26 17.11 0.00 0.00 chr1ptel1M 237 282 (999718) (A)n#Simple_repeat 1 46 (0) m_b1s252i1 1 chr1ptel1M 237 AAAAAAAAAAAAAAAAAAAGAATAAAAAAAATAAATTTAAAAATAA 282 i v v vvv v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 46 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 18 29.00 1.67 0.00 chr1ptel1M 236 295 (999705) (TAA)n#Simple_repeat 1 61 (0) m_b1s252i0 2 chr1ptel1M 236 TAA-AAAAAAAAAAAAAAAAAGAATAAAAAAAATAAATTTAAAAATAATC 284 - v v v v v v v v vvv v v (TAA)n#Simple 1 TAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATA 50 chr1ptel1M 285 ATAATATTAAT 295 v (TAA)n#Simple 51 ATAATAATAAT 61 Matrix = Unknown Transitions / transversions = 0.00 (0/14) Gap_init rate = 0.02 (1 / 59), avg. gap size = 1.00 (1 / 1) 31 0.00 0.00 0.00 chr1ptel1M 1087 1113 (998887) (AC)n#Simple_repeat 1 27 (0) c_b1s251i0 3 chr1ptel1M 1087 ACACACACACACACACACACACACACA 1113 (AC)n#Simple_ 1 ACACACACACACACACACACACACACA 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 12 26.58 0.00 2.38 chr1ptel1M 1116 1158 (998842) (GAGGG)n#Simple_repeat 1 42 (0) m_b1s252i2 4 chr1ptel1M 1116 GAAGGCAGAGAATGGGAGGGGTGGGGGAGGGGAGGTGGGAGGA 1158 i v i i v -i v i i (GAGGG)n#Simp 1 GAGGGGAGGGGAGGGGAGGGG-AGGGGAGGGGAGGGGAGGGGA 42 Matrix = Unknown Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.02 (1 / 42), avg. gap size = 1.00 (1 / 1) 11 12.96 8.82 0.00 chr1ptel1M 1321 1354 (998646) (TTTTTCC)n#Simple_repeat 1 37 (0) m_b1s252i3 5 chr1ptel1M 1321 TTTTTCC-TTTT--TAATTCCATTTTCCTTTTTACTT 1354 - -- vv v v (TTTTTCC)n#Si 1 TTTTTCCTTTTTCCTTTTTCCTTTTTCCTTTTTCCTT 37 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.50 (3 / 2) 505 26.66 12.44 1.29 chr1ptel1M 1702 1910 (998090) MIR#SINE/MIR 21 252 (10) m_b1s601i0 6 chr1ptel1M 1702 AGAGGGTGGTCT-TGGAGC-GGAGTACCCTAGTGCAAATCC-AACCTTG- 1747 vii v - -i v i ivi v i -ii ii - MIR#SINE/MIR 21 AGAGCACGGGCTCTGGAGCCAGACTGCCTGGGTTCGAATCCCGGCTCTGC 70 chr1ptel1M 1748 -AATTATTAA-TGTTTGATCCATAGCAAGTCACTTGATAGTTCT---TAT 1792 - v i i- v i ivvi i i ivvi ---iv MIR#SINE/MIR 71 CACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCT 120 chr1ptel1M 1793 CAGTTTCCTCTTCTGTAAAATGAGG-TAATAATAG-ACTTCTTTCCCACA 1840 v i - - i vii vi vi MIR#SINE/MIR 121 CAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTCATAGG 170 chr1ptel1M 1841 GTTG----GAGAATTAAATGAA-TAATA-ATGTAAAG---------CAAT 1875 ---- i i- - --------- i MIR#SINE/MIR 171 GTTGTTGTGAGGATTAAATGAGTTAATACATGTAAAGCGCTTAGAACAGT 220 chr1ptel1M 1876 GTTTAATGCACATAATAGGTGCTTGAATACTTGTT 1910 ii i-- i i i i- vv MIR#SINE/MIR 221 GCCTG--GCACATAGTAAGCGCTC-AATAAATGTT 252 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.32 CpG sites = 37, Kimura (unadjusted) = 34.39 Transitions / transversions = 2.06 (37/18) Gap_init rate = 0.08 (16 / 208), avg. gap size = 1.81 (29 / 16) 226 24.24 0.00 0.00 chr1ptel1M 2153 2218 (997782) DNM1r#Unknown 2478 2543 (2119) m_b1s502i0 7 chr1ptel1M 2153 GTGGAGGTGTGTGTGTGTGTGTGTATATATATATATATGTATATGTATAT 2202 v v i i i i i i i i i i DNM1r#Unknown 2478 GTGTATGTGTGTATATATGTGTGTATATGTGTGTATGTGTGTATATATGT 2527 chr1ptel1M 2203 GCATACATAAGGATAT 2218 i i v v ? DNM1r#Unknown 2528 GTATATATACGTATNT 2543 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 31.46 CpG sites = 12, Kimura (unadjusted) = 31.46 Transitions / transversions = 3.00 (12/4) Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0) 244 19.23 0.00 0.00 chr1ptel1M 2160 2211 (997789) DNM1r#Unknown 2495 2546 (2116) m_b1s502i1 7 chr1ptel1M 2160 TGTGTGTGTGTGTGTGTATATATATATATATGTATATGTATATGCATACA 2209 i i i i i i i i i ?i DNM1r#Unknown 2495 TGTGTGTATATGTGTGTATGTGTGTATATATGTGTATATATACGTATNTA 2544 chr1ptel1M 2210 TA 2211 DNM1r#Unknown 2545 TA 2546 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 22.07 CpG sites = 10, Kimura (unadjusted) = 24.89 Transitions / transversions = 1.00 (10/0) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 395 26.89 4.00 3.31 chr1ptel1M 2673 2822 (997178) L2d2_3end#LINE/L2 405 555 (0) m_b1s601i1 8 chr1ptel1M 2673 TCTCTCGTGT--ATGTTGTTCCTCCTTA-TTAGAATGTAAGAACATTGAG 2719 i v -- iv vi ii -i v vv v L2d2_3end#LIN 405 TTTCACGTGTTTATGTCTTGTCTCCCCAACTAGATTGTAAGCTCCTTGAG 454 chr1ptel1M 2720 GGCAGGGATTGACTTTCTTTTTGCTTATATTTGT-TTCCCCA-AGC-TTT 2766 iii-- v v -i v -- - i - -ii L2d2_3end#LIN 455 GGCAGGGACCA--TGTCTTAT-ACTTCT--TTGTATCCCCCACAGCGCCT 499 chr1ptel1M 2767 AGCACAATACTCAGCACAGAGTAATTCCTTAATAAATGATTGTTGACTTG 2816 i i iiv v iviv i iv i L2d2_3end#LIN 500 AGCACAGTGCCTTGCACACAGTAGGCGCTCAATAAATATTTGTTGATTTG 549 chr1ptel1M 2817 GCTTGA 2822 ii L2d2_3end#LIN 550 ATTTGA 555 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.21 CpG sites = 24, Kimura (unadjusted) = 34.30 Transitions / transversions = 1.60 (24/15) Gap_init rate = 0.07 (10 / 149), avg. gap size = 1.10 (11 / 10) 405 32.00 0.79 0.79 chr1ptel1M 2687 2812 (997188) L2a_3end#LINE/L2 382 507 (10) m_b1s601i2 8 chr1ptel1M 2687 TGTTCCTCCTTATTAGAATGTAAGAACATTGAGGGCAGGGATTGACTTTC 2736 ii i ii i vv vv i v-i v L2a_3end#LINE 382 TGTCTCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGACTT-TTGTC 430 chr1ptel1M 2737 T-TTTTGCTTATATTTGTTTCCCCAAGCTTTAGCACAATACTCAGCACAG 2785 - i i ivvi v ivvii v i i iii v L2a_3end#LINE 431 TGTTTTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACAT 480 chr1ptel1M 2786 AGTAATTCCTTAATAAATGATTGTTGA 2812 iviv i iv L2a_3end#LINE 481 AGTAGGCGCTCAATAAATATTTGTTGA 507 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.81 CpG sites = 24, Kimura (unadjusted) = 43.26 Transitions / transversions = 1.50 (24/16) Gap_init rate = 0.02 (2 / 125), avg. gap size = 1.00 (2 / 2) 296 24.68 0.00 0.00 chr1ptel1M 3018 3094 (996906) C DNM1r#Unknown (2107) 2555 2479 m_b1s502i2 9 chr1ptel1M 3018 GTCCTTTCCTATACATACATATATACATCCATACATATACAGACATATAC 3067 i v i ? i i iv i i v i i i C DNM1r#Unknown 2555 GCCCTGTTCTATANATACGTATATATACACATATATACACACATACACAC 2506 chr1ptel1M 3068 ATATATAGACATACATATATGCATACA 3094 i v i i ii C DNM1r#Unknown 2505 ATATACACACATATATACACACATACA 2479 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 30.34 CpG sites = 15, Kimura (unadjusted) = 32.43 Transitions / transversions = 3.75 (15/4) Gap_init rate = 0.00 (0 / 76), avg. gap size = 0.0 (0 / 0) 16 14.46 0.00 0.00 chr1ptel1M 3096 3126 (996874) (TATA)n#Simple_repeat 1 31 (0) m_b1s252i4 10 chr1ptel1M 3096 TATATATAAATACATATACATACATATATAT 3126 v i i i (TATA)n#Simpl 1 TATATATATATATATATATATATATATATAT 31 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 235 34.68 3.96 2.94 chr1ptel1M 3204 3304 (996696) L2b_3end#LINE/L2 357 458 (8) m_b1s601i3 11 chr1ptel1M 3204 TCCTTGAAAACAGGGATGGTTTCATTTTTGTCC----TTGTGTTTCTAGA 3249 v iii iv ?v vv i i ----i i ii i v L2b_3end#LINE 357 TCCGTGAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTGTATCCCCAGC 406 chr1ptel1M 3250 GGTCAATGAAGAGCCTGGCAAATCATAGGCACTCAATCGATCCTTTTTCT 3299 vii iiiv ? v ivi i i vi v--- v L2b_3end#LINE 407 GCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATA---TTTGT 453 chr1ptel1M 3300 TGAAT 3304 L2b_3end#LINE 454 TGAAT 458 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 48.29 CpG sites = 21, Kimura (unadjusted) = 50.44 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.04 (4 / 100), avg. gap size = 1.75 (7 / 4) 47 2.27 0.00 0.00 chr1ptel1M 4045 4089 (995911) (AC)n#Simple_repeat 1 45 (0) c_b1s251i1 12 chr1ptel1M 4045 ACACACGCACACACACACACACACACACACACACACACACACACA 4089 i (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACA 45 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 15 5.56 0.00 0.00 chr1ptel1M 4606 4624 (995376) (TC)n#Simple_repeat 1 19 (0) m_b1s252i5 13 chr1ptel1M 4606 TCTCTCTTTCTCTCTCTCT 4624 i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCT 19 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 26 38.47 0.62 1.90 chr1ptel1M 4768 4927 (995073) (AAAGAA)n#Simple_repeat 1 158 (0) m_b1s252i6 14 chr1ptel1M 4768 AAAGTAAACTAGAAAGAGCTAGAGAGTAAAAAAAAAAAAAAAAAAAAGAC 4817 - -v i vv i iv i i i v (AAAGAA)n#Sim 1 AAAG-AAA-AAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAA 48 chr1ptel1M 4818 TGAAAAAGAGTGAAAAAAGTCAGAAAGAGAAAGAGAAAGAGAAATAAAGC 4867 vi i i -i i ivv i i i v i iv (AAAGAA)n#Sim 49 AAAGAAAAAG-AAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAA 97 chr1ptel1M 4868 AAGCCAGAGGGTGAAAAGAAGATTGAGAAAAAGTAAAA-AACAACAACAA 4916 vv i iivi i i vvi v - v v v (AAAGAA)n#Sim 98 AAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAA 147 chr1ptel1M 4917 CAACAACAAAA 4927 v v v (AAAGAA)n#Sim 148 GAAAAAGAAAA 158 Matrix = Unknown Transitions / transversions = 1.09 (24/22) Gap_init rate = 0.03 (4 / 159), avg. gap size = 1.00 (4 / 4) 17 3.96 3.85 0.00 chr1ptel1M 4903 4928 (995072) (AAC)n#Simple_repeat 1 27 (0) m_b1s252i7 15 chr1ptel1M 4903 AAAAACAACAACAACAACAACAA-AAC 4928 v - (AAC)n#Simple 1 AACAACAACAACAACAACAACAACAAC 27 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.04 (1 / 25), avg. gap size = 1.00 (1 / 1) 16 10.07 5.88 2.86 chr1ptel1M 4961 4994 (995006) (AG)n#Simple_repeat 1 35 (0) m_b1s252i8 16 chr1ptel1M 4961 AGA-AGAGAG-GATGAGGGCAAGAGAGAGAGAGAGA 4994 - - - i vi (AG)n#Simple_ 1 AGAGAGAGAGAGA-GAGAGAGAGAGAGAGAGAGAGA 35 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.09 (3 / 33), avg. gap size = 1.00 (3 / 3) 71 12.08 0.91 0.00 chr1ptel1M 5244 5353 (994647) (GA)n#Simple_repeat 1 111 (0) m_b1s252i9 17 chr1ptel1M 5244 GAGGGAGAGAGAGGGAGGGAGGGAGGGAAGGAGAGAAAGAGAGAAAGAG- 5292 i i i i i ii i i - (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr1ptel1M 5293 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 5342 (GA)n#Simple_ 51 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 100 chr1ptel1M 5343 AACAGATAGAG 5353 i v v (GA)n#Simple_ 101 GAGAGAGAGAG 111 Matrix = Unknown Transitions / transversions = 5.00 (10/2) Gap_init rate = 0.01 (1 / 109), avg. gap size = 1.00 (1 / 1) 296 31.42 3.91 2.20 chr1ptel1M 5440 5618 (994382) C MamSINE1#SINE/tRNA-RTE (2) 288 107 m_b1s502i3 18 chr1ptel1M 5440 TGCTCTCCTTCCTATGTGAAGATGA---TCCTGACAC---ATCAACAACA 5483 v v ii --- v v --- ii iv C MamSINE1#SINE 288 TGCTGTCCTTCGTATACGAAGATGACGCTACTGACCCACTATCAGTAGGA 239 chr1ptel1M 5484 CGTTCCCTTTGACGTG-TTTTCTAATAGTGGGGAGAGACCTGCAGCGGTC 5532 i viv vv - i i ? vi ii ivi i? C MamSINE1#SINE 238 CATGTGCTTTGAGTTGTTTTTCCAGTAGTGGNGATGGATTTGCGCTGANC 189 chr1ptel1M 5533 AACCCATTAATTGGTGCTGGGCCTTCCTGGTGACCAAACTCCTGCATTAT 5582 v i -i v ivv i v -i v vvv vi - C MamSINE1#SINE 188 CATCCA-CACTCTCTGCCGGTCC-CCCTTGTGACCAACGGCACGCATT-T 142 chr1ptel1M 5583 ACAAGGACGCTGGCTGTGATCAATGCTGGTGGTCTG 5618 i i ivv v i i iv v - ii C MamSINE1#SINE 141 GCGAGACGGCTGGCTGGGGTTAGGGGT-GCAGTCTG 107 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.35 CpG sites = 29, Kimura (unadjusted) = 42.17 Transitions / transversions = 1.12 (29/26) Gap_init rate = 0.04 (7 / 178), avg. gap size = 1.57 (11 / 7) 4137 30.42 2.48 2.31 chr1ptel1M 6620 9082 (990918) L1M5_orf2#LINE/L1 828 3294 (0) m_b1s551i0 19 chr1ptel1M 6620 GAATGACAACAATGAGACAGCATACACAAATCTGTGGGATACAGTCAAAG 6669 ? ii vi v i ivv i i ii L1M5_orf2#LIN 828 GAATGANAATGAAAATACAACATATCAAAATTTGTGGGATGCAGCTAAAG 877 chr1ptel1M 6670 CTGTAAGAAGGGGAAATTTTATATTTTTAGAGGCTTACTTGAATAAAACA 6719 v ivvv i i v vi? i v ? iv --- i v L1M5_orf2#LIN 878 CAGTGCTTAGAGGGAAATTTATAGCNTTAAATGCNTATAT---TAGAAAA 924 chr1ptel1M 6720 GA-GAAAGAG--AAGGTCAATAAATTGGGCTTGCAACTTTAAAAGATAGA 6766 - iv-- ii i vi ii v v v i v L1M5_orf2#LIN 925 GAAGAAAGGCTTAAAATCAATGATCTAAGCTTCCACCTTAAGAAGCTAGA 974 chr1ptel1M 6767 AAAAGA---GCAAACTGAAAATGCTCAATAACATGCTAAAAGT---GAAA 6810 --- i i ---- i - i? v - i v--- L1M5_orf2#LIN 975 AAAAGAAGAGCAAATTAAA----CCCAA-AGNAAG-TAGAAGGAAGGAAA 1018 chr1ptel1M 6811 TTCTAAAATTAAAAGGAGAAAATGATAAAACTGAAAGTAAAAAAATTATA 6860 vv iv i v vii i iv ii ? ? iv L1M5_orf2#LIN 1019 TAATAAAGATAAGAGCAGAAATCAATGAAATAGAAAACAAANANACAATA 1068 chr1ptel1M 6861 TTGAATTAATAAATAAAACTAACAATTGGTATTATGAAAAAACCAACAAA 6910 vv -- v ii i i v ii vi v i i i L1M5_orf2#LIN 1069 GAGAA--AATCAACGAAGCCAAAAGCTGGTTCTTTGAAAAGATCAATAAA 1116 chr1ptel1M 6911 ATAG-TAAACCTTTGGTAAATCTGATTAGAAAAAGGAAAGAGGAAAATCA 6959 v - i i i? iv i ii ii i i i vv L1M5_orf2#LIN 1117 ATTGATAAACCTCTAGCNAGACTGATCAAGAAAAAAAGAGAGAAGACACA 1166 chr1ptel1M 6960 AATTGTTACC-TTAAAAATGAAAAGGGAGAACTTTCCACCAATGAAGAGG 7008 iii vi- i ii i vv iv i vi vvvivi L1M5_orf2#LIN 1167 AATTACCAATATCAGGAATGAAAAAGGAGACATCACTACAGATCCTACAG 1216 chr1ptel1M 7009 AAATTAAAGAAATAATAAGGGTTTACTTTGCCCAACTTTATGCCAATAAA 7058 v iii i vv i v vv L1M5_orf2#LIN 1217 ACATTAAAAGGATAATAAGAGAATATTATGAACAACTTTATGCCAATAAA 1266 chr1ptel1M 7059 TTTGATAACCTAAGTGAAATGGATGACTGCCTCCCAAAATATAGGCTTCC 7108 ? i ii ii v v ivv i i i?i v L1M5_orf2#LIN 1267 TTTGANAACTTAGATGAAATGGACAAATTCCTTGAAAAACACAANTTACC 1316 chr1ptel1M 7109 CAGAATAACAGAGGAGGAAGTAAATTACTTAAATAGTCCCATTTCAGAAA 7158 v i v i ?v i i i i vv ii i i i v vivv L1M5_orf2#LIN 1317 AAAACTGACNCAAGAAGAAATAGAAAATCTGAATAGCCCTATATCTATTA 1366 chr1ptel1M 7159 AAGAAATAGAACAAGATATTAATCAACTCCCTAAAAAAAAATCCCCAGGA 7208 v ivv vv vv v i i v i v i v L1M5_orf2#LIN 1367 AAGAAATTGAATTTGTAATTAAAAACCTTCCCACAAAGAAAACTCCAGGC 1416 chr1ptel1M 7209 CCAGATGTATTTACATATAAATTCTACCAAACATTTAAAGAACAATTAGC 7258 vv i vvi i i v v ii L1M5_orf2#LIN 1417 CCAGATGGCTTCACTGGTGAATTCTACCAAACATTTAAGGAAGAAATAAT 1466 chr1ptel1M 7259 CTCAATGCTATAGAAACTATTTGAAAAAATAGGGAATGAAGGAGTCCTAC 7308 vi vi i v v iv i ii v i iiv v L1M5_orf2#LIN 1467 ACCAATCTTACACAAACTCTTCCAGAAAATAGAAAAAGAGGGAACACTTC 1516 chr1ptel1M 7309 TAAATTCCTTTTATGACACAGACATGGTACTGATACCTAAACCAGGTAGG 7358 iv i v vi vii ?iiv v ? ii ii L1M5_orf2#LIN 1517 CCAACTCATTTTATGAGGCCAGCATNACCCTGATACCAAAACCNGACAAA 1566 chr1ptel1M 7359 TTGAAA--ACAGAGAAAGAAAATTATAGACCAATCTCCCTAATGAATATT 7406 -- v -- iii i v v i v L1M5_orf2#LIN 1567 --GACATTACAAGAAAAGAAAATTACAGACCAATATCCCTCATGAACATA 1614 chr1ptel1M 7407 GATGCTAAAATCTTAAATAAGATATTAGCAAAATGACTACAGAAAATCAT 7456 v i ? i i vi v v v vvi L1M5_orf2#LIN 1615 GATGCAAAAATCCTNAACAAAATATTAGCAAATCGAATCCAGCAATATAT 1664 chr1ptel1M 7457 CTCCAGGATAATACACCATGATCAAGTAGGATTTATACCAGGAATGCAGG 7506 vvvv i i i i v i L1M5_orf2#LIN 1665 AAAAAGGATAATACATCATGACCAAGTGGGGTTTATCCCAGGAATGCAAG 1714 chr1ptel1M 7507 GCTGGTTCAGTATTAGGAAAACTATCAGTATAATTGGCTATATTTATAAC 7556 i i ii v i v v i i vi i --- L1M5_orf2#LIN 1715 GTTGGTTTAACATTCGAAAATCAATCAATGTAATTCACCATAT---TAAC 1761 chr1ptel1M 7557 CAAATTA---ACAAAAACCATATGATCATCTCAATAAATACAGAAAAAGC 7603 vi v --- v i i i L1M5_orf2#LIN 1762 AGAATAAAGGAGAAAAATCATATGATCATCTCAATAGATGCAGAAAAAGC 1811 chr1ptel1M 7604 ATTTGATAAAATCCAACATCCATTCCTATTAAAAACACTTGAGAGTATAG 7653 i i i v iv v iiiv ivv L1M5_orf2#LIN 1812 ATTTGACAAAATTCAACACCCATTCATGATAAAAACTCTCAGCAAACTAG 1861 chr1ptel1M 7654 GAATAAATGGGCTTTTCCTTAAAATAATCAGTACCATCTATTTAAAACCA 7703 i v vvi i vv i v iviv ivv v L1M5_orf2#LIN 1862 GAATAGAAGGGAACTTCCTCAACCTGATAAAGGGCATCTACGAAAAACCT 1911 chr1ptel1M 7704 TCAATTATCATTAAATGTAATGGGGACAAACTGCAACCATTCCCAGTAAG 7753 v ii? v i v iv v v ? v ?v v vv L1M5_orf2#LIN 1912 ACAGCNAACATCATACTTAATGGTGAAANACTGAANGCTTTCCCCCTAAG 1961 chr1ptel1M 7754 ATCAGGAGTGAAACAAAGTTGTCTACTATCACCATTACTATTCAATATTG 7803 i iii i i v ii ? i v i L1M5_orf2#LIN 1962 ATCGGGAACAAGACAAGGATGTCCGCTNTCACCACTTCTATTCAACATTG 2011 chr1ptel1M 7804 TATTAGAAATGCTAGCTTTGGCAATAAGAGTTGAGAAAGAGATTAAAGGA 7853 i i ii v ivvv ivvv i i v v L1M5_orf2#LIN 2012 TACTGGAGGTCCTAGCCAGTGCAATAAGGCAAGAAAAAGAAATAAAAGGC 2061 chr1ptel1M 7854 ATTAGAGTAGGTAATGAGGAAACCAAATTATCACTCTTTGCTGATTATAT 7903 v iii v v v i iv i i ?i v i v v i L1M5_orf2#LIN 2062 ATAAAGATTGGAAAGGAAGAAATAAAACTGTCNTTATTCGCAGATGACAT 2111 chr1ptel1M 7904 GATGGTATACTTAGAGAACCCCAGAGATTCTACTAAAACGTTATAAGAAA 7953 v ? v i i ? i v v ? vii iv v L1M5_orf2#LIN 2112 GATTGTNTACGTAGAAAATCCNAAAGAATCTACAAANAAACTACTAGAAC 2161 chr1ptel1M 7954 CAATCCACACCTTTAGCAAAATTGCAGGATACAAAATAAACCCACATAAG 8003 i vviiivv ii i ? ii v ivi v i L1M5_orf2#LIN 2162 TAATAAGTGAATTTAGCAAGGTCGCNGGATACAAGGTCAATATACAAAAA 2211 chr1ptel1M 8004 TCATAAGCATTCTTATGTATCACTAACAA--AATCCAATAGTTAGAGTTA 8051 vvv i ii i ii vi -- ivi v i v i v - L1M5_orf2#LIN 2212 TCAATTGTATTTCTATATACTAGCAACAAACAATTGGAAAATGAAATTT- 2260 chr1ptel1M 8052 CAAAGAGAAATTCCATTTAAAGTAACTACTGATAGTATAAAATACTTAGG 8101 -? i iv v v i i vv vi v ii ? L1M5_orf2#LIN 2261 -NAAAAACAATACCATTTACAATAGCATCAAAAAACATNAAATACTTAGG 2309 chr1ptel1M 8102 AATATATCTGCCAAGGGAAAAT---CAGAAACTTTATGAGCAAAACTACA 8148 v iv --- ? --- ii v ? iivvv L1M5_orf2#LIN 2310 AATAAATCTAACAA---AANATGTGCAAGACCTNTACACTGAAAACTACA 2356 chr1ptel1M 8149 AAACACTTTCCACACAAATTAAGTCTGATCTAACCCATTGGATAAATATT 8198 i viiv v v ivvv i viv v v i v L1M5_orf2#LIN 2357 AAACATTGCTGAGAGAAATTAAAGAAGACCTAAATAAATGGAGAGATATA 2406 chr1ptel1M 8199 AAATGCTCTTGGATTGGGCGAGCAAATATAATAAAAATGACAATACTGCC 8248 vv i v iv viv vi ? i v v v L1M5_orf2#LIN 2407 CCATGTTCATGGATTGGAAGACTCAATATTGTNAAGATGTCAATTCTCCC 2456 chr1ptel1M 8249 TAAACTAATCTATTCACTTAGCATTATACCATTC-AGACCCCAAAAAAAA 8297 i i i vv i i iiiiv v v - i i ---- iv L1M5_orf2#LIN 2457 CAAATTGATCTATAGATTCAATGCAATCCCAATCAAAATCCC----AGCA 2502 chr1ptel1M 8298 AACTATTTTAATGACCTAGAAAAAATAA---CAAAGTTCATATAGAAAAA 8344 iii v ivv vv v v iv i ---i i i - i v L1M5_orf2#LIN 2503 GGTTTTTTTGTAGAAATTGACAAGCTGATTCTAAAATTTATAT-GGAAAT 2551 chr1ptel1M 8345 ACAAAAGGTCAAGAAT-TTCAAAAGATTAATGAAAAAAAAATCAAATGAA 8393 i i ii ? -vi v v vv i ---i ii L1M5_orf2#LIN 2552 GCAAAGGACCNAGAATAGCCAAAACAATCTTGAAAAAGAA---GAACAAA 2598 chr1ptel1M 8394 GGTGGTGGTCTAGCTGTACCAGATCT-AAAATTATATTATAAAGCAGCAG 8442 v v v vi vv ? ? - i i - vi L1M5_orf2#LIN 2599 GTTGGAGGACTTACACTACCNGATNTCAAGACT-TATTATAAAGCTACAG 2647 chr1ptel1M 8443 TTACCATAACCTTTTGGTATTGGC-TAAGAAATAGACTAGTTGATCAGTG 8491 v i vi vv v - -i v i v i L1M5_orf2#LIN 2648 TAATCAAGACAGTGTGGTATTGGCGTAAG-GATAGACAAATAGATCAATG 2696 chr1ptel1M 8492 AAACAGGTTAG---GTTCAAAGGACAAA-CCAGTCA-ATAACTTTAATAC 8536 i iv --- i i -i i i - vv - --- vi?i ? L1M5_orf2#LIN 2697 GAACAGAATAGAGAGTCCAGA-AATAGACCCACACATATA---TGGNCAN 2742 chr1ptel1M 8537 TCTAGTGTTTGACAAACTT---AAAG-ACCCCAGCTTTTGAGATAAGAAC 8582 - ii v vv --- ? - vii ---- i iv i i L1M5_orf2#LIN 2743 T-TGATTTTTGACAAAGGTGCCAANGCAATTCAG----TGGGGAAAGGAT 2787 chr1ptel1M 8583 TCACTGTTTGACAAAAATTGCTGGGAAAATTGGAAACTAGTATGGCAGAA 8632 vvv v ii viv i v v iivi v i L1M5_orf2#LIN 2788 AGTCTTTTCAACAAATGGTGCTGGAACAATTGGATATCCATATGGAAAAA 2837 chr1ptel1M 8633 ACTAGGCACTGATCCACACTTAACACCGTGTACCAAGATAAGGTCAAAAT 8682 v iii?vii i vi i v i ii v i v iv ? i L1M5_orf2#LIN 2838 AATGAANCTCGACCCCTACCTCACACCATACACAAAAATTAATTCNAGAT 2887 chr1ptel1M 8683 GGGTTCAT-GACCTAGGCATAAAGAATGAGATTATAAATAAATTAGAGG- 8730 i- - iiii ii? i i i vvvvi i - L1M5_orf2#LIN 2888 GGA-TCATAGACCTAAATGTAAAAGNTAAAACTATAAAACTTCTAGAAGA 2936 chr1ptel1M 8731 -AACACAGGATAGTTTACCTCTCAGACCTGTGGAAGAGGAAAGAATTT-- 8777 - i v i-- i iivv - i?v v ii -- L1M5_orf2#LIN 2937 AAACATAGGAGAA--TATCTTCGTGACCT-TGGGNTAGGCAAAGATTTCT 2983 chr1ptel1M 8778 -----ATGAC-CAATAAAGAACTAGAGATCATTACTGA------TCACAA 8815 ----- v - - v ? --- i v vv ------ v i L1M5_orf2#LIN 2984 TAAACAGGACACAA-AAAGCACNA---ACCATAAAAGAAAAAATTGATAA 3029 chr1ptel1M 8816 AATTTTGATTATATCAAATTGAAAAGTTTTTG--TAACAACAAAACTAAT 8863 -- v i ?i v v ii i --i?v - i - vi L1M5_orf2#LIN 3030 A--TTGGACTNCATCAAAATTAAAAACTTCTGCTCNTCAA-AAGAC-ACC 3075 chr1ptel1M 8864 GCAGACAAGATTAGAAGGGAA-CCACTAAACTGGGAAAACATTTTTACAG 8912 ivi v i v i v - - i ? i v v i i L1M5_orf2#LIN 3076 GTTAAGAAAATGAAAAGGCAAGCCAC-AGANTGGGAGAAAATATTTGCAA 3124 chr1ptel1M 8913 T-CAAAGGTTCTGATAAAGGTTTCATTTCCAAAATATATAGAGGATTGCC 8961 ?- v vi- i vi i v i i i i - L1M5_orf2#LIN 3125 NACATATA-TCTGACAAAGGACTCGTATCCAGAATATATAAAGAACT-CC 3172 chr1ptel1M 8962 TTTAATTT-ATAAGAAATCAAGCCATTC--TCCAATTGATAAATGGTCAA 9008 vi ? i- ? -- v vv --i v? v v L1M5_orf2#LIN 3173 TACAANTCAATAANAAA--AAGACAAACAACCCAATANAAAAATGGGCAA 3220 chr1ptel1M 9009 AGGATATAAACAGACAACTCTCAGACAAAGAAATTGAAACTACTTCTAGG 9058 i iv i vi v i vi v ?v ivi ivv i L1M5_orf2#LIN 3221 AAGACTTGAACAGACACTTCACAAAAGAAGATATNCAAATGGCCAATAAG 3270 chr1ptel1M 9059 CATATGAAAAGATGCTCCAAGTCA 9082 i v v? L1M5_orf2#LIN 3271 CACATGAAAAGATGCTCAACNTCA 3294 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.12 CpG sites = 399, Kimura (unadjusted) = 40.94 Transitions / transversions = 1.20 (399/333) Gap_init rate = 0.04 (88 / 2462), avg. gap size = 1.34 (118 / 88) 1123 27.57 0.00 1.99 chr1ptel1M 8939 9297 (990703) L1ME3Cz_3end#LINE/L1 7 358 (639) m_b1s551i1 19 chr1ptel1M 8939 TCCAAAATATATAGAGGATTGCCTTTAATTTATAAGAAATCAAGCCATTC 8988 i i i i v iviv iv -- v --v L1ME3Cz_3end# 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAA--AAGACA--A 52 chr1ptel1M 8989 TCCAATTGATAAATGGTCAAAGGATATAAACAGACAACTCTCAGACAAAG 9038 i v v v i i i v vi i L1ME3Cz_3end# 53 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chr1ptel1M 9039 AAATTGAAACTACTTCTAGGCATATGAAAAGATGCTCCAAGTCATTATTA 9088 iivi ivi ivv ii v vv i v L1ME3Cz_3end# 103 AAACCCGAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTA 152 chr1ptel1M 9089 ATCAGAGAAATGCAAATTAAGACAACTCTGAGATACCACTACACACCTGT 9138 i i ? vv i v ii L1ME3Cz_3end# 153 ATCAGGGAAATGCAAATTAAAACNACAATGAGATACCATTTCACACCCAT 202 chr1ptel1M 9139 CAGATTGGCTAGAATGACAGGGAAAGATAATGCAGAATGTTGGAGGGGAT 9188 v i vvv ii vvv i i vi i v i L1ME3Cz_3end# 203 CAGATTGGCAAAAATTTAAAAGTCTGACAATACCAAGTGTTGGCGAGGAT 252 chr1ptel1M 9189 ATGGGAAAACAGAGACACTAATAATTTGTTGGTGGAATTGTCAATACATC 9238 i ii i ii v v vvi i i v v vvi v L1ME3Cz_3end# 253 GTGGAGAAACGGGAACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTA 302 chr1ptel1M 9239 CAGCCATTCTGGAGAGCAATTTGGAACTATGCTCAAAAAGTTATCAAACT 9288 i i i v v - viv i-- iv L1ME3Cz_3end# 303 CAACCACTTTGGAGAGCAATTTGGCAATAT-CTAGTAAAGTTG--AAGAT 349 chr1ptel1M 9289 GTGCATACC 9297 i L1ME3Cz_3end# 350 GCGCATACC 358 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.71 CpG sites = 52, Kimura (unadjusted) = 35.03 Transitions / transversions = 1.16 (52/45) Gap_init rate = 0.02 (7 / 358), avg. gap size = 1.00 (7 / 7) 582 25.91 4.71 1.01 chr1ptel1M 9810 10000 (990000) L1ME3G_3end#LINE/L1 351 548 (376) m_b1s551i2 19 chr1ptel1M 9810 CACATACCCTTTGATCTAGCAGTGTTACTGCTGGGCTTATATCCCAAAGA 9859 i i i i vii v ? ?v v i ? L1ME3G_3end#L 351 CGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAGA 400 chr1ptel1M 9860 AAT-CTTAAAGAAG-GGAAAGGGACCTGTATGTGTAAGAATGTTTCTGGC 9907 - iiv v v - v v i --? i ii i iv v L1ME3G_3end#L 401 AATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTCATTGC 448 chr1ptel1M 9908 AGCCCTCTTTGTAGTGGCCAGAAACTGGAAACTGAGTGGATGCCCATCAA 9957 vi v i i v i i vivv ii i L1ME3G_3end#L 449 AGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCAA 498 chr1ptel1M 9958 T-------TGGCTGAATAAATTGTGGTATATGAATATTATAGAATATTAT 10000 ------- i i i vv i i i L1ME3G_3end#L 499 TAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACTAT 548 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 31.83 CpG sites = 30, Kimura (unadjusted) = 33.59 Transitions / transversions = 1.58 (30/19) Gap_init rate = 0.03 (5 / 190), avg. gap size = 2.20 (11 / 5) 298 30.14 7.89 4.88 chr1ptel1M 9814 10092 (989908) L1MA10_3end#LINE/L1 359 645 (436) m_b1s551i3 19 chr1ptel1M 9814 TACCCTTTGATCTAGCAGTGTTACTGCTGGGCTTATATCCCAAAGAAATC 9863 v v i i vii v iv v --i L1MA10_3end#L 359 TACCATATGATCCAGCAATCCCACTTCTGGGTATATATCCAAAAGAA--T 406 chr1ptel1M 9864 TTAAAGAAGGG----AAAGGGACCTGTATGTGTAA--GAATGTTTCTGGC 9907 v vv i----i i ---- v i v--vv iv v L1MA10_3end#L 407 TGAAATCAGGATCTCGAAGAGA----TATCTGCACTCCCATGTTCATTGC 452 chr1ptel1M 9908 AGCCCTCTTTGTAGTGGCCAGAAACTGGAAACTGAGTGGATGCCCATCAA 9957 vi v iii i i ii vv vivv ii i i L1MA10_3end#L 453 AGCATTATTCACAATAGCCAAGATATGGAAACAACCTAAATGTCCATCGA 502 chr1ptel1M 9958 T-------TGGCTGAATAAATTGTGGTATATGAATATTATAGAATATTAT 10000 i------- v i v v iv iv i L1MA10_3end#L 503 CGGATGAATGGATAAAGAAAATGTGGTATATACATACAATGGAATATTAT 552 chr1ptel1M 10001 TGTTCTTTAAGAAATGACCAGCAGGATA-------ATTTCAGAAAGTCCT 10043 vvv i i ------ v v ------- vv v i- v L1MA10_3end#L 553 TCAGCCTTAAAAA------AGAAGGAAATCCTGCCATTTGCGACAA-CAT 595 chr1ptel1M 10044 GGAGAAACTTACATGAACA-GATGCTGAGTGAAATGAGCAGGAC-CAGGA 10091 vi i iv - i -v i i vi ? - i L1MA10_3end#L 596 GGATGAACCTGGA-GGACATTATGCTAAGTGAAATAAGCCAGNCACAGAA 644 chr1ptel1M 10092 G 10092 L1MA10_3end#L 645 G 645 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.49 CpG sites = 40, Kimura (unadjusted) = 39.33 Transitions / transversions = 1.00 (40/40) Gap_init rate = 0.07 (20 / 278), avg. gap size = 1.80 (36 / 20) 375 25.90 7.46 5.88 chr1ptel1M 9881 10081 (989919) L1MC3_3end#LINE/L1 430 633 (1899) m_b1s551i4 19 chr1ptel1M 9881 ACCTGTATGTGTAAGAATGTTTCTGGCAGCCCTCTTTGTAGTGGCCAGAA 9930 i i i ---- v i ii v ii i v i L1MC3_3end#LI 430 ACCTGCACGCG----AATGTTTATAGCAGCTTTATTCATAATCGCCAAAA 475 chr1ptel1M 9931 ACTGGA---AACTGAGTGGATGCCCATCAAT-------TGGCTGAATAAA 9970 --- ii --- i v ------- v i i L1MC3_3end#LI 476 ACTGGAAGCAACCAA---GATGTCCTTCAATAGGTGAATGGATAAACAAA 522 chr1ptel1M 9971 TTGTGGTATATGAATATTATAGAATATTATTGTTCTTT---AAGAAATGA 10017 i i vv iv i vvv vv --- L1MC3_3end#LI 523 CTGTGGTACATCCATACAATGGAATATTATTCAGCGATAAAAAGAAATGA 572 chr1ptel1M 10018 -CCAGCAGGATAATTTCAGAAAGTCCTGGA-GAAACTTACATGAACAGAT 10065 - i v i vi ---- ii v v - v v v i v- L1MC3_3end#LI 573 GCTATCAAGCCA----CGAAAAGACATGGATGAATCTTAAATGCATAT-T 617 chr1ptel1M 10066 GCTGAGTGAAATGAGC 10081 i vi L1MC3_3end#LI 618 GCTAAGTGAAAGAAGC 633 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 30.01 CpG sites = 27, Kimura (unadjusted) = 32.34 Transitions / transversions = 1.23 (27/22) Gap_init rate = 0.09 (17 / 200), avg. gap size = 1.59 (27 / 17) 15 12.73 9.30 0.00 chr1ptel1M 10370 10412 (989588) (ATTTAT)n#Simple_repeat 1 47 (0) m_b1s252i10 20 chr1ptel1M 10370 ATGTATACTTAT-TTTGTATTTA-ATTTATACTT-TA-ATATATTTA 10412 v i - i - i - -v (ATTTAT)n#Sim 1 ATTTATATTTATATTTATATTTATATTTATATTTATATTTATATTTA 47 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.10 (4 / 42), avg. gap size = 1.00 (4 / 4) 270 28.56 12.26 0.58 chr1ptel1M 10865 11019 (988981) L1ME3Cz_3end#LINE/L1 357 529 (468) m_b1s551i5 21 chr1ptel1M 10865 CCCAATGATCCAGCAATACCACTACTAGATCTGTATCCCTAAAAGA---- 10910 v i i v v i v i - i ii ---- L1ME3Cz_3end# 357 CCCTACGACCCAGCAATTCCACTTCTAGGTATATA-CCCTAGAGAAACTC 405 chr1ptel1M 10911 TCA-GTAAGTGGAAAATGAG-TTCATACAAAAATAATTATT---GCATTT 10955 i-ii v v v v -ivii ii iv i --- v L1ME3Cz_3end# 406 TCGCACATGTGCACAAGGAGACATGTACAAGGATGTTCATTGCAGCATTG 455 chr1ptel1M 10956 TTTGTAATGGCAAAGAAATAG--ACAA-------GCCTATCATTTTGAGA 10996 i i i v i -- ------- i i v vv i L1ME3Cz_3end# 456 TTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCAATAGGGGA 505 chr1ptel1M 10997 ATGGCTGAAC-GACTGTGGTATAT 11019 v i i-i i L1ME3Cz_3end# 506 ATGGATAAATAAATTGTGGTATAT 529 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.15 CpG sites = 28, Kimura (unadjusted) = 37.33 Transitions / transversions = 1.75 (28/16) Gap_init rate = 0.05 (8 / 154), avg. gap size = 2.50 (20 / 8) 414 25.93 4.63 0.00 chr1ptel1M 11868 11975 (988025) MIRc#SINE/MIR 3 115 (153) m_b1s601i4 22 chr1ptel1M 11868 AGCTAGT-TGGTATAGTGGATAGAGCACCAGCCCTGAAGTCAAAAGGACA 11916 vi - ii v ii v i i ii i v MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chr1ptel1M 11917 -GAGTTCAAATCTGGCCTCAGATGCTTA---ACTGTGTGACCATGGGCAA 11962 - i i i iv v v vii ---i v MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 102 chr1ptel1M 11963 GTCACTAAACCCC 11975 v i MIRc#SINE/MIR 103 GTCACTTAACCTC 115 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.44 CpG sites = 18, Kimura (unadjusted) = 32.87 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.03 (3 / 107), avg. gap size = 1.67 (5 / 3) 258 35.53 4.44 5.06 chr1ptel1M 13234 13571 (986429) C L1ME3Cz_3end#LINE/L1 (469) 528 193 m_b1s551i6 23 chr1ptel1M 13234 TATATCACAACTTGTTGAGATATTCCCGAATTCATGGGCATCCACTTACT 13283 i i i v vvi vv v i ii vv vv C L1ME3Cz_3end# 528 TATACCACAATTTATTTATCCATTCCCCTATTGATGGACATTTAGGTTGT 479 chr1ptel1M 13284 TTCCAGTTCTTAGCCACAACAAAGAGAGTTGCTATAAATATTTTGGGACA 13333 i i v i iv v iv i v i i ii v v C L1ME3Cz_3end# 478 TTCCAATTTTTCGCTATTACAAACAATGCTGCAATGAACATCCTTGTACA 429 chr1ptel1M 13334 TAGGGGTTCCTTTT---CTT---------TTTCCTTTGACCACATAAGAA 13371 --- vi v --- v --------- ii v ivi i ---- C L1ME3Cz_3end# 428 T---GTCTCCTTGTGCACATGTGCGAGAGTTTCTCTAGGGTATATA---- 386 chr1ptel1M 13372 AACAAGCATAATAATGGTATTGCTGTTTAAAAGGTTATACACACTTTTAT 13421 ------ v iv i v vv viv v i i ii i - C L1ME3Cz_3end# 385 ------CCTAGAAGTGGAATTGCTGGGTCGTAGGGTATGCGCATCTTCA- 343 chr1ptel1M 13422 AACCCTCTGTGCATAATTTCAGATTGCTC-CCAAAATAATTGGATCATTT 13470 - ii vi- iv v vi i - i ii v i v C L1ME3Cz_3end# 342 -ACTTTAC-TAGATATTGCCAAATTGCTCTCCAAAGTGGTTGTACCAATT 295 chr1ptel1M 13471 CAGACATCTACAAAAGGTGCATTAGTATCCTAATTTTTCCACATCTCCTT 13520 i v vi i v ivi i v vi i ivi i ii vi C L1ME3Cz_3end# 294 TACACTCCCACCAGCAGTGTATGAGAGTTCCCGTTTCTCCACATCCTCGC 245 chr1ptel1M 13521 CAATATTT--TCCTTTCCACCTTCTATCATTTTAGCTAATCTGATAGTTC 13568 i i -- vi v viv i -v v i i v v C L1ME3Cz_3end# 244 CAACACTTGGTATTGTCAGACTTTTA-AATTTTTGCCAATCTGATGGGTG 196 chr1ptel1M 13569 TGA 13571 C L1ME3Cz_3end# 195 TGA 193 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 47.70 CpG sites = 62, Kimura (unadjusted) = 49.52 Transitions / transversions = 1.19 (62/52) Gap_init rate = 0.06 (21 / 337), avg. gap size = 1.52 (32 / 21) 264 31.52 0.00 0.00 chr1ptel1M 13234 13325 (986675) C L1ME1_3end#LINE/L1 (394) 532 441 m_b1s551i7 23 chr1ptel1M 13234 TATATCACAACTTGTTGAGATATTCCCGAATTCATGGGCATCCACTTACT 13283 i i v vvi v v?i v i iiivv vv C L1ME1_3end#LI 532 TATACCACAATTTGTTTATCCATTCACCNGTTGATGGACATTTGGGTTGT 483 chr1ptel1M 13284 TTCCAGTTCTTAGCCACAACAAAGAGAGTTGCTATAAATATT 13325 i i i iv i v i i i i C L1ME1_3end#LI 482 TTCCAGTTTTTGGCTATTACGAATAAAGCTGCTATGAACATT 441 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.90 CpG sites = 17, Kimura (unadjusted) = 42.86 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.00 (0 / 91), avg. gap size = 0.0 (0 / 0) 26 11.47 0.00 0.00 chr1ptel1M 14686 14723 (985277) (T)n#Simple_repeat 1 38 (0) m_b1s252i12 24 chr1ptel1M 14686 TTTTTTTTTTTTTTTTTTGATTTTTATTTTATTTTTTT 14723 vv v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 38 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 19 20.25 1.89 1.89 chr1ptel1M 14686 14738 (985262) (TTTTA)n#Simple_repeat 1 53 (0) m_b1s252i11 25 chr1ptel1M 14686 TTTTTTTTTTTTTTTTTTGATTTTTATTTTATTTT-TTTAATAGCCTTTT 14734 v v v v - - v vviv (TTTTA)n#Simp 1 TTTTATTTTATTTTATTTTA-TTTTATTTTATTTTATTTTATTTTATTTT 49 chr1ptel1M 14735 ATTT 14738 (TTTTA)n#Simp 50 ATTT 53 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.00 (2 / 2) 27 0.00 0.00 0.00 chr1ptel1M 16717 16742 (983258) (C)n#Simple_repeat 1 26 (0) c_b1s251i2 26 chr1ptel1M 16717 CCCCCCCCCCCCCCCCCCCCCCCCCC 16742 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCC 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 18 0.00 0.00 0.00 chr1ptel1M 18851 18870 (981130) (CT)n#Simple_repeat 1 20 (0) m_b1s252i13 27 chr1ptel1M 18851 CTCTCTCTCTCTCTCTCTCT 18870 (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCT 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 51 0.00 0.00 0.00 chr1ptel1M 18871 18914 (981086) (CA)n#Simple_repeat 1 44 (0) c_b1s251i3 28 chr1ptel1M 18871 CACACACACACACACACACACACACACACACACACACACACACA 18914 (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACA 44 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 15 7.67 0.00 6.67 chr1ptel1M 21313 21344 (978656) (GGACT)n#Simple_repeat 1 30 (0) m_b1s252i14 29 chr1ptel1M 21313 GGACTTGAACTGGACTTGAACTGGACTGGACT 21344 - i - i (GGACT)n#Simp 1 GGAC-TGGACTGGAC-TGGACTGGACTGGACT 30 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.06 (2 / 31), avg. gap size = 1.00 (2 / 2) 347 26.13 9.92 0.70 chr1ptel1M 21997 22127 (977873) MIR3#SINE/MIR 64 206 (2) m_b1s601i5 30 chr1ptel1M 21997 GACTCTGACACTCATAAAGGCTATGACCTTTGGACAAATCCCTTC----- 22041 i v v iv?ivvv i - i i v ----- MIR3#SINE/MIR 64 GGCTCTGCCACTAACTNGCTGTGTGACCTT-GGGCAAGTCACTTCACCTC 112 chr1ptel1M 22042 TCTGTGTTTCAGTTTCCTC--CTGTAATTGAAGAGGATTGGACTCTA-AA 22088 v ii -- vvvi i i vv -i MIR3#SINE/MIR 113 TCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGA 162 chr1ptel1M 22089 TCCAAAAGGT---TTCCAGCTCC-ATATCTTATGACTTT-TGAT 22127 ivv --- i- i ii i i - MIR3#SINE/MIR 163 TCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTATGAT 206 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.07 CpG sites = 19, Kimura (unadjusted) = 33.07 Transitions / transversions = 1.27 (19/15) Gap_init rate = 0.05 (7 / 130), avg. gap size = 2.00 (14 / 7) 12 20.64 2.44 2.44 chr1ptel1M 23331 23371 (976629) (CCACAAT)n#Simple_repeat 1 41 (0) m_b1s252i15 31 chr1ptel1M 23331 CCACAGACCCTC-ATCCTCAATCTACAATGCATGATCCACAA 23371 - i v - v i v ii (CCACAAT)n#Si 1 CCACA-ATCCACAATCCACAATCCACAATCCACAATCCACAA 41 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 15 3.66 0.00 12.50 chr1ptel1M 24984 25019 (974981) (ATTT)n#Simple_repeat 1 32 (0) m_b1s252i16 32 chr1ptel1M 24984 ATTTATGTCTATTATTTTTATTTATTTATTTGATTT 25019 - - - v - (ATTT)n#Simpl 1 ATTTAT-T-TATT-TATTTATTTATTTATTT-ATTT 32 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.11 (4 / 35), avg. gap size = 1.00 (4 / 4) 488 20.45 0.75 8.06 chr1ptel1M 25023 25155 (974845) C MIRc#SINE/MIR (141) 127 4 m_b1s601i6 33 chr1ptel1M 25023 CTGAGGC-AATTGGGGTTAAGTGACTTGCCCAGGGTCACACAGCCAGGAA 25071 -v vv i i i --- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG--- 81 chr1ptel1M 25072 GTGTTAAGTGTCTGAGGCCCCATTTGAACTCAGGTCCTCCTGACTTCAAG 25121 ---- v v v vvv i i i i i C MIRc#SINE/MIR 80 ----TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr1ptel1M 25122 GCTGGTGCTCTATCCACTGAGCCATCTAGCTGCC 25155 v ii v vi i---i C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTGCACCAC---ACTGCC 4 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 22.86 CpG sites = 13, Kimura (unadjusted) = 23.90 Transitions / transversions = 1.08 (13/12) Gap_init rate = 0.08 (11 / 132), avg. gap size = 1.00 (11 / 11) 236 37.62 4.95 0.00 chr1ptel1M 25572 25672 (974328) MIRc#SINE/MIR 11 116 (152) m_b1s601i7 34 chr1ptel1M 25572 TGGTGTAATAAATAGTGTGCAGAAGTTATAATTGGGGAGAGCTGACTTCA 25621 i i ii v v ii v i v iv i ii i v iv i MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr1ptel1M 25622 AATCCTGCCTCAGG-----ACGAGCTGTGAAACTGCAGGAAAGTCACTCA 25666 i i v v v----- v vi ivii v i MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTA 110 chr1ptel1M 25667 GTCCCT 25672 ii i MIRc#SINE/MIR 111 ACCTCT 116 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 51.28 CpG sites = 24, Kimura (unadjusted) = 55.69 Transitions / transversions = 1.71 (24/14) Gap_init rate = 0.01 (1 / 100), avg. gap size = 5.00 (5 / 1) 238 29.96 7.26 4.92 chr1ptel1M 25723 25901 (974099) L2b_3end#LINE/L2 274 456 (10) m_b1s601i8 35 chr1ptel1M 25723 CTCTG--CCCACTCCAGCCCT-CCCTGCC--TGTGAGCT-TGCTT-TTTG 25765 -- - i i - -- v i i - ?v - i L2b_3end#LINE 274 CTCTGGGCCC-CCCCAGTCCTACCCTGCCACTCTGGGTTATNATTGTCTG 322 chr1ptel1M 25766 GGTAC-TGTACA-ATCCCTGG--AGTTTGTAAACTCCTCCAGGTTAGAG- 25810 ?v - vii-v ivi-- vi i i viv vi i - L2b_3end#LINE 323 NTTACATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGA 372 chr1ptel1M 25811 CTGTCTTTCTTTTTTCTTCTTCT-TATTCAAATCCCAGTATTTTTTCTCA 25859 i ?v i v i v iiv iv - i ----- iiii ---vv L2b_3end#LINE 373 CCGNGTCTGTCTTGTTCACCGCTGTATCC-----CCAGCGCCT---AGCA 414 chr1ptel1M 25860 CAGTACCTGGTACATAATAGGGACTTAATAAATATTTGTTGA 25901 ?i i i i vi i i L2b_3end#LINE 415 CAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTTGTTGA 456 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.05 CpG sites = 33, Kimura (unadjusted) = 41.37 Transitions / transversions = 1.83 (33/18) Gap_init rate = 0.11 (19 / 178), avg. gap size = 1.16 (22 / 19) 297 30.47 0.00 6.25 chr1ptel1M 25785 25903 (974097) L2d2_3end#LINE/L2 436 547 (8) m_b1s601i9 35 chr1ptel1M 25785 AGTTTGTAAACTCCTCCAGGTTAGAGCTGTCTTTCTTTTTTCTTCTTCTT 25834 v i iv vi i --ii v vii v v iv L2d2_3end#LIN 436 AGATTGTAAGCTCCTTGAGGGCAGGG--ACCATGTCTTATACTTCTTTGT 483 chr1ptel1M 25835 ATTCAAATCCCAGTATTTTTTCTCACAGTACCTGGTACATAATAGGGACT 25884 i ---- -i vivii vv i v i i i vi L2d2_3end#LIN 484 ATCC----CCCA-CAGCGCCTAGCACAGTGCCTTGCACACAGTAGGCGCT 528 chr1ptel1M 25885 TAATAAATATTTGTTGATT 25903 i L2d2_3end#LIN 529 CAATAAATATTTGTTGATT 547 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.08 CpG sites = 20, Kimura (unadjusted) = 40.09 Transitions / transversions = 1.43 (20/14) Gap_init rate = 0.06 (7 / 118), avg. gap size = 1.00 (7 / 7) 211 22.22 14.29 0.00 chr1ptel1M 25911 25973 (974027) MIRb#SINE/MIR 109 180 (88) m_b1s601i10 36 chr1ptel1M 25911 ACTTAATCCCTCTA--CTTCCATTTTCTCATTTGTATAATGGGG------ 25952 i i i-- i vi i i v ------ MIRb#SINE/MIR 109 ACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATA 158 chr1ptel1M 25953 ACACCT-TATCACAGTGTTGTT 25973 i -iv i v MIRb#SINE/MIR 159 ATACCTACCTCGCAGGGTTGTT 180 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 25.12 CpG sites = 10, Kimura (unadjusted) = 27.37 Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.05 (3 / 62), avg. gap size = 3.00 (9 / 3) 886 27.60 2.26 0.00 chr1ptel1M 26200 26420 (973580) MIRb#SINE/MIR 40 265 (3) m_b1s601i11 37 chr1ptel1M 26200 TGGAA--AGGAAGATCTGAGTTCAAATCCAGTAGCAGACACTTACTAGCT 26247 i-- iv i i i v vvv v v MIRb#SINE/MIR 40 TGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCT 89 chr1ptel1M 26248 GTGTAACTCTAGGCAAGTCACTTCACCTCTATTTGCCTCAGTTTCCTTAA 26297 i ii i i v v vv i v MIRb#SINE/MIR 90 GTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCAT 139 chr1ptel1M 26298 TTGTAAAATGGTGATAATAACCTCTACCTCCTAATACTATTGCATAGATC 26347 i v ivi vi ivii i iivi i MIRb#SINE/MIR 140 CTGTAAAATGGGGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATT 189 chr1ptel1M 26348 AAATGAG---ATGTTTGTAAAGTACATAATAGAATGCCTGTTACACAGTA 26394 --- iv ii v ii v i vi i MIRb#SINE/MIR 190 AAATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTA 239 chr1ptel1M 26395 GGTGCTATATAAATGCTCATTCTTTT 26420 i i vv v vii v MIRb#SINE/MIR 240 AGCGCTCAATAAATGGTAGCTCTATT 265 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.01 CpG sites = 35, Kimura (unadjusted) = 35.20 Transitions / transversions = 1.35 (35/26) Gap_init rate = 0.01 (2 / 220), avg. gap size = 2.50 (5 / 2) 218 23.41 10.58 5.50 chr1ptel1M 26494 26597 (973403) MIR3#SINE/MIR 87 195 (13) m_b1s601i12 38 chr1ptel1M 26494 TGACCT-GGGTAG--CACTTTGGATGACTCTCGGGATCTC--TTTCCCTA 26538 - i i-- i-- i-- v ii -- ii MIR3#SINE/MIR 87 TGACCTTGGGCAAGTCACTTC--AC--CTCTCTGGGCCTCAGTTTCCTCA 132 chr1ptel1M 26539 TCAATAAAATGAA----TTGA--TGGATCCTCTCCAAGCTTCAGTCCAGC 26582 vi i---- i-- i vv i v i vv MIR3#SINE/MIR 133 TCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGC 182 chr1ptel1M 26583 TCTAAATCCTTCTAT 26597 i -- v MIR3#SINE/MIR 183 TCTGA--CATTCTAT 195 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.99 CpG sites = 15, Kimura (unadjusted) = 28.99 Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.11 (11 / 103), avg. gap size = 1.55 (17 / 11) 17 24.12 3.70 5.00 chr1ptel1M 27402 27482 (972518) (TGTA)n#Simple_repeat 1 80 (0) m_b1s252i17 39 chr1ptel1M 27402 TGTACATATGCATATAGGTATTTGTGTACATAAATCTATGTATGTA-G-A 27449 ii i i v v i -- iv v - - (TGTA)n#Simpl 1 TGTATGTATGTATGTATGTATGTATGT--ATGTATGTATGTATGTATGTA 48 chr1ptel1M 27450 TGT-CGTATGGGTATGTATACATGTTTCTATGTA 27482 -i -- ii v v (TGTA)n#Simpl 49 TGTATGTAT--GTATGTATGTATGTATGTATGTA 80 Matrix = Unknown Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.09 (7 / 80), avg. gap size = 1.00 (7 / 7) 296 28.74 4.60 0.00 chr1ptel1M 28135 28221 (971779) MIR3#SINE/MIR 115 205 (3) m_b1s601i13 40 chr1ptel1M 28135 TGAATCTAACTTTCCCCATCTGTAAAATGAAGGAGTTACAGTCTATAGCC 28184 iii v v i i i iv v vv iii MIR3#SINE/MIR 115 TGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATC 164 chr1ptel1M 28185 TGGCAGGTCCTTTCCAGTTT---CA-TCTATGTTCCTATAA 28221 vvv i i i--- - v i i MIR3#SINE/MIR 165 TCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTATGA 205 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.32 CpG sites = 15, Kimura (unadjusted) = 37.32 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.02 (2 / 86), avg. gap size = 2.00 (4 / 2) 292 30.08 7.69 0.90 chr1ptel1M 28308 28411 (971589) C L2d2_3end#LINE/L2 (5) 550 440 m_b1s601i14 41 chr1ptel1M 28308 TCAAATTAGTAAATA---ATTAAGTGCCTGCTTCATGGCA--GCCCTGGG 28352 i ii --- i i i vii - -- v v C L2d2_3end#LIN 550 TCAAATCAACAAATATTTATTGAGCGCCTACTGTGTG-CAAGGCACTGTG 502 chr1ptel1M 28353 CTACACACCA---GGAACATAAAGAGATGTAAGAGACATTCCCTGCTCTC 28399 vi i ii--- i i i ii i v iiv i C L2d2_3end#LIN 501 CTAGGCGCTGTGGGGGATACAAAGAAGTATAAGACATGGTCCCTGCCCTC 452 chr1ptel1M 28400 ATTGAGGTCACA 28411 vv v i C L2d2_3end#LIN 451 AAGGAGCTTACA 440 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.46 CpG sites = 22, Kimura (unadjusted) = 40.94 Transitions / transversions = 2.44 (22/9) Gap_init rate = 0.04 (4 / 103), avg. gap size = 2.25 (9 / 4) 262 30.40 8.55 1.60 chr1ptel1M 28313 28429 (971571) C L2b_3end#LINE/L2 (10) 456 332 m_b1s601i15 41 chr1ptel1M 28313 TTAGTAAATA---ATTAAGTGCCTGCTTCATGGCAG-CCCTGGGCTACAC 28358 i ii --- i i i i vii v - ? v vi C L2b_3end#LINE 456 TCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGC 407 chr1ptel1M 28359 ACCAGGAACATAAAGAGATG--TAAGA--GACAT--TCCCTGCTCTCATT 28402 i ii i -- v v i --i -- ?i-- i iv C L2b_3end#LINE 406 GCTGGGGA--TACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACG 359 chr1ptel1M 28403 GAGGTCACAGAATGGCAAGGCAGTCAG 28429 v vv i iii v v C L2b_3end#LINE 358 GAGCTCACAGTCTAGTGGGGGAGACAG 332 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.82 CpG sites = 23, Kimura (unadjusted) = 41.97 Transitions / transversions = 1.92 (23/12) Gap_init rate = 0.06 (7 / 116), avg. gap size = 1.71 (12 / 7) 213 32.63 5.26 0.00 chr1ptel1M 28349 28443 (971557) C L2c_3end#LINE/L2 (38) 440 341 m_b1s601i16 41 chr1ptel1M 28349 TGGGCTACACACCAGGAACATAAAGAGATGTAAGAGACATTCCCTGCTCT 28398 v i vi i ii i i i vivi v iv i C L2c_3end#LINE 440 TGTGCCAGGCGCTGGGGATACAAAGATGAATAAGACACGGTCCCTGCCCT 391 chr1ptel1M 28399 CATTGAGGTCACAG---AATGG-CAAGGCAGTCA-GTACACCAGCAACTA 28443 vv v --- i -vi i v - v vii i C L2c_3end#LINE 390 CAAGGAGCTCACAGTCTAGTGGAGGAGACAGACANGTAAACAGACAATTA 341 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.49 CpG sites = 18, Kimura (unadjusted) = 44.26 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.03 (3 / 94), avg. gap size = 1.67 (5 / 3) 473 26.42 12.58 0.00 chr1ptel1M 28603 28761 (971239) C MIRc#SINE/MIR (58) 210 32 m_b1s601i17 42 chr1ptel1M 28603 TGCATTGTCTTATTTTATCCTCAAGAGAACC---TGAGG---GCTTAGCC 28646 i i i v vi v --- --- vvi v C MIRc#SINE/MIR 210 TACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCA 161 chr1ptel1M 28647 ATTATTATTATGTCCATTTTACAGGTAAAGAAACTGAA--TCAAA----- 28689 iv vi i i i i-- i ----- C MIRc#SINE/MIR 160 GGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGT 111 chr1ptel1M 28690 -AAGTG----GTCCTA--TAACTTAACTAGCAAGGTTCTGAGGTGGGATT 28732 - ---- i v -- v vi i i vvv v vi i C MIRc#SINE/MIR 110 TAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACT 61 chr1ptel1M 28733 AAAACTCCAGTCTTCCTGATTCAAAGCCC 28761 vi i vi i v i C MIRc#SINE/MIR 60 CGAACCCAGGTCTTCCTGACTCCAAGTCC 32 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.23 CpG sites = 23, Kimura (unadjusted) = 33.11 Transitions / transversions = 1.21 (23/19) Gap_init rate = 0.04 (7 / 158), avg. gap size = 2.86 (20 / 7) 330 30.12 14.60 0.64 chr1ptel1M 28644 28780 (971220) C MIR1_Amn#SINE/MIR (65) 165 10 m_b1s601i18 42 chr1ptel1M 28644 GCCATTATTATTATGTCCATTTTACAGGTAAAGAAACTGAATCAAAAAGT 28693 i v i vi i i i iv ?v i v C MIR1_Amn#SINE 165 GTCAGTATCATTATCCCCATTTTACAGATGAGGAAACTGAGGCNCAGAGA 116 chr1ptel1M 28694 GGT-----------CCTA---TAACTTAACTAGCAAGGTTCTGAGGTGGG 28729 ----------- i --- v ?i i ?i ? vvv v vi C MIR1_Amn#SINE 115 GGTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNAGTGGCAGAGCCGGG 66 chr1ptel1M 28730 ATTAAAACTCCAGTCT------TCCTGATTCAAAGCCCTATCCATTGTGA 28773 ? ?i i vi ------ iii i iv i i i- C MIR1_Amn#SINE 65 ANTNGAACCCAGGTCTCCCGAGTCCCAGTCCAGTGCTCTATCCACTA-GA 17 chr1ptel1M 28774 TTATATT 28780 ii i i C MIR1_Amn#SINE 16 CCACACT 10 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.96 CpG sites = 28, Kimura (unadjusted) = 43.41 Transitions / transversions = 2.15 (28/13) Gap_init rate = 0.03 (4 / 136), avg. gap size = 5.25 (21 / 4) 44 6.13 0.00 0.00 chr1ptel1M 30995 31045 (968955) (TG)n#Simple_repeat 1 51 (0) c_b1s251i4 43 chr1ptel1M 30995 TGTGTGTGTGTTTGTGTGTGTGTGTGTATGTGTGTGTGTGTGTGTCTGTG 31044 v i v (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr1ptel1M 31045 T 31045 (TG)n#Simple_ 51 T 51 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 19 21.38 0.00 0.00 chr1ptel1M 31068 31105 (968895) (T)n#Simple_repeat 1 38 (0) m_b1s252i18 44 chr1ptel1M 31068 TTTGTTTTATTATTTCTTTTCTTTTCTTTTCTTTTTTT 31105 v v v i i i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 38 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 232 25.85 0.81 8.77 chr1ptel1M 32204 32326 (967674) L1MC4a_3end#LINE/L1 487 600 (2029) m_b1s551i9 45 chr1ptel1M 32204 TAGATGCCCAACAGGTAG-AGAATGGCTGAATAAGCTATGGTATATGAAC 32252 i -i??i - ? i i i vv L1MC4a_3end#L 487 TAAATGCCCA-TNNATAGGAGANTGGTTGAATAAACTATGGTACATCCAC 535 chr1ptel1M 32253 ATTATGGAATATTATTATTTTATAAGAAATGATCAGAGAAGCCAGAGAGA 32302 iv i i vvvvi i i vi -- i ------- L1MC4a_3end#L 536 ACAATGGAGTACTATGCAGCTGTAAAAAAGAAT--GAGGA-------AGA 576 chr1ptel1M 32303 GTTATATAAACTGATGTTAAGTGA 32326 vi v i i vi L1MC4a_3end#L 577 TCTCTATGAACTGATATGGAGTGA 600 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.45 CpG sites = 18, Kimura (unadjusted) = 33.45 Transitions / transversions = 1.64 (18/11) Gap_init rate = 0.09 (11 / 122), avg. gap size = 1.00 (11 / 11) 243 26.56 0.00 0.00 chr1ptel1M 32204 32267 (967733) L1ME3G_3end#LINE/L1 485 548 (376) m_b1s551i8 45 chr1ptel1M 32204 TAGATGCCCAACAGGTAGAGAATGGCTGAATAAGCTATGGTATATGAACA 32253 i i v ivvi i i i ii vv i L1ME3G_3end#L 485 TAAATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCATA 534 chr1ptel1M 32254 TTATGGAATATTAT 32267 i i L1ME3G_3end#L 535 CTATGGAATACTAT 548 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.42 CpG sites = 12, Kimura (unadjusted) = 34.42 Transitions / transversions = 2.40 (12/5) Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0) 19 0.00 0.00 0.00 chr1ptel1M 32615 32635 (967365) (A)n#Simple_repeat 1 21 (0) m_b1s252i20 46 chr1ptel1M 32615 AAAAAAAAAAAAAAAAAAAAA 32635 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAA 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 273 29.41 10.59 0.00 chr1ptel1M 33035 33119 (966881) MIRc#SINE/MIR 3 96 (172) m_b1s601i19 47 chr1ptel1M 33035 AGGCAATACAGTGGAATGGAAATATCATTAGATTTGGAATCA-GAGGTCA 33083 i iii v i v v i i i i - i v v MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chr1ptel1M 33084 TGAGTTGAAATTCTGATTCTG-----TAC---CTGTGTGGTCTT 33119 i vi i i i ii ----- --- ii MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTT 96 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.05 CpG sites = 19, Kimura (unadjusted) = 40.26 Transitions / transversions = 3.17 (19/6) Gap_init rate = 0.04 (3 / 84), avg. gap size = 3.00 (9 / 3) 232 25.30 3.61 0.00 chr1ptel1M 33729 33811 (966189) L1MC4a_3end#LINE/L1 466 551 (2078) m_b1s551i10 48 chr1ptel1M 33729 TGCAAAAGA---GAAATAAAATAGATGCTTTTCAGTTGGAGAATGTTTAA 33775 v --- i vv i iiv ??i v ? v i L1MC4a_3end#L 466 TGCAAAATATTGGAAACAACCTAAATGCCCATNNATAGGAGANTGGTTGA 515 chr1ptel1M 33776 ACAAATTGTGGTACATGAACAGAATAGGGTACTTTG 33811 i i i vv v i i v L1MC4a_3end#L 516 ATAAACTATGGTACATCCACACAATGGAGTACTATG 551 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.73 CpG sites = 11, Kimura (unadjusted) = 32.73 Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.01 (1 / 82), avg. gap size = 3.00 (3 / 1) 233 24.07 0.00 0.00 chr1ptel1M 33738 33791 (966209) L1MD1_3end#LINE/L1 480 533 (456) m_b1s551i11 48 chr1ptel1M 33738 GAAATAAAATAGATGCTTTTCAGTTGGAGAATGTTTAAACAAATTGTGGT 33787 i vvi iii iiv v v i L1MD1_3end#LI 480 GAAACAACCCAGATGTCCTTCAACGGGTGAATGGTTAAACAAACTGTGGT 529 chr1ptel1M 33788 ACAT 33791 L1MD1_3end#LI 530 ACAT 533 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 27.09 CpG sites = 8, Kimura (unadjusted) = 29.74 Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 562 21.37 0.85 0.85 chr1ptel1M 33845 33962 (966038) MIRc#SINE/MIR 10 127 (141) m_b1s601i20 49 chr1ptel1M 33845 GTGGTGCAGTGGATAGAGCACTAGCCCTTCAGTCAGAACAACCTGAGTTC 33894 v i v i vv i vi i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr1ptel1M 33895 AAATCTGGTCTTTAACACTTTCTTGGCTGTGTGACCTTGGGCAAATCACT 33944 i i iv v i iv v - i i MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTAC-TAGCTGTGTGACCTTGGGCAAGTCACT 108 chr1ptel1M 33945 TAACCCCAATT-GCCTCAG 33962 i vv v- MIRc#SINE/MIR 109 TAACCTCTCTGAGCCTCAG 127 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 24.25 CpG sites = 13, Kimura (unadjusted) = 25.38 Transitions / transversions = 1.08 (13/12) Gap_init rate = 0.02 (2 / 117), avg. gap size = 1.00 (2 / 2) 31 27.68 0.00 0.00 chr1ptel1M 33965 34043 (965957) (AAA)n#Simple_repeat 1 79 (0) m_b1s252i21 50 chr1ptel1M 33965 AAAAAAAAAAAAAAAAGAAAGAAAGAAAGAAAGAAAAGAAGAATAAGAAG 34014 i i i i i i i v i i (AAA)n#Simple 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr1ptel1M 34015 AAAGAAAAAGAAAAAGGAAGAAGAAGAAA 34043 i i ii i i i (AAA)n#Simple 51 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA 79 Matrix = Unknown Transitions / transversions = 16.00 (16/1) Gap_init rate = 0.00 (0 / 78), avg. gap size = 0.0 (0 / 0) 45 18.27 2.73 2.73 chr1ptel1M 33966 34075 (965925) (AAAG)n#Simple_repeat 1 110 (0) m_b1s252i22 50 chr1ptel1M 33966 AAAAAAAAAAAAAAAGAAAGAAAGAAAGAAAGAAAAGAAGAATAAGAAGA 34015 i i i ii - ii (AAAG)n#Simpl 1 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAA-AGAAAGA 49 chr1ptel1M 34016 AAGAAAAAGAAAAAGGAAG-AAG-AAGAAAG-GAGGAGGAAAGAGAAGGA 34062 i i i i - - -i i i - - (AAAG)n#Simpl 50 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA-AA-GA 97 chr1ptel1M 34063 AAGAAAAAGAGAA 34075 i i (AAAG)n#Simpl 98 AAGAAAGAAAGAA 110 Matrix = Unknown Transitions / transversions = 1.00 (16/0) Gap_init rate = 0.06 (6 / 109), avg. gap size = 1.00 (6 / 6) 242 17.54 17.54 0.00 chr1ptel1M 34077 34133 (965867) MIRc#SINE/MIR 84 150 (118) m_b1s601i21 51 chr1ptel1M 34077 GCTATGTGGCCCTGGGCAAGTCACTTAA----------CTTCAGTTACCT 34116 i i i ---------- i v MIRc#SINE/MIR 84 GCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCT 133 chr1ptel1M 34117 CAGCCAAAAAAGGGGGA 34133 v iiv v MIRc#SINE/MIR 134 CATCTGTAAAATGGGGA 150 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 20.25 CpG sites = 6, Kimura (unadjusted) = 20.25 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.02 (1 / 56), avg. gap size = 10.00 (10 / 1) 26 15.11 0.00 0.00 chr1ptel1M 34134 34179 (965821) (GGA)n#Simple_repeat 1 46 (0) m_b1s252i23 52 chr1ptel1M 34134 GGAGGAAAAGAAGGAAAAGGAGGAGGAGGAGGAGGAGAAGGAGGAG 34179 ii i ii i (GGA)n#Simple 1 GGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG 46 Matrix = Unknown Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 434 22.34 0.94 2.88 chr1ptel1M 34215 34320 (965680) MIRb#SINE/MIR 3 106 (162) m_b1s601i22 53 chr1ptel1M 34215 GAACAGCAGCTAGGTGGTGCAGTGAATAGATCCTGGGCCT-GGAGCCAGT 34263 ivi --- i v v vi i - i v MIRb#SINE/MIR 3 GAGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGA 49 chr1ptel1M 34264 AAGACCTGACATCAAATCTAACCTCTGACACTCACTAGCTGTGTGACCCT 34313 v ivv i iviv v i i MIRb#SINE/MIR 50 CAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTT 99 chr1ptel1M 34314 GGGCAAG 34320 MIRb#SINE/MIR 100 GGGCAAG 106 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 22.95 CpG sites = 12, Kimura (unadjusted) = 26.77 Transitions / transversions = 1.09 (12/11) Gap_init rate = 0.04 (4 / 105), avg. gap size = 1.00 (4 / 4) 465 20.43 1.08 0.00 chr1ptel1M 34228 34320 (965680) MIRc#SINE/MIR 10 103 (165) m_b1s601i23 53 chr1ptel1M 34228 GTGGTGCAGTGAATAGATC-CTGGGCCTGGAGCCAGTAAGACCTGACATC 34276 i v v - i i i v ivv MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr1ptel1M 34277 AAATCTAACCTCTGACACTCACTAGCTGTGTGACCCTGGGCAAG 34320 i i iviv v i i MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAG 103 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 21.41 CpG sites = 11, Kimura (unadjusted) = 24.19 Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.01 (1 / 92), avg. gap size = 1.00 (1 / 1) 15 19.85 0.00 0.00 chr1ptel1M 34736 34764 (965236) (G)n#Simple_repeat 1 29 (0) m_b1s252i24 54 chr1ptel1M 34736 GGGGGAGGGGGTGGGGGGGGTAGGAGGGG 34764 i v vi i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG 29 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 13 21.49 5.88 1.89 chr1ptel1M 34845 34895 (965105) (AAT)n#Simple_repeat 1 53 (0) m_b1s252i25 55 chr1ptel1M 34845 AATAA-AAAAATAATAATAATAGCTAA-AAAAAGAA-AAGAAAAAAAAAA 34891 - v -v - v v - v v v v (AAT)n#Simple 1 AATAATAATAATAATAATAATA-ATAATAATAATAATAATAATAATAATA 49 chr1ptel1M 34892 AGAA 34895 v (AAT)n#Simple 50 ATAA 53 Matrix = Unknown Transitions / transversions = 0.00 (0/9) Gap_init rate = 0.08 (4 / 50), avg. gap size = 1.00 (4 / 4) 255 26.84 7.04 5.56 chr1ptel1M 35741 35882 (964118) C L2c_3end#LINE/L2 (10) 468 325 m_b1s601i24 56 chr1ptel1M 35741 TCAACAGACACTAA---AACACTTATAAAATATCAGGTATACTTGGCAT- 35786 i i v --- i i i iv vi ii ii-- v v - C L2c_3end#LINE 468 TCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCG--CTGGGGATA 421 chr1ptel1M 35787 TAAGGAT---TCAGAGA-AGTCTCTGCCCTCAAAAAGCTGACATTTTCTG 35832 i i --- v v -i i ii v --v i C L2c_3end#LINE 420 CAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACA--GTCTA 373 chr1ptel1M 35833 CTGG-GGAGAGTGAAAACATGTATACGTGTAAATA-AATACAAAGTTAAT 35880 v - ---v i ? v ivii v - - C L2c_3end#LINE 372 GTGGAGGAGA---CAGACANGTAAACAGACAATTACAATAC-AAGTTAAT 327 chr1ptel1M 35881 GA 35882 C L2c_3end#LINE 326 GA 325 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 30.95 CpG sites = 22, Kimura (unadjusted) = 34.55 Transitions / transversions = 1.57 (22/14) Gap_init rate = 0.10 (14 / 141), avg. gap size = 1.29 (18 / 14) 352 38.84 5.62 7.46 chr1ptel1M 37071 37479 (962521) C L2b_3end#LINE/L2 (2) 464 63 m_b1s601i25 57 chr1ptel1M 37071 TCAATCATTTAACA----TTTATCAAACACTTATCATA-GC-AGGTTCTG 37114 v i ---- iii i i i iii i- - i? C L2b_3end#LINE 464 TCATTCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTG 415 chr1ptel1M 37115 TGATAAGTGCTGGGAATACAAAGG-GA--GGGGAAAACT------CTAGT 37155 v i i i iv - --ii iv i ?------ ivi C L2b_3end#LINE 414 TGCTAGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCC 365 chr1ptel1M 37156 CACAAAAAGCTTATAGCTTAATAAGAGAGACA-ACATATAAACAATTATG 37204 v vii i i ii i ii i - i ? ivi vv C L2b_3end#LINE 364 CTCACGGAGCTCACAGTCTAGTGGGGGAGACAGACATGTAANCAGACAAT 315 chr1ptel1M 37205 TACAAGCAAGATATAGACAGAATA-AATTGGGATGGTTTCCAAAGTTAGC 37253 ? i v v -i - i ii -i i iv --i i vvi v C L2b_3end#LINE 314 NATAACCCAGA-GT-GGCAGGGTAGGACTGGGGGGG--CCCAGAGGAGGG 269 chr1ptel1M 37254 CACTAG----GATTAAGAAGGCCTGAGAAAAGCTTTATGCAGAAGATGCA 37299 i iv ---- iiivi ii i v - i ii ivi v i i vv C L2b_3end#LINE 268 CGCCTGACCCGGCCTGGGGGGTCAG-GGAGGGCTTCCCGGAGGAGGTGAC 220 chr1ptel1M 37300 GCTTCAGTTATGATTTGAAGAAGCAAGGGGAATTTAGAAGATG--GAAAT 37347 ii v i iv ii i vv ivi i vivv ii -- ii C L2b_3end#LINE 219 ATTTGAGCTGAGACCTGAAGGATGAGTAGGAGTTGGCCAGGCGAAGAGGT 170 chr1ptel1M 37348 AAGGAGGGGATTATTAAATTATTAACCATTATTAAATTACAGGCATGAGG 37397 ii i ----------------- i -------- v vii C L2b_3end#LINE 169 GGGGAAGGG-----------------CGT--------TCCAGGCAGAGGG 145 chr1ptel1M 37398 GACAGACAGTGAAAAAGCTAGGAGTCTGGAGATAGACAGTCCCATGCAAG 37447 i vv? v i ivv v v ?v v?v v vii v i C L2b_3end#LINE 144 AACAGCANGTGCAAAGGCCCTGAGGCGGGAGNGAGCNTGGCGTGTTCGAG 95 chr1ptel1M 37448 GAATAATGAGGAGGTCCATGTCACTAGATTAG 37479 i iii i vi vi i vi C L2b_3end#LINE 94 GAACAGCAAGGAGGCCAGTGTGGCTGGAGCAG 63 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 56.01 CpG sites = 98, Kimura (unadjusted) = 61.38 Transitions / transversions = 2.00 (98/49) Gap_init rate = 0.10 (40 / 408), avg. gap size = 1.32 (53 / 40) 333 25.72 2.94 8.53 chr1ptel1M 38034 38169 (961831) MIR1_Amn#SINE/MIR 1 129 (101) m_b2s601i1 58 chr1ptel1M 38034 TATAGGGGCAGCTAGGTGGTACAGTG-ATAGAACAGTATCCCTGAAGTCA 38082 vi i i--- vi - i v ivv iv i v i MIR1_Amn#SINE 1 TAGGGAGGCAGT---GTGGTCTAGTGGATAGAGCACTGGACTGGGACTCG 47 chr1ptel1M 38083 GGAGGACCTGAGTTCAAATCTAGCTTCAGACACATAACACTTCCTAGCTG 38132 - i ? ? iv vi ------- iv ?v i? MIR1_Amn#SINE 48 GGAG-ACCTGGGTTCNANTCCCGGCTC-------TGCCACTNGCCNGCTG 89 chr1ptel1M 38133 TGTGACCTTGAATAAGTCAC--AACCTTAAT-TGCCTTAG 38169 ? iii --? ivv -? i MIR1_Amn#SINE 90 NGTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAG 129 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.20 CpG sites = 19, Kimura (unadjusted) = 34.52 Transitions / transversions = 1.46 (19/13) Gap_init rate = 0.10 (14 / 135), avg. gap size = 1.07 (15 / 14) 434 22.85 2.50 8.85 chr1ptel1M 38038 38157 (961843) MIRc#SINE/MIR 2 114 (154) m_b2s601i2 58 chr1ptel1M 38038 GGGGCAGCTAGGTGGTACAGTG-ATAGAACAGTATCCCTGAAGTCAGGAG 38086 i i--- i - v i v ivv i i i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr1ptel1M 38087 GACCTGAGTTCAAATCTAGCTTCAGACACATAACACTTCCTAGCTGTGTG 38136 i i i iv vi ------- iv v MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTC-------TGCCACTTACTAGCTGTGTG 91 chr1ptel1M 38137 ACCTTGAATAAGTCAC--AACCT 38157 iii -- MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACCT 114 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.67 CpG sites = 17, Kimura (unadjusted) = 27.98 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.10 (12 / 119), avg. gap size = 1.08 (13 / 12) 109 10.68 0.00 0.00 chr1ptel1M 38171 38326 (961674) (A)n#Simple_repeat 1 156 (0) m_b2s252i0 59 chr1ptel1M 38171 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAA 38220 i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr1ptel1M 38221 AAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAGAAAGAA 38270 i i i (A)n#Simple_r 51 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 100 chr1ptel1M 38271 AAGAAAAAGGAAAGAAAGAAAGAAAAGAAAAGAAAAAGAAAAAAGAAAGA 38320 i ii i i i i i i i i (A)n#Simple_r 101 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 150 chr1ptel1M 38321 AAAAAA 38326 (A)n#Simple_r 151 AAAAAA 156 Matrix = Unknown Transitions / transversions = 1.00 (15/0) Gap_init rate = 0.00 (0 / 155), avg. gap size = 0.0 (0 / 0) 17 17.75 0.00 2.56 chr1ptel1M 38514 38553 (961447) (ATT)n#Simple_repeat 1 39 (0) m_b2s252i1 60 chr1ptel1M 38514 ATTGTAATTTTTTTTATTATTATTATTATAACTTTTTATT 38553 i v v v v - v (ATT)n#Simple 1 ATTATTATTATTATTATTATTATTATTATTA-TTATTATT 39 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1) 13 4.34 3.85 3.85 chr1ptel1M 38620 38645 (961355) (CCCT)n#Simple_repeat 1 26 (0) m_b2s252i2 61 chr1ptel1M 38620 CCCTCCCTCCCTCCACCCCCT-CCTCC 38645 - i - (CCCT)n#Simpl 1 CCCTCCCTCCCTCC-CTCCCTCCCTCC 26 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.08 (2 / 25), avg. gap size = 1.00 (2 / 2) 1333 29.53 3.23 2.31 chr1ptel1M 38945 39502 (960498) C L1ME5_3end#LINE/L1 (291) 650 88 m_b2s551i0 62 chr1ptel1M 38945 ATCTC---CTGGTTCT-GCTCATTTCACTCAGCATCA-GTTCATGTAA-A 38988 --- v -i iv ii - -- v - C L1ME5_3end#LI 650 ATCTCATTCTGTTTCTTACTTTTTTCACTCAGCACTATGTT--TTTAAGA 603 chr1ptel1M 38989 TCTCCCCAATCCTCTCTGTATTCATCCTTCTGGTCATTTCTTACAGAAAA 39038 ivi vviiv v i v ivviiv iii v v vviv C L1ME5_3end#LI 602 TCCATCCATGTTGCTATGTGTACATCTAGTCCGTTGCTTCTAACTGCTGC 553 chr1ptel1M 39039 ATAATATTCCAAAACATTCATATACCACAATTTACCCAACCATTA----A 39084 i i viiii v vi v i v i v---- C L1ME5_3end#LI 552 ATAGTACTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCA 503 chr1ptel1M 39085 TTGATGGGCATCCATTCATTTTCCAGCTTCTTGCCACTACAAACAGGGCT 39134 v i i vvivvii i i ii i iv C L1ME5_3end#LI 502 GTGATGGACACCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCT 453 chr1ptel1M 39135 GTCACAAACATTTTGGCACATACAGGTCCCTTTCC---CTTATTT-AGTA 39180 iv ii ii ---- i v i vi--- i i v - v C L1ME5_3end#LI 452 GCAATGAACATCCT----CGTACATGTCCCCTTATGGACCTGTGTGAGAA 407 chr1ptel1M 39181 TCTCTTTGGGGTATAAGCCCAGTAGAAATACTGCTGGATCAAAGGGTATG 39230 i i vi v viiv i i v C L1ME5_3end#LI 406 TTTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATG 357 chr1ptel1M 39231 TACAGTTTGATAACTT--TTTGA--ACATAGTTCCAAATTGCTCTCCAGA 39276 i--- --- - -- -- vi v v i C L1ME5_3end#LI 356 C---GT---ATA-CTTAATTTGACTAAGTACTGCCAGATTGCTCTCCAGA 314 chr1ptel1M 39277 ATGGCTGGATGTGTTCACAGTTCCACCAACAATGTATCAGTGTCCCTGGT 39326 v ivv ii v i i i i v v i iv? C L1ME5_3end#LI 313 ATGGCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATN 264 chr1ptel1M 39327 TTCCCACATCCCCTCCAACATTTCGCATTATCTTTCCCTGTCATTCTAGC 39376 i i v i v ivv ii v v i v C L1ME5_3end#LI 263 TCCCCACATCCTCGCCAACACTTGGCATTATCCAGCTTTCTAATTTTTGC 214 chr1ptel1M 39377 CAGTCTGCCAGGTGTGTAGTGGTATCTCAGAATTGTCTTAATTTGCATTT 39426 ivi iv i vvi i C L1ME5_3end#LI 213 CAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATTT 164 chr1ptel1M 39427 CTCTGATTAATAATGACTTGGAGCATATTTTCATATGGCTAGAAGTAGTT 39476 v v v v i vi ivv ivv C L1ME5_3end#LI 163 CTCTGATTACTAATGAGTTTGAGCATCTCTTCATATGCTTGTTAGCCTTT 114 chr1ptel1M 39477 TCAATTTCTTTGTCTGAGAATTGTCT 39502 ivii i iv vi i C L1ME5_3end#LI 113 CGGGTTTCCTCTTCTGTAAATTGCCT 88 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.95 CpG sites = 89, Kimura (unadjusted) = 38.46 Transitions / transversions = 1.24 (89/72) Gap_init rate = 0.04 (22 / 557), avg. gap size = 1.41 (31 / 22) 576 25.74 2.19 0.72 chr1ptel1M 40283 40419 (959581) MIR#SINE/MIR 82 220 (42) m_b2s601i3 63 chr1ptel1M 40283 TGTATGGCCCCAGGCAAGTCACTTAACCCCAGTAGTTCTCAGTTTCCTCA 40332 i i iii i i vv ivvi MIR#SINE/MIR 82 TGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCA 131 chr1ptel1M 40333 TCTGTAAAATGGGGCTAGTAATAGCACTTGCCTCCTAGA---GTTGTGAA 40379 v i i i i v i--- i MIR#SINE/MIR 132 TCTGTAAAATGGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAG 181 chr1ptel1M 40380 GATCAAATGGAGTAACAGTGATAAAGTATTTTGCAACAAT 40419 i iiv i vvvi iii v - i MIR#SINE/MIR 182 GATTAAATGAGTTAATACATGTAAAGCGCTTAG-AACAGT 220 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.57 CpG sites = 24, Kimura (unadjusted) = 32.85 Transitions / transversions = 2.18 (24/11) Gap_init rate = 0.01 (2 / 136), avg. gap size = 2.00 (4 / 2) 22 4.00 0.00 0.00 chr1ptel1M 40515 40540 (959460) (T)n#Simple_repeat 1 26 (0) m_b2s252i3 64 chr1ptel1M 40515 TTTCTTTTTTTTTTTTTTTTTTTTTT 40540 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 949 29.35 4.04 4.28 chr1ptel1M 41007 41451 (958549) C L1ME5_3end#LINE/L1 (313) 628 185 m_b2s551i1 65 chr1ptel1M 41007 TTTCACTCAGCATCA-GTTCATGTAAG-TCTCTCCAGGC--CTTTCTGAA 41052 ii - -- v - iv v i-- v v v C L1ME5_3end#LI 628 TTTCACTCAGCACTATGTT--TTTAAGATCCATCCATGTTGCTATGTGTA 581 chr1ptel1M 41053 ATCATCCTGTTGGTCATTTCTTACAGAACAATAATATTCCATAATATTCA 41102 -- iv iv iii v v vvvv i i ii i v C L1ME5_3end#LI 580 --CATCTAGTCCGTTGCTTCTAACTGCTGCATAGTACTCCATGGTGTGCA 533 chr1ptel1M 41103 TATACCACAATTTA---ATGCCATTCTCCAACTGATGGACATCCATTCAG 41149 vi v --- - i v v i vviv C L1ME5_3end#LI 532 TCCACCACATTTTACCTAT-CCACTCTCCCAGTGATGGACACCCAGGTTG 484 chr1ptel1M 41150 TTTCCAGTTTCTAGCCACTACAAAAAGGGCTGCCACAAACATTCGTGCAC 41199 ii ii i iv i v iv v ii i vi i C L1ME5_3end#LI 483 CCTCCAACTCCCCGCCACCACAAACAACGCTGCAATGAACATCCTCGTAC 434 chr1ptel1M 41200 ATACAGGTCCCTTTC----CCTTCTTTATAATCTCTTTGGGATATAATCC 41245 ---- i v---- viv v v i vv C L1ME5_3end#LI 433 AT----GTCCCCTTATGGACCTGTGTGAGAATTTCTTTGGGATATATACC 388 chr1ptel1M 41246 CAGTAGTAACACTGCTGGATCAAAGGGTATGCACAGTTTGATCACTT--T 41293 v iiiv i i v ii -------i -- C L1ME5_3end#LI 387 CAGGAGCGGAATTGCTGGGTCATAGGGTATGCGTA-------TACTTAAT 345 chr1ptel1M 41294 TTGAGCA--TAGTTCCAAACTACTCTCCAAAATGGTTGGATTCGTTCACA 41341 vi -- v v i i i i i v iiv ii C L1ME5_3end#LI 344 TTGACTAAGTACTGCCAGATTGCTCTCCAGAATGGCTGCACCAGTCTACA 295 chr1ptel1M 41342 ACTCCACCAACAATGCATCAATGTCCCAGTTTTCCCGCATCCCCTCCAAC 41391 vii i i v iv i vi ? i i i v C L1ME5_3end#LI 294 CTCCCACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATCCTCGCCAAC 245 chr1ptel1M 41392 AATCATCATTATT---TTTTCCTGTCATCTTAGCCAATCTGACAGGTGTG 41438 v iiv i---i --- v i v i i i i C L1ME5_3end#LI 244 ACTTGGCATTATCCAGCTTTC---TAATTTTTGCCAGTCTAATAGGTGTA 198 chr1ptel1M 41439 TAGTGGTATCTTA 41451 v i i C L1ME5_3end#LI 197 AAGTGATATCTCA 185 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.15 CpG sites = 73, Kimura (unadjusted) = 38.37 Transitions / transversions = 1.40 (73/52) Gap_init rate = 0.06 (27 / 444), avg. gap size = 1.37 (37 / 27) 981 26.81 3.52 2.96 chr1ptel1M 41083 41451 (958549) C L1ME4c_3end#LINE/L1 (275) 555 185 m_b2s551i2 65 chr1ptel1M 41083 ATAATATTCCATAATATTCATATACCACAATTTAAT--GCCATTCTCCAA 41130 vivi ?v i i v --i i v C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chr1ptel1M 41131 CTGATGGACATCCATTCAGTTTCCAGTTTCTAGCCACTACAAAAAGGGCT 41180 i v ii vviv i i v i i i v iv C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCT 456 chr1ptel1M 41181 GCCACAAACAT--TCGTGCACATACAGGTCCCTTTCCCTTCTTT---ATA 41225 v ii -- i --- -- i i --- v C L1ME4c_3end#L 455 GCAATGAACATCTTCGTGCATATA---G--CTTTTTCCTTCTTTTGAATT 411 chr1ptel1M 41226 ATCTCTTTGGGATATAATCCCAGTAGTAACACTGCTGGATCAAAGGGTAT 41275 i i i v v v iiv i i i C L1ME4c_3end#L 410 ATTTCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTAT 361 chr1ptel1M 41276 GCACAGTTTGATCACTTTTTGAGCATAGTTCCAAACTACTCTCCAAAATG 41325 v v v vi i vivi i v v i i i v C L1ME4c_3end#L 360 GAACATTTTTATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAGG 311 chr1ptel1M 41326 GTTGGATTCGTTCACAACTCCACCAACAATGCATCAATGTCCCAGTTTTC 41375 v iivi i ?iv i i v i? v iv C L1ME4c_3end#L 310 GTTGTACCAATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCA 261 chr1ptel1M 41376 CCGCATCCCCTCCAACA------ATCATCATTATTTTTTCCTGTCATCTT 41419 ? i v i ------ i -- v----v i C L1ME4c_3end#L 260 CCGCANCCTCGCCAGCATTGGGTATTATCA--ATTTTTTA----AATTTT 217 chr1ptel1M 41420 AGCCAATCTGACAGGTGTGTAGTGGTATCTTA 41451 v i i i i i iv i i C L1ME4c_3end#L 216 TGCTAATTTAATAGGCGTAAAATGGTATCTCA 185 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.26 CpG sites = 58, Kimura (unadjusted) = 34.59 Transitions / transversions = 1.53 (58/38) Gap_init rate = 0.04 (15 / 368), avg. gap size = 1.60 (24 / 15) 192 28.57 0.00 0.00 chr1ptel1M 41666 41714 (958286) L2#LINE/L2 2430 2478 (604) m_b2s601i4 66 chr1ptel1M 41666 AGGCATCTCAAGCTCAACACATGTAAAACAGGACTGATTATTTTTACCC 41714 i i ii vi v i vv v i iv L2#LINE/L2 2430 AGGCATCTCAAACTTAACATGTCCAAAACTGAACTCCTGATCTTCCCCC 2478 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.82 CpG sites = 8, Kimura (unadjusted) = 36.82 Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 42 16.30 4.31 4.31 chr1ptel1M 41874 41989 (958011) (AGG)n#Simple_repeat 1 116 (0) m_b2s252i4 67 chr1ptel1M 41874 AGGA-GAGGAAGGA-GAGGAAGGAGGAGTGA-GAGAAGGAGGGAGAGAAG 41920 - - - - - - i - - i (AGG)n#Simple 1 AGGAGGAGG-AGGAGGAGG-AGGAGGAG-GAGGAGGAGGA-GGAG-GAGG 45 chr1ptel1M 41921 AAGAGGAGGAGAAGGAGGGGGAAGAGAAGG-GGAAGAAAAGGAGGA-AAC 41968 i i i i i - i ii -i v (AGG)n#Simple 46 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG 95 chr1ptel1M 41969 GAGGAAGAGGAAGAAGAGGAG 41989 i i i (AGG)n#Simple 96 GAGGAGGAGGAGGAGGAGGAG 116 Matrix = Unknown Transitions / transversions = 14.00 (14/1) Gap_init rate = 0.09 (10 / 115), avg. gap size = 1.00 (10 / 10) 184 27.78 0.00 0.00 chr1ptel1M 42016 42069 (957931) C MIRc#SINE/MIR (0) 268 215 m_b2s601i5 68 chr1ptel1M 42016 AACATTAATAATAGCTAGCATTTACATAGCACTTTAAGATTTGCAAACTT 42065 i v i?v vi ii vii i viv C MIRc#SINE/MIR 268 AATAATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCG 219 chr1ptel1M 42066 CTTT 42069 C MIRc#SINE/MIR 218 CTTT 215 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.56 CpG sites = 9, Kimura (unadjusted) = 36.57 Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 244 30.00 10.00 0.00 chr1ptel1M 42934 43023 (956977) L2d2_3end#LINE/L2 436 534 (21) m_b2s601i6 69 chr1ptel1M 42934 AAATTTTTAG-TCCTTGAGGGCAGGGATTATTTTTGATCTTTTTTTGAAT 42982 i v v - ii v i v vi i v L2d2_3end#LIN 436 AGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACTTCTTTGTAT 485 chr1ptel1M 42983 C----ATAGGAAATAACA----ATCTGGCACACGGTAAGCACATAGTAA 43023 ---- i vivv i ----ii v i i i vi i L2d2_3end#LIN 486 CCCCCACAGCGCCTAGCACAGTGCCTTGCACACAGTAGGCGCTCAATAA 534 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.80 CpG sites = 16, Kimura (unadjusted) = 39.49 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.03 (3 / 89), avg. gap size = 3.00 (9 / 3) 13 13.12 0.00 0.00 chr1ptel1M 43187 43212 (956788) (TTTTC)n#Simple_repeat 1 26 (0) m_b2s252i5 70 chr1ptel1M 43187 TTCTCTTTTCTTTTTTTTTCTTCTCT 43212 i i i (TTTTC)n#Simp 1 TTTTCTTTTCTTTTCTTTTCTTTTCT 26 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 555 30.60 7.10 0.00 chr1ptel1M 43806 43988 (956012) C MIRc#SINE/MIR (70) 198 3 m_b2s601i7 68 chr1ptel1M 43806 TTTAAGCCTCACAACAATCCTGTGATGTAGGT---GC---TATAATTA-- 43847 i v i v i--- --- v -- C MIRc#SINE/MIR 198 TTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATC 149 chr1ptel1M 43848 CTGAGTTTCTAGATTCAGAAAGTGAGGCTTAAAGAAATGAAGTGACTTGC 43897 iv v vi vvi v i i ii v C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr1ptel1M 43898 TCAGGATTACA----TAGTAAAATATGAAG-CAAGATACGATCACAGATC 43942 i i i i ---- ivviiii - ii iv v v i C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTC 49 chr1ptel1M 43943 TTCCTGTGCTCATGGTCAATACTCTTTCTATTAAACAATTCTTTCT 43988 vvii v vi i i i i iv v iv vi C MIRc#SINE/MIR 48 TTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTGCCT 3 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.60 CpG sites = 33, Kimura (unadjusted) = 40.55 Transitions / transversions = 1.43 (33/23) Gap_init rate = 0.03 (5 / 182), avg. gap size = 2.60 (13 / 5) 273 34.67 0.96 2.94 chr1ptel1M 44265 44368 (955632) C 7SLRNA#SINE/Alu (72) 248 147 m_b2s502i0 71 chr1ptel1M 44265 AGGC-TGATTCCATGGCTAATCAGCACAGAAACTTTGGTTTGCCCTATTT 44313 -i i ivi i i i ii iii i ii C 7SLRNA#SINE/A 248 AGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGACCTGCTCCGTTT 199 chr1ptel1M 44314 TCAACACTGATTGGTTCATCACTCCTCCTAATACCATCTGGTGTGCACCC 44363 i i viv iii --- i v vi v i vv v C 7SLRNA#SINE/A 198 CCGACCTGGGCCGGT---TCACCCCTCCTTAGGCAACCTGGTGGTCCCCC 152 chr1ptel1M 44364 TTTCC 44368 vi C 7SLRNA#SINE/A 151 GCTCC 147 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.47 CpG sites = 25, Kimura (unadjusted) = 50.59 Transitions / transversions = 2.50 (25/10) Gap_init rate = 0.04 (4 / 103), avg. gap size = 1.00 (4 / 4) 235 32.32 5.17 3.98 chr1ptel1M 44863 45036 (954964) C L1PA14_3end#LINE/L1 (490) 418 243 m_b2s551i3 72 chr1ptel1M 44863 AAAATAAGTTACCTTCTTCAGG---TATGACAAGTAGTAGAATATCTGGG 44909 i i v iv i v --- iv v i i i vv C L1PA14_3end#L 418 AGAATGATTTATATTCCTCTGGGTATATACCCAGTAATGGGATTGCTGGG 369 chr1ptel1M 44910 TCAAAGAATA-TACCATTTTAATCACTGTTTTTTTTACATAATT-CCAAA 44957 i vii - v iii v v ------- i iviv i- v C L1PA14_3end#L 368 TCGAATGGTAGTTCTGCTTTTAGC-------TCTTTGAGGAATCGCCATA 326 chr1ptel1M 44958 ATG-TTTCCAGAATGGT--AAC-ATTCCACAGTTGTACCAACAGTGTATT 45003 v - v -- - v ii v ivi v C L1PA14_3end#L 325 CTGCTTTCCACAATGGTTGAACTAATTTACACTCCCACCAACAGTGTATA 276 chr1ptel1M 45004 AGTGTGCCTATCTTCCCATAACCCTTCCAACAT 45036 v iv i ii ii iiv i C L1PA14_3end#L 275 AGTGTTCCCTTTTCTCCGCAACCTCGCCAGCAT 243 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.41 CpG sites = 31, Kimura (unadjusted) = 43.62 Transitions / transversions = 1.35 (31/23) Gap_init rate = 0.08 (13 / 173), avg. gap size = 1.23 (16 / 13) 424 28.89 2.73 1.62 chr1ptel1M 44892 45074 (954926) C L1ME4a_3end#LINE/L1 (482) 389 205 m_b2s551i4 72 chr1ptel1M 44892 AGTAGTAGAATATCTGGGTCAAAGAATATAC-CATTTTAATCACTGTTTT 44940 v i vv ii i?- ---i vv i C L1ME4a_3end#L 389 AGAAGTGGAATTACTGGGTCAAAGGGTATGNACATTTT---TAAGGCTTT 343 chr1ptel1M 44941 TTTTACATAATTCCAAAATGTT-TCCAGAATGGT---AACATTCCACAGT 44986 vv v v v ii- v --- v v ii v C L1ME4a_3end#L 342 TGATACATATTGCCAAATTGCCCTCCAGAAAGGTTGTACCAATTTACACT 293 chr1ptel1M 44987 TGTACCAACAGTGTATTAGTGTGCCTATCTTCCCATAACCCTTCCAACAT 45036 ivi i v v ii i i? i v iiv i C L1ME4a_3end#L 292 CCCACCAGCAGTGTATGAGAGTGCCCGTTTCNCCACACCCTCGCCAACAC 243 chr1ptel1M 45037 TAACTTTCCTCATTATTTTTCATCTTTGCTAACTTGAT 45074 iiv v iv v v vv i i C L1ME4a_3end#L 242 TGGGTATTATCAATCTTTTAAATCTTTGCCAATTTGAT 205 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.60 CpG sites = 26, Kimura (unadjusted) = 37.47 Transitions / transversions = 1.00 (26/26) Gap_init rate = 0.03 (6 / 182), avg. gap size = 1.33 (8 / 6) 20 10.11 0.00 0.00 chr1ptel1M 46137 46168 (953832) (AAC)n#Simple_repeat 1 32 (0) m_b2s252i6 73 chr1ptel1M 46137 AACAACAACAACAACAACAACAATAATACCAA 46168 i i v (AAC)n#Simple 1 AACAACAACAACAACAACAACAACAACAACAA 32 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 205 31.53 8.47 3.23 chr1ptel1M 47860 47977 (952023) L2c_3end#LINE/L2 331 454 (24) m_b2s601i8 74 chr1ptel1M 47860 ACTTGTGCTTTCCAATTTTTTTTT--CCTGTGTCTTGCCTACCATTAAAA 47907 ii v -- v i v -- ? v v iv - i i v L2c_3end#LINE 331 ACTTGTATTGT--AATTGTCTGTTTACNTGTCTGTCTCCT-CCACTAGAC 377 chr1ptel1M 47908 TGTAAGCTCCTTAAGGAC--------TATCTGTATTTATATATCTACAAT 47949 i i i -------- i - i v v v ivvi L2c_3end#LINE 378 TGTGAGCTCCTTGAGGGCAGGGACCGTGTCT-TATTCATCTTTGTATCCC 426 chr1ptel1M 47950 TAGTCCCTAGTGCACAGTAATCACTTAA 47977 i iv i ii i iv i i L2c_3end#LINE 427 CAGCGCCTGGCACATAGTAGGCGCTCAA 454 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.95 CpG sites = 22, Kimura (unadjusted) = 43.12 Transitions / transversions = 1.57 (22/14) Gap_init rate = 0.05 (6 / 117), avg. gap size = 2.33 (14 / 6) 15 9.10 8.57 0.00 chr1ptel1M 48193 48227 (951773) (GAGTCTG)n#Simple_repeat 1 38 (0) m_b2s252i7 75 chr1ptel1M 48193 GAGTCTGAAGTCTGGAGTCT-GAG-CTTGAG-CTTGAG 48227 i - - v - v (GAGTCTG)n#Si 1 GAGTCTGGAGTCTGGAGTCTGGAGTCTGGAGTCTGGAG 38 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.09 (3 / 34), avg. gap size = 1.00 (3 / 3) 194 36.16 1.33 4.11 chr1ptel1M 49441 49515 (950485) C MIRb#SINE/MIR (64) 204 132 m_b2s601i9 76 chr1ptel1M 49441 TATATTGTTTCATGAACTAGCCCTTATAGCAACCTTATAAG-TGGACAAT 49489 ii i i ---i ii i i i i iii - i ii v C MIRb#SINE/MIR 204 TGCATTATCTCAT---TTAATCCTCACAACAACCCTGCGAGGTAGGTATT 158 chr1ptel1M 49490 ATTGGCCTTATTTTAAAAATAAAGAA 49515 iv ii v i i i C MIRb#SINE/MIR 157 ATTATCCCCATTTTACAGATGAGGAA 132 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 55.06 CpG sites = 23, Kimura (unadjusted) = 59.23 Transitions / transversions = 7.67 (23/3) Gap_init rate = 0.05 (4 / 74), avg. gap size = 1.00 (4 / 4) 241 35.05 9.52 1.20 chr1ptel1M 49635 49865 (950135) L1ME4c_3end#LINE/L1 326 575 (255) m_b2s551i5 77 chr1ptel1M 49635 TTTGGAACTATGCCTCAAAGGGCACCAAAATCTGCATACCCTTTGACTCA 49684 v v i iv ii v iv v v i L1ME4c_3end#L 326 TTTGGCAATACGTATCAAGAGCCATAAAAATGTTCATACCCTTTGACCCA 375 chr1ptel1M 49685 GCAAT------------AA------CCAAAGAGA----TCAAAAAAGGTA 49712 i ------------ ------ i i i ---- i i v L1ME4c_3end#L 376 GTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAAGAAGGA 425 chr1ptel1M 49713 AAAGGGCTATTTTACAAGAAAATACTTATAGCAGCTCTTTTTGTGGTGGC 49762 -i - v i v i ii i v vi v i ii i L1ME4c_3end#L 426 AAA-AGCTA-TATGCACGAAGATGTTCATTGCAGCGTTATTTATAATAGC 473 chr1ptel1M 49763 AAAGAATCAGATTTTGTTGGTATGTCCATCAGTTAGGTAATGACTGAATG 49812 i i ii vviviiiviv v i vi v ii i i i L1ME4c_3end#L 474 GAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAATGGTTAAGTA 523 chr1ptel1M 49813 TGTTATAGTATATTAATGTAAAAAAAGTAGTGTTCTACTATAAGAAATGA 49862 vi i i i? ivii vii - v i v vi i v i L1ME4c_3end#L 524 AATTATGGTACATCNACTCGATGGAA-TATTATGCAGCCATTAAAAATGA 572 chr1ptel1M 49863 TAA 49865 L1ME4c_3end#L 573 TAA 575 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 47.77 CpG sites = 52, Kimura (unadjusted) = 50.64 Transitions / transversions = 1.86 (52/28) Gap_init rate = 0.03 (6 / 230), avg. gap size = 4.17 (25 / 6) 36 0.00 0.00 0.00 chr1ptel1M 50183 50213 (949787) (TG)n#Simple_repeat 1 31 (0) c_b2s251i0 78 chr1ptel1M 50183 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50213 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 896 24.48 4.40 1.95 chr1ptel1M 51216 51465 (948535) C MIRc#SINE/MIR (0) 268 13 m_b2s601i10 79 chr1ptel1M 51216 AATAATAATAATAGCT---AT--ATATAGTTCATTACAATTGGCCAACTC 51260 i?v --- --i iv v i vi v viv C MIRc#SINE/MIR 268 AATAATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCG 219 chr1ptel1M 51261 CTTTATCCCTTATGATTTTTCTC-TGTGAATTTCACAACACCCCTG--AG 51307 -- v v ii-- v - v vii v -- C MIRc#SINE/MIR 218 CTTT--CACATACA--TTATCTCATTTGATCCTCACAACAACCCTGTGAG 173 chr1ptel1M 51308 ATTGATAGCACAAATAA-ATTATCCCCATTTCATAGATGAGAGAACTGAG 51356 i v ii vi ii v- i i ii C MIRc#SINE/MIR 172 GTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAG 123 chr1ptel1M 51357 GCTCAGAGAGTTTTAAGCGATTTACCTACGGTCACACAGTAAATCAGTGG 51406 v - i i i i v iv i v C MIRc#SINE/MIR 122 GCTCAGAGAGGTT-AAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGG 74 chr1ptel1M 51407 CAGAGCTGGGATTAGAACTCAGGT-TCTCTAACTCTAA-TCCAATGCCAT 51454 i i v i - ii i i - i iv C MIRc#SINE/MIR 73 CAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCT 24 chr1ptel1M 51455 TCTCACTACAC 51465 ii i C MIRc#SINE/MIR 23 TTCCACTGCAC 13 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.43 CpG sites = 38, Kimura (unadjusted) = 30.65 Transitions / transversions = 1.73 (38/22) Gap_init rate = 0.05 (12 / 249), avg. gap size = 1.33 (16 / 12) 27 0.00 0.00 0.00 chr1ptel1M 51467 51496 (948504) (GT)n#Simple_repeat 1 30 (0) m_b2s252i8 80 chr1ptel1M 51467 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 51496 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 30 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 49 2.22 0.00 0.00 chr1ptel1M 51497 51542 (948458) (GA)n#Simple_repeat 1 46 (0) c_b2s251i1 81 chr1ptel1M 51497 GAGAAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 51542 i (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 46 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 14 14.08 0.00 6.06 chr1ptel1M 52108 52142 (947858) (TTA)n#Simple_repeat 1 33 (0) m_b2s252i9 82 chr1ptel1M 52108 TTTTTATAATTCATTAGTATTATTTATTGTTATTA 52142 v v - v - i (TTA)n#Simple 1 TTATTATTATT-ATTATTATTA-TTATTATTATTA 33 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 13 12.49 0.00 3.70 chr1ptel1M 53115 53142 (946858) (TAT)n#Simple_repeat 1 27 (0) m_b2s252i11 83 chr1ptel1M 53115 TATTGTATTTATTATTATTATTATATAT 53142 i vv - (TAT)n#Simple 1 TATTATTATTATTATTATTATTAT-TAT 27 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 31 15.83 6.98 1.10 chr1ptel1M 53112 53197 (946803) (ATATATT)n#Simple_repeat 1 91 (0) m_b2s252i10 84 chr1ptel1M 53112 ATATATTGTAT-TTAT-TATTAT-TATTATATA-TGTAAAATATATACTA 53157 i - - - - i v v i (ATATATT)n#Si 1 ATATATTATATATTATATATTATATATTATATATTATATATTATATATTA 50 chr1ptel1M 53158 TAAAGTA-A-AATATATGTTATATATTATACTTTAACATATT 53197 v v - - v i - v v i (ATATATT)n#Si 51 TATATTATATATTATATATTATATATTATA-TATTATATATT 91 Matrix = Unknown Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.08 (7 / 85), avg. gap size = 1.00 (7 / 7) 17 15.35 0.00 2.70 chr1ptel1M 53315 53352 (946648) (TAAA)n#Simple_repeat 1 37 (0) m_b2s252i12 85 chr1ptel1M 53315 TAAATAAAAAGCTATAATAAATAAATATATATATAAAT 53352 v iv - v v (TAAA)n#Simpl 1 TAAATAAATAAATA-AATAAATAAATAAATAAATAAAT 37 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 13 14.91 3.33 0.00 chr1ptel1M 53327 53356 (946644) (TATA)n#Simple_repeat 1 31 (0) m_b2s252i13 85 chr1ptel1M 53327 TATA-ATAAATAAATATATATATAAATTTAT 53356 - v v v v (TATA)n#Simpl 1 TATATATATATATATATATATATATATATAT 31 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 468 23.62 0.00 7.83 chr1ptel1M 54950 55073 (944927) MIRb#SINE/MIR 4 118 (150) m_b2s601i11 86 chr1ptel1M 54950 AGGGGCAGCTGGTGGTGTAGGTGATAGAGCACCAGCCCTGGAGTCGGGAG 54999 -- i vv v vi ii i ivi MIRb#SINE/MIR 4 AGGGGCAGC--GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACA 51 chr1ptel1M 55000 GATCCAAGTTCAAATCTGGCCTCAGACATTTAATATTTCCTAGCTGTGTG 55049 i iii i iv v v v i ------- MIRb#SINE/MIR 52 GACCTGGGTTCGAATCCCGGCTCTGCCACTTA-------CTAGCTGTGTG 94 chr1ptel1M 55050 ACCCTGGGTAAGTCACTTAACTTC 55073 i i i i MIRb#SINE/MIR 95 ACCTTGGGCAAGTTACTTAACCTC 118 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 27.81 CpG sites = 18, Kimura (unadjusted) = 29.08 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.07 (9 / 123), avg. gap size = 1.00 (9 / 9) 618 31.68 4.13 3.80 chr1ptel1M 56164 56478 (943522) HERVL66#LTR/ERVL 804 1119 (3210) m_b2s701i0 87 chr1ptel1M 56164 GCTTTTGACAAAGCAAAAATAGCAATGTAAATTGCCTTAGATTTGTGGCC 56213 vv v vv ii i v v i i i i HERVL66#LTR/E 804 GCTTTTGAACAAGCTAAACAAGCGGTGCAACTGGCCCTGGATCTATGGCC 853 chr1ptel1M 56214 C-TAAAGGAAGGGCCAGTAGAATTGCAAGTTTCTTTTTTTTTAATGACTA 56262 - vi v i vv -- v ii vi v vi HERVL66#LTR/E 854 CATACGGGATGGGCCAGTAGAACTGCAAGTAAC--TGTCCTAGATCAACA 901 chr1ptel1M 56263 TACAAATTGGAA-CTTGTGCAAAAACAGGGAAATAAAAATGTCCTGTTAG 56311 i v i- iv i i iviiv i iv v iv i HERVL66#LTR/E 902 TGCTAATTGGAGCCTTAGGCAGAAACAAGATGGGAAGAGGGTACCTTTGG 951 chr1ptel1M 56312 GATTTTGGTTCAGAAAACTGCCCAATTC-----AGGTTTGAACTACAGAC 56356 i vi v i vi vv ----- i i iv i- --- HERVL66#LTR/E 952 GGTTTTGGACCCGGAAACTGCCAGAGGCCGGCAAAGCTTATACC-C---C 997 chr1ptel1M 56357 TTTTGCGCAGTGGTTGCTAGCTGTATATCGGGCCTTAGTGGAAACAAAAC 56406 i v v iii i vvv i i iv ii HERVL66#LTR/E 998 TTTCGAGAAGCAATTGTTAGCTTGCTATTGGGCTTTGCTGGAAACGGAAC 1047 chr1ptel1M 56407 AATTGACTATTAATCTCAA-AGTGATAT-----TGAGATCATTAATTCCT 56450 vi -- ii ---- -vi i ----- ii vvv HERVL66#LTR/E 1048 ACCT--CTGCT----TCAACCATGATGTCTTTATGAGGCCTGAAATTCCT 1091 chr1ptel1M 56451 ATTATGAGTTGCATTATGAGCGCCCCTA 56478 v vi i iv i HERVL66#LTR/E 1092 ATTATGACTTGGGTCATGAGTTCCCCCA 1119 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.98 CpG sites = 54, Kimura (unadjusted) = 42.28 Transitions / transversions = 1.29 (54/42) Gap_init rate = 0.05 (17 / 314), avg. gap size = 1.47 (25 / 17) 16 19.86 0.00 0.00 chr1ptel1M 56572 56606 (943394) (AAG)n#Simple_repeat 1 35 (0) m_b2s252i14 88 chr1ptel1M 56572 AAAAAAAAGAAGAAGAAGAAGAATTAAAAGAGGAA 56606 i i vv i i (AAG)n#Simple 1 AAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAA 35 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 17 7.51 0.00 3.45 chr1ptel1M 57091 57120 (942880) (GGAG)n#Simple_repeat 1 29 (0) m_b2s252i15 89 chr1ptel1M 57091 GGAGGTGGGGAGGGAGGGAGAGGAGGGAGG 57120 vi - (GGAG)n#Simpl 1 GGAGGGAGGGAGGGAGGGAG-GGAGGGAGG 29 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 310 22.17 15.45 1.60 chr1ptel1M 57427 57536 (942464) MIRc#SINE/MIR 3 127 (141) m_b2s601i12 90 chr1ptel1M 57427 AGCCAG-GTGGTGCAGTGGATAGGACACCAACCCTGAAGTCAGGAGGACC 57475 v - v ii iiiv i i i MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chr1ptel1M 57476 CGAGTTCAAATCTGACCCCAGACACTTA-----------AC--TGGGCAA 57512 i i i i iviv i v v ----------- -- MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 102 chr1ptel1M 57513 GTCACTTAACGCCAATC---GCCTCAG 57536 vi -- --- MIRc#SINE/MIR 103 GTCACTTAACCTC--TCTGAGCCTCAG 127 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 24.56 CpG sites = 16, Kimura (unadjusted) = 27.14 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.06 (6 / 109), avg. gap size = 3.17 (19 / 6) 27 20.26 3.95 1.28 chr1ptel1M 57537 57612 (942388) (GAAA)n#Simple_repeat 1 78 (0) m_b2s252i16 91 chr1ptel1M 57537 GAAA-AAA-AAACAAAGAAAGAAAATAAAGCAAAAAAGACAGAAAGGCAG 57584 - - v - v v i v iv (GAAA)n#Simpl 1 GAAAGAAAGAAAGAAAGAAAG-AAAGAAAGAAAGAAAGAAAGAAAGAAAG 49 chr1ptel1M 57585 AAAG-AAGGAAGGGGGAAAAAAAGAGAGA 57612 - i iii i i (GAAA)n#Simpl 50 AAAGAAAGAAAGAAAGAAAGAAAGAAAGA 78 Matrix = Unknown Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.05 (4 / 75), avg. gap size = 1.00 (4 / 4) 18 19.79 2.17 0.00 chr1ptel1M 58402 58447 (941553) (TTTG)n#Simple_repeat 1 47 (0) m_b2s252i17 92 chr1ptel1M 58402 TTTGTTTGTTTGTTTGTTTGTTTTCCTGGTTATAT-TTTGATTCTTT 58447 vii v i v - v v (TTTG)n#Simpl 1 TTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTT 47 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1) 30 7.71 0.00 0.00 chr1ptel1M 59391 59432 (940568) (CATCA)n#Simple_repeat 1 42 (0) c_b2s251i2 93 chr1ptel1M 59391 CATCACATCACATCATATCATATCACATCACATTACATCACA 59432 i i i (CATCA)n#Simp 1 CATCACATCACATCACATCACATCACATCACATCACATCACA 42 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 33 5.62 0.00 0.00 chr1ptel1M 62409 62445 (937555) (AT)n#Simple_repeat 1 37 (0) c_b2s251i3 94 chr1ptel1M 62409 ATATATATCTATGTATATATATATATATATATATATA 62445 v i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATA 37 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 17 5.00 0.00 0.00 chr1ptel1M 62446 62466 (937534) (CA)n#Simple_repeat 1 21 (0) m_b2s252i18 95 chr1ptel1M 62446 CACACACACACACACACATAC 62466 i (CA)n#Simple_ 1 CACACACACACACACACACAC 21 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 25 16.50 0.00 0.00 chr1ptel1M 62728 62775 (937225) (GTT)n#Simple_repeat 1 48 (0) m_b2s252i19 96 chr1ptel1M 62728 GTTGTTGTTGTTTTTGGTGTGGTTGTGGTGGTGGTGGTTGTTGTTGTT 62775 v v v v v v v (GTT)n#Simple 1 GTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTT 48 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 20 8.02 0.00 0.00 chr1ptel1M 63266 63292 (936708) (AC)n#Simple_repeat 1 27 (0) m_b2s252i20 97 chr1ptel1M 63266 ACACATACACACACATACACACACACA 63292 i i (AC)n#Simple_ 1 ACACACACACACACACACACACACACA 27 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 257 31.71 0.00 2.97 chr1ptel1M 63462 63565 (936435) L1MB8_3end#LINE/L1 230 330 (595) m_b2s551i6 98 chr1ptel1M 63462 CAGATTTACTAATATGAGTTGCAGAGGATGTGGGAAAACTGGAAGAACTA 63511 -- v i v v vv ii i -vv v L1MB8_3end#LI 230 CAGAT--AATAACAAGTGTTGGCGAGGATGTGGAGAAATTGGAA-CCCTC 276 chr1ptel1M 63512 ATGTATTGTTGGTAGATTTGTGAACTGATCCGACCATTCTGGAAAGCAAT 63561 ii i i i ivv i v i v ii ii i i i L1MB8_3end#LI 277 ATACACTGCTGGTGGGAATGTAAAATGGTGCAGCCGCTTTGGAAAACAGT 326 chr1ptel1M 63562 TTGG 63565 i L1MB8_3end#LI 327 CTGG 330 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.14 CpG sites = 20, Kimura (unadjusted) = 42.95 Transitions / transversions = 1.67 (20/12) Gap_init rate = 0.03 (3 / 103), avg. gap size = 1.00 (3 / 3) 324 26.75 0.00 1.16 chr1ptel1M 63479 63565 (936435) L1ME5_3end#LINE/L1 245 330 (611) m_b2s551i7 98 chr1ptel1M 63479 GTTGCAGAGGATGTGGGAAAACTGGAAGAACTAATGTATTGTTGGTAGAT 63528 vv i ? iv vv- v i i i i iv L1ME5_3end#LI 245 GTTGGCGAGGATGTGGGGANATAGGAACC-CTCATGCACTGCTGGTGGGA 293 chr1ptel1M 63529 TTGTGAACTGATCCGACCATTCTGGAAAGCAATTTGG 63565 v ii i v ii i i L1ME5_3end#LI 294 GTGTAGACTGGTGCAGCCATTCTGGAGAGCAATCTGG 330 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.52 CpG sites = 14, Kimura (unadjusted) = 34.52 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.01 (1 / 86), avg. gap size = 1.00 (1 / 1) 305 26.17 0.92 1.85 chr1ptel1M 63485 63593 (936407) L1ME4c_3end#LINE/L1 251 358 (472) m_b2s551i8 98 chr1ptel1M 63485 GAGGATGTGGGAAAACTGGAAGAACTAATGTATTGTTGGTAGATTTGTGA 63534 ? i vi v v?- v ii i i vv? i L1ME4c_3end#L 251 GAGGNTGCGGTGAAACTGGTACN-CTCATACATTGCTGGTGGCANTGTAA 299 chr1ptel1M 63535 ACTGATCCGACCATTCTGGAAAGCAATTTGG-AACAAAGCCCAATGGGCT 63583 i i v i v i - i vivvi - i i L1ME4c_3end#L 300 ATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAA-GAGCC 348 chr1ptel1M 63584 ATAAAATTGT 63593 v L1ME4c_3end#L 349 ATAAAAATGT 358 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 31.15 CpG sites = 16, Kimura (unadjusted) = 34.06 Transitions / transversions = 1.33 (16/12) Gap_init rate = 0.03 (3 / 108), avg. gap size = 1.00 (3 / 3) 203 38.50 3.23 3.64 chr1ptel1M 64089 64336 (935664) L2#LINE/L2 2383 2629 (453) m_b2s601i13 99 chr1ptel1M 64089 CCCATACATCTAACTTCTTATCAGGCATTTTGCA-TCAGATAATCAAAT- 64136 i i i i v i iiv i i i- - ii i- v - L2#LINE/L2 2383 CTCGTATATCCAACTGCCTACTCGACATCTC-CACTTGGATG-TCTAATA 2430 chr1ptel1M 64137 GGCA---CAAATTCACCATACCCAAAATAAAACCCATTACCTTCCCCCTC 64183 --- i i v ii ivi i v v i L2#LINE/L2 2431 GGCATCTCAAACTTAACATGTCCAAAACTGAACTCCTGATCTTCCCCCTC 2480 chr1ptel1M 64184 CCCCCCATCATCCTCCTCTTCCAAATTTCCTTATTATTTAGAGGGTATCA 64233 vvv ----- v iiv ivi ii --i i v?ii iv L2#LINE/L2 2481 AAACC-----TGCTCCTCCCGCAGTCTTCCCCAT--CTCAGTNAATGGCA 2523 chr1ptel1M 64234 AAACTA---CTACAATCACTCAAATTCAACACCCTCATTTTATTCTTAAC 64280 vv i ---i v i ii iiiiv v i vivv i i i L2#LINE/L2 2524 ACTCCATCCTTCCAGTTGCTCAGGCCAAAAACCTTGGAGTCATCCTTGAC 2573 chr1ptel1M 64281 TTCTCACTATCTTTCAATTTTCATATCTAATCAACTGCCAAATTTGATCA 64330 i v v i vviii i i v iiiv iivi i L2#LINE/L2 2574 TCCTCTCTTTCTCTCACACCCCACATCCAATCCATCAGCAAATCCTGTCG 2623 chr1ptel1M 64331 TTTCTA 64336 vi L2#LINE/L2 2624 GCTCTA 2629 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 55.95 CpG sites = 61, Kimura (unadjusted) = 59.03 Transitions / transversions = 1.97 (61/31) Gap_init rate = 0.05 (13 / 247), avg. gap size = 1.31 (17 / 13) 220 27.95 13.51 3.28 chr1ptel1M 65332 65442 (934558) L2a_3end#LINE/L2 396 517 (0) m_b2s601i14 100 chr1ptel1M 65332 AGAATGTAAACTG---GAAACCAAGGGCTATT-TCTCTTTT--------C 65369 i v--- iiv i i v - v -------- L2a_3end#LINE 396 AGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTCTGTTTTGTTCACTGC 445 chr1ptel1M 65370 CTTTTCCTTAGTTATCCAGGATAGAGCCTGGCCCATAGT---TACTTAAT 65416 iv v ii -iii i i i v v ---ii i L2a_3end#LINE 446 TGTATCCCCAG-CGCCTAGAACAGTGCCTGGCACATAGTAGGCGCTCAAT 494 chr1ptel1M 65417 AAATGTAAGATGGATGATCAATGAAT 65442 i vv v i --- L2a_3end#LINE 495 AAATATTTGTTGAATG---AATGAAT 517 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.04 CpG sites = 19, Kimura (unadjusted) = 36.37 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.07 (8 / 110), avg. gap size = 2.38 (19 / 8) 570 35.80 4.07 8.48 chr1ptel1M 65637 66103 (933897) L3#LINE/CR1 3542 3989 (110) m_b2s601i15 101 chr1ptel1M 65637 AAGAAGGTGGTAGTATCACT-TACTCTGCCCTGCTCATACCAAGTCTGAA 65685 i i ii vi i - v v v vi i L3#LINE/CR1 3542 AGGGAGGTAATAGTCCCGCTGTACTCTGCGCTGGTCAGACCACATCTGGA 3591 chr1ptel1M 65686 ACAT-GTGATAACATCTGTG-ACCACAGCCTAGCCAAGATGCAGGTAAAT 65733 ii - i v v vv v -i vii ivvii iiiv ii i L3#LINE/CR1 3592 GTATTGCGTTCAGTTCTGGGCGCCACATTTTAAGAGGGACATTGACAAAC 3641 chr1ptel1M 65734 TGTAGAGCATCCAGAGGA-AGCGAGCCAGCATGGTGAAGGACCCCAAGTC 65782 v v i - - v ii ivi iv L3#LINE/CR1 3642 TGGAGCGCGTCCAGAGGAGAGCGA-CCAGGATGGTGAAGGGTCTGGAAAC 3690 chr1ptel1M 65783 TGTGCC--ATGAGGATCATTTGGAAGAACTAAGGAGCTTTAGTTAGGAGA 65830 ii i -- v iv i i ii vv iiv L3#LINE/CR1 3691 CATGTCATATGAGGAACGGTTGAAGGAACTGGGGATGTTTAGCCTGGAGA 3740 chr1ptel1M 65831 CCTGTGAGAATCTAAATCCATGTCAGTTAGAACCAGGATTGCCATCTTAA 65880 v-- v ii ii i ------------i iv v v ii v L3#LINE/CR1 3741 A--GAGAAGACTTAGA------------GGAGACATGATAGCTGTCTTCA 3776 chr1ptel1M 65881 GGTATCTGAAATCTTTTC------AAGTCTTCTTAGATTTTTTCC---TG 65921 ii i ivvi v ------ vvvvv i v i--- L3#LINE/CR1 3777 AATATTTGAAGGGCTGTCATGTGGAAGAGGGATTAGACTTATTCTGTGTG 3826 chr1ptel1M 65922 GCACATCAAGATGACCAGAATCAGAAGCAACGGTGGCAGAAGGCTGATTA 65971 --- v - iv ii i v i -- ii ----- L3#LINE/CR1 3827 GC---TCCAGA-GGGCAGAACTAGGACCAATG--GGTGGAAG-----TTA 3865 chr1ptel1M 65972 ACTTTTCAAGTTAAAAAAATAATAATAAACTTAA---AAAAAAAAACTTT 66018 ------ i -v iiv i -- -- vii i --- ii i - L3#LINE/CR1 3866 ------CAGG-GAGGCAGAT--T--TCGGCTCAATATAAGGAAGAAC-TT 3903 chr1ptel1M 66019 TTTAAGAATTTTAACTTCCCAGATGTGACATTATCTGCTCCAAGAGATGG 66068 i v ivv i vi i vi iv viv ii i? i i L3#LINE/CR1 3904 TCTAACAATCAGAGCTGTCCAAAAATGGAATGGGCTGCCTCGNGAGGTAG 3953 chr1ptel1M 66069 TGGGATCTTTTTTTC-AGAAATCTTTAAGCAAAGAC 66103 i v iiiv iv -i ii v i i i L3#LINE/CR1 3954 TGAGCTCCCCGTCACTGGAGGTGTTCAAGCAGAGGC 3989 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 47.46 CpG sites = 96, Kimura (unadjusted) = 51.33 Transitions / transversions = 1.68 (96/57) Gap_init rate = 0.10 (47 / 466), avg. gap size = 1.21 (57 / 47) 13 24.60 1.72 5.36 chr1ptel1M 67368 67425 (932575) (AGG)n#Simple_repeat 1 56 (0) m_b2s252i21 102 chr1ptel1M 67368 AGGATGAGG-GGCCGAGTCTGAGAGGGAGGCAGCTGGAGGAGGCAGCGGG 67416 v - vv vvv ii - vv - - i (AGG)n#Simple 1 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGG-AGGAGGAGGAGG-AG-GAG 47 chr1ptel1M 67417 GAGGAGGAG 67425 (AGG)n#Simple 48 GAGGAGGAG 56 Matrix = Unknown Transitions / transversions = 0.38 (3/8) Gap_init rate = 0.07 (4 / 57), avg. gap size = 1.00 (4 / 4) 266 20.19 9.57 9.57 chr1ptel1M 69609 69723 (930277) C MIRb#SINE/MIR (150) 118 4 m_b2s601i17 103 chr1ptel1M 69609 GGGGTTAAGTGAC------AGGGTCACACAGCTAGGAAGTGTGAAGTGTC 69652 i i ------ i v - v ---- C MIRb#SINE/MIR 118 GAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTG-GCAG---- 74 chr1ptel1M 69653 TGAAGCC-AGATTTGAACACAGGTCCTCC--ACTTCAGGG-CTG-GCTCT 69697 --- -i i v ivi -- i ii - i - C MIRb#SINE/MIR 73 ---AGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCT 27 chr1ptel1M 69698 ATCCACTATGATACCTAGCTGTCCCT 69723 v ---ii vv i C MIRb#SINE/MIR 26 TTCCACT---GCACCACGCTGCCCCT 4 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 21.59 CpG sites = 14, Kimura (unadjusted) = 24.13 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.14 (16 / 114), avg. gap size = 1.38 (22 / 16) 274 16.99 11.46 8.08 chr1ptel1M 69609 69704 (930296) C MIRc#SINE/MIR (153) 115 17 m_b2s601i16 103 chr1ptel1M 69609 GGGGTTAAGTGAC------AGGGTCACACAGCTAGGAAGTGTGAAGTGTC 69652 i ------ i v - v ---- C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTG-GCAG---- 71 chr1ptel1M 69653 TGAAGCC-AGATTTGAACACAGGTCCTCC--ACTTCAGGGCTG--GCTCT 69697 --- -i i i v i -- i i v ii-- C MIRc#SINE/MIR 70 ---AGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCT 24 chr1ptel1M 69698 ATCCACT 69704 v C MIRc#SINE/MIR 23 TTCCACT 17 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 18.32 CpG sites = 10, Kimura (unadjusted) = 19.73 Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.13 (12 / 95), avg. gap size = 1.58 (19 / 12) 441 22.06 3.01 4.58 chr1ptel1M 71154 71286 (928714) C MIRb#SINE/MIR (0) 268 138 m_b2s601i18 104 chr1ptel1M 71154 AAGAAGAAAACTGGCCATTATTATGAGGGGCTTATTAAGTGCCAGACA-T 71202 v v i i i- -- vii v i v i - C MIRb#SINE/MIR 268 AATAATAGAGCTA-CCATT--TATTGAGCGCTTACTATGTGCCAGGCACT 222 chr1ptel1M 71203 AAGTTAAACACCTTAC---CAGTATCTCCTGTGATCCTCACAACAAACCC 71249 iv i i i i --- v v v i - C MIRb#SINE/MIR 221 GTGCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAAC-AACCC 173 chr1ptel1M 71250 TGGAAGGGAGGTGTTTTTAATCCCCATTTTAACAAAT 71286 vi v i v - - i C MIRb#SINE/MIR 172 TGCGAGGTAGGTATTATT-ATCCCCATTTT-ACAGAT 138 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 24.38 CpG sites = 16, Kimura (unadjusted) = 26.50 Transitions / transversions = 1.33 (16/12) Gap_init rate = 0.06 (8 / 132), avg. gap size = 1.25 (10 / 8) 38 0.00 0.00 0.00 chr1ptel1M 71707 71739 (928261) (AC)n#Simple_repeat 1 33 (0) c_b2s251i4 105 chr1ptel1M 71707 ACACACACACACACACACACACACACACACACA 71739 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACA 33 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 360 31.49 7.51 3.75 chr1ptel1M 73603 73988 (926012) C L1M2_orf2#LINE/L1 (1459) 1832 1433 m_b2s551i9 106 chr1ptel1M 73603 AAAGACTGTTGTACTTTGACCAAA-GCATTTTCT----TTATTGTATTGA 73647 i iv v i - i - v ----i viv C L1M2_orf2#LIN 1832 AAGGGATGTTGAATTTT-ATCAAATGCTTTTTCTGCATCTATTGAGATGA 1784 chr1ptel1M 73648 CTATGTGCTTTTGGGTGTTCT-CATTTAG--AATGAGAT----TATGTTC 73690 ii i v --- i - iv --i v ----i i i C L1M2_orf2#LIN 1783 TCATATGGTTTT---TGTCCTTCATTCTGTTGATGTGATGTATCACGTTT 1737 chr1ptel1M 73691 ATTGCTCTCCCAATGTTGAACTACCCTTCCATCCCTACTGGCAATCCCAC 73740 v i v vv i i v ivvivv C L1M2_orf2#LIN 1736 ATTGATTTGCGTATGTTGAACCATCCTTGCATCCCTGGGATAAATCCCAC 1687 chr1ptel1M 73741 TTGATCATAATGAATGGTTTCTTGGACAATTCAC--TTGGAT--GTTTTG 73786 ii ? ?i i i ---i vii -- i -- v C L1M2_orf2#LIN 1686 TTGATCATGGTGNATNATCTTTT---TAATGTGCTGTTGAATTCGGTTTG 1640 chr1ptel1M 73787 ATAGGATTTTGTTTAAAATTAGAGGGAAGAGACA---GTGTTCATT---- 73829 v v v ii vvv -------- ---i i---- C L1M2_orf2#LIN 1639 CTAGTATTTTGTTGAGGATTTTTG--------CATCTATGTTCATCAGGG 1598 chr1ptel1M 73830 -CTTTAACTTCTAATTTACTCTTTGTGTTTAAATTTTCCTTGGTTTCAGT 73878 -iv ii i v i v i v vvivii vii ii C L1M2_orf2#LIN 1597 ATATTGGCCTGTAGTTTTCTTTTTTTGTTGTGTCCTTGTCTGGTTTTGGT 1548 chr1ptel1M 73879 ATTGGGTCTATGTTAGACTCCTAAAAGAATTTTTGTAGGATACTTTCTT- 73927 ii viv i i v v i vi v v v ? v ii i - C L1M2_orf2#LIN 1547 ATCAGGGTAATGCTGGCCTCGTAGAATGAGTTTGGAAGNATTCCCTCCTC 1498 chr1ptel1M 73928 ----ATTTGGTGGAATTAGTGGTGAGGTGTGGGTATTAACTGTTCTTTAT 73973 ---- vv viv v v i vi v ii v v C L1M2_orf2#LIN 1497 TTCAATTTTTTGGAATAGTTTGAGAAGAATTGGTATTAGTTCTTCTTTAA 1448 chr1ptel1M 73974 AGATCTGATAGAATT 73988 vi i i C L1M2_orf2#LIN 1447 ATGTTTGGTAGAATT 1433 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.86 CpG sites = 64, Kimura (unadjusted) = 42.34 Transitions / transversions = 1.21 (64/53) Gap_init rate = 0.07 (27 / 385), avg. gap size = 1.63 (44 / 27) 17 21.27 8.89 2.08 chr1ptel1M 74185 74274 (925726) (GTCATTTT)n#Simple_repeat 1 96 (0) m_b2s252i22 107 chr1ptel1M 74185 GTCATTTT-TAGTTTTGTCATTTT-T-ATTTATTTCCAATTTGTC-TTTT 74230 - vi - - - v - v - (GTCATTTT)n#S 1 GTCATTTTGTCATTTTGTCATTTTGTCATTT-TGT-CATTTTGTCATTTT 48 chr1ptel1M 74231 -TC-CCTGCTAATTTTAATATTTTGTC-TTTTGT-ACTTTCTAAGTTT 74274 - -ii vv v ivi - - i v v v (GTCATTTT)n#S 49 GTCATTTTGTCATTTTGTCATTTTGTCATTTTGTCATTTTGTCATTTT 96 Matrix = Unknown Transitions / transversions = 0.60 (6/10) Gap_init rate = 0.11 (10 / 89), avg. gap size = 1.00 (10 / 10) 339 26.65 8.03 1.37 chr1ptel1M 75833 75969 (924031) MIR3#SINE/MIR 51 196 (12) m_b3s601i0 108 chr1ptel1M 75833 GGATTTAAGAGTTGACTCTGACACTCATAAAGGGGATGACCTTTGGGCAG 75882 i iv vvii i v v iv?ivv vi - i MIR3#SINE/MIR 51 GGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTT-GGGCAA 99 chr1ptel1M 75883 ATC----C-CCTCTCTGTGTTT--GTTTCTT--TCTGTAAATTGAGGAGG 75923 i ---- - v ii -- i -- v - MIR3#SINE/MIR 100 GTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGG-GG 148 chr1ptel1M 75924 GTTGGACTTTTTAA-CTCTGAAGTGTTTTTCAGCTCT-ACATCTTATG 75969 vvv i - i i vii i - ii MIR3#SINE/MIR 149 GTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATG 196 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.88 CpG sites = 21, Kimura (unadjusted) = 34.04 Transitions / transversions = 1.40 (21/15) Gap_init rate = 0.06 (8 / 136), avg. gap size = 1.62 (13 / 8) 12 15.01 3.33 0.00 chr1ptel1M 76935 76964 (923036) (TCTCCA)n#Simple_repeat 1 31 (0) m_b3s252i1 109 chr1ptel1M 76935 TCTCCATCTTCATCTCTAACT-CATTTCCAT 76964 i i v - i (TCTCCA)n#Sim 1 TCTCCATCTCCATCTCCATCTCCATCTCCAT 31 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 190 32.84 1.49 0.00 chr1ptel1M 77213 77279 (922721) MIR3#SINE/MIR 114 181 (27) m_b3s601i1 110 chr1ptel1M 77213 CTGAATCTGGGTTTCC-CATCAACAAAATAAGTGGGTTGCAATCCATGGC 77261 iii vi - vii i v v v vv ii MIR3#SINE/MIR 114 CTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGAT 163 chr1ptel1M 77262 CCTGTATATCCCTTCCAG 77279 iivv vi MIR3#SINE/MIR 164 CTCTAAGGTCCCTTCCAG 181 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 44.27 CpG sites = 12, Kimura (unadjusted) = 44.27 Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.02 (1 / 66), avg. gap size = 1.00 (1 / 1) 199 33.65 9.57 1.98 chr1ptel1M 77369 77462 (922538) C L2b_3end#LINE/L2 (27) 439 339 m_b3s601i2 111 chr1ptel1M 77369 AGTGCCTGCTACATGCCAGGTCCTGGACTAAGTACCAGGAACATAAAGAG 77418 i i iii i? vi i ii ii i-- v v C L2b_3end#LINE 439 AGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGGG--ATACAGCG 392 chr1ptel1M 77419 ATGCAAAGGACA---------TCTGCTCTCCTGTAGGCCAAGGACTGGTG 77459 i v v i ---------i i vi v vi vi v i C L2b_3end#LINE 391 GTGAACAAGACAGACNCGGTCCCTGCCCTCACGGAGCTCACAGTCTAGTG 342 chr1ptel1M 77460 GGG 77462 C L2b_3end#LINE 341 GGG 339 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.86 CpG sites = 21, Kimura (unadjusted) = 48.57 Transitions / transversions = 2.10 (21/10) Gap_init rate = 0.03 (3 / 93), avg. gap size = 3.67 (11 / 3) 389 29.33 12.67 0.00 chr1ptel1M 77620 77769 (922231) C MIR#SINE/MIR (3) 259 91 m_b3s601i3 112 chr1ptel1M 77620 AATGACTAGCACTTCCACAGCACCTACTGTGTGCCATGAAC-------AG 77662 ii i i vivv i i i v v ------- C MIR#SINE/MIR 259 AATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAG 210 chr1ptel1M 77663 TGTT------GT-----CTTACTTTGTCCTCATGAGAACTCTATGAT-TA 77700 i i ------ ----- i i vi ii v i v- C MIR#SINE/MIR 209 CGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGGTA 160 chr1ptel1M 77701 GGTGTGATTGTTGTACCCATTTTACAGTTAAAGAAACTGAGGCAGACAGG 77750 iiv i i v v i i v v i C MIR#SINE/MIR 159 GGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGA 110 chr1ptel1M 77751 AATACTGTAAATTGACTAA 77769 ii vvv v v i C MIR#SINE/MIR 109 GGTTAAGTAACTTGCCCAA 91 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.09 CpG sites = 26, Kimura (unadjusted) = 38.29 Transitions / transversions = 1.44 (26/18) Gap_init rate = 0.03 (4 / 149), avg. gap size = 4.75 (19 / 4) 388 24.69 22.28 3.78 chr1ptel1M 77638 77839 (922161) C MIRb#SINE/MIR (23) 245 8 m_b3s601i4 112 chr1ptel1M 77638 AGCACCTACTGTGTGCCATGAACAGTG------------------TTGTC 77669 i i i v v v ------------------ i C MIRb#SINE/MIR 245 AGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACATGCATTATC 196 chr1ptel1M 77670 TTACTTTGTCCTCATGAGAACTCTATGAT-TAGGTGTGATTGTTGTACCC 77718 i i vi ii v i ii v- --- i i v C MIRb#SINE/MIR 195 TCATTTAATCCTCACAACAACCCTGCGAGGTAGGT---ATTATTATCCCC 149 chr1ptel1M 77719 ATTTTACAGTTAAAGAAACTGAGG--CAGACAGG--AATACTGTAAATTG 77764 v i i -- v -- ---- v C MIRb#SINE/MIR 148 ATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAA----GTAACTTG 103 chr1ptel1M 77765 ACTA-----ACCCATTTAT---------GAGGTGGGATTAAAACTCAGGT 77800 v i ----- v vi v--------- vi vi i C MIRb#SINE/MIR 102 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGT 53 chr1ptel1M 77801 CTTAATGATTAAAAACCCTAT--------CACTGTACCACCAACTGC 77839 vvv i vv v ii -------- i --i C MIRb#SINE/MIR 52 CTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCACCAC--GCTGC 8 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.23 CpG sites = 26, Kimura (unadjusted) = 30.65 Transitions / transversions = 1.18 (26/22) Gap_init rate = 0.08 (16 / 201), avg. gap size = 3.38 (54 / 16) 461 28.02 1.26 1.26 chr1ptel1M 82370 82528 (917472) L1ME4c_3end#LINE/L1 397 555 (275) m_b3s551i0 113 chr1ptel1M 82370 TATCCCAAAGAGATCAT--AAAGGAAGGAAAAGGACTCACATGTACAAAA 82417 i i i v -- i i - - i i i i L1ME4c_3end#L 397 TATCCTAAGGAAATAATTCAAAAGAAGGAAAAAG-CT-ATATGCACGAAG 444 chr1ptel1M 82418 ATGTTTGTGGCAGCCCTTTTTATAGTAGCAAGAAACTGAAAACTGAGGGA 82467 ii v vi v i i i i i vivvvi L1ME4c_3end#L 445 ATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAA 494 chr1ptel1M 82468 ATACCCATCACTTGGAGAATGGCTGAATAAGTTATGGTATATGAATGTTT 82517 ii v v v i i i i i i v? ivivv L1ME4c_3end#L 495 ATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGA 544 chr1ptel1M 82518 TGGAATATTAT 82528 L1ME4c_3end#L 545 TGGAATATTAT 555 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.74 CpG sites = 29, Kimura (unadjusted) = 36.89 Transitions / transversions = 1.93 (29/15) Gap_init rate = 0.02 (3 / 158), avg. gap size = 1.33 (4 / 3) 14 27.05 1.82 1.82 chr1ptel1M 84307 84361 (915639) (AGAGAG)n#Simple_repeat 1 55 (0) m_b3s252i2 114 chr1ptel1M 84307 AGAGAGCCAGAGGGAGAAAGAGAGAGATTGAAAGATCAGGTGGGGAGA-A 84355 vv i i vv i -v ivi i - (AGAGAG)n#Sim 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA-GAGAGAGAGAGAGA 49 chr1ptel1M 84356 GAGAGA 84361 (AGAGAG)n#Sim 50 GAGAGA 55 Matrix = Unknown Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.04 (2 / 54), avg. gap size = 1.00 (2 / 2) 34 14.49 0.00 0.00 chr1ptel1M 84850 84903 (915097) (A)n#Simple_repeat 1 54 (0) m_b3s252i3 115 chr1ptel1M 84850 AAAAACAAAAAAAAAAAAACAAAAAAAAAAAAAAAGGAAAAAAAGGAAAG 84899 v v ii ii i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr1ptel1M 84900 AAAA 84903 (A)n#Simple_r 51 AAAA 54 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 16 21.58 0.00 0.00 chr1ptel1M 86319 86350 (913650) (A)n#Simple_repeat 1 32 (0) m_b3s252i4 116 chr1ptel1M 86319 AAAAAAAAAAAAAAACAGAACTAAACAGAAAA 86350 v i vv v i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 32 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 17 23.06 3.41 7.06 chr1ptel1M 86649 86736 (913264) (AGAAG)n#Simple_repeat 1 85 (0) m_b3s252i5 117 chr1ptel1M 86649 AGAAGTAGGAAGATAAAGAGAAAAGAAAAGGGGCAGGATAGAAGGGAGAG 86698 - - -i i i ii - i v i - (AGAAG)n#Simp 1 AGAAG-A-GAAGA-GAAGAGAAGAGAAGAGAAG-AGAAGAGAAGAGA-AG 45 chr1ptel1M 86699 CAGAA-ACACTAGGAGAAAAGGTAAGAGAAGA-AAGA-AAG 86736 - - v vv i i iv - - (AGAAG)n#Simp 46 -AGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAG 85 Matrix = Unknown Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.10 (9 / 87), avg. gap size = 1.00 (9 / 9) 363 27.48 1.60 2.70 chr1ptel1M 86855 87041 (912959) L1MEj_5end#LINE/L1 1976 2160 (0) m_b3s551i1 118 chr1ptel1M 86855 AAAAGAAAAACAAAAGTATATACAAGGGAGAAAATAGGATGGA--GAAAA 86902 ? i --- v i i?i v i i -- v L1MEj_5end#LI 1976 AANAAAAAAACAAAA---TAAATAAANAATAAAGTAAGATGGAAGGAATA 2022 chr1ptel1M 86903 ACATGGAGCTGAT-AATCATAATTTTGAATGTGAATGGGATGAACTCTCC 86951 v vi ivv - i i v ivi i iv i L1MEj_5end#LI 2023 AAATCAAGTATATCAGTCGTTACACTAAATGTGAATGGACTGAATTCTCC 2072 chr1ptel1M 86952 CATAAAAAGGAAGCAAATAGCAGAGTGGATTAAAAAACATTATTCTATAA 87001 v iv vi v iv v i vv ii viiv L1MEj_5end#LI 2073 CATTAAAAGACAGAGACTGTCAGATTGGGTTAAAAAACAAAACCCAGCTA 2122 chr1ptel1M 87002 TATGTTGGTTATAAGAAACACATTTCACACAGAAAGAGAT 87041 i v i i v v -- v L1MEj_5end#LI 2123 TATGCTGTTTACAAGAAACACACTTAAAAC--AAAGTGAT 2160 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.32 CpG sites = 26, Kimura (unadjusted) = 35.18 Transitions / transversions = 1.08 (26/24) Gap_init rate = 0.04 (7 / 186), avg. gap size = 1.14 (8 / 7) 450 28.07 3.39 3.39 chr1ptel1M 86916 87151 (912849) L1M1_orf2#LINE/L1 27 262 (3032) m_b3s551i2 118 chr1ptel1M 86916 AATCATAATTTTGAATGTGAATGGGATGAACTCTCCCATAAAAAGGAAGC 86965 v iv i iv i v v iv vv L1M1_orf2#LIN 27 AATAATAACATTGAATGTAAATGGACTAAACTCTCCAATCAAAAGACATA 76 chr1ptel1M 86966 AAATAGCAGAGTGGATTAAAAAACATTATTCTATAATATGTTGGTTATAA 87015 i i i v i v vv ii v? i v vi i L1M1_orf2#LIN 77 GAGTGGCTGAATGGATGAAAAAACAAGACCCANTGATCTGTTGCCTACAA 126 chr1ptel1M 87016 GAAACACATTTCACACAGAAAGAGATAC--AGAGTAAAGGTAAAAGGCTA 87063 i vi v v i -- v i ii i v i L1M1_orf2#LIN 127 GAAACACACTTCACCTATAAAGACACACATAGACTGAAAATAAAGGGATG 176 chr1ptel1M 87064 AAAAAGAATTTATTATCCTTCAGCTGAAGTAAAAAAAAAAAAAGGGGGGG 87113 i ii -- -- v -- i-- i ii vv i vi L1M1_orf2#LIN 177 GAAAAAGA--TAT--TCCAT--GCC--AATGGAAACCAAAAAAGAGCAGG 218 chr1ptel1M 87114 AATAGCAATTCTGATCTCAGATAAAGCA------AAGATAAAAA 87151 i v v v v i ii ------ i L1M1_orf2#LIN 219 AGTAGCTATACTTATATCAGACAAAATAGATTTCAAGACAAAAA 262 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.12 CpG sites = 36, Kimura (unadjusted) = 36.12 Transitions / transversions = 1.29 (36/28) Gap_init rate = 0.04 (10 / 235), avg. gap size = 1.60 (16 / 10) 15 19.81 4.11 7.04 chr1ptel1M 87371 87443 (912557) (AAAAG)n#Simple_repeat 1 71 (0) m_b3s252i6 119 chr1ptel1M 87371 AATAGAAAA-ATCAGATCA-AAAAGGAAAGAAAATGAGTAAGAAAACAAA 87418 v - vv vv - i - -v v (AAAAG)n#Simp 1 AAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAA-GA-AAAGAAAAGAAA 48 chr1ptel1M 87419 ATGCAAATGAACAACAACA-AAAAGA 87443 - - v - v v - (AAAAG)n#Simp 49 A-G-AAAAGAA-AAGAAAAGAAAAGA 71 Matrix = Unknown Transitions / transversions = 0.10 (1/10) Gap_init rate = 0.11 (8 / 72), avg. gap size = 1.00 (8 / 8) 261 33.33 0.00 0.00 chr1ptel1M 87673 87810 (912190) C L1MC4a_3end#LINE/L1 (2052) 577 440 m_b3s551i3 120 chr1ptel1M 87673 ATCCTCCTGATAATTTCTTATAGAATAATAATATTCCATAACATTCACAT 87722 i v vv i i vvvv i i viii vv ii C L1MC4a_3end#L 577 ATCTTCCTCATTCTTTTTTACAGCTGCATAGTACTCCATTGTGTGGATGT 528 chr1ptel1M 87723 ACCATAACTTATTCAGCCATTCTGCAACTGATGGGCATCCACTCAGTTTC 87772 ii i ? v v i?? ii vviv C L1MC4a_3end#L 527 ACCATAGTTTATTCAACCANTCTCCTATNNATGGGCATTTAGGTTGTTTC 478 chr1ptel1M 87773 CAGTTACTTGCCACAACAAAAAGGGCTGCTACAAACAA 87810 i vvi v iv v iv v ii i C L1MC4a_3end#L 477 CAATATTTTGCAATTACAAACAATGCTGCAATGAATAA 440 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 46.40 CpG sites = 24, Kimura (unadjusted) = 46.40 Transitions / transversions = 1.09 (24/22) Gap_init rate = 0.00 (0 / 137), avg. gap size = 0.0 (0 / 0) 324 30.00 0.00 0.00 chr1ptel1M 87700 87809 (912191) C L1ME3G_3end#LINE/L1 (376) 548 439 m_b3s551i4 120 chr1ptel1M 87700 ATAATATTCCATAACATTCACATACCATAACTTATTCAGCCATTCTGCAA 87749 i ii vv i i i i iv v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr1ptel1M 87750 CTGATGGGCATCCACTCAGTTTCCAGTTACTTGCCACAACAAAAAGGGCT 87799 i i ii vviv i vi i i iv v iv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr1ptel1M 87800 GCTACAAACA 87809 v ii C L1ME3G_3end#L 448 GCAATGAACA 439 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.33 CpG sites = 21, Kimura (unadjusted) = 39.91 Transitions / transversions = 1.75 (21/12) Gap_init rate = 0.00 (0 / 109), avg. gap size = 0.0 (0 / 0) 2228 31.98 5.29 2.01 chr1ptel1M 87920 89754 (910246) L1M4_orf2#LINE/L1 392 2285 (1009) m_b3s551i5 121 chr1ptel1M 87920 AATTACAAGAAGAAATAGACAGCAAAACTATACTAATGGTAGGCCTCAAC 87969 iv i i iivv v v i v v i i i L1M4_orf2#LIN 392 AATTGAAGGGAGAAATAGACAATTCAACAATAATAGTTGGAGACTTCAAT 441 chr1ptel1M 87970 ATTCCCTTCTCA-----GAATCAGACAAATCTAATCACAAAATAAACAAA 88014 ii vi i ----- i vii -- iv v i v i L1M4_orf2#LIN 442 ACCCCACTTTCAATAATGGATAGAACAA--CTAGACAGAAGATCAACAAG 489 chr1ptel1M 88015 AAAGATCCTTGGAAGAAGGAAAGAATCCTAGAAA--ATCTAGATATGATA 88062 i i----- i vvvi v iv v -- v iv i i L1M4_orf2#LIN 490 GAAA-----TAGAAGACTTGAACAACACTATAAACCAACTAGACCTAACA 534 chr1ptel1M 88063 GACCTCTGGAGAAAATTGAAT--AGGGACAGAAAGAAATACATGTTTTTT 88110 v iv v i vv i-- ivi v i-- ii i - L1M4_orf2#LIN 535 GACATCTATAGAACACTCCACCCAACAACAGCAG--AATACACATTCTT- 581 chr1ptel1M 88111 TTCTCAGCAGTACATAGCACCTATACAAAAATAGACCATGCTTTAGGGCA 88160 -- ivv i i v v viv v ii iiv v L1M4_orf2#LIN 582 --CTCAAGTGCACATGGAACATTCTCCAGGATAGACCATATGTTAGGCCA 629 chr1ptel1M 88161 TAAAAACTTTATAAACAAATGCAGAAAGGCATT--AATAGTAAATGCTTC 88208 vvvv v v i vi - - -- vi v viv vi L1M4_orf2#LIN 630 TAAAACAAGTCTCAATAAATTTA-AAAGG-ATTGAAATCATACAAAGTAT 677 chr1ptel1M 88209 CTTTTTATACCACAATAAAA----ATTATAT-TCAATAAAGGGTCAAGGA 88253 v i ivv ii ---- v v- vi --- L1M4_orf2#LIN 678 GTTCTCCGACCACAATGGAATGAAATTAGAAATCAATAACAG---AAGGA 724 chr1ptel1M 88254 AA----GAGAGCCTAAAAACAATTAGAAATTATATAACCTAATTCTAAAA 88299 ---- ii iiii v i vv i v i vi v i v L1M4_orf2#LIN 725 AATTTGGGAAATTCACAAATATGTGGAAATTAAACAACACACTCCTAAAT 774 chr1ptel1M 88300 AATGAGTGGATCAAATAGCAAATCACAGAAACAATCCG----TAATTTCA 88345 iv i i v iv iiiiv iv ---- v v L1M4_orf2#LIN 775 AACCAATGGGTCAAAGAAGAAATCACAAGGGAAATTAGAAAATACTTTGA 824 chr1ptel1M 88346 --TCCATGAGAATGATAATGAGACAAACCAAAACCTATGGCATGCAGCCA 88393 -- vv i i v iivi v i v ? L1M4_orf2#LIN 825 GATGAATGAAAACGAAAACACAACATACCAAAACTTATGGGATGCAGCNA 874 chr1ptel1M 88394 AAGTAGTTCCTAG-GGGAACTTTTATATATCT-TAAAAGCTACTAAAATA 88441 i v i - v --- v - v -- v v L1M4_orf2#LIN 875 AAGCAGTGCTTAGAGGGAAATTT---ATAGCTGTAAATGC--CTATATTA 919 chr1ptel1M 88442 AAATAGAGAAAAAGG----AGATCCCTGAATTGGGCATGCAACCAAAACA 88487 v - i i---- i vv i vi iiv v v v iv iv L1M4_orf2#LIN 920 AAAAAGA-AGAAAGATCTCAAATCAATAACCTAACCTTCCACCTTAAGAA 968 chr1ptel1M 88488 GCTAAAAAAAGAA---TTAATTAAACCCCCTGTTAAATACCAAATTAGAA 88534 i i ---iv i vvv i- ii vv iivvi L1M4_orf2#LIN 969 ACTAGAAAAAGAAGAGCAAACTAAACCCAAAGC-AAGCAGAAGGAAGGAA 1017 chr1ptel1M 88535 ATTCTGAAATTCAAAGGAGAGATTAATAAAATAGAAATTAAGAGAATTAT 88584 vv i iv i i vi i v i i v ii i iv L1M4_orf2#LIN 1018 ATAATAAAGATTAGAGCGGAAATAAATGAAATAGAGAATAGAAAAACAAT 1067 chr1ptel1M 88585 TGA----ACTAATAAA--TAAGAGTTGGTTTTATGAAAACAATAACAAAA 88628 v ---- ii ii --i i i v v vi L1M4_orf2#LIN 1068 AGAGAAAATCAACGAAACCAAAAGTTGGTTCTTTGAAAAGATCAACAAAA 1117 chr1ptel1M 88629 T----AAAGGTTTAGTTAATTTTATCA-GAAAAAAAGAAAGAATAAAACC 88673 ---- vv i ivi v i - i --i vi L1M4_orf2#LIN 1118 TTGACAAACCTTTAGCTAGACTGACCAAGAAAAAAAGAGAGAA--GACTC 1165 chr1ptel1M 88674 ACATCACCAGTATCAAAAAATAAAGAGTAAAC-TTATTACCAATGAAAAA 88722 v i i iv ii vv vii - i i ivvv v L1M4_orf2#LIN 1166 AAATTACTAAAATCAGGAATGAAAGAGGGGACATTACTACCGACCTTACA 1215 chr1ptel1M 88723 GAAATTAAAGTAATAATTAGT---TATTTTACCCAACTGCATGTCAGCAA 88769 v ivi v v v--- i v ivv i i i i L1M4_orf2#LIN 1216 GAAATAAAAAGGATTATAAGGGAATACTATGAACAATTGTATGCCAACAA 1265 chr1ptel1M 88770 TTCAGACAATCTAACCTAAATGGATGAATATTTGAGATAATGTAAATTAT 88819 v i i i iviv ii vii iii vi iii i i L1M4_orf2#LIN 1266 ATTAGATAACCTAGATGAAATGGACAAATTCCTAGAAAGACACAAACTAC 1315 chr1ptel1M 88820 GCAGGTAAACAGAAGAGAAAATCAATTATTTAAATAGTCCCATTTTTGAA 88869 vv iiivi vv ii vi vv i i v i vviviiv L1M4_orf2#LIN 1316 CGAAACTGACTCAAGAAGAAATAGAAAATCTGAATAGACCTATAACAAGT 1365 chr1ptel1M 88870 AAAGAAATTGAATAAGCCATTAGTGAACTCCCTAAGAAATAATCTCCAGA 88919 i v iv i ivi i i vi iv vvi i L1M4_orf2#LIN 1366 AAAGAGATTGAATTAGTAATCAAAAAACTTCCCACAAAGAAAAGCCCAGG 1415 chr1ptel1M 88920 GCCAAATGGATTCATGAGTTAAATCTATCAAACATTTAAAGAAAAATTAA 88969 ? i v ivi v v i i L1M4_orf2#LIN 1416 NCCAGATGGCTTCACTGGTGAATTCTACCAAACATTTAAAGAAGAATTAA 1465 chr1ptel1M 88970 TTATAATACTCTGTAAACTATTTGGAAAAACAG----GTAAAGAAGTCCT 89015 ivvi v iiii v ivi i ---- v ii vv i L1M4_orf2#LIN 1466 CACCAATCCTTCACAAACTCTTCCAAAAAATAGAAGAGGAGGGAACACTT 1515 chr1ptel1M 89016 GCCAATTTTTTTCTGTGACACAAATATGATATTGATACTTAAACAAAGAA 89065 v i iv - i vi v i v ivi iv v iiv L1M4_orf2#LIN 1516 CCCAACTCATT-CTATGAGGCCAGTATTACCCTGATACCAAAACCAGACA 1564 chr1ptel1M 89066 GAGCCAAAACACAAAAAGAAAATTACATATTAATCTCCCTGATGAATATT 89115 i v vv vi i v ii v v v L1M4_orf2#LIN 1565 AAGACATCACAAGAAAAGAAAACTACAGACCAATATCCCTTATGAATATA 1614 chr1ptel1M 89116 GATGCAAAAATTTTAAATAAAATATTAGCAAAGAGATTACAGCAACTAAT 89165 ii v i i vv v v vv L1M4_orf2#LIN 1615 GATGCAAAAATCCTCAACAAAATACTAGCAAACCGAATCCAGCAACATAT 1664 chr1ptel1M 89166 AAGCAGGATAAGACACTATGACCAAGTCGGAGTTATAGCAGGAATTAAAG 89215 iv v v i v v vv vv L1M4_orf2#LIN 1665 AAAAAGGATTATACACCATGACCAAGTGGGATTTATCCCAGGAATGCAAG 1714 chr1ptel1M 89216 GCAGGTTCAATATCAGGAAA-AAATTACCATAACTAACCATCTCAATA-- 89262 iv i ?v i -v i vii ivv v i -- L1M4_orf2#LIN 1715 GTTGGTTCAACATNCGAAAATCAATCAATGTAATACACCATATTAATAGA 1764 chr1ptel1M 89263 ACAAAGCAAACAGAAATCATTTGATAATCTCAATAAATGCATAAAAA-CT 89311 i --i i i iv v i i v - v L1M4_orf2#LIN 1765 ATAAAG--GACAAAAACCACATGATCATCTCAATAGACGCAGAAAAAGCA 1812 chr1ptel1M 89312 TTCAACAAAATGCAGCACCCATTCCTATTAAAAACATTAGAGAGCATAGG 89361 ii v i v v iv i vi v ivv L1M4_orf2#LIN 1813 TTTGACAAAATCCAACACCCTTTCATGATAAAAACACTCAACAAACTAGG 1862 chr1ptel1M 89362 CATA-AAGGGAGCTTTC----CTTAATAAGCAGTATCAATCTAAAAGCAA 89406 v - i i ---- i i ivi i v ivv v v L1M4_orf2#LIN 1863 AATAGAAGGGAACTTCCTCAACCTGATAAAGGGCATCTACGAAAAACCCA 1912 chr1ptel1M 89407 CAGCAAGCATTATTTGTAATGGAGAGAAGCTATATTCATTCCCAATAAGA 89456 v i i viv v i ii iv ?v v vv L1M4_orf2#LIN 1913 CAGCTAACATCATACTTAATGGTGAAAGACTGAANGCTTTCCCCCTAAGA 1962 chr1ptel1M 89457 TCAGGGATGAAACAAGGATG-CTACTATCACCACTATTATTCAGCATTGT 89505 i ii i - ii v i vi i L1M4_orf2#LIN 1963 TCAGGAACAAGACAAGGATGTCCGCTCTCGCCACTTCTATTCAACATTGT 2012 chr1ptel1M 89506 ATTAGAAATATTGGCTTTAGCAATAAGAAAAAAAAAAAAAAAGAAATAAA 89555 i i ii vi i ivvi v iv i ----- L1M4_orf2#LIN 2013 ACTGGAGGTTCTAGCCAGGGCAATTAGGCAAGAAAAA-----GAAATAAA 2057 chr1ptel1M 89556 AGG-ATTTAGAAGCGACAGTGAG--GTAA--CTATCACTCTTTGCAGATG 89600 - ii vvv v vi -- -- v v i L1M4_orf2#LIN 2058 AGGCATCCAGATTGGAAAGGAAGAAGTAAAACTATCTCTATTCGCAGATG 2107 chr1ptel1M 89601 ATATGAT---ATACTTAGAGAATCCTAGAAAATC-ATCCAAAAACTA--- 89643 i ---i iv i iii - i?v --- L1M4_orf2#LIN 2108 ACATGATCTTGTATATAGAAAATCCTAAGGAATCCACNAAAAAACTATTA 2157 chr1ptel1M 89644 --ACT---------------CGAAGTTTCAGGATATAAAATAAACCAACA 89676 -- --------------- i i v i i v ivv L1M4_orf2#LIN 2158 GAACTAATAAACGAGTTCAGCAAGGTTGCAGGATACAAGATCAATATACA 2207 chr1ptel1M 89677 CAAATCATCAGTATTTCTATATATTA-CA---GACAAAGCCCAACAGCAA 89722 v viv i i - ---i --i i v iii L1M4_orf2#LIN 2208 AAAATCAATTGTATTTCTATACACTAGCAATGAACAA--TCCGAAAATGA 2255 chr1ptel1M 89723 AATATAGAAAGAGAAATCCCATTTAAAATAAC 89754 vv -- iv i v i L1M4_orf2#LIN 2256 AATTAAGAA--AACAATTCCATTTACAATAGC 2285 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.82 CpG sites = 311, Kimura (unadjusted) = 42.83 Transitions / transversions = 1.18 (311/264) Gap_init rate = 0.04 (74 / 1834), avg. gap size = 1.82 (135 / 74) 480 25.19 5.74 2.38 chr1ptel1M 89759 89880 (910120) MIRc#SINE/MIR 2 127 (141) m_b3s601i5 122 chr1ptel1M 89759 GAGGCAACTAGGTGGTATAGTGGAGAGAATACCAGTCCTGAAGTCAGGAG 89808 ii--- ii i ii ii v i i i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr1ptel1M 89809 GAGCTGAGTTCAAAT------TTTAACACTTCCTAGTTGTGTGACTCCGT 89852 v i i i ------ i iv v i iii v MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 98 chr1ptel1M 89853 GCAAGTCACTTAACCCCAATT-GCCTCAG 89880 i vv v- MIRc#SINE/MIR 99 GCAAGTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.01 CpG sites = 22, Kimura (unadjusted) = 32.33 Transitions / transversions = 2.75 (22/8) Gap_init rate = 0.04 (5 / 121), avg. gap size = 2.00 (10 / 5) 330 31.49 2.69 4.37 chr1ptel1M 89908 90279 (909721) L1P4_orf2#LINE/L1 2277 2642 (652) m_b3s551i6 123 chr1ptel1M 89908 TAAAATAACAGTAGACAAAATAAAATATTTTGGG-TCTATCTT-CCAAGA 89955 v i vii i v ii v i- vi v- i L1P4_orf2#LIN 2277 TACAATAGCCACAAAAAAAATAAAATACCTAGGAATACATCTAACCAAGG 2326 chr1ptel1M 89956 CAGATCTAAGAACTAAGTAGAAACACAATTACAAAACACTTCTCAAATAA 90005 - i vv v v-- v iv v i v v -i L1P4_orf2#LIN 2327 -AGGTGAAAGATCTC--TACAAGGAGAACTACAAAACACTGCTGAAA-GA 2372 chr1ptel1M 90006 AATCAAATCT-----AAAAAATTGGAAAAATATCAGTTGCTCATGGGTTG 90050 ? vv ----- v v i ivvv i L1P4_orf2#LIN 2373 AATCANAGATGACACAAACAAATGGAAAAACATTCCATGCTCATGGATTG 2422 chr1ptel1M 90051 ACCGAGCTAATAAAATAAAAATGACAATTTTACCTAAATTGGTCTACTTG 90100 ivv iii vvi v i v vi i i viii vvi L1P4_orf2#LIN 2423 GAAGAATCAATATCGTTAAAATGGCCATACTGCCCAAAGCAATCTACAGA 2472 chr1ptel1M 90101 TTCAGTGCCATACTAATCAAACTGCCAAAAAAATTATTTTATAAAATTAG 90150 ii i v iv i vivv - i i i L1P4_orf2#LIN 2473 TTCAACGCTATTCCTATCAAACTACCAACGTCATT-TTTCACAGAATTAG 2521 chr1ptel1M 90151 GAAAAATAATAACAAAATTCACCAGGAA-CATCAAAATGTCAAAAAAGAC 90199 i iv vvi ivv - vv iv i vi v -- L1P4_orf2#LIN 2522 AAAAAACTATTCTAAAATTCATATGGAACCAAAAAAGAGCCCGAATAG-- 2569 chr1ptel1M 90200 TATCAAGGGAAT--TAATGAAAAAAAAAAAATACAAAGGATGGTGTCTTG 90247 --i i v -- vv i v vv --- - ii --- L1P4_orf2#LIN 2570 --CCAAAGCAATCCTAAGCAAAAAGAACAAAGCC---GGA-GGCATC--- 2610 chr1ptel1M 90248 GCAGTAGCAAACCTAAAACTATACTATAAAGC 90279 i v v vi i v i i L1P4_orf2#LIN 2611 ACATTACCCGACTTCAAACTATACTACAAGGC 2642 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.13 CpG sites = 55, Kimura (unadjusted) = 41.47 Transitions / transversions = 0.96 (55/57) Gap_init rate = 0.06 (21 / 371), avg. gap size = 1.24 (26 / 21) 339 32.43 2.01 3.75 chr1ptel1M 89982 90279 (909721) L1PREC2_orf2#LINE/L1 2350 2642 (652) m_b3s551i7 123 chr1ptel1M 89982 AATTACAAAACACTTCTCAAATAAAATCAAATCT-----AAAAAATTGGA 90026 v -i i vv ----- v v L1PREC2_orf2# 2350 AATTACAAAACACTGCTCAAA-GAAATCAGAGATGACACAAACAAATGGA 2398 chr1ptel1M 90027 AAAATATCAGTTGCTCATGGGTTGACCGAGCTAATAAAATAAAAATGACA 90076 i ivvv i v ivv iii vvi v i v L1PREC2_orf2# 2399 AAAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTTAAAATGGCC 2448 chr1ptel1M 90077 ATTTTACCTAAATTGGTCTACTTGTTCAGTGCCATACTAATCAAACTGCC 90126 vi i i viii i vvi i i v iv i L1PREC2_orf2# 2449 ATACTGCCCAAAGCAATTTACAGATTCAATGCTATTCCTATCAAACTACC 2498 chr1ptel1M 90127 AAAAAAATTATTTTATAAAATTAGGAAAAATAATAACAAAATTCACCAGG 90176 vi v -i i i i i i iv vvi ivv L1PREC2_orf2# 2499 AATGACATT-CTTCACAGAACTAGAAAAAACTATTTTAAAATTCATATGG 2547 chr1ptel1M 90177 AA-CATCAAAATGTCAAAAAAGACTATCAAGGGAATTAATGAAAAAAAAA 90225 - vv iv i vi v ----i v i--iv iv L1PREC2_orf2# 2548 AACCAAAAAAGAGCCCGAATAG----CCAAGGCAATC--CTAAGCAAAAA 2591 chr1ptel1M 90226 AAATACAAAGGATGGTGTCTTGGCAGTAGCAAACCTAAAACTATACTATA 90275 i -- - v v v v vi iv v vi i v i L1PREC2_orf2# 2592 GA--ACAAA-GCTGGAGGCATCACGCTACCCGACTTCAAACTATACTACA 2638 chr1ptel1M 90276 AAGC 90279 ii L1PREC2_orf2# 2639 GGGC 2642 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.79 CpG sites = 48, Kimura (unadjusted) = 43.20 Transitions / transversions = 1.07 (48/45) Gap_init rate = 0.04 (13 / 297), avg. gap size = 1.31 (17 / 13) 233 21.52 6.33 0.00 chr1ptel1M 90638 90716 (909284) L1M2_orf2#LINE/L1 2803 2886 (405) m_b3s551i8 124 chr1ptel1M 90638 TGCTGAGAAAACTGGAAA---ATGT-CAGAAACAGGGCA-TAGACCTACA 90682 i v --- i - iv v iv - ivi L1M2_orf2#LIN 2803 TGCTGGGAAAACTGGATATCCATATGCAGAAGAATGAAACTAGACCCCTA 2852 chr1ptel1M 90683 TCTCACACCCTATACCAAAATAAGGTCAAAATGG 90716 v v v v iv L1M2_orf2#LIN 2853 TCTCTCACCATATACAAAAATCAACTCAAAATGG 2886 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 25.40 CpG sites = 7, Kimura (unadjusted) = 25.40 Transitions / transversions = 0.70 (7/10) Gap_init rate = 0.04 (3 / 78), avg. gap size = 1.67 (5 / 3) 228 26.63 4.32 4.97 chr1ptel1M 90835 90996 (909004) L1M5_orf2#LINE/L1 3010 3170 (124) m_b3s551i9 121 chr1ptel1M 90835 ATGAAAGGCAAAATGGACAACTTTGATTACATTAAA-TTAAAAAGTTTTG 90883 i iv v i v v i ? i - v i L1M5_orf2#LIN 3010 ATAAAAGAAAAAATTGATAAATTGGACTNCATCAAAATTAAAAACTTCTG 3059 chr1ptel1M 90884 G-----AACAAACAAAATTAATAGAAACAAGATTAAAATGGAAGT-ACAA 90927 v----- v i vvi -- ---- v v v i- i L1M5_orf2#LIN 3060 CTCNTCAAAAGACACCGTTAA--GAAA----ATGAAAAGGCAAGCCACAG 3103 chr1ptel1M 90928 AGTTGGGGAAAAAATCTTTCCAGCCAGTATTTCTAATAAAAGTCTCCCTT 90977 ? -- i v v i?vvi v i i i v viv L1M5_orf2#LIN 3104 ANT--GGGAGAAAATATTTGCAANACATATATCTGACAAAGGACTCGTAT 3151 chr1ptel1M 90978 CTAAAGTTTATAAAGAACT 90996 i i i v L1M5_orf2#LIN 3152 CCAGAATATATAAAGAACT 3170 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.03 CpG sites = 20, Kimura (unadjusted) = 34.02 Transitions / transversions = 0.95 (20/21) Gap_init rate = 0.07 (11 / 161), avg. gap size = 1.36 (15 / 11) 966 28.16 5.18 1.86 chr1ptel1M 90986 91506 (908494) L1ME4a_3end#LINE/L1 16 553 (318) m_b3s551i10 121 chr1ptel1M 90986 TATAAAGAACTGTGTCAAATTTTATAGGAATACAAGTCATTCCTCAATTG 91035 i v vv iv- i v vi vvv iv i v L1ME4a_3end#L 16 TATAAAGAGCTCTTACAAATCA-ATAAGAAAAAGACGAACACCCCAATAG 64 chr1ptel1M 91036 ATAAATGGTTAAGTGATAGGAACA----ATTTTTAGATGACAAAAT-TAA 91080 v vi iv i v ---- ivi i v vi -i L1ME4a_3end#L 65 AAAAATGGGCAAAGGACATGAACAGACAATTCACAAAAGAAGAAATACAA 114 chr1ptel1M 91081 A--GCCATTTGCAGTCATAAGAATAAATGTTCTAAATCACTATTGATCTG 91128 -- v --- iv v v ? v vv v i vi L1ME4a_3end#L 115 ATGGCCAAT---AAACATATGAAAANATGTTCAACCTCACTAGTAATCAA 161 chr1ptel1M 91129 AGAAATGCAAATTAAAATAACTCTGAC-TACCACTTCATACCTCTCAGAT 91177 i vv v- i ivi v i L1ME4a_3end#L 162 AGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCTATCAAAT 211 chr1ptel1M 91178 TGCCTAAGATGACAGGAAAAGAT-AATGATAC-----ATTGAAGGGGATG 91221 v v v----v -i i -----i iv i i L1ME4a_3end#L 212 TGGCAAAGATT----TAAAAGATTGATAATACCCAGTGTTGGCGAGGGTG 257 chr1ptel1M 91222 TGGGAAAACTGGGACACTAAAGCATTGTTGATGTAGTTGTGAAATGATCC 91271 ?i v v v v vi i i i viiv i v i v L1ME4a_3end#L 258 TGGNGAAACGGGCACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTAC 307 chr1ptel1M 91272 AACCAATCTGGAAA--AAATTGGAACTATGC-CCATAGG--TTATAAAT- 91315 vv ii-- v v v i-i v i -- v - L1ME4a_3end#L 308 AACCTTTCTGGAGGGCAATTTGGCAATATGTATCAAAAGCCTTAAAAATG 357 chr1ptel1M 91316 ----TACCCTTTGACCCAG-AGTGCTATTACTGGGTCTGTATCCCAGGGA 91360 ---- - i v i i v i vv v i i L1ME4a_3end#L 358 TNCATACCCTTTGACCCAGTAATTCCACTTCTAGGAATTTATCCTAAGGA 407 chr1ptel1M 91361 AATCATAAAGGA-G-GGAAAAAGACTCACATGTGCAAAAATGTTTGTAGC 91408 v v ii - - ? v i i -- i ii ii v L1ME4a_3end#L 408 AATAATCAGAGATGTGNACAAAGATTTA--TGTACAAGGATGTTCATCGC 455 chr1ptel1M 91409 AGCTGTTTTTGTGGTATCAAAGAATTGGAAAATGATTAGATGTCCATCAG 91458 vv v i ii v i i vvivi i v i L1ME4a_3end#L 456 AGCATTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAA 505 chr1ptel1M 91459 TTGGGGAATGGCTAAATAATTTGTGGTATATGCAGATTATGGAATATT 91506 v ? i v i i v v ?v L1ME4a_3end#L 506 TAGGGGANTGGTTAAATAAATTATGGTACATCCATANAATGGAATATT 553 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.80 CpG sites = 69, Kimura (unadjusted) = 36.11 Transitions / transversions = 0.92 (69/75) Gap_init rate = 0.05 (24 / 520), avg. gap size = 1.54 (37 / 24) 795 29.27 6.05 3.23 chr1ptel1M 91094 91605 (908395) L1ME3B_3end#LINE/L1 127 652 (337) m_b3s551i11 121 chr1ptel1M 91094 CATAAGAATAAATGTTCTAAATCACTATTGATCTGAGAAATGCAAATTAA 91143 v v ii i v vv i v i v i L1ME3B_3end#L 127 CATATGAAAAGGTGCTCAACCTCATTAGTAATCAGGGAAATGCAAATTAA 176 chr1ptel1M 91144 AATAACTCTGAC-TACCACTTCATACCTCTCAGATTGCCTAAGATGACAG 91192 iv vv v- v i ivi ? v v i v?--- L1ME3B_3end#L 177 AACCACAATGAGATACCACTACACACCCACCAGANTGGCAAAAATTN--- 223 chr1ptel1M 91193 GAAAAG-ATAATGATAC-----ATTGAAGGGGATGTGGGAAAACTGGGAC 91236 - -v i ii -----i iv i iiv v i L1ME3B_3end#L 224 -AAAAGTCTGACAATACCAAGTGTTGGCGAGGATGTGGAGCAACGGGAAC 272 chr1ptel1M 91237 ACTAAAGCATTGTTGATGTAGTTGTGAAATGATCCAACCAATCTGGAAAA 91286 v v vi i i i viiv i v i v v i L1ME3B_3end#L 273 TCTCATACACTGCTGGTGGGAGTGTAAATTGGTACAACCACTTTGGAAAA 322 chr1ptel1M 91287 AA--TTGGAACTATGCCCAT--AGGTTATAAAT-----TACCCTTTGACC 91327 v -- v i -- i ?-- i iv i ----- v L1ME3B_3end#L 323 CAGTTTGGCATTAT--CTANTAAAGTTGAAGATACGCATACCCTATGACC 370 chr1ptel1M 91328 CAG-AGTGCTATTACTGGGTCTGTATCCCAGGGAAAT-CATAAAGGAG-G 91374 - i v i i v i v i i i i i- i iv viv - L1ME3B_3end#L 371 CAGCAATTCCACTCCTAGGTATATACCCTAGAGAAACGCGTGCACATGTG 420 chr1ptel1M 91375 GAAAAAGACTCACATGTGCAAAAATGTTTGTAGCAGCTGTTTTTGTGGTA 91424 v vv i --? i i ii vv v i ii L1ME3B_3end#L 421 CACCAGGA--NACATGTACAAGAATGTTCATAGCAGCATTGTTCGTAATA 468 chr1ptel1M 91425 TCAAAGAATTGGAAAATGATTAGATGTCCATCAGTTGGGGAATGGCTAAA 91474 v v? i i vvivii i iiv vi v L1ME3B_3end#L 469 GCCNAAAACTGGAAACAACCCAAATGTCCATCAACAGTAGAATGGATAAA 518 chr1ptel1M 91475 TAATTTGTGGTATATGCAGATTATGGAATATTTTTGTTCTCTA-AGAAAT 91523 v v v iv -------- v - v L1ME3B_3end#L 519 TAAATTGTGGTATATTCATACAATGGAATA--------CTATACAGCAAT 560 chr1ptel1M 91524 G---ATGAACAAACTGATTTTA---G-AAAGGCCTGGAAAGATTTACATG 91566 --- i ivvvi --- - vii v vii i - ii L1ME3B_3end#L 561 GAAAATGAACGAACTACAGCTACACGCAACAACATGGATGAATCT-CACA 609 chr1ptel1M 91567 AAC-TGATTTTGAGCAAAACAAGTACAAC-C--AAGAATACAT 91605 - i v i v i vi - -- L1ME3B_3end#L 610 AACATAATGTTGAGCGAAAGAAGCAAGACACAAAAGAATACAT 652 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.69 CpG sites = 78, Kimura (unadjusted) = 38.34 Transitions / transversions = 1.16 (78/67) Gap_init rate = 0.06 (33 / 511), avg. gap size = 1.45 (48 / 33) 392 30.24 9.19 0.65 chr1ptel1M 93346 93628 (906372) L2#LINE/L2 2017 2323 (759) m_b3s601i6 125 chr1ptel1M 93346 TTTCTGAAACCAGGGAGCTCTTCTCAGTGTGCTTTTT-CTTAATCATTTC 93394 v i v iv iv vv viv v i - i i v? iv L2#LINE/L2 2017 TTGCTAAATCCAATGGTCAATTCTCAGTCCTCATCTTACTTGACCTNTCA 2066 chr1ptel1M 93395 CCAGCCTTTGACACAGGTGATCCCTCTCTCCTTCCTG--TTGCTCTCTTC 93442 v v v v i i --vii i L2#LINE/L2 2067 GCAGCATTTGACACAGTTGATCACTCCCTCCTTCTTGAAACACTTTCTTC 2116 chr1ptel1M 93443 TCTAAGGTTTTAGGACAAGACTCTCTCCTGGCTTACCTTTTCCCTCTATG 93492 v vi v ii vv v i v ii v vv L2#LINE/L2 2117 ACTTGGCTTCCAGGACACCACACTCTCCTGGTTTTCCTCCTACCTCACTG 2166 chr1ptel1M 93493 AC--TCCCTTCTCTGTCTTCTGTCCTGGATCATCCTCCAGATCACATGCT 93540 i --ii v i v v v v vvvvi v ivv L2#LINE/L2 2167 GCCGCTCCTTCTCAGTCTCCTTTGCTGGTTCCTCCTCATCTCCCCGACCT 2216 chr1ptel1M 93541 CTAATCATAG--GTATCCT----CTC---TCTTGGCTTCTCCTCTTTTCT 93581 ? v i v -- ii i---- ---i v-i i i L2#LINE/L2 2217 CTNAACGTTGGAGTGCCCCAGGGCTCAGTCCTTGGA-CCTCTTCTCTTCT 2265 chr1ptel1M 93582 CTCTCTACAC---------AAATGGATCTCATCAGCTGCCATGCTTTTA- 93621 v ---------?ii - viv vi vi - L2#LINE/L2 2266 CTATCTACACTCACTCCCTNGGT-GATCTCATCCAGTCTCATGGCTTTAA 2314 chr1ptel1M 93622 --ATCATCT 93628 -- i L2#LINE/L2 2315 ATACCATCT 2323 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.42 CpG sites = 39, Kimura (unadjusted) = 39.58 Transitions / transversions = 0.85 (39/46) Gap_init rate = 0.04 (11 / 282), avg. gap size = 2.55 (28 / 11) 213 31.33 17.59 2.18 chr1ptel1M 93743 93872 (906128) L2a_3end#LINE/L2 288 449 (68) m_b3s601i7 125 chr1ptel1M 93743 ACTCC---TCTTACTTGTTCTGCTTTCCTTCT-TCTA-ATTATTTCCTTT 93787 --- iiv iii vi i - i - vi i v-- i L2a_3end#LINE 288 ACTCCCTATCCCCCTTACCCTGCTTTATTTTTCTCCATAGCACTTA--TC 335 chr1ptel1M 93788 TTCATCTGTGCATAGTTTGCTTTGTATATTTTCATTTGCATATTGTCT-- 93835 vi -i v v iiv v iv v i iv -- L2a_3end#LINE 336 ACCATCTG-ACATACTATATATTTTACTTATTTATTTGTTTATTGTCTGT 384 chr1ptel1M 93836 ---CCCTCATTAGA-------CT---TGAGGGCAAGGACTGTCAT----- 93867 --- i i ------- --- i v ii ----- L2a_3end#LINE 385 CTCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTCTGTT 434 chr1ptel1M 93868 ----------ATGTA 93872 ----------v L2a_3end#LINE 435 TTGTTCACTGCTGTA 449 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.63 CpG sites = 37, Kimura (unadjusted) = 42.59 Transitions / transversions = 1.64 (23/14) Gap_init rate = 0.09 (11 / 129), avg. gap size = 3.45 (38 / 11) 300 26.05 10.56 5.37 chr1ptel1M 93800 93872 (906128) L2c_3end#LINE/L2 329 414 (64) m_b3s601i8 125 chr1ptel1M 93800 TAGTTTGCTTTGTATATTTTC-ATTTGCATAT-TGTCTCCCTCATTAGAC 93847 ii iv - v -i i ? i - ii i L2c_3end#LINE 329 TAACTTGTATTGTA-ATTGTCTGTTTACNTGTCTGTCTCCTCCACTAGAC 377 chr1ptel1M 93848 T----------TGAGGGCAAGGAC--TGTCATATGTA 93872 ---------- i -- v vi L2c_3end#LINE 378 TGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCA 414 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.51 CpG sites = 24, Kimura (unadjusted) = 34.18 Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.07 (5 / 72), avg. gap size = 3.00 (15 / 5) 33 3.13 0.00 0.00 chr1ptel1M 93873 93905 (906095) (TG)n#Simple_repeat 1 33 (0) c_b3s251i0 126 chr1ptel1M 93873 TGTGTATGTGTGTGTGTGTGTGTGTGTGTGTGT 93905 i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 33 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 300 26.05 10.56 5.37 chr1ptel1M 93906 93973 (906027) L2c_3end#LINE/L2 415 476 (2) m_b3s601i8 125 chr1ptel1M 93906 TAGCAGTTTGTA-GCAAAATATCTGACACATAGTAGGTATTCTGTAGCTC 93954 i----- -v vv iiii i iii vi iv v L2c_3end#LINE 415 C-----TTTGTATCCCCAGCGCCTGGCACATAGTAGGCGCTCAATAAATG 459 chr1ptel1M 93955 TTTATAGAATTGAAATGAA 93973 i v --i L2c_3end#LINE 460 TTTGTTGAAT--GAATGAA 476 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.51 CpG sites = 24, Kimura (unadjusted) = 34.18 Transitions / transversions = 1.86 (13/7) Gap_init rate = 0.12 (8 / 67), avg. gap size = 1.00 (8 / 8) 334 25.16 14.40 1.42 chr1ptel1M 95988 96112 (903888) MIR3#SINE/MIR 66 206 (2) m_b3s601i9 127 chr1ptel1M 95988 CTCTGACACTCATAAATAGTATGGCCTTTGAGCAAATCATTTC-----TC 96032 v v iv?iiv i i - i i i ----- MIR3#SINE/MIR 66 CTCTGCCACTAACTNGCTGTGTGACCTT-GGGCAAGTCACTTCACCTCTC 114 chr1ptel1M 96033 TGTGCTTCAGTTTCATC--CTGTAAATTGAAGAAGGTTGGA--------- 96071 v i v -- v - ii --------- MIR3#SINE/MIR 115 TGGGCCTCAGTTTCCTCATCTGTAAAATG-AGGGGGTTGGACTAGATGAT 163 chr1ptel1M 96072 CTCTGAAGTGTCTTTCACCTCT-ATATCTCATAAGTTT-TGAT 96112 i i vi i v - i iii i v i - MIR3#SINE/MIR 164 CTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTATGAT 206 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.25 CpG sites = 21, Kimura (unadjusted) = 32.25 Transitions / transversions = 2.10 (21/10) Gap_init rate = 0.06 (7 / 124), avg. gap size = 2.86 (20 / 7) 26 18.24 4.29 1.39 chr1ptel1M 96995 97064 (902936) (ATAA)n#Simple_repeat 1 72 (0) m_b3s252i7 128 chr1ptel1M 96995 ATACATCAAAAAATAAATAAATAAA-AAGTTTTTTAA-AAGAAAATAAAT 97042 v v v - i vvv v - iv (ATAA)n#Simpl 1 ATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAAT 50 chr1ptel1M 97043 AAATAATATAAATAAA-AAAGAA 97064 - - v (ATAA)n#Simpl 51 AAATAA-ATAAATAAATAAATAA 72 Matrix = Unknown Transitions / transversions = 0.22 (2/9) Gap_init rate = 0.06 (4 / 69), avg. gap size = 1.00 (4 / 4) 454 23.53 5.56 5.56 chr1ptel1M 98273 98398 (901602) MIRc#SINE/MIR 10 135 (133) m_b3s601i10 129 chr1ptel1M 98273 GTGGTGCAGTGGATAGAGCACCAGCCCTGAAGTCAGGAGGA-CTGGGTTC 98321 v ii v i i i - MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr1ptel1M 98322 AAATCTGACCTTAAACACTTAACACTTCCTGGCTGTGTGATTCTGAACAA 98371 i i iviv -------i iv v i iii ii MIRc#SINE/MIR 60 GAGTCCCGGCT-------CTGCCACTTACTAGCTGTGTGACCTTGGGCAA 102 chr1ptel1M 98372 GTCAC--AACCCC----AACCCCAATTGCCTCA 98398 -- i ---- i i i v MIRc#SINE/MIR 103 GTCACTTAACCTCTCTGAGCCTCAGTTTCCTCA 135 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 27.15 CpG sites = 21, Kimura (unadjusted) = 29.66 Transitions / transversions = 3.00 (21/7) Gap_init rate = 0.08 (10 / 125), avg. gap size = 1.40 (14 / 10) 28 18.85 0.00 0.00 chr1ptel1M 98401 98450 (901550) (A)n#Simple_repeat 1 50 (0) m_b3s252i8 130 chr1ptel1M 98401 AAAAAAAGAAAAAAAGAAAAACAAAAAGAAAGAAAAGAAAAGAAAAGAAA 98450 i i v i i i i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 Matrix = Unknown Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 358 22.22 3.57 3.57 chr1ptel1M 99593 99704 (900296) C MIRb#SINE/MIR (14) 254 143 m_b3s601i11 131 chr1ptel1M 99593 CAATTATTATGAGGGACCTATTAAGTGCCAGACACAA-GTTAAGCACCTT 99641 v -- v - i i v i vi- i i i C MIRb#SINE/MIR 254 CATTTATT--GAGCG-CTTACTATGTGCCAGGCACTGTGCTAAGCGCTTT 208 chr1ptel1M 99642 AT---CAATATTTCCCATGATCCTCACAACAAACCCTTATAGGGAGGTAT 99688 i--- v i viv i - vvv v C MIRb#SINE/MIR 207 ACATGCATTATCTCATTTAATCCTCACAACAA-CCCTGCGAGGTAGGTAT 159 chr1ptel1M 99689 TTATATCCCCATTTTA 99704 vv C MIRb#SINE/MIR 158 TATTATCCCCATTTTA 143 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 25.25 CpG sites = 11, Kimura (unadjusted) = 26.47 Transitions / transversions = 0.85 (11/13) Gap_init rate = 0.05 (6 / 111), avg. gap size = 1.33 (8 / 6) 21 16.78 0.00 7.02 chr1ptel1M 102645 102705 (897295) (TAAAATA)n#Simple_repeat 1 57 (0) m_b3s252i9 132 chr1ptel1M 102645 TAAAATGATAAAATAAAAGAATATGAAAATATGAAATATGCTTTATAGAA 102694 - v - - i ivvv - (TAAAATA)n#Si 1 TAAAAT-ATAAAATATAA-AATAT-AAAATATAAAATATAAAATATA-AA 46 chr1ptel1M 102695 ATGTGAAATAT 102705 i i (TAAAATA)n#Si 47 ATATAAAATAT 57 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.07 (4 / 60), avg. gap size = 1.00 (4 / 4) 212 30.86 11.11 0.00 chr1ptel1M 103085 103165 (896835) MIRc#SINE/MIR 54 143 (125) m_b3s601i12 133 chr1ptel1M 103085 GGATTTAAGAGTTGACTC--ACACTCACAAAGTATATGACTTCCAGCAAA 103132 i ii vvii i --v i v iv i i i ivi i MIRc#SINE/MIR 54 GGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAG 103 chr1ptel1M 103133 TCCCTTCAC-----TGTGTTTCAGTTTCCTC--CTGTAAA 103165 v v ----- v ii -- MIRc#SINE/MIR 104 TCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAA 143 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.02 CpG sites = 16, Kimura (unadjusted) = 41.56 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.04 (3 / 80), avg. gap size = 3.00 (9 / 3) 303 24.36 8.97 0.00 chr1ptel1M 103104 103181 (896819) MIR3#SINE/MIR 72 156 (52) m_b3s601i13 133 chr1ptel1M 103104 CACTCACAAAGTATATGACTTCCAGCAAATCCCTTCAC-----TGTGTTT 103148 v v?iv i i i ivi i v ----- v ii MIR3#SINE/MIR 72 CACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCT 121 chr1ptel1M 103149 CAGTTTCCTC--CTGTAAATTAAAAGGGTTGGACT 103181 -- v i ii MIR3#SINE/MIR 122 CAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACT 156 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 30.77 CpG sites = 12, Kimura (unadjusted) = 30.77 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.03 (2 / 77), avg. gap size = 3.50 (7 / 2) 253 28.97 6.67 4.67 chr1ptel1M 104220 104324 (895676) C MIR#SINE/MIR (50) 212 106 m_b3s601i14 134 chr1ptel1M 104220 AAGCACTTTGGAT------ACTTAATTCATCATCATAACAATTCTAGGAC 104263 i iv ------ i v v v i ii v v C MIR#SINE/MIR 212 AAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAG 163 chr1ptel1M 104264 -TAGATGTGATTGTTATGCCAATTTTATAGATAAAATATTTTGATTGATG 104312 - i iiv i v v i i iiv ----- i v C MIR#SINE/MIR 162 GTAGGTACTATTATTATCCCCATTTTACAGATGAGGAA-----ACTGAGG 118 chr1ptel1M 104313 CAAAAAGGGGTT 104324 v i i C MIR#SINE/MIR 117 CACAGAGAGGTT 106 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.03 CpG sites = 17, Kimura (unadjusted) = 37.67 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.07 (7 / 104), avg. gap size = 1.71 (12 / 7) 13 9.78 0.00 0.00 chr1ptel1M 105933 105954 (894046) (TGT)n#Simple_repeat 1 22 (0) m_b3s252i10 135 chr1ptel1M 105933 TGTTGTTTTTGTTGTTGTTTTT 105954 v v (TGT)n#Simple 1 TGTTGTTGTTGTTGTTGTTGTT 22 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 23 7.53 2.17 4.44 chr1ptel1M 106932 106977 (893023) (AATA)n#Simple_repeat 1 45 (0) m_b3s252i12 136 chr1ptel1M 106932 AATAGAATAAATAAAT-AATACAATAAATTAATAAATAAAAAAAAAA 106977 - - - v v v (AATA)n#Simpl 1 AATA-AATAAATAAATAAATA-AATAAATAAATAAATAAATAAATAA 45 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.07 (3 / 45), avg. gap size = 1.00 (3 / 3) 18 25.36 2.99 1.47 chr1ptel1M 107678 107744 (892256) (AAAG)n#Simple_repeat 1 68 (0) m_b3s252i13 137 chr1ptel1M 107678 AAAGAGAAGAAA-CCCGAGAGTAAGAAAGACTAAAAGAGA-TGAGTGAGA 107725 - -vvv i v vvi i -vi vi (AAAG)n#Simpl 1 AAAGA-AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA 49 chr1ptel1M 107726 AAGAAGGAAAGAAAGAAAG 107744 i (AAAG)n#Simpl 50 AAGAAAGAAAGAAAGAAAG 68 Matrix = Unknown Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.05 (3 / 66), avg. gap size = 1.00 (3 / 3) 670 29.48 4.04 2.72 chr1ptel1M 107856 108399 (891601) C L1M5_orf2#LINE/L1 (2005) 1289 739 m_b3s551i12 138 chr1ptel1M 107856 TCCATTCCACC-AAGTTTATCAATTTACTGATATATAATTGGAGAAAATA 107904 i i - ?viv i ii v i vvv v C L1M5_orf2#LIN 1289 TCCATTTCATCTAAGTTNTCAAATTTATTGGCATAAAGTTGTTCATAATA 1240 chr1ptel1M 107905 AATTCTAATTATTGCTCTCATTTCCTCTTCATTGGTGGAAAGGGCTCCCT 107954 vvi v ivi i v v ivivvv iv i vi v v i C L1M5_orf2#LIN 1239 TTCTCTTATTATCCTTTTAATGTCTGTAGGATCTGTAGTGATGTCTCCTT 1190 chr1ptel1M 107955 TTTCATTTTTGATATTAACAATTT-CATTTTCTTCTTTTCTTTTTCTAAT 108003 ii iii -ii i - i i ii i C L1M5_orf2#LIN 1189 TTTCATTCCTGATATTGGTAATTTGTGTCTTCT-CTCTTTTTTTCTTGAT 1141 chr1ptel1M 108004 CAAATTAACTAAAAGTTTATGTATTTTGTGGTTTTTTTTCCTTAAAACCA 108053 ivi ?i i i vv i v v i -- vv i C L1M5_orf2#LIN 1140 CAGTCTNGCTAGAGGTTTATCAATTTTATTGATCTTTT--CAAAGAACCA 1093 chr1ptel1M 108054 ACTCTT----TTATTTATTATTTCAGTAATTTTCTTACTTTCAATTTTAT 108099 i i ---- ii v v i vi vi ? ?i ii v i C L1M5_orf2#LIN 1092 GCTTTTGGCTTCGTTGATTTTCTCTATTGTNTNTTTGTTTTCTATTTCAT 1043 chr1ptel1M 108100 TAATCTCTTCT---ATTTTCAGAATTTCAAATTTGGTATTTAATTGGGAG 108146 i i v --- i i vv vvvii vv i ?v v i- C L1M5_orf2#LIN 1042 TGATTTCTGCTCTTATCTTTATTATTTCCTTCCTTCTACTTNCTTTGGG- 994 chr1ptel1M 108147 TTTTTTATTTG---TTCTTTTTCTAGCTTTTTTAGTTGCAGGCCCAAATC 108193 -- v --- i v v v i ii i C L1M5_orf2#LIN 993 --TTTAATTTGCTCTTCTTTTTCTAGCTTCTTAAGGTGGAAGCTTAGATC 946 chr1ptel1M 108194 ACTGATCTT---CTTTTTCTCTATTTTATGCAAT-TAAGCATCTAGAGAT 108239 i i --- i ii v i ---- - ? i i? v C L1M5_orf2#LIN 945 ATTGATTTTAAGCCTTTCTTCTTTTCT----AATATANGCATTTAANGCT 900 chr1ptel1M 108240 ATTAAACTTCCC-CAAAGAACTGCTTTGGCTGCATTCCATAAATTTTGTT 108288 - i - v v i i i v C L1M5_orf2#LIN 899 A-TAAATTTCCCTCTAAGCACTGCTTTAGCTGCATCCCACAAATTTTGAT 851 chr1ptel1M 108289 ATGTTGTCTCATTATTGTCATTCTCTTGGATGAAATTATC-AATTGTGAC 108337 v iv i ? vv vi -i v v - viv?i C L1M5_orf2#LIN 850 ATGTTGTATTTTCATTNTCATTCAGTTCAA-AATATTTTCTAATTTCCNT 802 chr1ptel1M 108338 TATGATTTGTTGTTTTACCAATCCTTTCTTTAGGATTA----GATTAGTT 108383 i v v v v vvv v i v i---- v i C L1M5_orf2#LIN 801 TGTGATTTCTTCTTTGACCCATGGGTTATTTAGAAGTGTGTTGTTTAATT 752 chr1ptel1M 108384 TCCAATTAATTTTTGG 108399 --- v C L1M5_orf2#LIN 751 TCCA---AATATTTGG 739 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.70 CpG sites = 84, Kimura (unadjusted) = 39.06 Transitions / transversions = 1.17 (84/72) Gap_init rate = 0.05 (25 / 543), avg. gap size = 1.48 (37 / 25) 252 29.15 11.03 0.62 chr1ptel1M 108726 108870 (891130) L1P3_orf2#LINE/L1 2749 2908 (386) m_b3s551i13 139 chr1ptel1M 108726 TTTGACAAATCC--CAAAGACT-----TGGGATAAGAACTCACTATTTAA 108768 i i-- i v----- iv i i v L1P3_orf2#LIN 2749 TTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAA 2798 chr1ptel1M 108769 CAAAAACTGCTGGGAAAATTAG-------TATGGCAG-AAACTAGGATTC 108810 i viv i i i ------- - - iii i v L1P3_orf2#LIN 2799 TAAATGGTGTTGGGAAAACTGGCTAGCCATAT-GCAGAAAACTGAAACTG 2847 chr1ptel1M 108811 AA-CCATACCTAACTCCCTGCACCAAGATAAAGTTGAAATGGGTTCATGA 108859 i - v v v v i ii v i v v ii i i v v L1P3_orf2#LIN 2848 GACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATTAAAGA 2897 chr1ptel1M 108860 TTTAGACATAA 108870 i i i L1P3_orf2#LIN 2898 CTTAAACGTAA 2908 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.27 CpG sites = 27, Kimura (unadjusted) = 38.46 Transitions / transversions = 1.80 (27/15) Gap_init rate = 0.04 (6 / 144), avg. gap size = 2.83 (17 / 6) 329 29.42 2.30 2.30 chr1ptel1M 109016 109189 (890811) L1P3_orf2#LINE/L1 3082 3255 (39) m_b3s551i14 139 chr1ptel1M 109016 AGATTGAA-AGGGAAGCGATAAACTGGGGAAATATTTTTTACATCTAATA 109064 v - v v v i i v ii v vvv - v L1P3_orf2#LIN 3082 AGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTA-TC 3130 chr1ptel1M 109065 GTTCTGAGAATGGCCTCATTTCTAAAATATATAGAGAATTGAATTGAATT 109114 vv v v v v v i i v i ii i v vii L1P3_orf2#LIN 3131 CATCTGACAAAGGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATT 3180 chr1ptel1M 109115 TATAAGAATT---CAAGCCATTTCCCAATTAATAAAGGGTCAAAGGATAT 109161 i vv--- i v --- v i v iv v i L1P3_orf2#LIN 3181 TACAAGAAAAAAACAAACAA---CCCCATCAAAAAGTGGGCGAAGGATAT 3227 chr1ptel1M 109162 GAACACACACTTTTCAGATGAAGGAATT 109189 v i i v iv L1P3_orf2#LIN 3228 GAACAGACACTTCTCAAAAGAAGACATT 3255 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.52 CpG sites = 20, Kimura (unadjusted) = 37.41 Transitions / transversions = 0.67 (20/30) Gap_init rate = 0.03 (6 / 173), avg. gap size = 1.33 (8 / 6) 604 32.42 5.77 2.48 chr1ptel1M 109079 109546 (890454) L1ME3_3end#LINE/L1 1 483 (426) m_b3s551i15 139 chr1ptel1M 109079 CTCATTTCTAAAATATATAGAGAATTGAATTGAATTTATAAGAA---TTC 109125 i v i i i i vvvvii iv ---vv L1ME3_3end#LI 1 CTCGTATCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAAAAGAC 50 chr1ptel1M 109126 AAGCCATTTCCCAATTAATAAAGGGTCAAAGGATATGAACACACACTTTT 109175 i v --- v v v i iv vi iv L1ME3_3end#LI 51 AAACAA---CCCAATTAAAAAATGGGCAAAAGACTTGAACAGGCACTTCA 97 chr1ptel1M 109176 CAGATGAAGGAATTGAGAGTATTTCTAGTCATATGAAAAG-CGCTCTAAA 109224 i v i iv iv i vviiivv iv -i v v L1ME3_3end#LI 98 CAAAAGAGGATATCCAAATGGCCAATAAGCATATGAAAAGGTGCTCAACA 147 chr1ptel1M 109225 TGACCCA--ATCAGAGAAATGCAAATTAAGACAACTCTGACATACCTCT- 109271 v iivi-- i i v vv v v - L1ME3_3end#LI 148 TCATTAGTCATCAGGGAAATGCAAATTAAAACCACAATGAGATACCACTA 197 chr1ptel1M 109272 CACATTGTCTAAGATGAC----AGTAAAA-----GATAATGATGAGTGTT 109312 iivv i ii i ---- v ----- i ivii L1ME3_3end#LI 198 CACACCCACCAGAATGGCTAAAATTAAAAAGACTGACAATACCAAGTGTT 247 chr1ptel1M 109313 AGAGGGAATGAAGGAAAACTGGGATGCTAATACATTGAGGGTGGAGCTGT 109362 i v i i vi iiv i iv v vv iiv L1ME3_3end#LI 248 GGCGAGGATGTGGAGCAACTGGAACTCTCATACATTGCTGGTGGGAGTGT 297 chr1ptel1M 109363 GAACTGATTCAACAATTTTGGAGTGCAATTTGGAACTATGCCCAAAGAGC 109412 i i i v v i ivi vi v v viv v - L1ME3_3end#LI 298 AAATTGGTACAACCACTTTGGAAAACTGTTTGGCAGTATCTACTAA-AGC 346 chr1ptel1M 109413 T-ATCAAACTGCATACCCTTTGATCCAGCAGTGTTTCTACTGGGCTTGTT 109461 - v v - v v i i viiv v i iv i v L1ME3_3end#LI 347 TAAACATAC-GCCTACCCTATGACCCAGCAATTCCACTCCTAGGTATATA 395 chr1ptel1M 109462 TCCCAAAGATATAAAAGAGAGAA-AGGAATCCACT--------TGTGCAA 109502 i v i ---- v v v - v -- i-------- i L1ME3_3end#LI 396 CCCAAGAG----AAATGAGTGCATATG--TCCACCAAAAGACATGTACAA 439 chr1ptel1M 109503 AAATGTTTG-GGCAGCCCTTTTTTGTAGTGGTCAGAAACAGAAAA 109546 i ii-i - i v ii i i i ?i v i L1ME3_3end#LI 440 GAATGTTCATAGCAG-CTTTATTCATAATAGCCNAAAACTGGAAA 483 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.19 CpG sites = 79, Kimura (unadjusted) = 43.58 Transitions / transversions = 1.14 (79/69) Gap_init rate = 0.05 (22 / 467), avg. gap size = 1.77 (39 / 22) 742 28.94 4.62 2.51 chr1ptel1M 109085 109474 (890526) L1ME3G_3end#LINE/L1 7 404 (520) m_b3s551i16 139 chr1ptel1M 109085 TCTAAAATATATAGAGAATTGAATTGAATTTATAAGAATTCAAGCCATTT 109134 i i i i vvvvii iv --v v v-- L1ME3G_3end#L 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAA--AAAGACAA-- 52 chr1ptel1M 109135 CCCAATTAATAAAGGGTCAAAGGATATGAACACACACTTTTCAGATGAAG 109184 vi v v v vi v iv v i L1ME3G_3end#L 53 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chr1ptel1M 109185 GAATTGAGAGTATTTCTAGTCATATGAAAAG-CGCTCTAAATGACC--CA 109231 i vv i vviiivv iv -i v vv v i--i L1ME3G_3end#L 103 AAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTA 152 chr1ptel1M 109232 ATCAGAGAAATGCAAATTAAGACAACTCTGACATACC---TCTCAC---- 109274 i i vv v --- i ---- L1ME3G_3end#L 153 ATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCAT 202 chr1ptel1M 109275 ---ATTGTCTAAGATGACAGTAAAAG----ATAATGATGAGTGTTAGAGG 109317 --- v v i v---- ---- ivi? i v i L1ME3G_3end#L 203 CAGATTGGCAAAAATT----TAAAAGNTTGATAATATCNAGTGTTGGCGA 248 chr1ptel1M 109318 GAATGAAGGAAAACTGGGATGCTAATACATTGAGGGTGGAGCTGTGAACT 109367 ii vi i v v iv v i vv iiv i i L1ME3G_3end#L 249 GGGTGTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATT 298 chr1ptel1M 109368 GATTCAACAATTTTGGAGTGCAATTTGGAACTATGCCCAAAGAGCTATCA 109417 i v i v? v v v viviv i vi -- L1ME3G_3end#L 299 GGTACAGCCNTTTTGGAGGGCAATTTGGCAGTATCTATTAAAATTTA--A 346 chr1ptel1M 109418 AAC-TGCATACCCTTTGATCCAGCAGTGTTTCTACTGGGCTTGTTTCCCA 109466 i-i i i viiv v ? ?v v v i L1ME3G_3end#L 347 AATGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTA 396 chr1ptel1M 109467 AAGATATA 109474 ? v L1ME3G_3end#L 397 NAGAAATA 404 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.07 CpG sites = 51, Kimura (unadjusted) = 37.49 Transitions / transversions = 0.86 (51/59) Gap_init rate = 0.04 (17 / 389), avg. gap size = 1.65 (28 / 17) 12 29.61 2.00 2.00 chr1ptel1M 109839 109888 (890112) (CTCCT)n#Simple_repeat 1 50 (0) m_b3s252i14 140 chr1ptel1M 109839 CTCCCCTCCT-TCTTTTACTCCTCTTTTTTCTTCTCTCCTCTCCCCATCC 109887 i - i i v ii i ii i i - (CTCCT)n#Simp 1 CTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTC-TCC 49 chr1ptel1M 109888 T 109888 (CTCCT)n#Simp 50 T 50 Matrix = Unknown Transitions / transversions = 10.00 (10/1) Gap_init rate = 0.04 (2 / 49), avg. gap size = 1.00 (2 / 2) 16 5.27 0.00 0.00 chr1ptel1M 110219 110238 (889762) (A)n#Simple_repeat 1 20 (0) m_b3s252i15 141 chr1ptel1M 110219 AAGAAAAAAAAAAAAAAAAA 110238 i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAA 20 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 22 18.88 0.00 0.00 chr1ptel1M 112239 112280 (887720) (A)n#Simple_repeat 1 42 (0) m_b4s252i0 142 chr1ptel1M 112239 AAACAAAAACCAAAAAAAAAAAGAAAAGAAAAAAATAGAAAA 112280 v vv i i v i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 42 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 13 22.64 2.44 0.00 chr1ptel1M 112250 112290 (887710) (AAAATAT)n#Simple_repeat 1 42 (0) m_b4s252i1 142 chr1ptel1M 112250 AAAAAAAAAAAGA-AAAGAAAAAAATAGAAAATATGAAATAT 112290 v v v - iv v v i (AAAATAT)n#Si 1 AAAATATAAAATATAAAATATAAAATATAAAATATAAAATAT 42 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 305 33.12 1.26 1.26 chr1ptel1M 112623 112781 (887219) L1ME4c_3end#LINE/L1 397 555 (275) m_b4s551i0 143 chr1ptel1M 112623 TATCCCAAATAGAT--CTTAAAGGAGGGAAAAGGACCCACAGGTCCAAAA 112670 i iv i --i i i i i -- i i v iv i i L1ME4c_3end#L 397 TATCCTAAGGAAATAATTCAAAAGAAGGAAAAAG--CTATATGCACGAAG 444 chr1ptel1M 112671 ATAGTTATGCCAGCCCTCTTTGTAGTAGCTAAAAACTGGAAACTGAATGG 112720 iv i vv vi v i i v i vivv ii L1ME4c_3end#L 445 ATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAA 494 chr1ptel1M 112721 ATGCCCATCAATTGGACAATGTCTGAATAAATTATGGCATATGAATGTTA 112770 i v v iv vi i i i i v? iviv L1ME4c_3end#L 495 ATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGA 544 chr1ptel1M 112771 CGGAATGTTAT 112781 i i L1ME4c_3end#L 545 TGGAATATTAT 555 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 43.87 CpG sites = 33, Kimura (unadjusted) = 46.34 Transitions / transversions = 1.74 (33/19) Gap_init rate = 0.02 (3 / 158), avg. gap size = 1.33 (4 / 3) 361 28.68 0.00 1.55 chr1ptel1M 112651 112781 (887219) L1ME3G_3end#LINE/L1 420 548 (376) m_b4s551i1 143 chr1ptel1M 112651 AAGGACCCACAGGTCCAAAAATAGTTATGCCAGCCCTCTTTGTAGTAGCT 112700 ?--i v v ii iv i vv vi v i v L1ME3G_3end#L 420 AAGGAN--GCATGTACAAGGATGTTCATTGCAGCATTGTTTGTAATAGCG 467 chr1ptel1M 112701 AAAAACTGGAAACTGAATGGATGCCCATCAATTGGACAATGTCTGAATAA 112750 i vivv ii i v iv vi i L1ME3G_3end#L 468 AAAAATTGGAAACAACCTAAATGTCCATCAATAGGGGAATGGTTAAATAA 517 chr1ptel1M 112751 ATTATGGCATATGAATGTTACGGAATGTTAT 112781 i vv ii i ii L1ME3G_3end#L 518 ATTATGGTATATCCATACTATGGAATACTAT 548 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.37 CpG sites = 21, Kimura (unadjusted) = 37.37 Transitions / transversions = 1.31 (21/16) Gap_init rate = 0.02 (2 / 130), avg. gap size = 1.00 (2 / 2) 1097 26.70 2.70 2.70 chr1ptel1M 112941 113348 (886652) L1ME4c_3end#LINE/L1 147 554 (276) m_b4s551i2 144 chr1ptel1M 112941 CTCTTTATTAATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACT 112990 vi v i ii vv i i L1ME4c_3end#L 147 CTCGCTAGTAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATT 196 chr1ptel1M 112991 ACACACCTGTCAGATTGGCTAAGATGACAGGAAAAAATAATGATGAT--- 113037 vi i i i i i v i ----vv -- i --- L1ME4c_3end#L 197 TTACGCCTATTAAATTAGCAAAAAT----TTAAAAAAT--TGATAATACC 240 chr1ptel1M 113038 ---TGTTGGAGGGGACGGGGGAAAACTGGGACATTGATGCATTGTTGGTG 113084 --- i v i ?i v vi v ?i v i i L1ME4c_3end#L 241 CAATGCTGGCGAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTG 290 chr1ptel1M 113085 GAGTTGTGAACGAATCCAACCATTTTGGAGAGTAGTTTGGAACTATGCTC 113134 vi? i ivii v v i i i v v i ivi L1ME4c_3end#L 291 GCANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTAT 340 chr1ptel1M 113135 AAAAAGTGATCAAACTGTGCATACCCTTTGATCCAGCAGTGTTACTACTG 113184 v i iv v v v i i i vii v L1ME4c_3end#L 341 CAAGAGCCATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTG 390 chr1ptel1M 113185 GGATTATATCCCAAAGAGATTAT---AAAGAAGGGAAAGGGACCTGTATG 113231 v v i i i v --- i i -----v i L1ME4c_3end#L 391 GGAATTTATCCTAAGGAAATAATTCAAAAGAAGGAAAAAG-----CTATA 435 chr1ptel1M 113232 TGCACGA--ATGTTTGTGGCAGCGCTTTTTGTAGTAGCTAGAAACTGGAA 113279 -- ii v i v i i v i i L1ME4c_3end#L 436 TGCACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAA 485 chr1ptel1M 113280 ACTGAATGGATGCCCATCAATTGGAGAATGGCTGAATAAATTGTGGTATA 113329 vivv ii i v v i i i i i i L1ME4c_3end#L 486 ACAACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACA 535 chr1ptel1M 113330 TGAATATTATGGAATATTA 113348 v? iviv L1ME4c_3end#L 536 TCNACTCGATGGAATATTA 554 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 33.15 CpG sites = 64, Kimura (unadjusted) = 34.34 Transitions / transversions = 1.52 (64/42) Gap_init rate = 0.04 (15 / 407), avg. gap size = 1.47 (22 / 15) 737 28.45 3.52 3.95 chr1ptel1M 112949 113431 (886569) L1MC4a_3end#LINE/L1 152 632 (1997) m_b4s551i3 144 chr1ptel1M 112949 TAATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACACCT 112998 v i v v i i v v L1MC4a_3end#L 152 TAATAAGAGAAATGCAAATTAAAACTACACTGAGATACCATTTCTCACCT 201 chr1ptel1M 112999 GTCAGATTGGCTAAGAT--GACAG---GAAAAAATAATGATGATTGTTGG 113043 i v i --i v --- v v i v -----i L1MC4a_3end#L 202 ATCAGATTGGCAAAAATTCAAAAGTTTGACAACACACT-----CTGTTGG 246 chr1ptel1M 113044 AGGGGACGGGGGAAAACTGGGACATTGATGCATTGTTGGTGGAGTTGTGA 113093 v i vi v i v v vi v i i iiv ii L1MC4a_3end#L 247 CGAGGCTGTGGGGAAACAGGCACTCTCATACATTGCTGGTGGGAATGCAA 296 chr1ptel1M 113094 ACGAATCCAACCATTTTGGAGAGTAGTTTGGAACTATGCTCAAAAAGTGA 113143 ?vii v v ? i v i v v - v v iiv L1MC4a_3end#L 297 ANTGGTACAACCCTTNTGGAGGGGAATTTGGCAATAT-CTAACAAAACTA 345 chr1ptel1M 113144 TCAAACTGTGCAT--ACCCTTTGATCCAGCAGTGTTACTACTGGGATTAT 113191 - --- i -- i i vii v i v v L1MC4a_3end#L 346 -CA---TATGCATTTACCCTTTGACCCAGCAATCCCACTTCTAGGAATTT 391 chr1ptel1M 113192 ATCCCAAAGAGATTATA-----AAGAAG-GGAAAGGGACCTGTATGTGCA 113235 i ii --- i ----- v v -iv iv? --i ii L1MC4a_3end#L 392 ACCCTGAAGA---TACACCTCCAACATGTACAAAATNAC--ATATGCACA 436 chr1ptel1M 113236 CGAATGTTTGTGGCAGCGCTTTTTGTAGTAGCTAGAAACTGGAAACTGAA 113285 v iv i ii v ii v i v v i v i vivv L1MC4a_3end#L 437 AGGTTATTCATTGCAGCATTGTTTGTAATTGCAAAATATTGGAAACAACC 486 chr1ptel1M 113286 TGGATGCCCATCAATTGGAGAATGGCTGAATAAATTGTGGTATATGAATA 113335 ii ?? v ? i i i i vv i L1MC4a_3end#L 487 TAAATGCCCATNNATAGGAGANTGGTTGAATAAACTATGGTACATCCACA 536 chr1ptel1M 113336 TTATGGAATATTACTGT-TCTGTAAGAAATGACCAACAGGATGATTTC-A 113383 iv i i - i-v i - -- vv v i - L1MC4a_3end#L 537 CAATGGAGTACTA-TGCAGCTGTAAAAAA-GA--ATGAGGAAGATCTCTA 582 chr1ptel1M 113384 GAAA--GGCCTGGAGAGACTTACACGAACTGATGCTGAGTGAAATGAGCA 113431 vi -- iiv v i v v vv iv i i vi L1MC4a_3end#L 583 TGAACTGATATGGAGTGATTTCCAGGATATATTGTTAAGTGAAAAAAGCA 632 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.98 CpG sites = 70, Kimura (unadjusted) = 36.98 Transitions / transversions = 1.13 (70/62) Gap_init rate = 0.06 (27 / 482), avg. gap size = 1.33 (36 / 27) 24 6.79 0.00 0.00 chr1ptel1M 113898 113928 (886072) (A)n#Simple_repeat 1 31 (0) m_b4s252i2 145 chr1ptel1M 113898 AAAAAAAAAAAAAAAAAACAAAAAAAAACAA 113928 v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 31 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 17 14.52 0.00 5.00 chr1ptel1M 114060 114101 (885899) (TTTTGT)n#Simple_repeat 1 40 (0) m_b4s252i3 146 chr1ptel1M 114060 TTTTGTTTTCCTTCTCTGGTTTTGTTTTTGTTTTTTGTCTTT 114101 iv - i v - i (TTTTGT)n#Sim 1 TTTTGTTTTTGTT-TTTGTTTTTGTTTTTG-TTTTTGTTTTT 40 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.05 (2 / 41), avg. gap size = 1.00 (2 / 2) 272 24.95 10.57 2.26 chr1ptel1M 114868 114990 (885010) MIR1_Amn#SINE/MIR 19 151 (79) m_b4s601i0 147 chr1ptel1M 114868 TAGTGCACAGAGCACTGGA---AGATTCA----ACTTCACTTGTTCCAGG 114910 v i ---i i i---- i vi--- ? ?v MIR1_Amn#SINE 19 TAGTGGATAGAGCACTGGACTGGGACTCGGGAGACCTGG---GTTCNANT 65 chr1ptel1M 114911 CCTACCTCAGACACTTTTCAGGTGTGTCAGCCTGG-----CCACTTAAGC 114955 iiv v v ?vi ? v ? v v i -----i ? v MIR1_Amn#SINE 66 CCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGTCACTTNACC 115 chr1ptel1M 114956 T-TGTTTGCCTCAGGTTCCTCACCTATGAAACTGGG 114990 - v v? v i i i iv MIR1_Amn#SINE 116 TCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGG 151 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.39 CpG sites = 15, Kimura (unadjusted) = 33.11 Transitions / transversions = 1.00 (15/15) Gap_init rate = 0.06 (7 / 122), avg. gap size = 2.29 (16 / 7) 563 29.04 4.40 3.57 chr1ptel1M 117035 117534 (882466) L1M5_orf2#LINE/L1 2791 3294 (0) m_b4s551i4 148 chr1ptel1M 117035 CTGTTTGACAAAAATTTCTGGGAAAATTGGAAATTAGTATGCAGAAACTA 117084 v ii viv v i v v ivi v i v- L1M5_orf2#LIN 2791 CTTTTCAACAAATGGTGCTGGAACAATTGGATATCCATATGGAAAAAA-A 2839 chr1ptel1M 117085 GGAA--TTGACCCACACATAACACCATACACCAAGATAAGCTCAAAATGG 117132 v -- i vi v v v i v ii ? i L1M5_orf2#LIN 2840 TGAANCTCGACCCCTACCTCACACCATACACAAAAATTAATTCNAGATGG 2889 chr1ptel1M 117133 GTTCAT-GACCTAGGCATAAAGAATGAGATTATAAA----TTGGAAGAA- 117176 i - - iiii ii? i i i ----i i - L1M5_orf2#LIN 2890 AT-CATAGACCTAAATGTAAAAGNTAAAACTATAAAACTTCTAGAAGAAA 2938 chr1ptel1M 117177 -CATAGGATAGTTTATCTCTCAGACCTGTGGAAGAGGAAGGAATTTATGA 117225 - v i -- iivv - i?v v iii v -- L1M5_orf2#LIN 2939 ACATAGGAGAAT--ATCTTCGTGACCT-TGGGNTAGGCAAAGATTTCT-- 2983 chr1ptel1M 117226 CCAAAGAAGAACTAGAGATCATTACTGATCACAAAACAGAAAATT----- 117270 -i v i vvi i i v i? --- i i v i ----- L1M5_orf2#LIN 2984 -TAAACAGGACACAAAAAGCACNA---ACCATAAAAGAAAAAATTGATAA 3029 chr1ptel1M 117271 --TTGATTATCTCAAATTGAAAAATTTTTGTACAAACAAATCTAATGCAG 117318 -- v i ?iv v v i i iv ?vvv vvi vi ivi L1M5_orf2#LIN 3030 ATTGGACTNCATCAAAATTAAAAACTTCTGCTCNTCAAAAGACACCGTTA 3079 chr1ptel1M 117319 ACAAGATTAGAAGGGAAGCAATAAACTGGGAAAACATTTTTACAGTCAAA 117368 v i v i v v i i ? i v v i i?- v L1M5_orf2#LIN 3080 AGAAAATGAAAAGGCAAGCCACAGANTGGGAGAAAATATTTGCAAN-ACA 3128 chr1ptel1M 117369 GGT-TCTGATAAAAGCCTCATCTCCAAAATATATAGAGAATTGACTCC-- 117415 vi - i i v i v i i ---- -- L1M5_orf2#LIN 3129 TATATCTGACAAAGGACTCGTATCCAGAATATATAAAGAA----CTCCTA 3174 chr1ptel1M 117416 CAATTTA-TAAGAAATCAAGCCATTC--TCCAATTGATAAATGGTCAAAG 117462 ? i - ? -- v vv --i v? v v i L1M5_orf2#LIN 3175 CAANTCAATAANAAA--AAGACAAACAACCCAATANAAAAATGGGCAAAA 3222 chr1ptel1M 117463 GATATGAACAGACAATTCTCAGATGAAGAAATTGAAACTATTTCTAGCCA 117512 iv v v i v v ?v iviiivv iv L1M5_orf2#LIN 3223 GACTTGAACAGACACTTCACAAAAGAAGATATNCAAATGGCCAATAAGCA 3272 chr1ptel1M 117513 TATGAAAAGATGCTCCAAGTCA 117534 i v v? L1M5_orf2#LIN 3273 CATGAAAAGATGCTCAACNTCA 3294 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.34 CpG sites = 74, Kimura (unadjusted) = 38.73 Transitions / transversions = 1.12 (74/66) Gap_init rate = 0.06 (28 / 499), avg. gap size = 1.43 (40 / 28) 1430 28.00 0.36 1.83 chr1ptel1M 117387 117939 (882061) L1ME3G_3end#LINE/L1 4 548 (376) m_b4s551i5 148 chr1ptel1M 117387 ATCTCCAAAATATATAGAGAATTGACTCCCAATTTATAAGAAATCAAGCC 117436 v i i i v- v v iv -- v L1ME3G_3end#L 4 ATATCCAGAATATATAAAGAACTC-CTACAAATCAATAAGAAA--AAGAC 50 chr1ptel1M 117437 ATTCTCCAATTGATAAATGGTCAAAGGATATGAACAGACAATTCTCAGAT 117486 --vi v v v i v v L1ME3G_3end#L 51 A--ACCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAA 98 chr1ptel1M 117487 GAAGAAATTGAAACTATTTCTAGCCATATGAAAAGATGCTCCAAGTCATT 117536 i vv iviiivv iv v vv i L1ME3G_3end#L 99 GAGGAAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACT 148 chr1ptel1M 117537 ATTAATCAGAGAAATGCAAATTAAGACAACTCTGAGATACTACTACACAT 117586 v i i vv i i viv i L1ME3G_3end#L 149 AGTAATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCAC 198 chr1ptel1M 117587 CTGTCATATTGGCTAGAATGACAGGGAAAGATAATGACGAATGTTGGAGG 117636 ii v v i vvv ii ?vv iv ? i v i L1ME3G_3end#L 199 CCATCAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGA 248 chr1ptel1M 117637 GGATGTGGGAAAACTGGGACACTAACACATTGTTAGTGGAGTTGGGAATA 117686 i i v v v v i i i i iiv vi v L1ME3G_3end#L 249 GGGTGTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATT 298 chr1ptel1M 117687 CATCCAGCCATTCTGGAGAGCAATTTGGAACTATACCCAAAAAGTTATCA 117736 vi v ? i i v v viviv v --- L1ME3G_3end#L 299 GGTACAGCCNTTTTGGAGGGCAATTTGGCAGTATCTATTAAAATTT---A 345 chr1ptel1M 117737 AACTGTGCATACCCTTTGATCCAGCAGTGTTACTACTGGTCTTATATCCC 117786 v i i i vii v ? v?v v i L1ME3G_3end#L 346 AAATGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCT 395 chr1ptel1M 117787 AAGGAGAT--TTTAAAGTAGGGAAAGGGACCTGTATGTGAAAGAATGTTT 117834 ?i i -- ivv vi iv v v i --? i iv i i L1ME3G_3end#L 396 ANAGAAATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTC 443 chr1ptel1M 117835 GTGGCAGACCTCTTTGTTGTGGCCAGAAGCTGGAAATTGAGTGGATGCCC 117884 i v vvi v vi i v i ii ivivv ii i L1ME3G_3end#L 444 ATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCC 493 chr1ptel1M 117885 ATCAACTGGAGAAGGGCTGAATAAATTGTGGTATATGAATATTATGGAAT 117934 iv i v i i i vv i L1ME3G_3end#L 494 ATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAAT 543 chr1ptel1M 117935 ATTAT 117939 i L1ME3G_3end#L 544 ACTAT 548 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.46 CpG sites = 76, Kimura (unadjusted) = 36.04 Transitions / transversions = 1.00 (76/76) Gap_init rate = 0.02 (11 / 552), avg. gap size = 1.09 (12 / 11) 12 18.27 5.41 0.00 chr1ptel1M 118312 118348 (881652) (TATACT)n#Simple_repeat 1 39 (0) m_b4s252i4 149 chr1ptel1M 118312 TATACATATA-TTGTATTTA-ACTTATACTTTAACATAT 118348 v - i i - vv v (TATACT)n#Sim 1 TATACTTATACTTATACTTATACTTATACTTATACTTAT 39 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 434 27.40 0.00 8.77 chr1ptel1M 121708 121831 (878169) C MIRb#SINE/MIR (150) 118 5 m_b4s601i1 150 chr1ptel1M 121708 GGGGTTAAGTTATTTTCCCAGGATCACACAGTTAGGAAGTGTTAATTGTC 121757 i v i v i i i v vi ------ C MIRb#SINE/MIR 118 GAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCA------ 75 chr1ptel1M 121758 TGAGACCAAATTTGAACTCAGGTTCTCCTGACTTCAGGGTTGGTGCTGCA 121807 - v vii i i iivi i ii iiv viv C MIRb#SINE/MIR 74 -GAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTT 26 chr1ptel1M 121808 TCTACTGTACCACCTAGCTGCCCC 121831 i i --- C MIRb#SINE/MIR 25 TCCACTGCACCAC---GCTGCCCC 5 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.84 CpG sites = 21, Kimura (unadjusted) = 35.28 Transitions / transversions = 2.10 (21/10) Gap_init rate = 0.08 (10 / 123), avg. gap size = 1.00 (10 / 10) 383 26.36 18.56 2.22 chr1ptel1M 121839 122032 (877968) MIRb#SINE/MIR 34 258 (10) m_b4s601i2 151 chr1ptel1M 121839 GGGCTTTTAA-TCATGAAGACCTGAATTTTAATCCC-------CCCCTTA 121880 vi - viv ii iv ------- v MIRb#SINE/MIR 34 GGGCTTTGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTA 83 chr1ptel1M 121881 TAATCT---TG---CTAGCCAATTTACAGGAC-TCCCTGTTTGCCT--GT 121921 iv v --- ---i i v v vvi - i v-- -- MIRb#SINE/MIR 84 CTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGA--GCCTCAGT 131 chr1ptel1M 121922 TTTTTTATTTGTAAAATAGGTATAACAACTGCACCTA-ATCCTAGGGTTC 121970 ii i i i v i ---i -v vi v MIRb#SINE/MIR 132 TTCCTCATCTGTAAAATGGGGATAATAA---TACCTACCTCGCAGGGTTG 178 chr1ptel1M 121971 TCATGAGGACAAAGTAAGA------------------TAGCACAGTGCAT 122002 ii iv i i ------------------ v MIRb#SINE/MIR 179 TTGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCT 228 chr1ptel1M 122003 AACACACAGTAGGTGCTATAGAAATGCTAG 122032 ii i i i vv v v MIRb#SINE/MIR 229 GGCACATAGTAAGCGCTCAATAAATGGTAG 258 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.64 CpG sites = 28, Kimura (unadjusted) = 33.24 Transitions / transversions = 1.27 (28/22) Gap_init rate = 0.07 (13 / 193), avg. gap size = 3.15 (41 / 13) 244 20.37 1.85 0.00 chr1ptel1M 121990 122043 (877957) L2d2_3end#LINE/L2 499 553 (2) m_b4s601i3 152 chr1ptel1M 121990 TAGCACAGTGCATAACACACAGTAGGTGCTATAGAAATGCTAGTC-ATTT 122038 v vi i vv v ii v i- L2d2_3end#LIN 499 TAGCACAGTGCCTTGCACACAGTAGGCGCTCAATAAATATTTGTTGATTT 548 chr1ptel1M 122039 GATTT 122043 L2d2_3end#LIN 549 GATTT 553 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 21.54 CpG sites = 5, Kimura (unadjusted) = 23.85 Transitions / transversions = 0.83 (5/6) Gap_init rate = 0.02 (1 / 53), avg. gap size = 1.00 (1 / 1) 185 31.43 8.93 3.39 chr1ptel1M 122181 122292 (877708) L2c_3end#LINE/L2 361 478 (0) m_b4s601i4 153 chr1ptel1M 122181 TATCATCCCTACCAGACCTTGGCCTCC---AGAA----GACTATCTCTTT 122223 i vi i i i iv iv --- ii---- ii v v L2c_3end#LINE 361 TGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTA 410 chr1ptel1M 122224 ATGTTCCTGGTCATTAGCCCAGCGCTAGGCATGTAGCAGACACT---TAA 122270 v vv i v - i-- iv ii i i i --- L2c_3end#LINE 411 TTCATCTTTGT-ATC--CCCAGCGCCTGGCACATAGTAGGCGCTCAATAA 457 chr1ptel1M 122271 ATCTTTGCTGACTTGAAGAAAT 122292 v i v- vi L2c_3end#LINE 458 ATGTTTGTTGAA-TGAATGAAT 478 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.02 CpG sites = 21, Kimura (unadjusted) = 42.48 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.06 (7 / 111), avg. gap size = 2.00 (14 / 7) 283 19.98 11.63 1.05 chr1ptel1M 122380 122465 (877535) C MIR3#SINE/MIR (3) 205 111 m_b4s601i5 154 chr1ptel1M 122380 TTATAGGATCATAGATGATCA---TTGGAAGGGATCTATAGGG-CCAT-- 122423 i i vvi ---i i - i -i -- C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCT-TAGAGATCATCT 157 chr1ptel1M 122424 AG---AGCGCACTCATTTTATAGATG-GGAAACTGAGATTCAGTGA 122465 --- i v v i - iii v C MIR3#SINE/MIR 156 AGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGA 111 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 23.99 CpG sites = 12, Kimura (unadjusted) = 23.99 Transitions / transversions = 2.40 (12/5) Gap_init rate = 0.07 (6 / 85), avg. gap size = 1.83 (11 / 6) 302 22.69 8.77 3.33 chr1ptel1M 123681 123794 (876206) C MIR3#SINE/MIR (1) 207 88 m_b4s601i6 155 chr1ptel1M 123681 AACCATCAGAAGTGATAAGATGT--GAGCTGAAAAACACTTCAG-CATTA 123727 i - - v ii -- i iiv i i -v i C MIR3#SINE/MIR 207 AATCAT-AGAA-TCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCA 160 chr1ptel1M 123728 AAAAGTCCAACCCTTTTCAATTTACAG--GAAGAAACTGAAACATAGA-- 123773 vvv ii - v -- i ii vi -- C MIR3#SINE/MIR 159 TCTAGTCCAACCCCCT-CATTTTACAGATGAGGAAACTGAGGCCCAGAGA 111 chr1ptel1M 123774 ---GAAGGGATTTGCCCAAAGGTC 123794 --- v i - C MIR3#SINE/MIR 110 GGTGAAGTGACTTGCCC-AAGGTC 88 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.79 CpG sites = 16, Kimura (unadjusted) = 27.79 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.08 (9 / 113), avg. gap size = 1.56 (14 / 9) 18 21.81 0.00 0.00 chr1ptel1M 125102 125138 (874862) (A)n#Simple_repeat 1 37 (0) m_b4s252i5 156 chr1ptel1M 125102 AAAAAAAAAAAAAAATTAGAAAAATAAATGAACAAAA 125138 vv i v vi v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 37 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 249 25.00 1.39 0.00 chr1ptel1M 125636 125707 (874293) L1M2_orf2#LINE/L1 1673 1745 (1546) m_b4s551i6 157 chr1ptel1M 125636 TTCATTGTGATCAAGTGGGACTGCTACTAGCAATGGAAGGATAGTTCAAC 125685 ? iii i vv v i vi v i L1M2_orf2#LIN 1673 TNCACCATGATCAAGTGGGATTTATCCCAGGGATGCAAGGATGGTTCAAC 1722 chr1ptel1M 125686 ATTGGGAAA-CAATGAACATAAT 125707 vv v - i i i L1M2_orf2#LIN 1723 ATACGCAAATCAATAAACGTGAT 1745 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 29.41 CpG sites = 10, Kimura (unadjusted) = 31.46 Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.01 (1 / 71), avg. gap size = 1.00 (1 / 1) 24 0.00 0.00 0.00 chr1ptel1M 126271 126296 (873704) (A)n#Simple_repeat 1 26 (0) m_b4s252i6 158 chr1ptel1M 126271 AAAAAAAAAAAAAAAAAAAAAAAAAA 126296 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAA 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 15 5.56 0.00 0.00 chr1ptel1M 126790 126808 (873192) (T)n#Simple_repeat 1 19 (0) m_b4s252i8 159 chr1ptel1M 126790 TTTCTTTTTTTTTTTTTTT 126808 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 17 18.60 0.00 4.44 chr1ptel1M 126789 126835 (873165) (ATTT)n#Simple_repeat 1 45 (0) m_b4s252i7 160 chr1ptel1M 126789 ATTTCTTTTTTTTTTTTTTTAAATTAATTAATTAATTTATTTATTTA 126835 v v v v -- v v v (ATTT)n#Simpl 1 ATTTATTTATTTATTTATTT--ATTTATTTATTTATTTATTTATTTA 45 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.04 (2 / 46), avg. gap size = 1.00 (2 / 2) 288 32.74 1.32 2.21 chr1ptel1M 128725 128952 (871048) L1ME4c_3end#LINE/L1 414 639 (191) m_b4s551i7 161 chr1ptel1M 128725 TTAAAGGAAGGAAAGAGACCCCCATGTGCAAAAATGTTTGTGGCAGCCCT 128774 i i i -- ivi ii i i ii v vi L1ME4c_3end#L 414 TCAAAAGAAGGAAAAAG--CTATATGCACGAAGATGTTCATTGCAGCGTT 461 chr1ptel1M 128775 TTTTGTTGTGG-AAGAAACTGGAAACTGAATAGATGTCCCTCAGGTGGGA 128823 v i vi i -i i i vivv i vv ivv i L1ME4c_3end#L 462 ATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGG 511 chr1ptel1M 128824 AATAGCTAAATAAGTTGTGGTATATAAATGTTATGGAATATTATTGTTCT 128873 i i i i i i v? iviv vvvv i L1ME4c_3end#L 512 AATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATATTATGCAGCC 561 chr1ptel1M 128874 GTAAGAAATGATCGGCAGGATGAT--TGCAGAAAGGTCTGGAAAGATTTA 128921 i v i vivi v v i-- i v --iv - v v L1ME4c_3end#L 562 ATTAAAAATGATAATTATGAAGACTATGTAGCAA--CATGGAAA-ATGTT 608 chr1ptel1M 128922 CATGAATTAATGCTAAGTGAAGTAAGCATAA 128952 i vv i iv v L1ME4c_3end#L 609 TATGATATAATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 42.09 CpG sites = 41, Kimura (unadjusted) = 44.53 Transitions / transversions = 1.28 (41/32) Gap_init rate = 0.03 (7 / 227), avg. gap size = 1.14 (8 / 7) 363 28.10 0.83 0.00 chr1ptel1M 128747 128867 (871133) L1ME3G_3end#LINE/L1 427 548 (376) m_b4s551i8 161 chr1ptel1M 128747 CATGTGCAAAAATGTTTGTGGCAGCCCTTTTTGTTGTGG-AAGAAACTGG 128795 i ii ii v vi v vi i -i i i L1ME3G_3end#L 427 CATGTACAAGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGG 476 chr1ptel1M 128796 AAACTGAATAGATGTCCCTCAGGTGGGAAATAGCTAAATAAGTTGTGGTA 128845 vivv i v ivv i i i i i L1ME3G_3end#L 477 AAACAACCTAAATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGTA 526 chr1ptel1M 128846 TATAAATGTTATGGAATATTAT 128867 vv ii i L1ME3G_3end#L 527 TATCCATACTATGGAATACTAT 548 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.23 CpG sites = 22, Kimura (unadjusted) = 36.60 Transitions / transversions = 1.83 (22/12) Gap_init rate = 0.01 (1 / 120), avg. gap size = 1.00 (1 / 1) 13 17.35 3.92 6.00 chr1ptel1M 129127 129177 (870823) (CTTTTT)n#Simple_repeat 1 50 (0) m_b4s252i9 162 chr1ptel1M 129127 CTTTTTCTTGTTTCTGTTT-GCTTGCATTTT-ATTTTCTGTTTCATTATT 129174 - v -vi v v -v v - - (CTTTTT)n#Sim 1 CTTTTTCTT-TTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTC-TT-TT 47 chr1ptel1M 129175 TCT 129177 (CTTTTT)n#Sim 48 TCT 50 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.10 (5 / 50), avg. gap size = 1.00 (5 / 5) 356 28.44 3.36 2.50 chr1ptel1M 129484 129602 (870398) MIRb#SINE/MIR 143 262 (6) m_b4s601i7 163 chr1ptel1M 129484 TAAAATGAGGATAAAAACACCTTCCTTCCAGTGTTTGTTCTGAGGATCAC 129533 i v i v iv - v v i v MIRb#SINE/MIR 143 TAAAATGGGGATAATAATACCTACCTCGCAG-GGTTGTTGTGAGGATTAA 191 chr1ptel1M 129534 AGGAAATATTG---GTAAGGTGTTTAAC-TTGTGTCTGGTACTTAATAGG 129579 v i v --- i i i i -iv i i v i i MIRb#SINE/MIR 192 ATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAG 241 chr1ptel1M 129580 TCCCTCATAATAATTGCAACTTT 129602 iv iiv -- v i i i MIRb#SINE/MIR 242 CGCTCAATA--AATGGTAGCTCT 262 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.76 CpG sites = 20, Kimura (unadjusted) = 36.87 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.04 (5 / 118), avg. gap size = 1.40 (7 / 5) 205 29.69 3.12 0.00 chr1ptel1M 129959 130022 (869978) AmnSINE2#SINE/tRNA-Deu 185 250 (108) m_b4s601i8 164 chr1ptel1M 129959 CTGCTCTGC-TGAACACAGGAGCTCCCATAAC-CTCTTTGAAATGGTAGG 130006 - i ivii v i ii - i i v vi AmnSINE2#SINE 185 CTGCTCTGCGTGGACATTAAAGATCCCGTGGCGCTTTTCGTAAGAGTAGG 234 chr1ptel1M 130007 GATCAGTCCCTGTGCC 130022 i iv i v AmnSINE2#SINE 235 GGTTTGCCCCGGTGCC 250 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.52 CpG sites = 13, Kimura (unadjusted) = 39.85 Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.03 (2 / 63), avg. gap size = 1.00 (2 / 2) 16 5.27 0.00 0.00 chr1ptel1M 130896 130915 (869085) (A)n#Simple_repeat 1 20 (0) m_b4s252i10 165 chr1ptel1M 130896 AAAAAAAAGAAAAAAAAAAA 130915 i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAA 20 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 336 26.99 6.47 1.37 chr1ptel1M 135479 135617 (864383) MIR3#SINE/MIR 62 207 (1) m_b4s601i9 166 chr1ptel1M 135479 CTGACTCTGACATTCATAAAGGATATGAGTTTTGGGAAG--AGT--GTTT 135524 i i v i v iv?ivvi i vi v v -- v --iii MIR3#SINE/MIR 62 CCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCT 111 chr1ptel1M 135525 CTCTGTGCTTCAGTTTCCTC--CTGTAAATTGATGAGGGCTGGAC-ATTT 135571 v i -- v - i i - vv MIR3#SINE/MIR 112 CTCTGGGCCTCAGTTTCCTCATCTGTAAAATGA-GGGGGTTGGACTAGAT 160 chr1ptel1M 135572 TAATTCTAAAGTTCCTTTAAGCTCT-ACATT-TATAAATGTGATGATT 135617 v vi i i iv - - i v v - MIR3#SINE/MIR 161 GATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCT-ATGATT 207 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.11 CpG sites = 19, Kimura (unadjusted) = 34.22 Transitions / transversions = 1.06 (19/18) Gap_init rate = 0.06 (8 / 138), avg. gap size = 1.38 (11 / 8) 298 28.57 3.57 0.00 chr1ptel1M 136404 136487 (863513) C MIR#SINE/MIR (72) 190 104 m_b4s601i10 167 chr1ptel1M 136404 CATCTTATCTCCACAGTAACCTTCCAAGTTAGGTGACACCGTTCTCCTCA 136453 i v ii ii i vii v ivi iii v i C MIR#SINE/MIR 190 CATTTAATCCTCACAACAACCCTATGAGGTAGGTACTATTATTATCCCCA 141 chr1ptel1M 136454 TTTAAGAGTTGAGGAAACTGAGGCA---AAAGTTTAA 136487 v v v --- i v C MIR#SINE/MIR 140 TTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAA 104 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.24 CpG sites = 15, Kimura (unadjusted) = 37.24 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.01 (1 / 83), avg. gap size = 3.00 (3 / 1) 203 24.71 0.95 15.22 chr1ptel1M 136410 136514 (863486) C MIR1_Amn#SINE/MIR (41) 189 98 m_b4s601i11 167 chr1ptel1M 136410 ATCTCCACAGTAACCTTCCAAGTTAGGTGA-CACCGTTCTCCTCATTTAA 136458 v - i - i v ivv v -i i i v i v C MIR1_Amn#SINE 189 ATCTCAA-AGCA-CTTTACAAAGGAGGTCAGTATCATTATCCCCATTTTA 142 chr1ptel1M 136459 GAGTTGAGGAAACTGAGGCAAAAGTTTAAAGGCAGAGAGCTCAGGGGATT 136508 v v ------------? v ? i v i C MIR1_Amn#SINE 141 CAGATGAGGAAACTGAGGC------------NCAGAGAGGTNAAGTGACT 104 chr1ptel1M 136509 TGGCTA 136514 v i C MIR1_Amn#SINE 103 TGCCCA 98 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.14 CpG sites = 10, Kimura (unadjusted) = 30.14 Transitions / transversions = 0.83 (10/12) Gap_init rate = 0.14 (15 / 104), avg. gap size = 1.00 (15 / 15) 335 25.29 4.60 0.00 chr1ptel1M 136981 137067 (862933) MIR3#SINE/MIR 111 201 (7) m_b4s601i12 168 chr1ptel1M 136981 TCACTGAACCTCAATTTACCCATTTCTAAAATGAGGAGGTTGGACCCCAT 137030 v ii i v i i v i ivv MIR3#SINE/MIR 111 TCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGAT 160 chr1ptel1M 137031 GGCCTTT-AGCTCTCATCCAG---TGGTCTTCTATGATCCT 137067 ii i - v i v --- iiv i MIR3#SINE/MIR 161 GATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCT 201 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.78 CpG sites = 14, Kimura (unadjusted) = 31.78 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.02 (2 / 86), avg. gap size = 2.00 (4 / 2) 221 28.62 14.91 4.52 chr1ptel1M 137165 137325 (862675) C L2a_3end#LINE/L2 (5) 512 336 m_b4s601i14 169 chr1ptel1M 137165 TTGACTCATCAAACATTTAT---GTGCCTACTACATGCTAGACCCTGGGT 137211 v i v i --- i ii i i v vvi C L2a_3end#LINE 512 TTCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTC 463 chr1ptel1M 137212 TAAG-----------CAGCAG-AAACAAAAAGAGATATATGGGTGACCCC 137249 i ----------- -i - v i v --i --- C L2a_3end#LINE 462 TAGGCGCTGGGGATACAGCAGTGAAC-AAAACAGACAAA--AGT---CCC 419 chr1ptel1M 137250 TGCTCCTATAGAGGTCAAAGGCTGGT-----GAGATTGACCATACAC--- 137291 i ii i v i v vv i ----- iv v v --- C L2a_3end#LINE 418 TGCCCTCATGGAGCTTACATTCTAGTGGGGGGAGACAGACAATAAACAAA 369 chr1ptel1M 137292 TAAGAGGGTAGAA-ACCTAATATGCATTAGATAAT 137325 ivii i - iv i -- i ii C L2a_3end#LINE 368 TAAATAAGTAAAATATATAGTATG--TCAGATGGT 336 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.57 CpG sites = 28, Kimura (unadjusted) = 37.67 Transitions / transversions = 1.75 (28/16) Gap_init rate = 0.09 (14 / 160), avg. gap size = 2.29 (32 / 14) 277 33.00 8.77 1.64 chr1ptel1M 137165 137278 (862722) C L2b_3end#LINE/L2 (5) 461 340 m_b4s601i13 169 chr1ptel1M 137165 TTGACTCATCAAACATTTAT---GTGCCTACTACATGCTAGACCCTGGGT 137211 v i v i i--- i iii i i ? v i C L2b_3end#LINE 461 TTCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGC 412 chr1ptel1M 137212 TAAGCA--GCAGAAACA-----AAAAGAGATATATGGGTGACCCCTGCTC 137254 i i-- vi v -----i vi i v i--?i ii i C L2b_3end#LINE 411 TAGGCGCTGGGGATACAGCGGTGAACAAGACAGAC--NCGGTCCCTGCCC 364 chr1ptel1M 137255 CTATAGAGGTCAAAGGCTGGTGAG 137278 ii ii v v v i i C L2b_3end#LINE 363 TCACGGAGCTCACAGTCTAGTGGG 340 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.15 CpG sites = 27, Kimura (unadjusted) = 48.61 Transitions / transversions = 2.70 (27/10) Gap_init rate = 0.04 (5 / 113), avg. gap size = 2.40 (12 / 5) 241 35.95 5.67 1.36 chr1ptel1M 137170 137310 (862690) C L2d2_3end#LINE/L2 (10) 545 399 m_b4s601i15 169 chr1ptel1M 137170 TCATCAAACATTTAT---GTGCCTACTACATGCTAGACCCTGGGTTAAGC 137216 v i --- i iii v i v v i i C L2d2_3end#LIN 545 TCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGC 496 chr1ptel1M 137217 AGC----AGAAACAAAAAGAGATATATGG-GTGACCCCTGCTCCTATAGA 137261 - ----i ii i v ii v i-i ii i ii vi C L2d2_3end#LIN 495 -GCTGTGGGGGATACAAAGAAGTATAAGACATGGTCCCTGCCCTCAAGGA 447 chr1ptel1M 137262 GGTCAAAGGCTGGTGAGATTGACCATACACTAAGAGGGTAGAAACCTAA 137310 v i v iv i vi ivv v v - iviv ii vi C L2d2_3end#LIN 446 GCTTACAATCTAGTTGGGGAGACAAGACA-TAAACACGTGAAAAGTTAA 399 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 50.51 CpG sites = 32, Kimura (unadjusted) = 52.06 Transitions / transversions = 1.78 (32/18) Gap_init rate = 0.04 (5 / 140), avg. gap size = 2.00 (10 / 5) 22 12.84 0.00 0.00 chr1ptel1M 137326 137359 (862641) (T)n#Simple_repeat 1 34 (0) m_b4s252i11 170 chr1ptel1M 137326 TTTTTTTCTTTTCTTTTTTTTTTTTTTAATTTTT 137359 i i vv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 34 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 20 18.50 6.56 0.00 chr1ptel1M 138888 138948 (861052) (AAGAAA)n#Simple_repeat 1 65 (0) m_b4s252i12 171 chr1ptel1M 138888 AAAAAACAGAATAAGAAAAA-AAAGAAAAACAG-AAAAGTAATA-CAAAA 138934 i v v - i i v - v v -v (AAGAAA)n#Sim 1 AAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAA 50 chr1ptel1M 138935 -CAAAAGAAAAAGAA 138948 -v (AAGAAA)n#Sim 51 GAAAAAGAAAAAGAA 65 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.07 (4 / 60), avg. gap size = 1.00 (4 / 4) 14 21.69 3.77 3.77 chr1ptel1M 139183 139235 (860765) (ATAC)n#Simple_repeat 1 53 (0) m_b4s252i13 172 chr1ptel1M 139183 ATACATATGCAGATATATACATAC--ACATAGATGCACACACACACATAT 139230 iii v i -- v -- i i i (ATAC)n#Simpl 1 ATACATACATACATACATACATACATACATACAT--ACATACATACATAC 48 chr1ptel1M 139231 ATACA 139235 (ATAC)n#Simpl 49 ATACA 53 Matrix = Unknown Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.06 (3 / 52), avg. gap size = 1.33 (4 / 3) 19 20.69 3.23 4.92 chr1ptel1M 139201 139262 (860738) (AC)n#Simple_repeat 1 61 (0) m_b4s252i14 172 chr1ptel1M 139201 ACATACACATAGATGCACACACACACATATATACAC-CCCATCAC-CAGC 139248 i i v ii i i i - v - - - (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACA-CACACA-C 48 chr1ptel1M 139249 TCTACACACACACA 139262 v - (AC)n#Simple_ 49 AC-ACACACACACA 61 Matrix = Unknown Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.08 (5 / 61), avg. gap size = 1.00 (5 / 5) 182 25.45 5.45 0.00 chr1ptel1M 139887 139941 (860059) MIRc#SINE/MIR 174 231 (37) m_b4s601i16 173 chr1ptel1M 139887 TCACAGATTTATTGTGAACATCCAATGTAATTATCCATGC---AGCTCAT 139933 iv i iv v vi v vi i--- v v MIRc#SINE/MIR 174 TCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTT 223 chr1ptel1M 139934 TGTAAACT 139941 MIRc#SINE/MIR 224 TGTAAACT 231 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.19 CpG sites = 6, Kimura (unadjusted) = 31.19 Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.02 (1 / 54), avg. gap size = 3.00 (3 / 1) 520 33.81 3.32 0.46 chr1ptel1M 140415 140625 (859375) L3#LINE/CR1 3489 3705 (394) m_b4s601i17 174 chr1ptel1M 140415 AGAAAGGGAGCACAGTATTAGGCTACATGAAAAGAGGCATTGTTGCTTGG 140464 i vv iii i v i v v i i v - iiii L3#LINE/CR1 3489 AAAAAGCTAATGCAATCTTAGGCTGCATTAATAGAAGTATAGT-GTCCAG 3537 chr1ptel1M 140465 AGTAAGA-AGATGGTAGTATTACT-TACTCTGCCCTGCTCAGACCAGATC 140512 ?i i- i ii viii - v v v L3#LINE/CR1 3538 ANCAAGGGAGGTAATAGTCCCGCTGTACTCTGCGCTGGTCAGACCACATC 3587 chr1ptel1M 140513 TGAAAC-TTGTGCTCACCTCTGTG-ACCACAACCTAGCCAAGATGTAGGT 140560 i ii- i i vi v -i vii ivvii ii v ii L3#LINE/CR1 3588 TGGAGTATTGCGTTCAGTTCTGGGCGCCACATTTTAAGAGGGACATTGAC 3637 chr1ptel1M 140561 AAATTGTAGAGCATCCAGAGAAAGGAAGCCAGCATAGTGAGGGACCT-CA 140609 i v v i i ii vii v i i ii -v L3#LINE/CR1 3638 AAACTGGAGCGCGTCCAGAGGAGAGCGACCAGGATGGTGAAGGGTCTGGA 3687 chr1ptel1M 140610 AGTCTTGTC--ATGAGGA 140625 ii v -- L3#LINE/CR1 3688 AACCATGTCATATGAGGA 3705 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.68 CpG sites = 49, Kimura (unadjusted) = 48.59 Transitions / transversions = 2.23 (49/22) Gap_init rate = 0.03 (7 / 210), avg. gap size = 1.14 (8 / 7) 290 21.43 0.00 0.00 chr1ptel1M 141377 141432 (858568) L3#LINE/CR1 4042 4097 (2) m_b4s601i18 175 chr1ptel1M 141377 AGCTTGGATTAGAAAACCTTTAAATTCCCTTCCAACTCTGAGAATCAGTG 141426 v i vi i iv v v L3#LINE/CR1 4042 AGGTTGGACTAGATGACCTCTAAGGTCCCTTCCAACTCTGAGATTCTGTG 4091 chr1ptel1M 141427 GCTCCA 141432 ii i L3#LINE/CR1 4092 ATTCTA 4097 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.64 CpG sites = 7, Kimura (unadjusted) = 25.64 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0) 850 30.66 3.03 3.84 chr1ptel1M 141670 142561 (857439) L1M5_orf2#LINE/L1 2410 3294 (0) m_b4s551i9 176 chr1ptel1M 141670 TGCTCCTGGATAGGTCGAGCGAATATAATAAAGATGACAATACTCCCTAA 141719 i v v vv viv vi ? v v i L1M5_orf2#LIN 2410 TGTTCATGGATTGGAAGACTCAATATTGTNAAGATGTCAATTCTCCCCAA 2459 chr1ptel1M 141720 ACTAATCTATTTATTATTTATTTAGTGCTATACCAATCAGACTTCCAAGA 141769 i i ----- v-- i i v v i v i iv L1M5_orf2#LIN 2460 ATTGATCTAT-----AG--ATTCAATGCAATCCCAATCAAAATCCCAGCA 2502 chr1ptel1M 141770 AAATATTTTAATGATCTAGAAAAAATAACAACAAAATTCATATGGAATAA 141819 iiv v ivv vv v v iv i ivvi i vvi L1M5_orf2#LIN 2503 GGTTTTTTTGTAGAAATTGACAAGCTGATTCTAAAATTTATATGGAAATG 2552 chr1ptel1M 141820 TAAAAGGTCTAGAAT-CTCAAAAGAATTAATGAAAAAAAAAAATCAAA-- 141866 i i ii ? -vi v iv- i i - -- L1M5_orf2#LIN 2553 CAAAGGACCNAGAATAGCCAAAACAATCT-TGAAAAAGAAGAA-CAAAGT 2600 chr1ptel1M 141867 TGAAGGTGGCCTAGCTGTACCTGATCT-AAAACTATATTATAAAGCAGCA 141915 i --i i - vv ? ? - i - vi L1M5_orf2#LIN 2601 TGGAGG--ACTTA-CACTACCNGATNTCAAGACT-TATTATAAAGCTACA 2646 chr1ptel1M 141916 GTCACCAAAACCATTTGGTATTGGC-TAAGAAATAGATTAGTTGATCAGT 141964 v i i vi v - i - iv i v i L1M5_orf2#LIN 2647 GTAATCAAGACAGTGTGGTATTGGCGTAAGGA-TAGACAAATAGATCAAT 2695 chr1ptel1M 141965 GGAACAGGTTAG---GTTCACAAGACAGA---ATAGTCAACTATAGCAAT 142008 iv --- i v - i --- i -- vv i ?v ? L1M5_orf2#LIN 2696 GGAACAGAATAGAGAGTCCAGAA-ATAGACCCACA--CATATATGGNCAN 2742 chr1ptel1M 142009 TTAGTGTTTGACAAAC---CCAAAGATCCTAACTT-TTGGGATAAGAATT 142054 ii v v--- ? ----i i i-v iv i v L1M5_orf2#LIN 2743 TTGATTTTTGACAAAGGTGCCAANG----CAATTCAGTGGGGAAAGGATA 2788 chr1ptel1M 142055 CATTATTTGACAAAAACTGCTGGGATAACTGGAAATTAGTATGTCAGAAA 142104 vvi v ii viv i i i v ivi vv i L1M5_orf2#LIN 2789 GTCTTTTCAACAAATGGTGCTGGAACAATTGGATATCCATATGGAAAAAA 2838 chr1ptel1M 142105 TTAGGCATGGACCCACACTTAGCACCATATACCAAGATAAGATCAAAATG 142154 v iii?v v vi i vi i v i v iv ? i L1M5_orf2#LIN 2839 ATGAANCTCGACCCCTACCTCACACCATACACAAAAATTAATTCNAGATG 2888 chr1ptel1M 142155 GGTCCAT-GATTTAGACATAAAGAACGAGATTATAAATAAATTAGAGGAA 142203 i - - ii i ii ii?ii i i vvvvi i L1M5_orf2#LIN 2889 GATC-ATAGACCTAAATGTAAAAGNTAAAACTATAAAACTTCTAGAAGAA 2937 chr1ptel1M 142204 --CATAGGATAGTTTATCTCTCAGACTTGTGGAAGAGGAAGAAATTTGTG 142251 -- v i -- iivv i - i?v v i i v v L1M5_orf2#LIN 2938 AACATAGGAGAAT--ATCTTCGTGACCT-TGGGNTAGGCAAAGATTTCTT 2984 chr1ptel1M 142252 ACTAAAGACAAACTAGAGACCATTATTGATCACAAAATAGAAAATT---- 142297 vvv i ---i i i v i? --- i i v i ---- L1M5_orf2#LIN 2985 AAACAGGACA---CAAAAAGCACNA---ACCATAAAAGAAAAAATTGATA 3028 chr1ptel1M 142298 ---TTGATTACATCAAATTAAAAAGCTTCTGTACAAACAAAACTAATGTA 142344 --- v i ? v v i iv ?vvv ivi vi v L1M5_orf2#LIN 3029 AATTGGACTNCATCAAAATTAAAAACTTCTGCTCNTCAAAAGACACCGTT 3078 chr1ptel1M 142345 AGCAAGATTAGAAGGGAAGCAACAAACTGGGAAAACATCTTCACAGTTGA 142394 iv i v i v v i ? i v v ii i?vv L1M5_orf2#LIN 3079 AAGAAAATGAAAAGGCAAGCCACAGANTGGGAGAAAATATTTGCAANACA 3128 chr1ptel1M 142395 AGGTTCTGATAAAGGCCTCATTTCCAAAATATATAGAGAACTGACTCTTA 142444 vivv i v i v i i -v viv L1M5_orf2#LIN 3129 TATATCTGACAAAGGACTCGTATCCAGAATATATAAAGAACT-CCTACAA 3177 chr1ptel1M 142445 ATTTATAAGAAACCAAGCCATTC--TCCAATTGATAAATGGTCAAAGGAT 142492 ? iv ? -- v vv --i v? v v i i L1M5_orf2#LIN 3178 NTCAATAANAAA--AAGACAAACAACCCAATANAAAAATGGGCAAAAGAC 3225 chr1ptel1M 142493 ATGAACAGACAGTTTTCAGATGATGAAATTGAAATCATTACCACTCATAT 142542 v v iv i v v v ?v viii vi vv i L1M5_orf2#LIN 3226 TTGAACAGACACTTCACAAAAGAAGATATNCAAATGGCCAATAAGCACAT 3275 chr1ptel1M 142543 GAAAGAGTGTTCCAAATCA 142561 iii i v v? L1M5_orf2#LIN 3276 GAAAAGATGCTCAACNTCA 3294 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.81 CpG sites = 136, Kimura (unadjusted) = 41.42 Transitions / transversions = 1.07 (136/127) Gap_init rate = 0.05 (47 / 891), avg. gap size = 1.30 (61 / 47) 1397 28.96 1.59 1.43 chr1ptel1M 142422 143048 (856952) L1ME4c_3end#LINE/L1 12 639 (191) m_b4s551i10 176 chr1ptel1M 142422 AATATATAGAGAACTGACTCTTAATTTATAAGAAACCAAGCCATTCTCCA 142471 ? i i v i v- v vv? v v vv i L1ME4c_3end#L 12 ANTATATAAAGAGCTCATTCA-AATTGATAAGAAAAANATCAAGACCCCA 60 chr1ptel1M 142472 ATTGATAAATGGTCAAAGGATATGAACAGACAGTTTTCAGATGATGAAAT 142521 v v i i iv ? v v L1ME4c_3end#L 61 ATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAGGAAAT 110 chr1ptel1M 142522 TGAAATCATTACCACTCATATGAAAGAGTGTTCCAAATCATTATTAATCA 142571 vv ? vi v v vv i i i i v vv ii v L1ME4c_3end#L 111 ACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTAGTAATCA 160 chr1ptel1M 142572 GAGAAATGCAAATTAAGACAACTCTGAGATACCACTACACACCTGTCAGA 142621 i ii vv i vi i i i i L1ME4c_3end#L 161 AAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCTATTAAA 210 chr1ptel1M 142622 TTGGCTAAGATGACAGGAAAAAATGATGAT------TGTTGGAGGGGATG 142665 i v i v---vi v i ------ i v i ? L1ME4c_3end#L 211 TTAGCAAAAATT---TAAAAAATTGATAATACCCAATGCTGGCGAGGNTG 257 chr1ptel1M 142666 TGGGAAAACTGGGACACTGATACATTGTTGGTGGAGCTGTGAAAGAATCC 142715 i vi v ? v i vi? i vvii v L1ME4c_3end#L 258 CGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGTAC 307 chr1ptel1M 142716 GACCATTCTGGAGAGCAATCTGGAATTATG-ACCAAAAAGTTATCAAACT 142764 i v i i i v v i - i i - ii v v L1ME4c_3end#L 308 AACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGA-GCCATAAAAAT 356 chr1ptel1M 142765 GTGCATACCCTTTGATCCAGCAGTGTTTCTACGGGGCTTATATCCCAAGG 142814 v i i i viiv v v vv v i L1ME4c_3end#L 357 GTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGG 406 chr1ptel1M 142815 AGATA---CTAAAGAAGGGAAAGGGACCAGTATGTGCCAAAATGTTTGTG 142861 i --- v i i -- i - ii v i ii v L1ME4c_3end#L 407 AAATAATTCAAAAGAAGGAAAAAG--CTA-TATGCACGAAGATGTTCATT 453 chr1ptel1M 142862 GCAGCCCTGTTTGTAGTGGCTAGAAGCTGGAAACTGAGTGGCTGCCCATC 142911 vi i i i i v i ii vivv iiv i v L1ME4c_3end#L 454 GCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAAC 503 chr1ptel1M 142912 AATTGGAGAATGGTTGGGTAAATTGTGGTATATGAATGTTATGGAATATT 142961 v i ii i i v? iviv L1ME4c_3end#L 504 AATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATATT 553 chr1ptel1M 142962 ATTGTTCTGTAAGAAATGACCAGCAGGATGAATACAGAGAGGCTTGGAGA 143011 vvvv ii v i iv vi v v v iiv vii v i L1ME4c_3end#L 554 ATGCAGCCATTAAAAATGATAATTATGAAGACTATGTAGCAACATGGAAA 603 chr1ptel1M 143012 GAATTACATGAACTGATGCTAAGTGAAATGAGCAGAA 143048 ivi -i vv i i vi L1ME4c_3end#L 604 ATGTT-TATGATATAATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.55 CpG sites = 95, Kimura (unadjusted) = 37.87 Transitions / transversions = 1.13 (95/84) Gap_init rate = 0.02 (12 / 626), avg. gap size = 1.58 (19 / 12) 12 9.24 0.00 4.17 chr1ptel1M 143361 143385 (856615) (GGGA)n#Simple_repeat 1 24 (0) m_b4s252i15 177 chr1ptel1M 143361 GGGAGGGGGTGGAGGGTGGGAGGGA 143385 i - v (GGGA)n#Simpl 1 GGGAGGGAG-GGAGGGAGGGAGGGA 24 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 18 8.53 0.00 0.00 chr1ptel1M 143469 143493 (856507) (A)n#Simple_repeat 1 25 (0) m_b4s252i16 178 chr1ptel1M 143469 AATAAAAAAAAAAAAACAAAAAAAA 143493 v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAA 25 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 16 19.56 0.00 0.00 chr1ptel1M 144704 144733 (855267) (G)n#Simple_repeat 1 30 (0) m_b4s252i17 179 chr1ptel1M 144704 GGGGGTGGAGGAGAGGGGGGGGGGGGGAGG 144733 v i i i i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 30 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 16 12.62 6.67 2.13 chr1ptel1M 145676 145720 (854280) (CCATCCT)n#Simple_repeat 1 47 (0) m_b4s252i18 180 chr1ptel1M 145676 CCATCC-CCATCCTCCATCTTCCCTGGCTCC--CCTCCCTCCTACATC 145720 - i v -v -- v v (CCATCCT)n#Si 1 CCATCCTCCATCCTCCATCCTCCAT-CCTCCATCCTCCATCCTCCATC 47 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.07 (3 / 44), avg. gap size = 1.33 (4 / 3) 13 17.67 6.12 4.00 chr1ptel1M 145870 145918 (854082) (AGG)n#Simple_repeat 1 50 (0) m_b4s252i19 181 chr1ptel1M 145870 AGGAGGATGGGGA-AAGGAGG-GAAGAGAAGAGGAGTA-AAGGAAGGAGG 145916 v i -i - i - i v -i - (AGG)n#Simple 1 AGGAGGAGGAGGAGGAGGAGGAGGAG-GAGGAGGAGGAGGAGG-AGGAGG 48 chr1ptel1M 145917 AG 145918 (AGG)n#Simple 49 AG 50 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.10 (5 / 48), avg. gap size = 1.00 (5 / 5) 12 17.88 7.69 0.00 chr1ptel1M 145881 145919 (854081) (GAAGA)n#Simple_repeat 1 42 (0) m_b4s252i20 181 chr1ptel1M 145881 GAA-AGGAGGGAAGAGAAGAGGAGTAAAG-GAAG-GAGGAGA 145919 - i i i vi - - i (GAAGA)n#Simp 1 GAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGA 42 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.08 (3 / 38), avg. gap size = 1.00 (3 / 3) 14 22.61 5.00 3.28 chr1ptel1M 148655 148714 (851286) (TTA)n#Simple_repeat 1 61 (0) m_b4s252i21 182 chr1ptel1M 148655 TTTTTATTATTATTCACT-TTGTTGTTAATGCTTAGTA-TATTTTTCTT- 148701 v - i - i i - vv v - v v - (TTA)n#Simple 1 TTATTATTATTATT-ATTATTATTATT-ATTATTATTATTATTATTATTA 48 chr1ptel1M 148702 TTTTTGTTATTAT 148714 v i (TTA)n#Simple 49 TTATTATTATTAT 61 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.08 (5 / 59), avg. gap size = 1.00 (5 / 5) 1103 31.51 3.65 0.77 chr1ptel1M 149136 149765 (850235) C L1ME4c_3end#LINE/L1 (171) 659 12 m_b5s551i0 183 chr1ptel1M 149136 AGTGTATA-ATGATCTCGTATTTCTGCTCATTTCACTTAGCATCAGTTCA 149184 i ? - ii i i - iv i i vv C L1ME4c_3end#L 659 AGCGTANATACAATTTTGTATT-CTGCTTTTTTCACTTAACATTATATCA 611 chr1ptel1M 149185 TATAAGTCTCTCCAGGCCTCTCTGTAGTCATCCTGCTGGTCATTTCTTAC 149234 v vi i - v iiv vii v v iv vi i v i C L1ME4c_3end#L 610 TAAACATTT-TCCATGTTGCTACATAGTCTTCATAATTATCATTTTTAAT 562 chr1ptel1M 149235 AGAACAATAATATTATATAACATTCATATACGACAGTTTATTCAGACATT 149284 i vvvv vi vivi ?v i v i i i i iv C L1ME4c_3end#L 561 GGCTGCATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATT 512 chr1ptel1M 149285 CTCCAGTTGATGGGCATCCATTCCATTTCCAGATTCTAGCCACTATGAAA 149334 i vi v i ii vviii iv i v i i i v C L1ME4c_3end#L 511 CCCCTATTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAAT 462 chr1ptel1M 149335 AGGGCTGCCACATACATTTTTGCACATACAGATTACTTTCC--CTTT--A 149380 iv v iiv i i ii i v -- -- -- C L1ME4c_3end#L 461 AACGCTGCAATGAACATCTTCGTGCATATAGCTT--TTTCCTTCTTTTGA 414 chr1ptel1M 149381 AT-ATCTCTTTAGGATATAAGCCCAGTAGAAACACTGCTGGATCAAAGGG 149429 - i i v vv v viiv i i i C L1ME4c_3end#L 413 ATTATTTCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGG 364 chr1ptel1M 149430 TATGTACAGTTTGATAACTTTTTGAGCTTACTTACAAATTGTTCTCCACA 149479 v v v ii i vivi v i vv i i v C L1ME4c_3end#L 363 TATGAACATTTTTATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAA 314 chr1ptel1M 149480 ------GTA---GTTCACAATTCCACCAATAATGCATCAATGTCCCTATT 149520 ------ ---i i ? v ii i v i? v vi C L1ME4c_3end#L 313 AGGGTTGTACCAATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTT 264 chr1ptel1M 149521 TTCCCACATCCCCTCCAACATTCGTCATTAACTTTTCCTGTCATCTTAGC 149570 iv i ? i v i v vi v vv ii vvv i v C L1ME4c_3end#L 263 TCACCGCANCCTCGCCAGCATTGGGTATTATCAATTTTTTAAATTTTTGC 214 chr1ptel1M 149571 CAATCTGACAGATATGTAATGGTATCTCAGAGTTGTCTTAATATGCATTT 149620 i i i i iii iv vv ii v C L1ME4c_3end#L 213 TAATTTAATAGGCGTAAAATGGTATCTCATTGTTGCTTTAATTTGCATTT 164 chr1ptel1M 149621 CTT-GATCAATAGTGATTTATAACACCTTTTCATGTGAGTAGAAATAGTT 149669 - i v i vv vv ii i vv ivvv ivi? C L1ME4c_3end#L 163 CTTTGATTACTAGCGAGGTTGAACATTTTTCCATGTGTTTGTTTACTANT 114 chr1ptel1M 149670 TCAATTTCATCATCTGAAAATTTTCTGTTCATTATCCTTTGCCCATTTAT 149719 vv v v ? vi v -i C L1ME4c_3end#L 113 TGTATTTCCTCTTNTGTGAATTGTCTGTTCAT-GTCCTTTGCCCATTTAT 65 chr1ptel1M 149720 CAATTGGAGAATGGCTTAATTTCTTAT-------AGTCAATTCTCTATAT 149762 v i vv v v ?vv ------- i v ii i C L1ME4c_3end#L 64 CTATTGGGGTCTTGATNTTTTTCTTATCAATTTGAATGAGCTCTTTATAT 15 chr1ptel1M 149763 ATT 149765 ? C L1ME4c_3end#L 14 ANT 12 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.80 CpG sites = 104, Kimura (unadjusted) = 42.52 Transitions / transversions = 1.12 (104/93) Gap_init rate = 0.02 (13 / 629), avg. gap size = 2.15 (28 / 13) 286 30.02 6.37 1.43 chr1ptel1M 149641 149907 (850093) C L1M5_orf2#LINE/L1 (8) 3286 3007 m_b5s551i1 183 chr1ptel1M 149641 AACACCTTTTCATGTGAGTAGAAATAGTTTCAATTTCATCATCTGAAAAT 149690 i i vv vviiivi v? v v v i vi v C L1M5_orf2#LIN 3286 AGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTTTTGTGAAG 3237 chr1ptel1M 149691 TTTCTGTTCATTATCCTTTGCCCATTTATCAATTGGA--GAATGGCTTAA 149738 v v-i i v ?v i-- vv v -- C L1M5_orf2#LIN 3236 TGTCTGTTCAA-GTCTTTTGCCCATTTTTNTATTGGGTTGTTTGTCTT-- 3190 chr1ptel1M 149739 TTTCTTAT--AGTC-----AATTCTCTATATATTTTTGAAATGGGGCCTT 149781 ? -- ? i----- i i i v v i i v C L1M5_orf2#LIN 3189 TTTNTTATTGANTTGTAGGAGTTCTTTATATATTCTGGATACGAGTCCTT 3140 chr1ptel1M 149782 TATCAGA-ACCTTTAACTGTAAAAATGTTTTCCCAATTTATTGCTTCCCT 149830 i - iv v -?i i v v i ? i i v v C L1M5_orf2#LIN 3139 TGTCAGATATATGT-NTTGCAAATATTTTCTCCCANTCTGTGGCTTGCCT 3091 chr1ptel1M 149831 TCTAATCTTGTCTACATTAGTTTTGTTTGTACAAAAGCTTTTTAACTTGA 149880 i v i v iv iv ivi vvv? vi i i v vi C L1M5_orf2#LIN 3090 TTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTTTAATTTTGA 3041 chr1ptel1M 149881 TATAATCAA-------AATTTTGTATTTTGTGAT 149907 i? i v ------- v v i i C L1M5_orf2#LIN 3040 TGNAGTCCAATTTATCAATTTTTTCTTTTATGGT 3007 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.11 CpG sites = 38, Kimura (unadjusted) = 40.40 Transitions / transversions = 0.93 (38/41) Gap_init rate = 0.03 (9 / 266), avg. gap size = 2.33 (21 / 9) 283 29.66 7.59 3.98 chr1ptel1M 151046 151361 (848639) C L1P3_orf2#LINE/L1 (2400) 894 568 m_b5s551i2 184 chr1ptel1M 151046 TTCCCCTCTGAGGACTGCTTTGGCTGAATTCCAGAAATTCTGGGATGTT- 151094 i i iv i vi i i v i - C L1P3_orf2#LIN 894 TTTCCCTCTAAACACTGCTTTAGCTGTGTCCCAGAGATTCTGGTACGTTG 845 chr1ptel1M 151095 TAATTAATCATTCTCATTTTGATTTGCA---AACTTG-TCATTTCCA--- 151137 ivi -- ii -- i - --- ?- i ii--- C L1P3_orf2#LIN 844 TGTCT--TTGTTCTCA--TTGGTTT-CAAAGAACTTNTTTATTTCTGCCT 800 chr1ptel1M 151138 -AAATTTGTTCTCTGACTCAGCCATTATTT---AACATGTTACTGGTAAA 151183 - v i v i - i ivi i i--- i v --- v v i C L1P3_orf2#LIN 799 TAATTTCGTTATTT-ACCCAGTAGTCATTCAGGAGCAGGT---TGTTCAG 754 chr1ptel1M 151184 TTTCCATTTAGGCTTGTATCTTTTTTTGGTGA--TCCCTGAACC-AATTT 151230 v -- i- vv vi -- i i i v -i v C L1P3_orf2#LIN 753 TTTCCATGTAG--TTGTG-CGGTTTTGAGTGAGTTTCTTAATCCTGAGTT 707 chr1ptel1M 151231 CTATTCTTATTTCATTAAGGAACAAAAGGATA-TAGTCATTATTGCTCCC 151279 v i v v i iv vvii i iv i- v i v v ivii C L1P3_orf2#LIN 706 CTAATTTGATTGCACTGTGGTCTGAGAGACTGTTTGTTATGATTTCCGTT 657 chr1ptel1M 151280 TTTTTACATTTGTCT--GCAATGAATTA-----ACTTA-GTGGTTAATTT 151321 i i - -- v i vv ----- v - i C L1P3_orf2#LIN 656 CTTTTGCATTTG-CTGAGGAGTGTTTTACTTCCAATTATGTGGTCAATTT 608 chr1ptel1M 151322 TTGTAGAAGTTCCATGTGTTGCAAAGAAATATGCATATTC 151361 v v v v v vi vi iv i C L1P3_orf2#LIN 607 TAGAATAAGTGCGATGTGGCGCTGAGAAGAATGTATATTC 568 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.73 CpG sites = 51, Kimura (unadjusted) = 38.92 Transitions / transversions = 1.31 (51/39) Gap_init rate = 0.08 (25 / 315), avg. gap size = 1.48 (37 / 25) 11 24.50 2.22 2.22 chr1ptel1M 152291 152335 (847665) (ATGAAAT)n#Simple_repeat 1 45 (0) m_b5s252i1 185 chr1ptel1M 152291 ATGAAGTA-GCCATAGGGAATGGGAAATATGAAATGTAGCAATATG 152335 i - vv v i iv i - v (ATGAAAT)n#Si 1 ATGAAATATGAAATATGAAATATGAAATATGAAATAT-GAAATATG 45 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.05 (2 / 44), avg. gap size = 1.00 (2 / 2) 224 32.22 7.78 0.00 chr1ptel1M 152523 152612 (847388) MIRc#SINE/MIR 54 150 (118) m_b5s601i0 186 chr1ptel1M 152523 GGATTTAAGAGGTGACTCTGACACTAATAAAGGGGATAACCTTTGGGAAA 152572 i ii vvvi i v v iv ivv vi i v v i MIRc#SINE/MIR 54 GGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAG 103 chr1ptel1M 152573 TCCCTT-----CCCTGTGTTTCAGTTTCCTC--CTGTACATTGAGGA 152612 v ----- i v ii -- v v i MIRc#SINE/MIR 104 TCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGA 150 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.73 CpG sites = 14, Kimura (unadjusted) = 42.62 Transitions / transversions = 0.93 (14/15) Gap_init rate = 0.02 (2 / 89), avg. gap size = 3.50 (7 / 2) 309 26.48 8.89 2.08 chr1ptel1M 152536 152670 (847330) MIR3#SINE/MIR 64 207 (1) m_b5s601i1 186 chr1ptel1M 152536 GACTCTGACACTAATAAAGGGGATAACCTTTGGGAAATCCCTTC-----C 152580 i v iv?ivv vi i v v i v -----i MIR3#SINE/MIR 64 GGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCT 113 chr1ptel1M 152581 CTGTGTTTCAGTTTCCTC--CTGTACATTGAGGAGGGTTGAACTTTTTAA 152628 v ii -- v v - i vvv i MIR3#SINE/MIR 114 CTGGGCCTCAGTTTCCTCATCTGTAAAATGAGG-GGGTTGGACTAGATGA 162 chr1ptel1M 152629 T-TCTGAAGTG---TACAGCTCT-ACATCTTAGGTCTTTTGATGATT 152670 - i i v--- v - ii v vi i -- MIR3#SINE/MIR 163 TCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCT--ATGATT 207 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.32 CpG sites = 17, Kimura (unadjusted) = 33.32 Transitions / transversions = 0.94 (17/18) Gap_init rate = 0.06 (8 / 134), avg. gap size = 1.88 (15 / 8) 356 22.08 5.75 1.10 chr1ptel1M 153927 154013 (845987) MIR3#SINE/MIR 115 205 (3) m_b5s601i2 187 chr1ptel1M 153927 TGAATCTTAGTTTCC-CATCTATAAAATAACAGGGTTGAACTCTGTGGCC 153975 iii i - i i vi i vvi ii MIR3#SINE/MIR 115 TGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATC 164 chr1ptel1M 153976 CTCTA-GATCCCTTCCAG---TGATCATCTATGATTCTATAA 154013 - - i --- ivv i MIR3#SINE/MIR 165 -TCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTATGA 205 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 27.29 CpG sites = 14, Kimura (unadjusted) = 27.29 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.05 (4 / 86), avg. gap size = 1.50 (6 / 4) 334 26.04 12.92 6.31 chr1ptel1M 154369 154577 (845423) C MIR1_Amn#SINE/MIR (5) 225 4 m_b5s601i3 188 chr1ptel1M 154369 AATGACTAGTATTTCTATAGCACCTGCTATATGTCATGCAGTATGATGTC 154418 iv ivi v i i v------- - - v C MIR1_Amn#SINE 225 AATACCTAGCTCTTATGTAGCACTTT-------TCAT-CAGTA-GATCTC 185 chr1ptel1M 154419 ATAGAACTCTAGGATTAGGGGGGCA--ATTGTTATGCCCATTTTGCAAAT 154466 v v i vi -- i v -- ii v i i C MIR1_Amn#SINE 184 AAAGCACTTTACAA--AGGAGGTCAGTATCATTATCCCCATTTTACAGAT 137 chr1ptel1M 154467 AAAGAAACTGAGGCAAATAGGGAT-------CTTGT------TGACT-AG 154502 i i ?v v i i ------- i------ v ?- C MIR1_Amn#SINE 136 GAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGCCCAAGGTCACNCAG 87 chr1ptel1M 154503 CACATTTATGA-AG---TGGGATTAAAACTCGGGTCTTCATGA---CTA- 154544 ?vii?vi i- ---i ? ?i i i i -i --- i - C MIR1_Amn#SINE 86 CNGGCNAGTGGCAGAGCCGGGANTNGAACCCAGGTCTCC-CGAGTCCCAG 38 chr1ptel1M 154545 ---AAAGTTCTATCCATTGTACCACCAACTGCATTC 154577 --- iv i i iv -- v i C MIR1_Amn#SINE 37 TCCAGTGCTCTATCCACTAGACCAC--ACTGCCTCC 4 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.99 CpG sites = 33, Kimura (unadjusted) = 34.67 Transitions / transversions = 1.83 (33/18) Gap_init rate = 0.11 (23 / 208), avg. gap size = 1.78 (41 / 23) 353 24.25 20.53 1.68 chr1ptel1M 154423 154573 (845427) C MIRc#SINE/MIR (85) 183 5 m_b5s601i4 188 chr1ptel1M 154423 AACTCTAGGAT-TAGG-GGGGCA---ATTGTTATGCCCATTTTGCAAATA 154467 i iv v- -i --- i v i i i C MIRc#SINE/MIR 183 AACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATG 134 chr1ptel1M 154468 AAGAAACTGAGGCAAATAGGGAT-------CTTGTT---GACTAGCACAT 154507 i vv v i i ------- ii--- iii - v C MIRc#SINE/MIR 133 AGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCA-CACAG 85 chr1ptel1M 154508 TTATGAAGT---------GGGATTAAAACTCGGGTCTTCATGACTAAAAG 154548 i vv --------- i vi i i v vv C MIRc#SINE/MIR 84 CTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr1ptel1M 154549 T-------TCTATCCATTGTACCACCAACTGC 154573 ------- v i i -- C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTGCACCAC--ACTGC 5 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.12 CpG sites = 22, Kimura (unadjusted) = 30.11 Transitions / transversions = 1.57 (22/14) Gap_init rate = 0.07 (10 / 150), avg. gap size = 3.40 (34 / 10) 223 30.43 2.90 0.00 chr1ptel1M 157176 157244 (842756) MIRc#SINE/MIR 3 73 (195) m_b5s601i5 189 chr1ptel1M 157176 AGGCAGCATGGGAGAATGGAAATATTACTAGATTTGGA-TCCAGAGGACA 157224 ii viv i v vi i i - vi i v MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chr1ptel1M 157225 TGGATTGAAATACC-ACTCTG 157244 i vi i v -i MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTG 73 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.03 CpG sites = 13, Kimura (unadjusted) = 40.53 Transitions / transversions = 1.62 (13/8) Gap_init rate = 0.03 (2 / 68), avg. gap size = 1.00 (2 / 2) 17 0.00 0.00 0.00 chr1ptel1M 158575 158593 (841407) (TA)n#Simple_repeat 1 19 (0) m_b5s252i2 190 chr1ptel1M 158575 TATATATATATATATATAT 158593 (TA)n#Simple_ 1 TATATATATATATATATAT 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 19 4.55 0.00 0.00 chr1ptel1M 158759 158781 (841219) (T)n#Simple_repeat 1 23 (0) m_b5s252i3 191 chr1ptel1M 158759 TTCTTTTTTTTTTTTTTTTTTTT 158781 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTT 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 333 24.28 4.55 9.52 chr1ptel1M 158782 158913 (841087) C MIRc#SINE/MIR (142) 126 1 m_b5s601i6 192 chr1ptel1M 158782 TGAGGCAATCGG---GGTTAAGTGACTTGCTCAGGATCACACAGCTACAA 158828 -- i --- i i i ---- C MIRc#SINE/MIR 126 TGAGGC--TCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCT---- 83 chr1ptel1M 158829 AGTATTAAGTGCCTGATACCAGATTTGAACTCGCGTCCTCCTGAGTTCAG 158878 --- v v vv vi i i i iv i v i i C MIRc#SINE/MIR 82 AG---TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAA 36 chr1ptel1M 158879 G---GATGTCCTATTCACTGAGCCACCTATCTGCCCCG 158913 ---ii ii v i vi v--- i C MIRc#SINE/MIR 35 GTCCAGTGCTCTTTCCACTGCACCACA---CTGCCTCG 1 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.86 CpG sites = 19, Kimura (unadjusted) = 30.10 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.11 (14 / 131), avg. gap size = 1.29 (18 / 14) 18 4.77 0.00 0.00 chr1ptel1M 159790 159811 (840189) (T)n#Simple_repeat 1 22 (0) m_b5s252i4 193 chr1ptel1M 159790 TTCTTTTTTTTTTTTTTTTTTT 159811 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTT 22 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 26 0.00 0.00 0.00 chr1ptel1M 159848 159872 (840128) (T)n#Simple_repeat 1 25 (0) c_b5s251i0 193 chr1ptel1M 159848 TTTTTTTTTTTTTTTTTTTTTTTTT 159872 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 1498 28.89 1.89 2.05 chr1ptel1M 160248 160883 (839117) C L1ME4c_3end#LINE/L1 (191) 639 5 m_b5s551i3 194 chr1ptel1M 160248 TTCTGCTCATTTCACTTAGCATCAGTTCATGGAAGTCTCTCCAAGCCTCT 160297 iv i i vv ii vi i - v iiv C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATAAACATTT-TCCATGTTGCT 591 chr1ptel1M 160298 CTGTATTCATCCTGTTGGCCATTTTTTACAGAACAATAATATTCCATAAC 160347 vii v v v iv vii v ii vvvv viv C L1ME4c_3end#L 590 ACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCGA 541 chr1ptel1M 160348 ATTCATATACCACAATTTACCCAACCATTCTCCAATTGATGGGCATCCAT 160397 i ?v i i ii i v v i ii v C L1ME4c_3end#L 540 GTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAG 491 chr1ptel1M 160398 TCATTTTCCAATTTCTGGCCACTACAAACAGGGCTGCCACAAACATTTTG 160447 vivv i v i i i i iv v ii i v C L1ME4c_3end#L 490 GTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTC 441 chr1ptel1M 160448 GCACATACAGGTCATTTTTCCTTCTTTAG---TATCTCCTTGGGATATAA 160494 ii i -- - v --- i i v v C L1ME4c_3end#L 440 GTGCATATAG--C-TTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAAT 394 chr1ptel1M 160495 GCCCAGTAGTAGCACTGCTGGGTCAAAAGGTATGCACAGTTTGATAACTT 160544 v v i v i i i v v v ii i C L1ME4c_3end#L 393 TCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTC 344 chr1ptel1M 160545 TTTGGGCATAATTCCAGATTGTTCTCCAGAATGGTTGGATTCATTCACAA 160594 vivi i v v i i i i v v iiv i ? C L1ME4c_3end#L 343 TTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACAN 294 chr1ptel1M 160595 CTCCAC---CAATGTATCAGTGTCCCAGTTTTCCCGCATCCCCTCCAACA 160641 iv --- v ? v iv ? i v i C L1ME4c_3end#L 293 TGCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGCA 244 chr1ptel1M 160642 ------ATCATCATTATTTTTTCCTGTCATCTTAGCCAATCTGACAAGTG 160685 ------ i -- v----v i v i i i i i i C L1ME4c_3end#L 243 TTGGGTATTATCA--ATTTTTTA----AATTTTTGCTAATTTAATAGGCG 200 chr1ptel1M 160686 TGTAGTGGTATCTCAGACTTGTCTTAATTTGCATTTCTCTGATTAATAAT 160735 iv i vvv ii i v ii C L1ME4c_3end#L 199 TAAAATGGTATCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACTAGC 150 chr1ptel1M 160736 GATTTGGAACACTCTTTCATATGAGTAGTAATAGTTTCAATTTCATCATC 160785 vv v i i i i vv iv v ivi? vv v v ? C L1ME4c_3end#L 149 GAGGTTGAACATTTTTCCATGTGTTTGTTTACTANTTGTATTTCCTCTTN 100 chr1ptel1M 160786 TGAAAATTGTCTGTTTTTATCCAACTGACCATTTGTCAATTGGAGAGATG 160835 vi iv i -vi v i v i vvv C L1ME4c_3end#L 99 TGTGAATTGTCTGTTCATGTCC-TTTGCCCATTTATCTATTGGGGTCTTG 51 chr1ptel1M 160836 AAAGCGATTTCTTATAAATTAGAGTCAGTTCTCTATATATTTTAAATA 160883 v?vi-- v v i v i i ? v? i C L1ME4c_3end#L 50 ATNTT--TTTCTTATCAATTTGAATGAGCTCTTTATATANTANAGATA 5 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.75 CpG sites = 95, Kimura (unadjusted) = 37.80 Transitions / transversions = 1.12 (95/85) Gap_init rate = 0.03 (16 / 635), avg. gap size = 1.56 (25 / 16) 1026 34.20 2.63 2.53 chr1ptel1M 160735 161760 (838240) C L1PREC2_orf2#LINE/L1 (0) 3294 2268 m_b5s551i4 194 chr1ptel1M 160735 TGATTTGGAACACTCTTTCATATGAGTAGTAATAGTTTCAATTTCATCAT 160784 v v i vi i vv iv iiiv iv vv v v v C L1PREC2_orf2# 3294 TGATGTTGAGCTTTTTTTCATATGCTTGTTGGCCGCATGTATGTCTTCTT 3245 chr1ptel1M 160785 CTGAAAATTGTCTGTTTTTATCCAACTGACCATTTGTCAATTGGAGAGAT 160834 i v iv i v-i v i v i v --- v C L1PREC2_orf2# 3244 TTGAAAAGTGTCTGTTCATGTCCT-TTGCCCACTTTTTAATGGG---GTT 3199 chr1ptel1M 160835 GAAAGCGATTT-CTTATAAATTAGAGTCAGTTCTCTATATATTTTAAATA 160883 vvv ivv - i v vv v ii v vi ii C L1PREC2_orf2# 3198 GTTTGTTTTTTTCTTGTAAATTTGTTTAAGTTCCTTATAGATGCTGGATA 3149 chr1ptel1M 160884 ---GGCCTTTATCAGAACCTTTAACTGTGAAGATATTTTCCCAGTTTATT 160930 --- i i vv v vivi ii ? v i v i i v C L1PREC2_orf2# 3148 TTAGACCTTTGTCAGATGCATAGTTTGCAAANATTTTCTCCCATTCTGTA 3099 chr1ptel1M 160931 TGCTTCCCTTCTAATCTTGTTTGCA-TTAGTTTTGTTTGTACAGAAGCTT 160979 v i vi iv i v - vii - vv i - i i C L1PREC2_orf2# 3098 GGTTGTCTGTTTACTCT-GTTGATAGTTTCTTTTGCT-GTGCAGAAGCTC 3051 chr1ptel1M 160980 TTTAATTTGATGTAATCAAAATTTTCTATTTTGTGATCA----ATAATGG 161025 i i vvi vv v v v - v iv----ii v C L1PREC2_orf2# 3050 TTTAGTTTAATTAGATCCCATTTGTCAATTTT-TGCTTTTGTTGCAATTG 3002 chr1ptel1M 161026 TCTCTAGTTCGTCTTTAGTCACAAATTTCTTCCTCCTCCACAAGTCT-GA 161074 ii i i -- i- ii v ii v i v i vi v i- C L1PREC2_orf2# 3001 CTTTTGG--CGTCTTC-GTCATGAAATCTTTGCCCGTTCCTATGTCCAGA 2955 chr1ptel1M 161075 AAGATAAACTATCCTATGTT--CCTCCAATTTATTTATAATCTCGATCTT 161122 v i --- vv v -- i ivv v i i i ivi C L1PREC2_orf2# 2954 ATGGTA---TTGCCTAGGTTGTCTTCCAGGGTTTTTATAGTTTTGGGTTT 2908 chr1ptel1M 161123 TATATCTAAATCATGGACCCATTTTGATCTTATCTTGGTATACAGTGTTA 161172 i i i v vi i i vi v i v ii v C L1PREC2_orf2# 2907 TACATTTAAGTCTTTAATCCATCTTGAGTTGATTTTTGTATATGGTGTAA 2858 chr1ptel1M 161173 AGTGTGGGTCCATGCCTAAT-TTCTGACATA---CTAATTTCCAGTTATC 161218 i viv vviii - - --- i--- C L1PREC2_orf2# 2857 GGAAGGGGTCCAGTTTCAATCTTCTG-CATATGGCTAG---CCAGTTATC 2812 chr1ptel1M 161219 CCAGCAGT-TTTGTCAAATAATGAATTCTTATCCCAAAAGTTAGGATCTT 161267 vi- i ii iv i i - v vv i v -- i C L1PREC2_orf2# 2811 CCAGCACCATTTATTGAATAGGGAGTCCTT-TCCCCATTGCTTG--TTTT 2765 chr1ptel1M 161268 TG---GGTTTGTCAAACACTAGATTGCTATAGTTGACTATTCTGTCTTGT 161314 --- v i v ii v i i v vviivi vvi v C L1PREC2_orf2# 2764 TGTCAGCTTTGTCGAAGATCAGATGGTTGTAGGTGTGCGGCCTTATTTCT 2715 chr1ptel1M 161315 GAAC---CTAACCTGTTCCACTGATCAACTAATCTATTTCTTAGCCAATA 161361 ii --- vi i i v ivvi i i vvi i C L1PREC2_orf2# 2714 GGGCTCTCTATTCTGTTCCATTGGTCTATGTGTCTGTTTTTGTACCAGTA 2665 chr1ptel1M 161362 CCAAATGGTTTTGGTGACTGCTGCTTTATAATATAGTTTTAGATCAGGTA 161411 viiv v iv ii i i v ii i C L1PREC2_orf2# 2664 CCATGCTGTTTTGGTTACTGTAGCCCTGTAGTATAGTTTGAAGTCGGGTA 2615 chr1ptel1M 161412 CAGCTAGGCCACCTTCATTTGATTTTTTTTTTTCATTAATTCTTTTGAGA 161461 vv iv v v vv - - i vi i vv v v i v vv C L1PREC2_orf2# 2614 GCGTGATGCCTCCAGC-TTTG-TTCTTTTTGCTTAGGATTGCCTTGGCTA 2567 chr1ptel1M 161462 TTCTAGACCTTTTATTATTCCATATGAATTTTGTTGTTATTTTTTCTAGG 161511 vi vi v vi ivvi vi v C L1PREC2_orf2# 2566 TTCGGGCTCTTTTTTGGTTCCATATGAATTTTAAAATAGTTTTTTCTAGT 2517 chr1ptel1M 161512 TCATTAAAATAGTTTC-TTGGGAGTCTGATTGCTATAGCACTAAATAAAT 161560 vv i i- i v - v i v vv i i vvi C L1PREC2_orf2# 2516 TCTGTGAAG-AATGTCATTGGTAGTTTGATAGGAATAGCATTGAATCTGT 2468 chr1ptel1M 161561 AGATTAATTTAGGGAGTATTGTCATCTTTATTATATTCGCTCGGCCTATC 161610 i iv i v v i i v iv vii vv C L1PREC2_orf2# 2467 AAATTGCTTTGGGCAGTATGGCCATTTTAACGATATTGATTCTTCCTATC 2418 chr1ptel1M 161611 TAGGAGCACTTAATATTTTTCCAATTATTTAAGTCTGACTTT-ATTTGTG 161659 i v ivv i v i iv -iv i - v v C L1PREC2_orf2# 2417 CATGAGCATGGAATGTTTTTCCATTTGTTTGTGTC-ATCTCTGATTTCTT 2369 chr1ptel1M 161660 TGGAAAGTTTTTTGTAATTTTGCTCATATA-ATTCCTGACTTTACTTTGG 161708 iiv v i vv ii v - iii v i -- ii C L1PREC2_orf2# 2368 TGAGCAGTGTTTTGTAATTCTCATTGTAGAGATCTTTCACCT--CCCTGG 2321 chr1ptel1M 161709 -TAGATAGATTCCCAAATATTTTATGCTGTCGACAGTTATTTTGAATGGA 161757 - v iv i ii v v iviii iv v i C L1PREC2_orf2# 2320 TTAGCTGTATTCCTAGGTATTTTATTCTTTTTGTGGCAATTGTGAATGGG 2271 chr1ptel1M 161758 ATT 161760 C L1PREC2_orf2# 2270 ATT 2268 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 45.67 CpG sites = 175, Kimura (unadjusted) = 46.61 Transitions / transversions = 1.05 (175/167) Gap_init rate = 0.04 (41 / 1025), avg. gap size = 1.29 (53 / 41) 1040 30.84 3.45 2.99 chr1ptel1M 160862 161760 (838240) C L1M5_orf2#LINE/L1 (124) 3170 2268 m_b5s551i5 194 chr1ptel1M 160862 AGTTCTCTATATATTTTAAATAGG---CCTTTATCAGA-ACCTTTAACTG 160907 i i ii v --- i - iv v ?-i C L1M5_orf2#LIN 3170 AGTTCTTTATATATTCTGGATACGAGTCCTTTGTCAGATATATGTN-TTG 3122 chr1ptel1M 160908 TGAAGATATTTTCCCAGTTTATTTGCTTCCCTTCTAATCTTGTTTGCATT 160957 ii v v i ? i i v- v i v i v vi iv C L1M5_orf2#LIN 3121 CAAATATTTTCTCCCANTCTGTG-GCTTGCCTTTTCATTTTCTTAACGGT 3073 chr1ptel1M 160958 AGTTTTGTTTGTACAGAAGCTTTTTAATTTGATGTAATCAAA-------A 161000 ivi vvv? vi i v v ? i v ------- C L1M5_orf2#LIN 3072 GTCTTTTGANGAGCAGAAGTTTTTAATTTTGATGNAGTCCAATTTATCAA 3023 chr1ptel1M 161001 TTTTCTATTTTGTGATCAATAATGGTCTCTAGTTCGTCTTTAGTCACAAA 161050 i v i i --- ?i v i i ivv v v --- v C L1M5_orf2#LIN 3022 TTTTTTCTTTTATGGT---TNGTGCTTTTTGTGTCCTGTTTA---AGAAA 2979 chr1ptel1M 161051 TTTCTTCCTCCTCCACAAGTCTGAAAGATAAACTATCCTATGTT--CCTC 161098 i i v v?i - i vvi --i v -- i C L1M5_orf2#LIN 2978 TCTTTGCCTANCCCA-AGGTCACGAAGATA--TTCTCCTATGTTTTCTTC 2932 chr1ptel1M 161099 CAATTTATTTATAATCTCGATCTTTATATCTAAATC-ATGGACCCATTTT 161147 i ivvvv i i ii?ii i i ii - - i i ? C L1M5_orf2#LIN 2931 TAGAAGTTTTATAGTTTTANCTTTTACATTTAGGTCTATG-ATCCATCTN 2883 chr1ptel1M 161148 GATCTTATCTTGGTATACAGTGTTAAGTGTGGGTCCATGCCTAATTTCTG 161197 vi v i v i ii v i iv v v?iii v i v C L1M5_orf2#LIN 2882 GAATTAATTTTTGTGTATGGTGTGAGGTAGGGGTCGAGNTTCATTTTTTT 2833 chr1ptel1M 161198 ACATACTAATTTCCAGTTATCCCAGCAGT-TTTGTCAAATAATGAATTCT 161246 v ivi v i i i vi- ii v ivvv i C L1M5_orf2#LIN 2832 CCATATGGATATCCAATTGTTCCAGCACCATTTGTTGAAAAGACTATCCT 2783 chr1ptel1M 161247 TATCCCAA-AAGTTAGGATCTTTGGG---TTTGTCAAACACTAGATTGCT 161292 vi v-i i i---- ? v--- v ii i? v? i C L1M5_orf2#LIN 2782 TTCCCCACTGAATTG----CNTTGGCACCTTTGTCAAAAATCAANTGNCC 2737 chr1ptel1M 161293 ATAGTTGACTAT---TCTGTCTTGTGAAC---CTAACCTGTTCCACTGAT 161336 vv -- i --- i - v i --- vi i C L1M5_orf2#LIN 2736 ATATATG--TGTGGGTCTAT-TTCTGGACTCTCTATTCTGTTCCATTGAT 2690 chr1ptel1M 161337 CAACTAATCTATTTCTTA-GCCAATACCAAATGGTTTTGGTGACTGCTGC 161385 v i vi i- - v iv i i v iv C L1M5_orf2#LIN 2689 CTATTTGTCTATC-CTTACGCCAATACCACACTGTCTTGATTACTGTAGC 2641 chr1ptel1M 161386 TTTATAATATAGTTTT-AGATCAGGTACAGCTAGGCCACCTTCA--TTTG 161432 - i - ? ? vv - i i -- i -- C L1M5_orf2#LIN 2640 TTTATAATA-AGTCTTGANATCNGGTAGTG-TAAGTC--CTCCAACTTTG 2595 chr1ptel1M 161433 ATTTTTTTTTTTCATTAATTCTTTTGAG-ATTCTAGACCTTTTATTATTC 161481 - i i v-i v iv- ? ii i iivv C L1M5_orf2#LIN 2594 -TTCTTCTTTTTCAA-GATTGTTTTGGCTATTCTNGGTCCTTTGCATTTC 2547 chr1ptel1M 161482 CATATGAATTTTGTTGTTATTTTTTCTAGGTCATTAAAATAGTTTCTTGG 161531 i ivvi i vi v v vv vvi v iii vi C L1M5_orf2#LIN 2546 CATATAAATTTTAGAATCAGCTTGTCAATTTCTACAAAAAAACCTGCTGG 2497 chr1ptel1M 161532 GAGTCTGATTGCTATAGCACTAAATAAATAGATTAATTTAGGGAGTATTG 161581 v i vv v i i vv i i v C L1M5_orf2#LIN 2496 GATTTTGATTGGGATTGCATTGAATCTATAGATCAATTTGGGGAGAATTG 2447 chr1ptel1M 161582 TCATCTTTATTATATTCGCTCGGCCTATCTAGGAGCACTTAATATTTTTC 161631 v ? iv viv vv v i v i ivvv i i C L1M5_orf2#LIN 2446 ACATCTTNACAATATTGAGTCTTCCAATCCATGAACATGGTATATCTCTC 2397 chr1ptel1M 161632 CAATTATTTAAGTCTGACTTTATTTGTGTGGAAAGTTTTTTGTAATTTTG 161681 v i vvi v v v viiv i v i v C L1M5_orf2#LIN 2396 CATTTATTTAGGTCTTCTTTAATTTCTCTCAGCAATGTTTTGTAGTTTTC 2347 chr1ptel1M 161682 CTCATATAATTCCTGACTTTACTTTGGTAGATAGATTCCCAAATATTTTA 161731 vvii ? iv i vviv ?i v vv i i ? C L1M5_orf2#LIN 2346 AGTGTANAGGTCTTGCACATNTTTTGTTAGATTTATTCCTAAGTATTTNA 2297 chr1ptel1M 161732 TG-CTGTCGACAGTTATTTTGAATGGAATT 161760 -i v i i- i v i v C L1M5_orf2#LIN 2296 TGTTTTTTGAT-GCTATTGTAAATGGTATT 2268 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.36 CpG sites = 144, Kimura (unadjusted) = 41.77 Transitions / transversions = 1.15 (144/125) Gap_init rate = 0.05 (42 / 898), avg. gap size = 1.38 (58 / 42) 501 31.69 11.94 2.05 chr1ptel1M 161964 162675 (837325) C L1PREC2_orf2#LINE/L1 (482) 2812 2032 m_b5s551i6 195 chr1ptel1M 161964 CCCAGCAGT-TTTGTCAAATAGTGAGTTCTATGCCAAAAGCTAGGGTTTT 162012 vi- i ii v i v v v vv -v v C L1PREC2_orf2# 2812 CCCAGCACCATTTATTGAATAGGGAGTCCTTTCCCCATTGCT-TGTTTTT 2764 chr1ptel1M 162013 G--GGGTTTGTCAAACACTAGATTGCTATAGTTATT--ACCT-ATTTTGT 162057 --i v i v ii v i i v i v--i - --- C L1PREC2_orf2# 2763 GTCAGCTTTGTCGAAGATCAGATGGTTGTAGGTGTGCGGCCTTATTT--- 2717 chr1ptel1M 162058 GCTGTGATC-CTAACCTACTCCACTAAT-----TGACTATTTCT-TACTC 162100 - v v - vi ii i ii ----- v i i - - C L1PREC2_orf2# 2716 -CTGGGCTCTCTATTCTGTTCCATTGGTCTATGTGTCTGTTTTTGTAC-C 2669 chr1ptel1M 162101 AGTATCAAATGGTTTTAATGACCACTACTTTATAATATAGTTTTAGGTCT 162150 i viiv ii v iiivi ii i i v i v C L1PREC2_orf2# 2668 AGTACCATGCTGTTTTGGTTACTGTAGCCCTGTAGTATAGTTTGAAGTCG 2619 chr1ptel1M 162151 GGCACAGCTGGACCACCTTCATTGCATT-TTTTTTTTCATTA--ATTCCC 162197 i -- vv i-i i -- v - i vv -- v C L1PREC2_orf2# 2618 GGTA--GCGTGAT-GCCTCCA--GCTTTGTTCTTTTTGCTTAGGATTGCC 2574 chr1ptel1M 162198 TTAAA-ATTCTTGACCTTTTGTTCTTCCAGTTGTACTCTGTCACTATTTT 162246 iiv- vv vi v vv vv v i i ivv ivi C L1PREC2_orf2# 2573 TTGGCTATTCGGGCTCTTTTTTGGTTCCATATGAATTTTAAAATAGTTTT 2524 chr1ptel1M 162247 TTCTAGATTTCTAAAA----TCATTTCT---TTGGTA----TGGCACTAA 162285 v i v i i---- vv --- i ---- i i i C L1PREC2_orf2# 2523 TTCTAGTTCTGTGAAGAATGTCATTGGTAGTTTGATAGGAATAGCATTGA 2474 chr1ptel1M 162286 ATAGGTAGATTA-----AATAGTATTGTCATTTTTGTTATATT--TGCTT 162328 vv i i-----iii v i viiv -- v C L1PREC2_orf2# 2473 ATCTGTAAATTGCTTTGGGCAGTATGGCCATTTTAACGATATTGATTCTT 2424 chr1ptel1M 162329 GACCTATCTATTAGTATTTGATATTTTTCTAACTGATTAGGTCG-----G 162373 -- i v i vvi i i vi v iv i----- C L1PREC2_orf2# 2423 --CCTATCCATGAGCATGGAATGTTTTTCCATTTGTTTGTGTCATCTCTG 2376 chr1ptel1M 162374 ---TCTTTG-----TGTTTTGTATTTGTCTTCATATAG----------TT 162405 --- ----- v v v ii v ---------- i C L1PREC2_orf2# 2375 ATTTCTTTGAGCAGTGTTTTGTAATTCTCATTGTAGAGATCTTTCACCTC 2326 chr1ptel1M 162406 CCTGACT--TTTCCTTCCCAAAT----TATC--------AACAATTATTT 162441 ii --i viv i ii ---- i--------ii i -- C L1PREC2_orf2# 2325 CCTGGTTAGCTGTATTCCTAGGTATTTTATTCTTTTTGTGGCAATTGT-- 2278 chr1ptel1M 162442 TGAATGGAATCTC-TTGCTG--------CTGGACTT---TGATGGTAATA 162479 - i iv - v -------- v i --- v v ii i C L1PREC2_orf2# 2277 -GAATGGGATTGCGTTCCTGATTTGGCTCTCGGCTTGGCTGTTGTTGGTG 2229 chr1ptel1M 162480 TATAAAAATGTTGATGATTTCTGTGGATTTATTTTGCATCCTGCAACTTT 162529 ii i ii i iv v i v C L1PREC2_orf2# 2228 TATAGGAATGCTAGTGATTTTTGTACATTGATTTTGTATCCTGAAACTTT 2179 chr1ptel1M 162530 GCTAAAGTTGTGAATTGTTTCTAGTAGTTTTTTAGTTGATTCTCTAGGGT 162579 i vv iivi ?v v i vi ii vv v i C L1PREC2_orf2# 2178 GCTGAAGTTGTTTATCAGCTNAAGGAGCTTTTGGGCCGAGACTATGGGGT 2129 chr1ptel1M 162580 TCTCTAAATATATCATCATATCATATGCAAAGAGTGACAATTTGG-TTTC 162628 i i vv i i v v v i i i- i C L1PREC2_orf2# 2128 TTTCTAGATATAGAATCATGTCGTCTGCAAACAGGGATAGTTTGACTTCC 2079 chr1ptel1M 162629 TCATGATCTACTCTAATTCCTTAAATCTCTTTTTCTTCTCTTATTGC 162675 vivvi i ivi v i vv i i vi v C L1PREC2_orf2# 2078 TCTCTTCCTATTTGGATGCCCTTTATTTCTTTCTCTTGCCTGATTGC 2032 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.50 CpG sites = 125, Kimura (unadjusted) = 42.53 Transitions / transversions = 1.30 (125/96) Gap_init rate = 0.06 (42 / 711), avg. gap size = 2.40 (101 / 42) 649 25.89 0.51 0.00 chr1ptel1M 162479 162675 (837325) C L1M1_orf2#LINE/L1 (1065) 2229 2032 m_b5s551i7 195 chr1ptel1M 162479 ATATAAAAATGTTGATGATTTCTGTGGATTTATTTTGCATCCTGCAACTT 162528 i i iv i ivi v i C L1M1_orf2#LIN 2229 ATATAGAAATGCTACTGATTTTTGTATGTTGATTTTGTATCCTGCAACTT 2180 chr1ptel1M 162529 TGCTAAAGTTGTGAATTGTTTCTAGTAGTTTTTTAGTTGATTCTCTAGGG 162578 i i v vv iiv i ? v v i v C L1M1_orf2#LIN 2179 TACTGAATTTGTTTATCAGTTCTAATAGTTTTTTNGTGGAGTCTTTAGGT 2130 chr1ptel1M 162579 TTCTCTAAATATATCATCATATCATATGCAAAGAGTGACAATTTGGTTTC 162628 i i vv v v iv i ii C L1M1_orf2#LIN 2129 TTTTCCAAATATAAGATCATATCATCTGCAAACAAGGATAATTTGACTTC 2080 chr1ptel1M 162629 TCATGATCTACTCT-AATTCCTTAAATCTCTTTTTCTTCTCTTATTGC 162675 ivivv i v i -i v i vv i i v v C L1M1_orf2#LIN 2079 TTCCTTTCCAATTTGGATGCCCTTTATTTCTTTCTCTTGTCTGATTGC 2032 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.39 CpG sites = 27, Kimura (unadjusted) = 32.39 Transitions / transversions = 1.12 (27/24) Gap_init rate = 0.01 (1 / 196), avg. gap size = 1.00 (1 / 1) 975 30.90 2.25 2.60 chr1ptel1M 162758 163335 (836665) L1MC4a_3end#LINE/L1 57 632 (1997) m_b5s551i9 196 chr1ptel1M 162758 CCAATTGATAAATGGTCAAAAGATATGAACAGATAATTTTTGGATTAAGA 162807 i v v v i i iviii -- L1MC4a_3end#L 57 CCGATAGAAAAATGGGCAAAAGACATGAACAGACAATTCACAAA--AAGA 104 chr1ptel1M 162808 AATAGAAACTATTTCTAACCATATGAAAAGATGCTCCAAAGTATTATTAA 162857 ? ? iviiiii v i v vvvi i vv L1MC4a_3end#L 105 NATANAAATGGCCCTTAAACATATGAAAAGATGTTCAACCTCACTCATAA 154 chr1ptel1M 162858 TCAGAAAAATGCAAATTAAGACAACTCTGTGATACCACTATATACCTCTC 162907 v i i v v v i vivi v L1MC4a_3end#L 155 TAAGAGAAATGCAAATTAAAACTACACTGAGATACCATTTCTCACCTATC 204 chr1ptel1M 162908 --ATTGGCTAGGAT--GACAG---GAAAAGATAATGCTGAATATTGGAGG 162950 -- v ii --i v --- v v i v - ---- v i L1MC4a_3end#L 205 AGATTGGCAAAAATTCAAAAGTTTGACAACACACT-CTG----TTGGCGA 249 chr1ptel1M 162951 GGATGTGGGAAAACTGGGACACTGATACATTGTTGGTGGAATTGTGAATG 163000 v i v v v v i i v ii ?v L1MC4a_3end#L 250 GGCTGTGGGGAAACAGGCACTCTCATACATTGCTGGTGGGAATGCAAANT 299 chr1ptel1M 163001 CATCAAACCATTCTGGAGAGCAATTTGGAACTATGTTCAAAGAGTTATCA 163050 vi vv v ? i v v v -i v v i ii - L1MC4a_3end#L 300 GGTACAACCCTTNTGGAGGGGAATTTGGCAATAT-CTAACAAAACTA-CA 347 chr1ptel1M 163051 AACTGTACATACTCTTTGATCCAGCAGCGTTACTACTGGGCTTATATCCC 163100 v - i iv i i iivii v i vv v i i L1MC4a_3end#L 348 TA-TGCATTTACCCTTTGACCCAGCAATCCCACTTCTAGGAATTTACCCT 396 chr1ptel1M 163101 --AGAGAGATCTTAAAGAAG-GGAAAGGGACCTGTATATGCAAGAATATT 163147 -- v v i iv v v -iv iv? --i iii iv L1MC4a_3end#L 397 GAAGATACACCTCCAACATGTACAAAATNAC--ATATGCACAAGGTTATT 444 chr1ptel1M 163148 TGTGGCAGCCCTTTTTGTAGTGGCTAGAAACTGGAAATTGAATGGATGCC 163197 ii v vi v i v v i v i ivivv ii L1MC4a_3end#L 445 CATTGCAGCATTGTTTGTAATTGCAAAATATTGGAAACAACCTAAATGCC 494 chr1ptel1M 163198 CATCAATTGGAGAATGGCTGAATAAGTTGTGGTATACAAATGTTATGGAA 163247 ?? v ? i ii i i ivv iiiv i L1MC4a_3end#L 495 CATNNATAGGAGANTGGTTGAATAAACTATGGTACATCCACACAATGGAG 544 chr1ptel1M 163248 TATTATTGTTCTCTAAGAAATGACCAACAGGATGATTTC---AAAAAGGT 163294 i vvvv v i - -- vv v i ---i vv i L1MC4a_3end#L 545 TACTATGCAGCTGTAAAAAA-GA--ATGAGGAAGATCTCTATGAACTGAT 591 chr1ptel1M 163295 CTGGAGAGACTTACATGAACTGATGCTGAGTGAAATGAGCA 163335 v v i v v vv iv i i vi L1MC4a_3end#L 592 ATGGAGTGATTTCCAGGATATATTGTTAAGTGAAAAAAGCA 632 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.87 CpG sites = 87, Kimura (unadjusted) = 41.17 Transitions / transversions = 1.00 (87/87) Gap_init rate = 0.04 (21 / 577), avg. gap size = 1.33 (28 / 21) 1369 29.53 0.81 1.01 chr1ptel1M 162758 163253 (836747) L1ME3G_3end#LINE/L1 54 548 (376) m_b5s551i8 196 chr1ptel1M 162758 CCAATTGATAAATGGTCAAAAGATATGAACAGATAATTTTTGGATTAAGA 162807 v v v i ii ivii vv i L1ME3G_3end#L 54 CCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGGA 103 chr1ptel1M 162808 AATAGAAACTATTTCTAACCATATGAAAAGATGCTCCAAAGTATTATTAA 162857 v iviiivv v v vvvi i v L1ME3G_3end#L 104 AATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTAA 153 chr1ptel1M 162858 TCAGAAAAATGCAAATTAAGACAACTCTGTGATACCACTATATACCTCTC 162907 ii i vv v i v vi iv L1ME3G_3end#L 154 TCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCATC 203 chr1ptel1M 162908 --ATTGGCTAGGATGACAGGAAAAGATAATGCTGAATATTGGAGGGGATG 162955 -- v ii vvv iii?vv iii? i i v i i L1ME3G_3end#L 204 AGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGTG 253 chr1ptel1M 162956 TGGGAAAACTGGGACACTGATACATTGTTGGTGGAATTGTGAATGCATCA 163005 i v v v v i i i v i vvi vv L1ME3G_3end#L 254 TGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTAC 303 chr1ptel1M 163006 AACCATTCTGGAGAGCAATTTGGAACTATGTTCAAAGAGTTATCAAACTG 163055 i ? i i v v v viv i v --- v L1ME3G_3end#L 304 AGCCNTTTTGGAGGGCAATTTGGCAGTATCTATTAAAATTT---AAAATG 350 chr1ptel1M 163056 TACATACTCTTTGATCCAGCAGCGTTACTACTGGGCTTATATCCCAGAGA 163105 ii i i iivii v ? ?v v i ? L1ME3G_3end#L 351 CGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAGA 400 chr1ptel1M 163106 GAT-CTTAAAGAAG-GGAAAGGGACCTGTATATGCAAGAATATTTGTGGC 163153 i - iiv v v - v v i --? i i i i i ii v L1ME3G_3end#L 401 AATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTCATTGC 448 chr1ptel1M 163154 AGCCCTTTTTGTAGTGGCTAGAAACTGGAAATTGAATGGATGCCCATCAA 163203 vi v i i v i i ivivv ii i L1ME3G_3end#L 449 AGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCAA 498 chr1ptel1M 163204 TTGGAGAATGGCTGAATAAGTTGTGGTATACAAATGTTATGGAATATTAT 163253 v i i i i i ivv ii i L1ME3G_3end#L 499 TAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACTAT 548 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.37 CpG sites = 81, Kimura (unadjusted) = 39.14 Transitions / transversions = 1.27 (81/64) Gap_init rate = 0.02 (8 / 495), avg. gap size = 1.12 (9 / 8) 2324 29.91 5.71 3.94 chr1ptel1M 164090 166209 (833791) C L1M5_orf2#LINE/L1 (1099) 2195 40 m_b5s551i10 194 chr1ptel1M 164090 TTGTGTCCTGCAACTTTGCTAAAGTTGTGAATTGTTTCTAGTAGCATTTT 164139 i ? i i v iiivv iv iv ? C L1M5_orf2#LIN 2195 TTGTATCCNGCGACCTTGCTAAATTCACTTATTAGTTCTAGTAGTTTNTT 2146 chr1ptel1M 164140 AGATGATTCTCTAGGGTTTTCTAAGTATGTCATCATATCATCTGCAAA-- 164187 v vv i ? i v ?iiv i i -- C L1M5_orf2#LIN 2145 TGTAGATTCTTTNGGATTTTCTACGTANACAATCATGTCATCTGCGAATA 2096 chr1ptel1M 164188 ATAATAATTTGACTTATTACCT----ACTTTAATTCCTTTGAT--CTTTT 164231 ?i i i v i v v i ---- ii v v v -- C L1M5_orf2#LIN 2095 ANGACAGTTTTATTTCTTCCTTTCCAATCTTTATGCCTTTTATTTCTTTT 2046 chr1ptel1M 164232 TCTTTGCTTATTGACAA-AGCTAACATTTCTAATA-----TTGAATAGTA 164275 vv - v-i iv ii i i ----- v C L1M5_orf2#LIN 2045 TCTTGCCTTATTG-CACTGGCTAGGACCTCCAGTACAATGTTGAATAGAA 1997 chr1ptel1M 164276 ATGTTAATAGTGGGCAACTTTGTTTCACCCCTGATCTTACTGGGAATGTT 164325 i v i ? i i v i i iiii i vv v i? C L1M5_orf2#LIN 1996 GTGGTGANAGCGGACATCCTTGTCTTGTTCCCGATCTTAGGGGGAAAGCN 1947 chr1ptel1M 164326 TGTAGTTTATTCCCAT--------ATGCTTGCTGATGGTTTTAGTAGGAG 164367 vi ? v iv -------- i ? vv -- v v C L1M5_orf2#LIN 1946 TTCAGTNTTTCACCATTAAGTATGATGTTNGCTGTAGGTTTT--TCGTAG 1899 chr1ptel1M 164368 ATGCTAATGATCAATTTATGGAATAATCCATTTATTCCTATATTCTTTTT 164417 ivv v iv iv vvvi v i vv vi vvv C L1M5_orf2#LIN 1898 ATGCCCTTTATCAGGTTGAGGAAGTTCCCTTCTATTCCTAGTTTGCTGAG 1849 chr1ptel1M 164418 TTTTTTTAAAAAAAACAGGAATGGGTGTTGGATTTTATCAAATGTCTTTT 164467 vv v------ v i i ii C L1M5_orf2#LIN 1848 AGTTTTTAT------CATGAATGGGTGTTGAATTTTGTCAAATGCTTTTT 1805 chr1ptel1M 164468 CTGCATCTAATGAGATAGTCAT--GATTTTTAT---TAGTTTGGTTACTG 164512 v ii -- v --- vi iv --- C L1M5_orf2#LIN 1804 CTGCATCTATTGAGATGATCATATGATTTTTCTCCTTTATTCTGTTA--- 1758 chr1ptel1M 164513 ATATAATCAATTATGCTAATACTTTTCCTAATAGTGAACCAATCCTGCAT 164562 ii v iii i vvv i v iv i i i C L1M5_orf2#LIN 1757 ATATGGTGAATTACATTGATTGATTTTCGAATGTTAAACCAACCTTGCAT 1708 chr1ptel1M 164563 -CCTGGTATAAATCCTATTTGGTCATAGTGAATTACCCTGGGGATGACTT 164611 - v i i i ii v i vvvv ivv C L1M5_orf2#LIN 1707 TCCTGGGATAAACCCCACTTGGTCATGATGTATTATCCTTTTTATATATT 1658 chr1ptel1M 164612 TCTGTAATCTCTTTACTAATATTTTATTTAAAATGTTTGCATCAATATTT 164661 v v v vv i i ? ii v v i i C L1M5_orf2#LIN 1657 GCTGGATTCGATTTGCTAATATTTTGTTNAGGATTTTTGCATCTATGTTC 1608 chr1ptel1M 164662 ATTAGGGAAATTGGTCTATAATTTTCTTTATTTTT----CCCGTATCTGG 164707 v v i vi v ----i iv i ? C L1M5_orf2#LIN 1607 ATGAGGGATATTGGTCTGTAATTTTCTTTTCTTGTAATGTCTTTGTCNGG 1558 chr1ptel1M 164708 TTTGGGTATTATTAGCATCATAACTGTGTCCTAAAAGGAATTTGGTAGGA 164757 v i --- vi ? iviv iv v v i v v vi C L1M5_orf2#LIN 1557 TTTTGGTATCA---GGGTNATGCTGGCCTCATAAAATGAGTTGGGAAGTG 1511 chr1ptel1M 164758 CTCCTGTCTCTACTTTTTTTTTC--AAATAACTTGCATAGTATTGGAATT 164805 i --- vi i v --i v ii ii iv v C L1M5_orf2#LIN 1510 TTCC---CTCTTTTTCTATTTTCTGGAAGAGTTTGTGTAAGATTGGTATT 1464 chr1ptel1M 164806 AATTGTTCTTTAAATGTTTGGTAGAATTCACATGTAAATCCATCTGGCTC 164855 v v i vv i v vi C L1M5_orf2#LIN 1463 ATTTCTTCCTTAAATGTTTGGTAGAATTCACCAGTGAAGCCATCTGGGCC 1414 chr1ptel1M 164856 TGGAGACTTTTTCTTAGAGAGTTGATTAATATCTTATATTTATTTTTTTT 164905 vi i iv i ii v vv vv -- v i v i C L1M5_orf2#LIN 1413 TGGAGTTTTCTTTGTGGGAAGGTTTTTAATTAC--AAATTCAATTTCTTT 1366 chr1ptel1M 164906 AA-----ATGTGACAAATTAAATAAGTCATTTCCTCTTCTGTTAATATGG 164950 ----- iv i v v i i vvvii i v? i i v v C L1M5_orf2#LIN 1365 AATAGATATAGGGCTATTCAGATTTTCTATTTCTTCTTGNGTCAGTTTTG 1316 chr1ptel1M 164951 GCAA--TCTAATTTTGTAGGCATTTCTCCATTTCACTTAGATTATCAAAT 164998 i -- v iv vv v v ii ii ? C L1M5_orf2#LIN 1315 GTAANTTGTGTTTTTCAAGGAATTTGTCCATTTCATCTAAGTTNTCAAAT 1266 chr1ptel1M 164999 TTATCGATATATATTTGGGCAAATTACTC-CTGATTATTGCTAATTTACA 165047 i ii v v vv v v i - v i- -- - C L1M5_orf2#LIN 1265 TTATTGGCATAAAGTTGTTCATAATATTCTCTTATTATC-CT--TTTA-A 1220 chr1ptel1M 165048 CTTCCTT--GATGAAAAGT----TCTCCCTTTTCATTTTTAAGACT---- 165087 iv iv -- vviv ---- i ii i v i ---- C L1M5_orf2#LIN 1219 TGTCTGTAGGATCTGTAGTGATGTCTCCTTTTTCATTCCTGATATTGGTA 1170 chr1ptel1M 165088 ATTTG-ATTTTTTCATTCCTTTTTCTAATCAAATTAACTGAAGGTTTATC 165136 -i i i vi ii ii i ivi ?i ii C L1M5_orf2#LIN 1169 ATTTGTGTCTTCTCTCTTTTTTTCTTGATCAGTCTNGCTAGAGGTTTATC 1120 chr1ptel1M 165137 CATTTTGTTAGTTTTTTTTCATAAAATCAA-----------GTCAATTTT 165175 v i ii-- i v i i i----------- ii C L1M5_orf2#LIN 1119 AATTTTATTGA--TCTTTTCAAAGAACCAGCTTTTGGCTTCGTTGATTTT 1072 chr1ptel1M 165176 ATTTATTAAATCAAGTTTTCTTACTTTCAATTTTTATTAATCTCCCCTTT 165225 v i ------- ? ?i ii v - i i i iv i C L1M5_orf2#LIN 1071 CTCTATT-------GTNTNTTTGTTTTCTA-TTTCATTGATTTCTGCTCT 1030 chr1ptel1M 165226 TCTGTTCAGAATTTCAAATCTGGTATTTAATTGGAGGATTTTAATTTG-- 165273 v v i vv vvvi vv i ?v v i --- -- C L1M5_orf2#LIN 1029 TATCTTTATTATTTCCTTCCTTCTACTTNCTTTGGG---TTTAATTTGCT 983 chr1ptel1M 165274 -TTCTTTTTCTAGCTTTTTTAGTTGCAAGCCCAATTCACTGATCTT--CT 165320 - i v v v ii iv i i --vi C L1M5_orf2#LIN 982 CTTCTTTTTCTAGCTTCTTAAGGTGGAAGCTTAGATCATTGATTTTAAGC 933 chr1ptel1M 165321 CTTTCTCTCTTTTATGCAAGTATGTTTCTAGAGATATAAAATTTCCCCTA 165370 - v i- vi ? iv i i? v v i i C L1M5_orf2#LIN 932 CTTTCT-TCTTTTCTA-ATATANGCATTTAANGCTATAAATTTCCCTCTA 885 chr1ptel1M 165371 ATAACCACTTTGGCTTCATACCACAAATTTTGATATGTTGTCTCATTATT 165420 vv ii i v v v iv i C L1M5_orf2#LIN 884 AGCACTGCTTTAGCTGCATCCCACAAATTTTGATATGTTGTATTTTCATT 835 chr1ptel1M 165421 GTCATTCTCTTGGATGAAATTACCAATTGTGTCTATGATGTGTTGGTTCA 165470 ? vv vi viv v v i viv?i i v v vv v C L1M5_orf2#LIN 834 NTCATTCAGTTCAAAATATTTTCTAATTTCCNTTGTGATTTCTTCTTTGA 785 chr1ptel1M 165471 CCTATTCATTGATTAGGATTAGATTATTTAGATTCCTTAATTTTTGGTCT 165520 i vvi iv i v ivi i - i iv v -vv C L1M5_orf2#LIN 784 CCCATGGGTTATTTAGAAGTGTGTTGTTTA-ATTTCCAAATATTTGG-GG 737 chr1ptel1M 165521 ATTTTCCCCTGGTCTT----TTATTGAATGTAATTTTTATTATATCATGA 165566 ivv?vi ---- v viv v v vi ii i C L1M5_orf2#LIN 736 ATTTTCTAGNTATCTTTTTGTTATTGATTTCTAATTTAATTCCATTGTGG 687 chr1ptel1M 165567 TCTGAAAAAAATATATATATTTACTATTTC-TTCTTTCTGCATTTGATTT 165615 --- i i i i- v v iv -v i i?iv i--- C L1M5_orf2#LIN 686 TC---AGAGAACATAC-TCTGTATGATTTCAATCCTTTNAAATTTA---T 644 chr1ptel1M 165616 TGAG----GTCTTTATGCCCTAATATATAGTCAATTTTTGTACAGGATCC 165661 ---- - v i i? i v i v v v v C L1M5_orf2#LIN 643 TGAGACTTGT-TTTATGGCCCAGNATATGGTCTATCTTGGTAAATGTTCC 595 chr1ptel1M 165662 ATGCACCACCCAGGAAAAAAAGGGTATTTCTGTTTTCATT-----CAATT 165706 ii- ii- i i v v - i?v ii -----? i v C L1M5_orf2#LIN 594 ATGTG-CACTT-GAAAAGAATGTGTA-TTCTGCNGTTGTTGGGTGNAGTG 548 chr1ptel1M 165707 TTCTCCAAAGATCTAGCACACCTAACT---------TTTTCTTT--ACCT 165745 vi vi v vi vii v ii --------- v v i-- i C L1M5_orf2#LIN 547 TTCTATAAATGTCAATTAGGTCAAGTTGGTTGATAGTGTTGTTCAAATCT 498 chr1ptel1M 165746 TCT-TATTTCTTATTTATTTTGTG---GTTTGATTTATCTAGTTCTGAAA 165791 - - i i v v ---ii v i v v v i C L1M5_orf2#LIN 497 TCTATA-TCCTTACTGATTTTTTGTCTACTTGTTCTATCAATTACTGAGA 449 chr1ptel1M 165792 GAGCAAGGTTGAGATCTCCTACT---ATTATAGTTTTCGTGTCTATTTCT 165838 v?iv i i ? --- i i v --- C L1M5_orf2#LIN 448 GAGGNGTGTTAAAATCTCCNACTATAATTGTGGATT---TGTCTATTTCT 402 chr1ptel1M 165839 TCTTGCAGCTTTCTTAACTT---CTCTAGGAATTTGGATGCTAAACCACT 165885 i vi i i v i ii --- ii v v v v vviii - C L1M5_orf2#LIN 401 CCTTTTAGTTCTGTCAGTTTTTGCTTCATGTATTTTGAAGCTCTGTTA-T 353 chr1ptel1M 165886 TTGGTGCACATATGTTTAGTATAGATATTACTTCATTATCTATGGTAGCC 165935 v i i ii v v v vv v v vv v - v C L1M5_orf2#LIN 352 TAGGTGCATACACATTTAGGATTGTTATGTCTTCTTGATGAATTG-ACCC 304 chr1ptel1M 165936 TTT----AGTAAGATAGTTTCTTTCCTTCACTCTT------TTTCCTTCA 165975 ---- v v - i v ii i vv v------ i v v C L1M5_orf2#LIN 303 TTTTATCATTATGA-AATGTCCCTCTTTATCTCTGGTAATATTTCTTGCC 255 chr1ptel1M 165976 CTG-TTTTTGCTTTTGTCTGATCTAGATCAGGATCACTACCCCTGTTTTT 166024 i -vv i i - ---- i iv vi i ? v i i C L1M5_orf2#LIN 254 TTGAAGTCTAC-TTTGTCTGAT----ATTAATATAGCCACNCCAGCTTTC 210 chr1ptel1M 166025 TTTTGTTGTTTTTTTTTTTTATATTTCACTTGAAGCATAATAGATTCCAC 166074 -----------? vi i -------- ii v iiivi C L1M5_orf2#LIN 209 TTTTG-----------NTTAGTGTTT--------GCATGGTATATCTTTT 179 chr1ptel1M 166075 TCCAGCCCTTTTCCTTT--ACTCTTATGTAGCGCTCTGCTTTAAATGTGT 166122 -i v -- ii? v iv vi v ii v i i C L1M5_orf2#LIN 178 TCCA-TCCTTTTACTTTCAACCTNTCTGTGTCTTTATATTTAAAGTGCGT 130 chr1ptel1M 166123 TTCTTGTAAACAACATATA---GGGTTTTGGCTTTTAATTCAGTCT-ACT 166168 i i i --- i vi v i - v C L1M5_orf2#LIN 129 CTCTTGTAGACAGCATATAGTTGGGTCTTGTTTTTTTATCCAGTCTGACA 80 chr1ptel1M 166169 ATCCACATCCATTTTATGCAAGAGTTGACATCATTCACATT 166209 i- vv v v vvi v v v?i i C L1M5_orf2#LIN 79 ATCT-CTGCCTTTTAATTGGAGTGTTTAGNCCATTTACATT 40 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.25 CpG sites = 317, Kimura (unadjusted) = 39.67 Transitions / transversions = 1.09 (317/292) Gap_init rate = 0.06 (123 / 2119), avg. gap size = 1.67 (206 / 123) 351 23.61 6.55 1.70 chr1ptel1M 166104 166271 (833729) C L1MEj_5end#LINE/L1 (2) 2158 1983 m_b5s551i11 194 chr1ptel1M 166104 CGCTCTGCTTTAAATGTGTTTCTTGTAAACAACATATA---GGGTTTTGG 166150 i i i i i --- v C L1MEj_5end#LI 2158 CACTTTGTTTTAAGTGTGTTTCTTGTAAACAGCATATAGCTGGGTTTTGT 2109 chr1ptel1M 166151 CTTTTAATTCAGTCT-ACTATCCACATCCATTTTATGCAAGAGTTGACAT 166199 i ii i - vi ivii i- v vi i v vvi C L1MEj_5end#LI 2108 TTTTTAACCCAATCTGACAGTCTCTGTCT-TTTAATGGGAGAATTCAGTC 2060 chr1ptel1M 166200 CATTCACATTCACAGTTACA---GAATTAGTT-ATTTTATTTCTTACCA- 166244 i vv v i--- vv v - i - - C L1MEj_5end#LI 2059 CATTCACATTTAGTGTAACGACTGATATACTTGATTTTATTCCTT-CCAT 2011 chr1ptel1M 166245 -TTATTTATATTTCTTA-CCATTTTATTT 166271 - i - ?i -ii i C L1MEj_5end#LI 2010 CTTACTT-TATTNTTTATTTATTTTGTTT 1983 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 28.52 CpG sites = 25, Kimura (unadjusted) = 29.42 Transitions / transversions = 1.79 (25/14) Gap_init rate = 0.06 (10 / 167), avg. gap size = 1.40 (14 / 10) 249 28.19 6.00 6.00 chr1ptel1M 166448 166647 (833353) C L1PA14_5end#LINE/L1 (352) 2435 2236 m_b5s551i12 197 chr1ptel1M 166448 TCTTCTTCCCTGTAAGATGATGCTCAGTTTAGCTGGATAGTTGATTCTTG 166497 i v v---- v i i vvvi C L1PA14_5end#L 2435 TCTCCTTCGCTT----ATGAAGCTTAGTTTGGCTGGATATGAAATTCTTG 2390 chr1ptel1M 166498 GCTGCAATCCAAGTTCTTTTCCTTTCATAATATCAGATTCCAGGCCGTTC 166547 i v ----- - v v i- v v vi -ii C L1PA14_5end#L 2389 GTTGGAAT-----TTCTTTT-CTTTAAGAATG-CTGAATATAGGCC-CCC 2348 chr1ptel1M 166548 AATC-CTTTAAG---GTAGAA--GCTGCCG---GATCCTGAGTAATCCTG 166588 - ivi --- ii--v i --- i vvv v v C L1PA14_5end#L 2347 AATCTCTTCTGGCTTGTAGGGTTTCTGCTGAAAGGTCCGCTGTTAGCCTG 2298 chr1ptel1M 166589 ATTGTGGCTCCTCAATATCTGAATTG---CTTCTTTTTAGCTGCTTACAA 166635 v v vii ivi vv vi --- i i i vi C L1PA14_5end#L 2297 ATGGGGTTCCCTTTGTAGGTGACCTGCCCCTTCTCTCTAGCTGCCTTTAA 2248 chr1ptel1M 166636 TATTTTTTCCTT 166647 i i C L1PA14_5end#L 2247 CATTTTTTCTTT 2236 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.72 CpG sites = 26, Kimura (unadjusted) = 35.72 Transitions / transversions = 0.96 (26/27) Gap_init rate = 0.09 (17 / 199), avg. gap size = 1.41 (24 / 17) 237 32.46 13.92 0.56 chr1ptel1M 172020 172177 (827823) MIRc#SINE/MIR 25 203 (65) m_b5s601i7 198 chr1ptel1M 172020 GAACCCTGAGATTTTAATAATGAAGACCTGAATTTTAATCCCACCTC--- 172066 i v iiv vv i v v ii iv i iv --- MIRc#SINE/MIR 25 GAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGC 74 chr1ptel1M 172067 -ATAAACAGGCTA-GTCAATTTA--CAGGATCAC----CGTTTC----CC 172104 - ivv vi i- v vi i-- i - ---- v i ---- MIRc#SINE/MIR 75 CACTTACTAGCTGTGTGACCTTGGGCAAG-TCACTTAACCTCTCTGAGCC 123 chr1ptel1M 172105 TCAATTTGTTATTCCGGAAAATGAGCATGACAAT---TGC---ATCTAT- 172147 i vi vv i v i v i i --- ---ii i- MIRc#SINE/MIR 124 TCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACC 173 chr1ptel1M 172148 TCCTAGGGTTCTCATGAGGATAAAATAAGA 172177 vi v ii v i MIRc#SINE/MIR 174 TCACAGGGTTGTTGTGAGGATCAAATGAGA 203 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.56 CpG sites = 29, Kimura (unadjusted) = 43.84 Transitions / transversions = 1.32 (29/22) Gap_init rate = 0.06 (10 / 157), avg. gap size = 2.30 (23 / 10) 335 31.54 12.75 0.00 chr1ptel1M 172077 172225 (827775) MIR#SINE/MIR 92 259 (3) m_b5s601i8 198 chr1ptel1M 172077 TAGTCAATTTACAGGATCACCGTTTCCCTCAATTTGTTATTCCGGAAAAT 172126 i v v vvi i v iv v v i vi vv i v MIR#SINE/MIR 92 TGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAAT 141 chr1ptel1M 172127 GAGCATGACAATTGCATCTA-TTCCTAGGGTTCTCATGAGGATAAAATAA 172175 i v i i v i i -i v v ii v i MIR#SINE/MIR 142 GGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGGATTAAATGA 191 chr1ptel1M 172176 G-----------AGAGC-------ACAGTGCATGACACACAGTAGATGTT 172207 ----------- i ------- v i i iii i MIR#SINE/MIR 192 GTTAATACATGTAAAGCGCTTAGAACAGTGCCTGGCACATAGTAAGCGCT 241 chr1ptel1M 172208 GCAGAAATGCTAGTCATT 172225 vv v i ii MIR#SINE/MIR 242 CAATAAATGTTAGCTATT 259 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.77 CpG sites = 26, Kimura (unadjusted) = 41.94 Transitions / transversions = 1.24 (26/21) Gap_init rate = 0.02 (3 / 148), avg. gap size = 6.33 (19 / 3) 274 37.18 5.74 0.78 chr1ptel1M 172399 172520 (827480) L2b_3end#LINE/L2 339 466 (0) m_b5s601i9 199 chr1ptel1M 172399 CCCCACCAATCCTTGGCTTTCAGGAGAGCAGGAGATGACACTA----GTT 172444 i iv iv ivi i iv i iivi ?vv i---- L2b_3end#LINE 339 CCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCTTGTT 388 chr1ptel1M 172445 TCTCTTTATGTTCCTGGTACTTAGCCAAGGGCCTGACATGTAGCAGACAC 172494 ivi vi i i i ii ii i vv ? i iii i i i L2b_3end#LINE 389 CACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGC 438 chr1ptel1M 172495 T---TAAATATTTGCTGACTTGAAGAAAT 172520 --- i v- vi L2b_3end#LINE 439 TCAGTAAATATTTGTTGAA-TGAATGAAT 466 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 50.12 CpG sites = 32, Kimura (unadjusted) = 58.24 Transitions / transversions = 2.46 (32/13) Gap_init rate = 0.02 (3 / 121), avg. gap size = 2.67 (8 / 3) 255 23.83 7.78 2.11 chr1ptel1M 172608 172697 (827303) C MIR3#SINE/MIR (3) 205 111 m_b5s601i10 200 chr1ptel1M 172608 TTATAGGGTAATA-AATGATCACAA----AAGAGATCT-AAAGAGCCATA 172651 i ii v - - v i---- i i - i -i v C MIR3#SINE/MIR 205 TCATAGAATCATAGAATG-TCAGAGCTGGAAGGGACCTTAGAGA-TCATC 158 chr1ptel1M 172652 GAGCACAACCCACTTATTTTATAGATG-GGAAACTGAGATTCAGTGA 172697 v iv v i i - iii v C MIR3#SINE/MIR 157 TAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGA 111 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.68 CpG sites = 14, Kimura (unadjusted) = 29.68 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.07 (6 / 89), avg. gap size = 1.50 (9 / 6) 198 22.86 5.41 5.41 chr1ptel1M 173945 174018 (825982) C MIR3#SINE/MIR (12) 196 123 m_b5s601i11 201 chr1ptel1M 173945 CATAAGATCT-AGAGCAGAAAAACACTTTAGA-ATTAAAAAGTCCAGTCC 173992 ii v - v i iiv i - i vvv ii C MIR3#SINE/MIR 196 CATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCC 147 chr1ptel1M 173993 CCCTATTCAATTTACAG--GAGGAAACT 174018 ---- v -- C MIR3#SINE/MIR 146 CC----TCATTTTACAGATGAGGAAACT 123 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 27.67 CpG sites = 9, Kimura (unadjusted) = 27.67 Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.10 (7 / 73), avg. gap size = 1.14 (8 / 7) 14 21.21 0.00 2.56 chr1ptel1M 174669 174708 (825292) (TAAAA)n#Simple_repeat 1 39 (0) m_b5s252i5 202 chr1ptel1M 174669 TATAATAAAATAAATTAAAAAAAAAAAAGAGTAACTTAAA 174708 v v v v - i vv (TAAAA)n#Simp 1 TAAAATAAAATAAAATAAAATAAAATAA-AATAAAATAAA 39 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1) 249 27.16 0.00 0.00 chr1ptel1M 176752 176832 (823168) L1M2_orf2#LINE/L1 1664 1744 (1547) m_b5s551i13 203 chr1ptel1M 176752 AAGAAACCATTCTTTATGATCAAGTGCGAATGGTACTAGGGATGGGAGGA 176801 i i i? ? vii v v vi v i vi L1M2_orf2#LIN 1664 AAAAGATNATNCACCATGATCAAGTGGGATTTATCCCAGGGATGCAAGGA 1713 chr1ptel1M 176802 TAGTTCAACAATGGGAAAACAATGAACATGA 176832 i vvv v v i i L1M2_orf2#LIN 1714 TGGTTCAACATACGCAAATCAATAAACGTGA 1744 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.28 CpG sites = 11, Kimura (unadjusted) = 35.20 Transitions / transversions = 1.00 (11/11) Gap_init rate = 0.00 (0 / 80), avg. gap size = 0.0 (0 / 0) 1334 27.43 2.26 3.97 chr1ptel1M 176942 177427 (822573) L1ME5_3end#LINE/L1 75 552 (389) m_b5s551i14 204 chr1ptel1M 176942 AAAGGATATGAACAGAAAATTCTCAGATGAAGAAA-TTGAAA--CTATTT 176988 iv iv v i -ii -- --v L1ME5_3end#LI 75 AAAGGATATGAACAGGCAATTTACAGAAGAGGAAACCCGAAAGGCTA--A 122 chr1ptel1M 176989 CTCGTCATATGAAAAGATGCTCCAAGTCATTATTAATCAGAGAAATGCAA 177038 vv - i v v v L1ME5_3end#LI 123 CAAG-CATATGAAGAGATGCTCAAACTCATTAGTAATCAGAGAAATGCAA 171 chr1ptel1M 177039 ATTAAGACAATTCTGAGATACCACTACACACCTGTGAGATTGGCTAGAAT 177088 i ivv i vi i v i v i L1ME5_3end#LI 172 ATTAAAACAACAATGAGATATCACTTTACACCTATTAGACTGGCAAAAAT 221 chr1ptel1M 177089 GACAGGAAA---AGATAATGATGAATGTTGGAGGGGATGTGGGAAAACTG 177135 v --- ---i vii i v i i ? iv L1ME5_3end#LI 222 TA---GAAAGCTGGATAATGCCAAGTGTTGGCGAGGATGTGGGGANATAG 268 chr1ptel1M 177136 GGACACTGATGCTTTGTTGATGGAATTGTGAATGGATCCAATCATTCTGA 177185 i v v vi i i i v ii iv i v ii i L1ME5_3end#LI 269 GAACCCTCATGCACTGCTGGTGGGAGTGTAGACTGGTGCAGCCATTCTGG 318 chr1ptel1M 177186 AGAGCAATTTGGAACTA--TACTCAAAAAGTTATCAATCTGTGCATACTC 177233 i v v -- v --- -- i v ii i L1ME5_3end#LI 319 AGAGCAATCTGGCAGTACTTAGTCAAA---TTA--AGTATACGCATACCC 363 chr1ptel1M 177234 TTTGATCCAGAAGTGCTACTACTTACTCGGTTTATATCCCAAAGAGATCT 177283 v i v i v ii - --- v v i ii L1ME5_3end#LI 364 TATGACCCAGCAATTCCGCT-C---CTGGGTATATATCCCAAAGAAATTC 409 chr1ptel1M 177284 T---AAAGGATGGAAAGGGATCCACATGTGCAAAAATGTTTGTGGCAGAC 177330 --- v viviv i--- i i ii ii v - L1ME5_3end#LI 410 TCACACAGGTCCATAAGGGG---ACATGTACGAGGATGTTCATTGCAG-C 455 chr1ptel1M 177331 CTTTTTCATAGTGACTAGAAACTGGAAATTAAATGGATGCTCATCAATTG 177380 v v ii i i vi i ii iiiv vv i ii v v L1ME5_3end#LI 456 GTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGGGTGTCCATCACTGG 505 chr1ptel1M 177381 GAGAATGGCTGAGTAAATTATGGTATATGAATCTAATGGAATATTAT 177427 i v ii v i iv v iviv i i L1ME5_3end#LI 506 GAGAGTGGATAGGTAAAATGTGGTGGATGCACACCATGGAGTACTAT 552 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.71 CpG sites = 76, Kimura (unadjusted) = 35.11 Transitions / transversions = 1.46 (76/52) Gap_init rate = 0.05 (24 / 485), avg. gap size = 1.25 (30 / 24) 21 3.71 0.00 0.00 chr1ptel1M 177909 177936 (822064) (ATA)n#Simple_repeat 1 28 (0) m_b5s252i6 205 chr1ptel1M 177909 ATAATAATAATAACAATAATAATAATAA 177936 i (ATA)n#Simple 1 ATAATAATAATAATAATAATAATAATAA 28 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 327 24.97 0.90 9.80 chr1ptel1M 179108 179218 (820782) MIRc#SINE/MIR 26 127 (141) m_b5s601i12 206 chr1ptel1M 179108 AGCACCAGCCCTGAAGTCAGGAGTAACTAAGGCCAAATCTGGTCTCTGAC 179157 ii v i i iv v ii vi i i iv v v MIRc#SINE/MIR 26 AGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCC 75 chr1ptel1M 179158 ACTTAACACTTCCTATAGCTGTTTGACCCT-GGCAAGTCAATTAAGCTCA 179206 - -------- v i - v v - MIRc#SINE/MIR 76 ACTT-AC--------TAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC- 115 chr1ptel1M 179207 ATTAAGCCTCAG 179218 vi i MIRc#SINE/MIR 116 TCTGAGCCTCAG 127 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.11 CpG sites = 14, Kimura (unadjusted) = 30.54 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.10 (11 / 110), avg. gap size = 1.00 (11 / 11) 24 0.00 0.00 0.00 chr1ptel1M 179222 179247 (820753) (A)n#Simple_repeat 1 26 (0) m_b5s252i7 207 chr1ptel1M 179222 AAAAAAAAAAAAAAAAAAAAAAAAAA 179247 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAA 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 258 29.27 4.95 1.92 chr1ptel1M 179336 179436 (820564) MIRb#SINE/MIR 156 259 (9) m_b5s601i13 208 chr1ptel1M 179336 ATAAAAACTAGCTTGCATTATTTTATTGTGAGGATCACAGAAGATATTG- 179384 v v v i vvi --i i v vi v - MIRb#SINE/MIR 156 ATAATACCTACCTCGCAGGGTT--GTTGTGAGGATTAAATGAGATAATGC 203 chr1ptel1M 179385 --GTAAGGTGCTTAAC-TTGTGTCTGGCACTTAATAGGTCCATAA-AAAT 179430 -- i i i -iv i v i i iv vi - MIRb#SINE/MIR 204 ATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAAAT 253 chr1ptel1M 179431 AATTGC 179436 ii v MIRb#SINE/MIR 254 GGTAGC 259 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.16 CpG sites = 16, Kimura (unadjusted) = 37.92 Transitions / transversions = 1.23 (16/13) Gap_init rate = 0.06 (6 / 100), avg. gap size = 1.17 (7 / 6) 16 17.44 7.02 3.39 chr1ptel1M 181486 181542 (818458) (CTC)n#Simple_repeat 1 59 (0) m_b5s252i8 209 chr1ptel1M 181486 CTCCTCC-CCTCCTTCT-TTCACTTTTTCT-CTTCTCCTCCCTCCT-CTC 181531 - i -i - ii i - i - - (CTC)n#Simple 1 CTCCTCCTCCTCCTCCTCCTC-CTCCTCCTCCTCCTCCT-CCTCCTCCTC 48 chr1ptel1M 181532 CCCATCCTCCT 181542 i v (CTC)n#Simple 49 CTCCTCCTCCT 59 Matrix = Unknown Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.11 (6 / 56), avg. gap size = 1.00 (6 / 6) 1323 30.09 3.84 3.84 chr1ptel1M 182973 184092 (815908) L1M5_orf2#LINE/L1 2140 3259 (35) m_b5s551i15 210 chr1ptel1M 182973 TCTACTAAAAAGCTATTAGAAATAATCCATAATTTTAGCAAAGTTGCAGG 183022 v ? i i v vvi i v i i ? L1M5_orf2#LIN 2140 TCTACAAANAAACTACTAGAACTAATAAGTGAATTTAGCAAGGTCGCNGG 2189 chr1ptel1M 183023 ATCCAAAATAAATATGCATAAATCCTCAGCGTTTTTATACATCACCAACA 183072 v ii v i v vviv ii i i ii v L1M5_orf2#LIN 2190 ATACAAGGTCAATATACAAAAATCAATTGTATTTCTATATACTAGCAACA 2239 chr1ptel1M 183073 AAATCCAACAGCAA---GAGATACAAAGAGAAATTCCATTC-CAAATTAA 183118 --- iv v --- i vi? i iv v i- -- i L1M5_orf2#LIN 2240 AA---CAATTGGAAAATGAAATTTNAAAAACAATACCATTTACAA--TAG 2284 chr1ptel1M 183119 CTGTCGATAG-CATAAAATATTTGAGAATCTATCTACCAAAGGAAAGTCA 183167 -i i v i- ? i ii vv v i? vivv L1M5_orf2#LIN 2285 C-ATCAAAAAACATNAAATACTTAGGAATAAATCTAACAAAANATGTGCA 2333 chr1ptel1M 183168 GCAATTATATGAGCAAAATTACAAAACACTTTCCATAAAAATAAAGTCAG 183217 iv vi ? iivvv i i viiv v i v ivv L1M5_orf2#LIN 2334 AGACCTNTACACTGAAAACTACAAAACATTGCTGAGAGAAATTAAAGAAG 2383 chr1ptel1M 183218 ATTTAAATAAGTGGAAAAATATTAAGTGCTCTTGGATAGGCCGATCAAAT 183267 ii i i i vvvi i v v vv iiv L1M5_orf2#LIN 2384 ACCTAAATAAATGGAGAGATATACCATGTTCATGGATTGGAAGACTCAAT 2433 chr1ptel1M 183268 ATAATAAAGATGACAATACTCCCTAAACTAATCTATTTATTTAGTGCCAT 183317 vi ? v v i i i vv i i v L1M5_orf2#LIN 2434 ATTGTNAAGATGTCAATTCTCCCCAAATTGATCTATAGATTCAATGCAAT 2483 chr1ptel1M 183318 ACCAATCAGACTCCCAAGAAACTATTTTAATGACCTAGAAA-----AAAA 183362 v i v iv iii v i------ ----- iv L1M5_orf2#LIN 2484 CCCAATCAAAATCCCAGCAGGTTTTTTTG------TAGAAATTGACAAGC 2527 chr1ptel1M 183363 TAACAACAAAATTCATATGGAACAACAAAAGGCTGAGAAT-TTCAAGGGA 183411 i ivvi i vvi i i i? -vi iiv L1M5_orf2#LIN 2528 TGATTCTAAAATTTATATGGAAATGCAAAGGACCNAGAATAGCCAAAACA 2577 chr1ptel1M 183412 A-CTAATGAAAAAAAAAATCAAATAAAGGTGGCCTCGCTGTACCTGAACT 183460 - -- i i v -ivv v v ii vv ? v? L1M5_orf2#LIN 2578 ATCT--TGAAAAAGAAGAACAAA-GTTGGAGGACTTACACTACCNGATNT 2624 chr1ptel1M 183461 -AAAACTATATTATAAAGCAGCAGTCACCAAAACCATTTGGTATTGGC-T 183508 - i - vi v i i vi v - L1M5_orf2#LIN 2625 CAAGACT-TATTATAAAGCTACAGTAATCAAGACAGTGTGGTATTGGCGT 2673 chr1ptel1M 183509 AAGAAATAGACTAGTTGATCAGTGGAATAGCTTAG---GTTCACAAGACA 183555 -i v i v i i vv --- i ------i L1M5_orf2#LIN 2674 AAG-GATAGACAAATAGATCAATGGAACAGAATAGAGAGTCCA------G 2716 chr1ptel1M 183556 AAATAG-TCAAC-----TATAGCAATCTAGTGTCTGACAAA---CCCAAA 183596 -i v ----- i ?v ?i ii v i ---v ? L1M5_orf2#LIN 2717 AAATAGACCCACACATATATGGNCANTTGATTTTTGACAAAGGTGCCAAN 2766 chr1ptel1M 183597 GATCCCAACTTC--TGGGATAAGAATTCATTATTTGACAAAAACTGCTGA 183644 ---- - -- iv i vvvi v ii viv i L1M5_orf2#LIN 2767 G----CAA-TTCAGTGGGGAAAGGATAGTCTTTTCAACAAATGGTGCTGG 2811 chr1ptel1M 183645 GATACCTGGAAATTAGTATGGCAGAAATTAGGCATGGACCCACACTTAAC 183694 i i vi v ivi v i v iii?v v vi i v L1M5_orf2#LIN 2812 AACAATTGGATATCCATATGGAAAAAAATGAANCTCGACCCCTACCTCAC 2861 chr1ptel1M 183695 ACCATATACCAAGACAAGATCAAAATGGGTCCAT-GACTTAGGCATAAAG 183743 i v i iv iv ? i i - - i iiii i L1M5_orf2#LIN 2862 ACCATACACAAAAATTAATTCNAGATGGAT-CATAGACCTAAATGTAAAA 2910 chr1ptel1M 183744 AATGAGATTATAAATAAATTGGAGG--AACATAGGATAGTTTACCTCTCA 183791 i? i i i vvvvi i i -- v i-- i iivv L1M5_orf2#LIN 2911 GNTAAAACTATAAAACTTCTAGAAGAAAACATAGGAGAA--TATCTTCGT 2958 chr1ptel1M 183792 GACTTGTGGGGGAGGAAGAAATTTGTGACCAAAGATGAACTAGAGATCAT 183841 i - ?v v i i v ---i v v vvi i i v i L1M5_orf2#LIN 2959 GACCT-TGGGNTAGGCAAAGATTTCT---TAAACAGGACACAAAAAGCAC 3004 chr1ptel1M 183842 TATTGACCACAAAATAGAAAAT-------TTTGATTACATC-AAATTAAA 183883 ? --- i v i ------- v i ? - L1M5_orf2#LIN 3005 NA---ACCATAAAAGAAAAAATTGATAAATTGGACTNCATCAAAATTAAA 3051 chr1ptel1M 183884 AAGTCTTTGTACAAACAAAACTAATGCAAACAAGATTAGAAGGGAAGCAA 183933 v - i iv ?vvv ivi vi iv v i v i v v L1M5_orf2#LIN 3052 AACT-TCTGCTCNTCAAAAGACACCGTTAAGAAAATGAAAAGGCAAGCCA 3100 chr1ptel1M 183934 CAAACTGGGAAAACATCTTCACAGTTAAAGGT-TCTGATAAAGGCCTCAT 183982 i ? i v v ii i-? v vi - i v i L1M5_orf2#LIN 3101 CAGANTGGGAGAAAATATTTGCAA-NACATATATCTGACAAAGGACTCGT 3149 chr1ptel1M 183983 TTCCAAAATACATAGAGAATTGACTCTAATTT-ATAAGAAATCAAGCCAT 184031 v i i i i -v vi ? i- ? -- v v L1M5_orf2#LIN 3150 ATCCAGAATATATAAAGAACT-CCTACAANTCAATAANAAA--AAGACAA 3196 chr1ptel1M 184032 TC--TCCAATTGATAAATGGTCAAAAGTTATGAACAGACAATTTCCAGAT 184079 v --i v? v v viv v iv i v L1M5_orf2#LIN 3197 ACAACCCAATANAAAAATGGGCAAAAGACTTGAACAGACACTTCACAAAA 3246 chr1ptel1M 184080 GATGAAATTGAAA 184092 v v ?v L1M5_orf2#LIN 3247 GAAGATATNCAAA 3259 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.86 CpG sites = 174, Kimura (unadjusted) = 40.51 Transitions / transversions = 1.16 (174/150) Gap_init rate = 0.06 (63 / 1119), avg. gap size = 1.37 (86 / 63) 937 28.92 1.81 1.81 chr1ptel1M 183984 184314 (815686) L1ME5_3end#LINE/L1 7 337 (604) m_b5s551i16 210 chr1ptel1M 183984 TCCAAAATACATAGAGAATTGACTCTAATTTATAAGAAATCAAGCCATT- 184032 i i i i ii i vviv v iv i -- v iv?- L1ME5_3end#LI 7 TCTAGAATATACAAGGAACTCCTGCAAATCAACAAGAAA--AAGACGGNA 54 chr1ptel1M 184033 -CTCCAATTGATAAATGGTCAAAAGTTATGAACAGACAATTTCCAGATGA 184081 - i v v v i v i v v L1ME5_3end#LI 55 ACCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGA 104 chr1ptel1M 184082 TGAAATT-GAAAGTATTTCCACTCATATGAAAGAGTGTTCCAAATAATTG 184130 v ii- -ii vv vv iiii i v v v i L1ME5_3end#LI 105 GGAAACCCGAAAG-GCTAACAAGCATATGAAGAGATGCTCAAACTCATTA 153 chr1ptel1M 184131 TTGATCGGAGAAATGTAAATTAAGACAACTCTGAGATACCACTACACACT 184180 v i i i i vv i vi i L1ME5_3end#LI 154 GTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACC 203 chr1ptel1M 184181 TGTTAGATTGGCTAAGATGACAGGAAAA---AATAATGATGAATGTTGGA 184227 i i v i v --- i---i vii i v L1ME5_3end#LI 204 TATTAGACTGGCAAAAATTA---GAAAGCTGGATAATGCCAAGTGTTGGC 250 chr1ptel1M 184228 GGGGATGTGGGAAAACTGCAATACTGATGCATTATTGGTGGAGTTATTAA 184277 i i ? iv v iv v i ii iiv i vi L1ME5_3end#LI 251 GAGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGA 300 chr1ptel1M 184278 TGAATCCAACCATTCTGGAGAACAATCTGGTACTACT 184314 ivii v i i i v L1ME5_3end#LI 301 CTGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACT 337 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.41 CpG sites = 56, Kimura (unadjusted) = 37.92 Transitions / transversions = 1.47 (56/38) Gap_init rate = 0.03 (10 / 330), avg. gap size = 1.20 (12 / 10) 258 29.92 4.62 5.70 chr1ptel1M 184286 184480 (815520) L1PREC2_3end#LINE/L1 360 552 (355) m_b5s551i17 211 chr1ptel1M 184286 ACCATTCTGGAGAACAATCTGGTACTACTGGGCTTATACCCCAAAGAGAT 184335 vivvv i i--i i iv - ii L1PREC2_3end# 360 ACCATTCGACCCAGCAATCC--CATTACTGGGTATATACCC-AAAGGAAT 406 chr1ptel1M 184336 ATTAAAGAA------GGGAAAGGGACCTGTATGTGCCAAAATGTTTGTGG 184379 - vv ------viv iv v i i i ?---- ii v L1PREC2_3end# 407 AT-AAATCATTCTACCATAAAGACACATGCACGCGN----ATGTTCATTG 451 chr1ptel1M 184380 CAGCCCTTTTTGTAGTGGCTAGAAAC-TGGAAAATGAA--TGGATGCCCA 184426 v v iii i i - i i - -- v -- ii L1PREC2_3end# 452 CAGCACTATTCACAATAGC-AAAGACATGGAA--TCAACCTAAATGCCCA 498 chr1ptel1M 184427 TCAATTGGACAATGGATGGGTAAATTGTGGTATATGAATGTCATGGAATA 184476 v v v v iiiv v i iv iii L1PREC2_3end# 499 TCAATGGCAGACTGGATAAAGAAAATGTGGTACATATACACCATGGAATA 548 chr1ptel1M 184477 TTAT 184480 i L1PREC2_3end# 549 CTAT 552 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.80 CpG sites = 33, Kimura (unadjusted) = 39.66 Transitions / transversions = 1.50 (33/22) Gap_init rate = 0.07 (14 / 194), avg. gap size = 1.43 (20 / 14) 474 32.03 3.77 2.23 chr1ptel1M 184310 184574 (815426) L1ME5_3end#LINE/L1 382 650 (291) m_b5s551i18 211 chr1ptel1M 184310 CTACTGGGCTTATACCCCAAAGAGATATTAAAGAAGG----GAAAGGGAC 184355 v iv i i vi v viv ----v i L1ME5_3end#LI 382 CTCCTGGGTATATATCCCAAAGAAATTCTCACACAGGTCCATAAGGGGAC 431 chr1ptel1M 184356 CTGTATGTGCCAAAATGTTTGTGGCAGCCCTTTTTGTAGTGGCTAGAAAC 184405 v i ---- ii ii v vi v i vi i ii L1ME5_3end#LI 432 ATGTACG----AGGATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGT 477 chr1ptel1M 184406 TGGAAAATGAATGGATGCCCATCAATTGGACAATGGATGGGTAAATTGTG 184455 iivvivv i i v v v i i v L1ME5_3end#LI 478 TGGAGGCAACCTGGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTG 527 chr1ptel1M 184456 GTATATGAATGTCATGGAATATTATTGTTCTGTAAGAAATGACCAGCAGG 184505 iv v iii i i vvvv v v iii vii vi L1ME5_3end#LI 528 GTGGATGCACACCATGGAGTACTATGCAGCAGTTAGAAGCAACGGACTAG 577 chr1ptel1M 184506 ATGAATACAGAGAGGCCTGGCGAGA-CTTACATGAAC-TAATGCTAAGTG 184553 v i v vii v vvi - v -- - i i L1ME5_3end#LI 578 ATGTACACATAGCAACATGGATGGATCTTAAA--AACATAGTGCTGAGTG 625 chr1ptel1M 184554 AAATGAGC-AGAACCAG---GAGAT 184574 vi i- v --- L1ME5_3end#LI 626 AAAAAAGTAAGAAACAGAATGAGAT 650 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.98 CpG sites = 44, Kimura (unadjusted) = 42.66 Transitions / transversions = 1.13 (44/39) Gap_init rate = 0.04 (11 / 264), avg. gap size = 1.45 (16 / 11) 1057 30.29 2.35 1.27 chr1ptel1M 184931 185398 (814602) L1ME4c_3end#LINE/L1 167 639 (191) m_b5s551i19 212 chr1ptel1M 184931 TGTAAATTAAGACAACTCTGAGATACCACTATATACCTCTCAGATTGGCT 184980 i ii vv i v ii v i i i v L1ME4c_3end#L 167 TGCAAATTAAAGCAACAATGAGATACCATTTTACGCCTATTAAATTAGCA 216 chr1ptel1M 184981 AAGGTGATAGGAAGAGATAATGACAAATGTTGG---AGATGTGGGAAAAC 185027 ii vvv ii vv iv v i ---i ? i vi L1ME4c_3end#L 217 AAAATTTAAAAAATTGATAATACCCAATGCTGGCGAGGNTGCGGTGAAAC 266 chr1ptel1M 185028 TGGGACACTGATACATTGTTGGTGGAATTGTGAAGGGATCCAACTATTCT 185077 v ? v i v ? i vv i v iv i L1ME4c_3end#L 267 TGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTT 316 chr1ptel1M 185078 GGAGAACAGTTTGGAACTATCC-TCAATAAGTTATCAAACTGGGCATACC 185126 i i i v v ivi- -i ii v v vv L1ME4c_3end#L 317 GGAAAGCAATTTGGCAATACGTATCAA-GAGCCATAAAAATGTTCATACC 365 chr1ptel1M 185127 CTTTGACCCAGCAGTGTTTCTGCTGGGCATATATTCCAGGGAGAT--CTT 185174 i i viiv v v v i i i i --i i L1ME4c_3end#L 366 CTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTC 415 chr1ptel1M 185175 AAAGGGGGGAAAATGACCCACATGTGCAAAAATGTTTGTGGCAGCTCTTT 185224 i ii -- v i i ii i i ii v vi v L1ME4c_3end#L 416 AAAAGAAGGAAAA--AGCTATATGCACGAAGATGTTCATTGCAGCGTTAT 463 chr1ptel1M 185225 TTATAGTAGCAAGAAGCTGGAAACTAAATGGATGCCCATCAATTAGAAAA 185274 i i i ii v vv ii i v vi ii L1ME4c_3end#L 464 TTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAA 513 chr1ptel1M 185275 TGGCTGAATAAATTATGGTACAT-GATT--ATGGAATATTACTGT-TCTG 185320 i i i -? i -- - i-v ii L1ME4c_3end#L 514 TGGTTAAGTAAATTATGGTACATCNACTCGATGGAATATTA-TGCAGCCA 562 chr1ptel1M 185321 TAAGAAACAACCAACAGGATGATTTCTGAGCAGCCTGGAGAG-ACTTACG 185369 v i ii iv vi v v i vivv i v i i-ii -- L1ME4c_3end#L 563 TTAAAAATGATAATTATGAAGACTATGTAGCAACATGGAAAATGTTTA-- 610 chr1ptel1M 185370 TGAACTAATGCTAAGGGAAATGAGCAGAA 185398 vv i v vi L1ME4c_3end#L 611 TGATATAATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.72 CpG sites = 85, Kimura (unadjusted) = 40.66 Transitions / transversions = 1.55 (85/55) Gap_init rate = 0.03 (13 / 467), avg. gap size = 1.31 (17 / 13) 1068 26.93 2.62 1.82 chr1ptel1M 184931 185312 (814688) L1ME3G_3end#LINE/L1 163 547 (377) m_b5s551i20 212 chr1ptel1M 184931 TGTAAATTAAGACAACTCTGAGATACCACTATATACCTCTCAGATTGGCT 184980 i i vv i v vi iv v L1ME3G_3end#L 163 TGCAAATTAAAACAACAATGAGATACCATTTTTCACCCATCAGATTGGCA 212 chr1ptel1M 184981 AAGGTGATAGGAAGA--GATAATGACAAATGTTGGAGA---TGTGGGAAA 185025 ii -- vii ?-- iv ? i v --- i L1ME3G_3end#L 213 AAAAT--TTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGTGTGGGGAA 260 chr1ptel1M 185026 ACTGGGACACTGATACATTGTTGGTGGAATTGTGAAGGGATCCAACTATT 185075 v v v v i i i v i vv i v i i? L1ME3G_3end#L 261 ACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTACAGCCNTT 310 chr1ptel1M 185076 CTGGAGAACAGTTTGGAACTATCCTCAATAAGTTATCAAACTGGGCATAC 185125 i ii i v v i-- v iv - i v v L1ME3G_3end#L 311 TTGGAGGGCAATTTGGCAGTATCT--ATTAAAAT-TTAAAATGCGCATAC 357 chr1ptel1M 185126 CCTTTGACCCAGCAGTGTTTCTGCTGGGCATATATTCCAGGGAGAT-CTT 185174 i viiv v ? ? v i i ?i i - i L1ME3G_3end#L 358 CCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAGAAATACTC 407 chr1ptel1M 185175 AAAGG-GGGGAAAATGACCCACATGTGCAAAAATGTTTGTGGCAGCTCTT 185223 iv vi- v v v v --?i i ii ii v vi v L1ME3G_3end#L 408 GCACATGTGCACAAGGA--NGCATGTACAAGGATGTTCATTGCAGCATTG 455 chr1ptel1M 185224 TTTATAGTAGCAAGAAGCTGGAAACTAAATGGATGCCCATCAATTAGAAA 185273 i i i i ii v vv ii i vi ii L1ME3G_3end#L 456 TTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCAATAGGGGA 505 chr1ptel1M 185274 ATGGCTGAATAAATTATGGTACATG---ATTATGGAATATTA 185312 i i i v--- i i L1ME3G_3end#L 506 ATGGTTAAATAAATTATGGTATATCCATACTATGGAATACTA 547 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.16 CpG sites = 60, Kimura (unadjusted) = 35.07 Transitions / transversions = 1.46 (60/41) Gap_init rate = 0.03 (12 / 381), avg. gap size = 1.42 (17 / 12) 25 9.18 0.00 0.00 chr1ptel1M 185844 185878 (814122) (A)n#Simple_repeat 1 35 (0) m_b6s252i0 213 chr1ptel1M 185844 AATAAAAAAAAAAAAAAGAAAAAGAAAAAAAAAAA 185878 v i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 35 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 12 21.84 2.70 0.00 chr1ptel1M 186126 186162 (813838) (AATTTG)n#Simple_repeat 1 38 (0) m_b6s252i1 214 chr1ptel1M 186126 AATTTAAATCTGTATTT-AGTTTGATTTTTAATTTTAA 186162 i i v - i v v v (AATTTG)n#Sim 1 AATTTGAATTTGAATTTGAATTTGAATTTGAATTTGAA 38 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 608 29.48 6.86 3.56 chr1ptel1M 186852 187259 (812741) HERVP71A#LTR/ERV1 4825 5245 (2345) m_b6s701i0 215 chr1ptel1M 186852 AATAACATTGGAACAAATTGTACTTAAGTATGGATTAATAGAGCCTACTG 186901 i i i i ii v vi ii i ivv i HERVP71A#LTR/ 4825 AATAATATTAGAACAGATTGTACCTAGATTTGGCCTGGTGGAAAATATTG 4874 chr1ptel1M 186902 ATTCTTATACA---GGAACATATTTTACTTCTAAGGTTTTTTAAGAAATA 186948 -- v --- i -i i i v i v vvii i v HERVP71A#LTR/ 4875 ATTC--AGACAATGGGAGC-CACTTTACCTCAAGGGTGTTAAGGGGAATT 4921 chr1ptel1M 186949 ATGGGGAAGGATTGCAAGTT-GA-GGAACAACTCTATATACCTGGCTATC 186996 -- v i i - - i iv - - i iv v vi HERVP71A#LTR/ 4922 ATGG--AAGGTTTACAAATTAGATGGGATTA-TC-ACACCCCTTGGCATC 4967 chr1ptel1M 186997 TGCCCTCATCAGGGGAAGTGGAAAGAATGAATCGGATTCCTAA---GCGT 187043 iv i v v ii i i ii i ii --- i HERVP71A#LTR/ 4968 CCCCTTCCTCTGGAAAGGTAGAAAGAATGAATCAAACTCTCAAAAAGCAT 5017 chr1ptel1M 187044 --TACAAAA--GATGTTAGAGACTCAATTGCTTTGGATCAAATGCCTCTT 187089 --i v --i v i v v i i i ii HERVP71A#LTR/ 5018 ATCACCAAACTAATCTTAGAAACTAAAATGCCTTGGACCAAATGTCTCCC 5067 chr1ptel1M 187090 ----GC-TTTGTTAAAGAATTACAACTGTTCCCTGAAGTGATCTGGGACT 187134 ---- -i iv -- i vi v ii vv iv ii i HERVP71A#LTR/ 5068 AATAGCACTCCTTA--GGATTAGGACAGCCCCAAGAAAAGACTTGGGATT 5115 chr1ptel1M 187135 TTTCCCATATGAGATTGTTTTAT----TTC---ATTTGGGAGGAAAAGGG 187177 v i v i - i v ---- i --- v---- i v HERVP71A#LTR/ 5116 GTCCCCCTACGAG-TTATTATATGGGCTCCCATATTTGGGC----AGGGC 5160 chr1ptel1M 187178 GAAAGACCCTC----TCTTGAAACAAAGGATAAGTTTTTAAGGAATTATA 187223 v v i i ---- v v v iv i i i HERVP71A#LTR/ 5161 TACAGATCTTCCTACTATGGAAACCAAGGACCAATTCTTAAGAAATTATA 5210 chr1ptel1M 187224 TACTGGCAGTGTCCTCATTCTTTTTCAGCCCTTAGG 187259 vi i -iv ii v v HERVP71A#LTR/ 5211 TACTGGCCATATCCTC-CACCCTGTCATCCCTTAGG 5245 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.52 CpG sites = 73, Kimura (unadjusted) = 38.96 Transitions / transversions = 1.70 (73/43) Gap_init rate = 0.06 (26 / 407), avg. gap size = 1.65 (43 / 26) 430 29.64 1.04 1.57 chr1ptel1M 188140 188331 (811669) L1ME5_3end#LINE/L1 58 248 (693) m_b6s551i2 216 chr1ptel1M 188140 CCAATTGATAATTGGTCAAAGGATATAAACAGACAATTTTCAGATGAAGA 188189 v v v v i i v v i L1ME5_3end#LI 58 CCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAGGA 107 chr1ptel1M 188190 AAATAAAACCATTTCTAGTCATATGAAAAGGTGCTTGAAATAACTGTTGA 188239 vivi vvii vvi iv i i ii v v i iv i L1ME5_3end#LI 108 AACCCGAAAGGCTAACAAGCATATGAAGAGATGCTCAAACTCATTAGTAA 157 chr1ptel1M 188240 TCAGAAAAATTTAAGTGAAGACAATTCTGAGGCATCACTACACACCTCTC 188289 i vi i v i ivv ii vi v i L1ME5_3end#LI 158 TCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCTATT 207 chr1ptel1M 188290 AAATTGTCTAAAATGACAGAAAAT--GATAATGACCATTTGTTG 188331 i i v v --i ii-- - vv L1ME5_3end#LI 208 AGACTGGCAAAAAT--TAGAAAGCTGGATAATG-CCAAGTGTTG 248 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.53 CpG sites = 30, Kimura (unadjusted) = 38.40 Transitions / transversions = 1.15 (30/26) Gap_init rate = 0.02 (4 / 191), avg. gap size = 1.25 (5 / 4) 27 0.00 0.00 0.00 chr1ptel1M 188676 188701 (811299) (T)n#Simple_repeat 1 26 (0) c_b6s251i0 217 chr1ptel1M 188676 TTTTTTTTTTTTTTTTTTTTTTTTTT 188701 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 394 32.32 4.60 4.00 chr1ptel1M 188883 189230 (810770) L1MC5a_3end#LINE/L1 233 582 (2195) m_b6s551i3 218 chr1ptel1M 188883 ACAACAAA---TATTGGTGGGCCTGTGGGAACACTGGGACACTAATGCAT 188929 v --- i i i v i v v v v v i L1MC5a_3end#L 233 ACAACATACTCTGTTGGCGAGGCTGTGGGGAAACAGGCACTCTCATACAT 282 chr1ptel1M 188930 TGTTGGTGGAGTTGTGAAATGATCCATGCATTCTGGAGAGCACTTTCAAA 188979 i iiv ii i v vv vi v i v v viv L1MC5a_3end#L 283 TGCTGGTGGGAATGCAAAATGGTACAACCCCTATGGAGGGGAATTTGGCA 332 chr1ptel1M 188980 CTATGCT--CAAAG--GGGTATGAAACTATATACCCTTTGATCCAGCAGT 189025 v - -- i--ivi ----i v i i L1MC5a_3end#L 333 ATAT-CTAGCAAAATTACATATG----CATTTACCCTTTGACCCAGCAAT 377 chr1ptel1M 189026 ---GTTTCTACTGACCTGTATCCCAAAGAGATAATA--AAGGAGAGAAAG 189070 ---ii vvi i -- i v i v ?-- ii v vi i L1MC5a_3end#L 378 CCCACTTCTAGGAATC--TATCCCGAAGATACACTNGCAAAAATACGAAA 425 chr1ptel1M 189071 AGACTCACATGTGCAGAA----ATTTTTGGCAGCCTTTTTTGTAGTGGGT 189116 ? ---- i i v ---- iv v v v i i vv L1MC5a_3end#L 426 NG----ACGTATGCACAAGGTTATTCATTGCAGCATTATTTGTAATAGCA 471 chr1ptel1M 189117 ATAAACTAGAACCTGAATAGATGCCCATCAGCTGAAGAATGGCTGAATAA 189166 v i i v vivvi i i iiv ii v i L1MC5a_3end#L 472 AAAGACTGGAAACAACCCAAATGTCCATCAATAGGGGACTGGTTGAATAA 521 chr1ptel1M 189167 GTTATGGTATATGAATGTTATAGAATATTATTATTCTGTAAGAAACAATC 189216 ii i vv iiiv i i i vvvv i iv - L1MC5a_3end#L 522 ACTATGGTACATCCACACAATGGAGTACTATGCAGCTGTAAAAAGGAAT- 570 chr1ptel1M 189217 AGCAGGAGGATTTC 189230 --v i i L1MC5a_3end#L 571 --GAGGAAGATCTC 582 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.57 CpG sites = 59, Kimura (unadjusted) = 43.70 Transitions / transversions = 1.20 (59/49) Gap_init rate = 0.06 (20 / 347), avg. gap size = 1.50 (30 / 20) 541 31.11 3.88 2.23 chr1ptel1M 188889 189197 (810803) L1ME4c_3end#LINE/L1 242 555 (275) m_b6s551i4 218 chr1ptel1M 188889 AATATTGGTGGGCCTGTGGGAACACTGGGACACTAATGCATTGTTGGTGG 188938 ii i i v? i vi v v ? v i i L1ME4c_3end#L 242 AATGCTGGCGAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGG 291 chr1ptel1M 188939 AGTTGTGAAATGATCCATGCATTCTGGAGAGCACTTTCAAACTATGCTCA 188988 vi? i v i v vv v i i v viv v i iviv L1ME4c_3end#L 292 CANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATC 341 chr1ptel1M 188989 AAGGGGTATGAAACTAT--ATACCCTTTGATCCAGCAGTGTTTCTACTGA 189036 i vi i v i -- i i i --- i -- L1ME4c_3end#L 342 AAGAGCCATAAAAATGTTCATACCCTTTGACCCAGTAAT---TCCACT-- 386 chr1ptel1M 189037 CCTG------TATCCCAAAGAGATAAT--AAAGGAGAGAAAGAGACTCAC 189078 i ------ i i i -- i ii i - - i L1ME4c_3end#L 387 TCTGGGAATTTATCCTAAGGAAATAATTCAAAAGAAGGAAAAAG-CT-AT 434 chr1ptel1M 189079 ATGTGCAGAAATTTT--TGGCAGCCTTTTTTGTAGTGGGTATAAACTAGA 189126 ii ii i v -- v v v i i i vv v i i L1ME4c_3end#L 435 ATGCACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGA 484 chr1ptel1M 189127 ACCTGAATAGATGCCCATCAGCTGAAGAATGGCTGAATAAGTTATGGTAT 189176 v vivv i i v iiv ii i i i i i L1ME4c_3end#L 485 AACAACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTAC 534 chr1ptel1M 189177 ATGAATGTTATAGAATATTAT 189197 v? iviv i L1ME4c_3end#L 535 ATCNACTCGATGGAATATTAT 555 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.70 CpG sites = 59, Kimura (unadjusted) = 42.71 Transitions / transversions = 1.69 (59/35) Gap_init rate = 0.04 (11 / 308), avg. gap size = 1.73 (19 / 11) 36 0.00 0.00 0.00 chr1ptel1M 190750 190780 (809220) (GT)n#Simple_repeat 1 31 (0) c_b6s251i1 219 chr1ptel1M 190750 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 190780 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 32 3.23 0.00 0.00 chr1ptel1M 190784 190815 (809185) (AG)n#Simple_repeat 1 32 (0) c_b6s251i2 220 chr1ptel1M 190784 AGAGAGAGAGAGAGAGAGAGAAAGAGAGAGAG 190815 i (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 32 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 18 23.72 0.00 0.00 chr1ptel1M 190917 190956 (809044) (A)n#Simple_repeat 1 40 (0) m_b6s252i2 221 chr1ptel1M 190917 AAAAAAAAAAAAAAACAGTGACAGAGAAAAAAAAAAAGAA 190956 v ivi v i i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 40 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 19 14.92 0.00 0.00 chr1ptel1M 192737 192767 (807233) (A)n#Simple_repeat 1 31 (0) m_b6s252i3 222 chr1ptel1M 192737 AAAAAAAAAAAAAAAAAAAAGGAGAAAGAAA 192767 ii i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 31 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 22 7.42 0.00 0.00 chr1ptel1M 193072 193100 (806900) (T)n#Simple_repeat 1 29 (0) m_b6s252i4 223 chr1ptel1M 193072 TTTTTTTTTTTTTTCTTTTTTCTTTTTTT 193100 i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 466 26.45 0.00 0.00 chr1ptel1M 193565 193685 (806315) C L1MD1_3end#LINE/L1 (436) 553 433 m_b6s551i5 224 chr1ptel1M 193565 AGTAATATTCCATAATATTCATATACCACAGTTTATTCAGCCATTCTCCA 193614 i ii vv i i i i v v C L1MD1_3end#LI 553 AGTAGTATTCCATGGTATGGATGTACCACAGTTTGTTTAACCATTCACCC 504 chr1ptel1M 193615 ACTGATGGACATCCATTCAGTTTCCAGTTTCTAGCCACTACAAAAAGGAC 193664 ii v iivviv i i i i i v iii C L1MD1_3end#LI 503 GTTGAAGGACATCTGGGTTGTTTCCAGTTTTTGGCTATTACGAATAAAGC 454 chr1ptel1M 193665 TGCCACAAACATTCGTGCACA 193685 i i i C L1MD1_3end#LI 453 TGCTATAAACATTCGTGTACA 433 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 31.68 CpG sites = 23, Kimura (unadjusted) = 34.33 Transitions / transversions = 2.56 (23/9) Gap_init rate = 0.00 (0 / 120), avg. gap size = 0.0 (0 / 0) 20 18.65 0.00 0.00 chr1ptel1M 193729 193765 (806235) (T)n#Simple_repeat 1 37 (0) m_b6s252i5 225 chr1ptel1M 193729 TTTTAGTTTTTTTTGTTGTTTTGTTTTTTGTTTTTTT 193765 vv v v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 37 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 20 10.82 2.38 2.38 chr1ptel1M 193737 193778 (806222) (TTTTTTG)n#Simple_repeat 1 42 (0) m_b6s252i6 225 chr1ptel1M 193737 TTTTTTGTTGTTTTGTTTTTTGTTTTTT-TAATTTGGGTTTTG 193778 - - vv vv (TTTTTTG)n#Si 1 TTTTTTGTT-TTTTGTTTTTTGTTTTTTGTTTTTTGTTTTTTG 42 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.05 (2 / 41), avg. gap size = 1.00 (2 / 2) 69 4.35 0.00 0.00 chr1ptel1M 195010 195081 (804919) (GA)n#Simple_repeat 1 72 (0) c_b6s251i3 226 chr1ptel1M 195010 GAGAGGGAGAGGGAGAGGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 195059 i i i (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr1ptel1M 195060 GAGAGAGAGAGAGAGAGAGAGA 195081 (GA)n#Simple_ 51 GAGAGAGAGAGAGAGAGAGAGA 72 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 71), avg. gap size = 0.0 (0 / 0) 246 37.75 2.14 9.16 chr1ptel1M 195977 196116 (803884) MIRc#SINE/MIR 18 148 (120) m_b6s601i0 227 chr1ptel1M 195977 GTGAAAAAAGCGAAGAA---AAAGACAAAGAAAACTGAGTTTTATTCTTA 196023 i i ivv i ---ii v iii i v i iv v iii MIRc#SINE/MIR 18 GTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCG 67 chr1ptel1M 196024 GTTCTGCCATTTGATGTCTACGGAATGTTCAGCAAAACATTCAACCTCAT 196073 i i iv iv ii vi iv vi iv i i - MIRc#SINE/MIR 68 GCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC-T 116 chr1ptel1M 196074 CTGAGGTTAAATGACATCTGAGACCTCTCATCTTTAAAAGGAG 196116 -----------i v viii v v i MIRc#SINE/MIR 117 CTGAG-----------CCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 52.42 CpG sites = 32, Kimura (unadjusted) = 56.23 Transitions / transversions = 2.00 (32/16) Gap_init rate = 0.09 (13 / 139), avg. gap size = 1.15 (15 / 13) 355 32.79 3.57 7.41 chr1ptel1M 196001 196168 (803832) MIR3#SINE/MIR 42 203 (5) m_b6s601i1 227 chr1ptel1M 196001 AAGAAAACTGAGTTTTATTCTTAGTTCTGCCATTTGATGTCTACGGAATG 196050 i i v i i v iii i i viv ?v ii vi iv MIR3#SINE/MIR 42 AGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACC 91 chr1ptel1M 196051 TTCAGCAAAACATTCAACCTCATCTGAGGTTAAATGACATCTGAGACCTC 196100 vi iv i iv - i -----------i v viii MIR3#SINE/MIR 92 TTGGGCAAGTCACTTCACCTC-TCTGGG-----------CCTCAGTTTCC 129 chr1ptel1M 196101 TCATCTTTAAAAGGAGTCCAGTGGACAAGGTG----CTAAGTCCCCTTCC 196146 v v vvviv v i ---- vi MIR3#SINE/MIR 130 TCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCC 179 chr1ptel1M 196147 AGCTGTA--ATTTTATGATTTGAT 196168 v i-- i iv MIR3#SINE/MIR 180 AGCTCTGACATTCTATGATTCTAT 203 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.33 CpG sites = 29, Kimura (unadjusted) = 44.64 Transitions / transversions = 1.32 (29/22) Gap_init rate = 0.08 (14 / 167), avg. gap size = 1.29 (18 / 14) 17 32.05 1.30 4.00 chr1ptel1M 196642 196718 (803282) (TA)n#Simple_repeat 1 75 (0) m_b6s252i7 228 chr1ptel1M 196642 TATATATCTCTAAATACACATATGGTA-ATATATGCACACACATATAGAA 196690 v v v i i -i - ii i i i v v (TA)n#Simple_ 1 TATATATATATATATATATATAT-ATATATATATATATATATATATATAT 49 chr1ptel1M 196691 ATGTACATCATATATACATCATGCATAT 196718 i i - i - ii (TA)n#Simple_ 50 ATATATAT-ATATATATAT-ATATATAT 75 Matrix = Unknown Transitions / transversions = 2.60 (13/5) Gap_init rate = 0.05 (4 / 76), avg. gap size = 1.00 (4 / 4) 19 32.91 2.06 2.06 chr1ptel1M 196643 196739 (803261) (ATATAC)n#Simple_repeat 1 97 (0) m_b6s252i8 228 chr1ptel1M 196643 ATATATCTCTAAATACACATAT-GGTA-ATATATGCACACACATATAGAA 196690 iv v v i -vi - i i i i v v (ATATAC)n#Sim 1 ATATACATATACATATACATATACATATACATATACATATACATATACAT 50 chr1ptel1M 196691 ATGTACATCATATATACATCATGCATATGCATGTGAGTATACACATACA 196739 ii i - i - i i i ivi i (ATATAC)n#Sim 51 ATACATAT-ACATATACAT-ATACATATACATATACATATACATATACA 97 Matrix = Unknown Transitions / transversions = 2.43 (17/7) Gap_init rate = 0.04 (4 / 96), avg. gap size = 1.00 (4 / 4) 19 8.13 0.00 0.00 chr1ptel1M 197060 197085 (802915) (C)n#Simple_repeat 1 26 (0) m_b6s252i10 229 chr1ptel1M 197060 CCCCCCCCCCCCCCCTCCCCACCCCC 197085 i v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCC 26 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 12 23.27 0.00 0.00 chr1ptel1M 197060 197094 (802906) (CCACCC)n#Simple_repeat 1 35 (0) m_b6s252i9 230 chr1ptel1M 197060 CCCCCCCCCCCCCCCTCCCCACCCCCAGTCCCTCC 197094 v v vi vi v (CCACCC)n#Sim 1 CCACCCCCACCCCCACCCCCACCCCCACCCCCACC 35 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 234 25.03 0.00 3.57 chr1ptel1M 197308 197365 (802635) MIRc#SINE/MIR 58 113 (155) m_b6s601i2 231 chr1ptel1M 197308 TTGAGTCATCAGCCTCAGACACTAATTAACCACATGATCCTGGGCAAGTC 197357 i -- v v v v v i i iiii i i MIRc#SINE/MIR 58 TCGAGTC--CCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTC 105 chr1ptel1M 197358 ACTTAACC 197365 MIRc#SINE/MIR 106 ACTTAACC 113 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.70 CpG sites = 9, Kimura (unadjusted) = 31.36 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.04 (2 / 57), avg. gap size = 1.00 (2 / 2) 325 22.96 0.00 8.86 chr1ptel1M 200012 200097 (799903) MIRc#SINE/MIR 37 115 (153) m_b6s601i3 232 chr1ptel1M 200012 TGCAGTCAGGAAGATGGGAGTTCAAATCCAGTCTCAAATATTTCACACTT 200061 v ivv i i i v v ------ v - MIRc#SINE/MIR 37 TGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTC------TGC-CACTT 79 chr1ptel1M 200062 GCTATTTTTGTGACCCTGGGCAAGTCATTTAACTCC 200097 i vi v i i ii MIRc#SINE/MIR 80 ACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.80 CpG sites = 10, Kimura (unadjusted) = 27.54 Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.08 (7 / 85), avg. gap size = 1.00 (7 / 7) 233 23.80 1.27 9.59 chr1ptel1M 200029 200107 (799893) MIR#SINE/MIR 50 122 (140) m_b6s601i4 232 chr1ptel1M 200029 GAGTTCAAATCCAGTCTCAAATATTTCACACTTGCTATTTTTGTGACCCT 200078 i i v v ------ v - i vi v i MIR#SINE/MIR 50 GGGTTCGAATCCCGGCTC------TGC-CACTTACTAGCTGTGTGACCTT 92 chr1ptel1M 200079 GGGCAAGTCATTTAACTCCAAT-TGCCCCA 200107 i i ii vv - i MIR#SINE/MIR 93 GGGCAAGTTACTTAACCTCTCTGTGCCTCA 122 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.94 CpG sites = 10, Kimura (unadjusted) = 28.91 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.10 (8 / 78), avg. gap size = 1.00 (8 / 8) 382 27.51 18.98 2.39 chr1ptel1M 200134 200349 (799651) MIRb#SINE/MIR 8 258 (10) m_b6s601i5 233 chr1ptel1M 200134 GCAGTTAGTGGTACAGTGGA-----TACAGCTTTT--AATCATGAGAACC 200176 i-- i -----i i vi -- i vivii MIRb#SINE/MIR 8 GCAGC--GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACC 55 chr1ptel1M 200177 TGAGCTTTAATCCCACCTC--------ATAAACTG----AC--TAGTCAA 200212 i i iv iv -------- iv i ---- -- i v MIRb#SINE/MIR 56 TGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 105 chr1ptel1M 200213 TTTCCAGGACCCCTATTTGCCTAAGTTTCTT-ATACTGTAAAATGAGCAT 200261 v v vvi i v vv v i - - i v MIRb#SINE/MIR 106 GTTACTTAACCTCTCTGAGCCTCAGTTTCCTCAT-CTGTAAAATGGGGAT 154 chr1ptel1M 200262 AACCATCACACTTAATTC-TAGGGTTCTCATGAGGATAAAATG------- 200303 --- v i i vi -i v ii v ------- MIRb#SINE/MIR 155 A---ATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAAT 201 chr1ptel1M 200304 ------AAAG-----AGCAAAGTGTATGATATACAGTAGGTGCTATAGAA 200342 ------ ----- v iv ii i i i i vv v MIRb#SINE/MIR 202 GCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAA 251 chr1ptel1M 200343 ATGGTAG 200349 MIRb#SINE/MIR 252 ATGGTAG 258 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.55 CpG sites = 33, Kimura (unadjusted) = 35.20 Transitions / transversions = 1.32 (33/25) Gap_init rate = 0.07 (16 / 215), avg. gap size = 2.94 (47 / 16) 259 35.19 4.83 2.01 chr1ptel1M 201754 201898 (798102) C MIRc#SINE/MIR (37) 231 83 m_b6s601i6 234 chr1ptel1M 201754 AATTTCTAAAGAGCTT---CATGCACAATAACATTGGATTCCCACGATAA 201800 i vi v --- i iv vv v i i i i C MIRc#SINE/MIR 231 AGTTTACAAAGCGCTTTCACATACATTATCTCATTTGATCCTCACAACAA 182 chr1ptel1M 201801 ATCTGTGACA---ACAAAGAAAGTGCCTTCATTCTTATTTTAAATACAAC 201847 vi vi---i ii v i iiiv i i ii v v ii v C MIRc#SINE/MIR 181 CCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAG 132 chr1ptel1M 201848 TCAGATTATCAGTTCAGAATGGCTGAGTGACTTGACCAA-ATCCCAGCAG 201896 vv iv v --i i iv i i v -i v - C MIRc#SINE/MIR 131 GAAACTGA--GGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACA-CAG 85 chr1ptel1M 201897 CT 201898 C MIRc#SINE/MIR 84 CT 83 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 49.71 CpG sites = 30, Kimura (unadjusted) = 49.71 Transitions / transversions = 1.50 (30/20) Gap_init rate = 0.04 (6 / 144), avg. gap size = 1.67 (10 / 6) 1477 31.16 3.05 3.05 chr1ptel1M 203511 204854 (795146) L1M5_orf2#LINE/L1 1951 3294 (0) m_b6s551i6 235 chr1ptel1M 203511 TTCCCAATAAGATCAGGAGTGAAACAAGGTTGACCACTATCACCGTTACT 203560 vv i iii i v v i ? ii v L1M5_orf2#LIN 1951 TTCCCCCTAAGATCGGGAACAAGACAAGGATGTCCGCTNTCACCACTTCT 2000 chr1ptel1M 203561 ATTTAATATTGTATTAGAAATGCTAGCTTTGGCAATAAGAGCTGAGAAAG 203610 i i i i ii v ivvv ivvv i L1M5_orf2#LIN 2001 ATTCAACATTGTACTGGAGGTCCTAGCCAGTGCAATAAGGCAAGAAAAAG 2050 chr1ptel1M 203611 AGATTAAAGGAATAAGAATAGCCAAGAAGGAAACCAAATTATCACTCTTT 203660 i v v ii v vv i i iv i i ?i v i L1M5_orf2#LIN 2051 AAATAAAAGGCATAAAGATTGGAAAGGAAGAAATAAAACTGTCNTTATTC 2100 chr1ptel1M 203661 GCTGATGATATGATGGTATACTTAGAGAACCCCAGAGATTCTACTAAAAA 203710 v i v ? v i i ? i v v ? L1M5_orf2#LIN 2101 GCAGATGACATGATTGTNTACGTAGAAAATCCNAAAGAATCTACAAANAA 2150 chr1ptel1M 203711 GTTATTAGAAATAATCCACAACTTTAGCAAAGTTGCTGGTTATAAAATAA 203760 ii i v vviii v i i ? v i ii v L1M5_orf2#LIN 2151 ACTACTAGAACTAATAAGTGAATTTAGCAAGGTCGCNGGATACAAGGTCA 2200 chr1ptel1M 203761 ACCCACATAAGTCATCAACATTCTTATATATCACTAACAA--AATCCAAC 203808 ivi v i vivii ii ii vi -- ivi v L1M5_orf2#LIN 2201 ATATACAAAAATCAATTGTATTTCTATATACTAGCAACAAACAATTGGAA 2250 chr1ptel1M 203809 AGTCAGCATTACAAAGAGAAATTTCATTTAAAGTAACTACTGATAGTATA 203858 i v i- v? - iv vi v i i vv vi v ii ? L1M5_orf2#LIN 2251 AATGAA-ATTTNAAA-AACAATACCATTTACAATAGCATCAAAAAACATN 2298 chr1ptel1M 203859 AAATATTTAGGAATCTATCTGCCAAGGGGAAAT---CAGAAACTTTA--- 203902 i vv iv ---i ? --- ii v ? --- L1M5_orf2#LIN 2299 AAATACTTAGGAATAAATCTAACAA---AANATGTGCAAGACCTNTACAC 2345 chr1ptel1M 203903 TGAGCCAAACTACAAAACACTTTCCACACAAATTAAGTCTGATATAACCA 203952 --- i viiv v v ivvv iv vi L1M5_orf2#LIN 2346 TGA---AAACTACAAAACATTGCTGAGAGAAATTAAAGAAGACCTAAATA 2392 chr1ptel1M 203953 ACTGGGAAAATATTAAATGCTCTTCGATTGGGTGAGCAAATATAATAAAG 204002 v ii i vvv i v v iv viv vi ? L1M5_orf2#LIN 2393 AATGGAGAGATATACCATGTTCATGGATTGGAAGACTCAATATTGTNAAG 2442 chr1ptel1M 204003 ATGACAATACTACCTAATCTAATCTATTTATTTAGCGCTATACCAATCAG 204052 v v v i vi i vv i ii v v i L1M5_orf2#LIN 2443 ATGTCAATTCTCCCCAAATTGATCTATAGATTCAATGCAATCCCAATCAA 2492 chr1ptel1M 204053 ACTTCCCAAAAACTATTTTGATGACCTAGAAAAAATAACAACAAAGTTCA 204102 v i viv iii v vv vv v v iv i ivvi i i L1M5_orf2#LIN 2493 AATCCCAGCAGGTTTTTTTGTAGAAATTGACAAGCTGATTCTAAAATTTA 2542 chr1ptel1M 204103 TATAGAAAAACAAAAGGTCAAGAAT-TTCAAGGGAATTAATGAAAAAACT 204151 i vi i ii ? -vi iiv i-v --- L1M5_orf2#LIN 2543 TATGGAAATGCAAAGGACCNAGAATAGCCAAAACAATC-TTGAAAAA--- 2588 chr1ptel1M 204152 AGTTGATCAATGGAATAGGTTAGG--TT-CTGTACCAGATCT-AAAATTA 204197 ---- vv iii i v -- -- - vv ? ? - i i - L1M5_orf2#LIN 2589 ----GAAGAACAAAGTTGG--AGGACTTACACTACCNGATNTCAAGACT- 2631 chr1ptel1M 204198 TATTATAAAGCAGCGGTTACTAAAACCATCTGGTATTGGC-TAAGAAATA 204246 vi i v ii i vi v - -i L1M5_orf2#LIN 2632 TATTATAAAGCTACAGTAATCAAGACAGTGTGGTATTGGCGTAAG-GATA 2680 chr1ptel1M 204247 GACTAGTTGATCAATGGAATAGGTTAG---GTTCAAAGGACAAAACAGC- 204292 v i v i iv --- i i -i i i v vi - L1M5_orf2#LIN 2681 GACAAATAGATCAATGGAACAGAATAGAGAGTCCAGA-AATAGACCCACA 2729 chr1ptel1M 204293 CAACTTTAATTACCTAGTGTTTGACAAA---CCCAAAGACCCCAGTTT-T 204338 vv v ii?i ?i ii v ---v ? ---- i i-v L1M5_orf2#LIN 2730 CATATATGGNCANTTGATTTTTGACAAAGGTGCCAANG----CAATTCAG 2775 chr1ptel1M 204339 TGGGATAAGAATGCACCATTTGACAAAAATTGCTGGGAAAATTGGAAATT 204388 iv i ivv iv ii viv i v v i L1M5_orf2#LIN 2776 TGGGGAAAGGATAGTCTTTTCAACAAATGGTGCTGGAACAATTGGATATC 2825 chr1ptel1M 204389 AGCATGGCAGAAATTAGGCATAGACCCACACTTAACACCGTACACCAAGA 204438 vii v i v iii?v v vi i v i v i L1M5_orf2#LIN 2826 CATATGGAAAAAAATGAANCTCGACCCCTACCTCACACCATACACAAAAA 2875 chr1ptel1M 204439 TAAGGTCAAAATGGGTTCAT-GACCTAGGCATAAAGAATGAGATTATAAA 204487 v iv ? i i- - iiii ii? i i i L1M5_orf2#LIN 2876 TTAATTCNAGATGGA-TCATAGACCTAAATGTAAAAGNTAAAACTATAAA 2924 chr1ptel1M 204488 TAAATTGGAAG--AGCATAGGATAGTTTACCTCTCAGACCTGTGGAAGAG 204535 vvvvi i -- i v i-- i iivv - i?v L1M5_orf2#LIN 2925 ACTTCTAGAAGAAAACATAGGAGAA--TATCTTCGTGACCT-TGGGNTAG 2971 chr1ptel1M 204536 GAAGGAATTTATGATCAA-AGAAC-TAGAGATCACTATTGACTACAAAAT 204583 v iii v -- v - i -i i i v ? --- i i v L1M5_orf2#LIN 2972 GCAAAGATTTCT--TAAACAGGACACAAAAAGCACNA---ACCATAAAAG 3016 chr1ptel1M 204584 AGAAAAT-------TTTGATTATATCAAATTGAAAAGTTTTTGTACAAAC 204626 i ------- v i ?i v v ii i iv -?v L1M5_orf2#LIN 3017 AAAAAATTGATAAATTGGACTNCATCAAAATTAAAAACTTCTGCTC-NTC 3065 chr1ptel1M 204627 AAAACTAATGCAGGCAAG---ATTAGAAGGGAAACAATAAACTGGGAAAA 204673 --i ii v vi --- v i v i v i i ? i L1M5_orf2#LIN 3066 AAAA--GACACCGTTAAGAAAATGAAAAGGCAAGCCACAGANTGGGAGAA 3113 chr1ptel1M 204674 CATTTTTATAGTCAAAGGT-TCTGATAAAGGACTCATTTCCAAAATATAT 204722 v v ii i-? v vi - i i v i L1M5_orf2#LIN 3114 AATATTTGCAA-NACATATATCTGACAAAGGACTCGTATCCAGAATATAT 3162 chr1ptel1M 204723 AGAGAATTGACTCTAATTT-ATAAGAAATCAAGCCATTC--TCCAATTGA 204769 i i -v vi ? i- ? -- v vv --i v? L1M5_orf2#LIN 3163 AAAGAACT-CCTACAANTCAATAANAAA--AAGACAAACAACCCAATANA 3209 chr1ptel1M 204770 TAAATGGTCAAAGGATATAAACAGATAACTCTCAGACAAAGAAATTGAAA 204819 v v i iv i i vi v i vi v ?v L1M5_orf2#LIN 3210 AAAATGGGCAAAAGACTTGAACAGACACTTCACAAAAGAAGATATNCAAA 3259 chr1ptel1M 204820 CTACTTCTAGGCATATGAAAAGATGCTCCAAGTCA 204854 ivi ivv i i v v? L1M5_orf2#LIN 3260 TGGCCAATAAGCACATGAAAAGATGCTCAACNTCA 3294 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.85 CpG sites = 227, Kimura (unadjusted) = 42.68 Transitions / transversions = 1.27 (227/179) Gap_init rate = 0.05 (62 / 1343), avg. gap size = 1.32 (82 / 62) 1447 29.46 2.49 2.33 chr1ptel1M 204711 205353 (794647) L1ME5_3end#LINE/L1 7 650 (291) m_b6s551i8 235 chr1ptel1M 204711 TCCAAAATATATAGAGAATTGACTCTAATTTATAAGAAATCAAGCCATT- 204759 i i i ii i vviv v iv i -- v iv?- L1ME5_3end#LI 7 TCTAGAATATACAAGGAACTCCTGCAAATCAACAAGAAA--AAGACGGNA 54 chr1ptel1M 204760 -CTCCAATTGATAAATGGTCAAAGGATATAAACAGATAACTCTCAGACAA 204808 - i v v v i ii i iv vi L1ME5_3end#LI 55 ACCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGA 104 chr1ptel1M 204809 AGAAATTGAAACTACTTCTAGGCATATGAAAAGATGCTCCAAGTCATTAT 204858 i iivi vvi vvi i i v v v L1ME5_3end#LI 105 GGAAACCCGAAAGGCTAACAAGCATATGAAGAGATGCTCAAACTCATTAG 154 chr1ptel1M 204859 TAATCAGAGAAATACAAATTAAGACAACTCTGAGATACCACTACCCACCT 204908 i i vv i viv L1ME5_3end#LI 155 TAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCT 204 chr1ptel1M 204909 GTCAGATTGGCTAGAATGACAGGGAAAGATAACGTGGAATGTTGGAGGGG 204958 i i i v i v v ii vvi i ivi i v i L1ME5_3end#LI 205 ATTAGACTGGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTGGCGAGG 254 chr1ptel1M 204959 ATGTGGGAAAACAGGGACACCGATACATTGTTGGTGGAATTGTGAACACA 205008 i ? i i v iv i i i i v ii vvi L1ME5_3end#LI 255 ATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACTGG 304 chr1ptel1M 205009 TCCAGCCATTCTGGAGAGCAATTTGGAACTATGT--TCAAA--AAGTTAT 205054 v i v v iv -- -- - L1ME5_3end#LI 305 TGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTAAG-TAT 353 chr1ptel1M 205055 CAAACTGTGCATACCCTTTGATCCAGCAGTGTTTCTACTGGGCTTATACC 205104 --- --- v i i viiv v iv i L1ME5_3end#LI 354 ---AC---GCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATATC 397 chr1ptel1M 205105 CCAAAGAGATACTAAAGAAGG----GAAAGGGACCTGTATGTGCCAAAAT 205150 i v v viv ----v i v i ---- ii L1ME5_3end#LI 398 CCAAAGAAATTCTCACACAGGTCCATAAGGGGACATGTACG----AGGAT 443 chr1ptel1M 205151 GTTTGTGGCAGCCCTGTTTGTAGTGGCTAGAAGCTGGAAAATGAATGGAT 205200 ii v vi i vi i i iivvivv i L1ME5_3end#LI 444 GTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGGGT 493 chr1ptel1M 205201 GCCAATCAATTGGAGAATGGTTGAGTAAATTGTGGCATATGAATGTTATG 205250 i v v v i v ii v iiv v iiii L1ME5_3end#LI 494 GTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACACCATG 543 chr1ptel1M 205251 GAATATTATTGTTCTGTAAGAAACAACCAGCACGATGAATACGGAG-AGG 205299 i i vvvv v v i vii vv v i iv - iv L1ME5_3end#LI 544 GAGTACTATGCAGCAGTTAGAAGCAACGGACTAGATGTACACATAGCAAC 593 chr1ptel1M 205300 ATTGGCGAGCCTTACATGAAC-TGATGCTGAGTGAAATGAGC-AGAACCA 205347 v ii iii v -- - ii vi i- v L1ME5_3end#LI 594 ATGGATGGATCTTAAA--AACATAGTGCTGAGTGAAAAAAGTAAGAAACA 641 chr1ptel1M 205348 G---GAGAT 205353 --- L1ME5_3end#LI 642 GAATGAGAT 650 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.39 CpG sites = 104, Kimura (unadjusted) = 38.45 Transitions / transversions = 1.28 (104/81) Gap_init rate = 0.04 (24 / 642), avg. gap size = 1.29 (31 / 24) 1524 27.42 0.36 1.66 chr1ptel1M 204711 205259 (794741) L1ME3G_3end#LINE/L1 7 548 (376) m_b6s551i7 235 chr1ptel1M 204711 TCCAAAATATATAGAGAATTGACTCTAATTTATAAGAAATCAAGCCATTC 204760 i i i vviv v iv -- v --v L1ME3G_3end#L 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAA--AAGACA--A 52 chr1ptel1M 204761 TCCAATTGATAAATGGTCAAAGGATATAAACAGATAACTCTCAGACAAAG 204810 i v v v i ii i v vi i L1ME3G_3end#L 53 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chr1ptel1M 204811 AAATTGAAACTACTTCTAGGCATATGAAAAGATGCTCCAAGTCATTATTA 204860 vv ivi ivv ii v vv i v L1ME3G_3end#L 103 AAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTA 152 chr1ptel1M 204861 ATCAGAGAAATACAAATTAAGACAACTCTGAGATACCACTACCCACCTGT 204910 i i i vv i vii ii L1ME3G_3end#L 153 ATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCAT 202 chr1ptel1M 204911 CAGATTGGCTAGAATGACAGGGAAAGATAACGTGGAATGTTGGAGGGGAT 204960 v i vvv ii ?vv ii v? i v i i L1ME3G_3end#L 203 CAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGT 252 chr1ptel1M 204961 GTGGGAAAACAGGGACACCGATACATTGTTGGTGGAATTGTGAACACATC 205010 i i v v iv i i i v i ivvi v L1ME3G_3end#L 253 GTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTA 302 chr1ptel1M 205011 CAGCCATTCTGGAGAGCAATTTGGAACTATGTTCAAAAAGTTATCAAACT 205060 ? i i v v v viv v --- v L1ME3G_3end#L 303 CAGCCNTTTTGGAGGGCAATTTGGCAGTATCTATTAAAATTT---AAAAT 349 chr1ptel1M 205061 GTGCATACCCTTTGATCCAGCAGTGTTTCTACTGGGCTTATACCCCAAAG 205110 i i i viiv v ? ?v v i i ? L1ME3G_3end#L 350 GCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAG 399 chr1ptel1M 205111 AGATACT-AAAGAAG-GGAAAGGGACCTGTATGTGCCAAAATGTTTGTGG 205158 i -iv v v - v v i --? i i v ii ii v L1ME3G_3end#L 400 AAATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTCATTG 447 chr1ptel1M 205159 CAGCCCTGTTTGTAGTGGCTAGAAGCTGGAAAATGAATGGATGCCAATCA 205208 vi i i v i ii vvivv ii i v L1ME3G_3end#L 448 CAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCA 497 chr1ptel1M 205209 ATTGGAGAATGGTTGAGTAAATTGTGGCATATGAATGTTATGGAATATTA 205258 v i i i i i vv ii i L1ME3G_3end#L 498 ATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACTA 547 chr1ptel1M 205259 T 205259 L1ME3G_3end#L 548 T 548 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.40 CpG sites = 80, Kimura (unadjusted) = 35.28 Transitions / transversions = 1.18 (80/68) Gap_init rate = 0.02 (11 / 548), avg. gap size = 1.00 (11 / 11) 13 4.76 0.00 4.35 chr1ptel1M 205660 205683 (794317) (GGGA)n#Simple_repeat 1 23 (0) m_b6s252i11 236 chr1ptel1M 205660 GGGAGGGGGTGGAGGGAGGGAGGG 205683 i - (GGGA)n#Simpl 1 GGGAGGGAG-GGAGGGAGGGAGGG 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 383 20.41 0.00 8.86 chr1ptel1M 206262 206347 (793653) MIRc#SINE/MIR 37 115 (153) m_b6s601i7 237 chr1ptel1M 206262 TGCAGTCAGGAGGACTTGAGTTCAAATGTGGTCTCTGAAACTTAATACGT 206311 v i i i i i viv v vv ------ MIRc#SINE/MIR 37 TGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTA------ 80 chr1ptel1M 206312 CCTGGCTATGTGACCCTGGGCAAGTCACTTAACCCC 206347 - i i i i MIRc#SINE/MIR 81 -CTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 22.41 CpG sites = 10, Kimura (unadjusted) = 24.08 Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.08 (7 / 85), avg. gap size = 1.00 (7 / 7) 365 29.59 13.49 2.52 chr1ptel1M 206385 206599 (793401) MIRc#SINE/MIR 5 242 (26) m_b6s601i8 238 chr1ptel1M 206385 GCAGTTAGCTGTACAGTGGATAGAGC-------TTTTAATCGTGAAGACC 206427 -- iv i v ------- vv i iv MIRc#SINE/MIR 5 GCAGT--GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chr1ptel1M 206428 TGATTTTTAATCCC---------ACTTCATAA----GTGAGCT-AGTCAA 206463 iv iv i --------- vv i---- v -i v MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 102 chr1ptel1M 206464 TTTGCAGGACCCCTATTTGTCTCAGTGTCTTTTTCTGTAAAATGAGCATA 206513 v ii vvi i v vv i v i iv i v MIRc#SINE/MIR 103 GTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATA 152 chr1ptel1M 206514 AAAATTCC------ACCTA-ATCCTAGGGTTCTCATGAGGACAAAATAAG 206556 v v ------i -v vi v ii iv i MIRc#SINE/MIR 153 ATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAG 202 chr1ptel1M 206557 ACAGCACAGTACATG-ATGCACAATAGTCATTTGTAAAATGCTA 206599 i ii--- ii - v i -v v v vi i MIRc#SINE/MIR 203 ATAAT---GTATGTGAAAGCGC-TTTGTAAACTGTAAAGTGCTA 242 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.71 CpG sites = 31, Kimura (unadjusted) = 38.23 Transitions / transversions = 1.00 (31/31) Gap_init rate = 0.06 (13 / 214), avg. gap size = 2.69 (35 / 13) 301 26.65 5.49 1.05 chr1ptel1M 206935 207025 (792975) C MIR3#SINE/MIR (3) 205 111 m_b6s601i9 239 chr1ptel1M 206935 TTATAGGGTCATAAATAATCA---TTGGAAGGAATCTACAGAG-CCACAG 206980 i ii i vvi ---i i i -i -i ivv C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCT-TAGAGATCATCT 157 chr1ptel1M 206981 AGCACAACCCACTTATTTTATAGATG-GGAAACTGAGATTCAGTGA 207025 iv v i i - iii v C MIR3#SINE/MIR 156 AGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGA 111 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.63 CpG sites = 17, Kimura (unadjusted) = 34.63 Transitions / transversions = 2.43 (17/7) Gap_init rate = 0.04 (4 / 90), avg. gap size = 1.50 (6 / 4) 366 25.53 7.25 3.50 chr1ptel1M 208285 208422 (791578) C MIR3#SINE/MIR (2) 206 64 m_b6s601i10 240 chr1ptel1M 208285 ATCAAAAGAT-ATAAGATGT-AGAGCTGGAAAACACTTTGGA-ATTAAAA 208331 v ii - ii - iiv i i - i vvv C MIR3#SINE/MIR 206 ATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCT 157 chr1ptel1M 208332 AGTCCAACCCCCTTTTTCAACTTGCAG--GAGGAAACTGAAATACGGA-- 208377 iv ---- i -- iiiv i -- C MIR3#SINE/MIR 156 AGTCCAACCCCCTCATT----TTACAGATGAGGAAACTGAGGCCCAGAGA 111 chr1ptel1M 208378 ---GAAGGGATTTGCCCAAAGGTCATCCCCTTTTTGAGTGTCAGAGTC 208422 --- v i - iv vvi?vv v v i C MIR3#SINE/MIR 110 GGTGAAGTGACTTGCCC-AAGGTCACACAGCNAGTTAGTGGCAGAGCC 64 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.11 CpG sites = 19, Kimura (unadjusted) = 32.11 Transitions / transversions = 1.27 (19/15) Gap_init rate = 0.08 (11 / 137), avg. gap size = 1.36 (15 / 11) 203 28.36 10.98 1.11 chr1ptel1M 208353 208434 (791566) C MIRc#SINE/MIR (126) 142 53 m_b6s601i11 240 chr1ptel1M 208353 TTGCAG--GAGGAAACTGAAATACGGAG-----AAGGGATTTGCCCAAAG 208395 i -- iiiv i ----- v i - C MIRc#SINE/MIR 142 TTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCC-AAG 94 chr1ptel1M 208396 GTCATCCCCTTTTTGAGTGTCAGAGTC--AACTCAGAGTCA 208434 iv vvi vv i v i --i ii vi C MIRc#SINE/MIR 93 GTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCA 53 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.79 CpG sites = 14, Kimura (unadjusted) = 36.80 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.05 (4 / 81), avg. gap size = 2.50 (10 / 4) 29 16.18 3.03 1.49 chr1ptel1M 209201 209266 (790734) (AAGG)n#Simple_repeat 1 67 (0) m_b6s252i12 241 chr1ptel1M 209201 AAAGAAGGAAGGAAGGATGGAGGGGAGGAAGGAAGGAA-GAAGAGAA-AA 209248 i v i i - - -i (AAGG)n#Simpl 1 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG-GAAGGA 49 chr1ptel1M 209249 AGAAAGAAAGAAAGAAAG 209266 i i i i (AAGG)n#Simpl 50 AGGAAGGAAGGAAGGAAG 67 Matrix = Unknown Transitions / transversions = 8.00 (8/1) Gap_init rate = 0.05 (3 / 65), avg. gap size = 1.00 (3 / 3) 11 11.32 10.00 2.33 chr1ptel1M 210384 210423 (789577) (AGCAAAT)n#Simple_repeat 1 43 (0) m_b6s252i13 242 chr1ptel1M 210384 AGTAAATA--AAATAGCAAATGGCAAA-AG-TAATATCACAATA 210423 i -- i - -v v - (AGCAAAT)n#Si 1 AGCAAATAGCAAATAGCAAATAGCAAATAGCAAATAGCA-AATA 43 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.10 (4 / 39), avg. gap size = 1.25 (5 / 4) 17 3.96 3.85 0.00 chr1ptel1M 211517 211542 (788458) (ATT)n#Simple_repeat 1 27 (0) m_b6s252i14 243 chr1ptel1M 211517 ATTATTATTATTATTATT-TTATTTTT 211542 - v (ATT)n#Simple 1 ATTATTATTATTATTATTATTATTATT 27 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.04 (1 / 25), avg. gap size = 1.00 (1 / 1) 12 17.57 3.12 0.00 chr1ptel1M 212115 212146 (787854) (ACAAA)n#Simple_repeat 1 33 (0) m_b6s252i15 244 chr1ptel1M 212115 ACAAAA-AAAAATAAATAAATAAAAACAAAACA 212146 - vv i vv (ACAAA)n#Simp 1 ACAAAACAAAACAAAACAAAACAAAACAAAACA 33 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 16 16.12 0.00 0.00 chr1ptel1M 212117 212144 (787856) (A)n#Simple_repeat 1 28 (0) m_b6s252i16 244 chr1ptel1M 212117 AAAAAAAAATAAATAAATAAAAACAAAA 212144 v v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA 28 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 354 20.48 3.77 7.84 chr1ptel1M 212148 212253 (787747) MIR#SINE/MIR 21 122 (140) m_b6s601i12 245 chr1ptel1M 212148 AGAGCACCAACCCTG-AGTTGG--TGAACTGAGTTCAAATCTGGTCTCAG 212194 vii i - iii -- v- i i iv v v MIR#SINE/MIR 21 AGAGCACGGGCTCTGGAGCCAGACTGC-CTGGGTTCGAATCCCGGCTCTG 69 chr1ptel1M 212195 ACACTTAACGTTCCCTAGCTGCGTGACCTTGGGCCAGTCACTTAACCTCA 212244 v ------- i v i v MIR#SINE/MIR 70 CCACTTA-------CTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCT 112 chr1ptel1M 212245 AT-TGCCTCA 212253 v - MIR#SINE/MIR 113 CTGTGCCTCA 122 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 22.76 CpG sites = 11, Kimura (unadjusted) = 24.09 Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.10 (11 / 105), avg. gap size = 1.09 (12 / 11) 18 0.00 0.00 0.00 chr1ptel1M 212256 212275 (787725) (A)n#Simple_repeat 1 20 (0) m_b6s252i17 246 chr1ptel1M 212256 AAAAAAAAAAAAAAAAAAAA 212275 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAA 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 340 28.68 3.20 2.38 chr1ptel1M 212351 212475 (787525) MIRb#SINE/MIR 143 268 (0) m_b6s601i13 247 chr1ptel1M 212351 TAAAATATGGATAAAAACTCCTCCCTTCCAGGGTTTTTGTAAGGATCACA 212400 iv v iv v iv v i i v MIRb#SINE/MIR 143 TAAAATGGGGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAA 192 chr1ptel1M 212401 GGAGATATTG---GTAAGGTGCTTAAC-TTGTGTCTAGCTCTCAATAGGT 212446 v v --- i i i -iv i i v vi i i - MIRb#SINE/MIR 193 TGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAG- 241 chr1ptel1M 212447 CCCTCAGAATAATTACCAGTTTTCTTCTT 212475 v -- v ivi i i v v MIRb#SINE/MIR 242 CGCTC--AATAAATGGTAGCTCTATTATT 268 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.12 CpG sites = 18, Kimura (unadjusted) = 36.66 Transitions / transversions = 1.06 (18/17) Gap_init rate = 0.04 (5 / 124), avg. gap size = 1.40 (7 / 5) 38 0.00 0.00 0.00 chr1ptel1M 218133 218165 (781835) (GA)n#Simple_repeat 1 33 (0) c_b6s251i4 248 chr1ptel1M 218133 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 218165 (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 33 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 67 4.41 0.00 0.00 chr1ptel1M 219230 219300 (780700) (AG)n#Simple_repeat 1 71 (0) c_b6s251i5 249 chr1ptel1M 219230 AGAGAGAGAAAAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAA 219279 i i i (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr1ptel1M 219280 AGAGAGAGAGAGAGAGAGAGA 219300 (AG)n#Simple_ 51 AGAGAGAGAGAGAGAGAGAGA 71 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0) 26 8.18 0.00 0.00 chr1ptel1M 221042 221080 (778920) (AGACAGAG)n#Simple_repeat 1 39 (0) c_b6s251i6 250 chr1ptel1M 221042 AGACAGAGAGACAGAGAAACAGAAAGACAGACAGACAGA 221080 i i v (AGACAGAG)n#S 1 AGACAGAGAGACAGAGAGACAGAGAGACAGAGAGACAGA 39 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 46 0.00 0.00 0.00 chr1ptel1M 221466 221504 (778496) (AC)n#Simple_repeat 1 39 (0) c_b6s251i7 251 chr1ptel1M 221466 ACACACACACACACACACACACACACACACACACACACA 221504 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACA 39 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 286 33.27 2.94 9.38 chr1ptel1M 221582 221717 (778283) MIRb#SINE/MIR 24 151 (117) m_b6s601i14 252 chr1ptel1M 221582 GAAAAAGTAAGAA----AAAGACAAAGAAAACTGAGTTTTAATCATAGCT 221627 i i v ii----ii v i v i v i iv vii MIRb#SINE/MIR 24 GAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCGAATCCCGGCT 73 chr1ptel1M 221628 TTGCCACTTGGTGTCTATGGGATATTCAGCAAGATATTTAACCACATTTG 221677 i iv iv i v iv vi v i v - i MIRb#SINE/MIR 74 CTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTC-TCTG 122 chr1ptel1M 221678 AGGTTAAATGAGATCTAAGACCTCTCATCTTTAAAATGAG 221717 -----------i v viii v i MIRb#SINE/MIR 123 AG-----------CCTCAGTTTCCTCATCTGTAAAATGGG 151 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.28 CpG sites = 25, Kimura (unadjusted) = 45.45 Transitions / transversions = 1.56 (25/16) Gap_init rate = 0.10 (13 / 135), avg. gap size = 1.23 (16 / 13) 390 28.67 4.76 8.64 chr1ptel1M 221602 221769 (778231) MIR3#SINE/MIR 42 203 (5) m_b6s601i15 252 chr1ptel1M 221602 AAGAAAACTGAGTTTTAATCATAGCTTTGCCACTTGGTGTCTATGGGATA 221651 i i v i i i vii i viv ?v i v iv MIR3#SINE/MIR 42 AGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACC 91 chr1ptel1M 221652 TTCAGCAAGATATTTAACCACATTTGAGGTTAAATGAGATCTAAGACCTC 221701 vi vi i v v - i i -----------i v viii MIR3#SINE/MIR 92 TTGGGCAAGTCACTTCACCTC-TCTGGG-----------CCTCAGTTTCC 129 chr1ptel1M 221702 TCATCTTTAAAATGAGTCCAGG--GGACAAGGTG----CTAAGTCCCCTT 221745 v v--i -- v i ---- vi MIR3#SINE/MIR 130 TCATCTGTAAAATGAGG--GGGTTGGACTAGATGATCTCTAAGGTCCCTT 177 chr1ptel1M 221746 CCAGCTGTA--ATTCTATGATTTGAT 221769 v i-- iv MIR3#SINE/MIR 178 CCAGCTCTGACATTCTATGATTCTAT 203 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.94 CpG sites = 25, Kimura (unadjusted) = 37.12 Transitions / transversions = 1.32 (25/19) Gap_init rate = 0.10 (17 / 167), avg. gap size = 1.29 (22 / 17) 12 18.44 0.00 3.12 chr1ptel1M 221961 221993 (778007) (AACACA)n#Simple_repeat 1 32 (0) m_b6s252i18 253 chr1ptel1M 221961 AACACCAACTCAAACAGAAACAGAAAAAACAAA 221993 v v v -v v (AACACA)n#Sim 1 AACACAAACACAAACACAAACA-CAAACACAAA 32 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 40 36.58 2.33 1.85 chr1ptel1M 222240 222454 (777546) (AT)n#Simple_repeat 1 216 (0) m_b6s252i19 254 chr1ptel1M 222240 ATATATCTCTAAATATACATATATGGTGATACATGCACATACACATATAA 222289 v v v i -i - i ii i i i v (AT)n#Simple_ 1 ATATATATATATATATATATATAT-AT-ATATATATATATATATATATAT 48 chr1ptel1M 222290 ATCTATATCATATGTACAT-TATACATATA-ATGTATATGTATACAT-TA 222336 v - i i - i - i i i - (AT)n#Simple_ 49 ATATATAT-ATATATATATATATATATATATATATATATATATATATATA 97 chr1ptel1M 222337 CAACAATGGGGA-ACACACATATGGAAGTACCTACATATATACATACATA 222385 i vvv iviv - i i i iv vi iv i i i (AT)n#Simple_ 98 TATATATATATATATATATATATATATATATATATATATATATATATATA 147 chr1ptel1M 222386 TGGGGATTTGTGCATATAAACACATATGTGTGAATATATATAGTA-ATAT 222434 iviv v i ii v i i i i iv - - (AT)n#Simple_ 148 TATATATATATATATATATATATATATATATATATATATATA-TATATAT 196 chr1ptel1M 222435 ATACATATGCATATATACAT 222454 i ii i (AT)n#Simple_ 197 ATATATATATATATATATAT 216 Matrix = Unknown Transitions / transversions = 2.22 (40/18) Gap_init rate = 0.04 (9 / 214), avg. gap size = 1.00 (9 / 9) 184 11.11 0.00 0.00 chr1ptel1M 222590 222616 (777384) MIR3#SINE/MIR 84 110 (98) m_b6s601i16 255 chr1ptel1M 222590 GTGTGATGCTGGGCAAGTCACTTCACC 222616 ivi MIR3#SINE/MIR 84 GTGTGACCTTGGGCAAGTCACTTCACC 110 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 12.16 CpG sites = 2, Kimura (unadjusted) = 12.16 Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 290 26.79 0.00 8.86 chr1ptel1M 226010 226095 (773905) MIRc#SINE/MIR 37 115 (153) m_b7s601i1 256 chr1ptel1M 226010 TGTAGTCAGGAGGACAGGAGTTCAAATCCGGCCTCAGACACTTAACACTT 226059 v i vv i i i v v v v ------ MIRc#SINE/MIR 37 TGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTA------ 80 chr1ptel1M 226060 CCTATTTTTGTGACCCTGATCAAGCCATTTAACTCC 226095 - vi v i iv i i ii MIRc#SINE/MIR 81 -CTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.38 CpG sites = 11, Kimura (unadjusted) = 33.26 Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.08 (7 / 85), avg. gap size = 1.00 (7 / 7) 198 28.01 1.27 9.59 chr1ptel1M 226027 226105 (773895) MIR#SINE/MIR 50 122 (140) m_b7s601i2 256 chr1ptel1M 226027 GAGTTCAAATCCGGCCTCAGACACTTAACACTTCCTATTTTTGTGACCCT 226076 i i v v v v ------- vi v i MIR#SINE/MIR 50 GGGTTCGAATCCCGGCTCTGCCACTTA-------CTAGCTGTGTGACCTT 92 chr1ptel1M 226077 GATCAAGCCATTTAACTCCAAT-TGCCCCA 226105 iv ii i ii vv - i MIR#SINE/MIR 93 GGGCAAGTTACTTAACCTCTCTGTGCCTCA 122 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.20 CpG sites = 11, Kimura (unadjusted) = 35.35 Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.10 (8 / 78), avg. gap size = 1.00 (8 / 8) 398 25.83 18.72 2.77 chr1ptel1M 226125 226343 (773657) MIRb#SINE/MIR 8 260 (8) m_b7s601i3 257 chr1ptel1M 226125 GCAGTTAGTGGTACAGTGGATATAGC-----TTTT--AATCATGAGAACC 226167 i-- i v v -----i -- i - v iv MIRb#SINE/MIR 8 GCAGC--GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCA-GACAGAC 54 chr1ptel1M 226168 CTGAGCTTTAATCCCA-------CA-TCATAAACTG----AC--TGGTCA 226203 i i iv i------- - i iv i ---- -- v MIRb#SINE/MIR 55 CTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 104 chr1ptel1M 226204 A-TTACTAGGACCCCTATTTGCCTCAGTTTCTTAGATTGTAAAATGAGCA 226252 - -vi i v vv i vivi i v MIRb#SINE/MIR 105 AGTTACT-TAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGA 153 chr1ptel1M 226253 TAACAATCACACTTA-ATCCTAGGGTTCTCATGATGATAAAATGAGA--- 226298 i --- i -v vi v ii v v --- MIRb#SINE/MIR 154 TAATAAT---ACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAA 200 chr1ptel1M 226299 -G--------------AGCATAATGCATGACACACAGTGGGTACTATAGA 226333 - -------------- i i v i i ii ii vv v MIRb#SINE/MIR 201 TGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATA 250 chr1ptel1M 226334 AATGGTAGTT 226343 i MIRb#SINE/MIR 251 AATGGTAGCT 260 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.65 CpG sites = 32, Kimura (unadjusted) = 32.53 Transitions / transversions = 1.39 (32/23) Gap_init rate = 0.08 (18 / 218), avg. gap size = 2.67 (48 / 18) 11 24.30 0.00 0.00 chr1ptel1M 228236 228269 (771731) (AACAAA)n#Simple_repeat 1 34 (0) m_b7s252i2 258 chr1ptel1M 228236 AAAAATAACAACAACAAAGAATAAAACAAATACA 228269 v v v i vv v (AACAAA)n#Sim 1 AACAAAAACAAAAACAAAAACAAAAACAAAAACA 34 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 12 13.86 0.00 0.00 chr1ptel1M 228286 228309 (771691) (ATAT)n#Simple_repeat 1 24 (0) m_b7s252i3 259 chr1ptel1M 228286 ATATACATACATATATATTTATAT 228309 i i v (ATAT)n#Simpl 1 ATATATATATATATATATATATAT 24 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 241 34.48 4.83 2.01 chr1ptel1M 228434 228578 (771422) C MIRc#SINE/MIR (37) 231 83 m_b7s601i4 260 chr1ptel1M 228434 AATTTCTAATGAGTTTCCA---GCATAATAACATTGGATTCCCACAATAA 228480 i vi v v i i ---i v vv v i i i C MIRc#SINE/MIR 231 AGTTTACAAAGCGCTTTCACATACATTATCTCATTTGATCCTCACAACAA 182 chr1ptel1M 228481 ACCTGTGACA-ACACAGGAT--GTGCCTTCATTCTTACTTTAAGTACAAC 228527 v vi- vi ii-- iiiv i i ii i viv ii v C MIRc#SINE/MIR 181 CCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAG 132 chr1ptel1M 228528 TCATATGATCAGCTCAGAATGGCTGAGTGACTTGACCAA-ATCCCAGCAG 228576 vv vv --i iv i i v -i v - C MIRc#SINE/MIR 131 GAAACTGA--GGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACA-CAG 85 chr1ptel1M 228577 CT 228578 C MIRc#SINE/MIR 84 CT 83 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 47.84 CpG sites = 28, Kimura (unadjusted) = 47.84 Transitions / transversions = 1.33 (28/21) Gap_init rate = 0.05 (7 / 144), avg. gap size = 1.43 (10 / 7) 20 11.25 0.00 0.00 chr1ptel1M 228768 228796 (771204) (T)n#Simple_repeat 1 29 (0) m_b7s252i4 261 chr1ptel1M 228768 TTTTCCTTTTTTTTTTTTTTTTTTTTGTT 228796 ii v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 410 19.14 0.00 8.86 chr1ptel1M 230221 230306 (769694) MIRc#SINE/MIR 37 115 (153) m_b7s601i5 262 chr1ptel1M 230221 TGCAGTCAAGAGGACTTGAGTTCAAATGTGGTCTCTGACACTTAATACTT 230270 v i i i i i i viv v v ------ MIRc#SINE/MIR 37 TGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTA------ 80 chr1ptel1M 230271 CCTAGCTGTGTGACCCTGGGTAAGTCACTTAACCCC 230306 - i i i MIRc#SINE/MIR 81 -CTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 20.77 CpG sites = 10, Kimura (unadjusted) = 22.41 Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.08 (7 / 85), avg. gap size = 1.00 (7 / 7) 273 31.23 17.33 1.72 chr1ptel1M 230361 230562 (769438) MIRb#SINE/MIR 28 260 (8) m_b7s601i6 263 chr1ptel1M 230361 GAACATAGCTTTT--AATCATGAAGACCTGAGTTTTAATCCCATCTC--- 230405 i ii vi -- i viv i iv iv --- MIRb#SINE/MIR 28 GAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTCTGC 77 chr1ptel1M 230406 ------ATAA----GTGAGCT-AGTCAATTTACAAGACCCCCGTTTGTCT 230444 ------v i---- v -i v v vvi i iv vv i MIRb#SINE/MIR 78 CACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCT 127 chr1ptel1M 230445 CAGTGTCTTATTCTATAAAATGAGCATAAAAAATTGCACCTA-ATCCTAG 230493 v i vv i i v v ----i -v vi MIRb#SINE/MIR 128 CAGTTTCCTCATCTGTAAAATGGGGATAATAA----TACCTACCTCGCAG 173 chr1ptel1M 230494 GATTCTC----------AATGGGATAAAATA---AGAG-----AGCACAG 230525 i v i---------- i vii --- i ----- MIRb#SINE/MIR 174 GGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAG 223 chr1ptel1M 230526 TACATAAAACACAGTAAATGCTATAGAAATGCTAGTT 230562 i v iiv i ii vv v v i MIRb#SINE/MIR 224 TGCCTGGCACATAGTAAGCGCTCAATAAATGGTAGCT 260 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.87 CpG sites = 33, Kimura (unadjusted) = 41.34 Transitions / transversions = 1.14 (33/29) Gap_init rate = 0.06 (13 / 201), avg. gap size = 3.00 (39 / 13) 296 30.30 12.82 0.57 chr1ptel1M 230410 230565 (769435) MIR#SINE/MIR 85 259 (3) m_b7s601i7 263 chr1ptel1M 230410 GTGAGCT-AGTCAATTTACAAGACCCCCGTTTGTCTCAGTGTCTTATTCT 230458 v -i v v vvi i iv v i v i vv MIR#SINE/MIR 85 GTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCT 134 chr1ptel1M 230459 ATAAAATGAGCATAAAAAATTGCACCTA-ATCCTAGGATTCTCAATGGGA 230507 i i v - v v i -v v i v iivvi MIR#SINE/MIR 135 GTAAAATGGGGAT-AATAATAGTACCTACCTCATAGGGTTGTTGTGAGGA 183 chr1ptel1M 230508 TAAAATAAG-----------AGAGC-------ACAGTACATAAAACACAG 230539 v i ----------- i ------- i v iiv i MIR#SINE/MIR 184 TTAAATGAGTTAATACATGTAAAGCGCTTAGAACAGTGCCTGGCACATAG 233 chr1ptel1M 230540 TAAATGCTATAGAAATGCTAGTTATT 230565 ii vv v i i MIR#SINE/MIR 234 TAAGCGCTCAATAAATGTTAGCTATT 259 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.26 CpG sites = 23, Kimura (unadjusted) = 39.30 Transitions / transversions = 0.96 (23/24) Gap_init rate = 0.03 (5 / 155), avg. gap size = 4.20 (21 / 5) 345 24.44 9.03 4.97 chr1ptel1M 230682 230836 (769164) L2b_3end#LINE/L2 306 466 (0) m_b7s601i8 264 chr1ptel1M 230682 TGGGTTTCTACATAGTTGTTTGTATA-GTGTCTG----CCCCAACAGTCT 230726 ----- ?i i ?v -i ---- vi v L2b_3end#LINE 306 TGGGTT-----ATNATTGTCTGNTTACATGTCTGTCTCCCCCACTAGACT 350 chr1ptel1M 230727 GTGGCCTCCAGGAGAGCAGG----GGATATCCCTTGTATCTCTTGTTG-- 230770 iv iv i ---- ?i v vi - v -i i -- L2b_3end#LINE 351 GTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCTTGT-TCAC-CGCTGTA 398 chr1ptel1M 230771 TTCCTAGTCCTTAACTCAGGGACTGGCATGCAGCAGGCACT---TAAATC 230817 i i iv i i v ? v ii i i --- v L2b_3end#LINE 399 TCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATA 448 chr1ptel1M 230818 TTTGCTGACTTGAAGAAAT 230836 i v- vi L2b_3end#LINE 449 TTTGTTGAA-TGAATGAAT 466 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.39 CpG sites = 22, Kimura (unadjusted) = 31.46 Transitions / transversions = 1.57 (22/14) Gap_init rate = 0.08 (13 / 154), avg. gap size = 1.69 (22 / 13) 346 30.30 5.26 0.72 chr1ptel1M 230698 230830 (769170) L2d2_3end#LINE/L2 412 550 (5) m_b7s601i9 264 chr1ptel1M 230698 TGTTTGTATAGTGTCTGCCCCAAC-AGTCTGTGGCCTCCAGGAGAGCAGG 230746 i i vv - - vi iiv vv i L2d2_3end#LIN 412 TGTTTATGTCTTGTCT-CCCCAACTAGATTGTAAGCTCCTTGAGGGCAGG 460 chr1ptel1M 230747 GGATATCCCTTGTATCTCTTGTTGTTCC---TAGTCCTTAACTCAGGGAC 230793 ivi vi i ii vv i i ---i iv i i v v v L2d2_3end#LIN 461 GACCATGTCTTATACTTCTTTGTATCCCCCACAGCGCCTAGCACAGTGCC 510 chr1ptel1M 230794 TGGCATGCAGCAGGCACT---TAAATCTTTGCTGACTTGA 230830 v ii i i --- v i i L2d2_3end#LIN 511 TTGCACACAGTAGGCGCTCAATAAATATTTGTTGATTTGA 550 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.53 CpG sites = 24, Kimura (unadjusted) = 40.11 Transitions / transversions = 1.50 (24/16) Gap_init rate = 0.03 (4 / 132), avg. gap size = 2.00 (8 / 4) 297 23.32 5.38 3.16 chr1ptel1M 230917 231009 (768991) C MIR3#SINE/MIR (3) 205 111 m_b7s601i10 265 chr1ptel1M 230917 TTATAGGGTCACATAAATAATCA---CTGGAAGGAATC-TAGAGATCCAC 230962 i ii i -i i- --- i i - - i C MIR3#SINE/MIR 205 TCATAGAATCATA-GAATG-TCAGAGCTGGAAGGGACCTTAGAGAT-CAT 159 chr1ptel1M 230963 AGAGCACAACCCACTTATTTTATAGCTG-GGAAACTGAGATTCAGTGA 231009 vv iv v i i v - iii v C MIR3#SINE/MIR 158 CTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGA 111 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.12 CpG sites = 15, Kimura (unadjusted) = 29.12 Transitions / transversions = 2.50 (15/6) Gap_init rate = 0.07 (6 / 92), avg. gap size = 1.33 (8 / 6) 160 9.99 0.43 0.00 chr1ptel1M 231595 231826 (768174) (AGAA)n#Simple_repeat 1 233 (0) m_b7s252i5 266 chr1ptel1M 231595 AGAAAGAGAAAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG 231644 i i (AGAA)n#Simpl 1 AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG 50 chr1ptel1M 231645 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG-AAGAAAGAAAGAA 231693 - (AGAA)n#Simpl 51 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAA 100 chr1ptel1M 231694 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG 231743 i i i i i i i i i i i i (AGAA)n#Simpl 101 AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG 150 chr1ptel1M 231744 GAAGGAAGGAAGGAAGGAAAAAAGAAAGAAAGAAAGAAAGAAAGAAAAAA 231793 i i i i i i i (AGAA)n#Simpl 151 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAA 200 chr1ptel1M 231794 AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 231826 (AGAA)n#Simpl 201 AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 233 Matrix = Unknown Transitions / transversions = 1.00 (21/0) Gap_init rate = 0.00 (1 / 231), avg. gap size = 1.00 (1 / 1) 361 26.30 7.41 1.40 chr1ptel1M 232480 232614 (767386) C MIR3#SINE/MIR (2) 206 64 m_b7s601i11 267 chr1ptel1M 232480 ATCA-AAAATCATAAGATGT-AGAGCTGAAAAACACTTCAGA-ATTAAAA 232526 - i ii - i iiv i i - i vvv C MIR3#SINE/MIR 206 ATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCT 157 chr1ptel1M 232527 AGTCCAGCCCTCTTCAATATACAGGTG--GAAACTGAAACACAGA----- 232569 i i - v v i -- ii v ----- C MIR3#SINE/MIR 156 AGTCCAACCCCCT-CATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGT 108 chr1ptel1M 232570 GAAGGGATTTCCCCAAAGGTCATCTCCTTTATGAGTGTCAGAGTC 232614 v i v - ivivvi?vi v v i C MIR3#SINE/MIR 107 GAAGTGACTTGCCC-AAGGTCACACAGCNAGTTAGTGGCAGAGCC 64 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.40 CpG sites = 20, Kimura (unadjusted) = 33.40 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.05 (7 / 134), avg. gap size = 1.71 (12 / 7) 219 32.56 7.78 1.04 chr1ptel1M 232537 232626 (767374) C MIRc#SINE/MIR (118) 150 55 m_b7s601i12 267 chr1ptel1M 232537 TCTTCAATATACAGGTG--GAAACTGAAACACAGAG-----AAGGGATTT 232579 ii v v i -- ii v ----- v i C MIRc#SINE/MIR 150 TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTT 101 chr1ptel1M 232580 CCCCAAAGGTCATCTCCTTTATGAGTGTCAGAGTCAACTCTTAAATC 232626 v - ivivvi vi i v i iivv ii i C MIRc#SINE/MIR 100 GCCC-AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACC 55 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.99 CpG sites = 17, Kimura (unadjusted) = 44.23 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.03 (3 / 89), avg. gap size = 2.67 (8 / 3) 55 25.91 0.69 0.69 chr1ptel1M 233379 233522 (766478) (GGAG)n#Simple_repeat 1 144 (0) m_b7s252i6 268 chr1ptel1M 233379 GGACGGATGGATGGATGGACAGACAGAAGGAAGGAAGGAAGGAAGGAAGG 233428 v v v v vi -i i i i i i i (GGAG)n#Simpl 1 GGAGGGAGGGAGGGAGGGAGGGA-GGGAGGGAGGGAGGGAGGGAGGGAGG 49 chr1ptel1M 233429 AAGGAAGGAAGGAAGGGAGGGAGGGAGAGAGGAAGGGAGGGA-GGAGGGA 233477 i i i i i i - (GGAG)n#Simpl 50 GAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGA 99 chr1ptel1M 233478 AGGAGGGAGAGAAGGAGAGAGGGAGAGAGAATGAGAGAGAGGCAG 233522 i i i i i iiv i i v (GGAG)n#Simpl 100 GGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAG 144 Matrix = Unknown Transitions / transversions = 3.29 (23/7) Gap_init rate = 0.01 (2 / 143), avg. gap size = 1.00 (2 / 2) 61 32.31 1.38 1.38 chr1ptel1M 233396 233613 (766387) (GAAA)n#Simple_repeat 1 218 (0) m_b7s252i7 268 chr1ptel1M 233396 GACAGACAG-AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG 233444 v v - i i i i i i i i i i (GAAA)n#Simpl 1 GAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA 50 chr1ptel1M 233445 GAGGGAGGGAGAGAGGAAGGGAGGGAGGAGGGAAGGAGGGAGAGAAGGAG 233494 i ii ii - i i i i i i ii i ii i -- (GAAA)n#Simpl 51 AAGAAAGAAAGA-AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAA--AG 97 chr1ptel1M 233495 AGAGGGAGAGAGAATGAGAGAGAGGCAGAAAGAGAAAAAGGAAGAAAGAA 233544 i ii i v i i iv i i i (GAAA)n#Simpl 98 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAA 147 chr1ptel1M 233545 AGAAAGAAAGACA-AAAAAAGGAAGGAAGGAAAGAAAAAAGGACAGAAGG 233593 v - i i i i i i v i (GAAA)n#Simpl 148 AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG 197 chr1ptel1M 233594 AGAGAAGGAAAGAAA-AAAGA 233613 i i - (GAAA)n#Simpl 198 AAAGAAAGAAAGAAAGAAAGA 218 Matrix = Unknown Transitions / transversions = 7.67 (46/6) Gap_init rate = 0.03 (6 / 217), avg. gap size = 1.00 (6 / 6) 16 13.35 0.00 2.94 chr1ptel1M 234564 234598 (765402) (AGAAAA)n#Simple_repeat 1 34 (0) m_b7s252i8 269 chr1ptel1M 234564 AGAAAAATAAACAAGCAAAAGTAAATGAAAAAGAA 234598 v - v v v (AGAAAA)n#Sim 1 AGAAAAAGAAA-AAGAAAAAGAAAAAGAAAAAGAA 34 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 11 11.32 10.00 2.33 chr1ptel1M 234739 234778 (765222) (AGCAAAT)n#Simple_repeat 1 43 (0) m_b7s252i9 270 chr1ptel1M 234739 AGTAAATA--AAATAGCAAATGGCAAA-AG-TAATATCACAATA 234778 i -- i - -v v - (AGCAAAT)n#Si 1 AGCAAATAGCAAATAGCAAATAGCAAATAGCAAATAGCA-AATA 43 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.10 (4 / 39), avg. gap size = 1.25 (5 / 4) 442 17.89 2.75 7.69 chr1ptel1M 236221 236329 (763671) MIRc#SINE/MIR 24 127 (141) m_b7s601i13 271 chr1ptel1M 236221 AGAGCACCAG-CCTGAAG-CAGGAGTAACTTGAGTTCAAATCTGGTCTCA 236268 ii - i i - i-i i i i i iv v v MIRc#SINE/MIR 24 AGAGCACTGGACTTGGAGTCAGGAA-GACCTGGGTTCGAGTCCCGGCTCT 72 chr1ptel1M 236269 GACACTTAACATTGCCTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 236318 v ------- MIRc#SINE/MIR 73 GCCACTTA-------CTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 chr1ptel1M 236319 AATTA-CCTCAG 236329 vv v - MIRc#SINE/MIR 116 TCTGAGCCTCAG 127 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 19.42 CpG sites = 11, Kimura (unadjusted) = 20.65 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.10 (11 / 108), avg. gap size = 1.00 (11 / 11) 324 28.69 3.17 3.17 chr1ptel1M 236417 236542 (763458) MIRb#SINE/MIR 143 268 (0) m_b7s601i14 272 chr1ptel1M 236417 TAAAATATGGATTAAAAACTCCTCCCTTCCAAGGTTTTTGTGAGGATCAC 236466 iv - v iv v iv i v i v MIRb#SINE/MIR 143 TAAAATGGGGAT-AATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAA 191 chr1ptel1M 236467 AGGAGATATTG---ATAAGGTGCTTAAC-TTGTGTCTAGCGCTCAATAGG 236512 v v ---i i i i -iv i i i vi i i MIRb#SINE/MIR 192 ATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAG 241 chr1ptel1M 236513 TCCCTCAAAATAATTGCCAGTTTTCTTCTT 236542 - v -- v vi i i v v MIRb#SINE/MIR 242 -CGCTC--AATAAATGGTAGCTCTATTATT 268 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.25 CpG sites = 19, Kimura (unadjusted) = 36.83 Transitions / transversions = 1.19 (19/16) Gap_init rate = 0.05 (6 / 125), avg. gap size = 1.33 (8 / 6) 707 26.16 6.07 1.71 chr1ptel1M 236604 236883 (763117) L1ME3G_3end#LINE/L1 257 548 (376) m_b7s551i0 273 chr1ptel1M 236604 GAAAACAGGGACACTGATACATTGTTGGTGGAATTGTGAATACATCCAGC 236653 i i v v v i i i v i vvi v L1ME3G_3end#L 257 GGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTACAGC 306 chr1ptel1M 236654 CATTCTGGAGAGC-------------CCA--AAAAGTTATCAAACTGTGC 236688 ? i i ------------- i -- v --- v i L1ME3G_3end#L 307 CNTTTTGGAGGGCAATTTGGCAGTATCTATTAAAATTTA---AAATGCGC 353 chr1ptel1M 236689 ATACCCTTTGATCCAGCAGTGTCTCTACTGGGCTTATACCCCAAAGAGAT 236738 i i vi v v ? ?v v i i ? i L1ME3G_3end#L 354 ATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAGAAAT 403 chr1ptel1M 236739 ACTAAAAAA-G-GGAAAGGGACCTGTATGTGCCAAAATGTTTGTGGCAGC 236786 viv v - - v v i --? i i v ii ii v L1ME3G_3end#L 404 ACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTCATTGCAGC 451 chr1ptel1M 236787 CCTGTTTGTAGTGGCCAGAAGCTGGAAAATGAATGGATGCCCATCAATTG 236836 vi i i v i ii vvivv ii i v L1ME3G_3end#L 452 ATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCAATAG 501 chr1ptel1M 236837 GAGAATGGTTGAGTAAATTGTGGTATATGAATGTTATGGAATATTAT 236883 i i i i vv ii i L1ME3G_3end#L 502 GGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACTAT 548 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 32.01 CpG sites = 42, Kimura (unadjusted) = 33.71 Transitions / transversions = 1.40 (42/30) Gap_init rate = 0.03 (9 / 279), avg. gap size = 2.44 (22 / 9) 687 30.54 4.68 0.80 chr1ptel1M 236606 236968 (763032) L1ME4c_3end#LINE/L1 263 639 (191) m_b7s551i1 273 chr1ptel1M 236606 AAACAGGGACACTGATACATTGTTGGTGGAATTGTGAATACATCCAGCCA 236655 v v ? v i v ? i vvi v i v L1ME4c_3end#L 263 AAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACAACCC 312 chr1ptel1M 236656 TTCTGGAGAGC------CCAA---------AAAGTTATCAAACTGTGCAT 236690 i i ------v --------- i ii v v v L1ME4c_3end#L 313 TTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAAAATGTTCAT 362 chr1ptel1M 236691 ACCCTTTGATCCAGCAGTGTCTCTACTGGGCTTATACCCCAAAGAGATAC 236740 i i i vi v v vv v i i i i v L1ME4c_3end#L 363 ACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAA 412 chr1ptel1M 236741 T--AAAAAAGGGAAAGGGACCTGTATGTGCCAAAATGTTTGTGGCAGCCC 236788 -- i i ii -- i ii v i ii v vi L1ME4c_3end#L 413 TTCAAAAGAAGGAAAAAG--CTATATGCACGAAGATGTTCATTGCAGCGT 460 chr1ptel1M 236789 TGTTTGTAGTGGCCAGAAGCTGGAAAATGAATGGATGCCCATCAATTGGA 236838 i i i i v i ii vvivv ii i v v i L1ME4c_3end#L 461 TATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGG 510 chr1ptel1M 236839 GAATGGTTGAGTAAATTGTGGTATATGAATGTTATGGAATATTATTGTTC 236888 i i i v? iviv vvvv L1ME4c_3end#L 511 GAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATATTATGCAGC 560 chr1ptel1M 236889 TGTAAGAAATGACCAGCAGGATGAATACAGAGAGGCTTGGAGAGAATTAC 236938 ii v i iv vi v v v iiv vii v i ivi -i L1ME4c_3end#L 561 CATTAAAAATGATAATTATGAAGACTATGTAGCAACATGGAAAATGTT-T 609 chr1ptel1M 236939 ATGAACTGATGCTAAGTGAAATGAGCAGAA 236968 vv i i vi L1ME4c_3end#L 610 ATGATATAATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.14 CpG sites = 61, Kimura (unadjusted) = 40.62 Transitions / transversions = 1.24 (61/49) Gap_init rate = 0.02 (6 / 362), avg. gap size = 3.33 (20 / 6) 297 32.41 3.83 1.88 chr1ptel1M 245952 246212 (753788) L1M3_orf2#LINE/L1 3016 3281 (7) m_b7s551i2 274 chr1ptel1M 245952 ATAGAAAATTTTGATTATATCAAATTAAAAAGCTTTTGTACAAACAAAAC 246001 v v vv i i i i i i- iv L1M3_orf2#LIN 3016 ATAGACAAGTGGGACTACATCAAACTAAAAAGCTTCTGCACAG-CAAAGG 3064 chr1ptel1M 246002 AAATG--CAGACAAGATTAGAAGGGAAGTAATAAGCTGGGGAAACATTTT 246049 ii-- - iii v i v viv iiiiv ii v v L1M3_orf2#LIN 3065 AAACAATCA-ACAGAGTGAAAAGGCAACCTACGGAATGGGAGAAAATATT 3113 chr1ptel1M 246050 TACAGTCAAAGGTTCTGATAAAAGCCTCATTTCCCAAATATAGAGAGAAT 246099 i iv v vivv ii vi v v v v ii i L1M3_orf2#LIN 3114 TGCAAACCATATATCTGATAAGGGGTTAATATCCAAAATATATAAGGAAC 3163 chr1ptel1M 246100 T-----GACTCTATA---AGAAATCAAGCCATTTTCCAATTGATAAATGG 246141 -----i v --- i v --- vvi i ? v L1M3_orf2#LIN 3164 TCNTACAACTCAATAGCAAAAAAACAA---ATAACCCGATTNAAAAATGG 3210 chr1ptel1M 246142 TCAAAGGAAATGAAAAGACAATTTTCAGATGAAGAAATGGAAACTATTTC 246191 v vv v v i vi v v iv iviiivv L1M3_orf2#LIN 3211 GCAAAGGACCTGAATAGACATTTCTCCAAAGAAGACATACAAATGGCCAA 3260 chr1ptel1M 246192 TAGCCACATGAAAAGATGCTC 246212 i vi i L1M3_orf2#LIN 3261 CAGGTATATGAAAAGATGCTC 3281 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 42.03 CpG sites = 43, Kimura (unadjusted) = 43.48 Transitions / transversions = 1.07 (43/40) Gap_init rate = 0.03 (8 / 260), avg. gap size = 1.88 (15 / 8) 424 25.15 2.92 2.33 chr1ptel1M 246081 246251 (753749) L1ME3G_3end#LINE/L1 7 178 (746) m_b7s551i3 274 chr1ptel1M 246081 TCCCAAATATAGAGAGAATT-----GACTCTATAAGAAATCAAGCCATTT 246125 vi v i i -----i v v -- v vi- L1ME3G_3end#L 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAA--AAGACAAC- 53 chr1ptel1M 246126 TCCAATTGATAAATGGTCAAAGGAAATGAAAAGACAATTTTCAGATGAAG 246175 - v v v v v i iv v i L1ME3G_3end#L 54 -CCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chr1ptel1M 246176 AAATGGAAACTATTTCTAGCCACATGAAAAGATGCTCCAGGTCATTATTA 246225 iv iviiivv iv i v vv i v L1ME3G_3end#L 103 AAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTA 152 chr1ptel1M 246226 ATCAGAGAAATGAAAATTGAGACAAC 246251 i v i i L1ME3G_3end#L 153 ATCAGGGAAATGCAAATTAAAACAAC 178 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 30.78 CpG sites = 19, Kimura (unadjusted) = 30.78 Transitions / transversions = 0.83 (19/23) Gap_init rate = 0.03 (5 / 170), avg. gap size = 1.80 (9 / 5) 111 4.42 0.00 0.00 chr1ptel1M 248283 248399 (751601) (AG)n#Simple_repeat 1 117 (0) c_b7s251i0 275 chr1ptel1M 248283 AGAGAGAGAGAGAGAGACAGAGAGACAGAGAGAGAGAGAGAGAGAGAGAG 248332 v v (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr1ptel1M 248333 AGAGAGAGAGACAGAGAGAGACAGAGAGAGAGAGAGACAGAGAGAGAGAG 248382 v v v (AG)n#Simple_ 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 100 chr1ptel1M 248383 AGAGAGAGAGAGAGAGA 248399 (AG)n#Simple_ 101 AGAGAGAGAGAGAGAGA 117 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.00 (0 / 116), avg. gap size = 0.0 (0 / 0) 23 17.04 0.00 0.00 chr1ptel1M 249085 249124 (750876) (T)n#Simple_repeat 1 40 (0) m_b7s252i10 276 chr1ptel1M 249085 TTTTTTTTATTTGTTTTTTTTTTTTTTTAATTTGATTTTT 249124 v v vv vv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 40 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 14 22.65 0.00 2.38 chr1ptel1M 250528 250570 (749430) (AAAAAGT)n#Simple_repeat 1 42 (0) m_b7s252i11 277 chr1ptel1M 250528 AAAAAGTGAAACAGTAAAAAAAAAAAAAAAAAAAAAAAAGAGT 250570 - v iv iv iv i (AAAAAGT)n#Si 1 AAAAAGT-AAAAAGTAAAAAGTAAAAAGTAAAAAGTAAAAAGT 42 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.02 (1 / 42), avg. gap size = 1.00 (1 / 1) 22 0.00 0.00 0.00 chr1ptel1M 250543 250566 (749434) (A)n#Simple_repeat 1 24 (0) m_b7s252i12 278 chr1ptel1M 250543 AAAAAAAAAAAAAAAAAAAAAAAA 250566 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAA 24 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 25 22.56 0.00 0.00 chr1ptel1M 251154 251205 (748795) (A)n#Simple_repeat 1 52 (0) m_b7s252i13 279 chr1ptel1M 251154 AAAAAAAAAAAAAAAAAAAAAAAGAATGAAAGACTAAGAAAAAGACAGAA 251203 i vi i vv i i v i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr1ptel1M 251204 AA 251205 (A)n#Simple_r 51 AA 52 Matrix = Unknown Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 16 13.72 0.00 0.00 chr1ptel1M 251250 251274 (748726) (T)n#Simple_repeat 1 25 (0) m_b7s252i14 280 chr1ptel1M 251250 TTTCTTCTTCTTTTTTTTTTTTTTT 251274 i i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 369 27.33 1.83 1.83 chr1ptel1M 251896 251973 (748027) C HERV3#LTR/ERV1 (503) 7923 7846 m_b7s701i0 281 chr1ptel1M 251896 GCCAAATGATCTAGTGCTTTAGCTGTCTGATTGGTGATAATCTCTACAAC 251945 ivv iv ? v ? ? v i i i v vv C HERV3#LTR/ERV 7923 GCCAGCAGATCTAAGGCNTTTGCNGTNTCATTAGTGATGATTTCAAGCAC 7874 chr1ptel1M 251946 TGCTTGAAGCCTAATTGTCCTGTTCAAC 251973 i v i v vi v v v i C HERV3#LTR/ERV 7873 TGCCTGCAACCTTATGATGCGGTTGAGC 7846 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.39 CpG sites = 16, Kimura (unadjusted) = 35.39 Transitions / transversions = 0.64 (9/14) Gap_init rate = 0.00 (0 / 77), avg. gap size = 0.0 (0 / 0) 60 0.00 0.00 0.00 chr1ptel1M 251974 252024 (747976) (AT)n#Simple_repeat 1 51 (0) c_b7s251i1 282 chr1ptel1M 251974 ATATATATATATATATATATATATATATATATATATATATATATATATAT 252023 (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr1ptel1M 252024 A 252024 (AT)n#Simple_ 51 A 51 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 369 27.33 1.83 1.83 chr1ptel1M 252025 252109 (747891) C HERV3#LTR/ERV1 (581) 7845 7761 m_b7s701i0 281 chr1ptel1M 252025 GGGGTTCTAT---GGTTCTATATTCCCAACTTCCATCTTGAGTCCAGGTG 252071 v --- vv --- v vi i vv?i vv i C HERV3#LTR/ERV 7845 TG---TAAATAGGGGTGCGGTATCCCCACGNCCCATCTTCTGCCCAGGTG 7799 chr1ptel1M 252072 GCTGGCCCACACTCTTCCATTATTCTCTCTGGAGGCCA 252109 i v v vv i v i C HERV3#LTR/ERV 7798 GCTGGCCCATAGTATTGGATTATTCTTTCAGGGGGCCA 7761 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.39 CpG sites = 16, Kimura (unadjusted) = 35.39 Transitions / transversions = 0.50 (7/14) Gap_init rate = 0.05 (4 / 84), avg. gap size = 1.50 (6 / 4) 407 30.00 1.67 0.00 chr1ptel1M 252155 252274 (747726) MIR3#SINE/MIR 82 203 (5) m_b7s601i15 283 chr1ptel1M 252155 CTATGGGATATTCAGCAAGAAATTCAACCTCATTATATCTCAGTTCTCTC 252204 i v iv vi vv i iv vi ivii ii MIR3#SINE/MIR 82 CTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTC 131 chr1ptel1M 252205 ATCTTTAAAATGAGTGCAGTGGACAAGATGATGTCTAAATCCCTTTGAAG 252254 v v viv v v ivi i vv MIR3#SINE/MIR 132 ATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAG 181 chr1ptel1M 252255 CTGTA--ATTCTATGATTTGAT 252274 v i-- iv MIR3#SINE/MIR 182 CTCTGACATTCTATGATTCTAT 203 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.66 CpG sites = 17, Kimura (unadjusted) = 38.66 Transitions / transversions = 0.89 (17/19) Gap_init rate = 0.01 (1 / 119), avg. gap size = 2.00 (2 / 1) 23 40.26 2.13 0.70 chr1ptel1M 252733 252873 (747127) (AT)n#Simple_repeat 1 143 (0) m_b7s252i15 284 chr1ptel1M 252733 ATATAAATGTACATCACATGTACAT-TATACATATATATGAATACA-ACA 252780 v i i - i i i - i iv i - i (AT)n#Simple_ 1 ATATATATATATAT-ATATATATATATATATATATATATATATATATATA 49 chr1ptel1M 252781 GGGA-ACACACATATAGAAATACCTACAAGTATACATAGATATGGGAAGA 252829 viv - i i i v v iv i vi i v iviv v (AT)n#Simple_ 50 TATATATATATATATATATATATATATATATATATATATATATATATATA 99 chr1ptel1M 252830 TGTGTGTATATATGTACATGTGTAAATATATATAGGAATATATA 252873 i i i i i i i v viv (AT)n#Simple_ 100 TATATATATATATATATATATATATATATATATATATATATATA 143 Matrix = Unknown Transitions / transversions = 1.80 (27/15) Gap_init rate = 0.03 (4 / 140), avg. gap size = 1.00 (4 / 4) 241 30.41 6.76 7.37 chr1ptel1M 253122 253476 (746524) C L1PREC2_orf2#LINE/L1 (2910) 384 32 m_b7s551i4 285 chr1ptel1M 253122 AACTTGTTCTCTAAGAATTTGGTTGCTATATCACCTAT------TACATA 253165 -- i v i v ------ i ------ i C L1PREC2_orf2# 384 AACTTG--CTTTATGAATCTGGGTGCT------CCTGTGTTGGGTGCATA 343 chr1ptel1M 253166 TATGTTTAGTATGGATATTACATCATTATCAATGGTACCATTTAGCAAGA 253215 i v i v vvv v v vv v v v v v vv C L1PREC2_orf2# 342 TATATTTAGGATAGTTAGGTCTTCTTGTTGAATTGAACCCTTTACCATTA 293 chr1ptel1M 253216 TATAGTTTCCTTCTTTAACTCTTTTAATTAGACACATTTTTGCTTT---- 253261 i i vi iv i i ------ v v v ---- C L1PREC2_orf2# 292 TGTAATGCCCTTCTTTGTCTTTTTTGAT------CTTTGTTGGTTTAAAG 249 chr1ptel1M 253262 --TGTTTGATCTGAGATCAGGATCATTACCCCTGCTTTTTTTTACTT--C 253307 -- vi i i iiiv i ii -- C L1PREC2_orf2# 248 TCTGTTTTGTCTGAAATTAGGATTGCAACCCCTGCTTTTTTCTGTTTTCC 199 chr1ptel1M 253308 ACCTGAAGCATAATACATTCCACCCCAGCCGTTTTCCTTCACTCTGTATG 253357 ii --- v ii v iiv i v v vii v vi i iv C L1PREC2_orf2# 198 ATTT---GCTTGGTAGATTTTTCTCCATCCCTTTATTTTGAGCCTATGGG 152 chr1ptel1M 253358 TATCATTCTGATTTAAATGAGTTTCTTATGAACAACAT---ATTGGAATA 253404 i viivv v i i i ivii i --- i--- C L1PREC2_orf2# 151 TGTCATTGCATGTGAGATGGGTCTCTTGAAGACAGCATACCATTGGG--- 105 chr1ptel1M 253405 TTCTGGCT--TTAATTCAGTCTGTTATCCACTTT---CATTTTA--TGTG 253447 - v -- v i ii ---- i --- v -- v C L1PREC2_orf2# 104 -TCTTGCTTCTTTATCCAGCTTG----CCACTCTGTGCCTTTTAATTGGG 60 chr1ptel1M 253448 AGAGTTGACATCATTCACATTCACAGTTA 253476 iv v ii -i i vi C L1PREC2_orf2# 59 GCATTTAGC-CCATTTACATTCAAGGTTA 32 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.76 CpG sites = 54, Kimura (unadjusted) = 39.76 Transitions / transversions = 1.17 (54/46) Gap_init rate = 0.10 (34 / 354), avg. gap size = 1.47 (50 / 34) 280 30.88 0.72 1.46 chr1ptel1M 253260 253397 (746603) C L1MC_orf2#LINE/L1 (3046) 248 112 m_b7s551i5 285 chr1ptel1M 253260 TTTGTTTGATCTGAGATCAGGATCATTACCCCTGCTTTTTTTTACTTCAC 253309 i i ivi i i iv vii i ? i iv vii C L1MC_orf2#LIN 248 TCTGCTCTGTCTGAAATTAATATAGCTACTCCNGCTTTCTTTTGATTAGT 199 chr1ptel1M 253310 CTGAAGCATAATACATTCCACCCCAGCCGTTTTCCTTCACTCTGTATGTA 253359 v v - ii i iiiv i v ? v i i v i i C L1MC_orf2#LIN 198 GTTA-GCATGGTATATCTTTCTCCATCCNTTTACTTTTAATCTATATGTG 150 chr1ptel1M 253360 TCATTCTGATTTAAA-TGAGTTTCTTATGAACAACATAT 253397 v v - - i i ii C L1MC_orf2#LIN 149 TCTTTAT-ATTTAAAGTGGGTTTCTTGTAGACAACATAT 112 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 43.13 CpG sites = 29, Kimura (unadjusted) = 43.13 Transitions / transversions = 2.23 (29/13) Gap_init rate = 0.02 (3 / 137), avg. gap size = 1.00 (3 / 3) 473 31.53 2.39 6.63 chr1ptel1M 253738 254114 (745886) L1HS_3end#LINE/L1 208 569 (333) m_b7s551i6 286 chr1ptel1M 253738 AGAATAACAATCATATTGGCTAAGATGACAGGAAAAAATAATGATGATTG 253787 ii ------ i v v v i iv------ L1HS_3end#LIN 208 AGAATGGCAATCAT------TAAAAAGTCAGGAAACAACAGG------TG 245 chr1ptel1M 253788 TTGGAGGGGATGCGGGAAAACTGGGACATTGATGCATTGTTGGTGGAGTT 253837 i i ii iv i i vv i i iii L1HS_3end#LIN 246 CTGGAGAGGATGCGGAGAAATAGGAACACTTTTACACTGTTGGTGGGACT 295 chr1ptel1M 253838 GTGAACGAATCCAACCATTTTGGAGAGTAGTTTGGAACTATGCTCAAAAA 253887 i v i i v iivi v viv - v iii L1HS_3end#LIN 296 GTAAACTAGTTCAACCATTGTGGAAGTCAGTGTGGCGAT-TCCTCAGGGA 344 chr1ptel1M 253888 GTTATCAAACTGTGCATCCCAGTAGATCCAGCAGTGTTACTACTGGGATT 253937 vi --i iviv v v v i vi vii i -- L1HS_3end#LIN 345 TCTA--GAACTAGAAATACCATTTGACCCAGCCATCCCATTACTGGG--T 390 chr1ptel1M 253938 ATAT-CCCAAAGAGATTATAAAGAAGGG------AAAGGGACCTGTATGT 253980 - - i vv v v------ iv ---- i L1HS_3end#LIN 391 ATATACCCAAAG-GACTATAAATCATGCTGCTATAAAGACAC----ATGC 435 chr1ptel1M 253981 GCACGAATGTTTGTGGCAGCCCTTTTTGTAGTGGCTAGAAACTGGAAACT 254030 i v i v i v v iii i i - i i v i i L1HS_3end#LIN 436 ACACGTATGTTTATTGCGGCACTATTCACAATAGC-AAAGACTTGGAACC 484 chr1ptel1M 254031 GA-ATGGATGTCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATATG 254079 i -viii v i viv v v v v v i i i L1HS_3end#LIN 485 AACCCAAATGTCCAACAATGATAGACTGGATTAAGAAAATGTGGCACATA 534 chr1ptel1M 254080 AAAATTATGGAATATTACTGT-TCTGTAAGAAATGA 254114 v v ii i - i-v ii i L1HS_3end#LIN 535 TACACCATGGAATACTA-TGCAGCCATAAAAAATGA 569 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.23 CpG sites = 67, Kimura (unadjusted) = 42.25 Transitions / transversions = 1.52 (67/44) Gap_init rate = 0.07 (28 / 376), avg. gap size = 1.18 (33 / 28) 764 27.81 3.36 2.11 chr1ptel1M 253770 254096 (745904) L1ME4c_3end#LINE/L1 224 554 (276) m_b7s551i7 286 chr1ptel1M 253770 AAAAAATAATGATGAT------TGTTGGAGGGGATGCGGGAAAACTGGGA 253813 -- i ------ i v i ? vi v L1ME4c_3end#L 224 AAAAAAT--TGATAATACCCAATGCTGGCGAGGNTGCGGTGAAACTGGTA 271 chr1ptel1M 253814 CATTGATGCATTGTTGGTGGAGTTGTGAACGAATCCAACCATTTTGGAGA 253863 ?i v i i vi? i ivii v v i L1ME4c_3end#L 272 CNCTCATACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAAA 321 chr1ptel1M 253864 GTAGTTTGGAACTATGCTCAAAAAGTTATCAAACTGTGCATCCCAGTAGA 253913 i i v v i iviv i ii v v v v vv v L1ME4c_3end#L 322 GCAATTTGGCAATACGTATCAAGAGCCATAAAAATGTTCATACCCTTTGA 371 chr1ptel1M 253914 TCCAGCAGTGTTACTACTGGGATTATATCCCAAAGAGATTAT---AAAGA 253960 i i i vii v v v i i i v --- L1ME4c_3end#L 372 CCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAAGA 421 chr1ptel1M 253961 AGGGAAAGGGACCTGTATGTGCACGAA--TGTTTGTGGCAGCCCTTTTTG 254008 i i v----- i -- ii v vi v i L1ME4c_3end#L 422 AGGAAAAAGC-----TATATGCACGAAGATGTTCATTGCAGCGTTATTTA 466 chr1ptel1M 254009 TAGTGGCTAGAAACTGGAAACTGAATGGATGTCCATCAGTTGGAGAATGG 254058 i i v i i vivv ii v i v i L1ME4c_3end#L 467 TAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAATGG 516 chr1ptel1M 254059 CTGAATAAATTGTGGTATATGAAAATTATGGAATATTA 254096 i i i i i v? vviv L1ME4c_3end#L 517 TTAAGTAAATTATGGTACATCNACTCGATGGAATATTA 554 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.13 CpG sites = 51, Kimura (unadjusted) = 36.14 Transitions / transversions = 1.34 (51/38) Gap_init rate = 0.03 (10 / 326), avg. gap size = 1.80 (18 / 10) 426 29.77 4.33 5.13 chr1ptel1M 253786 254178 (745822) L1MC1_3end#LINE/L1 244 633 (447) m_b7s551i8 286 chr1ptel1M 253786 TGTTGGAGGGGATGCGGGAAAACTGGGACATTGATGCATTGTTGGTGGAG 253835 i v i i iiv v i vi v v i ii L1MC1_3end#LI 244 TGCTGGCGAGGATGTGGAGCAACAGGAACTCTCATTCATTGCTGGTGGGA 293 chr1ptel1M 253836 TTGTGAACGAATCCAACCATTTTGGAGAGTAGTTTGGAACTATGCTCA-A 253884 v ii vvii v i i iiii v v - v i - L1MC1_3end#LI 294 ATGCAAAATGGTACAGCCACTTTGGAAGACAGTTTGGCAGT-TTCTTACA 342 chr1ptel1M 253885 AAAGTTATCAAACTGTGCATCCCAGTA-GATCCAGCAGTGTTACTACTGG 253933 v v v v v --- v - - i vvii v v L1MC1_3end#LI 343 AAACTAAACATACTCT---TACCA-TACGATCCAGCAATCGCGCTCCTTG 388 chr1ptel1M 253934 G-ATTATATCCCAAAGAGATTATAAA-----GAAGGGAAAGGGACCTGTA 253977 - - - iii iv ----- vvviv v iii i L1MC1_3end#LI 389 GTATT-TA-CCCAAAGGAGTTGAAAACTTATGTCCACACAAAAACCTGCA 436 chr1ptel1M 253978 TGTGCACGAATGTTTGTGGCAGCCCTTTTTGTAGTGGCTAGAAACTGGAA 254027 ---- i i i ii v ii i v i i vi L1MC1_3end#LI 437 ----CACGGATGTTTATAGCAGCTTTATTCATAATTGCCAAAACTTGGAA 482 chr1ptel1M 254028 ACTGAAT--GGATGTCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTA 254075 i -- i--i v v v v i i L1MC1_3end#LI 483 GC--AACCAAGATGTCCTTCAGTAGGTGAATGGATAAATAAACTGTGGTA 530 chr1ptel1M 254076 TATGAAAATTATGGAATATTACT--GTTCT-GTAAGAAATGA-CCAACAG 254121 i vv i iv i -- iv -iv - i v i L1MC1_3end#LI 531 CATCCAGACAATGGAATATTATTCAGCGCTAAAAAGAAATGAGCTATCAA 580 chr1ptel1M 254122 G--ATGATTTCAGAAAGGCCTGGA-GAGACTTACACGAACTGATGCTGAG 254168 -- ------ i v - i v i v - iv i i L1MC1_3end#LI 581 GCCATGA------AAAGACATGGAGGAAACTTAAATGCA-TATTACTAAG 623 chr1ptel1M 254169 TGAAATGAGC 254178 vi L1MC1_3end#LI 624 TGAAAGAAGC 633 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.97 CpG sites = 64, Kimura (unadjusted) = 38.92 Transitions / transversions = 1.36 (64/47) Gap_init rate = 0.08 (30 / 392), avg. gap size = 1.23 (37 / 30) 22 19.38 0.00 0.00 chr1ptel1M 254650 254690 (745310) (A)n#Simple_repeat 1 41 (0) m_b7s252i16 287 chr1ptel1M 254650 AAAAAAAAAAAAAAAAAAAAAAGAGAATAACAATCATAAAA 254690 i i v v vv v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 41 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 203 29.27 9.00 0.93 chr1ptel1M 255790 255889 (744111) C MIRc#SINE/MIR (157) 111 4 m_b7s601i16 288 chr1ptel1M 255790 TTAAATTACTTTGCTAAAAAACACAGAG---GTA-----CAGAACCCAAA 255831 i v - iv iiv v --- ----- i vii C MIRc#SINE/MIR 111 TTAAGTGACTT-GCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGA 63 chr1ptel1M 255832 TATCAACCCATGTCTTCA-GAATCCATATCTAGCCATCTTTACATTCCAC 255880 iviv v v- v vi i ivv v i v C MIRc#SINE/MIR 62 CTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCAC 13 chr1ptel1M 255881 CAGACTGCC 255889 v C MIRc#SINE/MIR 12 CACACTGCC 4 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.81 CpG sites = 13, Kimura (unadjusted) = 37.36 Transitions / transversions = 0.81 (13/16) Gap_init rate = 0.04 (4 / 99), avg. gap size = 2.50 (10 / 4) 21 0.00 0.00 0.00 chr1ptel1M 258373 258395 (741605) (A)n#Simple_repeat 1 23 (0) m_b7s252i17 289 chr1ptel1M 258373 AAAAAAAAAAAAAAAAAAAAAAA 258395 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAA 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 320 23.50 0.00 9.59 chr1ptel1M 260213 260292 (739708) MIRc#SINE/MIR 37 109 (159) m_b8s601i0 290 chr1ptel1M 260213 TGCAGTCAGGAAGAGCAGAGTTCAAATTTGGACTCAGGTACTTAACACTT 260262 v v v i i i iiv i --- i ---- MIRc#SINE/MIR 37 TGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTC---TGC----CACTT 79 chr1ptel1M 260263 GCTAACTTTGTGACCCTAGACAAGTCACTT 260292 i i v i i i MIRc#SINE/MIR 80 ACTAGCTGTGTGACCTTGGGCAAGTCACTT 109 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.99 CpG sites = 12, Kimura (unadjusted) = 29.00 Transitions / transversions = 2.40 (12/5) Gap_init rate = 0.09 (7 / 79), avg. gap size = 1.00 (7 / 7) 12 9.78 0.00 0.00 chr1ptel1M 260300 260321 (739679) (ATAA)n#Simple_repeat 1 22 (0) m_b8s252i0 291 chr1ptel1M 260300 ATCAAAAAATAAATAAATAAAT 260321 v v (ATAA)n#Simpl 1 ATAAATAAATAAATAAATAAAT 22 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 456 25.74 19.63 1.99 chr1ptel1M 260328 260541 (739459) MIRb#SINE/MIR 8 258 (10) m_b8s601i1 292 chr1ptel1M 260328 GCAGTTGATGGTACAGTGGATAGAGC-----TTTT--AATCATGAAGACC 260370 i--i i v -----i -- i viv MIRb#SINE/MIR 8 GCAGC--GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACC 55 chr1ptel1M 260371 TGAGTTTTAATCCCACCTCAAACAG--GCTAGTCA----ATTTT---CAG 260411 i iv iv viv v--i iii---- ii --- i MIRb#SINE/MIR 56 TGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 105 chr1ptel1M 260412 G--ACT---CCTGTTTG--CCTCAGTTTCTTAAACTGTAAAATGAGCATA 260454 -- --- v i -- i v v i v MIRb#SINE/MIR 106 GTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATA 155 chr1ptel1M 260455 ACAGTGACACTTAATTC-TAGGCTTCTCATGAGGATAAAATGAGACAA-- 260501 --- i i i vi -i v v ii v i -- MIRb#SINE/MIR 156 A---TAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATG 202 chr1ptel1M 260502 ----------------CACAGTGCATGACATACATTAGGTGCTATAGAAA 260535 ---------------- v i i i v i i vv v MIRb#SINE/MIR 203 CATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAAA 252 chr1ptel1M 260536 TGGTAG 260541 MIRb#SINE/MIR 253 TGGTAG 258 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.58 CpG sites = 33, Kimura (unadjusted) = 32.52 Transitions / transversions = 1.57 (33/21) Gap_init rate = 0.08 (16 / 213), avg. gap size = 2.94 (47 / 16) 16 9.78 0.00 0.00 chr1ptel1M 262814 262835 (737165) (T)n#Simple_repeat 1 22 (0) m_b8s252i1 293 chr1ptel1M 262814 TTTTTTTAATTTTTTTTTTTTT 262835 vv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTT 22 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 212 31.17 2.53 2.53 chr1ptel1M 264522 264600 (735400) MIRc#SINE/MIR 37 115 (153) m_b8s601i2 294 chr1ptel1M 264522 TGCAGTCAGGAGCACTTTAAATCTGAACTGAGACACTTAATACTTCCTAG 264571 v iv i -iii ii iiivv i v -ivi v MIRc#SINE/MIR 37 TGGAGTCAGGAAGACCT-GGGTTCGAGTCCCGGCTCT-GCCACTTACTAG 84 chr1ptel1M 264572 CTGTGTGACCCTGGGCATGTGAC--AACCCC 264600 i v v -- i MIRc#SINE/MIR 85 CTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.65 CpG sites = 15, Kimura (unadjusted) = 41.97 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.04 (3 / 78), avg. gap size = 1.33 (4 / 3) 188 18.37 6.12 0.00 chr1ptel1M 264563 264611 (735389) MIR#SINE/MIR 72 123 (139) m_b8s601i3 294 chr1ptel1M 264563 ACTTCCTAGCTGTGTGACCCTGGGCATGTGAC--AACCCCAAT-TACCCC 264609 v i v v -- i vv - i i MIR#SINE/MIR 72 ACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTC 121 chr1ptel1M 264610 AG 264611 MIR#SINE/MIR 122 AG 123 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 21.12 CpG sites = 4, Kimura (unadjusted) = 21.12 Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.04 (2 / 48), avg. gap size = 1.50 (3 / 2) 297 30.30 12.27 2.49 chr1ptel1M 264628 264847 (735153) MIRc#SINE/MIR 6 246 (22) m_b8s601i4 295 chr1ptel1M 264628 CAGAGTGGAGCTACTGGTACAGAGGATAAAGCTTTTAATCATGAAGACCT 264677 v v - v - v v iviii vv i v MIRc#SINE/MIR 6 CAGTGTGGTGC-AGTGG-AAAGAGCACTGGACTTGGAGTCAGGAAGACCT 53 chr1ptel1M 264678 GAGTTTTATTCGCACCTC----ATAAACTGGCTA-GTCAATTTA--TAGG 264720 i iv v v iv ---- ivv i i- v vi i--i i MIRc#SINE/MIR 54 GGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAG 103 chr1ptel1M 264721 ------ATCCTGTTTG--CCTCAGTTTCTTATTCTTTAAAATGCACATAA 264762 ------ v v i -- i vv v viv MIRc#SINE/MIR 104 TCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAA 153 chr1ptel1M 264763 CAAT-----CACT-CCTA-ATCCTAGGGTTCTCATGAAGATAAAGTAAGA 264805 i ----- v - -v vi v ii i v i i - MIRc#SINE/MIR 154 TAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAG- 202 chr1ptel1M 264806 GCATAGTGTAT-----AACACAGTAGATGCTGTAGAAATGCTATTCA 264847 -- i ----- i i vv iv vi - i v MIRc#SINE/MIR 203 --ATAATGTATGTGAAAGCGCTTTGTAAACTGTA-AAGTGCTATACA 246 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.09 CpG sites = 31, Kimura (unadjusted) = 39.32 Transitions / transversions = 0.91 (31/34) Gap_init rate = 0.07 (15 / 219), avg. gap size = 2.20 (33 / 15) 204 27.93 11.48 4.62 chr1ptel1M 264861 265104 (734896) L2d_3end#LINE/L2 249 508 (8) m_b8s601i5 296 chr1ptel1M 264861 TGACTATTCCCTCCCCAGTTGTTCTCT-CCTTCTTT-AACCATTA----- 264903 i i vv vvii v - i - ivi ----- L2d_3end#LINE 249 TGACCACTCCAGCCCACACTGATCTCTCCCTTCTCTGAACTCCTATAGCA 298 chr1ptel1M 264904 -TTATCCTCACTAATAAATGATTTAGTGAGGCACTAAATTGATCTAC--T 264950 - vv vv vi viii ----- v - v -- L2d_3end#LINE 299 CTTATAGTCTGTACCACGCAATTTA-----GCACTTAATT-ATATACTGT 342 chr1ptel1M 264951 TTTGTG--GTTCATGGTGTTG-TTCATGTTTGTATAG---TGTCTGCCCT 264994 i i-- - vvvi - v - --- v v L2d_3end#LINE 343 CTTGTATTGTTC-TCTAATTGTTTCATGTGTGT-TAGTCTTGTCTCCCCA 390 chr1ptel1M 264995 GGAAGTCTGTGGACTCCAGGAGAGCAGGGG--ATGACCCTTGTA-TCTCT 265041 ivv vi iii vv i i-- --i i - ? i L2d_3end#LINE 391 ACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATG--TCTTATACTNTTT 438 chr1ptel1M 265042 TGTTGTTTC---TAGTCCTTAACTCAGGGACTG-GTGC--AGCAGGCACT 265085 ? i i ---i iv i i v v - - ii -- i i L2d_3end#LINE 439 TNTCGTTCCCCACAGCGCCTAGCACAGTG-CTGAGCACATAGTAGGCGCT 487 chr1ptel1M 265086 ---TAAATTTTTGCTGACTTGA 265104 --- vi i - L2d_3end#LINE 488 CAATAAATACTTGTTGA-TTGA 508 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.46 CpG sites = 36, Kimura (unadjusted) = 36.18 Transitions / transversions = 1.24 (36/29) Gap_init rate = 0.11 (26 / 243), avg. gap size = 1.54 (40 / 26) 249 28.25 11.11 4.48 chr1ptel1M 264985 265110 (734890) L2b_3end#LINE/L2 333 466 (0) m_b8s601i6 296 chr1ptel1M 264985 TGTCTGCCCTGGAAGTCTGTGGACTCCAGGAGAGCAGGGGATGACCCTTG 265034 v iivv v ii iv i i----- v? L2b_3end#LINE 333 TGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGA-----CCGNG 377 chr1ptel1M 265035 TATCTCTTGT---------TGTTTCTAGTCCTTAACTCAGGGACTGG--T 265073 v v --------- i ii i iv i i v ? v --i L2b_3end#LINE 378 TCTGTCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCAC 427 chr1ptel1M 265074 GCAGCAGGCACT---TAAATTTTTGCTGACTTGAAGAAAT 265110 i i i --- v i v- vi L2b_3end#LINE 428 ACAGTAGGCGCTCAGTAAATATTTGTTGAA-TGAATGAAT 466 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.31 CpG sites = 20, Kimura (unadjusted) = 37.36 Transitions / transversions = 1.43 (20/14) Gap_init rate = 0.07 (9 / 125), avg. gap size = 2.22 (20 / 9) 252 28.07 6.67 1.05 chr1ptel1M 265191 265280 (734720) C MIR3#SINE/MIR (3) 205 111 m_b8s601i7 297 chr1ptel1M 265191 TTATAGGGTCATAAATAATCA---TTGGAAGGAATCTACAGAG-CCACAG 265236 i ii i vvi ---i i i -i -i ivv C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCT-TAGAGATCATCT 157 chr1ptel1M 265237 AGCACAACCTACTTATTTTATA-ATG-GGAAACTGAGATTCAGTGA 265280 iv iv i i - - iii v C MIR3#SINE/MIR 156 AGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGA 111 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.28 CpG sites = 18, Kimura (unadjusted) = 37.28 Transitions / transversions = 2.57 (18/7) Gap_init rate = 0.06 (5 / 89), avg. gap size = 1.40 (7 / 5) 28 4.69 4.55 0.00 chr1ptel1M 266316 266359 (733641) (AACAAA)n#Simple_repeat 1 46 (0) m_b8s252i2 298 chr1ptel1M 266316 AAAAAAAACAAAAATAAAAACAAAAACAAAAAC--AAACAAAAACA 266359 v i -- (AACAAA)n#Sim 1 AACAAAAACAAAAACAAAAACAAAAACAAAAACAAAAACAAAAACA 46 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.02 (1 / 43), avg. gap size = 2.00 (2 / 1) 321 25.73 8.15 2.10 chr1ptel1M 266559 266693 (733307) C MIR3#SINE/MIR (2) 206 64 m_b8s601i8 299 chr1ptel1M 266559 ATCA-AAAGCCATAAGATGT-AGAGCTGAAAAATACTTCAGA-ATTGAAA 266605 - i ii ii - i iiv i i - iivvv C MIR3#SINE/MIR 206 ATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCT 157 chr1ptel1M 266606 AGTCCAGCCCTCCTCCATTTACAG--GAGGAAACTGA-----AAAGCAGG 266648 i - vv -- ----- i vi v C MIR3#SINE/MIR 156 AGTCCAACCC-CCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGT 108 chr1ptel1M 266649 GAAAAGAATTGCCCCAAAGGTCATCCTTTTA-TGAGTGTCAGAGTC 266693 iv v -- iv vvi? - v v i C MIR3#SINE/MIR 107 GAAGTGACTTGCCC--AAGGTCACACAGCNAGTTAGTGGCAGAGCC 64 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.43 CpG sites = 19, Kimura (unadjusted) = 32.43 Transitions / transversions = 1.27 (19/15) Gap_init rate = 0.07 (9 / 134), avg. gap size = 1.56 (14 / 9) 213 27.54 10.11 2.08 chr1ptel1M 266618 266706 (733294) C MIRc#SINE/MIR (119) 149 54 m_b8s601i9 299 chr1ptel1M 266618 CTCCATTT-ACAG--GAGGAAACTGAAAAGCAGGGAA---AA--GAATTG 266659 i - -- iivv i i--- -- v C MIRc#SINE/MIR 149 CCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTG 100 chr1ptel1M 266660 CCCCAAAGGTCATCCTTTTA-TGAGTGTCAGAGTCAACCCTTAAATTC 266706 -- iv vvi - i v i iivv ii ii C MIRc#SINE/MIR 99 CCC--AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCC 54 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.72 CpG sites = 15, Kimura (unadjusted) = 35.53 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.08 (7 / 88), avg. gap size = 1.57 (11 / 7) 266 29.71 1.05 7.87 chr1ptel1M 267406 267500 (732500) MIRc#SINE/MIR 39 127 (141) m_b8s601i10 300 chr1ptel1M 267406 GAGATAGGAGAATGTGAGTTCAAATATGGTCTCAGATACTTAAAACTTCC 267455 vi ii iv i i i viv v v vi ------- MIRc#SINE/MIR 39 GAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTA-------C 81 chr1ptel1M 267456 TACCTGTGTGACCCTGGCCAAATCATTCAACCCCAATT-GCCTCAG 267500 v i v i i i i vv v- MIRc#SINE/MIR 82 TAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.43 CpG sites = 14, Kimura (unadjusted) = 38.27 Transitions / transversions = 1.17 (14/12) Gap_init rate = 0.09 (8 / 94), avg. gap size = 1.00 (8 / 8) 28 5.80 9.26 0.00 chr1ptel1M 267501 267554 (732446) (AAGAA)n#Simple_repeat 1 59 (0) m_b8s252i5 301 chr1ptel1M 267501 AAAAAAAGAAAAGAAAAG-AAA-TAAAGAAAAG-GAA-AAAAGAAAAG-A 267545 i - -v -i - - (AAGAA)n#Simp 1 AAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAA 50 chr1ptel1M 267546 AAGAAAAGA 267554 (AAGAA)n#Simp 51 AAGAAAAGA 59 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.09 (5 / 53), avg. gap size = 1.00 (5 / 5) 235 28.68 3.20 2.38 chr1ptel1M 269007 269131 (730869) L1M2_orf2#LINE/L1 1620 1745 (1546) m_b8s551i0 302 chr1ptel1M 269007 AATTTTAAACAATATCCTATCAAA----ATGCCACAGAAAATTATCTAAA 269052 ii v v v v ---- v v v v --- L1M2_orf2#LIN 1620 AATCCTCAACAAAATACTAGCAAACCGAATTCAACAGCACATTA---AAA 1666 chr1ptel1M 269053 AAACCATTCATTATGATCAAATGGGTATGGTACTGGGGATAGAAGGATAG 269102 i i? ? ii i vv vi v ii iv i L1M2_orf2#LIN 1667 AGATNATNCACCATGATCAAGTGGGATTTATCCCAGGGATGCAAGGATGG 1716 chr1ptel1M 269103 TTTGACAGTTGGAAAACAATGAACATTAT 269131 ii vvi v v i i v L1M2_orf2#LIN 1717 TTCAACATACGCAAATCAATAAACGTGAT 1745 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.74 CpG sites = 17, Kimura (unadjusted) = 37.32 Transitions / transversions = 0.94 (17/18) Gap_init rate = 0.03 (4 / 124), avg. gap size = 1.75 (7 / 4) 245 27.69 0.00 0.00 chr1ptel1M 269045 269109 (730891) L1PB_orf2#LINE/L1 1662 1726 (1568) m_b8s551i1 302 chr1ptel1M 269045 TATCTAAAAAACCATTCATTATGATCAAATGGGTATGGTACTGGGGATAG 269094 v i iv i ii i v vi ii iv L1PB_orf2#LIN 1662 TATCAAAAAGATAATCCACCATGATCAAGTGGGTTTCATACCAGGGATGC 1711 chr1ptel1M 269095 AAGGATAGTTTGACA 269109 i i i L1PB_orf2#LIN 1712 AGGGATGGTTTAACA 1726 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.58 CpG sites = 13, Kimura (unadjusted) = 36.58 Transitions / transversions = 2.60 (13/5) Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0) 14 18.34 2.50 2.50 chr1ptel1M 270314 270353 (729647) (CTTCT)n#Simple_repeat 1 40 (0) m_b8s252i6 303 chr1ptel1M 270314 CTTCTCCCCTACTTTTATTCCCTTCTCTTCTC-TCTCCTCT 270353 ii - i v i - i (CTTCT)n#Simp 1 CTTCTCTTCT-CTTCTCTTCTCTTCTCTTCTCTTCTCTTCT 40 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 12 17.67 2.38 4.88 chr1ptel1M 271203 271244 (728756) (TGGGAT)n#Simple_repeat 1 41 (0) m_b8s252i7 304 chr1ptel1M 271203 TGGGA-AGGGATTGGGACTCTGGAAATGGTTTAGGGATTGGGA 271244 -v - - i v vv v (TGGGAT)n#Sim 1 TGGGATTGGGATTGGGA-T-TGGGATTGGGATTGGGATTGGGA 41 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.07 (3 / 41), avg. gap size = 1.00 (3 / 3) 26 19.36 5.95 1.14 chr1ptel1M 271950 272033 (727967) (TATATTA)n#Simple_repeat 1 88 (0) m_b8s252i8 305 chr1ptel1M 271950 TAT-TTTTAT-TTAT-TCTTTTTTATTATATATCATATACAATATCATAT 271996 - v - - v v v i iv vv (TATATTA)n#Si 1 TATATTATATATTATATATTATATATTATATATTATATATTATATATTAT 50 chr1ptel1M 271997 ACAATTATGTATCATATA-CA-ATATTATATATCATATA 272033 -v i i -i - i (TATATTA)n#Si 51 A-TATTATATATTATATATTATATATTATATATTATATA 88 Matrix = Unknown Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.07 (6 / 83), avg. gap size = 1.00 (6 / 6) 17 2.94 11.43 0.00 chr1ptel1M 274494 274528 (725472) (ACATAT)n#Simple_repeat 1 39 (0) m_b8s252i9 306 chr1ptel1M 274494 ACATATA-A-AT-CATATACATATGCATATACATA-ACA 274528 - - - i - (ACATAT)n#Sim 1 ACATATACATATACATATACATATACATATACATATACA 39 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.12 (4 / 34), avg. gap size = 1.00 (4 / 4) 22 0.00 0.00 0.00 chr1ptel1M 275224 275247 (724753) (A)n#Simple_repeat 1 24 (0) m_b8s252i10 307 chr1ptel1M 275224 AAAAAAAAAAAAAAAAAAAAAAAA 275247 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAA 24 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 12 4.35 8.33 0.00 chr1ptel1M 275262 275285 (724715) (AGAGG)n#Simple_repeat 1 26 (0) m_b8s252i11 308 chr1ptel1M 275262 AGA-GAGAGG-GAGGGGAGGAGAGGA 275285 - - i (AGAGG)n#Simp 1 AGAGGAGAGGAGAGGAGAGGAGAGGA 26 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.09 (2 / 23), avg. gap size = 1.00 (2 / 2) 25 0.00 0.00 0.00 chr1ptel1M 279923 279949 (720051) (A)n#Simple_repeat 1 27 (0) m_b8s252i12 309 chr1ptel1M 279923 AAAAAAAAAAAAAAAAAAAAAAAAAAA 279949 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAA 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 224 26.65 9.21 1.22 chr1ptel1M 280279 280354 (719646) MIRc#SINE/MIR 69 150 (118) m_b8s601i11 310 chr1ptel1M 280279 CTCTGACACGCATAAATGGTATGGCCTTTGAGCAAATCACTT---CTCTT 280325 v vi iv iiv i i - i i --- i MIRc#SINE/MIR 69 CTCTGCCACTTACTAGCTGTGTGACCTT-GGGCAAGTCACTTAACCTCTC 117 chr1ptel1M 280326 TG--TTTCAGTTTCATC--CTCTAAATTGAAGA 280354 --ii v -- v v ii MIRc#SINE/MIR 118 TGAGCCTCAGTTTCCTCATCTGTAAAATGGGGA 150 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.16 CpG sites = 13, Kimura (unadjusted) = 34.16 Transitions / transversions = 1.86 (13/7) Gap_init rate = 0.05 (4 / 75), avg. gap size = 2.00 (8 / 4) 194 26.42 1.89 0.00 chr1ptel1M 281508 281560 (718440) C MIRb#SINE/MIR (7) 261 208 m_b8s601i12 311 chr1ptel1M 281508 GAGTAAGCATTTATTT-TCACCTACAATTTGCCAGGTGCTGTGCTATATG 281556 iv v v-v i i v v ii vii C MIRb#SINE/MIR 261 GAGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCG 212 chr1ptel1M 281557 CTTT 281560 C MIRb#SINE/MIR 211 CTTT 208 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.57 CpG sites = 7, Kimura (unadjusted) = 32.90 Transitions / transversions = 1.00 (7/7) Gap_init rate = 0.02 (1 / 52), avg. gap size = 1.00 (1 / 1) 504 28.25 4.84 1.04 chr1ptel1M 281877 282062 (717938) C MIR#SINE/MIR (64) 198 6 m_b8s601i13 311 chr1ptel1M 281877 TATTATGTCATCTTATCTTCACAATAATCTTCTAAGTTAGGTGATATTAT 281926 vv i v i i i i v i v iv C MIR#SINE/MIR 198 TATTAACTCATTTAATCCTCACAACAACCCTATGAGGTAGGTACTATTAT 149 chr1ptel1M 281927 TCTCCCCATTTAAGAGTC----AAAC--AGGCAAACAGAGTTCAAGT-AC 281969 v v v vi---- -- v v v i - C MIR#SINE/MIR 148 TATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAAC 99 chr1ptel1M 281970 TTGCTAAGGGGTACAGAGCTAGGAACTTCTTGAAGCTTGATTTAAGCTCA 282019 iv i vi v v v vviv iv vv ii i i C MIR#SINE/MIR 98 TTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCA 49 chr1ptel1M 282020 GGCACTTCTGGCTCTAT-GCTCAGGTCTCTCAA-CATTGTGGTAT 282062 -v i v- i iv - i - i i v C MIR#SINE/MIR 48 GGCA-GTCTGGCTCCAGAGCCCGTG-CTCTTAACCACTATGCTAT 6 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.98 CpG sites = 24, Kimura (unadjusted) = 35.71 Transitions / transversions = 0.86 (24/28) Gap_init rate = 0.04 (7 / 185), avg. gap size = 1.57 (11 / 7) 28 3.13 0.00 0.00 chr1ptel1M 283303 283335 (716665) (A)n#Simple_repeat 1 33 (0) m_b8s252i13 312 chr1ptel1M 283303 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAA 283335 i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 33 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 15 17.23 2.44 2.44 chr1ptel1M 284876 284916 (715084) (AAAAC)n#Simple_repeat 1 41 (0) m_b8s252i14 313 chr1ptel1M 284876 AAAACAAAAC-AAACAAATAAAAAACTGCTCAAAACTAAACA 284916 - - v vivv v (AAAAC)n#Simp 1 AAAACAAAACAAAACAAA-ACAAAACAAAACAAAACAAAACA 41 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 22 3.81 0.00 0.00 chr1ptel1M 285860 285886 (714114) (A)n#Simple_repeat 1 27 (0) m_b8s252i15 314 chr1ptel1M 285860 AAAAAAAAAAAACAAAAAAAAAAAAAA 285886 v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAA 27 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 17 0.00 0.00 0.00 chr1ptel1M 287158 287176 (712824) (A)n#Simple_repeat 1 19 (0) m_b8s252i16 315 chr1ptel1M 287158 AAAAAAAAAAAAAAAAAAA 287176 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAA 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 492 19.33 0.89 7.62 chr1ptel1M 287284 287395 (712605) MIRc#SINE/MIR 11 115 (153) m_b8s601i14 316 chr1ptel1M 287284 TGGCACAGTGGATAGAGCACCAGCCCTGAAGTCAGGAGGACCTGAGTTCA 287333 ii v ii v i i i i i MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr1ptel1M 287334 AAAATGGTCTCAGACACT-TAACACTTCCTAGCCGTGTGACCCTGGGCAA 287382 ----- i i --- - iv v i i MIRc#SINE/MIR 61 A-----GTCCCGG---CTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 102 chr1ptel1M 287383 ATCACTTAACCCC 287395 i i MIRc#SINE/MIR 103 GTCACTTAACCTC 115 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 20.67 CpG sites = 16, Kimura (unadjusted) = 23.25 Transitions / transversions = 4.00 (16/4) Gap_init rate = 0.08 (9 / 111), avg. gap size = 1.00 (9 / 9) 22 12.84 0.00 0.00 chr1ptel1M 287408 287441 (712559) (A)n#Simple_repeat 1 34 (0) m_b8s252i17 317 chr1ptel1M 287408 AAAAAAAAAAAAAAAAAAAAAATTGAAAGAAAAA 287441 vvi i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 34 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 35 0.00 0.00 0.00 chr1ptel1M 287504 287536 (712464) (AAATT)n#Simple_repeat 1 33 (0) c_b8s251i0 318 chr1ptel1M 287504 AAATTAAATTAAATTAAATTAAATTAAATTAAA 287536 (AAATT)n#Simp 1 AAATTAAATTAAATTAAATTAAATTAAATTAAA 33 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 12 17.72 3.12 0.00 chr1ptel1M 288272 288303 (711697) (TAAAT)n#Simple_repeat 1 33 (0) m_b8s252i18 319 chr1ptel1M 288272 TAAATTAAATT-AAGCAAATTCAACCAAATTAA 288303 - vi v ii (TAAAT)n#Simp 1 TAAATTAAATTAAATTAAATTAAATTAAATTAA 33 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 12 4.77 4.55 0.00 chr1ptel1M 288344 288365 (711635) (TCCT)n#Simple_repeat 1 23 (0) m_b8s252i19 320 chr1ptel1M 288344 TCCTT-CTTCCTTCCCTCCTTCC 288365 - i (TCCT)n#Simpl 1 TCCTTCCTTCCTTCCTTCCTTCC 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.05 (1 / 21), avg. gap size = 1.00 (1 / 1) 16 16.12 0.00 0.00 chr1ptel1M 288552 288579 (711421) (A)n#Simple_repeat 1 28 (0) m_b8s252i21 321 chr1ptel1M 288552 AAAAAAACAAAACAAAACAAAAAAACAA 288579 v v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA 28 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 26 0.00 0.00 0.00 chr1ptel1M 291373 291397 (708603) (AGAGGC)n#Simple_repeat 1 25 (0) c_b8s251i1 322 chr1ptel1M 291373 AGAGGCAGAGGCAGAGGCAGAGGCA 291397 (AGAGGC)n#Sim 1 AGAGGCAGAGGCAGAGGCAGAGGCA 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 22 11.35 0.00 0.00 chr1ptel1M 292159 292196 (707804) (AAATA)n#Simple_repeat 1 38 (0) m_b8s252i22 323 chr1ptel1M 292159 AAATGAAAAAAAATAAAATAAAAGAAAAGAAAATAAAA 292196 i v v v (AAATA)n#Simp 1 AAATAAAATAAAATAAAATAAAATAAAATAAAATAAAA 38 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 20 16.38 0.00 0.00 chr1ptel1M 292164 292197 (707803) (A)n#Simple_repeat 1 34 (0) m_b8s252i23 323 chr1ptel1M 292164 AAAAAAAATAAAATAAAAGAAAAGAAAATAAAAA 292197 v v i i v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 34 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 37 2.86 0.00 0.00 chr1ptel1M 294596 294631 (705369) (AG)n#Simple_repeat 1 36 (0) c_b8s251i2 324 chr1ptel1M 294596 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAAGAG 294631 i (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 36 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 30 0.00 0.00 0.00 chr1ptel1M 295091 295116 (704884) (AG)n#Simple_repeat 1 26 (0) c_b8s251i3 325 chr1ptel1M 295091 AGAGAGAGAGAGAGAGAGAGAGAGAG 295116 (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAG 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 539 31.08 4.06 1.99 chr1ptel1M 295165 295361 (704639) MIR3#SINE/MIR 3 203 (5) m_b8s601i15 326 chr1ptel1M 295165 GGCAGAGAAAGCATGCAGGAAAAAAGC-CAGAGTGAAAGACTAAGAAAAC 295213 viiviiv -- i i - i v ii v - i i v MIR3#SINE/MIR 3 GGCAGAGTGGCTGAGCAG--AGAGAGCACGGACTGGGAGTC-AGGAGACC 49 chr1ptel1M 295214 TGAGTTTTAATCTTAGCTTTGCCACTCAATGTCTATGAAATGTTCAGCAA 295263 i i i iii i v v ?v i vi iv vi MIR3#SINE/MIR 50 TGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAA 99 chr1ptel1M 295264 GACATTTAAA-----TGAGATCTGAGACCTCTCATCTTTAAAATGAATGG 295308 v i v v----- i -i v viii v iv MIR3#SINE/MIR 100 GTCACTTCACCTCTCTGGG-CCTCAGTTTCCTCATCTGTAAAATGAGGGG 148 chr1ptel1M 295309 AGTGGACAAGGTGATGTCTAAATCCCCTTCCAG--CTGCAATTCTATGAT 295356 iv v i v ivi -- vv MIR3#SINE/MIR 149 GTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGAT 198 chr1ptel1M 295357 TTGAT 295361 iv MIR3#SINE/MIR 199 TCTAT 203 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.62 CpG sites = 34, Kimura (unadjusted) = 41.52 Transitions / transversions = 1.31 (34/26) Gap_init rate = 0.04 (7 / 196), avg. gap size = 1.71 (12 / 7) 19 34.24 0.00 1.45 chr1ptel1M 295948 296017 (703983) (TA)n#Simple_repeat 1 69 (0) m_b8s252i24 327 chr1ptel1M 295948 TATATATGTACATGTGTGTGTATATATAGGATATATAATTGAATATATAC 295997 i i i i i i -v vv iv i (TA)n#Simple_ 1 TATATATATATATATATATATATATATA-TATATATATATATATATATAT 49 chr1ptel1M 295998 ATATGCACACATACATCTAT 296017 ii i i i v (TA)n#Simple_ 50 ATATATATATATATATATAT 69 Matrix = Unknown Transitions / transversions = 2.60 (13/5) Gap_init rate = 0.01 (1 / 69), avg. gap size = 1.00 (1 / 1) 239 15.91 2.27 0.00 chr1ptel1M 296121 296164 (703836) MIRc#SINE/MIR 69 113 (155) m_b8s601i16 328 chr1ptel1M 296121 CTCAGACACTAATTAGCC-TGTGATCCTGGGCAAGTCACTTAACC 296164 v v v i i- i i MIRc#SINE/MIR 69 CTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACC 113 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 18.05 CpG sites = 4, Kimura (unadjusted) = 18.05 Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.02 (1 / 43), avg. gap size = 1.00 (1 / 1) 26 0.00 0.00 0.00 chr1ptel1M 297613 297637 (702363) (T)n#Simple_repeat 1 25 (0) c_b9s251i0 329 chr1ptel1M 297613 TTTTTTTTTTTTTTTTTTTTTTTTT 297637 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 239 27.07 10.50 2.04 chr1ptel1M 304307 304487 (695513) L1MEi_5end#LINE/L1 2000 2195 (17) m_b9s551i0 330 chr1ptel1M 304307 GGAAGGGAAGGGAAAAGAAGGAGAAAAGCAT----------AAATAAGGG 304346 i ii i ? iiii ? ---------- i viii L1MEi_5end#LI 2000 GGAAAGGAGAGAAAAAGNAAAGAAAAAGNATGATAAACAGAAAACACAAA 2049 chr1ptel1M 304347 TTAAGATGGCA--AGTAA-TACAGA---ATTGGTAATTTTAACCATAAAT 304390 v i -- i - v i --- ii i--- v L1MEi_5end#LI 2050 ATAAGATGGTAGAAATAAGTCCAAATATATCAGTAATC---ACAATAAAT 2096 chr1ptel1M 304391 GTGAACAAGGTAAACTC-CCCATAAAGAGGAAACGATTAGCAGAATGGAT 304439 i iiiiv - i v i iv iv v v L1MEi_5end#LI 2097 GTAAATGGATTAAACTCACCTATTAAAAGACAGAGATTATCAGATTGGAT 2146 chr1ptel1M 304440 TAAAAGCCAAGAATCCTACAATATATTGTTT--AGGAAACACACCTGAAA 304487 i-v i vi v ii -- i i i L1MEi_5end#LI 2147 TAAAAA-AAAAAATCCAGCTATATGCTGTTTACAAGAGACACACCTAAAA 2195 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.17 CpG sites = 35, Kimura (unadjusted) = 36.17 Transitions / transversions = 2.69 (35/13) Gap_init rate = 0.06 (10 / 180), avg. gap size = 2.30 (23 / 10) 312 24.68 3.82 4.49 chr1ptel1M 304330 304486 (695514) L1M6_5end#LINE/L1 2350 2505 (10) m_b9s551i1 330 chr1ptel1M 304330 AAAAGCATAAATAAGGGTTAAGATGGCAAG--TAATACAGAAT-TGGTAA 304376 ? ----- ?- i i-- v vi i- ivi i L1M6_5end#LIN 2350 AAAAGCANAAA-----GN-AAGATGACAAANATAAGACCAAACATATCAG 2393 chr1ptel1M 304377 TTTTAACCATAAATGTGAACAAGGTAAACTCCCC-ATAAAGAGGAAACGA 304425 v i v i iii v - v i iv v L1M6_5end#LIN 2394 TTATGACAATAAATGTAAATGGGTTAAACTCCCCTATTAAAAGACAAAGA 2443 chr1ptel1M 304426 TTAGCAGAATGGATTAAAAGCCAAGAATCCTACAATATATTGTTT--AGG 304473 i vv v i iv - v v ii -- i L1M6_5end#LIN 2444 CTCTCAGATTGGGTTAAAAAACAA-AATCCAACTATATGCTGTTTACAAG 2492 chr1ptel1M 304474 AAACACACCTGAA 304486 i i L1M6_5end#LIN 2493 AGACACACCTAAA 2505 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 31.09 CpG sites = 22, Kimura (unadjusted) = 31.09 Transitions / transversions = 1.47 (22/15) Gap_init rate = 0.07 (11 / 156), avg. gap size = 1.18 (13 / 11) 1003 27.96 11.25 2.38 chr1ptel1M 304386 306199 (693801) L1M4_orf2#LINE/L1 38 2008 (1286) m_b9s551i2 330 chr1ptel1M 304386 TAAATGTGAACAAGGTAAACTCCCCA-TAAAGAGGAAACGATTAGCAGAA 304434 i iiiiv v i - v i v iv i L1M4_orf2#LIN 38 TAAATGTAAATGGATTAAACACTCCAATCAAAAGGCAGAGATTGGCAGAA 87 chr1ptel1M 304435 TGGATTAAAAGCCAAGAATCCTACAATATATTGTTT--AGGAAACACACC 304482 v iv v - v v ii i -- i i i L1M4_orf2#LIN 88 TGGATAAAAAAACATG-ATCCAACTATATGCTGTCTACAAGAGACACACT 136 chr1ptel1M 304483 TGAAAAGCAGGGAGATACATGCAGAATAAAGGTAAAA-GATGGAGCAAAA 304531 v i vv --i i vii iv i i - iv i L1M4_orf2#LIN 137 TTAGATTCA--AAGACACAAATAGGTTGAAAGTAAAAGGATGGAAAAAGA 184 chr1ptel1M 304532 TCTACTATGCTTCAGGTGAAGTAAAACAA----GGA-TAGCCATCAC--A 304574 v i vvvvi - vi v i---- - i i - -- L1M4_orf2#LIN 185 TATACCATGCAAACAGT-AACCAAAAGAGAGCTGGAGTGGCTAT-ACTAA 232 chr1ptel1M 304575 TCTCAGATCAACA--------AAAAC-AAAATTATAATTAAAGAGATAAG 304615 v - v -------- i - ? i v i -- i i L1M4_orf2#LIN 233 TATCAGA-CAAAATAGACTTTAAGACAAAAANTGTTACT--AGAGACAAA 279 chr1ptel1M 304616 GAAGGG-ACTATATCTTGCT-AAAGGGTAGCATAAATAATAAGAATATAA 304663 i- i v vv v - vi- vv v vi ii L1M4_orf2#LIN 280 GAAGGACATTTTATAATGATAAAAGGGTCA-ATCCATCAGGAAGATATAA 328 chr1ptel1M 304664 TTAT--TAAACATATAT--ACCAAGTGGTGTAGCATCTAAATTC-TAAAG 304708 iv -- -- v iiiiiiv vi v v - i L1M4_orf2#LIN 329 CAATTATAAACATATATGCACCTAACAACAGAGCCCCAAAATACATGAAG 378 chr1ptel1M 304709 ---AAATT-AGAGAGCTGCAAGAAGAAAATAGAAGCAA---AAT-ATAAT 304750 --- i - v ii v i i - -- --- i- L1M4_orf2#LIN 379 CAAAAACTGACAGAATTGAAGGGAG-AAATAGA--CAATTCAACAATAAT 425 chr1ptel1M 304751 AG-TGGA-ATCTCAA----CCACTCTCAAT--TAGATAAACCAAAT---C 304789 - - ii ---- i -- i i v v --- L1M4_orf2#LIN 426 AGTTGGAGACTTCAATACCCCACTTTCAATAATGGATAGAACAACTAGAC 475 chr1ptel1M 304790 TCAAAATAAATAAGAAAGAAGTCAAAGAGGTAAATAGAATACTAGAAA-A 304838 vv i v i --- i vi vv i i-- i v -v L1M4_orf2#LIN 476 AGAAGATCAACAAG---GAAATAGAAGACTTGAAC--AACACTATAAACC 520 chr1ptel1M 304839 AGTTAGATATGATAGACCTCTGGGAAAAA-------CAGAAATGGAACAG 304881 ii iv i i v ivii v ------- iv i-- i L1M4_orf2#LIN 521 AACTAGACCTAACAGACATCTATAGAACACTCCACCCAACAAC--AGCAG 568 chr1ptel1M 304882 AAAAGTACGTTCTTTTCAGCAGTTCATGGAACCTATACAAAAATAGACCA 304931 v -i i i ivv iv v viv v ii L1M4_orf2#LIN 569 AATA-CACATTCTTCTCAAGTGCACATGGAACATTCTCCAGGATAGACCA 617 chr1ptel1M 304932 TATATTAGGACA-AAAAC----CTCAAACTCAAATGCAGTAAGA--GAAA 304974 i v - ---- ---i vi iv i -- L1M4_orf2#LIN 618 TATGTTAGGCCATAAAACAAGTCTCAA---TAAATTTAAAAGGATTGAAA 664 chr1ptel1M 304975 TAGTG-AATGCATCCTTTTCAGACCACAATGCAATAAAATTAC-ACTCAA 305022 vi i- v i -v i v v i v- v L1M4_orf2#LIN 665 TCATACAAAGTAT-GTTCTCCGACCACAATGGAATGAAATTAGAAATCAA 713 chr1ptel1M 305023 CAAAAAGCCAGGAAAGTAGACCAA---AAAAATAATTGGAAACTAAATAA 305069 i v ii-- v v ivv --- v vv i i L1M4_orf2#LIN 714 TAACAGA--AGGAAATTTGGGAAATTCACAAATATGTGGAAATTAAACAA 761 chr1ptel1M 305070 TCTCA-TACTAAAGAA-TGATTGGTGAAAC-AGCAATCATAGACATAATT 305116 - v - v v -ii v v v- v i iiviv L1M4_orf2#LIN 762 -CACACTCCTAAATAACCAATGGGTCAAAGAAGAAATCACAAGGGAAATT 810 chr1ptel1M 305117 AATAACTTCACCCAAA-AAATGACAATAATGAGACATCATATCAAA---- 305161 iv v v viiv i -i v ii vi v v i ---- L1M4_orf2#LIN 811 AGAAAATACTTTGAGATGAATGAAAACGAAAACACAACATACCAAAACTT 860 chr1ptel1M 305162 ATGTGAT-C-GCCAAAGTGGTAA-TAAAGGAAATTTCAT-TCTCTAGACA 305207 v - - ? ii iv- i i v i -v v i ii L1M4_orf2#LIN 861 ATGGGATGCAGCNAAAGCAGTGCTTAGAGGGAAATTTATAGCTGTAAATG 910 chr1ptel1M 305208 CTTGCAT---AAAAGTAGAAAGA---AAGGTCAACGA---AATTGGGCAC 305248 i ii --- v ---v ii ii --- iivvv L1M4_orf2#LIN 911 CCTATATTAAAAAAGAAGAAAGATCTCAAATCAATAACCTAACCTTCCAC 960 chr1ptel1M 305249 AACTAAAAATCTAGAAAAGGAACAAATTAAAAAAAACCC-AGTCAAACAC 305297 -vi i v i -- i vi vv - iv i v L1M4_orf2#LIN 961 -CTTAAGAAACTAGAAAAAGA--AGAGCAAACTAAACCCAAAGCAAGCAG 1007 chr1ptel1M 305298 TAAACTTGAAATTCTAAAAATAAAAG-GAAGATCAAT-AAATTGAAAGTA 305345 v iivvv vv i v i - i i v - v i i L1M4_orf2#LIN 1008 AAGGAAGGAAATAATAAAGATTAGAGCGGAAATAAATGAAATAGAGAATA 1057 chr1ptel1M 305346 AAAAAACTAT-TAATTAATTAATGAAACTAAGAGTTGGTTCTAAGAAAA- 305393 i v -v ivv i i i i vv - L1M4_orf2#LIN 1058 GAAAAACAATAGAGAAAATCAACGAAACCAAAAGTTGGTTCTTTGAAAAG 1107 chr1ptel1M 305394 ATCAACAAAATAGACAAACCCCTTAGTAAATCTGATT---TAAAAAGGAA 305440 v - i iv iv ii---v i i L1M4_orf2#LIN 1108 ATCAACAAAATTGACAAA-CCTTTAGCTAGACTGACCAAGAAAAAAAGAG 1156 chr1ptel1M 305441 AGGAAAATCAAATTGTTAGTCTTAAAAAATGAA--AGGAGA-ATCCCCAC 305487 i i v ii ivv i- ii -- i - iv i L1M4_orf2#LIN 1157 AGAAGACTCAAATTACTAAAATC-AGGAATGAAAGAGGGGACATTACTAC 1205 chr1ptel1M 305488 TAA--TGAAAGAAATTAGAGCAATAATTAGGAATTACTTTC--CAACTTT 305533 ii -- v v v i ivi v v i v v v-- i v L1M4_orf2#LIN 1206 CGACCTTACAGAAATAAAAAGGATTATAAGGGAATACTATGAACAATTGT 1255 chr1ptel1M 305534 -TAGCAATAAATCA-ACAACTTAAATGAAA--GAAGAATACCTTCAAAAA 305579 - iv i i - i i i -- vi v vv i L1M4_orf2#LIN 1256 ATGCCAACAAATTAGATAACCTAGATGAAATGGACAAATTCCTAGAAAGA 1305 chr1ptel1M 305580 TAT-AGCTTCCCAGATTAA--CAGGAAGAAGTAAATATCCTAAACAGTCC 305626 i i- i v v i i i -- i i i v vi i i v L1M4_orf2#LIN 1306 CACAAACTACCGAAACTGACTCAAGAAGAAATAGAAAATCTGAATAGACC 1355 chr1ptel1M 305627 CATCTTAG--AAAAAAATAGAACAAGCTATTC----AACTCCC--TAAGA 305668 i vvi i-- i i v iv - v ---- i --i ii L1M4_orf2#LIN 1356 TATAACAAGTAAAGAGATTGAATTAG-TAATCAAAAAACTTCCCACAAAG 1404 chr1ptel1M 305669 AAAATCCCAGGACCAGATGGATTTA----TAAATTCTACCAAACATTCAA 305714 v ? v i ---- i i L1M4_orf2#LIN 1405 AAAAGCCCAGGNCCAGATGGCTTCACTGGTGAATTCTACCAAACATTTAA 1454 chr1ptel1M 305715 AGAACAATTAACCCCAAGC--TTATAAACTATT-TGAAAAATAG----GG 305757 v v v -- i i v -ii ---- L1M4_orf2#LIN 1455 AGAAGAATTAACACCAATCCTTCACAAACTCTTCCAAAAAATAGAAGAGG 1504 chr1ptel1M 305758 ACTGAAGAGTCCACCAAACTCCTTTTACAAA--CA--ACTAGACTGATAC 305803 vv v v i - - v i ii i-- -- i vv L1M4_orf2#LIN 1505 AGGGAACACTTC-CC-AACTCATTCTATGAGGCCAGTATTACCCTGATAC 1552 chr1ptel1M 305804 CTAAACCAGGTAGGCTGAAAAC------AGAAAAG-AAATTATAGACCAA 305846 v ii ----- i ------ - i i L1M4_orf2#LIN 1553 CAAAACCAGACA-----AAGACATCACAAGAAAAGAAAACTACAGACCAA 1597 chr1ptel1M 305847 T-TCTC-TAAGAATATCGATCTAAAA--TCTTAAAAAAATAATTAGAAA- 305891 - i - v v vi --i i v - i v - L1M4_orf2#LIN 1598 TATCCCTTATGAATATAGATGCAAAAATCCTCAACAAAAT-ACTAGCAAA 1646 chr1ptel1M 305892 ---AATTCAGAAAATCATTCTAGGAAAA----ACACTACAACCAA---TA 305931 --- i v -- viv ii ii ---- i ii ---vi L1M4_orf2#LIN 1647 CCGAATCCAGCAA--CATATAAAAAGGATTATACACCATGACCAAGTGGG 1694 chr1ptel1M 305932 ATTTATAC---AAAT-C-AGGACAATTCAATATTAAAAAA-CTATTAGCA 305975 v ---i - - viii i ?vi - v i iii L1M4_orf2#LIN 1695 ATTTATCCCAGGAATGCAAGGTTGGTTCAACATNCGAAAATCAATCAATG 1744 chr1ptel1M 305976 TAAT-TACTATATCAAT------AAG--CAAACTAACCCCATAATCATCT 306016 -i i i ------ -- -- v i L1M4_orf2#LIN 1745 TAATACACCATATTAATAGAATAAAGGACAAA--AACCACATGATCATCT 1792 chr1ptel1M 306017 CAATAGATGCAG-AAAAGCATTTATTAAA--TCAACATCCATTC-CAATA 306062 i - ivi --i i v -ii L1M4_orf2#LIN 1793 CAATAGACGCAGAAAAAGCATTTGACAAAATCCAACACCCTTTCATGATA 1842 chr1ptel1M 306063 AAATCAC----GAGAAT-GGAATA-AAG---ACTT--TCAA-ATAGTTAG 306100 v ----v i v - - --- -- -v ii v i L1M4_orf2#LIN 1843 AAAACACTCAACAAACTAGGAATAGAAGGGAACTTCCTCAACCTGATAAA 1892 chr1ptel1M 306101 GAGCAT----AAAAAACATCATA------AGCATATATGATGG-GAAA-A 306138 i ----i -i i ------ v iv i - - L1M4_orf2#LIN 1893 GGGCATCTACGAAAAAC-CCACAGCTAACATCATACTTAATGGTGAAAGA 1941 chr1ptel1M 306139 CTGAAT-CTTTCCCAGCAAGATCTAGTAA----ACAAGGTTGCC--CTGT 306181 ?- vvi - v ---- v i -- v L1M4_orf2#LIN 1942 CTGAANGCTTTCCCCCTAAGATC-AGGAACAAGACAAGGATGTCCGCTCT 1990 chr1ptel1M 306182 CACCGTTATTATTCAATA 306199 i ii vi i L1M4_orf2#LIN 1991 CGCCACTTCTATTCAACA 2008 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.38 CpG sites = 285, Kimura (unadjusted) = 36.04 Transitions / transversions = 1.36 (285/210) Gap_init rate = 0.08 (145 / 1813), avg. gap size = 1.73 (251 / 145) 1157 26.20 11.59 1.62 chr1ptel1M 304877 306222 (693778) L1MD_orf2#LINE/L1 561 2038 (1256) m_b9s551i3 330 chr1ptel1M 304877 AACAGAAAAGTACG--TTCTTTTCAGCAGTTCATGGAACCTATACAAAAA 304924 v i i i-- ivv ii i v ? v i L1MD_orf2#LIN 561 AACAGCAGAATACACATTCTTTTCAAGTGCCCACGGAACATNTACCAAGA 610 chr1ptel1M 304925 TAGACCATATATTAGG--ACAAAA---ACCTCAAACTCAAATGCAGTAAG 304969 vi i -- i --- --- vi i- L1MD_orf2#LIN 611 TAGACCATATCCTGGGCCATAAAACAAACCTCAA---CAAATTTAA-AAG 656 chr1ptel1M 304970 A---GAAATAGT---GAATGCATCCTTTTCAGACCACAATGCAATAAAAT 305013 --- vi --- i ii i i --- v v i L1MD_orf2#LIN 657 AATTGAAATCATACAGAGTGTGTTCTCT---GACCACAATGGAATCAAAC 703 chr1ptel1M 305014 TA-----CACTCAACAAAAAGC---CAGGAAAGTAGACCAAAAAAATAAT 305055 ----- v - i v--- i vv- ----i v L1MD_orf2#LIN 704 TAGAAATCAAT-AACAGAAAGATAACAGGAAAATCT-CCAAA----CACT 747 chr1ptel1M 305056 TGGAAACTAAATAATCTCA-TACTAAAGAATG-ATTGGTGAAACAGCAA- 305102 i - v - v v v- v v v v - L1MD_orf2#LIN 748 TGGAAACTAAACAA-CACACTTCTAAATAATCCATGGGTCAAAGAGGAAG 796 chr1ptel1M 305103 --TCATAGACATAATTAATAACTTCACCCAAA-AAATGACAATAATGAGA 305149 -- - iv - v v v iiv v-i v i vi v L1MD_orf2#LIN 797 TCTCA-AGGGA-AATTAAAAAATACATTGAACTGAATGAAAATGAAAATA 844 chr1ptel1M 305150 CATCATATCAAAAT--GTGA----TCGCCAAAGTGGTAATAA-AGGAAAT 305192 v -- i----iv i ii iv i - i v L1MD_orf2#LIN 845 CAACATATCAAAATTTGTGGGACGCAGCTAAAGCAGTGCTGAGAGGGAAA 894 chr1ptel1M 305193 TTCAT-TCTCTAGACACTTGCATAAAAGTAGAAAGAAAG-GTCAA--CGA 305238 i -v v i ii ? i v i iv iii -v -- i L1MD_orf2#LIN 895 TTTATAGCACTAAATGCNTACATTAGAAAAGAGGAAAAGTCTCAAATCAA 944 chr1ptel1M 305239 -AAT-TGGGC--ACAACT-AAAAATCTAGAAAAGGAACAAATTAAAAAAA 305283 - - ii --v v - i ? i v i--i v L1MD_orf2#LIN 945 TAATCTAAGCTCCCACCTCAAGAANCTAGAAAAAGAAGAG--CAAAATAA 992 chr1ptel1M 305284 ACCCAG-TCAAACACTAAACTTGAAATTCTAAAAATAAAAGGA-AGATCA 305331 i-v i vv iivvv vv i i v - i L1MD_orf2#LIN 993 ACCCAAAGCAAGCAGAAGGAAGGAAATAATAAAGATAAGAGCAGAAATCA 1042 chr1ptel1M 305332 AT-AAATTGAAAGTAAAAAAACTATTAATTAA-TTAATGAAACTAAGAGT 305379 - ii i v vi vv - i v i i L1MD_orf2#LIN 1043 ATGAAATTGAAAACAGAAAAACAATAGAGAAAATCAATGAAACAAAAAGC 1092 chr1ptel1M 305380 TGGTTCTAAGAAAA-ATCAACAAAATAGACAAACCCCTTAGTAAATCTGA 305428 vv - i v i - i iv L1MD_orf2#LIN 1093 TGGTTCTTTGAAAAGATCAATAAAATTGACAAACCTCT-AGCAAGACTGA 1141 chr1ptel1M 305429 T---TTAAAAAGGAAAGGAAAATCAAATTGTTAGTCTTAAAAAATGAAA- 305474 i---vv i i i i vv iii i v i ii - - L1MD_orf2#LIN 1142 CAAAGAAAAAAAGAGAGAAGACACAAATTACCAATATCAGGAA-TGAAAC 1190 chr1ptel1M 305475 -GGAGA-ATCCCCACTAA---TGAAAGAAATTAGAGCAATAATTAGGAAT 305519 - i - v i vi --- v - v i i ivi v i v L1MD_orf2#LIN 1191 AGGGGATATCACTACAGACCCTGCA-GACATCAAAAGGATAATAAGGGAA 1239 chr1ptel1M 305520 TACTTTC--CAACTTTTAGCA-ATAAATC-AACAACTTAAATGAAA--GA 305563 viv-- i vv - i-i i -- L1MD_orf2#LIN 1240 TACTACGAACAACTCTACGCACATAAATTTGACAACTTAGATGAAATGGA 1289 chr1ptel1M 305564 AGAATACCTTCAAAAATATAGCTTCCCAGA--TTAAC-AGGAAGAAGTAA 305610 vv v iv i i ivi v ? -- i v - i? v i i L1MD_orf2#LIN 1290 CCAATTCCTCGAAAAACACAAACTACCANAACTCACCCAANATGAAATAG 1339 chr1ptel1M 305611 ATATCCTAAACAGTCCCAT--CTTAGAAAAAAATAGAACAAGCTATTC-- 305656 vii i i i i -- vvv ii v ivv iv i-- L1MD_orf2#LIN 1340 ATAATTTGAATAGCCCTATAACTATTAAGGAAATTGAATTCGTAATTTNA 1389 chr1ptel1M 305657 -AACTCCCTAAGAA-AAATC-CCAGGACCAGATGGATTTAT----AAATT 305699 - i i - - v v i i----i L1MD_orf2#LIN 1390 AAACTCCCCAAAAAGAAATCTCCAGGCCCAGATGGTTTCACTGGAGAATT 1439 chr1ptel1M 305700 CTACCAAACATTCAAAGAACAATTAACCCCAAGCTTATAAA--CTATTTG 305747 i i v v vii i v -- v iv L1MD_orf2#LIN 1440 CTACCAAACGTTTAAAGAAGAATTAACACCAATTCTACACAATCTCTTCC 1489 chr1ptel1M 305748 A-AAAATAG----GGACTGAAGAGTCCACCAAACTCCTTTTACAAA--CA 305790 - ---- vv v v i - - v ii i-- L1MD_orf2#LIN 1490 AGAAAATAGAAGAGGAGGGAACACTTC-CC-AACTCATTTTATGAGGCCA 1537 chr1ptel1M 305791 --ACTAGACTGATACCTAAACCAGGT--AGGCTGAAAACAGAAAAGAAAT 305836 -- i vv v ii-- i v v v v i ii i L1MD_orf2#LIN 1538 GTATTACCCTGATACCAAAACCAGACAAAGACAGTACAAAAAAAGAAAAC 1587 chr1ptel1M 305837 TATAGACCAAT-TCTCTAA-GAATATCGATCTAAAA--TCTTAAAAAAAT 305882 i - i v - i v ivi --i i v L1MD_orf2#LIN 1588 TACAGACCAATATCCCTCATGAACATAGACGCAAAAATCCTCAACAAAAT 1637 chr1ptel1M 305883 AATTAGAAA----AATTCAGAAAATCATTCTAGGAA--AAACACTACAAC 305926 - v ---- v vvi vvv i -- v i ii L1MD_orf2#LIN 1638 -ATTAGCAAATNGAATTCAGCAATATATAAAAAGAATTATACACCATGAC 1686 chr1ptel1M 305927 CAA---TAATTTAT---ACAAAT-CAGGAC-AATTCAATATTAAAAAA-C 305967 ---vii --- vi? - i i -ii vi - L1MD_orf2#LIN 1687 CAAGTGGGGTTTATTCCAGGNATGCAAGGCTGGTTCAATATTCGAAAATC 1736 chr1ptel1M 305968 TATTAGCATAAT-TACTATATCAATAAGC------AAACTAACCCCATAA 306010 v i iii -i i i i i ------ i vv i v i L1MD_orf2#LIN 1737 AATCAATGTAATCCACCATATTAACAGGCTAAAGAAGAAAAATCACATGA 1786 chr1ptel1M 306011 TCATCTCAATAGATGCAG-AAAAGCATTTATTAAA--TCAACATCCATTC 306057 v v - ivi -- i L1MD_orf2#LIN 1787 TCATATCAATTGATGCAGAAAAAGCATTTGACAAAATTCAACACCCATTC 1836 chr1ptel1M 306058 -CAATAAAA----TCACGAGAAT-GGAATAAAG----ACTT--TCAAATA 306095 -ii ---- v? i v - i ---- -- v v L1MD_orf2#LIN 1837 ATGATAAAAACTCTCAGNAAACTAGGAATAGAGGGGAACTTCCTCAACTT 1886 chr1ptel1M 306096 G-TTAGGAGCAT----AAAAAACAT-CA--TAAG--CATATATGATGG-G 306134 - v i ---- v - -- v-- iv i - L1MD_orf2#LIN 1887 GATAAAGAGCATCTACAAAAAACCTACAGCTAACATCATACTTAATGGTG 1936 chr1ptel1M 306135 AAA-ACTGAAT-CTTTCCCAGCAAGATCTAGTAAA---CAAGGTTGCC-- 306177 - - vvi vi v v --- v i -- L1MD_orf2#LIN 1937 AAAGACTGAATGCTTTCCCCCTAAGATCGGGAACAAGGCAAGGATGTCCG 1986 chr1ptel1M 306178 CTGTCACCGTTATTATTCAATA-AG----AGAAACACTACCCA--GCAAT 306220 v ii v i - ----i iiv v -- L1MD_orf2#LIN 1987 CTCTCACCACTCTTATTCAACATAGTACTGGAAGTTCTAGCCAGTGCAAT 2036 chr1ptel1M 306221 AA 306222 L1MD_orf2#LIN 2037 AA 2038 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.40 CpG sites = 192, Kimura (unadjusted) = 33.09 Transitions / transversions = 1.24 (192/155) Gap_init rate = 0.08 (106 / 1345), avg. gap size = 1.70 (180 / 106) 278 25.26 13.11 0.49 chr1ptel1M 307006 307188 (692812) L1M3_orf2#LINE/L1 3031 3236 (52) m_b9s551i4 330 chr1ptel1M 307006 TACATCAA-TTAAAAA--CTCTGTACAA------AAACCATTAACAGATT 307046 -i --i i i------ v i v L1M3_orf2#LIN 3031 TACATCAAACTAAAAAGCTTCTGCACAGCAAAGGAAACAATCAACAGAGT 3080 chr1ptel1M 307047 AGAGGAAGCAACAAAC----TGGGAAAACATCTTCACAGTTAAAGGTTCT 307092 - ii i vv ---- i v v ii iviv vivv L1M3_orf2#LIN 3081 -GAAAAGGCAACCTACGGAATGGGAGAAAATATTTGCAAACCATATATCT 3129 chr1ptel1M 307093 GATAAAGGCCTCATTTCCAAAATATAGA--GAACGCT---AATTT-ATAG 307136 i vi v v v -- v ?--- i i- L1M3_orf2#LIN 3130 GATAAGGGGTTAATATCCAAAATATATAAGGAACTCNTACAACTCAATAG 3179 chr1ptel1M 307137 ----AAAAC-CATTCTCCAATTGATAAATGGTCAAAGGATATGAACAGAC 307181 ---- -v vvi i ? v v iv i L1M3_orf2#LIN 3180 CAAAAAAACAAATAACCCGATTNAAAAATGGGCAAAGGACCTGAATAGAC 3229 chr1ptel1M 307182 AATTTTC 307188 v i L1M3_orf2#LIN 3230 ATTTCTC 3236 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 30.74 CpG sites = 23, Kimura (unadjusted) = 31.55 Transitions / transversions = 1.00 (23/23) Gap_init rate = 0.05 (10 / 182), avg. gap size = 2.50 (25 / 10) 308 27.91 8.14 0.00 chr1ptel1M 307029 307200 (692800) L1PREC2_orf2#LINE/L1 3069 3254 (40) m_b9s551i5 330 chr1ptel1M 307029 AAAAACCATTAACAGATTAGA--GG-AAGCAACAAACTGGGAAAACATCT 307075 i i i v i -- i- v v i v i v ? L1PREC2_orf2# 3069 AGAAACTATCAACAGAGTAAACAGACAACCTACAGAATGGGAGAAAATNT 3118 chr1ptel1M 307076 TCACAGTTAAAGGTTCTGATAAAGGCCTCATTTCCAAAAT--ATAGAGAA 307123 ii iviv v vv i i v v iv -- ii L1PREC2_orf2# 3119 TTGCAAACTATGCATCTGACAAAGGTCTAATATCCAGCATCTATAAGGAA 3168 chr1ptel1M 307124 C----GCTAATTTATAG---AAAACCATTC--TCCAATTGATAAATGGTC 307164 ----i v i i--- v vv --i v i v i v L1PREC2_orf2# 3169 CTTAAACAAATTTACAAGAAAAAAACAAACAACCCCATTAAAAAGTGGGC 3218 chr1ptel1M 307165 AAAGGATATGAACAGACAATTTTCAGATGATGAAAT 307200 i v i v v v L1PREC2_orf2# 3219 AAAGGACATGAACAGACACTTTTCAAAAGAAGACAT 3254 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.56 CpG sites = 24, Kimura (unadjusted) = 35.56 Transitions / transversions = 1.00 (24/24) Gap_init rate = 0.04 (6 / 171), avg. gap size = 2.33 (14 / 6) 299 30.22 7.14 0.00 chr1ptel1M 307057 307238 (692762) L1PB_orf2#LINE/L1 3100 3294 (0) m_b9s551i6 330 chr1ptel1M 307057 ACAAACTGGGAAAACATCTTCACAGTTAAAGGTTCTGATAAAGGCCTCAT 307106 i v i v i iv vivv i v v L1PB_orf2#LIN 3100 ACAGAGTGGGAGAAAATCTTCACAATCTATACATCTGACAAAGGACTAAT 3149 chr1ptel1M 307107 TTCCAAAA--TATAGAGAACGCTAATTTAT-------AGAAAACCATTC- 307146 v i -- i i? v v ivv ------- i v vv - L1PB_orf2#LIN 3150 ATCCAGAATCTACAANGAACTCAAACAAATCAGCAAGAAAAAAACAAACA 3199 chr1ptel1M 307147 -TCCAATTGATAAATGGTCAAAGGATATGAACAGACAATTTTCAGATGAT 307195 - v ii v i v v i i i i v v L1PB_orf2#LIN 3200 ATCCCATCAAAAAGTGGGCTAAGGACATGAATAGACAATTCTCAAAAGAA 3249 chr1ptel1M 307196 GAAATTGAAATTATTACCACTCATGTG--AAAGTGTTCCAAATCA 307238 v vv viii v vv i -- i i v v L1PB_orf2#LIN 3250 GATATACAAATGGCCAACAAACATATGAAAAAATGCTCAACATCA 3294 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.16 CpG sites = 24, Kimura (unadjusted) = 39.16 Transitions / transversions = 0.77 (24/31) Gap_init rate = 0.03 (5 / 181), avg. gap size = 2.60 (13 / 5) 1451 25.51 5.25 2.31 chr1ptel1M 307128 307717 (692283) L1ME4c_3end#LINE/L1 33 639 (191) m_b9s551i7 330 chr1ptel1M 307128 AATTTATA-GAAAACCATT----CTCCAATTGATAAATGGTCAAAGGATA 307172 v - v? i---- i v v i L1ME4c_3end#L 33 AATTGATAAGAAAAANATCAAGACCCCAATAGATAAATGGGCAAAGGACA 82 chr1ptel1M 307173 TGAACAGACAATTTTCAGATGATGAAATTGAAATTATTACCA--CTCATG 307220 iv ? v v vv ? vi v v -- v L1ME4c_3end#L 83 TGAACAGACAATTCACANAAGAGGAAATACAANTAGTAAACAAACACATG 132 chr1ptel1M 307221 TGAAAGTGTTCCAAATCACTATTAATCAGAGAAATGCAAATTAAGACAAC 307270 vi i v vv i v i ii L1ME4c_3end#L 133 GAAAAATGTTCAACCTCGCTAGTAATCAAAGAAATGCAAATTAAAGCAAC 182 chr1ptel1M 307271 TCTGAGATACCACTACACACCTGTCAGATTGGCTAAGATGACAGGAAAAA 307320 vv i vi i i i i i v i ----vv L1ME4c_3end#L 183 AATGAGATACCATTTTACGCCTATTAAATTAGCAAAAAT----TTAAAAA 228 chr1ptel1M 307321 ATAATGATGAT------TGTTGAAGGGGATGCGGGAAAACTGGGACACTG 307364 -- i ------ i iv i ? vi v ? v L1ME4c_3end#L 229 AT--TGATAATACCCAATGCTGGCGAGGNTGCGGTGAAACTGGTACNCTC 276 chr1ptel1M 307365 ATACATTGTTGGTGGAGCTGGAACAAAT-----CAACCATTCTGGAGAGC 307409 i vi? ---i ----- v i i L1ME4c_3end#L 277 ATACATTGCTGGTGGCANTG---TAAATTGGTACAACCCTTTTGGAAAGC 323 chr1ptel1M 307410 AATCTGG-AAT---TATCCAAAAGTTATCAAACTG-TGATACCCTTTGAT 307454 i - --- - i ii v v - v i L1ME4c_3end#L 324 AATTTGGCAATACGTAT-CAAGAGCCATAAAAATGTTCATACCCTTTGAC 372 chr1ptel1M 307455 CCAGCAGTGTTTC-TCTGGG--CTTATCCTAAGGAGATA---CTAAAGAA 307498 i i viiv - --i i --- v L1ME4c_3end#L 373 CCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAAGAA 422 chr1ptel1M 307499 GGGAAAGGGACCAGTATGTGCCAAAATGTTTGTGGCAGCCCTGTTTGTAG 307548 i i -- i - ii v i ii v vi i i i L1ME4c_3end#L 423 GGAAAAAG--CTA-TATGCACGAAGATGTTCATTGCAGCGTTATTTATAA 469 chr1ptel1M 307549 TGGCTAGAAGCTGGCAACCAGGT-GGTGCCCATCAATTGGAGAATGGTTG 307597 i v i ii v v vv -ii i v v i i L1ME4c_3end#L 470 TAGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAATGGTTA 519 chr1ptel1M 307598 GGTAAATTGTGGTATATGAATGTTATGGAATATTAT-TGTTCTGTAGAAA 307646 i i i v? iviv -iivi vv i L1ME4c_3end#L 520 AGTAAATTATGGTACATCNACTCGATGGAATATTATGCAGCCATTAAAAA 569 chr1ptel1M 307647 TGACCAACAGGATGAATACAGAGAGGCTTGGAGAGAATTACATGAACTGA 307696 iv vi v v v iiv vii v i ivi -i vv i L1ME4c_3end#L 570 TGATAATTATGAAGACTATGTAGCAACATGGAAAATGTT-TATGATATAA 618 chr1ptel1M 307697 TGCTAAGTGAAATGAGCAGAA 307717 i vi L1ME4c_3end#L 619 TGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 31.47 CpG sites = 83, Kimura (unadjusted) = 32.26 Transitions / transversions = 1.30 (83/64) Gap_init rate = 0.05 (27 / 589), avg. gap size = 1.67 (45 / 27) 14 4.49 0.00 4.17 chr1ptel1M 308031 308055 (691945) (GGGA)n#Simple_repeat 1 24 (0) m_b9s252i1 331 chr1ptel1M 308031 GGGAGGGAGTGGAGGGTGGGAGGGA 308055 - v (GGGA)n#Simpl 1 GGGAGGGAG-GGAGGGAGGGAGGGA 24 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 19 8.91 8.33 0.00 chr1ptel1M 308140 308175 (691825) (TA)n#Simple_repeat 1 39 (0) m_b9s252i2 332 chr1ptel1M 308140 TATA-ATA-ATA-AAATTTTTATATATATATATATATAT 308175 - - - v v v (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATAT 39 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.09 (3 / 35), avg. gap size = 1.00 (3 / 3) 336 32.70 3.59 6.23 chr1ptel1M 308287 308648 (691352) C L1PREC2_orf2#LINE/L1 (2910) 384 32 m_b9s551i8 333 chr1ptel1M 308287 AACTTGTTCTCTAGGAATTTGGATGCTATATCACTTAGTGCATATATATT 308336 -- i v i i vivviii vi C L1PREC2_orf2# 384 AACTTG--CTTTATGAATCTGGGTGCTCCTGTGTTGGGTGCATATATATT 337 chr1ptel1M 308337 TAGTATGGATATTACATCATTTTATC-AATGGTACCCT--AGCAGAAGAT 308383 v i --- vi v i i i- v v -- v v--v C L1PREC2_orf2# 336 TAGGATAG---TTAGGTCTTCTTGTTGAATTGAACCCTTTACCAT--TAT 292 chr1ptel1M 308384 GTAGTGTCCTGCTTTAACTCTTTTAAATATGTTT-TTGCTTT------TG 308426 i i v iv i i --- v - v ------ C L1PREC2_orf2# 291 GTAATGCCCTTCTTTGTCTTTTTTGA---TCTTTGTTGGTTTAAAGTCTG 245 chr1ptel1M 308427 TTTCATCTGAGATCATGATCATTACTCCTGCTTTTTTTTTTTTTTTTACT 308476 ii i i v iiiv i i v ------ C L1PREC2_orf2# 244 TTTTGTCTGAAATTAGGATTGCAACCCCTGCTTTTTTCTGTTT------T 201 chr1ptel1M 308477 TCATCTGAAGCATTAATAGATTCCACTCCAGCCCTTTTCCTTCACTCTGA 308526 i i --- - ii iiv v vii v vi iv C L1PREC2_orf2# 200 CCATTT---GC-TTGGTAGATTTTTCTCCATCCCTTTATTTTGAGCCTAT 155 chr1ptel1M 308527 ATATATCACTCTGCTTTAAATGAATTTCTTGTAAGCAACATATTGT--GG 308574 ivi i i viiiv v i ii i v ii i iii -- C L1PREC2_orf2# 154 GGGTGTCATTGCATGTGAGATGGGTCTCTTGAAGACAGCATACCATTGGG 105 chr1ptel1M 308575 TATTCTGGCTTTAACTCAGTCTACTATCCACTTCCATTTTATGTAAGAC- 308623 v vivv v - ii i i ii vv v - vv ii i - C L1PREC2_orf2# 104 TCTTGCTTCTTTATC-CAGCTTGCCACTCTGTGCC-TTTTAATTGGGGCA 57 chr1ptel1M 308624 TTGACACCATTCACATTCACAGTTA 308648 v vv i vi C L1PREC2_orf2# 56 TTTAGCCCATTTACATTCAAGGTTA 32 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 44.45 CpG sites = 66, Kimura (unadjusted) = 44.45 Transitions / transversions = 1.47 (66/45) Gap_init rate = 0.08 (28 / 361), avg. gap size = 1.25 (35 / 28) 284 31.11 4.55 1.90 chr1ptel1M 308531 308684 (691316) C L1MEj_5end#LINE/L1 (0) 2160 2003 m_b9s551i9 333 chr1ptel1M 308531 ATCACTCTGCTTTAAATGAATTTCTTGTAAGCAACATATTGTGGTATTCT 308580 i i i vi i i v iv vi i C L1MEj_5end#LI 2160 ATCACTTTGTTTTAAGTGTGTTTCTTGTAAACAGCATATAGCTGGGTTTT 2111 chr1ptel1M 308581 G-GCTTTAACTCAGTCTACTATCCACTTCCATTTTATGTAAGACTTGACA 308629 -vi i i ivi vi v vi v v vi v v vv C L1MEj_5end#LI 2110 GTTTTTTAACCCAATCTGACAGTCTCTGTCTTTTAATGGGAGAATTCAGT 2061 chr1ptel1M 308630 CCATTCACATTC------ACAGTTAAAATAACTAATTCTGTATTTCCTAC 308673 i------ iii i v vi i i i--- v C L1MEj_5end#LI 2060 CCATTCACATTTAGTGTAACGACTGATATACTTGATTTTA---TTCCTTC 2014 chr1ptel1M 308674 CATTTTATTTT 308684 i i C L1MEj_5end#LI 2013 CATCTTACTTT 2003 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.40 CpG sites = 28, Kimura (unadjusted) = 41.57 Transitions / transversions = 1.47 (28/19) Gap_init rate = 0.03 (5 / 153), avg. gap size = 2.00 (10 / 5) 14 16.66 2.13 6.67 chr1ptel1M 308804 308850 (691150) (TTTCC)n#Simple_repeat 1 45 (0) m_b9s252i3 334 chr1ptel1M 308804 TTTCCCTTCTCTTAGCCTTCTCCTTTCCTTTTC-TTCTTTTCTCTTCC 308850 i - -v - i - i ii (TTTCC)n#Simp 1 TTTCCTTTC-CTT-TCCTT-TCCTTTCCTTTCCTTTCCTTTCCTTTCC 45 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.09 (4 / 46), avg. gap size = 1.00 (4 / 4) 533 29.56 4.53 2.97 chr1ptel1M 311760 312024 (687976) L1ME5_3end#LINE/L1 382 650 (291) m_b9s551i10 335 chr1ptel1M 311760 CTACTGGGCTTATATCCCAAAGAG-TTCTTAAAGAAG---GGAAAGGGAC 311805 v iv i- i v v i ---iv i L1ME5_3end#LI 382 CTCCTGGGTATATATCCCAAAGAAATTCTCACACAGGTCCATAAGGGGAC 431 chr1ptel1M 311806 CTGTATGTACAAGAATGTTTTTGGCAGCCCTTTTTGTAGTGGCCAGAAAC 311855 ---- i i iv v vi v i vi i ii L1ME5_3end#LI 432 ----ATGTACGAGGATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGT 477 chr1ptel1M 311856 TGGAAACTGAGTGGATGCCCATCAGTTGGAGAATGGTTGAATAAATTGTG 311905 ii vivv i i v v i v iii v L1ME5_3end#LI 478 TGGAGGCAACCTGGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTG 527 chr1ptel1M 311906 GTATATGAATATTATGGAATATTATTCTTCGATAAGAAATGACCAACAGG 311955 iv v i ii i i v vv ii v iii vi vi L1ME5_3end#LI 528 GTGGATGCACACCATGGAGTACTATGCAGCAGTTAGAAGCAACGGACTAG 577 chr1ptel1M 311956 ATGATTTCAGAAAG--GCCTGGAGAGA-CTTACATGAAC-TGATGCTGAG 312001 -- v v v --i v vi - v -- - ii L1ME5_3end#LI 578 ATG--TACACATAGCAACATGGATGGATCTTAAA--AACATAGTGCTGAG 623 chr1ptel1M 312002 TGAAATGAGC-AGAACCAG---GAGAT 312024 vi i- v --- L1ME5_3end#LI 624 TGAAAAAAGTAAGAAACAGAATGAGAT 650 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.86 CpG sites = 43, Kimura (unadjusted) = 38.51 Transitions / transversions = 1.30 (43/33) Gap_init rate = 0.06 (15 / 264), avg. gap size = 1.33 (20 / 15) 538 27.46 0.00 0.00 chr1ptel1M 311811 311952 (688048) L1ME2z_3end#LINE/L1 433 574 (617) m_b9s551i11 335 chr1ptel1M 311811 TGTACAAGAATGTTTTTGGCAGCCCTTTTTGTAGTGGCCAGAAACTGGAA 311860 iv i ii v ii i i i L1ME2z_3end#L 433 TGTACAAGAATGTTCATAGCAGCTTTATTCATAATAGCCAAAAACTGGAA 482 chr1ptel1M 311861 ACTGAGTGGATGCCCATCAGTTGGAGAATGGTTGAATAAATTGTGGTATA 311910 v vvii i i iiv v i i i L1ME2z_3end#L 483 ACAGCCCAGGTGTCCATCAACAGGAGAATGGATAAACAAACTGTGGTATA 532 chr1ptel1M 311911 TGAATATTATGGAATATTATTCTTCGATAAGAAATGACCAAC 311952 vv iv i i vv i i ivi v L1ME2z_3end#L 533 TTCATACAATGGAATACTACTCAGCAATAAAAAGGAACGAAC 574 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.45 CpG sites = 25, Kimura (unadjusted) = 35.45 Transitions / transversions = 1.79 (25/14) Gap_init rate = 0.00 (0 / 141), avg. gap size = 0.0 (0 / 0) 22 0.00 0.00 0.00 chr1ptel1M 312475 312498 (687502) (TA)n#Simple_repeat 1 24 (0) m_b9s252i4 336 chr1ptel1M 312475 TATATATATATATATATATATATA 312498 (TA)n#Simple_ 1 TATATATATATATATATATATATA 24 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 275 20.78 1.33 10.14 chr1ptel1M 313803 313877 (686123) MIRc#SINE/MIR 37 105 (163) m_b9s601i1 337 chr1ptel1M 313803 TGCAGTTAGGA-GACTTGAATTCAAATCTGGTCTCCCACATTTCATACTT 313851 v i - i ii i i iv v ------ v -i MIRc#SINE/MIR 37 TGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTC------TGC-CACTT 79 chr1ptel1M 313852 CCTAGCTGTGTGACCCTGGGCAAGTC 313877 v i MIRc#SINE/MIR 80 ACTAGCTGTGTGACCTTGGGCAAGTC 105 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 22.66 CpG sites = 9, Kimura (unadjusted) = 24.62 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.11 (8 / 74), avg. gap size = 1.00 (8 / 8) 13 9.55 0.00 0.00 chr1ptel1M 313891 313913 (686087) (AAAC)n#Simple_repeat 1 23 (0) m_b9s252i5 338 chr1ptel1M 313891 AAACAAACAAACAAATAAATAAA 313913 i i (AAAC)n#Simpl 1 AAACAAACAAACAAACAAACAAA 23 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 254 24.24 19.40 4.58 chr1ptel1M 313921 314054 (685946) MIRc#SINE/MIR 5 157 (111) m_b9s601i2 339 chr1ptel1M 313921 GCAGTTACTGGTACAGTGGAGAGAGC--TG---TT--AATTATGAAGACC 313963 v-- i i -- --- -- i i v MIRc#SINE/MIR 5 GCAGTG--TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chr1ptel1M 313964 TGAATTTTAATCACACCTC-ATAA------AG------------GGGCAA 313994 ii iv i v iv -iiv ------ ------------ MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 102 chr1ptel1M 313995 GTCCATTTTAAGGACCCCTGCTTGTCTCAGTTTCTTATTCTGTAAAATGA 314044 - i ----i i vivv i i vv i MIRc#SINE/MIR 103 GTC-ACTT----AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGG 147 chr1ptel1M 314045 GCATAACAAT 314054 v i MIRc#SINE/MIR 148 GGATAATAAT 157 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 27.97 CpG sites = 19, Kimura (unadjusted) = 30.26 Transitions / transversions = 1.58 (19/12) Gap_init rate = 0.10 (13 / 133), avg. gap size = 2.54 (33 / 13) 312 27.36 7.89 3.80 chr1ptel1M 313989 314140 (685860) MIR#SINE/MIR 93 250 (12) m_b9s601i3 339 chr1ptel1M 313989 GGGCAAGTCCATTTTAAGGACCCCTGCTTGTCTCAGTTTCTTATTCTGTA 314038 i- i ----i i viv i i vv MIR#SINE/MIR 93 GGGCAAGTT-ACTT----AACCTCTCTGTGCCTCAGTTTCCTCATCTGTA 137 chr1ptel1M 314039 AAATGAGCATAACAATTGCACTTA-ATCCTAGGCTTCTGGGGCGGG---- 314083 i v i v i i -v v v v v v v i---- MIR#SINE/MIR 138 AAATGGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGGATTAA 187 chr1ptel1M 314084 --GAGGGTAAAAAAAAAAAAG-----AGTACAGTGCATGACATATAGTAG 314126 -- - v v v viv ----- v v i i i MIR#SINE/MIR 188 ATGA-GTTAATACATGTAAAGCGCTTAGAACAGTGCCTGGCACATAGTAA 236 chr1ptel1M 314127 GTGCTGTAGAAATG 314140 i vv v MIR#SINE/MIR 237 GCGCTCAATAAATG 250 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.21 CpG sites = 17, Kimura (unadjusted) = 34.21 Transitions / transversions = 0.74 (17/23) Gap_init rate = 0.07 (10 / 151), avg. gap size = 1.80 (18 / 10) 295 27.68 9.09 4.00 chr1ptel1M 314278 314420 (685580) L2b_3end#LINE/L2 306 455 (11) m_b9s601i4 340 chr1ptel1M 314278 TGGGTTTCTACATAGTTGT--GGGTACAATGTCTGCC-CTGCCACT---C 314321 ----- ?i -- ?v - i - iv --- L2b_3end#LINE 306 TGGGTT-----ATNATTGTCTGNTTACA-TGTCTGTCTCCCCCACTAGAC 349 chr1ptel1M 314322 TGTGGCCTCCAGGAGAGCAGGAG--AAATCT--CTTGTTTCTCTTTATGT 314367 iv iv i ii--i?i -- ivi vi i i L2b_3end#LINE 350 TGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTGTAT 399 chr1ptel1M 314368 TCCTGGTCCTTAGTCCAGGGCCTGACATGTAGCAGATTCT---TAAATCT 314414 i ii iv i iv ? i iii i iiv --- v L2b_3end#LINE 400 CCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATAT 449 chr1ptel1M 314415 TTGTTG 314420 L2b_3end#LINE 450 TTGTTG 455 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.25 CpG sites = 28, Kimura (unadjusted) = 38.36 Transitions / transversions = 2.80 (28/10) Gap_init rate = 0.08 (12 / 142), avg. gap size = 1.58 (19 / 12) 208 30.32 6.67 1.05 chr1ptel1M 314513 314602 (685398) C MIR3#SINE/MIR (3) 205 111 m_b9s601i5 341 chr1ptel1M 314513 TTATA-AGTCATAAATGGTCA---CTG-AAGGAATCTATAG-CACCACAG 314556 i - i i vv --- - i i - -v i ivv C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCT-TAGAGATCATCT 157 chr1ptel1M 314557 GGCACAATCCACTTATTTTATAGATGGAGAAATTGAAAATCAGTGA 314602 i iv i v i i ii i iivi v C MIR3#SINE/MIR 156 AGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGA 111 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.87 CpG sites = 18, Kimura (unadjusted) = 40.87 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.06 (5 / 89), avg. gap size = 1.40 (7 / 5) 327 21.79 8.93 1.67 chr1ptel1M 315823 315934 (684066) C MIR3#SINE/MIR (2) 206 87 m_b9s601i6 342 chr1ptel1M 315823 ATCA-AAAGTCATAAGATG-AAGAACTGAAAAACACTTCAGA-ATTAAAA 315869 - i i ii -v i i iiv i i - i vvv C MIR3#SINE/MIR 206 ATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCT 157 chr1ptel1M 315870 AGTCCAACCCTTCTCAATTTATAG--GAGGAAACTGAAAC----ATAGG- 315912 i- v i -- ii ---- v - C MIR3#SINE/MIR 156 AGTCCAACCCC-CTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGT 108 chr1ptel1M 315913 GAAGGGATTTGCCCAAAGGTCA 315934 v i - C MIR3#SINE/MIR 107 GAAGTGACTTGCCC-AAGGTCA 87 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.53 CpG sites = 16, Kimura (unadjusted) = 26.53 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.07 (8 / 111), avg. gap size = 1.50 (12 / 8) 153 9.05 0.00 0.00 chr1ptel1M 317093 317306 (682694) (AGGA)n#Simple_repeat 1 214 (0) m_b9s252i6 343 chr1ptel1M 317093 AGGAGGGAGGGAGGGAATGAGGGAAAGAAGGAGGGAAGGAAGGAAGAAAG 317142 i i i v i i i i (AGGA)n#Simpl 1 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG 50 chr1ptel1M 317143 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 317192 (AGGA)n#Simpl 51 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 100 chr1ptel1M 317193 AGGAAAGAAGAAAGGACGGAAGGAAGGCAGGCAGGAAGAAGGGAAGGAAG 317242 i i v v v i i (AGGA)n#Simpl 101 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG 150 chr1ptel1M 317243 GAAGGAAGGAAGGAAGGAGGGAAGGAAGGAGGAAAGGAAGGAAGGAAGGA 317292 i i i (AGGA)n#Simpl 151 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 200 chr1ptel1M 317293 AGGAAGGAAGGAAG 317306 (AGGA)n#Simpl 201 AGGAAGGAAGGAAG 214 Matrix = Unknown Transitions / transversions = 3.50 (14/4) Gap_init rate = 0.00 (0 / 213), avg. gap size = 0.0 (0 / 0) 11 11.32 10.00 2.33 chr1ptel1M 319151 319190 (680810) (AGCAAAT)n#Simple_repeat 1 43 (0) m_b9s252i7 344 chr1ptel1M 319151 AGTAAATA--AAATAGCAAATGGCAAA-AG-TAATATCACAATA 319190 i -- i - -v v - (AGCAAAT)n#Si 1 AGCAAATAGCAAATAGCAAATAGCAAATAGCAAATAGCA-AATA 43 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.10 (4 / 39), avg. gap size = 1.25 (5 / 4) 230 28.84 9.87 5.15 chr1ptel1M 319535 319757 (680243) L1P1_orf2#LINE/L1 1665 1897 (1397) m_b9s551i12 345 chr1ptel1M 319535 CAAGAAACC-ATTCTTTATGATCAAGTGGAAATGATACTAGGGATGGAAG 319583 i i i- i vii ivv v v iv v L1P1_orf2#LIN 1665 CAAAAAGCTTATCCACCATGATCAAGTGGGCTTCATCCCTGGGATGCAAG 1714 chr1ptel1M 319584 GATAATGGGACATTGGAAAAACAATGAATATAATCT--CATTCTAAACCA 319631 v ii vvi vv v v i ii i-- - v vi L1P1_orf2#LIN 1715 GCTGGTTCAACATACGCAAATCAATAAACGTAATCCAGCA-TATAAACAG 1763 chr1ptel1M 319632 ATCCAAAACCA-----CACAT-------TCAGTATAATAAAGAGAATGCT 319669 v iv ----- ------- i -i iv i v i L1P1_orf2#LIN 1764 AACCAAAGACAAAAACCACATGATTATCTCAATA-GATGCAGAAAAGGCC 1812 chr1ptel1M 319670 TTCGTCAAAGTACAACAATCTTTTGTGGTTTAAAATTT------AATTAG 319713 i v i v i i ii - i v i i------ L1P1_orf2#LIN 1813 TTTGACAAAATTCAACAACCCTTCAT-GCTAAAAACTCTCAATAAATTAG 1861 chr1ptel1M 319714 GAGTATAGACCTAGTGGGACCAGAATTCTGAAA-AGTAAGAGCTA 319757 -- v ----- -- v iiii - i L1P1_orf2#LIN 1862 --GTATTGA-----TGGGAC--GTATCTCAAAATAATAAGAGCTA 1897 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.67 CpG sites = 36, Kimura (unadjusted) = 37.54 Transitions / transversions = 1.44 (36/25) Gap_init rate = 0.08 (18 / 222), avg. gap size = 1.89 (34 / 18) 40 19.93 0.00 0.00 chr1ptel1M 320326 320398 (679602) (A)n#Simple_repeat 1 73 (0) m_b9s252i8 346 chr1ptel1M 320326 AAAAAAAAAAAAAAAGAAAAAGAAAAAGAAAGAAAGAAAGAAGAAAGAAA 320375 i i i i i i i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr1ptel1M 320376 AGAAAAAAGAAAAAGAAAAGAAA 320398 i i i i (A)n#Simple_r 51 AAAAAAAAAAAAAAAAAAAAAAA 73 Matrix = Unknown Transitions / transversions = 1.00 (12/0) Gap_init rate = 0.00 (0 / 72), avg. gap size = 0.0 (0 / 0) 421 21.20 0.00 6.67 chr1ptel1M 321447 321542 (678458) MIRc#SINE/MIR 26 115 (153) m_b9s601i7 347 chr1ptel1M 321447 AGCACCAGCCCTGAAGTCAGGAGTAACTGAGTTCAAATCTGGTCTCAGAC 321496 ii v i i iv v i i i iv v v v MIRc#SINE/MIR 26 AGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCC 75 chr1ptel1M 321497 ACTTAACATTGCTTACTGTGTGACCCTGGGCAAGTCACTTAACCTC 321542 ------ vi i MIRc#SINE/MIR 76 ACTTA------CTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 23.69 CpG sites = 11, Kimura (unadjusted) = 25.17 Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.06 (6 / 95), avg. gap size = 1.00 (6 / 6) 249 28.93 5.98 2.48 chr1ptel1M 321647 321763 (678237) MIR#SINE/MIR 136 256 (6) m_b9s601i8 347 chr1ptel1M 321647 TAAAATATGGATAAAAAC--T-CCTCCCTTCCAGGGTTTTTGTGAGGATC 321693 iv v i-- - v ivi v i MIR#SINE/MIR 136 TAAAATGGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGGATT 185 chr1ptel1M 321694 ACAGGAG---ATATTGGTAAGGTGCTTA-ACTTGTGTCTAGCTCTCAATA 321739 v v --- ivv i i - viv i i v vi i MIR#SINE/MIR 186 AAATGAGTTAATACATGTAAAGCGCTTAGAACAGTGCCTGGCACATAGTA 235 chr1ptel1M 321740 GGTCCCTCAGAATAATTACCAGTT 321763 i - v -- v iii i MIR#SINE/MIR 236 AG-CGCTC--AATAAATGTTAGCT 256 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.88 CpG sites = 18, Kimura (unadjusted) = 37.29 Transitions / transversions = 1.20 (18/15) Gap_init rate = 0.06 (7 / 116), avg. gap size = 1.43 (10 / 7) 344 25.73 3.92 0.95 chr1ptel1M 321647 321748 (678252) MIRb#SINE/MIR 143 247 (21) m_b9s601i9 347 chr1ptel1M 321647 TAAAATATGGATAAAAACTCCTCCCTTCCAGGGTTTTTGTGAGGATCACA 321696 iv v iv v iv v i v MIRb#SINE/MIR 143 TAAAATGGGGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAA 192 chr1ptel1M 321697 GGAGATATTG---GTAAGGTGCTTAAC-TTGTGTCTAGCTCTCAATAGGT 321742 v v --- i i i -iv i i v vi i i - MIRb#SINE/MIR 193 TGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAG- 241 chr1ptel1M 321743 CCCTCA 321748 v MIRb#SINE/MIR 242 CGCTCA 247 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.02 CpG sites = 13, Kimura (unadjusted) = 31.84 Transitions / transversions = 1.00 (13/13) Gap_init rate = 0.03 (3 / 101), avg. gap size = 1.67 (5 / 3) 576 31.18 5.04 4.40 chr1ptel1M 326215 327207 (672793) L1M5_orf2#LINE/L1 2296 3294 (0) m_b9s551i13 348 chr1ptel1M 326215 ATAAAATATTTGGGGATCTATCTGCCAAGGGAAAGTCAGGAACTATATGA 326264 ? i i i vv iv ii? vivv i v ? iiv L1M5_orf2#LIN 2296 ATNAAATACTTAGGAATAAATCTAACAAAANATGTGCAAGACCTNTACAC 2345 chr1ptel1M 326265 GCAAAACTATAAAACACTTTCCACACAAATAAAGTCAAATCCAAGCAATT 326314 vv i i viiv v v v ivv i i i ii v L1M5_orf2#LIN 2346 TGAAAACTACAAAACATTGCTGAGAGAAATTAAAGAAGACCTAAATAAAT 2395 chr1ptel1M 326315 GGAAAAATATTAAGTGCTCTTGGATAGGTAAG---CAAGTATAATAAAGA 326361 i i vvvi i v v - --- - vi ? L1M5_orf2#LIN 2396 GGAGAGATATACCATGTTCATGGATTGG-AAGACTCAA-TATTGTNAAGA 2443 chr1ptel1M 326362 TGACAATACTACCTAAACTAATCTATTTATTTCATGT-ATACCAATCAGA 326410 v v v i i i vv iv i- v i L1M5_orf2#LIN 2444 TGTCAATTCTCCCCAAATTGATCTATAGATTCAATGCAATCCCAATCAAA 2493 chr1ptel1M 326411 CTCCCCCCCAAAATTATTTTAATGATCTAGAAAAAATAACAACAAAATTC 326460 v vv -- ii v ivv vv v v iv i ivvi i L1M5_orf2#LIN 2494 ATCCCAGC--AGGTTTTTTTGTAGAAATTGACAAGCTGATTCTAAAATTT 2541 chr1ptel1M 326461 ATCTGGAAGAACAAAAGGTCAAGACTTTCAAAGGAACTAATC-AAAAAAA 326509 v ivi i ii ? v vv v -- - -vi L1M5_orf2#LIN 2542 ATATGGAAATGCAAAGGACCNAGAATAGCCAA--AAC-AATCTTGAAAAA 2588 chr1ptel1M 326510 AAAAAAAAAAATCAAATGAAGGTGGCCTAATTGTACCAGATCT-AAAACT 326558 i i v i ---- i --- v v ivv ? ? - i L1M5_orf2#LIN 2589 GAAGAACAAAGT----TGGA---GGACTTACACTACCNGATNTCAAGACT 2631 chr1ptel1M 326559 ACATGATAAAGCAGCAGTCACCAAAACCCTTTGGTATTGGC-TAAGAAAT 326607 -i v vi v i i vv v - -i L1M5_orf2#LIN 2632 -TATTATAAAGCTACAGTAATCAAGACAGTGTGGTATTGGCGTAAG-GAT 2679 chr1ptel1M 326608 AGATTAGTTGATCAGTGCAATAGGTTAG---GTTCACAGGACAAAATAG- 326653 iv i v i v i iv --- i ------i - L1M5_orf2#LIN 2680 AGACAAATAGATCAATGGAACAGAATAGAGAGTCCA------GAAATAGA 2723 chr1ptel1M 326654 -TCA-ATAACTTTAATAATCTAGTGTTGGACAA---CCTCAAAG-ACTGC 326697 -i - i vv v ii?v ?i ii v v ---ivi ? - v v L1M5_orf2#LIN 2724 CCCACACATATATGGNCANTTGATTTTTGACAAAGGTGCCAANGCAATTC 2773 chr1ptel1M 326698 AGCTTCTGGGACAAGAGTTCACTATTTGACAAAAACTCCTGGAA-AATTG 326746 ---- iv ii vvv v ii viv v - L1M5_orf2#LIN 2774 AG----TGGGGAAAGGATAGTCTTTTCAACAAATGGTGCTGGAACAATTG 2819 chr1ptel1M 326747 GAAATTAGTATGGCAGAAACTAGGCATTGACCCACACTTAACACTGTACA 326796 v ivi v i v iii?v i vi i v ii L1M5_orf2#LIN 2820 GATATCCATATGGAAAAAAATGAANCTCGACCCCTACCTCACACCATACA 2869 chr1ptel1M 326797 CCAAGATAAGGTCAAAATGGGTTCAT-GATCTAGGTATAAAGAATGAGAT 326845 v i v iv ? i i- - i ii i ii? i i i L1M5_orf2#LIN 2870 CAAAAATTAATTCNAGATGGA-TCATAGACCTAAATGTAAAAGNTAAAAC 2918 chr1ptel1M 326846 TATAAATAAATTAGAAG--AACAAAGGATAGTTTACCTCTCAGACCTGTG 326893 vvvvi -- v v i-- i iivv - L1M5_orf2#LIN 2919 TATAAAACTTCTAGAAGAAAACATAGGAGAA--TATCTTCGTGACCT-TG 2965 chr1ptel1M 326894 GAATTTGTGACCAAAGA----------AGAAC-TAGAGATCATTATTGAT 326932 i? vv ---- ---------- i -i i i v i? --- i L1M5_orf2#LIN 2966 GGNTAGG----CAAAGATTTCTTAAACAGGACACAAAAAGCACNA---AC 3008 chr1ptel1M 326933 CACAAAATAGAAAAT-------TTCGATTATATCAAATTAAAAAGCTTTT 326975 i v i ------- v i ?i v v i i L1M5_orf2#LIN 3009 CATAAAAGAAAAAATTGATAAATTGGACTNCATCAAAATTAAAAACTTCT 3058 chr1ptel1M 326976 GTACTAACAAATGTAATGCAGACAAGATTAGAAGGGAAGTAATAAGCTGG 327025 iv ?vvv vii vi ivi v i v i v iv i ii? L1M5_orf2#LIN 3059 GCTCNTCAAAAGACACCGTTAAGAAAATGAAAAGGCAAGCCACAGANTGG 3108 chr1ptel1M 327026 AAAAACAT-TTTGACAGTCAAAGGTTCTGAAAAAAGCCTCATTTCCAAA- 327073 i i v - vv ?v v vi- v i v i v i - L1M5_orf2#LIN 3109 GAGAAAATATTTGCAANACATATA-TCTGACAAAGGACTCGTATCCAGAA 3157 chr1ptel1M 327074 ---ATAAAGAATTGACTCTAATTT-ATAAGAAATCAAGCCATTC--TCCA 327117 --- i -v vi ? i- ? -- v vv --i L1M5_orf2#LIN 3158 TATATAAAGAACT-CCTACAANTCAATAANAAA--AAGACAAACAACCCA 3204 chr1ptel1M 327118 ATTGATAAATGGTCAAATTATATGAAAAGACAATTTTCAAATGAAGAAAT 327167 v? v v vv iv v v iv v v L1M5_orf2#LIN 3205 ATANAAAAATGGGCAAAAGACTTGAACAGACACTTCACAAAAGAAGATAT 3254 chr1ptel1M 327168 TGAAA---CTATTTCAAGCCATATGAAAAGATAGTCCAAGTCA 327207 ?v --- i v -- - i iv v v? L1M5_orf2#LIN 3255 NCAAATGGCCAAT--AAG-CACATGAAAAGATGCTCAACNTCA 3294 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.57 CpG sites = 147, Kimura (unadjusted) = 42.31 Transitions / transversions = 0.99 (147/149) Gap_init rate = 0.07 (67 / 992), avg. gap size = 1.40 (94 / 67) 401 23.27 4.22 4.22 chr1ptel1M 327074 327239 (672761) L1ME4c_3end#LINE/L1 17 182 (648) m_b9s551i14 348 chr1ptel1M 327074 ATAAAGAATTGACTCTAATTTATAAGAAA----TCAAGCCATTCTCCAAT 327119 ii v i v v ---- v ----i L1ME4c_3end#L 17 ATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAAGAC----CCCAAT 62 chr1ptel1M 327120 TGATAAATGGTCAAATTATATGAAAAGACAATTTTCAAATGAAGAAATTG 327169 v v vv i v iv ? v i -i L1ME4c_3end#L 63 AGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAGGAAAT-A 111 chr1ptel1M 327170 AAACTATTTCAAGC---CATATGAAAAGATAGTCCAAGTCATTATTAATC 327216 v ? v -- i --- i i i iv v vv ii v L1ME4c_3end#L 112 CAANTAGT--AAACAAACACATGGAAAAATGTTCAACCTCGCTAGTAATC 159 chr1ptel1M 327217 AGAGAAATGCAAATTGAGACAAC 327239 i i ii L1ME4c_3end#L 160 AAAGAAATGCAAATTAAAGCAAC 182 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 27.68 CpG sites = 19, Kimura (unadjusted) = 28.57 Transitions / transversions = 1.06 (19/18) Gap_init rate = 0.05 (9 / 165), avg. gap size = 1.56 (14 / 9) 466 18.55 2.36 2.36 chr1ptel1M 327113 327239 (672761) L1ME5_3end#LINE/L1 56 182 (759) m_b9s551i15 348 chr1ptel1M 327113 CTCCAATTGATAAATGGTCAAATTATATGAAAAGACAATTTTCAAATGAA 327162 i v v v vv v i v i v i L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chr1ptel1M 327163 GAAATT-GAAA--CTATTTCAAGCCATATGAAAAGATAGTCCAAGTCATT 327209 ii- -- v-- - i iv v v L1ME5_3end#LI 106 GAAACCCGAAAGGCTAA--CAAGC-ATATGAAGAGATGCTCAAACTCATT 152 chr1ptel1M 327210 ATTAATCAGAGAAATGCAAATTGAGACAAC 327239 v i i L1ME5_3end#LI 153 AGTAATCAGAGAAATGCAAATTAAAACAAC 182 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 21.35 CpG sites = 10, Kimura (unadjusted) = 21.35 Transitions / transversions = 0.77 (10/13) Gap_init rate = 0.04 (5 / 126), avg. gap size = 1.20 (6 / 5) 40 0.00 0.00 0.00 chr1ptel1M 328817 328850 (671150) (GA)n#Simple_repeat 1 34 (0) c_b9s251i1 349 chr1ptel1M 328817 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 328850 (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 34 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 81 2.63 0.00 0.00 chr1ptel1M 329123 329200 (670800) (GA)n#Simple_repeat 1 78 (0) c_b9s251i2 350 chr1ptel1M 329123 GAGAGAGAGAGAGAAAGAGAGAGAGAAAGAGAGAGAGAGAGAGAGAGAGA 329172 i i (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr1ptel1M 329173 GAGAGAGAGAGAGAGAGAGAGAGAGAGA 329200 (GA)n#Simple_ 51 GAGAGAGAGAGAGAGAGAGAGAGAGAGA 78 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 77), avg. gap size = 0.0 (0 / 0) 32 11.96 0.00 0.00 chr1ptel1M 330158 330204 (669796) (A)n#Simple_repeat 1 47 (0) m_b9s252i9 351 chr1ptel1M 330158 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGAGAGAAAAGAA 330204 ii i i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 47 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 12 18.44 0.00 3.12 chr1ptel1M 330523 330555 (669445) (AACACA)n#Simple_repeat 1 32 (0) m_b9s252i10 352 chr1ptel1M 330523 AACACCAACTCAAACAAAAACAGAAAAAACAAA 330555 v v v -v v (AACACA)n#Sim 1 AACACAAACACAAACACAAACA-CAAACACAAA 32 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 51 0.00 0.00 0.00 chr1ptel1M 331115 331158 (668842) (AT)n#Simple_repeat 1 44 (0) c_b9s251i3 353 chr1ptel1M 331115 ATATATATATATATATATATATATATATATATATATATATATAT 331158 (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATAT 44 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 40 0.00 2.50 0.00 chr1ptel1M 331626 331665 (668335) (TCAG)n#Simple_repeat 1 41 (0) c_b9s251i4 354 chr1ptel1M 331626 TCAGTCAGTCAGTCAG-CAGTCAGTCAGTCAGTCAGTCAGT 331665 - (TCAG)n#Simpl 1 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGT 41 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1) 250 30.76 4.21 7.61 chr1ptel1M 331943 332227 (667773) C L1P4_orf2#LINE/L1 (2988) 306 31 m_b9s551i16 355 chr1ptel1M 331943 ACCATTTAGCAAGATATAGTTTCCTTCTTTAATTCTTTTAATTAGATACG 331992 v v vv i i vi i- i -- v---i C L1P4_orf2#LIN 306 ACCCTTTATCATTATGTAATGCCCTTCTTTG-TCCTTTT--TTAC---TG 263 chr1ptel1M 331993 TTTTTGCTTT----TCT---TTATTCTGATATCAGGATCATTAACCCTGG 332035 v v ---- --- - v i - vii iv C L1P4_orf2#LIN 262 TTGTTGGTTTAAAGTCTGTTTTAT-CTGATATAAGAAT-AGCGACCCCTG 215 chr1ptel1M 332036 CTTTTTTTTTTTTTTTAACTTCACTTGAAGCATAATAGATTCCACTCCAG 332085 i v ------ i ii --- i i iiiv ? C L1P4_orf2#LIN 214 CTCTTTTTTGTTT------TCCGTTT---GCGTGATAGATCTTTCTCCAN 174 chr1ptel1M 332086 CCCTTTTCCTTCACTCTGTATGTATCACTCTGCTTTAAATGAGTATCTTG 332135 v i v vi i iv i ii viiiv v i i v C L1P4_orf2#LIN 173 CCCTTTACTTTGAGCCTATGGGTGTCGTTACATGTGAGATGGGTCTCTTG 124 chr1ptel1M 332136 TAAACAACATATTGTGGCATTCTG-GCTTTAATTCAGTCTGTTATCCACT 332184 v i i v iv ?v vi ii -vi v i iii ---- C L1P4_orf2#LIN 123 AAGACAGCAGACGGNTGGGTCTTGTTTTTTTATCCAACTTG----CCACT 78 chr1ptel1M 332185 TT---TATTTTATGTGAGA-GTTGACACCATTCACATTCACAGTTAA 332227 i ---iv v i i- v v? i vi C L1P4_orf2#LIN 77 CTGTGCCTTTTAAGTGGGGCGTTTAGNCCATTTACATTCAAGGTTAA 31 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.01 CpG sites = 48, Kimura (unadjusted) = 41.37 Transitions / transversions = 1.45 (48/33) Gap_init rate = 0.09 (26 / 284), avg. gap size = 1.27 (33 / 26) 293 29.93 3.11 2.47 chr1ptel1M 332064 332224 (667776) C L1MC_orf2#LINE/L1 (3099) 195 34 m_b9s551i17 355 chr1ptel1M 332064 AGCATAATAGATTCCACTCCAGCCCTTTTCCTTCACTCTGTATGTATCAC 332113 ii v iiiv v ? v i i v i i vi C L1MC_orf2#LIN 195 AGCATGGTATATCTTTCTCCATCCNTTTACTTTTAATCTATATGTGTCTT 146 chr1ptel1M 332114 TCTGCTTTAAATGAGTATCTTGTAAACAACATATTGTGGCATTCTG-GCT 332162 v ii v i i v i v v vi ii -vi C L1MC_orf2#LIN 145 TATATTTAAAGTGGGTTTCTTGTAGACAACATATAGTTGGGTCTTGTTTT 96 chr1ptel1M 332163 TTAATTCAGTCTGTTA---TCCA-CTTTTATTTTATGTGAGAGTTGACAC 332208 i i v vi --- ii- v vi ----i v v C L1MC_orf2#LIN 95 TTGATCCACTCTGACAATCTCTGTCTTTTAATTGGTGT----ATTTAGAC 50 chr1ptel1M 332209 CATTCACATTCACAGT 332224 ? i v C L1MC_orf2#LIN 49 CATTNACATTTAAAGT 34 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.91 CpG sites = 27, Kimura (unadjusted) = 39.91 Transitions / transversions = 1.35 (27/20) Gap_init rate = 0.04 (7 / 160), avg. gap size = 1.29 (9 / 7) 308 27.39 6.81 2.51 chr1ptel1M 332109 332299 (667701) C L1MEj_5end#LINE/L1 (0) 2160 1962 m_b9s551i18 355 chr1ptel1M 332109 ATCACTCTGCTTTAAATGAGTATCTTGTAAACAACATATTGTGGCATTCT 332158 i i i v v i v iv vi i C L1MEj_5end#LI 2160 ATCACTTTGTTTTAAGTGTGTTTCTTGTAAACAGCATATAGCTGGGTTTT 2111 chr1ptel1M 332159 G-GCTTTAATTCAGTCTGTTATCCACTTTTATTTTATGTGAGAGTTGACA 332207 -vi ii i vi vi v v iv v v i v vv C L1MEj_5end#LI 2110 GTTTTTTAACCCAATCTGACAGTCTCTGTCTTTTAATGGGAGAATTCAGT 2061 chr1ptel1M 332208 CCATTCACATTC------ACAGTTAAAATAACTAATTCTGTATTTCCTAC 332251 i------ iii i v vi i i i--- v C L1MEj_5end#LI 2060 CCATTCACATTTAGTGTAACGACTGATATACTTGATTTTA---TTCCTTC 2014 chr1ptel1M 332252 CATCTTA-TTTA--CCTCA---AGTTTGCTTTTCTATTTCCTTTTCCCCT 332295 - --?i i --- v i i ? -- i ii C L1MEj_5end#LI 2013 CATCTTACTTTATTNTTTATTTATTTTGTTTTTTTNTTT--TTTTTCTTT 1966 chr1ptel1M 332296 TTCC 332299 C L1MEj_5end#LI 1965 TTCC 1962 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.75 CpG sites = 31, Kimura (unadjusted) = 35.63 Transitions / transversions = 1.55 (31/20) Gap_init rate = 0.05 (10 / 190), avg. gap size = 1.80 (18 / 10) 22 20.24 4.17 2.74 chr1ptel1M 332360 332431 (667569) (TCTTCC)n#Simple_repeat 1 73 (0) m_b9s252i11 356 chr1ptel1M 332360 TCTTTCCCTTACTACTTCTGTTTTCC-CTT-CTCTTAGTCTCCCT-TTCC 332406 i i v - -v i - - vv i - (TCTTCC)n#Sim 1 TCTTCCTCTTCCT-CTTC-CTCTTCCTCTTCCTCTTCCTCTTCCTCTTCC 48 chr1ptel1M 332407 TTTCCCTCTTTCTCTTCCACTTCCT 332431 i i i v (TCTTCC)n#Sim 49 TCTTCCTCTTCCTCTTCCTCTTCCT 73 Matrix = Unknown Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.07 (5 / 71), avg. gap size = 1.00 (5 / 5) 12 23.10 4.17 2.04 chr1ptel1M 332375 332422 (667578) (TTCTCTT)n#Simple_repeat 1 49 (0) m_b9s252i12 357 chr1ptel1M 332375 TTCTGTTTTCCCTTCTCT-TAGTCTCCCTT-TCCTTTCCCTCTTTCTCTT 332422 v i i - vv ii - i i - (TTCTCTT)n#Si 1 TTCTCTTTTCTCTTTTCTCTTTTCTCTTTTCTCTTTTCTCT-TTTCTCTT 49 Matrix = Unknown Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.06 (3 / 47), avg. gap size = 1.00 (3 / 3) 22 20.24 4.17 2.74 chr1ptel1M 332360 332431 (667569) (TCTTCC)n#Simple_repeat 1 73 (0) m_b9s252i11 356 chr1ptel1M 332360 TCTTTCCCTTACTACTTCTGTTTTCC-CTT-CTCTTAGTCTCCCT-TTCC 332406 i i v - -v i - - vv i - (TCTTCC)n#Sim 1 TCTTCCTCTTCCT-CTTC-CTCTTCCTCTTCCTCTTCCTCTTCCTCTTCC 48 chr1ptel1M 332407 TTTCCCTCTTTCTCTTCCACTTCCT 332431 i i i v (TCTTCC)n#Sim 49 TCTTCCTCTTCCTCTTCCTCTTCCT 73 Matrix = Unknown Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.07 (5 / 71), avg. gap size = 1.00 (5 / 5) 234 25.77 4.65 0.75 chr1ptel1M 332860 332988 (667012) C L1MCa_5end#LINE/L1 (911) 1523 1390 m_b9s551i19 355 chr1ptel1M 332860 AAGTCCTGGGTAATCTTGATTATGGCTCCTCGATATCTGAATTGGTTCTT 332909 ?viv ii v iv v v vv i iv v i C L1MCa_5end#LI 1523 AAGTCNGATGTAATTCTTATCTTTGCTCCTCTATAGGTAAGGTGTTTTTT 1474 chr1ptel1M 332910 ---TCTGGCTGCTTGCAATATTTTTTCCTTGAC-CTGATAATTCTGAAAT 332955 --- v v v i v -i -v v i C L1MCa_5end#LI 1473 CCCTCTGGCTTCTTTCAAGATTTTTTCTTTGTCTTTGAT-TTTCTGCAGT 1425 chr1ptel1M 332956 TTAACTATGCTATTCCTTGGAGT--TTTCATTTTG 332988 i v v v v v --? ? i? C L1MCa_5end#LI 1424 TTGAATATGATATGCCTAGGTGTAGNTNCGNTTTG 1390 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 31.75 CpG sites = 12, Kimura (unadjusted) = 32.88 Transitions / transversions = 0.57 (12/21) Gap_init rate = 0.03 (4 / 128), avg. gap size = 1.75 (7 / 4) 15 23.80 2.78 5.71 chr1ptel1M 333837 333908 (666092) (GAAAGA)n#Simple_repeat 1 70 (0) m_b10s252i0 358 chr1ptel1M 333837 GAAAGAGAAAGAG-AAGACAAGAATATAGGCAAAACAGAAAGGGAAGATG 333885 - v ii v - i vi v i - - (GAAAGA)n#Sim 1 GAAAGAGAAAGAGAAAGAGAAAGAGA-AAGAGAAAGAGAAAGAGAA-A-G 47 chr1ptel1M 333886 AACAAAGAGGAA-AGGGAGAGAAA 333908 - v i - ii (GAAAGA)n#Sim 48 -AGAAAGAGAAAGAGAAAGAGAAA 70 Matrix = Unknown Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.08 (6 / 71), avg. gap size = 1.00 (6 / 6) 12 21.70 0.00 0.00 chr1ptel1M 334580 334611 (665389) (ATTG)n#Simple_repeat 1 32 (0) m_b10s252i1 359 chr1ptel1M 334580 ATTAATTGATTGATTGATTTAATAATAAATTG 334611 i v v i vi (ATTG)n#Simpl 1 ATTGATTGATTGATTGATTGATTGATTGATTG 32 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 12 25.86 0.00 2.38 chr1ptel1M 334600 334642 (665358) (AATAAAA)n#Simple_repeat 1 42 (0) m_b10s252i2 360 chr1ptel1M 334600 AATAATAAATTGGAAGTAAAAAATCAAAATGACAAAACTAAAA 334642 v vii i v vv - v (AATAAAA)n#Si 1 AATAAAAAATAAAAAATAAAAAATAAAAAATA-AAAAATAAAA 42 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.02 (1 / 42), avg. gap size = 1.00 (1 / 1) 26 0.00 0.00 0.00 chr1ptel1M 337074 337098 (662902) (G)n#Simple_repeat 1 25 (0) c_b10s251i0 361 chr1ptel1M 337074 GGGGGGGGGGGGGGGGGGGGGGGGG 337098 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGG 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 386 30.46 3.57 3.57 chr1ptel1M 340299 340550 (659450) L1ME5_3end#LINE/L1 386 637 (304) m_b10s551i0 362 chr1ptel1M 340299 TGGGTTTATATCCCAAAGAGATTATAAAGAAGG----GAAAGGGTCCTGT 340344 v i v v viv ----v i v ---- L1ME5_3end#LI 386 TGGGTATATATCCCAAAGAAATTCTCACACAGGTCCATAAGGGGAC---- 431 chr1ptel1M 340345 ATGTGCACGAATGTTTGTGGCAGCCCTTTTTGTAGTGGCTAGAAACTGGA 340394 i iv i ii v vi v i vi i ii L1ME5_3end#LI 432 ATGTACGAGGATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGA 481 chr1ptel1M 340395 AACTGAATGGATGCCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTAT 340444 ii vivv i i v v i v iii v iv L1ME5_3end#LI 482 GGCAACCTGGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGG 531 chr1ptel1M 340445 ATGAATATTATGGAATATTACTGT-TCTGTAAGAAATGACCAACAGGATG 340493 v i ii i i - i-v v v iii vi vi L1ME5_3end#LI 532 ATGCACACCATGGAGTACTA-TGCAGCAGTTAGAAGCAACGGACTAGATG 580 chr1ptel1M 340494 ATTTCAGAAAG--ACCTGGAGAGA-CTTACACGAAC-TGATGCTGAGTGA 340539 -- v v v -- v vi - v -- - ii L1ME5_3end#LI 581 --TACACATAGCAACATGGATGGATCTTAAA--AACATAGTGCTGAGTGA 626 chr1ptel1M 340540 AATGAGCAGGA 340550 vi i i L1ME5_3end#LI 627 AAAAAGTAAGA 637 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.28 CpG sites = 41, Kimura (unadjusted) = 39.97 Transitions / transversions = 1.24 (41/33) Gap_init rate = 0.06 (14 / 251), avg. gap size = 1.29 (18 / 14) 466 25.62 0.00 0.00 chr1ptel1M 340346 340466 (659534) L1ME1_3end#LINE/L1 433 553 (373) m_b10s551i1 362 chr1ptel1M 340346 TGTGCACGAATGTTTGTGGCAGCCCTTTTTGTAGTGGCTAGAAACTGGAA 340395 i ii i ii v i i i i i L1ME1_3end#LI 433 TGTACACGAATGTTCATAGCAGCTTTATTCGTAATAGCCAAAAACTGGAA 482 chr1ptel1M 340396 ACTGAATGGATGCCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATA 340445 vivviii i ii? v v i i L1ME1_3end#LI 483 ACAACCCAAATGTCCATCAACNGGTGAATGGATAAACAAATTGTGGTATA 532 chr1ptel1M 340446 TGAATATTATGGAATATTACT 340466 vv iv i L1ME1_3end#LI 533 TCCATACAATGGAATACTACT 553 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 31.88 CpG sites = 22, Kimura (unadjusted) = 33.20 Transitions / transversions = 2.44 (22/9) Gap_init rate = 0.00 (0 / 120), avg. gap size = 0.0 (0 / 0) 244 34.23 3.09 3.97 chr1ptel1M 342042 342397 (657603) C L1PREC2_orf2#LINE/L1 (2910) 384 32 m_b10s551i2 363 chr1ptel1M 342042 AACTTGTTCTCTAGGAATTTGGATGCTATATCATTTAGTGCATATATGTT 342091 -- i v i i vivvii vi i C L1PREC2_orf2# 384 AACTTG--CTTTATGAATCTGGGTGCTCCTGTGTTGGGTGCATATATATT 337 chr1ptel1M 342092 TAATATGGATATTACATCTTTACCAATGGTAGCCTTTAGCAAGAAATAAT 342141 iv i v vvv v vviv v v v v vv vi C L1PREC2_orf2# 336 TAGGATAGTTAGGTCTTCTTGTTGAATTGAACCCTTTACCATTATGTAAT 287 chr1ptel1M 342142 -TTATTCTTTAACTCTTAATTAGATATGGTTTTTGCTTT------TGTTT 342184 -iiv iv i -- - v -- v v ------ C L1PREC2_orf2# 286 GCCCTTCTTTGTCTTTT--TT-GATCT--TTGTTGGTTTAAAGTCTGTTT 242 chr1ptel1M 342185 GATCTCAGATCAGGATCATTATCCCTGCTTTTTTTT-TACTTCACCTGAA 342233 vi v i i iiiv i i - vi i ii --- C L1PREC2_orf2# 241 TGTCTGAAATTAGGATTGCAACCCCTGCTTTTTTCTGTTTTCCATTT--- 195 chr1ptel1M 342234 GCATAATAGATTCCACTCCAGTCCTTT-TTCCATTCACACAGAATGTATC 342282 v ii iiv vi - iiivv vi ii --- i C L1PREC2_orf2# 194 GCTTGGTAGATTTTTCTCCATCCCTTTATTTTGAGCCTATGG---GTGTC 148 chr1ptel1M 342283 ATTCTGCTTTAAATGAGTTTCTTGTAAACAGCATATTGTAGGATTCTGGC 342332 viiiv v i i i v i iii v i- v C L1PREC2_orf2# 147 ATTGCATGTGAGATGGGTCTCTTGAAGACAGCATACCATTGGG-TCTTGC 99 chr1ptel1M 342333 T--TTAATTCAGTCTACTATCCACTTCCATTTTATGAGAGAGTTGACACC 342380 -- v i ii i i ii vv v v v vi i vi v vv C L1PREC2_orf2# 98 TTCTTTATCCAGCTTGCCACTCTGTGCCTTTTAATTGGGGCATTTAGCCC 49 chr1ptel1M 342381 ATTCACATTCACAGTTA 342397 i vi C L1PREC2_orf2# 48 ATTTACATTCAAGGTTA 32 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 46.85 CpG sites = 63, Kimura (unadjusted) = 46.85 Transitions / transversions = 1.17 (63/54) Gap_init rate = 0.05 (19 / 355), avg. gap size = 1.32 (25 / 19) 338 28.65 4.58 1.91 chr1ptel1M 342280 342432 (657568) C L1MEj_5end#LINE/L1 (0) 2160 2004 m_b10s551i3 363 chr1ptel1M 342280 ATCATTCTGCTTTAAATGAGTTTCTTGTAAACAGCATATTGTAGGATTCT 342329 i i i i v v iv i i C L1MEj_5end#LI 2160 ATCACTTTGTTTTAAGTGTGTTTCTTGTAAACAGCATATAGCTGGGTTTT 2111 chr1ptel1M 342330 G-GCTTTAATTCAGTCTACTATCCACTTCCATTTTATGAGAGAGTTGACA 342378 -vi ii i ivi vi v vi v v i i v vv C L1MEj_5end#LI 2110 GTTTTTTAACCCAATCTGACAGTCTCTGTCTTTTAATGGGAGAATTCAGT 2061 chr1ptel1M 342379 CCATTCACATTC------ACAGTTAAAATAACTAATTTTGTATTTCCTAC 342422 i------ iii i v vi i i--- v C L1MEj_5end#LI 2060 CCATTCACATTTAGTGTAACGACTGATATACTTGATTTTA---TTCCTTC 2014 chr1ptel1M 342423 CATTTTATTT 342432 i i C L1MEj_5end#LI 2013 CATCTTACTT 2004 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.32 CpG sites = 27, Kimura (unadjusted) = 37.43 Transitions / transversions = 1.69 (27/16) Gap_init rate = 0.03 (5 / 152), avg. gap size = 2.00 (10 / 5) 301 23.16 4.65 7.14 chr1ptel1M 342281 342452 (657548) C L1MEh_5end#LINE/L1 (1) 2234 2067 m_b10s551i4 363 chr1ptel1M 342281 TCATTCTGCTTTAAATGAGTTTCTTGTAAACAGCATATTGTAGGATTCTG 342330 v ? i i v i i v i C L1MEh_5end#LI 2234 TCCTTNTGTTTTAAGTGTGTCTCTTGTAGACAGCATATTGTTGGATTTTG 2185 chr1ptel1M 342331 GCTTT-AATTCAGTCTACTATCCACTTCCATTTTATGAGAGAGTTGACAC 342379 vi - i i iv? vi v vi v v vi v v vv C L1MEh_5end#LI 2184 TTTTTNAATCCAATCTGANAATCTCTGTCTTTTAATTGGTGAGTTTAACC 2135 chr1ptel1M 342380 CATTCACATTCACAGTTAAAATAACTAAT---TTTG----TATTTCCTAC 342422 i i --- iv v i? --- ? ---- - i C L1MEh_5end#LI 2134 CATTTACATTTA---TTGTAATTACTGNTATATTNGGACTTATTT-CTGC 2089 chr1ptel1M 342423 CATTTTATTTACCTCAAGTTTGCTTTCTAT 342452 i --------i i C L1MEh_5end#LI 2088 CATCTTATT--------ATTTGTTTTCTAT 2067 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 28.88 CpG sites = 20, Kimura (unadjusted) = 28.88 Transitions / transversions = 1.18 (20/17) Gap_init rate = 0.09 (15 / 171), avg. gap size = 1.33 (20 / 15) 217 28.51 8.74 4.67 chr1ptel1M 344074 344176 (655824) C MIRc#SINE/MIR (157) 111 5 m_b10s601i0 364 chr1ptel1M 344074 TTAAGTGAGATTACTTTGCTAAAAACACAGAG---GTA-----CAGAATC 344115 ----- vv i iiv v --- ----- ii C MIRc#SINE/MIR 111 TTAAGTGA-----CTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCC 67 chr1ptel1M 344116 CAAATTTCAACCCATGTCTTCA-GCATCCAAATCTAGCCATCTTTACATT 344164 vii i iv v v- vv i i ivv v i C MIRc#SINE/MIR 66 GGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACT 17 chr1ptel1M 344165 CCATCACACTGC 344176 v i C MIRc#SINE/MIR 16 GCACCACACTGC 5 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.81 CpG sites = 14, Kimura (unadjusted) = 36.39 Transitions / transversions = 1.00 (14/14) Gap_init rate = 0.08 (8 / 102), avg. gap size = 1.75 (14 / 8) 16 0.00 0.00 0.00 chr1ptel1M 347315 347331 (652669) (T)n#Simple_repeat 1 17 (0) m_b10s252i3 365 chr1ptel1M 347315 TTTTTTTTTTTTTTTTT 347331 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTT 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 289 26.71 4.20 8.77 chr1ptel1M 348637 348755 (651245) MIR#SINE/MIR 10 123 (139) m_b10s601i1 366 chr1ptel1M 348637 CATATTGGTTTCAAAATCA-GAA---TGCAGTCAGGAGGACTTGAGTTCA 348682 v -- i v - ii--- v i - vvi i i i MIR#SINE/MIR 10 CATAGTGGTT--AAGAGCACGGGCTCTGGAGCCAG-ACTGCCTGGGTTCG 56 chr1ptel1M 348683 AACTTGGTCTCTGACACTTCATACTTCCTAGCTGTGTAACCCTGGGCAAA 348732 iiiv v v v------- i i i MIR#SINE/MIR 57 AATCCCGGCTCTGCCACTTA-------CTAGCTGTGTGACCTTGGGCAAG 99 chr1ptel1M 348733 TCACTTAACACCAAT-TGCCCCAG 348755 i vi vv - i MIR#SINE/MIR 100 TTACTTAACCTCTCTGTGCCTCAG 123 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.22 CpG sites = 17, Kimura (unadjusted) = 33.63 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.11 (13 / 118), avg. gap size = 1.15 (15 / 13) 373 21.24 0.00 9.21 chr1ptel1M 348659 348741 (651259) MIRc#SINE/MIR 37 112 (156) m_b10s601i2 366 chr1ptel1M 348659 TGCAGTCAGGAGGACTTGAGTTCAAACTTGGTCTCTGACACTTCATACTT 348708 v i i i i iiiiv v v v------ MIRc#SINE/MIR 37 TGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTA------ 80 chr1ptel1M 348709 CCTAGCTGTGTAACCCTGGGCAAATCACTTAAC 348741 - i i i MIRc#SINE/MIR 81 -CTAGCTGTGTGACCTTGGGCAAGTCACTTAAC 112 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 23.67 CpG sites = 11, Kimura (unadjusted) = 25.47 Transitions / transversions = 2.20 (11/5) Gap_init rate = 0.09 (7 / 82), avg. gap size = 1.00 (7 / 7) 25 15.85 0.00 0.00 chr1ptel1M 348757 348798 (651202) (A)n#Simple_repeat 1 42 (0) m_b10s252i5 367 chr1ptel1M 348757 AAAAAAAAAAAAAAAAAAAAAAAAAGTAGATAAATAAATAAA 348798 iv i v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 42 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 18 20.94 0.00 3.92 chr1ptel1M 348757 348809 (651191) (AATA)n#Simple_repeat 1 51 (0) m_b10s252i4 368 chr1ptel1M 348757 AAAAAAAAAAAAAAAAAAAAAAAAAGTAGATAAATAAATAAATCAGAATG 348806 v v v v v v i i - - i (AATA)n#Simpl 1 AATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAAT-A-AATA 48 chr1ptel1M 348807 AAT 348809 (AATA)n#Simpl 49 AAT 51 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.00 (2 / 2) 354 27.67 21.57 0.81 chr1ptel1M 348813 349016 (650984) MIRb#SINE/MIR 13 258 (10) m_b10s601i3 369 chr1ptel1M 348813 GCAGTACAGTGGATAGAGC------TTTTGA-TCATAAAGACCTGAGTTT 348855 ii i v ------ v - v v i i MIRb#SINE/MIR 13 GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTC 62 chr1ptel1M 348856 TAATTACACCTC--------ATAAA----GGGGC--TAGTCCATTTACAG 348891 v iv iv -------- iv i---- v i -- i v v v vv MIRb#SINE/MIR 63 GAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTT 112 chr1ptel1M 348892 GACCACT----GTCTCAATTTCTTATTCTGTAAAATGAGCATAACAATCA 348937 i v ---- i i i vv i v i vv MIRb#SINE/MIR 113 AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAC 162 chr1ptel1M 348938 CTCCTAATCCTAGGGTTCTCATGAGGA-TAAATAAGA----G-------- 348974 v i-- vi v ii - i ---- -------- MIRb#SINE/MIR 163 CTACC--TCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAA 210 chr1ptel1M 348975 ------AGCACAGTGCATGACACACAGTAGATACTATAGAAATGCTAG 349016 ------ v i i iiii vv v v MIRb#SINE/MIR 211 GCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAAATGGTAG 258 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.68 CpG sites = 28, Kimura (unadjusted) = 35.00 Transitions / transversions = 1.00 (28/28) Gap_init rate = 0.06 (12 / 203), avg. gap size = 3.83 (46 / 12) 360 25.81 16.13 0.00 chr1ptel1M 348898 349021 (650979) MIR#SINE/MIR 116 259 (3) m_b10s601i4 369 chr1ptel1M 348898 TGTCTCAATTTCTTATTCTGTAAAATGAGCATAACAATCACTCCTA-ATC 348946 i i i vv i v i viiv -v MIR#SINE/MIR 116 TGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTC 165 chr1ptel1M 348947 CTAGGGTTCTCATGAGGA-TAAATAAG-----------AGAGC------- 348977 v v ii - i ----------- i ------- MIR#SINE/MIR 166 ATAGGGTTGTTGTGAGGATTAAATGAGTTAATACATGTAAAGCGCTTAGA 215 chr1ptel1M 348978 ACAGTGCATGACACACAGTAGATACTATAGAAATGCTAGTCATT 349021 v i i iiii vv v i ii MIR#SINE/MIR 216 ACAGTGCCTGGCACATAGTAAGCGCTCAATAAATGTTAGCTATT 259 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.19 CpG sites = 20, Kimura (unadjusted) = 32.56 Transitions / transversions = 1.67 (20/12) Gap_init rate = 0.03 (4 / 123), avg. gap size = 5.00 (20 / 4) 311 21.33 6.59 2.11 chr1ptel1M 349349 349439 (650561) C MIR3#SINE/MIR (3) 205 111 m_b10s601i5 370 chr1ptel1M 349349 TTATAGGGTCATA-AATGATCA---CTGGAAGGAATCTGCAGAG-CCACA 349393 i ii - - --- i i -i -i iv C MIR3#SINE/MIR 205 TCATAGAATCATAGAATG-TCAGAGCTGGAAGGGACCT-TAGAGATCATC 158 chr1ptel1M 349394 GAGGACAACCCACTTATTTTATAGATG-GGAAACTGAGATTCAGTGA 349439 v vv v i i - iii v C MIR3#SINE/MIR 157 TAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGA 111 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.90 CpG sites = 13, Kimura (unadjusted) = 25.90 Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.07 (6 / 90), avg. gap size = 1.33 (8 / 6) 237 35.96 2.61 0.85 chr1ptel1M 350682 350796 (649204) L3#LINE/CR1 3980 4096 (3) m_b10s601i6 371 chr1ptel1M 350682 AAGGAAAAGCTGCCTGCGCAATTTTCAGAACTTTGGAAGGCAAAATT--T 350729 v i i vv vv v v iiv v v v iviii -- L3#LINE/CR1 3980 AAGCAGAGGCTGGATGACCACTTGTCAGGGATGTTGTAGAAGGGATTCCT 4029 chr1ptel1M 350730 GCATCCAGATAG-AGGTTAAATGAAATCATCTCTGAGATTACTTCCATGT 350778 i-i i - ii iv i v i i i iv vv L3#LINE/CR1 4030 GCATT-GGATGGGAGGTTGGACTAGATGACCTCTAAGGTCCCTTCCAACT 4078 chr1ptel1M 350779 TTGAGATGCTTCCATTCT 350796 i v viv L3#LINE/CR1 4079 CTGAGATTCTGTGATTCT 4096 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 50.05 CpG sites = 21, Kimura (unadjusted) = 50.05 Transitions / transversions = 1.05 (21/20) Gap_init rate = 0.03 (3 / 114), avg. gap size = 1.33 (4 / 3) 309 25.33 7.69 3.36 chr1ptel1M 351152 351294 (648706) C MIR3#SINE/MIR (9) 199 51 m_b10s601i7 372 chr1ptel1M 351152 AACCATCAAAATGT-AGAGCTGAAAAACACTTAAGA-ATTAAAAAGTCCA 351199 i - i - i iiv i v - i vvv C MIR3#SINE/MIR 199 AATCAT-AGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCA 151 chr1ptel1M 351200 ACCCTCTTCAATATACAG--GAGAAAACTGAAACACAGA-----GAAGGG 351242 i - v v -- i ii v ----- v C MIR3#SINE/MIR 150 ACCCCCT-CATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTG 102 chr1ptel1M 351243 ATTCGCCCAAAGGTCATCCCCTTTAAG--AGTGTCAGAGTCAACTCTTAA 351290 i i - -- v vvi? -- v i iivv vi C MIR3#SINE/MIR 101 ACTTGCCC-AAGGTCA--CACAGCNAGTTAGTGGCAGAGCCGGGACTAGA 55 chr1ptel1M 351291 ATCC 351294 i C MIR3#SINE/MIR 54 ACCC 51 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.63 CpG sites = 19, Kimura (unadjusted) = 31.71 Transitions / transversions = 1.19 (19/16) Gap_init rate = 0.07 (10 / 142), avg. gap size = 1.60 (16 / 10) 19 3.54 3.45 0.00 chr1ptel1M 353503 353531 (646469) (ATT)n#Simple_repeat 1 30 (0) m_b10s252i6 373 chr1ptel1M 353503 ATTATTATTATTATTATTATT-TTATTTTT 353531 - v (ATT)n#Simple 1 ATTATTATTATTATTATTATTATTATTATT 30 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1) 18 22.67 0.00 3.77 chr1ptel1M 354174 354228 (645772) (AAAT)n#Simple_repeat 1 53 (0) m_b10s252i7 374 chr1ptel1M 354174 AAATAAATAAACAAACAAATAAAGCAAAATTTGAATTTAATAAAGTAAAT 354223 i i vv v vv - v v - (AAAT)n#Simpl 1 AAATAAATAAATAAATAAATAAATAAATAAAT-AAATAAATAAA-TAAAT 48 chr1ptel1M 354224 CAATA 354228 v (AAAT)n#Simpl 49 AAATA 53 Matrix = Unknown Transitions / transversions = 0.25 (2/8) Gap_init rate = 0.04 (2 / 54), avg. gap size = 1.00 (2 / 2) 273 27.24 6.93 1.89 chr1ptel1M 354271 354371 (645629) MIRb#SINE/MIR 143 248 (20) m_b10s601i8 375 chr1ptel1M 354271 TAAAATATGGATAAAAAT---TAGCTTCCAAAATTTATTGTGACAATCAC 354317 iv v --- v iv iii -i vi i v MIRb#SINE/MIR 143 TAAAATGGGGATAATAATACCTACCTCGCAGGGTT-GTTGTGAGGATTAA 191 chr1ptel1M 354318 AGGAGATATTG---GTAAGGTGTTTAACTT-GTGTCTGGCACATAATAGG 354363 v v --- i i i i vi- i i i MIRb#SINE/MIR 192 ATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAG 241 chr1ptel1M 354364 TCCATCAA 354371 iv - MIRb#SINE/MIR 242 CGC-TCAA 248 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.35 CpG sites = 17, Kimura (unadjusted) = 35.03 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.05 (5 / 100), avg. gap size = 1.80 (9 / 5) 13 18.67 7.41 3.57 chr1ptel1M 356497 356550 (643450) (CTC)n#Simple_repeat 1 56 (0) m_b10s252i8 376 chr1ptel1M 356497 CTCC-CCTCCTTCT-TTCACTTTTTCT-CTTCTCCTCCCTCCT-CTCCCC 356542 - i -i - ii i - i - - i (CTC)n#Simple 1 CTCCTCCTCCTCCTCCTC-CTCCTCCTCCTCCTCCT-CCTCCTCCTCCTC 48 chr1ptel1M 356543 ATCCTCCT 356550 v (CTC)n#Simple 49 CTCCTCCT 56 Matrix = Unknown Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.11 (6 / 53), avg. gap size = 1.00 (6 / 6) 286 29.27 1.22 0.00 chr1ptel1M 359170 359251 (640749) C L3#LINE/CR1 (2) 4097 4015 m_b10s601i9 377 chr1ptel1M 359170 TGGAGTCACTGATTCTCAGAGTTGGAAGGGAATTCAAAGATTGTCTAATC 359219 i i v v vi i i i ii i C L3#LINE/CR1 4097 TAGAATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTC 4048 chr1ptel1M 359220 CAAGGTAAAACCCCAAAGAGAGATCCC-TCTAC 359251 vv vvv i v viv ii - C L3#LINE/CR1 4047 CAACCTCCCATCCAATGCAGGAATCCCTTCTAC 4015 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.81 CpG sites = 13, Kimura (unadjusted) = 37.81 Transitions / transversions = 1.18 (13/11) Gap_init rate = 0.01 (1 / 81), avg. gap size = 1.00 (1 / 1) 17 22.31 4.11 4.11 chr1ptel1M 359308 359380 (640620) (ATTT)n#Simple_repeat 1 73 (0) m_b10s252i10 378 chr1ptel1M 359308 ATTTA-TTATTGTTTGTAAATGATTTAGTTTTTTTGTTTGTTT-TTT-GT 359354 - - v - v v v - v i i - -v (ATTT)n#Simpl 1 ATTTATTTATT-TAT-TTATTTATTTA-TTTATTTATTTATTTATTTATT 47 chr1ptel1M 359355 TGTTTTTTTTTTAATTTTTTTATTTA 359380 i v v v v (ATTT)n#Simpl 48 TATTTATTTATTTATTTATTTATTTA 73 Matrix = Unknown Transitions / transversions = 0.30 (3/10) Gap_init rate = 0.08 (6 / 72), avg. gap size = 1.00 (6 / 6) 25 17.77 0.00 0.00 chr1ptel1M 359335 359379 (640621) (T)n#Simple_repeat 1 45 (0) m_b10s252i11 379 chr1ptel1M 359335 TTTTTTTGTTTGTTTTTTGTTGTTTTTTTTTTAATTTTTTTATTT 359379 v v v v vv v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 45 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 14 11.56 3.57 0.00 chr1ptel1M 360576 360603 (639397) (AAC)n#Simple_repeat 1 29 (0) m_b10s252i12 380 chr1ptel1M 360576 AAAAACAACAACAACAAGAATAA-AACAA 360603 v v i - (AAC)n#Simple 1 AACAACAACAACAACAACAACAACAACAA 29 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 439 31.98 3.12 0.87 chr1ptel1M 366019 366242 (633758) L1ME4c_3end#LINE/L1 307 535 (295) m_b10s551i5 381 chr1ptel1M 366019 CAACTATTTTGGAGAGCAATTAGGAACAAAGTCCAAAAGGCTAGAAAATT 366068 iv i v v vv v viv ii i v v L1ME4c_3end#L 307 CAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAAAAT 356 chr1ptel1M 366069 GTCCATACCCTTTGATCCAGTAAGACCACTATTAGGTCTGTATCCTAAAG 366118 i i vv vi i vv v i L1ME4c_3end#L 357 GTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGG 406 chr1ptel1M 366119 AGATCAT---AAAAAGGGAAAAGGACCCCCATGTACAAAAAT----ATAG 366161 i v --- i i i -- ivi i i i ---- v L1ME4c_3end#L 407 AAATAATTCAAAAGAAGGAAAAAG--CTATATGCACGAAGATGTTCATTG 454 chr1ptel1M 366162 TGGCTCTTTTTGTGGTGTCAAAGAATTGGAAATTGAGGGGATGCCTATCA 366211 ii vi v i ii iv i i ivivvvii i i v L1ME4c_3end#L 455 CAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACA 504 chr1ptel1M 366212 AATGAGGAATGGTTGAACAAGTTGTGGTATA 366242 vv i i ii i i i L1ME4c_3end#L 505 ATAGGGGAATGGTTAAGTAAATTATGGTACA 535 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.51 CpG sites = 42, Kimura (unadjusted) = 43.14 Transitions / transversions = 1.45 (42/29) Gap_init rate = 0.02 (4 / 223), avg. gap size = 2.25 (9 / 4) 357 33.92 0.37 4.65 chr1ptel1M 369113 369381 (630619) HERVI#LTR/ERV1 4264 4521 (3263) m_b10s701i0 382 chr1ptel1M 369113 TGGCAAAACTGTTCATTGATAAGAGTTGAGGCTTGGAGATTGTCTAAAAC 369162 vi i v ??? vvi? i v v vv i i i v v HERVI#LTR/ERV 4264 TGGAGAAGCTCTNNNTGCGNAAGAATAGAGTCAGGAAGACTGCCTAATAA 4313 chr1ptel1M 369163 ATGGTCTTCCCAGACTTGTGAATTTTATGTACTCAATCTAGTAAACCCTG 369212 v v i ? ii v v i ii ---- i ii i HERVI#LTR/ERV 4314 TTGGTCTGCCCAAACNTGTGAGCTGTTTGCACTCAGCC----AAGCTTTA 4359 chr1ptel1M 369213 AAGTTATTGGCAAAGAAATAAAAAACTATTTATACTGATTCTAAATATAC 369262 ivv vv vv iv ii i i i ii HERVI#LTR/ERV 4360 AAGCACTTGCAAAACCAGGAAGGAACCATCTATACTGATTCTAAGTACGC 4409 chr1ptel1M 369263 TTGGGATATGGGGCATGGGGCATGTGTTTGAAAAAACTGAAGAAGAAAGA 369312 i v----- -- vv iii i i viiivv v HERVI#LTR/ERV 4410 CTT-----TGGGG--TGGCTCATACATTTGGAAAAATTCGGACTGAACGA 4452 chr1ptel1M 369313 GGTATGGTCAACAGTAATGGTAAGGAATTAGCCCACATGACATT-GTTAC 369361 v vi i i v iv i vi v ii i v ivi -i i HERVI#LTR/ERV 4453 GGTCTTATTAATAGTAAAGGCCAAGACCTTGTTCATAAGGAGTTAATCAC 4502 chr1ptel1M 369362 TGCAAGTCTTAAAAAACCTC 369381 i- v ? v HERVI#LTR/ERV 4503 C-CAAGTATTNAATAACCTC 4521 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 45.67 CpG sites = 49, Kimura (unadjusted) = 48.04 Transitions / transversions = 1.29 (49/38) Gap_init rate = 0.05 (13 / 268), avg. gap size = 1.00 (13 / 13) 370 34.60 0.42 5.29 chr1ptel1M 369149 369386 (630614) HERVP71A#LTR/ERV1 3983 4209 (3381) m_b10s701i1 382 chr1ptel1M 369149 AGATTGTCTAAAACATGGTCTTCCCAGACTTGTGAATTTTATGTACTCAA 369198 ii vivv vv i i v iv i HERVP71A#LTR/ 3983 AGATTACCTAATGGCTGGTCGGCCCAAACCTGTGAATTATATGCTCTTAA 4032 chr1ptel1M 369199 TCTAGTAAACCCTGAAGTTATTGGCAAAGAAATAAAAAACTATTTATACT 369248 i ---- ii i i vi v v iivv v iiv v HERVP71A#LTR/ 4033 CC----AGGCCCTAAAGCTCCTTGAAGGCCAAGAAGGCACTATATATACT 4078 chr1ptel1M 369249 GATTCTAAATATACTTGGGATATGGGGCATGGGGCATGTGTTTGAAAAAA 369298 i i i----- -- vi iiiv i HERVP71A#LTR/ 4079 GATTCCAAATATGCC-----TATGGGG--TGGTACACACTTTTGGAAAAA 4121 chr1ptel1M 369299 -CTGAAGAAGAAAGAGGTATGGTCAACAGTAATGGTAAGGAATTAGCCCA 369347 - i -v iv i iv ii v i i iv v i i iv HERVP71A#LTR/ 4122 TCTGGA-CAGAGCGGGGCCTAATAAATAGCAGGGGAAAAGAATTGGTACA 4170 chr1ptel1M 369348 CATGACATTGTTACTGCAAGTCTTAAAAAACCTCTTCCT 369386 iiv iv i v vvvi i i i i i v HERVP71A#LTR/ 4171 TGGGGAACTGGTCAAACAGGTTTTAGAAAGCCTCCTGCT 4209 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 48.29 CpG sites = 47, Kimura (unadjusted) = 48.29 Transitions / transversions = 1.52 (47/31) Gap_init rate = 0.05 (13 / 237), avg. gap size = 1.00 (13 / 13) 412 25.80 3.72 1.04 chr1ptel1M 369461 369648 (630352) L1ME4b_3end#LINE/L1 31 223 (669) m_b10s551i6 383 chr1ptel1M 369461 CAAATTTATAAGAAATCAAG-CCATTCTCCAAAT-GATAAATGGTCAA-G 369507 iv -- - vivv v - v v - L1ME4b_3end#L 31 CAAATCAATAAGAAA--AAGACCAACAACCCAATAGAAAAATGGGCAAAG 78 chr1ptel1M 369508 GATAAGAACAA----TTTTCAGTTGAAGAAATTGAAACTCTTTCTAGTCA 369553 v i---- iv vvi i vv ivvi ii iv L1ME4b_3end#L 79 GATATGAACAGACAGTTCACAGAAAAGGAAATACAAATGGCTCTTAAACA 128 chr1ptel1M 369554 TATGAAAAGGTGTTCCAAATCACTATTGATCAGAGAAATGCAAATTAAGA 369603 i i v vv vv i v i L1ME4b_3end#L 129 TATGAAAAGATGCTCAACCTCACTCATAATAAGAGAAATGCAAATTAAAA 178 chr1ptel1M 369604 CAACTCTGAGATACCACGACCCACTTCTAAGATTGGCTAAGATCA 369648 v v ivvii i v v v L1ME4b_3end#L 179 CTACACTGAGATACCATTTTTCACCTATCAGATTGGCAAAGATCA 223 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 31.67 CpG sites = 19, Kimura (unadjusted) = 31.67 Transitions / transversions = 0.66 (19/29) Gap_init rate = 0.03 (6 / 187), avg. gap size = 1.50 (9 / 6) 382 21.94 0.00 3.81 chr1ptel1M 369552 369660 (630340) L1ME3A_3end#LINE/L1 127 231 (689) m_b10s551i7 383 chr1ptel1M 369552 CATATGAAAAGGTGTTCCAAATCACTATTGATCAGAGAAATGCAAATTAA 369601 i v vv i v v i L1ME3A_3end#L 127 CATATGAAAAGGTGCTCAACTTCATTAGTCATCAGGGAAATGCAAATTAA 176 chr1ptel1M 369602 GACAACTCTGAGATACCACGACCCACTTCTAAGATTGGCTAAGATCACAG 369651 i v vv ? v v iiviv v i ---- L1ME3A_3end#L 177 AACCACAATGNGATACCACTACACACCCACCAGAATGGCTAAAAT----G 222 chr1ptel1M 369652 GAAAAGATA 369660 i i L1ME3A_3end#L 223 AAAAAGACA 231 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 26.28 CpG sites = 10, Kimura (unadjusted) = 26.28 Transitions / transversions = 0.77 (10/13) Gap_init rate = 0.04 (4 / 108), avg. gap size = 1.00 (4 / 4) 433 16.85 1.04 1.04 chr1ptel1M 369552 369647 (630353) L1MC1_3end#LINE/L1 127 222 (858) m_b10s551i8 383 chr1ptel1M 369552 CATATGAAAAGGTGTTCCAAATCACTAT-TGATCAGAGAAATGCAAATTA 369600 i i v - - v i L1MC1_3end#LI 127 CATATGAAAAGATGCTCCACATCA-TATGTCATCAGGGAAATGCAAATTA 175 chr1ptel1M 369601 AGACAACTCTGAGATACCACGACCCACTTCTAAGATTGGCTAAGATC 369647 i vv v v i v v v i i L1MC1_3end#LI 176 AAACAACAATGAGATACCACTACACACCTATTAGAATGGCCAAAATC 222 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 19.11 CpG sites = 7, Kimura (unadjusted) = 19.11 Transitions / transversions = 0.78 (7/9) Gap_init rate = 0.02 (2 / 95), avg. gap size = 1.00 (2 / 2) 385 30.77 1.17 1.17 chr1ptel1M 369667 369837 (630163) L1ME4c_3end#LINE/L1 385 555 (275) m_b10s551i9 383 chr1ptel1M 369667 CTGCTGGGCTTATATTCCAGGGAGAT--CTTAAAGTGGGGAACAAGACCT 369714 v vv v i i i i --i i ivii v -- L1ME4c_3end#L 385 CTTCTGGGAATTTATCCTAAGGAAATAATTCAAAAGAAGGAAAAAG--CT 432 chr1ptel1M 369715 GTATGTGCAAAAATGTTTGGGGCAGCCCTCTTTGTAGTGGCCGGAAACTG 369764 i ii i i iivv vi v i i i vii i L1ME4c_3end#L 433 ATATGCACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTG 482 chr1ptel1M 369765 GAAACTGAGTGAATGTCTATCAATTGGAGAATGGCTGAATAAATTATGGT 369814 vivv i i v v i i i i L1ME4c_3end#L 483 GAAACAACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGT 532 chr1ptel1M 369815 ATATGAATATTATGGAATATTAT 369837 i v? iviv L1ME4c_3end#L 533 ACATCNACTCGATGGAATATTAT 555 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.54 CpG sites = 33, Kimura (unadjusted) = 41.67 Transitions / transversions = 1.74 (33/19) Gap_init rate = 0.02 (3 / 170), avg. gap size = 1.33 (4 / 3) 342 32.48 0.00 1.95 chr1ptel1M 369715 369871 (630129) L1MC5a_3end#LINE/L1 430 583 (2194) m_b10s551i11 383 chr1ptel1M 369715 GTATGTGCAAAAATGTTTGGGGCAGCCCTCTTTGTAGTGGCCGGAAACTG 369764 ii iiv i iivv vi v i i vii i L1MC5a_3end#L 430 GTATGCACAAGGTTATTCATTGCAGCATTATTTGTAATAGCAAAAGACTG 479 chr1ptel1M 369765 GAAACTGAGTGAATGTCTATCAATTGGAGAATGGCTGAATAAATTATGGT 369814 vivvii i v i v i i L1MC5a_3end#L 480 GAAACAACCCAAATGTCCATCAATAGGGGACTGGTTGAATAAACTATGGT 529 chr1ptel1M 369815 ATATGAATATTATGGAATATTATTGTTCTGTAAGAAACAACCAACAGGAT 369864 i vv i iv i i vvvv i iv i---v v L1MC5a_3end#L 530 ACATCCACACAATGGAGTACTATGCAGCTGTAAAAAGGAAT---GAGGAA 576 chr1ptel1M 369865 GATTTCT 369871 i L1MC5a_3end#L 577 GATCTCT 583 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 43.93 CpG sites = 29, Kimura (unadjusted) = 43.93 Transitions / transversions = 1.38 (29/21) Gap_init rate = 0.02 (3 / 156), avg. gap size = 1.00 (3 / 3) 465 25.20 0.00 0.00 chr1ptel1M 369715 369837 (630163) L1ME3G_3end#LINE/L1 426 548 (376) m_b10s551i10 383 chr1ptel1M 369715 GTATGTGCAAAAATGTTTGGGGCAGCCCTCTTTGTAGTGGCCGGAAACTG 369764 i i ii iivv vi v i i vii i L1ME3G_3end#L 426 GCATGTACAAGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTG 475 chr1ptel1M 369765 GAAACTGAGTGAATGTCTATCAATTGGAGAATGGCTGAATAAATTATGGT 369814 vivv i i v i i i L1ME3G_3end#L 476 GAAACAACCTAAATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGT 525 chr1ptel1M 369815 ATATGAATATTATGGAATATTAT 369837 vv i i L1ME3G_3end#L 526 ATATCCATACTATGGAATACTAT 548 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 31.70 CpG sites = 20, Kimura (unadjusted) = 31.70 Transitions / transversions = 1.82 (20/11) Gap_init rate = 0.00 (0 / 122), avg. gap size = 0.0 (0 / 0) 75 2.82 0.00 0.00 chr1ptel1M 371003 371075 (628925) (AG)n#Simple_repeat 1 73 (0) c_b11s251i0 384 chr1ptel1M 371003 AGAGAAAGAAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 371052 i i (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr1ptel1M 371053 AGAGAGAGAGAGAGAGAGAGAGA 371075 (AG)n#Simple_ 51 AGAGAGAGAGAGAGAGAGAGAGA 73 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 72), avg. gap size = 0.0 (0 / 0) 17 0.00 0.00 0.00 chr1ptel1M 371315 371333 (628667) (A)n#Simple_repeat 1 19 (0) m_b11s252i0 385 chr1ptel1M 371315 AAAAAAAAAAAAAAAAAAA 371333 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAA 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 23 12.56 0.00 0.00 chr1ptel1M 371803 371837 (628163) (T)n#Simple_repeat 1 35 (0) m_b11s252i1 386 chr1ptel1M 371803 TTTTTTTTTTTTGTTTGTTTTTTTTTTTGATTTTT 371837 v v vv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 35 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 44 0.00 0.00 0.00 chr1ptel1M 372208 372245 (627755) (GA)n#Simple_repeat 1 38 (0) c_b11s251i1 387 chr1ptel1M 372208 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 372245 (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 38 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 36 0.00 0.00 0.00 chr1ptel1M 372398 372428 (627572) (AC)n#Simple_repeat 1 31 (0) c_b11s251i2 388 chr1ptel1M 372398 ACACACACACACACACACACACACACACACA 372428 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACA 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 chr1ptel1M 373610 373626 (626374) (A)n#Simple_repeat 1 17 (0) m_b11s252i2 389 chr1ptel1M 373610 AAAAAAAAAAAAAAAAA 373626 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 33 3.95 5.77 0.00 chr1ptel1M 375853 375904 (624096) (CCCCT)n#Simple_repeat 1 55 (0) m_b11s252i3 390 chr1ptel1M 375853 CCCCT-CCCT-CCCTCCAC-CCCCTCTCCTCCCCTCCCCTCCCCTCCCCT 375899 - - v - i (CCCCT)n#Simp 1 CCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCT 50 chr1ptel1M 375900 CCCCT 375904 (CCCCT)n#Simp 51 CCCCT 55 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.00 (3 / 3) 279 19.14 5.10 4.04 chr1ptel1M 376510 376607 (623393) MER50-int#LTR/ERV1 7098 7196 (9) m_b11s701i0 391 chr1ptel1M 376510 AACCCCCATGAACCCT-TGCCAGCTCAAAGCAGTTATAGAAGAAGAGACC 376558 v iviv - i vvi i vv- MER50-int#LTR 7098 AACCACCACCGCCCCTCTGTCAGCAGGAAGCAGTTACAGAAGACT-GACC 7146 chr1ptel1M 376559 TTGGCCCTTTATCCCAAATGAATTTAGGGGT----GACTGCTTGAGGGGG 376604 v i v v v v -- ---- - MER50-int#LTR 7147 TTCGTCCATTTTCCCCAAAGAATT--GGGGTCTTGGACT-CTTGAGGGGG 7193 chr1ptel1M 376605 GAA 376607 MER50-int#LTR 7194 GAA 7196 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 20.84 CpG sites = 6, Kimura (unadjusted) = 22.11 Transitions / transversions = 0.50 (6/12) Gap_init rate = 0.06 (6 / 97), avg. gap size = 1.50 (9 / 6) 32 0.00 0.00 0.00 chr1ptel1M 378361 378395 (621605) (A)n#Simple_repeat 1 35 (0) m_b11s252i4 392 chr1ptel1M 378361 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 378395 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 35 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 415 24.73 0.72 12.10 chr1ptel1M 379329 379466 (620534) C MIRc#SINE/MIR (143) 125 2 m_b11s601i0 393 chr1ptel1M 379329 GGGGCTGAGGGAATTGGGGTTAAGTGACTT-CCCAGAGTCACACAGCTAG 379377 i v i ----- - ii C MIRc#SINE/MIR 125 GAGGCTCAGAGA-----GGTTAAGTGACTTGCCCAAGGTCACACAGCTAG 81 chr1ptel1M 379378 GAAATGTTAAGTGTCTGAGGCCAGATTTGAACTCGGGCACTCCTGACTTC 379427 ------- v v v vi i i i i ivi i C MIRc#SINE/MIR 80 -------TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCC 38 chr1ptel1M 379428 AGGTCTAATGCTCTACACATGGTGCCACGAAGCTGCCCC 379466 i i i viv iv ii ---i i C MIRc#SINE/MIR 37 AAGTCCAGTGCTCTTTCCACTGCACCAC---ACTGCCTC 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.50 CpG sites = 21, Kimura (unadjusted) = 30.73 Transitions / transversions = 2.33 (21/9) Gap_init rate = 0.12 (16 / 137), avg. gap size = 1.00 (16 / 16) 13 17.39 3.92 6.00 chr1ptel1M 379580 379630 (620370) (CACAGA)n#Simple_repeat 1 50 (0) m_b11s252i5 394 chr1ptel1M 379580 CACAGA-ACAAACA-TGACACAAATATTCTGCACAGAGACACAGACACAA 379627 - i -v i i -- v - v i (CACAGA)n#Sim 1 CACAGACACAGACACAGACACAGACA--CAG-ACACAGACACAGACACAG 47 chr1ptel1M 379628 ACA 379630 (CACAGA)n#Sim 48 ACA 50 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.10 (5 / 50), avg. gap size = 1.00 (5 / 5) 19 0.00 0.00 0.00 chr1ptel1M 380530 380550 (619450) (T)n#Simple_repeat 1 21 (0) m_b11s252i6 395 chr1ptel1M 380530 TTTTTTTTTTTTTTTTTTTTT 380550 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTT 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 27 24.23 0.00 0.00 chr1ptel1M 381602 381669 (618331) (AAAAA)n#Simple_repeat 1 68 (0) m_b11s252i7 396 chr1ptel1M 381602 AAAAAAAAAAAAAAAAAAAAAAAAAAAAATCAGATCAAAAGGGAAAAAAT 381651 vv i vv iii v (AAAAA)n#Simp 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr1ptel1M 381652 GAGAAAGAAAACAAACAA 381669 i i i v v (AAAAA)n#Simp 51 AAAAAAAAAAAAAAAAAA 68 Matrix = Unknown Transitions / transversions = 1.00 (7/7) Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0) 249 30.69 8.91 0.00 chr1ptel1M 384018 384118 (615882) C MIRb#SINE/MIR (156) 112 3 m_b11s601i1 397 chr1ptel1M 384018 AAATTACTTTGCCAAGA--ACACAG-----AAATA-CAGAATGCAAATTT 384059 i v vv i-- ----- i i- iivvii i C MIRb#SINE/MIR 112 AAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTC 63 chr1ptel1M 384060 CAACCCATATCC-TCTAAATCCAAATCTAGTGATCTTTTCATTCGGCCAT 384108 v vi i- i v v iv v i i vvi i C MIRb#SINE/MIR 62 GAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCACCAC 13 chr1ptel1M 384109 GCTGCCCTTC 384118 i C MIRb#SINE/MIR 12 GCTGCCCCTC 3 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.29 CpG sites = 18, Kimura (unadjusted) = 40.63 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.04 (4 / 100), avg. gap size = 2.25 (9 / 4) 16 8.48 0.00 0.00 chr1ptel1M 385460 385484 (614516) (AAC)n#Simple_repeat 1 25 (0) m_b11s252i9 398 chr1ptel1M 385460 AAAAACAACAACAACAATAACAACA 385484 v i (AAC)n#Simple 1 AACAACAACAACAACAACAACAACA 25 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 20 3.22 2.94 2.94 chr1ptel1M 386694 386727 (613273) (TTAGGG)n#Simple_repeat 1 34 (0) m_b11s252i10 399 chr1ptel1M 386694 TTAGGGTTAGGGTTTAGGGCT-GGGTTAGGGTTAG 386727 - i - (TTAGGG)n#Sim 1 TTAGGGTTAGGG-TTAGGGTTAGGGTTAGGGTTAG 34 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2) 272 20.71 7.14 2.27 chr1ptel1M 386902 386985 (613015) C MIR3#SINE/MIR (10) 198 111 m_b11s601i2 400 chr1ptel1M 386902 ATCATA-AATGATCACAG---GAAGGAATCTACAGAG-CCACAGAGCACA 386946 - - v --- i i -i -i ivv iv C MIR3#SINE/MIR 198 ATCATAGAATG-TCAGAGCTGGAAGGGACCT-TAGAGATCATCTAGTCCA 151 chr1ptel1M 386947 ATCCACTCATTTTATAGATG-GGAAACTGAGATTCAGTGA 386985 i v i - iii v C MIR3#SINE/MIR 150 ACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGA 111 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.84 CpG sites = 11, Kimura (unadjusted) = 24.84 Transitions / transversions = 1.83 (11/6) Gap_init rate = 0.07 (6 / 83), avg. gap size = 1.33 (8 / 6) 29 0.00 0.00 0.00 chr1ptel1M 387711 387737 (612263) (TAGGGT)n#Simple_repeat 1 27 (0) c_b11s251i3 401 chr1ptel1M 387711 TAGGGTTAGGGTTAGGGTTAGGGTTAG 387737 (TAGGGT)n#Sim 1 TAGGGTTAGGGTTAGGGTTAGGGTTAG 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 237 33.62 4.39 0.85 chr1ptel1M 387754 387867 (612133) L3#LINE/CR1 3971 4088 (11) m_b11s601i3 402 chr1ptel1M 387754 GAGTTGT--AAGGAAAAGATGCCTGAGCAATTTTCAGAACT-TTGGAAGA 387800 v -- v i i v vv v v v iiv - v ii L3#LINE/CR1 3971 GAGGTGTTCAAGCAGAGGCTGGATGACCACTTGTCAGGGATGTTGTAGAA 4020 chr1ptel1M 387801 AAAATTT-TGCATCCAGATAG-AGGTTAAATGAAATCATCTCTGAGATTA 387848 iii i- i-i i - ii iv i v i i i iv L3#LINE/CR1 4021 GGGATTCCTGCATT-GGATGGGAGGTTGGACTAGATGACCTCTAAGGTCC 4069 chr1ptel1M 387849 CTTCCATATTTGAGATGCT 387867 vv i v L3#LINE/CR1 4070 CTTCCAACTCTGAGATTCT 4088 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 46.18 CpG sites = 22, Kimura (unadjusted) = 46.18 Transitions / transversions = 1.38 (22/16) Gap_init rate = 0.04 (5 / 113), avg. gap size = 1.20 (6 / 5) 19 19.25 0.00 0.00 chr1ptel1M 388027 388062 (611938) (A)n#Simple_repeat 1 36 (0) m_b11s252i12 403 chr1ptel1M 388027 AAAAAAAAAAAAAAAAACACAAACCACAAACAAAAA 388062 v v vv v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 36 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 365 26.53 7.69 1.45 chr1ptel1M 388272 388401 (611599) C MIR3#SINE/MIR (7) 201 64 m_b11s601i4 404 chr1ptel1M 388272 AAAGTCATAAGATGT-AGAGTTGAAAAATACTTTAGA-ATTAAA-AATCC 388318 i i ii - i i iiv i - i vv- i C MIR3#SINE/MIR 201 AGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCC 152 chr1ptel1M 388319 AATCTCCCTCAATTTACAG--GAAGAAACTGAAACACAGG-----GAAGG 388361 i - v -- i ii v i----- v C MIR3#SINE/MIR 151 AACC-CCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGT 103 chr1ptel1M 388362 GATTTGCCCAAAGGTCCTCCCCTTTATGAGTGTCAGAGTC 388401 i - viv vvi?vi v v i C MIR3#SINE/MIR 102 GACTTGCCC-AAGGTCACACAGCNAGTTAGTGGCAGAGCC 64 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.10 CpG sites = 21, Kimura (unadjusted) = 34.10 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.05 (7 / 129), avg. gap size = 1.71 (12 / 7) 11 16.10 4.26 6.52 chr1ptel1M 389329 389375 (610625) (GAAACA)n#Simple_repeat 1 46 (0) m_b11s252i13 405 chr1ptel1M 389329 GAAAGAGAAAACAAGAATC-TAGGCA-AAACAGAAAGAGAAGACAGAAA 389375 v - - v -v ii - v - (GAAACA)n#Sim 1 GAAACAG-AAAC-AGAAACAGAAACAGAAACAGAAACAGAA-ACAGAAA 46 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.11 (5 / 46), avg. gap size = 1.00 (5 / 5) 11 21.86 0.00 5.13 chr1ptel1M 389354 389394 (610606) (AAAGAG)n#Simple_repeat 1 39 (0) m_b11s252i14 405 chr1ptel1M 389354 AAACAGAAAGAGAAGACAGAAAATGAGGAGAGGGAGAGAAA 389394 v - v iv -i ii (AAAGAG)n#Sim 1 AAAGAGAAAGAGAA-AGAGAAAGAGA-AAGAGAAAGAGAAA 39 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 24 26.16 0.00 0.00 chr1ptel1M 390277 390344 (609656) (AAAAAAA)n#Simple_repeat 1 68 (0) m_b11s252i15 406 chr1ptel1M 390277 AAAAAAAAAAAAAAATGGAAAAATAAATAAACAAAAACAAAGTAAATACA 390326 vii v v v v iv v v (AAAAAAA)n#Si 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr1ptel1M 390327 AAAGATAAAATATAAAAA 390344 i v v v (AAAAAAA)n#Si 51 AAAAAAAAAAAAAAAAAA 68 Matrix = Unknown Transitions / transversions = 0.36 (4/11) Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0) 15 14.38 0.00 0.00 chr1ptel1M 391720 391743 (608257) (TG)n#Simple_repeat 1 24 (0) m_b11s252i16 407 chr1ptel1M 391720 TGTGTGTATGTGCATGTGTGTGTG 391743 i ii (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTG 24 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 334 25.24 4.00 0.97 chr1ptel1M 392283 392382 (607618) MIRb#SINE/MIR 143 245 (23) m_b11s601i5 408 chr1ptel1M 392283 TAAAATGGGGATATAAAGACCTCCCTACCAGGGTTTGTGGTGAGAATCAC 392332 vv v v vv - v i i v MIRb#SINE/MIR 143 TAAAATGGGGATAATAATACCTACCTCGCAGGG-TTGTTGTGAGGATTAA 191 chr1ptel1M 392333 AGGAGATATTG---GTAAGGTACTTAAC-TTGTGTCTGGTACTTAATAGG 392378 v v --- i ii i -iv i i v i i MIRb#SINE/MIR 192 ATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAG 241 chr1ptel1M 392379 TTCT 392382 iv MIRb#SINE/MIR 242 CGCT 245 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.04 CpG sites = 12, Kimura (unadjusted) = 31.02 Transitions / transversions = 0.92 (12/13) Gap_init rate = 0.03 (3 / 99), avg. gap size = 1.67 (5 / 3) 28 0.00 0.00 0.00 chr1ptel1M 394333 394363 (605637) (A)n#Simple_repeat 1 31 (0) m_b11s252i17 409 chr1ptel1M 394333 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 394363 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 189 26.09 0.00 0.00 chr1ptel1M 398278 398323 (601677) C L3#LINE/CR1 (2) 4097 4052 m_b11s601i6 410 chr1ptel1M 398278 TGGAATCACTGATGCTCAGAACTGGAAGGGAATTTAATGGTTTTCT 398323 i v vv ii vi iv iv C L3#LINE/CR1 4097 TAGAATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCT 4052 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.38 CpG sites = 6, Kimura (unadjusted) = 32.38 Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 21 19.94 0.00 0.00 chr1ptel1M 398435 398474 (601526) (T)n#Simple_repeat 1 40 (0) m_b11s252i18 411 chr1ptel1M 398435 TTTTTCTTTATTATTTTATTTTGTTTTTTCTTTATTTTTT 398474 i v v v v i v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 40 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 496 23.63 0.71 9.30 chr1ptel1M 398476 398615 (601385) C MIRb#SINE/MIR (138) 130 2 m_b11s601i7 412 chr1ptel1M 398476 CTGAGGC-AATTGGGGTTAAGTGACTTGCCCAGGGTCATACAACTAGGAA 398524 -v vv i i i i i --- C MIRb#SINE/MIR 130 CTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAG--- 84 chr1ptel1M 398525 GTGTTAAGTGTCTGAGGTCAGATTTGAACTCAGGTCCTTCTGACTTCAGG 398574 ---- v v vivi i i iv i ii C MIRb#SINE/MIR 83 ----TAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAA 38 chr1ptel1M 398575 GTTCATGCTCTATCTACACTGTGCCACCTAGATGCCCATTT 398615 ii i v -- ii --- v v i C MIRb#SINE/MIR 37 GCCCGTGCTCTTTC--CACTGCACCAC---GCTGCCCCTCT 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.54 CpG sites = 19, Kimura (unadjusted) = 28.84 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.09 (13 / 139), avg. gap size = 1.00 (13 / 13) 661 36.34 3.27 3.27 chr1ptel1M 398667 399033 (600967) C L3#LINE/CR1 (244) 3855 3489 m_b11s601i8 413 chr1ptel1M 398667 CCATTGCTTCTGATTCTGGTCATCTTGGGTCAGACAGGAAAAATCTAAGA 398716 v i ii vi - v i i v i v i vv C L3#LINE/CR1 3855 CCATTGGTCCTAGTTCTGCCC-TCTGGAGCCACACAGAATAAGTCTAATC 3807 chr1ptel1M 398717 AGACTT------GAGAAGATTTCAGATACTTGAAGATGGCAATCCTGGTT 398760 vvv ------ v ivvi i i ii v v vi C L3#LINE/CR1 3806 CCTCTTCCACATGACAGCCCTTCAAATATTTGAAGACAGCTATCATGTCT 3757 chr1ptel1M 398761 CTGACATGAATTTAGATTCTCACAGGTCTCCTAACTAAAGCTCCTTAGTT 398810 i-------- i ii ii v --v vii vv ii C L3#LINE/CR1 3756 CC--------TCTAAGTCTTCTC--TTCTCCAGGCTAAACATCCCCAGTT 3717 chr1ptel1M 398811 CTTCCAAATGATTATC--ATGGCACAGACATGAGGTCCTTCATCATGCTG 398858 i i vi v iv -- i ii viviv ii i v C L3#LINE/CR1 3716 CCTTCAACCGTTCCTCATATGACATGGTTTCCAGACCCTTCACCATCCTG 3667 chr1ptel1M 398859 CCTTCCTTCCTCTGGATGCTCTACAATTTACCTACATCTTGGCTAGGCTG 398908 viiv ii i v v i ii v ii iivvi iiv C L3#LINE/CR1 3666 GTCGCTCTCCTCTGGACGCGCTCCAGTTTGTCAATGTCCCTCTTAAAATG 3617 chr1ptel1M 398909 TGGT-CACAGAAGTTAGCACAA-GTTTCAGATCTGGTATGAGCAGGGCAG 398956 i- v v v i i -ii i v v v v C L3#LINE/CR1 3616 TGGCGCCCAGAACTGAACGCAATACTCCAGATGTGGTCTGACCAGCGCAG 3567 chr1ptel1M 398957 AACA-AGTGATACTACCACCT-TCTTAATCCAAGCAGCAATGCTTCTTGT 399004 ii - i iv ii -i i? iiii - v i vv C L3#LINE/CR1 3566 AGTACAGCGGGACTATTACCTCCCTTGNTCTGGACA-CTATACTTCTATT 3518 chr1ptel1M 399005 CATGTAGCCCAACACTGTGCTCCCTTTCT 399033 v i i v i iii vv i C L3#LINE/CR1 3517 AATGCAGCCTAAGATTGCATTAGCTTTTT 3489 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 48.90 CpG sites = 78, Kimura (unadjusted) = 52.44 Transitions / transversions = 1.53 (78/51) Gap_init rate = 0.05 (18 / 366), avg. gap size = 1.33 (24 / 18) 242 31.40 2.80 4.76 chr1ptel1M 399163 399269 (600731) C L2c_3end#LINE/L2 (0) 478 374 m_b11s601i9 414 chr1ptel1M 399163 ATTCATTGATAATCCATCAAGCATTTATTAAGTA---ACTATGGGCCAGG 399209 v ---i v i i ii--- v C L2c_3end#LINE 478 ATTCATTCAT---TCAACAAACATTTATTGAGCGCCTACTATGTGCCAGG 432 chr1ptel1M 399210 CTCTATAACTAAGGAAAAGGAAAAGAGAAACAGACCTTGGTTTCCAGGAA 399259 v iviiv - vi i v v - v i v i vii v i C L2c_3end#LINE 431 CGCTGGGGAT-ACAAAGATGAATA-AGACACGGTCCCTGCCCTCAAGGAG 384 chr1ptel1M 399260 TTTATATTCT 399269 i i i v C L2c_3end#LINE 383 CTCACAGTCT 374 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.18 CpG sites = 18, Kimura (unadjusted) = 41.71 Transitions / transversions = 1.29 (18/14) Gap_init rate = 0.06 (6 / 106), avg. gap size = 1.33 (8 / 6) 195 39.50 7.38 4.18 chr1ptel1M 399696 400020 (599980) C L2b_3end#LINE/L2 (118) 348 14 m_b11s601i10 414 chr1ptel1M 399696 TCTAATGAGTGAGA---ACATGCAAACAGCTAGTAA--AC-------AGC 399733 i i v --- i ? vi i ? -- -------i C L2b_3end#LINE 348 TCTAGTGGGGGAGACAGACATGTAANCAGACAATNATAACCCAGAGTGGC 299 chr1ptel1M 399734 AG--TAA-ATTGGAGATAATCTCAGAAAGACGTGAGGTGATGCTAGTAAC 399780 -- i- i i ivivi vv i i i iv--- i- ii i-- C L2b_3end#LINE 298 AGGGTAGGACTGGGGGGGCCCAGAGGAGGGCGCC---TGAC-CCGGC--C 255 chr1ptel1M 399781 TGAGAAGATAAGGAAAAGCTTCCTGTTATAGGAGCTTCTTCAGCTGTGTC 399830 i ii - v i ii i vviv v vivi v v v C L2b_3end#LINE 254 TGGGGGG-TCAGGGAGGGCTTCCCGGAGGAGGTGACATTTGAGCTGAGAC 206 chr1ptel1M 399831 TCAAAGGA--AACAAGGGACGAGAGGAAGCAGAGAGAAGGAATGAGAAGA 399878 iii -- ii i i vi ivvi iv v ivii --- iivi C L2b_3end#LINE 205 CTGAAGGATGAGTAGGAGTTGGCCAGGCGAAGAGGTGGGGAA---GGGCG 159 chr1ptel1M 399879 TTCCAGGCAAGAGGGACAGTCAGCTCAAAGTTGTTGAGGATGGAG---GT 399925 iii i iv? iv vivi vv --- i C L2b_3end#LINE 158 TTCCAGGCAGAGGGAACAGCANGTGCAAAGGCCCTGAGGCGGGAGNGAGC 109 chr1ptel1M 399926 TTGCTATGTGTAAGGAAGTACACAAAGAAGTACAATTTTGCTGGA-CTGT 399974 ? vii vii --- vv i vv i v v - v v C L2b_3end#LINE 108 NTGGCGTGTTCGAGGA---ACAGCAAGGAGGCCAGTGTGGCTGGAGCAGA 62 chr1ptel1M 399975 GTG---AAGGGAAGTAACAATCTATAATAACATTGGAAAGATGGTGAAG 400020 --- i - iiii vvivi i viii i i i i ii C L2b_3end#LINE 61 GTGAGCAAGGGGAG-AGTGGTAGGAGATGAGGCCGGAGAGGTAGCGGGG 14 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 56.17 CpG sites = 79, Kimura (unadjusted) = 62.09 Transitions / transversions = 1.80 (79/44) Gap_init rate = 0.07 (23 / 324), avg. gap size = 1.65 (38 / 23) 231 35.80 3.03 4.08 chr1ptel1M 399773 399970 (600030) C L2c_3end#LINE/L2 (214) 264 69 m_b11s601i11 414 chr1ptel1M 399773 CTAGTAACTGAGAAGATAAGGAAAAGCTTCCTGTTATAGGAGCTTCTTCA 399822 ?-- vi ii i v i i i vviv v vivii v C L2c_3end#LINE 264 CTAGN--CTTGGGGGGTCAGGGAAGGCTTCCCGGAGGAGGTGACATCTGA 217 chr1ptel1M 399823 GCTGTGTCTCAAAGGA-AACAAGGGACGAG--AGGAAGCAGAGAGAAGGA 399869 v ? ii -i vv iiiv -- vi v - ii i C L2c_3end#LINE 216 GCTGAGNCTTGAAGGATGAGTAGGAGTTAGCCAGGTGGAAG-GAGGGGGG 168 chr1ptel1M 399870 ATGAGAAGATTCCAGGCAAGAGGGACAGTCAGCTCAAAGTTGTTGAGGAT 399919 -- iv iii i ivv iv vi?iv vv C L2c_3end#LINE 167 A--AGAGCATTCCAGGCAGAGGGAACAGCATGTGCAAAGGCNCGGAGGCA 120 chr1ptel1M 399920 GG--AGGTTTGCTATGTG-TAAGGAAGTACACAAAGAAGTACAATTTTGC 399966 -- ivi vii - vi i i i --- ? v i v v C L2c_3end#LINE 119 GGAAAGAACTGCGGCGTGTTTGGGGAATGC---AAGNAGTTCAGTGTGGC 73 chr1ptel1M 399967 TGGA 399970 C L2c_3end#LINE 72 TGGA 69 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 48.85 CpG sites = 39, Kimura (unadjusted) = 52.16 Transitions / transversions = 1.34 (39/29) Gap_init rate = 0.06 (12 / 197), avg. gap size = 1.17 (14 / 12) 350 36.25 3.11 2.32 chr1ptel1M 400270 400526 (599474) C L2#LINE/L2 (454) 2628 2370 m_b11s601i12 414 chr1ptel1M 400270 AGAAATGACCGCATTTGACAGTTGATTAGATATGAAAATTGAAAGAATGT 400319 ivi v v viii v i i iiivv i v v C L2#LINE/L2 2628 AGAGCCGACAGGATTTGCTGATGGATTGGATGTGGGGTGTGAGAGAAAGA 2579 chr1ptel1M 400320 GAGAAGTTAACAATAAA-AGAGGGTTCTGAATTTGGTTGATTGTAGGAGT 400368 i i vi i v-vv i i viiii ivii i v i ii C L2#LINE/L2 2578 GAGGAGTCAAGGATGACTCCAAGGTTTTTGGCCTGAGCAACTGGAAGGAT 2529 chr1ptel1M 400369 AGAGATTTCCTCTAAAACAG-TAAGGAAATTTGGGAGAG----AGGTGTG 400413 i - v vi ? vvv - ii ivi v i ---- v C L2#LINE/L2 2528 GGAG-TTGCCATTNACTGAGATGGGGAAGACTGCGGGAGGAGCAGGTTTG 2480 chr1ptel1M 400414 ATATGCGGAAAAGGTAACAAGTTTTGTTTTGGATATGGTGAATTTGAGAT 400463 --- - ii i v vi iv i v i i C L2#LINE/L2 2479 A---G-GGGGAAGATCAGGAGTTCAGTTTTGGACATGTTAAGTTTGAGAT 2434 chr1ptel1M 400464 GCC-ATTGGCTATCTAATTCAAAGTTCTTGA-CAGGTAGTTAGATATATG 400511 - i vi i v -ii v v i -i i i i C L2#LINE/L2 2433 GCCTATTAGACATCCAAGT-GGAGATGTCGAGTAGGCAGTTGGATATACG 2385 chr1ptel1M 400512 GGACAGCATATCAGG 400526 i v v v vv C L2#LINE/L2 2384 AGTCTGGAGTTCAGG 2370 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 49.64 CpG sites = 54, Kimura (unadjusted) = 52.15 Transitions / transversions = 1.46 (54/37) Gap_init rate = 0.04 (11 / 256), avg. gap size = 1.27 (14 / 11) 257 33.91 6.70 1.27 chr1ptel1M 400724 400947 (599053) L1M1_orf2#LINE/L1 1490 1725 (1569) m_b11s551i3 415 chr1ptel1M 400724 GATAAATAAGGTAAGAAAGTATCCTATAAGAATCCTTTTAGGAGTCTAAC 400773 v ii v i ii v v viv i v v i v v i ii L1M1_orf2#LIN 1490 GAAAAATAGAGGAGGAGGGAATACTTCCAAACTCATTCTACGAGGCCAGT 1539 chr1ptel1M 400774 ATAGACCCAATACTGAAAACAAGGAAAGTCCAAGCACAGAAAGTAAATTA 400823 viv ii ii v iiv v vv v v i v i L1M1_orf2#LIN 1540 ATTACCCTGATACCAAAACCAGACAAAGACACATCAAAAAAAGAAAACTA 1589 chr1ptel1M 400824 CAAATCATTGTCTCC--------TTCCTCCAA---TTTTAAACAAAATCC 400862 iii v i i-------- vv v --- ii v v L1M1_orf2#LIN 1590 CAGGCCAATATCTCTGATGAATATTGATGCAAAAATCCTCAACAAAATAC 1639 chr1ptel1M 400863 TATCAAAACA----CCATAGTGAATTATCCAAGAACCCATTCATTATGAT 400908 v v i---- v i i iv --- i ivi i i L1M1_orf2#LIN 1640 TAGCAAACCGAATTCAACAATACATTA---AAAAGATCATTCATCATGAC 1686 chr1ptel1M 400909 CAAGTGGGATTGCTACTAGGGATGGAAGGGTAATTCAAC 400947 vv v i? v i ii L1M1_orf2#LIN 1687 CAAGTGGGATTTATCCCNGGGATGCAAGGATGGTTCAAC 1725 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 45.71 CpG sites = 40, Kimura (unadjusted) = 46.56 Transitions / transversions = 1.14 (40/35) Gap_init rate = 0.03 (6 / 223), avg. gap size = 3.00 (18 / 6) 269 26.25 3.92 2.91 chr1ptel1M 400846 400947 (599053) L1M2_orf2#LINE/L1 1620 1722 (1569) m_b11s551i4 415 chr1ptel1M 400846 AATTTTAAACAAAATCCTATCAAAACA----CCATAGTGAATTATCCAAG 400891 ii v v v v i---- v i iiv --- i L1M2_orf2#LIN 1620 AATCCTCAACAAAATACTAGCAAACCGAATTCAACAGCACATTA---AAA 1666 chr1ptel1M 400892 AACCCATTCATTATGATCAAGTGGGATTGCTACTAGGGATGGAAGGGTAA 400941 ivi? ? ii vv v i v i ii L1M2_orf2#LIN 1667 AGATNATNCACCATGATCAAGTGGGATTTATCCCAGGGATGCAAGGATGG 1716 chr1ptel1M 400942 TTCAAC 400947 L1M2_orf2#LIN 1717 TTCAAC 1722 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 32.32 CpG sites = 15, Kimura (unadjusted) = 33.90 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.04 (4 / 101), avg. gap size = 1.75 (7 / 4) 228 3.23 3.23 0.00 chr1ptel1M 401462 401492 (598508) U2#snRNA 4 35 (153) m_b11s502i0 416 chr1ptel1M 401462 GCTTCT-AGCCTTTTGGCTAAGATCAAGTGTA 401492 -i U2#snRNA 4 GCTTCTCGGCCTTTTGGCTAAGATCAAGTGTA 35 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 0.32 CpG sites = 1, Kimura (unadjusted) = 3.33 Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.03 (1 / 30), avg. gap size = 1.00 (1 / 1) 259 31.26 12.68 1.29 chr1ptel1M 402899 403316 (596684) C L1M5_orf2#LINE/L1 (1464) 1830 1366 m_b11s551i6 417 chr1ptel1M 402899 GTGTTGCATTTTGTCAAATTTTTTTTTTGCATTTATTGATTTAATGATA- 402947 v vi i i vv i v - C L1M5_orf2#LIN 1830 GTGTTGAATTTTGTCAAATGCTTTTTCTGCATCTATTGAGATGATCATAT 1781 chr1ptel1M 402948 -ATTTTTGTTTTTC---TTATTGATGT----AATTATGTTAAAGGTTTTC 402989 - v ii i---i i i i ---- ii i vv v i C L1M5_orf2#LIN 1780 GATTTTTCTCCTTTATTCTGTTAATATGGTGAATTACATTGATTGATTTT 1731 chr1ptel1M 402990 TTTTTATTGAAG-AGTCCTGAATTCCTTATATAAATCCTGTTTGGTCACA 403038 ivvv i i v- ii i v viv i iii ii C L1M5_orf2#LIN 1730 CGAATGTTAAACCAACCTTGCATTCCTGGGATAAACCCCACTTGGTCATG 1681 chr1ptel1M 403039 ATGTATAATCTT---------------GAT--GACATATTAATATTTTAG 403071 v i --------------- -- iv ii iv C L1M5_orf2#LIN 1680 ATGTATTATCCTTTTTATATATTGCTGGATTCGATTTGCTAATATTTTGT 1631 chr1ptel1M 403072 TTGGGCTTTTTGCATCAATATTAATGAA----ACTGGTCTGTG------- 403110 ?i v v i v i---- i i------- C L1M5_orf2#LIN 1630 TNAGGATTTTTGCATCTATGTTCATGAGGGATATTGGTCTGTAATTTTCT 1581 chr1ptel1M 403111 ---TGTGTG-TGTGTGTGTGTGAATGTAGCACCA------TATTTGTTTC 403150 ---iv i- v v v? iv v i i i ------ ii v ii C L1M5_orf2#LIN 1580 TTTCTTGTAATGTCTTTGTCNGGTTTTGGTATCAGGGTNATGCTGGCCTC 1531 chr1ptel1M 403151 ATAAAAGGAATTTGGTAGGACTTTTTTTTTTTTGCCTGTTATCGTAAATA 403200 v i v v vii iii i --- i v vvi v C L1M5_orf2#LIN 1530 ATAAAATGAGTTGGGAAGTGTTCCCTCTTTTT---CTATTTTCTGGAAGA 1484 chr1ptel1M 403201 ATTTATTTAATATGAGAATATTAG-----AATTAGAATAGTTGGTAAAAT 403245 i i v v vi -- v-----vv - iv i C L1M5_orf2#LIN 1483 GTTTGTGTAAGATTGG--TATTATTTCTTCCTTA-AATGTTTGGTAGAAT 1437 chr1ptel1M 403246 TCAGCAGTAAATCCATCTTGTCCTGAAGCTTTTTCCATAGAAAGCTCATT 403295 v i v v v i i i iii i i v iv C L1M5_orf2#LIN 1436 TCACCAGTGAAGCCATCTGGGCCTGGAGTTTTCTTTGTGGGAAGGTTTTT 1387 chr1ptel1M 403296 TATGGTCTGTTCAATTTCTTT 403316 v viivvi C L1M5_orf2#LIN 1386 AATTACAAATTCAATTTCTTT 1366 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.62 CpG sites = 75, Kimura (unadjusted) = 42.06 Transitions / transversions = 1.39 (75/54) Gap_init rate = 0.05 (19 / 417), avg. gap size = 3.11 (59 / 19) 318 23.80 15.17 0.41 chr1ptel1M 402899 403109 (596891) C L1MC_orf2#LINE/L1 (1464) 1830 1589 m_b11s551i5 417 chr1ptel1M 402899 GTGTTGCATTTTGTCAAATTTTTTTTTTGCATTTATTGATTTAATGA--T 402946 v vi i i v i v -- C L1MC_orf2#LIN 1830 GTGTTGGATTTTGTCAAATGCTTTTTCTGCATCTATTGATATGATCATGT 1781 chr1ptel1M 402947 AATTTTTGTTTTT---CTTATTGATGT----AATTATGTTAAAGGTTTTC 402989 i v i --- i i ----i ii vv v i C L1MC_orf2#LIN 1780 GATTTTTCTTCTTTAGCCTGTTGATGTGATGGATTACATTAATTGATTTT 1731 chr1ptel1M 402990 TTTTTATTGAA-GAGTCCTGAATTCCTTATATAAATCCTGTTTGGTCACA 403038 ivvv i -v i i v v viv iii iii C L1MC_orf2#LIN 1730 CGAATGTTGAACCAGCCTTGCATACCTGGGATAAATCCCACTTGGTCGTG 1681 chr1ptel1M 403039 ATGTATAA-TCTT--------------GAT--GACATATTAATATTTTAG 403071 i - -------------- -- iv ii - C L1MC_orf2#LIN 1680 GTGTATAATTCTTTTTATACATTGTTGGATTCGATTTGCTAATATTTT-G 1632 chr1ptel1M 403072 TTG-GGCTTTTTGCATCAATATTAATGAA----ACTGGTCTGT 403109 - v v i v i---- i C L1MC_orf2#LIN 1631 TTGAGGATTTTTGCATCTATGTTCATGAGAGATATTGGTCTGT 1589 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 27.90 CpG sites = 30, Kimura (unadjusted) = 29.26 Transitions / transversions = 1.50 (30/20) Gap_init rate = 0.05 (10 / 210), avg. gap size = 3.30 (33 / 10) 270 27.91 0.00 0.00 chr1ptel1M 403231 403316 (596684) C L1MC_orf2#LINE/L1 (1843) 1451 1366 m_b11s551i7 417 chr1ptel1M 403231 AATAGTTGGTAAAATTCAGCAGTAAATCCATCTTGTCCTGAAGCTTTTTC 403280 iv i v i i v v iv i v C L1MC_orf2#LIN 1451 AATGTTTGGTAGAATTCACCAGTGAACCCATCTGGGCCTGGTGCTTTCTG 1402 chr1ptel1M 403281 CATAGAAAGCTCATTTATGGTCTGTTCAATTTCTTT 403316 iv v i v i v vi ivi C L1MC_orf2#LIN 1401 TTTTGGAAGGTTATTAATTATTGATTCAATTTCTTT 1366 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.30 CpG sites = 12, Kimura (unadjusted) = 35.30 Transitions / transversions = 1.00 (12/12) Gap_init rate = 0.00 (0 / 85), avg. gap size = 0.0 (0 / 0) 20 17.83 0.00 0.00 chr1ptel1M 409904 409943 (590057) (AAAC)n#Simple_repeat 1 40 (0) m_b12s252i0 418 chr1ptel1M 409904 AAACAAACAAACAAACAAACGAGCGAGTAAACGAACAAAC 409943 i i i ii i (AAAC)n#Simpl 1 AAACAAACAAACAAACAAACAAACAAACAAACAAACAAAC 40 Matrix = Unknown Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 220 30.90 9.20 3.26 chr1ptel1M 410599 410772 (589228) C L2#LINE/L2 (591) 2491 2308 m_b12s601i0 419 chr1ptel1M 410599 GGAGCTGAACTGAAGGGCAAAGATAACAAGATCGGTTTTGCAAATGTTGA 410648 v ivi i -i v vi v i v v i C L2#LINE/L2 2491 GGAGCAGGTTTGAGGGG-GAAGATCAGGAGTTCAGTTTTGGACATGTTAA 2443 chr1ptel1M 410649 GATTCCCATGTTGGTAAGGTATCTAAGTTGAAATGTTCATT-GGTGGTTG 410697 v vvv iivi v ii i v i iv v - ii C L2#LINE/L2 2442 GTTTGAGATGCCTATTAGACATCCAAGTGGAGATGTCGAGTAGGCAGTTG 2393 chr1ptel1M 410698 G------GA---TG------AGAGGAAAGGAAAGGACAAGAGAGAAAAAT 410732 ------ --- ------ i i vvv i vi v v C L2#LINE/L2 2392 GATATACGAGTCTGGAGTTCAGGGGAGAGGTCCGGGCTGGAGATATAAAT 2343 chr1ptel1M 410733 TAGTTGGGAATGATTTGCAGATAGATTCCAACTTTAAAAC 410772 --- i v iv v vvi -- i C L2#LINE/L2 2342 ---TTGGGAGTCATCAGCATATAGATGGTA--TTTAAAGC 2308 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.37 CpG sites = 25, Kimura (unadjusted) = 40.35 Transitions / transversions = 0.93 (25/27) Gap_init rate = 0.06 (10 / 173), avg. gap size = 2.20 (22 / 10) 286 27.96 0.00 0.00 chr1ptel1M 410933 411025 (588975) L1ME3E_3end#LINE/L1 459 551 (438) m_b12s551i0 420 chr1ptel1M 410933 TTTGTAGTGGCAAGAAACTCGAGACTGAGGGGATGCCCATCAGTTGGAGA 410982 i i i v i vivvvii i iiiv L1ME3E_3end#L 459 TTTGTAATAGCAAAAAACTGGAAACAACCCAAATGTCCATCGACAGGAGA 508 chr1ptel1M 410983 ATGGATGAATAAATTATGGTATATGGATGTTATGGAATATCAT 411025 i i vv iiv ii L1ME3E_3end#L 509 ATGGATAAATAAATTGTGGTATATTCATACAATGGAATACTAT 551 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.64 CpG sites = 17, Kimura (unadjusted) = 36.41 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.00 (0 / 92), avg. gap size = 0.0 (0 / 0) 201 38.36 0.00 0.00 chr1ptel1M 411054 411126 (588874) L2a_3end#LINE/L2 431 503 (14) m_b12s601i1 421 chr1ptel1M 411054 TGATTTTTTTGTCACAGTATCCCTGGCACCTCGCCTAATCCCCAGAACAT 411103 v v iiiii v ii i v vvi i v ii v L2a_3end#LINE 431 TGTTTTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACAT 480 chr1ptel1M 411104 AATAGATGCTTCACAAATGCTTG 411126 i ii iv i ii L2a_3end#LINE 481 AGTAGGCGCTCAATAAATATTTG 503 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 52.21 CpG sites = 19, Kimura (unadjusted) = 58.70 Transitions / transversions = 2.11 (19/9) Gap_init rate = 0.00 (0 / 72), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 chr1ptel1M 412021 412037 (587963) (A)n#Simple_repeat 1 17 (0) m_b12s252i1 422 chr1ptel1M 412021 AAAAAAAAAAAAAAAAA 412037 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 400 27.10 0.81 7.76 chr1ptel1M 415628 415751 (584249) C MIRc#SINE/MIR (120) 148 33 m_b12s601i2 423 chr1ptel1M 415628 CTCATTTTATAGATGAGAAAACCAAAGCAAACAGGGTTAGGGTTAGGGTT 415677 i i i ii i v-- i ---i i v-- C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCT--CAGAG---AGGTTAAGT-- 106 chr1ptel1M 415678 AGCCTTGTCCAGAGTCACACAGTCAACAAGAGTCTTGAGTCCAGATTTGA 415727 - v i ii ii ii v v v- i vi i i C MIRc#SINE/MIR 105 -GACTTGCCCAAGGTCACACAGCTAGTAAGTGGCA-GAGCCGGGACTCGA 58 chr1ptel1M 415728 ACCCAAATCTCCCTGACTTC-AGTC 415751 ii i i - C MIRc#SINE/MIR 57 ACCCAGGTCTTCCTGACTCCAAGTC 33 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.30 CpG sites = 24, Kimura (unadjusted) = 35.77 Transitions / transversions = 3.43 (24/7) Gap_init rate = 0.08 (10 / 123), avg. gap size = 1.00 (10 / 10) 12 19.57 2.86 0.00 chr1ptel1M 416223 416257 (583743) (AAACAT)n#Simple_repeat 1 36 (0) m_b12s252i2 424 chr1ptel1M 416223 AAAAATAGA-AAAAACAGAAACAAATACATAAACAT 416257 v i - v v v v (AAACAT)n#Sim 1 AAACATAAACATAAACATAAACATAAACATAAACAT 36 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 276 31.39 1.15 1.15 chr1ptel1M 417230 417403 (582597) L1PB_orf2#LINE/L1 2283 2456 (838) m_b12s551i1 425 chr1ptel1M 417230 AGCTGTAAACAATGTAAAATACTTGGGAATCTACCTTACAAGATAGATTC 417279 i v vi i v v v iiv i vv L1PB_orf2#LIN 2283 AGCTGCAAAAAAAATAAAATACTTAGGAATATACCTAACCAAGGAGGTGA 2332 chr1ptel1M 417280 AGGAACTATATGAACACAATTACAAAAAACTTTTCATACAAATCA-AGTC 417328 i v v ii iv v i v vi v v v - v L1PB_orf2#LIN 2333 AAGACCTCTACAAGGAAAACTACAAAACACTGCTGAAAGAAATCATAGAC 2382 chr1ptel1M 417329 ATATCTAAACAACTGGAAAAATA-CCAGTGGCTTATGGGTAAGCCAAGCC 417377 i- ivi v v i - vi - i i ii ivi ii L1PB_orf2#LIN 2383 G-ACACAAACAAATGGAAACACATCCCAT-GCTCATGGATGGGTAGAATC 2430 chr1ptel1M 417378 AATAAAATAAAAATGACAATTCTGCC 417403 vvi i v v L1PB_orf2#LIN 2431 AATATTGTGAAAATGACCATACTGCC 2456 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.27 CpG sites = 27, Kimura (unadjusted) = 41.25 Transitions / transversions = 1.00 (27/27) Gap_init rate = 0.02 (4 / 173), avg. gap size = 1.00 (4 / 4) 296 26.34 2.94 1.74 chr1ptel1M 418534 418703 (581297) L1ME4c_3end#LINE/L1 21 192 (638) m_b12s551i2 426 chr1ptel1M 418534 AGAACTGAGTCAAATTTATAAGAATATAAGAAATTCCCCAATGGATAAAT 418583 i v v v v v? vv vv i L1ME4c_3end#L 21 AGAGCTCATTCAAATTGATAAGAAAAANATCAAGACCCCAATAGATAAAT 70 chr1ptel1M 418584 TGTTAAAGAATATGATCAGGCAA--CATTTA-GATGAATTAATCACATA- 418629 v vi i i v i -- iv? - v v -- v? - L1ME4c_3end#L 71 GGGCAAAGGACATGAACAGACAATTCACANAAGAGGAAATA--CAANTAG 118 chr1ptel1M 418630 TGTACAAGTATAAGAAGAAGTGTTCTAAGCTGGTT-TTGATTAGAAAAAT 418678 iv ii i v i i i - v v i -v i i i i L1ME4c_3end#L 119 TAAACAAACACATGGAAAAATGTTC-AACCTCGCTAGTAATCAAAGAAAT 167 chr1ptel1M 418679 GCAAATTAAAACAACTCTGAGGTAC 418703 i vv i L1ME4c_3end#L 168 GCAAATTAAAGCAACAATGAGATAC 192 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 33.47 CpG sites = 21, Kimura (unadjusted) = 33.47 Transitions / transversions = 0.91 (21/23) Gap_init rate = 0.04 (7 / 169), avg. gap size = 1.14 (8 / 7) 280 30.62 6.25 0.85 chr1ptel1M 418569 418792 (581208) L1ME5_3end#LINE/L1 56 291 (650) m_b12s551i3 426 chr1ptel1M 418569 CCCCAATGGATAAATTGTTAAAGAATATGATCAGGCAACATTTAGATGAA 418618 i v v vi i v iv vi v i L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chr1ptel1M 418619 TTAATCACATATGT--ACAAGTATAAGAAGAAGTGTTCTAAGCTGGTT-T 418665 vv i vv v v i-- i v ii i - i vi -v L1ME5_3end#LI 106 GAAACCCGAAAGGCTAACAAGCATATGAAGAGATGCTC-AAACTCATTAG 154 chr1ptel1M 418666 TGATTAGAAAAATGCAAATTAAAACAACTCTGAGGTA-CAGTCTGAGATT 418714 i i i vv i - v i - v ii L1ME5_3end#LI 155 TAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTT-ACACC 203 chr1ptel1M 418715 CATTAA--TGATAAAAAAAGGAAAAT--GATAATA------GTTGTAAAA 418754 i i-- ii vvi ii-- i------ vvi i L1ME5_3end#LI 204 TATTAGACTGGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTGGCGAG 253 chr1ptel1M 418755 GATGGGGGAAAATTAAGACACCAATGAAATGCTAGTAG 418792 v i ? viii v iv v v i i L1ME5_3end#LI 254 GATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGG 291 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.80 CpG sites = 38, Kimura (unadjusted) = 40.58 Transitions / transversions = 1.27 (38/30) Gap_init rate = 0.04 (8 / 223), avg. gap size = 2.00 (16 / 8) 222 24.08 8.33 1.11 chr1ptel1M 421433 421516 (578484) C MIR1_Amn#SINE/MIR (50) 180 91 m_b12s601i3 427 chr1ptel1M 421433 CACTTGACA--GGAATTC--TATT-TTATACCCATTTTACATTATGAAGA 421477 v -- iv -- i- v -v i C MIR1_Amn#SINE 180 CACTTTACAAAGGAGGTCAGTATCATTATCCCCATTTTACA-GATGAGGA 132 chr1ptel1M 421478 AAT--AGATCCAGAATGTAGAAGTCATGTGCCCCAAATCAC 421516 i-- ii? iv vv? v iv v ii C MIR1_Amn#SINE 131 AACTGAGGCNCAGAGAGGTNAAGTGACTTGCCCAAGGTCAC 91 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.22 CpG sites = 10, Kimura (unadjusted) = 30.22 Transitions / transversions = 1.00 (10/10) Gap_init rate = 0.06 (5 / 83), avg. gap size = 1.60 (8 / 5) 311 22.36 3.75 7.79 chr1ptel1M 422910 423069 (576931) C L1ME3Cz_3end#LINE/L1 (784) 213 60 m_b12s551i4 428 chr1ptel1M 422910 TTGCCAATCTGCAGGTTATGAGACAAAGGG---CTCAGAGTTCATTTCAT 422956 vv v i ---- v --- vv ?vv v C L1ME3Cz_3end# 213 TTGCCAATCTGATGGGTGTGA----AATGGTATCTCATTGTNGTTTTAAT 168 chr1ptel1M 422957 TTTCATCTCCCTTTTTAATTATTAATGATTTAGAGCATTTTTCTTCCATA 423006 v i ----i i i vv v i i--- C L1ME3Cz_3end# 167 TTGCATTTCCCT----GATTACTAGTGAGGTTGAGCATCTTTT---CATA 125 chr1ptel1M 423007 TGATAATTGATAGTTTGGGTTTCACCCTTCAA--AAATGCCTGTTCATAT 423054 v v iivi i - i vi-- v C L1ME3Cz_3end# 124 TGTTTATTGGCCATTCGGGTTTC-CTCTTCTGTGAATTGCCTGTTCATAT 76 chr1ptel1M 423055 -CTTTGGCCATTTATC 423069 - v v C L1ME3Cz_3end# 75 CCTTTGCCCATTTTTC 60 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 25.82 CpG sites = 13, Kimura (unadjusted) = 26.71 Transitions / transversions = 0.65 (13/20) Gap_init rate = 0.09 (15 / 159), avg. gap size = 1.20 (18 / 15) 239 32.06 7.27 9.26 chr1ptel1M 424365 424474 (575526) MIRb#SINE/MIR 3 110 (158) m_b12s601i4 429 chr1ptel1M 424365 GAAGAGCAACCAGATGGTACAATGGATAGAGAAC---C-----AGTCAAA 424406 i i i ---i i i v v --- ----- i MIRb#SINE/MIR 3 GAGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGA 49 chr1ptel1M 424407 AGGATTTACATTCAAATCTGGCCTCAGACATTTGATACTTGCTAATTGTG 424456 vi ii ivi i iv v ------- vi i ii MIRb#SINE/MIR 50 CAGACCTGGGTTCGAATCCCGGCTC-------TGCCACTTACTAGCTGTG 92 chr1ptel1M 424457 TGACTCCAAGAAAGTCAC 424474 iiiii v i MIRb#SINE/MIR 93 TGACCTTGGGCAAGTTAC 110 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.48 CpG sites = 24, Kimura (unadjusted) = 45.41 Transitions / transversions = 3.00 (24/8) Gap_init rate = 0.11 (12 / 109), avg. gap size = 1.50 (18 / 12) 249 32.56 8.33 7.22 chr1ptel1M 424379 424474 (575526) MIRc#SINE/MIR 11 107 (161) m_b12s601i5 429 chr1ptel1M 424379 TGGTACAATGGATAGAGAACC--------AGTCAAAAGGATTTACATTCA 424420 i i v v i-------- ii i ii ivi i MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr1ptel1M 424421 AATCTGGCCTCAGACATTTGATACTTGCTAATTGTGTGACTCCAAGAAAG 424470 i iv v ------- vi i ii iiiii v MIRc#SINE/MIR 61 AGTCCCGGCTC-------TGCCACTTACTAGCTGTGTGACCTTGGGCAAG 103 chr1ptel1M 424471 TCAC 424474 MIRc#SINE/MIR 104 TCAC 107 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.52 CpG sites = 22, Kimura (unadjusted) = 46.83 Transitions / transversions = 3.14 (22/7) Gap_init rate = 0.08 (8 / 95), avg. gap size = 1.88 (15 / 8) 512 28.53 5.68 3.04 chr1ptel1M 424523 425068 (574932) L1M5_orf2#LINE/L1 782 1341 (1953) m_b12s551i5 430 chr1ptel1M 424523 GAGTCAAAAAACAAACCATAA----AAT---AAAGGATTTC--ATTGAA- 424562 i i v i i ---- --- iv i-- i - L1M5_orf2#LIN 782 GGGTCAAAGAAGAAATCACAANGGAAATTAGAAAATATTTTGAACTGAAT 831 chr1ptel1M 424563 GAAAATGACCAAACAACATA-CAAAATTTACAGAATGGAGACAAAGGAAT 424611 ? vv v - iii i v vi v i L1M5_orf2#LIN 832 GANAATGAAAATACAACATATCAAAATTTGTGGGATGCAGCTAAAGCAGT 881 chr1ptel1M 424612 ACTTAGGGGTAAATTCATATCTTTAAATACTTACATTAATAAAATAAGAA 424661 i i v i v ? i ? i i- v L1M5_orf2#LIN 882 GCTTAGAGGGAAATTTATAGCNTTAAATGCNTATATTAG-AAAAGAAGAA 930 chr1ptel1M 424662 AAAGAGC---ACATCAATGACTT--GGTTACACAATTTAAAAAGCTAGAA 424706 ---i --- v ii -- v v --i i L1M5_orf2#LIN 931 A---GGCTTAAAATCAATGATCTAAGCTTCCAC--CTTAAGAAGCTAGAA 975 chr1ptel1M 424707 AAAGAA---CAAATTAAAAATCCCTAATTAAACACCAAATTAGAAACACT 424753 --- --- v v? ii vv iivvi i v L1M5_orf2#LIN 976 AAAGAAGAGCAAATTAAA---CCCAAAGNAAGTAGAAGGAAGGAAATAAT 1022 chr1ptel1M 424754 GAAAACCAAAGGAGAGGTTAATAAAATTAAAAGAAAACCACTGAACCAAT 424803 i i iv i v ii i i ---- v v?i? - L1M5_orf2#LIN 1023 AAAGATAAGAGCAGAAATCAATGAAAT----AGAAAACAAANANA-CAAT 1067 chr1ptel1M 424804 AGTGCAGGTTTTATGAGGGGAAAAA----------AAAAAAACACAATAA 424843 v v ii- iv i i vv i----------i i i- L1M5_orf2#LIN 1068 AGAGAAAA-TCAACGAAGCCAAAAGCTGGTTCTTTGAAAAGAT-CAATAA 1115 chr1ptel1M 424844 AATAGATAAACCATTGATTAATTTGCCCTA-AAAAAAAGGAAGAAAAAAA 424892 v vi iii? ivi vi v - ii i v v L1M5_orf2#LIN 1116 AATTGATAAACCTCTAGCNAGACTGATCAAGAAAAAAAGAGAGAAGACAC 1165 chr1ptel1M 424893 AAATTGCCGGTATCAAAAATGAAAGGAGTGAACTCACAACCAATAAAGAG 424942 i ii ii iii v vv v vi vvvivi L1M5_orf2#LIN 1166 AAATTACCAATATCAGGAATGAAAAAGGAGACATCACTACAGATCCTACA 1215 chr1ptel1M 424943 GAAATTGAGACAATTTTTAGAAGTCATT-TGACCCAATTATATGCCAATA 424991 v i i vi vv v iivi - -v i v L1M5_orf2#LIN 1216 GACATTAAAAGGATAATAAGAGAATATTATGA-ACAACTTTATGCCAATA 1264 chr1ptel1M 424992 AATTTGACAATCTAAATGAAACAGATGAATATTTACTAAAACATATATTA 425041 ? ii i ii ii vii vvv i v? L1M5_orf2#LIN 1265 AATTTGANAACTTAGATGAAATGGACAAATTCCTTGAAAAACACAANTTA 1314 chr1ptel1M 425042 TCCAGATTAACAGAAGAAGAAATAGAA 425068 i v i i i ?v L1M5_orf2#LIN 1315 CCAAAACTGACNCAAGAAGAAATAGAA 1341 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.59 CpG sites = 90, Kimura (unadjusted) = 37.91 Transitions / transversions = 1.48 (90/61) Gap_init rate = 0.05 (28 / 545), avg. gap size = 1.71 (48 / 28) 19 8.18 0.00 0.00 chr1ptel1M 425095 425120 (574880) (G)n#Simple_repeat 1 26 (0) m_b12s252i3 431 chr1ptel1M 425095 GGGGCTGGGGGGGGGGGGGGGGGGGG 425120 vv (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGG 26 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 741 24.32 9.30 1.20 chr1ptel1M 425959 426345 (573655) L1M5_orf2#LINE/L1 1493 1910 (1384) m_b12s551i6 430 chr1ptel1M 425959 AAATACACAAAG-GAGAAC--TTCCAAATTCTTTTTATGACACAAATATG 426005 v v - i -- v i v vi v ii ? L1M5_orf2#LIN 1493 AAATAGAAAAAGAGGGAACACTTCCCAACTCATTTTATGAGGCCAGCATN 1542 chr1ptel1M 426006 TTCCTCATACCTAA-CCAGA--AAGACA----GAGAAAGGAAA-TTATAG 426047 vi v v - ? -- ----i i - i L1M5_orf2#LIN 1543 ACCCTGATACCAAAACCNGACAAAGACATTACAAGAAAAGAAAATTACAG 1592 chr1ptel1M 426048 ATTAATTTCCCTAATGAATATTGATGCAAAA-TCTTCAAATAAAATATTA 426096 ii v v i v - i ? -i L1M5_orf2#LIN 1593 ACCAATATCCCTCATGAACATAGATGCAAAAATCCTNAA-CAAAATATTA 1641 chr1ptel1M 426097 GCAAGGTC--ATTACGCAATATAT---------------CTGTTACCAGG 426129 i- -- ivv ---------------iii v i L1M5_orf2#LIN 1642 GCAAA-TCGAATCCAGCAATATATAAAAAGGATAATACATCATGACCAAG 1690 chr1ptel1M 426130 TGGGATGTATAACAAAAATTCAGGGTTAGTTTAATACTAGGAAAACTATC 426179 i v vv ii v i i i i v i v v L1M5_orf2#LIN 1691 TGGGGTTTATCCCAGGAATGCAAGGTTGGTTTAACATTCGAAAATCAATC 1740 chr1ptel1M 426180 AGCATAAATGACCATATCAATAACAAAATCCACAGAAATCATATTTTTGT 426229 iii v v i i iv v vvv v i vv ii L1M5_orf2#LIN 1741 AATGTAATTCACCATATTAACAGAATAAAGGAGAAAAATCATATGATCAT 1790 chr1ptel1M 426230 CTTAATAGATGCAGAAAAAGTCTTTGACAAAAT---ACAACCATTCCTAT 426276 i iv --- v v iv L1M5_orf2#LIN 1791 CTCAATAGATGCAGAAAAAGCATTTGACAAAATTCAACACCCATTCATGA 1840 chr1ptel1M 426277 TAAAAA---TTAGAGAGCATAGGAGTA-AATGGCACTTACCTCAAAATTA 426322 --- i vi i - i - v v - vv v L1M5_orf2#LIN 1841 TAAAAACTCTCAGCAAAC-TAGGAATAGAAGGGAACTT-CCTCAACCTGA 1888 chr1ptel1M 426323 TTAAGTAGTATCTATCTAAAATC 426345 v -i i ivv i L1M5_orf2#LIN 1889 TAAAG-GGCATCTACGAAAAACC 1910 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 29.66 CpG sites = 48, Kimura (unadjusted) = 30.04 Transitions / transversions = 1.07 (48/45) Gap_init rate = 0.04 (17 / 386), avg. gap size = 2.41 (41 / 17) 281 29.88 2.41 1.19 chr1ptel1M 426343 426508 (573492) L1M2_orf2#LINE/L1 2107 2274 (1017) m_b12s551i8 432 chr1ptel1M 426343 ATCATATTATACTTGTAGAATCCTAGAGAATC-ATTTAAAAACTACCTGA 426391 v v i? iv i ? i v - iiv ?iiv L1M2_orf2#LIN 2107 ATGATCTTATATNTAGAAAANCCTAAAGACTCCACCAAAAAACTNTTAGA 2156 chr1ptel1M 426392 AATAATTAACAGCTTGCGTAAAGTTGCAGAAAATAAAGTAAACCCACATA 426441 v i v iiv vv i v i i v vi v L1M2_orf2#LIN 2157 ACTGATAAACGAATTCAGTAAAGTTGCAGGATACAAAATCAACATACAAA 2206 chr1ptel1M 426442 AATCATCAGTATTTCTATATATTACCAACAAAA---CTCAGGAGCAAATG 426488 vi i iiii v i v--- v ii iv v L1M2_orf2#LIN 2207 AATCAGTAGCATTTCTATACGCCAACAACGAACTATCTGAAAAAGAAATC 2256 chr1ptel1M 426489 AAGAAAGAGAAATTTCATTT 426508 -- v ii L1M2_orf2#LIN 2257 AAGAA--AGCAATCCCATTT 2274 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.73 CpG sites = 27, Kimura (unadjusted) = 39.92 Transitions / transversions = 1.23 (27/22) Gap_init rate = 0.02 (4 / 165), avg. gap size = 1.50 (6 / 4) 308 25.41 0.78 2.36 chr1ptel1M 426343 426471 (573529) L1M1_orf2#LINE/L1 2110 2236 (1058) m_b12s551i7 432 chr1ptel1M 426343 ATCATATTATACTTGTAGAATCCTAGAGAATC-ATTTAAAAACTACCTGA 426391 v v i v i v i v - i?v iiv L1M1_orf2#LIN 2110 ATGATCTTATATTTGGAAAAACCTAAAGACTCCACNAAAAAACTATTAGA 2159 chr1ptel1M 426392 AATAATTAACAGCTTGCGTAAAGTTGCAGAAAATAAAGTAAACCCACATA 426441 v i v iv vv i v i i v vi v L1M1_orf2#LIN 2160 ACTGATAAACAAATTCAGTAAAGTTGCAGGATACAAAATCAACATACAAA 2209 chr1ptel1M 426442 AATCATCAGTATTTCTATATATTACCAACA 426471 vi i --- i L1M1_orf2#LIN 2210 AATCAGTAGCATTTCTATA---TGCCAACA 2236 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 31.52 CpG sites = 15, Kimura (unadjusted) = 31.52 Transitions / transversions = 0.88 (15/17) Gap_init rate = 0.03 (4 / 128), avg. gap size = 1.00 (4 / 4) 264 30.63 5.60 2.54 chr1ptel1M 427165 427432 (572568) L1M2_orf2#LINE/L1 3016 3291 (0) m_b12s551i9 432 chr1ptel1M 427165 AAAATGGATAATTTTGGTTACATTTAATTAAAAAGATTTTGCACAAATAA 427214 i i v vv i iv i v i i-i L1M2_orf2#LIN 3016 AAAATAGACAAATGGGATTACATCAAACTAAAAAGCTTCTGCACAG-CAA 3064 chr1ptel1M 427215 AGCTAATGCAGCCAA--GATTAGAAGGGAAG-----CAGAAAGCTGGGAA 427257 vv -- ii -- v - i vi----- --- i L1M2_orf2#LIN 3065 AGGAAA--CAATCAACAGAGT-GAAGAGACAACCTACAGAA---TGGGAG 3108 chr1ptel1M 427258 ACAATTTGTACAGCCAATGTTTCTGATAAAGTCCTCATTTCTAAAATATA 427307 v v v i iv v ?iv i i vvi v v i i L1M2_orf2#LIN 3109 AAAATATTTGCAAACTATNCATCTGACAAGGGATTAATATCCAGAATATA 3158 chr1ptel1M 427308 TAGAGAACT-----GACTCA-CATTTTTAAGACT--TTCTCCAACTGATA 427349 ii -----i - vivvv i v-- vv i i ? v L1M2_orf2#LIN 3159 TAAGGAACTCAAACAACTCAACAGCAAAAAAACAAATAATCCGATTNAAA 3208 chr1ptel1M 427350 AATGGTCAAACGATAGGAACAGACAATTTTCAGGTGAAGAAATTAAAGTC 427399 v v ivv i v i iiv v vv i v L1M2_orf2#LIN 3209 AATGGGCAAAGGACCTGAATAGACATTTCTCAAAAGAAGACATACAAATG 3258 chr1ptel1M 427400 ATCTATAGTCATATGAAAAAATGCTTTAAATCA 427432 ii v i vi iv v L1M2_orf2#LIN 3259 GCCAACAGGTATATGAAAAAATGCTCAACATCA 3291 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.64 CpG sites = 39, Kimura (unadjusted) = 40.28 Transitions / transversions = 0.95 (39/41) Gap_init rate = 0.04 (12 / 267), avg. gap size = 1.83 (22 / 12) 613 31.59 4.26 2.35 chr1ptel1M 427291 427666 (572334) L1MD2_3end#LINE/L1 1 383 (723) m_b12s551i10 432 chr1ptel1M 427291 CTCATTTCTAAAATATATAGAGAACT-----GACTCA-CATTTTTAAGAC 427334 ?i v i i -----i - v vvv i L1MD2_3end#LI 1 CTNGTATCTAGAATATATAAAGAACTCTCAAAACTCAACAGTAAAAAAAC 50 chr1ptel1M 427335 TTTC--TCCAACTGATAAATGGTCAAACGATAGGAACAGACAATTTTCAG 427382 vvv -- i iiv v v i v v iv v L1MD2_3end#LI 51 AAACAATCCAATTAGAAAATGGGCAAAAGACATGAACAGACATTTCACCG 100 chr1ptel1M 427383 GTGAAGAAATTAAAGTCATCTATAGTCATATGAAAAAATGCTTTAAATCA 427432 iv i v vv ii viivv iv i i i iv v L1MD2_3end#LI 101 AAGAGGATATACAGATGGCAAATAAGCACATGAAAAGATGTTCAACATCA 150 chr1ptel1M 427433 TTATTGATTAGAGAAGTGCAAACTAAAACAACTCTTAGATACCATTTCAC 427482 viv i i i v vv v i i v L1MD2_3end#LI 151 TTAGCCATTAGGGAAATGCAAATTAAAACCACAATGAGATATCACTACAC 200 chr1ptel1M 427483 ACCTATCAGACTGGCTAAGGTGACAGAAAAGGAAAATGGTAAATATTAGA 427532 v ii i v i v iv v iivi ii i v L1MD2_3end#LI 201 ACCTATCAGAATGGCTAAAATAAAAAATAGTGACAACACCAAATGCTGGC 250 chr1ptel1M 427533 GGTGTTGTAAGGAAACTGGAACATCAATGC--TCTTAGTGGAGTTGTAAA 427580 iv v iiii v iiv i -- vi i iiv L1MD2_3end#LI 251 GAGGATGCGGAGAAACTGGATCACTCATACATTGCTGGTGGGAATGTAAA 300 chr1ptel1M 427581 CTGATCCAGCCATTCTGGAGGGCAATCTGGAACTATGTCCAAAAGGCTAT 427630 v i v i iii i i v v v v --------- L1MD2_3end#LI 301 ATGGTACAGCCACTCTGGAAAACAGTTTGGCAGTTTCT---------TAT 341 chr1ptel1M 427631 AAAACT----GTGTA--TACCTTTTGATCCAGCAATAACACT 427666 ----i i -- v vi i vi L1MD2_3end#LI 342 AAAACTAAACATGCANTTACCATACGACCCAGCAATTGCACT 383 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.05 CpG sites = 62, Kimura (unadjusted) = 42.05 Transitions / transversions = 1.15 (62/54) Gap_init rate = 0.04 (15 / 375), avg. gap size = 1.67 (25 / 15) 885 30.77 1.91 0.84 chr1ptel1M 427338 427809 (572191) L1ME4a_3end#LINE/L1 56 532 (339) m_b12s551i12 432 chr1ptel1M 427338 CTCCAACTGATAAATGGTCAAACGATAGGAACAGACAATTTTCAGGTGAA 427387 i iv v v v i v iv iiv L1ME4a_3end#L 56 CCCCAATAGAAAAATGGGCAAAGGACATGAACAGACAATTCACAAAAGAA 105 chr1ptel1M 427388 GAAATTAAAGTCATCTATAGTCATATGAAAAAATGCTTTAAATCATTATT 427437 vv i vii v iv ? i iv vv i v L1ME4a_3end#L 106 GAAATACAAATGGCCAATAAACATATGAAAANATGTTCAACCTCACTAGT 155 chr1ptel1M 427438 GATTAGAGAAGTGCAAACTAAAACAACTCTTAGATACCATTTCACACCTA 427487 i i i i i vv v iv L1ME4a_3end#L 156 AATCAAAGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCTA 205 chr1ptel1M 427488 TCAGACTGGCTAAGGTGACAGAAAAGGAAAATGGTAAATATTAGAGGTGT 427537 i i v i vvv i i vv v iviv i i i v iv v L1ME4a_3end#L 206 TCAAATTGGCAAAGATTTAAAAGATTGATAATACCCAGTGTTGGCGAGGG 255 chr1ptel1M 427538 TGTAAGGAAACTGGAAC-ATCA-ATGCTCTTAGTGGAGTTGTAAACTGAT 427585 ii? v v -v - ii vi i iiv i i L1ME4a_3end#L 256 TGTGGNGAAACGGGCACTCTCATACACTGCTGGTGGGAGTGTAAATTGGT 305 chr1ptel1M 427586 CCAGCCATTCTGGAGGGCAATCTGGAACTATGT-CCAAAAGGCTATAAAA 427634 v i v i v v -i v - L1ME4a_3end#L 306 ACAACCTTTCTGGAGGGCAATTTGGCAATATGTATCAAAAGCCT-TAAAA 354 chr1ptel1M 427635 CTGTGTATACCTTTTGATCCAGCAATAACACTACCAGGTCTGTATAATTA 427684 v ?i i i i vv v i vv v vv v L1ME4a_3end#L 355 ATGTNCATACCCTTTGACCCAGTAATTCCACTTCTAGGAATTTATCCTAA 404 chr1ptel1M 427685 AGATATATTTTAAAAA---GGAAAAGCACTCATATATATAAAAGTATTTA 427731 i v -v i i i --- ? v iv i -- i i iii i i L1ME4a_3end#L 405 GGAAATA-ATCAGAGATGTGNACAAAGATT--TATGTACAAGGATGTTCA 451 chr1ptel1M 427732 TAATAGC-TGCTTTTT--TGGTGGCAAATTGAAAATTGAAGGAATATCCA 427778 vii - vv v -- i i iv i ivivvvi i L1ME4a_3end#L 452 TCGCAGCATTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCA 501 chr1ptel1M 427779 TCAAATGGGGAATGGCTGAACAAATTGTTGT 427809 v vv ? i i i i v L1ME4a_3end#L 502 ACAATAGGGGANTGGTTAAATAAATTATGGT 532 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.14 CpG sites = 75, Kimura (unadjusted) = 40.88 Transitions / transversions = 1.09 (75/69) Gap_init rate = 0.02 (10 / 471), avg. gap size = 1.30 (13 / 10) 908 26.15 3.51 3.81 chr1ptel1M 427338 427679 (572321) L1ME5_3end#LINE/L1 56 396 (545) m_b12s551i11 432 chr1ptel1M 427338 CTCCAACTGATAAATGGTCAAACGATAGGAACAGACAATTTTCAGGTGAA 427387 i iv v v v v i v iv i L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chr1ptel1M 427388 GAAATT---AAAGTCATCTATAGTCATATGAAAAAATGCTTTAAATCATT 427434 ii--- i ii --- i iv i i iv v L1ME5_3end#LI 106 GAAACCCGAAAGGCTA---ACAAGCATATGAAGAGATGCTCAAACTCATT 152 chr1ptel1M 427435 ATTGATTAGAGAAGTGCAAACTAAAACAACTCTTAGATACCATTTCACAC 427484 v i i i i vv v i i i L1ME5_3end#LI 153 AGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACAC 202 chr1ptel1M 427485 CTATCAGACTGGCTAAGGTGACAGAAAA--GGAAAATGGTAAATATTAGA 427532 i v ii --i i-- v vi i i i v L1ME5_3end#LI 203 CTATTAGACTGGCAAAAAT--TAGAAAGCTGGATAATGCCAAGTGTTGGC 250 chr1ptel1M 427533 GGTGTTGTAAGGAAACTGGAACATCAATGCTCT--TAGTGGAGTTGTAAA 427580 iv v ii ? iv viiv v -- i iiv i L1ME5_3end#LI 251 GAGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGA 300 chr1ptel1M 427581 CTGATCCAGCCATTCTGGAGGGCAATCTGGAACTAT---GTCCAA--AAG 427625 i v i v v i--- v -- L1ME5_3end#LI 301 CTGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTAAG 350 chr1ptel1M 427626 GCTATAAAACTGTGTATACCTTTTGATCCAGCAATAACACTACCAGGTCT 427675 -- ------i i i v i vv i v ii v L1ME5_3end#LI 351 --TATA------CGCATACCCTATGACCCAGCAATTCCGCTCCTGGGTAT 392 chr1ptel1M 427676 GTAT 427679 i L1ME5_3end#LI 393 ATAT 396 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 32.17 CpG sites = 52, Kimura (unadjusted) = 33.11 Transitions / transversions = 1.53 (52/34) Gap_init rate = 0.05 (18 / 341), avg. gap size = 1.39 (25 / 18) 216 32.53 0.00 1.20 chr1ptel1M 427821 427904 (572096) C MamRTE1#LINE/RTE-BovB (7) 3805 3723 m_b12s601i6 433 chr1ptel1M 427821 TTGTTGTCCTTTGTACTTGAAGAGGACCAAAATGATGTTAGAATCAAATT 427870 i i i i v vvv v i v - v vvv i C MamRTE1#LINE/ 3805 TCGTTGTCCTTCGTATTCGAAGATGACGCTACTGACGGT-GATTGCTATC 3757 chr1ptel1M 427871 AGTGTGTCCAACTGTGGCTGACTACACCCATGTG 427904 vi v iiv vv v v i C MamRTE1#LINE/ 3756 TATGTGTGCGGGTGTGGCTGAAAAGACCGATGCG 3723 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.14 CpG sites = 10, Kimura (unadjusted) = 42.69 Transitions / transversions = 0.59 (10/17) Gap_init rate = 0.01 (1 / 83), avg. gap size = 1.00 (1 / 1) 225 26.98 2.17 3.30 chr1ptel1M 428777 428868 (571132) L1ME1_3end#LINE/L1 474 564 (362) m_b12s551i13 432 chr1ptel1M 428777 AAACTGGAAATGGG--GAATGCCCATTAATTGGAAGATGGATAAACAAAT 428824 iiiv--i i i i? vii L1ME1_3end#LI 474 AAACTGGAAACAACCCAAATGTCCATCAACNGGTGAATGGATAAACAAAT 523 chr1ptel1M 428825 TACAGTATATGACTCCAATGAGATATTAATACCCTGCAAGAAAA 428868 iii vvv v ii i--- i v v L1ME1_3end#LI 524 TGTGGTATATCCATACAATGGAATAC---TACTCAGCAATAAAA 564 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.32 CpG sites = 16, Kimura (unadjusted) = 35.32 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.04 (4 / 91), avg. gap size = 1.25 (5 / 4) 45 2.38 0.00 0.00 chr1ptel1M 429150 429192 (570808) (TG)n#Simple_repeat 1 43 (0) c_b12s251i0 434 chr1ptel1M 429150 TGTGTGTGTGTGTGTGTGTGTGTGCGTGTGTGTGTGTGTGTGT 429192 i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 43 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 187 22.22 0.00 0.00 chr1ptel1M 431961 431996 (568004) MIRb#SINE/MIR 219 254 (14) m_b12s601i7 435 chr1ptel1M 431961 CACAGTGCTTAACACATACCAAGCTGTTAATAAATG 431996 i ii vi vv i MIRb#SINE/MIR 219 CACAGTGCCTGGCACATAGTAAGCGCTCAATAAATG 254 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.96 CpG sites = 5, Kimura (unadjusted) = 26.96 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 412 28.46 17.95 0.88 chr1ptel1M 432664 432858 (567142) MIRc#SINE/MIR 2 229 (39) m_b12s601i8 436 chr1ptel1M 432664 GAAGCCAGGCAGCTCAGAGGATGGAACACTGTACCTGAAGTCAAGAATAC 432713 i viv ii iv v vi i v i i i v MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr1ptel1M 432714 CCGAGTTCAAATTCTGCCTCAGACACTCA----------GA-----GGCA 432748 i i i i i i v v v i ---------- ----- MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 101 chr1ptel1M 432749 GGGTAT-----CTCTCCCAGCCT--GTTTCCTCATATGTAAAATGGAAA- 432790 i vi i----- iv -- v ii - MIRc#SINE/MIR 102 AGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGAT 151 chr1ptel1M 432791 AATCAT------CACACCTGTCTCTCAGGGTCGTTATCACA---AAATGA 432831 v ------ vii ii v i i v vi--- MIRc#SINE/MIR 152 AATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGA 201 chr1ptel1M 432832 CATAACATA---GGAAGCAAACTTTATCAA 432858 v ii --- i --i i v MIRc#SINE/MIR 202 GATAATGTATGTGAAAGC--GCTTTGTAAA 229 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.65 CpG sites = 35, Kimura (unadjusted) = 37.20 Transitions / transversions = 1.75 (35/20) Gap_init rate = 0.05 (10 / 194), avg. gap size = 3.70 (37 / 10) 508 18.84 3.33 11.51 chr1ptel1M 434229 434378 (565622) MIRb#SINE/MIR 11 149 (119) m_b12s601i9 437 chr1ptel1M 434229 GCATGATG--GTGGATAGAGCACGAGCCCAGGAGTTAGGAGGAGGACCTG 434276 i i -- v i iiv i ivi --- MIRb#SINE/MIR 11 GCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGA---CCTG 57 chr1ptel1M 434277 ACTTCAAATCCTGCCTCCCATATTTCTGCCTAACACTTAGTAGTTAT-TA 434325 iv i i v --------- ---- v i i - i MIRb#SINE/MIR 58 GGTTCGAATCCCGGCTC---------TGCC----ACTTACTAGCTGTGTG 94 chr1ptel1M 434326 AC-TTGGGCAAGTCACTTCACC-CTGTTTGCCTCAGTTTCCTCATCTGTA 434373 - i v - v vv MIRb#SINE/MIR 95 ACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTA 144 chr1ptel1M 434374 AAATG 434378 MIRb#SINE/MIR 145 AAATG 149 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 18.98 CpG sites = 15, Kimura (unadjusted) = 21.77 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.13 (20 / 149), avg. gap size = 1.05 (21 / 20) 267 25.62 4.35 6.67 chr1ptel1M 434891 434982 (565018) C L2c_3end#LINE/L2 (15) 463 374 m_b12s601i10 438 chr1ptel1M 434891 AGACATTCATTAAGTGCCTCCCGTGAGCCTTGAGCACTGGGAATACAAA- 434939 i i i i v ii v --ii i i - C L2c_3end#LINE 463 AAACATTTATTGAGCGCCTACTATGTGCC--AGGCGCTGGGGATACAAAG 416 chr1ptel1M 434940 ---AGGAGGCCACGGACAACCCCTACTCCCAAGGAGCTCACAACCT 434982 --- iv i v ----i i i i ii C L2c_3end#LINE 415 ATGAATAAGACACGG----TCCCTGCCCTCAAGGAGCTCACAGTCT 374 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.96 CpG sites = 18, Kimura (unadjusted) = 33.73 Transitions / transversions = 4.50 (18/4) Gap_init rate = 0.09 (8 / 91), avg. gap size = 1.25 (10 / 8) 47 2.13 2.08 0.00 chr1ptel1M 435154 435201 (564799) (AC)n#Simple_repeat 1 49 (0) c_b12s251i1 439 chr1ptel1M 435154 ACACACATACACACACACACACACACACACACACACACACAC-CACACA 435201 i - (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACA 49 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.02 (1 / 47), avg. gap size = 1.00 (1 / 1) 185 28.79 0.00 0.00 chr1ptel1M 436732 436797 (563203) MIR1_Amn#SINE/MIR 60 125 (105) m_b12s601i12 440 chr1ptel1M 436732 TCAGATCCAGCCTCTGACACAGATTAGCTGGGTGATCCTAGACCAGACAC 436781 ?i? v v v v?iii? ? i i i i v v MIR1_Amn#SINE 60 TCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGTCAC 109 chr1ptel1M 436782 TTAAGGTGTTGGGGCC 436797 ? vv v iv ? MIR1_Amn#SINE 110 TTNACCTCTCTGNGCC 125 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.53 CpG sites = 9, Kimura (unadjusted) = 42.53 Transitions / transversions = 0.90 (9/10) Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0) 203 29.63 0.00 0.00 chr1ptel1M 436732 436785 (563215) MIRc#SINE/MIR 58 111 (157) m_b12s601i11 440 chr1ptel1M 436732 TCAGATCCAGCCTCTGACACAGATTAGCTGGGTGATCCTAGACCAGACAC 436781 iii v v v vv i v i i i i v v MIRc#SINE/MIR 58 TCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCAC 107 chr1ptel1M 436782 TTAA 436785 MIRc#SINE/MIR 108 TTAA 111 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.26 CpG sites = 8, Kimura (unadjusted) = 38.17 Transitions / transversions = 1.00 (8/8) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 365 25.01 4.72 5.56 chr1ptel1M 437611 437737 (562263) MIRb#SINE/MIR 5 130 (138) m_b12s601i13 441 chr1ptel1M 437611 GGGGCAGCCAGGTGCCC------GAGCACCAGCCCTGAAGTCAGGGGGAC 437654 vv vv------ vi ii i ivi MIRb#SINE/MIR 5 GGGGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGAC 54 chr1ptel1M 437655 CTGAGTTCAAATCTGGACCCAGACACTTAACACTGCCTGGCCGTGTGACC 437704 i i iv i i v v ------- i i MIRb#SINE/MIR 55 CTGGGTTCGAATCCCGGCTCTGCCACTTA-------CTAGCTGTGTGACC 97 chr1ptel1M 437705 CTGGGCGAGTCACTTAACCCCAATTACCCTCAG 437737 i i i i vv v v MIRb#SINE/MIR 98 TTGGGCAAGTTACTTAACCTCTCTGAGCCTCAG 130 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.74 CpG sites = 17, Kimura (unadjusted) = 30.96 Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.06 (8 / 126), avg. gap size = 1.62 (13 / 8) 412 24.39 0.00 6.80 chr1ptel1M 437628 437737 (562263) MIRc#SINE/MIR 25 127 (141) m_b12s601i14 441 chr1ptel1M 437628 GAGCACCAGCCCTGAAGTCAGGGGGACCTGAGTTCAAATCTGGACCCAGA 437677 ii v i i ii i i i iv i i v v MIRc#SINE/MIR 25 GAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGC 74 chr1ptel1M 437678 CACTTAACACTGCCTGGCCGTGTGACCCTGGGCGAGTCACTTAACCCCAA 437727 ------- i i i i i vv MIRc#SINE/MIR 75 CACTTA-------CTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTC 117 chr1ptel1M 437728 TTACCCTCAG 437737 v v MIRc#SINE/MIR 118 TGAGCCTCAG 127 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.96 CpG sites = 17, Kimura (unadjusted) = 30.41 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.06 (7 / 109), avg. gap size = 1.00 (7 / 7) 20 28.14 0.00 0.00 chr1ptel1M 438251 438311 (561689) (GGGGA)n#Simple_repeat 1 61 (0) m_b12s252i4 442 chr1ptel1M 438251 GGGGAGGGGCAGAGCGGGGAGGGGCAAGGAGCGGGGAGGAAGGGAGGGGG 438300 vi i v vii v i i i i (GGGGA)n#Simp 1 GGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGA 50 chr1ptel1M 438301 GGGGGGGTGAG 438311 i v (GGGGA)n#Simp 51 GGGGAGGGGAG 61 Matrix = Unknown Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 16 25.24 3.57 0.00 chr1ptel1M 438642 438697 (561303) (CCCCTC)n#Simple_repeat 1 58 (0) m_b12s252i5 443 chr1ptel1M 438642 CCCCTCCCCCACCTAGTCCCTGT-CCCCTCCCCCATCTAAT-CCCCGCCC 438689 v ivv iv - vi ivv - v (CCCCTC)n#Sim 1 CCCCTCCCCCTCCCCCTCCCCCTCCCCCTCCCCCTCCCCCTCCCCCTCCC 50 chr1ptel1M 438690 CCTCCCCC 438697 (CCCCTC)n#Sim 51 CCTCCCCC 58 Matrix = Unknown Transitions / transversions = 0.50 (4/8) Gap_init rate = 0.04 (2 / 55), avg. gap size = 1.00 (2 / 2) 18 8.59 0.00 9.76 chr1ptel1M 438925 438969 (561031) (GCCCC)n#Simple_repeat 1 41 (0) m_b12s252i6 444 chr1ptel1M 438925 GCCCCGCCCCGCCCAGGCCCCGCCCCCGCCCGAGGCCACGCCCCG 438969 -v - --v v (GCCCC)n#Simp 1 GCCCCGCCCCGCCC-CGCCCCG-CCCCGCCC--CGCCCCGCCCCG 41 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4) 250 37.78 2.89 8.29 chr1ptel1M 445515 445895 (554105) L2#LINE/L2 465 826 (2256) m_b13s601i0 445 chr1ptel1M 445515 ATCTGATTCTCTCCTGATGACACGGCCTCCCTGTTCTCCCTTTTTAGCAC 445564 i ii i v v i ivvivv i iv iiv L2#LINE/L2 465 ACCTGGCTCTCCCCTGAGGACACTGCTTCCCCTGCAGCCCTCTCAAGTGG 514 chr1ptel1M 445565 TGACTG----CACCTTCAGGCTCCCCAAATCAGTGGTCC---AGATGGGG 445607 i ---- v iii vi?i i iv i v v --- i L2#LINE/L2 515 TGGCTGTTTTCTCTCCCACANCCCTCGTACCACTGGGCCTGGAGGTGGGG 564 chr1ptel1M 445608 CAGTTGTAATACTCTAAACTCCCTATTGACACTTCTAGGTTCTCCTCTAC 445657 i v v--- ivvi ii v i i iiiv i -- L2#LINE/L2 565 TAGGTGTC---CTCCTTGCTCCTCATTGCCGCTTCCAGACCATTCTC--C 609 chr1ptel1M 445658 CTACCTCCATCACTTAGGAACTTCTCTTCCTTTGAGGTTCATGCAGTCCA 445707 v - - i -- viv i ivv ivi ivi vi L2#LINE/L2 610 CTCCCTCC-TC-CCTA--AAACACCCCAGCTTTGAATCTCATGTCATCAG 655 chr1ptel1M 445708 AATCTACCACCCAATCAAATTTTTTTGGCTTTAGGCCAAAAGGCTTAGGC 445757 v v i-- v viii ii v i vi v ------iii --- L2#LINE/L2 656 ACTATACCACCCG--CTACCCCTCCTTGTTGCAGTC------ATCTA--- 694 chr1ptel1M 445758 CCCAGTCTTTAGGATGCTTCCCTTT-TTCCTTCAGTAAGTCCAATGCCTG 445806 - iii iii vii i i i- v i-i v ii iiv L2#LINE/L2 695 -CCGACCTCCGGGTCACTCCCCCTCATTCCTTGAA-GATTTTAGCTCCTG 742 chr1ptel1M 445807 ATTCA-TGCCTTTCTCTCCTCCCCCTTCCTACTCCCTGCCCTCATACAAG 445855 ii - i vi vv -----v - i v v v vv L2#LINE/L2 743 GCTCACTGTCACTCTCTCCAAC-----ACTACT-CCTGTCATAATTCTTG 786 chr1ptel1M 445856 GGGATTTCAATAT--ATATAATCATACTCCCCCAGGTACCCT 445895 v -- ii i-- iv ii vii L2#LINE/L2 787 GTGATTTCAATATCCACGTAG--ATGATCCTTCCAATACCCT 826 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 51.72 CpG sites = 82, Kimura (unadjusted) = 55.68 Transitions / transversions = 1.64 (82/50) Gap_init rate = 0.09 (35 / 380), avg. gap size = 1.17 (41 / 35) 287 25.80 9.80 1.20 chr1ptel1M 449499 449651 (550349) L1PA13_3end#LINE/L1 17 182 (728) m_b13s551i0 446 chr1ptel1M 449499 ATAGAGAAATTAATCAAATTTATAA------AATAAATCACTCAATTGAA 449542 ii v v i ------ i iv i v i L1PA13_3end#L 17 ATAAGGAACTTAAACAAATTTACAAGAAAAAAACAAACAACCCCATTAAA 66 chr1ptel1M 449543 CAATGGTCAAAGGACATGAATAGGCAGTTTTCAGATAAA---ATAAGCAA 449589 v i v i i v i vi --- viiiv L1PA13_3end#L 67 AAGTGGGCAAAGGACATGAACAGACACTTTTCAAAAGAAGACATACATGC 116 chr1ptel1M 449590 AGGTAACTATAACTATGAAAAAA-----AATGTT-CTAATCCATTAGAAA 449633 i vi v v - ----- ii i- i - i L1PA13_3end#L 117 GGCCAACAATCA-TATGAAAAAAAGCTCAACATCACTGAT-CATTAGAGA 164 chr1ptel1M 449634 AATACACATTAAAACAAC 449651 i v i v L1PA13_3end#L 165 AATGCAAATCAAAACCAC 182 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 31.52 CpG sites = 24, Kimura (unadjusted) = 32.53 Transitions / transversions = 1.60 (24/15) Gap_init rate = 0.04 (6 / 152), avg. gap size = 2.83 (17 / 6) 288 22.78 7.59 0.00 chr1ptel1M 449499 449577 (550423) L1PREC2_orf2#LINE/L1 3161 3245 (49) m_b13s551i1 446 chr1ptel1M 449499 ATAGAGAAATTAATCAAATTTATAA------AATAAATCACTCAATTGAA 449542 ii v v i ------ i iv i v i L1PREC2_orf2# 3161 ATAAGGAACTTAAACAAATTTACAAGAAAAAAACAAACAACCCCATTAAA 3210 chr1ptel1M 449543 CAATGGTCAAAGGACATGAATAGGCAGTTTTCAGA 449577 v i v i i v i L1PREC2_orf2# 3211 AAGTGGGCAAAGGACATGAACAGACACTTTTCAAA 3245 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 27.75 CpG sites = 11, Kimura (unadjusted) = 27.75 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.01 (1 / 78), avg. gap size = 6.00 (6 / 1) 303 22.57 9.24 3.17 chr1ptel1M 449533 449651 (550349) L1ME5_3end#LINE/L1 57 182 (759) m_b13s551i2 446 chr1ptel1M 449533 CTCAATTGAACAATGGTCAAAGGACATGAATAGGCAGTTTTCAGATAAAA 449582 i v v v i i i v - i i L1ME5_3end#LI 57 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGA-AGAG 105 chr1ptel1M 449583 TAAGC---AAAGG-TAACTATAACTATGAAAAAAAATGTTCTAATCCATT 449628 v i --- - --- vi ivi i i i v ii L1ME5_3end#LI 106 GAAACCCGAAAGGCTAAC---AAGCATATGAAGAGATGCTCAAACTCATT 152 chr1ptel1M 449629 AG-------AAAAATACACATTAAAACAAC 449651 ------- i i v L1ME5_3end#LI 153 AGTAATCAGAGAAATGCAAATTAAAACAAC 182 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 27.67 CpG sites = 17, Kimura (unadjusted) = 27.67 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.06 (7 / 118), avg. gap size = 2.14 (15 / 7) 297 31.70 7.69 2.94 chr1ptel1M 450601 450795 (549205) C MamRTE1#LINE/RTE-BovB (2522) 1290 1087 m_b13s601i1 447 chr1ptel1M 450601 ACTCTGTGCCATACACGGCCTTCATTATTCTTA-CATCC--CA--TCTCT 450645 v i ii ii - v v v v - -- -- i v C MamRTE1#LINE/ 1290 ACTCGGCGCCACGCATAGC-TGCAGTAATCTAAACATCCTTCAGGTCCCG 1242 chr1ptel1M 450646 TCTCCTTACAATGATATAGTCTATTAAATACCAGTGTTTGCTTCAAGGGT 450695 iivi vv i i v v i i v i ivvi vv C MamRTE1#LINE/ 1241 CTGTCGAACGATGATATAATCAATGAGATGCCACTGCTTAGACCTTGGGT 1192 chr1ptel1M 450696 GCATCTCTGAAGT-TATGTTGCATTTAGTAAGTGAAAGA-GTTGATGGTG 450743 iv v - v v ivi ii i i i - v v C MamRTE1#LINE/ 1191 GCATCCATGATGTCTTTCTCTTATTCGGTAGGCGGAAGATGGTGTTGGTG 1142 chr1ptel1M 450744 AGAAGGTCATGA---GATGCCCAAGTC-CTCACTA---ATAAGT-GACCA 450785 ----- i i --- iiiivv -i i i--- vi - C MamRTE1#LINE/ 1141 A-----TTACGAGCTGATGCTTGGCACATTCGCTGAGCAGGAGTAGACCA 1097 chr1ptel1M 450786 TTGCTGTTGA 450795 ? C MamRTE1#LINE/ 1096 TTGCTGTTNA 1087 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.28 CpG sites = 34, Kimura (unadjusted) = 42.75 Transitions / transversions = 1.31 (34/26) Gap_init rate = 0.08 (15 / 194), avg. gap size = 1.40 (21 / 15) 500 20.07 0.89 6.60 chr1ptel1M 451716 451827 (548173) C MIRc#SINE/MIR (153) 115 10 m_b13s601i2 448 chr1ptel1M 451716 GAGGTTAAGTGACTTGCCCAGGGTCACACAGGTAGGAAGTGTTAAGTGTC 451765 i v ------- v C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGC 73 chr1ptel1M 451766 TGAGACCAGCTTTCAACTCAAGTCATCCTGACTTCAGG-CTGGTGCTTTA 451814 v v vi vi iv i i v i i - ii i v C MIRc#SINE/MIR 72 AGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTT 23 chr1ptel1M 451815 TCTACTGCACCAC 451827 i C MIRc#SINE/MIR 22 TCCACTGCACCAC 10 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 22.33 CpG sites = 12, Kimura (unadjusted) = 23.57 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.07 (8 / 111), avg. gap size = 1.00 (8 / 8) 265 33.33 0.00 0.00 chr1ptel1M 454491 454562 (545438) C Charlie1b#DNA/hAT-Charlie (431) 92 21 m_b13s502i0 449 chr1ptel1M 454491 TACTACTAGGGAAACACTTTTGACCTCACAAACCCTTGAAAAGGACATTA 454540 i i v i i v i ii iivi iiv ii C Charlie1b#DNA 92 TATTATTATGAAAATAGTTTTGACCTCGCGGACCCCCTGAAAGGGTCTCG 43 chr1ptel1M 454541 GGGATGCCCAGGTGTCTCCAAA 454562 iv v i ii C Charlie1b#DNA 42 GGGACCCCCAGGGGTCCCCGGA 21 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.31 CpG sites = 18, Kimura (unadjusted) = 48.33 Transitions / transversions = 3.00 (18/6) Gap_init rate = 0.00 (0 / 71), avg. gap size = 0.0 (0 / 0) 576 27.53 8.43 0.00 chr1ptel1M 455427 455604 (544396) C MIR#SINE/MIR (22) 240 48 m_b13s601i3 450 chr1ptel1M 455427 GCCCCTATTACGTACCAGGTTCTGTTCCAAGCACTTCATAAATAT---AT 455473 v i i i i iv i i i i vi ---v C MIR#SINE/MIR 240 GCGCTTACTATGTGCCAGGCACTGTTCTAAGCGCTTTACATGTATTAACT 191 chr1ptel1M 455474 CATTTGAACCTC-C--CTACTCTGCAAGCCAGGTGCTCCCATTATCTGCA 455520 i v - -- v i iii vi i vii iv C MIR#SINE/MIR 190 CATTTAATCCTCACAACAACCCTATGAGGTAGGTACTATTATTATCCCCA 141 chr1ptel1M 455521 CTTTACAATTGGGGAAACCGAGGCATTCAGAGGTTAAATGACTTGACCAA 455570 i iv i i ivv i i v C MIR#SINE/MIR 140 TTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCCAA 91 chr1ptel1M 455571 -GTCACAC--------GGTATCTGAGGCTGGATTTGAACTCGG 455604 - --------i iv v v v i i i C MIR#SINE/MIR 90 GGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAG 48 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.83 CpG sites = 32, Kimura (unadjusted) = 35.65 Transitions / transversions = 1.88 (32/17) Gap_init rate = 0.03 (5 / 177), avg. gap size = 3.00 (15 / 5) 439 24.39 14.37 1.02 chr1ptel1M 455455 455628 (544372) C MIRc#SINE/MIR (45) 223 27 m_b13s601i4 450 chr1ptel1M 455455 AAGCACTT---CATAAAT-ATATCATTTGAACCTC-C--CTACTCTGCAA 455497 i --- v - v v - -- v i ii C MIRc#SINE/MIR 223 AAGCGCTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGA 174 chr1ptel1M 455498 GCCAGGT---GC---TCCCATTATCTGCACTTTACAATTGGGGAAACCGA 455541 vi i--- --- vii iv i iv i i C MIRc#SINE/MIR 173 GGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGA 124 chr1ptel1M 455542 GGCATTCAGAGGTTAAATGACTTGACCAA-GTCACAC--------GGTAT 455582 vivv i v - --------i iv C MIRc#SINE/MIR 123 GGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGG 74 chr1ptel1M 455583 CTGAGGCTGGATTTGAACTCGGTTCTTACCCTG---CAAACTCTGGTGC 455628 v v v i i i i v -- --- v v ii C MIRc#SINE/MIR 73 CAGAGCCGGGACTCGAACCCAGGTCTT--CCTGACTCCAAGTCCAGTGC 27 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.32 CpG sites = 23, Kimura (unadjusted) = 29.97 Transitions / transversions = 1.21 (23/19) Gap_init rate = 0.06 (11 / 173), avg. gap size = 2.45 (27 / 11) 11 13.59 2.78 5.71 chr1ptel1M 456936 456971 (543029) (CTCAAC)n#Simple_repeat 1 35 (0) m_b13s252i0 451 chr1ptel1M 456936 CTCATCCGTC-ACCTCCACCCCCACCATCAACCTCAA 456971 v - - v i v - (CTCAAC)n#Sim 1 CTCAACC-TCAACCTCAACCTCAACC-TCAACCTCAA 35 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.09 (3 / 35), avg. gap size = 1.00 (3 / 3) 18 14.77 1.96 6.12 chr1ptel1M 457090 457140 (542860) (CCAGC)n#Simple_repeat 1 49 (0) m_b13s252i1 452 chr1ptel1M 457090 CCAGCCACCCCCACCCCAGTCCCTGTACCCAGCCCA-CCCACCCCAGCCC 457138 vvv v - v -- - v (CCAGC)n#Simp 1 CCAGCCCAGCCCAGCCCAG-CCCAG--CCCAGCCCAGCCCAGCCCAGCCC 47 chr1ptel1M 457139 AG 457140 (CCAGC)n#Simp 48 AG 49 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.08 (4 / 50), avg. gap size = 1.00 (4 / 4) 36 17.99 1.45 0.00 chr1ptel1M 457198 457266 (542734) (CA)n#Simple_repeat 1 70 (0) m_b13s252i2 453 chr1ptel1M 457198 CACACACACAGTCACAGACACACACATACTCTCACTCTCACACACACACA 457247 vv v i v v v v (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 chr1ptel1M 457248 CACTCACAC-CATACTCACA 457266 v - i v (CA)n#Simple_ 51 CACACACACACACACACACA 70 Matrix = Unknown Transitions / transversions = 0.22 (2/9) Gap_init rate = 0.01 (1 / 68), avg. gap size = 1.00 (1 / 1) 256 30.96 1.00 6.32 chr1ptel1M 458796 458895 (541105) MIR3#SINE/MIR 96 190 (18) m_b13s601i5 454 chr1ptel1M 458796 GCAGGTGACTCC-TCTGCCTGGACCTTAGTTTCCTCATGGAGAAAATGAG 458844 i v i -i vi i i vviv MIR3#SINE/MIR 96 GCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAG 145 chr1ptel1M 458845 GGAGCTGGATTGCCTGATGGCTGCCATGGCTGCAAACTTCAGCTCTAGCA 458894 i i i i--- iiiv i v iiv ---i i ii MIR3#SINE/MIR 146 GGGGTTGGACTA---GATGATCTCTAAGGTCCC---TTCCAGCTCTGACA 189 chr1ptel1M 458895 T 458895 MIR3#SINE/MIR 190 T 190 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 42.62 CpG sites = 21, Kimura (unadjusted) = 42.62 Transitions / transversions = 2.62 (21/8) Gap_init rate = 0.07 (7 / 99), avg. gap size = 1.00 (7 / 7) 191 25.45 9.09 0.00 chr1ptel1M 459341 459395 (540605) C MIRc#SINE/MIR (121) 147 88 m_b13s601i6 455 chr1ptel1M 459341 CCACTGTTCGAATGGGGAAACTGAGGTCAGGAGAG---AAGCGACTTGCT 459387 i v v ii i iivi --- i i C MIRc#SINE/MIR 147 CCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCC 98 chr1ptel1M 459388 --AGATCATA 459395 -- i i C MIRc#SINE/MIR 97 CAAGGTCACA 88 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.19 CpG sites = 11, Kimura (unadjusted) = 33.19 Transitions / transversions = 3.67 (11/3) Gap_init rate = 0.04 (2 / 54), avg. gap size = 2.50 (5 / 2) 14 14.53 2.27 7.14 chr1ptel1M 460610 460653 (539347) (CCCT)n#Simple_repeat 1 42 (0) m_b13s252i3 456 chr1ptel1M 460610 CCCTCCCCTCCCTCCCTCCC-GCCACAGGCCCTCCCCTCCCGTCC 460653 - -v v vvv - - (CCCT)n#Simpl 1 CCCT-CCCTCCCTCCCTCCCTCCCTCCCTCCCT-CCCTCCC-TCC 42 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.09 (4 / 43), avg. gap size = 1.00 (4 / 4) 14 5.01 8.16 8.16 chr1ptel1M 461305 461353 (538647) (AGGAGGG)n#Simple_repeat 1 49 (0) m_b13s252i4 457 chr1ptel1M 461305 AGG-GGGACGGAGGGATGCGCTGGAGGACGGGA-GA-GG-GGAGGGAGGA 461350 - - - - vv - - - - (AGGAGGG)n#Si 1 AGGAGGGA-GGAGGGA-G-GAGGGAGGA-GGGAGGAGGGAGGAGGGAGGA 46 chr1ptel1M 461351 GGG 461353 (AGGAGGG)n#Si 47 GGG 49 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.17 (8 / 48), avg. gap size = 1.00 (8 / 8) 108 19.76 6.29 0.31 chr1ptel1M 461704 462005 (537995) (TCTCTC)n#Simple_repeat 1 320 (0) m_b13s252i5 458 chr1ptel1M 461704 TCTCTCCCTCTGTCTCTCTTCCTC-CTC-CTCCTTCTC-CTCTCCCTC-C 461749 i v ii - - ii - i - (TCTCTC)n#Sim 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr1ptel1M 461750 TCTTCCTCT-TTTCTCACTGTCTCTCTCTCT-TCTCTCCATGTCTGTGTC 461797 ii - i v v - iv v v v (TCTCTC)n#Sim 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chr1ptel1M 461798 TGTCTCTCTCT-TCTGTCTCTCTCTCTTTACTC-CTC-CTC-CTC-CTC- 461841 v - v i - - - - - - (TCTCTC)n#Sim 101 TCTCTCTCTCTCTCTCTCTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCT 149 chr1ptel1M 461842 CTCT-TCTGTCTGTCTGTGTTTCTGTCTCTCTGTGTGTGTGTCTCTCTCT 461890 - v v v v i v v v v v v (TCTCTC)n#Sim 150 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 199 chr1ptel1M 461891 GTCTCTTTC-CTC-CTCCTTCTC-CTCTTCCTCT-TCT-TCTTCCTCCAT 461935 v i - - ii - ii - - ii iv (TCTCTC)n#Sim 200 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 249 chr1ptel1M 461936 CTCTGTGTCTGTCTCTCTGTCTCTGTTTCTGTCT-TGTCTCTCTTTCTCT 461984 v v v v v i v - v i (TCTCTC)n#Sim 250 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 299 chr1ptel1M 461985 CTCTCTCTCTCCCTCCCTCTC 462005 i i (TCTCTC)n#Sim 300 CTCTCTCTCTCTCTCTCTCTC 320 Matrix = Unknown Transitions / transversions = 0.86 (24/28) Gap_init rate = 0.07 (20 / 301), avg. gap size = 1.00 (20 / 20) 14 21.15 6.41 5.06 chr1ptel1M 462132 462209 (537791) (GAGAG)n#Simple_repeat 1 79 (0) m_b13s252i7 459 chr1ptel1M 462132 GAGAGTAGGAGGGGA-AAGAAGAGAGGAAAGG-GCCTAGAGAAGGAGGAG 462179 v - i -i i i - vvv i - (GAGAG)n#Simp 1 GAGAGGA-GAGGAGAGGAGAGGAGAGGAGAGGAGAGGAGAGGA-GAGGAG 48 chr1ptel1M 462180 AAGGAACTGGGGCGG-G-GGAGAGGA-AGGAGA 462209 - - vv i v - - - (GAGAG)n#Simp 49 -AGG-AGAGGAGAGGAGAGGAGAGGAGAGGAGA 79 Matrix = Unknown Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.12 (9 / 77), avg. gap size = 1.00 (9 / 9) 21 11.02 0.00 4.88 chr1ptel1M 462508 462550 (537450) (TCC)n#Simple_repeat 1 41 (0) m_b13s252i8 460 chr1ptel1M 462508 TCCTCCTCCTTCCTCCTCTTTCCTCCTCCTCCTGCTTCTGCTC 462550 - -i v i v (TCC)n#Simple 1 TCCTCCTCC-TCCTCCTC-CTCCTCCTCCTCCTCCTCCTCCTC 41 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.00 (2 / 2) 211 27.39 3.17 10.17 chr1ptel1M 463388 463513 (536487) MIR#SINE/MIR 14 131 (131) m_b13s601i7 461 chr1ptel1M 463388 GCAGTTA-GAGTGCTGGCCCTGAAGTCATGA--GGCTGGGAGTTCAAATC 463434 ii - ii v i i i - -- v -- i MIR#SINE/MIR 14 GTGGTTAAGAGCACGGGCTCTGGAGCCA-GACTGCCTGGG--TTCGAATC 60 chr1ptel1M 463435 CAGTCTCAGACATGCAATACTTGATCGATGTGTGACCTTTAAGAATTTTC 463484 v v ----- --i iv v v viiv v v MIR#SINE/MIR 61 CCGGCTC-----TGC--CACTTACTAGCTGTGTGACCTTGGGCAAGTTAC 103 chr1ptel1M 463485 ATTAATTTCACT-TGCATTCAACTACATCA 463513 - ii v - -i ii v v MIR#SINE/MIR 104 -TTAACCTCTCTGTGC-CTCAGTTTCCTCA 131 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.03 CpG sites = 17, Kimura (unadjusted) = 34.37 Transitions / transversions = 1.21 (17/14) Gap_init rate = 0.12 (15 / 125), avg. gap size = 1.07 (16 / 15) 19 23.22 0.00 0.00 chr1ptel1M 463996 464036 (535964) (A)n#Simple_repeat 1 41 (0) m_b13s252i10 462 chr1ptel1M 463996 AAAATAAAATAACAAAACAATAAACAAAAAAATAAAACAAA 464036 v v v v v v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 41 Matrix = Unknown Transitions / transversions = 0.00 (0/8) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 13 11.48 9.43 5.45 chr1ptel1M 463994 464046 (535954) (ATCAA)n#Simple_repeat 1 55 (0) m_b13s252i9 463 chr1ptel1M 463994 ATAAAATAAAATAACAAAAC-AAT-AAA-CAAA-AAAAT-AAAACAAATG 464038 v v -- v - - - -v - v - (ATCAA)n#Simp 1 ATCAAATCAAAT--CAAATCAAATCAAATCAAATCAAATCAAATCAAAT- 47 chr1ptel1M 464039 CAAATCAA 464046 (ATCAA)n#Simp 48 CAAATCAA 55 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.15 (8 / 52), avg. gap size = 1.00 (8 / 8) 452 20.34 1.65 2.50 chr1ptel1M 464716 464836 (535164) MER63D#DNA/hAT-Tip100 627 746 (315) m_b13s502i1 464 chr1ptel1M 464716 TTCAAGGAATAGCATTTGTATGATGGTAAGAAGTAGTTTAACAGTAGATC 464765 i v vv i v i i - MER63D#DNA/hA 627 TTTAATGAATATAATTTGTACGAGGGTGAGAAATAGTTTAACAGTAGAT- 675 chr1ptel1M 464766 ACACACCAG--ATAAAGGTAACACATTTCTTGGAAAAAGTTAGCAGATTG 464813 - i --? ? v i? i v v i -i MER63D#DNA/hA 676 -CACATCAGNTNTNATGANAATAAATTTATTGGAAAGAGTTA-TAGATTG 723 chr1ptel1M 464814 ATGTGCAATTGAATTGATCAAAT 464836 ivi i vv vi MER63D#DNA/hA 724 GGATGCAACTCCATTTGTCAAAT 746 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 23.58 CpG sites = 13, Kimura (unadjusted) = 24.72 Transitions / transversions = 1.18 (13/11) Gap_init rate = 0.03 (4 / 120), avg. gap size = 1.25 (5 / 4) 469 19.78 14.89 3.18 chr1ptel1M 464845 464985 (535015) MER63D#DNA/hAT-Tip100 816 972 (89) m_b13s502i2 465 chr1ptel1M 464845 AATTGCAGTTACAGGTTAGATTATCTATGGATGCAAG--CTTATCAAAAA 464892 iii i i ----- i i --i iiv MER63D#DNA/hA 816 AATTGCAACCATAGGTTGG-----CTACGGATACAAGAGTTCGGCAAAAA 860 chr1ptel1M 464893 TCAAC---AGAATAATGGGAGGATCTATTGACAATATGGAATTCACAATA 464939 --- v vv v i v i v i MER63D#DNA/hA 861 TCAACGAAAGCATTCTGTGAGAATCAATTGGCTATATGGAATTTACAATA 910 chr1ptel1M 464940 AAACGT----------------TTATTTGTAAATTTTGTGCTAGATATCT 464973 iv ---------------- v v i i MER63D#DNA/hA 911 AAGAGTATTGTATATTTTATTATTATTTGTAAATTGTGTGCTACACATCC 960 chr1ptel1M 464974 TTTCTATCAGTA 464985 v MER63D#DNA/hA 961 TTTATATCAGTA 972 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 21.41 CpG sites = 16, Kimura (unadjusted) = 23.41 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.06 (8 / 140), avg. gap size = 3.25 (26 / 8) 287 28.55 3.76 7.81 chr1ptel1M 465390 465522 (534478) C MIRc#SINE/MIR (124) 144 17 m_b13s601i8 466 chr1ptel1M 465390 TTCTCCAGATCAGAAAAGTGAA--TCCAACAGGATAAACTGACTTGCC-A 465436 i v v i v i-- vi v v i- - C MIRc#SINE/MIR 144 TTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAG-TGACTTGCCCA 96 chr1ptel1M 465437 GGGTCATGCAGCTTGTATGTGTCTTAAGGTCCAAGGT--GAGCTCAGAAA 465484 i ii v v v --- iv ii ii-- i i --- C MIRc#SINE/MIR 95 AGGTCACACAGCTAGTAAGTGGC---AGAGCCGGGACTCGAACCCAG--- 52 chr1ptel1M 465485 GATGTCTTCCTGACTACCAACCCAACCCTCTATGTACT 465522 --- v v ii iiv v vi C MIRc#SINE/MIR 51 ---GTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACT 17 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.32 CpG sites = 20, Kimura (unadjusted) = 36.62 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.10 (13 / 132), avg. gap size = 1.15 (15 / 13) 208 26.73 2.54 8.04 chr1ptel1M 465627 465744 (534256) MIR3#SINE/MIR 3 114 (94) m_b13s601i9 467 chr1ptel1M 465627 GGCAAACGAAGATGATCAGAGTGAAGGTGACCAACTGTGAATCATGGTTT 465676 i - vi v v v -- i- vi v i - --- MIR3#SINE/MIR 3 GGCAGA-GTGGCTGAGCAGAGAGA--GC-ACGGACTGGGAGTCA-GG--- 44 chr1ptel1M 465677 AG-CCTAGGTTCAAGTTGGGTGCTCAATCCCTC-CTGGCTCTGTGATCCA 465724 - i v ivv - vii v v- ? v i iv MIR3#SINE/MIR 45 AGACCTGGGTTCTAGTCCCG-GCTCTGCCACTAACTNGCTGTGTGACCTT 93 chr1ptel1M 465725 GGG-GAGTCACTTCATTCCTC 465744 -i iii MIR3#SINE/MIR 94 GGGCAAGTCACTTCACCTCTC 114 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.67 CpG sites = 15, Kimura (unadjusted) = 33.67 Transitions / transversions = 1.07 (15/14) Gap_init rate = 0.10 (12 / 117), avg. gap size = 1.00 (12 / 12) 233 30.27 7.42 5.77 chr1ptel1M 466011 466266 (533734) L1M2_orf2#LINE/L1 3032 3291 (0) m_b13s551i3 468 chr1ptel1M 466011 ATTGCATCAAACTAAAGAGATTTTTTGCA-TAAAGCCTATGCAATCAAGA 466059 i i v i vii -i v-- vi -- L1M2_orf2#LIN 3032 ATTACATCAAACTAAAAAGCTTCTGCACAGCAAAGG--AAACAATCAA-- 3077 chr1ptel1M 466060 TCAGAAGGAA-AG--------TAGAATGCTGGAAAACAGGTTTTTTTATG 466100 - iv - --------i vvi i ------ iii L1M2_orf2#LIN 3078 -CAGAGTGAAGAGACAACCTACAGAATGGGAGAAAATA------TTTGCA 3120 chr1ptel1M 466101 GTCAGTGTTTTTGATAACGGCTTTATTTCTAAACTATATAGAGAATTGAG 466150 iv vi ?iv i i v v v v i i v ii i v i L1M2_orf2#LIN 3121 AACTATNCATCTGACAAGGGATTAATATCCAGAATATATAAGGAACTCAA 3170 chr1ptel1M 466151 TCAAATT--TAG-AAGAACGCATTTTTTCC---TCAATAATGGTCAAAAG 466194 v v i--i - i vi vv vv --- ? v v - L1M2_orf2#LIN 3171 ACAACTCAACAGCAAAAAAACAAATAATCCGATTNAAAAATGGGCAAA-G 3219 chr1ptel1M 466195 GATACGAATAGATACCTTTCAGATGAAGAAATGTAA---GCCATTTATGG 466241 ivi i ii i i v v ii --- --- ii L1M2_orf2#LIN 3220 GACCTGAATAGACATTTCTCAAAAGAAGACATACAAATGGCCA---ACAG 3266 chr1ptel1M 466242 TCATATGAAAAAATTCTCTAAATCA 466266 vi v v v L1M2_orf2#LIN 3267 GTATATGAAAAAATGCTCAACATCA 3291 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.20 CpG sites = 41, Kimura (unadjusted) = 40.20 Transitions / transversions = 1.28 (41/32) Gap_init rate = 0.09 (22 / 255), avg. gap size = 1.55 (34 / 22) 1160 28.71 7.83 1.02 chr1ptel1M 466122 466670 (533330) L1ME4c_3end#LINE/L1 1 586 (244) m_b13s551i4 468 chr1ptel1M 466122 TTTATTTCTAAACTATATAGAGAATTGAGTCAAATTTAGAAGAACG-CAT 466170 v v ?v ? i ii v v v v vi-? L1ME4c_3end#L 1 TTAATATCTNTANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANAT 50 chr1ptel1M 466171 TTTTTCCTCAATA-----ATGGTCAAAAGGATACGAATAGATACCTTTCA 466215 ivvvv i ----- v - i i i i vi iv L1ME4c_3end#L 51 CAAGACCCCAATAGATAAATGGGCAAA-GGACATGAACAGACAATTCACA 99 chr1ptel1M 466216 GATGAAGAAATGTAAGCCATTTATGGTCATATGAAAAAATTCTCTAAATC 466265 ? v i ii ?ivi vv iiiv i i vi v vv L1ME4c_3end#L 100 NAAGAGGAAATACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTC 149 chr1ptel1M 466266 ACTATTGATTAAAGAAATGCAAATTAAAACAGCTCTGAGGTATCATCTCA 466315 i v i i i i vv i i i i L1ME4c_3end#L 150 GCTAGTAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTA 199 chr1ptel1M 466316 CACCTATCAGATTGGCTAATATGATAGAAAAGTGATAA-----AA----- 466355 i i i i v v v- i v ----- ----- L1ME4c_3end#L 200 CGCCTATTAAATTAGCAAAAATT-TAAAAAATTGATAATACCCAATGCTG 248 chr1ptel1M 466356 --GGGGATGTGGGAAAACTGAGACACTACGGCATTGTTGGTAGAGTTGT- 466402 -- i ? i vi iv ? vvvi i i vi? - L1ME4c_3end#L 249 GCGAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTA 298 chr1ptel1M 466403 --------CAACCGTTCTGGAGAACAATTTGG-ACTGATG-ACCAAAAGG 466442 -------- v i i i - v - i - i i - L1ME4c_3end#L 299 AATTGGTACAACCCTTTTGGAAAGCAATTTGGCAAT-ACGTATCAAGA-G 346 chr1ptel1M 466443 TCATAAAACTGTGCATACCCTTTGATCCAGAAATATCACTACTAGATCTT 466492 i v v i v vi v i ivv L1ME4c_3end#L 347 CCATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATT 396 chr1ptel1M 466493 TATCCCAAAGAAATCAT---AAAAAATGAAAAAGG---ATCCAC------ 466530 i i v --- i v v--- v ------ L1ME4c_3end#L 397 TATCCTAAGGAAATAATTCAAAAGAAGGAAAAAGCTATATGCACGAAGAT 446 chr1ptel1M 466531 GTTTGTAGCAGCTCTTCTTGTGGTGGCAAAGAATTGGAAACTGAAG--GG 466578 ii v vi vi i ii i i i -- v--ii L1ME4c_3end#L 447 GTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAAC--AACCTAA 494 chr1ptel1M 466579 ATGCCCATCAATCAGAAAATGGCTGAATAAGTTGTGGTAGATGAATGTAA 466628 i v vi ii i i i i i v v? ivii L1ME4c_3end#L 495 ATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGA 544 chr1ptel1M 466629 TGGAATACTATTGTTCTATAAGAAATGCTGAGCAGGAAGATT 466670 i vvvv i v i v i vi v i L1ME4c_3end#L 545 TGGAATATTATGCAGCCATTAAAAATGATAATTATGAAGACT 586 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.05 CpG sites = 89, Kimura (unadjusted) = 37.92 Transitions / transversions = 1.33 (89/67) Gap_init rate = 0.03 (18 / 548), avg. gap size = 2.72 (49 / 18) 771 29.98 7.38 4.44 chr1ptel1M 466180 466748 (533252) L1MB1_3end#LINE/L1 65 649 (266) m_b13s551i6 468 chr1ptel1M 466180 AATAATGGTCAAAAGGATACGAATAGATACCTTTCAGATGAAGAAATGTA 466229 v v - ivi i ii i vi v v ii L1MB1_3end#LI 65 AAAAATGGGCAAA-GGACTTGAATAGACATTTCTCCAAAGAAGACATACA 113 chr1ptel1M 466230 A---GCCATTTATGGTCATATGAAAAAATTCTCTAAATCACTATTGATTA 466276 --- --- ii vi i v v v v v i L1MB1_3end#LI 114 AATGGCCA---ACAGGTATATGAAAAGATGCTCAACATCACTAATCATCA 160 chr1ptel1M 466277 AAGAAATGCAAATTAAAACAGCTCTGAGGTATCATCTCACACCTATCAGA 466326 ii i vi vv i i i i i L1MB1_3end#LI 161 GGGAAATGCAAATCAAAACCACAATGAGATATCACCTCACACCTGTTAGG 210 chr1ptel1M 466327 TTGGCTAATATGATA-----GAAAAGTGATAA------AAGGGGATGTGG 466365 v v v v -----i i i i ------iv i L1MB1_3end#LI 211 ATGGCTATTATCAAAAAAACAAAAAATAACAAGTGTTGGCGAGGATGTGG 260 chr1ptel1M 466366 GAAAACTGAGACACTACGGCATTGTTGGTAGAGTTGT---------CAAC 466406 ii i ii v vvvi i i iiv --------- i L1MB1_3end#LI 261 AGAAATTGGAACCCTTGTACACTGTTGGTGGGAATGTAAAATGGTGCAGC 310 chr1ptel1M 466407 CGTTCTGGAGAACAATTTGGACTGATGAC-CAAAAGGTCATAAAACTGTG 466455 i v i i v -- i vv - ii i - iv vi L1MB1_3end#LI 311 CGCTATGGAAAACAGTATGGA--GGTTCCTCAAAAAATTA-AAAATAGAA 357 chr1ptel1M 466456 CATACCCTTTGATCCAGAAATATCACTACTAGATCTTTATCCCAAAGAAA 466505 - v v v vi v i i v v v L1MB1_3end#LI 358 C-TACCATATGATCCAGCAATCCCACTTCTGGGTATTTATCCAAAAGAAT 406 chr1ptel1M 466506 TCATAA--AAAAT---GAAAAAGGAT--------CCACGTTTGTAGCAGC 466542 v - -- ii --- i iiv -------- i ii v L1MB1_3end#LI 407 TGA-AATCAGGATCTCGAAGAGATATTTGCACTCCCATGTTCATTGCAGC 455 chr1ptel1M 466543 TCTTCTTGTGGTGGCAAAGAATTGGAAACTGAAG--GGATGCCCATCAAT 466590 vi vi iiiii i v vv -- v--ii i i - L1MB1_3end#LI 456 ATTATTCACAATAGCCAAGATGTGGAAAC--AACCTAAATGTCCATCGA- 502 chr1ptel1M 466591 CAGA-AAATGGCTGAATAAGTTGTGGTAGATGAATGTAATGGAATACTAT 466639 i -i v i v iv v iv ii i L1MB1_3end#LI 503 CGGATGAATGGATAAAGAAAATGTGGTATATACATACAATGGAATATTAT 552 chr1ptel1M 466640 TGTTCTATAAGAAATGCTGAGCAGGAAGATTTCTTGAAATGTCTGGAAAG 466689 vvv iv i ------ v i--- i vv i vi iv v L1MB1_3end#LI 553 TCAGCCTTAAAAA------AGAAGGAAA---TCCTGCCATATGCGACAAC 593 chr1ptel1M 466690 ATTTTTGATTTGATTTTGATGA-ATTGATGCGGAGTGAAGTGAG-CAGAA 466737 vvv ---- ii v - - vi i i - vv L1MB1_3end#LI 594 ATGGATGA----ACCTTGAGGACATT-ATGCTAAGTGAAATAAGCCAGTC 638 chr1ptel1M 466738 TCAGAAGGACA 466748 v L1MB1_3end#LI 639 ACAGAAGGACA 649 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.36 CpG sites = 92, Kimura (unadjusted) = 39.29 Transitions / transversions = 1.30 (92/71) Gap_init rate = 0.07 (38 / 568), avg. gap size = 1.79 (68 / 38) 1175 25.69 8.70 1.83 chr1ptel1M 466180 466639 (533361) L1ME4a_3end#LINE/L1 65 555 (316) m_b13s551i5 468 chr1ptel1M 466180 AATAATGGTCAAAAGGATACGAATAGATACCTTTCAGATGAAGAAATGTA 466229 v v - i i i i vi iv i v ii L1ME4a_3end#L 65 AAAAATGGGCAAA-GGACATGAACAGACAATTCACAAAAGAAGAAATACA 113 chr1ptel1M 466230 A---GCCATTTATGGTCATATGAAAAAATTCTCTAAATCACTATTGATTA 466276 --- --- iiv ? vi v vv v i i L1ME4a_3end#L 114 AATGGCCA---ATAAACATATGAAAANATGTTCAACCTCACTAGTAATCA 160 chr1ptel1M 466277 AAGAAATGCAAATTAAAACAGCTCTGAGGTATCATCTCACACCTATCAGA 466326 i vv i i i iv i L1ME4a_3end#L 161 AAGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCTATCAAA 210 chr1ptel1M 466327 TTGGCTAATATGATAGAAAAGTGATAAAA------------GGGGATGTG 466364 v v v- i i v v ------------ i i L1ME4a_3end#L 211 TTGGCAAAGATT-TAAAAGATTGATAATACCCAGTGTTGGCGAGGGTGTG 259 chr1ptel1M 466365 GGAAAACTGAGACACTACGGCATTGTTGGTAGAGTTGT---------CAA 466405 ?i v iv v vvvi i i i iiv --------- L1ME4a_3end#L 260 GNGAAACGGGCACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTACAA 309 chr1ptel1M 466406 CCGTTCTGGAGAACAATTTGG-ACTGATG-ACCAAAAGGTCATAAAACTG 466453 v ii - v - - i - i v v L1ME4a_3end#L 310 CCTTTCTGGAGGGCAATTTGGCAAT-ATGTATCAAAA-GCCTTAAAAATG 357 chr1ptel1M 466454 TGCATACCCTTTGATCCAGAAATATCACTACTAGATCTTTATCCCAAAGA 466503 ? i v vi v ivv i i L1ME4a_3end#L 358 TNCATACCCTTTGACCCAGTAATTCCACTTCTAGGAATTTATCCTAAGGA 407 chr1ptel1M 466504 AATCATAAAAAA--TGAAAAAGGATCC----------ACGTTTGTAGCAG 466541 v v i i -- ? v i ii---------- i ii v L1ME4a_3end#L 408 AATAATCAGAGATGTGNACAAAGATTTATGTACAAGGATGTTCATCGCAG 457 chr1ptel1M 466542 CTCTTCTTGTGGTGGCAAAGAATTGGAAACTGAAG--GGATGCCCATCAA 466589 vi vi i ii i i i -- v--ii i v L1ME4a_3end#L 458 CATTATTTATAATAGCGAAAAATTGGAAAC--AACCTAAATGTCCAACAA 505 chr1ptel1M 466590 TCAGAAAATGGCTGAATAAGTTGTGGTAGATGAATGTAATGGAATACTAT 466639 vi ii ? i i i i v vv i? i L1ME4a_3end#L 506 TAGGGGANTGGTTAAATAAATTATGGTACATCCATANAATGGAATATTAT 555 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 32.46 CpG sites = 69, Kimura (unadjusted) = 32.80 Transitions / transversions = 1.47 (69/47) Gap_init rate = 0.04 (17 / 459), avg. gap size = 2.88 (49 / 17) 184 34.50 9.94 0.00 chr1ptel1M 467273 467443 (532557) L2#LINE/L2 2171 2358 (724) m_b13s601i10 469 chr1ptel1M 467273 CCCTTTCTCAGCTTCATTTGCTTATTCTTATCAAAGTTAC--ATGTGATA 467320 i i ii v vi i viiv vv iv -- iv vv? L2#LINE/L2 2171 CTCCTTCTCAGTCTCCTTTGCTGGTTCCTCCTCATCTCCCCGACCTCTNA 2220 chr1ptel1M 467321 GCTATGGTCTCCTCCAAGATT--ATCCTTG-----CTTCTCTTCTCCCTC 467363 i vv vv v i i ii --i ----- iv L2#LINE/L2 2221 ACGTTGGAGTGCCCCAGGGCTCAGTCCTTGGACCTCTTCTCTTCTCTATC 2270 chr1ptel1M 467364 TAT-TTTACTT-----GTGATTTTATCAGTTCTCATAGA--TAATTCTCA 467405 i-i i i----- i i viv i v-- v vi L2#LINE/L2 2271 TACACTCACTCCCTNGGTGATCTCATCCAGTCTCATGGCTTTAAATACCA 2320 chr1ptel1M 467406 TCCTTATGATGATAATTGTCAAATATATTTATTCAGTC 467443 iv v i i vi v v v i i L2#LINE/L2 2321 TCTATATGCTGATGACTCCCAAATTTATATCTCCAGCC 2358 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 47.87 CpG sites = 32, Kimura (unadjusted) = 47.87 Transitions / transversions = 1.19 (32/27) Gap_init rate = 0.04 (6 / 170), avg. gap size = 2.83 (17 / 6) 275 31.67 5.00 0.00 chr1ptel1M 468008 468127 (531873) L3#LINE/CR1 3221 3346 (753) m_b13s601i11 470 chr1ptel1M 468008 GATGACAT----CTAAGAGGAACGATGAACGAACTGGTTGCCAGAGTCA- 468052 i---- ii i iiiiv iivi? v v i - L3#LINE/CR1 3221 GATGACACAAAGCTGGGAGGGATAGCTAATACGNTGGATGACAGAATCAA 3270 chr1ptel1M 468053 GAGTGAAGAACATCTTGCCAGGCTAAAACACTGGGAAATACCCACTAAGA 468102 v v i ?v i v ii iv vviv v vi L3#LINE/CR1 3271 GATTCAAAANGATCTCGACAGGCTGGAACGATGGGCCGAAACCAACAAGA 3320 chr1ptel1M 468103 TAAAATTTAAT-GGGAGAAATACAAA 468127 i i- v ii L3#LINE/CR1 3321 TGAAATTTAACAGGGATAAATGTAAA 3346 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.77 CpG sites = 23, Kimura (unadjusted) = 43.72 Transitions / transversions = 1.53 (23/15) Gap_init rate = 0.03 (3 / 119), avg. gap size = 2.00 (6 / 3) 26 0.00 0.00 0.00 chr1ptel1M 468175 468199 (531801) (ACC)n#Simple_repeat 1 25 (0) c_b13s251i0 471 chr1ptel1M 468175 ACCACCACCACCACCACCACCACCA 468199 (ACC)n#Simple 1 ACCACCACCACCACCACCACCACCA 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 20 6.57 6.25 0.00 chr1ptel1M 468290 468321 (531679) (TA)n#Simple_repeat 1 34 (0) m_b13s252i11 472 chr1ptel1M 468290 TATATATATATATATATATAT-TTTTTAT-TATA 468321 - v v - (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATA 34 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.06 (2 / 31), avg. gap size = 1.00 (2 / 2) 322 31.96 1.52 1.52 chr1ptel1M 468736 468932 (531068) C L1ME4c_3end#LINE/L1 (191) 639 443 m_b13s551i7 473 chr1ptel1M 468736 TTCTGCTCATTTCACTCA-CATCAGTTCATGTAAGTCTCTCCAAGCCTCT 468784 iv i - i vv i- vvi i v iiv C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATA-AACATTTTCCATGTTGCT 591 chr1ptel1M 468785 CTGTATTCATCCTGCTGGTCATTTCTTACAGAACAATAATATTCCATAAC 468834 vii v v v iv vi i v ii vvvv viv C L1ME4c_3end#L 590 ACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCGA 541 chr1ptel1M 468835 ATTCATATACCACAATTTACCCAACCATTCTCCAATTAATGGTCATCTA- 468883 i ?v i i ii i v iv v i - C L1ME4c_3end#L 540 GTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAG 491 chr1ptel1M 468884 -TTCATTTTCCAGTTTCTAGCCACTACAAACAGGGCTGCCACAAACATTT 468932 - v-- i i v i i i i iv v ii i C L1ME4c_3end#L 490 GTTG--TTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCT 443 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 42.05 CpG sites = 34, Kimura (unadjusted) = 42.97 Transitions / transversions = 1.21 (34/28) Gap_init rate = 0.03 (6 / 196), avg. gap size = 1.00 (6 / 6) 404 22.93 1.80 1.80 chr1ptel1M 468820 468930 (531070) C L1ME3G_3end#LINE/L1 (376) 548 438 m_b13s551i8 473 chr1ptel1M 468820 ATAATATTCCATAACATTCATATACCACAATTTACCCAACCATTCTCCAA 468869 i ii vv i iii i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr1ptel1M 468870 TTAATGGTCATCTA--TTCATTTTCCAGTTTCTAGCCACTACAAACAGGG 468917 i v i -- v-- i i v i i iv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTG--TTTCCAATTTTTCGCTATTACAAACAATG 451 chr1ptel1M 468918 CTGCCACAAACAT 468930 v ii C L1ME3G_3end#L 450 CTGCAATGAACAT 438 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 28.30 CpG sites = 17, Kimura (unadjusted) = 28.30 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.03 (3 / 110), avg. gap size = 1.33 (4 / 3) 248 26.67 1.32 1.32 chr1ptel1M 468933 469008 (530992) C L3#LINE/CR1 (1054) 3045 2970 m_b13s601i12 474 chr1ptel1M 468933 CACCAACTTATATTTTAATCTACCCAATGACTCCCCATCCT-TTCACAAG 468981 v vi i i v v i v v ivi i i - i C L3#LINE/CR1 3045 CACCTAACTGTACTATCATCCAGCCCATATTTCTCCATCTTGTCCACAAG 2996 chr1ptel1M 468982 GATTTCATGAGAGGTTTCTATCAAATG 469008 v ii - i C L3#LINE/CR1 2995 GATATCATGAGAGACTT-TGTCAAATG 2970 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.81 CpG sites = 12, Kimura (unadjusted) = 33.81 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.03 (2 / 75), avg. gap size = 1.00 (2 / 2) 562 30.95 6.04 6.23 chr1ptel1M 469201 469779 (530221) C L1ME4b_3end#LINE/L1 (311) 581 4 m_b13s551i9 475 chr1ptel1M 469201 AAAGCATCCTGTTCATCATTTCTTATAGGACAATAGTATTTCATCATAAT 469250 i v --- iv i ii vvvv i ii vv C L1ME4b_3end#L 581 AGAGCTTCCT---CATTCTTTTTTACGGCTGCATAGTATTCCATTGTATG 535 chr1ptel1M 469251 CATATACCACAATTTGGCCAACCTTTCTTCAATTGATGGACATCCCCTCT 469300 v i i ivii vv ii v iivvvi C L1ME4b_3end#L 534 GATGTACCATAATTTATTTAACCAGTCCCCTATTGATGGACATTTAGGTT 485 chr1ptel1M 469301 CAATTTCTAATTCTTTGCCCCCAGAAAAGA-GCTGCTATAAATATTTTTT 469349 --i i ii ivii v vi - v i -vii C L1ME4b_3end#L 484 --GTTTCCAATCTTTTGCTATTACAAACAATGCTGCAATGAATA-ACCTT 438 chr1ptel1M 469350 GTACATCTAGGTCCTTTTTCTTTTTT-----TATATCTCTTTTGGAACAT 469394 -- v v iv viv v ----- ----- v iv C L1ME4b_3end#L 437 GTACA--TACGTCATTTCGCACATGTGCGAGTATATC-----TGTAGGAT 395 chr1ptel1M 469395 AGAT--CTAGTCGTGGTATTGCTAAATCGAAAGATATGTGTGGTTTTATA 469442 i -- vv v iii i i i ii-- i C L1ME4b_3end#L 394 AAATTCCTAGAAGTGGAATTGCTGGGTCAAAGGGTATGTGCA--TTTGTA 347 chr1ptel1M 469443 GCCCTTTGGGCAGA-ATT-CCAAATTGTTTTACAGAATGGTTGAATCAGT 469490 i--- v ii - - iii v v iv v i i C L1ME4b_3end#L 346 A---TTTTGATAGATATTGCCAAATTGCCCTCCATAGAGGTTGTACCAAT 300 chr1ptel1M 469491 TCACAACTCCACCAATAGTGTATTACTGTCTCATTTTCCCCAC-CCCCCA 469539 i vii ii i v vv vi vv - i i C L1ME4b_3end#L 299 TTACACTCCCACCAGCAATGTATGAGAGTGCCTGTTTCCCCACACCCTCG 250 chr1ptel1M 469540 CCA------TTTGTCATTTTCCTTTTCTGTCCTATTAGCCAATCTGATA- 469582 ------ v i ivvv ivi --- v - C L1ME4b_3end#L 249 CCAACACAGTGTGTTATCAAACTTTTTGATC---TTTGCCAATCTGATAG 203 chr1ptel1M 469583 -TGAAGTATCATATTACATCAGAATTGTTTTTATTTATATATTTCCAATC 469631 - iv vi i--- vi v v ii v i iv i C L1ME4b_3end#L 202 GTGAAAAATGGTATC---TCAGTGTAGTTTTAATTTGCATTTCTCTTATT 156 chr1ptel1M 469632 AATAGTAAAGTAGAACAT-TTTTCATATGGCT-ATAGTTAGGTTTG-ATT 469678 vv i i v i - vi - v ii -- - C L1ME4b_3end#L 155 ATGAGTGAGGTTGAGCATCTTTTCATATGTTTAAGAGCCA--TTTGTATT 108 chr1ptel1M 469679 ACTTCATCTGAAAAC------TTCATAAGTTTTTTTTTTATCATTTATCA 469722 v i iv vi ------ ----- ii vvi v v C L1ME4b_3end#L 107 TCCTTTTCTGTGAACTGTCTGTTCATA-----TCCTTTGCCCATTTTTCT 63 chr1ptel1M 469723 ATTGGGGAAT--AACTTATTTTTGTAAATTTG-----ACTCTTTTCTCTA 469765 vvi --iv v i i vi -----i ----- C L1ME4b_3end#L 62 ATTGGGTTGTTGGTCTTTTTCTTATTGATTTGTAGGAGCTCTT-----TA 18 chr1ptel1M 469766 TATGTTTGAGAAAT 469779 i v i C L1ME4b_3end#L 17 TATATTAGGGAAAT 4 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.86 CpG sites = 93, Kimura (unadjusted) = 40.84 Transitions / transversions = 1.24 (93/75) Gap_init rate = 0.09 (51 / 578), avg. gap size = 1.39 (71 / 51) 660 30.36 4.84 4.24 chr1ptel1M 469214 469729 (530271) C L1ME4a_3end#LINE/L1 (297) 574 56 m_b13s551i10 475 chr1ptel1M 469214 CATCATTTCTTATAGGACAATAGTATTTCATCATAATCATATACCACAAT 469263 ? i v i vvvv i i i? vvv i i C L1ME4a_3end#L 574 CATNATTTTTAATGGCTGCATAATATTCCATTNTATGGATGTACCATAAT 525 chr1ptel1M 469264 TTGGCCAACCTTTCTTCAATTGATGGACATCCCCTCTCAATTTCTAATTC 469313 ivii v? ii v v iivvvi --i i i C L1ME4a_3end#L 524 TTATTTAACCANTCCCCTATTGTTGGACATTTAGGTT--GTTTCCAATTT 477 chr1ptel1M 469314 TTTGCCCCCAGAAAAGA-GCTGCTATAAATATTTTTTGTACATCTAGGTC 469362 i ivii v vi - v i i ii - -- ii C L1ME4a_3end#L 476 TTCGCTATTATAAATAATGCTGCGATGAACATCCTT-GTACAT--AAATC 430 chr1ptel1M 469363 CTTTTTCT--TTTTTTAT-ATCTCTTTTGGAACATAGAT--CTAGTCGTG 469407 i v ? v-- i i v - i i v --- i -- vv C L1ME4a_3end#L 429 TTTGTNCACATCTCTGATTATTTCCTTAGGA---TAAATTCCTAGAAGTG 383 chr1ptel1M 469408 GTATTGCTAAATCGAAAGATATGTGTGGTTTTATAGCCCTTTGG-GCAGA 469456 v i iii i i i ?iiiv - v i i-i v C L1ME4a_3end#L 382 GAATTACTGGGTCAAAGGGTATGNACATTTTTA-AGGCTTTTGATACATA 334 chr1ptel1M 469457 ATTCCAAATTGTTTTACAGAATGGTTGAATCAGTTCACAACTCCACCAAT 469506 v v iii v v v i i i vii ii C L1ME4a_3end#L 333 TTGCCAAATTGCCCTCCAGAAAGGTTGTACCAATTTACACTCCCACCAGC 284 chr1ptel1M 469507 AGTGTATTACTGT-CTCATTTTCCC-CACCCC--CCACCATTTGTCATTT 469552 v vv - i i i? - i-- v i v vi v C L1ME4a_3end#L 283 AGTGTATGAGAGTGCCCGTTTCNCCACACCCTCGCCAACACTGGGTATTA 234 chr1ptel1M 469553 TC---CTTTTCTGTCCTATTAGCCAATCTGATA--TGAAGTATCATATTA 469597 --- vvi --- v i -- iv vi iv C L1ME4a_3end#L 233 TCAATCTTTTAAATC---TTTGCCAATTTGATAGGTGAAAAATGGTATCT 187 chr1ptel1M 469598 CATCAGAATTGTTTTTATTTATATATTTCCAATCAATAGTAAAGTAGAAC 469647 i---i v ii v i iii i v i i v C L1ME4a_3end#L 186 CATT---GTTGTTTTAATTTGCATTTCTTTGATTACTAGTGAGGTTGAAC 140 chr1ptel1M 469648 AT-TTTTCATATGGCTA-TAGTTAGGTTTG-ATTACTTCATCTGAAAAC- 469693 - vi - i ii -- - v v i vi i- C L1ME4a_3end#L 139 ATNTTTTCATATGTTTATTGGCCA--TTTGTATTTCTTCTTTTGTGAATT 92 chr1ptel1M 469694 -----TTCATAAGTTTTTTTTTTATCATTTATCAATTGGGG 469729 ----- -- ii vi---i v v C L1ME4a_3end#L 91 GTCTGTTCAT--GTCCTTTGC---CCATTTTTCTATTGGGG 56 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.24 CpG sites = 91, Kimura (unadjusted) = 40.97 Transitions / transversions = 1.54 (91/59) Gap_init rate = 0.07 (37 / 515), avg. gap size = 1.27 (47 / 37) 58 1.88 0.00 0.00 chr1ptel1M 470526 470579 (529421) (CT)n#Simple_repeat 1 54 (0) c_b13s251i1 476 chr1ptel1M 470526 CTCTCTCACTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 470575 v (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chr1ptel1M 470576 CTCT 470579 (CT)n#Simple_ 51 CTCT 54 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 20 0.00 0.00 0.00 chr1ptel1M 470580 470601 (529399) (AT)n#Simple_repeat 1 22 (0) m_b13s252i12 477 chr1ptel1M 470580 ATATATATATATATATATATAT 470601 (AT)n#Simple_ 1 ATATATATATATATATATATAT 22 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 16 4.12 0.00 3.85 chr1ptel1M 471272 471298 (528702) (TTTGA)n#Simple_repeat 1 26 (0) m_b13s252i13 478 chr1ptel1M 471272 TTTGATATGATTTGATTTGATTTTGAT 471298 v - (TTTGA)n#Simp 1 TTTGATTTGATTTGATTTGA-TTTGAT 26 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.04 (1 / 26), avg. gap size = 1.00 (1 / 1) 241 34.24 6.94 2.67 chr1ptel1M 472149 472364 (527636) C L2a_3end#LINE/L2 (19) 498 274 m_b13s601i13 479 chr1ptel1M 472149 ATTTGTTAAG----TCCTATGTATCAGGAACTAGGCTTGGTGCTGACAGC 472194 i i ---- v ii v ivv v i iviii C L2a_3end#LINE 498 ATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGCGCTGGGGAT 449 chr1ptel1M 472195 ACAAGTATGATC----CTGAGACAGGTCCTGGCCC-CAGTGAGTTTACAT 472239 ivvi v ---- v v v i iv - vv i C L2a_3end#LINE 448 ACAGCAGTGAACAAAACAGACAAAAGTCCCTGCCCTCATGGAGCTTACAT 399 chr1ptel1M 472240 TCTACTAGAAGGATATGAAACATTCA--AGAGAAGTAAGTACACGATA-A 472286 v i ii v i- i v v -- i v i v vv - C L2a_3end#LINE 398 TCTAGTGGGGGGAGAC-AGACAATAAACAAATAAATAAGTAAAATATATA 350 chr1ptel1M 472287 ACCCAAAAGAAAGAGA-AAGTGCTTTGGGGAGAAGAGCACAAACAAATCA 472335 iiviivv vi v - v -- i ii - i iivi C L2a_3end#LINE 349 GTATGTCAGATGGTGATAAGTGCTAT--GGAGAAAAATA-AAGCAGGGTA 303 chr1ptel1M 472336 --GGGAATAAGAAATATTTTGGAGACGAAGG 472364 -- i i i i i--? i i? i C L2a_3end#LINE 302 AGGGGGATAGGGAGTG--NTGGGGGNGAGGG 274 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 47.27 CpG sites = 42, Kimura (unadjusted) = 48.22 Transitions / transversions = 1.40 (42/30) Gap_init rate = 0.06 (13 / 215), avg. gap size = 1.62 (21 / 13) 18 31.33 2.63 1.30 chr1ptel1M 473905 473980 (526020) (TC)n#Simple_repeat 1 77 (0) m_b13s252i14 480 chr1ptel1M 473905 TCTCTCTGTGTCTTTGTATCATTTTGCCTCTGTCTCTCCTTCTTTCT-TC 473953 v v i v v vi i vi v ii i - (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr1ptel1M 473954 TGTATGTCTCT-TCTCTATACTGTCTCT 473980 v v v - v - v (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCT-CTCTCTCT 77 Matrix = Unknown Transitions / transversions = 0.58 (7/12) Gap_init rate = 0.04 (3 / 75), avg. gap size = 1.00 (3 / 3) 834 31.51 5.44 0.29 chr1ptel1M 474038 474368 (525632) C L3#LINE/CR1 (661) 3438 3091 m_b13s601i14 481 chr1ptel1M 474038 ACTGCTACATTTTTTTTCTCTGAACTTCA---AAACCAGATC------AT 474078 iv vi i iviv v v--- i ------ C L3#LINE/CR1 3438 ACCCCTAGGTCTTTTTCACGTGAACTGCTGCTAAGCCAGATCCTCTCCAT 3389 chr1ptel1M 474079 GCT----TTCTATGGCTGATTTTGGGGAAACCAAGTGAACAATTTTACAT 474124 v ---- v iii i vv - v i i v vi i C L3#LINE/CR1 3388 CCTGTACTTGTGCAGTTGATTTTTTG-AACCTAAATGCAGGACTTTACAT 3340 chr1ptel1M 474125 TTATCTTTATTGAATTTCATTCTACTAGTTTCAGTGCAAACCTCTATCCT 474174 ii i i ii ii i i iv vvvi i v C L3#LINE/CR1 3339 TTATCCCTGTTAAATTTCATCTTGTTGGTTTCGGCCCATCGTTCCAGCCT 3290 chr1ptel1M 474175 GTCAATATCCTTTTAAATACTAATTGTTTTATTCAACAGGCTAACTTTAC 474224 i v ? i vi i v v i i ? ivii i v v C L3#LINE/CR1 3289 GTCGAGATCNTTTTGAATCTTGATTCTGTCATCCANCGTATTAGCTATCC 3240 chr1ptel1M 474225 CTCTCAGCTTTCTGTCATATGTAAATGTGATAAGCTTACCATATATGCCT 474274 i v v i v v i v v i C L3#LINE/CR1 3239 CTCCCAGCTTTGTGTCATCTGCAAATTTGATAAGCATGCCTTCTATGTCT 3190 chr1ptel1M 474275 TTTCCCAAG----TGATCACAA-GTTACCCAGCCCAGAGCAAAGCACAGA 474319 ivi ---- v v - ivv vv i v v C L3#LINE/CR1 3189 TCATCCAAGTCATTGATAAAAATGTTGAACAGGACAGGGCCAAGGACAGA 3140 chr1ptel1M 474320 TCTCTGGGACATCGCATTGGAAACTTCTTGCCATGTTGCCCTTGAACCA 474368 v i v i ivv i i i i iiv v v v i v C L3#LINE/CR1 3139 GCCCTGTGGCACGCCACTAGAGACCTCCCTCCAGGTTGACATCGATCCA 3091 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.93 CpG sites = 55, Kimura (unadjusted) = 42.03 Transitions / transversions = 1.12 (55/49) Gap_init rate = 0.02 (6 / 330), avg. gap size = 3.17 (19 / 6) 697 30.37 3.31 2.97 chr1ptel1M 474101 474402 (525598) C L3b_3end#LINE/CR1 (741) 465 163 m_b13s601i15 481 chr1ptel1M 474101 GAAACCAAGTGAACAATTTTACATTTATCTTTATTGAATTTCATTCTACT 474150 v v vi i i ii i ii ii C L3b_3end#LINE 465 GAACCCAAGTGCAGGACTTTACGTTTATCCCTGTTGAATTTCATCTTGTT 416 chr1ptel1M 474151 AGTTTCAGTGCAAACCTCTATCCTGTCAATATCCTTTTAAATACTAATTG 474200 i ? i iv i?vvi vi i v v ii v i - C L3b_3end#LINE 415 GGNTTCGGCCCGNCGTTCTAGTCTGTCGAGATCGTTTTGGATCCTGATT- 367 chr1ptel1M 474201 TTTTATTCAACAGGCTAACTTTACCTCTCAGCTTTCTGTCATATGTAAAT 474250 vi i ivii i iv vv i - i iv? i C L3b_3end#LINE 366 TTGCATCCAACGTATTAGCCGTCGCTCCCAGC-TTCTGCCACTNGCAAAT 318 chr1ptel1M 474251 GTGATAA---GCTTACCATATATGCCTTTTCCCAAGTGAT---CACAAGT 474294 v --- v i ---- ivi v ---i i C L3b_3end#LINE 317 TTGATAAGCTGCTTTCCGTAT----CTTCATCCAAGTCATTGATACAAAT 272 chr1ptel1M 474295 T-ACCCAGCCCAGAGCAAAGCACAGATCTCTGGGACATCGCATTGGAAAC 474343 - vv vv ii v v v i v i ivv i i i C L3b_3end#LINE 271 TCAGACAGGACAAGGCCAAGGACAGAGCCCTGCGGCACGCCACTAGAGAC 222 chr1ptel1M 474344 TTCTTGCCATGTTGCCCTTGAACCA-CAAACAATGACTCCATT-GGTCCA 474391 i i - v v v i ? -i? v i -- v - ? i C L3b_3end#LINE 221 TCCCT-CCAGGTTGACATCGANCCATTNATCAACG--TCCTTTGGGTNCG 175 chr1ptel1M 474392 GCCATCC-ACCA 474402 iii i - C L3b_3end#LINE 174 GTTGTTCAACCA 163 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.03 CpG sites = 54, Kimura (unadjusted) = 41.47 Transitions / transversions = 1.54 (54/35) Gap_init rate = 0.05 (15 / 301), avg. gap size = 1.27 (19 / 15) 467 24.21 0.00 8.65 chr1ptel1M 474991 475103 (524897) MIRc#SINE/MIR 10 113 (155) m_b13s601i16 482 chr1ptel1M 474991 GTGGTGCAGTGGATAGAGCACCAACCCTGAAGTCAGGAGGATCTGAGTTC 475040 v iiiv i i i i i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr1ptel1M 475041 AAATTTGGCCTCATATACATTTAACTCTTCCTGGCTGTGTGATCCTGGAC 475090 i i iiv v --- i ------ v v i i i i MIRc#SINE/MIR 60 GAGTCCCGGCTC---TGC------CACTTACTAGCTGTGTGACCTTGGGC 100 chr1ptel1M 475091 AAGTTACTTAATC 475103 i i MIRc#SINE/MIR 101 AAGTCACTTAACC 113 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.09 CpG sites = 19, Kimura (unadjusted) = 30.57 Transitions / transversions = 3.17 (19/6) Gap_init rate = 0.08 (9 / 112), avg. gap size = 1.00 (9 / 9) 258 30.96 4.27 3.39 chr1ptel1M 475139 475255 (524745) C L3#LINE/CR1 (1264) 2835 2718 m_b13s601i17 481 chr1ptel1M 475139 ACCACTTCCCTATCTGGACATTCACCAATCATACTGTC-ATTGACCCATT 475187 i i v iiiiii v i - i- v i i i C L3#LINE/CR1 2835 ACCGCTTCCTTTTCTAAGTGCTCACAAACCAT-CTGTTTAATAATCCGTT 2787 chr1ptel1M 475188 CTAGAATTTTCCCAGAAATCAAAGTCAGGCCCAAAAACCT----TTTATG 475233 v i ii i v i ii vviii ---- ?ii C L3#LINE/CR1 2786 CTAGAATTTTGCCGGGGATCGACGTCAAGCTTACCGGTCTGTAGTTTNCA 2737 chr1ptel1M 475234 GACATCAGCATATTTTTTCTTT 475255 - -- v ii C L3#LINE/CR1 2736 GA-ATC--CATCTTTTTTCCCT 2718 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.90 CpG sites = 27, Kimura (unadjusted) = 44.18 Transitions / transversions = 3.38 (27/8) Gap_init rate = 0.05 (6 / 116), avg. gap size = 1.50 (9 / 6) 434 35.22 6.98 3.23 chr1ptel1M 475339 475696 (524304) C L3#LINE/CR1 (1496) 2603 2233 m_b13s601i18 481 chr1ptel1M 475339 TCAGAATCCAAAGATAGAATGAATCTGGGCCAGGTGCCTTGAATTCATCT 475388 v i vii iv vvi v v v i i C L3#LINE/CR1 2603 TCAGTACCCTGGGATGTAATTCGTCTGGGCCTGGAGACTTGAACTCATTT 2554 chr1ptel1M 475389 --GGTAGCTAAATTGATCAC--ACT-----CTTTCTTATATTGGGGATGA 475429 --i ii ii- v v -- ----- iv i v vv v C L3#LINE/CR1 2553 AAAGCGGCTAGG-TGCTCTCTTACTATCTCCTCACCTATCTTGGGCTTCA 2505 chr1ptel1M 475430 ACT-CCTCTTGGTCATTTTTATTCTGTCACAGTCAGAGTAAAAGTCACAG 475478 i - iiiv v i ii vivvi vv i ii ivv C L3#LINE/CR1 2504 ATTCCCTCTTAACGATGTTTGTTCTACCCTTTCCAGTCTGAAGATCATTC 2455 chr1ptel1M 475479 TCCATTATAGA-AAGGCAAGACCAAAATGAGCACTAAGCAGCAGTGCTTC 475527 v v - i iii v ii vii i i ivv i C L3#LINE/CR1 2454 TCCTTGATAGAGAAGACGGAAGCAAAATAGGAGTTGAGTAGTTCTGCTTT 2405 chr1ptel1M 475528 CTTTTGATGGCA--GGTTTCCAATATTCTGTCTGCCACAGGTAGAGCCAA 475575 i i-- v --v vv v iv ii v i i --- ii C L3#LINE/CR1 2404 CTCTC--TGTCATCTGTTAACATTACGCCATCTGCCCCAAGCAG---CGG 2360 chr1ptel1M 475576 GCATTTATCCCTTCCTCGATGCTCCCTTTTCTCTTGACA------TTAAA 475619 --i i ? i --- vi i i v ivi ------ v C L3#LINE/CR1 2359 GC--CTGTCNCTTTCT---TTTTCCTTCTGCTCCGAACATAGCTTTGAAA 2315 chr1ptel1M 475620 AGAATCCTTTGTGTCGTCCTAAAC---TTCCCTCACCAAGATCGGTCCCT 475666 vv i? v i v i --- iii ii v ivv i ii v C L3#LINE/CR1 2314 AGCCTTNTTTTTGTTGTCCTTAGCATTTTTTTTTGCAAGCCTCAGCTCAT 2265 chr1ptel1M 475667 TCTGAGTTTTACCCTTC---ACAATAGTTTTTA 475696 i i v --- v - i C L3#LINE/CR1 2264 TCTGGGCTTTAGCCTTCCTGACACTA-TTCTTA 2233 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 45.89 CpG sites = 71, Kimura (unadjusted) = 49.96 Transitions / transversions = 1.39 (71/51) Gap_init rate = 0.06 (21 / 357), avg. gap size = 1.76 (37 / 21) 23 12.63 0.00 0.00 chr1ptel1M 476388 476422 (523578) (T)n#Simple_repeat 1 35 (0) m_b13s252i15 483 chr1ptel1M 476388 TTCTTTTTTTTTTTTTTTTTTTTTTTTGTCCTTTT 476422 i v ii (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 35 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 384 33.46 14.21 3.69 chr1ptel1M 476595 476740 (523260) C L2c_3end#LINE/L2 (10) 468 304 m_b13s601i19 484 chr1ptel1M 476595 TCCACAAACATTTGCTAAATGCCTACTCTATGCCAGGTAGCAGGGATTCT 476644 v ii i ii v i iivii v v C L2c_3end#LINE 468 TCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGATACA 419 chr1ptel1M 476645 TAGAAGGGCAAAAACCAATCCCTCCTCTCGAAGACCTCATAGTCCAATGC 476694 v v iii i vv ii v i i i v i i i v C L2c_3end#LINE 418 AAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAGTGG 369 chr1ptel1M 476695 AGGAGAT-------TAAA--------TACAA-AGAAG---GCGATGCATG 476725 i------- -------- - v ---ii ivi C L2c_3end#LINE 368 AGGAGACAGACANGTAAACAGACAATTACAATACAAGTTAATGATAAGTG 319 chr1ptel1M 476726 C-AT-ATGGATGTTCAT 476740 - - iv -- C L2c_3end#LINE 318 CTATAATGGGAGT--AT 304 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 44.46 CpG sites = 81, Kimura (unadjusted) = 47.67 Transitions / transversions = 1.87 (28/15) Gap_init rate = 0.06 (8 / 145), avg. gap size = 2.88 (23 / 8) 34 0.00 0.00 0.00 chr1ptel1M 476741 476769 (523231) (AC)n#Simple_repeat 1 29 (0) c_b13s251i2 485 chr1ptel1M 476741 ACACACACACACACACACACACACACACA 476769 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACA 29 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 384 33.46 14.21 3.69 chr1ptel1M 476770 477016 (522984) C L2c_3end#LINE/L2 (175) 303 36 m_b13s601i19 484 chr1ptel1M 476770 TACAGGGATAATATCAGAAAACATTAAGAAG--------GACTAG----- 476806 v - iv vi iv --i i -------- ----- C L2c_3end#LINE 303 GACAGGG-TGCTATGGGAGCACA--GAGGAGGGCACCTAGACTAGNCTTG 257 chr1ptel1M 476807 ---------GGAAGACTTCTTGAAGAAGGTGAAATTTGGA--GAAATCCA 476845 --------- i ii i i v i ii-- i?iiii C L2c_3end#LINE 256 GGGGGTCAGGGAAGGCTTCCCGGAGGAGGTGACATCTGAGCTGAGNCTTG 207 chr1ptel1M 476846 GAGAA--ACTTGGA-------AGAAGAGAGAAGGAGGGAATTGTGATTTC 476886 i i -- v v ------- iv ii i i -- v vv C L2c_3end#LINE 206 AAGGATGAGTAGGAGTTAGCCAGGTGGAAGGAGGGGGGAA--GAGCATTC 159 chr1ptel1M 476887 TAGGCATGGGGAACAATTGGTAAAAAAAAAAAAATGCCCAGAGTTGGGAG 476936 i vi iivv iv i-------- ? i vii i C L2c_3end#LINE 158 CAGGCAGAGGGAACAGCATGTGCAAAG--------GCNCGGAGGCAGGAA 117 chr1ptel1M 476937 ATAGA-GCCTCTTTTTTGAAAAACAGCAAAGAAATCAGTGTCATTGAATT 476985 v iv- vv v v iii i- i? iv vii i vi C L2c_3end#LINE 116 AGAACTGCGGCGTGTTTGGGGAAT-GCAAGNAGTTCAGTGTGGCTGGAGC 68 chr1ptel1M 476986 TCAGAGTATGTGGAGGAGCA-AAAGGATATGA 477016 vi v vii v i vi-ii v C L2c_3end#LINE 67 ATAGTGGGCGAGGAGGGGAGTGGAGGAGATGA 36 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 44.46 CpG sites = 81, Kimura (unadjusted) = 47.67 Transitions / transversions = 1.71 (53/31) Gap_init rate = 0.09 (22 / 246), avg. gap size = 2.23 (49 / 22) 489 36.71 10.67 0.51 chr1ptel1M 477622 477977 (522023) C L2#LINE/L2 (303) 2779 2388 m_b13s601i20 484 chr1ptel1M 477622 AGGATGGACTGAAATGAGGAC-----TTGAAGCA---AGATCTGC-AAGA 477662 i i ? i- i i ----- v --- i v i- i C L2#LINE/L2 2779 AGAATAGACTGNAG-GGGGGCAAGGGTGGAAGCAGGGAGACCAGTTAGGA 2731 chr1ptel1M 477663 AGCTATTGCAATAATTCAGATATGAGATGATAGGGAGCTGCACCAAGGCA 477712 i i i iiiv i v ivi v i ii C L2#LINE/L2 2730 GGCTATTGCAGTAATCCAGGCGAGAGATGATGGTGGCTTGGACCAGGGTG 2681 chr1ptel1M 477713 GGAGCAGTATCAGAGGAGAGGAG--G--GGACTCCAAA----------GG 477748 vi ivvi v v i -- -- i iii ----------i C L2#LINE/L2 2680 GTGGCAGTGGAGGTGGTGAGAAGTGGTCGGATTCTGGATATATTTTGAAG 2631 chr1ptel1M 477749 GTGAAATCAATAGGACTTGGAAAAAGTTTGGGTATAATGAGGTGAAAAAG 477798 ii ii i i i vvi vi v i i ii- iv i i i C L2#LINE/L2 2630 GTAGAGCCGACAGGATTTGCTGATGGATTGGATGTGG-GGTGTGAGAGAA 2582 chr1ptel1M 477799 TACGGGAAACCAAGGATGACATCTAGGTTGAAAAATTGAGTGACTGGA-G 477847 viv i i ii vi v vvviivi ii - C L2#LINE/L2 2581 AGAGAGGAGTCAAGGATGACTCCAAGGTTTTTGGCCTGAGCAACTGGAAG 2532 chr1ptel1M 477848 GATGGTGGTACCCTCAATAGCAATAAGGAAT----TAAAAGGAAAGAGTT 477893 v v i v i? iv vi ii v----iiii ivii C L2#LINE/L2 2531 GATGGAGTTGCCATTNACTGAGATGGGGAAGACTGCGGGAGGAGCAGGTT 2482 chr1ptel1M 477894 TAGGGCAAATGAT----AATTTAGTTTGAGGCACATTAAG------ATAC 477933 ii vii v ---- i i vi i ii ------ i C L2#LINE/L2 2481 TGAGGGGGAAGATCAGGAGTTCAGTTTTGGACATGTTAAGTTTGAGATGC 2432 chr1ptel1M 477934 TTATGAAATAACCAGTTTGAGATGTCCAATAAGCTGCTAGACAT 477977 i v i i v iv v v i i v i i i C L2#LINE/L2 2431 CTATTAGACATCCAAGTGGAGATGTCGAGTAGGCAGTTGGATAT 2388 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 53.34 CpG sites = 90, Kimura (unadjusted) = 55.49 Transitions / transversions = 2.25 (90/40) Gap_init rate = 0.03 (12 / 355), avg. gap size = 3.33 (40 / 12) 325 23.82 9.26 4.12 chr1ptel1M 477984 478145 (521855) C L2#LINE/L2 (736) 2346 2177 m_b13s601i21 484 chr1ptel1M 477984 AGACTTGAAAATCATCAGCATAGAAATGAGGATTGAAACCCTAGAAACT- 478032 i i ii i v i - v v v vv i - C L2#LINE/L2 2346 AAATTTGGGAGTCATCAGCATATAGATG-GTATTTAAAGCCATGAGACTG 2298 chr1ptel1M 478033 GATGAGATTACC-----AGTGAA-ATAGCT-GA-AAGATAAGAGGATCCA 478074 i ----- i-i v - - v vi v C L2#LINE/L2 2297 GATGAGATCACCNAGGGAGTGAGTGTAGATAGAGAAGAGAAGAGGTCCAA 2248 chr1ptel1M 478075 GGACCGAGCCCCATGGGGCA-TCT-ACAGTCA----TCAGGCATGACTTA 478118 i -- - i- iv ? ---- i v - i--- C L2#LINE/L2 2247 GGACTGAGCCC--TGGGGCACTCCAACGTTNAGAGGTCGGGGA-GAT--- 2204 chr1ptel1M 478119 GGGGAAGATTCAGCTACAGAGACCAAG 478145 i i vi v vi ii C L2#LINE/L2 2203 GAGGAGGAACCAGCAAAGGAGACTGAG 2177 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.71 CpG sites = 22, Kimura (unadjusted) = 29.57 Transitions / transversions = 1.47 (22/15) Gap_init rate = 0.09 (15 / 161), avg. gap size = 1.47 (22 / 15) 330 31.30 3.48 0.00 chr1ptel1M 479427 479541 (520459) C MIRc#SINE/MIR (15) 253 135 m_b13s601i22 486 chr1ptel1M 479427 TTATATCAATGCAGTGTTTTACTGTCTACAAAACTCTTG-GTATGCAATA 479475 i ivi ii iii v i i v v-ii i v C MIRc#SINE/MIR 253 TTACATTTGTATAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTA 204 chr1ptel1M 479476 TGCCATCTAATCATCACAATAAATTTATTGGATAGGTAA--CAG-TGTTA 479522 vi i i v i vii i vi i i i-- - i C MIRc#SINE/MIR 203 TCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTA 154 chr1ptel1M 479523 TTATCCCTATTTTATAGAT 479541 i i C MIRc#SINE/MIR 153 TTATCCCCATTTTACAGAT 135 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 43.94 CpG sites = 27, Kimura (unadjusted) = 43.94 Transitions / transversions = 3.00 (27/9) Gap_init rate = 0.03 (3 / 114), avg. gap size = 1.33 (4 / 3) 24 19.88 1.64 3.33 chr1ptel1M 479542 479602 (520398) (TA)n#Simple_repeat 1 60 (0) m_b13s252i16 487 chr1ptel1M 479542 TATATATATATATATATATATATGGCAGAAATATCTATA-ATAGCTATGT 479590 -ii v v v - vv i (TA)n#Simple_ 1 TATATATATATATATATATATAT-ATATATATATATATATATATATATAT 49 chr1ptel1M 479591 ATAGTAGAAATA 479602 - v v (TA)n#Simple_ 50 ATA-TATATATA 60 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.05 (3 / 60), avg. gap size = 1.00 (3 / 3) 12 13.67 0.00 0.00 chr1ptel1M 479752 479775 (520225) (TTG)n#Simple_repeat 1 24 (0) m_b13s252i17 488 chr1ptel1M 479752 TTGTCTTTTTTGTTGTTGTTGTTG 479775 iv v (TTG)n#Simple 1 TTGTTGTTGTTGTTGTTGTTGTTG 24 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 517 22.01 0.00 6.67 chr1ptel1M 479784 479895 (520105) C MIRc#SINE/MIR (153) 115 11 m_b13s601i23 486 chr1ptel1M 479784 GGGATTAAGTGACTTGCCCAGGGTCACACAACTAGGAAGTGTTAAGTGTC 479833 i i i i ------- v C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGC 73 chr1ptel1M 479834 TGAGGCCAGATTTGAACTCAGGTCCTCCTGACTTCAGGGCTGGTGCTCTA 479883 v v vi i i i i i i v ii v C MIRc#SINE/MIR 72 AGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTT 23 chr1ptel1M 479884 GCTACTGCATTA 479895 v i ii C MIRc#SINE/MIR 22 TCCACTGCACCA 11 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 25.45 CpG sites = 16, Kimura (unadjusted) = 26.79 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.06 (7 / 111), avg. gap size = 1.00 (7 / 7) 323 28.44 6.40 1.53 chr1ptel1M 479926 480050 (519950) C L1MC3_3end#LINE/L1 (1960) 572 442 m_b13s551i11 489 chr1ptel1M 479926 TCATTTCCT---ATCACAAAATAATTTTCCATTACA-----GTCAAACAC 479967 i --- i vi v ii ----- -- v C L1MC3_3end#LI 572 TCATTTCTTTTTATCGCTGAATAATATTCCATTGTATGGATGT--ACCAC 525 chr1ptel1M 479968 AGCTTGTTTAGCCATTCCTTGATTGATGGGCAGCCTTTTGACCTCCAATT 480017 i v viiv v i v i vv vi i i C L1MC3_3end#LI 524 AGTTTGTTTATCCATTCACCTATTGAAGGACATCTTGGTTGCTTCCAGTT 475 chr1ptel1M 480018 CTTAGCCACCACAAAAAGAGCTGCTAGAAATAT 480050 i i v ii ii v i v i C L1MC3_3end#LI 474 TTTGGCGATTATGAATAAAGCTGCTATAAACAT 442 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 35.51 CpG sites = 21, Kimura (unadjusted) = 36.83 Transitions / transversions = 1.50 (21/14) Gap_init rate = 0.03 (4 / 124), avg. gap size = 2.50 (10 / 4) 1624 27.10 0.57 1.74 chr1ptel1M 480127 480648 (519352) L1ME3G_3end#LINE/L1 33 548 (376) m_b13s551i12 490 chr1ptel1M 480127 AATTTATAAGAAATCAAGCCATTCTCCAATTGATAAGTGGTCAAAGAAAA 480176 iv -- v --vi v v i v i v L1ME3G_3end#L 33 AATCAATAAGAAA--AAGACA--ACCCAATAGAAAAATGGGCAAAGGATA 78 chr1ptel1M 480177 TGAACAGACAATTCTCAGACAAAGAAATTGAAACTATTTCTAGCCATATG 480226 i v vi i vv iviiivv iv L1ME3G_3end#L 79 TGAACAGGCAATTCACAGAAGAGGAAATACAAATGGCCAATAAACATATG 128 chr1ptel1M 480227 AAAAGATGCTCCAAGTCATTATTAATCAGAGAAATGCAAATTAAGACAAC 480276 v vv i v i i L1ME3G_3end#L 129 AAAAGATGCTCAACCTCACTAGTAATCAGGGAAATGCAAATTAAAACAAC 178 chr1ptel1M 480277 TCTGAGATACCACTACACATCTGTCAGATTGGCTAGAATGACAGGGAAAG 480326 vv i viv i ii v i vvv ii ?vv L1ME3G_3end#L 179 AATGAGATACCATTTTTCACCCATCAGATTGGCAAAAATTTAAAAGNTTG 228 chr1ptel1M 480327 ATAATGCGGAATGTTGGAGGGCATGTGGGAAAAGAGGGATAC-AATACAT 480375 iiv? i v i vi i vi v iv -v i L1ME3G_3end#L 229 ATAATATCNAGTGTTGGCGAGGGTGTGGGGAAACGGGTACTCTCATACAC 278 chr1ptel1M 480376 TGTTGGTGGAATTGTCAATACATCCAGCCATTCTGGAGAGCGATTTGGAA 480425 i i v v vvi v ? i i i v L1ME3G_3end#L 279 TGCTGGTGGGAGTGTAAATTGGTACAGCCNTTTTGGAGGGCAATTTGGCA 328 chr1ptel1M 480426 CTATGCTCAAAAAGTTATCAAACTGTGCATACCCTTTGATCCAGCAGTGT 480475 v - vvv i -- i v i i i vi L1ME3G_3end#L 329 GTAT-CTATTAAAAT--TTAAAATGCGCATACCCTTTGACCCAGCAATTC 375 chr1ptel1M 480476 TACTACTGGGATTATATCCCAAAGAGAT-CTTAAAGGAG-GGAAAGGGAC 480523 i v ? ?v v i ? i - iiv viv - v v i - L1ME3G_3end#L 376 CACTTCTNGGNATCTATCCTANAGAAATACTCGCACATGTGCACAAGGA- 424 chr1ptel1M 480524 CTGTATGTGCACAAATGTTTGTGGCAGCCCTGTTTGTAGTGACCAGAAAC 480573 -? i i vii ii v vi i ii v i i L1ME3G_3end#L 425 -NGCATGTACAAGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAAT 473 chr1ptel1M 480574 TGGAAACTGAGTAAATGCCCATCAATTGGAAAATGGCTGAATAAATTGTG 480623 vivv i v ii i i i L1ME3G_3end#L 474 TGGAAACAACCTAAATGTCCATCAATAGGGGAATGGTTAAATAAATTATG 523 chr1ptel1M 480624 ATATATGAATATTATGGAATATTAT 480648 i vv i i L1ME3G_3end#L 524 GTATATCCATACTATGGAATACTAT 548 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.76 CpG sites = 73, Kimura (unadjusted) = 34.70 Transitions / transversions = 1.11 (73/66) Gap_init rate = 0.02 (12 / 521), avg. gap size = 1.00 (12 / 12) 192 34.48 2.59 0.00 chr1ptel1M 481423 481538 (518462) C L2#LINE/L2 (995) 2087 1969 m_b13s601i24 484 chr1ptel1M 481423 ATCTAATTTGTCCAAAGCTTC-AAGAAAACGAG-AAGA-AAAGAATAAGA 481469 v v v v v v -i ? iiv i - -i i v i C L2#LINE/L2 2087 ATCAACTGTGTCAAATGCTGCTGANAGGTCAAGTAAGATGAGGACTGAGA 2038 chr1ptel1M 481470 AAAAAGCCCTAGATTCAGCGATTAGCAGGTCCATGGTGACCTTCTGCAGA 481519 vvi v vi i i i ivv v vv vvvv C L2#LINE/L2 2037 ATTGACCATTGGATTTAGCAACGTGGAGGTCATTGGTGACCTTGACAAGA 1988 chr1ptel1M 481520 GCAGTGTCAGTAGGATTGT 481538 v i i ii v C L2#LINE/L2 1987 GCAGTTTCGGTGGAGTGGT 1969 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 43.98 CpG sites = 17, Kimura (unadjusted) = 47.00 Transitions / transversions = 0.74 (17/23) Gap_init rate = 0.03 (3 / 115), avg. gap size = 1.00 (3 / 3) 543 33.99 6.82 3.42 chr1ptel1M 482285 482680 (517320) C L3#LINE/CR1 (70) 4029 3621 m_b14s601i0 491 chr1ptel1M 482285 AGGAATTCCTCCC-CTACATTACTGGTAAGTGGTCAGCCAGTTTTCTCTA 482333 i i i- v iv ii v ii iiv v C L3#LINE/CR1 4029 AGGAATCCCTTCTACAACATCCCTGACAAGTGGTCATCCAGCCTCTGCTT 3980 chr1ptel1M 482334 AAAGATT--------CAGGGAACTAA-TGGCTCATCAG-TAGCCCAT-CC 482372 i v ii-------- i i v - iv ?iv -i - C L3#LINE/CR1 3979 GAACACCTCCAGTGACGGGGAGCTCACTACCTCNCGAGGCAGCCCATTCC 3930 chr1ptel1M 482373 ACTTTGGCACAATTCCAATTATTAGAACTGTTTTC--------AAACTTA 482414 i v v ii ii i vvv i --------i i iv C L3#LINE/CR1 3929 ATTTTTGGACAGCTCTGATTGTTAGAAAGTTCTTCCTTATATTGAGCCGA 3880 chr1ptel1M 482415 AATCTACTTCCCTACCATTGTTTACTCCAAATC--TCCCAATTCAATTTC 482462 i i iiv i - ii i --- i-- i i -- vi C L3#LINE/CR1 3879 AATCTGCCTCCCTGTAACT-TCCACCC---ATTGGTCCTAGTTC--TGCC 3836 chr1ptel1M 482463 CTTTGG--CCAAATAGGACAAGTTTAATTAACTCCCTTGGTTTTGTGGCA 482510 i -- v i i i i --- i i --iivii i C L3#LINE/CR1 3835 CTCTGGAGCCACACAGAATAAGTCTAAT---CCCTCTT--CCACATGACA 3791 chr1ptel1M 482511 GTTCTTTAAATTCTTGGAAATAGCTAGCATGTCTCCACGAAGATTTTTCT 482560 ii i vi i i i v v v -- i - C L3#LINE/CR1 3790 GCCCTTCAAATATTTGAAGACAGCTATCATGTCTCCTCTAAG--TCTTC- 3744 chr1ptel1M 482561 TCTTCTCGTGACTAAATCTCCTCGTTTCTTCTAAATA-TCCTTATATTTC 482609 vv i iv i iv i ii vii- i vv C L3#LINE/CR1 3743 TCTTCTCCAGGCTAAACATCCCCAGTTCCTTCAACCGTTCCTCATATGAC 3694 chr1ptel1M 482610 TTGGGATTGAGGGAAGTCACCA-ACTAATTCCTTTTTTATAGATGCCTTC 482658 v vv iv ivvvv -v ii iv i ii v i i vi C L3#LINE/CR1 3693 ATGGTTTCCAGACCCTTCACCATCCTGGTCGCTCTCCTCTGGACGCGCTC 3644 chr1ptel1M 482659 CAGATTATC-ACAACCTTCCTAA 482680 v i - iiv i i C L3#LINE/CR1 3643 CAGTTTGTCAATGTCCCTCTTAA 3621 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 45.18 CpG sites = 86, Kimura (unadjusted) = 48.41 Transitions / transversions = 1.95 (86/44) Gap_init rate = 0.06 (25 / 395), avg. gap size = 1.64 (41 / 25) 548 32.86 5.99 0.44 chr1ptel1M 482965 483181 (516819) L3#LINE/CR1 3767 3995 (104) m_b14s601i1 492 chr1ptel1M 482965 GCAATTTCCAAGTATCTGTAGGATTTTTAGATGGAAAAAA---TGGATTT 483011 vi i i i i v ii v i vi i ii--- i i L3#LINE/CR1 3767 GCTGTCTTCAAATATTTGAAGGGCTGTCATGTGGAAGAGGGATTAGACTT 3816 chr1ptel1M 483012 ATTCTTTGTACCTCTTAAAAGGAAAAATTAGG-TCAAGGGCTAGAAGATA 483060 v iv i- i i v i i -i v v i v L3#LINE/CR1 3817 ATTCTGTGTGGCTCC-AGAGGGCAGAACTAGGACCAATGGGTGGAAGTTA 3865 chr1ptel1M 483061 CAAGGAGGCAGATTTCAGCTCAATATGAAGAGAAGCTTCCTAATAATTAA 483110 i i i i ii i i i i i L3#LINE/CR1 3866 CAGGGAGGCAGATTTCGGCTCAATATAAGGAAGAACTTTCTAACAATCAG 3915 chr1ptel1M 483111 ATGGATATGGAAGCAGGAAGTCCTACCTTCTGAAGCAATGGG------GT 483154 vvvi viii iii i v vv i iv? i i i i ------ L3#LINE/CR1 3916 AGCTGTCCAAAAATGGAATGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGT 3965 chr1ptel1M 483155 CATTGTAAGTGTTCA---AGAAGCTAGGTG 483181 i v i --- i i i L3#LINE/CR1 3966 CACTGGAGGTGTTCAAGCAGAGGCTGGATG 3995 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 45.39 CpG sites = 52, Kimura (unadjusted) = 47.30 Transitions / transversions = 2.74 (52/19) Gap_init rate = 0.02 (5 / 216), avg. gap size = 2.80 (14 / 5) 238 30.65 0.00 0.00 chr1ptel1M 485390 485451 (514549) C L2d_3end#LINE/L2 (4) 512 451 m_b14s601i2 493 chr1ptel1M 485390 TCAATGAATCAATAAGCATCTATTAGGTGCTCACTGTTTGCTGGTCCCTA 485439 v i i i ii i ii i v viv v i C L2d_3end#LINE 512 TCAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTG 463 chr1ptel1M 485440 TGCTAAGTGTTG 485451 i i i C L2d_3end#LINE 462 TGCTAGGCGCTG 451 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 36.54 CpG sites = 14, Kimura (unadjusted) = 42.39 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0) 13 11.56 3.57 0.00 chr1ptel1M 485740 485767 (514233) (TGTTT)n#Simple_repeat 1 29 (0) m_b14s252i0 494 chr1ptel1M 485740 TGTTCT-TTATGTTTTGTTTTGTTTTTTT 485767 i - v v (TGTTT)n#Simp 1 TGTTTTGTTTTGTTTTGTTTTGTTTTGTT 29 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 180 17.43 0.00 4.35 chr1ptel1M 487653 487700 (512300) C MIR3#SINE/MIR (41) 167 122 m_b14s601i3 495 chr1ptel1M 487653 AGAAGACATCTGAGGCAAACCCCCTCCATTCTACAGATGAGAAACCTG 487700 iiv - v v - i i v C MIR3#SINE/MIR 167 AGAGATCATCT-AGTCCAACCCCCTC-ATTTTACAGATGAGGAAACTG 122 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 19.89 CpG sites = 4, Kimura (unadjusted) = 19.89 Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.04 (2 / 47), avg. gap size = 1.00 (2 / 2) 412 20.55 0.00 9.73 chr1ptel1M 490568 490691 (509309) C MIR1_Amn#SINE/MIR (115) 115 3 m_b14s601i5 496 chr1ptel1M 490568 GGTTAAGTGACTTGCCCAGAGTCACACAACTAGTGAGTGTTAAGTGTCTG 490617 ? ii ? i ?i i? vi ------- C MIR1_Amn#SINE 115 GGTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNAGTGGCA-------G 73 chr1ptel1M 490618 AGGCCAGACTTGAACTCAGGTCCTCCTGACTCCAGGACCAGTGCTCTGTC 490667 v vi ? ? i - i v vi v i C MIR1_Amn#SINE 72 AGCCGGGANTNGAACCCAGGT-CTCCCGAGTCCCAGTCCAGTGCTCTATC 24 chr1ptel1M 490668 CACTGAGCCATCTAAGTGCCCCCC 490691 iii i--- v i C MIR1_Amn#SINE 23 CACTAGACCAC---ACTGCCTCCC 3 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 24.87 CpG sites = 16, Kimura (unadjusted) = 26.17 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.09 (11 / 123), avg. gap size = 1.00 (11 / 11) 533 15.61 0.00 6.80 chr1ptel1M 490568 490677 (509323) C MIRc#SINE/MIR (155) 113 11 m_b14s601i4 496 chr1ptel1M 490568 GGTTAAGTGACTTGCCCAGAGTCACACAACTAGTGAGTGTTAAGTGTCTG 490617 ii i ------- v v C MIRc#SINE/MIR 113 GGTTAAGTGACTTGCCCAAGGTCACACAGCTAGT-------AAGTGGCAG 71 chr1ptel1M 490618 AGGCCAGACTTGAACTCAGGTCCTCCTGACTCCAGGACCAGTGCTCTGTC 490667 v vi i i i i v v C MIRc#SINE/MIR 70 AGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTC 21 chr1ptel1M 490668 CACTGAGCCA 490677 vi C MIRc#SINE/MIR 20 CACTGCACCA 11 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 16.41 CpG sites = 9, Kimura (unadjusted) = 17.55 Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.06 (7 / 109), avg. gap size = 1.00 (7 / 7) 12 5.00 0.00 4.55 chr1ptel1M 490788 490810 (509190) (CCTC)n#Simple_repeat 1 22 (0) m_b14s252i1 497 chr1ptel1M 490788 CCTCCCTCCCTCCACCCCCTCCC 490810 - i (CCTC)n#Simpl 1 CCTCCCTCCCTCC-CTCCCTCCC 22 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.05 (1 / 22), avg. gap size = 1.00 (1 / 1) 485 32.11 4.29 4.70 chr1ptel1M 493273 493785 (506215) C L1MC4a_3end#LINE/L1 (1995) 634 124 m_b14s551i3 498 chr1ptel1M 493273 TTTGCTCATTTCACTCAGCATCAGTTCCTGTAAGTCTCTCCAAGCC--TC 493320 iv i i vi vv v i v vii -- i C L1MC4a_3end#L 634 TTTGCTTTTTTCACTTAACAATATATCCTGGAAATCACTCCATATCAGTT 585 chr1ptel1M 493321 CCT-GAAATCATCCCGCTGGTCGTTTCTTACAGAATAATAAAAGTCCATA 493369 v - i v --- vi iv i vvvv iv v v C L1MC4a_3end#L 584 CATAGAGATCTTCC---TCATTCTTTTTTACAGCTGCATAGTACTCCATT 538 chr1ptel1M 493370 ACATTCACATACTATAACTTATTCAGCCATTCTCC---AAATGCTCACTT 493416 iii vv ii i ii i ? ---?? vv - C L1MC4a_3end#L 537 GTGTGGATGTACCATAGTTTATTCAACCANTCTCCTATNNATGGGCA-TT 489 chr1ptel1M 493417 TCTACTCCTTTCCATCCACTCATTTTCCAATTCCT--TGA-GCTGCCACA 493463 vvii vi i v ------ v v v--ii - v ii C L1MC4a_3end#L 488 TAGGTTGTTTCCAAT------ATTTTGCAATTACAAACAATGCTGCAATG 445 chr1ptel1M 493464 AACATTTTTGCACATGTGGGTCCCATTCCCTCC---TTTAAGATCT--CT 493508 i vii ii i ----i? iiv v --- vi i v -- C L1MC4a_3end#L 444 AATAACCTTGTGCATATG----TNATTTTGTACATGTTGGAGGTGTATCT 399 chr1ptel1M 493509 TTGGGATAAAGGCCCAATAGTAACAATGCTGGATCAGAGGGGTATGTACA 493558 ii i vv i iv iiv v i i - vi i C L1MC4a_3end#L 398 TCAGGGTAAATTCCTAGAAGTGGGATTGCTGGGTCAAAGGG-TAAATGCA 350 chr1ptel1M 493559 TTTTGATAACTTCTTGCAGCTAGTTCCAAACTGTTCTCCAAAATGACTGG 493608 v --i ii iv -i v v v i vii ? v ii v C L1MC4a_3end#L 349 TAT--GTAGTTTTGT-TAGATATTGCCAAATTCCCCTCCANAAGGGTTGT 303 chr1ptel1M 493609 ATCCAC---GCACTGCTCCACCAACAATGAATCAGTGTCCCAGTTTTCCC 493655 - ?--- i --i i v v v v v i C L1MC4a_3end#L 302 A-CCANTTTGCATT--CCCACCAGCAATGTATGAGAGTGCCTGTTTCCCC 256 chr1ptel1M 493656 ACATCCCCTCCAACA---TTTGTCATTATCTTTTCCTGTCATCTTAGCCA 493702 v i v --- v ii i vvi -- -v i v C L1MC4a_3end#L 255 ACAGCCTCGCCAACAGAGTGTGTTGTCAAACTTT--TG-AATTTTTGCCA 209 chr1ptel1M 493703 ATATGACAGGTGTGCAGTGATATCTGAGTT--GCCTTAATTTGCATTTTT 493750 v i v v i i v v-- ii i C L1MC4a_3end#L 208 ATCTGATAGGTGAGAAATGGTATCTCAGTGTAGTTTTAATTTGCATTTCT 159 chr1ptel1M 493751 CTCAACAATAGTAATTTAAAGGACCTTTTCATATG 493785 i vi vv i vv vi iv i C L1MC4a_3end#L 158 CTTATTATGAGTGAGGTTGAACATCTTTTCATATG 124 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 43.55 CpG sites = 84, Kimura (unadjusted) = 43.55 Transitions / transversions = 1.15 (84/73) Gap_init rate = 0.07 (34 / 512), avg. gap size = 1.35 (46 / 34) 743 30.47 2.84 3.58 chr1ptel1M 493364 493785 (506215) C L1ME3G_3end#LINE/L1 (383) 541 123 m_b14s551i4 498 chr1ptel1M 493364 TCCATAACATTCACATACTATAACTTATTCAGCCATTCTCCAAATGCTC- 493412 ii vv i i i i i i v v v v- C L1ME3G_3end#L 541 TCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTATTGATGG 492 chr1ptel1M 493413 ACTTTCTACTCCTTTCCATCCACTCATT-TTCCAATTCCTTGAGCTGCCA 493461 v iviv iv viivi ii - v vivv --- v C L1ME3G_3end#L 491 ACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAAT---GCTGCAA 445 chr1ptel1M 493462 CAAACATTTTTGCACATGTGGGTCCC-ATTCCCTCCTTTAAG-ATCTCTT 493509 ii ii i i?-- i-i v v viv vii - i ? C L1ME3G_3end#L 444 TGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATTTCTN 397 chr1ptel1M 493510 TGGGATAAAGGCCCAATAGTAACAATGCTGGATCAGAGGGGTATGTACAT 493559 i i v? ? iv iiv v i i - ii C L1ME3G_3end#L 396 TAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGG-TATGCGCAT 348 chr1ptel1M 493560 TTTGATAACTTCTTGCAGCTAGTTCCAAACTGTTCTCCAAAATGACTGGA 493609 --- v i vii v v v i ii ? i v C L1ME3G_3end#L 347 TTT---AAATTTTAATAGATACTGCCAAATTGCCCTCCAAAANGGCTGTA 301 chr1ptel1M 493610 TCCA--CGCACTGCTCCACCAACAATGAATCAGTGTCCCAGTTTTCCCAC 493657 i v --ii --i i i v v v v v i C L1ME3G_3end#L 300 CCAATTTACACT--CCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCAC 253 chr1ptel1M 493658 ATCCCCTCCAACATTTGTCATTAT----CTTTTCCTGTCATCTTAGCCAA 493703 i i v i ? vi ---- v----v i v C L1ME3G_3end#L 252 ACCCTCGCCAACACTNGATATTATCAANCTTTTA----AATTTTTGCCAA 207 chr1ptel1M 493704 TATGACAGGTGTGCAGTGATATCTGA--GTTGCCTTAATTTGCATTTTTC 493751 v ii viv i i v -- ii ii C L1ME3G_3end#L 206 TCTGATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCC 157 chr1ptel1M 493752 TCAACAATAGTAATTTAAAGGACCTTTTCATATG 493785 v vi v i vv vi v i C L1ME3G_3end#L 156 TGATTACTAGTGAGGTTGAGCATCTTTTCATATG 123 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 39.53 CpG sites = 70, Kimura (unadjusted) = 40.91 Transitions / transversions = 1.30 (70/54) Gap_init rate = 0.05 (22 / 421), avg. gap size = 1.23 (27 / 22) 797 27.31 4.23 4.86 chr1ptel1M 493455 493785 (506215) C L1ME5_3end#LINE/L1 (486) 455 127 m_b14s551i5 498 chr1ptel1M 493455 GCTGCCACAAACATTTTTGCACATGTGGGTCCCATTC----CCTCCTTTA 493500 v ii ii i i ---- v v---- viv v C L1ME5_3end#LI 455 GCTGCAATGAACATCCTCGTACATGT----CCCCTTATGGACCTGTGTGA 410 chr1ptel1M 493501 AGATCTCTTTGGGATAAAGGCCCAATAGTAACAATGCTGGATCAGAGGGG 493550 ii i v vi iv iiiv v i v - C L1ME5_3end#LI 409 GAATTTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGG- 361 chr1ptel1M 493551 TATGTACATTTTGATAACTT--CTTGCAGCTAGTTCCAAACTGTTCTCCA 493598 iii vi -- i -- --- iv v v i i i C L1ME5_3end#LI 360 TATGCGTATACT--TAATTTGACT---AAGTACTGCCAGATTGCTCTCCA 316 chr1ptel1M 493599 AAATGACTGGATCCA---CGCACTGCTCCACCAACAATGAATCAGTGTCC 493645 i i v - ---ii --i i i v v v i C L1ME5_3end#LI 315 GAATGGCTGCA-CCAGTCTACACT--CCCACCAGCAGTGCATGAGGGTTC 269 chr1ptel1M 493646 CAGTTTTCCCACATCCCCTCCAACATTTGTCATTATCT---TTTCCTGTC 493692 vi ? i i v i v i--- --- v C L1ME5_3end#LI 268 CTATNTCCCCACATCCTCGCCAACACTTGGCATTATCCAGCTTTC---TA 222 chr1ptel1M 493693 ATCTTAGCCAATATGACAGGTGTGCAGTGATATCTGA--GTTGCCTTAAT 493740 i v i v i i iv v -- ii C L1ME5_3end#LI 221 ATTTTTGCCAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAAT 172 chr1ptel1M 493741 TTGCATTTTTCTCAACAATAGTAATTTAAAGGACCTTTTCATATG 493785 i v vi v i i v vi v i i C L1ME5_3end#LI 171 TTGCATTTCTCTGATTACTAATGAGTTTGAGCATCTCTTCATATG 127 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 33.43 CpG sites = 52, Kimura (unadjusted) = 35.05 Transitions / transversions = 1.53 (52/34) Gap_init rate = 0.06 (21 / 330), avg. gap size = 1.43 (30 / 21) 228 30.40 12.00 0.00 chr1ptel1M 493856 493980 (506020) C L2c_3end#LINE/L2 (4) 474 335 m_b14s601i6 499 chr1ptel1M 493856 ATTCAATTAACAA-CACTTCTTAAGT--CTACTACAGGCTAGGGATTGGG 493902 v i - i v i i-- iiv i vii C L2c_3end#LINE 474 ATTCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGG 425 chr1ptel1M 493903 CTTACAGAGATG----------GGTCTTGCCCCTTAAGAAGAGAATATTC 493942 vv i ---------- iivv i i vvv i v C L2c_3end#LINE 424 GATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTC 375 chr1ptel1M 493943 TAAAAGGGAAGA-GGAAATGGGCACAGATAATT-CAATAC 493980 ivi i i -i v ? viv i - C L2c_3end#LINE 374 TAGTGGAGGAGACAGACANGTAAACAGACAATTACAATAC 335 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 37.80 CpG sites = 22, Kimura (unadjusted) = 40.53 Transitions / transversions = 1.38 (22/16) Gap_init rate = 0.04 (5 / 124), avg. gap size = 3.00 (15 / 5) 286 26.39 14.65 3.45 chr1ptel1M 494355 494511 (505489) L3#LINE/CR1 3164 3337 (762) m_b14s601i7 500 chr1ptel1M 494355 AACATTTTTATCAATGA-----GTGAGG---TAAAA-------TTATTAA 494389 -----i i --- i ------- i L3#LINE/CR1 3164 AACATTTTTATCAATGACTTGGATGAAGACATAGAAGGCATGCTTATCAA 3213 chr1ptel1M 494390 ATTTGCAGACTATACAAAGTC--GAGAAATGGCAAATCCGCTGAAGCTCC 494437 iv i ii-- ii i v v ? i vvv v L3#LINE/CR1 3214 ATTTGCAGATGACACAAAGCTGGGAGGGATAGCTAATACGNTGGATGACA 3263 chr1ptel1M 494438 ATATCGGAGTCCAAAAAAATCT-----GG-TGAAGTCATGGTCTGGGACC 494481 iv iiii i ?i ----- - i iiv v i ii L3#LINE/CR1 3264 GAATCAAGATTCAAAANGATCTCGACAGGCTGGAACGATGGGCCGAAACC 3313 chr1ptel1M 494482 CAGTCTAAGAAGATAAAATTCAGTAGGGAT 494511 ------ v i i ii L3#LINE/CR1 3314 ------AACAAGATGAAATTTAACAGGGAT 3337 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 32.89 CpG sites = 29, Kimura (unadjusted) = 35.09 Transitions / transversions = 2.64 (29/11) Gap_init rate = 0.08 (12 / 156), avg. gap size = 2.42 (29 / 12) 247 27.74 7.30 0.00 chr1ptel1M 494524 494660 (505340) C L1P4_orf2#LINE/L1 (982) 2312 2166 m_b14s551i6 501 chr1ptel1M 494524 ACTCCCAGGTATTTTATATATTCTGTAGTTATGTTACATGAAGTTT--TT 494571 i i v v i i i vv v iii v-- C L1P4_orf2#LIN 2312 ATTCCTAGGTATTTTATTTTTTTTGTGGCTATTGTAAATGGGATTGCGTT 2263 chr1ptel1M 494572 CTT--TTT--CTCTCTTCCTA---TTTAT-GATATAAAGAAATACTGGTG 494613 -- -- vv i i---v - i i v i iv C L1P4_orf2#LIN 2262 CTTGATTTGGCTCTCAGCTTGAACGTTATTGGTGTATAGAAATGCTACTG 2213 chr1ptel1M 494614 ATGTATGTGGCTTTATTTTATATCAGGAAATTTTACTGAAACTGTTT 494660 v v ivv v i vv i iii C L1P4_orf2#LIN 2212 ATTTTTGTACATTGATTTTGTATCCTGAAACTTTACTGAAGTCGTTT 2166 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 34.02 CpG sites = 20, Kimura (unadjusted) = 35.15 Transitions / transversions = 1.11 (20/18) Gap_init rate = 0.04 (5 / 136), avg. gap size = 2.00 (10 / 5) 423 32.19 0.40 10.71 chr1ptel1M 494744 494990 (505010) L3#LINE/CR1 3474 3697 (402) m_b14s601i8 500 chr1ptel1M 494744 GTAATGAGGCAGCCCAAGAAACTAAGGCAATCTTGGCCCCCGTTTAGTAG 494793 i v v v i i v i v iv i - i L3#LINE/CR1 3474 GTGATGTGGCTGCCAAAAAAGCTAATGCAATCTTAGGCTGCATT-AATAG 3522 chr1ptel1M 494794 G-GTTGAGCTTCCAAGAAGAGTGGGGTAAAGATTCCCCTGGACTCTGACC 494842 i- vv iv ii?vi v i vii i v v vv L3#LINE/CR1 3523 AAGTATAGTGTCCAGANCAAGGGAGGTAATAGTCCCGCTGTACTCTGCGC 3572 chr1ptel1M 494843 TCATCGGACCACTTCTTATGCACACCAGACCTTATCAGATCAGTCATATG 494892 vi i ----------- i v i------------ vv ii L3#LINE/CR1 3573 TGGTCAGACC-----------ACATCTGG------------AGTATTGCG 3599 chr1ptel1M 494893 CTCAGTTCTGGGCACCAAGGTTTAAGATGGACCTTGGCCATCTGAAGAGT 494942 i i viv v v i v v i v i L3#LINE/CR1 3600 TTCAGTTCTGGGCGCCACATTTTAAGAGGGACATTGACAAACTGGAGCGC 3649 chr1ptel1M 494943 GTCTAGAGGAAAATACCTGACATTGGGAAGGGTCTGGAGTCCTTGCCA 494990 i i iiiv iiiv v v iv v i L3#LINE/CR1 3650 GTCCAGAGGAGAGCGACCAGGATGGTGAAGGGTCTGGAAACCATGTCA 3697 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 39.41 CpG sites = 38, Kimura (unadjusted) = 42.59 Transitions / transversions = 1.15 (38/33) Gap_init rate = 0.10 (25 / 246), avg. gap size = 1.00 (25 / 25) 395 30.51 6.67 3.23 chr1ptel1M 495213 495422 (504578) C L1MC_orf2#LINE/L1 (1458) 1836 1620 m_b14s551i7 498 chr1ptel1M 495213 GGATGGTTGTTACACTT-GTCCAAAACCTTTTTGGCATCTATTGACATAA 495261 i v iv i - v vi i iv i i C L1MC_orf2#LIN 1836 GAATGGGTGTTGGATTTTGTCAAATGCTTTTTCTGCATCTATTGATATGA 1787 chr1ptel1M 495262 TCATACAATTTT----------CTTATTAATGTGACTGATTATATTTACA 495301 iii ---------- i i i iv i v iv C L1MC_orf2#LIN 1786 TCATGTGATTTTTCTTCTTTAGCCTGTTGATGTGATGGATTACATTAATT 1737 chr1ptel1M 495302 ATTTTCCTAATATTTAACTGGCCCTACATTCTAGGTATAAATTCATCCTG 495351 iv i v i v ii i i v iv v i vv i C L1MC_orf2#LIN 1736 GATTTTCGAATGTTGAACCAGCCTTGCATACCTGGGATAAATCCCACTTG 1687 chr1ptel1M 495352 TTCATAGCATATGATCTTTGTGACACATTAT---AATCTCCTTGCTATTA 495398 v i i ii i ii v v i i --- v vvi v C L1MC_orf2#LIN 1686 GTCGTGGTGTATAATTCTTTTTATACATTGTTGGATTCGATTTGCTAATA 1637 chr1ptel1M 495399 TTTTATTTCAAACTGAGGAGTTTT 495422 i ------- v C L1MC_orf2#LIN 1636 TTTTGT-------TGAGGATTTTT 1620 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 39.80 CpG sites = 38, Kimura (unadjusted) = 40.67 Transitions / transversions = 1.58 (38/24) Gap_init rate = 0.05 (10 / 209), avg. gap size = 2.10 (21 / 10) 418 25.74 4.90 2.88 chr1ptel1M 495455 495658 (504342) C L1MD_orf2#LINE/L1 (2340) 954 747 m_b14s551i8 502 chr1ptel1M 495455 GCTGAGTTTGTTGATCTG---CTTTTTTTCTTTTATTGATGAAAGTGTTT 495501 v v i i --- ii -i i v ? ii C L1MD_orf2#LIN 954 GCTTAGATTATTGATTTGAGACTTTTCCTCTTTT-CTAATGTANGCATTT 906 chr1ptel1M 495502 AGAAATATAAATTTCCCCCTAAGCGCTGCTTTGGCTTCATACCA-AACTT 495550 viv i v i i v i v - v C L1MD_orf2#LIN 905 AGTGCTATAAATTTCCCTCTCAGCACTGCTTTAGCTGCGTCCCACAAATT 856 chr1ptel1M 495551 TGGAGAAG--GTAATCTCATTGTTGTCATTCCCTTTAATGAAATTATTGA 495598 v v v -- v i --- v vv i v v v i C L1MD_orf2#LIN 855 TTGATATGTTGTATTTTCA---TTTTCATTCAGTTCAATGTATTTTTTAA 809 chr1ptel1M 495599 -CTGCTTAGATGATTTCTTCTTTGAC---TGGCCCATTCTTGGAGATTGC 495644 -i v i v - i i --- vii - v i vv i C L1MD_orf2#LIN 808 TTTCCCTTGA-GACTTCCTCTTTGACCCATGGATTATT-TAGAAGTGTGT 761 chr1ptel1M 495645 TATTTAGTTTCTAA 495658 i i C L1MD_orf2#LIN 760 TGTTTAGTTTCCAA 747 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 31.36 CpG sites = 26, Kimura (unadjusted) = 32.10 Transitions / transversions = 1.04 (26/25) Gap_init rate = 0.05 (11 / 203), avg. gap size = 1.45 (16 / 11) 243 23.33 0.00 0.00 chr1ptel1M 496220 496279 (503721) C L1MEh_5end#LINE/L1 (1) 2234 2175 m_b14s551i9 502 chr1ptel1M 496220 TCTTTCTGTTTCAAATGTGTTTCTTATAAAGAATGTATTATTGGCTTCTG 496269 i ? i i i i i v iii i v i C L1MEh_5end#LI 2234 TCCTTNTGTTTTAAGTGTGTCTCTTGTAGACAGCATATTGTTGGATTTTG 2185 chr1ptel1M 496270 GTTTTTAATC 496279 v ? C L1MEh_5end#LI 2184 TTTTTNAATC 2175 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 30.93 CpG sites = 11, Kimura (unadjusted) = 30.93 Transitions / transversions = 3.67 (11/3) Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0) 15 19.46 0.00 0.00 chr1ptel1M 497052 497086 (502914) (GGGAG)n#Simple_repeat 1 35 (0) m_b14s252i2 503 chr1ptel1M 497052 GGGAGTGGAAGTGAGGGGAGTGGAGGTGAGGAGAG 497086 v i v v v i (GGGAG)n#Simp 1 GGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAG 35 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 333 32.81 10.76 3.55 chr1ptel1M 497104 497261 (502739) C MIR#SINE/MIR (10) 252 84 m_b14s601i9 504 chr1ptel1M 497104 AACATTTATTAAATGTCTGC--------AAGCATTGTACTAGGCATTTTA 497145 i ii ii i -------- i i v i ii C MIR#SINE/MIR 252 AACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGCGCTTTA 203 chr1ptel1M 497146 T---------CCCATTAGGTCTCCACAATAACCTTGGGAGTCCGACGCTA 497186 i--------- i vii ii i i iv viv iii C MIR#SINE/MIR 202 CATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGGTAGGTACTA 153 chr1ptel1M 497187 TGACTATCTCTATTTTGTGGATGAGACAAAAGAGGCAGACGAGGGTCAAG 497236 v i i i iii iv vv v viii i C MIR#SINE/MIR 152 TTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAG 103 chr1ptel1M 497237 TAAATAGTGAATGTCCGAGGTCCCA 497261 v ------ i i v C MIR#SINE/MIR 102 TAACT------TGCCCAAGGTCACA 84 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 44.47 CpG sites = 37, Kimura (unadjusted) = 47.16 Transitions / transversions = 2.85 (37/13) Gap_init rate = 0.05 (8 / 157), avg. gap size = 2.88 (23 / 8) 14 18.42 8.16 0.00 chr1ptel1M 497544 497592 (502408) (AAAGAC)n#Simple_repeat 1 53 (0) m_b14s252i3 505 chr1ptel1M 497544 AAAGATAAAAATTAAGACAAAGA-AAA-A-AATGAGAAA-ACAATGACAA 497589 i i iv - - - v v - v (AAAGAC)n#Sim 1 AAAGACAAAGACAAAGACAAAGACAAAGACAAAGACAAAGACAAAGACAA 50 chr1ptel1M 497590 TGA 497592 v (AAAGAC)n#Sim 51 AGA 53 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.08 (4 / 48), avg. gap size = 1.00 (4 / 4) 420 21.52 2.16 16.39 chr1ptel1M 499637 499775 (500225) MIRc#SINE/MIR 6 127 (141) m_b14s601i10 506 chr1ptel1M 499637 CAGCATGGTGACATGAGTAGAGTATCAGCCCTGAAGTCAGGAAGACCTGA 499686 ii vvi iiv i iii v i i i MIRc#SINE/MIR 6 CAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGG 55 chr1ptel1M 499687 GTTCAAATCCAGCCTCAGACACTTAACACTTAACACTTAACACCTAGCTG 499736 i i v v v v ------------------ MIRc#SINE/MIR 56 GTTCGAGTCCCGGCTCTGCCACTTA------------------CTAGCTG 87 chr1ptel1M 499737 TGTGACCCTGGGCAAGTCACTTAA---CTCCAATTGCCTCAG 499775 i --- ii -- MIRc#SINE/MIR 88 TGTGACCTTGGGCAAGTCACTTAACCTCTCTGA--GCCTCAG 127 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 24.22 CpG sites = 17, Kimura (unadjusted) = 25.38 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.15 (21 / 138), avg. gap size = 1.10 (23 / 21) 13 15.40 7.27 3.51 chr1ptel1M 500129 500148 (499852) (TCCTTC)n#Simple_repeat 1 19 (38) m_b14s252i4 507 chr1ptel1M 500129 TCATTCTCTCTCTCTCTTTC- 500148 v - - i - (TCCTTC)n#Sim 1 TCCTTCTC-CT-TCTCCTTCT 19 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.16 (3 / 19), avg. gap size = 1.00 (3 / 3) 18 11.88 5.26 0.00 chr1ptel1M 500133 500148 (499852) (TC)n#Simple_repeat 1 16 (24) m_b14s252i5 507 chr1ptel1M 500133 TCTCTCTCTCTCTTTC 500148 i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTC 16 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 15), avg. gap size = 0.0 (0 / 0) 27 8.35 0.00 0.00 chr1ptel1M 500149 500187 (499813) (TGTA)n#Simple_repeat 1 39 (0) c_b14s251i0 508 chr1ptel1M 500149 TGTATGTATGTATGTATGTATGTATATATATATATATGT 500187 i i i (TGTA)n#Simpl 1 TGTATGTATGTATGTATGTATGTATGTATGTATGTATGT 39 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 18 11.88 5.26 0.00 chr1ptel1M 500188 500208 (499792) (TC)n#Simple_repeat 17 39 (1) m_b14s252i5 509 chr1ptel1M 500188 CT-TGCCTCTC-CTCTCCCTCTC 500208 - vi - i (TC)n#Simple_ 17 CTCTCTCTCTCTCTCTCTCTCTC 39 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.10 (2 / 20), avg. gap size = 1.00 (2 / 2) 16 14.89 6.52 0.00 chr1ptel1M 500188 500216 (499784) (TCTCCC)n#Simple_repeat 17 48 (1) m_b14s252i6 510 chr1ptel1M 500188 CT-TGCCTCT-CCTCTCCCTCTCATTC-CCCT 500216 - v - vi - (TCTCCC)n#Sim 17 CTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCT 48 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.11 (3 / 28), avg. gap size = 1.00 (3 / 3) 376 33.30 6.33 2.17 chr1ptel1M 500430 500650 (499350) C L2b_3end#LINE/L2 (21) 445 216 m_b14s601i12 511 chr1ptel1M 500430 TTATTGAGTACCTACTATGTGCCAAGCACTGTACCAATCCCCATGGGTAC 500479 i ii i i ? i i iv v iiv i C L2b_3end#LINE 445 TTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGGGATAC 396 chr1ptel1M 500480 A-----AAAGAGGAAAAAGACAGTCCCCATTCTCAAGGACTTCATCTTCT 500524 -----i v i v i v? i iiii v vi ivv C L2b_3end#LINE 395 AGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGGAGCTCACAGTCT 346 chr1ptel1M 500525 AATGGAGGAGACA-ATATGCAAGCAAACACATGCAAA--GAAAATTATAG 500571 i i - i i ? i - ?vv --v i i vii C L2b_3end#LINE 345 AGTGGGGGAGACAGACATGTAANCAGACA-ATNATAACCCAGAGTGGCAG 297 chr1ptel1M 500572 ACT--GACTACATAGGAAATAACAGAGG-GAGAGCCTGA--AAGTAAGAG 500616 iv -- i---i iiii-v - i v --vi ivv i C L2b_3end#LINE 296 GGTAGGACTG---GGGGGGC-CCAGAGGAGGGCGCCTGACCCGGCCTGGG 251 chr1ptel1M 500617 GGG-CAGGGAAAGGCTCCTGTAAAAGATGGGATTT 500650 - ii vi i v ii i iv C L2b_3end#LINE 250 GGGTCAGGGAGGGCTTCCCGGAGGAGGTGACATTT 216 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 44.49 CpG sites = 49, Kimura (unadjusted) = 48.40 Transitions / transversions = 2.13 (49/23) Gap_init rate = 0.05 (12 / 220), avg. gap size = 1.58 (19 / 12) 407 23.20 2.16 10.08 chr1ptel1M 500430 500568 (499432) C L2c_3end#LINE/L2 (21) 457 329 m_b14s601i11 511 chr1ptel1M 500430 TTATTGAGTACCTACTATGTGCCAAGCACTGTACCAATCCCCATGGGTAC 500479 ii i i v------------ i C L2c_3end#LINE 457 TTATTGAGCGCCTACTATGTGCCAGGCGCTGG------------GGATAC 420 chr1ptel1M 500480 AAAAGAGGAAAAAGACA--GTCCCCATTCTCAAGGACTTCATCTTCTAAT 500527 - v v -- iiii vi ivv i C L2c_3end#LINE 419 AAA-GATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAGT 371 chr1ptel1M 500528 GGAGGAGACA-ATATGCAAGCAAACACATGCAAAGAAAATTA 500568 - i ? i i i vv i viv i C L2c_3end#LINE 370 GGAGGAGACAGACANGTAAACAGACAATTACAATACAAGTTA 329 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 26.18 CpG sites = 19, Kimura (unadjusted) = 28.58 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.11 (15 / 138), avg. gap size = 1.07 (16 / 15) 800 31.87 1.36 1.82 chr1ptel1M 500669 501109 (498891) L1M4_orf2#LINE/L1 1365 1803 (1491) m_b14s551i10 512 chr1ptel1M 500669 TAAAGAAATTGAACAAGCCACCAATGAAATCTCTA-AGAGAAAAAATTCT 500717 i iv iv i vi v ii i - i i----i L1M4_orf2#LIN 1365 TAAAGAGATTGAATTAGTAATCAAAAAACTTCCCACAAAGAAAAG----C 1410 chr1ptel1M 500718 CCAGGCTTAGATGAGTTCACACATGAATTCTACCAAACATTTAAACATCA 500767 ?ii iv vvi v vv L1M4_orf2#LIN 1411 CCAGGNCCAGATGGCTTCACTGGTGAATTCTACCAAACATTTAAAGAAGA 1460 chr1ptel1M 500768 GCTAATTCCAATACTTTATAAACTATTTGAAAGGATAGGTGAAGGATAAG 500817 ii iv v i i v iv ii iv i iivi i L1M4_orf2#LIN 1461 ATTAACACCAATCCTTCACAAACTCTTCCAAAAAATAGAAGAGGAGGGAA 1510 chr1ptel1M 500818 TCCATACAAATTCCTCTTAT-AGTACATATATAGTTCTAATACTAAA-TC 500865 iv v v v i v ii - vv -i viii i i -i L1M4_orf2#LIN 1511 CACTTCCCAACTCATTCTATGAGGCCA-GTATTACCCTGATACCAAAACC 1559 chr1ptel1M 500866 AGG-AAGAACAAAAATAGAGAAAGAGAACTATAGATGAATTTTCCCAATG 500914 i- ii vv vv - i i iv v i iv L1M4_orf2#LIN 1560 AGACAAAGACATCACAAGA-AAAGAAAACTACAGACCAATATCCCTTATG 1608 chr1ptel1M 500915 AATATATTGATGCAAAATTTTAAAATCAAATACTGACAAGAAGATTACAT 500964 -- v iivv iv ii ivv v v v L1M4_orf2#LIN 1609 AATATA--GATGCAAAAATCCTCAACAAAATACTAGCAAACCGAATCCAG 1656 chr1ptel1M 500965 CAATATACCACAAGATTCCTACACTTAGACAAGGTGTGATTTATAACAGG 501014 i iv v iv iv ivv v i v vv L1M4_orf2#LIN 1657 CAACATATAAAAAGGATTATACACCATGACCAAGTGGGATTTATCCCAGG 1706 chr1ptel1M 501015 AATGCAAGACTGGTTCAAGATAAGGAAA--ACTGAGTATGATTGATTATA 501062 ii v ?v i -- v v i i i vv ii L1M4_orf2#LIN 1707 AATGCAAGGTTGGTTCAACATNCGAAAATCAATCAATGTAATACACCATA 1756 chr1ptel1M 501063 TCAATAACAAAACCAACAGAAATCATATGATTATTTCAATACATGCA 501109 i iv v vvi i i i i i v i L1M4_orf2#LIN 1757 TTAATAGAATAAAGGACAAAAACCACATGATCATCTCAATAGACGCA 1803 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 42.45 CpG sites = 77, Kimura (unadjusted) = 42.86 Transitions / transversions = 1.26 (77/61) Gap_init rate = 0.03 (13 / 440), avg. gap size = 1.08 (14 / 13) 834 28.71 6.01 8.81 chr1ptel1M 501777 502708 (497292) L1MC_orf2#LINE/L1 1799 2706 (588) m_b14s551i12 513 chr1ptel1M 501777 ATGCAGAAAAAGTTTTTGATAAAATGTAGTATCCATTCCT-ATTAAAACA 501825 iv i vi ii i v - v v L1MC_orf2#LIN 1799 ATGCAGAAAAAGCATTTGACAAAATCCAACACCCATTCATGATAAAAACT 1848 chr1ptel1M 501826 CT-AGAGAGCATAGGAATAAATGA-AGCTT-----ACATGAAAAAGAAAA 501868 - vi i - i v i- i ----- v v -- L1MC_orf2#LIN 1849 CTCAGCAAAC-TAGGAATAGAGGGGAACTTCCTCAACTTGATAAAGAA-- 1895 chr1ptel1M 501869 GTAATATTCATCTA----AAACCATCAGCAAATATTATCAGTAATGGGGA 501914 -------- ---- vv v i i vvv v L1MC_orf2#LIN 1896 --------CATCTACAAAAAACCTACAGCTAACATCATACTTAATGGTGA 1937 chr1ptel1M 501915 TAAGCTAGAAGCATTCCCAATACAACCAGGGCTGAAACAAGAATGCTCAT 501964 v i ? v iv vi i ivii ii i ii vi L1MC_orf2#LIN 1938 GAAACTNGAAGCTTTCCCGCTAAGATCAGGAACAAGGCAAGGATGTCCCC 1987 chr1ptel1M 501965 TATTACCTTTATTATTTAATATTGTATGAGAAATGTTAGACATAGCAATA 502014 v i vi vi v i i i ivi i vi vi vv L1MC_orf2#LIN 1988 TCTCACCACTCCTTTTCAACATCGTACTGGAAGTCCTAGCTAATGCAATA 2037 chr1ptel1M 502015 AG---AGAAAAAAAAATTAAAAGAAT-TAGAATAGCAATGAGGAAACAAA 502060 --- ii v i v -i v i v v i i L1MC_orf2#LIN 2038 AGACAAGAAAAGGAAATAAAAGGTATACAGATTGGGAAGGAAGAAATAAA 2087 chr1ptel1M 502061 ACTATCACTCTTCACAGATGATATGACTA--TATTTAGAAAATGCTAGCA 502108 i vi v i i i i-- v v v ivi L1MC_orf2#LIN 2088 ACTGTCTTTGTTCGCAGATGACATGATTGTCTATGTAGAAAATCCGAAAG 2137 chr1ptel1M 502109 AATCAACAAAAAAAACCATCTGAAATTATTAA-TAATTTTAGCAAAGTTA 502157 i -- vi i i v -ii v i i L1MC_orf2#LIN 2138 AATCGACAAAAAAA--CTCCTGGAACTAATAAGCGATTATAGCAAGGTTG 2185 chr1ptel1M 502158 CAGCACACAAAATAAACCCATAGAAATCATGAGCATTTCTATATTACCAA 502207 v i ii v ivi i i i vvv v i - i L1MC_orf2#LIN 2186 CAGGATACAAGGTTAATATACAAAAGTCAATCGCTTTCCTATA-TACCAG 2234 chr1ptel1M 502208 TAAAGTCCAGCAGCAACATAGG---AAAAGTGAAATTCCATTTAAAATGA 502254 i v vv i?v v iv iii--- iiiv v ----v L1MC_orf2#LIN 2235 CAATGAACAANTGGAATTTGAAATTAAAAACACAATACCATTTA----CA 2280 chr1ptel1M 502255 TTATAGAC-----AACATAAAATACTTAG----AAATTTACC------TG 502289 -iv ----- v i ---- i v ------ L1MC_orf2#LIN 2281 TTA-GCACCCCCAAAAATGAAATACTTAGGTATAAATCTAACAAAATATG 2329 chr1ptel1M 502290 TTAAAGAACTATATGAACATAACTATAAAACGTTTTTCACAAAATAAGTC 502339 vv v iv v i --- i v ii v i L1MC_orf2#LIN 2330 TACAAGATCTATATGAGGAAAACTACAAAAC---TCTGATGAAAGAAATC 2376 chr1ptel1M 502340 -----AGATCCAAACAACTGGAAAAATATTAATTGCTCATGTGTAGACTG 502384 ----- ? i i v i i vvv i vi ivv L1MC_orf2#LIN 2377 AAAGAAGANCTAAATAAATGGAGAGATATTCCATGTTCATGGATAGGAAG 2426 chr1ptel1M 502385 AGTCAGTATAATAACATGATAATTGAAAAAAAATAACAGTTCTACCTAAA 502434 v i ------- ---- i----- i iv v i v L1MC_orf2#LIN 2427 ACTCAATAT-------TG----TC-----AAGATGTCAGTTCTTCCCAAC 2460 chr1ptel1M 502435 TTAATCCATTTATTCAATGTCAT----ATCAAACTATCA--AAATTTTTT 502478 i i vv iv ---- v vi -- i v L1MC_orf2#LIN 2461 TTGATCTATAGATTCAATGCAATCCCAATCAAAATCCCAGCAAGTTATTT 2510 chr1ptel1M 502479 TATAAAACTAGGAAAA--AATACAAGAAAATTCATCCGGAAGAACAAAAG 502526 i ii vv v iv --i v --v i i vi iiii L1MC_orf2#LIN 2511 TGTGGATATCGACAAACTGATTC--TAAAGTTTATATGGAGAGGCAAAAG 2558 chr1ptel1M 502527 -CTCAAGCATATCAAAGGAATTGAGAGACAGACAGAGACACACACAGAGA 502575 - i ------------ ---- v ------- - i vv L1MC_orf2#LIN 2559 ACCCA------------GAAT----AGCCA-------ACACA-ATATTGA 2584 chr1ptel1M 502576 GAGAGAGAGAGACAAAGAGAGAGAGAGGGTTTTTCTAGGCA-TACTAGAT 502624 ii - - vvi - -------- - i - iv i L1MC_orf2#LIN 2585 AGGAGA-AGA-ACAAAGTCGGAG-GA--------CT-GACACTACCCGAC 2622 chr1ptel1M 502625 CTCAA-ACTGTATTATAAA---ACAGTAATTATGAAAGCAATCTGCTACT 502670 i - - i --- i v --- i v v i L1MC_orf2#LIN 2623 TTCAAGACT-TACTATAAAGCTACAGTAATCAAGA---CAGTGTGGTATT 2668 chr1ptel1M 502671 GGCTAAGAAATAGAGTGGTAGATTCATGGAATAGAATA 502708 v ii vvii iv i L1MC_orf2#LIN 2669 GGCGAAAGAATAGACAAATAGATCAATGGAACAGAATA 2706 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.85 CpG sites = 136, Kimura (unadjusted) = 37.01 Transitions / transversions = 1.26 (136/108) Gap_init rate = 0.11 (101 / 931), avg. gap size = 1.35 (136 / 101) 1106 30.35 5.19 3.71 chr1ptel1M 501777 502546 (497454) L1P4_orf2#LINE/L1 1799 2579 (715) m_b14s551i11 513 chr1ptel1M 501777 ATGCAGAAAAAGTTTTTGATAAAATGTAGTATCCATTCCT-ATTAAAACA 501825 i i i vi ii v v - v v L1P4_orf2#LIN 1799 ACGCAGAAAAAGCTTTCGATAAAATCCAACATCCCTTCATGATAAAAACC 1848 chr1ptel1M 501826 CTAGAGAGCATAGGAATAAATGAAGCTTACATGAAAAAGAAAAGTAATAT 501875 vi v ivv v vi v i i v v v vi ---- v v L1P4_orf2#LIN 1849 CTCAACAAACTAGGCATCGAAGGAACATACCTCAAAATAA----TAAGAG 1894 chr1ptel1M 501876 TCATCTA----AAACCATCAGCAAATATTATCAGT-AATGGGGATAAGCT 501920 i ---- vv v i i - v - i v v L1P4_orf2#LIN 1895 CCATCTATGACAAACCCACAGCCAACATCAT-ACTGAACGGGCAAAAGCT 1943 chr1ptel1M 501921 AGAAGCATTCCCAATACAACCAGGGCTGAAACAAGAATGCTCATTATTAC 501970 i vv ivi v v ivii i i i i v i L1P4_orf2#LIN 1944 GGAAGCATTCCCCTTGAGAACTGGAACAAGACAAGGATGCCCACTCTCAC 1993 chr1ptel1M 501971 CTTTATTATTTAATATTGTATGAGAAATGTTAGACATAGCAATAAG---A 502017 vi vi i i v ivi i vi v v v --- L1P4_orf2#LIN 1994 CACTCCTATTCAACATAGTACTGGAAGTCCTAGCCAGAGCAATCAGGCAA 2043 chr1ptel1M 502018 GAAAAAAAAATTAAAAGAATTAGAATA-GCAATGAGGAAACAAAACTATC 502066 i i v i v ivi - v v i iiv L1P4_orf2#LIN 2044 GAGAAAGAAATAAAAGGCATCCAAATAGGAAAAGAAGAAGTCAAACTATC 2093 chr1ptel1M 502067 ACTCTTCACAGATGATATGA--CTATATTTAGAAAATGCTAGCAAATCAA 502114 v i v i -- ii iv ivi v vi L1P4_orf2#LIN 2094 TCTCTTCGCTGACGATATGATTCTATACCTAGAAAACCCTAAAGACTCCG 2143 chr1ptel1M 502115 CAAAAAAAACCATCTGAAATT-ATTAATAATTTTAGCAAAGTTACAGCAC 502163 v ii-- vi ii i - v ii i i i v v i L1P4_orf2#LIN 2144 CCAAAAGG--CTCCTAGAACTGATAAACGACTTCAGTAAAGTTTCAGGAT 2191 chr1ptel1M 502164 ACAAAATAAACCCATAGAAATCATGAGCATTTCTATATTACCAATAAAGT 502213 v ivi i i vv -i v L1P4_orf2#LIN 2192 ACAAAATCAATGTACAAAAATCAGTAGCATTTCTATA-CACCAATAACGT 2240 chr1ptel1M 502214 CC-AGC--AGCAACATAGGAAAAGTGAAATTCCATTTAAAATGATTATAG 502260 i - -- viv v vv i ii v i v iiii i i L1P4_orf2#LIN 2241 TCAAGCTGAGAGCCAAATCAAGAACGCAATCCCATTTACAATAGCCACAA 2290 chr1ptel1M 502261 ACAACATAAAATACTTAGAAATTTACCT----------GTTAAAGAACTA 502300 v v i i vi i ---------- v v v L1P4_orf2#LIN 2291 AAAAAATAAAATACCTAGGAATACATCTAACCAAGGAGGTGAAAGATCTC 2340 chr1ptel1M 502301 TATGAACATAACTATAAAACGTTTTTCACAAAATAAGTCA-----GATCC 502345 ii iv v i ii vi ---i v i ----- iv L1P4_orf2#LIN 2341 TACAAGGAGAACTACAAAACACTGCT---GAAAGAAATCANAGATGACAC 2387 chr1ptel1M 502346 AAACAACTGGAAAAATATTAATTGCTCATGTGTAGACTGAGTCAGTATAA 502395 v i vvv vi v ivv i i -- L1P4_orf2#LIN 2388 AAACAAATGGAAAAACATTCCATGCTCATGGATTGGAAGAATCAATAT-- 2435 chr1ptel1M 502396 TAACATGATAATTGAAAAAAAATAACAGTTCTACCTAAATTAATCCATTT 502445 --- i v----------- ii vi v i i vi i ivv L1P4_orf2#LIN 2436 ---CGTT-----------AAAATGGCCATACTGCCCAAAGCAATCTACAG 2471 chr1ptel1M 502446 ATTCAATG----TCATATCAAACTATCAAAAT--TTTTTTATAAAACTAG 502489 i ---- v i vi -- i i i i L1P4_orf2#LIN 2472 ATTCAACGCTATTCCTATCAAACTACCAACGTCATTTTTCACAGAATTAG 2521 chr1ptel1M 502490 GAAAAAATACAAGAAAATTCATCCGGAA--GAACAAAAGCTCAAGCATA- 502536 i v ivvv vi --i v i i i -- - L1P4_orf2#LIN 2522 AAAAAACTATTCTAAAATTCATATGGAACCAAAAAAGAGCCCGA--ATAG 2569 chr1ptel1M 502537 TCAAAGGAAT 502546 i v L1P4_orf2#LIN 2570 CCAAAGCAAT 2579 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 36.84 CpG sites = 123, Kimura (unadjusted) = 39.76 Transitions / transversions = 1.21 (123/102) Gap_init rate = 0.06 (44 / 769), avg. gap size = 1.57 (69 / 44) 698 30.65 5.17 3.04 chr1ptel1M 503137 503523 (496477) L1PA5_3end#LINE/L1 1 395 (506) m_b14s551i13 514 chr1ptel1M 503137 CTCATTTCTCAAATATATAGAGAATTGCATCAAATTTATAATAACA---C 503183 v v ivi v i i i vv v i v v --- L1PA5_3end#LI 1 CTAATATCCAGAATCTACAAAGAACTCAAACAAATTTACAAGAAAAAAAC 50 chr1ptel1M 503184 AAATCATTCC-TCAATTGATAGTCAAAGGATATAAACTGGAAGTTTTCAG 503232 iv ii - vvii i v i i v iv v i i L1PA5_3end#LI 51 AAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTTCTCAA 100 chr1ptel1M 503233 ACAAAGAAATCAAAGCTCTTCATAGTCATATGAAAAAAATGCTCTAAATC 503282 vi v iv v vviiv i v i - --- L1PA5_3end#LI 101 AAGAAGACATTTATGCAGCCAACAGACACATGAAAAAA-TGCTC---ATC 146 chr1ptel1M 503283 AT-ATTG---ATTGGAAAAATGAAACTTAAAA--ACAACTCTAAGGTACT 503326 - i --- ii i v v i -- --- i i i L1PA5_3end#LI 147 ATCACTGGCCATCAGAGAAATGCAAATCAAAACCACAA---TGAGATACC 193 chr1ptel1M 503327 ACTTCACACCTTTCAGAGTGATTAATATAATACAAA--TGGGAAA----- 503369 ii vv i i iiv vi -- v --ii ----- L1PA5_3end#LI 194 ATCTCACACCAGTTAGAATGGCGATCAT--TAAAAAGTCAGGAAACAACA 241 chr1ptel1M 503370 --TGTTGGAGAGGATATGGAAAACTGGGA-CACTAATGAACTGTTGGTAG 503416 -- i i i v i - vv iv i L1PA5_3end#LI 242 GGTGCTGGAGAGGATGTGGAGAAATAGGAACACTTTTACACTGTTGGTGG 291 chr1ptel1M 503417 ATTTGTGAACTGATTCAATCATTTTGGAGAGCAATTTGGAACTATACCCA 503466 ivi i ii i v iii i v -- v v iv L1PA5_3end#LI 292 GACTGTAAACTAGTTCAACCATTGTGGAAGACAGTGTGG--CGATTCCTC 339 chr1ptel1M 503467 AAGGGCCGTGAAACTGCGTATAATATTTGATCCAGTCATACCATTGCTAG 503516 ii - ii iviv vi i i v i i L1PA5_3end#LI 340 AAGGATC-TAGAACTAGAAATACCATTTGACCCAGCCATCCCATTACTGG 388 chr1ptel1M 503517 ATTTATA 503523 i v L1PA5_3end#LI 389 GTATATA 395 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 39.84 CpG sites = 69, Kimura (unadjusted) = 40.77 Transitions / transversions = 1.50 (69/46) Gap_init rate = 0.05 (21 / 386), avg. gap size = 1.52 (32 / 21) 554 28.95 5.82 4.19 chr1ptel1M 503140 503586 (496414) L1ME4c_3end#LINE/L1 4 457 (373) m_b14s551i14 514 chr1ptel1M 503140 ATTTCTCAAATATATAGAGAATTGCAT-CAAATTTATAATAACACAAATC 503188 v ?v ? i ii - - v v v - ? L1ME4c_3end#L 4 ATATCTNTANTATATAAAGAGCT-CATTCAAATTGATAAGAAAA-ANATC 51 chr1ptel1M 503189 ATT-CCTCAATTGATA----GTCAAAGGATATAAACTGGAAGTTTTCAGA 503233 vv- i v ---- v i i v iv i iv ? L1ME4c_3end#L 52 AAGACCCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANA 101 chr1ptel1M 503234 CAAAGAAATCAAAGCTCTTCATAGTCATATGAAAAAAATGCTCTAAATCA 503283 vi i vv ?ivv vv i iv i i - i v vv i L1ME4c_3end#L 102 AGAGGAAATACAANTAGTAAACAAACACATGGAAAAA-TGTTCAACCTCG 150 chr1ptel1M 503284 -TATTGATTGGAAAAATGAAACTTAAAAACAACTCTAAGGTACTACTTCA 503332 - v i iii i v v i- vv i i i i i L1ME4c_3end#L 151 CTAGTAATCAAAGAAATGCAAATTAAAG-CAACAATGAGATACCATTTTA 199 chr1ptel1M 503333 CACCTTTCAGAGTGATTAATATAA---TACAAA--TGGGAA------ATG 503371 i v i i ---- ii v --- v -- iv ------ L1ME4c_3end#L 200 CGCCTATTAAA----TTAGCAAAAATTTAAAAAATTGATAATACCCAATG 245 chr1ptel1M 503372 TTGGAGAGGATATGG-AAAACTGGGACACTAATGAACTGTTGGTAGATTT 503420 i v ? ii -i v ? v iv i i i vv? L1ME4c_3end#L 246 CTGGCGAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANT 295 chr1ptel1M 503421 GTGAACTGATTCAATCATTTTGGAGAGCAATTTGGAACTA--TACCCAAA 503468 i i i v i v i v v -- i -- L1ME4c_3end#L 296 GTAAATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATC--AA 343 chr1ptel1M 503469 GGGCCGTGAAACTGCGTATAATATTTGATCCAGTCATACCATTGCTAG-- 503516 i i i v ivi viv i v v i v i -- L1ME4c_3end#L 344 GAGCCATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGA 393 chr1ptel1M 503517 ATTTA---TATGTCAATGACATCTAAAAAATGGAAAGGAACCTATTTGTA 503563 --- v vv i-- ii i v -- v v i L1ME4c_3end#L 394 ATTTATCCTAAGGAAATA--ATTCAAAAGAAGGAAA--AAGCTATATGCA 439 chr1ptel1M 503564 AAAAATATATATATTTATAGCAG 503586 vi i----- i i v L1ME4c_3end#L 440 CGAAG-----ATGTTCATTGCAG 457 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 36.70 CpG sites = 67, Kimura (unadjusted) = 38.24 Transitions / transversions = 1.18 (67/57) Gap_init rate = 0.07 (30 / 446), avg. gap size = 1.50 (45 / 30) 212 36.87 5.32 3.59 chr1ptel1M 503850 504150 (495850) C L2#LINE/L2 (4) 3078 2773 m_b14s601i13 511 chr1ptel1M 503850 GGAGAACATTTCAGAAATTATGGGACAACCAGAGAAAATGTCAGGAGCCA 503899 i i i i iv v- v i i v v v v i vv v i C L2#LINE/L2 3078 GAAGAGCGTTCCAGGCAG-AGGGAACAGCAAGTGCAAAGGCCCTGAGGCG 3030 chr1ptel1M 503900 AAAG-ATGGAGGGTCTTATTTAAAGA-CAACCAGGAAGCCAGGGTCCCTG 503947 ii -i vvv - v i ii i - i v i v vv C L2#LINE/L2 3029 GGAGCGTGCCTGG-CGTGTTCGAGGAACAGCAAGGAGGCCAGTGTGGCTG 2981 chr1ptel1M 503948 GATCAAAAAGAACATATAGCAGAAT---AAGATATATATAGACTGGAATG 503994 v ii iv i ivivi v i --- i v i--- iiii iv C L2#LINE/L2 2980 GAGCGGAGTGAGCGAGGGGGAGAGTGGTAGGAGATG---AGGTCAGAGAG 2934 chr1ptel1M 503995 ATAG-GAGGGAGCCTACAATGAAGGGTTTTG--AATCCTGAGCAGAACAT 504041 i i- i v vv iv v ii --iii v vivv i v C L2#LINE/L2 2933 GTAACGGGGGACCAGATCATGTAGGGCCTTGTAGGCCATTGTAAGGACTT 2884 chr1ptel1M 504042 TGTCTATTTGATCT-AG-GAGGCCATGGGGAGCCTCT--AGGGTTTCCTG 504087 v - iv - - --- i vi -- -- C L2#LINE/L2 2883 TGGCT-TTTACTCTGAGTGAG---ATGGGAAGCCATTGGAGGGTTT--TG 2840 chr1ptel1M 504088 AGTAG----GTGACATGGTTGGGCCTATGCTTTAGGAAAATCACATTAGT 504133 i ---- i iv i i i i ii ii vi i i C L2#LINE/L2 2839 AGCAGAGGAGTGACATGATCTGACTTACGTTTTAAAAGGATCACTCTGGC 2790 chr1ptel1M 504134 GGCTGAATGGAGGGTAG 504150 v vi v ii C L2#LINE/L2 2789 TGCTGTGTTGAGAATAG 2773 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 48.22 CpG sites = 64, Kimura (unadjusted) = 53.33 Transitions / transversions = 1.49 (64/43) Gap_init rate = 0.07 (20 / 300), avg. gap size = 1.35 (27 / 20) 315 25.16 13.55 5.46 chr1ptel1M 504288 504678 (495322) C L2-1_AMi#LINE/L2 (584) 651 231 m_b14s551i15 515 chr1ptel1M 504288 GGATGTGGGAGGATGT-GAGAGATGATAGAGTCAAGGATGACTCCAAGTT 504336 -- iv - v viv i i v v v C L2-1_AMi#LINE 651 GGATGTG--AGGACCTAGAGAGAGGTCCGAGTCGAAGATGACGCCCAGGT 604 chr1ptel1M 504337 TTAGAGCCTG----------------GTGGTCTTTTTGACAGTAGT-AAG 504369 vv i ---------------- v v iv ii -i C L2-1_AMi#LINE 603 TACGGGCCTGAGTGACAGGCAGGATGGTGGTGTTGTCCACAGTGATCGAG 554 chr1ptel1M 504370 AAAGGTAGGAATTGGG-GAAGGTTTGGGGGGAAAGATAAAGAGCTTGATA 504418 i -- v - ? i - v ivi v C L2-1_AMi#LINE 553 AAAAG--GGAATGGGGAGNAGGCTTGGGGGG-AAGATTAAGAGCTCTGTT 507 chr1ptel1M 504419 TT-GGACATG-TGAGCAGAAGATGTCTGCTGGAAATCCAGCTAGAGATG- 504465 - v - vvi v v v i v vvvi - C L2-1_AMi#LINE 506 TTAGGCCATGTTGAGCTTGAGCTGACGGCTAGACATCCACGAGGAGATGT 457 chr1ptel1M 504466 -GGAGATGGCAGGTC---ATT-------------AAAGA-----GTTTGA 504493 -i - i i --- ------------- i ----- i i C L2-1_AMi#LINE 456 CAGAGA-GACAGGCCGAGATTTTAGTTTGGACAGAAGGAGACAGGTCTGG 408 chr1ptel1M 504494 AGCAGGATAGGTTAATTAGCGAATCCTTCCCATAGG-GGTCTTTAAATCT 504542 i - v vi iv i i ----- v i i- vv i i C L2-1_AMi#LINE 407 AGTA-GAGAGGTAGATCTGTGAGT-----CAACAGATGGTAGTTGAATTT 364 chr1ptel1M 504543 ATGGCTGC---TGAGATCTCCCAGTGAAGTAGGAAAGAGGGAGAAGAGAA 504589 i vi --- iv v -- i iviv i C L2-1_AMi#LINE 363 GTGTTTGCGGATGAGATTACCCAGAGA--TAAGGTGTAGAGAGAAGAGAA 316 chr1ptel1M 504590 GTGGGCCCAAGACAGAGCCTTGAGGGACAACCATGGTCAGAGGATGTAGT 504639 v i v i i v i vv ---- -- v i - C L2-1_AMi#LINE 315 GGGGACCAAGGACAGAGCCCTGTGGAACCCCCA----CAGA--AAGTGG- 273 chr1ptel1M 504640 GTGGAGGG--GGATCCAGCCAAGGAG-G--TAGAGAAGAAGCAG 504678 v i -- i i-- - -- i v v C L2-1_AMi#LINE 272 GAGGAAGGAAGAATT--GCCAAGGAGCGATTAGAGAGGTAGGAG 231 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 30.45 CpG sites = 47, Kimura (unadjusted) = 31.24 Transitions / transversions = 1.02 (47/46) Gap_init rate = 0.10 (39 / 390), avg. gap size = 1.95 (76 / 39) 17 28.75 6.35 6.35 chr1ptel1M 504825 505013 (494987) (AAGG)n#Simple_repeat 1 189 (0) m_b14s252i7 516 chr1ptel1M 504825 AAGGAGAGG--GGGAGGAAAGATAGGGGATGAAGAAAGGGAAGGAGAGAG 504872 - -- i i - - i v i - ii i (AAGG)n#Simpl 1 AAGGA-AGGAAGGAAGGAAGGA-A-GGAAGGAAGGAA-GGAAGGAAGGAA 46 chr1ptel1M 504873 GGAGGGAGAAGAA-AAATAGAGGAAAGAA-GAAGG-A-GAAGAAAGGAGG 504918 i - i -i vii i - - - i -i (AAGG)n#Simpl 47 GGAAGGA-AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA-A 94 chr1ptel1M 504919 GGAAGTGAATGGGAGAGGGACAAAGAGAGGGA-GAGGGAAAG-TGAAAGG 504966 - -- - i vi ii i - i i -v i (AAGG)n#Simpl 95 GGAAG-GAA--GGA-AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG 140 chr1ptel1M 504967 GGGTAAAGACAGAGAGGAA-ATAGGAGAGG--GGAGGGGAGGGA-GAAGG 505012 ii v i - ii -iv - -- i i i - (AAGG)n#Simpl 141 AAGGAAGGA-AGGAAGGAAGGAAGGA-AGGAAGGAAGGAAGGAAGGAAGG 188 chr1ptel1M 505013 A 505013 (AAGG)n#Simpl 189 A 189 Matrix = Unknown Transitions / transversions = 5.33 (32/6) Gap_init rate = 0.12 (22 / 188), avg. gap size = 1.09 (24 / 22) 17 26.25 2.78 4.23 chr1ptel1M 504841 504912 (495088) (AAG)n#Simple_repeat 1 71 (0) m_b14s252i8 516 chr1ptel1M 504841 AAGATAGGGGATGAAGAAAGGGAAGGAG-AGAGGGAGGGAGAAGAA-AAA 504888 - ii v iii i - -i i i - i (AAG)n#Simple 1 AAGA-AGAAGAAGAAGAAGAAGAAGAAGAAGA-AGAAGAAGAAGAAGAAG 48 chr1ptel1M 504889 TAGAGGAAAGAAGAAGGAGAAGAA 504912 v i - i (AAG)n#Simple 49 AAGAAG-AAGAAGAAGAAGAAGAA 71 Matrix = Unknown Transitions / transversions = 6.00 (12/2) Gap_init rate = 0.07 (5 / 71), avg. gap size = 1.00 (5 / 5) 14 16.89 2.27 4.65 chr1ptel1M 504988 505031 (494969) (AGGGG)n#Simple_repeat 1 43 (0) m_b14s252i9 517 chr1ptel1M 504988 AGGAGAGGGGAGGGGA-GGGAGAAGGAGGTGAGAGATAAGGGAGG 505031 i - -i v - iv i (AGGGG)n#Simp 1 AGGGGAGGGGAGGGGAGGGGAG-GGGAGGGGAG-GGGAGGGGAGG 43 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.07 (3 / 43), avg. gap size = 1.00 (3 / 3) 267 31.74 1.56 4.00 chr1ptel1M 505438 505565 (494435) L3#LINE/CR1 1715 1839 (2260) m_b14s601i14 518 chr1ptel1M 505438 TCTGCCCAAAGAAGAGAAGATGATGATTTCT-GATTTGCTGCAATAAAAA 505486 ? iv v v vv i v - i iviiv i v L3#LINE/CR1 1715 TCNGCTAAAAGCAGAGCATCTGATAAATTCTTGACTTGCCTTGCTGACAA 1764 chr1ptel1M 505487 TTCCCTCCTTCAAAAAAT-GAGGAGCCAAGGAAGGGGAGCCAGCACTTGC 505535 i v ii i ii - iv v i i -- v --- i L3#LINE/CR1 1765 TTTCATCTCTCAGAAGGTAGAGGAAGCAACGAGGGGAA--CTGC---TAC 1809 chr1ptel1M 505536 TCCAGATCTGATTCTGACCAGCAACAAGGA 505565 ii ii i i vi i L3#LINE/CR1 1810 TCTGGACTTAATTCTGACCAACAAGGAAGA 1839 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 43.70 CpG sites = 25, Kimura (unadjusted) = 43.70 Transitions / transversions = 1.79 (25/14) Gap_init rate = 0.06 (7 / 127), avg. gap size = 1.00 (7 / 7) 228 32.17 0.00 8.25 chr1ptel1M 505711 505815 (494185) L3#LINE/CR1 2843 2939 (1160) m_b14s601i15 518 chr1ptel1M 505711 AAGAGCCAATATGGCTTTGGCTATAATGAGTTGGGCCAGACTCACCTTGT 505760 i ii v iiviv v ii iiv i v ii L3#LINE/CR1 2843 AGGAGCCAGCATGGGTTCACTAAGAACAAGTCATGCCAAACTAACCTCAT 2892 chr1ptel1M 505761 TTCCTTTTTAGAAGCAAGGTCATTTAACTGATTTCCAGAATTAGAGAAAA 505810 v --i i i i vi i ---- - i - ii L3#LINE/CR1 2893 TTCCTTTTTTGA--TAGGGTTACTAGACTGGT----AG-ATCAG-GGGAA 2934 chr1ptel1M 505811 TGCTG 505815 i L3#LINE/CR1 2935 TGCCG 2939 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 43.13 CpG sites = 23, Kimura (unadjusted) = 45.18 Transitions / transversions = 2.88 (23/8) Gap_init rate = 0.08 (8 / 104), avg. gap size = 1.00 (8 / 8) 294 25.23 5.75 8.88 chr1ptel1M 507915 508088 (491912) L2c_3end#LINE/L2 308 476 (2) m_b14s601i16 519 chr1ptel1M 507915 TCCCATTG----ATCTTTCATATAACTTGCTTTGTATAGATATAGTTTGC 507960 i---- ii v - iv vvvi v - i L2c_3end#LINE 308 TCCCATTATAGCACTTATCAT-TAACTTGTATTGTAATTGTCT-GTTTAC 355 chr1ptel1M 507961 ATG-CTGTCTTCTCCA-TAGATTGCAACTTCCTTGAC--CAGTGAC--TC 508004 ? - i - i ii vi v-- v -- v L2c_3end#LINE 356 NTGTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTG 405 chr1ptel1M 508005 TTTTATTTCTTTTTGTATCCCCAGCACTTAGCTAGGATCCTGAAACATAT 508054 i iv i i i i ------------ v L2c_3end#LINE 406 TCTTATTCATCTTTGTATCCCCAGCGCCTGGC------------ACATAG 443 chr1ptel1M 508055 TAAGTGATTAATTAAATATTTATGAACTAATTGA 508088 i i v i - i i vi v i v L2c_3end#LINE 444 TAGGCGCTCAA-TAAATGTTTGTTGAATGAATGA 476 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 29.74 CpG sites = 24, Kimura (unadjusted) = 31.62 Transitions / transversions = 1.50 (24/16) Gap_init rate = 0.12 (20 / 173), avg. gap size = 1.25 (25 / 20) 296 24.58 7.81 1.47 chr1ptel1M 507965 508092 (491908) L2d_3end#LINE/L2 381 516 (0) m_b14s601i17 519 chr1ptel1M 507965 TGTCTTCTCCA-TAGATTGCAACTTCCTTGAC--CAGTGAC----TCTTT 508007 i i v - i vi v-- v ---- v L2d_3end#LINE 381 TGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTA 430 chr1ptel1M 508008 TATTTCTTTTT-GTATCCC-CAGCACTTAGCTAGGATCCTGAA-ACATAT 508054 i ?i ? - vi - i i - vii v i- v L2d_3end#LINE 431 TACTNTTTTNTCGTTCCCCACAGCGCCTAGC-ACAGTGCTGAGCACATAG 479 chr1ptel1M 508055 TAAGTGATTAATTAAATATTTATGAACTAATTGATTGA 508092 i i v i - i i vi i i L2d_3end#LINE 480 TAGGCGCTCAAT-AAATACTTGTTGATTGATTGATTGA 516 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 28.97 CpG sites = 20, Kimura (unadjusted) = 31.37 Transitions / transversions = 1.82 (20/11) Gap_init rate = 0.06 (8 / 127), avg. gap size = 1.50 (12 / 8) 180 22.47 11.11 1.12 chr1ptel1M 508107 508187 (491813) C MIR3#SINE/MIR (10) 198 110 m_b14s601i18 520 chr1ptel1M 508107 ATTATAGAATAG-AAAGCTGGAA-GGCCCTTAGCGCTC----AGCCTATC 508150 i iv- i - v v v ---- i i v C MIR3#SINE/MIR 198 ATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAAC 149 chr1ptel1M 508151 TCCCTACCTCTGAT-GGTGAGGAACCT--GGCCCAGTGAG 508187 i - v i v i- i v -- v C MIR3#SINE/MIR 148 CCCCT-CATTTTACAGATGAGGAAACTGAGGCCCAGAGAG 110 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 26.96 CpG sites = 9, Kimura (unadjusted) = 26.96 Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.07 (6 / 80), avg. gap size = 1.67 (10 / 6) 249 27.78 4.17 0.00 chr1ptel1M 510297 510368 (489632) MIR3#SINE/MIR 72 146 (62) m_b14s601i19 521 chr1ptel1M 510297 CATCAACTCTGTATGAGATCCTGAGCAAGTCTATTAATCTTTT---ACCT 510343 ii ?vv i v i i i vv v i i i---i MIR3#SINE/MIR 72 CACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCT 121 chr1ptel1M 510344 CGAGTTCCTCATCTGTAAAATGGGG 510368 iiv i MIR3#SINE/MIR 122 CAGTTTCCTCATCTGTAAAATGAGG 146 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 36.75 CpG sites = 13, Kimura (unadjusted) = 36.75 Transitions / transversions = 1.86 (13/7) Gap_init rate = 0.01 (1 / 71), avg. gap size = 3.00 (3 / 1) 400 23.60 13.25 1.79 chr1ptel1M 510308 510458 (489542) MIRc#SINE/MIR 86 253 (15) m_b14s601i21 521 chr1ptel1M 510308 TATGAGATCCTGAGCAAGTCTATTAATCTTTT---ACCTCGAGTTCCTCA 510354 i v i i i vv i i i---i iiv MIRc#SINE/MIR 86 TGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCA 135 chr1ptel1M 510355 TCTGTAAAATGGGGATAATATTA---GC---ACCTAACTCTTGAAGTTGT 510398 v --- ---i v viiii MIRc#SINE/MIR 136 TCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGT 185 chr1ptel1M 510399 --TGAGAATCATAT---AT------TATAAAAGCAGAGTTTTACAAGCCT 510437 -- i v --- ------ i i --- i ii i iv MIRc#SINE/MIR 186 TGTGAGGATCAAATGAGATAATGTATGTGAAAGC---GCTTTGTAAACTG 232 chr1ptel1M 510438 TAATGTACTATACAAATGAAA 510458 v i v MIRc#SINE/MIR 233 TAAAGTGCTATACAAATGTAA 253 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 29.45 CpG sites = 24, Kimura (unadjusted) = 29.45 Transitions / transversions = 2.18 (24/11) Gap_init rate = 0.06 (9 / 150), avg. gap size = 2.56 (23 / 9) 412 22.92 3.12 0.00 chr1ptel1M 510308 510403 (489597) MIR#SINE/MIR 82 180 (82) m_b14s601i20 521 chr1ptel1M 510308 TATGAGATCCTGAGCAAGTCTATTAATCTTT---TACCTCGAGTTCCTCA 510354 i v i i i ivv i i --- i iiv MIR#SINE/MIR 82 TGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCA 131 chr1ptel1M 510355 TCTGTAAAATGGGGATAATATTAGCACCTAACTCTTGAAGTTGTTGAGA 510403 v i v v iii v MIR#SINE/MIR 132 TCTGTAAAATGGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTGA 180 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 28.06 CpG sites = 14, Kimura (unadjusted) = 28.06 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.01 (1 / 95), avg. gap size = 3.00 (3 / 1) 15 39.90 0.00 0.00 chr1ptel1M 510464 510537 (489463) (GAG)n#Simple_repeat 1 74 (0) m_b14s252i10 522 chr1ptel1M 510464 GATGAGGAGGAGGAAGAAAAGAAGAAAGAAAAGGAGGAGAATGAAAAGGT 510513 v i ii i i i ii i v ii v (GAG)n#Simple 1 GAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA 50 chr1ptel1M 510514 TGACTCGAGGGAGGAAGAGGAAGA 510537 v vvv ii i i (GAG)n#Simple 51 GGAGGAGGAGGAGGAGGAGGAGGA 74 Matrix = Unknown Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.00 (0 / 73), avg. gap size = 0.0 (0 / 0) 11 14.08 0.00 8.82 chr1ptel1M 510761 510797 (489203) (TGCTTC)n#Simple_repeat 1 34 (0) m_b14s252i11 523 chr1ptel1M 510761 TGTTTCAGCTCGTGTCTTCTGCTTCTGCTGCTCTGCT 510797 i v iv - -- (TGCTTC)n#Sim 1 TGCTTCTGCTTCTG-CTTCTGCTTCTGCT--TCTGCT 34 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.08 (3 / 36), avg. gap size = 1.00 (3 / 3) 187 32.27 0.00 1.61 chr1ptel1M 511460 511522 (488478) L3b_3end#LINE/CR1 1142 1203 (3) m_b14s601i22 524 chr1ptel1M 511460 AGAGGAACAGATTGGACTGGGCGGTCACTGATGTTCTCCCCAACTTTTAA 511509 i ? vi - i ii ii v v i ii i i v i L3b_3end#LINE 1142 AGGGGNAGGGAT-GGACTAGATGACCTCTGAGGTCCTTTCCAATTCTGAG 1190 chr1ptel1M 511510 CTTCTATGACTTT 511522 v ii L3b_3end#LINE 1191 ATTCTATGGTTTT 1203 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 47.12 CpG sites = 15, Kimura (unadjusted) = 47.12 Transitions / transversions = 3.00 (15/5) Gap_init rate = 0.02 (1 / 62), avg. gap size = 1.00 (1 / 1) 245 32.69 8.93 1.67 chr1ptel1M 511746 511913 (488087) L3#LINE/CR1 3357 3536 (563) m_b14s601i23 525 chr1ptel1M 511746 TGGGTATAAAAAATCAGCTTCTTAAATGCAACACAG------TATTGATT 511789 i vi i v vi i i iv ii ------ v v v L3#LINE/CR1 3357 TAGGTTCAAAAAATCAACTGCACAAGTACAGGATGGAGAGGATCTGGCTT 3406 chr1ptel1M 511790 AACAGTTGTTC---TGAGGAGGATCTGGATATCTGAGGAAACTGCAAGCT 511836 i iv --- ii i i i ivi i v vvi i L3#LINE/CR1 3407 AGCAGCAGTTCACGTGAAAAAGACCTAGGGGTTTTAGTTGACCGCAAGCT 3456 chr1ptel1M 511837 CAAGATGAGGCAGCCAATTATGAGGCAGCT--CAAAAATAG--GATGTGA 511882 v v i -- v i v ii -- - --i ii L3#LINE/CR1 3457 CAATATGAGCCAAC--AGTGTGATGTGGCTGCCAAAAA-AGCTAATGCAA 3503 chr1ptel1M 511883 TCTGGGGCTG--TTAGTAGGGACACAGATTCCA 511913 vi -- i iiii i vv L3#LINE/CR1 3504 TCTTAGGCTGCATTAATAGAAGTATAGTGTCCA 3536 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 44.13 CpG sites = 35, Kimura (unadjusted) = 45.30 Transitions / transversions = 1.84 (35/19) Gap_init rate = 0.05 (8 / 167), avg. gap size = 2.25 (18 / 8) 246 26.44 6.67 2.75 chr1ptel1M 511788 511892 (488108) L3b_3end#LINE/CR1 507 615 (591) m_b14s601i24 525 chr1ptel1M 511788 TTAACAGTTGTTC---TGAGGAGGATCTGGATATCTGAGGAAACTGCAAG 511834 i iv i? --- ii i i ivi i v vvi i L3b_3end#LINE 507 TTAGCAGCAGCNCATGTGAAAAAGACCTGGGGGTTTTAGTTGACCGCAAG 556 chr1ptel1M 511835 CTCAAGATGAGGCAGCCAATTATGAGGCAGCT--CAAAAATAG--GATGT 511880 v v -- v ii v i -- - --i i L3b_3end#LINE 557 CTCAATATGAGTCAGC--AGTGCGACGCGGCTGCCAAAAA-AGCTAATGC 603 chr1ptel1M 511881 GATCTGGGGCTG 511892 v L3b_3end#LINE 604 GATCTTGGGCTG 615 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 28.17 CpG sites = 17, Kimura (unadjusted) = 34.12 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.06 (6 / 104), avg. gap size = 1.67 (10 / 6) 32 2.94 0.00 0.00 chr1ptel1M 512009 512043 (487957) (CTTC)n#Simple_repeat 1 35 (0) c_b14s251i1 526 chr1ptel1M 512009 CTTCCTTCCTTTCTTCCTTCCTTCCTTCCTTCCTT 512043 i (CTTC)n#Simpl 1 CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 35 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 20 10.76 0.00 0.00 chr1ptel1M 512044 512065 (487935) (T)n#Simple_repeat 10 31 (1) m_b14s252i12 527 chr1ptel1M 512044 TCTTTCTTTTTTTTTTTTTTTT 512065 i i (T)n#Simple_r 10 TTTTTTTTTTTTTTTTTTTTTT 31 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 249 26.15 13.53 1.05 chr1ptel1M 512223 512392 (487608) L3#LINE/CR1 3734 3924 (175) m_b14s601i25 528 chr1ptel1M 512223 CTGGAGAAGAGAGGATGGAGAGGGGA-------GCTGTCTTCAGGTACTT 512265 i ivv i ------- ii i L3#LINE/CR1 3734 CTGGAGAAGAGAAGACTTAGAGGAGACATGATAGCTGTCTTCAAATATTT 3783 chr1ptel1M 512266 GGGAGGTTGT---GTGGAGGAAGGTCTAGGCTTATTCATTGTGGAGCCAC 512312 iii i --- i i vi i vv vv v L3#LINE/CR1 3784 GAAGGGCTGTCATGTGGAAGAGGGATTAGACTTATTCTGTGTGGCTCCAG 3833 chr1ptel1M 512313 AGGG-AGAAC-AGG--CAGCTGGGGTGAGT----GGGA-GCAG----CAG 512349 - - -- iiv v vi ---- - ---- i L3#LINE/CR1 3834 AGGGCAGAACTAGGACCAATGGGTGGAAGTTACAGGGAGGCAGATTTCGG 3883 chr1ptel1M 512350 GCTGAGATTGGGAAAAACTCTACCCAGCAACAGGCGCTGTCCA 512392 viii v vi i i -- i i ivi v L3#LINE/CR1 3884 CTCAATATAAGGAAGAACTTT--CTAACAATCAGAGCTGTCCA 3924 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 32.33 CpG sites = 28, Kimura (unadjusted) = 33.26 Transitions / transversions = 1.75 (28/16) Gap_init rate = 0.06 (10 / 169), avg. gap size = 2.50 (25 / 10) 256 28.69 12.30 0.00 chr1ptel1M 512645 512766 (487234) L3#LINE/CR1 3957 4093 (6) m_b14s601i26 528 chr1ptel1M 512645 GCTCCCCTTCCTTGGAGCTCTCCGAGCAGACGCCTGCT--CCGCTGACCT 512692 v vi v v i i v iv v -- i vii v L3#LINE/CR1 3957 GCTCCCCGTCACTGGAGGTGTTCAAGCAGAGGCTGGATGACCACTTGTCA 4006 chr1ptel1M 512693 GGGATG--------GAGATTCTT---TTGGGGTGTGGGTTAAATTAGA-- 512729 -------- i i --- ivv vi ii i -- L3#LINE/CR1 4007 GGGATGTTGTAGAAGGGATTCCTGCATTGGATGGGAGGTTGGACTAGATG 4056 chr1ptel1M 512730 AACTTTCAGGTTTCTTCCAATTCAGAGATTATGAGAT 512766 v i v ii i v v v L3#LINE/CR1 4057 ACCTCTAAGGTCCCTTCCAACTCTGAGATTCTGTGAT 4093 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 36.66 CpG sites = 18, Kimura (unadjusted) = 36.66 Transitions / transversions = 1.06 (18/17) Gap_init rate = 0.03 (4 / 121), avg. gap size = 3.75 (15 / 4) 19 9.04 5.66 5.66 chr1ptel1M 514102 514154 (485846) (ACAAATT)n#Simple_repeat 1 53 (0) m_b14s252i13 529 chr1ptel1M 514102 ACACATTA-ACTTTACAAA-TACAAATTACAAAAATACAAATTTTACAAA 514149 v - vv - - v -- (ACAAATT)n#Si 1 ACAAATTACAAATTACAAATTACAAATTAC-AAATTACAAA--TTACAAA 47 chr1ptel1M 514150 -TACAA 514154 - (ACAAATT)n#Si 48 TTACAA 53 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.12 (6 / 52), avg. gap size = 1.00 (6 / 6) 458 24.14 2.59 0.00 chr1ptel1M 514156 514271 (485729) C MIR#SINE/MIR (57) 205 87 m_b14s601i27 530 chr1ptel1M 514156 TTACAAATAGCAACTCATTAGATCCTCACAGCCCTCCTGGGAGGAAAGTG 514205 vi vi vi i vvi iv v i i C MIR#SINE/MIR 205 TTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGGTAGGTA 156 chr1ptel1M 514206 TTATTATT---CCAATTTTACAGATGAGGAAACTAAGGCAGACAGAAGTT 514252 i --- v i v v i C MIR#SINE/MIR 155 CTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTT 106 chr1ptel1M 514253 AAGGGATTTGATCAGGCTC 514271 vi i vi i v C MIR#SINE/MIR 105 AAGTAACTTGCCCAAGGTC 87 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 29.50 CpG sites = 15, Kimura (unadjusted) = 29.50 Transitions / transversions = 1.15 (15/13) Gap_init rate = 0.01 (1 / 115), avg. gap size = 3.00 (3 / 1) 19 10.46 3.23 0.00 chr1ptel1M 515312 515342 (484658) (GA)n#Simple_repeat 1 32 (0) m_b14s252i14 531 chr1ptel1M 515312 GAGAG-GTGAAAGAGAGAAAGAGAGAGAGAGA 515342 - v i i (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 32 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.03 (1 / 30), avg. gap size = 1.00 (1 / 1) 43 24.41 5.49 3.23 chr1ptel1M 515652 515833 (484167) (CTTTC)n#Simple_repeat 1 186 (0) m_b14s252i15 532 chr1ptel1M 515652 CTTT-CTTTCCTTTCC--TCCCTT-CTTTCTCCTCCTCCCCCTTGCCCTC 515697 - -- i - iii -ii v i i (CTTTC)n#Simp 1 CTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCT-TTCCTTTCCTTT 49 chr1ptel1M 515698 CCTTCCATTCCCTTTCC-ACCCTTCCCTTCCCTTCTCC--TCCATTCCTT 515744 i v i -vi i i - -- v (CTTTC)n#Simp 50 CCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTT-TCCTTTCCTTTCCTT 98 chr1ptel1M 515745 CTCCTTTTCCTTCCCTTCTCCCTTACTTTCTCCTCTTTTCTCTTCTCTTC 515794 - - i - i v iii i ii ii (CTTTC)n#Simp 99 -TCC-TTTCCTTTCCTT-TCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTC 145 chr1ptel1M 515795 CCTTCTTCTCC--TCCTTTCTTTTCCCCTTCC-CTCCTTTCC 515833 i i i -- i - i -i (CTTTC)n#Simp 146 CTTTCCTTTCCTTTCCTTTCCTTT-CCTTTCCTTTCCTTTCC 186 Matrix = Unknown Transitions / transversions = 5.80 (29/5) Gap_init rate = 0.07 (13 / 181), avg. gap size = 1.23 (16 / 13) 709 23.56 7.80 2.62 chr1ptel1M 516372 516589 (483411) C MIRb#SINE/MIR (1) 267 39 m_b14s601i28 533 chr1ptel1M 516372 ATAATAATTAG-TAACATTTATAGAGCAACTGCTATGTGCTAAGTACTGT 516420 i-- - v v ivi i i i i C MIRb#SINE/MIR 267 ATAATAG--AGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGT 220 chr1ptel1M 516421 GCTAAAGCACTTTATGAATATTATCTCATTTGATCCTCAAA--------- 516461 - i iivii i v --------- C MIRb#SINE/MIR 219 GCTAA-GCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTG 171 chr1ptel1M 516462 -GAGGTAGGTGCAATTGTTATCCCTATTTTACACATAAGAAAATAGGGGA 516510 - --- i i v i i iv i v C MIRb#SINE/MIR 170 CGAGGTAGGT---ATTATTATCCCCATTTTACAGATGAGGAAACTGAGGC 124 chr1ptel1M 516511 AAATAGCAGTTAAGCAATTTGCTTAAGGCCA------TAATAAATGTCTG 516554 vv v vi i i ii i ------ i i v v C MIRb#SINE/MIR 123 TCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAG 74 chr1ptel1M 516555 TGGCTGGATTTGAATTCAAGTCTTTCTGACTTCAA 516589 v v v i ii i v i C MIRb#SINE/MIR 73 AGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAA 39 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 27.07 CpG sites = 32, Kimura (unadjusted) = 29.11 Transitions / transversions = 1.78 (32/18) Gap_init rate = 0.05 (10 / 217), avg. gap size = 2.30 (23 / 10) 316 31.58 3.47 8.48 chr1ptel1M 516459 516631 (483369) C MIR1_Amn#SINE/MIR (59) 171 7 m_b14s601i29 533 chr1ptel1M 516459 AAAGAGGTAGGTGCAATTGTTATCCCTATTTTACACATAAGAAAATAGGG 516508 i vi --- ii i v i i iv i C MIR1_Amn#SINE 171 AAGGAGGTCAGT---ATCATTATCCCCATTTTACAGATGAGGAAACTGAG 125 chr1ptel1M 516509 GAAAATAGCAGTTAAGCAATTTGCTTAAGGCCA------TAATAAATGTC 516552 v?v v vi ? ii i ii i ------?iii? i v C MIR1_Amn#SINE 124 GCNCAGAGAGGTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNAGTGGC 75 chr1ptel1M 516553 TGTGGCTGGATTTGAATTCAAGTCTTTCTGACTTCAAGATTTCCTGCCTG 516602 v v v v ? ? ii i ii --------- v i v i ii C MIR1_Amn#SINE 74 AGAGCCGGGANTNGAACCCAGGTCTCCC---------GAGTCCCAGTCCA 34 chr1ptel1M 516603 GCACTCTAATCACAGAGACTATAGCTGCC 516631 ii vi -v i i - C MIR1_Amn#SINE 33 GTGCTCTATCCAC-TAGACCACA-CTGCC 7 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 45.68 CpG sites = 34, Kimura (unadjusted) = 45.68 Transitions / transversions = 2.12 (34/16) Gap_init rate = 0.09 (15 / 172), avg. gap size = 1.33 (20 / 15) 316 35.45 0.00 2.78 chr1ptel1M 516638 516785 (483215) MIRc#SINE/MIR 11 154 (114) m_b14s601i30 534 chr1ptel1M 516638 TGATGTATAGGAGAGAGAATGACACCCGGAGTCAGAAAAAACTAAGTTTA 516687 i i vv i v iviv ii i i v ii ii MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr1ptel1M 516688 AATCCATCCTTAGACAACTAGCAGCTACATGACCAGCCTCGTCAGGTTCC 516737 i vvv iv v vi vi iii --- i v v i - v MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTACTAGCTGTGTGAC---CTTGGGCAAG-TCA 106 chr1ptel1M 516738 TTTCACCTCCATCCTTCTCAGTTCCCTCCTCTGTAGAATGGAGATGAT 516785 i v iv vvvi i v i i i MIRc#SINE/MIR 107 CTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAAT 154 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 48.12 CpG sites = 29, Kimura (unadjusted) = 49.66 Transitions / transversions = 1.32 (29/22) Gap_init rate = 0.03 (4 / 147), avg. gap size = 1.00 (4 / 4) 458 31.07 1.90 2.38 chr1ptel1M 517972 518182 (481818) MIRb#SINE/MIR 53 262 (6) m_b14s601i31 535 chr1ptel1M 517972 ACCCGAGTTTGAGTCTGGCCTCAGACACTTACT--CTCTGTGATCCCGGG 518019 i i i i iv v v v -- v i ii MIRb#SINE/MIR 53 ACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGG 102 chr1ptel1M 518020 CAAGTCACTGAACCTCTGTCTGCCTCAAGTTTTGTTAACTATAAAATTAA 518069 i v v vv - iv i v i vii MIRb#SINE/MIR 103 CAAGTTACTTAACCTCTCTGAGCCTCA-GTTTCCTCATCTGTAAAATGGG 151 chr1ptel1M 518070 -ATCAAGGCACCTGCGTCCCAAAGGTTGCAATGAGAACCAGATAACCTT- 518117 - v viii i v v i- ivi i ii i i vv v- MIRb#SINE/MIR 152 GATAATAATACCTACCTCGCAG-GGTTGTTGTGAGGATTAAATGAGATAA 200 chr1ptel1M 518118 TGTTTTTTAAAAGTTCCTTCGCCCTGTGTCCAGCACATAGTAGGTGCTTA 518167 iv v -- iv - v v v i ii i i i MIRb#SINE/MIR 201 TGCATGT--AAAGCGC-TTAGCACAGTGCCTGGCACATAGTAAGCGCTCA 247 chr1ptel1M 518168 ATCAATGCTTGTTCT 518182 v v v i MIRb#SINE/MIR 248 ATAAATGGTAGCTCT 262 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 38.56 CpG sites = 35, Kimura (unadjusted) = 41.02 Transitions / transversions = 1.21 (35/29) Gap_init rate = 0.03 (7 / 210), avg. gap size = 1.29 (9 / 7) 386 27.84 0.00 1.03 chr1ptel1M 518626 518723 (481277) C MIRb#SINE/MIR (14) 254 158 m_b15s601i1 536 chr1ptel1M 518626 CGTGTATCAAGGGCCTACTACGTGCCAGGCACAGCACTGAGCACTTGTTA 518675 i v ii v i i v ii i i vvi C MIRb#SINE/MIR 254 CATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACA 205 chr1ptel1M 518676 AAAATTAATCCTATTTAGTCCACACAACAACGCTGGAAGGCAGGTGTT 518723 viv - ii i v v vi i i C MIRb#SINE/MIR 204 TGCATT-ATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATT 158 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 32.71 CpG sites = 17, Kimura (unadjusted) = 35.99 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.01 (1 / 97), avg. gap size = 1.00 (1 / 1) 253 25.96 9.62 0.00 chr1ptel1M 518802 518905 (481095) C MIR1_Amn#SINE/MIR (82) 148 35 m_b15s601i2 537 chr1ptel1M 518802 CACTTTACAGTTGGTGGAGCTGAAGC----AGAGGTCAC-CGACTT--CC 518844 i v iv i i i ---- ? v-i -- C MIR1_Amn#SINE 148 CATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGCCC 99 chr1ptel1M 518845 GGGGTCACTCAGCTAGGGAAGATTTGAGACCAGATGGGAATCCAGG---C 518891 ii ? ?i v? iviviv v vi ?v? i --- C MIR1_Amn#SINE 98 AAGGTCACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAACCCAGGTCTC 49 chr1ptel1M 518892 CCAAGTCCCTGCCC 518905 i v i C MIR1_Amn#SINE 48 CCGAGTCCCAGTCC 35 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 33.63 CpG sites = 16, Kimura (unadjusted) = 35.24 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.04 (4 / 103), avg. gap size = 2.50 (10 / 4) 21 20.17 3.92 0.00 chr1ptel1M 519566 519616 (480384) (TC)n#Simple_repeat 1 53 (0) m_b15s252i0 538 chr1ptel1M 519566 TCTCTCTCT-TTTCTGTCTCTCTGTCTCTGTCTGTCCATCTCT-TGTGTC 519613 - i v v v v iv - v v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr1ptel1M 519614 TCT 519616 (TC)n#Simple_ 51 TCT 53 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.04 (2 / 50), avg. gap size = 1.00 (2 / 2) 186 26.67 1.64 1.64 chr1ptel1M 521117 521177 (478823) MIR3#SINE/MIR 85 145 (63) m_b15s601i3 539 chr1ptel1M 521117 TGAAACCCCGGGACAAGCCACTTGGCC-CTGTGCGCCTCAGGGTCCCTGT 521165 vi ii - i vi - v v vv iii MIR3#SINE/MIR 85 TGTGACCTTGGG-CAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCAT 133 chr1ptel1M 521166 CTGCAAAACGAG 521177 i i MIR3#SINE/MIR 134 CTGTAAAATGAG 145 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 33.98 CpG sites = 10, Kimura (unadjusted) = 33.98 Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.03 (2 / 60), avg. gap size = 1.00 (2 / 2) 201 23.53 1.96 0.00 chr1ptel1M 521127 521177 (478823) MIR1_Amn#SINE/MIR 99 150 (80) m_b15s601i4 539 chr1ptel1M 521127 GGACAAGCCACTTGGCC-CTGTGCGCCTCAGGGTCCCTGTCTGCAAAACG 521175 i i ?i - v ? vv iii i i MIR1_Amn#SINE 99 GGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATG 148 chr1ptel1M 521176 AG 521177 i MIR1_Amn#SINE 149 GG 150 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 31.25 CpG sites = 9, Kimura (unadjusted) = 31.25 Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.02 (1 / 50), avg. gap size = 1.00 (1 / 1) 11 10.27 2.70 8.57 chr1ptel1M 521969 522005 (477995) (GAGGAG)n#Simple_repeat 1 35 (0) m_b15s252i1 540 chr1ptel1M 521969 GAGGCAGGCGGAGGTGGGGGAGGGAGGAGGCAGG-GGA 522005 - v v i - - - (GAGGAG)n#Sim 1 GAGG-AGGAGGAGGAGGAGGA-GGAGGAGG-AGGAGGA 35 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.11 (4 / 36), avg. gap size = 1.00 (4 / 4) 16 14.49 6.25 2.00 chr1ptel1M 522152 522199 (477801) (GTCCTCCC)n#Simple_repeat 1 50 (0) m_b15s252i2 541 chr1ptel1M 522152 GTCCTCCCGGCCTCCC-TCCGCCCGTCC-CCGGT-GTCCCCTCCGCACCG 522198 v - v - v -v v v - (GTCCTCCC)n#S 1 GTCCTCCCGTCCTCCCGTCCTCCCGTCCTCCCGTCCTCCCGTCCTC-CCG 49 chr1ptel1M 522199 T 522199 (GTCCTCCC)n#S 50 T 50 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.09 (4 / 47), avg. gap size = 1.00 (4 / 4) 17 0.00 0.00 0.00 chr1ptel1M 522600 522618 (477382) (G)n#Simple_repeat 1 19 (0) m_b15s252i3 542 chr1ptel1M 522600 GGGGGGGGGGGGGGGGGGG 522618 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGG 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 234 22.04 1.67 1.67 chr1ptel1M 524661 524720 (475280) MIRb#SINE/MIR 114 173 (95) m_b15s601i5 543 chr1ptel1M 524661 ACCTCTGCTGA-CTCCAGCTTCCTCTTCTGTAAAATGGGCATCATGGCTT 524709 - - ii i v v v iiivi MIRb#SINE/MIR 114 ACCTCT-CTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAC 162 chr1ptel1M 524710 CGACCTTGCAG 524720 v i MIRb#SINE/MIR 163 CTACCTCGCAG 173 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 24.33 CpG sites = 8, Kimura (unadjusted) = 26.64 Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.03 (2 / 59), avg. gap size = 1.00 (2 / 2) 409 25.43 5.17 9.58 chr1ptel1M 526490 526663 (473337) MIRc#SINE/MIR 65 231 (37) m_b15s601i7 544 chr1ptel1M 526490 CTGCCCCTGCCAGTGTCTGGTAGTCGATGGGGCCATGGGACAACGGTCAC 526539 i v i v --- iv ii - v i v - -- MIRc#SINE/MIR 65 CCGGCTCTGCCACT---TACTAGCTG-TGTGACCTTGGG-CAA--GTCAC 107 chr1ptel1M 526540 TTCACTGACGCTGCCTGCTTCCGTTTCCTTGTCTGTAAAATGGGAATATC 526589 v iv- v v-- i v ii i vi MIRc#SINE/MIR 108 TTAACCT-CTCTGA--GCCTCAGTTTCCTCATCTGTAAAATGGGGATAAT 154 chr1ptel1M 526590 AAT-----CCCTACCTGC----CAGGGCTGTCATAAGAATCACATGAGAT 526630 ----- i i ---- i ii i i v MIRc#SINE/MIR 155 AATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGAT 204 chr1ptel1M 526631 AGTAACTGTAAACCTTAAAGGGCTCCGTAAATT 526663 i ivv i------ v ii i MIRc#SINE/MIR 205 AATGTATGTG------AAAGCGCTTTGTAAACT 231 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 30.81 CpG sites = 25, Kimura (unadjusted) = 31.76 Transitions / transversions = 1.67 (25/15) Gap_init rate = 0.10 (18 / 173), avg. gap size = 1.39 (25 / 18) 441 26.71 0.00 6.99 chr1ptel1M 526490 526642 (473358) MIRb#SINE/MIR 68 210 (58) m_b15s601i6 544 chr1ptel1M 526490 CTGCCCCTGCCAGTGTCTGGTAGTCGATGGGGCCATGGGACAACGGTCAC 526539 i v i v --- iv ii - v i v - -- i MIRb#SINE/MIR 68 CCGGCTCTGCCACT---TACTAGCTG-TGTGACCTTGGG-CAA--GTTAC 110 chr1ptel1M 526540 TTCACTGACGCTGCCTGCTTCCGTTTCCTTGTCTGTAAAATGGGAATATC 526589 v iv- v v-- i v ii i vi MIRb#SINE/MIR 111 TTAACCT-CTCTGA--GCCTCAGTTTCCTCATCTGTAAAATGGGGATAAT 157 chr1ptel1M 526590 AATCCCTACCTGCCAGGGCTGTCATAAGAATCACATGAGATAGTAACTGT 526639 v vv i ii i i i v i ivv MIRb#SINE/MIR 158 AATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCATGT 207 chr1ptel1M 526640 AAA 526642 MIRb#SINE/MIR 208 AAA 210 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 32.33 CpG sites = 21, Kimura (unadjusted) = 33.39 Transitions / transversions = 1.24 (21/17) Gap_init rate = 0.07 (10 / 152), avg. gap size = 1.00 (10 / 10) 16 16.57 0.00 0.00 chr1ptel1M 526689 526715 (473285) (G)n#Simple_repeat 1 27 (0) m_b15s252i4 545 chr1ptel1M 526689 GGGGAGGATGTGGGGGGGGGGGGGGGG 526715 i iv v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGG 27 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 444 23.57 2.42 7.63 chr1ptel1M 527164 527287 (472713) C MIRc#SINE/MIR (141) 127 10 m_b15s601i8 546 chr1ptel1M 527164 CTGAGGCAGTTGGAG---TTAAGTGACTTGCCCAGGGTCACACAATTAGG 527210 -- ii --- i ii v C MIRc#SINE/MIR 127 CTGAGGC--TCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGT 80 chr1ptel1M 527211 AAGTGTTAAATGTCTGAGGCCAGATTTGAACTCGGGTCCTCCTGGCTTCA 527260 vi ------- v vi i i i i i i i C MIRc#SINE/MIR 79 AAGTGGCA-------GAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCA 37 chr1ptel1M 527261 GGGCTGGTGCTGTGTCCACTGCGCTGC 527287 i v ii v v i ii C MIRc#SINE/MIR 36 AGTCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 28.21 CpG sites = 20, Kimura (unadjusted) = 29.52 Transitions / transversions = 2.86 (20/7) Gap_init rate = 0.08 (10 / 123), avg. gap size = 1.20 (12 / 10) 351 31.44 9.56 5.47 chr1ptel1M 527624 528010 (471990) C L1ME4c_3end#LINE/L1 (344) 486 85 m_b15s551i0 547 chr1ptel1M 527624 TTTCCAATTTTTTGCCACTACAGAAAGAACTGCTGTAAATAAATATATAA 527673 i i i i -- v - i --------- i C L1ME4c_3end#L 486 TTTCCAATTTTTCGCTATTATA--AATAAC-GCTGCAA---------TGA 449 chr1ptel1M 527674 ATATCTATTTATTTTTTTACAAATAAGTCATTTCCTCCCTTTTAAAAATC 527723 i -------- iv i v iv i- i i v vv i C L1ME4c_3end#L 448 ACATCT--------TCGTGCATATAGCTT-TTTCCTTCTTTTGAATTATT 408 chr1ptel1M 527724 TCTTTGGGATACAGATGTAGCCGTGGTATTGCTGACTCAAAGGATATCCA 527773 i i v vvivi vv v i iv i vv C L1ME4c_3end#L 407 TCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAA 358 chr1ptel1M 527774 TAATTTGATGACCCTAG------------------CTCGCCAGAATGGTT 527805 i v v i i v ------------------ iv i v C L1ME4c_3end#L 357 CATTTTTATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTT 308 chr1ptel1M 527806 AGGTCAGTTCCCAGCTCCACCA---CTGT-TG-GTGTCCCAATTTT-CCG 527849 ivii i iv ?iv ---v - - ? v i i- C L1ME4c_3end#L 307 GTACCAATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCACCG 258 chr1ptel1M 527850 TATCTTCTCCAGCATTTATCATTTTCCTTTTCTGTCATATGAATCAATCT 527899 i ? i v vivi v vv i vvv v vviii i C L1ME4c_3end#L 257 CANCCTCGCCAGCATTGGGTATTATCAATTTTTTAAATTTTTGCTAATTT 208 chr1ptel1M 527900 GATAGGGGTGAGATGGTGCCTCAGAGTTGTTTTTATATGCATTAATTAGA 527949 i v i i ii vv i v v vv v C L1ME4c_3end#L 207 AATAGGCGTAAAATGGTATCTCATTGTTGCTTTAATTTGCATTTCTTTGA 158 chr1ptel1M 527950 ATAT------------ATATTTTTTGATATGACTA-TAGCTAACTTTGAT 527986 v i------------ i iv i vi i- vi ?i v - C L1ME4c_3end#L 157 TTACTAGCGAGGTTGAACATTTTTCCATGTGTTTGTTTACTANTTGT-AT 109 chr1ptel1M 527987 TTCTTCCTTTGAAAACTGCCTGTT 528010 i i ? vi i i C L1ME4c_3end#L 108 TTCCTCTTNTGTGAATTGTCTGTT 85 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 41.58 CpG sites = 62, Kimura (unadjusted) = 42.55 Transitions / transversions = 1.17 (62/53) Gap_init rate = 0.08 (29 / 386), avg. gap size = 2.03 (59 / 29) 314 29.76 12.24 4.61 chr1ptel1M 527716 528099 (471901) C L1ME5_3end#LINE/L1 (529) 412 1 m_b15s551i1 547 chr1ptel1M 527716 TAAAAATCTCTTTGGGATACAGATGTAGCCGTGGTATTGCTGACTCAAAG 527765 i i i i v ivi vv i v iv v C L1ME5_3end#LI 412 TGAGAATTTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAG 363 chr1ptel1M 527766 GATATCCATA-ATTTGAT--GAC---------CC---TAGCTCGCCAGAA 527800 i v i - i i -- --------- --- v v C L1ME5_3end#LI 362 GGTATGCGTATACTTAATTTGACTAAGTACTGCCAGATTGCTCTCCAGAA 313 chr1ptel1M 527801 TGGTTAGGTCAGTTCCCAGCTCCACCA-CTGT---TG-GTGTCCCAATTT 527845 i ivii iiv vii - v --- - v i v ? C L1ME5_3end#LI 312 TGGCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATNT 263 chr1ptel1M 527846 TCC-GTATCTTCTCCAGCATTTATCATTTTCC--TTTTCTGTCATATGAA 527892 i -ii i v i i iv v --i i-- v vvi C L1ME5_3end#LI 262 CCCCACATCCTCGCCAACACTTGGCATTATCCAGCTTTCTA--ATTTTTG 215 chr1ptel1M 527893 TCAATCTGATAGGGGTGAGATGGTGCCTCAGAGTTGTTTTTATATGCAT- 527941 i i i v i ii i ii vv v v - C L1ME5_3end#LI 214 CCAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATT 165 chr1ptel1M 527942 ----TAATTA-----GAATAT--ATATTTTTTGATATGACTATAGCTAAC 527980 ---- i ----- i v --ii i i v vi i --- i C L1ME5_3end#LI 164 TCTCTGATTACTAATGAGTTTGAGCATCTCTTCATATGCTTGT---TAGC 118 chr1ptel1M 527981 TTT---GATTTCTTCCTTTGAAAACTGCCTGTTTTTTGCTAAGTGTTTTT 528027 i --- i i i i v i iv vv -------i C L1ME5_3end#LI 117 CTTTCGGGTTTCCTCTTCTGTAAATTGCCTGTTCATATC-------CTTT 75 chr1ptel1M 528028 GTTTTTGTTTTTGTT---GTTGTCGTTGCATGTCCAATTTATTGATTTAC 528074 iiiv v i i --- ?i -- v v i --- i i C L1ME5_3end#LI 74 GCCCATTTTTCTATTGGGGTTNCCGT--CTTTTTC---TTGTTGATTTGC 30 chr1ptel1M 528075 ------TCTTTCTCTATTTTATTGATGTTAA 528099 ------ i v v i -- i C L1ME5_3end#LI 29 AGGAGTTCCTTGTATATTCTA--GATATTAA 1 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 38.96 CpG sites = 69, Kimura (unadjusted) = 39.93 Transitions / transversions = 1.73 (69/40) Gap_init rate = 0.09 (35 / 383), avg. gap size = 1.89 (66 / 35) 376 30.01 14.77 0.54 chr1ptel1M 527722 528046 (471954) C L1MA4_3end#LINE/L1 (641) 406 36 m_b15s551i2 547 chr1ptel1M 527722 TCTCTTTGGGATACAGATGTAGCCGTGGTATTGCTGACTCAAAGGATA-- 527769 i v i v ivi v v iv v v i -- C L1MA4_3end#LI 406 TTTCTTTTGGATATATACCCAGCAGTGGGATTGCTGGATCATATGGTAGT 357 chr1ptel1M 527770 TCCAT----AATTTGATGA-------CCCTA--GCTCGCCAGAATGGTTA 527806 i ---- i vv ------- v -- i iv v i i i C L1MA4_3end#LI 356 TCTATTTTTAGTTTTTTGAGGAACCTCCATACTGTTTTCCATAGTGGCTG 307 chr1ptel1M 527807 GGTCAGTTCCCAGCTCCACCACTGTTG-----GTGT-CCCAATTTTCCGT 527850 viii i iv vii viiv ----- ? - vv i i C L1MA4_3end#LI 306 TACTAATTTACATTCCCACCAACAGTGTACGAGNGTTCCCCTTTCTCCGC 257 chr1ptel1M 527851 ATCTTCTCCAGCATTTATCATTTTCCTTTTCTGTCATATGAATCAATCTG 527900 i v i i i iv i i v v v? ii v i i C L1MA4_3end#LI 256 ATCCTCGCCAGCATCTGTTATTTTCTGTCTTTTTGATAANAGCCATTTTA 207 chr1ptel1M 527901 ATAGGGGTGAGATGGTGCCTCAGAGTTGTTTTTATATGCAT--------T 527942 iv i ii vv v v v -------- C L1MA4_3end#LI 206 ACTGGGGTGAGATGATATCTCATTGTGGTTTTGATTTGCATTTCCCTGAT 157 chr1ptel1M 527943 AATTAG-AATAT---ATATTTTTTGATATGACTA-TAGCTAACTTTG-AT 527986 i -i i ---ii v iv i- i i -- - C L1MA4_3end#LI 156 GATTAGTGATGTTGAGCATTTTTTCATATACCTGTTGGCCA--TTTGTAT 109 chr1ptel1M 527987 TTCTTCCTTTGAAAACTGCCTGTT------TTTTGCTAAGTGTTT----- 528025 v i i v i i ------ iv v v ?----- C L1MA4_3end#LI 108 GTCTTCTTTTGAGAAATGTCTATTCAGATCTTTTGCCCATTTTTNAATCG 59 chr1ptel1M 528026 --TTGTTTTTGTTTTTGTTGTTG 528046 -- i v v i i C L1MA4_3end#LI 58 GATTATTTGTTTTTTTGCTATTG 36 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 39.92 CpG sites = 56, Kimura (unadjusted) = 39.92 Transitions / transversions = 1.37 (56/41) Gap_init rate = 0.05 (16 / 324), avg. gap size = 3.12 (50 / 16) 16 0.00 0.00 0.00 chr1ptel1M 529127 529144 (470856) (C)n#Simple_repeat 1 18 (0) m_b15s252i5 548 chr1ptel1M 529127 CCCCCCCCCCCCCCCCCC 529144 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCC 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 16 9.26 0.00 0.00 chr1ptel1M 529572 529594 (470406) (C)n#Simple_repeat 1 23 (0) m_b15s252i6 549 chr1ptel1M 529572 CCCCCCTGCCCCCCCCCCCCCCC 529594 iv (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCC 23 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 488 31.71 8.60 1.68 chr1ptel1M 530450 530728 (469272) L3#LINE/CR1 3040 3337 (762) m_b15s601i9 550 chr1ptel1M 530450 TAGATGCATTCATGGGTGGTTTGA-GATCGTGGCTACAAAGAGTAGTCAT 530498 i v i i v vi - iii iv -- ii iv v L3#LINE/CR1 3040 TAGGTGGATTCGTAGCTGGTTGAACGACTATACC--CAAAAGGTGTTGAT 3087 chr1ptel1M 530499 TAAAGG-----------CCTGG---GAGGTGTCTTATGGAGCGCCCCGGG 530534 v ----------- --- v vi v i v i L3#LINE/CR1 3088 TAATGGATCGATGTCAACCTGGAGGGAGGTCTCTAGTGGCGTGCCACAGG 3137 chr1ptel1M 530535 ATGCC-TCGTTGGGCCTGTT---TTTGAAATTGTTTAT-AGTGGCTTGGA 530579 iiv i- v v i--- ii v - - i i L3#LINE/CR1 3138 GCTCTGTCCTTGGCCCTGTCCTGTTCAACATT-TTTATCAATGACTTGGA 3186 chr1ptel1M 530580 CAAAGGTACATCTGGGATGCAGATCAAGTTTTCAGTTGACACAGAACT-- 530627 ii ii i vvv v vv i v v i i -- L3#LINE/CR1 3187 TGAAGACATAGAAGGCATGCTTATCAAATTTGCAGATGACACAAAGCTGG 3236 chr1ptel1M 530628 GCAGGATAGCTAATGTTCTGTGTGGCAAAGTCAGCGTCTGAGAAAGATCT 530677 vi iiv? vi i i i ivi - v i ? L3#LINE/CR1 3237 GAGGGATAGCTAATACGNTGGATGACAGAATCAAGAT-TCAAAANGATCT 3285 chr1ptel1M 530678 CAA-AGACTTGAACTTTGGACCAGATTGAGCAGGGACACAAGTT-ACAAA 530725 i - i v vv i ii viv i -i iiv v - ii L3#LINE/CR1 3286 CGACAGGCTGGAACGATGGGCCGAAACCAACA-AGATGAAATTTAACAGG 3334 chr1ptel1M 530726 GAT 530728 L3#LINE/CR1 3335 GAT 3337 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 40.57 CpG sites = 52, Kimura (unadjusted) = 43.21 Transitions / transversions = 1.49 (52/35) Gap_init rate = 0.05 (14 / 278), avg. gap size = 2.07 (29 / 14) 199 29.87 5.19 0.00 chr1ptel1M 530885 530961 (469039) L3#LINE/CR1 3575 3655 (444) m_b15s601i10 550 chr1ptel1M 530885 GCCAGA--ACATGTAGACT-TTGTTCTTTGCTCTGTGAGTCACGTTG-AG 530930 i -- v i v - ivi iv i v v i i v- i L3#LINE/CR1 3575 GTCAGACCACATCTGGAGTATTGCGTTCAGTTCTGGGCGCCACATTTTAA 3624 chr1ptel1M 530931 GAAGGACATTGACATCTTGGAGGCCATCCAG 530961 i vvi vv i L3#LINE/CR1 3625 GAGGGACATTGACAAACTGGAGCGCGTCCAG 3655 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 34.61 CpG sites = 12, Kimura (unadjusted) = 38.72 Transitions / transversions = 1.09 (12/11) Gap_init rate = 0.04 (3 / 76), avg. gap size = 1.33 (4 / 3) 239 37.40 8.04 2.11 chr1ptel1M 531111 531334 (468666) L3#LINE/CR1 3838 4074 (25) m_b15s601i11 550 chr1ptel1M 531111 CAGAACCAGGAGCAGTGGGGAGCGGGGAAGGGGAGAGTCAGAGCCTGAGC 531160 i v i vi vi vv vi i-- -ii vi L3#LINE/CR1 3838 CAGAACTAGGACCAATGGGTGGAAGTTACAGGGAGG--CAGA-TTTCGGC 3884 chr1ptel1M 531161 TCTGACTGT-CGGAAGAATTCTCTGCCA---AGAACTGCCCCGAGGTAGG 531206 -- v i -v i i iv --- i i vi ii i i L3#LINE/CR1 3885 TC--AATATAAGGAAGAACTTTCTAACAATCAGAGCTGTCCAAAAATGGA 3932 chr1ptel1M 531207 ACAGTTTG-CTCAGGAGGAGGAGGACTTTCCCCCATCACAGGGTTTAAAG 531255 ii vi - i? vi v ii ii vi iiiv vv v L3#LINE/CR1 3933 ATGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGTCACTGGAGGTGTTCAAG 3982 chr1ptel1M 531256 CA-AGGTTTTAAGGTCAGTCGTTGGGGA-----CAACAAACATTTC---- 531295 - i vv v ii v i ii -----i iv iiv i ---- L3#LINE/CR1 3983 CAGAGGCTGGATGACCACTTGTCAGGGATGTTGTAGAAGGGATTCCTGCA 4032 chr1ptel1M 531296 ATGAATG---GGTTGAGCCATTAGGCCACTGAGGTCTCTCCC 531334 v i --- ii i vvv i v i i i L3#LINE/CR1 4033 TTGGATGGGAGGTTGGACTAGATGACCTCTAAGGTCCCTTCC 4074 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 53.63 CpG sites = 52, Kimura (unadjusted) = 55.73 Transitions / transversions = 1.73 (52/30) Gap_init rate = 0.05 (12 / 223), avg. gap size = 1.92 (23 / 12) 188 36.00 2.67 0.00 chr1ptel1M 532401 532475 (467525) MIRc#SINE/MIR 40 116 (152) m_b15s601i12 551 chr1ptel1M 532401 AGCCAGCAACACCTAATTCCAGCTCTTGCCCCTAACA--TGTTGACTGTG 532448 i v v iiv i iiv ii v i iv -- ii ii MIRc#SINE/MIR 40 AGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTG 89 chr1ptel1M 532449 TGATCCTGGTCATGTCATTTTACCTTT 532475 i i v v i v i MIRc#SINE/MIR 90 TGACCTTGGGCAAGTCACTTAACCTCT 116 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 47.01 CpG sites = 18, Kimura (unadjusted) = 52.68 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.01 (1 / 74), avg. gap size = 2.00 (2 / 1) 221 20.85 0.00 8.62 chr1ptel1M 532413 532475 (467525) MIR3#SINE/MIR 56 113 (95) m_b15s601i13 551 chr1ptel1M 532413 CTAATTCCAGCTCTTGCCCCTAACATGTTGACTGTGTGATCCTGGTCATG 532462 i i i - v ---- ?i i i v v MIR3#SINE/MIR 56 CTAGTCCCGGCTCT-GCCACTAAC----TNGCTGTGTGACCTTGGGCAAG 100 chr1ptel1M 532463 TCATTTTACCTTT 532475 i i i MIR3#SINE/MIR 101 TCACTTCACCTCT 113 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 23.32 CpG sites = 9, Kimura (unadjusted) = 25.76 Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.08 (5 / 62), avg. gap size = 1.00 (5 / 5) 203 29.01 7.07 6.00 chr1ptel1M 532415 532513 (467487) MIR#SINE/MIR 57 156 (106) m_b15s601i14 551 chr1ptel1M 532415 AATTCCAGCTCTTGCCCCTAACATGTTGACTGTGTGATCCTGGTCATGTC 532464 i i - v v ---- ii i i v v i MIR#SINE/MIR 57 AATCCCGGCTCT-GCCACTTAC----TAGCTGTGTGACCTTGGGCAAGTT 101 chr1ptel1M 532465 ATTTTACCTTTGAATGCCCCAAG----CAATGCTATAA---GAAGATAAT 532507 i v i vvi i iv----iv - i --- ii MIR#SINE/MIR 102 ACTTAACCTCTCTGTGCCTCAGTTTCCTCAT-CTGTAAAATGGGGATAAT 150 chr1ptel1M 532508 GATGGT 532513 i i MIR#SINE/MIR 151 AATAGT 156 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 36.61 CpG sites = 18, Kimura (unadjusted) = 38.45 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.08 (8 / 98), avg. gap size = 1.62 (13 / 8) 26 0.00 0.00 0.00 chr1ptel1M 532583 532607 (467393) (AATG)n#Simple_repeat 1 25 (0) c_b15s251i0 552 chr1ptel1M 532583 AATGAATGAATGAATGAATGAATGA 532607 (AATG)n#Simpl 1 AATGAATGAATGAATGAATGAATGA 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 223 28.33 1.67 0.00 chr1ptel1M 536686 536745 (463255) L2c_3end#LINE/L2 381 441 (37) m_b15s601i15 553 chr1ptel1M 536686 GAGCTCCTCCGGGG-AGGGGCTGGTTTTCGCCTCTCTTTGTATCCCCAGC 536734 ivi - i i vv i iiiiiv L2c_3end#LINE 381 GAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTATCCCCAGC 430 chr1ptel1M 536735 ACTTAGCACAT 536745 i i i L2c_3end#LINE 431 GCCTGGCACAT 441 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 32.57 CpG sites = 13, Kimura (unadjusted) = 38.23 Transitions / transversions = 3.25 (13/4) Gap_init rate = 0.02 (1 / 59), avg. gap size = 1.00 (1 / 1) 446 26.37 0.76 2.31 chr1ptel1M 536800 536931 (463069) C MIRc#SINE/MIR (104) 164 35 m_b15s601i16 554 chr1ptel1M 536800 GGCAGAGATCCTCCTCCAGCCCATTTTACAGATGAGGAAACTGAGGCA-A 536848 iv iv iv --- v- C MIRc#SINE/MIR 164 GGCAGGTATTATTATCC---CCATTTTACAGATGAGGAAACTGAGGCTCA 118 chr1ptel1M 536849 GCAGGATGAAATGACTTGCCCAGGCTCACTTGGCTAGGAAGTGTCTGGGG 536898 vii i v i i v vii v v v i v C MIRc#SINE/MIR 117 GAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGC 68 chr1ptel1M 536899 CTGCTCTGGAAGGCAGGAACTCCTAACTCCAGG 536931 v vv v vv vvi i i C MIRc#SINE/MIR 67 CGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 32.55 CpG sites = 14, Kimura (unadjusted) = 32.55 Transitions / transversions = 0.70 (14/20) Gap_init rate = 0.03 (4 / 131), avg. gap size = 1.00 (4 / 4) 391 27.78 0.70 4.35 chr1ptel1M 536819 536961 (463039) C MIRb#SINE/MIR (117) 151 14 m_b15s601i17 554 chr1ptel1M 536819 CCCATTTTACAGATGAGGAAACTGAGGC-AAGCAGGATGAAATGACTTGC 536867 -v vii i v i i C MIRb#SINE/MIR 151 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGC 102 chr1ptel1M 536868 CCAGGCTCACTTGGCTAGGAAGTGTCTGGGGCTGCTCTGGAAGGCAGGAA 536917 i v vii v v v i v v vvi v vv vv C MIRb#SINE/MIR 101 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTC 52 chr1ptel1M 536918 CTCCTAACTCCAGGATGCACGTAGCTTCCCGTTCTGGTGCATCA 536961 ivi i -- v v - --- v iiv i C MIRb#SINE/MIR 51 TGTCTGACTCCA--AAGCCCGT-GCT---CTTTCCACTGCACCA 14 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 34.74 CpG sites = 16, Kimura (unadjusted) = 34.74 Transitions / transversions = 0.73 (16/22) Gap_init rate = 0.05 (7 / 142), avg. gap size = 1.00 (7 / 7) 12 12.64 0.00 3.70 chr1ptel1M 538316 538343 (461657) (TGGA)n#Simple_repeat 1 27 (0) m_b15s252i7 555 chr1ptel1M 538316 TGGCTGGATTGGATCGATGTATGGATGG 538343 v - v v (TGGA)n#Simpl 1 TGGATGGA-TGGATGGATGGATGGATGG 27 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 188 35.77 5.15 2.00 chr1ptel1M 538782 538878 (461122) L2d2_3end#LINE/L2 446 545 (10) m_b15s601i18 553 chr1ptel1M 538782 CTCCTGCAGGGTGGTGATTAA----TATAGGCCTTTTTAGGTACCCC-CA 538826 vv ii v ii v---- -- i i ivi v - L2d2_3end#LIN 446 CTCCTTGAGGGCAGGGACCATGTCTTATA--CTTCTTTGTATCCCCCACA 493 chr1ptel1M 538827 GCAATCATCCCAGTGCCTGGCACATGACCGGTGCTTAATCAATGGTGACT 538876 ivii v v v iiiiv i i v iv vii L2d2_3end#LIN 494 GCGCCTAGCACAGTGCCTTGCACACAGTAGGCGCTCAATAAATATTTGTT 543 chr1ptel1M 538877 GA 538878 L2d2_3end#LIN 544 GA 545 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 46.54 CpG sites = 20, Kimura (unadjusted) = 50.74 Transitions / transversions = 1.43 (20/14) Gap_init rate = 0.04 (4 / 96), avg. gap size = 1.75 (7 / 4) 212 32.79 0.00 0.00 chr1ptel1M 538818 538878 (461122) L2a_3end#LINE/L2 447 507 (10) m_b15s601i19 553 chr1ptel1M 538818 GTACCCCCAGCAATCATCCCAGTGCCTGGCACATGACCGGTGCTTAATCA 538867 i ivii vvv iiiv i i v L2a_3end#LINE 447 GTATCCCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGGCGCTCAATAA 496 chr1ptel1M 538868 ATGGTGACTGA 538878 iv vii L2a_3end#LINE 497 ATATTTGTTGA 507 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 38.93 CpG sites = 12, Kimura (unadjusted) = 44.78 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 435 32.20 5.25 3.32 chr1ptel1M 539456 540046 (459954) L1M5_orf2#LINE/L1 865 1466 (1828) m_b15s551i3 556 chr1ptel1M 539456 GATGTAGCCGAAGAAATACTCAGGGGAAATTTTATATGTCTAATTGTTTA 539505 i ii v i i i i i v vv?i v i? L1M5_orf2#LIN 865 GATGCAGCTAAAGCAGTGCTTAGAGGGAAATTTATAGCNTTAAATGCNTA 914 chr1ptel1M 539506 CATCAGTAAAACAGAAAAAGGC---AGATCAATGAATTGAGTGTGCAAAT 539552 i i v iv -- --- i vi i iv v vv L1M5_orf2#LIN 915 TATTAGAAAAGAAGAAA--GGCTTAAAATCAATGATCTAAGCTTCCACCT 962 chr1ptel1M 539553 AAAAAAAAAACTAGAAAAAGAA---CAAATTTAAAACTCCCAATTAAACA 539599 v i i--- --- -- - v v? ii L1M5_orf2#LIN 963 TAAGAAG---CTAGAAAAAGAAGAGCAAATT--AAAC-CCAAAGNAAGTA 1006 chr1ptel1M 539600 TCAAATTATAAATCCTGAAAAATCAAAGGAGAGACTGATAAAATTGAAAT 539649 vv iivviv vv - i v i v i iii i v v L1M5_orf2#LIN 1007 GAAGGAAGGAAATAAT-AAAGATAAGAGCAGAAATCAATGAAATAGAAAA 1055 chr1ptel1M 539650 CAAGAAAATCATTGAACTAACAAATAAAACCAGAAGCTGGTTTTATGAGG 539699 i? ? iv v ivv iv ii i i i v --- L1M5_orf2#LIN 1056 CAAANANACAATAGAGAAAATCAACGAAGCCAAAAGCTGGTTCTTT---G 1102 chr1ptel1M 539700 AAAAACTCAATAAAATAAATAAACCTTTGTTTAATTTGATTTTTAGAAGG 539749 iv vi i ivi? ivi -- iv ii L1M5_orf2#LIN 1103 AAAAGATCAATAAAATTGATAAACCTCTAGCNAGACTGA--TCAAGAAAA 1150 chr1ptel1M 539750 AAAGAAGGAA---ACGAGT------TATCAAAAATGAAAGTGATGAACTC 539790 ii --- i i ------ ii iv iv vv L1M5_orf2#LIN 1151 AAAGAGAGAAGACACAAATTACCAATATCAGGAATGAAAAAGGAGACATC 1200 chr1ptel1M 539791 GCCATCAATGAAAAGGAAATTAAGACAATTGTTAGGAGCTATTTTATCCA 539840 i i ivi vvv vi v i vi vi v iiiv v ivv L1M5_orf2#LIN 1201 ACTACAGATCCTACAGACATTAAAAGGATAATAAGAGAATATTATGAACA 1250 chr1ptel1M 539841 GTTATAGGCCAACAAACTCAGCAATCTAAATGAAATGGATAAA-TATTTA 539889 ii v v i i iii? ii i i - vi i L1M5_orf2#LIN 1251 ACTTTATGCCAATAAATTTGANAACTTAGATGAAATGGACAAATTCCTTG 1300 chr1ptel1M 539890 CAAAATATAAATAATGCATATTAACAGAAGAAGAAATA---------AAT 539930 v i i ? v ivv v i i ?v --------- L1M5_orf2#LIN 1301 AAAAACACAANTTACCAAAACTGACNCAAGAAGAAATAGAAAATCTGAAT 1350 chr1ptel1M 539931 TACCCAAT-TTTAGAAAAAAGAAATTGAGCAATTCATCAGTGA----CTA 539975 vi v - i v--v --- ii v v i ---- v L1M5_orf2#LIN 1351 AGCCCTATATCTAT--TAAAGAAATTG---AATTTGTAATTAAAAACCTT 1395 chr1ptel1M 539976 CCTAGGGAAAAAATCCCCAGGATTAAATGGATTCACAAGCAAATTATACC 540025 i vii i - i vii i v vi ii v L1M5_orf2#LIN 1396 CCCACAAAGAAAA-CTCCAGGCCCAGATGGCTTCACTGGTGAATTCTACC 1444 chr1ptel1M 540026 -AATTTTTAGAGAAGAATTAAT 540046 - iv ii v L1M5_orf2#LIN 1445 AAACATTTAAGGAAGAAATAAT 1466 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 44.11 CpG sites = 107, Kimura (unadjusted) = 44.48 Transitions / transversions = 1.39 (107/77) Gap_init rate = 0.05 (29 / 590), avg. gap size = 1.76 (51 / 29) 1080 31.70 7.31 1.01 chr1ptel1M 540082 540916 (459084) L1M5_orf2#LINE/L1 1635 2521 (773) m_b15s551i4 556 chr1ptel1M 540082 AATATTAGTGATGAGATTTCAGCAAGATACTACAAGGATCAAATACTTTG 540131 ii vvv v i v iv v v v i iiv L1M5_orf2#LIN 1635 AATATTAGCAAATCGAATCCAGCAATATATAAAAAGGATAATACATCATG 1684 chr1ptel1M 540132 CTCAGGTAGAATTTATACCAGAAATGCAGGACTGGTTCAATACTAGGAAA 540181 vi i i ii v i i ii i i i v i L1M5_orf2#LIN 1685 ACCAAGTGGGGTTTATCCCAGGAATGCAAGGTTGGTTTAACATTCGAAAA 1734 chr1ptel1M 540182 ---ACCATTATATTTGACCACATCAATAGCAAGACCAATAGGAATCATAT 540228 --- i v i v v i i i v vi vvi v ii L1M5_orf2#LIN 1735 TCAATCAATGTAATTCACCATATTAACAGAATAAAGGAGAAAAATCATAT 1784 chr1ptel1M 540229 GATTATCTCAATA--TGCAGGAAAAGCCTTTGACAAAATACAGCCCCCAT 540276 i -- i v v i v L1M5_orf2#LIN 1785 GATCATCTCAATAGATGCAGAAAAAGCATTTGACAAAATTCAACACCCAT 1834 chr1ptel1M 540277 TCCTATTGAAAACATTAGAGAGAATAGGAATAAATGGAGTTTTCCTTAAA 540326 v iv i vi viiv i v i v iivi i v L1M5_orf2#LIN 1835 TCATGATAAAAACTCTCAGCAAACTAGGAATAGAAGGGAACTTCCTCAAC 1884 chr1ptel1M 540327 AT-ATACAGTAGCATCTATATAAAGCCATCAGCAATCATTATATGTAATG 540375 v - v -i iiv i vv ? v i iv L1M5_orf2#LIN 1885 CTGATAAAG-GGCATCTACGAAAAACCTACAGCNAACATCATACTTAATG 1933 chr1ptel1M 540376 GGAAGAAGCTAAAAGCATTCCTAATAAAATCAGGGGTGAAACAAGAGTG- 540424 vi i ?i i ? v ivv i i iiii i ii - L1M5_orf2#LIN 1934 GTGAAANACTGAANGCTTTCCCCCTAAGATCGGGAACAAGACAAGGATGT 1983 chr1ptel1M 540425 ---------------CTATTCAATATTGTACTGGAAATGTTAGCGCTAGC 540459 --------------- i ii vi vvvv L1M5_orf2#LIN 1984 CCGCTNTCACCACTTCTATTCAACATTGTACTGGAGGTCCTAGCCAGTGC 2033 chr1ptel1M 540460 AATCAGAGAAGAAAAA-----TAAAGGAATTAAAATAGGCAATGAGGAAA 540504 v iv -----v v v i v v v i L1M5_orf2#LIN 2034 AATAAGGCAAGAAAAAGAAATAAAAGGCATAAAGATTGGAAAGGAAGAAA 2083 chr1ptel1M 540505 CAAAACGATCACTCTTTGTAGATGATACGATGCTAT-------AATTACT 540547 i vi ?i v i i i i vv ? ------- v v ? L1M5_orf2#LIN 2084 TAAAACTGTCNTTATTCGCAGATGACATGATTGTNTACGTAGAAAATCCN 2133 chr1ptel1M 540548 AAAAAATATAT-TTGAAATTATTTAAA----------ATTTTAGCAAAGT 540586 i v i-vv? i i vi ---------- v i L1M5_orf2#LIN 2134 AAAGAATCTACAAANAAACTACTAGAACTAATAAGTGAATTTAGCAAGGT 2183 chr1ptel1M 540587 TGAAGGATACAAAACAAACTCACATAAATCATCAGTATCTATATATTTCT 540636 i v? iiiv ivi v viv i v - v L1M5_orf2#LIN 2184 CGCNGGATACAAGGTCAATATACAAAAATCAATTGTATTTCTATA-TACT 2232 chr1ptel1M 540637 ATTTCTACAAGGCCCAGCAGCAAAAGA----TAGAGA--AATTCCATTCA 540680 --v v i-- v vii v v ---- ?i i -- v i L1M5_orf2#LIN 2233 A--GCAACAAA--CAATTGGAAAATGAAATTTNAAAAACAATACCATTTA 2278 chr1ptel1M 540681 AAATAGCTGTAGACAATATTAAATACTTGGGAGTCTACCTGCCACCACAA 540730 v vvi i v i ? i i vv i iv vv ? v L1M5_orf2#LIN 2279 CAATAGCATCAAAAAACATNAAATACTTAGGAATAAATCTAACAAAANAT 2328 chr1ptel1M 540731 ACCCAGAAACTATA---TGAATACAGTTATAAAATGCTTTTGC-ACAAAT 540776 iiv ii v ? --- v --- i iii vi v- v L1M5_orf2#LIN 2329 GTGCAAGACCTNTACACTGAAAAC---TACAAAACATTGCTGAGAGAAAT 2375 chr1ptel1M 540777 AAAGTCAGATCTAAATAAATGGGAAAATATCCATTGCTAATGTGTAGATC 540826 v ivv i ii i v vv i v vi v ivv L1M5_orf2#LIN 2376 TAAAGAAGACCTAAATAAATGGAGAGATATACCATGTTCATGGATTGGAA 2425 chr1ptel1M 540827 AAATCAACATAATAAAAATGATAATTCTACTT--GTTAATCT----TTTC 540870 i v i vi ? i vi v ii--i i ----v L1M5_orf2#LIN 2426 GACTCAATATTGTNAAGATGTCAATTCTCCCCAAATTGATCTATAGATTC 2475 chr1ptel1M 540871 AGTAATATACCAATCAAATTTTCAAAAAATTATTTTCTAAAGTTTG 540916 i ivv v v ii iv ii v v i iv L1M5_orf2#LIN 2476 AATGCAATCCCAATCAAAATCCCAGCAGGTTTTTTTGTAGAAATTG 2521 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 42.10 CpG sites = 139, Kimura (unadjusted) = 42.99 Transitions / transversions = 1.13 (139/123) Gap_init rate = 0.03 (24 / 834), avg. gap size = 2.92 (70 / 24) 232 23.19 4.60 5.81 chr1ptel1M 542042 542128 (457872) L1ME4b_3end#LINE/L1 181 266 (626) m_b15s551i5 556 chr1ptel1M 542042 ACTCTGAGGTACCACTTTACACCTATCAGATTGATTAATATAACAAAAA- 542090 v i i v iiv v -- - L1ME4b_3end#L 181 ACACTGAGATACCATTTTTCACCTATCAGATTGGCAAAGAT--CAAAAAG 228 chr1ptel1M 542091 ---AGGAAAATGTTGATTGTTGGAAGGGGATGTGGGAAAAC 542128 ---iiv v iii -- -v i i i L1ME4b_3end#L 229 TTTGATAACACACTG--TGTTGG-CGAGGGTGTGGGGAAAC 266 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 28.42 CpG sites = 12, Kimura (unadjusted) = 28.42 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.08 (7 / 86), avg. gap size = 1.29 (9 / 7) 17 8.91 0.00 0.00 chr1ptel1M 542140 542163 (457837) (T)n#Simple_repeat 1 24 (0) m_b15s252i8 557 chr1ptel1M 542140 TTTTTTTTGTTTTTTTGTTTTTTT 542163 v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTT 24 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 27 30.19 1.61 3.28 chr1ptel1M 542141 542264 (457736) (TTTA)n#Simple_repeat 1 122 (0) m_b15s252i9 557 chr1ptel1M 542141 TTTTTTTGTTTTTTTGTTTTTTTCAGTTAATGAATTCATTTATTCATTCA 542190 v i v i v - - v vv i i i (TTTA)n#Simpl 1 TTTATTTATTTATTTATTTATTT-A-TTTATTTATTTATTTATTTATTTA 48 chr1ptel1M 542191 TTTGTTCAATTCTTTAGAATAGGTCTGAATTACTTTATTTTTTTATTTTT 542240 i i v v -vv vv v vv vv v v (TTTA)n#Simpl 49 TTTATTTATTTATTTA-TTTATTTATTTATTTATTTATTTATTTATTTAT 97 chr1ptel1M 542241 TTA-TTATTATAGTAACTT-TTTATT 542264 - - v v i - (TTTA)n#Simpl 98 TTATTTATT-TATTTATTTATTTATT 122 Matrix = Unknown Transitions / transversions = 0.38 (8/21) Gap_init rate = 0.05 (6 / 123), avg. gap size = 1.00 (6 / 6) 12 11.95 0.00 6.90 chr1ptel1M 542220 542250 (457750) (TTATT)n#Simple_repeat 1 29 (0) m_b15s252i10 558 chr1ptel1M 542220 TTACTTTATTTTTTTATTTTTTTATTATTAT 542250 i v - v - (TTATT)n#Simp 1 TTATTTTATTTTATT-TTATTTTATT-TTAT 29 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2) 17 8.91 0.00 0.00 chr1ptel1M 542140 542163 (457837) (T)n#Simple_repeat 1 24 (0) m_b15s252i8 557 chr1ptel1M 542140 TTTTTTTTGTTTTTTTGTTTTTTT 542163 v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTT 24 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 27 30.19 1.61 3.28 chr1ptel1M 542141 542264 (457736) (TTTA)n#Simple_repeat 1 122 (0) m_b15s252i9 557 chr1ptel1M 542141 TTTTTTTGTTTTTTTGTTTTTTTCAGTTAATGAATTCATTTATTCATTCA 542190 v i v i v - - v vv i i i (TTTA)n#Simpl 1 TTTATTTATTTATTTATTTATTT-A-TTTATTTATTTATTTATTTATTTA 48 chr1ptel1M 542191 TTTGTTCAATTCTTTAGAATAGGTCTGAATTACTTTATTTTTTTATTTTT 542240 i i v v -vv vv v vv vv v v (TTTA)n#Simpl 49 TTTATTTATTTATTTA-TTTATTTATTTATTTATTTATTTATTTATTTAT 97 chr1ptel1M 542241 TTA-TTATTATAGTAACTT-TTTATT 542264 - - v v i - (TTTA)n#Simpl 98 TTATTTATT-TATTTATTTATTTATT 122 Matrix = Unknown Transitions / transversions = 0.38 (8/21) Gap_init rate = 0.05 (6 / 123), avg. gap size = 1.00 (6 / 6) 12 9.24 0.00 4.17 chr1ptel1M 542333 542357 (457643) (TCCC)n#Simple_repeat 1 24 (0) m_b15s252i11 559 chr1ptel1M 542333 TCCCTCCCACCCTCCACCCCCTCCC 542357 v - i (TCCC)n#Simpl 1 TCCCTCCCTCCCTCC-CTCCCTCCC 24 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 1623 30.96 0.95 0.63 chr1ptel1M 542672 543305 (456695) C L1ME4c_3end#LINE/L1 (191) 639 4 m_b15s551i6 560 chr1ptel1M 542672 TTCTGCTCATTTCACTTAGCATCAGTTCATGTAATTCTCTCCAAGCTTCT 542721 iv i i vv i- ivi i v i v C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATA-AACATTTTCCATGTTGCT 591 chr1ptel1M 542722 CTGTATTCATCTTGCTGGTCATTTCTTACAGAACAATAATATTCTATAAC 542771 vii v v v iv vi i v ii vvvv i viv C L1ME4c_3end#L 590 ACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCGA 541 chr1ptel1M 542772 ATTCATATACCACAATTTACCCAACCATTCTTCAATTCATGGGCATCCAC 542821 i ?v i i ii ii v vv i ii v C L1ME4c_3end#L 540 GTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAG 491 chr1ptel1M 542822 TCAGTTTCCGGCTTCTAGCCACTACAAACAGGGCTGCCACAAACATTTTG 542871 viv iii i v i i i i iv v ii i v C L1ME4c_3end#L 490 GTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTC 441 chr1ptel1M 542872 GCACATACTGGTCCCTTTCCCTTCTTT---AGTATCTCCTTGGGGTATAA 542918 ii iv --- i i --- v i i i v v C L1ME4c_3end#L 440 GTGCATATAG---CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAAT 394 chr1ptel1M 542919 GCCCAGTAGAAACACTGCTGGATCAAAGGGTATGCACAGTTTGATAATTT 542968 v v viiv i i i v v v iii i C L1ME4c_3end#L 393 TCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTC 344 chr1ptel1M 542969 TTGGGGCATAATTCCAGATTGCAA-CCAGAATGGTCGGATTCTTTCACAG 543017 ivi i v v i vv- i v i v iivv i ? C L1ME4c_3end#L 343 TTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACAN 294 chr1ptel1M 543018 CTCCACCAACAATGTATCAGTGTCCCAGTTTTCCCGCATCCCCTCCAACA 543067 iv i v ? v iv ? i v i C L1ME4c_3end#L 293 TGCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGCA 244 chr1ptel1M 543068 ATCATCATTATTTTTTCCTGTCATCTTAGCCAATCTGACAGGTGTGTAGT 543117 v vivi ivv ii vvv i v i i i i i iv i C L1ME4c_3end#L 243 TTGGGTATTATCAATTTTTTAAATTTTTGCTAATTTAATAGGCGTAAAAT 194 chr1ptel1M 543118 GGTATCTCAGAGTTGTCTTAATTTGCATTTCTCTGATTAATAATGATTTG 543167 vv ii i v ii vv v C L1ME4c_3end#L 193 GGTATCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACTAGCGAGGTT 144 chr1ptel1M 543168 GAACACTCTTTCATATGAGTGGTAATGATTTCAATTTCATCATCTGAAAA 543217 i i i i vv v v iv ? vv v v ? vi C L1ME4c_3end#L 143 GAACATTTTTCCATGTGTTTGTTTACTANTTGTATTTCCTCTTNTGTGAA 94 chr1ptel1M 543218 TTGTCTGTTCATATCCTTTGACCATTTATCAATTGGAGAATGGCTTGGTT 543267 i v v i vv v v ?vv C L1ME4c_3end#L 93 TTGTCTGTTCATGTCCTTTGCCCATTTATCTATTGGGGTCTTGATNTTTT 44 chr1ptel1M 543268 GCTTATAAATT--AGTCAGTTCTCTATATATTTTGGAAAT 543305 v v -- i v i i ? v?i v C L1ME4c_3end#L 43 TCTTATCAATTTGAATGAGCTCTTTATATANTANAGATAT 4 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 40.29 CpG sites = 101, Kimura (unadjusted) = 41.39 Transitions / transversions = 1.07 (101/94) Gap_init rate = 0.01 (7 / 633), avg. gap size = 1.43 (10 / 7) 512 31.50 1.09 0.36 chr1ptel1M 543161 543434 (456566) C L1M2_orf2#LINE/L1 (0) 3291 3016 m_b15s551i7 560 chr1ptel1M 543161 TGATTTGGAACACTCTTTCATATGAGTGGTAATGATTTCAATTTCATCAT 543210 v v i i i ivv v iiiv vv v v v C L1M2_orf2#LIN 3291 TGATGTTGAGCATTTTTTCATATACCTGTTGGCCATTTGTATGTCTTCTT 3242 chr1ptel1M 543211 CTGAAAATTGTCTGTTCATATCCTTTGACCATTTATCAATTGGAGAATG- 543259 i i v i vi v v ? i vv v- C L1M2_orf2#LIN 3241 TTGAGAAATGTCTATTCAGGTCCTTTGCCCATTTTTNAATCGGATTATTT 3192 chr1ptel1M 543260 GCTTGGTTGCTTATAAATTAGTC-AGTTCTCTATATATTTTGGAAATGAG 543308 i vv vv i i iv i- ii i v v i C L1M2_orf2#LIN 3191 GTTTTTTTGCTGTTGAGTTGTTTGAGTTCCTTATATATTCTGGATATTAA 3142 chr1ptel1M 543309 GCCTTTATCAGAACCTTTAACTGTGAAGATGTTTTCCCAGTTTGTTGCTT 543358 v i i vv?v vivi ii v v i v i v v C L1M2_orf2#LIN 3141 TCCCTTGTCAGATGNATAGTTTGCAAATATTTTCTCCCATTCTGTAGGTT 3092 chr1ptel1M 543359 CCCTTCTAATCTTGTTTAC-ATTAGTTTTGTTTGTACAGAAGCTTTTTAA 543407 vi ii v iii v i-i vvi i - i i C L1M2_orf2#LIN 3091 GTCTCTTCACTCTGTTGATTGTTTCCTTTGCT-GTGCAGAAGCTTTTTAG 3043 chr1ptel1M 543408 TTTGATGTAATCAAAATTTTCTATTTT 543434 vv v v C L1M2_orf2#LIN 3042 TTTGATGTAATCCCATTTGTCTATTTT 3016 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 41.08 CpG sites = 41, Kimura (unadjusted) = 41.71 Transitions / transversions = 0.91 (41/45) Gap_init rate = 0.01 (4 / 273), avg. gap size = 1.00 (4 / 4) 308 36.59 6.56 1.85 chr1ptel1M 543494 543752 (456248) L1ME3Cz_3end#LINE/L1 270 540 (457) m_b15s551i8 561 chr1ptel1M 543494 CTAATGCATTGTTGATGGAACTGTGAACTGATTCAAGCATCT----GAG- 543538 v i i i i i v i i i v v ii ---- - L1ME3Cz_3end# 270 CTCATACACTGCTGGTGGGAGTGTAAATTGGTACAACCACTTTGGAGAGC 319 chr1ptel1M 543539 ---------ATGTCCAA-AGAGTTATAAAGCTATGTACACCCTTTAATAC 543578 --------- i i i- i i-- v ii i i vii iv L1ME3Cz_3end# 320 AATTTGGCAATATCTAGTAAAGTTG--AAGATGCGCATACCCTACGACCC 367 chr1ptel1M 543579 AGCAATACTACCGCTAGGTCCATCTCCCAACGATATTCCAAAAAAGGGGG 543628 v i iv vi vi i iv v i iviv v v v v L1ME3Cz_3end# 368 AGCAATTCCACTTCTAGGTATATACCCTAGAGAAACTCTCGCACATGTGC 417 chr1ptel1M 543629 A-AGGGATCTAATTGTACACAAAAAGTTAT-ATAGTTATTTTCTGTGGTG 543676 - i vvi -- vii viv i -ii i- v i ii i L1ME3Cz_3end# 418 ACAAGGAGACA--TGTACAAGGATGTTCATTGCAGC-ATTGTTTGTAATA 464 chr1ptel1M 543677 CCAAAAAACTGGAAATTGAAGGGATGCCCATCAATAGGTGAATGGCTAAA 543726 v i i ivivvvii i v v L1ME3Cz_3end# 465 GCGAAAAATTGGAAACAACCTAAATGTCCATCAATAGGGGAATGGATAAA 514 chr1ptel1M 543727 CGAGCTGTGGTGAATGATTATAATGG 543752 ii ii iv vvv i L1ME3Cz_3end# 515 TAAATTGTGGTATATTCATACAATGG 540 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 49.54 CpG sites = 57, Kimura (unadjusted) = 52.98 Transitions / transversions = 1.58 (57/36) Gap_init rate = 0.04 (11 / 258), avg. gap size = 2.00 (22 / 11) 372 36.91 4.92 4.19 chr1ptel1M 543758 544184 (455816) C L3#LINE/CR1 (2760) 1339 910 m_b15s601i20 562 chr1ptel1M 543758 TTCGCCTCCTTACATTAAAATCTGAAGCCCCCTTT--TTAAAATCCATCT 543805 ii iii i v ii?v -- vv i vi C L3#LINE/CR1 1339 TTTACCTCCTTGTGTTAAAATTTCAAGTTNACTTTNTTTATTACCCATAC 1290 chr1ptel1M 543806 TTTGTAGAT--GTATGGATAGACATGGAGAAAGATGAGTTTTATTACTAG 543853 i iv -- -- vviiiivv i v i v C L3#LINE/CR1 1289 TCTGTGCATTGGTAT--ATAGACATCTGAGGCCATAAGTATTGTTTCTAG 1242 chr1ptel1M 543854 CTTCTTTCTTGGACTTTAATAGTTTTTTGAAATT-CT--GTATGT-TTCA 543899 iii? --- v vvi ii v?i - -- i iv -i v C L3#LINE/CR1 1241 CTTCTTTTCCNG---TTATTTTCTCCTGNGAATTACTGGGCACCTCCTCC 1195 chr1ptel1M 543900 GCTGCCATTATTCTTTCTACA--ATGCC-GCTGCTCTCTACAGTAGCC-- 543944 i iii v ii-- i - ? iii i i v -- C L3#LINE/CR1 1194 ACTGTTGTTCTTCTTTCTATGTCATACCTGNTATCCTCCATAGTATCCGG 1145 chr1ptel1M 543945 CTTCACTGGACAGACATGAGAAGTTCGTCCCTCCTCTTTTGCATCTTATT 543994 i i -i vivv iv i v v iv ii iii ii iiv i i v C L3#LINE/CR1 1144 TTTTAC-AGTTTTATCTGGGCATTTTTTTTCCTTTCCCTCAAATTTCAGT 1096 chr1ptel1M 543995 TTCAAGTCATTTTGATTTAATTTGTGAAACACAAGGCAACCATATCCCTA 544044 v v i ivii iv i iv v v? ? v ii i i - C L3#LINE/CR1 1095 TTAAAGTCCTCTTGATCAGGTCGGCGAGTCTCCNGNCAAACACGTTCTT- 1047 chr1ptel1M 544045 AGGAACCCTCATCTC--TTAGGTGCTCTCCATCCCTGGCCAGAAACCTGT 544092 ------ ivi i-- v i v i ? i i ii C L3#LINE/CR1 1046 ------CCCGGTCTTCGTGAGATGCACTCCGTCCCTNGCCAGGAGCCCAT 1003 chr1ptel1M 544093 TATTCACAAATTTTTAAAGAGAATGGTCTAAGATTCCAGATAATCATTCT 544142 ii vviv i? -- -vv i ii vv i vv -i C L3#LINE/CR1 1002 CGTTCTGGTATCNT--AAG-CCATGGTCCAGAAAACCAAATCCT-GTTCT 957 chr1ptel1M 544143 CATATGTCATCTTTTTCGCCCA------ACTGCCCAAATCTTGCCTTT 544184 ivv iii viv v vi------ v v i - C L3#LINE/CR1 956 TCGACACCATCTACGTAGCCAGCTGTTCACTTCCCATATCCT-CCTTT 910 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 51.57 CpG sites = 94, Kimura (unadjusted) = 55.57 Transitions / transversions = 1.65 (94/57) Gap_init rate = 0.07 (28 / 426), avg. gap size = 1.39 (39 / 28) 16 15.91 0.00 0.00 chr1ptel1M 545173 545200 (454800) (T)n#Simple_repeat 1 28 (0) m_b15s252i12 563 chr1ptel1M 545173 TTCTTTTTTCTATTGTTTTTTTTTTTTT 545200 i i v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 28 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 639 24.10 0.00 8.59 chr1ptel1M 546238 546414 (453586) MIR#SINE/MIR 76 238 (24) m_b15s601i21 564 chr1ptel1M 546238 ACCAGCTGTGTGATCCTGGGCAAGCCACTTAGGCTCCGTTTGCCGCAGTT 546287 i i i ii iv iv v v MIR#SINE/MIR 76 ACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTT 125 chr1ptel1M 546288 TTTTCAACTGTAAAATGCAGATAATTCTAGGGCACCTGCCTCATAGGGTT 546337 ii v vi vv -- i i MIR#SINE/MIR 126 TCCTCATCTGTAAAATGGGGATAATAATA--GTACCTACCTCATAGGGTT 173 chr1ptel1M 546338 GCTGGGAGAATCAAAGGAGATAACCCTGGTAAAGTACGCAGTTAGGTTAG 546387 i v i i v v iv vv ii ---- ivi MIR#SINE/MIR 174 GTTGTGAGGATTAAATGAGTTAATACATGTAAAGCGC----TTAGAACAG 219 chr1ptel1M 546388 GGTCAGGGAGACTAGCACATAGTAGGC 546414 v i-------- i i MIR#SINE/MIR 220 TGC--------CTGGCACATAGTAAGC 238 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 28.41 CpG sites = 23, Kimura (unadjusted) = 29.40 Transitions / transversions = 1.44 (23/16) Gap_init rate = 0.08 (14 / 176), avg. gap size = 1.00 (14 / 14) 241 33.61 1.44 3.68 chr1ptel1M 547122 547260 (452740) L1ME3F_3end#LINE/L1 433 568 (422) m_b15s551i9 565 chr1ptel1M 547122 TGAACAAGAGTATTTACGGCAGCTCTTTTC-TCAGAGCAAAGAACTGGAA 547170 v i i i ii v v - v v i L1ME3F_3end#L 433 TGTACAAGAATGTTCATAGCAGCACTGTTCGTAATAGCAAAAAACTGGAA 482 chr1ptel1M 547171 GCGGAGGGGACGGATGCCCGTCTGTTGGGGAAGGGCCGGATAAATCGTGG 547220 i iivv---- ii i i viiv i v viii i L1ME3F_3end#L 483 ACAACC----CAAATGTCCATCGACAGGAGAATGGATAAATAAATTGTGG 528 chr1ptel1M 547221 TGTGTGATTGTGAGGGAATATTTTGT-GCCGTGAGAAATGA 547260 i i vvviiii v v ii- v - L1ME3F_3end#L 529 TATATTCACACAATGGAATATTATACAGCAGTGA-AAATGA 568 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 46.67 CpG sites = 28, Kimura (unadjusted) = 46.67 Transitions / transversions = 1.65 (28/17) Gap_init rate = 0.05 (7 / 138), avg. gap size = 1.00 (7 / 7) 14 26.88 1.25 6.58 chr1ptel1M 548108 548187 (451813) (GGAGGGG)n#Simple_repeat 1 76 (0) m_b15s252i13 566 chr1ptel1M 548108 GGAGGCGGGAGTGGGCAGCACCGGGGAGGGGGGAGGGAGGA-GCAGCAGC 548156 v - -- v vv i - vi v - (GGAGGGG)n#Si 1 GGAGGGGGGAG-GGG--GGAGGGGGGAGGGGGGAGGGGGGAGGGGGGAG- 46 chr1ptel1M 548157 CAGAGAGCCTGGTGGGGGGGGGGGCGGAGGG 548187 vi i vvv v i - (GGAGGGG)n#Si 47 GGGGGAGGGGGGAGGGGGGAGGGG-GGAGGG 76 Matrix = Unknown Transitions / transversions = 0.45 (5/11) Gap_init rate = 0.08 (6 / 79), avg. gap size = 1.00 (6 / 6) 73 16.30 3.30 3.30 chr1ptel1M 550691 550872 (449128) (TCTCTG)n#Simple_repeat 1 182 (0) m_b15s252i14 567 chr1ptel1M 550691 TCTCCCTCTCTGTGTCTGCCTCTCTCCCTCTCTCTGTGTCTG-C-CTCTC 550738 iv v i v i v v - - v (TCTCTG)n#Sim 1 TCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTC 50 chr1ptel1M 550739 TTTCTCTGTGTCTCTGTCTCTGTCTC--CCTCTCTCTCCGTCTCTCCCTC 550786 i v v --i v i vi (TCTCTG)n#Sim 51 TCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTC 100 chr1ptel1M 550787 TG-C-CTGTCTCTGTCTGTACATCTCTGTATCTGTCTGTCCGTCTCTGTC 550834 - - v --i v -- i (TCTCTG)n#Sim 101 TGTCTCTGTCTCTGTCTCT--GTCTCTGTCTCTGTC--TCTGTCTCTGTC 146 chr1ptel1M 550835 TCTGTCTGTCCGTCTCTGTCTCTCTCTCTCTCTCTCTC 550872 -- i v v v (TCTCTG)n#Sim 147 TCTGTC--TCTGTCTCTGTCTCTGTCTCTGTCTCTGTC 182 Matrix = Unknown Transitions / transversions = 0.67 (10/15) Gap_init rate = 0.06 (11 / 181), avg. gap size = 1.09 (12 / 11) 38 2.78 0.00 0.00 chr1ptel1M 550873 550909 (449091) (TG)n#Simple_repeat 1 37 (0) c_b15s251i1 568 chr1ptel1M 550873 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGTGTGT 550909 i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 37 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 11 26.41 5.56 0.00 chr1ptel1M 552342 552395 (447605) (GAGAAG)n#Simple_repeat 1 57 (0) m_b15s252i15 569 chr1ptel1M 552342 GAGAAGGAGATGGTGAA-AACAAAGA-AAGGATAAATA-TAGGAAAATAA 552388 v v -i v i - v iv -v i vi (GAGAAG)n#Sim 1 GAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGA 50 chr1ptel1M 552389 GAAGGAG 552395 (GAGAAG)n#Sim 51 GAAGGAG 57 Matrix = Unknown Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.06 (3 / 53), avg. gap size = 1.00 (3 / 3) 256 30.77 3.52 2.62 chr1ptel1M 552409 552635 (447365) L1MC_orf2#LINE/L1 23 251 (3043) m_b15s551i10 570 chr1ptel1M 552409 TATCAATCACAGCTCTAAGTTGGAATTGAATGAATTCACACAT---AATA 552455 v ivi i i vv? v vv i v vv --- v L1MC_orf2#LIN 23 TATCAATAATCACTTTAAATGTNAATGGTCTAAATACACCAATTAAAAGA 72 chr1ptel1M 552456 CAGGAGACAG-CAGAATGGAATAGAAA-CAAGAATCCAGCAGTTTAATGT 552503 - iv - i vi i - -i i vi v iv L1MC_orf2#LIN 73 CAG-AGATTGTCAGAGTGGATCAAAAAACAAGA-CCCAACTATATGTTGT 120 chr1ptel1M 552504 TTATAAGAAACACATTTGGAACAAAAAGATTCATATAGAGTTAAAATAAG 552553 i i v i vi i v iv v v i i L1MC_orf2#LIN 121 CTACAAGAAACCCACTTTAAATATAAAGACACATATAGATTAAAAGTAAA 170 chr1ptel1M 552554 GGGTTTGAGCAACATCTATTGTGTTTTAACTAAAGTAAAAAAAAAAGACA 552603 ? v v v v v iii i vvv -- v i --i ? L1MC_orf2#LIN 171 NGGATGGAGAAAGATATACCATGCTAACACTAA--TCAAAAGAAA--GCN 216 chr1ptel1M 552604 GAGGTGGC---AATGACTTCAGACAAAACTTACTT 552635 ii i --- v i i i i vv L1MC_orf2#LIN 217 GGAGTAGCTATATTAATTTCAGACAGAGCAGACTT 251 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 40.89 CpG sites = 34, Kimura (unadjusted) = 40.89 Transitions / transversions = 1.00 (34/34) Gap_init rate = 0.04 (10 / 226), avg. gap size = 1.40 (14 / 10) 12 15.86 5.71 0.00 chr1ptel1M 552793 552827 (447173) (AAATAA)n#Simple_repeat 1 37 (0) m_b15s252i16 571 chr1ptel1M 552793 AAATAAACCTAAACAT-AAAATAAAAA-AGAAATGAA 552827 vv v - - i i (AAATAA)n#Sim 1 AAATAAAAATAAAAATAAAAATAAAAATAAAAATAAA 37 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 13 20.99 0.00 5.00 chr1ptel1M 553477 553518 (446482) (AAATA)n#Simple_repeat 1 40 (0) m_b15s252i17 572 chr1ptel1M 553477 AAATAGGAAAACATAAAATATTATTTAAAAAAAAATAAAATA 553518 ii v v -- vv v (AAATA)n#Simp 1 AAATAAAATAAAATAAAATA--AAATAAAATAAAATAAAATA 40 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.05 (2 / 41), avg. gap size = 1.00 (2 / 2) 249 32.32 6.06 0.00 chr1ptel1M 557285 557383 (442617) L2b_3end#LINE/L2 347 451 (15) m_b16s601i0 573 chr1ptel1M 557285 GACTGTGGGCTCCCCTGGGCCAGAGACTTGGTCTTTTCTCTTAGCCTCAG 557334 i vivi v i iv? v ii v vi v v L2b_3end#LINE 347 GACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTG 396 chr1ptel1M 557335 GA--CTCAAC----AGCTCAGTGCTCCGCACACAGCAGGTGTCTAATAAA 557378 v -- i i ---- v ? iiv i i iii i L2b_3end#LINE 397 TATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAA 446 chr1ptel1M 557379 TGCTT 557383 ii L2b_3end#LINE 447 TATTT 451 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 41.66 CpG sites = 20, Kimura (unadjusted) = 45.51 Transitions / transversions = 1.67 (20/12) Gap_init rate = 0.02 (2 / 98), avg. gap size = 3.00 (6 / 2) 300 22.03 18.64 0.00 chr1ptel1M 557652 557769 (442231) C MIR1_Amn#SINE/MIR (78) 152 13 m_b16s601i2 574 chr1ptel1M 557652 TCTCTATTTGACAGGTGAGGAAACTGAGACCAACAG-GATTAGG-GACTT 557699 i i v i i ?v v - i ? i - C MIR1_Amn#SINE 152 TCCCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTT 103 chr1ptel1M 557700 GCTCAGGATCACA----TGGCTACTGGAAGA--TGAG--------CCA-- 557733 i i i ?----? ? v v --i i -------- -- C MIR1_Amn#SINE 102 GCCCAAGGTCACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAACCCAGG 53 chr1ptel1M 557734 --TCCCGCCTCC--ACCAGGCGCTCTATCCACCGGGCCAC 557769 -- vv --ii vi i ii i C MIR1_Amn#SINE 52 TCTCCCGAGTCCCAGTCCAGTGCTCTATCCACTAGACCAC 13 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 27.19 CpG sites = 18, Kimura (unadjusted) = 28.48 Transitions / transversions = 2.25 (18/8) Gap_init rate = 0.07 (8 / 117), avg. gap size = 2.75 (22 / 8) 328 23.88 2.99 0.00 chr1ptel1M 557652 557718 (442282) C MIRc#SINE/MIR (118) 150 82 m_b16s601i1 574 chr1ptel1M 557652 TCTCTATTTGACAGGTGAGGAAACTGAGAC-CAACAGGATTAGG-GACTT 557699 i i v i i - ivii i i - C MIRc#SINE/MIR 150 TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTT 101 chr1ptel1M 557700 GCTCAGGATCACATGGCTA 557718 i i i ii C MIRc#SINE/MIR 100 GCCCAAGGTCACACAGCTA 82 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 31.23 CpG sites = 14, Kimura (unadjusted) = 31.23 Transitions / transversions = 7.00 (14/2) Gap_init rate = 0.03 (2 / 66), avg. gap size = 1.00 (2 / 2) 288 30.54 6.85 1.30 chr1ptel1M 558128 558273 (441727) C Plat_L3#LINE/CR1 (341) 3232 3079 m_b16s551i0 575 chr1ptel1M 558128 TCACCCCTTAAGCTTCCATTTTCTAGCCTAAATAACCCCAATTTCTTCCA 558177 iv iv i i v i i iv C Plat_L3#LINE/ 3232 TCACCCCTTAGCCTTCTCTTCTCCAGGCTAAACAACCCCAATTCCTTTAA 3183 chr1ptel1M 558178 CTAGCCTTCCTGGGGCACAAACTTGCAGCTCTTTG------CTGGTCGC- 558220 ivvi i v i i - v vi v v i i------i v - C Plat_L3#LINE/ 3182 CCTTTCCTCATAGGAC-CTATTTTCCATCCCTTTAATCATTTTTGTCGCT 3134 chr1ptel1M 558221 CTGCTCCTGGATACACGCCAGCTTCTTAATGTTCTTCCTAAAAT---GTA 558267 v - iv v v i iv ii i ii i --- i C Plat_L3#LINE/ 3133 CTTCT-CTGGACCCTCTCCAGTTTCTCCACATCCTTTTTAAAGTGCGGTG 3085 chr1ptel1M 558268 ACCAGA 558273 i C Plat_L3#LINE/ 3084 ACCAAA 3079 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 40.70 CpG sites = 27, Kimura (unadjusted) = 40.70 Transitions / transversions = 1.59 (27/17) Gap_init rate = 0.03 (5 / 145), avg. gap size = 2.40 (12 / 5) 205 30.91 1.82 0.00 chr1ptel1M 558452 558506 (441494) MIRb#SINE/MIR 191 246 (22) m_b16s601i3 576 chr1ptel1M 558452 AATGAGAGAAAATGTGGAAAGCTCTTAGCACA-TATTTGGTGCCCAATAA 558500 v viii v v - iii ii vi i MIRb#SINE/MIR 191 AATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAA 240 chr1ptel1M 558501 ATGCTC 558506 ii MIRb#SINE/MIR 241 GCGCTC 246 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 39.13 CpG sites = 12, Kimura (unadjusted) = 42.48 Transitions / transversions = 2.40 (12/5) Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1) 354 18.58 7.10 0.00 chr1ptel1M 559139 559321 (440679) HERVIP10FH#LTR/ERV1 801 996 (4106) m_b16s701i0 577 chr1ptel1M 559139 CAGAGAGGG--GTGGGGAGACAGAGAGAAATAGGGAGGAAGAGACAGAGA 559186 i-- v i i v i v i v HERVIP10FH#LT 801 CAGAGAGGAAAGAGAGAAGAGAGAGAGAGAGAGAGAGGAAGAGAGAGAGA 850 chr1ptel1M 559187 TGGAC--AGAGAGAGATGGAGAGAGACAG---AAGACAGA--CAGAGACA 559229 vi v-- v v --- vi -- i v HERVIP10FH#LT 851 GAGAAAGAGAGAGAGAGGGAGAGAGAGAGACAAAGAGGGAGTCAAAGAGA 900 chr1ptel1M 559230 GAAAGAGATAGAGAGAGACAGAGAC--AGAGACAGACAGAGAGACAGACA 559277 i ii iv -- i v i v v HERVIP10FH#LT 901 GAGAGAGGCAGAGAGAGGAAGAGACAGAGAGACAAAGAGGGAGTCAGAGA 950 chr1ptel1M 559278 GAGAGAGACAGACAGACAG--ATAGAGAGACAGACAGAGAGACATA 559321 v v -- v v v v HERVIP10FH#LT 951 GAGAGAGAGAGACAGAAAGTCAAAGAGAGAAAGAAAGAGAGAGATA 996 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 21.38 CpG sites = 14, Kimura (unadjusted) = 21.38 Transitions / transversions = 0.70 (14/20) Gap_init rate = 0.03 (6 / 182), avg. gap size = 2.17 (13 / 6) 253 29.17 0.00 0.00 chr1ptel1M 561175 561246 (438754) C MIRc#SINE/MIR (146) 122 51 m_b16s601i4 578 chr1ptel1M 561175 GCTCGCAGAGGGGGAGGGACTTGCCTGAGCTCACTCAGCTAATAAGCAGC 561224 iv vvi v ii v v i ii C MIRc#SINE/MIR 122 GCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGC 73 chr1ptel1M 561225 ACGGTCACAACTCGAACGCGGG 561246 vi i ivi v i C MIRc#SINE/MIR 72 AGAGCCGGGACTCGAACCCAGG 51 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 35.59 CpG sites = 12, Kimura (unadjusted) = 37.85 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.00 (0 / 71), avg. gap size = 0.0 (0 / 0) 12 32.01 1.33 4.11 chr1ptel1M 561455 561529 (438471) (CCCGC)n#Simple_repeat 1 73 (0) m_b16s252i0 579 chr1ptel1M 561455 CCCGCCCCGCCTCCACTCCGCCCC-CCCACTCCTGCCGCAGCACTGTCCA 561503 - i i - vvi i - v v i - v (CCCGC)n#Simp 1 CCCGCCCCGCC-CCGCCCCGCCCCGCCCCGCCCCGCC-CCGCCCCG-CCC 47 chr1ptel1M 561504 TGAACAGCCCTCCCCTGTCCCGCCCC 561529 i vv v iv i i (CCCGC)n#Simp 48 CGCCCCGCCCCGCCCCGCCCCGCCCC 73 Matrix = Unknown Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.05 (4 / 74), avg. gap size = 1.00 (4 / 4) 17 12.63 2.86 0.00 chr1ptel1M 566023 566057 (433943) (TCCCT)n#Simple_repeat 1 36 (0) m_b16s252i1 580 chr1ptel1M 566023 TCTCTCCCCTTCCCTTGCTTTCCCTT-CCTTCCCTT 566057 i i v i - (TCCCT)n#Simp 1 TCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTT 36 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 267 37.61 7.40 3.69 chr1ptel1M 567913 568304 (431696) L2#LINE/L2 2654 3059 (23) m_b16s601i5 581 chr1ptel1M 567913 ACCACCTCTGCAGTATCTCTCCCATACATTGCCTTCGCTTCTCTGACCCT 567962 i - vi i ------- i vi i i--- ii v L2#LINE/L2 2654 ACCACTTCT-CACCACCTC-------CACTGCCACCACC---CTGGTCCA 2692 chr1ptel1M 567963 GGCCCTCATCTTCTCCTCCCTAGACTATTGCTAGAGC-TGCTCGTGGGTC 568011 i vi v iiv i i i v v - v viiv L2#LINE/L2 2693 AGCCACCATCATCTCTCGCCTGGATTACTGCAATAGCCTCCTAACTGGTC 2742 chr1ptel1M 568012 TCCCTGCCCCCATTCTCTCCCCATT---GTCCATTTTCTATGCAGTCACC 568058 ii ii iv vi --- i i v ii ivi L2#LINE/L2 2743 TCCCTGCTTCCACCCTTGCCCCCCTNCAGTCTATTCTCAACACAGCAGCC 2792 chr1ptel1M 568059 AAAGTGATTTTCCTGGAGCACAGGTGCAACCATGTAAA------ACT-AT 568101 i ii ii ii i ii i vvi i v v------i - v L2#LINE/L2 2793 AGAGTGATCCTTTTAAAACGTAAGTCAGATCATGTCACTCCTCTGCTCAA 2842 chr1ptel1M 568102 AA-TCGCCAGGAG-TCCCCGTCATCTTCAAAATCAAATATAAAATTC--A 568147 -i v ivi - i i vivi i i v vvi i i -- L2#LINE/L2 2843 AACCCTCCAATGGCTTCCCATCTCACTCAGAGTAAAAGCCAAAGTCCTTA 2892 chr1ptel1M 568148 CAGTCTGACATTCAGAAGCCTTCATAACCAG--CCCCCTCTCCCATCCCA 568195 i-- i v v iiiv v i i v -- vi v vii ii L2#LINE/L2 2893 CAA--TGGCCTACAAGGCCCTACATGATCTGGTCCCCCGTTACCTCTCTG 2940 chr1ptel1M 568196 GTCTCATTTTACAGCACACT-----TGGCCCACTC--CCGGGGTAACA-T 568237 ii i ivi v v ----- v i -- ivvi iv - L2#LINE/L2 2941 ACCTCATCTCCTACCACTCTCCCCCTCGCTCACTCCGCTCCAGCCACACT 2990 chr1ptel1M 568238 ATCCTCCCTGCTAGTCCTCCCACA----AGATCCTCCATCTCCTGACAAG 568283 iv i iv vv ---- iiv v ivi v -- i L2#LINE/L2 2991 GGCCTCCTTGCTGTTCCTCGAACACGCCAGGCACGCTCCCGCCT--CAGG 3038 chr1ptel1M 568284 ACACTTCCAGTGGCCGTTCCC 568304 i vi v v v i L2#LINE/L2 3039 GCCTTTGCACTTGCTGTTCCC 3059 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 54.32 CpG sites = 88, Kimura (unadjusted) = 55.53 Transitions / transversions = 1.63 (88/54) Gap_init rate = 0.07 (27 / 391), avg. gap size = 1.63 (44 / 27) 428 26.72 4.31 0.00 chr1ptel1M 568956 569071 (430929) MIRb#SINE/MIR 127 247 (21) m_b16s601i6 582 chr1ptel1M 568956 TCTGCTTCCTCAACTATAAAATGGGAATAATAACAGCTTCCT---GGGGT 569002 v i v i i i v v ---i MIRb#SINE/MIR 127 TCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTACCTCGCAGGGT 176 chr1ptel1M 569003 TGTTG-GAGGATTAAGTATAATAACATTTGTGAGGTAATTAGCATAGAG- 569050 - i ivi iiiv i i iiv i v - MIRb#SINE/MIR 177 TGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAGTGC 226 chr1ptel1M 569051 TGGGCACTTAATAAATGCTTA 569071 iv v i ii i MIRb#SINE/MIR 227 CTGGCACATAGTAAGCGCTCA 247 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 31.58 CpG sites = 21, Kimura (unadjusted) = 34.47 Transitions / transversions = 2.10 (21/10) Gap_init rate = 0.03 (3 / 115), avg. gap size = 1.67 (5 / 3) 234 24.99 3.96 0.96 chr1ptel1M 570844 570944 (429056) L1M6_5end#LINE/L1 1517 1620 (895) m_b16s551i1 583 chr1ptel1M 570844 AGAAATATTGTGGCCAAATTCTAGAACTATCAG-ACAAAGTCAAAAATAC 570892 v iv v i v i ?iv - i -v v L1M6_5end#LIN 1517 AGACATATCCTGGCAAAATTTTTGAATTNCAAGGATAAAG-AAAAAATCC 1565 chr1ptel1M 570893 TACAAGCAGCCAGAT---AAAAACAATTTAAATACCAAGGAGTCACAGTA 570939 v ii--- iv vv v i v v i v L1M6_5end#LIN 1566 TACAAGCATCCAGGCAGAAAAAACAGGTTACCTACAAAGGAATAAAAATC 1615 chr1ptel1M 570940 AGGCT 570944 L1M6_5end#LIN 1616 AGGCT 1620 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 30.84 CpG sites = 10, Kimura (unadjusted) = 30.84 Transitions / transversions = 0.67 (10/15) Gap_init rate = 0.03 (3 / 100), avg. gap size = 1.67 (5 / 3) 20 18.27 0.00 0.00 chr1ptel1M 571123 571159 (428841) (A)n#Simple_repeat 1 37 (0) m_b16s252i2 584 chr1ptel1M 571123 AAAAAAAAAAAAAAAAAAAAACAGAGCTAAACAAAAA 571159 v i ivv v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 37 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 357 25.67 8.79 3.66 chr1ptel1M 571688 571869 (428131) L1MEi_5end#LINE/L1 2007 2197 (15) m_b16s551i2 583 chr1ptel1M 571688 AGGGGGAAAGGAAAGAGAAAAGCATAAT---CTGGGGTTA----ACAAGA 571730 i ii ? - ? i --- v iiivi ---- i L1MEi_5end#LI 2007 AGAGAAAAAGNAAAGA-AAAAGNATGATAAACAGAAAACACAAAATAAGA 2055 chr1ptel1M 571731 TGGCAGGAA---ATTCAGA---ATTAGCAATCTTAACGATAAAGGTGAAT 571774 i i ---i i i --- i i --- i v i L1MEi_5end#LI 2056 TGGTAGAAATAAGTCCAAATATATCAGTAATC---ACAATAAATGTAAAT 2102 chr1ptel1M 571775 GGGATACACTCTCCCAT--AAAG-CGGAGGCCTATACCAGCCTGGATTAA 571821 iv v v i -- - i ii--- i vi L1MEi_5end#LI 2103 GGATTAAACTCACCTATTAAAAGACAGAGAT---TATCAGATTGGATTAA 2149 chr1ptel1M 571822 AAGTCAGAATCCTACAATATGTTGTTCACAGGAAACACACCTGAAGCA 571869 ivv i vi v i i i i i i L1MEi_5end#LI 2150 AAAAAAAAATCCAGCTATATGCTGTTTACAAGAGACACACCTAAAACA 2197 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 33.90 CpG sites = 34, Kimura (unadjusted) = 33.90 Transitions / transversions = 3.09 (34/11) Gap_init rate = 0.07 (13 / 181), avg. gap size = 1.77 (23 / 13) 351 32.46 3.55 1.49 chr1ptel1M 571723 571919 (428081) L1MEc_5end#LINE/L1 2278 2478 (49) m_b16s551i4 583 chr1ptel1M 571723 TAACAAGATGGCAGG---AAATTCAGAATTAGCAATCTTAACGATAAAGG 571769 i i i--- ii ivvv v vv v iv v L1MEc_5end#LI 2278 TAGCAAGATGGTAGATTTAAACCCAACCATATCAATAATCACATTAAATG 2327 chr1ptel1M 571770 TGAATGGGATACACTCTCCCAT---AAAGCGGAGGCCTATACCAGCCTGG 571816 i vv v v i v --- i i ii--- ii vi L1MEc_5end#LI 2328 TAAATGGTCTAAACACCCCAATTAAAAGGCAGAGAT---TGTCAGATTGG 2374 chr1ptel1M 571817 ATTAAAAGTCAGAATCCTACAATATGTTGTTCACAGGAAACACACCTGAA 571866 v iv ii i v v i iii i ? i v L1MEc_5end#LI 2375 ATAAAAAAGCAAGACCCAACTATATGCTGCCTACAAGAAACNCACTTTAA 2424 chr1ptel1M 571867 GCAGGGAGATAATAA-AGAATAAAGGTAAAAGGCTGGAACAGAATCTACT 571915 ii vii i vv - iv i v v ii v i L1MEc_5end#LI 2425 ATATAAAGACACAAATAGGTTAAAAGTAAAAGGATGGAAAAAGATATACC 2474 chr1ptel1M 571916 ATGC 571919 L1MEc_5end#LI 2475 ATGC 2478 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 44.18 CpG sites = 36, Kimura (unadjusted) = 44.18 Transitions / transversions = 1.33 (36/27) Gap_init rate = 0.03 (6 / 196), avg. gap size = 1.67 (10 / 6) 441 22.91 4.08 2.00 chr1ptel1M 571723 571869 (428131) L1MEh_5end#LINE/L1 2079 2228 (7) m_b16s551i3 583 chr1ptel1M 571723 TAACAAGATGGCAGGAA--ATTCAGAAT-TAGCAATCTTAACGATAAAGG 571769 i i -- v v? - ? i vv v i v L1MEh_5end#LI 2079 TAATAAGATGGCAGAAATAAGTCCNAATATANCAGTAATTACAATAAATG 2128 chr1ptel1M 571770 TGAATGGGATACACTCTCCCAT--AAAG-CGGAGGCCTATACCAGCCTGG 571816 i v v v v -- - i ii--- ?i vi L1MEh_5end#LI 2129 TAAATGGGTTAAACTCACCAATTAAAAGACAGAGAT---TNTCAGATTGG 2175 chr1ptel1M 571817 ATTAAAAGTCAGAATCCTACAATATGTTGTTCACAGGAAACACACCTGAA 571866 ? iv i v i ii i i i i L1MEh_5end#LI 2176 ATTNAAAAACAAAATCCAACAATATGCTGTCTACAAGAGACACACTTAAA 2225 chr1ptel1M 571867 GCA 571869 i L1MEh_5end#LI 2226 ACA 2228 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 28.92 CpG sites = 20, Kimura (unadjusted) = 28.92 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.05 (7 / 146), avg. gap size = 1.29 (9 / 7) 4606 30.38 3.52 2.92 chr1ptel1M 571764 575001 (424999) L1M5_orf2#LINE/L1 38 3294 (0) m_b16s551i5 583 chr1ptel1M 571764 TAAAGGTGAATGGGATACACTCTCCCAT---AAAGCGGAGGCCTATACCA 571810 v i ?v v v v --- i i ii--- ii L1M5_orf2#LIN 38 TAAATGTAAATGGNCTAAACACTCCAATTAAAAGGCAGAGAT---TGTCA 84 chr1ptel1M 571811 GCCTGGATTAAAAGTCAGAATCCTACAATATGTTGTTCACAGGAAACACA 571860 v v iv ii i v v i ii i i i L1M5_orf2#LIN 85 GACTGGATAAAAAAACAAGACCCAACTATATGCTGTCTACAAGAGACGCA 134 chr1ptel1M 571861 CCTGAAGCAGGGAGATA-ATAAAGAATAAAGGTAAAAGGCTGGAACAGAA 571909 i v ii vii i - v ? iv i i v v ii L1M5_orf2#LIN 135 CTTTAAATATAAAGACACAGANAGGTTGAAAGTAAAAGGATGGAAAAAGA 184 chr1ptel1M 571910 TCTACTATGCTTCAGGTGAAGTCAGA-AAAGGAGGGGTAGTCATCCTGAT 571958 v i v-v viiv ?iv i - vv ? i ii vi i L1M5_orf2#LIN 185 TATACCATGCA-AACACTAANCAAAAGAAAGCTGGNGTGGCTATATTAAT 233 chr1ptel1M 571959 CTCAGCTCAAGCA------AAAGCAAAAATTGATCTGATTAAAAGAGATA 572002 v viv i ------ i i --- --- vv L1M5_orf2#LIN 234 ATCAGACAAAGTAGACTTCAAGGCAAGAA---AT---ATTACCAGAGATA 277 chr1ptel1M 572003 AGGAAGGGCACTATATCTTGCTAAA-GGGT-AGTATAGGTAATGAAGCAA 572050 i i i i vi vv v - - i vi -- v v vv L1M5_orf2#LIN 278 AAGAGGGACATTTCATAATGATAAAAGGGTCAATTCA--TCAAGAAGACA 325 chr1ptel1M 572051 TGTCAATACTAAACATATACGCACCAAGTGGTATAGCATCTAAATTTCTA 572100 iv v ii i i v i iii v v v viv i L1M5_orf2#LIN 326 TAACAATCCTAAATGTGTATGCACCTAATAACAGAGCTTCAAAATACATG 375 chr1ptel1M 572101 AAGGAGAAGTTAAGAGAGCTGCAAGAAGAAATAGACAGCAAAACTATAAT 572150 v i ii i v i iv i --- v i i L1M5_orf2#LIN 376 AAGCAAAAACTGACAGAACTAAAAGGAGAAATAGACA---AATCCACAAT 422 chr1ptel1M 572151 ---AGTGGGAGATCTCAACATTGCTCTCTCAGAACTAGATAAATCAAAC- 572196 --- ? i i i?v v v v i v ii- L1M5_orf2#LIN 423 TATAGTNGGAGATTTTAACACNCCTCTCTCAGTAATTGATAGAACAAGTA 472 chr1ptel1M 572197 --CACAAAATAAGAAAAGTTAAAGAGGGAAATAGAACACCAGTAG----- 572239 -- v v v i v v i -- v v v v v----- L1M5_orf2#LIN 473 GACAAAAAATCAGTAAGGATATAGAAG--ATTTGAACAACACTATCAACC 520 chr1ptel1M 572240 AGTTAGGTATGATAGATCTTTGGAGAAAAATGAATGGAGATAGAAAAGAA 572289 ii v iiv i v iv iv v v ?v ivv ivv v?iv L1M5_orf2#LIN 521 AACTTGACCTAATTGACATTTATAGAACACTNCACCCAACAACNGCAGAA 570 chr1ptel1M 572290 TATACTTTCTTCTTGATAGTTGATGGAACCTATACAAAAACTGACCATAT 572339 i v i ii vv ivv v v v i iv L1M5_orf2#LIN 571 TACACATTCTTTTCAAGTGCACATGGAACATTTACCAAGATAGACCATAT 620 chr1ptel1M 572340 ATTAGGACATAAAGAC----CTCAAATTCAAATGCAGAAAGGCCGAACTA 572385 ?i i v - ---- ---i vi?i i iii v v L1M5_orf2#LIN 621 NCTGGGCCATAAA-ACAAGTCTCAA---TAAATTTNAAAGGATTGAAATC 666 chr1ptel1M 572386 GTA-AATGCATCCTTTCAGATCACAATGCAATGAAAATTACATTCAATAA 572434 i - iv i vi i v i v v v viv v L1M5_orf2#LIN 667 ATACAGAGTATGTTCTCTGACCACAATGGAATTAAATTAGAAATCAATAA 716 chr1ptel1M 572435 AATGCCAGGGGA-AAATAGACTAAA-----AAGTAATTGGAAACTAAATA 572478 ---- v iii - ?v -- ----- i v i i L1M5_orf2#LIN 717 ----CAAAAAGATANCTAGA--AAATCCCCAAATATTTGGAAATTAAACA 760 chr1ptel1M 572479 ATCTCA-TCCTAAAGAATGAATGGGTGAAACAGCAAATTAGACAC---AA 572524 - v - i v ivv v v iv i v - ?--- L1M5_orf2#LIN 761 A-CACACTTCTAAATAACCCATGGGTCAAAGAAGAAATCACA-ANGGAAA 808 chr1ptel1M 572525 TTAGTAATTTCATCCAAGAGAATGACAATAATGAGATGACATACCAAAAT 572574 v v viv iv vv ? i vi v ii i L1M5_orf2#LIN 809 TTAGAAAATATTTTGAACTGAATGANAATGAAAATACAACATATCAAAAT 858 chr1ptel1M 572575 GTGTGGGATGCAGCCAAAGTGTTAATGAGGGGAAATTTTATATCTCTAGA 572624 v i iiv iv v i i v v ?i i L1M5_orf2#LIN 859 TTGTGGGATGCAGCTAAAGCAGTGCTTAGAGGGAAATTTATAGCNTTAAA 908 chr1ptel1M 572625 GTCCTACTTGCAT--GAAATAGAGAAAG----AAAATTAATGAATTATGC 572668 ---- i ? ii -- vii ---- i vi v L1M5_orf2#LIN 909 ----TGCNTATATTAGAAAAGAAGAAAGGCTTAAAATCAATGATCTAAGC 954 chr1ptel1M 572669 TTGCAATTAAAAAAGCTAGAAAAAGA---GCAAATTAACACCCCATCAAA 572715 v vi v i --- - v -- i? L1M5_orf2#LIN 955 TTCCACCTTAAGAAGCTAGAAAAAGAAGAGCAAATTAA-ACCCAA--AGN 1001 chr1ptel1M 572716 AACTAAACTT---GAAATTCTAAAAATAAAAT--GAGATTAATACAATTG 572760 v i vvv--- vv i i v-- i i iv v L1M5_orf2#LIN 1002 AAGTAGAAGGAAGGAAATAATAAAGATAAGAGCAGAAATCAATGAAATAG 1051 chr1ptel1M 572761 AAAGTAAAAAGA-AGTATTTAATTAATAAATAAAACTAGGAGTTGGTTCT 572809 ii ? ? - i vvv -- v ii i i ii i L1M5_orf2#LIN 1052 AAAACAAANANACAATAGAGAA--AATCAACGAAGCCAAAAGCTGGTTCT 1099 chr1ptel1M 572810 ATAAAAAAATAAAATAAAATAGATAAACCCTTAGTAAATCTGATTAGAAA 572859 v i i v - v ii i? iv i ii L1M5_orf2#LIN 1100 TTGAAAAGATCAA-TAAAATTGATAAACCTCTAGCNAGACTGATCAAGAA 1148 chr1ptel1M 572860 AAGGAAAGAGGAAAATCAAATTGTTAGTCTTAAAAATGAAAAGGGAGAAC 572909 ii i i i vv iii i v i ii i vv L1M5_orf2#LIN 1149 AAAAAGAGAGAAGACACAAATTACCAATATCAGGAATGAAAAAGGAGACA 1198 chr1ptel1M 572910 TTGCCACTAAT---GAAGA-GTTAGAGCAATAATTATGAGT-TGCTTTGC 572954 ii i vi ---iv -i i ivi v - v- ii v v L1M5_orf2#LIN 1199 TCACTACAGATCCTACAGACATTAAAAGGATAATAA-GAGAATATTATGA 1247 chr1ptel1M 572955 CCAACTTTATGCCAATAAATTTGATAACTTAAACGAAATGGATGAATACC 573004 v ? i i ii v L1M5_orf2#LIN 1248 ACAACTTTATGCCAATAAATTTGANAACTTAGATGAAATGGACAAATTCC 1297 chr1ptel1M 573005 TTCAAAAATATAGACTTCACAGATTAACAGAGGAGGAAGTAAATTGGTTA 573054 v i i i?i v vv i i i ?v i i i i vvivi i L1M5_orf2#LIN 1298 TTGAAAAACACAANTTACCAAAACTGACNCAAGAAGAAATAGAAAATCTG 1347 chr1ptel1M 573055 AATAGTCCCAT-TTTAGAAAAAGAAATAGAAGAAGCTTTTAATCAA---- 573099 i i - i v-v v ----i v i ---- L1M5_orf2#LIN 1348 AATAGCCCTATATCTAT-TAAAGAAATTGAA----TTTGTAATTAAAAAC 1392 chr1ptel1M 573100 CTCCCTAAGAAAAAATCCCCAGGACCAGACGGATTTACAGGTGAATTCTA 573149 i i vi i v i v i v i v L1M5_orf2#LIN 1393 CTTCCCACAAAGAAAACTCCAGGCCCAGATGGCTTCACTGGTGAATTCTA 1442 chr1ptel1M 573150 ACAAACATTTAAAGAACAATTAACTCCAATGCTATATAAACTATTTGAAA 573199 v i v v iv vi i i -i vv i L1M5_orf2#LIN 1443 CCAAACATTTAAGGAAGAAATAATACCAATCTTACACAAACT-CTTCCAG 1491 chr1ptel1M 573200 AAAATAGGGAATGAAGCAGTCCTGCCAATTTCCTTTTATGACATGGACAT 573249 ii v i v iiv v v vi v viivii L1M5_orf2#LIN 1492 AAAATAGAAAAAGAGGGAACACTTCCCAACTCATTTTATGAGGCCAGCAT 1541 chr1ptel1M 573250 GGTGTCGATAACTAAATCAGGC-AGGACAATAACAGAGAAAGAAAATTAC 573298 ?iivii v v i ? i - i - v iii L1M5_orf2#LIN 1542 NACCCTGATACCAAAACCNGACAAAGAC-ATTACAAGAAAAGAAAATTAC 1590 chr1ptel1M 573299 AGACCAATCTCCCTAATGAACATCAATGTAAAAATCTTGAATAAAATATT 573348 v v vi i i ? i L1M5_orf2#LIN 1591 AGACCAATATCCCTCATGAACATAGATGCAAAAATCCTNAACAAAATATT 1640 chr1ptel1M 573349 AACAAAAAGGTTACAGAAAATCATCTCCAGGATGATCTCATCTCCATGAC 573398 i vv iv v v vvi vvvv i v- --- L1M5_orf2#LIN 1641 AGCAAATCGAATCCAGCAATATATAAAAAGGATAATA-CAT---CATGAC 1686 chr1ptel1M 573399 CAAGTAGGATGTATACCAAGAATGAAGGGCTGGTTCAATATTAGGAAAAC 573448 i i v v i v i i i i v i v L1M5_orf2#LIN 1687 CAAGTGGGGTTTATCCCAGGAATGCAAGGTTGGTTTAACATTCGAAAATC 1736 chr1ptel1M 573449 TATTGACATAATCGACTATATCAATA-ACCAATTAACAAAAACCATATAA 573497 v ii ii iv i i i - vi vvi v i i L1M5_orf2#LIN 1737 AATCAATGTAATTCACCATATTAACAGAATAAAGGAGAAAAATCATATGA 1786 chr1ptel1M 573498 TCATCTTAATAGATGCAGAAAAAGCATTTGATAAAACCCAACACTCATTC 573547 i i ii i L1M5_orf2#LIN 1787 TCATCTCAATAGATGCAGAAAAAGCATTTGACAAAATTCAACACCCATTC 1836 chr1ptel1M 573548 CTATTAAAAACACT-AGAGAGTAC-AGGAATA-AATGAACTTTTCTTAAA 573594 v iv v - vi -- - - v i vi i i v L1M5_orf2#LIN 1837 ATGATAAAAACTCTCAGCAA--ACTAGGAATAGAAGGGAACTTCCTCAAC 1884 chr1ptel1M 573595 ATAGTCAGTAGCATCTATTTAAAACCATCAGTAAGTATCATATGTAATAG 573644 v ii v ivi ivv vv i? ii iv i L1M5_orf2#LIN 1885 CTGATAAAGGGCATCTACGAAAAACCTACAGCNAACATCATACTTAATGG 1934 chr1ptel1M 573645 TGACAAACTGGAATCATCCCCAATAAAATCAGGAGTGAAACAAAGTTGCC 573694 v ? i ?v v i vv i i iii i i v i L1M5_orf2#LIN 1935 TGAAANACTGAANGCTTTCCCCCTAAGATCGGGAACAAGACAAGGATGTC 1984 chr1ptel1M 573695 CACTATCACCATTACTATTCAGTATTGTATCAGAAATGCTAGCTTTGGCA 573744 i ? i v ii iii ii v ivvv L1M5_orf2#LIN 1985 CGCTNTCACCACTTCTATTCAACATTGTACTGGAGGTCCTAGCCAGTGCA 2034 chr1ptel1M 573745 ATAAG--ATGAAAAAGAAATGAAAGGAATTAAAGTAGGCAATGGGGAAAC 573792 -- v i v v ii v v v ii i L1M5_orf2#LIN 2035 ATAAGGCAAGAAAAAGAAATAAAAGGCATAAAGATTGGAAAGGAAGAAAT 2084 chr1ptel1M 573793 CAAATTATCACTCTTTGCAGATGATATGATGGTATAGTTAGAGAACCCCA 573842 v i i ?i v i i v ? vv i i ? L1M5_orf2#LIN 2085 AAAACTGTCNTTATTCGCAGATGACATGATTGTNTACGTAGAAAATCCNA 2134 chr1ptel1M 573843 GAGATTCTACTAAAAAGCTATTAGAAATAATCCACAACTTTAGCAAAGTT 573892 i v v ? i i v vviii v i i L1M5_orf2#LIN 2135 AAGAATCTACAAANAAACTACTAGAACTAATAAGTGAATTTAGCAAGGTC 2184 chr1ptel1M 573893 GCAGGATACAAAGCAAATCCAC-ATAATCATTAACATTTTTGTACATCAC 573941 ? i iv vi - v v vii i i i ii v L1M5_orf2#LIN 2185 GCNGGATACAAGGTCAATATACAAAAATCAATTGTATTTCTATATACTAG 2234 chr1ptel1M 573942 TAACAAAATTCAACAAGCAA--GAGATACAAAGAGAAACTCCATTTAAAA 573989 i --- ivi v -- i vi? i iv iv v L1M5_orf2#LIN 2235 CAACAAA---CAATTGGAAAATGAAATTTNAAAAACAATACCATTTACAA 2281 chr1ptel1M 573990 TAACTGCTGATAGTATAAAATATTTGGGAATCTATCTGCCAAGGGAAAGT 574039 i vv vi v ii ? i i vv iv ii? vivv L1M5_orf2#LIN 2282 TAGCATCAAAAAACATNAAATACTTAGGAATAAATCTAACAAAANATGTG 2331 chr1ptel1M 574040 CAGGAACTATATGAGCAAAACTAGAAAACACTCTCCACACAAATAAAGTC 574089 i v ? iivvv v i viiv v v v ivv L1M5_orf2#LIN 2332 CAAGACCTNTACACTGAAAACTACAAAACATTGCTGAGAGAAATTAAAGA 2381 chr1ptel1M 574090 AGATTTAAACAACTGGAAAACTATTAAGTGCTCCTAGATAGATTGAGTAA 574139 ii i v i iv vvvi i v i v ivv v v L1M5_orf2#LIN 2382 AGACCTAAATAAATGGAGAGATATACCATGTTCATGGATTGGAAGACTCA 2431 chr1ptel1M 574140 ATATAATAAGGATGACAATACTACCTAAACTAATATATAG------TGCT 574183 vi ? i v v v i i i v ------ v L1M5_orf2#LIN 2432 ATATTGTNAAGATGTCAATTCTCCCCAAATTGATCTATAGATTCAATGCA 2481 chr1ptel1M 574184 ATACCAATCAGACTCCCAAGAAACTATTTTACTGACATAGAAAAAATAAC 574233 v i v iv iii v iiv v v v iv i i L1M5_orf2#LIN 2482 ATCCCAATCAAAATCCCAGCAGGTTTTTTTGTAGAAATTGACAAGCTGAT 2531 chr1ptel1M 574234 AATAAAATTCATCCGGAAGAACAAAAGGTCAAGAAT-TTCAAGAGAA-CT 574281 vv i vi ivi i ii ? -vi i v - L1M5_orf2#LIN 2532 TCTAAAATTTATATGGAAATGCAAAGGACCNAGAATAGCCAAAACAATCT 2581 chr1ptel1M 574282 AATGAAAAAAAAAATCAAATGAAGGTGGCCTAACTATATCTGATCT-AAA 574330 -- i i v - vv v v v vv i ? ? - i L1M5_orf2#LIN 2582 --TGAAAAAGAAGAACAAA-GTTGGAGGACTTACACTACCNGATNTCAAG 2628 chr1ptel1M 574331 ACTATATTATAAAGGAGTAGTCACCAAAACCATTTGGTATTGGT-TAAGA 574379 - vvii v i i vi v i- - L1M5_orf2#LIN 2629 ACT-TATTATAAAGCTACAGTAATCAAGACAGTGTGGTATTGGCGTAAG- 2676 chr1ptel1M 574380 AATAGCTTAGTTGATTGGTAGAATAAGTTAG---GTTCACAAGACAAAAT 574426 i viv i v iii i i iiv --- i v - i i -- L1M5_orf2#LIN 2677 GATAGACAAATAGATCAATGGAACAGAATAGAGAGTCCAGAA-ATAGA-- 2723 chr1ptel1M 574427 ATTCTATAGCAATAGCTATAGCAATCTAGTGTTTGACAAA---CCCAAAG 574473 --i i i - - -- i ?v ?i ii v ---v ? L1M5_orf2#LIN 2724 --CCCACA-C-ATA--TATGGNCANTTGATTTTTGACAAAGGTGCCAANG 2767 chr1ptel1M 574474 ACCCCAACTT-TTGGGATAAGAATGCACTATTTAACAAAAACTGCTGGGA 574522 ---- i i-v iv i ivv v i viv i L1M5_orf2#LIN 2768 ----CAATTCAGTGGGGAAAGGATAGTCTTTTCAACAAATGGTGCTGGAA 2813 chr1ptel1M 574523 AAATTGGAAATTAGTATGGCAGAAACTAGGCATTGACCCATACTTAACAC 574572 v v ivi v i v iii?v i v i v L1M5_orf2#LIN 2814 CAATTGGATATCCATATGGAAAAAAATGAANCTCGACCCCTACCTCACAC 2863 chr1ptel1M 574573 TGTACACCAAGATAAGGTCAAAATAGGTTCGT-GATCTAGGCATAAAGAA 574621 ii v i v iv ? i - v i - i iiii ii? L1M5_orf2#LIN 2864 CATACACAAAAATTAATTCNAGAT-GGATCATAGACCTAAATGTAAAAGN 2912 chr1ptel1M 574622 TGAGATTATAAATAAAT--TGGAAG--AACATAGGATAGTTTAGGTCTCA 574667 i i i -- v -- i -- v i v ---ii i L1M5_orf2#LIN 2913 TAAAACTATAA--AACTTCTAGAAGAAAACATAGGAGAATAT---CTTCG 2957 chr1ptel1M 574668 -GACCTGTGGAGAAGGAAGGAATTTGCAACCAAAGAAGAATTAGAGATCA 574716 - - i?v v iii - --ii v i vvi i i v L1M5_orf2#LIN 2958 TGACCT-TGGGNTAGGCAAAGATTT-C--TTAAACAGGACACAAAAAGCA 3003 chr1ptel1M 574717 TCATTGATCACAAAATAGAAACT-------TTTGATTATATCAAGTTAAA 574759 i? --- i i v i v ------- v i ?i iv v L1M5_orf2#LIN 3004 CNA---ACCATAAAAGAAAAAATTGATAAATTGGACTNCATCAAAATTAA 3050 chr1ptel1M 574760 AAGCTTTTG----TAGAAACAAAAC-TTATGCAGACACGATTAGAAGGGA 574804 i i ---- vi v v v - --- v -- v i v L1M5_orf2#LIN 3051 AAACTTCTGCTCNTCAAAAGACACCGTTA---AGAAA--ATGAAAAGGCA 3095 chr1ptel1M 574805 AGCAATAAAATGGGAAAACATCTTTACAGTGAAAGAT-TCTGATAAAGGC 574853 v i i ? i v v i i-? v v - i v L1M5_orf2#LIN 3096 AGCCACAGANTGGGAGAAAATATTTGCAA-NACATATATCTGACAAAGGA 3144 chr1ptel1M 574854 TTCATTTCCAAAATATATAACGAATTGACTCAAATTTATAAGAATTCAAG 574903 i i v i v i vviv ? iv ? --v L1M5_orf2#LIN 3145 CTCGTATCCAGAATATATAAAGAACTCCTACAANTCAATAANAA--AAAG 3192 chr1ptel1M 574904 CCATTC--TCCA--ACTGATGTGGTCAAAGGATATGAACAGACAATTTTC 574949 v vv --i -- ?vi vi v i iv v iv L1M5_orf2#LIN 3193 ACAAACAACCCAATANAAAAATGGGCAAAAGACTTGAACAGACACTTCAC 3242 chr1ptel1M 574950 AGATGATGAAATTGAAACTATTTCTACCCATATGAAAAGGTGTTCCAAAT 574999 i v v v ?v iviiivv vv i i i v v? L1M5_orf2#LIN 3243 AAAAGAAGATATNCAAATGGCCAATAAGCACATGAAAAGATGCTCAACNT 3292 chr1ptel1M 575000 CA 575001 L1M5_orf2#LIN 3293 CA 3294 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 40.21 CpG sites = 523, Kimura (unadjusted) = 40.82 Transitions / transversions = 1.21 (523/432) Gap_init rate = 0.05 (146 / 3237), avg. gap size = 1.43 (209 / 146) 1496 27.83 1.63 2.19 chr1ptel1M 574854 575404 (424596) L1ME3G_3end#LINE/L1 1 548 (376) m_b16s551i6 583 chr1ptel1M 574854 TTCATTTCCAAAATATATAACGAATTGACTCAAATTTATAAGAATTCAAG 574903 v v i v i vviv iv --v L1ME3G_3end#L 1 TTAATATCCAGAATATATAAAGAACTCCTACAAATCAATAAGAA--AAAG 48 chr1ptel1M 574904 CCATTCTCCAACTGATG--TGGTCAAAGGATATGAACAGACAATTTTCAG 574951 v --vi iv vi-- v i iv L1ME3G_3end#L 49 ACA--ACCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAG 96 chr1ptel1M 574952 ATGATGAAATTGAAACTATTTCTACCCATATGAAAAGGTGTTCCAAATCA 575001 v v vv iviiivv vv i i v vv L1ME3G_3end#L 97 AAGAGGAAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCA 146 chr1ptel1M 575002 TTATTGATCAGAGAAATGCAAATTAAGACAAT--TCAGATAACACTTCAC 575049 i v i i i i-- v v i iv L1ME3G_3end#L 147 CTAGTAATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTC 196 chr1ptel1M 575050 ACCAGTCAGATTGGCTAAGATGAAAGGAAAAGATAATGCAGAATGTTGGA 575099 vi v i vv iii?vv iiv? i v L1ME3G_3end#L 197 ACCCATCAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGC 246 chr1ptel1M 575100 GGGGATGTGGGAAAACTGGGACATTGATACATTATTGGTGGAGTTGTGAA 575149 i i i v v vi v i ii iiv i L1ME3G_3end#L 247 GAGGGTGTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAA 296 chr1ptel1M 575150 TGGATCCATCCATTCTGGGGACTGATTTGGAAGTATGC-TCAAAAAGCTG 575198 v i v v ? i i ivii v vi- i ----v L1ME3G_3end#L 297 TTGGTACAGCCNTTTTGGAGGGCAATTTGGCAGTATCTATTAAAA----T 342 chr1ptel1M 575199 TCAAACTGTGTATACCCTTTGATCCAGCAGTGTTACGACTGGGCTTATAT 575248 i v i i i i vii vv ? ?v v L1ME3G_3end#L 343 TTAAAATGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTAT 392 chr1ptel1M 575249 CCCAAAGAGAT-CTTAAAGAAG-GAAAAGGGAACTGTATGTGCAAAAATG 575296 i ? i - iiv v v - v v i --? i i ii L1ME3G_3end#L 393 CCTANAGAAATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATG 440 chr1ptel1M 575297 TTTGTGGCAGCCCTGTTTGTAGTGGCTAGAAACTGGAAAATGAA--TGGA 575344 ii v vi i i v i i --v -- ii L1ME3G_3end#L 441 TTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAA--CAACCTAAA 488 chr1ptel1M 575345 TGCCCATCAATTGGAGAATGGCTGAGTAAATTATGGTATATGAATGTGAT 575394 i v i i i i vv iiv L1ME3G_3end#L 489 TGTCCATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTAT 538 chr1ptel1M 575395 GGAATATTAT 575404 i L1ME3G_3end#L 539 GGAATACTAT 548 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 35.36 CpG sites = 81, Kimura (unadjusted) = 35.98 Transitions / transversions = 1.17 (81/69) Gap_init rate = 0.03 (18 / 550), avg. gap size = 1.17 (21 / 18) 1462 30.24 2.08 1.59 chr1ptel1M 574865 575489 (424511) L1ME4c_3end#LINE/L1 12 639 (191) m_b16s551i7 583 chr1ptel1M 574865 AATATATAACGAATTGACTCAAATTTATAAGAAT----TCAAGCCATTCT 574910 ? v ii v i v v---- v ----i L1ME4c_3end#L 12 ANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAAGAC----C 57 chr1ptel1M 574911 CCAACTGATG--TGGTCAAAGGATATGAACAGACAATTTTCAGATGATGA 574958 iv i-- v i iv ? v v L1ME4c_3end#L 58 CCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAGGA 107 chr1ptel1M 574959 AATTGAAACTATTTCTACCCATATGAAAAGGTGTTCCAAATCATTATTGA 575008 vv ?ivi vvvi vv i i ii v vv ii v i L1ME4c_3end#L 108 AATACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTAGTAA 157 chr1ptel1M 575009 TCAGAGAAATGCAAATTAAGACAAT--TCAGATAACACTTCACACCAGTC 575056 i ii i-- v v i i i vi i L1ME4c_3end#L 158 TCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCTATT 207 chr1ptel1M 575057 AGATTGGCTAAGATGAAAGGAAAAGATAATGCAGAATGTTGGAGGGGATG 575106 i i v i vv ii vv i vv i v i ? L1ME4c_3end#L 208 AAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGCTGGCGAGGNTG 257 chr1ptel1M 575107 TGGGAAAACTGGGACATTGATACATTATTGGTGGAGTTGTGAATGGATCC 575156 i vi v ?i v ii vi? i v i v L1ME4c_3end#L 258 CGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGTAC 307 chr1ptel1M 575157 ATCCATTCTGGGGACTGATTTGGAAGTATGCTCAAAAAGCTGTCAAACTG 575206 v v i ii vii v i i iviv i ii v v L1ME4c_3end#L 308 AACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAAAATG 357 chr1ptel1M 575207 TGTATACCCTTTGATCCAGCAGTGTTACGACTGGGCTTATATCCCAAAGA 575256 vi i i i vii vv vv v i i L1ME4c_3end#L 358 TTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGA 407 chr1ptel1M 575257 GAT-CTT--AAAGAAGGAAAAGGGAACTGTATGTGCAAAAATGTTTGTGG 575303 i -v -- --- i i ii i i ii v L1ME4c_3end#L 408 AATAATTCAAAAGAAGGAAAA---AGCTATATGCACGAAGATGTTCATTG 454 chr1ptel1M 575304 CAGCCCTGTTTGTAGTGGCTAGAAACTGGAAAATGAA--TGGATGCCCAT 575351 vi i i i i v i i --v -- ii i v L1ME4c_3end#L 455 CAGCGTTATTTATAATAGCGAAAAATTGGAAA--CAACCTAAATGTCCAA 502 chr1ptel1M 575352 CAATTGGAGAATGGCTGAGTAAATTATGGTATATGAATGTGATGGAATAT 575401 v i i i i v? ivi L1ME4c_3end#L 503 CAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATAT 552 chr1ptel1M 575402 TATTGTTCTGTAATAAATGACCGACAGGATGAATACAGAGAGGCCTGGGG 575451 vvvv ii v v ivivi v v v iiv vii v - i L1ME4c_3end#L 553 TATGCAGCCATTAAAAATGATAATTATGAAGACTATGTAGCAACAT-GGA 601 chr1ptel1M 575452 AGACTTATATGAACTGATGCTGAGTGAAATGAGCAGAA 575489 i iv v vv i i i vi L1ME4c_3end#L 602 AAATGTTTATGATATAATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 38.60 CpG sites = 104, Kimura (unadjusted) = 40.26 Transitions / transversions = 1.27 (104/82) Gap_init rate = 0.03 (16 / 624), avg. gap size = 1.44 (23 / 16) 289 30.92 2.69 10.10 chr1ptel1M 575957 576179 (423821) L1ME3D_3end#LINE/L1 121 328 (661) m_b16s551i8 585 chr1ptel1M 575957 AATAACTATAGGAAAGAATGGTCCAAATCCCAAAAATAATGCAAAATTGC 576006 vi v ii v -- i i vv i - i---- v L1ME3D_3end#L 121 AATAAACATATGAAAAGATGCTC--AACCTCATTAGTAAT-CAG----GG 163 chr1ptel1M 576007 AAATGCAAAATTGAAATGCACAAAAAACAATTCTGAAATTTTACTTCATA 576056 - i i- ---------- i vii i i L1ME3D_3end#L 164 AAATGCAAA-TTAAAAC-CACAA----------TGAGATACCATTTCACA 201 chr1ptel1M 576057 TCCCACAAATTGGCAAAGATGAGAAAGGATGGGAATAACCAATATTGGAA 576106 i vv i i v - vv iv v v i i vi L1ME3D_3end#L 202 CCCACCAGATTGGCAAAAATTA-AAAGTCTGACAATACCAAGTGTTGGCG 250 chr1ptel1M 576107 CAACTGTGG------GAGAGGCGCTAGTACATTGTTGATGGAGCTATGAA 576150 viiv ------ i i- v vi i i i iiv i i L1ME3D_3end#L 251 AGGATGTGGAGCAACGGGAA-CTCTCATACACTGCTGGTGGGAGTGTAAA 299 chr1ptel1M 576151 TCAATATAATCCTTTTGTAAAACAATTTG 576179 iii i i vi v L1ME3D_3end#L 300 TTGGTACAACCACTTTGGAAAACAATTTG 328 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 40.23 CpG sites = 39, Kimura (unadjusted) = 41.12 Transitions / transversions = 1.70 (39/23) Gap_init rate = 0.10 (22 / 222), avg. gap size = 1.23 (27 / 22) 302 33.32 4.97 1.20 chr1ptel1M 576019 576179 (423821) L1ME3Cz_3end#LINE/L1 159 325 (672) m_b16s551i9 585 chr1ptel1M 576019 GAAATGCACAA--AAAACAATTCTGAAATTTTACTTCATATCCCACAAAT 576066 - -- ? ivv i vii i i i vv i L1ME3Cz_3end# 159 GAAATGCA-AATTAAAACNACAATGAGATACCATTTCACACCCATCAGAT 207 chr1ptel1M 576067 TGGCAAAGATGAGAAAGGATGGGAATAACCAATATTGGAACAACTGTGGG 576116 i vvi vv iv v v i i viviiv - L1ME3Cz_3end# 208 TGGCAAAAATTTAAAAGTCTGACAATACCAAGTGTTGGCGAGGATGT-GG 256 chr1ptel1M 576117 AGAGGCG------CTAGTACATTGTTGATGGAGCTATGAATCAATATAAT 576160 ii ------ vi i i i iiv i i iii i i L1ME3Cz_3end# 257 AGAAACGGGAACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTACAAC 306 chr1ptel1M 576161 CCTTTTGTAAAACAATTTG 576179 vi v i i L1ME3Cz_3end# 307 CACTTTGGAGAGCAATTTG 325 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 45.62 CpG sites = 34, Kimura (unadjusted) = 46.87 Transitions / transversions = 1.79 (34/19) Gap_init rate = 0.03 (4 / 160), avg. gap size = 2.50 (10 / 4) 86 1.30 0.00 0.00 chr1ptel1M 576264 576341 (423659) (TG)n#Simple_repeat 1 78 (0) c_b16s251i0 586 chr1ptel1M 576264 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGTGTG 576313 i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr1ptel1M 576314 TGTGTGTGTGTGTGTGTGTGTGTGTGTG 576341 (TG)n#Simple_ 51 TGTGTGTGTGTGTGTGTGTGTGTGTGTG 78 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 77), avg. gap size = 0.0 (0 / 0) 348 24.34 0.79 9.40 chr1ptel1M 577415 577541 (422459) C MIR1_Amn#SINE/MIR (113) 117 1 m_b16s601i8 587 chr1ptel1M 577415 GGGGTTAAGTGACTTGCCCAGGGTCACACAGCTAGGAAGTGTTAAGTGTG 577464 i ? i ? ?i v? vi ------ C MIR1_Amn#SINE 117 GAGGTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNAGTGGCA------ 74 chr1ptel1M 577465 TGAGAC-AGATTTGAACTCGTGTCCTCCTGACTTCAGGGCTGGTCTTCTA 577513 - v -i ? ? i iv - i v i vi v ii vi C MIR1_Amn#SINE 73 -GAGCCGGGANTNGAACCCAGGT-CTCCCGAGTCCCAGTCCAGTGCTCTA 26 chr1ptel1M 577514 TCCACTGTGCCACCTAGCTGGCCCCCCA 577541 ivi ---i v i i C MIR1_Amn#SINE 25 TCCACTAGACCAC---ACTGCCTCCCTA 1 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.71 CpG sites = 18, Kimura (unadjusted) = 32.10 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.10 (12 / 126), avg. gap size = 1.00 (12 / 12) 484 21.99 0.89 6.60 chr1ptel1M 577415 577526 (422474) C MIRc#SINE/MIR (153) 115 10 m_b16s601i7 587 chr1ptel1M 577415 GGGGTTAAGTGACTTGCCCAGGGTCACACAGCTAGGAAGTGTTAAGTGTG 577464 i i v vi ------ C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCA------ 72 chr1ptel1M 577465 TGAGAC-AGATTTGAACTCGTGTCCTCCTGACTTCAGGGCTGGTCTTCTA 577513 - v -i i i i iv i i i v ii vi v C MIRc#SINE/MIR 71 -GAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTT 23 chr1ptel1M 577514 TCCACTGTGCCAC 577526 ii C MIRc#SINE/MIR 22 TCCACTGCACCAC 10 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 25.45 CpG sites = 16, Kimura (unadjusted) = 26.79 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.07 (8 / 111), avg. gap size = 1.00 (8 / 8) 522 24.11 11.70 0.53 chr1ptel1M 577884 578054 (421946) C MIRc#SINE/MIR (0) 268 79 m_b16s601i9 588 chr1ptel1M 577884 AATAATAGCTAGTCTTTAGAT----ACAGC-TTTTAAGCTTTGCAAAGCA 577928 iiv v? i v ---- i -i viv i i C MIRc#SINE/MIR 268 AATAATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCG 219 chr1ptel1M 577929 CTTT-GCAAACATGTCTTTC-TTGGATACTCACAATAAGTCTGAGAAGTA 577976 -i v - v i - v v i vi v i C MIRc#SINE/MIR 218 CTTTCACATACAT-TATCTCATTTGATCCTCACAACAACCCTGTGAGGTA 170 chr1ptel1M 577977 GGC------GTTATTATCACCCCCATCTTATAGATGTGGAAACTGAGG-- 578018 ------ v i i i i v -- C MIRc#SINE/MIR 169 GGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCT 120 chr1ptel1M 578019 --AAGACAGCA---GACTCACCTAAGGTGACATAGCTATTA 578054 --i vivi --- ii i v i v C MIRc#SINE/MIR 119 CAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTA 79 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.03 CpG sites = 24, Kimura (unadjusted) = 29.89 Transitions / transversions = 1.41 (24/17) Gap_init rate = 0.05 (9 / 170), avg. gap size = 2.33 (21 / 9) 21 15.87 4.08 0.00 chr1ptel1M 579616 579664 (420336) (AGAC)n#Simple_repeat 1 51 (0) m_b16s252i3 589 chr1ptel1M 579616 AGAGAGATGGACACACAGACAG--AGACGGACACACAGACAGACACACAG 579663 v ii v -- i v v (AGAC)n#Simpl 1 AGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAG 50 chr1ptel1M 579664 A 579664 (AGAC)n#Simpl 51 A 51 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.02 (1 / 48), avg. gap size = 2.00 (2 / 1) 429 30.64 2.14 0.53 chr1ptel1M 579906 580092 (419908) L1M3_orf2#LINE/L1 1426 1615 (1673) m_b16s551i10 590 chr1ptel1M 579906 GGAGAAATCTATCAATCTTTAAAAGAATAATTAGTACCTATGCTTCACAA 579955 v v i v v v v i v v v L1M3_orf2#LIN 1426 GGTGAATTCTACCAAACATTTAAAGAAGAATTAATACCAATCCTTCTCAA 1475 chr1ptel1M 579956 ATTCTTCTCAAAAATTGA----GAAAGAACCCCACCAAAATTTCTTTTAT 580001 i iv ---- ii v iv - i iv L1M3_orf2#LIN 1476 ACTCTTCCAAAAAATTGAAGAGGAGGGAACACTTCC-AAACTCATTTTAT 1524 chr1ptel1M 580002 GAGACAAATATAGTCCTACTACCTAAAGCAGGGAACGAAAAAACACAGAA 580051 i v ii vii iv v iv iv v v vv vii L1M3_orf2#LIN 1525 GAGGCCAGCATTACCCTGATACCAAAGCCAGACAAAGACACTACAAGAAA 1574 chr1ptel1M 580052 GGAAAATAGTAGGCCAATATCATTAGTAAATATTGACTCAA 580092 i ivii vi ii i i v iv L1M3_orf2#LIN 1575 AGAAAACTACAGGCCAATATCCCTGATGAACATAGATGCAA 1615 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.98 CpG sites = 29, Kimura (unadjusted) = 39.98 Transitions / transversions = 1.04 (29/28) Gap_init rate = 0.01 (2 / 186), avg. gap size = 2.50 (5 / 2) 304 25.37 9.04 3.54 chr1ptel1M 580130 580317 (419683) L1MEi_5end#LINE/L1 2010 2207 (5) m_b16s551i11 591 chr1ptel1M 580130 GAGAAAAGAAAGAGAAAAAACCATAATCTGGGGTTA----ACAAGACGGC 580175 i i? i i? iv v v iiivi ---- i i i L1MEi_5end#LI 2010 GAAAAAGNAAAGAAAAAGNATGATAAACAGAAAACACAAAATAAGATGGT 2059 chr1ptel1M 580176 AGGAAATA----CAGA---ATTAGTAATCTTAATCATAAAGGTGAATGGG 580218 - ---- i --- i --- iv v i i L1MEi_5end#LI 2060 AG-AAATAAGTCCAAATATATCAGTAATC---ACAATAAATGTAAATGGA 2105 chr1ptel1M 580219 ATAAACTCTCCCAT--AAAG-CAGAGGCCAATAGCAGACTGGATTAAAAA 580265 v v i -- - --- v v i L1MEi_5end#LI 2106 TTAAACTCACCTATTAAAAGACAGAG---ATTATCAGATTGGATTAAAAA 2152 chr1ptel1M 580266 CCAGAATCCTACAATA---TGTTAACAGGAAACACACTTGAAGCAGGGTG 580312 vv i vi v --- v i i i i i iiii L1MEi_5end#LI 2153 AAAAAATCCAGCTATATGCTGTTTACAAGAGACACACCTAAAACAAAACG 2202 chr1ptel1M 580313 ATACA 580317 i L1MEi_5end#LI 2203 ACACA 2207 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 31.83 CpG sites = 31, Kimura (unadjusted) = 32.71 Transitions / transversions = 2.07 (31/15) Gap_init rate = 0.07 (13 / 187), avg. gap size = 1.85 (24 / 13) 390 19.26 6.94 2.67 chr1ptel1M 580164 580307 (419693) L1MEh_5end#LINE/L1 2079 2228 (7) m_b16s551i12 591 chr1ptel1M 580164 TAACAAGACGGCAGGAAATA---CAGAAT-TAGTAATCTTAATCATAAAG 580209 i i - --- v? - ?i i vv v iv v L1MEh_5end#LI 2079 TAATAAGATGGCAG-AAATAAGTCCNAATATANCAGTAATTACAATAAAT 2127 chr1ptel1M 580210 GTGAATGGGATAAACTCTCCCAT--AAAG-CAGAGGCCAATAGCAGACTG 580256 i v v v -- - --- v ?v i L1MEh_5end#LI 2128 GTAAATGGGTTAAACTCACCAATTAAAAGACAGAG---ATTNTCAGATTG 2174 chr1ptel1M 580257 GATTAAAAACCAGAATCCTACAATATGTTA---ACAGGAAACACACTTGA 580303 ? v i v i i--- i i i L1MEh_5end#LI 2175 GATTNAAAAACAAAATCCAACAATATGCTGTCTACAAGAGACACACTTAA 2224 chr1ptel1M 580304 AGCA 580307 i L1MEh_5end#LI 2225 AACA 2228 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 23.24 CpG sites = 14, Kimura (unadjusted) = 23.24 Transitions / transversions = 1.08 (14/13) Gap_init rate = 0.06 (9 / 143), avg. gap size = 1.56 (14 / 9) 4602 28.48 4.06 3.20 chr1ptel1M 580205 583088 (416912) L1M5_orf2#LINE/L1 38 2945 (349) m_b16s551i13 591 chr1ptel1M 580205 TAAAGGTGAATGGGATAAACTCTCCCAT---AAAGCAGAGGCCAATAGCA 580251 v i ?v v v --- i --- v iv L1M5_orf2#LIN 38 TAAATGTAAATGGNCTAAACACTCCAATTAAAAGGCAGAG---ATTGTCA 84 chr1ptel1M 580252 GACTGGATTAAAAACCAGAATCCTACAATATGTTA---ACAGGAAACACA 580298 v v ii i v v i i--- i i i L1M5_orf2#LIN 85 GACTGGATAAAAAAACAAGACCCAACTATATGCTGTCTACAAGAGACGCA 134 chr1ptel1M 580299 CTTGAAGCAGGGTGATACATACAGAGTAAAGGTAAAAGGCTGAAGCAGAA 580348 v ii viiv i v ? iv i i v i iv ii L1M5_orf2#LIN 135 CTTTAAATATAAAGACACAGANAGGTTGAAAGTAAAAGGATGGAAAAAGA 184 chr1ptel1M 580349 TCTATTATGCTTCAGGTGAAGTCAAA-AAAGGAGAGGTAGCTATCCTGAT 580397 v ii v-v viiv ?iv - vv i? i vi i L1M5_orf2#LIN 185 TATACCATGCA-AACACTAANCAAAAGAAAGCTGGNGTGGCTATATTAAT 233 chr1ptel1M 580398 CTCAGATCAAGCA------AAAGCAAAAATTGATCTGATTAAAAGAGATA 580441 v iv i ------ i i --- --- vv L1M5_orf2#LIN 234 ATCAGACAAAGTAGACTTCAAGGCAAGAA---AT---ATTACCAGAGATA 277 chr1ptel1M 580442 AGGGAGGGCACTATATCTTGCTAAAGGG--CAGCATAGATAATGAAGCAA 580489 i ii i i vi vv v i -- -- vv v v vv L1M5_orf2#LIN 278 AAGAGGGACATTTCATAATGATAAAAGGGTCA--ATTCATCAAGAAGACA 325 chr1ptel1M 580490 TATCAATACTAAACAT--ATGCACCAAATTGTATAGCATCTAAATCCCTA 580537 v v ii -- v vii v v v v v i L1M5_orf2#LIN 326 TAACAATCCTAAATGTGTATGCACCTAATAACAGAGCTTCAAAATACATG 375 chr1ptel1M 580538 AAAGAGAAGTTGATAG--TTACAAAAAGAAATAGACAGTAAAACTATAAT 580585 iv i ii i --i v ii --- v i i L1M5_orf2#LIN 376 AAGCAAAAACTGACAGAACTAAAAGGAGAAATAGACA---AATCCACAAT 422 chr1ptel1M 580586 ---AGTAGTAGATGTCATCCTTGCTCTCTCAGAACTAGATAAATCAAACC 580632 --- ? v v i v vi?v v v v i v iiv L1M5_orf2#LIN 423 TATAGTNGGAGATTTTAACACNCCTCTCTCAGTAATTGATAGAACAAGTA 472 chr1ptel1M 580633 -ACAAAATAAATAAGAAAGAAGTTAAAGGGGTAAATAGAACACTAGAAA- 580680 - -- v v i vv i i iv vi - v vv - L1M5_orf2#LIN 473 GACAAAA--AATCAGTAAGGATATAGAAGATTTGA-ACAACACTATCAAC 519 chr1ptel1M 580681 -AGTTAGGTATGATAGATCTTTGGAGAACACTG-----AAGGGAGGCAGA 580724 - ii v iiv i v iv iv ?----- viiv? L1M5_orf2#LIN 520 CAACTTGACCTAATTGACATTTATAGAACACTNCACCCAACAACNGCAGA 569 chr1ptel1M 580725 AAGGAGTACACTTTCTTCTCGGCAGTTGATGGAACCTATACAAAAACTGA 580774 ----- v i iivv ivv v v v i iv L1M5_orf2#LIN 570 A-----TACACATTCTTTTCAAGTGCACATGGAACATTTACCAAGATAGA 614 chr1ptel1M 580775 CCATATATTAGGACATAAAA---ACCTCAAACTCAAATGCAGTAAGGCAG 580821 ?i i v ---ii ---i vi?iv i iiv L1M5_orf2#LIN 615 CCATATNCTGGGCCATAAAACAAGTCTCAA---TAAATTTNAAAGGATTG 661 chr1ptel1M 580822 AAATAGTA-AATGCATCCTTTTCAGATCATGATGCAATAAAAATTACATT 580870 vi - iv i v- i v i ii v v v viv v L1M5_orf2#LIN 662 AAATCATACAGAGTATG-TTCTCTGACCACAATGGAATTAAATTAGAAAT 710 chr1ptel1M 580871 CAATAAAAAGCCAAGTTCTATTTTCATAGAA----CAAAAAGTAATTGGA 580916 v i-- ---- v?ii v i ---- --- v L1M5_orf2#LIN 711 CAATAACAAA--AAG----ATANCTAGAAAATCCCCAAA---TATTTGGA 751 chr1ptel1M 580917 AACTAAATAATCTCA-TCCTAAAGAATGATTGGGTGAAACAGCAAATCAG 580965 i i - v - i v ivvv v v iv v L1M5_orf2#LIN 752 AATTAAACAA-CACACTTCTAAATAACCCATGGGTCAAAGAAGAAATCAC 800 chr1ptel1M 580966 ACAC---AATTA----ATAATTTCACCCAAGAGAATGACAATAATGAGAT 581008 - ?--- ---- v v v i---- ? i vi v i L1M5_orf2#LIN 801 A-ANGGAAATTAGAAAATATTTTGAACT----GAATGANAATGAAAATAC 845 chr1ptel1M 581009 GACATACCAAAATGTGTGGGATGTAGCTAAAGTGGTAATAAGGGGAAATT 581058 i i v i ii iv v i i v L1M5_orf2#LIN 846 AACATATCAAAATTTGTGGGATGCAGCTAAAGCAGTGCTTAGAGGGAAAT 895 chr1ptel1M 581059 TTATATCTCTAGAGGCTTACTTGCATAAAATAGAGAAAGAGA--AAAATC 581106 v ?i i v ? iv --- i v ii ii v-- L1M5_orf2#LIN 896 TTATAGCNTTAAATGCNTATAT---TAGAAAAGAAGAAAGGCTTAAAATC 942 chr1ptel1M 581107 AATGAATAAGGCTTGCAACTAGAAAAGCTAGAAAAA--AGAGCAAATTAA 581154 viv i v v vi i -- L1M5_orf2#LIN 943 AATGATCTAAGCTTCCACCTTAAGAAGCTAGAAAAAGAAGAGCAAATTAA 992 chr1ptel1M 581155 AAAACCCCAAA--CACTAAACTT---GAAATTCTAAAATTAAAAGGAGAA 581199 ---- --v v i vvv--- vv iv i v L1M5_orf2#LIN 993 A----CCCAAAGNAAGTAGAAGGAAGGAAATAATAAAGATAAGAGCAGAA 1038 chr1ptel1M 581200 ATTAATAAAATTGAAAGTAAAAAAACCTATTGAATTAATAAATAAAACTA 581249 i i v ii ? ? v- v ivv v ii i i L1M5_orf2#LIN 1039 ATCAATGAAATAGAAAACAAANANACA-ATAGAGAAAATCAACGAAGCCA 1087 chr1ptel1M 581250 AGAGGTGATTTTATGAAAAAACCAACAAAATAGATAAACCCTTGGTAAAT 581299 i v i i v i i i v ii i i? iv L1M5_orf2#LIN 1088 AAAGCTGGTTCTTTGAAAAGATCAATAAAATTGATAAACCTCTAGCNAGA 1137 chr1ptel1M 581300 TTGATCAGAAAAAGGAAAGAGGAAAATCAAATTGTTAGTCTTAAAAATGA 581349 i ii ii i i i vv iii i v i ii L1M5_orf2#LIN 1138 CTGATCAAGAAAAAAAGAGAGAAGACACAAATTACCAATATCAGGAATGA 1187 chr1ptel1M 581350 AAAGGGAGAATTTGTCACTAATGA----AGAGGAAAGTAGAGCAATAATT 581395 i ---ii vv ---- v - v v i ivi v L1M5_orf2#LIN 1188 AAAAGGAGA---CATCACTACAGATCCTACAG-ACATTAAAAGGATAATA 1233 chr1ptel1M 581396 AGGAGTTACTTTGCCCAACTTTATGCCAATAAATTTGATAACTTAAATGA 581445 iiiv i v vv ? i L1M5_orf2#LIN 1234 AGAGAATATTATGAACAACTTTATGCCAATAAATTTGANAACTTAGATGA 1283 chr1ptel1M 581446 --TGAGTA----CCTTCAAAAATATAGGTTGCACAGATTAAC---AGAAG 581486 -- iii ---- v i i i? i vv i i i --- L1M5_orf2#LIN 1284 AATGGACAAATTCCTTGAAAAACACAANTTACCAAAACTGACNCAAGAAG 1333 chr1ptel1M 581487 AAAAAGTAAATTGGTTAAATAGTCCCAT-TTTAGAAAAAGAAATAGAACA 581535 v v i--- i i i - i vv - v iv L1M5_orf2#LIN 1334 AAATAGAAAATC---TGAATAGCCCTATATCTATTAAA-GAAATTGAATT 1379 chr1ptel1M 581536 AGCTATTAATTAACTCCCTAAGAAAAAATTCCCAGAACCAGATGGATTTA 581585 v iv vv v i i vi i vii iv v i L1M5_orf2#LIN 1380 TGTAATTAAAAACCTTCCCACAAAGAAAACTCCAGGCCCAGATGGCTTCA 1429 chr1ptel1M 581586 CAGGTGAATTCTAACAAACATTTAAAGAACAATTAACTCCAATGCTATAT 581635 v v i v v iv vi i i L1M5_orf2#LIN 1430 CTGGTGAATTCTACCAAACATTTAAGGAAGAAATAATACCAATCTTACAC 1479 chr1ptel1M 581636 AAACTATTTGAAAAAATAGGGAATGAAGGAATCCTACCAAATTCCTTTTA 581685 v iv i ii v i iv v v i v L1M5_orf2#LIN 1480 AAACTCTTCCAGAAAATAGAAAAAGAGGGAACACTTCCCAACTCATTTTA 1529 chr1ptel1M 581686 TGACACGGACATGGTGCCGATAACTAAATCAGGTAG-GACAATAACAGAG 581734 vi vii ?iiv i v v i ? ii i- v vv - L1M5_orf2#LIN 1530 TGAGGCCAGCATNACCCTGATACCAAAACCNGACAAAGACATTACAAGA- 1578 chr1ptel1M 581735 AAAGAAAATTACAGACCAATCTCCCTAATGAACATCAATGCAAAAATCTT 581784 v v vi i L1M5_orf2#LIN 1579 AAAGAAAATTACAGACCAATATCCCTCATGAACATAGATGCAAAAATCCT 1628 chr1ptel1M 581785 AAATAAAATATTAGCAAAAAGATTACAGAAAATCATCTCCAGGATAAAAC 581834 ? i vv v v v vvi vvvv v L1M5_orf2#LIN 1629 NAACAAAATATTAGCAAATCGAATCCAGCAATATATAAAAAGGATAATAC 1678 chr1ptel1M 581835 ACCATGACCAAGTGGGATTTATACCAAGAATGCAGGGCTGGTTCAATATT 581884 i i v i i i i i L1M5_orf2#LIN 1679 ATCATGACCAAGTGGGGTTTATCCCAGGAATGCAAGGTTGGTTTAACATT 1728 chr1ptel1M 581885 AGGAAAACTACTATTAATATAATTGACTATATCAATA-ACTAAATTAACA 581933 -v ii -- i i v i i i - v -vi v L1M5_orf2#LIN 1729 -CGAAAATCA--ATCAATGTAATTCACCATATTAACAGAATAAA-GGAGA 1774 chr1ptel1M 581934 AAAAACATATAATCATCTCAATAGATGCAGAAAAAGCATTTGATAAAATC 581983 v i i i L1M5_orf2#LIN 1775 AAAATCATATGATCATCTCAATAGATGCAGAAAAAGCATTTGACAAAATT 1824 chr1ptel1M 581984 CAACATTCATTCCTATTAAAAACACT--GGAGAGTACAGGAATAAATGGA 582031 ii v iv v -- v i v -- i v i L1M5_orf2#LIN 1825 CAACACCCATTCATGATAAAAACTCTCAGCAAACT--AGGAATAGAAGGG 1872 chr1ptel1M 582032 CTTTTTCTTAAAATAGTCAGTAGCATCTATTTAAAACCATCAGTAAGCAT 582081 vvi i i vv ii v ivi ivv vv i? i L1M5_orf2#LIN 1873 AACTTCCTCAACCTGATAAAGGGCATCTACGAAAAACCTACAGCNAACAT 1922 chr1ptel1M 582082 CATATGTAATGGGACTAAACTGCAACCATTCCCAGTAAGATCAGGAATGA 582131 iv vivv ? v ?v v vv i ii L1M5_orf2#LIN 1923 CATACTTAATGGTGAAANACTGAANGCTTTCCCCCTAAGATCGGGAACAA 1972 chr1ptel1M 582132 AACAAGGTTGCCCACTATCACCATTACTATTCAGTATTGTATCAGAAATG 582181 i v i i ? i v ii iii ii v L1M5_orf2#LIN 1973 GACAAGGATGTCCGCTNTCACCACTTCTATTCAACATTGTACTGGAGGTC 2022 chr1ptel1M 582182 CTAGCTTTGGCAATAAG--ATGAAAAAGAAACGAAAGGAATTAGAGTAGG 582229 ivvv -- v ii v v iii v L1M5_orf2#LIN 2023 CTAGCCAGTGCAATAAGGCAAGAAAAAGAAATAAAAGGCATAAAGATTGG 2072 chr1ptel1M 582230 CAATGAGGAAACCAA----TCACTCTTTGAAGATGATATGACGGTATACT 582275 v v i iv ---- ?i v i v i iv ? v L1M5_orf2#LIN 2073 AAAGGAAGAAATAAAACTGTCNTTATTCGCAGATGACATGATTGTNTACG 2122 chr1ptel1M 582276 TAGAGAAGTCCAGAGATTCTACTAAAAAGCTATTAGAAATAATCCACAAC 582325 i vi ? i v v ? i i v vviii v L1M5_orf2#LIN 2123 TAGAAAATCCNAAAGAATCTACAAANAAACTACTAGAACTAATAAGTGAA 2172 chr1ptel1M 582326 TTTAGCAAAGTTGCAGGATACAAAGCAAATCCAC-ATAATCATTAATATT 582374 i i ? i iv vi - v v vi L1M5_orf2#LIN 2173 TTTAGCAAGGTCGCNGGATACAAGGTCAATATACAAAAATCAATTGTATT 2222 chr1ptel1M 582375 TCTATACAGCACTAACAAAATCCAACAGCAA---GAGATACAAAGAAAAA 582421 i vi vi --- iv v --- i vi? i v L1M5_orf2#LIN 2223 TCTATATACTAGCAACAAA---CAATTGGAAAATGAAATTTNAAAAACAA 2269 chr1ptel1M 582422 TTCCATTTAAAACAATTGCTGATAGTATAAAATATTTAGGAATCTATCTG 582471 v v i iivv vi v ii ? i vv i L1M5_orf2#LIN 2270 TACCATTTACAATAGCATCAAAAAACATNAAATACTTAGGAATAAATCTA 2319 chr1ptel1M 582472 CCAAGGGAAAAT---CAGGAACTATATGAGCAAAACTACAAAACACTCC- 582517 v --- ? --- i v ? iivvv i v - L1M5_orf2#LIN 2320 ACAA---AANATGTGCAAGACCTNTACACTGAAAACTACAAAACATTGCT 2366 chr1ptel1M 582518 -ACACAAATAAAGTCAGATTTAAACAACTGGAAAACTATTAAGTGCTCCT 582566 - v v v ivv ii i v i iv vvvi i v L1M5_orf2#LIN 2367 GAGAGAAATTAAAGAAGACCTAAATAAATGGAGAGATATACCATGTTCAT 2416 chr1ptel1M 582567 GGATAGGTCGAGTAAATATAATAAGGATGACAATAGTACCTAAACTAAT- 582615 v vv v v vi ? i v vv v i i i - L1M5_orf2#LIN 2417 GGATTGGAAGACTCAATATTGTNAAGATGTCAATTCTCCCCAAATTGATC 2466 chr1ptel1M 582616 -----ATTTAGTGCTATGCCAATCAGACTCCCAAGAAACTATTTTACTGA 582660 ----- i i v v i v iv iii v iiv L1M5_orf2#LIN 2467 TATAGATTCAATGCAATCCCAATCAAAATCCCAGCAGGTTTTTTTGTAGA 2516 chr1ptel1M 582661 CATAGAAAAAATAACAATAAAATTCATCTGGAAGAACAAA--ACTCAAGA 582708 v v v iv i ivv i v ivi -- - ? L1M5_orf2#LIN 2517 AATTGACAAGCTGATTCTAAAATTTATATGGAAATGCAAAGGAC-CNAGA 2565 chr1ptel1M 582709 AT-TTCAAGGGAA-CTAATGAAAAAAAAAATCAAATGAAGGTGGCCTAAC 582756 -vi iiv - -- i i v - vv v v v L1M5_orf2#LIN 2566 ATAGCCAAAACAATCT--TGAAAAAGAAGAACAAA-GTTGGAGGACTTAC 2612 chr1ptel1M 582757 TGTACCTGATTT-AAAACTATATTATAAAGCAGTAGTCACAAAAACCATT 582805 vv ? ? - i - vii v iv i vi v L1M5_orf2#LIN 2613 ACTACCNGATNTCAAGACT-TATTATAAAGCTACAGTAATCAAGACAGTG 2661 chr1ptel1M 582806 TGGTATTGGT-TAAGAAATAGCTTAGTTGATCAGTGGAATAAGTTAG--- 582851 i- -i viv i v i i iiv --- L1M5_orf2#LIN 2662 TGGTATTGGCGTAAG-GATAGACAAATAGATCAATGGAACAGAATAGAGA 2710 chr1ptel1M 582852 GTTCACAAGACAAAATATTCAATTAC---TATAGCAATCTAGTGTTTGAC 582898 i --- - v v ii --i --- i ?v ?i ii v L1M5_orf2#LIN 2711 GTCC---AGA-AATAGACCCA--CACATATATGGNCANTTGATTTTTGAC 2754 chr1ptel1M 582899 AAA---CCCAAAGACCCCAACTT-TTGGGATAAGAATGCACTATTTGACA 582944 ---v ? ---- i i-v iv i ivv v ii L1M5_orf2#LIN 2755 AAAGGTGCCAANG----CAATTCAGTGGGGAAAGGATAGTCTTTTCAACA 2800 chr1ptel1M 582945 AAAACTGCTGGGAAAATTGGAAACTAGCATGGCAGAAACTAGGCATTGAC 582994 viv i v v iivii v i v iii?v i L1M5_orf2#LIN 2801 AATGGTGCTGGAACAATTGGATATCCATATGGAAAAAAATGAANCTCGAC 2850 chr1ptel1M 582995 CCATACTCAACATTGTACAC-CAAGTTAAGATCAAAATTGGTTCAT-GAC 583042 v iiv iii -v i v- ? i - v - L1M5_orf2#LIN 2851 CCCTACCTCACACCATACACAAAAATTAAT-TCNAGA-TGGATCATAGAC 2898 chr1ptel1M 583043 CTAGGCAT-TAAAAAAAGAGATTATAAATAAAT--TAGAAG--AATATAG 583087 i-- - i?vi i i -- v -- -- i L1M5_orf2#LIN 2899 CTAA--ATGTAAAAGNTAAAACTATAA--AACTTCTAGAAGAAAACATAG 2944 chr1ptel1M 583088 G 583088 L1M5_orf2#LIN 2945 G 2945 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 36.64 CpG sites = 415, Kimura (unadjusted) = 37.17 Transitions / transversions = 1.09 (415/380) Gap_init rate = 0.05 (145 / 2883), avg. gap size = 1.45 (210 / 145) 806 32.78 4.65 2.88 chr1ptel1M 583110 583690 (416310) L1ME5_3end#LINE/L1 70 660 (281) m_b16s551i14 591 chr1ptel1M 583110 TGGAGGAAGGATATGAACAGACCATTTTCGGATGATGAAATT-GAAA--C 583156 ivi i v v i v v ii- -- L1ME5_3end#LI 70 TGGGCAAAGGATATGAACAGGCAATTTACAGAAGAGGAAACCCGAAAGGC 119 chr1ptel1M 583157 TATTTCTACTCATATGAAAAAGTGTTCTAAATCATTATTGATCAGA---- 583202 ---vi vv i ii i v v v i ---- L1ME5_3end#LI 120 TA---ACAAGCATATGAAGAGATGCTCAAACTCATTAGTAATCAGAGAAA 166 chr1ptel1M 583203 --CAATTCTGATCAACTCTGAGACACTACTACAACACTTATTAGATTAGC 583250 -- v ivi v vv i ii vi - i i i L1ME5_3end#LI 167 TGCAAATTAAAACAACAATGAGATATCACTTTA-CACCTATTAGACTGGC 215 chr1ptel1M 583251 TAGAATGACAGGGAAAGATAATGTAGAATATTGGAGGGGATGTGGGAAAA 583300 v i v v ii vvi ivi i i v i i ? L1ME5_3end#LI 216 AAAAATTAGAAAGCTGGATAATGCCAAGTGTTGGCGAGGATGTGGGGANA 265 chr1ptel1M 583301 ATGGGACACTGATGCATGGTTGGATGAATTGTGAAGGGATCCAACCATTC 583350 vv i v v iv i vv i v ii vv i v i L1ME5_3end#LI 266 TAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACTGGTGCAGCCATTC 315 chr1ptel1M 583351 TGTAGAGGAATTTTGAACTA--TACTCAAA--AAGTTATCAAACTGTGCA 583396 v v i v v v -- v -- - --- --- L1ME5_3end#LI 316 TGGAGAGCAATCTGGCAGTACTTAGTCAAATTAAG-TAT---AC---GCA 358 chr1ptel1M 583397 TATCCTTTGATTCAGAAGTGTTACTACTTAGACTTATATCCCAAAGAGA- 583445 i v ii v i viii - i i iiv i - L1ME5_3end#LI 359 TACCCTATGACCCAGCAATTCCGCT-CCTGGGTATATATCCCAAAGAAAT 407 chr1ptel1M 583446 TCTTAAAGAAG---GGAAAGGGACCCACATGTGCAAAAATG----TGGCA 583488 i v v i ---iv i ---- i i ii ---- v L1ME5_3end#LI 408 TCTCACACAGGTCCATAAGGGG----ACATGTACGAGGATGTTCATTGCA 453 chr1ptel1M 583489 GCCCTTTTTGTAGTGGCTAGAAACTGGAAATTAAATGGATGACTGTCAAT 583538 vi v i vi i ii iiiv vv i v ii v L1ME5_3end#LI 454 GCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGGGTGTCCATCACT 503 chr1ptel1M 583539 TACAGAATGGCTGAATAAATTGTGGCATATGAATGTTATGGAATATTATT 583588 viv i v iii v iiv v iiii i i v L1ME5_3end#LI 504 GGGAGAGTGGATAGGTAAAATGTGGTGGATGCACACCATGGAGTACTATG 553 chr1ptel1M 583589 GTTCTATAAGAAATGACCAGCAGGATGAATACAGAGAGGCTTGGAGAGA- 583637 vvv vi v iii vii vi v i v vii v vi - L1ME5_3end#LI 554 CAGCAGTTAGAAGCAACGGACTAGATGTACACATAGCAACATGGATGGAT 603 chr1ptel1M 583638 CTTACAATTACTGATGCTAAGTGAAATGAAC-AGAACCAG---GAGATC- 583682 v vi - ii i vi ii- v --- ?- L1ME5_3end#LI 604 CTTAAAAACA-TAGTGCTGAGTGAAAAAAGTAAGAAACAGAATGAGATNT 652 chr1ptel1M 583683 ATTATACA 583690 v i L1ME5_3end#LI 653 ATAACACA 660 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 43.91 CpG sites = 104, Kimura (unadjusted) = 44.60 Transitions / transversions = 1.28 (104/81) Gap_init rate = 0.05 (30 / 580), avg. gap size = 1.47 (44 / 30) 12 23.14 6.90 1.64 chr1ptel1M 583944 584001 (415999) (TATA)n#Simple_repeat 1 61 (0) m_b16s252i4 592 chr1ptel1M 583944 TATAAATATGTATACATATAT-TGTATTTA-ACATATACTTTA-ACATAT 583990 v i i - i v - i - v - i (TATA)n#Simpl 1 TATATATATATATATATATATATATATATATATATATA-TATATATATAT 49 chr1ptel1M 583991 TTA-ACATGTAT 584001 v - i i (TATA)n#Simpl 50 ATATATATATAT 61 Matrix = Unknown Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.09 (5 / 57), avg. gap size = 1.00 (5 / 5) 14 12.68 0.00 0.00 chr1ptel1M 584117 584142 (415858) (AAAT)n#Simple_repeat 1 26 (0) m_b16s252i5 593 chr1ptel1M 584117 AAATGCATAAATAAACAAATAAATAA 584142 iv i (AAAT)n#Simpl 1 AAATAAATAAATAAATAAATAAATAA 26 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 514 22.48 0.81 5.98 chr1ptel1M 584206 584328 (415672) C MIRc#SINE/MIR (141) 127 11 m_b16s601i10 594 chr1ptel1M 584206 CTGAGGC-AATTGGGGTTAAGTGACTTACCCAGGGTCACACAGCCAAGAA 584254 -v vv i i i i iv C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAA 78 chr1ptel1M 584255 GTGTTACATGTTTGAGACCAGATTTGAACTCAGGTCCTCCTGACTTCAGG 584304 --i ----- v vi i i i i i i C MIRc#SINE/MIR 77 GTG--GCA-----GAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr1ptel1M 584305 GCGGGTGCTTTATCTACTACACCA 584328 v vi i v i i C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTGCACCA 11 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 26.15 CpG sites = 17, Kimura (unadjusted) = 27.37 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.07 (8 / 122), avg. gap size = 1.00 (8 / 8) 460 29.90 10.01 4.50 chr1ptel1M 584344 585082 (414918) L1M1_orf2#LINE/L1 1871 2648 (646) m_b16s551i16 595 chr1ptel1M 584344 GAACTTGTTTTAATATGATAAAATCAGCAATCTAAAATAAAC-------- 584385 v iii i i i --- v v vi i i -------- L1M1_orf2#LIN 1871 GAACATACCTCAACATAATAAAA---GCCATATACGACAGACCCACAGCT 1917 chr1ptel1M 584386 AGTATCATATAAAATGAGGATATATTAAAA--CTTTCC-CCAATA----- 584427 ivi i v v i i -- - i v ----- L1M1_orf2#LIN 1918 AGTATCATACTGAATGGGGAAAAACTGAAAGCCTTTCCTCTAAGATCTGG 1967 chr1ptel1M 584428 AACACAATTAAATCAAGAATGTTCACTTTTTCCACCGTTATTTAATAT-G 584476 i ------ i ii iv i i i - L1M1_orf2#LIN 1968 AACACGA------CAAGGATGCCCACTTTCACCACTGTTATTCAACATAG 2011 chr1ptel1M 584477 TTCTGGAAATGTTAGAAACAGCAGGAAGACAAAAGATAGAAATTAAAGAT 584526 v i vi vv v ivv i v v i ii L1M1_orf2#LIN 2012 TACTGGAAGTCCTAGCTAGAGCAATCAGACAAGAGAAAGAAATAAAGGGC 2061 chr1ptel1M 584527 ATAAAGATAGGCAAAGAAGAGCTCAAACTATCTCTATTTGCTGATGGTAT 584576 vv i v v i iv i ii i v i L1M1_orf2#LIN 2062 ATCCAAATTGGAAAGGAAGAAGTCAAATTATCCTTGTTTGCAGATGATAT 2111 chr1ptel1M 584577 GATCATGTACTTGAAAAATCCTAGGAAATCAGCAAAGGTACTA--AGA-- 584622 v i i i v iii v vi ? iiv -- -- L1M1_orf2#LIN 2112 GATCTTATATTTGGAAAAACCTAAAGACTCCACNAAAAAACTATTAGAAC 2161 chr1ptel1M 584623 TGATTAAGAGA------ACAGTTGC-----------TT--CCT-TAAAAA 584652 v v i ------ v ----------- i-- v -i L1M1_orf2#LIN 2162 TGATAAACAAATTCAGTAAAGTTGCAGGATACAAAATCAACATACAAAAA 2211 chr1ptel1M 584653 TCAACTGCATTTCTATAT---AACACTACACAA---GAAACAGAAATAGA 584696 iiv --- v iv --- v vi L1M1_orf2#LIN 2212 TCAGTAGCATTTCTATATGCCAACAGTGAACAATCTGAAAAAGAAATCAA 2261 chr1ptel1M 584697 AAGGGAAATTTCATTCCAAATAACTCCAAAATGCACAAAATATATAAGGA 584746 ii v ii ivv i iv vviv iv iv - L1M1_orf2#LIN 2262 AAAAGTAATCCCATTTACAATAGCCACAAATAAAATTAAATACCT-AGGA 2310 chr1ptel1M 584747 ATGATCT--ACCAAAGCATTCAAA-ATGCTTAT--TACAAACTGT----- 584786 v v -- v v v - vii i-- iv i ----- L1M1_orf2#LIN 2311 ATTAACTTAACCAAAGAAGTGAAAGATCTCTACAATGAAAACTATAAAAC 2360 chr1ptel1M 584787 --TTCTTAAAGAAA-TAAAGAATAATTTAAATAGCTGGAGGAAAATTCAA 584833 -- vv v - i iv vvii - iv iii v v L1M1_orf2#LIN 2361 ACTGATGAAAGAAATTGAAGAGGACACCAAA-AAATGGAAAGATATTCCA 2409 chr1ptel1M 584834 TGCTCATTACT---AAGTAATGCAAATATAATAAAAATGATAATACTGCC 584880 i viv --- - - - vi v viv i L1M1_orf2#LIN 2410 TGTTCATGGATTGGAAG-AAT-C-AATATTGTTAAAATGTCCATACTACC 2456 chr1ptel1M 584881 AAAGTTAATTTATAGTCTTAATGTTATATCAATCAAATTACTAATAAAAC 584930 v ivi i i vi i iv vi v v i i v i L1M1_orf2#LIN 2457 CAAAGCAATCTACAGATTCAATGCAATCCCTATCAAAATACCAATGACAT 2506 chr1ptel1M 584931 TTTAAAATAATAACAAATAGTAATAAAAAGAGAAATAAATAATAATAGAA 584980 i ----------------- v i i v - i vv i L1M1_orf2#LIN 2507 TCT-----------------TCACAGAAATAGAAA-AAACAATCCTAAAA 2538 chr1ptel1M 584981 TTCATTTGGGAAAAAAGGAAAACATCTAGACT-GTCAAGGGCAAC--GAT 585027 i v --- vviv v i i v - i i vi v -- v L1M1_orf2#LIN 2539 TTTATATGG---AACCACAAAAGACCCAGAATAGCCAAAGCTATCCTGAG 2585 chr1ptel1M 585028 TAAAAGAAATA-------AGGAATAGCATT-TCAGATTTCCAATCATATT 585069 i ii i ------- vi -i v i v i i L1M1_orf2#LIN 2586 CAAAAAGAACAAAACTGGAGGAATCACATTACCTGACTTCAAATTATACT 2635 chr1ptel1M 585070 ATAAAGCATTAGT 585082 i i vv L1M1_orf2#LIN 2636 ACAGAGCTATAGT 2648 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 38.69 CpG sites = 116, Kimura (unadjusted) = 39.17 Transitions / transversions = 1.22 (116/95) Gap_init rate = 0.08 (59 / 738), avg. gap size = 1.85 (109 / 59) 617 28.16 10.80 2.25 chr1ptel1M 584344 584917 (415083) L1M5_orf2#LINE/L1 1872 2493 (801) m_b16s551i15 595 chr1ptel1M 584344 GAACTTGTTTTAATATGATAAA----ATC----AGCAATCTAAAATAAAC 584385 -ii i iv ---- ---- iv i v ii? L1M5_orf2#LIN 1872 GAACTT-CCTCAACCTGATAAAGGGCATCTACGAAAAACCTACAGCNAAC 1920 chr1ptel1M 584386 AGTATCATATAAAATGAGGATATATTAAAA-CTTTCCCCAATAAA--CAC 584432 --- ivv iv v ? i i ?- v- i-- iv L1M5_orf2#LIN 1921 A---TCATACTTAATGGTGAAANACTGAANGCTTTCCCCC-TAAGATCGG 1966 chr1ptel1M 584433 AATTAAATCAAGAATGTTCACTTTTTCCACCGTTATTTAATAT-GTTCTG 584481 i vi iv i i i ? iv ivi i i - v L1M5_orf2#LIN 1967 GAACAAGACAAGGATGTCCGCTNTCACCACTTCTATTCAACATTGTACTG 2016 chr1ptel1M 584482 GAAATGTTAGAAACAGCAGGAAGACAAAAGATAGAAATTAAAGATATAAA 584531 ii vi vv vv iv i i i v v ii L1M5_orf2#LIN 2017 GAGGTCCTAGCCAGTGCAATAAGGCAAGAAAAAGAAATAAAAGGCATAAA 2066 chr1ptel1M 584532 GATAGGCAAAGAAGAGCTCAAACTATCTCTATTTGCTGATGGTATGATCA 584581 v v i iv v i ?i i v ii ii L1M5_orf2#LIN 2067 GATTGGAAAGGAAGAAATAAAACTGTCNTTATTCGCAGATGACATGATTG 2116 chr1ptel1M 584582 TGTACTTGAAAAATCCTAGGAAATCAGCAAAGG---TACTAAGATGATTA 584628 ? v ii ? iii vi ?i--- ii iv v L1M5_orf2#LIN 2117 TNTACGTAGAAAATCCNAAAGAATCTACAAANAAACTACTAGAACTAATA 2166 chr1ptel1M 584629 AGAGAA-----CA--GTTGCT----------TCCTT----AAAAATCAAC 584657 v ----- -- i ?---------- vv ---- i L1M5_orf2#LIN 2167 AGTGAATTTAGCAAGGTCGCNGGATACAAGGTCAATATACAAAAATCAAT 2216 chr1ptel1M 584658 TGCATTTCTATATAACACTACACAAGAAACAGAAATAGAAAGGGAAATTT 584707 i --- -i v -- v i iv L1M5_orf2#LIN 2217 TGTATTTCTATAT---ACTA-GCAACAAAC--AATTGGAAAATGAAATTT 2260 chr1ptel1M 584708 C-------ATTCCA-----AATAACTCCAAAATGCACAAAATATATAAGG 584745 ?------- v ----- i vi vi i? i- v L1M5_orf2#LIN 2261 NAAAAACAATACCATTTACAATAGCATCAAAAAACATNAAATAC-TTAGG 2309 chr1ptel1M 584746 AAT-GATCTACCAAAGCA--TTCAAAATGCTT---------ATTACAAAC 584783 -i v i? -- v i ivi? --------- i v L1M5_orf2#LIN 2310 AATAAATCTAACAAAANATGTGCAAGACCTNTACACTGAAAACTACAAAA 2359 chr1ptel1M 584784 TGTTTCTTAAAGAAA-TAAAGAATAATTTAAATAGCTGGAGGAAAATTCA 584832 ii v v i - -i ii iv ii v v v L1M5_orf2#LIN 2360 CATTGCTGAGAGAAATTAAAGAA-GACCTAAATAAATGGAGAGATATACC 2408 chr1ptel1M 584833 ATGCTCAT-TACTAAGTAATGCAAATATAATAAAAATGATAATACTGCCA 584881 i -v i iiivi iv - vi ? i vi v v v L1M5_orf2#LIN 2409 ATGTTCATGGATTGGAAGACTC-AATATTGTNAAGATGTCAATTCTCCCC 2457 chr1ptel1M 584882 AAGTTAATTTATAGTCTTAATGTTATATCAATCAAA 584917 i i i vi i iv vi L1M5_orf2#LIN 2458 AAATTGATCTATAGATTCAATGCAATCCCAATCAAA 2493 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 36.52 CpG sites = 96, Kimura (unadjusted) = 37.73 Transitions / transversions = 1.55 (96/62) Gap_init rate = 0.05 (31 / 573), avg. gap size = 2.45 (76 / 31) 705 29.56 2.14 2.14 chr1ptel1M 585548 585827 (414173) C L1ME4c_3end#LINE/L1 (244) 586 307 m_b16s551i17 596 chr1ptel1M 585548 AATCTTCCTCCTGATCATTTCTTACAGAATA-ATAATATTTCATACCATT 585596 i v vv v - vv iv i- i vvvi ? C L1ME4c_3end#L 586 AGTCTTCATAATTATCATTT-TTAATGGCTGCATAATATTCCATCGAGTN 538 chr1ptel1M 585597 CATATACCACAATTTACTCAGCCATTCTCTAACTGATGGGCATCCA--TT 585644 v i i i i i iv i v i ii -- C L1ME4c_3end#L 537 GATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAGGTT 488 chr1ptel1M 585645 CAGTTTTCAGTTTCTTGCCACTACAAAAAGAGCTGCCACAAACATTTTTG 585694 -- i i i i i i i v iv v ii i i C L1ME4c_3end#L 487 --GTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTCG 440 chr1ptel1M 585695 CCCATGTGGGTCCTTTTTCCTCCTTT--AA-GATCTCTTTGGGATACAGA 585741 iv i i --- i -- -v i i i v vv C L1ME4c_3end#L 439 TGCATATAG---CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAATT 393 chr1ptel1M 585742 CCTAGGAGAGATACTGCTGGATCAAAGGATATGAATAGTATGATGGCCCT 585791 i i v iv i i i i i v v v i C L1ME4c_3end#L 392 CCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTCT 343 chr1ptel1M 585792 TTAGGCATAGTTCCTTATTGCTCTCCAGAATGGCTG 585827 v vi i v v vv i i v i C L1ME4c_3end#L 342 TGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTG 307 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 37.06 CpG sites = 48, Kimura (unadjusted) = 38.90 Transitions / transversions = 1.45 (48/33) Gap_init rate = 0.04 (10 / 279), avg. gap size = 1.20 (12 / 10) 722 28.70 12.45 2.75 chr1ptel1M 585579 586076 (413924) C L1ME3E_3end#LINE/L1 (438) 551 7 m_b16s551i18 596 chr1ptel1M 585579 ATAATATTTCATACCATTCATATACCACAATTTACTCAGCCATTCTCTAA 585628 i i vvi vv i i v ivi C L1ME3E_3end#L 551 ATAGTATTCCATTGTATGAATATACCACAATTTATTTATCCATTCTCCTG 502 chr1ptel1M 585629 CTGATGGGCATCC--ATTCAGTTTTCAGTTTCTTGCCACTACAAAAAGAG 585676 ii i ii--i -- i i i i v iv C L1ME3E_3end#L 501 TCGATGGACATTTGGGTT--GTTTCCAGTTTTTTGCTATTACAAACAATG 454 chr1ptel1M 585677 CTGCCACAAACATTTTTGCCCATGTGGGTCCTTTTTC-CTCCTTTAAGA- 585724 i ii i iv --v vv v - v v vi - C L1ME3E_3end#L 453 CTGCTATGAACATTCTTGTACATGT--CTCCTGGTGCACACGTGCAAGAG 406 chr1ptel1M 585725 TCTCTTTGGGATACAGACCTAGGAGAGATACTGCTGGATCAAAGGATATG 585774 i i i i i v v iv i i iv i C L1ME3E_3end#L 405 TTTCTCTAGGGTATATACCTAGGAGTGGAATTGCTGGGTCGTAGGGTATG 356 chr1ptel1M 585775 AATAGTATGATGGCCCTT--TAGGCATAGTTCCTTATTGCTCTCCAGAAT 585822 ---v i vv viv i -- -- i v vv i i i i C L1ME3E_3end#L 355 ---CGCATCTTCAACTTTACTAG--ATAATGCCAAATTGTTTTCCAAAGT 311 chr1ptel1M 585823 GGCTG----AA--TACATCCCCTCCAAC----------AGTTGTCATT-- 585854 i ---- -- ii v i ---------- vi i -- C L1ME3E_3end#L 310 GGTTGTACCAATTTACACTCCCACCAGCAGCGTATAAGAGTTCCCGTTGC 261 chr1ptel1M 585855 -----ATCTTTTCC------------TGTCA---TCTTA------GCCAA 585878 ----- i iv ------------ --- i ------ C L1ME3E_3end#L 260 TCCACATCCTCGCCAACACTTGGTATTGTCAGACTTTTAATTTTTGCCAA 211 chr1ptel1M 585879 TCTGAGAGATGTGTAATGGTACCTCAGAGCTGTCTTAATTTGCATTTCTA 585928 ivi i iv i vv iv i iv C L1ME3E_3end#L 210 TCTGGTGGGTGTAAAATGGTATCTCATTGTGGTTTTAATTTGCATTTCCC 161 chr1ptel1M 585929 TGATCAATAGTGATTTAGAACATTTTTTCA-----TTACTAGAAAT--GT 585971 i v i vv v i i ----- i i vv -- C L1ME3E_3end#L 160 TGATTACTAATGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTCGT 111 chr1ptel1M 585972 TTTTAATTTTTTTATCTGAAA--ATTGTTCTTATCCTTTGACCATTTATC 586019 v --- ii i v v --vi v i i v v C L1ME3E_3end#L 110 GTT---TCCTCTTCTGTGAAATGCCTGTTCATGTCTTTTGCCCATTTTTC 64 chr1ptel1M 586020 AGTTGAAGAATGGCTTGTA---TTCTTATAAATCTGAATCAATTCTCTCT 586066 vi --- ii v i v--- vi i v vv i i v C L1ME3E_3end#L 63 TATT---GGGTTGTTTGTCTTTTTCTTATCGATTTGTAGGAGTTCTTTAT 17 chr1ptel1M 586067 ATATTTTAGA 586076 i i C L1ME3E_3end#L 16 ATATTCTGGA 7 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 35.58 CpG sites = 81, Kimura (unadjusted) = 37.26 Transitions / transversions = 1.40 (81/58) Gap_init rate = 0.06 (31 / 497), avg. gap size = 2.48 (77 / 31) 267 30.30 10.25 5.40 chr1ptel1M 587127 587604 (412396) L1ME4a_3end#LINE/L1 70 569 (302) m_b16s551i19 595 chr1ptel1M 587127 TGGTCACAGGATATGAACA----ATTTCCACAAGAA---CTGCAAAATGT 587169 v v i ---- iv v ---v i vv i L1ME4a_3end#L 70 TGGGCAAAGGACATGAACAGACAATTCACAAAAGAAGAAATACAAATGGC 119 chr1ptel1M 587170 TTACAACCATATGAAAGAATATTTGAATTTACATCACCAATAAT---AAA 587216 iv i v i? i ii ----- v i i --- i L1ME4a_3end#L 120 CAATAAACATATGAAAANATGTTCAA-----CCTCACTAGTAATCAAAGA 164 chr1ptel1M 587217 AAGGAAAA----AAAAACTCTG--------------------CAAATTAG 587242 v v ---- v vv -------------------- i L1ME4a_3end#L 165 AATGCAAATTAAAACAACAATGAGATACCATTTTTCACCTATCAAATTGG 214 chr1ptel1M 587243 CAAAGATGAAAAAAATGGG-AATAGTTAATAATGGGAAGGTTATGGAATG 587291 vv i v i- vii i iv vi v i ?ivi L1ME4a_3end#L 215 CAAAGATTTAAAAGATTGATAATACCCAGTGTTGGCGAGGGTGTGGNGAA 264 chr1ptel1M 587292 ATATGTA-TATGA-ACCGTGTTGTTAGAACAATAAAATG-----ACTTAT 587334 iiv i - v v - vv i v i i vvi v ----- i - L1ME4a_3end#L 265 ACGGGCACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTACAACCT-T 313 chr1ptel1M 587335 TTTGGAAAGCAATTTGGAATTATATAAAAAAAAATGTGACAAAGATTTCC 587384 i ii v v i vv iviv --- i v ? L1ME4a_3end#L 314 TCTGGAGGGCAATTTGGCAATATGTATCAAAAGCCTT---AAAAATGTNC 360 chr1ptel1M 587385 ATACCCTCTGAACCAGAGACTTTA-TTATTGGAGTTTATGCCCCAAGAAC 587433 i v vi i ii - v v i -- i i v L1ME4a_3end#L 361 ATACCCTTTGACCCAGTAATTCCACTTCTAGGAATTTAT--CCTAAGGAA 408 chr1ptel1M 587434 ATCATTA---ATAAGAAGAAAGTCCCATATACACCAAAATATTTATAGCA 587480 v i --- iv ? v viii i -- ii i i v L1ME4a_3end#L 409 ATAATCAGAGATGTGNACAAAGATTTATGTACA--AGGATGTTCATCGCA 456 chr1ptel1M 587481 GCACTTTTTCTGATAGCAAAGAATTGAAAATAA---AGTTGATTAACACA 587527 i v v i i i i i --- iv vii -- L1ME4a_3end#L 457 GCATTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACA-- 504 chr1ptel1M 587528 GAATGAAGATTATTGAAGAATTATATGAAGAAATTATGGTATACGGATGT 587577 ----------- v ii ? vi - i v i ivv i? L1ME4a_3end#L 505 -----------ATAGGGGANTGGT-TAAATAAATTATGGTACATCCATAN 542 chr1ptel1M 587578 AATAGAATATTATTATGCTGTTAAAAA 587604 i vvv ii L1ME4a_3end#L 543 AATGGAATATTATGCAGCCATTAAAAA 569 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.38 CpG sites = 76, Kimura (unadjusted) = 40.58 Transitions / transversions = 1.25 (76/61) Gap_init rate = 0.08 (39 / 477), avg. gap size = 1.95 (76 / 39) 430 30.09 4.34 6.35 chr1ptel1M 587236 587604 (412396) L1ME4c_3end#LINE/L1 208 569 (261) m_b16s551i20 595 chr1ptel1M 587236 AAATTAGCAAAGATGAAAAAAATGGG-AATAGTTAATAATGGGAAGGTTA 587284 i vv v i- vii iv vi ? i L1ME4c_3end#L 208 AAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGCTGGCGAGGNTG 257 chr1ptel1M 587285 TGG----AATGATATGTATATGAACCGTGTTGTTAGAACAATAAAATGAC 587330 i ---- v i i?ivi -- vv i v i v ?vi v ii L1ME4c_3end#L 258 CGGTGAAACTGGTACNCTCAT--ACATTGCTGGTGGCANTGTAAATTGGT 305 chr1ptel1M 587331 TTA----TTTTGGAAAGCAATTTGGAATTATATAAAAAAAAATGTGACAA 587376 vi ---- v v ii vv i --- iv i L1ME4c_3end#L 306 ACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGA---GCCATAA 352 chr1ptel1M 587377 AGATTTCCATACCCTCTGAACCAGAGACTTTA-TTATTGGAGTTTATGCC 587425 i v i i v vi i ii - v v i -- L1ME4c_3end#L 353 AAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTAT--C 400 chr1ptel1M 587426 CCAAGAACATCATTAATAAGAAG---AAAGTCCCATATACACCAAAATAT 587472 i i v v v v --- -- i i v i i L1ME4c_3end#L 401 CTAAGGAAATAATTCAAAAGAAGGAAAAAG--CTATATGCACGAAGATGT 448 chr1ptel1M 587473 TTATAGCAGCACTTTTTCTGATAGCAAAGAATTGAAAATAA---AGTTGA 587519 i v ii v v i i i i i --- iv v L1ME4c_3end#L 449 TCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGT 498 chr1ptel1M 587520 TTAACACAGAATGAAGATTATTGAAGAATTATATGAAGAAATTATGGTAT 587569 ii ------------- v ii vi - i iv i L1ME4c_3end#L 499 CCAACA-------------ATAGGGGAATGGT-TAAGTAAATTATGGTAC 534 chr1ptel1M 587570 ACGGATGTAATAGAATATTATTATGCTGTTAAAAA 587604 iv? ivii i vvv ii L1ME4c_3end#L 535 ATCNACTCGATGGAATATTATGCAGCCATTAAAAA 569 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 37.11 CpG sites = 61, Kimura (unadjusted) = 40.17 Transitions / transversions = 1.42 (61/43) Gap_init rate = 0.08 (29 / 368), avg. gap size = 1.34 (39 / 29) 15 24.54 0.00 0.00 chr1ptel1M 588655 588697 (411303) (AAGAAA)n#Simple_repeat 1 43 (0) m_b16s252i6 597 chr1ptel1M 588655 AAGAATCAGTCAAACAAAAAGAAAAAGAAAAAATAGGAGAAAA 588697 vv vv v iv ii (AAGAAA)n#Sim 1 AAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAA 43 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 1102 30.38 1.44 0.00 chr1ptel1M 589190 589607 (410393) C L1M4_orf2#LINE/L1 (1797) 1497 1074 m_b16s551i21 598 chr1ptel1M 589190 TATCTTTT-----AATTTATAAAGCATTGGGGCTAATTGTTCTTTGAATG 589234 i ----- i i i v v i v i C L1M4_orf2#LIN 1497 TATTTTTTGGAAGAGTTTGTGAAGGATTGGTGTTAATTCTTCTTTAAATG 1448 chr1ptel1M 589235 TTTGGTAGAATTCACATGTAAATCCATCTGGTCCTGGGGAATTTTTTTTA 589284 vv i v ? vvv i v i C L1M4_orf2#LIN 1447 TTTGGTAGAATTCACCAGTGAAGCCATCTGGNCCTGGGCTTTTCTTTGTG 1398 chr1ptel1M 589285 GGGAGTTGATTAATAACTTGTTCTATTTCTTTTTCTGAAATGGGACTATT 589334 i vv i v vi v i vii vv i v C L1M4_orf2#LIN 1397 GGAAGTTTTTTGATTACTAATTCAATCTCTTTACTTGTTATAGGTCTATT 1348 chr1ptel1M 589335 TAAGCAATTTACTTCCTCCTCTGATAATCTGGGAAGCTTATATTTTTGGA 589384 i iiivv i i i i vv vi i i v v i i i i vv C L1M4_orf2#LIN 1347 CAGATTTTCTATTTCTTCTTGAGTCAGTTTCGGTAGTTTGTGTCTTTCTA 1298 chr1ptel1M 589385 GGTAGTCATCCATTTCACTTAGGTTATCAAATTTACTGGCATAAAGTTGG 589434 v v ii ii v ii v i v C L1M4_orf2#LIN 1297 GGAATTTGTCCATTTCATCTAGGTTATCTAATTTGTTGGCATACAATTGT 1248 chr1ptel1M 589435 GCAAAGTAACCCCTTATTATTTCTTTAATTTCTTCTTCATTGGGGGAAAG 589484 v v vi v iii v vivvvi i vi v v C L1M4_orf2#LIN 1247 TCATAGTATTCCCTTATAATCCTTTTTATTTCTGTAAGGTCGGTAGTAAT 1198 chr1ptel1M 589485 TTCTCCCTTTTCATTTTTAAGACTACTAATTTGA-TTTCCTCTCTCCTTT 589533 v i ii ii i vvi v - i i ii C L1M4_orf2#LIN 1197 GTCCCCTCTTTCATTCCTGATTTTAGTAATTTGAGTCTTCTCTCTTTTTT 1148 chr1ptel1M 589534 TTCTAATCAGATTTACCAAAGGTTTATCAATTTTACTGGTTTTTTCATAA 589583 ii ii vi vi i i ii i i v i C L1M4_orf2#LIN 1147 TCTTGGTCAGTCTAGCTAAAGGTTTGTCAATTTTGTTGATCTTTTCAAAG 1098 chr1ptel1M 589584 AACCAACTCTTAGTTTTATTTATT 589607 i i ii v C L1M4_orf2#LIN 1097 AACCAACTTTTGGTTTCGTTGATT 1074 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.35 CpG sites = 74, Kimura (unadjusted) = 40.22 Transitions / transversions = 1.40 (74/53) Gap_init rate = 0.00 (2 / 417), avg. gap size = 3.00 (6 / 2) 466 20.55 4.55 2.68 chr1ptel1M 589633 589742 (410258) MIRb#SINE/MIR 4 115 (153) m_b16s601i11 599 chr1ptel1M 589633 AGGAGCAGCTAGATGGTGCAGTGGATAGAGTGCAG-CCCTGAAGTCAGGA 589681 i ---i v ii i - ii i iv MIRb#SINE/MIR 4 AGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGAC 50 chr1ptel1M 589682 GGACTGGAGTTCAAATCTGGCCTCAG--AC--ACTAGCTGTGTGACCCTG 589727 i iv i i iv v v -- -- i MIRb#SINE/MIR 51 AGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTG 100 chr1ptel1M 589728 GGCAAGTCACTTAAC 589742 i MIRb#SINE/MIR 101 GGCAAGTTACTTAAC 115 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 21.14 CpG sites = 16, Kimura (unadjusted) = 24.91 Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.06 (6 / 109), avg. gap size = 1.33 (8 / 6) 480 18.56 5.15 0.00 chr1ptel1M 589646 589742 (410258) MIRc#SINE/MIR 11 112 (156) m_b16s601i12 599 chr1ptel1M 589646 TGGTGCAGTGGATAGAGTGC-AGCCCTGAAGTCAGGAGGACTGGAGTTCA 589694 v ii -i v i i i iv i i MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr1ptel1M 589695 AATCTGGCCTCAG--AC--ACTAGCTGTGTGACCCTGGGCAAGTCACTTA 589740 i iv v v -- -- i MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTA 110 chr1ptel1M 589741 AC 589742 MIRc#SINE/MIR 111 AC 112 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 20.48 CpG sites = 12, Kimura (unadjusted) = 21.80 Transitions / transversions = 2.00 (12/6) Gap_init rate = 0.03 (3 / 96), avg. gap size = 1.67 (5 / 3) 12 19.33 0.00 3.12 chr1ptel1M 590255 590287 (409713) (CCCTAC)n#Simple_repeat 1 32 (0) m_b16s252i7 600 chr1ptel1M 590255 CCCTCACCCCTACCCCCACCCTCACCTCTGCCC 590287 - i ii i i (CCCTAC)n#Sim 1 CCCT-ACCCCTACCCCTACCCCTACCCCTACCC 32 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 518 28.17 11.83 3.30 chr1ptel1M 592555 593281 (406719) HERVK14C#LTR/ERVK 2862 3648 (3786) m_b17s701i0 601 chr1ptel1M 592555 TGTTGAAGGTCTTCAAACTTTCATTATTCCTTTTCAATGGAAAAC---GA 592601 -- i i i ?ii ---- i vv ?i ---i HERVK14C#LTR/ 2862 TGTTGA--GCCTCCAGANCCT----ATTCCCTTAAAATGGANGACCCAAA 2905 chr1ptel1M 592602 ACACCGTATGGATAGAACAGTGGTAGGTAGC--------AACTTCAGGCC 592643 ?v ? v i ? ? iv v ?? -------- vvi HERVK14C#LTR/ 2906 ANCCNGTTTGGGTNGANCAGTGGCCGCTNNCTCAGGAAAAACTGGGGGCC 2955 chr1ptel1M 592644 TTATTAG-ATTAATCGA--AAC-ATTTGACCAAGGACA-------CCAAC 592682 ivi - i i -- - v ?v ------- v HERVK14C#LTR/ 2956 TTACAGGAATTAGTCAAAGAACAATTAGANAAAGGACACATNGAGCCCAC 3005 chr1ptel1M 592683 CTTCTCTAAGTCCTTGGAATTGCC--GTATTTGTTGT----AAAAAGTCT 592726 v i ---- ? v? -- i vi ---- i i HERVK14C#LTR/ 3006 ATTTTC----TCCNTGGAATTCNCCAGTGTTTGTAATNAAGAAAAAATCC 3051 chr1ptel1M 592727 GGAAAATGAAGGATGTTGACTGATTTAAGAA-AGTAAAAATGAAAGGGTG 592775 v i iv ? i i i i v i-v --v v ivvi ? HERVK14C#LTR/ 3052 GGCAGATGGCGNATGCTAACCGACTTACGAGCCGT--CAATGCAGTCATN 3099 chr1ptel1M 592776 GAAACTAT-GGAACTCTTCAGCCTGGGCTTCCTCTCCTC----TCATTCT 592820 v v ? - ii ? v v v ?ii i ---- v i HERVK14C#LTR/ 3100 CAACCNATGGGGGCNCTGCAGCCAGGGCTGCCNTCCCCCGCCATGATTCC 3149 chr1ptel1M 592821 TAGAG---GGCCTCTTTGGGTTATAGACATT---GGATTGTTTCTATTCT 592864 --- ?i vvvi i- --- i i v v HERVK14C#LTR/ 3150 TAGAGACTGGCCNTTAATAGTTATAGAT-TTGAAGGACTGCTTCTTTACT 3198 chr1ptel1M 592865 -TTCCTCTGGATAAGGAGGATGTGAAAAGATTTGCCTTTTCTG--CCCAA 592911 - i vvi vv? v vi i i v i-- iiv HERVK14C#LTR/ 3199 ATTCCTCTAGCAGAGCCNGATTTTGAAAAATTTGCTTTTACTATTCCTGC 3248 chr1ptel1M 592912 CGTTAACACTGAG--CCTTATAA--AGATATGAATGGACAGTTTTGCCAC 592957 ii v vii --v i?ii i-- ? v v v ? i HERVK14C#LTR/ 3249 TATGAACAACAAGGAACCNGCAGCCAGNTATCATTGGAAAGTNTTGCCGC 3298 chr1ptel1M 592958 AGGGAATGAAAAACAGCCCTACTATGTG---AAATGATTTG----CTGCT 593000 v vvi i i ? ? v --- v v? v ----vv HERVK14C#LTR/ 3299 AGGGCATGTTGAATAGTCCNACNATTTGTCAAACTTNTGTGGGGNAGGCT 3348 chr1ptel1M 593001 GTTT-TCCAGTAAAAAAGCA--TTTAAAAAAGTTATGCTATTACATTATA 593047 i i-v v ? i i v -- iv i vvv? iii - HERVK14C#LTR/ 3349 ATTCAACCTGTNAGAGATCAGTTTCCAGATTCNTATATCATT-CATTATA 3397 chr1ptel1M 593048 TATA-GATA-ATTGGGATGTGCACCTGA------GGAACA--------AA 593081 iv - i - ---? iv i ------i v -------- i HERVK14C#LTR/ 3398 TGGATGACATATT---NTGTGCGGCCGAAACTCGAGACCAACTTATCCAG 3444 chr1ptel1M 593082 TGTTAGAACATGTCTACAAAAAGACCATAGAAAACTAAGGGTTACAAACT 593131 v-v ii i - i i vi ? vvi vvv i i?vv i- HERVK14C#LTR/ 3445 TGTTAT-TCACATTTAC-AGAAGGCGGTNGCCGACGCTGGATTGNTCAT- 3491 chr1ptel1M 593132 AACAAGCTGCAGA-AAAATTCAGACA--TGCTCCTTTTCAATATTTAGGA 593178 ---- ?v ? - i i-- i i i HERVK14C#LTR/ 3492 ----AGCNCCNGATAAAATTCAAACGNCTACTCCTTTCCAATATTTGGGA 3537 chr1ptel1M 593179 TATGAATATCC----TAAGGTGCTTACAATTCAAAA-CTTCTAA---GAA 593220 - v vi i ----v i iiv vivi? -v v --- HERVK14C#LTR/ 3538 -ATGCAGGTTCAGGAAAGGGCAATTAAGCCNCAAAAGGTTCAAATTCGAA 3586 chr1ptel1M 593221 AAGA--AGCTAAACACATTGAATGATTTTTTAGAAATTGATAGGAGATAT 593268 --vv i v v i - i i iv i HERVK14C#LTR/ 3587 AAGACTCTCTGAAAACTTTAAATGA-TTTTCAAAAATTATTAGGGGATAT 3635 chr1ptel1M 593269 CCAATGGATTGGA 593281 iv v v HERVK14C#LTR/ 3636 TAATTGGATTCGA 3648 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 36.58 CpG sites = 104, Kimura (unadjusted) = 38.27 Transitions / transversions = 1.11 (104/94) Gap_init rate = 0.08 (57 / 726), avg. gap size = 1.96 (112 / 57) 575 31.09 6.20 8.74 chr1ptel1M 594210 594935 (405065) HERVK3#LTR/ERVK 4478 5186 (2016) m_b17s701i1 601 chr1ptel1M 594210 AAGCTAGGAGCATAGTAAAAACCTGTACAGCTTGCC------TTCCT--T 594251 ivi ? v i v vi ------ i --? HERVK3#LTR/ER 4478 AAGCTAGGGCTATNGTACAAGCCTGTCCTACTTGCCAGCATGTCCCTGGN 4527 chr1ptel1M 594252 GCCACACTCCTACACTGCCTCCAGGGAAGAACCCTCGTGATTTGAGACCC 594301 i iiv v -------- ?viv v v i ivv v HERVK3#LTR/ER 4528 GCCGCACCTGTAGA--------AGGNTGTAACCCACGAGGTTTGGCTCCA 4569 chr1ptel1M 594302 AATGAAATGTGGCAAATGGATGTGACCCATTATAA-ATCGTTTGG----- 594345 v v v -i i- v v ----- HERVK3#LTR/ER 4570 AATGAAATCTGGCAAATGGATGTTACACA-CATAGCAGCCTTTGGCAAGC 4618 chr1ptel1M 594346 TCGTCTATCTTTTATCCACATTATGGTAGACACCTTTTCGGGATTCAC-T 594394 iiv v i i vv? -- --- i v ----- i- HERVK3#LTR/ER 4619 TTAGCTATGTTCTGTGANC--TA---TAGACACTTATTC-----TCATAT 4658 chr1ptel1M 594395 TTTGCA------ATACCAGCAGCAAAAGAGACAGCCCGAGTGGTCAC--- 594435 vi ------ i -- i iiv ----- i--- HERVK3#LTR/ER 4659 GCTGCATGCTACATGCCA--AACAGGTGAGACAGC-----TGGTCATGTA 4701 chr1ptel1M 594436 ---TGAGTTCCTCACACAAGCATTTGCCATTATGGGTGTGCCACAAGCAA 594482 ---i vv iv -iiiv v ivv vi i -i i HERVK3#LTR/ER 4702 CGGCGACATTGTC-TGTCATCATTTGCTCATATGGGGATACC-TAAACAA 4749 chr1ptel1M 594483 -TAAAAACAGACAATGGTCCTGCTTATACTTCGAAACAT--TTTGCAAAC 594529 - v v i --- iv -- v v HERVK3#LTR/ER 4750 TTAAAAACTGACAATGGACCCGCTTATACT---AGTCATGCTTTTCAAAA 4796 chr1ptel1M 594530 TTTTGTGCACAGTATAAGATTTTA---CAGACCACTGGCATACCCTTTAA 594576 iv -- iv vi ii v --- v vv v v v i v HERVK3#LTR/ER 4797 TTTCTT--ACAGCTTTGGGCTATAACCCATAAAACAGGAATTCCTTATAA 4844 chr1ptel1M 594577 TCCTCAAGAAC-AGGCAATAGTAGAGAGGAGAAACAGAGACATTAAGACG 594625 vi i - v - v iv v i-v i vi HERVK3#LTR/ER 4845 TCCTAGAGGACAAGGCATTA-TAGAGCGGGCACAT-CAAACATTACAACG 4892 chr1ptel1M 594626 C-TCCTCCAAAAACAAAAGAAAGGG----GGAGCCACAGGTA--ACCTAG 594668 - vi vv iiii? ---- v - iv -- vi HERVK3#LTR/ER 4893 CATGTTGAAAAAACAAAAAGGGNGGTATAGGAGGC-CAACTACCACCTCA 4941 chr1ptel1M 594669 AGAACTTCTAAATCTACCTCTTTATACTATTAATTTCTT-GATTTTTGAC 594717 vv vvv v i v ii v v v v i - i ii ii HERVK3#LTR/ER 4942 ATCAAAACTACATTTAGCCTTATTTACTTTAAATTTTTTNGACTCCTGGT 4991 chr1ptel1M 594718 AAAGATGCACTGGTTCCGGCAGACAGGTTTTATAACCCACCGGAAGGACA 594767 vi vvvv ii i v iiv ivv vviiiii i i v HERVK3#LTR/ER 4992 ACGGATGGTAAGACTCCAGCAGAAAGACATTGGCAAGTGTTAGAGGAAAA 5041 chr1ptel1M 594768 GTGTCCAGTGCAAGCAGCTCTACTATCTTTAGATAATCGCCAGGTGATAT 594817 v ------ v i-------i i--- -------- i v HERVK3#LTR/ER 5042 GAG------GAAAGT-------TTATCC---GA--------AAGTGTTAT 5067 chr1ptel1M 594818 GGAGAGACCCAGA--AAGTGGTGGATGGAAGGGACCAGATAGGTTAACTG 594865 i vv i -- ? ii-i i v - i i i v HERVK3#LTR/ER 5068 GGAAATCCCCGGAAGAAGNGAC-AATGGAAAGGTCC-GGTGGATTTACTG 5115 chr1ptel1M 594866 -CTTGGGGGAGAGGGTTTGCTTGTATCTCTACAGGTGGAGAAGGAATCAG 594914 - v i? v i i i v iv i vi i iv HERVK3#LTR/ER 5116 ACGTGGGGANGAGGGTATGCTTGTGTTTTTACAGGAGATGGACAAACCGT 5165 chr1ptel1M 594915 ATGAGTGCCAACAAGCTGTAT 594935 i i vv v ii HERVK3#LTR/ER 5166 GTGGGTGCCCTCAAGGTGCGT 5186 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 39.18 CpG sites = 105, Kimura (unadjusted) = 41.25 Transitions / transversions = 1.04 (105/101) Gap_init rate = 0.11 (80 / 725), avg. gap size = 1.34 (107 / 80) 621 27.81 6.56 3.17 chr1ptel1M 594233 594659 (405341) HERVK14C#LTR/ERVK 4671 5111 (2323) m_b17s701i2 601 chr1ptel1M 594233 TGTACAGC-TTGCCTTCCTTGCCACACTCCTACA-CTGCC---TCCAGGG 594277 ? i - i ??v vi- v - --- v HERVK14C#LTR/ 4671 TGTNCAACATTGCCCTNNGTGCCAGG-TGCTACAACTGCCACATCAAGGG 4719 chr1ptel1M 594278 A----AG--AACCCTCGTGATTTGAGACCCAATGAAATGTGGCAAATGGA 594321 ----? -- ? v iv iv? i ?viv ? HERVK14C#LTR/ 4720 ACTGGNGTTAACCCNCGAGGATTGGCNCCTAATNCGCTNTGGCAAATGGA 4769 chr1ptel1M 594322 TGTGACCCATTATAAAT-CGTTTGGTCGTCTATCTTTTATCCACATTATG 594370 i ? -i vv - i vviv ? ? vii ii ? iv HERVK14C#LTR/ 4770 CGTNACCCAT-GTACCTNCATTTGGGAAACTNTCNTACGTCCATGTNACT 4818 chr1ptel1M 594371 GTAGACACCTTTTCGGGATTCACTTTTGCAA--TACCAGCAGCAAAAGAG 594418 i vviv iii? vv ? -- i -- i ii? HERVK14C#LTR/ 4819 GTAGATACCTTTTCTCATTTTGTNTGGGCNACTTGCCA--AACAGGNGAG 4866 chr1ptel1M 594419 ACAGCC---CGAGT----GGTCACTGAGTTCCTCACACAAGCATTTGCCA 594461 i ? i--- v ----i v i viv i iiii------- i ?i HERVK14C#LTR/ 4867 GCNGCTGCTCGTGTTAAAAGACATTTGCTTTCCTGT-------TTCGCNG 4909 chr1ptel1M 594462 TTATGGGTGTGCCACAAGCAATAAAAACAGACAATGGTCCTGCTTATACT 594511 i ii v iv? v ? i v vi i?? HERVK14C#LTR/ 4910 TCATGGGCATTCCACAAAANATTAAAACNGACAATGGCCCAGGCTACNNT 4959 chr1ptel1M 594512 TCGAAACATTTTGCAAACTTTTGTGCA-CAGTATAAGATTTTACAGACCA 594560 -v v v?i i? ?i v iv v - i iv? v vv v ?i HERVK14C#LTR/ 4960 -AGTAAANCTTTANANGCGTTCCTTCAACAATGGNACATTAAACACANTA 5008 chr1ptel1M 594561 CTGGCATACCCTTTAATCCTCAAGAACAGGCAATAGTAGAGAGGAGAAAC 594610 ? v v i i? i v v v iv iivv i HERVK14C#LTR/ 5009 CTGGNATCCCCTATAATTCTCAAGGNCAAGCCATTGTTGAACGAGCTAAT 5058 chr1ptel1M 594611 AGAGACATTAAGACGCTC--CTCCAAAAACAAA----AGAAAGGGGGAGC 594654 v - v i ?- --i v ---- i i HERVK14C#LTR/ 5059 CGA-ACCTTAAAAN-CTCAATTACAAAAACAAAAGACAGAAGGGGGGAAC 5106 chr1ptel1M 594655 CACAG 594659 v HERVK14C#LTR/ 5107 CAGAG 5111 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 37.22 CpG sites = 62, Kimura (unadjusted) = 38.97 Transitions / transversions = 1.17 (62/53) Gap_init rate = 0.06 (26 / 426), avg. gap size = 1.62 (42 / 26) 229 30.79 12.77 3.25 chr1ptel1M 596295 596435 (403565) C MIR3#SINE/MIR (52) 156 3 m_b17s601i0 602 chr1ptel1M 596295 AGTCCACCCCACCATCCGTTTTATGGA---GGATACTAAGGTCTAGGG-- 596339 v v i--- i ii --- v i i i i -- C MIR3#SINE/MIR 156 AGTCCAACCCCCT---CATTTTACAGATGAGGAAACTGAGGCCCAGAGAG 110 chr1ptel1M 596340 GAGGAGTTGGGTTTAACCAAGGTCACTTGGGCAATTAATGACC-AGCCAG 596388 v i -- ii iv vii v? i i i v- i C MIR3#SINE/MIR 109 GTGAAGT--GACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGG 62 chr1ptel1M 596389 -----GAAACCAGGTTTCTAG---CCCAATTCA----CTTCCCATTAAAC 596426 ----- v i iv --- i i i---- ii iii v i C MIR3#SINE/MIR 61 GACTAGAACCCAGGTCTCCTGACTCCCAGTCCGTGCTCTCTCTGCTCAGC 12 chr1ptel1M 596427 CACACAGCC 596435 v v C MIR3#SINE/MIR 11 CACTCTGCC 3 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 39.93 CpG sites = 29, Kimura (unadjusted) = 42.67 Transitions / transversions = 2.23 (29/13) Gap_init rate = 0.08 (11 / 140), avg. gap size = 2.09 (23 / 11) 211 33.39 4.20 12.03 chr1ptel1M 596310 596452 (403548) C MIRb#SINE/MIR (118) 150 18 m_b17s601i1 602 chr1ptel1M 596310 CCGTTTTATGGA---GGATACTAAGGTCTAGGGGAGGAGTTGGGT---TT 596353 i ii --- v i iii --- ii ii --- C MIRb#SINE/MIR 150 CCATTTTACAGATGAGGAAACTGAGGCTCAG---AGAGGTTAAGTAACTT 104 chr1ptel1M 596354 AACCAAGGTCACTTGGGCAATTAATGACCAGCCAGGAAACCAGGTTTCTA 596403 iv ----i ii i i vii - -- i i v v C MIRb#SINE/MIR 103 GCCCAAGGTCAC----ACAGCTAGTAAGTGGC-AG--AGCCGGGATTCGA 61 chr1ptel1M 596404 GCCCAATTCACTTCCCATTAAACCACACAGCCTGTTTCCTCTCCACTGC 596452 i iv ------ii ivi iv v i vii i C MIRb#SINE/MIR 60 ACCCAGGTC------TGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGC 18 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 44.69 CpG sites = 32, Kimura (unadjusted) = 47.98 Transitions / transversions = 3.20 (32/10) Gap_init rate = 0.13 (18 / 142), avg. gap size = 1.22 (22 / 18) 261 28.75 14.96 1.39 chr1ptel1M 596310 596436 (403564) C MIR1_Amn#SINE/MIR (81) 149 6 m_b17s601i2 602 chr1ptel1M 596310 CCGTTTTATGGA---GGATACTAAGGTCTAGGGGAG--GAGTTGGGTTTA 596354 i ii --- v i i?i i ii --i -- ii i C MIR1_Amn#SINE 149 CCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGT--GACTTG 102 chr1ptel1M 596355 ACCAAGGTCACTTGGGCAATTAATGACC-AGCCAGGA-----AACCAGGT 596398 v ?ii v?iii? i i v- i ----- v C MIR1_Amn#SINE 101 CCCAAGGTCACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAACCCAGGT 52 chr1ptel1M 596399 TTCTAG---CCCAATTCA-----CTTCCCATTAAACCACACAGCCT 596436 i iv --- i i ----- vi i i v C MIR1_Amn#SINE 51 CTCCCGAGTCCCAGTCCAGTGCTCTATCCACTAGACCACACTGCCT 6 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 39.63 CpG sites = 28, Kimura (unadjusted) = 41.18 Transitions / transversions = 3.50 (28/8) Gap_init rate = 0.06 (8 / 126), avg. gap size = 2.62 (21 / 8) 182 28.75 8.75 0.00 chr1ptel1M 596741 596820 (403180) L2d2_3end#LINE/L2 449 535 (20) m_b17s601i3 603 chr1ptel1M 596741 CTGGAGAACAAGGGC--TGGCTTCTGC--CTTTCTACCCCC---AGGGCC 596783 v ii i i -- v v i -- v i --- v L2d2_3end#LIN 449 CTTGAGGGCAGGGACCATGTCTTATACTTCTTTGTATCCCCCACAGCGCC 498 chr1ptel1M 596784 TGGCCCCGTGCCCCGCACACAGCGGGCCATTAGCAAA 596820 i v v ii ii vv i ii L2d2_3end#LIN 499 TAGCACAGTGCCTTGCACACAGTAGGCGCTCAATAAA 535 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 37.41 CpG sites = 14, Kimura (unadjusted) = 37.41 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.04 (3 / 79), avg. gap size = 2.33 (7 / 3) 29 0.00 0.00 0.00 chr1ptel1M 597679 597705 (402295) (CTG)n#Simple_repeat 1 27 (0) c_b17s251i0 604 chr1ptel1M 597679 CTGCTGCTGCTGCTGCTGCTGCTGCTG 597705 (CTG)n#Simple 1 CTGCTGCTGCTGCTGCTGCTGCTGCTG 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 180 29.35 5.47 1.50 chr1ptel1M 599207 599334 (400666) L2d2_3end#LINE/L2 117 249 (306) m_b17s601i4 605 chr1ptel1M 599207 TTCCCAC-TCTGGACATTT--TCAC--TGACCCCCCATGCCTACAGTGCT 599251 i - vi v -- --i vi -i iv i i L2d2_3end#LIN 117 TTCCCGCCTCTGCGCCTTTGCTCACGCCGTTCCCCC-CGCCTGGAATGCC 165 chr1ptel1M 599252 CTTCCCCCTCACCTCCACC--TCCCGGTCTTCCTGACTTCCTCCAGACCC 599299 i vi -- vii i v iv - i i v i L2d2_3end#LIN 166 CTTCCCCTTCCTCTCCACCTATCCAAATCCTACCCA-TCCTTCAAGGCCC 214 chr1ptel1M 599300 AGATCTAATCCCATCCACTGCAAAACGCTTTCCCT 599334 v v ? i iv v ivi v i L2d2_3end#LIN 215 AGCTCAAATNCCACCTCCTCCGTGAAGCCTTCCCT 249 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 32.40 CpG sites = 22, Kimura (unadjusted) = 38.79 Transitions / transversions = 1.47 (22/15) Gap_init rate = 0.05 (6 / 127), avg. gap size = 1.50 (9 / 6) 187 25.00 0.00 0.00 chr1ptel1M 600225 600268 (399732) L3#LINE/CR1 3930 3973 (126) m_b17s601i5 606 chr1ptel1M 600225 GAGATGGGCTTTCTCCGGAGGGAGTGACTCTCTCGTCACTGGAG 600268 ii vi v? v viii i L3#LINE/CR1 3930 GGAATGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGTCACTGGAG 3973 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 32.26 CpG sites = 7, Kimura (unadjusted) = 32.26 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 271 21.21 2.40 1.18 chr1ptel1M 601021 601187 (398813) HERVIP10FH#LTR/ERV1 835 1003 (4099) m_b17s701i3 607 chr1ptel1M 601021 GGGGGTGAGAGAGAAAGAGACAGAGACAGAGAGAAAAAGAGAGAGACACA 601070 i iv i v v ii i v HERVIP10FH#LT 835 GAGGAAGAGAGAGAGAGAGAAAGAGAGAGAGAGGGAGAGAGAGAGACAAA 884 chr1ptel1M 601071 GAGAGA--CACAGACAGAGACAGACAGTGACTGACAGAGAGAGAGAGAGA 601118 i -- v v v i v -- vii v HERVIP10FH#LT 885 GAGGGAGTCAAAGAGAGAGAGAGGCAGAGA--GAGGAAGAGACAGAGAGA 932 chr1ptel1M 601119 AACAGAGGGAG--AGAGAGAGAGAGAGAGAGACAATGACAGAGAGAGAGA 601166 v v -- v v v v i i HERVIP10FH#LT 933 CAAAGAGGGAGTCAGAGAGAGAGAGAGAGACAGAAAGTCAAAGAGAGAAA 982 chr1ptel1M 601167 GAGAGAATGAATGAGAACTAG 601187 i iv ivv v HERVIP10FH#LT 983 GAAAGAGAGAGATAGAAGTAG 1003 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 24.99 CpG sites = 15, Kimura (unadjusted) = 24.99 Transitions / transversions = 0.75 (15/20) Gap_init rate = 0.02 (4 / 166), avg. gap size = 1.50 (6 / 4) 276 20.84 0.00 1.39 chr1ptel1M 601027 601172 (398828) HERVIP10FH#LTR/ERV1 819 962 (4140) m_b17s701i4 607 chr1ptel1M 601027 GAGAGAGAAAGAGACAGAGACAGAGAGAAAAAGAGAGAGACACAGAGAGA 601076 i v iv i i i v v i HERVIP10FH#LT 819 GAGAGAGAGAGAGAGAGAGGAAGAGAGAGAGAGAGAAAGAGAGAGAGAGG 868 chr1ptel1M 601077 CACAGACAGAGACAGACAGTGACTGACAGAGAGAGAGAGAGAAACAGAGG 601126 v v v i v v v v v iv i v HERVIP10FH#LT 869 GAGAGAGAGAGACAAAGAGGGAGTCAAAGAGAGAGAGAGGCAGAGAGAGG 918 chr1ptel1M 601127 GAGAGAGAGAGAGAGAGAGAGACAATGACAGAGAGAGAGAGAGAGA 601172 i v v i iv i -- HERVIP10FH#LT 919 AAGAGACAGAGAGACAAAGAGGGAGT--CAGAGAGAGAGAGAGAGA 962 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 24.47 CpG sites = 13, Kimura (unadjusted) = 24.47 Transitions / transversions = 0.76 (13/17) Gap_init rate = 0.01 (2 / 145), avg. gap size = 1.00 (2 / 2) 14 7.50 3.33 3.33 chr1ptel1M 602028 602057 (397943) (GAGGG)n#Simple_repeat 1 30 (0) m_b17s252i0 608 chr1ptel1M 602028 GAGGGGAGGGGA-AGGAGGGGCAGGGGATGG 602057 -i - v (GAGGG)n#Simp 1 GAGGGGAGGGGAGGGGAGGGG-AGGGGAGGG 30 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.07 (2 / 29), avg. gap size = 1.00 (2 / 2) 205 20.83 8.33 0.00 chr1ptel1M 603177 603224 (396776) C X6A_LINE#LINE/CR1 (464) 614 563 m_b17s601i6 609 chr1ptel1M 603177 GAACTTCTCTGATTTCTGCTCTGTGATCTCTGAAATGA----ACCAAAAC 603222 i i i iv ? vv i i ---- C X6A_LINE#LINE 614 GGACCTTTCCTATTTCTGCTNTGTCTTCTTTGAGATGAAGTGACCAAAAC 565 chr1ptel1M 603223 CG 603224 i C X6A_LINE#LINE 564 TG 563 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 25.86 CpG sites = 7, Kimura (unadjusted) = 25.86 Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.02 (1 / 47), avg. gap size = 4.00 (4 / 1) 182 26.74 2.17 10.59 chr1ptel1M 605234 605325 (394675) C L2d_3end#LINE/L2 (248) 268 184 m_b17s601i7 610 chr1ptel1M 605234 AGTGTGTGTGAGAGTGTATGTCTGTTCAAGGGAAAGTTCCGTGGAGGTGG 605283 v ivi --- ------ i i i v C L2d_3end#LINE 268 AGTGTGGGCTGGAGTG---GTC------AGGGAAGGCTTCGTGGAGGAGG 228 chr1ptel1M 605284 GGACCCCTGAGCTGAACCTTGAAGAAGGAG--GGAGTCAGAGAG 605325 v ivv i ii i v i -- v ii v C L2d_3end#LINE 227 TGGGACTTGAGCTGGGCCTTGAAGGATGGGTAGGATTTGGATAG 184 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 33.49 CpG sites = 13, Kimura (unadjusted) = 33.49 Transitions / transversions = 1.44 (13/9) Gap_init rate = 0.11 (10 / 91), avg. gap size = 1.10 (11 / 10) 227 28.05 2.44 0.00 chr1ptel1M 605262 605343 (394657) C L2c_3end#LINE/L2 (230) 248 165 m_b17s601i8 610 chr1ptel1M 605262 AGGGAAAGTTCCGTGGAGGTGGGGACCCCTGAGCTGAACCTTGAAGAAGG 605311 i i i vi v v vi i? i v C L2c_3end#LINE 248 AGGGAAGGCTTCCCGGAGGAGGTGACATCTGAGCTGAGNCTTGAAGGATG 199 chr1ptel1M 605312 AG--GGAGTCAGAGAGCCGCAAGGCTGAAGAAAG 605343 -- i vv vi v vv ii i C L2c_3end#LINE 198 AGTAGGAGTTAGCCAGGTGGAAGGAGGGGGGAAG 165 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 34.29 CpG sites = 12, Kimura (unadjusted) = 36.21 Transitions / transversions = 1.09 (12/11) Gap_init rate = 0.01 (1 / 81), avg. gap size = 2.00 (2 / 1) 127 18.67 0.00 0.00 chr1ptel1M 605888 606123 (393877) (CA)n#Simple_repeat 1 236 (0) m_b17s252i1 611 chr1ptel1M 605888 CACGCAAATACACACACACACACACACACACACACACTTTCTCTCTCACA 605937 i v i viv v v v (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 chr1ptel1M 605938 CACACACACTCTCACACACTCACTCACATTCACACACACTCACATACACA 605987 v v v v iv v i (CA)n#Simple_ 51 CACACACACACACACACACACACACACACACACACACACACACACACACA 100 chr1ptel1M 605988 CTCATACACTCTCTCACACACACACACATACTCACACACTCATGCACACA 606037 v i v v v i v v ii (CA)n#Simple_ 101 CACACACACACACACACACACACACACACACACACACACACACACACACA 150 chr1ptel1M 606038 CTCACATACACACTCATACACTCACACACACATACTCACACACTCACACA 606087 v i v i v i v v (CA)n#Simple_ 151 CACACACACACACACACACACACACACACACACACACACACACACACACA 200 chr1ptel1M 606088 CACTCACACACTCTTACACACACACACACACACACA 606123 v v vi (CA)n#Simple_ 201 CACACACACACACACACACACACACACACACACACA 236 Matrix = Unknown Transitions / transversions = 0.50 (13/26) Gap_init rate = 0.00 (0 / 235), avg. gap size = 0.0 (0 / 0) 12 0.00 5.26 0.00 chr1ptel1M 610211 610229 (389771) (ATT)n#Simple_repeat 1 20 (0) m_b17s252i2 612 chr1ptel1M 610211 ATTATTATTA-TATTATTAT 610229 - (ATT)n#Simple 1 ATTATTATTATTATTATTAT 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.06 (1 / 18), avg. gap size = 1.00 (1 / 1) 350 32.99 10.82 1.59 chr1ptel1M 610352 610582 (389418) C L3#LINE/CR1 (872) 3227 2976 m_b17s601i9 613 chr1ptel1M 610352 TGTTATTTGGGGGTTTTTT--GCATGAAGCCATCTATACCTTTAACACAG 610399 i i viii vv -- --- v ii i v vv C L3#LINE/CR1 3227 TGTCATCTGCAAATTTGATAAGCATG---CCTTCTATGTCTTCATCCAAG 3181 chr1ptel1M 610400 TCATTGACGAAAATGTTGACCC--ACAGAGGTCAAGCTCATAACCTTGGG 610447 ii v v-- - i vv v i i v C L3#LINE/CR1 3180 TCATTGATAAAAATGTTGAACAGGACAG-GGCCAAGGACAGAGCCCTGTG 3132 chr1ptel1M 610448 ACTTTCCACCTGAAATGTCCTATGAAGCTGAGCT-------GTAATTAGC 610490 i viv iv i iv iviv i i vv -------v i i C L3#LINE/CR1 3131 GCACGCCACTAGAGACCTCCCTCCAGGTTGACATCGATCCATTAATCAAC 3082 chr1ptel1M 610491 -----TTGG----AACC---CAGCCAGGTCTGAAGCC-CCTGCTTGGCCT 610527 ----- ---- ii --- i v vi v - ivi vv C L3#LINE/CR1 3081 ACCTTTTGGGTATAGTCGTTCAACCAGCTACGAATCCACCTAACTGTACT 3032 chr1ptel1M 610528 GTTGTCTAGGGCTTAGCTCTCTATCTT-CCCACAAGAATTGCATGAAACT 610576 i ii i vv v vi i -i i vv i vv C L3#LINE/CR1 3031 ATCATCCAGCCCATATTTCTCCATCTTGTCCACAAGGATATCATGAGAGA 2982 chr1ptel1M 610577 CTTTGT 610582 C L3#LINE/CR1 2981 CTTTGT 2976 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 42.85 CpG sites = 39, Kimura (unadjusted) = 44.42 Transitions / transversions = 1.08 (39/36) Gap_init rate = 0.05 (12 / 230), avg. gap size = 2.42 (29 / 12) 13 20.44 2.44 2.44 chr1ptel1M 611499 611539 (388461) (GGCTG)n#Simple_repeat 1 41 (0) m_b17s252i3 614 chr1ptel1M 611499 GGCTGAGCCGGGCAGGG-AGGGATGAGGCTGGGGTGGGCAGG 611539 i i v -v v - v v (GGCTG)n#Simp 1 GGCTGGGCTGGGCTGGGCTGGGCTG-GGCTGGGCTGGGCTGG 41 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 41 10.20 1.54 0.00 chr1ptel1M 613419 613483 (386517) (GGA)n#Simple_repeat 1 66 (0) m_b17s252i4 615 chr1ptel1M 613419 GGAGG-GAAGGAGGAAGAGGGGGAGGAGGAGGAGGAGGAGGAGGAGGAGG 613467 - i i i (GGA)n#Simple 1 GGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGG 50 chr1ptel1M 613468 AAGAGGGAGAGGAGGA 613483 i ii (GGA)n#Simple 51 AGGAGGAGGAGGAGGA 66 Matrix = Unknown Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.02 (1 / 64), avg. gap size = 1.00 (1 / 1) 57 3.54 0.00 0.00 chr1ptel1M 614172 614229 (385771) (GT)n#Simple_repeat 1 58 (0) c_b17s251i1 616 chr1ptel1M 614172 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGAGTGTGTGTGTGAGT 614221 v v (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50 chr1ptel1M 614222 GTGTGTGT 614229 (GT)n#Simple_ 51 GTGTGTGT 58 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0) 630 17.21 3.15 0.45 chr1ptel1M 614233 615533 (384467) (TG)n#Simple_repeat 1 1336 (0) m_b17s252i5 617 chr1ptel1M 614233 TGTATATGTTTCTGTTTGTGTGTATTTGTGTATCTGTATGTCTGTGTTAA 614282 i i v v v i v i v i v vvi (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr1ptel1M 614283 TGTATGTGCTTGTGTGTATTTATATGTTTGTATTTGTGTCTGTGTGTATG 614332 i iv i v i i v i v v i (TG)n#Simple_ 51 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 100 chr1ptel1M 614333 TATATGCTTATATTTGTGCGTGTGTGTATATGTAT-TTTGTGTGTGTGTT 614381 i i iv i i v i i i i - v v (TG)n#Simple_ 101 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 150 chr1ptel1M 614382 TGTGTATCTGTATGTGTTTCTGTGTCAATGTTTGTATTTCTGTGTGTATG 614431 i v i v v vvi v i v v i (TG)n#Simple_ 151 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 200 chr1ptel1M 614432 TGTGGATATCTGTGTGTATGTGTGGATATCTGTGTGTGTGTATATATATT 614481 vi i v i vi i v i i i i v (TG)n#Simple_ 201 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 250 chr1ptel1M 614482 TGTGTGTGTGTGTGTCTCTGTGTGTCTCTGTGTGTGTGTGTCTCTGTGTG 614531 v v v v v v (TG)n#Simple_ 251 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 300 chr1ptel1M 614532 TGTGTGTCTCTGTCTCTGTGTCTCTGTGTGTGTCTCTCTGTGTGTCTCTG 614581 v v v v v v v v v v v (TG)n#Simple_ 301 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 350 chr1ptel1M 614582 TCTGTGTCTCTGT-TGTGTCT-TGTTTGTGTTCTTGGTTCTGTGTCTCTG 614629 v v v - v - v viv vv v v v (TG)n#Simple_ 351 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 400 chr1ptel1M 614630 TTTGTGT-TCTGT-TGTGT-TCTGT-TGTGTTTGTGT-TGTGT-TCTGTG 614673 v - v - - v - v - - v (TG)n#Simple_ 401 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 450 chr1ptel1M 614674 TGTGTGT-TCTGTGT-TGT-TCTGTGTGTGTGCTTGTGTGTGTCTCTGTG 614720 - v - - v iv v v (TG)n#Simple_ 451 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 500 chr1ptel1M 614721 TGTGT-TGTCTCTGTGT-TGTGTCTGTGTCT-TCTGTGTCTGTGTGTTTG 614767 - v v - v v - v v v (TG)n#Simple_ 501 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 550 chr1ptel1M 614768 TGTGTCGTGT-TGTGTGT-TCTGTGTCCGTGTGT-TGTGT-TGTGTCTCT 614813 - - - v vi - - v v (TG)n#Simple_ 551 TGTGT-GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 599 chr1ptel1M 614814 GTGTGTGTGTTCGTGTGTGTGTGTGTGT-TGTGTGTCT-TGTGTGTGCTG 614861 vi - v - - (TG)n#Simple_ 600 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG-TG 648 chr1ptel1M 614862 TTTGT-TGTGTGTGTCTCT-TGTGTGTGTTTCTGTGTGTGTGTGTGTCTG 614909 v - v v - v v v (TG)n#Simple_ 649 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 698 chr1ptel1M 614910 TGT-TGTGTGT-TGTGT-TGTGTGTTTCTGTGCTGT-TGTGTTCTTGTGT 614955 - - - v v - - viv (TG)n#Simple_ 699 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG-TGTGTGTGTGTGTGTGT 747 chr1ptel1M 614956 -TGTGTGTCT-TGTGT-TGTGTGT-TGTCGTTTGTGTGT-TGTGT-TGTG 614999 - v - - - - v - - (TG)n#Simple_ 748 GTGTGTGTGTGTGTGTGTGTGTGTGTGT-GTGTGTGTGTGTGTGTGTGTG 796 chr1ptel1M 615000 TGTCTGTGT-TGTGTGTGT-TCTTTGT-TGTGTGTTTCTGTGTCGTGT-T 615045 v - - v v - v v - - (TG)n#Simple_ 797 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT-GTGTGT 845 chr1ptel1M 615046 GTGTTTGTGTGTGTGTTCTTGTGTGTGTGT-TCTGTGTGTGTGTCTGTGT 615094 v viv - v v (TG)n#Simple_ 846 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 895 chr1ptel1M 615095 GTGCTTCTCTGTGTGTGTGT-TGTGTGTGTCTCTGTGTGTTTGTGT-TGT 615142 iv v v - v v v - (TG)n#Simple_ 896 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 945 chr1ptel1M 615143 GTGCTTTCTCTCTGTGTGTGTGTCTCTGTGTGTGT-TCTGTGTTTGTGTG 615191 - v v v v v v - v v (TG)n#Simple_ 946 GTG-TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 994 chr1ptel1M 615192 TATCTGTGTGTGTCTCTGTGTGTGTGTCTCTGTGTGTCTCTGTGTGTGTG 615241 i v v v v v v v (TG)n#Simple_ 995 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 1044 chr1ptel1M 615242 TCTCTGTGTGTGTGTCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 615291 v v v (TG)n#Simple_ 1045 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 1094 chr1ptel1M 615292 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTTGTGTGTGTGTGTGTGTG 615341 v (TG)n#Simple_ 1095 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 1144 chr1ptel1M 615342 TGTGTGTGTGTGTGTGTGTGTGTCTGTGTGTGTGTGTGTGTGTGTGTGTC 615391 v v (TG)n#Simple_ 1145 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 1194 chr1ptel1M 615392 TCTCATTGTGTGTGTCTCTGTGTGTGTCTCTGTGTGTGTGTGTGTCTCTG 615441 v vvv v v v v v v (TG)n#Simple_ 1195 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 1244 chr1ptel1M 615442 TGTGTGTGTGTGTCTGTGTGTGTGTCTCTGTGTGTGTCTCTGTGTGTGTG 615491 v v v v v (TG)n#Simple_ 1245 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 1294 chr1ptel1M 615492 TGTCTCTGTGTGTGTGTCTCTCTGTGTGTGTCTCTCTGTGTG 615533 v v v v v v v v (TG)n#Simple_ 1295 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 1336 Matrix = Unknown Transitions / transversions = 0.29 (44/154) Gap_init rate = 0.04 (47 / 1300), avg. gap size = 1.00 (47 / 47) 49 6.27 7.14 0.00 chr1ptel1M 616908 616991 (383009) (TTCC)n#Simple_repeat 1 90 (0) m_b17s252i6 618 chr1ptel1M 616908 TTCTTTCCTTCCATCCTTCCTCCCTCCCTCCCTTCCTTCCTT-CTT-CTT 616955 i v i i i - - (TTCC)n#Simpl 1 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 50 chr1ptel1M 616956 -CTTCCTTCCTTCCTT-CTT-CTT-CTTCCTTCCTTCCTT 616991 - - - - (TTCC)n#Simpl 51 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 90 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.07 (6 / 83), avg. gap size = 1.00 (6 / 6) 22 22.80 2.94 1.45 chr1ptel1M 620024 620091 (379909) (GAT)n#Simple_repeat 1 69 (0) m_b17s252i7 619 chr1ptel1M 620024 GATGATGATGGTGGTG-GGATGATGATGGTGGTG-GGATGATGATGGTTG 620071 i i -v i i -v - v (GAT)n#Simple 1 GATGATGATGATGATGATGATGATGATGATGATGATGATGATGAT-GATG 49 chr1ptel1M 620072 AGGAGAAGGAGGATGCTGAT 620091 v vi v v v (GAT)n#Simple 50 ATGATGATGATGATGATGAT 69 Matrix = Unknown Transitions / transversions = 0.62 (5/8) Gap_init rate = 0.04 (3 / 67), avg. gap size = 1.00 (3 / 3) 320 26.88 3.23 0.00 chr1ptel1M 620723 620815 (379185) C MIRb#SINE/MIR (77) 191 96 m_b17s601i10 620 chr1ptel1M 620723 TTGACCCTCACCACAAGCTTG--AGGTAGAAATTGTTATCATCCTCCTAG 620770 i i v v i -- iv i vi v ii v C MIRb#SINE/MIR 191 TTAATCCTCACAACAACCCTGCGAGGTAGGTATTATTATCCCCATTTTAC 142 chr1ptel1M 620771 ATCT-AGGAAACTGGAGCTCAGCTAGGTTAAGAGACTGGACCAGGG 620815 vv - ii vv vi v v i C MIRb#SINE/MIR 141 AGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGG 96 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 33.56 CpG sites = 12, Kimura (unadjusted) = 33.56 Transitions / transversions = 0.92 (12/13) Gap_init rate = 0.02 (2 / 92), avg. gap size = 1.50 (3 / 2) 307 31.53 0.00 5.71 chr1ptel1M 621845 622029 (377971) L1ME4b_3end#LINE/L1 460 634 (258) m_b17s551i0 621 chr1ptel1M 621845 TTTGGGGTAGCAAAAAATTGGAAAATAAGTAGAGGCCCATCAATTGGGGA 621894 vii i vv vv i v i v L1ME4b_3end#L 460 TTTGTAATAGCAAAAGATTGGAAACAACCTAAATGTCCATCAATAGGGGA 509 chr1ptel1M 621895 ATGGCTGAACAAGTTATAGCATATGAAGGTATTGGAATATTATTATTCCA 621944 v i i i i i i i vv vii v i vvvv i L1ME4b_3end#L 510 CTGGTTAAATAAATTATGGTACATCCATACAATGGAATACTATGCAGCCG 559 chr1ptel1M 621945 CAAAAAATAATGAACAAGCCAATTTTAAAAGGCCCTGGTAAGGCCAGGGA 621994 i v iv i--i ? --- v iv i -----v i L1ME4b_3end#L 560 TAAAAAAGAATGAGGAAGCT--CTNT---ATGTACTGATA-----TGGAA 599 chr1ptel1M 621995 AGATTTATAGGAACTAATGGTGAGCGAAACAAGCA 622029 ? i vi i vv v v i i v L1ME4b_3end#L 600 NGATCTCCAAGATATATTGTTAAGTGAAAAAAGCA 634 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 41.04 CpG sites = 28, Kimura (unadjusted) = 42.03 Transitions / transversions = 1.04 (28/27) Gap_init rate = 0.05 (10 / 184), avg. gap size = 1.00 (10 / 10) 291 31.77 0.47 6.00 chr1ptel1M 621852 622062 (377938) L1ME4c_3end#LINE/L1 470 669 (161) m_b17s551i1 621 chr1ptel1M 621852 TAGCAAAAAATTGGAAAATAAGTAGAGGCCCATCAATTGGGGAATGGCTG 621901 i vv vv i v i v v i i L1ME4c_3end#L 470 TAGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAATGGTTA 519 chr1ptel1M 621902 AACAAGTTATAGCATATGAAGGTATTGGAATATTATTATTCCACAAAAAA 621951 ii i i i i v? vviiv vvvv iv L1ME4c_3end#L 520 AGTAAATTATGGTACATCNACTCGATGGAATATTATGCAGCCATTAAAAA 569 chr1ptel1M 621952 TAATGAACAAGCCAATTTTAAAAGGCCCTGGTAAGGCCAGGGAAGATTTA 622001 i --------- v -i i iv - iviv v i v v L1ME4c_3end#L 570 TGAT---------AATTAT-GAAGACTAT-GTAGCAACATGGAAAATGTT 608 chr1ptel1M 622002 TAGGAACTAATGGTGAGCGAAACAAGCAGAAC-CAGGAATACAGTGCACA 622050 v vv v i i v i- ii v ii - ?i i L1ME4c_3end#L 609 TATGATATAATGTTAAGTGAAAAAAGCAGAATACAAAATTGTA-TNTACG 657 chr1ptel1M 622051 CAATAACCACAA 622062 v i ii L1ME4c_3end#L 658 CTATGATTACAA 669 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 39.79 CpG sites = 33, Kimura (unadjusted) = 42.48 Transitions / transversions = 1.10 (33/30) Gap_init rate = 0.06 (13 / 210), avg. gap size = 1.00 (13 / 13) 846 28.41 1.06 4.09 chr1ptel1M 622714 623091 (376909) L1MB2_3end#LINE/L1 43 409 (509) m_b17s551i2 622 chr1ptel1M 622714 AAAAATACAAATCATTCCCCAATTGATAAATGGTCAAAAGAGATGAATAG 622763 v v --- i ? v v i vv L1MB2_3end#LI 43 AAAAAAACAAATAA---CCCGATTNAAAAATGGGCAAAGGACTTGAATAG 89 chr1ptel1M 622764 ATATTTTCTTCAGCTAAAGAAAT-CAAA--GCTATCTCTAGTCATATGAA 622810 i - i iv-i v - -- i v --- iv L1MB2_3end#LI 90 ACATTT-CTCCAAA-GAAGATATACAAATGGCCAAC---AAGCATATGAA 134 chr1ptel1M 622811 AAAATATTGCTCTAAATCCTTACTTATTAGAGAAATGCAAATTAAAATAA 622860 i --- v v vi v i i i iv L1MB2_3end#LI 135 AAGAT---GCTCAACATCACTAATCATTAGGGAAATGCAAATCAAAACCA 181 chr1ptel1M 622861 TTCTGAGGTACCACCTCACACCTATTAGATTGCCTAATATGACAAAAAAG 622910 ivv i i i iv v v v v vi L1MB2_3end#LI 182 CAATGAGATATCACCTCACACCCATTAGGATGGCTACTATCAAAAAAACA 231 chr1ptel1M 622911 GAAAATGTTGGATGTTGATGGGGATGTGGGAAAATTGGGACGCTAATGAA 622960 iviiii ii i ii i v vi v L1MB2_3end#LI 232 GAAAATAACAAGTGTTGGCGAGGATGTGGAGAAATTGGAACCCTTGTGCA 281 chr1ptel1M 622961 CTGTTGGTAAAGTTGTGAAATGATCTTACTACTCTGGAGCACAATTTGGA 623010 iiiiv i i vivi ii v iv i v - L1MB2_3end#LI 282 CTGTTGGTGGGAATGTAAAATGGTGCAGCCGCTATGGAAAACAGTATGG- 330 chr1ptel1M 623011 ACTGTGGC-CAAAGGACTATAAAACTGGGCATAACTTTTGATGCAGAAAT 623059 - v vv - ii i-- v i ivv v v v v v L1MB2_3end#LI 331 -CGGTTCCTCAAAAAAT--TAAAAATAGAATTACCATATGATCCAGCAAT 377 chr1ptel1M 623060 AGCACTGCTTGGTCTATTGCTCAAAGAAATGA 623091 vv v v v vv iv v L1MB2_3end#LI 378 CCCACTTCTGGGTATATATCCAAAAGAATTGA 409 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 34.81 CpG sites = 50, Kimura (unadjusted) = 36.13 Transitions / transversions = 0.94 (50/53) Gap_init rate = 0.05 (18 / 377), avg. gap size = 1.06 (19 / 18) 86 18.18 3.24 0.00 chr1ptel1M 623096 623280 (376720) (GAGAGA)n#Simple_repeat 1 191 (0) m_b17s252i9 623 chr1ptel1M 623096 GAGGGA-AGA-AGGGAGGGA-AGAGAGAGATAG-GAGAGAGA-AGGGAGA 623140 i - - i i - v - - i (GAGAGA)n#Sim 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr1ptel1M 623141 GAAAGAGA-AGGGAGGGAAGGAGGAAGGAAGGGAGAGAGACAGAGACAGA 623189 i - i i ii ii ii i v v (GAGAGA)n#Sim 51 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 100 chr1ptel1M 623190 GACAGAGACAGAGACAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 623239 v v v (GAGAGA)n#Sim 101 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 150 chr1ptel1M 623240 GAGAAGGAGGGAGAGAGAGAGAAGGAGGGAGGGAGGAAGAG 623280 ii i ii i i ii (GAGAGA)n#Sim 151 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 191 Matrix = Unknown Transitions / transversions = 3.83 (23/6) Gap_init rate = 0.03 (6 / 184), avg. gap size = 1.00 (6 / 6) 252 35.17 2.50 0.49 chr1ptel1M 623292 623491 (376509) L1ME2z_3end#LINE/L1 430 633 (558) m_b17s551i3 624 chr1ptel1M 623292 ATTTGTACAAAAATATTTATAGCAGGGTTTTT--TTGTAGCAAAAAATTA 623339 i i i i vv v -- vi v i i L1ME2z_3end#L 430 ACTTGTACAAGAATGTTCATAGCAGCTTTATTCATAATAGCCAAAAACTG 479 chr1ptel1M 623340 GAAATTGAGGGGGTGCCCATCAATTGAGAAATGACTAAACAAGTAGTAGT 623389 iv vvvi i iv iii iv iiv i L1ME2z_3end#L 480 GAAACAGCCCAGGTGTCCATCAACAGGAGAATGGATAAACAAACTGTGGT 529 chr1ptel1M 623390 ATATG-ATGTGATAAAATATCATTATGCTGTGAGAAGTGACAAGCATGAT 623438 v- iii ii ii i vv vi i i vi i i - iv L1ME2z_3end#L 530 ATATTCATACAATGGAATACTACTCAGCAATAAAAAGGAACGAAC-TACT 578 chr1ptel1M 623439 GAT-TTCAGAAAAACTTGGA-AAGACTTAATGAAATGATGCAAAGTGAAG 623486 -iv iv v v -i iv i vi v v vi i L1ME2z_3end#L 579 GATACACGCAACAACATGGATGAATCTCAAAAACATTATGCTGAGTGAAA 628 chr1ptel1M 623487 TGAGC 623491 vi L1ME2z_3end#L 629 GAAGC 633 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 47.60 CpG sites = 42, Kimura (unadjusted) = 49.63 Transitions / transversions = 1.50 (42/28) Gap_init rate = 0.03 (5 / 199), avg. gap size = 1.20 (6 / 5) 49 24.32 2.36 0.00 chr1ptel1M 623657 623783 (376217) (TTTC)n#Simple_repeat 1 130 (0) m_b17s252i10 625 chr1ptel1M 623657 TTTCTCCCTTTCTTCCTTTCTTTCCTTCTTT-TTTCCTTCCTCCTCCCTC 623705 ii i i - i i i ii i (TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 50 chr1ptel1M 623706 CCTTTTTTTCCTTCTCTCTCTTTTTCTCTCTTTCTTTTGTTC-TACTTT- 623753 i i i i i i i iv - v - (TTTC)n#Simpl 51 TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC 100 chr1ptel1M 623754 TCTTTTTCCTTCTTTCTTTCTTGTTTTCTT 623783 i i i vi (TTTC)n#Simpl 101 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 130 Matrix = Unknown Transitions / transversions = 7.33 (22/3) Gap_init rate = 0.02 (3 / 126), avg. gap size = 1.00 (3 / 3) 12 18.26 4.88 2.38 chr1ptel1M 623666 623706 (376294) (TTCCTCC)n#Simple_repeat 1 42 (0) m_b17s252i11 626 chr1ptel1M 623666 TTCTTCCTT--TCTTTCCTTCTTTTTTCCTTCCTCCTCCCTCC 623706 i -- i - i ii i (TTCCTCC)n#Si 1 TTCCTCCTTCCTCCTTCC-TCCTTCCTCCTTCCTCCTTCCTCC 42 Matrix = Unknown Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.50 (3 / 2) 49 24.32 2.36 0.00 chr1ptel1M 623657 623783 (376217) (TTTC)n#Simple_repeat 1 130 (0) m_b17s252i10 625 chr1ptel1M 623657 TTTCTCCCTTTCTTCCTTTCTTTCCTTCTTT-TTTCCTTCCTCCTCCCTC 623705 ii i i - i i i ii i (TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 50 chr1ptel1M 623706 CCTTTTTTTCCTTCTCTCTCTTTTTCTCTCTTTCTTTTGTTC-TACTTT- 623753 i i i i i i i iv - v - (TTTC)n#Simpl 51 TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC 100 chr1ptel1M 623754 TCTTTTTCCTTCTTTCTTTCTTGTTTTCTT 623783 i i i vi (TTTC)n#Simpl 101 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 130 Matrix = Unknown Transitions / transversions = 7.33 (22/3) Gap_init rate = 0.02 (3 / 126), avg. gap size = 1.00 (3 / 3) 443 31.32 5.99 0.57 chr1ptel1M 624817 624983 (375017) C MIRc#SINE/MIR (18) 250 75 m_b17s601i11 627 chr1ptel1M 624817 CATTTATATAACCCTTTAAGAGTTACAAAGCATTTT-ACCTGAACTGTCT 624865 i i v viiv ii - v iv i i C MIRc#SINE/MIR 250 CATTTGTATAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATCT 201 chr1ptel1M 624866 TCCTTTATCCCCACAACAGCCCTGGGAGG-AGAT------GCTCTTATTG 624908 ivi v i i v - ii------ v v i C MIRc#SINE/MIR 200 CATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTA 151 chr1ptel1M 624909 TCTGTATCTTGTGGAAGAATAAAAAGGAGGTGGACAGAGACTAAGCAACT 624958 ivi i iii v i-i vv ivv v ii ii C MIRc#SINE/MIR 150 TCCCCATTTTACAGATGAG-GAAACTGAGGCTCAGAGAGGTTAAGTGACT 102 chr1ptel1M 624959 TGCTCA--GACACAGACCTAGCATGTG 624983 i -- v v v i v C MIRc#SINE/MIR 101 TGCCCAAGGTCACACAGCTAGTAAGTG 75 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 40.88 CpG sites = 31, Kimura (unadjusted) = 41.95 Transitions / transversions = 1.48 (31/21) Gap_init rate = 0.03 (5 / 166), avg. gap size = 2.20 (11 / 5) 280 18.33 5.00 0.00 chr1ptel1M 626045 626104 (373896) L2b_3end#LINE/L2 403 465 (1) m_b17s601i12 628 chr1ptel1M 626045 CAGCGCT--GTGCAGGACCTGGCACACAGTAGG-GCTGAATAAATGCTCA 626091 i-- ii ?i - v i ii ii L2b_3end#LINE 403 CAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTTG 452 chr1ptel1M 626092 TAGAATGAATGAA 626104 v L2b_3end#LINE 453 TTGAATGAATGAA 465 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 22.45 CpG sites = 9, Kimura (unadjusted) = 22.45 Transitions / transversions = 4.50 (9/2) Gap_init rate = 0.03 (2 / 59), avg. gap size = 1.50 (3 / 2) 271 33.38 13.78 2.81 chr1ptel1M 626163 626387 (373613) MIRb#SINE/MIR 6 254 (14) m_b17s601i13 629 chr1ptel1M 626163 GGGCAGCTAGATGGCACAACAGAGAGAGGGCTGAGCCTATGTGCAGGGAG 626212 ---i ii iii i vi - i i --- v vv MIRb#SINE/MIR 6 GGGCAGC---GTGGTGCAGTGGAAAGAGCAC-GGGCTT---TGGAGTCAG 48 chr1ptel1M 626213 ATGG---CGAGCTCGAATCCAGCCTCAGGCCCTCGCTAGCTGGGCTGCCT 626259 ii ---i i i v v v v v ii v ivi MIRb#SINE/MIR 49 ACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCT 98 chr1ptel1M 626260 C------CTCA---AATCTCCGTCTGCCTCCATTCTCTCAAGTATAAAGT 626300 i------v i --- i iv vv vi ii vv i i MIRb#SINE/MIR 99 TGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAAT 148 chr1ptel1M 626301 AGGGGTG-----ACCCAGCACCCGGGGCCGTTGTGAGGGTC-AGCGAGGC 626344 i i i----- i v v v i ii i i- ii ii MIRb#SINE/MIR 149 GGGGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGAT 198 chr1ptel1M 626345 GA------------GATTAGC-CGGGGCCTGGTGCACAGTAGGCACTTAG 626381 i ------------ v - i v ii i i i i i MIRb#SINE/MIR 199 AATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAA 248 chr1ptel1M 626382 TAAATG 626387 MIRb#SINE/MIR 249 TAAATG 254 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 45.60 CpG sites = 50, Kimura (unadjusted) = 47.46 Transitions / transversions = 2.17 (50/23) Gap_init rate = 0.06 (14 / 224), avg. gap size = 2.71 (38 / 14) 187 27.50 0.00 0.00 chr1ptel1M 626353 626392 (373608) L2c_3end#LINE/L2 426 465 (13) m_b17s601i14 630 chr1ptel1M 626353 CCGGGGCCTGGTGCACAGTAGGCACTTAGTAAATGCCCGT 626392 i v ii i i i i iii L2c_3end#LINE 426 CCAGCGCCTGGCACATAGTAGGCGCTCAATAAATGTTTGT 465 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 33.98 CpG sites = 10, Kimura (unadjusted) = 38.50 Transitions / transversions = 10.00 (10/1) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 16 15.91 0.00 0.00 chr1ptel1M 628585 628612 (371388) (A)n#Simple_repeat 1 28 (0) m_b17s252i12 631 chr1ptel1M 628585 AACAAAATAAAAAAAGAAAGAAAAAAAA 628612 v v i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA 28 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 305 16.25 8.75 0.00 chr1ptel1M 628645 628724 (371276) C L2d2_3end#LINE/L2 (66) 489 403 m_b17s601i15 632 chr1ptel1M 628645 GGGAATACAAAGAAATGTGT-ACA-GGTCCCTGCCTTCAAGGAGCTTTCA 628692 i i i iv- - i v C L2d2_3end#LIN 489 GGGGATACAAAGAAGTATAAGACATGGTCCCTGCCCTCAAGGAGCTTACA 440 chr1ptel1M 628693 ATCTAA-TGGAGATACAAAAGA-AAGCA---GAAAAG 628724 i- i v i v - i --- C L2d2_3end#LIN 439 ATCTAGTTGGGGAGACAAGACATAAACACGTGAAAAG 403 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 18.71 CpG sites = 9, Kimura (unadjusted) = 18.71 Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.06 (5 / 79), avg. gap size = 1.40 (7 / 5) 18 18.18 3.85 1.89 chr1ptel1M 629407 629458 (370542) (TTAA)n#Simple_repeat 1 53 (0) m_b18s252i1 633 chr1ptel1M 629407 TTAATTAATAAATTTATTAGTTAGCTAATTTAATTAA-AAATTGACT-AT 629454 v v i ii - -v i i - (TTAA)n#Simpl 1 TTAATTAATTAATTAATTAATTAATTAA-TTAATTAATTAATTAATTAAT 49 chr1ptel1M 629455 TAAT 629458 (TTAA)n#Simpl 50 TAAT 53 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.00 (3 / 3) 17 26.00 3.17 3.17 chr1ptel1M 630716 630778 (369222) (TC)n#Simple_repeat 1 63 (0) m_b18s252i2 634 chr1ptel1M 630716 TCTCTGACT-TTTCTGCCTCTGTCTCTCTCTGTGTCTCTC-CTTTACTGT 630763 vv - i vi v v v - i - v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT-CTCT 49 chr1ptel1M 630764 TCCTCTGCTCTTTCT 630778 ii - i (TC)n#Simple_ 50 CTCTCT-CTCTCTCT 63 Matrix = Unknown Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.06 (4 / 62), avg. gap size = 1.00 (4 / 4) 203 30.90 14.84 3.98 chr1ptel1M 631202 631383 (368617) L3#LINE/CR1 780 980 (3119) m_b18s601i1 635 chr1ptel1M 631202 GACAAAGGCAGAAGGAACCTGGAACAC-TTTATGAACACTCAGGACCTCT 631250 v v i ii - i v iivv iv i vii L3#LINE/CR1 780 GACACAGTCAGAAGAAACCTGGAATGCATCTCTAGTGACTTTGAAGTCCT 829 chr1ptel1M 631251 GAGCAATGGGGTGATGAAGGCTACT--GGGGCACAGGCAATCGTTCCATC 631298 i --- iviv -- -- iii vv i L3#LINE/CR1 830 GGGCA---GGAAACTGAAGG--ACTTGGGGGCACAGGTGGTGTTTTCATC 874 chr1ptel1M 631299 ------------GGAAAG----GAATTT-----AAAAAGAGAGATTTAGG 631327 ------------v i ---- v ----- i iii v i L3#LINE/CR1 875 TCTTCTTCCAGTTGAAGGTCGTGACTTTGGAAGAGAAAGGAGGATATGGG 924 chr1ptel1M 631328 GTGTGAGTAGCTGG---GAGAGATGAGAGTGTCTGGGAATGAGATTTGGA 631374 iv ii ---viv --- vii iii v L3#LINE/CR1 925 AAGTGAACAGCTGGCTACGTAGATG---GTGTCGAAGAACAGGATTTGGT 971 chr1ptel1M 631375 CATCTGAAC 631383 iv i L3#LINE/CR1 972 TTTCTGGAC 980 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 40.73 CpG sites = 34, Kimura (unadjusted) = 41.77 Transitions / transversions = 1.70 (34/20) Gap_init rate = 0.08 (14 / 181), avg. gap size = 2.50 (35 / 14) 228 34.44 8.18 3.93 chr1ptel1M 631521 631789 (368211) L3#LINE/CR1 1214 1493 (2606) m_b18s601i2 635 chr1ptel1M 631521 TCCTGGAAGGAGACCAGCGGAAGAGAAGTCA-AGACAG-ATTCAAGAA-- 631566 ?ii i i i iv v? i ii - i i- i i v iv-- L3#LINE/CR1 1214 TCNCAGGAGAAAATAACNGGAAAAGAAGCTAGAAACAATACTTATGGCCT 1263 chr1ptel1M 631567 -AAACATCTATGTATCAAAGAAGAAATTATGGTTAACTG-CAAAG--AGC 631612 - i ii i i v v v i v v ivi-? -- i L3#LINE/CR1 1264 CAGATGTCTATATACCAATGCACAGAGTATGGGTAATAAANAAAGTNAAC 1313 chr1ptel1M 631613 CCGGA-------CACAAGAAGACAAATCACAGGTTGGGAAATA--AATAA 631653 ii i ------- i ii - iivi viv ii -- vii L3#LINE/CR1 1314 TTGAAATTTTAACACAAGGAGGTAAAT-ACGATCTCATAGGTATCACCGA 1362 chr1ptel1M 631654 G-CTTGG-GGGATAAAATCTATGATGAGAATATATTTCCAGGTAAATATA 631701 - - iii iii ivi iivivvii iviii ? L3#LINE/CR1 1363 GACTTGGTGGGATGGGACTCATGACTGGAATACGGCGATGGAAGGGTANA 1412 chr1ptel1M 631702 CCTTAATCAAAAAAAGTGAAATC-AGTAGAGGGCTGAGGTAGGATTATGG 631750 iv i ii- i - ? i -v ? -------- L3#LINE/CR1 1413 CCTTGTTCAAAAGAAAC-AGATCTANTAGAAGG-GGAGGNA--------G 1452 chr1ptel1M 631751 ACTAGCATTGTCTGTGAAGGAGATATA-ATC-ACGTGAAAA 631789 v i v v i - i -i i L3#LINE/CR1 1453 AGTAGCACTGTATGTCAAGAAGATATACACCTGCGTGGAAA 1493 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 48.77 CpG sites = 65, Kimura (unadjusted) = 52.51 Transitions / transversions = 2.71 (65/24) Gap_init rate = 0.09 (24 / 268), avg. gap size = 1.38 (33 / 24) 12 21.71 0.00 0.00 chr1ptel1M 631929 631960 (368040) (AATAA)n#Simple_repeat 1 32 (0) m_b18s252i3 636 chr1ptel1M 631929 AACAAAATAAATAAAAATACAATCAAATACAA 631960 i vv v v v (AATAA)n#Simp 1 AATAAAATAAAATAAAATAAAATAAAATAAAA 32 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 50 0.00 0.00 0.00 chr1ptel1M 632426 632468 (367532) (TA)n#Simple_repeat 1 43 (0) c_b18s251i0 637 chr1ptel1M 632426 TATATATATATATATATATATATATATATATATATATATATAT 632468 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATAT 43 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 388 33.76 3.70 3.07 chr1ptel1M 632679 632840 (367160) L3#LINE/CR1 1767 1929 (2170) m_b18s601i3 635 chr1ptel1M 632679 TCACTCTTCAAAAAGTGAAGGAAGCAGCA----GAACTGCTTCACTGGGC 632724 iiii i i ii i i---- v v i L3#LINE/CR1 1767 TCATCTCTCAGAAGGTAGAGGAAGCAACGAGGGGAACTGCTACTCTGGAC 1816 chr1ptel1M 632725 CTGGACGACTCTGACCAACCA-AATGAACGGGCTGTTGGATTAGACGT-G 632772 i i---- i v -i v v i v i v i v - L3#LINE/CR1 1817 TTA----ATTCTGACCAACAAGGAAGAACTGGTTGGTGAAGTGGAAGTCG 1862 chr1ptel1M 632773 GTAGAAATCCTGAGAATGGGTGACTGCTTTATCTTGGAATTTGTATTAGG 632822 i i i i i ivii - iiiv i i i i v v L3#LINE/CR1 1863 ATAGGAACCTTGGGAGAAAGTG-CCATGTCATCTTAGAGTTCGTAATAGC 1911 chr1ptel1M 632823 AGAGAAGAGGTGAGCTAA 632840 vi ii ivi i L3#LINE/CR1 1912 CAAGAAAGGAAAAGTTAA 1929 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 46.31 CpG sites = 39, Kimura (unadjusted) = 49.00 Transitions / transversions = 2.79 (39/14) Gap_init rate = 0.05 (8 / 161), avg. gap size = 1.38 (11 / 8) 772 31.62 5.86 2.39 chr1ptel1M 633762 635297 (364703) L1M5_orf2#LINE/L1 1707 3294 (0) m_b18s551i0 638 chr1ptel1M 633762 AATGCAGGCATGGGTTAACATAAGGAAAACTACTAACATAATTGATTACA 633811 i vv v vv i v v ii ii v ii i L1M5_orf2#LIN 1707 AATGCAAGGTTGGTTTAACATTCGAAAATCAATCAATGTAATTCACCATA 1756 chr1ptel1M 633812 TCAATAACAAAAATAATAAAAATTGTATGATTATATCAATAAATAGAGAA 633861 i i iv v vi v ii i v i iv L1M5_orf2#LIN 1757 TTAACAGAATAAAGGAGAAAAATCATATGATCATCTCAATAGATGCAGAA 1806 chr1ptel1M 633862 AATGGATTTGACAAAATACAGTATTCATTCATATTAAAAACACTTGAGAG 633911 v v v ii ii iv v i--- L1M5_orf2#LIN 1807 AAAGCATTTGACAAAATTCAACACCCATTCATGATAAAAACTCTC---AG 1853 chr1ptel1M 633912 CA---TAG--ATATAAATGAATTTTTCCTTAAAATGATAAAAAGCATCTA 633956 --- -- v iv --i i vv ii L1M5_orf2#LIN 1854 CAAACTAGGAATAGAAGGGAA--CTTCCTCAACCTGATAAAGGGCATCTA 1901 chr1ptel1M 633957 CCTAATACCAATAAATAACATTATTTGTAACGGGGATAAGCTAGAAACCT 634006 vv v v i iv? i viv i v v ?i ii ?i i L1M5_orf2#LIN 1902 CGAAAAACCTACAGCNAACATCATACTTAATGGTGAAANACTGAANGCTT 1951 chr1ptel1M 634007 TCCCAATAAGAT--GGAATGAAA-GAGGATGCCCATCATCATCAATATTA 634053 vv -- ii i -i i iii? i v vi L1M5_orf2#LIN 1952 TCCCCCTAAGATCGGGAACAAGACAAGGATGTCCGCTNTCACCACTTCTA 2001 chr1ptel1M 634054 TTCAATGTTGCATTAGAAATGTTAGCAATTGCAATAAGAGAAGAATAAAT 634103 ii i i i ii vi v v iv v iv L1M5_orf2#LIN 2002 TTCAACATTGTACTGGAGGTCCTAGCCAGTGCAATAAGGCAAGAAAAAGA 2051 chr1ptel1M 634104 AATCAAAGGAATCAGAATGGGCAATGAGGTAATAAAACTCTTTCT-TTTG 634152 v v v ii v v v i v v i?i - i L1M5_orf2#LIN 2052 AATAAAAGGCATAAAGATTGGAAAGGAAGAAATAAAACTGTCNTTATTCG 2101 chr1ptel1M 634153 TAGACAAGATGATATTCTTGG--GGAAATCTTAGAGATTCAACTAAAAAT 634200 i ii v vv ? vv -- i i? i v v v ? v L1M5_orf2#LIN 2102 CAGATGACATGATTGTNTACGTAGAAAATCCNAAAGAATCTACAAANAAA 2151 chr1ptel1M 634201 TTAGTTGAAACAATTAATGATTTTAGCAAAGTAGCAGGGTATAAGATAAA 634250 i v v vi v i v i v ? i i i v L1M5_orf2#LIN 2152 CTACTAGAACTAATAAGTGAATTTAGCAAGGTCGCNGGATACAAGGTCAA 2201 chr1ptel1M 634251 TCCATATAAATCCTCAGCATTTCTATGTATCATCAACAAACCCCCATAAG 634300 vi i v vviv i i ii v vviiiv i L1M5_orf2#LIN 2202 TATACAAAAATCAATTGTATTTCTATATACTAGCAACAAACAATTGGAAA 2251 chr1ptel1M 634301 AAGCGATAGTAAGAAATACCCCCTTTAAAATAACCATGGAAAATATGAAA 634350 v vi vv? i vv iv v v i vviii i ? L1M5_orf2#LIN 2252 ATGAAATTTNAAAAACAATACCATTTACAATAGCATCAAAAAACATNAAA 2301 chr1ptel1M 634351 GAC--------AAACCTAGGAAC-----TATAAGA-----ACA-TG---A 634378 v -------- i iv v----- ii ----- - --- L1M5_orf2#LIN 2302 TACTTAGGAATAAATCTAACAAAANATGTGCAAGACCTNTACACTGAAAA 2351 chr1ptel1M 634379 TTAGAAAACACTTTTTGA-ACAAATAAAGTCAGATTTAAATAACTGCA-A 634426 i v - vi - v v ivv ii v v - L1M5_orf2#LIN 2352 CTACAAAACA-TTGCTGAGAGAAATTAAAGAAGACCTAAATAAATGGAGA 2400 chr1ptel1M 634427 AATTTTTAATTCTTCATTGGTGGAGAGAGCCAATATAATAAAAATG---A 634473 i v viv - v v i v ii vi vi ? i --- L1M5_orf2#LIN 2401 GATATACCA-TGTTCATGGATTGGAAGACTCAATATTGTNAAGATGTCAA 2449 chr1ptel1M 634474 TTTTACCTAAACTAA--TATATTTTTAATGGAAATATCATTGAATATACA 634521 i v i i i -- vv i - v vi v v v v v L1M5_orf2#LIN 2450 TTCTCCCCAAATTGATCTATAGATTCAAT-GCAATCCCAATCAAAATCCC 2498 chr1ptel1M 634522 AAATAGTTATTTTATTGAGCTAGA-AAAATAATAACAAAATTCATTTGGA 634570 ivvi v i v iv v - iv i vvi i v L1M5_orf2#LIN 2499 AGCAGGTTTTTTTGTAGAAATTGACAAGCTGATTCTAAAATTTATATGGA 2548 chr1ptel1M 634571 AGAACAAAAGGTGAAGAAT-GTCAAAAGAATTAATGAAAAA-ATGTA-AA 634617 ivi i iiv? - i v i-v - v v - L1M5_orf2#LIN 2549 AATGCAAAGGACCNAGAATAGCCAAAACAATC-TTGAAAAAGAAGAACAA 2597 chr1ptel1M 634618 AGAAGAAGGTCTTGCTATACTAGATCTTAAACCGCATCATTAGGCAGCAA 634667 vv i v i vv i? ? i iv vi i v i vi i L1M5_orf2#LIN 2598 AGTTGGAGGACTTACACTACCNGATNTCAAGACTTATTATAAAGCTACAG 2647 chr1ptel1M 634668 TTATCAAAATTATCTTATACTAGC-TAACAAATAGAAAGGTGGATCAATG 634716 v i ivi v vi i i - -ii v ii i L1M5_orf2#LIN 2648 TAATCAAGACAGTGTGGTATTGGCGTAA-GGATAGACAAATAGATCAATG 2696 chr1ptel1M 634717 TATCAAACTAGA-----CACATAATA----CACAGCAATTAATTGCTATA 634757 v v i v ----- v - ---- - -- ----- i L1M5_orf2#LIN 2697 GAACAGAATAGAGAGTCCAGA-AATAGACCCACA-CA--TA-----TATG 2737 chr1ptel1M 634758 ATAACTTTGTGTTTGACCAATGTAAATATTTAAGCTTGTGAGTTAAGAAT 634807 i?v ? vi v v v ivvv ?vi viiv i vv i L1M5_orf2#LIN 2738 GNCANTTGATTTTTGACAAAGGTGCCAANGCAATTCAGTGGGGAAAGGAT 2787 chr1ptel1M 634808 TCACTATTTGGTAAAAAAAAATTGTTGGGAATATTAGAAAGCAATCTCAT 634857 -- v v -- v v viv i i vv i v v v v viv L1M5_orf2#LIN 2788 --AGTCTTT--TCAACAAATGGTGCTGGAACAATTGGATATCCATATGGA 2833 chr1ptel1M 634858 AGAAATTGGATATAGAGCATTATCTTATACTATTTACCAATATGAGATCA 634907 i v i ?v v v vi i i i i vi v v v iv ? L1M5_orf2#LIN 2834 AAAAAATGAANCTCGACCCCTACCTCACACCATACACAAAAATTAATTCN 2883 chr1ptel1M 634908 AAATGGATTCAT-GGCCTAGACATAAATGG-AAATCTCATAAGTAAAT-- 634953 i - - i i ii v ?- v - -- v -- L1M5_orf2#LIN 2884 AGATGGA-TCATAGACCTAAATGTAAAAGNTAAAACT-ATAA--AACTTC 2929 chr1ptel1M 634954 TAGAAG--CACATAGAACCTAATATC----AGACTTATGTATAGGAGAAG 634997 --v i --v ----v i vv v? vi L1M5_orf2#LIN 2930 TAGAAGAAAACATAGGA--GAATATCTTCGTGACCTTGGGNTAGGCAAAG 2977 chr1ptel1M 634998 AATTTATAAACAAAAGATAGAGAGCATT----ATAAGATACAAAATGGAT 635043 v iv ii v i i i i?---- i v v v L1M5_orf2#LIN 2978 ATTTCTTAAACAGGACACAAAAAGCACNAACCATAAAAGAAAAAATTGAT 3027 chr1ptel1M 635044 AATTTTAATTACATTAAATTTAAAAA------------AAGATAAGACCA 635081 v vi i ? i v ------------ i -i v i L1M5_orf2#LIN 3028 AAATTGGACTNCATCAAAATTAAAAACTTCTGCTCNTCAAAA-GACACCG 3076 chr1ptel1M 635082 ATATATACAAGATTAGAAGAAAAG-CAGAAAATGGTGGAGAGAGGTTTTA 635130 v --- v i v i iv - v i ? -- i ivv i L1M5_orf2#LIN 3077 TTA---AGAAAATGAAAAGGCAAGCCACAGANTG--GGAGAAAATATTTG 3121 chr1ptel1M 635131 T-AGACAGCTTCTTGAATAAAGG--TC-TATCTCAAGTAAATAGAAAACT 635176 i- ? vv vii - i -- - ivi i v i i L1M5_orf2#LIN 3122 CAANACATATATCTG-ACAAAGGACTCGTATCCAGAATATATAAAGAACT 3170 chr1ptel1M 635177 TAGTCAAATTTATAAGAATATGA-ATATTTCCCAAT-GATAAATAATCAA 635224 ivvv ? iv ? v v - v ivv -? v iiv L1M5_orf2#LIN 3171 CCTACAANTCAATAANAAAAAGACAAACAACCCAATANAAAAATGGGCAA 3220 chr1ptel1M 635225 AAGATATAAACAGGCAGCGTTCAGAAAAAGAAATA---AAAGTATATATG 635271 iv i i - - v ii i --- vviivv i L1M5_orf2#LIN 3221 AAGACTTGAACAGACA-C-TTCACAAAAGAAGATATNCAAATGGCCAATA 3268 chr1ptel1M 635272 ATCATAGGAAAAAATGTTCCAAATCA 635297 v i v i i v v? L1M5_orf2#LIN 3269 AGCACATGAAAAGATGCTCAACNTCA 3294 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 42.48 CpG sites = 235, Kimura (unadjusted) = 42.83 Transitions / transversions = 0.98 (235/239) Gap_init rate = 0.05 (74 / 1535), avg. gap size = 1.73 (128 / 74) 774 33.40 4.96 2.25 chr1ptel1M 633763 634932 (365068) L1M3_orf2#LINE/L1 1702 2902 (386) m_b18s551i2 638 chr1ptel1M 633763 ATGCAGGCATGGGTTAACATAAGGAAAACTACTAACATAATTGATTACAT 633812 i v v i v ? v v i? ii i vv ii L1M3_orf2#LIN 1702 ATGCAAGGATGGTTCAACATACGNAAATCAATNAATGTGATACACCACAT 1751 chr1ptel1M 633813 CAATAACAAAAATAATAAAAATTGTATGATTATATCAATAAATAGAGAAA 633862 i i iv vi vi iii i v i iv L1M3_orf2#LIN 1752 TAACAGAATGAAGGATAAAAATCACATGATCATCTCAATAGATGCAGAAA 1801 chr1ptel1M 633863 ATGGATTTGACAAAATACAGTATTCATTCATATTAAAAACACTTGAGAGC 633912 v v v ii i v iv v ii v iv L1M3_orf2#LIN 1802 AAGCATTTGACAAAATTCAACATCCTTTCATGATAAAAACTCTCAACAAA 1851 chr1ptel1M 633913 ATAGATATAAATGAATTTTTCCTTAAAATGATAAAAAGCATCTACCTAAT 633962 v i? i v i v?? v i v i iiv v ivv v L1M3_orf2#LIN 1852 CTAGGNATAGAAGGAANNTACCTCAACATAATAAAGGCCATATATGAAAA 1901 chr1ptel1M 633963 ACCAATAAATAACATTATTTGTAACGGGGATAAGCTAGAAACCTTCCCAA 634012 i v i iv i vivi i v v i ii i i i vv L1M3_orf2#LIN 1902 GCCCACAGCTAACATCATACTCAATGGTGAAAAACTGAAAGCTTTTCCTC 1951 chr1ptel1M 634013 TAAGAT--GGAATGAAAG--AGGATGCCCATCATCATCAATATTATTCAA 634058 -- i- i -- iiv ii v vi L1M3_orf2#LIN 1952 TAAGATCAGGAAC-AAGGCAAGGATGCCCACTCTCGCCACTTCTATTCAA 2000 chr1ptel1M 634059 TGTTGCATTAGAAATGTTAGCAATTGCAATAAGAGAAGAATAAATAATCA 634108 ii v i i i i vi v vv v iv v iv v L1M3_orf2#LIN 2001 CATAGTACTGGAAGTCCTAGCCAGAGCAATTAGGCAAGAAAAAGAAATAA 2050 chr1ptel1M 634109 AAGGAATCAGAATGGGCAATGAGGTAATAAAACTCTTTCT-TTTGTAGAC 634157 v vi v v v i v i i v i - i i L1M3_orf2#LIN 2051 AAGGCATCCAAATCGGAAAGGAAGAAGTAAAATTATCTCTGTTTGCAGAT 2100 chr1ptel1M 634158 AAGATGATATTCT-TG-GGGAAATCTTAGAGATTCAACTAAAAATTTAGT 634205 i v v v - -i i i i i i v i vi - L1M3_orf2#LIN 2101 GACATGATCTTATATGTAGAAAACCCTAAAGACTCCACCAAAAAACT-GT 2149 chr1ptel1M 634206 TGAAAC-AATTAATGATTTTAGCAAAGTAGCAGGGTATAAGATAAATCCA 634254 ii - v i v i i v i i i v ivi L1M3_orf2#LIN 2150 TAGAACTAATAAACGAATTCAGTAAAGTTGCAGGATACAAAATCAACATA 2199 chr1ptel1M 634255 TATAAATCCTCAGCATTTCTATGTATCATCAACAAACCCCCATAAGAAGC 634304 i v vviv i ii ii v i ivi -ii i - L1M3_orf2#LIN 2200 CAAAAATCAGTTGCGTTTCTATACACTAACAACGAACTATC-CGAAAAG- 2247 chr1ptel1M 634305 GATAGTAAGAAA--TACCCCCTTTAAAATAACCATGGAAAAT-ATGAAAG 634351 v v --v i v v i- vi v- i v L1M3_orf2#LIN 2248 GAAATTAAGAAAACAATCCCATTTACAATAG-CATCAAAAAGAATAAAAT 2296 chr1ptel1M 634352 AC--------AAACCT-----AGGAACTATAAGA-----ACA-TG---AT 634379 -------- i ----- iv iv ----- - --- i L1M3_orf2#LIN 2297 ACTTAGGAATAAACTTAACCAAGGAGGTGAAAGACTTGTACACTGAAAAC 2346 chr1ptel1M 634380 TAGAAAACACTTTTTGAACAAA--TAAAGTCAGATTTAAATAACTGCAAA 634427 v - vv vi -- -v ivi v v L1M3_orf2#LIN 2347 TATAAAACA-TTGATGAAAGAAATTAAAG-AAGACACAAATAAATGGAAA 2394 chr1ptel1M 634428 ATTTTTAATTCTTCATTGGTGGAGAGAGCCAATATAATAAAAATG---AT 634474 iviv ivvv v v i v ii iii vi v --- L1M3_orf2#LIN 2395 GACATCCCGTGTTCATGGATTGGAAGAATTAATATTGTTAAAATGTCCAT 2444 chr1ptel1M 634475 TTTACCTAAACTAA--TATATTTTTAATGGAAATATCATTGAATATACAA 634522 vi i vii -- i vv i v vivii ii - - vv L1M3_orf2#LIN 2445 ACTACCCAAAGCGATCTACAGATTCAATGCAATCCCTATCAAA-AT-CCC 2492 chr1ptel1M 634523 AATAGT-TATTTTATTGAGCTAG-AAAAATAATAACAAAATTCATTTGGA 634570 i i- v iv iv - i vvi v L1M3_orf2#LIN 2493 AATGGCATTTTTTACAGAAATAGAAAAAACAATCCTAAAATTCATATGGA 2542 chr1ptel1M 634571 AGAACAAAAGGTGAAGAAT-GTCAAAAGAA--TTAATGAAAAAATGTAAA 634617 vv iivvv - i iv -- i - i vivv L1M3_orf2#LIN 2543 ACCACAAAAGACCCCGAATAGCCAAAGCAATCTTGA-GAAAGAAGAACAA 2591 chr1ptel1M 634618 AGAAGAAGGTCTTGCTATACTAGATCTTAAACCGCATCATTAGGCAGCAA 634667 vv i iv ii vv v iv i i viii i iv i vi i L1M3_orf2#LIN 2592 AGCTGGAGGCATCACACTTCCTGATTTCAAAATATATTACAAAGCTACAG 2641 chr1ptel1M 634668 TTATCAAAATTATCTTATACTAGC-TAACAAATAGAAAGGTGGATCAATG 634716 v ivi v vi i - - i v vi i i L1M3_orf2#LIN 2642 TAATCAAAACAGTATGGTACTGGCATAA-AAACAGACATATAGACCAATG 2690 chr1ptel1M 634717 TATCAAACTAGACACATAATACACAGCAATTAAT---TGC-TATA--ATA 634760 v v i v v ------i v v v i---i - --i v L1M3_orf2#LIN 2691 GAACAGAATAGAGA------GCCCAGAAATAAACCCACGCATATACGGTC 2734 chr1ptel1M 634761 ACTTTGTGTTTGACCAATGT-----AAATATTTAAGCTTGTGAGTTAAGA 634805 vi vi v i v iv -----i ivi ----- i vv i L1M3_orf2#LIN 2735 AACTGATCTTCGACAAGGGTGCCAAGAATACACAA-----TGGGGAAAGG 2779 chr1ptel1M 634806 ATTCACTATTTGGTAAAAAAAAATTGTTGGGAATATTAGAAAGCAATCT- 634854 -- v v i -- v v viv v i i v v v iv - L1M3_orf2#LIN 2780 AT--AGTCTCT--TCAACAAATGGTGTTGGGAAAACTGGATATCCACATG 2825 chr1ptel1M 634855 CATAGAAATTGGATATAGAGCATTATCTTATACTATTTACCAATATGAGA 634904 v ii vii - i v v i i vi v v v iv L1M3_orf2#LIN 2826 CAAAAGAATGAAAT-TGGACCCTTATCTTACACCATACACAAAAATCAAC 2874 chr1ptel1M 634905 TCAAAATGGATTCATGGCCTAGACATAA 634932 v v i i i i L1M3_orf2#LIN 2875 TCAAAATGGATTAAAGACTTAAACGTAA 2902 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 44.02 CpG sites = 202, Kimura (unadjusted) = 45.50 Transitions / transversions = 1.12 (202/180) Gap_init rate = 0.05 (53 / 1169), avg. gap size = 1.60 (85 / 53) 888 32.02 5.07 1.40 chr1ptel1M 633763 634728 (365272) L1MC_orf2#LINE/L1 1708 2708 (586) m_b18s551i1 638 chr1ptel1M 633763 ATGCAGGCATGGGTTAACATAAGGAAAACTACTAACATAATTGATTACAT 633812 i vv v i vv i v v i ii iv i L1MC_orf2#LIN 1708 ATGCAAGGCTGGTTCAACATTCGAAAATCAATTAATGTAATCCATCACAT 1757 chr1ptel1M 633813 CAATAACAAAAATAATAAAAATTGTATGATTATATCAATAAATAGAGAAA 633862 i ivvv v v iii i i iv L1MC_orf2#LIN 1758 CAACAGGCTAAAGAAGAAAAATCACATGATCATATCAATAGATGCAGAAA 1807 chr1ptel1M 633863 ATGGATTTGACAAAATACAGTATTCATTCATATTAAAAACACTTGAGAGC 633912 v v v ii ii iv v i--- L1MC_orf2#LIN 1808 AAGCATTTGACAAAATCCAACACCCATTCATGATAAAAACTCTC---AGC 1854 chr1ptel1M 633913 A---TAGATATAAATGAATTTTTCCTTAAAATGATAAAAAGCATCTACCT 633959 --- iv i v iivvi i vv i i vv L1MC_orf2#LIN 1855 AAACTAGGAATAGAGGGGAACTTCCTCAACTTGATAAAGAACATCTACAA 1904 chr1ptel1M 633960 AATACCAATAAATAACATTATTTGTAACGGGGATAAGCTAGAAACCTTCC 634009 v v i iv i viv i v v i ? i i L1MC_orf2#LIN 1905 AAAACCTACAGCTAACATCATACTTAATGGTGAGAAACTNGAAGCTTTCC 1954 chr1ptel1M 634010 CAATAAGAT--GGAATGAAAG--AGGATG-CCCATCATCATCAATATTAT 634054 iv -- i- i -- - v - i v vi v L1MC_orf2#LIN 1955 CGCTAAGATCAGGAAC-AAGGCAAGGATGTCCCCTC-TCACCACTCCTTT 2002 chr1ptel1M 634055 TCAATGTTGCATTAGAAATGTTAGCAATTGCAATAAGAGAAGAATAAATA 634104 ii i i i i i vi v v v v iiv L1MC_orf2#LIN 2003 TCAACATCGTACTGGAAGTCCTAGCTAATGCAATAAGACAAGAAAAGGAA 2052 chr1ptel1M 634105 ATCAAAGGAAT-CAGAATGGGCAATGAGGTAATAAAACTCTTTCT-TTTG 634152 v v - v - v i v v i i - i L1MC_orf2#LIN 2053 ATAAAAGGTATACAGATTGGG-AAGGAAGAAATAAAACTGTCTTTGTTCG 2101 chr1ptel1M 634153 TAGACAAGATGATATTCT-TG-GGGAAATCTTAGAGATTCAACTAAAAAT 634200 i ii v vv - -i i iv i v i v v L1MC_orf2#LIN 2102 CAGATGACATGATTGTCTATGTAGAAAATCCGAAAGAATCGACAAAAAAA 2151 chr1ptel1M 634201 TTAGTTGAAACAATTAATGATTTTAGCAAAGTAGCAGGGTATAAGATAAA 634250 i vv v vi v ii v i v i i i v L1MC_orf2#LIN 2152 CTCCTGGAACTAATAAGCGATTATAGCAAGGTTGCAGGATACAAGGTTAA 2201 chr1ptel1M 634251 TCCATATAAATCCTCAGCATTTCTATGTATCATCAACAAACCCCCATAAG 634300 vi i v i vviv v i i i v ii --- v ?vi L1MC_orf2#LIN 2202 TATACAAAAGTCAATCGCTTTCCTATATACCAGCAATGAA---CAANTGG 2248 chr1ptel1M 634301 AA-GCGATAGTAAGAAATAC---CCCCTTTAAAATAAC-CATGGAAAATA 634345 -vi v v - i ---v v v v i - vivv - L1MC_orf2#LIN 2249 AATTTGAAATTAA-AAACACAATACCATTTACATTAGCACCCCCAAAA-A 2296 chr1ptel1M 634346 TGAAAGAC--------AAACCTAGGAAC-----TATAAGA---ACATG-- 634377 v -------- i iv v----- i --- i -- L1MC_orf2#LIN 2297 TGAAATACTTAGGTATAAATCTAACAAAATATGTACAAGATCTATATGAG 2346 chr1ptel1M 634378 ----ATTAGAAAACACTTTTTGAACAAATAAAGTCAGATTTAAATAACTG 634423 ---- i v v vv vi v v ivv ?i v L1MC_orf2#LIN 2347 GAAAACTACAAAACTCTGATGAAAGAAATCAAAGAAGANCTAAATAAATG 2396 chr1ptel1M 634424 CA-AAATTTTTAATTCTTCATTGGTGGAGAGAGCCAATATAATAAAAATG 634472 v - i v iv - v v i i ii vi vi v i L1MC_orf2#LIN 2397 GAGAGATATTCCA-TGTTCATGGATAGGAAGACTCAATATTGTCAAGATG 2445 chr1ptel1M 634473 ---ATTTTACCTAAACTAA--TATATTTTTAATGGAAATATCATTGAATA 634517 ---i i v i vi i -- vv i - v vi v v v L1MC_orf2#LIN 2446 TCAGTTCTTCCCAACTTGATCTATAGATTCAAT-GCAATCCCAATCAAAA 2494 chr1ptel1M 634518 TACAAAATAGTTATTTTATTGAGCTAGA-AAAATAATAACAAAATTCATT 634566 v v ivv i v vv v - v i vvi i i v L1MC_orf2#LIN 2495 TCCCAGCAAGTTATTTTGTGGATATCGACAAACTGATTCTAAAGTTTATA 2544 chr1ptel1M 634567 TGGAAGAACAAAAGGTGAAGAAT-GTCAAAAGAATTAATGAA-AAAATGT 634614 iiii iivv - i v v - v -i i v v L1MC_orf2#LIN 2545 TGGAGAGGCAAAAGACCCAGAATAGCCAACACAA-TATTGAAGGAGAAGA 2593 chr1ptel1M 634615 A-AAAGAAGAAGGTCTTGCTATACTAGATCTTAAACCGCATCATTAGGCA 634663 - vv i v vi vv iv ii i iv vi ii v i v L1MC_orf2#LIN 2594 ACAAAGTCGGAGGACTGACACTACCCGACTTCAAGACTTACTATAAAGCT 2643 chr1ptel1M 634664 GCAATTATCAAAATTATCTTATACTAGCTAACAAATAGAAAGGTGGATCA 634713 i i v i ivi v vi i i v vi v ii i L1MC_orf2#LIN 2644 ACAGTAATCAAGACAGTGTGGTATTGGCGAAAGAATAGACAAATAGATCA 2693 chr1ptel1M 634714 ATGTATCAAACTAGA 634728 v v i v L1MC_orf2#LIN 2694 ATGGAACAGAATAGA 2708 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 41.45 CpG sites = 150, Kimura (unadjusted) = 42.53 Transitions / transversions = 0.97 (150/155) Gap_init rate = 0.04 (37 / 965), avg. gap size = 1.70 (63 / 37) 761 31.94 4.48 2.83 chr1ptel1M 635155 635779 (364221) L1ME4c_3end#LINE/L1 5 639 (191) m_b18s551i3 638 chr1ptel1M 635155 TATCTCAAGTAAATAGAAAACTTAGTCAAATTTATAAGAA---TATGAAT 635201 ?v ? v i i i i v v ---? v v L1ME4c_3end#L 5 TATCTNTANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAAG 54 chr1ptel1M 635202 ATTTCCCAAT-GATAAATAATCAAAAGATATAAACAGGCAGCGTTCAGAA 635250 i-- - iiv i i i i iiviv ? L1ME4c_3end#L 55 AC--CCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAA 102 chr1ptel1M 635251 AAAGAAATAAAAGTA-TATATGATCATAGGAAAAAATGTTCCAAATCATT 635299 i i v ? - v ii v i v i v vv ii L1ME4c_3end#L 103 GAGGAAATACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCT 152 chr1ptel1M 635300 CTTTATTAGACATATACAAATT-----------GAGATACCGTCTCATAC 635338 vv v i i v v i ----------- i i i ii L1ME4c_3end#L 153 AGTAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGC 202 chr1ptel1M 635339 TTTTAAGGTTGGCTAAAATGATGGAAGTGGGAAATGACAAATTACAAT-- 635386 i v v ii i v v- ii ----- v i vviv -- L1ME4c_3end#L 203 CTATTAAATTAGCAAAAATT-TAAAA-----AATTGATAATACCCAATGC 246 chr1ptel1M 635387 TAGAAAGGATATAGAAAACTTGAGACACTAATTGAGATACTATTGGGGGA 635436 i vi ? iii vi vi iv ? v ---- i i ii v v L1ME4c_3end#L 247 TGGCGAGGNTGCGGTGAAACTGGTACNCTCAT----ACATTGCTGGTGGC 292 chr1ptel1M 635437 ACTCTGAACTGACCCAGCTATTTTGGAGAGCAAACTGG-AATAAAGCTCA 635485 ? v i i iiv i iv i vi - vivv L1ME4c_3end#L 293 ANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCA 342 chr1ptel1M 635486 AAGAGTTTTGAGCA-GTCTGTACCCTTTGACCCAGTAATACCACTATTAG 635534 - iiv i iv - iii v vi i L1ME4c_3end#L 343 A-GAGCCATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGG 391 chr1ptel1M 635535 T--TCTACTTCCCAAGG---TGAT-CAAAGAAAAAGAGAACCCAAAAGTT 635578 v-- i -- i --- i - ii iii i v i v v iv L1ME4c_3end#L 392 GAATTTA--TCCTAAGGAAATAATTCAAAAGAAGGAAAAAGCTATATGCA 439 chr1ptel1M 635579 TTTAAATATTTATAGCAGCTCTCTTTGTAGTGGCAAAGAACTAGAGAATA 635628 ivv i i i v vi v i i i i i i i - i L1ME4c_3end#L 440 CGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGA-AACA 488 chr1ptel1M 635629 AG-GGGATGCCTATCAATCGGGGAATGGCTGAACAAATTATGGTACAT-G 635676 v-vii i i v v i i ii -? L1ME4c_3end#L 489 ACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCN 538 chr1ptel1M 635677 ATTGTGAGAGAATATTATTATGCTGTAAGAAATGATGAGCAGATTGATTT 635726 i -i vi vvv ii v i i vi vivv i v L1ME4c_3end#L 539 ACT-CGATGGAATATTATGCAGCCATTAAAAATGATAATTATGAAGACTA 587 chr1ptel1M 635727 TAGAAAAAGATGGAAAATTTTTCATGAAATAATGAAGAGTAAAATGAGCA 635776 iv iv v v - v vvi i vi L1ME4c_3end#L 588 TGTAGCAACATGGAAAATGTTT-ATGATATAATGTTAAGTGAAAAAAGCA 636 chr1ptel1M 635777 GAA 635779 L1ME4c_3end#L 637 GAA 639 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 41.53 CpG sites = 115, Kimura (unadjusted) = 44.03 Transitions / transversions = 1.46 (115/79) Gap_init rate = 0.05 (30 / 624), avg. gap size = 1.53 (46 / 30) 240 33.97 3.61 4.24 chr1ptel1M 636000 636165 (363835) L2#LINE/L2 1887 2051 (1031) m_b18s601i4 639 chr1ptel1M 636000 GAAAAGGATGTTCATGCTGACTCCCCTACAACATTTCTACCTCTCTCACT 636049 ii v ii i vi vi - v -- i - ii i i L2#LINE/L2 1887 GAAAGAGTTGTCTATACTCGCTGTC-TCCAA--TTCCT-CTCCTCCCATT 1932 chr1ptel1M 636050 GTCCTCTAAACTTTCTTCAATCTGACT--CCTAATCAC-ACTCAGCTGAA 636096 v iii i iiv i v i -- v vvi - vi i L2#LINE/L2 1933 CTCTCTTGAACCCACTCCAATCAGGCTTTCGTCCCCACCACTCCACCGAA 1982 chr1ptel1M 636097 ATTGCTCTCTCCAAAGTGAGCTTCAATCACTT--A-ATTGCTAGATCTAA 636143 i ivi i v ---i v i -- -i i i L2#LINE/L2 1983 ACTGCTCTTGTCAAGGTCA---CCAATGACCTCCACGTTGCTAAATCCAA 2029 chr1ptel1M 636144 TGGCCTTTTTTCCCTCCCAATC 636165 i vv i vv iv L2#LINE/L2 2030 TGGTCAATTCTCAGTCCTCATC 2051 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 44.13 CpG sites = 35, Kimura (unadjusted) = 47.85 Transitions / transversions = 1.84 (35/19) Gap_init rate = 0.07 (11 / 165), avg. gap size = 1.18 (13 / 11) 18 21.63 4.17 0.00 chr1ptel1M 638065 638112 (361888) (TA)n#Simple_repeat 1 50 (0) m_b18s252i4 640 chr1ptel1M 638065 TACATATA-ATGTTAATATATATA-ATGTTAATATATATGTTTATATATA 638112 i - i vv - i vv i v (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.04 (2 / 47), avg. gap size = 1.00 (2 / 2) 19 0.00 0.00 0.00 chr1ptel1M 638430 638450 (361550) (AC)n#Simple_repeat 1 21 (0) m_b18s252i5 641 chr1ptel1M 638430 ACACACACACACACACACACA 638450 (AC)n#Simple_ 1 ACACACACACACACACACACA 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 309 31.61 7.35 3.86 chr1ptel1M 638671 640072 (359928) L1M5_orf2#LINE/L1 84 1532 (1762) m_b18s551i4 642 chr1ptel1M 638671 AGACTGAATTAGAAATCATAATCCAATAGTATGTTGTTGACAAGAAACAT 638720 i v i v vi i ivi i iv i ii L1M5_orf2#LIN 84 AGACTGGATAAAAAAACAAGACCCAACTATATGCTGTCTACAAGAGACGC 133 chr1ptel1M 638721 ACTTGAAACAGAGAGACA--GAA---TTAAAAATACAGAGCTGGAATAGA 638765 v i v i -- ?--- i i v ii v v ii L1M5_orf2#LIN 134 ACTTTAAATATAAAGACACAGANAGGTTGAAAGTAAAAGGATGGAAAAAG 183 chr1ptel1M 638766 ATCTGTTTTACTGCAGCTAAAGTAAA-AAGGCAGTGAGAGCAATCATAAT 638814 v iiiv i vivvi ?vv - i v v?ivi v vv L1M5_orf2#LIN 184 ATATACCATGCAAACACTAANCAAAAGAAAGCTGGNGTGGCTATATTAAT 233 chr1ptel1M 638815 CTCAGACAAAGCA------AAAGCAAAAATAGATCTAATTAAAAGAGATA 638858 v i ------ i i --- --- vv L1M5_orf2#LIN 234 ATCAGACAAAGTAGACTTCAAGGCAAGAA---AT---ATTACCAGAGATA 277 chr1ptel1M 638859 AGCAAGGAAATTAAATCTTGGTAAAAGGCACCATAGATAATGAAGTCTTT 638908 iv i v vv vv i vv v vv v v v v v L1M5_orf2#LIN 278 AAGAGGGACATTTCATAATGATAAAAGGGTCAATTCATCAAGAAGACATA 327 chr1ptel1M 638909 TCAATACTAAACACATATGCACC-AATGGTATAGACTCCAAAATGT-TAA 638956 v v iiii - iii v - i ii- i L1M5_orf2#LIN 328 ACAATCCTAAATGTGTATGCACCTAATAACAGAG-CTTCAAAATACATGA 376 chr1ptel1M 638957 AGGAAAATTTAAATGAATTACAAGAGAAAATAGAGAG---TAAAATTGTA 639003 v vi i vv i v iii v i---i v --- L1M5_orf2#LIN 377 AGCAAAAACTGACAGAACTAAAAGGAGAAATAGACAAATCCACAATT--- 423 chr1ptel1M 639004 ATAATGGGGCCTCTCAATTTTCATCTCTCAGATCTAA---ATAAATTTAG 639050 i ? ivv i i ivi? v --- --- i viv L1M5_orf2#LIN 424 ATAGTNGGAGATTTTAACACNCCTCTCTCAG---TAATTGATAGAACAAG 470 chr1ptel1M 639051 TTATAAAATAAAT-AATAAAGATGTTAGGGAGAGT--AGGAATTTTAGAA 639097 - v v v - i i i --i i v -- iv ivi vv L1M5_orf2#LIN 471 T-AGACAAAAAATCAGTAAGGATAT--AGAAGATTTGAACAACACTATCA 517 chr1ptel1M 639098 A--AATTAGGTATAACAGATGTCTA-GGAAAAATTTAGTGGGAACAGAAA 639144 -- i v iiv iv ii i -i v v ?i viv-- - v? L1M5_orf2#LIN 518 ACCAACTTGACCTAATTGACATTTATAGAACACTNCACCC--AACA-ACN 564 chr1ptel1M 639145 GCA--ATATATCTTTTTCTCGACTATTTTTGGAACCTTTAAAAAAAATGA 639192 -- i iv i i i v iiviv v vv i vv L1M5_orf2#LIN 565 GCAGAATACACATTCTTTTCAAGTGCACATGGAACATTTACCAAGATAGA 614 chr1ptel1M 639193 CTCTGTATTAGAACATAAAAC----CCCATAAACAAATGCAGAAAAACAG 639238 iv i ?i i iv ---- i --- i vi?i ii iv L1M5_orf2#LIN 615 CCATATNCTGGGCCATAAAACAAGTCTCA---ATAAATTTNAAAGGATTG 661 chr1ptel1M 639239 AAATGTTA---AATATATTCTTTTCAGACCATAATTCAATAAAAATTACA 639285 vv --- i i i --- i vv v - v L1M5_orf2#LIN 662 AAATCATACAGAGTATGTTCTCT---GACCACAATGGAATTAAA-TTAGA 707 chr1ptel1M 639286 GTGAATAAAGGAATGAGGAGGCATAGATAAAATT------TAGTTAGAAA 639329 --- v v- ii ii ii ?vv v i------ v i L1M5_orf2#LIN 708 ---AATCAAT-AACAAAAAGATANCTAGAAAATCCCCAAATATTTGGAAA 753 chr1ptel1M 639330 CTAAATTATCTTATTCTAAAGAA----TAAGTCAAAAAACAAATCATAGA 639375 i iv ivivv v ---- ii i v i i? L1M5_orf2#LIN 754 TTAAACAACACACTTCTAAATAACCCATGGGTCAAAGAAGAAATCACAAN 803 chr1ptel1M 639376 TACAATCA-ATAATATC----ATTAAA--ACAATGAGA---CAACATACC 639415 viv i - v i---- i i -- ? i --- i L1M5_orf2#LIN 804 GGAAATTAGAAAATATTTTGAACTGAATGANAATGAAAATACAACATATC 853 chr1ptel1M 639416 AAAATTTGTGGAAAGTAGCCAAAACAGTATTTCAGAAAGAT-TTTATGTC 639464 i v i i i ii - ii v- iv L1M5_orf2#LIN 854 AAAATTTGTGGGATGCAGCTAAAGCAGTGCTT-AGAGGGAAATTTATAGC 902 chr1ptel1M 639465 TCTAAAAGTACATACATCAGTAAAAGAGACAAAGAAC--AGATGGATGAA 639512 ?i -- i ? i i - - v ivi-- i vi v L1M5_orf2#LIN 903 NTTAAA--TGCNTATATTAG-AAAAGA-AGAAAGGCTTAAAATCAATGAT 948 chr1ptel1M 639513 TTGAACATGCAACT-AAAAAACAATAAAAA--AGA-CAAATTTTAAATCC 639558 i i i v v v - i i v v -- - -- - L1M5_orf2#LIN 949 CTAAGCTTCCACCTTAAGAAGCTAGAAAAAGAAGAGCAAATT--AAA-CC 995 chr1ptel1M 639559 CCAATTAAGTATTAAAATGGAAATCTAAAAAATCAAAGAAGAAATAAAGT 639608 v v? vv ii v vvv i v i v v -- L1M5_orf2#LIN 996 CAAAGNAAGTAGAAGGAAGGAAATAATAAAGATAAGAGCAGAAATCAA-- 1043 chr1ptel1M 639609 TGAAAGTTTAAAAATGAAC---TAGTAAATAAAAGTA--GGACTTA---- 639649 -- vi ii ?---i i i v vi -- i vii ---- L1M5_orf2#LIN 1044 TGAAA--TAGAAAACAAANANACAATAGAGAAAATCAACGAAGCCAAAAG 1091 chr1ptel1M 639650 --GGTTTGTGGGAGAGA--AATAAAATAGATAAATCATGAGTTAGTCTGA 639695 -- iv v i i -- v i viv i? v L1M5_orf2#LIN 1092 CTGGTTCTTTGAAAAGATCAATAAAATTGATAAACCTCTAGCNAGACTGA 1141 chr1ptel1M 639696 TTTTTTTTTTAAAGAAGAAAATG----------AATTTACC-ATATCA-C 639733 i--------- i vi---------- v - -v L1M5_orf2#LIN 1142 TC---------AAGAAAAAAAGAGAGAAGACACAAATTACCAATATCAGG 1182 chr1ptel1M 639734 AATTAAAAGGGCAA-ATGCACTACAATGA----ATATGAAATTAAAGCAA 639778 v i vi - - -- ---- i - v ivi L1M5_orf2#LIN 1183 AATGAAAAAGGAGACAT-CACTACA--GATCCTACA-GACATTAAAAGGA 1228 chr1ptel1M 639779 TTGTTC---AGTATTACT--CAGTTATATACCATTAAAGCTAACAATCTA 639823 vi vv--- i iv-- ii v i v vi i ? ii L1M5_orf2#LIN 1229 TAATAAGAGAATATTATGAACAACTTTATGCCAATAAATTTGANAACTTA 1278 chr1ptel1M 639824 AATAAAATAGATGAATATTTTTAATAATAAAAATTTTCCAGATTAACAGA 639873 i i i ii vii v v i v ? vi v i i i ?v L1M5_orf2#LIN 1279 GATGAAATGGACAAATTCCTTGAAAAACACAANTTACCAAAACTGACNCA 1328 chr1ptel1M 639874 AGAGAAAATAGAATGCTTAAATAACCCTATCTTAGCAAAAGAAAGTGAAC 639923 ii viii i i v iviiv v i L1M5_orf2#LIN 1329 AGAAGAAATAGAAAATCTGAATAGCCCTATATCTATTAAAGAAATTGAAT 1378 chr1ptel1M 639924 AAGTCACAAATGAGCTCTCTG-AGAGAAATCCCCAGGACCGGATGGATTT 639972 vv v iv vi v ii ii- i v i v i v i L1M5_orf2#LIN 1379 TTGTAATTAAAAACCTTCCCACAAAGAAAACTCCAGGCCCAGATGGCTTC 1428 chr1ptel1M 639973 A-TGGTGAATTTTATCAAAAGTATACAAAACAATTACTCCCAATACTACA 640021 - i i vi v vii v v v v vi L1M5_orf2#LIN 1429 ACTGGTGAATTCTACCAAACATTTAAGGAAGAAATAATACCAATCTTACA 1478 chr1ptel1M 640022 TAAAGTATTTGAAAAAATGGCA----ATGAAACTCCTACCAAATTCCTTT 640067 i v v iv i i v ---- v i v i - v i v L1M5_orf2#LIN 1479 CAAACTCTTCCAGAAAATAGAAAAAGAGGGAACACTT-CCCAACTCATTT 1527 chr1ptel1M 640068 TATGA 640072 L1M5_orf2#LIN 1528 TATGA 1532 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 42.84 CpG sites = 234, Kimura (unadjusted) = 42.98 Transitions / transversions = 1.22 (234/192) Gap_init rate = 0.07 (97 / 1401), avg. gap size = 1.64 (159 / 97) 13 6.79 9.68 0.00 chr1ptel1M 640232 640262 (359738) (ATACAA)n#Simple_repeat 1 34 (0) m_b18s252i6 643 chr1ptel1M 640232 ATACATATAC-AAT-CACATA-AAATACAAATAC 640262 v - - v - (ATACAA)n#Sim 1 ATACAAATACAAATACAAATACAAATACAAATAC 34 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.10 (3 / 30), avg. gap size = 1.00 (3 / 3) 268 31.00 8.36 4.05 chr1ptel1M 640321 641934 (358066) L1M5_orf2#LINE/L1 1600 3280 (14) m_b18s551i5 642 chr1ptel1M 640321 TCTTTTATGAATATTGATGCAAAAATAATAATAAATAAAACACTGTCAAA 640370 ii i i v vv ? --- i i i iv L1M5_orf2#LIN 1600 TCCCTCATGAACATAGATGCAAAAATCCTNA---ACAAAATATTAGCAAA 1646 chr1ptel1M 640371 GAGATTGCAACAATATATCACTAAGATTCCATACTATTATCAGATGAGAT 640420 vv v v i v vv i vvi i ii v i ii i i L1M5_orf2#LIN 1647 TCGAATCCAGCAATATATAAAAAGGATAATACATCATGACCAAGTGGGGT 1696 chr1ptel1M 640421 TTATACCAGGAATTCAGGGCTGCTTCAATATTAGGACAATAATAAA---A 640467 v v i i v i i v i v vi v --- L1M5_orf2#LIN 1697 TTATCCCAGGAATGCAAGGTTGGTTTAACATTCGAAAATCAATCAATGTA 1746 chr1ptel1M 640468 ACACAAAATAATAACA--ACAAA----AAAAA----------ACCTCAA- 640500 iv vv v -- i ---- ---------- i - L1M5_orf2#LIN 1747 ATTCACCATATTAACAGAATAAAGGAGAAAAATCATATGATCATCTCAAT 1796 chr1ptel1M 640501 -AATGCAGAGAAAAGTTTTTGACAGAATGCAATATCCATTCCTATTAGAA 640549 -i - iv i v i i v iv i L1M5_orf2#LIN 1797 AGATGCAGA-AAAAGCATTTGACAAAATTCAACACCCATTCATGATAAAA 1845 chr1ptel1M 640550 A------GTA---TAG-AATAAATGAGGCCTTACATAAAATAATAAGTAG 640589 ------ i --- - i v i iv v vi vv i ivi L1M5_orf2#LIN 1846 ACTCTCAGCAAACTAGGAATAGAAGGGAACTTCCTCAACCTGATAAAGGG 1895 chr1ptel1M 640590 AATCT--------CCTATAATGGAAATAA-GCTAAA-----AAAAA---A 640622 v -------- i ii?i v v -i v ----- ? --- L1M5_orf2#LIN 1896 CATCTACGAAAAACCTACAGCNAACATCATACTTAATGGTGAAANACTGA 1945 chr1ptel1M 640623 AAACTTTCCAA-TAAAAGCAGCGTTAA-ATATGAATTCCCATTATCACCA 640670 ?i vv- i v i vivi - i v i vi ii ? L1M5_orf2#LIN 1946 ANGCTTTCCCCCTAAGATCGGGAACAAGACAAGGATGTCCGCTNTCACCA 1995 chr1ptel1M 640671 CCATTATCCCATAT---------AGTTATAGC------AATAAAACAGGA 640705 ivi i v i ---------i iv ------ ii i L1M5_orf2#LIN 1996 CTTCTATTCAACATTGTACTGGAGGTCCTAGCCAGTGCAATAAGGCAAGA 2045 chr1ptel1M 640706 AAAAGAAAGTGAAGGAATAAAAATAGGCTATGAGGAAATAAAATGCTCAC 640755 vvi v i v vv v i ivv ?i L1M5_orf2#LIN 2046 AAAAGAAATAAAAGGCATAAAGATTGGAAAGGAAGAAATAAAACTGTCNT 2095 chr1ptel1M 640756 ACTTTGCAAAT---ATCATAGTATAC-TAAAAAAAAAAAAAAAACTTTAA 640801 vv i i --- v v ? - i vvv? i - i v L1M5_orf2#LIN 2096 TATTCGCAGATGACATGATTGTNTACGTAGAAAATCCNAAAGAA-TCTAC 2144 chr1ptel1M 640802 GAACCAACTAC---AATTGA-AACTACAATTCTAGCAAAGTAATTTTATA 640847 i ?v --- i i - v i- - i vii?vv L1M5_orf2#LIN 2145 AAANAAACTACTAGAACTAATAAGTG-AATT-TAGCAAGGTCGCNGGATA 2192 chr1ptel1M 640848 TATAATACACCCACATAAATCATCAGCATTTCTATATATTACTAGCAAAA 640897 i vii vv ivi v viv i i vi i - L1M5_orf2#LIN 2193 CAAGGTCAATATACAAAAATCAATTGTATTTCTATATACTAGCAACAAA- 2241 chr1ptel1M 640898 TTCAACAGGAAAA--AAACAGAAAGAGAAATGCCACTTAAAATACTGGTA 640945 -- iv -- ivv? i iv i i v viivi L1M5_orf2#LIN 2242 --CAATTGGAAAATGAAATTTNAAAAACAATACCATTTACAATAGCATCA 2289 chr1ptel1M 640946 GA---CATAAAGTACCTATGAGTTTGTCTACCAAGACAAACCCAGGAACT 640992 i --- ? i i v i vvi v i ? viiv i v L1M5_orf2#LIN 2290 AAAAACATNAAATACTTAGGAATAAATCTAACAAAANATGTGCAAGACCT 2339 chr1ptel1M 640993 ATA---TGAACACAGTTACAAAATACTTTTTACACTAAAAATACATTTTA 641039 ? --- v --- i i ------i i i i- v vv L1M5_orf2#LIN 2340 NTACACTGAAAAC---TACAAAACATT------GCTGAGAG-AAATTAAA 2379 chr1ptel1M 641040 GAGAACCAAACAATTAGTGGAAAGATAGTTGTTGCTCATGGAT----AAA 641085 ii v -- v i i vvivv i ---- i L1M5_orf2#LIN 2380 GAAGACCTAA--ATAAATGGAGAGATATACCATGTTCATGGATTGGAAGA 2427 chr1ptel1M 641086 CTAAGCCAATATAACAAAAATGACAATTCCACCTAAGTAAATTTATTTAT 641135 ---- vii? i v iv i i vi i vv L1M5_orf2#LIN 2428 CT----CAATATTGTNAAGATGTCAATTCTCCCCAAATTGATCTATAGAT 2473 chr1ptel1M 641136 TCAGTG---------TCAAAACTACCAAAGAATTATTTTATAGAACTAGA 641176 i --------- - v iviii v i v v L1M5_orf2#LIN 2474 TCAATGCAATCCCAATCAAAA-TCCCAGCAGGTTTTTTTGTAGAAATTGA 2522 chr1ptel1M 641177 AAAGGCAATTTAAAAGTTCAAATGGGAGAACACAAAG--TCAAGAATA-T 641223 v vii iv i i v --i ii --i ? -i L1M5_orf2#LIN 2523 CAAGCTGATTCTAAAATTTATATGG--AAATGCAAAGGACCNAGAATAGC 2570 chr1ptel1M 641224 CAAGGGAATTAGTGGGAAAAAAAGTTGAAGGAAGGAGGCCTAGTAGTACC 641273 iiv i-- v i i vvv i vv v vii v L1M5_orf2#LIN 2571 CAAAACAATC--TTGAAAAAGAAGAACAAAGTTGGAGGACTTACACTACC 2618 chr1ptel1M 641274 A-CTCTCTA-ACTGTATTATAAAGGAGTAATTATCAAAACAACCAGATCG 641321 ?-v ? v - - vvii i v i iivv i vv L1M5_orf2#LIN 2619 NGATNTCAAGACT-TATTATAAAGCTACAGTAATCAAGACAGTGTGGTAT 2667 chr1ptel1M 641322 TGGCTACAAAAAAATTAG--AAGTAGATCAGTAGAATAGATTAG---GT- 641365 -ii ii --- -- i i i i v --- - L1M5_orf2#LIN 2668 TGGC-GTAAGGA---TAGACAAATAGATCAATGGAACAGAATAGAGAGTC 2713 chr1ptel1M 641366 -ATAAATACACGATAACTTATCCTAGTACTCTAGTGTTTGGTAAA---CC 641411 - v v vvvv v vivi?i ? - ii v ii ---v L1M5_orf2#LIN 2714 CAGAAATAGACCCACACATATATGGNCANT-TGATTTTTGACAAAGGTGC 2762 chr1ptel1M 641412 CAAAGACAAACATCA--GGGGCAAGAAC--TCCATTGAAGAAAAATGAGG 641457 ? - --v -- v i i-- iv v -- v iv L1M5_orf2#LIN 2763 CAANG-CAA--TTCAGTGGGGAAAGGATAGTCTTTTCA--ACAAATGGTG 2807 chr1ptel1M 641458 AGGGA--AGTTGAAAAACCATTTGGAAGAAACTAGGCATTGACCAGCACC 641505 vv -- i i v v v i v iii?v i vvi L1M5_orf2#LIN 2808 CTGGAACAATTGGATATCCATATGGAAAAAAATGAANCTCGACCCCTACC 2857 chr1ptel1M 641506 TCAAACTTCATACCAAAATAAGGTTTAAATGAATAAAGAATTTAGAATAA 641555 v ivi i v v iv i? i i v vii ii - iv L1M5_orf2#LIN 2858 TCACACCATACACAAAAATTAATTCNAGATGGATCATAGACCTA-AATGT 2906 chr1ptel1M 641556 AGAATGGTAGCATAAGAAAA---TTAGAGG--AACCT-GGAAATTTTTAT 641599 i - ? iv iv v ---i i -- v - i ---v L1M5_orf2#LIN 2907 AAAA-GNTAAAACTATAAAACTTCTAGAAGAAAACATAGGAGA---ATAT 2952 chr1ptel1M 641600 CTGTCACATCTATGGATTAGGGAAGAATTTATGACTAAAGAAGAGATAGA 641649 - iiiv iv i? v ii v --- v i v i i- L1M5_orf2#LIN 2953 CT-TCGTGACCTTGGGNTAGGCAAAGATTTCT---TAAACAGGACACAA- 2997 chr1ptel1M 641650 GTAAAGAAGAGAT----AAAGAAGTGAAATGGATAATTTTGATTACAG-G 641694 -- v v?i i---- --i v v v i ? v-i L1M5_orf2#LIN 2998 --AAAGCACNAACCATAAAAGAA--AAAATTGATAAATTGGACTNCATCA 3043 chr1ptel1M 641695 AAGTTAAAAAGATTTTGCACGAAAAAAAAATAAACCAATGT--AGCCAAA 641742 i -v i v ?vv i ------ vi -- -- L1M5_orf2#LIN 3044 AAATTAAAAA-CTTCTGCTCNTCAAAAGA------CACCGTTAAG--AAA 3084 chr1ptel1M 641743 ATTAGAAGGAAAGTAGGAAACTGGG-GAAAAT-TTTGTA--GCAAATTTC 641788 v i v iviv i ? - - i --i v v L1M5_orf2#LIN 3085 ATGAAAAGGCAAGCCACAGANTGGGAGAAAATATTTGCAANACATATATC 3134 chr1ptel1M 641789 TGATAAAAGCCACATTTCTCAAAAGTATGAGAAATGGAGCCAAACTTATA 641838 i i v v i v ivi vi i ii ivvvvv ?iiv L1M5_orf2#LIN 3135 TGACAAAGGACTCGTATCCAGAATATATAAAGAACTCCTACAANTCAATA 3184 chr1ptel1M 641839 AAATTAAGAGTCACTCTCCAATTGATAAATGGTC-AAAGACTATGAAGAG 641887 ? vv vvv vvi v? v v - - v L1M5_orf2#LIN 3185 ANAAAAAGACAAACAACCCAATANAAAAATGGGCAAAAGACT-TGAACAG 3233 chr1ptel1M 641888 GCAGTTTTCACAAGAAGA-ATTCAAAGCTAGCAAA-AGTCACATAAAAA 641934 i v iv v - ? -- i v - iv i L1M5_orf2#LIN 3234 ACACTTCACAAAAGAAGATATNCAAA--TGGCCAATAAGCACATGAAAA 3280 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 41.00 CpG sites = 252, Kimura (unadjusted) = 42.03 Transitions / transversions = 1.11 (252/228) Gap_init rate = 0.07 (118 / 1613), avg. gap size = 1.72 (203 / 118) 275 30.99 10.26 3.79 chr1ptel1M 640321 641363 (358637) L1M1_orf2#LINE/L1 1600 2707 (587) m_b18s551i6 642 chr1ptel1M 640321 TCTTTTATGAATATTGATGCAAAAATAATAATAAATAAAACACTGTCAAA 640370 i v vv v --- i i iv L1M1_orf2#LIN 1600 TCTCTGATGAATATTGATGCAAAAATCCTCA---ACAAAATACTAGCAAA 1646 chr1ptel1M 640371 GAGATTGCAACAATATATCACTAAGATTCCAT--ACTATTATCAGATGAG 640418 vv v v i i vv -- -- ii v i ii i L1M1_orf2#LIN 1647 CCGAATTCAACAATACATTAAAAAGAT--CATTCATCATGACCAAGTGGG 1694 chr1ptel1M 640419 ATTTATACCAGGAATTCAGGGCTGCTTCAATATTAGGACAATAATAAA-- 640466 v ? i v i v v i vv v v vi v -- L1M1_orf2#LIN 1695 ATTTATCCCNGGGATGCAAGGATGGTTCAACATACGCAAATCAATCAATG 1744 chr1ptel1M 640467 -AACACAAAATAATAACAACAAAA--------AAAAACC----------- 640496 -i i --- v v i -------- ----------- L1M1_orf2#LIN 1745 TGATACA---TCATATCAACAGAATGAAGGACAAAAACCATATGATCATT 1791 chr1ptel1M 640497 TCAA--AATGCAGAGAAAAGTTTTTGACAGAATGCAATATCCATTCCTAT 640544 --i v - iv i i v i v v iv L1M1_orf2#LIN 1792 TCAATTGATGCTGA-AAAAGCATTTGATAAAATTCAACATCCCTTCATGA 1840 chr1ptel1M 640545 TAGAAA---------------GTATAGAATAAATGAGGCCTTA-CATAA- 640577 i --------------- vi i- vi i - - L1M1_orf2#LIN 1841 TAAAAACCCTCAAAAAACTGGGTATAGAAGGAAC-ATACCTCAACATAAT 1889 chr1ptel1M 640578 AATA-----ATAAG-TAGA-----ATCTCCTATAATG-GAAATAAGCTAA 640615 v ----- v -i ----- v vv v i-vi ii vv L1M1_orf2#LIN 1890 AAAAGCCATATACGACAGACCCACAGCTAGTATCATACTGAATGGGGAAA 1939 chr1ptel1M 640616 AAAAAAAAAACTTTCCAATAAAAGCAGCGTTA-AATATGAATTCCCATTA 640664 vvi iv vv i v v vivi -i i v i v i v L1M1_orf2#LIN 1940 AACTGAAAGCCTTTCCTCTAAGATCTGGAACACGACAAGGATGCCCACTT 1989 chr1ptel1M 640665 TCACCACCATTATCCCATATAGT---------------TATAGCAATAAA 640699 ii i v i --------------- v v i L1M1_orf2#LIN 1990 TCACCACTGTTATTCAACATAGTACTGGAAGTCCTAGCTAGAGCAATCAG 2039 chr1ptel1M 640700 ACAGGAAAAAGAAAGTGAAGGA-ATAAAAATAGGCTATGAGGAAATAAAA 640748 i i - i i- vv v vv v i i v L1M1_orf2#LIN 2040 ACAAGAGAAAGAAA-TAAAGGGCATCCAAATTGGAAAGGAAGAAGTCAAA 2088 chr1ptel1M 640749 TGCTCACACTTTGCAAAT---ATCATAGTATACTAAAAAAAAAAAAAAAA 640795 vv vivv i --- v vv i vii vvv i L1M1_orf2#LIN 2089 TTATCCTTGTTTGCAGATGATATGATCTTATATTTGGAAAAACCTAAAGA 2138 chr1ptel1M 640796 CTTTAAGAACCAACTACAATTGAAACT-----ACAATTCTAGCAAAGTAA 640840 ii v? vv --- ii ----- v ii i vi L1M1_orf2#LIN 2139 CTCCACNAAAAAACTA---TTAGAACTGATAAACAAATTCAGTAAAGTTG 2185 chr1ptel1M 640841 TTTTATATATAATACACCCACATAAATCATCAGCATTTCTATATATTACT 640890 ivvv i v vv vi v vi iii vi L1M1_orf2#LIN 2186 CAGGATACAAAATCAACATACAAAAATCAGTAGCATTTCTATATGCCAAC 2235 chr1ptel1M 640891 AGCAAAATTCAACAGGAAAAAAACA--GAAAGAGAAATGCCACTTAAAAT 640938 ii --- ivv i v --i i v v i v L1M1_orf2#LIN 2236 AGTGAA---CAATCTGAAAAAGAAATCAAAAAAGTAATCCCATTTACAAT 2282 chr1ptel1M 640939 A----CTGGTAGACATAAAGTACCTATGAGTTTGTCTACCAAGACAAACC 640984 ---- vii i - v i v i viii v v i v iiv L1M1_orf2#LIN 2283 AGCCACAAATAAA-ATTAAATACCTAGGAATTAACTTAACCAAAGAAGTG 2331 chr1ptel1M 640985 CAGGAACTATA---TGAACACAGTTACAAAATACTTTTTACACTAAAAAT 641031 v i v v --- v --- i i ------iv i i- L1M1_orf2#LIN 2332 AAAGATCTCTACAATGAAAAC---TATAAAACACT------GATGAAAG- 2371 chr1ptel1M 641032 ACATTTTAGAGAAC--CAAACAATTAGTGGAAAGATAGTTGTTGCTCATG 641079 v vv i -- v ---- v ivv i L1M1_orf2#LIN 2372 AAATTGAAGAGGACACCAAAAAAT----GGAAAGATATTCCATGTTCATG 2417 chr1ptel1M 641080 GATAAACTAAGCCAATATAACAAAAATGACAATTCCACCTAAGTAAATTT 641129 viivvi ii viiv v v v i i ivv i L1M1_orf2#LIN 2418 GATTGGAAGAATCAATATTGTTAAAATGTCCATACTACCCAAAGCAATCT 2467 chr1ptel1M 641130 ATTTATTCAGTG---------TCAAAACTACCAAAGA-ATTATTTTATAG 641169 ivv i --------- - v - -i i i L1M1_orf2#LIN 2468 ACAGATTCAATGCAATCCCTATCAAAA-TACCAATGACATT-CTTCACAG 2515 chr1ptel1M 641170 AACTAGAAAAGGCAATTTAAAAGTTCAAATGGGAGAACACAAAGTCAAGA 641219 v ii iiv i i v i vv v iii v L1M1_orf2#LIN 2516 AAATAGAAAAAACAATCCTAAAATTTATATGGAACCACAAAAGACCCAGA 2565 chr1ptel1M 641220 ATA-TCAAGGGAATTAGTGGGAAAAAAAGTTGAAGGAA---GGAGGCCTA 641265 -i i vv i-v i v ---- vi --- vv v L1M1_orf2#LIN 2566 ATAGCCAAAGCTATC-CTGAGCAAAAA----GAACAAAACTGGAGGAATC 2610 chr1ptel1M 641266 GTAGTACC--ACTCTCTAACTGTATTATAAAGGAGTAATTATCAAAACAA 641313 ii v -- - v i i i i i vvi i v i i L1M1_orf2#LIN 2611 ACATTACCTGACT-TCAAATTATACTACAGAGCTATAGTAACCAAAACAG 2659 chr1ptel1M 641314 CCAGATCGTGGCTACAAAAAAATTAGAAGTAGATCAGTAGAATAGATTAG 641363 vv i vv - i v -v v vi i i i i v L1M1_orf2#LIN 2660 CATGGTACTGGC-ATAAAAACA-GACACATAGACCAATGGAACAGAATAG 2707 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 40.56 CpG sites = 153, Kimura (unadjusted) = 40.73 Transitions / transversions = 0.97 (153/158) Gap_init rate = 0.07 (68 / 1042), avg. gap size = 2.19 (149 / 68) 417 29.72 16.33 1.58 chr1ptel1M 641829 642269 (357731) L1ME4a_3end#LINE/L1 31 535 (336) m_b18s551i7 642 chr1ptel1M 641829 CAAACTTATAAAATTAAGAGTCACTCTCCAATTGATAAATGGTCAAAGAC 641878 iiv i vv vvv v i v v v iv L1ME4a_3end#L 31 CAAATCAATAAGAAAAAGACGAACACCCCAATAGAAAAATGGGCAAAGGA 80 chr1ptel1M 641879 TATGAAGAGGCAGTTTTCACAAGAAGAATT-CAAA--GCTAGCAAAAGTC 641925 i v i i iv v v - -- i ii --- L1ME4a_3end#L 81 CATGAACAGACAATTCACAAAAGAAGAAATACAAATGGCCAATAAA---C 127 chr1ptel1M 641926 ACATAAAAA------------------TGATTAGAGAAATGAAAAATTAA 641957 i i ------------------ i i i v - L1ME4a_3end#L 128 ATATGAAAANATGTTCAACCTCACTAGTAATCAAAGAAATGCAAA-TTAA 176 chr1ptel1M 641958 AACAACTCTGAGG--------------TATCAGATTGGCTAATAGGCAAA 641993 vv i-------------- i v v vvi L1ME4a_3end#L 177 AACAACAATGAGATACCATTTTTCACCTATCAAATTGGCAAAGATTTAAA 226 chr1ptel1M 641994 AAGAGGAAAATGACAAATGCTGCAGGAAATGTGGGAAACTAGGGACTGT- 642042 iivv v iv v i i vv iiii ?i vii v v - L1ME4a_3end#L 227 AGATTGATAATACCCAGTGTTGGCGAGGGTGTGGNGAAACGGGCACTCTC 276 chr1ptel1M 642043 -TGCATTGTTGGTGGAATTGTGAACTGGTCTAATCATGCTGGAGGACAAT 642091 - i i i i v i i vi i v v i L1ME4a_3end#L 277 ATACACTGCTGGTGGGAGTGTAAATTGGTACAACCTTTCTGGAGGGCAAT 326 chr1ptel1M 642092 TATGGTA-----------------TAAGACTGTGCATACCCTTTGATCTA 642124 - i ----------------- i v ? i i L1ME4a_3end#L 327 T-TGGCAATATGTATCAAAAGCCTTAAAAATGTNCATACCCTTTGACCCA 375 chr1ptel1M 642125 GGTCAATACCCC--ATAGAGAT-----CAAAGGAA------AAAGAAAAG 642161 --i v v --v ii ----- v ------ i viv L1ME4a_3end#L 376 G--TAATTCCACTTCTAGGAATTTATCCTAAGGAAATAATCAGAGATGTG 423 chr1ptel1M 642162 GACCGATATTAA--AAAAAGCAT-TTC-TCGCAGCTCTTTTTTGTGGTGG 642207 ? vi v v --v v v - - -v v i ii i L1ME4a_3end#L 424 NACAAAGATTTATGTACAAGGATGTTCATCGCAGC-ATTATTTATAATAG 472 chr1ptel1M 642208 CAAAGAATTGGAAGTGGAAAGGATGCCC-ATAATCTGGGAATCATTGAAC 642256 i i iiiivvvii i - i vv ? vi i i L1ME4a_3end#L 473 CGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGANTGGTTAAAT 522 chr1ptel1M 642257 AAGTTGTGATATA 642269 i i i i L1ME4a_3end#L 523 AAATTATGGTACA 535 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 38.50 CpG sites = 72, Kimura (unadjusted) = 39.33 Transitions / transversions = 1.26 (72/57) Gap_init rate = 0.05 (22 / 440), avg. gap size = 3.64 (80 / 22) 541 27.12 17.81 2.43 chr1ptel1M 641854 642246 (357754) L1ME5_3end#LINE/L1 56 507 (434) m_b18s551i8 642 chr1ptel1M 641854 CTCCAATTGATAAATGGTCAAAGACTATGAAGAGGCAGTTTTCACAAGAA 641903 i v v v iv v i v v i L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chr1ptel1M 641904 GAATTC---AAAGCTAGCAAAAGTCACATAAAAA---------------- 641934 vi --- i i i--- i i i ---------------- L1ME5_3end#LI 106 GAAACCCGAAAGGCTAACAAG---CATATGAAGAGATGCTCAAACTCATT 152 chr1ptel1M 641935 --TGATTAGAGAAATGAAAAATTAAAACAACTCTGAGGTATCAGATT--G 641980 -- i i v - vv i vv --i L1ME5_3end#LI 153 AGTAATCAGAGAAATGCAAA-TTAAAACAACAATGAGATATCACTTTACA 201 chr1ptel1M 641981 GCTAATA----GGCAAAA---AGA-----GGAAAATGACAAATGCTGCAG 642018 v v ---- --- ----- v v i i vv L1ME5_3end#LI 202 CCTATTAGACTGGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTGGCG 251 chr1ptel1M 642019 GAAATGTGGGAAACTAGGGACTGT--TGCATTGTTGGTGGAATTGTGAAC 642066 iii i ?v i iv -- i i i v ii L1ME5_3end#LI 252 AGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGAC 301 chr1ptel1M 642067 TGGTCTAATCATGCTGGAGGACAATTATGGTA--------------TAAG 642102 vi ii v ii i- i -------------- L1ME5_3end#LI 302 TGGTGCAGCCATTCTGGAGAGCAATC-TGGCAGTACTTAGTCAAATTAAG 350 chr1ptel1M 642103 ACTGTGCATACCCTTTGATCTAGGTCAATACC---CC-----ATAGAGAT 642144 vv ii v i i -- v --- ----- v vvi L1ME5_3end#LI 351 TATACGCATACCCTATGACCCAG--CAATTCCGCTCCTGGGTATATATCC 398 chr1ptel1M 642145 CAAAGGAA-------AAAG----AAAAGGACCGATATTAAAAAAAGCATT 642183 i ------- v ---- v i-- i vv vi iiiii L1ME5_3end#LI 399 CAAAGAAATTCTCACACAGGTCCATAAGGG--GACATGTACGAGGATGTT 446 chr1ptel1M 642184 TCTCGCAGCTCTTTTTTGTGGTGGCAAAGAATTGGAAGTGGAAAGGATGC 642233 iv i -v v iii i i iiivvv i i L1ME5_3end#LI 447 CATTGCAGC-GTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGGGTGT 495 chr1ptel1M 642234 CCATAATCTGGGA 642246 v - L1ME5_3end#LI 496 CCATCA-CTGGGA 507 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 33.54 CpG sites = 61, Kimura (unadjusted) = 34.77 Transitions / transversions = 1.42 (61/43) Gap_init rate = 0.06 (24 / 392), avg. gap size = 3.38 (81 / 24) 256 33.48 5.47 3.41 chr1ptel1M 642535 642735 (357265) L1ME3D_3end#LINE/L1 346 550 (439) m_b18s551i9 644 chr1ptel1M 642535 TGAATGTGCGCAGCCCTTGT---CCAGCCGCGCCGCCGCTTGGTCCGTAT 642581 ii vv i ii--- viiv i iv v vii i L1ME3D_3end#L 346 TGAACATGCGCATACCCTACGACCCAGCAATTCCACTCCTAGGTATATAC 395 chr1ptel1M 642582 CCCAGAGGGA----TGCAAAAGGG-GCCAGGAAAAACCTATTTAGGCAAA 642626 i ii ---- v v v -i i v v ------ i L1ME3D_3end#L 396 CCTAGAGAAACTCTTGCACATGTGCACCAGGAGACACGTA------CAAG 439 chr1ptel1M 642627 AATATTCATAGCAGGTTTGTCTG--GTGGCCAAGAAATAGAAACCGAGGG 642674 i vv ii --i i v i v i vivvvi L1ME3D_3end#L 440 AATGTTCATAGCAGCATTGTTCGTAATAGCAAAAAACTGGAAACAACCCA 489 chr1ptel1M 642675 AATGTCCAGCAATCAG-AGAACGGCTGAACCAGTTGTAGTCCGTGGCTGT 642723 v - - i v i iv i i vii vvv ii L1ME3D_3end#L 490 AATGTCCATCAA-CAGTAGAATGGATAAATAAATTGTGGTATATTCATAC 538 chr1ptel1M 642724 AATAAAATACTA 642735 ii L1ME3D_3end#L 539 AATGGAATACTA 550 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 44.07 CpG sites = 38, Kimura (unadjusted) = 46.01 Transitions / transversions = 1.41 (38/27) Gap_init rate = 0.06 (12 / 200), avg. gap size = 1.50 (18 / 12) 266 31.33 5.10 4.43 chr1ptel1M 642579 642735 (357265) L1ME2z_3end#LINE/L1 394 551 (640) m_b18s551i10 644 chr1ptel1M 642579 TATCCCAGAGGGATGCAAAA---GGGGCCAGGAAAAACCTATTTAGGCAA 642625 i v ii - ---iv v vi i--- i ivi L1ME2z_3end#L 394 TACCCAAGAGAAATG-AAAACATATGTCCACAAAAAG---ACTTGTACAA 439 chr1ptel1M 642626 AAATATTCATAGCAGGTTTGTC--TGGTGGCCAAGAAATAGAAACCG--- 642670 i i v i i-- ii i i v i v --- L1ME2z_3end#L 440 GAATGTTCATAGCAGCTTTATTCATAATAGCCAAAAACTGGAAACAGCCC 489 chr1ptel1M 642671 AGGGAATGTCCAGCAATCAGAGAACGGCTGAACCAGTTGTAGTCCGTGGC 642720 --- v ivi i v i v ii i vii vvv L1ME2z_3end#L 490 AGG---TGTCCATCAACAGGAGAATGGATAAACAAACTGTGGTATATTCA 536 chr1ptel1M 642721 TGTAATAAAATACTA 642735 ii ii L1ME2z_3end#L 537 TACAATGGAATACTA 551 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 42.70 CpG sites = 31, Kimura (unadjusted) = 42.70 Transitions / transversions = 1.94 (31/16) Gap_init rate = 0.06 (10 / 156), avg. gap size = 1.50 (15 / 10) 270 33.03 1.83 0.00 chr1ptel1M 642627 642735 (357265) L1ME1_3end#LINE/L1 441 551 (375) m_b18s551i11 644 chr1ptel1M 642627 AATATTCATAGCAGGTTTGTCTG--GTGGCCAAGAAATAGAAACCGAGGG 642674 i v i ii --i i i v i vivvvi L1ME1_3end#LI 441 AATGTTCATAGCAGCTTTATTCGTAATAGCCAAAAACTGGAAACAACCCA 490 chr1ptel1M 642675 AATGTCCAGCAATCAGAGAACGGCTGAACCAGTTGTAGTCCGTGGCTGTA 642724 v i?i v i v i v i i vii vvv ii L1ME1_3end#LI 491 AATGTCCATCAACNGGTGAATGGATAAACAAATTGTGGTATATCCATACA 540 chr1ptel1M 642725 ATAAAATACTA 642735 ii L1ME1_3end#LI 541 ATGGAATACTA 551 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 44.24 CpG sites = 22, Kimura (unadjusted) = 46.01 Transitions / transversions = 1.57 (22/14) Gap_init rate = 0.01 (1 / 108), avg. gap size = 2.00 (2 / 1) 227 18.01 0.00 2.00 chr1ptel1M 643117 643167 (356833) L1MC4a_3end#LINE/L1 479 528 (2101) m_b18s551i12 645 chr1ptel1M 643117 AAAAAATCATATATGCCCATCAACGGGAGAACGGTTGGGTAAACTGTGGT 643166 v i - v ?? ii ?i ii i L1MC4a_3end#L 479 AAACAACC-TAAATGCCCATNNATAGGAGANTGGTTGAATAAACTATGGT 527 chr1ptel1M 643167 A 643167 L1MC4a_3end#L 528 A 528 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 23.03 CpG sites = 7, Kimura (unadjusted) = 23.03 Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.02 (1 / 50), avg. gap size = 1.00 (1 / 1) 17 4.00 0.00 3.70 chr1ptel1M 643557 643584 (356416) (GGGA)n#Simple_repeat 1 27 (0) m_b18s252i7 646 chr1ptel1M 643557 GGGAGGGGGTGGAGGGAGGGAGGGAGGG 643584 i - (GGGA)n#Simpl 1 GGGAGGGAG-GGAGGGAGGGAGGGAGGG 27 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 268 19.61 19.57 5.77 chr1ptel1M 644806 644897 (355103) L2d2_3end#LINE/L2 444 547 (8) m_b18s601i5 647 chr1ptel1M 644806 AGTTCCTTAAGGGTAAGGACCAT------------TTTG------CCTCA 644837 i i i i ------------ ------ v L2d2_3end#LIN 444 AGCTCCTTGAGGGCAGGGACCATGTCTTATACTTCTTTGTATCCCCCACA 493 chr1ptel1M 644838 GCCCCGGGCACAGTGTCTGGCACACAGTAGGTCTTGGTTAGTGACTGATA 644887 v vi i v ---i v i i i --- L2d2_3end#LIN 494 GCGCCTAGCACAGTGCCTTGCACACAGTAGG---CGCTCAATAA---ATA 537 chr1ptel1M 644888 CTGGTTGATT 644897 i v L2d2_3end#LIN 538 TTTGTTGATT 547 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 21.92 CpG sites = 11, Kimura (unadjusted) = 23.45 Transitions / transversions = 1.83 (11/6) Gap_init rate = 0.09 (8 / 91), avg. gap size = 3.00 (24 / 8) 190 38.95 3.16 0.00 chr1ptel1M 645621 645715 (354285) L3#LINE/CR1 3720 3817 (282) m_b18s601i6 648 chr1ptel1M 645621 TGGAGACATCCAGGCTAGGAAGTGGAGGACTTGG-GGCCACCTACCAGCT 645669 i ii ii v i ii ivi i i - vv v ivi L3#LINE/CR1 3720 TGGGGATGTTTAGCCTGGAGAAGAGAAGACTTAGAGGAGACATGATAGCT 3769 chr1ptel1M 645670 GTCCTTGGATACCAAAAGACCT-TCCCATGGAAGAAAAATCAG-CTTA 645715 i iii iivi iv - vii iii i - L3#LINE/CR1 3770 GTCTTCAAATATTTGAAGGGCTGTCATGTGGAAGAGGGATTAGACTTA 3817 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 62.89 CpG sites = 28, Kimura (unadjusted) = 62.89 Transitions / transversions = 3.11 (28/9) Gap_init rate = 0.03 (3 / 94), avg. gap size = 1.00 (3 / 3) 13 23.72 2.50 0.00 chr1ptel1M 646534 646573 (353427) (AAGA)n#Simple_repeat 1 41 (0) m_b18s252i8 649 chr1ptel1M 646534 AAGAAAGAGAGAAAGTGAGATA-AAGGAGAACAAGAAAGAA 646573 i vi v - i i iv (AAGA)n#Simpl 1 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAA 41 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1) 121 1.73 9.14 0.00 chr1ptel1M 646574 646748 (353252) (AGAGAC)n#Simple_repeat 1 191 (0) c_b18s251i1 650 chr1ptel1M 646574 AGAGACAGAGACAGAGACAGAAACAGAGAGAGAGAGAGAGACAGAGACAG 646623 i v v (AGAGAC)n#Sim 1 AGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAG 50 chr1ptel1M 646624 AG--AGAGACAGAGACAGAG--AGAGACAGAGACAGAG--AGAGACAGAG 646667 -- -- -- (AGAGAC)n#Sim 51 AGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAG 100 chr1ptel1M 646668 ACAGAG--AGAGACAGAGACAGAG--AGAGACAGAGACAGAG--AGAGAC 646711 -- -- -- (AGAGAC)n#Sim 101 ACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGAC 150 chr1ptel1M 646712 AGAGACAGAG--AGAGACAGAGACAGAG--AGAGACAGAGA 646748 -- -- (AGAGAC)n#Sim 151 AGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGA 191 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.05 (8 / 174), avg. gap size = 2.00 (16 / 8) 489 33.87 4.35 3.12 chr1ptel1M 648330 648582 (351418) C L2b_3end#LINE/L2 (7) 459 204 m_b18s601i7 651 chr1ptel1M 648330 CAATCAATAAACATTAATTAAGCATCTAATATGTACCAGGCACTGTGCTC 648379 v i i v i i ii v i i ? v C L2b_3end#LINE 459 CATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTA 410 chr1ptel1M 648380 AGTGCT-GGGATATAACA--GACCACAAAAGACA--ATACTCATTCTCAA 648424 i i - i i i-- v vi v ?--i v iiiii v C L2b_3end#LINE 409 GGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCAC 360 chr1ptel1M 648425 AGAGTTTATGGCATAAT-CAGAAGACCCACAAGTAAACAGAT-ATAAACT 648472 i i i ii iv i -vi i vv v ? i- ? -- C L2b_3end#LINE 359 GGAGCTCACAGTCTAGTGGGGGAGACAGACATGTAANCAGACAATNA--T 312 chr1ptel1M 648473 AAGCAAGCGTTAGATAGGATCGG--TAGGAAATAATTAGCAGTAGGGAAA 648520 v v v -- ii i v -- i iii-ivii - v viv C L2b_3end#LINE 311 AACCCAGAGT--GGCAGGGTAGGACTGGGGGG-GCCCAG-AGGAGGGCGC 266 chr1ptel1M 648521 CT--CCAAAATTAAGAGGGATCGGGGAAGTTTTCCTGCAGAAGGTGGGAT 648568 -- viivi -- i i i i vi i v i iv C L2b_3end#LINE 265 CTGACCCGGCCT--GGGGGGTCAGGGAGGGCTTCCCGGAGGAGGTGACAT 218 chr1ptel1M 648569 TTTAGTTGAGGCTT 648582 v i i i C L2b_3end#LINE 217 TTGAGCTGAGACCT 204 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 43.34 CpG sites = 55, Kimura (unadjusted) = 49.11 Transitions / transversions = 1.96 (55/28) Gap_init rate = 0.06 (15 / 252), avg. gap size = 1.27 (19 / 15) 58 29.99 2.58 0.00 chr1ptel1M 648639 648688 (351312) (AGAT)n#Simple_repeat 1 50 (149) m_b18s252i9 652 chr1ptel1M 648639 AGATATATAGACAGACAGACAGATAGGTAAGTAGGTATATGAATAGACAG 648688 v i i i i ii i v ii i (AGAT)n#Simpl 1 AGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAG 50 Matrix = Unknown Transitions / transversions = 5.00 (10/2) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 31 5.82 9.72 0.00 chr1ptel1M 648689 648760 (351240) (AGATAGAC)n#Simple_repeat 1 79 (0) c_b18s251i2 653 chr1ptel1M 648689 AGATAGACAGATAGACAGACAGACAG--AGACATACAGACAGATAGA-AA 648735 i -- v i - i (AGATAGAC)n#S 1 AGATAGACAGATAGACAGATAGACAGATAGACAGATAGACAGATAGACAG 50 chr1ptel1M 648736 ATAGACAGAT-G---GATAGACAGATAGA 648760 - --- (AGATAGAC)n#S 51 ATAGACAGATAGACAGATAGACAGATAGA 79 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.06 (4 / 71), avg. gap size = 1.75 (7 / 4) 58 29.99 2.58 0.00 chr1ptel1M 648761 648903 (351097) (AGAT)n#Simple_repeat 51 198 (1) m_b18s252i9 654 chr1ptel1M 648761 TGGCTAAGTAGATAGGTAGACAGCCAGATAGACAAATA-A-AGATAGACA 648808 i v ii i i vi i i - - i (AGAT)n#Simpl 51 TAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATA 100 chr1ptel1M 648809 GACAAATAGAT-GAAAAATAGATAGA-AGATAGACAGACAGATAGGTAGG 648856 i i - v i - i i i i (AGAT)n#Simpl 101 GATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGA 150 chr1ptel1M 648857 TACGTAGGTGGGCAGACAGACAAACAGA-AGATATGCAGATAGACAGA 648903 vi i i ii i i i i - vii i (AGAT)n#Simpl 151 TAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGA 198 Matrix = Unknown Transitions / transversions = 5.60 (28/5) Gap_init rate = 0.04 (5 / 142), avg. gap size = 1.00 (5 / 5) 20 17.17 3.70 1.82 chr1ptel1M 650968 651021 (348979) (AGGGAA)n#Simple_repeat 1 55 (0) m_b18s252i10 655 chr1ptel1M 650968 AGGGAAATGG-GAGGGAAAGGGGAAAGAGAAAGGTAAAGACCAATGG-AA 651015 v -i - i v ivv v - (AGGGAA)n#Sim 1 AGGGAAAGGGAAAGGGAAA-GGGAAAGGGAAAGGGAAAGGGAAAGGGAAA 49 chr1ptel1M 651016 GGGAAA 651021 (AGGGAA)n#Sim 50 GGGAAA 55 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.06 (3 / 53), avg. gap size = 1.00 (3 / 3) 259 29.44 5.95 4.30 chr1ptel1M 651182 651433 (348567) L1P1_orf2#LINE/L1 28 283 (3011) m_b18s551i13 656 chr1ptel1M 651182 ATTTTAACTGTGAATGTGAATGGGATGAACTCCCCCATAAAACAGA-AGT 651230 v v i i iv i iv i v v - - vv L1P1_orf2#LIN 28 ATATTAACTTTAAATGTAAATGGACTAAATGCTCCAATTAAA-AGACACA 76 chr1ptel1M 651231 GAATCGCAGACTGGATTGAAAGCCAGAATCCTACAAAATGTTGTTTATAA 651280 v v i i vi i i ii i vv ivi i v vi i L1P1_orf2#LIN 77 GACTGGCAAATTGGATAAAGAGTCAAGACCCATCAGTGTGCTGTATTCAG 126 chr1ptel1M 651281 GTAACACATTTAAAG--CAGAGCGATACATA----CAGAGTGAAGAAGGC 651324 v v i v v -- vv i ---- i i i -- v L1P1_orf2#LIN 127 GAAACCCATCTCACGTGCAGAGACACACATAGGCTCAAAATAAAG--GGA 174 chr1ptel1M 651325 TGAAG-CAGA-CTATCATGCTTCGGGTGAAGTA-AAAAAAAAACAGGGGT 651371 i -v - i v ---iii i iv - ii L1P1_orf2#LIN 175 TGGAGGAAGATCTACCAAGC---AAATGGAAAACAAAAAAAGGCAGGGGT 221 chr1ptel1M 651372 AGAAACCCTAATCTCAGATCAAG-GGA----AAACAAAGATAGATCTAAT 651416 v v i i v v i-i ---- v v v ---- L1P1_orf2#LIN 222 TGCAATCCTAGTCTCTGATAAAACAGACTTTAAACCAACAAAGATC---- 267 chr1ptel1M 651417 TAAAAGAGATAAAGAAG 651433 - i L1P1_orf2#LIN 268 -AAAAGAGACAAAGAAG 283 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 38.10 CpG sites = 38, Kimura (unadjusted) = 38.10 Transitions / transversions = 1.15 (38/33) Gap_init rate = 0.08 (19 / 251), avg. gap size = 1.37 (26 / 19) 371 24.51 0.97 0.97 chr1ptel1M 651192 651294 (348706) L1M6_5end#LINE/L1 2403 2505 (10) m_b18s551i14 656 chr1ptel1M 651192 TGAATGTGAATGGGATGAACTCCCCCA-TAAAACAGAAGTGAATCGCAGA 651240 i i v i i - v v i- v v L1M6_5end#LIN 2403 TAAATGTAAATGGGTTAAACTCCCCTATTAAAAGACAAA-GACTCTCAGA 2451 chr1ptel1M 651241 CTGGATTGAAAGCCAGAATCCTACAAAATGTTGTTTATAAGTAACACATT 651290 i i i iv i v v v i i vi ii L1M6_5end#LIN 2452 TTGGGTTAAAAAACAAAATCCAACTATATGCTGTTTACAAGAGACACACC 2501 chr1ptel1M 651291 TAAA 651294 L1M6_5end#LIN 2502 TAAA 2505 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 30.35 CpG sites = 15, Kimura (unadjusted) = 30.35 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.02 (2 / 102), avg. gap size = 1.00 (2 / 2) 119 9.65 5.03 0.00 chr1ptel1M 652128 652326 (347674) (AG)n#Simple_repeat 1 209 (0) m_b18s252i11 657 chr1ptel1M 652128 AGAGACAAACAGAGACAGACAGACATTCAGAAACAGAGAGAGAGAGAGAG 652177 v i v v v v vvv i v (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr1ptel1M 652178 AGAGAGAGACAGACAGAGAGAGAGAGAGA-AGAGA-AGAGA-AGAGA-AG 652223 v v - - - - (AG)n#Simple_ 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 100 chr1ptel1M 652224 AGA-AGAGA-AGAGA-AGAGA-AGAGAGAGAGAGA-AGAGAG-GGGAGAG 652267 - - - - - - i (AG)n#Simple_ 101 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 150 chr1ptel1M 652268 AGAGAGAGAGAGAGAGAGAGAGAGAGACAGAGAGAGAGAGACAGAGAGAG 652317 v v (AG)n#Simple_ 151 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 200 chr1ptel1M 652318 AGAATGAGA 652326 iv (AG)n#Simple_ 201 AGAGAGAGA 209 Matrix = Unknown Transitions / transversions = 0.29 (4/14) Gap_init rate = 0.05 (10 / 198), avg. gap size = 1.00 (10 / 10) 44 0.00 0.00 0.00 chr1ptel1M 652893 652930 (347070) (AT)n#Simple_repeat 1 38 (0) c_b18s251i3 658 chr1ptel1M 652893 ATATATATATATATATATATATATATATATATATATAT 652930 (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATAT 38 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 310 31.82 11.68 0.62 chr1ptel1M 653903 654193 (345807) C L1ME4c_3end#LINE/L1 (452) 378 56 m_b18s551i15 659 chr1ptel1M 653903 TGCTGGGC--AAGGGGAAGAACAGTTTGACAGCCTTTGG-GTGTGGTTCC 653949 i i-- v v v v ii ii i-ii iv v C L1ME4c_3end#L 378 TACTGGGTCAAAGGGTATGAACATTTTTATGGCTCTTGATACGTATTGCC 329 chr1ptel1M 653950 AG-TTCCTTTCCAGAATGAGAAT-CCAGACCATGGCTCTATCAAGAGCAC 653997 i- v i v ivvi - ivii ii?iv i i iv iiii C L1ME4c_3end#L 328 AAATTGCTTTCCAAAAGGGTTGTACCAATTTACANTGCCACCAGCAATGT 279 chr1ptel1M 653998 ATG-GGGCGCCTGCTTTCCCACAACC-CTCCAGCATCTGTCATCATC--C 654043 - ? ii v i iv i ? - v iv vi i --i C L1ME4c_3end#L 278 ATGAGNGTACCAGTTTCACCGCANCCTCGCCAGCATTGGGTATTATCAAT 229 chr1ptel1M 654044 TTTTTGGTCAGTTCTGCTCATCTTATGGGCATGAGAGAGAACCTC----- 654088 ii-- v i v i v i i i i vi v i ----- C L1ME4c_3end#L 228 TTTTTAA--ATTTTTGCTAATTTAATAGGCGTAAAATGGTATCTCATTGT 181 chr1ptel1M 654089 --CCTTA-TTTGCATTTCTTTAATTACCAGGGATATAG---------CTA 654126 -- i - i i v vi v --------- i C L1ME4c_3end#L 180 TGCTTTAATTTGCATTTCTTTGATTACTAGCGAGGTTGAACATTTTTCCA 131 chr1ptel1M 654127 T-TGGTAG-------CTTGGATTTCCTATTTAGGAAAATGTGGGTTCATG 654168 - v v -------? v v ?v vi v vv C L1ME4c_3end#L 130 TGTGTTTGTTTACTANTTGTATTTCCTCTTNTGTGAATTGTCTGTTCATG 81 chr1ptel1M 654169 TCCTTTTACCATTTCTCAATTAGGG 654193 vv v v i C L1ME4c_3end#L 80 TCCTTTGCCCATTTATCTATTGGGG 56 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 41.85 CpG sites = 53, Kimura (unadjusted) = 43.75 Transitions / transversions = 1.36 (53/39) Gap_init rate = 0.05 (15 / 290), avg. gap size = 2.40 (36 / 15) 340 29.89 12.60 0.73 chr1ptel1M 653948 654193 (345807) C L1ME5_3end#LINE/L1 (611) 330 56 m_b18s551i16 659 chr1ptel1M 653948 CCAG-TTCCTTTCCAGAATGA--GAATCCAGACCATGGCTCTATCAAGAG 653994 - v i i-- v - v i iivii i i iv C L1ME5_3end#LI 330 CCAGATTGCTCTCCAGAATGGCTGCA-CCAGTCTACACTCCCACCAGCAG 282 chr1ptel1M 653995 CACATG-GGGCGCCTGCTTTCCCACAACC-CTCCAGCATCTGTCATCATC 654042 ii - iv ii? i v - v i ii v i C L1ME5_3end#LI 281 TGCATGAGGGTTCCTATNTCCCCACATCCTCGCCAACACTTGGCATTATC 232 chr1ptel1M 654043 CTTTTTGGTCAGTTCTGCTCATCTTATGGGCATGAGAGAGA-ACCTC--- 654088 vvi vv v v i ivi v i ii i - v - i --- C L1ME5_3end#LI 231 CAGCTTTCTAATTTTTGCCAGTCTAATAGGTGTAA-AGTGATATCTCATT 183 chr1ptel1M 654089 ----CCTTA-TTTGCATTTCTTTAATTACCAGGGA--TATAGC------- 654124 ----ii - i i i iv -- vv ------- C L1ME5_3end#LI 182 GTTGTTTTAATTTGCATTTCTCTGATTACTAATGAGTTTGAGCATCTCTT 133 chr1ptel1M 654125 --TA---TTGGTAGC---TTGGATTTCCTATTTAGGAAAATGTGGGTTCA 654166 -- --- v --- i i v iv v v ivv C L1ME5_3end#LI 132 CATATGCTTGTTAGCCTTTCGGGTTTCCTCTTCTGTAAATTGCCTGTTCA 83 chr1ptel1M 654167 TGTCCTTTTACCATTTCTCAATTAGGG 654193 i vv i v i C L1ME5_3end#LI 82 TATCCTTTGCCCATTTTTCTATTGGGG 56 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 38.72 CpG sites = 42, Kimura (unadjusted) = 39.42 Transitions / transversions = 1.35 (42/31) Gap_init rate = 0.06 (14 / 245), avg. gap size = 2.36 (33 / 14) 19 16.94 0.00 0.00 chr1ptel1M 654492 654524 (345476) (C)n#Simple_repeat 1 33 (0) m_b18s252i12 660 chr1ptel1M 654492 CCCTCTCCCCCCCCCCCACCACCCCCCACCCCC 654524 i i v v v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 33 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 59 12.54 0.00 0.00 chr1ptel1M 654666 654769 (345231) (AC)n#Simple_repeat 1 104 (0) c_b18s251i4 661 chr1ptel1M 654666 ACACACACTCACACAGACACACACACACACTCACACACACACTCATGCAC 654715 v v v v ii (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50 chr1ptel1M 654716 TTACACACACAGACACACACACACACTCACACTCACAGACACACACACAC 654765 vi v v v v (AC)n#Simple_ 51 ACACACACACACACACACACACACACACACACACACACACACACACACAC 100 chr1ptel1M 654766 ACAC 654769 (AC)n#Simple_ 101 ACAC 104 Matrix = Unknown Transitions / transversions = 0.33 (3/9) Gap_init rate = 0.00 (0 / 103), avg. gap size = 0.0 (0 / 0) 269 28.25 14.59 2.42 chr1ptel1M 654884 655068 (344932) L2#LINE/L2 2188 2394 (688) m_b18s601i8 662 chr1ptel1M 654884 TTGTTTGCTCCTCCTCCAGATCACGCCTCCCAAACACTGATGTCCCTCAG 654933 i v i vvvvi v v ii i? ii iv v i L2#LINE/L2 2188 TTGCTGGTTCCTCCTCATCTCCCCGACCTCTNAACGTTGGAGTGCCCCAG 2237 chr1ptel1M 654934 AGCTCGGTCCCGGGCCTGCTTCTCTTCTCCCTCTGTCCTTCACT-----G 654978 i i iv v iv iv iiv - ----- L2#LINE/L2 2238 GGCTCAGTCCTTGGACCTCTTCTCTTCTCTATCTACACT-CACTCCCTNG 2286 chr1ptel1M 654979 GTGATCTCAT---------TGACT------ACCATCTCTAGGCTGACGAT 655013 --------- i ------ v v i i L2#LINE/L2 2287 GTGATCTCATCCAGTCTCATGGCTTTAAATACCATCTATATGCTGATGAC 2336 chr1ptel1M 655014 TCTCTCCAGTCTCATTTCTTTAACT---GCCTTTCA---GACCTCTCAGA 655057 --- ivi i v ii i i---i i v--- v - L2#LINE/L2 2337 TC---CCAAATTTATATCTCCAGCCCGGACCTCTCCCCTGAACTC-CAGA 2382 chr1ptel1M 655058 C-CGGATGTCCA 655068 - v i L2#LINE/L2 2383 CTCGTATATCCA 2394 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 35.90 CpG sites = 30, Kimura (unadjusted) = 36.81 Transitions / transversions = 1.43 (30/21) Gap_init rate = 0.06 (11 / 184), avg. gap size = 2.91 (32 / 11) 205 33.82 0.00 0.00 chr1ptel1M 655017 655084 (344916) L2#LINE/L2 2376 2443 (639) m_b18s601i9 662 chr1ptel1M 655017 CTCCAGTCTCATTTCTTTAACTGCCTTTCAGACCTCTCAGACCGGATGTC 655066 v i v v ii viiv v vivii L2#LINE/L2 2376 CTCCAGACTCGTATATCCAACTGCCTACTCGACATCTCCACTTGGATGTC 2425 chr1ptel1M 655067 CAGGAGACGGCTTAAACT 655084 i iv i iv i L2#LINE/L2 2426 TAATAGGCATCTCAAACT 2443 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 43.66 CpG sites = 13, Kimura (unadjusted) = 46.40 Transitions / transversions = 1.30 (13/10) Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0) 228 22.77 10.34 1.59 chr1ptel1M 655726 655783 (344217) L2d_3end#LINE/L2 452 514 (2) m_b18s601i10 663 chr1ptel1M 655726 AGCCTCTGAGCACACCACCTAGCACACAGTAGGTGTGC------TACTTA 655769 vi - vii iv i i iv ------ i L2d_3end#LINE 452 AGCGCCT-AGCACAGTGCTGAGCACATAGTAGGCGCTCAATAAATACTTG 500 chr1ptel1M 655770 TTGATTGATTAATT 655783 i L2d_3end#LINE 501 TTGATTGATTGATT 514 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 25.66 CpG sites = 9, Kimura (unadjusted) = 28.17 Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.04 (2 / 57), avg. gap size = 3.50 (7 / 2) 35 31.82 1.95 1.29 chr1ptel1M 656766 656919 (343081) (GAGA)n#Simple_repeat 1 155 (0) m_b18s252i13 664 chr1ptel1M 656766 GAGACAGACAGACAGACAGAGACAGAGAGACAGAGAGAAGGTTAGGGGTA 656815 v v v v v v ii vv i iv (GAGA)n#Simpl 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr1ptel1M 656816 G-GAGAGACAGACAGACAGACGGGATAGGGGTAG-GGGAGACAAAGACAG 656863 - v v v - i v i iv - i v i v (GAGA)n#Simpl 51 GAGAGAGAGAGAGAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAG 99 chr1ptel1M 656864 AGAGAGGGTTAGGGGTAG-GGGAGGCAGACAGACAGACAGACAGAGACCA 656912 i vv i iv - i iv v v v v -v (GAGA)n#Simpl 100 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA-GA 148 chr1ptel1M 656913 GAGAGAG 656919 (GAGA)n#Simpl 149 GAGAGAG 155 Matrix = Unknown Transitions / transversions = 0.56 (14/25) Gap_init rate = 0.03 (5 / 153), avg. gap size = 1.00 (5 / 5) 13 34.53 3.23 2.13 chr1ptel1M 656791 656883 (343117) (AGGGAT)n#Simple_repeat 1 94 (0) m_b18s252i14 665 chr1ptel1M 656791 AGAGACAGAGAGAAGGTTAGGGGTAGGAGAGACAGACAGACAGACGGGAT 656840 i i i v i v i - v vi i iv v - (AGGGAT)n#Sim 1 AGGGATAGGGATAGGGATAGGGATAGG-GATAGGGATAGGGATA-GGGAT 48 chr1ptel1M 656841 AGGGGTAGGG---GAGACAAAGACAGAGAGAGGGTTAGGGGTAGGG 656883 i --- i i ii i i v v i (AGGGAT)n#Sim 49 AGGGATAGGGATAGGGATAGGGATAGGGATAGGGATAGGGATAGGG 94 Matrix = Unknown Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.03 (3 / 92), avg. gap size = 1.67 (5 / 3) 35 31.82 1.95 1.29 chr1ptel1M 656766 656919 (343081) (GAGA)n#Simple_repeat 1 155 (0) m_b18s252i13 664 chr1ptel1M 656766 GAGACAGACAGACAGACAGAGACAGAGAGACAGAGAGAAGGTTAGGGGTA 656815 v v v v v v ii vv i iv (GAGA)n#Simpl 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr1ptel1M 656816 G-GAGAGACAGACAGACAGACGGGATAGGGGTAG-GGGAGACAAAGACAG 656863 - v v v - i v i iv - i v i v (GAGA)n#Simpl 51 GAGAGAGAGAGAGAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAG 99 chr1ptel1M 656864 AGAGAGGGTTAGGGGTAG-GGGAGGCAGACAGACAGACAGACAGAGACCA 656912 i vv i iv - i iv v v v v -v (GAGA)n#Simpl 100 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA-GA 148 chr1ptel1M 656913 GAGAGAG 656919 (GAGA)n#Simpl 149 GAGAGAG 155 Matrix = Unknown Transitions / transversions = 0.56 (14/25) Gap_init rate = 0.03 (5 / 153), avg. gap size = 1.00 (5 / 5) 381 31.49 2.72 1.61 chr1ptel1M 657879 658062 (341938) L1MD1_3end#LINE/L1 448 633 (356) m_b18s551i18 666 chr1ptel1M 657879 ATGGCTACTTT--TTGTAGTGGCTAAAAACTGGAAACTGAA--TGGATGT 657924 i vi -- i i i i -- --ii L1MD1_3end#LI 448 ATAGCAGCTTTATTCGTAATAGCCAAAAACTGGAAAC--AACCCAGATGT 495 chr1ptel1M 657925 CCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATATGAATATTATGGA 657974 v iiv v i i i i i vv ii L1MD1_3end#LI 496 CCTTCAACGGGTGAATGGTTAAACAAACTGTGGTACATCCATACCATGGA 545 chr1ptel1M 657975 ATATTACTGTTCTGTAAGAAATGACCAACAGGATGAT-TTCAGAAAGGCC 658023 i vvv vi i ivi v -viv -iv iv vii L1MD1_3end#LI 546 ATACTACTCAGCAATAAAAAGGAACGAAC-TATTGATACACGCAACAACC 594 chr1ptel1M 658024 TGGAGAGACTTACACGAACTGATGCTGAGTGAAATGAGC 658062 vii ii v vii v v vi L1MD1_3end#LI 595 TGGATGAATCTCCAGAGAATTATGCTGAGTGAAAAAAGC 633 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.35 CpG sites = 34, Kimura (unadjusted) = 42.26 Transitions / transversions = 1.48 (34/23) Gap_init rate = 0.03 (6 / 183), avg. gap size = 1.33 (8 / 6) 406 20.58 3.85 1.89 chr1ptel1M 657879 657982 (342018) L1ME1_3end#LINE/L1 448 553 (373) m_b18s551i17 666 chr1ptel1M 657879 ATGGCTACTTT--TTGTAGTGGCTAAAAACTGGAAACTGAA--TGGATGT 657924 i vi -- i i i i -- --iii L1ME1_3end#LI 448 ATAGCAGCTTTATTCGTAATAGCCAAAAACTGGAAAC--AACCCAAATGT 495 chr1ptel1M 657925 CCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATATGAATATTATGGA 657974 ii? v v i i vv iv L1ME1_3end#LI 496 CCATCAACNGGTGAATGGATAAACAAATTGTGGTATATCCATACAATGGA 545 chr1ptel1M 657975 ATATTACT 657982 i L1ME1_3end#LI 546 ATACTACT 553 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 23.83 CpG sites = 15, Kimura (unadjusted) = 25.20 Transitions / transversions = 2.50 (15/6) Gap_init rate = 0.04 (4 / 103), avg. gap size = 1.50 (6 / 4) 409 17.78 2.17 2.17 chr1ptel1M 657889 657980 (342020) L1ME3G_3end#LINE/L1 456 547 (377) m_b18s551i19 666 chr1ptel1M 657889 TTTGTAGTGGCTAAAAACTGGAAACTGAA--TGGATGTCCATCAGTTGGA 657936 i i v i -- -- ii i v i L1ME3G_3end#L 456 TTTGTAATAGCGAAAAATTGGAAAC--AACCTAAATGTCCATCAATAGGG 503 chr1ptel1M 657937 GAATGGCTGAATAAATTGTGGTATATGAATATTATGGAATATTA 657980 i i i vv i i L1ME3G_3end#L 504 GAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACTA 547 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 20.96 CpG sites = 12, Kimura (unadjusted) = 20.96 Transitions / transversions = 3.00 (12/4) Gap_init rate = 0.03 (3 / 91), avg. gap size = 1.33 (4 / 3) 18 3.96 0.00 0.00 chr1ptel1M 658525 658550 (341450) (AAAC)n#Simple_repeat 1 26 (0) m_b18s252i15 667 chr1ptel1M 658525 AAACAAACAAACAAACAAACAAAGAA 658550 v (AAAC)n#Simpl 1 AAACAAACAAACAAACAAACAAACAA 26 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 211 19.60 3.85 1.89 chr1ptel1M 658687 658738 (341262) C MIRc#SINE/MIR (141) 127 75 m_b18s601i11 668 chr1ptel1M 658687 CTGAGGC--AGTTGAGGCTGAGTGACTTACCCAGGGCCACATGGCTAGGA 658734 -- v- i i i i i ii v C MIRc#SINE/MIR 127 CTGAGGCTCAGA-GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTA 79 chr1ptel1M 658735 AGCG 658738 i C MIRc#SINE/MIR 78 AGTG 75 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 23.81 CpG sites = 8, Kimura (unadjusted) = 23.81 Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.50 (3 / 2) 175 19.23 1.39 0.28 chr1ptel1M 659721 660079 (339921) (TCTC)n#Simple_repeat 1 363 (0) m_b18s252i17 669 chr1ptel1M 659721 TCTCTCCCTCTATCTC-CTACT-TCCCTGGC-CTCCTTCTCTCTCTCTCT 659767 i v - - - i vv - ii (TCTC)n#Simpl 1 TCTCTCTCTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 49 chr1ptel1M 659768 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCCTCCCTCTCTTTTTCT 659817 i i i i (TCTC)n#Simpl 50 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 99 chr1ptel1M 659818 TTTTCTTTGTTTCTGTCTTTCTATCTCTGTCTCTGTCTCTGTCTCTCTCT 659867 i i i v i v i v v v v (TCTC)n#Simpl 100 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 149 chr1ptel1M 659868 CCCCCTCCCTCCCTCTCTTTTTCTTTGTTTCTCTCTGTCTTTCTATCTCT 659917 i i i i i i i v i v i v (TCTC)n#Simpl 150 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 199 chr1ptel1M 659918 GTCTCTTTCTTACTCTCTGTCTCTGTCTCTGTCTCCCTCTCTCCTTCTCT 659967 v i iv v v v i ii (TCTC)n#Simpl 200 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 249 chr1ptel1M 659968 CTCTCTCTCTTTTTCTGTCTTTGTCTCTGTCTCT-TTTCTCTCT-TCTCT 660015 i i v i v v - i - (TCTC)n#Simpl 250 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 299 chr1ptel1M 660016 CTCTCTGTCTCTTTGTCTCTCTCCCTCTTTGTCTCTCTTTCTCTGTCTCT 660065 v i v i i v i v (TCTC)n#Simpl 300 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 349 chr1ptel1M 660066 CTCTGTCTCTCTCT 660079 v (TCTC)n#Simpl 350 CTCTCTCTCTCTCT 363 Matrix = Unknown Transitions / transversions = 1.40 (35/25) Gap_init rate = 0.02 (6 / 358), avg. gap size = 1.00 (6 / 6) 374 33.50 8.09 1.63 chr1ptel1M 660224 660396 (339604) C MIR3#SINE/MIR (24) 184 1 m_b18s601i12 670 chr1ptel1M 660224 GAGCTGGATG----TTTAGACATAATCTCATCCAACCCCTATCATTTTAC 660269 v ----i v v vi i- C MIR3#SINE/MIR 184 GAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCC-TCATTTTAC 136 chr1ptel1M 660270 TGATGTGGAAACTAATACTCAG-GAATCTAAGTAGCTTATCCAAAAGTA- 660317 v v i vi i - iviv ii ii iivi - C MIR3#SINE/MIR 135 AGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCAC 86 chr1ptel1M 660318 --AG-TAGGGAATATCAAAGTGGAGATTTGAACTTGGATCCTTCCCCTCT 660364 -- -? vv i iv i iv i i v iii i iiiivv i C MIR3#SINE/MIR 85 ACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGTCTCCTGACTCC 36 chr1ptel1M 660365 TAAC-----TTCTCTCATATCAAGCCAGCTCCACCAG 660396 i ii-----i - iiiv - ii C MIR3#SINE/MIR 35 CAGTCCGTGCTCTCTC-TGCTCAGCCA-CTCTGCCAG 1 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 47.96 CpG sites = 39, Kimura (unadjusted) = 47.96 Transitions / transversions = 2.17 (39/18) Gap_init rate = 0.05 (9 / 172), avg. gap size = 1.89 (17 / 9) 446 33.81 16.96 1.41 chr1ptel1M 660775 661452 (338548) L2#LINE/L2 1907 2688 (394) m_b18s601i13 671 chr1ptel1M 660775 CTGTCCACAATACATCACTTTCCACTTTTTAAAAAATCC--TTCCATCTG 660822 iv v v v i i i i i vvvi i -- i v v L2#LINE/L2 1907 CTGTCTCCAATTCCTCTCCTCCCATTCTCTCTTGAACCCACTCCAATCAG 1956 chr1ptel1M 660823 GTTTCCAACCTTATCATTCTCCCCAACCTGTTCTCTCCAAAGGTGCCTGT 660872 i i iv ii i i iv v v i ivi i vii vi L2#LINE/L2 1957 GCTTTCGTCCCCACCACTCCACCGAAACTGCTCTTGTCAAGGTCACCAAT 2006 chr1ptel1M 660873 GAACTCGGAGTTGCTGAATTTGATGACAGAGTTGAAGGC---ATCCTTCT 660919 v viv i iii iivi v ivv v --- i v L2#LINE/L2 2007 GACCTCCACGTTGCTAAATCCAATGGTCAATTCTCAGTCCTCATCTTACT 2056 chr1ptel1M 660920 TG---------CAGCATTCAGTGCTGTTGACCAC------CGTCT----- 660949 --------- iiiii v i ------ v ----- L2#LINE/L2 2057 TGACCTNTCAGCAGCATTTGACACAGTTGATCACTCCCTCCTTCTTGAAA 2106 chr1ptel1M 660950 ----------------CCTCCAAGACACTGCTCTCTTCTGCTTCTCCCCC 660983 ---------------- i i ii v i v i i L2#LINE/L2 2107 CACTTTCTTCACTTGGCTTCCAGGACACCACACTCTCCTGGTTTTCCTCC 2156 chr1ptel1M 660984 -ATCT-GTAGGAC----------AG-CTCCTTTGCAAG---CTCATCATC 661017 - i -iiv v ---------- - vi --- v L2#LINE/L2 2157 TACCTCACTGGCCGCTCCTTCTCAGTCTCCTTTGCTGGTTCCTCCTCATC 2206 chr1ptel1M 661018 CCTACGCCATCCCTTAGCGATG-ATTGTTCCCACAGATCAATCCT-GGAC 661065 i iv -- i i ? i v - v i- vi v i - L2#LINE/L2 2207 TCCCCG--ACCTCTNAACGTTGGAGTGC-CCCAGGGCTCAGTCCTTGGAC 2253 chr1ptel1M 661066 C----CAGTTCTCCCTCCACACTT--TTGCTTGGTGATCCC--TCAGCTC 661107 ---- vv iv i i-- iv ? i --i - L2#LINE/L2 2254 CTCTTCTCTTCTCTATCTACACTCACTCCCTNGGTGATCTCATCCAG-TC 2302 chr1ptel1M 661108 CCATAGGTTTCTCTATTATTTCT-TGC------------AATCTA----- 661139 i i v vvv ii i v - ------------ i ----- L2#LINE/L2 2303 TCATGGCTTTAAATACCATCTATATGCTGATGACTCCCAAATTTATATCT 2352 chr1ptel1M 661140 --ACCCCAG--TTCTCTCCTGAATTCCAGTCCCACACCACCAACCAACTA 661185 -- v i --i i i v i ii ivv iiv L2#LINE/L2 2353 CCAGCCCGGACCTCTCCCCTGAACTCCAGACTCGTATATCCAACTGCCTA 2402 chr1ptel1M 661186 CCGGTTCTTGCGATCTGGATGTCCCTTAAGCACCCAAAGTTCAACA--CC 661233 iv viv iv v ii ivv i i iv ii i --i L2#LINE/L2 2403 CTCGACATCTCCACTTGGATGTCTAATAGGCATCTCAAACTTAACATGTC 2452 chr1ptel1M 661234 CAAAATAGAGCTT---ATCCT-TCCTTCAAACT--CTCCCTCTTT--TCT 661275 iv i i--- i -i i i-- ii ivi-- L2#LINE/L2 2453 CAAAACTGAACTCCTGATCTTCCCCCTCAAACCTGCTCCTCCCGCAGTCT 2502 chr1ptel1M 661276 GTTCCCATTTTTGTT----GCAATTACCACCATCTTTCT-GTTTCCCAAG 661320 - i i iv ?---- i ---- i i- v i i L2#LINE/L2 2503 -TCCCCATCTCAGTNAATGGCAACT----CCATCCTTCCAGTTGCTCAGG 2547 chr1ptel1M 661321 CCTGAAACCTTCACATAATCTCTGATATTCCCTTCCCTTCCTCACCCTTT 661370 vi vivi v ii -- i ii ii ii v iii L2#LINE/L2 2548 CCAAAAACCTTGGAGTCATCCTTG--ACTCCTCTCTTTCTCTCACACCCC 2595 chr1ptel1M 661371 CCATCTAAGTAATGA-CCAATCTTGTT-GCTCCATGTCCAGTGCATGTCT 661418 v i viv v - v i i- i iv i ivii i i L2#LINE/L2 2596 ACATCCAATCCATCAGCAAATCCTGTCGGCTCTACCTTCAAAATATATCC 2645 chr1ptel1M 661419 ----TTCA--CAC-TCTCTTCA--TCCACGTTCTCCATCCTAG 661452 ---- i i-- - vi -- vvi v i i L2#LINE/L2 2646 AGAATCCGACCACTTCTCACCACCTCCACTGCCACCACCCTGG 2688 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 46.15 CpG sites = 146, Kimura (unadjusted) = 47.97 Transitions / transversions = 1.82 (146/80) Gap_init rate = 0.07 (45 / 677), avg. gap size = 2.80 (126 / 45) 235 22.77 2.86 5.88 chr1ptel1M 661614 661683 (338317) C L2d2_3end#LINE/L2 (269) 286 219 m_b18s601i14 672 chr1ptel1M 661614 TCAGACAAAGGGAGAGACCACAGCCCGGGTTT--GTGATCAGGACAGACT 661661 -ii i --i? i v-- i iv i C L2d2_3end#LIN 286 TCAGA-GGAGGGAGAGATCAC--TNCGGGCTGGAGTGGTCAGGGAAGGCT 240 chr1ptel1M 661662 TCATGAAGAAAGGTGACCTTTG 661683 i i -i i?v C L2d2_3end#LIN 239 TCACGGAG-GAGGTGGNATTTG 219 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 27.48 CpG sites = 12, Kimura (unadjusted) = 29.86 Transitions / transversions = 4.00 (12/3) Gap_init rate = 0.07 (5 / 69), avg. gap size = 1.20 (6 / 5) 294 35.70 4.02 4.95 chr1ptel1M 662003 662226 (337774) C L2#LINE/L2 (203) 2879 2658 m_b18s601i15 672 chr1ptel1M 662003 TTTTACAGTGAAGAGAAGGGGGATTCCCTGAAGTTATCTGAACAAGGGAG 662052 vv iviii v i vi vi i vvv i i ii C L2#LINE/L2 2879 TTTTACTCTGAGTGAGATGGGAAGCCATTGGAGGGTTTTGAGCAGAGGAG 2830 chr1ptel1M 662053 CTTCCCTGGCTTCCCTTGTATTTGAGAAAGAT---TTTGGCTG-TATGCT 662098 - vv v iii vv iii v i i --- i - i i C L2#LINE/L2 2829 -TGACATGATCTGACTTACGTTTTAAAAGGATCACTCTGGCTGCTGTGTT 2781 chr1ptel1M 662099 GAGGATGGATTTGAATAAAG--AGGAATTAGAAATGAGG-GACTAATTAG 662145 i i i v? iviii -- i-- i iiii - i i C L2#LINE/L2 2780 GAGAATAGACTGNAGGGGGGCAAGGG--TGGAAGCAGGGAGACCAGTTAG 2733 chr1ptel1M 662146 GAGGCTGTTGCAATAGCCTCTAG--GAGAGATGCTCAGGGCCTGGACTCC 662193 i i i-- i -- v viv i i-- C L2#LINE/L2 2732 GAGGCTATTGCAGTAA--TCCAGGCGAGAGATGATGGTGGCTTGGACC-- 2687 chr1ptel1M 662194 CTGAAGTAAGAGGGAAGGGGAGAAAGGGAGAAG 662226 ---- viv iv v v ivi v C L2#LINE/L2 2686 ----AGGGTGGTGGCAGTGGAGGTGGTGAGAAG 2658 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 50.75 CpG sites = 49, Kimura (unadjusted) = 51.88 Transitions / transversions = 1.81 (49/27) Gap_init rate = 0.07 (16 / 223), avg. gap size = 1.25 (20 / 16) 13 19.25 0.00 0.00 chr1ptel1M 662293 662322 (337678) (GACA)n#Simple_repeat 1 30 (0) m_b18s252i18 673 chr1ptel1M 662293 GACAGACAGAAACAGAGACAGAACGACAGA 662322 v v v vv (GACA)n#Simpl 1 GACAGACAGACAGACAGACAGACAGACAGA 30 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 19 25.73 1.96 0.00 chr1ptel1M 664550 664600 (335400) (AC)n#Simple_repeat 1 52 (0) m_b18s252i19 674 chr1ptel1M 664550 ACACACAGACATAGACACAGACACTCGCGCGCACACGCA-AGACACGCAC 664598 v i v v v i i i i - v i (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50 chr1ptel1M 664599 AC 664600 (AC)n#Simple_ 51 AC 52 Matrix = Unknown Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.02 (1 / 50), avg. gap size = 1.00 (1 / 1) 172 8.24 2.74 5.30 chr1ptel1M 664637 664965 (335035) (GGA)n#Simple_repeat 1 321 (0) m_b18s252i20 675 chr1ptel1M 664637 GGAGGGGGGGGAAGGAGGGAGGAGGAGCGATCAGGCGCGGGGGGTGG-GG 664685 i i - - - vv v vi i v - (GGA)n#Simple 1 GGAGGAGGAGG-AGGA-GGAGGAGGAG-GAGGAGGAGGAGGAGGAGGAGG 47 chr1ptel1M 664686 GGGAGCGGGCGGAGAAGGAAGAAGAAGAGGACTCCAGGA-GAGG-GGGGG 664733 i vi v i i i i --vv - - i (GGA)n#Simple 48 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA--GGAGGAGGAGGAGGAGG 95 chr1ptel1M 664734 AGGAGGAGG-GGAGGGGGAGGAGG-GGAGGAGGAGGAGGAGGAGGAGGAG 664781 - i - - (GGA)n#Simple 96 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA- 144 chr1ptel1M 664782 GGAGGAGGAGGGAGGAGGAGGGAGGAGGGAGGAGGGAGGAGGAGGAGGAG 664831 - - - - (GGA)n#Simple 145 GGAGGAGGA-GGAGGAGGA-GGAGGA-GGAGGA-GGAGGAGGAGGAGGAG 190 chr1ptel1M 664832 GAGGAGGAGGAGGAGG-GGAGGAGG-GGAGGAGGAGGGAGGAGGAGGAGG 664879 - - - - (GGA)n#Simple 191 GAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA-GGAGGAGGAGGA-G 238 chr1ptel1M 664880 GAGGGAGGAGGAGGAGGAGGGGGAGGGAGGAGGAGGAGGGAGGAGGAGGA 664929 - i - - (GGA)n#Simple 239 GA-GGAGGAGGAGGAGGAGGAGGA-GGAGGAGGAGGA-GGAGGAGGAGGA 285 chr1ptel1M 664930 GGGAGGAGGAGG-GG-GGAGGAGGGAGGGGGAGGAGGA 664965 - - - - i (GGA)n#Simple 286 -GGAGGAGGAGGAGGAGGAGGA-GGAGGAGGAGGAGGA 321 Matrix = Unknown Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.08 (26 / 328), avg. gap size = 1.00 (26 / 26) 17 16.71 0.00 4.76 chr1ptel1M 665041 665084 (334916) (GGGAG)n#Simple_repeat 1 42 (0) m_b18s252i22 676 chr1ptel1M 665041 GGGAGCGGAGGGCCGGGGAGGTGGGGGGAAGGGGCGGGGGAGGG 665084 v vv - i i -i (GGGAG)n#Simp 1 GGGAGGGGAGGGGAGGGGAGG-GGAGGGGAGGGG-AGGGGAGGG 42 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2) 13 8.32 3.57 3.57 chr1ptel1M 665160 665187 (334813) (CGG)n#Simple_repeat 1 28 (0) m_b18s252i23 677 chr1ptel1M 665160 CGGCGGCGGCGGCGAGTGGTGG-GGCGGC 665187 - i i - (CGG)n#Simple 1 CGGCGGCGGCGGCG-GCGGCGGCGGCGGC 28 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.07 (2 / 27), avg. gap size = 1.00 (2 / 2) 13 22.64 2.44 0.00 chr1ptel1M 665322 665362 (334638) (CCAGCCT)n#Simple_repeat 1 42 (0) m_b18s252i24 678 chr1ptel1M 665322 CCGGCGTCCAGCCTGACGCC-CGAGCCCGCAGCCTCCAGCCT 665362 i v vvv - v iv (CCAGCCT)n#Si 1 CCAGCCTCCAGCCTCCAGCCTCCAGCCTCCAGCCTCCAGCCT 42 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 183 22.67 3.33 6.90 chr1ptel1M 666115 666204 (333796) MIR3#SINE/MIR 6 92 (116) m_b18s601i16 679 chr1ptel1M 666115 AGGGTGGCCATTGGGCAGCCCGAGGACGCAGCTCTTGCAGTCAGGAGTCC 666164 i --- i vvv v v --- v v v MIR3#SINE/MIR 6 AGAGTGGC---TGAGCAGAGAGAGCACGGA---CTGGGAGTCAGGAGACC 49 chr1ptel1M 666165 TGGGTTCAAATCCCCCCCCCCCCATT--CTTGGTG-GTGACCT 666204 v i vv i iv i -- ? v - MIR3#SINE/MIR 50 TGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCT 92 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 27.31 CpG sites = 6, Kimura (unadjusted) = 27.31 Transitions / transversions = 0.46 (6/13) Gap_init rate = 0.09 (8 / 89), avg. gap size = 1.12 (9 / 8) 432 19.82 16.22 0.00 chr1ptel1M 667419 667529 (332471) C MIRb#SINE/MIR (57) 211 83 m_b19s601i0 680 chr1ptel1M 667419 CCTTACAT--ATTATCTCATTTCATCCTCA--ACATTCCTGGGAG----- 667459 i -- v -- vi v ----- C MIRb#SINE/MIR 211 CTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGG 162 chr1ptel1M 667460 -----TTATACTCACTTTGCAGATAAGGAAACTGAGGT----AGAGGTGA 667500 ----- v i i i i i---- v C MIRb#SINE/MIR 161 TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTA 112 chr1ptel1M 667501 AATGACTTATCTAGGGTCATCTAGCTAAT 667529 i i ii i i ivi i C MIRb#SINE/MIR 111 AGTAACTTGCCCAAGGTCACACAGCTAGT 83 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 23.81 CpG sites = 16, Kimura (unadjusted) = 23.81 Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.05 (5 / 110), avg. gap size = 3.60 (18 / 5) 187 27.07 7.08 5.22 chr1ptel1M 667619 667731 (332269) L2c_3end#LINE/L2 357 471 (7) m_b19s601i1 681 chr1ptel1M 667619 TGCTTTTCTCCTGCCCTATTAGACTGTGAGGTCCTCGGAGACAT---TTC 667665 ii v --- i i v i ii i v---iiv L2c_3end#LINE 357 TGTCTGTCTCCT---CCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCG 403 chr1ptel1M 667666 TTTCTATATTCAGTATTTAGTA----CAGTGCCGGCCATATGGTAAGCCC 667711 v - - v - ---- i v v i i i v L2c_3end#LINE 404 TGTCT-TATTCA-TCTTT-GTATCCCCAGCGCCTGGCACATAGTAGGCGC 450 chr1ptel1M 667712 TCTCT-AGTGCTTGTGGACTG 667731 vv - i i v v L2c_3end#LINE 451 TCAATAAATGTTTGTTGAATG 471 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 31.42 CpG sites = 16, Kimura (unadjusted) = 34.24 Transitions / transversions = 1.23 (16/13) Gap_init rate = 0.08 (9 / 112), avg. gap size = 1.56 (14 / 9) 443 25.69 1.23 9.27 chr1ptel1M 667890 668052 (331948) MIRb#SINE/MIR 1 151 (117) m_b19s601i2 682 chr1ptel1M 667890 CAGGAAGGCAGCTGGGAGGGTGCCATGGTGCAGAGTGTCAGAATTGGAGT 667939 iii ----iv vi -iv iiivi vv MIRb#SINE/MIR 1 CAGAGGGGCAGC----GTGGTGCAGTGG-AAAGAGCACGGGCTTTGGAGT 45 chr1ptel1M 667940 CAGGAAGACTCATCTCCCTGAGTTCAAATCCAGCCTCAGACACTCACTCA 667989 iv -------- i i v v v v i vi MIRb#SINE/MIR 46 CAGACAGAC--------CTGGGTTCGAATCCCGGCTCTGCCACTTACTAG 87 chr1ptel1M 667990 CTGGGGGACCCTGGGCAAGACACTT--CCTCCTGTTTGCCTCAGTTTCCT 668037 v v i vi -- - v vv MIRb#SINE/MIR 88 CTGTGTGACCTTGGGCAAGTTACTTAACCT-CTCTGAGCCTCAGTTTCCT 136 chr1ptel1M 668038 TATCCGTAAAATGAG 668052 i i i MIRb#SINE/MIR 137 CATCTGTAAAATGGG 151 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 28.69 CpG sites = 20, Kimura (unadjusted) = 31.57 Transitions / transversions = 1.11 (20/18) Gap_init rate = 0.09 (15 / 162), avg. gap size = 1.07 (16 / 15) 508 22.32 1.38 7.30 chr1ptel1M 667908 668052 (331948) MIRc#SINE/MIR 12 148 (120) m_b19s601i3 682 chr1ptel1M 667908 GGTGCCATGGTGCAGAGTGTCAGAATTGGAGTCAGGAAGACTCATCTCCC 667957 vi -iv iiiii v -------- MIRc#SINE/MIR 12 GGTGCAGTGG-AAAGAGCACTGGACTTGGAGTCAGGAAGAC--------C 52 chr1ptel1M 667958 TGAGTTCAAATCCAGCCTCAGACACTCACTCACTGGGGGACCCTGGGCAA 668007 i i i v v v v i vi v v i MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 102 chr1ptel1M 668008 GACACTT--CCTCCTGTTTGCCTCAGTTTCCTTATCCGTAAAATGAG 668052 v -- - v vv i i i MIRc#SINE/MIR 103 GTCACTTAACCT-CTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 25.64 CpG sites = 16, Kimura (unadjusted) = 26.64 Transitions / transversions = 1.14 (16/14) Gap_init rate = 0.08 (11 / 144), avg. gap size = 1.09 (12 / 11) 336 31.72 3.12 3.94 chr1ptel1M 668158 668285 (331715) MIRb#SINE/MIR 139 265 (3) m_b19s601i4 682 chr1ptel1M 668158 TCTGTAAACTGGG-ATAATGATGGCACCTGCTTCACAAAGCTGC---GAG 668203 v - i --- i i i ii i i--- MIRb#SINE/MIR 139 TCTGTAAAATGGGGATAATAAT---ACCTACCTCGCAGGGTTGTTGTGAG 185 chr1ptel1M 668204 GATCAAATCGAGTGAGATATGTGTAGGTTATCTGGAGCAGTGGCTGGCAC 668253 i - vv - iii iiviiii i vi v MIRb#SINE/MIR 186 GATTAAAT-GAGATA-ATGCATGTAAAGCGCTTAGCACAGTGCCTGGCAC 233 chr1ptel1M 668254 ACAGTAGGCATTTAATACACAATTGTTCCCTT 668285 i i ii i v iii v i iv MIRb#SINE/MIR 234 ATAGTAAGCGCTCAATAAATGGTAGCTCTATT 265 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 40.18 CpG sites = 30, Kimura (unadjusted) = 45.12 Transitions / transversions = 3.33 (30/9) Gap_init rate = 0.06 (7 / 127), avg. gap size = 1.29 (9 / 7) 411 27.02 3.54 1.74 chr1ptel1M 668158 668270 (331730) MIR#SINE/MIR 132 246 (16) m_b19s601i5 682 chr1ptel1M 668158 TCTGTAAACTGGG-ATAATGATGGCACCTGCTTCACAAAGCTGC---GAG 668203 v - i i i i i i ii i i--- MIR#SINE/MIR 132 TCTGTAAAATGGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAG 181 chr1ptel1M 668204 GATCAAATCGAGTGAGATATGTGTAGGTTATCTGGAGCAGTGGCTGGCAC 668253 i - v - ii iiviiii i i v MIR#SINE/MIR 182 GATTAAAT-GAGTTA-ATACATGTAAAGCGCTTAGAACAGTGCCTGGCAC 229 chr1ptel1M 668254 ACAGTAGGCATTTAATA 668270 i i ii i MIR#SINE/MIR 230 ATAGTAAGCGCTCAATA 246 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 33.64 CpG sites = 26, Kimura (unadjusted) = 36.98 Transitions / transversions = 6.50 (26/4) Gap_init rate = 0.04 (4 / 112), avg. gap size = 1.50 (6 / 4) 16 16.54 6.12 1.96 chr1ptel1M 668500 668548 (331452) (CCTT)n#Simple_repeat 1 51 (0) m_b19s252i1 683 chr1ptel1M 668500 CCTCCCTTCCTTGCGTCCTTCC--CCTGTGCTGCC-TCCTACCTCCCTTC 668546 i v v -- - v v - v i (CCTT)n#Simpl 1 CCTTCCTTCCTTCCTTCCTTCCTTCCT-TCCTTCCTTCCTTCCTTCCTTC 49 chr1ptel1M 668547 CT 668548 (CCTT)n#Simpl 50 CT 51 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.06 (3 / 48), avg. gap size = 1.33 (4 / 3) 513 23.25 2.04 6.38 chr1ptel1M 668903 669049 (330951) MIRc#SINE/MIR 6 146 (122) m_b19s601i6 684 chr1ptel1M 668903 CAGTG-GATAGAATGGCCAGAGCACCAGGCCTGGAATCAAGAAAACTCAT 668951 - i iv i vv ii i i i i i iiiv MIRc#SINE/MIR 6 CAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGG 55 chr1ptel1M 668952 CTTCTGGAATTCAGGTT-TGCCCCCAGACACTTCCTAGCTGTGTGACCCT 669000 v -- i i v i - ------- v i MIRc#SINE/MIR 56 GTTC--GAGTCCCGGCTCTGCC-------ACTTACTAGCTGTGTGACCTT 96 chr1ptel1M 669001 GGATAAGTCACTTAGCC-CTGTTTGCCTCTGTTTCCTCATCTGTCAAATG 669049 ii i - v vv v v MIRc#SINE/MIR 97 GGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATG 146 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 28.42 CpG sites = 20, Kimura (unadjusted) = 28.42 Transitions / transversions = 1.67 (20/12) Gap_init rate = 0.08 (12 / 146), avg. gap size = 1.00 (12 / 12) 96 19.77 0.53 0.00 chr1ptel1M 670349 670538 (329462) (CA)n#Simple_repeat 1 191 (0) m_b19s252i2 685 chr1ptel1M 670349 CACACACACACAGTCACACACTCACACACACACTTACACACACAGTTACA 670398 vv v vi vvi (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 chr1ptel1M 670399 TACACACTCACACAGTCATACACACTTAAACACATACACCTACACACTCA 670448 i v vv i vi v i vi v (CA)n#Simple_ 51 CACACACACACACACACACACACACACACACACACACACACACACACACA 100 chr1ptel1M 670449 CACACACTCACACACACACTCACATACACTCATACACACAGTCACACACA 670498 v v i v i vv (CA)n#Simple_ 101 CACACACACACACACACACACACACACACACACACACACACACACACACA 150 chr1ptel1M 670499 CACACTCACTCACACACACATACGTATACACAC-CACACAC 670538 v v i ii i - (CA)n#Simple_ 151 CACACACACACACACACACACACACACACACACACACACAC 191 Matrix = Unknown Transitions / transversions = 0.65 (13/20) Gap_init rate = 0.01 (1 / 189), avg. gap size = 1.00 (1 / 1) 450 21.36 11.52 6.36 chr1ptel1M 671033 671197 (328803) MIRb#SINE/MIR 5 177 (91) m_b19s601i7 686 chr1ptel1M 671033 GGGTCAGCTGGGTGGTGCCACAGTGAATAGAA-------TGTGGAGTCAT 671075 v --- --- i v i------- v v MIRb#SINE/MIR 5 GGGGCAGC---GTGGTGC---AGTGGAAAGAGCACGGGCTTTGGAGTCAG 48 chr1ptel1M 671076 GAAGACCTGAATTCGAAAACCCAGCCTCAAATACTTACT----------- 671114 iv ii - v i - vivi ----------- MIRb#SINE/MIR 49 ACAGACCTGGGTTCG-AATCCCGG-CTCTGCCACTTACTAGCTGTGTGAC 96 chr1ptel1M 671115 -CTGGGCGAGTCATTGCACCTTCACCTGCCTCAGTTTCCTCATCTGTAAA 671163 -i i i i vv iivivv MIRb#SINE/MIR 97 CTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAA 146 chr1ptel1M 671164 ATGGGGGTGGTGATAATACCTACCTCCCTGGGCT 671197 --- i i v v i MIRb#SINE/MIR 147 ATGGG---GATAATAATACCTACCTCGCAGGGTT 177 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 24.66 CpG sites = 18, Kimura (unadjusted) = 25.53 Transitions / transversions = 1.20 (18/15) Gap_init rate = 0.09 (14 / 164), avg. gap size = 2.14 (30 / 14) 371 26.58 4.44 5.22 chr1ptel1M 671112 671246 (328754) MIR1_Amn#SINE/MIR 94 227 (3) m_b19s601i8 686 chr1ptel1M 671112 ACTCTGGGCGAGTCATTGCACCTTCACCTGCCTCAGTTTCCTCATCTGTA 671161 ii i i v? iiviv? MIR1_Amn#SINE 94 ACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTA 143 chr1ptel1M 671162 AAATGGGGGTGGTGATAATACCTACCTCCCT------GGGCTTAGCACAG 671205 --- i i i iv i ------ v v --- MIR1_Amn#SINE 144 AAATGGG---GATAATGATACTGACCTCCTTTGTAAAGTGCTTTG---AG 187 chr1ptel1M 671206 TCCTGGCACATGGTAGCAGCCATACAAAAGTTAGTTATTAT 671246 vi -i vv iv ivv i i i i i v MIR1_Amn#SINE 188 ATCT-ACTGATGAAAAGTGCTACATAAGAGCTAGGTATTAT 227 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 34.46 CpG sites = 21, Kimura (unadjusted) = 34.46 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.06 (8 / 134), avg. gap size = 1.62 (13 / 8) 825 31.50 10.35 1.44 chr1ptel1M 671714 672225 (327775) L3#LINE/CR1 1275 1831 (2268) m_b19s601i9 687 chr1ptel1M 671714 ATACAGATACAAAATGTGTGGGTGAGAAGAACCCCAGACTAGCGACTAGA 671763 vi i v iv i i v i? vvvi?i v vi i vv L3#LINE/CR1 1275 ATACCAATGCACAGAGTATGGGTAATAAANAAAGTNAACTTGAAATTTTA 1324 chr1ptel1M 671764 ACCCAAAGGAGGTAAGATTGACCTCATGGGT----CCGA----------- 671798 v - ivvi i i ---- ----------- L3#LINE/CR1 1325 ACACAA-GGAGGTAAATACGATCTCATAGGTATCACCGAGACTTGGTGGG 1373 chr1ptel1M 671799 ATGAGACCCAGGATTGGACCTGAGAGA-GGAAAGCTCCACAGTTGTCAAA 671847 i i v i vivvi v - i v v? vv vv L3#LINE/CR1 1374 ATGGGACTCATGACTGGAATACGGCGATGGAAGGGTANACCTTGTTCAAA 1423 chr1ptel1M 671848 AAAACAAGGGGAGATAAATGGGGTGGAAGAATGGAGCATCATTGCACCGT 671897 i vv ivvvi? i v v ? i i ----- i i i- L3#LINE/CR1 1424 AGAAACAGATCTANTAGAAGGGGAGGNAGAGTAG-----CACTGTAT-GT 1467 chr1ptel1M 671898 CAGGA-GACCTAC--TTGTATGAGAAACCA------------GAGAA--- 671929 i - iv --i ii ii v ------------v --- L3#LINE/CR1 1468 CAAGAAGATATACACCTGCGTGGAAATCCACGAACCTGAGGGTAGAAGCG 1517 chr1ptel1M 671930 ------AGATTATT-GGGTAAAGATTAATGGAGTGAAAATCAGAGGCAAT 671972 ------ vi - i i v v v i v i ii L3#LINE/CR1 1518 CGNTGGAGAGCATTTGGGTGAGGATAAAAGGAGAGAGAAACAGAAGTGAT 1567 chr1ptel1M 671973 CTTGTCTT-----CATCACTACAAACTAGCTAGACAGAAAATGGGAATTC 672017 v i iv -----i - i iiv ii v viiv i? vv L3#LINE/CR1 1568 ATCGTTGTGGGAGTAT-ACTACAGACCGCCCGGCCAGATGGAGGANATGG 1616 chr1ptel1M 672018 ATGAGGACTTTGGGAAACA--TCGCAAGGCTGGCA-ATAG-CATATTGT- 672062 v vi ivv v -- ii ii - v - viv ?i- L3#LINE/CR1 1617 ATGATGCTTTCCTGATACAGATTACAAAACTGGCACAGAGGCAAGATNCA 1666 chr1ptel1M 672063 -TAGTGATGCGGGACTTCAATTATCCAGACAGCTGCTGGGACGCTCCCTC 672111 - v i i v i vv vi L3#LINE/CR1 1667 GTAGTGATGGGGGACTTCAACTATCCGGACATCTGCTGGAAGTCTCATTC 1716 chr1ptel1M 672112 TGCCAAAAGCAGAGCCGCTAATAACTTTTTGAC-TGCCTTAATGATAATT 672160 ? i vv i v i - iv i L3#LINE/CR1 1717 NGCTAAAAGCAGAGCATCTGATAAATTCTTGACTTGCCTTGCTGACAATT 1766 chr1ptel1M 672161 CCATCCTTCAAAAAGCGGAGTAAGGGAAATGAGCAAATTTTATTCTGCAC 672210 i ii i i ii v vi viv i v v vi i v L3#LINE/CR1 1767 TCATCTCTCAGAAGGTAGAGGAAGCAACGAGGGGAACTGCTACTCTGGAC 1816 chr1ptel1M 672211 TGGATTCTCACCAAC 672225 vi v L3#LINE/CR1 1817 TTAATTCTGACCAAC 1831 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 39.78 CpG sites = 84, Kimura (unadjusted) = 42.66 Transitions / transversions = 1.12 (84/75) Gap_init rate = 0.05 (24 / 511), avg. gap size = 2.54 (61 / 24) 23 14.35 0.00 2.13 chr1ptel1M 672520 672567 (327433) (AGAGAG)n#Simple_repeat 1 47 (0) m_b19s252i3 688 chr1ptel1M 672520 AGACGAGAGAGAGAGAAATAGAGAGACAGAGACAGACAGAGACAGAGA 672567 - i v v v v v (AGAGAG)n#Sim 1 AGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 47 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.02 (1 / 47), avg. gap size = 1.00 (1 / 1) 16 5.27 0.00 0.00 chr1ptel1M 672945 672964 (327036) (A)n#Simple_repeat 1 20 (0) m_b19s252i4 689 chr1ptel1M 672945 AAAAAAAAAAAAAAAAAGAA 672964 i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAA 20 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 524 14.15 5.66 0.00 chr1ptel1M 672989 673094 (326906) MER63D#DNA/hAT-Tip100 357 468 (593) m_b19s502i0 690 chr1ptel1M 672989 AAATCGGCAG--TCTACAAATCAGGGCTGGATT----GTTATGCTGATTG 673032 i--v v ---- v i MER63D#DNA/hA 357 AAATCGGCAAACGCTACAAATCAGGGCTTGATTTATTGTTTTGTTGATTG 406 chr1ptel1M 673033 TCTAGACCTTAGAAAGTGAAGGTAATTATGATAATAATGCAGATTAAACT 673082 i v v vi vv v MER63D#DNA/hA 407 TCTAGACTTAAGAAAGTGATGGAGAAAATGTTAATAATGCAGATTAAACT 456 chr1ptel1M 673083 TAAAAGTGCATC 673094 ii MER63D#DNA/hA 457 TAAAAGTGTGTC 468 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 15.69 CpG sites = 6, Kimura (unadjusted) = 15.69 Transitions / transversions = 0.67 (6/9) Gap_init rate = 0.02 (2 / 105), avg. gap size = 3.00 (6 / 2) 17 0.00 0.00 0.00 chr1ptel1M 673276 673294 (326706) (T)n#Simple_repeat 1 19 (0) m_b19s252i5 691 chr1ptel1M 673276 TTTTTTTTTTTTTTTTTTT 673294 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 262 31.11 4.44 0.00 chr1ptel1M 673903 674037 (325963) C L1ME2z_3end#LINE/L1 (618) 573 433 m_b19s551i0 692 chr1ptel1M 673903 TTCGTCCTTTCTTA---CTGGACAATCATCCATTACATTTAAATACCT-- 673947 i i i --- iii i vv ii vv v v-- C L1ME2z_3end#L 573 TTCGTTCCTTTTTATTGCTGAGTAGTATTCCATTGTATGAATATACCACA 524 chr1ptel1M 673948 GTTT-TTCAGCCATTCCCCAATTAATAGGCTCCTCCTCTGCTTTCAGTTT 673996 - i v i vi i i i v vvv i i C L1ME2z_3end#L 523 GTTTGTTTATCCATTCTCCTGTTGATGGACACCTGGGCTGTTTCCAGTTT 474 chr1ptel1M 673997 TTTGCTACCATAAAAAAGGTTTCAATGAATATTCTAATATA 674037 v ii i v i i v v i vi i C L1ME2z_3end#L 473 TTGGCTATTATGAATAAAGCTGCTATGAACATTCTTGTACA 433 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 41.54 CpG sites = 25, Kimura (unadjusted) = 41.54 Transitions / transversions = 1.47 (25/17) Gap_init rate = 0.02 (3 / 134), avg. gap size = 2.00 (6 / 3) 469 26.25 6.86 5.30 chr1ptel1M 674087 674625 (325375) L3#LINE/CR1 2793 3339 (760) m_b19s601i10 687 chr1ptel1M 674087 TTATTAAAAGGAT------TAAACATTTCGAGAGGGGATCAGGGATCACA 674130 vi ------ i i i v i i i v i v v L3#LINE/CR1 2793 TTATTAAACAGATGGTTTGTGAGCACTTAGAAAAGGAAGCGGTGATCACT 2842 chr1ptel1M 674131 AAGAACCTCTGTGATTTCAGTAAT--CCAG--ATGC--ATTTAAT----T 674170 i i vvii iv v v-- v -- -- vi i---- L3#LINE/CR1 2843 AGGAGCCAGCATGGGTTCACTAAGAACAAGTCATGCCAAACTAACCTCAT 2892 chr1ptel1M 674171 TTCCCTTTTTGACAG--TCGTCAAAATGGTAGATGGTAGAGGAACACTTT 674218 i i -- iiii i v --i i ii iv L3#LINE/CR1 2893 TTCCTTTTTTGATAGGGTTACTAGACTGGTAGAT--CAGGGGAATGCCGT 2940 chr1ptel1M 674219 CAGGGGATATTACTATTTTAAGGATGGCAGTCTGGGGAAATTTACTGGCA 674268 --i iv ? v i- i --- vv i---ii iv --- i L3#LINE/CR1 2941 --AGACANAGTG-TATCT---GGATTTCAGC---AAGGCATTT---GACA 2978 chr1ptel1M 674269 AATTTTTGCATGTCATTCTTATGAAAAGGA--GAGAAACATATTCATGAT 674316 v i iv vi i i i v i -- i ivv vv L3#LINE/CR1 2979 AAGTCTCTCATGATATCCTTGTGGACAAGATGGAGAAATATGGGCTGGAT 3028 chr1ptel1M 674317 GACACTGTGGGGAGGTTGAGGACGTTGAAGGGATGTTGCAG-TAGCTGAA 674365 i v iii vv -------------- - i i - i i L3#LINE/CR1 3029 GATAGTACAGTTAGGT--------------GGAT-TCGTAGCTGGTTGAA 3063 chr1ptel1M 674366 TG--TACA---AGGAAGAGTT-ATTAGTTGTTCAATATCAGCATG-ACTG 674408 i -- i --- ii i v - i v v i i i v - vv L3#LINE/CR1 3064 CGACTATACCCAAAAGGTGTTGATTAATGGATCGATGTCAACCTGGAGGG 3113 chr1ptel1M 674409 AGGTTTCCA-TGGAGTGTCCCATGG-TCTG--CTT---TCTGTNNNNNNN 674451 i i - v i v v - -- ---i ??????? L3#LINE/CR1 3114 AGGTCTCTAGTGGCGTGCCACAGGGCTCTGTCCTTGGCCCTGTCCTGTTC 3163 chr1ptel1M 674452 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 674501 ?????????????????????????????????????????????????? L3#LINE/CR1 3164 AACATTTTTATCAATGACTTGGATGAAGACATAGAAGGCATGCTTATCAA 3213 chr1ptel1M 674502 NNNNNNNNNNNNNNNNNNNNNNNNNNNNCC--CTGAGACGGTGGGTATCC 674549 ????????????????????????????vi-- i v ? i iv v L3#LINE/CR1 3214 ATTTGCAGATGACACAAAGCTGGGAGGGATAGCTAATACGNTGGATGACA 3263 chr1ptel1M 674550 GAGTAAGGATTCGAAAAGATCCTGTCAGGCTAGGACACTGGGCTGCATCC 674599 i v i i ? ii v i i iv i v v L3#LINE/CR1 3264 GAATCAAGATTCAAAANGATCTCGACAGGCTGGAACGATGGGCCGAAACC 3313 chr1ptel1M 674600 AACAAGAAGAGACACAATAGAGATAA 674625 v i ivi i i L3#LINE/CR1 3314 AACAAGATGAAATTTAACAGGGATAA 3339 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 39.70 CpG sites = 84, Kimura (unadjusted) = 43.11 Transitions / transversions = 1.68 (84/50) Gap_init rate = 0.09 (46 / 538), avg. gap size = 1.43 (66 / 46) 257 21.40 15.29 1.03 chr1ptel1M 674445 674529 (325471) CR1-L3A_Croc#LINE/CR1 3309 3405 (883) m_b19s551i1 687 chr1ptel1M 674445 TTGGTCCTATGCTGTGTAACATTTCTATCAATGACTTT---GAAAACATG 674491 i i i v i i v--- i CR1-L3A_Croc# 3309 TTGGCCCTACGCTATTTAACATTTTTATCAATGACCTGGAAGAAAACATA 3358 chr1ptel1M 674492 -----CTTGCAGA-----CTTGCAGATATCAGCAAAACTTGGAGGGGT 674529 -----v i v -----i iv - iv i i CR1-L3A_Croc# 3359 AAATCATTACTGATAAAGTTTGCAGATGACA-CAAAGATTGGGGGAGT 3405 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 24.31 CpG sites = 12, Kimura (unadjusted) = 25.95 Transitions / transversions = 2.00 (12/6) Gap_init rate = 0.05 (4 / 84), avg. gap size = 3.50 (14 / 4) 16 13.56 0.00 9.09 chr1ptel1M 675126 675173 (324827) (TTTCTTA)n#Simple_repeat 1 44 (0) m_b19s252i6 693 chr1ptel1M 675126 TTTCTTGGTTTCTTTTCTCTCATTATCTCTTCTTTCTTATTTCTAATT 675173 -i v - - - i v v (TTTCTTA)n#Si 1 TTTCTT-ATTTCTTAT-T-TC-TTATTTCTTATTTCTTATTTCTTATT 44 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.09 (4 / 47), avg. gap size = 1.00 (4 / 4) 276 22.74 15.91 3.38 chr1ptel1M 675503 675634 (324366) MIR1_Amn#SINE/MIR 6 153 (77) m_b19s601i11 694 chr1ptel1M 675503 AGCCAGTGTTGGATGGTGGATAGAA---TGGA---------GGAAGACCT 675540 v v vv i i--- --------- i MIR1_Amn#SINE 6 AGGCAGTGTGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGAGACCT 55 chr1ptel1M 675541 GGAT---------GTCTCTGCCCACATGCTGGGTTAGATGACCATAGGCA 675581 i --------- v - v? i? -i i?i v i MIR1_Amn#SINE 56 GGGTTCNANTCCCGGCTCTGCC-ACTNGCCNG-CTGNGTGACCTTGGGCA 103 chr1ptel1M 675582 AGTCACCGAATCGCTCTCACCCTCAGATATTTCTGTATTGGTAAAATGTT 675631 iv? i v v?v --- ivi iv vv MIR1_Amn#SINE 104 AGTCACTTNACCTCTCTGNGCCTCAG---TTTCCTCATCTGTAAAATGGG 150 chr1ptel1M 675632 GAT 675634 MIR1_Amn#SINE 151 GAT 153 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 28.78 CpG sites = 14, Kimura (unadjusted) = 28.78 Transitions / transversions = 0.93 (14/15) Gap_init rate = 0.06 (8 / 131), avg. gap size = 3.25 (26 / 8) 327 28.04 12.03 2.91 chr1ptel1M 675531 675688 (324312) MIRc#SINE/MIR 44 215 (53) m_b19s601i12 694 chr1ptel1M 675531 AGGAAGACCTGGAT----GTCTCTGC----CCACATGCTGGGTTAGATGA 675572 i ---- i v ---- v i i -i ivi MIRc#SINE/MIR 44 AGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAG-CTGTGTGA 92 chr1ptel1M 675573 CCATAGGCAAGTCACCGAATCGCTCTCACCCTCAGATATTTCTGTATTGG 675622 v i iv i v v v --- ivi iv MIRc#SINE/MIR 93 CCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAG---TTTCCTCATCTG 139 chr1ptel1M 675623 TAAAATGTTGAT-------TCTG---TACCTATACCACAGAGCTTCTG-G 675661 vv -------i --- i ivi i i vi - MIRc#SINE/MIR 140 TAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTG 189 chr1ptel1M 675662 ACAATGCAAATAAAAGAAGATATCTAA 675688 vi - i i v vi v i MIRc#SINE/MIR 190 AGGAT-CAAATGAGATAATGTATGTGA 215 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 36.10 CpG sites = 25, Kimura (unadjusted) = 36.10 Transitions / transversions = 1.39 (25/18) Gap_init rate = 0.06 (10 / 157), avg. gap size = 2.40 (24 / 10) 29 0.00 0.00 0.00 chr1ptel1M 675758 675784 (324216) (TTAGGG)n#Simple_repeat 1 27 (0) c_b19s251i0 695 chr1ptel1M 675758 TTAGGGTTAGGGTTAGGGTTAGGGTTA 675784 (TTAGGG)n#Sim 1 TTAGGGTTAGGGTTAGGGTTAGGGTTA 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 187 24.18 1.64 5.08 chr1ptel1M 675880 675940 (324060) C L2a_3end#LINE/L2 (92) 425 367 m_b19s601i13 696 chr1ptel1M 675880 AAGTGCTCTGCTCTTCAGGAGCTCCCACTCAAGTGGGGTAGTAAACAAAC 675929 - i i ivv iv i v -- v i i C L2a_3end#LINE 425 AAGT-CCCTGCCCTCATGGAGCTTACATTCTAGTGGGG--GGAGACAGAC 379 chr1ptel1M 675930 AA-AAATGAATA 675940 - ii C L2a_3end#LINE 378 AATAAACAAATA 367 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 29.99 CpG sites = 9, Kimura (unadjusted) = 29.99 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.07 (4 / 60), avg. gap size = 1.00 (4 / 4) 371 29.56 9.84 2.03 chr1ptel1M 676023 676205 (323795) C MIRb#SINE/MIR (44) 224 28 m_b19s601i14 697 chr1ptel1M 676023 ATTGGGCTGAGAGCTTGACA---A--ATATCATTT--------CAACAGC 676059 i v i v v --- -- v -------- i C MIRb#SINE/MIR 224 ACTGTGCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAAC 175 chr1ptel1M 676060 CCTGTGGTGTAGGTGCTG--GTCCCCA-TTTAGAGTTGAGGAAAGGGAGA 676106 i iv ii i--i - v v vv i C MIRb#SINE/MIR 174 CCTGCGAGGTAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGG 125 chr1ptel1M 676107 CAAATGAAAGATTAAAAGAGGATTTTCCTTGGGTCACACAG-TAGTAGGC 676155 vv - i i ---ivi i v ivi - i i C MIRb#SINE/MIR 124 CTCA-GAGAGGTTAA---GTAACTTGCCCAAGGTCACACAGCTAGTAAGT 79 chr1ptel1M 676156 ATCTGAGGTTAACTTTAAACTTGGGTCT-TCTCACTCCAAATCCAGCATT 676204 iv v viviiv ii iii - v v v iii C MIRb#SINE/MIR 78 GGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCT 29 chr1ptel1M 676205 C 676205 C MIRb#SINE/MIR 28 C 28 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 35.86 CpG sites = 31, Kimura (unadjusted) = 38.73 Transitions / transversions = 1.41 (31/22) Gap_init rate = 0.06 (11 / 182), avg. gap size = 2.00 (22 / 11) 250 32.48 2.48 3.33 chr1ptel1M 676589 676709 (323291) L2c_3end#LINE/L2 353 472 (6) m_b19s601i15 698 chr1ptel1M 676589 TACTTGTACATTTTCCTCCATTAAAAGGCAAGTTCCTTGAAGGAATGGGT 676638 ? - vv i i i vv ii i i v v ii L2c_3end#LINE 353 TACNTGT-CTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGAC 401 chr1ptel1M 676639 --TCTTTTAAGTTTTATCTTT-TATTTGTTGTGCCTGATGTACAGTAGGT 676685 -- v i --- i - iiviv i iiii i i L2c_3end#LINE 402 CGTGTCTTA---TTCATCTTTGTATCCCCAGCGCCTGGCACATAGTAGGC 448 chr1ptel1M 676686 GTTTAATAACTGCTCCTTAATTGA 676709 i i v i iv i v L2c_3end#LINE 449 GCTCAATAAATGTTTGTTGAATGA 472 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 42.57 CpG sites = 26, Kimura (unadjusted) = 45.91 Transitions / transversions = 2.17 (26/12) Gap_init rate = 0.05 (6 / 120), avg. gap size = 1.17 (7 / 6) 15 14.38 0.00 0.00 chr1ptel1M 678432 678455 (321545) (T)n#Simple_repeat 1 24 (0) m_b19s252i7 699 chr1ptel1M 678432 TTTTTTCTTTTTTTTTCCTTTTTT 678455 i ii (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTT 24 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 14 22.09 2.78 7.25 chr1ptel1M 678536 678607 (321393) (AACAA)n#Simple_repeat 1 69 (0) m_b19s252i8 700 chr1ptel1M 678536 AACTAAATACAAAATAAGAAAAAACACAATAGAAAAGAAAGAC-AGA-AA 678583 - - i - v - v v v - - i - (AACAA)n#Simp 1 AAC-AAA-ACAAAACAA-AACAAA-ACAAAACAAAACAAA-ACAAAACAA 45 chr1ptel1M 678584 AGGAAATTACAATAAAACAAAACA 678607 iv vi v i (AACAA)n#Simp 46 AACAAAACAAAACAAAACAAAACA 69 Matrix = Unknown Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.10 (7 / 71), avg. gap size = 1.00 (7 / 7) 279 31.85 15.84 1.99 chr1ptel1M 680593 680813 (319187) C L2b_3end#LINE/L2 (16) 450 200 m_b19s601i16 701 chr1ptel1M 680593 AACATTTGCTAAGTGTTTGTTTTGTGCCTGGCCCTGGGCTTGGACCC--- 680639 i i i i ii ii v v ? v v vv i--- C L2b_3end#LINE 450 AATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGG 401 chr1ptel1M 680640 -ATGAGGCG------AAGACGGAAGTGG-CTCTGCCTCTGAGGAGCTCGC 680681 - ivi ------ i v?i - i iiiiv i C L2b_3end#LINE 400 GATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGGAGCTCAC 351 chr1ptel1M 680682 TCCCTACCAGGG-----AGACAGGT--CCAGGAGGGAGTGTCTCAGAATA 680724 vvi vii ----- v --? iviiv?i iv i i i C L2b_3end#LINE 350 AGTCTAGTGGGGGAGACAGACATGTAANCAGACAATNATAACCCAGAGTG 301 chr1ptel1M 680725 AGTACAAGGTGGTCGGCTGGGGGC------AGGAG-----------CGGC 680757 i--- i i -- i v------ ----------- C L2b_3end#LINE 300 G---CAGGGTAG--GACTGGGGGGGCCCAGAGGAGGGCGCCTGACCCGGC 256 chr1ptel1M 680758 TGGGGAGATCAAGAGAGGCTTCCTGGAGGAAGTGGCTTTTATGTCGAACC 680807 iv i i i iii i i i v iv ii iv C L2b_3end#LINE 255 CTGGGGGGTCAGGGAGGGCTTCCCGGAGGAGGTGACATTTGAGCTGAGAC 206 chr1ptel1M 680808 CTGAAG 680813 C L2b_3end#LINE 205 CTGAAG 200 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 42.89 CpG sites = 48, Kimura (unadjusted) = 45.66 Transitions / transversions = 2.29 (48/21) Gap_init rate = 0.06 (13 / 220), avg. gap size = 3.08 (40 / 13) 250 26.79 0.00 2.82 chr1ptel1M 684686 684758 (315242) C L2#LINE/L2 (334) 2748 2678 m_b19s601i17 701 chr1ptel1M 684686 CAGGGAGACCAGTCACCAGGTTATCGCGATGCTCCAGGTGCGTGAGATGA 684735 i vv i i ii iv -- v C L2#LINE/L2 2748 CAGGGAGACCAGTTAGGAGGCTATTGCAGTAATCCAG--GCGAGAGATGA 2701 chr1ptel1M 684736 TGAGGTCCTATAACAGGATGTTG 684758 iv v i iv v i v C L2#LINE/L2 2700 TGGTGGCTTGGACCAGGGTGGTG 2678 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 33.56 CpG sites = 10, Kimura (unadjusted) = 33.56 Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.03 (2 / 72), avg. gap size = 1.00 (2 / 2) 678 32.54 16.52 1.39 chr1ptel1M 684817 685754 (314246) C L2#LINE/L2 (534) 2548 1471 m_b19s601i18 701 chr1ptel1M 684817 GCCTGGGTGAGTGGA-GGAGGGTGGTACCCTGGACAGCGACAGGAAAGTT 684865 i ii v - v v v i v v? v v ii i vi C L2#LINE/L2 2548 GCCTGAGCAACTGGAAGGATGGAGTTGCCATTNACTGAGATGGGGAAGAC 2499 chr1ptel1M 684866 TGTGATGGGGAGGAACT------GGAAAGAGTGGG-TTTCA--TCTGGGC 684906 i i- i v iv ------ i vii -v -- i i C L2#LINE/L2 2498 TGCGG-GAGGAGCAGGTTTGAGGGGGAAGATCAGGAGTTCAGTTTTGGAC 2450 chr1ptel1M 684907 ATTGGTGAGTTTCCGATGTCTACAGGACATCAAGTTCAAGATTTCTGA-- 684954 - v i vv i ivi v iv vi v - -- C L2#LINE/L2 2449 AT-GTTAAGTTTGAGATGCCTATTAGACATCCAAGTGGAGATGTC-GAGT 2402 chr1ptel1M 684955 -------TGGATTT--GAGGTTGAAGGTCAGC--AGAAGTGAGCACTGGA 684993 ------- v -- vi i v v-- i vv vi C L2#LINE/L2 2401 AGGCAGTTGGATATACGAGTCTGGAGTTCAGGGGAGAGGTCCGGGCTGGA 2352 chr1ptel1M 684994 GAAGGAGATCTGAGAATCCTGGGCAGAGGGACGATCGTTGAATCCATGAG 685043 viv i i i i v vi v vi i i vv i v C L2#LINE/L2 2351 GATATAAATTTGGGAGTCATCAGCATATAGATGGTATTTAAAGCCATGAG 2302 chr1ptel1M 685044 AACTGATGAGATCACCCAGTGAA---------ATAACAGGAAAGAAGAAA 685084 viv ? v i--------- i- i i ii C L2#LINE/L2 2301 ACTGGATGAGATCACCNAGGGAGTGAGTGTAGATAG-AGAAGAGAAGAGG 2253 chr1ptel1M 685085 TCCTGAGACAAAGCCTTGTGGGGATGTCCCTACAT--------------- 685119 vii vi i --- iiiii v i --------------- C L2#LINE/L2 2252 TCCAAGGACTGAGCCCTG---GGGCACTCCAACGTTNAGAGGTCGGGGAG 2206 chr1ptel1M 685120 -----AAAAAATCAGCAAAGGAGACTAAGAAAGAATGGTCAGTCAGGTGG 685164 -----i ii i i i ii i v i C L2#LINE/L2 2205 ATGAGGAGGAACCAGCAAAGGAGACTGAGAAGGAGCGGCCAGTGAGGTAG 2156 chr1ptel1M 685165 AAGGAGAACCAGGAGAGGGCAAGGTCATGAACAACCAGAAACAAGAGAGT 685214 i i v iiiv v i - i - ivv i C L2#LINE/L2 2155 GAGGAAAACCAGGAGAGTGTGGTGTCCTGGA-AGCCA-AGTGAAGAAAGT 2108 chr1ptel1M 685215 ATT---GGGGAGAAGACGTGACCAAATGTGT------CTGCAGAGAAATC 685255 i ---i iii i iv i v ------ v ? ii C L2#LINE/L2 2107 GTTTCAAGAAGGAGGGAGTGATCAACTGTGTCAAATGCTGCTGANAGGTC 2058 chr1ptel1M 685256 A---AAGACGAGGAGAGAAGACTCTCCCTTAGATTTTGTCATTGAGGGAG 685302 --- i vv ii i vv v i v - vi v ii C L2#LINE/L2 2057 AAGTAAGATGAGGACTGAGAATTGACCATTGGATTTAG-CAACGTGGAGG 2009 chr1ptel1M 685303 TCGCCAG---------CGAGAGCAGG---GGTAGGATGACAAGATCTGGA 685340 iiii --------- i v--- i ii iiii iv vii C L2#LINE/L2 2008 TCATTGGTGACCTTGACAAGAGCAGTTTCGGTGGAGTGGTGGGGACGAAA 1959 chr1ptel1M 685341 ACCAGATTGGG--GAGTTCAGAAGAGGGTGGGAG--AAGGAAGTGGGGAC 685386 i v i-- i ii ii --i v i C L2#LINE/L2 1958 GCCTGATTGGAGTGGGTTCAAGAGAGAATGGGAGGAGAGGAATTGGAGAC 1909 chr1ptel1M 685387 -----------------CTTTGCAAGA---TGGCCACAAAGATGAGGAGA 685416 ----------------- vv i --- v iii iv v C L2#LINE/L2 1908 AGCGAGTATAGACAACTCTTTCGAGGAGTTTTGCTGTAAAGGGGAGCAGA 1859 chr1ptel1M 685417 GACATGGAG-GGTGGCCAGTGGGAGCACAT-GGATCAGGTAAGG--TTTT 685462 v i - i ii v i - ?i - i i vi i-- C L2#LINE/L2 1858 GAAATGGGGCGGTAGCTGGAGGGGG-ANGTGGGGTCAAGGGAGAATTTTT 1810 chr1ptel1M 685463 CTTGTT----GATGGGGGGATGTGGC--CATGTTTGCA-ACCATAGGGAA 685505 v v ---- i i -i ?i -- i -i iivv C L2#LINE/L2 1809 GTTTTTTAAAGATGGGAGAA-ATNACAGCATGTTTGTATGCTGATGGGAA 1761 chr1ptel1M 685506 GCACCCAGGAGACTAGAGGAGACT--------AGAAG-GAGAGTGGGGA- 685545 vv i v vvi iii i i -------- i - v i - C L2#LINE/L2 1760 TGATCCAGTAGAGAGGGAAAAATTGATGATGCAGGAGAGAGAGGGGAGAA 1711 chr1ptel1M 685546 -----GGGGCAATCTTCTGGAGAAAAGAAGATGGAATGGGATC-ACTGTG 685589 ----- i i v i v v iivi v i - v ii C L2#LINE/L2 1710 TTGCTGGAGCGATGTCCTTGAGTAGGCGAGAGGGGATGGGATCTAGTGCA 1661 chr1ptel1M 685590 CCTGAGAAAAGTTTGTCCTCAGA-------------AACTC-TTCATGGG 685625 vv v i ii v v i ------------- ii - i i i v C L2#LINE/L2 1660 CAAGTGGAGGGGTTGGCCTTAGATAGGAGCACGGACAGTTCATCCGTAGT 1611 chr1ptel1M 685626 ACACAGGAGAGAAGATGGAGAAAGTGATGAAACTTAT-CTGGGAGATGTG 685674 - i iii v v -- iv vv - v v i v C L2#LINE/L2 1610 A-ACAGGAGGGAAGGCAGAGTATGTG--GGCACAGATGCAGGTAGGTGGG 1564 chr1ptel1M 685675 -AGAGAAGGGAGAAGGAGAGCATGCAA---------TGAATGGCCACATT 685714 - viv vi vi ??ii v --------- v viivi C L2#LINE/L2 1563 TAGATGTGGTGGTGGGAGNNTGTGGAAGTTCTCTTCTGATTGCTTCTATT 1514 chr1ptel1M 685715 TT-TCAGTGAG--AGCGAGTAAGGTTCTCAGGTGAAGGAGAAG 685754 - i-- vi i iv v ii v i C L2#LINE/L2 1513 TTCTCAGTGAAATAGGAAGCAAGGTCATCAGCTGAGAGTGAGG 1471 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 43.71 CpG sites = 186, Kimura (unadjusted) = 45.16 Transitions / transversions = 1.62 (186/115) Gap_init rate = 0.06 (53 / 937), avg. gap size = 3.21 (170 / 53) 186 35.13 3.92 3.25 chr1ptel1M 685840 685992 (314008) L3#LINE/CR1 2954 3107 (992) m_b19s601i19 702 chr1ptel1M 685840 CTAGGTGTCAGGGAGAGACTCGGGCAAGTCACCCACAACAGCCCTGTGGA 685889 i i v vi iv i i ivv v i ii i v i L3#LINE/CR1 2954 CTGGATTTCAGCAAGGCATTTGACAAAGTCTCTCATGATATCCTTGTGGA 3003 chr1ptel1M 685890 TGAGATGATCAAGCTCCTGCTGGA----ACTACAGTGAGCTGACTGACTC 685935 ii ivv iivivv ---- v v v --- i L3#LINE/CR1 3004 CAAGATGGAGAAATATGGGCTGGATGATAGTACAGTTAGGTG---GATTC 3050 chr1ptel1M 685936 AGATCTGATCCAAGGGC-AGAACCATCA-GTGTTCCGAGTAAAGGGTGGT 685983 iv v i iv v i - v v vv - -- v v i v v L3#LINE/CR1 3051 GTAGCTGGTTGAACGACTATACCCAAAAGGTGTT--GATTAATGGATCGA 3098 chr1ptel1M 685984 TGTCCACCT 685992 v L3#LINE/CR1 3099 TGTCAACCT 3107 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 46.68 CpG sites = 24, Kimura (unadjusted) = 47.91 Transitions / transversions = 0.86 (24/28) Gap_init rate = 0.05 (8 / 152), avg. gap size = 1.38 (11 / 8) 411 30.45 7.17 5.75 chr1ptel1M 686247 686469 (313531) L3#LINE/CR1 3872 4097 (2) m_b19s601i20 702 chr1ptel1M 686247 GGCAACTTTCTGCTCAATATGAGAGTAAACTTCCTAACTATTAGAGCTTG 686296 iv v i iivi i v i - L3#LINE/CR1 3872 GGCAGATTTCGGCTCAATATAAGGAAGAACTTTCTAACAATCAGAGCT-G 3920 chr1ptel1M 686297 GCCAA----------------CTTGAAAAGCAATGTGCTCCCCGTCTCTG 686330 v ---------------- i ?i i i i v v L3#LINE/CR1 3921 TCCAAAAATGGAATGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGTCACTG 3970 chr1ptel1M 686331 GGGGTCTTAGAGCCAAGACTAGATGGCAACTTGTAAGTTATTGTTGTTGT 686380 i v vi vi i i i v v vv ---- L3#LINE/CR1 3971 GAGGTGTTCAAGCAGAGGCTGGATGACCACTTGTCAGGGA----TGTTGT 4016 chr1ptel1M 686381 ATGTTGGGGTGCGGGCCCCGGACATGGTAAGGGTTGAACCGATCAATCGC 686430 - vv i v vv vii -- v -- i iiivii i v L3#LINE/CR1 4017 A-GAAGGGATTCCTGCATTGG--ATGGGA--GGTTGGACTAGATGACCTC 4061 chr1ptel1M 686431 TGGGATTGCTTCTTCCCCTTTGGGCTTTCTAGGATTCCA 686469 ii i iv -- vv i i v- iv i L3#LINE/CR1 4062 TAAGGTCCCTTC--CAACTCTGAGA-TTCTGTGATTCTA 4097 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 39.53 CpG sites = 36, Kimura (unadjusted) = 40.35 Transitions / transversions = 1.29 (36/28) Gap_init rate = 0.06 (14 / 222), avg. gap size = 2.07 (29 / 14) 256 27.50 9.09 0.84 chr1ptel1M 689869 689978 (310022) MIRb#SINE/MIR 7 125 (143) m_b19s601i21 703 chr1ptel1M 689869 GGCAAGGGGGTCCACGTGGAAGAATCCCAGGGCCCGGAGTC---CAGACC 689915 iv v v - ii v v i viii --- MIRb#SINE/MIR 7 GGCAGCGTGGTGCA-GTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACC 55 chr1ptel1M 689916 TGG------ACCCCTGCTCTGCTGCTAATTACCCATGTGGCC-TGGGCAA 689958 ------ i v ii v i v ii i - MIRb#SINE/MIR 56 TGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 105 chr1ptel1M 689959 GCCACTTCCTCTCACTGGGC 689978 ii vvi v i MIRb#SINE/MIR 106 GTTACTTAACCTCTCTGAGC 125 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 33.79 CpG sites = 18, Kimura (unadjusted) = 35.24 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.04 (4 / 109), avg. gap size = 2.75 (11 / 4) 487 34.44 7.43 1.76 chr1ptel1M 693189 693726 (306274) L2#LINE/L2 2043 2610 (472) m_b19s601i22 704 chr1ptel1M 693189 GTCTTCCTCCTTCTTGGCCTCTGTCTGCAGCCTTTGACAGTGCCAGTTGC 693238 i v i v i ? -- v v vv iiii ii L2#LINE/L2 2043 GTCCTCATCTTACTTGACCTNT--CAGCAGCATTTGACACAGTTGATCAC 2090 chr1ptel1M 693239 TTCTTGGCCCCCGT---ACTCTCACCTTTCTAGGTTTCCACGACAATCCC 693285 i i -- ii v --- v iv i iv v i v viv v L2#LINE/L2 2091 TCCCT--CCTTCTTGAAACACTTTCTTCACTTGGCTTCCAGGACACCACA 2138 chr1ptel1M 693286 CCCTCCTGGATTTT----TACCTTCCT------TCTTTCTCAGTCTCCTT 693325 i v i---- iv ------ i L2#LINE/L2 2139 CTCTCCTGGTTTTCCTCCTACCTCACTGGCCGCTCCTTCTCAGTCTCCTT 2188 chr1ptel1M 693326 AGC-AGCATTTCATCAGGGTTACACTCCCTAAAACTAGTGGTCCTCTAAC 693374 v -i ivii v vvviiv ivi i ? vv v vi v i i iv L2#LINE/L2 2189 TGCTGGTTCCTCCTCATCTCCCCGACCTCTNAACGTTGGAGTGCCCCAGG 2238 chr1ptel1M 693375 ACTCCCTCTTGAG---TCTTCTCTTTT---TCTAGATTATTTTTCTTGGT 693418 i vv i vi --- i --- v i vvi ii ? L2#LINE/L2 2239 GCTCAGTCCTTGGACCTCTTCTCTTCTCTATCTACACTCACTCCCTNGGT 2288 chr1ptel1M 693419 GATCTCATC-AACTGCAT----CCAATTATCATCTCTCTGCTGATGATTC 693463 - iiiv ----ii v i v v i L2#LINE/L2 2289 GATCTCATCCAGTCTCATGGCTTTAAATACCATCTATATGCTGATGACTC 2338 chr1ptel1M 693464 TCGACTCCTTTTAGACAACCAGAATCTCTTTC---ACCTCCAGACT---- 693506 i i v iiv v vvv i v i i ii --- v ---- L2#LINE/L2 2339 CCAAATTTATATCTCCAGCCCGGACCTCTCCCCTGAACTCCAGACTCGTA 2388 chr1ptel1M 693507 --TCCC-CTGCC-ATTTGACCTCTTGAATTGGAAGTCCCATAGACATCTT 693552 -- v- - i i v iv v v iv i i L2#LINE/L2 2389 TATCCAACTGCCTACTCGACATCTCCACTTGGATGTCTAATAGGCATCTC 2438 chr1ptel1M 693553 CAACATAGCATGTTCCAAACGCAATTAATTATCTTTCCTTCCAAACCT-T 693601 v v i i v vv i vv v i iii -i L2#LINE/L2 2439 AAACTTAACATGTCCAAAACTGAACTCCTGATCTTCCCCCTCAAACCTGC 2488 chr1ptel1M 693602 TCCTCCTTCCCCCCCCCCCTTCCTATTACCCAG-AGCTCTCTCTTCTTCC 693650 iv vvi ii v ii v ?vvii - i --- v i i L2#LINE/L2 2489 TCCTCCCGCAGTCTTCCCCATCTCAGTNAATGGCAACTC---CATCCTTC 2535 chr1ptel1M 693651 CAGACATTGGAGTTCACAGCTTTGCTGTTAGCC--AACTCCTCAGCCTCT 693698 viii vii iiv v i i vv i v --i vvii L2#LINE/L2 2536 CAGTTGCTCAGGCCAAAAACCTTGGAGTCATCCTTGACTCCTCTCTTTCT 2585 chr1ptel1M 693699 CGCAGACACTCCCACCCAAGTCCTATCA 693726 v v - i v i - - L2#LINE/L2 2586 CTCACAC-CCCACATCCAA-TCC-ATCA 2610 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 46.85 CpG sites = 99, Kimura (unadjusted) = 47.95 Transitions / transversions = 1.19 (99/83) Gap_init rate = 0.05 (26 / 537), avg. gap size = 1.92 (50 / 26) 188 31.76 3.49 1.14 chr1ptel1M 693903 693988 (306012) AmnL2-1#LINE/L2 2172 2259 (354) m_b19s601i23 705 chr1ptel1M 693903 TCCAGTAACTCCTTATTACCTCCAGGATCAGGT--AGAGCTCCCTTTGTT 693950 v ii ii vvi i vi -- i ii v i-i AmnL2-1#LINE/ 2172 TCCACTGGCTCCCCATTCATTTCAGGATCCAGTTCAAAATTGCCTTC-CT 2220 chr1ptel1M 693951 TGGTTTTAAAACCCTCTCT-AACCTGCCTCTTTCTACCT 693988 v iv -i i ii vvi AmnL2-1#LINE/ 2221 TGTTTTTAAAACCCTCCATGGACTTGCTCCAGCCTACCT 2259 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 43.64 CpG sites = 18, Kimura (unadjusted) = 43.64 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.04 (3 / 85), avg. gap size = 1.33 (4 / 3) 227 23.08 3.85 0.00 chr1ptel1M 694659 694710 (305290) L2c_3end#LINE/L2 423 476 (2) m_b19s601i24 706 chr1ptel1M 694659 TCCCCAGC--CTTGCACCCAGTAGGTATTTAATTAATGTTTCCTGAATGG 694706 -- v vi iii i v vi i L2c_3end#LINE 423 TCCCCAGCGCCTGGCACATAGTAGGCGCTCAATAAATGTTTGTTGAATGA 472 chr1ptel1M 694707 ATAA 694710 i L2c_3end#LINE 473 ATGA 476 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 25.42 CpG sites = 8, Kimura (unadjusted) = 28.45 Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.02 (1 / 51), avg. gap size = 2.00 (2 / 1) 335 21.36 11.36 0.68 chr1ptel1M 696069 696200 (303800) C MIR1_Amn#SINE/MIR (84) 146 1 m_b19s601i25 707 chr1ptel1M 696069 TTATATAGATGAG-AAACTGAGGCGAACAG---------GACTTGCCCAG 696108 v i - ?v v --------- i C MIR1_Amn#SINE 146 TTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGCCCAA 97 chr1ptel1M 696109 GATCACAGAGCTGGGAAGTGTCTGAGGCCAAATGTGA---TGAGTCTCCC 696155 i ?v ? v? v v v vii ?v? ---iii C MIR1_Amn#SINE 96 GGTCACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAACCCAGGTCTCCC 47 chr1ptel1M 696156 CACTCCAGGTCCGG-GCTCTAACCACTAG-CCTCCCTGGCTGCTCTA 696200 v v vi i - v - v v v - i C MIR1_Amn#SINE 46 GAGTCCCAGTCCAGTGCTCTATCCACTAGACCACACTGCCT-CCCTA 1 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 26.63 CpG sites = 11, Kimura (unadjusted) = 26.63 Transitions / transversions = 0.65 (11/17) Gap_init rate = 0.05 (6 / 131), avg. gap size = 2.67 (16 / 6) 22 0.00 0.00 0.00 chr1ptel1M 697681 697704 (302296) (AT)n#Simple_repeat 1 24 (0) m_b19s252i9 708 chr1ptel1M 697681 ATATATATATATATATATATATAT 697704 (AT)n#Simple_ 1 ATATATATATATATATATATATAT 24 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 358 34.94 3.35 1.41 chr1ptel1M 698213 698421 (301579) C L1ME4c_3end#LINE/L1 (275) 555 343 m_b19s551i2 709 chr1ptel1M 698213 ATAATATTCTACAACATTCATGAACCACAATTTACTTAGCCGTTCTACCA 698262 i ivivi ?v v i i i iv i C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chr1ptel1M 698263 CTGATGCACAGCCACCCAGTTTCCAATTTCTGGCCACTACACAAAGGGCT 698312 i v v vii vviv i v i i i v v iv C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCT 456 chr1ptel1M 698313 GCCACAGACATCTGTGCACACCTGGGTCCCTTTCCCTTCTTT---ATC-C 698358 v iii vi ii iv i --- i i --- i-i C L1ME4c_3end#L 455 GCAATGAACATCTTCGTGCATATAG---CTTTTTCCTTCTTTTGAATTAT 409 chr1ptel1M 698359 CTCTCTGGAATATGGAACC---AGTAGAGCGGCCGGACCAAAGGGGATGC 698405 i ii i i vivvv --- i iivi i ii v v C L1ME4c_3end#L 408 TTCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGA 359 chr1ptel1M 698406 AGAGTTTGCTGGCTCT 698421 v v vv C L1ME4c_3end#L 358 ACATTTTTATGGCTCT 343 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 47.51 CpG sites = 43, Kimura (unadjusted) = 49.47 Transitions / transversions = 1.48 (43/29) Gap_init rate = 0.03 (6 / 208), avg. gap size = 1.67 (10 / 6) 256 34.62 9.23 0.00 chr1ptel1M 699779 699908 (300092) MIRc#SINE/MIR 13 154 (114) m_b19s601i26 710 chr1ptel1M 699779 GCACAGCGCAGAGGGCACCGGGCTTGGAGCGAGGGAAACCCGGATTCAAG 699828 ii i v i i i i iv i i i i i MIRc#SINE/MIR 13 GTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAG 62 chr1ptel1M 699829 TCTTGCCACAGACAGTTAGCATCTGGCTGGCCCT------TCCACGCA-- 699870 ii v v v v v vi v vv i i ------vi vi -- MIRc#SINE/MIR 63 TCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAAC 112 chr1ptel1M 699871 ----CGGTGCCCCAATTCCTTCTTCTATAAAAGGGAGCTGAT 699908 ---- v v i i i i v i v i v i MIRc#SINE/MIR 113 CTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAAT 154 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 45.45 CpG sites = 27, Kimura (unadjusted) = 48.46 Transitions / transversions = 1.50 (27/18) Gap_init rate = 0.02 (3 / 129), avg. gap size = 4.00 (12 / 3) 180 20.00 0.00 0.00 chr1ptel1M 700125 700159 (299841) C L2c_3end#LINE/L2 (79) 399 365 m_b19s601i27 711 chr1ptel1M 700125 CCTTGACCTCAAGGAGCTTGCAGTGCAGTGGGGGA 700159 i v ii vi i C L2c_3end#LINE 399 CCCTGCCCTCAAGGAGCTCACAGTCTAGTGGAGGA 365 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 24.03 CpG sites = 5, Kimura (unadjusted) = 24.03 Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 384 36.18 5.41 1.96 chr1ptel1M 700249 700544 (299456) C L3#LINE/CR1 (1571) 2528 2223 m_b19s601i28 712 chr1ptel1M 700249 TCTCCCTAC--ATTTGGGGATTCACCTCCTTGTTA------TCTATCCCA 700290 ii -- i v v vi i v ------ i i i i C L3#LINE/CR1 2528 TCTCCTCACCTATCTTGGGCTTCAATTCCCTCTTAACGATGTTTGTTCTA 2479 chr1ptel1M 700291 C--TTTCTAGGCCAAACAGCATTCCCCCTGGCATTAAGAACAGAATTAAA 700338 -- i v ii v v i i ii vvi ii i vi C L3#LINE/CR1 2478 CCCTTTCCAGTCTGAAGATCATTCTCCTTGATAGAGAAGACGGAAGCAAA 2429 chr1ptel1M 700339 AATAGGAGCTGAGCACCTCTGACTCCTCTCTGCCATCTGTT---ATTATC 700385 - i i vi vi i i --- iv C L3#LINE/CR1 2428 A-TAGGAGTTGAGTAGTTCTGCTTTCTCTCTGTCATCTGTTAACATTACG 2380 chr1ptel1M 700386 CCATCAGCCATGAGCAATTCATCCTGCCCTTGTTCAATATTCTTTTCCAT 700435 v vii iiv-iv i ?i - -- v iii iii C L3#LINE/CR1 2379 CCATCTGCCCCAAGCAGCG-GGCCTGTCNCT-TTC--TTTTTCCTTCTGC 2334 chr1ptel1M 700436 GGTAAAGCTTTCCTTTCTTAAGCAGCCCTTTTGTGGTCCTG---GTTTCC 700482 vvii - v vv vvv vvi?i v v---i ii C L3#LINE/CR1 2333 TCCGAA-CATAGCTTTGAAAAGCCTTNTTTTTGTTGTCCTTAGCATTTTT 2285 chr1ptel1M 700483 TCGTCCCTGACTCAATCCCCTTGAGATTTCAGTCCTCCTGACGCTCCTCC 700532 iv v vv v iii vi ivi ii i i i i vi i C L3#LINE/CR1 2284 TTTTGCAAGCCTCAGCTCATTCTGGGCTTTAGCCTTCCTGACACTATTCT 2235 chr1ptel1M 700533 TCCGAGATTGTG 700544 v ii v C L3#LINE/CR1 2234 TACAGGCTTGTG 2223 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 49.71 CpG sites = 65, Kimura (unadjusted) = 52.75 Transitions / transversions = 1.62 (65/40) Gap_init rate = 0.04 (11 / 295), avg. gap size = 2.00 (22 / 11) 419 30.44 2.82 2.82 chr1ptel1M 700811 700952 (299048) C L3#LINE/CR1 (2184) 1915 1774 m_b19s601i29 712 chr1ptel1M 700811 CTCGGCTATTA---GTGCTGAGATTGCATTAGGGTCACTTTCCCGAAATA 700857 i ---iiv i vi ---- v i vv vi C L3#LINE/CR1 1915 CTTGGCTATTACGAACTCTAAGATGACAT----GGCACTTTCTCCCAAGG 1870 chr1ptel1M 700858 TGCCTAT-AATTTCTACTTCAGCAGCCAGCTGCCCTTTGCTGGTCAGAAT 700906 v -i i i v i i vii i i C L3#LINE/CR1 1869 TTCCTATCGACTTCCACTTCACCAACCAGTTCTTCCTTGTTGGTCAGAAT 1820 chr1ptel1M 700907 TAAATTCAATCTAGAAATTCCTCCCACTGTTTCCTCCATCGTTTAA 700952 i i ivv v i i i ii i i i v i i C L3#LINE/CR1 1819 TAAGTCCAGAGTAGCAGTTCCCCTCGTTGCTTCCTCTACCTTCTGA 1774 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 38.73 CpG sites = 29, Kimura (unadjusted) = 41.35 Transitions / transversions = 2.23 (29/13) Gap_init rate = 0.04 (6 / 141), avg. gap size = 1.33 (8 / 6) 487 20.61 4.58 0.00 chr1ptel1M 700975 701105 (298895) Charlie4a#DNA/hAT-Charlie 336 472 (36) m_b19s502i1 713 chr1ptel1M 700975 TCGTGAACTTGGTTTTGTAATATTTTCTTGACTGTATTACAATATAATAG 701024 iii i ? v vv i v v Charlie4a#DNA 336 TCACAAATTTGNTTTTTTAATATTTTGATAACTGTATTTCAATATAATTG 385 chr1ptel1M 701025 GTTTCCTTTCTAATCCTACATATTTTA----AGG-ACTTAAAAACATGAT 701069 v ii ---- v - i v Charlie4a#DNA 386 GTTTCCTTTGTAATCCTATGTATTTTATTTTATGCATTTAAAAACATTAT 435 chr1ptel1M 701070 TCAGAGAAGTGAT-TATAGACTTCGCCACATTATTAA 701105 v v i -i i i v i iii Charlie4a#DNA 436 TCTGAGAAGGGGTCCATAGGCTTCACCAGACTGCCAA 472 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 24.72 CpG sites = 16, Kimura (unadjusted) = 24.72 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.02 (3 / 130), avg. gap size = 2.00 (6 / 3) 452 33.72 8.61 1.53 chr1ptel1M 701599 701842 (298158) C L3#LINE/CR1 (2315) 1784 1524 m_b19s601i30 712 chr1ptel1M 701599 CCACATTTTAAAGGATGAAATT-----TAAGGAAAATCACAGA---TGTC 701640 i v i i ii -----i v i - --- i C L3#LINE/CR1 1784 CTACCTTCTGAGAGATGAAATTGTCAGCAAGGCAAGTCA-AGAATTTATC 1736 chr1ptel1M 701641 ATACTTGTTCGGCTTTTAACAGAA---AACT-CTGGTAGATAGTTGAAAA 701686 v -- i v i ? ---i - ii i ivii i v C L3#LINE/CR1 1735 AGA--TGCTCTGCTTTTAGCNGAATGAGACTTCCAGCAGATGTCCGGATA 1688 chr1ptel1M 701687 ACTAAAGTTTCTGATAACTACTATACCATGCCTCTGTATTGTGTCTGTCA 701736 ii i ii iv v i? i v iiiivv i - C L3#LINE/CR1 1687 GTTGAAGTCCCCCATCACTACTGNATCTTGCCTCTGTGCCAGTTTTGT-A 1639 chr1ptel1M 701737 AGTTTTCT----AAAGACCTAACTAT-TCTTCCTTCTGCCCAAGTGGTCT 701781 vi v v ---- vvii v i - i v v ii i C L3#LINE/CR1 1638 ATCTGTATCAGGAAAGCATCATCCATNTCCTCCATCTGGCCGGGCGGTCT 1589 chr1ptel1M 701782 ACAGCGAACTCTCATGACAATGGTGTTTCTGTT----TGCCCCTTGATCG 701827 ii iiv i ii i iviii ---- vi i v v C L3#LINE/CR1 1588 GTAGTATACTCCCACAACGATATCACTTCTGTTTCTCTCTCCTTTTATCC 1539 chr1ptel1M 701828 TTATCCAAATACACT 701842 i i i v C L3#LINE/CR1 1538 TCACCCAAATGCTCT 1524 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 45.31 CpG sites = 56, Kimura (unadjusted) = 48.75 Transitions / transversions = 2.24 (56/25) Gap_init rate = 0.05 (11 / 243), avg. gap size = 2.27 (25 / 11) 247 33.79 6.63 2.78 chr1ptel1M 702929 703275 (296725) C L1MC4a_3end#LINE/L1 (2065) 564 205 m_b19s551i3 714 chr1ptel1M 702929 TTTCTTACAGC---ACAG-ATTCCATATACTTGGGGA-GCACCATTGTGT 702973 i --- i - i - i-- v - i v v C L1MC4a_3end#L 564 TTTTTTACAGCTGCATAGTACTCCAT-TG--TGTGGATGTACCATAGTTT 518 chr1ptel1M 702974 G----GCCAGTCCCTAGTGAATGGGCCTC------GTTGCCATTTTTTTT 703013 i----i ? i ivi ?? v i------ v v v - C L1MC4a_3end#L 517 ATTCAACCANTCTCCTATNNATGGGCATTTAGGTTGTTTCCAATATTTT- 469 chr1ptel1M 703014 GACTATCACAAAAAGTGCT---ATGAATATTTTTATATATTTAGGCACTT 703060 -i v i v i --- vii i ii v - v? i C L1MC4a_3end#L 468 -GCAATTACAAACAATGCTGCAATGAATAACCTTGTGCATAT-GTNATTT 421 chr1ptel1M 703061 TCTTCTTATC--AGTTGCCTCTTTGGTATATAAGCCCAGTAACAGAATCT 703108 v v v i i-- v iv ii vi v vv i v iii i iv C L1MC4a_3end#L 420 TGTACATGTTGGAGGTGTATCTTCAGGGTAAATTCCTAGAAGTGGGATTG 371 chr1ptel1M 703109 ATGAATTTAACGGCA--TGGATTTTTAGTTACTTTATTTGCATAATTCTA 703156 v ii iv v i -- v v v --- i v - v v i C L1MC4a_3end#L 370 CTGGGTCAAAGGGTAAATGCATATGTAGTT---TTGTTAG-ATATTGCCA 325 chr1ptel1M 703157 AATTCCCTTTCAAAACAATCATGTGAATTCACAGCTCCACCAACAATGCA 703206 i i ? vii ii iiv ? ii vii i i C L1MC4a_3end#L 324 AATTCCCCTCCANAAGGGTTGTACCANTTTGCATTCCCACCAGCAATGTA 275 chr1ptel1M 703207 GTAGTGTATCTATCTTCCCACCACTTCTCCAACATTAACTATT-TCAATC 703255 vv v ii i i i vi i v vvivv i - v C L1MC4a_3end#L 274 TGAGAGTGCCTGTTTCCCCACAGCCTCGCCAACAGAGTGTGTTGTCAAAC 225 chr1ptel1M 703256 TTTGTCACCTTTACCAATTT 703275 vvv ii i i C L1MC4a_3end#L 224 TTTTGAATTTTTGCCAATCT 205 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 47.69 CpG sites = 65, Kimura (unadjusted) = 47.69 Transitions / transversions = 1.33 (65/49) Gap_init rate = 0.05 (19 / 346), avg. gap size = 1.74 (33 / 19) 318 35.16 3.23 2.13 chr1ptel1M 702997 703275 (296725) C L1ME4a_3end#LINE/L1 (382) 489 208 m_b19s551i4 714 chr1ptel1M 702997 TCGTTGCCATTTTTTTTGACTATCACAAAAAGTGCT---ATGAATATTTT 703043 i v v i--i i i v i --- i ii C L1ME4a_3end#L 489 TTGTTTCCAATTTTTC--GCTATTATAAATAATGCTGCGATGAACATCCT 442 chr1ptel1M 703044 TATATATTTAGGCACTTTCTTCTTATC---AGTTGCCTCTTTGGTATATA 703090 i i vv v--- v ? vi ---ii iii i i v v C L1ME4a_3end#L 441 TGTACATAAAT---CTTTGTNCACATCTCTGATTATTTCCTTAGGATAAA 395 chr1ptel1M 703091 AGCCCAGTAACAGAATCTATGAATTTAACGGCATGGA--TTTTTAGTTAC 703138 vv i v iii ivv ii iv v i ? -- iv-i C L1ME4a_3end#L 394 TTCCTAGAAGTGGAATTACTGGGTCAAAGGGTATGNACATTTTTAAG-GC 346 chr1ptel1M 703139 TTTATTTGCATAATTCTAAATTCCCTTTCAAAACAATCATGTGAATTCAC 703188 vvv i v v i v i i i vii ii iiv i C L1ME4a_3end#L 345 TTTTGATACATATTGCCAAATTGCCCTCCAGAAAGGTTGTACCAATTTAC 296 chr1ptel1M 703189 AGCTCCACCAACAATGCAGTAGTGTATCTATCTTCCCACCACTTCTCCAA 703238 vii i i i vv v ii ii i i? vv i v C L1ME4a_3end#L 295 ACTCCCACCAGCAGTGTATGAGAGTGCCCGTTTCNCCACACCCTCGCCAA 246 chr1ptel1M 703239 CATTAACTATT-TCAATCTTTGTCACCTTTACCAATTT 703275 i iiv - vvv i i C L1ME4a_3end#L 245 CACTGGGTATTATCAATCTTTTAAATCTTTGCCAATTT 208 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 48.97 CpG sites = 59, Kimura (unadjusted) = 50.68 Transitions / transversions = 1.59 (59/37) Gap_init rate = 0.04 (10 / 278), avg. gap size = 1.50 (15 / 10) 426 25.88 3.91 6.40 chr1ptel1M 703360 703487 (296513) MIRc#SINE/MIR 24 148 (120) m_b20s601i0 715 chr1ptel1M 703360 AGAACGTCAGACCTGAGGTCAGGAAGACTCATCATCATGAGTTCAAATCC 703409 i iiii i ii i-------- i i i MIRc#SINE/MIR 24 AGAGCACTGGACTTGGAGTCAGGAAGACC--------TGGGTTCGAGTCC 65 chr1ptel1M 703410 AGTCTCAGACACT----AGCTATTTGACTCTGGACAAGTCATTTAA-TTC 703454 v v v v ---- i v ii i i -i MIRc#SINE/MIR 66 CGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 chr1ptel1M 703455 GGTTTGCCTCCATTTCCTCATCTGTAAAATAAG 703487 vv vv vi ii MIRc#SINE/MIR 116 TCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.65 CpG sites = 21, Kimura (unadjusted) = 32.96 Transitions / transversions = 2.10 (21/10) Gap_init rate = 0.08 (10 / 127), avg. gap size = 1.30 (13 / 10) 327 32.98 5.85 5.39 chr1ptel1M 703592 704514 (295486) C L1M5_orf2#LINE/L1 (1141) 2153 1227 m_b20s551i2 714 chr1ptel1M 703592 AGTATTTTTGCTAATTCTTCACAATTTTCTAAGGCAACTTTCATTGCCA- 703640 v ? ivi i?vi v vv? vv - i - C L1M5_orf2#LIN 2153 AGTTTNTTTGTAGATTCTTTNGGATTTTCTACGTANACAATCAT-GTCAT 2105 chr1ptel1M 703641 --GCAAATAGGAATAGTTTTCTGTTCTCATGACCTATCTTTGCACTTTTA 703688 -- i i?i i v v ii v vv v iii i v C L1M5_orf2#LIN 2104 CTGCGAATAANGACAGTTTTATTTCTTCCTTTCCAATCTTTATGCCTTTT 2055 chr1ptel1M 703689 ATTTCTTTCTTTTGTCTCATTATATT-GCTAGGGTCTCCAGAACCATATG 703737 i i i i ii i - ii v v i v C L1M5_orf2#LIN 2054 ATTTCTTTTTCTTGCCTTATTGCACTGGCTAGGACCTCCAGTACAATGTT 2005 chr1ptel1M 703738 AAATAATAATGGAGAAAGTAAGCATCTTTGCTTTTCTTCTGAATTTATTA 703787 i iv i v ? iiii i ii vi i i vi vvi C L1M5_orf2#LIN 2004 GAATAGAAGTGGTGANAGCGGACATCCTTGTCTTGTTCCCGATCTTAGGG 1955 chr1ptel1M 703788 GAAAAAATTCTAATGTATCTCTATCACAGATGACACTTGATTTTAATTAT 703837 i iv? ii i ? v v i i viv ------- v ?ii i C L1M5_orf2#LIN 1954 GGAAAGCNTTCAGTNTTTCACCATTAAGTA-------TGATGTTNGCTGT 1912 chr1ptel1M 703838 ATATATATATATATAAATATATATAATATGCATATGTTTTAAGGGTCTCT 703887 vi --- v vii i iiviv v --- vi---- i ------ C L1M5_orf2#LIN 1911 AGGT---TTTTCGTAGATGCCCTTTAT---CAGG----TTGAGG------ 1878 chr1ptel1M 703888 TTGAAATCCC--TCTATATCTACACTTGT--AGGGATGTTAGTATAAATG 703933 --- i i -- vi -ii i-- i v v vi i C L1M5_orf2#LIN 1877 ---AAGTTCCCTTCTATTCCTA-GTTTGCTGAGAGTTTTTATCATGAATG 1832 chr1ptel1M 703934 ACCATTGTACTTTGTCAAAGGTTTTTCCCACA--TATTGAGATAATCATG 703981 ivii v i v i i ii -- i i C L1M5_orf2#LIN 1831 GGTGTTGAATTTTGTCAAATGCTTTTTCTGCATCTATTGAGATGATCATA 1782 chr1ptel1M 703982 GGATTTTTTTGTTTT-TGCTTTTGATAT----AATTATGCTGATTG-TTT 704025 v i vi - v v i ---- iii - C L1M5_orf2#LIN 1781 TGATTTTTCTCCTTTATTCTGTTAATATGGTGAATTACATTGATTGATTT 1732 chr1ptel1M 704026 TCCAACG----------CTTGTGTCCTTGGTATACATCTGACTTAGTCAT 704065 v i ---------- ii i i v v i iv i C L1M5_orf2#LIN 1731 TCGAATGTTAAACCAACCTTGCATTCCTGGGATAAACCCCACTTGGTCAT 1682 chr1ptel1M 704066 GATGAATGATTTCTTGGAGGAATCATTAG--TCTGTGTGATAGAGTTTTA 704113 v v iii vv viv iii i -- vi v v ivi i C L1M5_orf2#LIN 1681 GATGTATTATCCTTTTTATATATTGCTGGATTCGATTTGCTAATATTTTG 1632 chr1ptel1M 704114 TTTAAAATTTTTGAATCTATATTCATTGATAATATTGGTCTATATATTGG 704163 ? ii v i viivi i vv -- C L1M5_orf2#LIN 1631 TTNAGGATTTTTGCATCTATGTTCATGAGGGATATTGGTCTGTAATTT-- 1584 chr1ptel1M 704164 TCCATTTTT------TCTTT-TCATGCTTTAG-ATC-----TATATTTGT 704200 iv i ------ - ?v i i - -----? ii v i C L1M5_orf2#LIN 1583 TCTTTTCTTGTAATGTCTTTGTCNGGTTTTGGTATCAGGGTNATGCTGGC 1534 chr1ptel1M 704201 CCCATAAAAGAAATCTGGTAGGATTCTTTCTTTCTCACTTTTTGAGAATA 704250 i vi i iv v vi ii i vv ivi v C L1M5_orf2#LIN 1533 CTCATAAAATGAGTTGGGAAGTGTTCCCTCTTTTTCTATTTTCTGGAAGA 1484 chr1ptel1M 704251 ATTTGTATAATGCAGGTACTAAATGTTCTTTGAAAGTTTGAAACTATT-- 704298 i i viiv i vv v i i v iv vv -- C L1M5_orf2#LIN 1483 GTTTGTGTAAGATTGGTATTATTTCTTCCTTAAATGTTTGGTAGAATTCA 1434 chr1ptel1M 704299 -CTATGCTTCTGTCAGGACCAGGAATTTTAATTGGTGACAGGAATGGTAG 704347 - vi vvv ii v i v i -v v --- - -- C L1M5_orf2#LIN 1433 CCAGTGAAGCCATCTGGGCCTGGAGTTTT-CTTTGTG---GGAA-GGT-- 1391 chr1ptel1M 704348 TGGTGATAATTCCTTTACAGTTAGTTAAATTTCCTTTTATTGGAC-TGGA 704396 --- vv ----- --- i v -- v i i- i i C L1M5_orf2#LIN 1390 ---TTTTAA-----TTACA---AATTCAATTTC--TTTAATAGATATAGG 1354 chr1ptel1M 704397 TCGCTT---ATTATCTCTTT-GTCTTCTATTGGGTTGAGAATTGTATATT 704442 v vv --- v v -v v?i ii v vi v v?v i i C L1M5_orf2#LIN 1353 GCTATTCAGATTTTCTATTTCTTCTTGNGTCAGTTTTGGTAANTTGTGTT 1304 chr1ptel1M 704443 TTCGAAGGTGTTT---TATTTCTTTTGTGTTCT--GTTTTGTTAGCATAT 704487 iv vi ---i v i iv ? --iv i i v C L1M5_orf2#LIN 1303 TTTCAAGGAATTTGTCCATTTCATCTAAGTTNTCAAATTTATTGGCATAA 1254 chr1ptel1M 704488 CACTGTGCATAATAGATTTTTTTTCTC 704514 vii v vvi i v v C L1M5_orf2#LIN 1253 AGTTGTTCATAATATTCTCTTATTATC 1227 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 44.98 CpG sites = 165, Kimura (unadjusted) = 45.91 Transitions / transversions = 1.34 (165/123) Gap_init rate = 0.08 (72 / 922), avg. gap size = 1.44 (104 / 72) 466 34.15 5.65 4.03 chr1ptel1M 703592 704299 (295701) C L1M1_orf2#LINE/L1 (1141) 2153 1435 m_b20s551i1 714 chr1ptel1M 703592 AGTATTTTTGCTAATTCTTCACAATTTTCTAAGGC--AACTTTCATTGCC 703639 v ? ivi v i viv i ivv-- iv ivi iii C L1M1_orf2#LIN 2153 AGTTTTTTNGTGGAGTCTTTAGGTTTTTCCAAATATAAGATCATATCATC 2104 chr1ptel1M 703640 AGCAAATAGGAATAGTTTTCTGTTCTCATGACCTATCTTTGCACTTTTAA 703689 v i i i i vviv ii v vv v i vviii ii v C L1M1_orf2#LIN 2103 TGCAAACAAGGATAATTTGACTTCTTCCTTTCCAATTTGGATGCCCTTTA 2054 chr1ptel1M 703690 TTTCTTTCTTTTGTCTCATTA-TATTGCTAGGGTCTCCAGAACCATATGA 703738 i v i- v v iii v i i vi C L1M1_orf2#LIN 2053 TTTCTTTCTCTTGTCTGATTGCTCTAGCTAGGACTTCCAGTACTATGTTG 2004 chr1ptel1M 703739 AATAATAATGGAGAAAGTAAGCATCTTTGCTTTTCTTCTGAATTTATTAG 703788 i i v ii i iiv vi i v vi vvi C L1M1_orf2#LIN 2003 AATAACAGTGGTGAAAGTGGGCATCCTTGTCGTGTTCCAGATCTTAGAGG 1954 chr1ptel1M 703789 AAAAAATTCTAATGTATCTCTATCACAG-ATGACACTTGATTTTAATTAT 703837 iiv ii i v v i i i- - i ------- ii i C L1M1_orf2#LIN 1953 AAAGGCTTTCAGTTTTTCCCCATT-CAGTATGATACT-------AGCTGT 1912 chr1ptel1M 703838 ATATATAT-ATATATAAATATATATAATATGCATATGTTTTAAGGGTCTC 703886 ivi v i -i iiv v ------ --- ---ii v v C L1M1_orf2#LIN 1911 GGGTCTGTCGTATATGGCTTT------TAT---TATGTT---GAGGTATG 1874 chr1ptel1M 703887 TTTGAAATCCCTCTATATCTACACTTGT-AGGGATGTTAGTATAAATGAC 703935 ------ i i i vvi v - v v vi i v iv C L1M1_orf2#LIN 1873 TT------CCTTCTATACCCAGTTTTTTGAGGGTTTTTATCATGAAGGGA 1830 chr1ptel1M 703936 CATTGTACTTTGTCAAAGGTTTTTCCCACAT--ATTGAGATAATCATGGG 703983 ii v i i v i i vi -- i i iv C L1M1_orf2#LIN 1829 TGTTGAATTTTATCAAATGCTTTTTCAGCATCAATTGAAATGATCATATG 1780 chr1ptel1M 703984 ATTTTT-TTGTTTTTGCTTTTGATATAAT----TATGCTGATTGTTTT-- 704026 i - iv iv v v i ----i iii v -- C L1M1_orf2#LIN 1779 GTTTTTGTCCTTCATTCTGTTGATATGATGTATCACATTGATTGATTTGC 1730 chr1ptel1M 704027 ----------CCAACGCTTGTGTCCTTGGTATACATCTGACTTAGTCATG 704066 ---------- v - ii i? v v iv i C L1M1_orf2#LIN 1729 GTATGTTGAACCATC-CTTGCATCCCNGGGATAAATCCCACTTGGTCATG 1681 chr1ptel1M 704067 ATGAATGATTTCTTGGAGGAATCATT--AGTCTGTGTGATAGAGTTTTAT 704114 i i vi v v ii -- v v v v vi i C L1M1_orf2#LIN 1680 ATGAATGATCTTTTTAATGTATTGTTGAATTCGGTTTGCTAGTATTTTGT 1631 chr1ptel1M 704115 TTAAAATTTTTGAATCTATATTCATTGATAATATTGGTCTATATATTGGT 704164 v ii v v iiivi i i vv -- C L1M1_orf2#LIN 1630 TGAGGATTTTTGCATCAATATTCATCAGAGATATTGGCCTGTAGTTT--T 1583 chr1ptel1M 704165 CCATTTTT------TCTTTTCATGCTTTAGATCT-------ATATTTGTC 704201 iv ------ viv v v i v ------- i v i C L1M1_orf2#LIN 1582 CTTTTTTTGATGTGTCTTTGTCTGGTTTTGGTATCAGGGTAATACTGGCC 1533 chr1ptel1M 704202 CCATAAAAGAAATCTGGTAGGATTCTTTCTTTCTCACTTTTTGAGAATAA 704251 i i i vi i i v v ii i i vv vi i C L1M1_orf2#LIN 1532 TCGTAGAATGAGTTTGGAAGTATTCCCTCCTCCTCTATTTTTCGGAATAG 1483 chr1ptel1M 704252 TTTGTATAATGCAGGTACTAAATGTTCTTTGAAAGTTTGAAACTATTC 704299 vi iviiv i iv v i v iv vv C L1M1_orf2#LIN 1482 TTTGAGTAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAATTC 1435 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 46.29 CpG sites = 134, Kimura (unadjusted) = 47.44 Transitions / transversions = 1.37 (134/98) Gap_init rate = 0.06 (42 / 707), avg. gap size = 1.64 (69 / 42) 18 15.09 5.45 3.57 chr1ptel1M 704533 704587 (295413) (AATT)n#Simple_repeat 1 56 (0) m_b20s252i0 716 chr1ptel1M 704533 AAATAATTATAATCGTTAATTAATTGATTGATTAA-TAATTAA--AAATA 704579 v - v vi i i - -- v (AATT)n#Simpl 1 AATTAATTA-ATTAATTAATTAATTAATTAATTAATTAATTAATTAATTA 49 chr1ptel1M 704580 ATTATATT 704587 - (AATT)n#Simpl 50 ATTA-ATT 56 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.07 (4 / 54), avg. gap size = 1.25 (5 / 4) 181 22.45 16.33 0.00 chr1ptel1M 705949 705997 (294003) L3b_3end#LINE/CR1 557 613 (593) m_b20s601i1 717 chr1ptel1M 705949 CTCAATGTGAGTTCACAG--------GCCTCCCAGAGAAGCTGAGGCGAC 705990 i ivi -------- v v i i i v i L3b_3end#LINE 557 CTCAATATGAGTCAGCAGTGCGACGCGGCTGCCAAAAAAGCTAATGCGAT 606 chr1ptel1M 705991 CTTGGGC 705997 L3b_3end#LINE 607 CTTGGGC 613 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.35 CpG sites = 7, Kimura (unadjusted) = 27.35 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.02 (1 / 48), avg. gap size = 8.00 (8 / 1) 198 21.74 2.17 0.00 chr1ptel1M 706048 706093 (293907) C MIR#SINE/MIR (139) 123 77 m_b20s601i2 718 chr1ptel1M 706048 CTGAAGCG-ATCGGGGTTAAGTGACTTGGCCAGGGTCACAGAGCCAG 706093 i i- vv i i v i v i C MIR#SINE/MIR 123 CTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAG 77 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.15 CpG sites = 6, Kimura (unadjusted) = 26.15 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1) 205 14.29 0.00 0.00 chr1ptel1M 706059 706093 (293907) C MIRc#SINE/MIR (153) 115 81 m_b20s601i3 718 chr1ptel1M 706059 GGGGTTAAGTGACTTGGCCAGGGTCACAGAGCCAG 706093 i v i v i C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG 81 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 16.01 CpG sites = 3, Kimura (unadjusted) = 16.01 Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 31 22.47 0.00 3.53 chr1ptel1M 708807 708894 (291106) (CCCCGCT)n#Simple_repeat 1 85 (0) m_b20s252i1 719 chr1ptel1M 708807 CCCCACTCCCAGACACCCCGCTCCCTGGCTCCCAGATGCCCCACTCCCGG 708856 i v - v -v v v - i v (CCCCGCT)n#Si 1 CCCCGCTCCCCG-CTCCCCGCTCCC-CGCTCCCCGCT-CCCCGCTCCCCG 47 chr1ptel1M 708857 CGCCCGGCTCCCTGCTCCCCGGCACCCACTCCCCACTC 708894 v v i viv i i (CCCCGCT)n#Si 48 CTCCCCGCTCCCCGCTCCCCGCTCCCCGCTCCCCGCTC 85 Matrix = Unknown Transitions / transversions = 0.60 (6/10) Gap_init rate = 0.03 (3 / 87), avg. gap size = 1.00 (3 / 3) 12 31.98 1.45 2.94 chr1ptel1M 709652 709720 (290280) (GAGG)n#Simple_repeat 1 68 (0) m_b20s252i2 720 chr1ptel1M 709652 GAGAGAGGGCAGGGAGGGAGGCCCGGGCCAAAGAGATGG-GGGTGGGCTT 709700 i - -vv vvii i v - v vvv (GAGG)n#Simpl 1 GAGGGAGGG-AGGGAGGGAGG-GAGGGAGGGAGGGAGGGAGGGAGGGAGG 48 chr1ptel1M 709701 GAAGGGGAGAGTGAGGGAGG 709720 i i i v (GAGG)n#Simpl 49 GAGGGAGGGAGGGAGGGAGG 68 Matrix = Unknown Transitions / transversions = 0.70 (7/10) Gap_init rate = 0.04 (3 / 68), avg. gap size = 1.00 (3 / 3) 88 5.19 0.00 4.76 chr1ptel1M 709961 710092 (289908) (TCTCTCTG)n#Simple_repeat 1 126 (0) c_b20s251i0 721 chr1ptel1M 709961 TCTCTCTGTCTCTGTCTCTCTCTCTGTCTCTCTGTCTCTCTGTCTCTCTC 710010 -- v -- (TCTCTCTG)n#S 1 TCTCTCTGTCTC--TCTGTCTCTCTGTCTCTCTGTCTCTCTG--TCTCTC 46 chr1ptel1M 710011 TGTCTCTCTGTCTCTCTCTCTCTCTGTCTCTCTCTGTCTCTCTGTCTCTC 710060 v -- (TCTCTCTG)n#S 47 TGTCTCTCTGTCTCTCTGTCTCTCTG--TCTCTCTGTCTCTCTGTCTCTC 94 chr1ptel1M 710061 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 710092 v v v v (TCTCTCTG)n#S 95 TGTCTCTCTGTCTCTCTGTCTCTCTGTCTCTC 126 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.05 (6 / 131), avg. gap size = 1.00 (6 / 6) 38 0.00 0.00 0.00 chr1ptel1M 710093 710134 (289866) (AC)n#Simple_repeat 1 42 (0) m_b20s252i3 722 chr1ptel1M 710093 ACACACACACACACACACACACACACACACACACACACACAC 710134 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACAC 42 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 192 28.32 0.00 10.67 chr1ptel1M 713543 713625 (286375) C MIR3#SINE/MIR (103) 105 31 m_b20s601i4 723 chr1ptel1M 713543 AGTGGCCTTCATCCCGGGTCTCAGCAGCCAGGTGCCTCAGAGAGAGGGCT 713592 i i v -- vi v - ? ----- i v iv i i C MIR3#SINE/MIR 105 AGTGACTTGC--CCAAGGTCACA-CAGCNAG-----TTAGTGGCAGAGCC 64 chr1ptel1M 713593 GGGTCTAAAGTCAAGGAGTCCTGACTTCCAATC 713625 v i ii v vv i i C MIR3#SINE/MIR 63 GGGACTAGAACCCAGGTCTCCTGACTCCCAGTC 31 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.34 CpG sites = 12, Kimura (unadjusted) = 36.49 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.10 (8 / 82), avg. gap size = 1.00 (8 / 8) 495 32.19 2.05 0.00 chr1ptel1M 713566 713711 (286289) MIRc#SINE/MIR 5 153 (115) m_b20s601i5 724 chr1ptel1M 713566 GCAGCCAGGTGCCTCAGAGAGAGGGCTGGGTCTAAAGTCAAGGAGTCCTG 713615 ivv vvii i vi iii ii i i v MIRc#SINE/MIR 5 GCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTG 54 chr1ptel1M 713616 ACTTCCAATCTAGCCTCAAACACTTATTGGCTGAGTGACCCTGGGCAAGC 713665 iv v i iv v viv i i v i i MIRc#SINE/MIR 55 GGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGT 104 chr1ptel1M 713666 TACTT---CTTTGTCTTCCTCGGTTTCCTTAAATGTAAAATGGAAGTGA 713711 i --- i v vvv i i vv iii i MIRc#SINE/MIR 105 CACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAA 153 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.58 CpG sites = 28, Kimura (unadjusted) = 43.58 Transitions / transversions = 1.47 (28/19) Gap_init rate = 0.01 (1 / 145), avg. gap size = 3.00 (3 / 1) 433 27.02 5.56 1.79 chr1ptel1M 713574 713735 (286265) MIR3#SINE/MIR 9 176 (32) m_b20s601i6 724 chr1ptel1M 713574 GTGCCTCAG-AGAGAGGGCTGGGTCTAA-AGTCAAGGAGTCCTGACTTCC 713621 v v - i vv v ii- - v iv i MIR3#SINE/MIR 9 GTGGCTGAGCAGAGAGAGCACGGACTGGGAGTCA-GGAGACCTGGGTTCT 57 chr1ptel1M 713622 AATCTAGCCTCAAACACTTATTGGCTGAGTGACCCTGGGCAAGCTACTTC 713671 i iv v viv v i ? v i ii MIR3#SINE/MIR 58 AGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTC 107 chr1ptel1M 713672 -TTTGTCT--TCCTCGGTTTCCTTAAATGTAAAAT--GGAAGT--GAGGA 713714 -ii v --v i i vv -- ii -- vv MIR3#SINE/MIR 108 ACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTA 157 chr1ptel1M 713715 GATAGCATCTGTGAAGCCCTT 713735 i-- v i i i i MIR3#SINE/MIR 158 GATG--ATCTCTAAGGTCCCT 176 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.34 CpG sites = 23, Kimura (unadjusted) = 34.34 Transitions / transversions = 1.15 (23/20) Gap_init rate = 0.06 (9 / 161), avg. gap size = 1.33 (12 / 9) 193 26.83 0.00 0.00 chr1ptel1M 713713 713753 (286247) MIRb#SINE/MIR 194 234 (34) m_b20s601i7 725 chr1ptel1M 713713 GAGATAGCATCTGTGAAGCCCTTGGCCCAGTGCCTGGTGCA 713753 iiiiv i v i v ii MIRb#SINE/MIR 194 GAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACA 234 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.08 CpG sites = 8, Kimura (unadjusted) = 35.08 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 199 24.39 0.00 0.00 chr1ptel1M 713882 713922 (286078) L2d_3end#LINE/L2 462 502 (14) m_b20s601i9 726 chr1ptel1M 713882 ACAGTACTTAGTACACAGTAGGTGCTGGTTAAATGCTCGTT 713922 i v i i i viv i i L2d_3end#LINE 462 ACAGTGCTGAGCACATAGTAGGCGCTCAATAAATACTTGTT 502 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.12 CpG sites = 7, Kimura (unadjusted) = 30.73 Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 554 19.85 11.76 0.00 chr1ptel1M 715281 715416 (284584) MIRc#SINE/MIR 2 153 (115) m_b20s601i10 727 chr1ptel1M 715281 GAGGCAGTGTGGTTTAGTGGCAAGGGCACTGGACACGGAGCCAGGAC-AC 715329 vi v i vi i v- MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr1ptel1M 715330 TTGAGTTCCAGTCCCACCTCAGACAGT--CT-----TGTCACCTTGAGCA 715372 i i v iv v v v -- ----- v i MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 101 chr1ptel1M 715373 AGTCCCTTG--------GTACCTCAGTTTCCTGATCTGCAAAATGGAGGC 715414 v i-------- vi v i i ii MIRc#SINE/MIR 102 AGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGAT 151 chr1ptel1M 715415 AA 715416 MIRc#SINE/MIR 152 AA 153 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 22.30 CpG sites = 14, Kimura (unadjusted) = 23.24 Transitions / transversions = 1.08 (14/13) Gap_init rate = 0.03 (4 / 135), avg. gap size = 4.00 (16 / 4) 526 26.35 9.04 1.69 chr1ptel1M 715283 715448 (284552) MIR3#SINE/MIR 3 180 (28) m_b20s601i11 727 chr1ptel1M 715283 GGCAGTGTGGTTTAGTGGCAAGGGCACTGGACACGGAGCCAGGACACTTG 715332 v i v ii vi i - vv i v i MIR3#SINE/MIR 3 GGCAGAGTGGCTGAGCAGAGAGAGCAC-GGACTGGGAGTCAGGAGACCTG 51 chr1ptel1M 715333 AGTTCCAGTCCCACCTCAGACAGT------CT-TGTCACCTTGAGCAAGT 715375 i i iv v v v ------ - v i MIR3#SINE/MIR 52 GGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGT 101 chr1ptel1M 715376 CCCTT--------GGTACCTCAGTTTCCTGATCTGCAAAATGGAGGCAAG 715417 v --------v vi v i ii --i MIR3#SINE/MIR 102 CACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGG--GG 149 chr1ptel1M 715418 AGAAACCCAACAGCCTCTAAGATCCCTTCCA 715448 vvii ivi iiii i MIR3#SINE/MIR 150 TTGGACTAGATGATCTCTAAGGTCCCTTCCA 180 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.29 CpG sites = 25, Kimura (unadjusted) = 33.23 Transitions / transversions = 1.39 (25/18) Gap_init rate = 0.04 (6 / 165), avg. gap size = 3.00 (18 / 6) 239 36.89 0.00 0.00 chr1ptel1M 715895 715997 (284003) L1ME3F_3end#LINE/L1 431 533 (457) m_b20s551i3 728 chr1ptel1M 715895 CACGGACCAAAAGGTTCATAGCAGCGCTTTCTGGGGTGGCAAAGAACTGG 715944 i v v i v i v ii vii i i L1ME3F_3end#L 431 CATGTACAAGAATGTTCATAGCAGCACTGTTCGTAATAGCAAAAAACTGG 480 chr1ptel1M 715945 AAATTGAGGGGATAGCCGTTGGTCAGGGAATGGCTGAACAAGTTGTGAGA 715994 ivivvvii iv i i iivi i v i i i iv L1ME3F_3end#L 481 AAACAACCCAAATGTCCATCGACAGGAGAATGGATAAATAAATTGTGGTA 530 chr1ptel1M 715995 CAT 715997 i L1ME3F_3end#L 531 TAT 533 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 50.26 CpG sites = 25, Kimura (unadjusted) = 54.57 Transitions / transversions = 1.92 (25/13) Gap_init rate = 0.00 (0 / 102), avg. gap size = 0.0 (0 / 0) 15 19.81 4.35 0.00 chr1ptel1M 717942 717987 (282013) (CACTCTC)n#Simple_repeat 1 48 (0) m_b20s252i4 729 chr1ptel1M 717942 CACTCTCC-CCCTCCTC-CTCCCCCCTCCCCTGAACACTCTCCACTCT 717987 - i v - v i v vvv (CACTCTC)n#Si 1 CACTCTCCACTCTCCACTCTCCACTCTCCACTCTCCACTCTCCACTCT 48 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.04 (2 / 45), avg. gap size = 1.00 (2 / 2) 15 13.24 7.27 5.36 chr1ptel1M 717946 718000 (282000) (CTC)n#Simple_repeat 1 56 (0) m_b20s252i5 729 chr1ptel1M 717946 CTCCCCCTCCTCCTCC-CC-CCTCC-CCTGAACACT-CTCCACTCTGTCT 717991 i - - - vvv - - v - -i (CTC)n#Simple 1 CTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC-CTCCTCCTC-CT-CCT 47 chr1ptel1M 717992 CCTCCTCCT 718000 (CTC)n#Simple 48 CCTCCTCCT 56 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.13 (7 / 54), avg. gap size = 1.00 (7 / 7) 12 18.86 2.63 2.63 chr1ptel1M 719755 719792 (280208) (CCAGGGG)n#Simple_repeat 1 38 (0) m_b20s252i6 730 chr1ptel1M 719755 CCAGTGTCCAGAGGGGAGGGG-CAGCTGGCCAGGGGCCA 719792 v v i vv - -v (CCAGGGG)n#Si 1 CCAGGGGCCAGGGGCCAGGGGCCAG-GGGCCAGGGGCCA 38 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 12 17.72 3.12 0.00 chr1ptel1M 720269 720300 (279700) (CCCAGC)n#Simple_repeat 1 33 (0) m_b20s252i7 731 chr1ptel1M 720269 CCCAGCGTCAAACCCGGCCCCAG-CCCAGCCCC 720300 vi iv i - (CCCAGC)n#Sim 1 CCCAGCCCCAGCCCCAGCCCCAGCCCCAGCCCC 33 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 200 26.32 5.38 10.11 chr1ptel1M 722595 722687 (277313) C MIRb#SINE/MIR (54) 214 126 m_b20s601i12 732 chr1ptel1M 722595 GCGCTTGA--TGCACC-TCCC-TTTAATCCTCAC-GCAGCCGGGCAAGGA 722639 v -- ii- i - -i i vv i v C MIRb#SINE/MIR 214 GCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGT 165 chr1ptel1M 722640 GAGCACTGCAGCCCTGGAGAGCCCCGTTTTACAGTTGCAGAAACTGAG 722687 ii i i ii---------v v i v vi C MIRb#SINE/MIR 164 AGGTATTAT---------TATCCCCATTTTACAGATGAGGAAACTGAG 126 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.42 CpG sites = 14, Kimura (unadjusted) = 33.26 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.14 (13 / 92), avg. gap size = 1.08 (14 / 13) 185 32.81 9.03 5.62 chr1ptel1M 722613 722767 (277233) C MIR#SINE/MIR (74) 188 29 m_b20s601i14 732 chr1ptel1M 722613 TTTAATCCTCACG-CAGCCGGGCAAGGAGAGCACTGCAGCCCTGGAGAGC 722661 i- i vviii vii i i------ vivv v C MIR#SINE/MIR 188 TTTAATCCTCACAACAACCCTATGAGGTAGGTACTA------TTATTATC 145 chr1ptel1M 722662 CCCGTTTTACAGTTGCAGAAACTGAGTCACGG-----------CACCTGC 722700 i v vi v i -----------v i C MIR#SINE/MIR 144 CCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGC 95 chr1ptel1M 722701 CC-AGGCCATACATGCAGCCAGGGTCCCATCCCCGGGTCAGTTCTCCCTG 722749 - i i vvi iv v v vv v vv iv ii---v v C MIR#SINE/MIR 94 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGA---ACCCAG 48 chr1ptel1M 722750 AAAGTCTGGCCCCA-AGCC 722767 iv i - C MIR#SINE/MIR 47 GCAGTCTGGCTCCAGAGCC 29 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.60 CpG sites = 23, Kimura (unadjusted) = 43.79 Transitions / transversions = 0.92 (23/25) Gap_init rate = 0.08 (13 / 154), avg. gap size = 1.77 (23 / 13) 225 32.00 1.33 0.00 chr1ptel1M 722613 722687 (277313) C MIRc#SINE/MIR (70) 198 123 m_b20s601i13 732 chr1ptel1M 722613 TTTAATCCTCACG-CAGCCGGGCAAGGAGAGCACTGCAGCCCTGGAGAGC 722661 i i- i vv ii vii vv viv vivv v C MIRc#SINE/MIR 198 TTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATC 149 chr1ptel1M 722662 CCCGTTTTACAGTTGCAGAAACTGAG 722687 i v vi C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAG 123 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.07 CpG sites = 11, Kimura (unadjusted) = 42.07 Transitions / transversions = 0.85 (11/13) Gap_init rate = 0.01 (1 / 74), avg. gap size = 1.00 (1 / 1) 30 29.33 1.10 0.00 chr1ptel1M 725073 725163 (274837) (TGAA)n#Simple_repeat 1 92 (0) m_b20s252i8 733 chr1ptel1M 725073 TGAATGAAGGAAGGAACAAACACATGAACAAATGAATGAATGAATGAACC 725122 v v ii iiv ii iv (TGAA)n#Simpl 1 TGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATG 50 chr1ptel1M 725123 AATGAACAAACAGATGAATGAACGAACAAACAAATGAA-GAA 725163 ii iii i ii ii - (TGAA)n#Simpl 51 AATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAA 92 Matrix = Unknown Transitions / transversions = 4.25 (17/4) Gap_init rate = 0.01 (1 / 90), avg. gap size = 1.00 (1 / 1) 301 27.67 3.08 5.51 chr1ptel1M 725195 725324 (274676) C L2b_3end#LINE/L2 (76) 390 264 m_b20s601i15 734 chr1ptel1M 725195 TGAACAGAAGCAGATGCGGCCCCTGCCCTTGAGGAACTCACAATCCAATG 725244 ii - i? i iiv i i i i C L2b_3end#LINE 390 TGAACAAGA-CAGACNCGGTCCCTGCCCTCACGGAGCTCACAGTCTAGTG 342 chr1ptel1M 725245 GGGG-GACACGGGACAT---ACCCACCAAGTGTAGGGGAGCGTGGCTAGG 725290 - --- --- ? viv v?i ivvv v vi C L2b_3end#LINE 341 GGGGAGACA---GACATGTAANCAGACAATNATAACCCAGAGTGGCAGGG 295 chr1ptel1M 725291 ACCGATTCAGGAAGGGGCCCGGAAGCGGCCACCT 725324 vvv i --- ii i i v v i C L2b_3end#LINE 294 TAGGACT---GGGGGGGCCCAGAGGAGGGCGCCT 264 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.19 CpG sites = 20, Kimura (unadjusted) = 36.53 Transitions / transversions = 1.43 (20/14) Gap_init rate = 0.07 (9 / 129), avg. gap size = 1.22 (11 / 9) 25 11.83 2.17 0.00 chr1ptel1M 725535 725580 (274420) (TCCG)n#Simple_repeat 1 47 (0) m_b20s252i9 735 chr1ptel1M 725535 TCCATCCGTCCCTCCGTCCATCCCTCTGTCCGTCCGTCC-TCCGTCC 725580 i v i v i - (TCCG)n#Simpl 1 TCCGTCCGTCCGTCCGTCCGTCCGTCCGTCCGTCCGTCCGTCCGTCC 47 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1) 200 32.91 1.25 1.25 chr1ptel1M 730435 730514 (269486) MIRc#SINE/MIR 103 182 (86) m_b20s601i16 736 chr1ptel1M 730435 GTCACCAAACTCCCCTCCATCTTCAGTTCCCTCCTGGGTAAAA-GGGGGT 730483 iv ii i v- v i i v vv - i MIRc#SINE/MIR 103 GTCACTTAACCTCTCTG-AGCCTCAGTTTCCTCATCTGTAAAATGGGGAT 151 chr1ptel1M 730484 GATGGGGCCTGGAGTATCTCCCTGCCAGGGT 730514 i iivi vvv ii v vv MIRc#SINE/MIR 152 AATAATACCTGCCCTGCCTACCTCACAGGGT 182 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.01 CpG sites = 13, Kimura (unadjusted) = 44.01 Transitions / transversions = 1.00 (13/13) Gap_init rate = 0.03 (2 / 79), avg. gap size = 1.00 (2 / 2) 192 36.89 11.11 1.21 chr1ptel1M 731159 731383 (268617) L3#LINE/CR1 3849 4095 (4) m_b20s601i17 737 chr1ptel1M 731159 CCAACAGGTAAAGGAAGGTA-AAGGAAGCAGACTTAGGCTAGAGACCTGG 731207 ii --- v - i i i v vi v ivv L3#LINE/CR1 3849 CCAATGGGT---GGAAGTTACAGGGAGGCAGATTTCGGCTCAATATAAGG 3895 chr1ptel1M 731208 GCAGGCGTCCCCCAGAGGAGAGCTATCCCCATACTGAAGGAGATAATTC- 731256 iviii v i ivvvi vv i vv v iv v i v ivi - L3#LINE/CR1 3896 AAGAACTTTCTAACAATCAGAGCTGTCCAAAAATGGAATGGGCTGCCTCG 3945 chr1ptel1M 731257 ------AGGGGGCT-CCTGCCACTGG---------AGCAGAGAGTGG--G 731288 ------ v i - i i --------- iv -- L3#LINE/CR1 3946 NGAGGTAGTGAGCTCCCCGTCACTGGAGGTGTTCAAGCAGAGGCTGGATG 3995 chr1ptel1M 731289 GACACTAGGCAAGCACCTTATGGAGAAGACA-CTGATTTCGGTCG--GGT 731335 iv v v i v iv i i iii iv- vv v i v -- L3#LINE/CR1 3996 ACCACTTGTCAGGGATGTTGTAGAAGGGATTCCTGCATTGGATGGGAGGT 4045 chr1ptel1M 731336 TCAGATAGGTG--CCATGAGTTCCCTGCCAAGTCTGGGCTGAGGAGATTC 731383 viiv i -- iv i v v v i v vvv v L3#LINE/CR1 4046 TGGACTAGATGACCTCTAAGGTCCCTTCCAACTCTGAGATTCTGTGATTC 4095 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 50.75 CpG sites = 39, Kimura (unadjusted) = 51.63 Transitions / transversions = 0.91 (39/43) Gap_init rate = 0.05 (12 / 224), avg. gap size = 2.33 (28 / 12) 14 20.67 1.35 10.29 chr1ptel1M 735406 735479 (264521) (GGGGC)n#Simple_repeat 1 68 (0) m_b20s252i10 738 chr1ptel1M 735406 GGGGCGTCCCGGGCCAGGGCTGGGGTCGGGGTCGGCCCCGAAGGGCAAGG 735455 vvv v i - - - -vv -- ii (GGGGC)n#Simp 1 GGGGCGGGGCGGGGCGGGGC-GGGG-CGGGG-CGG-GGCG--GGGCGGGG 44 chr1ptel1M 735456 CCTGGCTGGGGC-GGGCGGGGCGGG 735479 vv - - (GGGGC)n#Simp 45 CGGGGC-GGGGCGGGGCGGGGCGGG 68 Matrix = Unknown Transitions / transversions = 0.38 (3/8) Gap_init rate = 0.11 (8 / 73), avg. gap size = 1.00 (8 / 8) 230 25.84 17.98 0.00 chr1ptel1M 735815 735903 (264097) L3#LINE/CR1 3796 3900 (199) m_b20s601i18 739 chr1ptel1M 735815 TGTGGGGGAGGGGTTAGGTCTGTCCTGCCTGACCCCAAAGGGCAGAATCT 735864 ii i iii i i iv i i i iiv L3#LINE/CR1 3796 TGTGGAAGAGGGATTAGACTTATTCTGTGTGGCTCCAGAGGGCAGAACTA 3845 chr1ptel1M 735865 GG-----TGGG----------GGGGAAGCAGATTTAGGCTCAGGGT-GGG 735898 ----- ----------i i v ivi -i L3#LINE/CR1 3846 GGACCAATGGGTGGAAGTTACAGGGAGGCAGATTTCGGCTCAATATAAGG 3895 chr1ptel1M 735899 AAGAA 735903 L3#LINE/CR1 3896 AAGAA 3900 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.28 CpG sites = 19, Kimura (unadjusted) = 34.28 Transitions / transversions = 4.75 (19/4) Gap_init rate = 0.03 (3 / 88), avg. gap size = 5.33 (16 / 3) 202 29.55 0.00 0.00 chr1ptel1M 738275 738318 (261682) C MIR3#SINE/MIR (20) 188 145 m_b20s601i19 740 chr1ptel1M 738275 GTTAGAACTGAAAGGGACCTCCGAGGCTGTCTGGTCCGACTGCC 738318 i i i iv iiii i i iv C MIR3#SINE/MIR 188 GTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCC 145 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.81 CpG sites = 11, Kimura (unadjusted) = 41.81 Transitions / transversions = 5.50 (11/2) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 18 20.07 2.50 0.00 chr1ptel1M 739765 739804 (260196) (CA)n#Simple_repeat 1 41 (0) m_b20s252i12 741 chr1ptel1M 739765 CATACACA-AAAAACACACACTCACTCACACAGACACAGAC 739804 i - v v v v v v (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACAC 41 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1) 277 27.91 6.98 0.00 chr1ptel1M 741539 741624 (258376) C L2d_3end#LINE/L2 (13) 503 412 m_b21s601i0 742 chr1ptel1M 741539 CAACAAGCACAGATCGAGTACCTACCACGTGCTGAGGACTGGTCTGAACG 741588 i ivv i ii i i v v vv iii C L2d_3end#LINE 503 CAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTGTGCTAGGCG 454 chr1ptel1M 741589 CT---GGGAATACAAAAAAAGT---GGAGCTGGTCTCTGCTC 741624 --- iiv? ? ---i vv i i C L2d_3end#LINE 453 CTGTGGGGAACGANAAAANAGTATAAGACATGGTCCCTGCCC 412 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.98 CpG sites = 15, Kimura (unadjusted) = 37.24 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.02 (2 / 85), avg. gap size = 3.00 (6 / 2) 463 24.56 7.02 0.00 chr1ptel1M 741689 741802 (258198) MIRb#SINE/MIR 124 245 (23) m_b21s601i1 743 chr1ptel1M 741689 GCCTCAGTTCCCTCATCTGTCAAATGGGAATAGCACTA------GCACAA 741732 i v i ii v ------v i i MIRb#SINE/MIR 124 GCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTACCTCGCAG 173 chr1ptel1M 741733 G-TTGC-ATCAGGATCGAGTGAGAGAATATCTGCAAAGCCCTGAGCACAG 741780 - i-i v ii i v iiv i v v MIRb#SINE/MIR 174 GGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAG 223 chr1ptel1M 741781 CACCTGGCACACGGTACGTGCT 741802 ii ii v i MIRb#SINE/MIR 224 TGCCTGGCACATAGTAAGCGCT 245 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.25 CpG sites = 19, Kimura (unadjusted) = 30.87 Transitions / transversions = 2.11 (19/9) Gap_init rate = 0.03 (3 / 113), avg. gap size = 2.67 (8 / 3) 317 29.37 0.00 13.46 chr1ptel1M 743183 743300 (256700) MIRc#SINE/MIR 12 115 (153) m_b21s601i2 744 chr1ptel1M 743183 GGCGCAGTGGATAGCTCTATCCTGAACCAGCCCTGAAAATAGGAGGACAT 743232 i v vv -------- ii v i i ivi i v MIRc#SINE/MIR 12 GGTGCAGTGGAAAGAGC--------ACTGGACTTGGAGTCAGGAAGACCT 53 chr1ptel1M 743233 GAGTTCAAATCTAGCCTCAGTTCTTAAGACTTCCTGGCTCTGTGACCCTG 743282 i i i iv v v ii------ v i v i MIRc#SINE/MIR 54 GGGTTCGAGTCCCGGCTCTGCC------ACTTACTAGCTGTGTGACCTTG 97 chr1ptel1M 743283 GGCAAGTCGCTTAGCCCC 743300 i i i MIRc#SINE/MIR 98 GGCAAGTCACTTAACCTC 115 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.18 CpG sites = 19, Kimura (unadjusted) = 37.79 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.12 (14 / 117), avg. gap size = 1.00 (14 / 14) 22 19.51 0.00 0.00 chr1ptel1M 743777 743817 (256183) (C)n#Simple_repeat 1 41 (0) m_b21s252i1 745 chr1ptel1M 743777 CCCCCCCGCCCCCCCCCCGCCGCCCCCAACTCCCCGCCCCC 743817 v v v vv i v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 41 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 281 26.96 4.44 1.08 chr1ptel1M 744887 744976 (255024) MIR3#SINE/MIR 85 177 (31) m_b21s601i3 746 chr1ptel1M 744887 TGGGAGCCTGCG-AAGTCACT-CACCGGTTTG--CCTCAGTTTGCTCATC 744932 v v i v - - vv i -- v MIR3#SINE/MIR 85 TGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATC 134 chr1ptel1M 744933 TGTAAAATGAGAAGGCGGTGACAAAGAACCCCCTGCGATCCTTT 744976 ii iv - v iivivi i iv i i MIR3#SINE/MIR 135 TGTAAAATGAGGGGGTTG-GACTAGATGATCTCTAAGGTCCCTT 177 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.97 CpG sites = 13, Kimura (unadjusted) = 33.97 Transitions / transversions = 1.18 (13/11) Gap_init rate = 0.04 (4 / 89), avg. gap size = 1.25 (5 / 4) 182 35.04 8.28 3.66 chr1ptel1M 746224 746380 (253620) MIR1_Amn#SINE/MIR 1 164 (66) m_b21s601i4 747 chr1ptel1M 746224 TAGGAGAGCTGCATGACCAGAGTGGTTAG--TTCTGGGTTTGGGATCA-- 746269 iii v ii ii -v v --iv ii v iv i-- MIR1_Amn#SINE 1 TAGGGAGGCAGTGTGGTC-TAGTGGATAGAGCACTGGACTGGGACTCGGG 49 chr1ptel1M 746270 AGGTCTGAATCTGAACCCAGCCTCAGACCCTAATGCTACCAGCCAAGGGA 746319 ii ii ii? ?i v v v v v ?i----- ? ii? v MIR1_Amn#SINE 50 AGACCTGGGTTCNANTCCCGGCTCTGCCACTNG-----CCNGCTGNGTGA 94 chr1ptel1M 746320 ACT-------GTCA--TAATCCCACGCAGACTCAGTTTCCCTATTTGTAA 746360 v ------- -- ? i i v vv? v ii i MIR1_Amn#SINE 95 CCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAA 144 chr1ptel1M 746361 AGTTGACATCCTAACAGTGA 746380 i v iv vv i i v MIR1_Amn#SINE 145 AATGGGGATAATGATACTGA 164 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 51.41 CpG sites = 31, Kimura (unadjusted) = 52.89 Transitions / transversions = 1.41 (31/22) Gap_init rate = 0.06 (10 / 156), avg. gap size = 1.90 (19 / 10) 223 33.81 9.52 3.76 chr1ptel1M 746251 746376 (253624) MIRc#SINE/MIR 26 158 (110) m_b21s601i5 747 chr1ptel1M 746251 AGTTCTGGGTTTGGGATCA---AGGTCTGAATCTGAACCCAGCCTCAGAC 746297 iv ii ii --- ii ii ii ii v v v v MIRc#SINE/MIR 26 AGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCC 75 chr1ptel1M 746298 CCTAATGCTACCAGCCAAGGGAACT-------GTCA--TAATCCCACGCA 746338 v ----- i iiv v v ------- -- i i v vv MIRc#SINE/MIR 76 ACT-----TACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGA 120 chr1ptel1M 746339 GACTCAGTTTCCCTATTTGTAAAGTTGACATCCTAACA 746376 v ii i i v iv vv i MIRc#SINE/MIR 121 GCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATA 158 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.19 CpG sites = 24, Kimura (unadjusted) = 46.77 Transitions / transversions = 1.41 (24/17) Gap_init rate = 0.06 (8 / 125), avg. gap size = 2.12 (17 / 8) 30 16.93 0.00 0.00 chr1ptel1M 746740 746792 (253208) (TG)n#Simple_repeat 1 53 (0) m_b21s252i2 748 chr1ptel1M 746740 TGTGTGTCTTTGTGCGTGTGAGTGTGTGTGTGTGTGCATGTGTGTGCCTG 746789 v v i v ii iv (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr1ptel1M 746790 TGT 746792 (TG)n#Simple_ 51 TGT 53 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 193 28.33 5.00 0.00 chr1ptel1M 747163 747222 (252778) C MIRc#SINE/MIR (65) 203 141 m_b21s601i6 749 chr1ptel1M 747163 TCTCTCTGGACTCTCACCACAGACCTGGGAAAAGCACAGGGCAGGT-TTA 747211 vi v ii v iv v iivivi - C MIRc#SINE/MIR 203 TCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTA 154 chr1ptel1M 747212 --GTCCCCATTCT 747222 --i i C MIRc#SINE/MIR 153 TTATCCCCATTTT 141 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.53 CpG sites = 10, Kimura (unadjusted) = 36.53 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.03 (2 / 59), avg. gap size = 1.50 (3 / 2) 233 32.10 3.64 0.88 chr1ptel1M 749880 749989 (250011) C L2a_3end#LINE/L2 (1) 516 404 m_b21s601i7 750 chr1ptel1M 749880 TTCAGTTAATCAACAACCATTCATTAAGCACTTTCTATTTCACAG--ACT 749927 v i v vi i i i i v v vv -- C L2a_3end#LINE 516 TTCATTCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACT 467 chr1ptel1M 749928 GTAATGAATGCTAGGAATACAA-AGAGAGCCAAAAATA-AATAGCTTTTG 749975 vv iiii i i i- v i v v v - v iiii C L2a_3end#LINE 466 GTTCTAGGCGCTGGGGATACAGCAGTGAACAAAACAGACAAAAGTCCCTG 417 chr1ptel1M 749976 CCCCCCAAGGAGTT 749989 - i v i C L2a_3end#LINE 416 -CCCTCATGGAGCT 404 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.94 CpG sites = 20, Kimura (unadjusted) = 43.17 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.04 (4 / 109), avg. gap size = 1.25 (5 / 4) 310 27.03 1.35 0.00 chr1ptel1M 749993 750066 (249934) MER99#DNA/hAT 1 75 (756) m_b21s502i0 751 chr1ptel1M 749993 TAGTGTTTCTAA-TTCTCAGCAGATATTAATCTTCAGAATCTGAAAATGA 750041 i - i ii i i ii ii i MER99#DNA/hAT 1 TAGTGTTTCCAAATTCCCGACAGATATTAATCTTCGGGATTCGGGAACGA 50 chr1ptel1M 750042 AGAATCAAAACTCCTGGCAGTTCCC 750066 ii ii i i v i i MER99#DNA/hAT 51 GAAATCGGAATTCCCGGGAATTCTC 75 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 24.67 CpG sites = 19, Kimura (unadjusted) = 38.12 Transitions / transversions = 19.00 (19/1) Gap_init rate = 0.01 (1 / 73), avg. gap size = 1.00 (1 / 1) 411 19.40 19.40 0.00 chr1ptel1M 750289 750422 (249578) MER99#DNA/hAT 109 268 (563) m_b21s502i1 752 chr1ptel1M 750289 TATTTCCAATATTATTCATACTCTTTCCTCATTATTATGGATATCTAAAC 750338 i i v v v MER99#DNA/hAT 109 TACTTCCAACATTCTTCATACTCTTTACTCATTATTATGGATATCTAAAA 158 chr1ptel1M 750339 ATGT--------------------------TAGTCATATTTATAAAGAAT 750362 v -------------------------- vi i i MER99#DNA/hAT 159 ATTTGTTTAATAAATAAGAAATATTAAGTTTAGTAGTATTTACAAAGAAC 208 chr1ptel1M 750363 TATAGCCTATAACAAATAATCAAATGGTAGAAAATGCCAGCAAAGAATAC 750412 i i i v iiv i i i v v i MER99#DNA/hAT 209 TGTAGCCTATAGCGAATATTCAAACACTGGAAAACGCCAGCGAACATTAT 258 chr1ptel1M 750413 TAAGTAGAAT 750422 ii v MER99#DNA/hAT 259 TGGGTAGTAT 268 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 19.99 CpG sites = 16, Kimura (unadjusted) = 22.84 Transitions / transversions = 1.60 (16/10) Gap_init rate = 0.01 (1 / 133), avg. gap size = 26.00 (26 / 1) 970 22.32 2.68 0.00 chr1ptel1M 750425 750648 (249352) C MER99#DNA/hAT (338) 493 264 m_b21s502i2 753 chr1ptel1M 750425 GTATGTTTGTGGCCTTCTTTGCTG------GTGAGTCATCTTTGCAAATA 750468 i i i v i ------ ii C MER99#DNA/hAT 493 GTGTGTTCGTGGCCCTGTCTGCTGCTAACGGTGAGTCATTCTTGCAAATA 444 chr1ptel1M 750469 AAATAAATATTAATAAGTATATATACAGAGCATATTTTATACATCTCCTA 750518 v ii v i i vv C MER99#DNA/hAT 443 AAATAAATATTAATAAGTTTATACGCATAGTATACTTTATACAAATCCTA 394 chr1ptel1M 750519 TGAATAGTGTTGTAAGACATGACAAGTTTTGGAAGCAAAATAATTTTTTA 750568 i i vi v i v ii C MER99#DNA/hAT 393 TGAGTGGTGTTCCAAGAAATAACAAGTTTTGGAAGCAAAATAAGTCCTTA 344 chr1ptel1M 750569 AATCAGCCATTTTAACTTGAGATTCCACGTAACATTGCTCACCTTGCTGG 750618 ii v ii vi v iii iiii i v i C MER99#DNA/hAT 343 AATTGGCAATTTCGACACGTGATTCTGTGTAGTGCTGTTAACCTTGCTAG 294 chr1ptel1M 750619 GAGATGTGAATGCTGGGTTATACAAATGCT 750648 vi i iv v i i C MER99#DNA/hAT 293 GAGATCCGAATGTTACGTTATTCGAATACT 264 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 23.58 CpG sites = 35, Kimura (unadjusted) = 27.45 Transitions / transversions = 2.33 (35/15) Gap_init rate = 0.00 (1 / 223), avg. gap size = 6.00 (6 / 1) 851 17.79 13.11 1.75 chr1ptel1M 750647 750852 (249148) MER99#DNA/hAT 603 831 (0) m_b21s502i3 754 chr1ptel1M 750647 CTCTGTATGTCACCATTTCCTGCTTTTGCTTTTGACTTAGCATCAGTGAA 750696 i ii v i i i ii i i MER99#DNA/hAT 603 CTCCGCGTGTCAGCGTTTCCTGCTCTTGCTTTCGACTTGACGTCAGTGGA 652 chr1ptel1M 750697 TTCCTTCAGACCAGCA--------ATGTTTATCGTTAACTTTCAATTCTC 750738 ii i -------- v i vi i MER99#DNA/hAT 653 TTCCTTCGAACCAGTAACGTCTCTATGTTGATTGTTAAGCTTTAATTCTC 702 chr1ptel1M 750739 ACAGGAGAATGAT-------------------CCAATTTCCTGACTGAAT 750769 i v ------------------- i ii - MER99#DNA/hAT 703 GCAGGAGAATTATAATACTTTTTCCCGTTTTCCCGATTTCTCGACTG-AT 751 chr1ptel1M 750770 TTTTTTCAATGGTATTTGGGAGTTAGAAAAACATATAAATTTCCCAAGAA 750819 i --- v i v ii i MER99#DNA/hAT 752 TTTTCTC---GGGATTCGGGATTCGGAAAAACATATAAATTTCCCGAGAA 798 chr1ptel1M 750820 ATACCAGGAAGAAATTCCTTCATGGAAACACTA 750852 i i i iv MER99#DNA/hAT 799 ATGCCGGGAAGGAATTCCCGCATGGAAACACTA 831 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 12.64 CpG sites = 29, Kimura (unadjusted) = 21.21 Transitions / transversions = 4.14 (29/7) Gap_init rate = 0.03 (6 / 205), avg. gap size = 5.17 (31 / 6) 192 31.30 7.69 3.23 chr1ptel1M 750938 751145 (248855) C L2d_3end#LINE/L2 (237) 279 63 m_b21s601i8 750 chr1ptel1M 750938 AGGGAAAGTATTTGTGGGGTGTGGAG-AGTGAGGAAAGACTTCCTGGAGA 750986 i - iv v vv -i v i i v i C L2d_3end#LINE 279 AGGGAGAG-ATCAGTGTGGGCTGGAGTGGTCAGGGAAGGCTTCGTGGAGG 231 chr1ptel1M 750987 AGATGGGACTTGACCTGAATCTTGAAGTAATTTAGAGAAGCTCAAAGGCA 751036 i v iii -i vviv i vi vi vi vi C L2d_3end#LINE 230 AGGTGGGACTTGAGCTGGGCCTTGAAG-GATGGGTAGGATTTGGATAGAG 182 chr1ptel1M 751037 GAAGCAAAAAGGGAAAGG-ATTTCAGCC---AAGAAAGGC---AG-ACAG 751078 ii vii i i - i v ---ii v --- - v C L2d_3end#LINE 181 AGAGAGGAAGGGGAAGGGCATTCCAGGCGGGGGGAACGGCGTGAGCAAAG 132 chr1ptel1M 751079 GCAGA-AGATGGGATATCACATGCAAGG-ATGTGCAGGG--CAGCAAAGT 751124 iv - ii ---- iii -i v i -- ii - C L2d_3end#LINE 131 GCGCAGAGGCGGGA----ATGCGCAAGGCGTGTTCGGGGGACAGTGAAG- 87 chr1ptel1M 751125 AGAAGAA---AACTGGAAAGGAGG 751145 vvii---i iv C L2d_3end#LINE 86 AGACCGGCCTGACTGGAGCGGAGG 63 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.19 CpG sites = 40, Kimura (unadjusted) = 42.41 Transitions / transversions = 1.74 (40/23) Gap_init rate = 0.08 (16 / 207), avg. gap size = 1.44 (23 / 16) 233 38.10 1.57 0.78 chr1ptel1M 750959 751085 (248915) C L2c_3end#LINE/L2 (221) 257 130 m_b21s601i9 750 chr1ptel1M 750959 TGGAGAGTGAGGAAAGACTTCCTGGAGAAGATGGGACTTGACCTGAATCT 751008 i i v i i i i i iv ii v i? C L2c_3end#LINE 257 TGGGGGGTCAGGGAAGGCTTCCCGGAGGAGGTGACATCTGAGCTGAGNCT 208 chr1ptel1M 751009 TGAAGTAATTTAGAGAAGCTCA-AAGGCAGAAGCAAAAAGGGAAAGGATT 751057 -i vviv i i vi-v ii v iiii i i v C L2c_3end#LINE 207 TGAAG-GATGAGTAGGAGTTAGCCAGGTGGAAGGAGGGGGGAAGAGCATT 159 chr1ptel1M 751058 TCAGCCAAGAAAGGCAG-ACAGGCAGAAG 751085 i v iiiiiii - iiv i i C L2c_3end#LINE 158 CCAGGCAGAGGGAACAGCATGTGCAAAGG 130 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 58.92 CpG sites = 36, Kimura (unadjusted) = 61.07 Transitions / transversions = 3.00 (36/12) Gap_init rate = 0.02 (3 / 126), avg. gap size = 1.00 (3 / 3) 292 34.62 3.85 1.12 chr1ptel1M 751219 751478 (248522) C L1M1_orf2#LINE/L1 (1594) 1700 1434 m_b21s551i0 755 chr1ptel1M 751219 ATAAATGTAATGTGGTTAT----AATGATTTTTTAAAAATGTAGCCATGC 751264 viv iv i ---- i v vi i v iiivii C L1M1_orf2#LIN 1700 ATAAATCCCACTTGGTCATGATGAATGATCTTTTTAATGTATTGTTGAAT 1651 chr1ptel1M 751265 CCT-TTTGCTAATGACTTATTCACTACTTTAGTATCAATATTCATTAGTA 751313 i v- i ivi i v vv i v i i vi C L1M1_orf2#LIN 1650 TCGGTTTGCTAGTATTTTGTTGAGGATTTTTGCATCAATATTCATCAGAG 1601 chr1ptel1M 751314 ATATTAATCCAAAGTTTTCTTTCAGTGGTCTATCACTG-CCAGTTTTGTG 751362 iii iiv ivv i v i vi - ii - C L1M1_orf2#LIN 1600 ATATTGGCCTGTAGTTTTCTTTTTTTGATGTGTCTTTGTCTGGTTTTG-G 1552 chr1ptel1M 751363 TATCT-AGTCATAGTTGTCTCAGAGAGGGAGTTTGATAAAGCA---CTTC 751408 v-i v v v i iv iv --i i --- i C L1M1_orf2#LIN 1551 TATCAGGGTAATACTGGCCTCGTAGAATGAGTTTG--GAAGTATTCCCTC 1504 chr1ptel1M 751409 TTTCTCTATTTCTGTGAATAGTTTATATTACATAAAGATTAGTTGTTCTG 751458 i i i vv ivi viv viiv v v C L1M1_orf2#LIN 1503 CTCCTCTATTTTTCGGAATAGTTTGAGTAGGATTGGTATTAGTTCTTCTT 1454 chr1ptel1M 751459 AAGGTGTTTAATTACACTCA 751478 v ii ii viv i C L1M1_orf2#LIN 1453 TAAATGTTTGGTAGAATTCA 1434 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 47.49 CpG sites = 52, Kimura (unadjusted) = 48.26 Transitions / transversions = 1.41 (52/37) Gap_init rate = 0.03 (8 / 259), avg. gap size = 1.62 (13 / 8) 24 0.00 3.12 0.00 chr1ptel1M 751600 751620 (248380) (AT)n#Simple_repeat 1 21 (12) m_b21s252i3 756 chr1ptel1M 751600 ATATATATATATATATATATA 751620 (AT)n#Simple_ 1 ATATATATATATATATATATA 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 38 0.00 0.00 0.00 chr1ptel1M 751621 751653 (248347) (TG)n#Simple_repeat 1 33 (0) c_b21s251i0 757 chr1ptel1M 751621 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 751653 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 33 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 24 0.00 3.12 0.00 chr1ptel1M 751654 751663 (248337) (AT)n#Simple_repeat 22 32 (1) m_b21s252i3 758 chr1ptel1M 751654 AT-TATATATA 751663 - (AT)n#Simple_ 22 ATATATATATA 32 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.11 (1 / 9), avg. gap size = 1.00 (1 / 1) 20 10.38 3.12 0.00 chr1ptel1M 752665 752696 (247304) (GA)n#Simple_repeat 1 33 (0) m_b21s252i4 759 chr1ptel1M 752665 GAGAGAGGGGGAG-GAGGGAGAGAGAGAGAGAG 752696 i i - i (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 33 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 275 30.82 14.38 0.00 chr1ptel1M 752704 752849 (247151) C L2b_3end#LINE/L2 (17) 449 283 m_b21s601i10 760 chr1ptel1M 752704 ACATTTACTAAGTGTTTACTGTGTGCCAGGCACTGTGCTAAGAACTGGAG 752753 i i i ii ? i vi i C L2b_3end#LINE 449 ATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGGG 400 chr1ptel1M 752754 ATA-------ATATAAGAT--------TCTCTGATCTCATGGAGATTACA 752788 -------iv i i-------- i vi i v i C L2b_3end#LINE 399 ATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGGAGCTCACA 350 chr1ptel1M 752789 ---TA-TGAGAAAACAAAACATAAAGGCAAGCTGTAAGGA-TGAGAGTGA 752833 --- - i ii ivv i iv i? ii vi ? vi -iv i C L2b_3end#LINE 349 GTCTAGTGGGGGAGACAGACATGTAANCAGACAATNATAACCCAGAGTGG 300 chr1ptel1M 752834 -AGGGGAAAGCAAAGGG 752849 - v iii vii C L2b_3end#LINE 299 CAGGGTAGGACTGGGGG 283 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.03 CpG sites = 33, Kimura (unadjusted) = 44.02 Transitions / transversions = 2.75 (33/12) Gap_init rate = 0.04 (6 / 145), avg. gap size = 3.50 (21 / 6) 337 20.75 17.92 0.00 chr1ptel1M 752704 752809 (247191) C L2d2_3end#LINE/L2 (17) 538 414 m_b21s601i11 760 chr1ptel1M 752704 ACATTTACTAAGTGTTTACTGTGTGCCAGGCACTGTGCTAAGAACT---G 752750 i i i i ii v i vi --- C L2d2_3end#LIN 538 ATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGTGG 489 chr1ptel1M 752751 GAGAT-------AATATAAGAT----TCTCTGATCTCATGGAGATTACA- 752788 i ------- i i---- i vi v v - C L2d2_3end#LIN 488 GGGATACAAAGAAGTATAAGACATGGTCCCTGCCCTCAAGGAGCTTACAA 439 chr1ptel1M 752789 --TA--TGAGAAAACAAAACATAAA 752809 -- -- i i i i C L2d2_3end#LIN 438 TCTAGTTGGGGAGACAAGACATAAA 414 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 22.80 CpG sites = 17, Kimura (unadjusted) = 25.41 Transitions / transversions = 3.40 (17/5) Gap_init rate = 0.06 (6 / 105), avg. gap size = 3.17 (19 / 6) 344 35.41 2.47 0.61 chr1ptel1M 753480 753641 (246359) C L3#LINE/CR1 (170) 3929 3765 m_b21s601i12 761 chr1ptel1M 753480 ATTTTTGAATACACAATAATTCTTGGAAAGTT-TTCCAGACATC-AGCT- 753526 i i -i vv i v i - vv i i- i- C L3#LINE/CR1 3929 ATTTTTGGACA-GCTCTGATTGTTAGAAAGTTCTTCCTTATATTGAGCCG 3881 chr1ptel1M 753527 AAGCCAATCTCTCTACAATTGTTGTCTATTGCTCTTGCTTCT-CTCTCTT 753575 ii vii i ii i viiii i v i iv - i v C L3#LINE/CR1 3880 AAATCTGCCTCCCTGTAACTTCCACCCATTGGTCCTAGTTCTGCCCTCTG 3831 chr1ptel1M 753576 AGACTGAACAAAATTAGCCCCCTCTCTCTTCCAGGTGACTGCCCCTCAAA 753625 iii iiv i v i ivv i vi v i C L3#LINE/CR1 3830 GAGCCACACAGAATAAGTCTAATCCCTCTTCCACATGACAGCCCTTCAAA 3781 chr1ptel1M 753626 AACTTGACTACCGTTA 753641 v i vv v i C L3#LINE/CR1 3780 TATTTGAAGACAGCTA 3765 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 49.65 CpG sites = 37, Kimura (unadjusted) = 50.98 Transitions / transversions = 1.85 (37/20) Gap_init rate = 0.03 (5 / 161), avg. gap size = 1.00 (5 / 5) 331 34.61 2.99 2.99 chr1ptel1M 753638 753771 (246229) C L3#LINE/CR1 (366) 3733 3600 m_b21s601i13 761 chr1ptel1M 753638 GTTAAAGCTCCCTATTGCCTTCAACCAGCGAATTTATGTAATATCAATTT 753687 i vv i v v iviv--i i i i i viv i C L3#LINE/CR1 3733 GCTAAACATCCCCAGTTCCTTCAACCGTTC--CTCATATGACATGGTTTC 3686 chr1ptel1M 753688 GAGCCCCTACACCATTTCAGCTGCTCTTTTCTGG-TGCTTTATAGCTTTT 753736 v v v iiii ii ii -i vi vi i v C L3#LINE/CR1 3685 CAGACCCTTCACCATCCTGGTCGCTCTCCTCTGGACGCGCTCCAGTTTGT 3636 chr1ptel1M 753737 CCATATGCTTCTTTAC---TGGCATCTCCAGAACTGAA 753771 v i v i v v--- i--i C L3#LINE/CR1 3635 CAATGTCCCTCTTAAAATGTGGCG--CCCAGAACTGAA 3600 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.61 CpG sites = 27, Kimura (unadjusted) = 48.46 Transitions / transversions = 1.50 (27/18) Gap_init rate = 0.05 (6 / 133), avg. gap size = 1.33 (8 / 6) 205 29.88 3.41 1.11 chr1ptel1M 753698 753785 (246215) C X6A_LINE#LINE/CR1 (442) 636 547 m_b21s601i14 761 chr1ptel1M 753698 ACCATTTCAGCTGCTCTTTTCTGGTGCTTTA-TAGCTTTTCCATATGCTT 753746 i i i i vv v- vi i v i? i - C X6A_LINE#LINE 636 ACCATTTTAGTTGCCCTTCTCTGGACCTTTCCTATTTCTGCTNTGT-CTT 588 chr1ptel1M 753747 CTTT--ACTGGCATCTCCAGAACTGAAACCGGGATTAAAGG 753785 --iv ivi vv i vv i v v C X6A_LINE#LINE 587 CTTTGAGATGAAGTGACCAAAACTGAACGCAGCATTCAAGG 547 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.21 CpG sites = 13, Kimura (unadjusted) = 39.21 Transitions / transversions = 1.00 (13/13) Gap_init rate = 0.03 (3 / 87), avg. gap size = 1.33 (4 / 3) 293 23.19 8.65 4.63 chr1ptel1M 754060 754163 (245837) MIR#SINE/MIR 35 142 (120) m_b21s601i15 762 chr1ptel1M 754060 GGAGTCAGACTCCTCTTCCTCAGTTCCAATCCACTTGCAGACACTCACT- 754108 i v ----- vi v vvviv v v i - MIR#SINE/MIR 35 GGAGCCAGACTGC-----CTGGGTTCGAATCCCGGCTCTGCCACTTACTA 79 chr1ptel1M 754109 --TGTATGA-----GGCAAGTCATTGCACCTTGTT-TGCCTCAGTTTCTT 754150 -- i ----- i i vv ivi - i MIR#SINE/MIR 80 GCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCT 129 chr1ptel1M 754151 GATCTGTAAAATG 754163 v MIR#SINE/MIR 130 CATCTGTAAAATG 142 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.89 CpG sites = 10, Kimura (unadjusted) = 27.89 Transitions / transversions = 0.77 (10/13) Gap_init rate = 0.09 (9 / 103), avg. gap size = 1.56 (14 / 9) 16 5.80 11.11 0.00 chr1ptel1M 755623 755658 (244342) (GAGGC)n#Simple_repeat 1 40 (0) m_b21s252i5 763 chr1ptel1M 755623 GAGGCGAGG-GAGGCGAGG-GAGGCGTGG-G-GGCGTGGC 755658 - - v - - v (GAGGC)n#Simp 1 GAGGCGAGGCGAGGCGAGGCGAGGCGAGGCGAGGCGAGGC 40 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.11 (4 / 35), avg. gap size = 1.00 (4 / 4) 216 31.12 1.09 5.68 chr1ptel1M 756323 756414 (243586) MIR1_Amn#SINE/MIR 31 118 (112) m_b21s601i16 764 chr1ptel1M 756323 CAGTGAGCTAGAGCTCAGCCAGGAAGGCCTGGCTCCTCGTCTTGTCTCTG 756372 v ii i ii ----- i i v i ?v? ii v MIR1_Amn#SINE 31 CACTGGACTGGGACTC-----GGGAGACCTGGGTTCNANTCCCGGCTCTG 75 chr1ptel1M 756373 ACCTGCACCGACTGTGTGACCCTCAATAAGGCAC-TGACTTCT 756414 v viv?i ?i ? i viii v - ? i MIR1_Amn#SINE 76 CCACTNGCCNGCTGNGTGACCTTGGGCAAGTCACTTNACCTCT 118 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.39 CpG sites = 18, Kimura (unadjusted) = 46.83 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.07 (6 / 91), avg. gap size = 1.00 (6 / 6) 246 30.58 1.01 7.53 chr1ptel1M 756339 756437 (243563) MIRc#SINE/MIR 40 132 (136) m_b21s601i17 764 chr1ptel1M 756339 AGCCAGGAAGGCCTGGCTCCTCGTCTTGTCTCTGACCTGCACCGACTGTG 756388 i i v i vv ii v v vivi iii MIRc#SINE/MIR 40 AGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTG 89 chr1ptel1M 756389 TGACCCTCAATAAGGCACTGACTTCTGGCTCTCTAAGAGCC-CAATTTTC 756437 i viii v v vi----- -- - i i MIRc#SINE/MIR 90 TGACCTTGGGCAAGTCACTTAAC-----CTCTCT--GAGCCTCAGTTTCC 132 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.54 CpG sites = 17, Kimura (unadjusted) = 40.41 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.08 (8 / 98), avg. gap size = 1.00 (8 / 8) 318 25.16 0.00 8.00 chr1ptel1M 756564 756671 (243329) C MIR1_Amn#SINE/MIR (47) 183 84 m_b21s601i18 765 chr1ptel1M 756564 AAGCACCTTATGTACACACATTAGATCTAATAACTATTATCCCCATCCTA 756613 i ------ v vv i - i v - ii C MIR1_Amn#SINE 183 AAGCACTTTA------CAAAGGAGGTC-AGTATC-ATTATCCCCATTTTA 142 chr1ptel1M 756614 CAGATGAGGAAATTGGGGCCACCAAAGCTTGGATGGCTTCCTCAGGGTCA 756663 i i ?vvv i v ?iii i v i i C MIR1_Amn#SINE 141 CAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGCCCAAGGTCA 92 chr1ptel1M 756664 CAGGGCCG 756671 ?vi ? C MIR1_Amn#SINE 91 CNCAGCNG 84 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.79 CpG sites = 15, Kimura (unadjusted) = 32.79 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.07 (8 / 107), avg. gap size = 1.00 (8 / 8) 348 25.11 10.27 4.55 chr1ptel1M 756596 756741 (243259) C MIRc#SINE/MIR (111) 157 4 m_b21s601i19 765 chr1ptel1M 756596 ACTATTATCCCCATCCTACAGATGAGGAAATTGGGGCCACCAAAGCTTGG 756645 i ii i i ivvv i v ii C MIRc#SINE/MIR 157 ATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAA 108 chr1ptel1M 756646 ATGGCTTCCTCAGGGTCACAGGGCCG--AAGGGTCTGCAGCCATTAAGAG 756693 i i v i i vi ii-- v v v - ----i ii C MIRc#SINE/MIR 107 GTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAG-AGCC----GGGA 63 chr1ptel1M 756694 CTC---CCCAGG-------GACAGCCCAGG--CAGGGCTCTTTCCCCTGC 756731 --- ------- --i i -- v v C MIRc#SINE/MIR 62 CTCGAACCCAGGTCTTCCTGAC--TCCAAGTCCAGTGCTCTTTCCACTGC 15 chr1ptel1M 756732 -TCTCGCTGCC 756741 -i v i C MIRc#SINE/MIR 14 ACCACACTGCC 4 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.64 CpG sites = 23, Kimura (unadjusted) = 31.74 Transitions / transversions = 1.92 (23/12) Gap_init rate = 0.08 (12 / 145), avg. gap size = 1.83 (22 / 12) 19 11.69 0.00 0.00 chr1ptel1M 756915 756942 (243058) (G)n#Simple_repeat 1 28 (0) m_b21s252i6 766 chr1ptel1M 756915 GGGGGGGGGGGGGGTGAGGAGGGGGGGG 756942 v i i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGG 28 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 25 11.68 0.00 0.00 chr1ptel1M 758473 758509 (241491) (G)n#Simple_repeat 1 37 (0) m_b21s252i7 767 chr1ptel1M 758473 GGGTGGGGGGCGGGGGCGGGGGGGGGAGGGGGGGGGG 758509 v v v i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 37 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 19 32.36 0.00 1.30 chr1ptel1M 758773 758850 (241150) (CGGGGGG)n#Simple_repeat 1 77 (0) m_b21s252i8 768 chr1ptel1M 758773 CGGGGGGCGGAGGGGCGGGGGGAGGGGGTGGTGGGGTGGGTGAAAAGAGA 758822 - v vv v i v ivii i i (CGGGGGG)n#Si 1 CGGGGGGCGG-GGGGCGGGGGGCGGGGGGCGGGGGGCGGGGGGCGGGGGG 49 chr1ptel1M 758823 TGGACGCAGGGTGCCGGGGGGGGGGGGG 758850 i iv vv v v v (CGGGGGG)n#Si 50 CGGGGGGCGGGGGGCGGGGGGCGGGGGG 77 Matrix = Unknown Transitions / transversions = 0.67 (8/12) Gap_init rate = 0.01 (1 / 77), avg. gap size = 1.00 (1 / 1) 13 16.36 9.30 0.00 chr1ptel1M 758987 759029 (240971) (GAGAAG)n#Simple_repeat 1 47 (0) m_b21s252i9 769 chr1ptel1M 758987 GAGGAGGAAGAGGAGAAGGAG--GGAGGAGG-GAGGGA-AAGGAAAA 759029 i ii -- i - i - i (GAGAAG)n#Sim 1 GAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAA 47 Matrix = Unknown Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.07 (3 / 42), avg. gap size = 1.33 (4 / 3) 17 7.39 0.00 6.45 chr1ptel1M 758987 759019 (240981) (GAG)n#Simple_repeat 1 31 (0) m_b21s252i10 770 chr1ptel1M 758987 GAGGAGGAAGAGGAGAAGGAGGGAGGAGGGAGG 759019 i i - - (GAG)n#Simple 1 GAGGAGGAGGAGGAGGAGGA-GGAGGA-GGAGG 31 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.06 (2 / 32), avg. gap size = 1.00 (2 / 2) 13 13.88 6.06 0.00 chr1ptel1M 758989 759021 (240979) (GGAG)n#Simple_repeat 1 35 (0) m_b21s252i11 770 chr1ptel1M 758989 GGAGGAAGAG-GAGAAGGAGGGA-GGAGGGAGGGA 759021 i i - i i - (GGAG)n#Simpl 1 GGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGA 35 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.06 (2 / 32), avg. gap size = 1.00 (2 / 2) 42 4.40 0.00 0.00 chr1ptel1M 759032 759078 (240922) (GAG)n#Simple_repeat 1 47 (0) c_b21s251i1 770 chr1ptel1M 759032 GAGGAGGAGGAGGAGGAGGAGGAGCAGCAGGAGGAGGAGGAGGAGGA 759078 v v (GAG)n#Simple 1 GAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA 47 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 24 3.54 0.00 0.00 chr1ptel1M 759323 759351 (240649) (CA)n#Simple_repeat 1 29 (0) m_b21s252i12 771 chr1ptel1M 759323 CACACAGACACACACACACACACACACAC 759351 v (CA)n#Simple_ 1 CACACACACACACACACACACACACACAC 29 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 190 37.02 0.00 5.83 chr1ptel1M 759754 759862 (240138) C MIRc#SINE/MIR (75) 193 91 m_b21s601i20 772 chr1ptel1M 759754 TCCTCCCGATGGCCCCGTGCGGCCTTCAGGGGGCATAGATGGAGCTTCTC 759803 v i iii i v ivvv ----i i ivvii vii C MIRc#SINE/MIR 193 TCCTCACAACAACCCTGTGAGGTAGGCAGGG----CAGGTATTATTATCC 148 chr1ptel1M 759804 CGACTTCAAAGCTGGGGAAGCTGAGAGTGTGAGAGGTCACGTGGCTGCGG 759853 v i i v v i i iv vv i v i --v C MIRc#SINE/MIR 147 CCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACT--TG 100 chr1ptel1M 759854 CCAAAGGCC 759862 v i C MIRc#SINE/MIR 99 CCCAAGGTC 91 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 52.54 CpG sites = 21, Kimura (unadjusted) = 52.54 Transitions / transversions = 1.24 (21/17) Gap_init rate = 0.06 (6 / 108), avg. gap size = 1.00 (6 / 6) 17 12.89 2.08 6.52 chr1ptel1M 760203 760250 (239750) (CCCT)n#Simple_repeat 1 46 (0) m_b21s252i13 773 chr1ptel1M 760203 CCCTCCCCTCCCTTCC-CAAACCCTCCCTCCCTCTCCATACCTCCCTCC 760250 - i - vvv - - v (CCCT)n#Simpl 1 CCCT-CCCTCCCTCCCTCCCTCCCTCCCTCCCTC-CC-TCCCTCCCTCC 46 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.09 (4 / 47), avg. gap size = 1.00 (4 / 4) 308 25.01 4.39 5.31 chr1ptel1M 760405 760518 (239482) MIRc#SINE/MIR 34 146 (122) m_b21s601i21 774 chr1ptel1M 760405 ACCTCAAATTACAAAAACCCCGGGGATGGAGGGGATCTGGCCTCGGACCC 760454 i vi i i vi i i-- v v ---- iv v v v v MIRc#SINE/MIR 34 ACTTGGAGTCAGGAAGACCT--GGGTTCGAG----TCCCGGCTCTGCCAC 77 chr1ptel1M 760455 TTCCCGGCTGTG--ACCCTGGGCTTGTCACTTCAC-TGTCTG--CCTCAA 760499 v ii -- i vv v - v -- i MIRc#SINE/MIR 78 TTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAG 127 chr1ptel1M 760500 TTTCCTCATCTGCAAAATG 760518 i MIRc#SINE/MIR 128 TTTCCTCATCTGTAAAATG 146 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.63 CpG sites = 13, Kimura (unadjusted) = 30.63 Transitions / transversions = 0.93 (13/14) Gap_init rate = 0.08 (9 / 113), avg. gap size = 1.22 (11 / 9) 312 10.53 5.26 0.00 chr1ptel1M 760463 760519 (239481) MIR3#SINE/MIR 85 144 (64) m_b21s601i22 774 chr1ptel1M 760463 TGTGACCCTGGGCTTGTCACTTCAC-TGTCTG--CCTCAATTTCCTCATC 760509 i vv - v -- i MIR3#SINE/MIR 85 TGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATC 134 chr1ptel1M 760510 TGCAAAATGA 760519 i MIR3#SINE/MIR 135 TGTAAAATGA 144 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 11.37 CpG sites = 3, Kimura (unadjusted) = 11.37 Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.04 (2 / 56), avg. gap size = 1.50 (3 / 2) 228 34.34 17.47 0.00 chr1ptel1M 760611 760776 (239224) L3b_3end#LINE/CR1 402 596 (610) m_b21s601i23 775 chr1ptel1M 760611 GTCGGGCAAATCTTGGTGAGATGAAACGGCATCGGGACAAACAAAAAGCT 760660 ? vi v?iiiiii ivvv iv i iv ii L3b_3end#LINE 402 GNCGGGCCGAANCCAACAAGATGAAATTCAACAGGGATAAACGTAAAGTC 451 chr1ptel1M 760661 TCCCACTTGTGCTCC--------------TGAATCCAAGAAAGGG---CC 760693 iiv v i v--------------i i v i vi ---v L3b_3end#LINE 452 CTGCACTTGGGTTCAAAAAANCAATCGCGCGAGTACAGGATGGGGGAGAC 501 chr1ptel1M 760694 GCGG----------GATTATGGGAAACCGGC-TGGAGATCTCAGTGGACC 760732 ---------- v?i v vv i - i i i i v L3b_3end#LINE 502 GCGGCTTAGCAGCAGCNCATGTGAAAAAGACCTGGGGGTTTTAGTTGACC 551 chr1ptel1M 760733 ACAAGCTT-ACACGAGTCCACAGTGGGGTGCGGAGGACAAAGAAG 760776 i i- i i vi v ii vv v i L3b_3end#LINE 552 GCAAGCTCAATATGAGTCAGCAGTGCGACGCGGCTGCCAAAAAAG 596 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.25 CpG sites = 34, Kimura (unadjusted) = 49.14 Transitions / transversions = 1.48 (34/23) Gap_init rate = 0.03 (5 / 165), avg. gap size = 5.80 (29 / 5) 12 12.49 0.00 3.70 chr1ptel1M 763284 763311 (236689) (CCCCA)n#Simple_repeat 1 27 (0) m_b21s252i14 776 chr1ptel1M 763284 CCCCTCCCCACCCCCACCCCACTCCTCC 763311 v - i v (CCCCA)n#Simp 1 CCCCACCCCA-CCCCACCCCACCCCACC 27 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 186 29.97 9.88 1.14 chr1ptel1M 764511 764591 (235409) MIRc#SINE/MIR 75 162 (106) m_b21s601i24 777 chr1ptel1M 764511 CACTCACTGATCACG--ACCATTGGACAGATCATTT-----CTCAGAGGT 764553 i iiiiii -- - i ii i ----- v vi MIRc#SINE/MIR 75 CACTTACTAGCTGTGTGACC-TTGGGCAAGTCACTTAACCTCTCTGAGCC 123 chr1ptel1M 764554 TCCCTTTACTCATCTGCAAATT-GAGACCATGATCCCTG 764591 vv v i v - i iv i v MIRc#SINE/MIR 124 TCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTG 162 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.24 CpG sites = 16, Kimura (unadjusted) = 40.24 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.05 (4 / 80), avg. gap size = 2.25 (9 / 4) 15 0.00 4.55 0.00 chr1ptel1M 764890 764911 (235089) (GGAG)n#Simple_repeat 1 23 (0) m_b21s252i15 778 chr1ptel1M 764890 GGAGGGA-GGAGGGAGGGAGGGA 764911 - (GGAG)n#Simpl 1 GGAGGGAGGGAGGGAGGGAGGGA 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.05 (1 / 21), avg. gap size = 1.00 (1 / 1) 23 22.87 4.35 0.00 chr1ptel1M 766757 766825 (233175) (GAGA)n#Simple_repeat 1 72 (0) m_b21s252i16 779 chr1ptel1M 766757 GAGAGA-AAAGAAAAAGAGGGAAAG-GAGGGAGGGAGGGAGGGAGAGGGA 766804 - i i i i i - i i i i i (GAGA)n#Simpl 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr1ptel1M 766805 GACAGAAAG-GAGAGACAGAGA 766825 v i - v (GAGA)n#Simpl 51 GAGAGAGAGAGAGAGAGAGAGA 72 Matrix = Unknown Transitions / transversions = 5.50 (11/2) Gap_init rate = 0.04 (3 / 68), avg. gap size = 1.00 (3 / 3) 333 36.90 5.34 3.50 chr1ptel1M 768086 768422 (231578) C L2#LINE/L2 (376) 2706 2364 m_b21s601i25 780 chr1ptel1M 768086 AAAAGATATTGGCCAGATACCAGAGAGGTGAAATCTACAAGGGATGCCCT 768135 i v iv iv i- i v iv v- iv i v i ---- C L2#LINE/L2 2706 AGATGATGGTGGCTTGG-ACCAGGGTGGTGGCAG-TGGAGGTGGTG---- 2663 chr1ptel1M 768136 AGAGGAGCATGGGACTCTGCAGAAGT---GAAAGTA------ATACACTT 768176 i v -i v i v v vi --- i ------ i viv C L2#LINE/L2 2662 AGAAGTG-GTCGGATTCTGGATATATTTTGAAGGTAGAGCCGACAGGATT 2614 chr1ptel1M 768177 TGGTACCATATTGTATATGGGG-GTGAGAAATAGTGAGGAATCCAGGATG 768225 v iviiv v i - i v v i v C L2#LINE/L2 2613 TGCTGATGGATTGGATGTGGGGTGTGAGAGAAAGAGAGGAGTCAAGGATG 2564 chr1ptel1M 768226 ATCCCTAAGGATCAGGGAACCTGAAGGACAGGGGTGATGG---TATCTTC 768272 ii - v ivv -- ivi v iiv --- ii v i C L2#LINE/L2 2563 ACTCC-AAGGTTTTTGG--CCTGAGCAACTGGAAGGATGGAGTTGCCATT 2517 chr1ptel1M 768273 AGGAGTGACAAAGAAAGGTAGGAGAGGGATATTTATTTAGGAGGAAAGAT 768322 ?ivv v iiii iiv iv i iii v--i ii i i C L2#LINE/L2 2516 NACTGAGATGGGGAAGACTGCGGGAGGAGCAG--GTTTGAGGGGGAAGAT 2469 chr1ptel1M 768323 AATGAGTTCTGTTTTAGACATGTTAAGTT-----TGTCTACTGAATACCT 768367 v v v i ----- i i ii i i i C L2#LINE/L2 2468 CAGGAGTTCAGTTTTGGACATGTTAAGTTTGAGATGCCTATTAGACATCC 2419 chr1ptel1M 768368 GATGTAAAATGTCTCAAAGGCAGCTAGAGATGTTCAATTGGAGGTTGGTG 768417 i vvvi i vviv i i v iivvivi v ii v C L2#LINE/L2 2418 AAGTGGAGATGTCGAGTAGGCAGTTGGATATACGAGTCTGGAGTTCAGGG 2369 chr1ptel1M 768418 GAAAG 768422 i C L2#LINE/L2 2368 GAGAG 2364 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 52.71 CpG sites = 70, Kimura (unadjusted) = 53.37 Transitions / transversions = 1.40 (70/50) Gap_init rate = 0.05 (17 / 336), avg. gap size = 1.76 (30 / 17) 358 34.16 4.04 4.39 chr1ptel1M 768667 768963 (231037) L1ME4a_3end#LINE/L1 366 661 (210) m_b21s551i2 781 chr1ptel1M 768667 CTTTGATCCAGAACTGTTTCTACTGGGTCTGTGTCCCAGAAAGATCATAA 768716 i v v viiv v i vv v i i iii i v v L1ME4a_3end#L 366 CTTTGACCCAGTAATTCCACTTCTAGGAATTTATCCTAAGGAAATAATCA 415 chr1ptel1M 768717 AAGAGG--GAAAAGGACCCACATGTGCAAAAATGTTTGTGGCAACTTT-T 768763 i v --? v i iii -- i ii ii v i v - L1ME4a_3end#L 416 GAGATGTGNACAAAGATTTA--TGTACAAGGATGTTCATCGCAGCATTAT 463 chr1ptel1M 768764 TTGTAATGTCAAGGAAATGGAAACTGAGTGGATGCCCAGCAGTTGGGGAA 768813 i iv i ii v vivv ii i i i v ? L1ME4a_3end#L 464 TTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAN 513 chr1ptel1M 768814 TGGCTGAATAAGTTATGGTAAGTGAATGCTATGGGATACTATTGTTCTGT 768863 i i i vi vv i?v i i vvvv ii L1ME4a_3end#L 514 TGGTTAAATAAATTATGGTACATCCATANAATGGAATATTATGCAGCCAT 563 chr1ptel1M 768864 AAGAAACAACCAGCAGGATGGTTTCAGAGA---------GGCTTGGGGAG 768904 v i i---------? v ii --------- i v i i L1ME4a_3end#L 564 TAAAAAT---------NATGTTTTCGAAGAATATTTAATGACATGGGAAA 604 chr1ptel1M 768905 ACTCACATGAACTGATGCTAAGTGAAGTGAGCAGAACCAAGAAAACACTG 768954 iv v vv i i ivi i?i-- v vv i L1ME4a_3end#L 605 ATGCTCATGATATAATGTTAAGTGAAAAAAGCAGGNT--ACAAAACTGTA 652 chr1ptel1M 768955 TACACAATA 768963 i i L1ME4a_3end#L 653 TATACAGTA 661 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 47.31 CpG sites = 58, Kimura (unadjusted) = 48.74 Transitions / transversions = 1.49 (58/39) Gap_init rate = 0.05 (16 / 296), avg. gap size = 1.56 (25 / 16) 451 32.09 1.59 1.05 chr1ptel1M 768667 768855 (231145) L1ME4c_3end#LINE/L1 366 555 (275) m_b21s551i1 781 chr1ptel1M 768667 CTTTGATCCAGAACTGTTTCTACTGGGTCTGTGTCCCAGAAAGATCAT-- 768714 i v v viiv v vv v i i iii i v -- L1ME4c_3end#L 366 CTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTC 415 chr1ptel1M 768715 AAAAGAGGGAAAAGGACCCACATGTGCAAAAATGTTTGTGGCAAC-TTTT 768763 i i -- i i ii i i ii v i - v L1ME4c_3end#L 416 AAAAGAAGGAAAAAG--CTATATGCACGAAGATGTTCATTGCAGCGTTAT 463 chr1ptel1M 768764 TTGTAATGTCAAGGAAATGGAAACTGAGTGGATGCCCAGCAGTTGGGGAA 768813 i iv i ii v vivv ii i i i v L1ME4c_3end#L 464 TTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAA 513 chr1ptel1M 768814 TGGCTGAATAAGTTATGGTAAGTGAATGCTATGGGATACTAT 768855 i i i i vi v? iv v i i L1ME4c_3end#L 514 TGGTTAAGTAAATTATGGTACATCNACTCGATGGAATATTAT 555 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 42.36 CpG sites = 39, Kimura (unadjusted) = 44.39 Transitions / transversions = 1.86 (39/21) Gap_init rate = 0.02 (4 / 188), avg. gap size = 1.25 (5 / 4) 15 5.48 0.00 0.00 chr1ptel1M 769146 769164 (230836) (TG)n#Simple_repeat 1 19 (0) m_b21s252i17 782 chr1ptel1M 769146 TGTCTGTGTGTGTGTGTGT 769164 v (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGT 19 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 13 34.65 0.00 1.72 chr1ptel1M 770216 770274 (229726) (AGGGG)n#Simple_repeat 1 58 (0) m_b21s252i18 783 chr1ptel1M 770216 AGGGGCGGGGGAGGGAAGGAAGGAGGGGGACAGGAAACAGGAAAGGAGGG 770265 v ii i i - i iv ii vi ii (AGGGG)n#Simp 1 AGGGGAGGGGAGGGGAGGGGAGG-GGAGGGGAGGGGAGGGGAGGGGAGGG 49 chr1ptel1M 770266 GAGGGGGGG 770274 i (AGGGG)n#Simp 50 GAGGGGAGG 58 Matrix = Unknown Transitions / transversions = 4.00 (12/3) Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1) 11 26.13 0.00 6.12 chr1ptel1M 770810 770861 (229139) (GGGGCG)n#Simple_repeat 1 49 (0) m_b21s252i19 784 chr1ptel1M 770810 GGGGCTGGGGGCCCCGGCCCTGGCAGGGGGGAGGGGGGGGGGCCCGGGGC 770859 - vvv vvv -- v v v v (GGGGCG)n#Sim 1 GGGGC-GGGGGCGGGGGCGGGGGC--GGGGGCGGGGGCGGGGGCGGGGGC 47 chr1ptel1M 770860 GG 770861 (GGGGCG)n#Sim 48 GG 49 Matrix = Unknown Transitions / transversions = 0.00 (0/10) Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.00 (3 / 3) 13 24.24 0.00 0.00 chr1ptel1M 771416 771454 (228546) (CCCCGGG)n#Simple_repeat 1 39 (0) m_b21s252i20 785 chr1ptel1M 771416 CCCCGTGCCCAGGGCCCCTTCCCCCAGCCCCGGGGCCCC 771454 v v vvv i v v (CCCCGGG)n#Si 1 CCCCGGGCCCCGGGCCCCGGGCCCCGGGCCCCGGGCCCC 39 Matrix = Unknown Transitions / transversions = 0.14 (1/7) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 21 21.82 4.23 1.37 chr1ptel1M 773930 774000 (226000) (GGGAGGA)n#Simple_repeat 1 73 (0) m_b21s252i21 786 chr1ptel1M 773930 GGGAAGAGGGAAGCAGGGA-AAGGGAGGAGGGCAGA-GCAGGAGGAAGGT 773977 i - v -i vi - v i v (GGGAGGA)n#Si 1 GGGAGGAGGG-AGGAGGGAGGAGGGAGGAGGGAGGAGGGAGGAGGGAGGA 49 chr1ptel1M 773978 GAGAGGA-GGAGCGGGGTGGGGGG 774000 i - vi v i (GGGAGGA)n#Si 50 GGGAGGAGGGAGGAGGGAGGAGGG 73 Matrix = Unknown Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.06 (4 / 70), avg. gap size = 1.00 (4 / 4) 200 41.48 0.00 1.63 chr1ptel1M 774423 774547 (225453) C L2c_3end#LINE/L2 (76) 402 280 m_b21s601i26 787 chr1ptel1M 774423 GATCCCTGCCCTCAAAAAATTTTCAGTCTATTGAGGGAAACGCAAATCTG 774472 i ii ii iv v ii i iv v ?v i C L2c_3end#LINE 402 GGTCCCTGCCCTCAAGGAGCTCACAGTCTAGTGGAGGAGACAGACANGTA 353 chr1ptel1M 774473 AAAGGGCTCCTGAGAAAGCAGGTGACAGCCATTCCTGTCATGAGAATGGG 774522 vi i vvi ivi v vv v i iiiiv v v i v i i ivi C L2c_3end#LINE 352 AACAGACAATTACAATACAAGTTAATGATAAGTGCTATAATGGGAGTATA 303 chr1ptel1M 774523 CACAAGAGTGCCCTCCAGAGCAGAG 774547 v - i iv -vi v C L2c_3end#LINE 302 GAC-AGGGTGCTAT-GGGAGCACAG 280 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 64.50 CpG sites = 29, Kimura (unadjusted) = 64.50 Transitions / transversions = 1.32 (29/22) Gap_init rate = 0.02 (2 / 124), avg. gap size = 1.00 (2 / 2) 512 26.15 17.10 3.91 chr1ptel1M 775125 775510 (224490) C L2b_3end#LINE/L2 (13) 453 19 m_b21s601i27 788 chr1ptel1M 775125 ACAAGCATCTATTAACCTTCTAGGGTGTGCTGGGCACCATGCAAAGCCCT 775174 ii i i i v vi vv ii ? ii v i v C L2b_3end#LINE 453 ACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCT 404 chr1ptel1M 775175 AGGGATACAA----GAA--AGACAGAAGGCCATCCCTGCCCTTCAGGGGC 775218 i i---- -- v?- vi ivv i C L2b_3end#LINE 403 GGGGATACAGCGGTGAACAAGACAGACN-CGGTCCCTGCCCTCACGGAGC 355 chr1ptel1M 775219 TGTCCCTCTAGCAGAAGAGA-AGCCATGCAAACA------TCTG---CAG 775258 vv vv ii ii - v i ? ------?v i--- C L2b_3end#LINE 354 TCACAGTCTAGTGGGGGAGACAGACATGTAANCAGACAATNATAACCCAG 305 chr1ptel1M 775259 ACAAACAGGCTACAGAACTGGGGGGGTCTCAGAGGGAAGGC-----ACCC 775303 vvii v -- i i - - i ----- C L2b_3end#LINE 304 AGTGGCAGGGTA--GGACTGGGGGGGCC-CAGAGG-AGGGCGCCTGACCC 259 chr1ptel1M 775304 GGATTGAGGA-CCAGGAAGGGCTTTTTGCACAGGGGAGGATGACTTTT-A 775351 vi i i-i i ---- v i i - v - C L2b_3end#LINE 258 GGCCTGGGGGGTCAGGGAGGGCTT----CCCGGAGGAGG-TGACATTTGA 214 chr1ptel1M 775352 GTTGGGGATTGAAGG-------GAAGCCGG------GAAGA--TGAGGAA 775386 i i ivi ------- i ii ------ -- i C L2b_3end#LINE 213 GCTGAGACCTGAAGGATGAGTAGGAGTTGGCCAGGCGAAGAGGTGGGGAA 164 chr1ptel1M 775387 GACCATTCCAGGTAGCCAGGGA-----ATGTGCTTA------GAGTTGGG 775425 iv i i -- ----- ? vv ------ vi C L2b_3end#LINE 163 GGGCGTTCCAGGCAG--AGGGAACAGCANGTGCAAAGGCCCTGAGGCGGG 116 chr1ptel1M 775426 AGA-------------TGGAGGACAAGCCAGAAGGCCACGGTCATTGGAT 775462 ?------------- v vv v i vv vii - C L2b_3end#LINE 115 AGNGAGCNTGGCGTGTTCGAGGAACAGCAAGGAGGCCAGTGTGGCTGGA- 67 chr1ptel1M 775463 GAAAGAGTGTATGTCAGGGAGAAAGAAGTAAG----GAGACTGGAAAAGT 775508 -iv vi--- i i i vi i ---- i i i i C L2b_3end#LINE 66 -GCAGAGTGAG---CAAGGGGAGAGTGGTAGGAGATGAGGCCGGAGAGGT 21 chr1ptel1M 775509 AG 775510 C L2b_3end#LINE 20 AG 19 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.31 CpG sites = 60, Kimura (unadjusted) = 34.03 Transitions / transversions = 1.62 (60/37) Gap_init rate = 0.08 (32 / 385), avg. gap size = 2.59 (83 / 32) 214 34.58 14.11 4.20 chr1ptel1M 775405 775730 (224270) C L2#LINE/L2 (52) 3030 2674 m_b21s601i28 788 chr1ptel1M 775405 GGGAATGTGCTTAGAGTTGGGAGATGGAGGACAAGCCAGAAGGCCACGGT 775454 ii i i v ----- v v vv v i vv C L2#LINE/L2 3030 GGGAGCGTGCCTGGCGT-----GTTCGAGGAACAGCAAGGAGGCCAGTGT 2986 chr1ptel1M 775455 CATTGGATGAAAGAGTGTATGTCAGGGAGAAAGAAGTAAG----GAGACT 775500 vii --ivi vii -- i i vi i ---- iii C L2#LINE/L2 2985 GGCTGGA--GCGGAGTGAGCG--AGGGGGAGAGTGGTAGGAGATGAGGTC 2940 chr1ptel1M 775501 GGAAAAGTAGGAGAGGGCCGAGTTAAAAAGGGCTTTGA-----ATGACAA 775545 i i i ivi i i iii i viv i v----- vii C L2#LINE/L2 2939 AGAGAGGTAACGGGGGACCAGATCATGTAGGGCCTTGTAGGCCATTGTAA 2890 chr1ptel1M 775546 CAACTTAGGGTGTATTTGGCCTTAGAAGTGACAGGGAGTC-CTGGAGCTG 775594 vi v v --- ivi v -v v ii i i -i vvv C L2#LINE/L2 2889 GGACTTTGGCT---TTTACTCTGAG-TGAGATGGGAAGCCATTGGAGGGT 2844 chr1ptel1M 775595 ATTGAGTAGTGATGTGTCA-GACCTGAT-----CTTTAGGAAAACCAATA 775638 v i v iv v - i i-----i ii ii i v v C L2#LINE/L2 2843 TTTGAGCAGAGGAGTGACATGATCTGACTTACGTTTTAAAAGGATCACTC 2794 chr1ptel1M 775639 T------TTTGATGAATGGATAGACTGG-----------------AGCAG 775665 ------ v v -- i ?----------------- C L2#LINE/L2 2793 TGGCTGCTGTGTTGA--GAATAGACTGNAGGGGGGCAAGGGTGGAAGCAG 2746 chr1ptel1M 775666 GGAGAC---TCA----GCTCTTGCACTAGTGCAAGTGTGAAGTGATGAAG 775708 --- i ---- v v i v i i v ii iv C L2#LINE/L2 2745 GGAGACCAGTTAGGAGGCTATTGCAGTAATCCAGGCGAGAGATGATGGTG 2696 chr1ptel1M 775709 GCCCGCCCCAGTGGAATGACAG 775730 ii vv v vii i C L2#LINE/L2 2695 GCTTGGACCAGGGTGGTGGCAG 2674 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.65 CpG sites = 64, Kimura (unadjusted) = 48.81 Transitions / transversions = 1.45 (64/44) Gap_init rate = 0.07 (24 / 325), avg. gap size = 2.54 (61 / 24) 370 33.12 3.16 0.62 chr1ptel1M 775926 776083 (223917) C L2#LINE/L2 (443) 2639 2478 m_b21s601i29 788 chr1ptel1M 775926 ACTATAGAAGTGAAATCGACAGGCCTTGGCACCAAGTTGGATCTGGGAAA 775975 i v ii i ii ii vi viiviiii v iv- C L2#LINE/L2 2639 ATTTTGAAGGTAGAGCCGACAGGATTTGCTGATGGATTGGATGTGGGGT- 2591 chr1ptel1M 775976 GTGAGAGACAGTGAGGAGTCCAGGATGACTCC-TGGTTGTGAGCCTGGGG 776024 v v v -v v vi i v C L2#LINE/L2 2590 GTGAGAGAAAGAGAGGAGTCAAGGATGACTCCAAGGTTTTTGGCCTGAGC 2541 chr1ptel1M 776025 GACTGGGAGGATGGGGATGTTTGTGACAATAATAGG---GGCCCTGGAAG 776071 i i i v iivv ? vivi i --- i ivi i C L2#LINE/L2 2540 AACTGGAAGGATGGAGTTGCCATTNACTGAGATGGGGAAGACTGCGGGAG 2491 chr1ptel1M 776072 GA-CAGGGCTGGG 776083 - vi i C L2#LINE/L2 2490 GAGCAGGTTTGAG 2478 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.83 CpG sites = 32, Kimura (unadjusted) = 46.07 Transitions / transversions = 1.60 (32/20) Gap_init rate = 0.03 (4 / 157), avg. gap size = 1.50 (6 / 4) 198 21.05 0.00 0.00 chr1ptel1M 776505 776542 (223458) MIR1_Amn#SINE/MIR 117 154 (76) m_b21s601i30 789 chr1ptel1M 776505 CCCTGGGCCTCAGCTGCCTCACCTACGAAATGGGGACA 776542 i ? i v i iii i MIR1_Amn#SINE 117 CTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGGATA 154 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.38 CpG sites = 7, Kimura (unadjusted) = 27.38 Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 189 30.46 0.00 2.90 chr1ptel1M 777565 777635 (222365) C MIR1_Amn#SINE/MIR (39) 191 123 m_b22s601i1 790 chr1ptel1M 777565 AGAACTCAAGTCATGACCACCATGGATGTTGGGCTCCTAGAGCCCCATTT 777614 v iv iv-ii v v v ii vv v -v v C MIR1_Amn#SINE 191 AGATCTCAAAGCACT-TTACAAAGGAGGTCAGTATCAT-TATCCCCATTT 144 chr1ptel1M 777615 TACAAATGGGGCAACAGAGGC 777635 i i v v C MIR1_Amn#SINE 143 TACAGATGAGGAAACTGAGGC 123 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.08 CpG sites = 8, Kimura (unadjusted) = 39.08 Transitions / transversions = 0.62 (8/13) Gap_init rate = 0.03 (2 / 70), avg. gap size = 1.00 (2 / 2) 15 16.90 4.00 4.00 chr1ptel1M 780137 780186 (219814) (GGGCCAG)n#Simple_repeat 1 50 (0) m_b22s252i0 791 chr1ptel1M 780137 GGGACAAGGGCCCCAGG-CAGGGGGC-GGGGCCAGGCCGCCCAGGGGCCA 780184 v i vvi - v - -- v (GGGCCAG)n#Si 1 GGGCCAGGGGCCAGGGGCCAGGGGCCAGGGGCCAGG--GGCCAGGGGCCA 48 chr1ptel1M 780185 GG 780186 (GGGCCAG)n#Si 49 GG 50 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.08 (4 / 49), avg. gap size = 1.00 (4 / 4) 30 5.46 2.63 0.00 chr1ptel1M 781583 781620 (218380) (CA)n#Simple_repeat 1 39 (0) c_b22s251i0 792 chr1ptel1M 781583 CACAC-CACACACACTCATACACACACACACACACACAC 781620 - v i (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACAC 39 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 38 23.06 0.00 3.37 chr1ptel1M 783284 783375 (216625) (GT)n#Simple_repeat 1 89 (0) m_b22s252i1 793 chr1ptel1M 783284 GTGTGTGCTGTGTGTGTACATGTGTGTGCTGTGTGTACATGTGTGTGTGC 783333 - iii - iii i (GT)n#Simple_ 1 GTGTGTG-TGTGTGTGTGTGTGTGTGTG-TGTGTGTGTGTGTGTGTGTGT 48 chr1ptel1M 783334 ATGTGTGTGCTGTGCATGTACACGTGTGTGTGCGTGCGTGTG 783375 i - ii iiii i i (GT)n#Simple_ 49 GTGTGTGTG-TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 89 Matrix = Unknown Transitions / transversions = 1.00 (16/0) Gap_init rate = 0.03 (3 / 91), avg. gap size = 1.00 (3 / 3) 50 0.00 0.00 0.00 chr1ptel1M 783388 783432 (216568) (G)n#Simple_repeat 1 45 (0) c_b22s251i1 794 chr1ptel1M 783388 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 783432 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 45 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 29 25.24 0.00 0.00 chr1ptel1M 783959 784031 (215969) (GATG)n#Simple_repeat 1 73 (0) m_b22s252i2 795 chr1ptel1M 783959 GACGGAGAGATGGACGGGCAGGTGGATGGATGGAGGGATGGATGGATAGA 784008 i vi i iii i v i (GATG)n#Simpl 1 GATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGA 50 chr1ptel1M 784009 CAGACAGATGGATGGCTGGATGG 784031 ii ii v (GATG)n#Simpl 51 TGGATGGATGGATGGATGGATGG 73 Matrix = Unknown Transitions / transversions = 4.00 (12/3) Gap_init rate = 0.00 (0 / 72), avg. gap size = 0.0 (0 / 0) 18 0.00 0.00 0.00 chr1ptel1M 786202 786221 (213779) (G)n#Simple_repeat 1 20 (0) m_b22s252i3 796 chr1ptel1M 786202 GGGGGGGGGGGGGGGGGGGG 786221 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGG 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 22 17.22 0.00 0.00 chr1ptel1M 790638 790676 (209324) (A)n#Simple_repeat 1 39 (0) m_b22s252i4 797 chr1ptel1M 790638 AAAAAATAAAGAAAAAAAACAAACAAAAAAAAGAACAAA 790676 v i v v i v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 39 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 17 15.49 0.00 0.00 chr1ptel1M 791201 791229 (208771) (A)n#Simple_repeat 1 29 (0) m_b22s252i5 798 chr1ptel1M 791201 AATAAAATAAAAAAAAAAAAAAACACAAA 791229 v v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA 29 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 25 15.69 0.00 0.00 chr1ptel1M 792991 793033 (206967) (AG)n#Simple_repeat 1 43 (0) m_b22s252i6 799 chr1ptel1M 792991 AGAGACAGAGAGAGAGAGACACAGAGAGAGACACAGAGATAGA 793033 v v v v v v (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 43 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 13 15.84 6.82 2.17 chr1ptel1M 794090 794133 (205867) (CTGGG)n#Simple_repeat 1 46 (0) m_b22s252i7 800 chr1ptel1M 794090 CTGTGCCGGG-TGGCCATGGGCTGGGCT-GGCTGTGCT-CGCTGTGC 794133 v i - v - - v -v v (CTGGG)n#Simp 1 CTGGGCTGGGCTGGGC-TGGGCTGGGCTGGGCTGGGCTGGGCTGGGC 46 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.09 (4 / 43), avg. gap size = 1.00 (4 / 4) 18 12.17 2.78 0.00 chr1ptel1M 794376 794411 (205589) (CCACCC)n#Simple_repeat 1 37 (0) m_b22s252i9 801 chr1ptel1M 794376 CCAGCCCCACCCCCA-CCCATGCCCCACCCCCACCCC 794411 v - vvv (CCACCC)n#Sim 1 CCACCCCCACCCCCACCCCCACCCCCACCCCCACCCC 37 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) 16 13.87 0.00 9.09 chr1ptel1M 794372 794419 (205581) (CACCC)n#Simple_repeat 1 44 (0) m_b22s252i8 802 chr1ptel1M 794372 CACACCAGCCCCACCCCCACCCATGCCCCACCCCCACCCCATCTCACC 794419 v - - -ii - i i (CACCC)n#Simp 1 CACCCCA-CCCCA-CCCCACCC-CACCCCA-CCCCACCCCACCCCACC 44 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.09 (4 / 47), avg. gap size = 1.00 (4 / 4) 243 29.62 0.00 10.98 chr1ptel1M 794985 795075 (204925) L2c_3end#LINE/L2 395 476 (2) m_b22s601i2 803 chr1ptel1M 794985 CGGAGACCAGGGCTAACTCATACCTCTTGTGCCCCCAGCGCTCAGCACTG 795034 i i iv v v i -- - ii ------ L2c_3end#LINE 395 CAGGGACCGTGTCTTATTCAT--CT-TTGTATCCCCAGCGC------CTG 435 chr1ptel1M 795035 GCATACAGGGGGCGCCTAATAAATGCTCACAAAGTGACCGA 795075 i i vi ii i iiivi i vi L2c_3end#LINE 436 GCACATAGTAGGCGCTCAATAAATGTTTGTTGAATGAATGA 476 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.65 CpG sites = 18, Kimura (unadjusted) = 39.85 Transitions / transversions = 3.00 (18/6) Gap_init rate = 0.10 (9 / 90), avg. gap size = 1.00 (9 / 9) 16 16.52 0.00 0.00 chr1ptel1M 797343 797369 (202631) (C)n#Simple_repeat 1 27 (0) m_b22s252i10 804 chr1ptel1M 797343 CCCCCCCCACCCCACCCCCCTCCACCC 797369 v v i v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCC 27 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 192 25.53 2.13 0.00 chr1ptel1M 797879 797925 (202075) MIR3#SINE/MIR 114 161 (47) m_b22s601i3 805 chr1ptel1M 797879 CCAGGCCTCGCTTTCCTCATCTGT-AAATCGGAGGCCTGGGCTCAATG 797925 ii iv - vi i vi i vi MIR3#SINE/MIR 114 CTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATG 161 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.38 CpG sites = 8, Kimura (unadjusted) = 32.38 Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.02 (1 / 46), avg. gap size = 1.00 (1 / 1) 13 17.81 5.26 0.00 chr1ptel1M 798286 798323 (201677) (CCCTCCG)n#Simple_repeat 1 40 (0) m_b22s252i11 806 chr1ptel1M 798286 CCCTGCCCCCTCCGCCCT-GGCCC-CCCCCCCCGGCCCTC 798323 v v -v - v i v (CCCTCCG)n#Si 1 CCCTCCGCCCTCCGCCCTCCGCCCTCCGCCCTCCGCCCTC 40 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 233 26.98 0.00 10.67 chr1ptel1M 798519 798601 (201399) C MIR3#SINE/MIR (21) 187 113 m_b22s601i4 807 chr1ptel1M 798519 TCAGGGACAGAATGGACGGCTCTCTGAGGCTACCAAGTCCAGCCCCTCCA 798568 i vii v ---- iv iii i v i ii C MIR3#SINE/MIR 187 TCAGAGCTGGAAGGGAC----CTTAGAGATCATCTAGTCCAACCCCCTCA 142 chr1ptel1M 798569 CTTTACAGAGAAGAAAACAGAGACTGGCCCAGA 798601 i vi i v ---- C MIR3#SINE/MIR 141 TTTTACAGATGAGGAAACTGA----GGCCCAGA 113 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.55 CpG sites = 14, Kimura (unadjusted) = 34.55 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.10 (8 / 82), avg. gap size = 1.00 (8 / 8) 14 21.54 4.00 1.96 chr1ptel1M 798957 799006 (200994) (CTGC)n#Simple_repeat 1 51 (0) m_b22s252i12 808 chr1ptel1M 798957 CTTCCTGCTCT-CCTCCCTCCATGCCTGTCTCCCTGCCT-TCAGCCTGGC 799004 v - - v v v i v -i v v (CTGC)n#Simpl 1 CTGCCTGC-CTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCC 49 chr1ptel1M 799005 TG 799006 (CTGC)n#Simpl 50 TG 51 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.06 (3 / 49), avg. gap size = 1.00 (3 / 3) 236 24.62 7.69 0.00 chr1ptel1M 799963 800027 (199973) HSAT5v1#Satellite 5210 5279 (619) m_b22s502i0 809 chr1ptel1M 799963 GCGTGTGTACAA-----GTGTGTATGTGCGTGTGCACATATGTGCGTGTG 800007 ii i ----- i i i i i i i i HSAT5v1#Satel 5210 GCGTGCATGCAATGTGTGTGTGCACGCGCGTGCGCGCGTGTGTGTGTGTG 5259 chr1ptel1M 800008 CACGTGCGTGCGTGTGTGTG 800027 ? i i i i i HSAT5v1#Satel 5260 NACGCGTGTGTGCGCGTGTG 5279 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 16.08 CpG sites = 16, Kimura (unadjusted) = 34.66 Transitions / transversions = 1.00 (16/0) Gap_init rate = 0.02 (1 / 64), avg. gap size = 5.00 (5 / 1) 15 13.67 0.00 0.00 chr1ptel1M 801061 801084 (198916) (G)n#Simple_repeat 1 24 (0) m_b22s252i13 810 chr1ptel1M 801061 GGGGGGACGGGGGTGGGGGGGGGG 801084 iv v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGG 24 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 207 33.33 1.39 0.00 chr1ptel1M 802291 802362 (197638) MIRb#SINE/MIR 173 245 (23) m_b22s601i5 811 chr1ptel1M 802291 GGATCCTTGAAAGGATCCAGCGGGGCCAGGGCGGTAAAGCGCCAAGCACA 802340 i iv vi iv ii i iiv v vvv iv MIRb#SINE/MIR 173 GGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGCACA 222 chr1ptel1M 802341 GCGCCT-GCACACAGTAGGTACT 802362 i - i i ii MIRb#SINE/MIR 223 GTGCCTGGCACATAGTAAGCGCT 245 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.26 CpG sites = 15, Kimura (unadjusted) = 46.20 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.01 (1 / 71), avg. gap size = 1.00 (1 / 1) 16 32.28 0.00 1.82 chr1ptel1M 802411 802466 (197534) (GT)n#Simple_repeat 1 55 (0) m_b22s252i14 812 chr1ptel1M 802411 GTGCGAGTGTGTACTTTGTAAGTGTGCATGTGTGTGTGTATATGGGCATG 802460 i v -v v iv ii i i v ii (GT)n#Simple_ 1 GTGTGTGTGTGT-GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 49 chr1ptel1M 802461 TGTCTG 802466 v (GT)n#Simple_ 50 TGTGTG 55 Matrix = Unknown Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.02 (1 / 55), avg. gap size = 1.00 (1 / 1) 22 16.46 3.57 1.75 chr1ptel1M 803239 803294 (196706) (CCGGCC)n#Simple_repeat 1 57 (0) m_b22s252i16 813 chr1ptel1M 803239 CCGGCCCC-GCCCCCGCCCCGCCCCCAGCCCGGGCGCCCCGCCCC-CTCC 803286 - v v i v - v -vi (CCGGCC)n#Sim 1 CCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGC-CCCGGCCCCGGCCC 49 chr1ptel1M 803287 CAGCCCCG 803294 i (CCGGCC)n#Sim 50 CGGCCCCG 57 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.05 (3 / 55), avg. gap size = 1.00 (3 / 3) 14 21.19 1.25 10.96 chr1ptel1M 804097 804176 (195824) (GCTGG)n#Simple_repeat 1 73 (0) m_b22s252i17 814 chr1ptel1M 804097 GCAGGGCCGGCCGTGGGCGGGGCCTAGGCGCGGACCGGGGTCTGGATTGG 804146 v i v - v - - - v iv v - ii (GCTGG)n#Simp 1 GCTGGGCTGGGC-TGGGCTGGG-CT-GG-GCTGGGCTGGG-CTGGGCTGG 45 chr1ptel1M 804147 G-TGAGACGTGGGCTGGGCTGGCGCAGGGCT 804176 - - i - - v (GCTGG)n#Simp 46 GCTG-GGC-TGGGCTGGGCTGG-GCTGGGCT 73 Matrix = Unknown Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.11 (9 / 79), avg. gap size = 1.00 (9 / 9) 35 0.00 0.00 0.00 chr1ptel1M 804229 804261 (195739) (G)n#Simple_repeat 1 33 (0) c_b22s251i2 815 chr1ptel1M 804229 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 804261 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 33 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 13 20.37 1.72 7.27 chr1ptel1M 804377 804434 (195566) (CGCGCTC)n#Simple_repeat 1 55 (0) m_b22s252i18 816 chr1ptel1M 804377 CGCGCTTCGCTGC-CCGCGCAGCGCCTGCTCCAGGATCCGCCCTCCGGGC 804425 i - - vv - - iv v v v (CGCGCTC)n#Si 1 CGCGCTCCGC-GCTCCGCGCTCCG-C-GCTCCGCGCTCCGCGCTCCGCGC 47 chr1ptel1M 804426 TCTCGGGCT 804434 - v (CGCGCTC)n#Si 48 TC-CGCGCT 55 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.09 (5 / 57), avg. gap size = 1.00 (5 / 5) 20 13.96 0.00 0.00 chr1ptel1M 804579 804610 (195390) (G)n#Simple_repeat 1 32 (0) m_b22s252i19 817 chr1ptel1M 804579 GGGGGGGGGGAGGGGGGAGGGGGGAGGGCGGG 804610 i i i v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 32 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 34 0.00 0.00 0.00 chr1ptel1M 806149 806177 (193823) (AC)n#Simple_repeat 1 29 (0) c_b22s251i3 818 chr1ptel1M 806149 ACACACACACACACACACACACACACACA 806177 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACA 29 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 81 24.05 0.00 0.00 chr1ptel1M 808210 808379 (191621) (G)n#Simple_repeat 1 170 (0) m_b22s252i20 819 chr1ptel1M 808210 GGAGGGGGGCGGGAGGGGGGAAGGTGGAGGGGGGGGAAGGGGGGAGGGGG 808259 i v i ii v i ii i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 50 chr1ptel1M 808260 AAGGGGGGGAGGGGGGGGGGAGGGGAAGGGGGGGGAGGGGAGGGAGGGGG 808309 ii i i ii i i i (G)n#Simple_r 51 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 100 chr1ptel1M 808310 GGGGAGGGGGGGAAGGGAAAGGGGGGGGGAGGGGGGGGGGAAGGAGGGGG 808359 i ii iii i ii i (G)n#Simple_r 101 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 150 chr1ptel1M 808360 GGGAGGGGGGGAATGGGGGG 808379 i iiv (G)n#Simple_r 151 GGGGGGGGGGGGGGGGGGGG 170 Matrix = Unknown Transitions / transversions = 10.00 (30/3) Gap_init rate = 0.00 (0 / 169), avg. gap size = 0.0 (0 / 0) 19 24.72 0.00 5.71 chr1ptel1M 808856 808929 (191071) (GCCCCCG)n#Simple_repeat 1 70 (0) m_b22s252i21 820 chr1ptel1M 808856 GCCCCCGGCCCCCGGTCCCCGTCTCCCCCGGTCTCGGGGCTCCCCCGGTC 808905 i --v - i vv - v vi (GCCCCCG)n#Si 1 GCCCCCGGCCCCCGGCCCCCG--GCCCCCGG-CCCCCGGC-CCCCGGCCC 46 chr1ptel1M 808906 TCTCCGCCCGGCTCCCGGTCCCCG 808929 i vv v i i (GCCCCCG)n#Si 47 CCGGCCCCCGGCCCCCGGCCCCCG 70 Matrix = Unknown Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.05 (4 / 73), avg. gap size = 1.00 (4 / 4) 12 8.66 0.00 7.41 chr1ptel1M 809583 809611 (190389) (GGGA)n#Simple_repeat 1 27 (0) m_b22s252i22 821 chr1ptel1M 809583 GGAAGGGAGGTGGGGGAGGGGAGGGAGGG 809611 i - i - (GGGA)n#Simpl 1 GGGAGGGAGG-GAGGGA-GGGAGGGAGGG 27 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.07 (2 / 28), avg. gap size = 1.00 (2 / 2) 29 2.61 5.13 0.00 chr1ptel1M 809712 809750 (190250) (AGAGAC)n#Simple_repeat 1 41 (0) c_b22s251i4 822 chr1ptel1M 809712 AGAGAGAGAGACAGAGACAGAGA-AGAGA-AGAGACAGAGA 809750 v - - (AGAGAC)n#Sim 1 AGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGA 41 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2) 819 7.75 0.00 0.00 chr1ptel1M 809783 810869 (189131) (A)n#Simple_repeat 1 1087 (0) m_b22s252i23 823 chr1ptel1M 809783 AAAAAAAGAACAAGAGACAGAAAAAAAGACAAGAGAAAAAAAAAAAAGAG 809832 i v i i v i i v i i i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr1ptel1M 809833 AACAAGAGAAAACAGAAAACAAAAAAACCAAAAGAAAAAAAAAAAAAAAA 809882 v i i v i v vv i (A)n#Simple_r 51 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 100 chr1ptel1M 809883 AAAAAAAACAACAAGAAAAAAAAAGCAAAAAAAAAAAAAAGGGAAAAAAA 809932 v v i iv iii (A)n#Simple_r 101 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 150 chr1ptel1M 809933 AAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 809982 v (A)n#Simple_r 151 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 200 chr1ptel1M 809983 AAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 810032 v (A)n#Simple_r 201 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 250 chr1ptel1M 810033 AAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 810082 v (A)n#Simple_r 251 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 300 chr1ptel1M 810083 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 810132 (A)n#Simple_r 301 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 350 chr1ptel1M 810133 AAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 810182 v (A)n#Simple_r 351 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 400 chr1ptel1M 810183 AAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAACAAAAAAAAAAAAC 810232 v v v (A)n#Simple_r 401 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 450 chr1ptel1M 810233 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAACAAA 810282 v v (A)n#Simple_r 451 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 500 chr1ptel1M 810283 AAAAACAAAAAAAAACAAAAAAAAAAACAAAAAAAAAAAACAAAAAAAAA 810332 v v v v (A)n#Simple_r 501 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 550 chr1ptel1M 810333 AAAAAAAAACAAAGAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAA 810382 v i v (A)n#Simple_r 551 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 600 chr1ptel1M 810383 AAAACAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAATTAAACAAAA 810432 v v vv v (A)n#Simple_r 601 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 650 chr1ptel1M 810433 AAAAAAAAAAAAAAACAAAAAACAAAAAAAAAAAAAAAAAAACAAAACAA 810482 v v v v (A)n#Simple_r 651 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 700 chr1ptel1M 810483 AAAAAAACAAACAAAAAAAACAAAACAAAAACAAAAAAAACAAAAAACAA 810532 v v v v v v v (A)n#Simple_r 701 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 750 chr1ptel1M 810533 AAAAAACAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACA 810582 v v v (A)n#Simple_r 751 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 800 chr1ptel1M 810583 AAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 810632 v (A)n#Simple_r 801 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 850 chr1ptel1M 810633 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGAA 810682 ii (A)n#Simple_r 851 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 900 chr1ptel1M 810683 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAA 810732 v (A)n#Simple_r 901 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 950 chr1ptel1M 810733 AAAAAAAAAAAACGGAAAAAAAGGGAAAAAAAAAAAAAAACAAAAAGAAA 810782 vii iii v i (A)n#Simple_r 951 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1000 chr1ptel1M 810783 AAAAAAAGCAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAA 810832 iv v (A)n#Simple_r 1001 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1050 chr1ptel1M 810833 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAA 810869 v (A)n#Simple_r 1051 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1087 Matrix = Unknown Transitions / transversions = 0.54 (28/52) Gap_init rate = 0.00 (0 / 1086), avg. gap size = 0.0 (0 / 0) 15 14.81 0.00 7.50 chr1ptel1M 811402 811444 (188556) (CCCGGG)n#Simple_repeat 1 40 (0) m_b22s252i24 824 chr1ptel1M 811402 CCCGGGCCGCTCTCCCGGCCCCGGGTCCGGGCCACTGGGCCCG 811444 - vvv v i - - (CCCGGG)n#Sim 1 CCCGGGCC-CGGGCCCGGGCCCGGGCCCGGGCC-C-GGGCCCG 40 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.07 (3 / 42), avg. gap size = 1.00 (3 / 3) 20 22.11 0.00 0.00 chr1ptel1M 811708 811749 (188251) (C)n#Simple_repeat 1 42 (0) m_b22s252i25 825 chr1ptel1M 811708 CCCGCGCCCCCCCGCCCCCCATCCCCCCTCCTCCCCTCCCCC 811749 v v v vi i i i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 42 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 17 12.68 0.00 0.00 chr1ptel1M 812661 812686 (187314) (G)n#Simple_repeat 1 26 (0) m_b22s252i26 826 chr1ptel1M 812661 GGGGCGGGGAGGGGGGGAGGGGGGGG 812686 v i i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGG 26 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 120 24.09 5.01 1.45 chr1ptel1M 816345 816743 (183257) (TC)n#Simple_repeat 1 413 (0) m_b23s252i0 827 chr1ptel1M 816345 TCTCTCTCTC-CTCTC-CTCCGTCT-TCTGTCTCTGTCTTTATCTCTGTC 816391 - - iv - v v i v v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr1ptel1M 816392 CCTCCCCCCCCCTC-CTCTCTCTGCCCATCTCT-TGTCTCTTTCTCTC-C 816438 i i i i i - - i - - v i - (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCT-CTC-TCTCTCTCTCTCTCTCTCTCTC 98 chr1ptel1M 816439 TCTCTGTCCATCTCTCT-TTTCTCTGTATGTATCTC-CTTTCTCTTTC-C 816485 v iv - i v v v v - i i - (TC)n#Simple_ 99 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 148 chr1ptel1M 816486 TCTCATTTCTCT-TCTTTGTCTCTGTCTCT-TGTGTCTCT-TGTGTCTGT 816532 - i - i v v - v v - v v v (TC)n#Simple_ 149 TCTC-TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 197 chr1ptel1M 816533 CTC-CTCTCTGTCTCTCTCAGTCTTTCTCTTCCTTTCCCTTTCTCTCCCC 816581 - v vv i ii i i i i i (TC)n#Simple_ 198 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 247 chr1ptel1M 816582 CCATCTTTCCCTCTCTCTC-CTGTTTCTGCT-TCTCTGTCTACCCCCTCC 816629 iv i i - v i - - v - i i i (TC)n#Simple_ 248 CTCTCTCTCTCTCTCTCTCTCTCTCTCT-CTCTCTCTCTCT-CTCTCTCT 295 chr1ptel1M 816630 CT-TCT-TTTCTCCCCCCATCTCTCTTTCCCTCTCCCTGTCTCTTTATCT 816677 - - i i i iv i i i v i v (TC)n#Simple_ 296 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 345 chr1ptel1M 816678 CTTTCTCT-TCT-TGTCTTTGCCTCTGTCCATCTCT-TCTCTGCCTTTCC 816724 i - - v i vi v iv - vi i i (TC)n#Simple_ 346 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 395 chr1ptel1M 816725 CCCGTCTCTCTCTCTCTCT 816743 i - (TC)n#Simple_ 396 CTC-TCTCTCTCTCTCTCT 413 Matrix = Unknown Transitions / transversions = 1.39 (46/33) Gap_init rate = 0.07 (26 / 398), avg. gap size = 1.00 (26 / 26) 415 30.19 3.34 1.09 chr1ptel1M 817253 817943 (182057) (TC)n#Simple_repeat 1 714 (0) m_b23s252i1 828 chr1ptel1M 817253 TCTCTCT-TTTTTCTTTTCCTCTCCCTCT-TTTCTGTCTGTCTCTCTCTC 817300 - i i i ii i - i v v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr1ptel1M 817301 ATATGTCTCTCTCT-TCTATCTCTTCCTTTCTCTTTCCCACTCTTTC-CC 817348 - v v - v ii i i i v i - i (TC)n#Simple_ 51 -TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 99 chr1ptel1M 817349 CCCTCTCTTTCCCTCTCCTTGTCTTTTTCTGTCTTTCTGTCTCTGTCCCT 817398 i i i ii v i i v i v v i (TC)n#Simple_ 100 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 149 chr1ptel1M 817399 TTCTCTGTTTTTCTCT-TTTCTCCCTTTCTCTC-CTTTTTC-CTCTC-CT 817444 i v i i - i i i - i i - - (TC)n#Simple_ 150 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 199 chr1ptel1M 817445 TTTTCTTTTTTCCCCTCTCT-TTTCTCCATTTCTCTCCCTCTTTC-CTTT 817492 i i i i ii i - i iv i i i - i (TC)n#Simple_ 200 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 249 chr1ptel1M 817493 CTTTCTCTTTCCCTTTCTCTC-CTCTTTCTTTCTCTCCCTTTTTCCTTTT 817541 i i i i - i i i i i ii i (TC)n#Simple_ 250 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 299 chr1ptel1M 817542 CCCTCT-TTTCTCTTTTCCTCTCTCTC-CTGTATCTTTCTCTTTCCCCCT 817589 i - i i ii - v v i i i i (TC)n#Simple_ 300 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 349 chr1ptel1M 817590 CTCTC-CTGTCTTTCTCTTTCCCCCTCTTTCTTTTTCTCTTCCTTTCTCT 817638 - v i i i i i i i ii i (TC)n#Simple_ 350 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 399 chr1ptel1M 817639 C-CTTTGTCTCTGTCTCTTTTTGTCTCTTCCTATCTCT-TCTGTCTCTTT 817686 - i v v i i v ii v - v i (TC)n#Simple_ 400 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 449 chr1ptel1M 817687 TTCTGTCTCTGTCTCTCCCTTTCTCTTTCCGTCTGTTTCTGTCTCT-TCT 817735 i v v i i i iv v i v - (TC)n#Simple_ 450 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 499 chr1ptel1M 817736 TTGTCTCT-TTTCT-TCTCTTTCTCTCTCTCCCTCTCCCCCTCT-TATCT 817782 i v - i - i i i i - v (TC)n#Simple_ 500 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 549 chr1ptel1M 817783 CTGTATTTCTCTTTTTCTTTTCCTCCCTCTC-CTGTCTTTCTTTCTGTCT 817831 v v i i i i ii i - v i i v (TC)n#Simple_ 550 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 599 chr1ptel1M 817832 CT-TCTGTCACTGTCTCTGTCTTTGATCTGTCTCACTCTCTCTCTTTCCC 817880 - v v v v i -v v v i i (TC)n#Simple_ 600 CTCTCTCTCTCTCTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTC 648 chr1ptel1M 817881 TC-CTCTTTGTTGCT-TTTTTCTGTCTCTCTCT-TCTGTTTCTCTTCCTT 817927 - i v iv - i i v - v i ii i (TC)n#Simple_ 649 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 698 chr1ptel1M 817928 TCTCTCTTTCCCTCTC 817943 i i (TC)n#Simple_ 699 TCTCTCTCTCTCTCTC 714 Matrix = Unknown Transitions / transversions = 2.74 (115/42) Gap_init rate = 0.04 (27 / 690), avg. gap size = 1.00 (27 / 27) 26 0.00 0.00 0.00 chr1ptel1M 817947 817971 (182029) (TGTCTC)n#Simple_repeat 1 25 (0) c_b23s251i0 829 chr1ptel1M 817947 TGTCTCTGTCTCTGTCTCTGTCTCT 817971 (TGTCTC)n#Sim 1 TGTCTCTGTCTCTGTCTCTGTCTCT 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 415 30.19 3.34 1.09 chr1ptel1M 818139 818891 (181109) (TC)n#Simple_repeat 885 1651 (0) m_b23s252i2 830 chr1ptel1M 818139 CCTCTCTTTTTCTGTCTCTGTCTCCATCTCCCTATCTCTCCCTCCCTCTC 818188 i i i v v iv i v i i (TC)n#Simple_ 885 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 934 chr1ptel1M 818189 TCTTTCTCT-TATCTCTTTCCCTTTCTCAC-CTGCCTCTCTCTCTTTCTC 818236 i - v i i i v - vi i (TC)n#Simple_ 935 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 984 chr1ptel1M 818237 TGTCTCTCATCTCTCTC-CTCATCT-TGTCTGTCTCCATCCATCTCT-TC 818283 v - - - - v v iv iv - (TC)n#Simple_ 985 TCTCTCTC-TCTCTCTCTCTC-TCTCTCTCTCTCTCTCTCTCTCTCTCTC 1032 chr1ptel1M 818284 TCTCTGTATCTGTCTCTGTCTCTTTCCCTCTC-CTCTGTCTCTTTTTCTC 818332 v v v v i i - v i i (TC)n#Simple_ 1033 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 1082 chr1ptel1M 818333 TTTTGGTGTCTCTGTTTCTGTGTCTCTCACTATCTCTTTCACTCTCTCT- 818381 i ivv v v i v v v v i v - (TC)n#Simple_ 1083 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 1132 chr1ptel1M 818382 TCTGTTTTTGGCTTTTTCTCT-TTTTTGTCACTGTCTCTGTCT-TCTGTC 818429 v i i vv i i - i i v v v v - v (TC)n#Simple_ 1133 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 1182 chr1ptel1M 818430 TGTCTC-CTTTCTCTCTCACTCTTTCCATCTCTC-CTCTCTCT-TCTCTA 818476 v - i v i iv - - v (TC)n#Simple_ 1183 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 1232 chr1ptel1M 818477 TCTCTCTTTCCCTCTCCTTGTCTCTC-CTGTTTCTGTGTCTCTTTTTTTG 818525 i i ii v - v i v v i i i v (TC)n#Simple_ 1233 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 1282 chr1ptel1M 818526 TCTGTCTCTTTCTGTCCCCGTCTTTCTCTCCCTACCTCTTTCCCTC-CTC 818574 v i v i iv i i vi i i - (TC)n#Simple_ 1283 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 1332 chr1ptel1M 818575 -CTGCCCTCCCTCTCGTCTGTCTCTTTTTCTCTTCCCCTGTCTCTCTTTT 818623 - - i i - v i i ii i v i i (TC)n#Simple_ 1333 TCT-CTCTCTCTCTC-TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 1380 chr1ptel1M 818624 TCTCTTTCTCTCTCTCT-TGTCTATATCTCT-TTTCTCTCTTCCTTTCTT 818671 i - v v v - i ii i i (TC)n#Simple_ 1381 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 1430 chr1ptel1M 818672 TTCCCCTCTTTCATCTCTTCCCCTTTCTCTCT-TCTCCCTCTCTGTCGCT 818720 ii i i - ii i i - i v v (TC)n#Simple_ 1431 TCTCTCTCTCTC-TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 1479 chr1ptel1M 818721 TTCTCTATCTCTCT-TGTCTCTGTATCTGTCTCTCTTCCTTTCTCTCTTC 818769 i v - v v v v ii i ii (TC)n#Simple_ 1480 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 1529 chr1ptel1M 818770 CCCTCTTTCTTTCTCTCCCTCTCTTTCATCTTTCTCTGTGTCTTTTTCTG 818819 i i i i i - i v v i i v (TC)n#Simple_ 1530 CTCTCTCTCTCTCTCTCTCTCTCTCTC-TCTCTCTCTCTCTCTCTCTCTC 1578 chr1ptel1M 818820 TCTCTGACTCTGTCTGTCTCTCTGTTTCTCTGTCTCTCTCCCTCCCTCCC 818869 vv v v v i v i i i (TC)n#Simple_ 1579 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 1628 chr1ptel1M 818870 TTCCTCCCTC-CTCCCTCGCTCT 818891 ii i - i v (TC)n#Simple_ 1629 TCTCTCTCTCTCTCTCTCTCTCT 1651 Matrix = Unknown Transitions / transversions = 1.36 (94/69) Gap_init rate = 0.03 (26 / 752), avg. gap size = 1.00 (26 / 26) 13 18.25 2.38 4.88 chr1ptel1M 818857 818898 (181102) (CTTC)n#Simple_repeat 1 41 (0) m_b23s252i3 831 chr1ptel1M 818857 CTCCCTCCCTCCCTTCC-TCCCTCCTCCCTCGCTCTTCCTTCC 818898 i i i - i i -v - (CTTC)n#Simpl 1 CTTCCTTCCTTCCTTCCTTCCTTCCTTCCT-TC-CTTCCTTCC 41 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.07 (3 / 41), avg. gap size = 1.00 (3 / 3) 306 30.97 13.37 0.52 chr1ptel1M 819616 819787 (180213) MIRc#SINE/MIR 10 203 (65) m_b23s601i0 832 chr1ptel1M 819616 GCGGGGCAATGGCTGGAGCTCTGGGCCTGT-GCCGGGAAG--------TC 819656 i v i vvi v i i v- i i -------- MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr1ptel1M 819657 AAAATCGGGCCTCCGATGCTTCCCGGCCACATGACACCAGGTAAGTCACT 819706 i ivi v - i vii v ii iiii viii i MIRc#SINE/MIR 60 GAGTCCCGGC-TCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACT 108 chr1ptel1M 819707 TAACGTATCT--GCCTCTGTTCCTGCAACTGTAATATGGAGCGA------ 819748 v v -- v i iv v v i vv ------ MIRc#SINE/MIR 109 TAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATA 158 chr1ptel1M 819749 ---GCGCCACCTCCCCCA---GGTTCCTGTGAGGCTCAAATGGGA 819787 --- v ii v i --- vi v i MIRc#SINE/MIR 159 CCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGA 203 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 40.20 CpG sites = 31, Kimura (unadjusted) = 41.22 Transitions / transversions = 1.41 (31/22) Gap_init rate = 0.04 (7 / 171), avg. gap size = 3.43 (24 / 7) 186 14.76 0.00 5.88 chr1ptel1M 821741 821776 (178224) C MIR#SINE/MIR (116) 146 113 m_b23s601i3 833 chr1ptel1M 821741 TCCCCATTTTGCGGATAAGGAAGCCGAGGCGGACAG 821776 i i i i i -- C MIR#SINE/MIR 146 TCCCCATTTTACAGATGAGGAAACTGAGGC--ACAG 113 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 17.42 CpG sites = 5, Kimura (unadjusted) = 17.42 Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 187 16.67 0.00 0.00 chr1ptel1M 821741 821770 (178230) C MIRb#SINE/MIR (115) 153 124 m_b23s601i2 833 chr1ptel1M 821741 TCCCCATTTTGCGGATAAGGAAGCCGAGGC 821770 i i i i i C MIRb#SINE/MIR 153 TCCCCATTTTACAGATGAGGAAACTGAGGC 124 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 20.27 CpG sites = 5, Kimura (unadjusted) = 20.27 Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 14 0.00 0.00 0.00 chr1ptel1M 822138 822155 (177845) (GGA)n#Simple_repeat 1 18 (0) m_b23s252i4 834 chr1ptel1M 822138 GGAGGAGGAGGAGGAGGA 822155 (GGA)n#Simple 1 GGAGGAGGAGGAGGAGGA 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 43 42.01 3.78 3.22 chr1ptel1M 822854 823409 (176591) (CTCCCTC)n#Simple_repeat 1 559 (0) m_b23s252i5 835 chr1ptel1M 822854 CTCCCTCCCCCCTCCTCCTTCCT-CCT-GTCTCTCTTGTCTCTGTCTTTC 822901 i i - -v i i vi ivi i i (CTCCCTC)n#Si 1 CTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTCC 50 chr1ptel1M 822902 TGTCTTCTCTGT-CTCTCTGTCTCTCTCTTCTCTTCTCTCT-GTCCCTTG 822949 vi i iv - i -i i i i i i -v iv (CTCCCTC)n#Si 51 TCCCTCCTCCCTCCTCCCT-CCTCCCTCCTCCCTCCTCCCTCCTCCCTCC 99 chr1ptel1M 822950 TCTCTTCT-TCTCTTCTCT-GTCTCTTTGTCTCTGTCTCTCTCTTCTCTT 822997 i i -i i i -v - i iv i -i i i i i (CTCCCTC)n#Si 100 TCCCTCCTCCCTCCTCCCTCCTC-CCTCCTCCCT-CCTCCCTCCTCCCTC 147 chr1ptel1M 822998 CTCTCT-GTCCCT-GTCTCTCTTTCCT--TCCCT-CTGTCTCTGTCTTTC 823042 i -v -v i i i -- - vi ivi i i (CTCCCTC)n#Si 148 CTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTCC 197 chr1ptel1M 823043 TCTTTTTTCTCTGTCTCTTCTTCTCTGTCTTCCCTCTTCTCTTCTTTCCT 823092 ii ii i -i -i i iv i i - i i i (CTCCCTC)n#Si 198 TCCCTCCTCCCT-CCTC-CCTCCTCCCTCCTCCCTCCTC-CCTCCTCCCT 244 chr1ptel1M 823093 TTTCCCTCTTCTCTTCTTCTTTCT-CCT-CTTCTTCTGTCCCTCTTTTCT 823140 ii i i i i i i - - i i -v i ii (CTCCCTC)n#Si 245 CCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTC-CTCCCTCCTCCCT 293 chr1ptel1M 823141 -CTATCTCTTCTCT-CTCTCTTCT-TCTCTTCTCTTCTATCTCTATCTCT 823187 - vi i i - i i -i i i i vi -v i (CTCCCTC)n#Si 294 CCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTC-CTCCCT 342 chr1ptel1M 823188 ATCTCTTTCTCTCTCTCTTCTCTTCTCTCT-CTGTCTCTTCCCTCTTCTC 823236 -i ii - i i i i i - vi i -- (CTCCCTC)n#Si 343 -CCTCCCTC-CTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTC--CTC 388 chr1ptel1M 823237 TCTCTTCTCTTCTCTTCTTCTCTTCTTCTTTCTCTTCTCTAC-CTCTTCT 823285 i i i i -i i -i i ii i i v - i i (CTCCCTC)n#Si 389 CCTCCTCCCTCCTC-CCTCCTC-CCTCCTCCCTCCTCCCTCCTCCCTCCT 436 chr1ptel1M 823286 CTCTTCTCTTTCCTTCCCTCTTCTCT-AT-CTTTATCCCTCTGTCTCTTC 823333 i i ii - i i -v - i iv -v i i (CTCCCTC)n#Si 437 CCCTCCTCCCTCC-TCCCTCCTCCCTCCTCCCTCCTCCCTC-CTCCCTCC 484 chr1ptel1M 823334 TCTCTTCTCTATCTCTCTTCTTCTTCTTCTTCTCTCTTCCCTCTTCTCTT 823383 i i iv - -i i i i i i i i i i (CTCCCTC)n#Si 485 TCCCTCCTCCCTC-CTC-CCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTC 532 chr1ptel1M 823384 CTCTCTCTTCTCTCTTCTCTCC-CCCT 823409 i i i i i - (CTCCCTC)n#Si 533 CTCCCTCCTCCCTCCTCCCTCCTCCCT 559 Matrix = Unknown Transitions / transversions = 5.50 (132/24) Gap_init rate = 0.07 (38 / 555), avg. gap size = 1.03 (39 / 38) 189 26.32 0.00 0.00 chr1ptel1M 825344 825381 (174619) L2d2_3end#LINE/L2 512 549 (6) m_b23s601i4 836 chr1ptel1M 825344 TGCACACAGTAGGTGCTTAATCAGTGTTCACTGGCTTG 825381 i i v i i iii ii L2d2_3end#LIN 512 TGCACACAGTAGGCGCTCAATAAATATTTGTTGATTTG 549 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 31.48 CpG sites = 9, Kimura (unadjusted) = 36.01 Transitions / transversions = 9.00 (9/1) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 261 37.42 9.18 0.47 chr1ptel1M 826565 826760 (173240) L3#LINE/CR1 857 1069 (3030) m_b23s601i5 837 chr1ptel1M 826565 ACAGCTGG-GTTTTCATCACCCCCGCCAATTAAGAGTCATGGTTTCCAAA 826613 v - v ii iv i i ii i ii ivi L3#LINE/CR1 857 ACAGGTGGTGTTTTCATCTCTTCTTCCAGTTGAAGGTCGTGACTTTGGAA 906 chr1ptel1M 826614 AAGAAAGGAAGTTG-GGGAAAT------CTAG-------GA-GGTTTGGA 826648 i i v i- i ------ i ------- - v v L3#LINE/CR1 907 GAGAAAGGAGGATATGGGAAGTGAACAGCTGGCTACGTAGATGGTGTCGA 956 chr1ptel1M 826649 ACCATGAGGCTTGTGTTTGTGCGCCTCCCTTTAAAAC-TTAGAAAGGGCA 826697 vv iii ii vv v vi vivvi ?i i-ii v ivvi L3#LINE/CR1 957 AGAACAGGATTTGGTTTTCTGGACCATGGCTTANGATACCAGAACGATGG 1006 chr1ptel1M 826698 GCTTCTGGCCACGGGCAGGAAATGTC-CACTGAGGGCTGAAAAAAATAGA 826746 i ? v i i iiviii - - i i i ii i iivi L3#LINE/CR1 1007 GCTCCTGGCNAGGGACGGAGTGCATCTCAC-GAAGACCGGGAAGAACGTG 1055 chr1ptel1M 826747 TTTGCCTAAAGTCT 826760 ? ?ii v L3#LINE/CR1 1056 TTTGNCNGGAGACT 1069 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 53.36 CpG sites = 50, Kimura (unadjusted) = 58.53 Transitions / transversions = 2.17 (50/23) Gap_init rate = 0.04 (8 / 195), avg. gap size = 2.38 (19 / 8) 17 24.01 0.00 0.00 chr1ptel1M 831995 832033 (167967) (TT)n#Simple_repeat 1 39 (0) m_b23s252i7 838 chr1ptel1M 831995 TTTTTTTTTTTTTCTGAGCTTTTTTTGTTGTTTATTTTT 832033 i vvvi v v v (TT)n#Simple_ 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 39 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 13 4.77 4.55 0.00 chr1ptel1M 839310 839331 (160669) (CCT)n#Simple_repeat 1 23 (0) m_b23s252i8 839 chr1ptel1M 839310 CCT-CTCCTCCTCCTCCTTCTCC 839331 - i (CCT)n#Simple 1 CCTCCTCCTCCTCCTCCTCCTCC 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.05 (1 / 21), avg. gap size = 1.00 (1 / 1) 17 14.33 6.25 2.00 chr1ptel1M 840841 840888 (159112) (TTGCTT)n#Simple_repeat 1 50 (0) m_b23s252i9 840 chr1ptel1M 840841 TTG-TTTTTATTTT-CTTCT-CTTGTGGTTTTTCTCTTTGCTTTTGCTTT 840887 - vv - i - v v v - (TTGCTT)n#Sim 1 TTGCTTTTGCTTTTGCTTTTGCTTTTGCTTTTGCT-TTTGCTTTTGCTTT 49 chr1ptel1M 840888 T 840888 (TTGCTT)n#Sim 50 T 50 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.09 (4 / 47), avg. gap size = 1.00 (4 / 4) 16 18.30 2.22 2.22 chr1ptel1M 840845 840889 (159111) (TTTTC)n#Simple_repeat 1 45 (0) m_b23s252i10 840 chr1ptel1M 840845 TTTTATTTTCTTCTCTTGTGGTTT-TTCTCTTTGCTTTTGCTTTTC 840889 v i v vv - i v - (TTTTC)n#Simp 1 TTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTT-CTTTTC 45 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.05 (2 / 44), avg. gap size = 1.00 (2 / 2) 33 8.70 3.85 2.53 chr1ptel1M 841103 841180 (158820) (GATGCCCCT)n#Simple_repeat 1 79 (0) c_b23s251i1 841 chr1ptel1M 841103 GATGCCCTTGATGCCCCCAATGCCCCTGATGCCCCT-ATTGCCCC-CACG 841150 i ii - - -v i (GATGCCCCT)n# 1 GATGCCCCTGATGCCCCTGATGCCCCTGATGCCCCTGA-TGCCCCTGATG 49 chr1ptel1M 841151 CCCCTGATGTCCCC-AATGCCCCTGATGCCC 841180 - -i (GATGCCCCT)n# 50 CCCCTGATG-CCCCTGATGCCCCTGATGCCC 79 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.06 (5 / 77), avg. gap size = 1.00 (5 / 5) 32 27.83 0.00 0.00 chr1ptel1M 841225 841312 (158688) (ACAC)n#Simple_repeat 1 88 (0) m_b23s252i11 842 chr1ptel1M 841225 ACACACACGCGCACATGCACACACAGACGCACAGACACGCACTCACGTGC 841274 i i ii v i v i v iii (ACAC)n#Simpl 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50 chr1ptel1M 841275 ACACGCAGACACACAGACACGCACTCACACGTACAGAC 841312 i v v i v ii v (ACAC)n#Simpl 51 ACACACACACACACACACACACACACACACACACACAC 88 Matrix = Unknown Transitions / transversions = 1.86 (13/7) Gap_init rate = 0.00 (0 / 87), avg. gap size = 0.0 (0 / 0) 16 13.08 0.00 0.00 chr1ptel1M 841400 841424 (158576) (C)n#Simple_repeat 1 25 (0) m_b23s252i12 843 chr1ptel1M 841400 CCCCCCGCCCCCCCCCCGTCCCCCC 841424 v vi (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCC 25 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 12 25.03 4.26 0.00 chr1ptel1M 841590 841636 (158364) (CTGCGGG)n#Simple_repeat 1 49 (0) m_b23s252i13 844 chr1ptel1M 841590 CTGCTGGCTGCGGGCTCCAGGCCCCGAG--GCTGGCGGCGGGCAGAGGG 841636 v v i iv i -- v v v v (CTGCGGG)n#Si 1 CTGCGGGCTGCGGGCTGCGGGCTGCGGGCTGCGGGCTGCGGGCTGCGGG 49 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.02 (1 / 46), avg. gap size = 2.00 (2 / 1) 406 29.91 0.00 0.00 chr1ptel1M 842030 842136 (157864) MIR#SINE/MIR 76 182 (80) m_b23s601i6 845 chr1ptel1M 842030 ATTCGCCACGTGACCCTGGACCAGTCATTCAGGCTTCATGTGCTTCAGTT 842079 i v iii i i v i i i iv iiv i MIR#SINE/MIR 76 ACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTT 125 chr1ptel1M 842080 TCTCCACCTGTAAAATGGGGATAATCGCAGCTCCTCCCTCTCAGGGCTCT 842129 ii i vii iv v vi i v MIR#SINE/MIR 126 TCCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTCATAGGGTTGT 175 chr1ptel1M 842130 GGAGAGG 842136 v v MIR#SINE/MIR 176 TGTGAGG 182 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 39.95 CpG sites = 21, Kimura (unadjusted) = 39.95 Transitions / transversions = 1.91 (21/11) Gap_init rate = 0.00 (0 / 106), avg. gap size = 0.0 (0 / 0) 13 28.17 0.00 5.17 chr1ptel1M 842294 842354 (157646) (CCCTCTG)n#Simple_repeat 1 58 (0) m_b23s252i14 846 chr1ptel1M 842294 CCATCCGCCCTCGGCTGCGGTTCCCGCTGGCCCCCGTGCCCTGGGCCCTT 842343 v i v -v vv v v - i - vv i (CCCTCTG)n#Si 1 CCCTCTGCCCTCTGC-CCTCTGCCCTCT-GCCCTC-TGCCCTCTGCCCTC 47 chr1ptel1M 842344 TGCCCACTGCC 842354 v (CCCTCTG)n#Si 48 TGCCCTCTGCC 58 Matrix = Unknown Transitions / transversions = 0.30 (3/10) Gap_init rate = 0.05 (3 / 60), avg. gap size = 1.00 (3 / 3) 16 20.82 0.00 0.00 chr1ptel1M 844623 844655 (155345) (C)n#Simple_repeat 1 33 (0) m_b23s252i15 847 chr1ptel1M 844623 CCCCATCTCCACCCCCCCACCCCCCCACCCCCC 844655 vi i v v v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 33 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 13 12.68 0.00 0.00 chr1ptel1M 846255 846280 (153720) (GGCCA)n#Simple_repeat 1 26 (0) m_b23s252i16 848 chr1ptel1M 846255 GGCCAGGCTGGGCCAGGCCACGCCAG 846280 ii v (GGCCA)n#Simp 1 GGCCAGGCCAGGCCAGGCCAGGCCAG 26 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 316 29.36 9.94 0.57 chr1ptel1M 846701 846861 (153139) MIR3#SINE/MIR 25 200 (8) m_b23s601i7 849 chr1ptel1M 846701 AGGATGGCATGGGAAT---GAGACCGGAGGCGGAGTGCTCACTCCGACTC 846747 v i vv i --- v i vivv v ivi i v v MIR3#SINE/MIR 25 AGCACGGACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCAC 74 chr1ptel1M 846748 TTGCTAGCTGTGTGACCTGGGGCAAGTCAC-TCA----TTTACTCCTCAG 846792 vi ? v - ---- i ivv MIR3#SINE/MIR 75 TAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAG 124 chr1ptel1M 846793 TTTCTCCATCTAGAATAT---GGGATT--ACAAGGCTGAATTCAAAAGGC 846837 ii iv v --- i -- v i- vi v i v MIR3#SINE/MIR 125 TTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGA-TGATCTCTAAGGTC 173 chr1ptel1M 846838 C---CCGATGAAGACAGTCTGTGACTC 846861 --- iiivvv v i i MIR3#SINE/MIR 174 CCTTCCAGCTCTGACATTCTATGATTC 200 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 35.93 CpG sites = 22, Kimura (unadjusted) = 37.89 Transitions / transversions = 0.88 (22/25) Gap_init rate = 0.04 (7 / 160), avg. gap size = 2.43 (17 / 7) 341 26.19 7.14 0.00 chr1ptel1M 846705 846830 (153170) MIR1_Amn#SINE/MIR 34 168 (62) m_b23s601i8 849 chr1ptel1M 846705 TGGCATGGGAAT---GAGACCGGAGGCGGAGTGCTCACTCCGACTCTTGC 846751 vv v --- v i viv? ? v ivi i v v ? MIR1_Amn#SINE 34 TGGACTGGGACTCGGGAGACCTGGGTTCNANTCCCGGCTCTGCCACTNGC 83 chr1ptel1M 846752 TAGCTGTGTGACCTGGGGCAAGTCACTCA-----TTTACTCCTCAGTTTC 846796 i? ? v i?----- i i?v MIR1_Amn#SINE 84 CNGCTGNGTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTC 133 chr1ptel1M 846797 TCCATCTAGAATAT-GGGATTACAAGGCTGAATTC 846830 ii iv v - v ii vi vi MIR1_Amn#SINE 134 CTCATCTGTAAAATGGGGATAATGATACTGACCTC 168 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 33.67 CpG sites = 16, Kimura (unadjusted) = 34.94 Transitions / transversions = 0.94 (16/17) Gap_init rate = 0.02 (3 / 125), avg. gap size = 3.00 (9 / 3) 370 26.00 5.00 0.00 chr1ptel1M 846718 846817 (153183) MIRc#SINE/MIR 48 152 (116) m_b23s601i9 849 chr1ptel1M 846718 AGACCGGAGGCGGAGTGCTCACTCCGACTCTTGCTAGCTGTGTGACCTGG 846767 v i viv v ivi i v v i v MIRc#SINE/MIR 48 AGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTG 97 chr1ptel1M 846768 GGCAAGTCACTCA-----TTTACTCCTCAGTTTCTCCATCTAGAATATGG 846812 i ----- i ivv ii iv v MIRc#SINE/MIR 98 GGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGG 147 chr1ptel1M 846813 GATTA 846817 iv MIRc#SINE/MIR 148 GGATA 152 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 30.79 CpG sites = 13, Kimura (unadjusted) = 32.24 Transitions / transversions = 1.00 (13/13) Gap_init rate = 0.01 (1 / 99), avg. gap size = 5.00 (5 / 1) 499 31.02 7.49 0.00 chr1ptel1M 847544 847730 (152270) MIRb#SINE/MIR 33 233 (35) m_b23s601i10 850 chr1ptel1M 847544 CAGGCTGTAGAGACAGGAGGGCCTGGATTCAAGCCCCACCTCCAATGTTT 847593 i v i v ivi i i i ii iv iiviii MIRb#SINE/MIR 33 CGGGCTTTGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTCTGCCACTT 82 chr1ptel1M 847594 AATAGTTGCCTGGCACCGGGAAGGTTACTTAACTTCCCCTGGCCTCAGTT 847643 v i iv i vii v i i i ivi MIRb#SINE/MIR 83 ACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTT 132 chr1ptel1M 847644 TCCTCAGGTTCAAAAT---GAT-ACAGCACCAACCTCATGGAGCTGT--T 847687 vv vi --- - i ii v iii i i -- MIRb#SINE/MIR 133 TCCTCATCTGTAAAATGGGGATAATAATACCTACCTCGCAGGGTTGTTGT 182 chr1ptel1M 847688 CAGGATCCCATGAG-TCAGGCAGGG-------TTGGCACAGTACCTGGCA 847729 v ivv - v v v v------- i i MIRb#SINE/MIR 183 GAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCA 232 chr1ptel1M 847730 C 847730 MIRb#SINE/MIR 233 C 233 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 38.06 CpG sites = 37, Kimura (unadjusted) = 41.83 Transitions / transversions = 1.76 (37/21) Gap_init rate = 0.03 (5 / 186), avg. gap size = 2.80 (14 / 5) 16 16.97 2.38 2.38 chr1ptel1M 849294 849335 (150665) (AATAAA)n#Simple_repeat 1 42 (0) m_b23s252i17 851 chr1ptel1M 849294 AATAAAAAGTTATAATAAAAAT-AAATTTAAAATAATAAAAAA 849335 - v v - v v v v (AATAAA)n#Sim 1 AATAAAAA-TAAAAATAAAAATAAAAATAAAAATAAAAATAAA 42 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.05 (2 / 41), avg. gap size = 1.00 (2 / 2) 260 29.87 14.94 0.00 chr1ptel1M 850495 850648 (149352) L2a_3end#LINE/L2 331 507 (10) m_b23s601i11 852 chr1ptel1M 850495 TTAATGCCAAGTGAAAT-CCATATATGT--CTTGTTTATATTTGCATAGT 850541 vii vv v - i v -- i v v vi v L2a_3end#LINE 331 TTATCACCATCTGACATACTATATATTTTACTTATTTATTTGTTTATTGT 380 chr1ptel1M 850542 CT-----CCTCCATTAAACTG--AGCTTCTTGAGAGCAGGAACT---AGC 850581 ----- i i i v -- i v i i ---iv L2a_3end#LINE 381 CTGTCTCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTC 430 chr1ptel1M 850582 TTTTTTCTTTCTT--TGCATCTCTAGCACTTAG-------TTTAGAA-AT 850621 v v ivi -- i i i i i -------ii i v - L2a_3end#LINE 431 TGTTTTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACAT 480 chr1ptel1M 850622 GGTAAATATTTAATAAATATCTGTTGA 850648 i iiiii i i L2a_3end#LINE 481 AGTAGGCGCTCAATAAATATTTGTTGA 507 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 37.46 CpG sites = 30, Kimura (unadjusted) = 39.84 Transitions / transversions = 1.88 (30/16) Gap_init rate = 0.05 (8 / 153), avg. gap size = 2.88 (23 / 8) 358 28.78 1.54 6.45 chr1ptel1M 850519 850648 (149352) L2c_3end#LINE/L2 345 468 (10) m_b23s601i12 852 chr1ptel1M 850519 TGTCTTGTTTATATTTGCATAGTCTCCTCCATTAAACTG--AGCTTCTTG 850566 - i? v ---iv i i -- i L2c_3end#LINE 345 TGTCT-GTTTACNTGT---CTGTCTCCTCCACTAGACTGTGAGCTCCTTG 390 chr1ptel1M 850567 AGAGCAGGAACTAGCTTTTTTCTTTCTTTGCATCTCTAGCACTTAGTTTA 850616 i i iivv i v iiv i i i i i i i--- L2c_3end#LINE 391 AGGGCAGGGACCGTGTCTTATTCATCTTTGTATCCCCAGCGCCTGGC--- 437 chr1ptel1M 850617 GAAATGGTAAATATTTAATAAATATCTGTTGA 850648 - v i iiiii i i i L2c_3end#LINE 438 -ACATAGTAGGCGCTCAATAAATGTTTGTTGA 468 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 35.08 CpG sites = 28, Kimura (unadjusted) = 39.84 Transitions / transversions = 4.00 (28/7) Gap_init rate = 0.07 (9 / 129), avg. gap size = 1.11 (10 / 9) 259 32.65 5.38 3.40 chr1ptel1M 850799 851058 (148942) C L1M2_orf2#LINE/L1 (1577) 1714 1450 m_b23s551i0 853 chr1ptel1M 850799 ATCCTGTTATATCTGCTATAAATCCAATTTTGCTAT----AATGATCTCT 850844 vvi vi vv v i viii ----? ? i C L1M2_orf2#LIN 1714 ATCCTTGCATCCCTGGGATAAATCCCACTTGATCATGGTGNATNATCTTT 1665 chr1ptel1M 850845 TGAATAAACTGCTATAGTCG---TGATAGAATTACATTTAAAAATTTTAA 850891 v ivi i iv v --- v v vii v ii v iv C L1M2_orf2#LIN 1664 TTAATGTGCTGTTGAATTCGGTTTGCTAGTATTTTGTTGAGGATTTTTGC 1615 chr1ptel1M 850892 ATCAATGTTCATTCATGATACTAGTGTATGGCTGTCTTTATCTGCTTTAT 850941 v iviv i i iv i i i v v i i v i C L1M2_orf2#LIN 1614 ATCTATGTTCATCAGGGATATTGGCCTGTAGTTTTCTTTTTTTGTTGTGT 1565 chr1ptel1M 850942 CCTTCCCTTGGTTTAGGAATCTGGACTATATTTGGCT--GAGAAGAAGCC 850989 vi - v v v iiv ii v v --v vi ii C L1M2_orf2#LIN 1564 CCTTGTC-TGGTTTTGGTATCAGGGTAATGCTGGCCTCGTAGAATGAGTT 1516 chr1ptel1M 850990 TGGCAATATGC---CTTCTTCA--TTTTTGGACATATCGTTCCTCAAAAA 851034 v i? v --- i -- --- v ivvv i C L1M2_orf2#LIN 1515 TGGAAGNATTCCCTCCTCTTCAATTTTTTGGA---ATAGTTTGAGAAGAA 1469 chr1ptel1M 851035 TTGAAAAAATGTTAGTTTTTTTTT 851058 -----i i i i C L1M2_orf2#LIN 1468 TTG-----GTATTAGTTCTTCTTT 1450 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 44.50 CpG sites = 43, Kimura (unadjusted) = 44.50 Transitions / transversions = 1.10 (43/39) Gap_init rate = 0.05 (14 / 259), avg. gap size = 1.64 (23 / 14) 443 28.12 0.00 4.39 chr1ptel1M 851721 851839 (148161) MIRc#SINE/MIR 2 115 (153) m_b24s601i2 854 chr1ptel1M 851721 GGGGCAGCTAGGTGGCACAGTGAATAGAGCATCAGTCTTGAAATGAGGAG 851770 i i--- ii i v iii v i i v i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr1ptel1M 851771 AACCTGAGTTCAAATCTAGCCTCAGATTAGCTAACTAGATGTGTGATCCT 851820 i i i i iv v v -ii - v v i i MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTG-CCA-CTTACTAGCTGTGTGACCTT 96 chr1ptel1M 851821 CGGCAAGTCACTTAGCTCC 851839 v i ii MIRc#SINE/MIR 97 GGGCAAGTCACTTAACCTC 115 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 35.73 CpG sites = 23, Kimura (unadjusted) = 37.23 Transitions / transversions = 2.56 (23/9) Gap_init rate = 0.04 (5 / 118), avg. gap size = 1.00 (5 / 5) 306 30.69 4.58 3.01 chr1ptel1M 851733 851863 (148137) MIR#SINE/MIR 7 139 (123) m_b24s601i3 854 chr1ptel1M 851733 TGGCACAGTGAATA-GAGCATCAGTCTTGAAATGAGGAGAACCTGAGTTC 851781 i i iv - ivi iii i iiv - vvi i MIR#SINE/MIR 7 TAGCATAGTGGTTAAGAGCACGGGCTCTGGAGCCAG-ACTGCCTGGGTTC 55 chr1ptel1M 851782 AAATCTAGCCTCAGATTAGCTAACTAGATGTGTGATCCTCGGCAAGTCAC 851831 i iv v v -ii - v v i i v i MIR#SINE/MIR 56 GAATCCCGGCTCTG-CCA-CTTACTAGCTGTGTGACCTTGGGCAAGTTAC 103 chr1ptel1M 851832 TTAGCTCCAAT-TGCC----TTCCCTCAACATGCAAA 851863 i ii vv - ---- i v - i MIR#SINE/MIR 104 TTAACCTCTCTGTGCCTCAGTTTCCTCATC-TGTAAA 139 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 38.50 CpG sites = 25, Kimura (unadjusted) = 41.28 Transitions / transversions = 1.79 (25/14) Gap_init rate = 0.05 (7 / 130), avg. gap size = 1.43 (10 / 7) 188 25.15 20.51 1.44 chr1ptel1M 852037 852153 (147847) C L2d_3end#LINE/L2 (4) 512 374 m_b24s601i4 855 chr1ptel1M 852037 TTAATCAATCAACAAGCAGTTATTAGG-----A--ATG-----AA-AGTT 852073 i i v ii ----- -- ----- i- v v C L2d_3end#LINE 512 TCAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTG 463 chr1ptel1M 852074 TGCAAAGCACTATGGTCACAACTATCAAAAGG---AAAACA--ATTTCTG 852118 v i i i --iv v ?v ?i --- i --i ii C L2d_3end#LINE 462 TGCTAGGCGCTGTGG--GGAACGANAAAANAGTATAAGACATGGTCCCTG 415 chr1ptel1M 852119 CCCTCAAGAAGTT-----TCCATTTGAAGAG-TAAGACCAA 852153 i i ----- i v ii -i i C L2d_3end#LINE 414 CCCTCAAGGAGCTTACAATCTAGTTGGGGAGACAAGACTAA 374 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 31.62 CpG sites = 21, Kimura (unadjusted) = 33.03 Transitions / transversions = 2.62 (21/8) Gap_init rate = 0.09 (10 / 116), avg. gap size = 2.60 (26 / 10) 189 20.57 23.44 1.28 chr1ptel1M 852596 852659 (147341) C MIRc#SINE/MIR (21) 247 170 m_b24s601i5 856 chr1ptel1M 852596 TTGTAGAATGCTTTGAAGTTTGCAAAG------CATATACATTTACCTCA 852639 v iii iv i ------ i - i C MIRc#SINE/MIR 247 TTGTATAGCACTTTACAGTTTACAAAGCGCTTTCACATACA-TTATCTCA 199 chr1ptel1M 852640 ATGGAT---------AACCCTGTAGGGTA 852659 v v --------- ii C MIRc#SINE/MIR 198 TTTGATCCTCACAACAACCCTGTGAGGTA 170 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 24.87 CpG sites = 9, Kimura (unadjusted) = 24.87 Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.05 (3 / 63), avg. gap size = 5.33 (16 / 3) 247 29.93 2.84 2.84 chr1ptel1M 855293 855433 (144567) Plat_L3#LINE/CR1 3151 3291 (282) m_b24s551i2 857 chr1ptel1M 855293 AAGAGGCGGCAAGTTCAGGCCCCATTAAGACTAAACTTAA-GGAATTGGG 855341 i ii v i -- i i v i -- iv - Plat_L3#LINE/ 3151 AAGGGATGGAAAAT--AGGTCCTATGAGGA--AAGGTTAAAGGAATTGGG 3196 chr1ptel1M 855342 GATGTTTCGGCTGGACAAAAGAACACTCTGGGA-GACACAAGAAGCATTT 855390 v v v v i vi vv i- vi v vii i Plat_L3#LINE/ 3197 GTTGTTTAGCCTGGAGAAGAGAAGGCTAAGGGGTGACTTAATAACTGTCT 3246 chr1ptel1M 855391 TCAAGCGTTAGAAGGGCTCCTCTGCGGAAGAGG--GATCAGATGT 855433 ii vv i ii v v i v -- i v Plat_L3#LINE/ 3247 TCAAGTATATGAAGGGTTTTTATGGGGAGGACGCTGACCAGTTGT 3291 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 38.92 CpG sites = 22, Kimura (unadjusted) = 38.92 Transitions / transversions = 1.16 (22/19) Gap_init rate = 0.05 (7 / 140), avg. gap size = 1.14 (8 / 7) 229 30.43 14.36 1.97 chr1ptel1M 855450 855630 (144370) L3#LINE/CR1 3830 4032 (67) m_b24s601i6 858 chr1ptel1M 855450 CCCGAGGAGCCGAACTGGGGACGATGGGATGGAGGCCCCAGGG-GGCCAA 855498 v - v i iv i - i iiv - vi L3#LINE/CR1 3830 CCAGAGG-GCAGAACTAGGACCAATGGG-TGGAAGTTACAGGGAGGCAGA 3877 chr1ptel1M 855499 GTGAGGCTTCATAT-----------------CCATCAG-------TAAGG 855524 v vv iv ----------------- v -------i ii L3#LINE/CR1 3878 TTTCGGCTCAATATAAGGAAGAACTTTCTAACAATCAGAGCTGTCCAAAA 3927 chr1ptel1M 855525 AGGGGACGGGCTGCCCTGGGAGGCAG-AACCTTGTTCCTCTTGGGAGGTC 855573 v i i ii ? i -i v i-ii v viv v L3#LINE/CR1 3928 ATGGAATGGGCTGCCTCGNGAGGTAGTGAGCTC-CCCGTCACTGGAGGTG 3976 chr1ptel1M 855574 TTCGAGCAAAGATCTGCACAACCCCTTGTGAGGGAGGTGGGGGCAAGGAC 855623 i i i- v ii v v v v vi v i i L3#LINE/CR1 3977 TTCAAGCAGAGG-CTGGATGACCACTTGTCAGGGATGTTGTAGAAGGGAT 4025 chr1ptel1M 855624 TCATTCA 855630 v v L3#LINE/CR1 4026 TCCTGCA 4032 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 39.29 CpG sites = 29, Kimura (unadjusted) = 40.25 Transitions / transversions = 1.16 (29/25) Gap_init rate = 0.04 (8 / 180), avg. gap size = 3.75 (30 / 8) 14 21.12 6.12 0.00 chr1ptel1M 856548 856596 (143404) (GGGCGC)n#Simple_repeat 1 52 (0) m_b24s252i0 859 chr1ptel1M 856548 GGGAGCGGGCGCGGGCGCGGG-GCTCTTGCAGG-GTGGGCTCGAG-GCGG 856594 v - vvvi i - i v i - (GGGCGC)n#Sim 1 GGGCGCGGGCGCGGGCGCGGGCGCGGGCGCGGGCGCGGGCGCGGGCGCGG 50 chr1ptel1M 856595 GC 856596 (GGGCGC)n#Sim 51 GC 52 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.06 (3 / 48), avg. gap size = 1.00 (3 / 3) 13 28.25 0.00 6.35 chr1ptel1M 859894 859960 (140040) (GCCC)n#Simple_repeat 1 63 (0) m_b24s252i1 860 chr1ptel1M 859894 GCCCTCCCTCCCGTGCTGCCACCCCCCCGCCACGGCCCAGCCCACAGGCC 859943 v v iv vv i v - - - i vv (GCCC)n#Simpl 1 GCCCGCCCGCCCGCCCGCCCGCCCGCCCGCC-C-GCCC-GCCCGCCCGCC 47 chr1ptel1M 859944 CGGGCAGCCAGCCCGCC 859960 - v v v (GCCC)n#Simpl 48 C-GCCCGCCCGCCCGCC 63 Matrix = Unknown Transitions / transversions = 0.27 (3/11) Gap_init rate = 0.06 (4 / 66), avg. gap size = 1.00 (4 / 4) 230 22.32 15.09 7.02 chr1ptel1M 861323 861428 (138572) MIRc#SINE/MIR 2 115 (153) m_b24s601i7 861 chr1ptel1M 861323 GGGGCAGCTGGGTAGCGCAGTGGTCAGAGCACCAGTCCTGGAGGCAGGA- 861371 i i--- i i vv ii v i v - MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr1ptel1M 861372 -----------GAATCCCAG----GGCAATGGGGGTCCTAGCTGTGTGAC 861406 ----------- i i ---- v v ----- v MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCCACT-----TACTAGCTGTGTGAC 93 chr1ptel1M 861407 ACTGGGCAAGCCCCTTGACCCC 861428 vi i v i i MIRc#SINE/MIR 94 CTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 25.76 CpG sites = 13, Kimura (unadjusted) = 27.17 Transitions / transversions = 1.44 (13/9) Gap_init rate = 0.10 (11 / 105), avg. gap size = 2.18 (24 / 11) 222 31.25 0.00 0.00 chr1ptel1M 865214 865277 (134723) L3#LINE/CR1 984 1047 (3052) m_b24s601i8 862 chr1ptel1M 865214 GACTTCAGATGCAGCAATGTCCAGTTCCTGGCCAGGGATGGAGGGCATCC 865263 i v? i viv i vivi i ? i v i L3#LINE/CR1 984 GGCTTANGATACCAGAACGATGGGCTCCTGGCNAGGGACGGAGTGCATCT 1033 chr1ptel1M 865264 GATAAGAACCGGGA 865277 v ii ii L3#LINE/CR1 1034 CACGAAGACCGGGA 1047 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 35.56 CpG sites = 13, Kimura (unadjusted) = 44.39 Transitions / transversions = 1.86 (13/7) Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0) 324 22.52 14.96 2.10 chr1ptel1M 865433 865559 (134441) MIR1_Amn#SINE/MIR 16 158 (72) m_b24s601i9 863 chr1ptel1M 865433 GTCTCAGGGAATATAAATACTGGGCTGTGAGGAGGGAAGACCTACACTCA 865482 - v i -i ii i v vvv - ivii ? MIR1_Amn#SINE 16 GTCT-AGTGGATA-GAGCACTGGACTGGGACTCGGGA-GACCTGGGTTCN 62 chr1ptel1M 865483 AGTCC-AGCTC---CAGACACTAGCTAGG-------GAGCTAGTT----- 865516 ? -i --- vv?i i? i? ------- i v i----- MIR1_Amn#SINE 63 ANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGTCACTTN 112 chr1ptel1M 865517 -CCTATTTG--CCTCAGTTCTCTCATCTGTAAAATGGGGATCATGA 865559 - v i -- ii v MIR1_Amn#SINE 113 ACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATGA 158 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 27.66 CpG sites = 17, Kimura (unadjusted) = 28.86 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.07 (9 / 126), avg. gap size = 2.44 (22 / 9) 618 23.64 10.77 2.37 chr1ptel1M 865454 865648 (134352) MIRb#SINE/MIR 34 244 (24) m_b24s601i10 863 chr1ptel1M 865454 GGGCTGTGAGGAGGGA-AGACCTACACTCAAGTCC-AGCTC---CAGACA 865498 v ii vvi - ivii i i -i --- vvi MIRb#SINE/MIR 34 GGGCTTTGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTA 83 chr1ptel1M 865499 CTAGCTAGG-------GAGCTAGTT------CCTATTTG--CCTCAGTTC 865533 iv ------- i v ------ v i -- i MIRb#SINE/MIR 84 CTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTT 133 chr1ptel1M 865534 TCTCATCTGTAAAATGGGGATCATGACTCTCCCTACACCTCCCAAGGCTG 865583 i v i --- v -- v i i MIRb#SINE/MIR 134 CCTCATCTGTAAAATGGGGATAATAA---TACCTAC--CTCGCAGGGTTG 178 chr1ptel1M 865584 TAATGAG-ATCAAATGAGATGATAACTCTAAAGCACTTAGCACGGTGCTT 865632 vi - i i ivv v i i i MIRb#SINE/MIR 179 TTGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCT 228 chr1ptel1M 865633 GGCCCACAGTAGGAGC 865648 v i i v MIRb#SINE/MIR 229 GGCACATAGTAAGCGC 244 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 26.83 CpG sites = 27, Kimura (unadjusted) = 29.07 Transitions / transversions = 1.50 (27/18) Gap_init rate = 0.06 (12 / 194), avg. gap size = 2.17 (26 / 12) 268 22.32 18.02 3.15 chr1ptel1M 865762 865872 (134128) C MIRc#SINE/MIR (140) 128 2 m_b24s601i11 864 chr1ptel1M 865762 ATTAAGGC--AAATAGGTTTAAGTGGCTTGCCCAACGTCCCACAGCTACT 865809 i i -- i v - i v v v C MIRc#SINE/MIR 128 ACTGAGGCTCAGAGAGGTT-AAGTGACTTGCCCAAGGTCACACAGCTAGT 80 chr1ptel1M 865810 A--TGTCTGAGGCCGGATT---------GTT-------CACCAGGCCCAA 865841 -- v v v v i --------- i------- v i i i C MIRc#SINE/MIR 79 AAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAG 30 chr1ptel1M 865842 CGCTCTGTTCACTGAACCACTTAGCTGCCCC 865872 i v i v ---i i C MIRc#SINE/MIR 29 TGCTCTTTCCACTGCACCAC---ACTGCCTC 2 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 26.97 CpG sites = 13, Kimura (unadjusted) = 26.97 Transitions / transversions = 1.18 (13/11) Gap_init rate = 0.07 (8 / 110), avg. gap size = 3.00 (24 / 8) 781 23.85 16.59 1.14 chr1ptel1M 867431 867659 (132341) MIRb#SINE/MIR 2 265 (3) m_b24s601i12 865 chr1ptel1M 867431 AAATGAACAGAGTGGTTCAATGTACAGAGCACTAGAGCTGGAGCCAGAAA 867480 i v ii v v i v v vi vvi i v MIRb#SINE/MIR 2 AGAGGGGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACA 51 chr1ptel1M 867481 GCCC------CGAATTCCA------CCA-----------TGTGCCCCCAG 867507 v ------ i i------ ----------- v iii MIRb#SINE/MIR 52 GACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 101 chr1ptel1M 867508 GCAAGTCATTTAACCTGTCTG--CCTTGATTTCCCCGTTTGCAAAATGGG 867555 i i v -- iii i i i i MIRb#SINE/MIR 102 GCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 151 chr1ptel1M 867556 GATAATAACAGTACCTATCTCCCAAGATTGTTGTAAGGATCAAATG-GAT 867604 --- i v i i i i - MIRb#SINE/MIR 152 GATAATAA---TACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGAT 198 chr1ptel1M 867605 AATATTTGTAAAGC------------ACCTGCCACACAGTAGGCACCTAA 867642 iiv ------------i v i i i ii MIRb#SINE/MIR 199 AATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAA 248 chr1ptel1M 867643 TACATGCTTGTTCTCTT 867659 v v v i v MIRb#SINE/MIR 249 TAAATGGTAGCTCTATT 265 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 28.33 CpG sites = 35, Kimura (unadjusted) = 29.63 Transitions / transversions = 1.84 (35/19) Gap_init rate = 0.04 (9 / 228), avg. gap size = 4.56 (41 / 9) 369 21.51 17.97 5.59 chr1ptel1M 867892 868019 (131981) C MIR#SINE/MIR (118) 144 2 m_b24s601i13 866 chr1ptel1M 867892 CTTATTTTACAGGTAAGGAAACTGAGGCA--------------AAC---- 867923 ii i i -------------- ---- C MIR#SINE/MIR 144 CCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGC 95 chr1ptel1M 867924 --AAGGTCATACAGCTAGTTTAACTCTCTGAGGTCCGATTTGAACTCAGG 867971 -- i -- v vv v vivv i i C MIR#SINE/MIR 94 CCAAGGTCACACAGCTAG--TAAGTGGCAGAGCCGGGATTCGAACCCAGG 47 chr1ptel1M 867972 AAGTTAAATCTTGGCTCCAGGACCTGCACTCTG---TACTATGCTTTCCT 868018 v ------i ii i ii v---i v v C MIR#SINE/MIR 46 CAGT------CTGGCTCCAGAGCCCGTGCTCTTAACCACTATGCTATACT 3 chr1ptel1M 868019 G 868019 C MIR#SINE/MIR 2 G 2 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 22.66 CpG sites = 15, Kimura (unadjusted) = 25.97 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.09 (12 / 127), avg. gap size = 2.58 (31 / 12) 12 24.33 4.00 1.96 chr1ptel1M 870865 870914 (129086) (GGC)n#Simple_repeat 1 51 (0) m_b24s252i2 867 chr1ptel1M 870865 GGCGGCGGCGGCGGCAGAGGGGGACTGCAGCATTGG-GGCGGGGTCGG-G 870912 i v v - v i ivi - v v - (GGC)n#Simple 1 GGCGGCGGCGGCGGCGGCGGCGG-CGGCGGCGGCGGCGGCGGCGGCGGCG 49 chr1ptel1M 870913 GC 870914 (GGC)n#Simple 50 GC 51 Matrix = Unknown Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.06 (3 / 49), avg. gap size = 1.00 (3 / 3) 16 19.25 0.00 0.00 chr1ptel1M 871533 871562 (128438) (C)n#Simple_repeat 1 30 (0) m_b24s252i3 868 chr1ptel1M 871533 CCCGCCGCGCCGCCCCCCGCCCCCCCCCCC 871562 v v v v v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 30 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 15 24.83 2.99 4.55 chr1ptel1M 872221 872287 (127713) (GCC)n#Simple_repeat 1 66 (0) m_b24s252i4 869 chr1ptel1M 872221 GCCTCGGCTGCCGCCG-CGCCGCCGCCACTTCCGCTTCCTCAGGCGCGCG 872269 v v i - i iv iv v v v - (GCC)n#Simple 1 GCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGC-CG 49 chr1ptel1M 872270 CTCTCTGCTCGCC-CCGCC 872287 - v i - - (GCC)n#Simple 50 C-CGCCGC-CGCCGCCGCC 66 Matrix = Unknown Transitions / transversions = 0.62 (5/8) Gap_init rate = 0.08 (5 / 66), avg. gap size = 1.00 (5 / 5) 692 31.02 14.29 0.00 chr1ptel1M 873297 873828 (126172) C L2#LINE/L2 (481) 2601 1994 m_b24s601i14 870 chr1ptel1M 873297 GGATATGGGG---GAGGGGG-GTGAGGAGCCCAGGATGACTTCCAGGCTC 873342 i --- i ii- v i v i v i i C L2#LINE/L2 2601 GGATGTGGGGTGTGAGAGAAAGAGAGGAGTCAAGGATGACTCCAAGGTTT 2552 chr1ptel1M 873343 ACAATCTG-GTGACTAGGAGGATGGGGGTGCTCTCCATCATAACAGGGAA 873391 viiii - ii i i i v iv i? iiivi ii C L2#LINE/L2 2551 TTGGCCTGAGCAACTGGAAGGATGGAGTTGCCATTNACTGAGATGGGGAA 2502 chr1ptel1M 873392 A---GTAGGAGG-----------GGGGGAAGAGAATGAATCCA-TTTGGG 873426 i--- ii ----------- vv v i i - v C L2#LINE/L2 2501 GACTGCGGGAGGAGCAGGTTTGAGGGGGAAGATCAGGAGTTCAGTTTTGG 2452 chr1ptel1M 873427 ACAGGGCGAATT-GAGATGTCTCCTGGATAACCA---------GTCTGAA 873466 v vii i - i vi i i v --------- viiv C L2#LINE/L2 2451 ACATGTTAAGTTTGAGATGCCTATTAGACATCCAAGTGGAGATGTCGAGT 2402 chr1ptel1M 873467 AGGCAGTTGGAGA-AGGAGATTGGAAGTCAGCAGAAGGGTTAGGGCAGGA 873515 v - v vi iv vi ii iv v C L2#LINE/L2 2401 AGGCAGTTGGATATACGAGTCTGGAGTTCAGGGGAGAGGTCCGGGCTGGA 2352 chr1ptel1M 873516 TAGTCAGCTCTGGGAGTAACT--CACAGAGATGGTCATTAAATCTATGGC 873563 v vvi iv i v ii-- i v vv v i iv C L2#LINE/L2 2351 GATATAAATTTGGGAGTCATCAGCATATAGATGGTATTTAAAGCCATGAG 2302 chr1ptel1M 873564 AGCTGAGGAGACCAAGTAGGA---GAGTGGA----------AGAAGAGGA 873600 viv v i vv? i--- v ---------- v C L2#LINE/L2 2301 ACTGGATGAGATCACCNAGGGAGTGAGTGTAGATAGAGAAGAGAAGAGGT 2252 chr1ptel1M 873601 CAAA--ACTG-----TGAGCAACACCTGTGGTTAGAGGGCATGGGCTGGA 873643 v -- ----- i vv v vii v ? v iv ivvv C L2#LINE/L2 2251 CCAAGGACTGAGCCCTGGGGCACTCCAACGTTNAGAGGTCGGGGAGATGA 2202 chr1ptel1M 873644 GGAGGATGCAGCAAAGGAGACAGAGAAGAAATCCTCAGAGAAGTGGGAGG 873693 vv v i iivvi v i i C L2#LINE/L2 2201 GGAGGAACCAGCAAAGGAGACTGAGAAGGAGCGGCCAGTGAGGTAGGAGG 2152 chr1ptel1M 873694 ACAA--AAGAGAAAG-GGT---CTGAAAACC---CCAGGCAAG------- 873727 v -- i iv - --- i i ---iv i v ------- C L2#LINE/L2 2151 AAAACCAGGAGAGTGTGGTGTCCTGGAAGCCAAGTGAAGAAAGTGTTTCA 2102 chr1ptel1M 873728 -GGCGGA--GAGTGATCCACAGCGTCCAAGGCTGCAGAGGAATCGGGGAG 873774 - iv -- v v i v v v ?iii ii v i C L2#LINE/L2 2101 AGAAGGAGGGAGTGATCAACTGTGTCAAATGCTGCTGANAGGTCAAGTAA 2052 chr1ptel1M 873775 GGGGA-GACTGGAAAGT---CATTAGATTGGGCAACTAGGAGATCCCTGG 873820 iv - ii v --- i vi vv i vi C L2#LINE/L2 2051 GATGAGGACTGAGAATTGACCATTGGATTTAGCAACGTGGAGGTCATTGG 2002 chr1ptel1M 873821 TGATTTTG 873828 ii C L2#LINE/L2 2001 TGACCTTG 1994 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 40.00 CpG sites = 90, Kimura (unadjusted) = 41.34 Transitions / transversions = 1.20 (90/75) Gap_init rate = 0.04 (23 / 531), avg. gap size = 3.30 (76 / 23) 16 13.08 0.00 0.00 chr1ptel1M 875266 875290 (124710) (T)n#Simple_repeat 1 25 (0) m_b24s252i5 871 chr1ptel1M 875266 TTTCTTTTTTTTATTTTTATTTTTT 875290 i v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 1491 28.45 2.04 0.81 chr1ptel1M 875822 876310 (123690) C L1ME5_3end#LINE/L1 (389) 552 58 m_b24s551i3 872 chr1ptel1M 875822 ATAATATTCCATAACATTCATATACCACAATTTACCCAACCATTCTCCAC 875871 i i iiii v vi v i v i vv C L1ME5_3end#LI 552 ATAGTACTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCA 503 chr1ptel1M 875872 TTGATGGGCATCCATTCATTTTCCAGCTTCTAGCCACTACAAACAGGGCT 875921 v i i vvivvii i i iv i iv C L1ME5_3end#LI 502 GTGATGGACACCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCT 453 chr1ptel1M 875922 GCCACAAATATTTTGGCACATATAGGTCTCTTTC----CCTTCTTTAGTA 875967 v ii i ii v i ---- i i v---- viv v v C L1ME5_3end#LI 452 GCAATGAACATCCTCGTACAT----GTCCCCTTATGGACCTGTGTGAGAA 407 chr1ptel1M 875968 TCTCTTTGGGGTATAAGCCCAGTAGTAACACTGCTGGATCAAAGGGTATG 876017 i i vi v iiiv i i v C L1ME5_3end#LI 406 TTTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATG 357 chr1ptel1M 876018 C--ACAGTT--TTTGAGCA--TAGTTCCAAATAGCTCTCCAGAATGGCTG 876061 -- i v -- vi -- v v i v C L1ME5_3end#LI 356 CGTATACTTAATTTGACTAAGTACTGCCAGATTGCTCTCCAGAATGGCTG 307 chr1ptel1M 876062 GATGTGTTCACAATTCCACCAACAATGTATCAGTGTCCCTGTTTTCCCAC 876111 v ivv ii v i i i i v v i i ? i C L1ME5_3end#LI 306 CACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATNTCCCCAC 257 chr1ptel1M 876112 ATCCCTTCCAACATTCCGCATTATCTTCCCCTGTCATTCTAGTCAATCTG 876161 iiv i iv ivv ii v v i v i i i C L1ME5_3end#LI 256 ATCCTCGCCAACACTTGGCATTATCCAGCTTTCTAATTTTTGCCAGTCTA 207 chr1ptel1M 876162 ACAGGTGTGTAGTGGTATCTCAGAGTTGTCTTAATTTGCATTTCTCTGAT 876211 i iv i vv i C L1ME5_3end#LI 206 ATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATTTCTCTGAT 157 chr1ptel1M 876212 TAATAATGATTTGGAGCATATTTTCATATGGCTAGAAATAGTTTTAGTTT 876261 v v v v i vi ivv iivv ivi C L1ME5_3end#LI 156 TACTAATGAGTTTGAGCATCTCTTCATATGCTTGTTAGCCTTTCGGGTTT 107 chr1ptel1M 876262 CTTTGCCTGAGAATTGTCTGTTCATATCCTTTGATCACTTATCAATTGG 876310 i ivi vi i vi i v v C L1ME5_3end#LI 106 CCTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGG 58 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 35.64 CpG sites = 78, Kimura (unadjusted) = 36.68 Transitions / transversions = 1.30 (78/60) Gap_init rate = 0.02 (8 / 488), avg. gap size = 1.75 (14 / 8) 1028 31.15 4.37 3.61 chr1ptel1M 876218 877316 (122684) C L1M5_orf2#LINE/L1 (0) 3294 2188 m_b24s551i4 872 chr1ptel1M 876218 TGATTTGGAGCATATTTTCATATGGCTAGAAATAGTTTTAGTTTCTTTGC 876267 ?v v v i vi vviiivi v?i v ivi C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr1ptel1M 876268 CTGAGAATTGTCTGTTCATATCCTTTGATCACTTATCAATTGGAAAATGG 876317 i v v vi i vi i v ?v i--- v C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGG---TTG 3198 chr1ptel1M 876318 CTTGA---TTTCTTACAGAGTC-----AATGCTCTATATATTTTGGAAAT 876359 i v--- ? iv ? i----- i v i i v i C L1M5_orf2#LIN 3197 TTTGTCTTTTTNTTATTGANTTGTAGGAGTTCTTTATATATTCTGGATAC 3148 chr1ptel1M 876360 GAGGCCTTTATCAGA-ACCTTTGACTGTAAAAATATTTTCCCAGTTTATT 876408 v i - iv v ?-i i v v i ? i i v C L1M5_orf2#LIN 3147 GAGTCCTTTGTCAGATATATGTN-TTGCAAATATTTTCTCCCANTCTGTG 3099 chr1ptel1M 876409 GTTTCCCTTCTAAT---CTCGCCTGCATTAGTTTTGTTGGTACAAAAACT 876455 i v i v --- iiv v ii i-- v? i-i i ii C L1M5_orf2#LIN 3098 GCTTGCCTTTTCATTTTCTTAACGGTGTC--TTTTGANGA-GCAGAAGTT 3052 chr1ptel1M 876456 TTTCAATTTGATATAATCAAAATTTTCAATTTTGTAGTCAATAGTGATCT 876505 v v i? i v v v v vv iv i ----- C L1M5_orf2#LIN 3051 TTTAATTTTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGGT----- 3007 chr1ptel1M 876506 CTAGTTCTTCTTTGGTCAT-------AAATTCCTTCCTCTTCCACAGGTC 876548 - ? v i vv v ------- iii v v?i - C L1M5_orf2#LIN 3006 -TNGTGCTTTTTGTGTCCTGTTTAAGAAATCTTTGCCTANCCCA-AGGTC 2959 chr1ptel1M 876549 TGAGAGGTAAACTATCCTATGCT--CTTCCAATTTATTTATAATCTTATT 876596 vvii i --i v i -- i ivvvv i i ?i C L1M5_orf2#LIN 2958 ACGAAGATA--TTCTCCTATGTTTTCTTCTAGAAGTTTTATAGTTTTANC 2911 chr1ptel1M 876597 CTTTATGCCTAGGTC-ATGAACCCATTTTGACCTTATCTTGGTGTACGGT 876645 i iiii - -i i ? vi v i v i C L1M5_orf2#LIN 2910 TTTTACATTTAGGTCTATGA-TCCATCTNGAATTAATTTTTGTGTATGGT 2862 chr1ptel1M 876646 GTTAGGTGTGGGTCAATGCCTAGTTTCTGCCATACTAATTTCCAATTTTC 876695 v iv i v?iii v i v ivi v v i C L1M5_orf2#LIN 2861 GTGAGGTAGGGGTCGAGNTTCATTTTTTTCCATATGGATATCCAATTGTT 2812 chr1ptel1M 876696 CCAGCAATTTTTGTCAAATAATGCATTCTTATCCCAA-AAACTGGGGTCT 876744 viv ii v ivvi i vi v-i i ---- ? C L1M5_orf2#LIN 2811 CCAGCACCATTTGTTGAAAAGACTATCCTTTCCCCACTGAATTG----CN 2766 chr1ptel1M 876745 TTGGG---TTTGTCAAACACTAGATGATTAAAGTTAT-TGGCTGTTTTGT 876790 v--- v ii i? ?ii v vv i - v v v -- C L1M5_orf2#LIN 2765 TTGGCACCTTTGTCAAAAATCAANTGNCCATATATGTGTGGGTCTATT-- 2718 chr1ptel1M 876791 CCTTTGAAC---CTAACCTATTCCATTGATCAACTAGTCTATTTCTTA-G 876836 -- i i --- vi i v i v i- - C L1M5_orf2#LIN 2717 --TCTGGACTCTCTATTCTGTTCCATTGATCTATTTGTCTATC-CTTACG 2671 chr1ptel1M 876837 CCAGTACCAAATGGTTTTAGTAACTGCTGCTTTATAATATCATTTTAGAT 876886 i v iv i ii v iv vvvi v ? C L1M5_orf2#LIN 2670 CCAATACCACACTGTCTTGATTACTGTAGCTTTATAATAAGTCTTGANAT 2621 chr1ptel1M 876887 CTGGTACAGCTAAGCTATCTTCA--TTTGATTTTTTTTTTCATTCATTCC 876934 ? vv - i--i i -- v i i -vv vi C L1M5_orf2#LIN 2620 CNGGTAGTG-TAAGT--CCTCCAACTTTGTTCTTCTTTTTCA-AGATTGT 2575 chr1ptel1M 876935 CTTGGA-ATTCTTGATCTTTTGTTTTTCCATATGAACTTTG--------T 876975 i v- ? i i iv i i i-------- C L1M5_orf2#LIN 2574 TTTGGCTATTCTNGGTCCTTTGCATTTCCATATAAATTTTAGAATCAGCT 2525 chr1ptel1M 876976 TGTT-TTTTCTAGGTCATCAAAATAGTTTTTGGGAGTCTAATTGGTATAG 877024 i-v --- -- v vi vi v i i v v C L1M5_orf2#LIN 2524 TGTCAATTTCTA---CA--AAAAAACCTGCTGGGATTTTGATTGGGATTG 2480 chr1ptel1M 877025 TGCTAAATAAATAGATTAGTTTAGGCAGTATTGTCATCTTTATTATATTT 877074 iii i vv i i i v v v ? iv v C L1M5_orf2#LIN 2479 CATTGAATCTATAGATCAATTTGGGGAGAATTGACATCTTNACAATATTG 2430 chr1ptel1M 877075 GCTCACCCAATCCGAGAGCATTTAATGTTTTTCCAGTTGGTTAGATCGGA 877124 iv vi iv i vvv i i i v iv i vvv C L1M5_orf2#LIN 2429 AGTCTTCCAATCCATGAACATGGTATATCTCTCCATTTATTTAGGTCTTC 2380 chr1ptel1M 877125 CTTAATTTGTGTAGAAAGTGTTTTGTAGTTTTGCTCATAAAGTTTCTG-- 877172 i v v viiv i vvvii ? v ii -- C L1M5_orf2#LIN 2379 TTTAATTTCTCTCAGCAATGTTTTGTAGTTTTCAGTGTANAGGTCTTGCA 2330 chr1ptel1M 877173 -ATTTTCCCTTGGCAGATAGATTCCTAAACATTTTATACAATCAGTAGTT 877221 - ? --- vi vv ii ? iivv iv vv i C L1M5_orf2#LIN 2329 CATNTT---TTGTTAGATTTATTCCTAAGTATTTNATGTTTTTTGATGCT 2283 chr1ptel1M 877222 ACTTTAAATGGAATTTCTCTTTGTAACTCTAATTGTTGGAT--TTTGTTA 877269 i v v vi i --? v i v v ivi -- i C L1M5_orf2#LIN 2282 ATTGTAAATGGTATTGTTTTT--NAAATTTCATTTTCCAATTGTTTGTTG 2235 chr1ptel1M 877270 GTGATATATAAGCATACTGATGACTTACATGGGTTTATTTTGTATCC 877316 v ii iiv viv i vii ivi v ii C L1M5_orf2#LIN 2234 CTAGTATATAGAAATACAATTGATTTTTGTATATTGACCTTGTATCC 2188 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 41.94 CpG sites = 176, Kimura (unadjusted) = 42.45 Transitions / transversions = 1.14 (176/154) Gap_init rate = 0.05 (59 / 1098), avg. gap size = 1.49 (88 / 59) 309 32.00 0.00 0.00 chr1ptel1M 877365 877464 (122536) C L1ME3F_3end#LINE/L1 (461) 529 430 m_b24s551i5 873 chr1ptel1M 877365 ACTGTAACTTATTCAGCCATTCTCCCACCCATGGGTGTCCCCTCAGTTCC 877414 iii i i v iii v iii iivvviv i C L1ME3F_3end#L 529 ACCACAATTTATTTATCCATTCTCCTGTCGATGGACATTTGGGTTGTTTC 480 chr1ptel1M 877415 CAGTTTCTTGCCACTACGAAAAGGGCTGCCACAAACATTTTTGCCCATGT 877464 i i i v v i ii i iv C L1ME3F_3end#L 479 CAGTTTTTTGCTATTACGAACAGTGCTGCTATGAACATTCTTGTACATGT 430 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 44.89 CpG sites = 23, Kimura (unadjusted) = 44.89 Transitions / transversions = 2.56 (23/9) Gap_init rate = 0.00 (0 / 99), avg. gap size = 0.0 (0 / 0) 246 9.76 2.44 0.00 chr1ptel1M 877850 877890 (122110) C MIR3#SINE/MIR (63) 145 104 m_b24s601i15 874 chr1ptel1M 877850 CTCATTTTAGAGATGAAGAAACTGAGGCACACAGA-GTGAAG 877890 v i v v - C MIR3#SINE/MIR 145 CTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAG 104 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 10.46 CpG sites = 1, Kimura (unadjusted) = 10.46 Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 35 13.91 0.00 0.00 chr1ptel1M 878373 878428 (121572) (T)n#Simple_repeat 1 56 (0) m_b24s252i6 875 chr1ptel1M 878373 TTTTCTTTTTTCTTTCTTTCTTTCTTTTTTTTTTTTTTTTTTTTGATTTT 878422 i i i i i vv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr1ptel1M 878423 TTTTTT 878428 (T)n#Simple_r 51 TTTTTT 56 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0) 1516 28.65 2.22 2.75 chr1ptel1M 878850 879434 (120566) C L1ME5_3end#LINE/L1 (304) 637 56 m_b24s551i6 876 chr1ptel1M 878850 TCCTGCTCATTTCACTCAGCATCA-GTTCATGTAAG-TCTCTCCAAGCCT 878897 i i iv ii - -- v - iv v iiv C L1ME5_3end#LI 637 TCTTACTTTTTTCACTCAGCACTATGTT--TTTAAGATCCATCCATGTTG 590 chr1ptel1M 878898 CTCTGCATTCATCCTGCTGGTCATTTCTTACAGAACAATAATATTCCATA 878947 v ii v iv iiv iii v v vvvv i i i C L1ME5_3end#LI 589 CTATGTGTACATCTAGTCCGTTGCTTCTAACTGCTGCATAGTACTCCATG 540 chr1ptel1M 878948 ACATTCATATACCACAATTTACCCAATCATTCTCCAATTGATGGGCATCC 878997 iii v vi v i vi i v v i i C L1ME5_3end#LI 539 GTGTGCATCCACCACATTTTACCTATCCACTCTCCCAGTGATGGACACCC 490 chr1ptel1M 878998 ATTCATTTTCCAGTTGCTAGCCACTACAAACAGGGCTGCCACAAACATTC 879047 vvivvii ii v iv i iv v ii i C L1ME5_3end#LI 489 AGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCTGCAATGAACATCC 440 chr1ptel1M 879048 TGGCACATACAGGTCCCTTTC----CCTTCTTTATGATCTCTTTGGGGTA 879093 ---- i v i v---- viv v vi i i C L1ME5_3end#LI 439 T----CGTACATGTCCCCTTATGGACCTGTGTGAGAATTTCTTTGGGATA 394 chr1ptel1M 879094 TAAGCCCAGTAGTAGCACTGCTGGCTCAAAGGGTATGCACAGTGTGATAA 879143 vi v ii v i v v --- i ---- C L1ME5_3end#LI 393 TATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATGC---GTAT----A 351 chr1ptel1M 879144 CTT--TTTGAGCA--TAGTTCCAAATTGCTCTCCAGAATGGTTGGATTCG 879189 -- vi -- v v i i v iiv C L1ME5_3end#LI 350 CTTAATTTGACTAAGTACTGCCAGATTGCTCTCCAGAATGGCTGCACCAG 301 chr1ptel1M 879190 TTCACAACTCCACCAACAATGCATCAGTGTCCCAGTTTTCCCACAGCCCC 879239 ii vii i i v v i vi ? i v i C L1ME5_3end#LI 300 TCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATCCTC 251 chr1ptel1M 879240 TCCAACATTCATCATTATTT---TTTCCTGTCATCTTAGCCAGTCTGACA 879286 v i iiv ii--- --- v i v i i C L1ME5_3end#LI 250 GCCAACACTTGGCATTATCCAGCTTTC---TAATTTTTGCCAGTCTAATA 204 chr1ptel1M 879287 GGTGTGTAGTGGTATCTCAGAGTTGTCTTAATTTGCATTTCTCTGATCAA 879336 iv i vv i i v C L1ME5_3end#LI 203 GGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATTTCTCTGATTAC 154 chr1ptel1M 879337 TAGTGATTTGGAACACTCTTTCATATGAGTGGGAATAGTTTCAATTTCTT 879386 i v v i iiii vv vv iivv ivii i C L1ME5_3end#LI 153 TAATGAGTTTGAGCATCTCTTCATATGCTTGTTAGCCTTTCGGGTTTCCT 104 chr1ptel1M 879387 CATCTGAAAATTGTCTGTTCATATCCTTTGACCATTTATCAATTGGAG 879434 v v i v v v i C L1ME5_3end#LI 103 CTTCTGTAAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGGGG 56 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 36.06 CpG sites = 91, Kimura (unadjusted) = 36.95 Transitions / transversions = 1.26 (91/72) Gap_init rate = 0.04 (22 / 584), avg. gap size = 1.32 (29 / 22) 202 12.22 7.84 3.77 chr1ptel1M 880885 880935 (119065) C Tigger19b#DNA/TcMar-Tigger (207) 343 291 m_b24s601i16 877 chr1ptel1M 880885 GCTGGGAAAGGCTGTCCA--TTCTTGACCCTGACTCCTCCCCAA--CCTC 880930 -- -- i v i v v -- C Tigger19b#DNA 343 GCTGGGAA--GCTGTCCAGTTTCCTCATCCTGCCTCCTGCCCAACTCCTC 296 chr1ptel1M 880931 TCTGC 880935 i C Tigger19b#DNA 295 CCTGC 291 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 13.41 CpG sites = 3, Kimura (unadjusted) = 13.41 Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.08 (4 / 50), avg. gap size = 1.50 (6 / 4) 18 8.48 0.00 0.00 chr1ptel1M 882882 882906 (117094) (C)n#Simple_repeat 1 25 (0) m_b24s252i7 878 chr1ptel1M 882882 CCCTCCCCCCCCCCCCCCCCCCACC 882906 i v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCC 25 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 247 29.71 4.41 5.97 chr1ptel1M 883200 883335 (116665) L2c_3end#LINE/L2 338 471 (7) m_b24s601i17 879 chr1ptel1M 883200 TTGT--TTGTGTGTTTGCTGGTC-ATCTTTTCCACAAGCTGGGGAGGACC 883246 -- v i ?v -i ii v viv v vv L2c_3end#LINE 338 TTGTAATTGTCTGTTTACNTGTCTGTCTCCTCCACTAGACTGTGAGCTCC 387 chr1ptel1M 883247 T-GAGAGCAGGA--TATCTCTCACTGGTCCCTTTGCATCTCAGCACTGCA 883293 - i i--ii v i i vi -- i i -- -- i L2c_3end#LINE 388 TTGAGGGCAGGGACCGTGTCTTATTCATC--TTTGTATCCC--CA--GCG 431 chr1ptel1M 883294 CCTGGCACACAGGACTCCTCCTTCACAAATGTGCACTGAGTG 883335 i v vv --v iv i viii i L2c_3end#LINE 432 CCTGGCACATAGTAGGC--GCTCAATAAATGTTTGTTGAATG 471 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 36.47 CpG sites = 22, Kimura (unadjusted) = 39.23 Transitions / transversions = 1.38 (22/16) Gap_init rate = 0.09 (12 / 135), avg. gap size = 1.17 (14 / 12) 22 7.28 0.00 0.00 chr1ptel1M 883892 883920 (116080) (AC)n#Simple_repeat 1 29 (0) m_b24s252i8 880 chr1ptel1M 883892 ACACACACACACAGACACACACACACTCA 883920 v v (AC)n#Simple_ 1 ACACACACACACACACACACACACACACA 29 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 567 31.74 9.13 1.94 chr1ptel1M 883973 884213 (115787) L3#LINE/CR1 2865 3122 (977) m_b24s601i18 881 chr1ptel1M 883973 AGAACATGTGATCCTTGGCCAATGTCATTTGCTTTTTTATTGGACAGGGT 884022 v v v ivii i iv v ---- i L3#LINE/CR1 2865 AGAACAAGTCATGCCAAACTAACCTCATTTCCTTTTTT----GATAGGGT 2910 chr1ptel1M 884023 TACTCTCCTGAAAGATGAAGGGA-TGGCATA--TGGAATTTACCTAGATC 884069 vvv iv v i - v i --ii? i v i i i L3#LINE/CR1 2911 TACTAGACTGGTAGATCAGGGGAATGCCGTAGACANAGTGTATCTGGATT 2960 chr1ptel1M 884070 TCAGCAAAACATTGGATAG---------TACTGCCACTGTAGATAATATG 884110 ii v i i--------- iv ii vi i i v L3#LINE/CR1 2961 TCAGCAAGGCATTTGACAAAGTCTCTCATGATATCCTTGTGGACAAGATG 3010 chr1ptel1M 884111 GAAAGAAGCAACCTAGATGACAGTCCAGGTAA-TGGATTGGACAACTGGC 884159 i i viiiiv i i v v i- v -i i i L3#LINE/CR1 3011 GAGAAATATGGGCTGGATGATAGTACAGTTAGGTGGATTCG-TAGCTGGT 3059 chr1ptel1M 884160 TGG---------CTCAAACAGTAATTACCAGTGGGTTGAAGTCAACATGG 884200 i--------- i vi iv v ii i i i v v L3#LINE/CR1 3060 TGAACGACTATACCCAAAAGGTGTTGATTAATGGATCGATGTCAACCTGG 3109 chr1ptel1M 884201 AGGAAGGTCTTTA 884213 i i L3#LINE/CR1 3110 AGGGAGGTCTCTA 3122 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 42.00 CpG sites = 48, Kimura (unadjusted) = 43.58 Transitions / transversions = 1.78 (48/27) Gap_init rate = 0.04 (10 / 240), avg. gap size = 2.70 (27 / 10) 214 33.07 9.19 5.21 chr1ptel1M 884310 884494 (115506) L3b_3end#LINE/CR1 1012 1203 (3) m_b24s601i19 881 chr1ptel1M 884310 AGTGATAAATGGTATATGCTTTTGGCTTGGGCTATCTTGGGAGCAAGTGG 884359 v iv v v ii --- vv i i vv vvv i L3b_3end#LINE 1012 AGTGAGAGTTGTTAAACACT---GGAATGGGTTACCGAGGGAGGTTGCGG 1058 chr1ptel1M 884360 GTTCCCCTTTACTAGAG-GTCTTCTTGGGAAGATTGGTTGGGT----AT- 884403 iv i iv i - ? i----i i v ivi i ---- - L3b_3end#LINE 1059 AATCTCCTTCTCTGGAGAGNCTTT----AAAAATAGAACGGATTCTCATC 1104 chr1ptel1M 884404 --TCTAGGCTAACTTAGAAAAGTA-TCCTATTT--------GTGTATGAG 884442 -- i v i -- i i - iii -------- v ? - i L3b_3end#LINE 1105 TGTCTGGGATGACTTA--AAGGCAGTCCTGCCTAGAGCTAGGGGNA-GGG 1151 chr1ptel1M 884443 TTGGACTCGATAGTCTCTAAAGTTCTTTCCAACTTGGAAATTTGGAGATT 884492 v v iii i i i i iv i iviv i L3b_3end#LINE 1152 ATGGACTAGATGACCTCTGAGGTCCTTTCCAATTCTGAGATTCTATGGTT 1201 chr1ptel1M 884493 TT 884494 L3b_3end#LINE 1202 TT 1203 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 44.30 CpG sites = 36, Kimura (unadjusted) = 46.53 Transitions / transversions = 1.64 (36/22) Gap_init rate = 0.09 (16 / 184), avg. gap size = 1.69 (27 / 16) 409 34.36 3.07 0.00 chr1ptel1M 884332 884494 (115506) L3#LINE/CR1 3929 4096 (3) m_b24s601i20 881 chr1ptel1M 884332 TGGCTTGGGCTATCTTGGGAGCAAGTGGGTTCCCCTTTACTAGAGGTCTT 884381 vv ii i ? vv i i v i i v L3#LINE/CR1 3929 TGGAATGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGTCACTGGAGGTGTT 3978 chr1ptel1M 884382 CTTGGGAAGATTGGTTGGGTATT---CTAGGCTAACTTAGAAAAGTATCC 884428 vv vii ii v ivi i --- vi v iviv ii vv L3#LINE/CR1 3979 CAAGCAGAGGCTGGATGACCACTTGTCAGGGATGTTGTAGAAGGGATTCC 4028 chr1ptel1M 884429 TAT-TTGTGTATGAG-TTGGACTCGATAGTCTCTAAAGTTCTTTCCAACT 884476 ii- vi iv - v iii i i i L3#LINE/CR1 4029 TGCATTGGATGGGAGGTTGGACTAGATGACCTCTAAGGTCCCTTCCAACT 4078 chr1ptel1M 884477 TGGAAATTTGGAGATTTT 884494 iv i iv v i L3#LINE/CR1 4079 CTGAGATTCTGTGATTCT 4096 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 46.99 CpG sites = 33, Kimura (unadjusted) = 48.21 Transitions / transversions = 1.43 (33/23) Gap_init rate = 0.02 (3 / 162), avg. gap size = 1.67 (5 / 3) 246 25.93 0.00 0.00 chr1ptel1M 884807 884887 (115113) C L1MC5a_3end#LINE/L1 (2639) 138 58 m_b24s551i7 882 chr1ptel1M 884807 TTTTTTCATATGACTAGAAATGCTTTTAATTTCTTCATCTGAAAATTGTC 884856 i vi iiiiivv vv iv vi i C L1MC5a_3end#L 138 TCTTTTCATATGTTTAAGGGCCATTTGCATTTCTTTTTCTGTGAACTGTC 89 chr1ptel1M 884857 TGTTCATATCTTTTGACCATTTATCAATTAG 884887 v v v i C L1MC5a_3end#L 88 TGTTCATATCTTTTGCCCATTTTTCTATTGG 58 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 32.22 CpG sites = 11, Kimura (unadjusted) = 32.22 Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.00 (0 / 80), avg. gap size = 0.0 (0 / 0) 275 25.45 0.00 0.00 chr1ptel1M 884835 884944 (115056) C L1ME4c_3end#LINE/L1 (720) 110 1 m_b24s551i8 882 chr1ptel1M 884835 ATTTCTTCATCTGAAAATTGTCTGTTCATATCTTTTGACCATTTATCAAT 884884 i v ? vi i i v v C L1ME4c_3end#L 110 ATTTCCTCTTNTGTGAATTGTCTGTTCATGTCCTTTGCCCATTTATCTAT 61 chr1ptel1M 884885 TAGAGAATGGCTTGAATTATTATAAATTTGAGTCACTTCTCTCTATATTT 884934 i i vv v v ?vvv v v i v vi i v ? v C L1ME4c_3end#L 60 TGGGGTCTTGATNTTTTTCTTATCAATTTGAATGAGCTCTTTATATANTA 11 chr1ptel1M 884935 TAGAAATGAA 884944 ? v v C L1ME4c_3end#L 10 NAGATATTAA 1 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 32.56 CpG sites = 9, Kimura (unadjusted) = 32.56 Transitions / transversions = 0.47 (9/19) Gap_init rate = 0.00 (0 / 109), avg. gap size = 0.0 (0 / 0) 549 34.77 2.78 3.35 chr1ptel1M 885208 885927 (114073) C L1P1_orf2#LINE/L1 (474) 2820 2105 m_b24s551i9 883 chr1ptel1M 885208 CCAGTTTTCCCAGAAATTTTTGTCAAATGGTGAGTTTTTATCCCAGAAAC 885257 v viv i i i v i ii vi vvi- C L1P1_orf2#LIN 2820 CCAGTTTTCCCAGCACCATTTATTAAATAGGGAATCCTTTCCCCATTG-C 2772 chr1ptel1M 885258 TGGAGTCTTTGAGTTTTATCAAACACTAGATTACTATCATCATTGAATAT 885307 v vv i i v v i v ii vii i vivi vviiii C L1P1_orf2#LIN 2771 TTGTTTTTCTCAGGTTTGTCAAAGATCAGATAGTTGTAGATATGCGGCGT 2722 chr1ptel1M 885308 TGTATCTTGTGAACCTAACCTATTCCACTGATCCATTACTCTATTTCTTA 885357 i v viv ivi ivi i i i vv i -- i C L1P1_orf2#LIN 2721 TATTTCTGAGGGCTCTGTTCTGTTCCATTGATCTATATCTCTGTTT--TG 2674 chr1ptel1M 885358 G--CCAGTACCAAATGGTTTTGATGACCACTGCTTTATAGTATTTTTTTA 885405 -- viiv i v iiiv i i vv v C L1P1_orf2#LIN 2673 GTACCAGTACCATGCTGTTTTGGTTACTGTAGCCTTGTAGTATAGTTTGA 2624 chr1ptel1M 885406 GGTCCGATACAGCTAGGCTACCTTTCTGTGCATTTTTCTCCTGTGCATTT 885455 i v i -- -iv v i iiv--- v v ii - v vv C L1P1_orf2#LIN 2623 AGTCAGGTA--GC-GTGATGCCTCCA---GCTTTGTTCTTTTG-GCTTAG 2581 chr1ptel1M 885456 AATTTACTTGACT-TTCTTGATCTTTTCTTCTTCCAGATGAATTTT---G 885501 i v i v- v vv v i vv v i --- C L1P1_orf2#LIN 2580 GATTGACTTGGCGATGCGGGCTCTTTTTTGGTTCCATATGAACTTTAAAG 2531 chr1ptel1M 885502 TTATTTTT-CTAGCTCTATCAAGCAATTTGGGGGCAGTTTGATTGGTATA 885550 vi - i ii i v v v iivv i i v v i C L1P1_orf2#LIN 2530 TAGTTTTTTCCAATTCTGTGAAGAAAGTCATTGGTAGCTTGATGGGGATG 2481 chr1ptel1M 885551 GCACC-AATATACAATTGGTATAGTAAACTAAAGTAGAATTGTCATTTTT 885599 ii- v i v -- i------ vii i v v i i C L1P1_orf2#LIN 2480 GCATTGAATCTATAAAT--TAC------CTTGGGCAGTATGGCCATTTTC 2439 chr1ptel1M 885600 GTTATATTAGTTCAGTCTACCCATGAGCACTTGATATTCTTTCAATTGTT 885649 iiv ii vvi ivvi i i v C L1P1_orf2#LIN 2438 ACGATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTCCATTTGTT 2389 chr1ptel1M 885650 TAGATCTAACTTTATTTTTTGTGGAAAGTGGTTTATAATTGTGTTCATAT 885699 iv ivvi i? - iiv i i v vi iiv v C L1P1_orf2#LIN 2388 TGTATCCTCTTTTATTTCNT-TGAGCAGTGGTTTGTAGTTCTCCTTGAAG 2340 chr1ptel1M 885700 AG-----TCA-ATGTCTTTGCAGG-TAGACTCCCAAATATTTTATATTAT 885742 ----- - -i i i i - i i i ii vi v C L1P1_orf2#LIN 2339 AGGTCCTTCACAT-CCCTTGTAAGTTGGATTCCTAGGTATTTTATTCTCT 2291 chr1ptel1M 885743 CTACAGCTATTTTAAATGGGACTTCTCTT-TGTATCT--CTTGCTGCTGG 885789 i iv v v i v v i- - i -- iv i v C L1P1_orf2#LIN 2290 TTGAAGCAATTGTGAATGGGAGTTCACTCATG-ATTTGGCTCTCTGTTTG 2242 chr1ptel1M 885790 ACT-TTGTTGGTAACATACAGAAATGCTGATGATTTATGTGAATTTGTTT 885838 v - i ---i i ii vi v iiv vi C L1P1_orf2#LIN 2241 TCTGTTATTGGT---GTATAAGAATGCTTGTGATTTTTGCACATTGATTT 2195 chr1ptel1M 885839 TGTATACTGCAGCTTTGCTAAAGTT-CTAAAATGTTTCTAATAGTTTTTA 885887 v vii i - v vvv i vviivii vi C L1P1_orf2#LIN 2194 TGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGGAGATTTTGG 2145 chr1ptel1M 885888 GTTGATTCTCTAGGATTCTCTAACTATACTATCATATTGT 885927 i vv vv i i i iv v i i C L1P1_orf2#LIN 2144 GCTGAGACGATGGGGTTTTCTAGATATACAATCATGTCGT 2105 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 46.87 CpG sites = 135, Kimura (unadjusted) = 48.29 Transitions / transversions = 1.26 (135/107) Gap_init rate = 0.05 (36 / 719), avg. gap size = 1.22 (44 / 36) 669 31.45 2.99 3.50 chr1ptel1M 885322 885924 (114076) C L1M2_orf2#LINE/L1 (587) 2704 2105 m_b24s551i10 883 chr1ptel1M 885322 CTAACCTATTCCACTGATCCATTACTCTATTTCTTAGCCAGTACCAAATG 885371 vi i i i i vvv i i vv viiv C L1M2_orf2#LIN 2704 CTATTCTGTTCCATTGGTCTATGTGTCTGTTTTTATGCCAGTACCATGCT 2655 chr1ptel1M 885372 GTTTTGATGACCACTGCTTTATAGTATTTTTTTAGGTCCGATACAGCTAG 885421 i v i iv i v v i v i vv iv v C L1M2_orf2#LIN 2654 GTTTTGGTTACTATAGCTTTGTAGTATATTTTGAAGTCAGGTAGTGTGAT 2605 chr1ptel1M 885422 GCTACC-TTTCTGTGCATTTTTCTCCTGTGCATTTAATTTACTTGACT-T 885469 iv -vi i v v v vv -------- vvi i - C L1M2_orf2#LIN 2604 GCCTCCAGCTTTGTTCTTTTTGCTCAGG--------ATTGCTTTGGCTAT 2563 chr1ptel1M 885470 TCTTGATCTTTTCTTCTTCCAGATGAATTTTG---TTATTTTT-CTAGCT 885515 vv i v vv v i i--- ? - vi C L1M2_orf2#LIN 2562 TCGGGGTCTTTTGTGGTTCCATACGAATTTTAGGATTNTTTTTTCTATTT 2513 chr1ptel1M 885516 CTATCAAGCAAT-TTGGGGGCAGTTTGATTGGTATAGCACC-AATATACA 885563 i v - - iivv i v v v v ii- v ii C L1M2_orf2#LIN 2512 CTGTGAAG-AATGTCATTGGTATTTTGATAGGGATTGCATTGAATCTGTA 2464 chr1ptel1M 885564 -ATTGGTATAGTAAACTAAAGTAGAATTGTCATTTTTGTTATATTAGTTC 885612 - i v v i --------- v v ? viiv i C L1M2_orf2#LIN 2463 GATCGCTTTGG---------GTAGTATGGNCATTTTAACAATATTAATTC 2423 chr1ptel1M 885613 AGTCTACCCATGAGCACTTGATATTCTTTCAATTGTTTAGATCTAACTTT 885662 vvi v i ivv ii i v ? ivi iv- i C L1M2_orf2#LIN 2422 TTCCAATCCATGAGCATGGGATATCTTTCCATTTNTTTGTGTCCT-CTTC 2374 chr1ptel1M 885663 ATTTTTTGTGGAAAGTGGTTTATAATTGTGTTCATATAG----TCAATGT 885708 v i v vivv v i v v? ii v ---- iv iv C L1M2_orf2#LIN 2373 AATTTCTTTCATCAGTGTTTTATAGTTTTCNTTGTAGAGATCTTTCACCT 2324 chr1ptel1M 885709 CTTTG--CAGGTAGACTCCCAAATATTTTATATTATCTACAGCTATTTTA 885756 i --i ii vv i i ii v v i ii v C L1M2_orf2#LIN 2323 CCTTGGTTAAATTTATTCCTAGGTATTTTATTTTTTTTGTAGCTATTGTA 2274 chr1ptel1M 885757 AATGGGACT--TCTCTTTGTATCTCTTGCTGCTGGACTTTGTTGGTAACA 885804 i -- i vi v i v v v i -- i v ii i C L1M2_orf2#LIN 2273 AATGGGATTGCTTTCTTGATTTCTTTTTCAGATAG--TTCGTTGTTGGCG 2226 chr1ptel1M 885805 TACAGAAATGCTGATGATTTATGTGAATTTGTTTTGTATACTGCAGCTTT 885854 i iv v ivi vi v i C L1M2_orf2#LIN 2225 TATAGAAATGCTACTGATTTTTGTATGTTGATTTTGTATCCTGCAACTTT 2176 chr1ptel1M 885855 GCTAAAGTTCTAAAATGTTTCTAATAG-TTTTTAGTTGATTCTCTAGGAT 885903 i i v iv vv viiv ? - i v v i ? C L1M2_orf2#LIN 2175 ACTGAATTCGTTTATCAGTTCTAANAGTTTTTTGGTGGAGTCTTTAGGNT 2126 chr1ptel1M 885904 TCTCTAACTATACTATCATAT 885924 i ?v vv i C L1M2_orf2#LIN 2125 TTTCTANATATAAGATCATGT 2105 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 40.50 CpG sites = 90, Kimura (unadjusted) = 41.97 Transitions / transversions = 0.97 (90/93) Gap_init rate = 0.05 (32 / 602), avg. gap size = 1.22 (39 / 32) 1837 28.57 0.84 0.98 chr1ptel1M 886462 887175 (112825) C L1M5_orf2#LINE/L1 (1180) 2114 1402 m_b24s551i11 882 chr1ptel1M 886462 ATCATATCATCTGCAAAGAGTGATAATTTTGTTTCCTCATTACTTACTCT 886511 i i v i? i i i i v v iv iii C L1M5_orf2#LIN 2114 ATCATGTCATCTGCGAATAANGACAGTTTTATTTCTTCCTTTCCAATCTT 2065 chr1ptel1M 886512 AATGCCTTCGATTTCTTTTTCTACTCTTATTCCTAAAACTAACCTTTCTG 886561 v iv vvi v vvvii ivvii ii C L1M5_orf2#LIN 2064 TATGCCTTTTATTTCTTTTTCTTGCCTTATTGCACTGGCTAGGACCTCCA 2015 chr1ptel1M 886562 GTACAATATTGAATCATACTGATGATAGTGGGATA-CCTTGTTTCACTCG 886610 i viv v i ? i - i - i iii v C L1M5_orf2#LIN 2014 GTACAATGTTGAATAGAAGTGGTGANAGCGG-ACATCCTTGTCTTGTTCC 1966 chr1ptel1M 886611 TGATCTTACCGGAAATGTTTCTAGTTTATCCAC----ACATATAATTCTT 886656 i vv i v i? ii ? - i ---- vi i vi ? C L1M5_orf2#LIN 1965 CGATCTTAGGGGGAAAGCNTTCAGTNT-TTCACCATTAAGTATGATGTTN 1917 chr1ptel1M 886657 CCTGATGGTTTTTAGATAGATATTACTTATCATTTTGAAGAAAACTCCAT 886706 v vv v - iiivi vv i ivii v C L1M5_orf2#LIN 1916 GCTGTAGGTTTTTCG-TAGATGCCCTTTATCAGGTTGAGGAAGTTCCCTT 1868 chr1ptel1M 886707 TTATTTCTATTCTCTCTAGAGTTTTTACTAGGAATGGGTGTTGTATTTTG 886756 i i v i viiv ii v v C L1M5_orf2#LIN 1867 CTATTCCTAGTTTGCTGAGAGTTTTTATCATGAATGGGTGTTGAATTTTG 1818 chr1ptel1M 886757 TCAAATGCTTTTTCTGCATCTATTGAGATTACCATATGATTTCTGTTGGT 886806 v i i v ivv C L1M5_orf2#LIN 1817 TCAAATGCTTTTTCTGCATCTATTGAGATGATCATATGATTTTTCTCCTT 1768 chr1ptel1M 886807 TTGGTTATTGATATGGTTGATTATGACAATAGTTTTCCTAATATTGAACC 886856 vvvi i i vi iivii v v i v i i C L1M5_orf2#LIN 1767 TATTCTGTTAATATGGTGAATTACATTGATTGATTTTCGAATGTTAAACC 1718 chr1ptel1M 886857 AATGCAGCATTCTTGTATTAAATCCCACTTAGTCATAGTGTACTATCCTG 886906 iviv i viv i i ii i v C L1M5_orf2#LIN 1717 AACCTTGCATTCCTGGGATAAACCCCACTTGGTCATGATGTATTATCCTT 1668 chr1ptel1M 886907 TTGATAAGTTGTTGTAATCTCTTTGCTAATGTTTTATTTAAAAATTTTGC 886956 v vi i v v vv i i ? ii v C L1M5_orf2#LIN 1667 TTTATATATTGCTGGATTCGATTTGCTAATATTTTGTTNAGGATTTTTGC 1618 chr1ptel1M 886957 ATCAATATTCATTAGGAAAATTGATCTGTAATTTTCTTTCTCCATTTTGG 887006 v i v i v i iiiii vv v C L1M5_orf2#LIN 1617 ATCTATGTTCATGAGGGATATTGGTCTGTAATTTTCTTTTCTTGTAATGT 1568 chr1ptel1M 887007 CTCCTCCTGGTTTAGGTATCTGCAACCTATTTGTGTCATAAAAGGAATTT 887056 iivi ? v v viv?v ii v iv v i- C L1M5_orf2#LIN 1567 CTTTGTCNGGTTTTGGTATCAGGGTNATGCTGGCCTCATAAAATGAG-TT 1519 chr1ptel1M 887057 GGCAAGAGTT-TTTCTTTACCTATTTTTCCAAATAGTTTGCATAGTATTG 887105 v v -ii vi iivi v ii iv C L1M5_orf2#LIN 1518 GGGAAGTGTTCCCTCTTTTTCTATTTTCTGGAAGAGTTTGTGTAAGATTG 1469 chr1ptel1M 887106 GAATTAAATGTTCTTTAAATGGTTGATAGAATTCATTTGTGAATCCATTT 887155 v vv v i v i iiv v i C L1M5_orf2#LIN 1468 GTATTATTTCTTCCTTAAATGTTTGGTAGAATTCACCAGTGAAGCCATCT 1419 chr1ptel1M 887156 GGCCCTGGAGAGTTTTTCTT 887175 v --- C L1M5_orf2#LIN 1418 GGGCCTGGAG---TTTTCTT 1402 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 36.57 CpG sites = 112, Kimura (unadjusted) = 37.26 Transitions / transversions = 1.24 (112/90) Gap_init rate = 0.01 (10 / 713), avg. gap size = 1.30 (13 / 10) 29 9.56 5.36 0.00 chr1ptel1M 887176 887231 (112769) (AGGGTT)n#Simple_repeat 1 59 (0) m_b24s252i9 884 chr1ptel1M 887176 AGGGTTAGGGTTAGGGTTAGAG-TCGGGTTAGAG-TCGGGTT-GGGTTAG 887222 i - v i - v - (AGGGTT)n#Sim 1 AGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAG 50 chr1ptel1M 887223 GGTTAGAGT 887231 i (AGGGTT)n#Sim 51 GGTTAGGGT 59 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.05 (3 / 55), avg. gap size = 1.00 (3 / 3) 596 30.88 6.28 4.01 chr1ptel1M 887725 888871 (111129) C L1M5_orf2#LINE/L1 (2085) 1209 38 m_b25s551i2 882 chr1ptel1M 887725 ATTTGTATTAA-GTTTACTCTTTTAGTTTTTGATATTGATAATTTG-ATT 887772 i v i - i v i i - ii i -i i C L1M5_orf2#LIN 1209 ATCTGTAGTGATGTCTCCTTTTTCA-TTCCTGATATTGGTAATTTGTGTC 1161 chr1ptel1M 887773 TTCT-TCTTTCCTTTTCCTAATCAAATTAACCAAAGGCTTATC--TTTTG 887819 - -- i i ivi ?i i i i -- i C L1M5_orf2#LIN 1160 TTCTCTCTTT--TTTTCTTGATCAGTCTNGCTAGAGGTTTATCAATTTTA 1113 chr1ptel1M 887820 GGGGGAT-TTTTCATAATATCAATTCTTAGTTTTGTTTATA--CTTCA-- 887864 vv -- - v iv i ii i i i i v v-- ii -- C L1M5_orf2#LIN 1112 TTG--ATCTTTTCAAAGAACCAGCTTTTGGCTTCGTTGATTTTCTCTATT 1065 chr1ptel1M 887865 GTAGTTTTCTTTTA-ATTTT-TTAATCTCTTCTTTTATTTTCAGAAATTC 887912 ?v? v v- i- i i v i i i vv v C L1M5_orf2#LIN 1064 GTNTNTTTGTTTTCTATTTCATTGATTTCTGCTCTTATCTTTATTATTTC 1015 chr1ptel1M 887913 AAATTTGACATTTACTTGGGGTTTTTAAATTTGTTCTT-----TC-AATG 887956 vvvii vvi i ? v --- i ----- - iiv C L1M5_orf2#LIN 1014 CTTCCTTCTACTTNCTTTGGGTTT---AATTTGCTCTTCTTTTTCTAGCT 968 chr1ptel1M 887957 TTTTAAGTTGCATGCCCAATTCATTAATCTT--TTCTTTCT-CTATTTTA 888003 i v v v ii iv i i --vi - v i C L1M5_orf2#LIN 967 TCTTAAGGTGGAAGCTTAGATCATTGATTTTAAGCCTTTCTTCTTTTCTA 918 chr1ptel1M 888004 TTCATGTAAGCATTTAAAGATATAAGATTTCCC-CTAAGAACTGTTCTGG 888052 --- i ? ? v - - v i i i C L1M5_orf2#LIN 917 ---ATATANGCATTTAANGCTATAA-ATTTCCCTCTAAGCACTGCTTTAG 872 chr1ptel1M 888053 TTGCATCCCATAAATTTTGGTATGTTGTCTGATTATTGTCATTCTGTTGG 888102 i i i v vv i ? v vi C L1M5_orf2#LIN 871 CTGCATCCCACAAATTTTGATATGTTGTATTTTCATTNTCATTCAGTTCA 822 chr1ptel1M 888103 ATGAAATTATCAATAGTTTC---TATGATTTGTTGTTTTACCCATTCATT 888149 -i v v -- i --- i v v v vvi C L1M5_orf2#LIN 821 A-AATATTTTC--TAATTTCCNTTGTGATTTCTTCTTTGACCCATGGGTT 775 chr1ptel1M 888150 CTTTAGGATTA----GATTAGTTTCCAATTA-------ATTTTTGATCTA 888188 v i v i---- v i v ------- iv v? C L1M5_orf2#LIN 774 ATTTAGAAGTGTGTTGTTTAATTTCCAAATATTTGGGGATTTTCTAGNTA 725 chr1ptel1M 888189 TTTTTCCCTGGCCCTTTATTACATGTAATTTTTACTGCATCATGATCTGA 888238 i --- v iiv v --- v - v i v ii i v C L1M5_orf2#LIN 724 TCTTT---TTGTTATTGATT---TCTAA-TTTAATTCCATTGTGGTCAGA 682 chr1ptel1M 888239 AAAAAGATGCATTTGCTATTTCTTTCTTTCTGCATTTGATTTTAAG---- 888284 i v v iv - v iiv vv i i?iv i--- i ---- C L1M5_orf2#LIN 681 GAACATACTC-TGTATGATTTCAATCCTTTNAAATTTA---TTGAGACTT 636 chr1ptel1M 888285 GTTTTATCCCCTAATACATGGTCATTTTTTGTATAGGTTTCATGTACCAC 888334 vv i i? i vv i v v v i i vvi C L1M5_orf2#LIN 635 GTTTTATGGCCCAGNATATGGTCTATCTTGGTAAATGTTCCATGTGCACT 586 chr1ptel1M 888335 CAAGAAAAAAG-ATATTCC-TTTTTGTCACCATTCAATTTTCTTCAAAAG 888382 ii i i v -i i-i?v ii-vi v? i v vi v C L1M5_orf2#LIN 585 TGAAAAGAATGTGTATTCTGCNGTTGTTG-GGTGNAGTGTTCTATAAATG 537 chr1ptel1M 888383 TCTATCATACCAAACTTTTCTAAAATCCTATTTACCTTTTTAACATCTTT 888432 v i vii ii vv iv v i vi i i vv i iv i i C L1M5_orf2#LIN 536 TCAATTAGGTCAAGTTGGTTGATAGTGTTGTTCAAATCTTCTATATCCTT 487 chr1ptel1M 888433 CCT-ATTTTGTG-------GTTCT-TAAA-----GAGCAAGGC----TGA 888464 v - v ------- - v ----- vi ?---- i C L1M5_orf2#LIN 486 ACTGATTTTTTGTCTACTTGTTCTATCAATTACTGAGAGAGGNGTGTTAA 437 chr1ptel1M 888465 GATCCCCCCTAGTACAGTTTTG---CTGTTTAAATCTTCTTGCAGTTTTC 888511 i -- i ? v i i v ---i i vv i vi i v C L1M5_orf2#LIN 436 AAT--CTCCNACTATAATTGTGGATTTGTCTATTTCTCCTTTTAGTTCTG 389 chr1ptel1M 888512 TTAACATCTTCTCTAGGAATTTGAATGCTATACCATTTGGTGCATATATG 888561 i iiv i v ii v v vi v v iii v i ii C L1M5_orf2#LIN 388 TCAGTTTTTGCTTCATGTATTTTGAAGCTCTGTTATTAGGTGCATACACA 339 chr1ptel1M 888562 TTTAATATTA--ATGT-TACTATATT-ATTTACCC-TTTACCAAGATGTA 888606 iv i-- - v vv v- v - i vv v C L1M5_orf2#LIN 338 TTTAGGATTGTTATGTCTTCTTGATGAATTGACCCTTTTATCATTATGAA 289 chr1ptel1M 888607 GTTTCCTTCCTTATCTCTTTTAATAAGTTCTATTTTTGCTTTTGCTTGAT 888656 i v i i vv vv ii iii vivv i i vi C L1M5_orf2#LIN 288 ATGTCCCTCTTTATCTCTGGTAATATTTCTTGCCTTGAAGTCTACTTTGT 239 chr1ptel1M 888657 CTGTGATCAGGATTGCTATCTCTGCTTTTTTTTTTTTAAC-TTCAGCTAA 888705 vv i iv v i i?i v i v? ii- i------ C L1M5_orf2#LIN 238 CTGATATTAATATAGCCACNCCAGCTTTCTTTTGNTTAGTGTTT------ 195 chr1ptel1M 888706 AGCATAATAGATCCTGCTACTGCCTTTTAACTTTACTCTGTATGTATCAT 888755 - ii v i vi v vv vi i vi ? v i v C L1M5_orf2#LIN 194 -GCATGGTATATCTTTTTCCATCCTTTTACTTTCAACCTNTCTGTGTCTT 146 chr1ptel1M 888756 TCTACTTTAAATGTGTTTCTTGTAAAAAAAAAAAAAAAGCATATTGTAGG 888805 v i v i i i ---------- i v v v C L1M5_orf2#LIN 145 TATATTTAAAGTGCGTCTCTTGT----------AGACAGCATATAGTTGG 106 chr1ptel1M 888806 ATTCTGGCTTTTGATCCAGTCTG-CTATCTGCTTCTGTTTTAT--GAGAA 888852 i ii vi v - v - v iv v -- vi C L1M5_orf2#LIN 105 GTCTTGTTTTTTTATCCAGTCTGACAATCT-CTGCCTTTTAATTGGAGTG 57 chr1ptel1M 888853 TTCACCCCATTAACATTCA 888871 i v? v i C L1M5_orf2#LIN 56 TTTAGNCCATTTACATTTA 38 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 41.32 CpG sites = 185, Kimura (unadjusted) = 41.64 Transitions / transversions = 1.19 (185/155) Gap_init rate = 0.07 (80 / 1146), avg. gap size = 1.49 (119 / 80) 262 25.95 2.76 12.73 chr1ptel1M 888751 888931 (111069) C L1MEj_5end#LINE/L1 (0) 2160 1996 m_b25s551i3 882 chr1ptel1M 888751 ATCATTCTACTTTAAATGTGTTTCTTGTAAAAAAAAAAAAAAAGCATATT 888800 i i ii i ---------- v v C L1MEj_5end#LI 2160 ATCACTTTGTTTTAAGTGTGTTTCTTGT----------AAACAGCATATA 2121 chr1ptel1M 888801 GTAGGATTCTGGCTTTTGATCCAGTCTGCTATCTGCTTCTGTTTT---AT 888847 iv i i vi i i i vi --- ii i --- C L1MEj_5end#LI 2120 GCTGGGTTTTGTTTTTTAACCCAATCTGACA---GTCTCTGTCTTTTAAT 2074 chr1ptel1M 888848 --GAGAATTCACCCCATTAACATTCACAGTTAAAATTACTAACTGTATTT 888895 -- vi v i vv --- iv i - i i C L1MEj_5end#LI 2073 GGGAGAATTCAGTCCATTCACATTTAGTGT---AACGACTGA-TATACTT 2028 chr1ptel1M 888896 CCCATTTTATTTTCCCCAAGTTAGACTTTTCTCTTT 888931 --v iiii vv -- vi ? C L1MEj_5end#LI 2027 --GATTTTATTCCTTCCATCTT--ACTTTATTNTTT 1996 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 31.77 CpG sites = 27, Kimura (unadjusted) = 32.74 Transitions / transversions = 1.93 (27/14) Gap_init rate = 0.13 (23 / 180), avg. gap size = 1.13 (26 / 23) 272 19.42 10.32 10.32 chr1ptel1M 888752 888906 (111094) C L1MEh_5end#LINE/L1 (1) 2234 2080 m_b25s551i4 882 chr1ptel1M 888752 TCATTCTACTTTAAATGTGTTTCTTGTAAAAAAAAAAAAAAAGCATATTG 888801 v ? ii i i i v ---------- C L1MEh_5end#LI 2234 TCCTTNTGTTTTAAGTGTGTCTCTTGTAGACA----------GCATATTG 2195 chr1ptel1M 888802 TAGGATTCTGGCTTTTGATCCAGTCTGCTA---TCTG-CTTCTGTTTTAT 888847 v i vi ?i i v? --- - i iv vi C L1MEh_5end#LI 2194 TTGGATTTTGTTTTTNAATCCAATCTGANAATCTCTGTCTTTTAATTGGT 2145 chr1ptel1M 888848 GAGAATTCACCCCATTAACATTCACAGTTAAAATTACT----------AA 888887 -- i v v i --- iv ----------i C L1MEh_5end#LI 2144 GAG--TTTAACCCATTTACATTTA---TTGTAATTACTGNTATATTNGGA 2100 chr1ptel1M 888888 CTGTATTTC--CCATTTTATT 888906 - -- i C L1MEh_5end#LI 2099 CT-TATTTCTGCCATCTTATT 2080 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 23.52 CpG sites = 17, Kimura (unadjusted) = 23.52 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.13 (20 / 154), avg. gap size = 1.60 (32 / 20) 15 17.69 6.35 4.69 chr1ptel1M 888996 889058 (110942) (CCTTCT)n#Simple_repeat 1 64 (0) m_b25s252i0 885 chr1ptel1M 888996 CCTTCCTCCTTC-CTTAGCCCCTTCCCCTTCTCCTTCTGCCCT-ACCTTC 889043 - - i -v i i - i -v (CCTTCT)n#Sim 1 CCTT-CTCCTTCTCCT-TCTCCTTCTCCTTCTCCTTCT-CCTTCTCCTTC 47 chr1ptel1M 889044 T-ATT-ACCTTCCCCTT 889058 -v -v i (CCTTCT)n#Sim 48 TCCTTCTCCTTCTCCTT 64 Matrix = Unknown Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.11 (7 / 62), avg. gap size = 1.00 (7 / 7) 11 13.83 2.78 5.71 chr1ptel1M 891439 891474 (108526) (AAAAGG)n#Simple_repeat 1 35 (0) m_b25s252i1 886 chr1ptel1M 891439 AAATGGGAAGGGAAAAGCGAAAAGG-GAAGGAATAAG 891474 v i i - -i - (AAAAGG)n#Sim 1 AAAAGGAAAAGGAAAAG-GAAAAGGAAAAGGAA-AAG 35 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.09 (3 / 35), avg. gap size = 1.00 (3 / 3) 336 23.61 3.40 7.80 chr1ptel1M 891615 891761 (108239) L1M6_5end#LINE/L1 2350 2490 (25) m_b25s551i5 887 chr1ptel1M 891615 AAAAGCATAAACAGGGGTTAACAAGATGGCAAG--TAACACAGAAT-TAA 891661 ? ---------i? i i-- v vi i- v L1M6_5end#LIN 2350 AAAAGCANAAA---------GNAAGATGACAAANATAAGACCAAACATAT 2390 chr1ptel1M 891662 TAATTTTAACCATAAATGTGAACGGGATAAACTCTCCCAT--AAAGACGA 891709 i i v i v i i v i i -- i L1M6_5end#LIN 2391 CAGTTATGACAATAAATGTAAATGGGTTAAACTCCCCTATTAAAAGACAA 2440 chr1ptel1M 891710 AGCGGTCAGCAGACTGGATTAAAGGCCAGAATCCTACAATTTGTTGTTTA 891759 -iv -v i i iiv i v v v i L1M6_5end#LIN 2441 AG-ACTC-TCAGATTGGGTTAAAAAACAAAATCCAACTATATGCTGTTTA 2488 chr1ptel1M 891760 CA 891761 L1M6_5end#LIN 2489 CA 2490 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 29.49 CpG sites = 20, Kimura (unadjusted) = 29.49 Transitions / transversions = 1.67 (20/12) Gap_init rate = 0.10 (14 / 146), avg. gap size = 1.14 (16 / 14) 368 20.95 6.20 3.79 chr1ptel1M 891633 891761 (108239) L1MEh_5end#LINE/L1 2079 2210 (25) m_b25s551i6 887 chr1ptel1M 891633 TAACAAGATGGCA--AGTAACACAGAAT----TAATAATTTTAACCATAA 891676 i -- i vv v? ----i i --- v L1MEh_5end#LI 2079 TAATAAGATGGCAGAAATAAGTCCNAATATANCAGTAATT---ACAATAA 2125 chr1ptel1M 891677 ATGTGAACGGGATAAACTCTCCCAT--AAAGACGAAGCGGTCAGCAGACT 891724 i i v v v -- -- v i i?v i L1MEh_5end#LI 2126 ATGTAAATGGGTTAAACTCACCAATTAAAAGAC--AGAGATTNTCAGATT 2173 chr1ptel1M 891725 GGATTAAAGGCCAGAATCCTACAATTTGTTGTTTACA 891761 ? iiv i v v i i L1MEh_5end#LI 2174 GGATTNAAAAACAAAATCCAACAATATGCTGTCTACA 2210 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 25.59 CpG sites = 14, Kimura (unadjusted) = 25.59 Transitions / transversions = 1.17 (14/12) Gap_init rate = 0.06 (8 / 128), avg. gap size = 1.62 (13 / 8) 4922 29.95 3.06 2.86 chr1ptel1M 891657 894863 (105137) L1M5_orf2#LINE/L1 24 3236 (58) m_b25s551i7 887 chr1ptel1M 891657 ATTAATAATTTTAACCATAAATGTGAACGGGATAAACTCTCCCATAAAGA 891706 i --- vv i i ?v v v v i L1M5_orf2#LIN 24 ATCAATAATT---ACATTAAATGTAAATGGNCTAAACACTCCAATTAAAA 70 chr1ptel1M 891707 CGAAGCGGTCAGCAGACTGGATTAAAGGCCAGAATCCTACAATTTGTTGT 891756 v v v i iiv v iiv ii i v v v i L1M5_orf2#LIN 71 GGCAGAGATTGTCAGACTGGATAAAAAAACAAGACCCAACTATATGCTGT 120 chr1ptel1M 891757 TTACATATTACATATTATACCCGAAGCAGGGAGATACATACAGAGTAAAG 891806 i vivv ii i v ----- ii vii i v ? iv i i L1M5_orf2#LIN 121 CTACAAGAGACGCACTTTA-----AATATAAAGACACAGANAGGTTGAAA 165 chr1ptel1M 891807 GCAAAAGGTTGGAGCATAATCTACTATGCTTCAGGTGAAGTCAAA-AAAG 891855 i v iv vi v i v-v viiv ?iv - L1M5_orf2#LIN 166 GTAAAAGGATGGAAAAAGATATACCATGCA-AACACTAANCAAAAGAAAG 214 chr1ptel1M 891856 CAGGGGTAGCCATCCTGGTCTCAGATCAAGCA------AAAGCAAAAATT 891899 v ? i i vi ii v iv i ------ i i -- L1M5_orf2#LIN 215 CTGGNGTGGCTATATTAATATCAGACAAAGTAGACTTCAAGGCAAGAA-- 262 chr1ptel1M 891900 GATCTAATTAAAAGAGATAAGGAAGGGCATGACATCTTGCTAAAAGGGTA 891949 - --- vv i i i vv vv v v L1M5_orf2#LIN 263 -AT---ATTACCAGAGATAAAGAGGGACATTTCATAATGATAAAAGGGTC 308 chr1ptel1M 891950 AATAGATAATGAAGCAATATCAATATTAAACATATATGCAGCAAGTGGTG 891999 vv v v vv v vi ii i v v i iiii L1M5_orf2#LIN 309 AATTCATCAAGAAGACATAACAATCCTAAATGTGTATGCACCTAATAACA 358 chr1ptel1M 892000 TAGCATTTAAATTCTTAAAAGAGAAATTAAGAGAGCTGCAAGAAGAAACA 892049 v v iv v v i iv i i i v i iv i i L1M5_orf2#LIN 359 GAGCTTCAAAATACATGAAGCAAAAACTGACAGAACTAAAAGGAGAAATA 408 chr1ptel1M 892050 GACAGCAAAACTATAAT---AGTGGAAGATCTCAA-ACTTGCACTCTTAA 892095 --- v i i --- ? i i i - ?i- v i i L1M5_orf2#LIN 409 GACA---AATCCACAATTATAGTNGGAGATTTTAACACNC-CTCTCTCAG 454 chr1ptel1M 892096 -AATT---AGAGAAATTAAACCACAAAATAAATAAGAAAGAAGTCAAAGA 892141 - --- iv v i v - v i --- vi vi L1M5_orf2#LIN 455 TAATTGATAGAACAAGTAGACAA-AAAATCAGTAAG---GATATAGAAGA 500 chr1ptel1M 892142 GTTAAATAGAATACTGGAAA--AGTTAGATATGATAGATCTCTGGAGAAA 892189 v i i -- i ivv -- ii v iv i v iv i iv v L1M5_orf2#LIN 501 TTTGAACA--ACACTATCAACCAACTTGACCTAATTGACATTTATAGAAC 548 chr1ptel1M 892190 ACTA-ACTGGA-GACAGAAATGAGTACACTTTCTTCTCAGCAGTTCATGG 892237 ?- ivi -i ? v -- i v i ivv iv L1M5_orf2#LIN 549 ACTNCACCCAACAACNGCA--GAATACACATTCTTTTCAAGTGCACATGG 596 chr1ptel1M 892238 AACCTATACAAAAATTGACCGTATATTAAGACATAAAA---ACCTCAAAC 892284 v v v i v i ?i ii v ---ii -- L1M5_orf2#LIN 597 AACATTTACCAAGATAGACCATATNCTGGGCCATAAAACAAGTCTCAA-- 644 chr1ptel1M 892285 TCAAATGCAGTAAGGCAGAAATAGTA-AATGCATCCTTTTCAGACCACAA 892333 -i vi?iv i iiv vi - iv i v- i v L1M5_orf2#LIN 645 -TAAATTTNAAAGGATTGAAATCATACAGAGTATG-TTCTCTGACCACAA 692 chr1ptel1M 892334 TGCAATGAAAATTACATTCAACAA----AAGCCAG-GGGAAAATAGACCA 892378 v v v viv v i ---- vi ?-vi --- v L1M5_orf2#LIN 693 TGGAATTAAATTAGAAATCAATAACAAAAAGATANCTAGAAAAT---CCC 739 chr1ptel1M 892379 AAAATAATTTGAAACTAAATAATCTCA-TAATAAAGAATGATTGGGTGAA 892427 v v v i i - v - vv v ivvv v L1M5_orf2#LIN 740 CAAATATTTGGAAATTAAACAA-CACACTTCTAAATAACCCATGGGTCAA 788 chr1ptel1M 892428 ACAGCAAATCATAGACATAATTAATAACT-TCATCAAAAAAATGGCAATA 892476 v iv i i?viv iv v - iv v vvi i? i L1M5_orf2#LIN 789 AGAAGAAATCACAANGGAAATTAGAAAATATTTTGAACTGAATGANAATG 838 chr1ptel1M 892477 ATGAAACATCATACCAAAATGTGTGGGATGCAGCCAAAGCAGTAATAAG- 892525 vi v v i v i iv v - L1M5_orf2#LIN 839 AAAATACAACATATCAAAATTTGTGGGATGCAGCTAAAGCAGTGCTTAGA 888 chr1ptel1M 892526 GGGAAATTTCATATCTCTAGAGGCCTACTTGCATAAAATAGA-GAAAGA- 892573 - v ?i i v ? iv --- i v - i- L1M5_orf2#LIN 889 GGGAAATTT-ATAGCNTTAAATGCNTATAT---TAGAAAAGAAGAAAGGC 934 chr1ptel1M 892574 -GAAGGTCAATGAATTGGGCTTGCAACTAAAAATGCTAGAAAAGGAA--- 892619 -v ii vi ii v v v i v i --- L1M5_orf2#LIN 935 TTAAAATCAATGATCTAAGCTTCCACCTTAAGAAGCTAGAAAAAGAAGAG 984 chr1ptel1M 892620 CAAATTAAAAACCCCTAGTCAAACATTAAACTTGAAATTCTAAAAATAAA 892669 --- v iv? ii vv iivvv vv i i L1M5_orf2#LIN 985 CAAATTAAA---CCCAAAGNAAGTAGAAGGAAGGAAATAATAAAGATAAG 1031 chr1ptel1M 892670 AGGAGAGATCAATAAAATTGAAAGTAAAAAATCTATTGAATTAATTAATA 892719 v i i v ii ? ?v v v ivv i ii L1M5_orf2#LIN 1032 AGCAGAAATCAATGAAATAGAAAACAAANANACAATAGAGAAAATCAACG 1081 chr1ptel1M 892720 AAACTAAGAGTTGGTTCTATGAAATAACCAACAAAATAGACAAACCCTTA 892769 i i i i v vi i i v i ii L1M5_orf2#LIN 1082 AAGCCAAAAGCTGGTTCTTTGAAAAGATCAATAAAATTGATAAACCTCTA 1131 chr1ptel1M 892770 GTAAATCTGATTAAAAAAAGGAAAG-GAAAAT-CAAATTGTTAGTCTTAA 892817 i? iv i i ii i - i i- iii i v i i L1M5_orf2#LIN 1132 GCNAGACTGATCAAGAAAAAAAGAGAGAAGACACAAATTACCAATATCAG 1181 chr1ptel1M 892818 AAATGAAAAGGGAGAACTTGCCACTTATGAAGAGGAAATTAGAGAAATAA 892867 i i vv ii i vv vvvivi v i iii L1M5_orf2#LIN 1182 GAATGAAAAAGGAGACATCACTACAGATCCTACAGACATTAAAAGGATAA 1231 chr1ptel1M 892868 TTAGGAGTTACTTTGTCCAAATTTATGTCAATAAAATCGACAACTTAAAT 892917 v iiiv i v vv v i v i ? i L1M5_orf2#LIN 1232 TAAGAGAATATTATGAACAACTTTATGCCAATAAATTTGANAACTTAGAT 1281 chr1ptel1M 892918 GAAATGGAATAATACCTTCAAAAATATAGCTTGCCCAAATTAACAGAGGA 892967 vv v v i i i? i v i i ?v i L1M5_orf2#LIN 1282 GAAATGGACAAATTCCTTGAAAAACACAANTTACCAAAACTGACNCAAGA 1331 chr1ptel1M 892968 AGAAGTAAATATCCTAAACAGTCCCAT-TTTAGAAAAAGAAATAGAACAA 893016 i i v vi i i i i - i vv - v ivv L1M5_orf2#LIN 1332 AGAAATAGAAAATCTGAATAGCCCTATATCTATTAAA-GAAATTGAATTT 1380 chr1ptel1M 893017 GCTATTAACCAACTCCCTAAGAAAAAATCCCCAGGACCAGATGGATTTAC 893066 iv vv v i i vi i v i v v i L1M5_orf2#LIN 1381 GTAATTAAAAACCTTCCCACAAAGAAAACTCCAGGCCCAGATGGCTTCAC 1430 chr1ptel1M 893067 ATGTGAATTCTACCAAACATTTAAAGAACAATTAACTCCAATGCTATATA 893116 vv i v v iv vi i i L1M5_orf2#LIN 1431 TGGTGAATTCTACCAAACATTTAAGGAAGAAATAATACCAATCTTACACA 1480 chr1ptel1M 893117 AACTATTTGAAAAAAAATAGGAATTGAAGGAGTCCTACCAAATTCCTTCT 893166 v iv i -- i vv i iiv v v i v i L1M5_orf2#LIN 1481 AACTCTTCCAGAAAA--TAGAAAAAGAGGGAACACTTCCCAACTCATTTT 1528 chr1ptel1M 893167 ATGACACAGACATGGTACTGATACCTAAACCAGGTAGGTTGAAA--ACAG 893214 vi vii ?iiv v ? ii ii-- v -- i L1M5_orf2#LIN 1529 ATGAGGCCAGCATNACCCTGATACCAAAACCNGACAAA--GACATTACAA 1576 chr1ptel1M 893215 AAAAAGAAAATTATAGACCAATCTCCCTAATGAATATTGATGCTAAAATC 893264 i i v v i v v L1M5_orf2#LIN 1577 GAAAAGAAAATTACAGACCAATATCCCTCATGAACATAGATGCAAAAATC 1626 chr1ptel1M 893265 TT----AAGATATTAGCAAAAAAGATTACAGAAAATCATCCTCAGGGTAA 893310 i ---- i vvii i- v vvi vvvv i L1M5_orf2#LIN 1627 CTNAACAAAATATTAGCAAATCGAATC-CAGCAATATATAAAAAGGATAA 1675 chr1ptel1M 893311 TACACTAGGACCAAGTAGGATTTATACCAGGAATTGCAGGGCTGGTTCAA 893360 ii v i i v - i i i L1M5_orf2#LIN 1676 TACATCATGACCAAGTGGGGTTTATCCCAGGAAT-GCAAGGTTGGTTTAA 1724 chr1ptel1M 893361 TATTAGGAAAACTATGAGCATAATTGATTATGTCAATAACCAAATTAAC- 893409 i v i v v v iii v ii i --- vi v v- L1M5_orf2#LIN 1725 CATTCGAAAATCAATCAATGTAATTCACCATAT---TAACAGAATAAAGG 1771 chr1ptel1M 893410 --AAAAACCATATGATCATCTCAATAGGTGCAGAAAACGCATTTGATAAA 893457 -- i i v i L1M5_orf2#LIN 1772 AGAAAAATCATATGATCATCTCAATAGATGCAGAAAAAGCATTTGACAAA 1821 chr1ptel1M 893458 ATCCAACATCCATTCGTAATAAAAACACTTGAGAGGATAGGAATAAATGG 893507 i i i i v iiiv iiv i v L1M5_orf2#LIN 1822 ATTCAACACCCATTCATGATAAAAACTCTCAGCAAACTAGGAATAGAAGG 1871 chr1ptel1M 893508 ACTTTTCCTTAAAATAATCAGGTGTATATATTTAAAACCATCAGTAAGCA 893557 ivvi i vv i v i v i v ivv vv i? i L1M5_orf2#LIN 1872 GAACTTCCTCAACCTGATAAAGGGCATCTACGAAAAACCTACAGCNAACA 1921 chr1ptel1M 893558 TCATATGCAATGGAGAAAAACTGGAACCTTTCCCAGTAAGATCTGGAGTA 893607 ivi v ? i ?v vv v ii L1M5_orf2#LIN 1922 TCATACTTAATGGTGAAANACTGAANGCTTTCCCCCTAAGATCGGGAACA 1971 chr1ptel1M 893608 AAGCAAGGTTGCCCACTATCACCATTTTTATTCAATATTG-AATG----- 893651 ii v i i ? i i i - v ----- L1M5_orf2#LIN 1972 AGACAAGGATGTCCGCTNTCACCACTTCTATTCAACATTGTACTGGAGGT 2021 chr1ptel1M 893652 -CTAGCCTCAGCAATAAGAGTCAAG--AAAGAGATTAAAGGAATTAAAGT 893698 - vvv i-- -- i v v v ii L1M5_orf2#LIN 2022 CCTAGCCAGTGCAATAAGG--CAAGAAAAAGAAATAAAAGGCATAAAGAT 2069 chr1ptel1M 893699 AGGCAATGAGGAAACCAAAATATCACTCTTTGCAGATGATGTGATGGTAT 893748 v v v i iv v i ?i v i ii v ? L1M5_orf2#LIN 2070 TGGAAAGGAAGAAATAAAACTGTCNTTATTCGCAGATGACATGATTGTNT 2119 chr1ptel1M 893749 ACTTAGAGAACCCCAGAGATCCTATTAAAAAGCTATTAGAA--AATAATT 893796 v i i ? i vi iv ? i i -- -- L1M5_orf2#LIN 2120 ACGTAGAAAATCCNAAAGAATCTACAAANAAACTACTAGAACTAATAA-- 2167 chr1ptel1M 893797 CATAACTTTAGCAAAGTTGCAGGATACAAAATAAATCCCCATAAATCCTC 893846 -i i v i i ? ii v viv v vvi L1M5_orf2#LIN 2168 -GTGAATTTAGCAAGGTCGCNGGATACAAGGTCAATATACAAAAATCAAT 2216 chr1ptel1M 893847 AGCATTTTTATACTTCACCAACAAAATCCAACAGCAA---GAGATACAAA 893893 v i i ivii v --- iv v --- i vi? L1M5_orf2#LIN 2217 TGTATTTCTATATACTAGCAACAAA---CAATTGGAAAATGAAATTTNAA 2263 chr1ptel1M 893894 GAGAAATTCCATTCAAAATAACTGTTGATAGCATAAAATATTTGGAAATC 893943 i iv v i v i vvivi v i ? i i i v L1M5_orf2#LIN 2264 AAACAATACCATTTACAATAGCATCAAAAAACATNAAATACTTAGGAATA 2313 chr1ptel1M 893944 TAGCTACCAAAGGAAAGTCAGGAATTATATGAGCAAAATTACAAAAAACT 893993 v v v i? vivv i vi ? iivvv i v i L1M5_orf2#LIN 2314 AATCTAACAAAANATGTGCAAGACCTNTACACTGAAAACTACAAAACATT 2363 chr1ptel1M 893994 TTCCACACAAATACAGTCAGATTTAAATAATTGGAAAAATATTAAGTGCT 894043 viiv v v vv ivv ii v i i vvvi i L1M5_orf2#LIN 2364 GCTGAGAGAAATTAAAGAAGACCTAAATAAATGGAGAGATATACCATGTT 2413 chr1ptel1M 894044 CTTGGATAGGCTGAGCGAATATAATAAAGATGACAATACTCCCTAAACTA 894093 v v vv viv vi ? v v i i i L1M5_orf2#LIN 2414 CATGGATTGGAAGACTCAATATTGTNAAGATGTCAATTCTCCCCAAATTG 2463 chr1ptel1M 894094 ACCTATTTATTTAGTGTTATACCAATCAGACTTCCAAGAAAATATTCTAA 894143 i vv i i iv v i v i iv iiv v i iv L1M5_orf2#LIN 2464 ATCTATAGATTCAATGCAATCCCAATCAAAATCCCAGCAGGTTTTTTTGT 2513 chr1ptel1M 894144 TGATCTAGAAAAAAGAACAACAAAATTCATATGGAAGAACAAAAGGTCGA 894193 v vv v v ivvi ivvi i ivi i ii ? L1M5_orf2#LIN 2514 AGAAATTGACAAGCTGATTCTAAAATTTATATGGAAATGCAAAGGACCNA 2563 chr1ptel1M 894194 GAATC-TCAAGGAAATTAATGAAAAA-AAAATCAAA--TGAAGGTGGCCT 894239 v-i iiv i-v - i v -- i -- i i L1M5_orf2#LIN 2564 GAATAGCCAAAACAATC-TTGAAAAAGAAGAACAAAGTTGGAG--GACTT 2610 chr1ptel1M 894240 ATCTGTACCTGATCT-AAAACTATATTATAAAGCGGCAGTCACCAAAACC 894288 - vv ? ? - i - vi v i i v L1M5_orf2#LIN 2611 A-CACTACCNGATNTCAAGACT-TATTATAAAGCTACAGTAATCAAGACA 2658 chr1ptel1M 894289 ATTTGGTATTGGC-TAAGAAAGAGATTAGTTGATCAGTGGAATAGATTAG 894337 i v - -i v iv i v i i v L1M5_orf2#LIN 2659 GTGTGGTATTGGCGTAAG-GATAGACAAATAGATCAATGGAACAGAATAG 2707 chr1ptel1M 894338 ---GTTCACAAGACAAAAGAGTCA-AC---TATAGCAATCTAGTGTTCGA 894380 --- i --- - v vi - --- i ?v ?i ii v i L1M5_orf2#LIN 2708 AGAGTCC---AGA-AATAGACCCACACATATATGGNCANTTGATTTTTGA 2753 chr1ptel1M 894381 CAAA---CCCAAAGATCTTAACTT-TTGGGATGAGAAT--TCATTAATTC 894424 ---v ? ----i i i-v ivi i -- v -- iv L1M5_orf2#LIN 2754 CAAAGGTGCCAANG----CAATTCAGTGGGGAAAGGATAGTCTTT--TCA 2797 chr1ptel1M 894425 ACAAAAACTGCTGGGATAACTGGAAATTAGTATGGCAGAAATTAGGCATG 894474 viv i i i v ivi v i v iii?v v L1M5_orf2#LIN 2798 ACAAATGGTGCTGGAACAATTGGATATCCATATGGAAAAAAATGAANCTC 2847 chr1ptel1M 894475 GACCCACACTTAACACCATATACTAAGGTAAGATCAAAATGGGTCCAT-G 894523 vi i v i v ii v iv ? i i - - L1M5_orf2#LIN 2848 GACCCCTACCTCACACCATACACAAAAATTAATTCNAGATGGAT-CATAG 2896 chr1ptel1M 894524 ATTTATGCATAAATAACGAGATTATAAATAAAT--TAGAGG--AACATGG 894569 ii viii vi?ii i i -- v -- i -- i L1M5_orf2#LIN 2897 ACCTAAATGTAAAAGNTAAAACTATAA--AACTTCTAGAAGAAAACATAG 2944 chr1ptel1M 894570 GATAGTTTATCTCTCAGACTTGTGGAGGAGGAAGAAATTTCTGACCAAAG 894619 v i-- iivv i - i?v v i i ---i v L1M5_orf2#LIN 2945 GAGAA--TATCTTCGTGACCT-TGGGNTAGGCAAAGATTTCT---TAAAC 2988 chr1ptel1M 894620 ATGAACTAGAGACCATTATTGATCACAAAATAGAAAAT-------TTTGA 894662 v vvi i i v i? --- i i v i ------- v L1M5_orf2#LIN 2989 AGGACACAAAAAGCACNA---ACCATAAAAGAAAAAATTGATAAATTGGA 3035 chr1ptel1M 894663 TTACATCAAATTAAAAAGCCTTTGTACAAACAAAACTAATGCCAACAAGA 894712 i ? v v i i i iv ?vvv ivi vi ii v i L1M5_orf2#LIN 3036 CTNCATCAAAATTAAAAACTTCTGCTCNTCAAAAGACACCGTTAAGAAAA 3085 chr1ptel1M 894713 TTAGAAAGGAAGCAACAAACTGGGAAAACATCTTCACAGTTAAAGGT-TC 894761 v i i v v i ? i v v ii i-? v vi - L1M5_orf2#LIN 3086 TGAAAAGGCAAGCCACAGANTGGGAGAAAATATTTGCAA-NACATATATC 3134 chr1ptel1M 894762 TGAAAAAGGCCTCATTTCCAGAATATATAGAGAATTGACTCTAATTT-AT 894810 v v i v i i -v vi ? i- L1M5_orf2#LIN 3135 TGACAAAGGACTCGTATCCAGAATATATAAAGAACT-CCTACAANTCAAT 3183 chr1ptel1M 894811 AAGAAATCAAGCCATTC--TCCAATTGATAAATGGTCAAAGGATATGACC 894858 ? -- v vv --i v? v v i iv v L1M5_orf2#LIN 3184 AANAAA--AAGACAAACAACCCAATANAAAAATGGGCAAAAGACTTGAAC 3231 chr1ptel1M 894859 AGACA 894863 L1M5_orf2#LIN 3232 AGACA 3236 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.35 CpG sites = 499, Kimura (unadjusted) = 39.91 Transitions / transversions = 1.15 (499/434) Gap_init rate = 0.04 (142 / 3206), avg. gap size = 1.34 (190 / 142) 338 32.71 2.55 1.81 chr1ptel1M 894646 894919 (105081) L1M1_orf2#LINE/L1 3019 3294 (0) m_b25s551i8 887 chr1ptel1M 894646 AAAATAGAAAATTTTGATTACATCAAATTAAAAAGCCTTTGTACA---AA 894692 i v v vv i i i i i --- L1M1_orf2#LIN 3019 AAAATGGACAAATGGGATCACATCAAGTTAAAAAGCTTCTGCACAGCAAA 3068 chr1ptel1M 894693 CAAAACTAATGCCAACAAGATTAGAAAGGAAGCAACAAACTGGGAAAACA 894742 vi - -- ii v ii iiv v v i v i v L1M1_orf2#LIN 3069 GGAAAC-AAT--CAACAAAGTGAAGAGACAACCCACAGAATGGGAGAAAA 3115 chr1ptel1M 894743 TCTTCACAGTTAAAGGTTCTGAAAAAGGCCTCATTTCCAGAATATATAGA 894792 v ii iviv vvvv v i vi v vv ii L1M1_orf2#LIN 3116 TATTTGCAAACTACCCATCTGACAAGGGATTAATAACCAGAATATATAAG 3165 chr1ptel1M 894793 GAATTGACTCTAATTTATAAGAAATCAAGCC--ATTCTCCAATTGATAAA 894840 ii v vv v v i i -- ii -- vv i i v L1M1_orf2#LIN 3166 GAGCTCAAACAACTCTATAGGAAA--AAATCTAATAATCCGATTAAAAAA 3213 chr1ptel1M 894841 TGGTCAAAGGATATGACCAGACAATGTTCAGATGATGAAATTGAAACAAT 894890 v i v vi v vi i v v v vv iiii L1M1_orf2#LIN 3214 TGGGCAAAAGATCTGAATAGACATTTCTCAAAAGAAGACATACAAATGGC 3263 chr1ptel1M 894891 TTCCACTCATATGAAA--GTGTTCCAAATCA 894919 vvv vv -- i v v L1M1_orf2#LIN 3264 AAACAGGCATATGAAAAGGTGCTCAACATCA 3294 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 42.70 CpG sites = 40, Kimura (unadjusted) = 43.33 Transitions / transversions = 0.83 (40/48) Gap_init rate = 0.03 (8 / 273), avg. gap size = 1.50 (12 / 8) 1425 29.67 2.88 2.55 chr1ptel1M 894783 895408 (104592) L1ME4c_3end#LINE/L1 12 639 (191) m_b25s551i9 887 chr1ptel1M 894783 AATATATAGAGAATTGACTCTAATTTATAAGAAA----TCAAGCCATTCT 894828 ? i ii v i v v ---- v ----i L1ME4c_3end#L 12 ANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAAGAC----C 57 chr1ptel1M 894829 CCAATTGATAAATGGTCAAAGGATATGACCAGACAATGTTCAGATGATGA 894878 v v i v viv ? v v L1ME4c_3end#L 58 CCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAGGA 107 chr1ptel1M 894879 AATTGAAACAATTTCCACTCATATG--AAAGTGTTCCAAATCACTATTGA 894926 vv ?i i vvv vv i -- i v vv i v i L1ME4c_3end#L 108 AATACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTAGTAA 157 chr1ptel1M 894927 TCAGAGAAATGCAAATTAACACAACTCTGAGATACCACTACACACCTGTC 894976 i vi vv i vi i i i L1ME4c_3end#L 158 TCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCTATT 207 chr1ptel1M 894977 AGATTGGCTAAGATGACAGGAAAAAATAATGATGAT------TGTTGGAG 895020 i i v i ----vv -- i ------ i v L1ME4c_3end#L 208 AAATTAGCAAAAAT----TTAAAAAAT--TGATAATACCCAATGCTGGCG 251 chr1ptel1M 895021 GGGATGTGGGAAAACTGGGACACTGATGTATTGTGGGTGGAGTTGTGAAC 895070 i ? i vi v ? v ii iv vi? i i L1ME4c_3end#L 252 AGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAAT 301 chr1ptel1M 895071 GAATCCAAGCATTCTGGACAGCAATCTGGAATTATGCCCCAAAAGTTATC 895120 vii v v v i v i v v i ivi i ii v L1ME4c_3end#L 302 TGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATA 351 chr1ptel1M 895121 AAATTGTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGCTTATACCC 895170 v v i i i vii v vv v i L1ME4c_3end#L 352 AAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCC 401 chr1ptel1M 895171 CAAAGAGATACT---AAAGAAGGGAAAGGGACCTGTATGTGCCAAAATGT 895217 i i i v --- i i --- i ii v i L1ME4c_3end#L 402 TAAGGAAATAATTCAAAAGAAGGAAAAAG---CTATATGCACGAAGATGT 448 chr1ptel1M 895218 TTGTGGGGGCCCTGTTTGTAGTGGCTAGCAACTGGAA--AATGGATGATG 895265 ii v vi vi i i i i v iv i -- ivv -i L1ME4c_3end#L 449 TCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTA-AATG 497 chr1ptel1M 895266 CCCATCAATTGGAGAATGATTGGGCAAATTGTGGTATATGAATGTTATGG 895315 i v v i i ii i i i v? iviv L1ME4c_3end#L 498 TCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGG 547 chr1ptel1M 895316 AATATCAT-TGTTTGGTAAGGAATGACCAGCAGAATGAATACAGAGAGGC 895364 i -iiviiiv -i iv vi vi v v iiv vii L1ME4c_3end#L 548 AATATTATGCAGCCATTAA-AAATGATAATTATGAAGACTATGTAGCAAC 596 chr1ptel1M 895365 TTGGAGAGACTTACATGAACTGATGCTAAGTGAAATGAGCAGAA 895408 v - i iv vi vv i i vi L1ME4c_3end#L 597 ATGGA-AAATGTTTATGATATAATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 37.85 CpG sites = 101, Kimura (unadjusted) = 39.23 Transitions / transversions = 1.26 (101/80) Gap_init rate = 0.04 (22 / 625), avg. gap size = 1.55 (34 / 22) 13 4.70 0.00 4.35 chr1ptel1M 895724 895747 (104253) (GGGA)n#Simple_repeat 1 23 (0) m_b25s252i2 888 chr1ptel1M 895724 GGGAGGGGATGGAGGGAGGGAGGG 895747 - v (GGGA)n#Simpl 1 GGGA-GGGAGGGAGGGAGGGAGGG 23 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 451 26.12 2.48 2.48 chr1ptel1M 895839 895999 (104001) L1M5_orf2#LINE/L1 1180 1340 (1954) m_b25s551i10 889 chr1ptel1M 895839 AAAAATGCAAAGGGAGAACTCGTCACTAGCAAA----GAGGAAATTAGAG 895884 ii v i --- i - i ----ivi v i i L1M5_orf2#LIN 1180 AGGAATGAAAAAGGAGA---CATCACTA-CAGATCCTACAGACATTAAAA 1225 chr1ptel1M 895885 TAATAATTAGGAGTTACTTTGCCCAACTTTATGCCAATAAATTCGACAAC 895934 vi v iiiv i v vv i ? L1M5_orf2#LIN 1226 GGATAATAAGAGAATATTATGAACAACTTTATGCCAATAAATTTGANAAC 1275 chr1ptel1M 895935 TTAAATGAAATGGAAGAATACCTTAAAAAATATAGCTTGCCCAGATTAAC 895984 i vi v i i i i? i v i i i L1M5_orf2#LIN 1276 TTAGATGAAATGGACAAATTCCTTGAAAAACACAANTTACCAAAACTGAC 1325 chr1ptel1M 895985 AGAGGAAGAAGTAAA 895999 ?v i i i L1M5_orf2#LIN 1326 NCAAGAAGAAATAGA 1340 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 34.34 CpG sites = 28, Kimura (unadjusted) = 34.34 Transitions / transversions = 2.15 (28/13) Gap_init rate = 0.03 (5 / 160), avg. gap size = 1.60 (8 / 5) 364 33.19 1.72 1.72 chr1ptel1M 896297 896529 (103471) C Cheshire#DNA/hAT-Charlie (286) 2134 1902 m_b25s502i0 890 chr1ptel1M 896297 TGCAAGTGTGCATCCATTAGTCTTGATCTGGTTGGAGATTTCAAATGTTT 896346 i v ii i vi vvvv i vi i C Cheshire#DNA/ 2134 TGCAAATGTTCATCTGTTAATGCTGATCTGTAATGAGATTTTACGTATTT 2085 chr1ptel1M 896347 CATTCTAGAAAAAGTCTATTCACAGACATAAGTGCTGCCAAAGATGGTTG 896396 ii v v v v v i i v iv v i C Cheshire#DNA/ 2084 CATCTTTGAAAATGTCTTTTCACACAGATAGGTACTGCCAAATACTGATA 2035 chr1ptel1M 896397 CCATTT--TGAATGCATGGTTCCTAAGATGAGGATATGTCTCAGAGGGGA 896444 i v i--i iiii i -i v- v viv ivvv i C Cheshire#DNA/ 2034 TCAATCCACGAGCATATGATT-TTAAT-TGAGCATATTCATCGCTTGGAA 1987 chr1ptel1M 896445 GAGATGCATAGAAAT-TATGAAGGCTTCTTGACTTGA-ATATGTCTTTCA 896492 iv vi v - v -- v vv - v i i C Cheshire#DNA/ 1986 GGCATTTATAGAATTCTATTA--GATTCTTCTCTTGATATTTGCCTTTTA 1939 chr1ptel1M 896493 GAGAGTCACAATTCTGCAGTTCAGCCAGTACCATTTG 896529 viv iv ivi v i ii v v v C Cheshire#DNA/ 1938 GCATGTCATTACATTGCAGATTAATCACTTCCAATTG 1902 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 42.14 CpG sites = 37, Kimura (unadjusted) = 44.42 Transitions / transversions = 0.95 (37/39) Gap_init rate = 0.03 (7 / 232), avg. gap size = 1.14 (8 / 7) 374 38.75 2.00 3.17 chr1ptel1M 896930 897630 (102370) C Cheshire#DNA/hAT-Charlie (921) 1499 807 m_b25s502i1 890 chr1ptel1M 896930 CAGAAAAGTTGTAATCTGTGGAAGTAAG-TCATAGAAACATTTCAAAACT 896978 i vi -i vvv i - v i v iivvi C Cheshire#DNA/ 1499 CAGAAAAATTTCAATCT-CGGCCCTGAGCTCAAAAAATCGCAATAAAACT 1451 chr1ptel1M 896979 CTCCCTCAACTCAGCCAATGGACTTCTGTGTAATATAGAACATCTTCAAA 897028 i v v vi v vi i v ii vi v vi vvv v C Cheshire#DNA/ 1450 TTACCACTGCTAAGCCATCGAACTGCTGTGTGGTAGGGCAAGTCAGGATA 1401 chr1ptel1M 897029 CTCAACATTTAGCTCAGACAGAAATCCCTGAAATTGTCTGTGATTTAGTG 897078 i i v i vi v i i vi i i v vi i v v C Cheshire#DNA/ 1400 TTCAGCTTCTATTTCTGACAAAAATTCACGGAACTGACGATGGTTAAGTC 1351 chr1ptel1M 897079 CATCAGCTCTAATGAAGTCAACACAAGATACCACAATTTTCATAACAGAG 897128 iv vv v iv vvvv i i viv iv v v C Cheshire#DNA/ 1350 CACGAGAGCGAATGAAGTTCACCGTTGACACTACTGGTTCAATAACACAT 1301 chr1ptel1M 897129 TCCCACTTCAGTGATTTACTATACAGCGCTTGTTGGTGGATGAGGCAGTG 897178 vviviv ivv v iii v ii i i i i i vi i C Cheshire#DNA/ 1300 GATAGATTCAAATATTTTCCGCAAAGTACCTGCTGATGAATAATACAATG 1251 chr1ptel1M 897179 TATGGCTATTGGATGAGAATG-GTTATGTTTGTCCATCTCTTGGCTAATG 897227 v ii i v v vvi ii-v ii viv -vv v iv v C Cheshire#DNA/ 1250 AATAACCATAGGCTTTAAACACCTTACATTTTCACA-AGCTTTGTAAATT 1202 chr1ptel1M 897228 CGAGCAATTACTCTTTTCTTAGACCCCTAC-CATGCTAGGAGCACCATCA 897276 i vv i vv i i iv -- i i - ii vvv v C Cheshire#DNA/ 1201 TGTCCAACTAAGCCTTTTTCTG--CTCCACACATATTTTTACCACCATCA 1154 chr1ptel1M 897277 GTGATCACGCTGGCTAGTTTAGCTCAGTCCAACAACAA-----ACC--AT 897319 vi v i ----- vi vv v - vv i----- i-- C Cheshire#DNA/ 1153 GTTGTAACAC-----ATCTTAGCAGATTCC-ACTTCAGGTTGTACTGAAT 1110 chr1ptel1M 897320 TCATAGTTTGGCAAACCTTTTCATAGATATCCTCTCCTGTAGTTGTTCCT 897369 vi iv vv - i i iiv i i v v C Cheshire#DNA/ 1109 TAGTGTTTTCTCA-ACTTCTTTGAAAATATTCTCGCCTGTAGTTGTTCCA 1061 chr1ptel1M 897370 TTGATGCTTTGCAGTGCATCAAGCGCTTCTATGACTTCAAAATAATCATT 897419 ivv vi v v vv viv v iiv vi v v viv C Cheshire#DNA/ 1060 CGCAGACTATTCATAGAGGCTAATTCTTCAGTCACTTCAAACTCGGCATT 1011 chr1ptel1M 897420 CATCCCACGAATAAAAATTAGAAGTTGTGCAGAATCAAGAACATC-ATTG 897468 v ii v ------v ii v v iiv -i i C Cheshire#DNA/ 1010 GACTCCTCGAATAAA------CAACTGAGCAGTATCGGTAACATCTGTCG 967 chr1ptel1M 897469 CTTTCGTCGATTGCCAAGGAAAAATA--TGAAATTTTTTTTTATGGAGTT 897516 v-i i i vv vi --i iv viiv --- C Cheshire#DNA/ 966 A-CTCATCAAGAGCCAAGGAAAACCACTCGAAATCATTTGCCTT---GTT 921 chr1ptel1M 897517 TTGCAAATGCTGATGCAGACTGTCTCCCATTTCTTCAA-TCTTCCATGTA 897565 vi v viv vv vii iii v v i - v - i C Cheshire#DNA/ 920 TTTTAATTGACTATTGATGTTGCTCCCAATGTCCTCAACTCTTCGA-GCA 872 chr1ptel1M 897566 ATTGTAGGTACTAAAAGACTCATTGTACGAAATAAATCAGCTTTCTCTGA 897615 i vvvii ii i v v viv i i ivii i C Cheshire#DNA/ 871 ACTGTTCTCGCCGAAAGGCTAATAGTCTTAAACAAGTTTATTTTCTCTGG 822 chr1ptel1M 897616 ACACATCTCTTTGGC 897630 i i C Cheshire#DNA/ 821 ACACATTTCTTCGGC 807 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 51.23 CpG sites = 127, Kimura (unadjusted) = 55.50 Transitions / transversions = 0.93 (127/136) Gap_init rate = 0.04 (30 / 700), avg. gap size = 1.20 (36 / 30) 265 27.69 0.00 0.00 chr1ptel1M 897993 898057 (101943) C Cheshire#DNA/hAT-Charlie (2355) 65 1 m_b25s502i2 891 chr1ptel1M 897993 GCGGGCCACATAAATGTCCTCAGCAGGCCGCATCTGGTCCGTGGGCCATA 898042 ii i viivvv i i v i i i i C Cheshire#DNA/ 65 GCGGGCCGTACAAAAACAGGCGGCGGGCCGGATTTGGCCCGCGGGCCGTA 16 chr1ptel1M 898043 GTTTGAGGACCCCTG 898057 vv C Cheshire#DNA/ 15 GTTTGCCGACCCCTG 1 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 24.45 CpG sites = 11, Kimura (unadjusted) = 35.61 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0) 3356 29.97 2.65 2.33 chr1ptel1M 898060 899945 (100055) L1M5_orf2#LINE/L1 1345 3236 (58) m_b25s551i11 889 chr1ptel1M 898060 CTAAATAGTCCCAT-TTTAGAAAAAGAAATAGAACAAGCTATTAACCAAC 898108 i i i - i vv - v ivv iv vv v L1M5_orf2#LIN 1345 CTGAATAGCCCTATATCTATTAAA-GAAATTGAATTTGTAATTAAAAACC 1393 chr1ptel1M 898109 TCCCTAAGAAAAAAATCACCAGGACTAGATGGATTTACATGTGAATTCTA 898158 i i vi i - v v i v i vv L1M5_orf2#LIN 1394 TTCCCACAAAGAAAA-CTCCAGGCCCAGATGGCTTCACTGGTGAATTCTA 1442 chr1ptel1M 898159 CCAAACATTTAAAGAACAATTAATTCCAATGCTATATAAAGTATTTGAAA 898208 i v v v vi i i v v iv i L1M5_orf2#LIN 1443 CCAAACATTTAAGGAAGAAATAATACCAATCTTACACAAACTCTTCCAGA 1492 chr1ptel1M 898209 AAATAGGGATTGAAGGAGTCCTACCAAATTTCTTCTATGACACAGACATG 898258 ii vv i iiv v v i iv i vi vii ? L1M5_orf2#LIN 1493 AAATAGAAAAAGAGGGAACACTTCCCAACTCATTTTATGAGGCCAGCATN 1542 chr1ptel1M 898259 GTACTGATACCTAAACCAGGTAGATTGAAA--ACAGATTAAGAAAATTAT 898306 iiv v ? ii i -- v -- iivv i L1M5_orf2#LIN 1543 ACCCTGATACCAAAACCNGACAAA--GACATTACAAGAAAAGAAAATTAC 1590 chr1ptel1M 898307 AGACCAATCTCCCTAATGAATATTGATGCTAAAATCTT----AAAGTATT 898352 v v i v v i ---- i L1M5_orf2#LIN 1591 AGACCAATATCCCTCATGAACATAGATGCAAAAATCCTNAACAAAATATT 1640 chr1ptel1M 898353 AGCAAAAAGACTACAGAAAATTATCCCCAAGATAATACACTATAACCAAG 898402 vv v v v vv vvvv i ii i L1M5_orf2#LIN 1641 AGCAAATCGAATCCAGCAATATATAAAAAGGATAATACATCATGACCAAG 1690 chr1ptel1M 898403 TAGGATTTATACCAGGAATTGCAGGGCTGGTTCAATATTAGGAAAACTAT 898452 i i v - i i i i v i v v L1M5_orf2#LIN 1691 TGGGGTTTATCCCAGGAAT-GCAAGGTTGGTTTAACATTCGAAAATCAAT 1739 chr1ptel1M 898453 GAGCATAATTGATTATGTCAATAACCAAATTAAC---AAAAACCATATGA 898499 v iii v ii i --- vi v v--- i L1M5_orf2#LIN 1740 CAATGTAATTCACCATAT---TAACAGAATAAAGGAGAAAAATCATATGA 1786 chr1ptel1M 898500 TCATCTCAATAGGTGCAGAAAACGCATTTGATAAAATCCAACATCCATTC 898549 i v i i i L1M5_orf2#LIN 1787 TCATCTCAATAGATGCAGAAAAAGCATTTGACAAAATTCAACACCCATTC 1836 chr1ptel1M 898550 CTAATAAAAACACTTGAGAGGATAGGAATAAATGGACTTTTCCTTAAAAT 898599 v i v iiiv iiv i v ivvi i vv L1M5_orf2#LIN 1837 ATGATAAAAACTCTCAGCAAACTAGGAATAGAAGGGAACTTCCTCAACCT 1886 chr1ptel1M 898600 AGTCAGGAGCATATATTTAAAATTGTCAGTAAGCATCATATGCAATGGGG 898649 ii v i i v ivv iivv i? i ivi v L1M5_orf2#LIN 1887 GATAAAGGGCATCTACGAAAAACCTACAGCNAACATCATACTTAATGGTG 1936 chr1ptel1M 898650 AAAAATTGGAACCTTTCCCAGTAAGGTCTGGCGTGAAGCAAGGTTGCCCA 898699 ? i i ?v vv i v viii ii v i i L1M5_orf2#LIN 1937 AAANACTGAANGCTTTCCCCCTAAGATCGGGAACAAGACAAGGATGTCCG 1986 chr1ptel1M 898700 CTATCACCATTATTATTCAATATTGTATTAGAAACGCTAGCCTCGGCTAT 898749 ? i vi i i i iiiv vvv v L1M5_orf2#LIN 1987 CTNTCACCACTTCTATTCAACATTGTACTGGAGGTCCTAGCCAGTGCAAT 2036 chr1ptel1M 898750 AAGAGTCGAGAAAGAGATTAAAGGAATTAGAGTAGGCAATGAGGAAACCA 898799 ivvv i i v v v iii v v v i iv L1M5_orf2#LIN 2037 AAGGCAAGAAAAAGAAATAAAAGGCATAAAGATTGGAAAGGAAGAAATAA 2086 chr1ptel1M 898800 AACTATCACTCTTTGCAGATGATATGATGGTATACTTAAGAGAACCCCAG 898849 i ?i v i i v ? v - i i ? i L1M5_orf2#LIN 2087 AACTGTCNTTATTCGCAGATGACATGATTGTNTACGT-AGAAAATCCNAA 2135 chr1ptel1M 898850 AGATCCTATTAAAAAGCTATTAGAAATAATTCATAACTTTAGTAAAGTTG 898899 vi iv ? i i v vvi i v i i i L1M5_orf2#LIN 2136 AGAATCTACAAANAAACTACTAGAACTAATAAGTGAATTTAGCAAGGTCG 2185 chr1ptel1M 898900 CAGGATACAAAATAAATCCCCATAAATCCTCAGCATTTTTATACTTCACC 898949 ? ii v viv v vviv i i ivii v L1M5_orf2#LIN 2186 CNGGATACAAGGTCAATATACAAAAATCAATTGTATTTCTATATACTAGC 2235 chr1ptel1M 898950 AACAAAATCCAACAGCAA---GAGATACAAAGAGAAATTCCATTCAAAAT 898996 --- iv v --- i vi? i iv v i v L1M5_orf2#LIN 2236 AACAAA---CAATTGGAAAATGAAATTTNAAAAACAATACCATTTACAAT 2282 chr1ptel1M 898997 AACTGTTGATAGCATAAAATATTTGGAAATCTAGCTACCAAAGGA-GT-C 899044 i vvivi v i ? i i i vv v v i? - - L1M5_orf2#LIN 2283 AGCATCAAAAAACATNAAATACTTAGGAATAAATCTAACAAAANATGTGC 2332 chr1ptel1M 899045 AGGAATTATATGAGCAAAATTACAAAAAACTTTCCACACAAATACAGTCA 899094 i vi ? iivvv i v i viiv v v vv ivv L1M5_orf2#LIN 2333 AAGACCTNTACACTGAAAACTACAAAACATTGCTGAGAGAAATTAAAGAA 2382 chr1ptel1M 899095 GATTTAAATAATTGGAAAAATATTAAGTGCTCTTGGATAGGCCAAGCGAA 899144 ii v i i vvvi i v v vvi viv L1M5_orf2#LIN 2383 GACCTAAATAAATGGAGAGATATACCATGTTCATGGATTGGAAGACTCAA 2432 chr1ptel1M 899145 TATAATAAAGATGACAATACTCCTTAAATTAATCTATTTATTTAGTGCTA 899194 vi ? v v ii i vv i i v L1M5_orf2#LIN 2433 TATTGTNAAGATGTCAATTCTCCCCAAATTGATCTATAGATTCAATGCAA 2482 chr1ptel1M 899195 TACCAATCAGACTTCCAAGAAAATATTCTAATGATCTAGAAAAAAGAACA 899244 v i v i iv iiv v i ivv vv v v ivvi iv L1M5_orf2#LIN 2483 TCCCAATCAAAATCCCAGCAGGTTTTTTTGTAGAAATTGACAAGCTGATT 2532 chr1ptel1M 899245 ACAAAATTCATATGGAAGAACAAAAGGTTGAGAATC-TCAAGGGAATTAA 899293 vi i ivi i iii? v-i iiv i-v L1M5_orf2#LIN 2533 CTAAAATTTATATGGAAATGCAAAGGACCNAGAATAGCCAAAACAATC-T 2581 chr1ptel1M 899294 TGAAAAA-AAAATCAAA--TGAAGGTGGCCTAGCTGTATCTGATCT-AAA 899339 - i v -- i -- i i - vv i ? ? - i L1M5_orf2#LIN 2582 TGAAAAAGAAGAACAAAGTTGGAG--GACTTA-CACTACCNGATNTCAAG 2628 chr1ptel1M 899340 ACTATATTATAAAGCGGTAGTCACCAAAACCATTTGGTATTGGC-TAAGA 899388 - vii v i i vi v - - L1M5_orf2#LIN 2629 ACT-TATTATAAAGCTACAGTAATCAAGACAGTGTGGTATTGGCGTAAG- 2676 chr1ptel1M 899389 AAGAGATTAGTTGATCAGTGGAATAGATTAG---GTTCACAAGACAAAAG 899435 i v iv i v i i v --- i --- - v L1M5_orf2#LIN 2677 GATAGACAAATAGATCAATGGAACAGAATAGAGAGTCC---AGA-AATAG 2722 chr1ptel1M 899436 AGTCA-AC---TATAGCAATCTAGTGTTTGACAAA---CCCAAAGATCTT 899478 vi - --- i ?v ?i ii v ---v ? ----i L1M5_orf2#LIN 2723 ACCCACACATATATGGNCANTTGATTTTTGACAAAGGTGCCAANG----C 2768 chr1ptel1M 899479 AATTT-TTGGGATGAGAAT--TCATTAATTCACAAAAACTGCTGGGATAA 899525 i-v ivi i -- v -- iv viv i i L1M5_orf2#LIN 2769 AATTCAGTGGGGAAAGGATAGTCTTT--TCAACAAATGGTGCTGGAACAA 2816 chr1ptel1M 899526 CTGGAAAGTAGTATGGTAGAAATTAGGCATGGACCCACACTTAACACCAT 899575 i v vivi v i v iii?v v vi i v L1M5_orf2#LIN 2817 TTGGATATCCATATGGAAAAAAATGAANCTCGACCCCTACCTCACACCAT 2866 chr1ptel1M 899576 ATACTAAGGTAAGATCAAAATGGGTCCAT-GATTTATGCATAAATAACGA 899624 i v ii v iv ? i i - - ii viii vi?ii L1M5_orf2#LIN 2867 ACACAAAAATTAATTCNAGATGGAT-CATAGACCTAAATGTAAAAGNTAA 2915 chr1ptel1M 899625 GATTATAAATAAAT--TAGAGG--AACATGGGATAGTTTATCTCTCAGAC 899670 i i -- v -- i -- i v i-- iivv L1M5_orf2#LIN 2916 AACTATAA--AACTTCTAGAAGAAAACATAGGAGAA--TATCTTCGTGAC 2961 chr1ptel1M 899671 TTGTGGAGGAGGAAGAAATTTCTGACCAAAGATGAACTAGAGACCATTAT 899720 i - i?v v i i ---i v v vvi i i v i? - L1M5_orf2#LIN 2962 CT-TGGGNTAGGCAAAGATTTCT---TAAACAGGACACAAAAAGCACNA- 3006 chr1ptel1M 899721 TGATCACAAAATAGAAAAT-------TTTGATTACATCAAATTAAAAAGC 899763 -- i i v i ------- v i ? v v i L1M5_orf2#LIN 3007 --ACCATAAAAGAAAAAATTGATAAATTGGACTNCATCAAAATTAAAAAC 3054 chr1ptel1M 899764 CTTTGTACAAACAAAACTAATGCCAACAAGATTAGAAGGGAAGCAACAAA 899813 i i iv ?vvv ivi vi ii v i v i v v i L1M5_orf2#LIN 3055 TTCTGCTCNTCAAAAGACACCGTTAAGAAAATGAAAAGGCAAGCCACAGA 3104 chr1ptel1M 899814 CTGGGAGAACATCTTCACAATTAAAGGT-TCTGATAAAGACCTCATTTCC 899862 ? v v ii -? v vi - i iv i v L1M5_orf2#LIN 3105 NTGGGAGAAAATATTTGCAA-NACATATATCTGACAAAGGACTCGTATCC 3153 chr1ptel1M 899863 AAAATTTATAGAGAATTGACTCTAATTT-ATAAGAAATCAAGCCATTC-- 899909 i v i i -v vi ? i- ? -- v vv -- L1M5_orf2#LIN 3154 AGAATATATAAAGAACT-CCTACAANTCAATAANAAA--AAGACAAACAA 3200 chr1ptel1M 899910 TCCAATTGATAAATGGTCAAAGGATATGACCAGGCA 899945 i v? v v i iv v i L1M5_orf2#LIN 3201 CCCAATANAAAAATGGGCAAAAGACTTGAACAGACA 3236 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.31 CpG sites = 295, Kimura (unadjusted) = 39.96 Transitions / transversions = 1.15 (295/257) Gap_init rate = 0.04 (69 / 1885), avg. gap size = 1.36 (94 / 69) 332 33.08 2.55 1.81 chr1ptel1M 899728 900001 (99999) L1M1_orf2#LINE/L1 3019 3294 (0) m_b25s551i12 889 chr1ptel1M 899728 AAAATAGAAAATTTTGATTACATCAAATTAAAAAGCCTTTGTA---CAAA 899774 i v v vv i i i i i --- L1M1_orf2#LIN 3019 AAAATGGACAAATGGGATCACATCAAGTTAAAAAGCTTCTGCACAGCAAA 3068 chr1ptel1M 899775 CAAAACTAATGCCAACAAGATTAGAAGGGAAGCAACAAACTGGGAGAACA 899824 vi - -- ii v ii iv v v i v v L1M1_orf2#LIN 3069 GGAAAC-AAT--CAACAAAGTGAAGAGACAACCCACAGAATGGGAGAAAA 3115 chr1ptel1M 899825 TCTTCACAATTAAAGGTTCTGATAAAGACCTCATTTCCAAAATTTATAGA 899874 v ii viv vvvv i i ivi v vv i v ii L1M1_orf2#LIN 3116 TATTTGCAAACTACCCATCTGACAAGGGATTAATAACCAGAATATATAAG 3165 chr1ptel1M 899875 GAATTGACTCTAATTTATAAGAAATCAAGCC--ATTCTCCAATTGATAAA 899922 ii v vv v v i i -- ii -- vv i i v L1M1_orf2#LIN 3166 GAGCTCAAACAACTCTATAGGAAA--AAATCTAATAATCCGATTAAAAAA 3213 chr1ptel1M 899923 TGGTCAAAGGATATGACCAGGCAATGTTCAGATGATGAAATTGAAACAAT 899972 v i v vi i v vi i v v v vv iiii L1M1_orf2#LIN 3214 TGGGCAAAAGATCTGAATAGACATTTCTCAAAAGAAGACATACAAATGGC 3263 chr1ptel1M 899973 TTCCACTCATATGAAA--GTGTTCCAAATCA 900001 vvv vv -- i v v L1M1_orf2#LIN 3264 AAACAGGCATATGAAAAGGTGCTCAACATCA 3294 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 43.40 CpG sites = 41, Kimura (unadjusted) = 44.05 Transitions / transversions = 0.85 (41/48) Gap_init rate = 0.03 (8 / 273), avg. gap size = 1.50 (12 / 8) 1496 29.32 2.74 2.24 chr1ptel1M 899869 900489 (99511) L1ME4c_3end#LINE/L1 16 639 (191) m_b25s551i13 889 chr1ptel1M 899869 TATAGAGAATTGACTCTAATTTATAAGAAA----TCAAGCCATTCTCCAA 899914 i ii v i v v ---- v ----i L1ME4c_3end#L 16 TATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAAGAC----CCCAA 61 chr1ptel1M 899915 TTGATAAATGGTCAAAGGATATGACCAGGCAATGTTCAGATGATGAAATT 899964 v v i v i viv ? v v v L1ME4c_3end#L 62 TAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAGGAAATA 111 chr1ptel1M 899965 GAAACAATTTCCACTCATATG--AAAGTGTTCCAAATCACCATTGATCAG 900012 v ?i i vvv vv i -- i v vv i i v i i L1ME4c_3end#L 112 CAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTAGTAATCAA 161 chr1ptel1M 900013 AGAAATGCAAATTAACACAACTCTGAGATACCACTACACACCTGTCAGAT 900062 vi vv i vi i i i i L1ME4c_3end#L 162 AGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCTATTAAAT 211 chr1ptel1M 900063 TGGCTAAGATGACAGGAAAAAATAATGATG---AATGTTGGAGAGGATGT 900109 i v i v---vi v i i i--- i v ? i L1ME4c_3end#L 212 TAGCAAAAATT---TAAAAAATTGATAATACCCAATGCTGGCGAGGNTGC 258 chr1ptel1M 900110 GGGAAAACTGGGACACTGATGTATTGTTGATGGAGTTGTGAACGAATCCA 900159 vi v ? v ii i i vi? i ivii v L1ME4c_3end#L 259 GGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACA 308 chr1ptel1M 900160 ACCATTCTGGAGAGCAATTTGGAACTATGCTCAAAAAGCTATCAAACTGT 900209 v i i v v i iviv i i v v L1ME4c_3end#L 309 ACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAAAATGT 358 chr1ptel1M 900210 GCATACCCTTTGATCCAGCAGTGTTACTACTGGGCTTATACCCCAAAGAG 900259 v i i i vii v vv v i i i i L1ME4c_3end#L 359 TCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAA 408 chr1ptel1M 900260 ATACT---AAAGAAGGGAAAGGGACCTGTATGTGCCAAAATGTTTGTGGG 900306 v --- i i --- i ii v i ii v v L1ME4c_3end#L 409 ATAATTCAAAAGAAGGAAAAAG---CTATATGCACGAAGATGTTCATTGC 455 chr1ptel1M 900307 GGCCTTGTTTGTAGTGGCTAGAAACTGGAAAATGAA--TGGATGCCCATC 900354 i v i i i i v i i --v -- ii i v L1ME4c_3end#L 456 AGCGTTATTTATAATAGCGAAAAATTGGAAA--CAACCTAAATGTCCAAC 503 chr1ptel1M 900355 AATTGGAGAATGGTTGGGCAAATTGTAGTATATGAATGTTATGCAATATT 900404 v i ii i i i i v? iviv v L1ME4c_3end#L 504 AATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATATT 553 chr1ptel1M 900405 AT-TATTTGGTAAGGAATGACCAGCAGGACGA--ATACAGAGGCTTGGAG 900451 -i viiiv -i iv vi v v -- ii vii v - L1ME4c_3end#L 554 ATGCAGCCATTAA-AAATGATAATTATGAAGACTATGTAGCAACATGGA- 601 chr1ptel1M 900452 AGACTTACATGAACTGATGCTAAGTAAAATGAGCAGAA 900489 i iv vi vv i i i vi L1ME4c_3end#L 602 AAATGTTTATGATATAATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 37.26 CpG sites = 102, Kimura (unadjusted) = 38.65 Transitions / transversions = 1.34 (102/76) Gap_init rate = 0.03 (21 / 620), avg. gap size = 1.48 (31 / 21) 247 31.16 8.25 6.13 chr1ptel1M 901135 901534 (98466) C L1PA10_5end#LINE/L1 (364) 2080 1673 m_b25s551i14 892 chr1ptel1M 901135 ATAATGCTTAGTTTTGCCGAACATTTGATTCTTGGCTGCAGTCCAACCTC 901184 i v v i i i vvi v i ------ vv i C L1PA10_5end#L 2080 ATGAAGCTTAGTTTGGCTGGATATGAAATTCTGGGTTG------AAAATT 2037 chr1ptel1M 901185 CTTTTCCCTCAGAATATC--ATATT-----CCATGCACTTTGAGCCTTTA 901227 ii v i i-- ----- iv v ivi i v C L1PA10_5end#L 2036 CTTTTCTTTAAGAATGTTGAATATTGGCCCCCACTCTCTTCTGGCTTGTA 1987 chr1ptel1M 901228 AAGTGGAAGCTGCTAAATCTG--GGAAATCCTGATTGTGGCT--CCTCGA 901273 ii vvvv ? vv ii i -- vv i - - - -- ivi C L1PA10_5end#L 1986 GGGTTTCTGCNGAGAGGTCCGCTGTTAGTC-TGAT-G-GGCTTCCCTTTG 1940 chr1ptel1M 901274 TATTTGAATTG---TTTCTTTTTGGCTGCTTGCAATATTTTCTTCTTGAT 901320 vv vi --- i i iivi i i i v C L1PA10_5end#L 1939 TAGGTGACCTGGCCTTTCTCTCTGGCTGCCCTTAACATTTTTTCCTTCAT 1890 chr1ptel1M 901321 TTAATGATTCTGAA--ATTTAGGTATGCTATTCCTTGGAGTTCATTTT-- 901366 --i iii i -- i iivv vv i vi i v? i -- C L1PA10_5end#L 1889 TT--CGACCTTGGAGAATCTGACGATTATGTGTCTTGGGGTTGNTCTTCT 1842 chr1ptel1M 901367 ---GGAGTATCTTTCAGGAA------GTAATTCATGAATTATTTCAATGA 901407 --- vvv vi------ v v --- v - C L1PA10_5end#L 1841 CGNGGAGTATCTTAGTGGTGTTCTCTGTATTTCCTGAATT---TGAATG- 1796 chr1ptel1M 901408 TTAACTCAACTCTCTGGTTCTAGAATGTCAGGGCAGTTTTCCTTGATGAT 901457 ii ---- v v -- --- ii v i v i C L1PA10_5end#L 1795 TTGGC----CTGTCTTG--CTAG---GTTGGGGAAGTTCTCCTGGATAAT 1755 chr1ptel1M 901458 TTCTTGAAAGATGTTGTTGA----GGCTCTTTTTTCCATTGTGGTTTTCA 901503 v i ivi v iv ---- i iv i -ii v?i C L1PA10_5end#L 1754 ATCCTGAAGTGTGTTTTCCAACTTGGTTCCATTCTCC-CCGTCNCTTTCA 1706 chr1ptel1M 901504 GGTAGTCCAATAATTCCTAGATT--GTCTCTCC 901534 v? v v v i -- i i C L1PA10_5end#L 1705 GGTACNCCAATCAATCGTAGGTTCGGTCTTTTC 1673 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 40.47 CpG sites = 64, Kimura (unadjusted) = 41.87 Transitions / transversions = 1.21 (64/53) Gap_init rate = 0.09 (36 / 399), avg. gap size = 1.61 (58 / 36) 251 30.38 5.14 2.22 chr1ptel1M 901144 901318 (98682) C L1M4c_5end#LINE/L1 (865) 1635 1456 m_b25s551i15 892 chr1ptel1M 901144 AGTTTTGCCGAACATTTGATTCTTGGCTG-CAGTCCAACCTCCTTTT--C 901190 i i vv? i - ii--ii i i-- C L1M4c_5end#LI 1635 AGTTTTGCCGGATATAGNATTCTTGGTTGACAGTTT--TTTTCTTTCAGC 1588 chr1ptel1M 901191 CCTCAGAATATCATATTCCA-TGCACTTTGAGCCTTTAAAGTGGAAGCTG 901239 v iv vvi ?i - - ivi ?i i vvvv ? C L1M4c_5end#LI 1587 ACTTTGAATATATCANCCCACTGC-CTTCTGGCCTNCAAGGTTTCTGNTG 1539 chr1ptel1M 901240 CTAAATCTG--GGAAATCCTGATTGTGGCTCCTCGATATTT---GAATTG 901284 vv i -- iv i - v v iivi v --- i i C L1M4c_5end#LI 1538 AGAAATCCGCTGATAATCTT-ATTGAGGATCCCTTGTATGTGACGAGTCG 1490 chr1ptel1M 901285 TTTCTTTTTGGCTGCTTGCAATATTTTCTTCTTG 901318 i i i i v v v i ii C L1M4c_5end#LI 1489 CTTTTCTCTTGCTGCTTTCAAGATTCTCTCTTTG 1456 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.50 CpG sites = 31, Kimura (unadjusted) = 41.60 Transitions / transversions = 1.48 (31/21) Gap_init rate = 0.05 (9 / 174), avg. gap size = 1.44 (13 / 9) 15 20.36 0.00 0.00 chr1ptel1M 901579 901607 (98393) (T)n#Simple_repeat 1 29 (0) m_b25s252i3 893 chr1ptel1M 901579 TTTTCTTGTTTTTTTCCTTCTTTTTTTTT 901607 i v ii i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 1189 27.26 2.91 3.11 chr1ptel1M 902670 903184 (96816) C L1ME4a_3end#LINE/L1 (321) 550 37 m_b25s551i17 894 chr1ptel1M 902670 ATTCCATAACATTCAAATACCATCATTTATTCAGCCATTCTTCAACTGAT 902719 v?i vv vi v i i ? ii v i v C L1ME4a_3end#L 550 ATTCCATTNTATGGATGTACCATAATTTATTTAACCANTCCCCTATTGTT 501 chr1ptel1M 902720 GGGTATTCACTCAACTTTCAGTTTCTAGCCACTACAAAGAGGGCTGCCAC 902769 ii i vvivii i i i v i i i v iv v i C L1ME4a_3end#L 500 GGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAATGCTGCGAT 451 chr1ptel1M 902770 AAACATTTGTGCACATA----TGGGTCCATTTCCCTCCTTTAAGATCTCT 902815 i iiv i ---- vv ? iv i vv ---- i i C L1ME4a_3end#L 450 GAACATCCTTGTACATAAATCTTTGTNCACATCTCTGATT----ATTTCC 405 chr1ptel1M 902816 TTGGGATATAATCCCAATAGAAAT---ACTGCTGGGTCAAAGGGTACACA 902862 i - i -- i --- i i ii? C L1ME4a_3end#L 404 TTAGGATA-AATTCC--TAGAAGTGGAATTACTGGGTCAAAGGGTATGNA 358 chr1ptel1M 902863 CAGTTTGATAACTTTTTCAGCATAATTCCAAATTGTTCTCCAGAATGGAT 902912 v v vii vvvi v v ii v v C L1ME4a_3end#L 357 CATTTTTAAGGCTTTTGATACATATTGCCAAATTGCCCTCCAGAAAGGTT 308 chr1ptel1M 902913 GGATCAGTTCACAACTCCACCAACAATGTATCAGTGTCCCAGTTTTCCCA 902962 v i i i vii i i v v v v i? C L1ME4a_3end#L 307 GTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTGCCCGTTTCNCCA 258 chr1ptel1M 902963 CATGCCT--CCAACATTCTTCATTATC--TTTTCCTATCATCTCAGCCAA 903008 i- -- i vvvi -- i iiv -- iv C L1ME4a_3end#L 257 CAC-CCTCGCCAACACTGGGTATTATCAATCTTTTAA--ATCTTTGCCAA 211 chr1ptel1M 903009 TCTGATAGGTGTGTAGTGGTATCTCAGAGTTGTTTTAATTTGCATTTCTC 903058 i viv i vv i C L1ME4a_3end#L 210 TTTGATAGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCTT 161 chr1ptel1M 903059 TGATCAATAGTGATTTGGAGCAACTTTTCATATGACTA--GGCCAATTGT 903106 i v vv v i v? vi -- v C L1ME4a_3end#L 160 TGATTACTAGTGAGGTTGAACATNTTTTCATATGTTTATTGGCCATTTGT 111 chr1ptel1M 903107 ACTTTCAAAGTTTTGTTGTTCATTTTTTTTTTTATTTCATCAGTTTATTA 903156 - ---- i v vv - v i v i v v iv iii v C L1ME4a_3end#L 110 A-TTTC----TTCTTTTGTGAA-TTGTCTGTTCATGTCCTTTGCCCATTT 67 chr1ptel1M 903157 TT-TAAGGGGTTGTTC-TCTTTTTTTCATT 903184 - vv v - i i C L1ME4a_3end#L 66 TTCTATTGGGGTGTTCGTCTTTTTCTTATT 37 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 34.92 CpG sites = 72, Kimura (unadjusted) = 34.92 Transitions / transversions = 1.12 (72/64) Gap_init rate = 0.04 (23 / 514), avg. gap size = 1.35 (31 / 23) 1272 25.52 2.71 2.71 chr1ptel1M 902670 903112 (96888) C L1ME3G_3end#LINE/L1 (381) 543 101 m_b25s551i16 894 chr1ptel1M 902670 ATTCCATAACATTCAAATACCATCATTTATTCAGCCATTCTTCAACTGAT 902719 ii vv v v i i ii v i C L1ME3G_3end#L 543 ATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTATTGAT 494 chr1ptel1M 902720 GGGTATTCACTCAACTTTCAGTTTCTAGCCACTACAAAGAGGGCTGCCAC 902769 ii i vvivii i i i v i i v iv v i C L1ME3G_3end#L 493 GGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCTGCAAT 444 chr1ptel1M 902770 AAACATTTGTGCACATATGGGTCCATTT-CCCTCCTTTAAG-ATCTCTTT 902817 i iiv i -- v? v v - v viv vii - i ? C L1ME3G_3end#L 443 GAACATCCTTGTACAT--GCNTCCTTGTGCACATGTGCGAGTATTTCTNT 396 chr1ptel1M 902818 GGGATATAATCCCAATAGAAAT---ACTGCTGGGTCAAAGGGTACACACA 902864 i -i ? ? -- i --- i ii i C L1ME3G_3end#L 395 AGGATA-GATNCCNA--GAAGTGGAATTGCTGGGTCAAAGGGTATGCGCA 349 chr1ptel1M 902865 GTTTGATAACTTTTTCAGCATAATTCCAAATTGTTCTCCAGAATGGATGG 902914 v i -- i vvi - v v ii i ? v v C L1ME3G_3end#L 348 TTTTAA--ATTTTAATAG-ATACTGCCAAATTGCCCTCCAAAANGGCTGT 302 chr1ptel1M 902915 ATCAGTTCACAACTCCACCAACAATGTATCAGTGTCCCAGTTTTCCCACA 902964 i i i vii i i v v v v i C L1ME3G_3end#L 301 ACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCACA 252 chr1ptel1M 902965 TGCCTC--CAACATTCTTCATTATC---TTTTCCTATCATCTCAGCCAAT 903009 i- -- i ?vvi ---i -- -v i iv C L1ME3G_3end#L 251 C-CCTCGCCAACACTNGATATTATCAANCTTT--TA-AATTTTTGCCAAT 206 chr1ptel1M 903010 CTGATAGGTGTGTAGTGGTATCTCAGAGTTGTTTTAATTTGCATTTCTCT 903059 i viv i vv i C L1ME3G_3end#L 205 CTGATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCT 156 chr1ptel1M 903060 GATCAATAGTGATTTGGAGCAACTTTTCATATGACTA--GGCCAATTGTA 903107 i v vv v v vi -- v C L1ME3G_3end#L 155 GATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGTA 106 chr1ptel1M 903108 CTTTC 903112 i i C L1ME3G_3end#L 105 TTTCC 101 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 31.63 CpG sites = 63, Kimura (unadjusted) = 32.38 Transitions / transversions = 1.34 (63/47) Gap_init rate = 0.04 (18 / 442), avg. gap size = 1.33 (24 / 18) 144 11.39 0.42 1.71 chr1ptel1M 905666 905902 (94098) (GAGCCG)n#Simple_repeat 1 234 (0) m_b25s252i4 895 chr1ptel1M 905666 GAGCTGGAGCCGGAGCCGGAGCTGGAGCCGGAGCTGGAGCCAGAACCGGA 905715 i i i i i (GAGCCG)n#Sim 1 GAGCCGGAGCCGGAGCCGGAGCCGGAGCCGGAGCCGGAGCCGGAGCCGGA 50 chr1ptel1M 905716 GCCAGAGCCGGAGCTGGAGCCAGAGCCGGACCGGGAGCCGGAGCC-GAGC 905764 i i i v v - (GAGCCG)n#Sim 51 GCCGGAGCCGGAGCCGGAGCCGGAGCCGGAGCCGGAGCCGGAGCCGGAGC 100 chr1ptel1M 905765 GGGAGCAGGAGCCGGAGCGGGAGCCGGAGCCGGAGCCAGAACCGGAGCGG 905814 v v v i i v (GAGCCG)n#Sim 101 CGGAGCCGGAGCCGGAGCCGGAGCCGGAGCCGGAGCCGGAGCCGGAGCCG 150 chr1ptel1M 905815 GAGCCGGAGCCGGAGCCGGAGCCGGAGTGGGAGCCAGAGCGGGAGCCGGA 905864 iv i v (GAGCCG)n#Sim 151 GAGCCGGAGCCGGAGCCGGAGCCGGAGCCGGAGCCGGAGCCGGAGCCGGA 200 chr1ptel1M 905865 ACCAGAGCCAGAGCCGGAGCGCCGGAGCGCCAGAGCCG 905902 i i i -- -- i (GAGCCG)n#Sim 201 GCCGGAGCCGGAGCCGGA--GCCGGA--GCCGGAGCCG 234 Matrix = Unknown Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.02 (5 / 236), avg. gap size = 1.00 (5 / 5) 13 8.41 13.16 0.00 chr1ptel1M 906297 906334 (93666) (CTCCCG)n#Simple_repeat 1 43 (0) m_b25s252i5 896 chr1ptel1M 906297 CTCCC-CTCCGGCTCCC-CTCCCGTTCCC-CT--CGTTCCCGC 906334 - v - i - -- i (CTCCCG)n#Sim 1 CTCCCGCTCCCGCTCCCGCTCCCGCTCCCGCTCCCGCTCCCGC 43 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.11 (4 / 37), avg. gap size = 1.25 (5 / 4) 18 29.86 0.00 0.00 chr1ptel1M 907372 907424 (92576) (CC)n#Simple_repeat 1 53 (0) m_b25s252i6 897 chr1ptel1M 907372 CCCCCCCCTCCCCCACAGCTTCCGCCGCCCCCCCCCAGCTCTCCCCCTCC 907421 i v vv ii v v vv i i i (CC)n#Simple_ 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 50 chr1ptel1M 907422 CCC 907424 (CC)n#Simple_ 51 CCC 53 Matrix = Unknown Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 1269 33.14 6.46 2.27 chr1ptel1M 910872 912140 (87860) L1PB_orf2#LINE/L1 1616 2936 (358) m_b25s551i18 898 chr1ptel1M 910872 ATGCAAAAATTTTACATAAAGTGTCGGTAAAGAGATTACAATAACTTATC 910921 ? ii vv i i iiii iv vv v v i i v L1PB_orf2#LIN 1616 ATGCNAAAATCCTCAACAAAATACTAGCTAACCGAATCCAACAGCATATC 1665 chr1ptel1M 910922 AGCGGGACGATGGGCCATGACCGAGCGGGATTTAGACCGGGGTCTGCTCA 910971 ivii ii vvi i i i v i v i -v --- L1PB_orf2#LIN 1666 AAAAAGATAATCCACCATGATCAAGTGGGTTTCATACCAGGG-ATGC--- 1711 chr1ptel1M 910972 AGGGCTGGCTCAAGGTCAGGAAGACTGCTGCCATAA--GCGAC-CATCTC 911018 v i i vi vv v ------v v -- i i- i v L1PB_orf2#LIN 1712 AGGGATGGTTTAACATACGCAAG------TCAATAAATGTGATACACCAC 1755 chr1ptel1M 911019 AGTCACAAAA---ACAGCACAACTCAAAGAGTTA-CTCACTAGAGGCAGA 911064 vvv i --- v i v v v vii i - v v L1PB_orf2#LIN 1756 ATAAACAGAATTAAAAACAAAAATCACATGATCATCTCAATAGATGCAGA 1805 chr1ptel1M 911065 AAAAGCTTTTGACGAACTACAGCACCTGCTCTTACTAAAAACACTAGGGA 911114 v i v v i ivi iv iv v v vi v L1PB_orf2#LIN 1806 AAAAGCATTTGACAAAATCCAGCATCCCTTTATGATTAAAACCCTCAGCA 1855 chr1ptel1M 911115 GCATAGGGATAAAAGGAAC-----TTAAAATAATAAGCAGCAGCCATCTA 911159 iv v v ? i ----- ?i i---- L1PB_orf2#LIN 1856 AAATCGGCATANAAGGGACATACCTTAANGTAATAAA----AGCCATCTA 1901 chr1ptel1M 911160 ----AAAACAACAGCAAGCATTAT-CTGTAATGGAGGGAGGATGGACACA 911204 ---- v v v i ? - - i ii i v i vi L1PB_orf2#LIN 1902 TGACAAACCCACAGCCAACATNATACTG-AATGGGGAAAAGTTGAAAGCA 1950 chr1ptel1M 911205 TTCCCCATGAGATCAGG-----GTCAAGGAGGCCCATTATCCCCACCATT 911249 v v v ----- v v i v v ivi L1PB_orf2#LIN 1951 TTCCCCCTGAGAACTGGAACAAGACAAGGATGCCCACTCTCACCACTTCT 2000 chr1ptel1M 911250 AAGCAACACTGCACTCGAAATGTTGGCTTTAGCAAG-----AAGAAAAGG 911294 ?vv iv i v i vi i ivv v----- i i L1PB_orf2#LIN 2001 NTTCAACATAGTACTGGAAGTCCTAGCCAGAGCAATCAGACAAGAGAAAG 2050 chr1ptel1M 911295 AAATTCAGGGAATTGGAATAGACAACTAGGAGATAAAACTATCACTCTTT 911344 vv v ivi v ii vv ii v i i v L1PB_orf2#LIN 2051 AAATAAAGGGCATCCAAATCGGTAAAGAGGAAGTCAAACTGTCGCTGTTT 2100 chr1ptel1M 911345 GCAGATGATAAGATGGTATACCTAGGGAACCCTAGAAAATCATCCAAAAA 911394 v v v ? ii i i v v i L1PB_orf2#LIN 2101 GCTGATGATATGATCGTNTACCTAGAAAACCCTAAAGACTCCTCCAGAAA 2150 chr1ptel1M 911395 ACTACTGGAAACAATTGACAGCTTTAGCAAAGCTGCAGAATACAAAA-TA 911443 i v i vii vi ?iiv i i v ? i - L1PB_orf2#LIN 2151 GCTCCTAGAACTGATAAANGAATTCAGCAAAGTTTCNGGATACAAAATTA 2200 chr1ptel1M 911444 A-------------------CCCCCATGAATCATCAGC------ATTAAG 911468 ------------------- i? i iv i v ------ii i L1PB_orf2#LIN 2201 ATGTACACAAATCAGTAGCTCTNCTATACACCAACAGCGACCAAGCTGAG 2250 chr1ptel1M 911469 AAGGAAA--GAGA----AATTCCATTGAAAATAACTGTTGCCAAAAGAAA 911512 vv --i ---- ii v v v i ivivv v L1PB_orf2#LIN 2251 AATCAAATCAAGAACTCAACCCCTTTTACAATAGCTGCAAAAAAAATAAA 2300 chr1ptel1M 911513 ATATGTCGGGGTCTATTT-GCCAAGACAAACCCAAGAACTACATGAACAC 911561 iv v ii v ii -i i- iiivv v vi ii iv v L1PB_orf2#LIN 2301 ATACTTAGGAATATACCTAACCAAGG-AGGTGAAAGACCTCTACAAGGAA 2349 chr1ptel1M 911562 AACTGCAAAACACTTCTCACACAAAAAAAGTAAGACCTATACAATTGGAA 911611 i v v v v vv viv v vi v v L1PB_orf2#LIN 2350 AACTACAAAACACTGCTGAAAGAAATCATAGACGACACAAACAAATGGAA 2399 chr1ptel1M 911612 AAAAAGCAAGTGCTCATGGGTAGGCTGAGCCAATAAAATAAAAATGACAA 911661 v v v vvi i i iv ii vvi i v L1PB_orf2#LIN 2400 ACACATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAATGACCA 2449 chr1ptel1M 911662 TCCGACC----TCAATCTACTTATTCAGTGCCATTCCACTCAAACTCCCA 911707 v vi ----v vv i v vv v v L1PB_orf2#LIN 2450 TACTGCCAAAAGCAATCTACAAATTCAATGCAATTCCCATCAAAATACCA 2499 chr1ptel1M 911708 AGA-AATTACTTCATAGAGCTAGAAAAAATAA---CAAAGTTCATCTGGA 911753 vv -v - i i i ---i i v L1PB_orf2#LIN 2500 CCATCATT-CTTCACAGAACTAGAAAAAACAATCCTAAAATTCATATGGA 2548 chr1ptel1M 911754 AGATCAAAA---GGTCAAGATTTTCAAGGGAATTACTGAGGAAAAAAATG 911800 -- i ---i i viv vvi i v -v i v i -i L1PB_orf2#LIN 2549 --ACCAAAAAAGAGCCCGCATAGCCAAAGCAA-GACTAAGCAAAAAGA-A 2594 chr1ptel1M 911801 CTAG--TAAAGGTGGCCCAGCTGGGCCAGAGCTAAAACTATATTATGAAG 911848 v i-- ii iiv v vi---i v vi v i i i L1PB_orf2#LIN 2595 CAAATCTGGAGGCATCACATT---ACCCGACTTCAAACTATACTATAAGG 2641 chr1ptel1M 911849 CAGTGGTCACCAAAACCATTTGGTATTGGCTAAGAGGTAGACTAGCTGAT 911898 vi i viiv i ivv i ii i vviiv i L1PB_orf2#LIN 2642 CCATAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGGCACATAGAC 2691 chr1ptel1M 911899 AAGTGG-ACAGGTTAG-GTTCACAG-GACAAACCAGTCAATAACTATAGC 911945 v i - iv - vv v -i i --iv vi i L1PB_orf2#LIN 2692 CAATGGAACAGAATAGAGAACCCAGAAATAAACC--CAAATACTTACAGC 2739 chr1ptel1M 911946 AATCTAGTGTTTGACAAACC---CAAAAGCCCTAACTTCTGGGACAAGAA 911992 v v ii v i v --- i viv ---v iv i L1PB_orf2#LIN 2740 CAACTGATCTTCGACAAAGCAAACAAAAACATAAA---GTGGGGAAAGGA 2786 chr1ptel1M 911993 TTCATTACTGGACAGAAACTGCTGGGAAAATTGG-AAACTAGTATGGCAG 912041 iv vi i vi i viv v - i i -i vvi L1PB_orf2#LIN 2787 CACCCTATTCAACAAATGGTGCTGGGATAATTGGCAAGCCA-CATGTAGG 2835 chr1ptel1M 912042 AAACTAGGCATGGACCCACACCTAACACTGTACACCAAGATAAGGTCGAA 912091 i v iiivv i v i vv iv i v i v iv i i L1PB_orf2#LIN 2836 AGAATGAAACTGGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAG 2885 chr1ptel1M 912092 ATGGGTTCATGATTTAGACAAAGGA--TGATACCATGAACAAATTAGGAG 912139 i iv v i i ivv i -- v i v vvi i L1PB_orf2#LIN 2886 ATGGATCAAGGACTTAAATCTAAGACCTGAAACCATAAAAATTCTAGAAG 2935 chr1ptel1M 912140 A 912140 L1PB_orf2#LIN 2936 A 2936 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 44.56 CpG sites = 208, Kimura (unadjusted) = 45.00 Transitions / transversions = 1.02 (208/203) Gap_init rate = 0.04 (56 / 1268), avg. gap size = 2.00 (112 / 56) 406 33.15 11.81 1.10 chr1ptel1M 912321 912811 (87189) L1ME4a_3end#LINE/L1 12 554 (317) m_b25s551i19 899 chr1ptel1M 912321 AATATAGAAAGGGCTGTGTCACATTTATAAGCATCCAAGTC--ATGCTCC 912368 v i v vv v iv v --v v -- ii i L1ME4a_3end#L 12 AATATATAAAGAGCTCTTACAAATCAATAAGAA--AAAGACGAACACCCC 59 chr1ptel1M 912369 AGTGCCTAACCGGTCAAAGGATAAGAAGAGACAATTTTCAGATGAAGAAA 912418 i ivvv vi v i v v iv i v L1ME4a_3end#L 60 AATAGAAAAATGGGCAAAGGACATGAACAGACAATTCACAAAAGAAGAAA 109 chr1ptel1M 912419 TTGAAACCATTTCTAGTCCTATGAAAAGGTGCTCTGAA--TCACCATT-- 912464 vv iviiivv iv v ?i i -- -- i v -- L1ME4a_3end#L 110 TACAAATGGCCAATAAACATATGAAAANATGTTC--AACCTCACTAGTAA 157 chr1ptel1M 912465 -----GAACCG-------AGACAACTCTGAGGTACCACTTCATACTGTGC 912502 ----- vi ------- i vv i i ivi ivvv L1ME4a_3end#L 158 TCAAAGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCTATC 207 chr1ptel1M 912503 AGATGGGC-TAGGCTGACAGGA---AAAGTAGCAAATGTTGGAGGGGATG 912548 i v -v ii v v i --- v i v v i v i i L1ME4a_3end#L 208 AAATTGGCAAAGATTTAAAAGATTGATAATACCCAGTGTTGGCGAGGGTG 257 chr1ptel1M 912549 TGGGAAAAGCGGAACACTGATGCATTGTTGGTGGAGCTGTGGAATGATCC 912598 ?i vv v v v i i i iiv ii v i v L1ME4a_3end#L 258 TGGNGAAACGGGCACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTAC 307 chr1ptel1M 912599 AGCACTTCTGGAGAACAATTTGGAACTCTGC-CCAAAGGGCTGTCACTCT 912647 i vi ii v v v i-i i v - v vvv L1ME4a_3end#L 308 AACCTTTCTGGAGGGCAATTTGGCAATATGTATCAAAAGCCT-TAAAAAT 356 chr1ptel1M 912648 GGGCAT--------ATCCAGCAGTGCCATTGCTGGGGCTGTGT-----GG 912684 v? -------- i i i v i v i iv v i ----- L1ME4a_3end#L 357 GTNCATACCCTTTGACCCAGTAATTCCACTTCTAGGAATTTATCCTAAGG 406 chr1ptel1M 912685 AAATCATAAAGGAGGCGA--------------------ATGTTCATAACG 912714 v v ii v i ?-------------------- vi i L1ME4a_3end#L 407 AAATAATCAGAGATGTGNACAAAGATTTATGTACAAGGATGTTCATCGCA 456 chr1ptel1M 912715 GCTCTTTTTGTGGTAGCAAAGAAATGGGAAATGAGC-GGATGCCTGTCAA 912763 vi v i ii i - v ii v -ii i iiv L1ME4a_3end#L 457 GCATTATTTATAATAGCGAA-AAATTGGAAACAACCTAAATGTCCAACAA 505 chr1ptel1M 912764 CTGGGCAATGGCTGAACAAGTCAT-GTGCATGAAGGTGATGGAACATTA 912811 iv v ? i i i i i - i vv vi?i i L1ME4a_3end#L 506 TAGGGGANTGGTTAAATAAATTATGGTACATCCATANAATGGAATATTA 554 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 44.75 CpG sites = 84, Kimura (unadjusted) = 45.52 Transitions / transversions = 1.09 (84/77) Gap_init rate = 0.04 (19 / 490), avg. gap size = 3.37 (64 / 19) 512 31.82 13.14 2.01 chr1ptel1M 912380 912828 (87172) L1MB7_3end#LINE/L1 71 568 (363) m_b25s551i21 899 chr1ptel1M 912380 GGTCAAAGGATAAGAAGAGACAATTTTCAGATGAAGAAATTGAAACCATT 912429 v vv v v i vi v v vv iviii L1MB7_3end#LI 71 GGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCC 120 chr1ptel1M 912430 TCTAGTCCTATGAAAAGGTGCTCTGAATCAC----CATTG---------- 912465 vv iv vi i viv i---- i---------- L1MB7_3end#LI 121 AATAAGCACATGAAAAGATGCTCAACATCATTAGTCATTAGGGAAATGCA 170 chr1ptel1M 912466 AACCGAGACAACTCTGAGGTACCACTTCATACTGTGCAGATGGGCTAGGC 912515 i i i v vv i i ivvvi ivv viv L1MB7_3end#LI 171 AATCAAAACCACAATGAGATACCACTTCACACCCACTAGGATGGCTATAA 220 chr1ptel1M 912516 TGACAGGAAAAG----TAGCAAATGTTGGAGGGGATGTGGGAAAAGCGGA 912561 ? v iii v ---- i i v i ii vi L1MB7_3end#LI 221 TNAAAAAGACAGACAATAACAAGTGTTGGCGAGGATGTGGAGAAATTGGA 270 chr1ptel1M 912562 ACACTGATGCATTGTTGGTGGAGCTGTGGAATGATCCAGCACTTCTGGAG 912611 v v i i iiv ii i v vvi i i L1MB7_3end#LI 271 ACCCTCATACATTGCTGGTGGGAATGTAAAATGGTGCAGCCGCTTTGGAA 320 chr1ptel1M 912612 AACAATTTGGAACTCTGCCCAAAGGGCT---------GTCACTCTGGGCA 912652 i v v - v i ii i --------- i ------ L1MB7_3end#LI 321 AACAGTTTGGCAGT-TCCTCAAAAAGTTAAACATAGAGTTAC------CA 363 chr1ptel1M 912653 TAT---CCAGCAGTGCCATTGCTGGGGCTGT-----------GTGGAAAT 912688 --- i v i v i vv i -----------? i i L1MB7_3end#LI 364 TATGACCCAGCAATTCCACTCCTAGGTATATACCCAAGAGAANTGAAAAC 413 chr1ptel1M 912689 ---------CATAAA-----GGAGGCGAATGTTCATAACGGCTCTTTTTG 912724 --------- i ----- v vi i i vi v ii L1MB7_3end#LI 414 ATATGTCCACACAAAAACTTGTACACGAATGTTCATAGCAGCATTATTCA 463 chr1ptel1M 912725 TGGTAGCAAAGAAATGGGAAATGA-GCGGATGCCTGTCAACTGGGCAATG 912773 ii v i i - ii -v ii i ii ivv L1MB7_3end#LI 464 TAATAGCCAAAAAGT-GGAAACAACCCAAATGTCCATCAACTGATGAATG 512 chr1ptel1M 912774 GCTGAACAAGTCATGTG---CATGAAGGTGATGGAACATTACTGTTCTAT 912820 v i i-- ---i vv viii i i vvv i L1MB7_3end#LI 513 GATAAACAAA--ATGTGGTATATCCATACAATGGAATATTATTCGGCCAT 560 chr1ptel1M 912821 AAAAACGA 912828 v L1MB7_3end#LI 561 AAAAAGGA 568 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 43.03 CpG sites = 80, Kimura (unadjusted) = 43.03 Transitions / transversions = 1.33 (80/60) Gap_init rate = 0.04 (20 / 448), avg. gap size = 3.45 (69 / 20) 534 31.40 7.44 0.00 chr1ptel1M 912380 912621 (87379) L1ME5_3end#LINE/L1 71 330 (611) m_b25s551i20 899 chr1ptel1M 912380 GGTCAAAGGATAAGAAGAGACAATTTTCAGATGAAGAAATTGAAACCATT 912429 v v v i v v i iivi vvii L1ME5_3end#LI 71 GGGCAAAGGATATGAACAGGCAATTTACAGAAGAGGAAACCCGAAAGGCT 120 chr1ptel1M 912430 TCTAGTCCTATGAAAAGGTGCTCTGAATCACCATTGAACCGAG------- 912472 vvi iv v i i vi v ii v i v v ------- L1ME5_3end#LI 121 AACAAGCATATGAAGAGATGCTCAAACTCATTAGTAATCAGAGAAATGCA 170 chr1ptel1M 912473 -------ACAACTCTGAGGTACCACTTCATACTGTGCAGATGGGCTAGGC 912515 ------- vv i i i i ivvvi iv v iiv L1ME5_3end#LI 171 AATTAAAACAACAATGAGATATCACTTTACACCTATTAGACTGGCAAAAA 220 chr1ptel1M 912516 T--GACAG--GAAAAGTAGCAAATGTTGGAGGGGATGTGGGAAAAGCGGA 912561 -- v -- i v i iv i v i i ? vv L1ME5_3end#LI 221 TTAGAAAGCTGGATAATGCCAAGTGTTGGCGAGGATGTGGGGANATAGGA 270 chr1ptel1M 912562 ACACTGATGCATTGTTGGTGGAGCTGTGGAATGATCCAGCACTTCTGGAG 912611 v v i i iiv i v i v vv L1ME5_3end#LI 271 ACCCTCATGCACTGCTGGTGGGAGTGTAGACTGGTGCAGCCATTCTGGAG 320 chr1ptel1M 912612 AACAATTTGG 912621 i i L1ME5_3end#LI 321 AGCAATCTGG 330 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 40.80 CpG sites = 38, Kimura (unadjusted) = 41.50 Transitions / transversions = 1.00 (38/38) Gap_init rate = 0.02 (4 / 241), avg. gap size = 4.50 (18 / 4) 13 18.66 2.08 6.52 chr1ptel1M 916048 916095 (83905) (CCTCC)n#Simple_repeat 1 46 (0) m_b25s252i7 900 chr1ptel1M 916048 CCCCCCCT-CCCTCCCCGCGCCTCCTCACCTGCTCGGCCTCGCCCTCCC 916095 i - v v i v -v -v - (CCTCC)n#Simp 1 CCTCCCCTCCCCTCCCCTCCCCTCCCCTCC-CCTC-CCCTC-CCCTCCC 46 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.09 (4 / 47), avg. gap size = 1.00 (4 / 4) 12 13.57 0.00 8.57 chr1ptel1M 916218 916255 (83745) (CCCTGC)n#Simple_repeat 1 35 (0) m_b25s252i8 901 chr1ptel1M 916218 CCCAGCCCCTGCCCGAGCCTCCTGGCCCGCCGCCCCTG 916255 v vv - - - i (CCCTGC)n#Sim 1 CCCTGCCCCTGCCCCTGCC-CCT-GCCC-CTGCCCCTG 35 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.08 (3 / 37), avg. gap size = 1.00 (3 / 3) 393 29.61 5.49 5.93 chr1ptel1M 918768 919004 (80996) C MIR#SINE/MIR (10) 252 17 m_b25s601i0 902 chr1ptel1M 918768 AGCATTTATGTGGCACCTCCCA-----CAGGCACCAGGCTG-GCATCTCA 918811 i vvi i i v i ----- iivv i- iii i C MIR#SINE/MIR 252 AACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGCGCTTTA 203 chr1ptel1M 918812 CAGATACTACCACACTGCATCTGACCAAGAACC-TACCCA-CAAGTACCC 918859 vi i v v i vv ivvv v - ivvi-i i iv C MIR#SINE/MIR 202 CATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGGTAGGTACTA 153 chr1ptel1M 918860 TCGTCACCCCCACTTTAAAGCTGAGGAAACGGAGGCAGAGAGAGAGGTGA 918909 ii i i i v v v -- v v C MIR#SINE/MIR 152 TTATTATCCCCATTTTACAGATGAGGAAACTGAGGC--ACAGAGAGGTTA 105 chr1ptel1M 918910 TGGCTTGTTTGCCCAGGGTCCTACAACTAATGAGCATTTCAG-GCTGGG- 918957 v -- vii i vi i i i -- vv - i - C MIR#SINE/MIR 104 AG--TAACTTGCCCAAGGTCACACAGCTAGTAAG--TGGCAGAGCCGGGA 59 chr1ptel1M 918958 TTTGAACCC---CAGTCTCTGCAGCTCCAGGTGCCGGCTGCCTTCTCAAC 919004 i --- ----i i- v - -- i C MIR#SINE/MIR 58 TTCGAACCCAGGCAGTCT----GGCTCCAGA-GCCCG-TGC--TCTTAAC 17 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 35.69 CpG sites = 38, Kimura (unadjusted) = 38.63 Transitions / transversions = 1.36 (38/28) Gap_init rate = 0.09 (21 / 236), avg. gap size = 1.29 (27 / 21) 2122 27.53 3.02 1.31 chr1ptel1M 920736 921563 (78437) L1M5_orf2#LINE/L1 1324 2165 (1129) m_b25s551i22 903 chr1ptel1M 920736 ATCCAAGAGGAAGTAAATTGCTTAAATAGTCCCATTTCAGAAAAAGAACT 920785 i? i i i vviii i i i v vivv v L1M5_orf2#LIN 1324 ACNCAAGAAGAAATAGAAAATCTGAATAGCCCTATATCTATTAAAGAAAT 1373 chr1ptel1M 920786 AGAACAAGTCATTGATCAACTCCCCAAGAAAAAATCCCCAGGACCAGATG 920835 v ivv v i vv v i vi i v i v L1M5_orf2#LIN 1374 TGAATTTGTAATTAAAAACCTTCCCACAAAGAAAACTCCAGGCCCAGATG 1423 chr1ptel1M 920836 TAGTTACATGTGAATTCTACCAAACATTTAAAGAATAATTGGCCCCAATG 920885 vvv i vv i v v iiiv v L1M5_orf2#LIN 1424 GCTTCACTGGTGAATTCTACCAAACATTTAAGGAAGAAATAATACCAATC 1473 chr1ptel1M 920886 CTATATAAACTATTGGAAAAACTAGGGAATGAAGGA-CTCTTACCAAATT 920934 i i i v vv i v ii v i - v v -i L1M5_orf2#LIN 1474 TTACACAAACTCTTCCAGAAAATAGAAAAAGAGGGAACACTTCCCAA-CT 1522 chr1ptel1M 920935 CCTTTTATGACACAGACATGGTACTGATACTTAAACCAGGTAGGTTGAAA 920984 v vi vii ?iiv iv ? ii ii-- v L1M5_orf2#LIN 1523 CATTTTATGAGGCCAGCATNACCCTGATACCAAAACCNGACAAA--GACA 1570 chr1ptel1M 920985 --ACAGAAAAAGAAAATTATAGACCAATCTCCCTAATGAATATTGATGCT 921032 -- ii i v v i v v L1M5_orf2#LIN 1571 TTACAAGAAAAGAAAATTACAGACCAATATCCCTCATGAACATAGATGCA 1620 chr1ptel1M 921033 AAAATC-TTAATAAGATATTAGCAAA--AAAGTTTACAGAAAATCATCCC 921079 - ? i i --i --- v v vvi vvv L1M5_orf2#LIN 1621 AAAATCCTNAACAAAATATTAGCAAATCGAA---TCCAGCAATATATAAA 1667 chr1ptel1M 921080 CAGGGTAATACATCATGATCAAGTAGGTTTTATACCAGGAATGCAGGGCT 921129 v i i i v v i i L1M5_orf2#LIN 1668 AAGGATAATACATCATGACCAAGTGGGGTTTATCCCAGGAATGCAAGGTT 1717 chr1ptel1M 921130 GGTTCAATATTAGGAAAACTATCAGTATAATTGATGACATTAATA-ACCA 921178 i i v i v v i i v iv i i - vi L1M5_orf2#LIN 1718 GGTTTAACATTCGAAAATCAATCAATGTAATTCACCATATTAACAGAATA 1767 chr1ptel1M 921179 AATTAACAAAAACCATATGATCATCTCAATAGATGCAGAAAAAGCATTTG 921228 vv i- i L1M5_orf2#LIN 1768 AAGGAG-AAAAATCATATGATCATCTCAATAGATGCAGAAAAAGCATTTG 1816 chr1ptel1M 921229 ATAAAATCCAATATCCATTCCTATTAAAAACACTTGAGAGTATAGGAATA 921278 i i i i v iv v iiiv ivv L1M5_orf2#LIN 1817 ACAAAATTCAACACCCATTCATGATAAAAACTCTCAGCAAACTAGGAATA 1866 chr1ptel1M 921279 AATGG--ACTTGTCCTTAAAATAATCAGTAGCATCTATTTAAAATCATCA 921326 i v -- -- i vv i v ivi ivv i vv L1M5_orf2#LIN 1867 GAAGGGAACTT--CCTCAACCTGATAAAGGGCATCTACGAAAAACCTACA 1914 chr1ptel1M 921327 ATGAGCATCATATGTAACCGGGATAAACTGCAACCATTCCCAATAAAATC 921376 ii? i iv iv v v ? v ?v v vv i L1M5_orf2#LIN 1915 GCNAACATCATACTTAATGGTGAAANACTGAANGCTTTCCCCCTAAGATC 1964 chr1ptel1M 921377 AGGAGCGA--------------CTATCACCATTATTATTCACTACTGTAT 921412 i i i -------------- ? i vi vi i i L1M5_orf2#LIN 1965 GGGAACAAGACAAGGATGTCCGCTNTCACCACTTCTATTCAACATTGTAC 2014 chr1ptel1M 921413 TAGAATCACTAGCTTTGGCAATAAGAGTTGAGAAAAAG--ATTAAAGGAA 921460 i iviv ivvv i--ii -- v v L1M5_orf2#LIN 2015 TGGAGGTCCTAGCCAGTGCAATAAGG--CAAGAAAAAGAAATAAAAGGCA 2062 chr1ptel1M 921461 TTAGAGTAGGTAATGAGGAAACCAAATTATCACTCTTTGCAGATGATATG 921510 v iii v v v i iv i i ?i v i i L1M5_orf2#LIN 2063 TAAAGATTGGAAAGGAAGAAATAAAACTGTCNTTATTCGCAGATGACATG 2112 chr1ptel1M 921511 ATGGTAAACTTAGAGAACTCCAGAGATTCTACTAGAAAGCTTTTAGAAAT 921560 v ?v v i ii ? i v v i? i vi v L1M5_orf2#LIN 2113 ATTGTNTACGTAGAAAATCCNAAAGAATCTACAAANAAACTACTAGAACT 2162 chr1ptel1M 921561 AAT 921563 L1M5_orf2#LIN 2163 AAT 2165 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 34.72 CpG sites = 118, Kimura (unadjusted) = 35.49 Transitions / transversions = 1.10 (118/107) Gap_init rate = 0.02 (19 / 827), avg. gap size = 1.89 (36 / 19) 882 27.31 1.33 2.36 chr1ptel1M 921572 921871 (78129) L1ME3G_3end#LINE/L1 252 548 (376) m_b25s551i23 903 chr1ptel1M 921572 TGTGGGAAAATAGGGACACTAATACATTGTTGGTGGAATTGTGAATATAT 921621 i ii v v v i i i v i vvi L1ME3G_3end#L 252 TGTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGT 301 chr1ptel1M 921622 CCAGTCATCCTGGAGAGAAATTTGGAACTATGCCCA--AAAGGTTATCAA 921669 v i ? ii i v v v -- i -- iv --- L1ME3G_3end#L 302 ACAGCCNTTTTGGAGGGCAATTTGGCAGTAT--CTATTAAAATTTA---A 346 chr1ptel1M 921670 ACTGTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGCTTATACCCCA 921719 v i i i vii v ? ?v v i i L1ME3G_3end#L 347 AATGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTA 396 chr1ptel1M 921720 AAGAGATACT-AAAGAAGAG-AAAGGGACCTGTATGTGCAAGAATATTTG 921767 ? i -iv v v v - v i --? i i i i ii L1ME3G_3end#L 397 NAGAAATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTCA 444 chr1ptel1M 921768 TGGCAGGTCTCTTTGTAGTGGCCAGAAACTGGAAACTGAGTGGATGCCCA 921817 v vvi v i i v i i vivv ii i L1ME3G_3end#L 445 TTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCA 494 chr1ptel1M 921818 TCAACTGGAGAATAGCTGAATAAATTGTGGTATATGAATGTTATGGAATA 921867 iv i i i i i vv ii L1ME3G_3end#L 495 TCAATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATA 544 chr1ptel1M 921868 TTAT 921871 i L1ME3G_3end#L 545 CTAT 548 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 33.95 CpG sites = 48, Kimura (unadjusted) = 35.67 Transitions / transversions = 1.50 (48/32) Gap_init rate = 0.03 (10 / 299), avg. gap size = 1.10 (11 / 10) 17 9.12 0.00 0.00 chr1ptel1M 922372 922395 (77605) (A)n#Simple_repeat 1 24 (0) m_b25s252i9 904 chr1ptel1M 922372 AAAAAAAAAAAAAAGAAAAAGAAA 922395 i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAA 24 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 20 7.86 0.00 0.00 chr1ptel1M 922926 922952 (77048) (A)n#Simple_repeat 1 27 (0) m_b25s252i10 905 chr1ptel1M 922926 AAAAAAAAAAAAAAAACAAAAACAAAA 922952 v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAA 27 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 18 12.16 0.00 0.00 chr1ptel1M 923980 924006 (75994) (A)n#Simple_repeat 1 27 (0) m_b25s252i11 906 chr1ptel1M 923980 AAATAAAAAGAAAAAAAGAAAAAAAAA 924006 v i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAA 27 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 27 3.10 0.00 2.94 chr1ptel1M 924389 924423 (75577) (TTAAAA)n#Simple_repeat 1 34 (0) c_b25s251i0 907 chr1ptel1M 924389 TTAAAATTAAAATTAAATTTTAAAATTAAAATTAA 924423 -v (TTAAAA)n#Sim 1 TTAAAATTAAAATTAAA-ATTAAAATTAAAATTAA 34 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 1173 28.57 3.61 2.83 chr1ptel1M 924451 924976 (75024) L1ME4a_3end#LINE/L1 56 585 (286) m_b25s551i24 908 chr1ptel1M 924451 CTCCAATTGATAAATGGTTAAAGGATGTGAACA----ATTTTCAGATGAA 924496 i v v vi ii ---- iv i v L1ME4a_3end#L 56 CCCCAATAGAAAAATGGGCAAAGGACATGAACAGACAATTCACAAAAGAA 105 chr1ptel1M 924497 GAAAT-TAAA--GCCATTTCTAGTCATATAAAAAAATGCTCTAAATCACT 924543 -i -- ---v iv i ? i v vv L1ME4a_3end#L 106 GAAATACAAATGGCCA---ATAAACATATGAAAANATGTTCAACCTCACT 152 chr1ptel1M 924544 ATTGATTAAAGAAATGCAAATTAAGACAACTCTGAGATACCACTCCGCAT 924593 v i i i vv i iiv i L1ME4a_3end#L 153 AGTAATCAAAGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCAC 202 chr1ptel1M 924594 CTCTCAGATTGACTAAG--TTAAAGGAAAAGATAATGATAAGTGATGGAG 924641 v i i v -- i vv- iviv v v L1ME4a_3end#L 203 CTATCAAATTGGCAAAGATTTAAAAGATT-GATAATACCCAGTGTTGGCG 251 chr1ptel1M 924642 GGGATGTGGGAAAATTGGGATACTAATACATAGTTAGTGGAGTTGTGAAC 924691 i i ?i iv v iv v iv i i iiv i i L1ME4a_3end#L 252 AGGGTGTGGNGAAACGGGCACTCTCATACACTGCTGGTGGGAGTGTAAAT 301 chr1ptel1M 924692 TGATCCAAACATTCTGGAGAACAATATGAAACCATA-ATCAAAGGGCTAC 924740 i v v v ii v iv vi i- i v -i L1ME4a_3end#L 302 TGGTACAACCTTTCTGGAGGGCAATTTGGCAATATGTATCAAAAGCCT-T 350 chr1ptel1M 924741 CAAACTATGCATACCCTTTGATTCAGCAGTGTCTCTACAAGGGCTGTATC 924790 v v i ? ii i i vi v v v iv v L1ME4a_3end#L 351 AAAAATGTNCATACCCTTTGACCCAGTAATTCCACTTCTAGGAATTTATC 400 chr1ptel1M 924791 CCAAAGAGATAATAAAGCAGAGAAAAGGACCCA----TAGGTGCAAAAGT 924836 i i i ---- viv ? vv ---- v i iii L1ME4a_3end#L 401 CTAAGGAAATAAT----CAGAGATGTGNACAAAGATTTATGTACAAGGAT 446 chr1ptel1M 924837 ----ATAGCAGCTCTTTTTGCAGTGGCAAGGAACTGCAAACCAAATGGAT 924882 ---- v vi v ii i i i ii i v v vv ii L1ME4a_3end#L 447 GTTCATCGCAGCATTATTTATAATAGCGAAAAATTGGAAACAACCTAAAT 496 chr1ptel1M 924883 GCCCACCAGTTGGAGAATGGTTGAATGAGTTATGGTATATTATGGATATA 924932 i v i v i ? i i i i i-----i L1ME4a_3end#L 497 GTCCAACAATAGGGGANTGGTTAAATAAATTATGGTACATC-----CATA 541 chr1ptel1M 924933 ATATGGTATATTATAT-GTTATGGAATATTATTGTTCTGTAAGAA 924976 ?v v ii- ii vi v ? - i vv L1ME4a_3end#L 542 NAATGGAATATTATGCAGCCATTAAAAATNA-TGTTTTCGAAGAA 585 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 36.83 CpG sites = 83, Kimura (unadjusted) = 37.48 Transitions / transversions = 1.32 (83/63) Gap_init rate = 0.04 (23 / 525), avg. gap size = 1.48 (34 / 23) 16 0.00 4.35 0.00 chr1ptel1M 925477 925499 (74501) (TAAA)n#Simple_repeat 1 24 (0) m_b26s252i0 909 chr1ptel1M 925477 TAAA-AAATAAATAAATAAATAAA 925499 - (TAAA)n#Simpl 1 TAAATAAATAAATAAATAAATAAA 24 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.05 (1 / 22), avg. gap size = 1.00 (1 / 1) 19 4.35 0.00 0.00 chr1ptel1M 925558 925581 (74419) (AC)n#Simple_repeat 1 24 (0) m_b26s252i1 910 chr1ptel1M 925558 ACACACACACATACACACACACAC 925581 i (AC)n#Simple_ 1 ACACACACACACACACACACACAC 24 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 183 30.80 3.64 5.56 chr1ptel1M 927269 927378 (72622) C L2a_3end#LINE/L2 (92) 425 318 m_b26s601i0 911 chr1ptel1M 927269 AAGCTCTCGCCCTCAAGAAGCTGATCTTCTATTGGGGGAAAACAG-CTAT 927317 ii ii v i v iv v i i - v C L2a_3end#LINE 425 AAGTCCCTGCCCTCATGGAGCTTACATTCTAGTGGGGGGAGACAGACAAT 376 chr1ptel1M 927318 AGCCTTAAGTGATACAAAAGGAGCATCTTTGGGGAAGGCAGTTGG-GAT- 927365 ----- vvi v v v iv v v -i v v v v - - C L2a_3end#LINE 375 A-----AACAAATAAATAAGTAAAATATAT-AGTATGTCAGATGGTGATA 332 chr1ptel1M 927366 -GTGACGTGAAGAA 927378 - vii i C L2a_3end#LINE 331 AGTGCTATGGAGAA 318 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.82 CpG sites = 14, Kimura (unadjusted) = 39.82 Transitions / transversions = 0.78 (14/18) Gap_init rate = 0.09 (10 / 109), avg. gap size = 1.00 (10 / 10) 314 27.32 4.24 6.96 chr1ptel1M 928220 928337 (71663) MIRc#SINE/MIR 12 126 (142) m_b26s601i1 912 chr1ptel1M 928220 GGCATAGGGGATAGAGCACCG----TGTGCTCAGGAGGACCCGACTTCAA 928265 iii v v i ---- viv i i iv i MIRc#SINE/MIR 12 GGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGA 61 chr1ptel1M 928266 ACCTGGCCTTAGACACTTAACACTTCCTAGCCTGTGTGAGCCCGGGCAAG 928315 ii iv v iv v ------- - v ii MIRc#SINE/MIR 62 GTCCCGGCTCTGCCACTTA-------CTAGC-TGTGTGACCTTGGGCAAG 103 chr1ptel1M 928316 TCATTTAACCCCACC-TGCCTCA 928337 i i v i-v MIRc#SINE/MIR 104 TCACTTAACCTCTCTGAGCCTCA 126 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.39 CpG sites = 18, Kimura (unadjusted) = 34.82 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.09 (10 / 117), avg. gap size = 1.30 (13 / 10) 194 24.50 0.00 2.04 chr1ptel1M 934269 934318 (65682) MIRb#SINE/MIR 139 187 (81) m_b26s601i2 913 chr1ptel1M 934269 TCTGTAAAACGGGGCTCACCGGCACCGACCTCCCAGGGTTATGGGGAGGA 934318 i v v i-iii v v i v v MIRb#SINE/MIR 139 TCTGTAAAATGGGGATAAT-AATACCTACCTCGCAGGGTTGTTGTGAGGA 187 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.91 CpG sites = 6, Kimura (unadjusted) = 29.91 Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.02 (1 / 49), avg. gap size = 1.00 (1 / 1) 31 18.64 0.00 5.13 chr1ptel1M 936305 936386 (63614) (GACCCT)n#Simple_repeat 1 78 (0) m_b26s252i2 914 chr1ptel1M 936305 GATCCCGACCCTGACTCTGGCCCTGACCCTGACTCCGACCCCTGACCCCA 936354 i i i i i i - ii (GACCCT)n#Sim 1 GACCCTGACCCTGACCCTGACCCTGACCCTGACCCTGA-CCCTGACCCTG 49 chr1ptel1M 936355 ACCCTGACCCCCAGCTCCGGCCCCTGATCCCT 936386 iv - - v v - (GACCCT)n#Sim 50 ACCCTGACCCTGA-C-CCTGACCCTGA-CCCT 78 Matrix = Unknown Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.05 (4 / 81), avg. gap size = 1.00 (4 / 4) 270 35.60 5.49 2.37 chr1ptel1M 936893 937056 (62944) MIRb#SINE/MIR 46 214 (54) m_b26s601i3 915 chr1ptel1M 936893 CGGACAGACCGCTGGACTGGAAGCCTGAGTCT--CACCT-CAGACCCTGA 936939 i -- ii v v i iv -- i - vii iv v MIRb#SINE/MIR 46 CAGACAGACC--TGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGT 93 chr1ptel1M 936940 CACTGCCAGCA-GTGGCTC--CTTCCCTG--CCTCAGTTTTCTCATCTGT 936984 v ivivi - vi i-- i i -- i MIRb#SINE/MIR 94 GACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGT 143 chr1ptel1M 936985 ACCATGGGCACAGAATGGCATCCATCTCCCAGGGCAACTGTG-GGCCTAT 937033 vv v i-- iii i i i v ivii - vi v MIRb#SINE/MIR 144 AAAATGGGGAT--AATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAA 191 chr1ptel1M 937034 GTGGCACAGTCTGTGGGAGGTGC 937056 i iv i i vii vi i i MIRb#SINE/MIR 192 ATGAGATAATGCATGTAAAGCGC 214 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 48.81 CpG sites = 37, Kimura (unadjusted) = 51.47 Transitions / transversions = 1.85 (37/20) Gap_init rate = 0.06 (10 / 163), avg. gap size = 1.30 (13 / 10) 30 2.62 2.33 4.76 chr1ptel1M 939050 939092 (60908) (AC)n#Simple_repeat 1 42 (0) c_b26s251i1 916 chr1ptel1M 939050 ACACACACAC-CTGCACACACACACACACACACACGACACACAC 939092 - -i - (AC)n#Simple_ 1 ACACACACACAC-ACACACACACACACACACACAC-ACACACAC 42 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.07 (3 / 42), avg. gap size = 1.00 (3 / 3) 40 31.75 3.42 0.00 chr1ptel1M 939116 939261 (60739) (AC)n#Simple_repeat 1 151 (0) m_b26s252i3 916 chr1ptel1M 939116 ACACACACACCTGCACACACACACATACA-ACACACACCCCTGCGTGCAT 939164 vii i - v vii iii i (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50 chr1ptel1M 939165 A-ATGCACCTGTACACACACACCTGCACACACACACATACA-ACACACAC 939212 - ii viii vii i - (AC)n#Simple_ 51 ACACACACACACACACACACACACACACACACACACACACACACACACAC 100 chr1ptel1M 939213 CCCTGCGTGCACA-ATGCACTTGCGCACACACACACACGCACA-ACACAC 939260 v vii iii - ii vii i i - (AC)n#Simple_ 101 ACACACACACACACACACACACACACACACACACACACACACACACACAC 150 chr1ptel1M 939261 A 939261 (AC)n#Simple_ 151 A 151 Matrix = Unknown Transitions / transversions = 3.50 (28/8) Gap_init rate = 0.03 (5 / 145), avg. gap size = 1.00 (5 / 5) 13 15.56 6.38 4.17 chr1ptel1M 942368 942414 (57586) (GGCGA)n#Simple_repeat 1 48 (0) m_b26s252i4 917 chr1ptel1M 942368 GGC-AGCCGATGCGAGGGGCCCCGGAGG-GAGGGCGAGGCGAGGCG-GGC 942414 - v v v vvv - - - - (GGCGA)n#Simp 1 GGCGAGGCGAGGCGAGGCGAGGC-GAGGCGA-GGCGAGGCGAGGCGAGGC 48 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.11 (5 / 46), avg. gap size = 1.00 (5 / 5) 16 15.26 2.56 2.56 chr1ptel1M 943786 943824 (56176) (GAGG)n#Simple_repeat 1 39 (0) m_b26s252i5 918 chr1ptel1M 943786 GAGGGATGGGAGGATGAGAGAG-GGGAGGGAGGGGGGGAG 943824 - iv i i - i (GAGG)n#Simpl 1 GAGGGA-GGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAG 39 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2) 12 27.30 3.23 3.23 chr1ptel1M 944187 944248 (55752) (GGTGGAA)n#Simple_repeat 1 62 (0) m_b26s252i6 919 chr1ptel1M 944187 GGCGGGAGG-GGTAGG-GGAGGGCGGGAGAGGGGGGGGGGAAGGTGGGAG 944234 i i - v - i i i iv ii v - i (GGTGGAA)n#Si 1 GGTGGAAGGTGGAAGGTGGAAGGTGGAAGGTGGAAGGTGGAAGGT-GGAA 49 chr1ptel1M 944235 GGGGGAAGGTTGGA 944248 v - (GGTGGAA)n#Si 50 GGTGGAAGG-TGGA 62 Matrix = Unknown Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.07 (4 / 61), avg. gap size = 1.00 (4 / 4) 186 25.00 0.00 0.00 chr1ptel1M 951748 951791 (48209) MIR#SINE/MIR 116 159 (103) m_b26s601i4 920 chr1ptel1M 951748 TGCCTCAGTTTCCCCAACTGTATGAAGGGGGAAACCCTAGAACC 951791 i v vi v iv ivv v MIR#SINE/MIR 116 TGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACC 159 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.42 CpG sites = 4, Kimura (unadjusted) = 30.42 Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 205 27.66 0.00 0.00 chr1ptel1M 951811 951857 (48143) L2d_3end#LINE/L2 452 498 (18) m_b26s601i5 921 chr1ptel1M 951811 AGTACCCTGGACAGTCCTGGGCACACAGTAGGCACTTTATCAACACT 951857 ii iv v v i i i iv v i L2d_3end#LINE 452 AGCGCCTAGCACAGTGCTGAGCACATAGTAGGCGCTCAATAAATACT 498 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.76 CpG sites = 8, Kimura (unadjusted) = 35.58 Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 17 20.09 3.77 1.85 chr1ptel1M 952893 952945 (47055) (CTCCC)n#Simple_repeat 1 54 (0) m_b26s252i7 922 chr1ptel1M 952893 CTGCCCCCCACTCCCCTCCCCCTGCCCTTCCCT-TGCTCCCCATCCCT-C 952940 v i v - v i -iv vi - (CTCCC)n#Simp 1 CTCCCCTCCCCTCCCCT-CCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCC 49 chr1ptel1M 952941 CCTCC 952945 (CTCCC)n#Simp 50 CCTCC 54 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.06 (3 / 52), avg. gap size = 1.00 (3 / 3) 18 14.50 2.63 0.00 chr1ptel1M 955821 955858 (44142) (ATTT)n#Simple_repeat 1 39 (0) m_b26s252i8 923 chr1ptel1M 955821 ATTTTTTTTTTTAACT-TTTATTTATTTATTTTTTTATT 955858 v v vi - v (ATTT)n#Simpl 1 ATTTATTTATTTATTTATTTATTTATTTATTTATTTATT 39 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 1485 28.35 1.26 2.07 chr1ptel1M 956319 956952 (43048) C L1ME3G_3end#LINE/L1 (292) 632 4 m_b26s551i2 924 chr1ptel1M 956319 CCTGCTCATTTCACTCAGCATCAGTTCGTGTAAGTCTCTCCAGGCCTTTC 956368 i iv i vi vv v v ii i v i vv v C L1ME3G_3end#L 632 CTTGCTTTTTTCACTCAACAATATGTCTTGGAGATCTTTCCATGTCAGTA 583 chr1ptel1M 956369 TG---AAATCCTCCTGTTGGTCATTTCTTACAG-AACAGTAATATTCCAT 956414 ii--- i iv vv -- - i v ? -vi - i C L1ME3G_3end#L 582 CATATAGATCTACCTCAT--TC-TTTTTAACNGCTGCA-TAGTATTCCAT 537 chr1ptel1M 956415 AATATTCATATACCACAATTTATTCAGCCATTCTCCAACTGATGGACATC 956464 i vv i i i i v i i C L1ME3G_3end#L 536 AGTATGGATATACCATAATTTATTTAACCATTCCCCTATTGATGGACATT 487 chr1ptel1M 956465 CATTCAGTTTCCAGTTTCTAGCCACTACAAAAAGGGCTGCCACAAACATT 956514 i vviv i i v i i v iv v ii i C L1ME3G_3end#L 486 TAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCTGCAATGAACATC 437 chr1ptel1M 956515 CGTGCACATACAGGTCCCTTT-CCCTTCTTTATG-ATCTCTTTGGGATAT 956562 v i i ?-- i v - v v v viiv - i ? i v C L1ME3G_3end#L 436 CTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATTTCTNTAGGATAG 389 chr1ptel1M 956563 AAGCCCAGTAGTAACACTGCTGGATCAAAGGGTACGCACAGTTTGGTAAC 956612 v? ? v iiv i i i i v i-- i C L1ME3G_3end#L 388 ATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGCATTTTA--AAT 341 chr1ptel1M 956613 TTTATGAGCATAGTTCCAAACTACTCTCCAAAATGATTGGATTCGTTCAC 956662 vv - v v i i i ? ii v iivi i C L1ME3G_3end#L 340 TTTAATAG-ATACTGCCAAATTGCCCTCCAAAANGGCTGTACCAATTTAC 292 chr1ptel1M 956663 AACTCCACCAACAATGCATCAATGTCCCAGTTTTCCCACATCCCCTGCAA 956712 vii i i i v iv v v i i i vv C L1ME3G_3end#L 291 ACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCACACCCTCGCCAA 242 chr1ptel1M 956713 CAATCATCATTATTTTTTCCTGTCATCTTAGCCAATCTGACATGTGTGTA 956762 v ?ivi ivv?iii vvv i v iiv viv C L1ME3G_3end#L 241 CACTNGATATTATCAANCTTTTAAATTTTTGCCAATCTGATGGGTGAAAA 192 chr1ptel1M 956763 GTGGTATCTCAGAGTTGTCTTAATTTGCATTTCTCTGATTAATAATGACT 956812 i vv i i v i vv C L1ME3G_3end#L 191 ATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGATTACTAGTGAGG 142 chr1ptel1M 956813 TGGAGCATCTTTTCATATGACTA--GAAAGTTTCGATTTCTTCATCTGAG 956860 v vi -- ivvi vv i v v C L1ME3G_3end#L 141 TTGAGCATCTTTTCATATGTTTATTGGCCATTTGTATTTCCTCTTCTGTG 92 chr1ptel1M 956861 AATTGTCTATTCATATCCTTTGACCATTTTTCAACTGGAGAATGGCTTGA 956910 i i v v i iv-- v -- C L1ME3G_3end#L 91 AATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGGGT--TGTCTT-- 46 chr1ptel1M 956911 TTTTTTATAAATTAGAATTAATTCTCTATATATTTTGGAAAT 956952 i vi v v vv i i i v C L1ME3G_3end#L 45 TTTCTTATTGATTTGTAGGAGTTCTTTATATATTCTGGATAT 4 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 36.20 CpG sites = 92, Kimura (unadjusted) = 36.75 Transitions / transversions = 1.10 (92/84) Gap_init rate = 0.03 (18 / 633), avg. gap size = 1.17 (21 / 18) 1489 28.23 1.10 2.03 chr1ptel1M 956404 956949 (43051) C L1ME3Cz_3end#LINE/L1 (450) 547 7 m_b26s551i3 924 chr1ptel1M 956404 TAATATTCCATAATATTCATATACCACAATTTATTCAGCCATTCTCCAAC 956453 i vi vv i v i v i C L1ME3Cz_3end# 547 TAGTATTCCATTGTATGAATATACCACAATTTATTTATCCATTCCCCTAT 498 chr1ptel1M 956454 TGATGGACATCCATTCAGTTTCCAGTTTCTAGCCACTACAAAAAGGGCTG 956503 ii vviv i i v i i v iv C L1ME3Cz_3end# 497 TGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCTG 448 chr1ptel1M 956504 CCACAAACATTCGTGCACATACAGGTCCCTTT---CCCTTCTTTATGA-T 956549 v ii i v i ---- i i --- v v v viiv - C L1ME3Cz_3end# 447 CAATGAACATCCTTGTACAT----GTCTCCTTGTGCACATGTGCGAGAGT 402 chr1ptel1M 956550 CTCTTTGGGATATAAGCCCAGTAGTAACACTGCTGGATCAAAGGGTACGC 956599 i i i i vi i v iiv i i iv i C L1ME3Cz_3end# 401 TTCTCTAGGGTATATACCTAGAAGTGGAATTGCTGGGTCGTAGGGTATGC 352 chr1ptel1M 956600 ACAGTTTGGTAACTTTATGAGCATAGTTCCAAACTACTCTCCAAAATGAT 956649 i vi --i iv - v v i i i i C L1ME3Cz_3end# 351 GCATCTT--CAACTTTACTAG-ATATTGCCAAATTGCTCTCCAAAGTGGT 305 chr1ptel1M 956650 TGGATTCGTTCACAACTCCACCAACAATGCATCAATGTCCCAGTTTTCCC 956699 v iivi i vii i i i v iv i v ii C L1ME3Cz_3end# 304 TGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTTCCCGTTTCTCC 255 chr1ptel1M 956700 ACATCCCCTGCAACAATCATCATTATTTTTTCCTGTCATCTTAGCCAATC 956749 i vv v iivi i ivvviii vvv i v C L1ME3Cz_3end# 254 ACATCCTCGCCAACACTTGGTATTGTCAGACTTTTAAATTTTTGCCAATC 205 chr1ptel1M 956750 TGACATGTGTGTAGTGGTATCTCAGAGTTGTCTTAATTTGCATTTCTCTG 956799 iiv v i vv ? i i C L1ME3Cz_3end# 204 TGATGGGTGTGAAATGGTATCTCATTGTNGTTTTAATTTGCATTTCCCTG 155 chr1ptel1M 956800 ATTAATAATGACTTGGAGCATCTTTTCATATGACTA--GAAAGTTTCGAT 956847 v i vv v vi -- ivvi iv i C L1ME3Cz_3end# 154 ATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTCGGGT 105 chr1ptel1M 956848 TTCTTCATCTGAGAATTGTCTATTCATATCCTTTGACCATTTTTCAACTG 956897 i v v i i v v i C L1ME3Cz_3end# 104 TTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTG 55 chr1ptel1M 956898 GAGAATGGCTTGATTTTTTATAAATTAGAATTAATTCTCTATATATTTTG 956947 iv-- v -- i vi v v vv i i i C L1ME3Cz_3end# 54 GGT--TGTCTT--TTTCTTATTGATTTGTAGGAGTTCTTTATATATTCTG 9 chr1ptel1M 956948 GA 956949 C L1ME3Cz_3end# 8 GA 7 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 35.04 CpG sites = 85, Kimura (unadjusted) = 36.26 Transitions / transversions = 1.29 (85/66) Gap_init rate = 0.03 (14 / 545), avg. gap size = 1.21 (17 / 14) 385 27.09 2.88 2.39 chr1ptel1M 956808 957015 (42985) C L1M4_orf2#LINE/L1 (0) 3294 3086 m_b26s551i4 924 chr1ptel1M 956808 TGACTTGGAGCATCTTTTCATATGACTA--GAAAGTTTCGATTTCTTCAT 956855 iv v i vi -- ivvi vv v v C L1M4_orf2#LIN 3294 TGATGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGTATATCTTCTT 3245 chr1ptel1M 956856 CTGAGAATTGTCTATTCATATCCTTTGACCATTTTTCAACTGGAGAATGG 956905 iv v v v ? i ivv -- C L1M4_orf2#LIN 3244 TGGAGAAATGTCTATTCAAATCCTTTGCCCATTTTTNAATTGGGTTAT-- 3197 chr1ptel1M 956906 CTTGATTTTTTA----TAAATTAGAATTAATTCTCTATATATTTTGGAAA 956951 - vi ---- i i iv -v i i i v C L1M4_orf2#LIN 3196 -TTGTCTTTTTATTGTTGAGTTGTAA-GAGTTCTTTATATATTCTGGATA 3149 chr1ptel1M 956952 TGAGGCCTTTATCAGAACCTTTAACTGTAAAAATATTTTCCCAGTTTATG 957001 i? v i vviv v vi i v v i v i i C L1M4_orf2#LIN 3148 CNAGTCCCTTATCAGATATATGATTTGCAAATATTTTCTCCCATTCTGTG 3099 chr1ptel1M 957002 AGCATTTTTTTTCA 957015 i i- v i C L1M4_orf2#LIN 3098 GGT-TGTCTTTTCA 3086 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 34.30 CpG sites = 26, Kimura (unadjusted) = 34.30 Transitions / transversions = 0.90 (26/29) Gap_init rate = 0.03 (7 / 207), avg. gap size = 1.57 (11 / 7) 21 21.76 0.00 0.00 chr1ptel1M 957420 957462 (42538) (T)n#Simple_repeat 1 43 (0) m_b26s252i10 925 chr1ptel1M 957420 TTTTTTTGTTTGTTTTCTTTTTCTCTCTTTTTTTTTCATTTTT 957462 v v i i i i iv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 43 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 183 20.00 0.00 0.00 chr1ptel1M 961798 961832 (38168) C L2c_3end#LINE/L2 (18) 460 426 m_b26s601i7 926 chr1ptel1M 961798 CATTTATAGAGCACCGACTGTGTGCCAGCTCCTGG 961832 v i v i viv C L2c_3end#LINE 460 CATTTATTGAGCGCCTACTATGTGCCAGGCGCTGG 426 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 16.58 CpG sites = 3, Kimura (unadjusted) = 23.31 Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 236 32.17 8.73 3.79 chr1ptel1M 963936 964061 (35939) C MIRb#SINE/MIR (23) 245 114 m_b27s601i2 927 chr1ptel1M 963936 AGGGTCTCCTGTCCATCAGGAACACAGATACTGAGCATGTGACGGTGACG 963985 v ii v i viii -- v - i i iiv v ivvv iv C MIRb#SINE/MIR 245 AGCGCTTACTATGTGCCAGG--CACTG-TGCTAAGCGCTTTACATGCATT 199 chr1ptel1M 963986 ATCTCGCCGGATCCTCCCAACCACCCC-TGA----------ATGATGCCC 964024 iiivi v v i-i ---------- v v C MIRb#SINE/MIR 198 ATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATTATCCCC 149 chr1ptel1M 964025 ATTTTACAGCTGAGGAAACAGAGGCCAGCAGGGGAGT 964061 v v i-- i ii C MIRb#SINE/MIR 148 ATTTTACAGATGAGGAAACTGAGGCT--CAGAGAGGT 114 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.41 CpG sites = 22, Kimura (unadjusted) = 43.32 Transitions / transversions = 1.29 (22/17) Gap_init rate = 0.06 (7 / 125), avg. gap size = 2.29 (16 / 7) 185 22.22 0.00 0.00 chr1ptel1M 964022 964066 (35934) C MIR3#SINE/MIR (63) 145 101 m_b27s601i3 927 chr1ptel1M 964022 CCCATTTTACAGCTGAGGAAACAGAGGCCAGCAGGGGAGTAGGGA 964066 i v v viv i v v v C MIR3#SINE/MIR 145 CTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGA 101 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.36 CpG sites = 3, Kimura (unadjusted) = 26.36 Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 22 0.00 0.00 0.00 chr1ptel1M 964525 964548 (35452) (A)n#Simple_repeat 1 24 (0) m_b27s252i0 928 chr1ptel1M 964525 AAAAAAAAAAAAAAAAAAAAAAAA 964548 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAA 24 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 17 23.79 3.28 1.61 chr1ptel1M 964634 964694 (35306) (TTAT)n#Simple_repeat 1 62 (0) m_b27s252i1 929 chr1ptel1M 964634 TTAATT-TTTATTTTCTTTTTTACTTAAAAATGCTGTTT-TTCATCTATT 964681 v - vi v i vvv -i i - i i (TTAT)n#Simpl 1 TTATTTATTTATTTATTTATTTATTTATTTAT-TTATTTATTTATTTATT 49 chr1ptel1M 964682 TATTTATTTATTT 964694 (TTAT)n#Simpl 50 TATTTATTTATTT 62 Matrix = Unknown Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.05 (3 / 60), avg. gap size = 1.00 (3 / 3) 244 31.34 1.75 2.96 chr1ptel1M 965015 965185 (34815) C L1ME3G_3end#LINE/L1 (272) 652 484 m_b27s551i0 930 chr1ptel1M 965015 CTGTGTATAACATTCTCCTGGTTCCGCTTATTTCACTCAGCGTCAAGCCG 965064 iii v i v viv -- v i ivi v i v C L1ME3G_3end#L 652 CTGTACGTATCGTTCTGCAACTT--GCTTTTTTCACTCAACAATATGTCT 605 chr1ptel1M 965065 TGTAAATCTTTCCAGGCCTTTCTACA-ATCAGTTTGT-TAATCATTTTTC 965112 v i v -- ivv - vii i ii- v iv v C L1ME3G_3end#L 604 TGGAGATCTTTCCATG--TCAGTACATATAGATCTACCTCATTCTTTTTA 557 chr1ptel1M 965113 ACAG-AACAGTAATATTCCATTACTTTCATCTACTATAATTTCTTTGGCC 965161 ? -vi - i viiv vv v i v ii C L1ME3G_3end#L 556 ACNGCTGCA-TAGTATTCCATAGTATGGATATACCATAATTTATTTAACC 508 chr1ptel1M 965162 ATTCCCCAACTGATGGGCATCCAG 965185 v i i ii C L1ME3G_3end#L 507 ATTCCCCTATTGATGGACATTTAG 484 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 39.57 CpG sites = 28, Kimura (unadjusted) = 41.76 Transitions / transversions = 1.17 (28/24) Gap_init rate = 0.05 (8 / 170), avg. gap size = 1.00 (8 / 8) 272 26.96 18.40 2.07 chr1ptel1M 965253 965377 (34623) MIRb#SINE/MIR 3 147 (121) m_b27s601i4 931 chr1ptel1M 965253 GAAGGGCAGCTAGATGGCACAGTGGATAAAGCACCAGCCCTCAAGT---- 965298 i ---i ii v i vi ii vi ---- MIRb#SINE/MIR 3 GAGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGA 49 chr1ptel1M 965299 CAAATCTGGTCTCAGA---CA--TTTAATACTTC----CTGTGTGACCCT 965339 i i vi ii --- i-- i ivi v---- i MIRb#SINE/MIR 50 CAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTT 99 chr1ptel1M 965340 GGGCAAGTCACTAAA----------CCCCAATTGCCTCATCAAAAAAA 965377 i v ---------- i i v viv MIRb#SINE/MIR 100 GGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAA 147 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.26 CpG sites = 23, Kimura (unadjusted) = 35.19 Transitions / transversions = 2.30 (23/10) Gap_init rate = 0.06 (8 / 124), avg. gap size = 3.25 (26 / 8) 19 24.15 2.30 5.95 chr1ptel1M 966046 966132 (33868) (ATAATAA)n#Simple_repeat 1 84 (0) m_b27s252i2 932 chr1ptel1M 966046 ATAAAATAATAATAAATAATAAATAAATAATAA-AATTCTTAAA-AAGAA 966093 v - vv - v vv - v (ATAATAA)n#Si 1 ATAATA-AATAATAAATAATAAATAATAAATAATAAATAATAAATAATAA 49 chr1ptel1M 966094 CAAAATATGATCTATGTATGATAAATTCATACATATTAA 966132 - v -i -v iv i - v v v (ATAATAA)n#Si 50 -ATAATA-AAT-AATAAATAATAAA-TAATAAATAATAA 84 Matrix = Unknown Transitions / transversions = 0.23 (3/13) Gap_init rate = 0.08 (7 / 86), avg. gap size = 1.00 (7 / 7) 454 24.38 4.76 2.33 chr1ptel1M 966570 966695 (33305) MIRb#SINE/MIR 2 130 (138) m_b27s601i5 933 chr1ptel1M 966570 AGAAGGGCAGCTAGGTGGCGCAGTGGGTAGAGCACCAGCCCTGAAGTCAG 966619 i --- i iv vi ii i MIRb#SINE/MIR 2 AGAGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAG 48 chr1ptel1M 966620 TCAAAACTGCTCTCAGACACC-----TAACACTTTCTAGATGTGTGACCC 966664 v i v vvi ii iv ----- iv v v i MIRb#SINE/MIR 49 ACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCT 98 chr1ptel1M 966665 TGGGCAAATCACTTAACCCCAAT-TGCCTCAG 966695 i i i vv -v MIRb#SINE/MIR 99 TGGGCAAGTTACTTAACCTCTCTGAGCCTCAG 130 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.84 CpG sites = 17, Kimura (unadjusted) = 30.01 Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.04 (5 / 125), avg. gap size = 1.80 (9 / 5) 294 39.49 0.85 0.85 chr1ptel1M 966910 967144 (32856) L1ME4a_3end#LINE/L1 244 478 (393) m_b27s551i1 934 chr1ptel1M 966910 TGTTGGAG-GGATATGGGAAATCTGGGACACTAATGTACTGTTGGCAGAG 966958 v - i i ?i v v v v v ii i ii ii L1ME4a_3end#L 244 TGTTGGCGAGGGTGTGGNGAAACGGGCACTCTCATACACTGCTGGTGGGA 293 chr1ptel1M 966959 CTATGGGCGGATTCAGCCATTCTAGAGGGCGATTTGTAGCTATGT-CCAA 967007 v i iiiiv i v i v i i vviv -i L1ME4a_3end#L 294 GTGTAAATTGGTACAACCTTTCTGGAGGGCAATTTGGCAATATGTATCAA 343 chr1ptel1M 967008 AGGGCTCGAATTCACCCGTACCCTTTGCTCCAGCAACACCAGTAGAAGAT 967057 i v ii vviii? i vi i iv v vvv iv L1ME4a_3end#L 344 AAGCCTTAAAAATGTNCATACCCTTTGACCCAGTAATTCCACTTCTAGGA 393 chr1ptel1M 967058 CTGTCTCCCAAAAAGATAAAAAACAAGAGGGAAAAGGAACTATATGTACA 967107 v v v i ii i vv ivi viv ? v i -- v L1ME4a_3end#L 394 ATTTATCCTAAGGAAATAATCAGAGATGTGNACAAAGA--TTTATGTACA 441 chr1ptel1M 967108 AAACCATTTCTAACAGCTCTTTTTGGGGTGGCAAAGA 967144 iivii iv vi vi v ivii i i i L1ME4a_3end#L 442 AGGATGTTCATCGCAGCATTATTTATAATAGCGAAAA 478 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 58.05 CpG sites = 53, Kimura (unadjusted) = 60.13 Transitions / transversions = 1.36 (53/39) Gap_init rate = 0.02 (4 / 234), avg. gap size = 1.00 (4 / 4) 295 23.86 4.49 1.09 chr1ptel1M 970522 970610 (29390) MIR3#SINE/MIR 15 106 (102) m_b27s601i6 935 chr1ptel1M 970522 GAGCAGCGAGAG-GTGCAGTGG-AGTCAGGAGGACCCGAGTTCAAATCT- 970568 v -ii v v - - i i v i i- MIR3#SINE/MIR 15 GAGCAGAGAGAGCACGGACTGGGAGTCAGGAG-ACCTGGGTTCTAGTCCC 63 chr1ptel1M 970569 -GCTCTCAAAACACTCCTCTGTGTGATCCTGGGCAAGTCACTT 970610 - vvv vi vii?v i i MIR3#SINE/MIR 64 GGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTT 106 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.85 CpG sites = 11, Kimura (unadjusted) = 29.46 Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.06 (5 / 88), avg. gap size = 1.00 (5 / 5) 251 22.22 5.81 5.81 chr1ptel1M 970540 970625 (29375) MIR#SINE/MIR 34 119 (143) m_b27s601i8 935 chr1ptel1M 970540 TGGAGTCAGGAGGACCCGAGTTCAAATCT--GCTCTCAAAACACTC-CT- 970585 i - vvi i i i i-- ---iv i- - MIR#SINE/MIR 34 TGGAGCCAG-ACTGCCTGGGTTCGAATCCCGGCTCT---GCCACTTACTA 79 chr1ptel1M 970586 -CTGTGTGATCCTGGGCAAGTCACTTAAGCCCAACTGTGTC 970625 - i i i - ivv i MIR#SINE/MIR 80 GCTGTGTGACCTTGGGCAAGTTACTTAA-CCTCTCTGTGCC 119 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 25.65 CpG sites = 13, Kimura (unadjusted) = 27.42 Transitions / transversions = 2.60 (13/5) Gap_init rate = 0.11 (9 / 85), avg. gap size = 1.11 (10 / 9) 327 15.70 6.85 4.00 chr1ptel1M 970540 970612 (29388) MIRc#SINE/MIR 37 111 (157) m_b27s601i7 935 chr1ptel1M 970540 TGGAGTCAGGAGGACCCGAGTTCAAATCT--GCTCTCAAAACACTC-CT- 970585 i i i i i i-- ---iv i- - MIRc#SINE/MIR 37 TGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCT---GCCACTTACTA 83 chr1ptel1M 970586 -CTGTGTGATCCTGGGCAAGTCACTTAA 970612 - i i MIRc#SINE/MIR 84 GCTGTGTGACCTTGGGCAAGTCACTTAA 111 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 16.75 CpG sites = 10, Kimura (unadjusted) = 18.56 Transitions / transversions = 10.00 (10/1) Gap_init rate = 0.10 (7 / 72), avg. gap size = 1.14 (8 / 7) 15 26.21 0.00 6.85 chr1ptel1M 972047 972115 (27885) (CCCCGG)n#Simple_repeat 1 64 (9) m_b27s252i3 936 chr1ptel1M 972047 CCCCAACCCCTGCTCCGGCCCCTGCCCTGAGGCCCGCGGGCCCCTCCCCA 972096 ii v i v --v - v vv i (CCCCGG)n#Sim 1 CCCCGGCCCCGGCCCCGGCCCCGGCCC--CGGCCC-CGGCCCCGGCCCCG 47 chr1ptel1M 972097 GCCCAAGGGCCCAGCACCA 972115 -v v i - v (CCCCGG)n#Sim 48 GCCC-CGGCCCCGGC-CCC 64 Matrix = Unknown Transitions / transversions = 0.56 (5/9) Gap_init rate = 0.07 (5 / 68), avg. gap size = 1.00 (5 / 5) 50 2.03 0.00 0.00 chr1ptel1M 972116 972165 (27835) (C)n#Simple_repeat 1 50 (0) c_b27s251i0 937 chr1ptel1M 972116 CCCCCCCCCCCGCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 972165 v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 50 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 18 0.00 0.00 0.00 chr1ptel1M 972881 972900 (27100) (C)n#Simple_repeat 1 20 (0) m_b27s252i4 938 chr1ptel1M 972881 CCCCCCCCCCCCCCCCCCCC 972900 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCC 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 37 0.00 0.00 0.00 chr1ptel1M 974823 974856 (25144) (C)n#Simple_repeat 1 34 (0) c_b27s251i1 939 chr1ptel1M 974823 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 974856 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 34 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 274 34.02 9.15 0.65 chr1ptel1M 976331 976472 (23528) C MIRb#SINE/MIR (69) 199 46 m_b27s601i9 940 chr1ptel1M 976331 TGTCTCTCTGGATCCCCTCAATGGCCC--CGAGAAGGGTGAT----TCCC 976374 i vi vi i v iii -- ivi iv ---- C MIRb#SINE/MIR 199 TATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATTATCCC 150 chr1ptel1M 976375 TGTGCTTACAGTGGAGGAAGCCAAGGCACACGAAGGCCAGGCGGCCTGCC 976424 ii -i vv i ii v vii ii i iii i C MIRb#SINE/MIR 149 CAT-TTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCC 101 chr1ptel1M 976425 C---GTGTCACAGCT----TGTGTCTGAAGCTGGATCTGAGCTCTGGTCT 976467 --- vv ----v v v iv v ii i i v C MIRb#SINE/MIR 100 CAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCT 51 chr1ptel1M 976468 GGCTG 976472 v C MIRb#SINE/MIR 50 GTCTG 46 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.24 CpG sites = 30, Kimura (unadjusted) = 47.65 Transitions / transversions = 1.67 (30/18) Gap_init rate = 0.04 (5 / 141), avg. gap size = 2.80 (14 / 5) 18 0.00 0.00 3.85 chr1ptel1M 977066 977092 (22908) (CGGTC)n#Simple_repeat 1 26 (0) m_b27s252i5 941 chr1ptel1M 977066 CGGTCCGGTCCGGTCCGGTCCGGATCC 977092 - (CGGTC)n#Simp 1 CGGTCCGGTCCGGTCCGGTCCGG-TCC 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.04 (1 / 26), avg. gap size = 1.00 (1 / 1) 80 27.30 1.80 5.59 chr1ptel1M 978027 978360 (21640) (GGGGGA)n#Simple_repeat 1 322 (0) m_b27s252i6 942 chr1ptel1M 978027 GGGGGAGGGGGGAGGATAGAGGGGGA-GGGGAGGGGGAGAAGGGAGGAGG 978075 - -vi - -i - (GGGGGA)n#Sim 1 GGGGGA-GGGGGAGG-GGGAGGGGGAGGGGGAGGGGGAG-GGGGAGG-GG 46 chr1ptel1M 978076 AAGGAGAAGAGGAAGGGAAGGAGGGGGAGGGAGGA-ATGGA-GGAGAAGG 978123 i i i i i -- - -iv - i i (GGGGGA)n#Sim 47 GAGGGGGAGGGGGAGGG--GGAGGGGGAGGG-GGAGGGGGAGGGGGAGGG 93 chr1ptel1M 978124 GGAGAGGGA-GGGGAGGGGGAGAAAGGGGAGGGGGAAAAGGGGAAAAGGA 978172 i - --- --- i ii i (GGGGGA)n#Sim 94 GGAGGGGGAGGGGGAGGGGGAG---GGGGAGGGGG---AGGGGGAGGGGG 137 chr1ptel1M 978173 AAGAGGGGAGGAAGGGGGA-AAAGAGGAGGAAGGGGGGAGAGGAAAGGGA 978221 i i i i i -iii - i ii i ii (GGGGGA)n#Sim 138 AGGGGGAGGGGGAGGGGGAGGGGGAGG-GGGAGGGGGAGGGGGAGGGGGA 186 chr1ptel1M 978222 AGGACATGGGAAGGGAGAGGGGTTTGGGGAGAGGAAGAGGAAGGAAAAAG 978271 i iv v i i vvv i i i i -iii (GGGGGA)n#Sim 187 GGGGGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGGAGG-GGGAG 235 chr1ptel1M 978272 TGGGAGAGGGAGGAAG-GGGGAATGGGGAGGAGGGGGGACAAGGAGAGGG 978320 v i ii - i v i i iv i i (GGGGGA)n#Sim 236 GGGGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGGAGGG 285 chr1ptel1M 978321 AGAGGAGGCAGGGGAAGATGGGAAGGGGAAGGGACAGGGG 978360 i - v -- v i i iv (GGGGGA)n#Sim 286 GGAGG-GGGAGGGG--GAGGGGGAGGGGGAGGGGGAGGGG 322 Matrix = Unknown Transitions / transversions = 4.08 (53/13) Gap_init rate = 0.07 (24 / 333), avg. gap size = 1.00 (24 / 24) 12 15.74 2.56 5.26 chr1ptel1M 978915 978953 (21047) (GGGTTTT)n#Simple_repeat 1 38 (0) m_b27s252i7 943 chr1ptel1M 978915 GGGTTTACTGGGCGTTGGG-TTTGGGTTTTGTGTGCTGGG 978953 -- iv - v vi (GGGTTTT)n#Si 1 GGGTTT--TGGGTTTTGGGTTTTGGGTTTTGGGTTTTGGG 38 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.08 (3 / 38), avg. gap size = 1.00 (3 / 3) 51 1.99 0.00 0.00 chr1ptel1M 982973 983023 (16977) (C)n#Simple_repeat 1 51 (0) c_b27s251i2 944 chr1ptel1M 982973 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCGCCCCCCCCCCCCCCCCCCC 983022 v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 50 chr1ptel1M 983023 C 983023 (C)n#Simple_r 51 C 51 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 12 16.57 0.00 0.00 chr1ptel1M 983060 983086 (16914) (CCTCC)n#Simple_repeat 1 27 (0) m_b27s252i8 945 chr1ptel1M 983060 CCTCCTCTGCCTGCCCCTCCCCTCCCC 983086 i v iv (CCTCC)n#Simp 1 CCTCCCCTCCCCTCCCCTCCCCTCCCC 27 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 14 21.84 0.00 0.00 chr1ptel1M 984743 984779 (15221) (TCCCCC)n#Simple_repeat 1 37 (0) m_b27s252i9 946 chr1ptel1M 984743 TCTCCCTCCCCCCACCTCGGCCCCTGCCCCTCCCCCT 984779 i iv i vv v (TCCCCC)n#Sim 1 TCCCCCTCCCCCTCCCCCTCCCCCTCCCCCTCCCCCT 37 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 13 20.98 5.77 1.85 chr1ptel1M 984754 984805 (15195) (CCCCCTG)n#Simple_repeat 1 54 (0) m_b27s252i10 946 chr1ptel1M 984754 CCACCTCGGCCCCTG-CCCCT-CCCCCTG-GGAGGGCCCCCTGGCCCCTG 984800 v - v - - -vvvvv v (CCCCCTG)n#Si 1 CCCCCT-GCCCCCTGCCCCCTGCCCCCTGCCCCCTGCCCCCTGCCCCCTG 49 chr1ptel1M 984801 ACCCC 984805 v (CCCCCTG)n#Si 50 CCCCC 54 Matrix = Unknown Transitions / transversions = 0.00 (0/9) Gap_init rate = 0.08 (4 / 51), avg. gap size = 1.00 (4 / 4) 12 25.52 0.00 0.00 chr1ptel1M 986087 986123 (13877) (TCCC)n#Simple_repeat 1 37 (0) m_b27s252i11 947 chr1ptel1M 986087 TCCTTCCCTCCCCCCATCCCACCCCCGCTGGCTCCCT 986123 i i v v i v vv (TCCC)n#Simpl 1 TCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCT 37 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 296 26.67 3.33 0.00 chr1ptel1M 991157 991246 (8754) L1MD1_3end#LINE/L1 435 527 (462) m_b27s551i2 948 chr1ptel1M 991157 TACACCGGTGTTTCTAGCCGTCTTTCTTGTTGTAATACAGATCTG-AAAC 991205 vii v v ii vi i vi iivv i v - L1MD1_3end#LI 435 TACACGAATGTTTATAGCAGCTTTATTCGTAATAGCCAAAAACTGGAAAC 484 chr1ptel1M 991206 AAC--AGATGCCCTTCAACGGGGGAGTGGCTGAACAAACTCTG 991246 -- i v i i i v L1MD1_3end#LI 485 AACCCAGATGTCCTTCAACGGGTGAATGGTTAAACAAACTGTG 527 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 32.01 CpG sites = 14, Kimura (unadjusted) = 33.71 Transitions / transversions = 1.40 (14/10) Gap_init rate = 0.02 (2 / 89), avg. gap size = 1.50 (3 / 2) 311 31.85 5.49 2.37 chr1ptel1M 991482 991645 (8355) MIRb#SINE/MIR 86 254 (14) m_b27s601i10 949 chr1ptel1M 991482 AGCAGTGTGACCT-GGGCAGGGAACTCCACTT------GACTCAGTTTCC 991524 v - i vv iv i ------ v MIRb#SINE/MIR 86 AGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCC 135 chr1ptel1M 991525 TCAGGGGCAAA-CGGAGAAGAGAGCAGCCCTGCCCTCCCAGGAATCTTAG 991573 vvv i -i i vi v ii -- i - v iv v iv MIRb#SINE/MIR 136 TCATCTGTAAAATGGGGATAATAATA--CCTACC-TCGCAGGGTTGTTGT 182 chr1ptel1M 991574 GAGAGTCAAACACCATGGTGGCTGTAAAGTCCTGTGCACAGAGCCGGGTA 991623 ii i iivv ii vv iv vv v v i MIRb#SINE/MIR 183 GAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCA 232 chr1ptel1M 991624 CCACAG-AAGTCCAGCATGAATG 991645 - i - iv vvv i MIRb#SINE/MIR 233 -CATAGTAAGCGCTCAATAAATG 254 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.85 CpG sites = 24, Kimura (unadjusted) = 41.92 Transitions / transversions = 0.89 (24/27) Gap_init rate = 0.05 (8 / 163), avg. gap size = 1.62 (13 / 8) 13 6.51 8.82 2.78 chr1ptel1M 994870 994903 (5097) (GCTCCCC)n#Simple_repeat 1 36 (0) m_b27s252i12 950 chr1ptel1M 994870 GCCCCCCGGCTCCCCGCT-CCCGC-CGCCG-TCCCCG 994903 i - - - v - (GCTCCCC)n#Si 1 GCTCCCC-GCTCCCCGCTCCCCGCTCCCCGCTCCCCG 36 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.12 (4 / 33), avg. gap size = 1.00 (4 / 4) 15 16.94 0.00 0.00 chr1ptel1M 994944 994976 (5024) (CCGCTT)n#Simple_repeat 1 33 (0) m_b27s252i13 951 chr1ptel1M 994944 CCGGTTCCGCTTCCGGCACTGCTTCCGCTTCCG 994976 v viv i (CCGCTT)n#Sim 1 CCGCTTCCGCTTCCGCTTCCGCTTCCGCTTCCG 33 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 22 10.01 0.00 0.00 chr1ptel1M 996370 996401 (3599) (G)n#Simple_repeat 1 32 (0) m_b27s252i14 952 chr1ptel1M 996370 GGGGGGGGGGGGGGGGGGGGGGGGACGGGCGG 996401 iv v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 32 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 317 35.86 3.21 1.58 chr1ptel1M 996819 997005 (2995) L1ME5_3end#LINE/L1 363 552 (389) m_b27s551i3 953 chr1ptel1M 996819 CTGTGCCCCGGCAGTGCTTCTCCTGGGCTTATCCCCCAAGGAGGCCCTAA 996868 i v i i v iv iv vi i iiii v L1ME5_3end#LI 363 CTATGACCCAGCAATTCCGCTCCTGGGTATATATCCCAAAGAAATTCTCA 412 chr1ptel1M 996869 AGCGGG---GAAAGGGACCCACGTGGGCAAGAAGGTTTGGGGCAGCCCTG 996915 vi i ---iv i--- i vi i i v iivv vi L1ME5_3end#LI 413 CACAGGTCCATAAGGGG---ACATGTACGAGGATGTTCATTGCAGCGTTG 459 chr1ptel1M 996916 CTCGTAGTGGCCAGAAGCTGGAAAGTGCATGGATGCCCATCAGCGGGACG 996965 i i i vi i i iivvi v i i vi vi L1ME5_3end#LI 460 TTTGTGGTGGCGGGGAGTTGGAGGCAACCTGGGTGTCCATCACTGGGAGA 509 chr1ptel1M 996966 --GGCTGAGTGAATTGTGGTACAT-CACGTTATGGAGTGTTAT 997005 -- v ii i v iv - iii ii L1ME5_3end#LI 510 GTGGATAGGTAAAATGTGGTGGATGCACACCATGGAGTACTAT 552 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 50.00 CpG sites = 44, Kimura (unadjusted) = 52.38 Transitions / transversions = 2.00 (44/22) Gap_init rate = 0.03 (6 / 186), avg. gap size = 1.50 (9 / 6) 328 30.00 2.50 0.00 chr1ptel1M 996886 997005 (2995) L1ME3A_3end#LINE/L1 430 552 (368) m_b27s551i4 953 chr1ptel1M 996886 ACGTGGGCAAGAAGGTTTGGGGCAGCCCTGCTCGTAGTGGCCAGAAGCTG 996935 i vi v iivi v ii i i ?? i L1ME3A_3end#L 430 ACATGTACAAGAATGTTCATAGCAGCACTATTCGTAATAGCCNNAAACTG 479 chr1ptel1M 996936 GAAAGTGCATGGATGCCCATCAGCGG--GACGGGCTGAGTGAATTGTGGT 996983 v?i viii i i i -- vv v i i i L1ME3A_3end#L 480 GAAACNACCCAAATGTCCATCAACAGTAGAATGGATAAATAAATTGTGGT 529 chr1ptel1M 996984 ACA-TCACGTTATGGAGTGTTAT 997005 i - iiv i ii L1ME3A_3end#L 530 ATATTCACACAATGGAATACTAT 552 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 42.43 CpG sites = 26, Kimura (unadjusted) = 42.43 Transitions / transversions = 2.60 (26/10) Gap_init rate = 0.02 (2 / 119), avg. gap size = 1.50 (3 / 2) 293 31.86 2.65 0.00 chr1ptel1M 996907 997019 (2981) L1MC5_3end#LINE/L1 451 566 (2128) m_b27s551i5 953 chr1ptel1M 996907 GCAGCCCTGCTCGTAGTGGCCAGAAGCTGGAAAGTGCATGGATGCCCATC 996956 v ii i i i v i ii vvi viii i L1MC5_3end#LI 451 GCAGCACTATTTGTAATAGCAAAAGACTGGAAACAACCCAAATGTCCATC 500 chr1ptel1M 996957 AGC--GGGACGGGCTGAGTGAATTGTGGTACAT-CACGTTATGGAGTGTT 997003 ii-- v i i i i i - iiv ii L1MC5_3end#LI 501 AATAGGGGACTGGTTGAATAAACTATGGTACATCCACACAATGGAGTACT 550 chr1ptel1M 997004 ATTGTTCTGTAACAAG 997019 vvvv v L1MC5_3end#LI 551 ATGCAGCTGTAAAAAG 566 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 43.82 CpG sites = 24, Kimura (unadjusted) = 43.82 Transitions / transversions = 2.00 (24/12) Gap_init rate = 0.02 (2 / 112), avg. gap size = 1.50 (3 / 2) 356 20.44 11.90 2.92 chr1ptel1M 997533 997658 (2342) C MER63D#DNA/hAT-Tip100 (588) 473 337 m_b27s502i0 954 chr1ptel1M 997533 GACATGTAACACTTTTAAGCTTAATCTGCACTGGATTAATGGATTTTCTC 997582 i vv i i -- i-- C MER63D#DNA/hA 473 GACACGACACACTTTTAAGTTTAATCTGCATT--ATTAAC--ATTTTCTC 428 chr1ptel1M 997583 CATC---CTGTTAAGTCTAGGCCATC-----------AAAGTAAGCCTTG 997618 ---i v i v ----------- vi i C MER63D#DNA/hA 427 CATCACTTTCTTAAGTCTAGACAATCAACAAAACAATAAATCAAGCCCTG 378 chr1ptel1M 997619 ATTTAAAGCATTTGCTGATTTTTA-AGTGTTAGTGCTCACA 997658 iv i i iii-i v i i v C MER63D#DNA/hA 377 ATTTGTAGCGTTTGCCGATTTCCGTGGTGTAAATACTCCCA 337 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 20.19 CpG sites = 17, Kimura (unadjusted) = 24.61 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.06 (7 / 125), avg. gap size = 2.71 (19 / 7) 650 35.20 3.63 2.83 chr1ptel1M 997687 998072 (1928) MamRTE1#LINE/RTE-BovB 883 1271 (2541) m_b27s601i11 955 chr1ptel1M 997687 GCCATGCCGCTGTCATCGGTACCTAGGCTCCCACCATGACAAA--CCCAT 997734 i? i i i ii v v i i -- v MamRTE1#LINE/ 883 GCTNTGCCACCGTCATCAGCGCATATGCCCCCACCATGACGAATACCGAT 932 chr1ptel1M 997735 GAAGTCAAAGAAAGATTCCATGAAGACCTGGAGAGCCTTATT--AACA-T 997781 i vv i ii i i v v i i-- i i- MamRTE1#LINE/ 933 GAGGAGAAAGAAAGATTCTACAAGGATCTGGACAGACTCATCGCAGCGGT 982 chr1ptel1M 997782 GCCAAGAA-GGACAAGCTTATTCT---GGGTGACTTTAATGCTAGAATAG 997827 i v v-v v iv --- v i i i vv vi v MamRTE1#LINE/ 983 ACCAACATCTGACAAGCTGATCGTCACGGGAGATTTCAACGCACGTGTCG 1032 chr1ptel1M 997828 GCTCAGACTACC-AGCCACGGCAGGGAGTCCTCTGGAGGAATGGAGCTGG 997876 vvv - i - iv ii viiii v v ivv?v i iii MamRTE1#LINE/ 1033 GCAGCGA-TGCCGAAACGTGGAGAAAAGTCATCGGACCNCACGGGATTGG 1081 chr1ptel1M 997877 AAATAGCAACAGCAGTGGGCATTTACAATTGAAGACTTGTGCATCTCATG 997926 vvv? i v vvi v vii v ivivv vvvv v MamRTE1#LINE/ 1082 AAAGCTNAACAGCAATGGTCTACTCCTGCTCAGCGAATGTGCCAAGCATC 1131 chr1ptel1M 997927 ACCTTCTCATCCACAACACTTTCTTTCATTTATCTAAATGCAATAAAACT 997976 v iv v vv iv i iii i v vviv iv i v MamRTE1#LINE/ 1132 AGCTCGTAATCACCAACACCATCTTCCGCCTACCGAATAAGAGAAAGACA 1181 chr1ptel1M 997977 TCACGGATGCACCC----TCGCAGCAAAGGTTGGCATTTAATCAACTATA 998022 i ---- vv i---- i v ii i MamRTE1#LINE/ 1182 TCATGGATGCACCCAAGGTCTAAGCAG----TGGCATCTCATTGATTATA 1227 chr1ptel1M 998023 TGATTGTAAGAGACAGAGAGGATGTGAGAGGAATCATGCAGAGTATTGTA 998072 v i --vv v - iv - --ii vi v i i MamRTE1#LINE/ 1228 TCATCGT--TCGACAGCG-GGACCTGA-AGGA--TGTTTAGATTACTGCA 1271 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.59 CpG sites = 66, Kimura (unadjusted) = 48.95 Transitions / transversions = 1.00 (66/66) Gap_init rate = 0.05 (18 / 385), avg. gap size = 1.39 (25 / 18) 545 40.09 5.47 3.66 chr1ptel1M 998319 999232 (768) MamRTE1#LINE/RTE-BovB 1560 2489 (1323) m_b27s601i12 955 chr1ptel1M 998319 CATCAAGAATGGTTTGATGAGAATGATGGGAAAAATCAGAAGCTGCTA-- 998366 i ii v ivvii i v v i v-- MamRTE1#LINE/ 1560 CACCAGAACTGGTTTGATGAGAATGACTCAGAGATTAAGAAGCTACTTGC 1609 chr1ptel1M 998367 AATGAAAAAAATAA---------AACA----AGAACTCCACAGGGTGT-G 998402 iii iv i? --------- ----iv i v v i vi- MamRTE1#LINE/ 1610 AGCAAAGCAAGNAATGCNTTGTCAACACCTTGCAGCTCCTCATGATCCAG 1659 chr1ptel1M 998403 CCGACAGAATAGTTCAACCAGCATTTCATCTCATCAAAGATAAAGTACCA 998452 v v ivv i i -- v viiii v i ---- i --- i vi MamRTE1#LINE/ 1660 ACGAAAGAGACGCTTA--CAGAAGCCTGTATCGT----GACA---TGCAG 1700 chr1ptel1M 998453 GTAAAGCTTAGAGACAC--AGGATTCTTGGCTCAGTTAGAAGGCAGATGA 998500 i v i v i i -- v iivv ivvii vvv v v MamRTE1#LINE/ 1701 ATCAAGTTAAGAAACGCGNATGACCAGTGGTGGGATGCCAAGGCTGAAGA 1750 chr1ptel1M 998501 AATTCAG--TTTTGTGG--TGATAACAATCCAAATCGTTTTTTATAATTC 998546 i i --i v ii --i ?i v v i-- vi i ivv? MamRTE1#LINE/ 1751 GATCCAGGACTATGCAGACCGNCACCAAACCAAG--GACTTCTATGCGNC 1798 chr1ptel1M 998547 ATTGAAGGCATTATATGGACCGAATACCTATGAT-ACATCTCAGCTACTC 998595 vi i iii ? - i viiiv - iv v v ivvv MamRTE1#LINE/ 1799 CCTAAAGATGTTATATGGNCC-AACACACGCCATCACGGCACCGCTGAGG 1847 chr1ptel1M 998596 AGTGCTGATGGAGCCACATTGAGTAGTGATAAGGACATGGTCTTGGAGAG 998645 ?v vv i vi v vi vv iii i vivii i ivi MamRTE1#LINE/ 1848 AGTGNAGATGGCTCCGCCCTCATCACAGACGGGAAGGGAATCCTACGGAG 1897 chr1ptel1M 998646 ATGGGTG-AACAATTCCATGGTGCTCTCAACA-GCCC---ATAATTACTA 998690 vv - v v i i vi ? - i--- iv iivvi MamRTE1#LINE/ 1898 ATGGCAGCAACACTTCAACGATCTTCTNAACACGCCTTCTACCATCGAGG 1947 chr1ptel1M 998691 CTGAAGT--TATTAACCATT---AACTT--CAAGATGAAATC-TGTTACT 998732 v -- iiv v i v--- i -- vi v-i? vi i MamRTE1#LINE/ 1948 ATGAAGTCCTGCGAAGCGTAGAGAACCTGCCAAGATGCGATAACNTGGCC 1997 chr1ptel1M 998733 TCCTAGCAGAAGTCACAACT---GAAGATGTTTTGAGTGCCATTAGACCT 998779 i -- ----- - --- v iv?v vi ii i v i MamRTE1#LINE/ 1998 TTC--GC-----TC-CAACTTTTGAAGAAGTCANCACCGCTGTCAGAGCC 2039 chr1ptel1M 998780 CTTTCATGTGACAAAGCACCAGCTGCTGAATCTATTCATGCTGAGATTTA 998829 v vvvivi ii v iv vvv vvvi v v v MamRTE1#LINE/ 2040 ATGAAGAATGGTAAAGCTCTCGGACCTGATGGCATACCTGCTGAGATTTT 2089 chr1ptel1M 998830 TAAA---GTGGGGGAGTCCATTGTTCAGACAAACCCGGACTGAAATTTTC 998876 i i--- vi -v ii i i i--i i v - iiiv MamRTE1#LINE/ 2090 CAAGCAGGAAGGGGAG-ACGCTGCTTAGACG--TCTGCA-TAGGCTTTTC 2135 chr1ptel1M 998877 CAAATTATGTGGCAAGAGGAGGTTATGCCCCAGGGGTTCCAGAGGATGCC 998926 ivv vi i vivivv vv v iv --i i MamRTE1#LINE/ 2136 TTCAGCATATGGAGTACCGAGGAAATGCCGCAGGATTTC--AAAGATGCC 2183 chr1ptel1M 998927 TCCATTGTC--CATCTCTAGAAAGGTAAAGG-AAATAGGTTGTCCTGTGA 998973 v i ii -- ii ii -- -i iv i i -v i i MamRTE1#LINE/ 2184 ACTATCATCACCATCTTCAAGAAG--AAAGGCGAGAAAGCTG-ACTGCGG 2230 chr1ptel1M 998974 CAGTCACAGGAAGGTCTCTC-ATTTATCATTGTTGGCAAAATTTTTGCCA 999022 iii iv viivi ? -ii ivi i i ii v MamRTE1#LINE/ 2231 CAACTATCGCGGCATCTCNCTGCTCTCCATTGCTGGCAAGATCCTGGCCA 2280 chr1ptel1M 999023 GAGTCATCCTCAATAGGCTGACCAAAC-ACCTGGAAAAAAGATCACCTAC 999071 v i vi v - ii - v v vv vv vv i i-- MamRTE1#LINE/ 2281 GAGTCCTTCTGGATCGGCT-ACTGAACAACATCGTCAACCGTGCGCT--C 2327 chr1ptel1M 999072 CTGAGAGC-CCATGTGGCTTCAGAAGGGGCTGAGGAACAGCCTATATGG- 999119 i ii v - v i ivv vivi v v ? vv ii i- MamRTE1#LINE/ 2328 CCGGAATCGCAATGTGGCTTTAGGCCGCAGCGCGGTANAGCGGACGTGAT 2377 chr1ptel1M 999120 -TTTATTGCCTGAAAACTCCAGGAGAAACTCCAGGAACAGAACAGAAATC 999168 - ii? v vv iv v i i v vi iv ivi i i MamRTE1#LINE/ 2378 CTTTGCNGCATGTCAGATACAGGAAAAGCGCAGGGAACAACATCAAGACC 2427 chr1ptel1M 999169 TGCCTATGACATGTATAGCTCTGACTGAGGATTTTGATATTGTCAGTGCT 999218 vivi ivii vi v vi v vi i vv iiiii i-- MamRTE1#LINE/ 2428 TCTGCACTGTATTCATCGACCTTACAAAAGCATTTGACGCCATCAGTA-- 2475 chr1ptel1M 999219 TGCCGGGATTCTGG 999232 vi v ii MamRTE1#LINE/ 2476 GACCTGGGCTCTGG 2489 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 54.64 CpG sites = 195, Kimura (unadjusted) = 61.09 Transitions / transversions = 1.23 (195/158) Gap_init rate = 0.06 (58 / 913), avg. gap size = 1.45 (84 / 58) 278 40.40 3.28 1.61 chr1ptel1M 999239 999482 (518) MamRTE1#LINE/RTE-BovB 2577 2824 (988) m_b27s601i13 955 chr1ptel1M 999239 GACAGTGCTCT---TGAGCTTTTCCCAGTCACCATTGGCGTGAAACAAGG 999285 i i ii ---i v iv vi v v i i i MamRTE1#LINE/ 2577 GACGGCGTCCTGTCCGACCCATTCCCCATCACCAATGGAGTGAAGCAGGA 2626 chr1ptel1M 999286 CCATGTGCTCTCTCCCATGCTTTTTAGCCTGATGTTTTTAGCCATG-TTG 999334 iiii iv vvv vi vi v i ii iv v v vi - i MamRTE1#LINE/ 2627 TTGCGTAATAGGTCCAGTCTTATTCAATCTATTTTATGCAGCCATGCTCG 2676 chr1ptel1M 999335 CAAACACTTTCAGGGAGGACAAACATGGTGTCAAGGTTAGATACC-ATAC 999383 vii ii vviv vvvvi vv iii vv v v -i v MamRTE1#LINE/ 2677 AGGATGCAACAAGGGACCTGGAAGCTGGTGTCAGAATACGCTTCCGGTCC 2726 chr1ptel1M 999384 TGAGGGTTAATTCTTCAACTTGAAAAGGCTGCAAGCCAGAACGAAAG--- 999430 vv -v i v vi v v i i vvv v --- MamRTE1#LINE/ 2727 TCTGGG-AAACTCTTCCAACTCAACAGGCTACGAGCATCATCGAAAGTCC 2775 chr1ptel1M 999431 TGGAAGGAGGGTCGGTGTGGGACTTTTTGTGTGCAGATGAATGTGTGCTC 999480 v -- vi -i vii vi vi i v v iv i MamRTE1#LINE/ 2776 TTGA--GACAGTC-ATCCAGGAACTGCTGTATGCCGATGACTGTGCTCTT 2822 chr1ptel1M 999481 AA 999482 i MamRTE1#LINE/ 2823 GA 2824 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 53.96 CpG sites = 47, Kimura (unadjusted) = 59.29 Transitions / transversions = 0.94 (47/50) Gap_init rate = 0.03 (8 / 243), avg. gap size = 1.50 (12 / 8) 19 0.00 0.00 0.00 chr1ptel1M 999670 999690 (310) (CA)n#Simple_repeat 1 21 (0) m_b27s252i15 956 chr1ptel1M 999670 CACACACACACACACACACAC 999690 (CA)n#Simple_ 1 CACACACACACACACACACAC 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 186 22.30 2.30 7.23 chr1qtel1M 48 134 (999866) MIR1_Amn#SINE/MIR 28 110 (120) m_b28s601i0 957 chr1qtel1M 48 GAGCA-TGGCCCGAGGC-CGGGAGCGCTTGGTCCCACTCTGACCTCAGAC 95 - v i i i - vv v i ? ? iviv v -- MIR1_Amn#SINE 28 GAGCACTGGACTGGGACTCGGGAGACCTGGGTTCNANTCCCGGCTCTG-- 75 chr1qtel1M 96 ACGCCCACTTAGCAGCTGGGTGGCCCTGGGCGAGTCACT 134 ---- ?iv ? ? i i i MIR1_Amn#SINE 76 ----CCACTNGCCNGCTGNGTGACCTTGGGCAAGTCACT 110 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 27.05 CpG sites = 10, Kimura (unadjusted) = 28.89 Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.09 (8 / 86), avg. gap size = 1.00 (8 / 8) 465 19.71 7.64 8.39 chr1qtel1M 833 976 (999024) MIRc#SINE/MIR 2 144 (124) m_b28s601i1 958 chr1qtel1M 833 GGGGCAGCAAGGTG--ATGTAACAGAGCATTGGGCCTGAAATTAGGAAGG 880 i iiv --i v - i i i i i i i MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAA-AGAGCACTGGACTTGGAGTCAGGAAGA 50 chr1qtel1M 881 --TGAGTTCAATAAGTGAGTGACCTCAGAACTGC-----AGTAGCTGTGT 923 -- i ------- --- i i vv ----- v MIRc#SINE/MIR 51 CCTGGGTTC-------GAGT---CCCGGCTCTGCCACTTACTAGCTGTGT 90 chr1qtel1M 924 GAACCTGGGCTAATCACTTAACCCCGTTT--GCCTCAGTTTCCTCATCTG 971 v i v i i - i -- MIRc#SINE/MIR 91 GACCTTGGGCAAGTCACTTAACCTC-TCTGAGCCTCAGTTTCCTCATCTG 139 chr1qtel1M 972 TTAAA 976 v MIRc#SINE/MIR 140 TAAAA 144 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 22.49 CpG sites = 18, Kimura (unadjusted) = 23.50 Transitions / transversions = 2.25 (18/8) Gap_init rate = 0.11 (16 / 143), avg. gap size = 1.44 (23 / 16) 1440 25.48 3.64 3.64 chr1qtel1M 1048 1487 (998513) L1ME5_3end#LINE/L1 113 552 (389) m_b28s551i0 959 chr1qtel1M 1048 GAAGGACAAAC---CATATGAAAATATGCTCCAAATCATTATTAATCAGA 1094 i i v --- i v v v v L1ME5_3end#LI 113 GAAAGGCTAACAAGCATATGAAGAGATGCTCAAACTCATTAGTAATCAGA 162 chr1qtel1M 1095 GAAATGCAAATTAAGGCAACTCTGAGATACCACTACACACCTGTCAGACT 1144 ii vv i vi i i L1ME5_3end#LI 163 GAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCTATTAGACT 212 chr1qtel1M 1145 GGCTAGAATGACAGGGAAAGATAACACGGAATGTTGGAGGGGATGTGGGA 1194 v i v v ii vvi ii vi i v i i L1ME5_3end#LI 213 GGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTGGCGAGGATGTGGGG 262 chr1qtel1M 1195 AAACAGGGACACTGATACATTGTTGGTGGAATTGTGAATGAATCCAACCA 1244 ? i i v v i i i i v ii ivii v i L1ME5_3end#LI 263 ANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACTGGTGCAGCCA 312 chr1qtel1M 1245 TTCTGGAGAGCAATTTGGAAGTGTGCCCCAAAAGTTA-TCAAACT--GT- 1290 i v ---------- v - i -- - L1ME5_3end#LI 313 TTCTGGAGAGCAATCTGGCAGT----------ACTTAGTCAAATTAAGTA 352 chr1qtel1M 1291 ---GCAAACCCTTTGATCCAGCAGTGCTACTACTGGGCTTATACCCCAAG 1337 --- v v i i v ii v iv i i L1ME5_3end#LI 353 TACGCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATATCCCAAA 402 chr1qtel1M 1338 GAAATACTAAAGAAGG----GAAAGGGACCTGTATGTGCCAGAATGTTTG 1383 v v viv ----v i v i ---- i ii L1ME5_3end#LI 403 GAAATTCTCACACAGGTCCATAAGGGGACATGTACG----AGGATGTTCA 448 chr1qtel1M 1384 TGGCAGCCCTGTTTGTAGTGGCTAGAAGCTGGAA--AATGAATGGATGCC 1431 v vi i vi i i i-- i--v i i L1ME5_3end#LI 449 TTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAAC--CTGGGTGTC 496 chr1qtel1M 1432 CATCCATTGGAGAATGGTTGGGTAAATTGTGGTATATGAATGTTATGGAA 1481 vv v i v i v iv v iiii i L1ME5_3end#LI 497 CATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACACCATGGAG 546 chr1qtel1M 1482 TATTAT 1487 i L1ME5_3end#LI 547 TACTAT 552 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 31.18 CpG sites = 64, Kimura (unadjusted) = 31.93 Transitions / transversions = 1.45 (64/44) Gap_init rate = 0.05 (23 / 439), avg. gap size = 1.39 (32 / 23) 14 18.15 0.00 5.13 chr1qtel1M 2148 2188 (997812) (GAAAAA)n#Simple_repeat 1 39 (0) m_b28s252i0 960 chr1qtel1M 2148 GAAAGAGAAATCAGAAAAGGGAAAAACCACAAGAAAAAGAA 2188 i -v -i vv v (GAAAAA)n#Sim 1 GAAAAAGAAA-AAGAAAA-AGAAAAAGAAAAAGAAAAAGAA 39 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 13 20.52 2.56 0.00 chr1qtel1M 2149 2187 (997813) (AAAGAGA)n#Simple_repeat 1 40 (0) m_b28s252i1 960 chr1qtel1M 2149 AAAGAGAAATCAGAAAAGGGAAAAACCACAAGA-AAAAGA 2187 vv i ivv v - (AAAGAGA)n#Si 1 AAAGAGAAAAGAGAAAAGAGAAAAGAGAAAAGAGAAAAGA 40 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.03 (1 / 38), avg. gap size = 1.00 (1 / 1) 12 14.84 13.46 0.00 chr1qtel1M 4579 4630 (995370) (CTGAGG)n#Simple_repeat 1 59 (0) m_b28s252i2 961 chr1qtel1M 4579 CTG-GGCTGAGGC---GGCAGAGACAGAGTGTGAGGC-GATACTGAGG-T 4622 - --- v i v vv - vi - (CTGAGG)n#Sim 1 CTGAGGCTGAGGCTGAGGCTGAGGCTGAGGCTGAGGCTGAGGCTGAGGCT 50 chr1qtel1M 4623 GAGG-TGAG 4630 - (CTGAGG)n#Sim 51 GAGGCTGAG 59 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.10 (5 / 51), avg. gap size = 1.40 (7 / 5) 236 30.36 5.56 2.40 chr1qtel1M 4745 4906 (995094) Cheshire#DNA/hAT-Charlie 426 592 (1828) m_b28s502i0 962 chr1qtel1M 4745 CAAGAAAA----AGAAAAATTGACTCAGAGTGTAGGATATTCAAAGAACA 4790 ---- i v iv i v viiv i i v Cheshire#DNA/ 426 CAAGAAAAGAAGAGAAAAGTGGACTTCGAATGTCGCGCTTTTAAGGCACA 475 chr1qtel1M 4791 GTAGACTTATGATTACTTTTTCATTCTG---TACAAGG-AAAG-AGCGTA 4835 i v vvv i v i i-- --- v v - - vi i Cheshire#DNA/ 476 GTGGAGTGTGGATTATTTTGTTATC--GAATTAGATGGCAAAGCATTGTG 523 chr1qtel1M 4836 TTTCTGATATGCCAGAATATAATGTCTGTGTTCAAAGAATATAATTTGCG 4885 v -- v vi i iv iv i v i v i Cheshire#DNA/ 524 TTTAT--TATGCAATGACACTATAGCTGTGCTAAAAGAATACAATATACG 571 chr1qtel1M 4886 TGGACATTATGAACCTCAACA 4906 v iv iv v i Cheshire#DNA/ 572 TCGACATTACCAGACTAAGCA 592 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 37.32 CpG sites = 23, Kimura (unadjusted) = 39.35 Transitions / transversions = 0.92 (23/25) Gap_init rate = 0.05 (8 / 161), avg. gap size = 1.62 (13 / 8) 505 37.37 1.98 2.92 chr1qtel1M 5122 5777 (994223) Cheshire#DNA/hAT-Charlie 807 1456 (964) m_b28s502i1 963 chr1qtel1M 5122 GCCAAAGAGATGTGTCCAGAGAAGGCTGATTTATTTAGTACAATGAGTCT 5171 i i iiivi i i iv v v i Cheshire#DNA/ 807 GCCGAAGAAATGTGTCCAGAGAAAATAAACTTGTTTAAGACTATTAGCCT 856 chr1qtel1M 5172 TTCAGGACCTACAATTACATGGAAGA-TTGAAGAAATGGGAGACAATCTG 5220 i vivvv i i - v - i v v iii iv v Cheshire#DNA/ 857 TTCGGCGAGAACAGTTGC-TCGAAGAGTTGAGGACATTGGGAGCAACATC 905 chr1qtel1M 5221 CATCAGCATTTGCAAAACTCCATAACAAA-AATTTC--ATATTTTCCCTT 5267 v viv v iv --- vii -i --i iv i Cheshire#DNA/ 906 AATAGTCAATTAAAAAA---CAAGGCAAATGATTTCGAGTGGTTTTCCTT 952 chr1qtel1M 5268 GGCACTCGACAAAAGCAAT-GATGTTTGTGATTCTGCACAACTTCTAATT 5316 v i i-i iv i i- vvi v v ii------ v Cheshire#DNA/ 953 GGCTCTTGAT-GAGTCGACAGATGTTACCGATACTGCTCAGT------TG 995 chr1qtel1M 5317 TTTATTTGTGGGACAAATGACTATTTTGAAGTCATAGAAGAGCTTGCTGC 5366 i v iiiv v v v v iv ii v iv Cheshire#DNA/ 996 TTTATTCGAGGAGTCAATGCCGAGTTTGAAGTGACTGAAGAATTAGCCTC 1045 chr1qtel1M 5367 ACTGCAAAACATCAAAGGAACAACTACAGGAGAGAATATCTATGAAAAGG 5416 vv v v iiv vviv v i vii i i Cheshire#DNA/ 1046 TATGAATAGTCTGCGTGGAACAACTACAGGCGAGAATATTTTCAAAGAAG 1095 chr1qtel1M 5417 TTTGCCAA--ACT-AT---GGATGGTTTGGAGCTGGACTGGGCTAAACTA 5460 vivv -- - --- v iiiii i - v vv iv - Cheshire#DNA/ 1096 TTGAGAAAACACTAATTCAGTACAACCTGAAG-TGGAATCTGCTAAGAT- 1143 chr1qtel1M 5461 GCCAGCGTGACAAGTGATGGTGCTCCTAGCATG-GTGGGGTCTAAGAAAG 5509 ---- i v v v vvv ii - i - vi i Cheshire#DNA/ 1144 ----GTGTTACAACTGATGGTGGTAAAAATATGTGTGGAG-CAGAAAAAG 1188 chr1qtel1M 5510 GAGTAATTTCTCATATTAACCAAGAGATGGACAAACATAA-CCATTCTTA 5558 vv i vvv v v v vv- viv ii -vii ivv Cheshire#DNA/ 1189 GCTTAGTTGGACAAATTTACAAAGCT-TGTGAAAATGTAAGGTGTTTAAA 1237 chr1qtel1M 5559 TCCAATAGCCATACACTGCCTCATTCACCAGCAAGCGCTGTGTAGTAAAT 5608 v v i ii v i iv i i i ii v ii v Cheshire#DNA/ 1238 GCCTATGGTTATTCATTGTATTATTCATCAGCAGGTACTTTGCGGAAAAT 1287 chr1qtel1M 5609 CACTGAAGTGGGACTCGGTTATGAAAATTTTGGTATCTTGTGTTAACTTC 5658 vvi vivivvv vv vi vivv i i vvvv v Cheshire#DNA/ 1288 ATTTGAATCTATCATGTGTTATTGAACCAGTAGTGTCAACGGTGAACTTC 1337 chr1qtel1M 5659 ATTAGAGCTAATGCACTAAATTACAGATAATTTCAGGAATTTCTGTCTGA 5708 v vv vi v v ii iv vi i i iv i v Cheshire#DNA/ 1338 ATTCGCTCTCGTGGACTTAACCATCGTCAGTTCCGTGAATTTTTGTCAGA 1387 chr1qtel1M 5709 GCTAAATGTTGAGTATGAAAATGTTCTATATCACACAGAGGTACATTGGC 5758 iv i v i i vvvi iv v iv i vi v iv Cheshire#DNA/ 1388 AATAGAAGCTGAATATCCTGACTTGCCCTACCACACAGCAGTTCGATGGC 1437 chr1qtel1M 5759 TGAGTCGAGGGAGAGTTTT 5777 v iv v v i Cheshire#DNA/ 1438 TTAGCAGTGGTAAAGTTTT 1456 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 49.12 CpG sites = 113, Kimura (unadjusted) = 52.50 Transitions / transversions = 0.90 (113/125) Gap_init rate = 0.04 (28 / 655), avg. gap size = 1.14 (32 / 28) 227 30.92 6.46 4.09 chr1qtel1M 5752 6014 (993986) Charlie5#DNA/hAT-Charlie 1624 1892 (732) m_b28s502i2 964 chr1qtel1M 5752 CATTGGCTGAGTCGAGGGAGAGTTTTG-AAACATTT-CTATGAT-TTACT 5798 i i v i i- v - i iv - vi Charlie5#DNA/ 1624 CGTTGGTTGAGTCGTGGAAGAGTTTTACAAAGATTTACTGTACTGTTAAC 1673 chr1qtel1M 5799 TCCACAGATCACAACTTTTCTGCTTTCAAAAAACAAAGAAG---TACCAG 5845 --- ivv iv ---- v v - i v--- i i Charlie5#DNA/ 1674 TCCA---ATTCAAGATTTTCT----TGAAACAA-AAGGAATGCTTGCCAA 1715 chr1qtel1M 5846 A-ATCCAAT-------GATGCAGAATGGAAATGCCACCTTGC-CTTTCTG 5886 - i ------- iiv i v i iv i- i -i v Charlie5#DNA/ 1716 ATATTCAATAATCAAAGACAAAAAATGGCAGTGTGAT-TTACGTTTTCTC 1764 chr1qtel1M 5887 ACAGATGGAACAGAGC-TACTCAACAATTTTAATATGCATCTTCAAGGAA 5935 v ivv vv - - v i vi v v v v i Charlie5#DNA/ 1765 ACCGATATCACACTGCATA-TGAACGAGCTAAATTTGAAGCTCCAAGGAA 1813 chr1qtel1M 5936 AGGGGAAGCTCATCTGTGATAT-GCGATCACATGTCAAAGCATTTGAAGT 5984 ii i i iv - v -v v vvi v iviv Charlie5#DNA/ 1814 AGGAAAAGCTTATTTGTGACCTAGCTA-GACAGGTACGAGAATTTATGTT 1862 chr1qtel1M 5985 AAAATTAGGCCTCCTCATCAAACAAGTGAA 6014 i iiiv ii v v i v Charlie5#DNA/ 1863 GAAATTGAAACTTTTCATAATACAAATCAA 1892 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 38.58 CpG sites = 40, Kimura (unadjusted) = 40.55 Transitions / transversions = 1.05 (40/38) Gap_init rate = 0.08 (20 / 262), avg. gap size = 1.40 (28 / 20) 458 29.95 2.58 2.58 chr1qtel1M 6225 6457 (993543) Cheshire#DNA/hAT-Charlie 1902 2134 (286) m_b28s502i3 965 chr1qtel1M 6225 CAAATGGAACTGATTGAACTGCAGAATTGTGACTCTCTGAAAGACGCAT- 6273 v v i v ivi vi viv i i iv - Cheshire#DNA/ 1902 CAATTGGAAGTGATTAATCTGCAATGTAATGACATGCTAAAAGGCAAATA 1951 chr1qtel1M 6274 TCAAGTCAAGCAACCTTCATA-ATTTCTATGCATCTCTCCCCTCTGAGAC 6322 vv - i -v - v iv vi i vvvi viv Cheshire#DNA/ 1952 TCAAGAGAAG-AATCT-AATAGAATTCTATAAATGCCTTCCAAGCGATGA 1999 chr1qtel1M 6323 ATATCCTCATCTTTGGAACCATGCACTCA--AAATGGCAACCATCTTTGG 6370 v v-- ii i iii i--i v ii v vi v Cheshire#DNA/ 2000 ATATGCTCAA--TTAAAATCATATGCTCGTGGATTGATATCAGTATTTGG 2047 chr1qtel1M 6371 CAGCACTTATGTCTGTGAAGAGACTTTTTCTAGAATGAAACATTTGAAAT 6420 i i v v i v v ii i iv i Cheshire#DNA/ 2048 CAGTACCTATCTGTGTGAAAAGACATTTTCAAAGATGAAATACGTAAAAT 2097 chr1qtel1M 6421 CTCCAAT--CAGATCAAGACTAACAGATGCACACTTGCA 6457 -- -- iv i v i Cheshire#DNA/ 2098 CTC--ATTACAGATCAGCATTAACAGATGAACATTTGCA 2134 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 36.77 CpG sites = 36, Kimura (unadjusted) = 38.92 Transitions / transversions = 1.12 (36/32) Gap_init rate = 0.04 (10 / 232), avg. gap size = 1.20 (12 / 10) 491 33.83 2.94 2.64 chr1qtel1M 8003 8342 (991658) C HERVK11D#LTR/ERVK (2469) 5283 4943 m_b28s701i0 966 chr1qtel1M 8003 TTCCCTTTTTTCTGTTTGTCAAGGAG----GATTTTAATATCCTTGTTGC 8048 i i i i --- v i----i vi i - i C HERVK11D#LTR/ 5283 TCCCCCTCTTTTTGTTT---AAGTAATTGTAATTTTAAAGTTCT-GTTAC 5238 chr1qtel1M 8049 ATCTTTT---AATGGCTTG-CCCGATAGGATTGTATGGA-TGCCAGTAGA 8093 v i--- i - ivi i - i v - i iv C HERVK11D#LTR/ 5237 TTCTTTCTACAATAGCTTGGCCTTGTGGG-TTATAAGGAATACCAGTAAT 5189 chr1qtel1M 8094 GTGAATGATATTATTATAGGTGAGACAAAATTGTGCAAAATTCCTACCAG 8143 i vv i -iii iv i v - v v -i viii iiv C HERVK11D#LTR/ 5188 ATGTTTAATAT-GCCACTGATCA-AGAAAATTTT-TAAAAGCTTTACTGC 5142 chr1qtel1M 8144 CATAGGTAGGACCATTGTCAGTCTTGAAGTGTCTTGGAATGCCAAGAATC 8193 v iv v i iv vv v v v v i C HERVK11D#LTR/ 5141 AATAGGCTGGACCATTGTCTGTTTTGAGCTCACTAGGAATTCCCATAACC 5092 chr1qtel1M 8194 CTAAAGCAGAATAATAAATGCTCAATTACATGGGTGGCAACTTCTCTGGT 8243 vi i vi v i v i ivv v i i vi iii i C HERVK11D#LTR/ 5091 GCAAAACATGAAAACATATGTTTTTTAACGTGAGAAGTGGCTTCTCCGGT 5042 chr1qtel1M 8244 TTGGGGGGTGGCCATAATAAACACAGAGAAGGGATTTACAGTCACATATA 8293 ivi i vvi i vvii i vi iv v v ii C HERVK11D#LTR/ 5041 TTGACAGGTAGCCCAGATGAAATTGGAAAAGGTGTCAACTGTGACATGCA 4992 chr1qtel1M 8294 TAT-GGTGAAGACTCCCAAAAGATGGATAATGAGTGACATCCATCTGCCA 8342 i -i iv v-i i v vv i i C HERVK11D#LTR/ 4991 CATAAGCTAAT-TTTCCAAAAGAAGGAACATGAGTAACATCCATTTGCCA 4943 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 45.56 CpG sites = 66, Kimura (unadjusted) = 46.73 Transitions / transversions = 1.43 (66/46) Gap_init rate = 0.04 (14 / 339), avg. gap size = 1.36 (19 / 14) 253 29.06 1.67 2.52 chr1qtel1M 8785 8904 (991096) C HERVK13#LTR/ERVK (3149) 4967 4849 m_b28s701i1 966 chr1qtel1M 8785 CACTTTAAATCATGGGAGCAGACATATACT--GTATAACTAATGTCAGAA 8832 v v vv v - i -- iiv v -- C HERVK13#LTR/E 4967 CAGTTTCAATGTTGCGAGCA-ACATGTACTACGTACGCCGAAT--CAGAA 4921 chr1qtel1M 8833 AAAATGTTGAAGGGTTCAGTAACATCTTTAGGGAGAAGGATAATTACTAA 8882 v i vv vi v i i v ivv ivi vi? C HERVK13#LTR/E 4920 ACAATGTTAACTGGTTCAGGGAAATCTTCAAGGACAGCCATAACAGCGGN 4871 chr1qtel1M 8883 AATTTCAGCCTTTTGTGCTGAA 8904 v vi iiv C HERVK13#LTR/E 4870 CAGCTCAGCTCGTTGTGCTGAA 4849 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 34.56 CpG sites = 14, Kimura (unadjusted) = 37.28 Transitions / transversions = 0.70 (14/20) Gap_init rate = 0.03 (4 / 119), avg. gap size = 1.25 (5 / 4) 253 29.27 6.98 6.24 chr1qtel1M 9380 9809 (990191) C HERVK14C#LTR/ERVK (3630) 3804 3372 m_b28s701i2 966 chr1qtel1M 9380 TATTCTTATTAAT-TGGGCCTCAGATCAATTTTTTTCTCTGCAAGATATA 9428 - ? i- -- ? v? ii viiv ?v i C HERVK14C#LTR/ 3804 TATTCT-ATTNACCTGGGCCT--GNTGNATTTTTTCTTCAATCANTTGTA 3758 chr1qtel1M 9429 GTTCATGTTTTGCCTCTGAAGACAGAGTTCTAGGAGAGTTTTACTA---- 9474 i v vv iv ? i v -- v ------ ---- C HERVK14C#LTR/ 3757 ATTCTTTGTCAGCCTCNGGAGTCAG--TTCTCG------TTTACTATTGA 3716 chr1qtel1M 9475 ---AAGGGTTTCCTTATAAAATGGAGAATAAATGAGAAAGTTGATGCAT- 9520 ---v i i iv i i i i v v -- -- - C HERVK14C#LTR/ 3715 GANCAGGATCTCCTCTTAAGATAGAGAACAGATTAGACA--TG--GCATA 3670 chr1qtel1M 9521 --TATGTAT-CGTAGCATGGGTCAAA----GTCAATATCATCTAACAATT 9563 -- v v - v ivi i i ----i i vi i C HERVK14C#LTR/ 3669 GGTAGGAATGCCTAAAGTAGGTCGAATCCAATTAATATCCCCTAATAATT 3620 chr1qtel1M 9564 TTTGAAAATCATTAAGATTTTGTAATGAATCTGTTCTTGTCTCAAGTTTC 9613 v i v vi iv i v vvi i v vi i C HERVK14C#LTR/ 3619 TTTGAAAATCATTTAAAGTTTTCAGAGAGTCTTTTCGAATTTGAACCTTT 3570 chr1qtel1M 9614 TGGAGTCAGATTA----TTTGAGAATCCATCAGATAGCCAAGATATAAAA 9659 ?i iivi i---- ivv i iii--- vv - vii C HERVK14C#LTR/ 3569 TGNGGCTTAATTGCCCTTTCCTGAACCTGC---ATTCCCAA-ATATTGGA 3524 chr1qtel1M 9660 AAAGACTTGTC-TCTGAATTTTTTCAGGAGTAATTAACAAATCTCATGAA 9708 i v v ? - i v ? ? iv v ? - ivii vv C HERVK14C#LTR/ 3523 AAGGAGTAGNCGTTTGAATTTTATCNGGNGCTATGANC-AATCCAGCGTC 3475 chr1qtel1M 9709 TATAA--GCTTGCTCTAAATCATCTATTAAGAA-ACTGAGATTATTTACA 9755 vii? -- i v v ----- i v v - - v v i-i C HERVK14C#LTR/ 3474 GGCNACCGCCTTCTGTAAA-----TGTGAATAACACTG-GATAAGTTG-G 3432 chr1qtel1M 9756 TCT----TTACTACTATATAAAATA--TCATCCATATAGTGAATTGTTTC 9799 ---- v vi iii i ? -- i vi v v C HERVK14C#LTR/ 3431 TCTCGAGTTTCGGCCGCACANAATATGTCATCCATATAATGAATGATATA 3382 chr1qtel1M 9800 GGGATCTGGA 9809 ? i C HERVK14C#LTR/ 3381 NGAATCTGGA 3372 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 38.21 CpG sites = 64, Kimura (unadjusted) = 39.54 Transitions / transversions = 1.19 (64/54) Gap_init rate = 0.09 (39 / 429), avg. gap size = 1.46 (57 / 39) 293 24.97 8.10 6.57 chr1qtel1M 9406 9615 (990385) C HERVK#LTR/ERVK (3657) 3879 3667 m_b28s701i3 966 chr1qtel1M 9406 AATTTTTTTCTCTGCAAGATATAGTTCATGTT-TTGCCTCTGAAGACAGA 9454 ii ?i v - v i iv v ?- ii vi iv C HERVK#LTR/ERV 3879 AATTTTTTCTTCNACTA-ATTTAATTTCTTTNGTTGCCTCTGGGGTTAAC 3831 chr1qtel1M 9455 GTTCTAGGAGAGTTTTACTA---AAG----GGTTTCCTTATAAAATGGAG 9497 -------- --- ---- ii iv i i C HERVK#LTR/ERV 3830 GTTCT--------TTTACTATTTAAGTCTGGGTCCCCTCTTAAGATAGAG 3789 chr1qtel1M 9498 AATAAATGAGAAAGTTGATGCAT---TATGTAT-CGTAGCATGGGTCAAA 9543 i vv v -- -- --- v v - v vi v i i C HERVK#LTR/ERV 3788 AACAAATTTGACA--TG--GCATAAGTAGGAATGCCTAGAGTTGGCCGAA 3743 chr1qtel1M 9544 ----GTCAATATCATCTAACAATTTTTGAAAATCA-TTAAGATTTTGTAA 9588 ----i i vi i i - vi - C HERVK#LTR/ERV 3742 TCCAATTAATATCTCCTAGCAATTTTTGAAAGTCATTTAATGTTTT-TAA 3694 chr1qtel1M 9589 TGAATCTGTTCTTGTCTCAAGTTTCTG 9615 vi v i i v v i C HERVK#LTR/ERV 3693 TGTGTCTTTTCTTATTTCTATTTTTTG 3667 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 30.62 CpG sites = 28, Kimura (unadjusted) = 31.38 Transitions / transversions = 1.33 (28/21) Gap_init rate = 0.10 (21 / 209), avg. gap size = 1.48 (31 / 21) 737 28.06 2.51 2.83 chr1qtel1M 9831 10149 (989851) C HERVK14C#LTR/ERVK (4129) 3305 2988 m_b28s701i4 966 chr1qtel1M 9831 ATACCTTGAGGTAACACTTTCCATTGAAATCTTTGTGGAGGTTCCTCCAC 9880 i i v i ? v v ? vvv v? ivvi C HERVK14C#LTR/ 3305 ATGCCCTGCGGCAANACTTTCCAATGATANCTGGCTGCNGGTTCCTTGTT 3256 chr1qtel1M 9881 ATTTATACTAGGAATAGGAAGGGCAAATTTAGGTTTA---TCCTCCTTTT 9927 i i vi v ii --- i --- ?vv i v C HERVK14C#LTR/ 3255 GTTCATAGCAGGAATAGTAAAAGCAAATTT---TTCAAAATCNGGCTCTG 3209 chr1qtel1M 9928 AAAGAGGAATAGCCAAGAAGCAGTCTTTTAAATCAGTTGCTATCAGTGGC 9977 vv iv i i vi vi i i? C HERVK14C#LTR/ 3208 CTAGAGGAATAGTAAAGAAGCAGTCCTTCAAATCTATAACTATTAANGGC 3159 chr1qtel1M 9978 CATTCAGCAGGCACCATGGTAGGGGGAACAAAGGCCAGGCTGAAAGGGAC 10027 v vvi v i i- ?viv v v v i? vv C HERVK14C#LTR/ 3158 CAGTCTCTAGGAATCATGGC-GGGGGANGGCAGCCCTGGCTGCAGNGCCC 3110 chr1qtel1M 10028 TCTTT--TTGACCATGGTATTATTTATTGCATGAAGGACATGTACCATTC 10075 i v ?-- --? iivvi v iv vi v i v ivv v ? C HERVK14C#LTR/ 3109 CCATNGGTTG--NATGACTGCATTGACGGCTCGTAAGTCGGTTAGCATNC 3062 chr1qtel1M 10076 ACCATTTCCTTGATTTTTTCTTTATTACAAATATCAGAGAATTCCAAGGA 10125 i i v iv ? i iii ? ? C HERVK14C#LTR/ 3061 GCCATCTGCCGGATTTTTTCTTNATTACAAACACTGGNGAATTCCANGGA 3012 chr1qtel1M 10126 CTA---GTAGGAAATTCAATATGTCCT 10149 vv --- i ---i ? i C HERVK14C#LTR/ 3011 GAAAATGTGGG---CTCNATGTGTCCT 2988 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 34.55 CpG sites = 42, Kimura (unadjusted) = 37.68 Transitions / transversions = 0.93 (42/45) Gap_init rate = 0.04 (12 / 318), avg. gap size = 1.42 (17 / 12) 524 32.97 7.58 4.41 chr1qtel1M 11142 11471 (988529) C L3#LINE/CR1 (483) 3616 3277 m_b28s601i2 967 chr1qtel1M 11142 TAGCTTCAAGACCTGAACCTTGTCGTCCAGGTGTGGTTTGGCCAGCACAG 11191 i vi v v vivi vv i i i i C L3#LINE/CR1 3616 TGGCGCCCAGAACTGAACGCAATACTCCAGATGTGGTCTGACCAGCGCAG 3567 chr1qtel1M 11192 AGGATAGCCTGATTCTTGCCTCCCTC-TTCTG--TGCTCAGCCTCTCCTG 11238 v i vv i v i i-? --ii vvi i vi i C L3#LINE/CR1 3566 AGTACAGCGGGACTATTACCTCCCTTGNTCTGGACACTATACTTCTATTA 3517 chr1qtel1M 11239 ATGTTTATAGCCCAAGACTG--GTGACT------GTAGCC------TACT 11274 ----i i i --v ii ------ i ------i C L3#LINE/CR1 3516 ATG----CAGCCTAAGATTGCATTAGCTTTTTTGGCAGCCACATCACACT 3471 chr1qtel1M 11275 GCTGACCTGTCCAGAGCTCAGAGTTATCTGAAACTCCCAGACCTTGTTCA 11324 i i iii viv iivi i v i i i ii v C L3#LINE/CR1 3470 GTTGGCTCATATTGAGCTTGCGGTCAACTAAAACCCCTAGGTCTTTTTCA 3421 chr1qtel1M 11325 ---GACCAGCTA-TAGGCCAACAATGCCCCTCTCTCTCCCACATGGCCCT 11370 --- v v i- i --i --- iv iii ----- C L3#LINE/CR1 3420 CGTGAACTGCTGCTAAGCCA--GAT---CCTCTCCATCCTGTA-----CT 3381 chr1qtel1M 11371 TTTGAAGTCAA--TATTGAGATCCACAT-CAAAA-TGGACATTTATCCTT 11416 v v ii -- v - i i v - ii - vv i C L3#LINE/CR1 3380 TGTGCAGTTGATTTTTTGA-ACCTAAATGCAGGACTTTACATTTATCCCT 3332 chr1qtel1M 11417 ATTACATTTCACAGAGTCCAACTCATACCAGTGCTTCAGCATGTTGAGAT 11466 i v ivvv ivivi ivv vi i i v i C L3#LINE/CR1 3331 GTTAAATTTCATCTTGTTGGTTTCGGCCCATCGTTCCAGCCTGTCGAGAT 3282 chr1qtel1M 11467 CTGTT 11471 ?v C L3#LINE/CR1 3281 CNTTT 3277 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 42.84 CpG sites = 64, Kimura (unadjusted) = 45.85 Transitions / transversions = 1.60 (64/40) Gap_init rate = 0.08 (25 / 329), avg. gap size = 1.60 (40 / 25) 29 15.36 0.00 0.00 chr1qtel1M 12015 12066 (987934) (CTTC)n#Simple_repeat 1 52 (0) m_b28s252i3 968 chr1qtel1M 12015 CTTCCTTTCTTCCTTCCTTCTTTCCTTTATTTCTTCCTTCCCTCCTTCCC 12064 i i iv i i i (CTTC)n#Simpl 1 CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT 50 chr1qtel1M 12065 TC 12066 (CTTC)n#Simpl 51 TC 52 Matrix = Unknown Transitions / transversions = 6.00 (6/1) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 295 26.32 10.53 0.00 chr1qtel1M 12193 12287 (987713) C L2#LINE/L2 (606) 2476 2372 m_b28s601i3 969 chr1qtel1M 12193 GGGAAGACT--GCATTTAGTTT-GGGTATGTTAAACTAAAGATGTCTATA 12239 ii-- vi i - ii ii vi i v C L2#LINE/L2 2476 GGGAAGATCAGGAGTTCAGTTTTGGACATGTTAAGTTTGAGATGCCTATT 2427 chr1qtel1M 12240 AAGCATCCAGTT-----TGTCCAGCAGACAATTGGAGAT--GAGATTGGA 12282 ii iv ----- v i i i v -- vi C L2#LINE/L2 2426 AGACATCCAAGTGGAGATGTCGAGTAGGCAGTTGGATATACGAGTCTGGA 2377 chr1qtel1M 12283 GGTCA 12287 v C L2#LINE/L2 2376 GTTCA 2372 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 33.79 CpG sites = 17, Kimura (unadjusted) = 33.79 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.04 (4 / 94), avg. gap size = 2.50 (10 / 4) 229 31.84 5.13 3.36 chr1qtel1M 13220 13336 (986664) L2#LINE/L2 2299 2417 (665) m_b28s601i4 970 chr1qtel1M 13220 AGTTTC-TGGGTTCAGTTATCATCTCTATGAAGACAAGTTTCAGAATTAT 13268 i - v i iv i v vv ii v ii i v L2#LINE/L2 2299 AGTCTCATGGCTTTAAATACCATCTATATGCTGATGACTCCCAAATTTAT 2348 chr1qtel1M 13269 ATTCCCGGCCTAG-CCTGTTTGGGGAATTCCAG-TTC-TGCAGC--ACTC 13313 ii i ii - v iivvv i -i - ii v -- v L2#LINE/L2 2349 ATCTCCAGCCCGGACCTCTCCCCTGAACTCCAGACTCGTATATCCAACTG 2398 chr1qtel1M 13314 CCTACCTGAACTACATGTCCACT 13336 ii ---- v L2#LINE/L2 2399 CCTACTCG----ACATCTCCACT 2417 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 39.78 CpG sites = 22, Kimura (unadjusted) = 43.12 Transitions / transversions = 1.57 (22/14) Gap_init rate = 0.08 (9 / 116), avg. gap size = 1.11 (10 / 9) 370 35.09 13.64 0.95 chr1qtel1M 13493 13866 (986134) L2#LINE/L2 2662 3082 (0) m_b28s601i5 970 chr1qtel1M 13493 TCACCCCTTGTACAGTTACCAATCTGGTTCAGACCCTCATCACCTC-CGC 13541 v i vi v ii vi i ii vi i - L2#LINE/L2 2662 TCACCACCTCCACTGCCACCACCCTGGTCCAAGCCACCATCATCTCTCGC 2711 chr1qtel1M 13542 CTGGTTGATCACAATGGCCTCTTAGCAGCTCCCAGTCTAATCTCATCACT 13591 v v iii i i i v v i --i iv ii i vi L2#LINE/L2 2712 CTGGATTACTGCAATAGCCTCCTAACTGGTCTC--CCTGCTTCCACCCTT 2759 chr1qtel1M 13592 CCCCCTCCCCAG--GGTTC---ACAGAGTAGTCAGG--GATTTGCCTAAA 13634 v i i? --vi --- v i i i-- iivii L2#LINE/L2 2760 GCCCCCCTNCAGTCTATTCTCAACACAGCAGCCAGAGTGATCCTTTTAAA 2809 chr1qtel1M 13635 GCATAGGTCTGATCATACTGCTC--TTACTCAACAGACTC--ATGGTTCC 13680 i i i v iiii --i i v vv -- i i L2#LINE/L2 2810 ACGTAAGTCAGATCATGTCACTCCTCTGCTCAAAACCCTCCAATGGCTTC 2859 chr1qtel1M 13681 CTAT-------AGAGCAGATATAAAACGTCCT-------------AAGAC 13710 i ------- i i viiv - ------------- i L2#LINE/L2 2860 CCATCTCACTCAGAGTAAAAGCCAAA-GTCCTTACAATGGCCTACAAGGC 2908 chr1qtel1M 13711 CTT-CACAGTCTGGACCTC--TCCCTTCTCTCA-GGGATC-CTCGCAATT 13755 i - iii v i -- iv i v -vvv - iii v i L2#LINE/L2 2909 CCTACATGATCTGGTCCCCCGTTACCTCTCTGACCTCATCTCCTACCACT 2958 chr1qtel1M 13756 CACTCCC-------CTCTACTCTTGGTGAACTAGCAACCCTCGC-ATTTG 13797 v i ------- ii iv viiv i -vi i -i iv L2#LINE/L2 2959 CTCCCCCTCGCTCACTCCGCTCCAGCCACACTGGC-CTCCTTGCTGTTCC 3007 chr1qtel1M 13798 TGG---ACGTGACCCCCACTCCAACTCT---GCCTTTCCCCTGGCTCTTC 13841 v --- iv vv v i vi iii--- v v v v L2#LINE/L2 3008 TCGAACACGCCAGGCACGCTCCCGCCTCAGGGCCTTTGCACTTGCTGTTC 3057 chr1qtel1M 13842 TCTATGCATGGGAAGTTCTCCCCTC 13866 i v v i v i i i L2#LINE/L2 3058 CCTCTGCCTGGAACGCTCTTCCCCC 3082 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 48.08 CpG sites = 83, Kimura (unadjusted) = 50.40 Transitions / transversions = 1.77 (83/47) Gap_init rate = 0.05 (20 / 373), avg. gap size = 2.75 (55 / 20) 37 40.50 2.11 2.42 chr1qtel1M 13958 14289 (985711) (TATG)n#Simple_repeat 1 331 (0) m_b28s252i4 971 chr1qtel1M 13958 TATGCATGTACATACGTGTGTATGTAGGTTTTTATCTATACATATATATG 14007 i ii i i v v v v --i i (TATG)n#Simpl 1 TATGTATGTATGTATGTATGTATGTATGTATGTATGTAT--GTATGTATG 48 chr1qtel1M 14008 CATG--TGTATGTCTTTATCTAGACATATATGAGCATGTGTATGCATGGT 14055 i -- v v v vii i viii i i vv (TATG)n#Simpl 49 TATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTA 98 chr1qtel1M 14056 TTTATCTATACATATATGTGCATGCATATATGTTTAGCTATATGTGTGCA 14105 v v ii i -- i i v ivv i i i (TATG)n#Simpl 99 TGTATGTATGTATGTATGT--ATGTATGTATGTATGTATGTATGTATGTA 146 chr1qtel1M 14106 TGTATGTTTTTATCTATACATATATGTGCATGTGTGCATG-CTTCATCTA 14154 v v v ii i -- i i -v vi v (TATG)n#Simpl 147 TGTATGTATGTATGTATGTATGTATGT--ATGTATGTATGTATGTATGTA 194 chr1qtel1M 14155 GACACTTATGTGTTTTTATTCATACACATATATGCATGTTCATGTCTTTA 14204 vii iv i v v i vii iii i i - - v v (TATG)n#Simpl 195 TGTATGTATGTATGTATGTATGTATGTATGTATGTATG-T-ATGTATGTA 242 chr1qtel1M 14205 TACACGCATG-A-GCATGTGTACACGTTTTAATCTATAAATATGTGTATG 14252 ii i i - - i i ii i v vv v iv i i (TATG)n#Simpl 243 TGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATG 292 chr1qtel1M 14253 T-TTTATCTATACATGTGTGCATGTATGT-TTTATCTAT 14289 - v v ii i i - v v (TATG)n#Simpl 293 TATGTATGTATGTATGTATGTATGTATGTATGTATGTAT 331 Matrix = Unknown Transitions / transversions = 1.55 (59/38) Gap_init rate = 0.04 (14 / 331), avg. gap size = 1.07 (15 / 14) 343 29.30 11.19 0.68 chr1qtel1M 14380 14513 (985487) L2b_3end#LINE/L2 317 464 (2) m_b28s601i6 970 chr1qtel1M 14380 TATATAATTATGT-TTTGTCTCCCCCATTGAAACATGAGCCTTG-GAGGA 14427 i v i? ii - i i ii vii iii - i L2b_3end#LINE 317 TGTCTGNTTACATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGG 366 chr1qtel1M 14428 CAGGGGTAGTTTTTGCCTT------CGCAGT---CCCGTGACTTGGCACA 14468 iiv ?v i i ------ v --- ivvi i i L2b_3end#LINE 367 CAGGGACCGNGTCTGTCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACA 416 chr1qtel1M 14469 GTGTCTGGCACATAGTA--CGTT--ATAAACGTTTGACAGACTGAATAA 14513 ? i i -- i --i ii -iv v i L2b_3end#LINE 417 GNGCCTGGCACACAGTAGGCGCTCAGTAAATATTTG-TTGAATGAATGA 464 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 38.69 CpG sites = 30, Kimura (unadjusted) = 41.56 Transitions / transversions = 3.33 (30/9) Gap_init rate = 0.05 (7 / 133), avg. gap size = 2.29 (16 / 7) 276 27.36 15.87 1.39 chr1qtel1M 14983 15108 (984892) MIRb#SINE/MIR 64 207 (61) m_b28s601i7 972 chr1qtel1M 14983 AAACCCGATTCTAGCCACAAAC-AGCTGTATGAC--TGGGCCAGTCCCTT 15029 v ii - vv - i -- v iv MIRb#SINE/MIR 64 AATCCCGGCTCT-GCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTT 112 chr1qtel1M 15030 -----------GCACTCAGGATCTTCATCTCTAAAACAAAGATAATAGCA 15068 ----------- - vv i v iiii ii MIRb#SINE/MIR 113 AACCTCTCTGAGC-CTCAGTTTCCTCATCTGTAAAATGGGGATAATAATA 161 chr1qtel1M 15069 TCTAC------AAGTTCTGAAAAGGCTAAAATGCAGTCATGCATAT 15108 i ------ii v vivi v v vii v i MIRb#SINE/MIR 162 CCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCATGT 207 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 34.80 CpG sites = 19, Kimura (unadjusted) = 34.80 Transitions / transversions = 1.27 (19/15) Gap_init rate = 0.05 (6 / 125), avg. gap size = 3.67 (22 / 6) 222 28.32 15.09 3.39 chr1qtel1M 15459 15564 (984436) MIRb#SINE/MIR 1 118 (150) m_b28s601i8 973 chr1qtel1M 15459 CACAAGGGCAGCTGGATGACATGGCGGACAGAGCACTGGCCT--GACCC- 15505 v i ---i iiiii i v v i -- vi - MIRb#SINE/MIR 1 CAGAGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCA 47 chr1qtel1M 15506 --CAGGCCT-----------CAGACTCATAATGCTTCCTAGTTGTGTGAC 15542 -- i ----------- v i - ivii v i MIRb#SINE/MIR 48 GACAGACCTGGGTTCGAATCCCGGCTC-TGCCACTTACTAGCTGTGTGAC 96 chr1qtel1M 15543 CCTGAGCTAGTCACTTAATCCC 15564 i i v i i i MIRb#SINE/MIR 97 CTTGGGCAAGTTACTTAACCTC 118 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 36.25 CpG sites = 21, Kimura (unadjusted) = 37.95 Transitions / transversions = 2.62 (21/8) Gap_init rate = 0.08 (8 / 105), avg. gap size = 2.50 (20 / 8) 229 17.95 0.00 0.00 chr1qtel1M 15526 15564 (984436) MIRc#SINE/MIR 77 115 (153) m_b28s601i9 973 chr1qtel1M 15526 CTTCCTAGTTGTGTGACCCTGAGCTAGTCACTTAATCCC 15564 v i i i v i i MIRc#SINE/MIR 77 CTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 21.09 CpG sites = 5, Kimura (unadjusted) = 21.09 Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 581 30.46 11.34 3.00 chr1qtel1M 19256 19996 (980004) L2#LINE/L2 2253 3053 (29) m_b28s601i10 974 chr1qtel1M 19256 CCTCTTCTTTTCCATCCCTTCATTC--TCCCTTGGAGAATTCACCCATTT 19303 i iv vi v i -- ? v vi i v i L2#LINE/L2 2253 CCTCTTCTCTTCTCTATCTACACTCACTCCCTNGGTGATCTCATCCAGTC 2302 chr1qtel1M 19304 CCATAGGTTCAACTACCTTCTCTATCCCAATGGCTCCCACATTGACAGAT 19353 i i v i v v v v ii i v v i vv L2#LINE/L2 2303 TCATGGCTTTAAATACCATCTATATGCTGATGACTCCCAAATTTATATCT 2352 chr1qtel1M 19354 CCTGCCTCAGCCTCTTTCTCGAGTTTCAGTATGACCTCACCAACTTCCCA 19403 v ivii ii ii ii i vv viiv vv v i L2#LINE/L2 2353 CCAGCCCGGACCTCTCCCCTGAACTCCAGACTCGTATATCCAACTGCCTA 2402 chr1qtel1M 19404 CAGG--------ATTTGG-----CAA-AGACATTTACAACTGGATATGTC 19439 vv -------- i -----i - i i vv vi i L2#LINE/L2 2403 CTCGACATCTCCACTTGGATGTCTAATAGGCATCTCAAACTTAACATGTC 2452 chr1qtel1M 19440 CCCCACT----TCCTTATCTTTCACCATCAAACCCATCTTTCTCCCAAAG 19485 vvv ---- v i - v -- vi i iv L2#LINE/L2 2453 CAAAACTGAACTCCTGATCTTCC-CCCTCAAACC--TGCTCCTCCCGCAG 2499 chr1qtel1M 19486 TC--CCCTATTGCTGTGGAGGAGGGTACTGCCATCCTCCCAGTCACCC-- 19531 -- i iv v ---?i v i viv i ii i -- L2#LINE/L2 2500 TCTTCCCCATCTCAGT---NAATGGCAACTCCATCCTTCCAGTTGCTCAG 2546 chr1qtel1M 19532 ------AATCTT-CAGTCTTGATGGAATCTTCCCTTCCT-----GCCCCA 19569 ------ i -v v vv v v i i i -----i L2#LINE/L2 2547 GCCAAAAACCTTGGAGTCATCCTTGACTCCTCTCTTTCTCTCACACCCCA 2596 chr1qtel1M 19570 ---CCAACTCA--AGC----------------ACTTTCCAGACAT-TCTA 19597 --- ii -- ---------------- i v i i - i L2#LINE/L2 2597 CATCCAATCCATCAGCAAATCCTGTCGGCTCTACCTTCAAAATATATCCA 2646 chr1qtel1M 19598 ACATCTGTCCCCATCTCTCCATTCATACAGTCATGNNNNNNNNNNNNNNN 19647 iv i v v v v iiivi v i iv??????????????? L2#LINE/L2 2647 GAATCCGACCACTTCTCACCACCTCCACTGCCACCACCCTGGTCCAAGCC 2696 chr1qtel1M 19648 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGCCTCCCAATGAATCTCCT 19697 ?????????????????????????????? i ivii i L2#LINE/L2 2697 ACCATCATCTCTCGCCTGGATTACTGCAATAGCCTCCTAACTGGTCTCCC 2746 chr1qtel1M 19698 TGCCTC--CTCTTTCCCCACCATAGGCTATTTTTCATTCAGTTTCTTCCT 19745 i -- i v v i?i v i iv iv --- vv - L2#LINE/L2 2747 TGCTTCCACCCTTGCCCCCCTNCAGTCTATTCTCAACACAG---CAGCC- 2792 chr1qtel1M 19746 CAAGGGATTTTCCTCAAGTATATGTCTTATCATGACACTCTGCCTGCTCA 19795 vi v ii ii v iii v vv v i-i L2#LINE/L2 2793 AGAGTGATCCTTTTAAAACGTAAGTCAGATCATGTCACTCC-TCTGCTCA 2841 chr1qtel1M 19796 ATTAA-GCTCAGCTGGCTCCCAATCAGCTCCAGGATTAAAGATAAATTCC 19844 -- -v viv i v vvvii ii v vi v L2#LINE/L2 2842 A--AACCCTCCAATGGCTTCCCATCTCACTCAGAGTAAAAGCCAAAGTCC 2889 chr1qtel1M 19845 TTTATTTGGCATTTAACGTCCTTTACGACCTGACCCAGCTCTACCTTTCT 19894 vvvv v vi v i vi i i ii vv vi i L2#LINE/L2 2890 TTACAATGGCCTACAAGGCCCTACATGATCTGGTCCCCCGTTACCTCTCT 2939 chr1qtel1M 19895 G-------TGCTTACCACAC---------ATGATTCCACTTAAAGCCAAA 19928 -------iv i v ---------v v i i i-v v L2#LINE/L2 2940 GACCTCATCTCCTACCACTCTCCCCCTCGCTCACTCCGCTC-CAGCCACA 2988 chr1qtel1M 19929 CTGACCTCACCCAATTTTCTGATTCCT--GACACTTCA-----TCTCCCA 19971 i ------i v - --i vi -----v i L2#LINE/L2 2989 CTGGCCTC------CTTGCTG-TTCCTCGAACACGCCAGGCACGCTCCCG 3031 chr1qtel1M 19972 CCTCCATGCCTTTGACCCATGTGCT 19996 viv --- iv L2#LINE/L2 3032 CCTCAGGGCCTTTG---CACTTGCT 3053 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 42.02 CpG sites = 115, Kimura (unadjusted) = 43.89 Transitions / transversions = 1.11 (115/104) Gap_init rate = 0.06 (44 / 740), avg. gap size = 2.45 (108 / 44) 235 17.78 0.00 0.00 chr1qtel1M 19633 19677 (980323) UCON86#LINE/L2 9 53 (629) m_b28s502i4 974 chr1qtel1M 19633 ATCTTCATCCTAGTTCTCATCTCCTCTTGCCTGGACTATGGCAAC 19677 i v? iii i v v ? UCON86#LINE/L 9 ATCCTCATCCANGCCTTCATCTCCTCTCGCCTTGACTATTGCANC 53 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 18.84 CpG sites = 5, Kimura (unadjusted) = 21.76 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 24 6.76 0.00 0.00 chr1qtel1M 22420 22450 (977550) (T)n#Simple_repeat 1 31 (0) m_b28s252i5 975 chr1qtel1M 22420 TTTTTTTTTTTTTTTTTTTTTTTGCTTTTTT 22450 vi (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 31 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 16 6.73 2.86 5.88 chr1qtel1M 22508 22542 (977458) (AATA)n#Simple_repeat 1 34 (0) m_b28s252i6 976 chr1qtel1M 22508 AATAAA-AAATAAATAAACTTAATAAATAGAACAAA 22542 - - v - i (AATA)n#Simpl 1 AATAAATAAATAAATAAA-TAAATAAATA-AATAAA 34 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.09 (3 / 34), avg. gap size = 1.00 (3 / 3) 22 3.81 0.00 0.00 chr1qtel1M 22797 22823 (977177) (C)n#Simple_repeat 1 27 (0) m_b28s252i7 977 chr1qtel1M 22797 CCCCCCCCCCCCCCCCCCCCCGCCCCC 22823 v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCC 27 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 244 21.28 4.26 0.00 chr1qtel1M 23814 23860 (976140) L2b_3end#LINE/L2 407 455 (11) m_b28s601i11 978 chr1qtel1M 23814 GCTTAGCACAG--CCTGGCATGCAGTAGGTGCTCGATAAGTGCCTGTTG 23860 i -- ii i ii i iii L2b_3end#LINE 407 GCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTTGTTG 455 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 24.49 CpG sites = 10, Kimura (unadjusted) = 27.72 Transitions / transversions = 1.00 (10/0) Gap_init rate = 0.02 (1 / 46), avg. gap size = 2.00 (2 / 1) 274 30.34 10.04 5.00 chr1qtel1M 24370 24598 (975402) L2c_3end#LINE/L2 233 472 (6) m_b28s601i12 979 chr1qtel1M 24370 CCCAGAAACCTTCC-TGACTTCCGGCAAGTCTCTTACAAGAAGCTTTTCC 24418 vi i - ii -- ? vv vi i viv i iii L2c_3end#LINE 233 CCGGGAAGCCTTCCCTGACCCCC--CAAGNCTAGTCTAGGTGCCCTCCTC 280 chr1qtel1M 24419 CG-GCTCCCCT--CTCTCCGTTAAGTACTCCC-------TACCTATCCTG 24458 i - v -- v i i iv - -------i i v - L2c_3end#LINE 281 TGTGCTCCCATAGCACCCTGTCTA-TACTCCCATTATAGCACTTATCAT- 328 chr1qtel1M 24459 TCTCAGATCTATCTGTACAGATTTGTTTGCTTGT-TGTTTTCTC------ 24501 -- v vv v - vvvi i i ? - i i ------ L2c_3end#LINE 329 --TAACTTGTAT-TGTAATTGTCTGTTTACNTGTCTGTCTCCTCCACTAG 375 chr1qtel1M 24502 --TCTGAGCTCCCC-AGGGCCAGAATCAC--CTTTTCCATCTCTTTGAAC 24546 -- v ii- vi i i ii-- v i -- v i L2c_3end#LINE 376 ACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCT--TTGTAT 423 chr1qtel1M 24547 CCTCAGTTCCCTGTACATGTGAGGGGCTTAATGAATGTTAACTATTGAAA 24596 i iv iv i ivv v i i --- i v L2c_3end#LINE 424 CCCCAGCGCCTGGCACATAGTAGGCGCTCAATAAATGTT---TGTTGAAT 470 chr1qtel1M 24597 GA 24598 L2c_3end#LINE 471 GA 472 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 39.13 CpG sites = 39, Kimura (unadjusted) = 40.74 Transitions / transversions = 1.44 (39/27) Gap_init rate = 0.09 (20 / 228), avg. gap size = 1.75 (35 / 20) 30 0.00 0.00 0.00 chr1qtel1M 24611 24638 (975362) (T)n#Simple_repeat 1 28 (0) c_b28s251i0 980 chr1qtel1M 24611 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 24638 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 20 13.72 0.00 0.00 chr1qtel1M 25162 25193 (974807) (T)n#Simple_repeat 1 32 (0) m_b28s252i8 981 chr1qtel1M 25162 TTTTTTTGTTTTTTCTTATTTTTTTTCTTTTT 25193 v i v i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 32 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 282 27.98 10.29 2.74 chr1qtel1M 25308 25443 (974557) MIR3#SINE/MIR 9 154 (54) m_b28s601i14 982 chr1qtel1M 25308 GTGGTGCAGTGGATAAAGCATCTGTCCTGAAGTCAGGACACCTGAGCTCA 25357 ivv ii v i - v v iv i v i i v MIR3#SINE/MIR 9 GTGGCTGAGCAGAGAGAGCA-CGGACTGGGAGTCAGGAGACCTGGGTTCT 57 chr1qtel1M 25358 AATCTAGTCTCGGACACTTAATACTTCCTGTGTGAC--TGAGCAAGTCA- 25404 i iv v v v - -- ?v -- i - MIR3#SINE/MIR 58 AGTCCCGGCTCTGCCAC-TA--ACTNGCTGTGTGACCTTGGGCAAGTCAC 104 chr1qtel1M 25405 --CAACTC---------CAATTGCCTCAGGCAAAAAAAAAAGGGAGTGGA 25443 -- v --------- i v vviiv vi i iv MIR3#SINE/MIR 105 TTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGA 154 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 35.68 CpG sites = 17, Kimura (unadjusted) = 35.68 Transitions / transversions = 0.85 (17/20) Gap_init rate = 0.06 (8 / 135), avg. gap size = 2.25 (18 / 8) 399 20.89 6.96 4.24 chr1qtel1M 25308 25422 (974578) MIRc#SINE/MIR 10 127 (141) m_b28s601i13 982 chr1qtel1M 25308 GTGGTGCAGTGGATAAAGCATCTGTCCTGAAGTCAGGAC-ACCTGAGCTC 25356 v i iiv v i i v- i i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr1qtel1M 25357 AAATCTAGTCTCGGACACTTAATACTTCCTGTGTGAC--TGAGCAAGTCA 25404 i i iv v v v v ---v -- i MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTA---GCTGTGTGACCTTGGGCAAGTCA 106 chr1qtel1M 25405 C--AA---CTCCAATTGCCTCAG 25422 -- --- ii -- MIRc#SINE/MIR 107 CTTAACCTCTCTGA--GCCTCAG 127 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 23.64 CpG sites = 13, Kimura (unadjusted) = 24.84 Transitions / transversions = 1.30 (13/10) Gap_init rate = 0.08 (9 / 114), avg. gap size = 1.44 (13 / 9) 268 33.12 0.00 2.03 chr1qtel1M 25542 25692 (974308) L1HS_3end#LINE/L1 121 268 (634) m_b28s551i1 983 chr1qtel1M 25542 AAAAAAGAAAAAAAATAACACTCCAAATCACTAATCATTAGAGAAATGCA 25591 v v vi iv ii vvv iii i L1HS_3end#LIN 121 AAAAAACACATGAAGAAATGCTCATCATCACTGGCCATCAGAGAAATGCA 170 chr1qtel1M 25592 AATTAAAGGAACTCTGAGGTTTCACCTCCCACCAATCAGGCTGACAAAAA 25641 i ivv v i v i v i i iv i vv L1HS_3end#LIN 171 AATCAAAACCACTATGAGATATCATCTCACACCAGTTAGAATGGCAATCA 220 chr1qtel1M 25642 TGGCAAAAAAAAAGAAAAATGATGATTGTTGCAGAGATTGTGGAAAGATA 25691 --i ivv -i ii iiiv i v iv i i i L1HS_3end#LIN 221 T--TAAAAAGTCAG-GAAACAACAGGTGCTGGAGAGGATGCGGAGAAATA 267 chr1qtel1M 25692 G 25692 L1HS_3end#LIN 268 G 268 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 44.04 CpG sites = 29, Kimura (unadjusted) = 45.31 Transitions / transversions = 1.45 (29/20) Gap_init rate = 0.02 (3 / 150), avg. gap size = 1.00 (3 / 3) 286 24.18 6.11 5.30 chr1qtel1M 25548 25678 (974322) L1PA11_3end#LINE/L1 132 263 (658) m_b28s551i2 983 chr1qtel1M 25548 GAAAAAAAATAACACTCCAAATCACTAATCATTAGAGAAATGCAAATTAA 25597 i----- v v i i L1PA11_3end#L 132 GAAAAAAAG-----CTCAACATCACTGATCATTAGAGAAATGCAAATCAA 176 chr1qtel1M 25598 AGGAACTCTGAGGTTTCACCTCCCACCAATCAGGCTGAC-------AAAA 25640 ivv vv i vi i v i i iv i ------- L1PA11_3end#L 177 AACCACAATGAGATACCATCTCACGCCAGTCAGAATGGCTATTATTAAAA 226 chr1qtel1M 25641 ATGGCAAAAAAAAAGAAA-AATGATGATTGTTGCAGAGA 25678 - v v v i -iv ii -v i L1PA11_3end#L 227 A-GTCAAAAAACAACAGATGCTGGCGA-GGTTGCGGAGA 263 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 26.23 CpG sites = 16, Kimura (unadjusted) = 29.58 Transitions / transversions = 1.14 (16/14) Gap_init rate = 0.07 (9 / 130), avg. gap size = 1.67 (15 / 9) 287 20.97 6.73 3.74 chr1qtel1M 25551 25654 (974346) L1PB4_3end#LINE/L1 133 239 (664) m_b28s551i3 983 chr1qtel1M 25551 AAAAAATAACACTCCAAATCACTAATCATTAGAGAAATGCAAATTAAAGG 25600 i--- v v i iv L1PB4_3end#LI 133 AAAAAATG---CTCAACATCACTAATCATCAGAGAAATGCAAATTAAAAC 179 chr1qtel1M 25601 AACTCTGAGGTTTCACCTCCCACCAATCAGGCTGAC-------AAAAATG 25643 v vv i vi i iv i iv i ------- - L1PB4_3end#LI 180 CACAATGAGATACCATCTTACACCAGTCAGAATGGCTATTATTAAAAA-G 228 chr1qtel1M 25644 GCAAAAAAAAA 25654 v v L1PB4_3end#LI 229 TCAAAAAACAA 239 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 24.76 CpG sites = 10, Kimura (unadjusted) = 24.76 Transitions / transversions = 0.91 (10/11) Gap_init rate = 0.05 (5 / 103), avg. gap size = 2.20 (11 / 5) 430 30.73 7.91 2.25 chr1qtel1M 25562 25814 (974186) L1ME5_3end#LINE/L1 141 407 (534) m_b28s551i4 983 chr1qtel1M 25562 CTCCAAATCACTAATCATTAGAGAAATGCAAATTAAAGGAACTCTGAGGT 25611 v v i i v i iv vv i L1ME5_3end#LI 141 CTCAAACTCATTAGTAATCAGAGAAATGCAAATTAAAACAACAATGAGAT 190 chr1qtel1M 25612 TTCACCTCCCACCAATCAGGCTGACAAAAATGGCAAAAAAAAAGAAAAAT 25661 v i iv v i i i v--- i ivv i v L1ME5_3end#LI 191 ATCACTTTACACCTATTAGACTGGCAAAAATT---AGAAAGCTGGATAAT 237 chr1qtel1M 25662 GATGATTGTTGCAGAGATTGTGGAAAGATAG--ACCCATTAGTGTGGCAC 25709 vii v vv iv ii ? -- - i - iivii L1ME5_3end#LI 238 GCCAAGTGTTGGCGAGGATGTGGGGANATAGGAACCC-TCA-TGCACTGC 285 chr1qtel1M 25710 TAG-GAAAGTTCCGAACTGATGGAGCCATTCCAGAAATCAA--------- 25749 i - ii viv - i v ii i v --------- L1ME5_3end#LI 286 TGGTGGGAGTGTAG-ACTGGTGCAGCCATTCTGGAGAGCAATCTGGCAGT 334 chr1qtel1M 25750 ----AGTGGAA--AACTGCAC-TGGACTCTA-GACCCAGCCATACTGCTT 25791 ---- vi -- v ii -iiv i - v v i i L1ME5_3end#LI 335 ACTTAGTCAAATTAAGTATACGCATACCCTATGACCCAGCAATTCCGCTC 384 chr1qtel1M 25792 CTAGACTGATGCTCCAAAGAGAT 25814 i iivv iii i L1ME5_3end#LI 385 CTGGGTATATATCCCAAAGAAAT 407 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 40.52 CpG sites = 46, Kimura (unadjusted) = 41.24 Transitions / transversions = 1.53 (46/30) Gap_init rate = 0.05 (13 / 252), avg. gap size = 2.00 (26 / 13) 280 34.32 0.00 0.00 chr1qtel1M 26084 26252 (973748) L1P4_orf2#LINE/L1 3109 3277 (17) m_b28s551i6 984 chr1qtel1M 26084 GAAAACATCTTCACAGTCAAAGGTTCTGATAAAGGCCTCATTTCCAAAAT 26133 i v v i iv v v vv i i i v v i L1P4_orf2#LIN 3109 GAGAAAATATTCGCAAACTATGCATCCGACAAAGGTCTAATATCCAGAAT 3158 chr1qtel1M 26134 ATATAGAGAATTGACTCTAATTTATAAGAAATGAAGCCATTCTCCAATTA 26183 v ii i v vv v ? iv i v vi vvv vvi v L1P4_orf2#LIN 3159 CTATAAGGAACTTAAACAANTCAACAAGCAAAAAACAAATAACCCCATTA 3208 chr1qtel1M 26184 ATAAATGGTCAAAGGATATGAACAGACAATTTTGAGATGATGAAACTGAA 26233 v i v i v i v i v v v ivv L1P4_orf2#LIN 3209 AAAAGTGGGCAAAGGACATGAACAGACACTTCTCAAAAGAAGACATACAA 3258 chr1qtel1M 26234 GCTATTACCACTCATATGA 26252 viii v vv L1P4_orf2#LIN 3259 GCGGCCAACAAACATATGA 3277 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 44.32 CpG sites = 22, Kimura (unadjusted) = 46.32 Transitions / transversions = 0.61 (22/36) Gap_init rate = 0.00 (0 / 168), avg. gap size = 0.0 (0 / 0) 304 31.58 0.00 0.00 chr1qtel1M 26084 26216 (973784) L1PB_orf2#LINE/L1 3109 3241 (53) m_b28s551i5 984 chr1qtel1M 26084 GAAAACATCTTCACAGTCAAAGGTTCTGATAAAGGCCTCATTTCCAAAAT 26133 i v i v vivv i v v v i L1PB_orf2#LIN 3109 GAGAAAATCTTCACAATCTATACATCTGACAAAGGACTAATATCCAGAAT 3158 chr1qtel1M 26134 ATATAGAGAATTGACTCTAATTTATAAGAAATGAAGCCATTCTCCAATTA 26183 v i i? i v vv v ivii vi vvv ivv v i L1PB_orf2#LIN 3159 CTACAANGAACTCAAACAAATCAGCAAGAAAAAAACAAACAATCCCATCA 3208 chr1qtel1M 26184 ATAAATGGTCAAAGGATATGAACAGACAATTTT 26216 v i v v i i i L1PB_orf2#LIN 3209 AAAAGTGGGCTAAGGACATGAATAGACAATTCT 3241 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 41.61 CpG sites = 18, Kimura (unadjusted) = 41.61 Transitions / transversions = 0.75 (18/24) Gap_init rate = 0.00 (0 / 132), avg. gap size = 0.0 (0 / 0) 323 32.41 0.00 0.00 chr1qtel1M 26108 26252 (973748) L1P3_orf2#LINE/L1 3133 3277 (17) m_b28s551i8 984 chr1qtel1M 26108 TCTGATAAAGGCCTCATTTCCAAAATATATAGAGAATTGACTCTAATTTA 26157 i v v v i v i ii i v vv v L1P3_orf2#LIN 3133 TCTGACAAAGGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTA 3182 chr1qtel1M 26158 TAAGAAATGAAGCCATTCTCCAATTAATAAATGGTCAAAGGATATGAACA 26207 i vi vvv ivvi v i v i v i L1P3_orf2#LIN 3183 CAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACA 3232 chr1qtel1M 26208 GACAATTTTGAGATGATGAAACTGAAGCTATTACCACTCATATGA 26252 v i v i v v v i v v viii v vv L1P3_orf2#LIN 3233 GACACTTCTCAAAAGAAGACATTTATGCGGCCAACAAACATATGA 3277 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 41.44 CpG sites = 19, Kimura (unadjusted) = 42.57 Transitions / transversions = 0.68 (19/28) Gap_init rate = 0.00 (0 / 144), avg. gap size = 0.0 (0 / 0) 337 27.52 0.00 0.00 chr1qtel1M 26108 26216 (973784) L1PREC2_orf2#LINE/L1 3133 3241 (53) m_b28s551i7 984 chr1qtel1M 26108 TCTGATAAAGGCCTCATTTCCAAAATATATAGAGAATTGACTCTAATTTA 26157 i i v v iv v ii i v vv v L1PREC2_orf2# 3133 TCTGACAAAGGTCTAATATCCAGCATCTATAAGGAACTTAAACAAATTTA 3182 chr1qtel1M 26158 TAAGAAATGAAGCCATTCTCCAATTAATAAATGGTCAAAGGATATGAACA 26207 i vi vvv ivvi v v i v i L1PREC2_orf2# 3183 CAAGAAAAAAACAAACAACCCCATTAAAAAGTGGGCAAAGGACATGAACA 3232 chr1qtel1M 26208 GACAATTTT 26216 v L1PREC2_orf2# 3233 GACACTTTT 3241 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 34.35 CpG sites = 12, Kimura (unadjusted) = 34.35 Transitions / transversions = 0.67 (12/18) Gap_init rate = 0.00 (0 / 108), avg. gap size = 0.0 (0 / 0) 1554 30.37 1.44 0.96 chr1qtel1M 26131 26755 (973245) L1ME4c_3end#LINE/L1 12 639 (191) m_b28s551i9 984 chr1qtel1M 26131 AATATATAGAGAATTGACTCTAATTTATAAGAAATGAAGCCATTCTCCAA 26180 ? i ii v i v v vi? v v vv i L1ME4c_3end#L 12 ANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAAGACCCCAA 61 chr1qtel1M 26181 TTAATAAATGGTCAAAGGATATGAACAGACAATTTTGAGATGATGAAACT 26230 vi v i ivv ? v v iv L1ME4c_3end#L 62 TAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAGGAAATA 111 chr1qtel1M 26231 GAAGCTATTACCACTCATATG----AGTGTTCCAAATCACTATTGATTAG 26276 v ?ivi v v vv i ---- i v vv i v i i i L1ME4c_3end#L 112 CAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTAGTAATCAA 161 chr1qtel1M 26277 AGAAATGCAAATTAAGACAACTCTGAGATACCACTACACACCTGTCAGAT 26326 ii vv i vi i i i i L1ME4c_3end#L 162 AGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCTATTAAAT 211 chr1qtel1M 26327 TGGCTAAGATGACAGGGAAAGATAATGATGATTGTTGGAGGGGATGCGGG 26376 i v i vvv iii vv iviv v i v i ? v L1ME4c_3end#L 212 TAGCAAAAATTTAAAAAATTGATAATACCCAATGCTGGCGAGGNTGCGGT 261 chr1qtel1M 26377 AAAACTGGGACACTGATACATTGTGGGTAGAGCTGTGAACGAATCCAACC 26426 i v ? v iv i vi? i ivii v L1ME4c_3end#L 262 GAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACAACC 311 chr1qtel1M 26427 ATTCTGGAGAGCAATTTGGAACTATGCCCCAAAAGTTATCAAACTGTGCA 26476 v i i v v i ivi i ii v v v L1ME4c_3end#L 312 CTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAAAATGTTCA 361 chr1qtel1M 26477 TACCCTTTGATCCAGCAGTGCTACTACTGGGCTTATACCTCAAGGAGAGA 26526 i i i v i v vv v i ii i v L1ME4c_3end#L 362 TACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATA 411 chr1qtel1M 26527 CT---AAAGAAGGGAAAGGGACCAGTATGTGCCAGAATGTTTGTGGCAGC 26573 v --- i i -- i - ii v ii ii v L1ME4c_3end#L 412 ATTCAAAAGAAGGAAAAAG--CTA-TATGCACGAAGATGTTCATTGCAGC 458 chr1qtel1M 26574 CCTGTTTGTAGTGGCCAGAAACTGGAAAATGAA--TGGATGCCCATCAAT 26621 vi i i i i v i i --v -- ii i v L1ME4c_3end#L 459 GTTATTTATAATAGCGAAAAATTGGAAA--CAACCTAAATGTCCAACAAT 506 chr1qtel1M 26622 TGGAGAATGGTTGAGTAAATTGTGGTATATGAATGTTACGGAATATTATT 26671 v i i i i v? iviv i v L1ME4c_3end#L 507 AGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATATTATG 556 chr1qtel1M 26672 GTTCTGTAAGAAATGACCAGGAGGATGAATACAGAGAGGCCTGGAGAGAC 26721 vvv ii v i iv vv v v v iiv vii v - i i L1ME4c_3end#L 557 CAGCCATTAAAAATGATAATTATGAAGACTATGTAGCAACATGGA-AAAT 605 chr1qtel1M 26722 TTACATGAACTGATGCTGAGTGAAATGAGCAGAA 26755 v vi vv i i i vi L1ME4c_3end#L 606 GTTTATGATATAATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.26 CpG sites = 100, Kimura (unadjusted) = 40.37 Transitions / transversions = 1.14 (100/88) Gap_init rate = 0.01 (9 / 624), avg. gap size = 1.67 (15 / 9) 14 8.85 0.00 0.00 chr1qtel1M 27070 27093 (972907) (GGGA)n#Simple_repeat 1 24 (0) m_b28s252i9 985 chr1qtel1M 27070 GGGAGGGGTGGAGGGAGGGAGGGA 27093 iv (GGGA)n#Simpl 1 GGGAGGGAGGGAGGGAGGGAGGGA 24 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 19 21.31 0.00 0.00 chr1qtel1M 27171 27208 (972792) (A)n#Simple_repeat 1 38 (0) m_b28s252i10 986 chr1qtel1M 27171 AATAATAAATAAATAAATAAAAAACAGAAAAAAAAAAA 27208 v v v v v v i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 38 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 194 32.39 10.62 1.63 chr1qtel1M 28168 28280 (971720) L2d2_3end#LINE/L2 409 531 (24) m_b28s601i15 987 chr1qtel1M 28168 ACACGTTTGTCGCTAGTCTCCCC-ATTAGA-------CTCCCCGA-GGCA 28208 ii i vv v - i ------- ii - L2d2_3end#LIN 409 ACGTGTTTATGTCTTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCA 458 chr1qtel1M 28209 GGAGCTGGGCTCCCTCTTTCTTTGTACCTC---CGGGGTTGAGCTCGGTG 28255 ii iiv iiiiv vi i i --- i v iiv v i L2d2_3end#LIN 459 GGGACCATGTCTTATACTTCTTTGTATCCCCCACAGCGCCTAGCACAGTG 508 chr1qtel1M 28256 CCTGAGGTACACAGCCGGCACTTAA 28280 --v i iv i i L2d2_3end#LIN 509 CCT--TGCACACAGTAGGCGCTCAA 531 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 41.92 CpG sites = 25, Kimura (unadjusted) = 45.40 Transitions / transversions = 2.27 (25/11) Gap_init rate = 0.05 (6 / 112), avg. gap size = 2.33 (14 / 6) 635 31.59 11.02 4.64 chr1qtel1M 29532 30039 (969961) L2#LINE/L2 1939 2477 (605) m_b28s601i16 988 chr1qtel1M 29532 TGATTTCTCTCCAATCTTCCCTCCAATCTCACCATTTCACTAAAATTGTT 29581 vii v vvv i i ivi i i i ii i i L2#LINE/L2 1939 TGAACCCACTCCAATCAGGCTTTCGTCCCCACCACTCCACCGAAACTGCT 1988 chr1qtel1M 29582 CTTCCCAAAGATGCCGGCGATCTT-A-GTTGCCAAATCTGATGGCCTTTT 29629 vi i vii iii i i- - i ii i vv L2#LINE/L2 1989 CTTGTCAAGGTCACCAATGACCTCCACGTTGCTAAATCCAATGGTCAATT 2038 chr1qtel1M 29630 CTCGGTCCT--TCTT-------CTCCC--------TTGACAC--TCAATC 29660 i -- ------- ?i -------- -- ii L2#LINE/L2 2039 CTCAGTCCTCATCTTACTTGACCTNTCAGCAGCATTTGACACAGTTGATC 2088 chr1qtel1M 29661 ACTCTTCTCTCTTTGACAATCTTTTTTC-CTAGGTTTTGGGGGTGTCCCT 29709 iiii ii v vv i - v i ivi iiii v v L2#LINE/L2 2089 ACTCCCTCCTTCTTGAAACACTTTCTTCACTTGGCTTCCAGGACACCACA 2138 chr1qtel1M 29710 CTGTCCTGATCCTCCTCCTTCCTATCTAATTGCTC---CTCAGTCTCCTT 29756 v i ii v vv iiii --- L2#LINE/L2 2139 CTCTCCTGGTTTTCCTCCTACCTCACTGGCCGCTCCTTCTCAGTCTCCTT 2188 chr1qtel1M 29757 TGCTG---CATCTTCATTCAGACCTTGCCCTTTAACCAT---ACTTAGCC 29800 --- v i ii--- ii v i ? v i --- v vvv L2#LINE/L2 2189 TGCTGGTTCCTCCTCATCT---CCCCGACCTCTNAACGTTGGAGTGCCCC 2235 chr1qtel1M 29801 A---TTCTGTCC-TGTACC----CTCTTCTCCCTCTAC-TTCA----TTT 29837 ---i v - v ---- iv -i ----i ? L2#LINE/L2 2236 AGGGCTCAGTCCTTGGACCTCTTCTCTTCTCTATCTACACTCACTCCCTN 2285 chr1qtel1M 29838 AATGATCTCATTT-TCCCCATAGATTCAGTTATCATCTCTAAGCTGATGA 29886 ii ii-vi i i v i iv i v v L2#LINE/L2 2286 GGTGATCTCATCCAGTCTCATGGCTTTAAATACCATCTATATGCTGATGA 2335 chr1qtel1M 29887 TCCTCAAATCTACTTATCAACCCCCCCCCCCACACACACACACACTTCTC 29936 ii i i -- ---------- i -----i v iv i L2#LINE/L2 2336 CTCCCAAATTTA--TAT----------CTCCA-----GCCCGGACCTCTC 2368 chr1qtel1M 29937 TTCTTGCTTCTAGTTTTCCACTTCTGAATGCCTA-TTGAAA-----ACTT 29980 ii vivi i vi ivi iv ii v - i v ----- L2#LINE/L2 2369 CCCTGAACTCCAGACTCGTATATCCAACTGCCTACTCGACATCTCCACTT 2418 chr1qtel1M 29981 AGGGTTCATATCAGGTGGACATATTAAATTCAACATGTTTGAAATTGAAC 30030 i ----- i vii i i v i i i iii i L2#LINE/L2 2419 GG-----ATGTCTAATAGGCATCTCAAACTTAACATGTCCAAAACTGAAC 2463 chr1qtel1M 30031 -----ATTTTCCCC 30039 ----- i L2#LINE/L2 2464 TCCTGATCTTCCCC 2477 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 41.03 CpG sites = 106, Kimura (unadjusted) = 44.23 Transitions / transversions = 2.26 (106/47) Gap_init rate = 0.09 (44 / 507), avg. gap size = 1.84 (81 / 44) 522 39.30 3.36 2.04 chr1qtel1M 30681 31067 (968933) L2#LINE/L2 2691 3082 (0) m_b28s601i17 988 chr1qtel1M 30681 CAGGCCTTTATCATCTCAATTCTGAATTATTGCACATTATCCTATGGGTG 30730 i vii vvvi i i - vii iiv iiv L2#LINE/L2 2691 CAAGCCACCATCATCTCTCGCCTGGATTACTGCA-ATAGCCTCCTAACTG 2739 chr1qtel1M 30731 AGTCTGCCTGCCTCAAGTATCTTTCCGCTACAATCTAACTTTCATTCAGG 30780 - v i v viv ivii v ? i vii iv iv - L2#LINE/L2 2740 -GTCTCCCTGCTTCCACCCTTGCCCCCCTNCAGTCTATTCTCAACACAG- 2787 chr1qtel1M 30781 CACACA-AGTGATTCTTTAAAGGTGCAAGCTTGACCACATCACTTTTCTC 30829 vv - i v iii i iiv i ii ii v L2#LINE/L2 2788 CAGCCAGAGTGATCCTTTTAAAACGTAAGTCAGATCATGTCACTCCTCTG 2837 chr1qtel1M 30830 TTCAATAAACTTCAGTGACTCCCTATTGCCTGCAGGAGCAAATG-CAAAA 30878 i v vv i i i i i iv viv - i v - i L2#LINE/L2 2838 CTCAAAACCCTCCAATGGCTTCCCATCTCACTCA-GAGTAAAAGCCAAAG 2886 chr1qtel1M 30879 TGCTCCGTTTGGCATTCAGAGCTTT--ATAATCTAATTCCCTCCTATCTT 30926 v ivvvv v v ii ii -- i ii i ivi i i L2#LINE/L2 2887 TCCTTACAATGGCCTACAAGGCCCTACATGATCTGGTCCCCCGTTACCTC 2936 chr1qtel1M 30927 TCCAGTCTTCTCATGCTTTAGTCACGAGACATCTT-----CTCCAGTTTA 30971 iii---i viii -i vvvv vi i----- iv ii L2#LINE/L2 2937 TCTGA---CCTCATCTCCTA-CCACTCTCCCCCTCGCTCACTCCGCTCCA 2982 chr1qtel1M 30972 GTGACACTGACCTTCTGGCTGTACCATAAACAAGCAAATCTGTTTCTTGG 31021 iv i i v v vii v v iv vvvi ii v L2#LINE/L2 2983 GCCACACTGGCCTCCTTGCTGTTCCTCGAACACGCCAGGCACGCTCCCGC 3032 chr1qtel1M 31022 CTCTGAGCATTT----TCTCTATCTCTCATGCCTGGAATGATCTCCATCC 31067 v i v ---- iv i ii iiv i v i vi L2#LINE/L2 3033 CTCAGGGCCTTTGCACTTGCTGTTCCCTCTGCCTGGAACGCTCTTCCCCC 3082 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 54.84 CpG sites = 89, Kimura (unadjusted) = 59.21 Transitions / transversions = 1.48 (89/60) Gap_init rate = 0.03 (13 / 386), avg. gap size = 1.62 (21 / 13) 292 35.46 5.65 4.37 chr1qtel1M 30806 31212 (968788) AmnL2-1#LINE/L2 2138 2549 (64) m_b28s601i18 988 chr1qtel1M 30806 AAGCTTGACCACATCACTTTTCTCTTCAATAAACTTCAGTGACTCCCTAT 30855 vi iiiiv i vv i v i i AmnL2-1#LINE/ 2138 AAGCGCGACCACATCACCCCCATCCTCAAACAACTCCACTGGCTCCCCAT 2187 chr1qtel1M 30856 TGCCTGCAGGAGCAAATGCAAAA-TGCTCCGTTTGGCATTCAGA-GCTTT 30903 vvi v v v i v - iiivi viv v i -v ii AmnL2-1#LINE/ 2188 TCATTTCAGGATCCAGTTCAAAATTGCCTTCCTTGTTTTTAAAACCCTCC 2237 chr1qtel1M 30904 ATAATCTAATTCCCTCCTATCTTTCCAGTCTTCTCATGCTTTAGTCACGA 30953 iiv vii vv i iv viii v viv i v v vv AmnL2-1#LINE/ 2238 ATGGACTTGCTCCAGCCTACCTCACGGACCTTGTCTCTCTCTACTCCCCT 2287 chr1qtel1M 30954 GACATCT-TCTCCA---GTTTAGTGACACTGACCTTCTGGCTGTACCATA 30999 vv vv -i i--- i --- i i i vv v v - AmnL2-1#LINE/ 2288 CCCCGCTCCCTCCGCTCGTCTAG---CACCGGCCTCCTCTCTGTCCCTT- 2333 chr1qtel1M 31000 AACAAGCAAATCTGT--TTCTTGGCTCT-GAGCATT-TTCTCTATCTCTC 31045 -- vi viii i--i v iv v- v - i iivv AmnL2-1#LINE/ 2334 --CACACAATCTCGCCACTGTTGGTGCGAGAGCCTTCTCCTCTGCAGCTC 2381 chr1qtel1M 31046 ATGC---CTGGAATGATCTCC----ATC-CTCTGCCCTTCCTA-TTTCCC 31086 v --- iiii i ---- - i iivi v - i v AmnL2-1#LINE/ 2382 CTGCCATCTGGAACAGCCTTCCTGTATCTCTCCGCCTCATCGACTCTCCA 2431 chr1qtel1M 31087 TGACTTTCTTTAAATTCCAACTAAAATCCCATTTTCTACTGGAAGTCTTC 31136 -- i?i i ii ? i v vi i i - ----vi v AmnL2-1#LINE/ 2432 T--CTCNTTTCAAATCTCANCTGAAAACATATCTTTT-CT----CCCTTG 2474 chr1qtel1M 31137 CCCA-ACCCCTCAATTCCAGTGCCTTCCCTCTGTTAACTATTTCCTATTT 31185 i - i i i ---v ii i - i vi AmnL2-1#LINE/ 2475 CCTATACCTCTTAATTTC---TCTCTCCCTCTGCT-ATTATTTATTATTT 2520 chr1qtel1M 31186 -ATAGTGTA--TGTAATTGTTTGAACCTAT 31212 - ivv -- - i i vi i AmnL2-1#LINE/ 2521 AACTCTGTAACTGT-ATTATTTAACTCTGT 2549 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 47.74 CpG sites = 80, Kimura (unadjusted) = 50.33 Transitions / transversions = 1.38 (80/58) Gap_init rate = 0.08 (32 / 406), avg. gap size = 1.28 (41 / 32) 354 28.94 16.51 4.66 chr1qtel1M 30900 31323 (968677) L2c_3end#LINE/L2 1 472 (6) m_b28s601i20 988 chr1qtel1M 30900 CTTTATAATCTAATTCCCTCCTATCTTTCCAGTCTTCTCATGCTTTAGTC 30949 ?i ii iiii iv i i i iv - v ii v L2c_3end#LINE 1 CTNCACGATCTGGCCCCTGCCTACCTCTCCAGCCTCATC-TCCTCCACTC 49 chr1qtel1M 30950 ACGAGACATCTTCTCCA----GTTT-AGTGACACTGACCTTCTGGCTGTA 30994 v ---- vi ivi ---- i i- iv v ? v -i v L2c_3end#LINE 50 CC----CTCCTCGCCCACTATGCTCCAGCCACACTGAACTNCTTGC-ATT 94 chr1qtel1M 30995 CCATAAACAAGCAA-ATCTGTTTCTTGGCTCTGAGCATTTTC---T-CTA 31039 vi v vi- vi v i v i ? v v --- - i L2c_3end#LINE 95 CCCCAAACACGCCGCAGTTCTTTCCTGCCTCCGNGCCTTTGCACATGCTG 144 chr1qtel1M 31040 TCTCTCATGCCTGGAATGATCTCCATCCTCTGCCCTTCCTATTTCCCTGA 31089 ii iiv v i -i i -- - ii vv i L2c_3end#LINE 145 TTCCCTCTGCCTGGAATGCTCTTC-CCCCCT--CCTTCC-ACCTGGCTAA 190 chr1qtel1M 31090 CT--------TTCTTTAAATTCCAACTAAAATCCCATTTTCTACTGGAAG 31131 -------- i i i?ii i v i vi ii i v v L2c_3end#LINE 191 CTCCTACTCATCCTTCAAGNCTCAGCTCAGATGTCACCTCCTCCGGGAAG 240 chr1qtel1M 31132 TCTTCCCCAACCCCTCAATTCCA------GTGCCTTCCCTCTGT------ 31169 i ii i v? i ------ i - ------ L2c_3end#LINE 241 CCTTCCCTGACCCCCCAAGNCTAGTCTAGGTGCCCT-CCTCTGTGCTCCC 289 chr1qtel1M 31170 -TAA--------CTAT-TTCCTATTTATAGTG--TAT--GTAA-TTGT-T 31203 - i-------- -i i - ii-- --v - - L2c_3end#LINE 290 ATAGCACCCTGTCTATACTCCCA-TTATAGCACTTATCATTAACTTGTAT 338 chr1qtel1M 31204 TGAACCTATTTGTTTGCG----TGTCTCCTTCA----------AGCTTCC 31239 v vi i i i ?---- i ---------- i i L2c_3end#LINE 339 TGTAATTGTCTGTTTACNTGTCTGTCTCCTCCACTAGACTGTGAGCTCCT 388 chr1qtel1M 31240 ---ATGCAGGGTCTTTGAT---TTCAT-TTTGTATGGACAAAACTTAACA 31282 ---iv v iv vi--- - -------- ii-- L2c_3end#LINE 389 TGAGGGCAGGGACCGTGTCTTATTCATCTTTGTAT--------CCC--CA 428 chr1qtel1M 31283 GTGTCTTGCAGACAGTAGCAGCT---TAAAACTTTATTGATTGA 31323 i i v v i vv --- vv i v L2c_3end#LINE 429 GCGCCTGGCACATAGTAGGCGCTCAATAAATGTTTGTTGAATGA 472 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 36.50 CpG sites = 75, Kimura (unadjusted) = 39.12 Transitions / transversions = 1.79 (75/42) Gap_init rate = 0.10 (43 / 423), avg. gap size = 2.14 (92 / 43) 366 34.54 6.56 5.90 chr1qtel1M 30900 31219 (968781) L2d2_3end#LINE/L2 1 322 (233) m_b28s601i19 988 chr1qtel1M 30900 CTTTATAATCTAATTCCCTCCTATCTTTCCAGTCTTCTCATGCTTTAGTC 30949 ii ii iiii vv ?i i v viv vi v L2d2_3end#LIN 1 CTCCACGATCTGGCCCCAACCTNCCTTTCCAGCCTTATCTCCCACTATTC 50 chr1qtel1M 30950 ------ACGAGACATCTTCTCCAGTTTAGTGACACTGACCTTCTGGCTGT 30993 ------ iv v iv ii----- v ii v vi L2d2_3end#LIN 51 CCCTNCACGAACCCTCCGCTCCAGCC-----AAACTGGTCTACTCACTGT 95 chr1qtel1M 30994 ACCATAAACAAGCAAATCTG---TTTCTTGGCTCTGAGCATTTTCTC--- 31037 v vii v ---ii ---? ii v v v v --- L2d2_3end#LIN 96 CCCCCGAACACGC---CTTGCGCNTTCCCGCCTCTGCGCCTTTGCTCACG 142 chr1qtel1M 31038 -TATCTCTCATGCCTGGAATGATCTCCATCCTCTGCCCTTCCTATTT--- 31083 -ii ii i vi vi i vi i iv i iv ii--- L2d2_3end#LIN 143 CCGTTCCCCCCGCCTGGAATGCCCTTCCCCTTCCTCTCCACCTATCCAAA 192 chr1qtel1M 31084 CCCTGACT-TTCTTTAAATTCCAACTAAAATCCCATTTTCTACTGGAAGT 31132 i iv i- i i ivi i v ? ii i v vv i L2d2_3end#LIN 193 TCCTACCCATCCTTCAAGGCCCAGCTCAAATNCCACCTCCTCCGTGAAGC 242 chr1qtel1M 31133 CTTCCCCAACCCCTCAATTCC--AGTG--CCTTCCCTCTGTTAACTATTT 31178 ii v v vi -- -- ii ivi i -- i i L2d2_3end#LIN 243 CTTCCCTGACCACTCCAGCCCGNAGTGATCTCTCCCTCCTCTGA--ACTC 290 chr1qtel1M 31179 CCTATTTATAGTGTATGTAATTGTTTGAACCTATTTGTTTG 31219 ----- ii---? v i v - ii L2d2_3end#LIN 291 C-----TATAGCA---NTTATTGTCTGTACC-ATTCATTTG 322 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 45.71 CpG sites = 67, Kimura (unadjusted) = 50.04 Transitions / transversions = 1.81 (67/37) Gap_init rate = 0.08 (26 / 319), avg. gap size = 1.54 (40 / 26) 324 39.39 3.61 0.58 chr1qtel1M 31651 31816 (968184) C L2#LINE/L2 (240) 2842 2672 m_b28s601i21 989 chr1qtel1M 31651 TTGAACAAAAGAAATTACACAGTCAGAACTGTGTTTTAGAAAAATCATTT 31700 i i i i- v iii v vi ii i ii i i C L2#LINE/L2 2842 TTGAGCAGAGGAG-TGACATGATCTGACTTACGTTTTAAAAGGATCACTC 2794 chr1qtel1M 31701 TGGTGACTTTACATAAAAGGAATT--AGAGAAACAAGATTTACATCAGGC 31748 ivi v iivv i vii i -- i iii iv viv v v C L2#LINE/L2 2793 TGGCTGCTGTGTTGAGAATAGACTGNAGGGGGGCAAGGGTGGAAGCAGGG 2744 chr1qtel1M 31749 AGACCCACCAAAAG--TGTTGAAACAATCCAGGCATGAATTGCTGGGAGC 31796 viii ii -- i v ii iv iv v vi C L2#LINE/L2 2743 AGACCAGTTAGGAGGCTATTGCAGTAATCCAGGCGAGAGATGATGGTGGC 2694 chr1qtel1M 31797 CTGCACTA--GTGATGGCTATG 31816 i v i -- i vi C L2#LINE/L2 2693 TTGGACCAGGGTGGTGGCAGTG 2672 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 58.26 CpG sites = 44, Kimura (unadjusted) = 61.37 Transitions / transversions = 2.10 (44/21) Gap_init rate = 0.02 (4 / 165), avg. gap size = 1.75 (7 / 4) 268 38.04 0.00 0.00 chr1qtel1M 32855 32946 (967054) C L2#LINE/L2 (1050) 2032 1941 m_b28s601i22 989 chr1qtel1M 32855 CCATTGGATTTGGCAATCAAGAGATCGTTAATAACTGTGGAAAAAGCAGT 32904 i ivvi i i ii i iv iv i C L2#LINE/L2 2032 CCATTGGATTTAGCAACGTGGAGGTCATTGGTGACCTTGACAAGAGCAGT 1983 chr1qtel1M 32905 CCTGACTGAGATTTGAGATCAGAAGTCCCATTATGGTGGGTT 32946 iii iiv vvv i iv ii i iv ivi C L2#LINE/L2 1982 TTCGGTGGAGTGGTGGGGACGAAAGCCTGATTGGAGTGGGTT 1941 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 50.52 CpG sites = 24, Kimura (unadjusted) = 58.10 Transitions / transversions = 2.18 (24/11) Gap_init rate = 0.00 (0 / 91), avg. gap size = 0.0 (0 / 0) 205 24.66 5.06 2.47 chr1qtel1M 33532 33610 (966390) Penelope1_Vert#LINE/Penelope 465 545 (534) m_b28s601i23 990 chr1qtel1M 33532 AAGTTTTTCAATAATAGGTGCATT---CCAGACCACTCCTCAATTCTACC 33578 v -ii v v --- - vv v i iv Penelope1_Ver 465 AAGTTGTT-GGTAAGAGCTGCATTAAACCAG-CCTGTCATCAATCCTGGC 512 chr1qtel1M 33579 TCTAAGCCATAAAATTCAAAGAGGTGCA-TACC 33610 v v vv iv i i - Penelope1_Ver 513 TCTCACCGCTGTAACTCAAAGAGATGCACTACC 545 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.94 CpG sites = 7, Kimura (unadjusted) = 29.94 Transitions / transversions = 0.58 (7/12) Gap_init rate = 0.05 (4 / 78), avg. gap size = 1.50 (6 / 4) 16 9.55 0.00 0.00 chr1qtel1M 35562 35584 (964416) (C)n#Simple_repeat 1 23 (0) m_b28s252i11 991 chr1qtel1M 35562 CCCCCCCCCTCCCCCCCCCTCCC 35584 i i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCC 23 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 15 7.84 0.00 3.57 chr1qtel1M 38715 38743 (961257) (ATTTT)n#Simple_repeat 1 28 (0) m_b29s252i0 992 chr1qtel1M 38715 ATTTCTTTTTTATTTTATTTTATTTTTTT 38743 - v v (ATTTT)n#Simp 1 ATTT-TATTTTATTTTATTTTATTTTATT 28 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1) 16 15.86 0.00 0.00 chr1qtel1M 38716 38743 (961257) (T)n#Simple_repeat 1 28 (0) m_b29s252i1 992 chr1qtel1M 38716 TTTCTTTTTTATTTTATTTTATTTTTTT 38743 i v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 28 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 402 31.41 3.74 1.83 chr1qtel1M 39154 39367 (960633) C L1ME5_3end#LINE/L1 (291) 650 433 m_b29s551i0 993 chr1qtel1M 39154 ATCTC---CTGGTTCT-GCTCATTTCACTCAGCATCA-GTTCATGTAAGT 39198 --- v -i iv ii - -- v v C L1ME5_3end#LI 650 ATCTCATTCTGTTTCTTACTTTTTTCACTCAGCACTATGTT--TTTAAGA 603 chr1qtel1M 39199 CTCGCCAATCCT-CTTTGTATTCATCCTGCTGGTCATTTCTTACAGAACA 39247 ii ii v vi - v i v iv iiv iii v v vvvv C L1ME5_3end#LI 602 TCCATCCATGTTGCTATGTGTACATCTAGTCCGTTGCTTCTAACTGCTGC 553 chr1qtel1M 39248 ATAATATTCCATAACATTCATATACCACAATTTACCCAACCACTCTCCAA 39297 i i iiii v vi v i v v C L1ME5_3end#LI 552 ATAGTACTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCA 503 chr1qtel1M 39298 CTGATGGGCATCCA--TTCATTTTCCAGTTTCTGGCCACTACAAACAGGG 39345 v i i -- --vii ii i iv i iv C L1ME5_3end#LI 502 GTGATGGACACCCAGGTT--GCCTCCAACTCCCCGCCACCACAAACAACG 455 chr1qtel1M 39346 CTGCCACAAACATTTTGGCACA 39367 v ii ii v i C L1ME5_3end#LI 454 CTGCAATGAACATCCTCGTACA 433 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 42.09 CpG sites = 39, Kimura (unadjusted) = 42.09 Transitions / transversions = 1.44 (39/27) Gap_init rate = 0.04 (9 / 213), avg. gap size = 1.33 (12 / 9) 411 26.27 1.67 1.67 chr1qtel1M 39248 39367 (960633) C L1ME3G_3end#LINE/L1 (376) 548 429 m_b29s551i1 993 chr1qtel1M 39248 ATAATATTCCATAACATTCATATACCACAATTTACCCAACCACTCTCCAA 39297 i ii vv i iii i i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr1qtel1M 39298 CTGATGGGCATCCA--TTCATTTTCCAGTTTCTGGCCACTACAAACAGGG 39345 i i ii -- --v i i v i i iv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTT--GTTTCCAATTTTTCGCTATTACAAACAATG 451 chr1qtel1M 39346 CTGCCACAAACATTTTGGCACA 39367 v ii ii v i C L1ME3G_3end#L 450 CTGCAATGAACATCCTTGTACA 429 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 34.23 CpG sites = 23, Kimura (unadjusted) = 34.23 Transitions / transversions = 2.88 (23/8) Gap_init rate = 0.03 (3 / 119), avg. gap size = 1.33 (4 / 3) 347 20.24 6.48 8.49 chr1qtel1M 39620 39727 (960273) C MIRc#SINE/MIR (153) 115 10 m_b29s601i0 994 chr1qtel1M 39620 GGGGTTAAGTGACTT-----AGGTCACACAGGTAAGAAGTGTTGAGTGTG 39664 i ----- v iv -------- C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTG--------G 74 chr1qtel1M 39665 TGAGAGC--AGATTTGAACTTGGGTCTTCCTGACTGCGGGGCCGGTGCTT 39712 i- --i i i iii v ii v i i C MIRc#SINE/MIR 73 C-AGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTC 25 chr1qtel1M 39713 TATCCACTGTGCCAC 39727 v ii C MIRc#SINE/MIR 24 TTTCCACTGCACCAC 10 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 23.09 CpG sites = 15, Kimura (unadjusted) = 24.47 Transitions / transversions = 3.00 (15/5) Gap_init rate = 0.10 (11 / 107), avg. gap size = 1.45 (16 / 11) 425 27.29 17.70 4.31 chr1qtel1M 41324 41549 (958451) C MIRb#SINE/MIR (12) 256 2 m_b29s601i1 995 chr1qtel1M 41324 ATCATTTATTAAGTACCTACTATGTATGA-ACTCTATCCTGAGCACTTGT 41372 i i ii i iiv -i v i v i i - C MIRb#SINE/MIR 256 ACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTT-T 208 chr1qtel1M 41373 ACAGATGTTATTTCATTT------------GACCCTGTGAGGAGGGTACA 41410 viii i ------------i i vi -- C MIRb#SINE/MIR 207 ACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTA-- 160 chr1qtel1M 41411 TTTATTATCTGTGTTTGACAGATGAGAAAAC------------------- 41441 - ivii v i ------------------- C MIRb#SINE/MIR 159 -TTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAA 111 chr1qtel1M 41442 ATGACTTGCCCGGAGTCGCAC----AGTAAGTAGT----CTGAGGATTTG 41483 i i iii i ---- i i---- i - i C MIRb#SINE/MIR 110 GTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG-GGATTCG 62 chr1qtel1M 41484 ACTTCAGGTCTTTCTGATCCCAGGCATTTCCCTTATACCTCATACATGCC 41533 vii v ii ii----v v iiv i ivi - v C MIRb#SINE/MIR 61 AACCCAGGTCTGTCTGACTCCAAA----GCCCGTGCTCTTTCCAC-TGCA 17 chr1qtel1M 41534 CCACAGCTGCCTCTTT 41549 - i i C MIRb#SINE/MIR 16 CCAC-GCTGCCCCTCT 2 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 32.56 CpG sites = 45, Kimura (unadjusted) = 36.54 Transitions / transversions = 3.21 (45/14) Gap_init rate = 0.07 (15 / 225), avg. gap size = 3.40 (51 / 15) 19 21.31 0.00 0.00 chr1qtel1M 41550 41587 (958413) (T)n#Simple_repeat 1 38 (0) m_b29s252i2 996 chr1qtel1M 41550 TTTTTTTTTTTTTTTTTTTTAATTATAGCTTTTTATTT 41587 vv v vvi v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 38 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 340 26.78 5.67 5.67 chr1qtel1M 42030 42223 (957777) C L1MC3_3end#LINE/L1 (1899) 633 440 m_b29s551i2 997 chr1qtel1M 42030 GCTCATTTCACTCAGCATCAGTTCATGTAAG--TAACTCCAAGTCTCTCT 42077 iv i vi - v v -- v - v i -- C L1MC3_3end#LI 633 GCTTCTTTCACTTAGCAATA-TGCATTTAAGATTCA-TCCATGTCTTT-- 588 chr1qtel1M 42078 GAAATCAT--CCTGCTGG-TCATTTCTT---ACCAAACAAAAATATTCCA 42121 ---- i -- i v i - --- i ivvv v C L1MC3_3end#LI 587 ----TCGTGGCTTGATAGCTCATTTCTTTTTATCGCTGAATAATATTCCA 542 chr1qtel1M 42122 TAACATTTATATACCACAGTTTACCCAACCATTTTCCAATTGATGGGCAT 42171 vii vv i iiii v iv v v i C L1MC3_3end#LI 541 TTGTATGGATGTACCACAGTTTGTTTATCCATTCACCTATTGAAGGACAT 492 chr1qtel1M 42172 CCACTTAAT---TTCCAGTTTCTGGTCACTACAAAGAGGGCTGCCACAAA 42218 --- ii --- i iv i ii v ii i i C L1MC3_3end#LI 491 ---CTTGGTTGCTTCCAGTTTTTGGCGATTATGAATAAAGCTGCTATAAA 445 chr1qtel1M 42219 CATTC 42223 C L1MC3_3end#LI 444 CATTC 440 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 31.43 CpG sites = 29, Kimura (unadjusted) = 33.94 Transitions / transversions = 1.45 (29/20) Gap_init rate = 0.08 (16 / 193), avg. gap size = 1.38 (22 / 16) 410 29.73 0.00 0.00 chr1qtel1M 42113 42223 (957777) C L1MD1_3end#LINE/L1 (439) 550 440 m_b29s551i3 997 chr1qtel1M 42113 AATATTCCATAACATTTATATACCACAGTTTACCCAACCATTTTCCAATT 42162 i iii vv i iiii iv vi C L1MD1_3end#LI 550 AGTATTCCATGGTATGGATGTACCACAGTTTGTTTAACCATTCACCCGTT 501 chr1qtel1M 42163 GATGGGCATCCACTTAATTTCCAGTTTCTGGTCACTACAAAGAGGGCTGC 42212 v i iivv vi i ii i i v ii C L1MD1_3end#LI 500 GAAGGACATCTGGGTTGTTTCCAGTTTTTGGCTATTACGAATAAAGCTGC 451 chr1qtel1M 42213 CACAAACATTC 42223 i i C L1MD1_3end#LI 450 TATAAACATTC 440 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 37.22 CpG sites = 24, Kimura (unadjusted) = 40.45 Transitions / transversions = 2.67 (24/9) Gap_init rate = 0.00 (0 / 110), avg. gap size = 0.0 (0 / 0) 226 13.77 10.17 1.56 chr1qtel1M 42247 42305 (957695) MIR3#SINE/MIR 82 145 (63) m_b29s601i2 998 chr1qtel1M 42247 CTGTGTGAC--TGTGCAGGTCACTTTACCTGCT---GGCCTCAG-GACCT 42290 -- v i i - --- -vv MIR3#SINE/MIR 82 CTGTGTGACCTTGGGCAAGTCACTTCACCT-CTCTGGGCCTCAGTTTCCT 130 chr1qtel1M 42291 TGCCTGTAAAATGAG 42305 iii MIR3#SINE/MIR 131 CATCTGTAAAATGAG 145 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 15.42 CpG sites = 5, Kimura (unadjusted) = 15.42 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.07 (4 / 58), avg. gap size = 1.75 (7 / 4) 190 28.77 10.96 0.00 chr1qtel1M 43273 43345 (956655) C MIRb#SINE/MIR (26) 242 162 m_b29s601i3 999 chr1qtel1M 43273 GTTTA-TGTTTGCTGAGTCTTGTGCTAAGCACTTTACA---AATATC--- 43315 i - i v iii ivi i --- v --- C MIRb#SINE/MIR 242 GCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACATGCATTATCTCA 193 chr1qtel1M 43316 TTTGGTCTTTACAACAGTTCCA-AAGGTAGG 43345 ii i i iii ii-i C MIRb#SINE/MIR 192 TTTAATCCTCACAACAACCCTGCGAGGTAGG 162 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 35.32 CpG sites = 18, Kimura (unadjusted) = 40.35 Transitions / transversions = 6.00 (18/3) Gap_init rate = 0.06 (4 / 72), avg. gap size = 2.00 (8 / 4) 217 27.08 13.54 0.00 chr1qtel1M 43717 43812 (956188) L3#LINE/CR1 3828 3936 (163) m_b29s601i4 1000 chr1qtel1M 43717 CCCCAAAGGACAGAA---GAA-----GGGGAGAAATTACTAAGAAGCAAA 43758 i i i --- i ----- vi i vii i i L3#LINE/CR1 3828 CTCCAGAGGGCAGAACTAGGACCAATGGGTGGAAGTTACAGGGAGGCAGA 3877 chr1qtel1M 43759 TTCAGGGTTAATA--AGGAAAAACTTC---ATAATTTGAGCTGTATATAA 43803 iv v i -- i i--- i iv vi v L3#LINE/CR1 3878 TTTCGGCTCAATATAAGGAAGAACTTTCTAACAATCAGAGCTGTCCAAAA 3927 chr1qtel1M 43804 ATGAAATAG 43812 i i L3#LINE/CR1 3928 ATGGAATGG 3936 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 35.57 CpG sites = 19, Kimura (unadjusted) = 35.57 Transitions / transversions = 2.71 (19/7) Gap_init rate = 0.04 (4 / 95), avg. gap size = 3.25 (13 / 4) 572 28.12 7.00 1.96 chr1qtel1M 43974 44216 (955784) C MIRb#SINE/MIR (1) 267 13 m_b29s601i5 1001 chr1qtel1M 43974 ATAATAATAGTTGACATTTAT-ATATATTTCCAATGTGTGAAAC----TG 44018 i- i iv -iviiii v v iv ii ---- C MIRb#SINE/MIR 267 ATAATAG-AGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTG 219 chr1qtel1M 44019 CTCAGTACTTTATA---ATTATTTCATTTGATTCTTACAACAACCCCGCG 44065 v ii i --- i i i i i - C MIRb#SINE/MIR 218 CTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGC- 170 chr1qtel1M 44066 GATGTAGGTGCTATCATTATGCCCATTTTA---GTTACAAAACTGAAA-- 44110 v --- i v ---i v vi ii-- C MIRb#SINE/MIR 169 GAGGTAGG---TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCT 123 chr1qtel1M 44111 TAATCAGGTTAAGTGACTTGCCCATGATCACACAG---ATAAATGTCTGA 44157 i ivv i v i ---i i v v C MIRb#SINE/MIR 122 CAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGA 73 chr1qtel1M 44158 AGCTGGTTTTGAAATTAGGTCTTCCTGAAGATAAACCTGGAGTTCTGACC 44207 iv v v i vii vi vvvi v iv v i vv C MIRb#SINE/MIR 72 GCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCC 23 chr1qtel1M 44208 A-TGTACCAC 44216 - i C MIRb#SINE/MIR 22 ACTGCACCAC 13 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 34.03 CpG sites = 39, Kimura (unadjusted) = 36.18 Transitions / transversions = 1.39 (39/28) Gap_init rate = 0.05 (12 / 242), avg. gap size = 1.83 (22 / 12) 492 19.25 0.00 9.09 chr1qtel1M 44980 45099 (954901) C MIRc#SINE/MIR (157) 111 2 m_b29s601i6 1002 chr1qtel1M 44980 TTAAGTGACTTGCTCAGGGTCACACAGATAGGAAGTGTTAAGTGTCTGAG 45029 i i v ------- v v C MIRc#SINE/MIR 111 TTAAGTGACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGCAGAG 69 chr1qtel1M 45030 GTCAGATTTGAACTCAGGTCTTCCTGACTTCAGGGCTAGTGCTCCATCCA 45079 vivi i i i i i v i iv C MIRc#SINE/MIR 68 CCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCA 19 chr1qtel1M 45080 CTGCTTCACCTAGCTGCCTC 45099 vi ---i C MIRc#SINE/MIR 18 CTGCACCAC---ACTGCCTC 2 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 20.10 CpG sites = 13, Kimura (unadjusted) = 22.42 Transitions / transversions = 1.62 (13/8) Gap_init rate = 0.08 (10 / 119), avg. gap size = 1.00 (10 / 10) 295 21.17 14.47 6.75 chr1qtel1M 47878 48029 (951971) C MIRc#SINE/MIR (0) 268 106 m_b29s601i7 1003 chr1qtel1M 47878 AACAACAATAGCAGCTGTCATTTATATAGCACCTACTACGTGCCAGGCAT 47927 i i i ?v vv i i -- ----- ---- C MIRc#SINE/MIR 268 AATAATAATAACNCCTTACATTTGTATAGCACTT--TAC-----AG---- 230 chr1qtel1M 47928 TGTACTAAGTACTT--AAAAAAATTAG-TCATTTGATCCTCACAACAACC 47974 v v ii -- v v v v- C MIRc#SINE/MIR 229 TTTACAAAGCGCTTTCACATACATTATCTCATTTGATCCTCACAACAACC 180 chr1qtel1M 47975 TTAGAAGGTAGGT------GTTGTTATCATCCC-----------TGAGGT 48007 i ivi i------ v i i ----------- v C MIRc#SINE/MIR 179 CTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGA 130 chr1qtel1M 48008 AACTGAGG--CAAATGAGTTGAGT 48029 -- i vii i C MIRc#SINE/MIR 129 AACTGAGGCTCAGAGAGGTTAAGT 106 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 24.52 CpG sites = 17, Kimura (unadjusted) = 25.59 Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.11 (16 / 151), avg. gap size = 2.06 (33 / 16) 547 20.15 9.70 0.00 chr1qtel1M 47884 48017 (951983) C MIR#SINE/MIR (0) 262 116 m_b29s601i8 1003 chr1qtel1M 47884 AATAGCAGCTGTCATTTATATAGCACCTACTACGTGCCAGGCATTGTACT 47933 ii iv vv i i i i v C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCT 213 chr1qtel1M 47934 AAGTACTTAAAAAA-ATTAG-TCATTTGATCCTCACAACAACCTTAGAAG 47981 ii v v vi- i- i i vi C MIR#SINE/MIR 212 AAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAG 163 chr1qtel1M 47982 GTAGGTGTTGTTATCATCCC-----------TGAGGTAACTGAGGCA 48017 ii i i ----------- v C MIR#SINE/MIR 162 GTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCA 116 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 21.98 CpG sites = 18, Kimura (unadjusted) = 24.07 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.02 (3 / 133), avg. gap size = 4.33 (13 / 3) 267 32.73 0.00 0.00 chr1qtel1M 48146 48255 (951745) C L1ME4b_3end#LINE/L1 (323) 569 460 m_b29s551i4 1004 chr1qtel1M 48146 TTGTTTCTTACAAAACCATAATATTCCATAACATTCATATACCATAACTT 48195 v i iivvv i vii vv i i C L1ME4b_3end#L 569 TTCTTTTTTACGGCTGCATAGTATTCCATTGTATGGATGTACCATAATTT 520 chr1qtel1M 48196 GTTCAGCCATTTCCCAACTGATGGGCATCCACTCAGTCTCCATTTCCTTG 48245 i i i v i v i i ii vviv i v iii C L1ME4b_3end#L 519 ATTTAACCAGTCCCCTATTGATGGACATTTAGGTTGTTTCCAATCTTTTG 470 chr1qtel1M 48246 CCAGTACAAA 48255 i v C L1ME4b_3end#L 469 CTATTACAAA 460 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 43.10 CpG sites = 22, Kimura (unadjusted) = 44.81 Transitions / transversions = 1.57 (22/14) Gap_init rate = 0.00 (0 / 109), avg. gap size = 0.0 (0 / 0) 335 27.66 0.00 0.00 chr1qtel1M 48162 48255 (951745) C L1ME3G_3end#LINE/L1 (375) 549 456 m_b29s551i5 1004 chr1qtel1M 48162 CATAATATTCCATAACATTCATATACCATAACTTGTTCAGCCATTTCCCA 48211 i ii vv i i i i i v C L1ME3G_3end#L 549 CATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCT 500 chr1qtel1M 48212 ACTGATGGGCATCCACTCAGTCTCCATTTCCTTGCCAGTACAAA 48255 i i ii vviv i v ii i i v C L1ME3G_3end#L 499 ATTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAA 456 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 34.46 CpG sites = 18, Kimura (unadjusted) = 36.23 Transitions / transversions = 2.25 (18/8) Gap_init rate = 0.00 (0 / 93), avg. gap size = 0.0 (0 / 0) 18 18.05 0.00 0.00 chr1qtel1M 50375 50407 (949593) (AT)n#Simple_repeat 1 33 (0) m_b29s252i3 1005 chr1qtel1M 50375 ATATATGTATATATATACACGCATATATATATA 50407 i i iii (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATA 33 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 226 32.26 4.84 0.00 chr1qtel1M 50888 51011 (948989) C L1MC4a_3end#LINE/L1 (2052) 577 448 m_b29s551i6 1006 chr1qtel1M 50888 ATCCTGCTGATTGTTTCTTGTAGA---ACAATATTTCATTTCATTCATGT 50934 i v v v i ii v--- i i i i vii vv C L1MC4a_3end#L 577 ATCTTCCTCATTCTTTTTTACAGCTGCATAGTACTCCATTGTGTGGATGT 528 chr1qtel1M 50935 ATCATAACTTACTCAACTATTCT---GTGGATGGGCATCCACTCAGTTTC 50981 i ii i i ? ---i ?? ii vviv C L1MC4a_3end#L 527 ACCATAGTTTATTCAACCANTCTCCTATNNATGGGCATTTAGGTTGTTTC 478 chr1qtel1M 50982 CAGTTCCTTTCCTCTACAAAAAGAGCTGCA 51011 i vii v vvi v iv C L1MC4a_3end#L 477 CAATATTTTGCAATTACAAACAATGCTGCA 448 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 45.32 CpG sites = 24, Kimura (unadjusted) = 45.32 Transitions / transversions = 1.50 (24/16) Gap_init rate = 0.02 (2 / 123), avg. gap size = 3.00 (6 / 2) 309 29.32 10.60 2.56 chr1qtel1M 50912 51128 (948872) C L1ME4c_3end#LINE/L1 (275) 555 322 m_b29s551i7 1006 chr1qtel1M 50912 ACAATATTTCATTTCATTCATGTATCATAACTTACTCAACTATTC---TG 50958 i i ivvi ?v i i i i --- i C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chr1qtel1M 50959 TGGATGGGCATCCACTCAGTTTCCAGTTCCTTTC-CT-CTACAAAAAGAG 51006 v v i ii vviv i -- - -i i v iv C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATT--TTTCGCTATTATAAATAACG 458 chr1qtel1M 51007 CTGCA-----CAT----GTGGGT----CCCTTACCCTCCTTTAAG--ATC 51041 ----- ---- vi ---- ii v i i i i-- i C L1ME4c_3end#L 457 CTGCAATGAACATCTTCGTGCATATAGCTTTTTCCTTCTTTTGAATTATT 408 chr1qtel1M 51042 TCTTTGGGAGACAGATTCACTAAAG--ACACTGCTAGACCAAGGGGTCTG 51089 i i --i i v vi --iv i i i ii i v C L1ME4c_3end#L 407 TCCTTAGGA--TAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATG 360 chr1qtel1M 51090 CACAGTTTGATAGCCCTTTTGG-GCATATTTCCAAATTGC 51128 v v v i -- i i-i i v C L1ME4c_3end#L 359 AACATTTTTATGGC--TCTTGATACGTATTGCCAAATTGC 322 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 37.80 CpG sites = 42, Kimura (unadjusted) = 39.47 Transitions / transversions = 2.10 (42/20) Gap_init rate = 0.07 (15 / 216), avg. gap size = 1.93 (29 / 15) 15 13.67 0.00 0.00 chr1qtel1M 52105 52128 (947872) (C)n#Simple_repeat 1 24 (0) m_b29s252i4 1007 chr1qtel1M 52105 CCCCCCCCCCATCCCCACCCCCCC 52128 vi v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCC 24 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 271 32.89 3.23 3.90 chr1qtel1M 53394 53548 (946452) C L2d2_3end#LINE/L2 (3) 552 399 m_b29s601i9 1008 chr1qtel1M 53394 AGTCAAGTCAAGAAGCTTTGATTAAATACTGACTGTATGCCCACACATGG 53443 i i v iiv v i iii iv i v- vi iv C L2d2_3end#LIN 552 AATCAAATCAACAAATATTTATTGAGCGCCTACTGTGTGCA-AGGCACTG 504 chr1qtel1M 53444 TAGTGAATACTG-GATGGCTAAAGAAAGGCAGGAGACA--GTCCCTGCTC 53490 iv iiiii - iv v v i i i i vi -- i C L2d2_3end#LIN 503 TGCTAGGCGCTGTGGGGGATACAAAGAAGTATAAGACATGGTCCCTGCCC 454 chr1qtel1M 53491 TCAAGGAACTTCCAATAGAATGGGTGAG--AGGACAGGCTAAACAACTGT 53538 i v vv i v v -- i --- --i C L2d2_3end#LIN 453 TCAAGGAGCTTACAATCTAGTTGGGGAGACAAGACA---TAAACA--CGT 409 chr1qtel1M 53539 GCACAATTAA 53548 v v i C L2d2_3end#LIN 408 GAAAAGTTAA 399 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 41.15 CpG sites = 30, Kimura (unadjusted) = 45.13 Transitions / transversions = 1.58 (30/19) Gap_init rate = 0.06 (9 / 154), avg. gap size = 1.22 (11 / 9) 214 35.10 10.77 2.86 chr1qtel1M 53649 54038 (945962) C L2#LINE/L2 (6) 3076 2657 m_b29s601i10 1008 chr1qtel1M 53649 AGAGCCTTTCAGGCCTGGGGGACAGTCAGAGAGAATTCCCGGAGCTGAGA 53698 v i vvi i iv v vi vv v vi i C L2#LINE/L2 3076 AGAGCGTTCCAGGCAGAGGGAACAGCAAGTGCAAAGGCCCTGAGGCGGGA 3027 chr1qtel1M 53699 G-ATG---GACAT-----------AGCCCGGAGACCAGTAACACTGGA-T 53732 -i --- i i ----------- vv i ivvi -i C L2#LINE/L2 3026 GCGTGCCTGGCGTGTTCGAGGAACAGCAAGGAGGCCAGTGTGGCTGGAGC 2977 chr1qtel1M 53733 AGAA--AAAGATGTTCAGGG-AATCAGATGTAAGATTAGAGATGTTGGGG 53779 i i-- iv v vvv i -ii vi vi i i i ------ C L2#LINE/L2 2976 GGAGTGAGCGAGGGGGAGAGTGGTAGGAGATGAGGTCAGAGA------GG 2933 chr1qtel1M 53780 TGG-GGAGGACAAGATTATGGAAGTCTTTGAATGCC--TAACAGAATTTT 53826 ii- i v i v i v i v v -- ivv i i C L2#LINE/L2 2932 TAACGGGGGACCAGATCATGTAGGGCCTTGTAGGCCATTGTAAGGACTTT 2883 chr1qtel1M 53827 GTATTTGTTCCTGAAGGCAATAGGGAGTCACTGGAGG------AG--GGG 53868 vv vvii iv vi i i i i ------ -- i C L2#LINE/L2 2882 GGCTTTTACTCTGAGTGAGATGGGAAGCCATTGGAGGGTTTTGAGCAGAG 2833 chr1qtel1M 53869 AAGTGA-------TGACCAGCACTTTAGAAACACCACTTTGAAGATTGAA 53911 i ------- ivi ii i iv i i ivvii vi C L2#LINE/L2 2832 GAGTGACATGATCTGACTTACGTTTTAAAAGGATCACTCTGGCTGCTGTG 2783 chr1qtel1M 53912 TGGAGGTTAGATTGAAGAAGGGAGATCTTGAGACAAGCAGGT-GCCC--T 53958 v iv i ? ii vi vvv i--- v- v -- C L2#LINE/L2 2782 TTGAGAATAGACTGNAGGGGGGCAAGGGTGG---AAGCAGGGAGACCAGT 2736 chr1qtel1M 53959 CAGTAG-TTATTGCCATAGTCTAGGCATGAGATGATGAAAGTCAGCATCA 54007 i v -i vi i i iv ivi iiv v i C L2#LINE/L2 2735 TAGGAGGCTATTGCAGTAATCCAGGCGAGAGATGATGGTGGCTTGGACCA 2686 chr1qtel1M 54008 GAGGAGAGAAGGGAGTGG-GGTGGGGAGATGT 54038 i v--- iv v - v v C L2#LINE/L2 2685 GGGT---GGTGGCAGTGGAGGTGGTGAGAAGT 2657 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 46.16 CpG sites = 75, Kimura (unadjusted) = 49.31 Transitions / transversions = 1.29 (75/58) Gap_init rate = 0.07 (27 / 389), avg. gap size = 2.00 (54 / 27) 386 26.61 2.22 5.34 chr1qtel1M 54759 54893 (945107) C L2d2_3end#LINE/L2 (0) 555 425 m_b29s601i11 1009 chr1qtel1M 54759 TCAAGTCGG-TCAAAAAACATTTAAGCAGCACCTACCGTGTGCTGGGTAC 54807 i ii- v i vvv i i vi i C L2d2_3end#LIN 555 TCAAATCAAATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCAC 506 chr1qtel1M 54808 TGTGCCAAGCCCTTTATAACCCTGGGGCTATAAAGAAAAGCAGGAGATGG 54857 i i v v i------- v i ivii i v C L2d2_3end#LIN 505 TGTGCTAGGCGCTGTG-------GGGGATACAAAGAAGTATAAGACATGG 463 chr1qtel1M 54858 TCTTTGCCACCAA-GAGCTCACAGTCT-GTTGAGGGGA 54893 ii vi - i i - i i C L2d2_3end#LIN 462 TCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGGAGA 425 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 32.93 CpG sites = 23, Kimura (unadjusted) = 34.18 Transitions / transversions = 2.09 (23/11) Gap_init rate = 0.07 (10 / 134), avg. gap size = 1.00 (10 / 10) 336 28.53 15.41 2.33 chr1qtel1M 54885 55189 (944811) C L2#LINE/L2 (600) 2482 2139 m_b29s601i12 1008 chr1qtel1M 54885 TTGAGGGGAAA---TAGTGAATTCAGTTTTGG-TGTGTTGAGTTCAAGAT 54930 i ---i - i -ii i ii C L2#LINE/L2 2482 TTGAGGGGGAAGATCAG-GAGTTCAGTTTTGGACATGTTAAGTTTGAGAT 2434 chr1qtel1M 54931 GTCTTCGAGGACATTCGCTTTGAGATGTCTAA----CAGTTGGAG----G 54972 i viv - i ivv v v i---- v---- C L2#LINE/L2 2433 GCCTATTAG-ACATCCAAGTGGAGATGTCGAGTAGGCAGTTGGATATACG 2385 chr1qtel1M 54973 GGT---GAATCTAGGAGAAAGGTAAGGGCTGGGTAAGTCAATCTGAGAGT 55019 i --- i ii i i vv iv vi v i i C L2#LINE/L2 2384 AGTCTGGAGTTCAGGGGAGAGGTCCGGGCTGGAGATATAAATTTGGGAGT 2335 chr1qtel1M 55020 TATCTGT-----GATGA----TAAACCCAGGGGAGCTGG-TGAGATCAGT 55059 i v i----- i---- v v i - - vi C L2#LINE/L2 2334 CATCAGCATATAGATGGTATTTAAAGCCATGAGA-CTGGATGAGATCACC 2286 chr1qtel1M 55060 CAGCACAC-----TAGAGAGAGAAGACAAAAGGGGCCAAGA--TAGACAC 55102 ? vivii----- v v i - v i-- iii v C L2#LINE/L2 2285 NAGGGAGTGAGTGTAGATAGAGAAGAGAAGA-GGTCCAAGGACTGAGCCC 2237 chr1qtel1M 55103 TAGA------CAGTGCTCA---GTT-----AATTGGGTGTAACCCTCATA 55138 i i------ ii i ? --- i-----i vi v v vv v C L2#LINE/L2 2236 TGGGGCACTCCAACGTTNAGAGGTCGGGGAGATGAGGAGGAACCAGCAAA 2187 chr1qtel1M 55139 -AAGATGCAGACAGAGTGATCAGTCAGACAAGTAGGAAGATAACCAGGAG 55187 -i ivv vi i ii v ---- i v C L2#LINE/L2 2186 GGAGACTGAGAAGGAGCGGCCAGTGAG----GTAGGAGGAAAACCAGGAG 2141 chr1qtel1M 55188 GG 55189 i C L2#LINE/L2 2140 AG 2139 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 35.87 CpG sites = 52, Kimura (unadjusted) = 37.55 Transitions / transversions = 1.58 (52/33) Gap_init rate = 0.07 (22 / 304), avg. gap size = 2.50 (55 / 22) 436 25.87 1.41 7.46 chr1qtel1M 55344 55485 (944515) C MIRc#SINE/MIR (133) 135 2 m_b29s601i13 1010 chr1qtel1M 55344 TGGGGGGGCTGAGGC-AATTGGGATTAAGTGACTTGTCCAGGGTCACGTA 55392 i iii -v vv i i i i ii C MIRc#SINE/MIR 135 TGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACA 86 chr1qtel1M 55393 GCTAGGAGGTGTTAAGTGTCTGAGGCCAGATTTAAACTCAAGCCCTCCTG 55442 ------- v v v vi i ii i i i i C MIRc#SINE/MIR 85 GCTAG-------TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTG 43 chr1qtel1M 55443 ACTTCAGG-GTGGTACTCTTCCCACTGCACCACCCAGCTGCCCC 55485 i i -vii i i ---i i C MIRc#SINE/MIR 42 ACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC---ACTGCCTC 2 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 32.17 CpG sites = 26, Kimura (unadjusted) = 33.54 Transitions / transversions = 3.25 (26/8) Gap_init rate = 0.09 (12 / 141), avg. gap size = 1.00 (12 / 12) 352 27.66 4.26 0.00 chr1qtel1M 56431 56524 (943476) C L2b_3end#LINE/L2 (12) 454 357 m_b29s601i14 1011 chr1qtel1M 56431 AGCAAATGTTTATTAAGCACCTACTGCGGGCCAGGTACTTTGCTAAACAC 56480 i i i i i i v i? v ii i C L2b_3end#LINE 454 AACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGC 405 chr1qtel1M 56481 TGGATATCCAA----GAAGAGGGAAAATACAGTCCCTGCCTCCAAGGA 56524 iv v i---- v i iv i i? i ii v C L2b_3end#LINE 404 TGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGGA 357 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 32.27 CpG sites = 19, Kimura (unadjusted) = 37.71 Transitions / transversions = 2.71 (19/7) Gap_init rate = 0.01 (1 / 93), avg. gap size = 4.00 (4 / 1) 27 0.00 0.00 0.00 chr1qtel1M 57249 57274 (942726) (C)n#Simple_repeat 1 26 (0) c_b29s251i0 1012 chr1qtel1M 57249 CCCCCCCCCCCCCCCCCCCCCCCCCC 57274 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCC 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 327 25.20 12.60 0.00 chr1qtel1M 57308 57434 (942566) MIRb#SINE/MIR 109 251 (17) m_b29s601i15 1013 chr1qtel1M 57308 ACTTAGCATCCCTCG--CTCAGTCTTCTCAGCTGTAAAATGGGGCCAATA 57355 i v i vi-- i i v vi MIRb#SINE/MIR 109 ACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATA 158 chr1qtel1M 57356 ACACTGACCCAGCAGAGTTG------GGA--AGATGAGAT-GTTTGTGT- 57395 i iv iv i ------ -- i -i vii - MIRb#SINE/MIR 159 ATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTA 208 chr1qtel1M 57396 ---CATTGAGCCCACTA-CTGGCACCCAGTAGGCCCTTAATAA 57434 --- ii v v v i- vi i v i MIRb#SINE/MIR 209 AAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAA 251 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 30.39 CpG sites = 20, Kimura (unadjusted) = 31.57 Transitions / transversions = 1.67 (20/12) Gap_init rate = 0.06 (7 / 126), avg. gap size = 2.29 (16 / 7) 11 21.01 5.13 0.00 chr1qtel1M 59438 59476 (940524) (CTGAATA)n#Simple_repeat 1 41 (0) m_b29s252i5 1014 chr1qtel1M 59438 CTGACTTGTGAAT-CT-CATACTGAATACTGACTTGTGAAT 59476 v vv - -v v vv (CTGAATA)n#Si 1 CTGAATACTGAATACTGAATACTGAATACTGAATACTGAAT 41 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2) 275 28.43 5.26 4.35 chr1qtel1M 59810 59923 (940077) L3#LINE/CR1 3980 4094 (5) m_b29s601i16 1015 chr1qtel1M 59810 AAGCAGAGGCTGGATGAACACTTGGTGGGCATGTTATAGGAGAGATTGAA 59859 v vii v i i i ---- L3#LINE/CR1 3980 AAGCAGAGGCTGGATGACCACTTGTCAGGGATGTTGTAGAAGGGAT---- 4025 chr1qtel1M 59860 TCCT---TTTGCTTATGGATTAGCTTGGCTGGCTGTTCAAAGTCCC-CCT 59905 --- v v vivi i i vi i v i i- ii i -i i L3#LINE/CR1 4026 TCCTGCATTGGATGGGAGGTTGGACTAGATGACC-TCTAAGGTCCCTTCC 4074 chr1qtel1M 59906 AACTT--AAATTCCGTCATT 59923 i-- i i v L3#LINE/CR1 4075 AACTCTGAGATTCTGTGATT 4094 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 37.48 CpG sites = 21, Kimura (unadjusted) = 37.48 Transitions / transversions = 2.10 (21/10) Gap_init rate = 0.07 (8 / 113), avg. gap size = 1.38 (11 / 8) 221 14.89 2.13 0.00 chr1qtel1M 60198 60244 (939756) MIR3#SINE/MIR 97 144 (64) m_b29s601i17 1016 chr1qtel1M 60198 CAAGTCACTTCACC-CTGTTTGCCTAGGTTTCCTTATCTGTATAATGA 60244 - v vv vi i v MIR3#SINE/MIR 97 CAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGA 144 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 16.61 CpG sites = 2, Kimura (unadjusted) = 16.61 Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.02 (1 / 46), avg. gap size = 1.00 (1 / 1) 1416 27.73 2.00 3.12 chr1qtel1M 60353 60903 (939097) C L1ME3G_3end#LINE/L1 (376) 548 4 m_b29s551i8 1017 chr1qtel1M 60353 ATAATATTCCATAGCATTCATATACCATAATTTATTCAACCATTCTCTAA 60402 i i vv i i iv C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr1qtel1M 60403 CTGATGGGCACCCACTTGATTTCCAGTTTCTTGTCACTACAAA-AATGGC 60451 i i iii vv vi i i i ii i - - C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAAT-GC 450 chr1qtel1M 60452 TGCCACAAACATTGTTGCACATGTGGGTCCCT-TTCCCTCCTTTGAG-AT 60499 v ii iv i i--? i - v v viv vi - C L1ME3G_3end#L 449 TGCAATGAACATCCTTGTACATGC--NTCCTTGTGCACATGTGCGAGTAT 402 chr1qtel1M 60500 CTCTTTGGGAGATAAGCCCAGTAGTAACACTGCTGGATCAAAGGGTAGGC 60549 i ? i v v v? ? v iiv i i v C L1ME3G_3end#L 401 TTCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGC 352 chr1qtel1M 60550 ACAGTTTGATAACTTTTTGAGCATAGTTCCAAGTTGCCCTTCAGAATGAT 60599 i v i-- i vvv - v v i i i ? ii C L1ME3G_3end#L 351 GCATTTTA--AATTTTAATAG-ATACTGCCAAATTGCCCTCCAAAANGGC 305 chr1qtel1M 60600 TGGATCCGTTCACAACTCCACCAACAATGTATCAGTGTCCCAGTTTTCCC 60649 v i vi i vii i i v v v v i C L1ME3G_3end#L 304 TGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCC 255 chr1qtel1M 60650 ACATTTCCCT--CCATCATTCATCATTAT----CTTTTCCTGTCACCTTA 60693 --- -- v i ?ivi ---- v----v ii v C L1ME3G_3end#L 254 ACA---CCCTCGCCAACACTNGATATTATCAANCTTTTA----AATTTTT 212 chr1qtel1M 60694 GCCATTCTGACAGGTGTGTGGTGGTA--TCAGAGTTGTCGTAATTTGCAT 60741 v ii vivii -- vv iv C L1ME3G_3end#L 211 GCCAATCTGATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCAT 162 chr1qtel1M 60742 TTCTCTGATCAATAGTAATGTGGAGCACCTTTTCATGTGGCTACAAATAG 60791 i i v i v v i i vi iviiivi C L1ME3G_3end#L 161 TTCCCTGATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCA 112 chr1qtel1M 60792 TTTCAATTTCTTCATCTGAAAATTGTCTGTTCATATCCTTTGAATATGTA 60841 vv i v vi i vvi v v C L1ME3G_3end#L 111 TTTGTATTTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTT 62 chr1qtel1M 60842 TCAATTGGAGAATGGCTTGAACTATTATAAATTTGAGTTAGTTCTCTATC 60891 v iv-- v v--i v vi vivv i v C L1ME3G_3end#L 61 TCTATTGGGT--TGTCTTT--TTCTTATTGATTTGTAGGAGTTCTTTATA 16 chr1qtel1M 60892 TATTTTAGAAAT 60903 i i v C L1ME3G_3end#L 15 TATTCTGGATAT 4 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 34.82 CpG sites = 80, Kimura (unadjusted) = 35.71 Transitions / transversions = 1.18 (80/68) Gap_init rate = 0.04 (23 / 550), avg. gap size = 1.22 (28 / 23) 370 30.66 0.93 1.87 chr1qtel1M 60757 60972 (939028) C L1M5_orf2#LINE/L1 (0) 3294 3081 m_b29s551i9 1017 chr1qtel1M 60757 TAATGTGGAGCACCTTTTCATGTGGCTACAAATAGTTTCAATTTCTTCAT 60806 i ? v i vi iviiivi v? v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr1qtel1M 60807 CTGAAAATTGTCTGTTCATATCCTTTGAATATGTATCAATTGGA--GAAT 60854 i vi v vi i vvi v v ?v i-- vv C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTT 3195 chr1qtel1M 60855 GGCTTGAACTATTATAAATTTGAGTTAGTTCTCTATCTATTTTAGAAATG 60904 v v--i ? vi ? vivv i v i i v i C L1M5_orf2#LIN 3194 GTCTTT--TTNTTATTGANTTGTAGGAGTTCTTTATATATTCTGGATACG 3147 chr1qtel1M 60905 AGGCCTTTATCAGATCCTTTGGCTGTAAAAATGTTTTCCCAGTTTATTGC 60954 v i viv vv?i i v v i ? i i v C L1M5_orf2#LIN 3146 AGTCCTTTGTCAGATATATGTNTTGCAAATATTTTCTCCCANTCTGTGGC 3097 chr1qtel1M 60955 ATAAGCATTTTTCTTTTC 60972 v -- v iv C L1M5_orf2#LIN 3096 TT--GCCTTTTCATTTTC 3081 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 40.69 CpG sites = 29, Kimura (unadjusted) = 41.49 Transitions / transversions = 0.81 (29/36) Gap_init rate = 0.02 (5 / 215), avg. gap size = 1.20 (6 / 5) 251 33.33 5.83 0.00 chr1qtel1M 61396 61515 (938485) C L1MC3_3end#LINE/L1 (1934) 598 472 m_b29s551i10 1018 chr1qtel1M 61396 TCCAGGTTTTTTTGAAATCCACTGGCTCATCATTTCTTATAGCACAATAG 61445 v i i viiiiiiv i ivi i v vv i C L1MC3_3end#LI 598 TCCATGTCTTTTCGTGGCTTGATAGCTCATTTCTTTTTATCGCTGAATAA 549 chr1qtel1M 61446 TATTCCATTATATACATTCATCACAACTCGTTCAAGTGTTCCCCAAATGA 61495 i iv vi i ii i i vvii v v v C L1MC3_3end#LI 548 TATTCCATTGTATGGATGTACCACAGTTTGTTTATCCATTCACCTATTGA 499 chr1qtel1M 61496 TGGGCATC-------CTTCCAATTTTT 61515 v i ------- i C L1MC3_3end#LI 498 AGGACATCTTGGTTGCTTCCAGTTTTT 472 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 44.59 CpG sites = 25, Kimura (unadjusted) = 46.20 Transitions / transversions = 1.67 (25/15) Gap_init rate = 0.01 (1 / 119), avg. gap size = 7.00 (7 / 1) 239 32.43 2.63 2.63 chr1qtel1M 61421 61534 (938466) C L1ME4b_3end#LINE/L1 (319) 573 460 m_b29s551i11 1018 chr1qtel1M 61421 CTCATCATTTCTTATAGCACAATAGTATTCCATTATATACATTCATCACA 61470 iv i ii vvv i iv vi i i C L1ME4b_3end#L 573 CTCATTCTTTTTTACGGCTGCATAGTATTCCATTGTATGGATGTACCATA 524 chr1qtel1M 61471 ACTCGTTCAAGTGTTCCCCAAATGATGGGCATCC---TTCCAATTTTTAA 61517 i ii i viiv v v i ii--- ---i ii C L1ME4b_3end#L 523 ATTTATTTAACCAGTCCCCTATTGATGGACATTTAGGTT---GTTTCCAA 477 chr1qtel1M 61518 TTCTTTGTCATTACAGA 61534 ii ii i C L1ME4b_3end#L 476 TCTTTTGCTATTACAAA 460 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 43.85 CpG sites = 26, Kimura (unadjusted) = 45.85 Transitions / transversions = 2.60 (26/10) Gap_init rate = 0.04 (4 / 113), avg. gap size = 1.50 (6 / 4) 238 36.17 2.08 2.08 chr1qtel1M 61543 61638 (938362) C L2c_3end#LINE/L2 (10) 468 373 m_b29s601i18 1019 chr1qtel1M 61543 TCAGCCAGCATTTATCAAATGCCTACAATGT--TAATTGCTGGGAATACA 61590 i v i ii ii v --i ivi i C L2c_3end#LINE 468 TCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGATACA 419 chr1qtel1M 61591 AATAAAGGCAAAAAGCATGATCTCCATCTTTGAGCAACTCATGTTTTA 61638 -- i v v v ii i i i iii i ii v i iiv i C L2c_3end#LINE 418 A--AGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTA 373 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 48.14 CpG sites = 26, Kimura (unadjusted) = 55.51 Transitions / transversions = 3.25 (26/8) Gap_init rate = 0.03 (3 / 95), avg. gap size = 1.33 (4 / 3) 209 19.05 4.76 0.00 chr1qtel1M 69106 69147 (930853) C MIRc#SINE/MIR (192) 76 33 m_b29s601i19 1020 chr1qtel1M 69106 TAGCAGA--CTGGATTCGAACTCAGGACTTCTTGACTCCAAACC 69147 i -- v i i v i ii C MIRc#SINE/MIR 76 TGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTC 33 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 22.78 CpG sites = 6, Kimura (unadjusted) = 22.78 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.02 (1 / 41), avg. gap size = 2.00 (2 / 1) 204 11.76 0.00 0.00 chr1qtel1M 69203 69236 (930764) C MIR#SINE/MIR (113) 149 116 m_b29s601i20 1021 chr1qtel1M 69203 TTGTCCCCATTTGACAGCTGAGGACACTGAGGCA 69236 i v v v C MIR#SINE/MIR 149 TTATCCCCATTTTACAGATGAGGAAACTGAGGCA 116 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 12.81 CpG sites = 1, Kimura (unadjusted) = 12.81 Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 chr1qtel1M 71075 71094 (928906) (TCC)n#Simple_repeat 1 20 (0) m_b29s252i6 1022 chr1qtel1M 71075 TCCTCCTCCTCCTCCTCCTC 71094 (TCC)n#Simple 1 TCCTCCTCCTCCTCCTCCTC 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 232 27.25 6.73 4.72 chr1qtel1M 71762 71865 (928135) C L2d2_3end#LINE/L2 (7) 548 443 m_b29s601i21 1023 chr1qtel1M 71762 AAATCAGGGAGCACTTATGAAGCACCTACTGTGTGTCAGGCCTTGAGCTT 71811 ivi ii i vi i iv vi v v C L2d2_3end#LIN 548 AAATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTA 499 chr1qtel1M 71812 GGGG--GTGGGG---AC--AGAGGTCTAAAAAATGAAACCATCTCTGCTT 71854 v -- --- -- i v i v -----i i ii C L2d2_3end#LIN 498 GGCGCTGTGGGGGATACAAAGAAGTATAAGACATG-----GTCCCTGCCC 454 chr1qtel1M 71855 ACATGGAGTTT 71865 v v i C L2d2_3end#LIN 453 TCAAGGAGCTT 443 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.19 CpG sites = 16, Kimura (unadjusted) = 34.77 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.08 (8 / 103), avg. gap size = 1.50 (12 / 8) 273 28.57 3.30 0.00 chr1qtel1M 71774 71864 (928136) C L2b_3end#LINE/L2 (19) 447 354 m_b29s601i22 1023 chr1qtel1M 71774 ACTTATGAAGCACCTACTGTGTGTCAGGCCTTGAGCTTGGGGGTGGGG-- 71821 i ivi i i ?i v v v v -- C L2b_3end#LINE 447 ATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGGGAT 398 chr1qtel1M 71822 ACAGAGGTCTAAAAAAT-GAAACCATCTCTGCTTACATGGAGTT 71864 v vv v i i- v? vi i iiv i i C L2b_3end#LINE 397 ACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGGAGCT 354 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 34.15 CpG sites = 14, Kimura (unadjusted) = 37.70 Transitions / transversions = 1.17 (14/12) Gap_init rate = 0.02 (2 / 90), avg. gap size = 1.50 (3 / 2) 210 35.02 5.97 3.40 chr1qtel1M 72807 73007 (926993) C L2#LINE/L2 (576) 2506 2301 m_b29s601i23 1023 chr1qtel1M 72807 GAAAAAACAGTTGGGAAGAG-GGGTTGGTTGGGGAAA--CAGAAATCATT 72853 ii i v i- i -i v vv i-- i i ---- C L2#LINE/L2 2506 GGGAAGACTGC-GGGAGGAGCAGGTTTGAGGGGGAAGATCAGGAGT---- 2462 chr1qtel1M 72854 TTCCATTTGGAGCATGTT------GAAATGCCTCTCAAAATGTCCCCTTT 72897 - vi v ii ------ i v i i -ii vvv v C L2#LINE/L2 2461 -TCAGTTTTGGACATGTTAAGTTTGAGATGCCTATTAGA-CATCCAAGTG 2414 chr1qtel1M 72898 GTAATGTCCAGTAGGCAGT-GGTGACCTGGGACCAAAGCTCAAGGGACA- 72945 vi v - vv ivi i v iii i i v - C L2#LINE/L2 2413 GAGATGTCGAGTAGGCAGTTGGATATACGAGTCTGGAGTTCAGGGGAGAG 2364 chr1qtel1M 72946 -CTGGGGGAGGAGAGAGAGCTCTGAGAGCCATCTACACAGAAATGGTAAC 72994 -iiv vv v v iv i i i vi i v i vi C L2#LINE/L2 2363 GTCCGGGCTGGAGATATAAATTTGGGAGTCATCAGCATATAGATGGTATT 2314 chr1qtel1M 72995 TAAATTCACAGGA 73007 vi iii C L2#LINE/L2 2313 TAAAGCCATGAGA 2301 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 47.14 CpG sites = 40, Kimura (unadjusted) = 49.19 Transitions / transversions = 1.43 (40/28) Gap_init rate = 0.07 (13 / 200), avg. gap size = 1.46 (19 / 13) 649 28.94 8.52 2.00 chr1qtel1M 73366 73975 (926025) C L1M5_orf2#LINE/L1 (640) 2654 2006 m_b29s551i12 1024 chr1qtel1M 73366 TTGATAATTACCATTTTATAATACCATTTGAGATCTGATAG---AACTGG 73412 v i iivii vvvi ? ? i --- v vv C L1M5_orf2#LIN 2654 TTGATTACTGTAGCTTTATAATAAGTCTTGANATCNGGTAGTGTAAGTCC 2605 chr1qtel1M 73413 ATCAACTTTAAAATGTTTCACT-----GATTCCCTTAA-TATCCTTGAGC 73456 vi i--- vi vi ----- vii ii- i ? iv C L1M5_orf2#LIN 2604 TCCAACTTTG---TTCTTCTTTTTCAAGATTGTTTTGGCTATTCTNGGTC 2558 chr1qtel1M 73457 TTTTCTTCTTCCAGATGAATTTTG---TTATTTTTTCTAGCTCTATAAAA 73503 i vivi v i i--- i vi v v vi i C L1M5_orf2#LIN 2557 CTTTGCATTTCCATATAAATTTTAGAATCAGCTTGTCAATTTCTACAAAA 2508 chr1qtel1M 73504 TAATTT--TGATAATTTGATTATTGTAGCACTGAA---A-AGATTAATTT 73547 v ii -- iv v ivvi v i --- - i C L1M5_orf2#LIN 2507 AAACCTGCTGGGATTTTGATTGGGATTGCATTGAATCTATAGATCAATTT 2458 chr1qtel1M 73548 AGGTAGAATTGTAATTTTATATTATATTGGCTCAGCCTACTCATGAGCA- 73596 i v vv i ?- iv iv vv v ii i - C L1M5_orf2#LIN 2457 GGGGAGAATTGACATCTTN-ACAATATTGAGTCTTCCAATCCATGAACAT 2409 chr1qtel1M 73597 -GTTAATATTTTTCCAGTTGTTTAGATCTTACTTTATTTGTGTGAAAAAG 73645 - -- i i v i i vi v v v v iv - C L1M5_orf2#LIN 2408 GGT--ATATCTCTCCATTTATTTAGGTCTTCTTTAATTTCTCTCAGCAA- 2362 chr1qtel1M 73646 TGTTTT-TAGTTCT--ATTTACCCAGTTCTTGGGTTTGCCTTGGCAGGTA 73692 - i --i v ?-- v viiv ?ii vi i v C L1M5_orf2#LIN 2361 TGTTTTGTAGTTTTCAGTGTAN--AGGTCTTGCACATNTTTTGTTAGATT 2314 chr1qtel1M 73693 GACTCCCAAGTAGTTTATATTC----A-GTTATTTTAA--GG-------- 73727 v i i v ? i i---- - i v -- -------- C L1M5_orf2#LIN 2313 TATTCCTAAGTATTTNATGTTTTTTGATGCTATTGTAAATGGTATTGTTT 2264 chr1qtel1M 73728 --GAAATTTCTCTTTCTA--TCTTTTCTGGTAATATATAGAAATGCTAAT 73773 --? vi i -- v vi v i i v v C L1M5_orf2#LIN 2263 TTNAAATTTCATTTTCCAATTGTTTGTTGCTAGTATATAGAAATACAATT 2214 chr1qtel1M 73774 GATTTATGTGGATTTATTTTGTATTCTGCAATTTTGCTGAAGTTG-TGAA 73822 v iv v ii i ? i ii i v ii- v v C L1M5_orf2#LIN 2213 GATTTTTGTATATTGACCTTGTATCCNGCGACCTTGCTAAATTCACTTAT 2164 chr1qtel1M 73823 TAATTACAAGTAGTTTCGTAGTTAATTCTCTAGGATTTTCGAAGTATAAC 73872 i - v ?v v vi i ? v v ? vv C L1M5_orf2#LIN 2163 TAGTT-CTAGTAGTTTNTTTGTAGATTCTTTNGGATTTTCTACGTANACA 2115 chr1qtel1M 73873 ATGATGTCATTTGCAGAGAATGATAGTTTTGTTTTCTTGTTATCC---TT 73919 v i ii v ? i i- vi v ---i C L1M5_orf2#LIN 2114 ATCATGTCATCTGCGAATAANGACAGTTTTA-TTTCTTCCTTTCCAATCT 2066 chr1qtel1M 73920 TTAAATTCCTTTAATTTTTTTT------CTTATCACTATAGCTAACGTTT 73963 -- v v i ------ ii vv i iviii C L1M5_orf2#LIN 2065 TT--ATGCCTTTTATTTCTTTTTCTTGCCTTATTGCACTGGCTAGGACCT 2018 chr1qtel1M 73964 CTAGTACAACGT 73975 i i C L1M5_orf2#LIN 2017 CCAGTACAATGT 2006 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 37.87 CpG sites = 94, Kimura (unadjusted) = 38.44 Transitions / transversions = 1.19 (94/79) Gap_init rate = 0.05 (33 / 609), avg. gap size = 1.97 (65 / 33) 775 30.51 7.43 0.71 chr1qtel1M 73451 73975 (926025) C L1P4_orf2#LINE/L1 (729) 2565 2006 m_b29s551i13 1024 chr1qtel1M 73451 TTGAGCTTTTCTTC--TTCCAGATGAATTTTG---TTATTTTTTCTAGCT 73495 i i i i i-- v i--- vi ii C L1P4_orf2#LIN 2565 TCGGGCTCTTTTTTGGTTCCATATGAATTTTAGAATAGTTTTTTCTAATT 2516 chr1qtel1M 73496 CTAT--AAAATAATTTTGATAATTTGATTATTGTAGCACTGAAA----AG 73539 i -- i iv i i vivvi ii v---- C L1P4_orf2#LIN 2515 CTGTGAAAAATGACGTTGGTAGTTTGATAGGAATAGCGTTGAATCTGTAG 2466 chr1qtel1M 73540 ATTAATTTAGGTAGAATTGTAATTTTATATTATATTGGCTCAGCCTACTC 73589 iv i i v v iv - iv ii vv v ii C L1P4_orf2#LIN 2465 ATTGCTTTGGGCAGTATGGCCATTTTA-ACGATATTGATTCTTCCAATCC 2417 chr1qtel1M 73590 ATGAGCAGTTAATATTTTTCCAGTTGTTTAGATCTTACTTTATTTGTGTG 73639 vvv i v ivi v vi? v v v v C L1P4_orf2#LIN 2416 ATGAGCATGGAATGTTTTTCCATTTGTTTGTGTCATCTNTGATTTCTTTC 2367 chr1qtel1M 73640 AAAAAGTGTTTT-TAGTTCTATTTACCCAGTTCTTGGGTTTGCCTTGGC- 73687 iv - - vi iivv v vviii - i- C L1P4_orf2#LIN 2366 AGCA-GTGTTTTGTAGTTCTCCTTGTAGAGATCTTTCACCT-CCTTGGTT 2319 chr1qtel1M 73688 AGGTAGACTCCCAAGTAGTTTATATTC-----AGTTATTTTAAGGGAAAT 73732 i iv i i i v v i-----i i v iv ii C L1P4_orf2#LIN 2318 AGATGTATTCCTAGGTATTTTATTTTTTTTGTGGCTATTGTAAATGGGAT 2269 chr1qtel1M 73733 TTC--TCTT--TCTATCTTTT--CTGG--------TAATATATAGAAATG 73768 v -- -- i iv i i-- v -------- ii i C L1P4_orf2#LIN 2268 TGCGTTCTTGATTTGGCTCTCAGCTTGAACGTTATTGGTGTATAGAAATG 2219 chr1qtel1M 73769 CTAATGATTTATGTGGATTTATTTTGTATTCTGCAATTTTGCTGAAGTTG 73818 v v iv v i v i i i C L1P4_orf2#LIN 2218 CTACTGATTTTTGTACATTGATTTTGTATCCTGAAACTTTACTGAAGTCG 2169 chr1qtel1M 73819 TGAATAATTACAAGTAGTTTCGTAGTTAATTCTCTAGGATTTTCGAAGTA 73868 vv v v v v v ii iv i ivi v i i v i C L1P4_orf2#LIN 2168 TTTATCAGTTCTAGGAGCCTTTTGGCGGAGTCTTTAGGGTTTTCTAGGTA 2119 chr1qtel1M 73869 TAACATGATGTCATTTGCAGAGAATGATAGTTTTGTTTTCTTGTTATCCT 73918 iv v i i iv ii iv - vi v v C L1P4_orf2#LIN 2118 TAGAATCATATCGTCAGCGAAGAGAGATAG-TTTGACTTCTTCTTTTCCT 2070 chr1qtel1M 73919 -TTTAAATTCCTTTAATTT-TTTTTCTT-----ATCACTATAGCTAACGT 73961 - ii v v - i ----- ii v i ivii C L1P4_orf2#LIN 2069 ATTTGGATGCCTTTTATTTCTTTCTCTTGCCTGATTGCTCTGGCTAGGAC 2020 chr1qtel1M 73962 TTCTAGTACAACGT 73975 i v i C L1P4_orf2#LIN 2019 TTCCAGTACTATGT 2006 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 37.71 CpG sites = 90, Kimura (unadjusted) = 40.30 Transitions / transversions = 1.30 (90/69) Gap_init rate = 0.03 (18 / 524), avg. gap size = 2.39 (43 / 18) 254 28.03 1.83 1.83 chr1qtel1M 74018 74126 (925874) C L1MEj_5end#LINE/L1 (4) 2156 2048 m_b29s551i14 1025 chr1qtel1M 74018 CTCTGCTTCAGATGTGCTACTTATAAATAATATATTGTAGGATTCTGGTT 74067 i i i ii i v i i ii v iv i i v C L1MEj_5end#LI 2156 CTTTGTTTTAAGTGTGTTTCTTGTAAACAGCATATAGCTGGGTTTTGTTT 2107 chr1qtel1M 74068 TTTAATCCATTCTT-CTGTGCATTTGTGTTTTA-TGGATAAGTTCATCCC 74115 i v v- v - - i v - ivi i vi C L1MEj_5end#LI 2106 TTTAACCCAATCTGACAGT-C-TCTGTCTTTTAATGGGAGAATTCAGTCC 2059 chr1qtel1M 74116 ATTCACAATTA 74126 v C L1MEj_5end#LI 2058 ATTCACATTTA 2048 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 36.37 CpG sites = 19, Kimura (unadjusted) = 36.37 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.04 (4 / 108), avg. gap size = 1.00 (4 / 4) 247 26.25 8.94 2.09 chr1qtel1M 74019 74197 (925803) C L1MEh_5end#LINE/L1 (5) 2230 2040 m_b29s551i15 1025 chr1qtel1M 74019 TCTGCTTCAGATGTGCTACTTATAAATAATATATTGTAGGATTCTGGTTT 74068 ? i i ii iiv i i i ii v i v C L1MEh_5end#LI 2230 TNTGTTTTAAGTGTGTCTCTTGTAGACAGCATATTGTTGGATTTTGTTTT 2181 chr1qtel1M 74069 TTAATCCATTCTTCTGTGCATTTGTGTTTT---ATGGATAAGTTCATCCC 74115 ? ---v v?v i v i --- v i i i v C L1MEh_5end#LI 2180 TNAATCCA---ATCTGANAATCTCTGTCTTTTAATTGGTGAGTTTAACCC 2134 chr1qtel1M 74116 ATTCACAATTATAGTTATGATAACTATAT-----CTCTCTTCATGCAATT 74160 i v v v v ivi? ----- ivi - v i C L1MEh_5end#LI 2133 ATTTACATTTATTGTAATTACTGNTATATTNGGACTTATTTC-TGCCATC 2085 chr1qtel1M 74161 T--TTGCTTGTT---TATT--TCCCCTCT-TGTTCCTCACTCTTT 74197 -- ii --- -- v - v i iv ? C L1MEh_5end#LI 2084 TTATTATTTGTTTTCTATTTGTCCCATCTGTTTTTCTTTCTNTTT 2040 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 34.38 CpG sites = 27, Kimura (unadjusted) = 34.38 Transitions / transversions = 1.42 (27/19) Gap_init rate = 0.06 (10 / 178), avg. gap size = 2.00 (20 / 10) 249 18.00 6.67 11.11 chr1qtel1M 75191 75265 (924735) C MamRTE1#LINE/RTE-BovB (603) 3209 3138 m_b30s601i0 1026 chr1qtel1M 75191 GTGGTAGACTGTCTGGGTTTCACAGGCATACAAACATGAGGTCAGGACAA 75240 i --- ii i v i ? i ---- i- ? C MamRTE1#LINE/ 3209 GTGGCAG---GTCCAGGTCTCACAGCCGTANAGA----AGGTT-GGACAN 3168 chr1qtel1M 75241 CA-----GCTCTGTGGACCTTCAGTCTGGT 75265 i----- i i i C MamRTE1#LINE/ 3167 CGCTATCGCTCTGTAGACCTTTAGTTTGGT 3138 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 18.51 CpG sites = 11, Kimura (unadjusted) = 22.62 Transitions / transversions = 11.00 (11/1) Gap_init rate = 0.12 (9 / 74), avg. gap size = 1.44 (13 / 9) 16 23.47 0.00 0.00 chr1qtel1M 75437 75471 (924529) (T)n#Simple_repeat 1 35 (0) m_b30s252i0 1027 chr1qtel1M 75437 TTTTTTTGCTTGTTTGTTTGTTTTATTTTTTATTT 75471 vi v v v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 35 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 216 33.06 3.12 3.12 chr1qtel1M 75611 75738 (924262) C MamRTE1#LINE/RTE-BovB (700) 3112 2985 m_b30s601i1 1026 chr1qtel1M 75611 CACACTTT-CCT-CCAGAGCCTCCCCAAAACTGAGCTGGTTCTGGTAATA 75658 i -i - -- v iiviiv iii vv i v C MamRTE1#LINE/ 3112 CACACTCTGTCTGCCAG--CCTCCCAAAGGACATGCTGGCCTTCTTGATT 3065 chr1qtel1M 75659 TGGGTACCAACCTCATTGTCAA--AGTGGACATCCCTGGAAAGTGTCCTG 75706 i v vi v i v ? -- -- vi v i v C MamRTE1#LINE/ 3064 CGGTTTTCTACTTCTTTGTCNATCAGTG--CATCATTGGACAGCGTGCTG 3017 chr1qtel1M 75707 CCAAAGGAGGTGAACTGATCCCCAGCATTCAG 75738 v i v vv i vivivv v C MamRTE1#LINE/ 3016 CCTAGGTAGCAGAATTCGGTGACAGCTTTCAG 2985 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 40.41 CpG sites = 19, Kimura (unadjusted) = 44.52 Transitions / transversions = 0.86 (19/22) Gap_init rate = 0.06 (7 / 127), avg. gap size = 1.14 (8 / 7) 682 28.56 4.51 2.41 chr1qtel1M 76783 77026 (922974) C MIRc#SINE/MIR (17) 251 3 m_b30s601i2 1028 chr1qtel1M 76783 ACATGTACATGGTGCTTTTAAGGTTAGTTAAGGACTTT-ACAGAGAGTTA 76831 v ii i ii vv v -iv vi - v v - C MIRc#SINE/MIR 251 ACATTTGTATAGCACTTTACAGTTTA-CAAAGCGCTTTCACATACA-TTA 204 chr1qtel1M 76832 TCTTATTTGAACCTTATCACAAGACTGAGAGGTTGGT------GGTGGTA 76875 i v i iv vv v v i------ iv C MIRc#SINE/MIR 203 TCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTA 154 chr1qtel1M 76876 ATATCCTCATTT-ACAG-TGAGAAAATTGAGGCTGAGGGAGATGAA-TGA 76922 v i - - i i v i i v - C MIRc#SINE/MIR 153 TTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGA 104 chr1qtel1M 76923 CTTGCCTAGTGTTCACATGATAGCTGGGAAAGTTCTGAGGCCAGATTTGA 76972 i iv - i--- i v ivvv v v vi i i C MIRc#SINE/MIR 103 CTTGCCCAAGGT-CACAC---AGCTAGTAAGTGGCAGAGCCGGGACTCGA 58 chr1qtel1M 76973 ATTCAGATTTTCCCGATTCCAGTTCCAGGGGTCTCTCCACTATGTTAC-C 77021 ii i i i i iv v v i iiiii - C MIRc#SINE/MIR 57 ACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACAC 8 chr1qtel1M 77022 TGACT 77026 v C MIRc#SINE/MIR 7 TGCCT 3 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 35.39 CpG sites = 38, Kimura (unadjusted) = 36.74 Transitions / transversions = 1.27 (38/30) Gap_init rate = 0.05 (12 / 243), avg. gap size = 1.42 (17 / 12) 29 0.00 0.00 0.00 chr1qtel1M 79118 79145 (920855) (AAAAC)n#Simple_repeat 1 28 (0) c_b30s251i0 1029 chr1qtel1M 79118 AAAACAAAACAAAACAAAACAAAACAAA 79145 (AAAAC)n#Simp 1 AAAACAAAACAAAACAAAACAAAACAAA 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 19 31.38 0.00 0.00 chr1qtel1M 79398 79464 (920536) (AGAC)n#Simple_repeat 1 67 (0) m_b30s252i2 1030 chr1qtel1M 79398 AGATATACATATAGATAGACACATAAATAGATAGGCAGACAGACATAGAT 79447 i v v i i v i i i i i v v v (AGAC)n#Simpl 1 AGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAG 50 chr1qtel1M 79448 ATATAGAGACAGACAGA 79464 i v v (AGAC)n#Simpl 51 ACAGACAGACAGACAGA 67 Matrix = Unknown Transitions / transversions = 1.12 (9/8) Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.0 (0 / 0) 209 27.47 22.36 0.51 chr1qtel1M 80162 80322 (919678) L2#LINE/L2 418 613 (2469) m_b30s601i3 1031 chr1qtel1M 80162 TCATCCTCTTCCCTTA-TGTTTCC---AGCTTCAGGCACT--CAGAGACC 80205 v i v -i i --- v vv v -- ? i L2#LINE/L2 418 TCAACCTCTTCTCTGAACGTTCCCTTCACCTTCTTGCTCTAACNGAAACC 467 chr1qtel1M 80206 TAGGCCCTCT-----GGACAACGCTTCCCTTTCTACCTTTTCCAGTA--- 80247 - i i----- vi i v vi i i v i--- L2#LINE/L2 468 T-GGCTCTCCCCTGAGGACACTGCTTCCCCTGCAGCCCTCTCAAGTGGTG 516 chr1qtel1M 80248 ------------CCCCCAACTT-------ACTGGTCAAGGTGGGGGAGTC 80278 ------------ v ? ii------- v vv v v i v L2#LINE/L2 517 GCTGTTTTCTCTCCCACANCCCTCGTACCACTGGGCCTGGAGGTGGGGTA 566 chr1qtel1M 80279 AGAAGCCTATGTGCTCCCCAGGGCCACTTCCAG---ATTCTTCCTCC 80322 i viv viv i vv i --- i L2#LINE/L2 567 GGTGTCCTCCTTGCTCCTCATTGCCGCTTCCAGACCATTCTCCCTCC 613 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 33.20 CpG sites = 21, Kimura (unadjusted) = 35.10 Transitions / transversions = 0.91 (21/23) Gap_init rate = 0.06 (9 / 160), avg. gap size = 4.11 (37 / 9) 222 21.74 0.00 0.00 chr1qtel1M 80826 80871 (919129) L2d_3end#LINE/L2 370 415 (101) m_b30s601i4 1032 chr1qtel1M 80826 TGTTTTAAAATTGTCTCCCCCAAAAGACTGGAAGCTCCTTAAGGGC 80871 v ivv v vv i v i L2d_3end#LINE 370 TGTGTTAGTCTTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGC 415 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 25.68 CpG sites = 3, Kimura (unadjusted) = 25.68 Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 211 25.32 18.99 0.00 chr1qtel1M 80836 80914 (919086) L2d2_3end#LINE/L2 422 515 (40) m_b30s601i5 1032 chr1qtel1M 80836 TTGTCTCCCCCAAAAGACTGGAAGCTCCTTAAGGGC----------TTTT 80875 v vv i v i ---------- i L2d2_3end#LIN 422 TTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTT 471 chr1qtel1M 80876 GC-CTTCTTAGTTTCC----CAACACTTAATCCAGAGTCTAGCA 80914 ii- v v ---- i i i iiv v i v L2d2_3end#LIN 472 ATACTTCTTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCA 515 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 29.54 CpG sites = 11, Kimura (unadjusted) = 31.38 Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.04 (3 / 78), avg. gap size = 5.00 (15 / 3) 190 26.67 21.11 0.00 chr1qtel1M 80837 80926 (919074) L2a_3end#LINE/L2 382 490 (27) m_b30s601i6 1032 chr1qtel1M 80837 TGTCTCCCCCAAA-AGACTGGAAGCTCCTTAAGGG------CTTTTGCCT 80879 v v- v v v i ------ i L2a_3end#LINE 382 TGTCTCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTCT 431 chr1qtel1M 80880 TCTTAGT-----------TTCCCAACACTTAATCCAGAGTCTAGCAGGTA 80918 vi v ----------- i i i i ivv v i i vi L2a_3end#LINE 432 GTTTTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACATA 481 chr1qtel1M 80919 -TGGGCCCT 80926 - i v L2a_3end#LINE 482 GTAGGCGCT 490 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 31.66 CpG sites = 12, Kimura (unadjusted) = 33.30 Transitions / transversions = 1.00 (12/12) Gap_init rate = 0.04 (4 / 89), avg. gap size = 4.75 (19 / 4) 12 26.07 0.00 0.00 chr1qtel1M 81165 81201 (918799) (GGGG)n#Simple_repeat 1 37 (0) m_b30s252i3 1033 chr1qtel1M 81165 GGCGGGGGGGGGGGGAGAAGGGGGGTTGGGAGGGAGG 81201 v i ii vv i i (GGGG)n#Simpl 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 37 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 187 23.05 7.35 4.29 chr1qtel1M 84522 84589 (915411) L2d2_3end#LINE/L2 467 536 (19) m_b30s601i7 1032 chr1qtel1M 84522 GTCCTCTCCTTCTTGTTTGTGTCCC---CGGCGCTTCGCACAGGGCCTGG 84568 i v v --- i --- i i v v v L2d2_3end#LIN 467 GTCTTATACTTC---TTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTG 513 chr1qtel1M 84569 --CACAGTACATGCTCGATGAGT 84589 -- vii i i i L2d2_3end#LIN 514 CACACAGTAGGCGCTCAATAAAT 536 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 25.99 CpG sites = 9, Kimura (unadjusted) = 28.14 Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.07 (5 / 67), avg. gap size = 1.60 (8 / 5) 236 18.97 13.79 0.00 chr1qtel1M 84532 84589 (915411) L2b_3end#LINE/L2 382 447 (19) m_b30s601i8 1032 chr1qtel1M 84532 TCTTGTT------TGTGTCCCCGGCGCTTCGCACAGGGCCTGG--CACAG 84573 ------ i i i v ? -- L2b_3end#LINE 382 TCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAG 431 chr1qtel1M 84574 TACATGCTCGATGAGT 84589 vii ii i i L2b_3end#LINE 432 TAGGCGCTCAGTAAAT 447 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 21.05 CpG sites = 9, Kimura (unadjusted) = 23.43 Transitions / transversions = 4.50 (9/2) Gap_init rate = 0.04 (2 / 57), avg. gap size = 4.00 (8 / 2) 18 0.00 0.00 0.00 chr1qtel1M 85905 85927 (914073) (AAAT)n#Simple_repeat 1 23 (0) m_b30s252i4 1034 chr1qtel1M 85905 AAATAAATAAATAAATAAATAAA 85927 (AAAT)n#Simpl 1 AAATAAATAAATAAATAAATAAA 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 388 36.29 10.25 1.53 chr1qtel1M 87165 87525 (912475) L2#LINE/L2 2553 2944 (138) m_b30s601i9 1035 chr1qtel1M 87165 AACCTAGGTGTTAGCTTTGACTCCTCACTCT---TAACCCCTCCTATGCA 87211 v v i v i v i --- v v i vi v L2#LINE/L2 2553 AACCTTGGAGTCATCCTTGACTCCTCTCTTTCTCTCACACCCCACATCCA 2602 chr1qtel1M 87212 ATCTGTTGCCAAGTTCTGTCAATTTTATCTTTTTAATATCTTATAAAT-- 87259 ii iiv i i iii i i ivv v ivvi -- L2#LINE/L2 2603 ATCCATCAGCAAATCCTGTCGGCTCTACCTTCAAAATATATCCAGAATCC 2652 chr1qtel1M 87260 GTTCCTTTCCCTTCTCTGATATCGCAGTTACTCTGGTGCAAGCCCCCATC 87309 vi vi i vi v ivvi ii viii i v v L2#LINE/L2 2653 GACCACTTCTCACCACCTCCACTGCCACCACCCTGGTCCAAGCCACCATC 2702 chr1qtel1M 87310 ACCTTGTGCCTGAA------CAATAGCCGCACTCCTGGTTGGTTTTCCCA 87353 i ivi i ------ ---- iii i i ii L2#LINE/L2 2703 ATCTCTCGCCTGGATTACTGCAATAGC----CTCCTAACTGGTCTCCCTG 2748 chr1qtel1M 87354 C-CCCATCTCTG-CCTGGTCTGGTCTGTTCTCCACTCAGTTGTC----TA 87397 -i i ii - ivv ?ii i v v iv i ---- i L2#LINE/L2 2749 CTTCCACCCTTGCCCCCCTNCAGTCTATTCTCAACACAGCAGCCAGAGTG 2798 chr1qtel1M 87398 ACC------AAGCACCTATC--ACCAT----CTTCCCAATTCAATAAACT 87435 i ------ i iivvi -- i ---- i i vii v vv L2#LINE/L2 2799 ATCCTTTTAAAACGTAAGTCAGATCATGTCACTCCTCTGCTCAAAACCCT 2848 chr1qtel1M 87436 CCACTTTTTCCTCCATTGATCTGCAGGATCAAATATAAAATTCTC----T 87481 v vvi i - ivvv - ii v vvi i i i---- L2#LINE/L2 2849 CCAATGGCTTC-CCATCTCACT-CAGAGTAAAAGCCAAAGTCCTTACAAT 2896 chr1qtel1M 87482 GGTGTTCAA-GCCCTTCAAAAGCTGGTCTCC---TACTTTTCTAGTCT 87525 iv v - v vi v i --- i i iii L2#LINE/L2 2897 GGCCTACAAGGCCCTACATGATCTGGTCCCCCGTTACCTCTCTGACCT 2944 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 50.90 CpG sites = 80, Kimura (unadjusted) = 52.73 Transitions / transversions = 1.63 (80/49) Gap_init rate = 0.05 (18 / 360), avg. gap size = 2.39 (43 / 18) 223 34.26 8.57 3.50 chr1qtel1M 87666 87910 (912090) L2b_3end#LINE/L2 198 454 (12) m_b30s601i10 1035 chr1qtel1M 87666 TCCTTCAAGTCTCATCTAAAA---CCTCTCCTTCAAGAAG-CCTCACTGA 87711 i v v --- vi i ii - v L2b_3end#LINE 198 TCCTTCAGGTCTCAGCTCAAATGTCACCTCCTCCGGGAAGCCCTCCCTGA 247 chr1qtel1M 87712 TAGCCTATAATG---CTAGTGCTGATTATCTGTACTTT----GTTCTA-- 87752 ivv i vivi --- vi i i-v iv vi iii---- i -- L2b_3end#LINE 248 CCCCCCAGGCCGGGTCAGGCGCC-CTCCTCTGGGCCCCCCCAGTCCTACC 296 chr1qtel1M 87753 TTG-AATTCCTATTTGTATATACTTGTTTTCATGT-TGTCTCCCTCATTA 87800 i -v i iviv i ?vv iii ? v - i i L2b_3end#LINE 297 CTGCCACTCTGGGTTATNATTGTCTGNTTACATGTCTGTCTCCCCCACTA 346 chr1qtel1M 87801 GAC--TGAGTTTCTCGAGAACCAGTAATGTCTTTTGTCTTTCTTCACATC 87848 -- i i vi ii vi v vi -?v i - v vv L2b_3end#LINE 347 GACTGTGAGCTCCGTGAGGGCAGGGACCG-NGTCTGTC-TTGTTCACCGC 394 chr1qtel1M 87849 TTTTAAAAAATTCTAA----TTTGCACAGTGTCTGGTACAATTTAGGTAT 87894 v ------ i iv ----i v ? i i vvv iii L2b_3end#LINE 395 TGT------ATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGC 438 chr1qtel1M 87895 TGAATAAATGCTTATT 87910 v i ii i L2b_3end#LINE 439 TCAGTAAATATTTGTT 454 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 44.69 CpG sites = 48, Kimura (unadjusted) = 48.97 Transitions / transversions = 1.45 (48/33) Gap_init rate = 0.07 (18 / 244), avg. gap size = 1.67 (30 / 18) 261 31.44 5.85 5.34 chr1qtel1M 87706 87910 (912090) L2d_3end#LINE/L2 297 502 (14) m_b30s601i11 1035 chr1qtel1M 87706 CACTGATAGCCTATA--ATGC----TAGTGCT-GATTATCTGTACTTTGT 87748 v i i -- i ---- ii -i --i v v L2d_3end#LINE 297 CACTTATAGTCTGTACCACGCAATTTAGCACTTAATTAT--ATACTGTCT 344 chr1qtel1M 87749 TCTATTGAATTC-CTATTTGTATATACTTGTTTTCATGTTGTCTCCCTCA 87797 v -- - v v -i iv v vi v iv L2d_3end#LINE 345 TGTATTG--TTCTCTAATTGTTT-CATGTGTGTTAGTCTTGTCTCCCCAA 391 chr1qtel1M 87798 TTAGACTG--AGTTTCTCGAGAACCAGTA--ATGTCTTTTGTCTTTCTTC 87843 i i -- i i i ii vi v -- v i- ? i ? L2d_3end#LINE 392 CTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATA-CTNTTTTN 440 chr1qtel1M 87844 ACATCTTTTAAAAAATTCTAATTTGCACAGTGTCTGGTACAATTTAGGTA 87893 v i iiiii v ivi-i ---- iivi i vvv ii L2d_3end#LINE 441 TCGTTCCCCACAGCG-CCTA----GCACAGTGCTGAGCACATAGTAGGCG 485 chr1qtel1M 87894 TTGAATAAATGCTTATT 87910 i v i i L2d_3end#LINE 486 CTCAATAAATACTTGTT 502 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 39.42 CpG sites = 39, Kimura (unadjusted) = 43.29 Transitions / transversions = 1.77 (39/22) Gap_init rate = 0.08 (17 / 204), avg. gap size = 1.35 (23 / 17) 270 27.37 16.33 0.59 chr1qtel1M 88025 88171 (911829) C L1ME4a_3end#LINE/L1 (485) 386 217 m_b30s551i1 1036 chr1qtel1M 88025 AATGGAATCCCTGAGTCAAAGGGTATAGATGTGTC----GTTTTCTTTAT 88070 i iv i i? ii v i---- i ivv i C L1ME4a_3end#L 386 AGTGGAATTACTGGGTCAAAGGGTATGNACATTTTTAAGGCTTTTGATAC 337 chr1qtel1M 88071 AAAATTCCAGATTGTTCTCCAGAATGGTTGGGCCAATT----------CT 88110 v v v i ii v vi ---------- i C L1ME4a_3end#L 336 ATATTGCCAAATTGCCCTCCAGAAAGGTTGTACCAATTTACACTCCCACC 287 chr1qtel1M 88111 AGCTAGT--------GTGCCTGTTTCTCCACAGCTCCTTCAGTATTAGTT 88152 - -------- i ? v ii vi ii i i v C L1ME4a_3end#L 286 AGC-AGTGTATGAGAGTGCCCGTTTCNCCACACCCTCGCCAACACTGGGT 238 chr1qtel1M 88153 ATTCCC--TTTTTTTCATCTT 88171 vi -- i vv C L1ME4a_3end#L 237 ATTATCAATCTTTTAAATCTT 217 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 34.73 CpG sites = 25, Kimura (unadjusted) = 35.86 Transitions / transversions = 1.67 (25/15) Gap_init rate = 0.03 (5 / 146), avg. gap size = 5.00 (25 / 5) 15 23.10 1.64 5.08 chr1qtel1M 88187 88247 (911753) (TTTCATT)n#Simple_repeat 1 59 (0) m_b30s252i5 1037 chr1qtel1M 88187 TTTAATTTCTTCCTTTTTCATTATTTCTCTCATCATTCTTAATCTTTTC- 88235 v - v - vi iv i v - - (TTTCATT)n#Si 1 TTTCATTT-TTCATTTTTCATT-TTTCATTTTTCATTTTTCAT-TTTTCA 47 chr1qtel1M 88236 TTCCTCAATTTT 88247 ii v (TTTCATT)n#Si 48 TTTTTCATTTTT 59 Matrix = Unknown Transitions / transversions = 0.83 (5/6) Gap_init rate = 0.07 (4 / 60), avg. gap size = 1.00 (4 / 4) 339 25.38 13.85 0.00 chr1qtel1M 88929 89058 (910942) MIRc#SINE/MIR 2 149 (119) m_b30s601i12 1038 chr1qtel1M 88929 GAAGCTAGGTGGTGTGGTGGATAGTGAAGTGAGCCTGGAGTCATT----C 88974 i viv ii v v v v ii i vv---- MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr1qtel1M 88975 CTC--TTTGTGGCC----TCAGACACTTACTAGCTGTGTG-----GG--A 89011 v-- i v v ---- v v ----- -- MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 101 chr1qtel1M 89012 AATCACTTAA-TTCTGTTTGCTCCACTTTGCTCATCTGTAAAATAAAG 89058 i -i v vv ii v v iii MIRc#SINE/MIR 102 AGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGG 149 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 30.06 CpG sites = 15, Kimura (unadjusted) = 31.15 Transitions / transversions = 0.83 (15/18) Gap_init rate = 0.05 (6 / 129), avg. gap size = 3.00 (18 / 6) 308 23.90 9.45 7.75 chr1qtel1M 88986 89112 (910888) MIR#SINE/MIR 65 193 (69) m_b30s601i13 1038 chr1qtel1M 88986 CTCAGACACTTACTAGCTGTGTG------GG-AAATCACTTAAT-TCTGT 89027 v v ------ - i i i- v MIR#SINE/MIR 65 CTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCT 114 chr1qtel1M 89028 TTGCTCCACTTTGCTCATCTGTAAAATAAAGTGGAGGAAATAGCAAACCC 89077 v ii v v ----- i iv ii ivv MIR#SINE/MIR 115 GTGCCTCAGTTTCCTCATCTGTAAAA-----TGGGGATAATAATAGTACC 159 chr1qtel1M 89078 TTCC----AGTATTTCTGTAAAGAAAACCCTAAATGGGT 89112 v ---- vi vi i i -----i i MIR#SINE/MIR 160 TACCTCATAGGGTTGTTGTGAGGA-----TTAAATGAGT 193 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 29.33 CpG sites = 16, Kimura (unadjusted) = 29.33 Transitions / transversions = 1.33 (16/12) Gap_init rate = 0.11 (14 / 126), avg. gap size = 1.57 (22 / 14) 2519 29.66 3.43 3.21 chr1qtel1M 89830 91724 (908276) C L1M5_orf2#LINE/L1 (1190) 2104 206 m_b30s551i2 1036 chr1qtel1M 89830 CTGAAAAGAGTGATAATTTGGTTTCCTCATTACCTACTCTGATTCCTTTA 89879 vi v i? i i vi i v v v iii v v v C L1M5_orf2#LIN 2104 CTGCGAATAANGACAGTTTTATTTCTTCCTTTCCAATCTTTATGCCTTTT 2055 chr1qtel1M 89880 ATCTCTTTTTTTTCTCTTATTGCCAAAGCTAGCATTTCTAATACAATATT 89929 i i vi vvvi v ii i i i C L1M5_orf2#LIN 2054 ATTTCTTTTTCTTGCCTTATTGCACTGGCTAGGACCTCCAGTACAATGTT 2005 chr1qtel1M 89930 GAATAATAATGGTAATAGTGGGCAACCTTGTTTCA-CCCCTATCTTATTA 89978 iv i i ? i i v i ii-i v vvi C L1M5_orf2#LIN 2004 GAATAGAAGTGGTGANAGCGGACATCCTTGTCTTGTTCCCGATCTTAGGG 1955 chr1qtel1M 89979 GGAATGGTTTCAGTTTATCCCCATTACATATGATACTTGCTGATTGTTTT 90028 v v? ? v v vi ii ? vvv C L1M5_orf2#LIN 1954 GGAAAGCNTTCAGTNTTTCACCATTAAGTATGATGTTNGCTGTAGGTTTT 1905 chr1qtel1M 90029 AAATAGATGC----TA-CAGATTGTTTCAAGGATAAGT--CCATTTATTC 90071 vvi ---- - i ----- -- -- v i C L1M5_orf2#LIN 1904 TCGTAGATGCCCTTTATCAGGTTG-----AGG--AAGTTCCCTTCTATTC 1862 chr1qtel1M 90072 CTATACTTTCT-AGTGTTTTTAATAGGAATGGCTGTTGGATTTTATCAAA 90120 -ii v - v vi v v i i C L1M5_orf2#LIN 1861 CTA-GTTTGCTGAGAGTTTTTATCATGAATGGGTGTTGAATTTTGTCAAA 1813 chr1qtel1M 90121 TGGTTTTTCTGCATCTATTAAGATAATCATATGGTTTTT---GTTAATTT 90167 v i i i ---v v i C L1M5_orf2#LIN 1812 TGCTTTTTCTGCATCTATTGAGATGATCATATGATTTTTCTCCTTTATTC 1763 chr1qtel1M 90168 GGTTATTGATATAGTCAATTATGCTAATAGTTTTCCTAATATTGAAGCAG 90217 v --- i v iii i v v i v i i v i C L1M5_orf2#LIN 1762 TGTTA---ATATGGTGAATTACATTGATTGATTTTCGAATGTTAAACCAA 1716 chr1qtel1M 90218 CCCTGCATTCCTGGTATAAATCCTACTTGGTCATGGTGTATTATCCTGGG 90267 i v i i i vvv C L1M5_orf2#LIN 1715 CCTTGCATTCCTGGGATAAACCCCACTTGGTCATGATGTATTATCCTTTT 1666 chr1qtel1M 90268 GATGATTTTCTATAAGCATTTTGCTAATATTTTATTTAAGATTTTTGCAT 90317 v ivv v iv vv iv i ? i C L1M5_orf2#LIN 1665 TATATATTGCTGGATTCGATTTGCTAATATTTTGTTNAGGATTTTTGCAT 1616 chr1qtel1M 90318 C-AT-CTCATGAGGGAGATTGGTCTATCATTTTCTTTCTCTGTTTTCATC 90365 - -i v i v iii vv -i C L1M5_orf2#LIN 1615 CTATGTTCATGAGGGATATTGGTCTGTAATTTTCTTTTCTTGTAAT-GTC 1567 chr1qtel1M 90366 TT--ACTGGTTTAGGTATCAATACCATGACTTTGTTATTTATTCCTTTCA 90413 --v ? v ivii? ---------i viiii v vv C L1M5_orf2#LIN 1566 TTTGTCNGGTTTTGGTATCAGGGTNATG---------CTGGCCTCATAAA 1526 chr1qtel1M 90414 AGGAATTAGGTAGGAGTCCTTCATTCCCTATTTTTGTCTAATAGTTTATA 90463 v i i v viv i v ii i- vv v i i C L1M5_orf2#LIN 1525 ATGAGTTGGGAAGTGTTCCCTCTTTTTCTATTTTC-TGGAAGAGTTTGTG 1477 chr1qtel1M 90464 TAGTATTGGAGTTAATTGTTCTTTAAATGTTTGGGAGAATTCACATATAA 90513 iv vi v v i v vvi i C L1M5_orf2#LIN 1476 TAAGATTGGTATTATTTCTTCCTTAAATGTTTGGTAGAATTCACCAGTGA 1427 chr1qtel1M 90514 ATCCATCTGGTCCTGGGGATTTTTTTCTTAGGGAATTGATTAATAGCTTC 90563 v v i - i iv i i iv vv vi vvv C L1M5_orf2#LIN 1426 AGCCATCTGGGCCTGGAG-TTTTCTTTGTGGGAAGGTTTTTAATTACAAA 1378 chr1qtel1M 90564 TTCTATTTTTTTTTTCTAAA-ATGGGAGTATTTAAGTAATTTATTTCCTC 90612 v -- i vv i - i iv i ii vv i i C L1M5_orf2#LIN 1377 TTCAA--TTTCTTTAATAGATATAGGGCTATTCAGATTTTCTATTTCTTC 1330 chr1qtel1M 90613 TTCTGTTCATCTGGGCAATCTCTACTTTTGTAGGTATTCCTCCATTTCGC 90662 v? ivi i v i ?i v ii vv v iv ii C L1M5_orf2#LIN 1329 TTGNGTCAGTTTTGGTAANTTGTGTTTTTCAAGGAATTTGTCCATTTCAT 1280 chr1qtel1M 90663 TTAGGTTATTAAATTTATTGGCATAAAGTTGGGCAAAATACATTCTAATT 90712 i i ? i vv v ivi v C L1M5_orf2#LIN 1279 CTAAGTTNTCAAATTTATTGGCATAAAGTTGTTCATAATATTCTCTTATT 1230 chr1qtel1M 90713 ATTGCTCTAATTTCCTCTTCATTTTAAAGT----TCTCCCTTTTCATTTT 90758 ivi i v - v vviv i iv ---- i ii C L1M5_orf2#LIN 1229 ATCCTTTTAATGT-CTGTAGGATCTGTAGTGATGTCTCCTTTTTCATTCC 1181 chr1qtel1M 90759 TGAGACTAACAATCTGATTTTCCTCTTTCTTTTTTCTAATCAAATTAACT 90808 v i iii i vv i i i i ii i ivi ?i C L1M5_orf2#LIN 1180 TGATATTGGTAATTTGTGTCTTCTCTCTTTTTTTCTTGATCAGTCTNGCT 1131 chr1qtel1M 90809 AAAGATTTATTTATTTTGTTGTTTTTTTCATAAAACCAAC--TCAGTTTT 90856 i i iv i v i v i i -- ii i i C L1M5_orf2#LIN 1130 AGAGGTTTATCAATTTTATTGATCTTTTCAAAGAACCAGCTTTTGGCTTC 1081 chr1qtel1M 90857 ATTTATTAATTCAATAGTTTTTTTATTTTCAGTTTTATTAAT-----CTT 90901 i v vvi v v ? ? i vi i i ----- i C L1M5_orf2#LIN 1080 GTTGATTTTCTCTATTGTNTNTTTGTTTTCTATTTCATTGATTTCTGCTC 1031 chr1qtel1M 90902 TCCTTTTTAGAATTCCAAGTTTGGTATTTAATTGGAAGTTTTTAATTTG- 90950 iv i vv i vvvii vv i ?v v ii--- - C L1M5_orf2#LIN 1030 TTATCTTTATTATTTCCTTCCTTCTACTTNCTTTGGG---TTTAATTTGC 984 chr1qtel1M 90951 --TTTTTTTCCTAGCTTTTTTACTTGCAAGCCCAATTCATTGATCTT--- 90995 -- i i i v vv v ii iv i --- C L1M5_orf2#LIN 983 TCTTCTTTTTCTAGCTTCTTAAGGTGGAAGCTTAGATCATTGATTTTAAG 934 chr1qtel1M 90996 CTCTTTCTCTATTTTATGCAAGTAAGCATCTAGAGATATATAATTTCCCA 91045 ii ii v i --- vi ? i i? v - v C L1M5_orf2#LIN 933 CCTTTCTTCTTTTCTA---ATATANGCATTTAANGCTATA-AATTTCCCT 888 chr1qtel1M 91046 TTATAAAATAAAATTAGGCTGCATCCTACATACTTTGGTATGTTGTCTCA 91095 i - iv ivivv - i v i i v iv C L1M5_orf2#LIN 887 CTA-AGCACTGCTTTA-GCTGCATCCCACAAATTTTGATATGTTGTATTT 840 chr1qtel1M 91096 TTATTGTCATTCTCTTGGATGAAATTATTGATTGTGTCTATAATTTGCTG 91145 i ? vv vi viv v vi i viv?i i i vi v C L1M5_orf2#LIN 839 TCATTNTCATTCAGTTCAAAATATTTTCTAATTTCCNTTGTGATTTCTTC 790 chr1qtel1M 91146 TTTCACCCATTCATTCTTTAGGA-TGAGATAGAGT----TTTCCAATTAC 91190 v vvi v i - v v --- ---- v i C L1M5_orf2#LIN 789 TTTGACCCATGGGTTATTTAGAAGTGTGTT---GTTTAATTTCCAAATAT 743 chr1qtel1M 91191 TT-----TTTGGTCTATTTTCCCCTGGTTTTTTATTGAATGTAGTTTTGA 91235 ----- -- v? vi ii--- v v viviv i C L1M5_orf2#LIN 742 TTGGGGATTT--TCTAGNTATCTT---TTTGTTATTGATTTCTAATTTAA 698 chr1qtel1M 91236 TTGCATCATGATCTGAAAAGGATGC-CTTTACTATTTCTGCCTTTCTGCA 91284 v ii i v i -v i - v iv vii i i?iv C L1M5_orf2#LIN 697 TTCCATTGTGGTCAGAGAA-CATACTCTGTATGATTTCAATCCTTTNAAA 649 chr1qtel1M 91285 TTTGAATTTGAGGT---CTTTATGTCCTATTATATGGTCAATTTTTGTAT 91331 i--- ii---i v i v? v i v v C L1M5_orf2#LIN 648 TTTA---TTGAGACTTGTTTTATGGCCCAGNATATGGTCTATCTTGGTAA 602 chr1qtel1M 91332 AGGTTCCATGAACTGCTGAGAAGAAAGTGTACTCT-TTTCTGTCTCCATT 91380 v vi vvi i v i -i?vi - vvi v C L1M5_orf2#LIN 601 ATGTTCCATGTGCACTTGAAAAGAATGTGTATTCTGCNGTTGT-TGGGTG 553 chr1qtel1M 91381 CAGTTTTCTCCAAAGATCTATCATATCTAATT--TTTCTAGTACTCTATT 91428 ? v vi vi v i vi v i -- vv i--i i C L1M5_orf2#LIN 552 NAGTGTTCTATAAATGTCAATTAGGTCAAGTTGGTTGATAGTG--TTGTT 505 chr1qtel1M 91429 TACCTCTTTAATCTCTTTTTTTTTCATTTTGT-GGTTTGATTTTTCTACT 91477 i vv iv v i vi vv i- -vii v i v v i C L1M5_orf2#LIN 504 CAAATCTTCTATATCCTTACTGATT-TTTTGTCTACTTGTTCTATCAATT 456 chr1qtel1M 91478 TCTGAGAGGGCAAGGTTGAAATCTCCCACTATTATAGT---TTTGCTGTC 91524 v i v?iv i ? v v --- --- C L1M5_orf2#LIN 455 ACTGAGAGAGGNGTGTTAAAATCTCCNACTATAATTGTGGATT---TGTC 409 chr1qtel1M 91525 CATTTCTTTTTGCAGCTCTCTTAATTTCTCCTTTAATAATTTAGATGCTA 91574 i ii vi i v i i i v i vvv v v v C L1M5_orf2#LIN 408 TATTTCTCCTTTTAGTTCTGTCAGTTTTTGCTTCATGTATTTTGAAGCTC 359 chr1qtel1M 91575 TACCACTTGGTGCGTATTTGTTTAATATTGATATTGCTACATTATCTA-T 91623 iii i v i ivii iv v vv v v v vv - C L1M5_orf2#LIN 358 TGTTATTAGGTGCATACACATTTAGGATTGTTATGTCTTCTTGATGAATT 309 chr1qtel1M 91624 GCCACCCTTTAGC--TATATAGTGCCCTTCCTTATCTCTTTTAATCAGAT 91671 v - i v -- iv i i i i vv --- C L1M5_orf2#LIN 308 GAC-CCTTTTATCATTATGAAATGTCCCTCTTTATCTCTGGTAAT---AT 263 chr1qtel1M 91672 CAATTTTTGCTTTG-------CTTGATCTGAGATCAGAATGGCTACCCCT 91714 --- i i ------- vi v i iv i i ? v C L1M5_orf2#LIN 262 ---TTCTTGCCTTGAAGTCTACTTTGTCTGATATTAATATAGCCACNCCA 216 chr1qtel1M 91715 GCTTTTTTTT 91724 i C L1M5_orf2#LIN 215 GCTTTCTTTT 206 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 38.71 CpG sites = 288, Kimura (unadjusted) = 39.18 Transitions / transversions = 1.12 (288/256) Gap_init rate = 0.05 (88 / 1894), avg. gap size = 1.43 (126 / 88) 13 7.99 3.45 3.45 chr1qtel1M 91849 91877 (908123) (CTCC)n#Simple_repeat 1 29 (0) m_b30s252i6 1039 chr1qtel1M 91849 CTCCCTTTCTCCCTCACCT-CCTCCCTCCC 91877 ii - - (CTCC)n#Simpl 1 CTCCCTCCCTCCCTC-CCTCCCTCCCTCCC 29 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.07 (2 / 28), avg. gap size = 1.00 (2 / 2) 294 29.17 10.83 0.00 chr1qtel1M 92392 92511 (907489) C L2#LINE/L2 (670) 2412 2280 m_b30s601i14 1040 chr1qtel1M 92392 AAATGTCTGATAGGCGGCTGGAGATTGGAGACTGGAG-----GGGAGAAG 92436 i vii i i v vv v ----- i C L2#LINE/L2 2412 AGATGTCGAGTAGGCAGTTGGATATACGAGTCTGGAGTTCAGGGGAGAGG 2363 chr1qtel1M 92437 GCCGGACTGGGGAAGTAGATCAGAGAATCATCCACATCGAGGTAATCATT 92486 v i i vi i iv i i vi vv i ii vv C L2#LINE/L2 2362 TCCGGGCTGGAGATATAAATTTGGGAGTCATCAGCATATAGATGGTATTT 2313 chr1qtel1M 92487 GAATCGGTGGGAC--------ATCACCAAGGGA 92511 i v vi i -------- ? C L2#LINE/L2 2312 AAAGCCATGAGACTGGATGAGATCACCNAGGGA 2280 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 38.27 CpG sites = 20, Kimura (unadjusted) = 38.27 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.02 (2 / 119), avg. gap size = 6.50 (13 / 2) 207 33.68 4.21 0.00 chr1qtel1M 93102 93196 (906804) MIR#SINE/MIR 154 252 (10) m_b30s601i15 1041 chr1qtel1M 93102 AGTCCCGGCATTGCAGGAGTCTTGGGAGGAACAAATGGGGTGA--CAT-T 93148 v vi v iii iv v v vi i v i -- - MIR#SINE/MIR 154 AGTACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATACATGT 203 chr1qtel1M 93149 AGGG-GCTTAGGACAGTGCCCAGTTCTCAGTAAGTGCAACATAAGTACT 93196 ii - i ii iv vi i vvv i ii MIR#SINE/MIR 204 AAAGCGCTTAGAACAGTGCCTGGCACATAGTAAGCGCTCAATAAATGTT 252 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 44.47 CpG sites = 19, Kimura (unadjusted) = 46.48 Transitions / transversions = 1.46 (19/13) Gap_init rate = 0.03 (3 / 94), avg. gap size = 1.33 (4 / 3) 215 27.40 5.48 0.00 chr1qtel1M 93112 93184 (906816) MIRb#SINE/MIR 168 244 (24) m_b30s601i16 1041 chr1qtel1M 93112 TTGCAGGAGTCTTGGGAGGAACAAATGGGGTGA--CAT-TAGGG-GCTTA 93157 i iv v v vi i i i -- - ii - MIRb#SINE/MIR 168 TCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTTA 217 chr1qtel1M 93158 GGACAGTGCCCAGTTCTCAGTAAGTGC 93184 v ii iv vi i MIRb#SINE/MIR 218 GCACAGTGCCTGGCACATAGTAAGCGC 244 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 31.09 CpG sites = 13, Kimura (unadjusted) = 35.40 Transitions / transversions = 1.86 (13/7) Gap_init rate = 0.04 (3 / 72), avg. gap size = 1.33 (4 / 3) 12 17.57 0.00 0.00 chr1qtel1M 94263 94289 (905711) (AGGGG)n#Simple_repeat 1 27 (0) m_b30s252i7 1042 chr1qtel1M 94263 AGGGGAAGGGGGGGGGGGGGAGGAGAG 94289 i i i i (AGGGG)n#Simp 1 AGGGGAGGGGAGGGGAGGGGAGGGGAG 27 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 193 26.19 0.00 0.00 chr1qtel1M 94336 94377 (905623) C L2b_3end#LINE/L2 (93) 373 332 m_b30s601i17 1043 chr1qtel1M 94336 GTTCCTGCCTTGTCGAAGCTCACATTCTAAGGGGGAGGAAAG 94377 i i vv i v iv ii v C L2b_3end#LINE 373 GTCCCTGCCCTCACGGAGCTCACAGTCTAGTGGGGGAGACAG 332 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 32.74 CpG sites = 6, Kimura (unadjusted) = 32.74 Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 304 26.50 3.57 1.16 chr1qtel1M 95875 95958 (904042) L2d2_3end#LINE/L2 434 519 (36) m_b30s601i18 1044 chr1qtel1M 95875 CCAGATCATGAGGTTCTTGAGGGCTGGGGCCCCGTTTCTGACTTTCTTTG 95924 i ii i v i v i vi i ivv - L2d2_3end#LIN 434 CTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATAC-TTCTTTG 482 chr1qtel1M 95925 TAACCC---TGGGGCTTAGCACAGTGCTTGGCACATA 95958 v ---ii v i i v i L2d2_3end#LIN 483 TATCCCCCACAGCGCCTAGCACAGTGCCTTGCACACA 519 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 33.79 CpG sites = 14, Kimura (unadjusted) = 33.79 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.02 (2 / 83), avg. gap size = 2.00 (4 / 2) 659 33.00 3.07 2.10 chr1qtel1M 96322 96745 (903255) L1ME4c_3end#LINE/L1 227 654 (176) m_b30s551i3 1045 chr1qtel1M 96322 AAATTTATAGATA---AATGTTGGAGGGGATGTGG-AAAACTGGGACACT 96367 v - --- i v i ? i -i v ? L1ME4c_3end#L 227 AAATTGATA-ATACCCAATGCTGGCGAGGNTGCGGTGAAACTGGTACNCT 275 chr1qtel1M 96368 GATACATCGTTGGTAGAGTTGTGAATACATCCAGTCATTCTGGAGAACAG 96417 v i i i vi? i vvi v ii v i i i i L1ME4c_3end#L 276 CATACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGCAA 325 chr1qtel1M 96418 TTTGGAACTCTGCTCAAAGGGCTATCACGCTGTGCATGCCCTTTGACCCA 96467 v v vi iviv i i v viv v i L1ME4c_3end#L 326 TTTGGCAATACGTATCAAGAGCCATAAAAATGTTCATACCCTTTGACCCA 375 chr1qtel1M 96468 GCAGTGCTTCTACTGTGGTTATATCCCAAATAGAT--CTTAAAGGAGAGA 96515 i i v iv v v iv v i iv i --i i i ii L1ME4c_3end#L 376 GTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAAGAAGGA 425 chr1qtel1M 96516 AAGGGCCCCGGGTGTCCAAACATGTTTGTGGCAGCCCTCTTTGTAGTGGC 96565 ii -- iivi iv i v ii v vi v i i i L1ME4c_3end#L 426 AAAAG--CTATATGCACGAAGATGTTCATTGCAGCGTTATTTATAATAGC 473 chr1qtel1M 96566 AAGAAACAGGAAAATGAATGGATGCCCATCCGTTGGAGAATGGCTGAATA 96615 i i iv vvivv ii i v vi v i i i i L1ME4c_3end#L 474 GAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAATGGTTAAGTA 523 chr1qtel1M 96616 AATGATGGCATATGGATGCTATGGGATATTATTT--CTATAAGAAATGAC 96663 v i i v? iv v i vi-- i v i i L1ME4c_3end#L 524 AATTATGGTACATCNACTCGATGGAATATTATGCAGCCATTAAAAATGAT 573 chr1qtel1M 96664 CAGCAGGATG---ATGTCAGAGAGGGCTGGAGAG-ACTTACAGGGATAAT 96709 v vi v v --- --- viivv i i-ii i- iv L1ME4c_3end#L 574 AATTATGAAGACTATGT---AGCAACATGGAAAATGTTTAT-GATATAAT 619 chr1qtel1M 96710 GCTGAGTGAAATGAGCAGAAC-CAGATCATTGTACAT 96745 i i vi i- i -- i? L1ME4c_3end#L 620 GTTAAGTGAAAAAAGCAGAATACAAA--ATTGTATNT 654 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 44.24 CpG sites = 83, Kimura (unadjusted) = 46.10 Transitions / transversions = 1.54 (83/54) Gap_init rate = 0.04 (16 / 423), avg. gap size = 1.38 (22 / 16) 12 27.18 1.75 3.57 chr1qtel1M 96897 96953 (903047) (ATTTTTT)n#Simple_repeat 1 56 (0) m_b30s252i8 1046 chr1qtel1M 96897 ATTTTCATCTTTTTTA-TTGTTATTTGCTTGCATTTTGCTTTCTTTTTTT 96945 -v v - v -i iiv ii i v (ATTTTTT)n#Si 1 ATTTT-TTATTTTTTATTTTTTATTT-TTTATTTTTTATTTTTTATTTTT 48 chr1qtel1M 96946 CATTTTTT 96953 i (ATTTTTT)n#Si 49 TATTTTTT 56 Matrix = Unknown Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.05 (3 / 56), avg. gap size = 1.00 (3 / 3) 232 34.12 10.63 0.88 chr1qtel1M 97509 97715 (902285) C L2#LINE/L2 (783) 2299 2073 m_b30s601i19 1047 chr1qtel1M 97509 TGAATGGGATTTCCAAAATAGAGAGT--AACTGGAATAGAGGA-----CT 97551 i i iv ? iiv v -- iv i iv i ----- i C L2#LINE/L2 2299 TGGATGAGATCACCNAGGGAGTGAGTGTAGATAGAGAAGAGAAGAGGTCC 2250 chr1qtel1M 97552 AAGGGTAGATTTCTGGGGGACACCAATCTTTAGGGGGTGTGCATAACACC 97601 iiv vii v v iv ? i vi v v v vv vv C L2#LINE/L2 2249 AAGGACTGAGCCCTGGGGCACTCCAACGTTNAGAGGTCGGGGAGATGAGG 2200 chr1qtel1M 97602 GGGAACCAGGAA--GTGACCGAGAGGGAATGGCTACCAGCATGGGAGAA- 97648 i v -- v i i ii i viiivi i i - C L2#LINE/L2 2199 AGGAACCAGCAAAGGAGACTGAGAAGGAGCGGCCAGTGAGGTAGGAGGAA 2150 chr1qtel1M 97649 -----GGAAAGTGGGCTA----GGAGGGGAAGCGAG---AGCATTTACCT 97686 ----- i v v i---- i vv i i--- ii -- v C L2#LINE/L2 2149 AACCAGGAGAGTGTGGTGTCCTGGAAGCCAAGTGAAGAAAGTGTTT--CA 2102 chr1qtel1M 97687 AGAGCAAGGGAGTGGGCAACAATGTCAAA 97715 ivi iv vi C L2#LINE/L2 2101 AGAAGGAGGGAGTGATCAACTGTGTCAAA 2073 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 44.97 CpG sites = 40, Kimura (unadjusted) = 47.79 Transitions / transversions = 1.33 (40/30) Gap_init rate = 0.04 (9 / 206), avg. gap size = 2.67 (24 / 9) 16 0.00 6.67 3.23 chr1qtel1M 100387 100416 (899584) (AGATAT)n#Simple_repeat 1 31 (0) m_b30s252i9 1048 chr1qtel1M 100387 AGATGATAG--ATAGATATAGATATAGATATA 100416 - -- (AGATAT)n#Sim 1 AGAT-ATAGATATAGATATAGATATAGATATA 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.07 (2 / 29), avg. gap size = 1.50 (3 / 2) 463 30.00 0.00 0.00 chr1qtel1M 100441 100550 (899450) C MIRc#SINE/MIR (157) 111 2 m_b30s601i20 1049 chr1qtel1M 100441 TTAAGTGACTGGCCCGGGGTCACACAGCCAGAAAGTATCTGAGGTCAAAT 100490 v ii i v iv v vivii i C MIRc#SINE/MIR 111 TTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGAC 62 chr1qtel1M 100491 TTGAACTCAGGTCCTCATGACTTCAGGACTGGTGCTCTATTCACGGTGCT 100540 i i i v i i v ii v i v ii i C MIRc#SINE/MIR 61 TCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACC 12 chr1qtel1M 100541 ACCTAGCTTC 100550 viv i C MIRc#SINE/MIR 11 ACACTGCCTC 2 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 36.79 CpG sites = 21, Kimura (unadjusted) = 39.91 Transitions / transversions = 1.75 (21/12) Gap_init rate = 0.00 (0 / 109), avg. gap size = 0.0 (0 / 0) 300 25.00 0.00 0.00 chr1qtel1M 103390 103457 (896543) C MIRb#SINE/MIR (8) 260 193 m_b30s601i21 1050 chr1qtel1M 103390 AGCAAGCATTTCTGGAGCACGGACTGAGTGCCAGGCACTGCGCCAGGTGC 103439 v v v v i vv iv i i i i C MIRb#SINE/MIR 260 AGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGC 211 chr1qtel1M 103440 TTTACAAACACTCTCTCA 103457 vi i v C MIRb#SINE/MIR 210 TTTACATGCATTATCTCA 193 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 26.58 CpG sites = 8, Kimura (unadjusted) = 30.60 Transitions / transversions = 0.89 (8/9) Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0) 262 29.11 17.63 0.78 chr1qtel1M 103550 103878 (896122) L2#LINE/L2 1805 2188 (894) m_b30s601i22 1051 chr1qtel1M 103550 AGAACCAGAATAGCCGCTTG-TCCTGCCCATCCCTCCCACT-CTGCTCCC 103597 i v i vvi v -i ii ?ivi vi - i i v L2#LINE/L2 1805 AAAACAAAAATTCTCCCTTGACCCCACNTCCCCCTCCAGCTACCGCCCCA 1854 chr1qtel1M 103598 TCTCTCTGC----CTTTAC--CAA--------------GGTGTCTACACT 103627 i ---- -- -------------- v i L2#LINE/L2 1855 TTTCTCTGCTCCCCTTTACAGCAAAACTCCTCGAAAGAGTTGTCTATACT 1904 chr1qtel1M 103628 GGCTG-CTCCCTTGCCCCTCGCCCC---CTCTCTTGGGCTC-------TC 103666 v - vv v i vi --- ii i ------- L2#LINE/L2 1905 CGCTGTCTCCAATTCCTCTCCTCCCATTCTCTCTTGAACCCACTCCAATC 1954 chr1qtel1M 103667 AACCTT--GTCC------TTCCACCCAAACTGCTCTCTCCAGAGGTGGCT 103708 iv -- ------i v ivi - vi i L2#LINE/L2 1955 AGGCTTTCGTCCCCACCACTCCACCGAAACTGCTCTTGTCA-AGGTCACC 2003 chr1qtel1M 103709 GATCACC-----------AAACCCGATGGCCTGCTCCCGGTCCGCATCCT 103747 i v ----------- i i i vii i i v i L2#LINE/L2 2004 AATGACCTCCACGTTGCTAAATCCAATGGTCAATTCTCAGTCCTCATCTT 2053 chr1qtel1M 103748 CCTTGACCACT--GCGGCCTTGGACACTGTTGGTCATTCCC----CCTGG 103791 v v? -- i v v v i i ----i v L2#LINE/L2 2054 ACTTGACCTNTCAGCAGCATTTGACACAGTTGATCACTCCCTCCTTCTTG 2103 chr1qtel1M 103792 ACACTCTTCTCTCAAAGACTTTCCAGGACACTTGGTCTCTCCTGCTGCCC 103841 v v iii vvvivi -iivv v vii L2#LINE/L2 2104 AAACACTTTCTTCACTTGGCTTCCAGGACAC-CACACTCTCCTGGTTTTC 2152 chr1qtel1M 103842 TTCCCCCCACCCAGGCCCTCTCCCCATGAGTGTCCCT 103878 i iv v v v - v iiv v v i L2#LINE/L2 2153 CTCCTACCTCACTGG-CCGCTCCTTCTCAGTCTCCTT 2188 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 37.37 CpG sites = 51, Kimura (unadjusted) = 37.87 Transitions / transversions = 1.16 (51/44) Gap_init rate = 0.05 (16 / 328), avg. gap size = 3.81 (61 / 16) 494 31.32 8.22 0.85 chr1qtel1M 103944 104162 (895838) MIRb#SINE/MIR 1 235 (33) m_b30s601i23 1052 chr1qtel1M 103944 CACAGAGGCAGCAGGGAGCAC-------AGCAGGGGGCCTGAAGTCAGAA 103986 v i iv v v------- v vii i v MIRb#SINE/MIR 1 CAGAGGGGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGAC 50 chr1qtel1M 103987 AGAACTGAGTTCAAATCCGGCCTGTGACACCTCCCAGCTGT-TGACTCTG 104035 v i i v v v v i v i - ii MIRb#SINE/MIR 51 AGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTG 100 chr1qtel1M 104036 GA-AAGGCGCTT--CCTCCTTGCTGACCTCAGTGTCCCCGGCTGTAAAGT 104082 i- vii -- ii --ii v i iv i MIRb#SINE/MIR 101 GGCAAGTTACTTAACCTCTCTG--AGCCTCAGTTTCCTCATCTGTAAAAT 148 chr1qtel1M 104083 GAGACTAAGAGCACTGA-CTCACAGAGTGGCTGCGAGCCCCAAACATGAG 104131 i iv v ii iv - i i v i i vvii iiv v MIRb#SINE/MIR 149 GGGGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGAT 198 chr1qtel1M 104132 CACATCTGTAAGGAGCTT------GCGCCGGGCACGT 104162 v iiiv i v ------ i v i MIRb#SINE/MIR 199 AATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACAT 235 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 39.47 CpG sites = 40, Kimura (unadjusted) = 41.89 Transitions / transversions = 1.43 (40/28) Gap_init rate = 0.04 (8 / 218), avg. gap size = 2.50 (20 / 8) 191 20.75 11.32 0.00 chr1qtel1M 104184 104236 (895764) MIRb#SINE/MIR 196 254 (14) m_b30s601i24 1053 chr1qtel1M 104184 GATACTGCAGG----GCACTCATCA-AG-GTCAAGCACACAGTAAGCACT 104227 v v ---- i i v - - i vi i i MIRb#SINE/MIR 196 GATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCT 245 chr1qtel1M 104228 TAATAAATG 104236 i MIRb#SINE/MIR 246 CAATAAATG 254 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 19.94 CpG sites = 7, Kimura (unadjusted) = 24.84 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.06 (3 / 52), avg. gap size = 2.00 (6 / 3) 11 12.84 8.82 0.00 chr1qtel1M 104361 104394 (895606) (GACTGAG)n#Simple_repeat 1 37 (0) m_b30s252i11 1054 chr1qtel1M 104361 GACTGAGG-CTGAGGGCTGAGTGC--AGGACAGAGGA 104394 - i vi -- v (GACTGAG)n#Si 1 GACTGAGGACTGAGGACTGAGGACTGAGGACTGAGGA 37 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.50 (3 / 2) 28 0.00 0.00 0.00 chr1qtel1M 105624 105649 (894351) (CTG)n#Simple_repeat 1 26 (0) c_b30s251i1 1055 chr1qtel1M 105624 CTGCTGCTGCTGCTGCTGCTGCTGCT 105649 (CTG)n#Simple 1 CTGCTGCTGCTGCTGCTGCTGCTGCT 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 276 35.73 7.85 1.61 chr1qtel1M 106368 106660 (893340) L2#LINE/L2 2518 2828 (254) m_b30s601i25 1051 chr1qtel1M 106368 ATGGAACATCCCCTCTTCCCAGCCCCAGAGGCTCCCACTCTAGAAGTCAC 106417 v - ii v i i iiv vv ivvv vi v i i L2#LINE/L2 2518 ATGGCA-ACTCCATCCTTCCAGTTGCTCAGGCCAAAAACCTTGGAGTCAT 2566 chr1qtel1M 106418 CCCGAACTCCTCACC----CTCAC-CCCCAGACCCGAT--GTGGGC---- 106456 ivi v i---- - v i i --i vi ---- L2#LINE/L2 2567 CCTTGACTCCTCTCTTTCTCTCACACCCCACATCCAATCCATCAGCAAAT 2616 chr1qtel1M 106457 --TGATGACTTCCCCTTGCAGCATCTCCTCAGGGT--GCCCCCTTCTC-- 106500 -- vi i iiv - iv v vii ii -- v v -- L2#LINE/L2 2617 CCTGTCGGCTCTACCTT-CAAAATATATCCAGAATCCGACCACTTCTCAC 2665 chr1qtel1M 106501 ---CGCCGCTTCATCCAGCCTGGT--AGGGAACCCTCATTACTGCACACC 106545 --- v i v vv v -- i vv v iv --- i L2#LINE/L2 2666 CACCTCCACTGCCACCACCCTGGTCCAAGCCACCATCATCTCT---CGCC 2712 chr1qtel1M 106546 TGGATCGCTGCAATAGCTGATGGAGGAGCCTGCCTGCCTC-AGTCTCTCT 106594 ii ivvivi vvi i v i - vi iv i L2#LINE/L2 2713 TGGATTACTGCAATAGCCTCCTAACTGGTCTCCCTGCTTCCACCCTTGCC 2762 chr1qtel1M 106595 CCATCCCAAACCATCCTCCAGCCATCCACTAAAGTGATCTTCCTAAATTA 106644 vii? iv i i v vv v vi i i i ii vii L2#LINE/L2 2763 CCCCTNCAGTCTATTCTCAACACAGCAGCCAGAGTGATCCTTTTAAAACG 2812 chr1qtel1M 106645 CAGGTCTGATCATGTC 106660 i i v L2#LINE/L2 2813 TAAGTCAGATCATGTC 2828 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 48.15 CpG sites = 56, Kimura (unadjusted) = 50.29 Transitions / transversions = 1.19 (56/47) Gap_init rate = 0.05 (14 / 292), avg. gap size = 2.00 (28 / 14) 243 20.22 4.44 1.08 chr1qtel1M 109442 109531 (890469) L1ME5_3end#LINE/L1 121 213 (728) m_b30s551i4 1056 chr1qtel1M 109442 AACAAGCACCTGAAAAAAATG-TCAAATTATCCAGTAATCAAAGAAATGC 109490 iv i i - - i vvii i L1ME5_3end#LI 121 AACAAGCATATGAAGAGA-TGCTCAAACTCATTAGTAATCAGAGAAATGC 169 chr1qtel1M 109491 AAATTAAATC-TCA--GAAATAAAACTTTACTTCTATTAAACTG 109531 v -v -- i vv vi i L1ME5_3end#LI 170 AAATTAAAACAACAATGAGATATCACTTTACACCTATTAGACTG 213 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 23.84 CpG sites = 10, Kimura (unadjusted) = 23.84 Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.04 (4 / 89), avg. gap size = 1.25 (5 / 4) 315 28.97 5.61 0.00 chr1qtel1M 109581 109687 (890313) C L3#LINE/CR1 (22) 4077 3965 m_b30s601i26 1057 chr1qtel1M 109581 GTTGAAAGGAAGCTCAAA--CCATTTATTCTAACC-CACATCTGAATTAA 109627 i i v i i --i i v i - v ii vvi i C L3#LINE/CR1 4077 GTTGGAAGGGACCTTAGAGGTCATCTAGTCCAACCTCCCATCCAATGCAG 4028 chr1qtel1M 109628 -AATACTCCCTACAACATATCTGACAAGTCGTGATGCAGCTTTTGCT--A 109674 - v iii vi v v v i i -- C L3#LINE/CR1 4027 GAATCCCTTCTACAACATCCCTGACAAGTGGTCATCCAGCCTCTGCTTGA 3978 chr1qtel1M 109675 GGAACTCCTGTGA 109687 iv v v C L3#LINE/CR1 3977 ACACCTCCAGTGA 3965 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 37.58 CpG sites = 18, Kimura (unadjusted) = 37.58 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.04 (4 / 106), avg. gap size = 1.50 (6 / 4) 15 7.53 3.33 3.33 chr1qtel1M 109750 109779 (890221) (CAA)n#Simple_repeat 1 30 (0) m_b30s252i12 1058 chr1qtel1M 109750 CAA-AAAAACAAACAACAACAACAACAAAAA 109779 - v - v (CAA)n#Simple 1 CAACAACAAC-AACAACAACAACAACAACAA 30 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.07 (2 / 29), avg. gap size = 1.00 (2 / 2) 30 13.67 0.00 0.00 chr1qtel1M 110199 110246 (889754) (TG)n#Simple_repeat 1 48 (0) m_b30s252i13 1059 chr1qtel1M 110199 TGTGTGAGTATGTATGTGTGTGTGTGTGTGTGTGTGAGTGATTGTGTG 110246 v i i v vv (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 48 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 565 31.75 8.84 3.31 chr1qtel1M 111338 111767 (888233) L2b_3end#LINE/L2 14 466 (0) m_b30s601i27 1060 chr1qtel1M 111338 CCTCTCTGCCTTTCCTGCC--ATGTTATAC-AGTATCCCACTTCACCCAT 111384 i v i i v -- v iv - v v - -i i i L2b_3end#LINE 14 CCCCGCTACCTCTCCGGCCTCATCTCCTACCACTCTCCC-CTT-GCTCAC 61 chr1qtel1M 111385 TTTG-TCCAGCCCAC-CTGGCCT---TGCTGTCCCT--ACTACAAGACAC 111427 i - - - --- i -- vi ivv ?i L2b_3end#LINE 62 TCTGCTCCAGCC-ACACTGGCCTCCTTGCTGTTCCTCGAACACGCCANGC 110 chr1qtel1M 111428 TCCATCCTGCCCCTCTGCCTTTGCAATGGCTGAACCCTAAAACCTAAAAT 111477 ?v i i vvv v?v vv vvi- ii i L2b_3end#LINE 111 TCNCTCCCGCCTCAGGGCCTTTGCACNTGCTGTTCCCTCTG-CCTGGAAC 159 chr1qtel1M 111478 GTGGTCTTTCCT--CTGCTCAGCTCTCAAAATCCT-----TTCTGAAAGT 111520 i--i i i-- vi iv vv v v ----- i vv i L2b_3end#LINE 160 GC--CCTTCCCCACCTCTTCGCCTGGCCAACTCCTACTCATCCTTCAGGT 207 chr1qtel1M 111521 CAAAGTTCTTAGTACCGCTTTATTCATGAA--------CAACTCCTCATA 111562 vv i v- i ii i i iv i iv --------ii i i vi L2b_3end#LINE 208 CTCAGCTCA-AATGTCACCTCCTCCGGGAAGCCCTCCCTGACCCCCCAGG 256 chr1qtel1M 111563 TC----CACCCCTCCCCCCAAAGGAGCTGCTAATCCCTGGACACTGT--- 111605 i ---- vv vi i ivvi vv iv i i i--- v i--- L2b_3end#LINE 257 CCGGGTCAGGCGCCCTCCTCTGGGCCCCCCCAGTCCT---ACCCTGCCAC 303 chr1qtel1M 111606 TCTGTATTTACATTGTACAGATTTTCTATAGTGTTTCCCCCAGTAGACTG 111655 vi vv? - v ? viv i v- i v L2b_3end#LINE 304 TCTGGGTTATNATTGT-CTGNTTACATGTC-TGTCTCCCCCACTAGACTG 351 chr1qtel1M 111656 TAAGTTCCTAGAGGCCAGGGA-----TTTATCAATTTAATCTTTGTGTCC 111700 i i vv v ----- i i vvv v i vi i L2b_3end#LINE 352 TGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTGTATCC 401 chr1qtel1M 111701 CT-GAGTCTAGCACAGTGCCTGGCATACAGTAGGGGCTCAATAGATACCT 111749 i- v i ? i v i i ii L2b_3end#LINE 402 CCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTT 451 chr1qtel1M 111750 GTTACAAAGTAAATGCAT 111767 ---i i i v L2b_3end#LINE 452 GTT---GAATGAATGAAT 466 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 41.01 CpG sites = 71, Kimura (unadjusted) = 43.15 Transitions / transversions = 1.16 (71/61) Gap_init rate = 0.07 (28 / 429), avg. gap size = 1.89 (53 / 28) 16 13.08 0.00 0.00 chr1qtel1M 112829 112853 (887147) (A)n#Simple_repeat 1 25 (0) m_b31s252i0 1061 chr1qtel1M 112829 AAAAAAGACTAAAAAAAAAAAAAAA 112853 i vv (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAA 25 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 30 0.00 0.00 0.00 chr1qtel1M 113126 113153 (886847) (T)n#Simple_repeat 1 28 (0) c_b31s251i0 1062 chr1qtel1M 113126 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 113153 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 268 34.57 1.83 1.83 chr1qtel1M 115432 115540 (884460) L3#LINE/CR1 3816 3924 (175) m_b31s601i2 1063 chr1qtel1M 115432 TATTCTTTGCTCCTATGAAATGCAGAGCTGGGATCAAAGAGTGGAAACTA 115481 v ivv viii iv i i i v i ii L3#LINE/CR1 3816 TATTCTGTGTGGCTCCAGAGGGCAGAACTAGGACCAATGGGTGGAAGTTA 3865 chr1qtel1M 115482 CAGGGGAGCCCCTTGCAACTTGGTCCAAGAATTTGAA--TTCCAACAATA 115529 ii vvv v ii iii vi i --v -- i v L3#LINE/CR1 3866 CAGGGAGGCAGATTTCGGCTCAATATAAGGA--AGAACTTTCTAACAATC 3913 chr1qtel1M 115530 AGTCCTGTTCA 115540 vv i L3#LINE/CR1 3914 AGAGCTGTCCA 3924 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 46.47 CpG sites = 22, Kimura (unadjusted) = 48.31 Transitions / transversions = 1.47 (22/15) Gap_init rate = 0.03 (3 / 108), avg. gap size = 1.33 (4 / 3) 603 27.17 11.59 0.43 chr1qtel1M 117261 117467 (882533) MIR#SINE/MIR 33 262 (0) m_b31s601i3 1064 chr1qtel1M 117261 CTGGAGTCAAGAGGAGCAGAATTCAAATCCGACCTCAGACACCGCCTAGC 117310 i - vviv v ii i viv v v ivv MIR#SINE/MIR 33 CTGGAGCCA-GACTGCCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGC 81 chr1qtel1M 117311 TAGGTGACCCTAGCCTAGCCA-TTGACCAGTTTG--ACTCAGTTTTCTCC 117357 iv i i v v ii - i vv i --v i v MIR#SINE/MIR 82 TGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCA 131 chr1qtel1M 117358 TTTGTAAAGTAGG--TAATAGTAGCACCTGCTTCCCAGG---GCTGTGAA 117402 i i i -- i i i i vi --- i i MIR#SINE/MIR 132 TCTGTAAAATGGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAG 181 chr1qtel1M 117403 GACCAAATGAGATGATA-ATAT---------------GTGTCTGACACAC 117436 ii v i - i --------------- i i i MIR#SINE/MIR 182 GATTAAATGAGTTAATACATGTAAAGCGCTTAGAACAGTGCCTGGCACAT 231 chr1qtel1M 117437 AATAAGTGCTAAATCAATGTTAGTTATTATT 117467 i i v v i MIR#SINE/MIR 232 AGTAAGCGCTCAATAAATGTTAGCTATTATT 262 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 32.55 CpG sites = 35, Kimura (unadjusted) = 34.85 Transitions / transversions = 1.67 (35/21) Gap_init rate = 0.03 (7 / 206), avg. gap size = 3.57 (25 / 7) 63 0.00 0.00 0.00 chr1qtel1M 121610 121663 (878337) (TA)n#Simple_repeat 1 54 (0) c_b31s251i1 1065 chr1qtel1M 121610 TATATATATATATATATATATATATATATATATATATATATATATATATA 121659 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr1qtel1M 121660 TATA 121663 (TA)n#Simple_ 51 TATA 54 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 192 31.51 1.37 0.00 chr1qtel1M 122816 122888 (877112) C L2#LINE/L2 (338) 2744 2671 m_b31s601i4 1066 chr1qtel1M 122816 GAGACAAAACATAAGACTGCTGCAATAATCCAGGAGGAAGGGGATGAGAG 122865 v ivi vi i ii i v ii iv ivi C L2#LINE/L2 2744 GAGACCAGTTAGGAGGCTATTGCAGTAATCCAGGCGAGAGATGATGGTGG 2695 chr1qtel1M 122866 C-TGGACGAGGGCAGTGACTGTGG 122888 - v ii i v C L2#LINE/L2 2694 CTTGGACCAGGGTGGTGGCAGTGG 2671 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 42.94 CpG sites = 15, Kimura (unadjusted) = 42.94 Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.01 (1 / 72), avg. gap size = 1.00 (1 / 1) 336 25.72 7.14 9.76 chr1qtel1M 125396 125563 (874437) C MIR1_Amn#SINE/MIR (66) 164 1 m_b31s601i5 1067 chr1qtel1M 125396 TCATTATTATTATTATTATTTTG--GCTGAGGCAATTGGGG--------- 125434 v i ivii i-- v v i i --------- C MIR1_Amn#SINE 164 TCAGTATCATTATCCCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAG 115 chr1qtel1M 125435 -TTAAGTGACTTGCCCAAGGTCACACAGCCAGGAAGTGTTAAGTGTCTGA 125483 - ? ? ?i v? vi ------- C MIR1_Amn#SINE 114 GTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNAGTGGCA-------GA 72 chr1qtel1M 125484 GACCAGATTTTAACTCAGGTCCTCCTGACTTTCGGGGTGCCCCCAATAAT 125533 v vi ? ?v i - i v ii i ------i i iv C MIR1_Amn#SINE 71 GCCGGGANTNGAACCCAGGT-CTCCCGAGTCCCAG------TCCAGTGCT 29 chr1qtel1M 125534 TATTTCTTTAGGAACCAAATTGCTTTCCTA 125563 ivv i vi -- v i i i C MIR1_Amn#SINE 28 CTATCCACTAG--ACCACACTGCCTCCCTA 1 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 32.92 CpG sites = 24, Kimura (unadjusted) = 33.99 Transitions / transversions = 1.60 (24/15) Gap_init rate = 0.11 (19 / 167), avg. gap size = 1.47 (28 / 19) 358 24.35 10.79 5.48 chr1qtel1M 125398 125536 (874464) C MIR#SINE/MIR (106) 156 11 m_b31s601i6 1067 chr1qtel1M 125398 ATTATTATTATTATTATTTT--------GG---CTGAGGCA-ATTGGGGT 125435 i ivii -------- --- - vv i C MIR#SINE/MIR 156 ACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGT 107 chr1qtel1M 125436 TAAGTGACTTGCCCAAGGTCACACAGCCAGGAAGTGTTAAGTGTCTGAGA 125485 i i ------- v v v C MIR#SINE/MIR 106 TAAGTAACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGCAGAGC 64 chr1qtel1M 125486 CCAGATTTTAACTCAGGTCCTCCTGACTTTCGGG---GTGCCCCCAATAA 125532 vi iv i ivv - i iiv i --- i ii iv C MIR#SINE/MIR 63 CGGGATTCGAACCCAGGCAGT-CTGGCTCCAGAGCCCGTGCTCTTAACCA 15 chr1qtel1M 125533 TTAT 125536 i C MIR#SINE/MIR 14 CTAT 11 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 29.22 CpG sites = 20, Kimura (unadjusted) = 30.35 Transitions / transversions = 1.67 (20/12) Gap_init rate = 0.09 (12 / 138), avg. gap size = 1.92 (23 / 12) 421 18.64 10.53 5.88 chr1qtel1M 125400 125513 (874487) C MIRc#SINE/MIR (110) 158 40 m_b31s601i7 1067 chr1qtel1M 125400 TATTATTATTATTATTTTG--GCTGAGGCAATTGGGG----------TTA 125437 ivii i-- v v i i ---------- C MIRc#SINE/MIR 158 TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTA 109 chr1qtel1M 125438 AGTGACTTGCCCAAGGTCACACAGCCAGGAAGTGTTAAGTGTCTGAGACC 125487 i ------- v v v v C MIRc#SINE/MIR 108 AGTGACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGCAGAGCCG 66 chr1qtel1M 125488 AGATTTTAACTCAGGTCCTCCTGACT 125513 i i iv i i C MIRc#SINE/MIR 65 GGACTCGAACCCAGGTCTTCCTGACT 40 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 20.63 CpG sites = 12, Kimura (unadjusted) = 21.82 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.08 (9 / 113), avg. gap size = 2.11 (19 / 9) 281 13.82 0.00 5.17 chr1qtel1M 125673 125733 (874267) Tigger1#DNA/TcMar-Tigger 173 230 (2188) m_b31s502i0 1068 chr1qtel1M 125673 ATGTCTAACTTTTTTCCCATCATTGTTATATTTATCATGGTGATCTGTGA 125722 v v --- i i i i i Tigger1#DNA/T 173 ATTTCAAACTTTTT---CATTATTATTATATCTGTTATGGTGATCTGTGA 219 chr1qtel1M 125723 TCAGTGATTTT 125733 i Tigger1#DNA/T 220 TCAGTGATCTT 230 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 15.60 CpG sites = 6, Kimura (unadjusted) = 15.60 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.05 (3 / 60), avg. gap size = 1.00 (3 / 3) 626 15.73 4.76 5.39 chr1qtel1M 126160 126327 (873673) C Charlie4#DNA/hAT-Charlie (0) 3378 3212 m_b31s502i1 1069 chr1qtel1M 126160 CAGAGGTTCATAACTTGTTTTGGTATGTTGGACCAACCCTGTGGCAATCT 126209 i v i v - iivv --- v i C Charlie4#DNA/ 3378 CAGGGGTTCTTAACCTTTTTTG-TGCCATGGACC---CCTTTGGCAGTCT 3333 chr1qtel1M 126210 AGGGAAGCCTAAGAACTCCT---CAGAATCATTTTTTTTTTTAATGTACA 126256 i v v i i --- v v v--- i i C Charlie4#DNA/ 3332 GGTGAAGCCTATGGACCCCTTCTCAGAATAATGTTTTTA---AATGCATA 3286 chr1qtel1M 126257 AAATAAAATACTTAGGATTGCAAAGGAAATCAATTAT-----AATAAAGT 126301 v i i ----- v C Charlie4#DNA/ 3285 AAATAAAATACATAGGATTACAAAGGAAACCAATTATATTGAAATATAGT 3236 chr1qtel1M 126302 TATCAAAATATCTTTAAAAATAAATT 126327 -- i C Charlie4#DNA/ 3235 TATCAAAATA--TTTAAAAACAAATT 3212 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 17.75 CpG sites = 13, Kimura (unadjusted) = 17.75 Transitions / transversions = 1.08 (13/12) Gap_init rate = 0.07 (11 / 167), avg. gap size = 1.55 (17 / 11) 300 25.28 5.79 8.47 chr1qtel1M 126328 126448 (873552) MIRb#SINE/MIR 1 118 (150) m_b31s601i8 1070 chr1qtel1M 126328 CACAAGAACAGCTAGATGGTTCAGTGGTTAGAGCAA------TGGAGAAA 126371 v i ii ---i v vv v------ vv MIRb#SINE/MIR 1 CAGAGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCA 47 chr1qtel1M 126372 GGAGGATCCGAGTTCAAATCTGCCCTCAGACACTTAATACTATCTAGCT- 126420 ivi i i i i ivvv v v ------- - MIRb#SINE/MIR 48 GACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTA-------CTAGCTG 90 chr1qtel1M 126421 TGTGACCCTGGGCAAGTCACTTAATCCC 126448 i i i i MIRb#SINE/MIR 91 TGTGACCTTGGGCAAGTTACTTAACCTC 118 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 28.59 CpG sites = 15, Kimura (unadjusted) = 31.17 Transitions / transversions = 1.15 (15/13) Gap_init rate = 0.10 (12 / 120), avg. gap size = 1.42 (17 / 12) 345 20.41 6.67 6.67 chr1qtel1M 126344 126448 (873552) MIRc#SINE/MIR 11 115 (153) m_b31s601i9 1070 chr1qtel1M 126344 TGGTTCAGTGGTTAGAGCAATGGA----GAA--AGGAGGATCCGAGTTCA 126387 v vv v ---- i-- i i i i i MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr1qtel1M 126388 AATCTGCCCTCAGACACTTAATACTATCTAGCT-TGTGACCCTGGGCAAG 126436 i ivvv v v ------- - i MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTGACCTTGGGCAAG 103 chr1qtel1M 126437 TCACTTAATCCC 126448 i i MIRc#SINE/MIR 104 TCACTTAACCTC 115 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 22.76 CpG sites = 11, Kimura (unadjusted) = 24.09 Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.10 (10 / 104), avg. gap size = 1.40 (14 / 10) 15 24.06 0.00 2.22 chr1qtel1M 127239 127284 (872716) (TTTC)n#Simple_repeat 1 45 (0) m_b31s252i2 1071 chr1qtel1M 127239 TTTCTTTTTTTGTTGTTATTGTTTACTTCTTTTTTTTTTTCTTTCT 127284 i v - iv v vi i i (TTTC)n#Simpl 1 TTTCTTTCTTTCTT-TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 45 Matrix = Unknown Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1) 21 25.42 0.00 0.00 chr1qtel1M 127238 127293 (872707) (TTT)n#Simple_repeat 1 56 (0) m_b31s252i1 1072 chr1qtel1M 127238 TTTTCTTTTTTTGTTGTTATTGTTTACTTCTTTTTTTTTTTCTTTCTCAT 127287 i v v v v vi i i i iv (TTT)n#Simple 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr1qtel1M 127288 TTTTTT 127293 (TTT)n#Simple 51 TTTTTT 56 Matrix = Unknown Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0) 18 21.81 0.00 0.00 chr1qtel1M 127690 127726 (872274) (CA)n#Simple_repeat 1 37 (0) m_b31s252i3 1073 chr1qtel1M 127690 CACACAAAATCACAGGCACACAGACACATACACACAC 127726 v vv vi v i (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACAC 37 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 214 30.19 1.96 15.56 chr1qtel1M 128030 128182 (871818) C L2c_3end#LINE/L2 (10) 468 334 m_b31s601i12 1074 chr1qtel1M 128030 TCTAAAAGCACTTATTAAGCACCTACTACATGCTAGGCATTGTGTTAAGT 128079 v v i i i i ii i ------------ C L2c_3end#LINE 468 TCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGC------------ 431 chr1qtel1M 128080 GCTGAGGACACAAATAAAGGCAAAAAAAGGCAGCCCCTGTCCTCAGGAAG 128129 i i v vi--- v i vi i i i i i C L2c_3end#LINE 430 GCTGGGGATACAAAGATG---AATAAGACACGGTCCCTGCCCTCAAGGAG 384 chr1qtel1M 128130 CAC-TGGATTAACTGCAGAGACAATGGCTACAAGCAA--AGGGGACTACA 128176 v -ii vi iiv vi i----- ? i -- ivi i - C L2c_3end#LINE 383 CTCACAGTCTAGTGGAGGAGACAG-----ACANGTAAACAGACAATTAC- 340 chr1qtel1M 128177 AATACA 128182 C L2c_3end#LINE 339 AATACA 334 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 37.68 CpG sites = 28, Kimura (unadjusted) = 40.41 Transitions / transversions = 2.55 (28/11) Gap_init rate = 0.15 (23 / 152), avg. gap size = 1.04 (24 / 23) 346 32.81 1.55 0.77 chr1qtel1M 128030 128158 (871842) C L2d_3end#LINE/L2 (12) 504 375 m_b31s601i11 1074 chr1qtel1M 128030 TCTAAAAGCACTTATTAAGCACCTACTACATGCTAGGCATTGTGTTAAGT 128079 v v i i i i ii vi i i i i C L2d_3end#LINE 504 TCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTGTGCTAGGC 455 chr1qtel1M 128080 GCTG-AGGACACAAATAAAGGCAAAAAAAGGCAGCCCCTGTCCTCAGGAA 128128 -i iv i ?v ?ivv v i viii i i i i C L2d_3end#LINE 454 GCTGTGGGGAACGANAAAANAGTATAAGACATGGTCCCTGCCCTCAAGGA 405 chr1qtel1M 128129 GCACTGGAT-TAACTGCAGAGACAATGGCTA 128158 vivvi - ii vi - i C L2d_3end#LINE 404 GCTTACAATCTAGTTGGGGAGACAA-GACTA 375 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 42.54 CpG sites = 29, Kimura (unadjusted) = 47.23 Transitions / transversions = 2.23 (29/13) Gap_init rate = 0.02 (3 / 128), avg. gap size = 1.00 (3 / 3) 355 31.68 1.98 0.00 chr1qtel1M 128030 128130 (871870) C L2a_3end#LINE/L2 (10) 507 405 m_b31s601i10 1074 chr1qtel1M 128030 TCTAAAAGCACTTATTAAGCACCTACTACATGCTAGGCATTGTGTTAAGT 128079 v v ii i i i ii i i vi i i C L2a_3end#LINE 507 TCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGC 458 chr1qtel1M 128080 GCTGAGGACACA--AATAAAGGCAAAAAAAGGCAGCCCCTGTCCTCAGGA 128127 i i -- i i viv v i viiv i i v i C L2a_3end#LINE 457 GCTGGGGATACAGCAGTGAACAAAACAGACAAAAGTCCCTGCCCTCATGG 408 chr1qtel1M 128128 AGC 128130 C L2a_3end#LINE 407 AGC 405 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 40.46 CpG sites = 23, Kimura (unadjusted) = 44.23 Transitions / transversions = 2.56 (23/9) Gap_init rate = 0.01 (1 / 100), avg. gap size = 2.00 (2 / 1) 263 31.39 3.25 1.60 chr1qtel1M 128946 129068 (870932) L3#LINE/CR1 3602 3726 (373) m_b31s601i13 1075 chr1qtel1M 128946 CAATTCTGGGACCCCTAAACTGGGAAGAAAAAAATGACAAGATGGAGCAC 128995 i -- v i v i vvi iiiii v v iv i L3#LINE/CR1 3602 CAGTTCTGGG--CGCCACATTTTAAGAGGGACATTGACAAACTGGAGCGC 3649 chr1qtel1M 128996 --CCGGAGATGCACCACCAGGCTGTTGAAAGGTCTTGAGAGCACGTCACT 129043 -- i iv vi v v v i v i v i iv L3#LINE/CR1 3650 GTCCAGAGGAGAGCGACCAGGATGGTGAAGGGTCTGGAAACCATGTCATA 3699 chr1qtel1M 129044 TG-GGATCCATTGAAGGAA-GGAGGAT 129068 - v vi -v i L3#LINE/CR1 3700 TGAGGAACGGTTGAAGGAACTGGGGAT 3726 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 40.05 CpG sites = 20, Kimura (unadjusted) = 41.46 Transitions / transversions = 1.11 (20/18) Gap_init rate = 0.04 (5 / 122), avg. gap size = 1.20 (6 / 5) 185 24.72 7.45 1.00 chr1qtel1M 130801 130894 (869106) MIR1_Amn#SINE/MIR 51 150 (80) m_b31s601i14 1076 chr1qtel1M 130801 GGCCTGGCGGGCAAGTCCAGCCTCAACTATTTGCCAGCTTCATGGCC--- 130847 i - vv ? ? v v vi i i ? ? v?i i --- MIR1_Amn#SINE 51 GACCTGG-GTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTG 99 chr1qtel1M 130848 --CAAGGCAGTCCGGCTGCC--AGCCTCAGTTTCCTCAGCTCTCAAACGG 130893 -- v v i?iv vi --? v v v i MIR1_Amn#SINE 100 GGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGG 149 chr1qtel1M 130894 G 130894 MIR1_Amn#SINE 150 G 150 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 33.20 CpG sites = 10, Kimura (unadjusted) = 33.20 Transitions / transversions = 0.77 (10/13) Gap_init rate = 0.04 (4 / 93), avg. gap size = 2.00 (8 / 4) 19 4.55 0.00 0.00 chr1qtel1M 132517 132539 (867461) (C)n#Simple_repeat 1 23 (0) m_b31s252i4 1077 chr1qtel1M 132517 CCCCCCCCCCCCCCCCCCTCCCC 132539 i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCC 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 34 7.32 0.00 0.00 chr1qtel1M 134405 134447 (865553) (TA)n#Simple_repeat 1 43 (0) c_b31s251i2 1078 chr1qtel1M 134405 TATAAATATTTATATATATATATATATATGTATATATATATAT 134447 v v i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATAT 43 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 12 16.16 4.26 6.52 chr1qtel1M 134692 134738 (865262) (AAGTA)n#Simple_repeat 1 46 (0) m_b31s252i5 1079 chr1qtel1M 134692 AAGTAAGGTTAAAGTATAGTTAAGGAAA-T-AAGTGAAGGTAGAAATAA 134738 i - v v v - - - i - i (AAGTA)n#Simp 1 AAGTAAAG-TAAAGTAAAGTAAAGTAAAGTAAAGT-AAAGTA-AAGTAA 46 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.11 (5 / 46), avg. gap size = 1.00 (5 / 5) 19 23.96 0.00 0.00 chr1qtel1M 136121 136164 (863836) (AG)n#Simple_repeat 1 44 (0) m_b31s252i6 1080 chr1qtel1M 136121 AGAGACACACAGAGAGAGAGAGAGACAGGCAGACAGACAGAAAG 136164 v v v v iv v v i (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 44 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 22 15.91 0.00 0.00 chr1qtel1M 136123 136164 (863836) (AGAC)n#Simple_repeat 1 42 (0) m_b31s252i7 1080 chr1qtel1M 136123 AGACACACAGAGAGAGAGAGAGACAGGCAGACAGACAGAAAG 136164 v v v v i v (AGAC)n#Simpl 1 AGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAG 42 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 300 23.53 4.41 0.00 chr1qtel1M 138621 138688 (861312) C MIR#SINE/MIR (114) 148 78 m_b31s601i15 1081 chr1qtel1M 138621 TATTCCCATTTCACAGATGAGGGAACTGAGGCAGGCATAAGT---GTGAT 138667 i i i viv v i --- i i C MIR#SINE/MIR 148 TATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAAC 99 chr1qtel1M 138668 TCTCTCAGGGCCCCACAGCTA 138688 iv i i i v C MIR#SINE/MIR 98 TTGCCCAAGGTCACACAGCTA 78 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 29.27 CpG sites = 11, Kimura (unadjusted) = 29.27 Transitions / transversions = 2.20 (11/5) Gap_init rate = 0.01 (1 / 67), avg. gap size = 3.00 (3 / 1) 278 29.94 16.77 0.00 chr1qtel1M 139643 139809 (860191) MIRc#SINE/MIR 74 268 (0) m_b31s601i16 1082 chr1qtel1M 139643 CCATTCACACCCTGGATGACCCCAAGCGAGTCAC--AA-------GGGCT 139683 i i vvv vi iiii i -- ------- i i MIRc#SINE/MIR 74 CCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCC 123 chr1qtel1M 139684 --ATCTCCCTAATCTGCAAAATGCG-----TCATACC---CCCGGCTCCC 139723 -- vi i v i v ----- v --- i v v MIRc#SINE/MIR 124 TCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACC 173 chr1qtel1M 139724 TTCCAGAGTTGCTGTGAGCATAAAGGGACGT-ATTTATG----AGCACTG 139768 iv i i v v iv vi - v ---- i v MIRc#SINE/MIR 174 TCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTT 223 chr1qtel1M 139769 TGTCCACTTGAAAGCATTGTAGAAATGC----TATTATTGTTGTT 139809 vv vv iii i v i----?i i i MIRc#SINE/MIR 224 TGTAAACTGTAAAGTGCTATACAAATGTAAGGNGTTATTATTATT 268 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 38.42 CpG sites = 28, Kimura (unadjusted) = 39.43 Transitions / transversions = 1.27 (28/22) Gap_init rate = 0.05 (8 / 166), avg. gap size = 3.50 (28 / 8) 22 3.96 0.00 0.00 chr1qtel1M 139999 140024 (859976) (C)n#Simple_repeat 1 26 (0) m_b31s252i8 1083 chr1qtel1M 139999 CCCCCCCCCCCCCCCCCCCACCCCCC 140024 v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCC 26 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 302 26.29 10.37 4.20 chr1qtel1M 140056 140190 (859810) C L2d2_3end#LINE/L2 (13) 542 400 m_b31s601i17 1084 chr1qtel1M 140056 ATAAGCATTTATTAAGTGCTTACTGTGCACCA-GCACTGTGCTAATGGCT 140104 i ii i i i ii v - ivv C L2d2_3end#LIN 542 ACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCT 493 chr1qtel1M 140105 TTGGG---TAAAAAGATG---AACGCATGGGCGGCGCACCCAAGCAGCCC 140148 v --- v v --- vi v vvi v i v ii C L2d2_3end#LIN 492 GTGGGGGATACAAAGAAGTATAAGACATGGTCCCTGCCCTCAAGGAGCTT 443 chr1qtel1M 140149 AC-------TGGGGGAGACGGTGCAAAGCATAAATGGCCTGGAAAGTCA 140190 ------- v ----- ii i-i v i i C L2d2_3end#LIN 442 ACAATCTAGTTGGGGAGA-----CAAGACATAAAC-ACGTGAAAAGTTA 400 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 32.05 CpG sites = 20, Kimura (unadjusted) = 33.23 Transitions / transversions = 1.43 (20/14) Gap_init rate = 0.07 (10 / 134), avg. gap size = 2.00 (20 / 10) 184 28.61 0.00 3.57 chr1qtel1M 141985 142042 (857958) C MIRc#SINE/MIR (204) 64 9 m_b31s601i18 1085 chr1qtel1M 141985 GATTCGAATCCAGATCTCTTCCCGACTCCAGATCTGGCCCGCCATCCACT 142034 i i i -- i ii ii iv v iv C MIRc#SINE/MIR 64 GACTCGAACCCAGGTCT--TCCTGACTCCAAGTCCAGTGCTCTTTCCACT 17 chr1qtel1M 142035 TCAGTACA 142042 v vi C MIRc#SINE/MIR 16 GCACCACA 9 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 37.82 CpG sites = 11, Kimura (unadjusted) = 37.82 Transitions / transversions = 2.20 (11/5) Gap_init rate = 0.04 (2 / 57), avg. gap size = 1.00 (2 / 2) 279 31.01 6.74 2.15 chr1qtel1M 142494 142671 (857329) L2a_3end#LINE/L2 298 483 (34) m_b31s601i19 1086 chr1qtel1M 142494 CCACTTGCCCTGTTTTATGGTTTCCCTGAGATTACTT----CCATATGTT 142539 v i i -- i iiv v vi ---- v vi L2a_3end#LINE 298 CCCCTTACCCTGCTTTAT--TTTTCTCCATAGCACTTATCACCATCTGAC 345 chr1qtel1M 142540 TATGCTACAT-TCATATCAGATTATTTATTTACT-TGTGTCTTTCCC-AT 142586 - i i - iv iiviv i i - v ii - i L2a_3end#LINE 346 -ATACTATATATTTTACTTATTTATTTGTTTATTGTCTGTCTCCCCCCAC 394 chr1qtel1M 142587 CCAAATGGGAGGTCCTTGAGGGTGGGGA---TCATCTTTTTCTCTTTCCT 142633 ivi vi v v ii --- ii v - v iv L2a_3end#LINE 395 TAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTCTGTTT-TGTTCACT 443 chr1qtel1M 142634 --TGCAAAACCAGGGAATAGCACAATGTCTGGCACATTGT 142671 -- i vvv v vv v i i v L2a_3end#LINE 444 GCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACATAGT 483 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 40.88 CpG sites = 29, Kimura (unadjusted) = 40.88 Transitions / transversions = 1.16 (29/25) Gap_init rate = 0.06 (10 / 177), avg. gap size = 1.60 (16 / 10) 280 31.86 4.42 0.00 chr1qtel1M 142559 142671 (857329) L2b_3end#LINE/L2 315 432 (34) m_b31s601i20 1086 chr1qtel1M 142559 ATTATTTATTTACTTGT--GTCTTTCCCATCCAAATGGGAGGTCCTTGAG 142606 i i i? v -- ii iivi v v v v L2b_3end#LINE 315 ATTGTCTGNTTACATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGTGAG 364 chr1qtel1M 142607 GGTGGGGATCATCTTTTTCTCTTTCCTTGCAAAA---CCAGGGAATAGCA 142653 ii i i?v i v iv vii viv --- v vv L2b_3end#LINE 365 GGCAGGGACCGNGTCTGTCTTGTTCACCGCTGTATCCCCAGCGCCTAGCA 414 chr1qtel1M 142654 CAATGTCTGGCACATTGT 142671 i? i iv L2b_3end#LINE 415 CAGNGCCTGGCACACAGT 432 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 40.94 CpG sites = 20, Kimura (unadjusted) = 44.17 Transitions / transversions = 1.25 (20/16) Gap_init rate = 0.02 (2 / 112), avg. gap size = 2.50 (5 / 2) 257 23.21 0.00 0.00 chr1qtel1M 143096 143151 (856849) L1ME3G_3end#LINE/L1 488 543 (381) m_b31s551i0 1087 chr1qtel1M 143096 ATGCCCATCAGCTGGGGGATGGCTGAATAAGTCATGGTATATGAATGTTA 143145 i iiv i i i i i vv ii L1ME3G_3end#L 488 ATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTA 537 chr1qtel1M 143146 TGGAAT 143151 L1ME3G_3end#L 538 TGGAAT 543 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 29.28 CpG sites = 10, Kimura (unadjusted) = 29.28 Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0) 260 32.09 8.21 0.00 chr1qtel1M 143764 143897 (856103) C L2b_3end#LINE/L2 (2) 464 320 m_b31s601i21 1088 chr1qtel1M 143764 TCAGTCAGTC--TAAATGAATAATAAATATTTATTGAGT--CAA-TTCTG 143808 v v --i ivv v i iiiii i v -- i-i? C L2b_3end#LINE 464 TCATTCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTG 415 chr1qtel1M 143809 TGCTAAGTGCCAGGGGTACAA-AATGAGGCAAAAAGATT--GTTCTTTTT 143855 i i ii i i-ii ivv i v i?-- i i vii C L2b_3end#LINE 414 TGCTAGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCC 365 chr1qtel1M 143856 CTCAAGGAGCT--CAGTCTCATGGGGGAGGCAAA-AGGCAAACAG 143897 v -- vi i i - v i ? C L2b_3end#LINE 364 CTCACGGAGCTCACAGTCTAGTGGGGGAGACAGACATGTAANCAG 320 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 41.66 CpG sites = 30, Kimura (unadjusted) = 46.27 Transitions / transversions = 2.31 (30/13) Gap_init rate = 0.05 (7 / 133), avg. gap size = 1.57 (11 / 7) 393 27.47 5.26 1.45 chr1qtel1M 143783 143915 (856085) C L2c_3end#LINE/L2 (12) 466 329 m_b31s601i22 1088 chr1qtel1M 143783 AATAAATATTTATTGAGT--CAATTCTGTGCTAAGTGCCAGGGGTACAAA 143830 i i i-- v i v i i i ii i C L2c_3end#LINE 466 AACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGATACAAA 417 chr1qtel1M 143831 -ATGAGGCAAAAAGATTGTTCTTTTTCTCAAGGAGCT--CAGTCTCATGG 143877 - iv-- i v iv i i vii -- vi C L2c_3end#LINE 416 GATGAAT--AAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAGTGG 369 chr1qtel1M 143878 GGGAGGCAAA-AGGCAAACAGCTGTGTGCAA-ACAAGCTA 143915 i i i - ? i viivv i - i C L2c_3end#LINE 368 AGGAGACAGACANGTAAACAGACAATTACAATACAAGTTA 329 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 32.76 CpG sites = 26, Kimura (unadjusted) = 36.58 Transitions / transversions = 2.60 (26/10) Gap_init rate = 0.05 (7 / 132), avg. gap size = 1.29 (9 / 7) 194 24.00 0.00 0.00 chr1qtel1M 144409 144458 (855542) MIRc#SINE/MIR 214 263 (5) m_b31s601i23 1089 chr1qtel1M 144409 GAACGTGCTTTGTGAACTTCAAAGTACATTTCAAATCTGAGCTGTTATTA 144458 v i i vi i vv v v i v? MIRc#SINE/MIR 214 GAAAGCGCTTTGTAAACTGTAAAGTGCTATACAAATGTAAGGNGTTATTA 263 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 26.98 CpG sites = 5, Kimura (unadjusted) = 29.72 Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 19 0.00 0.00 3.70 chr1qtel1M 145219 145246 (854754) (AAAC)n#Simple_repeat 1 27 (0) m_b31s252i9 1090 chr1qtel1M 145219 AAACAAAACAAACAAACAAACAAACAAA 145246 - (AAAC)n#Simpl 1 AAAC-AAACAAACAAACAAACAAACAAA 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 32 0.00 0.00 0.00 chr1qtel1M 150375 150404 (849596) (G)n#Simple_repeat 1 30 (0) c_b32s251i0 1091 chr1qtel1M 150375 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 150404 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 30 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 13 14.93 2.44 5.00 chr1qtel1M 150515 150555 (849445) (GGAGCCC)n#Simple_repeat 1 40 (0) m_b32s252i0 1092 chr1qtel1M 150515 GGAGGCCTGTGAGCCCGGAGCCCGGAGGCC-AAGGTCGGAGC 150555 - i - v -i vi (GGAGCCC)n#Si 1 GGA-GCCCG-GAGCCCGGAGCCCGGAGCCCGGAGCCCGGAGC 40 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.07 (3 / 40), avg. gap size = 1.00 (3 / 3) 16 13.08 0.00 0.00 chr1qtel1M 151318 151342 (848658) (G)n#Simple_repeat 1 25 (0) m_b32s252i1 1093 chr1qtel1M 151318 GGGGTGGGGGGGTGGGGGGAGGGGG 151342 v v i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGG 25 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 17 23.83 0.00 0.00 chr1qtel1M 151387 151422 (848578) (C)n#Simple_repeat 1 36 (0) m_b32s252i2 1094 chr1qtel1M 151387 CCCCTCTCCGCCCCTCCTCCCTCCCCCCCTCCCCCC 151422 i i v i i i i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 36 Matrix = Unknown Transitions / transversions = 6.00 (6/1) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 251 17.56 2.90 9.23 chr1qtel1M 152301 152369 (847631) C LTR78#LTR/ERV1 (1005) 299 235 m_b32s502i0 1095 chr1qtel1M 152301 CTCCCTGGGATTGAAA--ACGGGGGAGCACACATCCCCCTTCTCTCTGCC 152348 ? ? v ii-- v ---i i v i C LTR78#LTR/ERV 299 CTCNCTNGGCTTGAGGTGAAGGGGGAGCAC---CCCCCCTCCTCTCTCCT 253 chr1qtel1M 152349 TGAGGGTGGGATTTGGGGATT 152369 i i --- i C LTR78#LTR/ERV 252 TGGGGGTGGGGT---GGGACT 235 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 21.25 CpG sites = 8, Kimura (unadjusted) = 21.25 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.10 (7 / 68), avg. gap size = 1.14 (8 / 7) 484 23.94 0.00 7.62 chr1qtel1M 153984 154096 (845904) MIRc#SINE/MIR 11 115 (153) m_b32s601i0 1096 chr1qtel1M 153984 TAGTGCAGTGGATAGAGCACCAGCCCTGAAGTCAAGAGAACCTGACTTCA 154033 i v ii v i i i ii iv i MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr1qtel1M 154034 AATTTGGTCTTAGACACTTTAACACTTCCTGACTGTTTGACCCTGGGCAA 154083 ----- iii --- i iv v ii v i MIRc#SINE/MIR 61 A-----GTCCCGG---CTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 102 chr1qtel1M 154084 GTCACTTAACCCC 154096 i MIRc#SINE/MIR 103 GTCACTTAACCTC 115 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 27.17 CpG sites = 19, Kimura (unadjusted) = 30.19 Transitions / transversions = 3.17 (19/6) Gap_init rate = 0.07 (8 / 112), avg. gap size = 1.00 (8 / 8) 27 6.26 0.00 0.00 chr1qtel1M 154109 154142 (845858) (A)n#Simple_repeat 1 34 (0) m_b32s252i3 1097 chr1qtel1M 154109 AAAAAAAAAAAAAAAAAAAAAAAAAAAAGGAAAA 154142 ii (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 34 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 362 34.29 1.85 2.80 chr1qtel1M 154685 154900 (845100) C L1MD2_3end#LINE/L1 (452) 654 441 m_b32s551i0 1098 chr1qtel1M 154685 GTATATAATGATCTCCTGATACTG-CTCGTTTCACTCAGCATCAGTTCCT 154733 i i--- ii v i - iv - i i C L1MD2_3end#LI 654 GTATGTAAC---CTTTTGAGATTGGCTTTTTTCACTCAGCAT-AATTCCC 609 chr1qtel1M 154734 GTCAG-TCTCTCTAGGCC--TCTCTGTATTCATCCTGCTGGTCATTTCTT 154780 v v - iv i i ii-- viv iv v-- i v ivi i C L1MD2_3end#LI 608 TTGAGATCCATCCAAGTTGTTGCGTGTATCAATA--GTTCGTTCCTTTTT 561 chr1qtel1M 154781 ACAGAACAATAATATTCCATAACATTCATGTACCACAATTTACCCAGCCA 154830 iv vvv i i iii vv i iiii i C L1MD2_3end#LI 560 ATTGCTGAGTAGTATTCCATGGTATGGATGTACCACAGTTTGTTTAACCA 511 chr1qtel1M 154831 TTCTCCAATTGATGGGCATCCACTCAGTTTCCAGCTTCTAGCCACTACAA 154880 v vi v i iiivviv i i i i i i C L1MD2_3end#LI 510 TTCACCCGTTGAAGGACATTTGGGTTGTTTCCAGTTTTTGGCTATTACGA 461 chr1qtel1M 154881 ACAGGGCTGCCACAAACATT 154900 i ii i ii C L1MD2_3end#LI 460 ATAAAGCTGCTATGAACATT 441 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 46.16 CpG sites = 49, Kimura (unadjusted) = 49.10 Transitions / transversions = 2.13 (49/23) Gap_init rate = 0.04 (9 / 215), avg. gap size = 1.11 (10 / 9) 446 33.33 1.02 1.02 chr1qtel1M 154713 154909 (845091) C L1ME5_3end#LINE/L1 (313) 628 432 m_b32s551i1 1098 chr1qtel1M 154713 TTTCACTCAGCATCA-GTTCCTGTCAG-TCTCTCTAGGCCTCTCTGTATT 154760 ii - -- v v - iv i v iiv v i v C L1ME5_3end#LI 628 TTTCACTCAGCACTATGTT--TTTAAGATCCATCCATGTTGCTATGTGTA 581 chr1qtel1M 154761 CATCCTGCTGGTCATTTCTTACAGAACAATAATATTCCATAACATTCATG 154810 iv iiv iii v v vvvv i i iiii v v C L1ME5_3end#LI 580 CATCTAGTCCGTTGCTTCTAACTGCTGCATAGTACTCCATGGTGTGCATC 531 chr1qtel1M 154811 TACCACAATTTACCCAGCCATTCTCCAATTGATGGGCATCCACTCAGTTT 154860 i v i v i v v i i vviv ii C L1ME5_3end#LI 530 CACCACATTTTACCTATCCACTCTCCCAGTGATGGACACCCAGGTTGCCT 481 chr1qtel1M 154861 CCAGCTTCTAGCCACTACAAACAGGGCTGCCACAAACATTTTGGCACAT 154909 i i iv i iv v ii ii v i C L1ME5_3end#LI 480 CCAACTCCCCGCCACCACAAACAACGCTGCAATGAACATCCTCGTACAT 432 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 45.48 CpG sites = 37, Kimura (unadjusted) = 45.48 Transitions / transversions = 1.32 (37/28) Gap_init rate = 0.02 (4 / 196), avg. gap size = 1.00 (4 / 4) 327 30.24 0.65 4.00 chr1qtel1M 154788 154942 (845058) C L1MB5_3end#LINE/L1 (368) 553 404 m_b32s551i2 1098 chr1qtel1M 154788 AATAATATTCCATAACATTCATGTACCACAATTTACCCAGCCATTCTCCA 154837 vii vv i v iiii v vi v C L1MB5_3end#LI 553 AATAATATTCCATTGTATGGATATACCACATTTTGTTTATCCATTCATCC 504 chr1qtel1M 154838 ATTGATGGGCATCCACTCAGTTTCCAGCTTCTAGCCACTACAAACAGGGC 154887 i i iiivviv v i i i i iii i v C L1MB5_3end#LI 503 GTTGATGGACATTTGGGTTGTTTCCACCTTTTGGCTATTGTGAATAGTGC 454 chr1qtel1M 154888 TGCCACAAACATTTTGGCACATAAAGTATTGATTTTTAAGATAATT-TTT 154936 i ii ivv i --- ? -- v i - vi - C L1MB5_3end#LI 453 TGCTATGAACATTCGTGTAC---AAGTNTT--TGTTTGA-ATACCTGTTT 410 chr1qtel1M 154937 TCAATT 154942 C L1MB5_3end#LI 409 TCAATT 404 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 38.37 CpG sites = 29, Kimura (unadjusted) = 40.75 Transitions / transversions = 1.81 (29/16) Gap_init rate = 0.05 (7 / 154), avg. gap size = 1.00 (7 / 7) 451 33.83 0.97 0.97 chr1qtel1M 155190 155395 (844605) C L1ME5_3end#LINE/L1 (304) 637 432 m_b32s551i3 1099 chr1qtel1M 155190 TCCTGCTCGTTTCACTCAGCATCA-GTTCCTGTCAG-TCTCTCTAGGCCT 155237 i i iv ii - -- v v - iv i v iiv C L1ME5_3end#LI 637 TCTTACTTTTTTCACTCAGCACTATGTT--TTTAAGATCCATCCATGTTG 590 chr1qtel1M 155238 CTCTGTATTCATCCTGCTGGTCATTTCTTACAGAACAATAATATTCCATA 155287 v i v iv iiv iii v v vvvv i i i C L1ME5_3end#LI 589 CTATGTGTACATCTAGTCCGTTGCTTCTAACTGCTGCATAGTACTCCATG 540 chr1qtel1M 155288 ACATTCATGTACCACAATTTACCCAGCCATTCTCCAATTGATGGGCATCC 155337 iii v vi v i v i v v i i C L1ME5_3end#LI 539 GTGTGCATCCACCACATTTTACCTATCCACTCTCCCAGTGATGGACACCC 490 chr1qtel1M 155338 ACTCAGTTTCCAGCTTCTAGCCACTACAAACAGGGCTGCCACAAACATTT 155387 vviv ii i i iv i iv v ii ii C L1ME5_3end#LI 489 AGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCTGCAATGAACATCC 440 chr1qtel1M 155388 TGGCACAT 155395 v i C L1ME5_3end#LI 439 TCGTACAT 432 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 46.57 CpG sites = 40, Kimura (unadjusted) = 46.57 Transitions / transversions = 1.38 (40/29) Gap_init rate = 0.02 (4 / 205), avg. gap size = 1.00 (4 / 4) 327 30.24 0.65 4.00 chr1qtel1M 155274 155428 (844572) C L1MB5_3end#LINE/L1 (368) 553 404 m_b32s551i4 1099 chr1qtel1M 155274 AATAATATTCCATAACATTCATGTACCACAATTTACCCAGCCATTCTCCA 155323 vii vv i v iiii v vi v C L1MB5_3end#LI 553 AATAATATTCCATTGTATGGATATACCACATTTTGTTTATCCATTCATCC 504 chr1qtel1M 155324 ATTGATGGGCATCCACTCAGTTTCCAGCTTCTAGCCACTACAAACAGGGC 155373 i i iiivviv v i i i i iii i v C L1MB5_3end#LI 503 GTTGATGGACATTTGGGTTGTTTCCACCTTTTGGCTATTGTGAATAGTGC 454 chr1qtel1M 155374 TGCCACAAACATTTTGGCACATAAAGTATTGATTTTTAAGATAATT-TTT 155422 i ii ivv i --- ? -- v i - vi - C L1MB5_3end#LI 453 TGCTATGAACATTCGTGTAC---AAGTNTT--TGTTTGA-ATACCTGTTT 410 chr1qtel1M 155423 TCAATT 155428 C L1MB5_3end#LI 409 TCAATT 404 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 38.37 CpG sites = 29, Kimura (unadjusted) = 40.75 Transitions / transversions = 1.81 (29/16) Gap_init rate = 0.05 (7 / 154), avg. gap size = 1.00 (7 / 7) 625 25.56 9.77 2.18 chr1qtel1M 155759 156014 (843986) C L1ME3G_3end#LINE/L1 (376) 548 274 m_b32s551i5 1100 chr1qtel1M 155759 ATAACATTCCATAATATTCATATACCATAATTTATTCAGCTATTCTCCAC 155808 ii i vv i i i i vv C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr1qtel1M 155809 TTGATGGGCATCCTCAG----TTTCCAGTTT----CTGCCACAAACATTT 155850 i -- i ---- i ---- iii v v C L1ME3G_3end#L 498 TTGATGGACAT--TTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATG 451 chr1qtel1M 155851 TTGCACATGTGGGTCCCTTTCC---CTTCTTTA---ACAT---------- 155884 i - vivi i v v --- ? i i--- ---------- C L1ME3G_3end#L 450 CTGCA-ATGAACATCCTTGTACATGCNTCCTTGTGCACATGTGCGAGTAT 402 chr1qtel1M 155885 -TCTTTGGGATATGAGCCCAGTAGAAACACTGCTGGATCAAAGGGTATGC 155933 - ? i viv? ? v viiv i i C L1ME3G_3end#L 401 TTCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGC 352 chr1qtel1M 155934 ACAGTCTGATAACTTTTTGAGCATAGTTCCAAACTGCTCTCCAGAATGGC 155983 i v i i -- i vvv - v v i i i ? C L1ME3G_3end#L 351 GCATTTTAA--ATTTTAATAG-ATACTGCCAAATTGCCCTCCAAAANGGC 305 chr1qtel1M 155984 TGGATCCATTCTCGGTTCCACCAATAATGTA 156014 v i v iv iv i ii i C L1ME3G_3end#L 304 TGTACCAATTTACACTCCCACCAGCAGTGTA 274 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 32.35 CpG sites = 39, Kimura (unadjusted) = 32.98 Transitions / transversions = 1.56 (39/25) Gap_init rate = 0.05 (12 / 255), avg. gap size = 2.58 (31 / 12) 14 20.14 1.47 9.52 chr1qtel1M 156374 156441 (843559) (TTATAT)n#Simple_repeat 1 63 (0) m_b32s252i4 1101 chr1qtel1M 156374 TTATA-TTAGCATTATATTTTTATATACATTGTAAACTATATATTATATA 156422 - vvv v v i - v - v - (TTATAT)n#Sim 1 TTATATTTATATTTATATTTATATTTATATT-TATA-TTTATATT-TATA 47 chr1qtel1M 156423 TCATCATATCTTATAATTA 156441 -- i - v (TTATAT)n#Sim 48 T--TTATAT-TTATATTTA 63 Matrix = Unknown Transitions / transversions = 0.25 (2/8) Gap_init rate = 0.10 (7 / 67), avg. gap size = 1.00 (7 / 7) 17 14.19 5.77 5.77 chr1qtel1M 156386 156437 (843563) (TA)n#Simple_repeat 1 52 (0) m_b32s252i5 1102 chr1qtel1M 156386 TATATTTTTATATACAT-TGTAAACTATATAT-TATATATCATCATATCT 156433 v v i - i v - - - - v (TA)n#Simple_ 1 TATATATATATATATATATATATA-TATATATATATATAT-AT-ATATAT 47 chr1qtel1M 156434 -TATA 156437 - (TA)n#Simple_ 48 ATATA 52 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.12 (6 / 51), avg. gap size = 1.00 (6 / 6) 264 36.15 0.00 0.00 chr1qtel1M 159029 159158 (840842) HERVIP10FH#LTR/ERV1 4559 4688 (414) m_b32s701i0 1103 chr1qtel1M 159029 AATTACAGCAGAGAGGCGGTGAAGGAAATAACAAAATGGTCGGAAGCTGC 159078 i vi v v v i i i vi iiii ii ii i HERVIP10FH#LT 4559 AACTACACTAGAGATGCTGTTAAAGGAATAGCTGAGCAATTAGGGGCTAC 4608 chr1qtel1M 159079 AAGCAGAAGGGCGTGGGAAGATAGAACGACTCTAGAAAGGTTATTGGCAG 159128 v vii v v i i iii ii v v v i HERVIP10FH#LT 4609 TAGCCAGATGGCTTGGGAAAATAGGATAGCCTTAGACATGATATTAGCAG 4658 chr1qtel1M 159129 GAAGAGGAGGAACATGTGTTACCACTAGAA 159158 i iiv i i iv i i HERVIP10FH#LT 4659 AAAGAGGAGGAGTTTGCGTCATGATTAAAA 4688 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 52.07 CpG sites = 33, Kimura (unadjusted) = 53.84 Transitions / transversions = 2.36 (33/14) Gap_init rate = 0.00 (0 / 129), avg. gap size = 0.0 (0 / 0) 245 28.20 3.88 5.78 chr1qtel1M 161013 161347 (838653) C L1MC_orf2#LINE/L1 (2238) 1056 728 m_b32s551i6 1104 chr1qtel1M 161013 GTTTTC--TTATATTCAGGTTTCTTAACTTTAGTTTTTAGGATTTTCAAT 161060 -- vi -- i --i i i vv iivv C L1MC_orf2#LIN 1056 GTTTTCAATTTCATT--GATTTCT--GCTCTAATTTTTATTATTTCTTTT 1011 chr1qtel1M 161061 TTGGTGTTTAATTGGAAATTTTTAATGTGTTCTTTTTTTAAATTTTTATT 161110 i vv i v v i --- v i i ---- i vi C L1MC_orf2#LIN 1010 CTTCTGCTTACTTTGGA---TTTAATTTGCTCTTCTTTT----TCTAGTT 968 chr1qtel1M 161111 TATTTATTTTGCACCATCAGTTGCTTGATCT--GCTCTTTATT--GTACT 161156 vi v vv v v v - i v vv i -- v v --v v C L1MC_orf2#LIN 967 TCCTAAGGTGGAAGC-TTAGATTATTGATTTTAGATCTTTCTTCTTTTCT 919 chr1qtel1M 161157 GATGTATACAATAAGAGAGATGAATTTCCCTCTGATTACTGCTTTTGCTG 161206 i i i v v iv vv i i vi i C L1MC_orf2#LIN 918 AATATATGCATTCAATGCTATAAATTTCCCTCTAAGCACTGCTTTCGCTG 869 chr1qtel1M 161207 CATCACATTGATTTTGGTATGTTGTGTTATTATCCCTTCTCTTTAATAAT 161256 v ivi i v i v i --- iiv i -vi C L1MC_orf2#LIN 868 CATCCCACAAATTTTGATAAGTTGTATTTTCAT---TTTCATTTAGT-TC 823 chr1qtel1M 161257 AAAAT-TTTTTATTGTTTCTC-TGA-----CTTCTTTAACCCATGTATCC 161299 - -vi - ----- i i iv C L1MC_orf2#LIN 822 AAAATATTTTTA-AATTTCTCTTGAGATTTCTTCTTTGACCCATGTGTTA 774 chr1qtel1M 161300 TTTAAAATAAGATTATTTAGTCTCCAATTAATTTTAGTCTATTTCCAG 161347 i vvivi i i v - i vv - C L1MC_orf2#LIN 773 TTTAGAAGTGTGTTGTTTAATCTCCAAGT-ATTTTGGGAT-TTTCCAG 728 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 35.20 CpG sites = 44, Kimura (unadjusted) = 35.69 Transitions / transversions = 0.98 (44/45) Gap_init rate = 0.07 (25 / 334), avg. gap size = 1.28 (32 / 25) 301 30.50 5.70 2.45 chr1qtel1M 161077 161392 (838608) C L1M2_orf2#LINE/L1 (2289) 1002 677 m_b32s551i7 1104 chr1qtel1M 161077 AATTTTTAATGTGTTCTTTTTTTAAATTTTTATTTATTTATTTTGCACCA 161126 vii v v i v i ivv i v vi ivvv i i C L1M2_orf2#LIN 1002 AATTTTGGGTTTGGTTTGTTCTTGCTTTTCTAGTTCCTTGAGGTGCATCG 953 chr1qtel1M 161127 TCAG-TTGCTTGATCTG----CTCTTTATTGTACTGATGTATACAATAAG 161171 i - i - i ---- i i i v vi vi iv v v C L1M2_orf2#LIN 952 TTAGGTTGTTT-ATTTGAAATCTTTCTACTTTTTTGATGTAGGCGTTTAT 904 chr1qtel1M 161172 AGAGATGAATTTCCCTCTGATTACTGCTTTTGCTGCATCACATTGATTTT 161221 v vv i i v v? i v v i C L1M2_orf2#LIN 903 TGCTATAAACTTCCCTCTTAGNACTGCTTTTGCTGTATCCCATAGGTTTT 854 chr1qtel1M 161222 GGTATGTTGTGTTATTATCCCTTCTC-TTTAAT--AATAAAATTTTTTAT 161268 ---- v i - iv -- -i ? v C L1M2_orf2#LIN 853 GGTATGTTGTGTT----TCCATTTTCATTTGTTTCAA-GAAATTTTTNAA 809 chr1qtel1M 161269 TGTTTCTCTGA----CTTCTTTAACCCATGTATCCTTTAAAATAAGATTA 161314 v iii v ---- v i vvi v i ii vv vi i C L1M2_orf2#LIN 808 TTTCCTTCTTAATTTCTTCATTGACCCATTGGTCGTTCAGGAGCATGTTG 759 chr1qtel1M 161315 TTTAGTCTCCAATTAATTTTAGTCTATTTCCAGGGT--CCCTTATTA--A 161360 i i vv v v --?vi ii -- i i --i C L1M2_orf2#LIN 758 TTTAATTTCCATGTATTTGTA--NAGTTTCCAAAGTTCCTCTTGTTATTG 711 chr1qtel1M 161361 ATATC--ATTTTGTTGCAGCATGGGCTAAAAAGA 161392 v --i i v vii v ?i C L1M2_orf2#LIN 710 ATTTCTAGTTTTATTCCATTGTGGTCNGAAAAGA 677 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.45 CpG sites = 49, Kimura (unadjusted) = 40.56 Transitions / transversions = 1.09 (49/45) Gap_init rate = 0.05 (16 / 315), avg. gap size = 1.62 (26 / 16) 397 24.69 4.65 3.45 chr1qtel1M 161155 161326 (838674) C L1MD_orf2#LINE/L1 (2374) 920 747 m_b32s551i8 1104 chr1qtel1M 161155 CTGATGTATACAATAAGAGAGATGAATTTCCCTCTGATTACTGCTTTTGC 161204 i ?i v v v vv i v vi v C L1MD_orf2#LIN 920 CTAATGTANGCATTTAGTGCTATAAATTTCCCTCTCAGCACTGCTTTAGC 871 chr1qtel1M 161205 TGCATCACATTGATTTTGGTATGTTGTGTTATTA--TCCCTTCTCTTTAA 161252 i v ivi i i v i -- i v vv i C L1MD_orf2#LIN 870 TGCGTCCCACAAATTTTGATATGTTGTATTTTCATTTTCATTCAGTTCAA 821 chr1qtel1M 161253 TAATAAAATTTTTTATTGTTTCTCT---GACT---TCTTTAACCCATGTA 161296 -i --- --i i --- --- i v C L1MD_orf2#LIN 820 T-GT---ATTTTTTA--ATTTCCCTTGAGACTTCCTCTTTGACCCATGGA 777 chr1qtel1M 161297 TCCTTTAAAATAAGATTATTTAGTCTCCAA 161326 iv i vvivi i i C L1MD_orf2#LIN 776 TTATTTAGAAGTGTGTTGTTTAGTTTCCAA 747 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 29.72 CpG sites = 22, Kimura (unadjusted) = 30.59 Transitions / transversions = 1.16 (22/19) Gap_init rate = 0.05 (9 / 171), avg. gap size = 1.56 (14 / 9) 219 30.30 21.72 0.00 chr1qtel1M 161466 161663 (838337) C L2#LINE/L2 (617) 2465 2225 m_b32s601i1 1105 chr1qtel1M 161466 GGGTTTCGTTTTGAGTGTATGGAGCTTAAGAGGTTTCCTAGACATCCTTT 161515 i iv iiii i vi i i v ii vi vvv C L2#LINE/L2 2465 GAGTTCAGTTTTGGACATGTTAAGTTTGAGATGCCTATTAGACATCCAAG 2416 chr1qtel1M 161516 TCTAGATATTG----GGC--TTGGGTG-A-GAGACTGGAAGTCATCAGAG 161557 vv i i ---- -- i i- - v iv vvi C L2#LINE/L2 2415 TGGAGATGTCGAGTAGGCAGTTGGATATACGAGTCTGGAGTTCAGGGGAG 2366 chr1qtel1M 161558 AGGTGGAAGCAGGAAAAGTAGATCTGAG----------ATGGAGATGGTA 161597 vvii v i vi i i i ---------- iv C L2#LINE/L2 2365 AGGTCCGGGCTGGAGATATAAATTTGGGAGTCATCAGCATATAGATGGTA 2316 chr1qtel1M 161598 ATTCAAGCCATGGGA---GATAA--------AG---GTG-----AAATAG 161628 v v i --- i -------- --- ----- i C L2#LINE/L2 2315 TTTAAAGCCATGAGACTGGATGAGATCACCNAGGGAGTGAGTGTAGATAG 2266 chr1qtel1M 161629 GTCAG----GAGGTTTGGAGA--GAGCCCTGAGGGACTCCA 161663 ivv ---- iiiii -- i v C L2#LINE/L2 2265 AGAAGAGAAGAGGTCCAAGGACTGAGCCCTGGGGCACTCCA 2225 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 38.52 CpG sites = 37, Kimura (unadjusted) = 40.27 Transitions / transversions = 1.61 (37/23) Gap_init rate = 0.06 (11 / 197), avg. gap size = 3.91 (43 / 11) 247 24.58 6.20 5.38 chr1qtel1M 161673 161801 (838199) C AmnL2-1#LINE/L2 (1138) 1475 1346 m_b32s601i2 1106 chr1qtel1M 161673 AGAAGCAGAATCCATTAATGGTAGGAGGAGAACCAG-GA-GCCTCCATCA 161720 i i i ----- ii - - - v - C AmnL2-1#LINE/ 1475 AGGAGCGGAACC-----ATGACAGGAGG-GAACCAGAGACGCCTGCAT-A 1433 chr1qtel1M 161721 GCTAGAGAGT--GTTAGGGCAAAGAGAGTGA-CCACAGTGTCTGGGGCTT 161767 ?vi v-- ivi vii vi i i- vii v C AmnL2-1#LINE/ 1432 GCTNTGGAGGCGGTCCAGGAGGATGGAATGGTCCACAGTGTCGAAGGCTG 1383 chr1qtel1M 161768 CAGGGAGGTCAAGG---ATGGGGATGGAGAGAAGGCC 161801 vv --- i v i ii C AmnL2-1#LINE/ 1382 CACTGAGGTCAAGGAGAATGAGGAAGGAGAAAGAGCC 1346 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.74 CpG sites = 19, Kimura (unadjusted) = 30.97 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.09 (12 / 128), avg. gap size = 1.25 (15 / 12) 2700 29.02 1.96 1.30 chr1qtel1M 164819 165890 (834110) C L1P4_orf2#LINE/L1 (735) 2559 1481 m_b32s551i9 1107 chr1qtel1M 164819 TCTTTTGTTTTTCCATATGAACTTTGTTGTTATTTTTTCTAGGTC-ATCA 164867 v vv i ivvi vi iv -i v C L1P4_orf2#LIN 2559 TCTTTTTTGGTTCCATATGAATTTTAGAATAGTTTTTTCTAATTCTGTGA 2510 chr1qtel1M 164868 AAATTGTTTTTGGGGAGTCTGATTGGTATAGCGCTAAATTAGTTAGATTA 164917 v viv v- i v v i i iv - i C L1P4_orf2#LIN 2509 AAAATGACGTTGGT-AGTTTGATAGGAATAGCGTTGAATCTGT-AGATTG 2462 chr1qtel1M 164918 GTTTAGGTAGTATTGTTATCTTTATTATATTTGCTTGCCCAATCCAAGAG 164967 v i i v ii i v iv vii ivi v C L1P4_orf2#LIN 2461 CTTTGGGCAGTATGGCCATTTTAACGATATTGATTCTTCCAATCCATGAG 2412 chr1qtel1M 164968 CATTTAATATCTTTCCAGTTGGTTAGATCAGACTTAATTTGTGTGAAAAG 165017 vv i i v v ivi vvi? i v v v iv C L1P4_orf2#LIN 2411 CATGGAATGTTTTTCCATTTGTTTGTGTCATCTNTGATTTCTTTCAGCAG 2362 chr1qtel1M 165018 TGTTTTGTAGTTTTGCTCATAAAG-TTTCTGATTTTCCCTTGGC-AGATA 165065 i v ii i - i i v ii -- i- i C L1P4_orf2#LIN 2361 TGTTTTGTAGTTCTCCTTGTAGAGATCTTTCACCT--CCTTGGTTAGATG 2314 chr1qtel1M 165066 GTTTCCTAAATATTTTAT----------ACTATCAGTA--TAAAATTTC- 165102 vv ii ----------i i- -- iii v - C L1P4_orf2#LIN 2313 TATTCCTAGGTATTTTATTTTTTTTGTGGCTATT-GTAAATGGGATTGCG 2265 chr1qtel1M 165103 -TCTT--TGTAACTCTGACTGTTGGATTTTGTTACTGATATATAAGAATG 165149 - -- v ii v vi- i i--- i i i ii C L1P4_orf2#LIN 2264 TTCTTGATTTGGCTCTCAGC-TTGAAC---GTTATTGGTGTATAGAAATG 2219 chr1qtel1M 165150 CTGATGATTTATGTGGGTTTATTTTATAACCAGCAACTTTGCTAAAGTTG 165199 iv v ivi v i v v v i i i C L1P4_orf2#LIN 2218 CTACTGATTTTTGTACATTGATTTTGTATCCTGAAACTTTACTGAAGTCG 2169 chr1qtel1M 165200 TAGATTATTTCTAATAGCTTTTTAGTAGAATCTCTGGGGTTCTTTAAGTA 165249 vv i v iv i i ii i i i i i i C L1P4_orf2#LIN 2168 TTTATCAGTTCTAGGAGCCTTTTGGCGGAGTCTTTAGGGTTTTCTAGGTA 2119 chr1qtel1M 165250 TACCATCATATCGTTCAGCAAAGAGTGATAATTTGGTTTCCTCATTGCCT 165299 vv - i v i ii i v v C L1P4_orf2#LIN 2118 TAGAATCATATCGT-CAGCGAAGAGAGATAGTTTGACTTCTTCTTTTCCT 2070 chr1qtel1M 165300 ATTCTTGTTCCTTTAATCTCTTTCTCAACTCTTATTGCCAAAGCTAGCAT 165349 ivvi v v i vvvi v ivvi v i C L1P4_orf2#LIN 2069 ATTTGGATGCCTTTTATTTCTTTCTCTTGCCTGATTGCTCTGGCTAGGAC 2020 chr1qtel1M 165350 TTCTAATACAATATTAAATAGTAACGGTGATAGTGAGCAACCTTATTTCA 165399 i i v i i v ii v i v i i ii C L1P4_orf2#LIN 2019 TTCCAGTACTATGTTGAATAGGAGTGGTGAGAGTGGGCATCCTTGTCTTG 1970 chr1qtel1M 165400 CTCCTGATCTTATTGGGAATGGTTGCAGTTTGTCCCCATTACATATGATG 165449 i v v i vv v v i v v i vvi C L1P4_orf2#LIN 1969 TTCCAGTTCTCAAGGGGAATGCTTCCAGCTTTTGCCCGTTCAGTATGATG 1920 chr1qtel1M 165450 CTTACTGCTGGTTTTAAATAGATGCTACTGATTATTTTAAGGAAAAGTCC 165499 i vi iv vvv viv v i v viv C L1P4_orf2#LIN 1919 TTGGCTGTGGGTTTGTCATAGATGGCTCTTATTATTTTGAGGTATGTTCC 1870 chr1qtel1M 165500 ATTTATTCCTATACTCTCAAGCGTTTTTAATAGGAATGGATGTTGGATTT 165549 v iv v vvi v ii v vi v v C L1P4_orf2#LIN 1869 TTCGATGCCTAGTTTGTTGAGGGTTTTTATCATGAAGGGATGTTGGATTT 1820 chr1qtel1M 165550 TATCAAATGCTTTTTCTGCATCTATTGAGATGATCATATGGTTTTTGTTA 165599 i v i - C L1P4_orf2#LIN 1819 TATCGAAAGCTTTTTCTGCGTCTATTGAGATGATCATATGGTTTTTGTT- 1771 chr1qtel1M 165600 ATTTGGTT--ATTAATATGGCCAATTATACTGATAGTTTTCCTAATATTG 165647 - ii --i v i iv i i i v v v v vv i C L1P4_orf2#LIN 1770 -TTTAATTCTGTTTATGTGGTGAATCACATTTATTGATTTGCGTATGTTG 1722 chr1qtel1M 165648 AACCAGCCCTGCATTCCTGGTATAAATCCTACTTGATCGTGGTGTGTTAT 165697 i i i v v v vi v C L1P4_orf2#LIN 1721 AACCAACCTTGCATCCCAGGAATAAAGCCTACTTGATCGTGGTGAATTAA 1672 chr1qtel1M 165698 CCTGGGGATGATTTTCTGTAGTCTTTTTGCTAATATTTTATTTAAGATTT 165747 i vvv vvi v v v vv i i v i C L1P4_orf2#LIN 1671 CTTTTTGATGTGCTGCTGGATTCGGTTTGCTAGTATTTTGTTGAGGATTT 1622 chr1qtel1M 165748 TAGCATCAATATTCATTAGGGAGATTGGTCTATAATTTTCTTTCCCTGTT 165797 v i v i i v i i? i iiii C L1P4_orf2#LIN 1621 TTGCGTCTATGTTCATCAGGGATATTGGCCTGNAGTTTTCTTTTTTCGTT 1572 chr1qtel1M 165798 TTCAACCTACCTGGTTTAGGTATCAGTACCATGTCTGTGTCATAAAAGGA 165847 v vvvii i v v viiv iiv iv i i v C L1P4_orf2#LIN 1571 GTGTCTTTGCCAGGTTTTGGTATCAGGGTGATGCTGGCTTCGTAGAATGA 1522 chr1qtel1M 165848 ATTTGGTAGGACTCCTTCATTCCCTATTTTTTTCCAAATAGTT 165890 i v v v i v i i v --vi C L1P4_orf2#LIN 1521 GTTAGGGAGGAGTCCCTCCTCCTCGATTTTTT--GGAATAGTT 1481 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 35.37 CpG sites = 159, Kimura (unadjusted) = 37.33 Transitions / transversions = 1.07 (159/148) Gap_init rate = 0.02 (23 / 1071), avg. gap size = 1.52 (35 / 23) 226 33.09 5.15 0.00 chr1qtel1M 165902 166037 (833963) C L1MC1_3end#LINE/L1 (508) 572 430 m_b32s551i10 1108 chr1qtel1M 165902 TCATCTCTTAT-AGAAC--AGTAATATTCCATTACACTCATATACCATAA 165948 i v - vi -- i iivivv i i i C L1MC1_3end#LI 572 TCATTTCTTTTTAGCGCTGAATAATATTCCATTGTCTGGATGTACCACAG 523 chr1qtel1M 165949 CTTATTCAGCCATTCTCCAGCTGATGGGCATC-CAGT---TTCCAGTTTC 165994 i i v v vi v i -ii --- iv i C L1MC1_3end#LI 522 TTTATTTATCCATTCACCTACTGAAGGACATCTTGGTTGCTTCCAAGTTT 473 chr1qtel1M 165995 TTGCCACTACAAAATGGGCTGCCACAAAAATTTTTGCACATGT 166037 v v i ii vvii i i v iiv ii v C L1MC1_3end#LI 472 TGGCAATTATGAATAAAGCTGCTATAAACATCCGTGTGCAGGT 430 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 42.89 CpG sites = 28, Kimura (unadjusted) = 45.67 Transitions / transversions = 1.65 (28/17) Gap_init rate = 0.03 (4 / 135), avg. gap size = 1.75 (7 / 4) 675 30.82 2.88 1.21 chr1qtel1M 165920 166162 (833838) C L1ME4c_3end#LINE/L1 (276) 554 308 m_b32s551i11 1108 chr1qtel1M 165920 TAATATTCCATTACACTCATATACCATAACTTATTCAGCCATTCTCCAGC 165969 iivii?v i i i i i i vii C L1ME4c_3end#L 554 TAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTAT 505 chr1qtel1M 165970 TGATGGGCATCCAG----TTTCCAGTTTCTTGCCACTACAAAATGGGCTG 166015 v i ii ---- i i i i i i vviv C L1ME4c_3end#L 504 TGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCTG 455 chr1qtel1M 166016 CCACAAAAATTTTTGCACATGTGGATCCCTTTCCCTCCTTTAAG--ATCT 166063 v ii v i i ii i i -- ii i i i i-- i C L1ME4c_3end#L 454 CAATGAACATCTTCGTGCATATAG--CTTTTTCCTTCTTTTGAATTATTT 407 chr1qtel1M 166064 CTTTGGGATAGAAGCCCAGTGGGAACACTGCTGGGTCAAAGGGGATACAC 166113 i i i vv vi viiv i i v iv C L1ME4c_3end#L 406 CCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAAC 357 chr1qtel1M 166114 AGTTTGATAGCCCTGTGA-GCATAGTTCCAGATTGCTCTCCACAATGGTT 166162 v v i i - -i i v v i i v v C L1ME4c_3end#L 356 ATTTTTATGGCTCT-TGATACGTATTGCCAAATTGCTTTCCAAAAGGGTT 308 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.37 CpG sites = 52, Kimura (unadjusted) = 42.54 Transitions / transversions = 2.36 (52/22) Gap_init rate = 0.02 (6 / 242), avg. gap size = 1.67 (10 / 6) 12 4.53 4.00 4.00 chr1qtel1M 166354 166378 (833622) (CTCC)n#Simple_repeat 1 25 (0) m_b32s252i6 1109 chr1qtel1M 166354 CTCCCTTCCT-CCTCCACTCCCTCCC 166378 i - - (CTCC)n#Simpl 1 CTCCCTCCCTCCCTCC-CTCCCTCCC 25 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.08 (2 / 24), avg. gap size = 1.00 (2 / 2) 11 25.80 0.00 6.12 chr1qtel1M 166477 166528 (833472) (AAAAAT)n#Simple_repeat 1 49 (0) m_b32s252i7 1110 chr1qtel1M 166477 AAAAATGAGAAAGAAAACAAAAAGCAAGCAAACAACAACAAAGATAAAAA 166526 - i v vv ii -- i v i i (AAAAAT)n#Sim 1 AAAAAT-AAAAATAAAAATAAAAATAA--AAATAAAAATAAAAATAAAAA 47 chr1qtel1M 166527 TA 166528 (AAAAAT)n#Sim 48 TA 49 Matrix = Unknown Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.00 (3 / 3) 12 16.93 0.00 0.00 chr1qtel1M 168861 168887 (831113) (CCTCC)n#Simple_repeat 1 27 (0) m_b32s252i8 1111 chr1qtel1M 168861 CCTCCCCTCCTTACCTCTCCCCTCCCC 168887 iiv i (CCTCC)n#Simp 1 CCTCCCCTCCCCTCCCCTCCCCTCCCC 27 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 17 23.88 0.00 0.00 chr1qtel1M 168979 169022 (830978) (AAA)n#Simple_repeat 1 44 (0) m_b32s252i10 1112 chr1qtel1M 168979 AAAAAAGAAAAAAAACTACTAGAAAGAAAAAAACAAACAAAAAA 169022 i vv vv i i v v (AAA)n#Simple 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 44 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 158 34.65 4.22 3.20 chr1qtel1M 171686 172799 (827201) (TCCTCCC)n#Simple_repeat 1 1125 (0) m_b32s252i11 1113 chr1qtel1M 171686 TCCTACCTCCTTCCCCCCTCCCT-TTGCCTTTTCCCTCCTCCCACTGTTT 171734 v - i -i v ii v iviii (TCCTCCC)n#Si 1 TCCTCCCTCC-TCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCC 49 chr1qtel1M 171735 TTTTCCCTCTCTCCTACCCCCTTCTTACCTCCTTCCCCCTCCCT-TTGCC 171783 ii - iv i i i v i i -i v (TCCTCCC)n#Si 50 TCCTCCCTC-CTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCC 98 chr1qtel1M 171784 TTTTCCCTCCTCCCT--TCTCT-TTGTCTTTTCTCTCCAGTCTCCTTCCT 171830 ii -- i -i vi ii i vvi i (TCCTCCC)n#Si 99 TCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCT 148 chr1qtel1M 171831 CCTGTCTCTTCCCTCCTCCCCACCTTTCCCTCTTCCC-CCTCCCT-TTGC 171878 vi i - v -- i - -i v (TCCTCCC)n#Si 149 CCTCCCTCCTCCCTCCT-CCCTCC--TCCCTCCTCCCTCCTCCCTCCTCC 195 chr1qtel1M 171879 CTTTTCCCTCCTCCC-CCTCTCTGTTTTTTTCCTTTTCCTACTCCCTTCC 171927 ii - i -ii iii -- i v - (TCCTCCC)n#Si 196 CTCCTCCCTCCTCCCTCCTCCCT-CCTCCCTCC--TCCCTCCTCCC-TCC 241 chr1qtel1M 171928 TACATCCTTTCTCCCTCCCT-TTGCCTTTTCCCTCCTCCCT--TCTCT-T 171973 v v ii - -i v ii -- i -i (TCCTCCC)n#Si 242 TCCCTCCTCCCT-CCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTCC 290 chr1qtel1M 171974 TGTCTTTTCCCTCCTGTCTCCTCCCTTCTCCTCTCC-ACCT-TTCCCTCT 172021 vi ii vi i - -v -i i (TCCTCCC)n#Si 291 TCCCTCCTCCCTCCTCCCTCCTCCCTCCTCC-CTCCTCCCTCCTCCCTCC 339 chr1qtel1M 172022 TCCC-CCTCCCT-TTGCTTTTTCCCTCCTCCCT--TCTCT-TTGTCTTTT 172066 - -i v i ii -- i -i vi ii (TCCTCCC)n#Si 340 TCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCT 389 chr1qtel1M 172067 TCCTCTTGCCTCCT-CCTCC-CCCTCCATTTGTCGT-TTTTCTACCTTCT 172113 i i v - - - iiv v -ii i v i (TCCTCCC)n#Si 390 CCCTCCTCCCTCCTCCCTCCTCCCTCC-TCCCTCCTCCCTCCTCCCTCCT 438 chr1qtel1M 172114 CCCCACCTCCTCTTCCCCCCTTTTGCCTTTTCACAAATTCTTTGTCTTTT 172163 - v - - i ii v ii v vvv i i iv -ii (TCCTCCC)n#Si 439 -CCCTCCTCC-C-TCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTC-CCT 484 chr1qtel1M 172164 ACCTTCCCTTCCCCTCTCCT-TGTCCT-TCTTCTCCCTGTTTTTTCTTCT 172211 - - - i i -iv -i i vi iii i i (TCCTCCC)n#Si 485 -CC-TCCC-TCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCC 531 chr1qtel1M 172212 TTCTTATCTCCT-CCTCCT-CCTTTTGCTTTTTCCCTCCTCCCTTCTCCT 172259 i i vi - - ii v i ii i i (TCCTCCC)n#Si 532 CTCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCC 581 chr1qtel1M 172260 TCCTCCC-CCTCTCT-TTATCTTTTCCCTCCTTCCTCCTCCCCTCTTTGT 172307 - i -i vi ii i - i ivi (TCCTCCC)n#Si 582 TCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCT-CCCTCCTCCC 630 chr1qtel1M 172308 TTTTTCCTCTTTCCTATCTCTTCTCCTTCCCCTTGCTTTTTCCCTTCTTC 172357 ii i i i -i -i i i i v i ii i i (TCCTCCC)n#Si 631 TCCTCCCTCCTCCCT-CCTC-CCTCCTCCCTCCTCCCTCCTCCCTCCTCC 678 chr1qtel1M 172358 CTCCCTGTCTTTTCCCTCCTCCC-CCTCTCTTTCTCTTTTCTTCTTTCCT 172406 - vi ii - - i i -ii i ii (TCCTCCC)n#Si 679 CT-CCTCCCTCCTCCCTCCTCCCTCCTC-CCTCCTC-CCTCCTCCCTCCT 725 chr1qtel1M 172407 ACCTCCTCCCCACCT-CTTCTTCCC-CCT-TCTCTTTCCTCCTCCC-CCT 172452 v - v - i i - -i i i - (TCCTCCC)n#Si 726 CCCTCCT-CCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCT 774 chr1qtel1M 172453 CTCT-TTGTTTTTTCTTTTCCTATTTCCTTCCCACCT-CCTCTTCCC-CT 172499 i -i vii ii -ii vii - v - i - i (TCCTCCC)n#Si 775 CCCTCCTCCCTCCTC-CCTCCTCCCTCC-TCCCTCCTCCCTCCTCCCTCC 822 chr1qtel1M 172500 TGCCTTTTCCCTCTTGCCTCCTCTCCTTTGTTTTTCTCTTTCCTACCTCT 172549 v ii i v - iiviii i ii v i (TCCTCCC)n#Si 823 TCCCTCCTCCCTCCTCCCTCCTC-CCTCCTCCCTCCTCCCTCCTCCCTCC 871 chr1qtel1M 172550 TTCCCCCTCCCTTTGTCTTTTCCTTCTTCCTTCATCC-CCCTCTTTGACT 172598 i i - iv -ii i i i v - -i vv (TCCTCCC)n#Si 872 TCCCTCCTCCC-TCCTC-CCTCCTCCCTCCTCCCTCCTCCCTC-CTCCCT 918 chr1qtel1M 172599 TTTACTTCCCATCTCCTCCCTACTCCCTCTCCCCTCCTCCCTCCT-TCTC 172647 ii v i ivi v ii -i (TCCTCCC)n#Si 919 CCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTC 968 chr1qtel1M 172648 CCCACCT-TTTTTTCCTCCCTCTTTGTTTTTTTTTCCT--TTCCTACCTC 172694 i - -i iii i ivi ii iii --i v (TCCTCCC)n#Si 969 CTC-CCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTC 1017 chr1qtel1M 172695 TTCTCCACCT-ACTCTTCCC-CCTCACT-TTTTCTTCTCCCTCCTCCC-C 172740 i - v -v i - v -i ii i - (TCCTCCC)n#Si 1018 CTC-CCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTC 1066 chr1qtel1M 172741 CACCCATTGACTTTCCT-CCTCCTGCCTTTTCCTGCTCTTTCTCCTTCCT 172789 v - ivv ii - v ii iv - ii i (TCCTCCC)n#Si 1067 CTCCC-TCCTCCCTCCTCCCTCCTCCCTCCTCCCTC-CTCCCTCCTCCCT 1114 chr1qtel1M 172790 CCTCCC-CCTC 172799 - (TCCTCCC)n#Si 1115 CCTCCCTCCTC 1125 Matrix = Unknown Transitions / transversions = 3.15 (211/67) Gap_init rate = 0.07 (79 / 1113), avg. gap size = 1.05 (83 / 79) 223 24.20 4.62 4.62 chr1qtel1M 172808 172872 (827128) C MIR3#SINE/MIR (96) 112 48 m_b32s601i4 1114 chr1qtel1M 172808 GGGGTTAAATGACTTGTCCAGGTTCACACAGCTAATCATTTGACCCAGAG 172857 i v i i i v ? i i v v --- C MIR3#SINE/MIR 112 GAGGTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGG---CAGAG 66 chr1qtel1M 172858 TCT---CCAGACTCCAGG 172872 i v--- i vi C MIR3#SINE/MIR 65 CCGGGACTAGAACCCAGG 48 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.47 CpG sites = 9, Kimura (unadjusted) = 30.47 Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.06 (4 / 64), avg. gap size = 1.50 (6 / 4) 241 20.48 0.00 6.12 chr1qtel1M 172808 172859 (827141) C MIRc#SINE/MIR (153) 115 67 m_b32s601i3 1114 chr1qtel1M 172808 GGGGTTAAATGACTTGTCCAGGTTCACACAGCTAATCATTTGACCCAGAG 172857 i i i i v i v v v --- C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGG---CAGAG 69 chr1qtel1M 172858 TC 172859 i C MIRc#SINE/MIR 68 CC 67 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 24.22 CpG sites = 6, Kimura (unadjusted) = 24.22 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.00 (3 / 3) 401 27.18 6.58 3.18 chr1qtel1M 173202 173353 (826647) C MIRc#SINE/MIR (64) 204 48 m_b32s601i5 1115 chr1qtel1M 173202 ATTTCTTTGGATTCTCACTGC--CCCAG--GGGTGGG---GACAGATGCC 173244 i v v i vi -- v --i i --- i i i-- C MIRc#SINE/MIR 204 ATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTA-- 157 chr1qtel1M 173245 CTTACTATCCCCATTTTACCAGTGGGAACACTGA--CACAATTAGGGGTT 173292 - i vii i i v -- v i-- i C MIRc#SINE/MIR 156 -TTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAG--AGAGGTT 110 chr1qtel1M 173293 AGTTGACTTGTCCAGGGTCACTCAGCCAACAAGTGTCTGCCCCTGAATTT 173342 iv i i v i ii v v vv v i i i C MIRc#SINE/MIR 109 AAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTC 60 chr1qtel1M 173343 G-ACGCTGGTCT 173353 - v v C MIRc#SINE/MIR 59 GAACCCAGGTCT 48 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 33.64 CpG sites = 24, Kimura (unadjusted) = 34.72 Transitions / transversions = 1.50 (24/16) Gap_init rate = 0.07 (10 / 151), avg. gap size = 1.50 (15 / 10) 228 28.07 2.70 10.95 chr1qtel1M 173253 173400 (826600) C MIR3#SINE/MIR (62) 146 10 m_b32s601i6 1115 chr1qtel1M 173253 CCCCATTTTACCAGTGGGAACACTGA--CACAATTAGGGGTTAGTTGACT 173300 i vii i i v -- v i-- i v iv C MIR3#SINE/MIR 146 CCTCATTTTACAGATGAGGAAACTGAGGCCCAG--AGAGGTGAAGTGACT 99 chr1qtel1M 173301 TGTCCAGGGTCACTCAGCCAACAAGTGTCTGCCCCTGAATTTG-ACGCTG 173349 i i v ? iiv v v vv v i i v - v v C MIR3#SINE/MIR 98 TGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAG 49 chr1qtel1M 173350 GTCTGTGGGGTTCCTTCCTGGCCTAGCCCCCCGCCCTCCCTCTGC-CAGC 173398 -------- vv -- i ---i iv i - C MIR3#SINE/MIR 48 GTC--------TCCTGACT--CCCAG---TCCGTGCTCTCTCTGCTCAGC 12 chr1qtel1M 173399 TA 173400 i C MIR3#SINE/MIR 11 CA 10 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 35.56 CpG sites = 19, Kimura (unadjusted) = 35.56 Transitions / transversions = 1.06 (19/18) Gap_init rate = 0.12 (18 / 147), avg. gap size = 1.06 (19 / 18) 263 22.06 4.41 0.00 chr1qtel1M 174704 174771 (825229) C MIRc#SINE/MIR (101) 167 97 m_b32s601i7 1116 chr1qtel1M 174704 CAGTGCAGGTGTCTGTGTTCCCATTTTGCAGAAGAGGAGACTGAGGTTGA 174753 v i ivv i i i v i i v C MIRc#SINE/MIR 167 CAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCA 118 chr1qtel1M 174754 CAGAGG--AAGGGA-TTGTCC 174771 v -- v - i C MIRc#SINE/MIR 117 GAGAGGTTAAGTGACTTGCCC 97 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 26.41 CpG sites = 8, Kimura (unadjusted) = 26.41 Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.03 (2 / 67), avg. gap size = 1.50 (3 / 2) 273 16.98 1.89 0.00 chr1qtel1M 174838 174890 (825110) EutTc1-N1#DNA/TcMar-Tc1 1 54 (534) m_b32s502i1 1117 chr1qtel1M 174838 CAGGGGGTCCCCAAAGTCTTAGGGCACTTTTAAGCTGTAGGAACTTT-GA 174886 v v v v v iv i- EutTc1-N1#DNA 1 CAGGGTGTCCCAAAAGTCTTAGTGCAATTTTAAGCTTTAATAACTTCAGA 50 chr1qtel1M 174887 GGTA 174890 i EutTc1-N1#DNA 51 AGTA 54 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 19.25 CpG sites = 3, Kimura (unadjusted) = 19.25 Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.02 (1 / 52), avg. gap size = 1.00 (1 / 1) 641 31.57 2.88 3.55 chr1qtel1M 177615 177926 (822074) C HERVP71A#LTR/ERV1 (2299) 5291 4982 m_b32s701i1 1118 chr1qtel1M 177615 GAACTGCAAACTCCA-AGGTGTGGTCTGAGGTAGTAATACTTGCTT--CC 177661 i i v - i vi i vi v i v -- -- C HERVP71A#LTR/ 5291 GAACCGCGAACTCAAGAGGCGGAGTTTGAGTCAGAAGTCCTT--TTAACC 5244 chr1qtel1M 177662 TAAGGGCTAAAAGGGATAAGGACACTGCCAGTATATCATTCCTTAAAACC 177711 v i v vvi i iv v i i vi C HERVP71A#LTR/ 5243 TAAGGGATGACAGGGTGGAGGATATGGCCAGTATATAATTTCTTAAGAAT 5194 chr1qtel1M 177712 TTATTATTTGTTTCAA----AAGAGAGTCTTTCCTTCTCCCCTCCCTCTT 177757 vi iv v v ---- i iii v vv----- v - vv C HERVP71A#LTR/ 5193 TGGTCCTTGGTTTCCATAGTAGGAAGATCTGTAG-----CCCTGCC-CAA 5150 chr1qtel1M 177758 ACGTGGTAAACCAAACAACATCTCATATGGGGAAAGTCCTGGATCTCTCC 177807 ii v iv v i i v i v v i iiii i i C HERVP71A#LTR/ 5149 ATATGGGAGCCCATATAATAACTCGTAGGGGGACAATCCCAAGTCTTTTC 5100 chr1qtel1M 177808 TGGGGACAGTCCTAATTCCTTAACAAAGTG--ATTGGCAAACTTTTGGTC 177855 v i v i -- -ii -- v i v C HERVP71A#LTR/ 5099 TTGGGGCTGTCCTAATCC--TAA-GGAGTGCTATTGGGAGACATTTGGTC 5053 chr1qtel1M 177856 CAAAGCAATTTAATGTCTAACCTCAAATTAGCAATCTATTTTTAAAGAAC 177905 i v i v vv i iv i ii v ii vi ii C HERVP71A#LTR/ 5052 CAAGGCATTTTAGTTTCTAAGATTAGTTTGGTGATATGCTTTTTGAGAGT 5003 chr1qtel1M 177906 CTTATTCACTCTTTTCACTTT 177926 i v i ii i C HERVP71A#LTR/ 5002 TTGATTCATTCTTTCTACCTT 4982 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.89 CpG sites = 55, Kimura (unadjusted) = 42.22 Transitions / transversions = 1.38 (55/40) Gap_init rate = 0.05 (15 / 311), avg. gap size = 1.33 (20 / 15) 1065 29.26 4.81 3.05 chr1qtel1M 178078 178722 (821278) L1P4_orf2#LINE/L1 1981 2636 (658) m_b32s551i12 1119 chr1qtel1M 178078 TGCCCACTCTCACCATTACTTTTCAATATTGTATTAGAAATGCTAGTTTT 178127 i v v i v i i i v iivv L1P4_orf2#LIN 1981 TGCCCACTCTCACCACTCCTATTCAACATAGTACTGGAAGTCCTAGCCAG 2030 chr1qtel1M 178128 GGCAATAAGAGAGAAGGAAGAGATTCAAGGAATTAGAGTAGGTCAGGAGG 178177 i v iv ii i i vv v ivi i vv i i L1P4_orf2#LIN 2031 AGCAATCAGGCAAGAGAAAGAAATAAAAGGCATCCAAATAGGAAAAGAAG 2080 chr1qtel1M 178178 AAACTCAATTATCACTCTTTGCAGATGATATGATAGTATACTT-GAGAAC 178226 iiiv i v i v i vv i - i L1P4_orf2#LIN 2081 AAGTCAAACTATCTCTCTTCGCTGACGATATGATTCTATACCTAGAAAAC 2130 chr1qtel1M 178227 CCTAGAAAATCAATGAAAAAGCTATCAGAAATAATCCACAACTTTAGCCA 178276 i i v viiv i vii v i vv i i iv L1P4_orf2#LIN 2131 CCTAAAGACTCCGCCAAAAGGCTCCTAGAACTGATAAACGACTTCAGTAA 2180 chr1qtel1M 178277 AGTTGCAGGATACAAAATAAATACACATAAATCATCAGCATTTTTATACA 178326 v v ii v vi i -- L1P4_orf2#LIN 2181 AGTTTCAGGATACAAAATCAATGTACAAAAATCAGTAGCATTTCTATA-- 2228 chr1qtel1M 178327 TCACTAATAAAATTCAA-C--AGGGCGATGCAAAGA--GAAATTCCATTT 178371 - i vi - -- i v viiv -- v i L1P4_orf2#LIN 2229 -CACCAATAACGTTCAAGCTGAGAGCCAAATCAAGAACGCAATCCCATTT 2277 chr1qtel1M 178372 AAAGTAACCATTGATAGTATAAAATATTGGGGGAATCTGCCT-GCCAAGG 178420 v i i ivi v iv ii-vi viii -i L1P4_orf2#LIN 2278 ACAATAGCCACAAAAAAAATAAAATACC-TAGGAATACATCTAACCAAGG 2326 chr1qtel1M 178421 GAAAGT-CAGGAACTATATGAAAACAACTACAAAACATTTTCCACACAAA 178469 -- i -v i v v ii ii v i viiv v v L1P4_orf2#LIN 2327 --AGGTGAAAGATCTCTACAAGGAGAACTACAAAACACTGCTGAAAGAAA 2374 chr1qtel1M 178470 T-AAAGTCAGACCTAATCAGTTGGAAAAATATCGAGTGCTCATAGGTAGA 178518 - ? vi- vi v iv i ivvi i i v i L1P4_orf2#LIN 2375 TCANAGAT-GACACAAACAAATGGAAAAACATTCCATGCTCATGGATTGG 2423 chr1qtel1M 178519 CTAAGAA--AATATAATGAAAATG---ATACTACCCAAATTAATCT---- 178559 -- -- vi v --- i vi ---- L1P4_orf2#LIN 2424 --AAGAATCAATATCGTTAAAATGGCCATACTGCCCAAAGCAATCTACAG 2471 chr1qtel1M 178560 ATTTAGTAGCATATCAATCAAACTCCCAA-GAAATTATCTTACAGATCTA 178608 i iiivi vi v v - vv - i i vi L1P4_orf2#LIN 2472 ATTCAACGCTATTCCTATCAAACTACCAACGTCATT-TTTCACAGAATTA 2520 chr1qtel1M 178609 GAAAAAA------TAAGAATGTTCATCTGAAGGAACAAAAGA---TAAAA 178649 ------ i --- v i ivv v ---ii v L1P4_orf2#LIN 2521 GAAAAAACTATTCTAAAA---TTCATATGGAACCAAAAAAGAGCCCGAAT 2567 chr1qtel1M 178650 AATTTCAAAGGAAT--TAA-TGAAAAGAAAATGTCAATGAAGGTGGCCTA 178696 i--i v -- -ii ----- v vv v v v L1P4_orf2#LIN 2568 AG--CCAAAGCAATCCTAAGCAAAAAGAA-----CAAAGCCGGAGGCATC 2610 chr1qtel1M 178697 GCTTTACCAGACCTAAAACTATATTA 178722 i v v i v i L1P4_orf2#LIN 2611 ACATTACCCGACTTCAAACTATACTA 2636 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 35.85 CpG sites = 101, Kimura (unadjusted) = 37.98 Transitions / transversions = 1.23 (101/82) Gap_init rate = 0.05 (34 / 644), avg. gap size = 1.50 (51 / 34) 376 34.77 3.88 0.84 chr1qtel1M 178895 179126 (820874) C HERVP71A#LTR/ERV1 (4917) 2673 2435 m_b32s701i2 1118 chr1qtel1M 178895 TTTACTACCCTAAGGTCTAATATTAATCCACAAATCTCATATGATTTCTT 178944 ivi v i vii ii i i viv i vv ii C HERVP71A#LTR/ 2673 TTTATAGCCCTTAGATCTTGCACCAATCTATACGACCCATCAGGCTTCTT 2624 chr1qtel1M 178945 AAGGGGCAAAATAGGAATATTGAAAAGGGACATAACAAAGTTTTGAT--- 178991 i vv v i v i v vi v i- ii i i --- C HERVP71A#LTR/ 2623 GACTGGGAGAATTGGAGTATTGTATGGTGACATG-CAGGGTTCTAATAGT 2575 chr1qtel1M 178992 ----CTTTCAACAAATCCCTTTATTATTGATTATAATCTTATTTTTCTTC 179037 ---- - iv i ii i iv iv i v i i i i C HERVP71A#LTR/ 2574 CCATCTTT-AATCAATCCCTCTATTACCGGTTGGAGACCTTTTCTCCCTT 2526 chr1qtel1M 179038 CAGTGATAATAGGATATTGTTGAACAGACACCACATCT-CTGGATTTTCC 179086 i iv i vvviiv v i v - v v ii C HERVP71A#LTR/ 2525 CAATGGAAATGGGATATTGTTTTCTGCAAACTACTTCTCCTGGTTGTTTT 2476 chr1qtel1M 179087 AGGTTGATTT-TAAGCGGGGAATTTTTAAACCTCTCCTCTT 179126 v ii i - v v vi v i v C HERVP71A#LTR/ 2475 AGTTCAATCTGTAAGGGTGTGATTTTTAACCCTCCCCTGTT 2435 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 46.91 CpG sites = 47, Kimura (unadjusted) = 48.62 Transitions / transversions = 1.42 (47/33) Gap_init rate = 0.03 (6 / 231), avg. gap size = 1.83 (11 / 6) 12 27.80 3.85 0.00 chr1qtel1M 179718 179769 (820231) (ATAAT)n#Simple_repeat 1 54 (0) m_b32s252i12 1120 chr1qtel1M 179718 ATAACATGATAT-ATGTGAGATAACATATAATTATATAATTTAA-ATGTT 179765 i i - i i v i vv v v - iv (ATAAT)n#Simp 1 ATAATATAATATAATATAATATAATATAATATAATATAATATAATATAAT 50 chr1qtel1M 179766 ATAA 179769 (ATAAT)n#Simp 51 ATAA 54 Matrix = Unknown Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.00 (2 / 2) 371 21.03 1.18 4.88 chr1qtel1M 181647 181731 (818269) MIRb#SINE/MIR 2 83 (185) m_b32s601i8 1121 chr1qtel1M 181647 AAAGGGGCAGCTAGGTGGTGCAGTGGATAGAGCACCAGCCCTGAAGTCAG 181696 i --- v vi ii i MIRb#SINE/MIR 2 AGAGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAG 48 chr1qtel1M 181697 GAGGACCTGAATTCAAAT-TTGGCTTTAGACACTTA 181731 ivi ii i -ii i - v MIRb#SINE/MIR 49 ACAGACCTGGGTTCGAATCCCGGCTCT-GCCACTTA 83 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 22.32 CpG sites = 13, Kimura (unadjusted) = 25.73 Transitions / transversions = 3.25 (13/4) Gap_init rate = 0.06 (5 / 84), avg. gap size = 1.00 (5 / 5) 45 0.00 0.00 0.00 chr1qtel1M 183754 183794 (816206) (T)n#Simple_repeat 1 41 (0) c_b32s251i1 1122 chr1qtel1M 183754 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 183794 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 41 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 387 25.26 0.00 10.00 chr1qtel1M 183947 184056 (815944) MIRc#SINE/MIR 2 101 (167) m_b32s601i9 1123 chr1qtel1M 183947 GGGGCAGTTCAGTGGTATAGTGGATAGAACACCAGCCCTGAAGTCAGGAG 183996 i --- ii v i ii v i i i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr1qtel1M 183997 GACCCGAGTTCAAATCTGGCCTCAGATACTGAACATTTCCAGGCTGTGTG 184046 i i i i iv v --- i ---- i v vi MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTC---TGC----CACTTACTAGCTGTGTG 91 chr1qtel1M 184047 ACCCTGAGCA 184056 i i MIRc#SINE/MIR 92 ACCTTGGGCA 101 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.60 CpG sites = 19, Kimura (unadjusted) = 32.19 Transitions / transversions = 3.17 (19/6) Gap_init rate = 0.09 (10 / 109), avg. gap size = 1.00 (10 / 10) 340 17.16 7.00 0.94 chr1qtel1M 184164 184263 (815737) C EutTc1-N1#DNA/TcMar-Tc1 (41) 547 442 m_b32s502i2 1124 chr1qtel1M 184164 AACTTCAGAAGTACAAATGCTACAAACTTACCTAAAA----ATAGGAAGA 184209 i i vv ---- vv ii C EutTc1-N1#DNA 547 AACCTCAGAAGTATAAATGCTACAAACTTACAAAAAACGACATTTGAAAG 498 chr1qtel1M 184210 GATAATGACTTGAATTT---AAACATTCAGGTGCTGTTTATTTAAAATTC 184256 ??? v i i --- i ? v ?i i vi - C EutTc1-N1#DNA 497 NNNAATTATTTAAATTTTTAAAATANTGANATGTTTCTTA-TTAAAATTC 449 chr1qtel1M 184257 AACATAA 184263 C EutTc1-N1#DNA 448 AACATAA 442 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 20.96 CpG sites = 10, Kimura (unadjusted) = 20.96 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.03 (3 / 99), avg. gap size = 2.67 (8 / 3) 263 30.09 2.59 2.59 chr1qtel1M 184307 184422 (815578) L2-1_AMi#LINE/L2 495 610 (625) m_b32s551i13 1125 chr1qtel1M 184307 AACATGTCC-GAAATAAAACCTATGATCTTTCCCCCCTAAACCTT-TCCC 184354 v -i i i i iiv i i -- i ?- L2-1_AMi#LINE 495 AACATGGCCTAAAACAGAGCTCTTAATCTTCCCCCC--AAGCCTNCTCCC 542 chr1qtel1M 184355 TCTCCTGCCTTCCCAATCACTGTGAAGGACA-CACGCATCTTCCCAGTCG 184403 iv i ivii i i i vi - - i v v i L2-1_AMi#LINE 543 CATTCCCTTTTCTCGATCACTGTGGACAACACCAC-CATCCTGCCTGTCA 591 chr1qtel1M 184404 CTCAGGTTCCCAATTTAGG 184422 ii vi ii i L2-1_AMi#LINE 592 CTCAGGCCCGTAACCTGGG 610 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 40.52 CpG sites = 26, Kimura (unadjusted) = 42.22 Transitions / transversions = 3.25 (26/8) Gap_init rate = 0.05 (6 / 115), avg. gap size = 1.00 (6 / 6) 222 36.85 12.63 2.10 chr1qtel1M 184616 185003 (814997) L2#LINE/L2 2655 3082 (0) m_b32s601i10 1126 chr1qtel1M 184616 CCCCTTCTCTTCTTTTTCATCTTCCCCATCTTTGGGCACTGCC-TCATCA 184664 v vi vii i iivi v i i v vv v- -i L2#LINE/L2 2655 CCACTTCTCACCACCTCCACTGCCACCACCCTGGTCCAA-GCCACCATCA 2703 chr1qtel1M 184665 ATTCATATCTGGACTATGGTAAT----------CTGG-----CTGCTTTG 184699 vi viii i iv i ---------- ----- iv L2#LINE/L2 2704 TCTCTCGCCTGGATTACTGCAATAGCCTCCTAACTGGTCTCCCTGCTTCC 2753 chr1qtel1M 184700 --TTTTTCCCCATTCCACTCCATCCTTTATTCAGCTACCCAAGTGATCTT 184747 --ii v vi ? v i i iv iv vi vi i L2#LINE/L2 2754 ACCCTTGCCCCCCTNCAGTCTATTCTCAACACAGCAGCCAGAGTGATCCT 2803 chr1qtel1M 184748 CCTGAAGTGGAGAGCTGATCATATCAC---------CA----CTTCCTGT 184784 ii i ii v iiv v i --------- ---- i vi L2#LINE/L2 2804 TTTAAAACGTAAGTCAGATCATGTCACTCCTCTGCTCAAAACCCTCCAAT 2853 chr1qtel1M 184785 GGTTCCTTATTGCTCCCAGGAGCAAATTCAAAATGACTTGTT-TGGCTTT 184833 i i ii iv v i iivv vi i v- iiv- i - L2#LINE/L2 2854 GGCTTCCCATCTCACTCAGAGTAAAAGCCAAAGTC-CTTACAATGGCCT- 2901 chr1qtel1M 184834 TAGAGAAATCT-CAAAACCTGCCCCCTCCTAATTTTCCAG---TAATGCC 184879 - v iiivi - vi i vi i v v ii ii v --- v vi L2#LINE/L2 2902 -ACAAGGCCCTACATGATCTGGTCCCCCGTTACCTCTCTGACCTCATCTC 2950 chr1qtel1M 184880 TTAA-ACCCTGAC--TCGTACCCTTTGATCCAG------TGATCTCACCT 184920 i v- i vv -- iv v ii v ------ ii -- L2#LINE/L2 2951 CTACCACTCTCCCCCTCGCTCACTCCGCTCCAGCCACACTGGCCTC--CT 2998 chr1qtel1M 184921 GGCTGTTCCATGAACACAACCTTCCATG-TCTTGTCTCTGGGCCTTCTC- 184968 v vi i- vvv i - ii i v iv - L2#LINE/L2 2999 TGCTGTTCCTCGAACACG-CCAGGCACGCTCCCGCCTCAGGGCCTTTGCA 3047 chr1qtel1M 184969 --TGCCTTATCCTCTATGCCTGGAATATTCTTCCTTC 185003 -- -- i i i v iii ii L2#LINE/L2 3048 CTTGC--TGTTCCCTCTGCCTGGAACGCTCTTCCCCC 3082 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 49.32 CpG sites = 86, Kimura (unadjusted) = 53.96 Transitions / transversions = 1.59 (86/54) Gap_init rate = 0.06 (24 / 387), avg. gap size = 2.42 (58 / 24) 295 32.53 11.76 1.23 chr1qtel1M 184853 185073 (814927) L2d_3end#LINE/L2 13 256 (260) m_b32s601i11 1126 chr1qtel1M 184853 GCCCCCTCCTAATTTTCCAGTAATGCCT-----TAAACCCTGACTCGTAC 184897 vi vi ? ivv ii ----- vv iii v v L2d_3end#LINE 13 GCCCCACCCTACCTNTCCAGCCTTATCTCCCACTACTCCCCAGCACGAAC 62 chr1qtel1M 184898 CCTTTGATCCAGT--GATC--TCACCTGGCTGTTCCATGAACACAACCTT 184943 ii v -- ii -- v i vi i vi iv i v L2d_3end#LINE 63 CCTCCGCTCCAGTCAGGCCGGTCTCTTCACTGTCCCCCGAACACGCCTTG 112 chr1qtel1M 184944 C-CATGTCTTGTCTCTGGGCCTT--CTC-TGCCTTATCCTCTATGCCTGG 184989 - - ii i v -- -i v - i i-i L2d_3end#LINE 113 CGCAT-TCCCGCCTCTGCGCCTTTGCTCACGCCGT-TCCCCC-CGCCTGG 159 chr1qtel1M 184990 AATATTCTTCCTTCTCGTCTCTGTTT------------CCCGG-CTTCCA 185026 iii iii v v i ------------ iv- v L2d_3end#LINE 160 AATGCCCTTCCCCTTCCTCTCTCTCTATCCAAATCCTACCCATCCTTCAA 209 chr1qtel1M 185027 GTTCCAATTCAAATCCTGCCTTATACAGGAAGTCTTTCCCAATTCCT 185073 vi ii i ii iv v v i i ii iiv L2d_3end#LINE 210 GGCCCAGCTCAAGTCCCACCTCCTCCACGAAGCCTTCCCTGACCACT 256 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 40.16 CpG sites = 46, Kimura (unadjusted) = 45.28 Transitions / transversions = 1.84 (46/25) Gap_init rate = 0.05 (11 / 220), avg. gap size = 2.64 (29 / 11) 322 34.79 17.75 1.21 chr1qtel1M 184891 185245 (814755) L2b_3end#LINE/L2 53 465 (1) m_b32s601i12 1126 chr1qtel1M 184891 CTCGTACCCTTTGATCCAG------TGATCTCACCTGGCTGTTCCATGAA 184934 i iv v i v ------ ii -- v vi L2b_3end#LINE 53 CTTGCTCACTCTGCTCCAGCCACACTGGCCTC--CTTGCTGTTCCTCGAA 100 chr1qtel1M 184935 CACAACCTTCCATGTCTTGTCTCTGGGCCTTC---TCTGCCTTATCCTCT 184981 iv v?v iv?v ii i v i---i? -- i i i L2b_3end#LINE 101 CACGCCANGCTCNCTCCCGCCTCAGGGCCTTTGCACNTGC--TGTTCCCT 148 chr1qtel1M 184982 ATGCCTGGAATATTCTTCC-----TTCTCGTCT------CTGTTTCCCGG 185020 v iiii ----- ii i ------ vi v i iv L2b_3end#LINE 149 CTGCCTGGAACGCCCTTCCCCACCTCTTCGCCTGGCCAACTCCTACTCAT 198 chr1qtel1M 185021 CTTCCAGTTC-CAATTCAAATCCTGCCTTATACAGGAAGTCTTTCCCAAT 185069 i i v - ii viii iv v i i i i ii i L2b_3end#LINE 199 CCTTCAGGTCTCAGCTCAAATGTCACCTCCTCCGGGAAGCCCTCCCTGAC 248 chr1qtel1M 185070 TCCTT--------TTTAATG--TTTCACTTAA--TTCCTAAT--GATCCT 185105 i ii-------- iviii --i i v vii--ii i i --v i L2b_3end#LINE 249 CCCCCAGGCCGGGTCAGGCGCCCTCCTCTGGGCCCCCCCAGTCCTACCCT 298 chr1qtel1M 185106 GCACATATTTGTTTG-CATT-CCTG-TTAGAT---TGTGTTCCCTGTTAG 185149 - ivi v v i-? -i - v --- v i iii L2b_3end#LINE 299 GC-CACTCTGGGTTATNATTGTCTGNTTACATGTCTGTCTCCCCCACTAG 347 chr1qtel1M 185150 ATTGTGAGCTCC-------------CCCTGTCTGTTTT---------TGA 185177 i ------------- v? i --------- v L2b_3end#LINE 348 ACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTGT 397 chr1qtel1M 185178 ATTTCCAGCATTTGACACAGTCCTTGACAAATAATAGGCTCTTTAAAAAT 185227 ii iii ii ?v i i v i i v iviv L2b_3end#LINE 398 ATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAAT 447 chr1qtel1M 185228 GTTTACTGGCTAATTGAA 185245 i ii iv i v L2b_3end#LINE 448 ATTTGTTGAATGAATGAA 465 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 47.62 CpG sites = 85, Kimura (unadjusted) = 52.09 Transitions / transversions = 2.30 (85/37) Gap_init rate = 0.06 (20 / 354), avg. gap size = 3.40 (68 / 20) 18 7.56 0.00 0.00 chr1qtel1M 190157 190184 (809816) (CCCAG)n#Simple_repeat 1 28 (0) m_b33s252i0 1127 chr1qtel1M 190157 CCCAGCCCTGCCCAGCCCTGCCCAGCCC 190184 v v (CCCAG)n#Simp 1 CCCAGCCCAGCCCAGCCCAGCCCAGCCC 28 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 248 20.47 7.14 1.12 chr1qtel1M 191119 191202 (808798) C MER63D#DNA/hAT-Tip100 (602) 459 371 m_b33s502i0 1128 chr1qtel1M 191119 TTAGGTTTAATCTGCCTAATTAACATGTTCTCCACC----TCTACTGTC- 191163 i v v v i ---- vvv - C MER63D#DNA/hA 459 TTAAGTTTAATCTGCATTATTAACATTTTCTCCATCACTTTCTTAAGTCT 410 chr1qtel1M 191164 AG-CAGTCAGGGAAACAGTAAAACAAAGTCCTCCTTTGTA 191202 - i ivi i v - i vv C MER63D#DNA/hA 409 AGACAATCAACAAAACAATAAATC-AAGCCCTGATTTGTA 371 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 23.96 CpG sites = 7, Kimura (unadjusted) = 23.96 Transitions / transversions = 0.70 (7/10) Gap_init rate = 0.05 (4 / 83), avg. gap size = 1.75 (7 / 4) 393 29.81 3.66 1.80 chr1qtel1M 191764 191927 (808073) C L1HS_3end#LINE/L1 (600) 302 136 m_b33s551i0 1129 chr1qtel1M 191764 AGTTCACAACTGCACCAACAATGTATTAGTGTCCCAGTTTCCCTACATCC 191813 i iiiv i vv i vi i ii C L1HS_3end#LIN 302 AGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCGCATCC 253 chr1qtel1M 191814 CCTCCAATGTATATGATGTTTTCCTGTCATCTTGGTGAATG------TGA 191857 i -- i iv v - v v i ii v ------ i C L1HS_3end#LIN 252 TCTCCA--GCACCTGTTG-TTTCCTGACTTTTTAATGATTGCCATTCTAA 206 chr1qtel1M 191858 GAGGTGTGAAATGAAACCACCGAGTTGTCTCAATTTATTTTTCTCTAATG 191907 vv i v i v vv v i ii iiv i C L1HS_3end#LIN 205 CTGGTGTGAGATGATATCTCATAGTGGTTTTGATTTGCATTTCTCTGATG 156 chr1qtel1M 191908 AATAGTGATTTAGAGCATTT 191927 ivi vvv C L1HS_3end#LIN 155 GCCAGTGATGATGAGCATTT 136 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 37.76 CpG sites = 27, Kimura (unadjusted) = 38.91 Transitions / transversions = 1.29 (27/21) Gap_init rate = 0.02 (4 / 163), avg. gap size = 2.25 (9 / 4) 18 13.75 2.38 2.38 chr1qtel1M 193984 194025 (805975) (AAGAA)n#Simple_repeat 1 42 (0) m_b33s252i1 1130 chr1qtel1M 193984 AAGAAAA-AAAGAAAAAGAAAAGAAATACAAAACAAAAGAGAA 194025 - ii - v v i (AAGAA)n#Simp 1 AAGAAAAGAAAAGAAAAGAAAAGAAA-AGAAAAGAAAAGAAAA 42 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.05 (2 / 41), avg. gap size = 1.00 (2 / 2) 343 22.19 11.82 1.65 chr1qtel1M 196206 196315 (803685) C HERV30#LTR/ERV1 (2669) 5588 5468 m_b33s701i0 1131 chr1qtel1M 196206 TACAAGGGAAGGCTTTTTCCCAGTTAGTAAAGGTGTTGACAAAGACCAA- 196254 iiv i v i ii v - C HERV30#LTR/ER 5588 TACAAGGGAAGGCTTCCACCCAATTTGTAAAGGTATCAACACAGACCAAT 5539 chr1qtel1M 196255 AAGTCGTTTGAAGCCC---------CAGCATGT--GTAGGATCCATCTGC 196293 v-- ii ---------ii i -- ii i v C HERV30#LTR/ER 5538 AAGTA--TTGAAATCCTCTTGACTTTGGCATATGGGTAAAATCTAACTGC 5491 chr1qtel1M 196294 CGGTCCTCCCTTGGGT-ATGTCC 196315 i i iv i - C HERV30#LTR/ER 5490 CAGTCCTCTCCGGGATAATGTCC 5468 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 26.22 CpG sites = 18, Kimura (unadjusted) = 27.57 Transitions / transversions = 3.00 (18/6) Gap_init rate = 0.06 (6 / 109), avg. gap size = 2.50 (15 / 6) 13 11.53 3.23 3.23 chr1qtel1M 197510 197540 (802460) (GGAA)n#Simple_repeat 1 31 (0) m_b33s252i2 1132 chr1qtel1M 197510 GGAAGGAAGGAAGG-GGGAAGAAAGAGAAAGA 197540 -i i - i (GGAA)n#Simpl 1 GGAAGGAAGGAAGGAAGGAAGGAAG-GAAGGA 31 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2) 218 24.25 26.85 0.74 chr1qtel1M 197746 197853 (802147) C MIRb#SINE/MIR (51) 217 82 m_b33s601i2 1133 chr1qtel1M 197746 TAAGCACTTT---TGCAGT----CATGTGATCTTCACAACAGTC------ 197782 i --- v ---- v i i ii ------ C MIRb#SINE/MIR 217 TAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGA 168 chr1qtel1M 197783 -------ATTATTAGTGCTC--TCTACACATCAGAAAATTG-GGC----- 197817 ------- - v i -- i v v i i - ----- C MIRb#SINE/MIR 167 GGTAGGTATTATTA-TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGA 119 chr1qtel1M 197818 -AGATAAAATAATTTGCCAAAAATCATGTAGCTGATA 197853 - i v i i v ii iii ii C MIRb#SINE/MIR 118 GAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTA 82 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 29.36 CpG sites = 19, Kimura (unadjusted) = 30.79 Transitions / transversions = 2.71 (19/7) Gap_init rate = 0.07 (8 / 107), avg. gap size = 3.75 (30 / 8) 20 9.40 3.92 6.00 chr1qtel1M 198757 198807 (801193) (CACAGA)n#Simple_repeat 1 50 (0) m_b33s252i3 1134 chr1qtel1M 198757 CACAGA-ACAAACA-TGACACAGACATTCTGCACAGAGACACAGACACAG 198804 - i -v -- v - v (CACAGA)n#Sim 1 CACAGACACAGACACAGACACAGACA--CAG-ACACAGACACAGACACAG 47 chr1qtel1M 198805 ACA 198807 (CACAGA)n#Sim 48 ACA 50 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.10 (5 / 50), avg. gap size = 1.00 (5 / 5) 237 31.99 4.85 5.38 chr1qtel1M 200066 200663 (799337) C L1PREC2_orf2#LINE/L1 (652) 2642 2048 m_b33s551i1 1135 chr1qtel1M 200066 GCCTTACAATACAGTTTGAGGTATGGAAGTGTTATTTCCCC--CTTTGTT 200113 i ii i i i vv v i v vi i -- C L1PREC2_orf2# 2642 GCCCTGTAGTATAGTTTGAAGTCGGGTAGCGTGATGCCTCCAGCTTTGTT 2593 chr1qtel1M 200114 CCTACTTCTTTTCATCATTTCCCTTGATCAT---GGATCTTTT---GTTC 200157 i vi v --- vv v - iii --- v --- C L1PREC2_orf2# 2592 CTTTTTGCTT---AGGATTGCC-TTGGCTATTCGGGCTCTTTTTTGGTTC 2547 chr1qtel1M 200158 CAAATAAACTTTAT--TA--TTTTTATGATTTCCTACAAAGTATTCTTTT 200203 v i i v-- -- v ii -- iii v viiv C L1PREC2_orf2# 2546 CATATGAATTTTAAAATAGTTTTTTCTAGTT--CTGTGAAGAATGTCATT 2499 chr1qtel1M 200204 GATAATTTGGTTAATATAGCATTAAAAGTGTAAATTAACTTAG-TGGCAT 200252 i i i viiv i vv ivi i -ii i C L1PREC2_orf2# 2498 GGTAGTTTGATAGGAATAGCATTGAATCTGTAAATTGCTTTGGGCAGTAT 2449 chr1qtel1M 200253 TGTCATTTTTATTATATTGGCACAGCCTAACTCATGAGTTATGAGCCACT 200302 v i v iv iiv vv v - i- ------- C L1PREC2_orf2# 2448 GGCCATTTTAACGATATTGATTCTTCCTATC-CATGAGC-ATG------- 2408 chr1qtel1M 200303 GAATATTCCTTCAAGTTTTTGGGTTGTTCTTTGGTTT-TTTAAGC---TC 200348 i ii i vv v v ii - i i - i ---vi C L1PREC2_orf2# 2407 GAATGTTTTTCCATTTGTTTGTGTCAT-CTCTGATTTCTTTGAGCAGTGT 2359 chr1qtel1M 200349 TTTGTG--TTTGATTATACA-ATGTTTTGCATGCTTTGGTAGAATG-ATT 200394 i-- i v i v - v ii v - ii viiv - C L1PREC2_orf2# 2358 TTTGTAATTCTCATTGTAGAGATCTTTCACCT-CCCTGGTTAGCTGTATT 2310 chr1qtel1M 200395 CACCAGATTTTTTCTATGCATTTCATAGTTATTTGGTATTAGATTTCCCT 200444 - i i v -- v v ii i iv vv v vi v v- C L1PREC2_orf2# 2309 C-CTAGGTATTTT--ATTCTTTTTGTGGCAATTGTGAATGGGATTGCG-T 2264 chr1qtel1M 200445 TTCTATTATTGCTTCTCATGTTTTATTATTATTAGAATATAGGAAGGCTT 200494 i iv - vi i- i vii i i i vi v v C L1PREC2_orf2# 2263 TCCTGAT-TTGGCTCTCG-GCTTGGCTGTTGTTGGTGTATAGGAATGCTA 2216 chr1qtel1M 200495 TTGATTTCTAAGAATTTATTTTGTAGCCTGAAGCTTTGTTAAAGTTGTTA 200544 v i iviv v v i i i v C L1PREC2_orf2# 2215 GTGATTTTTGTACATTGATTTTGTATCCTGAAACTTTGCTGAAGTTGTTT 2166 chr1qtel1M 200545 GTTTCTTCAGTTAA--TATCTTT---GCTGATTCCCTGGGGTTTTTCCAA 200589 i ----- i ? --v v --- i vv iv - i i C L1PREC2_orf2# 2165 AT-----CAGCTNAAGGAGCTTTTGGGCCGAGACTATGGGG-TTTTCTAG 2122 chr1qtel1M 200590 GT---GAACCTTTATATTATCAGCAATTAAGAGTTTTTTTCCCTCCTCTT 200636 i --- --- i i ii v vi i ii vv vv i i C L1PREC2_orf2# 2121 ATATAGAA---TCATGTCGTCTGCAAACAGGGATAGTTTGACTTCCTCTC 2075 chr1qtel1M 200637 TACCAGTTTTAATGCCTCTAATTTCTT 200663 v vi vi ii v C L1PREC2_orf2# 2074 TTCCTATTTGGATGCCCTTTATTTCTT 2048 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 41.44 CpG sites = 104, Kimura (unadjusted) = 43.06 Transitions / transversions = 1.35 (104/77) Gap_init rate = 0.08 (46 / 597), avg. gap size = 1.33 (61 / 46) 17 11.68 5.41 0.00 chr1qtel1M 200725 200761 (799239) (TTTTA)n#Simple_repeat 1 39 (0) m_b33s252i4 1136 chr1qtel1M 200725 TTTTATTTTATTCT-TTTTA-AAAATTTTATTTTATTTT 200761 i - -vvv (TTTTA)n#Simp 1 TTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTT 39 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 195 30.12 3.49 3.49 chr1qtel1M 201016 201101 (798899) C L2d_3end#LINE/L2 (47) 469 384 m_b33s601i3 1137 chr1qtel1M 201016 AGCACTGTACTCAGGGAGT-TGGGCTGCCAAGAGAAAGCCCAAAACA--G 201062 i - viv - vvi v ?i i ? ivi i -- C L2d_3end#LINE 469 AGCACTGTGCT-AGGCGCTGTGGGGAACGANAAAANAGTATAAGACATGG 421 chr1qtel1M 201063 TCCCTGCTTTTAGGGAGTTCACATCCCAAGGTGGGAGAG 201101 ii i i i i vi i -- v i C L2d_3end#LINE 420 TCCCTGCCCTCAAGGAGCTTACAATCTA--GTTGGGGAG 384 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 39.79 CpG sites = 17, Kimura (unadjusted) = 42.05 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.06 (5 / 85), avg. gap size = 1.20 (6 / 5) 292 36.91 16.67 0.66 chr1qtel1M 204350 204739 (795261) C L2#LINE/L2 (78) 3004 2553 m_b33s601i4 1137 chr1qtel1M 204350 ATAGCCAGCAGACACATGTCACAGAATTGGAAAGAATGTGTGGGGAGAAA 204399 i v v i vvi vi v i vi iv ii v - iv C L2#LINE/L2 3004 ACAGCAAGGAGGCCAGTGTGGCTGGAGCGGAGTGAGCGAG-GGGGAGAGT 2956 chr1qtel1M 204400 GGT-GTAAA--AAATCTGGAAGGGAAGGAGGGG-------ATGAAAAGCT 204439 - v i -- ii v ii v v i i------- v ii i C L2#LINE/L2 2955 GGTAGGAGATGAGGTCAGAGAGGTAACGGGGGACCAGATCATGTAGGGCC 2906 chr1qtel1M 204440 TTGAATACCA--GACAGAATATTTTGTGTTTGTTCTGGAGGCAATGGAGA 204487 v vi -- vv i i- v iv ii iiv vi ii C L2#LINE/L2 2905 TTGTAGGCCATTGTAAGGAC-TTTGGCTTTTACTCTGAGTGAGATGGGAA 2857 chr1qtel1M 204488 GCCCCCCCCAAAATT------AAGGAAGTGACATGGTCAGCCTTTTGTTT 204531 viivv- iii ------ ii i i v v vi C L2#LINE/L2 2856 GCCATTGG-AGGGTTTTGAGCAGAGGAGTGACATGATCTGACTTACGTTT 2808 chr1qtel1M 204532 TAGGAAAATTA--------------------ATGGAGTAGAGAAATGCTT 204561 ii ii i -------------------- i v i? iiiv vv C L2#LINE/L2 2807 TAAAAGGATCACTCTGGCTGCTGTGTTGAGAATAGACTGNAGGGGGGCAA 2758 chr1qtel1M 204562 GGG-AAAGGCAGAG---CTAATT-GCAGGCCGTGGCAGTAATCTAGGGGT 204606 -ii i i --- i i - v ii v i v v C L2#LINE/L2 2757 GGGTGGAAGCAGGGAGACCAGTTAGGAGGCTATTGCAGTAATCCAGGCGA 2708 chr1qtel1M 204607 GA----ATGAGGGCCTGTGCCAAGGTGG--GTAGCAGAGTCAGAGAGAAG 204650 ---- iv i vi i -- i ii vii v C L2#LINE/L2 2707 GAGATGATGGTGGCTTGGACCAGGGTGGTGGCAGTGGAGGTGGTGAGAAG 2658 chr1qtel1M 204651 T------ACTTTGGAGATGCTGCCAAGGGGAAATCAGCTGGCCTTGGTAG 204694 ------ i i v ii viv vii ii ii v vi v ii C L2#LINE/L2 2657 TGGTCGGATTCTGGATATATTTTGAAGGTAGAGCCGACAGGATTTGCTGA 2608 chr1qtel1M 204695 CAAATTGG----------TGAGAGATACAGAGAAATCTAGGGTAACTACT 204734 iii ---------- v v i i v i i v v C L2#LINE/L2 2607 TGGATTGGATGTGGGGTGTGAGAGAAAGAGAGGAGTCAAGGATGACTCCA 2558 chr1qtel1M 204735 AGGTT 204739 C L2#LINE/L2 2557 AGGTT 2553 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 52.00 CpG sites = 90, Kimura (unadjusted) = 54.30 Transitions / transversions = 1.70 (90/53) Gap_init rate = 0.04 (16 / 389), avg. gap size = 4.25 (68 / 16) 235 25.42 12.38 2.61 chr1qtel1M 205155 205259 (794741) C MIR1_Amn#SINE/MIR (113) 117 3 m_b33s601i5 1138 chr1qtel1M 205155 GGGGTTAAGTGACTT-CTCTGGGTCACATAGTAAGTGTCAAGTGTCCAAG 205203 i ? - i vi ?i i?i --- ? v vi C MIR1_Amn#SINE 117 GAGGTNAAGTGACTTGCCCAAGGTCACNCAGCNGG---CNAGTGGCAGAG 71 chr1qtel1M 205204 GCAAGATTTGA----AGGAAT----ATTCTTGG----GTGCTTTATCTAC 205241 v ii ? ? ---- vv ---- v iii ---- i i C MIR1_Amn#SINE 70 CCGGGANTNGAACCCAGGTCTCCCGAGTCCCAGTCCAGTGCTCTATCCAC 21 chr1qtel1M 205242 TATACCACCCAGCTACCC 205259 v v v iv C MIR1_Amn#SINE 20 TAGACCACACTGCCTCCC 3 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 32.75 CpG sites = 15, Kimura (unadjusted) = 34.36 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.07 (7 / 104), avg. gap size = 2.29 (16 / 7) 234 32.46 18.47 3.73 chr1qtel1M 206901 207252 (792748) L2c_3end#LINE/L2 69 470 (8) m_b33s601i6 1139 chr1qtel1M 206901 TCCAGCCAAGCTGGATTCTTTATCGTCCCCCTA----GCTAACATTCTGT 206946 vi i i ?i i- i i v ---- iivvi -- L2c_3end#LINE 69 TCCAGCCACACTGAACTNCTTG-CATTCCCCAAACACGCCGCAGTTC--T 115 chr1qtel1M 206947 CTCCCATTTCCATAGATTTGTGCA-------CCCTCT------AATGAT- 206982 i iiii i?ivv ii ------- ------ v - L2c_3end#LINE 116 TTCCTGCCTCCGNGCCTTTGCACATGCTGTTCCCTCTGCCTGGAATGCTC 165 chr1qtel1M 206983 TTCCCTCCTCACTGCCCCT-CTTAGTATCCCTACCTGCCTTT---GGCTT 207028 i vi v v -vi -- ii iiii i --- ? i L2c_3end#LINE 166 TTCCCCCCTCCTTCCACCTGGCTA--ACTCCTACTCATCCTTCAAGNCTC 213 chr1qtel1M 207029 GGTTCAAGTGTCATCTTACACCAGAACCATTTCCTGATTTCCACAGTTAT 207078 i i ii i iviv vi v v i iii vv --?i L2c_3end#LINE 214 AGCTCAGATGTCACCTCCTCCGGGAAGCCTTCCCTGACCCCCCAAG--NC 261 chr1qtel1M 207079 TAGTCCC--TGCCCTCCCCAAGAAATTTATTGTGTACTTTGTCCATATTT 207126 iv-- i vivivviii --v i ii i i i L2c_3end#LINE 262 TAGTCTAGGTGCCCTCCTCTGTGCTCCCAT--AGCACCCTGTCTATACTC 309 chr1qtel1M 207127 ------TAG-ACTTAT--TTAGCACATAGTGT-------TGTTT------ 207154 ------ - -- i vii v ------- ------ L2c_3end#LINE 310 CCATTATAGCACTTATCATTAACTTGTATTGTAATTGTCTGTTTACNTGT 359 chr1qtel1M 207155 --------TCCAGTAG-CAGGAAGCTCTTGCAAGGCAGGAATC--ATCTA 207193 -------- v - v vi i vv i i i --i v L2c_3end#LINE 360 CTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTT 409 chr1qtel1M 207194 A---ATCTTCAGGG-CCTAGCAAGTTGCTTGGAAGATAGAAAGTG----A 207235 --- iiviv- i ----- i v v v i i ---- L2c_3end#LINE 410 ATTCATCTTTGTATCCCCAGC-----GCCTGGCACATAGTAGGCGCTCAA 454 chr1qtel1M 207236 TAAATGTTGGATTGAAT 207252 v - L2c_3end#LINE 455 TAAATGTTTG-TTGAAT 470 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 44.20 CpG sites = 72, Kimura (unadjusted) = 46.02 Transitions / transversions = 1.89 (72/38) Gap_init rate = 0.09 (32 / 351), avg. gap size = 2.50 (80 / 32) 218 27.91 30.26 1.02 chr1qtel1M 207323 207474 (792526) C L3#LINE/CR1 (86) 4013 3818 m_b33s601i7 1140 chr1qtel1M 207323 ACATC---AACAAGTGGTCATCCCATTTCCACTTA---ACCTATAAGGAG 207366 ---i viii ii i--- vi iv - C L3#LINE/CR1 4013 ACATCCCTGACAAGTGGTCATCCAGCCTCTGCTTGAACACCTCCAGTGA- 3965 chr1qtel1M 207367 TTGGGGACCTGGCC-CCTGTCGTGAC-GTTCATTCCACTTT--------- 207405 -i v vi i- v? v i - ii i --------- C L3#LINE/CR1 3964 -CGGGGAGCTCACTACCTCNCGAGGCAGCCCATTCCATTTTTGGACAGCT 3916 chr1qtel1M 207406 -------TTAGCAAGTTTTTTCTGACATCAA--------CT--------- 207431 ------- v i i v i ii -------- --------- C L3#LINE/CR1 3915 CTGATTGTTAGAAAGTTCTTCCTTATATTGAGCCGAAATCTGCCTCCCTG 3866 chr1qtel1M 207432 ----TTCCATCTATGACTCCTGGTTCTA-TCTCTGAGGTCAAACAGAA 207474 ---- i i viv i i-i ii i v C L3#LINE/CR1 3865 TAACTTCCACCCATTGGTCCTAGTTCTGCCCTCTGGAGCCACACAGAA 3818 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 36.24 CpG sites = 30, Kimura (unadjusted) = 37.40 Transitions / transversions = 2.50 (30/12) Gap_init rate = 0.07 (10 / 151), avg. gap size = 4.80 (48 / 10) 262 32.96 1.84 5.06 chr1qtel1M 207481 207643 (792357) C CR1-3_Croc#LINE/CR1 (813) 2792 2635 m_b33s551i2 1141 chr1qtel1M 207481 TCTTTCCTCCACATGATAGCTCTTCAAGTACGTGAAGACCCCTCTCATAC 207530 ii i ivi ii i iv iv v i- C CR1-3_Croc#LI 2792 TCCCTCTTCTTTATGGCAGCCCTTCAAGTATTTGAAGACTGCTATCATG- 2744 chr1qtel1M 207531 CTCCCCCTTCCCTCTCAGTCTTCTCTTCTCCAAACCAA--ATACCCACTC 207578 ------- i i iv vi i iv i ii -- i i vii C CR1-3_Croc#LI 2743 -------TCCCCTCTTAAGCGCCTTTTCCGCAAGCTGAACATGCCTAGCT 2701 chr1qtel1M 207579 CCTTCAGCTAATCTTCCTAGGACATGGACTCT-AGCCTTTTATCATCCAG 207627 ivv i v v v vvi i- i ivv C CR1-3_Croc#LI 2700 CCTTCAGCCTCTCCTCGTATGACTTGCCTTCCAAGCCCTTTATCATCTTT 2651 chr1qtel1M 207628 ACTGTCCTCCTCTGGA 207643 ii i v C CR1-3_Croc#LI 2650 GTTGCCCGCCTCTGGA 2635 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 44.39 CpG sites = 33, Kimura (unadjusted) = 45.64 Transitions / transversions = 1.83 (33/18) Gap_init rate = 0.06 (10 / 162), avg. gap size = 1.10 (11 / 10) 288 29.63 1.23 0.00 chr1qtel1M 207656 207736 (792264) C L3#LINE/CR1 (1304) 2795 2714 m_b33s601i8 1142 chr1qtel1M 207656 TATTCTAGTCCAGAATTTCCCCAGGAATCAAAGTCAAGCCCTCTGGCCTA 207705 v iiv i iv i i i v iiv i i i C L3#LINE/CR1 2795 TAATCCGTTCTAGAATTTTGCCGGGGATCGACGTCAAGCTTACCGGTCTG 2746 chr1qtel1M 207706 TAGTTTGTGGATTCTGT-TTTCTTCCCTTATT 207736 ?ii v ii - i v C L3#LINE/CR1 2745 TAGTTTNCAGAATCCATCTTTTTTCCCTTTTT 2714 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 32.05 CpG sites = 17, Kimura (unadjusted) = 40.73 Transitions / transversions = 2.43 (17/7) Gap_init rate = 0.01 (1 / 80), avg. gap size = 1.00 (1 / 1) 238 36.62 0.00 0.00 chr1qtel1M 207752 207822 (792178) C L3#LINE/CR1 (495) 3604 3534 m_b33s601i9 1140 chr1qtel1M 207752 CTAAACTTGCTACTCCAGATGTGGGCCGATTAAGGCAGAGCACAGTGGAG 207801 i viiv v i ii iv i i ii C L3#LINE/CR1 3604 CTGAACGCAATACTCCAGATGTGGTCTGACCAGCGCAGAGTACAGCGGGA 3555 chr1qtel1M 207802 CGGGCATTTCTCCCATTCCGG 207822 vivi ii i iii? i C L3#LINE/CR1 3554 CTATTACCTCCCTTGNTCTGG 3534 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 54.61 CpG sites = 20, Kimura (unadjusted) = 58.22 Transitions / transversions = 3.33 (20/6) Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0) 387 34.24 7.37 5.58 chr1qtel1M 207918 208446 (791554) C Plat_L3#LINE/CR1 (707) 2866 2329 m_b33s551i3 1143 chr1qtel1M 207918 CCTAACTTGTACTTGTGAAGTTACTTTTTTAGTATCCAAGTGAAAGATTT 207967 i v i i vi vv i- vi i v vv ii C Plat_L3#LINE/ 2866 CCCATCCTGTATTTGTGCGGTTTGTTTTTC-GTCCCTAAGTGCACTACCT 2818 chr1qtel1M 207968 TATAGTGATCTCTATTGAATTTGATC-----TTAGTAGATTGTCTAGTGC 208012 ii v vi i v ----- v ? --- v i v vi C Plat_L3#LINE/ 2817 TGCACTTGTCCCTATTGAATTTCATCCTGTTTTTGNAG---GACCATTTT 2771 chr1qtel1M 208013 TCTAGCCTGCCAGGCTAGATCTTTTGGAATCTTGACTCTCTCGTCCACTG 208062 i iii i ?---- i vi v i ivii v v vv C Plat_L3#LINE/ 2770 TCCAATTTGTCN----AGGTCACTTTGAATTTTATTCCTGTCTTCCAAAG 2725 chr1qtel1M 208063 TATCATACTAAGTATCCCTCCCAACTCGGGATCATTAACAAAC------- 208105 i -- vi ---i v i ii v ivi i------- C Plat_L3#LINE/ 2724 TGT--TAGCAA---CCCCGCCCAATTTAGTATCATCTGCAAATTTGATGA 2680 chr1qtel1M 208106 -CATCTT-----TGCCTTCATTCACATCATTGATCAACATATTAAATAGC 208149 - vi ----- v i i vi i v v i v C Plat_L3#LINE/ 2679 GCATGCTCTCGATTCCTTCGTCCAGGTCATCGATAAAGATATTGAATAGA 2630 chr1qtel1M 208150 ACAGGGCCAAGCATGGATCCTTACGGCACTCCATACGAGACCTCCTCTCA 208199 v v v v iv i ii v v iv v i? iii C Plat_L3#LINE/ 2629 ACCGGTCCCAGGACCGATCCCTGTGGGACACCACTCGATATNTCCCTCCA 2580 chr1qtel1M 208200 TACTAACACCAAACCACCGCCAACCACTC---AAGT----CCATCCGACC 208242 vii i i i ii vii i i ---ii ---- v vii C Plat_L3#LINE/ 2579 GGTTGACACCGAGCCATTGATGACTACCCTTTGGGTGCGACCCTCGAGCC 2530 chr1qtel1M 208243 AGCTCTTAACCTGTGTGATTGTATTACCGTGTGATGAATATC-T-CTCTG 208290 v vv iiiv i iv ----- i i v v i - - i v C Plat_L3#LINE/ 2529 AGCTGTGCACCCACCTAACGGTA-----GTATGGTCAAGACCATACTTTC 2485 chr1qtel1M 208291 TAAGCTTC---ATAAGAAC-TTAC-TGGAATCTTTTATCAAAAGCCTTGC 208335 iv v--- i i i- i i- i ivvv-- i C Plat_L3#LINE/ 2484 CCAGCTTGTCGATGAGGATGTCATGTGGGACGGA--ATCAAAAGCCTTAC 2437 chr1qtel1M 208336 TGAAATCTAATTGAACTCTATCCACAGCATCCTCCTGCTCTAC-TAGTTT 208384 i iv ii i vi i iv v i vv - i --- C Plat_L3#LINE/ 2436 TGAAGTCTAGATAGATTACATCTATTGCTTCCCCCTTGTCTACGTGG--- 2390 chr1qtel1M 208385 ATTCTGTCTCTTTCCCCTGTCAGAAAAGGGAATT------GTCTGGCACG 208428 --i v ----- i v i i ------ C Plat_L3#LINE/ 2389 --CCTGTCACT-----CTATCATAGAAGGAAATTAAATTNGTCTGGCACG 2347 chr1qtel1M 208429 ATGCATTCTTGATGGAGC 208446 viii v iii C Plat_L3#LINE/ 2346 ATTTGCTCTTCACAAAGC 2329 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 45.45 CpG sites = 103, Kimura (unadjusted) = 48.21 Transitions / transversions = 1.51 (103/68) Gap_init rate = 0.08 (43 / 528), avg. gap size = 1.60 (69 / 43) 284 29.53 9.94 5.36 chr1qtel1M 208320 208480 (791520) C CR1-3_Croc#LINE/CR1 (1642) 1963 1796 m_b33s551i4 1143 chr1qtel1M 208320 TTATCAAAAGCCTTGCTGAAATCTAATTGAACTCTATCCACAGCATCCTC 208369 i i i iv iv v i i C CR1-3_Croc#LI 1963 TTGTCAAAAGCCTTGCTGAAGTCCAGATACACTATATCCACAGCATTCCC 1914 chr1qtel1M 208370 CTGCTCTACTAGTTTATTCTGTCTCTTTCCCCTGTCAGAAAAGGGAA--- 208416 i vv i ivivv ---- iv ----- i i ii --- C CR1-3_Croc#LI 1913 TTCATCCACCCAAGTA----GTTACTT-----TGTCAAAGAAGGAGATCA 1873 chr1qtel1M 208417 ---TTGTCTGGCACGATGCATTCTTGATGGA---------GCTCTTGGTG 208454 --- i i vii i vi ii --------- vi v C CR1-3_Croc#LI 1872 AGTTTGTTTGACACGATTTGTTTTTCGTAAATCCATGCTGGCTGCTTGTG 1823 chr1qtel1M 208455 ATCA-CTATTCACTTTCTAGATGCTTG 208480 - iv viii i C CR1-3_Croc#LI 1822 ATCAGCCTTTCCTCCTCCAGATGCTTG 1796 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 38.34 CpG sites = 30, Kimura (unadjusted) = 39.50 Transitions / transversions = 2.00 (30/15) Gap_init rate = 0.08 (13 / 160), avg. gap size = 1.92 (25 / 13) 348 34.75 4.26 0.51 chr1qtel1M 211060 211247 (788753) C L1ME4c_3end#LINE/L1 (294) 536 342 m_b33s551i5 1144 chr1qtel1M 211060 ATATGCCATAATTTATTCAGCCATT--GATGCCAGTGGGCATCCACTCAG 211107 i i i i i --vv iiiiv i ii vviv C L1ME4c_3end#L 536 ATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAGGTTG 487 chr1qtel1M 211108 TTTCTAGTTTTCTTGCCACTACAAGGAGGGCTGTCACAAACATTTTTGCA 211157 i i - i i i i iv iv iv ii i i ii C L1ME4c_3end#L 486 TTTCCAATTTT-TCGCTATTATAAATAACGCTGCAATGAACATCTTCGTG 438 chr1qtel1M 211158 CATCTGG--GTCCCTTTCTTTTAAG--ATCTCTTTGGGATATAATCCCAG 211203 v i --v ii i i i-- i i i v v C L1ME4c_3end#L 437 CATATAGCTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAATTCCCAG 388 chr1qtel1M 211204 TAGAAACATTGTTGGATCAAAAGTTATG--CAGTTTGATAACTTTT 211247 v viiv ii i i v -- v v ii i C L1ME4c_3end#L 387 AAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTCTT 342 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 48.38 CpG sites = 46, Kimura (unadjusted) = 50.70 Transitions / transversions = 2.42 (46/19) Gap_init rate = 0.03 (5 / 187), avg. gap size = 1.80 (9 / 5) 13 4.76 0.00 4.35 chr1qtel1M 211341 211364 (788636) (CCCT)n#Simple_repeat 1 23 (0) m_b33s252i5 1145 chr1qtel1M 211341 CCCTCCCTCCCTCCACCCCCTCCC 211364 - i (CCCT)n#Simpl 1 CCCTCCCTCCCTCC-CTCCCTCCC 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 855 29.48 10.14 2.21 chr1qtel1M 211750 212252 (787748) C L1ME5_3end#LINE/L1 (396) 545 4 m_b33s551i6 1146 chr1qtel1M 211750 TCCATAACATTCATATACCACACTTTACCCAACCATTCTCCAATTGATAG 211799 iiii v vi i i v i v v i C L1ME5_3end#LI 545 TCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCAGTGATGG 496 chr1qtel1M 211800 GCATCCATTCGTT--TTCCAGTTTCTAGTCACTACAAACAGGGCCGCCAC 211847 i i v-- --i ii i iv i i iv i v i C L1ME5_3end#LI 495 ACACCCAG--GTTGCCTCCAACTCCCCGCCACCACAAACAACGCTGCAAT 448 chr1qtel1M 211848 AAACATTTTGGCACATACAGGTCCCTTTC----CCTTCTTTACAATCTCT 211893 i ii ---- i v i v---- viv v v i C L1ME5_3end#LI 447 GAACATCCT----CGTACATGTCCCCTTATGGACCTGTGTGAGAATTTCT 402 chr1qtel1M 211894 TTGGGGTATAAGCCCAATAGTAACACTGCTGGATCAAAGG------GTAC 211937 i vi iv iiiv i i v ------ i C L1ME5_3end#LI 401 TTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATGCGTAT 352 chr1qtel1M 211938 GCACAGTTTGA-TAA--------------CTTTC-----TGG--GCATAA 211965 i vi i - -------------- i ----- -- iv C L1ME5_3end#LI 351 ACTTAATTTGACTAAGTACTGCCAGATTGCTCTCCAGAATGGCTGCACCA 302 chr1qtel1M 211966 TTCCAGATTGCTCTCCAG-AATGGTTG--GATTCGT------TCACAACT 212006 v i v i - i v - i vv -- i v ------i v i C L1ME5_3end#LI 301 GTCTACACT-CCCACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATCC 253 chr1qtel1M 212007 CCACCAACAAT--GCAT----CAGTGTCCCAGTCATTTTAGCCAATCTGA 212050 i i v -- ---- iv i i --- v i i C L1ME5_3end#LI 252 TCGCCAACACTTGGCATTATCCAGCTTTCTA---ATTTTTGCCAGTCTAA 206 chr1qtel1M 212051 CAGGTGTATAGTGGTATCTCAGAATTATCTTAATTTGCATTTCTCTGATC 212100 i v i vvi i i i C L1ME5_3end#LI 205 TAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATTTCTCTGATT 156 chr1qtel1M 212101 AATGGTGATTTGGAACACTCTTTCATATGAGTGGAAATAGTTTCAATTTC 212150 v ii v v i iiii vv vv iivv ivii C L1ME5_3end#LI 155 ACTAATGAGTTTGAGCATCTCTTCATATGCTTGTTAGCCTTTCGGGTTTC 106 chr1qtel1M 212151 ATCATCTGAAAATTGTCTGTTCATATCCTTTGACCATTTATTAATTGGAG 212200 v v v i v v iv i C L1ME5_3end#LI 105 CTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGGGG 56 chr1qtel1M 212201 --AATGGCTTGATTTCTTATAAATTAGAGTCAATTCTCTATATATTTTGG 212248 --?vi v -- i vi v vivv i ii i i i C L1ME5_3end#LI 55 TTNCCGTCTT--TTTCTTGTTGATTTGCAGGAGTTCCTTGTATATTCTAG 8 chr1qtel1M 212249 AAAT 212252 v C L1ME5_3end#LI 7 ATAT 4 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 37.07 CpG sites = 87, Kimura (unadjusted) = 38.83 Transitions / transversions = 1.50 (87/58) Gap_init rate = 0.05 (25 / 502), avg. gap size = 2.52 (63 / 25) 312 30.35 1.63 3.31 chr1qtel1M 212103 212286 (787714) C L1P3_orf2#LINE/L1 (0) 3294 3114 m_b33s551i7 1146 chr1qtel1M 212103 TGGTGATTTGGAACACTCTTTCATATGAGTGGAAATAGTTTCAATTTCAT 212152 i --- i vi i vv vviiiv iv v v v C L1P3_orf2#LIN 3294 TGATGAT---GAGCTTTTTTTCATATGTTTGTTGGCCGCATAAATGTCTT 3248 chr1qtel1M 212153 CATCTGAAAATTGTCTGTTCATATCCTTTGACCATTTATTAATTGGAGAA 212202 v i i v i v i v i v ---i C L1P3_orf2#LIN 3247 CTTTTGAGAAGTGTCTGTTCATATCCTTCGCCCACTTTTTGATGGG---G 3201 chr1qtel1M 212203 TGGCTTG---ATTTCTTATAAATTAGAGTCAATTCTCTATATATTTTGGA 212249 v i ---v i v vv v i ii i v i C L1P3_orf2#LIN 3200 TTGTTTGTTTTTTTCTTGTAAATTTGTTTAAGTTCCTTGTAGATTCTGGA 3151 chr1qtel1M 212250 AATGAGGCCTTTATCAGAATCTTTGACTGTAAAAATT 212286 v v v i vvvv v i i C L1P3_orf2#LIN 3150 TATTAGCCCTTTGTCAGATGGATAGATTGCAAAAATT 3114 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 38.22 CpG sites = 24, Kimura (unadjusted) = 39.11 Transitions / transversions = 0.80 (24/30) Gap_init rate = 0.04 (7 / 183), avg. gap size = 1.29 (9 / 7) 319 26.09 2.13 2.13 chr1qtel1M 212146 212286 (787714) C L1PREC2_orf2#LINE/L1 (40) 3254 3114 m_b33s551i8 1146 chr1qtel1M 212146 ATTTCATCATCTGAAAATTGTCTGTTCATATCCTTTGACCATTTATTAAT 212195 v v v i v i v i v C L1PREC2_orf2# 3254 ATGTCTTCTTTTGAAAAGTGTCTGTTCATGTCCTTTGCCCACTTTTTAAT 3205 chr1qtel1M 212196 TGGAGAATGGCTTG---ATTTCTTATAAATTAGAGTCAATTCTCTATATA 212242 v ---i v i ---v i v vv v i ii v C L1PREC2_orf2# 3204 GGG---GTTGTTTGTTTTTTTCTTGTAAATTTGTTTAAGTTCCTTATAGA 3158 chr1qtel1M 212243 TTTTGGAAATGAGGCCTTTATCAGAATCTTTGACTGTAAAAATT 212286 vi v v i i vv v v vi i ? C L1PREC2_orf2# 3157 TGCTGGATATTAGACCTTTGTCAGATGCATAGTTTGCAAANATT 3114 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 32.39 CpG sites = 14, Kimura (unadjusted) = 32.39 Transitions / transversions = 0.64 (14/22) Gap_init rate = 0.03 (4 / 140), avg. gap size = 1.50 (6 / 4) 194 33.32 5.83 0.93 chr1qtel1M 212622 212724 (787276) C L2a_3end#LINE/L2 (60) 457 350 m_b33s601i10 1147 chr1qtel1M 212622 GCTGAATATACAAAAA--GATGAAAAAGACAA---TTCCTGTCTTTGGGA 212666 iiv iv i--i ii v --- i i i iiv i C L2a_3end#LINE 457 GCTGGGGATACAGCAGTGAACAAAACAGACAAAAGTCCCTGCCCTCATGG 408 chr1qtel1M 212667 CAGCTTACTATCTAA-GAGGGAAGGCAGCGAGCAAACACATCTATATGGA 212715 - vv i- i i i vv ii v vv v v C L2a_3end#LINE 407 -AGCTTACATTCTAGTGGGGGGAGACAGACAATAAACAAATAAATAAGTA 359 chr1qtel1M 212716 CAATATACA 212724 v i C L2a_3end#LINE 358 AAATATATA 350 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 45.71 CpG sites = 20, Kimura (unadjusted) = 45.71 Transitions / transversions = 1.43 (20/14) Gap_init rate = 0.04 (4 / 102), avg. gap size = 1.75 (7 / 4) 188 35.62 6.69 3.99 chr1qtel1M 212730 212998 (787002) C L2a_3end#LINE/L2 (217) 300 25 m_b33s601i11 1147 chr1qtel1M 212730 GAAAATAGGAGACAATTAAGAGAGAAGGCA-ATAATATTAAG-AAGGTGG 212777 iii - vvi? ii i ? i ii-ii? v i- i C L2a_3end#LINE 300 GGGGATAGG-GAGTGNTGGGGGNGAGGGTGTGCNATTTTAAATAGGGTGG 252 chr1qtel1M 212778 -CA---AATGCTTC-CTGTAGAATATGGGATTCTATTTGGGACTTGACTT 212822 - --- v i - - vi i-----i i vvvv i C L2a_3end#LINE 251 TCAGGGAAGGCCTCNCTG-AGAAGGTGA-----CATTTGAGCAAAGACCT 208 chr1qtel1M 212823 AAAGGAAGTCAGGG--CAATCAGTAGGCAGAGCTAAAAAGGGAGAATTCC 212870 i i v -- i v vi iv v v v iiiiiii vi C L2a_3end#LINE 207 GAAGGAGGTGAGGGAGCGAGCCATGCGGATATCTGGGGGAAGAGCGTTCC 158 chr1qtel1M 212871 AAATCTCAGGA-TGGCCAGAGAAAATGTCTGCACATGGA---GTGTCT-- 212914 iiivvvi -ii v v v v i ivv vii i--- i -- C L2a_3end#LINE 157 AGGCAGAGGGAACAGCAAGTGCAAAGGCCCTGAGGCGGGAGCGTGCCTGG 108 chr1qtel1M 212915 --TGTTTGGGGAACAACCAGTGAGCCCTATGACTGGACTGAAGAGGATGG 212962 -- i i i v - v vi -- - i v vv C L2a_3end#LINE 107 CGTGTTCGAGGAACAGCAAG-GAGGCCAGTG--TGG-CTGGAGCGGAGTG 62 chr1qtel1M 212963 GGTGAGGAGCAGAGTGGGAGGGGAC-AGGTCAGGAAG 212998 i i i v v i i- ii C L2a_3end#LINE 61 AGCGAGGGGGAGAGTGGTAGGAGATGAGGTCAGAGAG 25 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 47.84 CpG sites = 57, Kimura (unadjusted) = 51.91 Transitions / transversions = 1.63 (57/35) Gap_init rate = 0.08 (22 / 268), avg. gap size = 1.32 (29 / 22) 195 25.93 1.12 4.65 chr1qtel1M 212910 212998 (787002) C L2#LINE/L2 (63) 3019 2934 m_b33s601i12 1147 chr1qtel1M 212910 TGTCTTGTTTGGGGAACAACCAGTGAGCCCTATGACTGGACTGAAGAGGA 212959 v v i i i v - v vi -- - i v C L2#LINE/L2 3019 TGGCGTGTTCGAGGAACAGCAAG-GAGGCCAGTG--TGG-CTGGAGCGGA 2974 chr1qtel1M 212960 TGGGGTGAGGAGCAGAGTGGGAGGGGAC-AGGTCAGGAAG 212998 vv i i i v v i i- ii C L2#LINE/L2 2973 GTGAGCGAGGGGGAGAGTGGTAGGAGATGAGGTCAGAGAG 2934 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 28.84 CpG sites = 12, Kimura (unadjusted) = 32.25 Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.06 (5 / 88), avg. gap size = 1.00 (5 / 5) 687 31.76 6.85 2.63 chr1qtel1M 213003 213513 (786487) L2#LINE/L2 1483 2014 (1068) m_b33s601i13 1148 chr1qtel1M 213003 CTGAC-ACCTTGCCTCATATTTTA-TAGGAAAAAAATGACATTAACAAGA 213050 i- i v i - ii v ivii v v v L2#LINE/L2 1483 CTGATGACCTTGCTTCCTATTTCACTGAGAAAATAGAAGCAATCAGAAGA 1532 chr1qtel1M 213051 G---TTCTCTATTCTCCCTGCTTCCTCATGT---CATCTAAATGC-TTTG 213093 --- ivi ?? -i iv v v --- i vv - i L2#LINE/L2 1533 GAACTTCCACANNCTCCC-ACCACCACATCTACCCACCTACCTGCATCTG 1581 chr1qtel1M 213094 GGC-----TACTATGGCATCCTTCACCCTTATCTCACATGAAGAGATGGT 213138 v ----- v v v i - iv iiv iv v--- vi L2#LINE/L2 1582 TGCCCACATACTCTGCCTTCCCTC-CTGTTACTACGGATGAAC---TGTC 1627 chr1qtel1M 213139 CTTATTCCTTAGCCA-GGCCAACTCCTCCATCTGTACAGGTGATCTCATT 213187 v ii - v i - i ii i vvv i i L2#LINE/L2 1628 CGTGCTCCT-ATCTAAGGCCAACCCCTCCACTTGTGCACTAGATCCCATC 1676 chr1qtel1M 213188 GATCCATCCCGTTTCTTCTAACAAATTTATCCC-CTGTCCTCCCCAATCT 213236 --- v i ii vi v iv v ivv v- vi i vv L2#LINE/L2 1677 ---CCCTCTCGCCTACTCAAGGACATCGCTCCAGCAATTCTCCCCTCTCT 1723 chr1qtel1M 213237 CTCTT--ATTTTTCATCTTTCCCTTTCT------TCATTTTCTGCTTCCT 213278 i -- iv iv i i ------ ii vv vv v L2#LINE/L2 1724 CTCCTGCATCATCAATTTTTCCCTCTCTACTGGATCATTCCCATCAGCAT 1773 chr1qtel1M 213279 ACAAACATGCCCATGTTTCCCTAATCCTC------CAATACTCTTCCCTT 213322 ivv?i i iv i i------ v v ii L2#LINE/L2 1774 ACAAACATGCTGTNATTTCTCCCATCTTTAAAAAACAAAAATTCTCCCTT 1823 chr1qtel1M 213323 TATCC---TTCCATCCCCA-CTAACACCCTATATCTCCTCTGTACTTTGC 213368 v i ---? vi i - v i i v iv viv i L2#LINE/L2 1824 GACCCCACNTCCCCCTCCAGCTACCGCCCCATTTCTCTGCTCCCCTTTAC 1873 chr1qtel1M 213369 AACTAAACTTCTCCAAAGGGCCTGTCTACAAGAGGTGCCTCCACTTTCTC 213418 i v i v i i- i vvv v i v i L2#LINE/L2 1874 AGCAAAACTCCTCGAAAGAGT-TGTCTATACTCGCTGTCTCCAATTCCTC 1922 chr1qtel1M 213419 TCCTTTCATTCTCTTCTTAATCCCTTATAATCTGGCTTCTGACCTCATGG 213468 ii ii v i vi vi v ii v i ivi L2#LINE/L2 1923 TCCTCCCATTCTCTCTTGAACCCACTCCAATCAGGCTTTCGTCCCCACCA 1972 chr1qtel1M 213469 GTCCATCCAAAATACTCTGAATTGTTTA-GTCACCAGTGAGCCCCA 213513 v i v v i ---- iv - i v i L2#LINE/L2 1973 CTCCACCGAAACTGCTC----TTGTCAAGGTCACCAATGACCTCCA 2014 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 41.26 CpG sites = 84, Kimura (unadjusted) = 42.68 Transitions / transversions = 1.14 (84/74) Gap_init rate = 0.05 (28 / 510), avg. gap size = 1.75 (49 / 28) 189 30.00 21.11 0.00 chr1qtel1M 213882 213971 (786029) C MIRb#SINE/MIR (116) 152 44 m_b33s601i14 1149 chr1qtel1M 213882 CCCCACTCTATAGATGAGGAGCCTAAAGCGCA-AGA-------------- 213916 i i i iv i i v - -------------- C MIRb#SINE/MIR 152 CCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTG 103 chr1qtel1M 213917 ---AAGACTGCGCAGCTAGTCAGGGTGAGAGCCAAGACT-GACCCTCGGG 213962 --- iiii i v v vv ii i - v iv v C MIRb#SINE/MIR 102 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGT 53 chr1qtel1M 213963 TTTTCTAAC 213971 i v i C MIRb#SINE/MIR 52 CTGTCTGAC 44 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 37.92 CpG sites = 17, Kimura (unadjusted) = 39.84 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.04 (4 / 89), avg. gap size = 4.75 (19 / 4) 20 13.35 0.00 4.65 chr1qtel1M 214440 214484 (785516) (GGGGC)n#Simple_repeat 1 43 (0) m_b33s252i6 1150 chr1qtel1M 214440 GGGGCGGGGCGGGGCCACACGGGGGCGGGGCGGGGGCGGGGCAGG 214484 vivi - - i (GGGGC)n#Simp 1 GGGGCGGGGCGGGGCGGGGC-GGGGCGGGGC-GGGGCGGGGCGGG 43 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.05 (2 / 44), avg. gap size = 1.00 (2 / 2) 183 25.45 9.09 0.00 chr1qtel1M 215492 215546 (784454) C MIRc#SINE/MIR (113) 155 96 m_b33s601i15 1151 chr1qtel1M 215492 TGTTGTCCCC-TTTTAAAGGTGGAGAAACCGAGGCTCCCAGGGAT----G 215536 i i - v i ii i vv i i ----v C MIRc#SINE/MIR 155 TATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGT 106 chr1qtel1M 215537 GGCCTGCCCA 215546 i i C MIRc#SINE/MIR 105 GACTTGCCCA 96 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 32.60 CpG sites = 10, Kimura (unadjusted) = 32.60 Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.04 (2 / 54), avg. gap size = 2.50 (5 / 2) 188 32.37 5.66 0.90 chr1qtel1M 216269 216374 (783626) C MIR#SINE/MIR (36) 226 116 m_b33s601i16 1152 chr1qtel1M 216269 CCAGGAGCTGCTCCATTCTTCTTA---GTCCTGACCTCATTGAATG-TCC 216314 vi i i vv vii --- vi i - v v- v C MIR#SINE/MIR 226 CCAGGCACTGTTCTAAGCGCTTTACATGTATTAAC-TCATTTAATCCTCA 178 chr1qtel1M 216315 CATCCACCCCATGATGTCAGTGCTCCTGGTGACGTTCTCT--CTGATGAG 216362 v v i v vi i vi iv iv viiv i -- v C MIR#SINE/MIR 177 CAACAACCCTATGAGGTAGGTACTATTATTATCCCCATTTTACAGATGAG 128 chr1qtel1M 216363 GAAACTGAGGCA 216374 C MIR#SINE/MIR 127 GAAACTGAGGCA 116 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 42.83 CpG sites = 16, Kimura (unadjusted) = 42.83 Transitions / transversions = 0.89 (16/18) Gap_init rate = 0.04 (4 / 105), avg. gap size = 1.75 (7 / 4) 16 5.27 0.00 0.00 chr1qtel1M 216975 216994 (783006) (T)n#Simple_repeat 1 20 (0) m_b33s252i7 1153 chr1qtel1M 216975 TTTTTTTTTTTTTCTTTTTT 216994 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTT 20 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 12 18.86 2.63 2.63 chr1qtel1M 218403 218440 (781560) (TTATGTT)n#Simple_repeat 1 38 (0) m_b33s252i8 1154 chr1qtel1M 218403 TTATG-TTTCTGTTTTAAGTTTTGTGTGTGATTTTATTA 218440 - v v i v v v - (TTATGTT)n#Si 1 TTATGTTTTATGTTTTATGTTTTATGTTTTATGTT-TTA 38 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 554 21.74 0.00 8.00 chr1qtel1M 222539 222673 (777327) MIRb#SINE/MIR 6 130 (138) m_b33s601i17 1155 chr1qtel1M 222539 GGGCAGCTAGGTGGTACAGTGGATAGAGCACCAGCTCTGAAGTCAGGAGG 222588 --- i v vi i i ivi MIRb#SINE/MIR 6 GGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAG 52 chr1qtel1M 222589 ACCTGAGTTCAAATGTGGCCTCAGACACTTAACACTTCCTAGCTGTGTGA 222638 i i viv v v v ------- MIRb#SINE/MIR 53 ACCTGGGTTCGAATCCCGGCTCTGCCACTTA-------CTAGCTGTGTGA 95 chr1qtel1M 222639 CTCTGGGCAAGTCATTTAACCCCCAGTTGCCTCAG 222673 ii i i i ivvvv MIRb#SINE/MIR 96 CCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAG 130 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 24.73 CpG sites = 15, Kimura (unadjusted) = 25.80 Transitions / transversions = 1.25 (15/12) Gap_init rate = 0.07 (10 / 134), avg. gap size = 1.00 (10 / 10) 372 27.17 5.33 8.54 chr1qtel1M 222549 222717 (777283) MIR3#SINE/MIR 9 172 (36) m_b33s601i18 1155 chr1qtel1M 222549 GTGGTACAGTGGATAGAGCACCAGCTCTGAAGTCAGGAGGACCTGAGTTC 222598 ivv ii v vii v- i - i MIR3#SINE/MIR 9 GTGGCTGAGCAGAGAGAGCACGGACTG-GGAGTCAGGAG-ACCTGGGTTC 56 chr1qtel1M 222599 AAATGTGGCCTCAGACACTTAACACTTCCTAGCTGTGTGACTCTGGGCAA 222648 v i viv v v v - ------ ? ii MIR3#SINE/MIR 57 TAGTCCCGGCTCTGCCACT-AAC------TNGCTGTGTGACCTTGGGCAA 99 chr1qtel1M 222649 GTCATTTAAC---------CCCCAGTTGCCTCAGCAAAAAGCAAAAAAAG 222689 i v --------- i v v ----v i vi MIR3#SINE/MIR 100 GTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATC----TGTAAAATGAG 145 chr1qtel1M 222690 GAAATGAGTGTGGGAGAGTCTTTAAGGT 222717 iii vi vv i iv - i MIR3#SINE/MIR 146 GGGGTTGGACTAGATGA-TCTCTAAGGT 172 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 34.38 CpG sites = 22, Kimura (unadjusted) = 34.38 Transitions / transversions = 1.10 (22/20) Gap_init rate = 0.09 (15 / 168), avg. gap size = 1.53 (23 / 15) 245 28.38 4.05 0.00 chr1qtel1M 223142 223215 (776785) C MIR#SINE/MIR (142) 120 44 m_b34s601i2 1156 chr1qtel1M 223142 AAGCAAACAG-GGTTAAGTGACTTACTCCAGATCTCACA--TGGTGAGTG 223188 i v v - i i i v i v -- i i C MIR#SINE/MIR 120 AGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTG 71 chr1qtel1M 223189 ACTGAGGCCAGATTTTAACTCGGGAAG 223215 i v v vi iv i i v C MIR#SINE/MIR 70 GCAGAGCCGGGATTCGAACCCAGGCAG 44 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.34 CpG sites = 12, Kimura (unadjusted) = 36.49 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.03 (2 / 73), avg. gap size = 1.50 (3 / 2) 16 0.00 0.00 0.00 chr1qtel1M 224420 224437 (775563) (T)n#Simple_repeat 1 18 (0) m_b34s252i0 1157 chr1qtel1M 224420 TTTTTTTTTTTTTTTTTT 224437 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTT 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 254 26.44 3.33 3.33 chr1qtel1M 225313 225402 (774598) C L2c_3end#LINE/L2 (23) 455 366 m_b34s601i3 1158 chr1qtel1M 225313 ATTGAGCGCCATTTATGGGCCAGGCCCCGTG--TTGAGGGATGGGCTACA 225360 vvi v v i v -- vv ii i--- i C L2c_3end#LINE 455 ATTGAGCGCCTACTATGTGCCAGGCGCTGGGGATACAAAGATGA---ATA 409 chr1qtel1M 225361 AGTAACAGACCCTATCCTCAAGGAGTTTCCAGTCTGG-GGAGG 225402 vv i v ii i iv i - C L2c_3end#LINE 408 AGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAGTGGAGG 366 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.32 CpG sites = 12, Kimura (unadjusted) = 33.02 Transitions / transversions = 1.09 (12/11) Gap_init rate = 0.06 (5 / 89), avg. gap size = 1.20 (6 / 5) 360 30.39 9.38 4.37 chr1qtel1M 226622 227058 (772942) L1ME4c_3end#LINE/L1 31 488 (342) m_b34s551i0 1159 chr1qtel1M 226622 CAAATTTATGAAAATGAGAGCCATTCTCCAATTGATAAATGGTCAAAATA 226671 v i i vi ? v v vv i v v iv L1ME4c_3end#L 31 CAAATTGATAAGAAAAANATCAAGACCCCAATAGATAAATGGGCAAAGGA 80 chr1qtel1M 226672 TATGATCAGTCAGTTATCAGAAGA-----TAT----------CAAAGCTT 226706 i v v i vv ? ----- i---------- ---i L1ME4c_3end#L 81 CATGAACAGACAATTCACANAAGAGGAAATACAANTAGTAAACAAA---C 127 chr1qtel1M 226707 TCATGAAAAAATGCTCTTAAA--TCACTAATTATTAGAGAAA----AATT 226750 v i i --- -- i i v i i ---- L1ME4c_3end#L 128 ACATGGAAAAATGTTC---AACCTCGCTAGTAATCAAAGAAATGCAAATT 174 chr1qtel1M 226751 AAA--AATT-TTCGGTAACACTTCAAAACTATCAAATTGGCTAACACAAT 226797 -- iv- vv i v i i viv i i v --- L1ME4c_3end#L 175 AAAGCAACAATGAGATACCATTTTACGCCTATTAAATTAGCAAA---AAT 221 chr1qtel1M 226798 GGAAAAGG--GA-AATGACAAATGCTGGAGGAAATATGGTGAAAAATAGG 226844 vv ii-- - iv v v iii? ii -- iv L1ME4c_3end#L 222 TTAAAAAATTGATAATACCCAATGCTGGCGAGGNTGCGGTG--AAACTGG 269 chr1qtel1M 226845 TGGACTTAT-TATGCATGTTGGTGGAATTGTCAACTGATCCAACAC-TTT 226892 iv? i -i --- i v ? v i i v v - L1ME4c_3end#L 270 TACNCTCATACAT---TGCTGGTGGCANTGTAAATTGGTACAACCCTTTT 316 chr1qtel1M 226893 GGAGAATAAATTGGAACTATGTCCAAAGGGCTATAAAATTA--CATATTC 226940 i ii v v v i viv i i v i-- ii L1ME4c_3end#L 317 GGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAAAATGTTCATACCC 366 chr1qtel1M 226941 ATTGATATTGGACCATCATTTCTAG---TTTATAACCCTTAAAAGACCAA 226987 v iviv v vivi i i --- ---- i iii vi L1ME4c_3end#L 367 TTTGACCCAGTAATTCCACTTCTGGGAATTTAT----CCTAAGGAAATAA 412 chr1qtel1M 226988 TATAAAAGGAG-----ATCTTTATATATAAAACAAATTATATTGGCTCAT 227032 vi i ----- v v ii ii i- vi -i vvv i L1ME4c_3end#L 413 TTCAAAAGAAGGAAAAAGCTATATGCACGAAG-ATGTT-CATTGCAGCGT 460 chr1qtel1M 227033 --TTTATGGTGGCAAGGAATTGGAAACA 227058 -- ii i i ii L1ME4c_3end#L 461 TATTTATAATAGCGAAAAATTGGAAACA 488 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.95 CpG sites = 74, Kimura (unadjusted) = 40.89 Transitions / transversions = 1.40 (74/53) Gap_init rate = 0.08 (34 / 436), avg. gap size = 1.79 (61 / 34) 398 27.89 10.34 3.56 chr1qtel1M 226649 226938 (773062) L1MB8_3end#LINE/L1 58 366 (559) m_b34s551i1 1159 chr1qtel1M 226649 CCAATTGATAAATGGTCAAAATATATGATCAGTCAGTTATC---AGAAGA 226695 ? v v iv v vi v v v --- L1MB8_3end#LI 58 CCAATTNAAAAATGGGCAAAGGATCTGAATAGACATTTCTCCAAAGAAGA 107 chr1qtel1M 226696 TAT-CAAA--GCT------TTCATGAAAAAATGCTCTTAA-ATCACTAAT 226735 - -- i------iv i -- - i i L1MB8_3end#LI 108 TATACAAATGGCCAATAAGCACATGAAAAGATGCTC--AACATCATTAGT 155 chr1qtel1M 226736 TATTAGAGAA----AAATTAAAAAT---TTTCGGTAACACTTCAAAACTA 226778 i i i ---- i vi---v vv i v v v i L1MB8_3end#LI 156 CATCAGGGAAATGCAAATCAAAACCACAATGAGATACCACTTCACACCCA 205 chr1qtel1M 226779 TCAAATTGGCTAACACAATGGAAAAGGGA---AATGACAAATGCTGGAGG 226825 ii iiv --- i vi iv --- i i i v i L1MB8_3end#LI 206 CTAGGATGGCT---ATAATCAAAAAGACAGATAATAACAAGTGTTGGCGA 252 chr1qtel1M 226826 AAATATGGTGAAAAATAGGTGGACTTATTATGCA-TGTTGGTGGAATTGT 226874 ii i -- i --- viiv i i - i i v L1MB8_3end#LI 253 GGATGTG--GAGAAAT---TGGAACCCTCATACACTGCTGGTGGGAATGT 297 chr1qtel1M 226875 CAACTGATCCAA-CACTTTGGAGAATAAATTGGAACTATGTCCAAAGGGC 226923 v v i v i- i i i ivi v v - vii i i L1MB8_3end#LI 298 AAAATGGTGCAGCCGCTTTGGAAAACAGTCTGGCAGT-TCCTCAAAAGGT 346 chr1qtel1M 226924 T----ATAAAATTA-CATAT 226938 ---- i i - L1MB8_3end#LI 347 TAAACATAGAGTTACCATAT 366 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 35.68 CpG sites = 48, Kimura (unadjusted) = 36.27 Transitions / transversions = 1.60 (48/30) Gap_init rate = 0.08 (23 / 289), avg. gap size = 1.78 (41 / 23) 431 28.24 8.53 2.56 chr1qtel1M 226649 226906 (773094) L1MB4_3end#LINE/L1 58 330 (597) m_b34s551i2 1159 chr1qtel1M 226649 CCAATTGATAAATGGTCAAAATATATGATCAGTCAGTTATC---AGAAGA 226695 ? v v iv iv vi v v v --- L1MB4_3end#LI 58 CCAATTNAAAAATGGGCAAAGGACTTGAATAGACATTTCTCCAAAGAAGA 107 chr1qtel1M 226696 TAT-CAAA--GCT------TTCATGAAAAAATGCTCTTAA-ATCACTAAT 226735 - -- i------iv i -- - i L1MB4_3end#LI 108 TATACAAATGGCCAATAAGCACATGAAAAGATGCTC--AACATCACTAGT 155 chr1qtel1M 226736 TATTAGAGAA----AAATTAAAAAT---TTTCGGTAACACTTCAAAACTA 226778 i i ---- i vi---v vv i v v v i L1MB4_3end#LI 156 CATTAGGGAAATGCAAATCAAAACCACAATGAGATACCACTTCACACCCA 205 chr1qtel1M 226779 TCAAATTGGCTAACACAATGGAAAAGGGAAATGACAAATGCTGGAGGAAA 226828 ii iiv v? iv vii v i i i i v iii L1MB4_3end#LI 206 CTAGGATGGCTATNATCAAAAAAACGGAAAATAACAAGTGTTGGCGAGGA 255 chr1qtel1M 226829 TATGGTGAAAAATAGGTGGACTTATTATGCA-TGTTGGTGGAATTGTCAA 226877 i -- i --- viiv ii - i i v v L1MB4_3end#LI 256 TGTG--GAGAAAT---TGGAACCCTCGTGCATTGCTGGTGGGAATGTAAA 300 chr1qtel1M 226878 CTGATCCAA-CACTTTGGAGAATAAATTGG 226906 v i v i- i v i i iv L1MB4_3end#LI 301 ATGGTGCAGCCGCTGTGGAAAACAGTTTGG 330 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 35.40 CpG sites = 41, Kimura (unadjusted) = 36.77 Transitions / transversions = 1.37 (41/30) Gap_init rate = 0.06 (16 / 257), avg. gap size = 1.81 (29 / 16) 360 27.16 1.23 0.00 chr1qtel1M 227530 227610 (772390) C MIR3#SINE/MIR (20) 188 107 m_b34s601i4 1160 chr1qtel1M 227530 GTCAGTGCTAGAAGAAACTTT-TACATCATCTAGTTCATTTTCCTCATTT 227578 v i ii i -v v i viii C MIR3#SINE/MIR 188 GTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTT 139 chr1qtel1M 227579 TACAATTAAAAAAACTGAAACCCAAGGAGCTG 227610 iv i ii ii ii v C MIR3#SINE/MIR 138 TACAGATGAGGAAACTGAGGCCCAGAGAGGTG 107 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.67 CpG sites = 16, Kimura (unadjusted) = 35.67 Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.01 (1 / 80), avg. gap size = 1.00 (1 / 1) 211 33.01 5.50 5.50 chr1qtel1M 227564 227672 (772328) C MIRb#SINE/MIR (109) 159 51 m_b34s601i5 1160 chr1qtel1M 227564 TCATTTTCCTCATTTTACAATTAAAAAAACTGAAACCCAAGGAGCT---G 227610 i v i iv i ii ii i ii v --- C MIRb#SINE/MIR 159 TTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAG 110 chr1qtel1M 227611 T---TTGCCCCTAAGTTTAGTTGCCCTGGCAGTAAGGAATAGTGTCATAA 227657 --- -- ---- ii v v vi viii v i ivi C MIRb#SINE/MIR 109 TAACTTGCCC--AAG----GTCACACAGCTAGTAAGTGGCAGAGCCGGGA 66 chr1qtel1M 227658 TATGATCCAAGTTCT 227672 vi v v v C MIRb#SINE/MIR 65 TTCGAACCCAGGTCT 51 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 41.83 CpG sites = 21, Kimura (unadjusted) = 45.45 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.07 (8 / 108), avg. gap size = 1.50 (12 / 8) 434 30.05 3.72 3.72 chr1qtel1M 228598 228839 (771161) L1ME3B_3end#LINE/L1 405 646 (343) m_b34s551i3 1159 chr1qtel1M 228598 AACATGTACGTGTGTGTGTGAGAGAGTGTGTGTGACGAATGTTTGTGGCA 228647 ii i iii iiiv ii?iii iii - ii i L1ME3B_3end#L 405 AACGCGTGCACATGTGCACCAGGANACATGTACAA-GAATGTTCATAGCA 453 chr1qtel1M 228648 GCCCTTTTTGTAGTGGCTAAAAACTGGAAACTGAA--TGGATGTCCATCA 228695 vi v i i i i? -- --iii L1ME3B_3end#L 454 GCATTGTTCGTAATAGCCNAAAACTGGAAAC--AACCCAAATGTCCATCA 501 chr1qtel1M 228696 GTTGGAGAATGGCTGAATAAATTGTGGTATATGAATATTATGGAATATTA 228745 iiv v v i vv iv i L1ME3B_3end#L 502 ACAGTAGAATGGATAAATAAATTGTGGTATATTCATACAATGGAATACTA 551 chr1qtel1M 228746 CTGTTCTGTAA--GAAATGACCAACAGGATAATTTCA--GAAAGGCCTGG 228791 --- v v i --i v i - vv i ii v --v vii v L1ME3B_3end#L 552 ---TACAGCAATGAAAATGAACGA-ACTACAGCTACACGCAACAACATGG 597 chr1qtel1M 228792 A-GAGACTTACACGAAC-TGATGCTGAGTGAAATGAGCAGGAC-CAGGAG 228838 - iv i -- - i i i vi i - ii L1ME3B_3end#L 598 ATGAATCTCACA--AACATAATGTTGAGCGAAAGAAGCAAGACACAAAAG 645 chr1qtel1M 228839 A 228839 L1ME3B_3end#L 646 A 646 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.50 CpG sites = 50, Kimura (unadjusted) = 41.40 Transitions / transversions = 2.50 (50/20) Gap_init rate = 0.06 (15 / 241), avg. gap size = 1.20 (18 / 15) 455 25.57 1.47 2.22 chr1qtel1M 228610 228745 (771255) L1ME3G_3end#LINE/L1 413 547 (377) m_b34s551i4 1159 chr1qtel1M 228610 TGTGTGTGAGAGAGTGTGTGTGACGAATGTTTGTGGCAGCCCTTTTTGTA 228659 iiii ii? ii iii - i ii v vi v L1ME3G_3end#L 413 TGTGCACAAGGANGCATGTACAA-GGATGTTCATTGCAGCATTGTTTGTA 461 chr1qtel1M 228660 GTGGCTAAAAACTGGAAACTGAA--TGGATGTCCATCAGTTGGAGAATGG 228707 i i v i -- -- ii i v i L1ME3G_3end#L 462 ATAGCGAAAAATTGGAAAC--AACCTAAATGTCCATCAATAGGGGAATGG 509 chr1qtel1M 228708 CTGAATAAATTGTGGTATATGAATATTATGGAATATTA 228745 i i i vv i i L1ME3G_3end#L 510 TTAAATAAATTATGGTATATCCATACTATGGAATACTA 547 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.81 CpG sites = 27, Kimura (unadjusted) = 33.81 Transitions / transversions = 3.86 (27/7) Gap_init rate = 0.03 (4 / 135), avg. gap size = 1.25 (5 / 4) 517 29.69 2.04 2.04 chr1qtel1M 228632 228827 (771173) L1MD1_3end#LINE/L1 438 633 (356) m_b34s551i6 1159 chr1qtel1M 228632 ACGAATGTTTGTGGCAGCCCTTTTTGTAGTGGCTAAAAACTGGAAACTGA 228681 i i ii v i i i i -- L1MD1_3end#LI 438 ACGAATGTTTATAGCAGCTTTATTCGTAATAGCCAAAAACTGGAAAC--A 485 chr1qtel1M 228682 A--TGGATGTCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATATGA 228729 --ii v iiv v i i i i i vv L1MD1_3end#LI 486 ACCCAGATGTCCTTCAACGGGTGAATGGTTAAACAAACTGTGGTACATCC 535 chr1qtel1M 228730 ATATTATGGAATATTACTGTTCTGTAAGAAATGACCAACAG--GATAATT 228777 ii i vvv vi i ivi v vi-- vvi L1MD1_3end#LI 536 ATACCATGGAATACTACTCAGCAATAAAAAGGAACGAACTATTGATACAC 585 chr1qtel1M 228778 TCAGAAAGGCCTGGAGAGACTTACACGAACTGATGCTGAGTGAAATGAGC 228827 v iv -- vii ii v vii v v vi L1MD1_3end#LI 586 GCAACAA--CCTGGATGAATCTCCAGAGAATTATGCTGAGTGAAAAAAGC 633 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.36 CpG sites = 34, Kimura (unadjusted) = 38.97 Transitions / transversions = 1.48 (34/23) Gap_init rate = 0.03 (6 / 195), avg. gap size = 1.33 (8 / 6) 522 21.05 1.72 1.72 chr1qtel1M 228632 228747 (771253) L1ME1_3end#LINE/L1 438 553 (373) m_b34s551i5 1159 chr1qtel1M 228632 ACGAATGTTTGTGGCAGCCCTTTTTGTAGTGGCTAAAAACTGGAAACTGA 228681 ii i ii v i i i i -- L1ME1_3end#LI 438 ACGAATGTTCATAGCAGCTTTATTCGTAATAGCCAAAAACTGGAAAC--A 485 chr1qtel1M 228682 AT--GGATGTCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATATGA 228729 i--ii ii? v v i i vv L1ME1_3end#LI 486 ACCCAAATGTCCATCAACNGGTGAATGGATAAACAAATTGTGGTATATCC 535 chr1qtel1M 228730 ATATTATGGAATATTACT 228747 iv i L1ME1_3end#LI 536 ATACAATGGAATACTACT 553 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 24.79 CpG sites = 18, Kimura (unadjusted) = 26.04 Transitions / transversions = 3.00 (18/6) Gap_init rate = 0.03 (3 / 115), avg. gap size = 1.33 (4 / 3) 16 0.00 0.00 0.00 chr1qtel1M 229296 229313 (770687) (A)n#Simple_repeat 1 18 (0) m_b34s252i1 1161 chr1qtel1M 229296 AAAAAAAAAAAAAAAAAA 229313 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAA 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 16 15.86 0.00 0.00 chr1qtel1M 229316 229343 (770657) (GT)n#Simple_repeat 1 28 (0) m_b34s252i2 1162 chr1qtel1M 229316 GTGTGTGTGAGGGTGTGCTTGTGTGTGT 229343 v v iv (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGT 28 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 255 33.14 2.50 6.96 chr1qtel1M 229520 229639 (770361) MIR#SINE/MIR 142 256 (6) m_b34s601i6 1163 chr1qtel1M 229520 GGGCACAATAAAAGCCCCTTCCTCCCGAGGTTGA---GGGAATCAAATAA 229566 v i v iv v viii v--- i i i i MIR#SINE/MIR 142 GGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGGATTAAATGA 191 chr1qtel1M 229567 CGTAACACTTGAACAGGGCTTGGCCTGGTGCTTGGCATGTAATACATGTA 229616 vv i v v v v i vvii i ii i ------ MIR#SINE/MIR 192 GTTAATACATGTAAAGCGCTTAGAACAGTGCCTGGCACATAGTA------ 235 chr1qtel1M 229617 ATAACATGTAATAAATGTTAGTT 229639 -- i iivi i MIR#SINE/MIR 236 --AGCGCTCAATAAATGTTAGCT 256 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 43.53 CpG sites = 22, Kimura (unadjusted) = 45.20 Transitions / transversions = 1.47 (22/15) Gap_init rate = 0.08 (9 / 119), avg. gap size = 1.22 (11 / 9) 45 0.00 0.00 0.00 chr1qtel1M 231295 231335 (768665) (CGGGGT)n#Simple_repeat 1 41 (0) c_b34s251i0 1164 chr1qtel1M 231295 CGGGGTCGGGGTCGGGGTCGGGGTCGGGGTCGGGGTCGGGG 231335 (CGGGGT)n#Sim 1 CGGGGTCGGGGTCGGGGTCGGGGTCGGGGTCGGGGTCGGGG 41 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 16 33.58 0.00 0.00 chr1qtel1M 235744 235806 (764194) (TTTT)n#Simple_repeat 1 63 (0) m_b34s252i3 1165 chr1qtel1M 235744 TTTTTTTTTTTTCCTATTTCAAGAAATCTTTATTTTATTTATTTTTTATT 235793 ii v ivvvvvv i v v v v (TTTT)n#Simpl 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr1qtel1M 235794 TATTTTTTTATTT 235806 v v (TTTT)n#Simpl 51 TTTTTTTTTTTTT 63 Matrix = Unknown Transitions / transversions = 0.31 (4/13) Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0) 22 3.00 2.78 2.78 chr1qtel1M 235772 235807 (764193) (TTTA)n#Simple_repeat 1 36 (0) m_b34s252i4 1165 chr1qtel1M 235772 TTTATTTTATTTATTT-TTTATTTATTTTTTTATTTA 235807 - - v (TTTA)n#Simpl 1 TTTA-TTTATTTATTTATTTATTTATTTATTTATTTA 36 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 311 28.92 9.60 7.43 chr1qtel1M 236568 236765 (763235) C MIR#SINE/MIR (3) 259 58 m_b34s601i7 1166 chr1qtel1M 236568 AATAA-TAACATTTA----GTGCTTACCAACTGACAGGCATTGCTTAATG 236612 i- ---- i i vv v i i i---- C MIR#SINE/MIR 259 AATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTC---- 214 chr1qtel1M 236613 CAATTGTGTTAAGCCCTTCCCA---ATTA--TCATTCAGTCCTCATAACA 236657 --------- v iv --- -- i i i C MIR#SINE/MIR 213 ---------TAAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACA 173 chr1qtel1M 236658 ACTCTGGGAGATGGTATACCATTATTGTTTTCCTTCTTATAAGCCTTTTA 236707 i iv i i -i i i iii v - i iiivvvvv C MIR#SINE/MIR 172 ACCCTATGAGGTAG-GTACTATTATTATCCCCATT-TTACAGATGAGGAA 125 chr1qtel1M 236708 TATGAGGCAAACAAAG-----GTAATTTT----AAATCACAGAGCTAGTA 236748 vv v v i ----- i v---- ii v C MIR#SINE/MIR 124 ACTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTA 75 chr1qtel1M 236749 AATTTCTGAGACAGAAT 236765 i vv v v i i C MIR#SINE/MIR 74 AGTGGCAGAGCCGGGAT 58 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.81 CpG sites = 31, Kimura (unadjusted) = 37.59 Transitions / transversions = 1.41 (31/22) Gap_init rate = 0.11 (21 / 197), avg. gap size = 1.62 (34 / 21) 198 33.33 13.33 0.00 chr1qtel1M 236623 236802 (763198) C MIRc#SINE/MIR (45) 223 20 m_b34s601i8 1166 chr1qtel1M 236623 AAGCCCTTCC-CA---ATTATC--ATTCAGTCCTCATAACAACTCTGGGA 236666 v i - --- -- iii i i v C MIRc#SINE/MIR 223 AAGCGCTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGA 174 chr1qtel1M 236667 GAT-GGTATACCA-TTATTGTTTTCCT--TCTTATAAGCCTTTTATATGA 236712 i - i viv -v i v i-- i i iiivvvvv vv C MIRc#SINE/MIR 173 GGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGA 124 chr1qtel1M 236713 GGCAAACAAAGGT--AAT--TTT-----AAATCACAGAGCTAGTAAATTT 236753 vv v i -- i --i ----- ii v i vv C MIRc#SINE/MIR 123 GGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGG 74 chr1qtel1M 236754 CTGAGACAGAATGT-AACTGAGGTTTCTCT--CTTT--TTCCAGTATTTT 236798 v v i i ivi- iv i ii -- ii--v ii i C MIRc#SINE/MIR 73 CAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCT 24 chr1qtel1M 236799 TTTC 236802 i C MIRc#SINE/MIR 23 TTCC 20 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 43.76 CpG sites = 36, Kimura (unadjusted) = 45.86 Transitions / transversions = 1.50 (36/24) Gap_init rate = 0.07 (12 / 179), avg. gap size = 2.00 (24 / 12) 611 18.51 8.09 0.68 chr1qtel1M 240890 241025 (758975) C Charlie4a#DNA/hAT-Charlie (0) 508 363 m_b34s502i0 1167 chr1qtel1M 240890 CAAAGGTTCTTCAC-TTTTTTGTTTTCTGGACCACTTTGGCAGGCTACTG 240938 ii v - viiv v v iv C Charlie4a#DNA 508 CAGGGGTTCTTAACCTTTTTTGTGCCATGGACCCCTTTGGCAGTCTGGTG 459 chr1qtel1M 240939 AATTCTATGGATTCCTT---AGAACTCTGCCTTTAAAATGCATAAAA--- 240982 vi ii --- ivv ii - --- C Charlie4a#DNA 458 AAGCCTATGGACCCCTTCTCAGAATAATGTTTTTAAA-TGCATAAAATAA 410 chr1qtel1M 240983 ----CATGGGATTACAAAGGAAATGAGTTATATTGGAATACAGTTAT 241025 ---- i iv i i C Charlie4a#DNA 409 AATACATAGGATTACAAAGGAAACCAATTATATTGAAATACAGTTAT 363 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 21.58 CpG sites = 15, Kimura (unadjusted) = 21.58 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.04 (5 / 135), avg. gap size = 2.40 (12 / 5) 17 0.00 0.00 0.00 chr1qtel1M 241027 241045 (758955) (T)n#Simple_repeat 1 19 (0) m_b34s252i5 1168 chr1qtel1M 241027 TTTTTTTTTTTTTTTTTTT 241045 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 192 35.62 8.33 2.31 chr1qtel1M 242031 242234 (757766) L2#LINE/L2 1593 1808 (1274) m_b34s601i9 1169 chr1qtel1M 242031 TCTG--TTCACCTCTTGTCTC-ACAGAAAAAGTTTCTTTACT--TATTTA 242075 -- - i iv - i vi v v iv i -- i L2#LINE/L2 1593 TCTGCCTTC-CCTCCTGTTACTACGGATGAACTGTCCGTGCTCCTATCTA 1641 chr1qtel1M 242076 AAGTTAATTTTTCT---------TTCGGTTCTATCTCCTATTGTCTATTT 242116 i ii iiii i---------i v i i i i v i i i i L2#LINE/L2 1642 AGGCCAACCCCTCCACTTGTGCACTAGATCCCATCCCCTCTCGCCTACTC 1691 chr1qtel1M 242117 TAAAACATCACTCTGGTAATCTTATCCTCTCCCTCAATACTTCATATTCA 242166 v ii i ii i ii vi i ---- v vv L2#LINE/L2 1692 AAGGACATCGCTCCAGCAATTCTCCCCTCTCTCTC----CTGCATCATCA 1737 chr1qtel1M 242167 GTTTGTCCCTTAAACCT---TTTTTCTCAGCTGCCCACTCACATGCCCTG 242213 i v ivvvv --- iv i v v vi vv iv ? L2#LINE/L2 1738 ATTTTTCCCTCTCTACTGGATCATTCCCATCAGCATACAAACATGCTGTN 1787 chr1qtel1M 242214 CTCTCTCTAGTACTTAAAAAA 242234 v i ivi vi L2#LINE/L2 1788 ATTTCTCCCATCTTTAAAAAA 1808 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 47.27 CpG sites = 44, Kimura (unadjusted) = 51.43 Transitions / transversions = 1.63 (44/27) Gap_init rate = 0.05 (10 / 203), avg. gap size = 2.20 (22 / 10) 200 29.23 3.08 0.00 chr1qtel1M 242321 242385 (757615) C L3#LINE/CR1 (2508) 1591 1525 m_b34s601i10 1170 chr1qtel1M 242321 TCTGTAGCATACTCTGATAGTTGTATTCCTTCTGTTTCTATTTCTCTTCA 242370 i iv i iivi iv v i ii i C L3#LINE/CR1 1591 TCTGTAGTATACTCCCACAACGATATCACTTCTGTTTCTCTCTCCTTTTA 1542 chr1qtel1M 242371 TC--TAACCAAAAGTTC 242385 --i v v i C L3#LINE/CR1 1541 TCCTCACCCAAATGCTC 1525 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.34 CpG sites = 13, Kimura (unadjusted) = 39.00 Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.02 (1 / 64), avg. gap size = 2.00 (2 / 1) 368 27.58 2.56 0.84 chr1qtel1M 242758 242874 (757126) C L3#LINE/CR1 (3077) 1022 904 m_b34s601i11 1170 chr1qtel1M 242758 GTCTCTGCTCAAGGGCTC--CTTCCTGA-ATTTTAGGCCATGGTCCAGAA 242804 i ?vi i i i -- v i i- i? i C L3#LINE/CR1 1022 GTCCCTNGCCAGGAGCCCATCGTTCTGGTATCNTAAGCCATGGTCCAGAA 973 chr1qtel1M 242805 ACACAAATCCTTTTCTCAGATGCTGCATTCTTATTCAGCTTGTTCATTTC 242854 vv v iv ii iiiv v v vi - i C L3#LINE/CR1 972 AACCAAATCCTGTTCTTCGACACCATCTACGTAGCCAGC-TGTTCACTTC 924 chr1qtel1M 242855 CCATATTTGCCCTTCCCTTC 242874 iiv i i C L3#LINE/CR1 923 CCATATCCTCCTTTCTCTTC 904 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.63 CpG sites = 21, Kimura (unadjusted) = 36.63 Transitions / transversions = 1.91 (21/11) Gap_init rate = 0.03 (3 / 116), avg. gap size = 1.33 (4 / 3) 924 29.22 1.22 1.22 chr1qtel1M 244903 245148 (754852) MIRb#SINE/MIR 7 252 (16) m_b34s601i12 1171 chr1qtel1M 244903 GGCAGCTTGGTGGTATAATGGCTAGAGTTCTGAGCCTAATGTCAGGAAGA 244952 --- ii i vv iv v ivii iiv iv MIRb#SINE/MIR 7 GGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGA 53 chr1qtel1M 244953 CATGAATTTAAATCTGGATTCAGATATTCCCTAACTATGTAACTCTGGAC 245002 v ii ii iv ii v vi i iv i i i ii i MIRb#SINE/MIR 54 CCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGC 103 chr1qtel1M 245003 AAGTCACTTAACCTTTCTCAACCTCAGATTCCTCAACTGTAAAATCAGGA 245052 i i v i v v vi MIRb#SINE/MIR 104 AAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGA 153 chr1qtel1M 245053 TAAAAGCATCTA--TTACATGG-AGCTGTGAGAATCTAATGAGATAATAT 245099 v ii i -- ii v -v i i iv ii MIRb#SINE/MIR 154 TAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGC 203 chr1qtel1M 245100 TTGTAAAGTGCTTAGATCAGTTCTTGGCACAAAGTAAGTATTTAATAAA 245148 v i vv v i v iii i MIRb#SINE/MIR 204 ATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAAA 252 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.60 CpG sites = 46, Kimura (unadjusted) = 38.60 Transitions / transversions = 1.84 (46/25) Gap_init rate = 0.02 (5 / 245), avg. gap size = 1.20 (6 / 5) 16 26.77 3.95 2.60 chr1qtel1M 245550 245625 (754375) (ATATAC)n#Simple_repeat 1 77 (0) m_b34s252i6 1172 chr1qtel1M 245550 ATATACATATACATAT-TA-ATAAGTAGATATCTGCA-ATCACATACATA 245596 -i - vi v i v i - - i i (ATATAC)n#Sim 1 ATATACATATACATATACATATACATATACATATACATAT-ACATATACA 49 chr1qtel1M 245597 TATACACATTGCACATTCAAATGCATCTA 245625 i - i i v v i v (ATATAC)n#Sim 50 TATACATA-TACATATACATATACATATA 77 Matrix = Unknown Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.07 (5 / 75), avg. gap size = 1.00 (5 / 5) 20 19.50 0.00 4.44 chr1qtel1M 248176 248222 (751778) (AT)n#Simple_repeat 1 45 (0) m_b34s252i7 1173 chr1qtel1M 248176 ATATATATGTATACACACACACTATATATAGTACATATACATATATA 248222 i i i i i - - i i (AT)n#Simple_ 1 ATATATATATATATATATATA-TATATATA-TATATATATATATATA 45 Matrix = Unknown Transitions / transversions = 1.00 (7/0) Gap_init rate = 0.04 (2 / 46), avg. gap size = 1.00 (2 / 2) 302 24.68 10.42 2.91 chr1qtel1M 248273 248368 (751632) C MIRc#SINE/MIR (155) 113 11 m_b34s601i13 1174 chr1qtel1M 248273 GGTTAAGTGATTTGCCCAGGGTCACACAGCTAGGGAGTGTTA-AGTGTCT 248321 i i vi vi - --- i C MIRc#SINE/MIR 113 GGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAG---CC 67 chr1qtel1M 248322 GAGGCT--------GGTCTTCCTGAATTCAGAACTGATGCCATGTTAGCT 248363 i i -------- v i iiv iii iv v ivi C MIRc#SINE/MIR 66 GGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACT 17 chr1qtel1M 248364 GC-CCA 248368 - C MIRc#SINE/MIR 16 GCACCA 11 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.62 CpG sites = 16, Kimura (unadjusted) = 31.26 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.06 (6 / 95), avg. gap size = 2.17 (13 / 6) 236 27.29 2.74 7.14 chr1qtel1M 249265 249410 (750590) L2c_3end#LINE/L2 118 257 (221) m_b34s601i14 1175 chr1qtel1M 249265 CCTGCTTCCAGCTCATGTTTGCAGCTGACTGGCCCATCACCAAGCCTCCA 249314 i i?vi --- vv - vi v v---- vv L2c_3end#LINE 118 CCTGCCTCCGNGCC---TTTGCACATG-CTGTTCCCTCT----GCCTGGA 159 chr1qtel1M 249315 GTGCTCTTTCCTCTTTCTTCCTCTTGG--GATCCCTAGTC-CCCTTGAGG 249361 i i i i i v i --i ii v -i v i L2c_3end#LINE 160 ATGCTCTTCCCCCCTCCTTCCACCTGGCTAACTCCTACTCATCCTTCAAG 209 chr1qtel1M 249362 GCTCAGCTCAGGGGCCACCTTTTCCAGGGAGTGCTCTCCCCG-CTCCCCA 249410 ? iv i ii i i -- ii i - i L2c_3end#LINE 210 NCTCAGCTCAGATGTCACCTCCTCCGGGAA--GCCTTCCCTGACCCCCCA 257 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.55 CpG sites = 25, Kimura (unadjusted) = 35.99 Transitions / transversions = 2.08 (25/12) Gap_init rate = 0.09 (13 / 145), avg. gap size = 1.08 (14 / 13) 12 9.71 5.41 5.41 chr1qtel1M 249644 249680 (750320) (CCCCGCA)n#Simple_repeat 1 37 (0) m_b34s252i8 1176 chr1qtel1M 249644 CCCCG-ACCCCGCACCTGGCGCCCCAGC-CCCCGCCACC 249680 - iv i - - - (CCCCGCA)n#Si 1 CCCCGCACCCCGCACCCCGCACCCC-GCACCCCG-CACC 37 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.11 (4 / 36), avg. gap size = 1.00 (4 / 4) 355 27.35 2.52 1.67 chr1qtel1M 249706 249824 (750176) C L3#LINE/CR1 (222) 3877 3758 m_b34s601i15 1177 chr1qtel1M 249706 TCTGCCTTTTTGGACCTCCCCCTCCCCCTGCTCCTGGTTCTGCC-TCTGG 249754 iii v v i v -- vi v i - C L3#LINE/CR1 3877 TCTGCCTCCCTGTAACTTCCAC--CCATTGGTCCTAGTTCTGCCCTCTGG 3830 chr1qtel1M 249755 GACCA-GCGGAACAGGTC-AATCTCTCTTCTATATAATTGCCCTTCAAAC 249802 ii -i i i i - i i i i iv i C L3#LINE/CR1 3829 AGCCACACAGAATAAGTCTAATCCCTCTTCCACATGACAGCCCTTCAAAT 3780 chr1qtel1M 249803 CCTTGGAGATGGCCATCCCGTC 249824 vi i ii i vi C L3#LINE/CR1 3779 ATTTGAAGACAGCTATCATGTC 3758 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.24 CpG sites = 24, Kimura (unadjusted) = 36.24 Transitions / transversions = 3.00 (24/8) Gap_init rate = 0.04 (5 / 118), avg. gap size = 1.00 (5 / 5) 197 32.42 3.97 3.97 chr1qtel1M 249857 250007 (749993) MIRc#SINE/MIR 49 199 (69) m_b34s601i16 1178 chr1qtel1M 249857 GACATGGGGCCCTGGGCCCCGAG-CAGACACTTCCCAGCTTCCTGTGGGA 249905 v vi -- i i iv- v v v i ---- v MIRc#SINE/MIR 49 GACCTGGGTTC--GAGTCCCGGCTCTGCCACTTACTAGCT----GTGTGA 92 chr1qtel1M 249906 CCC-GGACAAGTCACAGAGCCCTGCCTA-TCTCAGTCTGTTCAACTGTAA 249953 i- i vv i iiv iv -i i vi v MIRc#SINE/MIR 93 CCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAA 142 chr1qtel1M 249954 AATGGGATTCATAAAAATAGCGCGCCCCAACTC---GGGCTGCTCCGGAG 250000 iv v v viv v vv i v --- i i vi ii MIRc#SINE/MIR 143 AATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGG 192 chr1qtel1M 250001 ACCAAGT 250007 i i MIRc#SINE/MIR 193 ATCAAAT 199 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 43.17 CpG sites = 24, Kimura (unadjusted) = 43.17 Transitions / transversions = 1.04 (24/23) Gap_init rate = 0.07 (10 / 150), avg. gap size = 1.20 (12 / 10) 213 29.66 3.23 7.56 chr1qtel1M 249884 250007 (749993) MIR#SINE/MIR 71 189 (73) m_b34s601i18 1178 chr1qtel1M 249884 CACTTCCCAGCTTCCTGTGGGACCC-GGACAAGTCACAGAGCC-CTGCCT 249931 v i ---- v i- i i vv i - viv MIR#SINE/MIR 71 CACTTACTAGCT----GTGTGACCTTGGGCAAGTTACTTAACCTCTCTGT 116 chr1qtel1M 249932 ATCTCAGTCTGTTCAACTGTAAAATGGGATTCATAAAAATAGCGC--GCC 249979 ii i vi v i--- v ii --i MIR#SINE/MIR 117 GCCTCAGTTTCCTCATCTGTAAAATGGGG---ATAATAATAGTACCTACC 163 chr1qtel1M 249980 CCAACTCGGGCTGCTCCGGAGACCAAGT 250007 i -- v i i vi ii ii i MIR#SINE/MIR 164 TCA--TAGGGTTGTTGTGAGGATTAAAT 189 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.53 CpG sites = 23, Kimura (unadjusted) = 39.53 Transitions / transversions = 2.09 (23/11) Gap_init rate = 0.10 (12 / 123), avg. gap size = 1.08 (13 / 12) 217 27.53 2.38 4.88 chr1qtel1M 249884 249967 (750033) MIRb#SINE/MIR 78 159 (109) m_b34s601i17 1178 chr1qtel1M 249884 CACTTCCCAGCTTCCTGTGGGACCC-GGACAAGTCACAGAGCCCTGCCTA 249932 v i ---- v i- i i vv i iiv iv MIRb#SINE/MIR 78 CACTTACTAGCT----GTGTGACCTTGGGCAAGTTACTTAACCTCTCTGA 123 chr1qtel1M 249933 -TCTCAGTCTGTTCAACTGTAAAATGGGATTCATAA 249967 -i i vi v iv v MIRb#SINE/MIR 124 GCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAA 159 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.86 CpG sites = 12, Kimura (unadjusted) = 34.86 Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.07 (6 / 83), avg. gap size = 1.00 (6 / 6) 187 23.21 5.36 0.00 chr1qtel1M 250902 250957 (749043) C L3#LINE/CR1 (2215) 1884 1826 m_b34s601i19 1177 chr1qtel1M 250902 CACTTCC-CCCAAGGTTCCTATC-ATCTCTA-TGCACTGATCAATTTCTC 250948 i - - ii i - v ii i i ii C L3#LINE/CR1 1884 CACTTTCTCCCAAGGTTCCTATCGACTTCCACTTCACCAACCAGTTCTTC 1835 chr1qtel1M 250949 CTTCTTGAT 250957 v i C L3#LINE/CR1 1834 CTTGTTGGT 1826 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.83 CpG sites = 11, Kimura (unadjusted) = 29.83 Transitions / transversions = 5.50 (11/2) Gap_init rate = 0.05 (3 / 55), avg. gap size = 1.00 (3 / 3) 485 31.33 5.70 4.12 chr1qtel1M 250968 251230 (748770) C L3#LINE/CR1 (2316) 1783 1517 m_b34s601i20 1177 chr1qtel1M 250968 TACTTTTTGAATAACAAAATTATCATTTTGTTGACTCAAG-TACATCAAG 251016 i i ivi ii i ------- --- -i vi C L3#LINE/CR1 1783 TACCTTCTGAGAGATGAAATTGTCA-------G---CAAGGCAAGTCAAG 1744 chr1qtel1M 251017 AAGTTATAAGCTTCCTTGCTTTTGGTAGA----GACTTCTAGTTGATGTC 251062 v v v v ii i i? ---- i iv C L3#LINE/CR1 1743 AATTTATCAGATGCTCTGCTTTTAGCNGAATGAGACTTCCAGCAGATGTC 1694 chr1qtel1M 251063 TGGTTAACCAAAGTTA---ATCACTAGTATAATCTTACCTATGTGAGAGA 251109 i v iiii iv--- v i? - i v vv v C L3#LINE/CR1 1693 CGGATAGTTGAAGTCCCCCATCACTACTGNA-TCTTGCCTCTGTGCCAGT 1645 chr1qtel1M 251110 TTTATAATCCATTTCCTGGAT---TTGTCTATTTTCTCCTTTTTTCCAGG 251156 i ii v vv i v--- ii i ? i v i vv i C L3#LINE/CR1 1644 TTTGTAATCTGTATCAGGAAAGCATCATCCATNTCCTCCATCTGGCCGGG 1595 chr1qtel1M 251157 GGCTCTACTTTAGGCTTCAAGGGAAAAATCACTT--GTTTCTCCATTCTA 251204 v v iivv vi i v viivi v -- iv i v C L3#LINE/CR1 1594 CGGTCTGTAGTATACTCCCACAACGATATCACTTCTGTTTCTCTCTCCTT 1545 chr1qtel1M 251205 --ATCTTCATCCAAATGCTCTATATTGC 251230 -- i i vi ?i C L3#LINE/CR1 1544 TTATCCTCACCCAAATGCTCTCCANCGC 1517 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.95 CpG sites = 46, Kimura (unadjusted) = 42.80 Transitions / transversions = 1.39 (46/33) Gap_init rate = 0.06 (17 / 262), avg. gap size = 1.53 (26 / 17) 387 22.59 13.67 1.28 chr1qtel1M 251296 251434 (748566) Charlie4#DNA/hAT-Charlie 3223 3378 (0) m_b34s502i1 1179 chr1qtel1M 251296 AAATATTCGGATACCTTTATTTCAGT-------GTTT--TTTA-AATACT 251335 iv v v i ------- -- i- v Charlie4#DNA/ 3223 AAATATTTTGATAACTATATTTCAATATAATTGGTTTCCTTTGTAATCCT 3272 chr1qtel1M 251336 ATGTGTTTTAT-----GTATT--AAAATATTATTCTGA--AGAAGATAAC 251376 i ----- i -- i -- ii viv i Charlie4#DNA/ 3273 ATGTATTTTATTTTATGCATTTAAAAACATTATTCTGAGAAGGGGTCCAT 3322 chr1qtel1M 251377 AAGGTTCATTAGGCTGCTAAAGGGGACTATGATACAAAAAAATTATTCAG 251426 i v ii i i v i ii i--i v Charlie4#DNA/ 3323 AGGCTTCACCAGACTGCCAAAGGGGTCCATGGCACAAAAAAG--GTTAAG 3370 chr1qtel1M 251427 AACTTCTG 251434 ii Charlie4#DNA/ 3371 AACCCCTG 3378 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 27.98 CpG sites = 22, Kimura (unadjusted) = 27.98 Transitions / transversions = 2.44 (22/9) Gap_init rate = 0.06 (8 / 138), avg. gap size = 2.62 (21 / 8) 260 28.44 0.00 3.41 chr1qtel1M 251885 251975 (748025) L1PREC2_orf2#LINE/L1 844 931 (2363) m_b34s551i8 1180 chr1qtel1M 251885 ACAAAATACCAGAATTTCTGGGAGGCAGTTAAAGTAGTCCTTGGAGGAAA 251934 v i vi i i i vi vi i L1PREC2_orf2# 844 ACAACATACCAGAATCTCTGGGACACAGCTAAGGCAGTGTTAAGAGGGAA 893 chr1qtel1M 251935 AATTATATCTCTGATAACATACATTTTTAAAAAATGGGAAA 251975 v v v i vvi vi --- i i vi L1PREC2_orf2# 894 ATTTATAGCACTAAATGCCCACA---TCAAAAAGTTAGAAA 931 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.47 CpG sites = 14, Kimura (unadjusted) = 36.47 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.03 (3 / 90), avg. gap size = 1.00 (3 / 3) 278 21.05 0.00 0.00 chr1qtel1M 251885 251941 (748059) L1P1_orf2#LINE/L1 844 900 (2394) m_b34s551i7 1180 chr1qtel1M 251885 ACAAAATACCAGAATTTCTGGGAGGCAGTTAAAGTAGTCCTTGGAGGAAA 251934 v i v v i i viv i i L1P1_orf2#LIN 844 ACAACATACCAGAATCTCTGGGACGCATTCAAAGCAGTGTGTAGAGGGAA 893 chr1qtel1M 251935 AATTATA 251941 v L1P1_orf2#LIN 894 ATTTATA 900 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 24.88 CpG sites = 6, Kimura (unadjusted) = 24.88 Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0) 413 28.51 15.20 1.55 chr1qtel1M 254998 255168 (744832) C MIRc#SINE/MIR (25) 243 50 m_b34s601i21 1181 chr1qtel1M 254998 ATACCATCTTA-GGTTTATAA------TTTACATAAATCATCCTTCACAC 255040 v ii -i i ------ i v i -- i-i C MIRc#SINE/MIR 243 ATAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATC--TCAT-T 197 chr1qtel1M 255041 TGATTTTCCCAACCACCTTATGAGATAAGT----C---CATTCTAAT--- 255080 ii v v i i i i i---- ---i v v --- C MIRc#SINE/MIR 196 TGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCC 147 chr1qtel1M 255081 -ATTATATAAATGAAGAAACTGGGGCTCAGAA--------TGGCTTGCCT 255121 - v i i i i i-------- i i C MIRc#SINE/MIR 146 CATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCC 97 chr1qtel1M 255122 AAGATCACATAACTAATGATTGGCAGAAACAAAAGTGGAGCTTAAAT 255168 i i i i i v iv iii v v i ii ii C MIRc#SINE/MIR 96 AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGT 50 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.69 CpG sites = 37, Kimura (unadjusted) = 38.77 Transitions / transversions = 3.36 (37/11) Gap_init rate = 0.06 (10 / 170), avg. gap size = 2.90 (29 / 10) 429 29.41 7.95 3.16 chr1qtel1M 255018 255168 (744832) C MIRb#SINE/MIR (58) 210 53 m_b34s601i22 1181 chr1qtel1M 255018 TTTACATAAATCATCCTTCACACTGATTTTCCCAACCACCTTATGAGATA 255067 iv i -- i-i i ii v v i ii i C MIRb#SINE/MIR 210 TTTACATGCATTATC--TCAT-TTAATCCTCACAACAACCCTGCGAGGTA 164 chr1qtel1M 255068 AGTCCATTCTAAT----ATTATATAAATGAAGAAACTGGGGCTCAGAATG 255113 i -- v v ---- v i i i i iv C MIRb#SINE/MIR 163 GGT--ATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAG 116 chr1qtel1M 255114 G--------CTTGCCTAAGATCACATAACTAATGATTGGCAGAAACAAAA 255155 -------- i i i i i i v iv iii C MIRb#SINE/MIR 115 GTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGA 66 chr1qtel1M 255156 GTGGAGCTTAAAT 255168 v v i ii ii C MIRb#SINE/MIR 65 TTCGAACCCAGGT 53 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.66 CpG sites = 32, Kimura (unadjusted) = 40.13 Transitions / transversions = 2.91 (32/11) Gap_init rate = 0.05 (7 / 150), avg. gap size = 2.43 (17 / 7) 378 29.13 11.35 2.61 chr1qtel1M 255055 255195 (744805) C MIR3#SINE/MIR (36) 172 20 m_b34s601i23 1181 chr1qtel1M 255055 ACCTTATGAGATAAGTCCATTCTAAT------ATTATATAAATGAAGAAA 255098 - v - i v i i------ v i i i C MIR3#SINE/MIR 172 ACCTTA-GAGATCA-TCTAGTCCAACCCCCTCATTTTACAGATGAGGAAA 125 chr1qtel1M 255099 CTGGGGCTCAGAA--------TGGCTTGCCTAAGATCACATAACTAATGA 255140 i i i-------- i i i i i ? i v C MIR3#SINE/MIR 124 CTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTA 75 chr1qtel1M 255141 TTGGCAGAAACAAAAGTGGAGCTTAAATATCCT--CTTTCATCCTGATGG 255188 v iv iii v i i ii ii v -- ii vi i --v C MIR3#SINE/MIR 74 GTGGCAGAGCCGGGACTAGAACCCAGGTCTCCTGACTCCCAGTCCG--TG 27 chr1qtel1M 255189 CTCTCCC 255195 i C MIR3#SINE/MIR 26 CTCTCTC 20 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.47 CpG sites = 30, Kimura (unadjusted) = 40.13 Transitions / transversions = 3.00 (30/10) Gap_init rate = 0.05 (7 / 140), avg. gap size = 2.86 (20 / 7) 345 33.32 7.69 0.72 chr1qtel1M 255081 255210 (744790) C MIR1_Amn#SINE/MIR (83) 147 9 m_b34s601i24 1181 chr1qtel1M 255081 ATTATATAAATGAAGAAACTGGGGCTCAGAA--------TGGCTTGCCTA 255122 v i i i i ? i-------- i i C MIR1_Amn#SINE 147 ATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGCCCA 98 chr1qtel1M 255123 AGATCACATAACTAATGATTGGCAGAAACAAAAGTGGAGCTTAAATATCC 255172 i ?i i ?iii? v iv iii ? ? i ii ii v C MIR1_Amn#SINE 97 AGGTCACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAACCCAGGTCTCC 48 chr1qtel1M 255173 T--CTTTCATCCTGATGGCTCTCCCCAAGGGACTGAACTG 255210 i--v ii vi iii - vi vvi iiv C MIR1_Amn#SINE 47 CGAGTCCCAGTCCAGT-GCTCTATCCACTAGACCACACTG 9 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 48.85 CpG sites = 33, Kimura (unadjusted) = 52.54 Transitions / transversions = 3.30 (33/10) Gap_init rate = 0.02 (3 / 129), avg. gap size = 3.67 (11 / 3) 22 14.24 0.00 6.12 chr1qtel1M 255491 255542 (744458) (ATA)n#Simple_repeat 1 49 (0) m_b34s252i9 1182 chr1qtel1M 255491 ATAATAAAGAATTATTATAAATAATAATAATAAAGAATAACAATAACAAT 255540 - v v v - - v i i (ATA)n#Simple 1 ATAAT-AATAATAATAAT-AATAATAATAAT-AATAATAATAATAATAAT 47 chr1qtel1M 255541 AA 255542 (ATA)n#Simple 48 AA 49 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.00 (3 / 3) 331 25.20 6.00 7.43 chr1qtel1M 255651 255800 (744200) MIR1_Amn#SINE/MIR 23 170 (60) m_b34s601i25 1183 chr1qtel1M 255651 GGCTAGATTATCTGGGCTTTGGGGGCT-GGATTATCTGGGTTGAAATTCC 255699 v vi - i --- i - ivv i v? ? i MIR1_Amn#SINE 23 GGATAGAGCA-CTGGACT---GGGACTCGGGAGACCTGGGTTCNANTCCC 68 chr1qtel1M 255700 ATCTCT----CTGGTTTATTACCATATGACCTTGGACAAATCACATAATC 255745 iv ---- ? ii?ii i?---i i i - -- ? MIR1_Amn#SINE 69 GGCTCTGCCACTNGCCNGCTGN---GTGACCTTGGGCAAGTCAC-T--TN 112 chr1qtel1M 255746 ATCTCTCTAAGGCTTAGTTTCCTCA----TAAACGAGAAATAAGGGAACT 255791 i i? v i ---- vvi ii v iv MIR1_Amn#SINE 113 ACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATGATACT 162 chr1qtel1M 255792 GGACTACCT 255800 - iv MIR1_Amn#SINE 163 -GACCTCCT 170 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.75 CpG sites = 23, Kimura (unadjusted) = 33.95 Transitions / transversions = 1.92 (23/12) Gap_init rate = 0.09 (14 / 149), avg. gap size = 1.43 (20 / 14) 454 32.76 2.26 3.43 chr1qtel1M 255670 255846 (744154) MIR3#SINE/MIR 34 208 (0) m_b34s601i26 1183 chr1qtel1M 255670 TGGGGGCTGGATTATCTGGGTTGAAATTCCATCTCTCTGGTTTATTA-CC 255718 i iii ivv i vv i i iv vivii v i ?- i MIR3#SINE/MIR 34 TGGGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCT 83 chr1qtel1M 255719 ATATGACCTTGGACAAATCACATAATCATCTCTCTAAGGCTTAGTTTCCT 255768 i i i i - -- i ii v i MIR3#SINE/MIR 84 GTGTGACCTTGGGCAAGTCAC-T--TCACCTCTCTGGGCCTCAGTTTCCT 130 chr1qtel1M 255769 CATAAACGAGAAATAAGGGAACTGGACTACCTGATACCTGTAGTTCCTTT 255818 v--i vi i iii vv vi ivi i i MIR3#SINE/MIR 131 CATC--TGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTC 178 chr1qtel1M 255819 CAACTCCAGATATT---TGGCCCTATTATCC 255846 i i- i --- iii v i MIR3#SINE/MIR 179 CAGCTCT-GACATTCTATGATTCTATGATTC 208 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 45.60 CpG sites = 40, Kimura (unadjusted) = 46.80 Transitions / transversions = 2.50 (40/16) Gap_init rate = 0.05 (8 / 176), avg. gap size = 1.25 (10 / 8) 217 26.87 2.90 2.90 chr1qtel1M 256026 256094 (743906) C L3#LINE/CR1 (117) 3982 3914 m_b34s601i27 1184 chr1qtel1M 256026 CTTGACTATAACTCC--TGGGGAGGAACTGAATATTCTCAGAGGCAGCAC 256073 -- i v -- iv i i v v iiii?v v C L3#LINE/CR1 3982 CTTGA--ACACCTCCAGTGACGGGGAGCTCACTACCTCNCGAGGCAGCCC 3935 chr1qtel1M 256074 ATTCCAGTTTGGGAAAACTCT 256094 v v v i C L3#LINE/CR1 3934 ATTCCATTTTTGGACAGCTCT 3914 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.27 CpG sites = 9, Kimura (unadjusted) = 34.27 Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.04 (3 / 68), avg. gap size = 1.33 (4 / 3) 232 34.06 0.99 4.08 chr1qtel1M 256597 256697 (743303) L2c_3end#LINE/L2 373 470 (8) m_b34s601i28 1185 chr1qtel1M 256597 TAGACTGTATACTCTTTGAGAACAAGAACTATGTCTT-TTTGTCCTTGGA 256645 ivi i ii i i ii - ii i v L2c_3end#LINE 373 TAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTA 422 chr1qtel1M 256646 GCCCAGGAAAGCATCTTTTACTAACTGGGAAATTAATTCATGCTTTTTGA 256695 v ----v ii vvi vv v i viv i vv i v L2c_3end#LINE 423 TCCC----CAGCGCCTGGCACATAGTAGGCGCTCAATAAATGTTTGTTGA 468 chr1qtel1M 256696 AT 256697 L2c_3end#LINE 469 AT 470 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 41.05 CpG sites = 19, Kimura (unadjusted) = 46.92 Transitions / transversions = 1.36 (19/14) Gap_init rate = 0.05 (5 / 100), avg. gap size = 1.00 (5 / 5) 185 28.89 0.00 0.00 chr1qtel1M 259188 259232 (740768) C MIRb#SINE/MIR (14) 254 210 m_b34s601i29 1186 chr1qtel1M 259188 CATTTATTGAATGTTTACAGCTCGCCAAGCACTTTACTAAACCCT 259232 ii i viivi i v i i v C MIRb#SINE/MIR 254 CATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCT 210 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.68 CpG sites = 9, Kimura (unadjusted) = 38.45 Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 15 14.50 2.38 4.88 chr1qtel1M 259727 259768 (740232) (ATTC)n#Simple_repeat 1 41 (0) m_b34s252i10 1187 chr1qtel1M 259727 ATTCACTGAAT-ATTCATTCATTCATTTATTTACTTCCATTCA 259768 i v v - i i - - (ATTC)n#Simpl 1 ATTCATTCATTCATTCATTCATTCATTCATTCA-TT-CATTCA 41 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.07 (3 / 41), avg. gap size = 1.00 (3 / 3) 366 22.09 3.49 0.00 chr1qtel1M 261593 261678 (738322) C L2d_3end#LINE/L2 (7) 509 421 m_b35s601i1 1188 chr1qtel1M 261593 ACCAATCAATGAGCATTTATAAAGTGCCTACTATGTGCCGGGCACAGGGC 261642 i ii i vi i ivi v v C L2d_3end#LINE 509 ATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTGTGC 460 chr1qtel1M 261643 TAAGCAC--TAGGGAAC-AGAAAGAGGCAGAAGACATGG 261678 i i -- i - ? i?i i v C L2d_3end#LINE 459 TAGGCGCTGTGGGGAACGANAAAANAGTATAAGACATGG 421 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 24.71 CpG sites = 14, Kimura (unadjusted) = 28.12 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.02 (2 / 85), avg. gap size = 1.50 (3 / 2) 28 6.97 0.00 4.26 chr1qtel1M 264378 264426 (735574) (GGGGTG)n#Simple_repeat 1 47 (0) m_b35s252i1 1189 chr1qtel1M 264378 GGGGTGGGGGAGGGGCGTGGAGGTGGGGGAGGGGCGTGGGGGTGGGGGT 264426 v - i v - (GGGGTG)n#Sim 1 GGGGTGGGGGTGGGG-GTGGGGGTGGGGGTGGGG-GTGGGGGTGGGGGT 47 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.04 (2 / 48), avg. gap size = 1.00 (2 / 2) 12 4.30 8.33 0.00 chr1qtel1M 267907 267930 (732070) (ATC)n#Simple_repeat 1 26 (0) m_b35s252i2 1190 chr1qtel1M 267907 ATCATCATCATCATCCTC-TCA-CAT 267930 v - - (ATC)n#Simple 1 ATCATCATCATCATCATCATCATCAT 26 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.09 (2 / 23), avg. gap size = 1.00 (2 / 2) 292 26.26 0.00 1.25 chr1qtel1M 268835 268915 (731085) Charlie4a#DNA/hAT-Charlie 63 142 (366) m_b35s502i0 1191 chr1qtel1M 268835 AAAAAATCTTTACCATTGTTTTCCTTAACCTCTAGCTGGAACTCGGTATT 268884 - vi i v i vi i i i ii i Charlie4a#DNA 63 AAAAAAT-TACATCTTTATTTTCACTAACCTCTAACTGAAATTTAGCATT 111 chr1qtel1M 268885 TATCTCAGGTCTGAATGTAGGCAATAATCCA 268915 vii iv v i v Charlie4a#DNA 112 TCCTTCAATTATGAATGTAGGCAACAAACCA 142 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 33.58 CpG sites = 14, Kimura (unadjusted) = 33.58 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.01 (1 / 80), avg. gap size = 1.00 (1 / 1) 705 26.82 14.55 0.00 chr1qtel1M 269062 269281 (730719) C MIRc#SINE/MIR (1) 267 16 m_b35s601i2 1192 chr1qtel1M 269062 ATAATTACAATAGTTGGTCTTTATATAGTATTTTAAGGTTTGAAAAGC-- 269109 v i i?vi viiv i i i vi iv -- C MIRc#SINE/MIR 267 ATAATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCGC 218 chr1qtel1M 269110 --------ACAT------ATTTGATCCTCACAATGACTCTGGGAGATTGG 269145 -------- ------ ii i v i v C MIRc#SINE/MIR 217 TTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGG 168 chr1qtel1M 269146 ---------TACCATTATTTCCATTTTACAGTTGAGGAAAATGAAGCAAG 269186 --------- ii ii v v i vvi C MIRc#SINE/MIR 167 CAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCA 118 chr1qtel1M 269187 TAGAGGTTACGGGACTTGTCTAGGATCA-------AATAAATGTCTGAGG 269229 v v v i i i i ------- i i v v v C MIRc#SINE/MIR 117 GAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGC 68 chr1qtel1M 269230 TCACATTTGAATTCAGGTCTTTCTGACTCCAGGTCCAGCACTCTAGACAC 269279 iviv i i ii i i ii vvv C MIRc#SINE/MIR 67 CGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCAC 18 chr1qtel1M 269280 TG 269281 C MIRc#SINE/MIR 17 TG 16 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 32.90 CpG sites = 36, Kimura (unadjusted) = 34.33 Transitions / transversions = 1.57 (36/23) Gap_init rate = 0.02 (5 / 219), avg. gap size = 6.40 (32 / 5) 17 12.69 0.00 0.00 chr1qtel1M 269541 269566 (730434) (A)n#Simple_repeat 1 26 (0) m_b35s252i3 1193 chr1qtel1M 269541 AAAAAACAAAACAAAATAAAAAAAAA 269566 v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAA 26 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 14 17.52 5.13 0.00 chr1qtel1M 271819 271857 (728143) (ACATAC)n#Simple_repeat 1 41 (0) m_b35s252i4 1194 chr1qtel1M 271819 ACATGGATATACACACACACACACACAT--TCATACACATA 271857 iv i i i --v (ACATAC)n#Sim 1 ACATACACATACACATACACATACACATACACATACACATA 41 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.03 (1 / 38), avg. gap size = 2.00 (2 / 1) 18 12.16 0.00 0.00 chr1qtel1M 271829 271855 (728145) (AC)n#Simple_repeat 1 27 (0) m_b35s252i5 1195 chr1qtel1M 271829 ACACACACACACACACATTCATACACA 271855 iv i (AC)n#Simple_ 1 ACACACACACACACACACACACACACA 27 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 16 18.19 0.00 9.26 chr1qtel1M 272791 272849 (727151) (GACGA)n#Simple_repeat 1 54 (0) m_b35s252i6 1196 chr1qtel1M 272791 GACTGAGAGGAGACGAGTAAGGGACTGAGAGGAGACGGGTAAGGGACTGA 272840 - v - v i - v i - v i - (GACGA)n#Simp 1 GAC-GAGACGAGACGAG-ACGAGAC-GAGACGAGACGAG-ACGAGAC-GA 45 chr1qtel1M 272841 GAGGAGACG 272849 v (GACGA)n#Simp 46 GACGAGACG 54 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.09 (5 / 58), avg. gap size = 1.00 (5 / 5) 15 19.46 0.00 0.00 chr1qtel1M 272905 272939 (727061) (GACAAG)n#Simple_repeat 1 35 (0) m_b35s252i7 1197 chr1qtel1M 272905 GACAGTGCCAAGGGCAAGGACAAGGAAAAGCACAA 272939 iv v i v v (GACAAG)n#Sim 1 GACAAGGACAAGGACAAGGACAAGGACAAGGACAA 35 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 chr1qtel1M 274816 274833 (725167) (T)n#Simple_repeat 1 18 (0) m_b35s252i8 1198 chr1qtel1M 274816 TTTTTTTTTTTTTTTTTT 274833 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTT 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 12 17.53 3.12 0.00 chr1qtel1M 274968 274999 (725001) (ATAAGT)n#Simple_repeat 1 33 (0) m_b35s252i9 1199 chr1qtel1M 274968 ATATGTTAAAGTATAAAT-TAAATATAAGTATA 274999 v vv i - i (ATAAGT)n#Sim 1 ATAAGTATAAGTATAAGTATAAGTATAAGTATA 33 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 311 35.35 0.55 0.55 chr1qtel1M 275280 275461 (724539) C L1MD1_3end#LINE/L1 (356) 633 452 m_b35s551i0 1200 chr1qtel1M 275280 GCTCATTTCACTCAGCATCAGTTCGTGTAAGTCTCTCCAGGCCTTTCTGA 275329 iv v v iiv v ii iiv iiv vi v C L1MD1_3end#LI 633 GCTTTTTTCACTCAGCATAATTCTCTGGAGATTCATCCAGGTTGTTGCGT 584 chr1qtel1M 275330 A-ATCATCCTGTTGGTCATTTCTTACAGAACAATAATATTCCATAATATT 275378 i- viv- v ivi i iv vvv i i ii v C L1MD1_3end#LI 583 GTATCAATA-GTTCGTTCCTTTTTATTGCTGAGTAGTATTCCATGGTATG 535 chr1qtel1M 275379 CATATACAACAGTTTATTCAGCCATTCTCCAACTTATGGGCATCCACTCA 275428 v i v i i i v vii v v i iivviv C L1MD1_3end#LI 534 GATGTACCACAGTTTGTTTAACCATTCACCCGTTGAAGGACATCTGGGTT 485 chr1qtel1M 275429 GTTTCCAGTTTCTGGCCACTACAAAGAGACCTG 275461 i i i i v i v C L1MD1_3end#LI 484 GTTTCCAGTTTTTGGCTATTACGAATAAAGCTG 452 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 46.06 CpG sites = 35, Kimura (unadjusted) = 49.25 Transitions / transversions = 1.21 (35/29) Gap_init rate = 0.01 (2 / 181), avg. gap size = 1.00 (2 / 2) 287 32.58 0.76 0.00 chr1qtel1M 275348 275479 (724521) C L1MC5_3end#LINE/L1 (2129) 565 433 m_b35s551i1 1200 chr1qtel1M 275348 TTCTTACAGAACAATAATATTCCATAATATTCATATACAACAGTTTATTC 275397 i vvvv i i vi i vv i v i C L1MC5_3end#LI 565 TTTTTACAGCTGCATAGTACTCCATTGTGTGGATGTACCATAGTTTATTC 516 chr1qtel1M 275398 AGCCATTCTCCAACTTATGGGCATCCACTCAGTTTCCAGTTTCTGGCCAC 275447 i v i v i v i iiivviv i i v i i C L1MC5_3end#LI 515 AACCAGTCCCCTATTGATGGACATTTGGGTTGTTTCCAGTCTTTTGCTAT 466 chr1qtel1M 275448 TACAAAGAGACCTGAAGGGCATTGTCTT-TGCA 275479 v vv v iv v v i - C L1MC5_3end#LI 465 TACAAATAGTGCTGCAATGAATAGCCTTGTGCA 433 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 43.30 CpG sites = 21, Kimura (unadjusted) = 43.30 Transitions / transversions = 0.95 (21/22) Gap_init rate = 0.01 (1 / 131), avg. gap size = 1.00 (1 / 1) 347 28.43 0.00 0.00 chr1qtel1M 275360 275461 (724539) C L1ME2z_3end#LINE/L1 (638) 553 452 m_b35s551i2 1200 chr1qtel1M 275360 AATAATATTCCATAATATTCATATACAACAGTTTATTCAGCCATTCTCCA 275409 i i vi vv v i i v v C L1ME2z_3end#L 553 AGTAGTATTCCATTGTATGAATATACCACAGTTTGTTTATCCATTCTCCT 504 chr1qtel1M 275410 ACTTATGGGCATCCACTCAGTTTCCAGTTTCTGGCCACTACAAAGAGACC 275459 ii v i i iivv v i i i ii v i v C L1ME2z_3end#L 503 GTTGATGGACACCTGGGCTGTTTCCAGTTTTTGGCTATTATGAATAAAGC 454 chr1qtel1M 275460 TG 275461 C L1ME2z_3end#L 453 TG 452 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 36.69 CpG sites = 17, Kimura (unadjusted) = 36.69 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.00 (0 / 101), avg. gap size = 0.0 (0 / 0) 16 23.53 4.44 0.00 chr1qtel1M 275794 275838 (724162) (AT)n#Simple_repeat 1 47 (0) m_b35s252i10 1201 chr1qtel1M 275794 ATTTATTTACA-AGATATATGCATATATATATGCA-AGATATATATA 275838 v v i - v ii ii - v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATA 47 Matrix = Unknown Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.05 (2 / 44), avg. gap size = 1.00 (2 / 2) 46 29.18 2.52 0.62 chr1qtel1M 276370 276528 (723472) (AG)n#Simple_repeat 1 162 (0) m_b35s252i11 1202 chr1qtel1M 276370 AGAGAGATAGAGACAAATGAG-GGGGGTGGGA-AGGGAGGGAGGGAGATG 276417 v v i - - i i v i - i i i vi (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 49 chr1qtel1M 276418 GAGAGAGACAGAGAAAGGCAGACAGAGACAAAGATTGACAGAGACAGAGA 276467 v i iv v v i vv v v (AG)n#Simple_ 50 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 99 chr1qtel1M 276468 GATA-AGAGACACACACACATAGAGAGACACACACAGAGAGACAGAAACA 276516 v - v v v v v v v v v v v i v (AG)n#Simple_ 100 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 149 chr1qtel1M 276517 GAGAGAAAG-GAG 276528 i - (AG)n#Simple_ 150 GAGAGAGAGAGAG 162 Matrix = Unknown Transitions / transversions = 0.52 (13/25) Gap_init rate = 0.03 (5 / 158), avg. gap size = 1.00 (5 / 5) 237 29.63 1.85 0.00 chr1qtel1M 276529 276582 (723418) C MIRb#SINE/MIR (4) 264 210 m_b35s601i3 1203 chr1qtel1M 276529 ACAGAGTTGT-ATTTATCAAGCACTTGCTATGTGCAAAACACTACACTAA 276577 i i ii- ii i i v ii iii C MIRb#SINE/MIR 264 ATAGAGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAA 215 chr1qtel1M 276578 ATGCT 276582 ii C MIRb#SINE/MIR 214 GCGCT 210 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 36.35 CpG sites = 15, Kimura (unadjusted) = 43.62 Transitions / transversions = 15.00 (15/1) Gap_init rate = 0.02 (1 / 53), avg. gap size = 1.00 (1 / 1) 298 23.57 2.78 5.71 chr1qtel1M 276538 276609 (723391) C L2d2_3end#LINE/L2 (18) 537 468 m_b35s601i4 1204 chr1qtel1M 276538 TATTTATCAAGCACTTGCTATGTGCAAAACACTACACTAAATGC--TGAG 276585 ii i i i i ii iii iii -- i C L2d2_3end#LIN 537 TATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGTGGG 488 chr1qtel1M 276586 GGATACAAAGACTATAGAATAAGA 276609 ---- v C L2d2_3end#LIN 487 GGATACAAAGA----AGTATAAGA 468 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 26.53 CpG sites = 15, Kimura (unadjusted) = 31.18 Transitions / transversions = 15.00 (15/1) Gap_init rate = 0.07 (5 / 71), avg. gap size = 1.20 (6 / 5) 487 20.04 4.07 6.67 chr1qtel1M 276701 276823 (723177) C MIRc#SINE/MIR (122) 146 27 m_b35s601i5 1205 chr1qtel1M 276701 CATTTTACAGACAAGGAAACTGAGGC--AGACAGAGTGAAGTGACTTGTC 276748 ii -- v - v i C MIRc#SINE/MIR 146 CATTTTACAGATGAGGAAACTGAGGCTCAGAGAG-GTTAAGTGACTTGCC 98 chr1qtel1M 276749 CAGGGTCATCCAGGTAATAAGTAAGATCAGAATT-AAACTCGGGAAGACT 276797 i iv v i ii--- iii-ii ----i i C MIRc#SINE/MIR 97 CAAGGTCACACAGCTAGTAAGTGG---CAGAGCCGGGACTCG----AACC 55 chr1qtel1M 276798 CA--TCTTCCTGACTGCAGGCCCATTGC 276823 -- v i i v C MIRc#SINE/MIR 54 CAGGTCTTCCTGACTCCAAGTCCAGTGC 27 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 22.94 CpG sites = 17, Kimura (unadjusted) = 24.13 Transitions / transversions = 2.83 (17/6) Gap_init rate = 0.09 (11 / 122), avg. gap size = 1.18 (13 / 11) 13 11.19 0.00 6.45 chr1qtel1M 277416 277448 (722552) (ATTAA)n#Simple_repeat 1 31 (0) m_b35s252i12 1206 chr1qtel1M 277416 ATTATAATGAAATAAAAATTAAATTCAATTAAA 277448 - v -v v (ATTAA)n#Simp 1 ATTA-AATTAAAT-TAAATTAAATTAAATTAAA 31 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.06 (2 / 32), avg. gap size = 1.00 (2 / 2) 21 29.38 0.00 0.00 chr1qtel1M 278837 278894 (721106) (AA)n#Simple_repeat 1 58 (0) m_b35s252i14 1207 chr1qtel1M 278837 AAAAAAAAAAAAAAAAAAAAATGGACAGAATAGAAAAACACCAGAGAAAC 278886 vii v i v i v vv i i v (AA)n#Simple_ 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr1qtel1M 278887 AAAAGAAA 278894 i (AA)n#Simple_ 51 AAAAAAAA 58 Matrix = Unknown Transitions / transversions = 1.00 (7/7) Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0) 197 25.58 0.00 0.00 chr1qtel1M 279308 279350 (720650) MIRb#SINE/MIR 212 254 (14) m_b35s601i6 1208 chr1qtel1M 279308 CGTTTAACCCGGTGCCTGGCACAGAGTACGCATGGAATCAATG 279350 i i v i v v iivv v MIRb#SINE/MIR 212 CGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAAATG 254 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 28.22 CpG sites = 5, Kimura (unadjusted) = 31.45 Transitions / transversions = 0.83 (5/6) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 188 26.67 0.00 0.00 chr1qtel1M 279315 279359 (720641) L2c_3end#LINE/L2 425 469 (9) m_b35s601i7 1209 chr1qtel1M 279315 CCCGGTGCCTGGCACAGAGTACGCATGGAATCAATGTTGGTCGGA 279359 i i v v iivv v v i i L2c_3end#LINE 425 CCCAGCGCCTGGCACATAGTAGGCGCTCAATAAATGTTTGTTGAA 469 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 27.04 CpG sites = 6, Kimura (unadjusted) = 33.30 Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 12 20.36 0.00 0.00 chr1qtel1M 282571 282599 (717401) (CGCA)n#Simple_repeat 1 29 (0) m_b35s252i15 1210 chr1qtel1M 282571 CGCACGCACGCGCACGCGCACACACTCAC 282599 i i i i v (CGCA)n#Simpl 1 CGCACGCACGCACGCACGCACGCACGCAC 29 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 306 31.82 2.27 0.00 chr1qtel1M 283196 283283 (716717) C MIR#SINE/MIR (74) 188 99 m_b35s601i8 1211 chr1qtel1M 283196 TTTGACCCTTACGGCACCTCTA--AGGCAGCTGCTCTGCTTATGCCCATC 283243 i i i ii v i -- i v i v vv v i C MIR#SINE/MIR 188 TTTAATCCTCACAACAACCCTATGAGGTAGGTACTATTATTATCCCCATT 139 chr1qtel1M 283244 TTACAGATAGGGAGACTGAAGTCCGCAATGGCTAAATGAC 283283 ii i i iv iv iv i i i C MIR#SINE/MIR 138 TTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAAC 99 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 43.91 CpG sites = 19, Kimura (unadjusted) = 43.91 Transitions / transversions = 2.11 (19/9) Gap_init rate = 0.01 (1 / 87), avg. gap size = 2.00 (2 / 1) 15 26.14 2.00 0.00 chr1qtel1M 283452 283501 (716499) (AAAAC)n#Simple_repeat 1 51 (0) m_b35s252i16 1212 chr1qtel1M 283452 AAAAAAAAAAGAATCGAAAAAATACAGAA-AAAACAAAACTGAACAGAAC 283500 v vi v i v v i - vi i (AAAAC)n#Simp 1 AAAACAAAACAAAACAAAACAAAACAAAACAAAACAAAACAAAACAAAAC 50 chr1qtel1M 283501 A 283501 (AAAAC)n#Simp 51 A 51 Matrix = Unknown Transitions / transversions = 0.83 (5/6) Gap_init rate = 0.02 (1 / 49), avg. gap size = 1.00 (1 / 1) 387 25.16 1.64 8.77 chr1qtel1M 283587 283708 (716292) MIRc#SINE/MIR 2 115 (153) m_b35s601i9 1213 chr1qtel1M 283587 GGGGCAGCTAGGTGGCCCAGTAGATAGAGGACCGGTCCTGAAGTCAGGAG 283636 i i--- iv i v v i v i i i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr1qtel1M 283637 GAAATGAGTTCAAATCTGGTCTCAGACATTTAACACTTCCTAGC--TGGG 283684 vv i i i iv v ------- iv v -- v MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTC-------TGCCACTTACTAGCTGTGTG 91 chr1qtel1M 283685 ACTCTGGGCAAGTCACTTCACCCC 283708 ii v i MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 29.67 CpG sites = 16, Kimura (unadjusted) = 30.98 Transitions / transversions = 1.33 (16/12) Gap_init rate = 0.09 (11 / 121), avg. gap size = 1.09 (12 / 11) 213 35.03 6.33 2.44 chr1qtel1M 283843 284079 (715921) C L2#LINE/L2 (497) 2585 2340 m_b35s601i10 1214 chr1qtel1M 283843 AGAGAGGGAGCAGACAAGGGTCAGGGGCTAAGCATGCAGG---GAGTAAC 283889 i i v v i -- ivv i vv viv --- i C L2#LINE/L2 2585 AGAAAGAGAGGAGTCAAGGAT--GACTCCAAGGTTTTTGGCCTGAGCAAC 2538 chr1qtel1M 283890 CAGAA---TGGAGC-ATCTTCAACAACAAAGAGG--GCCTAAGAGAGG-G 283932 ii --- i-ii v i? vivi v i -- v iv i - C L2#LINE/L2 2537 TGGAAGGATGGAGTTGCCATTNACTGAGATGGGGAAGACTGCGGGAGGAG 2488 chr1qtel1M 283933 CGGAGTTTTGTGAAAAAGACAGGGAATTCC-TGTTGGACACAGCGCCTTT 283981 i - viv iii ivi i v- v iiviivv C L2#LINE/L2 2487 CAG-GTTTGAGGGGGAAGATCAGGAGTTCAGTTTTGGACATGTTAAGTTT 2439 chr1qtel1M 283982 TAGATGTCTGAGGAATATCCT-GTGGAGACATCAAATGTAAGTAGCTGGA 284030 v i ivvii i v- ii i -- i i i C L2#LINE/L2 2438 GAGATGCCTATTAGACATCCAAGTGGAGATGTCGA--GTAGGCAGTTGGA 2391 chr1qtel1M 284031 GGTGCAGGACCGGAAGTT--GGGGAGAGGTTAGGGCTAG-GAAAAAAACC 284077 vi i ii v i - -- iv i - v v ii C L2#LINE/L2 2390 TATACGAGTCTGGA-GTTCAGGGGAGAGGTCCGGGCTGGAGATATAAATT 2342 chr1qtel1M 284078 TG 284079 C L2#LINE/L2 2341 TG 2340 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 48.21 CpG sites = 50, Kimura (unadjusted) = 50.00 Transitions / transversions = 1.61 (50/31) Gap_init rate = 0.06 (15 / 236), avg. gap size = 1.40 (21 / 15) 228 28.19 5.10 5.10 chr1qtel1M 284830 284986 (715014) L1MB5_3end#LINE/L1 366 522 (399) m_b35s551i3 1215 chr1qtel1M 284830 TGACCCAGCCATGCCATGATTAGGGATGTACCTCAAAAGGCTCAAATAAA 284879 v v ivvi v i - iv ii -- L1MB5_3end#LI 366 TGACCCAGCAATTCCACTCCTAGGTATATACC-CAAAAGAATTGA--AAA 412 chr1qtel1M 284880 CAAGGA---AAGGACCCAAAGGCT----CAAAAATAGTTATAGTAGCAAC 284922 i v --- i---- ?i ---- vi iv i i - L1MB5_3end#LI 413 CAGGTATTCAAA----CAAANACTTGTACACGAATGTTCATAGCAGC-AC 457 chr1qtel1M 284923 TTTTTA-AATAGCAAAAAGTTGGAAACAAAGTGGGTGCTCATCAACTGGG 284971 v i - v v vviiii ii v iv L1MB5_3end#LI 458 TATTCACAATAGCCAAAAGGTGGAAACAACCCAAATGTCCATCAACGGAT 507 chr1qtel1M 284972 GAAGAGTTGTACAAA 284986 vi v iv L1MB5_3end#LI 508 GAATGGATAAACAAA 522 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 35.26 CpG sites = 23, Kimura (unadjusted) = 36.34 Transitions / transversions = 1.21 (23/19) Gap_init rate = 0.07 (11 / 156), avg. gap size = 1.45 (16 / 11) 478 25.67 0.76 5.56 chr1qtel1M 286271 286402 (713598) C MIRc#SINE/MIR (141) 127 2 m_b35s601i11 1216 chr1qtel1M 286271 CTGAGGC-AATTGGGATTAAATGACTTGTGCAGGGTCCCACAGCTAGGAA 286319 -v vv i i i iv i v v C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAA 78 chr1qtel1M 286320 GTGTTAGGTGTCTGAGACCACATTTGAACTCAGGTCCTCCTGACTTCAGG 286369 vi i- i - i ----- i i i i i C MIRc#SINE/MIR 77 GTGGCAGA-GCC-GGGAC-----TCGAACCCAGGTCTTCCTGACTCCAAG 35 chr1qtel1M 286370 GCTGGTGCTCTAACCATTGCATCACCTGGCTTC 286402 v ii vv i i viv i C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTGCACCACACTGCCTC 2 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 31.00 CpG sites = 20, Kimura (unadjusted) = 32.22 Transitions / transversions = 1.67 (20/12) Gap_init rate = 0.06 (8 / 131), avg. gap size = 1.00 (8 / 8) 219 33.07 0.00 5.49 chr1qtel1M 286971 287066 (712934) C MIR3#SINE/MIR (40) 168 78 m_b35s601i12 1217 chr1qtel1M 286971 TAGAGAGGAGCCTGACCGGCCTCCTTCTTTTATTGGTTTGGAAGCTCAGA 287020 vv v iv v ii i iv iv i vv i v i C MIR3#SINE/MIR 168 TAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGG 119 chr1qtel1M 287021 CAGAGAGAAAAGGAATAACTTGCTCAATTAAGATCAGCAGAGCCAG 287066 vv iiv i i i i ---- i - v ? C MIR3#SINE/MIR 118 CCCAGAGAGGTGAAGTGACTTGCCC----AAGGTCA-CACAGCNAG 78 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 45.10 CpG sites = 16, Kimura (unadjusted) = 45.10 Transitions / transversions = 1.14 (16/14) Gap_init rate = 0.05 (5 / 95), avg. gap size = 1.00 (5 / 5) 318 28.41 6.14 4.31 chr1qtel1M 287514 287627 (712373) L2d2_3end#LINE/L2 430 545 (10) m_b35s601i13 1218 chr1qtel1M 287514 CCCATCAGATGGGCGACTCCTTGCGGACGGGG----TGGTTTTTGCCTCT 287559 v ii v vvii v i i ---- vi v i i L2d2_3end#LIN 430 CCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACTTCT 479 chr1qtel1M 287560 TTGCATCCTC---AGTGCTGAGCGCAGCCTTGCATTTGCTACACAGTAGG 287606 i i --- i iv i --- -i - L2d2_3end#LIN 480 TTGTATCCCCCACAGCGCCTAGCACAG---TGC-CTTGC-ACACAGTAGG 524 chr1qtel1M 287607 CATTTAATAAATGCTGACTGA 287627 ii i ii vii L2d2_3end#LIN 525 CGCTCAATAAATATTTGTTGA 545 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 34.70 CpG sites = 22, Kimura (unadjusted) = 37.81 Transitions / transversions = 2.44 (22/9) Gap_init rate = 0.06 (7 / 113), avg. gap size = 1.71 (12 / 7) 306 23.32 6.59 1.04 chr1qtel1M 287712 287802 (712198) L2c_3end#LINE/L2 378 473 (5) m_b35s601i14 1219 chr1qtel1M 287712 TGGAAACTCCT-GAGAGCAGGGACGGAGTC--AT--GGCTTTGCATCTCC 287756 vi i - i v v -- --iv i i L2c_3end#LINE 378 TGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTATCCCC 427 chr1qtel1M 287757 AGGGCCCGGCACACAGTAGGCCCTTTAACAAACGCTT-CTGTATGGA 287802 v i i v - i i i i -i v i L2c_3end#LINE 428 AGCGCCTGGCACATAGTAGGCGC-TCAATAAATGTTTGTTGAATGAA 473 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 28.85 CpG sites = 14, Kimura (unadjusted) = 28.85 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.06 (5 / 90), avg. gap size = 1.40 (7 / 5) 185 30.78 0.00 1.92 chr1qtel1M 288045 288097 (711903) L2d_3end#LINE/L2 465 516 (0) m_b35s601i15 1219 chr1qtel1M 288045 GTACTCATACACACAGTAGGCAATTACTCTGTGCTTGCTGATTGGCTGAT 288094 i v -i i iv i v vvi i i ii L2d_3end#LINE 465 GTGCTGA-GCACATAGTAGGCGCTCAATAAATACTTGTTGATTGATTGAT 513 chr1qtel1M 288095 TAA 288097 i L2d_3end#LINE 514 TGA 516 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 38.48 CpG sites = 11, Kimura (unadjusted) = 41.96 Transitions / transversions = 2.20 (11/5) Gap_init rate = 0.02 (1 / 52), avg. gap size = 1.00 (1 / 1) 16 0.00 0.00 0.00 chr1qtel1M 289504 289520 (710480) (G)n#Simple_repeat 1 17 (0) m_b35s252i17 1220 chr1qtel1M 289504 GGGGGGGGGGGGGGGGG 289520 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGG 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 13 20.25 6.67 3.23 chr1qtel1M 290376 290435 (709565) (GGGGGA)n#Simple_repeat 1 62 (0) m_b35s252i18 1221 chr1qtel1M 290376 GGGGCAGGGCCAAGGTCTGGGTG-GGG-GAGGGGGACGGAGGGA-GAGG- 290421 v vv i vvv v - - - - - i - (GGGGGA)n#Sim 1 GGGGGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGGA-GG-GGGAGGGGGA 48 chr1qtel1M 290422 GGGGGAGGGGAAGG 290435 i (GGGGGA)n#Sim 49 GGGGGAGGGGGAGG 62 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.10 (6 / 59), avg. gap size = 1.00 (6 / 6) 598 25.76 6.60 3.45 chr1qtel1M 291849 292045 (707955) C MIRb#SINE/MIR (5) 263 61 m_b35s601i16 1222 chr1qtel1M 291849 TAGAACGAGCACTTATTAGGCGCCTTCTATGTGCTAGGCACCAGCCTAAG 291898 i v v i ii i v i iivv C MIRb#SINE/MIR 263 TAGAGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAG 214 chr1qtel1M 291899 TGCTTT-CA---AATGTTGCATTTGGTCTT---AAGAACCTGGTGAGGGA 291941 i - --- v i iv ii i --- v iv i v C MIRb#SINE/MIR 213 CGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTA 164 chr1qtel1M 291942 GGTGCCGTTAGCCCTATTTTACAGTGGAAGAAACTGGGA--CAGAGACG- 291988 iiii v i vv i i i-- v - C MIRb#SINE/MIR 163 GGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGT 114 chr1qtel1M 291989 -AAGGGACTTG-CCAGAATCAAAC-GCTAATGAGTCCAGGAGGCAGGGCC 292035 - vi - iii v - i i ------ i - C MIRb#SINE/MIR 113 TAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGT------GGCAGAG-C 71 chr1qtel1M 292036 CGGGAATCAA 292045 v i C MIRb#SINE/MIR 70 CGGGATTCGA 61 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 30.30 CpG sites = 32, Kimura (unadjusted) = 32.71 Transitions / transversions = 1.88 (32/17) Gap_init rate = 0.08 (15 / 196), avg. gap size = 1.33 (20 / 15) 228 24.98 6.17 1.18 chr1qtel1M 292248 292328 (707672) L2c_3end#LINE/L2 202 286 (192) m_b35s601i17 1223 chr1qtel1M 292248 CCCTCCAGCCTCAGCTCAGG-ACCACCCCCTCCAAGGAAGCCTTCCCAGC 292296 i v ? i-ii i i- v v L2c_3end#LINE 202 CCTTCAAGNCTCAGCTCAGATGTCACCTCCTCCG-GGAAGCCTTCCCTGA 250 chr1qtel1M 292297 CTCCCTCA----AATCTGGGCAGTCACTTCTGTGCT 292328 i iv ---- i i iivi v i L2c_3end#LINE 251 CCCCCCAAGNCTAGTCTAGGTGCCCTCCTCTGTGCT 286 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 30.30 CpG sites = 14, Kimura (unadjusted) = 32.26 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.04 (3 / 80), avg. gap size = 2.00 (6 / 3) 12 15.26 3.45 0.00 chr1qtel1M 292592 292620 (707380) (AAGGG)n#Simple_repeat 1 30 (0) m_b35s252i19 1224 chr1qtel1M 292592 AAGGGATGGGAAGGGTAAGG-AGGGACGGG 292620 v v i - v (AAGGG)n#Simp 1 AAGGGAAGGGAAGGGAAGGGAAGGGAAGGG 30 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1) 497 23.98 11.34 3.77 chr1qtel1M 294329 294575 (705425) C L1MA9_3end#LINE/L1 (728) 331 67 m_b35s551i4 1225 chr1qtel1M 294329 TCCAGACTGCTCTTCCATAAGGGTTATACTGACTCACCATTC--ACCAAC 294376 v i - v i i ii i i - -- C L1MA9_3end#LI 331 TCCATACTGTT-TTCCATAATGGCTGTACCAATTTAC-ATTCCCACCAAC 284 chr1qtel1M 294377 AATGCATCAGGGTACCCGTCTTTCCACTAACTCTCCTGGGTCAACCCTTC 294426 i i iv v v i i -- ii ---- i v v C L1MA9_3end#LI 283 AGTGTACAAGGGTTCCCTTTTCTCCAC--ATCCTC----GCCAACACTTG 240 chr1qtel1M 294427 TCATCTTTTGTCATCTTTGCCAACTCGCTAT-----------GGAGCTAA 294465 i - i vi - v i -----------v v i C L1MA9_3end#LI 239 TTATCTTTTGTC-TTTTTGATAA-TAGCCATCCTAACAGGTGTGAGGTGA 192 chr1qtel1M 294466 AACCTCGGGGCTGGTCTGATTTGCATTTCGCTTATAATCAGTGATTTGGG 294515 v i ivv iv v i v v i i v v i C L1MA9_3end#LI 191 TATCTCATTGTGGTTTTGATTTGCATTTCCCTGATGATTAGTGATGTTGA 142 chr1qtel1M 294516 GCA----TTCATA-------TGGTC-TTTG--TGTC-TCTTTGGAGAAGC 294550 ---- ------- i - -- - ii C L1MA9_3end#LI 141 GCACCTTTTCATATACCTGTTGGCCATTTGTATGTCTTCTTTGGAGAAAT 92 chr1qtel1M 294551 GTTTCTTCATATCTTTTGATCATTT 294575 i v vi i vi C L1MA9_3end#LI 91 GTCTATTCAGGTCCTTTGCCCATTT 67 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 29.62 CpG sites = 34, Kimura (unadjusted) = 29.62 Transitions / transversions = 1.48 (34/23) Gap_init rate = 0.07 (17 / 246), avg. gap size = 2.24 (38 / 17) 222 23.16 11.58 0.00 chr1qtel1M 295367 295461 (704539) C L3#LINE/CR1 (1757) 2342 2237 m_b35s601i18 1226 chr1qtel1M 295367 TCCTTTCTCTCCCAATAAAGCT---AAAAACCAAAACTGTGT---CCTT- 295409 iiv v i v --- i vv?vi v --- - C L3#LINE/CR1 2342 TCCTTCTGCTCCGAACATAGCTTTGAAAAGCCTTNTTTTTGTTGTCCTTA 2293 chr1qtel1M 295410 -CACTTCCCTTT-CCAGCCTCAGCTCATTC--AGCTTTAGCGCTCCGGAC 295455 - i iii - v --i vi v C L3#LINE/CR1 2292 GCATTTTTTTTTGCAAGCCTCAGCTCATTCTGGGCTTTAGCCTTCCTGAC 2243 chr1qtel1M 295456 ACTTTT 295461 v C L3#LINE/CR1 2242 ACTATT 2237 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 28.29 CpG sites = 11, Kimura (unadjusted) = 28.29 Transitions / transversions = 1.00 (11/11) Gap_init rate = 0.06 (6 / 94), avg. gap size = 1.83 (11 / 6) 383 30.08 4.93 3.08 chr1qtel1M 295509 295731 (704269) C MIRb#SINE/MIR (9) 259 33 m_b35s601i19 1227 chr1qtel1M 295509 GCCAGCATTGATGAAGCGCCTATCCAGTGCCTGGTACAACGCAAAGCCCT 295558 i v v vi i iivv v i vii v v C MIRb#SINE/MIR 259 GCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCT 210 chr1qtel1M 295559 TTACA-GCAATTTTCCCATTTTAATAATCCCTCCTCCCCTGC-AGGT-GC 295605 - - v i - vv v vv vv - - v C MIRb#SINE/MIR 209 TTACATGC-ATTATCTCA-TTTAATCCTCACAACAACCCTGCGAGGTAGG 162 chr1qtel1M 295606 TGTTGCT-TCCCAACTTGACACTTGGGGAAACCGAGG--CAGGCAGATTT 295652 i ii - v i v vv i i -- iv i- C MIRb#SINE/MIR 161 TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGG-TT 113 chr1qtel1M 295653 AAGCGGCTTACTCGGGGCCACACAG--AGCTAGCGCCTGAGGCTAACAGG 295700 iii i i ii i -- iv i v v - --- i C MIRb#SINE/MIR 112 AAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGA-GC---CGGG 67 chr1qtel1M 295701 AACAGAA--CAGA-CCACCAGGCTTCAAGGCCCG 295731 viv -- i- iii v i i i C MIRb#SINE/MIR 66 ATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCG 33 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 38.56 CpG sites = 36, Kimura (unadjusted) = 39.33 Transitions / transversions = 1.24 (36/29) Gap_init rate = 0.07 (15 / 222), avg. gap size = 1.20 (18 / 15) 328 32.82 6.10 4.15 chr1qtel1M 296603 296815 (703185) L2b_3end#LINE/L2 249 465 (1) m_b35s601i20 1228 chr1qtel1M 296603 CCCCCAGGCCAG---AGTCTCCCTT-TCAGAATCGCACCCTGCCTCACTT 296648 i --- v v i- v iii v - v i ii ii L2b_3end#LINE 249 CCCCCAGGCCGGGTCAGGCGCCCTCCTCTGGGCCCC-CCCAGTCCTACCC 297 chr1qtel1M 296649 GGCT-CTGTGGAGATTTTTTGTTCTCATCAGCATTCACG-CTGCTTCCCC 296696 v i- v i------ i ?v ii v ?v v i - ii L2b_3end#LINE 298 TGCCACTCTGGG------TTATNATTGTCTGNTTACATGTCTGTCTCCCC 341 chr1qtel1M 296697 TCAATAGAATCTAAGTTCCTTAGGATCTGAGGA--GGTTTTGCTTTGGTC 296744 - v v v i i v ii iv v - -- ?v i ii v L2b_3end#LINE 342 -CACTAGACTGTGAGCTCCGTGAGGGCAG-GGACCGNGTCTGTCTTGTTC 389 chr1qtel1M 296745 TCTAC---ATCCT-AGTAATTAGCCCCAA-CCTGGAACACAGCAAGCAAC 296789 v ii --- i- iivi v vi?- v i i ivi L2b_3end#LINE 390 ACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCT 439 chr1qtel1M 296790 TAATAAATGCTTGTTGAATGAATGGA 296815 i i ii i L2b_3end#LINE 440 CAGTAAATATTTGTTGAATGAATGAA 465 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 42.55 CpG sites = 42, Kimura (unadjusted) = 46.56 Transitions / transversions = 1.68 (42/25) Gap_init rate = 0.08 (17 / 212), avg. gap size = 1.29 (22 / 17) 359 30.46 6.20 0.74 chr1qtel1M 296687 296815 (703185) L2a_3end#LINE/L2 381 516 (1) m_b35s601i21 1228 chr1qtel1M 296687 CTGCTTCCCCTCAATAGAATCTAAGTTCCTTAGGATCTGAGGAGGTTT-- 296734 ii i v v i v ii iv v - vv -- L2a_3end#LINE 381 CTGTCTCCCCCCACTAGAATGTAAGCTCCATGAGGGCAG-GGACTTTTGT 429 chr1qtel1M 296735 -TGCTTTGGTCTCTAC---ATCCT-AGTAATTAGCCCCA-ACCTGGAACA 296778 - i v v i --- i- iivi vv vi-i v L2a_3end#LINE 430 CTGTTTTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACA 479 chr1qtel1M 296779 CAGCAAGCAACTAATAAATGCTTGTTGAATGAATGGA 296815 i i i ivii ii i L2a_3end#LINE 480 TAGTAGGCGCTCAATAAATATTTGTTGAATGAATGAA 516 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 37.72 CpG sites = 24, Kimura (unadjusted) = 40.56 Transitions / transversions = 1.60 (24/15) Gap_init rate = 0.05 (6 / 128), avg. gap size = 1.50 (9 / 6) 287 31.79 7.80 2.55 chr1qtel1M 297167 297576 (702424) L1P1_orf2#LINE/L1 2857 3287 (7) m_b36s551i0 1229 chr1qtel1M 297167 CTTACACC--ATGTCAAAATGAACTCAAAAGTGGATTCAA-ACCTGAATA 297213 -- iiv v i i - v - i i ii L1P1_orf2#LIN 2857 CTTACACCTTATACAAAAATTAATTCAAGA-TGGATTAAAGACTTAAACG 2905 chr1qtel1M 297214 TCAAAAATCATACCATAAGAGC-----AAGAGA---TAGT--TTACCTAT 297253 i i vv v v i i ----- i --- v--? vv L1P1_orf2#LIN 2906 TTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCANTACCATT 2955 chr1qtel1M 297254 CAGATCTTTGG-AGAAGAGAGGGATTTATGGCCAAAGAACTAGAG--AAT 297300 iv v v - vii vi iv i v i iv i i i-- L1P1_orf2#LIN 2956 CAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAAT 3005 chr1qtel1M 297301 ATTATGAAATGC-AAAATGGACAACTCTGATTACATTAAATTAAAAAGTT 297349 ivi vv v - v v vv ivv i i i L1P1_orf2#LIN 3006 GGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCT 3055 chr1qtel1M 297350 TTTGCACAAACAAAACCAATGCACC-CAAGATTAGAAAGGAAAC--AAAG 297396 i i- vv i-i -iv v ii v v -- v L1P1_orf2#LIN 3056 TCTGCACAG-CAAAAGAAAC-TACCATCAGAGTGAACAGGCAACCTACAG 3103 chr1qtel1M 297397 C-TAGGAAAAAATATTTTATAGCCAATGTTTCTGATAAAGGCCTCATTTC 297445 v- i i - iii i v iviv i v v v L1P1_orf2#LIN 3104 AATGGGAGAAAAT-TTTCGCAACCTACTCATCTGACAAAGGGCTAATATC 3152 chr1qtel1M 297446 TAAAATATATAAAGAACTCAGTCAAATTTATAAGAATA---CAAGT--CC 297490 i i v i v iv i v --- ii-- L1P1_orf2#LIN 3153 CAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACC 3202 chr1qtel1M 297491 TTCCCAAAATGATAAACGGTTGAAAGATAGGAAG------TTTTCAGATA 297534 iivi ----- ii vi i i v v------ i i vi L1P1_orf2#LIN 3203 CCATCAAAA-----AGTGGGCGAAGGACATGAACAGACACTTCTCAAAAG 3247 chr1qtel1M 297535 AAGACATTAAAGTTATCTATAGTTGCATGAAAAAAAATGCTC 297576 v v ivii v v ivii -- L1P1_orf2#LIN 3248 AAGACATTTATGCAGCCAAAAAACACATGAA--AAAATGCTC 3287 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 41.17 CpG sites = 70, Kimura (unadjusted) = 42.59 Transitions / transversions = 1.23 (70/57) Gap_init rate = 0.06 (25 / 409), avg. gap size = 1.72 (43 / 25) 313 28.55 5.93 4.00 chr1qtel1M 297313 297582 (702418) L1M3_orf2#LINE/L1 3013 3287 (1) m_b36s551i1 1229 chr1qtel1M 297313 AAAATGGACAACTCTGATTACATTAAATTAAAAAGTTTTTGCACA--AAC 297360 i v vv i i i i i -- v L1M3_orf2#LIN 3013 AAAATAGACAAGTGGGACTACATCAAACTAAAAAGCTTCTGCACAGCAAA 3062 chr1qtel1M 297361 AAAACCAATGCACCCAAGATTAGAAAGGAAAC-----AAAGCTAGGAAAA 297405 ii v vv --- v ii v -----i -- i i L1M3_orf2#LIN 3063 GGAAACAATCAAC---AGAGTGAAAAGGCAACCTACGGAA--TGGGAGAA 3107 chr1qtel1M 297406 AATATTTTATAGCCAATGTTTCTGATAAAGGCCTCATTTCTAAAATATAT 297455 -ii iv v i v i vi v v i L1M3_orf2#LIN 3108 AATATTT-GCAAACCATATATCTGATAAGGGGTTAATATCCAAAATATAT 3156 chr1qtel1M 297456 AAAGAACTCAGTCAAATTTAT---AAGAATACAAGT--CCT--TCCCAAA 297498 i ?vv v iv --- i v i -- i-- i?v L1M3_orf2#LIN 3157 AAGGAACTCNTACAACTCAATAGCAAAAAAACAAATAACCCGATTNAAAA 3206 chr1qtel1M 297499 ATGATAAACGG--TTGAAAGATAGGAAGTTTTCAGATAAAGACATTAAAG 297546 ivv v --i --- iv v i vi vi vv i L1M3_orf2#LIN 3207 ATGGGCAAAGGACCTGA---ATAGACATTTCTCCAAAGAAGACATACAAA 3253 chr1qtel1M 297547 TTATCTATAGTTGCATGAAAAAAAATGCTCTAAATC 297582 vii v i v ii -- i v v L1M3_orf2#LIN 3254 TGGCCAACAGGTATATG--AAAAGATGCTCAACATC 3287 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 36.29 CpG sites = 39, Kimura (unadjusted) = 36.91 Transitions / transversions = 1.11 (39/35) Gap_init rate = 0.06 (17 / 269), avg. gap size = 1.59 (27 / 17) 928 31.35 6.42 1.69 chr1qtel1M 297441 298063 (701937) L1ME4c_3end#LINE/L1 4 655 (175) m_b36s551i2 1229 chr1qtel1M 297441 ATTTCTAAAATATATAAAGAACTCAGTCAAATTTATAAGAATA----CAA 297486 v ?v ? i v v v ---- L1ME4c_3end#L 4 ATATCTNTANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAA 53 chr1qtel1M 297487 GTCCTTCCCAAAATGATAAACGGTTGAAAGATAGGAA------GTTTTCA 297530 v --- v - i vii i i v ------i iv L1ME4c_3end#L 54 GACC---CCAATA-GATAAATGGGCAAAGGACATGAACAGACAATTCACA 99 chr1qtel1M 297531 GATAAAGACATTAAAGTTATCTATAGTTGCATGAAAAAAAATGCTCTAAA 297580 ? vi i v vv ? vi vv i ivii i -- i v vv L1ME4c_3end#L 100 NAAGAGGAAATACAANTAGTAAACAAACACATGGAAAAA--TGTTCAACC 147 chr1qtel1M 297581 TCTCTATTGATTAGAAAAATGCAAATTAAAACTATGCTGAGGTCCCACCT 297630 v v i i i i i v iiv i v ii L1ME4c_3end#L 148 TCGCTAGTAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTT 197 chr1qtel1M 297631 CTCATTTTTCAGATTGCTTAAGATGACAGGAAAAGATAATGATAAATGTT 297680 iv iii v i i iviv i vvv ii vv iviv i L1ME4c_3end#L 198 TACGCCTATTAAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGCT 247 chr1qtel1M 297681 GGAGGGGATGTGAGAAAACTGGGACACTAAT-----GTTTGTGG-ACTAT 297724 v i ? i ivi v ? v ----- i v - ? i L1ME4c_3end#L 248 GGCGAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGT 297 chr1qtel1M 297725 CAAATGATCCAACCATTCTGGAGAGCAATTTGCAACTATGGCCAAAGGGC 297774 v v i v v i i vv v i vviv i L1ME4c_3end#L 298 AAATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGC 347 chr1qtel1M 297775 TATCAAACTGTGCATACCCTTTGATCCAGCAACATCTCTACTGGGTCTGT 297824 i v v v i i ivi v v vv v L1ME4c_3end#L 348 CATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTT 397 chr1qtel1M 297825 GTCCCAAAGAAATCAT--AAAAGAGGGAAA----------TACAAAAATG 297862 i i i v -- i ----------i i i L1ME4c_3end#L 398 ATCCTAAGGAAATAATTCAAAAGAAGGAAAAAGCTATATGCACGAAGATG 447 chr1qtel1M 297863 TCTGTATCAGCTCTCTTTGTAGTGGCAAAGAATTGGAAAATGAATAGATG 297912 iii vv vi v i i i i i vvivv i L1ME4c_3end#L 448 TTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATG 497 chr1qtel1M 297913 CCCACCAACTGGGGAATGACTAAG----TTATGGCATATGAAAGTAATGG 297958 i v iv ii ---- i i v? vvii L1ME4c_3end#L 498 TCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGG 547 chr1qtel1M 297959 AATATTATTGTTCTATAAAAAA----GATTGAACAGGTTGGATTTTAGAA 298004 vvvv i v ----i iviv ii i--- v v L1ME4c_3end#L 548 AATATTATGCAGCCATTAAAAATGATAATTATGAAGACTA---TGTAGCA 594 chr1qtel1M 298005 ATGTCTGGAAAGATTACATGAACTGATG----GTGAGCAAAACAAAAAAA 298050 ii-- ivv vi vv i ---- iv i i v v L1ME4c_3end#L 595 ACA--TGGAAAATGTTTATGATATAATGTTAAGTGAAAAAAGCAGAATAC 642 chr1qtel1M 298051 AAAATTGTACATA 298063 i? L1ME4c_3end#L 643 AAAATTGTATNTA 655 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 40.47 CpG sites = 100, Kimura (unadjusted) = 42.21 Transitions / transversions = 1.09 (100/92) Gap_init rate = 0.03 (20 / 622), avg. gap size = 2.55 (51 / 20) 12 10.03 0.00 0.00 chr1qtel1M 299598 299619 (700381) (ATGT)n#Simple_repeat 1 22 (0) m_b36s252i0 1230 chr1qtel1M 299598 ATGTATGTATGTGTGCATGTAT 299619 i i (ATGT)n#Simpl 1 ATGTATGTATGTATGTATGTAT 22 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 220 24.40 5.56 4.40 chr1qtel1M 301700 301789 (698211) C MIRb#SINE/MIR (68) 200 110 m_b36s601i2 1231 chr1qtel1M 301700 TTTTCACATTCACTCTT----ACAACCTTCCAGGGTAGGTTTTCAGCTAT 301745 v v i v i ---- i v ii v --ii C MIRb#SINE/MIR 200 TTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATT--ATTAT 153 chr1qtel1M 301746 TAC-ATTTTCCAAATGAGAAAAATGAGGGCTCAGCTTAAGTTAAG 301789 iv - v i i v - v-v i C MIRb#SINE/MIR 152 CCCCATTTTACAGATGAGGAAACTGA-GGCTCAGA-GAGGTTAAG 110 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 28.25 CpG sites = 11, Kimura (unadjusted) = 29.89 Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.07 (6 / 89), avg. gap size = 1.50 (9 / 6) 425 27.15 14.94 0.50 chr1qtel1M 301799 301972 (698028) MIRc#SINE/MIR 4 202 (66) m_b36s601i3 1232 chr1qtel1M 301799 GGTGGTGGGTCATAATGGGCAAAGTGCCAGCTTTGGAGGCAGGAAGGTCT 301848 ii v viii i iv i ii ii vi v ii MIRc#SINE/MIR 4 GGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCT 53 chr1qtel1M 301849 GGGTTC----------------AC--ATTATCTGTGTGTCTGTGGGCCAG 301880 ---------------- -- i v v iv v MIRc#SINE/MIR 54 GGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAG 103 chr1qtel1M 301881 TAACTTCACCTTTTCTCAGCTGTAACTTCCTCATTTGTAA---GGTGATA 301927 v v - i v ivi ii i --- v MIRc#SINE/MIR 104 TCACTTAACC-TCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATA 152 chr1qtel1M 301928 AT--TAGCAGC---GTCTACTTCCCAGGGCTGTTGAGAGGAGGAGATGAG 301972 -- v v --- i i v i v vv i MIRc#SINE/MIR 153 ATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAG 202 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 34.48 CpG sites = 27, Kimura (unadjusted) = 34.48 Transitions / transversions = 1.35 (27/20) Gap_init rate = 0.03 (6 / 173), avg. gap size = 4.50 (27 / 6) 200 24.26 17.70 1.53 chr1qtel1M 301986 302098 (697902) C MIR1_Amn#SINE/MIR (66) 164 34 m_b36s601i4 1233 chr1qtel1M 301986 TTAGTAGTCAGTATTATTATTTTACAGTATGAG-----TGATGTCTATTG 302030 i - v ivii - ----- v i?i vv C MIR1_Amn#SINE 164 TCAGTA-TCATTATCCCCATTTTACAG-ATGAGGAAACTGAGGCNCAGAG 117 chr1qtel1M 302031 TGGTGA----------CCA---TCATC--ACTGACCAGTCCCAAAGCTGG 302065 v ? ---------- --- i?--i ? i ? vv i i C MIR1_Amn#SINE 116 AGGTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNAGTGGCAGAGCCGG 67 chr1qtel1M 302066 GACCACAACCAAGGTCTTCTGATTCCCAAGCCA 302098 ?i?v v i i v iv C MIR1_Amn#SINE 66 GANTNGAACCCAGGTCTCCCGAGTCCCAGTCCA 34 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 29.60 CpG sites = 15, Kimura (unadjusted) = 32.42 Transitions / transversions = 1.25 (15/12) Gap_init rate = 0.05 (6 / 112), avg. gap size = 3.67 (22 / 6) 256 20.06 0.00 5.45 chr1qtel1M 302057 302114 (697886) C MIR3#SINE/MIR (138) 70 16 m_b36s601i5 1233 chr1qtel1M 302057 CAAAGCTGGGACCACAACCAAGGTCTTCTGATTCCCAAGCCATGCAGGCC 302106 i i i v v i i iv i ---i C MIR3#SINE/MIR 70 CAGAGCCGGGACTAGAACCCAGGTCTCCTGACTCCCAGTCCGTGC---TC 24 chr1qtel1M 302107 TCTCTGCT 302114 C MIR3#SINE/MIR 23 TCTCTGCT 16 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 19.31 CpG sites = 8, Kimura (unadjusted) = 24.08 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.05 (3 / 57), avg. gap size = 1.00 (3 / 3) 554 29.37 0.00 0.00 chr1qtel1M 302262 302404 (697596) MIR#SINE/MIR 102 244 (18) m_b36s601i6 1234 chr1qtel1M 302262 ACTTCATTGCTGCCTACCTCAGTTTCCCCAATTATAAACTGGAGAACATA 302311 v iiv viv i i vi i v i vv MIR#SINE/MIR 102 ACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATA 151 chr1qtel1M 302312 ATAGCATCTACCTCACAGGGCTGTTGTGAGGATCAAATGACATATTGTTT 302361 i i i i i vv v iiv MIR#SINE/MIR 152 ATAGTACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATACAT 201 chr1qtel1M 302362 GTAAAGCACTCAGCATGGGGCCTGGATTATCTTGGGCACTTAA 302404 i i v ii v vvi vv ii i i MIR#SINE/MIR 202 GTAAAGCGCTTAGAACAGTGCCTGGCACATAGTAAGCGCTCAA 244 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 35.92 CpG sites = 24, Kimura (unadjusted) = 38.20 Transitions / transversions = 1.33 (24/18) Gap_init rate = 0.00 (0 / 142), avg. gap size = 0.0 (0 / 0) 568 24.21 0.00 2.42 chr1qtel1M 302278 302404 (697596) MIRb#SINE/MIR 125 248 (20) m_b36s601i7 1234 chr1qtel1M 302278 CCTCAGTTTCCCCAATTATAAACTGGAGAACATAATAGCATCTACCTCAC 302327 i vi i v i --- ii i i MIRb#SINE/MIR 125 CCTCAGTTTCCTCATCTGTAAAATGGGGA---TAATAATACCTACCTCGC 171 chr1qtel1M 302328 AGGGCTGTTGTGAGGATCAAATGACATATTGTTTGTAAAGCACTCAGCAT 302377 i i v v iv i i i MIRb#SINE/MIR 172 AGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGCAC 221 chr1qtel1M 302378 GGGGCCTGGATTATCTTGGGCACTTAA 302404 i v vvi vv ii i i MIRb#SINE/MIR 222 AGTGCCTGGCACATAGTAAGCGCTCAA 248 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 26.69 CpG sites = 20, Kimura (unadjusted) = 30.21 Transitions / transversions = 2.00 (20/10) Gap_init rate = 0.02 (3 / 126), avg. gap size = 1.00 (3 / 3) 57 0.00 0.00 0.00 chr1qtel1M 302707 302755 (697245) (TG)n#Simple_repeat 1 49 (0) c_b36s251i0 1235 chr1qtel1M 302707 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 302755 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 49 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 327 33.73 11.94 1.84 chr1qtel1M 303167 303610 (696390) L1ME5_3end#LINE/L1 40 527 (414) m_b36s551i3 1236 chr1qtel1M 303167 AATAAAAAGAGAGGAGGAGCAAATGAGAAATCATCAAAAGATACAAACTG 303216 v vi ? ivvv vv i viv i ii v L1ME5_3end#LI 40 AAGAAAAAGACGGNAACCCCAATAGAAAAATGGGCAAAGGATATGAACAG 89 chr1qtel1M 303217 GAAATTT-TAGATAAAATAATCT----------TAAGTCATGTAAAAAAA 303255 v -i vi iiv i i----------i - i i i i L1ME5_3end#LI 90 GCAATTTACAGAAGAGGAAACCCGAAAGGCTAACAAG-CATATGAAGAGA 138 chr1qtel1M 303256 ATGCTCTAAATTACTACTGACTTAAGAAATGCAAATTAAAACAATTCTGA 303305 - v v i i v i iivi ivv L1ME5_3end#LI 139 -TGCTCAAACTCATTAGTAATCAGAGAAATGCAAATTAAAACAACAATGA 187 chr1qtel1M 303306 -ACAACGCAACACACCTGTCAGATCGGCTAAAG--AGACGTACAA---GG 303349 - i v i vvi i i ii v i-- ----- --- L1ME5_3end#LI 188 GATATCACTTTACACCTATTAGACTGGCAAAAATTAGA-----AAGCTGG 232 chr1qtel1M 303350 AAAATGACAAATTTTGGAGGGGATCCAGGAGAATTAAAACACTAGTG--C 303397 v v i v v i vii ii? vii v vi -- L1ME5_3end#LI 233 ATAATGCCAAGTGTTGGCGAGGATGTGGGGANATAGGAACCCTCATGCAC 282 chr1qtel1M 303398 TGCTG----------AGCC-----CA-TCATTCTGGAGAGCCATTTGG-- 303429 ---------- v ----- -i v i -- L1ME5_3end#LI 283 TGCTGGTGGGAGTGTAGACTGGTGCAGCCATTCTGGAGAGCAATCTGGCA 332 chr1qtel1M 303430 ------AACCATGCTCAAGACCACACATATCCTGTGACCAAGCAA---CA 303470 ------ ii -iv i vvi i i i v --- i L1ME5_3end#LI 333 GTACTTAGTCA-AATTAAGTATACGCATACCCTATGACCCAGCAATTCCG 381 chr1qtel1M 303471 CTACTAGGTCTGCATGCCGAAGAGAT------AAAAAACCA-AAAATGAA 303513 v i v ii v i i ------ v iiv - iiv v L1ME5_3end#LI 382 CTCCTGGGTATATATCCCAAAGAAATTCTCACACAGGTCCATAAGGGGAC 431 chr1qtel1M 303514 AAGGACAAAAATACTGGTGGCGACTCTTTTAGTGGTGGCAAAGAACTGGA 303563 v v i ii ii vi v ii vi v v iii ii L1ME5_3end#LI 432 ATGTACGAGGATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGA 481 chr1qtel1M 303564 ACTCGAAGGGACGTCCATCAATTGGGGGAATGGCTGAACAAGCTGTG 303610 ivivivvv ii - i i i v iiii iv L1ME5_3end#LI 482 GGCAACCTGGGTGTCCATC-ACTGGGAGAGTGGATAGGTAAAATGTG 527 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 44.50 CpG sites = 89, Kimura (unadjusted) = 47.17 Transitions / transversions = 1.53 (89/58) Gap_init rate = 0.05 (23 / 443), avg. gap size = 2.70 (62 / 23) 256 32.14 10.89 3.90 chr1qtel1M 303236 303740 (696260) L1MC5_3end#LINE/L1 120 658 (2036) m_b36s551i4 1236 chr1qtel1M 303236 TCTTAAGTCATGTAAAAAAAATGCTCTAAATTACTACTGACTTAAGAAAT 303285 ?- i i i - v vv ii vv i ivvi L1MC5_3end#LI 120 TCTTAAN-CATATGAAAAGA-TGCTCAACCTCGCTCATAATAAGAGAAAT 167 chr1qtel1M 303286 GCAAATTAAAACAATTCTGA-ACAACGCAACACACCTGTCAGATCGGCTA 303334 v iv - i v iivv v i i v L1MC5_3end#LI 168 GCAAATTAAAACTACACTGAGATACCATTTCTCACCTATCAGATTGGCAA 217 chr1qtel1M 303335 AAGAGACGTACAAGGAAAATGACAAATT---TTGGAGGGGATCCAGGAGA 303381 --- ivi v vvvi ii v i --- v i v vii ii L1MC5_3end#LI 218 AA---ATCCAAAAGTTTGACAACATACTCTGTTGGCGAGGCTGTGGGGAA 264 chr1qtel1M 303382 ATTAAAACACT-------AGTGCTGCTGAGC-------------CCATCA 303411 i-- ii ------- v v i v------------- v i v L1MC5_3end#LI 265 AC--AGGCACTCTCATACATTGCTGGTGGGAATGCAAAATGGTACAACCC 312 chr1qtel1M 303412 TTCTGGAGAGCCATTTGGAACCATGCT--CAAGACCACACAT------AT 303453 i v i vv v vi - -- i ii i ------ i L1MC5_3end#LI 313 CTATGGAGGGGAATTTGGCAATAT-CTAGCAAAATTACATATGCATTTAC 361 chr1qtel1M 303454 CCTGTGACCAAGCAA---CACTACTAGGTCTGCATGCCGAAGAGATAAAA 303500 v v --- v vv vi v i v i vvi L1MC5_3end#LI 362 CCTTTGACCCAGCAATCCCACTTCTAGGAATCTATCCCAAAGATACACTG 411 chr1qtel1M 303501 AACCAAAAAT--GAAAAGG-------ACAAAAATACTGGTGGCGACTCTT 303541 i-- -- i------- iiv i vi v ii v v L1MC5_3end#LI 412 G--CAAAAATACGAAAAGACGTATGCACAAGGCTATTCATTGCAGCACTA 459 chr1qtel1M 303542 TTAGTGGTGGCAAAGAACTGGAA----CTCGAAGGGACGTCCATCAATTG 303587 v ii i ii ---- i i ----i - i L1MC5_3end#LI 460 TTTGTAATAGCAAAAGACTGGAAACAACCCAAA----TGTCCATCAA-TA 504 chr1qtel1M 303588 GGGGAATGGCTGAACAAGCTGT-GTATAGT--CGTGGTGGAATACAATCA 303634 v i i i i - i vi-- iiii i v -i L1MC5_3end#LI 505 GGGGACTGGTTGAATAAACTATGGTACATCCACACAATGGAGTACTAT-G 553 chr1qtel1M 303635 CAG-TGTAAGAAATGATGAACAGAATG-CTCTCAGAAAATCC--TGGAAA 303680 - i ivi --i i- - v v v v -- iv L1MC5_3end#LI 554 CAGCTGTAAAAAGGAATGA--GGAATATCTCT-ATATACTGCTATGGAGT 600 chr1qtel1M 303681 GACCTACGTGAACTTTCGCAAAGGGAAATGAGCAGGACCAGGAGAACATT 303730 i v iv vv v i iv v vi i ii-- v v L1MC5_3end#LI 601 GATCTCCAGGATATATTGTTAAGTGAAAAAAGCAAGGT--GGAGAAAAGT 648 chr1qtel1M 303731 ATATACAGTA 303740 i i i L1MC5_3end#LI 649 GTGTATAGTA 658 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 43.03 CpG sites = 88, Kimura (unadjusted) = 43.44 Transitions / transversions = 1.29 (88/68) Gap_init rate = 0.07 (36 / 504), avg. gap size = 2.11 (76 / 36) 402 31.36 11.54 2.65 chr1qtel1M 303239 303654 (696346) L1ME3_3end#LINE/L1 123 574 (335) m_b36s551i5 1236 chr1qtel1M 303239 TAAGTCATGTAAAAAAAATGCTCTAAATTACTACTGACTTAAGAAATGCA 303288 - i i ii- v v i i v v iivii L1ME3_3end#LI 123 TAAG-CATATGAAAAGG-TGCTCAACATCATTAGTCATCAGGGAAATGCA 170 chr1qtel1M 303289 AATTAAAACAATTCTGA-ACAACGCAACACACCTGTCAGATCGGCTAAAG 303337 v ivv - i v i v iii vi i L1ME3_3end#LI 171 AATTAAAACCACAATGAGATACCACTACACACCCACCAGAATGGCTAAAA 220 chr1qtel1M 303338 AGACGTACAAGGAAAATGACAAATTTTGGAGGGGATCCAGGAGAATTAAA 303387 vv viv v vv v iv i v v i vii iiv i ii L1ME3_3end#LI 221 TTAAAAAGACTGACAATACCAAGTGTTGGCGAGGATGTGGAGCAACTGGA 270 chr1qtel1M 303388 ACACT-----AGTGCTGCTGAGC-------------CCATCATTCTGGAG 303419 v ----- v v i v------------- v i i i i L1ME3_3end#LI 271 ACTCTCATACATTGCTGGTGGGAGTGTAAATTGGTACAACCACTTTGGAA 320 chr1qtel1M 303420 AGCCATTTGGAACCAT--GCTCAAG---ACCACACA--TATCCTGTGACC 303462 i ii v vi --i v --- v i i-- i i L1ME3_3end#LI 321 AACTGTTTGGCAGTATCTACTAAAGCTAAACATACGCCTACCCTATGACC 370 chr1qtel1M 303463 AAGCAA---CACTACTAGGTCTGCATGCCGAAGAGATAAAAA-------- 303501 v --- v v -- i v v vi i-------- L1ME3_3end#LI 371 CAGCAATTCCACTCCTAGGTAT--ATACCCAAGAGAAATGAGTGCATATG 418 chr1qtel1M 303502 ---ACCAAAAATGAAAAGGACAAAAATACTGGTGGCGACTCTTTTAGTGG 303548 --- -- v v v i ii vi i ii i v vi ii L1ME3_3end#LI 419 TCCACCAAAA--GACATGTACAAGAATGTTCATAGCAGCTTTATTCATAA 466 chr1qtel1M 303549 TGGCAAAGAACTGGAA----CTCGAAGGGACGTCCATCAATTGGGGGAAT 303594 i v? i ---- i i ----i -ii ?i L1ME3_3end#LI 467 TAGCCNAAAACTGGAAACAACCCAAA----TGTCCATCAA-CAGNAGAAT 511 chr1qtel1M 303595 GGCTGAACAAGCTGT-GTATAGTCGT--GGTGGAATACAATCACAGT-GT 303640 v i i ii - v i --ii v - i-i L1ME3_3end#LI 512 GGATAAATAAATTGTGGTATATTCATACAATGGAATACTA-CACAGCAAT 560 chr1qtel1M 303641 AAGAAATGATGAAC 303654 i vi i L1ME3_3end#LI 561 AAAAAAGAACGAAC 574 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 41.66 CpG sites = 77, Kimura (unadjusted) = 42.56 Transitions / transversions = 1.54 (77/50) Gap_init rate = 0.06 (25 / 415), avg. gap size = 2.40 (60 / 25) 12 20.46 2.44 2.44 chr1qtel1M 304032 304072 (695928) (AGAATTC)n#Simple_repeat 1 41 (0) m_b36s252i1 1237 chr1qtel1M 304032 AGAATTCAGAACTCAAAATT-TGAAAAAAGAATATCAAAATT 304072 i i -v vvv - i (AGAATTC)n#Si 1 AGAATTCAGAATTCAGAATTCAGAATTCAGAAT-TCAGAATT 41 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 13 10.66 0.00 9.09 chr1qtel1M 304094 304129 (695871) (AAAAAC)n#Simple_repeat 1 33 (0) m_b36s252i2 1238 chr1qtel1M 304094 AAAAAGAAAATACTAAAATTATAAAACAAAAACAAA 304129 v - - vi - (AAAAAC)n#Sim 1 AAAAACAAAA-AC-AAAAACA-AAAACAAAAACAAA 33 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.09 (3 / 35), avg. gap size = 1.00 (3 / 3) 27 16.62 2.82 2.82 chr1qtel1M 305515 305585 (694415) (TAACATA)n#Simple_repeat 1 71 (0) m_b36s252i3 1239 chr1qtel1M 305515 TAACATATAACATAT--GTTATATGTTGTAACATTAAACATGTAACATAT 305562 --vv vvv i vv i (TAACATA)n#Si 1 TAACATATAACATATAACATATAACATATAACATATAACATATAACATAT 50 chr1qtel1M 305563 AACATACATAACATATAACAAAT 305585 -- v (TAACATA)n#Si 51 AACAT--ATAACATATAACATAT 71 Matrix = Unknown Transitions / transversions = 0.25 (2/8) Gap_init rate = 0.04 (3 / 70), avg. gap size = 1.33 (4 / 3) 227 31.53 9.48 1.60 chr1qtel1M 306791 306906 (693094) MIRc#SINE/MIR 90 214 (54) m_b36s601i8 1240 chr1qtel1M 306791 TAACCCTGGACAGGTCACTGACCTTCGTCT--GCCCCAGGATCCTCAGCT 306838 i i i i v v i - -- i vv v MIRc#SINE/MIR 90 TGACCTTGGGCAAGTCACTTAACCTC-TCTGAGCCTCAGTTTCCTCATCT 138 chr1qtel1M 306839 ACACAGTAGGGCT-------CTTGTCC--CCGACTTCACAGGGGGACTGT 306879 ii v i i v ------- i i -- v i vvii MIRc#SINE/MIR 139 GTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGT 188 chr1qtel1M 306880 GAAGGCCCAAGAACACAGTACAGTGTG 306906 i ii v vi v i i ii - MIRc#SINE/MIR 189 GAGGATCAAATGAGATAATGTA-TGTG 214 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 42.91 CpG sites = 23, Kimura (unadjusted) = 42.91 Transitions / transversions = 1.77 (23/13) Gap_init rate = 0.04 (5 / 115), avg. gap size = 2.60 (13 / 5) 15 21.08 2.17 2.17 chr1qtel1M 309308 309353 (690647) (GGGAG)n#Simple_repeat 1 46 (0) m_b36s252i4 1241 chr1qtel1M 309308 GGGAGGGGGGGAGA-GAGACCAGAAGGGAGGCGATGGGGAGGGGAGG 309353 i i - i vvi i v - (GGGAG)n#Simp 1 GGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGA-GGGGAGGGGAGG 46 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.04 (2 / 45), avg. gap size = 1.00 (2 / 2) 43 19.76 6.25 2.00 chr1qtel1M 309870 310013 (689987) (CCAGCC)n#Simple_repeat 1 150 (0) m_b36s252i5 1242 chr1qtel1M 309870 CCTGCTCCAGCCCC-GCCCCTGCTGCAGCGGGCCCTGCTCCGGCTCCAGC 309918 v i - v iv --- v i i i (CCAGCC)n#Sim 1 CCAGCCCCAGCCCCAGCCCCAGCCCCAGC---CCCAGCCCCAGCCCCAGC 47 chr1qtel1M 309919 CCC-GCCCCTGCTCCAG--CGAG-CCCTGCTCC-GACCCCGCCCCTGCTC 309963 - v i -- v - v i - v v v i (CCAGCC)n#Sim 48 CCCAGCCCCAGCCCCAGCCCCAGCCCCAGCCCCAGCCCCAGCCCCAGCCC 97 chr1qtel1M 309964 CAGCCCC-GCCCCTGCTCCGGCCCC-GCCCCTGCTCCAGCCCCA-CCCCC 310010 - v i i - v i - v (CCAGCC)n#Sim 98 CAGCCCCAGCCCCAGCCCCAGCCCCAGCCCCAGCCCCAGCCCCAGCCCCA 147 chr1qtel1M 310011 GCC 310013 (CCAGCC)n#Sim 148 GCC 150 Matrix = Unknown Transitions / transversions = 0.85 (11/13) Gap_init rate = 0.08 (11 / 143), avg. gap size = 1.09 (12 / 11) 422 31.46 16.85 0.00 chr1qtel1M 310905 311082 (688918) MIRb#SINE/MIR 42 249 (19) m_b36s601i9 1243 chr1qtel1M 310905 GAGTCTGGAAGACCCAAATTCAAATCTGACCTTAGGCATTTG-------- 310946 v iv iiii i iviv iv v i i-------- MIRb#SINE/MIR 42 GAGTCAGACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGT 91 chr1qtel1M 310947 GTGACCT-GGGTAGAACACTTAGCTTCTGCCTACCTCAGTTTCCTCTTCC 310995 - i iivi i i vivvi v i MIRb#SINE/MIR 92 GTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCT 141 chr1qtel1M 310996 -------------AGCAATCCC--------AAGGATACCGTGAGGATCAA 311024 ------------- ii v -------- i v iii i MIRb#SINE/MIR 142 GTAAAATGGGGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAA 191 chr1qtel1M 311025 ATGAGATCAGATTTGTAAAGTGTTTAGTATAGTGCCTGCCACACAGCAGG 311074 v viiv i i i i v i i i MIRb#SINE/MIR 192 ATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAG 241 chr1qtel1M 311075 GGTTTAAT 311082 v i i MIRb#SINE/MIR 242 CGCTCAAT 249 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 40.08 CpG sites = 38, Kimura (unadjusted) = 43.20 Transitions / transversions = 2.11 (38/18) Gap_init rate = 0.02 (4 / 177), avg. gap size = 7.50 (30 / 4) 249 22.65 0.00 1.89 chr1qtel1M 311406 311459 (688541) L2c_3end#LINE/L2 416 468 (10) m_b36s601i10 1244 chr1qtel1M 311406 CTTTGGCTCACCGGATGCCTAGAACATAGTAAGCACTTAATAAATGCTTG 311455 vv v i -i i v i i i i L2c_3end#LINE 416 CTTTGTATCCCCAG-CGCCTGGCACATAGTAGGCGCTCAATAAATGTTTG 464 chr1qtel1M 311456 CTGA 311459 i L2c_3end#LINE 465 TTGA 468 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 22.60 CpG sites = 8, Kimura (unadjusted) = 27.78 Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.02 (1 / 53), avg. gap size = 1.00 (1 / 1) 242 23.40 0.00 0.00 chr1qtel1M 311421 311467 (688533) L2d2_3end#LINE/L2 507 553 (2) m_b36s601i11 1244 chr1qtel1M 311421 TGCCTAGAACATAGTAAGCACTTAATAAATGCTTGCTGACTTGACTT 311467 v v i i i i ii i i i L2d2_3end#LIN 507 TGCCTTGCACACAGTAGGCGCTCAATAAATATTTGTTGATTTGATTT 553 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 26.71 CpG sites = 9, Kimura (unadjusted) = 29.94 Transitions / transversions = 4.50 (9/2) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 271 21.57 0.00 0.00 chr1qtel1M 311521 311571 (688429) C L2d_3end#LINE/L2 (14) 502 452 m_b36s601i12 1245 chr1qtel1M 311521 AACAAGTGTTTATGAAGCACCTACTATGTGCTAGGCATGCTGCTAAGTGC 311570 i vi i vi ivv i i C L2d_3end#LINE 502 AACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTGTGCTAGGCGC 453 chr1qtel1M 311571 T 311571 C L2d_3end#LINE 452 T 452 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 20.85 CpG sites = 7, Kimura (unadjusted) = 26.03 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 620 28.34 5.88 1.41 chr1qtel1M 311529 311732 (688268) C MIRb#SINE/MIR (16) 252 40 m_b36s601i13 1246 chr1qtel1M 311529 TTTATGAAGCACCTACTATGTGCTAGGCATGCTGCTAAGTGCTTTACA-- 311576 vi i i i ivv i -- C MIRb#SINE/MIR 252 TTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACATG 203 chr1qtel1M 311577 -AAGATCCCATTTGGTCTTCACAACAACCTTGGGTGGCAAGGCTATTATT 311625 - vv i ii i i v v i i -- C MIRb#SINE/MIR 202 CATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGG--TATTATT 155 chr1qtel1M 311626 ATGCCCA---AATATATGGAGGAAAGCCAGG-TGAACAAGATGAGGTGAC 311671 v ---v i v - viv - v ivi i v i i C MIRb#SINE/MIR 154 ATCCCCATTTTACAGAT-GAGGAAACTGAGGCTCAGAGAGGTTAAGTAAC 106 chr1qtel1M 311672 TTGCCCAAAGTAACACCATTACTAA-----ACAACCCAGATTTGCACTTG 311716 i v vii v ----- v i vi i v iii C MIRb#SINE/MIR 105 TTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCA 56 chr1qtel1M 311717 GGCCTTCCCAATCCCA 311732 i vi ii ii C MIRb#SINE/MIR 55 GGTCTGTCTGACTCCA 40 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 34.36 CpG sites = 35, Kimura (unadjusted) = 36.77 Transitions / transversions = 1.59 (35/22) Gap_init rate = 0.04 (8 / 203), avg. gap size = 1.88 (15 / 8) 267 25.00 1.37 1.37 chr1qtel1M 312233 312305 (687695) MIRc#SINE/MIR 80 152 (116) m_b36s601i14 1247 chr1qtel1M 312233 ACTCGTTGGGTTGTCTGTGGGCCAGACA-TTAAATTCCTTGATTCTCAGT 312281 v i v vii - v v - vi ii vi MIRc#SINE/MIR 80 ACTAGCTGTGTGACCT-TGGGCAAGTCACTTAACCTCTCTGAGCCTCAGT 128 chr1qtel1M 312282 TTCCTCCTCCATAAAATGGGGGTA 312305 v ii i MIRc#SINE/MIR 129 TTCCTCATCTGTAAAATGGGGATA 152 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 30.91 CpG sites = 10, Kimura (unadjusted) = 30.91 Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.03 (2 / 72), avg. gap size = 1.00 (2 / 2) 180 37.19 6.89 5.00 chr1qtel1M 312371 312704 (687296) C L2#LINE/L2 (1074) 2008 1669 m_b36s601i15 1248 chr1qtel1M 312371 TCACTGGTAGGAAACCCCGAAGAGTGACATTTCAGGGGAATGGAAGGATC 312420 i i---- ii vi v vvi i v i vi iv C L2#LINE/L2 2008 TCATTGGTG----ACCTTGACAAGAGCAGTTTCGGTGGAGTGGTGGGGAC 1963 chr1qtel1M 312421 AAAAATGAGAAACTTCAAG-GAGCTGAGAAATGAGTGGGAAGAATAGAAG 312469 i iivv --- vi - i i v ii iv i i ivi v C L2#LINE/L2 1962 GAAAGCCTGA---TTGGAGTGGGTTCAAGAGAGAATGGGAGGAGAGGAAT 1916 chr1qtel1M 312470 TGGAGCTTATG-GTATAAGCAGATTTTCCTAGGAGTTTGGCTATAAAAGT 312518 vivii - ii iv i i v v i i v C L2#LINE/L2 1915 TGGAGACAGCGAGTATAGACAACTCTTTCGAGGAGTTTTGCTGTAAAGGG 1866 chr1qtel1M 312519 AAG-AAAGATATAAAGTGATACCTACAGGGAT-GGCTGCCTC-------- 312558 i - i v iii i i v iv iv-? iv vv -------- C L2#LINE/L2 1865 GAGCAGAGAAATGGGGCGGTAGCTGGAGGGGGANGTGGGGTCAAGGGAGA 1816 chr1qtel1M 312559 ATGTATGGCTTTCTTAAGGAGCGGATAAG-ACCTGCAATTGTTTATAGAC 312607 v v -- i i vv v i-?v v -- i vi C L2#LINE/L2 1815 ATTTTTG--TTTTTTAAAGATGGGAGAAATNACAGCA--TGTTTGTATGC 1770 chr1qtel1M 312608 AGCAGGGTATAAGAAACTGAGAGAGAAGGAAAACT-----AGGTAAGAAA 312652 v vv --- vi v iiiv i v ----- v i i i C L2#LINE/L2 1769 TGATGGG---AATGATCCAGTAGAGAGGGAAAAATTGATGATGCAGGAGA 1723 chr1qtel1M 312653 TAAAGG-----ATTCTCAAAGCAGTAAACTCCCTGAAGAGAATAGAAGGA 312697 v i ----- viiii ii i--- i iv ivv i i C L2#LINE/L2 1722 GAGAGGGGAGAATTGCTGGAGCGATG---TCCTTGAGTAGGCGAGAGGGG 1676 chr1qtel1M 312698 ATAGGAT 312704 i C L2#LINE/L2 1675 ATGGGAT 1669 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 51.08 CpG sites = 70, Kimura (unadjusted) = 54.51 Transitions / transversions = 1.46 (70/48) Gap_init rate = 0.08 (25 / 333), avg. gap size = 1.60 (40 / 25) 359 27.02 16.37 2.58 chr1qtel1M 312741 312911 (687089) L2d2_3end#LINE/L2 354 547 (8) m_b36s601i16 1249 chr1qtel1M 312741 CTTCTATTATTTTCT---------ATTTAA--CTTGTATATATGGCTTG- 312778 i v --------- -- - i vii i- L2d2_3end#LIN 354 CTTCTATTGTTGTCTTGAACTGTTATTTAAATCTTGTAT-TGTTATTTAA 402 chr1qtel1M 312779 CTTTGTATAAAGCTGTTTGCAAGTTATCTCCCT----------CAAGCTT 312818 vi ii---- iiivv i i----------i i L2d2_3end#LIN 403 CTTTTCACG----TGTTTATGTCTTGTCTCCCCAACTAGATTGTAAGCTC 448 chr1qtel1M 312819 TTTGAAGACAGGAAC--TGTCTTGCCTCTTTTTGTATCCC----AGCTCT 312862 i i i i -- iivii i ---- v i L2d2_3end#LIN 449 CTTGAGGGCAGGGACCATGTCTTATACTTCTTTGTATCCCCCACAGCGCC 498 chr1qtel1M 312863 TAGCACAGTGCCTGGCACATAGTAGGTACTTAATGTTTACCCATTGACT 312911 v i ii i ivv iiii i L2d2_3end#LIN 499 TAGCACAGTGCCTTGCACACAGTAGGCGCTCAATAAATATTTGTTGATT 547 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 33.82 CpG sites = 35, Kimura (unadjusted) = 36.09 Transitions / transversions = 3.50 (35/10) Gap_init rate = 0.06 (11 / 170), avg. gap size = 3.00 (33 / 11) 369 26.61 14.52 0.00 chr1qtel1M 312791 312914 (687086) L2b_3end#LINE/L2 320 461 (5) m_b36s601i17 1249 chr1qtel1M 312791 CTGTTTGCAAGT-TATCTCCCTCA----------AGCTTTTTGAAGACAG 312829 ? i v - i i ---------- iiv i i L2b_3end#LINE 320 CTGNTTACATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAG 369 chr1qtel1M 312830 GAAC------TGTCTTGCCTCTTTTTGTATCCC-AGCTCTTAGCACAGTG 312872 i ------ iiiviivi - v i ? L2b_3end#LINE 370 GGACCGNGTCTGTCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNG 419 chr1qtel1M 312873 CCTGGCACATAGTAGGTACTTAATGTTTACCCATTGACTGAA 312914 i ii i i ivv iiii v L2b_3end#LINE 420 CCTGGCACACAGTAGGCGCTCAGTAAATATTTGTTGAATGAA 461 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 31.58 CpG sites = 25, Kimura (unadjusted) = 35.77 Transitions / transversions = 3.12 (25/8) Gap_init rate = 0.03 (4 / 123), avg. gap size = 4.50 (18 / 4) 216 30.08 6.99 5.29 chr1qtel1M 313316 313501 (686499) C L2b_3end#LINE/L2 (248) 218 30 m_b36s601i18 1250 chr1qtel1M 313316 TTTGATCTAAGCCTTGACAA--GAGCTATGGAGTCTAAGAGGCTGAAGAG 313363 v i v i vii-- - - ivivv - C L2b_3end#LINE 218 TTTGAGCTGAGACCTGAAGGATGAG-TA-GGAGTTGGCCAGGC-GAAGAG 172 chr1qtel1M 313364 G------AGGGCTATTGCAGGCACAGGGGACACGACTTGTGTAAAGGCAC 313407 ------ -i v v i --i v? i v C L2b_3end#LINE 171 GTGGGGAAGGGC-GTTCCAGGCAGAGGGAACA--GCANGTGCAAAGGCCC 125 chr1qtel1M 313408 AAAGG---AAGGGGATAT--CATCTTCATGGAAAGGAACATAGGCCATTG 313452 vi ---i ? iii? -- i v iv vi v viv v C L2b_3end#LINE 124 TGAGGCGGGAGNGAGCNTGGCGTGTTCGAGGAACAGCAAGGAGGCCAGTG 75 chr1qtel1M 313453 TGGTTGGAATATACAAAATAAGCATGATGATGATTCTGGAATATGAGGC 313501 i ----i i i i v iv vii vv i i v C L2b_3end#LINE 74 TGGCTGGA----GCAGAGTGAGCAAGGGGAGAGTGGTAGGAGATGAGGC 30 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 37.36 CpG sites = 29, Kimura (unadjusted) = 40.25 Transitions / transversions = 1.21 (29/24) Gap_init rate = 0.08 (14 / 185), avg. gap size = 1.64 (23 / 14) 256 36.70 4.59 0.00 chr1qtel1M 315580 315688 (684312) MIRb#SINE/MIR 40 153 (115) m_b36s601i19 1251 chr1qtel1M 315580 TGACATCAGA-AGAATTGTGTTTAAATCCTGCTTTTGATA-TGAC---AT 315624 ivi - vi v ii i vi i vi - v ---v MIRb#SINE/MIR 40 TGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCT 89 chr1qtel1M 315625 ATGGGATTATGGGCGAATTGTGGAACTTCCTCGAGCCTCAATTTCCTTGC 315674 i v iiv i i iivv i iii i iii MIRb#SINE/MIR 90 GTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCAT 139 chr1qtel1M 315675 TTACAACATGGAGA 315688 i ii v i MIRb#SINE/MIR 140 CTGTAAAATGGGGA 153 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 50.67 CpG sites = 28, Kimura (unadjusted) = 55.11 Transitions / transversions = 2.33 (28/12) Gap_init rate = 0.03 (3 / 108), avg. gap size = 1.67 (5 / 3) 209 41.86 3.03 2.26 chr1qtel1M 315585 315716 (684284) MIR3#SINE/MIR 40 172 (36) m_b36s601i20 1251 chr1qtel1M 315585 TCAGAAGAATTGTGTTTAAATCCTGCTTTTGATA-TGAC---ATATGGGA 315630 i vi v iv i i vi i vi - i ---v i v MIR3#SINE/MIR 40 TCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGA 89 chr1qtel1M 315631 TTATGGGCGAATTGTGGAACTTCCTCGAGCCTCAATTTCCTTGCTTACAA 315680 iiv i i iiivvv i iii i i iiii ii MIR3#SINE/MIR 90 CCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAA 139 chr1qtel1M 315681 CATGGAGAAGGCAAACCAGTTAGGATGTTCTAAAAT 315716 v ii ii viii i -- v -i ii MIR3#SINE/MIR 140 AATGAGGGGGTTGGACTAG--ATGAT-CTCTAAGGT 172 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 68.83 CpG sites = 40, Kimura (unadjusted) = 71.34 Transitions / transversions = 2.86 (40/14) Gap_init rate = 0.04 (5 / 131), avg. gap size = 1.40 (7 / 5) 11 17.29 7.69 0.00 chr1qtel1M 316804 316842 (683158) (CAGGCCC)n#Simple_repeat 1 42 (0) m_b36s252i6 1252 chr1qtel1M 316804 CAGGCAGGAGGCCCCAGG-TCC-GGCTCC-GGCCCCAGACCC 316842 vvv -i - i - i (CAGGCCC)n#Si 1 CAGGCCCCAGGCCCCAGGCCCCAGGCCCCAGGCCCCAGGCCC 42 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.08 (3 / 38), avg. gap size = 1.00 (3 / 3) 16 10.41 0.00 6.06 chr1qtel1M 317257 317291 (682709) (AGG)n#Simple_repeat 1 33 (0) m_b36s252i7 1253 chr1qtel1M 317257 AGGAGGAAGGACAAGGAGGGGGAGGAGGATGGAGG 317291 - vi i - (AGG)n#Simple 1 AGGAGG-AGGAGGAGGAGGAGGAGGAGGA-GGAGG 33 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 17 3.44 2.94 6.06 chr1qtel1M 318870 318903 (681097) (CCCT)n#Simple_repeat 1 33 (0) m_b36s252i8 1254 chr1qtel1M 318870 CCCTCCCCTCCCTCCCTCCTTCCC-CCCTCCTCTC 318903 - i - - (CCCT)n#Simpl 1 CCCT-CCCTCCCTCCCTCCCTCCCTCCCTCC-CTC 33 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.09 (3 / 33), avg. gap size = 1.00 (3 / 3) 14 9.55 0.00 0.00 chr1qtel1M 319051 319073 (680927) (CCT)n#Simple_repeat 1 23 (0) m_b36s252i9 1255 chr1qtel1M 319051 CCTCCCCCTCCTCCTCCTCCCCC 319073 i i (CCT)n#Simple 1 CCTCCTCCTCCTCCTCCTCCTCC 23 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 237 30.26 0.00 0.00 chr1qtel1M 325370 325445 (674555) C MIR3#SINE/MIR (24) 184 109 m_b36s601i21 1256 chr1qtel1M 325370 GAGCAGGTGGGGACCCCAGAGACCATGTAGGCCAACCCCATTCCTTTGCA 325419 v vi ii i v v v ivi i C MIR3#SINE/MIR 184 GAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACA 135 chr1qtel1M 325420 GAGGTGGATGCCAAAGCACAAGGAGG 325445 v v vi ii i v ii C MIR3#SINE/MIR 134 GATGAGGAAACTGAGGCCCAGAGAGG 109 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 39.73 CpG sites = 13, Kimura (unadjusted) = 39.73 Transitions / transversions = 1.30 (13/10) Gap_init rate = 0.00 (0 / 75), avg. gap size = 0.0 (0 / 0) 348 36.62 2.83 1.60 chr1qtel1M 326608 326854 (673146) C L3#LINE/CR1 (1275) 2824 2575 m_b36s601i22 1257 chr1qtel1M 326608 TCTTAGATGTTTACTAATTGTCCCTTCAGTGATATTCTCTGGACTTTTTC 326657 ii ii i i v iii iv i i i vivi i v v C L3#LINE/CR1 2824 TTCTAAGTGCTCACAAACCATCTGTTTAATAATCCGTTCTAGAATTTTGC 2775 chr1qtel1M 326658 TCAGAATCAAAGTCAAACTCTCTAGCCTTGTATTTTATAGACTTCATTTG 326707 ivi i i v i iv ii i - v ?i v i i v C L3#LINE/CR1 2774 CGGGGATCGACGTCAAGCTTACCGGTCT-GTAGTTTNCAGAATCCATCTT 2726 chr1qtel1M 326708 TACTCC--TTTGAACAATTCTTGAAAACATTTGCCCATTTCT-GTCCCTT 326754 vi -- v - ? vvv? v? i i i- -- C L3#LINE/CR1 2725 TTTTCCCTTTTTAA-AANTAGGNACNACATTTGCCCGTCTCCAGT--CTT 2679 chr1qtel1M 326755 CTGCCCTGTCTT--ATTCCCAAT-ATCTTCCAAAAATCGGTCACTGTGGC 326801 v viv --i i vi - i ii i iiviv v i i C L3#LINE/CR1 2678 CTGGCACCTCTTCCGTTCTCCGTGATTTCTCAAAGATTACCGACAGCGGT 2629 chr1qtel1M 326802 TCATCAGTCATACCAGCTGGATC-TCCAGTTTGCTGGGATGTCTGTCAGC 326850 vv ii i i v vi v - i viv vvv iv C L3#LINE/CR1 2628 TCCGCGATCACATCTGCAAGTTCTTTCAGTACCCTGGGATGTAATTCGTC 2579 chr1qtel1M 326851 TGGG 326854 C L3#LINE/CR1 2578 TGGG 2575 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 44.68 CpG sites = 53, Kimura (unadjusted) = 54.05 Transitions / transversions = 1.47 (53/36) Gap_init rate = 0.04 (9 / 246), avg. gap size = 1.22 (11 / 9) 513 34.50 3.45 7.73 chr1qtel1M 327237 327613 (672387) L3#LINE/CR1 2864 3225 (874) m_b36s601i23 1258 chr1qtel1M 327237 AAGAAGAAATTAATGATTAACTGATTTC-TTTCCTTTTTTACATATATAT 327285 v i i - viv i ii - i----- v L3#LINE/CR1 2864 AAGAACAAGTCA-TGCCAAACTAACCTCATTTCCTTTTTTG-----ATAG 2907 chr1qtel1M 327286 GCTTTGTAAACTAGTGTAAATAGTGATAGATCAGGAGAATAACACAGAAA 327335 v ----- ------- v i i iv ii v L3#LINE/CR1 2908 GGTT-----ACTAG-------ACTGGTAGATCAGGGGAATGCCGTAGACA 2945 chr1qtel1M 327336 TGTTAGACATAGATTTCAACAAAGGCTTTGTTAACAAGCTCTCAGTCTTT 327385 ?iv iv iv i i i vv vi - iv vvv v L3#LINE/CR1 2946 NAGTGTATCTGGATTTCAGCAAGGCATTTGACAA-AGTCTCTCATGATAT 2994 chr1qtel1M 327386 GCTTG-AGATAAAATGTGAGGATTTGGGATAGTTGACTGACAAGGCAGGT 327434 v -i i i viiii v ---- i iv i ivi v L3#LINE/CR1 2995 CCTTGTGGACAAGATGGAGAAATATGG----GCTGGATGATAGTACAGTT 3040 chr1qtel1M 327435 AGG-GTTTTTGAAACTAGTACAGAGGCAGGACCCAAAA-TTAGTCATTAG 327482 - vv i v i i vv iv i viv -v iv v i L3#LINE/CR1 3041 AGGTGGATTCGTAGCTGGTTGAACGACTATACCCAAAAGGTGTTGATTAA 3090 chr1qtel1M 327483 TGAGT--ATGCTACCTTACAGAGAAATCTCCAATAGCATGCCCCATGAAT 327530 ii -- ii v i iv i ii i i i i v v iv L3#LINE/CR1 3091 TGGATCGATGTCAACCTGGAGGGAGGTCTCTAGTGGCGTGCCACAGGGCT 3140 chr1qtel1M 327531 TGGTCCTT-------TTCTGTTCAACATCTTTATTTGTCATAAATTAAGT 327573 iv ------- i i ---iv i v iii L3#LINE/CR1 3141 CTGTCCTTGGCCCTGTCCTGTTCAACATTTTTAT---CAATGACTTGGAT 3187 chr1qtel1M 327574 GAAGGCAGAGATGACACACTGATTGGTTTTAAGCAAACAA 327613 i v v i ii v iiiv -- i ii L3#LINE/CR1 3188 GAAGACATAGAAGGCATGCTTATCAAATTT--GCAGATGA 3225 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 46.49 CpG sites = 72, Kimura (unadjusted) = 48.19 Transitions / transversions = 1.50 (72/48) Gap_init rate = 0.09 (34 / 376), avg. gap size = 1.21 (41 / 34) 11 34.33 0.00 3.12 chr1qtel1M 327958 328023 (671977) (ATCTCT)n#Simple_repeat 1 64 (0) m_b36s252i10 1259 chr1qtel1M 327958 ATTTCTCCCTCTATCTCTGTTTATCTTTTTTTCTTTATGTGTATGTCTCA 328007 i vi i i v v i i v i v v v - (ATCTCT)n#Sim 1 ATCTCTATCTCTATCTCTATCTCTATCTCTATCTCTATCTCTATCTCT-A 49 chr1qtel1M 328008 GTCTCTGTTTCTCTCT 328023 - i i v (ATCTCT)n#Sim 50 -TCTCTATCTCTATCT 64 Matrix = Unknown Transitions / transversions = 1.12 (9/8) Gap_init rate = 0.03 (2 / 65), avg. gap size = 1.00 (2 / 2) 250 30.00 2.50 0.00 chr1qtel1M 328199 328278 (671722) C L3#LINE/CR1 (50) 4049 3968 m_b36s601i24 1260 chr1qtel1M 328199 TCCAATCTCCCACTCAATGCA-AAATCTTCTCTATATTATTCTGAACTGC 328247 i ii -i iii i vi i ivi viv C L3#LINE/CR1 4049 TCCAACCTCCCATCCAATGCAGGAATCCCTTCTACAACATCCCTGACAAG 4000 chr1qtel1M 328248 TGGTCAT-CACCCTCTACTTAAACATTTTGAG 328278 - v i i ii iv C L3#LINE/CR1 3999 TGGTCATCCAGCCTCTGCTTGAACACCTCCAG 3968 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 41.28 CpG sites = 18, Kimura (unadjusted) = 41.28 Transitions / transversions = 3.00 (18/6) Gap_init rate = 0.03 (2 / 79), avg. gap size = 1.00 (2 / 2) 192 22.96 0.00 4.17 chr1qtel1M 328638 328687 (671313) C MIR#SINE/MIR (139) 123 76 m_b36s601i25 1261 chr1qtel1M 328638 CTGAGGAACATAAAAGTTAAATAACATGATTTTGAGGTCACAGAGCTAGT 328687 v v i i i v --iiii v C MIR#SINE/MIR 123 CTGAGGCACAGAGAGGTTAAGTAACTTG--CCCAAGGTCACACAGCTAGT 76 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 28.06 CpG sites = 7, Kimura (unadjusted) = 28.06 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.04 (2 / 49), avg. gap size = 1.00 (2 / 2) 186 38.07 6.81 1.62 chr1qtel1M 331387 331621 (668379) L2d2_3end#LINE/L2 14 260 (295) m_b36s601i26 1262 chr1qtel1M 331387 CTTTAACTTGTCTTTCTGGG-TTATTTCATCTTGTTTCCCCTCATTCATT 331435 iii i ?i ii v- i vivi i i i? ivv ii L2d2_3end#LIN 14 CCCCAACCTNCCTTTCCAGCCTTATCTCCCACTATTCCCCTNCACGAACC 63 chr1qtel1M 331436 CTGATGTCCAAATGAATTGTCCAGCTTTCTGCTCCCCGAAC---CTTT-- 331480 vvvv ivii i vi vi iv ii --- i -- L2d2_3end#LIN 64 CTCCGCTCCAGCCAAACTGGTCTACTCACTGTCCCCCGAACACGCCTTGC 113 chr1qtel1M 331481 -CATTTCATCTTCT--GCCTTT----ACACCTTTCTGCTGGTCTAAAATG 331523 - ? i vv i -- ---- i v iv iv i ii L2d2_3end#LIN 114 GCNTTCCCGCCTCTGCGCCTTTGCTCACGCCGTTCCCCCCGCCTGGAATG 163 chr1qtel1M 331524 TTCT--CTCTTCCACCTTTTACATCTTGAAATTCCTAACT-CCTTTTAAG 331570 ii -- i v -- ii v v iv - v i-i i i L2d2_3end#LIN 164 CCCTTCCCCTTCCTC--TCCACCTATCCAAA-TCCTACCCATCCTTCAAG 210 chr1qtel1M 331571 GTTTAATTTAAGTGTTATCTCCTACATAATACCTTTACTTGGTCATTTCA 331620 iii ii i i ?ii i v i i vi i- i ii i i L2d2_3end#LIN 211 GCCCAGCTCAAATNCCACCTCCTCCGTGAAGCCTTC-CCTGACCACTCCA 259 chr1qtel1M 331621 G 331621 L2d2_3end#LIN 260 G 260 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 57.50 CpG sites = 63, Kimura (unadjusted) = 60.93 Transitions / transversions = 2.52 (63/25) Gap_init rate = 0.05 (12 / 234), avg. gap size = 1.67 (20 / 12) 190 33.71 9.49 2.37 chr1qtel1M 331464 331621 (668379) L2d_3end#LINE/L2 92 260 (256) m_b36s601i27 1262 chr1qtel1M 331464 CTGCTCCCCGAAC---CTTT---CATTTCATCTTCT--GCCTTT----AC 331501 ii --- i --- i vv i -- ---- L2d_3end#LINE 92 CTGTCCCCCGAACACGCCTTGCGCATTCCCGCCTCTGCGCCTTTGCTCAC 141 chr1qtel1M 331502 ACCTTTCTGCTGGTCTAAAATGTTCT--CTCTTCCACCTTTTACATCTTG 331549 i v iv iv i ii ii -- i v ii i vi i-- L2d_3end#LINE 142 GCCGTTCCCCCCGCCTGGAATGCCCTTCCCCTTCCTCTCTCTCTATCC-- 189 chr1qtel1M 331550 AAATTCCTAACT-CCTTTTAAGGTTTAATTTAAGTGTTATCTCCTACATA 331598 - v i-i i i iii ii i vii i v ii L2d_3end#LINE 190 AAA-TCCTACCCATCCTTCAAGGCCCAGCTCAAGTCCCACCTCCTCCACG 238 chr1qtel1M 331599 ATACCTTTACTTGGTCATTTCAG 331621 vi i- i ii i i L2d_3end#LINE 239 AAGCCTTC-CCTGACCACTCCAG 260 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 47.14 CpG sites = 41, Kimura (unadjusted) = 50.16 Transitions / transversions = 3.73 (41/11) Gap_init rate = 0.06 (10 / 157), avg. gap size = 1.90 (19 / 10) 184 28.60 1.25 3.85 chr1qtel1M 331714 331793 (668207) L2a_3end#LINE/L2 432 509 (8) m_b36s601i28 1262 chr1qtel1M 331714 GTTTTGTTT-CTGTCTTGTAATCTTCTGTACTTAATACAATGTCTTACAT 331762 i- i-- - ii v ii i iv i i vi i L2a_3end#LINE 432 GTTTTGTTCACTGC--TGTA-TCCCCAGCGCCTAGAACAGTGCCTGGCAC 478 chr1qtel1M 331763 TTAATTGGCACTTAATAAATCTTTATTGAAT 331793 v i v i i v i L2a_3end#LINE 479 ATAGTAGGCGCTCAATAAATATTTGTTGAAT 509 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 33.60 CpG sites = 16, Kimura (unadjusted) = 38.25 Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.05 (4 / 79), avg. gap size = 1.00 (4 / 4) 196 29.15 0.00 6.45 chr1qtel1M 331740 331805 (668195) L2d2_3end#LINE/L2 494 555 (0) m_b36s601i29 1262 chr1qtel1M 331740 GTACTTAATACAATGTCTTACATTTAATTGGCACTTAATAAATCTTTATT 331789 ii i ii i i i ivi i v i i v i L2d2_3end#LIN 494 GCGCCTAGCACAGTGCCTTGCACACAGTAGGCGCTCAATAAATATTTGTT 543 chr1qtel1M 331790 GAATTATTTGGTTTGA 331805 ---- i L2d2_3end#LIN 544 G----ATTTGATTTGA 555 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 34.38 CpG sites = 15, Kimura (unadjusted) = 40.54 Transitions / transversions = 5.00 (15/3) Gap_init rate = 0.06 (4 / 65), avg. gap size = 1.00 (4 / 4) 372 24.14 19.31 0.00 chr1qtel1M 332030 332174 (667826) C L3#LINE/CR1 (3) 4096 3924 m_b36s601i30 1263 chr1qtel1M 332030 AGAAAGACAAAATTTGAGACTTAGAAGGGAT-TCAAAGGC---------- 332068 vv i i v v i i- i i i---------- C L3#LINE/CR1 4096 AGAATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCC 4047 chr1qtel1M 332069 ---------TCTAA---AGGAATCCCTGCTCTAAAATACCTAATAAGTGG 332106 --------- i --- v vi v v i i C L3#LINE/CR1 4046 AACCTCCCATCCAATGCAGGAATCCCTTCTACAACATCCCTGACAAGTGG 3997 chr1qtel1M 332107 TCTTCTAGCCTCAACTTGAAGACTTCCAATGA--GGGAACTC-CAAGTTC 332153 v i vi v i i -- i - v vi C L3#LINE/CR1 3996 TCATCCAGCCTCTGCTTGAACACCTCCAGTGACGGGGAGCTCACTACCTC 3947 chr1qtel1M 332154 A--AGACAATCCATTTAATTTTT 332174 ?-- i ii iv C L3#LINE/CR1 3946 NCGAGGCAGCCCATTCCATTTTT 3924 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 30.03 CpG sites = 21, Kimura (unadjusted) = 30.03 Transitions / transversions = 1.50 (21/14) Gap_init rate = 0.05 (7 / 144), avg. gap size = 4.00 (28 / 7) 15 9.69 6.06 0.00 chr1qtel1M 332175 332207 (667793) (TGTTT)n#Simple_repeat 1 35 (0) m_b36s252i11 1264 chr1qtel1M 332175 TGTTTTGTTTTGTTTTG--TTGTTTAATTGTGTTT 332207 -- vi v (TGTTT)n#Simp 1 TGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTT 35 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.03 (1 / 32), avg. gap size = 2.00 (2 / 1) 189 31.67 0.00 0.00 chr1qtel1M 332274 332333 (667667) C L3b_3end#LINE/CR1 (168) 1038 979 m_b36s601i32 1265 chr1qtel1M 332274 CCATTCCACTTTAGGATGGCTCTAGTTGTCAGAAAATTCTTCCTGACCTC 332323 v v vvi iii vii i i v iv C L3b_3end#LINE 1038 CCATTCCAGTGTTTAACAACTCTCACTGTCAGGAAGTTCTTCCTTATATC 989 chr1qtel1M 332324 AAATATAAAT 332333 v iv C L3b_3end#LINE 988 TAACCTAAAT 979 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 41.93 CpG sites = 10, Kimura (unadjusted) = 41.93 Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0) 258 18.18 0.00 0.00 chr1qtel1M 332274 332317 (667683) C L3#LINE/CR1 (163) 3936 3893 m_b36s601i31 1265 chr1qtel1M 332274 CCATTCCACTTTAGGATGGCTCTAGTTGTCAGAAAATTCTTCCT 332317 i v ii ii i i C L3#LINE/CR1 3936 CCATTCCATTTTTGGACAGCTCTGATTGTTAGAAAGTTCTTCCT 3893 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 22.01 CpG sites = 7, Kimura (unadjusted) = 22.01 Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 713 35.98 4.65 1.56 chr1qtel1M 332334 332957 (667043) C CR1-3_Croc#LINE/CR1 (817) 2788 2146 m_b36s551i6 1266 chr1qtel1M 332334 TCTTCCTTCACATCACAATCCTTTAAATACCTGAGCACAGCTAACATGTC 332383 i --- vi ii i i ii iv v v C CR1-3_Croc#LI 2788 TCTTCTTT---ATGGCAGCCCTTCAAGTATTTGAAGACTGCTATCATGTC 2742 chr1qtel1M 332384 CTACC--AAGTTTATTTTTCTCCAATTCAATCCTCCCTATTTCTTTCAGT 332431 ivi -- iviv i v v ii v - v v vi i i C CR1-3_Croc#LI 2741 CCCTCTTAAGCGCCTTTTCCGCAAGCTGAA-CATGCCTAGCTCCTTCAGC 2693 chr1qtel1M 332432 CT----TCATATGTTATAAACTCAATGCCCTTCACCATTCTGATTACCTT 332477 ---- i viv ivvi v v i i ii vi i iv C CR1-3_Croc#LI 2692 CTCTCCTCGTATGACTTGCCTTCCAAGCCCTTTATCATCTTTGTTGCCCG 2643 chr1qtel1M 332478 CTTATGAACAC---CTAAGATGAGCAT-TATTTCTTAAATCATAATGTCC 332523 i v i v --- vv vvv i- vi i vii iiv i C CR1-3_Croc#LI 2642 CCTCTGGACCCTCTCTAACTTCTCCACGTCCTTTTTAAAATGTGGAGCCC 2593 chr1qtel1M 332524 AGAACTGAACA--ATTTTCCAGATGAGCCCTAGCCAGGGAATAGTACGAT 332571 v --i vi v i v vvv viiv C CR1-3_Croc#LI 2592 AGAACTGCACACAGTACTCCAGATGAGGCCTAACCAGTGCCGAGTAGAGA 2543 chr1qtel1M 332572 GGGATGAT----TCCTGTTACTGGAAGTCCTA-TGACCCT-CTGA---AT 332612 v iv ---- i vv v v -- - vii -i --- C CR1-3_Croc#LI 2542 GGCACTATCACCTCCCGTGTCTTGCA--CCTAATGCTTCTATTGATGCAT 2495 chr1qtel1M 332613 TTCAAGATTTCACTAGCTTTTAGGGCTGCCACATCACACTTCTGACTTAT 332662 ii i iiv i v i v v v ii v v i C CR1-3_Croc#LI 2494 CCCAAAACCGCATTCGCCTTTTGTGCGGCTGCATCACACTGCAGACTCAT 2445 chr1qtel1M 332663 ATTGAGTTCACAATCCACTCAAAAC-CCCAACTGTTTTTCAA----ACTG 332707 iiiii i - i - iv vi v ----i C CR1-3_Croc#LI 2444 ATTGAGTCTGTGATCTAC-CAAGACTCCCAGGTCCTTTTCCATAGTGCTG 2396 chr1qtel1M 332708 TTATTCAACCAT---CCACCCCATTTTGTACTTGTAAAGGTCAGATGATT 332754 ii i i v---i - i i--vv iv v C CR1-3_Croc#LI 2395 CCATCCAGCCAGGTGTCACCC-ATTTTGTATTTGTG--TTTTTGATTATT 2349 chr1qtel1M 332755 GGAACCAAAGTTTTAAACTTTACATTTACCATTACTAGATTGTATTTTGT 332804 vvvv i i v viv i i ii vvi i ii i vi ii C CR1-3_Croc#LI 2348 CCTCCCGAGGTGTAGCACCTTGCATTTGTCCGCATTGAACTTCATCCTGT 2299 chr1qtel1M 332805 TAGATTCAGCCAAAAGTTCCAACCTATCAACATCTTTTTGGATCCTGGAT 332854 v ii v ivv i i i v i i i ivi vvi C CR1-3_Croc#LI 2298 TAGCTCTAGCCCAGCTTTCCAATCTGTCGAGATCCTTCTGAATTGCGCTC 2249 chr1qtel1M 332855 TTGTCATCCAATAAATTAATGATCCCTAATAGCTTTGTGTCATCTGAAAA 332904 ?i v iivi viii i vvi i i i v C CR1-3_Croc#LI 2248 NCGTCCTCCAACGTGTTCGCAATCCTTCCCAGTTTCGTGTCGTCTGCAAA 2199 chr1qtel1M 332905 GTTGATGAGCATATTGTCTATGCCATTATTCATATCACTGATAAAAATGT 332954 v v v iv vii v vi i v i i v i C CR1-3_Croc#LI 2198 CTTGCTCAAGAAGCTTTCTATGCCAGCATCCAAATCATTAATAAACACGT 2149 chr1qtel1M 332955 TAA 332957 i C CR1-3_Croc#LI 2148 TGA 2146 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 46.15 CpG sites = 126, Kimura (unadjusted) = 51.02 Transitions / transversions = 1.33 (126/95) Gap_init rate = 0.04 (22 / 623), avg. gap size = 1.77 (39 / 22) 13 24.03 0.00 0.00 chr1qtel1M 333781 333815 (666185) (TCCC)n#Simple_repeat 1 35 (0) m_b37s252i0 1267 chr1qtel1M 333781 TCTCTCTCTCCTTCCCTCCCTGCCCCTCTGCCTCC 333815 i i i v i i v (TCCC)n#Simpl 1 TCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCC 35 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 330 36.98 8.05 0.53 chr1qtel1M 334031 334204 (665796) C L3#LINE/CR1 (921) 3178 2992 m_b37s601i0 1268 chr1qtel1M 334031 ATTAATAAAACATTTTAAA-AGGA-------AAAAAAAGA-TCCTGGGAA 334071 i - v i - ------- ii v -i v iv C L3#LINE/CR1 3178 ATTGATAAAA-ATGTTGAACAGGACAGGGCCAAGGACAGAGCCCTGTGGC 3130 chr1qtel1M 334072 ATGCCACTGAAAATCT---GTCAAGTTGATATATACTCATTAATTACTAC 334118 i ii i i ---vi i i vv ii i vi C L3#LINE/CR1 3129 ACGCCACTAGAGACCTCCCTCCAGGTTGACATCGATCCATTAATCAACAC 3080 chr1qtel1M 334119 TCTTTGAGTCTGAGCAACCACTTAGTTCTGAATTTATTTAATTATG--GT 334166 ii i v iiv ivi vii i vi ii ii i i i--i C L3#LINE/CR1 3079 CTTTTGGGTATAGTCGTTCAACCAGCTACGAATCCACCTAACTGTACTAT 3030 chr1qtel1M 334167 CACCTAATCTTTATTTCATTATCCTCCTCACAAGAATA 334204 i i ii iv vii i vii i C L3#LINE/CR1 3029 CATCCAGCCCATATTTCTCCATCTTGTCCACAAGGATA 2992 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 52.99 CpG sites = 48, Kimura (unadjusted) = 57.23 Transitions / transversions = 3.00 (48/16) Gap_init rate = 0.03 (6 / 173), avg. gap size = 2.50 (15 / 6) 251 34.10 2.97 13.02 chr1qtel1M 334214 334449 (665551) C CR1-3_Croc#LINE/CR1 (1639) 1966 1752 m_b37s551i1 1266 chr1qtel1M 334214 ATTTTATCAAACGCTTTGCTAAAATGCAGGTAGTTGGTATCTACAGTGTT 334263 ii i v i i i v i vvivi i ii C CR1-3_Croc#LI 1966 ACCTTGTCAAAAGCCTTGCTGAAGTCCAGATACACTATATCCACAGCATT 1917 chr1qtel1M 334264 CCTCTCATT-AC-----TAGTTTAGATCCTGTCTAGAAAGAAAATAAGTT 334307 ii i- ----- --- iii v ii i i ----- C CR1-3_Croc#LI 1916 CCCTTCATCCACCCAAGTAGTT---ACTTTGTCAAAGAAGGAGAT----- 1875 chr1qtel1M 334308 CTTTCTAGCAAGAAAGTTAGATTTGTTCTAGCAAGATTTGTTCTTGAGAA 334357 -------- --------- - ii v i viv C CR1-3_Croc#LI 1874 --------CAAG---------TTTGTT-TGACACGATTTGTTTTTCGTAA 1843 chr1qtel1M 334358 AGCACTGCTGACTTCTTGTGATCATCACTTTTCATTTTTTGGATATTCAC 334407 v vv i v --i i v ii iii ii ii C CR1-3_Croc#LI 1842 ATCCATGCTGGCTGCTTGTGATCA--GCCTTTCCTCCTCCAGATGCTTGC 1795 chr1qtel1M 334408 TAATCATCTCCTTTATTAC-CATTCTAGAAGTTTCCTAGGAAT 334449 v vii i i vv i-iii i v ii i v C CR1-3_Croc#LI 1794 AAATGGCCTTCCTTAGGATATGCTCCAGTAACTTCCCAGGTAT 1752 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 47.34 CpG sites = 50, Kimura (unadjusted) = 48.35 Transitions / transversions = 2.50 (50/20) Gap_init rate = 0.13 (31 / 235), avg. gap size = 1.13 (35 / 31) 240 29.86 3.85 1.25 chr1qtel1M 334570 334647 (665353) C L3#LINE/CR1 (0) 4099 4020 m_b37s601i1 1269 chr1qtel1M 334570 GACAGAGCCACAGGACTTTAGAAGTGGGAGGGAGCATGGTGCTCATCCAG 334619 i ii i ii i iv i v v i v v i C L3#LINE/CR1 4099 GATAGAATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAG 4050 chr1qtel1M 334620 TCCAA---TTCATACCAGAAAAAGAATCCCT 334647 ---ii - iviv i C L3#LINE/CR1 4049 TCCAACCTCCCAT-CCAATGCAGGAATCCCT 4020 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 40.33 CpG sites = 16, Kimura (unadjusted) = 40.33 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.03 (2 / 77), avg. gap size = 2.00 (4 / 2) 198 31.31 16.92 1.57 chr1qtel1M 334785 335115 (664885) C L2#LINE/L2 (921) 2161 1781 m_b37s601i2 1270 chr1qtel1M 334785 AGGTTGGTAGAGCCCCAGTAAAGAGCACTGTCACAAAAATCTAGAGAAAA 334834 v vi ivv v i v iiv viii ii v v i C L2#LINE/L2 2161 AGGTAGGAGGAAAACCAGGAGAGTGTGGTGTCCTGGAAGCCAAGTGAAGA 2112 chr1qtel1M 334835 GAGAATATTTAAGAGAAGAGGGAGC--TCA-CAGAGGTAGACACTGC--A 334879 i vi - i - i i-- - v v vi i ii -- C L2#LINE/L2 2111 AAGTGT-TTCAAGA-AGGAGGGAGTGATCAACTGTGTCAAATGCTGCTGA 2064 chr1qtel1M 334880 GAAGTCAAAGGGAATGAGGACTCCAAAGAGGCCTGTGGGT--AGCT-CTT 334926 ? i iviii vvi vv i vv i -- v- v C L2#LINE/L2 2063 NAGGTCAAGTAAGATGAGGACTGAGAATTGACCATTGGATTTAGCAACGT 2014 chr1qtel1M 334927 GAAAGATACTTGAGAACTTTGACTA---------TGGTGGTGGGGTAAGG 334967 i i vi - ivi i v ---------i v v ii C L2#LINE/L2 2013 GGAGGTCA-TTGGTGACCTTGACAAGAGCAGTTTCGGTGGAGTGGTGGGG 1965 chr1qtel1M 334968 AAGA-----TG-CTGAAAAGGGTT-GAGAAGTCACCGGAAGAGAGGAAGT 335010 v ----- -i i iv -i iivv iv i v C L2#LINE/L2 1964 ACGAAAGCCTGATTGGAGTGGGTTCAAGAGAGAATGGGAGGAGAGGAATT 1915 chr1qtel1M 335011 GGAGGAAATGA--AAAGACAAAGCTTTTTC--AGAATTTGGCACCAAAG- 335055 iv ii -- v -- i --i i v vvi - C L2#LINE/L2 1914 GGAGACAGCGAGTATAGACAA--CTCTTTCGAGGAGTTTTGCTGTAAAGG 1867 chr1qtel1M 335056 -----AAAGAAA-GGGAAGG--GCTG--------CATGAAGT-------G 335082 ----- i - iv -- --------?i ii ------- C L2#LINE/L2 1866 GGAGCAGAGAAATGGGGCGGTAGCTGGAGGGGGANGTGGGGTCAAGGGAG 1817 chr1qtel1M 335083 AA----TGTTTCTTAAGAATGGGGGGAAATCCCAGCA 335115 ---- i ii - i ?v C L2#LINE/L2 1816 AATTTTTGTTTTTTAAAGAT-GGGAGAAATNACAGCA 1781 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 41.51 CpG sites = 61, Kimura (unadjusted) = 42.63 Transitions / transversions = 1.49 (61/41) Gap_init rate = 0.07 (24 / 330), avg. gap size = 2.58 (62 / 24) 250 22.81 5.26 0.00 chr1qtel1M 335111 335167 (664833) L2d_3end#LINE/L2 451 510 (6) m_b37s601i3 1271 chr1qtel1M 335111 CAGCACTGAGCACAGTGCC-AGTA-ACA-CAGGTGCTTAATAAGTGCTTG 335157 i iv i- i - i -i i i i i L2d_3end#LINE 451 CAGCGCCTAGCACAGTGCTGAGCACATAGTAGGCGCTCAATAAATACTTG 500 chr1qtel1M 335158 CCGATTGATT 335167 ii L2d_3end#LINE 501 TTGATTGATT 510 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 24.43 CpG sites = 12, Kimura (unadjusted) = 29.76 Transitions / transversions = 12.00 (12/1) Gap_init rate = 0.05 (3 / 56), avg. gap size = 1.00 (3 / 3) 807 26.77 19.54 1.22 chr1qtel1M 335395 335742 (664258) C L3#LINE/CR1 (5) 4094 3684 m_b37s601i4 1272 chr1qtel1M 335395 AATCCCAGAATTCTAGAATTGGAAAGGACC----A----ATCTA------ 335430 v iii i i ---- ---- ------ C L3#LINE/CR1 4094 AATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCAA 4045 chr1qtel1M 335431 --------CCAA---AGAAATTCCTCCTACTTTATCTTTGACCAATGGTT 335469 -------- --- i i i vvi ii v i i C L3#LINE/CR1 4044 CCTCCCATCCAATGCAGGAATCCCTTCTACAACATCCCTGACAAGTGGTC 3995 chr1qtel1M 335470 GTCCAATCTCTGTTTGAAGACCTCTAAGAAGGAGAAACATATCTCCTCTG 335519 i ii i v i ivi v i i i vi iiv ?v C L3#LINE/CR1 3994 ATCCAGCCTCTGCTTGAACACCTCCAGTGACGGGGAGCTCACTACCTCNC 3945 chr1qtel1M 335520 AAGGCAGCC-ATTTCACGT--GGACGGATCAAACTGTT---AAGTT-TTC 335562 i - i iv -- i v vi i --- - C L3#LINE/CR1 3944 GAGGCAGCCCATTCCATTTTTGGACAGCTCTGATTGTTAGAAAGTTCTTC 3895 chr1qtel1M 335563 ----------ACTGACATTT-----------------ACTCATTGTTCCT 335585 ----------i i v i ----------------- i v C L3#LINE/CR1 3894 CTTATATTGAGCCGAAATCTGCCTCCCTGTAACTTCCACCCATTGGTCCT 3845 chr1qtel1M 335586 GATCCTGCTCTTTGGGGACAAATAGAACAA-----CTCCCTCCTC---AT 335627 ii i i i i v v i i -----v i --- C L3#LINE/CR1 3844 AGTTCTGCCCTCTGGAGCCACACAGAATAAGTCTAATCCCTCTTCCACAT 3795 chr1qtel1M 335628 GACAGTTCTACATATACTGGAAGTCACTTATCATAT-TCCTGAAAGTGTT 335676 ii v v i v v vi i - vv v C L3#LINE/CR1 3794 GACAGCCCTTCAAATATTTGAAGACAGCTATCATGTCTCCTCTAAGTCTT 3745 chr1qtel1M 335677 AATTGTTCTTTATGCTAAATATGCTCAGTTCCTTCCCCCGAATGCTCATG 335726 --i v ii v i v i vv -v v i C L3#LINE/CR1 3744 --CTCTTCTCCAGGCTAAACATCCCCAGTTCCTTCAACCG-TTCCTCATA 3698 chr1qtel1M 335727 TACCATGAATTTTCCA 335742 iv i-- C L3#LINE/CR1 3697 TGACATGG--TTTCCA 3684 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 33.48 CpG sites = 58, Kimura (unadjusted) = 34.41 Transitions / transversions = 1.71 (58/34) Gap_init rate = 0.05 (19 / 347), avg. gap size = 3.84 (73 / 19) 376 27.42 7.41 5.45 chr1qtel1M 336106 336267 (663733) C MIR3#SINE/MIR (28) 180 16 m_b37s601i5 1273 chr1qtel1M 336106 TGGCAAAGACTCTGGAGTGTCTTCTTCTCTAGC----TCATGTTACAGTT 336151 v ii ii i -i v vv i i ---- v v C MIR3#SINE/MIR 180 TGGAAGGGACCTTAGAG-ATCATCTAGTCCAACCCCCTCATTTTACAGAT 132 chr1qtel1M 336152 GAGGAAATTGAGGC--AAGGAGG---ACTGACTTGCCCAGGAGCACACAG 336196 i -- ii --- v i iv C MIR3#SINE/MIR 131 GAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAG 82 chr1qtel1M 336197 CTGGGCAATGTCTGAGGCCAGATTTTGACTCAGGAAGGAGTCTTCCTGA- 336245 ?i vi i v v v vi i vvi i ------ - - C MIR3#SINE/MIR 81 CNAGTTAGTGGCAGAGCCGGGACTAGAACCCAG------GTC-TCCTGAC 39 chr1qtel1M 336246 --CCAATTCAGCACTCTGTCCACT 336267 -- i i - ii v ii C MIR3#SINE/MIR 38 TCCCAGTCC-GTGCTCTCTCTGCT 16 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 35.56 CpG sites = 26, Kimura (unadjusted) = 35.56 Transitions / transversions = 1.62 (26/16) Gap_init rate = 0.09 (14 / 161), avg. gap size = 1.50 (21 / 14) 469 22.38 6.11 4.51 chr1qtel1M 336138 336268 (663732) C MIRc#SINE/MIR (120) 148 16 m_b37s601i6 1273 chr1qtel1M 336138 CTCATGTTACAGTTGAGGAAATTGAGGC--AAGGAGG---ACTGACTTGC 336182 i v v i -- ii --- v C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr1qtel1M 336183 CCAGGAGCACACAGCTGGGCAATGTCTGAGGCCAGATTTTGACTCAGGAA 336232 i iv i vv i v v v vi i ivi i --- C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAG--- 52 chr1qtel1M 336233 GGAGTCTTCCTGA--CCAA-TTCAGCACTCTGTCCACTG 336268 --- -- - i ii v C MIRc#SINE/MIR 51 ---GTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTG 16 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 25.92 CpG sites = 16, Kimura (unadjusted) = 27.02 Transitions / transversions = 1.33 (16/12) Gap_init rate = 0.08 (10 / 130), avg. gap size = 1.40 (14 / 10) 294 22.39 3.96 7.14 chr1qtel1M 336451 336551 (663449) C CR1-3_Croc#LINE/CR1 (948) 2657 2560 m_b37s551i2 1274 chr1qtel1M 336451 CATCTTTACTTGTCCCGGTTGTCCTCCTAACCCTCTCTAGCTTTTCACTG 336500 i- - ----- ivi i i vvi C CR1-3_Croc#LI 2657 CATCTTTG-TTG-CCCG-----CCTCTGGACCCTCTCTAACTTCTCCACG 2615 chr1qtel1M 336501 TTC---TTAAACTGTGG-TCCTAGACATGAACACAGTGTTCCAGAGGAGG 336546 i --- v -v i vv v ii v C CR1-3_Croc#LI 2614 TCCTTTTTAAAATGTGGAGCCCAGAACTGCACACAGTACTCCAGATGAGG 2565 chr1qtel1M 336547 TCTGA 336551 i i C CR1-3_Croc#LI 2564 CCTAA 2560 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 25.48 CpG sites = 12, Kimura (unadjusted) = 26.94 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.09 (9 / 100), avg. gap size = 1.22 (11 / 9) 302 24.65 7.41 4.82 chr1qtel1M 336463 336624 (663376) C CR1-11_Crp#LINE/CR1 (420) 1041 876 m_b37s551i3 1274 chr1qtel1M 336463 TCCCGGTTGTCCTCCTA---ACCCTCTCTAGCTT---TTCACTGTTCTTA 336506 ii v i i v--- ivi i i --- iiv i C CR1-11_Crp#LI 1041 TCCTAGTAGCCCTTCTCTGCACCTGTTCCAGTTTGAATTCATCTTTCTTG 992 chr1qtel1M 336507 AAC-TGTGGT-CCTAGACATGAACACAGTGTTCCAGAGGAGGTCTGAGGA 336554 - - -v i vv v i v v vv C CR1-11_Crp#LI 991 AACATG-GGTGACCAGAACTGTACACAGTATTCCAGATGAGGTCTCACCA 943 chr1qtel1M 336555 AGGCACTT-TACAATGGAATTACTACTTCCATAT---TCCTGAAAACTCT 336600 -- iv - v v v --- v i --- C CR1-11_Crp#LI 942 --GTCCTTGTACAATGGCATTAATACTTCCCTATCTCTACTGGAAA---T 898 chr1qtel1M 336601 GCTCCTCTTAAGGCATCCTGCGAT 336624 i-- ii ? v iv C CR1-11_Crp#LI 897 A--CCTTCTNATGCATCCTAGGAT 876 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 30.44 CpG sites = 19, Kimura (unadjusted) = 30.44 Transitions / transversions = 1.00 (19/19) Gap_init rate = 0.09 (14 / 161), avg. gap size = 1.43 (20 / 14) 245 25.29 14.79 2.52 chr1qtel1M 336688 336829 (663171) C L2#LINE/L2 (1666) 1416 1258 m_b37s601i7 1270 chr1qtel1M 336688 GTCCAGCAAAGTT----AGTGAATT-ACTAAGGGAGGCATGTAGAAGGAT 336732 i v i v---- v- i i --- v ? C L2#LINE/L2 1416 GTCTAGGAGAGTGGGAGAGTGAATGGACTAGGGAA---ATGTAGTANGAT 1370 chr1qtel1M 336733 TGCCCAGCACCAGTTAAAGG-CCAGTTG----TAATG----TGAACTT-- 336771 vi v - i - v ---- ?i ---- i -- C L2#LINE/L2 1369 TGCCGGGCAGCA-TTAAGGGCCCACTTGAGGTTNGTGGTCATGAATTTAA 1321 chr1qtel1M 336772 -GTGTGGGC--TCGACA--GTGATATGGTTTTCTCCATCTTCATGTAGCA 336816 - v iv -- ii -- vi i v v iv i vi v C L2#LINE/L2 1320 AGTGAGACCAGTCAGCATGGTTGTGTGTTTTTCTCCAGCCACGTTCAGCT 1271 chr1qtel1M 336817 GCACATGTGAAAG 336829 ? iv v i C L2#LINE/L2 1270 GCNCGGGTGCAGG 1258 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.03 CpG sites = 18, Kimura (unadjusted) = 32.18 Transitions / transversions = 1.06 (18/17) Gap_init rate = 0.09 (13 / 141), avg. gap size = 1.92 (25 / 13) 206 34.90 4.55 3.60 chr1qtel1M 337376 337485 (662515) L2d_3end#LINE/L2 140 250 (266) m_b37s601i8 1275 chr1qtel1M 337376 ACGCTGTTCCTC--ATCTAAGGCATGTCCTCTCCTTCCCTGGTGTCTTTG 337423 i i --ii -- v i ii i i v- v i i L2d_3end#LINE 140 ACGCCGTTCCCCCCGCCT--GGAATGCCCTTCCCCTTCCTC-TCTCTCTA 186 chr1qtel1M 337424 CCCACACTGTTATCCAATTACTAGAAT---GTTCAGGTATCACCTCCTTC 337470 i v - vi i viivii iiii--- i i vi i L2d_3end#LINE 187 TCCAAA-TCCTACCCATCCTTCAAGGCCCAGCTCAAGTCCCACCTCCTCC 235 chr1qtel1M 337471 ATGGAGCCTTTCCTG 337485 i i i L2d_3end#LINE 236 ACGAAGCCTTCCCTG 250 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 46.49 CpG sites = 29, Kimura (unadjusted) = 52.82 Transitions / transversions = 3.62 (29/8) Gap_init rate = 0.06 (6 / 109), avg. gap size = 1.50 (9 / 6) 22 15.04 0.00 0.00 chr1qtel1M 338014 338050 (661950) (C)n#Simple_repeat 1 37 (0) m_b37s252i1 1276 chr1qtel1M 338014 CCCCCTGCGCCCTTCCCCCCCCCCCCCCCCCCCCCCC 338050 iv v ii (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 37 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 24 39.19 0.00 0.00 chr1qtel1M 338858 338973 (661027) (CCC)n#Simple_repeat 1 116 (0) m_b37s252i2 1277 chr1qtel1M 338858 CCCCTCCTCCCACCGAGCCACCCCTCCCCCATTCCCCTCCCCCCCATTCC 338907 i i v vvv v i vii i vii (CCC)n#Simple 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 50 chr1qtel1M 338908 CCTCCCCCCAATTCCCCTCCCCCATTCCCCTCCCCCATTGGCCCCCCACA 338957 i vvii i vii i viivv v v (CCC)n#Simple 51 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 100 chr1qtel1M 338958 ACACCCCCCCCCCTCC 338973 v v i (CCC)n#Simple 101 CCCCCCCCCCCCCCCC 116 Matrix = Unknown Transitions / transversions = 1.06 (18/17) Gap_init rate = 0.00 (0 / 115), avg. gap size = 0.0 (0 / 0) 17 18.82 10.53 2.44 chr1qtel1M 340454 340529 (659471) (TA)n#Simple_repeat 1 82 (0) m_b37s252i4 1278 chr1qtel1M 340454 TATATATAT-TATAT-TACCGA-ATAT-TATGTA-ATTAATATAATTACA 340498 - - ivv - - i - vv vv i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr1qtel1M 340499 -ACACATATA-ATATCATATACATCATAT-TATA 340529 - i i - - i - - (TA)n#Simple_ 51 TATATATATATATAT-ATATATAT-ATATATATA 82 Matrix = Unknown Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.13 (10 / 75), avg. gap size = 1.00 (10 / 10) 25 27.51 3.51 2.61 chr1qtel1M 340450 340563 (659437) (TAATA)n#Simple_repeat 1 115 (0) m_b37s252i3 1279 chr1qtel1M 340450 TAATTATATATATTATATTACCGAATATTATGTAAT-TAATATAATTACA 340498 - - v v ivv v i - - i (TAATA)n#Simp 1 TAA-TATA-ATATAATATAATATAATATAATATAATATAATATAA-TATA 47 chr1qtel1M 340499 ACA-CATATAATATCATAT-ACATCATATTATACAACAT-TTTTTTTATT 340545 i -v v - i v v i i -v v vv v (TAATA)n#Simp 48 ATATAATATAATATAATATAATATAATATAATATAATATAATATAATATA 97 chr1qtel1M 340546 ACGTAATATAAAATTATA 340563 ii v v (TAATA)n#Simp 98 ATATAATATAATATAATA 115 Matrix = Unknown Transitions / transversions = 0.56 (9/16) Gap_init rate = 0.06 (7 / 113), avg. gap size = 1.00 (7 / 7) 877 28.51 3.68 4.78 chr1qtel1M 341317 341887 (658113) HERVK14C#LTR/ERVK 3108 3672 (3762) m_b37s701i0 1280 chr1qtel1M 341317 GGGAACTCTTCAGCCTGGGCTTCCATGTCCTACTCAGTTGCCTAGAGAAT 341366 ii ? v v v ? vi ii ivv v v v HERVK14C#LTR/ 3108 GGGGGCNCTGCAGCCAGGGCTGCCNTCCCCCGCCATGATTCCTAGAGACT 3157 chr1qtel1M 341367 GGCCTCTTTGGGTTACAGACATTAAGGATTATTTCTATTCTATCCCTCTA 341416 ?i vvvi i iv v i ii v v i HERVK14C#LTR/ 3158 GGCCNTTAATAGTTATAGATTTGAAGGACTGCTTCTTTACTATTCCTCTA 3207 chr1qtel1M 341417 G-ATAGGGAGGATATGAAAGATTTGCCTTTTC-ATTGCCCAGC-GTTAAC 341463 - v vv? iv v i i v - -- v -i v HERVK14C#LTR/ 3208 GCAGAGCCNGATTTTGAAAAATTTGCTTTTACTATT--CCTGCTATGAAC 3255 chr1qtel1M 341464 --TTAGCTGAGCCTTATAAA-AAATATGAATGGACAGTTTTGCCACAGGG 341510 --iv -- i ?-ii iv- i? v v v ? i HERVK14C#LTR/ 3256 AACAAG--GAACCN-GCAGCCAGNTATCATTGGAAAGTNTTGCCGCAGGG 3302 chr1qtel1M 341511 AATGAAAAACAGCCCCACTATGTGTCAAATGTATGTTGCTGCTGCTCTTA 341560 v vvi i i ? ? v iv ? v vv?vv v v HERVK14C#LTR/ 3303 CATGTTGAATAGTCCNACNATTTGTCAAACTTNTGTGGGGNAGGCTATTC 3352 chr1qtel1M 341561 GTCCAGTAAGAAAAGCATTTCCAAAAG-TTATGCTATTACATTACATGGA 341609 iv v ? i vvvi i vv-? iii - i HERVK14C#LTR/ 3353 AACCTGTNAGAGATCAGTTTCCAGATTCNTATATCATT-CATTATATGGA 3401 chr1qtel1M 341610 TGACATATTGGCATGTGCACCTGA-----GGAAC--ACTGAGGAAATGTT 341652 ---? iv i ----- ii -- v vvv i HERVK14C#LTR/ 3402 TGACATATT---NTGTGCGGCCGAAACTCGAGACCAACTTATCCAGTGTT 3448 chr1qtel1M 341653 AGAAGCATGTCTACAAAAGACCATAG-AAACACTAAGGAACTACAAAATG 341701 v--v ii i i i vi ? -vi i -- -- ------ HERVK14C#LTR/ 3449 AT--TCACATTTACAGAAGGCGGTNGCCGACGCT--GGA--T------TG 3486 chr1qtel1M 341702 CACATAGCTCCAGAAAAAATTCAAAGACATGCTCCTTTTCAATATTTAGG 341751 ?v ? ? v vi?v i i i HERVK14C#LTR/ 3487 NTCATAGCNCCNGATAAAATTCAAACGNCTACTCCTTTCCAATATTTGGG 3536 chr1qtel1M 341752 ATATG-AAGTATACCCTAAGGTGCTTACAGTTCAAAAACTCTCCTTAAGA 341800 - - i vi vvvv i iiv vivi? iv ---- i - HERVK14C#LTR/ 3537 A-ATGCAGGTTCAGGAAAGGGCAATTAAGCCNCAAAAGGT----TCAA-A 3580 chr1qtel1M 341801 ACAGAAAAG-----CTAAACACATTGAATGATTTTCAGAAATTGATAGGA 341845 viv ----- i v v i i iv i HERVK14C#LTR/ 3581 TTCGAAAAGACTCTCTGAAAACTTTAAATGATTTTCAAAAATTATTAGGG 3630 chr1qtel1M 341846 GATATCCAATGGATGCGACCAGTGTTAGGCTTGACTACCTAT 341887 iv v v viiv v vv HERVK14C#LTR/ 3631 GATATTAATTGGATTCGACCTACTTTAGGCATTCCTACCTAT 3672 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 35.80 CpG sites = 72, Kimura (unadjusted) = 37.91 Transitions / transversions = 0.87 (72/83) Gap_init rate = 0.07 (38 / 570), avg. gap size = 1.26 (48 / 38) 583 31.48 4.46 5.51 chr1qtel1M 341357 341961 (658039) HERVK3#LTR/ERVK 2953 3551 (3651) m_b37s701i1 1280 chr1qtel1M 341357 CCTAGAGAATGGCCTCTTTGGGTTACAGACATTAAGGATTATTTCTATTC 341406 v v ivvi v i iv i v v HERVK3#LTR/ER 2953 CCAAGAGACTGGCCTCTCGTAGTAATAGATCTTAAGGATTGTTTCTTTAC 3002 chr1qtel1M 341407 TATCCCTCTAGATAGGGAGGATATGAA-AGATTTGCCTTTTCATTGCCCA 341455 v ?i v iii i v vv-v i vv iv HERVK3#LTR/ER 3003 TATACCNTTACACGAGAAGGATAAGCCTCGATTTGCCTTCTCTGTGCCTT 3052 chr1qtel1M 341456 GCGTTAACTTAGCTGAGCCTTATAAAAAATATGAATGGACAGTTTTGCCA 341505 vii iiv ivv i vv vvvviv v v i v HERVK3#LTR/ER 3053 CTATTAATCAAAGAGAACCTGTTTCTCGTTATCAATGGAAAGTTTTACCC 3102 chr1qtel1M 341506 CAGGGAATGAAAAACAGCCCCACTATGTGTCAAATGTATGTTGCTG--CT 341553 i v vvv i i vv i --- i v iv -- v HERVK3#LTR/ER 3103 CAAGGCATGCTTAACAGTCCTACGCTATGTCA---GCATTTTGTAGGACG 3149 chr1qtel1M 341554 GCTCTTAGTCCAGTAA----GAAAAGCATTTCCAAAAG-TTATGCTATTA 341598 viv i--- v i---- i viii v vv - iiii - HERVK3#LTR/ER 3150 GGCATTAA---AGGAGCCTCGGAATATGTTTCCCACTGCTTACATCATT- 3195 chr1qtel1M 341599 CATTACATGGATGACATA---TTGGCATGTGCACCTGAGGAACACTGAGG 341645 ?i i v--- ---i v ----- -- vv HERVK3#LTR/ER 3196 CATTNTATGGATGATATTCTTTTGGC---CGCTCCT-----ACA--GATC 3235 chr1qtel1M 341646 AAATGTTAGAAGCATGTCTACAAAAGACCATAG-AAAC----ACTAA--G 341688 v v -v vv v v i ii v v -iii ---- -- HERVK3#LTR/ER 3236 AAATCTTACA-TCAGTTATTCAGAGAAACAAAGCGGGCTTTGACTAAATG 3284 chr1qtel1M 341689 GAACTACAAAATGCACATAGCTCCAGAAAAAATTCAAAGACATGCTCCTT 341738 iiv ?------ i ii v v vv v i v HERVK3#LTR/ER 3285 GAATCTCAAAATN------GCTCCAGAGAAGGTGCAAACAACTTCCCCAT 3328 chr1qtel1M 341739 TTCAATATTTAGGA--TATGAAGTATACCCTAAGGTGCTTACAGT-TCAA 341785 vi ? i -- v-- - vvvi iv iv i i- i HERVK3#LTR/ER 3329 ACCANTACTTAGGAACTATT--GT-TACGGAGAGAAGTGTACGGCCTCAG 3375 chr1qtel1M 341786 AAA----CTCTCCTTAAGAACAGAAAAGCTAAACACATTGAATGATTTTC 341831 ----i v ii ---- i v v v i HERVK3#LTR/ER 3376 AAAGTAGTTCTCCGTAAAGACAG----GTTACAGACTTTAAATGATTTTC 3421 chr1qtel1M 341832 AGAAATTGATAGGAGATATCCAATGGATGCGACCAGTGTTAGGCTTGACT 341881 iv iv i iv v v v ii i iv vi HERVK3#LTR/ER 3422 AACAATTATTAGGGGATATTAATTGGCTGCGCCCGATGCTAGGTATTGCT 3471 chr1qtel1M 341882 ACCTATCAA-TTACA-ACCATTATATGACATTTTAAGGGGAGACAGTGCT 341929 - - i v ivvi vi vi i vv -- v ? HERVK3#LTR/ER 3472 ACCTATCAACTTACACATCTTTACCAAACCCTGCAAGGAGATTC--TTCN 3519 chr1qtel1M 341930 TTAAATTCACCACGCCAGCTTACAAAAGAAGC 341961 v i v i ? v i HERVK3#LTR/ER 3520 TTAAATTCCCCGCGGCAACTNACTAAAGAGGC 3551 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.38 CpG sites = 83, Kimura (unadjusted) = 41.74 Transitions / transversions = 0.86 (83/97) Gap_init rate = 0.08 (46 / 604), avg. gap size = 1.30 (60 / 46) 583 25.77 7.98 4.51 chr1qtel1M 342875 343325 (656675) HERVK14C#LTR/ERVK 4643 5108 (2326) m_b37s701i2 1280 chr1qtel1M 342875 GAGTTAGCTAGGAGCATAGTAAAAGCC--TGTACGGC-TTGCCTTCCTTT 342921 ?i v? i i i -i i? i ? -- ? ii - i ??v v HERVK14C#LTR/ 4643 GNATTACNTGGAAACA-GGCNAAGGNCATTGTNCAACATTGCCCTNNGTG 4691 chr1qtel1M 342922 CCATGCTCCTACA-CTGCC---TCCAGGGA----AA--AACTCTCGTGAT 342961 v - v - --- v ----?i-- i ? v iv HERVK14C#LTR/ 4692 CCAGG-TGCTACAACTGCCACATCAAGGGACTGGNGTTAACCCNCGAGGA 4740 chr1qtel1M 342962 TTGAGACCCAGTGAAATTTGGCAAATGGATGTGACCCATTATAAATTT-T 343010 iv? i i ?viv ? i ? -i vv ?i- HERVK14C#LTR/ 4741 TTGGCNCCTAATNCGCTNTGGCAAATGGACGTNACCCAT-GTACCTNCAT 4789 chr1qtel1M 343011 TTGGTCGTCTGTCTTTTATCCATGTTGTGGTAGACCCTTTTTCAGGATTC 343060 vviv ? ? vii ?iiv iv i ----- HERVK14C#LTR/ 4790 TTGGGAAACTNTCNTACGTCCATGTNACTGTAGATACCTTTTC-----TC 4834 chr1qtel1M 343061 ACTTTT-----GCAA--TACCAGCAGCAAAAGAGATAGCC---CGAGT-- 343098 i v----- ? -- i -- i ii? ii? i--- v -- HERVK14C#LTR/ 4835 ATTTTGTNTGGGCNACTTGCCA--AACAGGNGAGGCNGCTGCTCGTGTTA 4882 chr1qtel1M 343099 --GGTCATTAAATTTCTTATACAAGCATTTGCAATTATGGGTATGCCACA 343146 --i v viv i i ------- i ?i i i v HERVK14C#LTR/ 4883 AAAGACATTTGCTTTCCTGT-------TTCGCNGTCATGGGCATTCCACA 4925 chr1qtel1M 343147 AGCCATAAAAACAGACAATGGACCTGCATATACTTCTAAACATTT-TGCA 343195 iv? v ? v v vv i?? vv ?v -?i?i HERVK14C#LTR/ 4926 AAANATTAAAACNGACAATGGCCCAGGCTACNNTAGTAAANCTTTANANG 4975 chr1qtel1M 343196 CATTTTTGTGCACAGTATAAGATTTTACACACCACTGGCATACCCTTTAA 343245 i ii - vv i iv? v vv ?i ? v v HERVK14C#LTR/ 4976 CGTTCCT-TCAACAATGGNACATTAAACACANTACTGGNATCCCCTATAA 5024 chr1qtel1M 343246 TCCTCAAGGACAGGCAATAGTAGAGAGGAGA-AACAGAGATATTAAGATG 343294 i ? i v v v - v v- iv - iv i ?- HERVK14C#LTR/ 5025 TTCTCAAGGNCAAGCCATTGTTGA-ACGAGCTAATCGA-ACCTTAAAAN- 5071 chr1qtel1M 343295 CTC--CTCCAAAAACAAA----AGAAAGGGGGAGCCA 343325 --i v ---- i i HERVK14C#LTR/ 5072 CTCAATTACAAAAACAAAAGACAGAAGGGGGGAACCA 5108 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 33.64 CpG sites = 61, Kimura (unadjusted) = 35.65 Transitions / transversions = 1.22 (61/50) Gap_init rate = 0.08 (37 / 450), avg. gap size = 1.54 (57 / 37) 430 31.09 7.15 9.77 chr1qtel1M 342880 343592 (656408) HERVK3#LTR/ERVK 4479 5174 (2028) m_b37s701i3 1280 chr1qtel1M 342880 AGCTAGGAGCATAGTAAAAGCCTGTACGGCTTGCCTTCCTTTCCATGCTC 342929 ivi ? v v vi vv v v v v?v HERVK3#LTR/ER 4479 AGCTAGGGCTATNGTACAAGCCTGTCCTACTTGCCAGCATGTCCCTGGNG 4528 chr1qtel1M 342930 CTACACTGCCTCCAGGGAAA---AACTCTCGTGATTTGAGACCCAGTGAA 342976 ii --- vi iiii?--- i v v i ivv v i HERVK3#LTR/ER 4529 CCGCAC---CTGTAGAAGGNTGTAACCCACGAGGTTTGGCTCCAAATGAA 4575 chr1qtel1M 342977 ATTTGGCAAATGGATGTGACCCATTATAA-ATTTTTTGGTCGTCTGTCTT 343025 i v v i- i- vii iviv ----- HERVK3#LTR/ER 4576 ATCTGGCAAATGGATGTTACACAC-ATAGCAGCCTTTGGCAAGCT----- 4619 chr1qtel1M 343026 TTATCCATGTT--GTGG----TAGACCCTTTTTCAGGATTCAC-TTTTGC 343068 - v i -- i---- v v ----- i- vi HERVK3#LTR/ER 4620 -TAGCTATGTTCTGTGANCTATAGACACTTATTC-----TCATATGCTGC 4663 chr1qtel1M 343069 A------ATACCAGCAGCAAAAGAGATAGCCCGAGTGGTCAT-TA----A 343107 ------ i -- i iiv i ----- - ----i HERVK3#LTR/ER 4664 ATGCTACATGCCA--AACAGGTGAGACAGC-----TGGTCATGTACGGCG 4706 chr1qtel1M 343108 ATTTCTTATACAAGCATTTGCAATTATGGGTATGCCACAAGCCAT-AAAA 343156 iv iv v iiv v vvv v i -i i v - HERVK3#LTR/ER 4707 ACATTGTCTGTCATCATTTGCTCATATGGGGATACC-TAAACAATTAAAA 4755 chr1qtel1M 343157 ACAGACAATGGACCTGCATATA---------CTTCTAAACATTTTGCACA 343197 v i v --------- i v v ivi HERVK3#LTR/ER 4756 ACTGACAATGGACCCGCTTATACTAGTCATGCTTTTCAAAATTTCTTACA 4805 chr1qtel1M 343198 TTTTTGTGCACAGTATAAGATTTTACACACCACTGGCATACCCTTTAATC 343247 vi v ---- -----iv i vv v v v i v HERVK3#LTR/ER 4806 GCTTTGGGC----TATAA-----CCCATAAAACAGGAATTCCTTATAATC 4846 chr1qtel1M 343248 CTCAAGGAC-AGGCAATAGTAGAGAGGAGAAACAGAGATATTAAGATGC- 343295 vi - v - v iv v i-v i i vi i - HERVK3#LTR/ER 4847 CTAGAGGACAAGGCATTA-TAGAGCGGGCACAT-CAAACATTACAACGCA 4894 chr1qtel1M 343296 TCCTCCAAAAACAAAAGAAAGGG----GGAGCCACAA--GCAACCCTAG- 343338 vi vv iiii? ---- v - --i v ii i- HERVK3#LTR/ER 4895 TGTTGAAAAAACAAAAAGGGNGGTATAGGAGGC-CAACTACCACCTCAAT 4943 chr1qtel1M 343339 -AGAACTTCTAAATCTAGCTCTTTATACTATTGATTTCTT-GATTTTTGA 343386 - i --- v i ii v v v vi i - i ii i HERVK3#LTR/ER 4944 CAAAA---CTACATTTAGCCTTATTTACTTTAAATTTTTTNGACTCCTGG 4990 chr1qtel1M 343387 CAAAGATGCACTGGCTCCGGCAGGCAGGTTTTATAACCCACTGGAAGGGC 343436 i vi vvvv i i iv i---------- i v ---- HERVK3#LTR/ER 4991 TACGGATGGTAAGACTCCAGCAGAAAGA----------CATTGGCA---- 5026 chr1qtel1M 343437 AGTGTC-----CAATGCGAGCAGCTCCACTATCTTTAGATAATCGCCAGG 343481 i-----v v v iiv i ---- i--- -------- i HERVK3#LTR/ER 5027 AGTGTTAGAGGAAAAGAGGAAAGTT----TATCC---GA--------AAG 5061 chr1qtel1M 343482 TGATGTGGAGAGATCCAGA--AAGTGGTGAATGAAGGGGCCAGATAGGTA 343529 v i i vvi i -- ? ii- i ii i v i i i v HERVK3#LTR/ER 5062 TGTTATGGAAATCCCCGGAAGAAGNGAC-AATGGAAAGGTCCGGTGGATT 5110 chr1qtel1M 343530 AACTG-CTTGGGGGAGAGGGTTTGCTTGTATCTCCACAGATGAAGAAGGA 343578 v - v i? v i i ii iv v i vi HERVK3#LTR/ER 5111 TACTGACGTGGGGANGAGGGTATGCTTGTGTTTTTACAGGAGATGGACAA 5160 chr1qtel1M 343579 ATCAGATGGGTGCC 343592 i ivi HERVK3#LTR/ER 5161 ACCGTGTGGGTGCC 5174 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.26 CpG sites = 109, Kimura (unadjusted) = 41.42 Transitions / transversions = 1.20 (109/91) Gap_init rate = 0.12 (88 / 712), avg. gap size = 1.35 (119 / 88) 495 29.85 6.00 3.67 chr1qtel1M 342980 343379 (656621) HERVK#LTR/ERVK 4858 5266 (2270) m_b37s701i4 1280 chr1qtel1M 342980 TGGCAAATGGATGTGACCCATTATAAATTT-TTTGGTCGTCTGTCTTTTA 343028 v v -i vv i- vv vi v ? i HERVK#LTR/ERV 4858 TGGCAAATGGATGTCACGCAT-GTACCTTCATTTGGAAGATTGTCATNTG 4906 chr1qtel1M 343029 TCCATGTTGTGGTAGACCCTTTTTCAGGATTCACTTTTGCAA--TACCAG 343076 viii v iv v viv iv vv -- i HERVK#LTR/ERV 4907 TCCATGTAACAGTTGATACTTATTCACATTTCATATGGGCAACCTGCCAG 4956 chr1qtel1M 343077 -CAGCAAAAGAGATAGCCCGAGTGGTCATTAA-ATTTCTTATACAAGCAT 343124 - v i iiv ivv i-- v v vv - v - vv i- HERVK#LTR/ERV 4957 ACAGGAGAAAGTACTTCCCA--TGTTAAAAAACATTTATTAT-CTTGT-T 5002 chr1qtel1M 343125 TTGCAATTATGGGTATGCCACAAGCCATAAAAACAGACAATGGACCTGCA 343174 vi i vi v v ivv v v i v v HERVK#LTR/ERV 5003 TTGCTGTCATGGGAGTTCCAGAAAAAATTAAAACTGACAATGGGCCAGGA 5052 chr1qtel1M 343175 TATACTTCTAAA-CATTTTGCACATTTTTGTGCACAGTATAAGATTTTAC 343223 ivv vv - ? iiiv v i ivii- iv i vi HERVK#LTR/ERV 5053 TACTGTAGTAAAGCNTTCCAAAAATTCTTAAAT-CAGTGGAAAATTACAC 5101 chr1qtel1M 343224 ACACCACTGGCATACCCTTTAATCCTCAAGGACAGGCAATAGTAGAGAGG 343273 i v v v v i v i i v v i i HERVK#LTR/ERV 5102 ATACAACAGGAATTCCTTATAATTCCCAAGGACAGGCCATAGTTGAAAGA 5151 chr1qtel1M 343274 AGAAACAGAGATATTAAGATGCTCCTCCAA------AAACAAAAGAAAGG 343317 vv i - i i v i - ---- ------ ii HERVK#LTR/ERV 5152 ACTAATAGA-ACACTCAAA-GCT----CAATTGGTTAAACAAAAAGAAGG 5195 chr1qtel1M 343318 GGGAGCCA-CAAGCAA---------CCCTAGAG--AACTTCTAAATCTAG 343355 v -i v i--------- i v-- --- HERVK#LTR/ERV 5196 GGGAGACAGTAAGGAGTGTANCACTCCCCAGATGCAACTT---AATCTAG 5242 chr1qtel1M 343356 CTCTTTATACTATTGATTTCTTGA 343379 v i v vi i i HERVK#LTR/ERV 5243 CACTCTATACTTTAAATTTTTTAA 5266 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 38.61 CpG sites = 52, Kimura (unadjusted) = 38.61 Transitions / transversions = 0.83 (52/63) Gap_init rate = 0.06 (24 / 399), avg. gap size = 1.62 (39 / 24) 292 29.78 19.10 0.42 chr1qtel1M 345048 345246 (654754) C MIRb#SINE/MIR (30) 238 3 m_b37s601i9 1281 chr1qtel1M 345048 ACTGTGTATCCGGCACT-TACTGTGGAC----CAGCCAGTAGCTCATTTT 345092 i ii v - i iv vi ---- vv v v v C MIRb#SINE/MIR 238 ACTATGTGCCAGGCACTGTGCTAAGCGCTTTACATGCATTATCTCATTTA 189 chr1qtel1M 345093 GTCTTCATCACTACCC--CCTGGTAGG---------CCTCATTTTATAAA 345131 i i iv v -- vv --------- i i i C MIRb#SINE/MIR 188 ATCCTCACAACAACCCTGCGAGGTAGGTATTATTATCCCCATTTTACAGA 139 chr1qtel1M 345132 TGGGGAAACTGAGGCC----GAG-----------CACCCAGGGTCACCTA 345166 i i---- -----------ii i vi C MIRb#SINE/MIR 138 TGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACA 89 chr1qtel1M 345167 CTTCTTCAGTGTGTGAGGCAGGTTTTGAACCTGGGGCTTGTGT-ACTCC- 345214 vi vv v vvv v i v i ii v - v - - C MIRb#SINE/MIR 88 GCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCT-GTCTGACTCCA 40 chr1qtel1M 345215 AGGCTACCACTCTG-----TGCACAATGGCACCCCTC 345246 i ivvii v----- v i vii C MIRb#SINE/MIR 39 AAGCCCGTGCTCTTTCCACTGCACCACGCTGCCCCTC 3 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 35.31 CpG sites = 30, Kimura (unadjusted) = 38.51 Transitions / transversions = 1.03 (30/29) Gap_init rate = 0.05 (10 / 198), avg. gap size = 3.90 (39 / 10) 265 29.33 10.16 1.44 chr1qtel1M 345513 345640 (654360) C L2b_3end#LINE/L2 (7) 459 321 m_b37s601i10 1282 chr1qtel1M 345513 CAGTCCGTACACATTGA-TAAGCACCTGCTGTGCACCAGGTTTTGTGCT- 345560 v vii v i v - i i i ii i?i - C L2b_3end#LINE 459 CATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTA 410 chr1qtel1M 345561 GGCTCTAGGGCTACAAAGA-----AAGCCAAAAAC-ATCCT--CCTTGGT 345602 v i v iv i----- v i v? -i i-- i vii C L2b_3end#LINE 409 GGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCAC 360 chr1qtel1M 345603 GGGGCT--TGGGCTAGGGAGGGAGGAACAG-CATGCAAGTA 345640 i --ii v v i -- - i ?i C L2b_3end#LINE 359 GGAGCTCACAGTCTAGTGGGGGAG--ACAGACATGTAANCA 321 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 37.63 CpG sites = 25, Kimura (unadjusted) = 40.49 Transitions / transversions = 2.08 (25/12) Gap_init rate = 0.07 (9 / 127), avg. gap size = 1.67 (15 / 9) 219 25.60 5.81 4.60 chr1qtel1M 345807 345892 (654108) C AmnL2-1#LINE/L2 (378) 2235 2149 m_b37s601i11 1283 chr1qtel1M 345807 AGAGCTTTAAACACCAAACAGTCAACTG-GTATTGGGTCCTGAAGAGAAG 345855 i i v v iiv v i v- v i i iv v C AmnL2-1#LINE/ 2235 AGGGTTTTAAAAACAAGGAAGGCAATTTTGAACTGGATCCTGAAATGAAT 2186 chr1qtel1M 345856 AGGGAGCCACTGGCAATTGT----GGACCCCAGGGGTGATG 345892 i v - i ---- i---i C AmnL2-1#LINE/ 2185 GGGGAGCCAGTGG-AGTTGTTTGAGGAT---GGGGGTGATG 2149 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 31.94 CpG sites = 12, Kimura (unadjusted) = 31.94 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.07 (6 / 85), avg. gap size = 1.50 (9 / 6) 507 27.66 5.67 0.00 chr1qtel1M 345913 346053 (653947) MIR#SINE/MIR 71 219 (43) m_b37s601i12 1284 chr1qtel1M 345913 CACTTCCTGGCTGTGTGACCCTGAGCAAGGCACTTCCCTCCACTTTGCTT 345962 v i i i vi vv ii v v i MIR#SINE/MIR 71 CACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCT 120 chr1qtel1M 345963 TGGTTTCCTCAACCGTAAAATTGAGAGGACAACGCTCCCTCCTTGCCAGG 346012 ii v i v i vi i iiv v v i vvi MIR#SINE/MIR 121 CAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTCATAGG 170 chr1qtel1M 346013 GCTGTGGTGAGGATCAAATGGGTTCA-----GCAAAGCATT---AACAG 346053 i v i i v ----- i ii --- MIR#SINE/MIR 171 GTTGTTGTGAGGATTAAATGAGTTAATACATGTAAAGCGCTTAGAACAG 219 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 34.27 CpG sites = 23, Kimura (unadjusted) = 35.40 Transitions / transversions = 1.44 (23/16) Gap_init rate = 0.01 (2 / 140), avg. gap size = 4.00 (8 / 2) 526 20.33 0.00 8.77 chr1qtel1M 346816 346939 (653061) MIRb#SINE/MIR 5 118 (150) m_b37s601i13 1285 chr1qtel1M 346816 GGGGCAGCTAGGTGGCACAGTGGTTAGAGCACCAGCTCTGAAGTCAGGAG 346865 --- ii vv vi i i ivi MIRb#SINE/MIR 5 GGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACA 51 chr1qtel1M 346866 GACCTGAGTTCAAATCCAACCTCAGACACTTAATACTTCCTAGCTGTAGG 346915 i i viv v v ------- iv MIRb#SINE/MIR 52 GACCTGGGTTCGAATCCCGGCTCTGCCACTTA-------CTAGCTGTGTG 94 chr1qtel1M 346916 ACCTTGGGCAAGTCACTTAATCCC 346939 i i i MIRb#SINE/MIR 95 ACCTTGGGCAAGTTACTTAACCTC 118 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 21.63 CpG sites = 14, Kimura (unadjusted) = 23.92 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.08 (10 / 123), avg. gap size = 1.00 (10 / 10) 286 23.84 25.71 1.15 chr1qtel1M 347495 347634 (652366) C MIR#SINE/MIR (15) 247 74 m_b37s601i14 1286 chr1qtel1M 347495 TTATTAAGCACCTACTGTGTGTCAGGC--------------TTTACA--- 347527 i i i i i -------------- --- C MIR#SINE/MIR 247 TTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGCGCTTTACATGT 198 chr1qtel1M 347528 ---AACT---GTGATTCTCCCAGCAACCAGA-AAGGTCGGGGTTGT-AGT 347569 --- ---v i i v i vv -i v vii i - v C MIR#SINE/MIR 197 ATTAACTCATTTAATCCTCACAACAACCCTATGAGGTAGGTACTATTATT 148 chr1qtel1M 347570 CTCTCCATTTTGCAG----------TCAGGCAGAGTGCAGTGCAGTGATT 347609 v i i ---------- v v v vi vv i i C MIR#SINE/MIR 147 ATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACT 98 chr1qtel1M 347610 TGCC-AGGGTCACACACAGCTAGGAA 347634 - i -- v C MIR#SINE/MIR 97 TGCCCAAGGTCACACA--GCTAGTAA 74 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 28.17 CpG sites = 18, Kimura (unadjusted) = 29.20 Transitions / transversions = 1.20 (18/15) Gap_init rate = 0.07 (10 / 139), avg. gap size = 3.80 (38 / 10) 216 25.80 17.80 1.46 chr1qtel1M 347533 347650 (652350) C MIRc#SINE/MIR (72) 196 60 m_b37s601i15 1286 chr1qtel1M 347533 TGATTCTCCCAGCAACC-----AGAAAGGTCGGG---GTTGTAGTCTCTC 347574 i v i ----- iv iv --- vv v v i C MIRc#SINE/MIR 196 TGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCC 147 chr1qtel1M 347575 CATTTTGCAG----------TCAGGCAGAGTGCAGTGCAGTGATTTG-CC 347613 i ---------- v vv v vi vv i - C MIRc#SINE/MIR 146 CATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCC 97 chr1qtel1M 347614 AGGGTCACACACAGCTAGGAACTTG--GACTCAGGCCTC 347650 i -- v v v -- vi i v C MIRc#SINE/MIR 96 AAGGT--CACACAGCTAGTAAGTGGCAGAGCCGGGACTC 60 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.54 CpG sites = 11, Kimura (unadjusted) = 31.73 Transitions / transversions = 0.58 (11/19) Gap_init rate = 0.06 (7 / 117), avg. gap size = 3.29 (23 / 7) 183 21.62 0.00 0.00 chr1qtel1M 348320 348356 (651644) MIR3#SINE/MIR 151 187 (21) m_b37s601i16 1287 chr1qtel1M 348320 TGGACTAGCTGGTCTCTCAGGTCTCTTATATCCCTGA 348356 v i v i vi v i MIR3#SINE/MIR 151 TGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGA 187 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 25.69 CpG sites = 4, Kimura (unadjusted) = 25.69 Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 223 32.38 12.40 3.03 chr1qtel1M 348364 348484 (651516) C L3#LINE/CR1 (155) 3944 3813 m_b37s601i17 1288 chr1qtel1M 348364 GAAGCTGCCTATCTGATTG--GGGCAGCTATAATTACCAAACTACAGGGT 348411 i v i iiv v-- i v i iii i ---- i v C L3#LINE/CR1 3944 GAGGCAGCCCATTCCATTTTTGGACAGCTCTGATTGTTAGA----AAGTT 3899 chr1qtel1M 348412 CT--CTTATGTTGAGCTGAAA-----------GTGCCCACCACCTATTTG 348448 -- i i ----------- iv iv i v C L3#LINE/CR1 3898 CTTCCTTATATTGAGCCGAAATCTGCCTCCCTGTAACTTCCACCCATTGG 3849 chr1qtel1M 348449 TCCTTGTCCCTCCCATTAGAACTTCAATGAGCAAGT 348484 v i iv vi i i iv vv ii C L3#LINE/CR1 3848 TCCTAGTTCTGCCCTCTGGAGCCACACAGAATAAGT 3813 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 42.97 CpG sites = 24, Kimura (unadjusted) = 44.58 Transitions / transversions = 1.71 (24/14) Gap_init rate = 0.06 (7 / 120), avg. gap size = 2.71 (19 / 7) 488 24.23 5.22 1.44 chr1qtel1M 348581 348714 (651286) C L2d2_3end#LINE/L2 (8) 547 409 m_b37s601i18 1289 chr1qtel1M 348581 AATCACCCAAT--CAATAAAGCACCTACTATGTGGTAGACCCTGTGCTAA 348628 v v --iv vi i i vv i v i C L2d2_3end#LIN 547 AATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAG 498 chr1qtel1M 348629 GCACTA---GGGATACAAAAAGAAGCAAAAGATA--GCTCTTGCACTCAA 348673 i i--- -- i v i -- ii i v C L2d2_3end#LIN 497 GCGCTGTGGGGGATACAAA--GAAGTATAAGACATGGTCCCTGCCCTCAA 450 chr1qtel1M 348674 GGAGTTCACAATCTAAATGGGGAGACAACATCCAAAAATGT 348714 i i iv v ivi v i C L2d2_3end#LIN 449 GGAGCTTACAATCTAGTTGGGGAGACAAGACATAAACACGT 409 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 26.67 CpG sites = 19, Kimura (unadjusted) = 29.90 Transitions / transversions = 1.46 (19/13) Gap_init rate = 0.04 (5 / 133), avg. gap size = 1.80 (9 / 5) 64 29.53 1.62 5.72 chr1qtel1M 348923 348949 (651051) (AT)n#Simple_repeat 1 26 (271) m_b37s252i5 1290 chr1qtel1M 348923 ATATATAGAGTATATATGTACATAAAG 348949 v - i i v v (AT)n#Simple_ 1 ATATATATA-TATATATATATATATAT 26 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.04 (1 / 26), avg. gap size = 1.00 (1 / 1) 31 6.38 1.89 3.85 chr1qtel1M 348950 349002 (650998) (TA)n#Simple_repeat 1 52 (0) c_b37s251i0 1291 chr1qtel1M 348950 TATATATATATATATACAGTATAGAGTATATATATATATATATA-AAATA 348998 i - v - - v (TA)n#Simple_ 1 TATATATATATATATATA-TATATA-TATATATATATATATATATATATA 48 chr1qtel1M 348999 TATA 349002 (TA)n#Simple_ 49 TATA 52 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.06 (3 / 52), avg. gap size = 1.00 (3 / 3) 64 29.53 1.62 5.72 chr1qtel1M 349003 349283 (650717) (AT)n#Simple_repeat 27 296 (1) m_b37s252i5 1292 chr1qtel1M 349003 GAGTGCATGTATGTATATACACACACATATATATAGCATATATA-AAATA 349051 v - ii i i i i i i -i - v (AT)n#Simple_ 27 TA-TATATATATATATATATATATATATATATATA-TATATATATATATA 74 chr1qtel1M 349052 TATGTGTATAGAGTATATACTTTATAAAGTATGTGTGTATATGTAAATAG 349101 i i v - - v v - i i i i v - (AT)n#Simple_ 75 TATATATATATA-TATATA-TATATATA-TATATATATATATATATATA- 120 chr1qtel1M 349102 CAT-TAGA-ATATATATGTATATA-ACATACTTTCTTCAGAGTATGTGTG 349148 i - v - i - i - v v vi v - i i i (AT)n#Simple_ 121 TATATATATATATATATATATATATATATA-TATATATATA-TATATATA 168 chr1qtel1M 349149 TATATACATATGTATACACACAGATATAGCATATAGAGTATATA-AAACA 349197 i i i i i v -i v - - v i (AT)n#Simple_ 169 TATATATATATATATATATATATATATA-TATATATA-TATATATATATA 216 chr1qtel1M 349198 TACTTTATAGAGTATGTGTATGTATATACATATAGCATGTGCACATAAAT 349247 - v v - i i i i -i i ii i v (AT)n#Simple_ 217 TA-TATATATA-TATATATATATATATATATATA-TATATATATATATAT 263 chr1qtel1M 349248 GGCATATATATAGTATATATGTGTAGAGAGTATATA 349283 -ii - i i v v - (AT)n#Simple_ 264 -ATATATATATA-TATATATATATATATA-TATATA 296 Matrix = Unknown Transitions / transversions = 2.21 (42/19) Gap_init rate = 0.07 (21 / 280), avg. gap size = 1.00 (21 / 21) 833 32.26 3.12 3.30 chr1qtel1M 349772 350348 (649652) C L1MA10_3end#LINE/L1 (448) 633 58 m_b37s551i4 1293 chr1qtel1M 349772 GTTCATTTCACTCAGCATCAGTTCATGTAAGTCTCTCCA-GCCCTCTCTG 349820 i i i v vv v vi i iiv - iiv v -- C L1MA10_3end#L 633 GCTTATTTCACTTAGCATAATGTCCTCCAGGTTCATCCATGTTGTCGC-- 586 chr1qtel1M 349821 AAATCATCAAGCTGGTCGTTTCTTATAAAGAACAATAATATTTAATAACA 349870 vi- i v vvi v i i v i vvv iv vii C L1MA10_3end#L 585 AAATGG-CAGGATTTCCTTCTTTTTTAAGGCTGAATAATATTCCATTGTA 537 chr1qtel1M 349871 TTTATATACTATAATTTATTCAGCCATTCTCCAATTGTTAAGCATCCACT 349920 v i i v v i v vi vi i v iii ii vv C L1MA10_3end#L 536 TGTATATACCACATTTTCTTTATCCATTCATCCGTCGATGGACATTTAGG 487 chr1qtel1M 349921 CAATTTCCAGTTTCTTG-CCACTACAAAAAGGGCTGCCACAAACATTTT- 349968 ivi - v - i i iii v iv v ii vvv- C L1MA10_3end#L 486 TTGTTTCCA-TATCTTGGCTATTGTGAATAATGCTGCAATGAACATGGGA 438 chr1qtel1M 349969 -TGCACATAGTAGTCTCTTT----CCCTTCTTTAAGATCTCCTTGGTATA 350013 - v ---- i----i vv v iv ii v i C L1MA10_3end#L 437 GTGCAGATA----TCTCTTCGAGATCCTGATTTCAATTCTTTTGGATATA 392 chr1qtel1M 350014 TAAGCCCAGTAGTAACACTGCTGGATCAAAGGGTAGGCACAGTTTGATAA 350063 -- v iiv i v v vivi v -- C L1MA10_3end#L 391 TA--CCCAGAAGTGGGATTGCTGGATCATATGGTAGTTCTATTTT--TAA 346 chr1qtel1M 350064 CTTTTGGAGCATAGTTCCAAATTGCTCTCCAGAATGGTTGGATCCACTCA 350113 i v v - vi v i i i v i i v i v?i i C L1MA10_3end#L 345 TTTTTTGAGGA-ACCTCCATACTGTTTTCCATAGTGGCTGCACCANTTTA 297 chr1qtel1M 350114 CAACTCCACCAACAATATATCAGAGTCCTAGTTT-TCC-CATCCCCTCCA 350161 vii i i iv i i i?? - - i v C L1MA10_3end#L 296 CATTCCCACCAACAGTGTACAAGGGTTCCNNTTTCTCCACATCCTCGCCA 247 chr1qtel1M 350162 ACATTTGTCATTATCTTTTCCTGTCATTTTAAT------CAGTCTCACAG 350205 i --- --- iv i ------ vi v C L1MA10_3end#L 246 ACACTTGT---TATCTTTT---GTTTTTTTGATAATAGCCATCCTAACAG 203 chr1qtel1M 350206 GTGTATAGTGGTATCTCAGAGTTGTCTTAATTTTCATTTCTTTAATCAAT 350255 ivi i vv v i i v ii i v v C L1MA10_3end#L 202 GTGTGAGGTGATATCTCATTGTGGTTTTGATTTGCATTTCCCTGATGATT 153 chr1qtel1M 350256 AGTGATTTGGAGCACCTTTTTGTGTGACTAAAAATAGTTTCAATTCCTTC 350305 v v ii i iv ivviiivi vv vi C L1MA10_3end#L 152 AGTGATGTTGAGCACCTTTTCATATACCTGTTGGCCATTTGTATGTCTTC 103 chr1qtel1M 350306 ATCTGA-AAAT-TCCATTCATATCCTTTGATCATTTATCAATTGG 350348 v iv - - i vi vi v i i C L1MA10_3end#L 102 TTTGGAGAAATGTCTATTCAGGTCCTTTGCCCATTTTTTAATCGG 58 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 42.17 CpG sites = 97, Kimura (unadjusted) = 43.45 Transitions / transversions = 1.17 (97/83) Gap_init rate = 0.05 (29 / 576), avg. gap size = 1.28 (37 / 29) 1314 29.69 2.01 1.64 chr1qtel1M 349855 350402 (649598) C L1ME4c_3end#LINE/L1 (275) 555 6 m_b37s551i5 1293 chr1qtel1M 349855 ATAATATTTAATAACATTTATATACTATAATTTATTCAGCCATTCTCCAA 349904 iv vivi ?v i i i i i i v C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chr1qtel1M 349905 TTGTTAAGCATCCACTCAATTTCCAGTTTCTTGCCACTACAAAAAGGGCT 349954 iii ii vvivi i i i i i i v iv C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCT 456 chr1qtel1M 349955 GCCACAAACATTTTTGCACATAGTAGTCTCTTTCCCTTCTTTAAG--ATC 350002 v ii i i ii - - i i ii i i-- i C L1ME4c_3end#L 455 GCAATGAACATCTTCGTGCATA-TAG-CTTTTTCCTTCTTTTGAATTATT 408 chr1qtel1M 350003 TCCTTGGTATATAAGCCCAGTAGTAACACTGCTGGATCAAAGGGTAGGCA 350052 i v v vv v iiv i i i v v C L1ME4c_3end#L 407 TCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAA 358 chr1qtel1M 350053 CAGTTTGATAACTTTTGGAGCATAGTTCCAAATTGCTCTCCAGAATGGTT 350102 v v ii i ivi i v v i i v C L1ME4c_3end#L 357 CATTTTTATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTT 308 chr1qtel1M 350103 GGATCCACTCACAACTCCACCAACAATATATCAGAGTCCTAGTTTTCC-- 350150 v i v i i ?iv i i v ? v i iv -- C L1ME4c_3end#L 307 GTACCAATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCACCG 258 chr1qtel1M 350151 CATCCCCTCCAACATTTGTCATTATCTTTTCCTGTCATTTTAATCAGTCT 350200 ? i v i v vi vv ii vvv viii i i C L1ME4c_3end#L 257 CANCCTCGCCAGCATTGGGTATTATCAATTTTTTAAATTTTTGCTAATTT 208 chr1qtel1M 350201 CACAGGTGTATAGTGGTATCTCAGAGTTGTCTTAATTTTCATTTCTTTAA 350250 v i i v i vv ii v i C L1ME4c_3end#L 207 AATAGGCGTAAAATGGTATCTCATTGTTGCTTTAATTTGCATTTCTTTGA 158 chr1qtel1M 350251 TCAATAGTGATTTGGAGCACCTTTTTGTGTGACTA-AAAATAGTTTCAAT 350299 i v i vv v i ii iii vi i-vv v ? vi v C L1ME4c_3end#L 157 TTACTAGCGAGGTTGAACATTTTTCCATGTGTTTGTTTACTANTTGTATT 108 chr1qtel1M 350300 TCCTTCATCTGAAAAT--TCCATTCATATCCTTTGATCATTTATCAATTG 350347 - v ? vi -- ii i vi v C L1ME4c_3end#L 107 TCC-TCTTNTGTGAATTGTCTGTTCATGTCCTTTGCCCATTTATCTATTG 59 chr1qtel1M 350348 GAGAATGGCTTGAAC----TATTATAAATTTGAGTCAATACTCTAAATAT 350393 i---- v v?---- v v i v --i vv C L1ME4c_3end#L 58 GG----GTCTTGATNTTTTTCTTATCAATTTGAATGA--GCTCTTTATAT 15 chr1qtel1M 350394 TTTAGAGAT 350402 v? ? C L1ME4c_3end#L 14 ANTANAGAT 6 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 37.82 CpG sites = 93, Kimura (unadjusted) = 39.73 Transitions / transversions = 1.39 (93/67) Gap_init rate = 0.03 (14 / 547), avg. gap size = 1.43 (20 / 14) 1253 22.81 12.13 3.94 chr1qtel1M 350903 351372 (648628) C Charlie1b#DNA/hAT-Charlie (16) 507 1 m_b37s502i0 1294 chr1qtel1M 350903 TTTTGGTCCCAGGACTCCTTTCCACTGCTAAAAACTATTGAGGATCCCAA 350952 i i v vi i i C Charlie1b#DNA 507 TTTTGGTCTCAGGACCCCTTTACACTCTTAAAAATTATTGAGGACCCCAA 458 chr1qtel1M 350953 AGGGTTTTTATTTATGTGAGTTATAGAT----ATATTTATCAT------- 350991 i i i i vv ---- i i ------- C Charlie1b#DNA 457 AGAGCTTTTGTTTATGTGGGTTATATCTATCGATATTTACCGTATTAGAA 408 chr1qtel1M 350992 -TTACAA-----AATCTTTTAAAA----CATTAAATCA-TTGAAAATAAT 351030 - v ----- vi ----i v - i C Charlie1b#DNA 407 ATTAAAACTGAGAAATTTTTAAAATATTTATTAATTCATTTAAAAATAAT 358 chr1qtel1M 351031 ----------TTATGTGCTAACATAAATAAC--ATTTTCATGAAAGATAA 351068 ---------- ii i -- i i C Charlie1b#DNA 357 AATAAACCCATTACATGTTAACATAAATAACATATTTTTATGAAAAATAA 308 chr1qtel1M 351069 CTAAACTCCCTCCCCCCAAAAA---TAGGGGTAAAATGGGCATTGCTTTA 351115 v i ii ivvvv v --- v iv i vv i - C Charlie1b#DNA 307 CTATATTTTCCAAAACAAAAAAATTTAGTGAGAAGAGTGGCATTGTTTT- 259 chr1qtel1M 351116 CACATTTTTGCAAATCTCTATAATGTGTGGCTTAAGAGAAAACATTAATC 351165 - v v v i --- iii C Charlie1b#DNA 258 -ACATTTTTGCAAATCTCTTTAATGTCTGGCTTAATAGAAGAC---AGCT 213 chr1qtel1M 351166 AGATCTGCTTCTATTAGTTTCTACATTCAATTTGTTGT-ATAT----TGT 351210 i i-- iv iv i i i i- ----i C Charlie1b#DNA 212 GGATT--CTCATATCTGCTTCTGCATTCAATCTGTTGCGATATCACACGT 165 chr1qtel1M 351211 CTTGGTTAAGGTTAAAAACAAAATTCAGCATCAGACAATTAAACAGTTGG 351260 v -- ivv ivii--- i -- iiiv v i----- vi C Charlie1b#DNA 164 CATG--TAGCCTCTGG---AAAACTC--CACTGTACACTC-----GTGAG 127 chr1qtel1M 351261 AAAAGGGGA---AAAAAGGCAAAAAAAAGTTTTAATATTATTGTGCAAAT 351307 i v i --- - v v i i i v C Charlie1b#DNA 126 AGAATGAGAGTGAAAAAGGC-AAATAACGTCTTAGTATTATTATGAAAAT 78 chr1qtel1M 351308 GGTTTTGACCTCACAGATCCTCT------------GGGATTCTCAGAAGT 351345 i i i i i ------------ ii i ii C Charlie1b#DNA 77 AGTTTTGACCTCGCGGACCCCCTGAAAGGGTCTCGGGGACCCCCAGGGGT 28 chr1qtel1M 351346 CCATAGGCCACACTTTGAGAAATGCTG 351372 vii i vi C Charlie1b#DNA 27 CCCCGGACCACACTTTGAGAACCGCTG 1 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 25.58 CpG sites = 68, Kimura (unadjusted) = 28.13 Transitions / transversions = 1.94 (68/35) Gap_init rate = 0.07 (33 / 469), avg. gap size = 2.33 (77 / 33) 22 13.55 0.00 2.33 chr1qtel1M 354694 354737 (645263) (GAGGAGG)n#Simple_repeat 1 43 (0) m_b37s252i6 1295 chr1qtel1M 354694 GAGGAGGGGGGAAGGAGGAGGGGAGGAGGGAAAAGGGAAGAGGG 354737 i i - ii i (GAGGAGG)n#Si 1 GAGGAGGGAGGAGGGAGGA-GGGAGGAGGGAGGAGGGAGGAGGG 43 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.02 (1 / 43), avg. gap size = 1.00 (1 / 1) 217 28.57 3.17 0.00 chr1qtel1M 359433 359495 (640505) L2d_3end#LINE/L2 439 503 (13) m_b37s601i19 1296 chr1qtel1M 359433 TTTTGTGTCCCACTGTGCTTA--ACAGTGCTGGGCAAATTGGAGCTACTT 359480 ? i vi v i i -- i v v v vii i L2d_3end#LINE 439 TNTCGTTCCCCACAGCGCCTAGCACAGTGCTGAGCACATAGTAGGCGCTC 488 chr1qtel1M 359481 AATGAGTGTTTGTTG 359495 i i ii L2d_3end#LINE 489 AATAAATACTTGTTG 503 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.38 CpG sites = 12, Kimura (unadjusted) = 38.45 Transitions / transversions = 2.00 (12/6) Gap_init rate = 0.02 (1 / 62), avg. gap size = 2.00 (2 / 1) 13 18.85 2.78 0.00 chr1qtel1M 359723 359758 (640242) (TAATT)n#Simple_repeat 1 37 (0) m_b37s252i8 1297 chr1qtel1M 359723 TAAATTAATTTAGGTTAATTTAA-ATAAACTAATTTA 359758 v iv -v vi (TAATT)n#Simp 1 TAATTTAATTTAATTTAATTTAATTTAATTTAATTTA 37 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) 320 29.67 13.82 0.61 chr1qtel1M 359906 360339 (639661) C L1M2_orf2#LINE/L1 (1011) 2280 1790 m_b37s551i6 1298 chr1qtel1M 359906 TATTTTAAGT---ATTTCTTTTTTT-TTTTTTTCTC------TTCCTGAT 359945 v i --- v i v- i i ------ v vi C L1M2_orf2#LIN 2280 TATTGTAAATGGGATTGCTTTCTTGATTTCTTTTTCAGATAGTTCGTTGT 2231 chr1qtel1M 359946 TTAAATGCAGAAAAGCTGATGATTTAGGCTAGCTTTATTTTATATCCTTC 359995 vivi ii v iv vv - vv v i v C L1M2_orf2#LIN 2230 TGGCGTATAGAAATGCTACTGATTTTTG-TATGTTGATTTTGTATCCTGC 2182 chr1qtel1M 359996 ACTTTTGCTGAAGTTATT-----GTTTCAA---TTTTGTACTTGA--CTG 360035 vi i v ii ----- ii --- v iv v -- v C L1M2_orf2#LIN 2181 AACTTTACTGAATTCGTTTATCAGTTCTAANAGTTTTTTGGTGGAGTCTT 2132 chr1qtel1M 360036 TAGGGTTCT-TAGATATACCATCAAATTATCAGAAAAAAGTGG--ATTT- 360081 ? i - ? vv vi i v v v v i-- - C L1M2_orf2#LIN 2131 TAGGNTTTTCTANATATAAGATCATGTCATCTGCAAACAGGGACAATTTG 2082 chr1qtel1M 360082 -TTTTCTCTTTCCCA-------------CAATTTTTTTTTCTT------- 360110 -i i i i -------------iv i i ------- C L1M2_orf2#LIN 2081 ACTTCCTCCTTTCCAATTTGGATGCCTTTTATTTCTTTCTCTTGCCTAAT 2032 chr1qtel1M 360111 TGCTATAGCTAACATTTTCAGAACTATGTTAAATAGA----------GTG 360150 v i iv i i v i ---------- C L1M2_orf2#LIN 2031 TGCTCTGGCTAGGACTTCCAGTACTATGTTGAATAGAAGTGGTGAAAGTG 1982 chr1qtel1M 360151 GGCATTCTTGCTTTAATCCCAGTCTTACTGGAAAGAATTCCAATTTATCC 360200 i ii iv vi? vv iv i i v C L1M2_orf2#LIN 1981 GGCATCCTTGTCTTGTTCCAGNTCTTAGAGGAAAGGCTTTCAACTTTTCC 1932 chr1qtel1M 360201 TCAATATATGTAATGTTGGATCTTAGTTTTAAATATATACAATTTCCCTT 360250 i v vvi i i i v v vi vvv ivvv viiv C L1M2_orf2#LIN 1931 CCATTCAGTATGATGTTAGCTGTGGGTTTGTCATATATGGCCTTTATTGT 1882 chr1qtel1M 360251 CTTAGGGAAAGGTCCTTGTA---CTCATGTTTTCTAGTGTTTTTAGTAAA 360297 v ii v v v v --- v - v iv v vi vi C L1M2_orf2#LIN 1881 GTTGAGGTACGTTCCTTCTATACCTAAT-TTGTTGAGAGTTTTTATCATG 1833 chr1qtel1M 360298 ATATGAGTGTTGTGTTTTGTCAAAACCTTTT--TGCATGTATTG 360339 - v ii vi i vv -- v C L1M2_orf2#LIN 1832 A-AGGGATGTTGAATTTTATCAAATGCTTTTTCTGCATCTATTG 1790 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 37.70 CpG sites = 60, Kimura (unadjusted) = 38.48 Transitions / transversions = 0.88 (60/68) Gap_init rate = 0.04 (17 / 433), avg. gap size = 3.71 (63 / 17) 394 28.57 13.47 1.15 chr1qtel1M 359954 360339 (639661) C L1PB_orf2#LINE/L1 (1069) 2225 1793 m_b37s551i7 1298 chr1qtel1M 359954 AGAAAAGCTGATGATTTAGGCTAGCTTTATTTTATATCCTTCACTTTTGC 360003 ? i iv iv - vv v i ?vv vi C L1PB_orf2#LIN 2225 AGNAGAGCTACTGATTTGTG-TACATTAATTTTGTATCCNGAAACTTTGC 2177 chr1qtel1M 360004 TGAAGTTATTGTTTCAATTTT--GTACTT-------GA--CTGTAGGGTT 360042 v i? - v i i -- vi ------- -- v C L1PB_orf2#LIN 2176 TGAATTCNTT-TATCAGTTCTAGGAGCTTTCTGGAGGAGTCTTTAGGGTT 2128 chr1qtel1M 360043 CT-TAGATATACCATCAAATTATCAGAAAAAAGTGG-ATTTT---TTTCT 360087 i - i ? v v i v v i i- v --- i C L1PB_orf2#LIN 2127 TTCTAGGTANACGATCATATCATCAGCAAACAGCGACAGTTTGACTTCCT 2078 chr1qtel1M 360088 CTTT-------------CCCACAATTTTTTTTTCTT-------TGCTATA 360117 ------------- viv i i ------- v i C L1PB_orf2#LIN 2077 CTTTACCGATTTGGATGCCCTTTATTTCTTTCTCTTGTCTGATTGCTCTG 2028 chr1qtel1M 360118 GCTAACATTTTCAGAACTATGTTAAATAGA----------GTGGGCATTC 360157 iv i i v i ? ---------- i C L1PB_orf2#LIN 2027 GCTAGGACTTCCAGTACTATGTTGAANAGAAGTGGTGAGAGTGGGCATCC 1978 chr1qtel1M 360158 TTGCTTTAATCCCAGTCTTACTGGAAAGAATTCCAATTTATCCTCAATAT 360207 ii iv viv i vv i viv i i v i v vv C L1PB_orf2#LIN 1977 TTGTCTTGTTCCAGTTCTCAGGGGGAATGCTTTCAACTTTTCCCCATTCA 1928 chr1qtel1M 360208 ATGTAATGTTGGATCTTAGTTTTAAATATATACAATTTCCCTT--CTTAG 360255 i i ? v v vi --ivi v iiii iiv --? i C L1PB_orf2#LIN 1927 GTATNATGTTGGCTGTGGGTTT--GTCATAGATGGCTTTTATTACNTTAA 1880 chr1qtel1M 360256 GGAAAGGTCCTTGTA--CTCATGTTTTCTAGTGTTTTTAGTAAAATATGA 360303 v v vi ? -- iv - v iiv v i v v v v i C L1PB_orf2#LIN 1879 GGTATGTCCCTTNTATGCCGAT-TTTGCTGAGGGTTTTAATCATAAAGGG 1831 chr1qtel1M 360304 GTGTTGTGTTTTGTCAAAACCTTTT--TGCATGTATTG 360339 i i vi vv -- v C L1PB_orf2#LIN 1830 ATGCTGGATTTTGTCAAATGCTTTTTCTGCATCTATTG 1793 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 36.65 CpG sites = 55, Kimura (unadjusted) = 37.51 Transitions / transversions = 1.02 (55/54) Gap_init rate = 0.04 (17 / 385), avg. gap size = 3.35 (57 / 17) 16 0.00 0.00 0.00 chr1qtel1M 360672 360692 (639308) (TCAG)n#Simple_repeat 1 21 (0) m_b37s252i9 1299 chr1qtel1M 360672 TCAGTCAGTCAGTCAGTCAGT 360692 (TCAG)n#Simpl 1 TCAGTCAGTCAGTCAGTCAGT 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 201 22.22 3.70 0.00 chr1qtel1M 360707 360760 (639240) L3#LINE/CR1 3244 3299 (800) m_b37s601i20 1300 chr1qtel1M 360707 AGCTAATCTGCAGTTGGGCAGAATCAAGATTCAGAGAGAGCTCG--AGGC 360754 vi ?v vvv i i i? v -- L3#LINE/CR1 3244 AGCTAATACGNTGGATGACAGAATCAAGATTCAAAANGATCTCGACAGGC 3293 chr1qtel1M 360755 TGAAGC 360760 i i L3#LINE/CR1 3294 TGGAAC 3299 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 25.22 CpG sites = 6, Kimura (unadjusted) = 27.80 Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.02 (1 / 53), avg. gap size = 2.00 (2 / 1) 15 11.66 0.00 3.45 chr1qtel1M 361117 361146 (638854) (TTA)n#Simple_repeat 1 29 (0) m_b37s252i10 1301 chr1qtel1M 361117 TTATTATTATTATTATAATATCTTTTTATT 361146 v - v v (TTA)n#Simple 1 TTATTATTATTATTATTAT-TATTATTATT 29 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 12 9.24 0.00 4.17 chr1qtel1M 361214 361238 (638762) (TCCC)n#Simple_repeat 1 24 (0) m_b37s252i11 1302 chr1qtel1M 361214 TCCCTCCCACCCTCCACCCCCTCCC 361238 v - i (TCCC)n#Simpl 1 TCCCTCCCTCCCTCC-CTCCCTCCC 24 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 1729 27.30 2.71 3.20 chr1qtel1M 361548 362175 (637825) C L1ME5_3end#LINE/L1 (313) 628 4 m_b37s551i8 1303 chr1qtel1M 361548 TTTCACTCAGCATCA-GTTCATGTAAG-TCTCTCCAAGCCTCTCTGTATT 361595 ii - -- v - iv v iiv v i v C L1ME5_3end#LI 628 TTTCACTCAGCACTATGTT--TTTAAGATCCATCCATGTTGCTATGTGTA 581 chr1qtel1M 361596 CATCCTGCTGGTCATTTCTTACAGAACAATAATATTCCATAACATTCATA 361645 iv iiv iii v v vvvv i i iiii v v C L1ME5_3end#LI 580 CATCTAGTCCGTTGCTTCTAACTGCTGCATAGTACTCCATGGTGTGCATC 531 chr1qtel1M 361646 TACCACAATTTACCCAACCATTCTCCAATTGATGGGCATCCATTCATTG- 361694 i v i v i v v i i v--i - C L1ME5_3end#LI 530 CACCACATTTTACCTATCCACTCTCCCAGTGATGGACACCCAG--GTTGC 483 chr1qtel1M 361695 -TCCAGTTTCTAGCCACTACAAACAGGGGTGCCACAAACATTTTGGCACA 361743 - ii i iv i iv v v ii ii ---- i C L1ME5_3end#LI 482 CTCCAACTCCCCGCCACCACAAACAACGCTGCAATGAACATCCT----CG 437 chr1qtel1M 361744 TACAGGTCCCTTTC----CCTTCTTTAGTATCTCTTTGGGGTATAAGCCC 361789 v i v---- viv v v i i vi C L1ME5_3end#LI 436 TACATGTCCCCTTATGGACCTGTGTGAGAATTTCTTTGGGATATATACCC 387 chr1qtel1M 361790 AGTAGTAGCACTGCTGGGTCAAAGGGTATGCACAGTTTGATAACTT--TT 361837 v ii v i v --- --- - -- C L1ME5_3end#LI 386 AGGAGCGGAATTGCTGGGTCATAGGGTATGC---GT---ATA-CTTAATT 344 chr1qtel1M 361838 TGAGTA--TAGTTCCTAATTGCTCTCCAGAATGGTTGGATTCATTCACAA 361885 v -- v v vi i v iivi ii v C L1ME5_3end#LI 343 TGACTAAGTACTGCCAGATTGCTCTCCAGAATGGCTGCACCAGTCTACAC 294 chr1qtel1M 361886 GTCCACCAACAATGTATCAGTGTCCCAGTTTTCCCACATCCCCTCCAACA 361935 vi i i i v v i vi ? i i v C L1ME5_3end#LI 293 TCCCACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATCCTCGCCAACA 244 chr1qtel1M 361936 CTCATCATTATTT---TTTCCTGTCATCTTAGCCAATCTGACAGGTGTGT 361982 iiv ii--- --- v i v i i i iv C L1ME5_3end#LI 243 CTTGGCATTATCCAGCTTTC---TAATTTTTGCCAGTCTAATAGGTGTAA 197 chr1qtel1M 361983 AGTGGTATCTCAGAGTTGTCTTAATTTGCATTTCTCTGATTAATAATGAT 362032 i vv i v v C L1ME5_3end#LI 196 AGTGATATCTCATTGTTGTTTTAATTTGCATTTCTCTGATTACTAATGAG 147 chr1qtel1M 362033 TTGGAACACTCTTTCATATGAGTGGTAATGATTTCAATTTCATCATCTGA 362082 v i iiii vv v iivv ivii v v v C L1ME5_3end#LI 146 TTTGAGCATCTCTTCATATGCTTGTTAGCCTTTCGGGTTTCCTCTTCTGT 97 chr1qtel1M 362083 AAATTGTCTGTTCATATCCTTTGACCATTTGTCAATTGGAG--AATGGCT 362130 i v v v i --?vi v C L1ME5_3end#LI 96 AAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGGGGTTNCCGTCT 47 chr1qtel1M 362131 TGGTTTCTTATAAATTAGAGTCAGTTCTCTATATATTTTGGAAAT 362175 -- i vi v vivv ii i i i v C L1ME5_3end#LI 46 T--TTTCTTGTTGATTTGCAGGAGTTCCTTGTATATTCTAGATAT 4 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 33.62 CpG sites = 90, Kimura (unadjusted) = 34.67 Transitions / transversions = 1.18 (90/76) Gap_init rate = 0.05 (29 / 627), avg. gap size = 1.28 (37 / 29) 506 28.63 2.54 2.54 chr1qtel1M 362029 362304 (637696) C L1M2_orf2#LINE/L1 (0) 3291 3016 m_b37s551i9 1303 chr1qtel1M 362029 TGATTTGGAACACTCTTTCATATGAGTGGTAATGATTTCAATTTCATCAT 362078 v v i i i ivv v iiiv vv v v v C L1M2_orf2#LIN 3291 TGATGTTGAGCATTTTTTCATATACCTGTTGGCCATTTGTATGTCTTCTT 3242 chr1qtel1M 362079 CTGAAAATTGTCTGTTCATATCCTTTGACCATTTGTCAATTGGAGAATGG 362128 i i v i vi v v ? i vv -- C L1M2_orf2#LIN 3241 TTGAGAAATGTCTATTCAGGTCCTTTGCCCATTTTTNAATCGGATTAT-- 3194 chr1qtel1M 362129 CTTGGTTTCTTA----TAAATTAGAGTCAGTTCTCTATATATTTTGGAAA 362174 - v i i---- i i - vv v ii i v C L1M2_orf2#LIN 3193 -TTGTTTTTTTGCTGTTGAGTT-GTTTGAGTTCCTTATATATTCTGGATA 3146 chr1qtel1M 362175 TGAGGCCTTTATCAGAACCTTTAACTGTGAAGATGTTTTCCCAGTTTGTT 362224 v iv i i vv?v vivi ii v v i v i v C L1M2_orf2#LIN 3145 TTAATCCCTTGTCAGATGNATAGTTTGCAAATATTTTCTCCCATTCTGTA 3096 chr1qtel1M 362225 GCTTCTCTTCTAATCTTGTTTGCATTAGTTTTGTTTG---TACAGAAGCT 362271 v v ii v iii - - - iv --- i C L1M2_orf2#LIN 3095 GGTTGTCTCTTCACTCTGTT-G-ATT-GTTTCCTTTGCTGTGCAGAAGCT 3049 chr1qtel1M 362272 TTTTAATTTGATGTAATCAAAATTTTCTATTTT 362304 i vv v v C L1M2_orf2#LIN 3048 TTTTAGTTTGATGTAATCCCATTTGTCTATTTT 3016 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 36.11 CpG sites = 36, Kimura (unadjusted) = 36.69 Transitions / transversions = 0.88 (36/41) Gap_init rate = 0.03 (9 / 275), avg. gap size = 1.56 (14 / 9) 391 30.40 3.47 1.13 chr1qtel1M 363094 363266 (636734) L1PB_orf2#LINE/L1 1440 1616 (1678) m_b37s551i10 1304 chr1qtel1M 363094 CTATCACATTTTCAAAGAACAGTTAATTCTAATACTACTTGA-ACTAT-C 363141 i v iv v i ii v i v - - - L1PB_orf2#LIN 1440 CTACCAGACATTCAAAGAAGAATTGGTACCAATCCTA-TTGACACTATTC 1488 chr1qtel1M 363142 TGCAACCATAAGAAAAGAAGGCATCATTTC--AGTC--TTTATGATACAA 363187 ii v- iii i v v ii -- i -- i vi v L1PB_orf2#LIN 1489 CACAAG-ATAGAGAAAGAGGGAATCCTCCCTAAATCATTCTATGAAGCCA 1537 chr1qtel1M 363188 GTAGAATCTCAGTACTTAAGCTGGGGAGAGACAAAACAGAAAAAGAAAGC 363237 vv i ii i iv i ii i ii v ?i i L1PB_orf2#LIN 1538 GTATCACCCTAATACCAAAACCAGGAAAGGACATAACNAAAAAAGAAAAC 1587 chr1qtel1M 363238 TGCAGACCAGTGGTCCTAATAAACATTGA 363266 i i ivi i i v L1PB_orf2#LIN 1588 TACAGACCAATATCCCTGATGAACATAGA 1616 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 41.67 CpG sites = 36, Kimura (unadjusted) = 41.67 Transitions / transversions = 2.25 (36/16) Gap_init rate = 0.03 (6 / 172), avg. gap size = 1.33 (8 / 6) 671 25.54 11.11 2.13 chr1qtel1M 364120 364335 (635665) MIRb#SINE/MIR 17 251 (17) m_b37s601i21 1305 chr1qtel1M 364120 TGCAGTGGATAGAGTACTGGGTATGAAGTCAAAAAGAGCTGGATTCAAAT 364169 v i v v v i i v v i i MIRb#SINE/MIR 17 TGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCGAAT 66 chr1qtel1M 364170 CCA------GCCAC-TAGTAGCTGTGTGACTCTAGACAAATCAGTTAA-- 364210 v------ - v ii i i i i v -- MIRb#SINE/MIR 67 CCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACC 116 chr1qtel1M 364211 --------CCTCAACTTTCTCATCTATAAAATGGGCATAAAAACAGCATC 364252 -------- ii i i v v i ---- MIRb#SINE/MIR 117 TCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATA----C 162 chr1qtel1M 364253 CTGCTTCTCA---TGATTGTAAGGATCAATTGAGGTCAC---TGCAAAGT 364296 i i v --- vi i i v i v i--- i i MIRb#SINE/MIR 163 CTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGC 212 chr1qtel1M 364297 ATGTGGGCACAAGCCCTGGTGGGTAGTAGGC-CTCCCTAA 364335 ii- vi ivv iivi i - vv MIRb#SINE/MIR 213 GC-TTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAA 251 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.62 CpG sites = 33, Kimura (unadjusted) = 32.13 Transitions / transversions = 1.57 (33/21) Gap_init rate = 0.06 (12 / 215), avg. gap size = 2.42 (29 / 12) 183 32.00 18.40 0.00 chr1qtel1M 364364 364488 (635512) L3#LINE/CR1 3818 3965 (134) m_b37s601i22 1300 chr1qtel1M 364364 TTCTCGGTAACCCCAGAAAGCTGAAGCAGGAGCAG-AGATAGAAGGCACA 364412 vv ii i ii v vi v i-i i i vi L3#LINE/CR1 3818 TTCTGTGTGGCTCCAGAGGGCAGAACTAGGACCAATGGGTGGAAGTTACA 3867 chr1qtel1M 364413 AGGAGGTTTATTTGAGTT-----TAGGGGAGA---------------GA- 364441 i ivv vi i ----- i i --------------- - L3#LINE/CR1 3868 GGGAGGCAGATTTCGGCTCAATATAAGGAAGAACTTTCTAACAATCAGAG 3917 chr1qtel1M 364442 -TACCCCAAAGTAGGGTGGGATACCTGGGGAGGCTGTGAGCAGCCCGT 364488 - ii v i i ii v i v ? iv vv L3#LINE/CR1 3918 CTGTCCAAAAATGGAATGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGT 3965 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 42.56 CpG sites = 25, Kimura (unadjusted) = 44.06 Transitions / transversions = 1.67 (25/15) Gap_init rate = 0.04 (5 / 124), avg. gap size = 4.60 (23 / 5) 218 27.59 3.45 0.00 chr1qtel1M 364830 364887 (635113) C L2d_3end#LINE/L2 (8) 508 449 m_b37s601i23 1306 chr1qtel1M 364830 TCGATTAATGAACATGTATTAAGCTCCTACTATGTGCT-AG-ATTGTGTC 364877 i i ii ii v i v - - i ii C L2d_3end#LINE 508 TCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTGTGCT 459 chr1qtel1M 364878 TGACACTTTG 364887 v i i v C L2d_3end#LINE 458 AGGCGCTGTG 449 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 33.76 CpG sites = 12, Kimura (unadjusted) = 36.67 Transitions / transversions = 3.00 (12/4) Gap_init rate = 0.04 (2 / 57), avg. gap size = 1.00 (2 / 2) 328 28.03 5.56 3.40 chr1qtel1M 365009 365152 (634848) MIRb#SINE/MIR 5 151 (117) m_b37s601i24 1307 chr1qtel1M 365009 GGGGCAACTAACTGCTACTGTGATAAAGTGC-TGGGCCC-AAAGTCAGGA 365056 i v--- v i v i- v -i ii-ii iv MIRb#SINE/MIR 5 GGGGCAGCG---TGGTGCAGTGG-AAAGAGCACGGGCTTTGGAGTCAGAC 50 chr1qtel1M 365057 AGATC-GAGCTTGAATGCAGTCTC-AACACTTA-TGGCTGGGTGACCCTG 365103 i - i i i v v v -iv - i v i MIRb#SINE/MIR 51 AGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTG 100 chr1qtel1M 365104 GGCAAGTTACTTTGCCCTGTTTG---CCAGGATGTCTTATATGTAAAATG 365150 - iv v i --- ivi v vi i v MIRb#SINE/MIR 101 GGCAAGTTAC-TTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATG 149 chr1qtel1M 365151 AG 365152 i MIRb#SINE/MIR 150 GG 151 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 33.79 CpG sites = 23, Kimura (unadjusted) = 36.07 Transitions / transversions = 1.44 (23/16) Gap_init rate = 0.08 (11 / 143), avg. gap size = 1.18 (13 / 11) 374 29.50 4.88 0.78 chr1qtel1M 365030 365152 (634848) MIRc#SINE/MIR 21 148 (120) m_b37s601i25 1307 chr1qtel1M 365030 GATAAAGTGCTGGGCCCAAAGTCAGGAAGATC-GAGCTTGAATGCAGTCT 365078 v i ii i iiii i - i i i i v v v MIRc#SINE/MIR 21 GAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCT 70 chr1qtel1M 365079 C-AACACTTA-TGGCTGGGTGACCCTGGGCAAGTTACTTTGCCCTGTTTG 365126 -iv - i v i i - iv v i MIRc#SINE/MIR 71 CTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCAC-TTAACCTCTCTG 119 chr1qtel1M 365127 ---CCAGGATGTCTTATATGTAAAATGAG 365152 --- ivi v vi i v i MIRc#SINE/MIR 120 AGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 37.89 CpG sites = 24, Kimura (unadjusted) = 39.32 Transitions / transversions = 2.00 (24/12) Gap_init rate = 0.04 (5 / 122), avg. gap size = 1.40 (7 / 5) 261 32.88 2.45 6.09 chr1qtel1M 365467 365670 (634330) C L2#LINE/L2 (246) 2836 2640 m_b37s601i26 1306 chr1qtel1M 365467 AGAAGAGGCTCTGAACTGGTCAGACCTGCTTTTCATAGGAAAGTCCCTTT 365516 i ---- vv i v i i v i v i i -- v i C L2#LINE/L2 2836 AGAGGAG----TGACATGATCTGACTTACGTTTTAAAAGGA--TCACTCT 2793 chr1qtel1M 365517 GGTGGCTGACTGGAGACTGAACTGGATGGGGG---AGACCGAGGCAGGCA 365563 iv vv v v ii ? v ---i iiv i v C L2#LINE/L2 2792 GGCTGCTGTGTTGAGAATAGACTGNAGGGGGGCAAGGGTGGAAGCAGGGA 2743 chr1qtel1M 365564 GATCCCTCAGCA-GCTGCTGCAG-AGGCTAAGCTGTGAGGTGATGAGGGC 365611 i vv i v - ii - iv i i - v i iv C L2#LINE/L2 2742 GACCAGTTAGGAGGCTATTGCAGTAATCCAGGC-GAGAGATGATGGTGGC 2694 chr1qtel1M 365612 CTGCACCAGTGCGGTGATGATGTCTGAGGAGAGGAGGGGATGTACATGAG 365661 i v v i iiii vvv v v i v vi ----- v C L2#LINE/L2 2693 TTGGACCAGGGTGGTGGCAGTGGAGGTGGTGAGAAGTGGTCG-----GAT 2649 chr1qtel1M 365662 ACTGGATAT 365670 v C L2#LINE/L2 2648 TCTGGATAT 2640 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 43.28 CpG sites = 32, Kimura (unadjusted) = 44.21 Transitions / transversions = 1.03 (32/31) Gap_init rate = 0.07 (15 / 203), avg. gap size = 1.13 (17 / 15) 264 19.97 7.69 3.70 chr1qtel1M 365769 365846 (634154) MIRb#SINE/MIR 73 153 (115) m_b37s601i27 1308 chr1qtel1M 365769 TTTGCTCCTTAAT-GCTATTTGTAACTATGGACAAGGTATTTAACCTGCT 365817 i iv v - i -- i iv i v i - MIRb#SINE/MIR 73 TCTGCCACTTACTAGCTGT--GTGACCTTGGGCAAGTTACTTAACCT-CT 119 chr1qtel1M 365818 ---AGCCTCAATTT-CTTAT-TGTAAGATGAGGA 365846 --- i - i - i i MIRb#SINE/MIR 120 CTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGA 153 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 24.10 CpG sites = 11, Kimura (unadjusted) = 24.10 Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.09 (7 / 77), avg. gap size = 1.29 (9 / 7) 234 23.06 7.58 1.43 chr1qtel1M 365788 365853 (634147) MIR3#SINE/MIR 85 154 (54) m_b37s601i28 1308 chr1qtel1M 365788 TGTAACTATGGACAAGGTATTTAACCTGCT---AGCCTCAATTTCTT-AT 365833 i iv i vi i v - ---i i i - MIR3#SINE/MIR 85 TGTGACCTTGGGCAAGTCACTTCACCT-CTCTGGGCCTCAGTTTCCTCAT 133 chr1qtel1M 365834 -TGTAAGATGAGGAATTTGGA 365853 - i iiv MIR3#SINE/MIR 134 CTGTAAAATGAGGGGGTTGGA 154 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 28.82 CpG sites = 11, Kimura (unadjusted) = 28.82 Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.06 (4 / 65), avg. gap size = 1.50 (6 / 4) 642 18.00 3.92 1.92 chr1qtel1M 365897 366049 (633951) Charlie4#DNA/hAT-Charlie 3223 3378 (0) m_b37s502i1 1309 chr1qtel1M 365897 AAATATTTTTAAATATTTATCTTTC----TACTTGGTTACCAT-GTGATC 365941 --i vi v ---- v v v - i Charlie4#DNA/ 3223 AAATATTTT--GATAACTATATTTCAATATAATTGGTTTCCTTTGTAATC 3270 chr1qtel1M 365942 TTATATATTTTACTTTATGCATTTAAAAACATAATTCTAAGAACTGATCC 365991 i i i v i vv i Charlie4#DNA/ 3271 CTATGTATTTTATTTTATGCATTTAAAAACATTATTCTGAGAAGGGGTCC 3320 chr1qtel1M 365992 ATA-GTTTTACCAGATTGCTACAGGAGTCCATGACATACAAAAAAGTTAA 366040 - i i i i v i i i - i Charlie4#DNA/ 3321 ATAGGCTTCACCAGACTGCCAAAGGGGTCCATGGCACA-AAAAAGGTTAA 3369 chr1qtel1M 366041 GTACTCCTG 366049 v i Charlie4#DNA/ 3370 GAACCCCTG 3378 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 20.94 CpG sites = 17, Kimura (unadjusted) = 20.94 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.04 (6 / 152), avg. gap size = 1.50 (9 / 6) 209 24.32 1.37 4.23 chr1qtel1M 369035 369107 (630893) C X7C_LINE#LINE/CR1 (155) 81 11 m_b37s601i29 1310 chr1qtel1M 369035 AAGTTTGCT-CCTGCTCTTTGACATAGCATTTCCTTTTTTTTGCTCCCTA 369083 ii - i v v vi i v --i C X7C_LINE#LINE 81 AAGTTTATTACCTACTGTGTGAAGTAGTATTTCCTTTTATTTG--TCCTA 34 chr1qtel1M 369084 GATCTGATATCGCTCATATTCCAA 369107 i - v iv vi i C X7C_LINE#LINE 33 AA-CTTACCTCGCTCAAGTTTCAA 11 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.94 CpG sites = 10, Kimura (unadjusted) = 29.94 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.06 (4 / 72), avg. gap size = 1.00 (4 / 4) 444 37.08 6.11 4.41 chr1qtel1M 369093 369583 (630417) L2#LINE/L2 2583 3081 (1) m_b37s601i30 1311 chr1qtel1M 369093 TCGCTCATATTCCAATTGCAATCAGTCTACAAGTCTTGTCAGTTCTATGT 369142 v i ii vv v vi vi i i i i iv L2#LINE/L2 2583 TCTCTCACACCCCACATCCAATCCATCAGCAAATCCTGTCGGCTCTACCT 2632 chr1qtel1M 369143 TCA---TATATC----ATT-G-----TTCTCATCCACTCAGCATATTTTA 369179 --- ---- i- ----- i vv -- i- vii L2#LINE/L2 2633 TCAAAATATATCCAGAATCCGACCACTTCTCACCACCTC--CAC-TGCCA 2679 chr1qtel1M 369180 CCACCTCATTCTAGACCTCC-TCATTTGTCAACAAGATCTTTGAAATTAT 369228 iiiv i ii v - i v iv vi ivi v vii L2#LINE/L2 2680 CCACCCTGGTCCAAGCCACCATCATCTCTCGCCTGGATTACTGCAATAGC 2729 chr1qtel1M 369229 CCCTCAGTTGGTCTCCCTGTTTCCA----TGCACCAAT-CAACATATC-- 369271 i ii ii i ---- v vv - iiv i-- L2#LINE/L2 2730 CTCCTAACTGGTCTCCCTGCTTCCACCCTTGCCCCCCTNCAGTCTATTCT 2779 chr1qtel1M 369272 --ACAGATTGTGCTGTCAGAAT-AGCCCCTTAGAGCAAAAGCCTGATTCT 369318 -- v ---- v i i - v ii i i iv i v iv L2#LINE/L2 2780 CAACACA----GCAGCCAGAGTGATCCTTTTAAAACGTAAGTCAGATCAT 2825 chr1qtel1M 369319 GAAAGGAGTCTATTTGAAAGCCTTCAATGGCTTTCTGTTCTCTCCTAG-G 369367 vv vvvv ii ii v i i ii- v ii - L2#LINE/L2 2826 GTCACTCCTCTGCTCAAAACCCTCCAATGGCTTCCCA-TCTCACTCAGAG 2874 chr1qtel1M 369368 TAAAATAGGAACTTCTTTTAGGGGTGCTTAAAGCCCCTCATATTCCAGAA 369417 vvvi v i vi iv ivivi i iv iv ii -- L2#LINE/L2 2875 TAAAAGCCAAAGTCCTTACAATGGCCTACAAGGCCCTACATGATCTGG-- 2922 chr1qtel1M 369418 TCATCC--TACCTTTCCAGA--TGAACTTC-ATGGTTGTTTCCCTTTACT 369462 vi -- i i- -- v v i - ivii -i i i ii L2#LINE/L2 2923 TCCCCCGTTACCTCTCT-GACCTCATCTCCTACCACT-CTCCCCCTCGCT 2970 chr1qtel1M 369463 TGCTTTGTATATTTCAACCACAATGGCCTATATTCCTTTCCATGGAGATG 369512 ii ii ----i i i v viv v iv vi i v i L2#LINE/L2 2971 CACTCCG----CTCCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACACG 3016 chr1qtel1M 369513 ATATCCCATCCCCTTCCTTTGTGCCTTTACACAAGCAACTGTTTAACTCT 369562 vi vv vvv i iv iv v i vv --- --- i L2#LINE/L2 3017 CCAGGCACGCTCCCGCCTCAGGGCCTTTGCACTTG---CTGTT---CCCT 3060 chr1qtel1M 369563 GTGCCTGGAGTAGCCTCCCTC 369583 v iiivi i i L2#LINE/L2 3061 CTGCCTGGAACGCTCTTCCCC 3081 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 49.61 CpG sites = 104, Kimura (unadjusted) = 53.78 Transitions / transversions = 1.49 (104/70) Gap_init rate = 0.07 (36 / 490), avg. gap size = 1.44 (52 / 36) 224 34.78 3.40 6.50 chr1qtel1M 369423 369628 (630372) L2b_3end#LINE/L2 19 218 (248) m_b37s601i31 1311 chr1qtel1M 369423 CTACCTTTCCAGATGAACTTCATGGTTGTTTCCCTTTACTTGCTTTGTAT 369472 i i vivv ii v ivivv i i i ii i --- L2b_3end#LINE 19 CTACCTCTCCGGCCTCATCTCCTACCACTCTCCCCTTGCTCACTCTG--- 65 chr1qtel1M 369473 ATTTCAACCACAATGGCCTATATTCCTTTCCATGGAGATGATATCCCATC 369522 -i i i v viv v iv vi i v i vi ?v iv? L2b_3end#LINE 66 -CTCCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACACGCCANGCTCNC 114 chr1qtel1M 369523 CCCTTCCTTTGTGCCTTTACACAAGCAACTGTTTAACTCTGTGCCTGGAG 369572 i iv iv v i ?v --- --- i v i L2b_3end#LINE 115 TCCCGCCTCAGGGCCTTTGCACNTG---CTGTT---CCCTCTGCCTGGAA 158 chr1qtel1M 369573 TAGCCTC-----CCTCTTCAGACTCTTAGACTCCATAGCTC--TTTTCAA 369615 iiv i----- - v vvivi - - --ii i L2b_3end#LINE 159 CGCCCTTCCCCACCTCTTC-GCCTGGCCAACTCC-TA-CTCATCCTTCAG 205 chr1qtel1M 369616 GGCTCGGATCAAA 369628 v i v L2b_3end#LINE 206 GTCTCAGCTCAAA 218 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 44.19 CpG sites = 38, Kimura (unadjusted) = 49.32 Transitions / transversions = 1.31 (38/29) Gap_init rate = 0.07 (15 / 205), avg. gap size = 1.33 (20 / 15) 500 25.90 9.15 1.13 chr1qtel1M 370148 370311 (629689) C L2d2_3end#LINE/L2 (28) 527 351 m_b37s601i32 1312 chr1qtel1M 370148 GCACCTACTATGTGCCAGGCACTGTGCTAAGTGCT----GGGATACAAAA 370193 i i v i i ---- i C L2d2_3end#LIN 527 GCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGTGGGGGATACAAAG 478 chr1qtel1M 370194 GGAGGCAAGACA--GTGCCTGTGTTCAAGAAGCTTGCAATCTAAGGAGGG 370241 iiivii -- v ivi i i ivvi C L2d2_3end#LIN 477 AAGTATAAGACATGGTCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGG 428 chr1qtel1M 370242 AGAC--------AACTTGCAAACAGTTTTAT-ACAAAGCAAGCCATATAT 370282 -------- vi ii v vv - vi viv v C L2d2_3end#LIN 427 AGACAAGACATAAACACGTGAAAAGTTAAATAACAATACAAGATTTAAAT 378 chr1qtel1M 370283 ACAAGTTAATTAGAAAATAATAGAAAAAA 370311 vv v -- v i i i C L2d2_3end#LIN 377 AACAGTTCA--AGACAACAATAGAAGAGA 351 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.71 CpG sites = 24, Kimura (unadjusted) = 32.45 Transitions / transversions = 1.33 (24/18) Gap_init rate = 0.04 (6 / 163), avg. gap size = 2.83 (17 / 6) 188 35.47 1.52 3.88 chr1qtel1M 370522 370653 (629347) L2#LINE/L2 1863 1991 (1091) m_b38s601i1 1313 chr1qtel1M 370522 CTTTCTTTTATAGCTAAACTCCTAGGAAAATTGACTTATAC-CATTGACT 370570 ii i i v v i i v viii - ii v L2#LINE/L2 1863 CTCCCCTTTACAGCAAAACTCCTCGAAAGAGTTGTCTATACTCGCTGTCT 1912 chr1qtel1M 370571 CCTCTTCTTTTCTTCCCACTCATTTCTCAACTC-CTTGAAGTTTCTCATT 370619 vv i i i i vi ii v i - iv --- vvii L2#LINE/L2 1913 CCAATTCCTCTCCTCCCATTCTCTCTTGAACCCACTCCAA---TCAGGCT 1959 chr1qtel1M 370620 TTTGATCCTTCCATTCCCCTGAAATGTCACTCTT 370653 i vi iv i v i --iii L2#LINE/L2 1960 TTCGTCCCCACCACTCCACCGAAA--CTGCTCTT 1991 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 46.44 CpG sites = 30, Kimura (unadjusted) = 51.38 Transitions / transversions = 2.00 (30/15) Gap_init rate = 0.05 (7 / 131), avg. gap size = 1.00 (7 / 7) 342 16.22 5.41 0.00 chr1qtel1M 370740 370813 (629187) C MIR1_Amn#SINE/MIR (76) 154 77 m_b38s601i3 1314 chr1qtel1M 370740 TACCTCCATTTTATAGAGGAGGAAACTGAGGCTCAAGGAATTTAA-TGGC 370788 i i i v ? ii iv ? - i C MIR1_Amn#SINE 154 TATCCCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGAC 105 chr1qtel1M 370789 TTGCCCAGGGAAACC---CCGGCGAGTG 370813 i vv ?--- ? ? C MIR1_Amn#SINE 104 TTGCCCAAGGTCACNCAGCNGGCNAGTG 77 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 20.20 CpG sites = 8, Kimura (unadjusted) = 20.20 Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.03 (2 / 73), avg. gap size = 2.00 (4 / 2) 345 16.95 1.69 0.00 chr1qtel1M 370740 370798 (629202) C MIRc#SINE/MIR (116) 152 93 m_b38s601i2 1314 chr1qtel1M 370740 TACCTCCATTTTATAGAGGAGGAAACTGAGGCTCAAGGAATTTAA-TGGC 370788 i i i v ii iv - i C MIRc#SINE/MIR 152 TATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGAC 103 chr1qtel1M 370789 TTGCCCAGGG 370798 i C MIRc#SINE/MIR 102 TTGCCCAAGG 93 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 19.95 CpG sites = 8, Kimura (unadjusted) = 19.95 Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1) 335 34.15 8.13 0.00 chr1qtel1M 371454 371576 (628424) C MIRc#SINE/MIR (126) 142 10 m_b38s601i4 1315 chr1qtel1M 371454 TCACAAATAAGAAA------GATTAGGAAGG--GAGCAATTTGCCTAGGG 371495 i i i i ------ v i ii --i ii i i i C MIRc#SINE/MIR 142 TTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGG 93 chr1qtel1M 371496 ACACACACTTAGTAAGTGAATGTGGCAGAATTTGCACTCGGCTCTCCTGG 371545 v vi ivv v v i i i i v i i v i iv C MIRc#SINE/MIR 92 TCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTG 43 chr1qtel1M 371546 ATTCCAAGTTC--TCCACTGTTCACTGTACTGC 371576 i i -- v v v i i ii C MIRc#SINE/MIR 42 ACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 45.64 CpG sites = 29, Kimura (unadjusted) = 48.98 Transitions / transversions = 2.23 (29/13) Gap_init rate = 0.02 (3 / 122), avg. gap size = 3.33 (10 / 3) 265 32.56 5.43 4.86 chr1qtel1M 372093 372276 (627724) C L3#LINE/CR1 (1596) 2503 2319 m_b38s601i5 1316 chr1qtel1M 372093 TCCCCACTTATTG-TATTTGT---GTCATTCCTGGTATAAAGTTCATTCT 372138 i v vi - i ---ii v i ii v i v C L3#LINE/CR1 2503 TTCCCTCTTAACGATGTTTGTTCTACCCTTTCCAGTCTGAAGATCATTCT 2454 chr1qtel1M 372139 TGTTGATGGGGAAAAAAGA--CAAAAGAGGAGTTCA-CAGCTCTTCCTTC 372185 iv i i i vi -- v v -i i v i C L3#LINE/CR1 2453 CCTTGATAGAGAAGACGGAAGCAAAATAGGAGTTGAGTAGTTCTGCTTTC 2404 chr1qtel1M 372186 TCCCTGCTG-CAGTTATGCTCATGTTCCTCGTGTCTCAGACAGATATTTA 372234 i iii- v vvv i i -i v - i i ii -----ii C L3#LINE/CR1 2403 TCTCTGTCATCTGTTAACATTACG-CCATC-TGCCCCAAGCAG-----CG 2361 chr1qtel1M 372235 AGCCT-TTATTAGCTCTCTCTCTCTCTCCTCT-AATACAGCTTT 372276 i - i?i --i i i ii v i- i i C L3#LINE/CR1 2360 GGCCTGTCNCT--TTCTTTTTCCTTCTGCTCCGAACATAGCTTT 2319 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 40.78 CpG sites = 41, Kimura (unadjusted) = 46.50 Transitions / transversions = 2.56 (41/16) Gap_init rate = 0.09 (16 / 183), avg. gap size = 1.19 (19 / 16) 350 30.05 12.36 6.20 chr1qtel1M 372388 372646 (627354) C L3#LINE/CR1 (2111) 1988 1715 m_b38s601i6 1316 chr1qtel1M 372388 TTTCTCTGAATCTCCCCAGACCCACTAAAATCTGCTTTCCCC----AAAC 372433 i ii---------- i i i---- ii C L3#LINE/CR1 1988 TTTCTCTGAATTTTT----------TGAAATCTGCTTTTCCTCGTAAAGT 1949 chr1qtel1M 372434 CTAAGGCGCATA-GCAGATTGATCTTAGTTTTC--TTCTTG---ATCATA 372477 -- vi - ii i -- i v v -- --- i ii C L3#LINE/CR1 1948 CT--GGAACATATGTGGACT--TTTAACTTTTCCTTTCTTGGCTATTACG 1903 chr1qtel1M 372478 AATTTTAGGAGGGAGAAATC-TACCCCCCCCTCAGATTCCCATC-ATTTT 372525 i i i v --- v v-i iii i iv i i - i i C L3#LINE/CR1 1902 AACTCTAAGATG---ACATGGCACTTTCTCCCAAGGTTCCTATCGACTTC 1856 chr1qtel1M 372526 CACCCTAACAATAA--TCT---------GACAAA--CAGGTGCAAAA--- 372559 iii v iv -- --------- v i --i i v i i--- C L3#LINE/CR1 1855 CACTTCACCAACCAGTTCTTCCTTGTTGGTCAGAATTAAGTCCAGAGTAG 1806 chr1qtel1M 372560 -AATTTCCCT---TGGTTCCTCTGCCTTTTGAAGGGTAAAATAATCTTCA 372605 - i i --- v i i ii i i vi vv C L3#LINE/CR1 1805 CAGTTCCCCTCGTTGCTTCCTCTACCTTCTGAGAGATGAAATTGTCAGCA 1756 chr1qtel1M 372606 AGGCAAGTCAAGATGCCATTTGCTGCTTTGCTCTTGGTGGA 372646 vvii iv v i i i i? C L3#LINE/CR1 1755 AGGCAAGTCAAGAATTTATCAGATGCTCTGCTTTTAGCNGA 1715 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 40.85 CpG sites = 54, Kimura (unadjusted) = 41.72 Transitions / transversions = 2.84 (54/19) Gap_init rate = 0.11 (29 / 258), avg. gap size = 1.69 (49 / 29) 246 33.68 13.04 2.25 chr1qtel1M 372674 372995 (627005) C L3#LINE/CR1 (2441) 1658 1303 m_b38s601i7 1316 chr1qtel1M 372674 GCTTCAGGGCTAGGCTTAGAACCTGT-TCCCCAACTCCTTGTCTCTCTTC 372722 i v v i vi iv i - vvv vv v ii iv ? i C L3#LINE/CR1 1658 GCCTCTGTGCCAGTTTTGTAATCTGTATCAGGAAAGCATCATCCATNTCC 1609 chr1qtel1M 372723 TTTCTTTCCAGCCAGGTTGTAAGATGACATACATCACTCACCAA-ATCAC 372771 -- iv ii i iv vv - iii - v v v i - C L3#LINE/CR1 1608 T--CCATCTGGCCGGGCGGTCTG-TAGTATAC-TCCCACAACGATATCAC 1563 chr1qtel1M 372772 TTCTATTTCTTCCTCCATAGACCTT-----GAATTTTCTCTGTAATGCTC 372816 i ii v vv i i -----i vi ii?vii i C L3#LINE/CR1 1562 TTCTGTTTCTCTCTCCTTTTATCCTCACCCAAATGCTCTCCANCGCGCTT 1513 chr1qtel1M 372817 CCACTCT--GGTTCCTGGACTTGCACACATGAGT-------TTTG----- 372852 i i -- v i v i v v -------i ----- C L3#LINE/CR1 1512 CTACCCTCAGGTTCGTGGATTTCCACGCAGGTGTATATCTTCTTGACATA 1463 chr1qtel1M 372853 ----------CCTTCTCCCTTT-------ACCTGTTGTTTGTGATGAAGG 372885 ---------- i?i i ------- i vi v vv C L3#LINE/CR1 1462 CAGTGCTACTCTNCCTCCCCTTCTANTAGATCTGTTTCTTTTGAACAAGG 1413 chr1qtel1M 372886 TAAACGC--CCATTCAAGCCATGGTC-AGACTTT-GTCCTTATCCCATTA 372931 ?v v -- i--- i iv - v v v- i- ii C L3#LINE/CR1 1412 TNTACCCTTCCATC---GCCGTATTCCAGTCATGAGTCCC-ATCCCACCA 1367 chr1qtel1M 372932 GGTCTCATTGCTGTCTGGAAGGTCAGACTTGACCCCTGGCATTAAGATCT 372981 i iv v ii ivi i iv i iv i v ii i i C L3#LINE/CR1 1366 AGTCTCGGTGATACCTATGAGATCGTATTTACCTCCTTGTGTTAAAATTT 1317 chr1qtel1M 372982 GAAGTTGTCTTTGT 372995 v ?v ? C L3#LINE/CR1 1316 CAAGTTNACTTTNT 1303 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 41.70 CpG sites = 61, Kimura (unadjusted) = 47.71 Transitions / transversions = 1.36 (61/45) Gap_init rate = 0.06 (19 / 321), avg. gap size = 2.63 (50 / 19) 19 8.18 0.00 0.00 chr1qtel1M 374388 374413 (625587) (T)n#Simple_repeat 1 26 (0) m_b38s252i0 1317 chr1qtel1M 374388 TTTTTTTTTTTTGGTTTTTTTTTTTT 374413 vv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 533 21.43 0.81 5.93 chr1qtel1M 374640 374763 (625237) C MIRc#SINE/MIR (141) 127 10 m_b38s601i8 1318 chr1qtel1M 374640 CTGAGGC-AATTGGGGTTAAGTGACTTGCCCAGGGTCACACAGCTAGGCT 374688 -v vv i i --- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG--- 81 chr1qtel1M 374689 GTGTTAAGGGTCTGAGGTCAAATTTGAACTCAGGTCCTCCTGACTTTAGG 374738 ---- v v v vivii i i i i ii i C MIRc#SINE/MIR 80 ----TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr1qtel1M 374739 ACTGGTGCTCTATCCACTGCGCCAC 374763 v ii v i C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 23.32 CpG sites = 15, Kimura (unadjusted) = 25.60 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.07 (8 / 123), avg. gap size = 1.00 (8 / 8) 200 26.76 14.08 0.00 chr1qtel1M 374886 374956 (625044) C L2a_3end#LINE/L2 (10) 507 427 m_b38s601i9 1319 chr1qtel1M 374886 TTAGTAAATATATATTTAGTACCAA--ATACACCAAGCACTGT-----AT 374928 i ii v v ii v -- iii i -----ii C L2a_3end#LINE 507 TCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGC 458 chr1qtel1M 374929 GCTGGGGATGCAAATGTG---AAAACAGCCA 374956 i ivv --- v C L2a_3end#LINE 457 GCTGGGGATACAGCAGTGAACAAAACAGACA 427 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.94 CpG sites = 13, Kimura (unadjusted) = 34.58 Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.04 (3 / 70), avg. gap size = 3.33 (10 / 3) 246 33.33 3.03 0.00 chr1qtel1M 375666 375764 (624236) C L2d_3end#LINE/L2 (4) 512 411 m_b38s601i11 1320 chr1qtel1M 375666 TCAGTCAGTTGGTAAGCATTTACTAAGTACCTATT-TTTGCCAGGAACTG 375714 i i iiii i i i ii i - v ivi v C L2d_3end#LINE 512 TCAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTG 463 chr1qtel1M 375715 CACTAAGCAGTTTGGGGATATATAGAAG-GTCTAA-AGATCATTCCTGCC 375762 ii i iv v vvv ? i ?- v - v vi i C L2d_3end#LINE 462 TGCTAGGCGCTGTGGGGAACGANAAAANAGTATAAGACATGGTCCCTGCC 413 chr1qtel1M 375763 TT 375764 i C L2d_3end#LINE 412 CT 411 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 43.95 CpG sites = 22, Kimura (unadjusted) = 48.28 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.03 (3 / 98), avg. gap size = 1.00 (3 / 3) 257 29.00 1.41 2.86 chr1qtel1M 375666 375736 (624264) C L2b_3end#LINE/L2 (2) 464 395 m_b38s601i10 1320 chr1qtel1M 375666 TCAGTCAGTTGGTAAGCATTTACTAAGTACCTATT-TTTGCCAGGAACTG 375714 v v iiii ii i ii i - v v? C L2b_3end#LINE 464 TCATTCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTG 415 chr1qtel1M 375715 CACTAAGCAGTTTGGGGATATA 375736 ii i i--i i C L2b_3end#LINE 414 TGCTAGGCG--CTGGGGATACA 395 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.21 CpG sites = 16, Kimura (unadjusted) = 40.82 Transitions / transversions = 4.00 (16/4) Gap_init rate = 0.04 (3 / 70), avg. gap size = 1.00 (3 / 3) 260 28.23 3.49 1.14 chr1qtel1M 375679 375764 (624236) C L2d2_3end#LINE/L2 (15) 540 453 m_b38s601i12 1320 chr1qtel1M 375679 AAGCATTTACTAAGTACCTATTTT-TGCCAGGAACTGCACTAAGCAGTTT 375727 ii i i ii i v - v v ii i iv v C L2d2_3end#LIN 540 AAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGT 491 chr1qtel1M 375728 GG-GGATATATAGAAGGTCTAA-AGATCATTCCTGCCTT 375764 - i v - v - v vi i i C L2d2_3end#LIN 490 GGGGGATACAAAGAA-GTATAAGACATGGTCCCTGCCCT 453 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.68 CpG sites = 15, Kimura (unadjusted) = 36.65 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.05 (4 / 85), avg. gap size = 1.00 (4 / 4) 806 27.78 2.87 9.39 chr1qtel1M 375763 376215 (623785) C L2#LINE/L2 (558) 2524 2099 m_b38s601i13 1320 chr1qtel1M 375763 TTACCCTTGACACATAATAGAGGATGTTGGAAGGGGAG-AGTGTCAAGGG 375811 i v ? vv -i i i i vii vii i - vv ii C L2#LINE/L2 2524 TTGCCATTNACTGA-GATGGGGAAGACTGCGGGAGGAGCAGGTTTGAGGG 2476 chr1qtel1M 375812 AAAAGATAATGAATTTAGTTTTGCACAT--TGAGTTTAAGATGTCTATCA 375859 ii v v i i v -- i i i i C L2#LINE/L2 2475 GGAAGATCAGGAGTTCAGTTTTGGACATGTTAAGTTTGAGATGCCTATTA 2426 chr1qtel1M 375860 GACACCCAATTTTGAGATGTATTAAAAAATCAGTTGATTGTATGAGATTG 375909 i v v- --ii iv iv iv i i vi C L2#LINE/L2 2425 GACATCCAAGTG-GAGATGT--CGAGTAGGCAGTTGGATATACGAGTCTG 2379 chr1qtel1M 375910 GAGGTCAGCAGAG-GGTCCGGGGCAGAAAAAGTAGATTTGAGAATCATCA 375958 v vi - vii i v - i i i C L2#LINE/L2 2378 GAGTTCAGGGGAGAGGTCCGGGCTGGAGATA-TAAATTTGGGAGTCATCA 2330 chr1qtel1M 375959 GCGTAGGAAGAATGAAAATGATATTATTTTAATTAAAATCCAATTGCTAC 376008 i v--------- i i -------- i- -- vv C L2#LINE/L2 2329 GCATAT---------AGATGGTAT--------TTAAAG-CCA--TGAGAC 2300 chr1qtel1M 376009 AAATAATTAAAT--CCATGGGAGCTAAAGTAAAGTAGTATAGAGGAATAA 376056 vi--i v i -- ?v i--i --- - ---- C L2#LINE/L2 2299 TG--GATGAGATCACCNAGGGAGT--GAGT---GTAG-ATAGAG----AA 2262 chr1qtel1M 376057 GAGATGAGGACTCAGGACAGATCTCTGAGGGACACTAATGGTTAAAACAT 376106 v v iv v v i i v v i i- ? i vi C L2#LINE/L2 2261 GAGAAGAGGTCCAAGGACTGAGCCCTGGGGCACTCCAAC-GTTNAGAGGT 2213 chr1qtel1M 376107 --GAGATCTGCAGGAGTATCCAACAAAGGAGACAGAGAAGGAGCAGTTGG 376154 -- i vv - v v i v i iii C L2#LINE/L2 2212 CGGGGAGATG-AGGAGGAACCAGCAAAGGAGACTGAGAAGGAGCGGCCAG 2164 chr1qtel1M 376155 TGAGGGAGAGAGAAAA-TAGGAGAG-G-AGTATCCCCCAAAACCTAGAGA 376201 v iii -i - -i i - ivi i v v C L2#LINE/L2 2163 TGAGGTAGGAGGAAAACCAGGAGAGTGTGGTGT-CCTGGAAGCCAAGTGA 2115 chr1qtel1M 376202 --GAAGTGTTTTGGGA 376215 --i iii C L2#LINE/L2 2114 AGAAAGTGTTTCAAGA 2099 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.88 CpG sites = 71, Kimura (unadjusted) = 35.89 Transitions / transversions = 1.65 (71/43) Gap_init rate = 0.11 (49 / 452), avg. gap size = 1.08 (53 / 49) 12 14.97 2.33 7.32 chr1qtel1M 376620 376662 (623338) (TTTAAAA)n#Simple_repeat 1 41 (0) m_b38s252i1 1321 chr1qtel1M 376620 TTTACAATTTCATATAATTT-TTATTTACACTTTAAAATTTAAA 376662 v - - - -vv v v (TTTAAAA)n#Si 1 TTTAAAATTT-A-A-AATTTAAAATTTAAAATTTAAAATTTAAA 41 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.10 (4 / 42), avg. gap size = 1.00 (4 / 4) 18 0.00 0.00 0.00 chr1qtel1M 377415 377434 (622566) (C)n#Simple_repeat 1 20 (0) m_b38s252i2 1322 chr1qtel1M 377415 CCCCCCCCCCCCCCCCCCCC 377434 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCC 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 243 29.59 4.69 2.29 chr1qtel1M 378095 378222 (621778) MamRTE1#LINE/RTE-BovB 308 438 (3374) m_b38s601i14 1323 chr1qtel1M 378095 TAGGGAGCCCAGATCATGGGGCCATCTTCTCATTGAAGCAGAGGTGGGA- 378143 vi ivi v -i iii vv ii ? vi vi ii v - MamRTE1#LINE/ 308 TAGGCGGCCCAGGATATTGG-TCGCTTAGTCGCTGANGAGGCAGCAGCAC 356 chr1qtel1M 378144 --TTCGGCATC-CCCTGGGTGTCTGAGGAGCTTTCTTAAGGACC-C-CCG 378188 -- v -? v ii v v ? - - i MamRTE1#LINE/ 357 CGTTCGGCAGCGNCCTGGGTGTCTGAGCAGCCCTGTTTAGGANCGCGCTG 406 chr1qtel1M 378189 CTGGCTCCTAATTGGAAAAGTTCCCCAGAAATGG 378222 vi v v i i --v? i v MamRTE1#LINE/ 407 CTCACTCCGAATGGGGAAGG--GNCTAGAAAAGG 438 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.04 CpG sites = 20, Kimura (unadjusted) = 40.09 Transitions / transversions = 1.18 (20/17) Gap_init rate = 0.06 (8 / 127), avg. gap size = 1.12 (9 / 8) 204 25.26 6.25 5.15 chr1qtel1M 378403 378498 (621502) L2d2_3end#LINE/L2 391 487 (68) m_b38s601i15 1324 chr1qtel1M 378403 ATTGTCATTTCA--TTTC---TGCTTGAAATGT-TTGTCTCTCCAAGAAG 378446 i v -- --- i --- - i vv L2d2_3end#LIN 391 ATTGTTATTTAACTTTTCACGTGTTT---ATGTCTTGTCTCCCCAACTAG 437 chr1qtel1M 378447 ACTGGGGACTCCTTGAGTCCAAAGACTATATTGAATGGTTCCTCTGTGAT 378496 i viii vv ii i i ivv iv - i - L2d2_3end#LIN 438 ATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACTT-CTTTGT-AT 485 chr1qtel1M 378497 CC 378498 L2d2_3end#LIN 486 CC 487 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.60 CpG sites = 14, Kimura (unadjusted) = 31.60 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.08 (8 / 95), avg. gap size = 1.38 (11 / 8) 260 30.54 4.46 3.54 chr1qtel1M 378417 378528 (621472) L2c_3end#LINE/L2 347 459 (19) m_b38s601i16 1324 chr1qtel1M 378417 TCTGCTTGAAATGTTTGTCTCTCCAAGAAGACTGGGGACTCCTTGAGTCC 378466 i - v? i ii v vv v ii vv L2c_3end#LINE 347 TCTGTTT-ACNTGTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGC 395 chr1qtel1M 378467 AAAGACTATATTGAATGGTTCCTCTGTG-ATCCTGAACAC----AATACA 378511 ii ii i i--- vi v v - iv i i ----v i i L2c_3end#LINE 396 AGGGACCGTGTC---TTATTCATCTTTGTATCCCCAGCGCCTGGCACATA 442 chr1qtel1M 378512 GTAGTCTCTCAAGAAAT 378528 v v v L2c_3end#LINE 443 GTAGGCGCTCAATAAAT 459 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.32 CpG sites = 18, Kimura (unadjusted) = 40.60 Transitions / transversions = 1.20 (18/15) Gap_init rate = 0.05 (6 / 111), avg. gap size = 1.50 (9 / 6) 17 13.12 0.00 0.00 chr1qtel1M 379357 379382 (620618) (T)n#Simple_repeat 1 26 (0) m_b38s252i3 1325 chr1qtel1M 379357 TTTTTCTTTCTTTCTTTTTTTTTTTT 379382 i i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 14 3.57 10.34 0.00 chr1qtel1M 379359 379387 (620613) (TTTC)n#Simple_repeat 1 32 (0) m_b38s252i4 1325 chr1qtel1M 379359 TTTCTTTCTTTCTTT-TTT-TTT-TTTCTCTC 379387 - - - i (TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC 32 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.11 (3 / 28), avg. gap size = 1.00 (3 / 3) 329 33.22 2.26 6.47 chr1qtel1M 380068 380244 (619756) L3#LINE/CR1 3487 3656 (443) m_b38s601i17 1326 chr1qtel1M 380068 CAAAAAAGCAACCCTAAGTAAATCTTAGTTTACAGTTGGGGAAGAATATG 380117 ----- vvv vi i v vivi v vv L3#LINE/CR1 3487 CAAAAAAGC-----TAATGCAATCTTAGGCTGCATTAATAGAAGTATAGT 3531 chr1qtel1M 380118 GTCTGAACTAAGATGATGAGATAACAGTTCTGA-GTCCTCTGCTCAGATC 380166 iii ?i i---- i i i i v- v v v i L3#LINE/CR1 3532 GTCCAGANCAAGG----GAGGTAATAGTCCCGCTGTACTCTGCGCTGGTC 3577 chr1qtel1M 380167 CAGACCACAGCTGGAGGA--GCACTT-GTCCATGGGAACCACACTTTGGG 380213 - v v -- ii i- i - vi i ii L3#LINE/CR1 3578 -AGACCACATCTGGAGTATTGCGTTCAGTTC-TGGGCGCCACATTTTAAG 3625 chr1qtel1M 380214 GAACACATTGGTGTACCAGGAAACATCTAGA 380244 iiiv iiiv ii iivi i i L3#LINE/CR1 3626 AGGGACATTGACAAACTGGAGCGCGTCCAGA 3656 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 40.70 CpG sites = 35, Kimura (unadjusted) = 46.36 Transitions / transversions = 1.75 (35/20) Gap_init rate = 0.08 (14 / 176), avg. gap size = 1.07 (15 / 14) 21 12.03 14.29 0.00 chr1qtel1M 381162 381224 (618776) (TA)n#Simple_repeat 1 72 (0) m_b38s252i5 1327 chr1qtel1M 381162 TAT-TATATATATATATAT-TTTTTTTACATAT-TAT-TAT-TATAT-TT 381205 - - v v v i - - - - v (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr1qtel1M 381206 TATGTAT-TTTAT-TAT-TATA 381224 i - v - - (TA)n#Simple_ 51 TATATATATATATATATATATA 72 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.15 (9 / 62), avg. gap size = 1.00 (9 / 9) 13 7.81 7.41 0.00 chr1qtel1M 383437 383463 (616537) (AGA)n#Simple_repeat 1 29 (0) m_b38s252i6 1328 chr1qtel1M 383437 AGAAGAAGAAG-AGAAATAGAAGAA-AAG 383463 - iv - (AGA)n#Simple 1 AGAAGAAGAAGAAGAAGAAGAAGAAGAAG 29 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.08 (2 / 26), avg. gap size = 1.00 (2 / 2) 261 36.29 8.44 1.18 chr1qtel1M 385141 385377 (614623) L2d2_3end#LINE/L2 8 261 (294) m_b38s601i18 1329 chr1qtel1M 385141 ACCCAGTCTCAACCGACCTTTCC---CATATACATCA----TCCCCTCTC 385183 i ii i i v? --- v vivi ---- ?iv L2d2_3end#LIN 8 ATCTGGCCCCAACCTNCCTTTCCAGCCTTATCTCCCACTATTCCCCTNCA 57 chr1qtel1M 385184 TGAAGTCATTGGTCCTGCCCAACTGGTGCTTTACCTCTTTCTCATACGAG 385233 i vi vii v v v vivi vv v ii i iv iv L2d2_3end#LIN 58 CGAACCCTCCGCTCCAGCCAAACTGGTCTACTCACTGTCCCCCGAACACG 107 chr1qtel1M 385234 CCA-GTCCAACCCCATCTCTGTGGTTTT----ATGTTGCTTTCCCTGTGT 385278 v- iv ?vi ii i vi ---- i ii i ii i iv L2d2_3end#LIN 108 CCTTGCGCNTTCCCGCCTCTGCGCCTTTGCTCACGCCGTTCCCCCCGCCT 157 chr1qtel1M 385279 TCAGAATGCACT--CACTCCCATCTCAATTTGCC----TCTTACAAAGTC 385322 --i v -- v i - v ii ii ---- i vv vi L2d2_3end#LIN 158 --GGAATGCCCTTCCCCTTCC-TCTCCACCTATCCAAATCCTACCCATCC 204 chr1qtel1M 385323 TTCAAGACTGAGCTCAAGTG--AGGTTTTGTTTGCAGCCTTACCTGATCT 385370 i iv i ?-- vv ii viv v v i v L2d2_3end#LIN 205 TTCAAGGCCCAGCTCAAATNCCACCTCCTCCGTGAAGCCTTCCCTGACCA 254 chr1qtel1M 385371 CTTCAGC 385377 i L2d2_3end#LIN 255 CTCCAGC 261 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 44.48 CpG sites = 49, Kimura (unadjusted) = 53.07 Transitions / transversions = 1.36 (49/36) Gap_init rate = 0.04 (10 / 236), avg. gap size = 2.30 (23 / 10) 52 2.08 0.00 0.00 chr1qtel1M 385416 385464 (614536) (TA)n#Simple_repeat 1 49 (0) c_b38s251i0 1330 chr1qtel1M 385416 TATATATGTATATATATATATATATATATATATATATATATATATATAT 385464 i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATAT 49 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 36 18.36 6.77 3.65 chr1qtel1M 386623 386755 (613245) (TTATAA)n#Simple_repeat 1 137 (0) m_b38s252i7 1331 chr1qtel1M 386623 TTATAATTATAATTAT-TTTATTTTTATTATTCTTAAT-TCATTATAATT 386670 -v vv v v v v - v (TTATAA)n#Sim 1 TTATAATTATAATTATAATTATAATTATAATTATAATTATAATTATAATT 50 chr1qtel1M 386671 -TAA-TAT-TTTATTATT-TACATAAAATT-TAATTAAAATTA-AGTATA 386714 - - -v v - vv v - v - i - (TTATAA)n#Sim 51 ATAATTATAATTATAATTATAATTATAATTATAATTATAATTATAAT-TA 99 chr1qtel1M 386715 TATATATATAAGTATTATTA-AATTACACATTAAACATTCTA 386755 - - v v - i - v - v (TTATAA)n#Sim 100 TA-AT-TATAATTATAATTATAATTATA-ATTATA-ATTATA 137 Matrix = Unknown Transitions / transversions = 0.11 (2/18) Gap_init rate = 0.11 (14 / 132), avg. gap size = 1.00 (14 / 14) 12 16.31 2.78 2.78 chr1qtel1M 391617 391652 (608348) (AGACTCC)n#Simple_repeat 1 36 (0) m_b38s252i8 1332 chr1qtel1M 391617 AGACTTCAGGCTCCAGACTCCCTAGTCCAAGA-TCCA 391652 i i vv v - - (AGACTCC)n#Si 1 AGACTCCAGACTCCAGACTCCAGACTCC-AGACTCCA 36 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 63 1.75 0.00 0.00 chr1qtel1M 391899 391956 (608044) (AT)n#Simple_repeat 1 58 (0) c_b38s251i1 1333 chr1qtel1M 391899 ATATATATATATATATATATATATATATATATATATATATATATTTATAT 391948 v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr1qtel1M 391949 ATATATAT 391956 (AT)n#Simple_ 51 ATATATAT 58 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 chr1qtel1M 391957 391973 (608027) (TG)n#Simple_repeat 3 19 (1) m_b38s252i9 1334 chr1qtel1M 391957 GTGTGTGTGTGTGTGTG 391973 (TG)n#Simple_ 3 GTGTGTGTGTGTGTGTG 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 352 27.42 0.93 8.00 chr1qtel1M 392913 393019 (606981) C MIRc#SINE/MIR (158) 110 11 m_b38s601i19 1335 chr1qtel1M 392913 TAAGTGATTTAATTAGGCTCACACAGCTAGTCAGTGTTAGGTGTCTTAGA 392962 i ivii i v v vi ------- v C MIRc#SINE/MIR 110 TAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAG-------AGC 68 chr1qtel1M 392963 CCAAATTTGAATTCAGGTCCTCCTTACTTTAGGGTCCA-TGATCTATCCA 393011 vii i i ii i v ii -i - v v C MIRc#SINE/MIR 67 CGGGACTCGAACCCAGGTCTTCCTGACTCCA-AGTCCAGTGCTCTTTCCA 19 chr1qtel1M 393012 TTGTACCA 393019 i i C MIRc#SINE/MIR 18 CTGCACCA 11 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.68 CpG sites = 18, Kimura (unadjusted) = 35.32 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.08 (9 / 106), avg. gap size = 1.00 (9 / 9) 252 32.92 0.84 8.11 chr1qtel1M 392914 393032 (606968) C MIR1_Amn#SINE/MIR (119) 111 1 m_b38s601i20 1335 chr1qtel1M 392914 AAGTGATTTAATTAGGCTCACACAGCTAGTCAGTGTTAGGTGTCTTAGAC 392963 i ivii i v ? ?i i? vi ------- v C MIR1_Amn#SINE 111 AAGTGACTTGCCCAAGGTCACNCAGCNGGCNAGTGGCAG-------AGCC 69 chr1qtel1M 392964 CAAATTTGAATTCAGGTCCTCCTTACTTTAGGGTCCA-TGATCTATCCAT 393012 vii ? ? ii ii vviiiii -- - v i C MIR1_Amn#SINE 68 GGGANTNGAACCCAGGTCTCCCGAGTCCCA--GTCCAGTGCTCTATCCAC 21 chr1qtel1M 393013 TGTACCATCTAGCAGCCCTA 393032 iv iviv vv C MIR1_Amn#SINE 20 TAGACCACACTGCCTCCCTA 1 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 48.38 CpG sites = 23, Kimura (unadjusted) = 48.38 Transitions / transversions = 1.77 (23/13) Gap_init rate = 0.08 (10 / 118), avg. gap size = 1.00 (10 / 10) 553 32.84 5.47 0.00 chr1qtel1M 393795 393995 (606005) MIRc#SINE/MIR 10 221 (47) m_b38s601i21 1336 chr1qtel1M 393795 GTGGTACAGTGGATTGATTATTGGGTTTCAAATCATGAAGACCCAAATTC 393844 i vv vi i ii vi i v iiii MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr1qtel1M 393845 CAATTCCACTTTAGAAACTTGCTAATTCTGTGATCCTAGATTAGTCCCAG 393894 v i i ivi iv vv i ii v i i i iiv v vv MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTT 109 chr1qtel1M 393895 GACCTCT----GCCACTGTTTCTTTATCTGTAAGATGGGTATAATAATA- 393939 i ---- v v i i i v - MIRc#SINE/MIR 110 AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAC 159 chr1qtel1M 393940 --GC---ACTTAAATCCTAAAATTCTCTTGAGGATAAAATGAGACCACAT 393984 -- ---i i vv vi iii v iv v iv ii MIRc#SINE/MIR 160 CTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGT 209 chr1qtel1M 393985 TTGT-ACAGTGC 393995 v - v i MIRc#SINE/MIR 210 ATGTGAAAGCGC 221 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 42.93 CpG sites = 39, Kimura (unadjusted) = 44.77 Transitions / transversions = 1.44 (39/27) Gap_init rate = 0.03 (5 / 200), avg. gap size = 2.20 (11 / 5) 194 25.16 6.35 11.67 chr1qtel1M 394169 394294 (605706) L2c_3end#LINE/L2 349 468 (10) m_b38s601i22 1337 chr1qtel1M 394169 TGTTGATGTATTT-TCTTTCCTACCAGTCTG--ACCTCCATGACAACAAT 394215 v i? i i - iii i i v -- v v vii i- L2c_3end#LINE 349 TGTTTACNTGTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAG- 397 chr1qtel1M 394216 GGATGCCACTTGTGTCTC-TTTATGTTCCTGCTGCTTATCCC-AGGTCCA 394263 -- ---- i- i v ----- -- - vv v L2c_3end#LINE 398 GGA--CC----GTGTCTTATTCATCTT-----TG--TATCCCCAGCGCCT 434 chr1qtel1M 394264 GGCATGTAGCAGGCACT---TAAATGTCTATTGA 394294 ii i i --- i i L2c_3end#LINE 435 GGCACATAGTAGGCGCTCAATAAATGTTTGTTGA 468 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.57 CpG sites = 19, Kimura (unadjusted) = 31.96 Transitions / transversions = 2.11 (19/9) Gap_init rate = 0.15 (19 / 125), avg. gap size = 1.16 (22 / 19) 351 32.67 0.00 5.30 chr1qtel1M 394413 394551 (605449) C MIR3#SINE/MIR (27) 181 50 m_b38s601i23 1338 chr1qtel1M 394413 CTGGAAGGGAGCAAAAAGGCCATGGTATGCAACCCCTTCATTTTATAGAT 394462 v vv i ii vvvi v i i C MIR3#SINE/MIR 181 CTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGAT 132 chr1qtel1M 394463 GGGGAAATTGAGATTCAGTGACAAGCCCAGAAAGGGATTTGCCCAAAGCT 394512 i i iii v viv ------ v i i - C MIR3#SINE/MIR 131 GAGGAAACTGAGGCCCAGAGAGGTG------AAGTGACTTGCCCAAGG-T 89 chr1qtel1M 394513 CATGCTTTTTATGAGTATCAGAATCAGTTCTTGAAACTA 394551 ii vvi?vi v iv ii i vv v v i C MIR3#SINE/MIR 88 CACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCA 50 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 42.78 CpG sites = 23, Kimura (unadjusted) = 44.15 Transitions / transversions = 1.15 (23/20) Gap_init rate = 0.05 (7 / 138), avg. gap size = 1.00 (7 / 7) 368 31.79 15.61 0.00 chr1qtel1M 395441 395613 (604387) MIRc#SINE/MIR 10 209 (59) m_b38s601i24 1339 chr1qtel1M 395441 GTAGTGCAGGAGATAAATC--TGGACATAGGGT-AAGAAGTGTTGAATTT 395487 i vi v i v -- v i i - i vvi ii i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr1qtel1M 395488 AAATCAAGACTCAGTTACTT------------------GACGAGTCTCTT 395519 i i vv i v ii ------------------ i i v MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTT 109 chr1qtel1M 395520 AAACTTTGTTTTCCTCAGTTTCCTCAATTCTCAAATGGGGAGGATAATAT 395569 v i v vvv vi v v vi i MIRc#SINE/MIR 110 AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAC 159 chr1qtel1M 395570 C------ATTTATCTTGGAAAGTTATTGTGAGGATGAAGTGACATACTAT 395613 ------iii i iiv ii i v i v v i MIRc#SINE/MIR 160 CTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGT 209 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 41.53 CpG sites = 32, Kimura (unadjusted) = 42.67 Transitions / transversions = 1.39 (32/23) Gap_init rate = 0.02 (4 / 172), avg. gap size = 6.75 (27 / 4) 375 28.57 0.00 0.00 chr1qtel1M 395508 395605 (604395) MIR#SINE/MIR 94 191 (71) m_b38s601i25 1339 chr1qtel1M 395508 GACGAGTCTCTTAAACTTTGTTTTCCTCAGTTTCCTCAATTCTCAAATGG 395557 i i iv v i v v v vi v v MIR#SINE/MIR 94 GGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGG 143 chr1qtel1M 395558 GGAGGATAATATCATTTATCTTGGAAAGTTATTGTGAGGATGAAGTGA 395605 vi vi ii i iiv ii i v i MIR#SINE/MIR 144 GGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGGATTAAATGA 191 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.82 CpG sites = 16, Kimura (unadjusted) = 36.82 Transitions / transversions = 1.33 (16/12) Gap_init rate = 0.00 (0 / 97), avg. gap size = 0.0 (0 / 0) 482 26.06 1.55 4.80 chr1qtel1M 398594 398722 (601278) C MIRc#SINE/MIR (141) 127 3 m_b38s601i26 1340 chr1qtel1M 398594 CTGAGGC-AATTGGGGTTAAGTGACTTGCACAGAGTCACACAGACAGGAA 398642 -v vv i v ii vi v C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAA 78 chr1qtel1M 398643 ATGTGAGTATCTGAGGCCAGATTTGAACTTAGATCCTCCTGACTTCAGGG 398692 i --- i --- v vi i i ii i i i i v C MIRc#SINE/MIR 77 GTG---GCA---GAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGT 34 chr1qtel1M 398693 TTGGTGCTCTATCTACTACACCA-ACTATCT 398722 iii v i i - ii C MIRc#SINE/MIR 33 CCAGTGCTCTTTCCACTGCACCACACTGCCT 3 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.05 CpG sites = 22, Kimura (unadjusted) = 33.34 Transitions / transversions = 2.20 (22/10) Gap_init rate = 0.06 (8 / 128), avg. gap size = 1.00 (8 / 8) 21 17.81 0.00 0.00 chr1qtel1M 400098 400135 (599865) (TG)n#Simple_repeat 1 38 (0) m_b38s252i10 1341 chr1qtel1M 400098 TGGGTGTTTGTGTGTATGTGTGTGTGAGTGTATATGTG 400135 v v i v i i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 38 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 16 15.40 2.78 0.00 chr1qtel1M 401063 401098 (598902) (GAGG)n#Simple_repeat 1 37 (0) m_b38s252i11 1342 chr1qtel1M 401063 GAGAGAGGGAGGGAGGCAGGCAGGCA-GCAGGGAGGG 401098 i v v v - v (GAGG)n#Simpl 1 GAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGG 37 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) 15 25.34 1.89 1.89 chr1qtel1M 402769 402821 (597179) (CTC)n#Simple_repeat 1 53 (0) m_b38s252i12 1343 chr1qtel1M 402769 CTGCTCCTCCCCCTCCAGCTCCTTCCTTCTCAGACTCC-CATCTTCCTCC 402817 v i vv - i vvv - v i (CTC)n#Simple 1 CTCCTCCTCCTCCTCCTCCTCC-TCCTCCTCCTCCTCCTCCTCCTCCTCC 49 chr1qtel1M 402818 TTCT 402821 i (CTC)n#Simple 50 TCCT 53 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.00 (2 / 2) 264 30.39 14.61 2.00 chr1qtel1M 403077 403254 (596746) C L3#LINE/CR1 (160) 3939 3740 m_b38s601i27 1344 chr1qtel1M 403077 AGTCTATTCCATTTTGGGACGGCTCTAATT-CGAGGAAGTTTCCTCTCAT 403125 i i v i i -iv i iiii i C L3#LINE/CR1 3939 AGCCCATTCCATTTTTGGACAGCTCTGATTGTTAGAAAGTTCTTCCTTAT 3890 chr1qtel1M 403126 ------CTGAAACCTGTGTCTCTA-AGCATTCACCAACTGCTCTTGATTC 403168 ------ i i iv i i- i v i v i v i ii C L3#LINE/CR1 3889 ATTGAGCCGAAATCTGCCTCCCTGTAACTTCCACCCATTGGTCCTAGTTC 3840 chr1qtel1M 403169 --------AGAGCAACA-AACATACTTGTAA-ACTTCCTCTATGTGAATA 403208 --------i v - iv vv v -v i i i ii --- C L3#LINE/CR1 3839 TGCCCTCTGGAGCCACACAGAATAAGTCTAATCCCTCTTCCACATG---A 3793 chr1qtel1M 403209 GAGTCCT-----TGTTCTCAGAGATC---CATATCTCCTAATAACTCTTT 403250 v i ----- i ivv v v --- i -v v i C L3#LINE/CR1 3792 CAGCCCTTCAAATATTTGAAGACAGCTATCATGTCTCCT-CTAAGTCTTC 3744 chr1qtel1M 403251 TCTT 403254 C L3#LINE/CR1 3743 TCTT 3740 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.79 CpG sites = 34, Kimura (unadjusted) = 40.82 Transitions / transversions = 1.79 (34/19) Gap_init rate = 0.07 (12 / 177), avg. gap size = 2.50 (30 / 12) 15 5.48 0.00 0.00 chr1qtel1M 403306 403324 (596676) (T)n#Simple_repeat 1 19 (0) m_b38s252i13 1345 chr1qtel1M 403306 TTTTTTTTTTTTTTTTGTT 403324 v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 365 26.08 5.88 7.28 chr1qtel1M 403428 403733 (596267) C L1PREC2_orf2#LINE/L1 (662) 2632 2331 m_b38s551i0 1346 chr1qtel1M 403428 ACAGTTTGAAATCTGGTATGGCTAGATCATCTCC--CTTTGAATTTTTTC 403475 i i v -- vv -ii -- vvi v C L1PREC2_orf2# 2632 ATAGTTTGAAGTCGGGTA--GCGTGAT-GCCTCCAGCTTTGTTCTTTTTG 2586 chr1qtel1M 403476 ATTA--ATTCCCTTGAC-ATCCTTGACCTTTTGTTCTTCCTGATGAATTT 403522 v -- v i - i vv vi v vv vv C L1PREC2_orf2# 2585 CTTAGGATTGCCTTGGCTATTCGGGCTCTTTTTTGGTTCCATATGAATTT 2536 chr1qtel1M 403523 T--GGTA-TTTTTTGTAGTTCTATGAATATTGTT-TTGATAGTTTG-TTT 403567 --ii - v i v v i- i - vv C L1PREC2_orf2# 2535 TAAAATAGTTTTTTCTAGTTCTGTGAAGAATGTCATTGGTAGTTTGATAG 2486 chr1qtel1M 403568 GTATGGCACTGAATCAGTAAATTAATTTAGGTAGAATTGTCATTTTTTAT 403617 v i i v iv i i v v i - v i C L1PREC2_orf2# 2485 GAATAGCATTGAATCTGTAAATTGCTTTGGGCAGTATGGCCA-TTTTAAC 2437 chr1qtel1M 403618 TATATATATTTTATTGTATAAGCTCAGCCTACCCATGAGCAAGTGAAC-T 403666 v vv i --------------v i v - i- C L1PREC2_orf2# 2436 GATATTGATTCT--------------TCCTATCCATGAGCATG-GAATGT 2402 chr1qtel1M 403667 TTCCCCAATTATTTAGATCTGGATTT---ATTTGTTTAAAAAATGTTTTG 403713 ii v i ivi --- i --- v i iv i C L1PREC2_orf2# 2401 TTTTCCATTTGTTTGTGTC---ATCTCTGATTTCTTTGAGCAGTGTTTTG 2355 chr1qtel1M 403714 GCATTTTTAATCT----ATCTTTC 403733 vv i i v v ---- C L1PREC2_orf2# 2354 TAATTCTCATTGTAGAGATCTTTC 2331 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 31.69 CpG sites = 34, Kimura (unadjusted) = 32.20 Transitions / transversions = 0.85 (34/40) Gap_init rate = 0.10 (32 / 305), avg. gap size = 1.25 (40 / 32) 1618 26.85 3.61 4.10 chr1qtel1M 406677 407313 (592687) C L1ME5_3end#LINE/L1 (304) 637 4 m_b38s551i1 1347 chr1qtel1M 406677 TCCTGCTCATTTCACTCAGCATCA-GTTCGTGTAAG-TCTCTCCAGGC-- 406722 i i iv ii - -- v - iv v i-- C L1ME5_3end#LI 637 TCTTACTTTTTTCACTCAGCACTATGTT--TTTAAGATCCATCCATGTTG 590 chr1qtel1M 406723 CTTTCTGAAATTATCCTGTTGGTCATTTCTTACAGA-ACAGTAATATTCC 406771 v v v --i iv iv iii v v v-i - i i C L1ME5_3end#LI 589 CTATGTGTA--CATCTAGTCCGTTGCTTCTAACTGCTGCA-TAGTACTCC 543 chr1qtel1M 406772 ATAATATTCATATACCACAATTTATTCAGCCATTCTCCAACTGATGGACA 406821 ii i v vi v iii v i v v C L1ME5_3end#LI 542 ATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCAGTGATGGACA 493 chr1qtel1M 406822 TCCA--TTCAGTTTCCAGTTTTTAGCCACTACAAAAAGGGCTGCCACAAA 406869 i -- -- ii ii iiiv i v iv v ii C L1ME5_3end#LI 492 CCCAGGTT--GCCTCCAACTCCCCGCCACCACAAACAACGCTGCAATGAA 445 chr1qtel1M 406870 CATTCGTGCACATACAGGTCCCTTT----CCCTTCTTTATAATCTCTTTG 406915 i vi i ---- i ----v viv v v i C L1ME5_3end#LI 444 CATCCTCGTACAT----GTCCCCTTATGGACCTGTGTGAGAATTTCTTTG 399 chr1qtel1M 406916 GGATATAATCCCAGTAGTAACACTGCTGGATCAAAGGGTATGCACAGTTT 406965 vv v iiiv i i v --- -- C L1ME5_3end#LI 398 GGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATGC---GT-- 354 chr1qtel1M 406966 GATAACTT--TTTGAGCA--TAGTTCCAAACTACTCTCCAAAATGGTTGG 407011 - - -- vi -- v v i i i i i v C L1ME5_3end#LI 353 -AT-ACTTAATTTGACTAAGTACTGCCAGATTGCTCTCCAGAATGGCTGC 306 chr1qtel1M 407012 ATTCGTTCACAACTCCACCAACAATGCATCAATGTCCCAGTTTTCCCGCA 407061 iiv ii vii i i v iv i vi ? i i C L1ME5_3end#LI 305 ACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATNTCCCCACA 256 chr1qtel1M 407062 TCCCCTCCAACAATCATCATTATT---TTTTCCTGTCATCTTAGCCAATC 407108 i v v iiv i---i --- v i v i C L1ME5_3end#LI 255 TCCTCGCCAACACTTGGCATTATCCAGCTTTC---TAATTTTTGCCAGTC 209 chr1qtel1M 407109 TGACAGGTGTGTAGTGGTATCTTAGAGTTGTCTTAATTTGCATTTCTCTG 407158 i i iv i i vv i C L1ME5_3end#LI 208 TAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATTTCTCTG 159 chr1qtel1M 407159 ATTAATAATGACTTGGAGCATCTTTTCATATGACTAGAAATAG--TTTC- 407205 v v v i - v --v -- - C L1ME5_3end#LI 158 ATTACTAATGAGTTTGAGCATCTCTTCATATG-CTTG--TTAGCCTTTCG 112 chr1qtel1M 407206 AATTTCTTCATCTGAGAATTGTCTGTTCATATCCTTTGACCATTTTTCAA 407255 ii i v vi i v v C L1ME5_3end#LI 111 GGTTTCCTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCCATTTTTCTA 62 chr1qtel1M 407256 TTGGAG--AATGGCTTGATTTTTTATAAATTAGAGTTAATTCTCTATATA 407303 i --?vi v -- i i vi v vivv i ii i C L1ME5_3end#LI 61 TTGGGGTTNCCGTCTT--TTTCTTGTTGATTTGCAGGAGTTCCTTGTATA 14 chr1qtel1M 407304 TTTTGGAAAT 407313 i i v C L1ME5_3end#LI 13 TTCTAGATAT 4 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.40 CpG sites = 97, Kimura (unadjusted) = 34.19 Transitions / transversions = 1.45 (97/67) Gap_init rate = 0.06 (38 / 636), avg. gap size = 1.29 (49 / 38) 1732 25.57 1.45 2.76 chr1qtel1M 406763 407313 (592687) C L1ME3G_3end#LINE/L1 (377) 547 4 m_b38s551i2 1347 chr1qtel1M 406763 TAATATTCCATAATATTCATATACCACAATTTATTCAGCCATTCTCCAAC 406812 i i vv i i i i v i C L1ME3G_3end#L 547 TAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTAT 498 chr1qtel1M 406813 TGATGGACATCCA--TTCAGTTTCCAGTTTTTAGCCACTACAAAAAGGGC 406860 ii -- -- i v i i v iv C L1ME3G_3end#L 497 TGATGGACATTTAGGTT--GTTTCCAATTTTTCGCTATTACAAACAATGC 450 chr1qtel1M 406861 TGCCACAAACATTCGTGCACATACAGGTCCCTTTCC-CTTCTTT-ATAAT 406908 v ii i v i i ?-- i v v - v v vi- vv C L1ME3G_3end#L 449 TGCAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTAT 402 chr1qtel1M 406909 CTCTTTGGGATATAATCCCAGTAGTAACACTGCTGGATCAAAGGGTATGC 406958 i ? i v v? ? v iiv i i C L1ME3G_3end#L 401 TTCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGC 352 chr1qtel1M 406959 ACAGTTTGATAACTTTTTGAGCATAGTTCCAAACTACTCTCCAAAATGGT 407008 i v i -- i vvv - v v i i i ? i C L1ME3G_3end#L 351 GCATTTTAA--ATTTTAATAG-ATACTGCCAAATTGCCCTCCAAAANGGC 305 chr1qtel1M 407009 TGGATTCGTTCACAACTCCACCAACAATGCATCAATGTCCCAGTTTTCCC 407058 v iivi i vii i i i v iv v v i C L1ME3G_3end#L 304 TGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCC 255 chr1qtel1M 407059 GCATCCCCTCCAACAATCATCATTATT----TTTTCCTGTCATCTTAGCC 407104 i i i v v ?ivi i---- vv---- i v C L1ME3G_3end#L 254 ACACCCTCGCCAACACTNGATATTATCAANCTTTTAA----ATTTTTGCC 209 chr1qtel1M 407105 AATCTGACAGGTGTGTAGTGGTATCTTAGAGTTGTCTTAATTTGCATTTC 407154 ii viv i i vv i C L1ME3G_3end#L 208 AATCTGATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTC 159 chr1qtel1M 407155 TCTGATTAATAATGACTTGGAGCATCTTTTCATATGACTAGAAATAGTTT 407204 i v i vv v vi vviiivi C L1ME3G_3end#L 158 CCTGATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTT 109 chr1qtel1M 407205 CAATTTCTTCATCTGAGAATTGTCTGTTCATATCCTTTGACCATTTTTCA 407254 vv i v v i v v C L1ME3G_3end#L 108 GTATTTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCT 59 chr1qtel1M 407255 ATTGGAGAATGGCTTGATTTTTTATAAATTAGAGTTAATTCTCTATATAT 407304 iv-- v -- i vi v vivv i i C L1ME3G_3end#L 58 ATTGGGT--TGTCTT--TTTCTTATTGATTTGTAGGAGTTCTTTATATAT 13 chr1qtel1M 407305 TTTGGAAAT 407313 i v C L1ME3G_3end#L 12 TCTGGATAT 4 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 31.58 CpG sites = 73, Kimura (unadjusted) = 32.14 Transitions / transversions = 1.14 (73/64) Gap_init rate = 0.03 (19 / 550), avg. gap size = 1.21 (23 / 19) 1470 29.70 3.51 3.61 chr1qtel1M 407167 408193 (591807) C L1M5_orf2#LINE/L1 (0) 3294 2269 m_b38s551i3 1347 chr1qtel1M 407167 TGACTTGGAGCATCTTTTCATATGACTAGAAATAGTTTCAATTTCTTCAT 407216 ?v v i vi vviiivi v? v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr1qtel1M 407217 CTGAGAATTGTCTGTTCATATCCTTTGACCATTTTTCAATTGGAGAATGG 407266 i v v vi i v ?v ---i v C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGG---GTTG 3198 chr1qtel1M 407267 CTTGATTTTTTATAAATTAGAGTT-----AATTCTCTATATATTTTGGAA 407311 i vi ? -v - ? ----- i i i v C L1M5_orf2#LIN 3197 TTTGTCTTTTTNT-TATT-GANTTGTAGGAGTTCTTTATATATTCTGGAT 3150 chr1qtel1M 407312 ATGAGGCCTTTATCAGA-ACCTTTGACTGTAAAAATATTTTCCCAGTTTA 407360 i v i - iv v -?i i v v i ? i i C L1M5_orf2#LIN 3149 ACGAGTCCTTTGTCAGATATATGT-NTTGCAAATATTTTCTCCCANTCTG 3101 chr1qtel1M 407361 TTGCTTCCCTTCTAATCTTGTCTGCATTAGTTTTGTTTGTACAAAAACTT 407410 v v i v i v ivi iv ivi vvv? vi i ii C L1M5_orf2#LIN 3100 TGGCTTGCCTTTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTT 3051 chr1qtel1M 407411 TTCAGTTTGGTATAATCGA-------AATTTTCTATTTTGTGATCAGTAA 407453 v v i i? i v ------- i v i i i? i- C L1M5_orf2#LIN 3050 TTAATTTTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGGTTNGTG- 3002 chr1qtel1M 407454 TGATCTCTAGTTCTGCTTTGGTCATAAAGACCTTCCCCT-TCCACAGGTC 407502 ---- i -- v iii v i - i i i iv -? vv C L1M5_orf2#LIN 3001 ----CTTT--TTGTGTCCTGTTTA-AGAAATCTTTGCCTANCCCAAGGTC 2959 chr1qtel1M 407503 TGAGAGGTAAACTATCCTATG--TTCCTCT--AATTTATTAATAATTTCA 407548 vvii i -- i v -- i -- v - - i i C L1M5_orf2#LIN 2958 ACGAAGAT--ATTCTCCTATGTTTTCTTCTAGAAGTT-TT-ATAGTTTTA 2913 chr1qtel1M 407549 TTCTTTATGCCTAGGTC-ATGAACCCATTTTGACCTTATCTTGGTGTACG 407597 ?ii iiii - - i i ? vi v i v i C L1M5_orf2#LIN 2912 NCTTTTACATTTAGGTCTATG-ATCCATCTNGAATTAATTTTTGTGTATG 2864 chr1qtel1M 407598 GCGTTAAGTATGGATCAATGCCTAGTTTCTGCCATATTAGTTTCCAATTT 407647 i v i v i i v?iii v i v vii v v C L1M5_orf2#LIN 2863 GTGTGAGGTAGGGGTCGAGNTTCATTTTTTTCCATATGGATATCCAATTG 2814 chr1qtel1M 407648 TCCCAGCAATTTTTATCAAACAG--TAAGTTCTTATCCCAAAAGCTGGGA 407695 i viv i ii v -- -- i vi ---- iiv C L1M5_orf2#LIN 2813 TTCCAGCACCATTTGTTGAAAAGACTA--TCCTTTCCCCA----CTGAAT 2770 chr1qtel1M 407696 T-CTTTGG---GTTTGTCAAAGACTAGGTTGCTATATTTGT-TGACTGTT 407740 - ? ---v i ii i? v? i v - --- v C L1M5_orf2#LIN 2769 TGCNTTGGCACCTTTGTCAAAAATCAANTGNCCATATATGTGTG---GGT 2723 chr1qtel1M 407741 TTATCCCTTGAAC---CTAATCTATTCCACTGATCAACTAATCTATTCCT 407787 i ii - i --- v i i v i vi - C L1M5_orf2#LIN 2722 CTATTTC-TGGACTCTCTATTCTGTTCCATTGATCTATTTGTCTA-TCCT 2675 chr1qtel1M 407788 TA-GCCAATACCAAATAGTTTTGGTAACTGCTGCTCTATAATATAATTTT 407836 - v iv i i v iv i - i i C L1M5_orf2#LIN 2674 TACGCCAATACCACACTGTCTTGATTACTGTAGCTTTATAATA-AGTCTT 2626 chr1qtel1M 407837 -AGATCTGGTACAGCTAAG-CCACCATCATTTGATTTTTTTTTTCATTAA 407884 - ? ? vv - - v v - v i i -vi C L1M5_orf2#LIN 2625 GANATCNGGTAGTG-TAAGTCCTCCAAC-TTTGTTCTTCTTTTTCA-AGA 2579 chr1qtel1M 407885 TTCCCTTGAA-ATTCTTGACCTTTTGTTTTTCCATATGAACTTTGTTGTT 407933 vii iv- ? ii i iv i i ivvi i C L1M5_orf2#LIN 2578 TTGTTTTGGCTATTCTNGGTCCTTTGCATTTCCATATAAATTTTAGAATC 2529 chr1qtel1M 407934 ATTTTTTCTAGGTCATTAAAATAGTTTTTTGGGAGTCTGATTGGTATAGC 407983 vi v v vv vvi v iii vi v i v v C L1M5_orf2#LIN 2528 AGCTTGTCAATTTCTACAAAAAAACCTGCTGGGATTTTGATTGGGATTGC 2479 chr1qtel1M 407984 GCTAAATAAATAGATTAGTTTAGGTAATATTGTCATCTTTATTATATTTG 408033 ii i vv i i i v iv v ? iv vi C L1M5_orf2#LIN 2478 ATTGAATCTATAGATCAATTTGGGGAGAATTGACATCTTNACAATATTGA 2429 chr1qtel1M 408034 CTCGCCCTATCCAAGAGCATTTAATATTTTTCCAATTGGTTAGATCAGAC 408083 v vi v v i vvv i i v iv i vvvi C L1M5_orf2#LIN 2428 GTCTTCCAATCCATGAACATGGTATATCTCTCCATTTATTTAGGTCTTCT 2379 chr1qtel1M 408084 TTAATTTGTGTGAAAAGTGGTCTGTAATTTTGCTCATAAAGTTTCTG--- 408130 v v v iv i v i i vvvii ? v ii --- C L1M5_orf2#LIN 2378 TTAATTTCTCTCAGCAATGTTTTGTAGTTTTCAGTGTANAGGTCTTGCAC 2329 chr1qtel1M 408131 ATTTTCCCTTGGCAGATAGATTCCTAAATATTTTATATTATCAGTAGTTA 408180 ? --- vi vv i ? i v iv vv i C L1M5_orf2#LIN 2328 ATNTT---TTGTTAGATTTATTCCTAAGTATTTNATGTTTTTTGATGCTA 2282 chr1qtel1M 408181 CTTTAAATGGAAT 408193 i v v C L1M5_orf2#LIN 2281 TTGTAAATGGTAT 2269 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.17 CpG sites = 160, Kimura (unadjusted) = 39.87 Transitions / transversions = 1.19 (160/134) Gap_init rate = 0.05 (54 / 1026), avg. gap size = 1.35 (73 / 54) 27 0.00 0.00 0.00 chr1qtel1M 408705 408730 (591270) (T)n#Simple_repeat 1 26 (0) c_b39s251i0 1348 chr1qtel1M 408705 TTTTTTTTTTTTTTTTTTTTTTTTTT 408730 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 13 44.26 0.94 0.94 chr1qtel1M 409312 409417 (590583) (ATAT)n#Simple_repeat 1 106 (0) m_b39s252i0 1349 chr1qtel1M 409312 ATACATACATGCACATATATTTATATGCACATACATACACATGTAT-TGC 409360 i i ii i v ii i i i i i - ii (ATAT)n#Simpl 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr1qtel1M 409361 ATACAGGCATGTATATATGTATGCATGCAAAATTATGCTATACATATTTC 409410 i vii i i ii ii v vv -v i v v (ATAT)n#Simpl 51 ATATATATATATATATATATATATATATATATATAT-ATATATATATATA 99 chr1qtel1M 409411 TATTTAT 409417 v (ATAT)n#Simpl 100 TATATAT 106 Matrix = Unknown Transitions / transversions = 2.67 (24/9) Gap_init rate = 0.02 (2 / 105), avg. gap size = 1.00 (2 / 2) 354 27.88 6.87 1.45 chr1qtel1M 409844 409974 (590026) C MIR3#SINE/MIR (7) 201 64 m_b39s601i0 1350 chr1qtel1M 409844 AAAGCCATAAGATGT-AAAACTGAAAGACACTTCAGA-ATTAGAGACTCC 409891 i ii ii - i i i iv i i - i vvv v C MIR3#SINE/MIR 201 AGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCC 152 chr1qtel1M 409892 AACCCTGATCGATTTACAG--GAGGAAACTGAAGCCCAGAGAAG-GA--- 409935 iv- iv -- i i - --- C MIR3#SINE/MIR 151 AACCCCC-TCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGT 103 chr1qtel1M 409936 -ATTTGTCCAAAGTTCATACCTTTCATGAGTGTCAGAATC 409974 - i i i - i vvi?vi v v ii C MIR3#SINE/MIR 102 GACTTGCCCAAGG-TCACACAGCNAGTTAGTGGCAGAGCC 64 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.82 CpG sites = 24, Kimura (unadjusted) = 36.82 Transitions / transversions = 2.00 (24/12) Gap_init rate = 0.06 (8 / 130), avg. gap size = 1.38 (11 / 8) 22 9.47 2.94 0.00 chr1qtel1M 410989 411022 (588978) (GT)n#Simple_repeat 1 35 (0) m_b39s252i2 1351 chr1qtel1M 410989 GTGTCTGTGTGTGTGTGT-TGTGTGTGGGTGGGTG 411022 v - v v (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 35 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 14 23.22 2.44 0.00 chr1qtel1M 410988 411028 (588972) (GGTG)n#Simple_repeat 1 42 (0) m_b39s252i1 1352 chr1qtel1M 410988 GGTGTCTGTGTGTGTGTGT-TGTGTGTGGGTGGGTGGGGGGG 411028 vv v v v -v v v (GGTG)n#Simpl 1 GGTGGGTGGGTGGGTGGGTGGGTGGGTGGGTGGGTGGGTGGG 42 Matrix = Unknown Transitions / transversions = 0.00 (0/8) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 198 18.16 6.90 5.08 chr1qtel1M 411506 411563 (588437) L3#LINE/CR1 3526 3584 (515) m_b39s601i1 1353 chr1qtel1M 411506 TATAGAGCTCAGAGCAGCAGGGA---AATGATCTCTCTG-ATTTTGCCCT 411551 v ii ? -- --- ii i v - i i v L3#LINE/CR1 3526 TATAGTGTCCAGANCA--AGGGAGGTAATAGTCCCGCTGTACTCTGCGCT 3573 chr1qtel1M 411552 GGATCAGACCAC 411563 - L3#LINE/CR1 3574 GG-TCAGACCAC 3584 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 21.85 CpG sites = 7, Kimura (unadjusted) = 21.85 Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.09 (5 / 57), avg. gap size = 1.40 (7 / 5) 12 23.37 3.70 3.70 chr1qtel1M 413277 413330 (586670) (AGAAAA)n#Simple_repeat 1 54 (0) m_b39s252i3 1354 chr1qtel1M 413277 AGAAAACAGTAGAAATTCAAACACAATTAAAAA-AAAAA-AAACAGAAAA 413324 - - i vvv v v vv - - v (AGAAAA)n#Sim 1 AGAAAA-AG-AAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAA 48 chr1qtel1M 413325 AGCAAA 413330 v (AGAAAA)n#Sim 49 AGAAAA 54 Matrix = Unknown Transitions / transversions = 0.11 (1/9) Gap_init rate = 0.08 (4 / 53), avg. gap size = 1.00 (4 / 4) 62 1.79 0.00 0.00 chr1qtel1M 413493 413549 (586451) (TC)n#Simple_repeat 1 57 (0) c_b39s251i1 1355 chr1qtel1M 413493 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTTCTC 413542 i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr1qtel1M 413543 TCTCTCT 413549 (TC)n#Simple_ 51 TCTCTCT 57 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0) 18 27.38 3.03 0.00 chr1qtel1M 414664 414729 (585271) (CCTCTT)n#Simple_repeat 1 68 (0) m_b39s252i4 1356 chr1qtel1M 414664 CCCCTACCTTTTTCTCTT-CTCATTGGCTTCC-CTTTCTCTTCCTCTCAC 414711 i v i i - v ivv - i iv (CCTCTT)n#Sim 1 CCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCC 50 chr1qtel1M 414712 TCTCCATCTCCCTATTCC 414729 i v i v (CCTCTT)n#Sim 51 TCTTCCTCTTCCTCTTCC 68 Matrix = Unknown Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.03 (2 / 65), avg. gap size = 1.00 (2 / 2) 234 32.88 11.50 0.39 chr1qtel1M 415329 415789 (584211) C L1MD_orf2#LINE/L1 (726) 2568 2057 m_b39s551i3 1357 chr1qtel1M 415329 TATTCTTGCCCTTTTGTACTTACAGCTGAATTGT----TATATTTGTCTA 415374 v ii i ivi v vv i v ---- v?i C L1MD_orf2#LIN 2568 TATTCTAGTTCCTTTGCCTTTCCATATAAATTTTAGAATAANCTTGTCTA 2519 chr1qtel1M 415375 GCTCTACAAAATATTT--CTGGTAGTTTGATTGCTATGGCACTAA----G 415418 vv v i -- v v v vv v ii ---- C L1MD_orf2#LIN 2518 TATCTACAAAAAATCTTGCTGGGATTTTGATAGGAATTGCGTTAAACCTG 2469 chr1qtel1M 415419 TAAATTAATTT-----------------TTCTTATATTGACTTGGCCTAC 415451 ? i ----------------- vi i v ivv v i C L1MD_orf2#LIN 2468 TANATCAATTTGGGGAGAATTGACATCTTTACTATGTTGAGTCTTCCAAT 2419 chr1qtel1M 415452 CCATGAGCA-ATTATGAATTTTCCAGTTACTTAAATCT-----GATTTTG 415495 i -iv v-i i v i i ----- iv C L1MD_orf2#LIN 2418 CCATGAACACGGTATGT-CTCTCCATTTATTTAGATCTTCTTTGATTTCT 2370 chr1qtel1M 415496 TATAAAAAGTATTTTGTAATTTTATTCACATAGCTCCTAGATTTGTCTTG 415545 - v vv ii i vvv i i iv iv iv i C L1MD_orf2#LIN 2369 T-TCATCAGCGTTTTGTAGTTTTCAGCATACAAGTCCTGTACATGTTTTG 2321 chr1qtel1M 415546 GCAGGTAGACA---------TTCATTGTCCA--AAGTTATTTTAAATAGA 415584 vi i vv i --------- v iiv--i iv v i v C L1MD_orf2#LIN 2320 TTAGATTTATACCTAAGTATTTCATTTTTTTTTGAGCGATTGTAAATGGT 2271 chr1qtel1M 415585 ATT---TCTTTACTTATCTTTTGCTCCTGGATGTTGGTAATATGTGAAAA 415631 --- i v vivv v v v vvii v i i ii C L1MD_orf2#LIN 2270 ATTGTATTTTTAATTTCGGTTTCCACGTGTTCATTGCTAGTATATAGAAA 2221 chr1qtel1M 415632 TGCTGATGATTTATTTGGCTTCATTTTATATTCTGTAACTTTGTTGAG-- 415679 i viv v v ivv ? i i i ii i i i-- C L1MD_orf2#LIN 2220 TACAATTGATTTTTGTATGTTNATCTTGTATCCTGCGACCTTGCTGAACT 2171 chr1qtel1M 415680 ---TTGTTATTTCAATTAATTTTTAACT-GATTCTGTATGATTTTCTAAA 415725 --- i v v vv i vvv - iv iv vi C L1MD_orf2#LIN 2170 CACTTATTAGTTCTAGGAGTTTTTTTGTAGATTCCTTGGGATTTTCTACG 2121 chr1qtel1M 415726 TCTACCATCATTTCATCTCCAAAGAGTGATCATTTTGTTTCCTTATTGCC 415775 vv v v v v v ivi i i iv v C L1MD_orf2#LIN 2120 TAGACAATCATGTCATCTGCAAATAGGGACAGTTTTATTTCTTCCTTTCC 2071 chr1qtel1M 415776 TATTCGAATTCCTT 415789 v ii v v C L1MD_orf2#LIN 2070 AATCTGTATGCCTT 2057 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.43 CpG sites = 70, Kimura (unadjusted) = 44.12 Transitions / transversions = 0.86 (70/81) Gap_init rate = 0.03 (14 / 460), avg. gap size = 3.93 (55 / 14) 289 31.64 5.00 0.87 chr1qtel1M 415570 415789 (584211) C L1M4_orf2#LINE/L1 (1009) 2285 2057 m_b39s551i4 1357 chr1qtel1M 415570 GTTATTTTAAATAGAATTTCTTTACTTATCTTTTGCTCCTGGAT-----G 415614 i v i vi - -v iii iii -----i C L1M4_orf2#LIN 2285 GCTATTGTAAATGGAATTGTTTT-CTTA-ATTTCATTTTCGGATTGTTCA 2238 chr1qtel1M 415615 TTGGTAATATGTGAAAATGCTGATGATTTATTTGGCTTCATTTTATATTC 415664 v i i i ii i viv v v ivv v i i i C L1M4_orf2#LIN 2237 TTGCTAGTGTATAGAAATACAATTGATTTTTGTATATTGATCTTGTATCC 2188 chr1qtel1M 415665 TGTAACTTTGTTGAG-----TTGTTATTTCAATTAATTTTTAACTG-ATT 415708 i i i i----- i v v v i v?v - C L1M4_orf2#LIN 2187 TGCAACCTTGCTGAACTCGTTTATTAGTTCTAATAGTTTTTTNGTGGATT 2138 chr1qtel1M 415709 CTGTATGATTTTCTAAATCTACCATCATTTCATCTCCAAAGAGTGATCAT 415758 iv v v vi vv v v i v v vi C L1M4_orf2#LIN 2137 CCTTAGGATTTTCTATATACAAGATCATGTCATCTGCGAATAGAGATAGT 2088 chr1qtel1M 415759 TTTGTTTCCTTATTGCCTATTCGAATTCCTT 415789 ii i iv v v ii i v C L1M4_orf2#LIN 2087 TTTACTTCTTCCTTTCCAATCTGGATGCCTT 2057 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.77 CpG sites = 38, Kimura (unadjusted) = 42.38 Transitions / transversions = 1.23 (38/31) Gap_init rate = 0.02 (5 / 219), avg. gap size = 2.60 (13 / 5) 311 28.29 4.38 0.60 chr1qtel1M 415630 415789 (584211) C L1P3_orf2#LINE/L1 (1072) 2222 2057 m_b39s551i5 1357 chr1qtel1M 415630 AATGCTGATGATTTATTTGGCTTCATTTTATATTCTGTAACTTTGTTGA- 415678 vi v viivv v i i vi i - C L1P3_orf2#LIN 2222 AATGCTTGTGATTTTTGCACATTGATTTTGTATCCTGAGACTTTGCTGAA 2173 chr1qtel1M 415679 GTTGTTATTTCAA-TTAA-----TTTTTAACTGATTCTGTATGATTTTCT 415722 i - v i- ----- vii vv vi iv i C L1P3_orf2#LIN 2172 GTTGCT-TATCAGCTTAAGGAGNTTTTGGGCTGAGACGATGGGGTTTTCT 2124 chr1qtel1M 415723 AAATCTACCATCATTTCATCTCCAAAGAGTGATCATTTTGTTTCCTTATT 415772 v v v v v v iv vii ivi C L1P3_orf2#LIN 2123 AAATATACAATCATGTCATCTGCAAACAGAGACAATTTGACTTCCTCTCT 2074 chr1qtel1M 415773 GCCTATTCGAATTCCTT 415789 v i v i C L1P3_orf2#LIN 2073 TCCTATTTGAATACCCT 2057 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.80 CpG sites = 21, Kimura (unadjusted) = 35.80 Transitions / transversions = 0.88 (21/24) Gap_init rate = 0.03 (4 / 159), avg. gap size = 2.00 (8 / 4) 39 24.79 1.72 2.61 chr1qtel1M 415994 416109 (583891) (AAAG)n#Simple_repeat 1 115 (0) m_b39s252i5 1358 chr1qtel1M 415994 AAAGAAA-AAAGGAAGGATGGAAGGAAGAAAGGAAAGAAAG-AAGGAAGG 416041 - i i v i i - - i i (AAAG)n#Simpl 1 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA-GAAAGAAAGAAAGAAAGA 49 chr1qtel1M 416042 AAGAAAAGAAGGAGGAAGGGAGGGAAAGGAGGGAGGAAGGAAAAGGAAGA 416091 ii i i -i ii i i i i i - i (AAAG)n#Simpl 50 AAGAAAGAAAGAAAGAA-AGAAAGAAAGAAAGAAAGAAAG-AAAGAAAGA 97 chr1qtel1M 416092 AATAAAGAAAGGAAGAAA 416109 v i (AAAG)n#Simpl 98 AAGAAAGAAAGAAAGAAA 115 Matrix = Unknown Transitions / transversions = 10.00 (20/2) Gap_init rate = 0.04 (5 / 115), avg. gap size = 1.00 (5 / 5) 595 32.24 13.06 1.06 chr1qtel1M 416223 416896 (583104) C L1M4_orf2#LINE/L1 (1265) 2029 1276 m_b39s551i6 1357 chr1qtel1M 416223 TAGCCAGCATTTTTAGTACAATACTGAATGATAGAGTTG-GA-TGGGTAT 416270 i i v ii ii ii iiv v vi - -i ii C L1M4_orf2#LIN 2029 TGGCTAGAACCTCCAGTACAATGTTGAATAGAAGTGGCGAGAGCGGACAT 1980 chr1qtel1M 416271 CATTCACC----CCTGATCTTATTGAGAAGGTCTCTAGTTTTTCTCCACT 416316 v vv i---- vv i i i? ii i v i C L1M4_orf2#LIN 1979 CCTTGTCTTGTTCCTGATCTTAGGGGGAAAGCNTTCAGTCTTTCACCATT 1930 chr1qtel1M 416317 AGATA--ATGCTTGGTGATGGTTTCAGATAGGTACTATTTATCATGTTAA 416364 ii -- i v v vv ivvi i i iv v i C L1M4_orf2#LIN 1929 AAGTATGATGTTAGCTGTGGGTTTTTCGTAGATGCCCTTTATCAGGTTGA 1880 chr1qtel1M 416365 GGAAAGTTCTATTTATTCCCA---TGTT------TTCTA----------- 416394 iv i iv i i --- ------ i ----------- C L1M4_orf2#LIN 1879 GGAAGTTCCCTTCTATTCCTAGTTTGTTGAGTGTTTTTATCATGAAAGGG 1830 chr1qtel1M 416395 -----------GTTAAAACCTTTTTCTGAGTCTATATACATAACAATATT 416433 ----------- i vv v vv v i iv i v C L1M4_orf2#LIN 1829 TGTTGGATTTTGTCAAATGCTTTTTCTGCGTCTATTGAGATGATCATGTG 1780 chr1qtel1M 416434 ATTTTTGT---------TATTAGTATG-------AC------------CC 416455 i --------- i ------- ------------i C L1M4_orf2#LIN 1779 GTTTTTGTCCTTTATTCTATTAATATGGTGTATTACATTGATTGATTTTC 1730 chr1qtel1M 416456 TAACATTAAGCCAGCCT--AATTCCTG--ATATGTCTCACCAGGTTATAA 416501 v? ii i i i --v -- vi i iv i ii C L1M4_orf2#LIN 1729 GNATGTTGAACCAACCTTGCATTCCTGGGATAAATCCCACTTGGTCATGG 1680 chr1qtel1M 416502 TGTATGATCTTTATTATATATTGCTGTAATCTACTTTCTTGTATTTTAAT 416551 i i v i v v vii v v iv C L1M4_orf2#LIN 1679 TGTATAATCCTTTTTATATGTTGCTGGATTCGGTTTGCTAGTATTTTGTT 1630 chr1qtel1M 416552 TAT--TTTTTTCATCAATGTTCACTACAGAAATTGGATGATAACTTTCTC 416599 v v-- v v i iv vi v vivi ii i C L1M4_orf2#LIN 1629 GAGGATTTTTGCATCTATATTCATAAGGGATATTGGTCTGTAGTTTTCTT 1580 chr1qtel1M 416600 TGTTTTTG--CTCATTGT--GGTTTAGGTATCAGCAATATATTTGTATTA 416645 vi v --v v -- v vivv i v iv i C L1M4_orf2#LIN 1579 TTCTTGTGATGTCTTTGTCTGGTTTTGGTATCAGGGTAATACTGGCCTCA 1530 chr1qtel1M 416646 TAAAGGGAACTTGATAGCATTGCTTATTTGGCTATTTTTCCAAGTTATTT 416695 i iv ii v iv ii v i vi ivv ivi ivvi C L1M4_orf2#LIN 1529 TAGAATGAGTTGGGAAGTGTTCCCTCCTCTTCTATTTTTTGGAAGAGTTT 1480 chr1qtel1M 416696 ATGGAGTA--GATGAATTAATTTTTTTTTA----TTTGGTAGGATTCACC 416739 i i v -- i -- i i ---- i C L1M4_orf2#LIN 1479 GTGAAGGATTGGTG--TTAATTCTTCTTTAAATGTTTGGTAGAATTCACC 1432 chr1qtel1M 416740 TTTGAATCCATCTGGCCCTTTATAGTTTTTCT---TAGGGAGTTCATTTA 416786 vv v ? ---vi i --- i i iv v C L1M4_orf2#LIN 1431 AGTGAAGCCATCTGGNCCT---GGGCTTTTCTTTGTGGGAAGTTTTTTGA 1385 chr1qtel1M 416787 TGGATTGTTCAAATTCTATTTTCTAAGATAGAGG--TACTTGAGTATTTT 416834 viv vi -- v v -v v v -- i iiii v i C L1M4_orf2#LIN 1384 TTACTAATTCAA--TCTCTTTACT-TGTTATAGGTCTATTCAGATTTTCT 1338 chr1qtel1M 416835 ATTTGATTTTCTGTTAATGTAGGTAATTAATATTTTTGCAAAGATTCATC 416884 vv i vv i i v v i vi i i vi iii ii C L1M4_orf2#LIN 1337 ATTTCTTCTTGAGTCAGTTTCGGTAGTTTGTGTCTTTCTAGGAATTTGTC 1288 chr1qtel1M 416885 CATCTCACTTAG 416896 i ii C L1M4_orf2#LIN 1287 CATTTCATCTAG 1276 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 42.95 CpG sites = 123, Kimura (unadjusted) = 43.77 Transitions / transversions = 1.34 (123/92) Gap_init rate = 0.04 (28 / 673), avg. gap size = 3.43 (96 / 28) 608 27.55 6.33 3.07 chr1qtel1M 416457 416898 (583102) C L1M5_orf2#LINE/L1 (1566) 1728 1273 m_b39s551i7 1357 chr1qtel1M 416457 AACATTAAGCCAGCCT--AATTCCTG--ATATGTCTCACCAGGTTATAAT 416502 ii i i --v -- vii i iv i i C L1M5_orf2#LIN 1728 AATGTTAAACCAACCTTGCATTCCTGGGATAAACCCCACTTGGTCATGAT 1679 chr1qtel1M 416503 GTATGATCTTTATTATATATTGCTGTAATCTACTTTCTTGTATTTTAATT 416552 v i v v v v i v vi iv ? C L1M5_orf2#LIN 1678 GTATTATCCTTTTTATATATTGCTGGATTCGATTTGCTAATATTTTGTTN 1629 chr1qtel1M 416553 AT--TTTTTTCATCAATGTTCACTACAGAAATTGGATGATAACTTTCTCT 416600 v-- v v iv vi v vivi i i- C L1M5_orf2#LIN 1628 AGGATTTTTGCATCTATGTTCATGAGGGATATTGGTCTGTAATTTTCTT- 1580 chr1qtel1M 416601 GTTTTTGC----TCATTGT--GGTTTAGGTATCAGCAATATATTTGTATT 416644 - i i---- v -- v viv? ii v iv i C L1M5_orf2#LIN 1579 -TTCTTGTAATGTCTTTGTCNGGTTTTGGTATCAGGGTNATGCTGGCCTC 1531 chr1qtel1M 416645 ATAAAGGGAACTTGATAGCATTGCTTATTTGGCTATTTTTCCAAGTTATT 416694 iv ii v iv ii v i v vv iivi ivvi C L1M5_orf2#LIN 1530 ATAAAATGAGTTGGGAAGTGTTCCCTCTTTTTCTATTTTCTGGAAGAGTT 1481 chr1qtel1M 416695 TATGGAGTAGAT--GAATTAATTTTTTTTTA----TTTGGTAGGATTCAC 416738 i v -- -- v v i ii ---- i C L1M5_orf2#LIN 1480 TGTGTA--AGATTGGTATTATTTCTTCCTTAAATGTTTGGTAGAATTCAC 1433 chr1qtel1M 416739 CTTTGAATCCATCTGGCCCTTTATAGTTTTTCTTA-GGGA--GTTCATTT 416785 vv v v -- iv ii i- -- -- C L1M5_orf2#LIN 1432 CAGTGAAGCCATCTGGGCC--TGGAGTTTTCTTTGTGGGAAGGTT--TTT 1387 chr1qtel1M 416786 ATGGATTGTTCAAATTCTATTT-TCTA--AGATAGAGG--TACTTGAGTA 416830 --- i-- v - i -- v -- i iiii v C L1M5_orf2#LIN 1386 A---ATTA--CAAATTCAATTTCTTTAATAGATATAGGGCTATTCAGATT 1342 chr1qtel1M 416831 TTTTATTTGATTTTCTGTTAATGTAGGTAATTAATATTTTTGCAAAG-AT 416879 i vv i v? i i v v ? vi i - i - C L1M5_orf2#LIN 1341 TTCTATTTCTTCTTGNGTCAGTTTTGGTAANTTGTGTTTTT-CAAGGAAT 1293 chr1qtel1M 416880 TCATCCATCTCA-CTTAGTT 416898 ii i - v C L1M5_orf2#LIN 1292 TTGTCCATTTCATCTAAGTT 1273 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.44 CpG sites = 65, Kimura (unadjusted) = 35.44 Transitions / transversions = 1.23 (65/53) Gap_init rate = 0.06 (28 / 441), avg. gap size = 1.50 (42 / 28) 362 35.59 1.80 2.41 chr1qtel1M 417410 417576 (582424) MIR3#SINE/MIR 30 195 (13) m_b39s601i2 1359 chr1qtel1M 417410 GGACTCTGGATTGGGGATATCTGGATGCAAATCTTACCTTGGAAATTTAT 417459 v- v vi v i i v v i iiiv iv vv i v i MIR3#SINE/MIR 30 GGACTG-GGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAAC 78 chr1qtel1M 417460 TAATGTTATTACCCTATTGGGCAAATTTTGTAAATGCTCTG--TCTCCAT 417507 ?iivv i v --- i iviv v viv --i vi MIR3#SINE/MIR 79 TNGCTGTGTGACC---TTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGT 125 chr1qtel1M 417508 TTTCTCATCTTCAAAAGGAGAGGTTTATACTGGACAATCCCTGAGATCCC 417557 i vi v i v iv i ii i i i MIR3#SINE/MIR 126 TTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCC 175 chr1qtel1M 417558 TCCCAGCCCC-ACATCCAAT 417576 i i i- i v MIR3#SINE/MIR 176 TTCCAGCTCTGACATTCTAT 195 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 49.08 CpG sites = 33, Kimura (unadjusted) = 50.47 Transitions / transversions = 1.32 (33/25) Gap_init rate = 0.04 (6 / 166), avg. gap size = 1.17 (7 / 6) 22 24.64 6.49 0.00 chr1qtel1M 419332 419408 (580592) (AT)n#Simple_repeat 1 82 (0) m_b39s252i6 1360 chr1qtel1M 419332 ATATATCT-TTTAT-TCAATATATATGCACATATATAGGTACATGTATTT 419379 v - v - vv ii i vi i i v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr1qtel1M 419380 ATATAT-TGCATACAT-TAAATA-ATATATAT 419408 - ii i - v - (AT)n#Simple_ 51 ATATATATATATATATATATATATATATATAT 82 Matrix = Unknown Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.07 (5 / 76), avg. gap size = 1.00 (5 / 5) 432 22.69 0.00 12.62 chr1qtel1M 420682 420797 (579203) C L2c_3end#LINE/L2 (11) 467 365 m_b39s601i3 1361 chr1qtel1M 420682 CAATAAAGATTTATTAAGTAACTGTTACCATGTATCAGACGGTATTAAAC 420731 i v i iiv --- i ii i --------- C L2c_3end#LINE 467 CAACAAACATTTATTGAGCGCCT---ACTATGTGCCAGGCG--------- 430 chr1qtel1M 420732 ACTGGGGATACAAAGAAATATACAAGTCAGTCCCTGCTCTGAAGGAGCTC 420781 - viv vi vv i i v C L2c_3end#LINE 429 -CTGGGGATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTC 381 chr1qtel1M 420782 ACAATCTAATGAAGGA 420797 i i i C L2c_3end#LINE 380 ACAGTCTAGTGGAGGA 365 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 24.40 CpG sites = 15, Kimura (unadjusted) = 27.24 Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.11 (13 / 115), avg. gap size = 1.00 (13 / 13) 393 29.00 13.64 3.23 chr1qtel1M 421009 421514 (578486) C L1PREC2_orf2#LINE/L1 (720) 2574 2018 m_b39s551i8 1362 chr1qtel1M 421009 CTTGA-TATTCTTGACCTTTTGTACTTACAAATGAATTGTTA------TT 421051 i- vv vi v iv v v - ------ C L1PREC2_orf2# 2574 CTTGGCTATTCGGGCTCTTTTTTGGTTCCATATGAATT-TTAAAATAGTT 2526 chr1qtel1M 421052 TTTTCTAGCTCTACAAAATATATC--TGGTAGTTTGATTGATATGGCACT 421099 i iii iv i -- v iv i i C L1PREC2_orf2# 2525 TTTTCTAGTTCTGTGAAGAATGTCATTGGTAGTTTGATAGGAATAGCATT 2476 chr1qtel1M 421100 GAACAAGTAAATTATCTTT--------------TTTT--TTATATTGATT 421133 ivv i- -------------- --iv C L1PREC2_orf2# 2475 GAATCTGTAAATTG-CTTTGGGCAGTATGGCCATTTTAACGATATTGATT 2427 chr1qtel1M 421134 TTGACTACCCATGAGCAATTATGAA----TTTTCC------TTACAT-AG 421172 i vv i ---- i ---- ------ iii - v C L1PREC2_orf2# 2426 CTTCCTATCCATGAGCA----TGGAATGTTTTTCCATTTGTTTGTGTCAT 2381 chr1qtel1M 421173 ATCTGTTTTTGTATAAAAAGTGTTTTGCAATTATGATCACACGGTTCCTA 421222 v v iv - i iv i v v iii vi v i v C L1PREC2_orf2# 2380 CTCTGATTTCTT-TGAGCAGTGTTTTGTAATTCTCATTGTAGAGATCTTT 2332 chr1qtel1M 421223 GATTTGTCTTGGCAGGTAGACATCCATGTATATTATATTGTCCAAAGTTA 421272 v ii vi v vi v iv ivi i v v vi v iiivi iv C L1PREC2_orf2# 2331 CACCTCCCTGGTTAGCTGTATTCCTAGGTATTTTATTCTTTTTGTGGCAA 2282 chr1qtel1M 421273 TTTTAAATAGAATT----TCTTTACCTATCTTTTGTTGCT-GGGTGTTGT 421317 v i i i ---- i v ii iv i i -- - v C L1PREC2_orf2# 2281 TTGTGAATGGGATTGCGTTCCTGATTTGGCTCTCG--GCTTGGCTGTTGT 2234 chr1qtel1M 421318 TGGTAATATATGGAAATGCTGATGAAAATCAATTTG-GC-TTGATTTTAT 421365 i--- i i ii --- i-- -i - i C L1PREC2_orf2# 2233 TGGTG---TATAGGAATGCTAGTGA---TT--TTTGTACATTGATTTTGT 2192 chr1qtel1M 421366 ATTCTATAATTTTGCTGAAGTTGTTATTTCAATTAATG----TTTT--GC 421409 i iv i - v ii ? v ---- -- C L1PREC2_orf2# 2191 ATCCTGAAACTTTGCTGAAGTTGTT-TATCAGCTNAAGGAGCTTTTGGGC 2143 chr1qtel1M 421410 TGATTCTTTATGATTTTCTAAGTATACCATCATTTCATCCACAAAGAGTG 421459 i vv v iv i ii vv v i ii v v C L1PREC2_orf2# 2142 CGAGACTATGGGGTTTTCTAGATATAGAATCATGTCGTCTGCAAACAGGG 2093 chr1qtel1M 421460 A-----TTATTTCCTCATTGCCTAT----------TCTAATTCCTTCTCT 421494 ----- v i vi v ---------- i v i C L1PREC2_orf2# 2092 ATAGTTTGACTTCCTCTCTTCCTATTTGGATGCCCTTTATTTCTTTCTCT 2043 chr1qtel1M 421495 T-----ATTGCATTGACTAGTATTT 421514 ----- vi i i v i C L1PREC2_orf2# 2042 TGCCTGATTGCTCTGGCCAGGACTT 2018 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.53 CpG sites = 82, Kimura (unadjusted) = 37.88 Transitions / transversions = 1.37 (82/60) Gap_init rate = 0.07 (35 / 505), avg. gap size = 2.49 (87 / 35) 48 30.04 2.79 3.27 chr1qtel1M 421696 421910 (578090) (AAGA)n#Simple_repeat 1 214 (0) m_b39s252i7 1363 chr1qtel1M 421696 AAG-AAGACACAAA-AAAGAAAGTTAGAAAGAAAAGACAAAAAGGAAGGA 421743 - v v - vv - - i i i (AAGA)n#Simpl 1 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG-AAAGA-AAGAAAGAAAGA 48 chr1qtel1M 421744 AAGGAGGAAGGGAAG-AAGAAAGAAATGAGGGAAAGGAAAGGACGAGGAG 421792 i i i i - - ii - i v -i (AAGA)n#Simpl 49 AAGAAAGAAAGAAAGAAAGAAAGAAA-GAAAGAAA-GAAAGAAAGA-AAG 95 chr1qtel1M 421793 GAAGGAGGGAAGGAAGGAAGAGA-AAAGAAAGTCAAG-GAGAAAGGAA-A 421839 i i i i i i i - -v -i i - (AAGA)n#Simpl 96 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG-AAAGAAAGAAAGAAAGA 144 chr1qtel1M 421840 AGGGGAGGATGGAGGGAGAAAAGGAATTAGGAAGTGAAGGAAGAAAAGGA 421889 i ii i v i i i ii i vv i -v i ii i (AAGA)n#Simpl 145 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAA-AGAAAGAAAGAAAGAA 193 chr1qtel1M 421890 AGGAATAAAGAAAGGAAGAAA 421910 i v i (AAGA)n#Simpl 194 AGAAAGAAAGAAAGAAAGAAA 214 Matrix = Unknown Transitions / transversions = 3.36 (37/11) Gap_init rate = 0.06 (13 / 214), avg. gap size = 1.00 (13 / 13) 398 31.44 16.23 0.95 chr1qtel1M 422026 422481 (577519) C L1MC_orf2#LINE/L1 (1265) 2029 1505 m_b39s551i9 1364 chr1qtel1M 422026 TAGCCACCATTTTTAGTACAATATTGGATAAT-GTGTTG-GATGAG-CAT 422072 i vv i ii i i i v iv- v - v i - C L1MC_orf2#LIN 2029 TAGCTAGGACTTCCAGTACGATGTTGAAAAGGAGTGGTGAGAGGGGACAT 1980 chr1qtel1M 422073 CTTT----CATCCCTGAACTTATTGAGAAGACCTCTAGTTTATCTTCACT 422118 i ----ii i v vi i ii i ? v vi i C L1MC_orf2#LIN 1979 CCTTGCCTTGTTCCTGATCTTAGCGGGAAAGCTTCNAGTTTCTCACCATT 1930 chr1qtel1M 422119 ACAGATAATACTTGGTGATAGTTTCAGATAGATA--CTATATCATTTCAA 422166 viv i ii v v vvi ivvi i-- v vv ii C L1MC_orf2#LIN 1929 AAGTATGATGTTAGCTGTAGGTTTTTTGTAGATGTTCTTTATCAAGTTGA 1880 chr1qtel1M 422167 GGAAAATTCTATTTATTCCCA---TGCT------TTCTA----------- 422196 iv i iv i i --- ------ i ----------- C L1MC_orf2#LIN 1879 GGAAGTTCCCCTCTATTCCTAGTTTGCTGAGAGTTTTTATCATGAATGGG 1830 chr1qtel1M 422197 -GTTAAA-------AAA--CTTTATCTGAGTCTATTGACACAATAATATT 422236 - ii ------- -- v vi i ii v i v C L1MC_orf2#LIN 1829 TGTTGGATTTTGTCAAATGCTTTTTCTGCATCTATTGATATGATCATGTG 1780 chr1qtel1M 422237 ATTTTTGTT---------ATTGGTATGAT-------------------CC 422258 v ---------i i i -------------------i C L1MC_orf2#LIN 1779 ATTTTTCTTCTTTAGCCTGTTGATGTGATGGATTACATTAATTGATTTTC 1730 chr1qtel1M 422259 CAACCTTAAGCTAGCCT-GATTTCCTAGTATAATTCTCTTCTGGTCACCA 422307 v iv i i i - vv v i v v i vii iivi C L1MC_orf2#LIN 1729 GAATGTTGAACCAGCCTTGCATACCTGGGATAAATCCCACTTGGTCGTGG 1680 chr1qtel1M 422308 TGTGCGATTTTTTGGATATATTGGTGTAATCTATTTGCTTGTATTTTATT 422357 iii i vv i v v v v vi i C L1MC_orf2#LIN 1679 TGTATAATTCTTTTTATACATTGTTGGATTCGATTTGCTAATATTTTGTT 1630 chr1qtel1M 422358 TAATTTTTTTGCATCAATGTTCATTAGAGAAATTGGACTATAACTTTC-T 422406 v ivv v v v v i ii - C L1MC_orf2#LIN 1629 GAGGATTTTTGCATCTATGTTCATGAGAGATATTGGTCTGTAGTTTTCTT 1580 chr1qtel1M 422407 TTCTC----TGTTTTTGCTCATTCTGATTTAGGTACTAGCACCATATTTG 422452 i---- i ----- i v i viiv ii v C L1MC_orf2#LIN 1579 TTCTTGTAATGTCTTTG-----TCTGGTTTTGGTATTAGGGTAATGCTGG 1535 chr1qtel1M 422453 TGTTGTA-ATTGAATTTGGTAGCATTCCTT 422481 iv ii - v i v v i i C L1MC_orf2#LIN 1534 CCTCATAGAATGAGTTAGGAAGTATTCCCT 1505 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.07 CpG sites = 83, Kimura (unadjusted) = 42.26 Transitions / transversions = 1.41 (83/59) Gap_init rate = 0.05 (22 / 455), avg. gap size = 3.59 (79 / 22) 480 30.54 0.49 0.00 chr1qtel1M 422279 422481 (577519) C L1M1_orf2#LINE/L1 (1586) 1708 1505 m_b39s551i10 1364 chr1qtel1M 422279 TTCCTAGTATAATTCTCTTCTGGTCACCATGTGCGATTTTTTGGATATAT 422328 i ?i v v i vii iv vii i vi i C L1M1_orf2#LIN 1708 TCCCNGGGATAAATCCCACTTGGTCATGATGAATGATCTTTTTAATGTAT 1659 chr1qtel1M 422329 TGGTGTAATCTATTTGCTTGTATTTTATTTAATTTTTTTGCATCAATGTT 422378 v v v vi v i v ivv i C L1M1_orf2#LIN 1658 TGTTGAATTCGGTTTGCTAGTATTTTGTTGAGGATTTTTGCATCAATATT 1609 chr1qtel1M 422379 CATTAGAGAAATTGGACTATAACTTTCTTTCTCTGTTTTTGCTCATTCTG 422428 i v v i ii i i v v vv ivv C L1M1_orf2#LIN 1608 CATCAGAGATATTGGCCTGTAGTTTTCTTTTTTTGATGTGTCTTTGTCTG 1559 chr1qtel1M 422429 ATTTAGGTACTAGCACCATATTTGTGTTGTA-ATTGAATTTGGTAGCATT 422477 i v ii viiv i v iv i - v i v i C L1M1_orf2#LIN 1558 GTTTTGGTATCAGGGTAATACTGGCCTCGTAGAATGAGTTTGGAAGTATT 1509 chr1qtel1M 422478 CCTT 422481 i C L1M1_orf2#LIN 1508 CCCT 1505 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.40 CpG sites = 33, Kimura (unadjusted) = 40.23 Transitions / transversions = 1.14 (33/29) Gap_init rate = 0.00 (1 / 202), avg. gap size = 1.00 (1 / 1) 17 8.85 0.00 0.00 chr1qtel1M 422601 422624 (577376) (T)n#Simple_repeat 1 24 (0) m_b39s252i8 1365 chr1qtel1M 422601 TTTGTTTTTTTTTTTTTTCTTTTT 422624 v i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTT 24 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 347 26.72 0.99 7.37 chr1qtel1M 422735 422835 (577165) C MIRc#SINE/MIR (154) 114 20 m_b39s601i4 1366 chr1qtel1M 422735 AGGTTAAGAAGTTTTACTAGGGTCACACAGTTGGTAAGTGTCAAGGATCT 422784 viii vv i i i i v ------- C MIRc#SINE/MIR 114 AGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCA------- 72 chr1qtel1M 422785 GAGGCTGGATTTGAACTCAGGTCCCCCTGACT-CAGGACTGATGTTCTAT 422833 v v i i i ii - i v iii i v C MIRc#SINE/MIR 71 GAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTT 22 chr1qtel1M 422834 CC 422835 C MIRc#SINE/MIR 21 CC 20 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.57 CpG sites = 17, Kimura (unadjusted) = 34.27 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.08 (8 / 100), avg. gap size = 1.00 (8 / 8) 235 21.82 0.00 0.00 chr1qtel1M 422958 423012 (576988) C L1M5_orf2#LINE/L1 (2385) 909 855 m_b39s551i11 1367 chr1qtel1M 422958 ATCTAAAAATATAAATTTTCCCCTAACTAATGCTTTGACTGCATCCCATA 423007 i ?iv i i vi v ii i C L1M5_orf2#LIN 909 ATTTAANGCTATAAATTTCCCTCTAAGCACTGCTTTAGCTGCATCCCACA 860 chr1qtel1M 423008 CATTT 423012 v C L1M5_orf2#LIN 859 AATTT 855 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 27.14 CpG sites = 8, Kimura (unadjusted) = 27.14 Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 470 26.39 5.56 0.76 chr1qtel1M 425695 425820 (574180) C MIRc#SINE/MIR (120) 148 17 m_b39s601i5 1368 chr1qtel1M 425695 CTTATTTTACAGTTGAGGAA-CTGAAACAAATAG-GGTTAAGTGACTTGC 425742 ii v - ii vv v - C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr1qtel1M 425743 CCAGGGTCACACAACTAGTAAATATCGGAACTCAGG--TAGA---TGAGT 425787 i i i iv i i - i -- v ---iii C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGC-CGGGACTCGAACCCAGGT 50 chr1qtel1M 425788 CTTCCTGATTCTTGACCTGGCACTTTGTGCACT 425820 i iviii ii ii i v v C MIRc#SINE/MIR 49 CTTCCTGACTCCAAGTCCAGTGCTCTTTCCACT 17 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.02 CpG sites = 24, Kimura (unadjusted) = 34.33 Transitions / transversions = 2.67 (24/9) Gap_init rate = 0.04 (5 / 125), avg. gap size = 1.60 (8 / 5) 14 13.19 4.26 6.52 chr1qtel1M 425843 425889 (574111) (AATGAA)n#Simple_repeat 1 46 (0) m_b39s252i9 1369 chr1qtel1M 425843 AATGGAAATTGCAAAGAGGAAAATGAAGGTG-AAATGTAAA-GAAAATG 425889 - v - - v ii - v - (AATGAA)n#Sim 1 AAT-GAAAATG-AAA-ATGAAAATGAAAATGAAAATGAAAATGAAAATG 46 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.11 (5 / 46), avg. gap size = 1.00 (5 / 5) 687 24.87 7.58 0.47 chr1qtel1M 427388 427585 (572415) C MIRc#SINE/MIR (33) 235 24 m_b39s601i6 1370 chr1qtel1M 427388 TTAAGATTTGCAAAGCCCTTT-AGAAATGTCATGTCATTTTATCTTCTCA 427436 vii i v - v v ii i v v i v C MIRc#SINE/MIR 235 TTACAGTTTACAAAGCGCTTTCACATACATTATCTCATTTGATCCTCACA 186 chr1qtel1M 427437 ACCACAATGAAAGGTAGG------AGCTGAAATTATCCCCATTTTACCCA 427480 v vv vi ------ v ivv vv C MIRc#SINE/MIR 185 ACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGA 136 chr1qtel1M 427481 TGAA-AAAC---GGGT---AGAAATCAAATGACTTGCCTAGGGTCAAACA 427523 i- --- v --- ii i i i i v C MIRc#SINE/MIR 135 TGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACA 86 chr1qtel1M 427524 GCTAGTAAATGTCCAAAGCT-GGATTTAAATTCAAGTCTCCCTGACTCCA 427572 i -v i i- i ii ii i i C MIRc#SINE/MIR 85 GCTAGTAAGTG-GCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCA 37 chr1qtel1M 427573 GGCCCAGCTCTCT 427585 i i iv C MIRc#SINE/MIR 36 AGTCCAGTGCTCT 24 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.31 CpG sites = 29, Kimura (unadjusted) = 30.88 Transitions / transversions = 1.45 (29/20) Gap_init rate = 0.04 (7 / 197), avg. gap size = 2.29 (16 / 7) 207 34.43 0.00 0.00 chr1qtel1M 431817 431877 (568123) L2c_3end#LINE/L2 368 428 (50) m_b39s601i7 1371 chr1qtel1M 431817 TCCATTGGAATGGAAACTCCTTAAATGTAGGAATCACTTCTATTTTATCT 431866 i i v vi i i iv i i i iiv vv i L2c_3end#LINE 368 TCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCT 417 chr1qtel1M 431867 CTCTGTCCCCA 431877 i v i L2c_3end#LINE 418 TTGTATCCCCA 428 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 45.81 CpG sites = 14, Kimura (unadjusted) = 49.16 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 262 33.92 5.26 8.84 chr1qtel1M 432431 432582 (567418) MIRc#SINE/MIR 32 178 (90) m_b39s601i8 1372 chr1qtel1M 432431 GGACTTGAAGTTAAGAATGTCAGAGTTTATATCCTGCCTCAGACGCCTAG 432480 i i i vii v i iivi i v v v i i v MIRc#SINE/MIR 32 GGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTAC 81 chr1qtel1M 432481 TACTCGTATGATCCTGGGGAAAACATTTCACTTT-----GTCTTTGTTTT 432525 vii i i i v iv i v i i----- i iv i MIRc#SINE/MIR 82 TAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTC 131 chr1qtel1M 432526 CCTGTGATTCAAGCTCTGTGATTCAA-GAGGATATT--TGCCCATCCTAT 432572 ------- --- i --- - i v -- i iii ii MIRc#SINE/MIR 132 C-------TCA---TCTGTAA---AATGGGGATAATAATACCTGCCCTGC 168 chr1qtel1M 432573 CTACATCCCA 432582 v v MIRc#SINE/MIR 169 CTACCTCACA 178 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 45.01 CpG sites = 32, Kimura (unadjusted) = 48.08 Transitions / transversions = 2.13 (32/15) Gap_init rate = 0.11 (16 / 151), avg. gap size = 1.31 (21 / 16) 33 24.72 0.00 0.00 chr1qtel1M 434172 434247 (565753) (GA)n#Simple_repeat 1 76 (0) m_b39s252i10 1373 chr1qtel1M 434172 GAGAGAGAGAAAAACAGAAAGAGAGCCAGAGAATCAGAGAGATAAAGACA 434221 i i v i vv ivv v i v (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr1qtel1M 434222 GAGAGACACAGAGACAGAGAGAAAGA 434247 v v v i (GA)n#Simple_ 51 GAGAGAGAGAGAGAGAGAGAGAGAGA 76 Matrix = Unknown Transitions / transversions = 0.60 (6/10) Gap_init rate = 0.00 (0 / 75), avg. gap size = 0.0 (0 / 0) 225 29.11 4.02 5.23 chr1qtel1M 435809 435982 (564018) L1M3_orf2#LINE/L1 3059 3230 (58) m_b39s551i12 1374 chr1qtel1M 435809 CAAAGAAAACCAACACAGCCAGGATTACAAGGGAA---GCAGAAAGCTGG 435855 i v v v--- ii v v v ---i i v -- L1M3_orf2#LIN 3059 CAAAGGAAACAATCAA---CAGAGTGAAAAGGCAACCTACGGAATG--GG 3103 chr1qtel1M 435856 AAACAGTGTTTACAGCCAGTGTTTCTGATAAAGGCCTCATTTCTCAACTA 435905 i v i i i iv vi i v i vi v v iv v L1M3_orf2#LIN 3104 AGAAAATATTTGCAAACCATATATCTGATAAGGGGTTAATATCCAAAATA 3153 chr1qtel1M 435906 GATAGAGAACTGAGTCTAATTTA----CAAGAATACAAATTATTCCCCAA 435951 v ii -v? vi i i ---- i v v --- i L1M3_orf2#LIN 3154 TATAAGGAACT-CNTACAACTCAATAGCAAAAAAACAAATAA---CCCGA 3199 chr1qtel1M 435952 TTGATAAATGATCAAAGGACATGAACAGACA 435982 ? v iv v i L1M3_orf2#LIN 3200 TTNAAAAATGGGCAAAGGACCTGAATAGACA 3230 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.93 CpG sites = 24, Kimura (unadjusted) = 37.86 Transitions / transversions = 1.00 (24/24) Gap_init rate = 0.06 (11 / 173), avg. gap size = 1.45 (16 / 11) 326 23.68 3.62 5.15 chr1qtel1M 435845 435982 (564018) L1PREC2_orf2#LINE/L1 3101 3236 (58) m_b39s551i13 1374 chr1qtel1M 435845 CAGAAAGCTGGAAACAGTGTTTACAGCCAGTGTTTCTGATAAAGGCCTCA 435894 v -- i v i ? i iv vi iv i i v L1PREC2_orf2# 3101 CAGAATG--GGAGAAAATNTTTGCAAACTATGCATCTGACAAAGGTCTAA 3148 chr1qtel1M 435895 TTTCT--CAACTAGATAGAGAACTGAGTCTAATTTACAAG---AATACAA 435939 v i-- v -- ii v iv v --- v L1PREC2_orf2# 3149 TATCCAGCATCTA--TAAGGAACTTAAACAAATTTACAAGAAAAAAACAA 3196 chr1qtel1M 435940 ATTATTCCCCAATTGATAAATGATCAAAGGACATGAACAGACA 435982 iv -- - i v i iv L1PREC2_orf2# 3197 ACAA--CCCC-ATTAAAAAGTGGGCAAAGGACATGAACAGACA 3236 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 28.99 CpG sites = 16, Kimura (unadjusted) = 28.99 Transitions / transversions = 1.07 (16/15) Gap_init rate = 0.07 (9 / 137), avg. gap size = 1.33 (12 / 9) 809 30.30 7.31 1.89 chr1qtel1M 435897 436498 (563502) L1ME4c_3end#LINE/L1 7 640 (190) m_b39s551i14 1374 chr1qtel1M 435897 TCTCAACTAGATAGAGAACTGAGTCTAATTTACAAGAATACAAATTATT- 435945 ?v ? v i i v v v v i - v ? i vv- L1ME4c_3end#L 7 TCTNTANTATATAAAGAGCTCATTCAAATTGATAAGAA-AAANATCAAGA 55 chr1qtel1M 435946 CCCCAATTGATAAATGATCAAAGGACATGAACAGACAACATTCAGAT--- 435992 v iv -- v ?--- L1ME4c_3end#L 56 CCCCAATAGATAAATGGGCAAAGGACATGAACAGACAA--TTCACANAAG 103 chr1qtel1M 435993 ------TCTAATTA-----------CATGAAAGAAAATGCTC--TTTTG- 436022 ------ vi ? ----------- i -- i --ii i - L1ME4c_3end#L 104 AGGAAATACAANTAGTAAACAAACACATGGAA--AAATGTTCAACCTCGC 151 chr1qtel1M 436023 ----AAT-AGAGAAATGCAAACTAAGACAACTCTGAGGTTATACAAT--- 436064 ---- - i i ii vv --- v --- L1ME4c_3end#L 152 TAGTAATCAAAGAAATGCAAATTAAAGCAACAATGAG---ATACCATTTT 198 chr1qtel1M 436065 --GCCTATCCCATTGGGTGAAAT--GACAGA--GAAGATACTAAATATTG 436108 -- ivv i vvi --i v i -- vi iv ii L1ME4c_3end#L 199 ACGCCTATTAAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGCTG 248 chr1qtel1M 436109 GAAGGAATGTGG-GAAAAGGGGACAC--ATGCATTTTTGGTAATATTGAG 436155 vii i? i - vv v ? -- i vi iii ? vi L1ME4c_3end#L 249 GCGAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTA 298 chr1qtel1M 436156 AACTGATTGAACCATTTTGGAGAGCAACTGGGAGTTATGT-CCAAAAGAC 436204 i i vv v i i v viv i -i i - L1ME4c_3end#L 299 AATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAG-C 347 chr1qtel1M 436205 CATAAAATTGTGCATACCCTTTGATCCAACAAGATCTCTATTATGTCTGT 436254 v v i ii vvi v vi iv vv v L1ME4c_3end#L 348 CATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTT 397 chr1qtel1M 436255 ATCACACAGTGATTATCAAAGAGGGGAAAAAATCCACATATGGAAAAATG 436304 vi vi vi v iv i ii i v i i iiivi i L1ME4c_3end#L 398 ATCCTAAGGAAATAATTCAAAAGAAGGAAAAAGCTATATGCACGAAGATG 447 chr1qtel1M 436305 TTTGTAGCAAGAGTT-TTTGTAGTGGCAAGTAATCAGAAATTGAATGGAT 436353 ii v - v - i i i i iv ii ivivv ii L1ME4c_3end#L 448 TTCATTGC-AGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAAT 496 chr1qtel1M 436354 GCCCATGAATTTGGGAATGACTGAATTACTTATTGTGTATGAATATAATG 436403 i vv vv ii i i v v v ii v? ivii L1ME4c_3end#L 497 GTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATG 546 chr1qtel1M 436404 GAATATTATCCTTCTATAAGAAATGATGATCAAGATGATTGCTGAGAAGC 436453 v vv i v i i i v v i iivv v i L1ME4c_3end#L 547 GAATATTATGCAGCCATTAAAAATGATAATTATGAAGACTATGTAGCAAC 596 chr1qtel1M 436454 ATGGAAAG-GCTTACAGGAACAGATGCTGAGTGAAATAAGCAGAAT 436498 i- i i- iv i - i i v L1ME4c_3end#L 597 ATGGAAAATGTTTAT-GATATA-ATGTTAAGTGAAAAAAGCAGAAT 640 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.62 CpG sites = 101, Kimura (unadjusted) = 40.70 Transitions / transversions = 1.29 (101/78) Gap_init rate = 0.04 (27 / 601), avg. gap size = 2.07 (56 / 27) 15 30.10 3.08 0.00 chr1qtel1M 436693 436757 (563243) (TTTTCT)n#Simple_repeat 1 67 (0) m_b39s252i11 1375 chr1qtel1M 436693 TTTTTTTTTTTACTTGCTTTTTCTTTTTC-TTCCCCGTAT-TTTTCCCTT 436740 i ivi v - ii iv v - i i (TTTTCT)n#Sim 1 TTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTT 50 chr1qtel1M 436741 TTAGTTTGATTTTTCTT 436757 vv vv (TTTTCT)n#Sim 51 TTCTTTTTCTTTTTCTT 67 Matrix = Unknown Transitions / transversions = 1.00 (8/8) Gap_init rate = 0.03 (2 / 64), avg. gap size = 1.00 (2 / 2) 226 30.63 0.89 0.89 chr1qtel1M 437906 438017 (561983) L1M2_orf2#LINE/L1 20 131 (3160) m_b39s551i15 1376 chr1qtel1M 437906 ACCTAGTATTTACAACTTTGAACTAGAATGAAATGAATTCACATATCAAG 437955 vi v v i i ivvi i v i v vv i i L1M2_orf2#LIN 20 ACCTATCAATAATAACCTTGAATGTAAATGGATTAAATTCTCCAATTAAA 69 chr1qtel1M 437956 TAGAAACAGA-TATCAGAATGGATTAAAAACCAGAACCTGACACTATGTT 438004 - v i - iv v v v ii ii vv i L1M2_orf2#LIN 70 -AGACATAGANTGGCTGAATGGATAAAAAAACAAGACCCAACTATATGCT 118 chr1qtel1M 438005 GCTTACATGAAAC 438017 i v L1M2_orf2#LIN 119 GCCTACAAGAAAC 131 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.90 CpG sites = 17, Kimura (unadjusted) = 39.90 Transitions / transversions = 1.00 (17/17) Gap_init rate = 0.02 (2 / 111), avg. gap size = 1.00 (2 / 2) 247 22.00 8.00 0.00 chr1qtel1M 437932 438031 (561969) L1MEh_5end#LINE/L1 2125 2232 (3) m_b39s551i16 1376 chr1qtel1M 437932 AATG-AAATGAATTCA-CATATCAAGTAGAA-ACAGA---TATCAGAATG 437975 - ii v - vi i v i - --- ? v L1MEh_5end#LI 2125 AATGTAAATGGGTTAAACTCACCAATTAAAAGACAGAGATTNTCAGATTG 2174 chr1qtel1M 437976 GATTAAAAACCAGAACCTGACACTATGTTGCTTACATGAA--ACATTTAA 438023 ? v i i ii v i ii v i-- i L1MEh_5end#LI 2175 GATTNAAAAACAAAATCCAACAATATGCTGTCTACAAGAGACACACTTAA 2224 chr1qtel1M 438024 AACAACAG 438031 ?v L1MEh_5end#LI 2225 AACANAAG 2232 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 27.70 CpG sites = 14, Kimura (unadjusted) = 27.70 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.05 (5 / 99), avg. gap size = 1.60 (8 / 5) 350 30.08 6.15 4.86 chr1qtel1M 438365 438689 (561311) L1ME3G_3end#LINE/L1 75 403 (521) m_b39s551i17 1377 chr1qtel1M 438365 GAAATAAGCAGACAAT--------GAAGAAATCCAAATATATATCATAA- 438405 v i i i -------- i v ivvi -- - L1ME3G_3end#L 75 GATATGAACAGGCAATTCACAGAAGAGGAAATACAAATGGCCA--ATAAA 122 chr1qtel1M 438406 --TATAACAAG--GTTGAACATCAGCTTTGATTAGAGGAATTTAAATAAA 438451 -- i v -- i v v vivv i i i i vi v L1ME3G_3end#L 123 CATATGAAAAGATGCTCAACCTCACTAGTAATCAGGGAAATGCAAATTAA 172 chr1qtel1M 438452 AATGGCTTTGAGATATCATTTTACACCAACCAGATTGCTTAAAATGATAG 438501 iii vv i v v i viv v- i L1ME3G_3end#L 173 AACAACAATGAGATACCATTTTTCACCCATCAGATTGGCAAAAATT-TAA 221 chr1qtel1M 438502 AAGGG-GAAATTGACAAGCGTTAGAAGGAATATGGAGAAATTAGGGCAGT 438550 ?v- v v iv ? i i vii ii i i ivi vi vv L1ME3G_3end#L 222 AAGNTTGATAATATCNAGTGTTGGCGAGGGTGTGGGGAAACGGGTACTCT 271 chr1qtel1M 438551 AATTCATTGTTGGTGGGACTGTGAATT-GTCTAACTATTT--GAGAGCAA 438597 v v i i v i - vi i i? -- i L1ME3G_3end#L 272 CATACACTGCTGGTGGGAGTGTAAATTGGTACAGCCNTTTTGGAGGGCAA 321 chr1qtel1M 438598 TCTAGAATTGTAAAATGGTTTTAATTGGAA-TTAAAATAGTTTGTGCCAT 438646 i i v -- ------ i -- ii - - ivii i v L1ME3G_3end#L 322 TTTGGCA--GTA------TCT--ATTAAAATTTAAAAT-GCGCATACCCT 360 chr1qtel1M 438647 TTGAGCCATCATTATCACTACTAGG--TCCAATTCCCAAAGTAAT 438689 v v v vi v ? -- i -- i ? v L1ME3G_3end#L 361 TTGACCCAGCAATTCCACTTCTNGGNATCTA--TCCTANAGAAAT 403 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.60 CpG sites = 52, Kimura (unadjusted) = 40.26 Transitions / transversions = 1.27 (52/41) Gap_init rate = 0.08 (25 / 324), avg. gap size = 1.44 (36 / 25) 399 30.61 7.14 1.19 chr1qtel1M 438365 438602 (561398) L1ME3Cz_3end#LINE/L1 75 326 (671) m_b39s551i18 1377 chr1qtel1M 438365 GAAATAAGCAGACAAT--------GAAGAAATCCAAATATATATCATAA- 438405 v i i i -------- i i i ivvi -- - L1ME3Cz_3end# 75 GATATGAACAGGCAATTCACAGAAGAGGAAACCCGAATGGCCA--ATAAA 122 chr1qtel1M 438406 --TATAACAAG--GTTGAACATCAGCTTTGATTAGAGGAATTTAAATAAA 438451 -- i v -- i v v vivv i i i i vi v L1ME3Cz_3end# 123 CATATGAAAAGATGCTCAACCTCACTAGTAATCAGGGAAATGCAAATTAA 172 chr1qtel1M 438452 AATGGCTTTGAGATATCATTTTACACCAACCAGATTGCTTAAAATGATAG 438501 i?i vv i i v i viv v- i L1ME3Cz_3end# 173 AACNACAATGAGATACCATTTCACACCCATCAGATTGGCAAAAATT-TAA 221 chr1qtel1M 438502 AAGGG-GAAATTGACAAGCGTTAGAAGGAATATGGAGAAATTAGGGCAGT 438550 vv- v v iv i i vii i i ivi ii vv L1ME3Cz_3end# 222 AAGTCTGACAATACCAAGTGTTGGCGAGGATGTGGAGAAACGGGAACTCT 271 chr1qtel1M 438551 AATTCATTGTTGGTGGGACTGTGAATT-GTCTAACTATTT--GAGAGCAA 438597 v v i i v i - vi i i -- L1ME3Cz_3end# 272 CATACACTGCTGGTGGGAGTGTAAATTGGTACAACCACTTTGGAGAGCAA 321 chr1qtel1M 438598 TCTAG 438602 i i L1ME3Cz_3end# 322 TTTGG 326 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.60 CpG sites = 42, Kimura (unadjusted) = 40.80 Transitions / transversions = 1.40 (42/30) Gap_init rate = 0.04 (10 / 237), avg. gap size = 2.00 (20 / 10) 408 32.67 1.49 0.00 chr1qtel1M 438377 438578 (561422) L1MB5_3end#LINE/L1 99 303 (618) m_b39s551i19 1377 chr1qtel1M 438377 CAATGAAGAAATCCAAATATATATCATA-ATATAACAAG--GTTGAACAT 438423 v v v ivvi v vi- i i v -- i v L1MB5_3end#LI 99 CAAAGAAGATATACAAATGGCCAACAAGCACATGAAAAGATGCTCAACAT 148 chr1qtel1M 438424 CAGCTTTGATTAGAGGAATTTAAATAAAAATGGCTTTGAGATATCATTTT 438473 vivv v i i vi v ivi vv i i i L1MB5_3end#LI 149 CATTAGTCATTAGGGAAATGCAAATCAAAACCACAATGAGATACCACTTC 198 chr1qtel1M 438474 ACACCAACCAGATTGCTTAAAATGATAGAAGGGGAAATTGACAAGCGTTA 438523 v i iv vi v v v i iv v i i i L1MB5_3end#LI 199 ACACCCACTAGGATGGCTATAATTAAAAAAACGGAAAATAACAAGTGTTG 248 chr1qtel1M 438524 GAAGGAATATGGAGAAATTAGGGCAGTAATTCATTGTTGGTGGGACTGTG 438573 vii i i i ii vv vi v i v i L1MB5_3end#LI 249 GCGAGGATGTGGAGAAATTGGAACCCTCGTACATTGCTGGTGGGAATGTA 298 chr1qtel1M 438574 AATTG 438578 v L1MB5_3end#LI 299 AAATG 303 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.85 CpG sites = 33, Kimura (unadjusted) = 43.57 Transitions / transversions = 1.00 (33/33) Gap_init rate = 0.01 (2 / 201), avg. gap size = 1.50 (3 / 2) 348 32.36 4.29 5.80 chr1qtel1M 438415 438834 (561166) L1ME1_3end#LINE/L1 140 553 (373) m_b39s551i20 1377 chr1qtel1M 438415 GTTGAACATCAGCTTTGATTAGAGGAATTTAAATAAAAATGGCTTTGAGA 438464 i v vivv v i i vi v ivi vv L1ME1_3end#LI 140 GCTCAACATCATTAGTCATTAGGGAAATGCAAATTAAAACCACAATGAGA 189 chr1qtel1M 438465 TATCATTTTACACCAACCAGATTGCTTAAAATGATAGAAGGG--GAAATT 438512 i i vi v ii v vi -- i i i-- v v L1ME1_3end#LI 190 TACCACTACACACCTATTAGAATGGCTAAAAT--TAAAAAGACTGACAAT 237 chr1qtel1M 438513 GACAAGCGTTAGAAGGAATATGGAGAAATTAGGGCAGTAATTCATTGTTG 438562 iv i i vii i i v i i ii vv v v i L1ME1_3end#LI 238 ACCAAGTGTTGGCGAGGATGTGGAGCAACTGGAACTCTCATACATTGCTG 287 chr1qtel1M 438563 GTGGGACTGT-GAATTGTCTAACTATTT--GAGAGCAATCTAGAATTGTA 438609 v i-i v vi i i i -- i i i i i v ----- L1ME1_3end#LI 288 GTGGGAATGCAAAATGGTACAGCCACTTTGGAAAACAGTTTGGCA----- 332 chr1qtel1M 438610 AAATGGTTTTAATTGGAA--TTAAA-ATAGTTTGTGCCATTTGAGCCATC 438656 ----- i-- i? -- - vvi - i v v v L1ME1_3end#LI 333 -----GTTTC--TTANAAAGTTAAACATACACT-TACCATATGACCCAGC 374 chr1qtel1M 438657 ATTATCACTACTAGGTCCAATTCCCAAAGTAATTAGTGAAAAAGGAATAG 438706 v vi v -- v v v vi -- i ---v v L1ME1_3end#LI 375 AATTCCACTCCTAGGT--ATTTACCCAAGAGA--AATGAAAA---CATAT 417 chr1qtel1M 438707 TTCTTTTC-----CTTTTAAA--AATATGGATAGCATTTCTCTTTGGAAT 438749 v iviv ----- v v -- i vv vi i v i v L1ME1_3end#LI 418 GTCCACACAAAGACTTGTACACGAATGTTCATAGCAGCTTTATTCGTAAT 467 chr1qtel1M 438750 GGCAAAGAACTGGAAATTGAGGGGATGCCCCTCAACTGCAGAA--AACTA 438797 i v i ivivvvii i v ? vv --i iv L1ME1_3end#LI 468 AGCCAAAAACTGGAAACAACCCAAATGTCCATCAACNGGTGAATGGATAA 517 chr1qtel1M 438798 ACAAAGT-TGGCATATATAATTGTAATGGAACACTACT 438834 v - i vi -- ii i L1ME1_3end#LI 518 ACAAATTGTGGTATATCCA--TACAATGGAATACTACT 553 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 42.46 CpG sites = 66, Kimura (unadjusted) = 43.35 Transitions / transversions = 1.06 (66/62) Gap_init rate = 0.08 (33 / 419), avg. gap size = 1.27 (42 / 33) 379 31.45 2.76 6.10 chr1qtel1M 438432 438685 (561315) L1PA5_3end#LINE/L1 157 402 (499) m_b39s551i22 1377 chr1qtel1M 438432 ATTAGAGGAATTTAAATAAAAATGGCTTTGAGATATCATTTTACACCAAC 438481 i i vi v ivi vv i i i ii L1PA5_3end#LI 157 ATCAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTCACACCAGT 206 chr1qtel1M 438482 CAGATTGCTTAAAATGATAGAAGG---GGAAATTGACAAGCGTTAGAAGG 438528 i v viv vv -- i i --- i-i i i i i ii L1PA5_3end#LI 207 TAGAATGGCGATCAT--TAAAAAGTCAGGAAAC-AACAGGTGCTGGAGAG 253 chr1qtel1M 438529 AATATGGAGAAATTAGGGCAGTAATTCATTGTTGGTGGGACTGTGAATT- 438577 i i vi ii v vv v i i i - L1PA5_3end#LI 254 GATGTGGAGAAATAGGAACACTTTTACACTGTTGGTGGGACTGTAAACTA 303 chr1qtel1M 438578 GTCTAACTATT-TGAGAG-CAATCTAG-AATTGTAAAATGGTTTTAATTG 438624 ii i - ii - i v i -i vivv - v i ---- L1PA5_3end#LI 304 GTTCAACCATTGTGGAAGACAGTGTGGCGATTCCTCAA-GGATCTA---- 348 chr1qtel1M 438625 GAATTAAAATAGTTTGTGCCATTTGAGCCATCATTATCACTACTAGGTCC 438674 i i ------i i v v vv vi i i vi L1PA5_3end#LI 349 GAACTAGAA------ATACCATTTGACCCAGCCATCCCATTACTGGGTAT 392 chr1qtel1M 438675 AATTCCCAAAG 438685 - v L1PA5_3end#LI 393 -ATACCCAAAG 402 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.02 CpG sites = 48, Kimura (unadjusted) = 42.55 Transitions / transversions = 1.78 (48/27) Gap_init rate = 0.08 (20 / 253), avg. gap size = 1.10 (22 / 20) 440 29.58 2.92 1.15 chr1qtel1M 438432 438602 (561398) L1ME5_3end#LINE/L1 157 330 (611) m_b39s551i21 1377 chr1qtel1M 438432 ATTAGAGGAATTTAAATAAAAATGGCTTTGAGATATCATTTTACACCAAC 438481 i i vi v iii vv i v i L1ME5_3end#LI 157 ATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCTAT 206 chr1qtel1M 438482 CAGATTGCTTAAAATGATAGAAGG--GGAAATTGACAAGCGTTAGAAGGA 438529 i i viv -- i -- v v v i i vii i L1ME5_3end#LI 207 TAGACTGGCAAAAAT--TAGAAAGCTGGATAATGCCAAGTGTTGGCGAGG 254 chr1qtel1M 438530 ATATGGAGAAATTAGGGCAGTAATTCATTGTTGGTGGGACTGTGAATT-G 438578 i i ? vi ii vv v v i i v ii i - L1ME5_3end#LI 255 ATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACTGG 304 chr1qtel1M 438579 TCTAACTATTT--GAGAGCAATCTAG 438602 vi i i i-- i L1ME5_3end#LI 305 TGCAGCCATTCTGGAGAGCAATCTGG 330 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.47 CpG sites = 32, Kimura (unadjusted) = 39.51 Transitions / transversions = 1.78 (32/18) Gap_init rate = 0.03 (5 / 170), avg. gap size = 1.40 (7 / 5) 25 30.55 5.30 1.46 chr1qtel1M 439473 439604 (560396) (TA)n#Simple_repeat 1 137 (0) m_b39s252i12 1378 chr1qtel1M 439473 TAT-TATATATATATATGGGTGTACAAGTGTACACCCTGTATATA-ATAA 439520 - ivi i i vi i i -iv i - v (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATA-TATATATATATATAT 49 chr1qtel1M 439521 ATATAT-TTTATATTTATATA-ATATCTCTGGGTATA-ATAAACAGATAT 439567 - v v - v v ivi - v i v (TA)n#Simple_ 50 ATATATATATATATATATATATATATATATATATATATATATATATATAT 99 chr1qtel1M 439568 ACATATGTAGATGTGTTAAAATAT-TATA-AAATAGTAT 439604 i i v i i vv v - - v - (TA)n#Simple_ 100 ATATATATATATATATATATATATATATATATATA-TAT 137 Matrix = Unknown Transitions / transversions = 1.00 (16/16) Gap_init rate = 0.07 (9 / 131), avg. gap size = 1.00 (9 / 9) 421 39.12 6.38 2.17 chr1qtel1M 440227 440712 (559288) L2#LINE/L2 2565 3070 (12) m_b39s601i9 1379 chr1qtel1M 440227 ACCCTCAACTCCTCACCGTCTCTCACCCCCTTTATATGATC--------- 440267 i ii v iv v ivi vii --------- L2#LINE/L2 2565 ATCCTTGACTCCTCTCTTTCTCTCACACCCCACATCCAATCCATCAGCAA 2614 chr1qtel1M 440268 ----TGTTGATTCCATTTTTGTAACTTCTC-----TCTAATAAGTTCACC 440308 ---- i ii i ii iiv iv v ----- ii iv v v v L2#LINE/L2 2615 ATCCTGTCGGCTCTACCTTCAAAATATATCCAGAATCCGACCACTTCTCA 2664 chr1qtel1M 440309 TCCTCTCCTCTGCTAT-----TGGAGCA-TCCCTCATGACTTCACACCTG 440352 i vi v i i----- vv -v vi v ii v i L2#LINE/L2 2665 CCACCTCCACTGCCACCACCCTGGTCCAAGCCACCATCATCTCTCGCCTG 2714 chr1qtel1M 440353 CACTATTTCCATAGCCTTTTACTGGGTGTCTCTATCACAAGTGTCTTTTC 440402 v i i v v ii viv v i iiiv v viv iviii L2#LINE/L2 2715 GATTACTGCAATAGCCTCCTAACTGGTCTCCCTGCTTCCACCCTTGCCCC 2764 chr1qtel1M 440403 CTTCTACTCCATTCTCCATTCTGTTTTGACAGTGATGTTTTGAAAGTGCA 440452 i ?i v i v iv v ivviv v vi v ii i L2#LINE/L2 2765 CCTNCAGTCTATTCTCAACACAGCAGCCAGAGTGATCCTTTTAAAACGTA 2814 chr1qtel1M 440453 AGTTGGACCACGTCATTCCCAAATTCAATGAATTCTAGTGGCTCTCTCCC 440502 ii i i i ivvii vivvi i i --- L2#LINE/L2 2815 AGTCAGATCATGTCACTCCTCTGCTCAAAACCCTCCAATGGCT---TCCC 2861 chr1qtel1M 440503 ACCTC---CAGAATAAACTACAAAAACATT-CATGTGACATTCAAAGCAC 440548 i --- i vvv iv v - -i i v v i v L2#LINE/L2 2862 ATCTCACTCAGAGTAAAAGCCAAAGTCCTTACA-ATGGCCTACAAGGCCC 2910 chr1qtel1M 440549 TCAATGCACTAATCCCCCTATACCTTTCCA--TTCTTCTTGTACTGTACA 440596 vv vv ii vv i ii--i v iv ---- L2#LINE/L2 2911 TACATGATCTGGTCCCCCGTTACCTCTCTGACCTCATCTCCTAC----CA 2956 chr1qtel1M 440597 CCATCCATCCCCACCTGTTCCTTAATACAGAGATACCGGTCTTCTTGCTG 440646 iv -i i i iiii --iv v vv i i i i L2#LINE/L2 2957 CTCTCC-CCCTCGCTCACTCC--GCTCCAGCCACACTGGCCTCCTTGCTG 3003 chr1qtel1M 440647 TTCCATGGAGAAGACACTCCATCTCATACCTCAGACATTTTGT-CTGTCT 440695 vi i v v v vv vvv vii ivvi i- vv L2#LINE/L2 3004 TTCCTCGAACACGCCAGGCACGCTCCCGCCTCAGGGCCTTTGCACTTGCT 3053 chr1qtel1M 440696 GTCTTTCATTCGTGGAA 440712 iiiiiv v v L2#LINE/L2 3054 GTTCCCTCTGCCTGGAA 3070 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 53.89 CpG sites = 102, Kimura (unadjusted) = 57.71 Transitions / transversions = 1.21 (102/84) Gap_init rate = 0.04 (20 / 485), avg. gap size = 2.10 (42 / 20) 22 22.26 3.03 1.49 chr1qtel1M 441009 441074 (558926) (ACAT)n#Simple_repeat 1 67 (0) m_b39s252i13 1380 chr1qtel1M 441009 ACATTACTGACATA-AT-CATATATACACATGTACATACCTATATACATA 441056 - vv - - i i ii v i (ACAT)n#Simpl 1 ACA-TACATACATACATACATACATACATACATACATACATACATACATA 49 chr1qtel1M 441057 CATGCACACACACACACA 441074 i i i i (ACAT)n#Simpl 50 CATACATACATACATACA 67 Matrix = Unknown Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.05 (3 / 65), avg. gap size = 1.00 (3 / 3) 11 20.74 5.13 0.00 chr1qtel1M 441018 441056 (558944) (ACATAT)n#Simple_repeat 1 41 (0) m_b39s252i14 1381 chr1qtel1M 441018 ACATAATCATAT--ATACACATGTACATACCTATATACATA 441056 vv -- i i ivi (ACATAT)n#Sim 1 ACATATACATATACATATACATATACATATACATATACATA 41 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.03 (1 / 38), avg. gap size = 2.00 (2 / 1) 15 14.38 0.00 0.00 chr1qtel1M 441052 441075 (558925) (AC)n#Simple_repeat 1 24 (0) m_b39s252i15 1382 chr1qtel1M 441052 ACATACATGCACACACACACACAC 441075 i ii (AC)n#Simple_ 1 ACACACACACACACACACACACAC 24 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 22 22.26 3.03 1.49 chr1qtel1M 441009 441074 (558926) (ACAT)n#Simple_repeat 1 67 (0) m_b39s252i13 1380 chr1qtel1M 441009 ACATTACTGACATA-AT-CATATATACACATGTACATACCTATATACATA 441056 - vv - - i i ii v i (ACAT)n#Simpl 1 ACA-TACATACATACATACATACATACATACATACATACATACATACATA 49 chr1qtel1M 441057 CATGCACACACACACACA 441074 i i i i (ACAT)n#Simpl 50 CATACATACATACATACA 67 Matrix = Unknown Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.05 (3 / 65), avg. gap size = 1.00 (3 / 3) 63 1.75 0.00 0.00 chr1qtel1M 441076 441133 (558867) (AT)n#Simple_repeat 1 58 (0) c_b39s251i2 1383 chr1qtel1M 441076 ATATATATATATATATATATATATATATATATATATATATATATATATAC 441125 i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr1qtel1M 441126 ATATATAT 441133 (AT)n#Simple_ 51 ATATATAT 58 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0) 12 20.03 0.00 0.00 chr1qtel1M 441181 441209 (558791) (AATA)n#Simple_repeat 1 29 (0) m_b39s252i16 1384 chr1qtel1M 441181 AATAAATACCTAAAAAAATACCTAAATAA 441209 vv v vv (AATA)n#Simpl 1 AATAAATAAATAAATAAATAAATAAATAA 29 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 287 32.55 12.22 1.00 chr1qtel1M 444347 444526 (555474) MIRc#SINE/MIR 36 235 (33) m_b39s601i10 1385 chr1qtel1M 444347 TTGGCATCAAGAAGACTTGAGAT-GAATTTT-TTTCAGTTAGTTATTAGC 444394 vi i i i v - i iii-vi v ii v i MIRc#SINE/MIR 36 TTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGC 85 chr1qtel1M 444395 TGCATGAT----AGCA----ACTTAATTTTTCTCACTCTCAGTAGCTTCC 444436 ii i----i ---- ii i v vi vv i v MIRc#SINE/MIR 86 TGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCA 135 chr1qtel1M 444437 TTT-TGAAACGGGAACAATGAAA---GA---ACCTACCTAATGGGTTTTG 444479 i - i i i i i v --- v---i v ii -v MIRc#SINE/MIR 136 TCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAGG-GTTG 184 chr1qtel1M 444480 AAGTGAAAACCAAA--AAATACATATAT---AAGGCATTTTTAAAATTTT 444524 vv ii i -- i - i --- i ii vv i v MIRc#SINE/MIR 185 TTGTGAGGATCAAATGAGATA-ATGTATGTGAAAGCGCTTTGTAAACTGT 233 chr1qtel1M 444525 AA 444526 MIRc#SINE/MIR 234 AA 235 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.20 CpG sites = 39, Kimura (unadjusted) = 45.37 Transitions / transversions = 2.05 (39/19) Gap_init rate = 0.06 (11 / 179), avg. gap size = 2.18 (24 / 11) 14 35.38 0.00 0.00 chr1qtel1M 444561 444621 (555379) (TAC)n#Simple_repeat 1 61 (0) m_b40s252i0 1386 chr1qtel1M 444561 TACTATGACTATAACTACTACTACTGCTGCTGCTGCTGCTGTTCCTCCTT 444610 iv iv i i i i i ii v v v (TAC)n#Simple 1 TACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTA 50 chr1qtel1M 444611 CTCCTCCTCCT 444621 v v v (TAC)n#Simple 51 CTACTACTACT 61 Matrix = Unknown Transitions / transversions = 1.12 (9/8) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 44 23.06 0.00 0.00 chr1qtel1M 444575 444675 (555325) (CTC)n#Simple_repeat 1 101 (0) m_b40s252i1 1386 chr1qtel1M 444575 CTACTACTACTGCTGCTGCTGCTGCTGTTCCTCCTTCTCCTCCTCCTCTT 444624 v v v v v v v v vi i i (CTC)n#Simple 1 CTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT 50 chr1qtel1M 444625 CCTCTTCCTCTTCTTCCTAATCCTCCTCCTCTTCCTCTTTCTCCTCCTCC 444674 i i i vv i i i (CTC)n#Simple 51 CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC 100 chr1qtel1M 444675 T 444675 (CTC)n#Simple 101 T 101 Matrix = Unknown Transitions / transversions = 0.82 (9/11) Gap_init rate = 0.00 (0 / 100), avg. gap size = 0.0 (0 / 0) 216 36.70 1.83 0.00 chr1qtel1M 448879 448987 (551013) C MIR3#SINE/MIR (15) 193 83 m_b40s601i1 1387 chr1qtel1M 448879 AGAAT-TCAGATCTCTTAGAGACTTTGGAGTTAAGTTGTTATTAAATCTT 448927 - v vvv i i i v v vi iv viv vvi i C MIR3#SINE/MIR 193 AGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCT 144 chr1qtel1M 448928 TACTTTGCAAATGAAGAAA-TGATGTCCAGGAAATTAGAATGACTTGCTT 448976 i i i i i - v i ii iv ii i ii C MIR3#SINE/MIR 143 CATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCC 94 chr1qtel1M 448977 ACAATTACACA 448987 vii i C MIR3#SINE/MIR 93 AAGGTCACACA 83 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 53.41 CpG sites = 25, Kimura (unadjusted) = 53.41 Transitions / transversions = 1.67 (25/15) Gap_init rate = 0.02 (2 / 108), avg. gap size = 1.00 (2 / 2) 208 30.86 12.59 2.55 chr1qtel1M 448899 449041 (550959) C MIRb#SINE/MIR (92) 176 20 m_b40s601i2 1387 chr1qtel1M 448899 ACTTTG-GAGTTAAGTTGTTATTAAATCTTTACTTTGCAAATGAAGAAA- 448946 ii - v i -i -- iii i i i i - C MIRb#SINE/MIR 176 ACCCTGCGAGGTAGGT-ATTATTA--TCCCCATTTTACAGATGAGGAAAC 130 chr1qtel1M 448947 TGATGTCCAG-GAAATTAGAATGACTTGCTTACAATTACACAATTTGGA- 448994 v ii - ii - i i ii vii i ii v v - C MIRb#SINE/MIR 129 TGAGGCTCAGAGAGGTTA-AGTAACTTGCCCAAGGTCACACAGCTAGTAA 81 chr1qtel1M 448995 ---GCAGATC----ATT-----CTGGGTT--TTTAAATCCAAAGCCAATC 449030 --- v ---- ----- ii i-- i i v vi v C MIRb#SINE/MIR 80 GTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTG 31 chr1qtel1M 449031 CACTTCTTACT 449041 v iii C MIRb#SINE/MIR 30 CTCTTTCCACT 20 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 42.04 CpG sites = 33, Kimura (unadjusted) = 43.45 Transitions / transversions = 3.30 (33/10) Gap_init rate = 0.08 (12 / 142), avg. gap size = 1.83 (22 / 12) 12 9.71 0.00 0.00 chr1qtel1M 455430 455451 (544549) (TTCT)n#Simple_repeat 1 22 (0) m_b40s252i2 1388 chr1qtel1M 455430 TTCTTTCTTTCTTTTTTTATTT 455451 i v (TTCT)n#Simpl 1 TTCTTTCTTTCTTTCTTTCTTT 22 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 561 28.88 8.85 0.41 chr1qtel1M 456066 456291 (543709) C MIRc#SINE/MIR (0) 268 24 m_b40s601i3 1389 chr1qtel1M 456066 AGTAACAACAATAGCTAGAATATACACAGCACTTTAAGGTTTGCACAGC- 456114 i i i i?v viv v ii i vi i v - C MIRc#SINE/MIR 268 AATAATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCG 219 chr1qtel1M 456115 TTTTAGCA-ATGTCATCTCGTTTTATCCTTCCAACCACC----AAAAAAG 456159 i vi - ii i i v iv v ----i iiv C MIRc#SINE/MIR 218 CTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAG 169 chr1qtel1M 456160 ATAGG--AGCTAATGTTACCCC----------ATGAGGAA-CTGAGGCAA 456196 ii -- v v i i ---------- - vv C MIRc#SINE/MIR 168 GCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC 119 chr1qtel1M 456197 GTAGAAATCAAATGACTTGCCCAGGGTCATACAGCTAGTATGTGTTCCAA 456246 iv ii i i i i v -v vi C MIRc#SINE/MIR 118 AGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTG-GCAGA 70 chr1qtel1M 456247 GCTAGT-TTTGAATTAAGGTCTCCCTGATTCCAGGCCAAGTTCTCT 456291 ii v-i i iiv i i i i v v C MIRc#SINE/MIR 69 GCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCT 24 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 36.62 CpG sites = 42, Kimura (unadjusted) = 38.22 Transitions / transversions = 1.83 (42/23) Gap_init rate = 0.04 (8 / 225), avg. gap size = 2.62 (21 / 8) 524 29.07 4.06 0.49 chr1qtel1M 456360 456556 (543444) MIRc#SINE/MIR 39 242 (26) m_b40s601i4 1390 chr1qtel1M 456360 GAGTCGGGAGGACCTGAGTTCAAATCTGGTCTCAGATTCTTACTAGTTAT 456409 i i i i i iv v v viv i i MIRc#SINE/MIR 39 GAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGT 88 chr1qtel1M 456410 GTAAAGCTCCACAAGTCATTTTGCCTCTGCCTGCCTCCGTTTCCTCATCT 456459 i vvi vvi i vi vivv v MIRc#SINE/MIR 89 GTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCT 138 chr1qtel1M 456460 ATGAAAAAGGGGAGACAATAACAGCCC-AC--ACCCC-CAGAGTTGTTGT 456505 i i vi ivi i v v -i -- i - i MIRc#SINE/MIR 139 GTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGT 188 chr1qtel1M 456506 GTGGATTAAAATAAGCTCATCT---TTAAAGCATCTTGTGCTATGTGAAG 456552 v i- i v v v --- v iii ivvv i MIRc#SINE/MIR 189 GAGGATC-AAATGAGATAATGTATGTGAAAGCGCTTTGTAAACTGTAAAG 237 chr1qtel1M 456553 -GCTA 456556 - MIRc#SINE/MIR 238 TGCTA 242 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 35.87 CpG sites = 31, Kimura (unadjusted) = 37.51 Transitions / transversions = 1.19 (31/26) Gap_init rate = 0.03 (6 / 196), avg. gap size = 1.50 (9 / 6) 322 17.91 1.49 0.00 chr1qtel1M 456934 457000 (543000) C MIR3#SINE/MIR (63) 145 78 m_b40s601i5 1391 chr1qtel1M 456934 CTCATTTTACAGGTGAGGGA-CCGAGGGCAAACAAAGCTAAGTGACTTGC 456982 i i - i v v ivi i iv C MIR3#SINE/MIR 145 CTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGC 96 chr1qtel1M 456983 CCAGGGTCACACAGCCAG 457000 i ? C MIR3#SINE/MIR 95 CCAAGGTCACACAGCNAG 78 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 21.28 CpG sites = 8, Kimura (unadjusted) = 21.28 Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.02 (1 / 66), avg. gap size = 1.00 (1 / 1) 19 31.74 1.20 1.20 chr1qtel1M 457202 457284 (542716) (AGAGAG)n#Simple_repeat 1 83 (0) m_b40s252i3 1392 chr1qtel1M 457202 AGAAAGAGCTA-AGATCGAGAGAGACAAAAGGACAGACAGAGGCAGAGAG 457250 i vv - vv v i ii v v iv (AGAGAG)n#Sim 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr1qtel1M 457251 AGACAGAGACAGAGACATTGACATGAGACAAAGA 457284 v v v vv v - v i (AGAGAG)n#Sim 51 AGAGAGAGAGAGAGAGAGAGAGA-GAGAGAGAGA 83 Matrix = Unknown Transitions / transversions = 0.40 (6/15) Gap_init rate = 0.02 (2 / 82), avg. gap size = 1.00 (2 / 2) 106 0.00 7.81 0.00 chr1qtel1M 459878 460005 (539995) (TTTCT)n#Simple_repeat 1 138 (0) c_b40s251i0 1393 chr1qtel1M 459878 TTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCT 459927 (TTTCT)n#Simp 1 TTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCT 50 chr1qtel1M 459928 TTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTC-TTTC-TTTC-TTTC- 459973 - - - - (TTTCT)n#Simp 51 TTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCT 100 chr1qtel1M 459974 TTTC-TTTC-TTTC-TTTC-TTTC-TTTC-TTTCTTTT 460005 - - - - - - (TTTCT)n#Simp 101 TTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTT 138 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.08 (10 / 127), avg. gap size = 1.00 (10 / 10) 193 35.90 3.12 5.48 chr1qtel1M 462154 462377 (537623) L2#LINE/L2 1266 1484 (1598) m_b40s601i6 1394 chr1qtel1M 462154 CAGGCTATTGATTGGAGTTGGATAAAATCATGGAAC--TGCCGACCGGAT 462201 i? vii vi vi i v v iiv -- i i vi L2#LINE/L2 1266 CGNGCAGCTGAACGTGGCTGGAGAAAAACACACAACCATGCTGACTGGTC 1315 chr1qtel1M 462202 CTATTATAAAATGGTGTCCTCCCTCTGATCTGAAGTGGACCTTCAGTGCA 462251 ii i v v vi ----v v ?i i v i i i i v L2#LINE/L2 1316 TCACTTTAAATTCATG----ACCACNAACCTCAAGTGGGCCCTTAATGCT 1361 chr1qtel1M 462252 ACCAACCAATTACCCTTCTCTTCCCTACAAGATTCCAAATCTCACACTGT 462301 i viv i?iv v vi vvvv -- v v v L2#LINE/L2 1362 GCCCGGCAATCNTACTACATTTCCCTAGTCCATTC--ACTCTCCCACTCT 1409 chr1qtel1M 462302 ACCTGA--GCTAGTCCAAA---TCTTCTTTTTCCTCAGGCTTCTCATGGT 462346 v iv --i v i v --- i i i ii i iv iivi L2#LINE/L2 1410 CCTAGACGACTATTTCACACCTTCTCCTCTCTCCTCAAACCTCCAACACC 1459 chr1qtel1M 462347 TTCTCATGCCTGCACCTGCACCCTCTCAGCT 462377 i --v -- i iv -- L2#LINE/L2 1460 TCCTC--CCCT--ATCCTCA--CTCTCAGCT 1484 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 48.53 CpG sites = 42, Kimura (unadjusted) = 51.41 Transitions / transversions = 1.24 (42/34) Gap_init rate = 0.07 (15 / 223), avg. gap size = 1.27 (19 / 15) 18 8.72 0.00 0.00 chr1qtel1M 464184 464208 (535792) (T)n#Simple_repeat 1 25 (0) m_b40s252i4 1395 chr1qtel1M 464184 TTTTTTTTTTCTTTTTCTTTTTTTT 464208 i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 183 22.22 4.44 0.00 chr1qtel1M 464664 464708 (535292) C L2d2_3end#LINE/L2 (81) 474 428 m_b40s601i7 1396 chr1qtel1M 464664 TATAAAAGTCAGTCCCCGCCCCCAAGAAGCTTACATCCT--TTGGGG 464708 i vvii i i i vi -- C L2d2_3end#LIN 474 TATAAGACATGGTCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGG 428 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 27.30 CpG sites = 7, Kimura (unadjusted) = 27.30 Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.02 (1 / 44), avg. gap size = 2.00 (2 / 1) 12 8.85 4.17 0.00 chr1qtel1M 465582 465605 (534395) (CTC)n#Simple_repeat 1 25 (0) m_b40s252i5 1397 chr1qtel1M 465582 CTCCT-CTCCTTCTCATCCTCCTCC 465605 - i v (CTC)n#Simple 1 CTCCTCCTCCTCCTCCTCCTCCTCC 25 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 18 0.00 4.55 0.00 chr1qtel1M 466137 466158 (533842) (GT)n#Simple_repeat 1 23 (0) m_b40s252i6 1398 chr1qtel1M 466137 GTGTGTGTGTGTGTGTGTG-GTG 466158 - (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTG 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.05 (1 / 21), avg. gap size = 1.00 (1 / 1) 15 5.56 0.00 0.00 chr1qtel1M 466515 466533 (533467) (A)n#Simple_repeat 1 19 (0) m_b40s252i7 1399 chr1qtel1M 466515 AAAAAAAAAAAAAGAAAAA 466533 i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAA 19 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 183 29.13 0.00 3.64 chr1qtel1M 466618 466674 (533326) L3#LINE/CR1 2754 2808 (1291) m_b40s601i8 1400 chr1qtel1M 466618 TAATCTTGCAACACTGATTCTGGGGAAAACTCTAGAATGGATCATTGAAG 466667 v -- iii i iv v i i i i v L3#LINE/CR1 2754 TAAGCTTG--ACGTCGATCCCCGGCAAAATTCTAGAACGGATTATTAAAC 2801 chr1qtel1M 466668 AAATAAT 466674 i ii L3#LINE/CR1 2802 AGATGGT 2808 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 30.39 CpG sites = 12, Kimura (unadjusted) = 39.50 Transitions / transversions = 3.00 (12/4) Gap_init rate = 0.04 (2 / 56), avg. gap size = 1.00 (2 / 2) 35 21.22 1.83 4.72 chr1qtel1M 466744 466852 (533148) (ATATGT)n#Simple_repeat 1 106 (0) m_b40s252i9 1401 chr1qtel1M 466744 ATATGTATGTGTATATGTGTGTGTATATGTATATATATA-G-AGAGAGAT 466791 i i i i - - v viv (ATATGT)n#Sim 1 ATATGTATATGTATATGTATATGTATATGTATATGTATATGTATATGTAT 50 chr1qtel1M 466792 ATGTGTGATGTGAGTGTGGATATGTGCAGATACATACATATGTATGTATG 466841 i - - - i v ii vi i ii -- (ATATGT)n#Sim 51 ATGTAT-ATGT-A-TATGTATATGTATATGTATATGTATATGTA--TATG 95 chr1qtel1M 466842 TATATGTATAT 466852 (ATATGT)n#Sim 96 TATATGTATAT 106 Matrix = Unknown Transitions / transversions = 2.60 (13/5) Gap_init rate = 0.06 (7 / 108), avg. gap size = 1.00 (7 / 7) 28 35.96 0.00 2.59 chr1qtel1M 466744 466862 (533138) (AT)n#Simple_repeat 1 116 (0) m_b40s252i8 1402 chr1qtel1M 466744 ATATGTATGTGTATATGTGTGTGTATATGTATATATATAGAGAGAGATAT 466793 i i i i i i i i v v v v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr1qtel1M 466794 GTGTGATGTGAGTGTGGATATGTGCAGATACATACATATGTATGTATGTA 466843 i i - i - - i iv i ii v i i i i i (AT)n#Simple_ 51 ATAT-ATAT-A-TATATATATATATATATATATATATATATATATATATA 97 chr1qtel1M 466844 TATGTATATAGAAATACAT 466862 i v v i (AT)n#Simple_ 98 TATATATATATATATATAT 116 Matrix = Unknown Transitions / transversions = 2.88 (23/8) Gap_init rate = 0.03 (3 / 118), avg. gap size = 1.00 (3 / 3) 13 29.85 2.53 3.85 chr1qtel1M 466902 466980 (533020) (AGAAA)n#Simple_repeat 1 78 (0) m_b40s252i10 1403 chr1qtel1M 466902 AGAAAAGGGGAGAAAAGAATA-AAGTAAAAAGTGCACAGCAGAAAAAAAA 466950 iii v - ivi viv v iv i (AGAAA)n#Simp 1 AGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAA 50 chr1qtel1M 466951 AGAATAATCTACAAG-GAAGCAAAGAAAAGA 466980 - --v v -i v (AGAAA)n#Simp 51 AGAA-AA--GAAAAGAAAAGAAAAGAAAAGA 78 Matrix = Unknown Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.06 (5 / 78), avg. gap size = 1.00 (5 / 5) 12 19.15 2.63 2.63 chr1qtel1M 467129 467166 (532834) (TTTTGTA)n#Simple_repeat 1 38 (0) m_b40s252i11 1404 chr1qtel1M 467129 TTTTTTATTTGCTTTTTTCTTATTTTGTATTTAGT-TTT 467166 v vv v -v v - (TTTTGTA)n#Si 1 TTTTGTATTTTGTATTTT-GTATTTTGTATTTTGTATTT 38 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 12 17.40 0.00 5.88 chr1qtel1M 468829 468864 (531136) (AGAAG)n#Simple_repeat 1 34 (0) m_b40s252i12 1405 chr1qtel1M 468829 AGAATGAGATTAGAAGAGAGAAAGAAGGGAAGTGAA 468864 - vv - i i v (AGAAG)n#Simp 1 AGAA-GAGAAGAGAAGAGA-AGAGAAGAGAAGAGAA 34 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 524 26.70 2.14 7.17 chr1qtel1M 473596 473829 (526171) C L1ME1_3end#LINE/L1 (271) 655 433 m_b40s551i0 1406 chr1qtel1M 473596 AGTATATAATGATCTCCTG-GTCCTGCTCATTTCACTCAGCATCAGTTCG 473644 i ? --- ii - iv iv - i v?v C L1ME1_3end#LI 655 AGTATGTANT---CTTTTGTGTCTGGCTTCTTTCACTCAGCAT-AATGNT 610 chr1qtel1M 473645 TGTAAGTCTC-TCCAGGCTTTTCTGAAATCGCGGACGTGACCGT-GTTGG 473692 v i vi - v i v -------- --i iv v - v C L1ME1_3end#LI 609 TTTGAGATTCATCCATGTTGTT--------GCG--TGTATCAGTAGTTCG 570 chr1qtel1M 473693 TCATTTCTTACTGAACAATAATATTCCATAATATTCATATACCACGATTT 473742 ivi i i vvv i i vi vv i C L1ME1_3end#LI 569 TTCCTTTTTATTGCTGAGTAGTATTCCATTGTATGGATATACCACAATTT 520 chr1qtel1M 473743 ATTCAGCCATTCTCCAACTGATGGACATCCA--TTCAGTTTCCAGTTTCT 473790 i i v v ?ii iii-- -- i C L1ME1_3end#LI 519 GTTTATCCATTCACCNGTTGATGGACATTTGGGTT--GTTTCCAGTTTTT 472 chr1qtel1M 473791 AGCCACTACAAAGAGGGCTGCCACAAACATTCGTGCACA 473829 i i i i v ii i ii i C L1ME1_3end#LI 471 GGCTATTACGAATAAAGCTGCTATGAACATTCGTGTACA 433 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 33.85 CpG sites = 37, Kimura (unadjusted) = 34.59 Transitions / transversions = 1.76 (37/21) Gap_init rate = 0.09 (20 / 233), avg. gap size = 1.05 (21 / 20) 310 27.90 4.83 8.05 chr1qtel1M 473609 473877 (526123) C L1MA10_3end#LINE/L1 (436) 645 385 m_b40s551i1 1406 chr1qtel1M 473609 CTCCTG-GTCCTGCTCATTTCACTCAGCATCAGTTCGTGTAAGTCTCTCC 473657 i - ? iv i i v vv v vi i iiv C L1MA10_3end#L 645 CTTCTGTGNCTGGCTTATTTCACTTAGCATAATGTCCTCCAGGTTCATCC 596 chr1qtel1M 473658 AGGCTTTTCTGAAATCGCGGACGTGACCGTGTTGGTCATTTCTTA---CT 473704 v - v vv v i ---- i---- vv iv i --- C L1MA10_3end#L 595 ATG-TTGTCGCAAATGGCAG----GAT----TTCCTTCTTTTTTAAGGCT 555 chr1qtel1M 473705 GAACAATAATATTCCATAATATTCATATACCACGATTTATTCAGCCATTC 473754 --- vi vi iv v i v C L1MA10_3end#L 554 GAA---TAATATTCCATTGTATGTATATACCACATTTTCTTTATCCATTC 508 chr1qtel1M 473755 -TCCAACTGATGGACATCCA--TTCAGTTTCCAGTTTCTAGCCACTACAA 473801 - iv - ii -- -- vv ii i i i iii C L1MA10_3end#L 507 ATCCGTC-GATGGACATTTAGGTT--GTTTCCATATCTTGGCTATTGTGA 461 chr1qtel1M 473802 AGAGGGCTGCCACAAACAT--TCGTGCACATACAGGTCCCTTT----CCC 473845 v iv v ii --vv v ---- i i----i C L1MA10_3end#L 460 ATAATGCTGCAATGAACATGGGAGTGCAGATA----TCTCTTCGAGATCC 415 chr1qtel1M 473846 TTCTTTATAATCTCTTTGGGATATAAGCCTAG 473877 vv -i - v vi i C L1MA10_3end#L 414 TGATTT-CAAT-TCTTTTGGATATATACCCAG 385 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 34.20 CpG sites = 36, Kimura (unadjusted) = 35.45 Transitions / transversions = 1.09 (36/33) Gap_init rate = 0.10 (27 / 268), avg. gap size = 1.26 (34 / 27) 466 23.68 4.40 4.40 chr1qtel1M 473710 473868 (526132) C L1ME4c_3end#LINE/L1 (275) 555 397 m_b40s551i2 1406 chr1qtel1M 473710 ATAATATTCCATAATATTCATATACCACGATTTATTCAGCCATTCTCCAA 473759 vivi ?v i ii i i i i v C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chr1qtel1M 473760 CTGATGGACATCCA--TTCAGTTTCCAGTTTCTAGCCACTACAAAGAGGG 473807 i v ii -- -- i i v i i i v iv C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTT--GTTTCCAATTTTTCGCTATTATAAATAACG 458 chr1qtel1M 473808 CTGCCACAAACA--TTCGTGCACATACAGGTCCCTTTCCCTTCTTT---A 473852 v ii -- -- i --- i i --- C L1ME4c_3end#L 457 CTGCAATGAACATCTTCGTG--CATATAG---CTTTTTCCTTCTTTTGAA 413 chr1qtel1M 473853 TAATCTCTTTGGGATA 473868 v i i i C L1ME4c_3end#L 412 TTATTTCCTTAGGATA 397 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 28.98 CpG sites = 26, Kimura (unadjusted) = 29.98 Transitions / transversions = 2.60 (26/10) Gap_init rate = 0.06 (10 / 158), avg. gap size = 1.40 (14 / 10) 344 27.67 0.81 5.98 chr1qtel1M 474295 474417 (525583) MIRc#SINE/MIR 11 127 (141) m_b40s601i9 1407 chr1qtel1M 474295 TGGTGGAGTGGATAGAGCACCAACCCTGAAGTCAGGAAGGCACGAGTTCA 474344 v v iiiv i i i vi i i MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr1qtel1M 474345 AATTTGGCCTAGACAAGTAACACTTCCTAGCTTTGTGATCCTGGG-AAAT 474393 i iiv v --- --- iv v v i i - i MIRc#SINE/MIR 61 AGTCCCGGCT---C---TGCCACTTACTAGCTGTGTGACCTTGGGCAAGT 104 chr1qtel1M 474394 CAAATAACTTCCCATTTACCTCAG 474417 vv i i - vvi MIRc#SINE/MIR 105 CACTTAACCTCTC-TGAGCCTCAG 127 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.94 CpG sites = 19, Kimura (unadjusted) = 35.30 Transitions / transversions = 1.46 (19/13) Gap_init rate = 0.07 (8 / 122), avg. gap size = 1.00 (8 / 8) 48 28.02 0.73 0.73 chr1qtel1M 474420 474556 (525444) (AAAT)n#Simple_repeat 1 137 (0) m_b40s252i13 1408 chr1qtel1M 474420 AAATAAATAGAT-GATAAATAGATGGATGGATGAGTAAATGAATGAACAA 474468 i -i i ii ii i i i i i (AAAT)n#Simpl 1 AAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAA 50 chr1qtel1M 474469 ATAAACAAACAAATCAATGAAGGAATGAATGAATAAATAAGTGAACAAAC 474518 i i v i vi i i i i i i (AAAT)n#Simpl 51 ATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAAT 100 chr1qtel1M 474519 AAATAACTAAACAAAACAAACAATTAAATAAGTAAATA 474556 v -v i i v i (AAAT)n#Simpl 101 AAATAAATAAA-TAAATAAATAAATAAATAAATAAATA 137 Matrix = Unknown Transitions / transversions = 5.00 (25/5) Gap_init rate = 0.01 (2 / 136), avg. gap size = 1.00 (2 / 2) 203 29.41 1.47 0.00 chr1qtel1M 474711 474778 (525222) MIRc#SINE/MIR 169 237 (31) m_b40s601i10 1407 chr1qtel1M 474711 CTACCTTCCAGCATCACTGTGAGGATCTCATGAGATCCTAGAAGTGAAAG 474760 iv vi iii vv vv iv v MIRc#SINE/MIR 169 CTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAG 218 chr1qtel1M 474761 -ATTTTGCCAACCTTAAAG 474778 -ii iv iv MIRc#SINE/MIR 219 CGCTTTGTAAACTGTAAAG 237 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 35.49 CpG sites = 10, Kimura (unadjusted) = 37.80 Transitions / transversions = 1.00 (10/10) Gap_init rate = 0.01 (1 / 67), avg. gap size = 1.00 (1 / 1) 181 31.43 4.29 0.00 chr1qtel1M 476329 476398 (523602) C L2d2_3end#LINE/L2 (7) 548 476 m_b40s601i11 1409 chr1qtel1M 476329 AAGTTAATAAACACTTCACAAGGGCCTAATTCATGTGAGTTACTGTCCTA 476378 i i i i i vvii v v vii ii vi v C L2d2_3end#LIN 548 AAATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTA 499 chr1qtel1M 476379 --CA-TATGGAGGATACAAAGAA 476398 -- i- i i C L2d2_3end#LIN 498 GGCGCTGTGGGGGATACAAAGAA 476 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 40.52 CpG sites = 15, Kimura (unadjusted) = 43.18 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.03 (2 / 69), avg. gap size = 1.50 (3 / 2) 626 28.98 2.65 4.03 chr1qtel1M 476999 477300 (522700) C L1ME4c_3end#LINE/L1 (191) 639 342 m_b40s551i3 1410 chr1qtel1M 476999 TTCTGCTCATTTCACTCAGCATCAGTTCATATAAGTCTTGCCAATCTTCT 477048 iv i i i vv v vi i - vvi v C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATAAACATTTT-CCATGTTGCT 591 chr1qtel1M 477049 CTGTATTCATCATCCTCCTGGTCATTTCTTATAGAACAATAATATTCCAT 477098 vii v v vv i---i i v i vvvv C L1ME4c_3end#L 590 ACATAGTCTTCATAATT---ATCATTTTTAATGGCTGCATAATATTCCAT 544 chr1qtel1M 477099 AACATTCATATACCACAATTTACTCAACCATTCTCCAATTGATGGGCATC 477148 vivi ?v i i i i v v i i C L1ME4c_3end#L 543 CGAGTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATT 494 chr1qtel1M 477149 CA--TTCATTTTCCAGCTTCTAGCCACTACAAACAGGGCTGCCACAAACA 477196 i -- v-- ii i v i i i i iv v ii C L1ME4c_3end#L 493 TAGGTTG--TTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACA 446 chr1qtel1M 477197 TTTTGGCACATACAGGTCCCTTTCCCTTCTTT---AGTCTCTCATTGGGG 477243 i v ii i --- i i --- v v i v i i C L1ME4c_3end#L 445 TCTTCGTGCATATAG---CTTTTTCCTTCTTTTGAATTATTTCCTTAGGA 399 chr1qtel1M 477244 TATAAGCCCAG---TGGAAACACTGCTGGATCAAAGGGTATGCACAGTTT 477290 v vv --- ---i i i v v C L1ME4c_3end#L 398 TAAATTCCCAGAAGTGGAA---TTACTGGGTCAAAGGGTATGAACATTTT 352 chr1qtel1M 477291 GATAACTTTT 477300 v ii i C L1ME4c_3end#L 351 TATGGCTCTT 342 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 37.02 CpG sites = 47, Kimura (unadjusted) = 37.59 Transitions / transversions = 1.27 (47/37) Gap_init rate = 0.05 (15 / 301), avg. gap size = 1.33 (20 / 15) 216 18.44 7.35 4.29 chr1qtel1M 477339 477406 (522594) L2d2_3end#LINE/L2 443 512 (43) m_b40s601i12 1411 chr1qtel1M 477339 AAGCTCTTTGAGGGCAGATAC--TGTCTAACTTACTTCATTTGTATATC- 477385 i iv -- v -- - vi - L2d2_3end#LIN 443 AAGCTCCTTGAGGGCAGGGACCATGTCTTA--TACTTC-TTTGTATCCCC 489 chr1qtel1M 477386 --AGGAGCTCAGCACAGTGCATT 477406 --vi v ii v L2d2_3end#LIN 490 CACAGCGCCTAGCACAGTGCCTT 512 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 21.31 CpG sites = 6, Kimura (unadjusted) = 21.31 Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.09 (6 / 67), avg. gap size = 1.33 (8 / 6) 36 37.52 1.73 2.62 chr1qtel1M 477982 478212 (521788) (AT)n#Simple_repeat 1 229 (0) m_b40s252i14 1412 chr1qtel1M 477982 ATATATACTATAAATATTTATGTATATATACAAGTTTACATATTTAAATA 478031 - v v i i vi v i v v (AT)n#Simple_ 1 ATATATA-TATATATATATATATATATATATATATATATATATATATATA 49 chr1qtel1M 478032 TACATATCGACTATATCCA-ATGTACACACATATATGCACAAATATGTAC 478080 i vv - vi - i i i i ii i v i i (AT)n#Simple_ 50 TATATATATA-TATATATATATATATATATATATATATATATATATATAT 98 chr1qtel1M 478081 ATACATGGAAAGAAATCATACGTAAAT-TCTACCT-TATACCCTCAGATA 478128 i iv v v v - ii v - v iv - -iv - v (AT)n#Simple_ 99 ATATATATATATATAT-ATATATATATATATATATATATA-TAT-ATATA 145 chr1qtel1M 478129 GCAT-TATATATGTTCGTGTTTATATGCATATACACACATTTATATAAAT 478177 -i - i vii i v ii i i i v v (AT)n#Simple_ 146 -TATATATATATATATATATATATATATATATATATATATATATATATAT 194 chr1qtel1M 478178 ATGCATATAGACATATGTGTAACTATATCTAAATA 478212 ii v i i i vv v v (AT)n#Simple_ 195 ATATATATATATATATATATATATATATATATATA 229 Matrix = Unknown Transitions / transversions = 1.29 (36/28) Gap_init rate = 0.04 (10 / 230), avg. gap size = 1.00 (10 / 10) 350 25.95 1.61 6.78 chr1qtel1M 479487 479610 (520390) MIRc#SINE/MIR 10 127 (141) m_b40s601i13 1413 chr1qtel1M 479487 GTGGTGGAGTGGATAGAACACCAACCCTGAAGTCAGGAGGACACGAGTTC 479536 v v i iiiv i i i vi i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr1qtel1M 479537 AAATCTGATCTAGACAAGTAACACTTCCTAGCTTTGTGACCCTGGG-AAA 479585 i i iviv --- --- iv v v i - i MIRc#SINE/MIR 60 GAGTCCCGGCT---C---TGCCACTTACTAGCTGTGTGACCTTGGGCAAG 103 chr1qtel1M 479586 TCAAATAACTTC-CCAATTGCCTCAG 479610 vv i - ii -- MIRc#SINE/MIR 104 TCACTTAACCTCTCTGA--GCCTCAG 127 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 30.09 CpG sites = 19, Kimura (unadjusted) = 32.70 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.08 (10 / 123), avg. gap size = 1.00 (10 / 10) 35 4.59 2.22 0.00 chr1qtel1M 479619 479663 (520337) (ATAG)n#Simple_repeat 1 46 (0) c_b40s251i1 1414 chr1qtel1M 479619 ATAGAT-GATAGATAGATAGATAGAAAGATGGATAGATAGATAGAT 479663 - v i (ATAG)n#Simpl 1 ATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGAT 46 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 34 22.06 2.27 0.00 chr1qtel1M 479664 479745 (520255) (AATG)n#Simple_repeat 7 89 (1) m_b40s252i15 1415 chr1qtel1M 479664 GAGTGAATGAATGAACAAATAAAGAAATAAATGAATGAACGAATGAATGA 479713 i ii i vi i i (AATG)n#Simpl 7 GAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGA 56 chr1qtel1M 479714 ATAAATCAATGAACAAACAAATAAAT-AATTAA 479745 i v ii ii i - v (AATG)n#Simpl 57 ATGAATGAATGAATGAATGAATGAATGAATGAA 89 Matrix = Unknown Transitions / transversions = 4.33 (13/3) Gap_init rate = 0.01 (1 / 81), avg. gap size = 1.00 (1 / 1) 50 22.20 0.00 0.00 chr1qtel1M 479669 479776 (520224) (AATA)n#Simple_repeat 1 108 (0) m_b40s252i16 1415 chr1qtel1M 479669 AATGAATGAACAAATAAAGAAATAAATGAATGAACGAATGAATGAATAAA 479718 i i i v i i ii i i (AATA)n#Simpl 1 AATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAA 50 chr1qtel1M 479719 TCAATGAACAAACAAATAAATAATTAAACAAACAAATAAACAATTAAATA 479768 v i i i v i i i v (AATA)n#Simpl 51 TAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATA 100 chr1qtel1M 479769 AGTAAATA 479776 i (AATA)n#Simpl 101 AATAAATA 108 Matrix = Unknown Transitions / transversions = 4.00 (16/4) Gap_init rate = 0.00 (0 / 107), avg. gap size = 0.0 (0 / 0) 206 27.94 1.47 0.00 chr1qtel1M 479931 479998 (520002) MIRc#SINE/MIR 169 237 (31) m_b40s601i14 1413 chr1qtel1M 479931 CTACCTTCCAGGGTCAAGGTGAGGATCTCATGAGATCCTAGAAGTGAAAG 479980 iv iivv vv vv iv v MIRc#SINE/MIR 169 CTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAG 218 chr1qtel1M 479981 -ATTTTGCCAACCTTAAAG 479998 -ii iv iv MIRc#SINE/MIR 219 CGCTTTGTAAACTGTAAAG 237 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 32.92 CpG sites = 8, Kimura (unadjusted) = 35.07 Transitions / transversions = 0.73 (8/11) Gap_init rate = 0.01 (1 / 67), avg. gap size = 1.00 (1 / 1) 339 22.34 5.26 1.01 chr1qtel1M 481597 481691 (518309) MIRb#SINE/MIR 1 99 (169) m_b41s601i0 1416 chr1qtel1M 481597 CAAAGCAGCAGAGTGGTCCTGTGGATATAGCACTGGCTGTGGAGTC---C 481643 i vi v v v v v v v --- MIRb#SINE/MIR 1 CAGAGGGGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGAC 50 chr1qtel1M 481644 ATACATTGGGCTCTAAACCTGTCTCTGATACTTA--ATCTGTGTGACATT 481691 v -i i v v i v vi -- v v MIRb#SINE/MIR 51 AGAC-CTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTT 99 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 25.21 CpG sites = 6, Kimura (unadjusted) = 26.54 Transitions / transversions = 0.40 (6/15) Gap_init rate = 0.03 (3 / 94), avg. gap size = 2.00 (6 / 3) 201 37.47 7.02 1.67 chr1qtel1M 482160 482330 (517670) L2c_3end#LINE/L2 283 462 (16) m_b41s601i1 1417 chr1qtel1M 482160 TGC-CCCTTAATGCTGCTGCCT-TCCTTCCATTATTTCCAATTTATCCTG 482207 - v iii i- i - v i vv -- i v v L2c_3end#LINE 283 TGCTCCCATAGCACC-CTGTCTATACTCCCATTATAGC--ACTTATCATT 329 chr1qtel1M 482208 AA--TGTAGAGAATTTGTTCAGTTGCTTGCACGTTCTCTTAATCAAACAG 482255 -- vv v v iiiv i ? ivi iii iv ii i v L2c_3end#LINE 330 AACTTGTATTGTAATTGTCTGTTTACNTGTCTGTCTCCTCCACTAGACTG 379 chr1qtel1M 482256 TCAACAACTCAAACACAG---CCACTTTTTGGCTTTCTCCGCATCTCCAG 482302 v i vv ii ivi --- iiv i iviiv ii i i L2c_3end#LINE 380 TGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTATCCCCAG 429 chr1qtel1M 482303 TGCTTAG-----AATAGGTACTGAATAAATGTT 482330 i i i ----- i ii v L2c_3end#LINE 430 CGCCTGGCACATAGTAGGCGCTCAATAAATGTT 462 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 52.13 CpG sites = 41, Kimura (unadjusted) = 56.39 Transitions / transversions = 1.86 (41/22) Gap_init rate = 0.05 (8 / 170), avg. gap size = 1.88 (15 / 8) 13 20.91 3.77 3.77 chr1qtel1M 483814 483866 (516134) (ATTATTT)n#Simple_repeat 1 53 (0) m_b41s252i0 1418 chr1qtel1M 483814 ATTATTTATTATCTCCATTATTTAATATTT-CTCCATAAT-TTTATAAAT 483861 - -i v -i viv v - v v (ATTATTT)n#Si 1 ATTATTTATTAT-T-TATTATTTATTATTTATTATTTATTATTTATTATT 48 chr1qtel1M 483862 TATTA 483866 (ATTATTT)n#Si 49 TATTA 53 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.08 (4 / 52), avg. gap size = 1.00 (4 / 4) 13 15.86 0.00 0.00 chr1qtel1M 483971 483998 (516002) (AAAGA)n#Simple_repeat 1 28 (0) m_b41s252i1 1419 chr1qtel1M 483971 AATGAAAAGATAAGAAAAGCAAAAAAAA 483998 v v v i (AAAGA)n#Simp 1 AAAGAAAAGAAAAGAAAAGAAAAGAAAA 28 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 230 25.00 6.67 0.00 chr1qtel1M 485554 485613 (514387) C L2b_3end#LINE/L2 (6) 460 397 m_b41s601i2 1420 chr1qtel1M 485554 TCAATCAACCAACATT----AGATACCTACTAAGTGCCAGGCCCTGTGCT 485599 v v i ----iiiii iv ? C L2b_3end#LINE 460 TCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCT 411 chr1qtel1M 485600 ACCTTCTAGGGATA 485613 vviv i C L2b_3end#LINE 410 AGGCGCTGGGGATA 397 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 26.64 CpG sites = 9, Kimura (unadjusted) = 31.79 Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.02 (1 / 59), avg. gap size = 4.00 (4 / 1) 27 0.00 0.00 0.00 chr1qtel1M 485972 485997 (514003) (TAGA)n#Simple_repeat 1 26 (0) c_b41s251i0 1421 chr1qtel1M 485972 TAGATAGATAGATAGATAGATAGATA 485997 (TAGA)n#Simpl 1 TAGATAGATAGATAGATAGATAGATA 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 472 37.51 4.52 2.00 chr1qtel1M 486296 486782 (513218) MamRTE1#LINE/RTE-BovB 828 1326 (2486) m_b41s601i3 1422 chr1qtel1M 486296 CCCAAAGGAATGAATGGGGGGCTCGTGATAATGTGATTGCCTCTTGGGGA 486345 i v ? i ivv v vi ivv ii vi i ? viiiv MamRTE1#LINE/ 828 CCCAGAGGCATNAGTGACCGTCTGATGACCCTACGCCTACNTCTGAAACA 877 chr1qtel1M 486346 AAACC-CCATCCCACCATCATCAAGGTCTGTGCTCCCACTATGACTGAC- 486393 v - i? v i iv iv i i i vi i- MamRTE1#LINE/ 878 AAAGCGCTNTGCCACCGTCATCAGCGCATATGCCCCCACCATGACGAATA 927 chr1qtel1M 486394 CCCATGAGGCCAAAGAAAAACGGTACAAAGATCTGAAGATCCTCATCCTT 486443 v vv i ivv i i v vv viv MamRTE1#LINE/ 928 CCGATGAGGAGAAAGAAAGATTCTACAAGGATCTGGACAGACTCATCGCA 977 chr1qtel1M 486444 GATGTGCCCAAGA--GAACCAGCTTGTAATTCTGGGTGACTTTAATGCTA 486491 vv i- v --vi v vi vi ivi v i i i vv MamRTE1#LINE/ 978 GCGGTA-CCAACATCTGACAAGCTGATCGTCACGGGAGATTTCAACGCAC 1026 chr1qtel1M 486492 GTGTGGGCTGGGACTACC-AGACATGGCAGGGGTTCCTGGGA-GGGATGG 486539 v v v - i - i i viiiiiv v v -v?v i MamRTE1#LINE/ 1027 GTGTCGGCAGCGA-TGCCGAAACGTGGAGAAAAGTCATCGGACCNCACGG 1075 chr1qtel1M 486540 AGCTGGAAA---CAGCAGCCACATGGGTGGTTACT----AGTGAAGACTT 486582 iii ---? i --v vivii v ---- i ---- MamRTE1#LINE/ 1076 GATTGGAAAGCTNAACAGC--AATGGTCTACTCCTGCTCAGCGAA----T 1119 chr1qtel1M 486583 GTGCACCTCATGACCTTCTCCTCTCCAACAGGGTATCCCATTTACCTAAA 486632 vvvv v v iv vv v vvi v i iii v v MamRTE1#LINE/ 1120 GTGCCAAGCATCAGCTCGTAATCACCAACACCATCTTCCGCCTACCGAAT 1169 chr1qtel1M 486633 AGCATTAAGACATGCTGGACACACCCTTGCAGCAAACACTGACATTTAAT 486682 iv vv vv ii vv vvvi i v i i v MamRTE1#LINE/ 1170 AAGAGAAAGACATCATGGATGCACCCAAGGTCTAAGCAGTGGCATCTCAT 1219 chr1qtel1M 486683 AGACTGTGTGATTGGTAAAGAAAAGA----GACAGATG--TGGATGCAAT 486726 v i i i v i v vi v ivi i---- vi -- i -i v MamRTE1#LINE/ 1220 TGATTATATCATCGTTCGACAGCGGGACCTGAAGGATGTTTAGAT-TACT 1268 chr1qtel1M 486727 GAAAGCAATGTGTGGTGCAGAG---TGGACTGATCTCTACAAGATCAGAT 486773 -v v i i v --- i i viii vv vv v MamRTE1#LINE/ 1269 G-CAGCTATGCGTGGCGCCGAGTGCTGGACCGACCATCGCCTGATACGCT 1317 chr1qtel1M 486774 TCGAACCCT 486782 i i i MamRTE1#LINE/ 1318 CCAAACTCT 1326 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 46.80 CpG sites = 86, Kimura (unadjusted) = 53.74 Transitions / transversions = 0.92 (86/93) Gap_init rate = 0.04 (20 / 486), avg. gap size = 1.60 (32 / 20) 275 22.27 0.00 4.76 chr1qtel1M 486771 486836 (513164) C MIRc#SINE/MIR (204) 64 2 m_b41s601i4 1423 chr1qtel1M 486771 GATTCGAACCCTAGTCCTTCTGATTTCAGGGCCAGAACTCTATGCACTGC 486820 i vi i i i i i v vi v v C MIRc#SINE/MIR 64 GACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGC 15 chr1qtel1M 486821 ACCATCTCACTGCCCC 486836 --- i C MIRc#SINE/MIR 14 ACCA---CACTGCCTC 2 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.03 CpG sites = 9, Kimura (unadjusted) = 27.03 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.05 (3 / 65), avg. gap size = 1.00 (3 / 3) 304 30.86 8.00 1.50 chr1qtel1M 487136 487260 (512740) C Charlie4#DNA/hAT-Charlie (3243) 135 3 m_b41s502i0 1424 chr1qtel1M 487136 TAAAAGAAATGCTAAAATTGCCA--TAGATGTCAGGGAAAATAAAAGTGC 487183 i i v -- -- v i v ii i C Charlie4#DNA/ 135 TGAAGGAAATGCTAAATTT--CAGTTAGAGGTTAGTGAAAATAAAGATGT 88 chr1qtel1M 487184 CAATTTCCTTCATC---ATCCCTGGTCACCCTA-----TATCCACAGATT 487225 v v iiii ---i i vi v v i----- i ii C Charlie4#DNA/ 87 AATTTTTTCCCATCCAAGTTCACGGACCCCCTGAATTCTATCCACGGACC 38 chr1qtel1M 487226 CCTGAGGGAATTATAGACTTCAGGTTAATCACCTC 487260 vi iviii i ii vv i C Charlie4#DNA/ 37 CCTTGGGGGTCCGTGGACCCCAGGTTAAGAACCCC 3 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.63 CpG sites = 26, Kimura (unadjusted) = 42.16 Transitions / transversions = 2.17 (26/12) Gap_init rate = 0.04 (5 / 124), avg. gap size = 2.40 (12 / 5) 203 13.89 2.78 0.00 chr1qtel1M 487296 487331 (512669) MIR#SINE/MIR 87 123 (139) m_b41s601i5 1425 chr1qtel1M 487296 GACCTTGGGCAAGTCACTTAACCCCAAT-TGCCTTAG 487331 i i vv - i MIR#SINE/MIR 87 GACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAG 123 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 15.51 CpG sites = 3, Kimura (unadjusted) = 15.51 Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) 20 0.00 0.00 0.00 chr1qtel1M 487334 487355 (512645) (A)n#Simple_repeat 1 22 (0) m_b41s252i2 1426 chr1qtel1M 487334 AAAAAAAAAAAAAAAAAAAAAA 487355 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAA 22 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 236 33.63 8.70 0.90 chr1qtel1M 487752 487958 (512042) L1PB_orf2#LINE/L1 1403 1625 (1669) m_b41s551i0 1427 chr1qtel1M 487752 AAAAAACTTTAGGATCAAATGCATTTACAAGTGAGTTGCGATAAATATTG 487801 v ii i i i v i iv? i viivi i i v L1PB_orf2#LIN 1403 AAAAAAGTCCAGGACCAGACGGATTCACAGCNGAATTCTACCAGACATTC 1452 chr1qtel1M 487802 AAAGAATAATT----TCAATATCA-----AATA----ACCAGTTAGCAAA 487838 v ----i vii ----- v ---- v v vi L1PB_orf2#LIN 1453 AAAGAAGAATTGGTACCAATCCTATTGACACTATTCCACAAGATAGAGAA 1502 chr1qtel1M 487839 AATCAGAGAGACCCTACTAGATTA--CGATAAA---AATATGATTTTTGT 487883 i-- i iv iiv i i -- v i --- i v iii vi L1PB_orf2#LIN 1503 AG--AGGGAATCCTCCCTAAATCATTCTATGAAGCCAGTATCACCCTAAT 1550 chr1qtel1M 487884 ACCTAAAATGGGGAGAAATGAAGCAGAGAAAGAAAAGTATAGACCAATAT 487933 v vii i iii iiv i ?i i v i L1PB_orf2#LIN 1551 ACCAAAACCAGGAAAGGACATAACNAAAAAAGAAAACTACAGACCAATAT 1600 chr1qtel1M 487934 CCTTTATGAACATTGACACAATAAT 487958 i v v ii ? v L1PB_orf2#LIN 1601 CCCTGATGAACATAGATGCNAAAAT 1625 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 47.32 CpG sites = 45, Kimura (unadjusted) = 48.33 Transitions / transversions = 1.88 (45/24) Gap_init rate = 0.03 (7 / 206), avg. gap size = 2.86 (20 / 7) 246 29.45 0.00 3.92 chr1qtel1M 487870 487975 (512025) L1P1_orf2#LINE/L1 1537 1638 (1656) m_b41s551i2 1427 chr1qtel1M 487870 AATATGATTTTTGTACCTAAAATGGGGAGAAATGAAGCAGAGAAAGAAAA 487919 ii v ii vi v ivi? v i iiv i vi i i L1P1_orf2#LIN 1537 AGCATCATCCTGATACCAAAGCCNGGCAGAGACACAACCAAAAAAGAGAA 1586 chr1qtel1M 487920 GTATAGACCAATATCCTTTATGAACATTGACACAATAATAGCTTTTAATA 487969 v v v ii v ---ii i L1P1_orf2#LIN 1587 TTTTAGACCAATATCCTTGATGAACATTGATGCAAAAAT---CCTCAATA 1633 chr1qtel1M 487970 ACAATA 487975 - L1P1_orf2#LIN 1634 A-AATA 1638 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.34 CpG sites = 19, Kimura (unadjusted) = 39.34 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.04 (4 / 105), avg. gap size = 1.00 (4 / 4) 259 31.46 0.00 0.00 chr1qtel1M 487870 487958 (512042) L1PREC2_orf2#LINE/L1 1537 1625 (1669) m_b41s551i1 1427 chr1qtel1M 487870 AATATGATTTTTGTACCTAAAATGGGGAGAAATGAAGCAGAGAAAGAAAA 487919 ii v ii vi v viv v i iiv i i i L1PREC2_orf2# 1537 AGCATCATCCTGATACCAAAACCTGGCAGAGACACAACAAAAAAAGAAAA 1586 chr1qtel1M 487920 GTATAGACCAATATCCTTTATGAACATTGACACAATAAT 487958 v vi i v i ii v L1PREC2_orf2# 1587 CTTCAGGCCAATATCCTTGATGAACATCGATGCAAAAAT 1625 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.32 CpG sites = 17, Kimura (unadjusted) = 42.32 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.00 (0 / 88), avg. gap size = 0.0 (0 / 0) 267 19.77 0.00 6.06 chr1qtel1M 487907 487976 (512024) L1MD_orf2#LINE/L1 1574 1639 (1655) m_b41s551i3 1427 chr1qtel1M 487907 CAGAGAAAGAAAAGTATAGACCAATATCCTTTATGAACATTGACACAATA 487956 i i v i i i v i v L1MD_orf2#LIN 1574 CAAAAAAAGAAAACTACAGACCAATATCCCTCATGAACATAGACGCAAAA 1623 chr1qtel1M 487957 ATAGCTTTTAATAACAATAT 487976 ---ii i i - L1MD_orf2#LIN 1624 AT---CCTCAACAA-AATAT 1639 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 21.76 CpG sites = 10, Kimura (unadjusted) = 23.81 Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.06 (4 / 69), avg. gap size = 1.00 (4 / 4) 260 32.87 10.56 3.65 chr1qtel1M 489324 489503 (510497) MIR3#SINE/MIR 1 192 (16) m_b41s601i6 1428 chr1qtel1M 489324 CTAGTATAGTGG-------GAAAAAG-ACAAATTTGGAATTAGGC--TCT 489363 i i v ------- i i - ii i v i i v--i MIR3#SINE/MIR 1 CTGGCAGAGTGGCTGAGCAGAGAGAGCACGGACTGGGAGTCAGGAGACCT 50 chr1qtel1M 489364 AGGTTCAAATTCCAGATCAGCGACAAGCTAGTTTTGTTACTTCATGTTTC 489413 i v i i i v v v v i ? i v v i -- vviv MIR3#SINE/MIR 51 GGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCT--TGGGCA 98 chr1qtel1M 489414 TGTC-TTTAACCTCTCTCTGCTCCAGTTTCATC--CAGTAAGGTAAGAAG 489460 v -i v vv ii v -- v ii i ii MIR3#SINE/MIR 99 AGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGG 148 chr1qtel1M 489461 CAGATGGCTTAG------TTCAAAGTCAAGTTCAGCTTCTATGACCTTC 489503 -- v vi ------ ii i vvv i i--- v MIR3#SINE/MIR 149 --GTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTC---TGACATTC 192 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 42.90 CpG sites = 32, Kimura (unadjusted) = 45.02 Transitions / transversions = 1.28 (32/25) Gap_init rate = 0.07 (13 / 179), avg. gap size = 2.00 (26 / 13) 336 29.19 7.41 3.57 chr1qtel1M 489325 489459 (510541) MIR#SINE/MIR 7 146 (116) m_b41s601i7 1428 chr1qtel1M 489325 TAGTATAGTGGGAAAAAG-ACAAATT-TGGAATTAGGCT--CTAGGTTCA 489370 i vv i - iiii - iii i -- i i MIR#SINE/MIR 7 TAGCATAGTGGTTAAGAGCACGGGCTCTGGAGCCAGACTGCCTGGGTTCG 56 chr1qtel1M 489371 AATTCCAGATCAGCGACAAGCTAGTTTTGTTACTT----CATGTTTCTGT 489416 i i v v v vvi i v v i ---- v v -- MIR#SINE/MIR 57 AATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACT-- 104 chr1qtel1M 489417 CTTTAACCTCTCTCTGCTCCAGTTTCATC--CAGTAAGGTAAGAA 489459 --- v ii v -- v ii ii i MIR#SINE/MIR 105 ---TAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGA 146 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.64 CpG sites = 24, Kimura (unadjusted) = 38.47 Transitions / transversions = 1.71 (24/14) Gap_init rate = 0.07 (10 / 134), avg. gap size = 1.50 (15 / 10) 31 12.26 0.00 0.00 chr1qtel1M 493781 493826 (506174) (T)n#Simple_repeat 1 46 (0) m_b41s252i3 1429 chr1qtel1M 493781 TTTTTTTTTCCTTTCTTTTTTTCTTTTCTTTTTTTTTTTTTTTTTT 493826 ii i i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 46 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 23 3.71 0.00 0.00 chr1qtel1M 494266 494293 (505707) (GT)n#Simple_repeat 1 28 (0) m_b41s252i4 1430 chr1qtel1M 494266 GTGTGTGTGTGTGTGTGTGTGTGTATGT 494293 i (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGT 28 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 17 12.68 0.00 0.00 chr1qtel1M 494475 494500 (505500) (G)n#Simple_repeat 1 26 (0) m_b41s252i5 1431 chr1qtel1M 494475 GGTGGGGGGGGGGGGGGGGAGGAGGG 494500 v i i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGG 26 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 27 0.00 2.63 5.41 chr1qtel1M 494594 494631 (505369) (TTTG)n#Simple_repeat 1 37 (0) c_b41s251i1 1432 chr1qtel1M 494594 TTTGTTTGTTTGTTTGTTTGTTTTGTTTTGTTT-TTTGT 494631 - - - (TTTG)n#Simpl 1 TTTGTTTGTTTGTTTGTTTG-TTTG-TTTGTTTGTTTGT 37 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.08 (3 / 37), avg. gap size = 1.00 (3 / 3) 23 7.03 0.00 0.00 chr1qtel1M 495097 495126 (504874) (A)n#Simple_repeat 1 30 (0) m_b41s252i6 1433 chr1qtel1M 495097 AAAAAAACAAAACAAAAAAAAAAAAAAAAA 495126 v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 30 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 19 22.11 1.79 1.79 chr1qtel1M 496897 496952 (503048) (TCCTT)n#Simple_repeat 1 56 (0) m_b41s252i7 1434 chr1qtel1M 496897 TCCTCCCCTTTCCTTTCTTCTCCCTTTCCCTT-CTTACTTACCCCTTCCT 496945 ii i - i i - v i vi i (TCCTT)n#Simp 1 TCCTTTCCTTTCCTTTCCT-TTCCTTTCCTTTCCTTTCCTTTCCTTTCCT 49 chr1qtel1M 496946 TTCCTTT 496952 (TCCTT)n#Simp 50 TTCCTTT 56 Matrix = Unknown Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.04 (2 / 55), avg. gap size = 1.00 (2 / 2) 185 28.24 10.09 2.56 chr1qtel1M 497541 497649 (502351) C L2d2_3end#LINE/L2 (52) 503 387 m_b41s601i8 1435 chr1qtel1M 497541 TGCTAAACACTA---GAGATACAAAGAGGTAAGAGA---GCCCCCTGCTC 497584 ii i i--- i i vi --- vi i C L2d2_3end#LIN 503 TGCTAGGCGCTGTGGGGGATACAAAGAAGTATAAGACATGGTCCCTGCCC 454 chr1qtel1M 497585 TCAAAG-GCT---GATCTAAAGAGAGGGACAAGGTACAAAACAGACTAAG 497630 i - ---i ivvi i i ii i- viiv - C L2d2_3end#LIN 453 TCAAGGAGCTTACAATCTAGTTGGGGAGACAAGACAT-AAACACGTGAA- 406 chr1qtel1M 497631 GAAGCTAAA-AACAGGATAA 497649 - i - iv i C L2d2_3end#LIN 405 -AAGTTAAATAACAATACAA 387 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.91 CpG sites = 23, Kimura (unadjusted) = 38.20 Transitions / transversions = 3.29 (23/7) Gap_init rate = 0.07 (8 / 108), avg. gap size = 1.75 (14 / 8) 624 33.63 12.46 5.27 chr1qtel1M 497998 498832 (501168) C L2#LINE/L2 (219) 2863 1972 m_b41s601i9 1435 chr1qtel1M 497998 ATTAGAGGTCAGTGAAGTTTATTGAATCGGGAGGTAATGTGGTCAAGCCT 498047 vi i i v i vv v iiv i ii i ii i vii i C L2#LINE/L2 2863 ATGGGAAGCCATTGGAGGGTTTTGAGCAGAGGAGTGACATGATCTGACTT 2814 chr1qtel1M 498048 ATACTTTCAGAAAATCACTTTAGTGACTGAATGGAGGATGGACTAGA--- 498094 iii v i ii i i ivi vi v i i i? --- C L2#LINE/L2 2813 ACGTTTTAAAAGGATCACTCTGGCTGCTGTGTTGAGAATAGACTGNAGGG 2764 chr1qtel1M 498095 ----AAAAGTAGAGGCAGGCGGACCCCTCCCCACCCCTACCCTCCAGCAG 498140 ---- ii i i vi vv --------- ------i vi C L2#LINE/L2 2763 GGGCAAGGGTGGAAGCAGGGAGACCAGT---------TA------GGAGG 2729 chr1qtel1M 498141 CTATTCCAATAGTCCAGGCATGAGATATAATGA-GTCTTGGAGAAGAAGA 498189 v i i -- v i i- v vv i- v C L2#LINE/L2 2728 CTATTGCAGTAATCCAGGC--GAGAGATGATGGTGGCTTGGACCAGG-GT 2682 chr1qtel1M 498190 AGTT-TATTCAAAATGCTAA-AAGTGA---AATT--GGAGATATTGTAAA 498232 i v-i v vi ii v i - i---i -- v v i C L2#LINE/L2 2681 GGTGGCAGTGGAGGTGGTGAGAAGTGGTCGGATTCTGGATATATTTTGAA 2632 chr1qtel1M 498233 GATTGACATGTCTTGGTAACAATTTGTATATGGTGGCAGCAGTGGCCAGG 498282 i v --- i -- ii i-i i--- i ---- v viiv C L2#LINE/L2 2631 GGTAGA---GCC--GACAG-GATTTGC---TGATGG----ATTGGATGTG 2595 chr1qtel1M 498283 GGGAAGGAGGAGGAAAATGAGTGGGAAATCCTAGATGACTCTTGGGTTGG 498332 viv - i i ----- i i i vvi ivi vv C L2#LINE/L2 2594 GGGTGTGAG-AGAAAGA-----GAGGAGTCAAGGATGACTCCAAGGTTTT 2551 chr1qtel1M 498333 GAGCCTAAGGGCTTAGGAGGATGG-GATGTTCCCTACAGTAATAGGGAAG 498381 vi i vivi i i - v iivii? v vi i C L2#LINE/L2 2550 TGGCCTGAGCAACTGGAAGGATGGAGTTGCCATTNACTGAGATGGGGAAG 2501 chr1qtel1M 498382 ---GTAGGAGGGGGAAATCTTTAAGGGGAAAGATAA-------------- 498414 --- ii i v ii -- i i v -------------- C L2#LINE/L2 2500 ACTGCGGGAGGAGCAGGT--TTGAGGGGGAAGATCAGGAGTTCAGTTTTG 2453 chr1qtel1M 498415 -------TGAGTTTAAAATGCCTATTGGATGTCCAGTTGGAAATCTGGGG 498457 ------- i i i i ii iv i v v i C L2#LINE/L2 2452 GACATGTTAAGTTTGAGATGCCTATTAGACATCCAAGTGGAGATGTCGAG 2403 chr1qtel1M 498458 TGGAAAGTAGG------------------CAG---AGAGATT-GGGCAGG 498485 i iv v ------------------ --- i i- v C L2#LINE/L2 2402 TAGGCAGTTGGATATACGAGTCTGGAGTTCAGGGGAGAGGTCCGGGCTGG 2353 chr1qtel1M 498486 A-AGAGAGATTTGAAAATCGCCAGCACAGAGATAGAAAGTGATGAATCCA 498534 - v v i ii i ii i v i v -- v- i v C L2#LINE/L2 2352 AGATATAAATTTGGGAGTCATCAGCATATAGATGGTA--TT-TAAAGCCA 2306 chr1qtel1M 498535 TGGGAGCTGATGAAATCTC-----------ATGTGAATAGAGGGAAAAGG 498573 i viv i v -----------i ii iii i i C L2#LINE/L2 2305 TGAGACTGGATGAGATCACCNAGGGAGTGAGTGTAGATAGAGAAGAGAAG 2256 chr1qtel1M 498574 AGGCCCA-GGATGGAGCACTGAGGGACATGTACAGTTAGGAGGT------ 498616 i - iv v i v - vi vv ?i ------ C L2#LINE/L2 2255 AGGTCCAAGGACTGAGCCCTGGGGCAC-TCCAACGTTNAGAGGTCGGGGA 2207 chr1qtel1M 498617 GAT---------CCAGAAGAGGATATTAAGAAA---CCGCTGATGGAAGG 498654 --------- v i v i i i--- v iii iiivi C L2#LINE/L2 2206 GATGAGGAGGAACCAGCAAAGGAGACTGAGAAGGAGCGGCCAGTGAGGTA 2157 chr1qtel1M 498655 GGAAGAAAACCCAAGGAGTGT-----CCCCAAAACT---TAAAGAAAAGA 498696 i viii ----- ivi i i--- i ivi C L2#LINE/L2 2156 GGAGGAAAACCAGGAGAGTGTGGTGTCCTGGAAGCCAAGTGAAGAAAGTG 2107 chr1qtel1M 498697 TTATCATGGAAGAAGAAAGTGAGCACTAGTATCCAGGGCTGT--AGAGGA 498744 - -i i ii v viv i v iv i-- ? v C L2#LINE/L2 2106 TT-TCA-AGAAGGAGGGAGTGATCAACTGTGTCAAATGCTGCTGANAGGT 2059 chr1qtel1M 498745 CAAGGAGAATCGGGATTGAGGGAAAGACCCTTGGATTTGGCCAC-TGACA 498793 v ii vi i i- vv v i v - i- C L2#LINE/L2 2058 CAAGTAAGATGAGGACTGAGA-ATTGACCATTGGATTTAGCAACGTGG-A 2011 chr1qtel1M 498794 GATCACTGGTAATTGTGGAGAGAGTATTTCGGGTAGAAT 498832 i i i iiv ivi i v iv i i C L2#LINE/L2 2010 GGTCATTGGTGACCTTGACAAGAGCAGTTTCGGTGGAGT 1972 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 47.36 CpG sites = 175, Kimura (unadjusted) = 47.94 Transitions / transversions = 1.92 (175/91) Gap_init rate = 0.08 (70 / 834), avg. gap size = 2.16 (151 / 70) 16 0.00 0.00 0.00 chr1qtel1M 498874 498890 (501110) (T)n#Simple_repeat 1 17 (0) m_b41s252i8 1436 chr1qtel1M 498874 TTTTTTTTTTTTTTTTT 498890 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTT 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 395 31.19 2.75 0.00 chr1qtel1M 499803 499911 (500089) C MIRc#SINE/MIR (151) 117 6 m_b41s601i10 1437 chr1qtel1M 499803 GACAGATTAAGTGACTTGCCTGAGATCAAATGGCTATT--TTGTCTGGGG 499850 v i ii i v ii v --v v v i v C MIRc#SINE/MIR 117 GAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGC 68 chr1qtel1M 499851 CAGGGTTCAAATTCAA-TTTTCCTAACTTCAAGTCCAGCAATCTATTCAC 499899 i ii i ii i- i i i iiv v i C MIRc#SINE/MIR 67 CGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCAC 18 chr1qtel1M 499900 TATCCCAAATTG 499911 iiv v i C MIRc#SINE/MIR 17 TGCACCACACTG 6 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.29 CpG sites = 23, Kimura (unadjusted) = 42.64 Transitions / transversions = 2.09 (23/11) Gap_init rate = 0.02 (2 / 108), avg. gap size = 1.50 (3 / 2) 24 9.39 0.00 0.00 chr1qtel1M 500051 500084 (499916) (T)n#Simple_repeat 1 34 (0) m_b41s252i9 1438 chr1qtel1M 500051 TTATTTCTTTTTTTTTTTTTTTTTTTTTTTATTT 500084 v i v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 34 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 1626 26.52 3.61 4.10 chr1qtel1M 500546 501182 (498818) C L1ME5_3end#LINE/L1 (304) 637 4 m_b41s551i4 1439 chr1qtel1M 500546 TCCTGCTCATTTCACTCAGCATCA-GTTCGTGTAAG-TCTCTCCAGGC-- 500591 i i iv ii - -- v - iv v i-- C L1ME5_3end#LI 637 TCTTACTTTTTTCACTCAGCACTATGTT--TTTAAGATCCATCCATGTTG 590 chr1qtel1M 500592 CTTTCTGAAATCATCCTGTTGGTCATTTCTTACAGA-ACAGTAATATTCC 500640 v v v -- iv iv iii v v v-i - i i C L1ME5_3end#LI 589 CTATGTGTA--CATCTAGTCCGTTGCTTCTAACTGCTGCA-TAGTACTCC 543 chr1qtel1M 500641 ATAATTTTCATATACCACAATTTATTCAGCCATTCTCCAACTGATGGACA 500690 ii v v vi v iii v i v v C L1ME5_3end#LI 542 ATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCAGTGATGGACA 493 chr1qtel1M 500691 TCCA--TTCAGTTTCCAGTTTCTAGCCACTACAAAAAGGGCTGCCACAAA 500738 i -- -- ii ii i iv i v iv v ii C L1ME5_3end#LI 492 CCCAGGTT--GCCTCCAACTCCCCGCCACCACAAACAACGCTGCAATGAA 445 chr1qtel1M 500739 CATTCGTGCACATACAGGTCCCTTTC----CCTTCTTTATAATCTCTTTG 500784 i vi i ---- i v---- viv v v i C L1ME5_3end#LI 444 CATCCTCGTACAT----GTCCCCTTATGGACCTGTGTGAGAATTTCTTTG 399 chr1qtel1M 500785 GGATATAATCCCAGTAGTAACACTGCTGGATCAAAGGGTATGCACAGTTT 500834 vv v iiiv i i v --- -- C L1ME5_3end#LI 398 GGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATGC---GT-- 354 chr1qtel1M 500835 GATAACTT--TTTGAGCA--TAGTTCCAAACTACTCTCCAAAATGGTTGG 500880 - - -- vi -- v v i i i i i v C L1ME5_3end#LI 353 -ATA-CTTAATTTGACTAAGTACTGCCAGATTGCTCTCCAGAATGGCTGC 306 chr1qtel1M 500881 ATTCGTTCACAACTCCACCAACAATGAATCAATGTCCCAGTTTTCCCACA 500930 iiv ii vii i i v v iv i vi ? i C L1ME5_3end#LI 305 ACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATNTCCCCACA 256 chr1qtel1M 500931 TCCCCTCCAACAATCATCATTATTT---TTTCCTGTCATCTTAGCCAATC 500977 i v v iiv ii--- --- v i v i C L1ME5_3end#LI 255 TCCTCGCCAACACTTGGCATTATCCAGCTTTC---TAATTTTTGCCAGTC 209 chr1qtel1M 500978 TGACAGGTGTGTAGTGGTATCTTAGAGTTGTCTTAATTTGCATTTCTCTG 501027 i i iv i i vv i C L1ME5_3end#LI 208 TAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATTTCTCTG 159 chr1qtel1M 501028 ATTAATAATGACTTGGAGCATCTTTTCATATGACTAGAAATAG--TTTCA 501075 v v v i - v v-- -- i C L1ME5_3end#LI 158 ATTACTAATGAGTTTGAGCATCTCTTCATATG-CTTGT--TAGCCTTTCG 112 chr1qtel1M 501076 A-TTTCTTCATCTGAGAATTGTCTGTTCATATCCTTTGACCATTTTTCAA 501124 i- i v vi i v v C L1ME5_3end#LI 111 GGTTTCCTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCCATTTTTCTA 62 chr1qtel1M 501125 TTGGAG--AATGGCTTGATTTTTTATAAATTAGAGTTAATTCTCTATATA 501172 i --?vi v -- i i vi v vivv i ii i C L1ME5_3end#LI 61 TTGGGGTTNCCGTCTT--TTTCTTGTTGATTTGCAGGAGTTCCTTGTATA 14 chr1qtel1M 501173 TTTTGGAAAT 501182 i i v C L1ME5_3end#LI 13 TTCTAGATAT 4 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 32.52 CpG sites = 93, Kimura (unadjusted) = 33.55 Transitions / transversions = 1.35 (93/69) Gap_init rate = 0.06 (38 / 636), avg. gap size = 1.29 (49 / 38) 1694 25.76 1.45 2.76 chr1qtel1M 500632 501182 (498818) C L1ME3G_3end#LINE/L1 (377) 547 4 m_b41s551i5 1439 chr1qtel1M 500632 TAATATTCCATAATTTTCATATACCACAATTTATTCAGCCATTCTCCAAC 500681 i i v vv i i i i v i C L1ME3G_3end#L 547 TAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTAT 498 chr1qtel1M 500682 TGATGGACATCCA--TTCAGTTTCCAGTTTCTAGCCACTACAAAAAGGGC 500729 ii -- -- i i v i i v iv C L1ME3G_3end#L 497 TGATGGACATTTAGGTT--GTTTCCAATTTTTCGCTATTACAAACAATGC 450 chr1qtel1M 500730 TGCCACAAACATTCGTGCACATACAGGTCCCTTTCC-CTTCTTT-ATAAT 500777 v ii i v i i ?-- i v v - v v vi- vv C L1ME3G_3end#L 449 TGCAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTAT 402 chr1qtel1M 500778 CTCTTTGGGATATAATCCCAGTAGTAACACTGCTGGATCAAAGGGTATGC 500827 i ? i v v? ? v iiv i i C L1ME3G_3end#L 401 TTCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGC 352 chr1qtel1M 500828 ACAGTTTGATAACTTTTTGAGCATAGTTCCAAACTACTCTCCAAAATGGT 500877 i v i -- i vvv - v v i i i ? i C L1ME3G_3end#L 351 GCATTTTAA--ATTTTAATAG-ATACTGCCAAATTGCCCTCCAAAANGGC 305 chr1qtel1M 500878 TGGATTCGTTCACAACTCCACCAACAATGAATCAATGTCCCAGTTTTCCC 500927 v iivi i vii i i v v iv v v i C L1ME3G_3end#L 304 TGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCC 255 chr1qtel1M 500928 ACATCCCCTCCAACAATCATCATTATT----TTTTCCTGTCATCTTAGCC 500973 i i v v ?ivi i---- vv---- i v C L1ME3G_3end#L 254 ACACCCTCGCCAACACTNGATATTATCAANCTTTTAA----ATTTTTGCC 209 chr1qtel1M 500974 AATCTGACAGGTGTGTAGTGGTATCTTAGAGTTGTCTTAATTTGCATTTC 501023 ii viv i i vv i C L1ME3G_3end#L 208 AATCTGATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTC 159 chr1qtel1M 501024 TCTGATTAATAATGACTTGGAGCATCTTTTCATATGACTAGAAATAGTTT 501073 i v i vv v vi vviiivi C L1ME3G_3end#L 158 CCTGATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTT 109 chr1qtel1M 501074 CAATTTCTTCATCTGAGAATTGTCTGTTCATATCCTTTGACCATTTTTCA 501123 vv i v v i v v C L1ME3G_3end#L 108 GTATTTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCT 59 chr1qtel1M 501124 ATTGGAGAATGGCTTGATTTTTTATAAATTAGAGTTAATTCTCTATATAT 501173 iv-- v -- i vi v vivv i i C L1ME3G_3end#L 58 ATTGGGT--TGTCTT--TTTCTTATTGATTTGTAGGAGTTCTTTATATAT 13 chr1qtel1M 501174 TTTGGAAAT 501182 i v C L1ME3G_3end#L 12 TCTGGATAT 4 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 31.83 CpG sites = 72, Kimura (unadjusted) = 32.39 Transitions / transversions = 1.09 (72/66) Gap_init rate = 0.03 (19 / 550), avg. gap size = 1.21 (23 / 19) 1284 28.81 4.83 3.89 chr1qtel1M 501036 502028 (497972) C L1M5_orf2#LINE/L1 (0) 3294 2293 m_b41s551i6 1439 chr1qtel1M 501036 TGACTTGGAGCATCTTTTCATATGACTAGAAATAGTTTCAATTTCTTCAT 501085 ?v v i vi vviiivi v? v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr1qtel1M 501086 CTGAGAATTGTCTGTTCATATCCTTTGACCATTTTTCAATTGGAGAATGG 501135 i v v vi i v ?v ---i v C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGG---GTTG 3198 chr1qtel1M 501136 CTTGATTTTTTATAAATTAGAGTT-----AATTCTCTATATATTTTGGAA 501180 i vi ? -v - ? ----- i i i v C L1M5_orf2#LIN 3197 TTTGTCTTTTTNT-TATT-GANTTGTAGGAGTTCTTTATATATTCTGGAT 3150 chr1qtel1M 501181 ATGAGGCCTTTATCAGA-ACCTTTGACTGTAAAAATATTTTCCCAGTTTA 501229 i v i - iv v -?i i v v i ? i i C L1M5_orf2#LIN 3149 ACGAGTCCTTTGTCAGATATATGT-NTTGCAAATATTTTCTCCCANTCTG 3101 chr1qtel1M 501230 TTGCTT-CCTTCTAATCTTGTCTGCATTAGTTTTGTTTGTACA--AAAAC 501276 v - i v i v ---i vii v iv v?v -- i v C L1M5_orf2#LIN 3100 TGGCTTGCCTTTTCATTTTCT---TAACGGTGTCTTTTGANGAGCAGAAG 3054 chr1qtel1M 501277 TTTTCAGTTTAGGTATAATCGA-------AATTTTCTATTTTGTGATCAG 501319 i i v i i? i v ------- i v i i --- C L1M5_orf2#LIN 3053 TTTTTAATTTTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGGT--- 3007 chr1qtel1M 501320 TAATGATCTCTA-GTTCTGCTTTGGTCATAAAACCTTCCCT-TCCACAGG 501367 ?i v i i i- i i vi ---- v i v -? vv C L1M5_orf2#LIN 3006 TNGTGCTTTTTGTGTCCTGTTTAAG----AAATCTTTGCCTANCCCAAGG 2961 chr1qtel1M 501368 TCTGAGAGGTAAACTATCCTATGTTCCTTT----AATTTATTAATAATTT 501413 vvii i -- i v iii ---- v - - i C L1M5_orf2#LIN 2960 TCACGAAGAT--ATTCTCCTATGTTTTCTTCTAGAAGTT-TT-ATAGTTT 2915 chr1qtel1M 501414 CATTCTTTATGCCTAGGTC-ATGAACCCATTTTGACCTTATCTTGGTGTA 501462 i ?ii iiii - - i i ? vi v i v C L1M5_orf2#LIN 2914 TANCTTTTACATTTAGGTCTATG-ATCCATCTNGAATTAATTTTTGTGTA 2866 chr1qtel1M 501463 CAGCGTTAAGTATGGATCAATGCCTAGTTTCTGCCATATTAGTTTCCAAT 501512 ii i v i v i i v?iii v i v vii v C L1M5_orf2#LIN 2865 TGGTGTGAGGTAGGGGTCGAGNTTCATTTTTTTCCATATGGATATCCAAT 2816 chr1qtel1M 501513 T-TTCCAGCAAT-TTTATCAAACAG--TAAGTTCTTATCCCAAAAGCTGG 501558 - vi- i ii v -- -- i vi ---- i C L1M5_orf2#LIN 2815 TGTTCCAGCACCATTTGTTGAAAAGACTA--TCCTTTCCCCA----CTGA 2772 chr1qtel1M 501559 GAT-CTTTGG---GTTTGTCAAAGACTAGGTTGCTATATTTGT-TGACTG 501603 iv - ? ---v i ii i? v? i v - --- C L1M5_orf2#LIN 2771 ATTGCNTTGGCACCTTTGTCAAAAATCAANTGNCCATATATGTGTG---G 2725 chr1qtel1M 501604 TTTTATCCCTTGAAC---CTAATCTATTCCACTGATCTACTAATCTATTC 501650 v i ii - i --- v i i i vi - C L1M5_orf2#LIN 2724 GTCTATTTC-TGGACTCTCTATTCTGTTCCATTGATCTATTTGTCTA-TC 2677 chr1qtel1M 501651 CTTA-GCCAATACCAAATAGTTTTGGTAACTGCTGCTCTATAGTATAGTT 501699 - v iv i i v iv i i - i C L1M5_orf2#LIN 2676 CTTACGCCAATACCACACTGTCTTGATTACTGTAGCTTTATAATA-AGTC 2628 chr1qtel1M 501700 TT-AGATCTGGTACAGCTAAG-CCACCATCATTTGATTTTTTTTTTTTAT 501747 - ? ? vv - - v v - - i i i v C L1M5_orf2#LIN 2627 TTGANATCNGGTAGTG-TAAGTCCTCCAAC-TTTG-TTCTTCTTTTTCAA 2581 chr1qtel1M 501748 TAATTCCTTGAA-ATTCTTGACCTTTTGT-TTTCCATATGAACTTTGTTG 501795 v v vii iv- ? ii i i- i i ivvi C L1M5_orf2#LIN 2580 GATTGTTTTGGCTATTCTNGGTCCTTTGCATTTCCATATAAATTTTAGAA 2531 chr1qtel1M 501796 TTATTTTTTCTAGGTCATTAAAATAGTTTTTTGGGAGTCTGATTGGTATA 501845 i vi v v vv vvi v iii vi v i v v C L1M5_orf2#LIN 2530 TCAGCTTGTCAATTTCTACAAAAAAACCTGCTGGGATTTTGATTGGGATT 2481 chr1qtel1M 501846 GCGCTAAATAAATAG-----TTTAGGTAATATTGTCATCTTTATTATATT 501890 ii i vv ----- i v iv v ? iv C L1M5_orf2#LIN 2480 GCATTGAATCTATAGATCAATTTGGGGAGAATTGACATCTTNACAATATT 2431 chr1qtel1M 501891 TGCTCGCCCTATCCAAGAGCATTTAATATTTTTCCAATTGGTTAGATCAG 501940 viv vi v v i vvv i i v iv i vv C L1M5_orf2#LIN 2430 GAGTCTTCCAATCCATGAACATGGTATATCTCTCCATTTATTTAGGTCTT 2381 chr1qtel1M 501941 ACTTAATTTGTGTGAAAAGTGGTCTGTAATTTTGCTCATAAAGTTTCTG- 501989 vi v v v iv i v i i vvvii ? v ii - C L1M5_orf2#LIN 2380 CTTTAATTTCTCTCAGCAATGTTTTGTAGTTTTCAGTGTANAGGTCTTGC 2331 chr1qtel1M 501990 --ATTTTCCCTTGGCAGATAGATTCCTAAATATTTTATATT 502028 -- ? --- vi vv i ? i C L1M5_orf2#LIN 2330 ACATNTT---TTGTTAGATTTATTCCTAAGTATTTNATGTT 2293 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.68 CpG sites = 152, Kimura (unadjusted) = 38.41 Transitions / transversions = 1.24 (152/123) Gap_init rate = 0.06 (63 / 992), avg. gap size = 1.38 (87 / 63) 346 26.77 25.25 0.00 chr1qtel1M 502467 502664 (497336) MIRc#SINE/MIR 3 250 (18) m_b41s601i11 1440 chr1qtel1M 502467 AGATAG-GTGGTGCAGGGAATACAATTATGAACCTGGAGGCAGAAA---T 502512 ii - v i v v iivv i i v i ---i MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chr1qtel1M 502513 TAAGTTTGAATCCCACCT----CATTTAC------TGTAACCTTGGA-AA 502551 ii i i iv ---- i ------ i i- MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 102 chr1qtel1M 502552 GTTGCTTAGTCTC----AGCCATAGTTCTCTCACTTTTCAAAC----ATA 502593 ii ii ---- vi ii ii v v i---- MIRc#SINE/MIR 103 GTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATA 152 chr1qtel1M 502594 ATTATAAC------ACCTATGTAACAAGGCTAC-----GGA-------AG 502625 v v ------i iv v i i ii----- ------- MIRc#SINE/MIR 153 ATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAG 202 chr1qtel1M 502626 -TA----ATATGAAA---TTTTGTAACCT-TAAAGCACTATATAAATG 502664 - ---- i ---i v - ii i MIRc#SINE/MIR 203 ATAATGTATGTGAAAGCGCTTTGTAAACTGTAAAGTGCTATACAAATG 250 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.22 CpG sites = 38, Kimura (unadjusted) = 34.88 Transitions / transversions = 2.53 (38/15) Gap_init rate = 0.07 (14 / 197), avg. gap size = 3.57 (50 / 14) 212 20.51 0.00 0.00 chr1qtel1M 503675 503713 (496287) L3#LINE/CR1 3752 3790 (309) m_b41s601i12 1441 chr1qtel1M 503675 AGAAGAGCCATAATAGCGATCTTCAAGCATCTGAAGGGC 503713 i v i vi ii i L3#LINE/CR1 3752 AGAGGAGACATGATAGCTGTCTTCAAATATTTGAAGGGC 3790 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 24.94 CpG sites = 6, Kimura (unadjusted) = 24.94 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 236 25.34 4.17 1.35 chr1qtel1M 503722 503793 (496207) L3#LINE/CR1 3832 3905 (194) m_b41s601i13 1441 chr1qtel1M 503722 AGAGAAGAGGATCTAGCAACAACAGGTAGAAGTTTCAGAGAG--AAATTT 503769 iiv i - v v ii i v i -- i L3#LINE/CR1 3832 AGAGGGCAGAA-CTAGGACCAATGGGTGGAAGTTACAGGGAGGCAGATTT 3880 chr1qtel1M 503770 -GGCTTGATGTCAGGAAAAACTTCC 503793 - ii i v i i L3#LINE/CR1 3881 CGGCTCAATATAAGGAAGAACTTTC 3905 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.49 CpG sites = 13, Kimura (unadjusted) = 32.49 Transitions / transversions = 2.60 (13/5) Gap_init rate = 0.04 (3 / 71), avg. gap size = 1.33 (4 / 3) 511 32.84 11.29 4.39 chr1qtel1M 506610 506972 (493028) C L3#LINE/CR1 (766) 3333 2947 m_b41s601i14 1442 chr1qtel1M 506610 CTATTAGATCTCTCCTCATAAGATTTGGACCAGGGCTTCCACCTGTCAAG 506659 i i i vi ii vi v i v vv i i vi i C L3#LINE/CR1 3333 CTGTTAAATTTCATCTTGTTGGTTTCGGCCCATCGTTCCAGCCTGTCGAG 3284 chr1qtel1M 506660 GTCTTTCTGGATGTTGATTCATTCATTCCATGAGTTAATCCATACCACCC 506709 i ? i i v vv i v?i vi ------i i i C L3#LINE/CR1 3283 ATCNTTTTGAATCTTGATTCTGTCATCCANCGTATTA------GCTATCC 3240 chr1qtel1M 506710 CTCCCTCTAAGCTTTGGGTCCTATGTACATTTCTCTTGAAGGCTTCTTAG 506759 ---- v v v i v vvivv v v i ii v C L3#LINE/CR1 3239 CTCCC----AGCTTTGTGTCATCTGCAAATTTGATAAGCATGCCTTCTAT 3194 chr1qtel1M 506760 GCCTTGATCCACATCACTAAGGAAAAAAGCTTTCAATAAAACA---CTAA 506806 i v vi i --- v iiv v i ii --- i C L3#LINE/CR1 3193 GTCTTCATCCAAGTCATT---GATAAAAATGTTGAACAGGACAGGGCCAA 3147 chr1qtel1M 506807 ACCTAACAGATCCCAAGGGCATTCCGCCAAGAGTCTCCCTGTAAGCTAAC 506856 i---i v viv iv i i iiiii vi i i i C L3#LINE/CR1 3146 G---GACAGAGCCCTGTGGCACGCCACTAGAGACCTCCCTCCAGGTTGAC 3100 chr1qtel1M 506857 A----------GATCA---------------AGTCATTC-ACCAGTTCCA 506880 ----------i --------------- i - i v i C L3#LINE/CR1 3099 ATCGATCCATTAATCAACACCTTTTGGGTATAGTCGTTCAACCAGCTACG 3050 chr1qtel1M 506881 AA-CCACCCAACTGAACTATTATCAAA--TACATTTCTCCACCTCATTCA 506927 - i v i v i--i i i ii i C L3#LINE/CR1 3049 AATCCACCTAACTGTACTATCATCCAGCCCATATTTCTCCATCTTGTCCA 3000 chr1qtel1M 506928 GCAAG-----CGT--GAGACTCC-TCAAACATTGTACTAAAGTTTAAA-G 506968 - ----- i -- ii- iiiiv i i i ii i -i C L3#LINE/CR1 2999 -CAAGGATATCATGAGAGACTTTGTCAAATGCCTTGCTGAAATCCAGATA 2951 chr1qtel1M 506969 CACT 506972 C L3#LINE/CR1 2950 CACT 2947 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 43.16 CpG sites = 77, Kimura (unadjusted) = 46.57 Transitions / transversions = 2.08 (77/37) Gap_init rate = 0.07 (27 / 362), avg. gap size = 2.15 (58 / 27) 262 23.08 0.00 0.00 chr1qtel1M 507181 507232 (492768) L2a_3end#LINE/L2 452 503 (14) m_b41s601i15 1443 chr1qtel1M 507181 CCCATTACCAAGCACAGTGCCTGGCACATAGTACATCCTTGATAAATGTT 507230 vii v v viiv ii i L2a_3end#LINE 452 CCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGGCGCTCAATAAATATT 501 chr1qtel1M 507231 TG 507232 L2a_3end#LINE 502 TG 503 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 22.63 CpG sites = 7, Kimura (unadjusted) = 28.08 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 32 3.23 0.00 0.00 chr1qtel1M 507415 507446 (492554) (TG)n#Simple_repeat 1 32 (0) c_b41s251i2 1444 chr1qtel1M 507415 TGTGTGTGTGTGTGTGTGTATGTGTGTGTGTG 507446 i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 32 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 31 0.00 0.00 0.00 chr1qtel1M 507464 507490 (492510) (AT)n#Simple_repeat 1 27 (0) c_b41s251i3 1445 chr1qtel1M 507464 ATATATATATATATATATATATATATA 507490 (AT)n#Simple_ 1 ATATATATATATATATATATATATATA 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 18 4.13 4.00 0.00 chr1qtel1M 510061 510085 (489915) (AT)n#Simple_repeat 1 26 (0) m_b41s252i10 1446 chr1qtel1M 510061 ATATTTAT-TATATATATATATATAT 510085 v - (AT)n#Simple_ 1 ATATATATATATATATATATATATAT 26 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 51 2.00 0.00 0.00 chr1qtel1M 510189 510239 (489761) (T)n#Simple_repeat 1 51 (0) c_b41s251i4 1447 chr1qtel1M 510189 TTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 510238 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr1qtel1M 510239 T 510239 (T)n#Simple_r 51 T 51 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 329 32.37 2.16 0.00 chr1qtel1M 510337 510475 (489525) L1ME2z_3end#LINE/L1 424 565 (626) m_b41s551i7 1448 chr1qtel1M 510337 AAAATGGCTGTTGCAAAAAT-TTC-TAGCAGCTCT-TTTGTAGTGACAAA 510383 v i vv i i - - i - ii i ii v L1ME2z_3end#L 424 AAAAAGACTTGTACAAGAATGTTCATAGCAGCTTTATTCATAATAGCCAA 473 chr1qtel1M 510384 GAACTGGAAATTGAGTGGATGCCCATCAGTTGGGGAATGACTGAATAAGT 510433 i iv vvii i i iiv i iv i i ii L1ME2z_3end#L 474 AAACTGGAAACAGCCCAGGTGTCCATCAACAGGAGAATGGATAAACAAAC 523 chr1qtel1M 510434 TGTGGTATGTGAATGTAATAAAATATTTTTCTTCTATAAAAA 510475 i vv ii ii i vi vv v L1ME2z_3end#L 524 TGTGGTATATTCATACAATGGAATACTACTCAGCAATAAAAA 565 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 44.86 CpG sites = 30, Kimura (unadjusted) = 44.86 Transitions / transversions = 2.00 (30/15) Gap_init rate = 0.02 (3 / 138), avg. gap size = 1.00 (3 / 3) 17 0.00 0.00 0.00 chr1qtel1M 511747 511765 (488235) (A)n#Simple_repeat 1 19 (0) m_b41s252i11 1449 chr1qtel1M 511747 AAAAAAAAAAAAAAAAAAA 511765 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAA 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 259 31.10 7.34 2.63 chr1qtel1M 511766 511874 (488126) C MIR3#SINE/MIR (78) 130 17 m_b41s601i16 1450 chr1qtel1M 511766 AAAAAACTAAGGCT--AAGAAGTGATTTAATGACTTGCTCAAAGTCACTC 511813 ii i i--i i --- i i i v C MIR3#SINE/MIR 130 AGGAAACTGAGGCCCAGAGAGGTGA---AGTGACTTGCCCAAGGTCACAC 84 chr1qtel1M 511814 AACA--T--GTATCAAAGCTAGGCATAAAAACAAGGCTTATT--CTACTA 511857 i ?-- -- iv i ii vv i v v ii vi -- v i C MIR3#SINE/MIR 83 AGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGTCTCCTGACTCCCA 34 chr1qtel1M 511858 CATTGTACTGTCTCTGC 511874 vvii i v C MIR3#SINE/MIR 33 GTCCGTGCTCTCTCTGC 17 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.31 CpG sites = 22, Kimura (unadjusted) = 42.97 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.06 (7 / 108), avg. gap size = 1.57 (11 / 7) 411 26.89 5.00 0.80 chr1qtel1M 512499 512618 (487382) C MIR3#SINE/MIR (31) 177 53 m_b41s601i17 1451 chr1qtel1M 512499 AAGAAACCT--AAGCTCATCTAGTCTAACAC--TCATTTTACAGATGAGG 512544 ii --i v i v -- C MIR3#SINE/MIR 177 AAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGG 128 chr1qtel1M 512545 AAACTAAGACCAAGACAGGTTAAACGACCTA--TGATTTCATACAATTAA 512592 i i v v v ii i i--ii vv i ii? i C MIR3#SINE/MIR 127 AAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGCNAG 78 chr1qtel1M 512593 TTTGCAATAGATGTGGGACTCAAAAC 512618 v iiii vvi - i C MIR3#SINE/MIR 77 TTAGTGGCAGAGCCGGGACT-AGAAC 53 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.85 CpG sites = 22, Kimura (unadjusted) = 35.23 Transitions / transversions = 2.20 (22/10) Gap_init rate = 0.03 (4 / 119), avg. gap size = 1.75 (7 / 4) 342 32.31 11.54 0.00 chr1qtel1M 512527 512656 (487344) C MIRc#SINE/MIR (120) 148 4 m_b41s601i18 1451 chr1qtel1M 512527 CTCATTTTACAGATGAGGAAACTAAGACCAAGACAGGTTAAACGACCTA- 512575 i i i iv v ii i i- C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr1qtel1M 512576 -TGATTTCATACAATTAATTTGCAATAGATGTGGGACTCAAAACTA---- 512620 -ii vv i ii i vv iiii vvi i v i ---- C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTC 49 chr1qtel1M 512621 TTCC--------AATTCGGGGCTCATTTCAC-ATCCTATTCTGCC 512656 -------- i i i v v i -iiv i iv C MIRc#SINE/MIR 48 TTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTGCC 4 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 42.12 CpG sites = 29, Kimura (unadjusted) = 45.08 Transitions / transversions = 2.23 (29/13) Gap_init rate = 0.03 (4 / 129), avg. gap size = 3.75 (15 / 4) 263 32.24 14.07 4.19 chr1qtel1M 512768 513094 (486906) C L2c_3end#LINE/L2 (6) 472 115 m_b41s601i20 1452 chr1qtel1M 512768 TCAGTCAACAAGCACTTATTAAGTAC--ATTGTGTGCGAAGTGGAATGCT 512815 v i i i ii -- i i v i i vviv vv C L2c_3end#LINE 472 TCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGA 423 chr1qtel1M 512816 TAGCACTGGTGAAACATAAGGCAAAAATAATCTCTGCTTTAGAGGAGCCC 512865 - vv i --- i ----iii i ii vi i C L2c_3end#LINE 422 TA-CAAAGATGAA---TAAGACA----CGGTCCCTGCCCTCAAGGAGCTC 381 chr1qtel1M 512866 ACAGCCTTGTGG-GGAAA-AACCAT-------GACAACT-CTGTACAA-- 512903 i v - i - iv ?------- i - vi -- C L2c_3end#LINE 380 ACAGTCTAGTGGAGGAGACAGACANGTAAACAGACAATTACAATACAAGT 331 chr1qtel1M 512904 -----ATAAGATTTAGAATGAATAATATAGAAAAAAT---------TCAC 512939 ----- vvi v ii- i v iii ---------v C L2c_3end#LINE 330 TAATGATAAGTGCTATAATGGG-AGTATAGACAGGGTGCTATGGGAGCAC 282 chr1qtel1M 512940 GGA-GAGGG------GACTAACCTTAAAGAGGACTGGGAAAGGCTTCTTG 512982 i - ------ i? --i i iiii i ii C L2c_3end#LINE 281 AGAGGAGGGCACCTAGACTAGNCTT--GGGGGGTCAGGGAAGGCTTCCCG 234 chr1qtel1M 512983 AAGATAGTGGGACTTTAGCCCCTTA-TCTTCA---ACAAG-AAAATCTAA 513027 i ivi iv ii v --- v -? v --- ii - ii vi i C L2c_3end#LINE 233 GAGGAGGTGACATCTGAG---CTGAGNCTTGAAGGATGAGTAGGAGTTAG 187 chr1qtel1M 513028 -GAGGTGAA---AGAGGGAAAGA--ATTTCGGAATTGGGGGACAACTAAT 513071 -v i --- i i -- i i ivvvi i i vvi C L2c_3end#LINE 186 CCAGGTGGAAGGAGGGGGGAAGAGCATTCCAGGCAGAGGGAACAGCATGT 137 chr1qtel1M 513072 GAAAATGCTTTAGAGTTAGGAAA 513094 v v -?ii vi C L2c_3end#LINE 136 GCAAAGGC-NCGGAGGCAGGAAA 115 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 42.47 CpG sites = 68, Kimura (unadjusted) = 45.81 Transitions / transversions = 2.06 (68/33) Gap_init rate = 0.10 (31 / 326), avg. gap size = 1.97 (61 / 31) 338 37.52 9.83 3.21 chr1qtel1M 512768 513001 (486999) C L2b_3end#LINE/L2 (6) 460 212 m_b41s601i19 1452 chr1qtel1M 512768 TCAGTCAACAAGCACTTATTAAGTAC--ATTGTGTGCGAAGTGGAATGCT 512815 v ii i i i ii -- i v i i?vvi C L2b_3end#LINE 460 TCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCT 411 chr1qtel1M 512816 TAGCACTGGTGAAACA--------TAAGGCAAAAATAATCTCTGCTTTAG 512857 vi i v v --------i i i v?iii i ii vi C L2b_3end#LINE 410 AGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCA 361 chr1qtel1M 512858 AGGAGCCCACAGCCTTGTGGGGAAAAACCATGACAACTCTGTA--CAAAT 512905 v i i v i i -- - ---- -- i i C L2b_3end#LINE 360 CGGAGCTCACAGTCTAGTGGGGGAGA--CA-GACA----TGTAANCAGAC 318 chr1qtel1M 512906 AA----GATTTAGAAT----GAATAATATAGAAAAAATTCACGGAGAGGG 512947 ----i iii i ---- ii iv iv iiiiiiii - ii C L2b_3end#LINE 317 AATNATAACCCAGAGTGGCAGGGTAGGACTGGGGGGGCCCA-GAGGAGGG 269 chr1qtel1M 512948 -GACTAACCTTAA--AGAGGACTGGGAAAGGCTTCTTGAAGATAGTGGGA 512994 - v i iviv--i i iiii i i ii i ivi iv C L2b_3end#LINE 268 CGCCTGACCCGGCCTGGGGGGTCAGGGAGGGCTTCCCGGAGGAGGTGACA 219 chr1qtel1M 512995 CTTTAGC 513001 i v C L2b_3end#LINE 218 TTTGAGC 212 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 54.65 CpG sites = 66, Kimura (unadjusted) = 60.71 Transitions / transversions = 3.47 (66/19) Gap_init rate = 0.06 (15 / 233), avg. gap size = 2.07 (31 / 15) 369 22.37 6.58 0.00 chr1qtel1M 513117 513192 (486808) MER58C#DNA/hAT-Charlie 10 90 (125) m_b41s502i1 1453 chr1qtel1M 513117 GTAAACTATAGTCTGAGGGTCAAATTTGGCCCAG----TGTTTTTATATG 513162 i ii i i v i ii iv---- i i MER58C#DNA/hA 10 GCAAACTACGGCCCGCGGGCCAAATCCGGCCCGCGGCCTGTTTTTGTACG 59 chr1qtel1M 513163 GCCT-CAAGCTAAGAATGATTTTTATATTTT 513192 i- i i i MER58C#DNA/hA 60 GCCCGCGAGCTAAGAATGGTTTTTACATTTT 90 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 15.91 CpG sites = 15, Kimura (unadjusted) = 28.68 Transitions / transversions = 7.50 (15/2) Gap_init rate = 0.03 (2 / 75), avg. gap size = 2.50 (5 / 2) 212 23.68 0.00 0.00 chr1qtel1M 513913 513950 (486050) C L2#LINE/L2 (2819) 263 226 m_b41s601i21 1454 chr1qtel1M 513913 AGTCTTGGACTTCTTGTGATAATTCACACAACCAGGAA 513950 i i i i v ii v i C L2#LINE/L2 263 AGTCTTGGGCTTCTTGTGGTGACTGACGTAAACAGGGA 226 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 26.18 CpG sites = 7, Kimura (unadjusted) = 30.11 Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 234 30.21 6.25 6.92 chr1qtel1M 514796 514955 (485045) L3b_3end#LINE/CR1 637 795 (411) m_b41s601i22 1455 chr1qtel1M 514796 CAAATTAAATGGCAGTGGCCTTCCATCTCTA----GCACTGGTCAAGCTT 514841 i ?i i- vi ii?? vv ---- i i i? L3b_3end#LINE 637 CAGANCAAG-GGAGGTGATNNTCCCGCTCTACTCTGCGCTGGTCAGGCCN 685 chr1qtel1M 514842 GATCCAGGGCCTTGGGGTCAGTTCTGA--CCCAAACTTTAAGCTGGACGT 514889 v ? ii i ivi v v i--? v ? ivv L3b_3end#LINE 686 CANCTGGAGTACTGCGTTCAGTTCTGGGCNCCACANTTTAAAAGGGACGT 735 chr1qtel1M 514890 T----AACTGGGCATTATTCAGAGAAGGCCCATTTATCCAGAAACGAATA 514935 v---- ?i iv vvi i iv v ------ i i v L3b_3end#LINE 736 GGAGAANTTGGAGAGAGTTCAGAGGAGAGCAA------CAAAAATGATTA 779 chr1qtel1M 514936 GAATGGGGACTGGAGGGTGG 514955 i ---- i iii L3b_3end#LINE 780 AA----GGGCTGGAAAATGG 795 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 42.05 CpG sites = 28, Kimura (unadjusted) = 43.36 Transitions / transversions = 1.65 (28/17) Gap_init rate = 0.09 (14 / 159), avg. gap size = 1.50 (21 / 14) 13 7.52 7.14 0.00 chr1qtel1M 515526 515553 (484447) (ACAA)n#Simple_repeat 1 30 (0) m_b41s252i12 1456 chr1qtel1M 515526 ACAAA-GAA-AAACAAACAAACAAAAAAAC 515553 -i - v (ACAA)n#Simpl 1 ACAAACAAACAAACAAACAAACAAACAAAC 30 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.07 (2 / 27), avg. gap size = 1.00 (2 / 2) 265 31.33 2.79 10.84 chr1qtel1M 515573 515751 (484249) C L2b_3end#LINE/L2 (91) 375 210 m_b41s601i23 1457 chr1qtel1M 515573 CAATCACTGTTCTCATCAAATGAGTTCATACTTTAATGGAGGATTCA-AT 515621 ii v ii - i--- i i v i i i vv - i C L2b_3end#LINE 375 CGGTCCCTGCCCTCA-CG---GAGCTCACAGTCTAGTGGGGGAGACAGAC 330 chr1qtel1M 515622 ATGTAA--AAAAAACTATGTAAAACAAGCTATTAGCAGGGTAA-ATTGGA 515668 -- i v i? --- v v -- v i i- i i C L2b_3end#LINE 329 ATGTAANCAGACAATNAT---AACCCAG--AGTGGCAGGGTAGGACTGGG 285 chr1qtel1M 515669 GATAATCATGAGG-GGGAAAAAGTTCTAGCATTAGGGAGGTGTGTGTCAG 515717 ivivi - - vivvv vi ii v --- i ----- C L2b_3end#LINE 284 GGGGCCCA-GAGGAGGGCGCCTGACCCGGCCT---GGGGG-----GTCAG 244 chr1qtel1M 515718 GAAAAGCTTCCTGGAGAAAGTGAGATTTTAACTG 515751 i ii i i i v v i C L2b_3end#LINE 243 GGAGGGCTTCCCGGAGGAGGTGACATTTGAGCTG 210 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.72 CpG sites = 32, Kimura (unadjusted) = 42.30 Transitions / transversions = 1.78 (32/18) Gap_init rate = 0.12 (22 / 178), avg. gap size = 1.05 (23 / 22) 18 8.35 2.27 7.14 chr1qtel1M 516155 516198 (483802) (GGGGACC)n#Simple_repeat 1 42 (0) m_b41s252i13 1458 chr1qtel1M 516155 GGGGACCGAGGGACC-GAGACCGGGGAGCGGGGAGCCGAGGGGCC 516198 - - i v - - i (GGGGACC)n#Si 1 GGGGACCG-GGGACCGGGGACCGGGGACCGGGGA-CCG-GGGACC 42 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.09 (4 / 43), avg. gap size = 1.00 (4 / 4) 12 24.08 0.00 0.00 chr1qtel1M 517120 517153 (482847) (GGG)n#Simple_repeat 1 34 (0) m_b41s252i14 1459 chr1qtel1M 517120 GGTGGGGCGGAGGGTGGTGGGGGCAGGGGGGGGG 517153 v v i v v vi (GGG)n#Simple 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 34 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 378 37.95 3.26 0.71 chr1qtel1M 519869 520144 (479856) L3#LINE/CR1 1293 1575 (2524) m_b42s601i0 1460 chr1qtel1M 519869 TGGGCATTCAATAAAAT-AACCAGATGTTCCAACACCAAGAGGCGGAC-T 519916 i v v ? i - iv vi ii v i iii i-i L3#LINE/CR1 1293 TGGGTAATAAANAAAGTNAACTTGAAATTTTAACACAAGGAGGTAAATAC 1342 chr1qtel1M 519917 GATCTT-TAGCGTGCCTTTCAGCCT--GTGGAATAAGACT-ATGACTGCA 519962 i- - ii viiv v -- i ii - v L3#LINE/CR1 1343 GATCTCATAG-GTATCACCGAGACTTGGTGGGATGGGACTCATGACTGGA 1391 chr1qtel1M 519963 GTGGAGCTGTGGAGGCATTTACTTTATTCACAAGAAATAGAGATA--AGA 520010 i ivi vi i vi v? i i v i vv -- L3#LINE/CR1 1392 ATACGGCGATGGAAGGGTANACCTTGTTCAAAAGAAACAGATCTANTAGA 1441 chr1qtel1M 520011 AGTAGAGTTGGGGGGGCTTTGTATATGGAAAAAAAATCTTAACAGGGCAA 520060 vi v?i i vi vi i vi i i v v-i v v v iii L3#LINE/CR1 1442 AGGGGAGGNAGAGTAGCACTGTATGTCAAGAAGATATA-CACCTGCGTGG 1490 chr1qtel1M 520061 GAAACCAGAAAACCAGTGGGAAAAGCCTGTTGACGAACACCTGAGTGTAG 520110 i v vi v iiiv v i vi ? iv i ii i vi L3#LINE/CR1 1491 AAATCCACGAACCTGAGGGTAGAAGCGCGNTGGAGAGCATTTGGGTGAGG 1540 chr1qtel1M 520111 GTTGGGGGAAGGCG-TACAAAAGGGATTTTGTCAT 520144 i viii ii v -v i v v i ii L3#LINE/CR1 1541 ATAAAAGGAGAGAGAAACAGAAGTGATATCGTTGT 1575 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 52.61 CpG sites = 65, Kimura (unadjusted) = 57.69 Transitions / transversions = 1.67 (65/39) Gap_init rate = 0.03 (9 / 275), avg. gap size = 1.22 (11 / 9) 17 4.35 0.00 0.00 chr1qtel1M 520573 520596 (479404) (AAAT)n#Simple_repeat 1 24 (0) m_b42s252i0 1461 chr1qtel1M 520573 AAATAAGTAAATAAATAAATAAAT 520596 i (AAAT)n#Simpl 1 AAATAAATAAATAAATAAATAAAT 24 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 298 20.31 1.56 0.00 chr1qtel1M 521420 521483 (478517) MIR3#SINE/MIR 81 145 (63) m_b42s601i1 1462 chr1qtel1M 521420 GCAGTGTGACCCTGGGCAGGTCACC-CACTCCTGTTTGCCTCAATTTCCT 521468 v i i i- ii v vv i MIR3#SINE/MIR 81 GCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCT 130 chr1qtel1M 521469 CGTGTGTAAAGTGAG 521483 i v i MIR3#SINE/MIR 131 CATCTGTAAAATGAG 145 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 24.13 CpG sites = 8, Kimura (unadjusted) = 24.13 Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.02 (1 / 63), avg. gap size = 1.00 (1 / 1) 191 37.30 7.41 2.35 chr1qtel1M 521796 521957 (478043) C L3#LINE/CR1 (2613) 1486 1317 m_b42s601i2 1463 chr1qtel1M 521796 GTAGGTGTGACTTATTCTCTTAATATGCACTG--AGCCCCATTCCCTGTG 521843 i i--- ii i i i v -- vi i?vi iv v C L3#LINE/CR1 1486 GCAGGTGTA---TATCTTCTTGACATACAGTGCTACTCTNCCTCCCCTTC 1440 chr1qtel1M 521844 TGACCTCTCTCATCTCTTTTAAATAAGACTTG-TGTCTCATGGCTGTGTT 521892 i?ivvv -i i i i ii? i-iv ii v i i C L3#LINE/CR1 1439 TANTAGATCT-GTTTCTTTTGAACAAGGTNTACCCTTCCATCGCCGTATT 1391 chr1qtel1M 521893 CCCATCATTGGTCTCATTTCAGCAAGATTCA--GA-------GAGGTTAG 521933 vi vi i ii v vi i-- ------- i iiv C L3#LINE/CR1 1390 CCAGTCATGAGTCCCATCCCACCAAGTCTCGGTGATACCTATGAGATCGT 1341 chr1qtel1M 521934 ATTTGCTTTTTTACCTTAAGTTTT 521957 i i ii iiv iv C L3#LINE/CR1 1340 ATTTACCTCCTTGTGTTAAAATTT 1317 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 53.98 CpG sites = 42, Kimura (unadjusted) = 58.91 Transitions / transversions = 2.47 (42/17) Gap_init rate = 0.05 (8 / 161), avg. gap size = 2.00 (16 / 8) 16 12.51 2.70 2.70 chr1qtel1M 522784 522820 (477180) (TAATA)n#Simple_repeat 1 37 (0) m_b42s252i1 1464 chr1qtel1M 522784 TACTAT-ATATTATATAATATAAGAATAATATTATATA 522820 v - v -v v (TAATA)n#Simp 1 TAATATAATATAATATAATATAA-TATAATATAATATA 37 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 16 9.10 11.43 0.00 chr1qtel1M 522787 522821 (477179) (TA)n#Simple_repeat 1 39 (0) m_b42s252i2 1464 chr1qtel1M 522787 TATATAT-TATATA-ATATAAGAATA-ATAT-TATATAT 522821 - - viv - - (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATAT 39 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.12 (4 / 34), avg. gap size = 1.00 (4 / 4) 253 28.24 5.88 0.00 chr1qtel1M 525035 525119 (474881) C MIR3#SINE/MIR (1) 207 118 m_b42s601i3 1465 chr1qtel1M 525035 AATCATAGGATTCTA-CATGT-GGAACTCAAGGGGACCTCAGA--CCTTT 525080 i iv -v -i i vi i i --i v i C MIR3#SINE/MIR 207 AATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATC 158 chr1qtel1M 525081 GAGTTTAAGCCC-TCATTTCACATATAAAGGGCCTGAGGC 525119 v ii v - i v i i iiv C MIR3#SINE/MIR 157 TAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGC 118 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 37.01 CpG sites = 16, Kimura (unadjusted) = 37.01 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.05 (4 / 84), avg. gap size = 1.25 (5 / 4) 21 0.00 0.00 0.00 chr1qtel1M 525792 525814 (474186) (G)n#Simple_repeat 1 23 (0) m_b42s252i3 1466 chr1qtel1M 525792 GGGGGGGGGGGGGGGGGGGGGGG 525814 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGG 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 222 28.54 6.11 3.73 chr1qtel1M 525936 526066 (473934) C L2c_3end#LINE/L2 (8) 470 337 m_b42s601i4 1467 chr1qtel1M 525936 ATTCCACAAACATATTATTCA----CAATTATATGGAAAGCACTATGCTT 525981 v - v ---- v i i vv i i iv -vv C L2c_3end#LINE 470 ATTCAACAAACAT-TTATTGAGCGCCTACTATGTGCCAGGCGCTGGG-GA 423 chr1qtel1M 525982 TACTTTGATA---GAAACACGGATATTCCTGCCCTGATGGAACTTATAGT 526028 vvv i---i i --- i v v i i i C L2c_3end#LINE 422 TACAAAGATGAATAAGACACGG---TCCCTGCCCTCAAGGAGCTCACAGT 376 chr1qtel1M 526029 CTAGTAATGGTGACATAAAGGTACACAAAT-ATAATAAT 526066 iiv v v v ? v i i- v i C L2c_3end#LINE 375 CTAGTGGAGGAGACAGACANGTAAACAGACAATTACAAT 337 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 35.41 CpG sites = 17, Kimura (unadjusted) = 36.64 Transitions / transversions = 0.89 (17/19) Gap_init rate = 0.06 (8 / 130), avg. gap size = 1.62 (13 / 8) 226 24.32 1.37 4.23 chr1qtel1M 525993 526065 (473935) C L2b_3end#LINE/L2 (86) 380 310 m_b42s601i5 1467 chr1qtel1M 525993 AAACACGGATATTCCTGCCCTGATGGAACTTATAGTCTAGTAATGGTGAC 526042 i ? --- i v i i i i iiv v C L2b_3end#LINE 380 AGACNCGG---TCCCTGCCCTCACGGAGCTCACAGTCTAGTGGGGGAGAC 334 chr1qtel1M 526043 ATAAAGGTACACAAAT-ATAATAA 526065 v v v v? i i- ? C L2b_3end#LINE 333 AGACATGTAANCAGACAATNATAA 310 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 29.45 CpG sites = 10, Kimura (unadjusted) = 31.65 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.06 (4 / 72), avg. gap size = 1.00 (4 / 4) 266 26.74 5.81 0.00 chr1qtel1M 527684 527769 (472231) C MIR3#SINE/MIR (1) 207 117 m_b42s601i6 1468 chr1qtel1M 527684 AATCATAGGATTCTA-CATGT-GGAGCTTACGGGGAC--TGCAGACCTTT 527729 i iv -v -i vivi -- iv i v i C MIR3#SINE/MIR 207 AATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATC 158 chr1qtel1M 527730 GAGTTTAACCCC-TCATTTCACATATAAAGGACCTGAGGCC 527769 v ii - i v i i i v C MIR3#SINE/MIR 157 TAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCC 117 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 34.00 CpG sites = 14, Kimura (unadjusted) = 34.00 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.05 (4 / 85), avg. gap size = 1.25 (5 / 4) 213 24.52 1.85 1.85 chr1qtel1M 527860 527913 (472087) L2d_3end#LINE/L2 462 515 (1) m_b42s601i7 1469 chr1qtel1M 527860 ATAGTGCTTGGCACAATAATGGGCACTTACTAAATAC-TGCTTACTGACT 527908 i vi - i i i i v - i v i i L2d_3end#LINE 462 ACAGTGCTGAGCACA-TAGTAGGCGCTCAATAAATACTTGTTGATTGATT 510 chr1qtel1M 527909 GACTG 527913 i L2d_3end#LINE 511 GATTG 515 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 28.54 CpG sites = 10, Kimura (unadjusted) = 31.46 Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.04 (2 / 53), avg. gap size = 1.00 (2 / 2) 246 28.75 1.25 0.00 chr1qtel1M 528773 528852 (471148) L1ME4a_3end#LINE/L1 121 201 (670) m_b42s551i0 1470 chr1qtel1M 528773 AAAAAGCATCTGAACACATATTCAGATTCTCTGATGATCAGAGAGGTACA 528822 v i v v ? i ivi v ii i i ii i L1ME4a_3end#L 121 AATAAACATATGAAAANATGTTCAACCTCACTAGTAATCAAAGAAATGCA 170 chr1qtel1M 528823 AATTAAAACAACTCGGAGGT-TCATCTTCCA 528852 vvv i -i i i L1ME4a_3end#L 171 AATTAAAACAACAATGAGATACCATTTTTCA 201 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 38.45 CpG sites = 15, Kimura (unadjusted) = 38.45 Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.01 (1 / 79), avg. gap size = 1.00 (1 / 1) 209 21.64 0.00 5.88 chr1qtel1M 529106 529159 (470841) L2a_3end#LINE/L2 464 514 (3) m_b42s601i8 1471 chr1qtel1M 529106 AATAGTGCCTGGCACAATAATGGGCACTTACTAAATACTACTTCTGACTG 529155 i - i i i i v i -- vi v L2a_3end#LINE 464 AACAGTGCCTGGCAC-ATAGTAGGCGCTCAATAAATATT--TGTTGAATG 510 chr1qtel1M 529156 ACTG 529159 v L2a_3end#LINE 511 AATG 514 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 23.38 CpG sites = 7, Kimura (unadjusted) = 26.03 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.06 (3 / 53), avg. gap size = 1.00 (3 / 3) 245 21.87 4.62 1.49 chr1qtel1M 532110 532174 (467826) C MIR3#SINE/MIR (64) 144 78 m_b42s601i9 1472 chr1qtel1M 532110 TCATTTGGCAGATGAGGAAACTGAGGC---AAACAGTTAAGTGGCCAGCT 532156 vi ---i ivi v i iv i C MIR3#SINE/MIR 144 TCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCC 95 chr1qtel1M 532157 CAGGACCACACATGCAAG 532174 i ii - ? C MIR3#SINE/MIR 94 CAAGGTCACACA-GCNAG 78 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 27.37 CpG sites = 10, Kimura (unadjusted) = 27.37 Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.03 (2 / 64), avg. gap size = 2.00 (4 / 2) 254 22.41 5.17 0.00 chr1qtel1M 532111 532168 (467832) C MIRc#SINE/MIR (122) 146 86 m_b42s601i10 1472 chr1qtel1M 532111 CATTTGGCAGATGAGGAAACTGAGGC---AAACAGTTAAGTGGCCAGCTC 532157 vi ---i ivi i iv i C MIRc#SINE/MIR 146 CATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCC 97 chr1qtel1M 532158 AGGACCACACA 532168 i ii C MIRc#SINE/MIR 96 AAGGTCACACA 86 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 27.98 CpG sites = 10, Kimura (unadjusted) = 27.98 Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.02 (1 / 57), avg. gap size = 3.00 (3 / 1) 339 31.64 17.68 0.47 chr1qtel1M 532219 532399 (467601) C MIRc#SINE/MIR (20) 248 37 m_b42s601i11 1473 chr1qtel1M 532219 TTTACATGGTACTTTAAGGTTTGCAAAGCACTTG-ACAAATACTCCATCG 532267 ii i i vi i i v- v i i viv i C MIRc#SINE/MIR 248 TTTGTATAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATCTCA 199 chr1qtel1M 532268 TTTGATCCTTACAATAACCCTACAA---AAGTGGGTGCA----------- 532303 i i iii --- i ii - ----------- C MIRc#SINE/MIR 198 TTTGATCCTCACAACAACCCTGTGAGGTAGGCAGG-GCAGGTATTATTAT 150 chr1qtel1M 532304 ----ATTTCACAGATGAGTAAAGGGAAGCT-----------GGCGACTTA 532338 ---- i v vv i -----------i i i C MIRc#SINE/MIR 149 CCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTG 100 chr1qtel1M 532339 TCTAGAATCA-ATGGCTGCGAAAGCCCCGAGGCAGGATTGGGACACAGGT 532387 i i iii - ii ivv ivvv v v i i v i v C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGT 50 chr1qtel1M 532388 TTATCT-ACTGCA 532399 i vi - v C MIRc#SINE/MIR 49 CTTCCTGACTCCA 37 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 41.37 CpG sites = 38, Kimura (unadjusted) = 43.44 Transitions / transversions = 2.00 (38/19) Gap_init rate = 0.04 (8 / 180), avg. gap size = 4.12 (33 / 8) 222 31.14 8.07 6.53 chr1qtel1M 533315 533661 (466339) L2#LINE/L2 2095 2446 (636) m_b42s601i12 1474 chr1qtel1M 533315 TCCTTTTTGCAACGTGCTTCCCTCTGGGCTTCTTTGCTGCT-CACTCCTC 533363 i v iivi iii v v ivv vii i- - L2#LINE/L2 2095 TCCTTCTTGAAACACTTTCTTCACTTGGCTTCCAGGACACCACACTC-TC 2143 chr1qtel1M 533364 ATGGAT--CCTCTCTCTTCTCTAG--GCT--TTCT-AGACCCCTCCTTCT 533406 v v -- iiv i v i -- -- - ---i - L2#LINE/L2 2144 CTGGTTTTCCTCCTACCTCACTGGCCGCTCCTTCTCAG---TCTCCTT-T 2189 chr1qtel1M 533407 CTTGGTTCTCCCCCTTCCTCTCTGACCAAATCCGGTGTCACCTTTAACGG 533456 vi ii i v - i i -------- v ? v v --- L2#LINE/L2 2190 GCTGGTTCCTCCTCATC-TCCCCGACC--------TCTNAACGTT---GG 2227 chr1qtel1M 533457 AGGTTATCCCACAAGGCTCTAAGC--TGGACTCTCATCTGTTTTCCCTCC 533504 ---- v v i - iv -- - v v i iv i L2#LINE/L2 2228 AG----TGCCCCAGGGCTC-AGTCCTTGGAC-CTCTTCTCTTCTCTATCT 2271 chr1qtel1M 533505 AAACTACTTCACTTGTTGATCTCATCTATTCCCATCAACTACAAT--CAC 533552 v vvi v ? v i v i vivi vv -- i L2#LINE/L2 2272 ACACTCACTCCCTNGGTGATCTCATCCAGTCTCATGGCTTTAAATACCAT 2321 chr1qtel1M 533553 CTTTGTGCTGAT-ATTCTCCAATCTGCTTTTCCAG-------CTCT---- 533590 v i - i i v i iiv i ------- ---- L2#LINE/L2 2322 CTATATGCTGATGACTCCCAAATTTATATCTCCAGCCCGGACCTCTCCCC 2371 chr1qtel1M 533591 --AA--CCAATATTGCATCTTCAACTGTCTGATGGACACTCAGAACTGGA 533636 -- -- ivv i i v i i iv v iiivv vi L2#LINE/L2 2372 TGAACTCCAGACTCGTATATCCAACTGCCTACTCGACATCTCCACTTGGA 2421 chr1qtel1M 533637 TGTCCTGTAGACATCATCAACTCAA 533661 ivi i viv i L2#LINE/L2 2422 TGTCTAATAGGCATCTCAAACTTAA 2446 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 40.47 CpG sites = 55, Kimura (unadjusted) = 41.54 Transitions / transversions = 1.20 (55/46) Gap_init rate = 0.10 (35 / 346), avg. gap size = 1.46 (51 / 35) 345 27.48 7.06 5.81 chr1qtel1M 533810 533979 (466021) L2c_3end#LINE/L2 297 468 (10) m_b42s601i13 1474 chr1qtel1M 533810 CTTGATTAT-CTCCAATT-TATCCTTTACAA--AGCTTGT-TTCTACATA 533854 i vi - v - v vi iv -- i - v vv i L2c_3end#LINE 297 CCTGTCTATACTCCCATTATAGCACTTATCATTAACTTGTATTGTAATTG 346 chr1qtel1M 533855 GTTAT---CTTGCTCATTTCTTCCATTAAACTGTAATCTCCTTGAGAGCA 533901 vi i --- ? iiii i i i i i v i L2c_3end#LINE 347 TCTGTTTACNTGTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCA 396 chr1qtel1M 533902 GCGAC--TGTCTTACTTTTATTAGTAGCTCCAGCTCTCTGTAGTGTTTGG 533949 v -- i iv v v v i ---------- ii L2c_3end#LINE 397 GGGACCGTGTCTTATTCATCTTTGTATCCCCAGC----------GCCTGG 436 chr1qtel1M 533950 CACATGGTAGGTACTTAAT--ATGTTTATCGA 533979 i ii i -- i i L2c_3end#LINE 437 CACATAGTAGGCGCTCAATAAATGTTTGTTGA 468 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 34.81 CpG sites = 29, Kimura (unadjusted) = 35.96 Transitions / transversions = 1.93 (29/15) Gap_init rate = 0.10 (17 / 169), avg. gap size = 1.29 (22 / 17) 350 23.95 3.06 2.02 chr1qtel1M 534349 534446 (465554) C MIRc#SINE/MIR (155) 113 15 m_b42s601i14 1472 chr1qtel1M 534349 GGTCCGATGACTTGCCCAAAGTCACACAGCTAGACAGTGTCTGAGAAGGA 534398 ivii i vv v v vv i C MIRc#SINE/MIR 113 GGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGG 64 chr1qtel1M 534399 ATCTGAACTCGGCTCTTGCTGGCTCTA--TCCATTGTGCTATCTCC-CTG 534445 iii i i v v i i -- -- v i - C MIRc#SINE/MIR 63 ACTCGAACCCAGGTCTTCCTGACTCCAAGTCCA--GTGCTCTTTCCACTG 16 chr1qtel1M 534446 C 534446 C MIRc#SINE/MIR 15 C 15 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 27.86 CpG sites = 13, Kimura (unadjusted) = 29.34 Transitions / transversions = 1.30 (13/10) Gap_init rate = 0.04 (4 / 97), avg. gap size = 1.25 (5 / 4) 413 28.69 4.92 0.00 chr1qtel1M 535038 535159 (464841) C L2d2_3end#LINE/L2 (19) 536 409 m_b42s601i15 1475 chr1qtel1M 535038 ATTTATTAGGCACCAGTGGTGTGTCAGGCACCGTGCAAAGTACCA---GG 535084 ii i viiv iv i v i ii ii--- C L2d2_3end#LIN 536 ATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGTGGGG 487 chr1qtel1M 535085 GATACAAAG--GCAGAA-ACAGAGTCCTTGCTCTCAAGGAGCTTATCTTC 535131 -- i v - vi i i ivv C L2d2_3end#LIN 486 GATACAAAGAAGTATAAGACATGGTCCCTGCCCTCAAGGAGCTTACAATC 437 chr1qtel1M 535132 TAATGGGGGAAACAGCAAATGGCCATGT 535159 i v i iv v iiv i C L2d2_3end#LIN 436 TAGTTGGGGAGACAAGACATAAACACGT 409 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 33.54 CpG sites = 23, Kimura (unadjusted) = 37.73 Transitions / transversions = 1.92 (23/12) Gap_init rate = 0.02 (3 / 121), avg. gap size = 2.00 (6 / 3) 18 0.00 0.00 0.00 chr1qtel1M 535706 535725 (464275) (GT)n#Simple_repeat 1 20 (0) m_b42s252i4 1476 chr1qtel1M 535706 GTGTGTGTGTGTGTGTGTGT 535725 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGT 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 180 13.51 5.41 0.00 chr1qtel1M 537735 537771 (462229) C MIRc#SINE/MIR (195) 73 35 m_b42s601i16 1477 chr1qtel1M 537735 CAGAAGCGGGACTCGGACC--GGCCTTCCTGAGTCCAAG 537771 iv i -- i v C MIRc#SINE/MIR 73 CAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 15.04 CpG sites = 3, Kimura (unadjusted) = 15.04 Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.03 (1 / 36), avg. gap size = 2.00 (2 / 1) 63 14.47 2.63 0.00 chr1qtel1M 539476 539589 (460411) (CT)n#Simple_repeat 1 117 (0) m_b42s252i5 1478 chr1qtel1M 539476 CTCTCGCTCTCTCTCT-TTTCTCTGTCTCTCTGTCACTCTCTCT-TTTCT 539523 v - i v v v - i (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chr1qtel1M 539524 CTGCCTCTCTCTCTTTGTCTCTCTCTCT-TTTCTCTGTCTCTCTCTCTCT 539572 vi i v - i v (CT)n#Simple_ 51 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 100 chr1qtel1M 539573 CTGTCTCTGTGTCTCTC 539589 v v v (CT)n#Simple_ 101 CTCTCTCTCTCTCTCTC 117 Matrix = Unknown Transitions / transversions = 0.50 (5/10) Gap_init rate = 0.03 (3 / 113), avg. gap size = 1.00 (3 / 3) 243 27.92 17.93 3.64 chr1qtel1M 542701 542845 (457155) C MIRc#SINE/MIR (34) 234 70 m_b42s601i17 1479 chr1qtel1M 542701 TATAGTTGATAAGAAGCTTTCACA----------------ATCCTCATAC 542734 i v i iiv ---------------- i v C MIRc#SINE/MIR 234 TACAGTTTACAAAGCGCTTTCACATACATTATCTCATTTGATCCTCACAA 185 chr1qtel1M 542735 AAACTTTATAAGGTAGATCAGTCAG------TTATTCC--TTTTACAAAT 542776 v ii i i iivi v ------ i -- i C MIRc#SINE/MIR 184 CAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGAT 135 chr1qtel1M 542777 GAGGAAACTGGGACTTA-AGATTTATTTATTTAATAACTTACCCAA-CTT 542824 i i i - ---iv --- i i i -v i C MIRc#SINE/MIR 134 GAGGAAACTGAGGCTCAGAGA---GGTTA---AGTGACTTGCCCAAGGTC 91 chr1qtel1M 542825 ATACCACCAATAAATGTTAAA 542845 i vi i i i vi i C MIRc#SINE/MIR 90 ACACAGCTAGTAAGTGGCAGA 70 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 37.47 CpG sites = 29, Kimura (unadjusted) = 37.47 Transitions / transversions = 2.90 (29/10) Gap_init rate = 0.08 (11 / 144), avg. gap size = 2.91 (32 / 11) 260 27.53 3.28 7.69 chr1qtel1M 542724 542845 (457155) C MIRb#SINE/MIR (79) 189 73 m_b42s601i18 1479 chr1qtel1M 542724 AATCCTCATACAAACTTTATAAGGTAGATCAGTCAGTTATTCC--TTTTA 542771 i vv ii iii i --i i - i -- C MIRb#SINE/MIR 189 AATCCTCACAACAACCCTGCGAGGTAGGT--ATTA-TTATCCCCATTTTA 143 chr1qtel1M 542772 CAAATGAGGAAACTGGGACTTA-AGATTTATTTATTTAATAACTTACCCA 542820 i i i i - ---iv --- i i C MIRb#SINE/MIR 142 CAGATGAGGAAACTGAGGCTCAGAGA---GGTTA---AGTAACTTGCCCA 99 chr1qtel1M 542821 A-CTTATACCACCAATAAATGTTAAA 542845 -v i i vi i i i vi i C MIRb#SINE/MIR 98 AGGTCACACAGCTAGTAAGTGGCAGA 73 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 35.30 CpG sites = 25, Kimura (unadjusted) = 37.02 Transitions / transversions = 4.17 (25/6) Gap_init rate = 0.10 (12 / 121), avg. gap size = 1.08 (13 / 12) 356 34.02 4.75 3.34 chr1qtel1M 542939 543233 (456767) C Plat_L3#LINE/CR1 (96) 3477 3179 m_b42s551i1 1480 chr1qtel1M 542939 ACAAATGGTTGCCCAGTCTCCCCTTCAAGACCACCAAGGAGGGAGAGGGA 542988 i ? i i v iii v i v i v v--- C Plat_L3#LINE/ 3477 ACAGATGGNTGTCTATTCTTTTCTTAAAGATCTCCAGGGATGGAGAC--- 3431 chr1qtel1M 542989 GCCCACTACTTC--TCAAGAGACC----CA-TGTTTGGACAGCTCTAAGT 543031 -i v i -- iiv v ---- - viv - i i vv C Plat_L3#LINE/ 3430 -TCCACAACCTCCCTCGGTAGCCCGTTCCAGTGTTTTATCA-CCCTGACA 3383 chr1qtel1M 543032 TTCAGGAACTTTCCCCTGGCATTTAGCTTCTAAAT-TAGCCTGTTTGCAC 543080 v i v iii viii ii i -- v - vv i vv i C Plat_L3#LINE/ 3382 GTCAAGAAGTTCTTCCTTATGTCCAAC--CGAAATCTCTCCTGCTTTAAT 3335 chr1qtel1M 543081 ACTAAACCCACAATTCCTGGTTCTGCCCTCTGTGACCAAATGGAAGATAT 543130 -i i ivviii v v i ? iv -- ii i v C Plat_L3#LINE/ 3334 -TTAAGCCCATTTCCTCTTGTTCGGTCCTCNGTGGACA--TGGAGAACAA 3288 chr1qtel1M 543131 CAAATC--CCTTTTCCATGTCACAACCTTTCAAATACTTGAAGCCTGTCA 543178 vii -- v ii vii v v i v v v i C Plat_L3#LINE/ 3287 CTGGTCAGCGTCCTCCCCATAAAAACCCTTCATATACTTGAAGACAGTTA 3238 chr1qtel1M 543179 TT---TC-TCTGTTGGTCTTCTCTTCTCTAGACCAGCCATGCCCAGTTCT 543224 --- -i iv i i i i i iv vv i i C Plat_L3#LINE/ 3237 TTAAGTCACCCCTTAGCCTTCTCTTCTCCAGGCTAAACAACCCCAATTCC 3188 chr1qtel1M 543225 TTTAGTCCT 543233 ii i C Plat_L3#LINE/ 3187 TTTAACCTT 3179 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 47.18 CpG sites = 59, Kimura (unadjusted) = 47.88 Transitions / transversions = 1.55 (59/38) Gap_init rate = 0.06 (17 / 294), avg. gap size = 1.41 (24 / 17) 37 0.00 0.00 0.00 chr1qtel1M 543668 543699 (456301) (GT)n#Simple_repeat 1 32 (0) c_b42s251i0 1481 chr1qtel1M 543668 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 543699 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 32 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 15 22.11 8.54 2.30 chr1qtel1M 543843 543924 (456076) (TGCTTT)n#Simple_repeat 1 87 (0) m_b42s252i6 1482 chr1qtel1M 543843 TGTTTTTGCTCTT-TTTTTGCTGTTTGC--TTGCATTTTG-TTTT-CTTT 543887 i i -i - -- - - - (TGCTTT)n#Sim 1 TGCTTTTGCTTTTGCTTTTGCT-TTTGCTTTTGC-TTTTGCTTTTGCTTT 48 chr1qtel1M 543888 CTCACTT--TTTTCCTTTTTGATCTGATTTTTCTTGTGC 543924 iv vi -- v vvv i v v v (TGCTTT)n#Sim 49 TGCTTTTGCTTTTGCTTTTGCTTTTGCTTTTGCTTTTGC 87 Matrix = Unknown Transitions / transversions = 0.67 (6/9) Gap_init rate = 0.09 (7 / 81), avg. gap size = 1.29 (9 / 7) 16 5.20 0.00 0.00 chr1qtel1M 544277 544296 (455704) (A)n#Simple_repeat 1 20 (0) m_b42s252i7 1483 chr1qtel1M 544277 AAAAAAAAAAAAAAAAACAA 544296 v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAA 20 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 15 18.89 2.17 4.44 chr1qtel1M 544883 544928 (455072) (TCC)n#Simple_repeat 1 45 (0) m_b42s252i8 1484 chr1qtel1M 544883 TCCTTCTGCCAGCTGCT-CTCCTCCCTCTCCTCCTCCCCCTCCCTCC 544928 i - vv v - ii i - (TCC)n#Simple 1 TCCTCCT-CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT-CCTCC 45 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.07 (3 / 45), avg. gap size = 1.00 (3 / 3) 351 23.57 22.29 0.00 chr1qtel1M 545065 545184 (454816) Charlie7#DNA/hAT-Charlie 1869 2021 (594) m_b42s502i0 1485 chr1qtel1M 545065 TTGTTGAAAACAAAACAAGTCTATC---TACAAAAATTCT---ATCTGTC 545108 ii i vii i v i --- i i --- iv Charlie7#DNA/ 1869 TTGCCGAAAACGATGTAAATGTGTCACCTATAAAAACTCTCATATCTGCA 1918 chr1qtel1M 545109 CACTCTAAAATCTTGGAGA---------------GGTTCGACAATCTTCC 545143 i v i ---------------v ii v Charlie7#DNA/ 1919 CACTTTAAAAACTTGGAAACAGAATTTTCTAACCTGTTTAAAAATCTTCC 1968 chr1qtel1M 545144 AGAAGAAGAGTTCCAGTGGTTTTTCAACCTGTCTCTTAAAA--------- 545184 i v i v v ii i v --------- Charlie7#DNA/ 1969 AAATGAAGAGTTTCAGTGGGTTTTGAACCCATTTGTTAAAAATATAAAAA 2018 chr1qtel1M 545184 --- 545184 --- Charlie7#DNA/ 2019 TGC 2021 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 26.39 CpG sites = 22, Kimura (unadjusted) = 29.10 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.03 (4 / 119), avg. gap size = 8.25 (33 / 4) 31 0.00 0.00 0.00 chr1qtel1M 545185 545211 (454789) (AC)n#Simple_repeat 1 27 (0) c_b42s251i1 1486 chr1qtel1M 545185 ACACACACACACACACACACACACACA 545211 (AC)n#Simple_ 1 ACACACACACACACACACACACACACA 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 351 23.57 22.29 0.00 chr1qtel1M 545212 545247 (454753) Charlie7#DNA/hAT-Charlie 2022 2059 (556) m_b42s502i0 1485 chr1qtel1M 545212 AAACTTTCCAATGAGTTTCCAACAACAGAT--TTGACA 545247 v i i v v v iv -- Charlie7#DNA/ 2022 ACACCTTCCGATTAGTTTGCAAGAACAACTGATTGACA 2059 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 26.39 CpG sites = 22, Kimura (unadjusted) = 29.10 Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.03 (1 / 35), avg. gap size = 2.00 (2 / 1) 202 20.50 24.78 0.71 chr1qtel1M 545721 545833 (454167) C L3b_3end#LINE/CR1 (667) 539 400 m_b42s601i19 1487 chr1qtel1M 545721 CCCCCAGGCTTTTTTGGACAAAGTCT----CTAA-CCACGACTCCTCC-T 545764 ii v- vi?v ---- - i v i - C L3b_3end#LINE 539 CCCCCAGGTCTTTTTC-ACATGNGCTGCTGCTAAGCCGCGTCTCCCCCAT 491 chr1qtel1M 545765 CCT--ACC-------TTGACTCTGTGAACCCAAGTGC--------ACATT 545797 -- i------- ?i i v -------- i C L3b_3end#LINE 490 CCTGTACTCGCGCGATTGNTTTTTTGAACCCAAGTGCAGGACTTTACGTT 441 chr1qtel1M 545798 TATCCCT-----AGTTCACGTTGTTAGGTCTGGCTCAACAT 545833 ----- v iv i ? ii i i? i C L3b_3end#LINE 440 TATCCCTGTTGAATTTCATCTTGTTGGNTTCGGCCCGNCGT 400 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 19.74 CpG sites = 16, Kimura (unadjusted) = 25.87 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.07 (8 / 112), avg. gap size = 3.62 (29 / 8) 220 35.24 9.03 4.15 chr1qtel1M 545814 546112 (453888) C L3#LINE/CR1 (638) 3461 3149 m_b42s601i20 1488 chr1qtel1M 545814 TGTTAGGTCTG-GCTCAACATAAACCACCTGCACCAGCTCGTTTCCAC-- 545860 i ii ii - v - v v ----- v v i -- C L3#LINE/CR1 3461 TATTGAGCTTGCGGTCAAC-TAAAACCCCT-----AGGTCTTTTTCACGT 3418 chr1qtel1M 545861 -AACTCTCGCGAGGGTCCATC-TGGCCAGCCTCTACCTGCAAAGTTAAAA 545908 - vii v i vivv - vv v v i iiv i -- C L3#LINE/CR1 3417 GAACTGCTGCTAAGCCAGATCCTCTCCATCCTGTACTTGTGCAGTTGA-- 3370 chr1qtel1M 545909 GGTTTATTTAGCTCAAGTGTAGACCCTGCTGTCCATTTCAGTAAAGATTT 545958 -- v v i ii i i iv i vvii ii ii v v iv i C L3#LINE/CR1 3369 --TTTTTTGAACCTAAATGCAGGACTTTACATTTATCCCTGTTAAATTTC 3322 chr1qtel1M 545959 GGTTTGTTGG--TCAGCCCGATCGTCTTTTCCTCATGGGAGCTTTACTGT 546006 ivi -- i - iiivv vvi i v ? -i v C L3#LINE/CR1 3321 ATCTTGTTGGTTTCGGCCC-ATCGTTCCAGCCTGTCGAGATCNTT-TTGA 3274 chr1qtel1M 546007 GTC-CGCTGCC-TCATACGA-ATATTAACT-----------CTCTG-GTC 546041 i -i v v i- v i?-i i ----------- i - C L3#LINE/CR1 3273 ATCTTGATTCTGTCATCCANCGTATTAGCTATCCCTCCCAGCTTTGTGTC 3224 chr1qtel1M 546042 TTCCACAAGTGTAACAATTACACCAGCTCTACCTCTAT----GCCACTGA 546087 v ii i v i i vi ii vv v ii ii ---- i i C L3#LINE/CR1 3223 ATCTGCAAATTTGATAAGCATGCCTTCTATGTCTTCATCCAAGTCATTGA 3174 chr1qtel1M 546088 CAAAAATGGGGAACTAGGA-AGGGCC 546112 i vv - - C L3#LINE/CR1 3173 TAAAAATGTTGAAC-AGGACAGGGCC 3149 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 48.21 CpG sites = 60, Kimura (unadjusted) = 50.36 Transitions / transversions = 1.46 (60/41) Gap_init rate = 0.08 (25 / 298), avg. gap size = 1.60 (40 / 25) 256 28.02 11.11 0.84 chr1qtel1M 546345 546452 (453548) C L2c_3end#LINE/L2 (10) 468 350 m_b42s601i21 1489 chr1qtel1M 546345 TCAATAAACATTGATTAAGCACCTACTGTGTTTC-----------ATACA 546383 i v i i i vi ----------- C L2c_3end#LINE 468 TCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGATACA 419 chr1qtel1M 546384 AAACAAGGCAAAAACCCAGTCACTGCCCTCAAAGGCCTTCCACTGGAACA 546433 i- v ivv i v i v i iv iv v vv iii C L2c_3end#LINE 418 AAG-ATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAGTG 370 chr1qtel1M 546434 GGGGAGCCA-ACATGCAAAC 546452 i v - ? i C L2c_3end#LINE 369 GAGGAGACAGACANGTAAAC 350 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 33.37 CpG sites = 17, Kimura (unadjusted) = 36.33 Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.03 (3 / 107), avg. gap size = 4.33 (13 / 3) 438 22.87 1.65 6.03 chr1qtel1M 547030 547150 (452850) C MIRc#SINE/MIR (141) 127 12 m_b42s601i22 1490 chr1qtel1M 547030 CTGAGGC-AACTGGGATTAAGTGACTTGCCCAGGGTCACACAGCTAGGAA 547078 -v vv i i i --- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG--- 81 chr1qtel1M 547079 GTGTTAAGTGTCTAAGGGCAGATTTGAACTCGGGTCCTCCTGACTTCAGG 547128 ---- v vi vvvi i i i i i i i C MIRc#SINE/MIR 80 ----TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr1qtel1M 547129 GCTGGTGTTC-ATCCACTGCGCC 547150 v ii i -v i C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTGCACC 12 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 26.56 CpG sites = 16, Kimura (unadjusted) = 27.80 Transitions / transversions = 1.60 (16/10) Gap_init rate = 0.07 (9 / 120), avg. gap size = 1.00 (9 / 9) 17 0.00 0.00 4.76 chr1qtel1M 548550 548571 (451429) (CA)n#Simple_repeat 1 21 (0) m_b42s252i9 1491 chr1qtel1M 548550 CACTACACACACACACACACAC 548571 - (CA)n#Simple_ 1 CAC-ACACACACACACACACAC 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.05 (1 / 21), avg. gap size = 1.00 (1 / 1) 58 33.40 0.00 0.00 chr1qtel1M 548638 548826 (451174) (TGGCCC)n#Simple_repeat 1 189 (0) m_b42s252i10 1492 chr1qtel1M 548638 TGGCCCTGGTCCTGCTCCTGACCCTGATCCTGCCTCTGGCCCTTGCCCAG 548687 i vi i ii v i v v (TGGCCC)n#Sim 1 TGGCCCTGGCCCTGGCCCTGGCCCTGGCCCTGGCCCTGGCCCTGGCCCTG 50 chr1qtel1M 548688 GTCCTGACTCTGATACTGGTTCTGGTCCTGACTCTGATACTGGTTCTGGT 548737 i i i iiv ii i i i iiv ii i (TGGCCC)n#Sim 51 GCCCTGGCCCTGGCCCTGGCCCTGGCCCTGGCCCTGGCCCTGGCCCTGGC 100 chr1qtel1M 548738 CCTGCCTCTGGCCCTTGCCCAGGTCCTGACTCTGGCCCTGACTCTGGCCT 548787 v i v v i i i i i i (TGGCCC)n#Sim 101 CCTGGCCCTGGCCCTGGCCCTGGCCCTGGCCCTGGCCCTGGCCCTGGCCC 150 chr1qtel1M 548788 TGGTCCTGCTCTTGTTCCTGCTTCTGAACCTGTCCCTGG 548826 i vi i vi vii iv v (TGGCCC)n#Sim 151 TGGCCCTGGCCCTGGCCCTGGCCCTGGCCCTGGCCCTGG 189 Matrix = Unknown Transitions / transversions = 2.50 (35/14) Gap_init rate = 0.00 (0 / 188), avg. gap size = 0.0 (0 / 0) 16 22.03 2.04 2.04 chr1qtel1M 548871 548919 (451081) (AGGG)n#Simple_repeat 1 49 (0) m_b42s252i11 1493 chr1qtel1M 548871 AGGGA-AGAGGCAGAGTGGGAGTGGAGGGTGGGAAGGAGGCAGTTAGGGA 548919 -i v i v - v i v vv (AGGG)n#Simpl 1 AGGGAGGGAGGGAGGGAGGGAG-GGAGGGAGGGAGGGAGGGAGGGAGGGA 49 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.04 (2 / 48), avg. gap size = 1.00 (2 / 2) 317 27.68 7.14 0.00 chr1qtel1M 549486 549597 (450403) MIRc#SINE/MIR 122 241 (27) m_b42s601i23 1494 chr1qtel1M 549486 CCTCTGTTTCACCATCTGCAAAATGAGACTAATAAG---TGC---ACCAA 549529 v vi i i iv v--- ---i v MIRc#SINE/MIR 122 CCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTA 171 chr1qtel1M 549530 GTTC-CAGGGTGGCTGTGAAGGTGAAGTGAGATCAAATGGGCAAGAG-GC 549577 vi - v i i i v i v vi iv ii i - MIRc#SINE/MIR 172 CCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGC 221 chr1qtel1M 549578 TTTGGCAAACATAAAGTGCT 549597 vv vii MIRc#SINE/MIR 222 TTTGTAAACTGTAAAGTGCT 241 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 35.17 CpG sites = 17, Kimura (unadjusted) = 35.17 Transitions / transversions = 1.21 (17/14) Gap_init rate = 0.04 (4 / 111), avg. gap size = 2.00 (8 / 4) 18 16.26 0.00 4.65 chr1qtel1M 551286 551330 (448670) (CCCTC)n#Simple_repeat 1 43 (0) m_b42s252i12 1495 chr1qtel1M 551286 CCCTCTCCTCCCAGCGCCTCCCCTCCGGCCTCCTCTCCCCTTCCC 551330 i vv v -- i i (CCCTC)n#Simp 1 CCCTCCCCTCCCCTCCCCTCCCCTCC--CCTCCCCTCCCCTCCCC 43 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.05 (2 / 44), avg. gap size = 1.00 (2 / 2) 13 16.94 3.03 0.00 chr1qtel1M 551557 551589 (448411) (CCCGCC)n#Simple_repeat 1 34 (0) m_b42s252i13 1496 chr1qtel1M 551557 CCCGCCCCCG-CCGCGTCCTGCCCCCCGCCCCCG 551589 - v i ivv (CCCGCC)n#Sim 1 CCCGCCCCCGCCCCCGCCCCCGCCCCCGCCCCCG 34 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 13 17.64 0.00 3.03 chr1qtel1M 551713 551746 (448254) (GGGAA)n#Simple_repeat 1 33 (0) m_b42s252i14 1497 chr1qtel1M 551713 GGGAAGGGGAGGGAAAGGAAGGACCAGGGGAGGG 551746 i i -vv i (GGGAA)n#Simp 1 GGGAAGGGAAGGGAAGGGAAGG-GAAGGGAAGGG 33 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 346 30.34 12.56 1.30 chr1qtel1M 552966 553172 (446828) L3#LINE/CR1 3648 3877 (222) m_b42s601i24 1498 chr1qtel1M 552966 GCGGTTAGAAGGGCAGCGATGAGGCTGCTGAAGCATC-----ACTCTGC- 553009 vii i i - iv v v vi ----- iv i- L3#LINE/CR1 3648 GCGTCCAGAGGAG-AGCGACCAGGATGGTGAAGGGTCTGGAAACCATGTC 3696 chr1qtel1M 553010 ---TGGGGAATCGCTGAAAGAGCTGGGAAGGGTTAGTCTGGAGAAGAGAA 553056 --- i iv i i i i v v i L3#LINE/CR1 3697 ATATGAGGAACGGTTGAAGGAACTGGGGATGTTTAGCCTGGAGAAGAGAA 3746 chr1qtel1M 553057 TCTTTGGAAGGAGGCTTCTTAGCTCTCTTCAG------GGAGGAC----- 553095 vvi i - i v vv v i------ i i ----- L3#LINE/CR1 3747 GACTTAG-AGGAGACATGATAGCTGTCTTCAAATATTTGAAGGGCTGTCA 3795 chr1qtel1M 553096 -GGGAAAGAGGCACCAGGCTCTTGCT---TGGCCCTGGAGGGTAAGACCG 553141 - v i v ii i iv v --- i ii i ii ii L3#LINE/CR1 3796 TGTGGAAGAGGGATTAGACTTATTCTGTGTGGCTCCAGAGGGCAGAACTA 3845 chr1qtel1M 553142 GGA--AAAGGACGGAAGCAACAAAGATGACAAA 553172 -- v ii iv ii - i i L3#LINE/CR1 3846 GGACCAATGGGTGGAAGTTACAGGGA-GGCAGA 3877 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 40.03 CpG sites = 41, Kimura (unadjusted) = 40.91 Transitions / transversions = 1.95 (41/21) Gap_init rate = 0.05 (11 / 206), avg. gap size = 2.64 (29 / 11) 13 20.57 0.00 4.88 chr1qtel1M 554071 554113 (445887) (GAGCTGG)n#Simple_repeat 1 41 (0) m_b42s252i15 1499 chr1qtel1M 554071 GAGCCTGGGCGCTGGGAGCTGGAGGCTGTTAGCATAGGGGCTG 554113 - v ii vv - i i (GAGCTGG)n#Si 1 GAG-CTGGGAGCTGGGAGCTGGGAGCTGGGAGC-TGGGAGCTG 41 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.00 (2 / 2) 270 31.72 4.76 0.92 chr1qtel1M 554160 554264 (445736) MIR#SINE/MIR 10 118 (144) m_b42s601i25 1500 chr1qtel1M 554160 CATAG-GGCAGAGAGC-TAGTCTC-AGAGCTAGGAGTGATTGGGTTTGAG 554206 - ivi -ii v -i i - v vi i i MIR#SINE/MIR 10 CATAGTGGTTAAGAGCACGGGCTCTGGAGCCAG-ACTGCCTGGGTTCGAA 58 chr1qtel1M 554207 TCTTAACT--GACACATATTAGCTGTGTTACCCTGAGCAAGACATTCAGC 554254 iiii -- v v i v i i vi i i i MIR#SINE/MIR 59 TCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAAC 108 chr1qtel1M 554255 CCCCTAATGC 554264 i iivi MIR#SINE/MIR 109 CTCTCTGTGC 118 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 38.65 CpG sites = 24, Kimura (unadjusted) = 44.46 Transitions / transversions = 2.67 (24/9) Gap_init rate = 0.05 (5 / 104), avg. gap size = 1.20 (6 / 5) 313 32.22 2.22 0.00 chr1qtel1M 554168 554257 (445743) MIRc#SINE/MIR 24 115 (153) m_b42s601i26 1500 chr1qtel1M 554168 AGAGAGCTAGTCTCAGAGCTAGGAGTGATTGGGTTTGAGTCTTAACT--G 554215 vi i v ii ii ivivi i iiii -- MIRc#SINE/MIR 24 AGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTG 73 chr1qtel1M 554216 ACACATATTAGCTGTGTTACCCTGAGCAAGACATTCAGCCCC 554257 v v i v i i v i i i i MIRc#SINE/MIR 74 CCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 40.90 CpG sites = 21, Kimura (unadjusted) = 45.44 Transitions / transversions = 2.62 (21/8) Gap_init rate = 0.01 (1 / 89), avg. gap size = 2.00 (2 / 1) 325 23.97 14.88 0.00 chr1qtel1M 554492 554612 (445388) C MIRc#SINE/MIR (39) 229 91 m_b42s601i27 1501 chr1qtel1M 554492 TTTCCAAAACACTTT-GTAAACAT---CTCTTTCGATCCTCACAAC---C 554534 v i i -ii v --- v i --- C MIRc#SINE/MIR 229 TTTACAAAGCGCTTTCACATACATTATCTCATTTGATCCTCACAACAACC 180 chr1qtel1M 554535 CTGAAAAGTAGTTAC------TATGGTTTTCCCCAATTTACAGATGAGGA 554578 vi i vi v------ vi v v C MIRc#SINE/MIR 179 CTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGA 130 chr1qtel1M 554579 CACCAAAGCT----GAGATTAGGAGA-TGGCTCAGTGTC 554612 v ii i ---- i i v - v i iv C MIRc#SINE/MIR 129 AACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTC 91 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 28.13 CpG sites = 16, Kimura (unadjusted) = 29.30 Transitions / transversions = 1.23 (16/13) Gap_init rate = 0.05 (6 / 120), avg. gap size = 3.00 (18 / 6) 590 27.62 13.45 1.12 chr1qtel1M 555246 555483 (444517) C MIRc#SINE/MIR (0) 268 2 m_b42s601i28 1502 chr1qtel1M 555246 AATAATATTAAGAGAGAGCATTTATGGAGGGCATTAAGGTTTACAAAGCA 555295 v v?vvvvi i iv vi v vi i C MIRc#SINE/MIR 268 AATAATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCG 219 chr1qtel1M 555296 CTT--------GTGATTTCATTGGATTCTCCAAACAGC----TGAGAGAG 555333 --------i v i v i vv i ---- iv C MIRc#SINE/MIR 218 CTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAG 169 chr1qtel1M 555334 GTAAGT--GCTATTACTATC--------ATAGATAAGGAAAT-------- 555365 i i v-- v i -------- i i i-------- C MIRc#SINE/MIR 168 GCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC 119 chr1qtel1M 555366 --AAAGATTGATTGACTTTCCCAGGGTCATCCAGTTAGTAAGCATCTTGG 555413 -- i i i v v i iv i iiv vvi C MIRc#SINE/MIR 118 AGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAG 69 chr1qtel1M 555414 TCTGAATTTAAACTCAGGTCTTACTGATTCTAAGTCCAACTCTCTTGCCC 555463 i v i i ii i v i i iiv -i C MIRc#SINE/MIR 68 CCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTT-TCC 20 chr1qtel1M 555464 ACTGTAGCCCCACCTGCCTC 555483 i - v - C MIRc#SINE/MIR 19 ACTGCA-CCACA-CTGCCTC 2 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 34.14 CpG sites = 38, Kimura (unadjusted) = 35.57 Transitions / transversions = 1.41 (38/27) Gap_init rate = 0.04 (9 / 237), avg. gap size = 3.89 (35 / 9) 315 28.71 3.45 8.70 chr1qtel1M 556086 556230 (443770) L2c_3end#LINE/L2 339 476 (2) m_b43s601i3 1503 chr1qtel1M 556086 TGTACTTAATTACTTACATGTC-ATTTTCCCCACTGGAATATAAAC-CCT 556133 v ivi ii ? -i i i i i v i i i - L2c_3end#LINE 339 TGTAATTGTCTGTTTACNTGTCTGTCTCCTCCACTAGACTGTGAGCTCCT 388 chr1qtel1M 556134 TGAAGA---AAATAATGGCTTTTGCCACTCTTTGTATACCCAGTTCAGCA 556180 i i---ii ivi v v -i - v i------ L2c_3end#LINE 389 TGAGGGCAGGGACCGTGTCTTAT-TCA-TCTTTGTATCCCCAGC------ 430 chr1qtel1M 556181 CTATGCCTGGCAGTTAATAAGTGTTTCATGAATGCTTGTTGACTGAATGA 556230 ---- vv i i i i iv i i v L2c_3end#LINE 431 ----GCCTGGCACATAGTAGGCGCTCAATAAATGTTTGTTGAATGAATGA 476 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 34.59 CpG sites = 27, Kimura (unadjusted) = 38.46 Transitions / transversions = 2.45 (27/11) Gap_init rate = 0.10 (15 / 144), avg. gap size = 1.13 (17 / 15) 20 32.20 2.60 0.00 chr1qtel1M 556553 556629 (443371) (AG)n#Simple_repeat 1 79 (0) m_b43s252i0 1504 chr1qtel1M 556553 AGGGAGAAAAAAAGGGA-AGGGGGTGAGTGA-AGAACAAGAGAGAGATAG 556600 i i i i i - i i v v - ivi v (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr1qtel1M 556601 AGACAGAGAGACCCAGAGAGAAACACAGA 556629 v vvv i v v (AG)n#Simple_ 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGA 79 Matrix = Unknown Transitions / transversions = 1.00 (10/10) Gap_init rate = 0.03 (2 / 76), avg. gap size = 1.00 (2 / 2) 3353 28.40 3.38 1.92 chr1qtel1M 557560 559096 (440904) L1M5_orf2#LINE/L1 1084 2642 (652) m_b43s551i0 1505 chr1qtel1M 557560 GCTAAGAGTTGGTTTTATGAAAAAAAACCCCAACAAAATAGATAAACCTT 557609 i i i i v i ----i i v i L1M5_orf2#LIN 1084 GCCAAAAGCTGGTTCTTTGAAAAGA----TCAATAAAATTGATAAACCTC 1129 chr1qtel1M 557610 TAGCTAATTTGATTAG--AAAAAGGAAAGAAGAAAATCAAATTGTTAATT 557657 ? ivi i i-- i i v -- iii v L1M5_orf2#LIN 1130 TAGCNAGACTGATCAAGAAAAAAAGAGAGAAGACA--CAAATTACCAATA 1177 chr1qtel1M 557658 TCAAAAATGAAAAGAAAGAACTTTCCGCCAATTAAGAAGAAATCAGAGCA 557707 ii iii vv iv ii vi ivviv v i i ivi L1M5_orf2#LIN 1178 TCAGGAATGAAAAAGGAGACATCACTACAGATCCTACAGACATTAAAAGG 1227 chr1qtel1M 557708 ATAATTAGCAGTTATTTTGCCCAATTATATGCCAATAAATTTGATAACCT 557757 v viiv v vv i v ? i L1M5_orf2#LIN 1228 ATAATAAGAGAATATTATGAACAACTTTATGCCAATAAATTTGANAACTT 1277 chr1qtel1M 557758 AAGTGAAATGGAGGAATACCT-ACAAAATATAGATTGCCCAGGTTAACAG 557806 ii vi v -iv i i i? i v iii i ?v L1M5_orf2#LIN 1278 AGATGAAATGGACAAATTCCTTGAAAAACACAANTTACCAAAACTGACNC 1327 chr1qtel1M 557807 AAGAGGAAATAAATTATTTAAATAGTTTCAT-TTTAGAAAAAGAAATAGA 557855 i i vv i i iiii - i vv - v L1M5_orf2#LIN 1328 AAGAAGAAATAGAAAATCTGAATAGCCCTATATCTATTAAA-GAAATTGA 1376 chr1qtel1M 557856 ACAAACTATTAATCAACCCCCTAAGAAAAAAATCTCCAGGGCCAGATAGA 557905 ivviiv -v ii iv v i v v i v L1M5_orf2#LIN 1377 ATTTGTAATTAA-AAACCTTCCCACAAAGAAAACTCCAGGCCCAGATGGC 1425 chr1qtel1M 557906 TTTACATGTGAATTCTACCAAACATTTAAAGAACAATTAATTCCAATACT 557955 i vv i v v v vi L1M5_orf2#LIN 1426 TTCACTGGTGAATTCTACCAAACATTTAAGGAAGAAATAATACCAATCTT 1475 chr1qtel1M 557956 AGGCAAACTATTTGAAAAAATAGGAGAAGAAGGAGTCCTACCAAATTCCT 558005 vi v iv i i i i iiv v v i v L1M5_orf2#LIN 1476 ACACAAACTCTTCCAGAAAATAGAAAAAGAGGGAACACTTCCCAACTCAT 1525 chr1qtel1M 558006 TTTATGACACAGATACAGTGTTGATACCTAAACCAGGTAGGATGAAA--A 558053 vi viii i?iivi v ? ii -- v v -- L1M5_orf2#LIN 1526 TTTATGAGGCCAGCATNACCCTGATACCAAAACCNGACA--AAGACATTA 1573 chr1qtel1M 558054 CAGAGAAAGAAAATTATAGACCAGTTTCCCTAATGAATATTGATGCAAAA 558103 iii i i v v i v L1M5_orf2#LIN 1574 CAAGAAAAGAAAATTACAGACCAATATCCCTCATGAACATAGATGCAAAA 1623 chr1qtel1M 558104 ATCTTAAATAAAATATTAGCAATGAGATTACAGAAA---GTCAACCCCAG 558150 i ? i vvv v v v ---i v v--- L1M5_orf2#LIN 1624 ATCCTNAACAAAATATTAGCAAATCGAATCCAGCAATATATAAAA---AG 1670 chr1qtel1M 558151 GCTAATACACCATGACCAAGTAGGATTTATACCAGGAATGCAGGGTTGGT 558200 v i i i v i L1M5_orf2#LIN 1671 GATAATACATCATGACCAAGTGGGGTTTATCCCAGGAATGCAAGGTTGGT 1720 chr1qtel1M 558201 TCAATATTAGGAAAATTATTAGCATAGTCAACTATATCAATA-ACCAAAC 558249 i i v i viv i iii i iv i i i - vi v L1M5_orf2#LIN 1721 TTAACATTCGAAAATCAATCAATGTAATTCACCATATTAACAGAATAAAG 1770 chr1qtel1M 558250 TAACAAAAATCATATGATTATCTCAATAGATTCA-AAAAAGCATTCGATA 558298 v i- i v - i i L1M5_orf2#LIN 1771 GAG-AAAAATCATATGATCATCTCAATAGATGCAGAAAAAGCATTTGACA 1819 chr1qtel1M 558299 AAATCTAACACTCATTCCTTTTAAAAACT-TGAGAGAGTATAGGAATAAA 558347 ii i v vv - v vi ii- i L1M5_orf2#LIN 1820 AAATTCAACACCCATTCATGATAAAAACTCTCAGCAAAC-TAGGAATAGA 1868 chr1qtel1M 558348 TGGACTTTTCTTTAAAATGATCAGTAGTATCTA----AAACCATCAGCAT 558393 v ivvi i i vv v ivi i ---- vv ?v L1M5_orf2#LIN 1869 AGGGAACTTCCTCAACCTGATAAAGGGCATCTACGAAAAACCTACAGCNA 1918 chr1qtel1M 558394 GCATCATATGTAATAGGGACAAACTAGAACCATTCCAAATAAGATTAGGG 558443 i iv i v v ? ii ?v v vvv ii i L1M5_orf2#LIN 1919 ACATCATACTTAATGGTGAAANACTGAANGCTTTCCCCCTAAGATCGGGA 1968 chr1qtel1M 558444 GTGAAACAAGGTTGTCCACTATCACCATTACTATTCAACATTCTATTAGA 558493 iii i v i ? i v v i i L1M5_orf2#LIN 1969 ACAAGACAAGGATGTCCGCTNTCACCACTTCTATTCAACATTGTACTGGA 2018 chr1qtel1M 558494 GATGTTAGCTTTGGCAATAAGAGAAGAAAAAGAGATTAAAGG------AA 558537 i vi ivvv iv i v ------i L1M5_orf2#LIN 2019 GGTCCTAGCCAGTGCAATAAGGCAAGAAAAAGAAATAAAAGGCATAAAGA 2068 chr1qtel1M 558538 TTAGAG---------TAAA-TTATCACTCTTTGTAGGTGATATGATGGTA 558577 i i--------- -i i ?i v i i i i v ? L1M5_orf2#LIN 2069 TTGGAAAGGAAGAAATAAAACTGTCNTTATTCGCAGATGACATGATTGTN 2118 chr1qtel1M 558578 TTCTTAGAGAATCCTAG------TACTAAAAAACTACTAGAAACAATTCA 558621 v v i ? i------ v ? vi vvi L1M5_orf2#LIN 2119 TACGTAGAAAATCCNAAAGAATCTACAAANAAACTACTAGAACTAATAAG 2168 chr1qtel1M 558622 CAACTTTAGCAAAGTTACAGGATACAAAATAAATTCACAGAAATCATCAG 558671 ii v i ii ? ii v vi i viv L1M5_orf2#LIN 2169 TGAATTTAGCAAGGTCGCNGGATACAAGGTCAATATACAAAAATCAATTG 2218 chr1qtel1M 558672 CATTTTTATATATTATCAACAAAGTCCCGCAGCAAGAGATACAAAGAGAA 558721 i i i v vvvii v iv v i vi? i iv L1M5_orf2#LIN 2219 TATTTCTATATACTAGCAACAAACAATTGGAAAATGAAATTTNAAAAACA 2268 chr1qtel1M 558722 ATTCCATTCAAAATAACTGTAGATGGTATGAAATATTTGGGAATCTATCT 558771 v i v i vvi i viii ? i i vv L1M5_orf2#LIN 2269 ATACCATTTACAATAGCATCAAAAAACATNAAATACTTAGGAATAAATCT 2318 chr1qtel1M 558772 TCCAAGGGAAAGTCAGGGACTATA---TGAACACAACTACAAAACACTTT 558818 vv ii? vivv i iv ? --- --- - v L1M5_orf2#LIN 2319 AACAAAANATGTGCAAGACCTNTACACTGAA---AACTACAAAACA-TTG 2364 chr1qtel1M 558819 CCAACAAA---TAAAGTCAGATCTAATCAGTTGAAAAAATATCAAATGCT 558865 ii v i --- -v i vi iv i i i vvv i L1M5_orf2#LIN 2365 CTGAGAGAAATTAAAG-AAGACCTAAATAAATGGAGAGATATACCATGTT 2413 chr1qtel1M 558866 CATGGGT--AAATTGAGTGAATATAATAAAAATGACAATATTACCTAAAT 558913 i --i -- v v vi ? i v vi v i L1M5_orf2#LIN 2414 CATGGATTGGAA--GACTCAATATTGTNAAGATGTCAATTCTCCCCAAAT 2461 chr1qtel1M 558914 TAATCTACTTATTTAATGCCATACCAATCAAACTCCCAAGAAATTATTT- 558962 i ivv i v v v iv ii v - L1M5_orf2#LIN 2462 TGATCTATAGATTCAATGCAATCCCAATCAAAATCCCAGCAGGTTTTTTT 2511 chr1qtel1M 558963 -TACAAATTTAGAAAAAATAATAACACAGTTCATCTGGAAGGACAAAAGA 559011 - v -- v iv i vvi v i i v ivi i L1M5_orf2#LIN 2512 GTAGAAATT--GACAAGCTGATTCTAAAATTTATATGGAAATGCAAAGGA 2559 chr1qtel1M 559012 TCAAGAAT-TTCAAGGGAA--TTGATGAAAAAAGAAATGCCAATGAAGGT 559058 i ? -vi iiv -- -i i ---- v vv v L1M5_orf2#LIN 2560 CCNAGAATAGCCAAAACAATCTTGA-AAAAGAAGAA----CAAAGTTGGA 2604 chr1qtel1M 559059 GGCCTAGCTGTGCCAGACCT-AAAATTATATTATAAAGC 559096 v vi vv i ? i? - i i - L1M5_orf2#LIN 2605 GGACTTACACTACCNGATNTCAAGACT-TATTATAAAGC 2642 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 36.81 CpG sites = 242, Kimura (unadjusted) = 37.27 Transitions / transversions = 1.30 (242/186) Gap_init rate = 0.03 (51 / 1536), avg. gap size = 1.61 (82 / 51) 190 21.97 0.00 2.44 chr1qtel1M 559217 559258 (440742) C L2#LINE/L2 (1173) 1909 1869 m_b43s601i4 1506 chr1qtel1M 559217 CAGGGATGTATAGACAGCTTTTTCAAGAAGTTTCATTGTGAA 559258 v - i i i i iii i C L2#LINE/L2 1909 CAGCGA-GTATAGACAACTCTTTCGAGGAGTTTTGCTGTAAA 1869 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 24.41 CpG sites = 8, Kimura (unadjusted) = 28.03 Transitions / transversions = 8.00 (8/1) Gap_init rate = 0.02 (1 / 41), avg. gap size = 1.00 (1 / 1) 559 20.55 7.53 0.00 chr1qtel1M 559304 559449 (440551) MIRc#SINE/MIR 84 240 (28) m_b43s601i5 1507 chr1qtel1M 559304 GTTCTATGTCCCTGAGCAAATCACTGAACCTCTTTCAGCCTCAGTATCCT 559353 i v i v i i i v i v v MIRc#SINE/MIR 84 GCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCT 133 chr1qtel1M 559354 CATCCATAAATCGGGGATAATAATA-GTGCCTGG--GACC---CAGAGTT 559397 ii vi -v iv --v --- i MIRc#SINE/MIR 134 CATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTT 183 chr1qtel1M 559398 GTTGTGAACATCAAGTGAGA-AA---ATGTGAAGG-GCTTTGCAAACCCT 559442 iv i - --- i - i iv MIRc#SINE/MIR 184 GTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTTTGTAAACTGT 233 chr1qtel1M 559443 GAAGCAC 559449 i ii MIRc#SINE/MIR 234 AAAGTGC 240 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 24.53 CpG sites = 19, Kimura (unadjusted) = 24.53 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.04 (6 / 145), avg. gap size = 1.83 (11 / 6) 323 16.67 28.70 0.00 chr1qtel1M 559921 560028 (439972) MIRb#SINE/MIR 13 151 (117) m_b43s601i6 1508 chr1qtel1M 559921 GTGGGGTTGTGAAAAAGGCACCAGCTCTGGAGT-AGAAAGACCTAGTT-- 559967 v iv i ii vi i - v i v -- MIRb#SINE/MIR 13 GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTC 62 chr1qtel1M 559968 --ATCC------TGCCTTTTA------------------GCAAGTAACTT 559991 -- ------ vi ------------------ v MIRb#SINE/MIR 63 GAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTT 112 chr1qtel1M 559992 AA--TCTGTGGGTCTCAGTTTCCTCATCTGTAAAATGGG 560028 -- v i i MIRb#SINE/MIR 113 AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 151 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 19.01 CpG sites = 10, Kimura (unadjusted) = 19.01 Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.06 (6 / 107), avg. gap size = 5.17 (31 / 6) 306 19.30 11.24 1.02 chr1qtel1M 560686 560774 (439226) MER63D#DNA/hAT-Tip100 340 437 (624) m_b43s502i0 1509 chr1qtel1M 560686 GAGCATTTCCACCTGGGAAACTGGCAAAC--TATAAATTAGGATTTGATT 560733 i v vv ii -- i i ii MER63D#DNA/hA 340 GAGTATTTACACCACGGAAATCGGCAAACGCTACAAATCAGGGCTTGATT 389 chr1qtel1M 560734 TGT-ATTTTGAGGGATTGTCTACACTTAA-------ATTGATAAAATGT 560774 i -i -vv v ------- v v MER63D#DNA/hA 390 TATTGTTTTG-TTGATTGTCTAGACTTAAGAAAGTGATGGAGAAAATGT 437 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 21.10 CpG sites = 9, Kimura (unadjusted) = 22.53 Transitions / transversions = 1.12 (9/8) Gap_init rate = 0.05 (4 / 88), avg. gap size = 2.75 (11 / 4) 419 17.95 1.27 1.27 chr1qtel1M 561083 561161 (438839) MIR3#SINE/MIR 93 171 (37) m_b43s601i7 1510 chr1qtel1M 561083 TAGGCAAATCACTTGACTTC-CTGGGACTCAGTTTCTTCATCTGTAAAAA 561131 i i v i - v i - MIR3#SINE/MIR 93 TGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGT-AAAA 141 chr1qtel1M 561132 TGAGGGGGTTGGATTAAATGGCTCCCAAAG 561161 i i iiii i i MIR3#SINE/MIR 142 TGAGGGGGTTGGACTAGATGATCTCTAAGG 171 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 21.59 CpG sites = 12, Kimura (unadjusted) = 21.59 Transitions / transversions = 6.00 (12/2) Gap_init rate = 0.03 (2 / 78), avg. gap size = 1.00 (2 / 2) 400 32.64 8.04 1.51 chr1qtel1M 561536 561846 (438154) L2#LINE/L2 2301 2631 (451) m_b43s601i8 1511 chr1qtel1M 561536 TCTCATGGACTCACTCATCATCCCTATGTTGATGAGTCTTAAATTTATTT 561585 vi i vvi i iv i v ii v L2#LINE/L2 2301 TCTCATGGCTTTAAATACCATCTATATGCTGATGACTCCCAAATTTATAT 2350 chr1qtel1M 561586 CTCTAATGGCCAAG--CTCTCTGCTGACCTCCAATATCACATCTCCCACT 561633 i --- vi -- iv v ivv ii v v L2#LINE/L2 2351 CTCCA---GCCCGGACCTCTCCCCTGAACTCCAGACTCGTATATCCAACT 2397 chr1qtel1M 561634 --CTAGCAGATAT-TCAAATTGGATGTACTATACACATCTTAAACTCAAC 561680 -- viv i - v v viv vi i i L2#LINE/L2 2398 GCCTACTCGACATCTCCACTTGGATGTCTAATAGGCATCTCAAACTTAAC 2447 chr1qtel1M 561681 --------AACT-------TGATCTTTTCCCCACAATTCTTCCCGCTTCC 561715 -------- ------- - i v vi v i - i L2#LINE/L2 2448 ATGTCCAAAACTGAACTCCTGATC-TTCCCCCTCAAACCTGCTC-CTCCC 2495 chr1qtel1M 561716 AT-GTTTT--CTATTATTGCCCAAGACGTTGCCATCCTGCCAGTGACTCC 561762 ii- i -- i iviv i?v v i iviv v vi v L2#LINE/L2 2496 GCAGTCTTCCCCATCTCAGTNAATGGCAACTCCATCCTTCCAGTTGCTCA 2545 chr1qtel1M 561763 AGCTTACAACCAAGGTGTC--TCTCAACTCCTCAATTTCCCTCCCCCCTA 561810 i iv v vv v --i ii vv i v v iv L2#LINE/L2 2546 GGCCAAAAACCTTGGAGTCATCCTTGACTCCTCTCTTTCTCTCACACCCC 2595 chr1qtel1M 561811 ATATCCAATCTGTTGACAAGGATCGTCAATCTTACC 561846 i ii iii ivvii iiiii L2#LINE/L2 2596 ACATCCAATCCATCAGCAAATCCTGTCGGCTCTACC 2631 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 41.97 CpG sites = 56, Kimura (unadjusted) = 44.33 Transitions / transversions = 1.27 (56/44) Gap_init rate = 0.04 (13 / 310), avg. gap size = 2.31 (30 / 13) 543 25.46 1.43 12.11 chr1qtel1M 561909 562118 (437882) C MIR#SINE/MIR (0) 262 73 m_b43s601i9 1512 chr1qtel1M 561909 AATAATAACTCATGTTTAAACAGCATCTTACTTTGTGACAGGCACTGTGT 561958 i v ii vvv i- v v vi C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCG-CTTACTATGTGCCAGGCACTGTTC 214 chr1qtel1M 561959 TAAGTATTTTATAAATATTATCTCAGTTAATATTCACAACAATCCTGGGA 562008 iii i vi v v vi i iv C MIR#SINE/MIR 213 TAAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGA 164 chr1qtel1M 562009 GGCAGACACTGTGATTA-ATCCATTTTACAGATGGGAGGCAGACACTGTT 562057 i ii i v -vi i ----- v -- C MIR#SINE/MIR 163 GGTAGGTACTATTATTATCCCCATTTTACAGATGAG-----GAAACTG-- 121 chr1qtel1M 562058 ATTAACCCAATTTATAGATTTACAGAAGTT--GTGACTTGCCTAGCATTA 562105 --------------- iivi v i -- i i ivi i C MIR#SINE/MIR 120 ---------------AGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCA 86 chr1qtel1M 562106 CACAGCTACTAAG 562118 v C MIR#SINE/MIR 85 CACAGCTAGTAAG 73 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 29.64 CpG sites = 28, Kimura (unadjusted) = 31.31 Transitions / transversions = 1.47 (28/19) Gap_init rate = 0.12 (25 / 209), avg. gap size = 1.04 (26 / 25) 555 23.61 1.09 14.81 chr1qtel1M 561935 562118 (437882) C MIRb#SINE/MIR (27) 241 80 m_b43s601i10 1512 chr1qtel1M 561935 CTTACTTTGTGACAGGCACTGTGTTAAGTATTTTATAAATATTATCTCAG 561984 v v i iii i vii v C MIRb#SINE/MIR 241 CTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACATGCATTATCTCAT 192 chr1qtel1M 561985 TTAATATTCACAACAATCCTGGGAGGCAGACACTGTGATTAATCCATTTT 562034 vi i v i ii i i v i--i C MIRb#SINE/MIR 191 TTAATCCTCACAACAACCCTGCGAGGTAGGTATTATTATC--CCCATTTT 144 chr1qtel1M 562035 ACAGATGGGAGGCAGACACTGTTATTAACCCAATTTATAGATTTACAGAA 562084 i ----- v ----------------- ii i v i C MIRb#SINE/MIR 143 ACAGATGAG-----GAAACTG-----------------AGGCTCAGAGAG 116 chr1qtel1M 562085 GTT--GTGACTTGCCTAGCATTACACAGCTACTAAG 562118 -- i i ivi i v C MIRb#SINE/MIR 115 GTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAG 80 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 27.70 CpG sites = 26, Kimura (unadjusted) = 28.72 Transitions / transversions = 2.36 (26/11) Gap_init rate = 0.14 (25 / 183), avg. gap size = 1.04 (26 / 25) 296 28.20 3.39 0.83 chr1qtel1M 564743 564860 (435140) C MIR#SINE/MIR (81) 181 61 m_b43s601i11 1513 chr1qtel1M 564743 CTCATAGCCACCAGAAGAGGTAAG-ACTGTC-TTATTTCCATTCTAGAGC 564790 i i v vv v i - i i- ii i v v C MIR#SINE/MIR 181 CTCACAACAACCCTATGAGGTAGGTACTATTATTATCCCCATTTTACAGA 132 chr1qtel1M 564791 TGAGGAAAC--GCTCTCTGAGACATGAAGTGACTTTTCCATAGTCAGCAC 564838 --ivv v v vi v i vi vi - C MIR#SINE/MIR 131 TGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCA-CAC 83 chr1qtel1M 564839 AGCTAGTGAGGGCCAGGGGCAG 564860 i v v i v i C MIR#SINE/MIR 82 AGCTAGTAAGTGGCAGAGCCGG 61 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 34.41 CpG sites = 16, Kimura (unadjusted) = 35.72 Transitions / transversions = 0.94 (16/17) Gap_init rate = 0.03 (4 / 117), avg. gap size = 1.25 (5 / 4) 340 21.14 13.82 0.00 chr1qtel1M 565189 565311 (434689) C L2d_3end#LINE/L2 (12) 504 365 m_b43s601i12 1514 chr1qtel1M 565189 TCAATAAGCATTTGTTAAGTCCCAAA---------AGCACTGTGCTAAAC 565229 i i i i iv v v--------- ii C L2d_3end#LINE 504 TCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTGTGCTAGGC 455 chr1qtel1M 565230 CCTG--GGGAACAAAAAAGAGGCAAAAGACA--GTTCCTGCCCTCAAGGA 565275 v -- i ? i?i i v -- i C L2d_3end#LINE 454 GCTGTGGGGAACGANAAAANAGTATAAGACATGGTCCCTGCCCTCAAGGA 405 chr1qtel1M 565276 CATTACAGTCTACCT---GCAACAAG-CAAACACACAGGA 565311 vv i vi --- vi - v v C L2d_3end#LINE 404 GCTTACAATCTAGTTGGGGAGACAAGACTAACACACATGA 365 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 23.50 CpG sites = 15, Kimura (unadjusted) = 25.70 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.04 (5 / 122), avg. gap size = 3.40 (17 / 5) 13 15.24 0.00 3.33 chr1qtel1M 566219 566249 (433751) (CCCCA)n#Simple_repeat 1 30 (0) m_b43s252i1 1515 chr1qtel1M 566219 CCCCGCCCCACCTCACCCGGACCCCACCACA 566249 i i -v v (CCCCA)n#Simp 1 CCCCACCCCACCCCACCC-CACCCCACCCCA 30 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.03 (1 / 30), avg. gap size = 1.00 (1 / 1) 181 4.00 0.00 0.00 chr1qtel1M 567125 567149 (432851) MIR3#SINE/MIR 117 141 (67) m_b43s601i13 1516 chr1qtel1M 567125 GGCCTCAGTTTCCTCATCTGTATAA 567149 v MIR3#SINE/MIR 117 GGCCTCAGTTTCCTCATCTGTAAAA 141 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 4.13 CpG sites = 0, Kimura (unadjusted) = 4.13 Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 24 2.77 0.00 7.50 chr1qtel1M 567174 567216 (432784) (CCCCTC)n#Simple_repeat 1 40 (0) m_b43s252i2 1517 chr1qtel1M 567174 CCCCTCCCCCCGTCCCTCTCCCTCCTCCCCCTCCCCCTCCCCC 567216 - - i - (CCCCTC)n#Sim 1 CCCCT-CCCCC-TCCCCCTCCC-CCTCCCCCTCCCCCTCCCCC 40 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.07 (3 / 42), avg. gap size = 1.00 (3 / 3) 279 33.00 5.02 3.14 chr1qtel1M 571181 571399 (428601) L1MC3_3end#LINE/L1 426 648 (1884) m_b43s551i1 1518 chr1qtel1M 571181 AAATGCCTGCATGTAGAAAAATATAGCAGCTTT-TTTGTGGTGGCACAGA 571229 vi i iii vivv - ii ii v vv i L1MC3_3end#LI 426 AAAAACCTGCACGCGAATGTTTATAGCAGCTTTATTCATAATCGCCAAAA 475 chr1qtel1M 571230 ATTGGAAATTGAAT--AGATGCCCATCAACTGGGGAATAGCTGAGCAAGC 571277 i ii-- i-- i v iv v i v i i i L1MC3_3end#LI 476 ACTGGAAGC--AACCAAGATGTCCTTCAATAGGTGAATGGATAAACAAAC 523 chr1qtel1M 571278 TGTGGCTCATGAATGTAATGGAATACTGTTGTGCCCTAAGAACTGATGAG 571327 iv vv ii i i vv vv i vvi L1MC3_3end#LI 524 TGTGGTACATCCATACAATGGAATATTATTCAGCGATAAAAAGAAATGAG 573 chr1qtel1M 571328 CAGGCAGGTTTTAGAAAAACTGGAAATGCATGAA--TTGAA-GCAAAGTG 571374 viv i iiviii i ----- v -- i - v v L1MC3_3end#LI 574 CTATCAAGCCACGAAAAGAC-----ATGGATGAATCTTAAATGCATATTG 618 chr1qtel1M 571375 --AAGTGAACAGAACCAA---GAGAAGGTT 571399 -- vii i i--- i i L1MC3_3end#LI 619 CTAAGTGAAAGAAGCCAGTCTGAAAAGGCT 648 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 42.58 CpG sites = 43, Kimura (unadjusted) = 45.42 Transitions / transversions = 1.59 (43/27) Gap_init rate = 0.06 (13 / 218), avg. gap size = 1.38 (18 / 13) 289 28.43 5.93 1.63 chr1qtel1M 571189 571306 (428694) L1ME3G_3end#LINE/L1 426 548 (376) m_b43s551i2 1518 chr1qtel1M 571189 GCATGTAGAAAAAT----ATAGCAGC-TTTTTTGTGGTGGCACAGAATTG 571233 v ii ---- v - v ii i iv i L1ME3G_3end#L 426 GCATGTACAAGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTG 475 chr1qtel1M 571234 GAAATTGAA--TAGATGCCCATCAACTGGGGAATAGCTGAGCAAGCTGTG 571281 i-- -- i i iv i i i ii ii i L1ME3G_3end#L 476 GAAAC--AACCTAAATGTCCATCAATAGGGGAATGGTTAAATAAATTATG 523 chr1qtel1M 571282 GCTCATGAATGTAATGGAATACTGT 571306 ivi vv iiv i L1ME3G_3end#L 524 GTATATCCATACTATGGAATACTAT 548 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 36.52 CpG sites = 24, Kimura (unadjusted) = 38.02 Transitions / transversions = 2.67 (24/9) Gap_init rate = 0.04 (5 / 117), avg. gap size = 1.80 (9 / 5) 357 23.07 2.83 1.87 chr1qtel1M 571202 571307 (428693) L1MD3_3end#LINE/L1 447 553 (2189) m_b43s551i3 1518 chr1qtel1M 571202 TATAGCAGCTTT-TTTGTGGTGGCACAGAATTGGAAATTGAA--TAGATG 571248 - ii ii ? vv i ?i i-- --? L1MD3_3end#LI 447 TATAGCAGCTTTATTCATAATNGCCAAAANCTGGAAAC--AACCNAGATG 494 chr1qtel1M 571249 CCCATCAACTGGGGAATAGCTGAGCAAGCTGTGGCTCATGAATGTAATGG 571298 i ? v v i v i i i iv vv ii L1MD3_3end#LI 495 TCCNTCAACAGGTGAATGGATAAACAAACTGTGGTACATCCATACAATGG 544 chr1qtel1M 571299 AATACTGTT 571307 i L1MD3_3end#LI 545 AATACTATT 553 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 29.90 CpG sites = 16, Kimura (unadjusted) = 29.90 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.04 (4 / 105), avg. gap size = 1.25 (5 / 4) 303 30.47 2.31 1.53 chr1qtel1M 571203 571332 (428668) L1ME4b_3end#LINE/L1 448 578 (314) m_b43s551i4 1518 chr1qtel1M 571203 ATAGCAGC-TTTTTTGTGGTGGCACAGAATTGGAAATTGAA--TAGATGC 571249 v - v ii i v ii i-- -- i i L1ME4b_3end#L 448 ATTGCAGCATTGTTTGTAATAGCAAAAGATTGGAAAC--AACCTAAATGT 495 chr1qtel1M 571250 CCATCAACTGGGGAATAGCTGAGCAAGCTGTGGCTCATGAATGTAATGGA 571299 iv v i i i ii ii i iv vv ii L1ME4b_3end#L 496 CCATCAATAGGGGACTGGTTAAATAAATTATGGTACATCCATACAATGGA 545 chr1qtel1M 571300 ATACTGTTGTGCCCTAAGAACTGATGAGCAGGC 571332 i vvv v i vvi v i L1ME4b_3end#L 546 ATACTATGCAGCCGTAAAAAAGAATGAGGAAGC 578 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 40.56 CpG sites = 24, Kimura (unadjusted) = 40.56 Transitions / transversions = 1.60 (24/15) Gap_init rate = 0.03 (4 / 129), avg. gap size = 1.25 (5 / 4) 229 27.77 2.20 1.09 chr1qtel1M 575162 575252 (424748) C L1ME4a_3end#LINE/L1 (495) 376 285 m_b43s551i5 1519 chr1qtel1M 575162 CTGTGTCCCAGGTAATGTACATTTTGAGAATTTTGTGGC-CATAGCTCCA 575210 v vv vv ? v iiii - ii- viv C L1ME4a_3end#L 376 CTGGGTCAAAGGGTATGNACATTTTTAAGGCTTT-TGATACATATTGCCA 328 chr1qtel1M 575211 AATTGCTTTCCAGAATGTTTGGACCAA-CTGCAGCCCCTCCAG 575252 ii v v v -i i vi v C L1ME4a_3end#L 327 AATTGCCCTCCAGAAAGGTTGTACCAATTTACACTCCCACCAG 285 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.51 CpG sites = 12, Kimura (unadjusted) = 35.51 Transitions / transversions = 0.92 (12/13) Gap_init rate = 0.03 (3 / 90), avg. gap size = 1.00 (3 / 3) 319 28.99 15.09 0.38 chr1qtel1M 575206 575437 (424563) C L1PA17_3end#LINE/L1 (581) 332 67 m_b43s551i6 1519 chr1qtel1M 575206 CTCCAAATTGCTTTCCAGAATGTTTGGACCAACT-GCAGCCCCTCCAG-- 575252 i v iv vi i i i -i vi v i-- C L1PA17_3end#L 332 CTCCAAACTGCTTTCCACAGGGGCTGAACTAATTTACATTCCCACCAACA 283 chr1qtel1M 575253 -------AG-GTTCTCTAGCC--CACCTTTTGGCCA-----TTTTACTTT 575287 ------- - i vvi -- i v?ii v ----- v i C L1PA17_3end#L 282 GTGTATAAGCGTTCCCTTTTCTCCGCANCCTCGCCAACATCTGTTATTTT 233 chr1qtel1M 575288 TTGTCTTCTTG------GCTATTTTG-CTGGCAGTAAGGGGGAACTTCTA 575330 v i i------ i i - i- i iv v ii vv C L1PA17_3end#L 232 TTGACTTTTTAATAATAGCCATTCTGACTGGT-GTGAGATGGTATCTCAT 184 chr1qtel1M 575331 AGTCTCCTTAATTTGCATTTCTATAATTATTATTGCTCTAGAGCATTTTT 575380 v vvii i v i v v v v v C L1PA17_3end#L 183 TGTGGTTTTGATTTGCATTTCTCTGATGATTAGTGATGTTGAGCATTTTT 134 chr1qtel1M 575381 T---------GTTGACAGCTTAAATTTGTCCCTTTGAGAAATGCTTGTTC 575421 --------- i v iv v v i i i ii C L1PA17_3end#L 133 TCATATGTTTGTTGGCCGCTTGTATGTCTTCTTTTGAGAAGTGTCTGTTC 84 chr1qtel1M 575422 ATA-CCCTTGACCATTT 575437 i- i v i C L1PA17_3end#L 83 ATGTCCTTTGCCCACTT 67 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 37.04 CpG sites = 38, Kimura (unadjusted) = 37.75 Transitions / transversions = 1.31 (38/29) Gap_init rate = 0.05 (11 / 231), avg. gap size = 3.27 (36 / 11) 226 26.32 11.40 0.00 chr1qtel1M 575336 575449 (424551) C L1ME4c_3end#LINE/L1 (652) 178 52 m_b43s551i7 1519 chr1qtel1M 575336 CCTTAATTTGCATTTCTATAATTATTATTGCTCTAGAGCATTT------- 575378 i v i i vi vvv v i ------- C L1ME4c_3end#L 178 CTTTAATTTGCATTTCTTTGATTACTAGCGAGGTTGAACATTTTTCCATG 129 chr1qtel1M 575379 --TTTGTTGACAGCTTAAATTTGTCCCTTTGAGAAATGCTTGTTCATA-C 575425 -- v vi? iv vii i ? v v ii i- C L1ME4c_3end#L 128 TGTTTGTTTACTANTTGTATTTCCTCTTNTGTGAATTGTCTGTTCATGTC 79 chr1qtel1M 575426 CCTTGACCATTTGTGTGT---GGTCTT 575449 i v i v i --- C L1ME4c_3end#L 78 CTTTGCCCATTTATCTATTGGGGTCTT 52 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 32.29 CpG sites = 16, Kimura (unadjusted) = 33.63 Transitions / transversions = 1.14 (16/14) Gap_init rate = 0.04 (4 / 113), avg. gap size = 3.25 (13 / 4) 21 13.26 0.00 0.00 chr1qtel1M 575569 575601 (424399) (T)n#Simple_repeat 1 33 (0) m_b43s252i3 1520 chr1qtel1M 575569 TTTTTTGTTTCATCTTTTTTTTTTTTTTTTTTT 575601 v iv i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 33 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 28 0.00 3.33 0.00 chr1qtel1M 576206 576235 (423765) (TCTTTT)n#Simple_repeat 1 31 (0) c_b43s251i0 1521 chr1qtel1M 576206 TCTTTTT-TTTTTCTTTTTCTTTTTCTTTTT 576235 - (TCTTTT)n#Sim 1 TCTTTTTCTTTTTCTTTTTCTTTTTCTTTTT 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 12 9.24 0.00 4.17 chr1qtel1M 577059 577083 (422917) (TCCC)n#Simple_repeat 1 24 (0) m_b43s252i4 1522 chr1qtel1M 577059 TCCCTCCCACCCTCCACCCCCTCCC 577083 v - i (TCCC)n#Simpl 1 TCCCTCCCTCCCTCC-CTCCCTCCC 24 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 1634 28.12 2.72 2.72 chr1qtel1M 577651 578275 (421725) C L1ME5_3end#LINE/L1 (313) 628 4 m_b43s551i8 1523 chr1qtel1M 577651 TTTCACTTAGCATCA-GTTCATGTAAT-TCTCTCCAAGCTTCTCTGTATT 577698 i ii - -- v v- iv v i v v i v C L1ME5_3end#LI 628 TTTCACTCAGCACTATGTT--TTTAAGATCCATCCATGTTGCTATGTGTA 581 chr1qtel1M 577699 CATCTTGCTGGTCATTTCTTACAGAACAATAATATTCCATAACATTCATA 577748 v iiv iii v v vvvv i i iiii v v C L1ME5_3end#LI 580 CATCTAGTCCGTTGCTTCTAACTGCTGCATAGTACTCCATGGTGTGCATC 531 chr1qtel1M 577749 TACCACAATTTACCCAACCATTCTCCAATTGATGAGCAGCCACTCAGTTT 577798 i v i v i v v ii v vviv ii C L1ME5_3end#LI 530 CACCACATTTTACCTATCCACTCTCCCAGTGATGGACACCCAGGTTGCCT 481 chr1qtel1M 577799 CCAGCTTCTAGCCACTACAAACAGGGCTGCCACAAACATTTAGCACATAC 577848 i i iv i iv v ii i--- v i C L1ME5_3end#LI 480 CCAACTCCCCGCCACCACAAACAACGCTGCAATGAACATC---CTCGTAC 434 chr1qtel1M 577849 AGGTCCCTTTC----CCTTCTTTAGTATCTCCTTGGGGTATAAGCCCAGT 577894 v i v---- viv v v i i i vi v C L1ME5_3end#LI 433 ATGTCCCCTTATGGACCTGTGTGAGAATTTCTTTGGGATATATACCCAGG 384 chr1qtel1M 577895 AGAAACACTGCTGGATCAAAGGGTATGCACAGTTTGATAACTT--TTTGG 577942 viiv i i v --- --- - -- i C L1ME5_3end#LI 383 AGCGGAATTGCTGGGTCATAGGGTATGC---GT---ATA-CTTAATTTGA 341 chr1qtel1M 577943 GCA--TAATTCCAGATTGCTCTCCAGAATGGTTGGATTCGTTCACAACTC 577990 vi -- v v i v iiv ii vii C L1ME5_3end#LI 340 CTAAGTACTGCCAGATTGCTCTCCAGAATGGCTGCACCAGTCTACACTCC 291 chr1qtel1M 577991 CACCAAT-GT-CATCAGTGTCCCAGTTTTCCCACATCCCCTCCAACACTC 578038 ii- - v v i vi ? i i v i C L1ME5_3end#LI 290 CACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATCCTCGCCAACACTT 241 chr1qtel1M 578039 ATCATTATTT---TTTCCTGTCATCTTAGCCAATCTGACAGGTGTGTAGT 578085 iv ii--- --- v i v i i i iv C L1ME5_3end#LI 240 GGCATTATCCAGCTTTC---TAATTTTTGCCAGTCTAATAGGTGTAAAGT 194 chr1qtel1M 578086 GGTATCTCAGAGTTGTCTTAATTTGCATTTCTCTGATTAATAATGATTTG 578135 i vv i v v v C L1ME5_3end#LI 193 GATATCTCATTGTTGTTTTAATTTGCATTTCTCTGATTACTAATGAGTTT 144 chr1qtel1M 578136 GAACACTCTTTCATATGAGTGGTAATGATTTTAATTTCATCATCTGAAAA 578185 i iiii vv v iivv ivii v v v C L1ME5_3end#LI 143 GAGCATCTCTTCATATGCTTGTTAGCCTTTCGGGTTTCCTCTTCTGTAAA 94 chr1qtel1M 578186 TTGTCTGTTCATATCCTTTGACCATTTATCAATTGGAG--AATGGCTTGG 578233 i v v v i --?vi v -- C L1ME5_3end#LI 93 TTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGGGGTTNCCGTCTT-- 46 chr1qtel1M 578234 TTTCTTATAAATTAGAGTCAGCTCTCTATATATTTTGGAAAT 578275 i vi v vivv i ii i i i v C L1ME5_3end#LI 45 TTTCTTGTTGATTTGCAGGAGTTCCTTGTATATTCTAGATAT 4 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 34.97 CpG sites = 92, Kimura (unadjusted) = 36.01 Transitions / transversions = 1.16 (92/79) Gap_init rate = 0.04 (26 / 624), avg. gap size = 1.31 (34 / 26) 539 30.95 3.13 3.13 chr1qtel1M 578129 578575 (421425) C L1M5_orf2#LINE/L1 (0) 3294 2848 m_b43s551i9 1523 chr1qtel1M 578129 TGATTTGGAACACTCTTTCATATGAGTGGTAATGATTTTAATTTCATCAT 578178 ?v v i iii i vv iv iiiv v? v v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr1qtel1M 578179 CTGAAAATTGTCTGTTCATATCCTTTGACCATTTATCAATTGGA--GAAT 578226 i vi v vi i v v ?v i-- vv C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTT 3195 chr1qtel1M 578227 GGCTTGGTTTCTTA-TAAATTAGAGTCAGCTCTCTATATATTTTGGAAAT 578275 v -- ? - i ? iv -v i i i v i C L1M5_orf2#LIN 3194 GTCTT--TTTNTTATTGANTTGTAG-GAGTTCTTTATATATTCTGGATAC 3148 chr1qtel1M 578276 GAGGCCTTTATCAGA-ACCTTTAACTGTGAAGATGTTTTCCCAGTTTGTT 578324 v i - iv v -?i ii v v i ? i v C L1M5_orf2#LIN 3147 GAGTCCTTTGTCAGATATATGT-NTTGCAAATATTTTCTCCCANTCTGTG 3099 chr1qtel1M 578325 GCTTCCCTTCTAATCTTGTTTACATTAGTTTTGTTTGTACAGAAGCTTTT 578374 v i v i v v iv ivi vvv? vi i C L1M5_orf2#LIN 3098 GCTTGCCTTTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTTT 3049 chr1qtel1M 578375 TAATTTGATGTAATCAA-------AATTTTCTATTTTGTGATCAATAATG 578417 v v ? i v ------- i v i i --- ?i C L1M5_orf2#LIN 3048 AATTTTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGGT---TNGTG 3002 chr1qtel1M 578418 GTCTCTAGTTCGTCTTTAGTCACAAATTTCTTCCTCTTCCACAAGTCTGA 578467 v i i ivv v v --- v i i v v?i - i vvi C L1M5_orf2#LIN 3001 CTTTTTGTGTCCTGTTTA---AGAAATCTTTGCCTANCCCA-AGGTCACG 2956 chr1qtel1M 578468 GAGATAAACTATCCTTTG--TTCCTCCAATTTGTTTATAATCTCGTTCTT 578515 i -- i v v -- i i ivvvv i i ii?ii C L1M5_orf2#LIN 2955 AAGAT--ATTCTCCTATGTTTTCTTCTAGAAGTTTTATAGTTTTANCTTT 2908 chr1qtel1M 578516 TATGTCTAAATC-ATGGACCCATTTTGATCTTATCTTGGTATACGGTGTT 578564 ii i ii - - i i ? vi v i v i i v C L1M5_orf2#LIN 2907 TACATTTAGGTCTAT-GATCCATCTNGAATTAATTTTTGTGTATGGTGTG 2859 chr1qtel1M 578565 AAGTGTGGGTC 578575 i iv C L1M5_orf2#LIN 2858 AGGTAGGGGTC 2848 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 41.16 CpG sites = 71, Kimura (unadjusted) = 42.40 Transitions / transversions = 1.13 (71/63) Gap_init rate = 0.04 (20 / 446), avg. gap size = 1.40 (28 / 20) 358 27.09 4.94 4.29 chr1qtel1M 579020 579181 (420819) C MIRc#SINE/MIR (31) 237 75 m_b43s601i14 1524 chr1qtel1M 579020 CTTTATATGGCTTACAAGGTGTGCGCTGT-ACAGAGATGATCTCATTTGA 579068 i -- i i ---- v - v v v C MIRc#SINE/MIR 237 CTTTACA--GTTTACAAAG----CGCTTTCACATACATTATCTCATTTGA 194 chr1qtel1M 579069 CCCTCACGCCAGTTCTTGGAGGTAT------CTGCTATTTTCAGTCCTCA 579112 i iv iii vv v------ v v v i - i C MIRc#SINE/MIR 193 TCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTA-TCCCCA 145 chr1qtel1M 579113 TTTCACAGATGAAGAAAGTAAGGC-AAGCCCAGTTAAGTGCCTTGTCCAG 579161 i i v i -v vvvi v i i C MIRc#SINE/MIR 144 TTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAA 95 chr1qtel1M 579162 CTGTGTCCAGCTGGTCAGTG 579181 vvviiiv i v C MIRc#SINE/MIR 94 GGTCACACAGCTAGTAAGTG 75 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.89 CpG sites = 20, Kimura (unadjusted) = 33.89 Transitions / transversions = 0.91 (20/22) Gap_init rate = 0.06 (10 / 161), avg. gap size = 1.50 (15 / 10) 388 30.21 0.71 0.71 chr1qtel1M 579042 579181 (420819) C MIR#SINE/MIR (52) 210 71 m_b43s601i15 1524 chr1qtel1M 579042 GCGCTGTACAGAGATGATCTCATTTGACCCTCACGCCAGTTCTTGGAGGT 579091 v viv v v i i iv iii vv C MIR#SINE/MIR 210 GCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGGT 161 chr1qtel1M 579092 ATCTGCTATTTTCAGTCCTCATTTCACAGATGAAGAAAGTAAGGCA-AGC 579140 vv i v i - i i i v i - v C MIR#SINE/MIR 160 AGGTACTATTATTA-TCCCCATTTTACAGATGAGGAAACTGAGGCACAGA 112 chr1qtel1M 579141 CCAGTTAAGTGCCTTGTCCAGCTGTGTCCAGCTGGTCAGTG 579181 vvi iv i ivvviiiv i v C MIR#SINE/MIR 111 GAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTG 71 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 39.18 CpG sites = 21, Kimura (unadjusted) = 39.18 Transitions / transversions = 1.00 (21/21) Gap_init rate = 0.01 (2 / 139), avg. gap size = 1.00 (2 / 2) 216 30.41 14.80 3.99 chr1qtel1M 579348 579597 (420403) C L3#LINE/CR1 (224) 3875 3600 m_b43s601i16 1525 chr1qtel1M 579348 TGTCTCTGGGCAACTCTCACCCATGACTCCTGATCTTGCACTTTGAGGCC 579397 i ivv i ii viv ii ii v i ii C L3#LINE/CR1 3875 TGCCTCCCTGTAACTTCCACCCATTGGTCCTAGTTCTGCCCTCTGGAGCC 3826 chr1qtel1M 579398 AAACATACAAGGGCCAATAATGTCTCCTC-ACGGGTTAGCTCTTCAGCTG 579446 v v vv i v --- vi i - iv vi i iv i C L3#LINE/CR1 3825 ACACAGAATAAGTC---TAATCCCTCTTCCACATGACAGCCCTTCAAATA 3779 chr1qtel1M 579447 CCGGAAGGAAGGCTGTTCTCAGAGCCTCC-CTAAGACTGCTCCATCCCCA 579495 iiv iv - i iv ---- i - v v i- i C L3#LINE/CR1 3778 TTTGAAGACAG-CTATCAT----GTCTCCTCTAAGTCTTCTCT-TCTCCA 3735 chr1qtel1M 579496 --TT---CA--CCCAGTTCC-CCAATC--TC---------------TTCC 579520 --i --- -- -i i -- --------------- C L3#LINE/CR1 3734 GGCTAAACATCCCCAGTTCCTTCAACCGTTCCTCATATGACATGGTTTCC 3685 chr1qtel1M 579521 AAAAGCTCTTCACTATCCTGGTTG-----CCCTGGACATTCTCTGGCTAA 579565 i -- i i i ----- i iiv ii i vi C L3#LINE/CR1 3684 AGA--CCCTTCACCATCCTGGTCGCTCTCCTCTGGACGCGCTCCAGTTTG 3637 chr1qtel1M 579566 GAAATATTCCT----AAAC-TGGTGTCCCAAACTGAA 579597 vv i i ---- i- i i vi C L3#LINE/CR1 3636 TCAATGTCCCTCTTAAAATGTGGCGCCCAGAACTGAA 3600 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 38.33 CpG sites = 49, Kimura (unadjusted) = 41.32 Transitions / transversions = 2.04 (49/24) Gap_init rate = 0.09 (22 / 249), avg. gap size = 2.18 (48 / 22) 15 9.12 0.00 0.00 chr1qtel1M 579644 579667 (420333) (CCT)n#Simple_repeat 1 24 (0) m_b43s252i5 1526 chr1qtel1M 579644 CCCCCTCCTCCTCCTCCTCTTCCT 579667 i i (CCT)n#Simple 1 CCTCCTCCTCCTCCTCCTCCTCCT 24 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 194 23.86 8.82 1.37 chr1qtel1M 581302 581369 (418631) L2b_3end#LINE/L2 313 385 (81) m_b43s601i17 1527 chr1qtel1M 581302 TAGTTATCTG----CATCTC-GTTTTCCCTGTTAGACTATGAGTGCT-TG 581345 ?i i ---- v - i i iii i iv i- L2b_3end#LINE 313 TNATTGTCTGNTTACATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGTG 362 chr1qtel1M 581346 CAGGGCAAGGACCAGTTTTGTCTT 581369 - i i?v i L2b_3end#LINE 363 -AGGGCAGGGACCGNGTCTGTCTT 385 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 27.20 CpG sites = 13, Kimura (unadjusted) = 31.96 Transitions / transversions = 4.33 (13/3) Gap_init rate = 0.06 (4 / 67), avg. gap size = 1.75 (7 / 4) 238 24.43 16.55 1.20 chr1qtel1M 581706 581850 (418150) L1ME5_3end#LINE/L1 7 173 (768) m_b43s551i10 1528 chr1qtel1M 581706 TCCAAGATATACAAGAAACTGATTCAAATTGATAAGAACAGAAC--CATT 581753 i ii i vv v ii i v ii --? vi L1ME5_3end#LI 7 TCTAGAATATACAAGGAACTCCTGCAAATCAACAAGAAAAAGACGGNAAC 56 chr1qtel1M 581754 CCCAGTAGATAAAGGGTCAGAGAATAGGAATAGG----------AAGA-- 581791 i v v v i i v i ---------- -- L1ME5_3end#LI 57 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAGG 106 chr1qtel1M 581792 --ATCC--AAGATTATCA-GCAATCATGAAAA-ATGCTCCAAACCATTAA 581835 -- i -- ii v - --i i - v vi i L1ME5_3end#LI 107 AAACCCGAAAGGCTAACAAGCA--TATGAAGAGATGCTCAAACTCATTAG 154 chr1qtel1M 581836 GG----GAGAAATGCAAAT 581850 vi---- L1ME5_3end#LI 155 TAATCAGAGAAATGCAAAT 173 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 30.71 CpG sites = 22, Kimura (unadjusted) = 30.71 Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.07 (10 / 144), avg. gap size = 2.60 (26 / 10) 264 24.32 2.70 0.00 chr1qtel1M 581713 581786 (418214) L1ME4c_3end#LINE/L1 14 89 (741) m_b43s551i11 1528 chr1qtel1M 581713 TATACAAGAAACTGATTCAAATTGATAAGAACAGAACCA--TTCCCAGTA 581760 i ii i v v i? i --vi i L1ME4c_3end#L 14 TATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAAGACCCCAATA 63 chr1qtel1M 581761 GATAAAGGGTCAGAGAATAGGAATAG 581786 v v i i i v i L1ME4c_3end#L 64 GATAAATGGGCAAAGGACATGAACAG 89 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 30.95 CpG sites = 12, Kimura (unadjusted) = 30.95 Transitions / transversions = 2.00 (12/6) Gap_init rate = 0.01 (1 / 73), avg. gap size = 2.00 (2 / 1) 19 16.94 0.00 0.00 chr1qtel1M 582443 582475 (417525) (T)n#Simple_repeat 1 33 (0) m_b43s252i6 1529 chr1qtel1M 582443 TTTTTTTTTTTTTCTTTTTTAAATTTCTTTTTT 582475 i vvv i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 33 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 37 8.35 0.00 0.00 chr1qtel1M 583094 583145 (416855) (TCC)n#Simple_repeat 1 52 (0) c_b43s251i1 1530 chr1qtel1M 583094 TCCTCCTCCTCCTCCTCTTCCTCCTCCTCCTCCTCCTTTTCCTCCTTCTC 583143 i ii i (TCC)n#Simple 1 TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC 50 chr1qtel1M 583144 CT 583145 (TCC)n#Simple 51 CT 52 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 209 24.78 22.39 0.61 chr1qtel1M 584406 584539 (415461) C MIRb#SINE/MIR (66) 202 40 m_b43s601i18 1531 chr1qtel1M 584406 CATTATCTCATTGAGTCTTCCCCACAGTCCTGGGACG---GCACTGTTGT 584452 v i i v v ii v v --- i i i i C MIRb#SINE/MIR 202 CATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATTAT 153 chr1qtel1M 584453 T----------------GGAACACTGAGGC--AGACGGGTTGTTGAACTT 584484 i---------------- - -- vi ivvv C MIRb#SINE/MIR 152 CCCCATTTTACAGATGAGGAA-ACTGAGGCTCAGAGAGGTTAAGTAACTT 104 chr1qtel1M 584485 GCCC-AGGTCGCACA-----CAAGTGTCTGGGGCCAGATCTGAATCCTGG 584528 - i -----i v v i v vi ii i v C MIRb#SINE/MIR 103 GCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGG 54 chr1qtel1M 584529 CC---CTGACTCCA 584539 i --- C MIRb#SINE/MIR 53 TCTGTCTGACTCCA 40 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 29.61 CpG sites = 19, Kimura (unadjusted) = 30.70 Transitions / transversions = 1.36 (19/14) Gap_init rate = 0.05 (7 / 133), avg. gap size = 4.43 (31 / 7) 16 0.00 0.00 0.00 chr1qtel1M 586694 586711 (413289) (T)n#Simple_repeat 1 18 (0) m_b43s252i7 1532 chr1qtel1M 586694 TTTTTTTTTTTTTTTTTT 586711 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTT 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 11 16.66 5.88 0.00 chr1qtel1M 587482 587515 (412485) (TAATTAT)n#Simple_repeat 1 36 (0) m_b43s252i8 1533 chr1qtel1M 587482 TAATAATTTAGTATTAA--ATTAATTTTTATTTATT 587515 v v v -- v v (TAATTAT)n#Si 1 TAATTATTAATTATTAATTATTAATTATTAATTATT 36 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.03 (1 / 33), avg. gap size = 2.00 (2 / 1) 486 17.39 0.77 15.93 chr1qtel1M 587647 587776 (412224) MIRc#SINE/MIR 3 115 (153) m_b43s601i19 1534 chr1qtel1M 587647 AGGTAG-GTGGGGCAGTGGATAGAGCACCAGCCCTGAAGTCAGGAAGACC 587695 i - v v ii v i i MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chr1qtel1M 587696 TGAGTTCAAGTCTGGTTTCAGACACTTAACACTTCCTAGACACTTCCTAG 587745 i i iv vi v v ------------------ MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCACTTA------------------CTAG 84 chr1qtel1M 587746 CTGTGTGACTCTGGGCAAGTCACTTAACCCC 587776 ii i MIRc#SINE/MIR 85 CTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 18.44 CpG sites = 12, Kimura (unadjusted) = 19.54 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.15 (19 / 129), avg. gap size = 1.00 (19 / 19) 27 0.00 0.00 0.00 chr1qtel1M 587786 587811 (412189) (G)n#Simple_repeat 1 26 (0) c_b43s251i2 1535 chr1qtel1M 587786 GGGGGGGGGGGGGGGGGGGGGGGGGG 587811 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGG 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 310 20.36 0.00 13.33 chr1qtel1M 589437 589538 (410462) MIRc#SINE/MIR 2 91 (177) m_b43s601i20 1536 chr1qtel1M 589437 GGGGCAGCTAGGTGGTGCAGTGGATAGAGCACTACCCCTGAAGTCAGGAG 589486 i i--- v ivv i i i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr1qtel1M 589487 GACCTAAGTGAGTTCAAATCTGGCCTCAGACACAACATTTCCTAGCTGTG 589536 ---- i i i iv v v v ----- v MIRc#SINE/MIR 49 GACC----TGGGTTCGAGTCCCGGCTCTGCCAC-----TTACTAGCTGTG 89 chr1qtel1M 589537 TG 589538 MIRc#SINE/MIR 90 TG 91 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 22.10 CpG sites = 10, Kimura (unadjusted) = 23.53 Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.12 (12 / 101), avg. gap size = 1.00 (12 / 12) 230 31.79 11.86 5.87 chr1qtel1M 592551 592921 (407079) L2#LINE/L2 2231 2622 (460) m_b44s601i0 1537 chr1qtel1M 592551 GCTCCAGTGCTCTGTCCTGAGCCCCCTTTTGTTCT------AGGCTT--T 592592 i v v vi v i i v ------ vi i-- L2#LINE/L2 2231 GCCCCAGGGCTCAGTCCTTGGACCTCTTCTCTTCTCTATCTACACTCACT 2280 chr1qtel1M 592593 CACTCGGTGATCTC-TGCAGCTTC----CTTCAATT--CATTTATCGAGT 592635 v ? - v ii ---- i v -- i v---- L2#LINE/L2 2281 CCCTNGGTGATCTCATCCAGTCTCATGGCTTTAAATACCATCTATA---- 2326 chr1qtel1M 592636 TTATAGATGATTCCCAAATCTA-ATATTTAGCCTTAGTCTCTCACCCGAG 592684 - iiv i i - v ii iviii v i i L2#LINE/L2 2327 -TGCTGATGACTCCCAAATTTATATCTCCAGCCCGGACCTCTCCCCTGAA 2375 chr1qtel1M 592685 -TTCAAATTGCCCTTCCTGTCACTGACCTGCTTATTAGACA--TTCAC-- 592729 - i i ------i v i - iiv v i i v -- i -- L2#LINE/L2 2376 CTCCAGA------CTCGTAT-ATCCAACTGCCTACTCGACATCTCCACTT 2418 chr1qtel1M 592730 -GATGAACCACAG--ATCCCA---TCAACAT---CACAAACTCAAGCAAC 592770 - vviv i -- i --- i --- - --- - L2#LINE/L2 2419 GGATGTCTAATAGGCATCTCAAACTTAACATGTCCA-AAACT---G-AAC 2463 chr1qtel1M 592771 TCATTAGCTTTTCCC-CAAACTCTACTTTTCTTGAAAATT----AATTT- 592814 v v v ii - - i ii ii v ivi ----v i - L2#LINE/L2 2464 TCCTGATCTTCCCCCTCAAAC-CTGCTCCTCCCGCAGTCTTCCCCATCTC 2512 chr1qtel1M 592815 --TCAAGAGCACCACCTTTCTTCTGTTTGTTGAGTTTCACAGCTTCAGCG 592862 -- ? vi v v v i iiv i v viiv v i i ii v L2#LINE/L2 2513 AGTNAATGGCAACTCCATCCTTCCAGTTGCTCAGGCCAAAAACCTTGGAG 2562 chr1qtel1M 592863 CCAGTCTCAGGT------TTCCACTCTCACCCTTCCTCTAATCAGAGATC 592906 i vi iiiv ------ i v v iv v i ---v L2#LINE/L2 2563 TCATCCTTGACTCCTCTCTTTCTCTCACACCCCACATCCAATC---CATC 2609 chr1qtel1M 592907 AGCTCACATTCTCTC 592921 -- v i v L2#LINE/L2 2610 AG--CAAATCCTGTC 2622 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 42.21 CpG sites = 65, Kimura (unadjusted) = 43.26 Transitions / transversions = 1.41 (65/46) Gap_init rate = 0.11 (40 / 370), avg. gap size = 1.68 (67 / 40) 194 27.27 0.00 0.00 chr1qtel1M 594046 594100 (405900) C MIRb#SINE/MIR (9) 259 205 m_b44s601i1 1538 chr1qtel1M 594046 GCTGGCATTTATACAGCACTGACAGTATCCCAGGCACTTGGCTAAGCCCA 594095 iv vv i v vi i v vv v v C MIRb#SINE/MIR 259 GCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCT 210 chr1qtel1M 594096 TCACA 594100 i C MIRb#SINE/MIR 209 TTACA 205 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 31.39 CpG sites = 5, Kimura (unadjusted) = 33.90 Transitions / transversions = 0.50 (5/10) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 208 32.29 5.88 2.86 chr1qtel1M 594265 594366 (405634) C L2a_3end#LINE/L2 (23) 494 390 m_b44s601i2 1539 chr1qtel1M 594265 ATTAAGCACCTGCTCTGTTCTGGTGACTGT--TAAGCCCTGGGGATATAA 594312 i i i v v ii vv -- i v i i C L2a_3end#LINE 494 ATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGCGCTGGGGATACAG 445 chr1qtel1M 594313 ----AAAAAAAGTCAATTATAGTCTCTGCAACCTATATCTAGGATACTTT 594358 ----i v iivi iv v i -- -i vv vv v C L2a_3end#LINE 444 CAGTGAACAAAACAGACAAAAGTCCCTGC--CCT-CATGGAGCTTACATT 398 chr1qtel1M 594359 ATAATAGG 594366 v i i C L2a_3end#LINE 397 CTAGTGGG 390 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 41.41 CpG sites = 17, Kimura (unadjusted) = 43.18 Transitions / transversions = 1.13 (17/15) Gap_init rate = 0.05 (5 / 101), avg. gap size = 1.80 (9 / 5) 408 28.30 19.43 1.20 chr1qtel1M 594378 594588 (405412) MIRb#SINE/MIR 3 251 (17) m_b44s601i3 1540 chr1qtel1M 594378 GGAGGGCAGCCAGATGGAGTAGCGGAGAGAATACTGGTTCTGAAGTCAGG 594427 ii ---i v i i i ii v i i i i MIRb#SINE/MIR 3 GAGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGA 49 chr1qtel1M 594428 -AGGCCTG----CG----CC--CTCAAACAAT-ACTAGCTGTGTGACCCT 594465 - i ---- ---- -- viv v - i MIRb#SINE/MIR 50 CAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTT 99 chr1qtel1M 594466 GGGCAAGTCATCTAACCCCTATT-GCTTC--CTTCCTC-TCC-CCAAATA 594510 i ii i v v- i --i - i-iv i MIRb#SINE/MIR 100 GGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATG 149 chr1qtel1M 594511 -----AATAATGTCCA----ATGAGATGCTTGTAA-----AAACAA---A 594543 ----- ii i ----iiii i vv i ----- ii --- MIRb#SINE/MIR 150 GGGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATA 199 chr1qtel1M 594544 ACGCA-------CATTTAGCACAGTGCTCGGTACATCGGAGATGCTTTGT 594586 i ------- ii ii i v v iii ivi MIRb#SINE/MIR 200 ATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAAT 249 chr1qtel1M 594587 AA 594588 MIRb#SINE/MIR 250 AA 251 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 35.10 CpG sites = 46, Kimura (unadjusted) = 38.48 Transitions / transversions = 3.54 (46/13) Gap_init rate = 0.08 (17 / 210), avg. gap size = 2.59 (44 / 17) 21 4.13 0.00 0.00 chr1qtel1M 595578 595602 (404398) (G)n#Simple_repeat 1 25 (0) m_b44s252i0 1541 chr1qtel1M 595578 GGGCGGGGGGGGGGGGGGGGGGGGG 595602 v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGG 25 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 14 16.97 4.76 2.33 chr1qtel1M 597544 597585 (402415) (TCC)n#Simple_repeat 1 43 (0) m_b44s252i1 1542 chr1qtel1M 597544 TCCTCGCT-CTCCTCGTCGGCC-CCTCCTCCTGAGCCTCCTCCT 597585 - - v vv - vvv (TCC)n#Simple 1 TCCTC-CTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT 43 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.07 (3 / 41), avg. gap size = 1.00 (3 / 3) 30 28.87 2.80 0.92 chr1qtel1M 598039 598145 (401855) (TG)n#Simple_repeat 1 109 (0) m_b44s252i2 1543 chr1qtel1M 598039 TGTGTGTGTGTGTGTGTGTGTGGGAGAGGGTGTGGAGGTGAGTCT-TGTG 598087 v v v v viv v v - (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr1qtel1M 598088 GGTGAGTGTAAGAAATGGGGGGGAGTGTGTGTGGAGGGGTG-GTGTGTG- 598135 v v iv -vi v v v v viv v - - (TG)n#Simple_ 51 TGTGTGTGTGTG-TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 99 chr1qtel1M 598136 GAGTGAGTGT 598145 v v (TG)n#Simple_ 100 GTGTGTGTGT 109 Matrix = Unknown Transitions / transversions = 0.19 (4/21) Gap_init rate = 0.04 (4 / 106), avg. gap size = 1.00 (4 / 4) 39 18.96 1.28 0.00 chr1qtel1M 598584 598661 (401339) (GT)n#Simple_repeat 1 79 (0) m_b44s252i3 1544 chr1qtel1M 598584 GTGTGTGAGT-TCAGTGTGTGTGTGAGTGAGTGTGTGTGAGTGAGTGTGT 598632 v - vv v v v v (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50 chr1qtel1M 598633 AAGAATGAGTGTGTGTGAGTGTGTGTGTG 598661 iv vi v v (GT)n#Simple_ 51 GTGTGTGTGTGTGTGTGTGTGTGTGTGTG 79 Matrix = Unknown Transitions / transversions = 0.18 (2/11) Gap_init rate = 0.01 (1 / 77), avg. gap size = 1.00 (1 / 1) 39 18.96 1.28 0.00 chr1qtel1M 598865 598942 (401058) (GT)n#Simple_repeat 1 79 (0) m_b44s252i4 1545 chr1qtel1M 598865 GTGTGTGAGT-TCAGTGTGTGTGTGAGTGAGTGTGTGTGAGTGAGTGTGT 598913 v - vv v v v v (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50 chr1qtel1M 598914 AAGAATGAGTGTGTGTGAGTGTGTGTGTG 598942 iv vi v v (GT)n#Simple_ 51 GTGTGTGTGTGTGTGTGTGTGTGTGTGTG 79 Matrix = Unknown Transitions / transversions = 0.18 (2/11) Gap_init rate = 0.01 (1 / 77), avg. gap size = 1.00 (1 / 1) 34 18.91 0.00 1.37 chr1qtel1M 599146 599219 (400781) (GTGT)n#Simple_repeat 1 73 (0) m_b44s252i5 1546 chr1qtel1M 599146 GTGTGTGAGTGCAGTGTGTGTGTGAGTGAGTGTGTGAGTGAGTGTGTAAG 599195 v -v v v v v iv (GTGT)n#Simpl 1 GTGTGTGTGTG-TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 49 chr1qtel1M 599196 AATGAGTGTGTGAGTGTGTGTGTG 599219 vi v v (GTGT)n#Simpl 50 TGTGTGTGTGTGTGTGTGTGTGTG 73 Matrix = Unknown Transitions / transversions = 0.20 (2/10) Gap_init rate = 0.01 (1 / 73), avg. gap size = 1.00 (1 / 1) 18 12.52 0.00 2.78 chr1qtel1M 600634 600670 (399330) (TTTTTAA)n#Simple_repeat 1 36 (0) m_b44s252i6 1547 chr1qtel1M 600634 TTTTTTTTTTTTAATTTTTAAATTTTTATTATTTAAT 600670 vv - v v (TTTTTAA)n#Si 1 TTTTTAATTTTTAATTTTT-AATTTTTAATTTTTAAT 36 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 255 31.79 2.84 1.69 chr1qtel1M 601125 601300 (398700) C L1MC5a_3end#LINE/L1 (2140) 637 460 m_b44s551i0 1548 chr1qtel1M 601125 CCCTGCTTGTTTCCCTCAGCCTCAGTTCCTGTCGGTCTCTCCAGGCCTTT 601174 i v v i i vvi vv vv i v vi? vv C L1MC5a_3end#L 637 CCTTGCTTTTTTCACTTAACAATATATCCTGGAGATCACTCCATANCAGT 588 chr1qtel1M 601175 CT---GAAATCTTCCTGTTGGTCATTTCTTACAGAACAATAATATTCCCT 601221 v --- i vv -- v - vvvv i i v C L1MC5a_3end#L 587 ATATAGAGATCTTCCTCAT--TCCTTT-TTACAGCTGCATAGTACTCCAT 541 chr1qtel1M 601222 AATATTTATATACCACAATTTATTCAGCCATTCTCCAACTGATGGGCATC 601271 vi i vv i i i i v i v i i i C L1MC5a_3end#L 540 TGTGTGGATGTACCATAGTTTATTCAACCAGTCCCCTATTGATGGACATT 491 chr1qtel1M 601272 CACTCAGTTTCCAGTTTCTAG--ATTGCAAA 601300 iivviv i i v -- i C L1MC5a_3end#L 490 TGGGTTGTTTCCAGTCTTTTGCTATTACAAA 460 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 42.01 CpG sites = 25, Kimura (unadjusted) = 42.01 Transitions / transversions = 0.83 (25/30) Gap_init rate = 0.03 (5 / 175), avg. gap size = 1.60 (8 / 5) 267 27.28 1.61 2.44 chr1qtel1M 601177 601300 (398700) C L1MC4a_3end#LINE/L1 (2049) 580 458 m_b44s551i1 1548 chr1qtel1M 601177 GAAATCTTCCTGTTGGTCATTTCTTACAGAACAATAATATTCCCTAATAT 601226 i vv -- - i vvvv i i v vi i C L1MC4a_3end#L 580 GAGATCTTCCTCAT--TC-TTTTTTACAGCTGCATAGTACTCCATTGTGT 534 chr1qtel1M 601227 TTATATACCACAATTTATTCAGCCATTCTCCAACTGATGGGCATCCACTC 601276 vv i i i i ? v i?? ii vvi C L1MC4a_3end#L 533 GGATGTACCATAGTTTATTCAACCANTCTCCTATNNATGGGCATTTAGGT 484 chr1qtel1M 601277 AGTTTCCAGTTTCTAG--ATTGCAAA 601300 v i v i v -- i C L1MC4a_3end#L 483 TGTTTCCAATATTTTGCAATTACAAA 458 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 35.47 CpG sites = 17, Kimura (unadjusted) = 35.47 Transitions / transversions = 1.06 (17/16) Gap_init rate = 0.03 (4 / 123), avg. gap size = 1.25 (5 / 4) 338 24.18 2.20 0.00 chr1qtel1M 601210 601300 (398700) C L1ME3G_3end#LINE/L1 (376) 548 456 m_b44s551i2 1548 chr1qtel1M 601210 ATAATATTCCCTAATATTTATATACCACAATTTATTCAGCCATTCTCCAA 601259 i v i vv i i i i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr1qtel1M 601260 CTGATGGGCATCCACTCAGTTTCCAGTTTCTAG--ATTGCAAA 601300 i i ii vviv i i v -- i C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAA 456 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 30.01 CpG sites = 14, Kimura (unadjusted) = 30.01 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.01 (1 / 90), avg. gap size = 2.00 (2 / 1) 233 28.30 3.46 14.35 chr1qtel1M 601821 602051 (397949) C L2c_3end#LINE/L2 (17) 461 253 m_b44s601i4 1549 chr1qtel1M 601821 ACATTTATAATTAAGCACCTAGTTAAATGCTAGGCTCTGCGTTAAGCAGT 601870 --- i i -i vi i v --------- - C L2c_3end#LINE 461 ACATTTAT---TGAGCGCCTA-CTATGTGCCAGGCGCTG---------G- 426 chr1qtel1M 601871 GGGTATAGAGAGGCAGAA---ACAG--CCTGCTCTCAAGG-GCTTTTGGT 601914 i i i v v v --- i -- i - ivii C L2c_3end#LINE 425 GGATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGT 376 chr1qtel1M 601915 CCATTGGTAGATGC-TACAAGCAAAAAACTAAGTACAA-ACAAGGTATAT 601962 i v vi vi -v ? i v ivi v - ----- C L2c_3end#LINE 375 CTAGTGGAGGAGACAGACANGTAAACAGACAATTACAATACAAG-----T 331 chr1qtel1M 601963 TGATGATAATCCTTAAAAAGGAGGGACTATGTAAGGACAGCACTGATGTG 602012 i vivi v ---v v ----i -iv v i C L2c_3end#LINE 330 TAATGATAAGTGCTATAA---TGGGAGTAT----AGACAG-GGTGCTATG 289 chr1qtel1M 602013 GGGGGGAATGAGGATCGGGGACTGAGGCTTTTCTTTGGG 602051 i viv - -- v iv i vv? v C L2c_3end#LINE 288 GGAGCACA-GAGGA--GGGCACCTAGACTAGNCTTGGGG 253 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 34.22 CpG sites = 29, Kimura (unadjusted) = 35.77 Transitions / transversions = 1.07 (29/27) Gap_init rate = 0.15 (35 / 230), avg. gap size = 1.09 (38 / 35) 246 30.26 13.99 0.62 chr1qtel1M 601830 601972 (398028) C L2a_3end#LINE/L2 (23) 494 333 m_b44s601i5 1549 chr1qtel1M 601830 ATTAAGCACCTAGTTAAATGCTAGGCTCTGCGTTAAGCAGTGGGTATAGA 601879 i i -i vi i v ivi i iv v v C L2a_3end#LINE 494 ATTGAGCGCCTA-CTATGTGCCAGGCACTGTTCTAGGCGCTGGGGATACA 446 chr1qtel1M 601880 G---------AGGCAGA-AACAG--CCTGCTCTCAAGG-GCTTTTGGTCC 601916 --------- ii - v -- i v - viiv i C L2a_3end#LINE 445 GCAGTGAACAAAACAGACAAAAGTCCCTGCCCTCATGGAGCTTACATTCT 396 chr1qtel1M 601917 ATTGGTAGATG-----CTACAAGCAAAAAACTAAGTACAA-ACAAGGTAT 601960 v vi iv ----- v i i v v v - i vi C L2a_3end#LINE 395 AGTGGGGGGAGACAGACAATAAACAAATAAATAAGTAAAATATATAGTAT 346 chr1qtel1M 601961 ATT-GATGATAAT 601972 i i- i i C L2a_3end#LINE 345 GTCAGATGGTGAT 333 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 37.52 CpG sites = 25, Kimura (unadjusted) = 39.90 Transitions / transversions = 1.39 (25/18) Gap_init rate = 0.06 (8 / 142), avg. gap size = 2.62 (21 / 8) 13 27.96 0.00 2.08 chr1qtel1M 602371 602419 (397581) (ATTTA)n#Simple_repeat 1 48 (0) m_b44s252i7 1550 chr1qtel1M 602371 ATTTAATATTACTCATTTTACTTAATTTTAAATTAGTTTAAATTTTATT 602419 v v i i v v v v v i - v (ATTTA)n#Simp 1 ATTTAATTTAATTTAATTTAATTTAATTTAATTTAATTT-AATTTAATT 48 Matrix = Unknown Transitions / transversions = 0.38 (3/8) Gap_init rate = 0.02 (1 / 48), avg. gap size = 1.00 (1 / 1) 498 31.27 9.59 6.42 chr1qtel1M 603722 604326 (395674) C L2#LINE/L2 (401) 2681 2059 m_b44s601i6 1549 chr1qtel1M 603722 GGTGGTCGTGTGGGTGCAGAGAAGGGGGCCTAAGGGAGAGCTGTCATGGA 603771 iv vi vv v v vv vvvvi vv i iv i C L2#LINE/L2 2681 GGTGGCAGTGGAGGTGGTGAGAAGTGGTCGGATTCTGGATATATTTTGAA 2632 chr1qtel1M 603772 GGTAGAAT-GACAAGCCTTGGCAGCAGGTTGG--GCTGAGTGGGA----- 603813 ii- i vi viiiii i -- iv i v ----- C L2#LINE/L2 2631 GGTAGAGCCGACAGGATTTGCTGATGGATTGGATGTGGGGTGTGAGAGAA 2582 chr1qtel1M 603814 --AGGGCTGCCAAGGATGACTTGGCTGAGCTTGGAAGCC---GCGACTGC 603858 -- i vv i --- ii v vvvi --- i - C L2#LINE/L2 2581 AGAGAGGAGTCAAGGATGACT---CCAAGGTTTTTGGCCTGAGCAACTG- 2536 chr1qtel1M 603859 TGGGAAACTGGTGGAG----CATTGGACAGGACTAGGAAGAGGGGA---- 603900 --- i-- i ---- ?------ ii v -- ---- C L2#LINE/L2 2535 ---GAAG--GATGGAGTTGCCATTN------ACTGAGATG--GGGAAGAC 2499 chr1qtel1M 603901 ------------AGGTTTGGTGGGAAAGACCAAGAGGTCAGCTTGGGAAA 603938 ------------ iv i i i v i v v C L2#LINE/L2 2498 TGCGGGAGGAGCAGGTTTGAGGGGGAAGATCAGGAGTTCAGTTTTGGACA 2449 chr1qtel1M 603939 GTTTGAGCTTAAAATGCCAATTAGAGCCTGTCCTGGTTAAGGTGTCCAGT 603988 vv i i i i v ---ii vi vi i v C L2#LINE/L2 2448 TGTTAAGTTTGAGATGCCTATTAGA---CATCCAAGTGGAGATGTCGAGT 2402 chr1qtel1M 603989 GGATCCTTGG-----------TG--ATTGAGGCAGGAGATTAGTGCTGGG 604025 i iivv ----------- --i v vii i iv v i C L2#LINE/L2 2401 AGGCAGTTGGATATACGAGTCTGGAGTTCAGGGGAGAGGTCCGGGCTGGA 2352 chr1qtel1M 604026 TATACAAATGGGGGTATAATCTTCCTGGAGATGATCATTAA--CCCTGGG 604073 v i vv vi v vv v iv i vv -- v i C L2#LINE/L2 2351 GATATAAATTTGGGAGTCATCAGCATATAGATGGTATTTAAAGCCATGAG 2302 chr1qtel1M 604074 AACTGATGAGATCACCCAGTGACATAGTATAGAAGAAGAAGAGGAGAAAG 604123 viv ? v vvv i vii i -- C L2#LINE/L2 2301 ACTGGATGAGATCACCNAGGGAGTGAGTGTAGATAGAGAAGAGAAG--AG 2254 chr1qtel1M 604124 AACCAGAAA--GACCCTTGGGG-A-TTCAGCTGGGGGATGAGAGCTAAGG 604169 iv iii -- v i - - i i ----- v ? v vi C L2#LINE/L2 2253 GTCCAAGGACTGAGCCCTGGGGCACTCCAAC-----GTTNAGAGGTCGGG 2209 chr1qtel1M 604170 TGTGTGTGTGAGGGGGTAGTTGAAGGTCCAGCAAAGGAAACTGAGAGGGA 604219 - v ---i i ------ --- i i C L2#LINE/L2 2208 -GAG---ATGAGGAG------GAA---CCAGCAAAGGAGACTGAGAAGGA 2172 chr1qtel1M 604220 GC-ATCATTCAGGTAGGAGAAGAACCAGGAGAGAACAGGGACAAGAAAAT 604268 -ii v v i i viii v v vv i ii C L2#LINE/L2 2171 GCGGCCAGTGAGGTAGGAGGAAAACCAGGAGAGTGTGGTGTCCTGGAAGC 2122 chr1qtel1M 604269 CTATTGGAGAGAAATTATTGTGGAGAAGGG-GTG----GCTGTATTAAAG 604313 v v i i ivv v iiv i i - ----i i i v C L2#LINE/L2 2121 CAAGTGAAGAAAGTGTTTCAAGAAGGAGGGAGTGATCAACTGTGTCAAAT 2072 chr1qtel1M 604314 GCTGCACAAAAGT 604326 vv ? i C L2#LINE/L2 2071 GCTGCTGANAGGT 2059 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 41.45 CpG sites = 94, Kimura (unadjusted) = 41.76 Transitions / transversions = 1.13 (94/83) Gap_init rate = 0.09 (56 / 604), avg. gap size = 1.75 (98 / 56) 21 29.15 0.00 0.00 chr1qtel1M 604455 604512 (395488) (TT)n#Simple_repeat 1 58 (0) m_b44s252i8 1551 chr1qtel1M 604455 TTTTTCTTTTTGTTTTGTTCCTCATGTATGTGTTTTTTAATTATTTTTTT 604504 i v v ii iv v v v v vv v (TT)n#Simple_ 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr1qtel1M 604505 TTTTTTTT 604512 (TT)n#Simple_ 51 TTTTTTTT 58 Matrix = Unknown Transitions / transversions = 0.40 (4/10) Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0) 503 21.38 3.79 7.87 chr1qtel1M 604762 604893 (395107) C MIRb#SINE/MIR (138) 130 4 m_b44s601i7 1552 chr1qtel1M 604762 CTGAGGC-AATTGGGGTTAAGTGACTTT----GGGTCCCACAGCTAGGAA 604806 -v vv i i v----i v --- C MIRb#SINE/MIR 130 CTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAG--- 84 chr1qtel1M 604807 GTATTAAATGGCTGAGCTCAGATTTAAACTCAGGTCCATCTGACTTCAGG 604856 ---- i v ivi ii i ii i ii C MIRb#SINE/MIR 83 ----TAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAA 38 chr1qtel1M 604857 ACTAGTGCTCTATCCACTGTACCACCTAGCTGCCCCT 604893 i iv v i --- C MIRb#SINE/MIR 37 GCCCGTGCTCTTTCCACTGCACCAC---GCTGCCCCT 4 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 23.37 CpG sites = 17, Kimura (unadjusted) = 25.72 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.09 (12 / 131), avg. gap size = 1.25 (15 / 12) 187 31.48 0.00 0.00 chr1qtel1M 605136 605189 (394811) L3#LINE/CR1 4043 4096 (3) m_b44s601i8 1553 chr1qtel1M 605136 GACTGGACTGGAGGGCAGCTGAGGAATCTTCCAATACTTAAACTCTGGGA 605185 ii i v i vv i vvi iv v i i v L3#LINE/CR1 4043 GGTTGGACTAGATGACCTCTAAGGTCCCTTCCAACTCTGAGATTCTGTGA 4092 chr1qtel1M 605186 TTCT 605189 L3#LINE/CR1 4093 TTCT 4096 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 41.62 CpG sites = 9, Kimura (unadjusted) = 41.62 Transitions / transversions = 1.12 (9/8) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 211 29.51 1.64 0.00 chr1qtel1M 605310 605370 (394630) MIRb#SINE/MIR 186 247 (21) m_b44s601i9 1554 chr1qtel1M 605310 GATCAAAGGAGATTATATTTGTAGATTGCTTAGTGGAGCGCTTGGCATGT 605359 i v v iiv i vi iiv i i ii MIRb#SINE/MIR 186 GATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACAT 235 chr1qtel1M 605360 AGT-AGTTCTCA 605370 - iv MIRb#SINE/MIR 236 AGTAAGCGCTCA 247 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 33.83 CpG sites = 12, Kimura (unadjusted) = 39.32 Transitions / transversions = 2.00 (12/6) Gap_init rate = 0.02 (1 / 60), avg. gap size = 1.00 (1 / 1) 246 31.17 8.18 0.85 chr1qtel1M 606301 606410 (393590) C L2a_3end#LINE/L2 (23) 494 377 m_b44s601i10 1555 chr1qtel1M 606301 ATTAAGTGTTTGCT--GCACTTAACACAATGCCAAGTGATGGAGATATAA 606348 i i ii i -- ii ivii vi v i i i v i i - C L2a_3end#LINE 494 ATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGCGCTGGGGATACA- 446 chr1qtel1M 606349 GCAG-GAA--AGTCAGACAA---TCCCTTCCCTCCAGAAGCTCCCCTACT 606392 - -- iv --- v vv i iv v v C L2a_3end#LINE 445 GCAGTGAACAAAACAGACAAAAGTCCCTGCCCTCATGGAGCTTACATTCT 396 chr1qtel1M 606393 AATGGGGGAACA-AAACAA 606410 i i v - i C L2a_3end#LINE 395 AGTGGGGGGAGACAGACAA 377 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 38.98 CpG sites = 22, Kimura (unadjusted) = 42.27 Transitions / transversions = 1.83 (22/12) Gap_init rate = 0.06 (6 / 109), avg. gap size = 1.67 (10 / 6) 195 32.69 1.96 13.04 chr1qtel1M 607116 607217 (392783) C L2d2_3end#LINE/L2 (50) 505 414 m_b44s601i11 1556 chr1qtel1M 607116 TGTTTCAGGTATTGTGGGAAGTTCAAGGGATACAGAAATGAAATATAAAA 607165 vii iii --------- i --- i i C L2d2_3end#LIN 505 TGTGCTAGGCGCTGTGG---------GGGATACAAA---GAAGTATAAGA 468 chr1qtel1M 607166 TATACTTTCT--CTTCAAAGAATCTTCACTGTATTGGGGGAAATAATATG 607213 i iv ii -- i i iii v v v v v i i v ii C L2d2_3end#LIN 467 CATGGTCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGGAGACAAGACA 418 chr1qtel1M 607214 TAAA 607217 C L2d2_3end#LIN 417 TAAA 414 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 43.00 CpG sites = 21, Kimura (unadjusted) = 45.44 Transitions / transversions = 2.62 (21/8) Gap_init rate = 0.13 (13 / 101), avg. gap size = 1.08 (14 / 13) 15 14.38 0.00 0.00 chr1qtel1M 607518 607541 (392459) (A)n#Simple_repeat 1 24 (0) m_b44s252i10 1557 chr1qtel1M 607518 AAAAAAAGAAAAGAAAAGAAAAAA 607541 i i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAA 24 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 711 36.84 9.69 2.32 chr1qtel1M 610249 611012 (388988) L2#LINE/L2 2196 3014 (68) m_b44s601i12 1558 chr1qtel1M 610249 TCCTCTTCCAAATCAGCCC--TCTCTTCATAT----GTGCCCTCAAGCTT 610292 i --- vv --i ?v ii ---- - i vi L2#LINE/L2 2196 TCCTCCTC---ATCTCCCCGACCTCTNAACGTTGGAGTGCCC-CAGGGCT 2241 chr1qtel1M 610293 TAATAAT--AATCTCTTTTCTT---TATATATACTTCTTCATTTGGTGAT 610337 i i vv --i i i --- v i ivi vi ? L2#LINE/L2 2242 CAGTCCTTGGACCTCTTCTCTTCTCTATCTACACTCACTCCCTNGGTGAT 2291 chr1qtel1M 610338 CTCATCAGCTCCCGTGGATTGAATTACTGTCTCTATTTTAATGATGATCG 610387 viv i i v v v ii v vi i ivvi i L2#LINE/L2 2292 CTCATCCAGTCTCATGGCTTTAAATACCATCTATATGCTGATGACTCCCA 2341 chr1qtel1M 610388 AATCT---TTCTTGTCCCAG---TCCCTATTGAACTCTAG--TCACATCT 610429 i --- iiiiiv i --- i ivi i -- ii v L2#LINE/L2 2342 AATTTATATCTCCAGCCCGGACCTCTCCCCTGAACTCCAGACTCGTATAT 2391 chr1qtel1M 610430 CCAGTTGCCTTTCAAACATGTTAAATTG-----CTAGTAGGTATCTTTAA 610474 ii viivi v iv v ----- i i iv L2#LINE/L2 2392 CCAACTGCCTACTCGACATCTCCACTTGGATGTCTAATAGGCATCTCAAA 2441 chr1qtel1M 610475 CTCAATA-ATTTGAAACAAATCTGATCATCTTTCTTCTTACCTTACCTGT 610523 i i -i iii vi v vv v i ii i v--- i L2#LINE/L2 2442 CTTAACATGTCCAAAACTGAACTCCTGATCTTCCCCCTCAA---ACCTGC 2488 chr1qtel1M 610524 TACTGTCAACGGTATT-ATCAT-TC--TTGATAGTA---TCATTCTTCCA 610566 v -i vi i v -vi - -- ?i i i ---i i L2#LINE/L2 2489 TCCT-CCCGCAGTCTTCCCCATCTCAGTNAATGGCAACTCCATCCTTCCA 2537 chr1qtel1M 610567 GCCTTTCAGGTTCTCAGACTGGGAGACATCTTGGATTGCCCATTATCTAT 610616 iivi iivvv iv v v i v i v i vi v v L2#LINE/L2 2538 GTTGCTCAGGCCAAAAACCTTGGAGTCATCCTTGACTCCTCTCTTTCTCT 2587 chr1qtel1M 610617 CAACCCCCCATTTCCACATGGTGCCCAAGGCTTGTTGATGCCACCTTTGC 610666 - v iv vvivi vvv iv i i iiv i iiv L2#LINE/L2 2588 C-ACACCCCACATCCAATCCATCAGCAAATCCTGTCGGCTCTACCTTCAA 2636 chr1qtel1M 610667 AAGATCTCTCAAATACATTGCCTTCTCTTGA----CATTGCCTTCG-CCT 610711 v v ivi v ivivv viv ---- i vi i- L2#LINE/L2 2637 AATATATCCAGAATCCGACCACTTCTCACCACCTCCACTGCCACCACCCT 2686 chr1qtel1M 610712 GGTGCAGGCCCTTGTCACTTCCCACTTTGATTACTATAATGTCCTGCGGG 610761 v i viii ii i i i v ii iv v vii L2#LINE/L2 2687 GGTCCAAGCCACCATCATCTCTCGCCTGGATTACTGCAATAGCCTCCTAA 2736 chr1qtel1M 610762 TAGGTCAACCTGCCTTAAACCTCTGTCCATTACAA---ATTCTCTCTTCA 610808 iv vv i iv v ivvi vi ? i--- vviv L2#LINE/L2 2737 CTGGTCTCCCTGCTTCCACCCTTGCCCCCCTNCAGTCTATTCTCAACACA 2786 chr1qtel1M 610809 GCA-CTAAACTGATTTTCCTAAAA-------CAGAT-------------T 610837 - i i v ii ii ------- ------------- L2#LINE/L2 2787 GCAGCCAGAGTGATCCTTTTAAAACGTAAGTCAGATCATGTCACTCCTCT 2836 chr1qtel1M 610838 TCTTAAG---CTCCAATGGATTATTGTCTCCATTAAAAAACAAAACAAAA 610884 v i i--- v viii - i ------ i ii L2#LINE/L2 2837 GCTCAAAACCCTCCAATGGCTTCCCATCT-CACT------CAGAGTAAAA 2879 chr1qtel1M 610885 CACAAAATCAGTA----GGCATTTAAAGATCTTCACAACCTG---TGCCA 610927 vv i vv ---- v vi i vi v ii i ---iv i L2#LINE/L2 2880 GCCAAAGTCCTTACAATGGCCTACAAGGCCCTACATGATCTGGTCCCCCG 2929 chr1qtel1M 610928 TTCAATCTTTCCAGTTT--TCTTACACC-TTATCCTCTGCAATGTACTCT 610974 -- i i iiiii -- ivi -i v i iv iv -i i L2#LINE/L2 2930 TT--ACCTCTCTGACCTCATCTCCTACCACTCTCCCCCTCGCT-CACTCC 2976 chr1qtel1M 610975 GATCTACTGGCCCTAGCCTTCTGTCTGTTCCATGAACA 611012 v i vivi v i i vv vi L2#LINE/L2 2977 GCTCCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACA 3014 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 50.30 CpG sites = 164, Kimura (unadjusted) = 53.78 Transitions / transversions = 1.48 (164/111) Gap_init rate = 0.06 (43 / 763), avg. gap size = 2.16 (93 / 43) 252 27.28 0.00 1.52 chr1qtel1M 611190 611256 (388744) MIRc#SINE/MIR 87 152 (116) m_b44s601i13 1559 chr1qtel1M 611190 GCGTGACCCTCAACAAGTCACTTAAGCCATCCCAGCCTCACTTTACTCAT 611239 i i vii v iv iv v v MIRc#SINE/MIR 87 GTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCAT 136 chr1qtel1M 611240 TTGTGGCACAGTGGATA 611256 i iiv ii - MIRc#SINE/MIR 137 CTGTAAAATGG-GGATA 152 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 34.90 CpG sites = 11, Kimura (unadjusted) = 34.90 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.02 (1 / 66), avg. gap size = 1.00 (1 / 1) 431 27.64 4.23 5.71 chr1qtel1M 611241 611382 (388618) MIRc#SINE/MIR 9 148 (120) m_b44s601i14 1560 chr1qtel1M 611241 TGTGGCACAGTGGATACAATTCTG--TTTGGAATCAGGAAGACTCTTCTT 611288 ii v v iiv --i i ------- MIRc#SINE/MIR 9 TGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC------- 51 chr1qtel1M 611289 CCTAAGTGCAAACTTGGATTCAGACACTTGCTGGCTG-GTTATTCTGGAC 611337 - ii v i iiiiv ii v v i i - v iii i MIRc#SINE/MIR 52 -CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGC 100 chr1qtel1M 611338 AAGTCACTTAACC-CTATTGGCCT--GTTTGCTGATCTGAAAAATAAG 611382 - v vi -- v v v ii MIRc#SINE/MIR 101 AAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 34.54 CpG sites = 24, Kimura (unadjusted) = 35.76 Transitions / transversions = 1.85 (24/13) Gap_init rate = 0.09 (12 / 141), avg. gap size = 1.17 (14 / 12) 292 27.20 10.34 4.92 chr1qtel1M 612116 612231 (387769) L2b_3end#LINE/L2 333 454 (12) m_b44s601i15 1558 chr1qtel1M 612116 TGTCTTTCAGATTAGACTGTGACCTTT-TGGGGG----------GGCTGT 612154 ii vv i v ii- i ---------- v L2b_3end#LINE 333 TGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGT 382 chr1qtel1M 612155 TTTCTGCTCCCCGTTTT-TCCCCAACCCGTGTTTAGCAAAGTGCCTGGCA 612203 i -- i v i v - i ---- ii v ? L2b_3end#LINE 383 CTT--GTTCACCGCTGTATCCCCAGC----GCCTAGCACAGNGCCTGGCA 426 chr1qtel1M 612204 CAGAATGGGTGCTTCATGAATACTCATT 612231 v i i i ivi i i ii L2b_3end#LINE 427 CACAGTAGGCGCTCAGTAAATATTTGTT 454 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 33.05 CpG sites = 21, Kimura (unadjusted) = 36.06 Transitions / transversions = 2.33 (21/9) Gap_init rate = 0.08 (9 / 115), avg. gap size = 2.00 (18 / 9) 14 21.98 2.38 0.00 chr1qtel1M 614374 614415 (385585) (GAGGGTG)n#Simple_repeat 1 43 (0) m_b44s252i11 1561 chr1qtel1M 614374 GAGGGTGGTGGGGGTAGGG-GGAGGCCGTGGGGTGGAAGGTGG 614415 v v v - vi vi i (GAGGGTG)n#Si 1 GAGGGTGGAGGGTGGAGGGTGGAGGGTGGAGGGTGGAGGGTGG 43 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.02 (1 / 41), avg. gap size = 1.00 (1 / 1) 18 0.00 0.00 0.00 chr1qtel1M 616620 616639 (383361) (T)n#Simple_repeat 1 20 (0) m_b44s252i12 1562 chr1qtel1M 616620 TTTTTTTTTTTTTTTTTTTT 616639 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTT 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 414 26.38 1.65 6.03 chr1qtel1M 616641 616761 (383239) C MIRc#SINE/MIR (141) 127 12 m_b44s601i16 1563 chr1qtel1M 616641 CTGAGGC-AATTGGGGTTAAGTGACTTGTCTAGGACCACACAACTTGGAA 616689 -v vv i i i i ii i v v C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAA 78 chr1qtel1M 616690 GTATTAGGTGGCTGAGGTCATATTTGAACACAAGTCCTCCTGACTTAAGG 616739 ivi i-- i i ----- i i v i i iv i C MIRc#SINE/MIR 77 GTGGCAGA--GCCGGG-----ACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr1qtel1M 616740 GCTGGTGCTCTATCCACT-CACC 616761 v ii v - C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTGCACC 12 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.95 CpG sites = 20, Kimura (unadjusted) = 33.69 Transitions / transversions = 2.00 (20/10) Gap_init rate = 0.07 (9 / 120), avg. gap size = 1.00 (9 / 9) 19 0.00 0.00 0.00 chr1qtel1M 617115 617135 (382865) (AT)n#Simple_repeat 1 21 (0) m_b44s252i13 1564 chr1qtel1M 617115 ATATATATATATATATATATA 617135 (AT)n#Simple_ 1 ATATATATATATATATATATA 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 232 23.80 5.88 1.12 chr1qtel1M 617271 617355 (382645) DNM1r#Unknown 2498 2586 (2076) m_b44s502i0 1565 chr1qtel1M 617271 GTTTATATGTATGTATGTATGTATGTATAC--ATACATACATATATTTAG 617318 v i i i ii-- i i ? v DNM1r#Unknown 2498 GTGTATATGTGTGTATGTGTGTATATATGTGTATATATACGTATNTATAG 2547 chr1qtel1M 617319 AATCACCCCAT---CATACCTCAGCCCAAGCCCAAGTTTT 617355 - vvv v--- v vvvii v DNM1r#Unknown 2548 AA-CAGGGCAGGGGCATACCACAGAGGGGGCACAAGTTTT 2586 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 27.55 CpG sites = 9, Kimura (unadjusted) = 29.19 Transitions / transversions = 0.82 (9/11) Gap_init rate = 0.04 (3 / 84), avg. gap size = 2.00 (6 / 3) 184 30.43 2.28 0.16 chr1qtel1M 619182 619795 (380205) (CTCT)n#Simple_repeat 1 627 (0) m_b44s252i14 1566 chr1qtel1M 619182 CTCTCTCTCCCCCTCCCT-TCTCTC-CTCTGTCAGTCTGTCCCTCCTTCT 619229 i i i - - v vv v i ii (CTCT)n#Simpl 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chr1qtel1M 619230 CACTGTCCCTCCCCCTCTCTGTCCCTCCCTCTCACTGTCCCTCCCCCTCA 619279 v v i i i v i i v v i i i v (CTCT)n#Simpl 51 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 100 chr1qtel1M 619280 CTGTCCCTCCCCCTCACTGTCCCTCCCCCTCACTGTCCCTCCCTCTCTCC 619329 v i i i v v i i i v v i i i (CTCT)n#Simpl 101 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 150 chr1qtel1M 619330 TTCCCCCTCACTGTCCCTCCCCCTCTCTGTCCCTCCCCCTCTCTGTCCCT 619379 i i i v v i i i v i i i v i (CTCT)n#Simpl 151 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 200 chr1qtel1M 619380 CCCTCTCTCTGTCCCTC-CCCCCTCTGTCCCTCCCTCTCACTGTCCCTCC 619428 i v i - i i v i i v v i i (CTCT)n#Simpl 201 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 250 chr1qtel1M 619429 CTCTCCCTCCCTCTCACTGTCCCTC-CCCTCTGTCCCTC-CCCTCTCCCT 619476 i i v v i - i v i - i i (CTCT)n#Simpl 251 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 300 chr1qtel1M 619477 CCCTCTC-CTGTCCCTC-CTCTCTGCTCCCCCCCCCTCTGTCCCTCCCTC 619524 i - v i - - i i i i v i i (CTCT)n#Simpl 301 CTCTCTCTCTCTCTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTC 349 chr1qtel1M 619525 TCACTGTC-CCCTCCCTCTCTGTCCCTC-CCCCCTCTGTCCCTCCCTCTC 619572 v v - i i v i - i i v i i (CTCT)n#Simpl 350 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 399 chr1qtel1M 619573 ACTGTCCCTC-CCCTCTCTGTCCCTC-CCCCCTCTGTCCCTCCCTCTCTC 619620 v v i - i v i - i i v i i (CTCT)n#Simpl 400 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 449 chr1qtel1M 619621 CCTCCCTCCCTCTCACTGTC-CTCCCCCTCTGTCCCTCCCTCTCACTGTC 619669 i i i v v - i i v i i v v (CTCT)n#Simpl 450 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 499 chr1qtel1M 619670 CCTCCCCCTCTGTCCCTC-CCCTCTGTCCCTCCCTCTCACTGTCCCTC-C 619717 i i i v i - i v i i v v i - (CTCT)n#Simpl 500 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 549 chr1qtel1M 619718 CCTCTCCCTCCCTCTCACTGTCCCTCCCCCTCTCCCTCCCTCTCACTGTT 619767 i i i v v i i i i i v v i (CTCT)n#Simpl 550 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 599 chr1qtel1M 619768 CCTCCCCCCCTCTGTCTCTCCCTCTCTC 619795 i i i i v i (CTCT)n#Simpl 600 TCTCTCTCTCTCTCTCTCTCTCTCTCTC 627 Matrix = Unknown Transitions / transversions = 1.98 (99/50) Gap_init rate = 0.02 (15 / 613), avg. gap size = 1.00 (15 / 15) 13 25.49 0.00 4.17 chr1qtel1M 619838 619887 (380113) (TGTATC)n#Simple_repeat 1 48 (0) m_b44s252i15 1567 chr1qtel1M 619838 TGTTTCTGTATCTGTCCACGTGCACCTGTATCTCTATGGTTACCTGTATC 619887 v -- iv i i v vvv i (TGTATC)n#Sim 1 TGTATCTGTATCTGT--ATCTGTATCTGTATCTGTATCTGTATCTGTATC 48 Matrix = Unknown Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.04 (2 / 49), avg. gap size = 1.00 (2 / 2) 13 14.94 0.00 3.23 chr1qtel1M 621247 621278 (378722) (AAAGAA)n#Simple_repeat 1 31 (0) m_b44s252i16 1568 chr1qtel1M 621247 AAACAAAACAAAAAAGGAAGAAGAAAAAGAAA 621278 v - i i i (AAAGAA)n#Sim 1 AAAGAAAA-AGAAAAAGAAAAAGAAAAAGAAA 31 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 255 26.91 5.06 1.22 chr1qtel1M 621452 621530 (378470) MIRb#SINE/MIR 186 267 (1) m_b44s601i17 1569 chr1qtel1M 621452 GATCAAATGAGAT----TTTGTTAATTGCTTATTAGGGTACCTTGGCACA 621497 i ----iv v vi vi vi i - MIRb#SINE/MIR 186 GATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCT-GGCACA 234 chr1qtel1M 621498 CAGTAGGTGCTACATAAATACTTGCTCCCTTAT 621530 i i i vv iv v iv MIRb#SINE/MIR 235 TAGTAAGCGCTCAATAAATGGTAGCTCTATTAT 267 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.04 CpG sites = 11, Kimura (unadjusted) = 33.81 Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.03 (2 / 78), avg. gap size = 2.50 (5 / 2) 260 34.80 2.48 1.85 chr1qtel1M 621578 621738 (378262) C L1PA15_3end#LINE/L1 (517) 395 234 m_b44s551i3 1570 chr1qtel1M 621578 TATAGAGCCATTAATGGCATTGTCGGGTCAGAAGGTA-CTCAGAATGTTA 621626 v v v v ii ii v -i v -- v C L1PA15_3end#L 395 TATATACCCAATAATGGGATTGCTGGGTCGAATGGTAGTTCTG--TTTTA 348 chr1qtel1M 621627 AGAAATTGGGGGCATAATTCAGAATTCTCTTCAGAATCACTGAACTGTTT 621676 vvv v i iv vii- i v v i i v i vi iv C L1PA15_3end#L 347 AGTTCTTTGAGAAATCGC-CAAACTGCTTTCCACAGTGGCTGAACTAATT 299 chr1qtel1M 621677 CCTAGTTTCCTCAGCAGTGCAT---CGTGCCTTTCTTCCCAGAGCCCCTC 621723 ivi v ii vi i --- v i i ii iv i i v C L1PA15_3end#L 298 TACATTCCCACCAGCAGTGTATAAGCGTTCCCTTTTCTCCGCAACCTCGC 249 chr1qtel1M 621724 CAGTTTCTGTCATTT 621738 iv i C L1PA15_3end#L 248 CAGCATCTGTTATTT 234 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 44.55 CpG sites = 30, Kimura (unadjusted) = 48.12 Transitions / transversions = 1.20 (30/25) Gap_init rate = 0.03 (5 / 160), avg. gap size = 1.40 (7 / 5) 234 22.54 5.61 4.63 chr1qtel1M 624028 624134 (375866) C L1ME3D_3end#LINE/L1 (760) 229 122 m_b44s551i4 1571 chr1qtel1M 624028 GACTTTCATCTTATTTTT-CAAATTTGCTAGATATGAAA----ATCTTCA 624072 i ---- - v i v i i i ---- - C L1ME3D_3end#L 229 GACTTTTA----ATTTTTGCCAATCTGGTGGGTGTGAAATGGTATCT-CA 185 chr1qtel1M 624073 AGGTTGTTTTAATTTACATTTATCTTACTCCTAAAGACGTGGAATAT-TT 624121 vv v i vi v i v v v v ii - C L1ME3D_3end#L 184 TTGTGGTTTTAATTTGCATTTCCCTGATTACTAATGAGGTTGAGCATCTT 135 chr1qtel1M 624122 TTCATATGGTTGT 624134 v i C L1ME3D_3end#L 134 TTCATATGTTTAT 122 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 26.98 CpG sites = 11, Kimura (unadjusted) = 26.98 Transitions / transversions = 0.92 (11/12) Gap_init rate = 0.08 (8 / 106), avg. gap size = 1.38 (11 / 8) 249 25.43 5.22 0.83 chr1qtel1M 624040 624154 (375846) C L1MC5_3end#LINE/L1 (2473) 221 102 m_b44s551i5 1571 chr1qtel1M 624040 ATTTTT-CAAATTTGCTAGATATGAAA----ATCTTCAAGGTTGTTTTAA 624084 - v i v i iv ---- - iv v C L1MC5_3end#LI 221 ATTTTTGCCAATCTGATAGGTGAGAAATGGTATCT-CAGTGTAGTTTTAA 173 chr1qtel1M 624085 TTTACATTTATCTTACTCCTAAAGACGTGGAATAT-TTTTCATATGGTTG 624133 i v i viv iv v v ii - ? i C L1MC5_3end#LI 172 TTTGCATTTCTCTTATTATGAGCGAGGTTGAGCATCTTTTCATATGNTTA 123 chr1qtel1M 624134 TAAATAGTTTACATTTCTTTT 624154 vi iivi i C L1MC5_3end#LI 122 AGAGCCATTTGCATTTCTTTT 102 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 31.93 CpG sites = 16, Kimura (unadjusted) = 31.93 Transitions / transversions = 1.23 (16/13) Gap_init rate = 0.04 (4 / 114), avg. gap size = 1.75 (7 / 4) 277 28.42 5.36 2.61 chr1qtel1M 624449 624560 (375440) C L2d_3end#LINE/L2 (22) 494 380 m_b44s601i18 1572 chr1qtel1M 624449 TTTATAGTCTACCAATTATGTTCCCAGCATTGTGGTAAG---TATAGGGA 624495 v vvii v i v i i v i --- i i C L2d_3end#LINE 494 TTTATTGAGCGCCTACTATGTGCTCAGCACTGTGCTAGGCGCTGTGGGGA 445 chr1qtel1M 624496 TGTAGAATCTAAAAATGAAATAC-TA--CCTTGTCCTCAAGGAGCTTACA 624542 vvv ? --- ? i iv v - i-- i i C L2d_3end#LINE 444 ACGANAA---AANAGTATAAGACATGGTCCCTGCCCTCAAGGAGCTTACA 398 chr1qtel1M 624543 CTATATCGGGGAAGATAA 624560 v v viv i i C L2d_3end#LINE 397 ATCTAGTTGGGGAGACAA 380 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 35.51 CpG sites = 16, Kimura (unadjusted) = 37.15 Transitions / transversions = 1.07 (16/15) Gap_init rate = 0.05 (6 / 111), avg. gap size = 1.50 (9 / 6) 219 33.72 2.17 3.30 chr1qtel1M 624479 624570 (375430) C L2c_3end#LINE/L2 (38) 440 350 m_b44s601i19 1572 chr1qtel1M 624479 TGTGGTAAGTA-TAGGGATGTAGAATCTAAAAATGAAATACTA-CCTTGT 624526 vi i ii- i ii i i--- vi i i i vi- i i C L2c_3end#LINE 440 TGTGCCAGGCGCTGGGGATACAAAG---ATGAATAAGACACGGTCCCTGC 394 chr1qtel1M 624527 CCTCAAGGAGCTTACACTATATCGGGGAAGATAATAATGTAAAC 624570 i v v vi i i i ivv ? C L2c_3end#LINE 393 CCTCAAGGAGCTCACAGTCTAGTGGAGGAGACAGACANGTAAAC 350 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 47.00 CpG sites = 22, Kimura (unadjusted) = 49.71 Transitions / transversions = 2.75 (22/8) Gap_init rate = 0.05 (5 / 91), avg. gap size = 1.00 (5 / 5) 480 24.63 0.00 5.26 chr1qtel1M 624834 624953 (375047) MIRc#SINE/MIR 2 115 (153) m_b44s601i20 1573 chr1qtel1M 624834 GGGGCAGCTAGGTGGCACAATGGATAGAGCACTGGCCCTGGACTCAGGAG 624883 i i--- ii i v v i v i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr1qtel1M 624884 GACTTGAATTCAAATCTGGCTTCAGACAATACTTTCCAGATATGTTACCT 624933 i ii i i iv vi v v --- v i v i v MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCC---ACTTACTAGCTGTGTGACCT 95 chr1qtel1M 624934 TGGGCAATTCACTTAACCCC 624953 v i MIRc#SINE/MIR 96 TGGGCAAGTCACTTAACCTC 115 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.18 CpG sites = 17, Kimura (unadjusted) = 30.46 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.05 (6 / 119), avg. gap size = 1.00 (6 / 6) 12 25.39 4.69 3.08 chr1qtel1M 627985 628048 (371952) (AGATGA)n#Simple_repeat 1 65 (0) m_b44s252i17 1574 chr1qtel1M 627985 AGATGACTATGGAGTTGAATGTTAA-ATGAAGAT-AA-ATGAGTTTGAAA 628031 vv i v vi v - - - ivv -- (AGATGA)n#Sim 1 AGATGAAGATGAAGATGAAGATGAAGATGAAGATGAAGATGAAGATG--A 48 chr1qtel1M 628032 AGATGAAGGGGAAAATG 628048 iv i (AGATGA)n#Sim 49 AGATGAAGATGAAGATG 65 Matrix = Unknown Transitions / transversions = 0.62 (5/8) Gap_init rate = 0.08 (5 / 63), avg. gap size = 1.00 (5 / 5) 17 0.00 0.00 0.00 chr1qtel1M 628316 628334 (371666) (T)n#Simple_repeat 1 19 (0) m_b44s252i18 1575 chr1qtel1M 628316 TTTTTTTTTTTTTTTTTTT 628334 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 17 0.00 0.00 0.00 chr1qtel1M 628679 628697 (371303) (T)n#Simple_repeat 1 19 (0) m_b44s252i19 1576 chr1qtel1M 628679 TTTTTTTTTTTTTTTTTTT 628697 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 192 24.07 7.41 0.00 chr1qtel1M 629940 629993 (370007) C L2#LINE/L2 (607) 2475 2418 m_b45s601i0 1577 chr1qtel1M 629940 GGGAATTTGGGGATTC--TTTTGGACATGTTAAATTTGGGATGCTTG--A 629985 i iv ii ii -- i i i i-- C L2#LINE/L2 2475 GGAAGATCAGGAGTTCAGTTTTGGACATGTTAAGTTTGAGATGCCTATTA 2426 chr1qtel1M 629986 AATATCCA 629993 i i C L2#LINE/L2 2425 GACATCCA 2418 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 32.03 CpG sites = 12, Kimura (unadjusted) = 32.03 Transitions / transversions = 12.00 (12/1) Gap_init rate = 0.04 (2 / 53), avg. gap size = 2.00 (4 / 2) 69 1.53 0.00 0.00 chr1qtel1M 631727 631792 (368208) (C)n#Simple_repeat 1 66 (0) c_b45s251i0 1578 chr1qtel1M 631727 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 631776 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 50 chr1qtel1M 631777 CCCCCCCCCCGCCCCC 631792 v (C)n#Simple_r 51 CCCCCCCCCCCCCCCC 66 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0) 300 32.12 12.13 2.04 chr1qtel1M 633893 634337 (365663) C L1PREC2_orf2#LINE/L1 (2692) 602 114 m_b45s551i0 1579 chr1qtel1M 633893 TGTATGCCATGTGCTGCTGAGAAAAAGGTATATTTCTTTTTATTTCTATT 633942 i i vi v i v iiv v v ?vvi v C L1PREC2_orf2# 602 TATGTGCCATGTGGCGATGAGAAGAATGTATATTCTGTTGTTTTNGGGTG 553 chr1qtel1M 633943 CAGTTTTCTCCAGAGGTCTATCATACCTA---------------AATT-- 633975 v vv vi v vii i --------------- i -- C L1PREC2_orf2# 552 GAGAGTTCTGTAGATGTCTATCAGGTCCATTTGGTCCAGTGTTGAGTTCA 503 chr1qtel1M 633976 --TTCT-----TTTTTGTTTCTTTTGTGGTTAAAT---TTATCTAATTCT 634015 -- i ----- i vv v vi vi ---i i v C L1PREC2_orf2# 502 GGTCCTGAATATCTTTGTTAATTTTCTGCCTCGATGATCTGTCTAATACT 453 chr1qtel1M 634016 GAGAGGGAGAAGTTTAGATCCTCCACTAATAT--------------AGTT 634051 vv v i iv v ii ii v -------------- i C L1PREC2_orf2# 452 GTCAGTGGGGTGTTGAAGTCTCCCACTATTATTGTGTGGGAGTCTAAGTC 403 chr1qtel1M 634052 TTGCTGTAATTGGCT--TAACTT-CTTTAAGAATTTGGATGCTC-TACGA 634097 ivi ? iv vv --v - v i i - ii - C L1PREC2_orf2# 402 TCTTTGNAGGTCTCTAAGAACTTGCTTTATGAATCTGGGTGCTCCTGTG- 354 chr1qtel1M 634098 CTTGGTGCATATACATTTAATATCCTTACTACTTCATTG-TGTATGGTAC 634146 i v i iv vv vvv - - v v v C L1PREC2_orf2# 353 TTGGGTGCATATATATTTAGGATAGTTAGGTCTTC-TTGTTGAATTGAAC 305 chr1qtel1M 634147 CCTTTAACAAGATATAGTTTCCTTCCTTAGCTCATTTAATTAAATCTTTT 634196 v vv i i vi i iv iv -----i v C L1PREC2_orf2# 304 CCTTTACCATTATGTAATGCCCTTCTTTGTCTTTTTT-----GATCTTTG 260 chr1qtel1M 634197 TTTACTTA-----TGTTTTATCTGGGATCAGAATTGCTACTCCTGGTTTT 634241 vii ----- i ii i i v i v C L1PREC2_orf2# 259 TTGGTTTAAAGTCTGTTTTGTCTGAAATTAGGATTGCAACCCCTGCTTTT 210 chr1qtel1M 634242 TTTTGCTT--CAGCTGAAGCATAATAAATTCTGTTGCA-GCCTTCACTGT 634288 i i -- vi --- v ii i i vi v -v i i v C L1PREC2_orf2# 209 TTCTGTTTTCCATTT---GCTTGGTAGATTTTTCTCCATCCCTTTATTTT 163 chr1qtel1M 634289 TACTCTGTATGTATCTCTGTAATTCAAATGTATTTCTTGTAAATAACAT 634337 v vi i iv i vi i vv v i vi i v i i i C L1PREC2_orf2# 162 GAGCCTATGGGTGTCATTGCATGTGAGATGGGTCTCTTGAAGACAGCAT 114 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 42.25 CpG sites = 72, Kimura (unadjusted) = 43.05 Transitions / transversions = 1.06 (72/68) Gap_init rate = 0.05 (23 / 444), avg. gap size = 2.78 (64 / 23) 413 32.00 7.05 2.60 chr1qtel1M 633968 634336 (365664) C L1P3_orf2#LINE/L1 (2795) 499 115 m_b45s551i1 1579 chr1qtel1M 633968 CCTAAATTTTCTTTTTTGTTTCTTTTGTGGTTAAATTTATCTAATTCTGA 634017 i v i v vi ii v v v i - i i vi C L1P3_orf2#LIN 499 CCTGAATATCCTTGTTAATTTTCTGTCTCGTTGA-TCTGTCTAATATTGA 451 chr1qtel1M 634018 GAGGGAGAAGTTTAGATCCTCCACTAATAT--------------AGTTTT 634053 v v i iv v ii ii v -------------- i i C L1P3_orf2#LIN 450 CAGTGGGGTGTTAAAGTCTCCCACTATTATTGTGTGGGAGTCTAAGTCTC 401 chr1qtel1M 634054 GCTGTAATTGGCT--TAACTT-CTTTAAGAATTTGGATGCTCTACGACTT 634100 vi iv vv --v - v i i ivvv i v C L1P3_orf2#LIN 400 TTTGTAGGTCTCTAAGAACTTGCTTTATGAATCTGGGTGCTCCTGTATTG 351 chr1qtel1M 634101 GGTGCATATACATTTAATATCCTTACTACTTCATTGT-GTATGGTACCCT 634149 i iv vv viv - - i v vv C L1P3_orf2#LIN 350 GGTGCATATATATTTAGGATAGTTAGCTCTTC-TTGTTGCATTGATCCCT 302 chr1qtel1M 634150 TTAACAAGATATAGTTTCCTTCCTTAGCTCATTTAATTAAATCTTTTTTT 634199 v vv i i vi i iv iv i ----- v v C L1P3_orf2#LIN 301 TTACCATTATGTAATGCCCTTCTTTGTCTTTTTTGAT-----CTTTGTTG 257 chr1qtel1M 634200 ACTTA-----TGTTTTATCTGGGATCAGAATTGCTACTCCTGGTTTTTTT 634244 ii ----- v i ii i v i v C L1P3_orf2#LIN 256 GTTTAAAGTCTGTTTTATCAGAGACTAGGATTGCAACCCCTGCTTTTTTT 207 chr1qtel1M 634245 TGCTT--CAGCTGAAGCATAATAAATTCTGTTGCA-GCCTTCACTGTTAC 634291 -- vi --- v ii ?i vi v -v i i v v v C L1P3_orf2#LIN 206 TGCTTTCCATTT---GCTTGGTAAATNTTCCTCCATCCCTTTATTTTGAG 160 chr1qtel1M 634292 TCTGTATGTATCTCTGTAATTCAAATGTATTTCTTGTAAATAACA 634336 i i i i i i vv v i vi i i v v i i C L1P3_orf2#LIN 159 CCTATGTGTGTCTTTGCACGTGAGATGGGTCTCCTGAATACAGCA 115 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 42.73 CpG sites = 60, Kimura (unadjusted) = 42.73 Transitions / transversions = 1.09 (60/55) Gap_init rate = 0.05 (17 / 368), avg. gap size = 2.12 (36 / 17) 398 31.52 7.74 1.72 chr1qtel1M 633975 634413 (365587) C L1M1_orf2#LINE/L1 (2801) 493 29 m_b45s551i2 1579 chr1qtel1M 633975 TTTCTTTTTTG-TTTCTTTTGTGGTTAAATTTATCTAATTCTGAGAGGGA 634023 v - ii v v v- i i i i v i v i C L1M1_orf2#LIN 493 TTTCTTTGTTGATTTTCTGTCTGGA-AGATCTGTCCAATGCTGAAAGTGG 445 chr1qtel1M 634024 GAAGTTTAGATCCTCCACTAATATAGTTTTG----------CTGTAATTG 634063 iv v ii ii vi v v v ---------- v vv i C L1M1_orf2#LIN 444 GGTGTTGAAGTCTCCAGCTATTATTGTATTGGGGTCTATCTCTCTCTTTA 395 chr1qtel1M 634064 GCT----TAAC---TTCTTTAAGAATTTGGATGCTCTACGACTTGGTGCA 634106 ---- i--- v viv i i i vvii v C L1M1_orf2#LIN 394 GCTCTAATAATATTTGCTTTATATATCTGGGTGCTCCAGTGTTGGGTGCA 345 chr1qtel1M 634107 TATACATTTAATATCCTTACTACTTCATTG-TGTATGGTACCCTTTAACA 634155 i ?v iv ivv i - - v v vv v C L1M1_orf2#LIN 344 TATATATTTANAATTGTTATATCCTC-TTGCTGAATTGACCCCTTTATCA 296 chr1qtel1M 634156 AGATATAGTTTCCTTCCTTAGCTCATTTAATTAAATCTTTTTTT--ACTT 634203 vv vv i iv v i v -- i i v i -- vv C L1M1_orf2#LIN 295 TTATATAGTGACCTTCTTTGTCTCTTCTTAT--AGTTTTTGTCTTGAAAT 248 chr1qtel1M 634204 ATGTTTTATCTGGGATCAGAATTGCTACTCCTGGTTTTTTTT-GCTTCAG 634252 v i i iv v v v v i - i vi C L1M1_orf2#LIN 247 CTATTTTGTCTGATATAAGTATAGCTACTCCTGCTCTTTTTTGGTTTCCA 198 chr1qtel1M 634253 CTGAAGCATAATAAATTCTGTTGCA-GCCTTCACTGTTACTCTGTATGTA 634301 i -- iiv v ii v v -v i i v i v i i i C L1M1_orf2#LIN 197 TTG--GCATGGAATATCTTTTTCCATCCCTTTATTTTCAGTCTATGTGTG 150 chr1qtel1M 634302 TCTCTGTAATTCAAATGTATTTCTTGTAAATAAC--ATTGTAGAGTTCTG 634349 i i iv v i i iii -- ii?v i ii C L1M1_orf2#LIN 149 TCTTTATAGGTGAAGTGTGTTTCTTGTAGGCAACAGATCANTGGGTCTTG 100 chr1qtel1M 634350 TGCTTTAATCTGTT-ATTTGCT-TCTGTTTTATGA---GAGAGTTCATAA 634394 vi v ii - viii - v i v --- -- i C L1M1_orf2#LIN 99 TTTTTTCATCCATTCAGCCACTCTATGTCTTTTGATTGGAGAGTT--TAG 52 chr1qtel1M 634395 TCC----ACAGTTAAGATTATTA 634413 ---- v i vi C L1M1_orf2#LIN 51 TCCATTTACATTCAATGTTATTA 29 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 42.02 CpG sites = 72, Kimura (unadjusted) = 42.02 Transitions / transversions = 1.12 (72/64) Gap_init rate = 0.05 (21 / 438), avg. gap size = 2.00 (42 / 21) 413 32.35 3.23 2.49 chr1qtel1M 634081 634359 (365641) C L1MC_orf2#LINE/L1 (2924) 370 90 m_b45s551i3 1579 chr1qtel1M 634081 ATTTGGATGCTCTACGACTTGGTGCATATACATTTAATATCCTTACTACT 634130 v i iivii v i i i v iv iv ivv C L1MC_orf2#LIN 370 ATTTTGACGCTCTGTTGTTAGGCGCATACACGTTAAGGATTGTTATGTCT 321 chr1qtel1M 634131 TCATTGTGTATGGTACCCTTTAACAAGATATAGTTTCCTTCCTTAGCTCA 634180 v v v v v vv v vv i i vi i i v i - C L1MC_orf2#LIN 320 TCTTGGAGAATTGACCCCTTTATCATTATGTAATGCCCCTCTTTATCCC- 272 chr1qtel1M 634181 TTTAATTAAATCTTTTTTTACT------TATGTTTTATCTGGGATCAGAA 634224 -- i -- - ii i ------ v i i i ii i iv C L1MC_orf2#LIN 271 --TGAT--AA-CTTTCCTTGCTCTGAAGTCTGCTCTGTCTGAAATTAATA 227 chr1qtel1M 634225 TTGCTACTCCTGGTTTTTTTTGCTTCAGCTGAAGCATAATAAATTCTGTT 634274 v ? v i v - ivvv ii v ii vi C L1MC_orf2#LIN 226 TAGCTACTCCNGCTTTCTTTTGATT-AGTGTTAGCATGGTATATCTTTCT 178 chr1qtel1M 634275 GCAGCC-TTCACTGTTACTCTGTATGTATCTCTGTAATTCAAATGTATTT 634323 v v - i v v i i i i v v i vi C L1MC_orf2#LIN 177 CCATCCNTTTACTTTTAATCTATATGTGTCTTTATATTTAAAGTGGGTTT 128 chr1qtel1M 634324 CTTGTAAATAACAT-T-GTAGAGTTCTGTGCTTTAATC 634359 i i - - v i ii vi i C L1MC_orf2#LIN 127 CTTGTAGACAACATATAGTTGGGTCTTGTTTTTTGATC 90 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 41.72 CpG sites = 49, Kimura (unadjusted) = 43.70 Transitions / transversions = 1.26 (49/39) Gap_init rate = 0.04 (11 / 278), avg. gap size = 1.45 (16 / 11) 226 35.38 2.29 2.76 chr1qtel1M 634575 634792 (365208) C L1MA5A_3end#LINE/L1 (386) 658 442 m_b45s551i4 1580 chr1qtel1M 634575 TGCTGTGTGTAATGATCTCCTGGTTCTG-CTCATTTCACTTACTATCAAT 634623 v v i---i i v i - i vi - C L1MA5A_3end#L 658 TGCGGTGTTTAAC---TTTCTGTTCCTGGCTTATTTCACTTAACAT-AAT 613 chr1qtel1M 634624 -TCCTGTAAGTCTCTCCAGGCCTCTCTGAAT--CATCCTGCTGGTCTTTT 634670 - vi iv iv v iiv ivi -- vvv viiiv C L1MA5A_3end#L 612 GTCCTCCAGTTCCATCCATGTTGCCGCGAATGACAGGATTTCATTCTTTT 563 chr1qtel1M 634671 CTTATAGAACAATAATATTCCATAACATTGATATACCATAACTTATTTAG 634720 - i vvv i viii vv i vi v v C L1MA5A_3end#L 562 -TTATGGCTGAATAGTATTCCATTGTGTATATATACCACATTTTCTTTAT 514 chr1qtel1M 634721 CCATCCTCCTACTAGTGGGCATCCA-CTCAATTTCCAATTTCTAGCCACT 634769 i vi ii iv i i i -v ii i vv i - i i i C L1MA5A_3end#L 513 CCATTCATCTGTTGTTGGACACCTAGGTTGATTCCATATCT-TGGCTATT 465 chr1qtel1M 634770 ACAAAGAGGGCTGTCACAAACAT 634792 iii v v iv i C L1MA5A_3end#L 464 GTGAATAGTGCTGCAATAAACAT 442 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 47.77 CpG sites = 43, Kimura (unadjusted) = 49.65 Transitions / transversions = 1.34 (43/32) Gap_init rate = 0.05 (10 / 217), avg. gap size = 1.10 (11 / 10) 322 32.68 1.95 1.46 chr1qtel1M 634599 634803 (365197) C L1MC4a_3end#LINE/L1 (1995) 634 429 m_b45s551i5 1580 chr1qtel1M 634599 TCTGCTCATTTCACTTACTATCAATTCCTGTAAGTCTCTCCAGGCC---T 634645 i iv vi vi vv v i v vii --- C L1MC4a_3end#L 634 TTTGCTTTTTTCACTTAACAATATATCCTGGAAATCACTCCATATCAGTT 585 chr1qtel1M 634646 CTCTGA-ATCATCCTGCTGGTCTTTTCTTATAGAACAATAATATTCCATA 634694 viv - v vv -- - i vvvv i i v C L1MC4a_3end#L 584 CATAGAGATCTTCCTCAT--TCTTTT-TTACAGCTGCATAGTACTCCATT 538 chr1qtel1M 634695 ACATTGATATACCATAACTTATTTAGCCATCCTCCTACTAGTGGGCATCC 634744 iii v i ii i i ?i i??i ii C L1MC4a_3end#L 537 GTGTGGATGTACCATAGTTTATTCAACCANTCTCCTATNNATGGGCATTT 488 chr1qtel1M 634745 ACTCAATTTCCAATTTCTAGCCACTACAAAGAGGGCTGTCACAAACATTT 634794 vvivi v i v v i v iv iv ii i vii C L1MC4a_3end#L 487 AGGTTGTTTCCAATATTTTGCAATTACAAACAATGCTGCAATGAATAACC 438 chr1qtel1M 634795 TTGCACATA 634803 ii C L1MC4a_3end#L 437 TTGTGCATA 429 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 45.06 CpG sites = 37, Kimura (unadjusted) = 45.06 Transitions / transversions = 1.28 (37/29) Gap_init rate = 0.02 (5 / 204), avg. gap size = 1.40 (7 / 5) 353 31.73 2.01 4.83 chr1qtel1M 634660 634808 (365192) C L1MC3_3end#LINE/L1 (1958) 574 430 m_b45s551i6 1580 chr1qtel1M 634660 GCTGGTCTTTTCTTATAGAACAATAATATTCCATAACATTGATATACCAT 634709 vi i i i v vvv vii v i i C L1MC3_3end#LI 574 GCTCATTTCTTTTTATCGCTGAATAATATTCCATTGTATGGATGTACCAC 525 chr1qtel1M 634710 AACTTATTTAGCCATCCTCCTACTAGTGGGCATCCACTCAAT---TTCCA 634756 ii i v i v i iiv i --- iii --- C L1MC3_3end#LI 524 AGTTTGTTTATCCATTCACCTATTGAAGGACAT---CTTGGTTGCTTCCA 478 chr1qtel1M 634757 ATTTCTAGCCACTACAAAGAGGGCTGTCACAAACATTTTTGCACATACAG 634806 i i i v i ii v ii ii i ---- i i i C L1MC3_3end#LI 477 GTTTTTGGCGATTATGAATAAAGCTGCTATAAACATT----CGCGTGCAG 432 chr1qtel1M 634807 GT 634808 C L1MC3_3end#LI 431 GT 430 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 41.74 CpG sites = 33, Kimura (unadjusted) = 44.48 Transitions / transversions = 2.75 (33/12) Gap_init rate = 0.05 (8 / 148), avg. gap size = 1.25 (10 / 8) 478 28.27 0.00 2.17 chr1qtel1M 634682 634822 (365178) C L1ME4c_3end#LINE/L1 (275) 555 418 m_b45s551i7 1580 chr1qtel1M 634682 ATAATATTCCATAACATTGATATACCATAACTTATTTAGCCATCCTCCTA 634731 vivi ? i i i i i i C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chr1qtel1M 634732 CTAGTGGGCATCCACTCAATTTCCAATTTCTAGCCACTACAAAGAGGGCT 634781 i iv i ii vvivi i v i i i v iv C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCT 456 chr1qtel1M 634782 GTCACAAACATTTTTGCACATACAGGTCCCTTTTCCTTCTT 634822 iv ii i i ii i --- i C L1ME4c_3end#L 455 GCAATGAACATCTTCGTGCATATAG---CTTTTTCCTTCTT 418 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.70 CpG sites = 29, Kimura (unadjusted) = 38.24 Transitions / transversions = 2.90 (29/10) Gap_init rate = 0.02 (3 / 140), avg. gap size = 1.00 (3 / 3) 494 27.64 0.00 0.00 chr1qtel1M 634682 634804 (365196) C L1ME3G_3end#LINE/L1 (376) 548 426 m_b45s551i8 1580 chr1qtel1M 634682 ATAATATTCCATAACATTGATATACCATAACTTATTTAGCCATCCTCCTA 634731 i ii v i i i i C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr1qtel1M 634732 CTAGTGGGCATCCACTCAATTTCCAATTTCTAGCCACTACAAAGAGGGCT 634781 i ii i ii vvivi i v i i v iv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr1qtel1M 634782 GTCACAAACATTTTTGCACATAC 634804 iv ii ii i i C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACATGC 426 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 36.94 CpG sites = 26, Kimura (unadjusted) = 36.94 Transitions / transversions = 3.25 (26/8) Gap_init rate = 0.00 (0 / 122), avg. gap size = 0.0 (0 / 0) 668 29.71 3.42 2.03 chr1qtel1M 637453 637744 (362256) C L1ME4c_3end#LINE/L1 (179) 651 356 m_b45s551i9 1581 chr1qtel1M 637453 TACAAT---ATATTCTGCTTGTTTCCCTCAGTGTCAGTTTGTGTAAATCT 637499 ---i v v i iii i vv ii iv v - C L1ME4c_3end#L 651 TACAATTTTGTATTCTGCTTTTTTCACTTAACATTATATCATAAACAT-T 603 chr1qtel1M 637500 TTCCAGGCCTTTCTAAA-AATCAGC----TTGTTCATTTCTTACAGATCA 637544 v -- v v - i vv ---- i- i v ii v vv C L1ME4c_3end#L 602 TTCCATG--TTGCTACATAGTCTTCATAATTA-TCATTTTTAATGGCTGC 556 chr1qtel1M 637545 GTAATATTCCATTACCTTTGTATACCCCAGCTTACCCAGCCATTCCCCAA 637594 i iivv ?vi i vi ii ii i v C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chr1qtel1M 637595 TCGGTGGATATCTACTCACTTTCCAATTCTTTGCCATCACAGAAAGAGCT 637644 i v i i vvivv i i i i i i v iv C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCT 456 chr1qtel1M 637645 GCTATAAACATTTTTGCACATGTAGGTCCTTTTCTTTCCTTT--ATGATT 637692 v i i i ii i -- i i i -- v C L1ME4c_3end#L 455 GCAATGAACATCTTCGTGCATATAG--CTTTTTCCTTCTTTTGAATTATT 408 chr1qtel1M 637693 TCCTTGGGATACAGCCCTAGGAATGGCACTGCTGGGTCAAAGGGTATGCA 637742 i v vi i i i v i i v C L1ME4c_3end#L 407 TCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAA 358 chr1qtel1M 637743 CA 637744 C L1ME4c_3end#L 357 CA 356 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 37.49 CpG sites = 52, Kimura (unadjusted) = 39.35 Transitions / transversions = 1.58 (52/33) Gap_init rate = 0.03 (10 / 291), avg. gap size = 1.60 (16 / 10) 572 30.44 6.81 2.37 chr1qtel1M 637465 637787 (362213) C L1ME3Cz_3end#LINE/L1 (367) 630 294 m_b45s551i10 1581 chr1qtel1M 637465 TGCTTGTTTCCCTCAGTGTCA-GTTTGTGTAAATCTTTCCAGGCC--TTT 637511 v v iii i - v - i i v v ii-- vi C L1ME3Cz_3end# 630 TGCTTTTTTCACTCAACATTATGTTTTTG-AGATTTATCCATGTTGATAC 582 chr1qtel1M 637512 CTAAAAATC-AGCTTGTTCATTTCTTACAGATCAGTAATATTCCATTACC 637560 v iv i - i ii - v v v vvi i iiv C L1ME3Cz_3end# 581 ATGTAGATCTAGTTCATTCATTT-TAACTGCTGTATAGTATTCCATTGTA 533 chr1qtel1M 637561 TTTGTATACCCCAGCTTACCCAGCCATTCCCCAATCGGTGGATATCTACT 637610 vvi v ii iii v v i i i i vv C L1ME3Cz_3end# 532 TGAATATACCACAATTTATTTATCCATTCCCCTATTGATGGACATTTAGG 483 chr1qtel1M 637611 CACTTTCCAATTCTTTGCCATCACAGAAAGAGCTGCTATAAACATTTTTG 637660 ivv i i i i i v iv v i ii C L1ME3Cz_3end# 482 TTGTTTCCAATTTTTCGCTATTACAAACAATGCTGCAATGAACATCCTTG 433 chr1qtel1M 637661 CACATGTAGGTCCTTTTCTTTCCTTTATGA---TTTCCTTGGGATACAGC 637707 i v-- v viv- v v ii --- ii i i i vv C L1ME3Cz_3end# 432 TACATGTC--TCCTTGTGCA-CATGTGCGAGAGTTTCTCTAGGGTATATA 386 chr1qtel1M 637708 CCTAGGAATGGCACTGCTGGGTCAAAGGGTATGCACAGCT--AATT---C 637752 i i v i iv i v -- i --- C L1ME3Cz_3end# 385 CCTAGAAGTGGAATTGCTGGGTCGTAGGGTATGCGCATCTTCAACTTTAC 336 chr1qtel1M 637753 TAG----------ACTGTTCTCCAGAATGGTTGGATCTTAAATTT 637787 ---------- i i i i v i --- C L1ME3Cz_3end# 335 TAGATATTGCCAAATTGCTCTCCAAAGTGGTTGTACC---AATTT 294 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 38.27 CpG sites = 58, Kimura (unadjusted) = 40.46 Transitions / transversions = 1.53 (58/38) Gap_init rate = 0.05 (15 / 322), avg. gap size = 2.00 (30 / 15) 599 30.24 6.37 2.16 chr1qtel1M 637521 637787 (362213) C L1ME3E_3end#LINE/L1 (415) 574 297 m_b45s551i11 1581 chr1qtel1M 637521 AGCTTGTTCATTTCTTACAGATCAGTAATATTCCATTACCTTTGTATACC 637570 i ii - i v v vvi i iiv vvi C L1ME3E_3end#L 574 AGTTCATTCATTT-TCACTGCTGTATAGTATTCCATTGTATGAATATACC 526 chr1qtel1M 637571 CCAGCTTACCCAGCCATTCCCCAATCGGTGGATATCTACTCACTTTCCAA 637620 v ii iii v i vi i i i ivvivv i C L1ME3E_3end#L 525 ACAATTTATTTATCCATTCTCCTGTCGATGGACATTTGGGTTGTTTCCAG 476 chr1qtel1M 637621 TTCTTTGCCATCACAGAAAGAGCTGCTATAAACATTTTTGCACATGTAGG 637670 i i i i v iv i i i v-- C L1ME3E_3end#L 475 TTTTTTGCTATTACAAACAATGCTGCTATGAACATTCTTGTACATGTC-- 428 chr1qtel1M 637671 TCCTTTT-CTTTCCTTTATGA-TTTCCTTGGGATACAGCCCTAGGAATGG 637718 vv - viv v vi v - ii i i i vv i C L1ME3E_3end#L 427 TCCTGGTGCACACGTGCAAGAGTTTCTCTAGGGTATATACCTAGGAGTGG 378 chr1qtel1M 637719 CACTGCTGGGTCAAAGGGTATGCAC---------------AGCTAATTCT 637753 v i iv i --------------- v v i C L1ME3E_3end#L 377 AATTGCTGGGTCGTAGGGTATGCGCATCTTCAACTTTACTAGATAATGCC 328 chr1qtel1M 637754 AGACTGTTCTCCAGAATGGTTGGATCTTAAATTT 637787 i i i i i v i --- C L1ME3E_3end#L 327 AAATTGTTTTCCAAAGTGGTTGTACC---AATTT 297 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 38.79 CpG sites = 48, Kimura (unadjusted) = 40.11 Transitions / transversions = 1.55 (48/31) Gap_init rate = 0.03 (9 / 266), avg. gap size = 2.56 (23 / 9) 204 22.45 0.00 0.00 chr1qtel1M 637879 637927 (362073) C L3#LINE/CR1 (327) 3772 3724 m_b45s601i1 1582 chr1qtel1M 637879 GACAGCTTTCCTATCTCTGCTGAGTCTTGTCTTCTGTAGTCTAAACACC 637927 v v i iv i v vi v i C L3#LINE/CR1 3772 GACAGCTATCATGTCTCCTCTAAGTCTTCTCTTCTCCAGGCTAAACATC 3724 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 26.79 CpG sites = 5, Kimura (unadjusted) = 26.79 Transitions / transversions = 0.83 (5/6) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 269 31.36 13.57 2.26 chr1qtel1M 638776 638974 (361026) C MIRb#SINE/MIR (6) 262 42 m_b45s601i2 1583 chr1qtel1M 638776 AGAATAAGCATTGATCTAGCACCTAATACGTGTGAGGCGCCTTGCTAAGC 638825 iiv v v iv i i v i iv i iv C MIRb#SINE/MIR 262 AGAGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGC 213 chr1qtel1M 638826 ACTTTACAAGTGT------------TCCTCACAAGTGCTTTTC-AGAGAG 638862 i v ii ------------ vvi ii v - iv C MIRb#SINE/MIR 212 GCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAG 163 chr1qtel1M 638863 GTGCTGCTGTCACCTTATTTTTAAGTTAAGACAACT-AGG-TCCGAGTGG 638910 ii ii i -- ii vv v i iv - - v v C MIRb#SINE/MIR 162 GTATTATTAT--CCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGG 115 chr1qtel1M 638911 ACATTCTGTGACTTGCCC-AGGC-----------TGAGTACCTGAGGTAG 638948 --- vv i - i----------- i iv v vii C MIRb#SINE/MIR 114 ---TTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGG 68 chr1qtel1M 638949 GATTTGAACTCCGGTCTTCCCGGCTC 638974 i i v vi i i C MIRb#SINE/MIR 67 GATTCGAACCCAGGTCTGTCTGACTC 42 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 38.43 CpG sites = 36, Kimura (unadjusted) = 42.11 Transitions / transversions = 1.44 (36/25) Gap_init rate = 0.06 (11 / 198), avg. gap size = 2.91 (32 / 11) 247 27.35 10.00 2.48 chr1qtel1M 640464 640613 (359387) C L2a_3end#LINE/L2 (1) 516 356 m_b45s601i3 1584 chr1qtel1M 640464 TTCATT-AGTCAGCAAGTAGTTGTTTAGCAACTACAGTATACCAGATATT 640512 - v i i v i v iv vi i i ii i C L2a_3end#LINE 516 TTCATTCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACT 467 chr1qtel1M 640513 TGTT---AGTGCTGGG--TACAA-AG---ACAAAA---ATAAATGAGCCC 640550 - ---i i -- i- --- --- i -- i C L2a_3end#LINE 466 -GTTCTAGGCGCTGGGGATACAGCAGTGAACAAAACAGACAAA--AGTCC 420 chr1qtel1M 640551 TTTCCTTCTGAGGACTGGCATTC-AGTTGGGGGAAACA-CCATGTATATA 640598 i v i vvi ii vi - v i -v -i v i C L2a_3end#LINE 419 CTGCCCTCATGGAGCTTACATTCTAGTGGGGGGAGACAGACA-ATAAACA 371 chr1qtel1M 640599 GAAAAGTAAATAAAA 640613 i v i i C L2a_3end#LINE 370 AATAAATAAGTAAAA 356 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.38 CpG sites = 27, Kimura (unadjusted) = 35.61 Transitions / transversions = 2.08 (27/13) Gap_init rate = 0.08 (12 / 149), avg. gap size = 1.58 (19 / 12) 305 27.11 5.04 0.81 chr1qtel1M 640661 640779 (359221) L2c_3end#LINE/L2 345 468 (10) m_b45s601i4 1585 chr1qtel1M 640661 TATATGTTTATATAGTGTGTC-CTTCCA-TACTCTGTGGGCTTCTGAAGG 640708 i v i? - v - i - vv i i vi L2c_3end#LINE 345 TGTCTGTTTACNT-GTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGG 393 chr1qtel1M 640709 GCAGGTACTGGATTTT-CTC--CTTTATCTCCTCAGCACTT-ACTCATAG 640754 v i vi i -i -- i v i i i -i v L2c_3end#LINE 394 GCAGGGACCGTGTCTTATTCATCTTTGTATCCCCAGCGCCTGGCACATAG 443 chr1qtel1M 640755 AAAGCACTTAATTAATGCCTCTTGA 640779 v i i i v ii v L2c_3end#LINE 444 TAGGCGCTCAATAAATGTTTGTTGA 468 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 31.14 CpG sites = 20, Kimura (unadjusted) = 35.13 Transitions / transversions = 1.67 (20/12) Gap_init rate = 0.05 (6 / 118), avg. gap size = 1.17 (7 / 6) 606 27.65 10.62 0.81 chr1qtel1M 641225 641450 (358550) MIRb#SINE/MIR 13 260 (8) m_b45s601i5 1586 chr1qtel1M 641225 GTGGTACAGGGGACAGAGCTCTGCCCTTGGA----------CCTCAGTTC 641264 i v v v v v i ---------- vi MIRb#SINE/MIR 13 GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTC 62 chr1qtel1M 641265 AAGTCCTGCCTCAAACACTGCCTAGCCCTGTGACCCTGAGCAAATCAGTG 641314 i i i v viv vv iv i i i i v v MIRb#SINE/MIR 63 GAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTT 112 chr1qtel1M 641315 CATCCATCT--ACCTCAGTTTCCTCATCTCTAAAATGG---------CAT 641353 v i iv --i v ---------i i MIRb#SINE/MIR 113 AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAC 162 chr1qtel1M 641354 CTGCTTCTCAAGGTGGTTGGTGGGGATCATCTTGAGATAATAATTATAAA 641403 i i v i v - i i -vv ivv i MIRb#SINE/MIR 163 CTACCTCGCAGGGTTGTT-GTGAGGATTA-AATGAGATAATGCATGTAAA 210 chr1qtel1M 641404 GTGTTTATCAAAATACTTGGTGCACACTAAGCAT---ATAAATATTAGCT 641450 i i v v i i i ii i v ii--- iv MIRb#SINE/MIR 211 GCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAAATGGTAGCT 260 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 32.51 CpG sites = 35, Kimura (unadjusted) = 35.27 Transitions / transversions = 1.30 (35/27) Gap_init rate = 0.03 (6 / 225), avg. gap size = 4.33 (26 / 6) 417 29.19 7.84 4.05 chr1qtel1M 641892 642248 (357752) L1MC4a_3end#LINE/L1 257 626 (2003) m_b45s551i12 1587 chr1qtel1M 641892 GAAAAACTGGGACATTAATACATTATTGGTGGAGTTGTGAACTGATCCAA 641941 ii v v vi v ii iiv ii ? i v L1MC4a_3end#L 257 GGGAAACAGGCACTCTCATACATTGCTGGTGGGAATGCAAANTGGTACAA 306 chr1qtel1M 641942 CCATTCTGGAGAGCAATCTGGAACTACGCT--CAAAGGTCTATCAAACTG 641989 v ? i v i v v i- -- i-- - --- i L1MC4a_3end#L 307 CCCTTNTGGAGGGGAATTTGGCAATAT-CTAACAAAA--CTA-CA---TA 349 chr1qtel1M 641990 TGCAC--ACCCTTTGACCTAGCATTATATCCCAA----AGAGATCTTA-- 642031 i-- i ---- v---- ii - -- L1MC4a_3end#L 350 TGCATTTACCCTTTGACCCAGCA----ATCCCACTTCTAGGAAT-TTACC 394 chr1qtel1M 642032 --AAAGAGG-------AAAAGGGAC----CCACATGTGTAAAAA--TATT 642066 --i vi------- v v v ----i? i i v i-- L1MC4a_3end#L 395 CTGAAGATACACCTCCAACATGTACAAAATNACATATGCACAAGGTTATT 444 chr1qtel1M 642067 TGTGGAAGCCCTTTTAGTAGTGGTGAGAAACTGAAAACTGAGTGAATGCC 642116 ii v v vi v v i v ii i v i i vivv i L1MC4a_3end#L 445 CATTGCAGCATTGTTTGTAATTGCAAAATATTGGAAACAACCTAAATGCC 494 chr1qtel1M 642117 TATGAACTGGAGAATGGCTGAATAAATTGTGGTATAGGAATACTATGGAA 642166 i ?? iv ? i i i i vvv i v i L1MC4a_3end#L 495 CATNNATAGGAGANTGGTTGAATAAACTATGGTACATCCACACAATGGAG 544 chr1qtel1M 642167 TACTATTGTTCTATAAGAAACAATCAGCAGAAACATTTC-AGGGAGT--C 642213 vvvv i i v v -- i- i - v i v --i L1MC4a_3end#L 545 TACTATGCAGCTGTAAAAAAGAATGAG--GAAG-ATCTCTATGAACTGAT 591 chr1qtel1M 642214 CTGGAGAGACTCACATGAACTGATGGTAAGTGAAA 642248 v v i iv v vv iv v L1MC4a_3end#L 592 ATGGAGTGATTTCCAGGATATATTGTTAAGTGAAA 626 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 38.59 CpG sites = 53, Kimura (unadjusted) = 38.59 Transitions / transversions = 1.13 (53/47) Gap_init rate = 0.07 (25 / 356), avg. gap size = 1.72 (43 / 25) 696 28.81 6.83 1.37 chr1qtel1M 641895 642172 (357828) L1ME4c_3end#LINE/L1 263 555 (275) m_b45s551i13 1587 chr1qtel1M 641895 AAACTGGGACATTAATACATTATTGGTGGAGTTGTGAACTGATCCAACCA 641944 v ?i v ii vi? i i i v v L1ME4c_3end#L 263 AAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACAACCC 312 chr1qtel1M 641945 TTCTGGAGAGCAATCTGGAACTACGC-TCAAAGGTCTATCAAACTGTGCA 641993 i i i v v i- ii i - v v v L1ME4c_3end#L 313 TTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCC-ATAAAAATGTTCA 361 chr1qtel1M 641994 CACCCTTTGACCTAG------CATT------A---TATCCCAAAGAGAT- 642027 i i ------ i ------ --- i i i - L1ME4c_3end#L 362 TACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATA 411 chr1qtel1M 642028 -CTTAAAAG-AGGAAAAGGGACCCACATGTGTAAAAATATTTGTGGAAGC 642075 -i i - i --- i i iiii i i ii v v L1ME4c_3end#L 412 ATTCAAAAGAAGGAAAAAG---CTATATGCACGAAGATGTTCATTGCAGC 458 chr1qtel1M 642076 CCTTTTAGTAGTGGTGAGAAACTGAAAACTGAGTGAATGCCTATGAACTG 642125 vi v vi i i i i i i vivv i i i vv iv L1ME4c_3end#L 459 GTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAG 508 chr1qtel1M 642126 GAGAATGGCTGAATAAATTGTGGTATAGGAATACTATGGAATACTAT 642172 i i i i i i vv? iv v i L1ME4c_3end#L 509 GGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATATTAT 555 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 37.48 CpG sites = 54, Kimura (unadjusted) = 38.84 Transitions / transversions = 2.16 (54/25) Gap_init rate = 0.04 (11 / 277), avg. gap size = 2.09 (23 / 11) 22 18.86 0.00 0.00 chr1qtel1M 645581 645622 (354378) (T)n#Simple_repeat 1 42 (0) m_b45s252i1 1588 chr1qtel1M 645581 TTTTTTTAATTGATATTTTCCTTTTTTTTTTTTTTTTTTTTT 645622 vv vv v ii (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 42 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 213 23.08 10.77 0.00 chr1qtel1M 646527 646591 (353409) C L2a_3end#LINE/L2 (37) 480 409 m_b45s601i6 1589 chr1qtel1M 646527 ATGTGCCAGGTACTATGCTAAGAACTGGGGATAAA--AGT--ACAAGCCA 646572 i i v i vi v -- -- iv C L2a_3end#LINE 480 ATGTGCCAGGCACTGTTCTAGGCGCTGGGGATACAGCAGTGAACAAAACA 431 chr1qtel1M 646573 ---AAGAGTATCTACCTCCATG 646591 --- i vi i ii C L2a_3end#LINE 430 GACAAAAGTCCCTGCCCTCATG 409 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 26.25 CpG sites = 10, Kimura (unadjusted) = 28.45 Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.05 (3 / 64), avg. gap size = 2.33 (7 / 3) 339 34.99 15.01 1.26 chr1qtel1M 647071 647976 (352024) L2#LINE/L2 1562 2590 (492) m_b45s601i7 1590 chr1qtel1M 647071 TACCCAGAAATCTGTCATC-ATCCTCCCAT-TTCCTCCTTCACGCCAGGC 647118 vvv i - -i v i v -i iv v v v vi L2#LINE/L2 1562 TACCCACCTACCTG-CATCTGTGCCCACATACTCTGCCTTCCCTCCTGTT 1610 chr1qtel1M 647119 TCTAAGGAAGAGATGTCC---CTTCGTGCTAAGGCTGACCTCTCTATGTG 647165 v v v iv --- i vvv ii i i iv L2#LINE/L2 1611 ACTACGGATGAACTGTCCGTGCTCCTATCTAAGGCCAACCCCTCCACTTG 1660 chr1qtel1M 647166 TACCCTAAATCTTTGTTCCTTTT--TTATT--------TTACTT-ATCA- 647203 i v i iivvii i i--i i -------- ii i- v - L2#LINE/L2 1661 TGCACTAGATCCCATCCCCTCTCGCCTACTCAAGGACATCGCTCCAGCAA 1710 chr1qtel1M 647204 -TCTTCCCTCTCTA---------ATCAGTCTCTCCCTACCTACTCTTTCC 647243 - i v--------- i i i vi vvv v L2#LINE/L2 1711 TTCTCCCCTCTCTCTCCTGCATCATCAATTTTTCCCTCTCTACTGGATCA 1760 chr1qtel1M 647244 TTTCCTGAT-GGC-TGTCAATGTATCCAAATCTCCCTCATCCTTTAAGAA 647291 i -- -i - iiv ii iiivv? i i i i v i L2#LINE/L2 1761 TTCCC--ATCAGCATACAAACATGCTGTNATTTCTCCCATCTTTAAAAAA 1808 chr1qtel1M 647292 C------TTTCACAAGATTCTACCAGGGCTGCCAACTATAACCCTATATT 647335 ------ i v vv ii i ?vvvv iv i ivi i v i L2#LINE/L2 1809 CAAAAATTCTCCCTTGACCCCACNTCCCCCTCCAGCTACCGCCCCATTTC 1858 chr1qtel1M 647336 TCTTCTTCTC-----AGGTCAAGTTCTTGAAA-AGGTGTTTATTTTCCAA 647379 v i i ----- vvv v i i - v i vi -iv L2#LINE/L2 1859 TCTGCTCCCCTTTACAGCAAAACTCCTCGAAAGAGTTGTCTATACTC-GC 1907 chr1qtel1M 647380 TGTTTCTATTTCAACACATACCTA----CTTCTGAACC-ATTCG---CAG 647421 i i v vv v v - i ---- ii - i v--- L2#LINE/L2 1908 TGTCTCCAATTCCTCTCCT-CCCATTCTCTCTTGAACCCACTCCAATCAG 1956 chr1qtel1M 647422 AGTTGATTCTTCATCATTAAACTGAAATTGCTCTC--TGAACTTATTAAT 647469 iv vvv ii i i vv i i i--ii iv i ii L2#LINE/L2 1957 GCTTTCGTCCCCACCACTCCACCGAAACTGCTCTTGTCAAGGTCACCAAT 2006 chr1qtel1M 647470 GAGCTGTTTA-ATCTCCAAATACAATGGACTTTTGGCAATCCTCATCCCA 647518 v --ii -i iv i v v vv vv i ii L2#LINE/L2 2007 GACCT--CCACGTTGCTAAATCCAATGGTCAATTCTCAGTCCTCATCTTA 2054 chr1qtel1M 647519 TTTG---------CAACATTT--TGTAGTTAACTACTTTTTCCTC--TGG 647555 i --------- i --iii i ii iii i-- i L2#LINE/L2 2055 CTTGACCTNTCAGCAGCATTTGACACAGTTGATCACTCCCTCCTTCTTGA 2104 chr1qtel1M 647556 GATA--TTCTGCACTT----TCCAGG--------TGCTTGAGGTTCTCC- 647590 i i -- v ---- --------iv ivv i - L2#LINE/L2 2105 AACACTTTCTTCACTTGGCTTCCAGGACACCACACTCTCCTGGTTTTCCT 2154 chr1qtel1M 647591 -------------CCTCTCCTCCTC-----CCTGT-CTGACTACTACTCA 647621 ------------- v i ----- v - ii v v L2#LINE/L2 2155 CCTACCTCACTGGCCGCTCCTTCTCAGTCTCCTTTGCTGGTTCCTCCTCA 2204 chr1qtel1M 647622 GATGTTATACCTACTTAACACTTAGGGTATCCC----CTAAGCATCTGCA 647667 vv viivv - ? i- i i ii ---- v ivii v L2#LINE/L2 2205 TCTCCCCGACCT-CTNAACG-TTGGAGTGCCCCAGGGCTCAGTCCTTGGA 2252 chr1qtel1M 647668 CTCTGTTCTCCTTTCCTTATACATT--------AAGTGATCTTATCAACT 647709 - v i i iv v i --------?i i v v L2#LINE/L2 2253 C-CTCTTCTCTTCTCTATCTACACTCACTCCCTNGGTGATCTCATCCAGT 2301 chr1qtel1M 647710 CTCAAAGACTTAG---TTATCTATGCAGATGATGATTCTCAGACCCA-AT 647755 vi vi i---ii ii- v i i i iii - L2#LINE/L2 2302 CTCATGGCTTTAAATACCATCTATAT-GCTGATGACTCCCAAATTTATAT 2350 chr1qtel1M 647756 CTTTG-------CCTCTATCCTGAGCTCCATTTTCACACTACCAACTGCC 647798 iii------- vi i vvi ii ivv L2#LINE/L2 2351 CTCCAGCCCGGACCTCTCCCCTGAACTCCAGACTCGTATATCCAACTGCC 2400 chr1qtel1M 647799 TATTAGATGTTTTGAACAGGATGCCTTACAGAGATCTTAAACTCCATATA 647848 i v ii i iv viv i v i iv i iv i i L2#LINE/L2 2401 TACTCGACATCTCCACTTGGATGTCTAATAGGCATCTCAAACTTAACATG 2450 chr1qtel1M 647849 TCCAAAAC--AACTTATA----TTTCCCTCAAATC--CTCCTC---CAAA 647887 -- iv i---- ii i -- --- iv L2#LINE/L2 2451 TCCAAAACTGAACTCCTGATCTTCCCCCTCAAACCTGCTCCTCCCGCAGT 2500 chr1qtel1M 647888 CTTCACTATTCTTATTGACGACAATACCATCTTCATAATCATCTAGTTTT 647937 v i iiivi ?i i i iv i ivi i iiiii viiv L2#LINE/L2 2501 CTTCCCCATCTCAGTNAATGGCAACTCCATCCTTCCAGTTGCTCAGGCCA 2550 chr1qtel1M 647938 GTAATCTC---GTCAACTCTTGACTCACATTTGTTCACTCAC 647976 iv i i--- v - - vi iv v L2#LINE/L2 2551 AAAACCTTGGAGTCATC-CTTGACTC-CTCTCTTTCTCTCAC 2590 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 47.95 CpG sites = 193, Kimura (unadjusted) = 50.05 Transitions / transversions = 1.61 (193/120) Gap_init rate = 0.06 (52 / 905), avg. gap size = 2.87 (149 / 52) 20 8.02 0.00 0.00 chr1qtel1M 649088 649114 (350886) (T)n#Simple_repeat 1 27 (0) m_b45s252i2 1591 chr1qtel1M 649088 TTTTTTCTTTTTTCTTTTTTTTTTTTT 649114 i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTT 27 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 184 27.59 0.00 0.00 chr1qtel1M 649135 649192 (350808) C MamRTE1#LINE/RTE-BovB (1707) 2105 2048 m_b45s601i8 1592 chr1qtel1M 649135 CCCTCCTTCCACCTTGTAAATTTCAGCTGGAATAGAATCAGCACCAAGTG 649184 i i vv v i v v ivv vv i v C MamRTE1#LINE/ 2105 CTCCCCTTCCTGCTTGAAAATCTCAGCAGGTATGCCATCAGGTCCGAGAG 2056 chr1qtel1M 649185 CTTTGCCA 649192 i C MamRTE1#LINE/ 2055 CTTTACCA 2048 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 31.98 CpG sites = 6, Kimura (unadjusted) = 34.42 Transitions / transversions = 0.60 (6/10) Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0) 333 32.72 4.62 2.84 chr1qtel1M 649500 649672 (350328) C MamRTE1#LINE/RTE-BovB (2509) 1303 1128 m_b45s601i9 1592 chr1qtel1M 649500 TGATCAGTCCAGCACTCTGCACCACAC---GCTATC----TTTCACCATT 649542 i i v i i --- iiv---- i v v i C MamRTE1#LINE/ 1303 TGGTCGGTCCAGCACTCGGCGCCACGCATAGCTGCAGTAATCTAAACATC 1254 chr1qtel1M 649543 CTTCCACACTGTCTCTCCTCCTTACAATCATGTAGCCTATTAAATGCCAG 649592 vi---- i v ivi vv i v i ii v v i v C MamRTE1#LINE/ 1253 CTTCAG----GTCCCGCTGTCGAACGATGATATAATCAATGAGATGCCAC 1208 chr1qtel1M 649593 TATCTACTGCAAGGGGGCATCCATGAAGT-TCTATTGCATTTAGGTAAGT 649641 iii vvv vv v v - i v ivi i- i i C MamRTE1#LINE/ 1207 TGCTTAGACCTTGGGTGCATCCATGATGTCTTTCTCTTATTC-GGTAGGC 1159 chr1qtel1M 649642 AGAAGACAGTGCTGGTGATGAGGAGGTGATG 649672 i ii i v v v C MamRTE1#LINE/ 1158 GGAAGATGGTGTTGGTGATTACGAGCTGATG 1128 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 37.87 CpG sites = 30, Kimura (unadjusted) = 44.09 Transitions / transversions = 1.20 (30/25) Gap_init rate = 0.05 (8 / 172), avg. gap size = 1.62 (13 / 8) 394 24.63 9.03 1.29 chr1qtel1M 649906 650049 (349951) C MamRTE1#LINE/RTE-BovB (3347) 465 311 m_b45s601i10 1592 chr1qtel1M 649906 TTGGGTAAGCAGACTATTTTTGGAGCACCTTTTCTAGTCCCT--CACATC 649953 vv i i v iv i i ? -- v i C MamRTE1#LINE/ 465 TTGGCGAGGCAGGCAACGTTTAGGGCACCTTTTCTAGNCCCTTCCCCATT 416 chr1qtel1M 649954 TGGAG------GTGCGGTCCTTAA-AAGGCTGTTCAAACA-CCGGGGGGC 649995 i ------ i ? v - i i i - i ?v C MamRTE1#LINE/ 415 CGGAGTGAGCAGCGCGNTCCTAAACAGGGCTGCTCAGACACCCAGGNCGC 366 chr1qtel1M 649996 TACTGAATCCCACTGCTGCTTC--CAGCGAGAAGAGGAGCCTAAGAT-CT 650042 i i ivvii i -- vv iiv -- i v - C MamRTE1#LINE/ 365 TGCCGAACGGTGCTGCTGCCTCNTCAGCGACTAAGCGA--CCAATATCCT 318 chr1qtel1M 650043 GGGCTGC 650049 i C MamRTE1#LINE/ 317 GGGCCGC 311 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 25.38 CpG sites = 22, Kimura (unadjusted) = 31.56 Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.06 (8 / 143), avg. gap size = 1.88 (15 / 8) 23 3.03 2.94 0.00 chr1qtel1M 650643 650676 (349324) (TTTTTC)n#Simple_repeat 1 35 (0) m_b45s252i3 1593 chr1qtel1M 650643 TTTTTC-TTTTCTTTTTTTTTTTCTTTTTCTTTTT 650676 - i (TTTTTC)n#Sim 1 TTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTT 35 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 359 22.79 0.96 2.94 chr1qtel1M 650679 650782 (349218) C MIR#SINE/MIR (139) 123 22 m_b45s601i11 1594 chr1qtel1M 650679 CTGAAGCA-ATTGGGGCTAAGTGACTTGCCCAGGGTCACACAGCTAGGAA 650727 i - vv i i i i v C MIR#SINE/MIR 123 CTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAA 74 chr1qtel1M 650728 GTGTGTCTGAGGACAGATTTGAACTCAGGTCCTCCTGACTTCAGGGCTAG 650777 - - v vvvi i i ivv - i i i iv C MIR#SINE/MIR 73 GTG-G-CAGAGCCGGGATTCGAACCCAGGCAGT-CTGGCTCCAGAGCCCG 27 chr1qtel1M 650778 TGCTC 650782 C MIR#SINE/MIR 26 TGCTC 22 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 26.19 CpG sites = 13, Kimura (unadjusted) = 27.55 Transitions / transversions = 1.30 (13/10) Gap_init rate = 0.04 (4 / 103), avg. gap size = 1.00 (4 / 4) 512 18.88 0.00 1.89 chr1qtel1M 650690 650797 (349203) C MIRc#SINE/MIR (153) 115 10 m_b45s601i12 1594 chr1qtel1M 650690 GGGGCTAAGTGACTTGCCCAGGGTCACACAGCTAGGAAGTGTGTCTGAGG 650739 i i i v - - v v C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTG-G-CAGAGC 68 chr1qtel1M 650740 ACAGATTTGAACTCAGGTCCTCCTGACTTCAGGGCTAGTGCTCCATCTAC 650789 vvi i i i i i i v i iv i C MIRc#SINE/MIR 67 CGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCAC 18 chr1qtel1M 650790 TGCACCAC 650797 C MIRc#SINE/MIR 17 TGCACCAC 10 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 20.97 CpG sites = 13, Kimura (unadjusted) = 22.19 Transitions / transversions = 1.86 (13/7) Gap_init rate = 0.02 (2 / 107), avg. gap size = 1.00 (2 / 2) 215 38.99 7.66 1.72 chr1qtel1M 651011 651284 (348716) L2#LINE/L2 2672 2961 (121) m_b45s601i13 1595 chr1qtel1M 651011 CACTGTTCCCACATTATTGCACACCCTCATCACTTCACTCTTGGGCTATT 651060 iiv vi iv v vi vi ii v v i ii i L2#LINE/L2 2672 CACTGCCACCACCCTGGTCCAAGCCACCATCATCTCTCGCCTGGATTACT 2721 chr1qtel1M 651061 GAAATAGT-----------TCAGCCTGCTTTGTGTCT--CCCTATTCTGG 651097 v i----------- vv ivvvi -- ivi ?ii L2#LINE/L2 2722 GCAATAGCCTCCTAACTGGTCTCCCTGCTTCCACCCTTGCCCCCCTNCAG 2771 chr1qtel1M 651098 TCCACCCTCCATTTAGCCACCAAAATGATTTTCCTAAAGTAAAAGTTCAA 651147 i ii v ivi vi i i ii ii iiiv ivi L2#LINE/L2 2772 TCTATTCTCAACACAGCAGCCAGAGTGATCCTTTTAAAACGTAAGTCAGA 2821 chr1qtel1M 651148 TCATGTCATCTCCACC-CCCAATAGAAAAACGCCAATGGCTCTTTATTGC 651196 - v i- i ---- vv v iiii iv L2#LINE/L2 2822 TCATGTCA-CTCCTCTGCTCA----AAACCCTCCAATGGCTTCCCATCTC 2866 chr1qtel1M 651197 CTCCGGGATCAAATACAA----CATGCAGTA---TTCAAAGCCCTTCACA 651239 vii i ii v vv ---- v i i i--- v i v ii L2#LINE/L2 2867 ACTCAGAGTAAAAGCCAAAGTCCTTACAATGGCCTACAAGGCCCTACATG 2916 chr1qtel1M 651240 ACCTATTCTCTTTCTACCTTTCCAATCTCCTTACCTCTCATTCCC 651284 i iv i iivi i ii i v iv vi i i L2#LINE/L2 2917 ATCTGGTCCCCCGTTACCTCTCTGACCTCATCTCCTACCACTCTC 2961 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 57.97 CpG sites = 68, Kimura (unadjusted) = 59.93 Transitions / transversions = 1.84 (68/37) Gap_init rate = 0.04 (10 / 273), avg. gap size = 2.60 (26 / 10) 329 33.56 11.76 3.14 chr1qtel1M 651399 651721 (348279) C L1ME5_3end#LINE/L1 (297) 644 295 m_b45s551i14 1596 chr1qtel1M 651399 TTCTGGTTCT-GCTCCCTCCACTCAGCATCA-GTTCATGTAAG-TCTCCC 651445 v -i iii i ii - -- v - ivi C L1ME5_3end#LI 644 TTCTGTTTCTTACTTTTTTCACTCAGCACTATGTT--TTTAAGATCCATC 597 chr1qtel1M 651446 CAGGCCTCTCTGAAATCATCCTGTTGTTCATTTCTTATA------GAATA 651489 v iiv v vivv --- v i i v v ------ v C L1ME5_3end#LI 596 CATGTTGCTATGTGTACATC---TAGTCCGTTGCTTCTAACTGCTGCATA 550 chr1qtel1M 651490 ATATCCCCCTAACATTCATATACTGTAACTCACTCAGCCATTCTCCAACT 651539 i - i v iiii v vi iii vi i ii v i v v C L1ME5_3end#LI 549 GTA-CTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCAGT 501 chr1qtel1M 651540 GATGGGCATCTA------CTC-GGTTTCTTGCCACCACAATAAAGGCTGC 651582 i i i ------ -iii i ii vv v C L1ME5_3end#LI 500 GATGGACACCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCTGC 451 chr1qtel1M 651583 CACAAATATTTTTGCATAT--------ATGGG------------TTTCTT 651612 v ii i ii i i i -------- i------------ C L1ME5_3end#LI 450 AATGAACATCCTCGTACATGTCCCCTTATGGACCTGTGTGAGAATTTCTT 401 chr1qtel1M 651613 TGGGATACAGGCCCAGTAGAGACATAGTTGGATCAAAAGATATGCAGAGT 651662 i vi v v iv v i i v i i iv vv C L1ME5_3end#LI 400 TGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATGCGTATA 351 chr1qtel1M 651663 TTGATAACCCTTTGGGCA--TAGTTCCAAATTATTCTCTAGAATGGTTGG 651710 i -- --- ivi -- v v i ii i i v C L1ME5_3end#LI 350 CT--TAA---TTTGACTAAGTACTGCCAGATTGCTCTCCAGAATGGCTGC 306 chr1qtel1M 651711 ATCCATTCACA 651721 i vi ii C L1ME5_3end#LI 305 ACCAGTCTACA 295 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 44.54 CpG sites = 67, Kimura (unadjusted) = 47.05 Transitions / transversions = 1.76 (67/38) Gap_init rate = 0.06 (20 / 322), avg. gap size = 2.45 (49 / 20) 390 34.06 13.02 1.67 chr1qtel1M 651507 651721 (348279) C L1ME3E_3end#LINE/L1 (457) 532 294 m_b45s551i15 1596 chr1qtel1M 651507 ATATACTGTAACTCACTCAGCCATTCTCCAACTGATGGGCATCTA----- 651551 iii i i i i v viii i i i----- C L1ME3E_3end#L 532 ATATACCACAATTTATTTATCCATTCTCCTGTCGATGGACATTTGGGTTG 483 chr1qtel1M 651552 --CTCGGTTTCTTGCCACCACAATAAAGGCTGCCACAAATATTTTTGCAT 651599 --ii i i i ii vv v i ii i i i i C L1ME3E_3end#L 482 TTTCCAGTTTTTTGCTATTACAAACAATGCTGCTATGAACATTCTTGTAC 433 chr1qtel1M 651600 ATAT--------------------GGGTTTCTTTGGGATACAGGCCCAGT 651629 i -------------------- i i i i i vi i v C L1ME3E_3end#L 432 ATGTCTCCTGGTGCACACGTGCAAGAGTTTCTCTAGGGTATATACCTAGG 383 chr1qtel1M 651630 AGAGACATAGTTGGATCAAAAGATATGCAGAGTTTGATAACCCT-TTGGG 651678 v iv v i i iv i i iv vi --i ii -i i - C L1ME3E_3end#L 382 AGTGGAATTGCTGGGTCGTAGGGTATGCGCATCTT--CAACTTTACTAG- 336 chr1qtel1M 651679 CATAGTTCCAAATTATTCTCTAGAATGGTTGGATCCATTCACA 651721 - i v i i i i i v i v i C L1ME3E_3end#L 335 -ATAATGCCAAATTGTTTTCCAAAGTGGTTGTACCAATTTACA 294 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 47.61 CpG sites = 56, Kimura (unadjusted) = 50.76 Transitions / transversions = 3.50 (56/16) Gap_init rate = 0.04 (8 / 214), avg. gap size = 4.00 (32 / 8) 232 27.81 7.07 4.23 chr1qtel1M 652038 652221 (347779) L2#LINE/L2 2109 2297 (785) m_b45s601i14 1597 chr1qtel1M 652038 CTCTCCTCCTTAAGTTCTTGAGGTACTGCTCTCTTCTGGTTCTCCTCCT- 652086 i i vi vi i iiiii ii ii v i i - L2#LINE/L2 2109 CTTTCTTCACTTGGCTTCCAGGACACCACACTCTCCTGGTTTTCCTCCTA 2158 chr1qtel1M 652087 --TT-CTGACTGTTCCTTCTCCATCTCCTTTGTTGGATGTTCTTCCAGAT 652133 -- i- i i i vi i --- i --- L2#LINE/L2 2159 CCTCACTGGCCGCTCCTTCTCAGTCTCCTTTGCTG---GTTCCTCC---T 2202 chr1qtel1M 652134 CATGTGTC------CTGATCATAGGTGTTCCACAGGGATCTGTCCTGGGC 652177 v vi ------ ? v i v v v v v v v v L2#LINE/L2 2203 CATCTCCCCGACCTCTNAACGTTGGAGTGCCCCAGGGCTCAGTCCTTGGA 2252 chr1qtel1M 652178 CCTCTCTCCTTCCCCTATATAC---CACTTCACCTGTTGATCTCCTC 652221 - ii i i v --- i - i? v v L2#LINE/L2 2253 CCTCT-TCTCTTCTCTATCTACACTCACTCC-CTNGGTGATCTCATC 2297 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 34.70 CpG sites = 31, Kimura (unadjusted) = 36.58 Transitions / transversions = 1.72 (31/18) Gap_init rate = 0.07 (13 / 183), avg. gap size = 1.62 (21 / 13) 562 33.90 13.08 2.11 chr1qtel1M 653000 653641 (346359) L2#LINE/L2 2304 3014 (68) m_b45s601i15 1597 chr1qtel1M 653000 CATGGATATAATTCTCATCTCTAGGCTGATAATTTTCAAATGTAATTTTC 653049 v v v vi v v i i ii v vv i L2#LINE/L2 2304 CATGGCTTTAAATACCATCTATATGCTGATGACTCCCAAATTTATATCTC 2353 chr1qtel1M 653050 TTCCTCCAGTTTCCCTCCT----TCCAATTTAACATTGCCAGCTACATTG 653095 ivv i viiii i i ---- ivi vii vv i i v vv L2#LINE/L2 2354 CAGCCCGGACCTCTCCCCTGAACTCCAGACTCGTATATCCAACTGCCTAC 2403 chr1qtel1M 653096 CAGATATCTTAAACTGGACCTACAGTAAATATCTAAAAGTCAATATGTCC 653145 iv i iv vi iv vi i iii v v i i L2#LINE/L2 2404 TCGACATCTCCACTTGGATGTCTAATAGGCATCTCAAACTTAACATGTCC 2453 chr1qtel1M 653146 AGAATGGAATTCATTATCTTTCCCTCCAAACTCTCTTCTCCTTCCAAATT 653195 i iv i v v i ii iiv i -iv ivi L2#LINE/L2 2454 AAAACTGAACTCCTGATCTTCCCCCTCAAACCTGCTCCTCC-CGCAGTCT 2502 chr1qtel1M 653196 TCCCTATTGAGGTTGAGGTCAACGCCAT-CTCCCACTCCCTTAGGCTCAC 653244 i ivvi ?i v v v - i v iv i iv v L2#LINE/L2 2503 TCCCCATCTCAGTNAATGGCAACTCCATCCTTCCAGTTGCTCAGGCCAAA 2552 chr1qtel1M 653245 AACCTAGGA-TCATCTTGGGCTTTCCACTTT-TTTCTCACCCC------- 653285 v - i v i iii v - i v ------- L2#LINE/L2 2553 AACCTTGGAGTCATCCTTGACTCCTCTCTTTCTCTCACACCCCACATCCA 2602 chr1qtel1M 653286 ---------CAAGGCCTGTCAGATTAACCTTCACAACGCATT-----TCC 653321 --------- iv i v iv v iii i----- L2#LINE/L2 2603 ATCCATCAGCAAATCCTGTCGGCTCTACCTTCAAAATATATCCAGAATCC 2652 chr1qtel1M 653322 AA-TACTTCTCCTTCTCTCCTGTGGGGACACTCTCCCCACTCTGAT-GAA 653369 i -i viivi --------- vi v i i -v L2#LINE/L2 2653 GACCACTTCTCACCACCTC---------CACTGCCACCACCCTGGTCCAA 2693 chr1qtel1M 653370 G--ACCATCACTTCACCCCT-GACTATGGCA----------AGCTG---- 653402 -- ii v v - i iv ---------- i ---- L2#LINE/L2 2694 GCCACCATCATCTCTCGCCTGGATTACTGCAATAGCCTCCTAACTGGTCT 2743 chr1qtel1M 653403 -CCTGCCTCCAGC--TGACTCTTCCCAGTTCAATCTCCATTCAGCCACCA 653449 - i v -- v i iii? ii v v iv vi L2#LINE/L2 2744 CCCTGCTTCCACCCTTGCCCCCCTNCAGTCTATTCTCAACACAGCAGCCA 2793 chr1qtel1M 653450 AAGTGATTTTTCTAAAGCA-----CAGATC-TGTTAC-CCCCTACTCACT 653492 i ii i i i----- - i - i i --- L2#LINE/L2 2794 GAGTGATCCTTTTAAAACGTAAGTCAGATCATGTCACTCCTCTGCTC--- 2840 chr1qtel1M 653493 AAAA---GCCAGTGGTTCCCTATTACTTCCATGATA-----------CTT 653528 ---v i i i i iv vii vii ----------- i L2#LINE/L2 2841 AAAACCCTCCAATGGCTTCCCATCTCACTCAGAGTAAAAGCCAAAGTCCT 2890 chr1qtel1M 653529 TGTAA----CT-CAAAGCCCTTCATAA-CCAGTTTCCTCCTGCCTTTCCA 653572 ii ---- - i v i - ii ii ivi i i ii L2#LINE/L2 2891 TACAATGGCCTACAAGGCCCTACATGATCTGGTCCCCCGTTACCTCTCTG 2940 chr1qtel1M 653573 GGC----CTTTTAGGCCTTACTCCCCAACACTC---TTGATTCAGTGACA 653615 iv ---- ii -- viv vv i ---ii v i iv L2#LINE/L2 2941 ACCTCATCTCCTA--CCACTCTCCCCCTCGCTCACTCCGCTCCAGCCACA 2988 chr1qtel1M 653616 CTAGCCATGTGGCTATTCCCCAAACA 653641 i viv v i i i L2#LINE/L2 2989 CTGGCCTCCTTGCTGTTCCTCGAACA 3014 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 44.96 CpG sites = 134, Kimura (unadjusted) = 47.79 Transitions / transversions = 1.70 (134/79) Gap_init rate = 0.06 (40 / 641), avg. gap size = 2.48 (99 / 40) 186 20.00 0.00 0.00 chr1qtel1M 654599 654638 (345362) L2d_3end#LINE/L2 471 510 (6) m_b45s601i16 1598 chr1qtel1M 654599 AGCACATTTTAGGTGACTAATAAATGCTTATTGATTGATT 654638 vv i vii i i L2d_3end#LINE 471 AGCACATAGTAGGCGCTCAATAAATACTTGTTGATTGATT 510 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 20.49 CpG sites = 5, Kimura (unadjusted) = 23.72 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 477 29.13 3.93 1.65 chr1qtel1M 654637 654814 (345186) MIR#SINE/MIR 74 255 (7) m_b45s601i18 1599 chr1qtel1M 654637 TTACTGGCTATGTGACTCTAGGCAAATCAC--AATTTTTCTCAGGCTCAG 654684 i i ii i i i -- ii i vv v MIR#SINE/MIR 74 TTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAG 123 chr1qtel1M 654685 TTTCCTCTTCTGTAAAATAGAAATAACA--AGTGATTGTTTTCTAGGGTT 654732 v i ii i -- ivi iii iv MIR#SINE/MIR 124 TTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTCATAGGGTT 173 chr1qtel1M 654733 GCTATAGGAATTAAATGCGATAATGCACCAAAAG-GCTTTGCA-AAT-CC 654779 i i ii i v v i ivv - v v - i - MIR#SINE/MIR 174 GTTGTGAGGATTAAATGAGTTAATACATGTAAAGCGCTTAGAACAGTGCC 223 chr1qtel1M 654780 TAAACTACAGTATAGTGTGTTCCACAAATCTTAGC 654814 iivvi i - -- i i v i v MIR#SINE/MIR 224 TGGCACATAGTA-A--GCGCTCAATAAATGTTAGC 255 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 37.85 CpG sites = 35, Kimura (unadjusted) = 38.86 Transitions / transversions = 2.19 (35/16) Gap_init rate = 0.05 (8 / 177), avg. gap size = 1.25 (10 / 8) 510 28.03 7.64 0.00 chr1qtel1M 654637 654793 (345207) MIRc#SINE/MIR 78 246 (22) m_b45s601i19 1599 chr1qtel1M 654637 TTACTGGCTATGTGACTCTAGGCAAATCAC--AATTTTTCTCAGGCTCAG 654684 i i ii i i -- ii i v v MIRc#SINE/MIR 78 TTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAG 127 chr1qtel1M 654685 TTTCCTCTTCTGTAAAATAGAAATAACAA-----G---TGATTGTTTTCT 654726 v i ii i ----- --- vi iii ivi MIRc#SINE/MIR 128 TTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCAC 177 chr1qtel1M 654727 AGGGTTGCTATAGGAATTAAATGCGATAATGCAC-CAAAAG-GCTTTGCA 654774 i i ii i i v i i-ii - i MIRc#SINE/MIR 178 AGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTTTGTA 227 chr1qtel1M 654775 AATCCTAAACTACAGTATA 654793 iiv v i vi i MIRc#SINE/MIR 228 AACTGTAAAGTGCTATACA 246 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 38.02 CpG sites = 35, Kimura (unadjusted) = 38.02 Transitions / transversions = 3.89 (35/9) Gap_init rate = 0.03 (5 / 156), avg. gap size = 2.40 (12 / 5) 531 26.28 2.17 0.71 chr1qtel1M 654637 654774 (345226) MIRb#SINE/MIR 81 220 (48) m_b45s601i17 1599 chr1qtel1M 654637 TTACTGGCTATGTGACTCTAGGCAAATCAC--AATTTTTCTCAGGCTCAG 654684 i i ii i i i -- ii i v v MIRb#SINE/MIR 81 TTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAG 130 chr1qtel1M 654685 TTTCCTCTTCTGTAAAATAGAAATAACAAGTGATTGTTTTCTAGGGTTGC 654734 v i ii i - ivi iii ivi i MIRb#SINE/MIR 131 TTTCCTCATCTGTAAAATGGGGATAATAA-TACCTACCTCGCAGGGTTGT 179 chr1qtel1M 654735 TATAGGAATTAAATGCGATAATGCACCAAAAG-GCTTTGCA 654774 i ii i v ivv - v MIRb#SINE/MIR 180 TGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGCA 220 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.12 CpG sites = 27, Kimura (unadjusted) = 34.32 Transitions / transversions = 3.00 (27/9) Gap_init rate = 0.02 (3 / 137), avg. gap size = 1.33 (4 / 3) 13 7.37 3.03 6.25 chr1qtel1M 656891 656923 (343077) (CCTCCC)n#Simple_repeat 1 32 (0) m_b45s252i5 1600 chr1qtel1M 656891 CCTCCGCCCTTCCCCCTCTTCCT-CCCCTCCCCC 656923 - - ii - (CCTCCC)n#Sim 1 CCTCC-CCC-TCCCCCTCCCCCTCCCCCTCCCCC 32 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.09 (3 / 32), avg. gap size = 1.00 (3 / 3) 293 32.43 6.31 0.00 chr1qtel1M 658964 659074 (340926) L2d2_3end#LINE/L2 435 552 (3) m_b45s601i20 1601 chr1qtel1M 658964 TAGATGATGAGCTTCTTGAGAGCAG--ACTATTTTGCCTGTTT-TTTGTA 659010 vi i i i -- i v iviv ii - L2d2_3end#LIN 435 TAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACTTCTTTGTA 484 chr1qtel1M 659011 TCCTT---AGCAGTTAACATACTGTCTCACACATGATAAACATTGAATAA 659057 ii--- ivi i i v i ii iii ii ii v L2d2_3end#LIN 485 TCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAGTAGGCGCTCAATAA 534 chr1qtel1M 659058 ATATTTACTAA-CTGATT 659074 ii i -i L2d2_3end#LIN 535 ATATTTGTTGATTTGATT 552 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 43.65 CpG sites = 29, Kimura (unadjusted) = 47.41 Transitions / transversions = 4.14 (29/7) Gap_init rate = 0.04 (4 / 110), avg. gap size = 1.75 (7 / 4) 16 10.47 3.23 0.00 chr1qtel1M 659509 659539 (340461) (TTATTT)n#Simple_repeat 1 32 (0) m_b45s252i6 1602 chr1qtel1M 659509 TTAGTTTT-TTTTTATTTTTATTTTTTTTATT 659539 v - v v (TTATTT)n#Sim 1 TTATTTTTATTTTTATTTTTATTTTTATTTTT 32 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.03 (1 / 30), avg. gap size = 1.00 (1 / 1) 18 12.17 0.00 0.00 chr1qtel1M 659513 659539 (340461) (T)n#Simple_repeat 1 27 (0) m_b45s252i7 1602 chr1qtel1M 659513 TTTTTTTTTATTTTTATTTTTTTTATT 659539 v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTT 27 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 321 23.95 11.85 4.14 chr1qtel1M 660587 660721 (339279) C MIRc#SINE/MIR (120) 148 4 m_b45s601i22 1603 chr1qtel1M 660587 CTCATTTTACAGAAGGGGAAACTGAGGCAATTAG---GCTTCAGTAATTT 660633 i v i -- i --- v v i i C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGC--TCAGAGAGGTTAAGTGACTT 101 chr1qtel1M 660634 GCCCAGGATCATACAACTCTTAA-----------GGGTCT-GAGGCCAGG 660671 i i i i vv ----------- v - iv C MIRc#SINE/MIR 100 GCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGG 51 chr1qtel1M 660672 TCTTACTGAGCGCCGCCAGGTCTGCTGCTCCATTCGCTGGGCTGC-CTGC 660720 v ---- v i iiv iv i i vi ii - C MIRc#SINE/MIR 50 TCTTCCTGA----CTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTGC 5 chr1qtel1M 660721 C 660721 C MIRc#SINE/MIR 4 C 4 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 29.66 CpG sites = 19, Kimura (unadjusted) = 29.66 Transitions / transversions = 1.58 (19/12) Gap_init rate = 0.07 (10 / 134), avg. gap size = 2.20 (22 / 10) 326 19.71 4.27 8.93 chr1qtel1M 660587 660703 (339297) C MIRb#SINE/MIR (117) 151 40 m_b45s601i21 1603 chr1qtel1M 660587 CTCATTTTACAGAAGGGGAAACTGAGGCAATTAG---GCTTCAGTAATTT 660633 i v i -- i --- v v i C MIRb#SINE/MIR 151 CCCATTTTACAGATGAGGAAACTGAGGC--TCAGAGAGGTTAAGTAACTT 104 chr1qtel1M 660634 GCCCAGGATCATACAACTCTTAAGGGTCTGAGGCCAGGTCTTACTGAGCG 660683 i i i i vv v v v - i vi ---i i - C MIRb#SINE/MIR 103 GCCCAAGGTCACACAGCTAGTAAGTGGCAGA-GCCGGGATT---CGAAC- 59 chr1qtel1M 660684 CCGCCAGGTCTG-CTG-CTCCA 660703 --- - - C MIRb#SINE/MIR 58 ---CCAGGTCTGTCTGACTCCA 40 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 20.67 CpG sites = 12, Kimura (unadjusted) = 23.04 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.11 (13 / 116), avg. gap size = 1.15 (15 / 13) 46 4.29 0.00 0.00 chr1qtel1M 661941 661988 (338012) (AC)n#Simple_repeat 1 48 (0) c_b45s251i1 1604 chr1qtel1M 661941 ACACACACACACACACACACACACACACACACACACACTTACACACAC 661988 vi (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACAC 48 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 241 25.18 11.97 1.55 chr1qtel1M 662110 662226 (337774) L2a_3end#LINE/L2 386 514 (3) m_b45s601i23 1605 chr1qtel1M 662110 TCTTCTCATTAGAATG--AGTTCCTCCAGGGCAGGGACTCTTTTCACCTT 662157 ii i i -- i viv i v vvi L2a_3end#LINE 386 TCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTCTGTTT 435 chr1qtel1M 662158 TCTT------TCTAACCTTGGCGCTGAGCCACA--GCCTGGCACATAATA 662199 v ------ v v iii iv -v -- i L2a_3end#LINE 436 TGTTCACTGCTGTATCCCCAGCGCCTAG-AACAGTGCCTGGCACATAGTA 484 chr1qtel1M 662200 AAC-CT---TAAATTTTCTGATTAGTGAATG 662226 ii - --- v - v v i L2a_3end#LINE 485 GGCGCTCAATAAATATT-TGTTGAATGAATG 514 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 31.23 CpG sites = 16, Kimura (unadjusted) = 31.23 Transitions / transversions = 1.23 (16/13) Gap_init rate = 0.06 (7 / 116), avg. gap size = 2.29 (16 / 7) 236 15.08 5.56 1.79 chr1qtel1M 662574 662627 (337373) C MIR3#SINE/MIR (59) 149 94 m_b45s601i24 1606 chr1qtel1M 662574 CCTTCTCATTGGTACAAATGGGGAAACTGAGG--CAG-GGGGTGAGGCGA 662620 ii v- i i -- - i i i C MIR3#SINE/MIR 149 CCCCCTCATTT-TACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGA 101 chr1qtel1M 662621 CTTGCCC 662627 C MIR3#SINE/MIR 100 CTTGCCC 94 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 17.60 CpG sites = 7, Kimura (unadjusted) = 17.60 Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.06 (3 / 53), avg. gap size = 1.33 (4 / 3) 460 25.99 11.33 6.37 chr1qtel1M 664734 665033 (334967) C L2c_3end#LINE/L2 (2) 476 163 m_b45s601i25 1607 chr1qtel1M 664734 TCAGTCAGCCAACAAGCATTTATTAAGCACCTTCTTCTATTTGTCAGGCA 664783 v vi i i i v --- v i i C L2c_3end#LINE 476 TCATTCATTCAACAAACATTTATTGAGCGCCTACT---ATGTGCCAGGCG 430 chr1qtel1M 664784 TTGGCTGAAGGGCTAAGAATACAGAGAAAGGTAA-AGACAGACCCTGCTC 664832 i ------------ i i viii - v i v i C L2c_3end#LINE 429 CTGG------------GGATACAAAGATGAATAAGACACGGTCCCTGCCC 392 chr1qtel1M 664833 TCAAGGAGCTTACAGGTTAA-GGGGGAGATA-ACATGCAAA---ACTATG 664877 i vi i- i i - ? i --- v - C L2c_3end#LINE 391 TCAAGGAGCTCACAGTCTAGTGGAGGAGACAGACANGTAAACAGACAAT- 343 chr1qtel1M 664878 TACATATACAAGCTACGGATGGG----ATA-----AGT-TA--------G 664909 - i vv ii ---- ----- - -------- C L2c_3end#LINE 342 TACA-ATACAAGTTAATGATAAGTGCTATAATGGGAGTATAGACAGGGTG 294 chr1qtel1M 664910 CTAT--GATCAACAGAAGGAAGGCACTAAGATTAA----GGAAAGCTGGT 664953 -- v - - i iv i i---- iii iii v C L2c_3end#LINE 293 CTATGGGAGC-ACAG-AGGAGGGCACCTAGACTAGNCTTGGGGGGTCAGG 246 chr1qtel1M 664954 AAAGGCTTCTTGAAGAAAGTAAGATTTTCCCTGGACCTTCACGGA--AGT 665001 i ii i i i i v i vvv ii? v v -- C L2c_3end#LINE 245 GAAGGCTTCCCGGAGGAGGTGACATCTGAGCTGAGNCTTGAAGGATGAGT 196 chr1qtel1M 665002 CGGGAG--ATCCGGGAGGCAGAAATGAGGAAGGG 665033 -i -- v i v v i iv i i C L2c_3end#LINE 195 -AGGAGTTAGCCAGGTGGAAGGAGGGGGGAAGAG 163 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 31.37 CpG sites = 49, Kimura (unadjusted) = 33.63 Transitions / transversions = 2.04 (49/24) Gap_init rate = 0.11 (32 / 299), avg. gap size = 1.69 (54 / 32) 256 28.38 14.35 1.88 chr1qtel1M 666561 666797 (333203) C L1ME1_3end#LINE/L1 (373) 553 288 m_b46s551i0 1608 chr1qtel1M 666561 AATAGTATCCTATT---------TACCATAATGTGTATATGCCTTCA--- 666598 i i i --------- i v v v v --- C L1ME1_3end#LI 553 AGTAGTATTCCATTGTATGGATATACCACAATTTGTTTATCCATTCACCN 504 chr1qtel1M 666599 -TAAATGGTCACTT---TCAAATTC-GTTTTTTGCTATTAGGCAAAGAGC 666643 - vi v i --- iivv i - v v v v i C L1ME1_3end#LI 503 GTTGATGGACATTTGGGTTGTTTCCAGTTTTTGGCTATTACGAATAAAGC 454 chr1qtel1M 666644 TTTTAT--ACATT--TTTATGAGTCCTTTTCT---CATTCTGTGATCACT 666686 vi -- -- v ii i v v --- -v vv i C L1ME1_3end#LI 453 TGCTATGAACATTCGTGTACAAGTCTTTGTGTGGACAT-ATGTTTTCATT 405 chr1qtel1M 666687 CTATTTAGG------CCTACAAGTGCCATTGCTGGTTCAAAGGGTA--TG 666728 iivi i ------ vi vv v v v -- C L1ME1_3end#LI 404 TCTCTTGGGTAAATACCTAGGAGTGGAATTGCTGGGTCATATGGTAAGTG 355 chr1qtel1M 666729 TACACATAGACTTTT--GGGGACTAGTTCCTAATTGTTTTCCAGAATGGC 666776 iiiv - ?--i ii i--- v i i i C L1ME1_3end#LI 354 TATGTTTA-ACTTTNTAAGAAACTG---CCAAACTGTTTTCCAAAGTGGC 309 chr1qtel1M 666777 TGAATTAATCCACAGTCCCAC 666797 v ii v iii v C L1ME1_3end#LI 308 TGTACCATTTTGCATTCCCAC 288 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 36.56 CpG sites = 35, Kimura (unadjusted) = 36.56 Transitions / transversions = 1.13 (35/31) Gap_init rate = 0.07 (16 / 236), avg. gap size = 2.44 (39 / 16) 291 27.65 15.73 1.64 chr1qtel1M 666621 666995 (333005) C L1ME3G_3end#LINE/L1 (452) 472 46 m_b46s551i1 1608 chr1qtel1M 666621 TTTTTTGCTATTAGGCAAAGA--GCTTTTAT--ACATTTTT----ATGAG 666662 i -- v -- viv -- ii ---- v? C L1ME3G_3end#L 472 TTTTTCGCTATTA--CAAACAATGCTGCAATGAACATCCTTGTACATGCN 425 chr1qtel1M 666663 TCCTTTT-CTCATTCTGTGATCACTCTATTTAGG-------CCTACAAGT 666704 v - v v- i vi i - v ? ------- ? v C L1ME3G_3end#L 424 TCCTTGTGCACATG-TGCGAGTATT-TCTNTAGGATAGATNCCNAGAAGT 377 chr1qtel1M 666705 GCCATTGCTGGTTCAAAGGGTATGTACACATAGACTTTTGGGGACTAGTT 666754 vv v ii iv vi v iiviiv v v C L1ME3G_3end#L 376 GGAATTGCTGGGTCAAAGGGTATGCGCATTTTAAATTTTAATAGATACTG 327 chr1qtel1M 666755 CCTAATTGTTTTCCAGAATGGCTGAATTAATCCACAGTCCCAC--GC--- 666799 v iii i ? v ii ii v -- --- C L1ME3G_3end#L 326 CCAAATTGCCCTCCAAAANGGCTGTACCAATTTACACTCCCACCAGCAGT 277 chr1qtel1M 666800 ---TCA---CACAC-TTTTCCCATATTCCCTCCAACATCTCATTTT---- 666838 --- v ---i v - i i ii i v ii?v v ---- C L1ME3G_3end#L 276 GTATGAGAGTACCCGTTTCCCCACACCCTCGCCAACACTNGATATTATCA 227 chr1qtel1M 666839 -TCTTTGTCATCTTTGCTTTTCTGACGGCTGTGGGGCAGAATATCA---- 666883 -? vvv i ivv i v viiiiii v v ---- C L1ME3G_3end#L 226 ANCTTTTAAATTTTTGCCAATCTGATGGGTGAAAAATGGTATCTCATTGT 177 chr1qtel1M 666884 ------AAATTGC-TCCCTCCAATTATTATGTG-----GAGCAATTTTTC 666921 ------ v - ii i ii i - ----- vi C L1ME3G_3end#L 176 TGTTTTAATTTGCATTTCCCTGATTACTA-GTGAGGTTGAGCATCTTTTC 128 chr1qtel1M 666922 TTATATTGA-TAGC--TTTG-ATTTCC---TTTGAAAATTTC---TTTAT 666961 v i v - i -- - --- i vi v --- i C L1ME3G_3end#L 127 ATATGTTTATTGGCCATTTGTATTTCCTCTTCTGTGAATTGCCTGTTCAT 78 chr1qtel1M 666962 ATTCTTTTACTATTTGTCTATTGAAGGGTGGCTT 666995 i vv i v -- v v C L1ME3G_3end#L 77 ATCCTTTGCCCATTTTTCTATTG--GGTTGTCTT 46 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 34.55 CpG sites = 54, Kimura (unadjusted) = 35.89 Transitions / transversions = 1.12 (54/48) Gap_init rate = 0.07 (26 / 374), avg. gap size = 2.54 (66 / 26) 345 25.78 15.66 0.62 chr1qtel1M 666696 666976 (333024) C L1MA7_3end#LINE/L1 (649) 389 67 m_b46s551i2 1608 chr1qtel1M 666696 CCTACAAGTGCCATTGCTGGTTCAAAGGGTA--TGTACACATAGACTTTT 666743 i v vv v v v -- v iviv vi C L1MA7_3end#LI 389 CCCAGAAGTGGGATTGCTGGATCATATGGTAGTTCTATTTTTAGTTTTTT 340 chr1qtel1M 666744 GGGGACTAGTTCCTAATTGTTTTCCAGAATGGCTGAATTAATCCACAGTC 666793 i -- vi vv i v v i ii v C L1MA7_3end#LI 339 GAGGA--ACCTCCATACTGTTTTCCATAATGGCTGTACTAATTTACATTC 292 chr1qtel1M 666794 CCAC-----GCTCACA------CACTTTTC-CCATATTCCCTCCAACA-- 666829 ----- ivi ------ v - i i i v -- C L1MA7_3end#LI 291 CCACCAACAGTGTACAAGGGTTCCCTTTTCTCCACATCCTCGCCAACACT 242 chr1qtel1M 666830 TCTCATTTT---TCTTTGTCATCTTTGCTTTTCTGACGGCTGTGGGGCAG 666876 v i i --- v v vv v iv i i v i iii C L1MA7_3end#LI 241 TGTTATCTTTCGTCTTTTTGATAATAGCCATTCTAACAGGTGTGAGGTGA 192 chr1qtel1M 666877 AATATCA----------AAATTGC---TCCCT-CCAATTA-TTATGTGGA 666911 v v ---------- v --- -vii - v v C L1MA7_3end#LI 191 TATCTCATTGTGGTTTTAATTTGCATTTCCCTGATGATTAGTGATGTTGA 142 chr1qtel1M 666912 GCAATTTTTCTTATAT-TGATAGC--TTTG-AT---TTCCTTTGA-AAAT 666953 v v - v i -- - --- i - C L1MA7_3end#LI 141 GCATTTTTTCATATATCTGTTGGCCATTTGTATGTCTTCTTTTGAGAAAT 92 chr1qtel1M 666954 TTC--TTTATATTCTTTTACTATTT 666976 v -- i vi i vv i C L1MA7_3end#LI 91 GTCTATTCAGGTCCTTTGCCCATTT 67 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 31.77 CpG sites = 32, Kimura (unadjusted) = 31.77 Transitions / transversions = 0.80 (32/40) Gap_init rate = 0.06 (18 / 280), avg. gap size = 2.56 (46 / 18) 18 8.48 0.00 0.00 chr1qtel1M 667533 667557 (332443) (T)n#Simple_repeat 1 25 (0) m_b46s252i0 1609 chr1qtel1M 667533 TTTGTCTTTTTTTTTTTTTTTTTTT 667557 v i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 232 21.43 0.00 0.00 chr1qtel1M 667877 667918 (332082) C L1M2_orf2#LINE/L1 (1269) 2022 1981 m_b46s551i3 1608 chr1qtel1M 667877 TAGCATTTTTAGTACCATATCAAATAGAAGTGGTGACAGTGG 667918 v i ii i i ii v C L1M2_orf2#LIN 2022 TAGGACTTCCAGTACTATGTTGAATAGAAGTGGTGAAAGTGG 1981 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 26.48 CpG sites = 7, Kimura (unadjusted) = 26.48 Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 12 18.86 2.63 2.63 chr1qtel1M 667923 667960 (332040) (TATTT)n#Simple_repeat 1 38 (0) m_b46s252i1 1610 chr1qtel1M 667923 TATTTT-TTTCCTTAAAATTTATTTTATTTTTAATTTAT 667960 - iv vv v - v (TATTT)n#Simp 1 TATTTTATTTTATTTTATTTTATTTTA-TTTTATTTTAT 38 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 415 23.66 12.50 4.46 chr1qtel1M 667998 668205 (331795) C L1M3_orf2#LINE/L1 (1303) 1985 1762 m_b46s551i4 1608 chr1qtel1M 667998 GACAGTCGACATCCTTGCCTTATTTCTGATCATACTGGAAAGGCTTTTAA 668047 v v i i i v vv i i i C L1M3_orf2#LIN 1985 GAGAGTGGGCATCCTTGCCTTGTTCCTGATCTTAGAGGAAAAGCTTTCAG 1936 chr1qtel1M 668048 CTTTTCTCCAGTACCTAAAATGTTTGCTCTTGG--TTTTAGATATGAC-- 668093 i v v ivv vi v v v -- i v i -- C L1M3_orf2#LIN 1935 TTTTTCACCATTGAGTATGATGTTAGCTGTGGGCTTTTCATATATGGCCT 1886 chr1qtel1M 668094 TTACCATATGAAGGAAAATTCCTTTTATTTTCATGCTTCCTAGTTTGT-- 668141 ii i vi v ?? i --------- ? -- C L1M3_orf2#LIN 1885 TTATTATGTTGAGGTANNTTCCTTCTA---------TNCCTAGTTTGTTG 1845 chr1qtel1M 668142 ----TTTTTA--AAGAAACTGATGTCAGATTGTGTCA------TTTTTAG 668179 ---- -- v -v iii v ------ iv C L1M3_orf2#LIN 1844 AGAGTTTTTATCATGAAA-GGATGTTGAATTTTGTCAAATGCTTTTTCTG 1796 chr1qtel1M 668180 CCTCTAT--------CCATATGGCTTTTATTTTT 668205 v --------i i ii ii C L1M3_orf2#LIN 1795 CATCTATTGAGATGATCATGTGATTTTTATCCTT 1762 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 29.51 CpG sites = 26, Kimura (unadjusted) = 29.51 Transitions / transversions = 1.24 (26/21) Gap_init rate = 0.08 (17 / 207), avg. gap size = 2.12 (36 / 17) 238 30.52 5.59 6.53 chr1qtel1M 668249 668588 (331412) C L1MD_orf2#LINE/L1 (1630) 1664 1328 m_b46s551i5 1611 chr1qtel1M 668249 ATATGCTGTGGTATCCTATTTGTAAATATTTTATTTTACATTTTATAATA 668298 ii iv v i ? iv i vviv ------ C L1MD_orf2#LIN 1664 ATATATTGCTGAATTCNATTTGCTAATATTTTGTTGAGGATTTT------ 1621 chr1qtel1M 668299 TTAATGTCACTTTTCCTTAGCAGTATGGGTCTGTAGTTTTCTTATTCTAT 668348 - i-i vv v v v vii v v i i C L1MD_orf2#LIN 1620 -TG-CGTCTATGTTCATGAGGGATATTGGTCTGTAGTTTTCTTTTTTTGT 1573 chr1qtel1M 668349 TCTTTTTCTCCCTGGCTTACATACCAAGCCTATATTTGTATTACAGAAGA 668398 v v i i vi i vvi i i viv i v iv i i i vi C L1MD_orf2#LIN 1572 ACTGTCTTTGTCTGGTTTTGGTATCAGGGTAATACTGGCCTCATAAAATG 1523 chr1qtel1M 668399 GATTTGGAAGT------TTCTCTTTTCTTTTCTTCAATTGTTTATATAAC 668442 ii v ------ i i v vv vv v i i iv C L1MD_orf2#LIN 1522 AGTTGGGAAGTGTTCCCTCCTCTTCTATTTTCTGGAAGAGATTGTGTAGA 1473 chr1qtel1M 668443 ATTGGAGTTACTTGTTTTCTGAATGTTTGATAGAATTCACTTGTAA---- 668488 v v v i i i i i v iv i ---- C L1MD_orf2#LIN 1472 ATTGGTGTTAATTCTTCTTTAAACGTTTGGTAGAATTCTCCAGTGAAACC 1423 chr1qtel1M 668489 GTCTTGGATTCTGTA-ATTTTTTTCCTTTGGGAGTTT---ACTTATGGCC 668534 i v --i v - i -- v --- v i i-- C L1MD_orf2#LIN 1422 ATCTGGG--CCTGGAGATTTCTTT--TTGGGGAGTTTTNAAATTACGA-- 1379 chr1qtel1M 668535 TGTTCAGTTTCTTT-----TTATGGGATTTAATTATTTGGAAAATATCTA 668579 -i i i ----- i -----ii i-- v C L1MD_orf2#LIN 1378 -ATTCAATTTCCTTAATAGTTATAGG-----GCTATTC--AAATTATCTA 1337 chr1qtel1M 668580 TGTTATTTT 668588 v i ? C L1MD_orf2#LIN 1336 TTTCATNTT 1328 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 38.82 CpG sites = 54, Kimura (unadjusted) = 40.43 Transitions / transversions = 1.26 (54/43) Gap_init rate = 0.08 (27 / 339), avg. gap size = 1.52 (41 / 27) 276 32.34 3.26 3.64 chr1qtel1M 668249 668524 (331476) C L1PB_orf2#LINE/L1 (1630) 1664 1390 m_b46s551i6 1611 chr1qtel1M 668249 ATATGCTGTGGTATCCTATTTGTAAATATTTTATTTTACATTTTATAATA 668298 v v i vi v iv i i vviv -- ?ii C L1PB_orf2#LIN 1664 ATATGCTGTTGGATTCGGTTAGCTAGTATTTTGTTGAGGATTT--TNGCA 1617 chr1qtel1M 668299 TTAATGTCACTTTTCCTTAGCAGTATGGGTCTGTAGTTTTCTTATTCTAT 668348 iv ------ v i vii v v i?i C L1PB_orf2#LIN 1616 TCTATG------TTCATCAGGGATATTGGTCTGTAGTTTTCTTTTTTNGT 1573 chr1qtel1M 668349 TCTTTTTCTCCCTGGCTTACATACCAAGCCTATATTTGTATTACAGAAGA 668398 v v iii i i vvi ii i viv i v iv i i v- C L1PB_orf2#LIN 1572 TATGTCCTTTCCTGGTTTTGGTATTAGGGTGATACTGGCTTCATAGAAT- 1524 chr1qtel1M 668399 GATTT--GGAAGTTTCTCT-TTTCTTT-TCTT---CAATTGTTTATATAA 668441 -- i v i - i - ---v v v vv i C L1PB_orf2#LIN 1523 GATTTAGGGAGGATTCCCTCTTTCTCTATCTTGTGGAATAGTGTCAATAG 1474 chr1qtel1M 668442 CATTGGAGTTACTTGTTTTCTGAATGTTTGATAGAATTCACTTGTAAGTC 668491 v viii v v i i i i ?vi i i C L1PB_orf2#LIN 1473 GATTGGTACCAATTCTTCTTTGAATGTCTGGTAGAATTCNGCTGTGAATC 1424 chr1qtel1M 668492 --TTGGATTCTGTAATTTTTTTCCTTTGGGAGTTT 668524 -- iv i i -i i iiv v i C L1PB_orf2#LIN 1423 CGTCTGGTCCTG-GACTTTTTTTTGTTGGTAATTT 1390 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 44.40 CpG sites = 50, Kimura (unadjusted) = 44.40 Transitions / transversions = 1.39 (50/36) Gap_init rate = 0.05 (15 / 275), avg. gap size = 1.27 (19 / 15) 369 23.58 8.49 0.00 chr1qtel1M 668758 668863 (331137) C L2d2_3end#LINE/L2 (2) 553 439 m_b46s601i0 1612 chr1qtel1M 668758 AAGTCAAATCAGTAAGTATTCAT-----GCCCCCTGGGTGCCAGGCACTG 668802 i ii i i ----- iv v v C L2d2_3end#LIN 553 AAATCAAATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTG 504 chr1qtel1M 668803 GGATAAGTGCTA---GGGATACAAAGAATGGCAAAA-ACTGCCCTTGCCC 668848 v v i i i--- vvii i - iv i i C L2d2_3end#LIN 503 TGCTAGGCGCTGTGGGGGATACAAAGAAGTATAAGACATGGTCCCTGCCC 454 chr1qtel1M 668849 TCAAGAAGCTCACAA 668863 i i C L2d2_3end#LIN 453 TCAAGGAGCTTACAA 439 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 27.93 CpG sites = 17, Kimura (unadjusted) = 29.32 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.03 (3 / 105), avg. gap size = 3.00 (9 / 3) 497 25.62 7.55 1.79 chr1qtel1M 669041 669199 (330801) MIRc#SINE/MIR 75 242 (26) m_b46s601i1 1613 chr1qtel1M 669041 CACTTAAATAACTGTGGGACACCGGGCAAGTCATTTGGAATCTATC---A 669087 v- i v vii i -- i v ---i MIRc#SINE/MIR 75 CACTTAC-TAGCTGTGTGACCTTGGGCAAGTCACTT--AACCTCTCTGAG 121 chr1qtel1M 669088 CCTCAGTTTTCTCATCCATAAAATGGAGTTAATCACA---GC---ACCTA 669131 i ii i v v i --- ---i MIRc#SINE/MIR 122 CCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTA 171 chr1qtel1M 669132 TCTCCCAGGATTGTCATAAAGATCGAATGACATAACACACAT---AGTAC 669178 i v i ii i i i v iii ii --- ii MIRc#SINE/MIR 172 CCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGC 221 chr1qtel1M 669179 TTGGCAAATCTTAAAATGCTA 669199 v i iiv i MIRc#SINE/MIR 222 TTTGTAAACTGTAAAGTGCTA 242 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 32.06 CpG sites = 30, Kimura (unadjusted) = 33.21 Transitions / transversions = 3.00 (30/10) Gap_init rate = 0.04 (7 / 158), avg. gap size = 2.14 (15 / 7) 847 19.00 8.66 2.03 chr1qtel1M 669383 669613 (330387) C MIRb#SINE/MIR (1) 267 22 m_b46s601i2 1614 chr1qtel1M 669383 ATAATA-AGTTAACATTTATATAA-----TACTATGTGCCAGATACTGCG 669426 - i v - i ----- ii i C MIRb#SINE/MIR 267 ATAATAGAGCTACCATTTAT-TGAGCGCTTACTATGTGCCAGGCACTGTG 219 chr1qtel1M 669427 CTAAGCTC-----ATG----AGATCATTTGATCTTCACAACCCCCCTGGG 669467 v ----- ---- vv i i vv v C MIRb#SINE/MIR 218 CTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCG 169 chr1qtel1M 669468 AGGTAGGTGTTATTATCCCCATTTTGCAGATGGATAAACTGAGATAAACA 669517 i i iiv iivv v C MIRb#SINE/MIR 168 AGGTAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGA 119 chr1qtel1M 669518 GTGGTTAAGTGACTTGCCCACTGGGGTCACACAACTAGTAAATGTCTGA- 669566 v i ---i i i v v - C MIRb#SINE/MIR 118 GAGGTTAAGTAACTTGCCCA---AGGTCACACAGCTAGTAAGTGGCAGAG 72 chr1qtel1M 669567 -CTGGATTTGAACT--ACTCTTCTTTACTCC-AGGCCCGATGCTCTCTTC 669612 - v i i--iv vii v - i - i i C MIRb#SINE/MIR 71 CCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCG-TGCTCTTTCC 23 chr1qtel1M 669613 A 669613 C MIRb#SINE/MIR 22 A 22 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 21.67 CpG sites = 25, Kimura (unadjusted) = 22.23 Transitions / transversions = 1.39 (25/18) Gap_init rate = 0.06 (13 / 230), avg. gap size = 1.92 (25 / 13) 17 9.74 0.00 5.71 chr1qtel1M 672140 672176 (327824) (ATTATA)n#Simple_repeat 1 35 (0) m_b46s252i2 1615 chr1qtel1M 672140 ATTAGTTATTATCATTATAAATATATATTATAATTAT 672176 - v v v - (ATTATA)n#Sim 1 ATTA-TAATTATAATTATAATTATA-ATTATAATTAT 35 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 406 25.37 4.44 3.68 chr1qtel1M 672318 672452 (327548) MIRc#SINE/MIR 3 138 (130) m_b46s601i3 1616 chr1qtel1M 672318 AGGCAGCTAGATGGTACAGTGGATAAAAACCCTGCATCTAGAGAGAGTAA 672367 i---i i - i i v v ii i vv v MIRc#SINE/MIR 3 AGGCAGT---GTGGTGCAGTGGA-AAGAGCACTGGACTTGGAGTCAGGAA 48 chr1qtel1M 672368 GACCTGAGTTCAAATCCTGCTTCTG------ACTGGATGTGTTTAGCTGG 672411 i i i i vi ------ i v vvvvi MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 98 chr1qtel1M 672412 GCAAGTCACTTAAGTTCTTTTTGACTCAAGTTTCCTCAACT 672452 vi i vv v - v MIRc#SINE/MIR 99 GCAAGTCACTTAACCTCTCTGAGCCTC-AGTTTCCTCATCT 138 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 29.14 CpG sites = 17, Kimura (unadjusted) = 31.34 Transitions / transversions = 1.06 (17/16) Gap_init rate = 0.04 (6 / 134), avg. gap size = 1.83 (11 / 6) 297 17.02 10.00 2.06 chr1qtel1M 672563 672652 (327348) C MIRc#SINE/MIR (141) 127 31 m_b46s601i4 1617 chr1qtel1M 672563 CTGAGGCAAACAG-GGTT--GTGACTTGCCCAGGGTCACAAAGCTATTAA 672609 vv v - -- i v v C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAA 78 chr1qtel1M 672610 GTCTCTGAGGCCC----CATGAACTCAGGTCTTCTGGACTCTA--TCCA 672652 vv v -- ---- vi i iv i -- C MIRc#SINE/MIR 77 GTGGCAGAG--CCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCA 31 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 18.03 CpG sites = 5, Kimura (unadjusted) = 19.34 Transitions / transversions = 0.50 (5/10) Gap_init rate = 0.07 (6 / 89), avg. gap size = 1.83 (11 / 6) 237 33.80 8.45 0.00 chr1qtel1M 672659 672800 (327200) MIRc#SINE/MIR 115 268 (0) m_b46s601i6 1616 chr1qtel1M 672659 CCCCGAGCCACTCCTTCCCCAACTGTAAAATGAAAATACTAAGATT---- 672704 i i v vvi i v iii v v ii---- MIRc#SINE/MIR 115 CTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCC 164 chr1qtel1M 672705 ----ATATCTCCAAAGACTATGGTAGGGATAAAATGAAATAGT---TGT- 672746 ----v i vv i ii i v ii v i i --- - MIRc#SINE/MIR 165 CTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTG 214 chr1qtel1M 672747 AAAGCACTTAGCACAATGCCTGGTACTATATAAATGCTACTTATTACTAC 672796 i v i v v ivvi i i iv vv?i i i MIRc#SINE/MIR 215 AAAGCGCTTTGTAAACTGTAAAGTGCTATACAAATGTAAGGNGTTATTAT 264 chr1qtel1M 672797 TACT 672800 i MIRc#SINE/MIR 265 TATT 268 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 45.96 CpG sites = 29, Kimura (unadjusted) = 47.34 Transitions / transversions = 1.53 (29/19) Gap_init rate = 0.02 (3 / 141), avg. gap size = 4.00 (12 / 3) 411 26.61 3.17 1.56 chr1qtel1M 672659 672784 (327216) MIRb#SINE/MIR 118 245 (23) m_b46s601i5 1616 chr1qtel1M 672659 CCCCGAGCCACTCCTTCCCCAACTGTAAAATGAAAATACTAAGATTATAT 672708 i i v vvi i v iii v v ii- i MIRb#SINE/MIR 118 CTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACC-TAC 166 chr1qtel1M 672709 CTCCAAAGACTATGGTAGGGATAAAATGAAATAGT---TGTAAAGCACTT 672755 vv i ii i v ii v i i --- i MIRb#SINE/MIR 167 CTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTT 216 chr1qtel1M 672756 AGCACAATGCCTGGTACTATA-TAAATGCT 672784 i i - - ii MIRb#SINE/MIR 217 AGCACAGTGCCTGGCAC-ATAGTAAGCGCT 245 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 31.86 CpG sites = 23, Kimura (unadjusted) = 34.44 Transitions / transversions = 2.30 (23/10) Gap_init rate = 0.03 (4 / 125), avg. gap size = 1.50 (6 / 4) 13 29.56 0.00 0.00 chr1qtel1M 673748 673790 (326210) (AAAGG)n#Simple_repeat 1 43 (0) m_b46s252i3 1618 chr1qtel1M 673748 AAAGAAGAAGAAAGGAAAGGAGTTAAAGGGAAGGGAAAGAAAA 673790 i i i ivvi i i i (AAAGG)n#Simp 1 AAAGGAAAGGAAAGGAAAGGAAAGGAAAGGAAAGGAAAGGAAA 43 Matrix = Unknown Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 230 25.00 3.95 0.00 chr1qtel1M 674389 674464 (325536) C L3#LINE/CR1 (703) 3396 3318 m_b46s601i7 1619 chr1qtel1M 674389 CTTCCCATCTTATACCTGT-CAGTT--TTTTAAAAAACAAAGTGTAGAAC 674435 ii i i i - -- vvi v v i i i C L3#LINE/CR1 3396 CTCTCCATCCTGTACTTGTGCAGTTGATTTTTTGAACCTAAATGCAGGAC 3347 chr1qtel1M 674436 CTTATATTTATCACTATTAAATTTTATTT 674464 i i v i i i C L3#LINE/CR1 3346 TTTACATTTATCCCTGTTAAATTTCATCT 3318 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 32.00 CpG sites = 14, Kimura (unadjusted) = 32.00 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.03 (2 / 75), avg. gap size = 1.50 (3 / 2) 309 31.13 8.49 0.00 chr1qtel1M 674584 674689 (325311) L2b_3end#LINE/L2 321 435 (31) m_b46s601i8 1620 chr1qtel1M 674584 TGTTTACATGTTT-----TCTGATTAGACTCTGAGCTCCTTGAAAGCAGG 674628 ? i -----i iv i v v ii L2b_3end#LINE 321 TGNTTACATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGG 370 chr1qtel1M 674629 AACTG---CT-TTTTGCCTTTCTTTTTATTCCCAGTACTTAGTACAATGT 674674 i i --- - i iiivi vi v i ii i i i? i L2b_3end#LINE 371 GACCGNGTCTGTCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGC 420 chr1qtel1M 674675 CTAGTATATAGCAAG 674689 i i i i i i L2b_3end#LINE 421 CTGGCACACAGTAGG 435 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 41.93 CpG sites = 27, Kimura (unadjusted) = 46.08 Transitions / transversions = 4.50 (27/6) Gap_init rate = 0.03 (3 / 105), avg. gap size = 3.00 (9 / 3) 261 31.63 8.51 1.32 chr1qtel1M 675082 675222 (324778) C L3#LINE/CR1 (2303) 1796 1646 m_b46s601i9 1619 chr1qtel1M 675082 TTGTCATTTCTTCT-CCACCTAAGGCAAGTTAAATTATTATTAAGGTAAA 675130 i iii i - vi i -- ii v i i vi i i C L3#LINE/CR1 1796 TCGTTGCTTCCTCTACCTTCTGAG--AGATGAAATTGTCAGCAAGGCAAG 1749 chr1qtel1M 675131 TTGCAAAATTATAATTTACTTTACTTT-----GACAGAGAGTTCCAGTAT 675175 iivi v v vv i i i ----- vv v i v C L3#LINE/CR1 1748 TCAAGAATTTATCAGATGCTCTGCTTTTAGCNGAATGAGACTTCCAGCAG 1699 chr1qtel1M 675176 ATGTCTGGATAATTTAAGTTCTCCATTA-----ATATCCTTTTTCTGT-C 675219 i i v i i i -----i? i vii - C L3#LINE/CR1 1698 ATGTCCGGATAGTTGAAGTCCCCCATCACTACTGNATCTTGCCTCTGTGC 1649 chr1qtel1M 675220 CAG 675222 C L3#LINE/CR1 1648 CAG 1646 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 41.35 CpG sites = 30, Kimura (unadjusted) = 44.09 Transitions / transversions = 2.14 (30/14) Gap_init rate = 0.04 (6 / 140), avg. gap size = 2.33 (14 / 6) 257 34.97 4.91 0.00 chr1qtel1M 675263 675425 (324575) C L3#LINE/CR1 (2559) 1540 1370 m_b46s601i10 1619 chr1qtel1M 675263 CTTCGCCAGAATGTTCTCCACTATGCTTCTCTCTTCTGGTTCCTGGATTT 675312 i i vi i ?iii vi i v v C L3#LINE/CR1 1540 CCTCACCCAAATGCTCTCCANCGCGCTTCTACCCTCAGGTTCGTGGATTT 1491 chr1qtel1M 675313 CCTCATA--TGTACAATTTCTTA--GTACAGAGTTAGAAAGTCAAGCATT 675358 v ii -- i vi i--i v i vvvv?i vvv v C L3#LINE/CR1 1490 CCACGCAGGTGTATATCTTCTTGACATACAGTGCTACTCTNCCTCCCCTT 1441 chr1qtel1M 675359 TTACC---TTTGTTTCTCTCAAGTCAAGTAT-CCAGTACAGAGCCAGCTT 675404 i ?i--- i i ii iiv i ? - vv v vv ivv C L3#LINE/CR1 1440 CTANTAGATCTGTTTCTTTTGAACAAGGTNTACCCTTCCATCGCCGTATT 1391 chr1qtel1M 675405 CCACTCATGGATTTCATTTCA 675425 v ii ii ii C L3#LINE/CR1 1390 CCAGTCATGAGTCCCATCCCA 1370 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 45.63 CpG sites = 33, Kimura (unadjusted) = 50.72 Transitions / transversions = 1.38 (33/24) Gap_init rate = 0.02 (4 / 162), avg. gap size = 2.00 (8 / 4) 279 28.16 10.81 0.82 chr1qtel1M 675881 675991 (324009) C L2b_3end#LINE/L2 (0) 466 345 m_b46s601i11 1621 chr1qtel1M 675881 ATTTATGCCATTCAGTAGATATTTACTAAGCATCTCTTTTGAGCCAGACA 675930 i -i ii i i ii vi v v i ? C L2b_3end#LINE 466 ATTCAT-TCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCN 418 chr1qtel1M 675931 CTAGGCTAGGTACTGATAATGTA---------AAGACAGAAT---TCAAA 675968 iv ii ivi ii --------- v?--- vvv C L2b_3end#LINE 417 CTGTGCTAGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCT 368 chr1qtel1M 675969 GCCCTTAAGGACTTCACATTCTA 675991 i v vi v C L2b_3end#LINE 367 GCCCTCACGGAGCTCACAGTCTA 345 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 34.19 CpG sites = 19, Kimura (unadjusted) = 37.37 Transitions / transversions = 1.58 (19/12) Gap_init rate = 0.03 (3 / 110), avg. gap size = 4.33 (13 / 3) 276 24.72 1.30 5.41 chr1qtel1M 676055 676131 (323869) Charlie4a#DNA/hAT-Charlie 3 76 (432) m_b46s502i0 1622 chr1qtel1M 676055 GGGGTTCTTAATATAGGGGCCTACCATATATAAATTTCAAGGGATCCATG 676104 iv i v---- i iv i v i i i Charlie4a#DNA 3 GGGGTTCTTAACCTGGGGT----CCGTGGATAGAATTCAGGGGGTCCGTG 48 chr1qtel1M 676105 AATTTTGGTGAGGGAAAAAA-TGCATCT 676131 i v i i i - i Charlie4a#DNA 49 AACTTGGATGGGGAAAAAAATTACATCT 76 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 27.21 CpG sites = 13, Kimura (unadjusted) = 31.32 Transitions / transversions = 2.60 (13/5) Gap_init rate = 0.07 (5 / 76), avg. gap size = 1.00 (5 / 5) 356 23.34 10.16 2.92 chr1qtel1M 676133 676260 (323740) Charlie4a#DNA/hAT-Charlie 371 507 (1) m_b46s502i1 1623 chr1qtel1M 676133 ATTTCAATATAATTTATTTCCT---------TATG--TTTTATTTTACAT 676171 vi --------- -- iii Charlie4a#DNA 371 ATTTCAATATAATTGGTTTCCTTTGTAATCCTATGTATTTTATTTTATGC 420 chr1qtel1M 676172 ATTTAAAAAAAAACGTGATTCTAAGGAAGGTCCCATGAGATTCATC--AC 676219 ---- i v i i i vi ii v i -- Charlie4a#DNA 421 ATTT----AAAAACATTATTCTGAGAAGGGGTCCATAGGCTTCACCAGAC 466 chr1qtel1M 676220 TTTTAAACCAATCTATTTCACCAAAAAAGTTAAGAACCTCT 676260 vii vvii i vv v i i Charlie4a#DNA 467 TGCCAAAGGGGTCCATGGCACAAAAAAGGTTAAGAACCCCT 507 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 28.87 CpG sites = 19, Kimura (unadjusted) = 28.87 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.06 (7 / 127), avg. gap size = 2.43 (17 / 7) 200 23.08 0.00 0.00 chr1qtel1M 681520 681558 (318442) L2d_3end#LINE/L2 465 503 (13) m_b46s601i12 1624 chr1qtel1M 681520 GTTCCAAGCACATAGTAAGTGCTTAATAAGTCCTTATTG 681558 v ii i i i i v i L2d_3end#LINE 465 GTGCTGAGCACATAGTAGGCGCTCAATAAATACTTGTTG 503 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 25.34 CpG sites = 7, Kimura (unadjusted) = 29.11 Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 200 23.08 0.00 0.00 chr1qtel1M 682644 682682 (317318) C L2d_3end#LINE/L2 (13) 503 465 m_b46s601i13 1625 chr1qtel1M 682644 CAATAAGGACTTATTAAGCACTTACTATGTGCTTGGAAC 682682 i v i i i i ii v C L2d_3end#LINE 503 CAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCAC 465 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 25.34 CpG sites = 7, Kimura (unadjusted) = 29.11 Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 201 11.76 2.94 0.00 chr1qtel1M 684251 684284 (315716) C L2c_3end#LINE/L2 (12) 466 432 m_b46s601i14 1626 chr1qtel1M 684251 AACAAGCATTTATAG-GCACTTACTATGTGCCAGG 684284 i v - i i C L2c_3end#LINE 466 AACAAACATTTATTGAGCGCCTACTATGTGCCAGG 432 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 9.81 CpG sites = 3, Kimura (unadjusted) = 13.04 Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 231 16.33 2.04 0.00 chr1qtel1M 684301 684349 (315651) MIR1_Amn#SINE/MIR 111 160 (70) m_b46s601i15 1627 chr1qtel1M 684301 TGATCCTTGTTTGCCTCAGTTTCCTCATATGTAAAATGGGG-TGATAATA 684349 ? i ii v v? v - i i MIR1_Amn#SINE 111 TNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATGATA 160 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 19.60 CpG sites = 5, Kimura (unadjusted) = 19.60 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.02 (1 / 48), avg. gap size = 1.00 (1 / 1) 362 19.54 4.60 0.00 chr1qtel1M 684312 684398 (315602) MIR#SINE/MIR 116 206 (56) m_b46s601i16 1627 chr1qtel1M 684312 TGCCTCAGTTTCCTCATATGTAAAATGGGG-TGATAATAGCACCTTTTTC 684360 v - i i vii MIR#SINE/MIR 116 TGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTC 165 chr1qtel1M 684361 CCCAGGTTGTTGTAGATATCAAATGA--TAGTAAA-GTAAA 684398 vivi iiiv i -- i v - MIR#SINE/MIR 166 ATAGGGTTGTTGTGAGGATTAAATGAGTTAATACATGTAAA 206 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 23.13 CpG sites = 11, Kimura (unadjusted) = 23.13 Transitions / transversions = 1.83 (11/6) Gap_init rate = 0.03 (3 / 86), avg. gap size = 1.33 (4 / 3) 270 27.50 2.50 0.00 chr1qtel1M 684409 684488 (315512) C MIRc#SINE/MIR (173) 95 14 m_b46s601i17 1628 chr1qtel1M 684409 AGGTCAGA--GCTAAGAAGTGTCTAAGGCTGGATTTGAACTCAGGTCTTC 684456 v -- iv v vi v v i i i C MIRc#SINE/MIR 95 AGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTC 46 chr1qtel1M 684457 CTGCAGTCAGGTCAAGCACTCTGTGCACTACA 684488 vvvi i v ii v v i C MIRc#SINE/MIR 45 CTGACTCCAAGTCCAGTGCTCTTTCCACTGCA 14 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 32.62 CpG sites = 10, Kimura (unadjusted) = 34.46 Transitions / transversions = 0.83 (10/12) Gap_init rate = 0.01 (1 / 79), avg. gap size = 2.00 (2 / 1) 187 28.33 1.67 0.00 chr1qtel1M 684982 685041 (314959) MIRc#SINE/MIR 11 71 (197) m_b46s601i18 1629 chr1qtel1M 684982 TGGTG-AGGGAACAGAGTGCTGGGACTGGAGTCAGGAACACCCAAGGTCC 685030 - v i v ii ivi v iii v v MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr1qtel1M 685031 AATCCTGCCTC 685041 i i v MIRc#SINE/MIR 61 AGTCCCGGCTC 71 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.88 CpG sites = 10, Kimura (unadjusted) = 36.53 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.02 (1 / 59), avg. gap size = 1.00 (1 / 1) 12 19.80 2.27 4.65 chr1qtel1M 686409 686452 (313548) (ATCAACA)n#Simple_repeat 1 43 (0) m_b46s252i4 1630 chr1qtel1M 686409 ATCAACAGTCATCAATCACATAATTAA-AATGAAGAATTCAAAAA 686452 i v - i i - v v - v (ATCAACA)n#Si 1 ATCAACAATCAACAATCA-ACAATCAACAATCAACAA-TCAACAA 43 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.07 (3 / 43), avg. gap size = 1.00 (3 / 3) 41 18.54 9.02 0.00 chr1qtel1M 687558 687679 (312321) (AT)n#Simple_repeat 1 133 (0) m_b46s252i5 1631 chr1qtel1M 687558 ATATATATATGTATATATATGTGTGTGTTTGTATAAATTAATATATATA- 687606 i i i i i v i v vv - (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr1qtel1M 687607 ATATATA-ACAT-TGCATAT-TAT-TAT-TATATA-ATATATA-ATA-AT 687648 - i - ii - - - - - - (AT)n#Simple_ 51 ATATATATATATATATATATATATATATATATATATATATATATATATAT 100 chr1qtel1M 687649 ATAGTTAATTATATTAATAT-TCTATATA-ATA 687679 vv vv vv - v - (AT)n#Simple_ 101 ATATATATATATATATATATATATATATATATA 133 Matrix = Unknown Transitions / transversions = 0.82 (9/11) Gap_init rate = 0.09 (11 / 121), avg. gap size = 1.00 (11 / 11) 16 18.33 1.75 7.41 chr1qtel1M 687622 687678 (312322) (TAT)n#Simple_repeat 1 54 (0) m_b46s252i6 1632 chr1qtel1M 687622 TATTATTATTATATAATATATAATAATATAGTTAATTA-TATTAATATTC 687670 - v - v v vi - - v v (TAT)n#Simple 1 TATTATTATTAT-TATTAT-TATTATTATTATT-ATTATTATTATTATTA 47 chr1qtel1M 687671 TATATAAT 687678 - v (TAT)n#Simple 48 T-TATTAT 54 Matrix = Unknown Transitions / transversions = 0.14 (1/7) Gap_init rate = 0.09 (5 / 56), avg. gap size = 1.00 (5 / 5) 618 33.45 0.66 2.01 chr1qtel1M 688381 688682 (311318) L1ME4c_3end#LINE/L1 342 639 (191) m_b46s551i7 1633 chr1qtel1M 688381 AAGGGCTATTAAAACGTGCATGCCCTTTGACCCAGCAGTGTTTCTACTGA 688430 i i v i v i i i viiv v i L1ME4c_3end#L 342 AAGAGCCATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGG 391 chr1qtel1M 688431 GCTTATATCCCAAAGTGAT--CTTAAAGGAGGGAAAGGGACCCCATATGT 688478 vv v i i vi --i i i i ii --- i i L1ME4c_3end#L 392 GAATTTATCCTAAGGAAATAATTCAAAAGAAGGAAAAAG---CTATATGC 438 chr1qtel1M 688479 ACAAAAATGTTTGTGGCAGCCCTGTTTGTAGTGGCAGGAAACTGGAAACT 688528 i i ii v vi i i i i iii i v L1ME4c_3end#L 439 ACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACA 488 chr1qtel1M 688529 GAGTGGATGCCCATCAGGTGGGGAATGGCTGAGTAAGTTGTGATATATGA 688578 ivv ii i v ivv i i i i i i v? L1ME4c_3end#L 489 ACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCN 538 chr1qtel1M 688579 ATGTTATGGAATATTATTGTTCTATAAGAAACGATGAGCAGGATGATTTC 688628 iviv vvvv i v i i i vi v v i vi L1ME4c_3end#L 539 ACTCGATGGAATATTATGCAGCCATTAAAAATGATAATTATGAAGACTAT 588 chr1qtel1M 688629 AGAGAGGCCTGGAGAGACTTACATGAACTGATGCTAAAAGTGAAATGAGC 688678 iv vii v - i iv vi vv i i -- vi L1ME4c_3end#L 589 GTAGCAACATGGA-AAATGTTTATGATATAATGTT--AAGTGAAAAAAGC 635 chr1qtel1M 688679 AGAA 688682 L1ME4c_3end#L 636 AGAA 639 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 44.70 CpG sites = 62, Kimura (unadjusted) = 46.68 Transitions / transversions = 1.68 (62/37) Gap_init rate = 0.02 (7 / 301), avg. gap size = 1.14 (8 / 7) 457 22.53 0.74 7.94 chr1qtel1M 689359 689493 (310507) MIRc#SINE/MIR 2 127 (141) m_b46s601i19 1634 chr1qtel1M 689359 GGGGCAGTTGGGTGGCTCGGTGGATAGAACACAGGCCCTGAAGTCAGGAG 689408 i --- iv i v i v v i i i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr1qtel1M 689409 GACCTGAATTCAAATCTGGTCTCAGACACTTAACACTTCTTGGCTGTGTG 689458 ii i i iv v v v -------i i MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTG 91 chr1qtel1M 689459 ACCCTGGGCAAGTCACTTAGCCCCAATT-GCCTCAG 689493 i i i vv v- MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 26.04 CpG sites = 17, Kimura (unadjusted) = 27.15 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.08 (11 / 134), avg. gap size = 1.00 (11 / 11) 368 23.97 2.40 3.23 chr1qtel1M 690463 690587 (309413) C MIR1_Amn#SINE/MIR (57) 173 50 m_b46s601i20 1635 chr1qtel1M 690463 CAAAGGAACTCAAGAAGTTTGGCCATTTCC-TTTTCTAGATGAGGAAATC 690511 iv ---- v viii ii - vi ii C MIR1_Amn#SINE 173 CAAAGGAGGTCA----GTATCATTATCCCCATTTTACAGATGAGGAAACT 128 chr1qtel1M 690512 GAGGCA-AACAACGTGAAGTGA-TTGTCCAGGGTCACATAGCTAGGAAGT 690559 ?- ivi v ? - i i ?i ?i v? C MIR1_Amn#SINE 127 GAGGCNCAGAGAGGTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNAGT 78 chr1qtel1M 690560 GTCTGACGCTGGATTTGAACTCAGATCT 690587 v v vv v ? ? i i C MIR1_Amn#SINE 77 GGCAGAGCCGGGANTNGAACCCAGGTCT 50 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 31.74 CpG sites = 17, Kimura (unadjusted) = 31.74 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.06 (7 / 124), avg. gap size = 1.00 (7 / 7) 378 22.77 3.92 0.95 chr1qtel1M 690487 690588 (309412) C MIRb#SINE/MIR (114) 154 50 m_b46s601i21 1635 chr1qtel1M 690487 ATTTCC-TTTTCTAGATGAGGAAATCGAGGC--AAACAACGTGAAGTGA- 690532 ii - vi ii -- i v i- v i - C MIRb#SINE/MIR 154 ATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAG-GTTAAGTAAC 106 chr1qtel1M 690533 TTGTCCAGGGTCACATAGCTAGGAAGTGTCTGACGCTGGATTTGAACTCA 690582 i i i v v v vv v i i C MIRb#SINE/MIR 105 TTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCA 56 chr1qtel1M 690583 GATCTG 690588 i C MIRb#SINE/MIR 55 GGTCTG 50 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 26.33 CpG sites = 14, Kimura (unadjusted) = 27.72 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.04 (4 / 101), avg. gap size = 1.25 (5 / 4) 17 13.79 5.00 0.00 chr1qtel1M 693902 693941 (306059) (GGGGAGG)n#Simple_repeat 1 42 (0) m_b46s252i8 1636 chr1qtel1M 693902 GGGGA-GGGGGAAGGAGGCGGGGGGAGGGGAGA-GTGGGAGG 693941 - i i v i - v (GGGGAGG)n#Si 1 GGGGAGGGGGGAGGGGGGAGGGGGGAGGGGGGAGGGGGGAGG 42 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 14 10.43 3.03 3.03 chr1qtel1M 694021 694053 (305947) (CCCGC)n#Simple_repeat 1 33 (0) m_b46s252i9 1637 chr1qtel1M 694021 CCCGCCCCGCCCCCGGCCC-CGCCGCCCGGCCCC 694053 - v - v v (CCCGC)n#Simp 1 CCCGCCCCG-CCCCGCCCCGCCCCGCCCCGCCCC 33 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.06 (2 / 32), avg. gap size = 1.00 (2 / 2) 194 17.59 12.68 3.90 chr1qtel1M 695121 695191 (304809) MIR3#SINE/MIR 88 164 (44) m_b46s601i23 1638 chr1qtel1M 695121 GATCCCGGGCAAGTCGCGCAGTCCCGTTTCT----CTCAGTT-CCTCATC 695165 i ii i v--- v v i ---- - MIR3#SINE/MIR 88 GACCTTGGGCAAGTCACT---TCACCTCTCTGGGCCTCAGTTTCCTCATC 134 chr1qtel1M 695166 TGTAAAAT---GGGGTCACACTGGA-GATC 695191 --- iiv i - MIR3#SINE/MIR 135 TGTAAAATGAGGGGGTTGGACTAGATGATC 164 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 20.54 CpG sites = 8, Kimura (unadjusted) = 20.54 Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.10 (7 / 70), avg. gap size = 1.71 (12 / 7) 210 16.64 8.77 5.08 chr1qtel1M 695121 695177 (304823) MIRc#SINE/MIR 91 149 (119) m_b46s601i22 1638 chr1qtel1M 695121 GATCCCGGGCAAGTCGCGCAGTCCCGTTTCT----CTCAGTT-CCTCATC 695165 i ii i vi ii --- i ---- - MIRc#SINE/MIR 91 GACCTTGGGCAAGTCACTTAACC---TCTCTGAGCCTCAGTTTCCTCATC 137 chr1qtel1M 695166 TGTAAAATGGGG 695177 MIRc#SINE/MIR 138 TGTAAAATGGGG 149 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 19.85 CpG sites = 8, Kimura (unadjusted) = 19.85 Transitions / transversions = 8.00 (8/1) Gap_init rate = 0.09 (5 / 56), avg. gap size = 1.60 (8 / 5) 360 28.18 8.18 0.00 chr1qtel1M 696099 696208 (303792) L2b_3end#LINE/L2 321 439 (27) m_b46s601i24 1639 chr1qtel1M 696099 TGTTTGCATAT-TGGCTCTCCCAGCACATTGTGAGCTCGTTGAGAATAGG 696147 ? i i - v i vi v i vv iii L2b_3end#LINE 321 TGNTTACATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGG 370 chr1qtel1M 696148 GGCTG--------TTTTTTGCCTTTTCATCCCTAGTGCTTGACATAGGAC 696189 i i -------- v ii vi vi i i i ii i ?i L2b_3end#LINE 371 GACCGNGTCTGTCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGC 420 chr1qtel1M 696190 CTGGCACATAGTAGGTGCT 696208 i i L2b_3end#LINE 421 CTGGCACACAGTAGGCGCT 439 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.90 CpG sites = 23, Kimura (unadjusted) = 38.67 Transitions / transversions = 2.88 (23/8) Gap_init rate = 0.02 (2 / 109), avg. gap size = 4.50 (9 / 2) 199 28.14 21.05 0.88 chr1qtel1M 697789 697978 (302022) C MIRb#SINE/MIR (38) 230 3 m_b46s601i25 1640 chr1qtel1M 697789 CCAGGATCGGTGTTAAGCATTTTCT---CATCAT---ATTTCACCTTCCC 697832 vv v i ii vi--- i --- v i i v C MIRb#SINE/MIR 230 CCAGGCACTGTGCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCAC 181 chr1qtel1M 697833 AACAACTAGGCAAAGAAGGTGCTA--------------CAGGCTGAGGAA 697868 ivv i i v ii -------------- i- C MIRb#SINE/MIR 180 AACAACCCTGCGAGGTAGGTATTATTATCCCCATTTTACAGA-TGAGGAA 132 chr1qtel1M 697869 ACTGCAGCTCCACG-GGTTAAGTGACTTGTT---GGGGAGACA------A 697908 vi viv - i ii--- vv v ------ C MIRb#SINE/MIR 131 ACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTA 82 chr1qtel1M 697909 A--GGCAGAA--GGG----GAACTCAAGTGTTCTTGTCTCCAGGTCCAGT 697950 -- i-- ---- i i v vii v iiv v C MIRb#SINE/MIR 81 AGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGT 32 chr1qtel1M 697951 ACCCTCCCCCACC-CTCCA-GCTGCCTCCC 697978 i i -ii i- v - i i C MIRb#SINE/MIR 31 GCTCT-TTCCACTGCACCACGCTGCCCCTC 3 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 34.69 CpG sites = 32, Kimura (unadjusted) = 36.41 Transitions / transversions = 1.52 (32/21) Gap_init rate = 0.07 (13 / 189), avg. gap size = 3.23 (42 / 13) 262 21.62 16.39 1.43 chr1qtel1M 697855 697976 (302024) C MIRc#SINE/MIR (127) 141 2 m_b46s601i26 1640 chr1qtel1M 697855 TACAGGCTGAGGAAACTGCAGCTCCACG-GGTTAAGTGACTTGTT---GG 697900 i- vi viv - ii--- C MIRc#SINE/MIR 141 TACAGA-TGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGG 93 chr1qtel1M 697901 GGAGACA------AAG--GCAGAA--GGG----GAACTCAAGTGTTCTTG 697936 vv v ------ -- i-- ---- i i v i C MIRc#SINE/MIR 92 TCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTG 43 chr1qtel1M 697937 TCTCCAGGTCCAGTACCC--TCCCCCACCCTCCAGCTGCCTC 697976 v i i i -- v ii v iv - C MIRc#SINE/MIR 42 ACTCCAAGTCCAGTGCTCTTTCCACTGCACCACA-CTGCCTC 2 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 25.97 CpG sites = 15, Kimura (unadjusted) = 25.97 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.07 (9 / 121), avg. gap size = 2.44 (22 / 9) 15 11.83 5.56 7.55 chr1qtel1M 698791 698844 (301156) (GGAGA)n#Simple_repeat 1 53 (0) m_b46s252i10 1641 chr1qtel1M 698791 GGACAGGAGAGGAGAGAGGGAGG-GATGGA-AGGAAGGAGGAAAGAAG-G 698837 v - i - - - - - i i - (GGAGA)n#Simp 1 GGAGAGGAGAGGAGAG-GAGAGGAGA-GGAGAGG-A-GAGGAGAGGAGAG 46 chr1qtel1M 698838 AAGAGGA 698844 i (GGAGA)n#Simp 47 GAGAGGA 53 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.13 (7 / 53), avg. gap size = 1.00 (7 / 7) 17 21.21 0.00 4.26 chr1qtel1M 698796 698844 (301156) (GGAG)n#Simple_repeat 1 47 (0) m_b46s252i11 1641 chr1qtel1M 698796 GGAGAGGAGAGAGGGAGGGATGGAAGGAAGGAGGAAAGAAGGAAGAGGA 698844 - i v i i i i i i - (GGAG)n#Simpl 1 GGAG-GGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAG-GGA 47 Matrix = Unknown Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.04 (2 / 48), avg. gap size = 1.00 (2 / 2) 307 35.59 2.54 0.00 chr1qtel1M 698954 699071 (300929) L2d2_3end#LINE/L2 435 555 (0) m_b46s601i27 1642 chr1qtel1M 698954 TAGATTGGGAACCCTTTGAGAACAGCGCCTGCTCTTTGCTTTTCTTTGTA 699003 vi i i i ii v v iiivii iivi L2d2_3end#LIN 435 TAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACTTCTTTGTA 484 chr1qtel1M 699004 TCCCC---AGAACTTGGCAGGGTGCCTGGCACATAAAGGTCATTTAATAA 699050 --- vi i i vi v i ivi v ii i L2d2_3end#LIN 485 TCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAGTAGGCGCTCAATAA 534 chr1qtel1M 699051 ATGTTGATTAGTCATATTTGA 699071 i vi ii ivv L2d2_3end#LIN 535 ATATTTGTTGATTTGATTTGA 555 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 48.56 CpG sites = 29, Kimura (unadjusted) = 52.25 Transitions / transversions = 2.23 (29/13) Gap_init rate = 0.01 (1 / 117), avg. gap size = 3.00 (3 / 1) 26 0.00 0.00 0.00 chr1qtel1M 699920 699944 (300056) (C)n#Simple_repeat 1 25 (0) c_b46s251i0 1643 chr1qtel1M 699920 CCCCCCCCCCCCCCCCCCCCCCCCC 699944 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCC 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 13 19.20 0.00 6.82 chr1qtel1M 701539 701585 (298415) (GAAAAAA)n#Simple_repeat 1 44 (0) m_b46s252i12 1644 chr1qtel1M 701539 GAAAGAAGAAAACAGAACAAAAGGGAAAAAACCAAAGTGAAAATAGA 701585 i v - -- vv iv v (GAAAAAA)n#Si 1 GAAAAAAGAAAAAAGAA-AAAA--GAAAAAAGAAAAAAGAAAAAAGA 44 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.07 (3 / 46), avg. gap size = 1.00 (3 / 3) 21 0.00 0.00 0.00 chr1qtel1M 701656 701678 (298322) (T)n#Simple_repeat 1 23 (0) m_b46s252i13 1645 chr1qtel1M 701656 TTTTTTTTTTTTTTTTTTTTTTT 701678 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTT 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 387 29.20 0.00 0.00 chr1qtel1M 701681 701793 (298207) C L1M5_orf2#LINE/L1 (1933) 1361 1249 m_b46s551i8 1646 chr1qtel1M 701681 GAAATGGGACTATTTAAGCAATTTACTTCCTCCTTTGTTAATCTGGGAAG 701730 v i i i iiivv i i i i v? i i i v v i C L1M5_orf2#LIN 1361 GATATAGGGCTATTCAGATTTTCTATTTCTTCTTGNGTCAGTTTTGGTAA 1312 chr1qtel1M 701731 CCTATATTTTTGGAGGTAGTCATCCATTTCGCTTAGGTTATCAAATTTAT 701780 ?i i i vi v v ii iii i ? C L1M5_orf2#LIN 1311 NTTGTGTTTTTCAAGGAATTTGTCCATTTCATCTAAGTTNTCAAATTTAT 1262 chr1qtel1M 701781 TGGCATAAAGTTG 701793 C L1M5_orf2#LIN 1261 TGGCATAAAGTTG 1249 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 40.98 CpG sites = 24, Kimura (unadjusted) = 40.98 Transitions / transversions = 2.67 (24/9) Gap_init rate = 0.00 (0 / 112), avg. gap size = 0.0 (0 / 0) 557 26.16 2.32 5.10 chr1qtel1M 701801 702102 (297898) C L1MC4_5end#LINE/L1 (61) 2494 2201 m_b46s551i9 1646 chr1qtel1M 701801 CTTCACTGTCTATAGTACCCTTTAGCAAGATATAGTTTCCTTCCTTATCT 701850 i vv v ??? ? vv v i v? i i C L1MC4_5end#LI 2494 CTTCATTGTGAATTGNNNCCTTTANCATTATAAAATGNCCTTCTTTGTCT 2445 chr1qtel1M 701851 CTTTTAATTAGATCAATTTTTGCTTT------TGCTTGATCTGAGATAGG 701894 ? ------iv ?i ------ i vi v ?ii C L1MC4_5end#LI 2444 CNTTTAAT------GCTTTTTGNCTTGAANTCTACTTTGTCTGATATNAA 2401 chr1qtel1M 701895 GATGGCTACCCCTGCTTTTTTGATTTCACCTGAAGCATAATAGATTCTGC 701944 ? v v i - v i ii --- v ii v ii v? C L1MC4_5end#LI 2400 NATTGCAACCCTT-CTTTTTTGTTTCCATTTG---CCTGGTATATCTTTN 2355 chr1qtel1M 701945 TCCAGCCTTTTACCTTTACTCTGTATGTATCTCCCTGTTTTAAATGTGTT 701994 v i ii i vi v v v v ii - ii i C L1MC4_5end#LI 2354 TCCATCCCTTTATTTTCAGCCTTTCTGAATCACTTT-TTTTAGGTGTGTC 2306 chr1qtel1M 701995 TCCTGTAAACAATATAAGGTAGGGTTCTGACTTTTGATCCAGTCTGCTA- 702043 i ? ii vi v ii vi ? ? ? i?i vv - C L1MC4_5end#LI 2305 TCTTGTANACAGCATATAGTTGGGTCTTGCTTTNTNANCCAANTTGAAAA 2256 chr1qtel1M 702044 TCTGCCTCCACTTTATGGGAGAGTTCATCCCATTCACATTTACGGTTAAA 702093 vi? i-i v ? v ? v i --- i?v C L1MC4_5end#LI 2255 TCTTTNTCT-TTTAATNGGTGAGTTNAGCCCATTTACATTTA---TTGNT 2210 chr1qtel1M 702094 ATGACTAAT 702102 ? i C L1MC4_5end#LI 2209 ATNACTGAT 2201 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 36.02 CpG sites = 43, Kimura (unadjusted) = 36.02 Transitions / transversions = 1.34 (43/32) Gap_init rate = 0.06 (17 / 301), avg. gap size = 1.29 (22 / 17) 410 24.72 5.73 5.18 chr1qtel1M 701973 702164 (297836) C L1MEj_5end#LINE/L1 (0) 2160 1968 m_b46s551i10 1646 chr1qtel1M 701973 ATCTCCCTGTTTTAAATGTGTTTCCTGTAAACAATATAAGGTAGGGTTCT 702022 v ii i i ii vi iv i C L1MEj_5end#LI 2160 ATCACTTTGTTTTAAGTGTGTTTCTTGTAAACAGCATATAGCTGGGTTTT 2111 chr1qtel1M 702023 GACTTTTGATCCAGTCTGCTA---TCTGCCTCCACTTTATGGGAGAGTTC 702069 vi i i i vi --- i i--- v i C L1MEj_5end#LI 2110 GTTTTTTAACCCAATCTGACAGTCTCTGTCTT---TTAATGGGAGAATTC 2064 chr1qtel1M 702070 ATCCCATTCACATTTACGGTTAAAATGACTAAT-T-CTGTAT----TTCC 702113 vi vv --- i i - - vv ---- C L1MEj_5end#LI 2063 AGTCCATTCACATTTAGTGT---AACGACTGATATACTTGATTTTATTCC 2017 chr1qtel1M 702114 TGCCATCCTAA--TATTCCCAGATTATGCATTTCTTTTTCTTGCCCTCCT 702161 v i v-- ?i---- vi iv i ?iii ii C L1MEj_5end#LI 2016 TTCCATCTTACTTTATTNT----TTATTTATTTTGTTTTTTTNTTTTTTT 1971 chr1qtel1M 702162 TCT 702164 C L1MEj_5end#LI 1970 TCT 1968 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 30.66 CpG sites = 30, Kimura (unadjusted) = 31.51 Transitions / transversions = 2.00 (30/15) Gap_init rate = 0.08 (15 / 191), avg. gap size = 1.40 (21 / 15) 13 26.67 4.84 1.56 chr1qtel1M 702248 702309 (297691) (TCCCTT)n#Simple_repeat 1 64 (0) m_b46s252i14 1647 chr1qtel1M 702248 TCCCTTCCCCTTT-CTTGTACCCTTCTCTTATTAC--TCTTTTTCCTTTT 702294 i - i v v i i - iv -- ii i (TCCCTT)n#Sim 1 TCCCTTTCCCTTTCCCTTTCCCTTTCCCTT-TCCCTTTCCCTTTCCCTTT 49 chr1qtel1M 702295 CCCTTTTCCTCTCCC 702309 i i (TCCCTT)n#Sim 50 CCCTTTCCCTTTCCC 64 Matrix = Unknown Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.05 (3 / 61), avg. gap size = 1.33 (4 / 3) 11 25.48 6.06 2.94 chr1qtel1M 702249 702314 (297686) (CCTTTCC)n#Simple_repeat 1 68 (0) m_b46s252i15 1647 chr1qtel1M 702249 CCCTTCCCCTTT--CTTGTACCC-TTCTCTTATTACTCTTTTTCCTTTTC 702295 i -- i v v - i i - v i ii i (CCTTTCC)n#Si 1 CCTTTCCCCTTTCCCCTTTCCCCTTTCCCCT-TTCCCCTTTCCCCTTTCC 49 chr1qtel1M 702296 CCTTT-TCCTCTCCCACTTT 702314 -i i - (CCTTTCC)n#Si 50 CCTTTCCCCTTTCCC-CTTT 68 Matrix = Unknown Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.08 (5 / 65), avg. gap size = 1.20 (6 / 5) 245 23.23 8.87 6.30 chr1qtel1M 702879 703002 (296998) C L1M6_5end#LINE/L1 (925) 1590 1464 m_b46s551i11 1646 chr1qtel1M 702879 TGTTTTTTC---CTGGTTGCTTGTAATATTGTTTCTTTAGTCTGAAAATT 702925 --- v iv v vi vi? C L1M6_5end#LIN 1590 TGTTTTTTCTGCCTGGATGCTTGTAGGATTTTTTCTTTATCCTTGNAATT 1541 chr1qtel1M 702926 CTGAAATTTGGCCACAATATTCCT-----TGGGT---TTTTTATTTTAGG 702967 vi v vi vi ----- --- i ----? C L1M6_5end#LIN 1540 CAAAAATTTTGCCAGGATATGTCTAGATGTGGGTCTCTTTTCATT----N 1495 chr1qtel1M 702968 ATCTTTTTCAGAAGATGTTCGATGAATTCTTTCAA 703002 i viiii v ---- i iii C L1M6_5end#LIN 1494 ATTTTGCCTGGAATA----CGGTGAGCCCTTTCAA 1464 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 29.04 CpG sites = 16, Kimura (unadjusted) = 29.04 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.09 (11 / 123), avg. gap size = 1.73 (19 / 11) 277 21.74 1.45 0.00 chr1qtel1M 706808 706876 (293124) C DNM1r#Unknown (2111) 2551 2482 m_b47s502i0 1648 chr1qtel1M 706808 TGATCTATAG-TAAATATATGTATATGTATATATATACATACATACATAC 706856 v ?- vi i i ii i i i i C DNM1r#Unknown 2551 TGTTCTATANATACGTATATATACACATATATACACACATACACACATAT 2502 chr1qtel1M 706857 ACACACATATATGTATATAT 706876 ii i i C DNM1r#Unknown 2501 ACACACATATATACACACAT 2482 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 25.85 CpG sites = 13, Kimura (unadjusted) = 28.05 Transitions / transversions = 6.50 (13/2) Gap_init rate = 0.01 (1 / 68), avg. gap size = 1.00 (1 / 1) 277 25.35 0.00 0.00 chr1qtel1M 706824 706894 (293106) C DNM1r#Unknown (2116) 2546 2476 m_b47s502i1 1648 chr1qtel1M 706824 TATGTATATGTATATATATACATACATACATACACACACATATATGTATA 706873 i? i i i i i i ii i C DNM1r#Unknown 2546 TATANATACGTATATATACACATATATACACACATACACACATATACACA 2497 chr1qtel1M 706874 TATGTATATATATATATATAT 706894 i i i i i i ii C DNM1r#Unknown 2496 CATATATACACACATACACGT 2476 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 30.81 CpG sites = 18, Kimura (unadjusted) = 36.11 Transitions / transversions = 1.00 (18/0) Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0) 18 12.17 0.00 0.00 chr1qtel1M 706895 706921 (293079) (AT)n#Simple_repeat 1 27 (0) m_b47s252i0 1649 chr1qtel1M 706895 ATATATATATATATATATAAAACTATA 706921 v vv (AT)n#Simple_ 1 ATATATATATATATATATATATATATA 27 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 13 10.36 6.45 0.00 chr1qtel1M 708306 708336 (291664) (AAAGGA)n#Simple_repeat 1 33 (0) m_b47s252i1 1650 chr1qtel1M 708306 AAAGGAAAGGGAAAA--AAAAGCAAAAGGATAA 708336 i -- v v (AAAGGA)n#Sim 1 AAAGGAAAAGGAAAAGGAAAAGGAAAAGGAAAA 33 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.03 (1 / 30), avg. gap size = 2.00 (2 / 1) 202 30.61 8.16 0.00 chr1qtel1M 708947 709044 (290956) C L2d2_3end#LINE/L2 (36) 519 414 m_b47s601i1 1651 chr1qtel1M 708947 TATGTGTCAGACACTGTGCCAA-TACTGTGA---ATGCAAACACA-AGCA 708991 i iv i i i-ii i--- i v vi- vv C L2d2_3end#LIN 519 TGTGTGCAAGGCACTGTGCTAGGCGCTGTGGGGGATACAAAGAAGTATAA 470 chr1qtel1M 708992 GGCAAGA---CTGACCCCCAGAAGCTTACATTCTAATAGGAACGACAAGT 709038 i v i--- v i v i v i v iiv v C L2d2_3end#LIN 469 GACATGGTCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGGAGACAAGA 420 chr1qtel1M 709039 CATAGA 709044 i C L2d2_3end#LIN 419 CATAAA 414 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 38.71 CpG sites = 18, Kimura (unadjusted) = 40.67 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.04 (4 / 97), avg. gap size = 2.00 (8 / 4) 234 21.19 14.63 2.17 chr1qtel1M 708947 709028 (290972) C L2a_3end#LINE/L2 (36) 481 390 m_b47s601i0 1651 chr1qtel1M 708947 TATGTGTCAGACACTGTGCCAA-TACTGTGAATGCA------AACACAAG 708989 i i v i i-ii v i i ------ - i C L2a_3end#LINE 481 TATGTGCCAGGCACTGTTCTAGGCGCTGGGGATACAGCAGTGAACA-AAA 433 chr1qtel1M 708990 CAGGCAAGA----CTGACCCCCA-GAAGCTTACATTCTAATAGG 709028 i i ---- - i - i i i C L2a_3end#LINE 432 CAGACAAAAGTCCCTG-CCCTCATGGAGCTTACATTCTAGTGGG 390 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 24.78 CpG sites = 15, Kimura (unadjusted) = 26.82 Transitions / transversions = 7.50 (15/2) Gap_init rate = 0.07 (6 / 81), avg. gap size = 2.33 (14 / 6) 717 26.30 3.30 8.05 chr1qtel1M 709426 709698 (290302) C MIRb#SINE/MIR (0) 268 8 m_b47s601i3 1652 chr1qtel1M 709426 AATAATAG--CTAATGTTTATAAAGTGCCTAATAAGTGCCAGGCAGTGTA 709473 -- vii vi i i v v v i C MIRb#SINE/MIR 268 AATAATAGAGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTG 219 chr1qtel1M 709474 GTAAGCACTTTATAAATATTATTATATTGGATCCTCACAAC--TCTTA-G 709520 v i i vii ivi vi --i i i- C MIRb#SINE/MIR 218 CTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCG 169 chr1qtel1M 709521 AGGTAGATGCTACTATCATCACGATTTTTGCAGATGAGGAAATTGAGGCA 709570 i ii i vi ---- i i v C MIRb#SINE/MIR 168 AGGTAGGTATTATTATCCCCA----TTTTACAGATGAGGAAACTGAGGCT 123 chr1qtel1M 709571 AATAGAAGTTAAGTGACTTGTCTTGGGTCACACAG----TAGGGGTCCGA 709616 v v i i i ivi ---- i v v v C MIRb#SINE/MIR 122 CAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGA 73 chr1qtel1M 709617 GGCCATCTTTGAAGTCAGGAAGACGAATATTCCTGACTCCTGACCTATCT 709666 v vivv i vi -------- v vi vi v ----- C MIRb#SINE/MIR 72 GCCGGGATTCGAACCCAGG--------TCTGTCTGACTCCAAAGC----- 36 chr1qtel1M 709667 ACTGTGCTCCATTCACTGTGCCACCTAGCTGC 709698 - i iv i ii --- C MIRb#SINE/MIR 35 -CCGTGCTCTTTCCACTGCACCAC---GCTGC 8 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 30.59 CpG sites = 39, Kimura (unadjusted) = 32.98 Transitions / transversions = 1.44 (39/27) Gap_init rate = 0.09 (25 / 272), avg. gap size = 1.20 (30 / 25) 765 21.79 1.67 0.55 chr1qtel1M 709426 709605 (290395) C MIR#SINE/MIR (0) 262 81 m_b47s601i2 1652 chr1qtel1M 709426 AATAATAGCTAATGTTTATAAAGTGCCTAATAAGTGCCAGGCAGTGTAGT 709475 ii vi i i v v v vv C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCT 213 chr1qtel1M 709476 AAGCACTTTATAAATATTATTATATTGGATCCTCACAAC--TCTTA-GAG 709522 i i vi vivi vi --i i - C MIR#SINE/MIR 212 AAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAG 163 chr1qtel1M 709523 GTAGATGCTACTATCATCACGATTTTTGCAGATGAGGAAATTGAGGCAAA 709572 i i i i v v - i i v C MIR#SINE/MIR 162 GTAGGTACTATTATTATCCCCA-TTTTACAGATGAGGAAACTGAGGCACA 114 chr1qtel1M 709573 TAGAAGTTAAGTGACTTGTCTTGGGTCACACAG 709605 v i i i ivi C MIR#SINE/MIR 113 GAGAGGTTAAGTAACTTGCCCAAGGTCACACAG 81 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 24.75 CpG sites = 24, Kimura (unadjusted) = 26.28 Transitions / transversions = 1.60 (24/15) Gap_init rate = 0.02 (3 / 179), avg. gap size = 1.33 (4 / 3) 29 19.09 1.45 2.94 chr1qtel1M 709861 709929 (290071) (TA)n#Simple_repeat 1 68 (0) m_b47s252i2 1653 chr1qtel1M 709861 TATATAGTATTTATATATATGTATTGATATACAAATGTTTATATAGTATT 709910 - v i vv i v i v - v (TA)n#Simple_ 1 TATATA-TATATATATATATATATATATATATATATATATATATA-TATA 48 chr1qtel1M 709911 TATATATATTTGTAT-TATA 709929 v i - (TA)n#Simple_ 49 TATATATATATATATATATA 68 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.04 (3 / 68), avg. gap size = 1.00 (3 / 3) 15 5.56 0.00 0.00 chr1qtel1M 710419 710437 (289563) (C)n#Simple_repeat 1 19 (0) m_b47s252i3 1654 chr1qtel1M 710419 CCCCCCCCCCCCCCCCTCC 710437 i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCC 19 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 14 4.94 0.00 0.00 chr1qtel1M 711103 711123 (288877) (GAGG)n#Simple_repeat 1 21 (0) m_b47s252i4 1655 chr1qtel1M 711103 GAGGGAGGCAGGGAGGGAGGG 711123 v (GAGG)n#Simpl 1 GAGGGAGGGAGGGAGGGAGGG 21 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 189 24.36 5.60 4.76 chr1qtel1M 711511 711635 (288365) C L2#LINE/L2 (818) 2264 2139 m_b47s601i4 1656 chr1qtel1M 711511 GAAGAGAAGAGGGTCCAGGACAGAGCCCTGGGAGACCTCGCCCGGGTTAG 711560 vi v v iv ii iv --- ?i C L2#LINE/L2 2264 GAAGAGAAGAGGTCCAAGGACTGAGCCCTGGGGCACTCCAAC---GTTNA 2218 chr1qtel1M 711561 CAGGT------AATCCGGAGGAGGATCAAGAAAATGAGACTTGGAAGGAG 711604 v ------i --- v v v v vi C L2#LINE/L2 2217 GAGGTCGGGGAGAT---GAGGAGGAACCAGCAAAGGAGACTGAGAAGGAG 2171 chr1qtel1M 711605 AAG-CAGAGAGTCGGGAGGAGAAGCAGAGGAG 711635 vi - v vii i v ii C L2#LINE/L2 2170 CGGCCAGTGAGGTAGGAGGAAAACCAGGAGAG 2139 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 28.81 CpG sites = 14, Kimura (unadjusted) = 29.99 Transitions / transversions = 0.93 (14/15) Gap_init rate = 0.06 (8 / 124), avg. gap size = 1.62 (13 / 8) 263 32.71 3.57 1.75 chr1qtel1M 712712 712823 (287177) L2b_3end#LINE/L2 139 252 (214) m_b47s601i5 1657 chr1qtel1M 712712 GCTGTCCTTTAGGCCTGGAATGCCCTCCCTCA--TTTTCGCCTTTTGCTT 712759 i ii vv i i i -- i -- v iv L2b_3end#LINE 139 GCTGTTCCCTCTGCCTGGAACGCCCTTCCCCACCTCTTCGCC--TGGCCA 186 chr1qtel1M 712760 TCTCTGACT--TCCTTCAAGTTGCAGATGAAATTCTACCTTTTACAGGAA 712807 v iv -- i iv v v vii ii v i L2b_3end#LINE 187 ACTCCTACTCATCCTTCAGGTCTCAGCTCAAATGTCACCTCCTCCGGGAA 236 chr1qtel1M 712808 ATCTTTGTTAGCTCCC 712823 ii i ivi ii i L2b_3end#LINE 237 GCCCTCCCTGACCCCC 252 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 42.10 CpG sites = 24, Kimura (unadjusted) = 45.58 Transitions / transversions = 2.00 (24/12) Gap_init rate = 0.04 (4 / 111), avg. gap size = 1.50 (6 / 4) 261 32.43 6.96 2.42 chr1qtel1M 712819 712976 (287024) L2b_3end#LINE/L2 283 447 (19) m_b47s601i6 1657 chr1qtel1M 712819 CTCCCA--TTTATCCTGCG---TTGGGCT-TCTTTGTACAGTTACCTGCT 712862 i --ii i v---i i - ?v vii? v i- L2b_3end#LINE 283 CCCCCAGTCCTACCCTGCCACTCTGGGTTATNATTGTCTGNTTACATGT- 331 chr1qtel1M 712863 ACCCTCTCCCCCATTAGAATGCGATTTCCTCCAGCGAAGGGACTGGCTTT 712912 - iv i v i vi viv v v i ?v i L2b_3end#LINE 332 -CTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCT 380 chr1qtel1M 712913 CACCTT-----CTGTTTGTGTCCCTGGTGCTTAAGCTAATATCTGACACA 712957 -ii ----- i -i i ii i i ivvi i?ii i L2b_3end#LINE 381 -GTCTTGTTCACCG-CTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACA 428 chr1qtel1M 712958 TAGTTGGCACTGAATAAAT 712976 i v i v i L2b_3end#LINE 429 CAGTAGGCGCTCAGTAAAT 447 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 41.87 CpG sites = 34, Kimura (unadjusted) = 47.05 Transitions / transversions = 2.12 (34/16) Gap_init rate = 0.05 (8 / 157), avg. gap size = 1.88 (15 / 8) 288 29.09 7.48 3.60 chr1qtel1M 712870 712976 (287024) L2a_3end#LINE/L2 388 498 (19) m_b47s601i7 1657 chr1qtel1M 712870 CCCCCATTAGAATGCGATTTCCTCCAGCGAAGGGACTGGCTTTCACCT-- 712917 i ii vi viv v v ---- iii -- L2a_3end#LINE 388 CCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGACT----TTTGTCTGT 433 chr1qtel1M 712918 TCTGTT------TGTGTCCCTGGTGCTTAAGCTAATATCTGACACATAGT 712961 i ------ i ii i i iivi i ii i L2a_3end#LINE 434 TTTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACATAGT 483 chr1qtel1M 712962 TGGCACTGAATAAAT 712976 v i v L2a_3end#LINE 484 AGGCGCTCAATAAAT 498 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 35.96 CpG sites = 22, Kimura (unadjusted) = 39.37 Transitions / transversions = 2.75 (22/8) Gap_init rate = 0.06 (6 / 106), avg. gap size = 2.00 (12 / 6) 189 26.10 0.00 2.17 chr1qtel1M 713541 713587 (286413) L3#LINE/CR1 3967 4012 (87) m_b47s601i8 1658 chr1qtel1M 713541 ACAGGAGGCTCTCAAGCAAAAAGCTGGATGACTACTTGTTGAAGACG 713587 v ivi i i- i iiii i L3#LINE/CR1 3967 ACTGGAGGTGTTCAAGCAGAG-GCTGGATGACCACTTGTCAGGGATG 4012 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 34.80 CpG sites = 10, Kimura (unadjusted) = 34.80 Transitions / transversions = 5.00 (10/2) Gap_init rate = 0.02 (1 / 46), avg. gap size = 1.00 (1 / 1) 434 21.11 2.17 2.17 chr1qtel1M 713623 713714 (286286) Charlie1a#DNA/hAT-Charlie 1 92 (1363) m_b47s502i2 1659 chr1qtel1M 713623 CAGGGGTTCTCA--GTGTTATTTGCAGACAACTGGGGGTACCCCAAGATT 713670 v -- vi ii i vv - i ii Charlie1a#DNA 1 CAGCGGTTCTCAAAGTGTGGTCCGCGGACCCCTGGGGGT-CCCCGAGACC 49 chr1qtel1M 713671 TTTTCAGGGGGGTCTGCAAGATCAAAACTATGTCTGTAATAATA 713714 i - i i i v iii Charlie1a#DNA 50 CTTTCAGGGGG-TCCGCGAGGTCAAAACTATTTTCATAATAATA 92 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 18.45 CpG sites = 14, Kimura (unadjusted) = 25.78 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.03 (3 / 91), avg. gap size = 1.33 (4 / 3) 1275 18.51 9.67 1.53 chr1qtel1M 713740 714101 (285899) Charlie1a#DNA/hAT-Charlie 1065 1455 (0) m_b47s502i3 1660 chr1qtel1M 713740 TGAGGTTAGATTTTCTTCATGAAATTTAACCAAAACAATATCTCACAACA 713789 iii iv v i i v i Charlie1a#DNA 1065 TGAGGCCGGATTTTCTTCATATACTTCAACCAAAACAACATATCGCAACA 1114 chr1qtel1M 713790 G--TGAAGGCAGAAACATTTATGAGAATGCAACTGTCATCTATTAAGC-- 713835 -- v i vv v i v -- Charlie1a#DNA 1115 GATTGAATGCAGAAGCAGATATGAGAATCCAGCTGTCTTCTATTAAGCCA 1164 chr1qtel1M 713836 -ATTTTA-----ATTTGCAAAAATATATGAAAAATACCACTCTTTTCATT 713879 - iv ----- i -i v i i i Charlie1a#DNA 1165 GACATTAAAGAGATTTGCAAAAATGTA-AAACAATGCCACTCTTCTCACT 1213 chr1qtel1M 713880 -AATTTTTTTATTTTGGAAAA-------GTCTTTTATTAAAATATA--AC 713919 - i -------i i i v i-- i Charlie1a#DNA 1214 AAATTTTTTTGTTTTGGAAAATATAGTTATTTTTCATAAAAATATGTTAT 1263 chr1qtel1M 713920 TAATGTAAACTACATGTCAGTAGTTTATTATTATTTTT-AATGAGTT--- 713965 v v --- v vvi - i --- Charlie1a#DNA 1264 TTATGTTA---ACATGTAATGGGTTTATTATTATTTTTAAATGAATTAAT 1310 chr1qtel1M 713966 -AATATTCTAGCATTTT----GTT----TTCCTATTTTGGTAAATATCAA 714006 - i iv v ---- ---- i v v i Charlie1a#DNA 1311 AAATATTTTAAAAATTTCTCAGTTTTAATTTCTAATATGGTAAATATCGA 1360 chr1qtel1M 714007 GAAATATCACCCACCTAAGCAAAA-CTCTTGGGAGAGGCCTCAAAAAATT 714055 v i v v i - v -- i v v v Charlie1a#DNA 1361 TAGATATAACCCACATAAACAAAAGCTCTTTG--GGGTCCTCAATAATTT 1408 chr1qtel1M 714056 TTAAGGGCATAAA-AGGTCCTGAGAACAAAAGGTTTGAGACTCACTG 714101 i ii -i v i vi i Charlie1a#DNA 1409 TTAAGAGTGTAAAGGGGTCCTGAGACCAAAAAGTTTGAGAACCGCTG 1455 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 20.08 CpG sites = 37, Kimura (unadjusted) = 21.52 Transitions / transversions = 1.28 (37/29) Gap_init rate = 0.06 (20 / 361), avg. gap size = 2.05 (41 / 20) 444 20.58 3.76 8.66 chr1qtel1M 714137 714269 (285731) C MIRb#SINE/MIR (138) 130 4 m_b47s601i9 1661 chr1qtel1M 714137 CTGAGGC-AATTGGGATTAAGTGACTTGCCCGGGGTCACACAGCTAGGAA 714185 -v vv i i i ii v C MIRb#SINE/MIR 130 CTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAA 81 chr1qtel1M 714186 GTGTTAAATGTCTGAAGCC-AGATTTGAACTCAGGTC---CTGACTTCAG 714231 vi --------i -i i i --- i i C MIRb#SINE/MIR 80 GTGGCA--------GAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAA 39 chr1qtel1M 714232 GGCTGGTGCTCTACCCACTGTGCCACCTAGCTGCCCTT 714269 i iv vi ii --- i C MIRb#SINE/MIR 38 AGCCCGTGCTCTTTCCACTGCACCAC---GCTGCCCCT 4 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 23.65 CpG sites = 18, Kimura (unadjusted) = 24.78 Transitions / transversions = 2.57 (18/7) Gap_init rate = 0.11 (14 / 132), avg. gap size = 1.14 (16 / 14) 196 25.43 8.26 2.61 chr1qtel1M 714688 714796 (285204) C MIR3#SINE/MIR (22) 186 72 m_b47s601i10 1662 chr1qtel1M 714688 CAGAGATACTGGAAGGG---TCGGCCATTTTCCTCTCCAGTCCC----TT 714730 --- --- ii vv iv ivv ii ---- C MIR3#SINE/MIR 186 CAGAG---CTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATT 140 chr1qtel1M 714731 TTAGAGATG-GGAAACTGAGGCAAGCAGGGCTGA-GTGGTGAGCCCAGGG 714778 v - vviv i v - iivv i C MIR3#SINE/MIR 139 TTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGG 90 chr1qtel1M 714779 TCACATGGGTAGTAAGTG 714796 ii v? v C MIR3#SINE/MIR 89 TCACACAGCNAGTTAGTG 72 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 31.73 CpG sites = 13, Kimura (unadjusted) = 31.73 Transitions / transversions = 0.93 (13/14) Gap_init rate = 0.06 (7 / 108), avg. gap size = 1.71 (12 / 7) 246 22.54 2.82 0.00 chr1qtel1M 714726 714796 (285204) C MIR#SINE/MIR (119) 143 71 m_b47s601i11 1662 chr1qtel1M 714726 CCCTTTTAGAGATG-GGAAACTGAGGCA-AGCAGGGCTGAGTGGTGAGCC 714773 v v - - vii i i iiivv C MIR#SINE/MIR 143 CCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCC 94 chr1qtel1M 714774 CAGGGTCACATGGGTAGTAAGTG 714796 i ii v C MIR#SINE/MIR 93 CAAGGTCACACAGCTAGTAAGTG 71 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 27.43 CpG sites = 10, Kimura (unadjusted) = 27.43 Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.03 (2 / 70), avg. gap size = 1.00 (2 / 2) 181 33.33 5.05 0.00 chr1qtel1M 714837 714935 (285065) L2d2_3end#LINE/L2 375 478 (77) m_b47s601i12 1663 chr1qtel1M 714837 GTCATTTA--TTCTATGTTGTTGCTTTGCCTAT-ATTTGTTCCCATGTTG 714883 i -- ii i i ii vi i v - iv ivii v L2d2_3end#LIN 375 GTTATTTAAATCTTGTATTGTTATTTAACTTTTCACGTGTTTATGTCTTG 424 chr1qtel1M 714884 TCTTCCCTACTAGGCTCTAAACTTCTCGAGGACAGGAGC--TGCCTTTTG 714931 i v ii v i i i i ii -- i v i L2d2_3end#LIN 425 TCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATA 474 chr1qtel1M 714932 CCTC 714935 i L2d2_3end#LIN 475 CTTC 478 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 46.34 CpG sites = 25, Kimura (unadjusted) = 48.48 Transitions / transversions = 3.12 (25/8) Gap_init rate = 0.03 (3 / 98), avg. gap size = 1.67 (5 / 3) 194 25.00 4.17 0.00 chr1qtel1M 714881 714928 (285072) L2d_3end#LINE/L2 380 429 (87) m_b47s601i13 1663 chr1qtel1M 714881 TTGTCTTCCCTACTAGGCTCTAAACTTCTCGAGGACAGGAGC--TGCCTT 714928 i v ii v i i i i ii -- i L2d_3end#LINE 380 TTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTT 429 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 32.83 CpG sites = 10, Kimura (unadjusted) = 32.83 Transitions / transversions = 5.00 (10/2) Gap_init rate = 0.02 (1 / 47), avg. gap size = 2.00 (2 / 1) 180 20.98 0.00 4.65 chr1qtel1M 715922 715966 (284034) C L2d2_3end#LINE/L2 (0) 555 513 m_b47s601i14 1664 chr1qtel1M 715922 TTAAATGGAAATTTAACAAAGATTTATTAAACACCTACTATGTGC 715966 i vi -- i v i i i i C L2d2_3end#LIN 555 TCAAATCAAA--TCAACAAATATTTATTGAGCGCCTACTGTGTGC 513 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 22.48 CpG sites = 7, Kimura (unadjusted) = 25.71 Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.05 (2 / 44), avg. gap size = 1.00 (2 / 2) 283 28.88 3.30 1.08 chr1qtel1M 715932 716022 (283978) C L2c_3end#LINE/L2 (8) 470 378 m_b47s601i15 1664 chr1qtel1M 715932 ATTTAACAAAGATTTATTAAACACCTACTATGTGCTGAGCTGCTGCGAAT 715981 i v i i i iii - v i C L2c_3end#LINE 470 ATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGC-GCTGGGGAT 422 chr1qtel1M 715982 CCCAGG--GAA-AAAAGAAAATTCCTGCCTCCTTGGGGTCCACA 716022 v v i -- - i v vii i ii vv i ii C L2c_3end#LINE 421 ACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACA 378 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 34.68 CpG sites = 18, Kimura (unadjusted) = 38.45 Transitions / transversions = 2.25 (18/8) Gap_init rate = 0.03 (3 / 90), avg. gap size = 1.33 (4 / 3) 194 30.99 0.99 7.37 chr1qtel1M 716462 716562 (283438) C L2d2_3end#LINE/L2 (19) 536 442 m_b47s601i16 1665 chr1qtel1M 716462 ATTTCCTTACCGCTAACTGCGTGCAGGGCATCTTGCCAGATGCTGGGGGG 716511 vi v v iv i i iiv i ii v C L2d2_3end#LIN 536 ATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGTGGGG 487 chr1qtel1M 716512 TAAGGGGGAGACAGGGAAAAAGGAAA-AGGTTCCCTGTGCTCAAGGCCCT 716560 ------- v ii iv vi i - v v iv vv C L2d2_3end#LIN 486 -------GATACAAAGAAGTATAAGACATGGTCCCTGCCCTCAAGGAGCT 444 chr1qtel1M 716561 TA 716562 C L2d2_3end#LIN 443 TA 442 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 38.64 CpG sites = 15, Kimura (unadjusted) = 40.40 Transitions / transversions = 1.07 (15/14) Gap_init rate = 0.08 (8 / 100), avg. gap size = 1.00 (8 / 8) 216 34.86 5.71 0.00 chr1qtel1M 718315 718489 (281511) L2#LINE/L2 1883 2067 (1015) m_b47s601i17 1666 chr1qtel1M 718315 CCTTGAAATCATCATCTGTCCTGGGTGTCTCC----CCTCGCTTTCCCTG 718360 i vvi ii i v v v ---- v i i v v L2#LINE/L2 1883 CCTCGAAAGAGTTGTCTATACTCGCTGTCTCCAATTCCTCTCCTCCCATT 1932 chr1qtel1M 718361 ATGT-TTAAACCTCCTGCCACCTCACTTCTGACATCCTCATGCAGTAGCA 718409 v v - i iv v v i vvi ii v vi vi iv viiv v L2#LINE/L2 1933 CTCTCTTGAACCCACTCCAATCAGGCTTTCGTCCCCACCACTCCACCGAA 1982 chr1qtel1M 718410 ACAGCTCTGTTCAAGGTTACCTGTGATAACAATG--ACCAAATCCAATGT 718457 v vv i vi ivv v i --i i v L2#LINE/L2 1983 ACTGCTCTTGTCAAGGTCACCAATGACCTCCACGTTGCTAAATCCAATGG 2032 chr1qtel1M 718458 CTCTTCCTCAGTCCTCATC---CTTGATCTTACAG 718489 iivv i --- i ?v L2#LINE/L2 2033 TCAATTCTCAGTCCTCATCTTACTTGACCTNTCAG 2067 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 44.66 CpG sites = 28, Kimura (unadjusted) = 47.74 Transitions / transversions = 0.85 (28/33) Gap_init rate = 0.02 (4 / 174), avg. gap size = 2.50 (10 / 4) 371 26.41 5.59 2.03 chr1qtel1M 718695 718837 (281163) C L2c_3end#LINE/L2 (2) 476 329 m_b47s601i18 1667 chr1qtel1M 718695 TCACTCACAGTCAGCAA-TGCCTACTAAGTGTCAGCTGTCATGCTAAGGG 718743 i i-- i -iiii i i i i vi i -i i i v C L2c_3end#LINE 476 TCATTCAT--TCAACAAACATTTATTGAGCGCCTACTAT-GTGCCAGGCG 430 chr1qtel1M 718744 CTACGGATACAAAGA-----AAGGCACAGACCCAGCTCTCAAGGAGCTCA 718788 iv ----- i i v v i C L2c_3end#LINE 429 CTGGGGATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCA 380 chr1qtel1M 718789 CAGTCTAA-GGAGGAAAACAACCTGCAAACAGCTATGTACAA-ACAAGGT 718836 i- i vvi v? i vi vv - v C L2c_3end#LINE 379 CAGTCTAGTGGAGGAGACAGACANGTAAACAGACAATTACAATACAAGTT 330 chr1qtel1M 718837 A 718837 C L2c_3end#LINE 329 A 329 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 31.99 CpG sites = 25, Kimura (unadjusted) = 34.27 Transitions / transversions = 2.08 (25/12) Gap_init rate = 0.05 (7 / 142), avg. gap size = 1.57 (11 / 7) 15 5.48 0.00 0.00 chr1qtel1M 719205 719223 (280777) (T)n#Simple_repeat 1 19 (0) m_b47s252i5 1668 chr1qtel1M 719205 TTGTTTTTTTTTTTTTTTT 719223 v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 33 0.00 0.00 0.00 chr1qtel1M 719248 719278 (280722) (T)n#Simple_repeat 1 31 (0) c_b47s251i0 1668 chr1qtel1M 719248 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 719278 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 433 22.06 0.81 7.83 chr1qtel1M 719281 719403 (280597) C MIRc#SINE/MIR (141) 127 13 m_b47s601i19 1669 chr1qtel1M 719281 CTGAGGC-AATTGGGGTTAAATGACTTGCCCAAGGATCACACAGCTAGGT 719329 -v vv i i - vv C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGG-TCACACAGCTAGTA 79 chr1qtel1M 719330 AGTGTTAAAATGTCTGAGGCCAGATTTGAACTCGGGTCCTCCTGACTTCA 719379 vi -------- v vi i i i i i i C MIRc#SINE/MIR 78 AGTGGCA--------GAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCA 37 chr1qtel1M 719380 GAGCTGGCGCTCTATCCACTGCAC 719403 iiv ii i v C MIRc#SINE/MIR 36 AGTCCAGTGCTCTTTCCACTGCAC 13 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 25.23 CpG sites = 15, Kimura (unadjusted) = 26.43 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.08 (10 / 122), avg. gap size = 1.00 (10 / 10) 185 29.40 4.55 3.37 chr1qtel1M 720498 720585 (279415) MIRb#SINE/MIR 144 232 (36) m_b47s601i21 1670 chr1qtel1M 720498 AAAACAAGAATAATAATGTACCTCTCTCATCAAGTCACTGTAAGGCTCAA 720547 iii i -- vi iivii iii i v i MIRb#SINE/MIR 144 AAAATGGGGATAATAAT--ACCTACCTCGCAGGGTTGTTGTGAGGATTAA 191 chr1qtel1M 720548 ATGAGTCAA-GCATCCTAAAGAGCTTTGTAAA---CCTGACA 720585 vi - -v v v i v --- i MIRb#SINE/MIR 192 ATGAGATAATGCAT-GTAAAGCGCTTAGCACAGTGCCTGGCA 232 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 37.24 CpG sites = 17, Kimura (unadjusted) = 39.29 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.06 (5 / 87), avg. gap size = 1.40 (7 / 5) 237 25.67 2.67 1.32 chr1qtel1M 720498 720572 (279428) MIR#SINE/MIR 137 212 (50) m_b47s601i20 1670 chr1qtel1M 720498 AAAACAAGAATAATAAT-GTACCTCTCTCATCAAGTCACTGTAAGGCTCA 720546 iii i - vi vii iii i v i MIR#SINE/MIR 137 AAAATGGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGGATTA 186 chr1qtel1M 720547 AATGAGTCAA-GCATCCTAAAGAGCTT 720572 i -i -v v MIR#SINE/MIR 187 AATGAGTTAATACAT-GTAAAGCGCTT 212 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.15 CpG sites = 14, Kimura (unadjusted) = 33.15 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.04 (3 / 74), avg. gap size = 1.00 (3 / 3) 370 23.61 5.43 1.49 chr1qtel1M 721487 721615 (278385) MIR3#SINE/MIR 12 145 (63) m_b47s601i22 1671 chr1qtel1M 721487 GCTGGGCAAAGAGAGCCCACCCT-GGAGTCAGGAAGGGCTGAGCTCAAAT 721535 i i v ivv - - iv i i v i MIR3#SINE/MIR 12 GCTGAGCAGAGAGAGCACGGACTGGGAGTCAGG-AGACCTGGGTTCTAGT 60 chr1qtel1M 721536 GTGATCCCAGACACTTACTGG----GTGAGCCTGGGCAAGGCCTTTCACC 721581 viviv i v v v ? ---- v i v vi - MIR3#SINE/MIR 61 CCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCA-C 109 chr1qtel1M 721582 CTGCCT--GCCTCAGTTTTCTCATCTGTAGAATGAG 721615 vi -- i i MIR3#SINE/MIR 110 CTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAG 145 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 26.72 CpG sites = 15, Kimura (unadjusted) = 28.89 Transitions / transversions = 1.00 (15/15) Gap_init rate = 0.04 (5 / 128), avg. gap size = 1.80 (9 / 5) 23 13.95 1.89 3.85 chr1qtel1M 722292 722344 (277656) (TTTTCC)n#Simple_repeat 1 52 (0) m_b47s252i6 1672 chr1qtel1M 722292 TTTTCCTTTTCTCTTGTTCCTTCTCCTTTTTCTTTTTTTTTTTC-TTTCT 722340 - - i i ii i - i (TTTTCC)n#Sim 1 TTTTCCTTTTC-CTT-TTCCTTTTCCTTTTCCTTTTCCTTTTCCTTTTCC 48 chr1qtel1M 722341 TTTT 722344 (TTTTCC)n#Sim 49 TTTT 52 Matrix = Unknown Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.06 (3 / 52), avg. gap size = 1.00 (3 / 3) 404 33.97 3.45 1.89 chr1qtel1M 722499 722759 (277241) L2#LINE/L2 2305 2569 (513) m_b47s601i23 1673 chr1qtel1M 722499 ATAGATTCAATTATCAGCTCTATTCTGATCATTCTCACATCTACCTGTAC 722548 i v i v i v v v v i i v i iv v v L2#LINE/L2 2305 ATGGCTTTAAATACCATCTATATGCTGATGACTCCCAAATTTATATCTCC 2354 chr1qtel1M 722549 GGGCTTAATCTCTCGCTT-------AGCCTCCCATCTCCAACTGCCAATT 722591 i v ivi i v i ------- v vi v v i L2#LINE/L2 2355 AGCCCGGACCTCTCCCCTGAACTCCAGACTCGTATATCCAACTGCCTACT 2404 chr1qtel1M 722592 CGCCATCTTGAATGAGTTATCCTAAAAACATCTAAATCTCAGCATATCCA 722641 v iv v vi v i iv v ii v v i i i L2#LINE/L2 2405 CGACATCTCCACTTGGATGTCTAATAGGCATCTCAAACTTAACATGTCCA 2454 chr1qtel1M 722642 AACCTGCACTCATTAGCTTTCCTCTCGACCCTTTTCTGCCTCTTCCA-AA 722690 v v v v v i i i v ----- ii i i- i L2#LINE/L2 2455 AAACTGAACTCCTGATCTTCCCCCTCAAAC-----CTGCTCCTCCCGCAG 2499 chr1qtel1M 722691 TCTTACCCTTACTTGTTGATGTT-ACCCCATCCTCTCAATCTCTCAAGCT 722739 v v viiv ?i vi- i ii i iv i i L2#LINE/L2 2500 TCTTCCCCATCTCAGTNAATGGCAACTCCATCCTTCCAGTTGCTCAGGCC 2549 chr1qtel1M 722740 TGCAACTTGGGTATCATCCT 722759 viv i v vi L2#LINE/L2 2550 AAAAACCTTGGAGTCATCCT 2569 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 45.00 CpG sites = 45, Kimura (unadjusted) = 46.44 Transitions / transversions = 1.07 (45/42) Gap_init rate = 0.03 (8 / 260), avg. gap size = 1.75 (14 / 8) 230 32.12 2.84 2.84 chr1qtel1M 722824 722964 (277036) L2#LINE/L2 2683 2823 (259) m_b47s601i24 1673 chr1qtel1M 722824 CCCTGCTTTAAGCCCTCATCACCTTAAACCTTATGACTATCGCAAGAGGC 722873 v ii vi i ivvi v-- i ii v v L2#LINE/L2 2683 CCCTGGTCCAAGCCACCATCATCTCTCGCCTG--GATTACTGCAATAGCC 2730 chr1qtel1M 722874 TATCGGTTGGTATCCCCACCCTAGCAGTCTCGCCCTACTCCAGTCTAATC 722923 viiiii v ii iii-- vi i iv ? v L2#LINE/L2 2731 TCCTAACTGGTCTCCCTGCTTC--CACCCTTGCCCCCCTNCAGTCTATTC 2778 chr1qtel1M 722924 CCTACTCAGCTCCCCGAGTCATCTTCCTAAAA-GTA---CAGATC 722964 i v v vv v v i ii - --- L2#LINE/L2 2779 TCAACACAGCAGCCAGAGTGATCCTTTTAAAACGTAAGTCAGATC 2823 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 42.49 CpG sites = 26, Kimura (unadjusted) = 43.84 Transitions / transversions = 1.44 (26/18) Gap_init rate = 0.04 (6 / 140), avg. gap size = 1.33 (8 / 6) 461 20.44 0.00 11.40 chr1qtel1M 723244 723370 (276630) MIRc#SINE/MIR 2 115 (153) m_b47s601i25 1674 chr1qtel1M 723244 GGGGCAGCTAGGTGGTGCCACTGTGGATAGAGCACCAGCCCTGAAGTCAG 723293 i i--- v--- v ii v i i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCA---GTGGAAAGAGCACTGGACTTGGAGTCAG 45 chr1qtel1M 723294 GAAGACTTGAGTTCAAATCTGGTTTCAGACACTTAACATTTCCTGGCTGT 723343 i i i i iv vi v v ------- i MIRc#SINE/MIR 46 GAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTA-------CTAGCTGT 88 chr1qtel1M 723344 GTAACCCTGGGCAAGTCACTTAACCCC 723370 i i i MIRc#SINE/MIR 89 GTGACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 23.03 CpG sites = 16, Kimura (unadjusted) = 24.21 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.10 (13 / 126), avg. gap size = 1.00 (13 / 13) 19 11.70 0.00 0.00 chr1qtel1M 723383 723410 (276590) (A)n#Simple_repeat 1 28 (0) m_b47s252i7 1675 chr1qtel1M 723383 AAAAAAAATAAAAAATAAAAAAAATAAA 723410 v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA 28 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 13 22.56 3.64 3.64 chr1qtel1M 723385 723439 (276561) (AATAAAT)n#Simple_repeat 1 55 (0) m_b47s252i8 1675 chr1qtel1M 723385 AAAAAATAAAAAATAA-AAAAAATAAA-GTTAAATGTTGGTCTAATTAAA 723432 v v - v -iv iv -ivv - (AATAAAT)n#Si 1 AATAAATAATAAATAATAAATAATAAATAATAAATAAT-AAATAA-TAAA 48 chr1qtel1M 723433 TAATAAA 723439 (AATAAAT)n#Si 49 TAATAAA 55 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.07 (4 / 54), avg. gap size = 1.00 (4 / 4) 359 16.93 23.53 0.68 chr1qtel1M 724129 724247 (275753) MIRc#SINE/MIR 3 148 (120) m_b47s601i26 1676 chr1qtel1M 724129 AGGTAG-GTGGTCCAGTGGATAGAGCAATAAGTTC--AGTCAGGAAGAC- 724174 i - v v v iiii i-- - MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chr1qtel1M 724175 -ACAT---AGTC---------------ACAAG---TGTAAATCTGGGCAA 724202 -ivi --- --------------- v --- i vii MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 102 chr1qtel1M 724203 GTCACTTAACCTTGTTTGA--CTCAGTTTCCTCATCTGTAAAATGAG 724247 i- i -- i MIRc#SINE/MIR 103 GTCACTTAACCTC-TCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 19.67 CpG sites = 14, Kimura (unadjusted) = 19.67 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.08 (9 / 118), avg. gap size = 3.22 (29 / 9) 336 14.54 4.35 10.34 chr1qtel1M 724187 724278 (275722) MIR1_Amn#SINE/MIR 89 175 (55) m_b47s601i27 1676 chr1qtel1M 724187 GTGTAAATCTGGGCAAGTCACTTAACCTTGTTTGA--CTCAGTTTCCTCA 724234 ? i vii ? i- i ?-- MIR1_Amn#SINE 89 GNGTGACCTTGGGCAAGTCACTTNACCTC-TCTGNGCCTCAGTTTCCTCA 137 chr1qtel1M 724235 TCTGTAAAATGAGCTGGAGAAGAAAATGATA--AACCTCTCTGGTA 724278 i -------- v --i ii v MIR1_Amn#SINE 138 TCTGTAAAATGGG--------GATAATGATACTGACCTCCTTTGTA 175 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 17.17 CpG sites = 9, Kimura (unadjusted) = 17.17 Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.12 (11 / 91), avg. gap size = 1.18 (13 / 11) 23 12.41 0.00 0.00 chr1qtel1M 726203 726237 (273763) (T)n#Simple_repeat 1 35 (0) m_b47s252i9 1677 chr1qtel1M 726203 TTTTCTTTTTTTTTTTTTTTTTAAATTTTTTTTTT 726237 i vvv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 35 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 439 23.33 1.63 5.93 chr1qtel1M 728547 728669 (271331) C MIRc#SINE/MIR (141) 127 10 m_b47s601i28 1678 chr1qtel1M 728547 CTGAGGC-AATTGGGGTTAAGTGACTTGCT-AGGGCCACACAGCTAGGAA 728594 -v vv i i- i i --- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG--- 81 chr1qtel1M 728595 GTATTAAGTGTCTGAGGTCATATTTGAACTCAGGTCCTCCTGACTTCAGG 728644 ---- v v viviv i i i i i i C MIRc#SINE/MIR 80 ----TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr1qtel1M 728645 GTTGGTACTCTATTCACTGCACCAC 728669 viii i v i C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 26.14 CpG sites = 17, Kimura (unadjusted) = 28.58 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.07 (9 / 122), avg. gap size = 1.00 (9 / 9) 254 25.30 4.82 0.00 chr1qtel1M 729809 729891 (270109) L1ME3C_3end#LINE/L1 130 216 (654) m_b47s551i1 1679 chr1qtel1M 729809 AAAAAATGCTCAACATCACAAAGAACTA-GAAAATGTGAATTAAAGCAAC 729857 i v v iv ii - i ii i ? L1ME3C_3end#L 130 AAAAGATGCTCAACCTCACTAGTAATCAGGGAAATGCAAATTAAAACNAC 179 chr1qtel1M 729858 TCTGAGGTTCTACCTCATA---ATAAGATTGGCAGAA 729891 vv i v i ii i --- v i L1ME3C_3end#L 180 AATGAGATACCATTTCACACCCATCAGATTGGCAAAA 216 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 32.51 CpG sites = 14, Kimura (unadjusted) = 32.51 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.02 (2 / 82), avg. gap size = 2.00 (4 / 2) 242 28.26 3.26 0.00 chr1qtel1M 730103 730194 (269806) L1ME3G_3end#LINE/L1 453 547 (377) m_b47s551i2 1680 chr1qtel1M 730103 TTTTTTGTTATAGCAAATATCTATAAATAACATTAGTACCCCTCAACTAA 730152 v v i v vi iv i v v i ii v ivii L1ME3G_3end#L 453 TTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCAATAGG 502 chr1qtel1M 730153 GGAATGGTTAGACAAATTATAGTATAT---TATTGTTGAATAGTA 730194 i i i --- i i v v L1ME3G_3end#L 503 GGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACTA 547 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 34.60 CpG sites = 15, Kimura (unadjusted) = 36.33 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.01 (1 / 91), avg. gap size = 3.00 (3 / 1) 11 21.63 0.00 5.13 chr1qtel1M 730632 730672 (269328) (ATAATTT)n#Simple_repeat 1 39 (0) m_b47s252i10 1681 chr1qtel1M 730632 ATAATTTAAAAATTATAATTCTATGGTTTTTTTTTTAATAA 730672 v v - ii v vv - (ATAATTT)n#Si 1 ATAATTTATAATTTATAATT-TATAATTTATAATTT-ATAA 39 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 198 33.67 14.36 0.47 chr1qtel1M 730707 730894 (269106) L3#LINE/CR1 1694 1907 (2192) m_b47s601i29 1682 chr1qtel1M 730707 GACTTCTGCCAGCACTCTC-----GCTGAAAGGAAGGCG-CTAGTGATGT 730750 v ii v v ----- i v ii i- ii i vv L3#LINE/CR1 1694 GACATCTGCTGGAAGTCTCATTCNGCTAAAAGCAGAGCATCTGATAAATT 1743 chr1qtel1M 730751 CCTGACTTATCTTGGT---AATTTTATGCTTC---------------CCC 730782 i ii v --- i vii --------------- vv L3#LINE/CR1 1744 CTTGACTTGCCTTGCTGACAATTTCATCTCTCAGAAGGTAGAGGAAGCAA 1793 chr1qtel1M 730783 CCAAGGGAAATGCTACTC-AAAC-TGATTCCCACCAAGAAGGCAGAACAA 730830 v i v -ii - i iv v v vi L3#LINE/CR1 1794 CGAGGGGAACTGCTACTCTGGACTTAATTCTGACCAACAAGGAAGAACTG 1843 chr1qtel1M 730831 ACTGTTGGGGTAGAAAAAG-TGGGAACAGCAGGAAGAAGAGAATACTCCA 730879 ii v ii i ivv - i vvii ii v -vi ivi L3#LINE/CR1 1844 GTTGGTGAAGTGGAAGTCGATAGGAACCTTGGGAGAAAGTG-CCATGTCA 1892 chr1qtel1M 730880 ATTAAGAGTTTGTAA 730894 vi v i L3#LINE/CR1 1893 TCTTAGAGTTCGTAA 1907 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 45.38 CpG sites = 37, Kimura (unadjusted) = 46.41 Transitions / transversions = 1.42 (37/26) Gap_init rate = 0.04 (8 / 187), avg. gap size = 3.50 (28 / 8) 284 30.09 10.78 2.26 chr1qtel1M 731138 731341 (268659) L3#LINE/CR1 2524 2744 (1355) m_b47s601i30 1682 chr1qtel1M 731138 GGAGCTCTTAAGAGAGCCCCCGGCTGCCTCAA-TGAGTGC------TCAG 731180 v vv v ii i i i - v ------i L3#LINE/CR1 2524 GGAGATAGTAAGAGAGCACCTAGCCGCTTTAAATGAGTTCAAGTCTCCAG 2573 chr1qtel1M 731181 GTGCAGG------ACATCCTTAAGGACAGAAAGGGCCAGCAGGGGTCATT 731224 iv i------ ivii v v ii iv iv v i L3#LINE/CR1 2574 GCCCAGACGAATTACATCCCAGGGTACTGAAAGAACTTGCAGATGTGATC 2623 chr1qtel1M 731225 CCTGAGCCACTGCCAGTGACCTCTGAG--ATCAGGGTGAAGGGGAGAGAC 731272 v v i i i i i i i -- v v v i ii L3#LINE/CR1 2624 GCGGAACCGCTGTCGGTAATCTTTGAGAAATCACGGAGAACGGAAGAGGT 2673 chr1qtel1M 731273 GTC-----ACTTG-GTCAAATGAATGTTGTCCC-AATCTAAGGAACAAAA 731315 i ----- v - v iiiii ? ? - ? i v ii vii L3#LINE/CR1 2674 GCCAGAAGACTGGAGACGGGCAAATGTNGTNCCTANTTTTAAAAAGGGAA 2723 chr1qtel1M 731316 AAGGAAGTGAATGGATGCTGCAGACT 731341 -- --- v ? i L3#LINE/CR1 2724 AA--AAG---ATGGATTCTGNAAACT 2744 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 36.87 CpG sites = 38, Kimura (unadjusted) = 41.31 Transitions / transversions = 1.73 (38/22) Gap_init rate = 0.06 (12 / 203), avg. gap size = 2.25 (27 / 12) 225 30.59 1.18 0.00 chr1qtel1M 731393 731477 (268523) C L3#LINE/CR1 (514) 3585 3500 m_b47s601i31 1683 chr1qtel1M 731393 TGTGATCTGGTCAGGGCTGGATACAAGGAGACTCTCACCTCCCCT-TTCT 731441 i ii v v ii iv i v i i -? C L3#LINE/CR1 3585 TGTGGTCTGACCAGCGCAGAGTACAGCGGGACTATTACCTCCCTTGNTCT 3536 chr1qtel1M 731442 CAGCTCTGTGCTTCCCTAAATGCTGACTGAGCTTGC 731477 vii v i i iv v v v i v C L3#LINE/CR1 3535 GGACACTATACTTCTATTAATGCAGCCTAAGATTGC 3500 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 41.07 CpG sites = 15, Kimura (unadjusted) = 41.07 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.01 (1 / 84), avg. gap size = 1.00 (1 / 1) 231 34.47 2.42 4.10 chr1qtel1M 731711 731834 (268166) L3#LINE/CR1 3802 3923 (176) m_b47s601i32 1682 chr1qtel1M 731711 AGAGAACTTAACTGACCCGTTCTGTTTGGCCCCAGGGGGTGTAAGGAGGA 731760 iiv --- iii v i i iiv vv L3#LINE/CR1 3802 AGAGGGATTA---GACTTATTCTGTGTGGCTCCAGAGGGCAGAACTAGGA 3848 chr1qtel1M 731761 ACAATGAGT---ATTTGGGGAAAGAGGCAAACCGAGGCTTGATGTTACAG 731807 v i --- v --iv ii i iivv ii i v vii L3#LINE/CR1 3849 CCAATGGGTGGAAGTT--ACAGGGAGGCAGATTTCGGCTCAATATAAGGA 3896 chr1qtel1M 731808 AAAACTTCCTAAGGATCACAACCATCC 731834 i i vi v i ii L3#LINE/CR1 3897 AGAACTTTCTAACAATCAGAGCTGTCC 3923 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 49.07 CpG sites = 27, Kimura (unadjusted) = 49.07 Transitions / transversions = 1.93 (27/14) Gap_init rate = 0.05 (6 / 123), avg. gap size = 1.33 (8 / 6) 241 25.00 1.79 0.00 chr1qtel1M 733067 733122 (266878) C MIRb#SINE/MIR (7) 261 205 m_b47s601i33 1684 chr1qtel1M 733067 GGGCGAGCACTGATTAAGTGCCTACTATGTACAAAGCACT-TGCTAAATA 733115 i v v i v i i i i v i - iii C MIRb#SINE/MIR 261 GAGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCG 212 chr1qtel1M 733116 CTTTACA 733122 C MIRb#SINE/MIR 211 CTTTACA 205 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 26.22 CpG sites = 10, Kimura (unadjusted) = 31.83 Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.02 (1 / 55), avg. gap size = 1.00 (1 / 1) 227 24.75 1.28 6.76 chr1qtel1M 733069 733146 (266854) C MIR#SINE/MIR (7) 255 182 m_b47s601i34 1684 chr1qtel1M 733069 GCGAGCACTGATTAAGTGCCTACTATGTACAAAGCACT-TGCTAAATACT 733117 v i i v i i i i v i - v iii C MIR#SINE/MIR 255 GCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGCGCT 206 chr1qtel1M 733118 TTACAAAGTGTTTTACAAATCATTTGACC 733146 --- v -- v i i C MIR#SINE/MIR 205 TTACA---TGTATT--AACTCATTTAATC 182 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 26.72 CpG sites = 12, Kimura (unadjusted) = 30.95 Transitions / transversions = 2.00 (12/6) Gap_init rate = 0.08 (6 / 77), avg. gap size = 1.00 (6 / 6) 378 28.79 9.73 1.64 chr1qtel1M 733274 733499 (266501) L1PA16_3end#LINE/L1 88 331 (582) m_b47s551i3 1685 chr1qtel1M 733274 AGTCAGTTTTCAAAGAAGGAAATCCAAATGATCAAAAGCCACATGAAAAA 733323 v v i ii i v v ii ii v iv i L1PA16_3end#L 88 AGACACTTCTCAAAAGAAGACATACAAGCGGCCAACAAACATATGAAAAA 137 chr1qtel1M 733324 ATGTT-----TCA--AATCA-CAGAGAAATACCAATCAAAGGGACACTTA 733365 i ----- -- - i v ivv v- i L1PA16_3end#L 138 ATGCTCAACATCACTAATCATCAGAGAAATGCAAATCAAAACCACAA-TG 186 chr1qtel1M 733366 AGGTTTAACCTCCCACT--TCAGGGTGGCAAAGTTAACAGAAAAGTAAAA 733413 i viv i v i-- ii v -- vi - v L1PA16_3end#L 187 AGATACCATCTCACACCAGTCAGAATGGCTA--TTATTA-AAAAGTCAAA 233 chr1qtel1M 733414 GGGTGAC---TACTGGAGGGGCTACAG-GAAAATGG---GC----ATATT 733452 iiiii --- i v i i i - v --- ---- i i L1PA16_3end#L 234 AAACAACAGATGCTGGCGAGGCTGCGGAGAAAAGGGAACGCTTATACACT 283 chr1qtel1M 733453 GTT-GTATTGCTGCCAGTCAGTTTAGCCATTCTGGAAAGCACTTGGGA 733499 - ivviv iv i i i i v v v L1PA16_3end#L 284 GTTGGTGGGAATGTAAATTAGTTCAGCCACTGTGGAAAGCAGTTTGGA 331 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 36.07 CpG sites = 39, Kimura (unadjusted) = 37.56 Transitions / transversions = 1.56 (39/25) Gap_init rate = 0.06 (13 / 225), avg. gap size = 2.00 (26 / 13) 21 3.30 0.00 3.12 chr1qtel1M 734153 734185 (265815) (AATTA)n#Simple_repeat 1 32 (0) m_b47s252i11 1686 chr1qtel1M 734153 AATTAAATTAATTTAAATTTAAATTAAATTAAA 734185 v - (AATTA)n#Simp 1 AATTAAATTAAATTAAA-TTAAATTAAATTAAA 32 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 241 0.00 0.00 0.00 chr1qtel1M 734688 734716 (265284) C MIR3#SINE/MIR (65) 143 115 m_b47s601i35 1687 chr1qtel1M 734688 CATTTTACAGATGAGGAAACTGAGGCCCA 734716 C MIR3#SINE/MIR 143 CATTTTACAGATGAGGAAACTGAGGCCCA 115 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 0.00 CpG sites = 0, Kimura (unadjusted) = 0.00 Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 219 25.55 4.55 7.48 chr1qtel1M 734895 735004 (264996) C MIR1_Amn#SINE/MIR (102) 128 22 m_b47s601i36 1688 chr1qtel1M 734895 TGAGGCA-ATTGGGGTTAAATGGCTTGCTCAGGGTCATGTAGCAAGTAAG 734943 ?- vv i ? i i i i i?i ?i i? C MIR1_Amn#SINE 128 TGAGGCNCAGAGAGGTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNAG 79 chr1qtel1M 734944 TATTAAGTGTCTGAGGCCACATTTGAACTCGGGTCCTCCTGA---CTA-T 734989 ivi ------- v viv ? ? i i - i --- i - C MIR1_Amn#SINE 78 TGGCA-------GAGCCGGGANTNGAACCCAGGT-CTCCCGAGTCCCAGT 37 chr1qtel1M 734990 CCACTGGGCCATCCA 735004 v vv i C MIR1_Amn#SINE 36 CCAGTGCTCTATCCA 22 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.68 CpG sites = 17, Kimura (unadjusted) = 35.38 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.10 (11 / 109), avg. gap size = 1.18 (13 / 11) 273 27.87 0.00 9.21 chr1qtel1M 734905 734987 (265013) C MIRc#SINE/MIR (153) 115 40 m_b47s601i37 1688 chr1qtel1M 734905 GGGGTTAAATGGCTTGCTCAGGGTCATGTAGCAAGTAAGTATTAAGTGTC 734954 i i i i i iii v ivi ------ C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCA------ 72 chr1qtel1M 734955 TGAGGCCACATTTGAACTCGGGTCCTCCTGACT 734987 - v viv i i i i i C MIRc#SINE/MIR 71 -GAGCCGGGACTCGAACCCAGGTCTTCCTGACT 40 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 34.63 CpG sites = 16, Kimura (unadjusted) = 36.89 Transitions / transversions = 3.20 (16/5) Gap_init rate = 0.09 (7 / 82), avg. gap size = 1.00 (7 / 7) 16 17.84 4.35 0.00 chr1qtel1M 736625 736657 (263343) (CTTTCT)n#Simple_repeat 1 35 (13) m_b47s252i12 1689 chr1qtel1M 736625 CTTTCT-TTTCT-TTTCTCTCTCTCTCTCCCTTGC 736657 - - i i i v (CTTTCT)n#Sim 1 CTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCTTTC 35 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.06 (2 / 32), avg. gap size = 1.00 (2 / 2) 109 1.57 1.40 5.07 chr1qtel1M 736658 736800 (263200) (TCCT)n#Simple_repeat 1 138 (0) c_b47s251i1 1690 chr1qtel1M 736658 TCCTTCCTTTTCTTCCTTCCTTTCCTTCCCTTCCTTCCCTTCCCTCCTTC 736707 - i - - - i (TCCT)n#Simpl 1 TCCTTCC-TTCCTTCCTTCC-TTCCTT-CCTTCCTT-CCTTCCTTCCTTC 46 chr1qtel1M 736708 CTTCCTTCCTTCCCTT-CTTCCCTT-CTTCCCTTCCTTCCTTCCTTCCTT 736755 - - - - - (TCCT)n#Simpl 47 CTTCCTTCCTT-CCTTCCTT-CCTTCCTT-CCTTCCTTCCTTCCTTCCTT 93 chr1qtel1M 736756 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC 736800 (TCCT)n#Simpl 94 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC 138 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.06 (9 / 142), avg. gap size = 1.00 (9 / 9) 16 17.84 4.35 0.00 chr1qtel1M 736801 736812 (263188) (CTTTCT)n#Simple_repeat 36 47 (1) m_b47s252i12 1691 chr1qtel1M 736801 TTTTTTGTTTCT 736812 i i v (CTTTCT)n#Sim 36 CTTTCTCTTTCT 47 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 11), avg. gap size = 0.0 (0 / 0) 356 23.99 2.46 7.76 chr1qtel1M 736814 736935 (263065) C MIR#SINE/MIR (139) 123 8 m_b47s601i38 1692 chr1qtel1M 736814 CTGAGGCA-ACTGGGTTTAAGTGACTTGCCTAGGGTCACACAGCTAGGAA 736862 - vv i v i i i --- C MIR#SINE/MIR 123 CTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAG--- 77 chr1qtel1M 736863 GTGTTAAGTGTCTAAAGTC-AAATTTGAACTCAGGTCCTCTTGACTTCAG 736911 ---- v - i i -ii i i ivv - i i C MIR#SINE/MIR 76 ----TAAGTGGC-AGAGCCGGGATTCGAACCCAGGCAGTC-TGGCTCCAG 33 chr1qtel1M 736912 GGCTGGTGCTC-TATCCATTGCGTT 736935 i iv - v i ii i C MIR#SINE/MIR 32 AGCCCGTGCTCTTAACCACTATGCT 8 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 28.63 CpG sites = 19, Kimura (unadjusted) = 29.95 Transitions / transversions = 2.38 (19/8) Gap_init rate = 0.10 (12 / 121), avg. gap size = 1.00 (12 / 12) 448 22.22 0.83 10.00 chr1qtel1M 736829 736948 (263052) C MIRc#SINE/MIR (157) 111 2 m_b47s601i39 1692 chr1qtel1M 736829 TTAAGTGACTTGCCTAGGGTCACACAGCTAGGAAGTGTTAAGTGTCTAAA 736878 i i ------- v - i C MIRc#SINE/MIR 111 TTAAGTGACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGC-AGA 70 chr1qtel1M 736879 GTC-AAATTTGAACTCAGGTCCTCTTGACTTCAGGGCTGGTGCTCTATCC 736927 i -ii i i i i i i i v ii v C MIRc#SINE/MIR 69 GCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCC 20 chr1qtel1M 736928 ATTGCGTTGCCTAACTGCCCC 736948 i iiii --- i C MIRc#SINE/MIR 19 ACTGCACCAC---ACTGCCTC 2 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 26.65 CpG sites = 21, Kimura (unadjusted) = 28.04 Transitions / transversions = 7.00 (21/3) Gap_init rate = 0.10 (12 / 119), avg. gap size = 1.00 (12 / 12) 26 19.27 4.48 0.00 chr1qtel1M 738336 738402 (261598) (AAGAGG)n#Simple_repeat 1 70 (0) m_b47s252i14 1693 chr1qtel1M 738336 AAAAGGAAGAGGAGGAGG-AGA--AAGAAGAAAAAGAGGAACAAGACGAG 738382 i i - -- i i i i iv v i (AAGAGG)n#Sim 1 AAGAGGAAGAGGAAGAGGAAGAGGAAGAGGAAGAGGAAGAGGAAGAGGAA 50 chr1qtel1M 738383 GAGGAAGAGGAAGAGGGAGA 738402 i (AAGAGG)n#Sim 51 GAGGAAGAGGAAGAGGAAGA 70 Matrix = Unknown Transitions / transversions = 4.50 (9/2) Gap_init rate = 0.03 (2 / 66), avg. gap size = 1.50 (3 / 2) 23 27.27 0.00 0.00 chr1qtel1M 738339 738398 (261602) (AGG)n#Simple_repeat 1 60 (0) m_b47s252i15 1693 chr1qtel1M 738339 AGGAAGAGGAGGAGGAGAAAGAAGAAAAAGAGGAACAAGACGAGGAGGAA 738388 i i i i ii i iv i v i (AGG)n#Simple 1 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG 50 chr1qtel1M 738389 GAGGAAGAGG 738398 i (AGG)n#Simple 51 GAGGAGGAGG 60 Matrix = Unknown Transitions / transversions = 5.50 (11/2) Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0) 22 17.86 6.17 3.61 chr1qtel1M 738749 738829 (261171) (TGTCTC)n#Simple_repeat 1 83 (0) m_b47s252i16 1694 chr1qtel1M 738749 TGTCTCTGTCTCTGTCTCTGCTTCTCTGAATCTCTCTACATCTCTGCCTC 738798 -- vv v vii i (TGTCTC)n#Sim 1 TGTCTCTGTCTCTGTCTCTG--TCTCTGTCTCTGTCTCTGTCTCTGTCTC 48 chr1qtel1M 738799 ACTCTACT-TCTCT-CCACT-TC-CT-TCTCTTTCT 738829 vv - - -i v - - - v (TGTCTC)n#Sim 49 TGTCT-CTGTCTCTGTCTCTGTCTCTGTCTCTGTCT 83 Matrix = Unknown Transitions / transversions = 0.50 (4/8) Gap_init rate = 0.10 (8 / 80), avg. gap size = 1.00 (8 / 8) 254 37.82 0.00 1.83 chr1qtel1M 739439 739605 (260395) L1ME4c_3end#LINE/L1 410 573 (257) m_b47s551i4 1695 chr1qtel1M 739439 TAACTGGAAAGGAGGGAAAGGGACCCACATATGGAAAAATATTTGTGGCA 739488 i vi i i i --- i i iiivi i i ii v L1ME4c_3end#L 410 TAATTCAAAAGAAGGAAAAAG---CTATATGCACGAAGATGTTCATTGCA 456 chr1qtel1M 739489 GCCCTTTCTGTAGTGGTAACAAACTGGAAACTGAGTGGTTGCCCATCAGC 739538 vi v i i i i ii v i vivv iiv i v ii L1ME4c_3end#L 457 GCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAAT 506 chr1qtel1M 739539 TGGAGAATGGCTGAATAAGTTATGGTATATGAATGTTGTAGAGTATTGTT 739588 v i i i i i i v? ivivi i i i v L1ME4c_3end#L 507 AGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATATTATG 556 chr1qtel1M 739589 GTTCTATAAAAAATGAT 739605 vvv i v L1ME4c_3end#L 557 CAGCCATTAAAAATGAT 573 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 53.32 CpG sites = 42, Kimura (unadjusted) = 57.85 Transitions / transversions = 2.10 (42/20) Gap_init rate = 0.02 (3 / 166), avg. gap size = 1.00 (3 / 3) 361 30.77 0.00 0.00 chr1qtel1M 739465 739568 (260432) L1ME3F_3end#LINE/L1 430 533 (457) m_b47s551i5 1695 chr1qtel1M 739465 ACATATGGAAAAATATTTGTGGCAGCCCTTTCTGTAGTGGTAACAAACTG 739514 i iv i i ii i v v ii i i i v L1ME3F_3end#L 430 ACATGTACAAGAATGTTCATAGCAGCACTGTTCGTAATAGCAAAAAACTG 479 chr1qtel1M 739515 GAAACTGAGTGGTTGCCCATCAGCTGGAGAATGGCTGAATAAGTTATGGT 739564 vivviiiv i ii v v i i i L1ME3F_3end#L 480 GAAACAACCCAAATGTCCATCGACAGGAGAATGGATAAATAAATTGTGGT 529 chr1qtel1M 739565 ATAT 739568 L1ME3F_3end#L 530 ATAT 533 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 38.48 CpG sites = 22, Kimura (unadjusted) = 41.96 Transitions / transversions = 2.20 (22/10) Gap_init rate = 0.00 (0 / 103), avg. gap size = 0.0 (0 / 0) 303 32.83 3.60 1.41 chr1qtel1M 739466 739604 (260396) L1ME3G_3end#LINE/L1 427 568 (356) m_b47s551i6 1695 chr1qtel1M 739466 CATATGGAAAAATATTTGTGGCAGCCCTTTCTGTAGTGGTAACAAACTGG 739515 i iv ii i ii v vi v i i i ii v i L1ME3G_3end#L 427 CATGTACAAGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGG 476 chr1qtel1M 739516 AAACTGAGTGGTTGCCCATCAGCTGGAGAATGGCTGAATAAGTTATGGTA 739565 vivv iiv i iiv i i i i L1ME3G_3end#L 477 AAACAACCTAAATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGTA 526 chr1qtel1M 739566 TATGAATGTTGTAGAGTATT-----GTTGTTCTATAAAAAATGA 739604 vv ii i i i i ----- i? -- v i L1ME3G_3end#L 527 TATCCATACTATGGAATACTATGCAGCNGT--TAAAAAGAATGA 568 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 45.39 CpG sites = 32, Kimura (unadjusted) = 47.06 Transitions / transversions = 2.46 (32/13) Gap_init rate = 0.02 (3 / 138), avg. gap size = 2.33 (7 / 3) 16 23.27 0.00 0.00 chr1qtel1M 739868 739902 (260098) (T)n#Simple_repeat 1 35 (0) m_b47s252i17 1696 chr1qtel1M 739868 TTTGTTTATTTTTCTTTCTTGTGATTTTTTTTTTT 739902 v v i i v vv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 35 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 19 4.50 0.00 0.00 chr1qtel1M 740463 740485 (259515) (T)n#Simple_repeat 1 23 (0) m_b48s252i1 1697 chr1qtel1M 740463 TTTTTTTTTGTTTTTTTTTTTTT 740485 v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTT 23 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 231 24.44 0.00 0.00 chr1qtel1M 741493 741537 (258463) C L2d_3end#LINE/L2 (8) 508 464 m_b48s601i0 1698 chr1qtel1M 741493 TCAATTAATGAGCATTTATTAAGCACCTATTATGTGTTAGCCACT 741537 i ii i i i i i viv C L2d_3end#LINE 508 TCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACT 464 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.24 CpG sites = 9, Kimura (unadjusted) = 31.72 Transitions / transversions = 4.50 (9/2) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 13 19.80 4.88 0.00 chr1qtel1M 743032 743072 (256928) (ATTCAGA)n#Simple_repeat 1 43 (0) m_b48s252i2 1699 chr1qtel1M 743032 ATTCACAAGTCAGTATTCAGCA-TGAG-ATTCACAAGTCAGAA 743072 v v v v - v - v v (ATTCAGA)n#Si 1 ATTCAGAATTCAGAATTCAGAATTCAGAATTCAGAATTCAGAA 43 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 16 0.00 0.00 0.00 chr1qtel1M 744375 744391 (255609) (T)n#Simple_repeat 1 17 (0) m_b48s252i3 1700 chr1qtel1M 744375 TTTTTTTTTTTTTTTTT 744391 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTT 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 257 33.33 7.62 0.00 chr1qtel1M 744438 744542 (255458) C MIRc#SINE/MIR (139) 129 17 m_b48s601i1 1701 chr1qtel1M 744438 AATTGGGATCTTGATAGGTAAAG--ATCTATTCAGGGTTACATAGGTATT 744485 i i iiiiv v v -- ii iii i i i v v C MIRc#SINE/MIR 129 AACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGT 80 chr1qtel1M 744486 AAGTTATATCCCAGGGATTCAAACCTTGGTCTT-ATGATTGCAAGTC--- 744531 vii vvv v i i iv -v i v --- C MIRc#SINE/MIR 79 AAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAG 30 chr1qtel1M 744532 --ATCTTGCCACT 744542 --v v C MIRc#SINE/MIR 29 TGCTCTTTCCACT 17 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.74 CpG sites = 20, Kimura (unadjusted) = 45.51 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.04 (4 / 104), avg. gap size = 2.00 (8 / 4) 292 23.06 12.10 0.57 chr1qtel1M 746387 746543 (253457) L1MEj_5end#LINE/L1 1977 2151 (9) m_b48s551i3 1702 chr1qtel1M 746387 AGAAAAAGAAAAAATAAACAAAAGAAAAAATAGGATTGAGGGAAAGACAG 746436 ? i v i ?i v i i v i vi v v L1MEj_5end#LI 1977 ANAAAAAAACAAAATAAATAAANAATAAAGTAAGATGGAAGGAATAAAAT 2026 chr1qtel1M 746437 TAATTATA-----------ACTGAATATGAATGGGATGAACTCTCCCATA 746475 i v ----------- i i iv i v L1MEj_5end#LI 2027 CAAGTATATCAGTCGTTACACTAAATGTGAATGGACTGAATTCTCCCATT 2076 chr1qtel1M 746476 AAACAGAAGGGGATAG-CAAAATGGATTA-----CAA--TCCAACAATAT 746517 - vi i iv - i v i ----- --i i v L1MEj_5end#LI 2077 AAA-AGACAGAGACTGTCAGATTGGGTTAAAAAACAAAACCCAGCTATAT 2125 chr1qtel1M 746518 GTTGTTTGCAAAAAACACACTTGAAA 746543 i i i i L1MEj_5end#LI 2126 GCTGTTTACAAGAAACACACTTAAAA 2151 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 28.78 CpG sites = 23, Kimura (unadjusted) = 28.78 Transitions / transversions = 1.77 (23/13) Gap_init rate = 0.03 (5 / 156), avg. gap size = 4.00 (20 / 5) 338 23.41 6.25 0.85 chr1qtel1M 746434 746545 (253455) L1M4_5end#LINE/L1 2562 2679 (7) m_b48s551i4 1702 chr1qtel1M 746434 CAGTAATTATAACTGAATATGAATGGGATGAACTCTCCCATAAAACAGAA 746483 i -i i i i iv i ? v v vi v L1M4_5end#LIN 2562 CAGTAATTACA-TTAAATGTAAATGGATTAAACNCTCCAATCAAAAGGCA 2610 chr1qtel1M 746484 GGGGATAGCAAAATGGATT-----ACA--ATCCAACAATATGTTGTTTGC 746526 i iv i i ----- -- v i i i L1M4_5end#LIN 2611 GAGATTGGCAGAATGGATTAAAAAACATGATCCAACTATATGCTGTCTAC 2660 chr1qtel1M 746527 AAAAAACACACTTGAAATT 746545 i i ? v i L1M4_5end#LIN 2661 AAGAGACNCACTTTAGATT 2679 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 29.82 CpG sites = 18, Kimura (unadjusted) = 29.82 Transitions / transversions = 2.25 (18/8) Gap_init rate = 0.03 (3 / 111), avg. gap size = 2.67 (8 / 3) 424 20.59 0.98 0.00 chr1qtel1M 746850 746951 (253049) L1P4_orf2#LINE/L1 817 919 (2375) m_b48s551i5 1702 chr1qtel1M 746850 TTCATTAAAGAGAATGACAATGAAG-CACAATATACCAAAATTTATGGGA 746898 v i iv? v iii - i i v L1P4_orf2#LIN 817 TTCTTTGAAATNAATGAAAACAGAGACACAACATACCAAAATCTCTGGGA 866 chr1qtel1M 746899 TGCAGCCAAAGCAGTATTTAGGGGAAATTTTATATCTCTATATGCTTAGA 746948 ? i v i v v v v i i v L1P4_orf2#LIN 867 TGCAGCNAAAGCAGTGTTAAGAGGAAAGTTTATAGCGCTAAACGCCTACA 916 chr1qtel1M 746949 TCA 746951 L1P4_orf2#LIN 917 TCA 919 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 23.56 CpG sites = 11, Kimura (unadjusted) = 24.86 Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.01 (1 / 101), avg. gap size = 1.00 (1 / 1) 450 16.85 1.12 0.00 chr1qtel1M 746861 746949 (253051) L1M4_orf2#LINE/L1 828 917 (2377) m_b48s551i6 1702 chr1qtel1M 746861 GAATGACAATGAAG-CACAATATACCAAAATTTATGGGATGCAGCCAAAG 746909 v i i- i i ? L1M4_orf2#LIN 828 GAATGAAAACGAAAACACAACATACCAAAACTTATGGGATGCAGCNAAAG 877 chr1qtel1M 746910 CAGTATTTAGGGGAAATTTTATATCTCTATATGCTTAGAT 746949 ii i i v v v v i v L1M4_orf2#LIN 878 CAGTGCTTAGAGGGAAATTTATAGCTGTAAATGCCTATAT 917 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 18.20 CpG sites = 9, Kimura (unadjusted) = 19.59 Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.01 (1 / 88), avg. gap size = 1.00 (1 / 1) 504 26.47 5.15 0.00 chr1qtel1M 747532 747667 (252333) MIRc#SINE/MIR 3 145 (123) m_b48s601i2 1703 chr1qtel1M 747532 AAGCAAAATGTTTCAGGGGATAATGC--CAGGCCTGAAGTCAGGAAGAAC 747579 i ivi v v v v iv --ii i i i v MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chr1qtel1M 747580 TGAATTCAAATTA-GGCTACAGAA---ACTAGCTATGTGACCCTGGACAA 747625 ii i i iv- viivv --- i i i MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 102 chr1qtel1M 747626 GTCACTTAGCC-CTGTTTACCTCAGTTTCCTCTTCTGTAAAAT 747667 i - v vvi v MIRc#SINE/MIR 103 GTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAAT 145 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.26 CpG sites = 21, Kimura (unadjusted) = 33.39 Transitions / transversions = 1.40 (21/15) Gap_init rate = 0.03 (4 / 135), avg. gap size = 1.75 (7 / 4) 247 23.73 13.11 3.29 chr1qtel1M 752858 753162 (246838) L1MC4_5end#LINE/L1 2204 2537 (18) m_b48s551i7 1704 chr1qtel1M 752858 AATCATAACTATGAATGTGAATGGGATGAACTCTCCCAT--AAAACAAAA 752905 i ? ? v i i v ? v ? -- iv? L1MC4_5end#LI 2204 AGTNATANCAATAAATGTAAATGGGCTNAACTCACCNATTAAAAGANAAA 2253 chr1qtel1M 752906 G----------TGAATCAA----CAGAATCTTACAATATGTTGTTTACAA 752941 ---------- i? ? ?---- ii i iv v i ? L1MC4_5end#LI 2254 GATTTTCAANTTGGNTNANAAAGCAAGACCCAACTATATGCTGTNTACAA 2303 chr1qtel1M 752942 GAAACATATA-AAAAAAAGACATACAAAA----TAATGGTAAAAGGTTGG 752986 i i iv- vv v i ---- i vii i v L1MC4_5end#LI 2304 GAGACACACCTAAAAAAAGTGATTCAGAAAGGCTGAAAATAAAGGGATGG 2353 chr1qtel1M 752987 AATGGAATATATGATGCTCAGCTAAAGCAAACAAAGCAGGGTAGCAATTC 753036 ?viii iv v -v iivi i - v v ?i L1MC4_5end#LI 2354 ANAAAGATATACCAGGC-AAATGGAAACAAA-AAAGAAGGGTTGCAATNT 2401 chr1qtel1M 753037 TGATCT----CAAAGCA------AAAGCAAAAATACATCTACTTAAAAGA 753076 ? v ---- i ------ i? -i ----- ? L1MC4_5end#LI 2402 TNATATCAGACAAAGTAGANTTCAAGNCAAAAA-GCA-----TTAAANGA 2445 chr1qtel1M 753077 GATAGGAAAGGAAGCTATCT-----TGTTAAAAAGTACCATAGACAAT-- 753119 i--- i i ?i i ----- ? ii??? v vv -- L1MC4_5end#LI 2446 GAC---AAAGAAGGNCATTTTATAATGNTAAAGGNNNCAATTCACAATGA 2492 chr1qtel1M 753120 --ATATGTCAATATTAAATACATATGCACTAAGGGATACAGCATC 753162 -- iv vv i? i ivi i ? ? L1MC4_5end#LI 2493 AGATATAACAATTATAAATATNTATGCACCAAATAACANAGCANC 2537 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 32.38 CpG sites = 43, Kimura (unadjusted) = 32.38 Transitions / transversions = 1.59 (43/27) Gap_init rate = 0.07 (21 / 304), avg. gap size = 2.43 (51 / 21) 247 26.39 8.33 0.00 chr1qtel1M 752903 753046 (246954) L1MC_orf2#LINE/L1 84 239 (3055) m_b48s551i8 1704 chr1qtel1M 752903 AAAGTGAATCAA----CAGAATCTTACAATATGTTGTTTACAAGAAACAT 752948 i i ---- ii i iv v i vi L1MC_orf2#LIN 84 AGAGTGGATCAAAAAACAAGACCCAACTATATGTTGTCTACAAGAAACCC 133 chr1qtel1M 752949 A---TAAA---AAAAAGACATACAAAATAATGGTAAAAGGTTGGAATGGA 752992 --- --- i v i i v vi ? v iviii L1MC_orf2#LIN 134 ACTTTAAATATAAAGACACATATAGATTAAAAGTAAANGGATGGAGAAAG 183 chr1qtel1M 752993 ATATATGATGCTCA-GCTAAAGCAAACAAAGCAGG-GTAGCAATTCTGAT 753040 iv v -i vvv v ? - v vi i L1MC_orf2#LIN 184 ATATACCATGCTAACACTAATCAAAAGAAAGCNGGAGTAGCTATATTAAT 233 chr1qtel1M 753041 CTCAAA 753046 i i L1MC_orf2#LIN 234 TTCAGA 239 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 33.84 CpG sites = 22, Kimura (unadjusted) = 33.84 Transitions / transversions = 1.38 (22/16) Gap_init rate = 0.03 (5 / 143), avg. gap size = 2.40 (12 / 5) 242 31.11 5.88 3.10 chr1qtel1M 753370 753777 (246223) L1MC_orf2#LINE/L1 568 986 (2308) m_b48s551i10 1704 chr1qtel1M 753370 GAATATATCTTTTTCTCAGCAGTACATCGATACCTACATAAAAACTGACC 753419 i iv i ivvvi v - v v iv i iv L1MC_orf2#LIN 568 GAATACACATTCTTCTCAAGCTCACATGGA-ACATTCACCAAGATAGACC 616 chr1qtel1M 753420 ATTTACTAGAGCATAAAA-ACTTCACATCAAATGCAGAAAGGCAGAAATA 753468 iv v i iv - vi vi v vi i iiii v L1MC_orf2#LIN 617 ACATTCTGGGCCATAAAACACACCTTAACAAATTTAAAAGAATAGAAATC 666 chr1qtel1M 753469 GTA-AATGCATCCCTTTCAGATCAAGACACAACAAAAATTAAACTCAATA 753517 i - ? i? v - i i vi iiv iv v vi v L1MC_orf2#LIN 667 ATACAANGTNTGC-TCTCAGACCACAATGGAATTAAACTAGAAATCAATA 715 chr1qtel1M 753518 AAGGGTCAAGGAAAGATAGATGA------CCAA-----TTAGAAATTAAA 753556 ----- -- v i------ ----- i i L1MC_orf2#LIN 716 A-----CA--GAAAGATAGCTGGAAAATCCCAAAATACTTGGAGATTAAA 758 chr1qtel1M 753557 TAATCTAACCCTAAAGAATAAATGGGTTAAACAATAAATCATAAAAACAA 753606 i ivi vii v i v i v v vi i iv L1MC_orf2#LIN 759 CAACACACTTCTAAATAACACATGGGTCAAAGAAGAAATCTCAAGAGAAA 808 chr1qtel1M 753607 T-----AATTTATCCAAGAGAATGACAATAATGAGACAATATACCAAAAC 753651 ----- v v iv vvi v i vi v iv i i L1MC_orf2#LIN 809 TTTAAAAATATTTTGAACTAAATGAAAATGAAAATACAACTTATCAAAAT 858 chr1qtel1M 753652 CTATGGGATGCAGCCAAAGCAGTTCTT--AGGAAAATTTTTCTATTTTTA 753699 i i v v -- i -- v viv i L1MC_orf2#LIN 859 TTGTGGGATGCAGCGAAAGCAGTGCTTAGAGGGAAA--TTTATAGCATTG 906 chr1qtel1M 753700 ACTACTTATAT--GAATAAAATAAAGA--GGAGATCAATGAATTGGGCAT 753745 v i v -- v i v --vi i i vi ii v L1MC_orf2#LIN 907 AATGCATATATTAGAAAAGAAGAAAGATCTAAAATCAATAATCTAAGCTT 956 chr1qtel1M 753746 ACAAACTAAAAAAGCTAGGAAAAAAAATAGCA 753777 v vvi ii - - i v L1MC_orf2#LIN 957 CCACCTTAGGAAA-CTA-GAAAAAGAAGAGCA 986 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.28 CpG sites = 65, Kimura (unadjusted) = 41.28 Transitions / transversions = 1.12 (65/58) Gap_init rate = 0.05 (21 / 407), avg. gap size = 1.76 (37 / 21) 316 33.22 4.39 0.91 chr1qtel1M 753370 753688 (246312) L1P3_orf2#LINE/L1 568 897 (2397) m_b48s551i9 1704 chr1qtel1M 753370 GAATATATCTTTTTCTCAGCAGTACATCGATACCTACATAAAAACTGACC 753419 iv i ivi -i i iviv i L1P3_orf2#LIN 568 GAATATACATTCTTCTCAGCGCCACATCG-CACTTATTCTAAAATTGACC 616 chr1qtel1M 753420 ATTTACTAGAGCATAAAA-ACTTCACATCAAATGCAGAAAGGCAGAAATA 753468 iv v v iivi - i v v i iii i v L1P3_orf2#LIN 617 ACATAATTGGAAGTAAAACACTCCTCAGCAAATGCAAAAGAACGGAAATC 666 chr1qtel1M 753469 GTAA-ATGCATCCCTTTCAGATCAAGACACAACAAAAATTAAACTCA--A 753515 i - vi vi - i i viiii iv v vi -- L1P3_orf2#LIN 667 ATAACAAACAGTC-TCTCAGACCACAGTGCAATCAAATTAGAACTCAGGA 715 chr1qtel1M 753516 TAAAGGG--TCAAGGAAAGATAGATGACCAATTAGAAATTAAATAATCTA 753563 v ii-- vvv iviiv ii i vv i i i i i i L1P3_orf2#LIN 716 TTAAGAAACTCACTCAAAACCGCACAACTACATGGAAACTGAACAACCTG 765 chr1qtel1M 753564 ACCCTAAAGAATAAATGGGTTAAACAAT-AAATCA---TAAAAACAA-TA 753608 vi i vi iv v - i i- i ---i i i -? L1P3_orf2#LIN 766 CTCCTGAATGACTACTGGGT-AAATAACGAAATTAAGGCAGAAATAAANA 814 chr1qtel1M 753609 ATTTATCCAAGAG-AATGACAATAATGAGACAATATACCAAAACCTATGG 753657 v v iii i v- v i v v ii i i v L1P3_orf2#LIN 815 AGTTCTTTGAAACCAATGAGAACAAAGACACAACGTACCAGAATCTCTGG 864 chr1qtel1M 753658 GATGCAGCCAAAGCAGTTCTT--AGGAAAATTT 753688 ii i vi -- i L1P3_orf2#LIN 865 GACACAGCTAAAGCAGTGTTTAGAGGGAAATTT 897 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 43.33 CpG sites = 68, Kimura (unadjusted) = 46.53 Transitions / transversions = 1.84 (68/37) Gap_init rate = 0.04 (12 / 318), avg. gap size = 1.42 (17 / 12) 405 26.62 4.72 1.67 chr1qtel1M 753545 753777 (246223) L1M5_orf2#LINE/L1 747 986 (2308) m_b48s551i11 1704 chr1qtel1M 753545 TTAGAAATTAAATAATCTAACCCTAAAGAATAAATGGGTTAAACAATAAA 753594 i i ivi vii v ivv i v v L1M5_orf2#LIN 747 TTGGAAATTAAACAACACACTTCTAAATAACCCATGGGTCAAAGAAGAAA 796 chr1qtel1M 753595 TCATAAAAACAAT-----AATTTATCCAAGAGAATGACAATAATGAGACA 753639 i ?iiv ----- v v iv vv ? i vi v L1M5_orf2#LIN 797 TCACAANGGAAATTAGAAAATATTTTGAACTGAATGANAATGAAAATACA 846 chr1qtel1M 753640 ATATACCAAAACCTATGGGATGCAGCCAAAGCAGTTCTT--AGGAAAATT 753687 i i ii i i v -- i -- L1M5_orf2#LIN 847 ACATATCAAAATTTGTGGGATGCAGCTAAAGCAGTGCTTAGAGGGAAA-- 894 chr1qtel1M 753688 TTTCTATTTTTAACTACTTATATGAATAAAATAAAGAGG----AGATCAA 753733 v vi? v i ? v iv iv i i ---- i L1M5_orf2#LIN 895 TTTATAGCNTTAAATGCNTATATTAGAAAAGAAGAAAGGCTTAAAATCAA 944 chr1qtel1M 753734 TGAATTGGGCATACAAACTAAAAAAGCTAGGAAAAAAAATAGCA 753777 vi ii - v v v v i - i v L1M5_orf2#LIN 945 TGATCTAAGC-TTCCACCTTAAGAAGCTA-GAAAAAGAAGAGCA 986 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.20 CpG sites = 33, Kimura (unadjusted) = 34.20 Transitions / transversions = 1.18 (33/28) Gap_init rate = 0.03 (7 / 232), avg. gap size = 2.14 (15 / 7) 713 26.07 7.76 0.81 chr1qtel1M 755294 755525 (244475) MIRc#SINE/MIR 3 250 (18) m_b48s601i3 1705 chr1qtel1M 755294 AGGCAAAGTGATGTAGTGCATAGAACACTAGACCTGGAGGGAGGAAGACT 755343 iv i i v v i i i vv i MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chr1qtel1M 755344 AAAGTTTGAATCCAATCTCAGAAA---ACAAAAAA-ATGAACTTAGGCTA 755389 vii i i viv v vv --- v ivvi-i v i v MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 102 chr1qtel1M 755390 ATCACTTAAACTCTTTCTGCCTCAATTTCCTCACCTGAAAAATCGGGATA 755439 i v i vv i i v v MIRc#SINE/MIR 103 GTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATA 152 chr1qtel1M 755440 ATAACA---GA---GCCTACTTCTCAGTGTTTTTGTGAGGA-CAAAT--- 755479 i --- v--- i v v v - --- MIRc#SINE/MIR 153 ATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAG 202 chr1qtel1M 755480 ---ATATTTGT-AAAGTACCTGGGAAACCATAAAAAATGCCAAATAAATG 755525 --- i v - ii i v v ii -- i i v i MIRc#SINE/MIR 203 ATAATGTATGTGAAAGCGCTTTGTAAACTGT--AAAGTGCTATACAAATG 250 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.47 CpG sites = 31, Kimura (unadjusted) = 32.44 Transitions / transversions = 1.07 (31/29) Gap_init rate = 0.04 (10 / 231), avg. gap size = 2.00 (20 / 10) 514 33.78 9.00 4.92 chr1qtel1M 756379 756789 (243211) L3#LINE/CR1 1641 2067 (2032) m_b48s601i4 1706 chr1qtel1M 756379 CAAGCCTGACATAGAG-CATGATACAGGCAATGAAAAAAAAAACTTTAAT 756427 iv i i - v ? -i i viiiii -- i i L3#LINE/CR1 1641 CAAAACTGGCACAGAGGCAAGATNCAG-TAGTGATGGGGGA--CTTCAAC 1687 chr1qtel1M 756428 TATCTAGACATCTGCTGGTATTTTCTCCCTACCCCAAACAGAATACAGCT 756477 ii v v i vii ?i ivv i --i v L3#LINE/CR1 1688 TATCCGGACATCTGCTGGAAGTCTCATTCNGCTAAAAGCAGA--GCATCT 1735 chr1qtel1M 756478 AATGATTTCCTGAC-TACTT---TAAAAATTCCATCTTTCAAAATGTGGC 756523 i i v i - i i --- i v i i i v i v L3#LINE/CR1 1736 GATAAATTCTTGACTTGCCTTGCTGACAATTTCATCTCTCAGAAGGTAGA 1785 chr1qtel1M 756524 TATACCAACAA----AAC-----------------TTCTGACCAAGAAAG 756552 viv v i ---- ----------------- v i L3#LINE/CR1 1786 GGAAGCAACGAGGGGAACTGCTACTCTGGACTTAATTCTGACCAACAAGG 1835 chr1qtel1M 756553 CAGAACTGGCTGCTGGGATAGAAAT-GATGAGAATTTTGGGAAGAAAAGA 756601 v i v iii i i - ii ii - ivi L3#LINE/CR1 1836 AAGAACTGGTTGGTGAAGTGGAAGTCGATAGGAACCTTGGG-AGAAAGTG 1884 chr1qtel1M 756602 ATAAATACTCTACCTTGCAAATTGTAA----CAGAAAAGGCTACTTCTAC 756647 vi vi ----i i iv iv i ---- ii vv vv iv v L3#LINE/CR1 1885 CCATGT----CATCTTAGAGTTCGTAATAGCCAAGAAAGGAAAAGTTAAA 1930 chr1qtel1M 756648 CTTTCA-AGA-ACCATAGACTTCAGGAG----AGCAGATTTTAAGGGATT 756691 vv i - v -iiivi i v ---- i iii L3#LINE/CR1 1931 AGTCCACATATGTTCCAGACTTTACGAGGAAAAGCAGATTTCAAAAAATT 1980 chr1qtel1M 756692 CAGAAAAAAAAAAAAAAAAAAGGATTACATGAGCCAAAATTCTCCAAGAT 756741 ------ i i iiv v v iv ?i i -- v i v L3#LINE/CR1 1981 CAG------AGAAAAGAGGTATGATTCCATGGCCNGAGA--CTCAAAAAG 2022 chr1qtel1M 756742 GAAGTTACCAATCCATTAAAGTTAAAAAGCTTTCAAGGATGACATTCT 756789 i v iv ---i vv ii ? iii i i ii v L3#LINE/CR1 2023 AAAGATGGC---TCAAGAGGGNTGGGAAGCTCTTAAAAATGAAATTCT 2067 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 46.76 CpG sites = 86, Kimura (unadjusted) = 48.40 Transitions / transversions = 1.87 (86/46) Gap_init rate = 0.08 (31 / 410), avg. gap size = 1.87 (58 / 31) 355 29.22 5.30 1.46 chr1qtel1M 756804 756935 (243065) MIR1_Amn#SINE/MIR 13 149 (81) m_b48s601i5 1707 chr1qtel1M 756804 GTGGTCTAGTA-ACGG----CTGGATGTGGTAAAAAAAAAGATGTGGAGT 756848 i- ii ---- i- -i vvviii iv iv MIR1_Amn#SINE 13 GTGGTCTAGTGGATAGAGCACTGGAC-TGG-GACTCGGGAGACCTGGGTT 60 chr1qtel1M 756849 CAAATCCAGCTTCAAACATTTCCTAGCAATGTGAATCTGGGCAAGTCATT 756898 ? ? v vi viv i ?v i? vi? vii i MIR1_Amn#SINE 61 CNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGTCACT 110 chr1qtel1M 756899 TAGC--TTCTGTGCTTTAGTTTCCCCACTTGTAACATGG 756935 ?i --i ? i i i ii v MIR1_Amn#SINE 111 TNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGG 149 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.35 CpG sites = 25, Kimura (unadjusted) = 41.83 Transitions / transversions = 1.92 (25/13) Gap_init rate = 0.04 (5 / 131), avg. gap size = 1.80 (9 / 5) 449 32.60 2.88 0.70 chr1qtel1M 756819 756957 (243043) MIRc#SINE/MIR 30 171 (97) m_b48s601i6 1707 chr1qtel1M 756819 CTGGATGTGGTAAAAAAAAAGATGTGGAGTCAAATCCAGCTTCAAACATT 756868 iv - ivv ii iv iv i i v vi viv i MIRc#SINE/MIR 30 CTGGACTTGG-AGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACT 78 chr1qtel1M 756869 TCCTAGCAATGTGAATCTGGGCAAGTCATTTAGCTTCTGT--GCTTTAGT 756916 v vi vii i i i v -- i i MIRc#SINE/MIR 79 TACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGT 128 chr1qtel1M 756917 TTCCCCACTTGTAACATGGATACAGC--TACTTGTCCCACCTA 756957 i ii v iv i ii-- i i ii MIRc#SINE/MIR 129 TTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTA 171 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.93 CpG sites = 30, Kimura (unadjusted) = 45.33 Transitions / transversions = 2.00 (30/15) Gap_init rate = 0.02 (3 / 138), avg. gap size = 1.67 (5 / 3) 298 30.71 11.00 2.30 chr1qtel1M 757323 757522 (242478) L3#LINE/CR1 2532 2748 (1351) m_b48s601i7 1706 chr1qtel1M 757323 TAAGAGAGCCCCCGGCTGCCTC-GATGAGTGC------TCAGGTGCAGG- 757364 v ii i i i-i v ------i iv i- L3#LINE/CR1 2532 TAAGAGAGCACCTAGCCGCTTTAAATGAGTTCAAGTCTCCAGGCCCAGAC 2581 chr1qtel1M 757365 -----ATATCCTTAAGGACAGAAAGGGCCGGCAGGGGTCATTCCTGAGCC 757409 ----- i ivii v v ii iv iv v iv v i L3#LINE/CR1 2582 GAATTACATCCCAGGGTACTGAAAGAACTTGCAGATGTGATCGCGGAACC 2631 chr1qtel1M 757410 ACTGCCAGTGACCTCTGAG--ATCAGGGTGAAGGGGAGAGACGTC----- 757452 i i i i i i -- v v v i ii i ----- L3#LINE/CR1 2632 GCTGTCGGTAATCTTTGAGAAATCACGGAGAACGGAAGAGGTGCCAGAAG 2681 chr1qtel1M 757453 ACTTG-GTCGCATGAATGTTGTCCC-AATCTAAGGAACAAAAAAGGAAGC 757500 v - v viii ? ? - ? i v ii vii -- - L3#LINE/CR1 2682 ACTGGAGACGGGCAAATGTNGTNCCTANTTTTAAAAAGGGAAAA--AAG- 2728 chr1qtel1M 757501 GAATGGATGCTGCAGACTTTAG 757522 -- v ? i vi L3#LINE/CR1 2729 --ATGGATTCTGNAAACTACAG 2748 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.96 CpG sites = 39, Kimura (unadjusted) = 42.73 Transitions / transversions = 1.86 (39/21) Gap_init rate = 0.07 (13 / 199), avg. gap size = 2.08 (27 / 13) 224 29.70 2.94 0.96 chr1qtel1M 757550 757651 (242349) C L3#LINE/CR1 (493) 3606 3503 m_b48s601i8 1708 chr1qtel1M 757550 AACAGAAC-CACACAC-CCTGCTGTGATCTGGTCAGGGCTGGATACAAGG 757597 v - - i - v v i ii v v ii iv C L3#LINE/CR1 3606 AACTGAACGCA-ATACTCCAGATGTGGTCTGACCAGCGCAGAGTACAGCG 3558 chr1qtel1M 757598 AGACTCTCACCTCCCCT-TTCTCAGCTCTGTGCTTCCCTAAATGCTGACT 757646 i v i i -? vii v i i iv v v v C L3#LINE/CR1 3557 GGACTATTACCTCCCTTGNTCTGGACACTATACTTCTATTAATGCAGCCT 3508 chr1qtel1M 757647 GTGAT 757651 iv C L3#LINE/CR1 3507 AAGAT 3503 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.02 CpG sites = 16, Kimura (unadjusted) = 39.02 Transitions / transversions = 1.14 (16/14) Gap_init rate = 0.04 (4 / 101), avg. gap size = 1.00 (4 / 4) 200 27.69 1.54 0.00 chr1qtel1M 757639 757703 (242297) C L3b_3end#LINE/CR1 (633) 573 508 m_b48s601i9 1709 chr1qtel1M 757639 TGCTGACT-GTGATGAGCTTGCGGTCCACTCAAAGCCCTGAATCATTTCC 757687 -i iv v v v iiii v i C L3b_3end#LINE 573 TGCTGACTCATATTGAGCTTGCGGTCAACTAAAACCCCCAGGTCTTTTTC 524 chr1qtel1M 757688 CAATTATCTTCTGATA 757703 vv v?v v v C L3b_3end#LINE 523 ACATGNGCTGCTGCTA 508 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.30 CpG sites = 7, Kimura (unadjusted) = 35.30 Transitions / transversions = 0.64 (7/11) Gap_init rate = 0.02 (1 / 64), avg. gap size = 1.00 (1 / 1) 225 30.96 18.53 3.99 chr1qtel1M 757729 758014 (241986) L3#LINE/CR1 3598 3923 (176) m_b48s601i10 1706 chr1qtel1M 757729 CGTTCACTTCTGGGCACCTCA----------------GCCAA---GAAGC 757759 v i v ---------------- v --- i L3#LINE/CR1 3598 CGTTCAGTTCTGGGCGCCACATTTTAAGAGGGACATTGACAAACTGGAGC 3647 chr1qtel1M 757760 AC--CCAGAGCTGGGAAACCAGGATGTTGGGGGGCCCCGGGGGCTTAAGT 757807 i -- vv i vi v ii i i- iii ------ L3#LINE/CR1 3648 GCGTCCAGAGGAGAGCGACCAGGATGGTGAAGGGTCT-GGAAAC------ 3690 chr1qtel1M 757808 TCCTGCCATCACACAACTCGACAAAGGAAGTGGGGGTGTTTAGT---GAG 757854 - v i vvv vi viv vii v i i--- L3#LINE/CR1 3691 -CATGTCATATGAGGAACGGTTGAAGGAACTGGGGATGTTTAGCCTGGAG 3739 chr1qtel1M 757855 AAGAGAAGATCTGGGGCCGG--TGACAAC-ATC-------------AGG- 757887 ii i i vv i-- i i -i ------------- - L3#LINE/CR1 3740 AAGAGAAGACTTAGAGGAGACATGATAGCTGTCTTCAAATATTTGAAGGG 3789 chr1qtel1M 757888 ---TCATC---AAGAAAGCTTAACTGCCCTGTTCTGTTTGGCCCCAGAGG 757931 --- v--- ii v --- v i i v i L3#LINE/CR1 3790 CTGTCATGTGGAAGAGGGATTA---GACTTATTCTGTGTGGCTCCAGAGG 3836 chr1qtel1M 757932 GTGTAAGGAGGAGCAATGGGT---ATTTAAGAAAAGAGGTAAACCGAGGC 757978 iiv vv v --- v --v ii i i iivv L3#LINE/CR1 3837 GCAGAACTAGGACCAATGGGTGGAAGTTA--CAGGGAGGCAGATTTCGGC 3884 chr1qtel1M 757979 TTGATGTTACAGAAAACT---TAATGATCTCAACCATCC 758014 ii i v vii i --- ii vv i ii L3#LINE/CR1 3885 TCAATATAAGGAAGAACTTTCTAACAATCAGAGCTGTCC 3923 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.08 CpG sites = 51, Kimura (unadjusted) = 41.64 Transitions / transversions = 1.50 (51/34) Gap_init rate = 0.09 (25 / 285), avg. gap size = 2.64 (66 / 25) 273 29.78 4.17 2.04 chr1qtel1M 759276 759371 (240629) C L2c_3end#LINE/L2 (11) 467 370 m_b48s601i11 1710 chr1qtel1M 759276 CAACAGATATTTAT-AAGTGTTTCCTATGTACCAGACACTGTTAAATCCA 759324 i i -i i ii v i i i v-ii v C L2c_3end#LINE 467 CAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGG-GGATACA 419 chr1qtel1M 759325 AACAAGAACTGAAA---AGTCACTCCCTTCAAGGAATCCACCCTCTAATG 759371 v v - i i ---i v v i iii vv i C L2c_3end#LINE 418 AAGATGAA-TAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAGTG 370 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.53 CpG sites = 19, Kimura (unadjusted) = 39.97 Transitions / transversions = 2.11 (19/9) Gap_init rate = 0.04 (4 / 95), avg. gap size = 1.50 (6 / 4) 15 7.50 3.33 3.33 chr1qtel1M 759852 759881 (240119) (CTT)n#Simple_repeat 1 30 (0) m_b48s252i4 1711 chr1qtel1M 759852 CTTTTTCCTTCTTCTTCTT-TTCATCTTCTT 759881 i - - v (CTT)n#Simple 1 CTTCTT-CTTCTTCTTCTTCTTCTTCTTCTT 30 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.07 (2 / 29), avg. gap size = 1.00 (2 / 2) 238 34.25 3.80 1.60 chr1qtel1M 760394 760577 (239423) L2#LINE/L2 2391 2578 (504) m_b48s601i12 1712 chr1qtel1M 760394 TTCAAGTAC--ACATGGCAGCTTCAATGGGATGACCCACAGATTTCTTAA 760441 i v i -- vi i v i v v v iv i iiv i L2#LINE/L2 2391 TCCAACTGCCTACTCGACATCTCCACTTGGATGTCTAATAGGCATCTCAA 2440 chr1qtel1M 760442 AACTCCTCGGTCCAAAGCTGGACTCACT--CCCTCTGTCCCAAACCCTCC 760489 vi vvivv i i - --i i ivi i iv i L2#LINE/L2 2441 ACTTAACATGTCCAAAACTGAACTC-CTGATCTTCCCCCTCAAACCTGCT 2489 chr1qtel1M 760490 TCTCCTCCTCCCTTCCCC--CACAATGCTGAGGGCACCGCCATCCTCCTG 760537 i iv vvi -- v i ?--i v v v i ii L2#LINE/L2 2490 CCTCCCGCAGTCTTCCCCATCTCAGTN--AATGGCAACTCCATCCTTCCA 2537 chr1qtel1M 760538 GTCCCTTGGGCTTGAA-TCTTGGTGTCATCCTCCACTCCTC 760577 iv ii ivi -i v iv L2#LINE/L2 2538 GTTGCTCAGGCCAAAAACCTTGGAGTCATCCTTGACTCCTC 2578 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.69 CpG sites = 36, Kimura (unadjusted) = 47.84 Transitions / transversions = 1.38 (36/26) Gap_init rate = 0.04 (7 / 183), avg. gap size = 1.43 (10 / 7) 772 25.64 6.03 2.50 chr1qtel1M 761272 761503 (238497) MIRb#SINE/MIR 13 252 (16) m_b48s601i13 1713 chr1qtel1M 761272 GTGGTTCAGTGCAGAGAGCCTTAG-TCTGGGATCATGACAAA-----GTT 761315 v v i vivi - i ii - i ----- MIRb#SINE/MIR 13 GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCA-GACAGACCTGGGTT 61 chr1qtel1M 761316 CAAATCCAGCCTTAGACACATACCAGCTATAGGACCCTGAGTCAAGCTAT 761365 i v v iv v v i i iv i i - i i MIRb#SINE/MIR 62 CGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGG-CAAGTTAC 110 chr1qtel1M 761366 TTGACCTTT----GCCTCAGTTTTCTTAATTGTGAAAAAGGGGCAATAAT 761411 i i ---- i i vi - v -- MIRb#SINE/MIR 111 TTAACCTCTCTGAGCCTCAGTTTCCTCATCTGT-AAAATGGGG--ATAAT 157 chr1qtel1M 761412 AGCACCACTCTCCTAGGGTTGTTG-GAACATCAAATGAGATATT---TAT 761457 ii vvi vi - iv i v --- i MIRb#SINE/MIR 158 AATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCATGT 207 chr1qtel1M 761458 AAACTACTTAGTACAGTGTTTGGCGCAGAGTAGATGTGCCAATAAA 761503 vii i ii i v iii i-i MIRb#SINE/MIR 208 AAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGC-TCAATAAA 252 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.85 CpG sites = 39, Kimura (unadjusted) = 32.64 Transitions / transversions = 2.05 (39/19) Gap_init rate = 0.05 (11 / 231), avg. gap size = 1.82 (20 / 11) 436 35.13 7.55 1.70 chr1qtel1M 761728 762005 (237995) L2b_3end#LINE/L2 160 453 (13) m_b48s601i14 1712 chr1qtel1M 761728 GCTCCTTCTCATTTCGGTCTCCTGGC----TTCT-CTCAT-------GTC 761765 i i i i ii v- v ---- i - ------- L2b_3end#LINE 160 GCCCTTCCCCACCTCT-TCGCCTGGCCAACTCCTACTCATCCTTCAGGTC 208 chr1qtel1M 761766 CCAGCTAAAATCCCACCTTCTCCAGGAAGTCTTTCTTAAACTCCCTGAAT 761815 i v vi i i i i i i i v i v ivi L2b_3end#LINE 209 TCAGCTCAAATGTCACCTCCTCCGGGAAGCCCTCCCTGACCCCCCAGGCC 258 chr1qtel1M 761816 A--TTAG-TGCCTTATCTCTCAATTATTTCCGATCCAGCCCGAATAAGAT 761862 i-- i -i i -i viiii-iii ii vi vivi v-- L2b_3end#LINE 259 GGGTCAGGCGCCCT-CCTCTGGGCC-CCCCCAGTCCTACCCTGCCAC--T 304 chr1qtel1M 761863 CTATTTGCACATGATTTATTTCCTTGTG-ATCTCCCC-ATTAGACTGTGA 761910 ivv vvv? vi i i? v v v-i - i L2b_3end#LINE 305 CTGGGTTATNATTGTCTGNTTACATGTCTGTCTCCCCCACTAGACTGTGA 354 chr1qtel1M 761911 GGTCTTTGAAGGCTGGGATCTTCTTTTTCCTCTTTCTCAAGG----CTCA 761956 v iv i v i v?v i v i v ivi ivv ---- i L2b_3end#LINE 355 GCTCCGTGAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTGTATCCCCA 404 chr1qtel1M 761957 GTGCTTAGAACAGTGCCTGCCACATAGTAGGAACTTTACATCTATTTAT 762005 i i v ? v i vi ivii vv i L2b_3end#LINE 405 GCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTTGT 453 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.65 CpG sites = 59, Kimura (unadjusted) = 50.97 Transitions / transversions = 1.59 (59/37) Gap_init rate = 0.05 (13 / 277), avg. gap size = 2.00 (26 / 13) 19 21.38 7.46 1.41 chr1qtel1M 762006 762072 (237928) (AT)n#Simple_repeat 1 71 (0) m_b48s252i5 1714 chr1qtel1M 762006 ATATAT-TGTGTTTATACGATATATAT-TATGTA-ACATCTGT-TATAAA 762051 - i i v -v - i - i v i - v (AT)n#Simple_ 1 ATATATATATATATATA-TATATATATATATATATATATATATATATATA 49 chr1qtel1M 762052 CATATTTATATATA-ACATATA 762072 i v - i (AT)n#Simple_ 50 TATATATATATATATATATATA 71 Matrix = Unknown Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.09 (6 / 66), avg. gap size = 1.00 (6 / 6) 16 0.00 0.00 0.00 chr1qtel1M 762388 762404 (237596) (T)n#Simple_repeat 1 17 (0) m_b48s252i6 1715 chr1qtel1M 762388 TTTTTTTTTTTTTTTTT 762404 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTT 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 11 24.11 6.67 1.59 chr1qtel1M 763082 763141 (236859) (GGCGGG)n#Simple_repeat 1 63 (0) m_b48s252i7 1716 chr1qtel1M 763082 GGCAGGGACCCGGCCGGGGGAAGGGGGAGCTGG-AGGAG-GGGGGC-GGG 763128 i i vv v -v v vv -i i - - (GGCGGG)n#Sim 1 GGCGGGGGCGGGGGCGGGGG-CGGGGGCGGGGGCGGGGGCGGGGGCGGGG 49 chr1qtel1M 763129 GC-GGGGCGGCGGC 763141 - v (GGCGGG)n#Sim 50 GCGGGGGCGGGGGC 63 Matrix = Unknown Transitions / transversions = 0.50 (4/8) Gap_init rate = 0.08 (5 / 59), avg. gap size = 1.00 (5 / 5) 16 19.74 2.08 2.08 chr1qtel1M 763093 763140 (236860) (GGGCGGG)n#Simple_repeat 1 48 (0) m_b48s252i8 1716 chr1qtel1M 763093 GGCCGGGGGAAGGGGGAGCTGGAGGAGGGGGGCGGGGCG-GGGCGGCGG 763140 v iv - v i v v - v (GGGCGGG)n#Si 1 GGGCGGGGGGCGGGGG-GCGGGGGGCGGGGGGCGGGGGGCGGGGGGCGG 48 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.04 (2 / 47), avg. gap size = 1.00 (2 / 2) 13 11.99 0.00 3.57 chr1qtel1M 763113 763141 (236859) (GGCGG)n#Simple_repeat 1 28 (0) m_b48s252i9 1716 chr1qtel1M 763113 GGAGGAGGGGGGCGGGGCGGGGCGGCGGC 763141 v i v - (GGCGG)n#Simp 1 GGCGGGGCGGGGCGGGGCGGGGCGG-GGC 28 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1) 204 23.26 0.00 0.00 chr1qtel1M 764220 764262 (235738) C MIRc#SINE/MIR (150) 118 76 m_b48s601i15 1717 chr1qtel1M 764220 AGAGAAGATAATTGACTTGTCCGGGATCCCAGAGCTACTAAGT 764262 i v v i ii i v v v C MIRc#SINE/MIR 118 AGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGT 76 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.07 CpG sites = 5, Kimura (unadjusted) = 28.07 Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 297 29.43 6.10 6.75 chr1qtel1M 764317 764480 (235520) MIR3#SINE/MIR 18 180 (28) m_b48s601i16 1718 chr1qtel1M 764317 CAGATGGGGCAGAGCATTGGGACTATATCAGATGACTCATGAGTTCCAGT 764366 vi i vi - i ----i iv i-- i i MIR3#SINE/MIR 18 CAGAGAGAGCACGG-ACTGGGA----GTCAGGAGACC--TGGGTTCTAGT 60 chr1qtel1M 764367 CT-GGCTGCAGACCCTTCCTCGTTGGGTGACCCTGGGGAA--TGCTTCAG 764413 i- - v v v vv ? i v i v --ii v MIR3#SINE/MIR 61 CCCGGCT-CTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCAC 109 chr1qtel1M 764414 TTT-----GCCTCAGTTTCTTTATGTGTAAACT--GGAGATTAAAATGGA 764456 i i----- i i v v -- i i ii v i MIR3#SINE/MIR 110 CTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGA 159 chr1qtel1M 764457 GAAACCATTCCAGCGTCTCTGCCA 764480 vi v --- i iv i v MIR3#SINE/MIR 160 TGATC---TCTAAGGTCCCTTCCA 180 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.74 CpG sites = 27, Kimura (unadjusted) = 38.85 Transitions / transversions = 1.50 (27/18) Gap_init rate = 0.09 (15 / 163), avg. gap size = 1.40 (21 / 15) 302 23.76 6.20 5.38 chr1qtel1M 764319 764447 (235553) MIR1_Amn#SINE/MIR 24 153 (77) m_b48s601i17 1718 chr1qtel1M 764319 GATGGGGCAGAGCATTGGGACTATATCAGATGACTCATGAGTTCCAGTCT 764368 i i vv v i ---- i iv i-- i ? ? i MIR1_Amn#SINE 24 GATAGAGCACTGGACTGGGACT----CGGGAGACC--TGGGTTCNANTCC 67 chr1qtel1M 764369 -GGCTGCAGACCCTTCCTCGTTGGGTGACCCTGGGGAA--TGCTTCAGTT 764415 - - v v v ?v i? i ? i v --ii ? vi MIR1_Amn#SINE 68 CGGCT-CTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGTCACTTNACCT 116 chr1qtel1M 764416 -----TGCCTCAGTTTCTTTATGTGTAAACTGGAGAT 764447 -----? i i v v i MIR1_Amn#SINE 117 CTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGGAT 153 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.11 CpG sites = 17, Kimura (unadjusted) = 31.39 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.08 (10 / 128), avg. gap size = 1.50 (15 / 10) 235 30.61 10.20 0.00 chr1qtel1M 766878 766975 (233025) L3#LINE/CR1 3832 3939 (160) m_b48s601i18 1719 chr1qtel1M 766878 AAAAGGCCCAGATAGTAACAATGAAAGGAAACTTCAG--AAGCAGCTTT- 766924 i i vv iv v v iiv ii v -- i v - L3#LINE/CR1 3832 AGAGGGCAGAACTAGGACCAATGGGTGGAAGTTACAGGGAGGCAGATTTC 3881 chr1qtel1M 766925 AGTTTGATGGAAGAAAAAACTTCCTAA-------AACTGTTGAAAAACGG 766967 i i ii iv i i i ------- i iv i L3#LINE/CR1 3882 GGCTCAATATAAGGAAGAACTTTCTAACAATCAGAGCTGTCCAAAAATGG 3931 chr1qtel1M 766968 GATGGGCT 766975 i L3#LINE/CR1 3932 AATGGGCT 3939 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.55 CpG sites = 20, Kimura (unadjusted) = 41.39 Transitions / transversions = 2.00 (20/10) Gap_init rate = 0.03 (3 / 97), avg. gap size = 3.33 (10 / 3) 15 21.18 0.00 0.00 chr1qtel1M 768098 768135 (231865) (AAATA)n#Simple_repeat 1 38 (0) m_b48s252i10 1720 chr1qtel1M 768098 AAATATAATAAATTAGAATAAAATAGAATTAAGGAAAA 768135 v v i i v iv (AAATA)n#Simp 1 AAATAAAATAAAATAAAATAAAATAAAATAAAATAAAA 38 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 15 21.09 0.00 2.56 chr1qtel1M 768228 768267 (231733) (GAA)n#Simple_repeat 1 39 (0) m_b48s252i11 1721 chr1qtel1M 768228 GAGGAAAAACAGAGAATCTGAAGAAGAAGAAGAAGAGGAA 768267 i i v - vvv i (GAA)n#Simple 1 GAAGAAGAAGA-AGAAGAAGAAGAAGAAGAAGAAGAAGAA 39 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1) 21 13.48 0.00 0.00 chr1qtel1M 771938 771970 (228030) (T)n#Simple_repeat 1 33 (0) m_b48s252i12 1722 chr1qtel1M 771938 TTTATTTTTTTCCTTTTTTCTTTTTTTTTTTTT 771970 v ii i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 33 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 34 0.00 0.00 0.00 chr1qtel1M 772095 772123 (227877) (AC)n#Simple_repeat 1 29 (0) c_b48s251i0 1723 chr1qtel1M 772095 ACACACACACACACACACACACACACACA 772123 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACA 29 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 31 0.00 0.00 0.00 chr1qtel1M 772125 772153 (227847) (ATATAC)n#Simple_repeat 1 29 (0) c_b48s251i1 1724 chr1qtel1M 772125 ATATACATATACATATACATATACATATA 772153 (ATATAC)n#Sim 1 ATATACATATACATATACATATACATATA 29 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 251 33.70 1.09 0.00 chr1qtel1M 772155 772246 (227754) L3#LINE/CR1 1778 1870 (2229) m_b48s601i19 1725 chr1qtel1M 772155 AAGTTGGAAGTACCAACAAGGGAAAATGTTCTTCTATATATGGTTCTTGC 772204 v i i v v i i v i vi iv iv ii vi L3#LINE/CR1 1778 AAGGTAGAGGAAGCAACGAGGGGAACTGCTACTCTGGACTTAATTCTGAC 1827 chr1qtel1M 772205 CAACAAGGTAGAACTGATTTTTATGGTGTAAAT-ATTGGGAAC 772246 v i vv ivi v i -iv i L3#LINE/CR1 1828 CAACAAGGAAGAACTGGTTGGTGAAGTGGAAGTCGATAGGAAC 1870 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.02 CpG sites = 17, Kimura (unadjusted) = 45.95 Transitions / transversions = 1.21 (17/14) Gap_init rate = 0.01 (1 / 91), avg. gap size = 1.00 (1 / 1) 245 29.51 1.01 4.17 chr1qtel1M 772624 772722 (227278) L3#LINE/CR1 2494 2589 (1510) m_b48s601i20 1725 chr1qtel1M 772624 TAATAGGGAATTGATACCTAAG-CAGCATAAGGATTTCCTAAAAGAGCCC 772672 v vi i -i -i i vv vv i v L3#LINE/CR1 2494 TAAGAGGGAATTGAAGCCCAAGATAG-GTGAGGAGATAGTAAGAGAGCAC 2542 chr1qtel1M 772673 ATAGTTGCTACCACTGATGAATTCAAGACACCTGGGCTTGACAAATCACA 772722 v ii viv --- i v v v v iv i i L3#LINE/CR1 2543 CTAGCCGCTTTAA---ATGAGTTCAAGTCTCCAGGCCCAGACGAATTACA 2589 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.50 CpG sites = 13, Kimura (unadjusted) = 37.73 Transitions / transversions = 0.87 (13/15) Gap_init rate = 0.05 (5 / 98), avg. gap size = 1.00 (5 / 5) 191 37.38 1.85 0.92 chr1qtel1M 773259 773366 (226634) C MamRTE1#LINE/RTE-BovB (2826) 986 878 m_b48s601i21 1726 chr1qtel1M 773259 TGGCACC--TGATGACAAGGATCTCCAGGTCTTCACAGCAGCTTTCTTTC 773306 i -- -i ii vv v i i iii v v C MamRTE1#LINE/ 986 TGGTACCGCTG-CGATGAGTCTGTCCAGATCCTTGTAGAATCTTTCTTTC 938 chr1qtel1M 773307 CCTTCACCAGGATCCATGGCCGTGGGCGGGTGCATGTTGATGGGGATGGA 773356 i i i i v i i viiv v vi iiii i iv i v C MamRTE1#LINE/ 937 TCCTCATCGGTATTCGTCATGGTGGGGGCATATGCGCTGATGACGGTGGC 888 chr1qtel1M 773357 TTGGTGCTTT 773366 v?i i C MamRTE1#LINE/ 887 ANAGCGCTTT 878 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 46.65 CpG sites = 27, Kimura (unadjusted) = 57.03 Transitions / transversions = 2.08 (27/13) Gap_init rate = 0.02 (2 / 107), avg. gap size = 1.50 (3 / 2) 232 29.84 10.14 8.31 chr1qtel1M 773722 774017 (225983) L3#LINE/CR1 3648 3948 (151) m_b48s601i22 1725 chr1qtel1M 773722 GCATCCAAAGGTGGGAAACCAGAATGCTGGGAGGGGGTGCCTTAAGTTCC 773771 i i v i vi i -- v i ---i vi ivi v L3#LINE/CR1 3648 GCGTCCAGAGGAGAGCGACCAGGATG--GTGAAGGG---TCTGGAAACCA 3692 chr1qtel1M 773772 TGCCAT-CAAACAACTCAATGAAAAAACTGGGGGTGTTCAG--TGG-GAA 773817 i -ii iv v-iv ii i i -- - L3#LINE/CR1 3693 TGTCATATGAGGAACG-GTTGAAGGAACTGGGGATGTTTAGCCTGGAGAA 3741 chr1qtel1M 773818 GAGAAGATCTGGGGCAGGTGAGAACATCA-AGTTG-CT--GAGTCTGTGA 773863 ii i i ----- - v - i - --i i v v L3#LINE/CR1 3742 GAGAAGACTTAGAG-----GAG-ACATGATAGCTGTCTTCAAATATTTGA 3785 chr1qtel1M 773864 AAGGCTGACACACTACAGCGAGATGAACTCAACATGTTCTGTTCTGCCCC 773913 i v --- iii -i v i i vi v i viv i L3#LINE/CR1 3786 AGGGCTGTCA---TGTGG-AAGAGGGATTAGACTTATTCTGTGTGGCTCC 3831 chr1qtel1M 773914 AGATGG--GAA--AGG-------------AGTTA----GAGACAGATCAA 773942 v -- -- ------------- ---- i ivv L3#LINE/CR1 3832 AGAGGGCAGAACTAGGACCAATGGGTGGAAGTTACAGGGAGGCAGATTTC 3881 chr1qtel1M 773943 GGCCTGACATTACAGAAG-ACTTCCCGGCAATTACAACCATCCTCCAGAG 773991 iii i - vi - i iii i v i ii--- i i L3#LINE/CR1 3882 GGCTCAATA-TAAGGAAGAACTTTCTAACAATCAGAGCTG---TCCAAAA 3927 chr1qtel1M 773992 ATCAGGTGCAATGAGAGGCCTTGGGA 774017 -- --- i vv i ? L3#LINE/CR1 3928 AT--GG---AATGGGCTGCCTCGNGA 3948 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.53 CpG sites = 56, Kimura (unadjusted) = 40.52 Transitions / transversions = 2.24 (56/25) Gap_init rate = 0.12 (36 / 295), avg. gap size = 1.53 (55 / 36) 222 34.85 0.00 0.00 chr1qtel1M 775262 775327 (224673) C L2d2_3end#LINE/L2 (12) 543 478 m_b48s601i23 1727 chr1qtel1M 775262 AACTAAGATGTATGAAATGTTTCCTATGTGTCAAACACTGGGTTAAGTGC 775311 v v v vi ii ii v i iv ii v i i i C L2d2_3end#LIN 543 AACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGC 494 chr1qtel1M 775312 TGAAGGGAATACAAGG 775327 vi i i C L2d2_3end#LIN 493 TGTGGGGGATACAAAG 478 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.77 CpG sites = 15, Kimura (unadjusted) = 49.81 Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0) 201 32.95 0.00 3.95 chr1qtel1M 775561 775639 (224361) C L2a_3end#LINE/L2 (79) 438 363 m_b48s601i24 1727 chr1qtel1M 775561 ACAAAGTAAAAAATAGTCCCTGTATTTATGGAACTGATATTCCAACAAGG 775610 ii i v v ivi i i v i i ii-- C L2a_3end#LINE 438 ACAAAACAGACAAAAGTCCCTGCCCTCATGGAGCTTACATTCTAGT--GG 391 chr1qtel1M 775611 GAAAAAACATGCATCTTAACGAATAGATA 775639 iii i vi -v v i i C L2a_3end#LINE 390 GGGGAGACAGACA-ATAAACAAATAAATA 363 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 46.80 CpG sites = 18, Kimura (unadjusted) = 46.80 Transitions / transversions = 2.57 (18/7) Gap_init rate = 0.04 (3 / 78), avg. gap size = 1.00 (3 / 3) 245 31.94 19.42 1.23 chr1qtel1M 775886 776091 (223909) L2#LINE/L2 2140 2382 (700) m_b48s601i25 1728 chr1qtel1M 775886 TCTCCTATTCCTCCATCCAACTTGCCTGACAACTCATTCCCACTCTCCTT 775935 iv ii - v i vv i vi v i v L2#LINE/L2 2140 TCTCCTGGTTTTCC-TCCTACCTCACTGGCCGCTCCTTCTCAGTCTCCTT 2188 chr1qtel1M 775936 GATTAAT-----CTTATCTCGCCCACGGCCGA------GGGTATATCCAA 775974 vii ii ----- i v v vv i? ------ i ii-i i L2#LINE/L2 2189 TGCTGGTTCCTCCTCATCTCCCCGACCTCTNAACGTTGGAGTGC-CCCAG 2237 chr1qtel1M 775975 AGCTCGG-----------------------AGCCATATTC-CTTTTTGGG 776000 i i ----------------------- v i i i - iii ? L2#LINE/L2 2238 GGCTCAGTCCTTGGACCTCTTCTCTTCTCTATCTACACTCACTCCCTNGG 2287 chr1qtel1M 776001 T-ACCTCATCAGGGTCCCATTACTTTA----CCATCGTTATACTGATGAT 776045 - i vi - i vi ---- vv i i L2#LINE/L2 2288 TGATCTCATCCAG-TCTCATGGCTTTAAATACCATCTATATGCTGATGAC 2336 chr1qtel1M 776046 TTCCAGCTTTGTATATCTATCCCTAGTCTCTCTTCTGAGTCCCAGA 776091 i iv i v i v viii ii iii L2#LINE/L2 2337 TCCCAAATTTATATCTCCAGCCCGGACCTCTCCCCTGAACTCCAGA 2382 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.97 CpG sites = 44, Kimura (unadjusted) = 44.94 Transitions / transversions = 2.10 (44/21) Gap_init rate = 0.04 (9 / 205), avg. gap size = 4.78 (43 / 9) 180 27.64 7.63 4.96 chr1qtel1M 776146 776263 (223737) L2d_3end#LINE/L2 372 492 (24) m_b48s601i26 1728 chr1qtel1M 776146 TGTTAGGAATGATCTTTCCCATGAGAGTGGAAGCTTCTGGAGGGCAAGGG 776195 vvv - ii v iv v v i v i i L2d_3end#LINE 372 TGTTAGTCTTG-TCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGA 420 chr1qtel1M 776196 GC-TTTCTTGT--TGCTTGCAGATGT-GTT-GCCAC--CACTTAG--CAG 776236 v - v i -- ?i ----- ? - -v -- i i -- L2d_3end#LINE 421 CCATGTCTTATACTNTTT-----TNTCGTTCCCCACAGCGCCTAGCACAG 465 chr1qtel1M 776237 TGCCTGACACATAGGAAGCATCGAATA 776263 ivii v i iiiv L2d_3end#LINE 466 TGCTGAGCACATAGTAGGCGCTCAATA 492 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.19 CpG sites = 17, Kimura (unadjusted) = 36.01 Transitions / transversions = 1.21 (17/14) Gap_init rate = 0.10 (12 / 117), avg. gap size = 1.25 (15 / 12) 302 26.98 5.94 0.94 chr1qtel1M 776163 776263 (223737) L2a_3end#LINE/L2 390 495 (22) m_b48s601i27 1728 chr1qtel1M 776163 CCCATGAGAGTGGAAGCTTCTGGAGGGCAAGGGGCTTT---CT-TGTTGC 776208 iv i v i vv - i --- - v i L2a_3end#LINE 390 CCCACTAGAATGTAAGCTCCATGAGGGCA-GGGACTTTTGTCTGTTTTGT 438 chr1qtel1M 776209 TTGCAGATGTGTTGCCACCACTTAG--CAGTGCCTGACACATAGGAAGCA 776256 ii v v i iv v i i -- i v i i L2a_3end#LINE 439 TCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGGCG 488 chr1qtel1M 776257 TCGAATA 776263 iiv L2a_3end#LINE 489 CTCAATA 495 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.26 CpG sites = 16, Kimura (unadjusted) = 34.32 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.04 (4 / 100), avg. gap size = 1.75 (7 / 4) 354 24.71 0.00 1.18 chr1qtel1M 776558 776643 (223357) C Charlie4#DNA/hAT-Charlie (3263) 115 31 m_b48s502i0 1729 chr1qtel1M 776558 AGTTAGAGGGTAATGAAAATAAAGATGTAATTTTCCCCACAGTTATATTC 776607 v i ii - vii vi C Charlie4#DNA/ 115 AGTTAGAGGTTAGTGAAAATAAAGATGTAATTTTTTCC-CATCCAAGTTC 67 chr1qtel1M 776608 ACAAACTCCCAGAAATACATTCATAGGCCCCTCGGG 776643 ii i v v vi i ii i i C Charlie4#DNA/ 66 ACGGACCCCCTGAATTCTATCCACGGACCCCTTGGG 31 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 27.61 CpG sites = 15, Kimura (unadjusted) = 31.35 Transitions / transversions = 2.50 (15/6) Gap_init rate = 0.01 (1 / 85), avg. gap size = 1.00 (1 / 1) 14 21.53 0.00 7.69 chr1qtel1M 777172 777227 (222773) (GCTGGGA)n#Simple_repeat 1 52 (0) m_b48s252i13 1730 chr1qtel1M 777172 GCTGGGAGATGGGAGCTGAGAGGCTCCGTGTCTGGTCAGCTGGTGTGCTT 777221 v i - vv v - -v - v v (GCTGGGA)n#Si 1 GCTGGGAGCTGGGAGCTGGGA-GCTGGGAG-CTGG-GAGCTGG-GAGCTG 46 chr1qtel1M 777222 GGACCT 777227 v (GCTGGGA)n#Si 47 GGAGCT 52 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.07 (4 / 55), avg. gap size = 1.00 (4 / 4) 11 18.73 0.00 7.69 chr1qtel1M 777601 777642 (222358) (AAAGAG)n#Simple_repeat 1 39 (0) m_b49s252i1 1731 chr1qtel1M 777601 AAAGAAAAAGAGGAAGAGAATAAGCAAATTCAGAAAGAGCAA 777642 i i vi - --v v (AAAGAG)n#Sim 1 AAAGAGAAAGAGAAAGAGAAAGAG-AAA--GAGAAAGAGAAA 39 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.07 (3 / 41), avg. gap size = 1.00 (3 / 3) 236 33.18 8.33 0.70 chr1qtel1M 778185 778448 (221552) L1ME3Cz_3end#LINE/L1 123 406 (591) m_b49s551i0 1732 chr1qtel1M 778185 CACATGAAAAATATGCTCTAAAACACCAATAA---AAGAAAC-CAGTATC 778230 i i- v vvv i i ---ii i- i- i L1ME3Cz_3end# 123 CATATGAAAAG-ATGCTCAACCTCACTAGTAATCAGGGAAATGCAA-ATT 170 chr1qtel1M 778231 AAAACAACCCCAAGGTTTTATTTCTTACCTG-GAAATTGGCAAAAAT--- 778276 ? vvii i vii vi ii-v i --- L1ME3Cz_3end# 171 AAAACNACAATGAGATACCATTTCACACCCATCAGATTGGCAAAAATTTA 220 chr1qtel1M 778277 -------GAGAATAGTCAGTGTAGGAGAAT-TGTGGAAATACTGGAATAA 778318 ------- v viv v v iv- i v v ivv L1ME3Cz_3end# 221 AAAGTCTGACAATACCAAGTGTTGGCGAGGATGTGGAGAAACGGGAACTC 270 chr1qtel1M 778319 AAATACACTTCTGGTGGAGCAGTGAACTACAATGGCCCTTCTGGCAAGCA 778368 vv v iivv i i ivv iii vi i vi L1ME3Cz_3end# 271 TCATACACTGCTGGTGGGAGTGTAAATTGGTACAACCACTTTGGAGAGCA 320 chr1qtel1M 778369 ATGTGGAATTAT---GCAAA--TAAAG-TGCTTGTGTTCTTGAACCCCGA 778412 v v v --- i -- i - vii iii vvi v v L1ME3Cz_3end# 321 ATTTGGCAATATCTAGTAAAGTTGAAGATGCGCATACCCTACGACCCAGC 370 chr1qtel1M 778413 GATCCCACTGCTAAATATATACCCCCAAGAAGGTCT 778448 i i v ii ivi iv L1ME3Cz_3end# 371 AATTCCACTTCTAGGTATATACCCTAGAGAAACTCT 406 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 44.58 CpG sites = 48, Kimura (unadjusted) = 45.29 Transitions / transversions = 1.23 (48/39) Gap_init rate = 0.04 (11 / 263), avg. gap size = 2.18 (24 / 11) 751 31.75 1.17 1.57 chr1qtel1M 778503 778758 (221242) C MIRb#SINE/MIR (12) 256 2 m_b49s601i1 1733 chr1qtel1M 778503 ACCATTTCTATGGCACCTACTATGTGCAAGGCACTGTG-TAAACACTTTT 778551 v vvi i i v - i i - C MIRb#SINE/MIR 256 ACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTT- 208 chr1qtel1M 778552 TAAATAAAT-ATCTCATTTTACCGTCAGAACCACCCT-CAAGATAGGAGA 778599 - v iv - v i v v v - i i viv C MIRb#SINE/MIR 207 -ACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTAT 159 chr1qtel1M 778600 TGTTATTCCCACTTTACAGATGAGAAAATTGAGATGCACAGAAGTTCAGT 778649 i i i i i iiv v i v C MIRb#SINE/MIR 158 TATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGT 109 chr1qtel1M 778650 TACATATCCGGGGTCACAGGGCTAAAAAGCATCTGAGTCCACATTAGAGC 778699 v v ii ii vi iv iiv v i viv v i C MIRb#SINE/MIR 108 AACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAAC 59 chr1qtel1M 778700 TTGGAGCTTCCTCCCTCCAGCTCTAGCACGCTGTCCGTTGTGCTACCAGC 778749 iii iv vi vv ivv iv ii v v ii ii i -- C MIRb#SINE/MIR 58 CCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCACCAC--GC 11 chr1qtel1M 778750 CACCTCACT 778758 ii i v C MIRb#SINE/MIR 10 TGCCCCTCT 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.42 CpG sites = 46, Kimura (unadjusted) = 42.52 Transitions / transversions = 1.35 (46/34) Gap_init rate = 0.03 (7 / 255), avg. gap size = 1.00 (7 / 7) 35 0.00 0.00 0.00 chr1qtel1M 779257 779289 (220711) (G)n#Simple_repeat 1 33 (0) c_b49s251i0 1734 chr1qtel1M 779257 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 779289 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 33 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 446 23.83 0.00 7.89 chr1qtel1M 781042 781164 (218836) MIRc#SINE/MIR 2 115 (153) m_b49s601i2 1735 chr1qtel1M 781042 GAGGCAGCGAGGAGGTGCAGTGAATAGAGCCCCAGCCCTGAAGTCAGGAG 781091 i v --- i v v ii v i i i MIRc#SINE/MIR 2 GAGGCAGTGTGG---TGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr1qtel1M 781092 GACCTGAGTTCAAATGTGACCTTAGACACTTAACACTTCCAACTGGGTGA 781141 i i i viviv iv v ------ i i v MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCCACTTA------CTAGCTGTGTGA 92 chr1qtel1M 781142 CCCTGGGCAAGTCACTTAACCCC 781164 i i MIRc#SINE/MIR 93 CCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.70 CpG sites = 17, Kimura (unadjusted) = 29.21 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.07 (9 / 122), avg. gap size = 1.00 (9 / 9) 663 22.93 10.23 2.60 chr1qtel1M 781565 781779 (218221) C MIRb#SINE/MIR (23) 245 15 m_b49s601i3 1736 chr1qtel1M 781565 AGCATATACTTTGTGCCAGGCACTATGATAAATACTTT---TGCA-AATA 781610 iiv v i v iii --- -v v C MIRb#SINE/MIR 245 AGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACATGCATTATC 196 chr1qtel1M 781611 TTATATA-----------AACCCTCCAAGGCAGGTGCTATTATTAACACT 781649 i v ----------- v i i --- v v i C MIRb#SINE/MIR 195 TCATTTAATCCTCACAACAACCCTGCGAGGTAGG---TATTATTATCCCC 149 chr1qtel1M 781650 ATTTTACAGATAGGGAAACAGAAGCAAGCAGAGATG----GTCACTTGCC 781695 ii v i --v v ---- v C MIRb#SINE/MIR 148 ATTTTACAGATGAGGAAACTGAGGC--TCAGAGAGGTTAAGTAACTTGCC 101 chr1qtel1M 781696 CAGGGTCACACAACTTGTGAGAGTCTGAGGCTGGTTTTGA--CCTTGTCT 781743 i i v i v v v v v v i -- vv C MIRb#SINE/MIR 100 CAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCT 51 chr1qtel1M 781744 TCCTGACTCC-AGGCTCATTGCTCAATACACTGTACC 781779 vi - i i i- vv v i C MIRb#SINE/MIR 50 GTCTGACTCCAAAGCCCG-TGCTCTTTCCACTGCACC 15 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.34 CpG sites = 22, Kimura (unadjusted) = 27.55 Transitions / transversions = 0.85 (22/26) Gap_init rate = 0.06 (12 / 214), avg. gap size = 2.33 (28 / 12) 203 28.35 4.35 2.86 chr1qtel1M 782180 782248 (217752) L2d2_3end#LINE/L2 474 543 (12) m_b49s601i4 1737 chr1qtel1M 782180 ACTTGTTTGTATCCCAGACTGGATACCCTGT---GTGCCTAGCACGTAGT 782226 v vv v --ii iv i--- v ii L2d2_3end#LIN 474 ACTTCTTTGTATCCCCCACAG--CGCCTAGCACAGTGCCTTGCACACAGT 521 chr1qtel1M 782227 AGACACTATATAAATGCTTATT 782248 i i vv ii i L2d2_3end#LIN 522 AGGCGCTCAATAAATATTTGTT 543 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.62 CpG sites = 11, Kimura (unadjusted) = 36.51 Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.04 (3 / 68), avg. gap size = 1.67 (5 / 3) 207 28.26 0.00 0.00 chr1qtel1M 782203 782248 (217752) L2c_3end#LINE/L2 421 466 (12) m_b49s601i5 1737 chr1qtel1M 782203 TACCCTGTGTGCCTAGCACGTAGTAGACACTATATAAATGCTTATT 782248 i ivv i i i i i vv i i L2c_3end#LINE 421 TATCCCCAGCGCCTGGCACATAGTAGGCGCTCAATAAATGTTTGTT 466 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.32 CpG sites = 9, Kimura (unadjusted) = 37.31 Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 232 26.71 0.00 13.59 chr1qtel1M 782605 782721 (217279) L2d_3end#LINE/L2 327 429 (87) m_b49s601i6 1738 chr1qtel1M 782605 CTCAATTAGTTATTATTTCCTATTTATCTTATAAGTAGCTTGCTTTATAT 782654 i vv i i i iv vv i- ----- i i i L2d_3end#LINE 327 CTTAATTATATACTGTCTTGTATTGTTCTC-TAA-----TTGTTTCATGT 370 chr1qtel1M 782655 ATATTTGTTTGCATGCTGTCATCCCATATTAGCTTGTGAGCTCCTTATGG 782704 i i v i ------ vi - i v i iv L2d_3end#LINE 371 GTGTTAGTCT------TGTCTCCCCA-ACTAGATTGTAAGCTCCTTGAGG 413 chr1qtel1M 782705 GCAGGGACTCATGGTTT 782721 - vi L2d_3end#LINE 414 GCAGGGAC-CATGTCTT 429 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.26 CpG sites = 17, Kimura (unadjusted) = 33.26 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.12 (14 / 116), avg. gap size = 1.00 (14 / 14) 298 25.01 1.01 3.09 chr1qtel1M 782632 782730 (217270) L2c_3end#LINE/L2 321 417 (61) m_b49s601i7 1738 chr1qtel1M 782632 CTTATAAGTAGCTTGCTTTATATATATTTGTTTGCATG-CTGTCATCCCA 782680 v v i iv i vv i i i ? - - iv L2c_3end#LINE 321 CTTATCATTAACTTGTATTGTAATTGTCTGTTTACNTGTCTGTC-TCCTC 369 chr1qtel1M 782681 TATTAGCTTGTGAGCTCCTTATGGGCAGGGACTCATGGTTTTGATCCTCT 782730 i i vi iv - i - i iv v L2c_3end#LINE 370 CACTAGACTGTGAGCTCCTTGAGGGCAGGGAC-CGT-GTCTTATTCATCT 417 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.90 CpG sites = 14, Kimura (unadjusted) = 31.45 Transitions / transversions = 1.40 (14/10) Gap_init rate = 0.04 (4 / 98), avg. gap size = 1.00 (4 / 4) 16 0.00 0.00 0.00 chr1qtel1M 783227 783244 (216756) (A)n#Simple_repeat 1 18 (0) m_b49s252i2 1739 chr1qtel1M 783227 AAAAAAAAAAAAAAAAAA 783244 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAA 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 21 8.62 0.00 5.13 chr1qtel1M 783894 783934 (216066) (CCCT)n#Simple_repeat 1 39 (0) m_b49s252i3 1740 chr1qtel1M 783894 CCCTCCCTCCCTCCATTCCCTCCCTCCCTCTATCCCCTCCC 783934 -i iv - (CCCT)n#Simpl 1 CCCTCCCTCCCTCC-CTCCCTCCCTCCCTCCCT-CCCTCCC 39 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 18 13.69 0.00 0.00 chr1qtel1M 786241 786272 (213728) (GCG)n#Simple_repeat 1 32 (0) m_b49s252i4 1741 chr1qtel1M 786241 GCGGCGACGGCGGCGGCGGCGGAGGAGGAGGC 786272 i v v v (GCG)n#Simple 1 GCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC 32 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 237 28.47 8.06 2.29 chr1qtel1M 788306 788553 (211447) L1M5_orf2#LINE/L1 2447 2708 (586) m_b49s551i1 1742 chr1qtel1M 788306 CAATTCTACTTAAAT----CTATTTATTCAGTTCCATGCCA-TTAAACTA 788350 v ii ---- vv i v v v - i v v L1M5_orf2#LIN 2447 CAATTCTCCCCAAATTGATCTATAGATTCAATGCAATCCCAATCAAAATC 2496 chr1qtel1M 788351 TCAAAAATTATTTTTGTAGAGCTAGAAAAAAT-----TAACATTTCATCT 788395 i iv iv v iv v v iv ----- v - v L1M5_orf2#LIN 2497 CCAGCAGGTTTTTTTGTAGAAATTGACAAGCTGATTCTAAAATTT-ATAT 2545 chr1qtel1M 788396 GAAAGAACAAAAGACCAATGATA-TCAAGGGAATCAATGAAAAGAATGTG 788444 i ivi i ? vi -i iiv vvvi --- L1M5_orf2#LIN 2546 GGAAATGCAAAGGACCNAGAATAGCCAAAACAATCTTGAAAAAGAA---G 2592 chr1qtel1M 788445 AAGGAAGGTGGT---CTAGCCATACTAGATCTCAA-ACT-ATTATTGAGC 788489 vi v v--- vi vv i? ? - - vi L1M5_orf2#LIN 2593 AACAAAGTTGGAGGACTTACACTACCNGATNTCAAGACTTATTATAAAGC 2642 chr1qtel1M 788490 AGTAATAATCAAGATGGTCTAGTACTGGC-TAAG---AAACAGTGGTAGA 788535 vii i ii v i i - --- i --ii L1M5_orf2#LIN 2643 TACAGTAATCAAGACAGTGTGGTATTGGCGTAAGGATAGACA--AATAGA 2690 chr1qtel1M 788536 TCAGTAGAATGGATTAGA 788553 i i ii v L1M5_orf2#LIN 2691 TCAATGGAACAGAATAGA 2708 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.01 CpG sites = 36, Kimura (unadjusted) = 37.01 Transitions / transversions = 1.09 (36/33) Gap_init rate = 0.06 (15 / 247), avg. gap size = 1.73 (26 / 15) 225 33.57 2.05 2.05 chr1qtel1M 788986 789131 (210869) L1P3_orf2#LINE/L1 3134 3279 (15) m_b49s551i2 1742 chr1qtel1M 788986 CTGATAAAGGCCTCACTTCTTAAATATATAGAGAACGGAGTAAAATTTAT 789035 i v v iv ivi v i ii vv ivv i L1P3_orf2#LIN 3134 CTGACAAAGGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTAC 3183 chr1qtel1M 789036 AA---AAACACATGTCATTTCCCTATTGAAAAATGGACAAAGGATATGAG 789082 --- v viiv --- i ii i i i i L1P3_orf2#LIN 3184 AAGAAAAAAACAAACAA---CCCCATCAAAAAGTGGGCGAAGGATATGAA 3230 chr1qtel1M 789083 CAGGCAGTTTTCAGACAAAGAAATCAAAGCAACCTCTAGTCATATAAAA 789131 i v i i vi v iv v ii vvi iv i L1P3_orf2#LIN 3231 CAGACACTTCTCAAAAGAAGACATTTATGCGGCCAACAAACATATGAAA 3279 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 43.49 CpG sites = 28, Kimura (unadjusted) = 46.11 Transitions / transversions = 1.40 (28/20) Gap_init rate = 0.03 (4 / 145), avg. gap size = 1.50 (6 / 4) 477 28.50 8.01 2.09 chr1qtel1M 789008 789369 (210631) L1MA2_3end#LINE/L1 12 394 (657) m_b49s551i4 1742 chr1qtel1M 789008 AATATATAGAGAACGGAGTAAAATTTATAAAAACACATGTCATTTCCCTA 789057 ii i vv ivv v i ii v v v v vvi v L1MA2_3end#LI 12 AATATATAAGGAGCTCAAACAACTCTATAGGAAAAAATCTAATAATCCGA 61 chr1qtel1M 789058 TTGAAAAATGGACAAAGGATATGAGCAGGCAGTTTTCAGACAAAGAAAT- 789106 i i i v ii i v i i vi v - L1MA2_3end#LI 62 TTAAAAAATGGGCAAAAGATTTGAATAGACATTTCTCAAAAGAAGACATA 111 chr1qtel1M 789107 CAAA--GCAACCTCTAGTCATAT--AAAAGTGCTCAAGTCACTATTG--- 789149 -- v --- v -- i -- ii --- L1MA2_3end#LI 112 CAAATGGCAAAC---AGGCATATGAAAAGGTGCTCAA--CATCATTGATC 156 chr1qtel1M 789150 ATTAGAAAAATGCAGATT-AAACAACTCTGCGGTATAACTTCACACCTAT 789198 i i i i- v vv v i v ii v vi L1MA2_3end#LI 157 ATCAGAGAAATGCAAATCAAAACTACAATGAGATATCATCTCACCCCAGT 206 chr1qtel1M 789199 CAGACTGGCTAATATGACAAAAAA-GGAAAATGATAAACA-TGG-GAGG- 789244 i i v v? -v i -i iv i i ii- - - L1MA2_3end#LI 207 TAAAATGGCTTNTAT-CCAAAAGACAGGCAATAACAAATGCTGGCGAGGA 255 chr1qtel1M 789245 ---GGA-AAATGGGGCCACTAATGCATTGTTGGTGAAGTAGTAAATTGAT 789290 --- - v iv v vi i i iiivv ii L1MA2_3end#LI 256 TGTGGAGAAAAGGGAACCCTCGTACACTGTTGGTGGGAATGTAAATTAGT 305 chr1qtel1M 789291 -CCATCATTCTGAAGAACAATTTGGAACT--CT-----GACCAA----AG 789328 - v i i v i i iv -- -----i i ---- L1MA2_3end#LI 306 ACAACCACTATGGAGAACAGTTTGGAGGTTCCTCAAAAAACTAAAAATAG 355 chr1qtel1M 789329 GGTTATCCATTTGGTCCAGTGATACCACTGTTAGACTATAT 789369 i i - v i ii v i i i- L1MA2_3end#LI 356 AGCTA-CCATATGATCCAGCAATCCCACTGCTGGG-TATAT 394 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.67 CpG sites = 61, Kimura (unadjusted) = 37.13 Transitions / transversions = 1.52 (61/40) Gap_init rate = 0.06 (23 / 361), avg. gap size = 1.61 (37 / 23) 560 27.14 4.56 1.58 chr1qtel1M 789008 789314 (210686) L1ME3C_3end#LINE/L1 12 327 (543) m_b49s551i3 1742 chr1qtel1M 789008 AATATATAGAGAACGGAGTA-AAATTTATAAAAACACATGTCATTTCCCT 789056 i vvv- - iv i v - v v-- v L1ME3C_3end#L 12 AATATATAAAGAACTCC-TACAAATCAATAAGAAAACA-GACAA--CCCA 57 chr1qtel1M 789057 ATTGAAAAATGGACAAAGGATATGAGCAGGCAGTTTTCAGACAAAGAAAT 789106 v i i i i iv vi i i L1ME3C_3end#L 58 ATAGAAAAATGGGCAAAAGATATGAACAGGCAATTCACAGAAGAGGAAAC 107 chr1qtel1M 789107 CAAAGCAACCTCTAGTCATAT-AAAAG-TGCTCAA-GTCACTATTGATTA 789153 ?vi iiii vv iv - - -v v i i L1ME3C_3end#L 108 NCGAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTAATCA 157 chr1qtel1M 789154 GAAAAATGCAGATT-AAACAACTCTGCGGTATAACTTCACACCTATCAGA 789202 ii i - ? vv v i iv i i L1ME3C_3end#L 158 GGGAAATGCAAATTAAAACNACAATGAGATACCATTTCACACCCATCAGA 207 chr1qtel1M 789203 CTGGCTAATATGACAAAAAAGGAAAATGATAAACAT--GGGAGG----GG 789246 i v v vvv ivvv v ivi iii -- v ---- L1ME3C_3end#L 208 TTGGCAAAAATTTAAAAGTCTGACAATACCAAGTGTTGGCGAGGATGTGG 257 chr1qtel1M 789247 AA-AATGGGGCCACTAATGCATTGTTGGT-GAAGTAGTAAATTGAT-CCA 789293 i- i iv v v i i i - i - i - v L1ME3C_3end#L 258 AGCAACGGGAACTCTCATACACTGCTGGTGGGAGT-GTAAATTGGTACAA 306 chr1qtel1M 789294 TCATTCTGAAGAACAATTTGG 789314 i i i i i L1ME3C_3end#L 307 CCACTTTGGAGAGCAATTTGG 327 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 33.64 CpG sites = 46, Kimura (unadjusted) = 34.68 Transitions / transversions = 1.28 (46/36) Gap_init rate = 0.05 (15 / 306), avg. gap size = 1.27 (19 / 15) 574 30.11 7.41 0.58 chr1qtel1M 789053 789376 (210624) L1MA7_3end#LINE/L1 57 402 (636) m_b49s551i6 1742 chr1qtel1M 789053 CCCTATTGAAAAATGGACAAAGGATATGAGCAGGCAGTTTTCAGACAAAG 789102 v i i iv ii i v i i vi L1MA7_3end#LI 57 CCCGATTAAAAAATGGGCAAAGGACCTGAATAGACATTTCTCAAAAGAAG 106 chr1qtel1M 789103 AAATCAAAGCAACCTCTAGTCATAT--AAAAGTGCTCAA-GTCACTATTG 789149 v vv iiii vvi vi -- i -i v v L1MA7_3end#LI 107 ACATACAAATGGCCAACAGATATATGAAAAAATGCTCAACATCACTAATC 156 chr1qtel1M 789150 ATTAGAAAAATGCAGATTAAA-CAACTCTGCGGTATAACTTCACACCTAT 789198 i ii i - v vv v i v i i L1MA7_3end#LI 157 ATCAGGGAAATGCAAATTAAAACCACAATGAGATATCACCTCACACCTGT 206 chr1qtel1M 789199 CAGACTGGCTAATATGACAAAAAAGGAAAATGATAAACATGGGAGGGGA- 789247 i v v v v i v i i i i iii v v i - L1MA7_3end#LI 207 TAGAATGGCTATTATCAAAAAGACGAAAGATAACAAGTGTTGGCGAGGAT 256 chr1qtel1M 789248 ------AAATGGGGCCACTAATGCATTGTTGGTGAAGTAGTAAATTGATC 789291 ------ v iv v vi i i iiivv ii v L1MA7_3end#LI 257 GTGGAGAAAAGGGAACCCTTGTACACTGTTGGTGGGAATGTAAATTAGTA 306 chr1qtel1M 789292 CA-TCATTCTGAAGAACAATTTGGAACT--CT-----GACCAA----AGG 789329 -i v i i i v iv -- -----i i ---- i L1MA7_3end#LI 307 CAGCCATTATGGAAAACAGTATGGAGGTTCCTCAAAAAACTAAAAATAGA 356 chr1qtel1M 789330 GTTATCCATTTGGTCCAGTGATACCACTGTTAGACTATAT-TTCAAAG 789376 ii - v i ii v vi i i- - i L1MA7_3end#LI 357 ACTA-CCATATGATCCAGCAATCCCACTTCTGGG-TATATATCCAAAG 402 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.96 CpG sites = 60, Kimura (unadjusted) = 39.96 Transitions / transversions = 1.62 (60/37) Gap_init rate = 0.04 (12 / 323), avg. gap size = 2.17 (26 / 12) 702 23.32 6.49 1.82 chr1qtel1M 789053 789314 (210686) L1ME5_3end#LINE/L1 57 330 (611) m_b49s551i5 1742 chr1qtel1M 789053 CCCTATTGAAAAATGGACAAAGGATATGAGCAGGCAGTTTTCAGACAAAG 789102 v v i i i v vi i L1ME5_3end#LI 57 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAGG 106 chr1qtel1M 789103 AAATC---AAAGC-AACCTCTAGTCATAT-AAAAG-TGCTCAAG-TCACT 789145 i --- i - ---- iv - i - i- i L1ME5_3end#LI 107 AAACCCGAAAGGCTAAC----AAGCATATGAAGAGATGCTCAAACTCATT 152 chr1qtel1M 789146 ATTGATTAGAAAAATGCAGATT-AAACAACTCTGCGGTATAACTTCACAC 789194 v i i i i - vv v i v i L1ME5_3end#LI 153 AGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACAC 202 chr1qtel1M 789195 CTATCAGACTGGCTAATATGACAAAAAAGGAAAATGATAAACATGGGAG- 789243 i v v v v ivv v vi iii v v - L1ME5_3end#LI 203 CTATTAGACTGGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTGGCGA 252 chr1qtel1M 789244 ------GGGAAAATGGGGCCACTAATGCATTGTTGGT-GAAGTAGTAAAT 789286 ------ i ? i iv v v i i - i - i i L1ME5_3end#LI 253 GGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGT-GTAGAC 301 chr1qtel1M 789287 TGATCCA-TCATTCTGAAGAACAATTTGG 789314 i v -i i i i L1ME5_3end#LI 302 TGGTGCAGCCATTCTGGAGAGCAATCTGG 330 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 28.69 CpG sites = 36, Kimura (unadjusted) = 28.69 Transitions / transversions = 1.50 (36/24) Gap_init rate = 0.06 (15 / 261), avg. gap size = 1.47 (22 / 15) 555 36.46 4.47 2.68 chr1qtel1M 789735 790137 (209863) C MamRTE1#LINE/RTE-BovB (2791) 1021 612 m_b49s601i8 1743 chr1qtel1M 789735 TTAAAATCATCCAGAATTATTAGTTTGTC---TTTTGGCAT-ATTGATCA 789780 i vi ivi iv i i --- v i i-ii -iv C MamRTE1#LINE/ 1021 TTGAAATCTCCCGTGACGATCAGCTTGTCAGATGTTGGTACCGCTG-CGA 973 chr1qtel1M 789781 TAAGGGTCTCCAGGTA--TGCAAACTTTTTCTTCTTTGGCCTCATCAGGA 789828 i vv v i v-- i i v i ii --- i v C MamRTE1#LINE/ 972 TGAGTCTGTCCAGATCCTTGTAGAATCTTTCTTTCT---CCTCATCGGTA 926 chr1qtel1M 789829 TTTGTCTTGGTGGAAGCATAAGCACTGAGGATGGTAGCAG-GTGTTTTCC 789877 i v ii v i v i i ?- i i iv C MamRTE1#LINE/ 925 TTCGTCATGGTGGGGGCATATGCGCTGATGACGGTGGCANAGCGCTTTTG 876 chr1qtel1M 789878 TGCAAGTGGCAATCACATTGTCATAAGCCAATC-CTT---CCTTTTGGAA 789923 viv v? i iv ii vv v v ii - ?--- i v v C MamRTE1#LINE/ 875 TTTCAGANGTAGGCGTAGGGTCATCAGACGGTCACTNATGCCTCTGGGCA 826 chr1qtel1M 789924 GGCATATGAG-CTTGTTTACCAAATTAGT-TTTGATTGCAAAACCTACAC 789971 iiiv iv - --viv i v v - i i iv i C MamRTE1#LINE/ 825 AATTTGGGAGNCTTG--AGACAAGTGACTGTCTGATTGCAAAGCTGACGC 778 chr1qtel1M 789972 CAACTTCAATGTGCTCCCTTTTACTGT----GACCACTGCAGAAAAATGT 790017 ---- v iv ivv v i v vviv---- v v i v i C MamRTE1#LINE/ 777 C----TGAGAGCCGTCGCTCTGAAGAGGGAAGACCTCTCCAGAAGAAGGC 732 chr1qtel1M 790018 ATTTACAGC-TCTGACTTCAGTAAGTTGATCTTTGTCTGCCAACCTTGTT 790066 i v?v i -i v i - i i vi ii v vv ii v C MamRTE1#LINE/ 731 GTANCCGGCACCTGTCTCC-GTGAGCTGTCCTTCATCAGGAAGTCTGGTT 683 chr1qtel1M 790067 TCACTGAGGGCTGCTATGTGGATGGGATACTTATTAAGTTTTCTTGCAAC 790116 i v v v v v ivvvi ii ivvv iv v i C MamRTE1#LINE/ 682 TCGCTCAGTGCGGCGATGTCGACTCCGTATCTGGACAGTTCACGTGCGAC 633 chr1qtel1M 790117 GAGAGCAGTTTATCTCTCAGG 790137 v v iv i v C MamRTE1#LINE/ 632 GAGTGCCGTTCTTCTTTCTGG 612 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.68 CpG sites = 74, Kimura (unadjusted) = 51.96 Transitions / transversions = 1.07 (74/69) Gap_init rate = 0.05 (21 / 402), avg. gap size = 1.38 (29 / 21) 13 14.78 0.00 6.06 chr1qtel1M 790931 790965 (209035) (GGAA)n#Simple_repeat 1 33 (0) m_b49s252i5 1744 chr1qtel1M 790931 GGAAGGAAGGAAGAAAGAAGAGAAAAGAAGAGAAG 790965 i i - i i - (GGAA)n#Simpl 1 GGAAGGAAGGAAGGAAGGA-AGGAAGGAAG-GAAG 33 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 13 15.51 3.33 0.00 chr1qtel1M 790941 790970 (209030) (AAGAA)n#Simple_repeat 1 31 (0) m_b49s252i6 1744 chr1qtel1M 790941 AAG-AAAGAAGAGAAAAGAAGAGAAGAGGAA 790970 - i i i i (AAGAA)n#Simp 1 AAGAAAAGAAAAGAAAAGAAAAGAAAAGAAA 31 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 19 0.00 0.00 0.00 chr1qtel1M 791044 791064 (208936) (AT)n#Simple_repeat 1 21 (0) m_b49s252i7 1745 chr1qtel1M 791044 ATATATATATATATATATATA 791064 (AT)n#Simple_ 1 ATATATATATATATATATATA 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 600 27.16 5.42 2.64 chr1qtel1M 791374 791668 (208332) L1M2_orf2#LINE/L1 1936 2238 (1053) m_b49s551i7 1746 chr1qtel1M 791374 AAGCTAGAAGCCTTCCCAATAAGAACAGAAGTGAAACAAGGATGCCCATT 791423 i ii i vv ? v i iii i i L1M2_orf2#LIN 1936 AAGTTGAAAGCCTTTCCTCTAAGANCTGGAACAAGACAAGGATGCCCACT 1985 chr1qtel1M 791424 GATATCATTATTTTTGAATATTGTATTAGAAATTCTAGCAATAGTAATTG 791473 vvi i i vi v v i v i i i i v v i i L1M2_orf2#LIN 1986 TTCACCACTTCTATTCAACATAGTACTGGAAGTCCTAGCCAGAGCAATTA 2035 chr1qtel1M 791474 GAGAAG----ATAAATTAAAGGCATCAGAATGGATAATGATGTAAT--GA 791517 iv ---- v v vi v iv v v v i --i L1M2_orf2#LIN 2036 GGCAAGAGAAAGAAATAAAAGGCATCCAAATTGGAAAGGAGGAAGTCAAA 2085 chr1qtel1M 791518 TTATCTCCTTTTGCAAGTGATATGATGATATACTCA-AAAATCCTAGAGA 791566 i i iv ii i vv i?i - ? i L1M2_orf2#LIN 2086 TTGTCCCTGTTTGCAGATGACATGATCTTATATNTAGAAAANCCTAAAGA 2135 chr1qtel1M 791567 TTCAATTAAAAATTAATTACTTGAAATGATTTTTTAAAC-AAT---ATA- 791611 i v ii --- i ?i v v ----- - ---i - L1M2_orf2#LIN 2136 CTCCACCAAAA---AACTNTTAGAACTGA-----TAAACGAATTCAGTAA 2177 chr1qtel1M 791612 ----GCAGGATATAAAATAAACCTACACAAATCATCAGCATTTCTATATA 791657 ---- i v v v vi ii L1M2_orf2#LIN 2178 AGTTGCAGGATACAAAATCAACATACAAAAATCAGTAGCATTTCTATACG 2227 chr1qtel1M 791658 GCACCAACAAA 791668 v v i L1M2_orf2#LIN 2228 CCAACAACGAA 2238 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.06 CpG sites = 46, Kimura (unadjusted) = 35.24 Transitions / transversions = 1.44 (46/32) Gap_init rate = 0.05 (15 / 294), avg. gap size = 1.60 (24 / 15) 434 31.32 5.13 3.14 chr1qtel1M 791377 791844 (208156) L1M4_orf2#LINE/L1 1942 2418 (876) m_b49s551i8 1746 chr1qtel1M 791377 CTAGAAGCCTTCCCAATAAGAACAGAAGTGAAACAAGGATGCCCATTGAT 791426 ii ? i vv v i iii i i ii vvi L1M4_orf2#LIN 1942 CTGAANGCTTTCCCCCTAAGATCAGGAACAAGACAAGGATGTCCGCTCTC 1991 chr1qtel1M 791427 ATCATTATTTTTGAATATTGTATTAGAAATTCTAGCAATAGTAATTGGAG 791476 ii i vi v v i i i ii v vi i i iv L1M4_orf2#LIN 1992 GCCACTTCTATTCAACATTGTACTGGAGGTTCTAGCCAGGGCAATTAGGC 2041 chr1qtel1M 791477 AAG----ATAAATTAAAGGCAT-CAGAATGGATA--ATGATGTAATGATT 791519 ---- v v - v v -- v v -i i L1M4_orf2#LIN 2042 AAGAAAAAGAAATAAAAGGCATCCAGATTGGAAAGGAAGAAGTAA-AACT 2090 chr1qtel1M 791520 ATCTCCTTTTGCAAGTGATATGATGATATAC-TCAAAAATCCTAGAGATT 791568 iv i ii i vv i i- vi ii v L1M4_orf2#LIN 2091 ATCTCTATTCGCAGATGACATGATCTTGTATATAGAAAATCCTAAGGAAT 2140 chr1qtel1M 791569 CAATTAAAA----ATT--AATTACTTGAAATGATTTTTTAAACAATATAG 791612 v i? ---- -- i v -- i v i--- i vi v L1M4_orf2#LIN 2141 CCACNAAAAAACTATTAGAACTAAT--AAACGAGTTC---AGCAAGGTTG 2185 chr1qtel1M 791613 CAGGATATAAAATAAACCTACACAAATCATCAGCATTTCTATATAGCACC 791662 i i v iv v viv i --- i L1M4_orf2#LIN 2186 CAGGATACAAGATCAATATACAAAAATCAATTGTATTTCTATA---CACT 2232 chr1qtel1M 791663 AACAA--AACCCTTCAAGAACATGCAG-TAAGAGA--TGCCCCATTTAAA 791707 i -- vv i -- v v i- i --viii v L1M4_orf2#LIN 2233 AGCAATGAACAATCC--GAAAATGAAATTAAGAAAACAATTCCATTTACA 2280 chr1qtel1M 791708 ATAATTGTAGACTGTATGAAATACCTGAAAGGATACCTATCAAAACAAAC 791757 iivvi i vv v i i iii iv v ii v v ii L1M4_orf2#LIN 2281 ATAGCATCAAAAAGAATAAAATACTTAGGAATAAATTTAACAAAAGAAGT 2330 chr1qtel1M 791758 CCAGAAAC---TACA-TGAACATAATTATGAAATACTATTTATACAAATT 791803 v - i --- - --- i ii i i i v v v L1M4_orf2#LIN 2331 GCA-AGACTTGTACACTGAA---AACTACAAAACATTGTTGAAAGAAATT 2376 chr1qtel1M 791804 AAGTTAAATTTAAGTTACTGGAAA-ATATTAATTGTTCATGG 791844 ivv i ii i v v - i ivvv L1M4_orf2#LIN 2377 AAAGAAGACCTAAATAAATGGAAAGACATCCCATGTTCATGG 2418 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.58 CpG sites = 84, Kimura (unadjusted) = 42.20 Transitions / transversions = 1.45 (84/58) Gap_init rate = 0.06 (27 / 467), avg. gap size = 1.44 (39 / 27) 943 28.57 4.55 4.35 chr1qtel1M 792453 792957 (207043) L1ME5_3end#LINE/L1 145 650 (291) m_b49s551i9 1747 chr1qtel1M 792453 AAATCACTATTGATCAGAGAAATGCAAATTAAGACAACTCTGAGATTCCA 792502 v i v i i vv vi L1ME5_3end#LI 145 AACTCATTAGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCA 194 chr1qtel1M 792503 CCACACACCTCTCGGATTGGCTAAGATGACAGGAAA---AGATAATGATA 792549 ivi v ii i v i v --- ---i vi L1ME5_3end#LI 195 CTTTACACCTATTAGACTGGCAAAAATTA---GAAAGCTGGATAATGCCA 241 chr1qtel1M 792550 AATGTTGGAGGGGATGTGGGAAAATTGGGACACTGATTCATTGTTGATGG 792599 i v i i ? v i v v v i i i L1ME5_3end#LI 242 AGTGTTGGCGAGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGG 291 chr1qtel1M 792600 AGCTGTGAACTGAGTCAACTGATTCTGGAGAGCAGTTTGGAACTA--TGC 792647 iiv ii ivv i i- i i v v -- iv L1ME5_3end#LI 292 GAGTGTAGACTGGTGCAGCC-ATTCTGGAGAGCAATCTGGCAGTACTTAG 340 chr1qtel1M 792648 TCAAA--AAGTTATCAAACTGTGCGTACCCTTTGATTCAGCGGTGTTTCC 792695 -- - --- --- i v ii ii viiv i L1ME5_3end#LI 341 TCAAATTAAG-TAT---AC---GCATACCCTATGACCCAGCAATTCCGCT 383 chr1qtel1M 792696 ACTGAACTTATATCCCAAAGTGATCTTAAAGGAGG---GAAAGGGATCCA 792742 v iiiv vi ii v viv ---iv i--- L1ME5_3end#LI 384 CCTGGGTATATATCCCAAAGAAATTCTCACACAGGTCCATAAGGGG---A 430 chr1qtel1M 792743 CATGTGCAAAAATATTCGTGGCAGCCCTCTTTGTAATGACAAGAAAT--- 792789 i i ii i i v vi v ii i ii i i --- L1ME5_3end#LI 431 CATGTACGAGGATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGG 480 chr1qtel1M 792790 --GGAATCTGAGTGGATTCCCATCACTGGGAGAATAGCTGAATAAGTTGT 792837 -- v i i ----i i i v iii iv L1ME5_3end#LI 481 AGGCAACCTGGGTG----TCCATCACTGGGAGAGTGGATAGGTAAAATGT 526 chr1qtel1M 792838 GGTATATGAATATTATGGAATATTATTGTTCTGTAAGAAACAACCAACAG 792887 iv v i ii i i vvvv v v i vi vi L1ME5_3end#LI 527 GGTGGATGCACACCATGGAGTACTATGCAGCAGTTAGAAGCAACGGACTA 576 chr1qtel1M 792888 GATGATTTCAGAAAG--GCCTGGAGAGA-CTTACAGGAAC-TGATGCTGA 792933 -- v v v --i v vi - v -- - ii L1ME5_3end#LI 577 GATG--TACACATAGCAACATGGATGGATCTTAAA--AACATAGTGCTGA 622 chr1qtel1M 792934 GTGAAACAAGC-AGAACCAG---GAGAT 792957 v i- v --- L1ME5_3end#LI 623 GTGAAAAAAGTAAGAAACAGAATGAGAT 650 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.12 CpG sites = 83, Kimura (unadjusted) = 37.15 Transitions / transversions = 1.51 (83/55) Gap_init rate = 0.07 (33 / 504), avg. gap size = 1.36 (45 / 33) 235 19.35 0.00 5.26 chr1qtel1M 793422 793474 (206526) C DNM1r#Unknown (2132) 2530 2481 m_b49s502i1 1748 chr1qtel1M 793422 TACACATATATGCATGTATATATACATAAACACATGTATATACATAATAC 793471 i iii i i v ii --- i C DNM1r#Unknown 2530 TACACATATATACACACATACACACATATACACACATATATAC---ACAC 2484 chr1qtel1M 793472 ATA 793474 C DNM1r#Unknown 2483 ATA 2481 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 23.94 CpG sites = 9, Kimura (unadjusted) = 23.94 Transitions / transversions = 9.00 (9/1) Gap_init rate = 0.06 (3 / 52), avg. gap size = 1.00 (3 / 3) 35 0.00 0.00 0.00 chr1qtel1M 793475 793504 (206496) (TG)n#Simple_repeat 1 30 (0) c_b49s251i1 1749 chr1qtel1M 793475 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 793504 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 30 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 263 26.97 0.00 1.12 chr1qtel1M 793761 793850 (206150) L1MD_orf2#LINE/L1 3084 3172 (122) m_b49s551i10 1750 chr1qtel1M 793761 GATCAGAAGGAAAGCAGAAAACTAGGAAAAAACTTTTTATAGACTGTTTA 793810 v i iv viv i i i - v ii i iiiv L1MD_orf2#LIN 3084 GATGAAAAGACAAGCTACAGACTGGGAGAAAA-TATTTGCAAACCACATA 3132 chr1qtel1M 793811 TCAGACAAAGGTTTCATATCTCGAATATATAAAGAACTTT 793850 v vi ?i v i L1MD_orf2#LIN 3133 TCCGACAAAGGACTNGTATCTAGAATATATAAAGAACTCT 3172 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.00 CpG sites = 15, Kimura (unadjusted) = 35.00 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.01 (1 / 89), avg. gap size = 1.00 (1 / 1) 238 25.63 0.00 4.65 chr1qtel1M 793775 793864 (206136) L1PREC2_orf2#LINE/L1 3101 3186 (108) m_b49s551i11 1750 chr1qtel1M 793775 CAGAAAACTAGGAAAAAACTTTTTATAGACTGTTTATCAGACAAAGGTTT 793824 --- i i - ? ii i i vi v i L1PREC2_orf2# 3101 CAGAA---TGGGAGAAAA-TNTTTGCAAACTATGCATCTGACAAAGGTCT 3146 chr1qtel1M 793825 CATATCTCGAATATATAAAGAACTTTGTCAGATCTATAAG 793864 v iv v v i viv i i i L1PREC2_orf2# 3147 AATATCCAGCATCTATAAGGAACTTAAACAAATTTACAAG 3186 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 32.76 CpG sites = 14, Kimura (unadjusted) = 32.76 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.04 (4 / 89), avg. gap size = 1.00 (4 / 4) 279 35.46 2.83 1.55 chr1qtel1M 793910 794227 (205773) L1ME4c_3end#LINE/L1 134 455 (375) m_b49s551i13 1746 chr1qtel1M 793910 AAAAATTTTCTAAATCATTATTTATTATAGAAATGCTAATTAAAATATTA 793959 v v vv ii v v i v v ii -- L1ME4c_3end#L 134 AAAAATGTTCAACCTCGCTAGTAATCAAAGAAATGCAAATTAAAGCA--A 181 chr1qtel1M 793960 TGTTGGGATATCATTTTATACCTATCAGATTTGTTTAAA-TGACAGAAGA 794008 iiv i i ii i i v ivv - v v i vv L1ME4c_3end#L 182 CAATGAGATACCATTTTACGCCTATTAAATTAGCAAAAATTTAAAAAATT 231 chr1qtel1M 794009 GGTAAGTGACAAATATCGAAGAGAATGTAGAAAAATTGAGACACTGATTC 794058 i - iv v iii iv i? ii vi i iv ? v v L1ME4c_3end#L 232 GATAA-TACCCAATGCTGGCGAGGNTGCGGTGAAACTGGTACNCTCATAC 280 chr1qtel1M 794059 ACTGTTGATGGATCTGTTAACTGACCCAATCATTTTAGAAAG--ATGTGG 794106 i i i vv? v i iiv i v i -- v L1ME4c_3end#L 281 ATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGG 330 chr1qtel1M 794107 ATTTATGC-TC---AGTTATTAAACTGCCTGTACTTTTTGAACTAGCAAT 794152 vvv i i- --- ii v v iiii ii v i i L1ME4c_3end#L 331 CAATACGTATCAAGAGCCATAAAAATGTTCATACCCTTTGACCCAGTAAT 380 chr1qtel1M 794153 ACTACTATT--AAATCTATTTTCTAAGGGGATTAGGGAAAATGGAAAAGA 794200 v i vi --i i -- i ii v vvv viiii i L1ME4c_3end#L 381 TCCACTTCTGGGAATTTA--TCCTAAGGAAATAATTCAAAAGAAGGAAAA 428 chr1qtel1M 794201 ATCTACCTGTTTGAAGACATTTATAGC 794227 v iv ivi ii i v L1ME4c_3end#L 429 AGCTATATGCACGAAGATGTTCATTGC 455 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 47.35 CpG sites = 65, Kimura (unadjusted) = 50.74 Transitions / transversions = 1.41 (65/46) Gap_init rate = 0.03 (10 / 317), avg. gap size = 1.40 (14 / 10) 379 34.33 2.55 2.18 chr1qtel1M 793910 794183 (205817) L1ME5_3end#LINE/L1 134 408 (533) m_b49s551i12 1746 chr1qtel1M 793910 AAAAATTTTCTAAATCATTATTTATTATAGAAATGCTAATTAAAATATTA 793959 i i vi v v v v i v v i -- L1ME5_3end#LI 134 AGAGATGCTCAAACTCATTAGTAATCAGAGAAATGCAAATTAAAACA--A 181 chr1qtel1M 793960 TGTTGGGATATCATTTTATACCTATCAGATTTGTTTAAATGACAGAAG-- 794007 iiv i i i i i v ivv v v - -- L1ME5_3end#LI 182 CAATGAGATATCACTTTACACCTATTAGACTGGCAAAAATTAGA-AAGCT 230 chr1qtel1M 794008 AGGTAAGTGACAAATATCGAAGAGAATGTAGAAAAATTGAGACACTGATT 794057 i i - v i i i iv i i ii ? v ii v v v L1ME5_3end#LI 231 GGATAA-TGCCAAGTGTTGGCGAGGATGTGGGGANATAGGAACCCTCATG 279 chr1qtel1M 794058 CACTGTTGATGGATCTGTTAACTGACCCAATCATTTTAGAAAG--ATGTG 794105 i i ivv vi iiv ii i i i -- v L1ME5_3end#LI 280 CACTGCTGGTGGGAGTGTAGACTGGTGCAGCCATTCTGGAGAGCAATCTG 329 chr1qtel1M 794106 GATTTATGCTCAGTT--ATTAAAC-TGCCTGTACTTTTTGAACTAGCAAT 794152 --ivi i i i-- ii- i vii ii v v i L1ME5_3end#LI 330 G--CAGTACTTAGTCAAATTAAGTATACGCATACCCTATGACCCAGCAAT 377 chr1qtel1M 794153 ACTACTATTAAATCTATTTTCTAAGGGGATT 794183 v ii vi iii v v i i i ii L1ME5_3end#LI 378 TCCGCTCCTGGGTATATATCCCAAAGAAATT 408 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 48.10 CpG sites = 60, Kimura (unadjusted) = 48.97 Transitions / transversions = 1.88 (60/32) Gap_init rate = 0.04 (10 / 273), avg. gap size = 1.30 (13 / 10) 18 19.16 0.00 4.44 chr1qtel1M 794283 794317 (205683) (AT)n#Simple_repeat 1 33 (12) m_b49s252i8 1751 chr1qtel1M 794283 ATATATATGTATGAGTGTGTGTATATATATATATA 794317 i - - i i i (AT)n#Simple_ 1 ATATATATATAT-A-TATATATATATATATATATA 33 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 43 0.00 0.00 0.00 chr1qtel1M 794318 794354 (205646) (TG)n#Simple_repeat 1 37 (0) c_b49s251i2 1752 chr1qtel1M 794318 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 794354 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 37 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 18 19.16 0.00 4.44 chr1qtel1M 794355 794365 (205635) (AT)n#Simple_repeat 34 44 (1) m_b49s252i8 1753 chr1qtel1M 794355 ATGTTTATTTA 794365 i v v (AT)n#Simple_ 34 ATATATATATA 44 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 10), avg. gap size = 0.0 (0 / 0) 25 19.81 0.00 6.76 chr1qtel1M 794413 794491 (205509) (AACAA)n#Simple_repeat 1 74 (0) m_b49s252i9 1754 chr1qtel1M 794413 AAAAAAATAAAGTAAAAAAAATACACAGCAGAGAACAAAAGAAAATCAAA 794462 v i ii v - v i - - v - (AACAA)n#Simp 1 AACAAAACAAAACAAAACAAA-ACAAAACA-A-AACAAAACAAAA-CAAA 46 chr1qtel1M 794463 AAAGAAGCAGGACAAAACAAAACAAAACA 794491 v - i ii (AACAA)n#Simp 47 ACA-AAACAAAACAAAACAAAACAAAACA 74 Matrix = Unknown Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.06 (5 / 78), avg. gap size = 1.00 (5 / 5) 213 34.23 8.33 2.63 chr1qtel1M 794623 794730 (205270) C L2d2_3end#LINE/L2 (5) 550 437 m_b49s601i9 1755 chr1qtel1M 794623 TTAAAATAAAAAATAT-----AAGAACTCAATAAGTATCAAACATTGTGT 794667 i vi v -----i vi ii v iv iiv ii i i C L2d2_3end#LIN 550 TCAAATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGC 501 chr1qtel1M 794668 TAATTGCTGGGAGTATAAATACAAGGAG--ACAAGACA--GTCCTTATCC 794713 ivi v i ---ii i i-- i -- i ii C L2d2_3end#LIN 500 TAGGCGCTGTGGG---GGATACAAAGAAGTATAAGACATGGTCCCTGCCC 454 chr1qtel1M 794714 TCAAAGTGCTTATATTC 794730 i v i v C L2d2_3end#LIN 453 TCAAGGAGCTTACAATC 437 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.90 CpG sites = 26, Kimura (unadjusted) = 49.92 Transitions / transversions = 2.60 (26/10) Gap_init rate = 0.06 (6 / 107), avg. gap size = 2.00 (12 / 6) 231 34.04 5.38 2.08 chr1qtel1M 794638 794730 (205270) C L2a_3end#LINE/L2 (25) 492 397 m_b49s601i10 1755 chr1qtel1M 794638 TAAGAACTCAATAAGTATCAAACATTGTGTTAATTGCTGGGAGTATA--A 794685 i vi ii v v ii ii i vi ivi ii i -- C L2a_3end#LINE 492 TGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGCGCTGGGGATACAGCA 443 chr1qtel1M 794686 AT--ACAAGG-AGACAAGACAGTCCTTATCCTCAAAGTGCTTATATTC 794730 i -- ii- i-- i ii vi v i C L2a_3end#LINE 442 GTGAACAAAACAGACAAA--AGTCCCTGCCCTCATGGAGCTTACATTC 397 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.78 CpG sites = 24, Kimura (unadjusted) = 50.54 Transitions / transversions = 3.43 (24/7) Gap_init rate = 0.05 (5 / 92), avg. gap size = 1.40 (7 / 5) 222 27.28 1.49 1.49 chr1qtel1M 794922 794988 (205012) C L3#LINE/CR1 (2667) 1432 1366 m_b49s601i11 1756 chr1qtel1M 794922 TTTGTTCCTTATGAATAAAGTATGCT-TTCCAAAAATATATTCCAACCCA 794970 i i v i i ? i i- vvivii ii - C L3#LINE/CR1 1432 TCTGTTTCTTTTGAACAAGGTNTACCCTTCCATCGCCGTATTCCAGTC-A 1384 chr1qtel1M 794971 TGAGCCAGATCCCACCAA 794988 i vv C L3#LINE/CR1 1383 TGAGTCCCATCCCACCAA 1366 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.90 CpG sites = 12, Kimura (unadjusted) = 36.05 Transitions / transversions = 2.00 (12/6) Gap_init rate = 0.03 (2 / 66), avg. gap size = 1.00 (2 / 2) 308 34.51 0.00 0.00 chr1qtel1M 795012 795153 (204847) C CR1-3_Croc#LINE/CR1 (898) 2707 2566 m_b49s551i14 1757 chr1qtel1M 795012 CCCAACTCCTTTAATCAATCCCCATATGAAATAAACTCAATGCCCTTCCT 795061 i i i ii vv i i vv ivvi v v iv C CR1-3_Croc#LI 2707 CCTAGCTCCTTCAGCCTCTCCTCGTATGACTTGCCTTCCAAGCCCTTTAT 2658 chr1qtel1M 795062 CTTCTTGTTCGACTTTCTCTGGATACTCTCTAGATTATCAAAATCCCTCT 795111 v vv i v ivi iv iv v v vi i i C CR1-3_Croc#LI 2657 CATCTTTGTTGCCCGCCTCTGGACCCTCTCTAACTTCTCCACGTCCTTTT 2608 chr1qtel1M 795112 TAAACTGTGGAATCCAGAACTGTATAAAATATTCTCAATAAG 795153 v ii i i v i i ivi i C CR1-3_Croc#LI 2607 TAAAATGTGGAGCCCAGAACTGCACACAGTACTCCAGATGAG 2566 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 43.65 CpG sites = 27, Kimura (unadjusted) = 47.58 Transitions / transversions = 1.23 (27/22) Gap_init rate = 0.00 (0 / 141), avg. gap size = 0.0 (0 / 0) 273 35.25 8.95 5.07 chr1qtel1M 795367 795880 (204120) C L2#LINE/L2 (1559) 1523 991 m_b49s601i12 1755 chr1qtel1M 795367 TGTTCTTAATTTTTCTATAAAATGGGAGACAAATTTCTCAGCTGAGAGTG 795416 i ii v i vi i i ii iv iv C L2#LINE/L2 1523 TGCTTCTATTTTCTCAGTGAAATAGGAAGCAAGGTCATCAGCTGAGAGTG 1474 chr1qtel1M 795417 GATAGAATCAGAAGGAGAAGAGCAGAGAATTTGAAGAGGGATGAAAAACT 795466 --- i - ii ii i v iv iiii i i v i iv C L2#LINE/L2 1473 ---AGGAT-AGGGGAGGAGGTGTTGGAGGTTTGAGGAGAGAGGAGAAGGT 1428 chr1qtel1M 795467 TTGGGAGA-TCCTCTGTGAAGAATGGGATAGTG-ATG----AGGGAGACA 795510 v ii v - v i- i i v - ---- i ii C L2#LINE/L2 1427 GTGAAATAGTCGTCTA-GGAGAGTGGGAGAGTGAATGGACTAGGGAAATG 1379 chr1qtel1M 795511 TACTAGGAT----------------GGGCCCTGTTAAGTCTATGTAG-CA 795543 v ? ---------------- vv i vi -? i - C L2#LINE/L2 1378 TAGTANGATTGCCGGGCAGCATTAAGGGCCCACTTGAGGTT-NGTGGTCA 1330 chr1qtel1M 795544 TAAATTTGTACTTGATTTAGTTAGAACAGTTGCAAAATTTTCTCCACTTT 795593 i iv v viivii i v ii iiviv viiv C L2#LINE/L2 1329 TGAATTTAAAGTGAGACCAGTCAGCATGGTTGTGTGTTTTTCTCCAGCCA 1280 chr1qtel1M 795594 TGTTCAACT-CATCTGTGGAGGCACAAAGGTGATGAATAAGGAGAGT--G 795640 i i - ?ivv v i ii vv ii------ -- C L2#LINE/L2 1279 CGTTCAGCTGCNCGGGTGCAGGCGCGGAGTAGGC------GGAGAGTTGG 1236 chr1qtel1M 795641 ATCCATTGAGTATTAACTGGGTTTAATGGGTGA-TATGAAAAGGTTCCTA 795689 ii viv vi i--? v ivii i - i vi i --- v C L2#LINE/L2 1235 ATTTAACCAGGGTTG--NGGTTTTGCCAGGCGAGTACGACGAAG---CGA 1191 chr1qtel1M 795690 GGTA--TTCAAGAGAG--GAGGGCAGTATAGAGCTAAGT--------TGC 795727 iv --vv i -- i - iv ivvi -------- v C L2#LINE/L2 1190 GAGAGGGGCAAGGGAGTTGAGGGTA-TATGCAAGGGAGTGATTATAATGA 1142 chr1qtel1M 795728 TTCACCAAGGAGTC-AAGATGGG-GAGAAAGAGAGAGAGAGAGTGAATGG 795775 ?v v i - v -i i i ii v iivi iv C L2#LINE/L2 1141 TNGACCATGGAATCTAAGCTGGGTAAGGAGGGAAGTGAGGACATGAGGGG 1092 chr1qtel1M 795776 TGCAATAAAGA-TGATCTGGGAGATAATTGAGAGGTAAGAGATTGAAGGT 795824 v ii vii v - ----ii i ii -- iivi vi i C L2#LINE/L2 1091 GGTGAGGGACAGTGA----AAAGGTGGT--AGGATCAATGGATTGGAGGT 1048 chr1qtel1M 795825 CATGGTGTGAATGAAAAGTAAGTTATGGAAGAAGAG-AC-AGAGGGA--G 795870 vi v ivi i i -v -- ivvi i - - -- C L2#LINE/L2 1047 CCCGGTGGGGTCGAAGAAT-TGT--TGGAGTCGGGGTACTAGAGGGAGTG 1001 chr1qtel1M 795871 AGATGAAAAG 795880 v i C L2#LINE/L2 1000 AGCTGGAAAG 991 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 46.70 CpG sites = 110, Kimura (unadjusted) = 51.42 Transitions / transversions = 1.77 (110/62) Gap_init rate = 0.09 (44 / 513), avg. gap size = 1.66 (73 / 44) 203 31.58 9.14 4.64 chr1qtel1M 795988 796173 (203827) L2c_3end#LINE/L2 273 466 (12) m_b49s601i13 1758 chr1qtel1M 795988 CCTTCTTCT---CTTTCATAGTAGAAGTGTCTTTCCTCC--TGATA---- 796028 i i --- ii i vvv- v v -- v ---- L2c_3end#LINE 273 CCCTCCTCTGTGCTCCCATAGCACCC-TGTCTATACTCCCATTATAGCAC 321 chr1qtel1M 796029 --ATCTCCAACTGGTCCTGT--CTGT-TGTTTGCC-ACTGGTCTTCCCCT 796072 -- vii v vi --i - i ?-iiiv i i v L2c_3end#LINE 322 TTATCATTAACTTGTATTGTAATTGTCTGTTTACNTGTCTGTCTCCTCCA 371 chr1qtel1M 796073 TTAGACCATCAGTTCCCAGTGAG-AAGGATTGGGCATTTTGTGCCTTTTT 796121 i ii v i iv v i - i ii v -- i i v v i L2c_3end#LINE 372 CTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTG--TCTTATTCATCTTT 419 chr1qtel1M 796122 CGTATTCTCAATCCCAATGATGGAAGATAGTAGGTGCTTAA-AAATACTT 796170 - i i iiv ----- v v i i - ii L2c_3end#LINE 420 -GTATCCCCAGCGCC-----TGGCACATAGTAGGCGCTCAATAAATGTTT 463 chr1qtel1M 796171 CTT 796173 v L2c_3end#LINE 464 GTT 466 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.13 CpG sites = 35, Kimura (unadjusted) = 43.21 Transitions / transversions = 1.67 (35/21) Gap_init rate = 0.10 (18 / 185), avg. gap size = 1.44 (26 / 18) 181 30.43 8.07 6.10 chr1qtel1M 796030 796190 (203810) L2d_3end#LINE/L2 353 516 (0) m_b49s601i14 1758 chr1qtel1M 796030 TCTCCAACTGGTCC-TGTCTGTTGTTTGCCACTGGTCTTCCCCTTTAGAC 796078 i i v i - v iv ----- v i vvi i L2d_3end#LINE 353 TCTCTAATTGTTTCATGTGTGTTAGT-----CTTGTCTCCCCAACTAGAT 397 chr1qtel1M 796079 CATCAGTTCCCAGTGAG-AAGGATTGGGCATTTTGTGCCTTTTTCGTATT 796127 ii v i iv v i - i iiiv -- i i i i? ?vii L2d_3end#LINE 398 TGTAAGCTCCTTGAGGGCAGGGACCATG--TCTTATACTNTTTTNTCGTT 445 chr1qtel1M 796128 CTCAAT----CC-----CAATGATG-GAAGATAGTAGGTGCTTAA-AAAT 796166 i v i---- ----- i v - v v i i - L2d_3end#LINE 446 CCCCACAGCGCCTAGCACAGTGCTGAGCACATAGTAGGCGCTCAATAAAT 495 chr1qtel1M 796167 ACTTCTTTAGTATTGTCTTATTGA 796190 v -- - vi v L2d_3end#LINE 496 ACTTGTT--G-ATTGATTGATTGA 516 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.77 CpG sites = 28, Kimura (unadjusted) = 41.24 Transitions / transversions = 1.56 (28/18) Gap_init rate = 0.10 (16 / 160), avg. gap size = 1.44 (23 / 16) 218 33.33 8.33 0.00 chr1qtel1M 796268 796363 (203637) C MIRb#SINE/MIR (51) 217 114 m_b49s601i15 1759 chr1qtel1M 796268 TAGACCTTTTACATACATTTTTTAATTTG---CTCTTAACAATTGGATAA 796314 ii vi i v i v i--- vi iivviii C MIRb#SINE/MIR 217 TAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGA 168 chr1qtel1M 796315 GTTAG---CCATGACCTCAATTTTCCAG--GAGAAAACATAGACTCAGAG 796359 v ---ii v i i v v -- i vv i C MIRb#SINE/MIR 167 GGTAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAG 118 chr1qtel1M 796360 GAGT 796363 ii C MIRb#SINE/MIR 117 AGGT 114 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.98 CpG sites = 20, Kimura (unadjusted) = 46.20 Transitions / transversions = 1.67 (20/12) Gap_init rate = 0.03 (3 / 95), avg. gap size = 2.67 (8 / 3) 262 27.84 3.75 1.22 chr1qtel1M 796371 796450 (203550) C L3#LINE/CR1 (2667) 1432 1351 m_b49s601i16 1760 chr1qtel1M 796371 TTTGTTCCTTGTGAATAAAGTAT-CCCTTCCAAAAATATATTCCAACCCA 796419 i i v i i ? - vvivii ii - C L3#LINE/CR1 1432 TCTGTTTCTTTTGAACAAGGTNTACCCTTCCATCGCCGTATTCCAGTC-A 1384 chr1qtel1M 796420 TAAGCCAGATCCCACCAAG--GTGATGATGTCT 796450 i i vv --vi i ii C L3#LINE/CR1 1383 TGAGTCCCATCCCACCAAGTCTCGGTGATACCT 1351 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.70 CpG sites = 15, Kimura (unadjusted) = 37.10 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.04 (3 / 79), avg. gap size = 1.33 (4 / 3) 447 22.64 1.67 4.27 chr1qtel1M 796599 796718 (203282) MIR#SINE/MIR 6 122 (140) m_b49s601i17 1761 chr1qtel1M 796599 ATGGGATAGTAGATAA-AGTACTGGCTCTTGAGTCAGGAAGACCTGATTT 796647 i v i v - i v v i - vvi iv MIR#SINE/MIR 6 ATAGCATAGTGGTTAAGAGCACGGGCTCTGGAGCCAG-ACTGCCTGGGTT 54 chr1qtel1M 796648 CAAATCTCATCTCAGACACTTAACACTAGCTGTGTGACCCT-GGCAAGTC 796696 i i iv v v --- i - i MIR#SINE/MIR 55 CGAATCCCGGCTCTGCCACTTA---CTAGCTGTGTGACCTTGGGCAAGTT 101 chr1qtel1M 796697 ACTTAATCTCAACTGCCTCTCA 796718 i -v ivi MIR#SINE/MIR 102 ACTTAACCTC-TCTGTGCCTCA 122 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.88 CpG sites = 14, Kimura (unadjusted) = 27.22 Transitions / transversions = 1.17 (14/12) Gap_init rate = 0.06 (7 / 119), avg. gap size = 1.00 (7 / 7) 411 26.87 7.95 2.70 chr1qtel1M 796600 796775 (203225) MIR1_Amn#SINE/MIR 14 198 (32) m_b49s601i19 1761 chr1qtel1M 796600 TGGGATAGTAGATAAAGTACTGGCTCTTGAGTCAGGAAGACCTGATTTCA 796649 vv i i i viivv v i - iv ? MIR1_Amn#SINE 14 TGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGA-GACCTGGGTTCN 62 chr1qtel1M 796650 AATCTCATCTCAGACACTTAACACTAGCTGTGTGACCCT-GGCAAGTCAC 796698 ? i iv v v ---?i i? ? i - MIR1_Amn#SINE 63 ANTCCCGGCTCTGCCACT---NGCCNGCTGNGTGACCTTGGGCAAGTCAC 109 chr1qtel1M 796699 TTAATCTCAACTGCCTCTCAAAAACCCC------AAAGCAG----AATGA 796738 ? i -v ?vi ivvv i ------ iii ---- MIR1_Amn#SINE 110 TTNACCTC-TCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATGA 158 chr1qtel1M 796739 TAGCTAC--CATTTACATAATACTTAAAGATCTA-TAATG 796775 viv -- v ii v i i vi - i MIR1_Amn#SINE 159 TACTGACCTCCTTTGTAAAGTGCTTTGAGATCTACTGATG 198 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.97 CpG sites = 26, Kimura (unadjusted) = 35.89 Transitions / transversions = 1.30 (26/20) Gap_init rate = 0.06 (10 / 175), avg. gap size = 1.90 (19 / 10) 529 21.17 0.93 2.86 chr1qtel1M 796600 796706 (203294) MIRc#SINE/MIR 11 115 (153) m_b49s601i18 1761 chr1qtel1M 796600 TGGGATAGTAGATAAAGTACTGGCTCTTGAGTCAGGAAGACCTGATTTCA 796649 vii i v i i vii v iv i MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr1qtel1M 796650 AATCTCATCTCAGACACTTAACACTAGCTGTGTGACCCT-GGCAAGTCAC 796698 i i iv v v --- i - MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTT---ACTAGCTGTGTGACCTTGGGCAAGTCAC 107 chr1qtel1M 796699 TTAATCTC 796706 i MIRc#SINE/MIR 108 TTAACCTC 115 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 22.84 CpG sites = 14, Kimura (unadjusted) = 25.42 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.04 (4 / 106), avg. gap size = 1.00 (4 / 4) 654 29.01 6.79 1.72 chr1qtel1M 796734 796954 (203046) C MIRc#SINE/MIR (3) 265 34 m_b49s601i20 1762 chr1qtel1M 796734 AATGATAGCTAC---CATTTACATAATACTTAAAGATCTATAATGCTCTT 796780 i i ?v --- ii ii v vii i i v v C MIRc#SINE/MIR 265 AATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCGCTT 216 chr1qtel1M 796781 TTACA--CATGATTTTATTTGATCCTCAAAATGACCCATTAAGGTAGAT- 796827 i -- v i i v ii vv i ii- C MIRc#SINE/MIR 215 TCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCA 166 chr1qtel1M 796828 --GC------TATTATCTTAATTTTAGAGAAAAGGAAGCTAAGACTGAGA 796869 -- ------ iiv v vi i i i v C MIRc#SINE/MIR 165 GGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGA 116 chr1qtel1M 796870 GAGGTTAAAGAAGTTTCTAAAAATCACAAAGCTGGCTTTTAAATGTCTGA 796919 ivi v v iv ii v i ---- i v v C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG----TAAGTGGCAGA 70 chr1qtel1M 796920 GATAAGGTTTAAACTAAGGTCTT-CTGGCTCCAAAT 796954 viii ii ii iv - i i C MIRc#SINE/MIR 69 GCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGT 34 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.78 CpG sites = 41, Kimura (unadjusted) = 38.53 Transitions / transversions = 1.86 (41/22) Gap_init rate = 0.05 (10 / 220), avg. gap size = 1.90 (19 / 10) 332 33.58 3.88 0.75 chr1qtel1M 798280 798408 (201592) MIRc#SINE/MIR 21 153 (115) m_b49s601i21 1763 chr1qtel1M 798280 GATAGAGTACTAGAATTGGGAACAG-ATCCCTTGAACTTGAGTGATTTAT 798328 v i i v iiv - vvv i iii i vvivvv MIRc#SINE/MIR 21 GAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCT 70 chr1qtel1M 798329 CTGATGTTTACTA----TGCAATTTGTAGGTAAGTTGCTTTATCTCTAAG 798374 viii ---- ii ii - i i ii v i vv MIRc#SINE/MIR 71 CTGCCACTTACTAGCTGTGTGACCT-TGGGCAAGTCACTTAACCTCTCTG 119 chr1qtel1M 798375 GGCCTCAGTCTCCTTATCTTTAAAATGGTGATGA 798408 i i i v v i MIRc#SINE/MIR 120 AGCCTCAGTTTCCTCATCTGTAAAATGGGGATAA 153 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.48 CpG sites = 26, Kimura (unadjusted) = 46.44 Transitions / transversions = 1.53 (26/17) Gap_init rate = 0.02 (3 / 128), avg. gap size = 2.00 (6 / 3) 490 17.90 2.90 10.94 chr1qtel1M 798407 798544 (201456) MIRb#SINE/MIR 3 130 (138) m_b49s601i22 1764 chr1qtel1M 798407 GAGGGACAGCTAGGTGGTACAATGGATAGAGCACCAGCCT-GAAGTCAGG 798455 i --- i i v vi i - i - MIRb#SINE/MIR 3 GAGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAG- 48 chr1qtel1M 798456 AGGAC-GACCTGAGTTCAAATCTGGTCTCAGACCCTTAACACTTCCTAAC 798504 --- - i i iv v ------- iv v i MIRb#SINE/MIR 49 ---ACAGACCTGGGTTCGAATCCCGGCTC-------TGCCACTTACTAGC 88 chr1qtel1M 798505 TGTGTGACCCTGGGCAAG-TACTTAACCCCAATT-GCCTCAG 798544 i - i vv v- MIRb#SINE/MIR 89 TGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAG 130 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 19.50 CpG sites = 13, Kimura (unadjusted) = 20.50 Transitions / transversions = 1.44 (13/9) Gap_init rate = 0.13 (18 / 137), avg. gap size = 1.00 (18 / 18) 468 30.13 6.00 7.07 chr1qtel1M 798420 798619 (201381) MIR3#SINE/MIR 9 206 (2) m_b49s601i23 1764 chr1qtel1M 798420 GTGGTACAATGGATAGAGCACCAGCCTGAAGTCAGGAGGACGACCTGAGT 798469 ivv iii v vii iv i ---- i MIR3#SINE/MIR 9 GTGGCTGAGCAGAGAGAGCACGGACTGGGAGTCAGGAG----ACCTGGGT 54 chr1qtel1M 798470 TCAAATCTGGTCTCAGACCCTTAACACTTCCTAACTGTGTGACCCTGGGC 798519 ----- i i i -- ii iv vv ?i i MIR3#SINE/MIR 55 TC-----TAGTCCCGG--CTCTGCCACTAACTNGCTGTGTGACCTTGGGC 97 chr1qtel1M 798520 AAGT-ACTTAACCCC----------AATTGCCTCAGGAAAAAAAAAAAGT 798558 - v i ---------- i v vvviv vi i v MIR3#SINE/MIR 98 AAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGG 147 chr1qtel1M 798559 GATTAGAATGTTAGACCGCTTCTAAGGTCTTTTCCCATTTTAAC-CCCAA 798607 i i ---i iviii ii vii i i -ii v MIR3#SINE/MIR 148 GGTTGGA---CTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTA 194 chr1qtel1M 798608 TGATTCTATGAT 798619 MIR3#SINE/MIR 195 TGATTCTATGAT 206 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.71 CpG sites = 37, Kimura (unadjusted) = 40.68 Transitions / transversions = 1.95 (37/19) Gap_init rate = 0.09 (17 / 199), avg. gap size = 1.53 (26 / 17) 32 30.07 3.36 2.67 chr1qtel1M 800021 800169 (199831) (TC)n#Simple_repeat 1 150 (0) m_b49s252i10 1765 chr1qtel1M 800021 TCTCTCTGTTTCTCTTTGTCGC-CTCCATGTTTGTACTCATGTCTCTTTG 800069 v i i v v - iv v i v - - v i - (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT-CTC-TCTCTCTCT- 47 chr1qtel1M 800070 GTTTCTATTTGTTTCTCTGTTTGTATCTCTCTCTCTCTCTTTATCT-TTT 800118 v i v i v i v i v v i v - i (TC)n#Simple_ 48 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 97 chr1qtel1M 800119 CTCCCTAGCTCTCTCTCTTTTTC-CTGTATTTCTCTC-CTGTACT-TCTC 800165 i vv i i - v v i - v - - (TC)n#Simple_ 98 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT-CTCTCTC 146 chr1qtel1M 800166 TTTC 800169 i (TC)n#Simple_ 147 TCTC 150 Matrix = Unknown Transitions / transversions = 0.84 (16/19) Gap_init rate = 0.06 (9 / 148), avg. gap size = 1.00 (9 / 9) 37 2.86 0.00 0.00 chr1qtel1M 800792 800827 (199173) (AC)n#Simple_repeat 1 36 (0) c_b49s251i3 1766 chr1qtel1M 800792 ACACACACACACACACACACACACATACACACACAC 800827 i (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACAC 36 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 292 29.64 2.68 3.60 chr1qtel1M 801021 801132 (198868) C MIR#SINE/MIR (33) 229 119 m_b49s601i24 1767 chr1qtel1M 801021 GTGCC---TACTGTTCTTCTTAAGTGAATTATAGTTGTTATTGAAATTGA 801067 ---i ---- i vv i vv i vivv v i C MIR#SINE/MIR 229 GTGCCAGGCACTGTTCT----AAGCGCTTTACATGTATTAACTCATTTAA 184 chr1qtel1M 801068 TCCATATAACTGCCCTCCCATAGAAGTGCTATTTTTATACCCATTTTGCA 801117 vi i vi viv viv i i v v i C MIR#SINE/MIR 183 TCCTCACAACAACCCTATGAGGTAGGTACTATTATTATCCCCATTTTACA 134 chr1qtel1M 801118 GATGAGAAAACAGAG 801132 i v C MIR#SINE/MIR 133 GATGAGGAAACTGAG 119 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.56 CpG sites = 15, Kimura (unadjusted) = 38.01 Transitions / transversions = 0.88 (15/17) Gap_init rate = 0.05 (5 / 111), avg. gap size = 1.40 (7 / 5) 244 21.02 7.59 3.66 chr1qtel1M 801064 801142 (198858) C MIRc#SINE/MIR (71) 197 116 m_b49s601i25 1767 chr1qtel1M 801064 TTGATCCATATAACTGCCCTCCCA--TAGA-AGTGC---TATTTTTATAC 801107 vi i vi viv -- i- v --- v v C MIRc#SINE/MIR 197 TTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCC 148 chr1qtel1M 801108 CCATTTTGCAGATGAGAAAACAGAGAAAGGTCAGA 801142 i i v --- v C MIRc#SINE/MIR 147 CCATTTTACAGATGAGGAAACTGAG---GCTCAGA 116 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.78 CpG sites = 7, Kimura (unadjusted) = 24.78 Transitions / transversions = 0.78 (7/9) Gap_init rate = 0.08 (6 / 78), avg. gap size = 1.50 (9 / 6) 14 8.51 0.00 3.85 chr1qtel1M 801268 801294 (198706) (AAC)n#Simple_repeat 1 26 (0) m_b49s252i11 1768 chr1qtel1M 801268 AACAACAACAACAACAAAAAGAGACAA 801294 v v - (AAC)n#Simple 1 AACAACAACAACAACAACAACA-ACAA 26 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.04 (1 / 26), avg. gap size = 1.00 (1 / 1) 535 20.92 0.74 7.94 chr1qtel1M 802552 802686 (197314) C MIRc#SINE/MIR (141) 127 2 m_b49s601i26 1767 chr1qtel1M 802552 CTGAGGC-CATTGGAGTTAAGTGACTTGCCCAGGATCACACAGCCAGGAC 802600 - vv ii i i i --- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG--- 81 chr1qtel1M 802601 ATATTAAGTGTCTGAGGTCACATTTGAACTCAGGTCCTCCTGACTTCAGG 802650 ---- v v viviv i i i i i i C MIRc#SINE/MIR 80 ----TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr1qtel1M 802651 GCTGGTGCTCTATCCACTGCACCACCTCGCTGCCCC 802686 v ii v --- i i C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTGCACCA---CACTGCCTC 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 22.82 CpG sites = 17, Kimura (unadjusted) = 24.97 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.08 (11 / 134), avg. gap size = 1.00 (11 / 11) 20 23.33 0.00 0.00 chr1qtel1M 803440 803484 (196516) (AC)n#Simple_repeat 1 45 (0) m_b49s252i12 1769 chr1qtel1M 803440 ACACACAAATACACACACACAGTCACACATAAACACAATCTCACA 803484 v i vv i v vv v (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACA 45 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 662 22.74 0.63 2.58 chr1qtel1M 803587 803744 (196256) C MIR#SINE/MIR (21) 241 87 m_b49s601i27 1770 chr1qtel1M 803587 AGTGCCTACCGAGTGCCACGTACTACCTGTCAAGCA-TTTACAGTTATTA 803635 i i iiv v i i-- vii i- vv C MIR#SINE/MIR 241 AGCGCTTACTATGTGCCAGGCACTG--TTCTAAGCGCTTTACATGTATTA 194 chr1qtel1M 803636 TCTCATTCGATCCTTACAACTGCCCTGCCAGAGAGGTGCTATTATTATTC 803685 v ii i vi iiv iv i i C MIR#SINE/MIR 193 ACTCATTTAATCCTCACAACAACCCTATGAGGTAGGTACTATTATTATCC 144 chr1qtel1M 803686 TCATTTTTACATATGAGGAAACTGATGCAGGCAGAGGTTTAAGTGACTTG 803735 i - v v viv - i C MIR#SINE/MIR 143 CCA-TTTTACAGATGAGGAAACTGAGGCACAGAGAGG-TTAAGTAACTTG 96 chr1qtel1M 803736 CCCAGGGTC 803744 i C MIR#SINE/MIR 95 CCCAAGGTC 87 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.91 CpG sites = 22, Kimura (unadjusted) = 27.74 Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.03 (5 / 157), avg. gap size = 1.00 (5 / 5) 449 25.09 1.61 6.78 chr1qtel1M 803940 804063 (195937) C MIRc#SINE/MIR (140) 128 11 m_b49s601i28 1771 chr1qtel1M 803940 ACTGAGGC-AATTGGGGTTCAGTGACTTTCCTAGGATCACACAGCTAGAA 803988 -v vv i v v i i i v C MIRc#SINE/MIR 128 ACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTA 79 chr1qtel1M 803989 AGTGTTTTAATATGTGAGGCCGGATTTGAATTCAGATCCTCTTGATATCA 804038 -----ii --- v v i i ii i i i ivi C MIRc#SINE/MIR 78 AGTG-----GCA---GAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCA 37 chr1qtel1M 804039 GG-CTAATGCTCTATCCACTACACCA 804063 i - i i v i C MIRc#SINE/MIR 36 AGTCCAGTGCTCTTTCCACTGCACCA 11 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.13 CpG sites = 19, Kimura (unadjusted) = 31.44 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.08 (10 / 123), avg. gap size = 1.00 (10 / 10) 230 29.75 22.99 3.38 chr1qtel1M 804429 804602 (195398) MIRb#SINE/MIR 1 207 (61) m_b49s601i29 1772 chr1qtel1M 804429 CAAAGGTACAACAGTGGT----TGGAAGGA---CAGG-TCTCAAGTCAAA 804470 i vi i - ---- i --- i - i vi i MIRb#SINE/MIR 1 CAGAGGGGCAGC-GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGA 49 chr1qtel1M 804471 AAAAC--GTACTTAAATCTGGTTTCAGATGCTTACTGGCTGT----CC-- 804512 v i -- vii ii iv vi v vii i ---- -- MIRb#SINE/MIR 50 CAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTT 99 chr1qtel1M 804513 ------GTT------CCCCTCT---------TTTTTCCATTTTTGAAATG 804541 ------ ------ i --------- iii i v i MIRb#SINE/MIR 100 GGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATG 149 chr1qtel1M 804542 GGAATAATAATAGTAGGATATATCTCCTGAGGTTGTCATGAAGAT---AT 804588 i ------ iv i viii ii i --- MIRb#SINE/MIR 150 GGGATAATAAT------ACCTACCTCGCAGGGTTGTTGTGAGGATTAAAT 193 chr1qtel1M 804589 AATATATTATATAT 804602 i v v ii i MIRb#SINE/MIR 194 GAGATAATGCATGT 207 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.71 CpG sites = 37, Kimura (unadjusted) = 41.03 Transitions / transversions = 2.85 (37/13) Gap_init rate = 0.10 (17 / 173), avg. gap size = 2.76 (47 / 17) 248 29.38 1.04 4.30 chr1qtel1M 804507 804602 (195398) MIR#SINE/MIR 109 201 (61) m_b49s601i30 1772 chr1qtel1M 804507 CTGTCCGTTCCCCTCTTTTTTCCATTTTTGAAATGGGAATAATAATAGTA 804556 v i v i vv ii - i v i i - MIR#SINE/MIR 109 CTCTCTGTGCCTCAGTTTCCTC-ATCTGTAAAATGGGGATAATAATAGT- 156 chr1qtel1M 804557 GGATATATCTCCTGAGGTTGTCATGAAGATATAATATATT-ATATAT 804602 -- iv i v ii ii i vv ivi - i MIR#SINE/MIR 157 --ACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATACAT 201 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.66 CpG sites = 17, Kimura (unadjusted) = 38.66 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.05 (5 / 95), avg. gap size = 1.00 (5 / 5) 24 19.82 6.67 2.13 chr1qtel1M 804611 804700 (195300) (TATATTA)n#Simple_repeat 1 94 (0) m_b49s252i13 1773 chr1qtel1M 804611 TATAGTAATATATTATACATTACATA-T-TATATTACATGCTGTATATAA 804658 - v i i - - i ii i v (TATATTA)n#Si 1 TATA-TTATATATTATATATTATATATTATATATTATATATTATATATTA 49 chr1qtel1M 804659 TGTAATATA-ATCTATATAATA-ATA-GATA-ATAATAAATTAAAT 804700 i v - - v - -v - v v v (TATATTA)n#Si 50 TATATTATATAT-TATATATTATATATTATATATTATATATTATAT 94 Matrix = Unknown Transitions / transversions = 0.88 (7/8) Gap_init rate = 0.09 (8 / 89), avg. gap size = 1.00 (8 / 8) 28 17.78 5.26 6.19 chr1qtel1M 804612 804725 (195275) (ATATA)n#Simple_repeat 1 113 (0) m_b49s252i14 1773 chr1qtel1M 804612 ATAGTAATATATTATACAT-TACATATTATATTACATGCTGT-ATATAAT 804659 - v - - - v v i iv i - (ATATA)n#Simp 1 ATA-TAATATAATATA-ATATA-ATATAATATAATATAATATAATATAAT 47 chr1qtel1M 804660 GTAATATAATCT-ATATAATAATAGATAATAATA-AAT-TAA-ATTAAAT 804705 i v - - - - - - - v v (ATATA)n#Simp 48 ATAATATAATATAATATAAT-ATA-AT-ATAATATAATATAATATAATAT 94 chr1qtel1M 804706 GGATAAAATAGATAATAATA 804725 -i v v vv (ATATA)n#Simp 95 -AATATAATATAATATAATA 113 Matrix = Unknown Transitions / transversions = 0.45 (5/11) Gap_init rate = 0.12 (13 / 113), avg. gap size = 1.00 (13 / 13) 555 23.55 14.97 2.38 chr1qtel1M 805258 805444 (194556) C MIRc#SINE/MIR (50) 218 9 m_b49s601i31 1774 chr1qtel1M 805258 CTTACAAATACATTAGCTCACTTGGTCCTCCCAACAACCCTGTGAGACAA 805307 v v v i i v ii i C MIRc#SINE/MIR 218 CTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAG 169 chr1qtel1M 805308 GT---GC---TGTT-TTATTCCCAATT----------GAAAT----GCAC 805336 i--- --- i - i v ---------- i---- v C MIRc#SINE/MIR 168 GCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC 119 chr1qtel1M 805337 AGGAAGATTA--TAACTTGCCCATGGTCGCCCAACCAGTAA-----AGAT 805379 ii i -- i v i v i i ----- v C MIRc#SINE/MIR 118 AGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAG 69 chr1qtel1M 805380 CTAAGGACTTATTTGAACTCAAATCTTCCTAATTCCAGATTCAATGCTCC 805429 i-i ---- i i ii i i ii i i i C MIRc#SINE/MIR 68 CC-GGGAC----TCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCT 24 chr1qtel1M 805430 ATTCACTGAATCCCA 805444 v i v i v C MIRc#SINE/MIR 23 TTCCACTGCACCACA 9 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.90 CpG sites = 31, Kimura (unadjusted) = 29.63 Transitions / transversions = 2.58 (31/12) Gap_init rate = 0.06 (12 / 186), avg. gap size = 2.75 (33 / 12) 243 36.73 2.00 2.00 chr1qtel1M 805460 805659 (194341) C L2#LINE/L2 (889) 2193 1994 m_b49s601i32 1775 chr1qtel1M 805460 CAGGAGAAAAGACTAAAGAGAATCAGTCA-TGCAGGTAGCAGGAGAACTA 805508 v i ii i ii i v i i - - v i i C L2#LINE/L2 2193 CAGCAAAGGAGACTGAGAAGGAGCGGCCAGTG-AGGTAGGAGGAAAACCA 2145 chr1qtel1M 805509 GAAAACAAAGAGTAACAGAAAAACAAACAGAAGACAAGCTATCGGGA-GA 805557 i i vviv - iv vvii i v vv v ivv v ii - i C L2#LINE/L2 2144 GGAGAGTGTG-GTGTCCTGGAAGCCAAGTGAAGAAAGTGTTTCAAGAAGG 2096 chr1qtel1M 805558 AGAACATGATTCATAGCATGGAAAGCTGCAGAGATATCAATAGGGATGAG 805607 iivi iv iv ii vi v v ? vi vvii C L2#LINE/L2 2095 AGGGAGTGATCAACTGTGTCAAATGCTGCTGANAGGTCAAGTAAGATGAG 2046 chr1qtel1M 805608 GACTTCAAAAAGTTA--ATTTGATTTGACAATAAAGGGGTCATAGGTGAC 805655 --i i v v -- v ii iivi i v C L2#LINE/L2 2045 GACT--GAGAATTGACCATTGGATTTAGCAACGTGGAGGTCATTGGTGAC 1998 chr1qtel1M 805656 TTTG 805659 i C L2#LINE/L2 1997 CTTG 1994 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 50.83 CpG sites = 42, Kimura (unadjusted) = 53.12 Transitions / transversions = 1.40 (42/30) Gap_init rate = 0.04 (7 / 199), avg. gap size = 1.14 (8 / 7) 392 34.15 1.83 7.75 chr1qtel1M 807480 807752 (192248) C L3#LINE/CR1 (519) 3580 3323 m_b49s601i33 1776 chr1qtel1M 807480 TCTAAACAGGGTAGTATACAATGGAGCCCTCAAAAAACTCATATTCTGGA 807529 i v v i vi ii ii iv i vvv-- i v i? C L3#LINE/CR1 3580 TCTGACCAGCGCAGAGTACAGCGGGACTATTACCT--CCCTTGNTCTGGA 3533 chr1qtel1M 807530 AACTACATCAGTTTTGATTTACTGTGATATTTT-TTAGCTTTATGGGACT 807578 v i iivv v i vi viv i v vi- v v - v C L3#LINE/CR1 3532 CACTATACTTCTATTAATGCAGCCTAAGATTGCATTAGCTTTTTTGG-CA 3484 chr1qtel1M 807579 GTTGGA-CACAATGTTAGCATATAGTAAACTT-TAGTCAACTAAAACTCT 807626 iiiv - v i vi v i i -ii i i C L3#LINE/CR1 3483 GCCACATCACACTGTTGGCTCATATTGAGCTTGCGGTCAACTAAAACCCC 3434 chr1qtel1M 807627 GGATATTTTCTTTTCACATGAATTATTACAAAGCTTCTTAAAATTATCTC 807676 --- vv ii i i ii i v i----- i iv C L3#LINE/CR1 3433 ---TAGGTCTTTTTCACGTGAACTGCTGCTAAGCC-----AGATCCTCTC 3392 chr1qtel1M 807677 ACCCACCTTATACTTATTCTTATGAAAATGATTTCTTGAACTTAGA--AA 807724 --- i i i i v ------ iv i i i --v C L3#LINE/CR1 3391 ---CATCCTGTACTTGTGC------AGTTGATTTTTTGAACCTAAATGCA 3351 chr1qtel1M 807725 GCACTTTCCTTTTCTCTCTATTACATTT 807752 v v v v i i v C L3#LINE/CR1 3350 GGACTTTACATTTATCCCTGTTAAATTT 3323 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.85 CpG sites = 50, Kimura (unadjusted) = 47.20 Transitions / transversions = 1.39 (50/36) Gap_init rate = 0.09 (24 / 272), avg. gap size = 1.04 (25 / 24) 213 36.35 10.70 5.31 chr1qtel1M 807839 808268 (191732) L2b_3end#LINE/L2 8 459 (7) m_b49s601i34 1777 chr1qtel1M 807839 ATCTGGTTCACCTCATAACTTTCCAGTCTTTTTATGTCTT-CCACTACAC 807887 -- v v - v i i i i--- v i - viv L2b_3end#LINE 8 ATCTGG--CCCCGC-TACCTCTCCGGCCTC---ATCTCCTACCACTCTCC 51 chr1qtel1M 807888 TTTAACACACTTTTTGATCTAGTGACACTGGGTTTTTTATAGTTTCTCAT 807937 ii vi v i -- v i iv vi ii iiv i iv L2b_3end#LINE 52 CCTTGCTCACTCT--GCTCCAGCCACACTGGCCTCCTTGCTGTTCCTCGA 99 chr1qtel1M 807938 ACAAAATACTTCCCTTTCCTACTA------TTTTCACTGACTATCCTCTG 807981 vivi ?vii ?i i vv v------ v ?vi i i i v L2b_3end#LINE 100 ACACGCCANGCTCNCTCCCGCCTCAGGGCCTTTGCACNTGCTGTTCCCTC 149 chr1qtel1M 807982 TGACTAAAATTTTCTCCTTC-CCTCTTTCCATTGTCC--TTCCTACT--T 808026 v ii ivii i ii - iv -i v --i -- L2b_3end#LINE 150 TGCCTGGAACGCCCTTCCCCACCTCTTCGC-CTGGCCAACTCCTACTCAT 198 chr1qtel1M 808027 TCTTCCATTCCATTTTTGGATTTCACTTTATTTGGATAGTTTTTTTCCTA 808076 i viv ivvvi iii v i iv ii iv iii i-- i L2b_3end#LINE 199 CCTTCAGGTCTCAGCTCAAATGTCACCTCCTCCGGGAAGCCCTC--CCTG 246 chr1qtel1M 808077 ATCCATCTTAATGCTA---CTGAT--TTTCCTCTGG---TGATTATTTCT 808118 i vi --- v ii--- v ii--ii ---ivvii v i L2b_3end#LINE 247 ACCCCCC---AGGCCGGGTCAGGCGCCCTCCTCTGGGCCCCCCCAGTCCT 293 chr1qtel1M 808119 ATCCATTAAGATACTGTTTTGA--TACAAGT-TCT--TTGCATGT-TGTC 808162 i ------- i iii i i-- i? v - -- i - L2b_3end#LINE 294 ACCC-------TGCCACTCTGGGTTATNATTGTCTGNTTACATGTCTGTC 336 chr1qtel1M 808163 ------AC---ATTGTGAGTATCTTGAGGGAATGGA------TTGTCTTT 808197 ------ --- i ivi v v v ------i v L2b_3end#LINE 337 TCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCTTG 386 chr1qtel1M 808198 TGCATTTCTACATAACTCCA-TATTTAGCAGAGTGCCTAGAACATAGTAA 808246 v iiv ii -- i -iiii v ? i v i i L2b_3end#LINE 387 TTCACCGCTGTAT--CCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAG 434 chr1qtel1M 808247 GTGTATCAG----TGTTTGTTGACTG 808268 i i- ---- i v L2b_3end#LINE 435 GCGC-TCAGTAAATATTTGTTGAATG 459 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 48.46 CpG sites = 97, Kimura (unadjusted) = 54.54 Transitions / transversions = 1.90 (97/51) Gap_init rate = 0.10 (41 / 429), avg. gap size = 1.71 (70 / 41) 280 32.04 6.80 0.00 chr1qtel1M 808165 808267 (191733) L2d2_3end#LINE/L2 438 547 (8) m_b49s601i35 1777 chr1qtel1M 808165 ATTGTGAGTATCTTGAGGGAATGGATTGTCTTTTGCATTTCTACATA-AC 808213 i ivi v v iii v i ii i vii -v L2d2_3end#LIN 438 ATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACTTCTTTGTATCC 487 chr1qtel1M 808214 TCCATA---TTTAGCAGAGTGCCTAGAACATAGTAAGTGT---ATCAGTG 808257 i i ---ii v v v i i i i--- v i i L2d2_3end#LIN 488 CCCACAGCGCCTAGCACAGTGCCTTGCACACAGTAGGCGCTCAATAAATA 537 chr1qtel1M 808258 TTTGTTGACT 808267 i L2d2_3end#LIN 538 TTTGTTGATT 547 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.75 CpG sites = 23, Kimura (unadjusted) = 44.63 Transitions / transversions = 2.30 (23/10) Gap_init rate = 0.03 (3 / 102), avg. gap size = 2.33 (7 / 3) 314 29.10 2.90 2.90 chr1qtel1M 808329 808466 (191534) L2#LINE/L2 2210 2347 (735) m_b49s601i36 1778 chr1qtel1M 808329 CTGTCCTGTTAACCTTGG-GTGTCCCACAGGATTCTGTCCTTAG--CTCG 808375 i v v ? v - i -- ii v i -- v L2#LINE/L2 2210 CCGACCTCTNAACGTTGGAGTGCCCCA--GGGCTCAGTCCTTGGACCTCT 2257 chr1qtel1M 808376 TCTCCTTGATCT-TTTATAATATTTCATTGGGGGATCTCAGTTGCTCCTA 808424 i i-- - i i v vvi vi ? v viiiv ii L2#LINE/L2 2258 TCTCTTC--TCTATCTACACTCACTCCCTNGGTGATCTCATCCAGTCTCA 2305 chr1qtel1M 808425 TGGTTTCAATTATCATCACTATGCTGATGACTTTTACTTTTA 808466 i i v i vv iii vv L2#LINE/L2 2306 TGGCTTTAAATACCATCTATATGCTGATGACTCCCAAATTTA 2347 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.20 CpG sites = 22, Kimura (unadjusted) = 38.45 Transitions / transversions = 1.29 (22/17) Gap_init rate = 0.05 (7 / 137), avg. gap size = 1.14 (8 / 7) 361 36.29 1.90 2.88 chr1qtel1M 808881 809090 (190910) L2#LINE/L2 2301 2508 (574) m_b49s601i37 1778 chr1qtel1M 808881 TCTC-TAGCTTCTATTTACTTCATTCATATGTTGATAATTATTGAATCT- 808928 - i - vv -- ii i i i viii i - L2#LINE/L2 2301 TCTCATGGCTT-TAAATAC--CATCTATATGCTGATGACTCCCAAATTTA 2347 chr1qtel1M 808929 --TAGCCAGTACTGATTTCTCTGTTGATTTCCAATTCTGCATGGTCAGCT 808976 -- vv iv v ii ivi vi iviii i ivi i L2#LINE/L2 2348 TATCTCCAGCCCGGACCTCTCCCCTGAACTCCAGACTCGTATATCCAACT 2397 chr1qtel1M 808977 GTCAATTAGATATCTTTTTAACTGGACTTCATATATACATTTAAAAGTAA 809026 i v i v i ii-- vi iv vv vi i v v v L2#LINE/L2 2398 GCCTACTCGACATCTCC--ACTTGGATGTCTAATAGGCATCTCAAACTTA 2445 chr1qtel1M 809027 ACATGACCAAAACTGAACTCATTATTATTCCCTCTAATCGCTCTCCTTTC 809076 v v v iv i iii v viv - i L2#LINE/L2 2446 ACATGTCCAAAACTGAACTCCTGATCTTCCCCCTCAAACCTGCTCC-TCC 2494 chr1qtel1M 809077 CAAAGTTTGTCACA 809090 iv i vi v L2#LINE/L2 2495 CGCAGTCTTCCCCA 2508 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 49.64 CpG sites = 43, Kimura (unadjusted) = 51.67 Transitions / transversions = 1.39 (43/31) Gap_init rate = 0.04 (9 / 209), avg. gap size = 1.11 (10 / 9) 13 18.91 0.00 0.00 chr1qtel1M 810187 810216 (189784) (AACC)n#Simple_repeat 1 30 (0) m_b49s252i15 1779 chr1qtel1M 810187 AACCGTCCAACCATCCATCCAACCAACGAA 810216 iv v v v (AACC)n#Simpl 1 AACCAACCAACCAACCAACCAACCAACCAA 30 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 234 30.36 0.00 0.00 chr1qtel1M 810443 810498 (189502) C L2b_3end#LINE/L2 (15) 451 396 m_b49s601i38 1780 chr1qtel1M 810443 AATTGTTTATTAGGTATTTTCTTTGTGTTAGGCCCTGTACTAGATACTGG 810492 v i i ii iiii v v ii ? i iii C L2b_3end#LINE 451 AAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGG 402 chr1qtel1M 810493 GGATAC 810498 C L2b_3end#LINE 401 GGATAC 396 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.64 CpG sites = 14, Kimura (unadjusted) = 44.35 Transitions / transversions = 4.67 (14/3) Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0) 389 37.78 2.60 2.60 chr1qtel1M 811493 811723 (188277) C L2#LINE/L2 (2479) 603 373 m_b49s601i39 1781 chr1qtel1M 811493 TGATCTGGAAGCGGTAATGGGGAACAAGGAGTA-ATCTGACTCCTCCATC 811541 i i i i v - i - i v vi C L2#LINE/L2 603 TGGTCTGGAAGCGGCAATGAGGAGCAAGGAGGACACCT-ACCCCACCTCC 555 chr1qtel1M 811542 ATGATCAACAAATCAGGAGATTTTGGGAGATGTGTAAACAA----AACCT 811587 v vi ii-ii vv ii i? v --- v i----v i C L2#LINE/L2 554 AGGCCCAGT-GGTACGAGGGNTGTGGGAGA---GAAAACAGCCACCACTT 509 chr1qtel1M 811588 GAAAGAGTAAGAAAGAAAGCAATATTTTCAGGATGGAATTATATTTTAGT 811637 i i iviv ii i i i ii ivi iii vi i? C L2#LINE/L2 508 GAGAGGGCTGCAGGGGAAGCAGTGTCCTCAGGGGAGAGCCAGGTTTCNGT 459 chr1qtel1M 811638 GAAGGCTTGAAGACAAAGTGAATG-AAAAAGAAGTAAGTGTAAGGTGAAA 811686 v ii vv iii v i -vv i - i vv i i ivii C L2#LINE/L2 458 TAGAGCAAGAAGGTGAAGGGAACGTTCAGAGAAG-AGGTTGAGGATACGG 410 chr1qtel1M 811687 GTAAGTTTGCTAATAATGGGTCAGGCCTTACAGAAGG 811723 vi v i i i ii iv vv v i C L2#LINE/L2 409 GGGATTTTGCTGATGACGGACCGTGAGTTCCAGAGGG 373 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 53.35 CpG sites = 56, Kimura (unadjusted) = 57.55 Transitions / transversions = 1.93 (56/29) Gap_init rate = 0.04 (9 / 230), avg. gap size = 1.33 (12 / 9) 12 28.89 0.00 0.00 chr1qtel1M 811965 812006 (187994) (TTTT)n#Simple_repeat 1 42 (0) m_b49s252i16 1782 chr1qtel1M 811965 TTTCTTTTTTTTCCAGTCTTTGTTTCTTTATTTGTTTTTTTT 812006 i iivv i v i v v (TTTT)n#Simpl 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 42 Matrix = Unknown Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 346 27.99 4.43 4.95 chr1qtel1M 812437 812639 (187361) C L1MC2_3end#LINE/L1 (458) 633 432 m_b49s551i15 1783 chr1qtel1M 812437 GCTCATTTCATTCAGCATCAGTTCATGTAAG-TCTCTCCAGGCCTTTCTG 812485 iv i i vi - v v - ii v i --- C L1MC2_3end#LI 633 GCTTCTTTCACTTAGCAATA-TGCATTTAAGGTTCCTCCATGTCTTT--- 588 chr1qtel1M 812486 AAATCAT--CCTGCTGG-TCGTTTCTT---ACCGAACAATAATATTCCAT 812529 --- i -- i v i - i --- i vvv C L1MC2_3end#LI 587 ---TCGTGGCTTGATAGCTCATTTCTTTTTATCGCTGAATAATATTCCAT 541 chr1qtel1M 812530 AATATTCATATACCACAATTTATTCAGCCATTCTCCAATTGATGGGCATC 812579 vi vv i i i i v v v v i - C L1MC2_3end#LI 540 TGTATGGATGTACCACAGTTTGTTTATCCATTCACCTATTGAAGGACAT- 492 chr1qtel1M 812580 CACTCAA--GTTTCCAGTTTCTGGCCACTACAAACAGGGCTGCCACAGAC 812627 -- iii-- i iv i v i ii i ii i i i C L1MC2_3end#LI 491 --CTTGGTTGCTTCCAAGTTTTGGCAATTATGAATAAAGCTGCTATAAAC 444 chr1qtel1M 812628 ATTCTTGCACAG 812639 v ii C L1MC2_3end#LI 443 ATTCGTGTGCAG 432 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.54 CpG sites = 35, Kimura (unadjusted) = 36.40 Transitions / transversions = 1.84 (35/19) Gap_init rate = 0.07 (15 / 202), avg. gap size = 1.27 (19 / 15) 621 24.88 1.90 2.39 chr1qtel1M 812518 812727 (187273) C L1ME3G_3end#LINE/L1 (376) 548 340 m_b49s551i16 1783 chr1qtel1M 812518 ATAATATTCCATAATATTCATATACCACAATTTATTCAGCCATTCTCCAA 812567 i i vv i i i i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr1qtel1M 812568 TTGATGGGCATCCA--CTCAAGTTTCCAGTTTCTGGCCACTACAAACAGG 812615 i ii --i --- i i v i i iv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTT---GTTTCCAATTTTTCGCTATTACAAACAAT 452 chr1qtel1M 812616 GCTGCCACAGACATTCTTGCACAGACAGGTCTTTTTCC-CTTCTTTAAA- 812663 v iii i i vi --? i v v - v v vii i- C L1ME3G_3end#L 451 GCTGCAATGAACATCCTTGTACATGC--NTCCTTGTGCACATGTGCGAGT 404 chr1qtel1M 812664 ATCTCTTTGGGATATAAGCCCAGTAGTAACACTGCTGGATCAAAGGGTAT 812713 i ? i v v? ? v iiv i i C L1ME3G_3end#L 403 ATTTCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTAT 354 chr1qtel1M 812714 TCACCTTTTGAATT 812727 v i v i C L1ME3G_3end#L 353 GCGCATTTTAAATT 340 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 30.39 CpG sites = 33, Kimura (unadjusted) = 31.99 Transitions / transversions = 1.83 (33/18) Gap_init rate = 0.04 (8 / 209), avg. gap size = 1.12 (9 / 8) 190 31.25 1.56 0.00 chr1qtel1M 812904 812967 (187033) C MIRb#SINE/MIR (141) 127 63 m_b49s601i40 1784 chr1qtel1M 812904 AAGCCCAGAGAAAATGAATTAATTGCCACAGA-CACAGAGTTAATAAGTG 812952 i i iiv i i v v vv i- v i i C MIRb#SINE/MIR 127 AGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTG 78 chr1qtel1M 812953 GGTGAGGCAGAATTC 812967 vv v i i C MIRb#SINE/MIR 77 GCAGAGCCGGGATTC 63 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.72 CpG sites = 11, Kimura (unadjusted) = 41.37 Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.02 (1 / 63), avg. gap size = 1.00 (1 / 1) 309 33.59 3.97 0.77 chr1qtel1M 814328 814453 (185547) C MIR3#SINE/MIR (38) 170 41 m_b50s601i0 1785 chr1qtel1M 814328 CTTAAA-ATGGTCTAGCACAAAACTCTCATTTTACAAATTACAAAACTCA 814376 i - vi iv vv i i v vi v C MIR3#SINE/MIR 170 CTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGA 121 chr1qtel1M 814377 AATCCCAAAGAAGTTAACAGTTTCAGTCAAATTTCCACAGCG----GATG 814422 ii- i i v vv vi iivi iv iv ?----ii C MIR3#SINE/MIR 120 GG-CCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTG 72 chr1qtel1M 814423 ACAGAGATAGGACTAGAAAGGAGATCCCTTG 814453 i vii vvv i i i C MIR3#SINE/MIR 71 GCAGAGCCGGGACTAGAACCCAGGTCTCCTG 41 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 44.87 CpG sites = 24, Kimura (unadjusted) = 46.57 Transitions / transversions = 1.33 (24/18) Gap_init rate = 0.02 (3 / 125), avg. gap size = 2.00 (6 / 3) 229 12.82 0.00 0.00 chr1qtel1M 814942 814980 (185020) DNM1r#Unknown 2475 2513 (2149) m_b50s502i0 1786 chr1qtel1M 814942 CATGTGTGTGTATGTATATATGTGTGTATATGTATATAT 814980 i i i i i DNM1r#Unknown 2475 CACGTGTATGTGTGTATATATGTGTGTATATGTGTGTAT 2513 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 11.80 CpG sites = 5, Kimura (unadjusted) = 14.81 Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 314 30.47 1.53 2.31 chr1qtel1M 815525 815655 (184345) C L1ME2z_3end#LINE/L1 (623) 568 439 m_b50s551i0 1787 chr1qtel1M 815525 TCCTTTCTTATAACACAGTATTATTCCACTTTAACTATACATTACAACTT 815574 - vi vv v i v vvv i ii ii C L1ME2z_3end#L 568 TCCTTT-TTATTGCTGAGTAGTATTCCATTGTATGAATATACCACAGTTT 520 chr1qtel1M 815575 GGTCAGTCACTTTCCAAGTGATGGGCATCCCTGAA--ATTTCCAGTTCTT 815622 v i vi i i viv i -- ii--i i C L1ME2z_3end#L 519 GTTTATCCATTCTCCTGTTGATGGACA--CCTGGGCTGTTTCCAGTTTTT 472 chr1qtel1M 815623 TGCCATTATAAAAAGAGCTGCAAGGAATACTTT 815655 v i i v i v v i i i C L1ME2z_3end#L 471 GGCTATTATGAATAAAGCTGCTATGAACATTCT 439 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 40.31 CpG sites = 23, Kimura (unadjusted) = 40.31 Transitions / transversions = 1.44 (23/16) Gap_init rate = 0.03 (4 / 130), avg. gap size = 1.25 (5 / 4) 15 15.79 7.84 1.85 chr1qtel1M 815902 815952 (184048) (TTAATT)n#Simple_repeat 1 54 (0) m_b50s252i0 1788 chr1qtel1M 815902 TTAATTTTAATTTTATGTTTTCATGGT-ACTTT-A-TTTAA-TATAATTT 815947 -i v vv - i - - - v (TTAATT)n#Sim 1 TTAATTTTAATTTTA-ATTTTAATTTTAATTTTAATTTTAATTTTAATTT 49 chr1qtel1M 815948 TTATT 815952 v (TTAATT)n#Sim 50 TAATT 54 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.10 (5 / 50), avg. gap size = 1.00 (5 / 5) 244 30.52 4.04 4.04 chr1qtel1M 816295 816393 (183607) C MIRb#SINE/MIR (66) 202 104 m_b50s601i1 1789 chr1qtel1M 816295 CATTGTCTATGGTACTTAATTCTTACAATTACCTTGGATGGTGG----TA 816340 i ----i i i i iv i viv i ---- C MIRb#SINE/MIR 202 CATTATCT----CATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTA 157 chr1qtel1M 816341 ATATCTCTCTTTTACACATGTGGAAATTGACACAAAAAGATATTTATTAA 816390 v i iv v v i vi vv i vi v v C MIRb#SINE/MIR 156 TTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAA 107 chr1qtel1M 816391 TTT 816393 i C MIRb#SINE/MIR 106 CTT 104 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 38.32 CpG sites = 16, Kimura (unadjusted) = 40.09 Transitions / transversions = 1.23 (16/13) Gap_init rate = 0.05 (5 / 98), avg. gap size = 1.60 (8 / 5) 337 28.81 7.74 3.73 chr1qtel1M 816983 817137 (182863) C L2a_3end#LINE/L2 (20) 497 337 m_b50s601i3 1790 chr1qtel1M 816983 TTTATTAAGCACCTACTTAGTGTTAGGAACAGTTTTAAGTGATGGTGACA 817032 i i vv ii v v i i i v v i C L2a_3end#LINE 497 TTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGCGCTGGGGATA 448 chr1qtel1M 817033 CATAAAAAAGCAAAAC------TATTTTCTGCACTCAAGAAGTTCACCTT 817076 vv ivi i ------v v ii v v i i i v C L2a_3end#LINE 447 CAGCAGTGAACAAAACAGACAAAAGTCCCTGCCCTCATGGAGCTTACATT 398 chr1qtel1M 817077 GTAGTAGGGA-----AGACAATGTGTAACTAGCAAAGTAACTATTGAATA 817121 v i i----- i--- v ii - v --i C L2a_3end#LINE 397 CTAGTGGGGGGAGACAGACAATA---AACAAATAAA-TAAGTA--AAATA 354 chr1qtel1M 817122 TATA-CAAGATAGATGG 817137 -i v vi C L2a_3end#LINE 353 TATAGTATGTCAGATGG 337 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 35.07 CpG sites = 24, Kimura (unadjusted) = 37.22 Transitions / transversions = 1.26 (24/19) Gap_init rate = 0.06 (9 / 154), avg. gap size = 2.00 (18 / 9) 374 30.58 4.96 0.00 chr1qtel1M 816983 817103 (182897) C L2b_3end#LINE/L2 (20) 446 320 m_b50s601i2 1790 chr1qtel1M 816983 TTTATTAAGCACCTACTTAGTGTTAGGAACAGTTTTAAGTGATGGTGACA 817032 i i i vv ii v? v vi i i v v i C L2b_3end#LINE 446 TTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGGGATA 397 chr1qtel1M 817033 CA----TAAAAAAG-CAAAACTATTTTCTGCACTCAAGAAGTTCACCTTG 817077 ---- i v - i v?iiv ii v v i i vv v C L2b_3end#LINE 396 CAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGGAGCTCACAGTC 347 chr1qtel1M 817078 TAGTAGGGAAGACA-ATGTGTAACTAG 817103 i i - ii ?i C L2b_3end#LINE 346 TAGTGGGGGAGACAGACATGTAANCAG 320 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 37.46 CpG sites = 22, Kimura (unadjusted) = 41.99 Transitions / transversions = 1.47 (22/15) Gap_init rate = 0.03 (3 / 120), avg. gap size = 2.00 (6 / 3) 1070 30.08 2.11 2.54 chr1qtel1M 818780 819253 (180747) L1M3_orf2#LINE/L1 1830 2301 (987) m_b50s551i1 1791 chr1qtel1M 818780 CATATTAAAAACACTAGAGAGTATAGGAATAAACGGACTTTTCTTTTAAA 818829 iv v vi v ivv ? i v v?? v i i---- L1M3_orf2#LIN 1830 CATGATAAAAACTCTCAACAAACTAGGNATAGAAGGAANNTACCTC---- 1875 chr1qtel1M 818830 AACAGTTAGTAA----CATCTATCTAAAACTGTCAGCAAGCAACATATGT 818875 -- i ---- v vv i ivv v i v ivi L1M3_orf2#LIN 1876 AACA--TAATAAAGGCCATATATGAAAAGCCCACAGCTAACATCATACTC 1923 chr1qtel1M 818876 AATGAGGATAAACTAGAACCATTCCCAGTAAGATCAGGAGTGAAACAAGG 818925 iv v ii v v i vv iii ii L1M3_orf2#LIN 1924 AATGGTGAAAAACTGAAAGCTTTTCCTCTAAGATCAGGAACAAGGCAAGG 1973 chr1qtel1M 818926 TTGCCCACTATCACTATTACTTTTCAATATTGTATTAGAAATGCTAGTTT 818975 v v i i i v v i v i i i v iiv L1M3_orf2#LIN 1974 ATGCCCACTCTCGCCACTTCTATTCAACATAGTACTGGAAGTCCTAGCCA 2023 chr1qtel1M 818976 CGGCAATAAGAGTTGAGAAAGAAAATAAAGGCATTAGAGTGGGTAATGAA 819025 vi v ivvv i vv ivi i v v v L1M3_orf2#LIN 2024 GAGCAATTAGGCAAGAAAAAGAAATAAAAGGCATCCAAATCGGAAAGGAA 2073 chr1qtel1M 819026 GAAACCAAATTATCACTCTTTGCAGATGATATGATGGCATACTTAGAGAA 819075 iiv v v i vvi iv i L1M3_orf2#LIN 2074 GAAGTAAAATTATCTCTGTTTGCAGATGACATGATCTTATATGTAGAAAA 2123 chr1qtel1M 819076 TCCCAGAGATTCTATTAAAAAGCTATTAAAAATAATCCACAACTTTAGCA 819125 i i i i i ii i i i v vv i v i i L1M3_orf2#LIN 2124 CCCTAAAGACTCCACCAAAAAACTGTTAGAACTAATAAACGAATTCAGTA 2173 chr1qtel1M 819126 AAGTTGAAGGATACAAAATAAGTTCACATAAATCATCAGCATTCTTATAC 819175 v v iivi v viv i ii L1M3_orf2#LIN 2174 AAGTTGCAGGATACAAAATCAACATACAAAAATCAGTTGCGTTTCTATAC 2223 chr1qtel1M 819176 ATCACTAACAAA--ATCCAACAGCAAGAGAGATAAAGAGA--AATTCCAT 819221 ii vi i -- i ---- ii i v i -- i L1M3_orf2#LIN 2224 ACTAACAACGAACTATCCGA----AAAGGAAATTAAGAAAACAATCCCAT 2269 chr1qtel1M 819222 TTAAAAT--CATTGTTGATGGGATAAAATATTTA 819253 v -- ii--i vi i i L1M3_orf2#LIN 2270 TTACAATAGCATCA--AAAAGAATAAAATACTTA 2301 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 37.90 CpG sites = 78, Kimura (unadjusted) = 39.73 Transitions / transversions = 1.28 (78/61) Gap_init rate = 0.03 (16 / 473), avg. gap size = 1.38 (22 / 16) 1120 29.55 1.25 1.25 chr1qtel1M 818828 819228 (180772) L1P4_orf2#LINE/L1 1882 2282 (1012) m_b50s551i2 1791 chr1qtel1M 818828 AAAACAGTTAGTAACATCTATCTAAAACTGTCAGCAAGCAACATATGTAA 818877 i i v viv vvv ivv v i v ivv L1P4_orf2#LIN 1882 AAAATAATAAGAGCCATCTATGACAAACCCACAGCCAACATCATACTGAA 1931 chr1qtel1M 818878 TGAGGATAAACTAGAACCATTCCCAGTAAGATCAGGAGTGAAACAAGGTT 818927 i i v v i i v vv i v v iii i v L1P4_orf2#LIN 1932 CGGGCAAAAGCTGGAAGCATTCCCCTTGAGAACTGGAACAAGACAAGGAT 1981 chr1qtel1M 818928 GCCCACTATCACTATTACTTTTCAATATTGTATTAGAAATGCTAGTTTCG 818977 v i i v v i v i i i v iivvi L1P4_orf2#LIN 1982 GCCCACTCTCACCACTCCTATTCAACATAGTACTGGAAGTCCTAGCCAGA 2031 chr1qtel1M 818978 GCAATAAGAGTTGAGAAAGAAAATAAAGGCATTAGAGTGGGTAATGAAGA 819027 v ivvv vv ivi i i v v L1P4_orf2#LIN 2032 GCAATCAGGCAAGAGAAAGAAATAAAAGGCATCCAAATAGGAAAAGAAGA 2081 chr1qtel1M 819028 AACCAAATTATCACTCTTTGCAGATGATATGATGGCATACTTAGAGAATC 819077 ii i v i v i vvi i i i L1P4_orf2#LIN 2082 AGTCAAACTATCTCTCTTCGCTGACGATATGATTCTATACCTAGAAAACC 2131 chr1qtel1M 819078 CCAGAGATTCTATTAAAAAGCTATTAAAAATAATCCACAACTTTAGCAAA 819127 i i i iiii i vi i v i vv i i i L1P4_orf2#LIN 2132 CTAAAGACTCCGCCAAAAGGCTCCTAGAACTGATAAACGACTTCAGTAAA 2181 chr1qtel1M 819128 GTTGAAGGATACAAAATAAGTTCACATAAATCATCAGCATTCTTATACAT 819177 vv v i vi v vi ii i L1P4_orf2#LIN 2182 GTTTCAGGATACAAAATCAATGTACAAAAATCAGTAGCATTTCTATACAC 2231 chr1qtel1M 819178 CACTAACAAAATCCAACAGC-AAGAG--AGATAAAGA--GAAATTCCATT 819222 v ---i i -- -i -- i v -- v i L1P4_orf2#LIN 2232 CAATAAC---GTTCA--AGCTGAGAGCCAAATCAAGAACGCAATCCCATT 2276 chr1qtel1M 819223 TAAAAT 819228 v L1P4_orf2#LIN 2277 TACAAT 2282 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 35.78 CpG sites = 63, Kimura (unadjusted) = 38.27 Transitions / transversions = 1.17 (63/54) Gap_init rate = 0.02 (8 / 400), avg. gap size = 1.25 (10 / 8) 502 32.32 6.06 4.38 chr1qtel1M 819271 820079 (179921) L1M5_orf2#LINE/L1 2473 3294 (0) m_b50s551i3 1792 chr1qtel1M 819271 TTTAGTGCTATGCCAATCAAC-TCCCAAGAAACTGTTTTACTGACCTAGA 819319 i i v v v- iv i--- vi --- L1M5_orf2#LIN 2473 TTCAATGCAATCCCAATCAAAATCCCAGCAG---GTTTTTTTG---TAGA 2516 chr1qtel1M 819320 AA-----AAAATAACAACAAAATTCATCTAGAAGAACAAAAGATAAAGAA 819364 ----- iv i ivvi i v i ivi i iv? L1M5_orf2#LIN 2517 AATTGACAAGCTGATTCTAAAATTTATATGGAAATGCAAAGGACCNAGAA 2566 chr1qtel1M 819365 T-TTCAAGGGAATTAAGGAAAAGAAAAGCAAA--TGAAGTTTCTAGCTGT 819411 -vi iiv ivv i i i -- i vvii - vv L1M5_orf2#LIN 2567 TAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGAGGACTTA-CACT 2615 chr1qtel1M 819412 CCCAGATCT-AAAACTATATTATAAAGCAGCGGTCACCAAAACCATTTGG 819460 v ? ? - i - vi i v i i vi v L1M5_orf2#LIN 2616 ACCNGATNTCAAGACT-TATTATAAAGCTACAGTAATCAAGACAGTGTGG 2664 chr1qtel1M 819461 TATTGGC-TAAGAAATAGAGCAGTGGATTAAAAGAATATGTTCACAGAAC 819509 - -i vv i i i vi -------- i L1M5_orf2#LIN 2665 TATTGGCGTAAG-GATAGACAAATAGATCAATGGA--------ACAGAAT 2705 chr1qtel1M 819510 AAAATAGTC----AAT-GACTC---------TAGCAATCTAGTATTTGAC 819545 i i- ---- - i --------- i ?v ?i ii v L1M5_orf2#LIN 2706 AGAG-AGTCCAGAAATAGACCCACACATATATGGNCANTTGATTTTTGAC 2754 chr1qtel1M 819546 AAA---CCCAAAG-ACCCCAGCTTTTGTAATAAGAATTCACTATTTGACA 819591 ---v ? - vii ---- viiv i vvv v ii L1M5_orf2#LIN 2755 AAAGGTGCCAANGCAATTCAG----TGGGGAAAGGATAGTCTTTTCAACA 2800 chr1qtel1M 819592 AAAACTGCTGGGAAAATTGGAAACTAGTATGGCAGAAACTAGGCACTGAC 819641 viv i v v iivi v i v iii?vii L1M5_orf2#LIN 2801 AATGGTGCTGGAACAATTGGATATCCATATGGAAAAAAATGAANCTCGAC 2850 chr1qtel1M 819642 CCACACCTAACACTGTATTCCAAGATAAGGTTGAAATGGGTTCATA-ATC 819690 vi v ii iv v i v iv i? i i- - i L1M5_orf2#LIN 2851 CCCTACCTCACACCATACACAAAAATTAATTCNAGATGGA-TCATAGACC 2899 chr1qtel1M 819691 TAGACATAAAGAAAGATATTATAAACAAATTAGAAG--AACATAGGATAG 819738 i ii ii?vi v i vvvvi -- v i L1M5_orf2#LIN 2900 TAAATGTAAAAGNTAAAACTATAAAACTTCTAGAAGAAAACATAGGAGAA 2949 chr1qtel1M 819739 TTTACCTCTCAGATCTGTGGAGGAGGAAAGAATTTTTGACCAAAGAGGAA 819788 -- i iivv i - i?v v ii i ---i v v L1M5_orf2#LIN 2950 --TATCTTCGTGACCT-TGGGNTAGGCAAAGATTTCT---TAAACAGGAC 2993 chr1qtel1M 819789 CTAGAGATTATTATTGAT----CACAAAATAGATAATTTTGATTCTATT- 819833 vi i i vi i? viv ----v v v v v i ?i i- L1M5_orf2#LIN 2994 ACAAAAAGCACNAACCATAAAAGAAAAAATTGATAAATTGGACTNCATCA 3043 chr1qtel1M 819834 CAGTTAAAAAAGTTTTTGTATAAATAAAACCAATGCAGACAAGATTAGAA 819883 v i --i i ivi?vvv iv vi ivi v i v i L1M5_orf2#LIN 3044 AAATTAAAAA--CTTCTGCTCNTCAAAAGACACCGTTAAGAAAATGAAAA 3091 chr1qtel1M 819884 GG-AAATTA------GGGAAAACATGTTTACATTCAAAGGT---TCTGAT 819923 - iii ------ i v i i --- ? vi --- i L1M5_orf2#LIN 3092 GGCAAGCCACAGANTGGGAGAAAATATTTGCA---ANACATATATCTGAC 3138 chr1qtel1M 819924 AAAGGCCTCATTCCTAAAATATATTGAGAACTGACTCATATTTATAATAA 819973 v i vi i i vi vviv v? iv ? L1M5_orf2#LIN 3139 AAAGGACTCGTATCCAGAATATATAAAGAACTCCTACAANTCAATAANAA 3188 chr1qtel1M 819974 TTCAAGCCATTC--TCCAATTGATTAATGGTCAAAGGATATAAACAGACA 820021 --v v vv --i v? vv v i iv i L1M5_orf2#LIN 3189 --AAAGACAAACAACCCAATANAAAAATGGGCAAAAGACTTGAACAGACA 3236 chr1qtel1M 820022 ATTTTCAGATGAAGAAATTGAAATTATTTGTAGTCACATGAAAAAGTGCT 820071 v iv i v v ?v viiivi iv ii L1M5_orf2#LIN 3237 CTTCACAAAAGAAGATATNCAAATGGCCAATAAGCACATGAAAAGATGCT 3286 chr1qtel1M 820072 CCAAATCA 820079 v v? L1M5_orf2#LIN 3287 CAACNTCA 3294 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 43.98 CpG sites = 138, Kimura (unadjusted) = 44.95 Transitions / transversions = 1.23 (138/112) Gap_init rate = 0.07 (55 / 808), avg. gap size = 1.55 (85 / 55) 1507 28.79 1.10 1.66 chr1qtel1M 819937 820480 (179520) L1ME3G_3end#LINE/L1 8 548 (376) m_b50s551i4 1792 chr1qtel1M 819937 CTAAAATATATTGAGAACTGACTCATATTTATAATAATTCAAGCCATTCT 819986 i i vi vviv v iv v --v v --vi L1ME3G_3end#L 8 CCAGAATATATAAAGAACTCCTACAAATCAATAAGAA--AAAGACA--AC 53 chr1qtel1M 819987 CCAATTGATTAATGGTCAAAGGATATAAACAGACAATTTTCAGATGAAGA 820036 v vv v i i iv v i L1ME3G_3end#L 54 CCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGGA 103 chr1qtel1M 820037 AATTGAAATTATTTGTAGTCACATGAAAAAGTGCTCCAAATCACTATTGA 820086 vv viiivi iv i ii v vv v i L1ME3G_3end#L 104 AATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTAA 153 chr1qtel1M 820087 TCAGAGAAAGGCAAATTAAGACAACTCTGAGATACCACTACATACCTGTC 820136 i v i vv i vivi ii L1ME3G_3end#L 154 TCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCATC 203 chr1qtel1M 820137 AGATTGGCTAAGATGACAGGAAACGATAATGAACAATGTTGGAGGGAACG 820186 v i vvv iii?vi ivv? i v i iii L1ME3G_3end#L 204 AGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGTG 253 chr1qtel1M 820187 TGGGAAAACTGGGACACTAATACATTGTTTGTGGAACTGTGAATGGATCC 820236 i v v v v i i v i v i v i v L1ME3G_3end#L 254 TGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTAC 303 chr1qtel1M 820237 AACCATTTTGGAGAGCAATTTGGAACTATGTTCAAAAAGTTATCAAACTG 820286 i ? i v v v viv v --- v L1ME3G_3end#L 304 AGCCNTTTTGGAGGGCAATTTGGCAGTATCTATTAAAATTT---AAAATG 350 chr1qtel1M 820287 TGCATACCCTTTAATCCAGCAGTGTTACTACTGGGCTTATATTCCAAAGA 820336 i i i i vii v ? ?v v i i ? L1ME3G_3end#L 351 CGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAGA 400 chr1qtel1M 820337 GAT-CTTAAAGA-ATGGATAAGGAGCCACATGTGCAAAACTG----TGGC 820380 i - iiv v -i v i --?i i iiv ---- v L1ME3G_3end#L 401 AATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTCATTGC 448 chr1qtel1M 820381 AACCTTCTTTGTAGTCGTTACAAACTGGAAACTGAGTGGATGCCCATCAA 820430 i v v i v iv v i vivv ii i L1ME3G_3end#L 449 AGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCAA 498 chr1qtel1M 820431 TTGAAGAATGACTGAATAAATTGTGGTATATGAATGTTATAGAATATTAT 820480 v ii ii i i vv ii i i L1ME3G_3end#L 499 TAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACTAT 548 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.59 CpG sites = 81, Kimura (unadjusted) = 37.54 Transitions / transversions = 1.11 (81/73) Gap_init rate = 0.02 (12 / 543), avg. gap size = 1.25 (15 / 12) 1083 30.73 2.60 2.60 chr1qtel1M 819987 820564 (179436) L1MC4a_3end#LINE/L1 57 634 (1995) m_b50s551i5 1792 chr1qtel1M 819987 CCAATTGATTAATGGTCAAAGGATATAAACAGACAATTTTCAGATGAAGA 820036 i v vv v i i i iv i -- L1MC4a_3end#L 57 CCGATAGAAAAATGGGCAAAAGACATGAACAGACAATTCACAAA--AAGA 104 chr1qtel1M 820037 AATTGAAATTATTTGTAGTCACATGAAAAAGTGCTCCAAATCACTATTGA 820086 ? v? viiiiv iv i ii i v vv vv i L1MC4a_3end#L 105 NATANAAATGGCCCTTAAACATATGAAAAGATGTTCAACCTCACTCATAA 154 chr1qtel1M 820087 TCAGAGAAAGGCAAATTAAGACAACTCTGAGATACCACTACATACCTGTC 820136 v v i v v i v vi i L1MC4a_3end#L 155 TAAGAGAAATGCAAATTAAAACTACACTGAGATACCATTTCTCACCTATC 204 chr1qtel1M 820137 AGATTGGCTAAGATGACAGGAAA---CGATAATGAACAATGTTGGAGGGA 820183 v i v- -- ---i i iiv vv v i i L1MC4a_3end#L 205 AGATTGGCAAAAATT-CA--AAAGTTTGACAACACACTCTGTTGGCGAGG 251 chr1qtel1M 820184 ACGTGGGAAAACTGGGACACTAATACATTGTTTGTGGAACTGTGAATGGA 820233 vi i v v v v i v i v ii ?v i L1MC4a_3end#L 252 CTGTGGGGAAACAGGCACTCTCATACATTGCTGGTGGGAATGCAAANTGG 301 chr1qtel1M 820234 TCCAACCATTTTGGAGAGCAATTTGGAACTATGTTCAAAAAGTTATCAAA 820283 v v ? i v v v -i v v ii - -- L1MC4a_3end#L 302 TACAACCCTTNTGGAGGGGAATTTGGCAATAT-CTAACAAAACTA-CA-- 347 chr1qtel1M 820284 CTGTGCA--TACCCTTTAATCCAGCAGTGTTACTACTGGGCTTATATTCC 820331 - i -- i i i vii v i vv v ii i L1MC4a_3end#L 348 -TATGCATTTACCCTTTGACCCAGCAATCCCACTTCTAGGAATTTACCCT 396 chr1qtel1M 820332 AAAGAGAT-CTTAAAGAATGGATAAGGAGCCACATGTGCAAAA------C 820374 i v i- i vv iv v i -- ii? i v ------i L1MC4a_3end#L 397 GAAGATACACCTCCAACATGTACAA--AATNACATATGCACAAGGTTATT 444 chr1qtel1M 820375 TGTGGCAACCTTCTTTGTAGTCGTTACAAACTGGAAACTGAGTGGATGCC 820424 ii v i v v i i iv v v i vivv ii L1MC4a_3end#L 445 CATTGCAGCATTGTTTGTAATTGCAAAATATTGGAAACAACCTAAATGCC 494 chr1qtel1M 820425 CATCAATTGAAGAATGACTGAATAAATTGTGGTATATGAATGTTATAGAA 820474 ?? v i ? ii i i i vv iiiv i i L1MC4a_3end#L 495 CATNNATAGGAGANTGGTTGAATAAACTATGGTACATCCACACAATGGAG 544 chr1qtel1M 820475 TATTATTGTTTTGTAAGAAATGACCAGCAGGATGATTTCAAAGA---GGC 820521 i vvvvi i - -- vv v i v v --- ii L1MC4a_3end#L 545 TACTATGCAGCTGTAAAAAA-GA--ATGAGGAAGATCTCTATGAACTGAT 591 chr1qtel1M 820522 CTGGAGAGACTAACATGAACTGATGCTGAGTGAAATCAGCAGA 820564 v v i vv v vv iv i i vv i L1MC4a_3end#L 592 ATGGAGTGATTTCCAGGATATATTGTTAAGTGAAAAAAGCAAA 634 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 40.65 CpG sites = 89, Kimura (unadjusted) = 40.95 Transitions / transversions = 1.06 (89/84) Gap_init rate = 0.03 (20 / 577), avg. gap size = 1.50 (30 / 20) 17 0.00 0.00 0.00 chr1qtel1M 821471 821491 (178509) (TAA)n#Simple_repeat 1 21 (0) m_b50s252i1 1793 chr1qtel1M 821471 TAATAATAATAATAATAATAA 821491 (TAA)n#Simple 1 TAATAATAATAATAATAATAA 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 389 30.25 5.17 1.67 chr1qtel1M 821924 822155 (177845) C L1ME4c_3end#LINE/L1 (178) 652 413 m_b50s551i6 1794 chr1qtel1M 821924 ACACCATTTTG-GTTCTGCTCACTTCACTTGATATCACTTCATGTAATAT 821972 i v -i ivi i i i iv i- i C L1ME4c_3end#L 652 ATACAATTTTGTATTCTGCTTTTTTCACTTAACATTATATCATA-AACAT 604 chr1qtel1M 821973 TTTCC----TG-----TACTTTTGA-AAGCATTATTTCTTATGGATTAAT 822012 ---- ----- v i v - vi i i v v vv C L1ME4c_3end#L 603 TTTCCATGTTGCTACATAGTCTTCATAATTATCATTTTTAATGGCTGCAT 554 chr1qtel1M 822013 AATATTC-ATCACAACCATATACCACAAATTGCTCAACTATTTCCCAATT 822061 - iviv?v i i v i i i i v C L1ME4c_3end#L 553 AATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTATT 504 chr1qtel1M 822062 GATGAACATTCCCTCAGTTTCCAATTCTTTGTCACCACAATAAGAGCTGT 822111 v i ivvviv i i ii ii i vv iv i C L1ME4c_3end#L 503 GTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGC 454 chr1qtel1M 822112 TATAAATATTTTTGGGCATATATGTCATTTTTGTTTTTCTTAAA 822155 v i i i i v - i-- vi i i i C L1ME4c_3end#L 453 AATGAACATCTTCGTGCATATA-GC--TTTTTCCTTCTTTTGAA 413 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 38.21 CpG sites = 43, Kimura (unadjusted) = 40.50 Transitions / transversions = 1.65 (43/26) Gap_init rate = 0.04 (9 / 231), avg. gap size = 1.78 (16 / 9) 322 36.22 4.25 2.31 chr1qtel1M 822531 822742 (177258) MamRTE1#LINE/RTE-BovB 250 465 (3347) m_b50s601i4 1795 chr1qtel1M 822531 CAACTGAAGTATCATGTGCAGGT-ACAATGGGAG--CTGTAGCACCAAGT 822577 v ii- v v v - ii i-- ivv i v- MamRTE1#LINE/ 250 CAACTCAAGCG-CATGTCCTGCTGACGGTGGGAAAACCTAAACAA-AAGT 297 chr1qtel1M 822578 C---TGCACACAAGTGGACTAGACCATAAGATAACATTCTCACT--AGAA 822622 --- ivii i i v i ivi vi - vi v vv i --? i MamRTE1#LINE/ 298 CCTNTGCGAGTAGGCGGCCCAGGATATTGG-TCGCTTAGTCGCTGANGAG 346 chr1qtel1M 822623 GCAATAGTAGAATTTCTCAGTTCCCTAGGTGTCTAAGCAGCCTT-TTAAG 822671 ii i vvi ivv iv? i i i - v MamRTE1#LINE/ 347 GCAGCAGCACCGTTCGGCAGCGNCCTGGGTGTCTGAGCAGCCCTGTTTAG 396 chr1qtel1M 822672 GATCAAATTCTTGCCTCCAGATGTGAGGAATAGGCTAGAAACAGTACACT 822721 ? ivii vi vv ii -- i vi ? vi i v MamRTE1#LINE/ 397 GANCGCGCTGCTCACTCCGAA--TGGGGAAGGGNCTAGAAAAGGTGCCCT 444 chr1qtel1M 822722 AAAAACTAAGTGCTTATCCAA 822742 vii ivv i vv MamRTE1#LINE/ 445 AAACGTTGCCTGCCTCGCCAA 465 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 40.65 CpG sites = 42, Kimura (unadjusted) = 52.77 Transitions / transversions = 1.27 (42/33) Gap_init rate = 0.05 (10 / 211), avg. gap size = 1.40 (14 / 10) 13 15.50 9.30 0.00 chr1qtel1M 823068 823110 (176890) (ATTTAT)n#Simple_repeat 1 47 (0) m_b50s252i2 1796 chr1qtel1M 823068 ATGTATACTTAT-TGTGTATCTA-ATTTATATTTA-A-ATATATTTA 823110 v i - v i i - - -v (ATTTAT)n#Sim 1 ATTTATATTTATATTTATATTTATATTTATATTTATATTTATATTTA 47 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.10 (4 / 42), avg. gap size = 1.00 (4 / 4) 14 5.00 0.00 0.00 chr1qtel1M 823253 823273 (176727) (AAAG)n#Simple_repeat 1 21 (0) m_b50s252i3 1797 chr1qtel1M 823253 AAAAAAAGAAAGAAAGAAAGA 823273 i (AAAG)n#Simpl 1 AAAGAAAGAAAGAAAGAAAGA 21 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 247 37.50 8.33 0.00 chr1qtel1M 823301 823444 (176556) L3#LINE/CR1 3673 3828 (271) m_b50s601i5 1798 chr1qtel1M 823301 GATAAGAAGCCTGGAAACCCTGCCATATGAAGATTATCTGAAGGTTCTGG 823350 i i iii i v i i viivi vv L3#LINE/CR1 3673 GGTGAAGGGTCTGGAAACCATGTCATATGAGGAACGGTTGAAGGAACTGG 3722 chr1qtel1M 823351 GAATACCTAA-ATGCAGAATTGA----TAAGAAGGGATACAGTGGTTTTC 823395 i iii i-v v vv ---- v i i i iii i i v L3#LINE/CR1 3723 GGATGTTTAGCCTGGAGAAGAGAAGACTTAGAGGAGACATGATAGCTGTC 3772 chr1qtel1M 823396 ATTAACTATTTA-------TTTATTTAGAAATGTAATTTTATTTATATTC 823438 v i v i-------v i v i iv vi vv i vi v L3#LINE/CR1 3773 TTCAAATATTTGAAGGGCTGTCATGTGGAAGAGGGATTAGACTTATTCTG 3822 chr1qtel1M 823439 TGTGAC 823444 i L3#LINE/CR1 3823 TGTGGC 3828 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 53.23 CpG sites = 33, Kimura (unadjusted) = 54.96 Transitions / transversions = 1.57 (33/21) Gap_init rate = 0.02 (3 / 143), avg. gap size = 4.00 (12 / 3) 663 27.40 4.60 1.49 chr1qtel1M 823743 824068 (175932) C L1M1_orf2#LINE/L1 (1009) 2285 1950 m_b50s551i7 1794 chr1qtel1M 823743 GCTATTTAAAATGGCAT--ATCTCTTACTTTCTCTTT----TTGCATA-T 823785 vv v --v i i iv i ---- ivi - C L1M1_orf2#LIN 2285 GCTATTGTAAATGGGATTACTTTTTTGATTTCTTTTTCAGATTGTTCACT 2236 chr1qtel1M 823786 GT-GTTATATAGAAATGCTGTTGATTTTCATGTGTTTACTTTATATTTTG 823834 - vi ii ii i v i i ii C L1M1_orf2#LIN 2235 GTTGGCATATAGAAATGCTACTGATTTTTGTATGTTGATTTTGTATCCTG 2186 chr1qtel1M 823835 CTACTTTGCTAAAATCATTAATTATTTCAACTATGTTTTTAATTGAGTC- 823883 v i i v ii v i v v v vv ?i v - C L1M1_orf2#LIN 2185 CAACTTTACTGAATTTGTTTATCAGTTCTAATAGTTTTTTNGTGGAGTCT 2136 chr1qtel1M 823884 -TGGGATTTTCCAACTGT---ATCATGATGTCTGCAAAAAAGAGAAATTT 823929 - i v v i --- ivii v iiv C L1M1_orf2#LIN 2135 TTAGGTTTTTCCAAATATAAGATCATATCATCTGCAAACAAGGATAATTT 2086 chr1qtel1M 823930 TTGTTACATCAGTTCTTATTTTGATTCTATCCACTTCTTTTTCATTTCTT 823979 vvv - v vv iv v v iv ii i i v v v C L1M1_orf2#LIN 2085 GACTT-CTTCCTTTCCAATTTGGATGCCCTTTATTTCTTTCTCTTGTCTG 2037 chr1qtel1M 823980 ATAGCTCTATTCTAGGATTTCAAGTACAATATTGAATAATATTGATGGCC 824029 v -v i v v i i v i ivv C L1M1_orf2#LIN 2036 ATTGCTCTA-GCTAGGACTTCCAGTACTATGTTGAATAACAGTGGTGAAA 1988 chr1qtel1M 824030 ATGAGCATCCTTTTGTCAT-CTCTA-ATCTTACAGTGAAAG 824068 i i -- i -i i - v - C L1M1_orf2#LIN 1987 GTGGGCATCC--TTGTCGTGTTCCAGATCTTAGAG-GAAAG 1950 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 34.21 CpG sites = 45, Kimura (unadjusted) = 34.69 Transitions / transversions = 1.05 (45/43) Gap_init rate = 0.04 (14 / 325), avg. gap size = 1.43 (20 / 14) 596 29.80 2.54 7.78 chr1qtel1M 823790 824262 (175738) C L1M5_orf2#LINE/L1 (1064) 2230 1781 m_b50s551i8 1794 chr1qtel1M 823790 TATATAGAAATGCTGTTGATTTTCATGTGTTTACTTTATATTTTGCTACT 823839 i vi ii i i v i i ii? v i C L1M5_orf2#LIN 2230 TATATAGAAATACAATTGATTTTTGTATATTGACCTTGTATCCNGCGACC 2181 chr1qtel1M 823840 TTGCTAAAATCATTAATTATTTCAACTATGTTTTTAATTGAGTC--TGGG 823887 v i v v v v vv ? vi v v -- ? C L1M5_orf2#LIN 2180 TTGCTAAATTCACTTATTAGTTCTAGTAGTTTNTTTGTAGATTCTTTNGG 2131 chr1qtel1M 823888 ATTTTCCAACTGT---ATCATGATGTCTGCAAAAAAGAGAAATTTTTGTT 823934 i vv i?--- vii i v -? v v i C L1M5_orf2#LIN 2130 ATTTTCTACGTANACAATCATGTCATCTGCGAATAA-NGACAGTTTTATT 2082 chr1qtel1M 823935 ACATCAGTTCTTATTTTGATTCTATCCACTTCTTTTTCATTTCTTATAGC 823984 v v vv iv i v v iv ii i v vi v C L1M5_orf2#LIN 2081 TCTTCCTTTCCAATCTTTATGCCTTTTATTTCTTTTTCTTGCCTTATTGC 2032 chr1qtel1M 823985 TCTATTCTAGGATTTCAAGTACAATATTGAATAATATTGATGGCCATGAG 824034 v i-v ii v i iv v i i?vii ii C L1M5_orf2#LIN 2031 ACTG-GCTAGGACCTCCAGTACAATGTTGAATAGAAGTGGTGANAGCGGA 1983 chr1qtel1M 824035 CATCCTTTTGTCATCTCTAATCTTACAGTGAAAGATTAATGGAAAAATCT 824084 v v ii ii ii vi v -------------- ? C L1M5_orf2#LIN 1982 CATCCTTGTCTTGTTCCCGATCTTAGGGGGAAAG--------------CN 1947 chr1qtel1M 824085 TATTAGCTTTTCTCTATCATAGATGAGGCTTGCTAATGGTTTTAGGTAAA 824134 - i i? v i i viv v i ? ivv vv i C L1M5_orf2#LIN 1946 T-TCAGTNTTTCACCATTAAGTATGATGTTNGCTGTAGGTTTTTCGTAGA 1898 chr1qtel1M 824135 TGCATTAAAAATCAATTTAAGAATAATTGATCAATAGCTATACTTACAAT 824184 vi --vv iv i i - i --i vv -- v i -- i C L1M5_orf2#LIN 1897 TGCCCT--TTATCAGGTTGAGGA-AGTT--CCCTT--CTATTCCT--AGT 1857 chr1qtel1M 824185 TTATT-ATAATTATTATAGATTATAATAGAAATGGGTGTT---CTTTATC 824230 ii - v i v ---------i vi ---i i C L1M5_orf2#LIN 1856 TTGCTGAGAGTTTTTAT---------CATGAATGGGTGTTGAATTTTGTC 1816 chr1qtel1M 824231 AAG---TTTTTCTGCATCTTTTGGCATAATCATAT 824262 i--- v iv i C L1M5_orf2#LIN 1815 AAATGCTTTTTCTGCATCTATTGAGATGATCATAT 1781 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 38.38 CpG sites = 70, Kimura (unadjusted) = 39.59 Transitions / transversions = 1.17 (70/60) Gap_init rate = 0.08 (40 / 472), avg. gap size = 1.18 (47 / 40) 279 28.41 1.37 15.62 chr1qtel1M 824315 824460 (175540) C MIRc#SINE/MIR (37) 231 104 m_b50s601i6 1799 chr1qtel1M 824315 AATTTTCAAAGTACTTT-ACATATGTTATCTTCTTTGAAACTCAAAACAA 824363 i v ii - ii iv vv v C MIRc#SINE/MIR 231 AGTTTACAAAGCGCTTTCACATACATTATCTCATTTGATCCTCACAACAA 182 chr1qtel1M 824364 TCTATATTATGTTATGTGTTTTTTATATATGTTATGTAGGTGTTATTATT 824413 i i----------- ------ vi v iviv i --- C MIRc#SINE/MIR 181 CCC-----------TGTG------AGGTAGGCAGGGCAGG---TATTATT 152 chr1qtel1M 824414 ATCCCC-TTTTACAGATCACACAAGTTAAACTAGGCAAAGTTAAGTAA 824460 - v viv v v ii vi vi i i C MIRc#SINE/MIR 151 ATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGA 104 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 33.94 CpG sites = 19, Kimura (unadjusted) = 35.31 Transitions / transversions = 1.19 (19/16) Gap_init rate = 0.15 (22 / 145), avg. gap size = 1.00 (22 / 22) 374 31.34 5.22 0.00 chr1qtel1M 824968 825101 (174899) MIRc#SINE/MIR 16 156 (112) m_b50s601i7 1800 chr1qtel1M 824968 CAGTAGAGATAGCTCTGTACTTGAAATCAT-ATCCCCTGAACACGAATGA 825016 i i v v v i i v- vvv iiiv i vv MIRc#SINE/MIR 16 CAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCC 65 chr1qtel1M 825017 TTTATCTGCTGCTTATTAAAT-----ACCCTGA-TGTGTTACTTTACCTC 825060 ivvv ii i iv ----- i i-iiv i v MIRc#SINE/MIR 66 CGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 chr1qtel1M 825061 TATGGGCCTCAGTTTCCATATCTTTAAAATGGAGATGAAAA 825101 v i vi v i i v MIRc#SINE/MIR 116 TCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAA 156 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 40.06 CpG sites = 22, Kimura (unadjusted) = 41.33 Transitions / transversions = 1.10 (22/20) Gap_init rate = 0.02 (3 / 133), avg. gap size = 2.33 (7 / 3) 390 29.80 0.95 0.95 chr1qtel1M 825048 825152 (174848) MIR3#SINE/MIR 100 204 (4) m_b50s601i8 1800 chr1qtel1M 825048 GTTACTTTACCTCTATGGGCCTCAGTTTCCATATCTTTAAAATGGAGATG 825097 i i v vi v - iv MIR3#SINE/MIR 100 GTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAAT-GAGGGG 148 chr1qtel1M 825098 AAAAAATTAGGTAGATTTTGAAGTCTCTTCTCATTATAA-GTTCCATGAT 825146 ivvii i i iivi i i i i ivii v i -i i MIR3#SINE/MIR 149 GTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGAT 198 chr1qtel1M 825147 TCTATG 825152 MIR3#SINE/MIR 199 TCTATG 204 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 40.38 CpG sites = 22, Kimura (unadjusted) = 40.38 Transitions / transversions = 2.44 (22/9) Gap_init rate = 0.02 (2 / 104), avg. gap size = 1.00 (2 / 2) 28 34.72 1.22 3.11 chr1qtel1M 826485 826648 (173352) (TTCTTT)n#Simple_repeat 1 161 (0) m_b50s252i4 1801 chr1qtel1M 826485 TTCTTTTTCTTGGTCTCTCTGTCTCTATCTTTTTCTTTTTTCCACTT-TA 826533 -- i i v i v - ivi - v (TTCTTT)n#Sim 1 TTCTTTTTCTT--TTTCTTTTTCTTTTTCTTTTTC-TTTTTCTTTTTCTT 47 chr1qtel1M 826534 AATCATTGTCCTTTTTGTTTCAGTTTCTCTCTGACTTTGTTTCTTTCTTT 826583 vv - v i v ivv i i vv v i i (TTCTTT)n#Sim 48 TTTC-TTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTT 96 chr1qtel1M 826584 GTCTCTGTCTTGATATATCTCCTTTTCTTAGTTCTGTCTCTATCTCAGTT 826633 v i v vv v v i i -v v i v i vv (TTCTTT)n#Sim 97 TTCTTTTTCTTTTTCTTTTTCTTTTTCTT-TTTCTTTTTCTTTTTCTTTT 145 chr1qtel1M 826634 TC-TCTACCTTTTCTT 826648 - i v i (TTCTTT)n#Sim 146 TCTTTTTCTTTTTCTT 161 Matrix = Unknown Transitions / transversions = 0.72 (18/25) Gap_init rate = 0.04 (7 / 163), avg. gap size = 1.00 (7 / 7) 33 0.00 0.00 0.00 chr1qtel1M 827302 827329 (172671) (CA)n#Simple_repeat 1 28 (0) c_b50s251i0 1802 chr1qtel1M 827302 CACACACACACACACACACACACACACA 827329 (CA)n#Simple_ 1 CACACACACACACACACACACACACACA 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 396 31.61 14.37 0.00 chr1qtel1M 827641 827814 (172186) MIRc#SINE/MIR 39 237 (31) m_b50s601i9 1803 chr1qtel1M 827641 GAGTCAAAAATATTTCAGT-GAAATCCTGTCTCAGATATTCATTAATTTT 827689 ii v ii vi -vi i i v v vi i i i ii v MIRc#SINE/MIR 39 GAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGT 88 chr1qtel1M 827690 GGGATGTAGGGAAAAACACTCAACTTTGCTGTGCCT-----------TCT 827728 v iv v v iv i i iv v ----------- MIRc#SINE/MIR 89 GTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCT 138 chr1qtel1M 827729 ------TGTGGATAATAACAG------TACTTACTTCCCAGGATGCTTCT 827766 ------ v i v------ i i i v i vv v MIRc#SINE/MIR 139 GTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGT 188 chr1qtel1M 827767 GAGGATCAAATCAGATCACATATAT-AAAGCATTTTGAAAACCTCAAAG 827814 v v ii i - ii v ivi MIRc#SINE/MIR 189 GAGGATCAAATGAGATAATGTATGTGAAAGCGCTTTGTAAACTGTAAAG 237 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 39.18 CpG sites = 31, Kimura (unadjusted) = 42.16 Transitions / transversions = 1.29 (31/24) Gap_init rate = 0.03 (5 / 173), avg. gap size = 5.00 (25 / 5) 406 30.07 11.89 0.00 chr1qtel1M 827662 827804 (172196) MIR#SINE/MIR 57 216 (46) m_b50s601i10 1803 chr1qtel1M 827662 AATCCTGTCTCAGATATTCATTAATTTTGGGATGTAGGGAAAAACACTCA 827711 i v v vi i i i ii v v iv v v ivi i MIR#SINE/MIR 57 AATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTA 106 chr1qtel1M 827712 ACTTTGCTGTGCCT-----------TCT------TGTGGATAATAACAGT 827744 i iv ----------- ------ v i MIR#SINE/MIR 107 ACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGT 156 chr1qtel1M 827745 ACTTACTTCCCAGGATGCTTCTGAGGATCAAATCAGATCACATATATAAA 827794 i i vi i vv v i v v v i i i MIR#SINE/MIR 157 ACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATACATGTAAA 206 chr1qtel1M 827795 GCATTTTGAA 827804 ii v MIR#SINE/MIR 207 GCGCTTAGAA 216 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 37.01 CpG sites = 24, Kimura (unadjusted) = 39.33 Transitions / transversions = 1.26 (24/19) Gap_init rate = 0.01 (2 / 142), avg. gap size = 8.50 (17 / 2) 13 14.64 0.00 3.23 chr1qtel1M 827932 827963 (172037) (TTTAT)n#Simple_repeat 1 31 (0) m_b50s252i5 1804 chr1qtel1M 827932 TTTATTTTGTTTTAATTAATTTGTTTTTTATT 827963 i v v - v (TTTAT)n#Simp 1 TTTATTTTATTTTATTTTATTT-TATTTTATT 31 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 325 32.73 5.11 4.52 chr1qtel1M 828526 828701 (171299) C L2a_3end#LINE/L2 (0) 517 341 m_b50s601i11 1805 chr1qtel1M 828526 ATTTATTAATTTAACTGGCATTTATC-ATCACCTACCA-GTGCTGAGTGC 828573 i v i viii i- v i i - iii ii C L2a_3end#LINE 517 ATTCATTCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCAC 468 chr1qtel1M 828574 TATGCTACACTCTGGTGATATAA----GAATAAGA-ATGTGAGAGTTCCT 828618 i v vi v v i i---- i i - viii i i C L2a_3end#LINE 467 TGTTCTAGGCGCTGGGGATACAGCAGTGAACAAAACAGACAAAAGTCCCT 418 chr1qtel1M 828619 GCTTTTAAGGATCTTTCATGCTAAT--GGAAAGAAAAACAAATTTCTTTA 828666 ii i v v v v i -- ii v i ------- C L2a_3end#LINE 417 GCCCTCATGGAGCTTACATTCTAGTGGGGGGAGACAGACAA-------TA 375 chr1qtel1M 828667 AAAATACAAAGAGAATAAAATGAATACCAGGTGAG 828701 v v i v - i iv vi v v C L2a_3end#LINE 374 AACAAATAAATA-AGTAAAATATATAGTATGTCAG 341 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 44.02 CpG sites = 35, Kimura (unadjusted) = 45.16 Transitions / transversions = 1.75 (35/20) Gap_init rate = 0.07 (13 / 175), avg. gap size = 1.31 (17 / 13) 424 27.24 2.15 9.20 chr1qtel1M 829322 829507 (170493) C MIRb#SINE/MIR (1) 267 94 m_b50s601i12 1806 chr1qtel1M 829322 ATAATAC--CCACTACTCAT--AGTGCTGGCAAAGTGCCACATAGTGTGC 829367 v-- i i i i -- i vi v v vii v C MIRb#SINE/MIR 267 ATAATAGAGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGC 218 chr1qtel1M 829368 TCACTGCTCCTGTTAAGTTGTACAATTATTGTCTCATTTGATCCTCACAA 829417 v vi i----------- vvi i i C MIRb#SINE/MIR 217 TAAGCGCTT-----------TACATGCATTATCTCATTTAATCCTCACAA 179 chr1qtel1M 829418 CCATCCTTCCAGAGAATAGCTATTATTATGCCAATTTTTATTTGGGAGGA 829467 v i v v ---i v v v - ivviv C MIRb#SINE/MIR 178 CAACCCTGCGAG---GTAGGTATTATTATCCCCA-TTTTACAGATGAGGA 133 chr1qtel1M 829468 AACTGAGGCACACCGGCATTTATGTGACTTGCTCAGGGTC 829507 v vv ivi- v i i i C MIRb#SINE/MIR 132 AACTGAGGCTCAGAGAGG-TTAAGTAACTTGCCCAAGGTC 94 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 32.10 CpG sites = 22, Kimura (unadjusted) = 33.84 Transitions / transversions = 0.92 (22/24) Gap_init rate = 0.10 (18 / 185), avg. gap size = 1.11 (20 / 18) 430 28.98 9.43 2.35 chr1qtel1M 830016 830174 (169826) MIR#SINE/MIR 4 173 (89) m_b50s601i13 1807 chr1qtel1M 830016 GTACAACA--GTGCTTATAAGGACAGATTTCAAGTGAGGAAGA-----TG 830058 i i -- v vi v i ii iii--- vv ----- MIR#SINE/MIR 4 GTATAGCATAGTGGTTAAGAGCACGGGCTCTG---GAGCCAGACTGCCTG 50 chr1qtel1M 830059 GGTTTAAATCCAGTTTCAACCACTTACCAGCTGTGTGACTCTGGACAAAT 830108 ii v vi vi i ii i i MIR#SINE/MIR 51 GGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGT 100 chr1qtel1M 830109 TAGTTTGCCTCTATTTCTCTAAGTTTTC-CATTT------TCAGGATAAT 830151 v vi v v vi v i - i ------ vi MIR#SINE/MIR 101 TACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAAT 150 chr1qtel1M 830152 AGTAATACATTGTCTTA-AGAGTT 830174 i i -i ii i - i MIR#SINE/MIR 151 AATAGTAC-CTACCTCATAGGGTT 173 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 36.13 CpG sites = 30, Kimura (unadjusted) = 38.45 Transitions / transversions = 2.00 (30/15) Gap_init rate = 0.06 (9 / 158), avg. gap size = 2.11 (19 / 9) 13 30.01 1.37 4.23 chr1qtel1M 831610 831649 (168351) (AGAA)n#Simple_repeat 1 40 (31) m_b50s252i6 1808 chr1qtel1M 831610 AGCAAGTCAGAGAGAGAGGAAGAAAG-AGGAAGGATTGAAT 831649 v vv i i i - i i vv - (AGAA)n#Simpl 1 AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAA- 40 Matrix = Unknown Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 27 21.28 2.99 0.00 chr1qtel1M 831618 831649 (168351) (AG)n#Simple_repeat 1 34 (35) m_b50s252i7 1808 chr1qtel1M 831618 AGAGAGAGAGGAAGAAAGAG-GAAGGATTGA-AT 831649 ii i - ii vv - v (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 34 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.06 (2 / 31), avg. gap size = 1.00 (2 / 2) 43 0.00 0.00 0.00 chr1qtel1M 831650 831686 (168314) (AC)n#Simple_repeat 1 37 (0) c_b50s251i1 1809 chr1qtel1M 831650 ACACACACACACACACACACACACACACACACACACA 831686 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACA 37 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 27 21.28 2.99 0.00 chr1qtel1M 831687 831720 (168280) (AG)n#Simple_repeat 35 68 (1) m_b50s252i7 1810 chr1qtel1M 831687 GCAAGAGAGAGAGAGAAAGAGAGGGAGAGAGAGA 831720 vi i i (AG)n#Simple_ 35 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 68 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 18 10.85 3.33 0.00 chr1qtel1M 832229 832258 (167742) (TA)n#Simple_repeat 1 31 (0) m_b50s252i8 1811 chr1qtel1M 832229 TAGATATATATATATTTAAATATATAT-TAT 832258 v v v - (TA)n#Simple_ 1 TATATATATATATATATATATATATATATAT 31 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 384 26.54 1.97 3.33 chr1qtel1M 832451 832602 (167398) C L1ME3Cz_3end#LINE/L1 (722) 275 126 m_b50s551i9 1812 chr1qtel1M 832451 TATGAATTAGTCTCCATATTTTCTATATCCCCTCCAACATTTGTCACTTT 832500 i-- ii i - i i i i v i vi i v C L1ME3Cz_3end# 275 TATGAG--AGTTCCCGT-TTCTCCACATCCTCGCCAACACTTGGTATTGT 229 chr1qtel1M 832501 CT--CTTTCTATTATTTTAGCCAATATGGTAGATGTAAAATGATATCCCA 832548 v-- iv -- v v i i i i i i C L1ME3Cz_3end# 228 CAGACTTTTAA--ATTTTTGCCAATCTGATGGGTGTGAAATGGTATCTCA 181 chr1qtel1M 832549 AGGTTGTTTTAATTTGCATGTTTCTAATCTATACTGACTTAGAACAT-TT 832597 vv ? v ii i ivv v vv v i - C L1ME3Cz_3end# 180 TTGTNGTTTTAATTTGCATTTCCCTGATTACTAGTGAGGTTGAGCATCTT 131 chr1qtel1M 832598 TTCAT 832602 C L1ME3Cz_3end# 130 TTCAT 126 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 32.76 CpG sites = 23, Kimura (unadjusted) = 33.82 Transitions / transversions = 1.44 (23/16) Gap_init rate = 0.05 (7 / 151), avg. gap size = 1.14 (8 / 7) 343 35.29 0.53 0.00 chr1qtel1M 832463 832649 (167351) C L1MB1_3end#LINE/L1 (645) 270 83 m_b50s551i10 1812 chr1qtel1M 832463 TCCATATTTTCTATATCCCCTCCAACATTTGTCACTTTCTCTTTCTATTA 832512 vv i i i i v i i i i v i v v C L1MB1_3end#LI 270 TCCAATTTCTCCACATCCTCGCCAACACTTGTTATTTTTTGTTTTTTTGA 221 chr1qtel1M 832513 TTTTAGCCAATATGGTAGATGTAAAATGATATCCCAAGGTTGTTTTAATT 832562 vv viv iii i i ii i vv v i C L1MB1_3end#LI 220 TAATAGCCATCCTAACAGGTGTGAGGTGATATCTCATTGTGGTTTTGATT 171 chr1qtel1M 832563 TGCATGTTTCTAATCTATACTGACTTAGAACAT-TTTTCATGAAACTACA 832611 v ii i vvv v iv v i - iv v iiv C L1MB1_3end#LI 170 TGCATTTCCCTGATGATTAGTGATGTTGAGCATCTTTTCATATACCTGTT 121 chr1qtel1M 832612 AATTGTTTTGATTTCTTCAATGAAAAAATGCTTCTTTA 832649 iiiii vv v vv i i ii v i C L1MB1_3end#LI 120 GGCCATTTGTATGTCTTCTTTGGAGAAATGTCTATTCA 83 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 49.30 CpG sites = 37, Kimura (unadjusted) = 49.30 Transitions / transversions = 1.28 (37/29) Gap_init rate = 0.01 (1 / 186), avg. gap size = 1.00 (1 / 1) 450 23.44 2.31 1.53 chr1qtel1M 832473 832602 (167398) C L1ME5_3end#LINE/L1 (681) 260 130 m_b50s551i11 1812 chr1qtel1M 832473 CTATATCCCCTCCAACATTTGTCACTTTCT--CTTTCTATTATTTTAGCC 832520 i i i v i v i v i-- -- v C L1ME5_3end#LI 260 CCACATCCTCGCCAACACTTGGCATTATCCAGCTTTCTA--ATTTTTGCC 213 chr1qtel1M 832521 AATATGGTAGATGTAAAATGATATCCCAAGGTTGTTTTAATTTGCATGTT 832570 i v ii i i i vv v i C L1ME5_3end#LI 212 AGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATTTC 163 chr1qtel1M 832571 TCTAATCTATACTGACTTAGAACAT-TTTTCAT 832602 i ivv v v v i - i C L1ME5_3end#LI 162 TCTGATTACTAATGAGTTTGAGCATCTCTTCAT 130 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 28.56 CpG sites = 17, Kimura (unadjusted) = 28.56 Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.03 (4 / 129), avg. gap size = 1.25 (5 / 4) 254 33.01 7.22 2.23 chr1qtel1M 832958 833428 (166572) C L1M1_orf2#LINE/L1 (406) 2888 2395 m_b50s551i12 1813 chr1qtel1M 832958 CATTTTTATCCCATCCTGGTATAGGGTGAAAAATACTGGTCT-CTGTCAA 833006 v iiv ii v v i i i vv -v v v C L1M1_orf2#LIN 2888 CATTTTGATTTGATTTTTGTATATGGCGAGAGATAGGGGTCTAGTTTCAT 2839 chr1qtel1M 833007 GTTTCTGCCATAGTGTTTTCCAGTTTTCCC--CACAATTTTTACCAAATA 833054 vi - vv v v -- v v vvv i v C L1M1_orf2#LIN 2838 TCTTCTGC-ATATGGATATCCAGTTTTCCCAGCACCATTTATTGAAGAGA 2790 chr1qtel1M 833055 ATAACTTTAGATCCCCAA---AT---CTTAATAC--TTGACAAATACAAA 833096 v iv --- i--- --- iii -- v i v ii i C L1M1_orf2#LIN 2789 CTGTCTTT---TCCCCAGTGTATGTTCTTGGCACCTTTGTCGAAAATGAG 2743 chr1qtel1M 833097 GTTATTATATTTATTTG----TGGCTGTAAGTTGTATGTCTACTCTATTC 833142 v i i i vv i v ---- vi v ii v ---- i i C L1M1_orf2#LIN 2742 TTCACTGTAGGTGTGTGGATTTGTTTCTGGGTTCT----CTATTCTGTTC 2697 chr1qtel1M 833143 CACT----TATCTTTCTATTTCTTAGCCAGTACC-TGATAATTTTGATAA 833187 i ---- v v i i vv - v -i i v C L1M1_orf2#LIN 2696 CATTGGTCTATGTGTCTGTTTTTATGCCAGTACCATGCT-GTTTTGGTTA 2648 chr1qtel1M 833188 TTATTA-TCTGATAATATAGTTTAAGATCTCATACTGCTAAATCTCCTGT 833236 i vi- - i i i ii vvi v iv vvi v C L1M1_orf2#LIN 2647 CTATAGCTCTG-TAGTATAATTTGAAGTCAGGTAATGTGATTCCTCCAGT 2599 chr1qtel1M 833237 CTTTCTTTTATTTGTTT-------CTGTGAC-ATTCTTGACTTTATGTTC 833278 - v i v i i------- v i - v iii v vv C L1M1_orf2#LIN 2598 -TTTGTTCTTTTTGCTCAGGATAGCTTTGGCTATTCTGGGTCTTTTGTGG 2550 chr1qtel1M 833279 TTCCAAATAAGTTTTGTGATT-TTTTTCCT-TATCGATAACATACCTTTT 833326 v i iv - i - v vi i viv iv iv C L1M1_orf2#LIN 2549 TTCCATATAAATTTTAGGATTGTTTTTTCTATTTCTGTGAAGAATGTCAT 2500 chr1qtel1M 833327 TGGTTATTTAGTTGGTATGATATTGCTTCTTTAAATTAGTTTTGGTAATG 833376 vv ii v v vii vv v i iv v i i C L1M1_orf2#LIN 2499 TGGTATTTTGATAGGGATTGCATTGAATCTGTAGATTGCTTTGGGTAGTA 2450 chr1qtel1M 833377 T---CATTTTTGTTTTATTGGCCCTTCCTACCCACGAATAATTAATATTT 833423 --- viivv iii v i i i vvv i C L1M1_orf2#LIN 2449 TGGACATTTTAACAATATTGATTCTTCCAATCCATGAACATGGAATATCT 2400 chr1qtel1M 833424 CTCCA 833428 i C L1M1_orf2#LIN 2399 TTCCA 2395 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 43.43 CpG sites = 75, Kimura (unadjusted) = 44.20 Transitions / transversions = 0.97 (75/77) Gap_init rate = 0.05 (25 / 470), avg. gap size = 1.80 (45 / 25) 186 28.89 0.00 0.00 chr1qtel1M 833879 833923 (166077) C L3#LINE/CR1 (1077) 3022 2978 m_b50s601i14 1814 chr1qtel1M 833879 CTCATATTTTCCCATCTCTTCTACAGGAATAGCATGAAGTACCTT 833923 i ii iv i i i v iiv i C L3#LINE/CR1 3022 CCCATATTTCTCCATCTTGTCCACAAGGATATCATGAGAGACTTT 2978 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 39.36 CpG sites = 10, Kimura (unadjusted) = 39.36 Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 285 38.12 3.55 1.39 chr1qtel1M 833914 834054 (165946) MIRb#SINE/MIR 5 148 (120) m_b50s601i15 1815 chr1qtel1M 833914 GAAGTACCTTAGTATAATGGAATGCACATTTTTTCTTGGTTCAGA--GGA 833961 ii i v v i ii i v vi ivvvi i v iv -- iv MIRb#SINE/MIR 5 GGGGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGAC 54 chr1qtel1M 833962 CTGGATTAAAATCTAATCTCAACTATTTACTAATTTTATGACTTTGTGGC 834011 i vi iviv vi i i ii v i i - MIRb#SINE/MIR 55 CTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTG-GGC 103 chr1qtel1M 834012 ---TTGGTGTAATCTCACTGAAACCTAGTTTTCTTTCCCATAAAAT 834054 --- iv - i v iv ii i ivi ii MIRb#SINE/MIR 104 AAGTTACT-TAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAAT 148 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 52.21 CpG sites = 34, Kimura (unadjusted) = 57.15 Transitions / transversions = 1.79 (34/19) Gap_init rate = 0.03 (4 / 140), avg. gap size = 1.75 (7 / 4) 393 21.61 6.19 1.69 chr1qtel1M 834574 834686 (165314) C MIRc#SINE/MIR (141) 127 10 m_b50s601i16 1816 chr1qtel1M 834574 CTGAGGCT-ATTGCGGTT----GACTTGCCCAGGGTCACACAGCTAGGAA 834618 - vv v ---- i v C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAA 78 chr1qtel1M 834619 GTGTTAAATGTCTGAGGCCAGA--TCAAGTCCTCCTGACTTCAGGGCTGG 834666 vi i - - i i i iv --i i i i i v ii C MIRc#SINE/MIR 77 GTGGCAGA-G-CCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAG 30 chr1qtel1M 834667 TGTTCTATCCACTGCTCCAC 834686 i v v C MIRc#SINE/MIR 29 TGCTCTTTCCACTGCACCAC 10 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 24.83 CpG sites = 15, Kimura (unadjusted) = 26.07 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.04 (5 / 112), avg. gap size = 1.80 (9 / 5) 276 21.93 1.83 12.12 chr1qtel1M 834590 834698 (165302) C MIR3#SINE/MIR (105) 103 5 m_b50s601i17 1816 chr1qtel1M 834590 TGACTTGCCCAGGGTCACACAGCTAGGAAGTGTTAAATGTCTGAGGCCAG 834639 i ? vv vi i - - i i i i C MIR3#SINE/MIR 103 TGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGA-G-CCGGGACTAG 56 chr1qtel1M 834640 A--TCAAGTCCTCCTGACTTCAGGGCTGGTGTTCTATCCACTGCTCCACC 834687 --i i - i vi v i- i v --- ---- C MIR3#SINE/MIR 55 AACCCAGGT-CTCCTGACTCCCAGTCC-GTGCTCTCT---CTGCTC---- 15 chr1qtel1M 834688 TAGCTACCCTG 834698 - i i C MIR3#SINE/MIR 14 -AGCCACTCTG 5 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 23.93 CpG sites = 15, Kimura (unadjusted) = 26.84 Transitions / transversions = 2.50 (15/6) Gap_init rate = 0.12 (13 / 108), avg. gap size = 1.08 (14 / 13) 379 35.81 2.63 3.41 chr1qtel1M 837214 837479 (162521) C L3#LINE/CR1 (516) 3583 3320 m_b50s601i18 1817 chr1qtel1M 837214 TGATTTAAGCAGAAAAATATACAGTGGAGCCATTAAAATGCGTTTTCTGG 837263 i i i v viv ivi i ii i vvviv v v? C L3#LINE/CR1 3583 TGGTCTGACCAGCGCAGAGTACAGCGGGACTATTACCTCCCTTGNTCTGG 3534 chr1qtel1M 837264 AAATTATATCTGACTTCATTC--TCTGTGCTATTTTTAGCTTTGTGGGGC 837311 v i ii vvv v v --i iv v vviv v v - C L3#LINE/CR1 3533 ACACTATACTTCTATTAATGCAGCCTAAGATTGCATTAGCTTTTTTGG-C 3485 chr1qtel1M 837312 TGTCTGGACAGAATGTTAGCACATATTAAGCTT-TAACCAACTAAAATTC 837360 v i vviv v v i v i -iiii ii C L3#LINE/CR1 3484 AGCCACATCACACTGTTGGCTCATATTGAGCTTGCGGTCAACTAAAACCC 3435 chr1qtel1M 837361 -TGGATTTTGTTCTCATGAATCATTTCATAGCCACCTGGAATAGCTTCAC 837409 - i i i v v i iiii v vv -----i -- i -i C L3#LINE/CR1 3434 CTAGGTCTTTTTCACGTGAACTGCTGCTAAGCCA-----GAT--CCTC-T 3393 chr1qtel1M 837410 CCAACTTATGTCTGTGAAAAT-ATTTTTGGAACGTACA--AAGCACTTTA 837456 v i i iii v iv - v v v --v v C L3#LINE/CR1 3392 CCATCCTGTACTTGTGCAGTTGATTTTTTGAACCTAAATGCAGGACTTTA 3343 chr1qtel1M 837457 CTTTTATCTCTATAACATTTCAT 837479 v i i v v C L3#LINE/CR1 3342 CATTTATCCCTGTTAAATTTCAT 3320 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 46.82 CpG sites = 46, Kimura (unadjusted) = 49.86 Transitions / transversions = 1.00 (46/46) Gap_init rate = 0.05 (14 / 265), avg. gap size = 1.14 (16 / 14) 291 38.39 6.59 5.59 chr1qtel1M 837573 837997 (162003) L2b_3end#LINE/L2 31 459 (7) m_b50s601i19 1818 chr1qtel1M 837573 CCCCATATCTTTCCAATCTCCTTATGTCTTAAACATGTACTTTGAGATCC 837622 i v i v v iiv - i -------- i v-- L2b_3end#LINE 31 CCTCATCTCCTACCACTCTCCCCTTG-CTCA--------CTCTGC--TCC 69 chr1qtel1M 837623 AGTGACACAGGTTACCTTAGAGTTTCTC--ACACAA-AAACCTTCACCTC 837669 iv v iiv ivv i -- iv- ?i ii? v iv L2b_3end#LINE 70 AGCCACACTGGCCTCCTTGCTGTTCCTCGAACACGCCANGCTCNCTCCCG 119 chr1qtel1M 837670 CCT---AGTGTTTTCATTGACGGCCCCCTGTGACTG-AACTTCTCTCCCT 837715 ---i iv v i?vi v ii v v - vi ii i L2b_3end#LINE 120 CCTCAGGGCCTTTGCACNTGCTGTTCCCTCTGCCTGGAACGCCCTTCCCC 169 chr1qtel1M 837716 CCTTTCTTACATTTTCTGTCTTTACTAG--CTTCAATTC-CAGATTTAAT 837762 v i ii ii v vvi viiiii vi-- iv - v iv L2b_3end#LINE 170 ACCTCTTCGCCTGGCCAACTCCTACTCATCCTTCAGGTCTCAGCTCAAAT 219 chr1qtel1M 837763 TTCACTTTCTTTAGGCAGTTTTTTT---CTTAATAGATTTTAATGAGACT 837809 v i i iii v iii iii--- iivvi iiiv-ii v i - L2b_3end#LINE 220 GTCACCTCCTCCGGGAAGCCCTCCCTGACCCCCCAGGCCG-GGTCAGGC- 267 chr1qtel1M 837810 GATTTTCTTCTGGTAAATATTTCCA-TTCTCCCCTTTAGGTATCTTTTTG 837858 -iiii i ---iiviii - i v --- vi - i vv L2b_3end#LINE 268 -GCCCTCCTCTGG---GCCCCCCCAGTCCTACCCT---GCCA-CTCTGGG 309 chr1qtel1M 837859 GTACAAATTATCTGC--ACAT---TGTCACCCCCA--ACATTATGAATTT 837901 v i? - i ?-- --- v -- v i i ii i L2b_3end#LINE 310 TTATNA-TTGTCTGNTTACATGTCTGTCTCCCCCACTAGACTGTGAGCTC 358 chr1qtel1M 837902 CTTGAGTGAAGGGAT------TGTCATTTGCATTTCTATATAACTCCA-T 837944 v v v i------ v v v iiv i -- i -i L2b_3end#LINE 359 CGTGAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTGTAT--CCCCAGC 406 chr1qtel1M 837945 GTTTAAGAGAGTGCCTAGAATATACTAAGTACTTAATCAATACTTGTTGA 837994 ii iv v ? i v i i v i ii i i v i L2b_3end#LINE 407 GCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTTGTTGA 456 chr1qtel1M 837995 CTG 837997 v L2b_3end#LINE 457 ATG 459 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 53.58 CpG sites = 98, Kimura (unadjusted) = 59.14 Transitions / transversions = 1.75 (98/56) Gap_init rate = 0.09 (37 / 424), avg. gap size = 1.41 (52 / 37) 335 33.60 5.83 0.79 chr1qtel1M 837877 837996 (162004) L2d2_3end#LINE/L2 422 547 (8) m_b50s601i20 1818 chr1qtel1M 837877 TTGTCACCCCCAAC---ATTATGAATTTCTTGAGTGAAGGGATTGTCATT 837923 -i --- i i ii i v v iii vvi L2d2_3end#LIN 422 TTGTC-TCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCT 470 chr1qtel1M 837924 TGCATTTCTATATAACTCC----ATGTTTAAGAGAGTGCCTAGAATATAC 837969 ii i v i v i ----ii ii iv v v v i i v L2d2_3end#LIN 471 TATACTTCTTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAG 520 chr1qtel1M 837970 TAAGTACTTAATCAATACTTGTTGACT 837996 i ii i v i i L2d2_3end#LIN 521 TAGGCGCTCAATAAATATTTGTTGATT 547 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 44.40 CpG sites = 28, Kimura (unadjusted) = 48.00 Transitions / transversions = 2.33 (28/12) Gap_init rate = 0.03 (3 / 119), avg. gap size = 2.67 (8 / 3) 200 31.94 5.56 3.10 chr1qtel1M 838062 838187 (161813) L2#LINE/L2 2223 2351 (731) m_b50s601i21 1819 chr1qtel1M 838062 GTTGGGTGTCTCCCAAGATTCTGTC-----ATCCATTCTCTTTTGTGCTC 838106 i- vi i ii v ----- i iv i v i- L2#LINE/L2 2223 GTTGGA-GTGCCCCAGGGCTCAGTCCTTGGACCTCTTCTCTTCTCTA-TC 2270 chr1qtel1M 838107 TTCCTTGAG--ATTTGGTGATCCTAATAGTTCCTATGGTTTCAGTTATCA 838154 v vi v v--vi ? ii viviv ii i i iv i L2#LINE/L2 2271 TACACTCACTCCCTNGGTGATCTCATCCAGTCTCATGGCTTTAAATACCA 2320 chr1qtel1M 838155 TCAATATGCTGGTGACTCTTTCATTTTTATATC 838187 v i --i vv L2#LINE/L2 2321 TCTATATGCTGATGACTC--CCAAATTTATATC 2351 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 43.59 CpG sites = 23, Kimura (unadjusted) = 43.59 Transitions / transversions = 1.44 (23/16) Gap_init rate = 0.05 (6 / 125), avg. gap size = 1.83 (11 / 6) 238 39.57 0.72 0.00 chr1qtel1M 839095 839233 (160767) L2#LINE/L2 2353 2492 (590) m_b50s601i22 1819 chr1qtel1M 839095 CTAACCCTCATCTCTCTGTTGATCTCCAGTTTTGTATATTCAGCTTTCTA 839144 i i vv i ivi v vi i i i vi L2#LINE/L2 2353 CCAGCCCGGACCTCTCCCCTGAACTCCAGACTCGTATATCCAACTGCCTA 2402 chr1qtel1M 839145 -TTAATATTTTGAACTGAATTTCATGTATATATTTTAAAATCAACATGAC 839193 - ii i i iv vi i v vvi vii i i v i v L2#LINE/L2 2403 CTCGACATCTCCACTTGGATGTCTAATAGGCATCTCAAACTTAACATGTC 2452 chr1qtel1M 839194 CTGAATTTCACTAAATATGATTCCCTTTAAATATTCCCCT 839233 vi i vv vvvv vv i i i iv v i L2#LINE/L2 2453 CAAAACTGAACTCCTGATCTTCCCCCTCAAACCTGCTCCT 2492 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 55.02 CpG sites = 30, Kimura (unadjusted) = 58.42 Transitions / transversions = 1.20 (30/25) Gap_init rate = 0.01 (1 / 138), avg. gap size = 1.00 (1 / 1) 280 38.67 4.66 2.49 chr1qtel1M 839596 839831 (160169) C L2#LINE/L2 (2479) 603 363 m_b50s601i23 1820 chr1qtel1M 839596 TGATCCAAAAGTAGTTATAGGGAGCAAGGAGTTCTGCCTTCTCCACC--- 839642 i iii ii iv ii vv -i v i --- C L2#LINE/L2 603 TGGTCTGGAAGCGGCAATGAGGAGCAAGGAGGAC-ACCTACCCCACCTCC 555 chr1qtel1M 839643 ATAATCAATAA-ACTAGGAAATATGGGGGAAAGTAGAGCCAAACCCTGAA 839691 vivi i ii- v i?- i i i iv v vvv i i C L2#LINE/L2 554 AGGCCCAGTGGTACGAGGGN-TGTGGGAGAGAAAACAGCCACCACTTGAG 506 chr1qtel1M 839692 CGGGTAAGAAAGGAATCA-TGATTTTTCAGCATGGAGCTATAGCTTTAGT 839740 v iviv ii v - -- ii vivi i -i i i? C L2#LINE/L2 505 AGGGCTGCAGGGGAAGCAGTG--TCCTCAGGGGAGAGCCA-GGTTTCNGT 459 chr1qtel1M 839741 GAGGATTTGAAGATGAAATGAATG-----AAAAGTAAGTTTAAAATG-AA 839784 v iiivv i iv i ----- i - i v ii i-ii C L2#LINE/L2 458 TAGAGCAAGAAGGTGAAGGGAACGTTCAGAGAAG-AGGTTGAGGATACGG 410 chr1qtel1M 839785 CGAACTTTGCTGGTTATGGTGCAGGCATTGTAGGGGGCATTGTGGGA 839831 v i i i v i vv iv vi vi i iv i C L2#LINE/L2 409 GGGATTTTGCTGATGACGGACCGTGAGTTCCAGAGGGCACAGTGGAA 363 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 54.30 CpG sites = 58, Kimura (unadjusted) = 59.68 Transitions / transversions = 1.87 (58/31) Gap_init rate = 0.05 (11 / 235), avg. gap size = 1.55 (17 / 11) 290 33.33 1.75 0.00 chr1qtel1M 840226 840339 (159661) C MIRb#SINE/MIR (116) 152 37 m_b50s601i24 1821 chr1qtel1M 840226 CCTCACTTTACAGATGTTTCTATTAAGTC-CAGAGAAGATGAGTTAATTG 840274 i i vvvvv i i v - i v i v v C MIRb#SINE/MIR 152 CCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTG 103 chr1qtel1M 840275 CCCACAGACATAGAATTAATAAGTGGGTGAGGCAGAATTCTATCTC-CAT 840323 vi v i v ii i vv v i i v v i -vi C MIRb#SINE/MIR 102 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGT 53 chr1qtel1M 840324 ATATCACCCTCCAAAG 840339 v i vvv C MIRb#SINE/MIR 52 CTGTCTGACTCCAAAG 37 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 42.81 CpG sites = 16, Kimura (unadjusted) = 44.29 Transitions / transversions = 0.73 (16/22) Gap_init rate = 0.02 (2 / 113), avg. gap size = 1.00 (2 / 2) 274 27.78 4.17 0.00 chr1qtel1M 840891 840962 (159038) C MIR3#SINE/MIR (23) 185 111 m_b50s601i25 1822 chr1qtel1M 840891 AGAACAGAAAGATGCTTTAAAGGTCATCTTGTCCA--CCTCT-ATTTGAC 840937 i v i ivi i i i v -- i - v C MIR3#SINE/MIR 185 AGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTAC 136 chr1qtel1M 840938 AGCTAAGAAAATGGAGGTTCAGAAA 840962 v i i iv ii i C MIR3#SINE/MIR 135 AGATGAGGAAACTGAGGCCCAGAGA 111 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 36.51 CpG sites = 14, Kimura (unadjusted) = 36.51 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.03 (2 / 71), avg. gap size = 1.50 (3 / 2) 285 24.98 8.85 0.82 chr1qtel1M 842165 842277 (157723) MER63D#DNA/hAT-Tip100 342 463 (598) m_b50s502i1 1823 chr1qtel1M 842165 GTATTTACACGGAGGTAATAAGCCAATGTTGTTCATCAGAGTTTGATTTG 842214 viv v vi v i i iivv i i i MER63D#DNA/hA 342 GTATTTACACCACGGAAATCGGCAAACGCTACAAATCAGGGCTTGATTTA 391 chr1qtel1M 842215 CTTGTCTT--------TC-AGACTTAGGAAAAGGATGTAGAAAAGGTTGA 842255 - i -------- - i iv v v i MER63D#DNA/hA 392 -TTGTTTTGTTGATTGTCTAGACTTAAGAAAGTGATGGAGAAAATGTTAA 440 chr1qtel1M 842256 TAATGTGCATT-CACTTATAAGT 842277 iiv -v v MER63D#DNA/hA 441 TAATGCAGATTAAACTTAAAAGT 463 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 28.28 CpG sites = 15, Kimura (unadjusted) = 30.82 Transitions / transversions = 1.15 (15/13) Gap_init rate = 0.04 (4 / 112), avg. gap size = 2.75 (11 / 4) 17 14.04 8.82 4.23 chr1qtel1M 842575 842642 (157358) (ATGAAGAAT)n#Simple_repeat 1 71 (0) m_b50s252i9 1824 chr1qtel1M 842575 ATGAAGTTATAT-AA-AATATG-AGAATCAGGGGGAAAATAAAG-TTTTG 842620 -v - - - - v ii v i -v v (ATGAAGAAT)n# 1 ATGAAG-AATATGAAGAATATGAAGAAT-ATGAAGAATATGAAGAATATG 48 chr1qtel1M 842621 AAG-A-ATGAAGAATATGAGAGAA 842642 - - - (ATGAAGAAT)n# 49 AAGAATATGAAGAATATGA-AGAA 71 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.13 (9 / 67), avg. gap size = 1.00 (9 / 9) 18 3.67 3.57 0.00 chr1qtel1M 843562 843589 (156411) (TTTA)n#Simple_repeat 1 29 (0) m_b50s252i10 1825 chr1qtel1M 843562 TTTATTTATTTATTTATTT-TTAATTTAT 843589 - v (TTTA)n#Simpl 1 TTTATTTATTTATTTATTTATTTATTTAT 29 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 591 33.11 3.34 0.00 chr1qtel1M 843758 844056 (155944) C L1PREC2_orf2#LINE/L1 (1055) 2239 1931 m_b50s551i13 1826 chr1qtel1M 843758 TGTTTGTGATATATAGGAATGCTGATAATTTATGTGAATTTGCTTTATAT 843807 vv i i ii i v iv vii i C L1PREC2_orf2# 2239 TGTTGTTGGTGTATAGGAATGCTAGTGATTTTTGTACATTGATTTTGTAT 2190 chr1qtel1M 843808 TCTGTTATTTTGTGAAAACTATTAATTGTTTT---TAACTTTTAAGTTG- 843853 i vv i ivi ii i v iivi ?---v i ii ii - C L1PREC2_orf2# 2189 CCTGAAACTTTGCTGAAGTTGTTTATCAGCTNAAGGAGCTTTTGGGCCGA 2140 chr1qtel1M 843854 TATTA-GGGATTTCCTAAGTATATCATCATATCATTTACAAA-AGAAATA 843901 v i - i i ii vv i i i i - ii C L1PREC2_orf2# 2139 GACTATGGGGTTTTCTAGATATAGAATCATGTCGTCTGCAAACAGGGATA 2090 chr1qtel1M 843902 GTTTGATCACCTCATTGTGCATTTTAATTTCTTCTATTACTTTTTCT--C 843949 iiv vi vivi vi vi i i v i -- C L1PREC2_orf2# 2089 GTTTGACTTCCTCTCTTCCTATTTGGATGCCCTTTATTTCTTTCTCTTGC 2040 chr1qtel1M 843950 TTG-TTGCTATTGCTAAAATTTCCAATACAATATTGAATAATA-TTGTGA 843997 i - v v i ii i v i iv - v C L1PREC2_orf2# 2039 CTGATTGCTCTGGCCAGGACTTCCAATACTATGTTGAATAGGAGTGGTGA 1990 chr1qtel1M 843998 TAGTGAGCATACTTCTTTCACACCTGATGTTACTGGGAATGCTTCTAGAT 844047 v v i v v i iiii v v v i vv i v C L1PREC2_orf2# 1989 GAGAGGGCATCCTTGTCTTGTGCCGGTTTTCAAGGGGAATGCTTCCAGCT 1940 chr1qtel1M 844048 TATTCACAT 844056 v v v C L1PREC2_orf2# 1939 TTTGCCCAT 1931 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 44.44 CpG sites = 60, Kimura (unadjusted) = 45.72 Transitions / transversions = 1.54 (60/39) Gap_init rate = 0.02 (7 / 298), avg. gap size = 1.43 (10 / 7) 362 31.10 9.28 3.93 chr1qtel1M 845071 846449 (153551) C L1M3_orf2#LINE/L1 (1448) 1840 391 m_b50s551i14 1827 chr1qtel1M 845071 TTTTTAAAATAGAAATGAATTTTATACTTTATTAAAACATTCCTCTATAT 845120 vv - - i v iv i i i vvv ii ii C L1M3_orf2#LIN 1840 TTTTTATCAT-GAAA-GGATGTTGAATTTTGTCAAATGCTTTTTCTGCAT 1793 chr1qtel1M 845121 CTATTGATATAATCTTATGATTTTAA-GTTTCA--ATATTGAT-TGCATC 845166 v i v i v -vi --v i i - -i v C L1M3_orf2#LIN 1792 CTATTGAGATGATCATGTGATTTTTATCCTTCATTCTGTTAATGTG-GTG 1744 chr1qtel1M 845167 AATTATATTAAT-AATTTT----TGTTATATTACCCTTGAATTCCTGACA 845211 v i i ? -i ?---- iv ii i v i v iv C L1M3_orf2#LIN 1743 TATCACATTNATTGATTTNCGTATGTTGAACCATCCTTGCATCCCAGGGA 1694 chr1qtel1M 845212 TAAATCCCACATGCTCATGATCTAAAATCTTTGTAATGTATAAACT-TTG 845260 v v i v vi i v i---- - C L1M3_orf2#LIN 1693 TAAATCCCACTTGGTCATGGTGTATGATCCTTTTAATGTG----CTGTTG 1648 chr1qtel1M 845261 ---TCATTTTTTAATTACTGTTTTAATTAGGATTTTCACATCCATGTTCT 845307 --- iv ---ii v i iv v ii i v C L1M3_orf2#LIN 1647 AATTCGGTTT---GCTAGTATTTTGTTGAGGATTTTTGCATCTATGTTCA 1601 chr1qtel1M 845308 TTA-----ATTTTCCT-------TCTTTATTTTTACTCTTCCTTTTTATA 845345 i ----- vv ------- vi v v v -- v v i C L1M3_orf2#LIN 1600 TCAGGGATATTGGCCTGTAGTTTTCTTTTCTTGTAGTGT--CTTTGTCTG 1553 chr1qtel1M 845346 -TTTTAGCATCA------TATTTGTTTCATAAAAGAAATTTGGTAGTACC 845388 -i i i ------ ii v ii vi i v iii C L1M3_orf2#LIN 1552 GCTTTGGTATCAGGGTAATGCTGGCCTCATAAAATGAGTTTGGAAGTGTT 1503 chr1qtel1M 845389 CCTTCTTTATCTATTATTAACAATTGTTTAATA----CTGGAATTAGGTC 845434 i i iv v v viv vv i v ----i v iv C L1M3_orf2#LIN 1502 CCCTCCTCTTCAATTTTTTGGAAGAGTTTGAGAAGGATTGGTATTAATTC 1453 chr1qtel1M 845435 TT-----AAT--TTGATAGAATTCACTTTTGAATCCATCTGGCCATAGG- 845476 ----- -- i ivv v i v i - C L1M3_orf2#LIN 1452 TTCTTTAAATGTTTGGTAGAATTCACCAGTGAAGCCATCTGGTCCTGGGC 1403 chr1qtel1M 845477 -TTTTTTTCTTGGGAACTTCATTTATGAT--CTG-TTCAATTTCTTTTTC 845522 - i v i----i v -- - i i vii C L1M3_orf2#LIN 1402 TTTTCTTTGTTGGGAG----GTTTTTGATTACTGATTCAATCTCCTTACT 1357 chr1qtel1M 845523 AAAAATAGATCTATTTAGATATTTTATTTCACCTTC-TGCTT--GTCCAG 845569 vivv v i i i v i --- - v -- iv C L1M3_orf2#LIN 1356 CGTTATTGGTCTGTTCAGATTTTCTATTT---CTTCATGATTCAGTCTTG 1310 chr1qtel1M 845570 GCAGTTTTTATTTTTGTCAATATTCTTCCATTTCACTTA--------AAT 845611 i v v v v viiv iv vii -------- C L1M3_orf2#LIN 1309 GTAGGTTGTATGTTTCTAGGAATTTATCCATTTCTTCTAGGTTATCCAAT 1260 chr1qtel1M 845612 TTATTGAC--ATAATTTAGCAAAATAACTCCTTATAGTTGCTTTAATTTC 845659 i i -- vvv v i iiii ii ivi v C L1M3_orf2#LIN 1259 TTGTTGGCGTATAATTGTTCATAGTAGTCTCTTATGATCCTTTTTATTTC 1210 chr1qtel1M 845660 ACCTTCATTAGTGGCATATTTATCC-CTTTCATTTTTAATACTAGTTATT 845708 vvivv i v i - v v - i i vi v C L1M3_orf2#LIN 1209 TGTGGCATCAGTTGTA-ATGTCTCCTCTTTCATTTCTGATTTTATTTATT 1161 chr1qtel1M 845709 TGA---TTTCCTTTTCTCCCATTAAAATCATATCTGCCAATATATTATAT 845755 --- ii i i -- -- i - v ivvii v i i - C L1M3_orf2#LIN 1160 TGAGTCTTCTCTTTTTTTC--TT--AGTC-TAGCTAAAGGTTTGTCA-AT 1117 chr1qtel1M 845756 TTTTATTTTATTTTTTT--AAAACCAAATC-CATTTTTATTTATTAATTC 845802 --v i i-- v -i v ii v vv C L1M3_orf2#LIN 1116 TTT--GTTTATCTTTTCAAAAAACCAACTCTTAGTTTCGTTGATTTTTTC 1069 chr1qtel1M 845803 -AGTGATTTTCTTATATCCAAT--ATTAGTAATTTTACCCTCAATTTTAG 845849 - v v v? v i v -- -- v i i i v vi v C L1M3_orf2#LIN 1068 TATTGTTTTTCTANTCTCTATTTCATT--TATTTCTGCTCTAATCTTTAT 1021 chr1qtel1M 845850 GGTTTCAAGTTTAGGGTCTAA--TTGGGGCTCCTTAGTTTGTTC----TT 845893 vi vvvii vvv - -- ---- ---- C L1M3_orf2#LIN 1020 TATTTCCTTCCTTCTG-CTAACTTTGGG----CTTAGTTTGTTCTTCTTT 976 chr1qtel1M 845894 TTGTAATTTTAAAAGTTGCATATCTAATTCATTGGTGTGCTCTTTTTCTA 845943 v i iivvi v i v vi iv ii vi v vvv i v C L1M3_orf2#LIN 975 TTCTAGTTCCTTGAGGTGTAAAGTTAGGTTGTTTATTTGAGATCTTTCTT 926 chr1qtel1M 845944 TTTTTTATTCTCTCTACTGCAGTAATCATTAGAGATATAAAATATTACTC 845993 i -------- v i vvi -- vv v v - iv C L1M3_orf2#LIN 925 CTTTTT--------TAATGTAGGCGT--TTATCGCTATAAACT-TCCCTC 887 chr1qtel1M 845994 TT---ATTACTTTTGATATGTCTCATAAGTTTTTCTGTGCTATTTTATTA 846040 --- i i v iii i vv i i i v v i C L1M3_orf2#LIN 886 TTAGNACTGCTTTTGCTGCATCCCATAAGTTTTGGTATGTTGTGTTTTCA 837 chr1qtel1M 846041 TTTTCATTC-TCTAATGAAATTATT--GTTTC---TATGATTT----TTC 846080 i- v v v v i--i --- v ---- i C L1M3_orf2#LIN 836 TTTTCATTTGTCTCAAGATATTTTCTAATTTCCCTTTTGATTTCTTCTTT 787 chr1qtel1M 846081 AACTTACTCATTATTTAATATTAGGTAGTTTAGTGTCCAATTAATT-TAA 846129 i ii i vi i i iv v iv v i v vv v - i C L1M3_orf2#LIN 786 GACCCATTGGTTGTTCAGGAGTGTGTTGTTTAATTTCCACATATTTGTGA 737 chr1qtel1M 846130 ATTTTAT-GTTTCTATGGTCCTTTATTTA-CTATAATTTTATGGCCTTAT 846177 vi- iiv -- iv v -i v i i ?v v i C L1M3_orf2#LIN 736 ATTTTCCAGTTTTCCT--TCTGTTATTGATTTCTAGTTTCATNCCATTGT 689 chr1qtel1M 846178 GATATGAAAAAGATGC--------ATTTCATATTTT-------------- 846205 i -i i i -------- - i -------------- C L1M3_orf2#LIN 688 GGT-CGGAAAAGATACTTGGTATGATTTCA-ATCTTCTTAAATTTGTTAA 641 chr1qtel1M 846206 GGCTT-TTCTGT--CCTCATATATGATC-ATTATTTAAAAGATACCATAA 846251 i - i -- v i i - iv vv i vi v i iv C L1M3_orf2#LIN 640 GACTTGTTTTGTGGCCTAACATGTGATCTATCCTGGAGAATGTTCCGTGT 591 chr1qtel1M 846252 ACCACTGAGAA-AATGTATATTCTTGTCAATTCTT--ATTCACTTCTCTC 846298 i vvi - i - - vii v --i vv v vi v C L1M3_orf2#LIN 590 GCGCTTGAGAAGAATGTGTATTC-TG-CTGCTGTTGGGTGGAATGTTCTG 543 chr1qtel1M 846299 CAGATATCTAT----TCTATTTAGCTTATCTAAAATTCTATTCACTTCCA 846344 i v i i ---- i i ---- v i vi i vv i C L1M3_orf2#LIN 542 TATATGTCTGTTAGGTCCATTTGG----TCTATAGTGTTGTTCAAGTCCG 497 chr1qtel1M 846345 -TGACTTCTTTCTCATTTACTGTTTGGTTAGATTTCTCTAATTCTGAGAG 846393 - vi i vi v v i v - ? i v i v vi i C L1M3_orf2#LIN 496 CTGTTTCCTTATTGATTTTCTGTCTGGAT-GNTCTATCCATTGTTGAAAG 448 chr1qtel1M 846394 AGGAAGATTAGAGTC-CCCACTATTATTGTCCTACTATTTATTTCCACTT 846442 v iiv ii - i vi i i i iv i C L1M3_orf2#LIN 447 TGGGGTATTGAAGTCTCCTACTATTATTGTATTGCTGTCTATTTCTCCCT 398 chr1qtel1M 846443 GCAATTC 846449 v i C L1M3_orf2#LIN 397 TCAGTTC 391 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 40.36 CpG sites = 219, Kimura (unadjusted) = 41.28 Transitions / transversions = 1.13 (219/193) Gap_init rate = 0.08 (105 / 1378), avg. gap size = 1.76 (185 / 105) 589 28.65 9.69 2.93 chr1qtel1M 845084 845723 (154277) C L1M5_orf2#LINE/L1 (1459) 1835 1154 m_b50s551i15 1827 chr1qtel1M 845084 AATGAATTTTATACTTTATTAAAACATTCCTCTATATCTATTGATATAAT 845133 ii v iv i i i vvv ii ii v i C L1M5_orf2#LIN 1835 AATGGGTGTTGAATTTTGTCAAATGCTTTTTCTGCATCTATTGAGATGAT 1786 chr1qtel1M 845134 CTTATGATTTTAAGTTTCAAT---ATTGAT-TGCATCAATTATATTAAT- 845178 v vvvii iv ---i i - -i v i i - C L1M5_orf2#LIN 1785 CATATGATTTTTCTCCTTTATTCTGTTAATATG-GTGAATTACATTGATT 1737 chr1qtel1M 845179 AATTTT----TGTTATATTACCCTTGAATTCCTGACATAAATCCCACATG 845224 i ---- v ii v v iv i v C L1M5_orf2#LIN 1736 GATTTTCGAATGTTAAACCAACCTTGCATTCCTGGGATAAACCCCACTTG 1687 chr1qtel1M 845225 CTCATGATCTAAAATCTTTGTAATGTAT----AAACTTTGTCATTTTTTA 845270 v v vv i v v i ----ii - i -- vi C L1M5_orf2#LIN 1686 GTCATGATGTATTATCCTTTTTATATATTGCTGGA-TTCG--ATTTGCTA 1640 chr1qtel1M 845271 ATTACTGTTTTAATTAGGATTTTCACATCCATGTTC-------------- 845306 ----i iv ? ii i -------------- C L1M5_orf2#LIN 1639 AT----ATTTTGTTNAGGATTTTTGCATCTATGTTCATGAGGGATATTGG 1594 chr1qtel1M 845307 --TTTAATTTTCCTTCTTTATTTTTACTCT-TCC--TTTTTATATTTTAG 845351 -- v i ii i vv vv i - ?-- vi i-- C L1M5_orf2#LIN 1593 TCTGTAATTTTCTTTTCTTGTAATGTCTTTGTCNGGTTTTGGTATC--AG 1546 chr1qtel1M 845352 CATCATATTTGTTTCATAAAAGAAATTTGGTAGTACCCCTTCTTTATCTA 845401 vi ? ii v ii vi i v v iii i v C L1M5_orf2#LIN 1545 GGTNATGCTGGCCTCATAAAATGAGTTGGGAAGTGTTCCCTCTTTTTCTA 1496 chr1qtel1M 845402 TTATT---AACAATT-GTTTAATACTGGAATTAGGTCTT-----AAT--T 845440 v i--- v i - v v i v vv ----- -- C L1M5_orf2#LIN 1495 TTTTCTGGAAGAGTTTGTGTAAGATTGGTATTATTTCTTCCTTAAATGTT 1446 chr1qtel1M 845441 TGATAGAATTCACTTTTGAATCCATCTGGCCATAG-GTTTTTTTCTTGGG 845489 i ivv v v v i - i iv C L1M5_orf2#LIN 1445 TGGTAGAATTCACCAGTGAAGCCATCTGGGCCTGGAGTTTTCTTTGTGGG 1396 chr1qtel1M 845490 AA---CTTCATTTATGATCTGTTCAATTTCTTTTTCAAAAATAGATCTAT 845536 ---i i v ii ---i vvi i v iv C L1M5_orf2#LIN 1395 AAGGTTTTTAATTACAA---ATTCAATTTCTTTAATAGATATAGGGCTAT 1349 chr1qtel1M 845537 TTAGATATTTTATTTCACCTTCTGCTTGTCCAGGCAGTTTTTATTTTTGT 845586 i v i vi v? iiv iiv i i? v i -- C L1M5_orf2#LIN 1348 TCAGATTTTCTATTTCTTCTTGNGTCAGTTTTGGTAANTTGTGTTTT--T 1301 chr1qtel1M 845587 CAAT--ATTCTTCCATTTCA--------CTTAAATTTATTGACATAATTT 845626 v-- iv --------? i i vv C L1M5_orf2#LIN 1300 CAAGGAATTTGTCCATTTCATCTAAGTTNTCAAATTTATTGGCATAAAGT 1251 chr1qtel1M 845627 AG--CAAAATAACTCCTTATAGTTGCTTTAATTTC---ACCTTCATTAGT 845671 v -- v viii vi ivi v --- vvv vv C L1M5_orf2#LIN 1250 TGTTCATAATATTCTCTTATTATCCTTTTAATGTCTGTAGGATCTGTAGT 1201 chr1qtel1M 845672 GGCATATTTATCCCTTTCATTTTTAATACTAGTTATTTGATTTCCTTTTC 845721 -- i i -i ii ii i i i v -- vi i C L1M5_orf2#LIN 1200 G--ATGTCT-CCTTTTTCATTCCTGATATTGGTAATTTG--TGTCTTCTC 1156 chr1qtel1M 845722 TC 845723 C L1M5_orf2#LIN 1155 TC 1154 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 37.21 CpG sites = 100, Kimura (unadjusted) = 37.47 Transitions / transversions = 1.28 (100/78) Gap_init rate = 0.06 (39 / 639), avg. gap size = 2.10 (82 / 39) 438 29.96 10.61 2.41 chr1qtel1M 845979 846515 (153485) C L1M2_orf2#LINE/L1 (2391) 900 321 m_b50s551i16 1827 chr1qtel1M 845979 TATAAAATATTACTCTTA---TTACTTTTGATATGTCTCATAAGTTTTTC 846025 v - iv ---i i v i i i i vv C L1M2_orf2#LIN 900 TATAAACT-TCCCTCTTAGNACTGCTTTTGCTGTATCCCATAGGTTTTGG 852 chr1qtel1M 846026 TGTGCTATTTTATTATTTTCATTC-TCTAATGAAATTATTG------TTT 846068 i i i v vii i- i v v v ?------i C L1M2_orf2#LIN 851 TATGTTGTGTTTCCATTTTCATTTGTTTCAAGAAATTTTTNAATTTCCTT 802 chr1qtel1M 846069 CTATGATTTTTCAACTTACTCATTA----TTTAATATTAGGTAGTTTAGT 846114 - i i iv i v i i---- i iv vi v v i C L1M2_orf2#LIN 801 CT-TAATTTCTTCATTGACCCATTGGTCGTTCAGGAGCATGTTGTTTAAT 753 chr1qtel1M 846115 GTCCAATTAATT-TAAATTTT---ATGTTTCTATGGTCCTTTATTTACTA 846160 v vv v - ? v --- v i v v iv v - C L1M2_orf2#LIN 752 TTCCATGTATTTGTANAGTTTCCAAAGTTCCTCTTGTTATTGATTT-CTA 704 chr1qtel1M 846161 TAATTTTATGGCCTTATGATATGAAAAAGATGC--------ATTTC-ATA 846201 --i vv v i i v? - i -------- - v C L1M2_orf2#LIN 703 --GTTTTATTCCATTGTGGTCNGAAAA-GATACTTGATATGATTTCGATT 657 chr1qtel1M 846202 TTTT------------GGCTT-TTCTGT--CCTCATATATGATC-ATTAT 846235 ------------ i - i -- v i i - iv C L1M2_orf2#LIN 656 TTTTNAAATTTGTTGAGACTTGTTTTGTGGCCTAACATATGGTCTATCCT 607 chr1qtel1M 846236 TTAAAAGATACCATAAACCACTGAGAA-AATGTATATTCTTGTCAATTCT 846284 vv i vi v ivi iiv - i - - ii v C L1M2_orf2#LIN 606 GGAGAATGTTCCATGTGCTGATGAGAAGAATGTGTATTCT-G-CAGCTGT 559 chr1qtel1M 846285 T--ATTCACTTCTCTCCAGATATCTATT----CTATTTAGCTTATCTAAA 846328 -- vv v vi vi i i i ---- i i ---- ? C L1M2_orf2#LIN 558 TGGATGAAATGTTCTGTAAATGTCTGTTAGGTCCATTTGG----TCTANA 513 chr1qtel1M 846329 ATTCTATTCACTTCC-ATGACTTCTTTCTC-ATTTACTGTTTGGTTAGAT 846376 i v vi i vv - -i v i- v i v - C L1M2_orf2#LIN 512 GTGCAGTTTAAGTCCGATG-TTTCTTTGTTGATTTTCTGTCTGGAT-GAT 465 chr1qtel1M 846377 TTCTCTAATTCTGAGAGAGGAAGATTAGAGTCCCC-ACTATTATTGTCCT 846425 i v i ? v v iivi ii - vi C L1M2_orf2#LIN 464 CTGTCCANTGCTGAGAGTGGGGTGTTGAAGTCCCCNACTATTATTGTATT 415 chr1qtel1M 846426 ACTATTTATTTC-CACTTGCAATTCATTTA-ACTTTTTTTAAATAGATGA 846473 i?vi i i - v vvi ii ? v - i vi v vv i C L1M2_orf2#LIN 414 GNAGTCTATCTCTCCCTTTAGATCTANTAATATTTGCTTTATATATCTGG 365 chr1qtel1M 846474 ATGCTATAGTATTTGCTGTTTGTAAGTTTAG--TGATTATATTC 846515 i vii i v v iv i vi ?-- vi i C L1M2_orf2#LIN 364 GTGCTCCGGTGTTGGGTGCATATATATTTANAATTGTTATATCC 321 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 39.57 CpG sites = 85, Kimura (unadjusted) = 39.93 Transitions / transversions = 1.18 (85/72) Gap_init rate = 0.07 (35 / 536), avg. gap size = 2.03 (71 / 35) 356 34.62 2.56 0.00 chr1qtel1M 846524 846679 (153321) C MIRb#SINE/MIR (68) 200 41 m_b50s601i26 1828 chr1qtel1M 846524 TTATAGTATGTAATCATTACAAATACCTTGCATAAT-GGTAATATT-TCT 846571 vvi v v i vv i ivii - v - i C MIRb#SINE/MIR 200 TTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATTATCC 151 chr1qtel1M 846572 C--TTTTATGTGTGTGCAAATTGACATAAACAGATATTAATTAACTTGGC 846619 -- iivi v v i viivv v vi v v C MIRb#SINE/MIR 150 CCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCC 101 chr1qtel1M 846620 CAAGATCATTCACCTAATAAAGGTCTGAGGTTAGATTTGTACTCAAGTCA 846669 i iv v i iv v v vivi i v i i v C MIRb#SINE/MIR 100 CAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCT 51 chr1qtel1M 846670 TCCTTATTCC 846679 vi v i C MIRb#SINE/MIR 50 GTCTGACTCC 41 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 43.54 CpG sites = 25, Kimura (unadjusted) = 46.92 Transitions / transversions = 0.86 (25/29) Gap_init rate = 0.02 (3 / 155), avg. gap size = 1.33 (4 / 3) 182 33.67 7.49 1.52 chr1qtel1M 849057 849243 (150757) L2a_3end#LINE/L2 313 510 (7) m_b50s601i27 1829 chr1qtel1M 849057 TAATTTTCTTC-TGGTGATTATCTCCATTTTCCCCTTTAGAAATATTTTT 849105 v i - i iiv v i vv vivi v -- v L2a_3end#LINE 313 TATTTTTCTCCATAGCACTTATCACCATCTGACATACTATA--TATTTTA 360 chr1qtel1M 849106 GTTATATATC-ATTTGCATGT-TGCCACCCCGAAC---ATTGTGAGCTTT 849150 v v i-i ii- - i v vv --- v i ii L2a_3end#LINE 361 CTTATTTATTTGTTTAT-TGTCTGTCTCCCCCCACTAGAATGTAAGCTCC 409 chr1qtel1M 849151 TTGAGGGAGGTGA---TTATCTTTTGTCTTT-CTA-TGTAACTCCA-TAT 849194 v vi v --- i v v v i- i- v i -iii L2a_3end#LINE 410 ATGAGGGCAGGGACTTTTGTCTGTTTTGTTCACTGCTGTATCCCCAGCGC 459 chr1qtel1M 849195 TTACTGGAGTGCCTAGAACA--ATAAATGTTTAATTAATGCTTGTTGACT 849242 i vviv i v --i iii i i v ii v L2a_3end#LINE 460 CTAGAACAGTGCCTGGCACATAGTAGGCGCTCAATAAATATTTGTTGAAT 509 chr1qtel1M 849243 G 849243 L2a_3end#LINE 510 G 510 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 43.84 CpG sites = 34, Kimura (unadjusted) = 45.95 Transitions / transversions = 1.21 (34/28) Gap_init rate = 0.06 (12 / 186), avg. gap size = 1.42 (17 / 12) 261 31.64 5.56 7.80 chr1qtel1M 849100 849243 (150757) L2c_3end#LINE/L2 331 471 (7) m_b50s601i28 1829 chr1qtel1M 849100 ATTTTTGTTATA--TATC-ATTTGCATGT-TGCCACCCCGA--ACATTGT 849143 i v i i -- i -i i ? - i v i v -- v i L2c_3end#LINE 331 ACTTGTATTGTAATTGTCTGTTTACNTGTCTGTCTCCTCCACTAGACTGT 380 chr1qtel1M 849144 GAGCTTTTTGAGGGAGGTGATTATCTTTTGTCTTTCTATGTAACTCCATA 849193 ii vi v iii v i i iiv v v i --- L2c_3end#LINE 381 GAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTATCCCC--- 427 chr1qtel1M 849194 TTTACTGGAGTGCCTAGAAC--AATAAATGTTTAATTAATGCTTGTTGAC 849241 -------- i i v -- i iii i i v i v L2c_3end#LINE 428 --------AGCGCCTGGCACATAGTAGGCGCTCAATAAATGTTTGTTGAA 469 chr1qtel1M 849242 TG 849243 L2c_3end#LINE 470 TG 471 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 39.69 CpG sites = 29, Kimura (unadjusted) = 44.08 Transitions / transversions = 2.23 (29/13) Gap_init rate = 0.11 (16 / 143), avg. gap size = 1.19 (19 / 16) 291 33.33 6.35 0.00 chr1qtel1M 849117 849242 (150758) L2d2_3end#LINE/L2 414 547 (8) m_b50s601i29 1829 chr1qtel1M 849117 TTTGCATGTTGCCACCCCGA--ACATTGTGAGCTTTTTGAGGGAGGTGAT 849164 iii v i v i -- v i ii vi v i L2d2_3end#LIN 414 TTTATGTCTTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGAC 463 chr1qtel1M 849165 TATCTTTTGTCTTTCTATGTA-ACTCCATATTTACTGG---AGTGCCTAG 849210 i v i i vi v -v i i vivv i --- v L2d2_3end#LIN 464 CATGTCTTATACTTCTTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTG 513 chr1qtel1M 849211 --AACAATAAATGTTTAATTAATGCTTGTTGACT 849242 --v i iii i i v ii i L2d2_3end#LIN 514 CACACAGTAGGCGCTCAATAAATATTTGTTGATT 547 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 43.40 CpG sites = 27, Kimura (unadjusted) = 46.46 Transitions / transversions = 1.80 (27/15) Gap_init rate = 0.03 (4 / 125), avg. gap size = 2.00 (8 / 4) 17 6.55 2.94 2.94 chr1qtel1M 850071 850104 (149896) (CAATGA)n#Simple_repeat 1 34 (0) m_b50s252i11 1830 chr1qtel1M 850071 CAATGACAATTGAC-ATGACAATGTCCATGACAAT 850104 - - v v (CAATGA)n#Sim 1 CAATGACAA-TGACAATGACAATGACAATGACAAT 34 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2) 185 24.00 2.00 0.00 chr1qtel1M 850108 850157 (149843) L2#LINE/L2 2301 2351 (731) m_b50s601i30 1831 chr1qtel1M 850108 TCCTATGGTTTCAATTATCATCAATATGCTGATGACTTTT-ATTTTTTAT 850156 ii i i v i v iii- v v L2#LINE/L2 2301 TCTCATGGCTTTAAATACCATCTATATGCTGATGACTCCCAAATTTATAT 2350 chr1qtel1M 850157 C 850157 L2#LINE/L2 2351 C 2351 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 29.90 CpG sites = 8, Kimura (unadjusted) = 29.90 Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.02 (1 / 49), avg. gap size = 1.00 (1 / 1) 12 12.49 0.00 3.70 chr1qtel1M 850682 850709 (149291) (CTCC)n#Simple_repeat 1 27 (0) m_b50s252i12 1832 chr1qtel1M 850682 CTCCATCTCTCCCTCCCTTCCCACCCTC 850709 v i - v (CTCC)n#Simpl 1 CTCCCTCCCTCCCTCCC-TCCCTCCCTC 27 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 29 0.00 0.00 0.00 chr1qtel1M 850726 850750 (149250) (AT)n#Simple_repeat 1 25 (0) c_b50s251i2 1833 chr1qtel1M 850726 ATATATATATATATATATATATATA 850750 (AT)n#Simple_ 1 ATATATATATATATATATATATATA 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 367 37.30 6.09 2.09 chr1qtel1M 852035 852264 (147736) C L2#LINE/L2 (2479) 603 365 m_b51s601i0 1834 chr1qtel1M 852035 TGATCTGGAAGTGGTAATGGGGAGCAAGGAATACTTTTCCTTCTCTACTA 852084 i i i i iv vii v ii v iv i C L2#LINE/L2 603 TGGTCTGGAAGCGGCAATGAGGAGCAAGGAGGACACCTACCCCACCTCCA 554 chr1qtel1M 852085 TGCTCAATTAATCAGGAGATATGGGTTAAAGTGTAGTCAAACCTTGAAAG 852134 v i i vivv ii i ? i vv i ivii i vvv i C L2#LINE/L2 553 GGCCCAGTGGTACGAGGGNTGTGGGAGAGAAAACAGCCACCACTTGAGAG 504 chr1qtel1M 852135 AG-TAAAAAAGAAA--------TCAGGATGGAGCTATATTTTAGTGAAGG 852175 i - iv iii i-------- ivi i vi i? v ii C L2#LINE/L2 503 GGCTGCAGGGGAAGCAGTGTCCTCAGGGGAGAGCCAGGTTTCNGTTAGAG 454 chr1qtel1M 852176 CTGAAATGAAAATGAAATGAAT-----GAAAAGTAAGTTTAAGATGAAAA 852220 -- -- ii iv i----- i - i v i iviii C L2#LINE/L2 453 C--AA--GAAGGTGAAGGGAACGTTCAGAGAAG-AGGTTGAGGATACGGG 409 chr1qtel1M 852221 GAAGTTTGCTAACTATGGAACAGGCATTGAAGAGGGCACAATGG 852264 i v i iv i v iv vi vv i C L2#LINE/L2 408 GGATTTTGCTGATGACGGACCGTGAGTTCCAGAGGGCACAGTGG 365 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 50.30 CpG sites = 55, Kimura (unadjusted) = 56.35 Transitions / transversions = 1.90 (55/29) Gap_init rate = 0.03 (8 / 229), avg. gap size = 2.38 (19 / 8) 263 23.16 2.86 7.46 chr1qtel1M 853178 853247 (146753) C MIR3#SINE/MIR (31) 177 111 m_b51s601i1 1835 chr1qtel1M 853178 AAAGGTCATCTTAAAGATCATC--ATTTAAAGACCTCTTTTTTTGACAGA 853225 i -- i i --i ii --- i i iv v C MIR3#SINE/MIR 177 AAGGG--ACCTTAGAGATCATCTAGTCCAA---CCCCCTCATTTTACAGA 133 chr1qtel1M 853226 TAAGAAAACTGAGGTCCAGAAA 853247 i i i i C MIR3#SINE/MIR 132 TGAGGAAACTGAGGCCCAGAGA 111 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.76 CpG sites = 13, Kimura (unadjusted) = 29.76 Transitions / transversions = 6.50 (13/2) Gap_init rate = 0.09 (6 / 69), avg. gap size = 1.17 (7 / 6) 450 24.75 0.00 8.77 chr1qtel1M 853368 853491 (146509) MIRc#SINE/MIR 2 115 (153) m_b51s601i2 1836 chr1qtel1M 853368 GGGGCAGCTAGGTGGCGCTGTGGATAGAGCACCAGCCCTGAAATTGGGAG 853417 i i--- i v v ii v i i i ii i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr1qtel1M 853418 AACTTGAGTTCAAATATGACCTCAGGCATTGAACACTTCCTAGCTGTGTG 853467 i i i i i ----- i - vi v- v MIRc#SINE/MIR 49 GACCTGGGTTCGAGT-----CCC-GGCTCTGC-CACTTACTAGCTGTGTG 91 chr1qtel1M 853468 ACTCTGGGCAAATCACTTAACCCC 853491 ii i i MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.26 CpG sites = 22, Kimura (unadjusted) = 31.65 Transitions / transversions = 3.67 (22/6) Gap_init rate = 0.08 (10 / 123), avg. gap size = 1.00 (10 / 10) 11 31.90 0.00 2.04 chr1qtel1M 855305 855354 (144646) (TATATG)n#Simple_repeat 1 49 (0) m_b51s252i1 1837 chr1qtel1M 855305 TATGTGTATATGTATATATGTGTGTGCGTGTGAATGTACATATTAGATGT 855354 i i i i iii iv i -v v (TATATG)n#Sim 1 TATATGTATATGTATATGTATATGTATATGTATATGTATAT-GTATATGT 49 Matrix = Unknown Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.02 (1 / 49), avg. gap size = 1.00 (1 / 1) 355 24.38 6.45 0.76 chr1qtel1M 855483 855606 (144394) MER63D#DNA/hAT-Tip100 334 464 (597) m_b51s502i0 1838 chr1qtel1M 855483 TAGTGTAAGTATTTATACAGAGGATATAAGCCAATGTTATTAATTAGAGT 855532 i vi i viv v vi v i i iv i i i MER63D#DNA/hA 334 TGGTGGGAGTATTTACACCACGGAAATCGGCAAACGCTACAAATCAGGGC 383 chr1qtel1M 855533 TTGATTTG----TTTGTTGAT----TAGACTTAGGAAAAGGATGTTAGAA 855574 i---- ---- i iv -v MER63D#DNA/hA 384 TTGATTTATTGTTTTGTTGATTGTCTAGACTTAAGAAAGTGATG-GAGAA 432 chr1qtel1M 855575 AATGTTGATAATATATATTCAATTTACAAGTG 855606 i ii v v i v MER63D#DNA/hA 433 AATGTTAATAATGCAGATTAAACTTAAAAGTG 464 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 27.82 CpG sites = 18, Kimura (unadjusted) = 30.16 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.02 (3 / 123), avg. gap size = 3.00 (9 / 3) 225 26.46 13.10 3.26 chr1qtel1M 858229 858396 (141604) C L1M5_orf2#LINE/L1 (2786) 508 325 m_b51s551i0 1839 chr1qtel1M 858229 TATTCATACCTTTGAC-TTCTTATTTATTTAGTTTTGGTTA---GATCTA 858274 i v i iv i- i i v --- vi --- v C L1M5_orf2#LIN 508 TGTTCAAATCTTCTATATCCTTACTGATTT---TTTGTCTACTTGTTCTA 462 chr1qtel1M 858275 TCTAGTTCTGAGAGAGGAAGTTTGAAATCCCTTACTATTATAATTTT--- 858321 v v v ?ivv i i --- ? i v --- C L1M5_orf2#LIN 461 TCAATTACTGAGAGAGGNGTGTTAAAATCTC---CNACTATAATTGTGGA 415 chr1qtel1M 858322 CCTATCTATTTCCCCCTGTAATTC---------------AAAAAATTTTG 858356 ii i i i v i ---------------v viv C L1M5_orf2#LIN 414 TTTGTCTATTTCTCCTTTTAGTTCTGTCAGTTTTTGCTTCATGTATTTTG 365 chr1qtel1M 858357 ATGCTATACTATTTGCTGCATATAGATTTAGTATTGGTAT 858396 v v ii v v i v v v C L1M5_orf2#LIN 364 AAGCTCTGTTATTAGGTGCATACACATTTAGGATTGTTAT 325 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.58 CpG sites = 21, Kimura (unadjusted) = 33.58 Transitions / transversions = 0.95 (21/22) Gap_init rate = 0.06 (10 / 167), avg. gap size = 2.80 (28 / 10) 18 5.60 7.69 2.44 chr1qtel1M 860842 860880 (139120) (ATTAA)n#Simple_repeat 1 41 (0) m_b51s252i2 1840 chr1qtel1M 860842 ATT-AATTAAATTAAAATTAAAAT-AATTAAA-TAAATCAAA 860880 - - v - - i (ATTAA)n#Simp 1 ATTAAATTAAATT-AAATTAAATTAAATTAAATTAAATTAAA 41 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.11 (4 / 38), avg. gap size = 1.00 (4 / 4) 20 26.21 0.00 0.00 chr1qtel1M 860912 860961 (139039) (TT)n#Simple_repeat 1 50 (0) m_b51s252i3 1841 chr1qtel1M 860912 TTTTATATATTCATTTTTTTATTAAAGCTTTTTTTTTTTTTTTTTTTTTT 860961 v v v iv v vvvvi (TT)n#Simple_ 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 Matrix = Unknown Transitions / transversions = 0.22 (2/9) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 15 20.52 2.56 0.00 chr1qtel1M 861362 861400 (138600) (TAA)n#Simple_repeat 1 40 (0) m_b51s252i4 1842 chr1qtel1M 861362 TAGTATTAATAATAATGCTACAAATAATAATACT-ATAAT 861400 i v iv vv v - (TAA)n#Simple 1 TAATAATAATAATAATAATAATAATAATAATAATAATAAT 40 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.03 (1 / 38), avg. gap size = 1.00 (1 / 1) 287 38.02 2.56 1.52 chr1qtel1M 861402 861596 (138404) C MIRc#SINE/MIR (70) 198 2 m_b51s601i3 1843 chr1qtel1M 861402 TTTGATTTACAGAACAGCCTTATGAATCA--CAGTGCAAGGAGTCATTTG 861449 iiv v i i i ivi -- v i v - i -i C MIRc#SINE/MIR 198 TTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTA-TTATT-A 151 chr1qtel1M 861450 TCTCCCAATTTAAAGAAGAGACATCTGCATCTGAGGAAAGCTTGCAAACA 861499 - v v v iv v viv v ii i i vivvi v C MIRc#SINE/MIR 150 TC-CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACT 102 chr1qtel1M 861500 CACTCTTCACCACAGAGCTTGTATACATCAGGG--GAGATTCCATTTCTG 861547 ii i vvvii v v viiiv i -- i i v vii v C MIRc#SINE/MIR 101 TGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAG 52 chr1qtel1M 861548 GTCTTCTCAACCCCAGGGC-AATGCTCTTTTCCCCAAAACAAGCTGCCTC 861596 iii i i v - i i v iiv v vi C MIRc#SINE/MIR 51 GTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTGCCTC 2 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 55.18 CpG sites = 41, Kimura (unadjusted) = 55.18 Transitions / transversions = 1.28 (41/32) Gap_init rate = 0.03 (6 / 194), avg. gap size = 1.33 (8 / 6) 480 23.81 10.88 0.00 chr1qtel1M 862428 862574 (137426) C MIRc#SINE/MIR (8) 260 98 m_b51s601i4 1844 chr1qtel1M 862428 TGACAACTAGCACTGATATACTGCTCCAAGGTTTGTGATGTTCTTT-ATA 862476 i ?v vi i vi vii ii vi iii v iv - i C MIRc#SINE/MIR 260 TAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCGCTTTCACA 211 chr1qtel1M 862477 TTTACTATCTCATTTGACCCTCATAAC--TCCTCTGAGGTAGGT---GC- 862520 vi i i i --i v i--- - C MIRc#SINE/MIR 210 TACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCA 161 chr1qtel1M 862521 --CATTATCA-CTCCATTTTACAAATGAGGAAACTGAGTCT----GAGAT 862563 --i i - i i v ---- i C MIRc#SINE/MIR 160 GGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGT 111 chr1qtel1M 862564 T--GTGACTTGCC 862574 -- C MIRc#SINE/MIR 110 TAAGTGACTTGCC 98 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.11 CpG sites = 25, Kimura (unadjusted) = 30.15 Transitions / transversions = 2.50 (25/10) Gap_init rate = 0.05 (8 / 146), avg. gap size = 2.00 (16 / 8) 491 17.45 7.62 1.80 chr1qtel1M 862470 862574 (137426) C MIRb#SINE/MIR (57) 211 101 m_b51s601i5 1844 chr1qtel1M 862470 CTTTATATTTACTATCTCATTTGACCCTCATAAC--TCCTCTGAGGTAGG 862517 i vi i i i i --i vi C MIRb#SINE/MIR 211 CTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGG 162 chr1qtel1M 862518 TGCCATTATCACTCCATTTTACAAATGAGGAAACTGAGTCT----GAGAT 862563 iii --i i v ---- i C MIRb#SINE/MIR 161 TATTATTATC--CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGT 114 chr1qtel1M 862564 T--GTGACTTGCC 862574 -- i C MIRb#SINE/MIR 113 TAAGTAACTTGCC 101 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 19.54 CpG sites = 15, Kimura (unadjusted) = 20.81 Transitions / transversions = 5.00 (15/3) Gap_init rate = 0.05 (5 / 104), avg. gap size = 2.00 (10 / 5) 319 18.23 11.34 3.85 chr1qtel1M 862510 862606 (137394) C MIR1_Amn#SINE/MIR (62) 168 65 m_b51s601i6 1844 chr1qtel1M 862510 GAGGTAGGTGCCATTATCACTCCATTTTACAAATGAGGAAACTGAGTCT- 862558 vi ii --i i v ?- C MIR1_Amn#SINE 168 GAGGTCAGTATCATTATC--CCCATTTTACAGATGAGGAAACTGAGGCNC 121 chr1qtel1M 862559 ---GAGATT--GTGACTTGCC--AG---ATACAGCAATGGCCAATTATGA 862598 --- i ?-- -- --- i? --? ? i viiii C MIR1_Amn#SINE 120 AGAGAGGTNAAGTGACTTGCCCAAGGTCACNCAGC--NGGCNAGTGGCAG 73 chr1qtel1M 862599 ATCCAGGA 862606 v i C MIR1_Amn#SINE 72 AGCCGGGA 65 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 21.70 CpG sites = 13, Kimura (unadjusted) = 23.23 Transitions / transversions = 3.25 (13/4) Gap_init rate = 0.09 (9 / 96), avg. gap size = 1.67 (15 / 9) 245 23.59 11.34 3.85 chr1qtel1M 862525 862621 (137379) C MIR3#SINE/MIR (58) 150 47 m_b51s601i7 1844 chr1qtel1M 862525 ATCACTCCATTTTACAAATGAGGAAACTGAGTCT----GAGATT--GTGA 862568 i v ii i v i---- i v-- C MIR3#SINE/MIR 150 ACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGA 101 chr1qtel1M 862569 CTTGCC--AG---ATACAGCAATGGCCAATTATGAATCCAGGAACTAGTA 862613 -- --- i ? -- ii i viiii v - i v C MIR3#SINE/MIR 100 CTTGCCCAAGGTCACACAGCNA--GTTAGTGGCAGAGCC-GGGACTAGAA 54 chr1qtel1M 862614 CAACAGGT 862621 -v C MIR3#SINE/MIR 53 C-CCAGGT 47 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.85 CpG sites = 15, Kimura (unadjusted) = 29.85 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.08 (8 / 96), avg. gap size = 1.88 (15 / 8) 248 28.29 3.70 1.82 chr1qtel1M 864060 864167 (135833) C L1ME4c_3end#LINE/L1 (444) 386 277 m_b51s551i1 1845 chr1qtel1M 864060 AGTGGACT--CTGAGTCAAATTATACCGGCATTTTAATCCCCTTCTTCCC 864107 v -- i vvi ivii v vv -- vvi C L1ME4c_3end#L 386 AGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGC--TCTTGAT 339 chr1qtel1M 864108 A-GAATT-TCAAACTGCTTTCCAAAATGGTGGTGCTGACTTACAGCTCTA 864155 - v -i i v v i ii i ?iv i C L1ME4c_3end#L 338 ACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACANTGCCA 289 chr1qtel1M 864156 TAAGCAATGCAT 864167 iv i C L1ME4c_3end#L 288 CCAGCAATGTAT 277 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.58 CpG sites = 16, Kimura (unadjusted) = 36.58 Transitions / transversions = 1.14 (16/14) Gap_init rate = 0.05 (5 / 107), avg. gap size = 1.20 (6 / 5) 268 30.68 6.72 5.15 chr1qtel1M 864241 864374 (135626) MIR#SINE/MIR 6 141 (121) m_b51s601i8 1846 chr1qtel1M 864241 ATGGCACACTGATTACAGGGGCTGAGC-CTGGATTTAGACAGCATTTTCC 864289 i i v i - i vvi i - vii v ------ MIR#SINE/MIR 6 ATAGCATAGTGGTTA-AGAGCACGGGCTCTGGAGCCAGACTGC------C 48 chr1qtel1M 864290 TAAATTCAAATCT--ACCCT--CAGACACCAGCTGTGTGATCCTGAGCAA 864335 iii i i--i i -- vvi i i i i MIR#SINE/MIR 49 TGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 98 chr1qtel1M 864336 ATGAA--AAATCCTGTTTGCCT--GTTTCCCCATCAATAGAAT 864374 i v v-- vii v v -- i vi i MIR#SINE/MIR 99 GTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAAT 141 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.76 CpG sites = 26, Kimura (unadjusted) = 41.58 Transitions / transversions = 2.00 (26/13) Gap_init rate = 0.09 (12 / 133), avg. gap size = 1.33 (16 / 12) 262 31.30 1.74 0.00 chr1qtel1M 864454 864568 (135432) C L1PB4_3end#LINE/L1 (713) 190 74 m_b51s551i2 1847 chr1qtel1M 864454 ACCTCAGGATGGTCTTAATTTGTATTTTCTTTATTATTGGTGATTTGGAG 864503 i vvi i i iii v v i v v C L1PB4_3end#LI 190 ATCTCATTGTGGTTTTAATTTGCATTTCTCTGATGATTAGTGATGTTGAG 141 chr1qtel1M 864504 CACTTTTTCTTTTGGCTGCTAATAGCTTTTTTTTCCCCCCT--AAAAAGG 864551 i v v vi i iiiv v v v ii ii -- v C L1PB4_3end#LI 140 CATTTTTTCATATGTTTGTTGGCCGCTTGTATGTCTTCTTTTGAAAAATG 91 chr1qtel1M 864552 CCTGTTTCTATCCTTTG 864568 i iv i C L1PB4_3end#LI 90 TCTGTTCATGTCCTTTG 74 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.78 CpG sites = 21, Kimura (unadjusted) = 41.78 Transitions / transversions = 1.40 (21/15) Gap_init rate = 0.01 (1 / 114), avg. gap size = 2.00 (2 / 1) 18 17.53 0.00 0.00 chr1qtel1M 865414 865445 (134555) (AT)n#Simple_repeat 1 32 (0) m_b51s252i5 1848 chr1qtel1M 865414 ATATATACATATATATCTCCATATTTATATAT 865445 i v vi v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATAT 32 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 1015 34.71 2.73 2.92 chr1qtel1M 866779 867327 (132673) L3#LINE/CR1 3194 3741 (358) m_b51s601i9 1849 chr1qtel1M 866779 ATGAATGACATATCTCATCAAATCTGTAAATGAAACAAAGCAAGGAGGGA 866828 ii v i i- i i i i v vi L3#LINE/CR1 3194 ATAGAAGGCATG-CTTATCAAATTTGCAGATGACACAAAGCTGGGAGGGA 3242 chr1qtel1M 866829 AAGCTAAAATATGGGATAGCAGAGTCGAGAACCAAAAAGGGCT-GCCAAG 866877 v v ii?v ii i i vi ? iv - v - L3#LINE/CR1 3243 TAGCTAATACGNTGGATGACAGAATCAAGATTCAAAANGATCTCGAC-AG 3291 chr1qtel1M 866878 GATAGAACTTTGGGTTATATTTACTAAAATGTAATTAAAATGAAGTAAAT 866927 v i vv iiiv vii vi i v v vv iii L3#LINE/CR1 3292 GCTGGAACGATGGGCCGAAACCAACAAGATGAAATTTAACAGGGATAAAT 3341 chr1qtel1M 866928 GCAAAGTCTTATGCTTTGATTAAAAAAAAAAAATCTATTTCTCAAA-ACA 866976 i i iiii v i -----v v i v v i- L3#LINE/CR1 3342 GTAAAGTCCTGCATTTAGGTT-----CAAAAAATCAACTGCACAAGTACA 3386 chr1qtel1M 866977 AAAT-GAGAAGACATGATTGACCAGCAATTTATGAGGGAAAAAAAAGATC 867025 ii - i iv ii v v i i i v ----- i L3#LINE/CR1 3387 GGATGGAGAGGATCTGGCTTAGCAGCAGTTCACGTG-----AAAAAGACC 3431 chr1qtel1M 867026 TGGGAATTTAAATAGACTATAAGCTCAAAATGGGTCAGCAGTGTGATTTA 867075 i ii v i v iii v i i i v i L3#LINE/CR1 3432 TAGGGGTTTTAGTTGACCGCAAGCTCAATATGAGCCAACAGTGTGATGTG 3481 chr1qtel1M 867076 GAAGTTGTAAAAGCT--T---ATCTTGAGTCACATTAA---GAGTA-AAA 867116 vv iiiv -- --- ii iii ---i - iv L3#LINE/CR1 3482 GCTGCCAAAAAAGCTAATGCAATCTTAGGCTGCATTAATAGAAGTATAGT 3531 chr1qtel1M 867117 GCTCAGAGATATAAGAAATTAGTAGTC---CTGTACTTAAGTCCCAGTTG 867163 ii -?i - i i iv i --- i-v iv ii ii L3#LINE/CR1 3532 GTCCAGA-NCA-AGGGAGGTAATAGTCCCGCTGTACTC-TGCGCTGGTCA 3578 chr1qtel1M 867164 AACTACATGTAGAATAACCAATTCAGAACTCAGTATAGTAGCTTCAGAAG 867213 i i v i i vivvi vv vi iiivii vi v i L3#LINE/CR1 3579 GACCACATCTGGAGTATTGCGTTCAGTTCTGGGCGCCACATTTTAAGAGG 3628 chr1qtel1M 867214 GACAATGTTAAGATAGAAAGCATCCAGAAGAGGTAAAATCCTGAAGGTGA 867263 v vi iv i iv i i i-ivi i vv v L3#LINE/CR1 3629 GACATTGACAAACTGGAGCGCGTCCAGAGGAGA-GCGACCAGGATGGTGA 3677 chr1qtel1M 867264 AGAAACTTTAGCCAATGTTATATGCAGAAGGCTTAAAACGACTTAGGATA 867313 iiv vv iv v i vi v v i ivi vi i L3#LINE/CR1 3678 AGGGTCTGGAAACCATGTCATATGAGGAACGGTTGAAGGAACTGGGGATG 3727 chr1qtel1M 867314 TTTATCTTGGAAAA 867327 v i i L3#LINE/CR1 3728 TTTAGCCTGGAGAA 3741 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 45.99 CpG sites = 117, Kimura (unadjusted) = 49.59 Transitions / transversions = 1.72 (117/68) Gap_init rate = 0.04 (24 / 548), avg. gap size = 1.29 (31 / 24) 418 33.86 5.65 1.16 chr1qtel1M 867336 867583 (132417) L3#LINE/CR1 3780 4038 (61) m_b51s601i10 1849 chr1qtel1M 867336 ATTTGAAGAA-TGTAATGTAGATAGTTGATTA--CTTGTTCTG----GCA 867378 ii- v i viivv -- i ---- - L3#LINE/CR1 3780 ATTTGAAGGGCTGTCATGTGGAAGAGGGATTAGACTTATTCTGTGTGGC- 3828 chr1qtel1M 867379 TGCA-AGGACTGACTCAGGAGCAATGGGTTAATTTCGTAAGGACG-AGAA 867426 v - i v vii v vi vv iii i v - v L3#LINE/CR1 3829 TCCAGAGGGCAGAACTAGGACCAATGGGTGGAAGTTACAGGGAGGCAGAT 3878 chr1qtel1M 867427 TTTAGCTTGATTCCAGGAAAAGTCGATCTTACAATGAGAACTGTCCCAAA 867476 ii ii viv i i- vv v v i v L3#LINE/CR1 3879 TTCGGCTCAATATAAGGAAGAA-CTTTCTAACAATCAGAGCTGTCCAAAA 3927 chr1qtel1M 867477 GTGGATTGGTAAGCCATAATAGGACACAAGTTTCCCCATAATTGGAAATT 867526 i v vvv vii?v vviii -i i v i ii v L3#LINE/CR1 3928 ATGGAATGGGCTGCCTCGNGAGGTAGTGAG-CTCCCCGTCACTGGAGGTG 3976 chr1qtel1M 867527 ATTAA--AGAAACGAGAT-ATCACATGTCAGGAACATCATAGTGGTGA-- 867571 v i -- ii vi - i v i ii ii vi v -- L3#LINE/CR1 3977 TTCAAGCAGAGGCTGGATGACCACTTGTCAGGGATGTTGTAGAAGGGATT 4026 chr1qtel1M 867572 CTTGTTTTAGAT 867583 i iv i L3#LINE/CR1 4027 CCTGCATTGGAT 4038 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 44.31 CpG sites = 47, Kimura (unadjusted) = 46.79 Transitions / transversions = 1.31 (47/36) Gap_init rate = 0.04 (11 / 247), avg. gap size = 1.55 (17 / 11) 278 18.00 2.00 0.00 chr1qtel1M 867591 867640 (132360) Plat_L3#LINE/CR1 3520 3570 (3) m_b51s551i3 1850 chr1qtel1M 867591 GGATGAGATGGCTTCT-GAGGTCCCTTCCAACTCTAGAATTTTCTAATTC 867639 iv i i - i ?i i v i Plat_L3#LINE/ 3520 GGACCAGATGACCTCTCGAGGTCCCTTCCAGCTCTANGATTCTATGATTC 3569 chr1qtel1M 867640 T 867640 Plat_L3#LINE/ 3570 T 3570 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 21.89 CpG sites = 7, Kimura (unadjusted) = 21.89 Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.02 (1 / 49), avg. gap size = 1.00 (1 / 1) 16 0.00 0.00 0.00 chr1qtel1M 867869 867885 (132115) (T)n#Simple_repeat 1 17 (0) m_b51s252i6 1851 chr1qtel1M 867869 TTTTTTTTTTTTTTTTT 867885 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTT 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 270 27.27 9.09 0.00 chr1qtel1M 869453 869551 (130449) C L2a_3end#LINE/L2 (24) 493 386 m_b51s601i11 1852 chr1qtel1M 869453 TTAAGTTTCAACAATGTGTCAAGCACTAAACTGAGTGCTGGG--TACAG- 869499 i ivi v v i i ivv ii i -- - C L2a_3end#LINE 493 TTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGCGCTGGGGATACAGC 444 chr1qtel1M 869500 AG---ACAAAGAAGA-AACAATAGCT--CTTTAAAGAGCTTATATTCTAT 869543 --- iv - v i vv -- i i vi i v C L2a_3end#LINE 443 AGTGAACAAAACAGACAAAAGTCCCTGCCCTCATGGAGCTTACATTCTAG 394 chr1qtel1M 869544 TGGGGGAA 869551 i C L2a_3end#LINE 393 TGGGGGGA 386 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.66 CpG sites = 16, Kimura (unadjusted) = 34.77 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.05 (5 / 98), avg. gap size = 1.80 (9 / 5) 262 31.58 9.65 0.00 chr1qtel1M 869454 869567 (130433) C L2b_3end#LINE/L2 (25) 441 317 m_b51s601i12 1852 chr1qtel1M 869454 TAAGTTTCAACAATGTGTCAAGCACTAAACTGAGTGCTGGG--TACAGAG 869501 i ivi v vi i i ? ivi ii i -- v C L2b_3end#LINE 441 TGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGGGATACAGCG 392 chr1qtel1M 869502 ----ACAAAGAAGAAACAATAGCT--CTTTAAAGAGCTTATATTCTATTG 869545 ---- iiv v? ii vv -- i i vi i i v v C L2b_3end#LINE 391 GTGAACAAGACAGACNCGGTCCCTGCCCTCACGGAGCTCACAGTCTAGTG 342 chr1qtel1M 869546 GGGGAAACA---ATATAACCACATA 869567 i --- i ? v i C L2b_3end#LINE 341 GGGGAGACAGACATGTAANCAGACA 317 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.10 CpG sites = 23, Kimura (unadjusted) = 44.59 Transitions / transversions = 1.77 (23/13) Gap_init rate = 0.04 (4 / 113), avg. gap size = 2.75 (11 / 4) 681 36.65 9.13 1.80 chr1qtel1M 869741 870518 (129482) L2#LINE/L2 2232 3065 (17) m_b51s601i13 1853 chr1qtel1M 869741 CCACAGGGCTCTGTTCTGGG--CTCTTCTCTTCACCCTCTATGCTACTTC 869788 v v i v -- v iv ii vvi L2#LINE/L2 2232 CCCCAGGGCTCAGTCCTTGGACCTCTTCTCTTCTCTATCTACACTCACTC 2281 chr1qtel1M 869789 CCTTGCTGATCCCAT-CAGCCACATGAATC----TGTCATC--TCTGCGG 869831 ? v i - i v iv i---- ii -- v v L2#LINE/L2 2282 CCTNGGTGATCTCATCCAGTCTCATGGCTTTAAATACCATCTATATGCTG 2331 chr1qtel1M 869832 ATGATTCTCCAATC----TCCCTATGGGCCCGAATCTCTGGC--GATCTT 869875 i i v i---- i i --- i i vv -- v i L2#LINE/L2 2332 ATGACTCCCAAATTTATATCTCCA---GCCCGGACCTCTCCCCTGAACTC 2378 chr1qtel1M 869876 CAGTCTTACATCTCCAAACATCTTTCAGACACCTCCAACTGCATATTCAG 869925 v iii v viii viiv i vi v i ii i L2#LINE/L2 2379 CAGACTCGTATATCCAACTGCCTACTCGACATCTCCACTTGGATGTCTAA 2428 chr1qtel1M 869926 GAGACACCTTACACTCAACAGGTCCTAAAGAGATCTC---AGCTTTTCCC 869972 v i i i v i v v vv v --- v ii L2#LINE/L2 2429 TAGGCATCTCAAACTTAACATGTCCAAAACTGAACTCCTGATCTTCCCCC 2478 chr1qtel1M 869973 TAAATCTTCCCTCTATC-TGGACTTCCC-----------ATTGC------ 870004 v v i v ii vi -ii v ----------- v ------ L2#LINE/L2 2479 TCAAACCTGCTCCTCCCGCAGTCTTCCCCATCTCAGTNAATGGCAACTCC 2528 chr1qtel1M 870005 -TTCTCCCAGTTCCTCAGACCCACGGTCTAGACATTATCCTGCACTCCT- 870052 - i i v i v viii v ivi i vv - L2#LINE/L2 2529 ATCCTTCCAGTTGCTCAGGCCAAAAACCTTGGAGTCATCCTTGACTCCTC 2578 chr1qtel1M 870053 ----------------CACATACAATCTGTCACCAAGACTTATTTATCTC 870086 ---------------- v ii v iv i i iviiiii L2#LINE/L2 2579 TCTTTCTCTCACACCCCACATCCAATCCATCAGCAAATCCTGTCGGCTCT 2628 chr1qtel1M 870087 ACCTTTGCCACATCACTCAG-ATATGCCCCTTTCTCTCCTCTGACCCGGT 870135 iivv i - ii - vi v vi v v ivv v v i L2#LINE/L2 2629 ACCTTCAAAATAT-ATCCAGAATCCGACCACTTCTCACCACCTCCACTGC 2677 chr1qtel1M 870136 CA-CGTTCAGGGCCAGGCCCTCATTGCCTCACACCTGGAGCATTACAACT 870184 - iii v v i vi iii v i vi i i iv L2#LINE/L2 2678 CACCACCCTGGTCCAAGCCACCATCATCTCTCGCCTGGATTACTGCAATA 2727 chr1qtel1M 870185 GTTTTTTGATGGCTCTGTCTTACCCCAGTCTCTTCCCCACTCTGATCCAT 870234 ii ii i iv v -i i i ii vii ii v v ?iii i L2#LINE/L2 2728 GCCTCCTAACTGGTCT-CCCTGCTTCCACCCTTGCCCCCCTNCAGTCTAT 2776 chr1qtel1M 870235 TCT--GTTCAGCTCACAAACTGATCTTTCTAAACTGCACGTCTGACCATG 870282 --iiv vvv i v i i vi i v v i L2#LINE/L2 2777 TCTCAACACAGCAGCCAGAGTGATCCTTTTAAAACGTAAGTCAGATCATG 2826 chr1qtel1M 870283 TCATCCCTTTACCTGCCCCCACTACCTACATTCCAATGGCTTCCAACTTG 870332 ii ---- i vv -- ----i v ii v L2#LINE/L2 2827 TCACTCCT----CTGCTCAAA--ACC----CTCCAATGGCTTCCCATCTC 2866 chr1qtel1M 870333 CCTCCATCTGGAGGC----ACCTCTAT-GTGGCCCCCCAATCCTTTTATA 870377 v vivv ii i ----ii ii i-i iv v iv i vi i L2#LINE/L2 2867 ACTCAGAGTAAAAGCCAAAGTCCTTACAATGGCCTACAAGGCCCTACATG 2916 chr1qtel1M 870378 ACCTGGCAATTTTCTACTTTTCTATTCTCATACCTGACC---TTGCCTCA 870424 i ivviiivi i i ivi vi iv ---i v i v L2#LINE/L2 2917 ATCTGGTCCCCCGTTACCTCTCTGACCTCATCTCCTACCACTCTCCCCCT 2966 chr1qtel1M 870425 GACTT-TTCTG--CCTG--ACACTGGCCTCCTGGCTGTTCCAGGAACAAG 870469 vi i-i i -- v -- v vv v L2#LINE/L2 2967 CGCTCACTCCGCTCCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACACG 3016 chr1qtel1M 870470 ACCTTTTCTATCTTGGCTCCAAGTATTTTCTCTGGCTATTTCCCATGCC 870518 v vvviv vv ii v vii iv v v v i i iv L2#LINE/L2 3017 CCAGGCACGCTCCCGCCTCAGGGCCTTTGCACTTGCTGTTCCCTCTGCC 3065 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 50.25 CpG sites = 162, Kimura (unadjusted) = 52.75 Transitions / transversions = 1.37 (162/118) Gap_init rate = 0.05 (36 / 777), avg. gap size = 2.39 (86 / 36) 490 31.28 2.41 1.80 chr1qtel1M 870615 870780 (129220) L2b_3end#LINE/L2 292 458 (8) m_b51s601i14 1853 chr1qtel1M 870615 CTACTTCTGTCTTCCTGGTATTAACTATTCCCCATCTATCTTGCCATCTT 870664 i- i vii -i -i? vi ii?i iv vv ii i L2b_3end#LINE 292 CTACC-CTGCCACTCTGG-GTTA-TNATTGTCTGNTTACATGTCTGTCTC 338 chr1qtel1M 870665 CCCCATAAGGTTGTGAGCTCCTTGAGCACAGGGAT--TGTCT--TTTGCT 870710 iv ii v vi i--? --i i L2b_3end#LINE 339 CCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCTTGTT 388 chr1qtel1M 870711 CTTTTTGGTAATCCTAGCACTTAGCACAGTGCCCGACACACAGGAGGTGC 870760 viiviv vi i i i ? i i v i L2b_3end#LINE 389 CACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGC 438 chr1qtel1M 870761 TTAATAAATGTTTACTAAGT 870780 i i i ii i i L2b_3end#LINE 439 TCAGTAAATATTTGTTGAAT 458 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 41.77 CpG sites = 38, Kimura (unadjusted) = 45.48 Transitions / transversions = 2.92 (38/13) Gap_init rate = 0.03 (5 / 165), avg. gap size = 1.40 (7 / 5) 511 26.94 4.17 2.04 chr1qtel1M 870635 870778 (129222) L2d2_3end#LINE/L2 399 545 (10) m_b51s601i15 1853 chr1qtel1M 870635 TTAACTATTCCC-CATCTAT--CTTGCCATCTTCCCCATAAGGTTGTGAG 870681 v v -ii i -- --- i v iv i i L2d2_3end#LIN 399 TTAACTTTTCACGTGTTTATGTCTTG---TCTCCCCAACTAGATTGTAAG 445 chr1qtel1M 870682 CTCCTTGAGCACAGGGATTGTCTTTTGCTCTTTTTGGTAATCCT---AGC 870728 vi iii v i iiv i v vi i--- L2d2_3end#LIN 446 CTCCTTGAGGGCAGGGACCATGTCTTATACTTCTTTGTATCCCCCACAGC 495 chr1qtel1M 870729 ACTTAGCACAGTGCCCGACACACAGGAGGTGCTTAATAAATGTTTACTAA 870778 i i ivi v i i i ii i L2d2_3end#LIN 496 GCCTAGCACAGTGCCTTGCACACAGTAGGCGCTCAATAAATATTTGTTGA 545 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.83 CpG sites = 27, Kimura (unadjusted) = 35.14 Transitions / transversions = 2.45 (27/11) Gap_init rate = 0.04 (6 / 143), avg. gap size = 1.50 (9 / 6) 263 35.37 1.36 0.00 chr1qtel1M 872678 872824 (127176) L2#LINE/L2 2177 2325 (757) m_b51s601i16 1854 chr1qtel1M 872678 CTCTGTTTCCTTTGCTAGGCCCTCCCCCAGATCATGCCCTCTGGCCAC-- 872725 v i i vi i vvvvi vi v ?iv ii-- L2#LINE/L2 2177 CTCAGTCTCCTTTGCTGGTTCCTCCTCATCTCCCCGACCTCTNAACGTTG 2226 chr1qtel1M 872726 GAGTCCCTCAGGGCTCTGTCCAGGGTCCTCCCTTTTCCCTTCTCTAGACT 872775 v i v vv v iii i i ii v v L2#LINE/L2 2227 GAGTGCCCCAGGGCTCAGTCCTTGGACCTCTTCTCTTCTCTATCTACACT 2276 chr1qtel1M 872776 CATGGCCTTAGTGGCCACAGCCAATCACCCAAATTTAATCACCATTCAT 872824 ivv ?i ii v v i v viiiv vi ii L2#LINE/L2 2277 CACTCCCTNGGTGATCTCATCCAGTCTCATGGCTTTAAATACCATCTAT 2325 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 47.47 CpG sites = 28, Kimura (unadjusted) = 50.17 Transitions / transversions = 1.17 (28/24) Gap_init rate = 0.01 (1 / 146), avg. gap size = 2.00 (2 / 1) 200 25.75 2.99 1.47 chr1qtel1M 873370 873436 (126564) L2#LINE/L2 2807 2874 (208) m_b51s601i17 1854 chr1qtel1M 873370 AAAAGGCAGATCTGATTATGTCATTTCTCCTACTCAATAAACTCC-ATGC 873418 v i ii v i i i - i v vv - v L2#LINE/L2 2807 AAAACGTAAGTCAGATCATGTCACTCCT-CTGCTCAAAACCCTCCAATGG 2855 chr1qtel1M 873419 CTCCCCATCAC-CTCAAGG 873436 i v - ii L2#LINE/L2 2856 CTTCCCATCTCACTCAGAG 2874 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.26 CpG sites = 10, Kimura (unadjusted) = 32.26 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.05 (3 / 66), avg. gap size = 1.00 (3 / 3) 195 19.09 8.33 5.41 chr1qtel1M 874498 874569 (125431) L3#LINE/CR1 4022 4095 (4) m_b51s601i18 1855 chr1qtel1M 874498 GGAATCCTCC-TTAAAT---AAGTTGGACTAGAAAGATATC-GAGGTCC- 874541 v v - ii --- i v- iv -i - L3#LINE/CR1 4022 GGATTCCTGCATTGGATGGGAGGTTGGACTAGAT-GACCTCTAAGGTCCC 4070 chr1qtel1M 874542 TTCCAACTCACAAATTCTGCACTAATTC 874569 vv i --- i L3#LINE/CR1 4071 TTCCAACTCTGAGATTCTG---TGATTC 4095 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 22.27 CpG sites = 7, Kimura (unadjusted) = 22.27 Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.11 (8 / 71), avg. gap size = 1.25 (10 / 8) 239 38.48 1.49 3.03 chr1qtel1M 874806 875006 (124994) C L2#LINE/L2 (569) 2513 2316 m_b51s601i19 1856 chr1qtel1M 874806 TGAAGTGCTGAGAAGTTTGGGGGAGAGCTGGGTATGAGGGGAAAGATC-G 874854 ii -- i vi v iivii v i - C L2#LINE/L2 2513 TGAGATG--GGGAAGACTGCGGGAGGAGCAGGTTTGAGGGGGAAGATCAG 2466 chr1qtel1M 874855 GAGCCCTGTTTAGAGCACAGCGATTCTGACTCGACCTCAGGACATCCGGT 874904 ii v v ii iivii v i vvi v ivivi iiv C L2#LINE/L2 2465 GAGTTCAGTTTTGGACATGTTAAGTTTGAGATGCCTATTAGACATCCAAG 2416 chr1qtel1M 874905 CTGAAACGTCCAGTGGACAATGTGCCAGGTGGGTCTGAAGCTTGGGGGAG 874954 iv i i v i i i vv vi vii i i i ii C L2#LINE/L2 2415 TGGAGATGTCGAGTAGGCAGTTGGATATACGAGTCTGGAGTTCAGGGGAG 2366 chr1qtel1M 874955 AGGCCAGGTCTGTGG--GTGGACCTACGAGCCATCACTAGGCAGACGGAT 875002 i v v vi --i ii ii iv i ---- v ii C L2#LINE/L2 2365 AGGTCCGGGCTGGAGATATAAATTTGGGAGTCATCA----GCATATAGAT 2320 chr1qtel1M 875003 GGCA 875006 i C L2#LINE/L2 2319 GGTA 2316 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 57.36 CpG sites = 50, Kimura (unadjusted) = 58.63 Transitions / transversions = 2.00 (50/25) Gap_init rate = 0.04 (8 / 200), avg. gap size = 1.12 (9 / 8) 14 13.72 3.12 0.00 chr1qtel1M 876368 876399 (123601) (CAAGGG)n#Simple_repeat 1 33 (0) m_b51s252i7 1857 chr1qtel1M 876368 CAAGGGCAAGGGC-AGGGCCAGGGTTAGGGTAA 876399 - v iv i (CAAGGG)n#Sim 1 CAAGGGCAAGGGCAAGGGCAAGGGCAAGGGCAA 33 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 22 9.10 0.00 2.70 chr1qtel1M 876584 876621 (123379) (TCCC)n#Simple_repeat 1 37 (0) m_b51s252i8 1858 chr1qtel1M 876584 TCCCTCCCTCCTTCCCTCTTTCCCTCCCTCCCTCACCT 876621 i ii - (TCCC)n#Simpl 1 TCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTC-CCT 37 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 188 22.86 0.00 0.00 chr1qtel1M 878521 878555 (121445) C L2c_3end#LINE/L2 (14) 464 430 m_b51s601i20 1859 chr1qtel1M 878521 CAAGCATTTATGAGGCACCTGCTGTGTGCTAGGCG 878555 i vii i i i i C L2c_3end#LINE 464 CAAACATTTATTGAGCGCCTACTATGTGCCAGGCG 430 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 25.14 CpG sites = 7, Kimura (unadjusted) = 29.45 Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 181 20.00 0.00 0.00 chr1qtel1M 879337 879376 (120624) MIRb#SINE/MIR 211 250 (18) m_b51s601i21 1860 chr1qtel1M 879337 GCGCTCAGCCCCGTGCCTGGCACACAGCAGGCGCTTCATA 879376 i v v i i i iv MIRb#SINE/MIR 211 GCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATA 250 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 23.72 CpG sites = 5, Kimura (unadjusted) = 23.72 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 15 16.89 5.88 0.00 chr1qtel1M 881164 881197 (118803) (AT)n#Simple_repeat 1 36 (0) m_b51s252i9 1861 chr1qtel1M 881164 ATGTATTCATATATAT-TATACACATATA-ATATAT 881197 i vi - i i - (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATAT 36 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2) 16 0.00 0.00 0.00 chr1qtel1M 881247 881263 (118737) (A)n#Simple_repeat 1 17 (0) m_b51s252i10 1862 chr1qtel1M 881247 AAAAAAAAAAAAAAAAA 881263 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 66 3.18 0.00 0.00 chr1qtel1M 883022 883086 (116914) (AT)n#Simple_repeat 1 65 (0) c_b51s251i1 1863 chr1qtel1M 883022 ATATATATATATATATATATATATATATATATATATATATATACATATAT 883071 i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr1qtel1M 883072 ATATATATATGTATA 883086 i (AT)n#Simple_ 51 ATATATATATATATA 65 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0) 233 27.40 6.85 0.00 chr1qtel1M 884333 884405 (115595) MIR3#SINE/MIR 2 79 (129) m_b51s601i22 1864 chr1qtel1M 884333 TGGAAGATGGGCT----AGAAGGAGCACTGAGTGGAAAACAGAA-AGCTG 884377 v vv ---- ii v v i iv i - v MIR3#SINE/MIR 2 TGGCAGAGTGGCTGAGCAGAGAGAGCACGGACTGGGAGTCAGGAGACCTG 51 chr1qtel1M 884378 AATGATAGTCCCATTTCTGCTACTAACT 884405 ii vv ivi i MIR3#SINE/MIR 52 GGTTCTAGTCCCGGCTCTGCCACTAACT 79 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.42 CpG sites = 10, Kimura (unadjusted) = 34.47 Transitions / transversions = 1.00 (10/10) Gap_init rate = 0.03 (2 / 72), avg. gap size = 2.50 (5 / 2) 295 28.30 2.75 2.75 chr1qtel1M 884852 884960 (115040) MIR3#SINE/MIR 93 201 (7) m_b51s601i23 1864 chr1qtel1M 884852 TGGACCAATCACT--ACCTTTATATGGCTCAGTTTCTT-ATTTATGTCAA 884898 i v i -- i v iv v i - i -- v MIR3#SINE/MIR 93 TGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCT--GTAAA 140 chr1qtel1M 884899 ATGACATGGCTGAGCAAGATGAGCTTTCAAGTCCATTTCAGCTCTCTCTC 884948 viv i ii v v i v i v i vv vi MIR3#SINE/MIR 141 ATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACAT 190 chr1qtel1M 884949 TCCAATGATTTT 884960 i- i MIR3#SINE/MIR 191 TCT-ATGATTCT 201 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.12 CpG sites = 16, Kimura (unadjusted) = 36.12 Transitions / transversions = 1.14 (16/14) Gap_init rate = 0.05 (5 / 108), avg. gap size = 1.20 (6 / 5) 333 28.78 5.98 7.26 chr1qtel1M 886856 887106 (112894) MIRc#SINE/MIR 2 249 (19) m_b51s601i24 1865 chr1qtel1M 886856 GAGGCATTGTGAAGTACTGGATAAAGTGCATCCAGTGGATAAAGTATCAA 886905 v iv i v -- v i---- ivvi vi i MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGA--AAGAGCAC----TGGACTTGGAGTCAG 45 chr1qtel1M 886906 ATCAGAAGCTCTGAGTT-GATTCCTGTCTCAGGCTATTACT--CTGTCAT 886952 ---- vi i - v i v v v vv -- -i MIRc#SINE/MIR 46 ----GAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGT-GT 90 chr1qtel1M 886953 G-CCTGAAAAGGGGGAACCTTTTCAATCTTTCACAGACT--GTCACCTAA 886999 - v---- vi ii vi - i i vv v -- iv v MIRc#SINE/MIR 91 GACCTT----GGGCAAGTCACTT-AACCTCTCTGAGCCTCAGTTTCCTCA 135 chr1qtel1M 887000 A--GTAGATCATCAGAGTAATAAT---TAAAATG---AACTCTCATGGTT 887041 v-- i -- vi ii --- ivvv --- v v v MIRc#SINE/MIR 136 TCTGTAAA--ATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTT 183 chr1qtel1M 887042 CTTGTGAGAATAAAATGAAATAATGC-TTTGAAAGTGCTTTGTACTCCTT 887090 v i v i i- v i vv iv MIRc#SINE/MIR 184 GTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTTTGTAAACTGT 233 chr1qtel1M 887091 GGTGTGCTATACAAAT 887106 iiv MIRc#SINE/MIR 234 AAAGTGCTATACAAAT 249 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.17 CpG sites = 30, Kimura (unadjusted) = 36.47 Transitions / transversions = 0.81 (30/37) Gap_init rate = 0.10 (26 / 250), avg. gap size = 1.27 (33 / 26) 397 30.33 5.69 4.69 chr1qtel1M 887136 887346 (112654) L3#LINE/CR1 3620 3832 (267) m_b51s601i25 1866 chr1qtel1M 887136 TTTAGTAAGGGAATAAGCAAGCTAGAGATTGCTCAAATAAGA-CAACCAG 887184 iv i iv vii i i vvi ii i vi - i L3#LINE/CR1 3620 TTTAAGAGGGACATTGACAAACTGGAGCGCGTCCAGAGGAGAGCGACCAG 3669 chr1qtel1M 887185 GATTGCGAGGTGAGGTCTATTTAAACCTTGAAATACAAG-AGTGGTTTTG 887233 v i i --- iv-- v vv ii - ii -- L3#LINE/CR1 3670 GATGGTGAAG---GGTCTGG--AAACCATGTCATATGAGGAACGGTT--G 3712 chr1qtel1M 887234 ATAGAACTAAGAATATTTATTTTTAGGAAGAGAAG-CTTAGAGGCACCAT 887282 vi ii i i vii vii - viv L3#LINE/CR1 3713 AAGGAACTGGGGATGTTTAGCCTGGAGAAGAGAAGACTTAGAGGAGACAT 3762 chr1qtel1M 887283 GGTAATTGTCTTTTTCAATATTTTAA----TGTTCACATGGAAGA-AAAT 887327 i ii -- iv v ---- - ii -ii L3#LINE/CR1 3763 GATAGCTGTC--TTCAAATATTTGAAGGGCTG-TCATGTGGAAGAGGGAT 3809 chr1qtel1M 887328 TTGAATT----TGAGTGACTCTA 887346 v v ---- v i i L3#LINE/CR1 3810 TAGACTTATTCTGTGTGGCTCCA 3832 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.14 CpG sites = 40, Kimura (unadjusted) = 40.77 Transitions / transversions = 1.90 (40/21) Gap_init rate = 0.08 (16 / 210), avg. gap size = 1.38 (22 / 16) 245 31.87 3.21 2.66 chr1qtel1M 887753 887939 (112061) C L1P4_orf2#LINE/L1 (654) 2640 2453 m_b51s551i4 1867 chr1qtel1M 887753 CTTACAATATAGTTTAAGATCTGGAACAGCTAAACTTCCTTCTT-GTACA 887801 ii i i ii v v vv iv vi i vv - v v C L1P4_orf2#LIN 2640 CTTGTAGTATAGTTTGAAGTCGGGTAATGTGATGCCTCCGGCTTTGTTCT 2591 chr1qtel1M 887802 TTTTCCCCTTTATTTCCTTTGCTATTCTTGAACTTTTTGTTTTG---CCA 887848 v iivvv v i v -- ii i -- --- C L1P4_orf2#LIN 2590 TTTTGCTTAGGATTGCTTTGGCTATTC--GGGCTCTTT--TTTGGTTCCA 2545 chr1qtel1M 887849 AATGAATTTTATTATGATTTTTTTCTAATTCAGC--AAAATAATTTTGGT 887896 v vv - v v i-- i iv C L1P4_orf2#LIN 2544 TATGAATTTTAGAAT-AGTTTTTTCTAATTCTGTGAAAAATGACGTTGGT 2496 chr1qtel1M 887897 AATTTAGTTATGATGGCATTGAATATAGAAATTAGTTTAAGTA 887939 i ii vivi i i v iv i iv ii i C L1P4_orf2#LIN 2495 AGTTTGATAGGAATAGCGTTGAATCTGTAGATTGCTTTGGGCA 2453 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.47 CpG sites = 31, Kimura (unadjusted) = 42.37 Transitions / transversions = 1.15 (31/27) Gap_init rate = 0.04 (8 / 186), avg. gap size = 1.38 (11 / 8) 13 18.79 3.70 5.66 chr1qtel1M 888054 888107 (111893) (TATTTA)n#Simple_repeat 1 53 (0) m_b51s252i11 1868 chr1qtel1M 888054 TATCTAAATTTATTTTTAAATATTTATATATA-ATATTCT-TTTCTTTTT 888101 i v v -- v - - v - v v (TATTTA)n#Sim 1 TATTTATATTTATATTT--ATATTTATATTTATAT-TTATATTTATATTT 47 chr1qtel1M 888102 AAATTT 888107 v (TATTTA)n#Sim 48 ATATTT 53 Matrix = Unknown Transitions / transversions = 0.14 (1/7) Gap_init rate = 0.09 (5 / 53), avg. gap size = 1.00 (5 / 5) 402 27.44 14.10 1.91 chr1qtel1M 888687 888920 (111080) C L1ME5_3end#LINE/L1 (544) 397 136 m_b52s551i1 1869 chr1qtel1M 888687 GAGATAGACCTAATAGTGATATTGTTAG-----AGTGTATGCAAAGATTT 888731 v v i iv i iv i i ----- v iv v i C L1ME5_3end#LI 397 GATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATGCGTATACTT 348 chr1qtel1M 888732 ATAATTT--TTAAGGTATACTTCCAAATTGTTCTTCAGAATGGTTGGACC 888779 -- --i --- v i i i i v C L1ME5_3end#LI 347 A--ATTTGACTAAG---TACTGCCAGATTGCTCTCCAGAATGGCTGCACC 303 chr1qtel1M 888780 AGTTCACAACTCTACCAATAGTTTATTAGTATACCTGTTATCCCTCAT-- 888827 ii vii i ii vi v vi v i ?vi v -- C L1ME5_3end#LI 302 AGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATCC 253 chr1qtel1M 888828 --GTC----CTT---------CAGCTTTTTAAACT-------TCTGATAG 888855 -- i ---- --------- i vi ------- i C L1ME5_3end#LI 252 TCGCCAACACTTGGCATTATCCAGCTTTCTAATTTTTGCCAGTCTAATAG 203 chr1qtel1M 888856 GTGCAATGTATTTTCTCAAAGTTGTATTAATTTGAATT--TTTAATCAAT 888903 i v iv v vv v v -- i i i v C L1ME5_3end#LI 202 GTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATTTCTCTGATTACT 153 chr1qtel1M 888904 TATGATTTAAAGCATTT 888920 v v vi i C L1ME5_3end#LI 152 AATGAGTTTGAGCATCT 136 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.77 CpG sites = 35, Kimura (unadjusted) = 35.14 Transitions / transversions = 1.25 (35/28) Gap_init rate = 0.06 (13 / 233), avg. gap size = 2.92 (38 / 13) 371 28.31 14.15 2.20 chr1qtel1M 888689 889013 (110987) C L1ME3G_3end#LINE/L1 (531) 393 31 m_b52s551i2 1869 chr1qtel1M 888689 GATAGA--CCTAATAGTGATATTGTTAG-----AGTGTATGCAAAGATTT 888731 -- ? iv iv i i ----- v iv -- C L1ME3G_3end#L 393 GATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGCA--TTT 346 chr1qtel1M 888732 ATAATTTTTAAGGTATACTTCCAAATTGTTCTTCAGAATGGTTGGACCAG 888781 - v viv v ii i i ? i v i C L1ME3G_3end#L 345 -TAAATTTTAATAGATACTGCCAAATTGCCCTCCAAAANGGCTGTACCAA 297 chr1qtel1M 888782 TTCACAACTCTACCAATAGTTTATTAGTATACCTGTTATCCCTCATGTCC 888831 i vii i ii v v vi i - - iii C L1ME3G_3end#L 296 TTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTT-TCCC-CACACCC 249 chr1qtel1M 888832 T------------------TCAGCTTTTTAAACT--------TCTGATAG 888855 ------------------ i?i i -------- i C L1ME3G_3end#L 248 TCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATCTGATGG 199 chr1qtel1M 888856 GTGCAATGTATTTTCTCAAAGTTGTATTAATTTGAATTT--TTAATCAAT 888903 v vi iv v vv v v --i i i v C L1ME3G_3end#L 198 GTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGATTACT 149 chr1qtel1M 888904 TATGATTTAAAGCA---TTTTATGTGACTATAGATCACTACAGATTT--T 888948 vi vv vi --- i i vi v ii i -iiv -- C L1ME3G_3end#L 148 AGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATT-TGTATTTCCT 100 chr1qtel1M 888949 CATCTAAAAATTGTATG---AT---CTTTGACTATTTACATTTAATGAAT 888992 v ivi iv --- --- v i --v i v ii C L1ME3G_3end#L 99 CTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTT--TTCTATTGGGT 52 chr1qtel1M 888993 GATTCTTTTTTTATAGATTTG 889013 vi ii i v C L1ME3G_3end#L 51 TGTCTTTTTCTTATTGATTTG 31 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.06 CpG sites = 53, Kimura (unadjusted) = 37.11 Transitions / transversions = 1.43 (53/37) Gap_init rate = 0.05 (17 / 324), avg. gap size = 3.18 (54 / 17) 14 15.24 0.00 7.69 chr1qtel1M 889320 889361 (110639) (TTTTAT)n#Simple_repeat 1 39 (0) m_b52s252i1 1870 chr1qtel1M 889320 TTTCATTTGCTTTTTTTGATATTATATTTTTATTTTTACTTT 889361 i -- v v - v i (TTTTAT)n#Sim 1 TTTTATTT--TTATTTTTAT-TTTTATTTTTATTTTTATTTT 39 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.07 (3 / 41), avg. gap size = 1.00 (3 / 3) 34 3.03 0.00 0.00 chr1qtel1M 889723 889756 (110244) (CA)n#Simple_repeat 1 34 (0) c_b52s251i0 1871 chr1qtel1M 889723 CACACACACACACATACACACACACACACACACA 889756 i (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACA 34 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 12 16.82 9.52 0.00 chr1qtel1M 889762 889803 (110197) (ATAC)n#Simple_repeat 1 46 (0) m_b52s252i2 1872 chr1qtel1M 889762 ATACACACA-A-ATATGTGTATACATACATACA-A-ATATATACAT 889803 i - - ii ii - - i (ATAC)n#Simpl 1 ATACATACATACATACATACATACATACATACATACATACATACAT 46 Matrix = Unknown Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.10 (4 / 41), avg. gap size = 1.00 (4 / 4) 19 4.50 0.00 0.00 chr1qtel1M 889988 890010 (109990) (T)n#Simple_repeat 1 23 (0) m_b52s252i3 1873 chr1qtel1M 889988 TTTTTTGTTTTTTTTTTTTTTTT 890010 v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTT 23 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 19 27.13 1.47 1.47 chr1qtel1M 890730 890797 (109203) (TTTTCTT)n#Simple_repeat 1 68 (0) m_b52s252i4 1874 chr1qtel1M 890730 TTTTCTTTGTTTCCTTATAGATTATTCTTTTGT-TATCTACTGTTCACTT 890778 - i v vvv v v - v i v v iv (TTTTCTT)n#Si 1 TTTTCTTT-TTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCTT 49 chr1qtel1M 890779 TTTACTTTATTCTTTTTTC 890797 v v (TTTTCTT)n#Si 50 TTTTCTTTTTTCTTTTTTC 68 Matrix = Unknown Transitions / transversions = 0.25 (3/12) Gap_init rate = 0.03 (2 / 67), avg. gap size = 1.00 (2 / 2) 18 22.66 4.26 6.52 chr1qtel1M 890846 890939 (109061) (ATAC)n#Simple_repeat 1 92 (0) m_b52s252i5 1875 chr1qtel1M 890846 ATATATTTATACAT--ATACATACATGCACATTTATACCCACACATATAT 890893 i vi -- -- vi vi i i i (ATAC)n#Simpl 1 ATACATACATACATACATACATACAT--ACATACATACATACATACATAC 48 chr1qtel1M 890894 CTGCAGAC--ACATACATAGATTTACATGCATACATATCCATATATAC 890939 v i v -- v -- i -- i (ATAC)n#Simpl 49 ATACATACATACATACATACA--TACATACATACATA--CATACATAC 92 Matrix = Unknown Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.09 (8 / 93), avg. gap size = 1.25 (10 / 8) 14 22.44 1.52 8.06 chr1qtel1M 892397 892462 (107538) (TTTC)n#Simple_repeat 1 62 (0) m_b52s252i6 1876 chr1qtel1M 892397 TTTCTTATATTTCCCATTCTGTTCTATTTTTTTTTTCATTCTTTCTAT-T 892445 - v -- v - - i i v v - (TTTC)n#Simpl 1 TTTCTT-TCTTT--CTTTCT-TTCT-TTCTTTCTTTCTTTCTTTCTTTCT 45 chr1qtel1M 892446 TTGTTTTGCTATTTCTT 892462 v ivi v (TTTC)n#Simpl 46 TTCTTTCTTTCTTTCTT 62 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.09 (6 / 65), avg. gap size = 1.00 (6 / 6) 24 26.09 0.00 0.00 chr1qtel1M 892557 892615 (107385) (TT)n#Simple_repeat 1 59 (0) m_b52s252i7 1877 chr1qtel1M 892557 TTTTTTTTTTTTTCATAATCTTCTTGTTTTTCTTGAATTTTTTTTTTTTT 892606 iv vv i i v i vvv (TT)n#Simple_ 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr1qtel1M 892607 TTAGTTTTT 892615 vv (TT)n#Simple_ 51 TTTTTTTTT 59 Matrix = Unknown Transitions / transversions = 0.44 (4/9) Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.0 (0 / 0) 14 13.14 9.52 0.00 chr1qtel1M 892882 892923 (107077) (CCTCTCA)n#Simple_repeat 1 46 (0) m_b52s252i9 1878 chr1qtel1M 892882 CCTCT-AGCT-TCA-CT-TCACCTCTCCCCTCTGACCTAGCACCTC 892923 - v - - - v v vv (CCTCTCA)n#Si 1 CCTCTCACCTCTCACCTCTCACCTCTCACCTCTCACCTCTCACCTC 46 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.10 (4 / 41), avg. gap size = 1.00 (4 / 4) 244 31.40 4.07 4.46 chr1qtel1M 894863 895132 (104868) L1M3_orf2#LINE/L1 3020 3288 (0) m_b52s551i3 1879 chr1qtel1M 894863 ACAATTTGG-TTACATTAAATTAAAAAGATTTTGCACA--AATAAAACCA 894909 v v -i i i v i -- vii v L1M3_orf2#LIN 3020 ACAAGTGGGACTACATCAAACTAAAAAGCTTCTGCACAGCAAAGGAAACA 3069 chr1qtel1M 894910 GTGCAGCCAAGATTAAAAGGGAAACAGAAAGATGGAGATGGGGTGAAAT- 894958 i - i -- v i i v vv ----i - ivi - L1M3_orf2#LIN 3070 AT-CAAC--AGAGTGAAAAGGCAACCTA----CGGA-ATGGGAGAAAATA 3111 chr1qtel1M 894959 TTTGCATTCAGTATTTCTGATAAAGGCCTCATTTCTATGACATGTAGAGA 895008 vv vi v i vi v v i vi i i ii L1M3_orf2#LIN 3112 TTTGCAAACCATATATCTGATAAGGGGTTAATATCCAAAATATATAAGGA 3161 chr1qtel1M 895009 CCTAATTCAAATTGAT---AAGAATATAAGTCATTCATCAATTGATTAAT 895055 v v? v v ii --- i v i i v i---i i ? vv L1M3_orf2#LIN 3162 ACTCNTACAACTCAATAGCAAAAAAACAAATAAC---CCGATTNAAAAAT 3208 chr1qtel1M 895056 GGTCAGAGGATATGAATTGAC-TATATTCAGATGAAGTTA---AAACAAT 895101 v i iv v - v v i i - vi --- iiii L1M3_orf2#LIN 3209 GGGCAAAGGACCTGAATAGACATTTCTCCAAA-GAAGACATACAAATGGC 3257 chr1qtel1M 895102 TTCTAGTCATATTAAAAAATGCTCCAAATCA 895132 ivvi vi v i v v L1M3_orf2#LIN 3258 CAACAGGTATATGAAAAGATGCTCAACATCA 3288 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.58 CpG sites = 43, Kimura (unadjusted) = 41.92 Transitions / transversions = 1.13 (43/38) Gap_init rate = 0.07 (18 / 269), avg. gap size = 1.28 (23 / 18) 567 29.25 9.81 4.01 chr1qtel1M 894992 895511 (104489) L1ME4c_3end#LINE/L1 7 555 (275) m_b52s551i5 1879 chr1qtel1M 894992 TCTATGACATGTAGAGACCTAATTCAAATTGATAAGAATATAAGTCATT- 895040 ? i?i i i v v v - ?i vv- L1ME4c_3end#L 7 TCTNTANTATATAAAGAGCTCATTCAAATTGATAAGAAAA-ANATCAAGA 55 chr1qtel1M 895041 CATCAATTGATTAATGGTCAGAGGATATGAATTGACTATATTCAGATGAA 895090 vi v v v i i iv v viv ? v i L1ME4c_3end#L 56 CCCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAG 105 chr1qtel1M 895091 GTTAAA-ACAATTTCTAGT-------CATATTAAAAAATGCTCCAAATCA 895132 -- - ? --- ------- i vi i v vv i L1ME4c_3end#L 106 G--AAATACAANT---AGTAAACAAACACATGGAAAAATGTTCAACCTCG 150 chr1qtel1M 895133 CTATTGATTAGAGAATTT----------------TGAGGTACTACTCAAC 895166 v i i i v v---------------- i i i iv L1ME4c_3end#L 151 CTAGTAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTAC 200 chr1qtel1M 895167 GTACCTCAGATGGGCTAAGATGGGCTATAGGAAAA--GATGATGACAAAT 895214 iviv i i vi v i ---i ---i -- i iv v L1ME4c_3end#L 201 GCCTATTAAATTAGCAAAAAT---TTA---AAAAATTGATAATACCCAAT 244 chr1qtel1M 895215 GTTGA-GGGGAGGTGGTAAAATTGGAATATTAATGTATTGTTGGTGA-AG 895262 i i- i ?v i i i v i?i v ii i i- ? L1ME4c_3end#L 245 GCTGGCGAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCAN 294 chr1qtel1M 895263 T-TAA--TGATCTAACCATTCTAGAAAGCATTTTGGAGCTATAC------ 895303 - -- i vi v i i v -- v ------ L1ME4c_3end#L 295 TGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGG--CAATACGTATCA 342 chr1qtel1M 895304 ----CCATAG----GTCTATACTCTTTGATCCAGCAGTATCAC--AAGGG 895343 ---- i---- ii i i i i vi --vv L1ME4c_3end#L 343 AGAGCCATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGG 392 chr1qtel1M 895344 AGTCTGTATCCCAAAGAGATAAT--AAAAAATGGAAAAGGACCCATATGC 895391 i i -- i i i -- i v i -- i L1ME4c_3end#L 393 AATTT--ATCCTAAGGAAATAATTCAAAAGAAGGAAAAAG--CTATATGC 438 chr1qtel1M 895392 AAAAAAAAAAAAGTTTGTAGCA-CTTTTTTTGTTGTAGTGAGAAAGTAAA 895440 vi i v---- ii v - v v i vi i i v ii L1ME4c_3end#L 439 ACGAAGAT----GTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGA 484 chr1qtel1M 895441 AATTAAATGGATGCCCACCAGTTGGTTAATGACTGAATAAGTTATGGTAT 895490 iv vv ii i v i v vv ii i i i i L1ME4c_3end#L 485 AACAACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTAC 534 chr1qtel1M 895491 ATGAAGGTAACAGTATATTAT 895511 v? vvii ii v L1ME4c_3end#L 535 ATCNACTCGATGGAATATTAT 555 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.61 CpG sites = 89, Kimura (unadjusted) = 39.39 Transitions / transversions = 1.56 (89/57) Gap_init rate = 0.07 (37 / 519), avg. gap size = 1.97 (73 / 37) 11 26.89 3.64 1.79 chr1qtel1M 898932 898986 (101014) (AAAACAT)n#Simple_repeat 1 56 (0) m_b52s252i10 1880 chr1qtel1M 898932 AAAACATAAATGGGTAAAA-A-AAGAAAAGAAACAAGAAAGAGAAAACAT 898979 -ivi - - i v vi vi v v (AAAACAT)n#Si 1 AAAACATAAA-ACATAAAACATAAAACATAAAACATAAAACATAAAACAT 49 chr1qtel1M 898980 AAAAGAT 898986 v (AAAACAT)n#Si 50 AAAACAT 56 Matrix = Unknown Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.06 (3 / 54), avg. gap size = 1.00 (3 / 3) 254 27.08 8.76 2.93 chr1qtel1M 899427 899620 (100380) L1MEh_5end#LINE/L1 2028 2232 (3) m_b52s551i6 1881 chr1qtel1M 899427 GAGAAAGGGTGAAAGGAGAGAGAA-------TAGGACAAACAGGAGGAAA 899469 i i vi i? i ------- i i i iiv L1MEh_5end#LI 2028 GAAAAAAGGAAAAAANAGAAAGAAAAACAGATGGGACAAATAGAAAACAA 2077 chr1qtel1M 899470 A-ATTAGGACGGAGGGAAAAA--CACAGTA----AGTAATCGTAACAGTG 899512 - v i i vi i v -- v? i ---- i--- i i L1MEh_5end#LI 2078 ATAATAAGATGGCAGAAATAAGTCCNAATATANCAGTAATT---ACAATA 2124 chr1qtel1M 899513 AATGTGAATGTGATGAACACTTTCAT---AAAACAGAAACAGCCATCAGA 899559 i v v i v viiv --- i i i---i? L1MEh_5end#LI 2125 AATGTAAATGGGTTAAACTCACCAATTAAAAGACAGAGAT---TNTCAGA 2171 chr1qtel1M 899560 ATGGATTAAAAAACAAAATCCTACAATATACTGCTCACAGGAAACATCCT 899609 v ? v i iii i i iv L1MEh_5end#LI 2172 TTGGATTNAAAAACAAAATCCAACAATATGCTGTCTACAAGAGACACACT 2221 chr1qtel1M 899610 TGATGCACAGG 899620 i vi ? i L1MEh_5end#LI 2222 TAAAACANAAG 2232 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.73 CpG sites = 36, Kimura (unadjusted) = 36.73 Transitions / transversions = 2.40 (36/15) Gap_init rate = 0.06 (11 / 193), avg. gap size = 2.09 (23 / 11) 391 25.17 4.23 2.07 chr1qtel1M 899469 899610 (100390) L1MEj_5end#LINE/L1 2003 2147 (13) m_b52s551i7 1881 chr1qtel1M 899469 AAATTAGGACGGAGGGAA--AAACACAGTA-AGTAATCGTAACAGTGAAT 899515 v i i i -- ivv - vi i v v i L1MEj_5end#LI 2003 AAAGTAAGATGGAAGGAATAAAATCAAGTATATCAGTCGTTACACTAAAT 2052 chr1qtel1M 899516 GTGAATGTGATGAACACTTTCAT---AAAACAGAAACAGCCATCAGAATG 899562 viv iv ii --- i i v --- v L1MEj_5end#LI 2053 GTGAATGGACTGAATTCTCCCATTAAAAGACAGAGACTG---TCAGATTG 2099 chr1qtel1M 899563 GATTAAAAAACAAAATCCTACAATATACTGCTCACAGGAAACATCCTT 899610 i i vi v i i i i iv L1MEj_5end#LI 2100 GGTTAAAAAACAAAACCCAGCTATATGCTGTTTACAAGAAACACACTT 2147 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 31.41 CpG sites = 21, Kimura (unadjusted) = 31.41 Transitions / transversions = 1.50 (21/14) Gap_init rate = 0.04 (6 / 141), avg. gap size = 1.50 (9 / 6) 589 35.31 3.03 6.25 chr1qtel1M 900124 900552 (99448) MamRTE1#LINE/RTE-BovB 336 751 (3061) m_b52s601i1 1882 chr1qtel1M 900124 TCACTGGACTGAAGCAGCAGTGGGATTCAGCAGTCTGTTGGGTGTTTGAG 900173 i i?-- i iivvi i iv?vi i MamRTE1#LINE/ 336 TCGCTGAN--GAGGCAGCAGCACCGTTCGGCAGCGNCCTGGGTGTCTGAG 383 chr1qtel1M 900174 AAGCCTTTTGGAAGGTCTGCACTGCTCACGTCCTGGCACAAGGAAGGGGC 900223 v i v vv i i? - i - -- v iii ? MamRTE1#LINE/ 384 CAGCCCTGTTTAGGANC-GCGCTGCTCAC-TCC--GAATGGGGAAGGGNC 429 chr1qtel1M 900224 TAGAAAATATGTCCTAAAAATTGTCTCCTTCA-CATAATC----CTG--- 900265 vi i vi i v i i- v ? ---- --- MamRTE1#LINE/ 430 TAGAAAAGGTGCCCTAAACGTTGCCTGCCTCGCCAAANTCAAANCTGGCT 479 chr1qtel1M 900266 -ACCTGCTTACCATGGCAGGCAGGAATCCTGTTGCTATGGTCTAAACAGA 900314 - v v i ii v v ii -- ii i? vi ii vi - ?v MamRTE1#LINE/ 480 CACCAGATTATCGCGTCTGGTGGG--TTTTANTCTTGCGGTGCAAA-ANC 526 chr1qtel1M 900315 AAAAAAAAAAATGTACAAAACTTTTTGTGAAAATGGTTCTACTGACTATT 900364 v i v iiv? ?? ----viv --------- i i MamRTE1#LINE/ 527 AAATAGAAAACTACCNANNAC----AAAGAAAA---------TAACCATT 563 chr1qtel1M 900365 G-GTACATGGAATGTGTGCACACTTAAGGGTAACATGAAATCTAGTAAGC 900413 - - ii vv v i vviv i i iv ---i i iv MamRTE1#LINE/ 564 GCGT-CATGGAACATCAGGACGCTATGCGATGACGAGAA---CAGCAGTC 609 chr1qtel1M 900414 AT---GGAAGAGGAACAGCTTTTGTTGAGAGAGAATTCAGTAGGTATCAC 900460 i --- i i i vi i i viv v i vvvi i iviv MamRTE1#LINE/ 610 GTCCAGAAAGAAGAACGGCACTCGTCGCACGTGAACTGTCCAGATACGGA 659 chr1qtel1M 900461 ATCCAAATAACGCCTCTGAGTGAAATAAGGCTGGCAAATGAAGGTCAGTT 900510 i v v vi vv v i iv i vv vi v i MamRTE1#LINE/ 660 GTCGACATCGCCGCACTGAGCGAAACCAGACTTCCTGATGAAGGACAGCT 709 chr1qtel1M 900511 TGCAGAAATCAGAGCTGGATGCAGGTCTTTCTGGAATGGCCT 900552 ii i i ivi v i ? i ivv ii iv i MamRTE1#LINE/ 710 CACGGAGACAGGTGCCGGNTACGCCTTCTTCTGGAGAGGTCT 751 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.04 CpG sites = 84, Kimura (unadjusted) = 51.74 Transitions / transversions = 1.45 (84/58) Gap_init rate = 0.07 (32 / 428), avg. gap size = 1.22 (39 / 32) 239 30.06 4.08 2.68 chr1qtel1M 901245 901391 (98609) L1PREC2_orf2#LINE/L1 3133 3281 (13) m_b52s551i8 1883 chr1qtel1M 901245 TCTGATAAAGGTCTCATTTCTCAG-ATACATAGAGAAGTGAGACAAATTT 901293 i v v - - vi ii v v i L1PREC2_orf2# 3133 TCTGACAAAGGTCTAATATC-CAGCATCTATAAGGAACTTAAACAAATTT 3181 chr1qtel1M 901294 ATGAGAATACAAGGCATTTTCTAATTGATGAATGGTCAAAAAATATCAAC 901343 ii v v viv ivvi iv i vi i v ii i v L1PREC2_orf2# 3182 ACAAGAAAAAAACAAACAACCCCATTAAAAAGTGGGCAAAGGACATGAAC 3231 chr1qtel1M 901344 AGGCAGTTTTC---AGAGAAC-TAAAT-CAGTCAATGTTAGACATGTGAA 901388 i v --- ii - v - i i ---i ii i L1PREC2_orf2# 3232 AGACACTTTTCAAAAGAAGACATACATGCGGCCAA---CAAGCATATGAA 3278 chr1qtel1M 901389 AAA 901391 L1PREC2_orf2# 3279 AAA 3281 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.52 CpG sites = 26, Kimura (unadjusted) = 39.73 Transitions / transversions = 1.53 (26/17) Gap_init rate = 0.05 (8 / 146), avg. gap size = 1.25 (10 / 8) 406 30.29 9.80 6.64 chr1qtel1M 901269 901809 (98191) L1ME3G_3end#LINE/L1 13 569 (355) m_b52s551i9 1883 chr1qtel1M 901269 ATACATAGAGAAGTGAGACAAATTTATGAGAATACAAGGCATTTTCTAAT 901318 i i v vvv iv i --v i vi-- i L1ME3G_3end#L 13 ATATATAAAGAACTCCTACAAATCAATAAGAA--AAAGACAAC--CCAAT 58 chr1qtel1M 901319 TGATGAATGGTCAAAAAATATCAACAGGCAGTTTTCAGAGAACTAAAT-C 901367 v vi v ii v i iv ii vv - L1ME3G_3end#L 59 AGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGGAAATAC 108 chr1qtel1M 901368 A----GTCAATGTTAGACATGTGAAAA-ATGCTC---------------- 901396 ---- i --- i i - ---------------- L1ME3G_3end#L 109 AAATGGCCAAT---AAACATATGAAAAGATGCTCAACCTCACTAGTAATC 155 chr1qtel1M 901397 ---------TAAATTAAA-CAACTGTGAACTAATACCTCACATCTATCAG 901436 ---------i - vi iv vi ii iv i i L1ME3G_3end#L 156 AGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCATCAG 205 chr1qtel1M 901437 ATTGATTAATATGACAAGAAAAGTAAAA---TGATTACTATCAAAAG--- 901480 i--------- - vv --- - v ? iv --- L1ME3G_3end#L 206 ATTGG---------CAA-AAATTTAAAAGNTTGAT-AATATCNAGTGTTG 244 chr1qtel1M 901481 ----GAATATGAGGAAACTGGGCCACTAATGCACTATTGGTGTATTTGTG 901526 ---- ii i i v vv v v i ii vivv i L1ME3G_3end#L 245 GCGAGGGTGTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTA 294 chr1qtel1M 901527 ATCTTATCTGACCATTCTGGAGAGCAACTTTGTACTATTCACAAAGGACT 901576 vi vi viii ? i i i v i v ii iv -- v L1ME3G_3end#L 295 AATTGGTACAGCCNTTTTGGAGGGCAATTTGGCAGTATCTATTAA--AAT 342 chr1qtel1M 901577 GTAGAACTTTGTGTACTCTTTGATTCAGCAATATAATTGCT--GTATCTG 901624 v i - vi ii i ii viv i v -- ? - L1ME3G_3end#L 343 TTAAAA-TGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCT- 390 chr1qtel1M 901625 AATCTCAAAGAGTTTTAAAAGGGCAGCTGAGGTGAAGAACCTATTTGCAT 901674 - ii ? iv ---- vvv vv v vvv i ?vi -- i i L1ME3G_3end#L 391 -ATCCTANAGAAAT----ACTCGCACATGTGCACAAGGANGCAT--GTAC 433 chr1qtel1M 901675 AAAAATACCTATAGCAGCTCTTTTTGTGAAATCCAAGACTAGAAATTGAA 901724 ii iiii v vi v -- --- - v i i L1ME3G_3end#L 434 AAGGATGTTCATTGCAGCATTGTTTGT--AAT---AG-CGAAAAATTGGA 477 chr1qtel1M 901725 AG-------GATGCCCATCAATTGGGGAATAGTTGAACAAGCTATTGTAT 901767 i-------i i v i i i ii v L1ME3G_3end#L 478 AACAACCTAAATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGTAT 527 chr1qtel1M 901768 ATAACTGTA--ATGGAATATTATTGTGCTATCAGAAATGATAAG 901809 -- ii -- i vvv ?i i i vi i L1ME3G_3end#L 528 AT--CCATACTATGGAATACTATGCAGCNGTTAAAAAGAATGAG 569 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.41 CpG sites = 90, Kimura (unadjusted) = 40.76 Transitions / transversions = 1.43 (90/63) Gap_init rate = 0.09 (49 / 540), avg. gap size = 1.84 (90 / 49) 426 33.32 4.70 4.05 chr1qtel1M 902056 902374 (97626) L1ME3Cz_3end#LINE/L1 228 548 (449) m_b52s551i10 1884 chr1qtel1M 902056 GAAAATGATAAATATTGAAGATGATGGAGAAAATTGGGA-CAGTAATTCA 902104 v ivi i i iv v vi i vi - vv v v L1ME3Cz_3end# 228 GACAATACCAAGTGTTGGCGAGGATGTGGAGAAACGGGAACTCTCATACA 277 chr1qtel1M 902105 CTGTTGGTAG-------AATTGATCCATCCATTCTGGAGAACAATTTGG- 902146 i i ------- i v v i i i - L1ME3Cz_3end# 278 CTGCTGGTGGGAGTGTAAATTGGTACAACCACTTTGGAGAGCAATTTGGC 327 chr1qtel1M 902147 ---AGCTAGGCTTAAAGTGTTTGATTATCAAACACTTTAACTCTTGGCTC 902193 --- v --- --- vv ---i i v -- i vv vi L1ME3Cz_3end# 328 AATATCTAG---TAAAGT---TGAAGAT---GCGCAT--ACCCTACGACC 366 chr1qtel1M 902194 CAACAATACCACTACTAGATCTGTATCTCAAAGACATT---GCAAAAAGG 902240 i v v i v i i ii i v i --- v viv L1ME3Cz_3end# 367 CAGCAATTCCACTTCTAGGTATATACCCTAGAGAAACTCTCGCACATGTG 416 chr1qtel1M 902241 GAAAAGGACTTATAGGCATAAAAATATTTATAATAGCTCTTTCTAGGGTA 902290 v v v-- i v i i ii i i vii vi v i ivii L1ME3Cz_3end# 417 CACAAGGAG--ACATGTACAAGGATGTTCATTGCAGCATTGTTTGTAATA 464 chr1qtel1M 902291 GTAAAGAATTGGAAATTGAAGGAATGTCCATCAATTGAGGAATGACTGAA 902340 ii i ivivvvi v i iv i L1ME3Cz_3end# 465 GCGAAAAATTGGAAACAACCTAAATGTCCATCAATAGGGGAATGGATAAA 514 chr1qtel1M 902341 CAAATTGCAATGAATAAATGTAATCAAATACTAT 902374 i iii iv vv ii vi L1ME3Cz_3end# 515 TAAATTGTGGTATATTCATACAATGGAATACTAT 548 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.59 CpG sites = 58, Kimura (unadjusted) = 45.48 Transitions / transversions = 1.32 (58/44) Gap_init rate = 0.06 (18 / 318), avg. gap size = 1.56 (28 / 18) 391 33.94 4.02 3.76 chr1qtel1M 902066 902463 (97537) L1ME4c_3end#LINE/L1 242 640 (190) m_b52s551i11 1884 chr1qtel1M 902066 AATATTGAAGATGATGGAG-AAAATTGGGACAGTAATTCACTGTTGGTAG 902114 ii iv v ? vi -i i v ?v v v i i i L1ME4c_3end#L 242 AATGCTGGCGAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGG 291 chr1qtel1M 902115 -------AATTGATCCATCCATTCTGGAGAACAATTTGGAGCTAGGCTTA 902157 ------- i v v v i i i viv v iv v L1ME4c_3end#L 292 CANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATC 341 chr1qtel1M 902158 AAGTGTTTGATTATCAAACACTTTA-ACTCTTGGCTCCAACAATACCACT 902206 v ii----- v vvv i - i v vi ii v L1ME4c_3end#L 342 AAGAGCC-----ATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACT 386 chr1qtel1M 902207 ACTAGATCTGTATCTCAAAGACAT--TGCAAAA-AGGGAAAAGGACTTAT 902253 v i ivv v ii i v -- v - i i --i L1ME4c_3end#L 387 TCTGGGAATTTATCCTAAGGAAATAATTCAAAAGAAGGAAAAAG--CTAT 434 chr1qtel1M 902254 AGGCATAAAAATATTTATAATAGCTCTTTCTAGGGTAGTAAAGAATTGGA 902303 v ii i i i vii vi v i vii ii i L1ME4c_3end#L 435 ATGCACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGA 484 chr1qtel1M 902304 AATTGAAGGAATGTCCATCAATTGAGGAATGACTGAACAAATTGCAATGA 902353 ivivvvi v v i ii i ii iiii iv L1ME4c_3end#L 485 AACAACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTAC 534 chr1qtel1M 902354 ATAAATGTAATCAAATACTATTGGTA--TATAAGAAATGATGAGCAGGAG 902401 v? ivii vi i -- i --i v i i vi v i L1ME4c_3end#L 535 ATCNACTCGATGGAATATTAT--GCAGCCATTAAAAATGATAATTATGAA 582 chr1qtel1M 902402 GATTCCAGAAAAAAAATTTAGAAAG-GCTTATGTGAAT-TAATGTAAAGT 902449 i viiv iv v --- i i- i --- - v L1ME4c_3end#L 583 GACTATGTAGCAACA---TGGAAAATGTTTATG---ATATAATGTTAAGT 626 chr1qtel1M 902450 GAAATGAGCAGAAT 902463 vi L1ME4c_3end#L 627 GAAAAAAGCAGAAT 640 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 45.32 CpG sites = 77, Kimura (unadjusted) = 47.52 Transitions / transversions = 1.45 (77/53) Gap_init rate = 0.06 (23 / 397), avg. gap size = 1.35 (31 / 23) 356 29.83 1.95 12.95 chr1qtel1M 903145 903298 (96702) C MIRc#SINE/MIR (120) 148 10 m_b52s601i2 1885 chr1qtel1M 903145 CTCACTTCACAGATGAAGCCATGGCAAAAAAGGGAGG---GGGCAGTTTA 903191 i i i i ---------- vv ---i iv v C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGG----------AAACTGAGGCTCAGAGAGGTTA 109 chr1qtel1M 903192 AGTGCCATGCCCAATATCATACAAGTAGTAAGAAGCTAAAACTGAATTGA 903241 v v vi i iv vi vi iv v i i vi C MIRc#SINE/MIR 108 AGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCG 59 chr1qtel1M 903242 AATTCCAGAAGATGAGATTTCCTGACCTTAGGTCCAGCACTCTATCCATT 903291 i- ------- vi iii i ii v i C MIRc#SINE/MIR 58 AAC-CCAG-------GTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACT 17 chr1qtel1M 903292 GCATCAC 903298 i C MIRc#SINE/MIR 16 GCACCAC 10 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.48 CpG sites = 25, Kimura (unadjusted) = 38.73 Transitions / transversions = 1.67 (25/15) Gap_init rate = 0.12 (19 / 153), avg. gap size = 1.11 (21 / 19) 12 5.00 0.00 4.55 chr1qtel1M 903309 903331 (96669) (ATGT)n#Simple_repeat 1 22 (0) m_b52s252i11 1886 chr1qtel1M 903309 ATGTATGTATTATATGTATGTAT 903331 - i (ATGT)n#Simpl 1 ATGTATGTA-TGTATGTATGTAT 22 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.05 (1 / 22), avg. gap size = 1.00 (1 / 1) 16 32.30 0.00 0.00 chr1qtel1M 903354 903414 (96586) (AGATAT)n#Simple_repeat 1 61 (0) m_b52s252i12 1887 chr1qtel1M 903354 AGAGAAAGATGAAAATATAGATATGCATATATTTATAGATCTATATGTAT 903403 v v iv i iv vv v v i v (AGATAT)n#Sim 1 AGATATAGATATAGATATAGATATAGATATAGATATAGATATAGATATAG 50 chr1qtel1M 903404 ATGTGTATATA 903414 i iv (AGATAT)n#Sim 51 ATATAGATATA 61 Matrix = Unknown Transitions / transversions = 0.60 (6/10) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 27 22.53 2.99 0.00 chr1qtel1M 903463 903529 (96471) (TC)n#Simple_repeat 1 69 (0) m_b52s252i13 1888 chr1qtel1M 903463 TCTCTCTATCTCTGTCTTTGTCTTTGTGTTTCTCTTTTTATCTCTCT-TT 903511 v v i v i v v i i i v - i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr1qtel1M 903512 TCTCTGTCTCTC-CTCTCT 903529 v - (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCT 69 Matrix = Unknown Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.03 (2 / 66), avg. gap size = 1.00 (2 / 2) 263 36.41 5.83 5.52 chr1qtel1M 903688 904030 (95970) C L2#LINE/L2 (1571) 1511 1168 m_b52s601i3 1889 chr1qtel1M 903688 CTCAATTAAA-ATGAAGCAAACTTCTCAGTGGAAAGAGTTGGCAGGA-AG 903735 i v - v iv iv iv i --- -- - C L2#LINE/L2 1511 CTCAGTGAAATAGGAAGCAAGGTCATCAGCTGAGAG---TG--AGGATAG 1467 chr1qtel1M 903736 GGGAAAAGTTTGAGGAATTAAAAGTTTT----GAAAAATCAATGTGGTGA 903781 i------ vi ii i v---- i iivv v vvi C L2#LINE/L2 1466 GGGAG------GAGGTGTTGGAGGTTTGAGGAGAGAGGAGAAGGTGTGAA 1423 chr1qtel1M 903782 ATGACTGT--AAACCAATTAGGATGTGTATAAA--AAGAACACAATACAA 903827 iiii -- iivv i vi iiv v ii -- i i --- ii i C L2#LINE/L2 1422 ATAGTCGTCTAGGAGAGTGGGAGAGTGAATGGACTAGGGA---AATGTAG 1376 chr1qtel1M 903828 TCAAAATTGTCTTTCTGCAGTAAGGGCCCTGTTGAGATTATGTAA-CGTT 903876 - ?i i vvv v v vv i ?- ii- i v C L2#LINE/L2 1375 T-ANGATTGCCGGGCAGCATTAAGGGCCCACTTGAGGTTN-GTGGTCATG 1328 chr1qtel1M 903877 AAATTGTAGTTATAT-AGTCAAGAAGGTTTCATGGTTTTCTCCAGCTTCT 903925 v iv v v i- iv v vii v iv v C L2#LINE/L2 1327 AATTTAAAGTGAGACCAGTCAGCATGGTTGTGTGTTTTTCTCCAGCCACG 1278 chr1qtel1M 903926 TTCAGCAGTGTGGAAATAAATGTAAA--AGACAGTAAGAGGTAGAAGTAA 903973 v i?i ivii iii iii -- i i -- v i vv C L2#LINE/L2 1277 TTCAGCTGCNCGGGTGCAGGCGCGGAGTAGGCGG--AGAGTTGGATTTAA 1230 chr1qtel1M 903974 CATAGAATTGATG-CATATCAGGACAATATTAT----TGACAG-GGAGCA 904017 -i ii ?v -iv ii vv i iv i----i v - i C L2#LINE/L2 1229 C-CAGGGTTGNGGTTTTGCCAGGCGAGTACGACGAAGCGAGAGAGGGGCA 1181 chr1qtel1M 904018 AGGGACTCAAGAG 904030 v ii i C L2#LINE/L2 1180 AGGGAGTTGAGGG 1168 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 48.07 CpG sites = 71, Kimura (unadjusted) = 53.35 Transitions / transversions = 1.51 (71/47) Gap_init rate = 0.09 (30 / 342), avg. gap size = 1.30 (39 / 30) 18 18.73 0.00 0.00 chr1qtel1M 904461 904492 (95508) (T)n#Simple_repeat 1 32 (0) m_b52s252i14 1890 chr1qtel1M 904461 TTTCTTTTCTTCTTCTTTTTTTTTTTTCTTTT 904492 i i i i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 32 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 352 25.12 1.01 7.53 chr1qtel1M 904494 904592 (95408) C MIR#SINE/MIR (140) 122 30 m_b52s601i4 1891 chr1qtel1M 904494 TGAGACA-ATTGTGGCTAAGTGATTTGCCCAAGATCACACAACTAGTAAT 904542 i - vv v i i i i i v C MIR#SINE/MIR 122 TGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAG 73 chr1qtel1M 904543 TGTTAAAAGTCTGAAGCCTGATTTGAACTCGGGTTTCCTGGCTTCAGAGC 904592 vi- i i v ------ i i i ivvi i C MIR#SINE/MIR 72 TGGC-AGAGCCGG------GATTCGAACCCAGGCAGTCTGGCTCCAGAGC 30 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.78 CpG sites = 15, Kimura (unadjusted) = 31.42 Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.08 (8 / 98), avg. gap size = 1.00 (8 / 8) 341 28.33 1.72 2.61 chr1qtel1M 906065 906180 (93820) C MIRc#SINE/MIR (151) 117 3 m_b52s601i5 1892 chr1qtel1M 906065 GAGAGGTTAAGGGACTTGGCCGAAGTCATACTGCCATTATGTAGCTGAGA 906114 v v i i i v i v v i v v C MIRc#SINE/MIR 117 GAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGC 68 chr1qtel1M 906115 TAGCTTCTCAAACTT-GGCCCTCCAGATTCTGAGGTTCA-TTCTCTAACC 906162 ii -vv i ii- i i v i i- i i - v vv C MIRc#SINE/MIR 67 CGG-GACTCGAACCCAGGTCTTCCTGACTCC-AAGTCCAGTGCTCTTTCC 20 chr1qtel1M 906163 ATTGTACCACAATAGCCT 906180 i i v - C MIRc#SINE/MIR 19 ACTGCACCACACT-GCCT 3 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.40 CpG sites = 18, Kimura (unadjusted) = 36.33 Transitions / transversions = 1.29 (18/14) Gap_init rate = 0.04 (5 / 115), avg. gap size = 1.00 (5 / 5) 17 26.05 0.00 0.00 chr1qtel1M 906730 906779 (93221) (CACT)n#Simple_repeat 1 50 (0) m_b52s252i15 1893 chr1qtel1M 906730 CAGTCACTCAATCATTCACTCACAGAATCACTCACTAATTAATTCATTCA 906779 v v i vv v v i v i i (CACT)n#Simpl 1 CACTCACTCACTCACTCACTCACTCACTCACTCACTCACTCACTCACTCA 50 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 213 31.30 7.14 1.12 chr1qtel1M 906818 906901 (93099) C L3#LINE/CR1 (10) 4089 4001 m_b52s601i6 1894 chr1qtel1M 906818 CAGAGTTTGAAATTTTGAAGTCAACCCAGAAGTCATCTAATCTAACATTC 906867 i i v i v v vv v ii i i i -i C L3#LINE/CR1 4089 CAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCAAC-CTC 4041 chr1qtel1M 906868 TCA--CA----AGGAATCCCCACCATAATATTTCCTATAA 906901 i -- ---- iv i i i ii iv i C L3#LINE/CR1 4040 CCATCCAATGCAGGAATCCCTTCTACAACATCCCTGACAA 4001 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.12 CpG sites = 18, Kimura (unadjusted) = 43.12 Transitions / transversions = 2.25 (18/8) Gap_init rate = 0.04 (3 / 83), avg. gap size = 2.33 (7 / 3) 20 14.08 1.89 5.88 chr1qtel1M 906920 906972 (93028) (AATA)n#Simple_repeat 1 51 (0) m_b52s252i16 1895 chr1qtel1M 906920 AAGAAATAAATAAAGAAATCCTCTAAAATTAA-AAATAAATAAATAAATG 906968 v v -vvv - v - - (AATA)n#Simpl 1 AATAAATAAATAAATAAAT-AAAT-AAATAAATAAATAAATAAATAAAT- 47 chr1qtel1M 906969 AAAT 906972 (AATA)n#Simpl 48 AAAT 51 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.08 (4 / 52), avg. gap size = 1.00 (4 / 4) 49 0.00 2.22 0.00 chr1qtel1M 907563 907607 (92393) (GT)n#Simple_repeat 1 46 (0) c_b52s251i1 1896 chr1qtel1M 907563 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT-TGTGTGTGTGTGT 907607 - (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 46 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 24 19.82 1.16 7.41 chr1qtel1M 907769 907854 (92146) (AGAC)n#Simple_repeat 1 81 (0) m_b52s252i17 1897 chr1qtel1M 907769 AGACAGACAGACAGACAGAGCTGTAAATACAGACACAGATGAGGAGACAG 907818 - v - v v v v - -v - (AGAC)n#Simpl 1 AGACAGACAGACAGACAGA-CAG-ACAGACAGACAGACA-GA-CAGACA- 45 chr1qtel1M 907819 GAAAATACA-AAAGACAAACAGGGAGACAAACAGACA 907854 - v v - v i iv i (AGAC)n#Simpl 46 G-ACAGACAGACAGACAGACAGACAGACAGACAGACA 81 Matrix = Unknown Transitions / transversions = 0.30 (3/10) Gap_init rate = 0.08 (7 / 85), avg. gap size = 1.00 (7 / 7) 541 32.70 5.73 3.00 chr1qtel1M 909097 909323 (90677) C MIRc#SINE/MIR (2) 266 34 m_b52s601i7 1898 chr1qtel1M 909097 TAATAATACAATCAAGTATTTTTGTAATGCCTTAAAGTTTGTAAAGCATT 909146 vv?i vvii v i iii i v ii ii C MIRc#SINE/MIR 266 TAATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCGCT 217 chr1qtel1M 909147 TT-ACATTTATTATCAAATTTTATTCTCACAACTCTTTTGTGAAATAGG- 909194 - vi vv v i vviii ii - C MIRc#SINE/MIR 216 TTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGC 167 chr1qtel1M 909195 --------TACTATTGTCTCCATTTTA---ATGAAGAAACAGCCAAATAG 909233 -------- i i i --- i v v-----i C MIRc#SINE/MIR 166 AGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGA-----GG 122 chr1qtel1M 909234 TCCAGAGAAAGATCCAATGTTTTCACTAGGATCTCACAATAAAAATGTAA 909283 ii -- i iv i vi vv i i i v iiv iv v ii C MIRc#SINE/MIR 121 CTCAGAGA--GGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGG 74 chr1qtel1M 909284 CTGAGGAAAGATTCAAATTCAGGTCTTCCTGATTCTAAAT 909323 v vvii i i ii i i i C MIRc#SINE/MIR 73 CAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGT 34 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.04 CpG sites = 47, Kimura (unadjusted) = 45.67 Transitions / transversions = 1.88 (47/25) Gap_init rate = 0.05 (11 / 226), avg. gap size = 1.82 (20 / 11) 282 29.21 5.62 0.00 chr1qtel1M 909835 909923 (90077) C MIRc#SINE/MIR (120) 148 55 m_b52s601i8 1899 chr1qtel1M 909835 CTTATTTTAGAAATGA---AACCGAGG-TAAACAAGATTAAGTGTCTTGT 909880 ii v i --- i - v ivi i v i C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr1qtel1M 909881 CCATGGTTACCCAGTTAATGA-TGCCAGATTCAGGTCTGGCATC 909923 v i v i i i - v vi i v v v i C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACC 55 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.13 CpG sites = 15, Kimura (unadjusted) = 37.97 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.03 (3 / 88), avg. gap size = 1.67 (5 / 3) 364 35.34 2.62 3.70 chr1qtel1M 909940 910130 (89870) MIRb#SINE/MIR 43 231 (37) m_b52s601i9 1900 chr1qtel1M 909940 AGTCAGCAATACCTTATTTTAAAATCCTATTTCACAGACACTGAT--GCT 909987 vv v viv ii vi vii iii --- v i-- MIRb#SINE/MIR 43 AGTCAGACAGACCTGGGTTCGAATCCCGGCTCTGC---CACTTACTAGCT 89 chr1qtel1M 909988 GTG--ATCATAAACAAGTCTGAGTCAACGTTTGTCTGCCTCAGTTTCCTC 910035 -- i v iii i-- v i v i v vv MIRb#SINE/MIR 90 GTGTGACCTTGGGCAAGTT--ACTTAACCTCTCTGAGCCTCAGTTTCCTC 137 chr1qtel1M 910036 TACTGGAAAATCAAGAAAAAATAGCATGTGGCCCTCACAATTGTT-TGAG 910084 vv v --i ii v ii iv iv i v vii - MIRb#SINE/MIR 138 ATCTGTAAAAT--GGGGATAATAATACCTACCTCGCAGGGTTGTTGTGAG 185 chr1qtel1M 910085 AATCGAATAATATAATACTTGTAAAGTCTTCAACAAAATTCCTGAC 910130 i ii i v i v ivi i i v i v i MIRb#SINE/MIR 186 GATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGC 231 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 47.42 CpG sites = 38, Kimura (unadjusted) = 49.71 Transitions / transversions = 1.41 (38/27) Gap_init rate = 0.05 (10 / 190), avg. gap size = 1.20 (12 / 10) 370 30.00 2.78 2.78 chr1qtel1M 909987 910130 (89870) MIR#SINE/MIR 84 227 (35) m_b52s601i10 1900 chr1qtel1M 909987 TGTGATCATAAACAAGTCTGAGTCAACGTTTGTCTGCCTCAGTTTCCTCT 910036 i v iii i-- v i v i v v v MIR#SINE/MIR 84 TGTGACCTTGGGCAAGTT--ACTTAACCTCTCTGTGCCTCAGTTTCCTCA 131 chr1qtel1M 910037 ACTGGAAAATCAAGA-AAAAATAGCATGTGGCCCTCACA--ATTGTT-TG 910082 v v vii - v i iv i-- i --i - MIR#SINE/MIR 132 TCTGTAAAATGGGGATAATAATAGTACCTA--CCTCATAGGGTTGTTGTG 179 chr1qtel1M 910083 AGAATCGAATAATATAATACTTGTAAAGTCTTCAACAAAATTCCTGAC 910130 i ii i vv v ivi i iv v i v i MIR#SINE/MIR 180 AGGATTAAATGAGTTAATACATGTAAAGCGCTTAGAACAGTGCCTGGC 227 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.11 CpG sites = 24, Kimura (unadjusted) = 39.31 Transitions / transversions = 1.33 (24/18) Gap_init rate = 0.05 (7 / 143), avg. gap size = 1.14 (8 / 7) 225 25.32 2.47 2.47 chr1qtel1M 910411 910491 (89509) MIR#SINE/MIR 173 253 (9) m_b52s601i12 1901 chr1qtel1M 910411 TGTTGGGAA-ATCAAACTAATATAATA-ATGGTAAAGTGCTTAACACAAG 910458 v i- i iv i - - - i iv iv MIR#SINE/MIR 173 TGTTGTGAGGATTAAATGAGT-TAATACATG-TAAAGCGCTTAGAACAGT 220 chr1qtel1M 910459 GACTAGCATATACTAAGCACTACATTATTGTTA 910491 v i i v i vv v v MIR#SINE/MIR 221 GCCTGGCACATAGTAAGCGCTCAATAAATGTTA 253 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 27.63 CpG sites = 10, Kimura (unadjusted) = 31.18 Transitions / transversions = 1.00 (10/10) Gap_init rate = 0.05 (4 / 80), avg. gap size = 1.00 (4 / 4) 237 22.39 2.90 2.90 chr1qtel1M 910411 910479 (89521) MIRb#SINE/MIR 177 245 (23) m_b52s601i11 1901 chr1qtel1M 910411 TGTTGGGAA-ATCAAACTAATATAATA-ATGGTAAAGTGCTTAACACAAG 910458 v i- i - i v i- - i i iv MIRb#SINE/MIR 177 TGTTGTGAGGATTAAA-TGAGATAATGCATG-TAAAGCGCTTAGCACAGT 224 chr1qtel1M 910459 GACTAGCATATACTAAGCACT 910479 v i i v i MIRb#SINE/MIR 225 GCCTGGCACATAGTAAGCGCT 245 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 23.28 CpG sites = 10, Kimura (unadjusted) = 27.39 Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.06 (4 / 68), avg. gap size = 1.00 (4 / 4) 251 31.12 7.61 2.84 chr1qtel1M 910900 911438 (88562) L1M2_orf2#LINE/L1 568 1131 (2160) m_b52s551i12 1902 chr1qtel1M 910900 GAATATACTATTTTTTTCATCAGGACATGC--CATTT----GGACAAAAA 910943 i - i i v v-- i---- i i -- L1M2_orf2#LIN 568 GAATACAC-ATTCTTCTCATCAGCACATGGAACATTCTCCAGGATAGA-- 614 chr1qtel1M 910944 GTAACAACATATTAGGACACAAAA-ACTTCACAATAAAATGCAGAAAATC 910992 ---- v i i v - vv v i v v? i L1M2_orf2#LIN 615 ----CCATATGTTAGGCCACAAAACAAGTCTCAACAAATTTNAAAAAATC 660 chr1qtel1M 910993 ATAA--GTAGTAAATGCATCTTTATCAGATAATAATGTATGTAAGGGCCA 911040 iv --i vi i -- - ? iv i v -i ii- i L1M2_orf2#LIN 661 GAAATCATATCAAGT--ATCTTT-TCNGACCACAATGGA-ATAAAA-CTA 705 chr1qtel1M 911041 TGAAA--AATAA--------ACC---AAAAATTAAC-------TGGAAAC 911070 - -- -------- i---i v ?v ------- i L1M2_orf2#LIN 706 -GAAATCAATAACAAGAGGAACTTTGGAAACTNTACAAATACATGGAAAT 754 chr1qtel1M 911071 TAAATAATCTAATCTAAAAGAATGAATGTGTCAAATAATAAATCATAGAA 911120 i iv iv ivi vi iv v vv v i - L1M2_orf2#LIN 755 TAAACAACATGCTCCTGAACGACCAATGGGTCAATGAAGAAATTA-AGAA 803 chr1qtel1M 911121 AGAA-TCAATAAATTCATCCAGGAGAATGAAATTATTAAGACAACATATC 911169 i - i? v iv iv iivi v ivv v i L1M2_orf2#LIN 804 GGAAATTNAAAAATTTCTTGAAACAAATGAAAATGGAAACACAACATACC 853 chr1qtel1M 911170 AAAATCTATGAGATGTAGCCAAAAAAGTTTTTAGGGAAAATTTTATATCT 911219 i i ii v iv ?i v i ii v v v L1M2_orf2#LIN 854 AAAACCTATGGGATACAGCAAAAGCAGTNCTAAGAGGGAAGTTTATAGCA 903 chr1qtel1M 911220 TTAGATGCTTATGTGAATAAAACAGGAAAAGAGAAGATCAATAAATTGTG 911269 v i i i ii v v ii i i vvvv i v i vi ivv L1M2_orf2#LIN 904 ATAAACGCCTACATCAAAAAAGTAGAAAGATTTCAAATAAACAACCTAAC 953 chr1qtel1M 911270 CATGCAACTAAAAAAACTAGAAAA--AAGAAT---TGAAACCTCCAATTA 911314 v v v ii -- i---iv ivv - L1M2_orf2#LIN 954 GATGCACCTCAAGGAACTAGAAAAGCAAGAACAAACCAAACCCAAAATT- 1002 chr1qtel1M 911315 AATACCAAATTAGAAATTCTGAAAATCAAAGGAGAGATTAATAAAATTAA 911364 i vv iivv vv i i i v i v i vi L1M2_orf2#LIN 1003 AGTAGAAGGAAAGAAATAATAAAGATCAGAGCAGAAATAAATGAAATAGA 1052 chr1qtel1M 911365 AAATAAGAAAACTATTGA----ACTTATAAAACT--GAGTTGGTTTTATG 911408 i v i v vv ---- iiv ii v--i v L1M2_orf2#LIN 1053 GACTAAAAAAACAATACAAAAGATCAACGAAACGAAAAGTTGGTTTTTTG 1102 chr1qtel1M 911409 AAAAAAACCAATAAAACAAATAAACTTTTA 911438 - i iv i ivi i i? L1M2_orf2#LIN 1103 -AAAAGATAAACAAAATCGACAAACCNTTA 1131 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.19 CpG sites = 90, Kimura (unadjusted) = 41.90 Transitions / transversions = 1.23 (90/73) Gap_init rate = 0.05 (29 / 538), avg. gap size = 1.97 (57 / 29) 470 32.70 3.73 1.30 chr1qtel1M 911064 911438 (88562) L1M4_orf2#LINE/L1 748 1131 (2163) m_b52s551i13 1902 chr1qtel1M 911064 TGGAAACTAAATAATCTAATCTAAAAGAATGAATGTGTCAAATAATAAAT 911113 i i ivi v iv v iv v v v L1M4_orf2#LIN 748 TGGAAATTAAACAACACACTCCTAAATAACCAATGGGTCAAAGAAGAAAT 797 chr1qtel1M 911114 CATAGAAAGAATCAATAAATTCATCCAGGAGAATGAAATTATTAAGACAA 911163 i iiiii i iv v v iv iv viivv v L1M4_orf2#LIN 798 CACAAGGGAAATTAGAAAATACTTTGAGATGAATGAAAACGAAAACACAA 847 chr1qtel1M 911164 CATATCAAAATCTATGAGATGTAGCCAAAAAAGTTTTTAGGGAAAATTTT 911213 i ii i i ? iv vi i ii v L1M4_orf2#LIN 848 CATACCAAAACTTATGGGATGCAGCNAAAGCAGTGCTTAGAGGGAAATTT 897 chr1qtel1M 911214 ATATCTTTAGATGCTTATGTGAATAAAACAGGAAAAGAGA----AGATCA 911259 v v i i i --- - i i i ---- i L1M4_orf2#LIN 898 ATAGCTGTAAATGCCTATAT---TAAAA-AAGAAGAAAGATCTCAAATCA 943 chr1qtel1M 911260 ATAAATTGTGCATGCAACTAAAAAAACTAGAAAAAAGAATTGAAAC---- 911305 vi ivv v v v v i ii ivvv ---- L1M4_orf2#LIN 944 ATAACCTAACCTTCCACCTTAAGAAACTAGAAAAAGAAGAGCAAACTAAA 993 chr1qtel1M 911306 CTCCAATTAAATACCAAATTAGAAATTCTGAAAATCAAAGGAGAGATTAA 911355 i v vi ii vv iivvi vv i i i i vi i v L1M4_orf2#LIN 994 CCCAAAGCAAGCAGAAGGAAGGAAATAATAAAGATTAGAGCGGAAATAAA 1043 chr1qtel1M 911356 TAAAATTAAAAATAAGAAAACTATTG----AACTTATAAAACT--GAGTT 911399 i vi i ii v v ---- iiv ii i--i L1M4_orf2#LIN 1044 TGAAATAGAGAATAGAAAAACAATAGAGAAAATCAACGAAACCAAAAGTT 1093 chr1qtel1M 911400 GGTTTTATGAAAAAAACCAATAAAACAAATAAACTTTTA 911438 i v - i i i ivi i i L1M4_orf2#LIN 1094 GGTTCTTTG-AAAAGATCAACAAAATTGACAAACCTTTA 1131 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.20 CpG sites = 73, Kimura (unadjusted) = 44.83 Transitions / transversions = 1.52 (73/48) Gap_init rate = 0.02 (9 / 374), avg. gap size = 2.11 (19 / 9) 13 22.06 3.57 3.57 chr1qtel1M 912618 912673 (87327) (AAACAAT)n#Simple_repeat 1 56 (0) m_b52s252i18 1903 chr1qtel1M 912618 AAACAAGTAAAGATTAAGCAATAAGGCAA-AAA-AAAAAAAAAAAAAAAA 912665 - v v i -i - - v v v v (AAACAAT)n#Si 1 AAACAA-TAAACAATAAACAATAA-ACAATAAACAATAAACAATAAACAA 48 chr1qtel1M 912666 TGAAAAAT 912673 i v (AAACAAT)n#Si 49 TAAACAAT 56 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.07 (4 / 55), avg. gap size = 1.00 (4 / 4) 21 7.52 0.00 0.00 chr1qtel1M 912645 912672 (87328) (A)n#Simple_repeat 1 28 (0) m_b52s252i19 1904 chr1qtel1M 912645 AAAAAAAAAAAAAAAAAAAAATGAAAAA 912672 vi (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA 28 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 36 22.91 3.88 0.00 chr1qtel1M 914640 914742 (85258) (ATAT)n#Simple_repeat 1 107 (0) m_b52s252i20 1905 chr1qtel1M 914640 ATATAGAAATATATTTATTTATATTTA-AAATATATTTATTTATATA-AT 914687 v v v v v - v v v - (ATAT)n#Simpl 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr1qtel1M 914688 ACTTAAATTTATATA-ATATTTA-AAATATATTTATTTATATAAATAAAA 914735 iv v v - v - v v v v v v (ATAT)n#Simpl 51 ATATATATATATATATATATATATATATATATATATATATATATATATAT 100 chr1qtel1M 914736 ATATTTA 914742 v (ATAT)n#Simpl 101 ATATATA 107 Matrix = Unknown Transitions / transversions = 0.05 (1/19) Gap_init rate = 0.04 (4 / 102), avg. gap size = 1.00 (4 / 4) 415 24.38 2.54 6.14 chr1qtel1M 914948 915065 (84935) C MIR#SINE/MIR (105) 157 44 m_b52s601i13 1906 chr1qtel1M 914948 TGCTATTTCATTCTCTAGCTCATTTCACAGGTAAGAAAACTGAGGCAAAC 914997 i -- v --- i i i i i v v C MIR#SINE/MIR 157 TACTATT--ATTATC---CCCATTTTACAGATGAGGAAACTGAGGCACAG 113 chr1qtel1M 914998 AAGAGTTA--TGACTTGCTCAGGGTCATACAGCTACTAAGTATCTGAAGG 915045 iii -- i i i i v iv v -- C MIR#SINE/MIR 112 AGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGA--G 65 chr1qtel1M 915046 CC-AAATTTAAACTCGGGAAG 915065 -ii ii i i v C MIR#SINE/MIR 64 CCGGGATTCGAACCCAGGCAG 44 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.36 CpG sites = 20, Kimura (unadjusted) = 30.90 Transitions / transversions = 2.86 (20/7) Gap_init rate = 0.08 (9 / 117), avg. gap size = 1.11 (10 / 9) 340 21.25 4.23 13.85 chr1qtel1M 914955 915096 (84904) C MIR1_Amn#SINE/MIR (72) 158 29 m_b52s601i14 1906 chr1qtel1M 914955 TCATTCTCTAGCTCATTTCACAGGTAAGAAAACTGAGGCAAACAAGAGTT 915004 v --- i i i i i ?v v iii ? C MIR1_Amn#SINE 158 TCATTATC---CCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTN 112 chr1qtel1M 915005 A--TGACTTGCTCAGGGTCATACAGCTACTAAGTATCTGAAGGCCAAATT 915052 -- i i i? ?ivi? ------- ------ C MIR1_Amn#SINE 111 AAGTGACTTGCCCAAGGTCACNCAGCNGGCNAGT-------GGC------ 75 chr1qtel1M 915053 TAAACTCGGGAAGAGAACTCGAGGT---CCAACCCCCA-TCCATTGCT 915096 - i vi ?v? i - --- i vi - v C MIR1_Amn#SINE 74 -AGAGCCGGGANTNGAACCC-AGGTCTCCCGAGTCCCAGTCCAGTGCT 29 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.04 CpG sites = 18, Kimura (unadjusted) = 27.26 Transitions / transversions = 2.25 (18/8) Gap_init rate = 0.15 (21 / 141), avg. gap size = 1.14 (24 / 21) 382 24.14 12.43 4.40 chr1qtel1M 915109 915277 (84723) C LSU-rRNA_Hsa#rRNA (1236) 3799 3618 m_b52s551i14 1907 chr1qtel1M 915109 CCATTCATGGGTATCA---ATTAGATGATGGCATAAGGCATTT---CACC 915152 v ii --- i ----- ---i C LSU-rRNA_Hsa# 3799 CCATTCATGCGCGTCACTAATTAGATGACG-----AGGCATTTGGCTACC 3755 chr1qtel1M 915153 ATAAATGAATCA--GCTAATGCTGCTGTTTACATGTTCTTGGGCAAATTT 915200 v iv i -- i v v i i vi iv vivii C LSU-rRNA_Hsa# 3754 TTAAGAGAGTCATAGTTACTCCCGCCGTTTACCCGCGCTTCATTGAATTT 3705 chr1qtel1M 915201 CTCCACTTTGACATTC------CTA---AGAATTCACATC-TATCAACAG 915240 i ------ i--- v -ii - C LSU-rRNA_Hsa# 3704 CTTCACTTTGACATTCAGAGCACTGGGCAGAAATCACATCGCGTCAACA- 3656 chr1qtel1M 915241 TACCATGGATGGATCTTTGTGGTGCTTTA---TAATTAAA 915277 -v iiv -i ii i i i i--- ? C LSU-rRNA_Hsa# 3655 -CCCGCCG-CGGGCCTTCGCGATGCTTTGTTTTNATTAAA 3618 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 20.92 CpG sites = 27, Kimura (unadjusted) = 30.66 Transitions / transversions = 2.25 (27/12) Gap_init rate = 0.09 (15 / 168), avg. gap size = 1.93 (29 / 15) 361 27.88 17.31 0.00 chr1qtel1M 915492 915595 (84405) L2a_3end#LINE/L2 373 494 (23) m_b52s601i15 1908 chr1qtel1M 915492 TTTGTTTCCTAATTTCTCCTAGTAGACTGTGAGCTCCTTGAAAGCAAGGA 915541 i vi ivi i i i v v i v ii i L2a_3end#LINE 373 TTTATTGTCTGTCTCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGA 422 chr1qtel1M 915542 CTTTT------------------TGTATCTCCACTGCTTAGCTCAGTGCC 915573 ------------------ i vi i vv L2a_3end#LINE 423 CTTTTGTCTGTTTTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCC 472 chr1qtel1M 915574 TGGCATATAATAAATACTTAAT 915595 i i iiii i L2a_3end#LINE 473 TGGCACATAGTAGGCGCTCAAT 494 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.55 CpG sites = 21, Kimura (unadjusted) = 36.95 Transitions / transversions = 2.62 (21/8) Gap_init rate = 0.01 (1 / 103), avg. gap size = 18.00 (18 / 1) 369 25.00 19.44 0.00 chr1qtel1M 915504 915611 (84389) L2b_3end#LINE/L2 335 463 (3) m_b52s601i16 1908 chr1qtel1M 915504 TTTCTCCTAGTAGACTGTGAGCTCCTTGAAAGCAAGGAC--------TTT 915545 i i i v v ii i -------- i L2b_3end#LINE 335 TCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCT 384 chr1qtel1M 915546 T---------TGTATCTCCACTGCTTAGCTCAGTGCCTGGCATATAATAA 915586 --------- i vi i v ? i i i i L2b_3end#LINE 385 TGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAG 434 chr1qtel1M 915587 ATACTT----AATGTTTTTTGGCTGTATG 915611 iii i---- i v iv v L2b_3end#LINE 435 GCGCTCAGTAAATATTTGTTGAATGAATG 463 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.36 CpG sites = 20, Kimura (unadjusted) = 32.43 Transitions / transversions = 2.86 (20/7) Gap_init rate = 0.03 (3 / 107), avg. gap size = 7.00 (21 / 3) 222 26.92 5.13 0.00 chr1qtel1M 915614 915691 (84309) C L2#LINE/L2 (329) 2753 2672 m_b52s601i17 1909 chr1qtel1M 915614 GGATGGAGGGAAA----TTAGGAGGCTGTTGAAGTAATTTAGGTGGGAGG 915659 v v i ---- i v ii i i i C L2#LINE/L2 2753 GGAAGCAGGGAGACCAGTTAGGAGGCTATTGCAGTAATCCAGGCGAGAGA 2704 chr1qtel1M 915660 TGATGAGTGTCTGAAACAAAGTGGTAGCTGTG 915691 ivv ii i v ii i v C L2#LINE/L2 2703 TGATGGTGGCTTGGACCAGGGTGGTGGCAGTG 2672 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.67 CpG sites = 14, Kimura (unadjusted) = 34.72 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.01 (1 / 77), avg. gap size = 4.00 (4 / 1) 20 23.85 0.00 0.00 chr1qtel1M 915748 915792 (84208) (TA)n#Simple_repeat 1 45 (0) m_b52s252i21 1910 chr1qtel1M 915748 TATATACACACATTTATATATACACACATATATAAAAATATATAT 915792 i i i v i i i v v (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATAT 45 Matrix = Unknown Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 215 24.13 3.33 3.33 chr1qtel1M 917285 917344 (82656) MIRb#SINE/MIR 161 220 (48) m_b52s601i18 1911 chr1qtel1M 917285 ATCTATTTTCATAGGATTGTTATAAGGATAAAGTGAGATGATG--TGTAA 917332 i ii - ii i i i v i i -- MIRb#SINE/MIR 161 ACCTACCT-CGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAA 209 chr1qtel1M 917333 AGGCACTTTACA 917344 - i vi MIRb#SINE/MIR 210 A-GCGCTTAGCA 220 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.19 CpG sites = 12, Kimura (unadjusted) = 31.52 Transitions / transversions = 6.00 (12/2) Gap_init rate = 0.05 (3 / 59), avg. gap size = 1.33 (4 / 3) 306 23.61 5.56 0.00 chr1qtel1M 917293 917364 (82636) MIRc#SINE/MIR 174 249 (19) m_b52s601i19 1911 chr1qtel1M 917293 TCATAGGATTGTTATAAGGATAAAGTGAGATGATG--TGTAAAGGCACTT 917340 i i i i v i i -- i i i MIRc#SINE/MIR 174 TCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTT 223 chr1qtel1M 917341 TACAACCTTCAAA--GCTACATAAAT 917364 ii v vi -- i i MIRc#SINE/MIR 224 TGTAAACTGTAAAGTGCTATACAAAT 249 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.18 CpG sites = 14, Kimura (unadjusted) = 30.33 Transitions / transversions = 4.67 (14/3) Gap_init rate = 0.03 (2 / 71), avg. gap size = 2.00 (4 / 2) 17 15.60 0.00 0.00 chr1qtel1M 917599 917627 (82373) (T)n#Simple_repeat 1 29 (0) m_b52s252i22 1912 chr1qtel1M 917599 TTTTTTTTTTTTTTTCTTTCTCATTTTTT 917627 i i iv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 636 24.99 4.66 0.50 chr1qtel1M 917980 918172 (81828) MIRc#SINE/MIR 65 265 (3) m_b52s601i20 1913 chr1qtel1M 917980 CCAGCTTTCAAATTTA-TAACATGTGTGATCCTGGGCAAATCAATTAACC 918028 i i vvv i - i - i i i v MIRc#SINE/MIR 65 CCGGCTCTGCCACTTACTAGC-TGTGTGACCTTGGGCAAGTCACTTAACC 113 chr1qtel1M 918029 TCTGTCTGCCTCAGTCTCCTCACCTATTAAATGAGGACCATAATAAC-AC 918077 v vv i i i v i iv v -i MIRc#SINE/MIR 114 TCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGC 163 chr1qtel1M 918078 CTT--CCATC---CAGGTTGGTTGTGAGGATAAAATGACAAAATGCTTGT 918122 i -- i i --- v v v v v iv MIRc#SINE/MIR 164 CCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGT 213 chr1qtel1M 918123 -AAAACATTTTGTAAAC-ATTAATTCAAATCTAAATGTTAATTATTATTA 918170 - i ii -i v v vvv vi v iv?i MIRc#SINE/MIR 214 GAAAGCGCTTTGTAAACTGTAAAGTGCTATACAAATGTAAGGNGTTATTA 263 chr1qtel1M 918171 TT 918172 MIRc#SINE/MIR 264 TT 265 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.40 CpG sites = 24, Kimura (unadjusted) = 30.89 Transitions / transversions = 1.00 (24/24) Gap_init rate = 0.04 (7 / 192), avg. gap size = 1.43 (10 / 7) 304 32.73 9.09 0.00 chr1qtel1M 920372 920481 (79519) L3#LINE/CR1 3977 4096 (3) m_b52s601i21 1914 chr1qtel1M 920372 TTTAATGAGGAGCTGCAAGATCATCTATTAGGAATAACATAAAGAGGAT- 920420 i vv ii v v i ii i i i ivii i ii - L3#LINE/CR1 3977 TTCAAGCAGAGGCTGGATGACCACTTGTCAGGGATGTTGTAGAAGGGATT 4026 chr1qtel1M 920421 CCAGCATTGAGTCAGAGGCTGGACTCAACTACTCCTCAGTTTCC-----A 920465 v ii vi i vi iv ii v v i ----- L3#LINE/CR1 4027 CCTGCATTGGATGGGAGGTTGGACTAGATGACCTCTAAGGTCCCTTCCAA 4076 chr1qtel1M 920466 C----AGATTCTATGATTCT 920481 ---- i L3#LINE/CR1 4077 CTCTGAGATTCTGTGATTCT 4096 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 46.01 CpG sites = 25, Kimura (unadjusted) = 46.01 Transitions / transversions = 2.27 (25/11) Gap_init rate = 0.03 (3 / 109), avg. gap size = 3.33 (10 / 3) 596 21.76 12.82 2.33 chr1qtel1M 923149 923421 (76579) Charlie1a#DNA/hAT-Charlie 1044 1344 (111) m_b52s502i0 1915 chr1qtel1M 923149 TTTTCCAACTACCTATCTGCATGTGGCTGCCTCTTCTTCATG---CTCGC 923195 v ii v i vv i i---i iv Charlie1a#DNA 1044 TTTTCCAACTACATATCTGTGTGAGGCCGGATTTTCTTCATATACTTCAA 1093 chr1qtel1M 923196 CCAAAAGAGCAGA---CGGCAGAGTGAATGCAGAAGCAG--GTGCTTCTC 923240 v i v --- ii v --i vvvv Charlie1a#DNA 1094 CCAAAACAACATATCGCAACAGATTGAATGCAGAAGCAGATATGAGAATC 1143 chr1qtel1M 923241 CAGCTGCTCTCCATTAACTGAGACAGGAAGGAG--TTGCAAAAACAATGT 923288 iii i viv vv i -- --- Charlie1a#DNA 1144 CAGCTGTCTTCTATTAAGCCAGACATTAAAGAGATTTGCAAA---AATGT 1190 chr1qtel1M 923289 ATAACGATA--------CTCACCCAATGTATTTGTTGGTGGAAA--ATAG 923328 v i i-------- iv v v -v -- Charlie1a#DNA 1191 AAAACAATGCCACTCTTCTCACTAAATTTTTTTGTT-TTGGAAAATATAG 1239 chr1qtel1M 923329 TTA-TTTTGGT--AAATATAATATTTTTGTTGCCATGTAATCATAGGTTT 923375 - vi -- iv v iv --- i Charlie1a#DNA 1240 TTATTTTTCATAAAAATATGTTATTTATGTTAACATGTA---ATGGGTTT 1286 chr1qtel1M 923376 CTTGTTA-TTTTAAAGAAGTT----ACTATTTTACAA-------GGTTTT 923413 v i - vi i ---- v v -------i Charlie1a#DNA 1287 ATTATTATTTTTAAATGAATTAATAAATATTTTAAAAATTTCTCAGTTTT 1336 chr1qtel1M 923414 ACTTTCTA 923421 v Charlie1a#DNA 1337 AATTTCTA 1344 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 25.42 CpG sites = 28, Kimura (unadjusted) = 25.92 Transitions / transversions = 0.93 (28/30) Gap_init rate = 0.07 (18 / 272), avg. gap size = 2.33 (42 / 18) 448 22.73 5.45 0.00 chr1qtel1M 923427 923536 (76464) MIRc#SINE/MIR 33 148 (120) m_b52s601i22 1916 chr1qtel1M 923427 GGCCTGGAATCAGGAAGACCCGAGTTCAAATCCAGGCTCAAACCCTTCTT 923476 i i i i i i i v viv v vi MIRc#SINE/MIR 33 GACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACT 82 chr1qtel1M 923477 GGCTATGTCCCCCTGGGCAAG-----GAACC-CCGTGTGCCTCAGTTTCC 923520 i i vv i -----v - iv v MIRc#SINE/MIR 83 AGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCC 132 chr1qtel1M 923521 TCATCTGTAAAGTGAG 923536 i i MIRc#SINE/MIR 133 TCATCTGTAAAATGGG 148 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.35 CpG sites = 15, Kimura (unadjusted) = 27.62 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.02 (2 / 109), avg. gap size = 3.00 (6 / 2) 16 9.78 0.00 0.00 chr1qtel1M 923775 923796 (76204) (C)n#Simple_repeat 1 22 (0) m_b52s252i23 1917 chr1qtel1M 923775 CCCCCCCCCCCCCCACCCCGCC 923796 v v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCC 22 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 21 10.15 2.17 4.44 chr1qtel1M 924216 924261 (75739) (AAGCGG)n#Simple_repeat 1 45 (0) m_b52s252i24 1918 chr1qtel1M 924216 AAGCGGAAGCGGAAGGGGAGGAGCGGAAGCGGAAGTGG-CGGGGAAG 924261 v -- i -v v (AAGCGG)n#Sim 1 AAGCGGAAGCGGAAGCGGA--AGCGGAAGCGGAAGCGGAAGCGGAAG 45 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.07 (3 / 45), avg. gap size = 1.00 (3 / 3) 463 36.59 7.20 2.16 chr1qtel1M 925225 925710 (74290) L2#LINE/L2 437 946 (2136) m_b53s601i0 1919 chr1qtel1M 925225 TTTCATTC-CCTTCTTAGAGTCACTAAGATGCTAGTGC-CTTCTGCTGAC 925272 i v - ivvv v ?i i i- i iv - ii vv L2#LINE/L2 437 TTCCCTTCACCTTCTTGCTCTAACNGAAAC-CTGGCTCTCCCCTGAGGAC 485 chr1qtel1M 925273 ACCTCTTTCCTGGTTCCCCTTTTCAG----AGCTATACTTTCTCTTAT-T 925317 iv i iv ivv i iv ----i i vi i ii i-? L2#LINE/L2 486 ACTGCTTCCCCTGCAGCCCTCTCAAGTGGTGGCTGTTTTCTCTCCCACAN 535 chr1qtel1M 925318 TTCT-GAACTCACTAA---TGAAGGTGGGGGGATTGAAATAGTTCTTGTT 925363 ii - v - ii--- i viiv --- vv i i L2#LINE/L2 536 CCCTCGTAC-CACTGGGCCTGGAGGTGGGGTAGGTG---TCCTCCTTGCT 581 chr1qtel1M 925364 CCTCATTACCACTTCTAGGC---TCTCCTTTGCCTCTATCACTTGGTAAC 925410 i i i i --- i i- i- v viivv L2#LINE/L2 582 CCTCATTGCCGCTTCCAGACCATTCTCCCTC-CCTCC-TCCCTAAAACAC 629 chr1qtel1M 925411 CTTC-CTTTGAAGTTCATTTAATC----CACACCACTCACTCAAGATTCC 925455 iiv- vi v v ----i i i i - vvvi L2#LINE/L2 630 CCCAGCTTTGAATCTCATGTCATCAGACTATACCACCCGCT-ACCCCTCC 678 chr1qtel1M 925456 --GGTG--GCTATTGAGGCAACTCCTGGGATACTTCT-----TTCCC--A 925494 -- v -- ii iv v- i ii i vi i i----- i-- L2#LINE/L2 679 TTGTTGCAGTCATCTAC-CGACCTCCGGGTCACTCCCCCTCATTCCTTGA 727 chr1qtel1M 925495 AGGAGTTAATACCTGGCTCACAATCTTTCTCTCCTTCCCAACTCCTGCCC 925544 ivv iiv vi vi vv v v i v L2#LINE/L2 728 AGATTTTAGCTCCTGGCTCACTGTCACTCTCTCCAACACTACTCCTGTCA 777 chr1qtel1M 925545 TCCAATTA--GAAGATATAAA-AGACATACTAATATTCCCTCTAAAAATC 925591 -- v-- iv v v - vv iiivi iv i i v vi L2#LINE/L2 778 T--AATTCTTGGTGATTTCAATATCCACGTAGATGATCCTTCCAATACCC 825 chr1qtel1M 925592 TAACCTCCCAGTTCTTCAATTTACCCATTTCCCACAATCTCCTCTTCTAC 925641 ii i i ii ii v i vii v ii iv i i L2#LINE/L2 826 TGGCCTCTCAGTTCCTTGACCTCCTCTCCTCCAATGATCTTGTCCTCCAC 875 chr1qtel1M 925642 CCTACCTCATCTACTCA--GAAAGAGTCACATTTGTGATCTTGCTATCAC 925689 v i --vvv vi i iiivv i ii i L2#LINE/L2 876 CCTACCTCAGCCACTCACTCCCATGGTCATACCCTAGACCTTGTCATTAC 925 chr1qtel1M 925690 ATACAAATGGACTACTTCCAT 925710 vv i v v viv i L2#LINE/L2 926 CAATAACTGCAACCCCTCCAT 946 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 50.68 CpG sites = 103, Kimura (unadjusted) = 52.97 Transitions / transversions = 1.45 (103/71) Gap_init rate = 0.06 (27 / 485), avg. gap size = 1.70 (46 / 27) 442 33.69 7.44 3.36 chr1qtel1M 925847 926276 (73724) L2#LINE/L2 2364 2810 (272) m_b53s601i1 1919 chr1qtel1M 925847 CTCTCCTTTGCTGATCCCCAGTTTC-TATCTCCAACTGCCTGTTGGATAT 925895 i--- v i vi - v ii v i L2#LINE/L2 2364 CTCTCCC---CTGAACTCCAGACTCGTATATCCAACTGCCTACTCGACAT 2410 chr1qtel1M 925896 ATCAAATT--ATGTGT--------TCTTAAACTCCAATTGTGAAAAACTG 925935 v v v -- v -------- i iv vv vv L2#LINE/L2 2411 CTCCACTTGGATGTCTAATAGGCATCTCAAACTTAACATGTCCAAAACTG 2460 chr1qtel1M 925936 AACTTAACATCTTTCATCTCAATCCCTTCTGTCTTCCGAA--CTTTCATA 925983 ivvv i vi -v v -i i v -- i vi L2#LINE/L2 2461 AACTCCTGATCTTCCCCCTCAA-ACCTGCT-CCTCCCGCAGTCTTCCCCA 2508 chr1qtel1M 925984 TTACAATGGAGG---ATGCCATCTTTGCCCTAATAACACACTCTCCCAAT 926030 iv i ?i v --- iv i --- i i vi v vv - vv v L2#LINE/L2 2509 TCTCAGTNAATGGCAACTCCATCCTT---CCAGTTGCTCAGGC-CAAAAA 2554 chr1qtel1M 926031 CCATATA---ATTCTCAACTCTTCT-TTTCTT--------CATATCCAAT 926068 v iv --- i ii i - i-------- i L2#LINE/L2 2555 CCTTGGAGTCATCCTTGACTCCTCTCTTTCTCTCACACCCCACATCCAAT 2604 chr1qtel1M 926069 TGTT----AAATCTTACTCGCAATTCACCTTCATAGCATCTCTTCTATAT 926114 ivv ---- i iiiv -- ii v ii v ivvv vi L2#LINE/L2 2605 CCATCAGCAAATCCTGTCGGC--TCTACCTTCAAAATATATCCAGAATCC 2652 chr1qtel1M 926115 ACCTGCTTTTTTCCCCTGGCACTGTTACCACCCTGGTAGAGATTCTCATC 926164 iv ii i iv v ivv ii vv iiiivi L2#LINE/L2 2653 GACCACTTCTCACCACCTCCACTGCCACCACCCTGGTCCAAGCCACCATC 2702 chr1qtel1M 926165 ACTTCATACTTGGATTACTACAATATCCTATTAGTTGCCTCAATTCTTTG 926214 ii vii i i v vi ii -v --- ii L2#LINE/L2 2703 ATCTCTCGCCTGGATTACTGCAATAGCCTCCTAACTG-GTC---TCCCTG 2748 chr1qtel1M 926215 CTTCAAATCCATTCCCACTCCAGTCCATTCTCCACTCTGCTACCCAAATC 926264 v vi ivvi v ? i v v v vi vi i v L2#LINE/L2 2749 CTTCCACCCTTGCCCCCCTNCAGTCTATTCTCAACACAGCAGCCAGAGTG 2798 chr1qtel1M 926265 ATGTTTCTAAAA 926276 vi i L2#LINE/L2 2799 ATCCTTTTAAAA 2810 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 44.70 CpG sites = 74, Kimura (unadjusted) = 46.13 Transitions / transversions = 1.12 (74/66) Gap_init rate = 0.06 (24 / 429), avg. gap size = 1.96 (47 / 24) 2695 28.72 3.38 1.74 chr1qtel1M 926367 927610 (72390) L1M5_orf2#LINE/L1 1015 2278 (1016) m_b53s551i0 1920 chr1qtel1M 926367 GAAATTCTAAAAATAAAAGGAGAGATTCGTAAAATTGAAAGTAAAAAAAA 926416 vv i i v i ivi i v ii ? ? v L1M5_orf2#LIN 1015 GAAATAATAAAGATAAGAGCAGAAATCAATGAAATAGAAAACAAANANAC 1064 chr1qtel1M 926417 AACTATTGAATAC--ATAAAACAAAGAGTTGGTTTTATGAAAAAGCCAAC 926464 - vv v i-- ii i v i i i v iii i L1M5_orf2#LIN 1065 AA-TAGAGAAAATCAACGAAGCCAAAAGCTGGTTCTTTGAAAAGATCAAT 1113 chr1qtel1M 926465 AAAATGAATAAACCTTTAGTTAATTTGATTAGACAAATGAAAGCAGAAAA 926514 vi i i? ivi i iiv vi i - i L1M5_orf2#LIN 1114 AAAATTGATAAACCTCTAGCNAGACTGATCAAGAAAAAAAGAG-AGAAGA 1162 chr1qtel1M 926515 T-CAAACTGTTAGTTTCAAAAATGAAAAGGGAGAACTTTCCACCAATGAA 926563 i- i iii i v ii i vv iv i vi vvv L1M5_orf2#LIN 1163 CACAAATTACCAATATCAGGAATGAAAAAGGAGACATCACTACAGATCCT 1212 chr1qtel1M 926564 AAAGACATTAGAGCAATAATTAGGACTTATTTTGCTCAGCTTTATGCCAA 926613 v i ivi v iivv v vv i L1M5_orf2#LIN 1213 ACAGACATTAAAAGGATAATAAGAGAATATTATGAACAACTTTATGCCAA 1262 chr1qtel1M 926614 AAAGTTTAACATCTTAAGTGAAATGGAGGAATACCTACAAAAATATAGAT 926663 v i i ? v ii vi v vv i i i? L1M5_orf2#LIN 1263 TAAATTTGANAACTTAGATGAAATGGACAAATTCCTTGAAAAACACAANT 1312 chr1qtel1M 926664 TGCCCAGATTAACAGAAGAGGAAATAAATTACTTAAATAGTCCCAT-TTT 926712 i v i i i ?v i i vv ii i i i - i L1M5_orf2#LIN 1313 TACCAAAACTGACNCAAGAAGAAATAGAAAATCTGAATAGCCCTATATCT 1362 chr1qtel1M 926713 AGAAAAAGAAATAGAATAAGCTATTAATCAACTCCCTAAGAAAAAAAATG 926762 vv - v vv iv vv v i i v- i i- L1M5_orf2#LIN 1363 ATTAAA-GAAATTGAATTTGTAATTAAAAACCTTCCCAC-AAAGAAAAC- 1409 chr1qtel1M 926763 TCCAGGGCCAGATGGATTTACATGTGAATTCTACTAAATATTTAAAGAAC 926812 v v i vv i i i v L1M5_orf2#LIN 1410 TCCAGGCCCAGATGGCTTCACTGGTGAATTCTACCAAACATTTAAGGAAG 1459 chr1qtel1M 926813 AATTAACTCTAATATTATATAAACTATTTGAAAAAATAAA--------GA 926854 v iv i v i i v iv i i -------- L1M5_orf2#LIN 1460 AAATAATACCAATCTTACACAAACTCTTCCAGAAAATAGAAAAAGAGGGA 1509 chr1qtel1M 926855 CTCCTACAAAATTCCTTTTATAA---CAGAGATATAGTACTGATAGCTAA 926901 viv v vv i v i --- ---i ?iiv v v L1M5_orf2#LIN 1510 ACACTTCCCAACTCATTTTATGAGGCCAG---CATNACCCTGATACCAAA 1556 chr1qtel1M 926902 ACCTAGGATGAAAACA---------GACAAAATTATAGACCAATTTCCCT 926942 ?-- ii i ---------i v i v L1M5_orf2#LIN 1557 ACCN--GACAAAGACATTACAAGAAAAGAAAATTACAGACCAATATCCCT 1604 chr1qtel1M 926943 AATGAATATTGATGCAAAAATCTT-----AAATATTAGCAAAGAGATTAC 926987 v i v i ----- vv v v L1M5_orf2#LIN 1605 CATGAACATAGATGCAAAAATCCTNAACAAAATATTAGCAAATCGAATCC 1654 chr1qtel1M 926988 ACCAAGTCATCAGCAGAATAATGCTCCATGATCAAGAAGTATCTATATCA 927037 v vvi v iv i i vi i vi vi i vi L1M5_orf2#LIN 1655 AGCAATATATAAAAAGGATAATACATCATGACCAAGTGGGGTTTATCCCA 1704 chr1qtel1M 927038 GGAATGCAAAGTTGGTTCAATATTAGGAAAACTCTTAGCATAATTGACTG 927087 i i i v i v vv i iii v ii L1M5_orf2#LIN 1705 GGAATGCAAGGTTGGTTTAACATTCGAAAATCAATCAATGTAATTCACCA 1754 chr1qtel1M 927088 TATCAAT--AATCAAACTAACAAAAACCATATGATTATTTCAGTAGATGC 927135 i i-- v i--i v i i i i L1M5_orf2#LIN 1755 TATTAACAGAATAAAG--GAGAAAAATCATATGATCATCTCAATAGATGC 1802 chr1qtel1M 927136 AGAAAAACCATTTGATAAAATCCAATACCCATTCCTATTTTTTAAAAAAA 927185 v i i i v i------ v L1M5_orf2#LIN 1803 AGAAAAAGCATTTGACAAAATTCAACACCCATTCATG------ATAAAAA 1846 chr1qtel1M 927186 CACTACAG-AATATAGGAATAAATGGAATTTTCCTTAAAAGAATCAGTAG 927234 v - - vv i v i vi i vvvi v ivi L1M5_orf2#LIN 1847 CTCT-CAGCAAACTAGGAATAGAAGGGAACTTCCTCAACCTGATAAAGGG 1895 chr1qtel1M 927235 TATCTATTTAAAATCATCATCAAGAATCATATGTGATGGGGATAAACTGG 927284 i ivv i vv v ? iv iv i v v ? i L1M5_orf2#LIN 1896 CATCTACGAAAAACCTACAGCNAACATCATACTTAATGGTGAAANACTGA 1945 chr1qtel1M 927285 AACCATTCCCAATAAGATCAGGAGTGAAGCAAGACTGCCCACTATCACCA 927334 ?v v vv i iii ii iv i i ? L1M5_orf2#LIN 1946 ANGCTTTCCCCCTAAGATCGGGAACAAGACAAGGATGTCCGCTNTCACCA 1995 chr1qtel1M 927335 TTACTATTCAGTTTTGTATTAGAAATGCTAGCTTTGGCAATCAGAGAAGG 927384 i v iiv i i ii v ivvv v iv i L1M5_orf2#LIN 1996 CTTCTATTCAACATTGTACTGGAGGTCCTAGCCAGTGCAATAAGGCAAGA 2045 chr1qtel1M 927385 AAAAG-------AGGAATTAGAGTAGGTAATGAGGAAACCAAATTATCAC 927427 ------- v v iii v v v i iv i i ?i L1M5_orf2#LIN 2046 AAAAGAAATAAAAGGCATAAAGATTGGAAAGGAAGAAATAAAACTGTCNT 2095 chr1qtel1M 927428 TCTTTGCAGATGATATGATAGTATACTTAGAGAACCCTAGAGAATCAACT 927477 v i i v ? v i i ? i v v L1M5_orf2#LIN 2096 TATTCGCAGATGACATGATTGTNTACGTAGAAAATCCNAAAGAATCTACA 2145 chr1qtel1M 927478 AAAAAACTATTAGAAATAATTCACAAGTTTAGCAAAGTTGCAGGATACAA 927527 ? i v vviii i i i ? L1M5_orf2#LIN 2146 AANAAACTACTAGAACTAATAAGTGAATTTAGCAAGGTCGCNGGATACAA 2195 chr1qtel1M 927528 AACAAATCCACAGAAATTATTGGCATTTTTATACATCACCAACAAAGTCC 927577 iiiv vi i i v v i i i ii v --- L1M5_orf2#LIN 2196 GGTCAATATACAAAAATCAATTGTATTTCTATATACTAGCAACAAA---C 2242 chr1qtel1M 927578 AACAGCAA---GAGATACAAAGAGAAATTCCATTTA 927610 iv v --- i vi? i iv v L1M5_orf2#LIN 2243 AATTGGAAAATGAAATTTNAAAAACAATACCATTTA 2278 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 36.94 CpG sites = 198, Kimura (unadjusted) = 37.77 Transitions / transversions = 1.29 (198/153) Gap_init rate = 0.03 (33 / 1243), avg. gap size = 1.94 (64 / 33) 381 29.66 3.29 2.87 chr1qtel1M 929787 930029 (69971) C L1M2_orf2#LINE/L1 (876) 2415 2172 m_b53s551i1 1921 chr1qtel1M 929787 CCGTGAGCACTTCATATTTTTCCTACTGATTAGGTC----TGACTTTCTT 929832 i ivvv i vvi ?v iv ---- v v C L1M2_orf2#LIN 2415 CCATGAGCATGGGATATCTTTCCATTTNTTTGTGTCCTCTTCAATTTCTT 2366 chr1qtel1M 929833 TGGTGGAAAGTGTTTTGTAGTTGTATTAATATA-ATTCCTGACTTTCCCT 929881 vi v--- i v v? vi v - iii v i -- C L1M2_orf2#LIN 2365 TCATC---AGTGTTTTATAGTTTTCNTTGTAGAGATCTTTCACCT--CCT 2321 chr1qtel1M 929882 TGGC-AGATAGATTCCCAAATATTTTATAATATTGACAGTTATTTTGAAT 929930 i- i vv i ii vv v vii i v i C L1M2_orf2#LIN 2320 TGGTTAAATTTATTCCTAGGTATTTTATTTTTTTTGTAGCTATTGTAAAT 2271 chr1qtel1M 929931 GGAATTTCTCTTTGTATCGCTTGTT--GATGAACTTTGTTGGTAACATAT 929978 i v i i vv iv v -- -- v i v ii i C L1M2_orf2#LIN 2270 GGGATTGCTTTCTTGATTTCTTTTTCAGAT--AGTTCGTTGTTGGCGTAT 2223 chr1qtel1M 929979 AAAAATGCTGATGATTTATGTGGATTTAATTTGTATCCTACAACTTTGCT 930028 i iv v ivi v v i i C L1M2_orf2#LIN 2222 AGAAATGCTACTGATTTTTGTATGTTGATTTTGTATCCTGCAACTTTACT 2173 chr1qtel1M 930029 G 930029 C L1M2_orf2#LIN 2172 G 2172 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 37.29 CpG sites = 35, Kimura (unadjusted) = 38.66 Transitions / transversions = 1.00 (35/35) Gap_init rate = 0.05 (11 / 242), avg. gap size = 1.36 (15 / 11) 700 25.08 2.48 2.48 chr1qtel1M 930058 930380 (69620) C L1M5_orf2#LINE/L1 (1426) 1868 1546 m_b53s551i2 1921 chr1qtel1M 930058 TTTATTCCTATGTTCTCCTGTG---TTTTAATAAAAATGGGTGCTATATT 930104 i - - v v --- vi vi i iv C L1M5_orf2#LIN 1868 TCTATTCCTA-GTT-TGCTGAGAGTTTTTATCATGAATGGGTGTTGAATT 1821 chr1qtel1M 930105 TTGTCAAAAGTTTTTCCTAGATCTATTGAGATAATAATATGATTTCTTTC 930154 v i i iv i v i i C L1M5_orf2#LIN 1820 TTGTCAAATGCTTTTTCTGCATCTATTGAGATGATCATATGATTTTTCTC 1771 chr1qtel1M 930155 A---ATTTTG-TGATTTAGTTGATTATATTGA-TAATTTTCTTAATATTG 930199 v--- i - i v i vi i - i -v i i C L1M5_orf2#LIN 1770 CTTTATTCTGTTAATATGGTGAATTACATTGATTGATTTTC-GAATGTTA 1722 chr1qtel1M 930200 AAACAATCCCTGTTTTCTTGGTATTATAGATCCCACATGGTCTTACTGTA 930249 v - i iv i ---v i i v v iv C L1M5_orf2#LIN 1721 AACCAA-CCTTGCATTCCTGG---GATAAACCCCACTTGGTCATGATGTA 1676 chr1qtel1M 930250 TTAAACTGATGATAAATTTTTGTAATCTCTTTAATAATAGTTTATTTAAA 930299 vv vv v v vi v v vv iv v i ? ii C L1M5_orf2#LIN 1675 TTATCCTTTTTATATATTGCTGGATTCGATTTGCTAATATTTTGTTNAGG 1626 chr1qtel1M 930300 ATTTTTGCATCAATATTTTTTGGGAAAATTGGTCTACAATTTTATTTTCT 930349 v i iv vi i v ii v C L1M5_orf2#LIN 1625 ATTTTTGCATCTATGTTCATGAGGGATATTGGTCTGTAATTTTCTTTTCT 1576 chr1qtel1M 930350 CTGTTTTGGCTTGTCCCGGTTTAGGTATCAG 930380 - vv v vvi ? v C L1M5_orf2#LIN 1575 -TGTAATGTCTTTGTCNGGTTTTGGTATCAG 1546 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 30.96 CpG sites = 37, Kimura (unadjusted) = 30.96 Transitions / transversions = 0.88 (37/42) Gap_init rate = 0.04 (12 / 322), avg. gap size = 1.33 (16 / 12) 397 30.32 3.11 3.11 chr1qtel1M 930080 930433 (69567) C L1M3_orf2#LINE/L1 (1449) 1839 1486 m_b53s551i3 1921 chr1qtel1M 930080 TTTTA--ATAAAAATGGGTGCTATATTTTGTCAAAAGTTTTTCCTAGATC 930127 -- i -- i i iv v i i iv C L1M3_orf2#LIN 1839 TTTTATCATGAAA--GGATGTTGAATTTTGTCAAATGCTTTTTCTGCATC 1792 chr1qtel1M 930128 TATTGAGATAATAATATGATTT----CTTTCAATTTTGT-GATTTAGTTG 930172 i v i ---- i - i -i v i vv C L1M3_orf2#LIN 1791 TATTGAGATGATCATGTGATTTTTATCCTTCA-TTCTGTTAATGTGGTGT 1743 chr1qtel1M 930173 ATTATATTGAT-AATTTTCTTAATATTGAAACAATCCCTGTTTTCTTGGT 930221 i i ? -i ? v - i v - i iv i iv v C L1M3_orf2#LIN 1742 ATCACATTNATTGATTTNCGTA-TGTTGAACCA-TCCTTGCATCCCAGGG 1695 chr1qtel1M 930222 ATTATAGATCCCACATGGTCTTACTGTATTAAACTGATGATAAATTTTTG 930271 --- i v v iv v vv vv i ivii v C L1M3_orf2#LIN 1694 AT---AAATCCCACTTGGTCATGGTGTATGATCCTTTTAATGTGCTGTTG 1648 chr1qtel1M 930272 TAATCTCTTTAATAATAGTTTATTTAAAATTTTTGCATCAATATTTTTTG 930321 v v vv iv i v i v ii v i iv ii C L1M3_orf2#LIN 1647 AATTCGGTTTGCTAGTATTTTGTTGAGGATTTTTGCATCTATGTTCATCA 1598 chr1qtel1M 930322 GGAAAATTGGTCTACAATTTTATTTTCTCTGTTTTGGCTTGTCCCGGTTT 930371 i v i ii i v - vv v vvi i i C L1M3_orf2#LIN 1597 GGGATATTGGCCTGTAGTTTTCTTTTCT-TGTAGTGTCTTTGTCTGGCTT 1549 chr1qtel1M 930372 AGGTATCAGCAT--TG-TAGTTGTATTTAATTGGAGTTTAAAAATTTGTT 930418 v vi -- - i iivi vv -- ii i v vii C L1M3_orf2#LIN 1548 TGGTATCAGGGTAATGCTGGCCTCATAAAAT--GAGTTTGGAAGTGTTCC 1501 chr1qtel1M 930419 ATTTTTCTCAATTTT 930433 v ii ii C L1M3_orf2#LIN 1500 CTCCTCTTCAATTTT 1486 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 40.09 CpG sites = 58, Kimura (unadjusted) = 40.09 Transitions / transversions = 1.26 (58/46) Gap_init rate = 0.05 (17 / 353), avg. gap size = 1.29 (22 / 17) 280 31.90 8.14 4.63 chr1qtel1M 930389 931223 (68777) C L1M5_orf2#LINE/L1 (2285) 1009 147 m_b53s551i4 1921 chr1qtel1M 930389 TTGTATTTAATTGGAGTTTAAAAATTTG---TTATTTTTCTCAATTTTGA 930435 v i ?v v i --- --- v viv i v C L1M5_orf2#LIN 1009 TTCTACTTNCTTTGGGTTTAA---TTTGCTCTTCTTTTTCTAGCTTCTTA 963 chr1qtel1M 930436 AAATTACATGCCTAATTCACTGATCT----CCTCTTTCCTTATTTTATTC 930481 ii viv - i iv i i ---- i i i - i --- C L1M5_orf2#LIN 962 AGGTGGAA-GCTTAGATCATTGATTTTAAGCCTTTCTTCTT-TTCTA--- 918 chr1qtel1M 930482 ATGTAAGAATTTAAAG----AAAC--------GAGGACTGCTTTGGCTGC 930519 i ? v ? ---- i--------i v i C L1M5_orf2#LIN 917 ATATANGCATTTAANGCTATAAATTTCCCTCTAAGCACTGCTTTAGCTGC 868 chr1qtel1M 930520 ATCCCATAAGTTTTGGCATGTTGTTTTATTGCTGCTACTTTCATGGATGA 930569 i i ii v v iii ?ii -- -- v v C L1M5_orf2#LIN 867 ATCCCACAAATTTTGATATGTTGTATTTTCATTNTCA--TTCA--GTTCA 822 chr1qtel1M 930570 AATTATT-----GTTTCTC---TGACTTGTTGTTTGACCTACTCATATTT 930611 v -----i i?--- i v v i ivvi vv C L1M5_orf2#LIN 821 AAATATTTTCTAATTTCCNTTGTGATTTCTTCTTTGACCCATGGGTTATT 772 chr1qtel1M 930612 TAGAATTAGATCACTTAGTTTCCAATTAGT------TTTTTAAACTATCT 930655 v ivi iii i v v ------ iv i? C L1M5_orf2#LIN 771 TAGAAGTGTGTTGTTTAATTTCCAAATATTTGGGGATTTTCTAGNTATCT 722 chr1qtel1M 930656 TTCATTTATTG-CATGTAATTTTATGGCACCATGATCTGGAAAGGATGCA 930704 ivv -iv v v vv iii i --- i i iii C L1M5_orf2#LIN 721 TTTTGTTATTGATTTCTAATTTAATTCCATTGTGGTC---AGAGAACATA 675 chr1qtel1M 930705 TTTAATAT--TTTTG--CCTTTC---TGCATTGGAATGTGGGGTTTTATG 930747 i ivi -- ii-- ?--- vi ii iv --- C L1M5_orf2#LIN 674 CTCTGTATGATTTCAATCCTTTNAAATTTATTGAGACTT---GTTTTATG 628 chr1qtel1M 930748 CCTTAATATATGGTCAGTTTTTGTGTCGGTGGCATGTACTGCTGAGAAAA 930797 v ii i? vi i v ivvv vv i vvi i i C L1M5_orf2#LIN 627 GCCCAGNATATGGTCTATCTTGGTAAATGTTCCATGTGCACTTGAAAAGA 578 chr1qtel1M 930798 AGGTATATTTCTTCCTCTCTC-----CAGTTTTCTCCAGAAGTTTATCAT 930842 v i - v ?vi v i-----? v vi i v iv i v C L1M5_orf2#LIN 577 ATGTGTA-TTCTGCNGTTGTTGGGTGNAGTGTTCTATAAATGTCAATTAG 529 chr1qtel1M 930843 ATCTAACTT--------------TTCAAAAATTCTAATCACTTTCTTAAC 930878 i - v -------------- vv ----- v i v C L1M5_orf2#LIN 528 GTC-AAGTTGGTTGATAGTGTTGTTCAAATCTTCTA-----TATCCTTAC 485 chr1qtel1M 930879 TTCTTTCTTGTTTATTTTGTGATTAGATTTATCTAGTTTTGAGAGGGGGG 930928 vv i i -i ------- i v v vi i ? C L1M5_orf2#LIN 484 TGATTTTTTGTCTA-CTTGT-------TCTATCAATTACTGAGAGAGGNG 443 chr1qtel1M 930929 TGTTGAGGTTCCCCACTAGTAAAGTGTTG--CTGTCTATTTCTTCTTGTA 930976 i ii ii ? v-- v v --i i v C L1M5_orf2#LIN 442 TGTTAAAATCTCCNACTAT--AATTGTGGATTTGTCTATTTCTCCTTTTA 395 chr1qtel1M 930977 ACTCACTTCATTTCTCCTAAAGGAATTTGGATACTATACCATTTGTTGAA 931026 ii vv ivi i v vv v v v vi v iii v v v C L1M5_orf2#LIN 394 GTTCTGTCAGTTTTTGCTTCATGTATTTTGAAGCTCTGTTATTAGGTGCA 345 chr1qtel1M 931027 -AAATATTTAATATTCACATTACTCCATTGTCCATGG---GAACC-TTTA 931071 - v i iv vvi vv i - --- i--- v - C L1M5_orf2#LIN 344 TACACATTTAGGATTGTTATGTCTTC-TTG---ATGAATTGACCCTTTTA 299 chr1qtel1M 931072 GTAAGATGTAATTTCCTTCCCTGTCTCTTTTAATAAGACCTACTTTTGCT 931121 vi vv v v i ii i vv vvv i i i vivv C L1M5_orf2#LIN 298 TCATTATGAAATGTCCCTCTTTATCTCTGGTAATATTTCTTGCCTTGAAG 249 chr1qtel1M 931122 TTTATTTTCTCTGAGATCAGGATTGCTACCCCTACTTT-TTTTGCTTCAG 931170 i i v v i iv v i ? vi - ? - C L1M5_orf2#LIN 248 TCTACTTTGTCTGATATTAATATAGCCACNCCAGCTTTCTTTTGNTT-AG 200 chr1qtel1M 931171 CTGAAGCAGAGCATCTCCTATTCCAGCCTTTTGCCTTTATTTTGCGTGTT 931220 ivvvv vi i v i v v i i i vii ?iv v C L1M5_orf2#LIN 199 TGTTTGCATGGTATATCTTTTTCCATCCTTTTACTTTCAACCTNTCTGTG 150 chr1qtel1M 931221 TCT 931223 C L1M5_orf2#LIN 149 TCT 147 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 43.56 CpG sites = 133, Kimura (unadjusted) = 43.56 Transitions / transversions = 1.10 (133/121) Gap_init rate = 0.07 (58 / 834), avg. gap size = 1.86 (108 / 58) 557 30.21 7.91 5.42 chr1qtel1M 930503 931223 (68777) C L1M2_orf2#LINE/L1 (2407) 884 147 m_b53s551i5 1921 chr1qtel1M 930503 AGGACTGCTTTGGCTGCATCCCATAAGTTTTGGCATGTTGTTTTATTGCT 930552 ? v i i i ------ i C L1M2_orf2#LIN 884 AGNACTGCTTTTGCTGTATCCCATAGGTTTTGGTATGTTG------TGTT 841 chr1qtel1M 930553 GCTACTTTCATGGAT-----GAAATTATTG--TTTC--TC-TGACTTGTT 930592 v i i vvi ----- v ?-- -- - i i v C L1M2_orf2#LIN 840 TCCATTTTCATTTGTTTCAAGAAATTTTTNAATTTCCTTCTTAATTTCTT 791 chr1qtel1M 930593 GTTTGACCTACTCATATTTTAGAATTAGATCACTTAGTTTCCA---ATTA 930639 vv i i vi vv i i vi vi iii i --- v C L1M2_orf2#LIN 790 CATTGACCCATTGGTCGTTCAGGAGCATGTTGTTTAATTTCCATGTATTT 741 chr1qtel1M 930640 GT----TTTTTAAACTATCTTTCATTTATTG-CATGTAATTTTATGGCAC 930684 ---- ii v vi i ii- -iv v i vv i C L1M2_orf2#LIN 740 GTANAGTTTCCAAAGTTCCTCTTG-TTATTGATTTCTAGTTTTATTCCAT 692 chr1qtel1M 930685 CATGATCTGGAAAGGATGCATTTAATAT--TTTTGCCTTTCTGCA----- 930727 ii i -? i -- i i -- i vi i ?v ----- C L1M2_orf2#LIN 691 TGTGGTC-NGAAAAGAT--ACTTGATATGATTTCGATTTTTTNAAATTTG 645 chr1qtel1M 930728 TTGGAATGTGGGGTTTTATGCCTTAATATATGGTCAGTTTTTGTGTCGGT 930777 ii iv --- i v i i vi ii v v vvv C L1M2_orf2#LIN 644 TTGAGACTT---GTTTTGTGGCCTAACATATGGTCTATCCTGGAGAATGT 598 chr1qtel1M 930778 GGCATGTACTGCTGAGAAAAAGGTATATTTCTTCCTCTCTC-----CAGT 930822 vv i v i v i - v vv v i-----v i C L1M2_orf2#LIN 597 TCCATGTGCTGATGAGAAGAATGTGTA-TTCTGCAGCTGTTGGATGAAAT 549 chr1qtel1M 930823 TTTCTCCAGAAGTTTATCATATCTAACTTT--TCAAAAATTCTAATCACT 930870 v vi i v i i i vi i -- -- v ? i v - i ---- C L1M2_orf2#LIN 548 GTTCTGTAAATGTCTGTTAGGTCCA--TTTGGTCTANAGTGC-AGT---- 506 chr1qtel1M 930871 TTCTTAACTTC----TTTC-TTGTTTATTTTGTGATTA---GATTTATCT 930912 --- v i ---- - v v vi i--- i i i C L1M2_orf2#LIN 505 ---TTAAGTCCGATGTTTCTTTGTTGATTTTCTGTCTGGATGATCTGTCC 459 chr1qtel1M 930913 AGTTTTGAGAGGGGGGTGTTGAGGTTCCCCACTAGTAAAGTGTTGCTGTC 930962 ? vi v i i ? v vv i ?v C L1M2_orf2#LIN 458 ANTGCTGAGAGTGGGGTGTTGAAGTCCCCNACTATTATTGTATTGNAGTC 409 chr1qtel1M 930963 TATTTCTTCTTGTAACTCACTTCATTTCTCCTAAAGGAATTTGGATACTA 931012 i i i v iv vv? v v i v vv viv i i i v C L1M2_orf2#LIN 408 TATCTCTCCCTTTAGATCTANTAATATTTGCTTTATATATCTGGGTGCTC 359 chr1qtel1M 931013 TACCATTTGTTGAA-AAATATTTA--------ATATTCACATTACTCCAT 931053 iivii v v v - v -------- i v - i vv C L1M2_orf2#LIN 358 CGGTGTTGGGTGCATATATATTTANAATTGTTATATCCTC-TTGCTGAAT 310 chr1qtel1M 931054 TGTCCATGGGAACCTTTAGTAAGATGTAATTTCCTTCCCTGTCTCTTTTA 931103 v ------- vi vv i vv ii v C L1M2_orf2#LIN 309 TGACC-------CCTTTATCATTATATAATGACCTTCTTTGTCTCTTTTT 267 chr1qtel1M 931104 ATAAGACCTACTTTTG-CT-----TTTATTTTCTCTGAGATCAGGATTGC 931147 i ------ii - ----- i v v v v v C L1M2_orf2#LIN 266 ACA------GTTTTTGACTTAAAGTCTATTTTATCTGATATAAGTATAGC 223 chr1qtel1M 931148 TACCCCTACTTTTTTT--GCTTCAGCTGAAGCAGAGCATCTCCTATTCCA 931195 i i i?i -- i v i v-- vi v v i v C L1M2_orf2#LIN 222 TACTCCTGCTCNCTTTTGGTTTCCGTTT--GCATGGAATATCTTTTTCCA 175 chr1qtel1M 931196 GCCTTTTGCCTTTATTTTGCGTGTTTCT 931223 v i ii i i v i ii v C L1M2_orf2#LIN 174 TCCCTTCACTTTCAGTCTATGTGTGTCT 147 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.73 CpG sites = 110, Kimura (unadjusted) = 40.26 Transitions / transversions = 1.15 (110/96) Gap_init rate = 0.08 (59 / 720), avg. gap size = 1.64 (97 / 59) 13 18.47 6.98 0.00 chr1qtel1M 931533 931575 (68425) (AAAATG)n#Simple_repeat 1 46 (0) m_b53s252i1 1922 chr1qtel1M 931533 AAAATGTAAATGAAAA-GAACA-G-AAATAAAAAAGCAAAAGCAAA 931575 v - v - - i v v v v (AAAATG)n#Sim 1 AAAATGAAAATGAAAATGAAAATGAAAATGAAAATGAAAATGAAAA 46 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.07 (3 / 42), avg. gap size = 1.00 (3 / 3) 14 13.61 0.00 5.88 chr1qtel1M 931540 931575 (68425) (AAAAG)n#Simple_repeat 1 34 (0) m_b53s252i2 1922 chr1qtel1M 931540 AAATGAAAAGAACAGAAATAAAAAAGCAAAAGCAAA 931575 v v - i - v (AAAAG)n#Simp 1 AAAAGAAAAGAAAAGAAA-AGAAAAG-AAAAGAAAA 34 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 13 25.72 3.51 1.72 chr1qtel1M 931974 932030 (67970) (AATAGT)n#Simple_repeat 1 58 (0) m_b53s252i3 1923 chr1qtel1M 931974 AATACTAATA-TAGAAG-AAGAGAACAAGATAATAATCAAAATAATAGTA 932021 v - iv - v v vv - i v v i (AATAGT)n#Sim 1 AATAGTAATAGTAATAGTAATAGTAATAG-TAATAGTAATAGTAATAGTA 49 chr1qtel1M 932022 ATATTAATA 932030 v (AATAGT)n#Sim 50 ATAGTAATA 58 Matrix = Unknown Transitions / transversions = 0.33 (3/9) Gap_init rate = 0.05 (3 / 56), avg. gap size = 1.00 (3 / 3) 17 14.17 0.00 0.00 chr1qtel1M 932001 932031 (67969) (ATA)n#Simple_repeat 1 31 (0) m_b53s252i4 1923 chr1qtel1M 932001 ATAATAATCAAAATAATAGTAATATTAATAA 932031 v v i v (ATA)n#Simple 1 ATAATAATAATAATAATAATAATAATAATAA 31 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 16 16.93 0.00 0.00 chr1qtel1M 932784 932810 (67190) (A)n#Simple_repeat 1 27 (0) m_b53s252i5 1924 chr1qtel1M 932784 AAAAGGAAAAAAAGATAAAAAAAAAAA 932810 ii i v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAA 27 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 504 33.31 5.60 2.72 chr1qtel1M 932977 933476 (66524) C L1ME4c_3end#LINE/L1 (190) 640 127 m_b53s551i6 1925 chr1qtel1M 932977 ATTCTGCTCAATTCACTTTTAATCAGTTTGTATAATAAG--GTTTCCATG 933024 ivv -- - -- i v i--v C L1ME4c_3end#L 640 ATTCTGCTTTTTTCACTT--AA-CA--TTATATCATAAACATTTTCCATG 596 chr1qtel1M 933025 TTTTTTTTTGAAATCCACATGCTCACCATTTCTCATTGTACTACTATATT 933074 vi viv -- i iv iv i i i v v ivvi iv C L1ME4c_3end#L 595 TTGCTACAT--AGTCTTCATAATTATCATTTTTAATGGCTGCATAATATT 548 chr1qtel1M 933075 CCACTGCAATC-ATATGCCACAGCTTGTCCAACTATTCTTGAATTGGTG- 933122 ii - i ?- i i i ii iiii i iivv v - C L1ME4c_3end#L 547 CCATCG-AGTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGG 499 chr1qtel1M 933123 ACATCTCAATT---TCCAATTCTTTGCCACCACAAAAAGAGTTGCTGTAA 933169 i vii --- i i i ii i v iv i vi i C L1ME4c_3end#L 498 ACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGA 449 chr1qtel1M 933170 ATTTTTTTGTATACATATAG-----------TTTTGAAA-ATCTCTTTGA 933207 iv i i i-- ----------- v- i i ii C L1ME4c_3end#L 448 ACATCTTCGTG--CATATAGCTTTTTCCTTCTTTTGAATTATTTCCTTAG 401 chr1qtel1M 933208 GATATAGACCTAGCCACAGGTATTGCTGGGTCAAAGGGTATGCATAGTTC 933257 v vv i v- vv v i v i v i C L1ME4c_3end#L 400 GATAAATTCCCAGA-AGTGGAATTACTGGGTCAAAGGGTATGAACATTTT 352 chr1qtel1M 933258 TGAAGCCCTTTGGACAGAGTTCCAAATGGCTTTCTAGAATTGTTGAACCA 933307 ivi i viv iv v v v i i vv v C L1ME4c_3end#L 351 TATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCA 302 chr1qtel1M 933308 CTTCACATTTCTGCCAAGAGTACATTAGTGTTCCAGATTTCCCATACCTT 933357 v i ? v ii iv i ii v ? v v iv ii ? i C L1ME4c_3end#L 301 ATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCT 252 chr1qtel1M 933358 CTCCCATACTTGTCATTTTTCTTTTCTGTAATATTAACCAATGTGATACA 933407 v vii i v vi v ivv i vv v vi i v i vi C L1ME4c_3end#L 251 CGCCAGCATTGGGTATTATCAATTTTTTAAATTTTTGCTAATTTAATAGG 202 chr1qtel1M 933408 TGTGAAG-GGT---TCCTTGGAACTTTTCTACTTTGCATTTCTCTATTTA 933453 i i i- --- v vvi --- v i iv C L1ME4c_3end#L 201 CGTAAAATGGTATCTCATTGTTGCTT---TAATTTGCATTTCTTTGATTA 155 chr1qtel1M 933454 ATA-----TTTACACCATTTTTCATGTG 933476 v -----v iv vv i C L1ME4c_3end#L 154 CTAGCGAGGTTGAACATTTTTCCATGTG 127 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 43.57 CpG sites = 90, Kimura (unadjusted) = 45.87 Transitions / transversions = 1.25 (90/72) Gap_init rate = 0.05 (23 / 499), avg. gap size = 1.83 (42 / 23) 608 30.34 7.03 2.83 chr1qtel1M 933054 933494 (66506) C L1ME3A_3end#LINE/L1 (355) 565 107 m_b53s551i7 1925 chr1qtel1M 933054 TTCTCATTGTACTACTATATTCCACTGCAATCATATGCCACAGCTTGTCC 933103 ivv ivi i iivvv i ii i ii C L1ME3A_3end#L 565 TTCTCATTGCTGTATAGTATTCCATTGTGTGAATATACCACAATTTATTT 516 chr1qtel1M 933104 AACTATTCTTGAATTGGTG-ACATCT---CAATTTCCAATTCTTTGCCAC 933149 v i vvvi i - i ---i?i i i??v i i C L1ME3A_3end#L 515 ATCCATTCTACTGTTGATGGACATTTGGGTNGTTTCCAGTTTNNGGCTAT 466 chr1qtel1M 933150 CACAAAAAGAGTTGCTGTAAATTTTTTTGTATACATATAGTTT--TGAAA 933197 i i v v i i i iv i -- i vv -- v C L1ME3A_3end#L 465 TACGAATAGTGCTGCTATGAACATTCTTGTA--CATGTCTTTTGGTGAAC 418 chr1qtel1M 933198 AT----------CTCTTTGAGATATAGACCTAGCCACAGGTATTGCTGGG 933237 ----------i v vi i v v- vv v C L1ME3A_3end#L 417 ATATGTACGCATTTCTGTTGGGTATATACCTAGG-AGTGGAATTGCTGGG 369 chr1qtel1M 933238 TCAAAGGGTATGCATA-GTTCTGAAGCCCTTTGG-ACAGAGTTCCAAATG 933285 v - --- -- i - v v v v ii C L1ME3A_3end#L 368 TCATAGGGTATGCATATGTTC---AG--CTTTAGTAGATACTGCCAAACA 324 chr1qtel1M 933286 GCTTTCTAGAATTGTTGAACCACTTCACATTTCTGCCAAGAGTACATTAG 933335 i i i i v v v i i i ii iv ii v C L1ME3A_3end#L 323 GTTTTCCAAAGTGGTTGTACCAATTTACACTCCCACCAGCAGTGTATGAG 274 chr1qtel1M 933336 TGTTCCAGATTTCCCATACCTTCTCCCATACTTGTCATTTTTCTTTTCTG 933385 v i v vii i i i v v i vi v iiv i i v C L1ME3A_3end#L 273 AGTTCCGGTTGCTCCACATCCTCGCCAACACTTGGTATTGTCTGTCTTTT 224 chr1qtel1M 933386 TAATATTAACCAATGTGATACATGTGAAG-GGT---TCCTTGGAACTTTT 933431 v v i v v i ivi v - ---? v vii--- C L1ME3A_3end#L 223 TCATTTTAGCCATTCTGGTGGGTGTGTAGTGGTATCNCATTGTGG---TT 177 chr1qtel1M 933432 CTACTTTGCATTTCTCT-AT--TTAAT--ATTT--ACACCATTTTTCATG 933474 i v i - --i -- v --i -- i C L1ME3A_3end#L 176 TTAATTTGCATTTCCCTGATGACTAATGAAGTTGAGCACC--TTTTCATA 129 chr1qtel1M 933475 TGACTA--AGCCCTTTACATAT 933494 vi --i v iv C L1ME3A_3end#L 128 TGTTTATTGGCCATTTGGATAT 107 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.66 CpG sites = 74, Kimura (unadjusted) = 40.47 Transitions / transversions = 1.32 (74/56) Gap_init rate = 0.06 (26 / 440), avg. gap size = 1.69 (44 / 26) 689 30.80 6.18 3.13 chr1qtel1M 933085 933456 (66544) C L1ME5_3end#LINE/L1 (407) 534 152 m_b53s551i8 1925 chr1qtel1M 933085 CATATGCCACAGCTTGTCCAACTATTCTTGAATTGGTG-ACATCTCAATT 933133 vii vi ii i v i i ivv v i - i ivii C L1ME5_3end#LI 534 CATCCACCACATTTTACCTATCCACTCTCCCAGTGATGGACACCCAGGTT 485 chr1qtel1M 933134 ---TCCAATTCTTTGCCACCACAAAAAGAGTTGCTGTAAATTTTTTTGTA 933180 --- i iii v iv i vi i iv ii i C L1ME5_3end#LI 484 GCCTCCAACTCCCCGCCACCACAAACAACGCTGCAATGAACATCCTCGTA 435 chr1qtel1M 933181 TA------CATATAG----TTTTGAAAATCTCTTTGAGATATAGACCTAG 933220 i ------ v i ----v v i i i v i C L1ME5_3end#LI 434 CATGTCCCCTTATGGACCTGTGTGAGAATTTCTTTGGGATATATACCCAG 385 chr1qtel1M 933221 CCACAGGTATTGCTGGGTCAAAGGGTATGCATAGTTCTGAAGCCCTTTGG 933270 vvi - v v i - v v ----- v C L1ME5_3end#LI 384 GAGC-GGAATTGCTGGGTCATAGGGTATGCGTA-TACTTAA-----TTTG 342 chr1qtel1M 933271 ACAGAG---TTCCAAATGGCTTTCTAGAATTGTTGAACCACTTCACATTT 933317 vi --- v i v i i v i v v ii i i C L1ME5_3end#LI 341 ACTAAGTACTGCCAGATTGCTCTCCAGAATGGCTGCACCAGTCTACACTC 292 chr1qtel1M 933318 CTGCCAAGAGTACATTAGTGTTCCAGATTTCCCATACCTTCTCCCATACT 933367 ii iv i v v viv? i i i i v v i C L1ME5_3end#LI 291 CCACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATCCTCGCCAACACT 242 chr1qtel1M 933368 TGTCATTTTTC--TTTTCTGTAATATTAACCAATGTGATACATGTGAAGG 933415 v v i --i -- v vi i v i vi i v C L1ME5_3end#LI 241 TGGCATTATCCAGCTTTC--TAATTTTTGCCAGTCTAATAGGTGTAAAGT 194 chr1qtel1M 933416 G----TTCCTTGGAACTTTTCTACTTTGCATTTCTCTATTTAATA 933456 ----i v ---i v i v iv v C L1ME5_3end#LI 193 GATATCTCATTG---TTGTTTTAATTTGCATTTCTCTGATTACTA 152 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.56 CpG sites = 64, Kimura (unadjusted) = 41.01 Transitions / transversions = 1.36 (64/47) Gap_init rate = 0.05 (19 / 371), avg. gap size = 1.84 (35 / 19) 928 29.67 5.46 2.74 chr1qtel1M 933484 934124 (65876) C L1M5_orf2#LINE/L1 (1360) 1934 1277 m_b53s551i9 1925 chr1qtel1M 933484 CCTTTACATATAATGCTTGTTGATGGTCGTAGAGAGATACTCCTTAACA- 933532 v vi i i ? i vv iv vviv i i i v - C L1M5_orf2#LIN 1934 CCATTAAGTATGATGTTNGCTGTAGGTTTTTCGTAGATGCCCTTTATCAG 1885 chr1qtel1M 933533 -TTTAAAAGGAAACCCCCATTTATTCCTATGCTCTCTAATTTTTTTTTTA 933581 - ---i iii v i - i iv i vvv v - C L1M5_orf2#LIN 1884 GTT---GAGGAAGTTCCCTTCTATTCCTA-GTTTGCTGAGAGTTTTTAT- 1840 chr1qtel1M 933582 ACAAAAATGGAATGTTATATTTGGTCAATAGGTTTTGCTGCATCAATTGA 933631 - vi i- iv v vv v v v C L1M5_orf2#LIN 1839 -CATGAATGGG-TGTTGAATTTTGTCAAATGCTTTTTCTGCATCTATTGA 1792 chr1qtel1M 933632 GATAATTTTACGATTTTTCTAAGTTTTAT------AATTTAGTTGATTAT 933675 i iv i v--i ------ v i vi i C L1M5_orf2#LIN 1791 GATGATCATATGATTTTTCTC--CTTTATTCTGTTAATATGGTGAATTAC 1744 chr1qtel1M 933676 ACTGACAGTTTTCCTAATATTGA--CAAAATCCCTATTTTCCTGGTATTA 933723 i iv v i v i i -- --- i iiv v -- C L1M5_orf2#LIN 1743 ATTGATTGATTTTCGAATGTTAAACCAA---CCTTGCATTCCTGGGAT-- 1699 chr1qtel1M 933724 TAGATCTCACCTGCTCCTAGGATATCATCCTGGTGATAAATTCTTGTAAT 933773 - i i i i v v iivi i vv v v vi v v C L1M5_orf2#LIN 1698 -AAACCCCACTTGGTCATGATGTATTATCCTTTTTATATATTGCTGGATT 1650 chr1qtel1M 933774 CTCTTTATTGATACTTTACTTAAAATTTTTGCATCAGTATTCTTTGGGAA 933823 vv ii i i ii ? ii vi i v vi i C L1M5_orf2#LIN 1649 CGATTTGCTAATATTTTGTTNAGGATTTTTGCATCTATGTTCATGAGGGA 1600 chr1qtel1M 933824 AATTGGTCTGTAATTTTCTTTTCTCTATTTTGGC-TTGTCGCAGTTTAAG 933872 v - i vv v - -?i vi C L1M5_orf2#LIN 1599 TATTGGTCTGTAATTTTCTTTTCT-TGTAATGTCTTTGTC-NGGTTTTGG 1552 chr1qtel1M 933873 GATCAGCATCTTAGTTGTGTCATAAAAGGAATTGGGCAGACTTGCATATT 933922 v vi ?v iv v iv v i v vv v v v C L1M5_orf2#LIN 1551 TATCAGGGTNATGCTGGCCTCATAAAATGAGTTGGGAAGTGTTCCCTCTT 1502 chr1qtel1M 933923 GT---------TGTAAGAGTTTAT------TTGGAATTAATTGTTCTTT- 933956 v --------- v i ------ v v v i - C L1M5_orf2#LIN 1501 TTTCTATTTTCTGGAAGAGTTTGTGTAAGATTGGTATTATTTCTTCCTTA 1452 chr1qtel1M 933957 AATGTTTGGCAGAATTCCCTTGT-ACTACATCAAGCCCTGGAACATTTTT 934005 i v iv - vvv vi v iiv i C L1M5_orf2#LIN 1451 AATGTTTGGTAGAATTCACCAGTGAAGCCATCTGGGCCTGGAGTTTTCTT 1402 chr1qtel1M 934006 CTTGGGGAGCTCACTGATGACTCGTTCCATTTCTTGTCCTAAA-ATGGGG 934054 iv i v ivi i v vvi v - vv i - i C L1M5_orf2#LIN 1401 TGTGGGAAGGTTTTTAATTACAAATTCAATTTCTT-TAATAGATATAGGG 1353 chr1qtel1M 934055 CTACTTAG-TATTTTATTTCCTCTTCCATTAATGTGGACAACTGGTATTT 934103 i i - v i i v?i i i v v ii ? v i C L1M5_orf2#LIN 1352 CTATTCAGATTTTCTATTTCTTCTTGNGTCAGTTTTGGTAANTTGTGTTT 1303 chr1qtel1M 934104 T---GGTCATT--TCCATTTCATCCA 934124 ---i vv -- i C L1M5_orf2#LIN 1302 TTCAAGGAATTTGTCCATTTCATCTA 1277 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 38.47 CpG sites = 91, Kimura (unadjusted) = 38.73 Transitions / transversions = 0.97 (91/94) Gap_init rate = 0.05 (31 / 640), avg. gap size = 1.71 (53 / 31) 346 30.36 5.47 4.95 chr1qtel1M 935042 935242 (64758) MIR1_Amn#SINE/MIR 4 205 (25) m_b53s601i2 1926 chr1qtel1M 935042 GGGGGCCGTGGGGTGTAGTGGGCAGAGCAGAGCCCTGAAGTCAGGGGGAC 935091 i v v v ii vv vv iiiiiv i MIR1_Amn#SINE 4 GGAGGCAGTGTGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGAGAC 53 chr1qtel1M 935092 CTGGATTCAAATCTGGCCTCAGACACCTAACGCGTCCTGGCTGTGGGGCC 935141 i ? ? iv v v v i?i------- i? ? v i MIR1_Amn#SINE 54 CTGGGTTCNANTCCCGGCTCTGCCACTNG-------CCNGCTGNGTGACC 96 chr1qtel1M 935142 CTGGGCAAGTCACTT----------AGCCCCAATTTCCTCAGGAAAGAAA 935181 i ----------? i i -vvviv MIR1_Amn#SINE 97 TTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCA-TCTGTAAA 145 chr1qtel1M 935182 ATGAAGGTGCATT-TACTGACCCACTAGATGTGCTGCCTGGAGCCTTTGT 935230 ii i i- v- iv vvi iviv i v vii vv MIR1_Amn#SINE 146 ATGGGGATA-ATGATACTGACCTCCTTTGTAAAGTGCTTTGAGATCTACT 194 chr1qtel1M 935231 GACTGAAGAGTG 935242 - i MIR1_Amn#SINE 195 GA-TGAAAAGTG 205 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 41.43 CpG sites = 31, Kimura (unadjusted) = 41.43 Transitions / transversions = 1.15 (31/27) Gap_init rate = 0.06 (12 / 200), avg. gap size = 1.75 (21 / 12) 430 22.73 8.46 5.22 chr1qtel1M 935043 935172 (64828) MIRb#SINE/MIR 5 138 (130) m_b53s601i3 1926 chr1qtel1M 935043 GGGGCCGTGGGGTGTAGTGGGCAGAGCA-GAGCCCTGAAGTCAGGGGGAC 935091 v i v i iv - i ii i ivi MIRb#SINE/MIR 5 GGGGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGAC 54 chr1qtel1M 935092 CTGGATTCAAATCTGGCCTCAGACACCTAACGCGTCCTGGCTGTGGGGCC 935141 i i iv v v v i ------- i v i MIRb#SINE/MIR 55 CTGGGTTCGAATCCCGGCTCTGCCACTTA-------CTAGCTGTGTGACC 97 chr1qtel1M 935142 CTGGGCAAGTCACTTA----------GCCCCAATTTCCTCA 935172 i i ---------- i i MIRb#SINE/MIR 98 TTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCA 138 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 25.71 CpG sites = 19, Kimura (unadjusted) = 28.03 Transitions / transversions = 2.11 (19/9) Gap_init rate = 0.07 (9 / 129), avg. gap size = 2.00 (18 / 9) 16 13.25 0.00 0.00 chr1qtel1M 935250 935274 (64726) (AC)n#Simple_repeat 1 25 (0) m_b53s252i6 1927 chr1qtel1M 935250 ACACACAGACACAGACACACACTCA 935274 v v v (AC)n#Simple_ 1 ACACACACACACACACACACACACA 25 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 13 14.85 5.13 2.50 chr1qtel1M 935624 935662 (64338) (CCAGCC)n#Simple_repeat 1 40 (0) m_b53s252i7 1928 chr1qtel1M 935624 CCAGCCCC-GCCCC-CTCCCAGCCCCATCCCAGGCTCCCAG 935662 - -vi v vi - (CCAGCC)n#Sim 1 CCAGCCCCAGCCCCAGCCCCAGCCCCAGCCCCAGC-CCCAG 40 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.08 (3 / 38), avg. gap size = 1.00 (3 / 3) 202 29.42 0.00 1.47 chr1qtel1M 937716 937784 (62216) MIRb#SINE/MIR 127 194 (74) m_b53s601i4 1926 chr1qtel1M 937716 TCAGCTTTTCTTGTCTGTTAAATATGTATAACAGTCCCTACCTCCTGTTG 937765 - i ii v iv v i i v viivv MIRb#SINE/MIR 127 TCAG-TTTCCTCATCTGTAAAATGGGGATAATAATACCTACCTCGCAGGG 175 chr1qtel1M 937766 CTCTTTGGAGGATAAAATG 937784 i v vv v MIRb#SINE/MIR 176 TTGTTGTGAGGATTAAATG 194 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 37.57 CpG sites = 9, Kimura (unadjusted) = 37.57 Transitions / transversions = 0.82 (9/11) Gap_init rate = 0.01 (1 / 68), avg. gap size = 1.00 (1 / 1) 256 32.69 0.79 8.47 chr1qtel1M 938475 938601 (61399) C L2c_3end#LINE/L2 (11) 467 350 m_b53s601i5 1929 chr1qtel1M 938475 CACCCAGCATTCCTTATGTACCTGCTCTGCATCAGATACAAAGCTCTGAG 938524 v v i iv iv ii i v iii ------- v i C L2c_3end#LINE 467 CAACAAACATTTATTGAGCGCCTACTATGTGCCAG-------GCGCTGGG 425 chr1qtel1M 938525 GATACAAAGAAAGGGAAATGACCATCCCAGATTCCCAAGAGCTCTCAACC 938574 viiiv ivv vi v viii v i v ii C L2c_3end#LINE 424 GATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTC 375 chr1qtel1M 938575 TAAGGGTAGAGGAGACAGA-ATGAAAAC 938601 --- i - ? v C L2c_3end#LINE 374 TA---GTGGAGGAGACAGACANGTAAAC 350 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 42.73 CpG sites = 22, Kimura (unadjusted) = 44.48 Transitions / transversions = 1.38 (22/16) Gap_init rate = 0.09 (11 / 126), avg. gap size = 1.00 (11 / 11) 15 11.64 3.33 3.33 chr1qtel1M 939147 939176 (60824) (TA)n#Simple_repeat 1 30 (0) m_b53s252i8 1930 chr1qtel1M 939147 TATACTA-AAATATATATATATATACACATA 939176 - - v i i (TA)n#Simple_ 1 TATA-TATATATATATATATATATATATATA 30 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.07 (2 / 29), avg. gap size = 1.00 (2 / 2) 411 25.33 1.59 12.28 chr1qtel1M 939493 939618 (60382) MIRc#SINE/MIR 2 115 (153) m_b53s601i6 1931 chr1qtel1M 939493 GAAGTAGTGTAGTGTAGTGGATAGAGCCCCAGCCCTGAAGTCAGGAGGAC 939542 i i i i v v ii v i i i MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr1qtel1M 939543 CTGA--TCAAACGGGGCCTCAGACACTTAGCATTTAACGTTTCTTGGTTG 939590 i-- i iivvv v v v --------------i i i MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTA--------------CTAGCTG 87 chr1qtel1M 939591 TGTGTCCTTGGGCAAGTTACTTAACCCC 939618 v i i MIRc#SINE/MIR 88 TGTGACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.01 CpG sites = 18, Kimura (unadjusted) = 31.36 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.12 (15 / 125), avg. gap size = 1.07 (16 / 15) 33 25.20 0.00 2.25 chr1qtel1M 939633 939723 (60277) (AAGG)n#Simple_repeat 1 89 (0) m_b53s252i9 1932 chr1qtel1M 939633 AAGAAAGAAAGGTAGGAAGGAAGGAAGGAAGGGGAGGTAGGGAGGGAGGG 939682 i i v - i v i i i (AAGG)n#Simpl 1 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAA-GGAAGGAAGGAAGGAAGGA 49 chr1qtel1M 939683 AGAAAAGGAGAGAGGGAAGGAGGAAAAAAAGGAAGCAATGA 939723 -i ii i i i ii v v (AAGG)n#Simpl 50 AG-GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 89 Matrix = Unknown Transitions / transversions = 3.50 (14/4) Gap_init rate = 0.02 (2 / 90), avg. gap size = 1.00 (2 / 2) 19 11.32 5.00 2.44 chr1qtel1M 939785 939824 (60176) (AC)n#Simple_repeat 1 41 (0) m_b53s252i11 1933 chr1qtel1M 939785 ACACACA-AAAGACACACACATAAACACA-ACACAGCACACA 939824 - v v i v - - (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACA-CACACA 41 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.08 (3 / 39), avg. gap size = 1.00 (3 / 3) 13 14.85 5.13 2.50 chr1qtel1M 940184 940222 (59778) (CCAGCC)n#Simple_repeat 1 40 (0) m_b53s252i12 1934 chr1qtel1M 940184 CCAGCCCC-GCCCC-CTCCCAGCCCCATCCCAGGCTCCCAG 940222 - -vi v vi - (CCAGCC)n#Sim 1 CCAGCCCCAGCCCCAGCCCCAGCCCCAGCCCCAGC-CCCAG 40 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.08 (3 / 38), avg. gap size = 1.00 (3 / 3) 13 9.69 9.09 0.00 chr1qtel1M 943024 943056 (56944) (AGAAAAT)n#Simple_repeat 1 36 (0) m_b53s252i13 1935 chr1qtel1M 943024 AGAAAACA-AAATTA-AAAATAGAAAA-AGTAAATA 943056 i - v - - v (AGAAAAT)n#Si 1 AGAAAATAGAAAATAGAAAATAGAAAATAGAAAATA 36 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.09 (3 / 32), avg. gap size = 1.00 (3 / 3) 30 22.63 2.53 0.00 chr1qtel1M 943051 943129 (56871) (TATA)n#Simple_repeat 1 81 (0) m_b53s252i14 1936 chr1qtel1M 943051 TAAATACATACACATATTTCCATATATATAT-TATATATGTATATATATA 943099 v i i i v vi - i (TATA)n#Simpl 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr1qtel1M 943100 CATAT-TGTATGTATGTATGTATGTAAATAT 943129 i - i i i i i v (TATA)n#Simpl 51 TATATATATATATATATATATATATATATAT 81 Matrix = Unknown Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.03 (2 / 78), avg. gap size = 1.00 (2 / 2) 24 23.14 2.82 1.39 chr1qtel1M 943072 943142 (56858) (ATGT)n#Simple_repeat 1 72 (0) m_b53s252i15 1936 chr1qtel1M 943072 ATATATATAT-TATATATGTATATATATACATATTGTATGTATGTATGTA 943120 i i - i i i ii - (ATGT)n#Simpl 1 ATGTATGTATGTATGTATGTATGTATGTATGTA-TGTATGTATGTATGTA 49 chr1qtel1M 943121 TGTAAATAT-TGCATATGTGTGT 943142 vi - iii i (ATGT)n#Simpl 50 TGTATGTATGTATGTATGTATGT 72 Matrix = Unknown Transitions / transversions = 12.00 (12/1) Gap_init rate = 0.04 (3 / 70), avg. gap size = 1.00 (3 / 3) 311 30.32 3.14 2.50 chr1qtel1M 943144 943302 (56698) L1MB7_3end#LINE/L1 415 574 (357) m_b53s551i10 1937 chr1qtel1M 943144 TATATACACACACACACTCACACATATGCAATATTTACAGCAGCCCT-TT 943192 i v v v iii ii--- i i i vi - L1MB7_3end#LI 415 TATGTCCACACAAAAACTTGTACACG---AATGTTCATAGCAGCATTATT 461 chr1qtel1M 943193 CATAGTAACCTCAAAAAGAAACCTAACTGATTG-CCATGCTTTCGTTGAA 943241 i i vv iv i v v v ii v - - vvii v L1MB7_3end#LI 462 CATAATAGCCAAAAAGTGGAAACAACCCAAATGTCCAT-CAACTGATGAA 510 chr1qtel1M 943242 CGGCTAAACAAATTGTGATATATTAACGTAATGGATTATTATTGTGCCAT 943291 i v v i iv iii v vv L1MB7_3end#LI 511 TGGATAAACAAAATGTGGTATATCCATACAATGGAATATTATTCGGCCAT 560 chr1qtel1M 943292 ---GAGACATGAAG 943302 ---i iv L1MB7_3end#LI 561 AAAAAGGAATGAAG 574 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 38.53 CpG sites = 26, Kimura (unadjusted) = 39.74 Transitions / transversions = 1.24 (26/21) Gap_init rate = 0.04 (7 / 158), avg. gap size = 1.29 (9 / 7) 332 25.52 4.20 1.36 chr1qtel1M 943165 943307 (56693) L1ME3A_3end#LINE/L1 430 576 (344) m_b53s551i11 1937 chr1qtel1M 943165 ACATATGCAA---TATTTACAGCAGCCCT-TTCATAGTAACCTCAAAAAG 943210 i i --- i i i v - i i i ?? vv L1ME3A_3end#L 430 ACATGTACAAGAATGTTCATAGCAGCACTATTCGTAATAGCCNNAAACTG 479 chr1qtel1M 943211 AAACCTAACTGATTG-CCATGCTTTCGTTGAACGGCTAAACAAATTGTGA 943259 i v ? v ii v - - vviv v i v i i L1ME3A_3end#L 480 GAAACNACCCAAATGTCCAT-CAACAGTAGAATGGATAAATAAATTGTGG 528 chr1qtel1M 943260 TATATTAACGTAATGGATTATTATTGTGCCATGAGACATGAA-GAAATA 943307 v ii v i vvv v - - v L1ME3A_3end#L 529 TATATTCACACAATGGAATACTATACAGCAATGAGA-ATGAACGAACTA 576 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 31.32 CpG sites = 18, Kimura (unadjusted) = 32.38 Transitions / transversions = 1.00 (18/18) Gap_init rate = 0.04 (6 / 142), avg. gap size = 1.33 (8 / 6) 594 28.33 10.00 2.11 chr1qtel1M 944103 944322 (55678) C MIRc#SINE/MIR (8) 260 24 m_b53s601i7 1938 chr1qtel1M 944103 TAACAGCTAGTAGTTATATGGTGTTTTAAACGTTT--------TTTTCAC 944144 ?v vii v i i iii v - --------i C MIRc#SINE/MIR 260 TAACNCCTTACATTTGTATAGCACTTTACA-GTTTACAAAGCGCTTTCAC 212 chr1qtel1M 944145 ACTTTTTTATCT--TTTGGTTTTCACAAAAACTGAGTGA----------- 944181 - viv -- i ii v ivv ----------- C MIRc#SINE/MIR 211 A-TACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGG 163 chr1qtel1M 944182 -AGGTGTTGCTACTTTAGAGATTGTACAAATAAGGAAACTGAGGTTGGAA 944230 - i ii iiiiv--- v i i i vii C MIRc#SINE/MIR 162 CAGGTATTATTATCCCC---ATTTTACAGATGAGGAAACTGAGGCTCAGA 116 chr1qtel1M 944231 GAAGTTAAGTATCTTTCTCAAGGTCACATGAATAGTAAGTGTATGAGGCA 944280 i iv v i iiiv vvv v i C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 66 chr1qtel1M 944281 GGATCTAAACTAAGATCTTTATGACTCCAAGTACAGTGCTCT 944322 iiii iv i iv v C MIRc#SINE/MIR 65 GGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCT 24 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 35.60 CpG sites = 39, Kimura (unadjusted) = 37.24 Transitions / transversions = 1.77 (39/22) Gap_init rate = 0.04 (9 / 219), avg. gap size = 3.00 (27 / 9) 350 29.01 4.84 4.56 chr1qtel1M 945839 946210 (53790) C HERVK14C#LTR/ERVK (2333) 5101 4729 m_b53s701i0 1939 chr1qtel1M 945839 CTTCCTCTTTCTTTTGTTTTTGGAG--GAATATCTTAATATCTCTGTT-T 945885 ii i v v i-- i?- i vi - vi -v C HERVK14C#LTR/ 5101 CCCCTTCTGTCTTTTGTTTTTGTAATTGAGN-TTTTAAGGT-TCGATTAG 5054 chr1qtel1M 945886 CTCCTCTCTATTATTGCCTGTACTTGAGAATTAAAAGATATGCCAATGGT 945935 v - v iv v i ?v v i iv ? i i? C HERVK14C#LTR/ 5053 CTCGT-TCAACAATGGCTTGNCCTTGAGAATTATAGGGGATNCCAGTANT 5005 chr1qtel1M 945936 GTG-AAAATCTTGTACTGTGCACAAAAATGTGCA-AAATGTTTAGAAGTA 945983 -vv v ?vi i vv - ii i i?i?- v? vv ??i C HERVK14C#LTR/ 5004 GTGTTTAATGTNCCATTGTTGA-AGGAACGCNTNTAAAGNTTTACTANNG 4956 chr1qtel1M 945984 TATGCAGGTCCATTGTCTGTTTTTATGTCTTGTAACACACCCATAATTGC 946033 vv v v ? v ? i iiv ii i i? C HERVK14C#LTR/ 4955 TAGCCTGGGCCATTGTCNGTTTTAATNTTTTGTGGAATGCCCATGACNGC 4906 chr1qtel1M 946034 AAATGCTTGGATATGGAAT-TCAGTGACCAC--TCAGGCTGTCTCTTTTG 946080 i --viv v vvi - vv v v --v - ? i ?ii C HERVK14C#LTR/ 4905 GAA--ACAGGAAAGCAAATGTCTTTTAACACGAGCA-GCNGCCTCNCCTG 4859 chr1qtel1M 946081 CGGCTGGCA--TGGC-----AAAAGTGAATCCTGAAAACGTGTCTAGAAC 946123 i--i -- ? -----v i ----- v i v ii C HERVK14C#LTR/ 4858 T--TTGGCAAGTNGCCCANACAAAATGA-----GAAAAGGTATCTACAGT 4816 chr1qtel1M 946124 AACATGGATAAAAGACAGACGACCAAA---AGATTTATGATAGGTCACAT 946170 ? iiv ? ? vivv --- i vi --- ? i C HERVK14C#LTR/ 4815 NACATGGACGTANGANAGTTTCCCAAATGNAGGTACATG---GGTNACGT 4769 chr1qtel1M 946171 TCATTTGCCAAATTTCATTGGGTCTCAAAACATGAGGGTT 946210 i ? viv? i ?vi vv vi ? C HERVK14C#LTR/ 4768 CCATTTGCCANAGCGNATTAGGNGCCAATCCTCGNGGGTT 4729 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 37.76 CpG sites = 52, Kimura (unadjusted) = 40.79 Transitions / transversions = 1.02 (52/51) Gap_init rate = 0.07 (26 / 371), avg. gap size = 1.35 (35 / 26) 119 10.81 6.01 0.82 chr1qtel1M 947340 947572 (52428) (AGAGAC)n#Simple_repeat 1 245 (0) m_b53s252i16 1940 chr1qtel1M 947340 AGAGCCAGAGAC--ACACAGAGGCAG-G-CAGAGAC--AGACAGAGAC-- 947381 v -- v i - - -- -- (AGAGAC)n#Sim 1 AGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAG 50 chr1qtel1M 947382 AGACAAAGACAGAGGGAAACACAGAGACAGAGACAGAGGCAGAGAC--AG 947429 i iv i v i -- (AGAGAC)n#Sim 51 AGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAG 100 chr1qtel1M 947430 ACAGAGACAGAGGCAAACACAGATACAGAGACAGAGACAGAGACAGAGAC 947479 i i v v (AGAGAC)n#Sim 101 ACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGAC 150 chr1qtel1M 947480 --ACACAGAGACAGGGAGAGACGGACAGAGAC--AGACAAAGACAGAGGC 947525 -- v i v -- -- i i (AGAGAC)n#Sim 151 AGAGACAGAGACAGAGACAGA--GACAGAGACAGAGACAGAGACAGAGAC 198 chr1qtel1M 947526 AAACACAGAGACAGAGACAGAGACAGAGACAGAGACAGACAGAGGGA 947572 i v v v i (AGAGAC)n#Sim 199 AGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGA 245 Matrix = Unknown Transitions / transversions = 1.09 (12/11) Gap_init rate = 0.04 (10 / 232), avg. gap size = 1.60 (16 / 10) 383 28.80 5.45 5.45 chr1qtel1M 948170 948371 (51629) MIR1_Amn#SINE/MIR 4 205 (25) m_b53s601i8 1941 chr1qtel1M 948170 GGGGGCCGTGGGGTGTAGTGGGCAGAGCCCAGCCCTGAAGTCAGGGGGAC 948219 i v v v ii v v vv iiiiiv i MIR1_Amn#SINE 4 GGAGGCAGTGTGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGAGAC 53 chr1qtel1M 948220 CCGAGTTCAAATCCGGCCTCAGACACCTAACACTTCCTGGCTGTGGGACC 948269 i i ? ? v v ------- iv ?v i? ? v MIR1_Amn#SINE 54 CTGGGTTCNANTCCCGGCT-------CTGCCACTNGCCNGCTGNGTGACC 96 chr1qtel1M 948270 CTGGGCAAGTCACTT----------AGCCCCAATTTCCTCAGGAAAGAAA 948309 i ----------? i i v--vv v MIR1_Amn#SINE 97 TTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCAT--CTGTAA 144 chr1qtel1M 948310 AATGAAGGTGCATT-TACTGACCCACTAGATGTGCTGCCTGGAGCCTTTG 948358 ii i i- v- iv vvi iviv i v vii vv MIR1_Amn#SINE 145 AATGGGGATA-ATGATACTGACCTCCTTTGTAAAGTGCTTTGAGATCTAC 193 chr1qtel1M 948359 TGACTGAAGAGTG 948371 - i MIR1_Amn#SINE 194 TGA-TGAAAAGTG 205 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 38.40 CpG sites = 28, Kimura (unadjusted) = 38.40 Transitions / transversions = 1.04 (28/27) Gap_init rate = 0.06 (13 / 201), avg. gap size = 1.69 (22 / 13) 448 21.91 8.46 5.22 chr1qtel1M 948171 948300 (51700) MIRc#SINE/MIR 2 135 (133) m_b53s601i9 1941 chr1qtel1M 948171 GGGGCCGTGGGGTGTAGTGGGCAGAGC-CCAGCCCTGAAGTCAGGGGGAC 948219 i v v i iv - ii v i i ii MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr1qtel1M 948220 CCGAGTTCAAATCCGGCCTCAGACACCTAACACTTCCTGGCTGTGGGACC 948269 i i i i v v ------- iv v i v MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTC-------TGCCACTTACTAGCTGTGTGACC 94 chr1qtel1M 948270 CTGGGCAAGTCACTTA----------GCCCCAATTTCCTCA 948300 i ---------- i i MIRc#SINE/MIR 95 TTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCA 135 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 25.59 CpG sites = 18, Kimura (unadjusted) = 26.73 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.07 (9 / 129), avg. gap size = 2.00 (18 / 9) 16 13.25 0.00 0.00 chr1qtel1M 948379 948403 (51597) (AC)n#Simple_repeat 1 25 (0) m_b53s252i17 1942 chr1qtel1M 948379 ACACACAGACACAGACACACACTCA 948403 v v v (AC)n#Simple_ 1 ACACACACACACACACACACACACA 25 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 15 10.85 3.33 0.00 chr1qtel1M 948753 948782 (51218) (CCAGCC)n#Simple_repeat 1 31 (0) m_b53s252i18 1943 chr1qtel1M 948753 CCAGCCCC-GCCCCCTCCCCAGCCCCATCCC 948782 - vv v (CCAGCC)n#Sim 1 CCAGCCCCAGCCCCAGCCCCAGCCCCAGCCC 31 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 41 15.61 0.00 2.47 chr1qtel1M 949819 949901 (50099) (TATA)n#Simple_repeat 1 81 (0) m_b53s252i19 1944 chr1qtel1M 949819 TATTTATATCCTTTATATATATTTATTTATATATATATATATATATTTAT 949868 v -v v v v v (TATA)n#Simpl 1 TATATATAT-ATATATATATATATATATATATATATATATATATATATAT 49 chr1qtel1M 949869 ATATTTATTTATATCCTTTATATATATTTATAT 949901 v v -v v v (TATA)n#Simpl 50 ATATATATATATAT-ATATATATATATATATAT 81 Matrix = Unknown Transitions / transversions = 0.00 (0/11) Gap_init rate = 0.02 (2 / 82), avg. gap size = 1.00 (2 / 2) 259 30.48 2.86 0.00 chr1qtel1M 952895 952999 (47001) C HERVK11#LTR/ERVK (6646) 1307 1200 m_b53s701i1 1945 chr1qtel1M 952895 GTTCCAGTCATCAGGAGTCAA---GACTTCGAAAGCCAAATTCTGTAACA 952941 i vvv iv --- i iiv vvv v i i C HERVK11#LTR/E 1307 GTCCCAGTCTAAAGGAAGCAAAATGACCTCAGTACAAAAAGTTTGTAATA 1258 chr1qtel1M 952942 GCATCTTAACATAAGCTGATGTAGCCCCATAATTAGTGCAGGCCTTTTTA 952991 v i vv v vv v v i i v ii C HERVK11#LTR/E 1257 CCATTTTAACATAAGGAGAAGTAGGACCATACTGAGTACAAGCATCCTTA 1208 chr1qtel1M 952992 AGATCTTT 952999 iv C HERVK11#LTR/E 1207 AATTCTTT 1200 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.21 CpG sites = 13, Kimura (unadjusted) = 39.21 Transitions / transversions = 0.68 (13/19) Gap_init rate = 0.01 (1 / 104), avg. gap size = 3.00 (3 / 1) 216 33.18 0.61 13.10 chr1qtel1M 954039 954201 (45799) L2#LINE/L2 2608 2752 (330) m_b53s601i10 1946 chr1qtel1M 954039 TTATTAAATCTTGCTTGAATTCACCTTCATAGCATCTCTTATATCCTATA 954088 i vi i - i iv ii v ii v iviv v iv L2#LINE/L2 2608 TCAGCAAATCCTG-TCGGCTCTACCTTCAAAATATATCCAGAATCCGACC 2656 chr1qtel1M 954089 AGAAGGATATACCTTCTTATTTCCCCTGGCCCTGCTACCACCCTGGT-AG 954137 ----------- i iiv i --- v i -vi L2#LINE/L2 2657 A-----------CTTCTCACCACCTC---CACTGCCACCACCCTGGTCCA 2692 chr1qtel1M 954138 AGACACTCTCATCACTTCACACTTGGACTACTACAACATCCTGGTAATTT 954187 v --- ii v i i i i i v vv -i L2#LINE/L2 2693 AGCCAC---CATCATCTCTCGCCTGGATTACTGCAATAGCCTCCTAA-CT 2738 chr1qtel1M 954188 GGTTTTCTTTTTTC 954201 i i i vi L2#LINE/L2 2739 GGTCTCCCTGCTTC 2752 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 42.37 CpG sites = 30, Kimura (unadjusted) = 44.99 Transitions / transversions = 1.76 (30/17) Gap_init rate = 0.12 (20 / 162), avg. gap size = 1.00 (20 / 20) 234 18.97 0.00 7.55 chr1qtel1M 954458 954514 (45486) C L1M2_orf2#LINE/L1 (2407) 884 832 m_b53s551i12 1947 chr1qtel1M 954458 AGGACTGCTTTGGCTGTAGCCCATAAACTTTGGCATGTTTTTTTAATTGC 954507 ? v v iii i v ----i v C L1M2_orf2#LIN 884 AGNACTGCTTTTGCTGTATCCCATAGGTTTTGGTATGTTGT----GTTTC 839 chr1qtel1M 954508 TATTTTC 954514 i C L1M2_orf2#LIN 838 CATTTTC 832 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 22.56 CpG sites = 6, Kimura (unadjusted) = 22.56 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.07 (4 / 56), avg. gap size = 1.00 (4 / 4) 240 23.00 2.94 1.94 chr1qtel1M 954948 955049 (44951) C L1MC4_5end#LINE/L1 (16) 2539 2437 m_b53s551i13 1948 chr1qtel1M 954948 TGGATGCTATACTACTTGTTGCAAAAATATTAGTATTAACATTACACC-- 954995 ? ? ii i v v ? -- v vii i i -- C L1MC4_5end#LI 2539 TGGNTGCTNTGTTATTTGGTGCATANATATT--TATAATTGTTATATCTT 2492 chr1qtel1M 954996 -ATTGCCTATAGGGCCCTTCAGTAAGATGTAGTTTCCTTCTTTGTCTCTT 955044 - ivv v ??? i ?i vv iv i v? ? C L1MC4_5end#LI 2491 CATTGTGAATTGNNNCCTTTANCATTATAAAATGNCCTTCTTTGTCTCNT 2442 chr1qtel1M 955045 TTAAT 955049 C L1MC4_5end#LI 2441 TTAAT 2437 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 31.19 CpG sites = 12, Kimura (unadjusted) = 31.19 Transitions / transversions = 1.09 (12/11) Gap_init rate = 0.04 (4 / 101), avg. gap size = 1.25 (5 / 4) 236 30.40 0.00 0.98 chr1qtel1M 955545 955647 (44353) C L1M1_orf2#LINE/L1 (3046) 248 147 m_b53s551i14 1947 chr1qtel1M 955545 TCTGTTTTGTGTGAGATTAGGATTTCGACCCCTGCTCTTTATTACTTCAC 955594 i v v v v vv v i v iv i- C L1M1_orf2#LIN 248 TCTATTTTGTCTGATATAAGTATAGCTACTCCTGCTCTTTTTTGGTTT-C 200 chr1qtel1M 955595 CGGAAGCAGAGCATCTCCTATTCCAGCCCTTTGCCTTTATTCTGTGTGTA 955644 ivvi vi v v i v v iii i v i i C L1M1_orf2#LIN 199 CATTGGCATGGAATATCTTTTTCCATCCCTTTATTTTCAGTCTATGTGTG 150 chr1qtel1M 955645 TCT 955647 C L1M1_orf2#LIN 149 TCT 147 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.23 CpG sites = 14, Kimura (unadjusted) = 39.23 Transitions / transversions = 0.82 (14/17) Gap_init rate = 0.01 (1 / 102), avg. gap size = 1.00 (1 / 1) 242 12.50 0.00 0.00 chr1qtel1M 955545 955584 (44416) C L1PREC2_orf2#LINE/L1 (3046) 248 209 m_b53s551i15 1947 chr1qtel1M 955545 TCTGTTTTGTGTGAGATTAGGATTTCGACCCCTGCTCTTT 955584 v i v i i C L1PREC2_orf2# 248 TCTGTTTTGTCTGAAATTAGGATTGCAACCCCTGCTTTTT 209 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 13.79 CpG sites = 3, Kimura (unadjusted) = 13.79 Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 374 30.53 4.21 0.00 chr1qtel1M 956946 957135 (42865) C L1PA14_3end#LINE/L1 (584) 324 127 m_b53s551i16 1949 chr1qtel1M 956946 TGCTTTCTCGAATTGTTGAACCACTTCACATTTTTGCCAAGACTACATTA 956995 ivv v i v i i iiii v v ii v C L1PA14_3end#L 324 TGCTTTCCACAATGGTTGAACTAATTTACACTCCCACCAACAGTGTATAA 275 chr1qtel1M 956996 GTGCCCCAGTTTCTC-ATATCATCTCCCACACCTGTCATTTTTT--TTCT 957042 ii vv -ii v v v vi i i --i i C L1PA14_3end#L 274 GTGTTCCCTTTTCTCCGCAACCTCGCCAGCATCTGTTATTTTTTGACTTT 225 chr1qtel1M 957043 GTAATATTAGCCAATCAGATAGGTGTGA-AGGGTTCCTCAGATTTCTTCT 957091 v v v v iv - v vi vvv vv i C L1PA14_3end#L 224 TTAATAATAGCCATTCTGACTGGTGTGAGATGGTATCTCATTGTGGTTTT 175 chr1qtel1M 957092 ACACTACATTTCTCTATTGAATAGTTA----GACCTTTTTTTCATGTG 957135 ivvi i v vi v ---- v i C L1PA14_3end#L 174 GATTTGCATTTCTCTAATGATCAGTGATATTGAGCTTTTTTTCATATG 127 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 38.68 CpG sites = 27, Kimura (unadjusted) = 39.53 Transitions / transversions = 0.87 (27/31) Gap_init rate = 0.02 (4 / 189), avg. gap size = 2.00 (8 / 4) 619 27.93 9.92 1.80 chr1qtel1M 957252 957765 (42235) C L1M5_orf2#LINE/L1 (1485) 1809 1255 m_b53s551i17 1950 chr1qtel1M 957252 TTTTGCTGCATCAATTGAGATAATCATATGATTT----CCTGTTAGTTTG 957297 v v i ---- - v i C L1M5_orf2#LIN 1809 TTTTTCTGCATCTATTGAGATGATCATATGATTTTTCTCCT-TTATTCTG 1761 chr1qtel1M 957298 T-AGTTTAGTTAATTATATTGACAGTTTTCCTAATACTGAA--AACATCC 957344 - i v i v i iv v i v ii i -- v iv C L1M5_orf2#LIN 1760 TTAATATGGTGAATTACATTGATTGATTTTCGAATGTTAAACCAACCTTG 1711 chr1qtel1M 957345 CGTTCTCTTGAT------CACCTTGTCCTAGTGTATTAT--------TGT 957380 i iivv ------ i v v ii -------- i C L1M5_orf2#LIN 1710 CATTCCTGGGATAAACCCCACTTGGTCATGATGTATTATCCTTTTTATAT 1661 chr1qtel1M 957381 ATTGGTCCCTTAATCTC--TTTGCTAATACTTTACTTAAATTTTTTGCAT 957428 ---- vi - -- i ii ? iiv C L1M5_orf2#LIN 1660 ATTG----CTGGAT-TCGATTTGCTAATATTTTGTTNAGGATTTTTGCAT 1616 chr1qtel1M 957429 CAGGATTCTTTGGGAAAGTTGGTCTGTCATTTTCTTTTCTCGATTTTGGC 957478 vivi v vi i vi v i - vv v C L1M5_orf2#LIN 1615 CTATGTTCATGAGGGATATTGGTCTGTAATTTTCTTTTCTTG-TAATGTC 1567 chr1qtel1M 957479 TTGTCCCAGTTTACGTTTCAGCATCTTAATTGTGTCATAAAAGGAACTAG 957528 vvi ?i vv v vi ?v iv v iv v ii i C L1M5_orf2#LIN 1566 TTTGTCNGGTTTTGGTATCAGGGTNATGCTGGCCTCATAAAATGAGTTGG 1517 chr1qtel1M 957529 GGAGACTCCCATATTTTTCT---------AATAGTTTAT------TTGGA 957563 i vv i v v --------- v i ------ v C L1M5_orf2#LIN 1516 GAAGTGTTCCCTCTTTTTCTATTTTCTGGAAGAGTTTGTGTAAGATTGGT 1467 chr1qtel1M 957564 ATTCATTGTTCTTT-AATGTTTGGCAGAATTCCCTTGT-ACTACATCAAG 957611 vv v i - i v iv - vvv vi C L1M5_orf2#LIN 1466 ATTATTTCTTCCTTAAATGTTTGGTAGAATTCACCAGTGAAGCCATCTGG 1417 chr1qtel1M 957612 CCCTGGAACTTATGTTTCTTGGGAA--TACTTGATGACTTGTTCCATTTC 957659 v ii - v -v -- vi i v vvi v C L1M5_orf2#LIN 1416 GCCTGGAGTTT-TCTTT-GTGGGAAGGTTTTTAATTACAAATTCAATTTC 1369 chr1qtel1M 957660 TTGTACTAAA-ATGGGGCCAATTAAGTGTTTTGCTTCCTCTTCTGCTACT 957708 - v i - i i v i ii v i ii i v? ii v C L1M5_orf2#LIN 1368 TT-TAATAGATATAGGGCTATTCAGATTTTCTATTTCTTCTTGNGTCAGT 1320 chr1qtel1M 957709 GTGGACAACTGGTATTTT----GGTCCTT-TCCATTTCATCCA---TTTC 957750 v v ii ? v i ---- vvi - i --- ? C L1M5_orf2#LIN 1319 TTTGGTAANTTGTGTTTTTCAAGGAATTTGTCCATTTCATCTAAGTTNTC 1270 chr1qtel1M 957751 TATTTCATTGTCACA 957765 v v i v i C L1M5_orf2#LIN 1269 AAATTTATTGGCATA 1255 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 35.91 CpG sites = 69, Kimura (unadjusted) = 35.91 Transitions / transversions = 0.96 (69/72) Gap_init rate = 0.05 (25 / 513), avg. gap size = 2.44 (61 / 25) 12 13.21 5.71 2.78 chr1qtel1M 958373 958407 (41593) (CAGA)n#Simple_repeat 1 36 (0) m_b53s252i20 1951 chr1qtel1M 958373 CAGAGACACAGGCAG--AGACAGGCGAGACAGACAGA 958407 v v i -- i - (CAGA)n#Simpl 1 CAGACAGACAGACAGACAGACAGAC-AGACAGACAGA 36 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.50 (3 / 2) 455 23.91 1.77 7.48 chr1qtel1M 959007 959119 (40881) MIRc#SINE/MIR 8 114 (154) m_b53s601i11 1952 chr1qtel1M 959007 GTGTGGTGTAGTGGGCAGAGCA-GAGCCCTGAAGTCAGGAGGACTTGAGT 959055 i iv -vi v i i i i i MIRc#SINE/MIR 8 GTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGT 57 chr1qtel1M 959056 TCAAATCT-AGCTTCAGACACCTAACACTTCCTCACTGTGTGACTCTGGA 959104 i i i-i -------- iv v vi ii i MIRc#SINE/MIR 58 TCGAGTCCCGGCT--------CTGCCACTTACTAGCTGTGTGACCTTGGG 99 chr1qtel1M 959105 CAAGTCACTTCACTT 959119 v i MIRc#SINE/MIR 100 CAAGTCACTTAACCT 114 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 27.10 CpG sites = 18, Kimura (unadjusted) = 29.92 Transitions / transversions = 2.57 (18/7) Gap_init rate = 0.09 (10 / 112), avg. gap size = 1.00 (10 / 10) 61 0.00 3.39 0.00 chr1qtel1M 959699 959757 (40243) (AC)n#Simple_repeat 1 61 (0) c_b53s251i0 1953 chr1qtel1M 959699 ACACACACACACACACACACACACACACACACAC-CACACACACACACAC 959747 - (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50 chr1qtel1M 959748 A-ACACACACA 959757 - (AC)n#Simple_ 51 ACACACACACA 61 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.03 (2 / 58), avg. gap size = 1.00 (2 / 2) 14 30.86 0.00 3.08 chr1qtel1M 962497 962563 (37437) (ATAAAAA)n#Simple_repeat 1 65 (0) m_b54s252i0 1954 chr1qtel1M 962497 ATAAAAACAGAAAAATACACAAACAATATTTTTAAAAAAAGAGAAAACAA 962546 vvi - v i - vvv v v i i v v (ATAAAAA)n#Si 1 ATAAAAAATAAAAAATA-AAAAATAA-AAAATAAAAAATAAAAAATAAAA 48 chr1qtel1M 962547 TATAAAAAATTAAAAAT 962563 v v (ATAAAAA)n#Si 49 AATAAAAAATAAAAAAT 65 Matrix = Unknown Transitions / transversions = 0.33 (4/12) Gap_init rate = 0.03 (2 / 66), avg. gap size = 1.00 (2 / 2) 17 13.96 0.00 0.00 chr1qtel1M 963447 963478 (36522) (CTTTCC)n#Simple_repeat 1 32 (0) m_b54s252i1 1955 chr1qtel1M 963447 CTTTCCCTTTCTCTTTTCCTTCCCCATTCCCT 963478 i i i v (CTTTCC)n#Sim 1 CTTTCCCTTTCCCTTTCCCTTTCCCTTTCCCT 32 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 303 33.29 4.10 5.17 chr1qtel1M 963801 964386 (35614) C L1ME4c_3end#LINE/L1 (221) 609 30 m_b54s551i0 1956 chr1qtel1M 963801 AGACAGTTTTCATGTT-TTACTGAAATCTTCATGCTCGCCATTTCTTATT 963849 i v i -i -iv i iv iii i v v C L1ME4c_3end#L 609 AAACATTTTCCATGTTGCTAC-ATAGTCTTCATAATTATCATTTTTAATG 561 chr1qtel1M 963850 GCACAATATTATTCCATTTA--CAATCCTGTGCCTCCAATTTCATTCAAC 963897 vvv v iv --?i --- i -vi - i i C L1ME4c_3end#L 560 GCTGCATAATATTCCATCGAGTNGAT---GTACC-ATAATTT-ACTTAAC 516 chr1qtel1M 963898 TGTTATTCTTGAATTGGCGGACATCT----TAATTTCAATTCTT-GCCAC 963942 ii vii --- vi i ---- iv i i - i i C L1ME4c_3end#L 515 CATTCCCCT---ATTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTAT 469 chr1qtel1M 963943 CACAAAGAGTTTATATGATAAGCATTTTTGTACACATACATTTTCCCCTC 963992 i i v iivi- iii i i i i i i vv i i C L1ME4c_3end#L 468 TATAAATAACGC-TGCAATGAACATCTTCGTGCATATAGCTTTTTCCTTC 420 chr1qtel1M 963993 TTTAAAA--ATCTCAT--GGATATGAACTACAATCAGATATAGACCTGTT 964038 vi -- i v -- -- i v --- vi i vi i-- C L1ME4c_3end#L 419 TTTTGAATTATTTCCTTAGGATA--AATTCC---CAGAAGTGGAATTA-- 377 chr1qtel1M 964039 CTGGAACAAGAAATTTACTCACAGTTCACAAAGAAGCCCTTTGGACATAG 964088 iv iiii v ivv i-v i ii----- i viv i v C L1ME4c_3end#L 376 CTGGGTCAAAGGGTATGAACAT-TTTTATG-----GCTCTTGATACGTAT 333 chr1qtel1M 964089 TTCCAAATGAAACTTTCTCAA----TTACGAACTGCTTCACATTTCTACC 964134 v vi-- iv ---- -- v iiv i ? v i C L1ME4c_3end#L 332 TGCCAAATTG--CTTTCCAAAAGGGTT--GTACCAATTTACANTGCCACC 287 chr1qtel1M 964135 AAGGACTATATAAAT-TACCAATTTC-CCATACACTCTCCCATATTTGTC 964182 - v v i i i?- i - ii ?v v vii v vi C L1ME4c_3end#L 286 A-GCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGCATTGGGT 238 chr1qtel1M 964183 CTTCTTTTTTTCTGTAATATTAGCCAATCTGATAGGTGTGAAG-GGTTCC 964231 v v ivv i vv v v i i i i i i- vi C L1ME4c_3end#L 237 ATTATCAATTTTTTAAATTTTTGCTAATTTAATAGGCGTAAAATGGTATC 188 chr1qtel1M 964232 TCAGAGTTGTTCTACTTTGCATTTCTCT-ATT-CAATC---GTTAGACCA 964276 vv i i v i - - v v --- - v C L1ME4c_3end#L 187 TCATTGTTGCTTTAATTTGCATTTCTTTGATTACTAGCGAGGTT-GAACA 139 chr1qtel1M 964277 TTTTTTTCAAGTGACTATAGGTAGCTTTAATTTCTTCTTCAGAAAATCAC 964326 - i v vi i vviivi? vv i ?v vi iii C L1ME4c_3end#L 138 -TTTTTCCATGTGTTTGTTTACTANTTGTATTTCCTCTTNTGTGAATTGT 90 chr1qtel1M 964327 CTGTTCATCTTCTTTAAGAATTTGTCAATTGGGGAATGGCTTTTATTTTT 964376 v i ivvv i v vv v v ? v i C L1ME4c_3end#L 89 CTGTTCATGTCCTTTGCCCATTTATCTATTGGGGTCTTGATNTTTTTCTT 40 chr1qtel1M 964377 ATAAATCTGA 964386 v i C L1ME4c_3end#L 39 ATCAATTTGA 30 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 44.19 CpG sites = 106, Kimura (unadjusted) = 46.24 Transitions / transversions = 1.34 (106/79) Gap_init rate = 0.07 (43 / 585), avg. gap size = 1.26 (54 / 43) 393 30.50 4.11 2.90 chr1qtel1M 964072 964412 (35588) C L1PA15_3end#LINE/L1 (564) 348 4 m_b54s551i1 1956 chr1qtel1M 964072 AAGCCCTTTG-GACATAGTTCCAAA-TGAAACTTTCT-CAATTAC-GAAC 964117 ii - v v -- - --- i- i vi - C L1PA15_3end#L 348 AAGTTCTTTGAGAAATCG--CCAAACTG---CTTTCCACAGTGGCTGAAC 304 chr1qtel1M 964118 TGCTTCACATTTCTACCAAGGACTATATAAA--TTACCAATTTCCCATAC 964165 iv i i i - v v i i-- v vv ii ii v C L1PA15_3end#L 303 TAATTTACATTCCCACCA-GCAGTGTATAAGCGTTCCCTTTTCTCCGCAA 255 chr1qtel1M 964166 ACTCTCCCATATTTGTCCTTCTTTTTTTCTGTAATATTAGCCAATCTGAT 964215 v v vii i iv i vvi i v v v i C L1PA15_3end#L 254 CCTCGCCAGCATCTGTTATTTTTTGACTTTTTAATAATAGCCATTCTGAC 205 chr1qtel1M 964216 AGGTGTGA-AGGGTTCCTCAGAGTTGTTCTACTTTGCATTTCTCTATTCA 964264 v - v vi vv v i iv v v C L1PA15_3end#L 204 TGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTAATGA 155 chr1qtel1M 964265 ATCGTTA----GACCATTTTTTTCAAGTGACTATAGGTAGCTTTAATTTC 964310 v v v ---- v - vi vi i v iv v vv v C L1PA15_3end#L 154 TTAGTGATGTTGAGCATTTTTT-CATATGCTTGTTGGCCGCGTGTATGTC 106 chr1qtel1M 964311 TTCTTCAGAAAATCACCTGTTCATCTTCTTTAAGAATTTGTCAATTGGGG 964360 iv viii v i ivvv i v i -- C L1PA15_3end#L 105 TTCTTTTGAAAAGTGTCTGTTCATGTCCTTTGCCCACTTTTTAAT--GGG 58 chr1qtel1M 964361 AATGGCTTTTATTT--TTATAAATCTGATTTGTATT-CTTATAAATTTTG 964407 iv vi v v -- i v i - ivi - i i C L1PA15_3end#L 57 GTTGTTTGTTTTTTGCTTGTTAATTTG-TTTAAGTTCCTTATAGATTCTG 9 chr1qtel1M 964408 ATTAT 964412 iv C L1PA15_3end#L 8 GATAT 4 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 39.02 CpG sites = 47, Kimura (unadjusted) = 39.51 Transitions / transversions = 0.87 (47/54) Gap_init rate = 0.06 (19 / 340), avg. gap size = 1.26 (24 / 19) 427 32.09 2.68 0.99 chr1qtel1M 964114 964412 (35588) C L1PA17_3end#LINE/L1 (606) 307 4 m_b54s551i2 1956 chr1qtel1M 964114 GAACTGCTTCACATTTCTACCAAGGACTATATAAA--TTACCAATTTCCC 964161 iv i i i v- v i i-- v vv ii C L1PA17_3end#L 307 GAACTAATTTACATTCCCACCAAC-AGTGTATAAGCGTTCCCTTTTCTCC 259 chr1qtel1M 964162 ATACACTCTCCCATATTTGTCCTTCTTTTTTTCTGTAATATTAGCCAATC 964211 ii ?v v v i i iv i vvi i v v v C L1PA17_3end#L 258 GCANCCTCGCCAACATCTGTTATTTTTTGACTTTTTAATAATAGCCATTC 209 chr1qtel1M 964212 TGATAGGTGTGA-AGGGTTCCTCAGAGTTGTTCTACTTTGCATTTCTCTA 964260 iv - v vi vv v i iv i C L1PA17_3end#L 208 TGACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTG 159 chr1qtel1M 964261 TTCAATCGTTA----GACCATTTTTTTCAAGTGACTATAGGTAGCTTTAA 964306 v v v v v ---- v - vi vi i v iv vv C L1PA17_3end#L 158 ATGATTAGTGATGTTGAGCATTTTTT-CATATGTTTGTTGGCCGCTTGTA 110 chr1qtel1M 964307 TTTCTTCTTCAGAAAATCACCTGTTCATCTTCTTTAAGAATTTGTCAATT 964356 v iv i viii v i ivvv i v i v C L1PA17_3end#L 109 TGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTTGCCCACTTTTTAATG 60 chr1qtel1M 964357 GGGGAATGGCTTTTATTTTTATAAATCTGATTTGTATT-CTTATAAATTT 964405 vv vvv v i i vi i - ivi - i i C L1PA17_3end#L 59 GGGTTATTTGTTTTTTTCTTGTTGATTTG-TTTAAGTTCCTTATAGATTC 11 chr1qtel1M 964406 TGATTAT 964412 iv C L1PA17_3end#L 10 TGGATAT 4 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 41.83 CpG sites = 43, Kimura (unadjusted) = 42.40 Transitions / transversions = 0.83 (43/52) Gap_init rate = 0.02 (7 / 298), avg. gap size = 1.57 (11 / 7) 23 32.22 0.00 0.00 chr1qtel1M 965425 965508 (34492) (AGAG)n#Simple_repeat 1 84 (0) m_b54s252i2 1957 chr1qtel1M 965425 AGAGGGAGGGTCAGAGAGACACAGGCAGAGACAGGCAGAGACAGACAGAG 965474 i i vv v v iv v iv v v (AGAG)n#Simpl 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr1qtel1M 965475 ACAGAGGCAAACACAGAGAAAGAGACAGACAGAG 965508 v iv i v v i v v (AGAG)n#Simpl 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 84 Matrix = Unknown Transitions / transversions = 0.47 (7/15) Gap_init rate = 0.00 (0 / 83), avg. gap size = 0.0 (0 / 0) 34 10.31 8.22 0.00 chr1qtel1M 965439 965511 (34489) (AGAGAC)n#Simple_repeat 1 79 (0) m_b54s252i3 1957 chr1qtel1M 965439 AGAGACACAGGCAGAGACAG-G-CAGAGAC--AGACAGAGACAGAGGCAA 965484 v i - - -- i i (AGAGAC)n#Sim 1 AGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAG 50 chr1qtel1M 965485 ACACAGAGAAAGAGAC--AGACAGAGGCA 965511 v v -- i (AGAGAC)n#Sim 51 AGACAGAGACAGAGACAGAGACAGAGACA 79 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.06 (4 / 72), avg. gap size = 1.50 (6 / 4) 40 16.07 0.00 2.53 chr1qtel1M 966471 966551 (33449) (TATA)n#Simple_repeat 1 79 (0) m_b54s252i4 1958 chr1qtel1M 966471 TATTTATATCCTTTATATATATTTATTTATATATATATATATATTTATAT 966520 v -v v v v v (TATA)n#Simpl 1 TATATATAT-ATATATATATATATATATATATATATATATATATATATAT 49 chr1qtel1M 966521 ATTTATTTATATCCTTTATATATATTTATAT 966551 v v -v v v (TATA)n#Simpl 50 ATATATATATAT-ATATATATATATATATAT 79 Matrix = Unknown Transitions / transversions = 0.00 (0/11) Gap_init rate = 0.03 (2 / 80), avg. gap size = 1.00 (2 / 2) 232 26.97 1.22 5.06 chr1qtel1M 970759 970840 (29160) L2#LINE/L2 2674 2752 (330) m_b54s601i0 1959 chr1qtel1M 970759 CTGCTACCACCCTGGT-AGAGACACTCTCATCACTTCACACTTGGACTAC 970807 i -vi v --- ii v i i i L2#LINE/L2 2674 CTGCCACCACCCTGGTCCAAGCCAC---CATCATCTCTCGCCTGGATTAC 2720 chr1qtel1M 970808 TACAACATCCTGGTAATTTGGTTTTCTTTTTTC 970840 i i v vv -i i i i vi L2#LINE/L2 2721 TGCAATAGCCTCCTAA-CTGGTCTCCCTGCTTC 2752 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 32.67 CpG sites = 14, Kimura (unadjusted) = 34.72 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.06 (5 / 81), avg. gap size = 1.00 (5 / 5) 232 18.97 0.00 7.55 chr1qtel1M 971097 971153 (28847) C L1M2_orf2#LINE/L1 (2407) 884 832 m_b54s551i3 1960 chr1qtel1M 971097 AGGACTGCTTTGGCTGTAGCCCATAAACTTTGGCATGTTTTTTTAATTGC 971146 ? v v iii i v ----i v C L1M2_orf2#LIN 884 AGNACTGCTTTTGCTGTATCCCATAGGTTTTGGTATGTTGT----GTTTC 839 chr1qtel1M 971147 TATTTTC 971153 i C L1M2_orf2#LIN 838 CATTTTC 832 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 22.56 CpG sites = 6, Kimura (unadjusted) = 22.56 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.07 (4 / 56), avg. gap size = 1.00 (4 / 4) 228 30.69 0.00 0.99 chr1qtel1M 972182 972283 (27717) C L1M3_orf2#LINE/L1 (3040) 248 148 m_b54s551i4 1960 chr1qtel1M 972182 TCTGTTTTGTGTGAGATTAGGATTTCGACCCCTGCTCTTTATTACTTCAC 972231 i v v v v vv v i v iv - C L1M3_orf2#LIN 248 TCTATTTTGTCTGATATAAGTATAGCCACCCCTGCTCTCTTTTGGTT-AC 200 chr1qtel1M 972232 CGGAAGCAGAGCATCTCCTATTCCAGCCCTTTGCCTTTATTCTGTGTGTA 972281 ivvv vi v v i v v ii i i vi i i C L1M3_orf2#LIN 199 CATTTGCATGGAATATCTTTTTCCATCCCTTCACTTTCAGCCTATGTGTG 150 chr1qtel1M 972282 TC 972283 C L1M3_orf2#LIN 149 TC 148 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 39.62 CpG sites = 13, Kimura (unadjusted) = 39.62 Transitions / transversions = 0.72 (13/18) Gap_init rate = 0.01 (1 / 101), avg. gap size = 1.00 (1 / 1) 242 12.50 0.00 0.00 chr1qtel1M 972182 972221 (27779) C L1PREC2_orf2#LINE/L1 (3046) 248 209 m_b54s551i5 1960 chr1qtel1M 972182 TCTGTTTTGTGTGAGATTAGGATTTCGACCCCTGCTCTTT 972221 v i v i i C L1PREC2_orf2# 248 TCTGTTTTGTCTGAAATTAGGATTGCAACCCCTGCTTTTT 209 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 13.79 CpG sites = 3, Kimura (unadjusted) = 13.79 Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 375 30.53 4.21 0.00 chr1qtel1M 973609 973798 (26202) C L1PA14_3end#LINE/L1 (584) 324 127 m_b54s551i6 1961 chr1qtel1M 973609 TGCTTTCTCGAATTGTTGAACCACTTCACATTTTTGCCAAGACTACATTA 973658 ivv v i v i i iiii v v ii v C L1PA14_3end#L 324 TGCTTTCCACAATGGTTGAACTAATTTACACTCCCACCAACAGTGTATAA 275 chr1qtel1M 973659 GTGCCCCAGTTTCTC-ATATCATCTCCCACACCTGTCATTTTTT--TTCT 973705 ii vv -ii v v v vi i i --i i C L1PA14_3end#L 274 GTGTTCCCTTTTCTCCGCAACCTCGCCAGCATCTGTTATTTTTTGACTTT 225 chr1qtel1M 973706 GTAATATTAGCCAATCAGATAGGTGTGA-AGGGTTCCTCAGATTTCTTCT 973754 v v v v iv - v vi vvv vv i C L1PA14_3end#L 224 TTAATAATAGCCATTCTGACTGGTGTGAGATGGTATCTCATTGTGGTTTT 175 chr1qtel1M 973755 ACACTACATTTCTCTATTGAATAGTTA----GACCTTTTTTTCATGTG 973798 ivvi i v vi v ---- v i C L1PA14_3end#L 174 GATTTGCATTTCTCTAATGATCAGTGATATTGAGCTTTTTTTCATATG 127 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 38.68 CpG sites = 27, Kimura (unadjusted) = 39.53 Transitions / transversions = 0.87 (27/31) Gap_init rate = 0.02 (4 / 189), avg. gap size = 2.00 (8 / 4) 520 30.50 10.62 0.95 chr1qtel1M 973805 974284 (25716) C L1PB_orf2#LINE/L1 (1359) 1935 1410 m_b54s551i7 1962 chr1qtel1M 973805 CCCATCCCATATAATGCTTACTAATGGCTTTAG-ATAGATAACTTTTAAC 973853 i vi ? i vi i- v iv- ii vi C L1PB_orf2#LIN 1935 CCCATTCAGTATNATGTTGGCTG-TGGGTTTGTCATAGATGGCTTTTATT 1887 chr1qtel1M 973854 ATTTTAAAGGAAAGCGCCATTTATTTCTATGCTCTCTAGTGTTTTTAATA 973903 i? - v v iv v ? vi v -i iv iiv v v C L1PB_orf2#LIN 1886 ACNTTAA-GGTATGTCCCTTNTATGCCGAT-TTTGCTGAGGGTTTTAATC 1839 chr1qtel1M 973904 AT-----GATG----ATTTTG-------------CTGCATCAATTGAGAT 973931 ----- ---- ------------- v C L1PB_orf2#LIN 1838 ATAAAGGGATGCTGGATTTTGTCAAATGCTTTTTCTGCATCTATTGAGAT 1789 chr1qtel1M 973932 AATCATATGATTTCTGTT---AGTTTTATG-ATTTAGTTAATTATATTGA 973977 i i i --- i i i v- v i vv i i v C L1PB_orf2#LIN 1788 GATCATGTGATTTTTGTTTTTAATTCTGTTTATGTGGTGTATCACATTTA 1739 chr1qtel1M 973978 CAGTTTTCCTAATACTGAAAACATCCC-GTTCTCTTGAT------CCCAC 974020 iv vi v vv ii - v - ivii i i ------ C L1PB_orf2#LIN 1738 TTGACTTGCGTATGTT-AAACCATCCCTGCATCCCTGGTATGAAACCCAC 1690 chr1qtel1M 974021 CTTGTCCTGGTGTATTATTGTGGTGATAAATTCTTGTAATCTCTTTGCTA 974070 i vi v v iv vv vii v v v vv v C L1PB_orf2#LIN 1689 TTGATCATGGTGGATTATCTTTTTGATATGCTGTTGGATTCGGTTAGCTA 1640 chr1qtel1M 974071 ATACTTTACTTAAATTTTTTGCATCAGGATTCTTTGGGAAAGTTGGTCTG 974120 i i ii v iiv ? vivi v ii i vi C L1PB_orf2#LIN 1639 GTATTTTGTTGAGGATTTTNGCATCTATGTTCATCAGGGATATTGGTCTG 1590 chr1qtel1M 974121 TCATTTTCTTTTCTCGATTTTGGCTTGTCCCAGTTTATGTTTCAGCATCT 974170 vi i ? - v v i v ii vv v i vi vv C L1PB_orf2#LIN 1589 TAGTTTTCTTTTTTNG-TTATGTCCTTTCCTGGTTTTGGTATTAGGGTGA 1541 chr1qtel1M 974171 TAATTGTGTCATAAAAGGAACTAGGGAGACTCCCATATTTTTCT------ 974214 v v iv i v vi iv i v v i ------ C L1PB_orf2#LIN 1540 TACTGGCTTCATAGAATGATTTAGGGAGGATTCCCTCTTTCTCTATCTTG 1491 chr1qtel1M 974215 ---AATAGTTT--AT----TTGGAATTCATTGTTCTTT-AATGTTTGGCA 974254 --- v -- ---- v iiv v - i i C L1PB_orf2#LIN 1490 TGGAATAGTGTCAATAGGATTGGTACCAATTCTTCTTTGAATGTCTGGTA 1441 chr1qtel1M 974255 GAATTCCCTTGT-ACTACATCAAGCCCTGGA 974284 ?vi - v v i vi i C L1PB_orf2#LIN 1440 GAATTCNGCTGTGAATCCGTCTGGTCCTGGA 1410 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 40.03 CpG sites = 72, Kimura (unadjusted) = 40.38 Transitions / transversions = 0.99 (72/73) Gap_init rate = 0.04 (19 / 479), avg. gap size = 2.95 (56 / 19) 755 30.59 6.86 0.36 chr1qtel1M 973907 974431 (25569) C L1M5_orf2#LINE/L1 (1481) 1813 1255 m_b54s551i8 1962 chr1qtel1M 973907 ATGATTTTGCTGCATCAATTGAGATAATCATATGATTT----CTGTTAGT 973952 v v v i ---- iv v C L1M5_orf2#LIN 1813 ATGCTTTTTCTGCATCTATTGAGATGATCATATGATTTTTCTCCTTTATT 1764 chr1qtel1M 973953 TTTATGATTTAGTTAATTATATTGACAGTTTTCCTAATACTGAA--AACA 974000 i vv i v i v i iv v i v ii i -- v C L1M5_orf2#LIN 1763 CTGTTAATATGGTGAATTACATTGATTGATTTTCGAATGTTAAACCAACC 1714 chr1qtel1M 974001 TCCCGTTCTCTTGAT----CCCACCTTGTCCTGGTGTATTATTGTGGTGA 974046 iv i iivv ---- i v v i iv vv v C L1M5_orf2#LIN 1713 TTGCATTCCTGGGATAAACCCCACTTGGTCATGATGTATTATCCTTTTTA 1664 chr1qtel1M 974047 TAAATTCTTGTAATCTCTTTGCTAATACTTTACTTAAATTTTTTGCATCA 974096 v vi v v vv i ii ? iiv v C L1M5_orf2#LIN 1663 TATATTGCTGGATTCGATTTGCTAATATTTTGTTNAGGATTTTTGCATCT 1614 chr1qtel1M 974097 GGATTCTTTGGGAAAGTTGGTCTGTCATTTTCTTTTCTCGATTTTGGCTT 974146 ivi v vi i vi v i - vv v C L1M5_orf2#LIN 1613 ATGTTCATGAGGGATATTGGTCTGTAATTTTCTTTTCTTG-TAATGTCTT 1565 chr1qtel1M 974147 GTCCCAGTTTATGTTTCAGCATCTTAATTGTGTCATAAAAGGAACTAGGG 974196 vvi ?i vv v vi ?v iv v iv v ii i i C L1M5_orf2#LIN 1564 TGTCNGGTTTTGGTATCAGGGTNATGCTGGCCTCATAAAATGAGTTGGGA 1515 chr1qtel1M 974197 AGACTCCCATATTTTTCT---------AATAGTTTAT------TTGGAAT 974231 vv i v v --------- v i ------ v C L1M5_orf2#LIN 1514 AGTGTTCCCTCTTTTTCTATTTTCTGGAAGAGTTTGTGTAAGATTGGTAT 1465 chr1qtel1M 974232 TCATTGTTCTTT-AATGTTTGGCAGAATTCCCTTGT-ACTACATCAAGCC 974279 vv v i - i v iv - vvv vi v C L1M5_orf2#LIN 1464 TATTTCTTCCTTAAATGTTTGGTAGAATTCACCAGTGAAGCCATCTGGGC 1415 chr1qtel1M 974280 CTGGAACATGTTTCTTGGGGAGCTCACTGATGACTTGTTCCATTTCTTGT 974329 iiv vi iv i v ivi i v vvi v - C L1M5_orf2#LIN 1414 CTGGAGTTTTCTTTGTGGGAAGGTTTTTAATTACAAATTCAATTTCTT-T 1366 chr1qtel1M 974330 ACTAAA-ATGGGGCCAATTAAGTGTTTTGCTTCCTCTTCTGCTACTGTGG 974378 v i - i i v i ii v i ii i v? ii v v v C L1M5_orf2#LIN 1365 AATAGATATAGGGCTATTCAGATTTTCTATTTCTTCTTGNGTCAGTTTTG 1316 chr1qtel1M 974379 ACAACTGGTATTTT----GGTCCTT-TCCATTTCATCCA---TTTCTATT 974420 ii ? v i ---- vvi - i --- ? v v C L1M5_orf2#LIN 1315 GTAANTTGTGTTTTTCAAGGAATTTGTCCATTTCATCTAAGTTNTCAAAT 1266 chr1qtel1M 974421 TCATTGTCACA 974431 i v i C L1M5_orf2#LIN 1265 TTATTGGCATA 1255 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 40.21 CpG sites = 73, Kimura (unadjusted) = 40.21 Transitions / transversions = 0.84 (73/87) Gap_init rate = 0.02 (13 / 524), avg. gap size = 2.92 (38 / 13) 12 13.21 5.71 2.78 chr1qtel1M 975045 975079 (24921) (CAGA)n#Simple_repeat 1 36 (0) m_b54s252i5 1963 chr1qtel1M 975045 CAGAGACACAGGCAG--AGACAGGCGAGACAGACAGA 975079 v v i -- i - (CAGA)n#Simpl 1 CAGACAGACAGACAGACAGACAGAC-AGACAGACAGA 36 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.50 (3 / 2) 408 23.91 1.77 7.48 chr1qtel1M 975699 975811 (24189) MIRc#SINE/MIR 8 114 (154) m_b54s601i1 1964 chr1qtel1M 975699 GTGTGGTGTAGTGGGCAGAGCAG-AGCCCTGAAGTCAGGAGGACTTGAGT 975747 i iv v-i v i i i i i MIRc#SINE/MIR 8 GTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGT 57 chr1qtel1M 975748 TCAAATCT-AGCTTCAGACACCTAACACTTCCTCACTGTGTGACTCTGGA 975796 i i i-i -------- iv v vi ii i MIRc#SINE/MIR 58 TCGAGTCCCGGCT--------CTGCCACTTACTAGCTGTGTGACCTTGGG 99 chr1qtel1M 975797 CAAGTCACTTCACTT 975811 v i MIRc#SINE/MIR 100 CAAGTCACTTAACCT 114 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 27.10 CpG sites = 18, Kimura (unadjusted) = 29.92 Transitions / transversions = 2.57 (18/7) Gap_init rate = 0.09 (10 / 112), avg. gap size = 1.00 (10 / 10) 64 0.00 1.72 0.00 chr1qtel1M 976402 976459 (23541) (AC)n#Simple_repeat 1 59 (0) c_b54s251i0 1965 chr1qtel1M 976402 ACACACACACACACACACACACACACACACACACACACACACACACACA- 976450 - (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50 chr1qtel1M 976451 ACACACACA 976459 (AC)n#Simple_ 51 ACACACACA 59 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.02 (1 / 57), avg. gap size = 1.00 (1 / 1) 17 26.64 0.00 4.62 chr1qtel1M 979207 979274 (20726) (ATAAAAA)n#Simple_repeat 1 65 (0) m_b54s252i6 1966 chr1qtel1M 979207 ATAAAAAACAGAAAAATACACAAACAATATTTTTAAAAAAAGAGAAAACA 979256 i - - v i - vvv v v i i v v (ATAAAAA)n#Si 1 ATAAAAAATA-AAAAATA-AAAAATAA-AAAATAAAAAATAAAAAATAAA 47 chr1qtel1M 979257 ATATAAAAAATTAAAAAT 979274 v v (ATAAAAA)n#Si 48 AAATAAAAAATAAAAAAT 65 Matrix = Unknown Transitions / transversions = 0.40 (4/10) Gap_init rate = 0.04 (3 / 67), avg. gap size = 1.00 (3 / 3) 17 13.96 0.00 0.00 chr1qtel1M 980164 980195 (19805) (CTTTCC)n#Simple_repeat 1 32 (0) m_b54s252i7 1967 chr1qtel1M 980164 CTTTCCCTTTCTCTTTTCCTTCCCCATTCCCT 980195 i i i v (CTTTCC)n#Sim 1 CTTTCCCTTTCCCTTTCCCTTTCCCTTTCCCT 32 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 770 33.57 2.43 1.90 chr1qtel1M 980518 981094 (18906) C L1ME4c_3end#LINE/L1 (221) 609 30 m_b54s551i9 1968 chr1qtel1M 980518 AGACAGTTTTCATGTT-TTACTGAAATCTTCATGCTCGCCATTTCTTATT 980566 i v i -i -iv i iv iii i v v C L1ME4c_3end#L 609 AAACATTTTCCATGTTGCTAC-ATAGTCTTCATAATTATCATTTTTAATG 561 chr1qtel1M 980567 GCACAATATTATTCCATTACAATCC-TGTGCCTCAGCTGGTCCAACTGTT 980615 vvv v ii- i ?v- i vi ii viiii ii C L1ME4c_3end#L 560 GCTGCATAATATTCCATCG-AGTNGATGTACCATAATTTACTTAACCATT 512 chr1qtel1M 980616 CTTGAATTGGCGGACATCT---TAATTTCCAATTCTTTGCCACCACAAA- 980661 iivv vi i --- vi i i i ii i - C L1ME4c_3end#L 511 CCCCTATTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAAT 462 chr1qtel1M 980662 AAAGTTGCCATAAATATTTTTGTACACATACATTTTTCCCCCTCTTTAAA 980711 v i v i i i i i i vv ii - i C L1ME4c_3end#L 461 AACGCTGCAATGAACATCTTCGTGCATATAGCTTTTTCCTTCT-TTTGAA 413 chr1qtel1M 980712 --ATCTCTTTGGGATATAGACCTAGTCAGATATAGACCTGTTCTGGAACA 980759 -- i i i v vv ---- vi i vi i-- iv C L1ME4c_3end#L 412 TTATTTCCTTAGGATAAATTCC----CAGAAGTGGAATTA--CTGGGTCA 369 chr1qtel1M 980760 AGGGGTACTCACAGTTCTGAAGCCCTTTGGACATAGTTCCAAATGGCTTT 980809 i ivv v i ivi i viv i v v v C L1ME4c_3end#L 368 AAGGGTATGAACATTTTTATGGCTCTTGATACGTATTGCCAAATTGCTTT 319 chr1qtel1M 980810 CTCGAATTTTTGAACTGCTTCACATTTCTACCAGGACTATATAAGTGCAC 980859 ivi vvv v iiv i ? v i v v i i ? i C L1ME4c_3end#L 318 CCAAAAGGGTTGTACCAATTTACANTGCCACCAGCAATGTATGAGNGTAC 269 chr1qtel1M 980860 CAAATTTCCCATACACTCTCCCATATTTGTCCTTCTTTTTTTCTGTAATA 980909 iv iv ii ?v v vii v viv v ivv i vv v C L1ME4c_3end#L 268 CAGTTTCACCGCANCCTCGCCAGCATTGGGTATTATCAATTTTTTAAATT 219 chr1qtel1M 980910 TTAGCCAATCTGATAGGTGTGAAG-GGTTCCTCAGAGTTGTTCTACTTTG 980958 v i i i i i i- vi vv i i v C L1ME4c_3end#L 218 TTTGCTAATTTAATAGGCGTAAAATGGTATCTCATTGTTGCTTTAATTTG 169 chr1qtel1M 980959 CATTTCTCT-ATT-CAATC---GTTAGACCATTTTTTTCAAGTGACTATA 981003 i - - v v --- - v - i v vi i v C L1ME4c_3end#L 168 CATTTCTTTGATTACTAGCGAGGTT-GAACA-TTTTTCCATGTGTTTGTT 121 chr1qtel1M 981004 GGTAGCTTTAATTTCTTCTTCAGAAAATCACCTGTTCATCTTCTTTAAGA 981053 viivi? vv i ?v vi iii v i ivvv C L1ME4c_3end#L 120 TACTANTTGTATTTCCTCTTNTGTGAATTGTCTGTTCATGTCCTTTGCCC 71 chr1qtel1M 981054 ATTTGTCAATTGGGGAATGGCTTTTATTTTTATAAATCTGA 981094 i v vv v v ? v i v i C L1ME4c_3end#L 70 ATTTATCTATTGGGGTCTTGATNTTTTTCTTATCAATTTGA 30 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 44.48 CpG sites = 104, Kimura (unadjusted) = 46.51 Transitions / transversions = 1.21 (104/86) Gap_init rate = 0.03 (20 / 576), avg. gap size = 1.25 (25 / 20) 23 32.22 0.00 0.00 chr1qtel1M 982149 982232 (17768) (AGAG)n#Simple_repeat 1 84 (0) m_b54s252i8 1969 chr1qtel1M 982149 AGAGGGAGGGTCAGAGAGACACAGGCAGAGACAGGCAGAGACAGACAGAG 982198 i i vv v v iv v iv v v (AGAG)n#Simpl 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr1qtel1M 982199 ACAGAGGCAAACACAGAGAAAGAGACAGACAGAG 982232 v iv i v v i v v (AGAG)n#Simpl 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 84 Matrix = Unknown Transitions / transversions = 0.47 (7/15) Gap_init rate = 0.00 (0 / 83), avg. gap size = 0.0 (0 / 0) 34 10.31 8.22 0.00 chr1qtel1M 982163 982235 (17765) (AGAGAC)n#Simple_repeat 1 79 (0) m_b54s252i9 1969 chr1qtel1M 982163 AGAGACACAGGCAGAGACAG-G-CAGAGAC--AGACAGAGACAGAGGCAA 982208 v i - - -- i i (AGAGAC)n#Sim 1 AGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAG 50 chr1qtel1M 982209 ACACAGAGAAAGAGAC--AGACAGAGGCA 982235 v v -- i (AGAGAC)n#Sim 51 AGACAGAGACAGAGACAGAGACAGAGACA 79 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.06 (4 / 72), avg. gap size = 1.50 (6 / 4) 381 30.16 0.79 0.00 chr1qtel1M 983359 983484 (16516) C MIRb#SINE/MIR (15) 253 127 m_b54s601i2 1970 chr1qtel1M 983359 ATTTACAATGCATCTACTCTGTGCTACGCAATAGACCAAGTACTTGTCAA 983408 iviv iii v i v v ivi i ii vv v C MIRb#SINE/MIR 253 ATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACAT 204 chr1qtel1M 983409 ATATTATTTTATTTGATCTTCACAACAACTCTGGGTGG-AGGTATTTTTA 983457 ii i i i i i v v - v C MIRb#SINE/MIR 203 GCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATTA 154 chr1qtel1M 983458 TCCATATTTAATACTTAAGCAAACTGA 983484 vi v i vv i v C MIRb#SINE/MIR 153 TCCCCATTTTACAGATGAGGAAACTGA 127 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 36.68 CpG sites = 21, Kimura (unadjusted) = 39.44 Transitions / transversions = 1.24 (21/17) Gap_init rate = 0.01 (1 / 125), avg. gap size = 1.00 (1 / 1) 332 25.64 14.04 3.57 chr1qtel1M 983393 983570 (16430) C MIRc#SINE/MIR (42) 226 31 m_b54s601i3 1970 chr1qtel1M 983393 ACCAAGTACTTGTCAAATA--TTATTTTATTTGATCTTCACAACAACTCT 983440 v ii - v -- i i i i C MIRc#SINE/MIR 226 ACAAAGCGCTT-TCACATACATTATCTCATTTGATCCTCACAACAACCCT 178 chr1qtel1M 983441 G---GGTGG-------AGGTATTTTTATCCATATTTAATACTTAAGCAAA 983480 --- i ------- v vi v i vv i v C MIRc#SINE/MIR 177 GTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAA 128 chr1qtel1M 983481 CTGA---TC--------TAAATGAACTGATGAGGGTAAGAGATCGCAACT 983519 --- -------- i vi viv i v ----- i i - C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCA-----CACAGC- 84 chr1qtel1M 983520 TAGTAATCATCTGAGACACTATGTGAACCT--GTTTTCCTGACTCTAGGT 983567 viiv v v ivv ivi i-- i i i C MIRc#SINE/MIR 83 TAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGT 34 chr1qtel1M 983568 CCA 983570 C MIRc#SINE/MIR 33 CCA 31 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 29.45 CpG sites = 25, Kimura (unadjusted) = 32.12 Transitions / transversions = 1.32 (25/19) Gap_init rate = 0.07 (13 / 177), avg. gap size = 2.46 (32 / 13) 13 9.69 9.09 0.00 chr1qtel1M 987572 987604 (12396) (AGAAAAT)n#Simple_repeat 1 36 (0) m_b54s252i10 1971 chr1qtel1M 987572 AGAAAACA-AAATTA-AAAATAGAAAA-AGTAAATA 987604 i - v - - v (AGAAAAT)n#Si 1 AGAAAATAGAAAATAGAAAATAGAAAATAGAAAATA 36 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.09 (3 / 32), avg. gap size = 1.00 (3 / 3) 23 24.45 2.90 0.00 chr1qtel1M 987599 987667 (12333) (TATA)n#Simple_repeat 1 71 (0) m_b54s252i11 1972 chr1qtel1M 987599 TAAATACATACACATATTTCCATATATAT-TATATATATACATAT-TGTA 987646 v i i i v vi - i - i (TATA)n#Simpl 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr1qtel1M 987647 TGTATGTATGTATGTAAATAT 987667 i i i i v (TATA)n#Simpl 51 TATATATATATATATATATAT 71 Matrix = Unknown Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.03 (2 / 68), avg. gap size = 1.00 (2 / 2) 19 23.24 3.33 1.64 chr1qtel1M 987621 987680 (12320) (TATG)n#Simple_repeat 1 61 (0) m_b54s252i12 1972 chr1qtel1M 987621 TATATAT-TATATATATACATATTGTATGTATGTATGTATGTAAATAT-T 987668 i - i i ii - vi - (TATG)n#Simpl 1 TATGTATGTATGTATGTATGTA-TGTATGTATGTATGTATGTATGTATGT 49 chr1qtel1M 987669 GCATATGTGTGT 987680 iii i (TATG)n#Simpl 50 ATGTATGTATGT 61 Matrix = Unknown Transitions / transversions = 10.00 (10/1) Gap_init rate = 0.05 (3 / 59), avg. gap size = 1.00 (3 / 3) 300 30.51 3.21 1.26 chr1qtel1M 987681 987836 (12164) L1MB5_3end#LINE/L1 416 574 (347) m_b54s551i10 1973 chr1qtel1M 987681 GTATACACACACACACACACATATGCAATATTTACAGCAGCCCT-TTCAT 987729 v v v ? viii i i - i i i v - i L1MB5_3end#LI 416 GTATTCAAACAAANACTTGTACACG-AATGTTCATAGCAGCACTATTCAC 464 chr1qtel1M 987730 AGTAACCTCAAAAAGAAACCTAACTGATTG-CCATGCTTTCGTTGAACGG 987778 i i vv iiv i v v v ii v - - vviv v i L1MB5_3end#LI 465 AATAGCCAAAAGGTGGAAACAACCCAAATGTCCAT-CAACGGATGAATGG 513 chr1qtel1M 987779 CTAAACAAATTGTGATATATTAATGTAATGGATTATTATTGTGCCAT--- 987825 v v i iv ii v vv --- L1MB5_3end#LI 514 ATAAACAAAATGTGGTATATCCATACAATGGAATATTATTCAGCCATAAA 563 chr1qtel1M 987826 GAGACATGAAG 987836 i iv L1MB5_3end#LI 564 AAGGAATGAAG 574 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 37.98 CpG sites = 24, Kimura (unadjusted) = 40.13 Transitions / transversions = 1.04 (24/23) Gap_init rate = 0.03 (5 / 155), avg. gap size = 1.40 (7 / 5) 321 26.23 4.20 1.36 chr1qtel1M 987699 987841 (12159) L1ME3A_3end#LINE/L1 430 576 (344) m_b54s551i11 1973 chr1qtel1M 987699 ACATATGCAA---TATTTACAGCAGCCCT-TTCATAGTAACCTCAAAAAG 987744 i i --- i i i v - i i i ?? vv L1ME3A_3end#L 430 ACATGTACAAGAATGTTCATAGCAGCACTATTCGTAATAGCCNNAAACTG 479 chr1qtel1M 987745 AAACCTAACTGATTG-CCATGCTTTCGTTGAACGGCTAAACAAATTGTGA 987793 i v ? v ii v - - vviv v i v i i L1ME3A_3end#L 480 GAAACNACCCAAATGTCCAT-CAACAGTAGAATGGATAAATAAATTGTGG 528 chr1qtel1M 987794 TATATTAATGTAATGGATTATTATTGTGCCATGAGACATGAA-GAAATA 987841 v iii v i vvv v - - v L1ME3A_3end#L 529 TATATTCACACAATGGAATACTATACAGCAATGAGA-ATGAACGAACTA 576 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 32.50 CpG sites = 19, Kimura (unadjusted) = 33.58 Transitions / transversions = 1.06 (19/18) Gap_init rate = 0.04 (6 / 142), avg. gap size = 1.33 (8 / 6) 535 27.19 7.61 2.06 chr1qtel1M 988664 988847 (11153) C MIRc#SINE/MIR (51) 217 24 m_b54s601i4 1974 chr1qtel1M 988664 TTTCACACTTTTTTATCT--TTTGGTTTTCACAAAAACTGAGTGA----- 988706 - viv -- i ii v ivv ----- C MIRc#SINE/MIR 217 TTTCACA-TACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAG 169 chr1qtel1M 988707 -------AGGTGTTGCTACTTTAGAGATTGTACAAATAAGGAAACTGAGG 988749 ------- i ii iiiiv--- v i i C MIRc#SINE/MIR 168 GCAGGGCAGGTATTATTATCCCC---ATTTTACAGATGAGGAAACTGAGG 122 chr1qtel1M 988750 TTGGAAGAAGTTAAGTATCTTTCTCAAGGTCACATGAATAGTAAGTGTAT 988799 i vii i iv v i iiiv vvv C MIRc#SINE/MIR 121 CTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCA 72 chr1qtel1M 988800 GAGGCAGGATCTAAACTAAGATCTTTATGACTCCAAGTACAGTGCTCT 988847 v i iiii iv i iv v C MIRc#SINE/MIR 71 GAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCT 24 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.10 CpG sites = 31, Kimura (unadjusted) = 34.97 Transitions / transversions = 1.72 (31/18) Gap_init rate = 0.04 (7 / 183), avg. gap size = 2.57 (18 / 7) 39 6.93 3.28 0.00 chr1qtel1M 991688 991748 (8252) (AGAGAC)n#Simple_repeat 1 63 (0) c_b54s251i1 1975 chr1qtel1M 991688 AGAGACAGAGAC--AGACAAAGACAGAGGCAAACACAGAGACAGAGACAG 991735 -- i i i v (AGAGAC)n#Sim 1 AGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAG 50 chr1qtel1M 991736 AGACAGAGACAGA 991748 (AGAGAC)n#Sim 51 AGACAGAGACAGA 63 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.02 (1 / 60), avg. gap size = 2.00 (2 / 1) 17 26.64 0.00 4.62 chr1qtel1M 995165 995232 (4768) (ATAAAAA)n#Simple_repeat 1 65 (0) m_b54s252i13 1976 chr1qtel1M 995165 ATAAAAAACAGAAAAATACACAAACAATATTTTTAAAAAAAGAGAAAACA 995214 i - - v i - vvv v v i i v v (ATAAAAA)n#Si 1 ATAAAAAATA-AAAAATA-AAAAATAA-AAAATAAAAAATAAAAAATAAA 47 chr1qtel1M 995215 ATATAAAAAATTAAAAAT 995232 v v (ATAAAAA)n#Si 48 AAATAAAAAATAAAAAAT 65 Matrix = Unknown Transitions / transversions = 0.40 (4/10) Gap_init rate = 0.04 (3 / 67), avg. gap size = 1.00 (3 / 3) 14 18.13 0.00 0.00 chr1qtel1M 996063 996094 (3906) (CTTTCC)n#Simple_repeat 1 32 (0) m_b54s252i14 1977 chr1qtel1M 996063 CTTTCCCTTTCTCTTTTTCTTCCCCATTCCCT 996094 i ii i v (CTTTCC)n#Sim 1 CTTTCCCTTTCCCTTTCCCTTTCCCTTTCCCT 32 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 334 29.93 9.80 4.53 chr1qtel1M 996511 996867 (3133) C L1ME5_3end#LINE/L1 (440) 501 127 m_b54s551i12 1978 chr1qtel1M 996511 TGGTGGACATCTCAATT---TCCA--CCCTTGCCACCACAAAA---GTTG 996552 i i ivii --- --i ii v--- i C L1ME5_3end#LI 501 TGATGGACACCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCTG 452 chr1qtel1M 996553 CCATAAATATTTCCA-ACATACAATTTTTC---CCTCTTTAAAAATCTCT 996598 v i i iii i- iivvii vi--- v v i i i C L1ME5_3end#LI 451 CAATGAACATCCTCGTACATGTCCCCTTATGGACCTGTGTGAGAATTTCT 402 chr1qtel1M 996599 TTGGGATATAGACCTAGTCAGATATAGACCTGTTCTGGG--AACGGGTAC 996646 v i --- -iii vi -- -- vv i C L1ME5_3end#LI 401 TTGGGATATATACCCAG---GA-GCGGAATTG--CTGGGTCATAGGGTAT 358 chr1qtel1M 996647 A---GTTCTGAAGCCCTTGGAC---ATAGTTCCAAA---CTTT---GAAT 996684 i---i v v ---- v ---i v v i --- i --- C L1ME5_3end#LI 357 GCGTATACTTAA----TTTGACTAAGTACTGCCAGATTGCTCTCCAGAAT 312 chr1qtel1M 996685 TTTTGAACTGCTTCACATTTCTACCAG-GTTATATAAGGCACCCCAAATT 996733 vvi v iiv ii i i i -iv ii i vvi i -- ? C L1ME5_3end#LI 311 GGCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTA--TN 264 chr1qtel1M 996734 TCCCCATACAACCTCCTCCCATATTTGTCCTTCTTT---TTTCTGTAATA 996780 -- v v- v i i v v v ii--- -- v C L1ME5_3end#LI 263 TCCCCA--CATCCTCG-CCAACACTTGGCATTATCCAGCTTTCT--AATT 219 chr1qtel1M 996781 TTAGCCAATCTGATAGGTGTGAAG-GGTTCCTCAGAGTTGTCCTACTTTG 996829 v i i i - i vi vv ii v C L1ME5_3end#LI 218 TTTGCCAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTG 169 chr1qtel1M 996830 CATTTCTCT-ATT--CAAT-CGTTAGACCATTTTTTCATGTG 996867 - --i -v v v i i i C L1ME5_3end#LI 168 CATTTCTCTGATTACTAATGAGTTTGAGCATCTCTTCATATG 127 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 38.30 CpG sites = 63, Kimura (unadjusted) = 39.88 Transitions / transversions = 1.62 (63/39) Gap_init rate = 0.09 (33 / 356), avg. gap size = 1.58 (52 / 33) 345 26.74 8.12 6.16 chr1qtel1M 996597 996867 (3133) C L1PA16_3end#LINE/L1 (511) 402 127 m_b54s551i13 1978 chr1qtel1M 996597 CTTTGGGATATAGACCTAGTCAGATATAGACCTGTTCTGGG---AACGGG 996643 - v i v ---- i ivi -- --- i - C L1PA16_3end#L 402 CTTTGGG-TATATACCCAGTAA----TGGGATTG--CTGGGTCGAATGG- 361 chr1qtel1M 996644 TACAGTTCTG----AAGCCCTTGGACATAGTTCCAAACT---TTG---AA 996683 --i ---- ii v v v vi --- v--- i C L1PA16_3end#L 360 --TAGTTCTGTTTTAAGTTCTTTGAGAAATCTCCAAACTGCTTTCCACAG 313 chr1qtel1M 996684 TTTTTGAACTGCTTCACATTTCTACCAG-GTTATATAAG-GCACCCCAAA 996731 vvi iv i i i i-iv i - iv i--- C L1PA16_3end#L 312 TGGCTGAACTAATTTACATTCCCACCAACAGTGTATAAGCGTTCCCT--- 266 chr1qtel1M 996732 TTTCCCCATACAACCTCCTCCCATATTTGTCCTTCTTT--TTTCTGTAAT 996779 i i-- i v- vii i iv i --i i - C L1PA16_3end#L 265 TTTCTCCG--CAGCCTCG-CCAGCATCTGTTGTTTTTTGACTTTT-TAAT 220 chr1qtel1M 996780 ATTAGCCAATCTGATAGGTGTGA-AGGGTTCCTCAGAGTTGTCCTACTTT 996828 v v iv - v vi vv v ii iv C L1PA16_3end#L 219 AATAGCCATTCTGACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTT 170 chr1qtel1M 996829 GCATTTCTCTATTCAATCGTTA----GACCATTTTTTCATGTG 996867 iv v v v v ---- v i C L1PA16_3end#L 169 GCATTTCTCTGATGATTAGTGATGTTGAGCATTTTTTCATATG 127 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 33.06 CpG sites = 37, Kimura (unadjusted) = 33.67 Transitions / transversions = 1.19 (37/31) Gap_init rate = 0.10 (26 / 270), avg. gap size = 1.50 (39 / 26) 355 25.42 5.00 3.85 chr1qtel1M 996688 996867 (3133) C L1PA15_3end#LINE/L1 (604) 308 127 m_b54s551i14 1978 chr1qtel1M 996688 TGAACTGCTTCACATTTCTACCAG-GTTATATAAG-GCACCCCAAATTTC 996735 iv i i i -iv i - iv i--- C L1PA15_3end#L 308 TGAACTAATTTACATTCCCACCAGCAGTGTATAAGCGTTCCCT---TTTC 262 chr1qtel1M 996736 CCCATACAACCTCCTCCCATATTTGTCCTTCTTT--TTTCTGTAATATTA 996783 i i-- v- vii i iv i --i i - v C L1PA15_3end#L 261 TCCG--CAACCTCG-CCAGCATCTGTTATTTTTTGACTTTT-TAATAATA 216 chr1qtel1M 996784 GCCAATCTGATAGGTGTGA-AGGGTTCCTCAGAGTTGTCCTACTTTGCAT 996832 v iv - v vi vv v ii iv C L1PA15_3end#L 215 GCCATTCTGACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCAT 166 chr1qtel1M 996833 TTCTCTATTCAATCGTTA----GACCATTTTTTCATGTG 996867 v v v v v ---- v i C L1PA15_3end#L 165 TTCTCTAATGATTAGTGATGTTGAGCATTTTTTCATATG 127 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 30.60 CpG sites = 23, Kimura (unadjusted) = 31.44 Transitions / transversions = 1.10 (23/21) Gap_init rate = 0.07 (12 / 179), avg. gap size = 1.33 (16 / 12) 303 20.49 5.43 5.43 chr1qtel1M 996758 996886 (3114) C L1ME1_3end#LINE/L1 (690) 236 108 m_b54s551i15 1978 chr1qtel1M 996758 TTGTCCTTCTTTTTTCTGTAATATTAGCCAATCTGATAGGTGTGAAG-GG 996806 vv ----- v v i v - C L1ME1_3end#LI 236 TTGTCAGTCTTTTT-----AATTTTAGCCATTCTAATAGGTGTGTAGTGG 192 chr1qtel1M 996807 TTCCTCAGAGTTGTCCTACTTTGCATTTCTCTATT---CAAT--CGTTAG 996851 vi vv v ii v i v ---i --i - C L1ME1_3end#LI 191 TATCTCATTGTGGTTTTAATTTGCATTTCCCTAATGACTAATGATGTT-G 143 chr1qtel1M 996852 ACCATTTTTTCATGTGACTAAGT-CCATCCCATATA 996886 v i vi vv - - i C L1ME1_3end#LI 142 AGCATCTTTTCATGTGCTTATTTGCCAT-CCGTATA 108 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 22.94 CpG sites = 10, Kimura (unadjusted) = 23.96 Transitions / transversions = 0.67 (10/15) Gap_init rate = 0.09 (11 / 128), avg. gap size = 1.27 (14 / 11) 51 11.49 8.44 4.38 chr1qtel1M 998042 998195 (1805) (CAGAGA)n#Simple_repeat 1 160 (0) m_b54s252i15 1979 chr1qtel1M 998042 CAGAGAGAGAACACCAGAGACAGGCAGA-ATGGACAGAGACAGAGAC--A 998088 v - v - - - - vi -- (CAGAGA)n#Sim 1 CAGAGACAG-AGA-CAGAGACA-G-AGACAGAGACAGAGACAGAGACAGA 46 chr1qtel1M 998089 CACAGAGACAG-G-CAGAGA-TG-GACAGAGAC--AGACAAAGACAGAGA 998132 v - - -v - -- i (CAGAGA)n#Sim 47 GACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGA 96 chr1qtel1M 998133 C--AGACAAACACAGGAGGGCAGAGATAGAGAACAGAGA-AGAGACAGAC 998179 -- i v - - i i - - v (CAGAGA)n#Sim 97 CAGAGACAGAGACA-GA-GACAGAGACAGAG-ACAGAGACAGAGACAGAG 143 chr1qtel1M 998180 A-GGAGAAGGAGACAGA 998195 -i vi (CAGAGA)n#Sim 144 ACAGAGACAGAGACAGA 160 Matrix = Unknown Transitions / transversions = 0.88 (7/8) Gap_init rate = 0.11 (17 / 153), avg. gap size = 1.18 (20 / 17) 263 26.20 3.77 2.80 chr1qtel1M 998772 998877 (1123) MIRc#SINE/MIR 12 118 (150) m_b54s601i5 1980 chr1qtel1M 998772 GGGGTAGTGGCA-GAGC-CCAGCCT--AAGTCAGGGGGACCTGAGTTCAA 998817 v i v - - ii v --i ii i i MIRc#SINE/MIR 12 GGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGA 61 chr1qtel1M 998818 ACCCCAGACACCCAACGCCTTCCTGGCTGTGGGGCCCTGGGCAAGTCACT 998867 ii i --- i vi vv v i v i i MIRc#SINE/MIR 62 GTCCCGG---CTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACT 108 chr1qtel1M 998868 TAGCCCCACT 998877 i i v MIRc#SINE/MIR 109 TAACCTCTCT 118 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 30.51 CpG sites = 18, Kimura (unadjusted) = 33.52 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.06 (6 / 105), avg. gap size = 1.17 (7 / 6) 21 13.23 0.00 0.00 chr2ptel1M 70 102 (999898) (T)n#Simple_repeat 1 33 (0) m_b55s252i0 1981 chr2ptel1M 70 TTTTTTTAGATCTTTTTTTTTTTTTTTTTTTTT 102 vvv i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 33 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 19 34.30 1.59 5.79 chr2ptel1M 365 490 (999510) (GGAG)n#Simple_repeat 1 121 (0) m_b55s252i1 1982 chr2ptel1M 365 GGAAGAAGGGGGGGAAAGGGGGAGGGAAGGCCAGGAGGGCGGGGATGGGA 414 i i i ii i - vvi -i - - (GGAG)n#Simpl 1 GGAGGGAGGGAGGGAGGGAGGGAGGG-AGGGAGGGAGGG-AGGGA-GGG- 46 chr2ptel1M 415 AGGGGAAGAAAGAGGCAAGGA-GGAGAAAGTGGGGGAAGGGAAAAGGGGA 463 iii ii v i - ii - i i iiii (GGAG)n#Simpl 47 AGGGAGGGAGGGAGGGAGGGAGGGAGGGAG-GGAGGGAGGGAGGGAGGGA 95 chr2ptel1M 464 GGGACAAGAGGGAAAGGAGGG-GGAAGG 490 -ii - i - i (GGAG)n#Simpl 96 GGGA-GGGAGGG-AGGGAGGGAGGGAGG 121 Matrix = Unknown Transitions / transversions = 8.67 (26/3) Gap_init rate = 0.07 (9 / 125), avg. gap size = 1.00 (9 / 9) 12 19.57 2.86 0.00 chr2ptel1M 1116 1150 (998850) (GGGGCC)n#Simple_repeat 1 36 (0) m_b55s252i2 1983 chr2ptel1M 1116 GGGGAAGGGGCCTGAG-CGGCCCCGGGGCCGGGGCC 1150 vv v i - vv (GGGGCC)n#Sim 1 GGGGCCGGGGCCGGGGCCGGGGCCGGGGCCGGGGCC 36 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 16 7.52 3.57 0.00 chr2ptel1M 2441 2468 (997532) (CTCC)n#Simple_repeat 1 29 (0) m_b55s252i3 1984 chr2ptel1M 2441 CTCCCTCCCTCCCTCCC-CCATCCTTCCC 2468 - v i (CTCC)n#Simpl 1 CTCCCTCCCTCCCTCCCTCCCTCCCTCCC 29 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 17 28.50 0.00 4.29 chr2ptel1M 2692 2764 (997236) (GGGAG)n#Simple_repeat 1 70 (0) m_b55s252i4 1985 chr2ptel1M 2692 GGGAGGGGAGGGGGGTTTGGGGGAGGAGAGGGTTGGGGGAAGGGTGTGGT 2741 i vvvi i -vi i v v v (GGGAG)n#Simp 1 GGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGG-GAGGGGAGGGGAGGGGA 49 chr2ptel1M 2742 ATGGTGGGGAGGCCTGAGGGGAG 2764 iv v --v (GGGAG)n#Simp 50 GGGGAGGGGAGG--GGAGGGGAG 70 Matrix = Unknown Transitions / transversions = 0.60 (6/10) Gap_init rate = 0.04 (3 / 72), avg. gap size = 1.00 (3 / 3) 277 22.45 8.16 0.00 chr2ptel1M 4841 4938 (995062) MIRb#SINE/MIR 96 201 (67) m_b55s601i0 1986 chr2ptel1M 4841 CCTTTGGCAAG---ATTAAACTCTGTTTGCCTCAGTTTCCTTAATTTT-A 4886 v ---v v v vv i vi v - MIRb#SINE/MIR 96 CCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAA 145 chr2ptel1M 4887 AATGGAGAGAAT-ATCCATAACTTGT--GGTTGTTTTGAAGGTAAAGTGA 4933 i v - v v v i i-- v i i v i MIRb#SINE/MIR 146 AATGGGGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGA 195 chr2ptel1M 4934 -ATAAT 4938 - MIRb#SINE/MIR 196 GATAAT 201 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 25.38 CpG sites = 8, Kimura (unadjusted) = 26.68 Transitions / transversions = 0.57 (8/14) Gap_init rate = 0.05 (5 / 97), avg. gap size = 1.60 (8 / 5) 785 25.33 11.54 2.35 chr2ptel1M 5419 5964 (994036) C L1ME4c_3end#LINE/L1 (191) 639 45 m_b55s551i0 1987 chr2ptel1M 5419 TTCTGCTATTT-CACTTAGCATCAGTTCATCTAAGTCTTCCAAGCTCTTC 5467 v - i i vv vv vi i v i vi v C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATAAACATTTTCCATGTTGCTA 590 chr2ptel1M 5468 TGTATTCATCCTGTTGGTCATTTCTTAAGA--ACAAAATATTCCAT-AAA 5514 ii v v v iv vi i v v i--i v -i i C L1ME4c_3end#L 589 CATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCGAG 540 chr2ptel1M 5515 TT--TCTATAACAATTTACCCAAC-ATTCTCCAAAATGGATGGGATCCAT 5561 ?-- v iv i ii - i v -- v v i--- C L1ME4c_3end#L 539 TNGATGTACCATAATTTACTTAACCATTCCCCTA--TTGTTGGA---CAT 495 chr2ptel1M 5562 TCAT----TTTCCAGTTTCTAGCCACT-CAAATAG-GATCCA-CAAACAT 5604 i v---- i i v i i -i i- v v -ii C L1ME4c_3end#L 494 TTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACAT 445 chr2ptel1M 5605 TTTTGGACATACAGGTCCTTTTCCCTTTTT---AGTATT-CCTTGGGGTA 5650 i i vi i -- i i i --- v - i i C L1ME4c_3end#L 444 CTTCGTGCATATAG--CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATA 397 chr2ptel1M 5651 TAAGCCCATA-GTAG---CACCGGAT-AAAGGG-ATGCAGGTTTG-ATAA 5693 v vv v - i ---i i i - - v vi v- ii C L1ME4c_3end#L 396 AATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGG 347 chr2ptel1M 5694 CTTTTGGGGATA---ATT-CCAGATTGC---CCAGAATGGCTGGATGTAT 5736 i --- --- - i --- i v i v ivv C L1ME4c_3end#L 346 CTCTTG---ATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAAT 300 chr2ptel1M 5737 TCACAATTCCACCAACAATGTATCAGTGTCCCAGTTT--TCGCATCCTT- 5783 i ? v i v ? v --i ? i- C L1ME4c_3end#L 299 TTACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCG 250 chr2ptel1M 5784 CCAAAAT----CATTAT---TTTTCCCTGTCATCTTAGCCAATCTGA-AG 5825 iv ----i --- --- vvv i v i i i - C L1ME4c_3end#L 249 CCAGCATTGGGTATTATCAATTTT---TTAAATTTTTGCTAATTTAATAG 203 chr2ptel1M 5826 GTGTGTAGTGGTATCTGA--GTTGTTTTAATGTGCATTTTTCTGATTAAT 5873 i iv i v -- i v i i v C L1ME4c_3end#L 202 GCGTAAAATGGTATCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACT 153 chr2ptel1M 5874 AATGA-CTTGAGCATCTTTTCA-ATG-------ACTAGTTTTAATTTCTT 5914 ii -v i i i -i ------- ? v - i C L1ME4c_3end#L 152 AGCGAGGTTGAACATTTTTCCATGTGTTTGTTTACTANTTGT-ATTTCCT 104 chr2ptel1M 5915 CATCT---AATTTTCTGTTCA-ATCCTTTGACCATTTA---A--AGAATT 5955 v ? --- v -i v --- --i ii i C L1ME4c_3end#L 103 CTTNTGTGAATTGTCTGTTCATGTCCTTTGCCCATTTATCTATTGGGGTC 54 chr2ptel1M 5956 TTGATTTTT 5964 ? C L1ME4c_3end#L 53 TTGATNTTT 45 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 30.75 CpG sites = 79, Kimura (unadjusted) = 32.18 Transitions / transversions = 1.41 (79/56) Gap_init rate = 0.08 (46 / 545), avg. gap size = 1.67 (77 / 46) 786 24.06 10.47 1.85 chr2ptel1M 5499 5947 (994053) C L1ME3G_3end#LINE/L1 (375) 549 63 m_b55s551i1 1987 chr2ptel1M 5499 CAAAATATTCCATAA-ATTTCTATA--ACAATTTACCCAAC-ATTCTCCA 5544 v i i- vvv -- i iii - i v C L1ME3G_3end#L 549 CATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCT 500 chr2ptel1M 5545 AAATGGATGGGATCCATTCAT----TTTCCAGTTTCTAGCCACT-CAAAT 5589 -- v i--- i v---- i i v i i - i C L1ME3G_3end#L 499 A--TTGATGGA---CATTTAGGTTGTTTCCAATTTTTCGCTATTACAAAC 455 chr2ptel1M 5590 AG-GATCCA-CAAACATTTTTGGACATACAGGTCCTTTTCCCTTTTT--- 5634 i- v v -ii ii v i ?-- v v viv v --- C L1ME3G_3end#L 454 AATGCTGCAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCG 407 chr2ptel1M 5635 AGTATTCCT-TGGGGTATAAGCCCATA-GTAGCA---CCGGAT-AAAGGG 5678 i - i i v v? ? v - i v --- i i - C L1ME3G_3end#L 406 AGTATTTCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGG 357 chr2ptel1M 5679 -ATGCAGGTTTGATAACTTTTGG-GGATAATTCCAGATTGCCC---AGAA 5723 - ivi -- v ii-i v v i --- i C L1ME3G_3end#L 356 TATGCGCATTT--TAAATTTTAATAGATACTGCCAAATTGCCCTCCAAAA 309 chr2ptel1M 5724 TGGCTGGATGTATTCACAATTCCACCAACAATGTATCAGTGTCCCAGTTT 5773 ? v ivv i v i i i v v v v C L1ME3G_3end#L 308 NGGCTGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTT 259 chr2ptel1M 5774 --TCGCATCCTT-CCAA-AATCATTATTTTT--CCCTGT-CATCTTAGCC 5816 --i i i i- - v ?iv v i--? i v -v i v C L1ME3G_3end#L 258 CCCCACACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCC 209 chr2ptel1M 5817 AATCTGA-AGGTGTGTAGTGGTATCTGA--GTTGTTTTAATGTGCATTTT 5863 -i viv i v -- v i C L1ME3G_3end#L 208 AATCTGATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTC 159 chr2ptel1M 5864 TCTGATTAATAATGA-CTTGAGCATCTTTTCA-ATG---ACTAG---TTT 5905 i v i -v - --- i i --- C L1ME3G_3end#L 158 CCTGATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTT 109 chr2ptel1M 5906 TAATTTCTTCATCT---AATTTTCTGTTCA-ATCCTTTGACCATTT 5947 vv i v --- vi - v C L1ME3G_3end#L 108 GTATTTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTT 63 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 29.28 CpG sites = 57, Kimura (unadjusted) = 29.94 Transitions / transversions = 1.16 (57/49) Gap_init rate = 0.08 (37 / 448), avg. gap size = 1.51 (56 / 37) 20 4.35 0.00 0.00 chr2ptel1M 7514 7537 (992463) (T)n#Simple_repeat 1 24 (0) m_b55s252i6 1988 chr2ptel1M 7514 TTTCTTTTTTTTTTTTTTTTTTTT 7537 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTT 24 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 15 28.35 0.00 4.84 chr2ptel1M 7513 7577 (992423) (ATTT)n#Simple_repeat 1 62 (0) m_b55s252i5 1989 chr2ptel1M 7513 ATTTCTTTTTTTTTTTTTTTTTTTTCATATTAGATTTATTTATTTGGGGA 7562 v v v v v viv -v ivvv (ATTT)n#Simpl 1 ATTTATTTATTTATTTATTTATTTATTTATT-TATTTATTTATTTATTTA 49 chr2ptel1M 7563 TTTAATTTTGTTTAT 7577 - - i (ATTT)n#Simpl 50 TTT-A-TTTATTTAT 62 Matrix = Unknown Transitions / transversions = 0.27 (3/11) Gap_init rate = 0.05 (3 / 64), avg. gap size = 1.00 (3 / 3) 598 26.25 10.44 4.20 chr2ptel1M 8011 8527 (991473) C L1ME4c_3end#LINE/L1 (275) 555 8 m_b55s551i2 1990 chr2ptel1M 8011 ATAATATTCCAT-AAATT-ATAGACCACG-TTTAC--AGCCATTTCCA-A 8054 -i i ?- iv ii- -- i i v- C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chr2ptel1M 8055 TTGATGGGCATCT-----GTT--CAATTTATTTCGCCAC-AGAAA-AGGG 8095 v i i ----- -- -- i i- v - iv C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTT--TTCGCTATTATAAATAACG 458 chr2ptel1M 8096 CTGCCA----CATTTT-ATCCATATAGGTCCCTTTCCTTCTTT---AT-A 8136 v ---- i -i v -- ii --- - C L1ME4c_3end#L 457 CTGCAATGAACATCTTCGTGCATATAG--CTTTTTCCTTCTTTTGAATTA 410 chr2ptel1M 8137 TCACTTTGGGATATAAGCATCACTTTGGGATATAAGTAACACTGTTGGAT 8186 iv i i - v-- v -------- v iiv i ii i C L1ME4c_3end#L 409 TTTCCTTAGGATA-AAT--TCCC--------AGAAGTGGAATTACTGGGT 371 chr2ptel1M 8187 CAAAGA-TATACACAGGTTGATGACTTTT--TGAGTATATTCCAAATTGC 8233 i- iv vv v i i -- iv - v C L1ME4c_3end#L 370 CAAAGGGTATGAACATTTTTATGGCTCTTGATACGTAT-TGCCAAATTGC 322 chr2ptel1M 8234 TT-CCAGACTGATTGGGATCGTTCACAACTCCA-----AATGCATCAGTA 8277 - i vv i vivivi i ?iv ----- i v ?i C L1ME4c_3end#L 321 TTTCCAAAAGGGTTGTACCAATTTACANTGCCACCAGCAATGTATGAGNG 272 chr2ptel1M 8278 TCCCAGTTTTCCCATATCCCC--CAACATTCATCATTAT--ATTTTCCTG 8323 v iv ii ? i -- i vivi -- -- v C L1ME4c_3end#L 271 TACCAGTTTCACCGCANCCTCGCCAGCATTGGGTATTATCAATTTT--TT 224 chr2ptel1M 8324 TCATCTTAGCCAATT-GACAGGTGTG--------TCTCAAAGTTATCTTA 8364 vv i v i -i i i i-------- vv iii C L1ME4c_3end#L 223 AAATTTTTGCTAATTTAATAGGCGTAAAATGGTATCTCATTGTTGCTTTA 174 chr2ptel1M 8365 ATTTGCATTTCTCTGATCAATAATAATTTGGAACACCTTTTCATGTAAGT 8414 i i v iii vv v ii i ivv C L1ME4c_3end#L 173 ATTTGCATTTCTTTGATTACTAGCGAGGTTGAACATTTTTCCATGTGTTT 124 chr2ptel1M 8415 G-AAAATAGTTTTGATTTTAAC-AATCTAAA-CAT-TATTCATATCCTTT 8460 -vv v ? v - ivv -v? v i -ii - i i C L1ME4c_3end#L 123 GTTTACTANTTGT-ATTTCCTCTTNTGTGAATTGTCTGTTCATGTCCTTT 75 chr2ptel1M 8461 GCCCATTTATCAATTGGGGAATGGCTTGA----TTTCTCATAAATTAGAG 8506 v ---- v ---- i v v i C L1ME4c_3end#L 74 GCCCATTTATCTATTGGG----GTCTTGATNTTTTTCTTATCAATTTGAA 29 chr2ptel1M 8507 TCAATTCTATATATATTTTAG 8527 v ii v ? v? C L1ME4c_3end#L 28 TGAGCTCTTTATATANTANAG 8 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 32.16 CpG sites = 74, Kimura (unadjusted) = 33.76 Transitions / transversions = 1.32 (74/56) Gap_init rate = 0.09 (49 / 516), avg. gap size = 1.57 (77 / 49) 664 31.77 4.26 4.97 chr2ptel1M 8447 9337 (990663) C L1M5_orf2#LINE/L1 (62) 3232 2348 m_b55s551i3 1990 chr2ptel1M 8447 TATTCATATCCTTTGCCCATTTATCAATTGGG--GAATGGCTTGATTTCT 8494 i vi i v ?v -- vv v -- ? C L1M5_orf2#LIN 3232 TGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTTGTCTT--TTTNT 3185 chr2ptel1M 8495 CAT-AAATTAGAGTCAATTCTATATATATTTTAGCAATGAGGC--TAATC 8541 i -i ? iv -v i v i i vv i v -- vi C L1M5_orf2#LIN 3184 TATTGANTTGTAG-GAGTTCTTTATATATTCTGGATACGAGTCCTTTGTC 3136 chr2ptel1M 8542 AGAACCTTCAACTGTAAAAATGTTTTCCCAGTTTATTGCTTCCCTTTTAA 8591 vviv vv?i i v v i ? i i v v v C L1M5_orf2#LIN 3135 AGATATATGTNTTGCAAATATTTTCTCCCANTCTGTGGCTTGCCTTTTCA 3086 chr2ptel1M 8592 TCTTGTCTGCATTAGTTTTGTTTGTGCAAAAGCTTTTTAACTTGATATAA 8641 i v ivi iv ivi vvv? v i i v vi i? i C L1M5_orf2#LIN 3085 TTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTTTAATTTTGATGNAG 3036 chr2ptel1M 8642 TCAAA-------ATTTTCTATTTTGTGATCAAGGATGATCTCTAGTTCTT 8684 v ------- i v i i i?i--- v i i ivv i C L1M5_orf2#LIN 3035 TCCAATTTATCAATTTTTTCTTTTATGGTTNG---TGCTTTTTGTGTCCT 2989 chr2ptel1M 8685 CTTTGGTCACAAATTCCTTCCTCCTCCACAGGTCTGAAAGATAAACTATC 8734 v i--- v iii v v?i - vvi --i v C L1M5_orf2#LIN 2988 GTTTA---AGAAATCTTTGCCTANCCCA-AGGTCACGAAGATA--TTCTC 2945 chr2ptel1M 8735 CTATGTTT--TTCTAACTTATTTATAATCTCATTCTTTATGCCTA-GTAC 8781 -- ivvvv i i i ?ii iiii - vi C L1M5_orf2#LIN 2944 CTATGTTTTCTTCTAGAAGTTTTATAGTTTTANCTTTTACATTTAGGTCT 2895 chr2ptel1M 8782 ATGAACCATTTTGACCTTACCTTGGTATACAGTGTTAAGTGTGGGTCCAT 8831 v i ? vi v ii v i ii v i iv v v C L1M5_orf2#LIN 2894 ATGATCCATCTNGAATTAATTTTTGTGTATGGTGTGAGGTAGGGGTCGAG 2845 chr2ptel1M 8832 GCCTAGTTTCTGCCATAGTAATTTCCAATTTTCCCAGTTGGTTTTGTCAA 8881 ?iii v i v vvi v v i ivvvv ii C L1M5_orf2#LIN 2844 NTTCATTTTTTTCCATATGGATATCCAATTGTTCCAGCACCATTTGTTGA 2795 chr2ptel1M 8882 ATAGTGAATTCTTATCCCAA-AAGTTGGGCTCTTTGG---GTTTATCAAA 8927 v vvv i vi v-i i ---- ? ---v i C L1M5_orf2#LIN 2794 AAAGACTATCCTTTCCCCACTGAATTG----CNTTGGCACCTTTGTCAAA 2749 chr2ptel1M 8928 CACTATATTG---ATATA-GTCATTGACGATTTTTTCCTGTGAAC---CT 8970 v ii - ? --- - v-- -- i i v i -- i --- C L1M5_orf2#LIN 2748 AATCA-ANTGNCCATATATGTG--TG--GGTCTATTTC--TGGACTCTCT 2706 chr2ptel1M 8971 AACCTATTTCACCGATTAACTAGTCCATTTCTTA-GCCAGTACCACATGG 9019 vi i i ii iv i v i - i - i iv C L1M5_orf2#LIN 2705 ATTCTGTTCCATTGATCTATTTGTCTA-TCCTTACGCCAATACCACACTG 2657 chr2ptel1M 9020 TTTTGTTGACTGCTGCTTTATAATATAATTTT-AGATCAGATACAGCTAG 9068 i v v iv - i i - ? ? i vv - i C L1M5_orf2#LIN 2656 TCTTGATTACTGTAGCTTTATAATA-AGTCTTGANATCNGGTAGTG-TAA 2609 chr2ptel1M 9069 G----CCACCTTCATTTGATTTTTTCCCCCCATTATTTCCCTTGAAATTC 9114 ---- v ii i-- i ii vvv i --- v vv C L1M5_orf2#LIN 2608 GTCCTCCAACTTTGTTC--TTCTTTTTCAAGATTGTTT---TGGCTATTC 2564 chr2ptel1M 9115 TTGATCTTTTGTTCTTCCAGATGAATTTT---GTT-GTTTTTTTTTTTCC 9160 ? i i ivi v i ---i i- i v ivv i C L1M5_orf2#LIN 2563 TNGGTCCTTTGCATTTCCATATAAATTTTAGAATCAGCTTGTCAATTTCT 2514 chr2ptel1M 9161 CCTGGGTCATTAAACCAGTTTTTTGGGAGTCTGATTAGTATAGCACTAAA 9210 v --------- vv iii vi v i i v v i i C L1M5_orf2#LIN 2513 AC---------AAAAAAACCTGCTGGGATTTTGATTGGGATTGCATTGAA 2473 chr2ptel1M 9211 TAAATAGATTATTTTAGGTAGTATTGTCATCTTTAATACATTTGCTAGAA 9260 vv i v i v v v ? vv i viv vvvv C L1M5_orf2#LIN 2472 TCTATAGATCAATTTGGGGAGAATTGACATCTTNACAATATTGAGTCTTC 2423 chr2ptel1M 9261 CTATCCAAGAACACTTAATATTTTTCCAATTG-TTAGATCTGACTTTATT 9309 v v ivvv i i v i- i vvi v C L1M5_orf2#LIN 2422 CAATCCATGAACATGGTATATCTCTCCATTTATTTAGGTCTTCTTTAATT 2373 chr2ptel1M 9310 TGTG-CAGAAAGTGTAGTTTTGTAGTTTT 9337 v v- v v---- C L1M5_orf2#LIN 2372 TCTCTCAGCAAT----GTTTTGTAGTTTT 2348 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 42.57 CpG sites = 136, Kimura (unadjusted) = 43.20 Transitions / transversions = 1.02 (136/133) Gap_init rate = 0.07 (62 / 890), avg. gap size = 1.32 (82 / 62) 580 31.36 3.62 1.78 chr2ptel1M 10237 10512 (989488) C L1ME3F_3end#LINE/L1 (635) 355 75 m_b55s551i4 1991 chr2ptel1M 10237 GAATATTACACTTTAGAGAAGAACATTACA--GCTCTCCAAAATGGTTGG 10284 i vv viii v iiii v -- i i i v C L1ME3F_3end#L 355 GAATGTTCAACTTTACGAGATAATGCCAAATTGTTTTCCAAAGTGGTTGT 306 chr2ptel1M 10285 ATTCATTCACAACTCCACCAACAATGCATCAGTGTCCAGGTTT-CCCTCA 10333 iiv i vii i i i v v i vv v-i v C L1ME3F_3end#L 305 ACCAATTTACACTCCCACCAGCAGTGTATAAGAGTTCCCGTTGATCCACA 256 chr2ptel1M 10334 TCCCCTCCAGTACTCATCATTATTTT-TTTCTGTCATCTTAGCCAATCTG 10382 i ii iivi i ivv-i - v i v vi C L1ME3F_3end#L 255 TCCTCTCCAACACTTGGTATTGTCAGACTTCT-TAATTTTTGCCAATCGA 207 chr2ptel1M 10383 ACAGGTGTGTAGTGGTATCTCAGAGTTATTTTAATTTGCATTTCTCTGAT 10432 ii i iv i vv vi i i C L1ME3F_3end#L 206 ATGGGTATAAAATGGTATCTCATTGTGGTCTTAATTTGCATTTCCCTGAT 157 chr2ptel1M 10433 CAATAGTGATTTGGAACA--CTTTCATATG---AGTGGAAATAGTTTCA- 10476 i v i vv v i --i --- v vv ---- i- C L1ME3F_3end#L 156 TACTAATGAGGTTGAGCATCTTTTCATATGTTTATTGGCCA----TTCGT 111 chr2ptel1M 10477 ATTTCATCATCTGAAAATTGTCTGTTCATATCCTTT 10512 i v v vi v i i i C L1ME3F_3end#L 110 GTTTCCTCTTCTGTGAAATGCCTGTTCATGTCTTTT 75 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.64 CpG sites = 50, Kimura (unadjusted) = 41.94 Transitions / transversions = 1.43 (50/35) Gap_init rate = 0.04 (11 / 275), avg. gap size = 1.36 (15 / 11) 845 24.06 3.25 2.01 chr2ptel1M 10267 10512 (989488) C L1ME5_3end#LINE/L1 (618) 323 75 m_b55s551i5 1991 chr2ptel1M 10267 GCTCTCCAAAATGGTTGGATTCATTCACAACTCCACCAACAATGCATCAG 10316 i i v iivi ii vii i i v C L1ME5_3end#LI 323 GCTCTCCAGAATGGCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAG 274 chr2ptel1M 10317 TGTCCAGGTTTCCCT-CATCCCCTCCAGTACTCATCATTATTT--TTTTC 10363 v i vvi ? i- i v ii iiv ii--i C L1ME5_3end#LI 273 GGTTCCTATNTCCCCACATCCTCGCCAACACTTGGCATTATCCAGCTTTC 224 chr2ptel1M 10364 TGTCATCTTAGCCAATCTGACAGGTGTGTAGTGGTATCTCAGAGTTATTT 10413 i-- i v i i i iv i vv i C L1ME5_3end#LI 223 TA--ATTTTTGCCAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTT 176 chr2ptel1M 10414 TAATTTGCATTTCTCTGATCAATAGTGATTTGGAACA-CT-TTCATATGA 10461 i v i v v i - - v C L1ME5_3end#LI 175 TAATTTGCATTTCTCTGATTACTAATGAGTTTGAGCATCTCTTCATATGC 126 chr2ptel1M 10462 GTGGAAATAG--TTTC-AATTTCATCATCTGAAAATTGTCTGTTCATATC 10508 v v--- -- -ii v v v i C L1ME5_3end#LI 125 TTGT---TAGCCTTTCGGGTTTCCTCTTCTGTAAATTGCCTGTTCATATC 79 chr2ptel1M 10509 CTTT 10512 C L1ME5_3end#LI 78 CTTT 75 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 29.91 CpG sites = 36, Kimura (unadjusted) = 29.91 Transitions / transversions = 1.64 (36/22) Gap_init rate = 0.04 (11 / 245), avg. gap size = 1.18 (13 / 11) 36 2.92 0.00 0.00 chr2ptel1M 10689 10723 (989277) (AC)n#Simple_repeat 1 35 (0) c_b55s251i0 1992 chr2ptel1M 10689 ACACACACACACACACACACAAACACACACACACA 10723 v (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACA 35 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 15 33.69 0.00 0.00 chr2ptel1M 11365 11413 (988587) (AA)n#Simple_repeat 1 49 (0) m_b55s252i7 1993 chr2ptel1M 11365 AAATATATAAAACAAAAAAAAAAAGAGAGTGAGAAAAAGAGGAAAAAAA 11413 v v v v i i ivi i i ii (AA)n#Simple_ 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 49 Matrix = Unknown Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 167 33.49 2.79 0.27 chr2ptel1M 11388 12103 (987897) (AGAG)n#Simple_repeat 1 734 (0) m_b55s252i8 1993 chr2ptel1M 11388 AGAGAGTGAGAAAAAGAG-GAAAAAAACAGAGAGACAGAAACAGTAAGAG 11436 v i i - i i i v v i v vi (AGAG)n#Simpl 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr2ptel1M 11437 A-AGGGA-AGACAGAGATTGAGAGAGAAAGAAAGA-AAAGAAATGATTAA 11483 - i - v vv i i - i i - vvi (AGAG)n#Simpl 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA-GAGAGA 99 chr2ptel1M 11484 AAGAAATAAAGTGA-AAAAATACAGAGAGAGACAGAACCAGAGCCAGAAA 11532 i i v i v - i i v v v ivv vv i (AGAG)n#Simpl 100 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 149 chr2ptel1M 11533 GAGCAAGACAGAGTGAACAAGAAAGAAAAAG-GAGAGA-AAAGA-AGTGC 11579 vi v v ivi i i i - - i - v v (AGAG)n#Simpl 150 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 199 chr2ptel1M 11580 CAGATGGAG-GAGAGAGGGAGAG-GGGGGTGGGTGGGGGAGTGAGAAACG 11627 v vi - i - i i v i v i i v i vi (AGAG)n#Simpl 200 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 249 chr2ptel1M 11628 GGGAAAGAGGGAGAGAGACAGAGAGAGAGATAGAGACAGTGAGATAAACA 11677 i i i v v v v v i v (AGAG)n#Simpl 250 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 299 chr2ptel1M 11678 TAAAGACAGAGAAACAGAACAAGAGGGACAGTGAGAGAGACAGACAGAGA 11727 v i v i v ivi i v v v v (AGAG)n#Simpl 300 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 349 chr2ptel1M 11728 GAACCAGTGCTAGAGAGAGCAAGACGGAGTGAACAAGAAAGAGAAAG-GA 11776 ivv v vv vi vi v ivi i i - (AGAG)n#Simpl 350 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 399 chr2ptel1M 11777 GAGA-AAAGA-AGTGCCAGATGGAG-GAGAGAGGGAGTG-GGGTGGGTG- 11821 - i - v vv vi - i v - i v i v - (AGAG)n#Simpl 400 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 449 chr2ptel1M 11822 GGGAG-GAGAAACGGGGAAAGAGGGAGAGAAACAGAGAGAGAAAGAGAGA 11870 i - i vi i i i i v i (AGAG)n#Simpl 450 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 499 chr2ptel1M 11871 TAAAGACAGTGAGATAAACAGAAAGACAGAGAAACAGAACAAGAGGGACA 11920 v i v v v i v i v i v ivi i v (AGAG)n#Simpl 500 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 549 chr2ptel1M 11921 GTGAGAAAGACAGAGAGAACCAGTGCTAGAGAGAGTAAGACAGAATGAAC 11970 v i v ivv v vv vi v iv iv (AGAG)n#Simpl 550 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 599 chr2ptel1M 11971 AAGAAAGAGAAAG-GAGAGAAAG-GATGTGCCAGATGGAGAGAAAGAGAG 12018 i i i - i - - v vv vi i (AGAG)n#Simpl 600 GAGAGAGAGAGAGAGAGAGAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAG 648 chr2ptel1M 12019 GGAGAGGGA-AGGGAGGGAGAGAGGGAGGGAGGGAAGGAGGGAGAGAGAG 12067 i i - i i i i i ii i (AGAG)n#Simpl 649 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 698 chr2ptel1M 12068 GGGGGGAGGAAGGGAGGGGAAAAGAGAGAGAGAGAG 12103 i i i ii i i ii i (AGAG)n#Simpl 699 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 734 Matrix = Unknown Transitions / transversions = 1.18 (103/87) Gap_init rate = 0.03 (22 / 715), avg. gap size = 1.00 (22 / 22) 314 22.10 1.25 3.85 chr2ptel1M 13826 13905 (986095) MIR1_Amn#SINE/MIR 87 164 (66) m_b55s601i2 1994 chr2ptel1M 13826 CTGTGTGACTCTAGGCAAGACACCCAGTC-CTGTTTGCCTCAGTTTCCTC 13874 ? ii i v ii?ii - v v? MIR1_Amn#SINE 87 CTGNGTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTC 136 chr2ptel1M 13875 ATCTGTAAAGTAAGCTGGAGAAAGAAATTGA 13905 i ii--- v v v i MIR1_Amn#SINE 137 ATCTGTAAAATGG---GGATAATGATACTGA 164 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.19 CpG sites = 11, Kimura (unadjusted) = 28.19 Transitions / transversions = 1.83 (11/6) Gap_init rate = 0.05 (4 / 79), avg. gap size = 1.00 (4 / 4) 315 22.22 1.59 0.00 chr2ptel1M 13826 13888 (986112) MIR#SINE/MIR 81 144 (118) m_b55s601i1 1994 chr2ptel1M 13826 CTGTGTGACTCTAGGCAAGACACCCAGTC-CTGTTTGCCTCAGTTTCCTC 13874 ii i vi ii ii - v v MIR#SINE/MIR 81 CTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTC 130 chr2ptel1M 13875 ATCTGTAAAGTAAG 13888 i ii MIR#SINE/MIR 131 ATCTGTAAAATGGG 144 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.78 CpG sites = 11, Kimura (unadjusted) = 27.78 Transitions / transversions = 3.67 (11/3) Gap_init rate = 0.02 (1 / 62), avg. gap size = 1.00 (1 / 1) 472 23.48 5.30 0.00 chr2ptel1M 16384 16515 (983485) MIRc#SINE/MIR 10 148 (120) m_b55s601i3 1995 chr2ptel1M 16384 GTGGT-CAGAGGATAGAGCAGTGGACTCGGAGTCAGCAAGA-CTCATCTC 16431 - v v v i v - vivi MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr2ptel1M 16432 AAATCCAGCCTCAGACACACAGTAGCTGTATGACTCTGGGTGCGTCACTG 16481 i i v v v v vi v i ii iiv v MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTT 109 chr2ptel1M 16482 AA-GTCT----GCCTCAGGTTCCTCCTTTGTAAAAGGAG 16515 -v ---- v v i v i MIRc#SINE/MIR 110 AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.22 CpG sites = 13, Kimura (unadjusted) = 28.23 Transitions / transversions = 0.72 (13/18) Gap_init rate = 0.03 (4 / 131), avg. gap size = 1.75 (7 / 4) 434 16.99 5.19 8.40 chr2ptel1M 17005 17139 (982861) Charlie7a#DNA/hAT-Charlie 141 271 (1) m_b55s502i0 1996 chr2ptel1M 17005 TGCACATACACATATATGTATACA-TACATACATATAAATATATAATTTA 17053 i --- vvi - -i i ---- Charlie7a#DNA 141 TGTACATA---ATATATTAGTACAGTA-GTACATGTA----TATAATTTA 182 chr2ptel1M 17054 TAAATAAGCA------CATACATTAGAGGCACATGTTTAAAAATGTTTTA 17097 ii ------ i i i ii i i v Charlie7a#DNA 183 TAAATAAATAAATATACATATATTGGGGGTGCATGCTCAAAAATTTTTTA 232 chr2ptel1M 17098 CTGATAGAAGTGAATTTGATCAAAACAAGTTAGGAGACTACT 17139 ii v -- - v i Charlie7a#DNA 233 CTGATAGGGGTGCA--TGATCAAAA-AAGTTTGGAGACCACT 271 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 19.82 CpG sites = 16, Kimura (unadjusted) = 19.82 Transitions / transversions = 3.20 (16/5) Gap_init rate = 0.10 (13 / 134), avg. gap size = 1.38 (18 / 13) 488 29.06 1.24 3.82 chr2ptel1M 17141 17301 (982699) C MIR3#SINE/MIR (37) 171 15 m_b55s601i4 1997 chr2ptel1M 17141 CCTTTGAGATCATCTAATCTACTCTCCTCCTCACTTTCCAGATGAGAAAA 17190 v i i v--- i i v i C MIR3#SINE/MIR 171 CCTTAGAGATCATCTAGTCCAA---CCCCCTCATTTTACAGATGAGGAAA 125 chr2ptel1M 17191 CATAGAACCAACAAGGTTAACTTAATGTACCCAAGATCACTCAGCTAAAA 17240 vv iv ivi v -v i iv i i v ? ivv C MIR3#SINE/MIR 124 CTGAGGCCCAGAGAGGTGAA-GTGACTTGCCCAAGGTCACACAGCNAGTT 76 chr2ptel1M 17241 GGTGGAAGATTAGGATCTAG-ACTCAGGTCCTCTGG-TCCCAAAGCCAGT 17288 i v viv iv - i ii i- -- i v C MIR3#SINE/MIR 75 AGTGGCAGAGCCGGGACTAGAACCCAGGTCTCCTGACTCCC--AGTCCGT 28 chr2ptel1M 17289 ACTTTTTTCACTC 17301 i i i iii C MIR3#SINE/MIR 27 GCTCTCTCTGCTC 15 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.17 CpG sites = 27, Kimura (unadjusted) = 38.17 Transitions / transversions = 1.50 (27/18) Gap_init rate = 0.05 (8 / 160), avg. gap size = 1.00 (8 / 8) 512 28.79 1.50 0.75 chr2ptel1M 17168 17300 (982700) C MIRb#SINE/MIR (115) 153 20 m_b55s601i5 1997 chr2ptel1M 17168 TCCTCACTTTCCAGATGAGAAAACATAGAACCAACAAGGTTAACTTAATG 17217 i i v i vv ivi ivi -v iv C MIRb#SINE/MIR 153 TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAA-GTAACT 105 chr2ptel1M 17218 TACCCAAGATCACTCAGCTAAAAGGTGGAAGA-TTAGGATCTAGACTCAG 17266 i i v iv i v -iii iiii i C MIRb#SINE/MIR 104 TGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAG 55 chr2ptel1M 17267 GTCC-TCTGGTCCCAAAGCCAGTACTTTTTTCACT 17300 i- iii v i i i C MIRb#SINE/MIR 54 GTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACT 20 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.56 CpG sites = 27, Kimura (unadjusted) = 38.46 Transitions / transversions = 2.45 (27/11) Gap_init rate = 0.02 (3 / 132), avg. gap size = 1.00 (3 / 3) 12 16.93 0.00 0.00 chr2ptel1M 17485 17511 (982489) (TGGCA)n#Simple_repeat 1 27 (0) m_b55s252i9 1998 chr2ptel1M 17485 TGGCATAGAATAGCATGGCATGACATG 17511 i v i i (TGGCA)n#Simp 1 TGGCATGGCATGGCATGGCATGGCATG 27 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 255 27.62 13.33 0.00 chr2ptel1M 21048 21152 (978848) C MIRc#SINE/MIR (139) 129 11 m_b55s601i6 1999 chr2ptel1M 21048 AACTGAGCTCCAGTCAAAATAAATTACTTTCCCAAG----CCCAG----- 21088 vii vv iiv i v v ---- v ----- C MIRc#SINE/MIR 129 AACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGT 80 chr2ptel1M 21089 -AGTTGCAGAACCAGAATTTCAACCTATG--TTCC-GACT-CAAATATAG 21133 - v i i i i iv i v -- - - i vi C MIRc#SINE/MIR 79 AAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAG 30 chr2ptel1M 21134 TGATCTTTCCATTCTGCCA 21152 v i vii C MIRc#SINE/MIR 29 TGCTCTTTCCACTGCACCA 11 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.18 CpG sites = 16, Kimura (unadjusted) = 35.09 Transitions / transversions = 1.23 (16/13) Gap_init rate = 0.06 (6 / 104), avg. gap size = 2.33 (14 / 6) 14 20.12 0.00 0.00 chr2ptel1M 22819 22852 (977148) (AAGA)n#Simple_repeat 1 34 (0) m_b55s252i10 2000 chr2ptel1M 22819 AAAAAAGAAAGAAAGAAAACAACAATTAAAGAAA 22852 i iv v vv (AAGA)n#Simpl 1 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 34 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 429 18.38 7.48 8.49 chr2ptel1M 23551 23657 (976343) MIRc#SINE/MIR 10 115 (153) m_b55s601i7 2001 chr2ptel1M 23551 GTGGCACAGTGGATAGAATGCTGAA------GTCAGGAGGACCTGAGTTC 23594 ii v iii i ------ i i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr2ptel1M 23595 AAATCT--GCTCTCAGACACTTAACACTTCCTGCCTGTGTGATCCTGGGC 23642 i i i-- -- v ------- iv i i MIRc#SINE/MIR 60 GAGTCCCGGCTCT--GCCACTTA-------CTAGCTGTGTGACCTTGGGC 100 chr2ptel1M 23643 AAGTCACTTAACCCC 23657 i MIRc#SINE/MIR 101 AAGTCACTTAACCTC 115 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 20.74 CpG sites = 15, Kimura (unadjusted) = 22.11 Transitions / transversions = 5.00 (15/3) Gap_init rate = 0.10 (11 / 106), avg. gap size = 1.55 (17 / 11) 308 29.58 13.64 2.04 chr2ptel1M 24797 24972 (975028) MIRb#SINE/MIR 9 204 (64) m_b55s601i8 2002 chr2ptel1M 24797 CAGAGTGGATGGAATGGGAATAG----GGTCTTGAACCTGGA-AAACCAG 24841 v - v i i v ---- ii i viii - i v MIRb#SINE/MIR 9 CAGCGTGG-TGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTG 57 chr2ptel1M 24842 GGTTTTACTTCCACTTCAGAAATTTGCT--------------GGTCAAGT 24877 iv v i ivi v vv i i -------------- v MIRb#SINE/MIR 58 GGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGT 107 chr2ptel1M 24878 TATAAGACCTCTGTTAGATTCAGTTT--TTATCTGTCAAATGGGCATAAT 24925 ivvi v v vi -- i v v MIRb#SINE/MIR 108 TACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAAT 157 chr2ptel1M 24926 AGCAGTTAAGTCCTTGGAGG---CACATGAGGATAAAATAAGAGAATGCA 24972 ii vi --- i v ---vvii v i v MIRb#SINE/MIR 158 AATACCTA---CCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCA 204 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.50 CpG sites = 26, Kimura (unadjusted) = 38.27 Transitions / transversions = 1.04 (26/25) Gap_init rate = 0.05 (9 / 175), avg. gap size = 3.11 (28 / 9) 218 32.57 6.99 3.38 chr2ptel1M 25125 25267 (974733) L2d2_3end#LINE/L2 403 550 (5) m_b55s601i9 2003 chr2ptel1M 25125 CTCTCCACAGTCGTTGGTATATTGTTTGCCCCACCACTGTGTGACCTCCA 25174 i i - - vi i v i v v i vvv i v v L2d2_3end#LIN 403 CTTTTCAC-GT-GTTTATGTCTTGTCTCCCCAACTAGATTGTAAGCTCCT 450 chr2ptel1M 25175 GGAGAGCAGG--CGATGTTCCTCACATCTCTTTGTGTTCC---TGGTGTT 25219 v i -- v -- i i ii i i ---ii i ii L2d2_3end#LIN 451 TGAGGGCAGGGACCATGT--CTTATACTTCTTTGTATCCCCCACAGCGCC 498 chr2ptel1M 25220 TAGCCCAAGGC--TGCCATGTAATAGGTCCTTAAT---TGTTTACTGACT 25264 v iv -- - iii i iv i --- i ii i L2d2_3end#LIN 499 TAGCACAGTGCCTTG-CACACAGTAGGCGCTCAATAAATATTTGTTGATT 547 chr2ptel1M 25265 AGA 25267 v L2d2_3end#LIN 548 TGA 550 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 42.56 CpG sites = 30, Kimura (unadjusted) = 45.33 Transitions / transversions = 2.00 (30/15) Gap_init rate = 0.06 (9 / 142), avg. gap size = 1.67 (15 / 9) 196 26.94 5.49 2.13 chr2ptel1M 25359 25449 (974551) C MIR3#SINE/MIR (6) 202 109 m_b55s601i10 2004 chr2ptel1M 25359 TGGGATCACAGA-TG--AGCACTGGAAGGGCCCTACAGGAGCCAT-GGGC 25404 i i i - -- vi v -i iiii -vi i C MIR3#SINE/MIR 202 TAGAATCATAGAATGTCAGAGCTGGAAGGGACCT-TAGAGATCATCTAGT 154 chr2ptel1M 25405 GCAGCCCACTCATTTTGTAGATG-GGAAACGCGAGGTTCACTGAGG 25449 v i v ii - -i ii vv C MIR3#SINE/MIR 153 CCAACCCCCTCATTTTACAGATGAGGAAAC-TGAGGCCCAGAGAGG 109 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.15 CpG sites = 17, Kimura (unadjusted) = 35.15 Transitions / transversions = 2.43 (17/7) Gap_init rate = 0.07 (6 / 90), avg. gap size = 1.17 (7 / 6) 395 31.97 4.46 2.43 chr2ptel1M 26075 26276 (973724) MIRc#SINE/MIR 2 207 (61) m_b55s601i11 2005 chr2ptel1M 26075 GAGGCCG-GTAGTTCAATGGAAAG--TCCTGGACATAGAATCAAAGCGTA 26121 v - i v i --iv v i i i--- v MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAG---GAA 48 chr2ptel1M 26122 CACTAGAGTCTGAAGTGAGCCTTGGACAAT-ACTAACTGTGCACCTCTGG 26170 v iv i ii ivivv v iv v v - i iiv ii MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 98 chr2ptel1M 26171 ACAAGTCAATTAAACTGCTGTTTTCCACAGTTTCCACAACTTTCAATTGG 26220 i v v - v vvv v v v v v v MIRc#SINE/MIR 99 GCAAGTCACTTAACCT-CTCTGAGCCTCAGTTTCCTCATCTGTAAAATGG 147 chr2ptel1M 26221 AGATAACAATATC-AC----CCTAACTTGGAAAGTTAAGATGAGGATAAA 26265 i i i -i ---- v iiv ii ivvi v MIRc#SINE/MIR 148 GGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAA 197 chr2ptel1M 26266 AGTGATACAAT 26276 - v i MIRc#SINE/MIR 198 A-TGAGATAAT 207 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 41.28 CpG sites = 30, Kimura (unadjusted) = 42.14 Transitions / transversions = 0.91 (30/33) Gap_init rate = 0.05 (10 / 201), avg. gap size = 1.40 (14 / 10) 20 3.81 3.70 0.00 chr2ptel1M 26530 26556 (973444) (AC)n#Simple_repeat 1 28 (0) m_b55s252i11 2006 chr2ptel1M 26530 ACACACACACACACAGACACA-ACACAC 26556 v - (AC)n#Simple_ 1 ACACACACACACACACACACACACACAC 28 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.04 (1 / 26), avg. gap size = 1.00 (1 / 1) 274 22.46 17.14 2.50 chr2ptel1M 26960 27064 (972936) C MIR3#SINE/MIR (2) 206 87 m_b55s601i12 2007 chr2ptel1M 26960 ATCA-AAAGTCAGAAGATGT-GGAGCTGAAAGACCCGTCAGAAGTAGAAT 27007 - i i v ii -i i ivv v i ii v-- C MIR3#SINE/MIR 206 ATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATC--AT 159 chr2ptel1M 27008 CT----CAGCCCCTTCATTTTATAGC--AGGAAACTGAAGCTCAGG---- 27047 ---- i i i v-- i i i---- C MIR3#SINE/MIR 158 CTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGG 109 chr2ptel1M 27048 ------GATTTGCCCAAAGGTCA 27064 ------ i - C MIR3#SINE/MIR 108 TGAAGTGACTTGCCC-AAGGTCA 87 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.02 CpG sites = 17, Kimura (unadjusted) = 28.02 Transitions / transversions = 2.83 (17/6) Gap_init rate = 0.09 (9 / 104), avg. gap size = 2.33 (21 / 9) 37 0.00 0.00 0.00 chr2ptel1M 30186 30217 (969783) (GT)n#Simple_repeat 1 32 (0) c_b55s251i1 2008 chr2ptel1M 30186 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 30217 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 32 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 199 26.82 7.08 4.31 chr2ptel1M 31015 31127 (968873) MIRb#SINE/MIR 3 118 (150) m_b55s601i13 2009 chr2ptel1M 31015 GAGGGAGCACTAGGGGTGGCAGTGGGTAGA-CACCAGCC--GGAATTCAG 31061 - vi- v - iv - vi i-- i - MIRb#SINE/MIR 3 GAGGG-GCAGC-GTGGTG-CAGTGGAAAGAGCACGGGCTTTGGAGT-CAG 48 chr2ptel1M 31062 GAGGCCCGGAGTCCAAATTAACACCTTAACC-----CTGGCTGTGTGACC 31106 ivi v v i i i iv- iv ivi ----- i MIRb#SINE/MIR 49 ACAGACCTGGGTTCGAATCC-CGGCTCTGCCACTTACTAGCTGTGTGACC 97 chr2ptel1M 31107 CTGGGAAAGTCACTTAACCCC 31127 i v i i MIRb#SINE/MIR 98 TTGGGCAAGTTACTTAACCTC 118 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.02 CpG sites = 18, Kimura (unadjusted) = 34.26 Transitions / transversions = 1.64 (18/11) Gap_init rate = 0.07 (8 / 112), avg. gap size = 1.62 (13 / 8) 280 23.05 7.53 2.04 chr2ptel1M 31035 31127 (968873) MIR1_Amn#SINE/MIR 20 117 (113) m_b55s601i14 2009 chr2ptel1M 31035 AGTGGGTAGA-CACCAG-CCGGAATTCAGGAGGCCCGGAGTCCAAATTAA 31082 i - ii - i i i i i i - i ? ? iv- MIR1_Amn#SINE 20 AGTGGATAGAGCACTGGACTGGGACTCGGGAGACCTGG-GTTCNANTCC- 67 chr2ptel1M 31083 CACCTTAACC-----CTGGCTGTGTGACCCTGGGAAAGTCACTTAACCCC 31127 iv ivi ----- i? ? i v ? i MIR1_Amn#SINE 68 CGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGTCACTTNACCTC 117 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.98 CpG sites = 17, Kimura (unadjusted) = 31.60 Transitions / transversions = 4.25 (17/4) Gap_init rate = 0.05 (5 / 92), avg. gap size = 1.80 (9 / 5) 229 17.39 2.17 0.00 chr2ptel1M 31093 31138 (968862) MIR#SINE/MIR 77 123 (139) m_b55s601i15 2009 chr2ptel1M 31093 CTGGCTGTGTGACCCTGGGAAAGTCACTTAACCCCAAT-TGCCTAAG 31138 i i v i i vv - v MIR#SINE/MIR 77 CTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAG 123 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 19.89 CpG sites = 4, Kimura (unadjusted) = 19.89 Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1) 18 15.00 1.96 6.12 chr2ptel1M 31203 31253 (968747) (CTCCT)n#Simple_repeat 1 49 (0) m_b55s252i12 2010 chr2ptel1M 31203 CTCC-CTCCATCTTTTACTCCTCTTCTCTCCCCTCCTCTCCCATCCTTCT 31251 - - ii - i i iv - (CTCCT)n#Simp 1 CTCCTCTCC-TCTCCT-CTCCTCTCCTCTCCTCTCCTCTCCTCTCC-TCT 47 chr2ptel1M 31252 CC 31253 (CTCCT)n#Simp 48 CC 49 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.08 (4 / 50), avg. gap size = 1.00 (4 / 4) 14 14.13 3.57 9.43 chr2ptel1M 32344 32399 (967601) (CTC)n#Simple_repeat 1 53 (0) m_b55s252i13 2011 chr2ptel1M 32344 CTCCTCCTCC-CCGCGGCC-CGTCACTTCCTCCCTCCCCACTCGCCCCTC 32391 - v vv - v - - - i - - i (CTC)n#Simple 1 CTCCTCCTCCTCCTCCTCCTCCTC-C-TCCT-CCTCCTC-CTC-CTCCTC 45 chr2ptel1M 32392 CTCCTCCT 32399 (CTC)n#Simple 46 CTCCTCCT 53 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.13 (7 / 55), avg. gap size = 1.00 (7 / 7) 428 28.88 1.99 3.54 chr2ptel1M 33661 33861 (966139) MIRb#SINE/MIR 4 201 (67) m_b55s601i16 2012 chr2ptel1M 33661 AAGGGGAGC-TGGTAGAATAAGGAAGAGAGACCTGGGCAT-AGAATCAGA 33708 i v - iv i -- - - vi v -i i MIRb#SINE/MIR 4 AGGGGCAGCGTGGTGCAGT--GGAA-AGAG-CACGGGCTTTGGAGTCAGA 49 chr2ptel1M 33709 AGTTCCTGAGCTTAAATCAAGGTTCAAAACAGTTCTTAGGTCGGTGCCCT 33758 vivv i i ii vv i viv- v vi v vv v MIRb#SINE/MIR 50 CAGACCTGGGTTCGAATCCCGGCTCTGC-CACTTACTAGCTGTGTGACCT 98 chr2ptel1M 33759 TGG-CAAGT-ACTTAAATTCTGTGTGCCTCAGATACCTCAACTCTTAAAT 33806 - - vi v v v v v v v MIRb#SINE/MIR 99 TGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAAT 148 chr2ptel1M 33807 GGGAGAATAATATCACATAACTTGAAATGTTGTTTTGAAGGTAAAGTTAC 33856 -- i vi v v i v iv v i i v i v v MIRb#SINE/MIR 149 GG--GGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAG 196 chr2ptel1M 33857 ATAAT 33861 MIRb#SINE/MIR 197 ATAAT 201 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.15 CpG sites = 22, Kimura (unadjusted) = 36.50 Transitions / transversions = 0.65 (22/34) Gap_init rate = 0.06 (11 / 200), avg. gap size = 1.00 (11 / 11) 290 23.13 17.71 0.89 chr2ptel1M 35510 35605 (964395) C MIR3#SINE/MIR (7) 201 90 m_b55s601i17 2013 chr2ptel1M 35510 AAAGTCATGAGATGT-AGAGCTGAAAGACACTCCAGAT---------TCC 35549 i i iii - i iv iii v--------- C MIR3#SINE/MIR 201 AGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCC 152 chr2ptel1M 35550 AACTTTCTTCAATTTACAG--GAAGATACTGAAGCACAGA-----GAAGT 35592 iii - v -- i v i v ----- C MIR3#SINE/MIR 151 AACCCCCT-CATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGT 103 chr2ptel1M 35593 GACTTGCTCATGG 35605 i v C MIR3#SINE/MIR 102 GACTTGCCCAAGG 90 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.92 CpG sites = 16, Kimura (unadjusted) = 28.92 Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.05 (5 / 95), avg. gap size = 3.60 (18 / 5) 13 9.26 0.00 0.00 chr2ptel1M 35730 35752 (964248) (CCTC)n#Simple_repeat 1 23 (0) m_b55s252i14 2014 chr2ptel1M 35730 CCTCCTTCCCTCCATCCCTCCCT 35752 i v (CCTC)n#Simpl 1 CCTCCCTCCCTCCCTCCCTCCCT 23 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 1302 30.01 3.70 1.42 chr2ptel1M 36101 36722 (963278) C L1ME4c_3end#LINE/L1 (191) 639 4 m_b55s551i6 2015 chr2ptel1M 36101 TTCTGCTCATTTCA-TTAACATCAGTTCATGTAAGTCTCTCCAGCCCTCT 36149 iv - i vv i- vvi i vviiv C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATA-AACATTTTCCATGTTGCT 591 chr2ptel1M 36150 CTGTATTAATCCTGATGGTCATTTCTTACAGAACAATAATATTCCATAAC 36199 vii v vv v i vi i v ii vvvv viv C L1ME4c_3end#L 590 ACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCGA 541 chr2ptel1M 36200 ATTCATAGACCACAATTTATTCAGCCATTCTCCAACTGATAGGCATCC-- 36247 i ?v iv i i i i i v i v i i ii-- C L1ME4c_3end#L 540 GTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAG 491 chr2ptel1M 36248 GTTCAATTTCCAGTTTCTTTCCACTACGAAAAGGGCTGCCACAAACATTT 36297 --i i i iv i i ii v iv v ii i C L1ME4c_3end#L 490 GTT--GTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCT 443 chr2ptel1M 36298 AATCA--CATACAGGTCCCTTTCCCTTCTTT-GA--TATCTCTTT-GGAT 36341 -- i-- i --- i i - -- i i - C L1ME4c_3end#L 442 --TCGTGCATATAG---CTTTTTCCTTCTTTTGAATTATTTCCTTAGGAT 398 chr2ptel1M 36342 ATAAGCCCAGTAGTAACATTGCTGGAT-AAAGAGTATACACAGTTTGATA 36390 v vv v iiv i i - i iv v v i C L1ME4c_3end#L 397 AAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATG 348 chr2ptel1M 36391 ACTTTTTGAGCATAGTTCCAAATTGCTCTCCAGAATGGTTGGATCTGTTC 36440 i i vivi i v v i i v v i vi i C L1ME4c_3end#L 347 GCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTT 298 chr2ptel1M 36441 ACAACTCCACCAACAATGCATTAGTGTCCCAGTTTTCCCACATCCCCTCC 36490 ?iv i i v ? v iv i ? i v C L1ME4c_3end#L 297 ACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCC 248 chr2ptel1M 36491 AACATTCGTCATTATC------TTA-------GCCAATCTGATAGGTGTG 36527 i v vi ------ ------- i i i i i C L1ME4c_3end#L 247 AGCATTGGGTATTATCAATTTTTTAAATTTTTGCTAATTTAATAGGCGTA 198 chr2ptel1M 36528 TAGTCTTATCTCAAAGTTGTCTTAATTTGCATTGCTCTGATCAATAATGA 36577 v i vv vv ii v i i v ii C L1ME4c_3end#L 197 AAATGGTATCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACTAGCGA 148 chr2ptel1M 36578 TTTGGAACACCTTTTCATGTAGGTGAAAATAATTTCAATTTCAAAATTCT 36627 vv v ii i ivv vvv iv ? vv -vvv ? C L1ME4c_3end#L 147 GGTTGAACATTTTTCCATGTGTTTGTTTACTANTTGTATTTC-CTCTTNT 99 chr2ptel1M 36628 AAACATTGTCTGTTCATATCTTTTGCCCATTTATCAATTGAAGAATTGCT 36677 iviv i i v ii vv v C L1ME4c_3end#L 98 GTGAATTGTCTGTTCATGTCCTTTGCCCATTTATCTATTGGGGTCTTGAT 49 chr2ptel1M 36678 TGATTTCTTATAAATTAGAGTCGATTTTATATATATTTTAGAAAT 36722 ?vv v v i viii i v ? v? v C L1ME4c_3end#L 48 NTTTTTCTTATCAATTTGAATGAGCTCTTTATATANTANAGATAT 4 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.91 CpG sites = 98, Kimura (unadjusted) = 39.83 Transitions / transversions = 1.14 (98/86) Gap_init rate = 0.03 (18 / 621), avg. gap size = 1.78 (32 / 18) 3774 29.15 4.27 2.94 chr2ptel1M 36634 38952 (961048) C L1M5_orf2#LINE/L1 (58) 3236 888 m_b55s551i7 2015 chr2ptel1M 36634 TGTCTGTTCATATCTTTTGCCCATTTATCAATTGAAGAATTGCTTGA--- 36680 vi v ?v ii--- i v--- C L1M5_orf2#LIN 3236 TGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGG---TTGTTTGTCTT 3190 chr2ptel1M 36681 TTTCTTAT-AAATTAGAGTCGA-TTTTATATATATTTTAGAAATGAGGCC 36728 ? -i ? iv -- - i v i i v i v C L1M5_orf2#LIN 3189 TTTNTTATTGANTTGTAG--GAGTTCTTTATATATTCTGGATACGAGTCC 3142 chr2ptel1M 36729 TTTATCAGAACTTTCAACTGTAAA-ATGTTTTCCCAGTTTATTGCTTCCC 36777 i vv v vv?i i - v i ? i i v v C L1M5_orf2#LIN 3141 TTTGTCAGATATATGTNTTGCAAATATTTTCTCCCANTCTGTGGCTTGCC 3092 chr2ptel1M 36778 TTCTAATCTT---------GTCT--------GCATTAGCTT---ACTT-G 36806 i v i --------- -------- vv i --- i - C L1M5_orf2#LIN 3091 TTTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTTTAATTTTG 3042 chr2ptel1M 36807 ATATAATCAAA-------ATTTTCTTTTTTGTGATCAATGATGATCTCTA 36849 i? i v ------- i i i i --- ?i v i i i C L1M5_orf2#LIN 3041 ATGNAGTCCAATTTATCAATTTTTTCTTTTATGGT---TNGTGCTTTTTG 2995 chr2ptel1M 36850 GTTCTTCTTTGGTCACAAATTCCTTCCTCCTCCACAGGTCTGAAAGATAA 36899 vv i v i--- v iii v v?i - vvi - C L1M5_orf2#LIN 2994 TGTCCTGTTTA---AGAAATCTTTGCCTANCCCA-AGGTCACGAAGATA- 2950 chr2ptel1M 36900 ACTATCCTATGTT--CTTCTA--ATTTATTTATAATCTCATTCTTTATGC 36945 -i v -- -- v -- i i i ?ii iii C L1M5_orf2#LIN 2949 -TTCTCCTATGTTTTCTTCTAGAAGTT--TTATAGTTTTANCTTTTACAT 2903 chr2ptel1M 36946 CTAG-TACATGAACCATTTTGACTTTATCTTGGTATACAGTGTTAAATGT 36994 i - vi v i ? v v i v i ii v ii iv C L1M5_orf2#LIN 2902 TTAGGTCTATGATCCATCTNGAATTAATTTTTGTGTATGGTGTGAGGTAG 2853 chr2ptel1M 36995 GGGTCCATGCCTAGTTTCTGCCATAGTAATTTCCAATTTTCCCAGC--CA 37042 v v?iii v i v vvi v v i -- C L1M5_orf2#LIN 2852 GGGTCGAGNTTCATTTTTTTCCATATGGATATCCAATTGTTCCAGCACCA 2803 chr2ptel1M 37043 TTTTTGGCAAATAGTGAATTTTTATGCCAA-AAGTTGGGCTCTTTGGG-- 37089 v v v v v -- ii viv v-i i ---- ? v-- C L1M5_orf2#LIN 2802 TTTGTTGAAAAGACT--ATCCTTTCCCCACTGAATTG----CNTTGGCAC 2759 chr2ptel1M 37090 -TTTGTCAAACAATAAATTG-CTATAGTCAT-TGACGATTTTTTTCCTGT 37136 - - v ? - i --i - vv i i v iv v C L1M5_orf2#LIN 2758 CTTTGTCAAA-AATCAANTGNCCATA--TATGTGTGGGTCTATTTCTGGA 2712 chr2ptel1M 37137 TAACCTAACCTATTCCAGTGATCAACTAGTTCATTTCTTA-GATAGTACT 37185 ivvi vi i v v i v ii i- - vi i i C L1M5_orf2#LIN 2711 CTCTCTATTCTGTTCCATTGATCTATTTGTCTATC-CTTACGCCAATACC 2663 chr2ptel1M 37186 ACATGGTAC--ATTACTGCTGCTTTATAATAAAATTTTAGATCAGATACA 37233 iv vi-- iv ivi v ? ? i vv C L1M5_orf2#LIN 2662 ACACTGTCTTGATTACTGTAGCTTTATAATAAGTCTTGANATCNGGTAGT 2613 chr2ptel1M 37234 GCTAGG----CCACCTTTATTTGATTTATTTTTCACTAG-TTCCTTTGAA 37278 - i ---- v i i--- v -- - vi iv C L1M5_orf2#LIN 2612 G-TAAGTCCTCCAACTTTGTTC---TTCTTTTTCA--AGATTGTTTTGGC 2569 chr2ptel1M 37279 -ATTCTTGACTTTTTATTCTTCCAGATGAATTTTG---TT-GTTTTTTTT 37323 - ? iiii iivi v i i--- i- i v ivv C L1M5_orf2#LIN 2568 TATTCTNGGTCCTTTGCATTTCCATATAAATTTTAGAATCAGCTTGTCAA 2519 chr2ptel1M 37324 TTTCTAGGTCATTAAACTATTTTTTTGGGAGTCTGATTAGTATAGCACTA 37373 ------i vv vii vi v i i v v i i C L1M5_orf2#LIN 2518 TTTCTA------CAAAAAAACCTGCTGGGATTTTGATTGGGATTGCATTG 2475 chr2ptel1M 37374 AATAAATAGATTAGTTTAAGTAGTATTGTCATCTTTAATATATTTGCTAG 37423 vv i i ii v v v ? vv viv vv C L1M5_orf2#LIN 2474 AATCTATAGATCAATTTGGGGAGAATTGACATCTTNACAATATTGAGTCT 2425 chr2ptel1M 37424 AACTATCCAAGAATACTTAATATTTTTCCAATTGTT-AGATCTGACTTTA 37472 vv v v i ivvv i i v i - i vvi v C L1M5_orf2#LIN 2424 TCCAATCCATGAACATGGTATATCTCTCCATTTATTTAGGTCTTCTTTAA 2375 chr2ptel1M 37473 TTTGTG-CAGAAAGTGTTTTGTAGTTTTGCTCTATATAGTTGTTG-ACTT 37520 v v- v - - vv i ? v v - v C L1M5_orf2#LIN 2374 TTTCTCTCAGCAA-TGTTTTGTAGTTTT-CAGTGTANAGGTCTTGCACAT 2327 chr2ptel1M 37521 TCCTTGGTAGTCATAGATTCCTCAAATATTTTATATTATCAACAGTTATT 37570 ?ii v -- vv - i ? i v ivivv i C L1M5_orf2#LIN 2326 NTTTTGTTAG--ATTTATTCCT-AAGTATTTNATGTTTTTTGATGCTATT 2280 chr2ptel1M 37571 TTAAGTGGAATTTCTCTT----TTTTATTT--CTGTTGGATTTTGTTATT 37614 v i v vi i ---- i -- vi --- ii C L1M5_orf2#LIN 2279 GTAAATGGTATTGTTTTTNAAATTTCATTTTCCAATTG---TTTGTTGCT 2233 chr2ptel1M 37615 GATATATAAAAATGCTGAGGATTTATGT----------TGTATCCTGCAA 37654 ii i i vivv v ---------- ? i C L1M5_orf2#LIN 2232 AGTATATAGAAATACAATTGATTTTTGTATATTGACCTTGTATCCNGCGA 2183 chr2ptel1M 37655 CTTTGATAAAGTTATGGATTATTGCTAATAGCTTTTTAGTAGAAGCCCTG 37704 i v v i ivv v v i i ? v vv ii ? C L1M5_orf2#LIN 2182 CCTTGCTAAATTCACTTATTAGTTCTAGTAGTTTNTTTGTAGATTCTTTN 2133 chr2ptel1M 37705 GGGTTCTCTAAGTATACCATCATATCATCTGTGAAGAGCCATAATTTG-- 37752 i i v ? v i i v i?v i i v-- C L1M5_orf2#LIN 2132 GGATTTTCTACGTANACAATCATGTCATCTGCGAATAANGACAGTTTTAT 2083 chr2ptel1M 37753 TTCCTCATTACCTACTCTAATTCCTTTAATCACTTTTTCATCTCTTATTG 37802 i v v v iii v v v iv v vi C L1M5_orf2#LIN 2082 TTCTTCCTTTCCAATCTTTATGCCTTTTATTTCTTTTTCTTGCCTTATTG 2033 chr2ptel1M 37803 CAGAAGCTAACATTTCTAATACAGTACTGAATAGTAATGTTGATAGTGGG 37852 vvi iv ii i i i ii v i v ? i i C L1M5_orf2#LIN 2032 CACTGGCTAGGACCTCCAGTACAATGTTGAATAGAAGTGGTGANAGCGGA 1983 chr2ptel1M 37853 CAATCTTGTTTCACTCCTGATTTTATTTGGAATAATTCCAGTTTATCACC 37902 vi i iii i i vvv viv? i ? v C L1M5_orf2#LIN 1982 CATCCTTGTCTTGTTCCCGATCTTAGGGGGAAAGCNTTCAGTNTTTCACC 1933 chr2ptel1M 37903 ATTACACATGATGCTTACTGATGGTTTTAAATAGGTGTTACTGACTATTT 37952 vii i ?i vv vvi i iivi v ii vv C L1M5_orf2#LIN 1932 ATTAAGTATGATGTTNGCTGTAGGTTTTTCGTAGATGCCCTTTATCAGGT 1883 chr2ptel1M 37953 TCATGAAAAGTCCATTTATTTTTATAATATCTAGTGTTTTTTAATAAGAA 38002 v v ivvi v i ii vvv iiiv v - vi v C L1M5_orf2#LIN 1882 TGAGGAAGTTCCCTTCTATTCCTAGTTTGCTGAGAGTTTTT-ATCATGAA 1834 chr2ptel1M 38003 TGGGTGTTGGATTTTATCAAATGCTTTTTCTATATATATTGAGATGATCA 38052 i i ii v C L1M5_orf2#LIN 1833 TGGGTGTTGAATTTTGTCAAATGCTTTTTCTGCATCTATTGAGATGATCA 1784 chr2ptel1M 38053 TATGATTTTTGT---TAATTTGGTTATTGCTATGGTTAATTATGTTAATA 38099 v --- v iv ---v v ii i v C L1M5_orf2#LIN 1783 TATGATTTTTCTCCTTTATTCTGTTA---ATATGGTGAATTACATTGATT 1737 chr2ptel1M 38100 GTTTCCCCAATATTGAACCACCCCTGCATTCCTGGTATAAATCTTACTTG 38149 v ii v i i v i v i ii C L1M5_orf2#LIN 1736 GATTTTCGAATGTTAAACCAACCTTGCATTCCTGGGATAAACCCCACTTG 1687 chr2ptel1M 38150 GTCATGGTGTATTATCCTGGGGATGATTTTCTTTAAAT-ATTTTGCTAAT 38198 i vvvv - v vi vi v -iv C L1M5_orf2#LIN 1686 GTCATGATGTATTATCCTTTTTAT-ATATTGCTGGATTCGATTTGCTAAT 1638 chr2ptel1M 38199 GTTTTATTTAAGATTTTTTGCATCACTGTTCAGTAAGAATATTGGTCTAT 38248 i i ? i - vv vv i i i C L1M5_orf2#LIN 1637 ATTTTGTTNAGGATTTTT-GCATCTATGTTCATGAGGGATATTGGTCTGT 1589 chr2ptel1M 38249 AATTTTCTTTCTCTATTTCATCCT-ACCTGGTTTAGGTATCAGTACCATG 38297 iii i vvii i -ii ? v vii? C L1M5_orf2#LIN 1588 AATTTTCTTTTCTTGTAATGTCTTTGTCNGGTTTTGGTATCAGGGTNATG 1539 chr2ptel1M 38298 ATACCC----AAAAGGAATTTGGTAGGACTCCTTTAATCCCTATTTTTTC 38343 v iv ---- v i v v vii i ivv ii i v C L1M5_orf2#LIN 1538 CTGGCCTCATAAAATGAGTTGGGAAGTGTTCCCTCTTTTTCTATTTTCTG 1489 chr2ptel1M 38344 AAATAATTTATATAGGATTGGAGTTAATTTTTCTTTAAATGTTTGGTAGA 38393 i v i i i i vi v i i C L1M5_orf2#LIN 1488 GAAGAGTTTGTGTAAGATTGGTATTATTTCTTCCTTAAATGTTTGGTAGA 1439 chr2ptel1M 38394 ATTCACATGTAAATCCATCTGGTCCTGGGGATTTTGTCTTAGGGAGTTGA 38443 vv i v v i v iv iv i i v vv C L1M5_orf2#LIN 1438 ATTCACCAGTGAAGCCATCTGGGCCTGGAGTTTTCTTTGTGGGAAGGTTT 1389 chr2ptel1M 38444 TTAATAGTTTGTTCTGTTTCTTTTTCTAAA-ATGGGACTATGTAACCAAT 38492 viivvi vi - vv i - i i vi ivivv C L1M5_orf2#LIN 1388 TTAATTACAAATTCAATTTC-TTTAATAGATATAGGGCTATTCAGATTTT 1340 chr2ptel1M 38493 TTACTTCTTCCTCTGTTAATCTTGGCAACTTATATTTTTGAAGGTATTCA 38542 i i i v? i i i i ? i i v v ii C L1M5_orf2#LIN 1339 CTATTTCTTCTTGNGTCAGTTTTGGTAANTTGTGTTTTTCAAGGAATTTG 1290 chr2ptel1M 38543 TCCATTTCATTTAAGTTATCAAATTCATTGACATAAAGTTAGGCAAAGTA 38592 i ? i i ivv v i C L1M5_orf2#LIN 1289 TCCATTTCATCTAAGTTNTCAAATTTATTGGCATAAAGTTGTTCATAATA 1240 chr2ptel1M 38593 -AGTCTTAATTATTGCTTTAATTTGCTCT-TCATTGATGGCAAGGTATCC 38640 -vv - ivi v - v -vv ivi i ii v v C L1M5_orf2#LIN 1239 TTCTCTT-ATTATCCTTTTAATGT-CTGTAGGATCTGTAGTGATGTCTCC 1192 chr2ptel1M 38641 CTTTTCATTTTTGAGACTAACAATTTGATTTTCCTCTTTCATTTTTCTAA 38690 i ii v i iii vv i i i iv ii i C L1M5_orf2#LIN 1191 TTTTTCATTCCTGATATTGGTAATTTGTGTCTTCTCTCTTTTTTTCTTGA 1142 chr2ptel1M 38691 TCAAATTAACAAAATGTTTATTTATTTTGTTGGTTTTTTTTTATAAAACG 38740 ivi ?i v i v iv i i-- i i v i v C L1M5_orf2#LIN 1141 TCAGTCTNGCTAGAGGTTTATCAATTTTATTGA--TCTTTTCAAAGAACC 1094 chr2ptel1M 38741 AACTCTTAATTTTATTTATTATTTTAATAGTTTTTTTTTTAACTTTCCAT 38790 i i iii ii v v i iv v ? ? v ---- i C L1M5_orf2#LIN 1093 AGCTTTTGGCTTCGTTGATTTTCTCTATTGTNTNTTTGT----TTTCTAT 1048 chr2ptel1M 38791 TTTATTAATTTCTCCTTTTATTTTTAGAATTTCAAATTTGGTATTTGACT 38840 i i v i i vv vvvii vv i ?vi C L1M5_orf2#LIN 1047 TTCATTGATTTCTGCTCTTATCTTTATTATTTCCTTCCTTCTACTTNCTT 998 chr2ptel1M 38841 GGGGTTTTTAATTTGC---TCTTTTTCTAACTTTTTTATTTGCAAGCCCA 38887 v -- --- i i v vv v ii C L1M5_orf2#LIN 997 TGGG--TTTAATTTGCTCTTCTTTTTCTAGCTTCTTAAGGTGGAAGCTTA 950 chr2ptel1M 38888 ATTGATTGATCTT---CCTTTTTTTCTATTTTATACAAGTAAGCATTTAG 38934 iv v i --- i ii v i v ---- ? i C L1M5_orf2#LIN 949 GATCATTGATTTTAAGCCTTTCTTCTTTTCTAATA----TANGCATTTAA 904 chr2ptel1M 38935 TGATATAAAATTTTCCCT 38952 ? v -- C L1M5_orf2#LIN 903 NGCTATAAA--TTTCCCT 888 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.86 CpG sites = 354, Kimura (unadjusted) = 38.54 Transitions / transversions = 1.17 (354/302) Gap_init rate = 0.05 (110 / 2318), avg. gap size = 1.53 (168 / 110) 3011 29.69 3.06 2.66 chr2ptel1M 36963 39246 (960754) C L1M5_orf2#LINE/L1 (410) 2884 592 m_b56s551i0 2015 chr2ptel1M 36963 TTGACTTTATCTTGGTATACAGTGTTAAATGTGGGTCCATGCCTAGTTTC 37012 ? v v i v i ii v ii iv v v?iii v i C L1M5_orf2#LIN 2884 TNGAATTAATTTTTGTGTATGGTGTGAGGTAGGGGTCGAGNTTCATTTTT 2835 chr2ptel1M 37013 TGCCATAGTAATTTCCAATTTTCCCAGC--CATTTTTGGCAAATAGTGAA 37060 v vvi v v i -- v v v v v -- C L1M5_orf2#LIN 2834 TTCCATATGGATATCCAATTGTTCCAGCACCATTTGTTGAAAAGACT--A 2787 chr2ptel1M 37061 TTTTTATGCCAA-AAGTTGGGCTCTTTGGG---TTTGTCAAACAATAAAT 37106 ii viv v-i i ---- ? v--- - v ? C L1M5_orf2#LIN 2786 TCCTTTCCCCACTGAATTG----CNTTGGCACCTTTGTCAAA-AATCAAN 2742 chr2ptel1M 37107 TG-CTATAGTCAT-TGACGATTTTTTTCCTGTTAACCTAACCTATTCCAG 37154 - i --i - vv i i v iv vivvi vi i v C L1M5_orf2#LIN 2741 TGNCCATA--TATGTGTGGGTCTATTTCTGGACTCTCTATTCTGTTCCAT 2694 chr2ptel1M 37155 TGATCAACTAGTTCATTTCTTA-GATAGTACTACATGGTAC--ATTACTG 37201 v i v ii i- - vi i i iv vi-- C L1M5_orf2#LIN 2693 TGATCTATTTGTCTATC-CTTACGCCAATACCACACTGTCTTGATTACTG 2645 chr2ptel1M 37202 CTGCTTTATAATAAAATTTTAGATCAGATACAGCTAGG----CCACCTTT 37247 iv ivi v ? ? i vv - i ---- v C L1M5_orf2#LIN 2644 TAGCTTTATAATAAGTCTTGANATCNGGTAGTG-TAAGTCCTCCAACTTT 2596 chr2ptel1M 37248 ATTTGATTTATTTTTCACTAG-TTCCTTTGAA-ATTCTTGACTTTTTATT 37295 i i--- v -- - vi iv- ? iiii iiv C L1M5_orf2#LIN 2595 GTTC---TTCTTTTTCA--AGATTGTTTTGGCTATTCTNGGTCCTTTGCA 2551 chr2ptel1M 37296 CTTCCAGATGAATTTTG---TT-GTTTTTTTTTTTCTAGGTCATTAAACT 37341 i v i i--- i- i v ivv ------i vv C L1M5_orf2#LIN 2550 TTTCCATATAAATTTTAGAATCAGCTTGTCAATTTCTA------CAAAAA 2507 chr2ptel1M 37342 ATTTTTTTGGGAGTCTGATTAGTATAGCACTAAATAAATAGATTAGTTTA 37391 vii vi v i i v v i i vv i i i C L1M5_orf2#LIN 2506 AACCTGCTGGGATTTTGATTGGGATTGCATTGAATCTATAGATCAATTTG 2457 chr2ptel1M 37392 AGTAGTATTGTCATCTTTAATATATTTGCTAGAACTATCCAAGAATACTT 37441 i v v v ? vv viv vvvv v v i ivv C L1M5_orf2#LIN 2456 GGGAGAATTGACATCTTNACAATATTGAGTCTTCCAATCCATGAACATGG 2407 chr2ptel1M 37442 AATATTTTTCCAATTGTT-AGATCTGACTTTATTTGTG-CAGAAAGTGTT 37489 v i i v i - i vvi v v v- v - C L1M5_orf2#LIN 2406 TATATCTCTCCATTTATTTAGGTCTTCTTTAATTTCTCTCAGCAA-TGTT 2358 chr2ptel1M 37490 TTGTAGTTTTGCTCTATATAGTTGTTG-ACTTTCCTTGGTAGTCATAGAT 37538 - vv i ? v v - v ?ii v -- vv C L1M5_orf2#LIN 2357 TTGTAGTTTT-CAGTGTANAGGTCTTGCACATNTTTTGTTAG--ATTTAT 2311 chr2ptel1M 37539 TCCTCAAATATTTTATATTATCAACAGTTATTTTAAGTGGAATTTCTCTT 37588 - i ? i v ivivv i v i v vi i C L1M5_orf2#LIN 2310 TCCT-AAGTATTTNATGTTTTTTGATGCTATTGTAAATGGTATTGTTTTT 2262 chr2ptel1M 37589 ----TTTTATTT--CTGTTGGATTTTGTTATTGATATATAAAAATGCTGA 37632 ---- i -- vi --- ii ii i i viv C L1M5_orf2#LIN 2261 NAAATTTCATTTTCCAATTG---TTTGTTGCTAGTATATAGAAATACAAT 2215 chr2ptel1M 37633 GGATTTATGT----------TGTATCCTGCAACTTTGATAAAGTTATGGA 37672 v v ---------- ? i i v v i ivv C L1M5_orf2#LIN 2214 TGATTTTTGTATATTGACCTTGTATCCNGCGACCTTGCTAAATTCACTTA 2165 chr2ptel1M 37673 TTATTGCTAATAGCTTTTTAGTAGAAGCCCTGGGGTTCTCTAAGTATACC 37722 v v i i ? v vv ii ? i i v ? v C L1M5_orf2#LIN 2164 TTAGTTCTAGTAGTTTNTTTGTAGATTCTTTNGGATTTTCTACGTANACA 2115 chr2ptel1M 37723 ATCATATCATCTGTGAAGAGCCATAATTTG--TTCCTCATTACCTACTCT 37770 i i v i?v i i v-- i v v v iii C L1M5_orf2#LIN 2114 ATCATGTCATCTGCGAATAANGACAGTTTTATTTCTTCCTTTCCAATCTT 2065 chr2ptel1M 37771 AATTCCTTTAATCACTTTTTCATCTCTTATTGCAGAAGCTAACATTTCTA 37820 v v v iv v vi vvi iv ii i C L1M5_orf2#LIN 2064 TATGCCTTTTATTTCTTTTTCTTGCCTTATTGCACTGGCTAGGACCTCCA 2015 chr2ptel1M 37821 ATACAGTACTGAATAGTAATGTTGATAGTGGGCAATCTTGTTTCACTCCT 37870 i i ii v i v ? i i vi i iii i C L1M5_orf2#LIN 2014 GTACAATGTTGAATAGAAGTGGTGANAGCGGACATCCTTGTCTTGTTCCC 1965 chr2ptel1M 37871 GATTTTATTTGGAATAATTCCAGTTTATCACCATTACACATGATGCTTAC 37920 i vvv viv? i ? v vii i ?i C L1M5_orf2#LIN 1964 GATCTTAGGGGGAAAGCNTTCAGTNTTTCACCATTAAGTATGATGTTNGC 1915 chr2ptel1M 37921 TGATGGTTTTAAATAGGTGTTACTGACTATTTTCATGAAAAGTCCATTTA 37970 vv vvi i iivi v ii vv v v ivvi v i C L1M5_orf2#LIN 1914 TGTAGGTTTTTCGTAGATGCCCTTTATCAGGTTGAGGAAGTTCCCTTCTA 1865 chr2ptel1M 37971 TTTTTATAATATCTAGTGTTTTTTAATAAGAATGGGTGTTGGATTTTATC 38020 ii vvv iiiv v - vi v i i C L1M5_orf2#LIN 1864 TTCCTAGTTTGCTGAGAGTTTTT-ATCATGAATGGGTGTTGAATTTTGTC 1816 chr2ptel1M 38021 AAATGCTTTTTCTATATATATTGAGATGATCATATGATTTTTGT---TAA 38067 ii v v --- v C L1M5_orf2#LIN 1815 AAATGCTTTTTCTGCATCTATTGAGATGATCATATGATTTTTCTCCTTTA 1766 chr2ptel1M 38068 TTTGGTTATTGCTATGGTTAATTATGTTAATAGTTTCCCCAATATTGAAC 38117 iv ---v v ii i v v ii v i i C L1M5_orf2#LIN 1765 TTCTGTTA---ATATGGTGAATTACATTGATTGATTTTCGAATGTTAAAC 1719 chr2ptel1M 38118 CACCCCTGCATTCCTGGTATAAATCTTACTTGGTCATGGTGTATTATCCT 38167 v i v i ii i C L1M5_orf2#LIN 1718 CAACCTTGCATTCCTGGGATAAACCCCACTTGGTCATGATGTATTATCCT 1669 chr2ptel1M 38168 GGGGATGATTTTCTTTAAAT-ATTTTGCTAATGTTTTATTTAAGATTTTT 38216 vvvv - v vi vi v -iv i i ? i C L1M5_orf2#LIN 1668 TTTTAT-ATATTGCTGGATTCGATTTGCTAATATTTTGTTNAGGATTTTT 1620 chr2ptel1M 38217 TGCATCACTGTTCAGTAAGAATATTGGTCTATAATTTTCTTTCTCTATTT 38266 - vv vv i i i iii i vv C L1M5_orf2#LIN 1619 -GCATCTATGTTCATGAGGGATATTGGTCTGTAATTTTCTTTTCTTGTAA 1571 chr2ptel1M 38267 CATCCT-ACCTGGTTTAGGTATCAGTACCATGATACCC----AAAAGGAA 38311 ii i -ii ? v vii? v iv ---- v i C L1M5_orf2#LIN 1570 TGTCTTTGTCNGGTTTTGGTATCAGGGTNATGCTGGCCTCATAAAATGAG 1521 chr2ptel1M 38312 TTTGGTAGGACTCCTTTAATCCCTATTTTTTCAAATAATTTATATAGGAT 38361 v v vii i ivv ii i vi v i i i i C L1M5_orf2#LIN 1520 TTGGGAAGTGTTCCCTCTTTTTCTATTTTCTGGAAGAGTTTGTGTAAGAT 1471 chr2ptel1M 38362 TGGAGTTAATTTTTCTTTAAATGTTTGGTAGAATTCACATGTAAATCCAT 38411 vi v i i vv i v C L1M5_orf2#LIN 1470 TGGTATTATTTCTTCCTTAAATGTTTGGTAGAATTCACCAGTGAAGCCAT 1421 chr2ptel1M 38412 CTGGTCCTGGGGATTTTGTCTTAGGGAGTTGATTAATAGTTTGTTCTGTT 38461 v i v iv iv i i v vv viivvi vi C L1M5_orf2#LIN 1420 CTGGGCCTGGAGTTTTCTTTGTGGGAAGGTTTTTAATTACAAATTCAATT 1371 chr2ptel1M 38462 TCTTTTTCTAAAATGGGACTATGTAACCAATTTACTTCTTCCTCTGTTAA 38511 vvivi v i i vi ivivv i i i v? i i C L1M5_orf2#LIN 1370 TCTTTAATAGATATAGGGCTATTCAGATTTTCTATTTCTTCTTGNGTCAG 1321 chr2ptel1M 38512 TCTTGGCAACTTATATTTTTGAAGGTATTCATCCATTTCATTTAAGTTAT 38561 i i ? i i v v ii i ? C L1M5_orf2#LIN 1320 TTTTGGTAANTTGTGTTTTTCAAGGAATTTGTCCATTTCATCTAAGTTNT 1271 chr2ptel1M 38562 CAAATTCATTGACATAAAGTTAGGCAAAGTAAGTCTTAATTATTGCTTTA 38611 i i ivv v i vviii v ivi C L1M5_orf2#LIN 1270 CAAATTTATTGGCATAAAGTTGTTCATAATATTCTCTTATTATCCTTTTA 1221 chr2ptel1M 38612 ATTTGCTCT-TCATTGATGGCAAGGTATCCCTTTTCATTTTTGAGACTAA 38660 v - v -vv ivi i ii v v i ii v i ii C L1M5_orf2#LIN 1220 ATGT-CTGTAGGATCTGTAGTGATGTCTCCTTTTTCATTCCTGATATTGG 1172 chr2ptel1M 38661 CAATTTGATTTTCCTCTTTCATTTTTCTAATCAAATTAACAAAATGTTTA 38710 i vv i i i iv ii i ivi ?i v i v C L1M5_orf2#LIN 1171 TAATTTGTGTCTTCTCTCTTTTTTTCTTGATCAGTCTNGCTAGAGGTTTA 1122 chr2ptel1M 38711 TTTATTTTGTTGGTTTTTTTTTATAAAACGAACTCTTAATTTTATTTATT 38760 iv i i-- i i v i v i i iii ii v C L1M5_orf2#LIN 1121 TCAATTTTATTGA--TCTTTTCAAAGAACCAGCTTTTGGCTTCGTTGATT 1074 chr2ptel1M 38761 ATTTTAATAGTTTTTTTTTTAACTTTCCATTTTATTAATTTCTCCTTTTA 38810 v i iv v ? ? v ---- i i i v i C L1M5_orf2#LIN 1073 TTCTCTATTGTNTNTTTGT----TTTCTATTTCATTGATTTCTGCTCTTA 1028 chr2ptel1M 38811 TTTTTAGAATTTCAAATTTGGTATTTGACTGGGGTTTTTAATTTGC---T 38857 i vv vvvii vv i ?vi v -- --- C L1M5_orf2#LIN 1027 TCTTTATTATTTCCTTCCTTCTACTTNCTTTGGG--TTTAATTTGCTCTT 980 chr2ptel1M 38858 CTTTTTCTAACTTTTTTATTTGCAAGCCCAATTGATTGATCTT---CCTT 38904 i i v vv v ii iv v i --- C L1M5_orf2#LIN 979 CTTTTTCTAGCTTCTTAAGGTGGAAGCTTAGATCATTGATTTTAAGCCTT 930 chr2ptel1M 38905 TTTTTCTATTTTATACAAGTAAGCATTTAGTGATATAAAATTTTCCCTTA 38954 i ii v i v ---- ? i? v v ii i v C L1M5_orf2#LIN 929 TCTTCTTTTCTAATA----TANGCATTTAANGCTATAAATTTCCCTCTAA 884 chr2ptel1M 38955 TTACTGTTTTGGCTGCATCCCACAAATTTTGGTATGTTGTTTCATTATTG 39004 vi i i i v iv i ? C L1M5_orf2#LIN 883 GCACTGCTTTAGCTGCATCCCACAAATTTTGATATGTTGTATTTTCATTN 834 chr2ptel1M 39005 TCATTCTCTTGGATGAAATTATTAATTGTGTCTATGATTTGGTGTTTCAC 39054 vv vi viv v vi viv?i i vv v v C L1M5_orf2#LIN 833 TCATTCAGTTCAAAATATTTTCTAATTTCCNTTGTGATTTCTTCTTTGAC 784 chr2ptel1M 39055 CCATTTATTCTTTAGGA-TGAGATTATTTAGTTTCCAATTTCTTTTGGTC 39103 vvi v i - v - i i v vi vv -- C L1M5_orf2#LIN 783 CCATGGGTTATTTAGAAGTGTG-TTGTTTAATTTCCAAATATTTGGGG-- 737 chr2ptel1M 39104 CATTTTCC-CCTGGCTTT---TTATTGAATGTAATTTTTATTGCATTGTG 39149 - i-v? iv --- v viv v v v C L1M5_orf2#LIN 736 -ATTTTCTAGNTATCTTTTTGTTATTGATTTCTAATTTAATTCCATTGTG 688 chr2ptel1M 39150 ATCTGAAAAGAATGCATTTACTATTTTTGCCTTTTCTGCATTTCAAT--- 39196 i --- i -- -- v v v vi ivv v v ?v --- C L1M5_orf2#LIN 687 GTC---AGAGAA--CA--TACTCTGTATGATTTCAATCCTTTNAAATTTA 645 chr2ptel1M 39197 TTGAG----GTCTTTATGTCCTAATATATGGTCAGTTTTTGTATAGGTTC 39242 ---- - v i i? vi i v v v C L1M5_orf2#LIN 644 TTGAGACTTGT-TTTATGGCCCAGNATATGGTCTATCTTGGTAAATGTTC 596 chr2ptel1M 39243 CATG 39246 C L1M5_orf2#LIN 595 CATG 592 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.70 CpG sites = 340, Kimura (unadjusted) = 39.23 Transitions / transversions = 1.06 (340/320) Gap_init rate = 0.04 (92 / 2283), avg. gap size = 1.42 (131 / 92) 744 26.63 2.03 0.80 chr2ptel1M 40970 41215 (958785) C L1ME5_3end#LINE/L1 (618) 323 75 m_b56s551i1 2016 chr2ptel1M 40970 GCTCTCCAGAATGGTTGGATTCATTAACAACTCCACCAACAATGCATCAG 41019 i v iivi iv vii i i v C L1ME5_3end#LI 323 GCTCTCCAGAATGGCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAG 274 chr2ptel1M 41020 TGTCCAGGTTTCCCT-CATCCCCTCTAACATTCATCATTATTT--TTTTC 41066 v i vvi ? i- i v i i iiv ii--i C L1ME5_3end#LI 273 GGTTCCTATNTCCCCACATCCTCGCCAACACTTGGCATTATCCAGCTTTC 224 chr2ptel1M 41067 TGTCATCTTAGCCAATCTGACAGGTGTGTAGTGGTATCTCAGAGTTATTT 41116 i-- i v i i i iv i vv i C L1ME5_3end#LI 223 TA--ATTTTTGCCAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTT 176 chr2ptel1M 41117 TAATTTGCATTTCTCTGATCAATAGTGATTTGGAACA-CT-TTCATATGA 41164 i v i v v i - - v C L1ME5_3end#LI 175 TAATTTGCATTTCTCTGATTACTAATGAGTTTGAGCATCTCTTCATATGC 126 chr2ptel1M 41165 GTGGAAATAGTTTCAATTTTATCATCTGAAAATTGTCTGTTCATATCCTT 41214 v vv iivv ivii iv v v i C L1ME5_3end#LI 125 TTGTTAGCCTTTCGGGTTTCCTCTTCTGTAAATTGCCTGTTCATATCCTT 76 chr2ptel1M 41215 T 41215 C L1ME5_3end#LI 75 T 75 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 33.22 CpG sites = 38, Kimura (unadjusted) = 33.85 Transitions / transversions = 1.41 (38/27) Gap_init rate = 0.02 (6 / 245), avg. gap size = 1.17 (7 / 6) 36 2.92 0.00 0.00 chr2ptel1M 41392 41426 (958574) (AC)n#Simple_repeat 1 35 (0) c_b56s251i0 2017 chr2ptel1M 41392 ACACACACACACACACACACAAACACACACACACA 41426 v (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACA 35 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 15 33.69 0.00 0.00 chr2ptel1M 42067 42115 (957885) (AA)n#Simple_repeat 1 49 (0) m_b56s252i0 2018 chr2ptel1M 42067 AAATATATAAAAACAAAAAAAAAAGAGAGTGAGAAAAAGAGGAAAAAAA 42115 v v v v i i ivi i i ii (AA)n#Simple_ 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 49 Matrix = Unknown Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 130 28.49 3.77 0.61 chr2ptel1M 42090 42566 (957434) (AGAG)n#Simple_repeat 1 492 (0) m_b56s252i2 2018 chr2ptel1M 42090 AGAGAGTGAGAAAAAGAG-GAAAAAAACAGAGAGAGACAGAAACGGTAAG 42138 v i i - i i i v v i vi vi (AGAG)n#Simpl 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr2ptel1M 42139 AGA-AGGGA-AGACAGAGATTGAGAGAGAAAGAAAGA-AAAGAAATGATT 42185 - i - v vv i i - i i - vv (AGAG)n#Simpl 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA-GAGA 99 chr2ptel1M 42186 AAAAGA-AGTAAAGTGA-AAAAATACAGAGAGAGACAGAACCAGAGCCAG 42233 i i - - i v - i i v v v ivv vv (AGAG)n#Simpl 100 GAGAGAGAG-AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 148 chr2ptel1M 42234 AAAGAGCAAGACAGAGTGAACAAGAAAGAAAAAG-GAGAGA-AAAGA-AG 42280 i vi v v ivi i i i - - i - (AGAG)n#Simpl 149 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 198 chr2ptel1M 42281 TGCCAGATGGAG-GAGAGAGGGAGAG-GGGTGGTGGGGAG-GAGAAAG-G 42326 v vv vi - i - i v ivi i - i - (AGAG)n#Simpl 199 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 248 chr2ptel1M 42327 GGAAAGAGGGAGAGAGACAGAGAGAGAAAGAGAGATAGAGACAGTGAGAT 42376 i i i v i v v v v (AGAG)n#Simpl 249 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 298 chr2ptel1M 42377 AAACAGAAAGACAGAGAAACAGAACAAGAGGGACAGTGAGAGAGAGAGAC 42426 i v i v i v ivi i v v v (AGAG)n#Simpl 299 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 348 chr2ptel1M 42427 AGAGAGAACCAGTGCTAGAGAGAGCAAGACGGAGTGAACAAGAAAGAGAA 42476 ivv v vv vi vi v ivi i i (AGAG)n#Simpl 349 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 398 chr2ptel1M 42477 AG-GAGAGAAAG-GATGTGCCAGATGGAGAGAAAGAGAGGGAGAGTG-GA 42523 - i - - v vv vi i i v - (AGAG)n#Simpl 399 AGAGAGAGAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 447 chr2ptel1M 42524 GGGAG-GAGTGAGAGA-AGAGAGAGAGAGAGAGAGAGAGAGAGAG 42566 i - v - (AGAG)n#Simpl 448 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 492 Matrix = Unknown Transitions / transversions = 1.02 (56/55) Gap_init rate = 0.04 (21 / 476), avg. gap size = 1.00 (21 / 21) 19 16.12 3.92 1.92 chr2ptel1M 42290 42340 (957660) (GAGGGGA)n#Simple_repeat 1 52 (0) m_b56s252i3 2019 chr2ptel1M 42290 GAGGAGAGA-GGGAGAGGGGTG-GTGGGGAGGAGAAAGGGGAAAGAGGGA 42337 i - v - v i i i i - (GAGGGGA)n#Si 1 GAGGGGAGAGGGGAGAGGGGAGAGGGGAGAGGGGAGAGGGGAGAG-GGGA 49 chr2ptel1M 42338 GAG 42340 (GAGGGGA)n#Si 50 GAG 52 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.06 (3 / 50), avg. gap size = 1.00 (3 / 3) 15 33.69 0.00 0.00 chr2ptel1M 42067 42115 (957885) (AA)n#Simple_repeat 1 49 (0) m_b56s252i0 2018 chr2ptel1M 42067 AAATATATAAAAACAAAAAAAAAAGAGAGTGAGAAAAAGAGGAAAAAAA 42115 v v v v i i ivi i i ii (AA)n#Simple_ 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 49 Matrix = Unknown Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 130 28.49 3.77 0.61 chr2ptel1M 42090 42566 (957434) (AGAG)n#Simple_repeat 1 492 (0) m_b56s252i2 2018 chr2ptel1M 42090 AGAGAGTGAGAAAAAGAG-GAAAAAAACAGAGAGAGACAGAAACGGTAAG 42138 v i i - i i i v v i vi vi (AGAG)n#Simpl 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr2ptel1M 42139 AGA-AGGGA-AGACAGAGATTGAGAGAGAAAGAAAGA-AAAGAAATGATT 42185 - i - v vv i i - i i - vv (AGAG)n#Simpl 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA-GAGA 99 chr2ptel1M 42186 AAAAGA-AGTAAAGTGA-AAAAATACAGAGAGAGACAGAACCAGAGCCAG 42233 i i - - i v - i i v v v ivv vv (AGAG)n#Simpl 100 GAGAGAGAG-AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 148 chr2ptel1M 42234 AAAGAGCAAGACAGAGTGAACAAGAAAGAAAAAG-GAGAGA-AAAGA-AG 42280 i vi v v ivi i i i - - i - (AGAG)n#Simpl 149 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 198 chr2ptel1M 42281 TGCCAGATGGAG-GAGAGAGGGAGAG-GGGTGGTGGGGAG-GAGAAAG-G 42326 v vv vi - i - i v ivi i - i - (AGAG)n#Simpl 199 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 248 chr2ptel1M 42327 GGAAAGAGGGAGAGAGACAGAGAGAGAAAGAGAGATAGAGACAGTGAGAT 42376 i i i v i v v v v (AGAG)n#Simpl 249 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 298 chr2ptel1M 42377 AAACAGAAAGACAGAGAAACAGAACAAGAGGGACAGTGAGAGAGAGAGAC 42426 i v i v i v ivi i v v v (AGAG)n#Simpl 299 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 348 chr2ptel1M 42427 AGAGAGAACCAGTGCTAGAGAGAGCAAGACGGAGTGAACAAGAAAGAGAA 42476 ivv v vv vi vi v ivi i i (AGAG)n#Simpl 349 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 398 chr2ptel1M 42477 AG-GAGAGAAAG-GATGTGCCAGATGGAGAGAAAGAGAGGGAGAGTG-GA 42523 - i - - v vv vi i i v - (AGAG)n#Simpl 399 AGAGAGAGAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 447 chr2ptel1M 42524 GGGAG-GAGTGAGAGA-AGAGAGAGAGAGAGAGAGAGAGAGAGAG 42566 i - v - (AGAG)n#Simpl 448 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 492 Matrix = Unknown Transitions / transversions = 1.02 (56/55) Gap_init rate = 0.04 (21 / 476), avg. gap size = 1.00 (21 / 21) 360 16.90 1.25 3.85 chr2ptel1M 44152 44231 (955769) MIR1_Amn#SINE/MIR 87 164 (66) m_b56s601i0 2020 chr2ptel1M 44152 CTGTGTGACCCTGGGCAAGACACCCAGTC-CTGTTTGCCTCAGTTTCCTC 44200 ? i v ii?ii - v v? MIR1_Amn#SINE 87 CTGNGTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTC 136 chr2ptel1M 44201 ATCTGTAAAATGAGCTGGAGAAAGAAATTGA 44231 i--- v v v i MIR1_Amn#SINE 137 ATCTGTAAAATGG---GGATAATGATACTGA 164 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 20.18 CpG sites = 7, Kimura (unadjusted) = 20.18 Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.05 (4 / 79), avg. gap size = 1.00 (4 / 4) 300 24.51 5.50 2.68 chr2ptel1M 44265 44373 (955627) EuthAT-N1#DNA/hAT-Tip100 114 225 (110) m_b56s502i0 2021 chr2ptel1M 44265 TACATTTAGATGGTGCTGACAGCTTTTGCTTTCTTTCAGCAAACTAGAAA 44314 v ---i viv vi i ivv EuthAT-N1#DNA 114 TACATTTACATG---TTGACAGCACATGCACTCCTTCAGCAGCGTAGAAA 160 chr2ptel1M 44315 CAGC-AAGTTT-GTACGTGGTTAGTAAGAA----TACTTAAAATTGATAG 44358 i -i i - i v i i ---- v v iv EuthAT-N1#DNA 161 CAACTGAGCTTAGCACCTAGTTAGCAAGAATAATTAGTTAAAATAGGAAG 210 chr2ptel1M 44359 GTACTAGATGGCATG 44373 v i ii EuthAT-N1#DNA 211 CTACCAGATGGCGCG 225 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 27.57 CpG sites = 15, Kimura (unadjusted) = 30.27 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.06 (6 / 108), avg. gap size = 1.50 (9 / 6) 900 28.47 2.37 2.61 chr2ptel1M 45061 45482 (954518) C L1ME4c_3end#LINE/L1 (398) 432 12 m_b56s551i2 2022 chr2ptel1M 45061 AGCTTTTGATAATCATTTTTTGGGAAGATGTCTTGGGGATATAATCCCAG 45110 ----- v i v i vv v i vi v v C L1ME4c_3end#L 432 AGCTTTT-----TCCTTCTTTTGAATTATTTCCTTAGGATAAATTCCCAG 388 chr2ptel1M 45111 TAGAAATATTGCTTAATCAAACGGTATGCATAGTTTGATAAATTTTTGA- 45159 v viiv i vii v v i v v ii-i i - C L1ME4c_3end#L 387 AAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGG-CTCTTGAT 339 chr2ptel1M 45160 GCATAGTTCCAAACTGCTCTCCAGAAATGTTGGATCCGTTCACAGTTCCA 45209 i i v v i i i iv v i vi i ? v C L1ME4c_3end#L 338 ACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACANTGCCA 289 chr2ptel1M 45210 CTAACAATGTATCAGCATCCTAGTTTTCCCACATCCCCTCCAACATTGGT 45259 i i v ?i v i iv i ? i v i v C L1ME4c_3end#L 288 CCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGCATTGGG 239 chr2ptel1M 45260 CATTATCATTTCCTGTCATCTTAGCCAGTCTAACAGGTGTGTAGTTGTAT 45309 i v ii vvv i v i i i i i iv i v C L1ME4c_3end#L 238 TATTATCAATTTTTTAAATTTTTGCTAATTTAATAGGCGTAAAATGGTAT 189 chr2ptel1M 45310 CTCAGAGTTGTCTTAATTTGTATTTCTCTGATGAATAGTGATTTGGAGCA 45359 vv ii i i v v i vv v i C L1ME4c_3end#L 188 CTCATTGTTGCTTTAATTTGCATTTCTTTGATTACTAGCGAGGTTGAACA 139 chr2ptel1M 45360 CCTTTTCATGTGACTACATA-TAGTTTTAATTTCTTCATCTGAAAAT--- 45405 ii i vi iiv - ? v - i v ? vi --- C L1ME4c_3end#L 138 TTTTTCCATGTGTTTGTTTACTANTTGT-ATTTCCTCTTNTGTGAATTGT 90 chr2ptel1M 45406 -TGTTCATATCCTTTGACCATTTATCAATTGGAGAATGGCTTGAAC---- 45450 - i v v i---- v v?---- C L1ME4c_3end#L 89 CTGTTCATGTCCTTTGCCCATTTATCTATTGGG----GTCTTGATNTTTT 44 chr2ptel1M 45451 CATTATAAATTTGAGTCAATTCGCTATATATT 45482 iv v i v ii vi ? C L1ME4c_3end#L 43 TCTTATCAATTTGAATGAGCTCTTTATATANT 12 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.68 CpG sites = 63, Kimura (unadjusted) = 37.26 Transitions / transversions = 1.17 (63/54) Gap_init rate = 0.04 (15 / 421), avg. gap size = 1.40 (21 / 15) 976 25.36 3.35 3.06 chr2ptel1M 45081 45438 (954562) C L1ME5_3end#LINE/L1 (527) 414 56 m_b56s551i3 2022 chr2ptel1M 45081 TGGGAAGATGTCTTGGGGATATAATCCCAGTAGAAATATTGCTTAATCAA 45130 v ii v v vv v viiv vii v C L1ME5_3end#LI 414 TGTGAGAATTTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCAT 365 chr2ptel1M 45131 ACGGTATGCATAGTTTGATAAATTT--TTGAGCATAGTTCCAAACTGCTC 45178 v i --- iv v --i i -- v v i i C L1ME5_3end#LI 364 AGGGTATGCGTA---TACTTAATTTGACTAAG--TACTGCCAGATTGCTC 320 chr2ptel1M 45179 TCCAGAAATGTTGGATCCGTTCACAGTTCCACTAACAATGTATCAGCAT- 45227 vv i v i v ii v i i i i i v vi - C L1ME5_3end#LI 319 TCCAGAATGGCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTT 270 chr2ptel1M 45228 CCTAGTTTTCCCACATCCCCTCCAACATTGGTCATTATC--ATTTCCTGT 45275 - ? i i v i v v --ii i i- C L1ME5_3end#LI 269 CCTA-TNTCCCCACATCCTCGCCAACACTTGGCATTATCCAGCTTTCTA- 222 chr2ptel1M 45276 CATCTTAGCCAGTCTAACAGGTGTGTAGTTGTATCTCAGAGTTGTCTTAA 45325 - i v i iv vi vv i C L1ME5_3end#LI 221 -ATTTTTGCCAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAA 173 chr2ptel1M 45326 TTTGTATTTCTCTGATGAATAGTGATTTGGAGCACCTTTTCATGTGACTA 45375 i v v i v v i i i vi i C L1ME5_3end#LI 172 TTTGCATTTCTCTGATTACTAATGAGTTTGAGCATCTCTTCATATGCTTG 123 chr2ptel1M 45376 CATATAGTTTT---AATTTCTTCATCTGAAAAT----TGTTCATATCCTT 45418 i--- ii ---ii i v v ---- C L1ME5_3end#LI 122 T---TAGCCTTTCGGGTTTCCTCTTCTGTAAATTGCCTGTTCATATCCTT 76 chr2ptel1M 45419 TGACCATTTATCAATTGGAG 45438 v v v i C L1ME5_3end#LI 75 TGCCCATTTTTCTATTGGGG 56 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 30.69 CpG sites = 48, Kimura (unadjusted) = 31.54 Transitions / transversions = 1.20 (48/40) Gap_init rate = 0.04 (16 / 357), avg. gap size = 1.44 (23 / 16) 247 31.40 2.87 0.94 chr2ptel1M 45348 45556 (954444) C L1M5_orf2#LINE/L1 (0) 3294 3082 m_b56s551i4 2022 chr2ptel1M 45348 TGATTTGGAGCACCTTTTCATGTGACTACATATAGTTTTAATTTCTTCAT 45397 ?v v i vi ivviivi v? v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr2ptel1M 45398 CTG-AAAAT---TGTTCATATCCTTTGACCATTTATCAATTGGA--GAAT 45441 i -i i --- vi i v v ?v i-- vv C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTT 3195 chr2ptel1M 45442 GGCTTGAACCATTATAAATTTGAGTCAATTCGCTATATATTTTAAAAATG 45491 v v--ii? vi ? vivv i vi i ii v i C L1M5_orf2#LIN 3194 GTCTTT--TTNTTATTGANTTGTAGGAGTTCTTTATATATTCTGGATACG 3147 chr2ptel1M 45492 AGTCCTTTATCAGATCCTTTGGATGTAAAAGTGTTTTCCCAGGTTATTGC 45541 i viv vv?v i vi v i ?vi i v C L1M5_orf2#LIN 3146 AGTCCTTTGTCAGATATATGTNTTGCAAATATTTTCTCCCANTCTGTGGC 3097 chr2ptel1M 45542 TTTCCTTCTAATCTT 45556 v i v i C L1M5_orf2#LIN 3096 TTGCCTTTTCATTTT 3082 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 42.23 CpG sites = 31, Kimura (unadjusted) = 43.08 Transitions / transversions = 0.91 (31/34) Gap_init rate = 0.02 (5 / 208), avg. gap size = 1.60 (8 / 5) 334 29.96 5.62 5.32 chr2ptel1M 46475 46830 (953170) C L1MC2_3end#LINE/L1 (458) 633 277 m_b56s551i5 2023 chr2ptel1M 46475 GCTCATTTCACTCAGCATCAGTTCATGTAAG--TCTCTCAGGCCTTTCTG 46522 iv i vi - v v -- iii v i ii C L1MC2_3end#LI 633 GCTTCTTTCACTTAGCAATA-TGCATTTAAGGTTCCTCCATGTCTTTTCG 585 chr2ptel1M 46523 AAATTATCCTGTTGG-TCATTTCTT------ACAGAACAGTAATATTCCA 46565 ---- iv i v i - ------i v --- C L1MC2_3end#LI 584 ----TGGCTTGATAGCTCATTTCTTTTTATCGCTGAA---TAATATTCCA 542 chr2ptel1M 46566 TAATTTTCATATACCACAATTTATTCAACTATTCTCCAACTGATGGACAT 46615 vi v vv i i i i v i v v i v C L1MC2_3end#LI 541 TTGTATGGATGTACCACAGTTTGTTTATCCATTCACCTATTGAAGGACAT 492 chr2ptel1M 46616 CC--ATTCAGTTTCC-AGTTTTAGCCACTACAAA-AGGGCTGCCACAAAC 46661 i--i -- i - i v i ii - ii i i C L1MC2_3end#LI 491 CTTGGTT--GCTTCCAAGTTTTGGCAATTATGAATAAAGCTGCTATAAAC 444 chr2ptel1M 46662 ATTCGTGCACATACAGGTCCCTTT-----CCTTCTTTATAATCTCTTTGG 46706 ---- i iii v ----- v vvv v v v v v C L1MC2_3end#LI 443 ATTCGTG----TGCAGGTTTTTGTGTGGACATAAGTTTTCAACTCATTTG 398 chr2ptel1M 46707 GATATAAT-CCCAGTAGTAACACTTCTGGATCAAAGGGTATGCACA-GTT 46754 i - - v v iivv i v iv v v v?i - C L1MC2_3end#LI 397 GGTA-AATACCAAGGAGCGCGATTGCTGGATCGTATGGTAAGANTATGTT 349 chr2ptel1M 46755 TGATAACTTTTTGAGTATAGTTCCAAACTACTCTCCAAAATGGTTGGATT 46804 --- i v i - v v v iiii i i v ii C L1MC2_3end#LI 348 ---TAGCTTTGTAAG-AAACTGCCAAACTGTCTTCCAAAGTGGCTGTACC 303 chr2ptel1M 46805 CGTTCACAACTCCACCAACAATGCAT 46830 vv ii vii i v C L1MC2_3end#LI 302 ATTTTGCATTCCCACCAGCAATGAAT 277 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.26 CpG sites = 56, Kimura (unadjusted) = 39.28 Transitions / transversions = 1.24 (56/45) Gap_init rate = 0.08 (28 / 355), avg. gap size = 1.39 (39 / 28) 702 25.79 4.21 2.06 chr2ptel1M 46556 46840 (953160) C L1ME4c_3end#LINE/L1 (276) 554 264 m_b56s551i6 2023 chr2ptel1M 46556 TAATATTCCATAATTTTCATATACCACAATTTATTCAACTATTCTCCAAC 46605 vivv ?v i i i i i i v i C L1ME4c_3end#L 554 TAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTAT 505 chr2ptel1M 46606 TGATGGACATCCATTCAGTTTCCAGTTTT-AGCCACTACAAA-AGGGCTG 46653 v ii vviv i -v i i i - iv C L1ME4c_3end#L 504 TGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCTG 455 chr2ptel1M 46654 CCACAAACAT--TCGTGCACATACAGGTCCCTTTCCTTCTTT---ATAAT 46698 v ii -- i v---- ii --- v C L1ME4c_3end#L 454 CAATGAACATCTTCGTGCATATAG----CTTTTTCCTTCTTTTGAATTAT 409 chr2ptel1M 46699 CTCTTTGGGATATAATCCCAGTAGTAACACTTCTGGATCAAAGGGTATGC 46748 i i i v v v iiv i v i v C L1ME4c_3end#L 408 TTCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGA 359 chr2ptel1M 46749 ACAGTTTGATAACTTTT--TGAGTATAGTTCCAAACTACTCTCCAAAATG 46796 v v ii i -- iv -- v i i i v C L1ME4c_3end#L 358 ACATTTTTATGGCTCTTGATACGTAT--TGCCAAATTGCTTTCCAAAAGG 311 chr2ptel1M 46797 GTTGGATTCGTTCACAACTCCACCAACAATGCATCAAT---CCAGTT 46840 v iivi i ?iv i i v i?--- C L1ME4c_3end#L 310 GTTGTACCAATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTT 264 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 32.29 CpG sites = 43, Kimura (unadjusted) = 32.85 Transitions / transversions = 1.48 (43/29) Gap_init rate = 0.04 (12 / 284), avg. gap size = 1.50 (18 / 12) 276 33.42 3.86 3.86 chr2ptel1M 47869 48257 (951743) L1P1_orf2#LINE/L1 23 411 (2883) m_b56s551i7 2024 chr2ptel1M 47869 TAGTAATTTTAACTATAAATGTGAATAGGATGATCTCTCCCATAAAACAG 47918 ii v v i i iv i viv v v - L1P1_orf2#LIN 23 TAACAATATTAACTTTAAATGTAAATGGACTAAATGCTCCAATTAAA-AG 71 chr2ptel1M 47919 AAGTGGG-TAGCAGACTGGATTAAAAGCCAGAATCCTACAATTTGTTGTT 47967 viii i- i i i v i i ii i vv i v i v L1P1_orf2#LIN 72 ACACAGACTGGCAAATTGGATAAAGAGTCAAGACCCATCAGTGTGCTGTA 121 chr2ptel1M 47968 TATAAGAAACTAATGTAAAGCAGAGTGACACATACAGAGTAAAGGTACAA 48017 vi i iv v v v iiv v i i iv v ii v i L1P1_orf2#LIN 122 TTCAGGAAACCCATCTCACGTGCAGAGACACACATAGGCTCAAAATAAAG 171 chr2ptel1M 48018 GGCTAGAGCACAAACTATTATGCTTCAGGTG--AAGTTAGAAAAG-CAGG 48064 v i v vi v ii v --- ii -- iiv i - L1P1_orf2#LIN 172 GGATGGAGGAAGATCTACCAAGC---AAATGGAAAACAAAAAAAGGCAGG 218 chr2ptel1M 48065 CATAGCCATCCTGATCTCAGATCAAGCA------AAAGCAAAAATAGATC 48108 vi v v ii v v i ------ v v - L1P1_orf2#LIN 219 GGTTGCAATCCTAGTCTCTGATAAAACAGACTTTAAACCAACAA-AGATC 267 chr2ptel1M 48109 TAATTAAAAATGACAAGGAAGAAAAGTACATCCTACTAAAAGG-----TA 48153 ----- iv i ivv v vv iv i ----- v L1P1_orf2#LIN 268 -----AAAAGAGACAAAGAAGGCCATTACATAATGGTAAAGGGATCAATT 312 chr2ptel1M 48154 CCACAGAGAATAAAGTAATGTCAATACCAAATATATATGCACCAAGTGGC 48203 v - -i iv --- v v i v i ivv L1P1_orf2#LIN 313 CAACA-AGAA-GAGCTAA---CTATCCTAAATATATATGCACCCAATACA 357 chr2ptel1M 48204 ATAGCATCCAAATTCCTAGAGGAGACATTGAGAGAGCTGCAAGAAGAATT 48253 iv i i v i v iiivi v v i ii v L1P1_orf2#LIN 358 GGAGCACCCAGATTCATAAAGCAAGTCCTGAGTGACCTACAAAGAGACTT 407 chr2ptel1M 48254 AAAC 48257 i L1P1_orf2#LIN 408 AGAC 411 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 45.29 CpG sites = 67, Kimura (unadjusted) = 45.29 Transitions / transversions = 1.16 (67/58) Gap_init rate = 0.05 (20 / 388), avg. gap size = 1.50 (30 / 20) 309 23.99 2.36 4.84 chr2ptel1M 47870 47996 (952004) L1MEh_5end#LINE/L1 2112 2235 (0) m_b56s551i8 2024 chr2ptel1M 47870 AGTAATTTTAACTATAAATGTGAATAGGATGATCTCTCCCAT---AAAAC 47916 --- v i i v i v v v --- i L1MEh_5end#LI 2112 AGTAATT---ACAATAAATGTAAATGGGTTAAACTCACCAATTAAAAGAC 2158 chr2ptel1M 47917 AGAAGTGGGTAGCAGACTGGATTAAAAGCCAGAATCCTACAATTTGTTGT 47966 ii --- ?v i ? iv i v v i L1MEh_5end#LI 2159 AGAGAT---TNTCAGATTGGATTNAAAAACAAAATCCAACAATATGCTGT 2205 chr2ptel1M 47967 TTATAAGAAACTAATGTAAAGCAGAGTGAC 47996 i i i vv iv i ? iv L1MEh_5end#LI 2206 CTACAAGAGACACACTTAAAACANAAGGAC 2235 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 30.23 CpG sites = 16, Kimura (unadjusted) = 30.23 Transitions / transversions = 1.23 (16/13) Gap_init rate = 0.06 (7 / 126), avg. gap size = 1.29 (9 / 7) 257 35.46 5.79 2.97 chr2ptel1M 47873 48494 (951506) L1PREC2_orf2#LINE/L1 27 665 (2629) m_b56s551i9 2024 chr2ptel1M 47873 AATTTTAACTATAAATGTGAATAGGATGATCTCTCCCATAAAACAGAAGT 47922 vi iv i i i v i viv i v v vi v vv L1PREC2_orf2# 27 AATACTAACCTTGAATGTAAATGGGCTAAATGCCCCAATTAAAAGGCACA 76 chr2ptel1M 47923 GGGTAGCAGACTGGATTAAAAGCCAGAATCCTACAATTTGTTGTTTATAA 47972 i i ii v i iv ii i v iii v i i vi L1PREC2_orf2# 77 GAGTGGCAAGCTGGATAAAGAAGCAAGACCCAATGGTATGCTGTCTTCAA 126 chr2ptel1M 47973 GAAACTAATGTAAAGCAGAGTGACACATACAGAGTAAAGGTACAAGGCTA 48022 i iv v v viiiv i vi i iv v ii v i v i L1PREC2_orf2# 127 GAGACCCATCTCACATGCAATGACACCCATAGGCTCAAAATAAAGGGATG 176 chr2ptel1M 48023 GAGCACAAACTATTATGCTTCAGGTG-AAGTTAGAAAA--GCAGGCATAG 48069 v v v ii v --- ii - ivi -- vi v L1PREC2_orf2# 177 GAGAAAAATCTACCAAGC---AAATGGAAAACAGAAAAAAGCAGGGGTTG 223 chr2ptel1M 48070 CCATCCTGATCTCAGATCAAGCA------AAAGCAAAAATAGATCTAATT 48113 v i i iv i ------ v v - ----- L1PREC2_orf2# 224 CAATCCTAATTTCAGACAAAACAGACTTTAAACCAACAA-AGATC----- 267 chr2ptel1M 48114 AAAAATGACAAGGAAGAAAAGTACATCCTACTAAAAGGTAC----CACAG 48159 v i iiv v vv iv i v ---- vvi L1PREC2_orf2# 268 AAAAAAGACAAAGAAGGGCATTACATAATGGTAAAGGGTTCAATTCAACA 317 chr2ptel1M 48160 AGAATAAAGTAATGTCAATACCAAATATATATGCACCAAGTGGCATAGCA 48209 -i vv --- v v i v iiivviv L1PREC2_orf2# 318 AGAA-GACCTAA---CTATCCTAAATATATATGCACCCAACACAGGAGCA 363 chr2ptel1M 48210 TCCAAATTCCTAGAGGAGACATTGAGAGAGCTGCAAGAAGAATTAAA--- 48256 i i v i v iiivi v v ? ii v i --- L1PREC2_orf2# 364 CCCAGATTCATAAAGCAAGTTCTTAGAGACCTNCAAAGAGACTTAGACTC 413 chr2ptel1M 48257 CAGAACTGTACTAGTGGGGTATCTCA--ACCTTGATCTCAGAACTAAATA 48304 viv vi v iv ii -- iiiv vv v i i i L1PREC2_orf2# 414 CCACACAATAATAGTGGGAGACTTCAACACCCCACTGACAGTATTAGACA 463 chr2ptel1M 48305 A---ATTGAAATACAAAATAAATTAGAAAGAAGTTAAGGAGGTAAATAGA 48351 i--- i iii v v i--- vi v vv i ivv L1PREC2_orf2# 464 GATCATCGAGGCAGAAAATTAAC---AAAGATATTCAGGACCTGAACTCA 510 chr2ptel1M 48352 ATTCTAGAAAAGTTAGCTCTCCTAGACCTTTAGAGAA-----------AA 48390 iv i vv iv i vi vv v i v ----------- L1PREC2_orf2# 511 ACACTGGACCAAATGGACCTGATAGACATCTACAGAACTCTCCACCCNAA 560 chr2ptel1M 48391 ATGAATGGACTATGTGTTTTTCTCAGAAGTACATGGAAC-TAATAAAAAA 48439 vv ii v iii i vvivi v - v vv L1PREC2_orf2# 561 AACAACAGAATATACATTCTTCTCATCGCCACATGGCACATACTCTAAAA 610 chr2ptel1M 48440 TTGACCGTACATTAGGGCATAAGAA---CCTCAAAATCAAATGCACAAAG 48486 i ii i v v i i v--- i--- v ii L1PREC2_orf2# 611 TCGACCACATAATCGGACATAAAACAATCCTCAG---CAAATGCAAAAGA 657 chr2ptel1M 48487 ACAGAAAT 48494 v L1PREC2_orf2# 658 ACCGAAAT 665 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 48.42 CpG sites = 113, Kimura (unadjusted) = 49.39 Transitions / transversions = 1.12 (113/101) Gap_init rate = 0.05 (29 / 621), avg. gap size = 1.90 (55 / 29) 321 26.12 0.89 0.89 chr2ptel1M 47884 47995 (952005) L1MEj_5end#LINE/L1 2048 2159 (1) m_b56s551i10 2024 chr2ptel1M 47884 TAAATGTGAATAGGATGATCTCTCCCATAAAACAGA-AGTGGGTAGCAGA 47932 i iv vi v - - v iv iv L1MEj_5end#LI 2048 TAAATGTGAATGGACTGAATTCTCCCATTAAA-AGACAGAGACTGTCAGA 2096 chr2ptel1M 47933 CTGGATTAAAAGCCAGAATCCTACAATTTGTTGTTTATAAGAAACTAATG 47982 i i iv i i vi v v i i vv iv L1MEj_5end#LI 2097 TTGGGTTAAAAAACAAAACCCAGCTATATGCTGTTTACAAGAAACACACT 2146 chr2ptel1M 47983 TAAAGCAGAGTGA 47995 i i L1MEj_5end#LI 2147 TAAAACAAAGTGA 2159 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 32.67 CpG sites = 16, Kimura (unadjusted) = 32.67 Transitions / transversions = 1.23 (16/13) Gap_init rate = 0.02 (2 / 111), avg. gap size = 1.00 (2 / 2) 264 30.26 2.63 0.00 chr2ptel1M 48540 48615 (951385) C MIRc#SINE/MIR (159) 109 32 m_b56s601i1 2025 chr2ptel1M 48540 AAGTGAGTTGTCCAGTTTCACAAAGCTAGTCAATATTTGAGGCAG--TTG 48587 v i ivv v v i iviv v i --i v C MIRc#SINE/MIR 109 AAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTC 60 chr2ptel1M 48588 GAATCCAGTTTTTCCTGATTCTATGTTC 48615 i v i i i v i C MIRc#SINE/MIR 59 GAACCCAGGTCTTCCTGACTCCAAGTCC 32 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.25 CpG sites = 12, Kimura (unadjusted) = 39.40 Transitions / transversions = 1.09 (12/11) Gap_init rate = 0.01 (1 / 75), avg. gap size = 2.00 (2 / 1) 493 20.00 2.36 1.56 chr2ptel1M 48639 48765 (951235) C MER63D#DNA/hAT-Tip100 (590) 471 344 m_b56s502i1 2026 chr2ptel1M 48639 CACAACAGGCTTTAAAATTTTAATTTACAATAT---CATTTTTTTCATCA 48685 i vi v i - i i v --- i i C MER63D#DNA/hA 471 CACGACACACTTTTAAGTTT-AATCTGCATTATTAACATTTTCTCCATCA 423 chr2ptel1M 48686 CTTTCTTAAGTCTATACAATCATCAGAACAATGGATCAAGTCCTGCTAAT 48735 v v i ii i v -v C MER63D#DNA/hA 422 CTTTCTTAAGTCTAGACAATCAACAAAACAATAAATCAAGCCCTGAT-TT 374 chr2ptel1M 48736 GTAGCATTTGTCTCTTTCAGAGGTGTAGAT 48765 i i vv v v i C MER63D#DNA/hA 373 GTAGCGTTTGCCGATTTCCGTGGTGTAAAT 344 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 21.49 CpG sites = 14, Kimura (unadjusted) = 23.54 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.02 (3 / 126), avg. gap size = 1.67 (5 / 3) 468 33.18 1.07 3.28 chr2ptel1M 49028 49214 (950786) MIR3#SINE/MIR 23 205 (3) m_b56s601i2 2027 chr2ptel1M 49028 AGATTACTGCATTTGAAATTAGGAAAACCTGTCTTCAAGTTGTACCTTAG 49077 vi v - i v i i i i - vv v iviiv iv MIR3#SINE/MIR 23 AGAGCACGG-ACTGGGAGTCAGGAGA-CCTGGGTTCTAGTCCCGGCTCTG 70 chr2ptel1M 49078 AGATTTCCTAGCTTTGTGAAACTGAATAAGTCATTTAATCCTTATAGGCC 49127 vv i vv ? v vvi iii i v i ii v i MIR3#SINE/MIR 71 CCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCC 120 chr2ptel1M 49128 TCAGTTCCCTCATTATCTCTAGAATGACGCAGCCAGACTGAACGACTTCT 49177 i --- v i v vi iii ii i ii MIR3#SINE/MIR 121 TCAGTTTCCTC---ATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCT 167 chr2ptel1M 49178 AAGGTGCCTTTTCACTCT-ACA-CCTGTGGGTTCTATGA 49214 v iivi - -i i - i MIR3#SINE/MIR 168 AAGGTCCCTTCCAGCTCTGACATTCTAT-GATTCTATGA 205 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.89 CpG sites = 37, Kimura (unadjusted) = 46.08 Transitions / transversions = 1.61 (37/23) Gap_init rate = 0.04 (8 / 186), avg. gap size = 1.00 (8 / 8) 12 18.61 5.41 0.00 chr2ptel1M 49450 49486 (950514) (GGATTA)n#Simple_repeat 1 39 (0) m_b56s252i4 2028 chr2ptel1M 49450 GGACTAGAATTA--TTTAGGGTTAGGATTAGTGTTAGGA 49486 i i --v i vi (GGATTA)n#Sim 1 GGATTAGGATTAGGATTAGGATTAGGATTAGGATTAGGA 39 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.03 (1 / 36), avg. gap size = 2.00 (2 / 1) 19 22.18 1.64 3.33 chr2ptel1M 49580 49640 (950360) (TCTT)n#Simple_repeat 1 60 (0) m_b56s252i5 2029 chr2ptel1M 49580 TCTCTCTGTTTTTATTTGCTTGCATTGTGT-TTTCTTTCTGTTTTTCTTT 49628 i v i v - v v v v - v i (TCTT)n#Simpl 1 TCTTTCTTTCTTTCTTT-CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT 49 chr2ptel1M 49629 TTCTTCTTTCTT 49640 i - (TCTT)n#Simpl 50 CT-TTCTTTCTT 60 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.05 (3 / 60), avg. gap size = 1.00 (3 / 3) 44 0.00 0.00 0.00 chr2ptel1M 49905 49942 (950058) (TC)n#Simple_repeat 1 38 (0) c_b56s251i1 2030 chr2ptel1M 49905 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 49942 (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 38 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 22 25.74 2.44 2.44 chr2ptel1M 50414 50495 (949505) (TTTTCT)n#Simple_repeat 1 82 (0) m_b56s252i6 2031 chr2ptel1M 50414 TTTTCTGTTTCTTGCTCATTTTCTTTTTTGGGGGTATTCTTTCTTTTCCT 50463 v vi v - vvvvv v - i (TTTTCT)n#Sim 1 TTTTCTTTTTCTTTTTCTTTTTC-TTTTTCTTTTTCTT-TTTCTTTTTCT 48 chr2ptel1M 50464 TTTT-TCCCCCTTTTT-TCTTTCTTTTTTTTTTT 50495 - iiii - i i (TTTTCT)n#Sim 49 TTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTT 82 Matrix = Unknown Transitions / transversions = 0.89 (8/9) Gap_init rate = 0.05 (4 / 81), avg. gap size = 1.00 (4 / 4) 16 16.12 0.00 0.00 chr2ptel1M 53313 53340 (946660) (T)n#Simple_repeat 1 28 (0) m_b56s252i7 2032 chr2ptel1M 53313 TTTTTTTTTTTTGTTGTTGTTGTTTTTT 53340 v v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 28 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 36 6.46 7.58 0.00 chr2ptel1M 53372 53437 (946563) (TC)n#Simple_repeat 1 71 (0) c_b56s251i2 2033 chr2ptel1M 53372 TCTCTCTCTCTC-CTCTCTCTCTCTCTCTCTCT-TCT-TCCCTC-CTTTC 53417 - - - i - i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr2ptel1M 53418 -CTCTTTCCCTCTCTCTCTCT 53437 - i i (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCT 71 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.08 (5 / 65), avg. gap size = 1.00 (5 / 5) 409 22.41 7.53 8.28 chr2ptel1M 54477 54622 (945378) MIRc#SINE/MIR 4 148 (120) m_b56s601i3 2034 chr2ptel1M 54477 GGCAGCTAGGTGCCACAGTAGAGAG-GC------CTTG-AG-CAGGAAGA 54517 ivv --- i i - ------ - - MIRc#SINE/MIR 4 GGCAGTGTGGTGC---AGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA 50 chr2ptel1M 54518 CTTCTATTTATGAACTCAAATCT-GGCTCTTGCCACTTACTAGCTATGTG 54566 i -------- iii i i i- - i MIRc#SINE/MIR 51 CCT--------GGGTTCGAGTCCCGGCTCT-GCCACTTACTAGCTGTGTG 91 chr2ptel1M 54567 ACCCCGGCCAAATCACCTAACC-CTGTTTTTCTCAGCTTTGTCAATTATA 54615 ii v i i - v vvvi i iv vi i MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTA 141 chr2ptel1M 54616 AAATGAG 54622 i MIRc#SINE/MIR 142 AAATGGG 148 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.48 CpG sites = 21, Kimura (unadjusted) = 27.56 Transitions / transversions = 2.33 (21/9) Gap_init rate = 0.12 (18 / 145), avg. gap size = 1.28 (23 / 18) 338 24.97 6.45 3.12 chr2ptel1M 54539 54662 (945338) MIR3#SINE/MIR 62 189 (19) m_b56s601i4 2034 chr2ptel1M 54539 CTGGCTCTTGCCACTTACTAGCTATGTGACCCCGGCCAAATCACCTAACC 54588 i - v ? i ii v i i v MIR3#SINE/MIR 62 CCGGCTCT-GCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACC 110 chr2ptel1M 54589 -CTGTTTTTCTCAGCTTTGTCAATTATAAAATGAGCTGGAGGGAG-AAAT 54636 - v vvvi i iv vi i vv vv v- i MIR3#SINE/MIR 111 TCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGAT 160 chr2ptel1M 54637 GG---CCAA---CCATTCCAGTACCTTTGACA 54662 i--- i --- v --- i MIR3#SINE/MIR 161 GATCTCTAAGGTCCCTTCCAG---CTCTGACA 189 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.81 CpG sites = 15, Kimura (unadjusted) = 31.02 Transitions / transversions = 1.00 (15/15) Gap_init rate = 0.07 (8 / 123), avg. gap size = 1.50 (12 / 8) 17 19.47 0.00 0.00 chr2ptel1M 54948 54978 (945022) (A)n#Simple_repeat 1 31 (0) m_b56s252i8 2035 chr2ptel1M 54948 AAAAAAAAAAAGAGAGAAAAAAAGAAAAGAA 54978 i i i i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 31 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 40 4.81 0.00 0.00 chr2ptel1M 55090 55132 (944868) (AC)n#Simple_repeat 1 43 (0) c_b56s251i3 2036 chr2ptel1M 55090 ACACATACACAGACACACACACACACACACACACACACACACA 55132 i v (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACA 43 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 22 12.61 6.82 0.00 chr2ptel1M 55597 55640 (944360) (TC)n#Simple_repeat 1 47 (0) m_b56s252i9 2037 chr2ptel1M 55597 TCTCTCTCTCCTTTTCTCTC-CTCTC-CTCTC-CACTCTCTCTTTCT 55640 ii i - - - v i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 47 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.07 (3 / 43), avg. gap size = 1.00 (3 / 3) 24 28.44 4.69 2.29 chr2ptel1M 55775 55902 (944098) (TCTCTG)n#Simple_repeat 1 131 (0) m_b56s252i10 2038 chr2ptel1M 55775 TCTCT-CCTCTTTCTCTGGTTTC-CCCTCTGT-T-TATAACTGTCTCTGT 55820 -i v - i -vi - - i vv (TCTCTG)n#Sim 1 TCTCTGTCTCTGTCTCT-GTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGT 49 chr2ptel1M 55821 CTC--TCTCAATCTCTTTGGCTGTCTCCCTCTCTCTTTCTGGCCCATTCA 55868 -- vi v vv iv v i v i vv v (TCTCTG)n#Sim 50 CTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCT 99 chr2ptel1M 55869 CTCTCTAGCTTGCTCTGGCTCATTCTCTGACTCT 55902 v -- vv v vv v (TCTCTG)n#Sim 100 CTGTCT--CTGTCTCTGTCTCTGTCTCTGTCTCT 131 Matrix = Unknown Transitions / transversions = 0.38 (8/21) Gap_init rate = 0.06 (8 / 127), avg. gap size = 1.12 (9 / 8) 12 9.24 0.00 4.17 chr2ptel1M 56157 56181 (943819) (TCC)n#Simple_repeat 1 24 (0) m_b56s252i11 2039 chr2ptel1M 56157 TCCTGCTCCTCCTTCTCCATCCTCC 56181 v i - (TCC)n#Simple 1 TCCTCCTCCTCCTCCTCC-TCCTCC 24 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 229 25.23 6.73 4.72 chr2ptel1M 56782 56885 (943115) Charlie7a#DNA/hAT-Charlie 166 271 (1) m_b56s502i2 2040 chr2ptel1M 56782 TACACATACACGCTTTATAAATAA-------CACACACATTAGAGGCACA 56824 ii i iiv -------i i i i i ii Charlie7a#DNA 166 TACATGTATATAATTTATAAATAAATAAATATACATATATTGGGGGTGCA 215 chr2ptel1M 56825 TGTTTTAAAAAACATTTTACTGTTAGAGGTGAATTTAATCAAAACCAATT 56874 i i-- iv v i v -- i -v i Charlie7a#DNA 216 TGCTC--AAAAATTTTTTACTGATAGGGGTGCA--TGATCAAAA-AAGTT 260 chr2ptel1M 56875 AGGAGACTACT 56885 v i Charlie7a#DNA 261 TGGAGACCACT 271 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 32.62 CpG sites = 19, Kimura (unadjusted) = 32.62 Transitions / transversions = 3.17 (19/6) Gap_init rate = 0.06 (6 / 103), avg. gap size = 2.00 (12 / 6) 416 29.89 1.88 3.82 chr2ptel1M 56887 57046 (942954) C MIR3#SINE/MIR (37) 171 15 m_b56s601i5 2041 chr2ptel1M 56887 CCTTCCAGATCATCTATTCTACCCTCCTCCTCAATTTCCAGATGAGAAAA 56936 vv v i v i v --- v i C MIR3#SINE/MIR 171 CCTTAGAGATCATCTAGTCCAACCCCCTCAT---TTTACAGATGAGGAAA 125 chr2ptel1M 56937 CATAGAACAAAGAAGGTTAACTTAATGTATCCAAGATCACTCAGCTAAAA 56986 vv iv v iii v v v v - ii i v ? ivv C MIR3#SINE/MIR 124 CTGAGGCCCAGAGAGGTGAAGTGACT-TGCCCAAGGTCACACAGCNAGTT 76 chr2ptel1M 56987 GGTGGAAGA-TTAGCTCTAG-ACTCAGGTCCTCTGG-TCCCAAAGCCAGT 57033 i v -iii vv - i ii i- -- i v C MIR3#SINE/MIR 75 AGTGGCAGAGCCGGGACTAGAACCCAGGTCTCCTGACTCCC--AGTCCGT 28 chr2ptel1M 57034 ACTTTTTTTACTC 57046 i i i i i C MIR3#SINE/MIR 27 GCTCTCTCTGCTC 15 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.00 CpG sites = 25, Kimura (unadjusted) = 39.21 Transitions / transversions = 1.19 (25/21) Gap_init rate = 0.06 (9 / 159), avg. gap size = 1.00 (9 / 9) 425 32.06 2.27 0.75 chr2ptel1M 56914 57045 (942955) C MIRb#SINE/MIR (115) 153 20 m_b56s601i6 2041 chr2ptel1M 56914 TCCTCAATTTCCAGATGAGAAAACATAGAACAAAGAAGGTTAACTTAATG 56963 i v v i vv iviv iii v - iv C MIRb#SINE/MIR 153 TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGT-AACT 105 chr2ptel1M 56964 TATCCAAGATCACTCAGCTAAAAGGTGGAAGA--TTAGCTCTAGACTCAG 57011 ii i v iv i v --ivi v iiii i C MIRb#SINE/MIR 104 TGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAG 55 chr2ptel1M 57012 GTCC-TCTGGTCCCAAAGCCAGTACTTTTTTTACT 57045 i- iii v i i ii C MIRb#SINE/MIR 54 GTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACT 20 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.21 CpG sites = 28, Kimura (unadjusted) = 44.23 Transitions / transversions = 2.00 (28/14) Gap_init rate = 0.02 (3 / 131), avg. gap size = 1.33 (4 / 3) 307 27.08 7.36 9.38 chr2ptel1M 57102 57264 (942736) C MIRb#SINE/MIR (81) 187 28 m_b56s601i7 2042 chr2ptel1M 57102 TCTTCCCAAAGATACTGGCGTAGTGGCTATTTCCTTCTCTGGCTCATTTC 57151 i v vi iv - vi i v --v v --- i i C MIRb#SINE/MIR 187 TCCTCACAACAACCCTG-CGAGGTAGGTATT--ATTATC---CCCATTTT 144 chr2ptel1M 57152 ACACAGGAGGAAAC----------AG-GGTTAAGTGACTTACCCAAAGTA 57190 v v ---------- - i i i v C MIRb#SINE/MIR 143 ACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTC 94 chr2ptel1M 57191 ACATAGTTATTGAGTGTCTGAGGTCAGATTTGGACTAATGAACATGAGTC 57240 i i v i v v vivi i i i------ --i C MIRb#SINE/MIR 93 ACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACC------CA--GGTC 52 chr2ptel1M 57241 TTCTCTG-TTCCAAACCTAATGCTC 57264 - v -i v ivi C MIRb#SINE/MIR 51 -TGTCTGACTCCAAAGCCCGTGCTC 28 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.07 CpG sites = 22, Kimura (unadjusted) = 34.11 Transitions / transversions = 1.22 (22/18) Gap_init rate = 0.11 (18 / 162), avg. gap size = 1.50 (27 / 18) 288 24.99 9.03 8.28 chr2ptel1M 57144 57287 (942713) C MIR3#SINE/MIR (63) 145 1 m_b56s601i9 2042 chr2ptel1M 57144 CTCATTTCACACAGGAGGAAAC----------AG-GGTTAAGTGACTTAC 57182 i v v ---------- - v i C MIR3#SINE/MIR 145 CTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGC 96 chr2ptel1M 57183 CCAAAGTAACATAGTTATTGAGTGTCTGAGGTCAGATTTGGACTAATGAA 57232 i v i i? v v v v -- v ---- -- C MIR3#SINE/MIR 95 CCAAGGTCACACAGCNAGTTAGTGGCAGAG--CCG----GGACTA--GAA 54 chr2ptel1M 57233 CATGAGTCTTCTCTGTTCCAAACCTAATGCTCAATTCTGTTT--TCCCTC 57280 viii i vvv i iv --i -vi i i--i v C MIR3#SINE/MIR 53 CCCAGGTCTCCTGACTCCCAGTCC--GTGCTC-TCTCTGCTCAGCCACTC 7 chr2ptel1M 57281 TATCCAG 57287 i- C MIR3#SINE/MIR 6 TG-CCAG 1 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.94 CpG sites = 17, Kimura (unadjusted) = 31.04 Transitions / transversions = 1.06 (17/16) Gap_init rate = 0.10 (15 / 143), avg. gap size = 1.67 (25 / 15) 365 24.74 9.09 6.45 chr2ptel1M 57144 57264 (942736) C MIRc#SINE/MIR (120) 148 25 m_b56s601i8 2042 chr2ptel1M 57144 CTCATTTCACACAGGAGGAAAC----------AG-GGTTAAGTGACTTAC 57182 i i v v ---------- - i C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr2ptel1M 57183 CCAAAGTAACATAGTTATTGAGTGTCTGAGGTCAGATTTGGACTAATGAA 57232 i v i i v i v v -- v ---- --i C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAG--CCG----GGACT--CGAA 57 chr2ptel1M 57233 CATGAGTCTTCTCTGTTCCAAACCTAATGCTC 57264 viii iivii ii i i C MIRc#SINE/MIR 56 CCCAGGTCTTCCTGACTCCAAGTCCAGTGCTC 25 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.88 CpG sites = 19, Kimura (unadjusted) = 31.22 Transitions / transversions = 2.11 (19/9) Gap_init rate = 0.08 (10 / 120), avg. gap size = 1.90 (19 / 10) 13 11.09 3.23 3.23 chr2ptel1M 57812 57842 (942158) (TTGAA)n#Simple_repeat 1 31 (0) m_b56s252i12 2043 chr2ptel1M 57812 TTGAGTTGGAATTGAATAGAAATGAA-TGAAT 57842 i - v v - (TTGAA)n#Simp 1 TTGAATT-GAATTGAATTGAATTGAATTGAAT 31 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2) 19 19.25 0.00 0.00 chr2ptel1M 60327 60362 (939638) (A)n#Simple_repeat 1 36 (0) m_b56s252i13 2044 chr2ptel1M 60327 AAAAACAAACTAAAACAAACAAACAAAAAAAAAAAA 60362 v vv v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 36 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 12 23.34 2.04 4.17 chr2ptel1M 60593 60641 (939359) (TTTGAA)n#Simple_repeat 1 48 (0) m_b56s252i14 2045 chr2ptel1M 60593 TTGGAATTATCACTGTCAATTTGAATTTTAAATTTTAATTT-AAGATGAA 60641 v - v v v v - i v - vv (TTTGAA)n#Sim 1 TTTGAATT-TGAATTTGAATTTGAA-TTTGAATTTGAATTTGAATTTGAA 48 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.06 (3 / 48), avg. gap size = 1.00 (3 / 3) 306 23.10 16.36 1.59 chr2ptel1M 60991 61100 (938900) C MIRc#SINE/MIR (140) 128 3 m_b56s601i10 2046 chr2ptel1M 60991 ACTGAGCCCATCAAA----TTAAATTACTTTCCCAAG----CCCAG---- 61028 v -- i ---- i v v ---- v ---- C MIRc#SINE/MIR 128 ACTGAGGC--TCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG 81 chr2ptel1M 61029 --AGTTGCAGAACCAGAATTTCAACCCATGTC---CCGACTC-AAATATA 61072 -- v i i i i iv v --- i - i vi C MIRc#SINE/MIR 80 TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCA 31 chr2ptel1M 61073 GTGATCTTTCCATTCTGCCATGCTGCCT 61100 v i vii ii C MIRc#SINE/MIR 30 GTGCTCTTTCCACTGCACCACACTGCCT 3 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.67 CpG sites = 15, Kimura (unadjusted) = 28.25 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.07 (8 / 109), avg. gap size = 2.50 (20 / 8) 37 0.00 0.00 0.00 chr2ptel1M 62819 62850 (937150) (AT)n#Simple_repeat 1 32 (0) c_b56s251i4 2047 chr2ptel1M 62819 ATATATATATATATATATATATATATATATAT 62850 (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATAT 32 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 448 24.30 0.74 6.20 chr2ptel1M 63497 63632 (936368) MIR1_Amn#SINE/MIR 1 129 (101) m_b56s601i11 2048 chr2ptel1M 63497 TGGGGAAGCTAGGTGGTCCAATGGATAGAGCACCAGTCCTGAAGTCAGGA 63546 i i viv i i ii v iv i v i MIR1_Amn#SINE 1 TAGGGAGGCAGTGTGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGA 50 chr2ptel1M 63547 GGAAATGAGTTCAAATCTGGTCTCAGACATTTAACACTTCCTGGCTGTGT 63596 - vv i ? ? iv v ------- iv ?v i? ? MIR1_Amn#SINE 51 G-ACCTGGGTTCNANTCCCGGCTC-------TGCCACTNGCCNGCTGNGT 92 chr2ptel1M 63597 GATCCTGGGCAAGTCACTTAACC-CCAAATGCCTCAG 63632 i i ? - ivvi? MIR1_Amn#SINE 93 GACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAG 129 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.77 CpG sites = 18, Kimura (unadjusted) = 32.00 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.07 (9 / 135), avg. gap size = 1.00 (9 / 9) 494 24.65 0.00 6.14 chr2ptel1M 63501 63621 (936379) MIRc#SINE/MIR 2 115 (153) m_b56s601i12 2048 chr2ptel1M 63501 GAAGCTAGGTGGTCCAATGGATAGAGCACCAGTCCTGAAGTCAGGAGGAA 63550 i viv v i v ii v i i i v MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr2ptel1M 63551 ATGAGTTCAAATCTGGTCTCAGACATTTAACACTTCCTGGCTGTGTGATC 63600 v i i i iv v ------- iv v i i MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTC-------TGCCACTTACTAGCTGTGTGACC 94 chr2ptel1M 63601 CTGGGCAAGTCACTTAACCCC 63621 i i MIRc#SINE/MIR 95 TTGGGCAAGTCACTTAACCTC 115 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.18 CpG sites = 17, Kimura (unadjusted) = 30.46 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.06 (7 / 120), avg. gap size = 1.00 (7 / 7) 361 26.71 5.81 5.81 chr2ptel1M 64749 64903 (935097) MIR#SINE/MIR 46 200 (62) m_b56s601i13 2049 chr2ptel1M 64749 GCCTTGAATCAGGAATCCCAGGGTTTTACTTCCACTTCATTAATTTT--- 64795 v iv -- -- i --- v - i ii v --- MIR#SINE/MIR 46 GCCTGGGTTC--GAATCCC--GGCT---CTGCCACTT-ACTAGCTGTGTG 87 chr2ptel1M 64796 ---CTGGTCAAGTTATGGTACCTCTGTGAGATTCAGTTTTTTTATCTGTC 64842 ---i v ivvv v v vi ii i v MIR#SINE/MIR 88 ACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTA 137 chr2ptel1M 64843 AAATGGGTATAATAATAGCAGTTAAGTTCA---GATTCTCATGATGATAA 64889 v i vi - vi --- i v ii v v MIR#SINE/MIR 138 AAATGGGGATAATAATAGTACCT-ACCTCATAGGGTTGTTGTGAGGATTA 186 chr2ptel1M 64890 AATAAGACAACACA 64903 i vi i MIR#SINE/MIR 187 AATGAGTTAATACA 200 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.42 CpG sites = 20, Kimura (unadjusted) = 33.42 Transitions / transversions = 1.05 (20/19) Gap_init rate = 0.08 (12 / 154), avg. gap size = 1.50 (18 / 12) 213 30.14 1.37 0.00 chr2ptel1M 65292 65364 (934636) C MIR3#SINE/MIR (26) 182 109 m_b56s601i14 2050 chr2ptel1M 65292 GCTGGAAGGGCCCTACAGGGCCATGGCGTGTGACCCACTCATTTTGTAGA 65341 v vvii ii vvv vii v ii C MIR3#SINE/MIR 182 GCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGA 133 chr2ptel1M 65342 TG-GGAAATCGAGGTTCACCGAGG 65364 - ii ii vv C MIR3#SINE/MIR 132 TGAGGAAACTGAGGCCCAGAGAGG 109 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.35 CpG sites = 12, Kimura (unadjusted) = 39.35 Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.01 (1 / 72), avg. gap size = 1.00 (1 / 1) 623 29.03 4.30 0.00 chr2ptel1M 65946 66131 (933869) MIRc#SINE/MIR 16 209 (59) m_b56s601i15 2051 chr2ptel1M 65946 CAGTGGA--GAGTCCTGGACATAGAGTCAAGTGTACTTGAGTTTGAAGTG 65993 -- iv v i i viv i i i iviv MIRc#SINE/MIR 16 CAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCC 65 chr2ptel1M 65994 AGCCTTGGACAATTACTAACTGTGTACCTCTGGGCAAGTCAATTAAACTC 66043 v v iv v v i iv ii v v MIRc#SINE/MIR 66 CGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 chr2ptel1M 66044 TGTT-TCCTTAGTTTCCTCAACTCTCAAATGAGGATAACAATATC-AC-- 66089 v v-v i v v v i i i -i -- MIRc#SINE/MIR 116 TCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCC 165 chr2ptel1M 66090 --TCTAACTTGGAAAGTTAAGATGAGGATAAAATGATACAATAT 66131 --i v iiv ii ivvi v v i i MIRc#SINE/MIR 166 TGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGT 209 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.41 CpG sites = 28, Kimura (unadjusted) = 37.27 Transitions / transversions = 1.08 (28/26) Gap_init rate = 0.03 (5 / 185), avg. gap size = 1.60 (8 / 5) 44 1.95 0.00 0.00 chr2ptel1M 66364 66399 (933601) (AC)n#Simple_repeat 1 36 (17) m_b56s252i15 2052 chr2ptel1M 66364 ACACACACACACACACACACACACACACACACACAC 66399 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACAC 36 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 48 0.00 0.00 0.00 chr2ptel1M 66400 66440 (933560) (AT)n#Simple_repeat 1 41 (0) c_b56s251i5 2053 chr2ptel1M 66400 ATATATATATATATATATATATATATATATATATATATATA 66440 (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATA 41 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 44 1.95 0.00 0.00 chr2ptel1M 66441 66456 (933544) (AC)n#Simple_repeat 37 52 (1) m_b56s252i15 2054 chr2ptel1M 66441 CACACAGACACACACA 66456 v (AC)n#Simple_ 37 CACACACACACACACA 52 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 15), avg. gap size = 0.0 (0 / 0) 286 25.63 11.61 2.46 chr2ptel1M 66856 66967 (933033) C MIR3#SINE/MIR (2) 206 85 m_b56s601i16 2055 chr2ptel1M 66856 ATCA-AAAGTCATAAGATGT-GGAACTGAAAGACTCATCAGAAGTAG--- 66900 - i i ii -i i i ivv v i ii vi--- C MIR3#SINE/MIR 206 ATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCT 157 chr2ptel1M 66901 AATCCAACTCCCTTCAATTCATAG--GAGGAGACTGAAACTCAGAGCAGG 66948 i - i v i i -- i ii i - C MIR3#SINE/MIR 156 AGTCCAAC-CCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAG-AGG 109 chr2ptel1M 66949 ------GATTTGCTCAAAGGTCATA 66967 ------ i i - i C MIR3#SINE/MIR 108 TGAAGTGACTTGCCC-AAGGTCACA 85 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.95 CpG sites = 23, Kimura (unadjusted) = 33.95 Transitions / transversions = 4.60 (23/5) Gap_init rate = 0.07 (8 / 111), avg. gap size = 2.00 (16 / 8) 207 31.35 9.09 2.13 chr2ptel1M 66912 66999 (933001) C MIRc#SINE/MIR (119) 149 56 m_b56s601i17 2055 chr2ptel1M 66912 CTTCAATTCATAG--GAGGAGACTGAAACTCAGAGCAGG------GATTT 66953 ii v i i -- i ii - ------ i C MIRc#SINE/MIR 149 CCCCATTTTACAGATGAGGAAACTGAGGCTCAGAG-AGGTTAAGTGACTT 101 chr2ptel1M 66954 GCTCAAAGGTCATAGGCTTTCTAAGAATCAGGGTCAGCTCTTAAAC 66999 i - i vivi vv viv i i i vv ii C MIRc#SINE/MIR 100 GCCC-AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAAC 56 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.48 CpG sites = 18, Kimura (unadjusted) = 42.91 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.05 (4 / 87), avg. gap size = 2.50 (10 / 4) 15 16.57 0.00 0.00 chr2ptel1M 68310 68336 (931664) (TG)n#Simple_repeat 1 27 (0) m_b56s252i16 2056 chr2ptel1M 68310 TGTGTGTAAGAGTGTGTATGTGTGTGT 68336 iv v i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGT 27 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 chr2ptel1M 69392 69409 (930591) (GT)n#Simple_repeat 1 18 (0) m_b56s252i17 2057 chr2ptel1M 69392 GTGTGTGTGTGTGTGTGT 69409 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGT 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 253 27.07 6.36 2.63 chr2ptel1M 70211 70320 (929680) MIRc#SINE/MIR 2 115 (153) m_b56s601i18 2058 chr2ptel1M 70211 GGGGCACTAGGGGTGGCAGTGGGTAGA-CACCAG-CCGGAATTCAGGAGG 70258 i v - v - iv - ii - iv i v i MIRc#SINE/MIR 2 GAGGCAGT-GTGGTG-CAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAG 49 chr2ptel1M 70259 CCCCGAGTCCAAATTAACACCTTAACC-----CTGGCTGTGTGACCCTGG 70303 v i i i i i iv- iv ivi ----- i i MIRc#SINE/MIR 50 ACCTGGGTTCGAGTCC-CGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 98 chr2ptel1M 70304 GAAAGTCACTTAACCCC 70320 v i MIRc#SINE/MIR 99 GCAAGTCACTTAACCTC 115 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.98 CpG sites = 19, Kimura (unadjusted) = 34.94 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.06 (6 / 109), avg. gap size = 1.67 (10 / 6) 228 17.39 2.17 0.00 chr2ptel1M 70286 70331 (929669) MIR#SINE/MIR 77 123 (139) m_b56s601i19 2058 chr2ptel1M 70286 CTGGCTGTGTGACCCTGGGAAAGTCACTTAACCCCAAT-TGCCTAAG 70331 i i v i i vv - v MIR#SINE/MIR 77 CTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAG 123 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 19.89 CpG sites = 4, Kimura (unadjusted) = 19.89 Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1) 18 31.42 2.97 1.96 chr2ptel1M 71518 71618 (928382) (CCCCCTC)n#Simple_repeat 1 102 (0) m_b56s252i18 2059 chr2ptel1M 71518 CCCCCTTCCCCCTCCCCCTTCCCCGCCAGGCTGCTCCTCTCTGAGAGCT- 71566 i i - vvv iv i i vvvvv - (CCCCCTC)n#Si 1 CCCCCTCCCCCCTCCCCCCTCCCC-CCTCCCCCCTCCCCCCTCCCCCCTC 49 chr2ptel1M 71567 CCTCCTCCCCTGCGGCCCCGT--CACTTCCTCCCTCCCCACTCGCCCCTC 71614 i -v vv v -- v i i v v (CCCCCTC)n#Si 50 CCCCCTCCCC-CCTCCCCCCTCCCCCCTCCCCCCTCCCCCCTCCCCCCTC 98 chr2ptel1M 71615 CTCC 71618 i (CCCCCTC)n#Si 99 CCCC 102 Matrix = Unknown Transitions / transversions = 0.56 (9/16) Gap_init rate = 0.04 (4 / 100), avg. gap size = 1.25 (5 / 4) 225 29.98 5.19 2.53 chr2ptel1M 73305 73458 (926542) L2b_3end#LINE/L2 286 443 (23) m_b56s601i20 2060 chr2ptel1M 73305 CCAGTT-TATCCTGTGCACAGCGCGTTTCTATC-TCATTGTTGATGTGT- 73351 i- i i- vvi v vi? i- -- ? v ii - L2b_3end#LINE 286 CCAGTCCTACCCTGC-CACTCTGGGTTATNATTGTC--TGNTTACATGTC 332 chr2ptel1M 73352 TGTCTGCCCCACCAGTCTGTGACCTCCGTGACACCAGGG---GAGGTT-C 73397 v i v v viv --- ? vi -i L2b_3end#LINE 333 TGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGT 382 chr2ptel1M 73398 CTCAAACCTCCTTATGCTCCTGGTGCTTAGCCCAGAGCCTGGCAT-TTGC 73446 iivv vi vi i iii ii i i v ? i-iv i L2b_3end#LINE 383 CTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGT 432 chr2ptel1M 73447 AGGCCCTTCAGT 73458 v - L2b_3end#LINE 433 AGGCGC-TCAGT 443 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.85 CpG sites = 27, Kimura (unadjusted) = 41.06 Transitions / transversions = 1.50 (27/18) Gap_init rate = 0.07 (10 / 153), avg. gap size = 1.20 (12 / 10) 218 34.09 5.30 0.00 chr2ptel1M 73341 73472 (926528) L2d2_3end#LINE/L2 412 550 (5) m_b56s601i21 2060 chr2ptel1M 73341 TGTTGATGTGTTGTCTGCCCCACCAGTCTGTGACCTCCGTGACACCAGGG 73390 v v v v i vi i v v viv L2d2_3end#LIN 412 TGTTTATGTCTTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGG 461 chr2ptel1M 73391 GAGGTTCCTCAAACCTCCTTATGCTCC---TGGTGCTTAGCCCAGAGCCT 73437 ivvi vi i v i i i iii ---ii i i v v L2d2_3end#LIN 462 ACCATGTCTTATACTTCTTTGTATCCCCCACAGCGCCTAGCACAGTGCCT 511 chr2ptel1M 73438 GGCAT-TTGCAGGCCCT---TCAGTGTTTGCCGACTTGA 73472 v i-iv i v --- v i i ii i L2d2_3end#LIN 512 TGCACACAGTAGGCGCTCAATAAATATTTGTTGATTTGA 550 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.63 CpG sites = 26, Kimura (unadjusted) = 47.08 Transitions / transversions = 1.37 (26/19) Gap_init rate = 0.02 (3 / 131), avg. gap size = 2.33 (7 / 3) 316 22.22 4.94 0.00 chr2ptel1M 73557 73637 (926363) C MIR3#SINE/MIR (3) 205 121 m_b56s601i22 2061 chr2ptel1M 73557 TTATAGGATCCTAGAGGATCA---CTGGAAGGGACCTACCAGGCCATCGA 73603 i i v ivi --- vvv ii v C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTA 156 chr2ptel1M 73604 GTGCA-CCTTCTCATGTTACAGATGGGGAAACAGA 73637 v - ii v i v C MIR3#SINE/MIR 155 GTCCAACCCCCTCATTTTACAGATGAGGAAACTGA 121 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.56 CpG sites = 9, Kimura (unadjusted) = 26.56 Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.03 (2 / 80), avg. gap size = 2.00 (4 / 2) 326 23.66 14.88 2.21 chr2ptel1M 74132 74252 (925748) C MIR3#SINE/MIR (7) 201 66 m_b56s601i23 2062 chr2ptel1M 74132 AAAGTCATGAGATAT-AGAAGTGAAAGGCACTTCAGAG---------TCC 74171 i i iii i - iv i v i i --------- C MIR3#SINE/MIR 201 AGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCC 152 chr2ptel1M 74172 AACCTTCTCCAATTTACAG--GAAGATACTGAAGCTCAGA-----GAAAT 74214 ii - v -- i v i i ----- i C MIR3#SINE/MIR 151 AACCCCCTC-ATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGT 103 chr2ptel1M 74215 GATTTGCTCAAGGGTCATCACATTTA-TGGATGTCAGAG 74252 i i - - vi? - vii v C MIR3#SINE/MIR 102 GACTTGCCCAA-GGTCA-CACAGCNAGTTAGTGGCAGAG 66 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.32 CpG sites = 21, Kimura (unadjusted) = 30.32 Transitions / transversions = 3.00 (21/7) Gap_init rate = 0.07 (8 / 120), avg. gap size = 2.62 (21 / 8) 15 21.70 6.00 1.92 chr2ptel1M 74391 74440 (925560) (TA)n#Simple_repeat 1 52 (0) m_b56s252i19 2063 chr2ptel1M 74391 TAAATATGT-TAAAGTATATGT-TAAATGCA-ATATATGTATATATATTT 74437 v i - v - i - v ii - i v (TA)n#Simple_ 1 TATATATATATATA-TATATATATATATATATATATATATATATATATAT 49 chr2ptel1M 74438 ATA 74440 (TA)n#Simple_ 50 ATA 52 Matrix = Unknown Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.08 (4 / 49), avg. gap size = 1.00 (4 / 4) 1225 29.12 3.40 4.25 chr2ptel1M 74681 75297 (924703) C L1ME5_3end#LINE/L1 (274) 667 56 m_b57s551i0 2064 chr2ptel1M 74681 ATGGTATTGTTGTTAAAGTATATAATGATCTACTGCTTCT-GCTCATTTC 74729 - --- ? v- v i-- i -i iv C L1ME5_3end#LI 667 ATGGTATTGT-GTTA---TANATC-TCATT--CTGTTTCTTACTTTTTTC 625 chr2ptel1M 74730 ATTTAGCATCA-GTTCATGTAAG-TCTCTCCAGGCCTCTCTGTTTTCATC 74777 i i ii - -- v - iv v iiv v v v C L1ME5_3end#LI 624 ACTCAGCACTATGTT--TTTAAGATCCATCCATGTTGCTATGTGTACATC 577 chr2ptel1M 74778 CTGCTGGTCATTTCTTACAAAACAATAATATTCCATAATATTCATGTACC 74827 iv iiv iii v vivvvv i i ii i v vi C L1ME5_3end#LI 576 TAGTCCGTTGCTTCTAACTGCTGCATAGTACTCCATGGTGTGCATCCACC 527 chr2ptel1M 74828 ACAATTTATTTAGCCATTCTCCAATTGATGGGCATCTATTCAATTTCCAA 74877 v ii v i v v i i i vviviii C L1ME5_3end#LI 526 ACATTTTACCTATCCACTCTCCCAGTGATGGACACCCAGGTTGCCTCCAA 477 chr2ptel1M 74878 TTTCTTGCCACTATGAAAAGGGCTGCCACAAACATTTTATCACCTACAGG 74927 i i ii i ii v iv v ii ii ---- v v C L1ME5_3end#LI 476 CTCCCCGCCACCACAAACAACGCTGCAATGAACATCCT----CGTACATG 431 chr2ptel1M 74928 TCCCTTTCC---CTTCTTTGATA-TCTATTTGGGATATAAGCCCAGTAGT 74973 i vi--- i v v v - i v vi v i C L1ME5_3end#LI 430 TCCCCTTATGGACCTGTGTGAGAATTTCTTTGGGATATATACCCAGGAGC 381 chr2ptel1M 74974 AACACTGCTGGATCAAAGGGTGTACACAGTTTGATAACTT--TTTGAGTA 75021 iiv i i v i i --- --- - -- v C L1ME5_3end#LI 380 GGAATTGCTGGGTCATAGGGTATGC---GT---ATA-CTTAATTTGACTA 338 chr2ptel1M 75022 --TAGTTCCAAACTGCTTTCTAGAATGGTTGGATCTGTTCACAACTCCAC 75069 -- v v i i i i i v i v ii vii C L1ME5_3end#LI 337 AGTACTGCCAGATTGCTCTCCAGAATGGCTGCACCAGTCTACACTCCCAC 288 chr2ptel1M 75070 CACCAATGTATCAGTGTCCCAGTTTTCCCACATCTCTTCCAACATTTGTC 75119 v i i v v i vi ? i iiiv i v C L1ME5_3end#LI 287 CAGCAGTGCATGAGGGTTCCTATNTCCCCACATCCTCGCCAACACTTGGC 238 chr2ptel1M 75120 ATTATCT---TTTCCTGTCATCTTAGTCAATCTGACATGTGTGTAGTCTT 75166 i--- --- v i v i i i i v iv vv C L1ME5_3end#LI 237 ATTATCCAGCTTTC---TAATTTTTGCCAGTCTAATAGGTGTAAAGTGAT 191 chr2ptel1M 75167 ATCTCAAAGTTGTCTTAATTTGCATTTCTCTGATCTATAATAATTTGGAA 75216 vv i ivv i v v i C L1ME5_3end#LI 190 ATCTCATTGTTGTTTTAATTTGCATTTCTCTGATTACTAATGAGTTTGAG 141 chr2ptel1M 75217 CACCTTTTCATGTGGGTGAAAATAG--TTTC-AATTTCATTATCTAAAAA 75263 i i i vv ---v -- -ii v iv iv C L1ME5_3end#LI 140 CATCTCTTCATATGCTTG---TTAGCCTTTCGGGTTTCCTCTTCTGTAAA 94 chr2ptel1M 75264 T----TGTTCATGTCCTTTGAGCATTTATCAATTGGAG 75297 ---- i vv v v i C L1ME5_3end#LI 93 TTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGGGG 56 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.99 CpG sites = 97, Kimura (unadjusted) = 37.85 Transitions / transversions = 1.29 (97/75) Gap_init rate = 0.06 (37 / 616), avg. gap size = 1.27 (47 / 37) 759 28.31 4.51 5.13 chr2ptel1M 74721 75230 (924770) C L1MC1_3end#LINE/L1 (447) 633 127 m_b56s551i11 2064 chr2ptel1M 74721 GCTCATTTCATTTAGCATCAGTTCATGTAAGTCTC-TCCAGGCCTCTCTG 74769 iv i i vi - v v i - v i ----- C L1MC1_3end#LI 633 GCTTCTTTCACTTAGTAATA-TGCATTTAAGTTTCCTCCATGTCT----- 590 chr2ptel1M 74770 TTTTCAT--CCTGCTGG-TCATTTCTTAC-AAAAC--AATAATATTCCAT 74813 - -- i v i - vi- ivi -- C L1MC1_3end#LI 589 -TTTCATGGCTTGATAGCTCATTTCTTTTTAGCGCTGAATAATATTCCAT 541 chr2ptel1M 74814 AATATTCATGTACCACAATTTATTTAGCCATTCTCCAATTGATGGGCATC 74863 vi v vv i v v v i v i C L1MC1_3end#LI 540 TGTCTGGATGTACCACAGTTTATTTATCCATTCACCTACTGAAGGACATC 491 chr2ptel1M 74864 T--ATTCAATTTCCAATTTCTTGCCACTATGAAAAGGGCTGCCACAAACA 74911 --i --ii v i v v i v ii i i C L1MC1_3end#LI 490 TTGGTT--GCTTCCAAGTTTTGGCAATTATGAATAAAGCTGCTATAAACA 443 chr2ptel1M 74912 TTTTATCACCTACAGGTCCCTTTCCCTTCTTTGATAT----------CTA 74951 i---- iiv i --- --- viv v i ---------- v C L1MC1_3end#LI 442 TC----CGTGTGCAGGT---TTT---TGTGTGGACATAAGTTTTCAACTC 403 chr2ptel1M 74952 TTTGGGATATAAGCCCAGTAGTAACACTGCTGGATCAAAGGGTGTACACA 75001 i v i v vi v v iivv i iv v i--- v C L1MC1_3end#LI 402 CTTTGGGTAAATACCAAGGAGCGCGATTGCTGGATCGTATGGTA---AGA 356 chr2ptel1M 75002 GTTTGATAACTTTT-TGAGTATAGTTCCAAACTGCTTTCTAGAATGGTTG 75050 v v v v - i v - v v ii i i i i C L1MC1_3end#LI 355 GTATGTTTAGTTTTGTAAGAA-ACTGCCAAACTGTCTTCCAAAGTGGCTG 307 chr2ptel1M 75051 GATCTGTTCACAACTCCACCACCAATGTATCAGTGTCCCAGTTTTCCCAC 75100 v i vv ii vii v v v v i v vii C L1MC1_3end#LI 306 TACCATTTTGCATTCCCACCAGCAATGAATGAGAGTTCCTGTTGCTCCAC 257 chr2ptel1M 75101 ATCTCTTCCAACATTTGTCATTATC--TTTTCCTGTCATCTTAGTCAATC 75148 iiiv i vii i -- v iv -- i i i v C L1MC1_3end#LI 256 ATCCTCGCCAGCATTTGGTGTTGTCAGTGTTCTGG--ATTTTGGCCATTC 209 chr2ptel1M 75149 TGACATGTGTGTAGTCTTATCTCAAAGTTGTCTTAATTTGCATTTCTCTG 75198 i i v vv vv i i C L1MC1_3end#LI 208 TAATAGGTGTGTAGTGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTG 159 chr2ptel1M 75199 ATC-TATAATAATTTGGAACACCTTTTCATGTG 75230 v-i - i v i i i C L1MC1_3end#LI 158 ATGACAT-ATGATGTGGAGCATCTTTTCATATG 127 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.48 CpG sites = 73, Kimura (unadjusted) = 36.13 Transitions / transversions = 1.14 (73/64) Gap_init rate = 0.07 (36 / 509), avg. gap size = 1.36 (49 / 36) 1273 29.33 2.43 1.67 chr2ptel1M 74802 75335 (924665) C L1ME4c_3end#LINE/L1 (275) 555 18 m_b57s551i1 2064 chr2ptel1M 74802 ATAATATTCCATAATATTCATGTACCACAATTTATTTAGCCATTCTCCAA 74851 vivi ?v i i i i v C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chr2ptel1M 74852 TTGATGGGCATCTATTCAATTTCCAATTTCTTGCCACTATGAAAAGGGCT 74901 v i i vvivi i i i i i v iv C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCT 456 chr2ptel1M 74902 GCCACAAACATTTTATCACCTACAGGTCCCTTTCCCTTCTTT-GA--TAT 74948 v ii i vvii v i --- i i - -- C L1ME4c_3end#L 455 GCAATGAACATCTTCGTGCATATAG---CTTTTTCCTTCTTTTGAATTAT 409 chr2ptel1M 74949 CTATTTGGGATATAAGCCCAGTAGTAACACTGCTGGATCAAAGGGTGTAC 74998 i vi i v vv v iiv i i i i iv C L1ME4c_3end#L 408 TTCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGA 359 chr2ptel1M 74999 ACAGTTTGATAACTTTT--TGAGTATAGTTCCAAACTGCTTTCTAGAATG 75046 v v ii i -- iv v -- i i i v C L1ME4c_3end#L 358 ACATTTTTATGGCTCTTGATACGTATTG--CCAAATTGCTTTCCAAAAGG 311 chr2ptel1M 75047 GTTGGATCTGTTCACAACTCCACCACCAATGTATCAGTGTCCCAGTTTTC 75096 v i vi i ?iv v v ? v iv C L1ME4c_3end#L 310 GTTGTACCAATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCA 261 chr2ptel1M 75097 CCACATCTCTTCCAACATTTGTCATTATCTTTTCCTGTCATCTTAGTCAA 75146 i ? iiiv i v vi vv ii vvv i v ii C L1ME4c_3end#L 260 CCGCANCCTCGCCAGCATTGGGTATTATCAATTTTTTAAATTTTTGCTAA 211 chr2ptel1M 75147 TCTGACATGTGTGTAGTCTTATCTCAAAGTTGTCTTAATTTGCATTTCTC 75196 i i i v i iv i vv vv ii i C L1ME4c_3end#L 210 TTTAATAGGCGTAAAATGGTATCTCATTGTTGCTTTAATTTGCATTTCTT 161 chr2ptel1M 75197 TGATCTATAATAATTTGGAACACCTTTTCATGTGGGTGAAAATAGTTTCA 75246 ivv iii vv v ii i vv vvv ivi? vv C L1ME4c_3end#L 160 TGATTACTAGCGAGGTTGAACATTTTTCCATGTGTTTGTTTACTANTTGT 111 chr2ptel1M 75247 ATTTCATTATCTAAAAAT----TGTTCATGTCCTTTGAGCATTTATCAAT 75292 v iv ? ivi ---- vv v C L1ME4c_3end#L 110 ATTTCCTCTTNTGTGAATTGTCTGTTCATGTCCTTTGCCCATTTATCTAT 61 chr2ptel1M 75293 TGGAGAATAGCTTGA----TTTCTTATAAATTAGAGTCAATTCTCTA 75335 i ----v ---- v v i v ii i C L1ME4c_3end#L 60 TGGGG----TCTTGATNTTTTTCTTATCAATTTGAATGAGCTCTTTA 18 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.58 CpG sites = 83, Kimura (unadjusted) = 38.49 Transitions / transversions = 1.17 (83/71) Gap_init rate = 0.03 (14 / 533), avg. gap size = 1.57 (22 / 14) 237 23.60 5.30 7.43 chr2ptel1M 75265 75415 (924585) C L1MC_orf2#LINE/L1 (62) 3232 3085 m_b57s551i2 2064 chr2ptel1M 75265 TGTTCATGTCCTTTGAGCATTTATCAATTGGAGAATAGCTTGATTTCTTA 75314 v i vv v ? i i--- v i v C L1MC_orf2#LIN 3232 TGTTCAGGTCTTTTGCCCATTTTTNAATCGGG---TTGTTTGTTTTCTTA 3186 chr2ptel1M 75315 TAAATTAGAGTCAATTCTCTAATTCTCTATATATTTTGGAAATGAGGCCT 75364 vi- - --- ivvv i i i v vv v C L1MC_orf2#LIN 3185 TTG-TT-GAGT---TTTAAGAGTTCTTTGTATATTTTGGATAACAGTCCT 3141 chr2ptel1M 75365 TTATCAGA---ACCTTTGACTGCAAA----CTC-CCCAGTTTATTGCTTC 75406 ---ii --- ----i - i i v v C L1MC_orf2#LIN 3140 TTATCAGATATGTCTTT---TGCAAATATTTTCTCCCAGTCTGTGGCTTG 3094 chr2ptel1M 75407 CCTTCTAAT 75415 i i v C L1MC_orf2#LIN 3093 TCTTTTCAT 3085 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 27.76 CpG sites = 16, Kimura (unadjusted) = 28.75 Transitions / transversions = 0.94 (16/17) Gap_init rate = 0.09 (14 / 150), avg. gap size = 1.36 (19 / 14) 3777 29.60 5.02 3.32 chr2ptel1M 75335 77372 (922628) C L1M5_orf2#LINE/L1 (124) 3170 1105 m_b57s551i3 2064 chr2ptel1M 75335 AATTCTCTATATATTTTGGAAATGAGGCCTTTATCAGAACCTTTG-ACTG 75383 i i i v i v i -iv v -?i C L1M5_orf2#LIN 3170 AGTTCTTTATATATTCTGGATACGAGTCCTTTGTCAGA-TATATGTNTTG 3122 chr2ptel1M 75384 CAAAC----TC-CCCAGTTTATTGCTTCCCTTCTAATCTTGTCTGCATTA 75428 i---- - ? i i v v i v i v ivi iv - C L1M5_orf2#LIN 3121 CAAATATTTTCTCCCANTCTGTGGCTTGCCTTTTCATTTTCTTAACGGT- 3073 chr2ptel1M 75429 GTTTTTT--TGTACAAAAACTTTTCCATTTGATATAATCAAATTT-TCTA 75475 i --? vi i ii vvv i? i v - v C L1M5_orf2#LIN 3072 GTCTTTTGANGAGCAGAAGTTTTTAATTTTGATGNAGTCCAATTTATCAA 3023 chr2ptel1M 75476 TTTTGTGATCAATGAT--GTGCTCTAGTTCTTCTTTGGTCACAAATTCCT 75523 v vv iv i -- i -- v viii v i vi v i C L1M5_orf2#LIN 3022 TTTTTTCTTTTATGGTTNGTGCTTT--TTGTGTCCTGTTTAAGAAATCTT 2975 chr2ptel1M 75524 T-CCTACTCCACAGATCTGAGAGGAAAATAT---CCTATATTCTTTT--- 75566 - ?i - i ---- v i --- i i i --- C L1M5_orf2#LIN 2974 TGCCTANCCCA-AGGTC----ACGAAGATATTCTCCTATGTTTTCTTCTA 2930 chr2ptel1M 75567 -AATTTATTTATAATCTCATTTTTTATGCCTAGATC-ATGAATCCATTTT 75614 - v -- i i i ?i iiii i - - i ? C L1M5_orf2#LIN 2929 GAAGTT--TTATAGTTTTANCTTTTACATTTAGGTCTATGA-TCCATCTN 2883 chr2ptel1M 75615 GATCTTATCTTAGTGTACAGTGTTAAGCGCGGCTCCATGCCTAGTTTCTG 75664 vi v i v ii v i iiv v v v?iii v i v C L1M5_orf2#LIN 2882 GAATTAATTTTTGTGTATGGTGTGAGGTAGGGGTCGAGNTTCATTTTTTT 2833 chr2ptel1M 75665 CCATACTAATTTCCAATTTTCCCAGCCGGTTTTGTCAAATAGTGAATTCT 75714 ivi v v i vvvv ii v vvv i C L1M5_orf2#LIN 2832 CCATATGGATATCCAATTGTTCCAGCACCATTTGTTGAAAAGACTATCCT 2783 chr2ptel1M 75715 TATCCCCA--AAGTTGGGCTCTTTGGG---TTTGTCAAACACTAGATTGC 75759 - --i i ---- ? v--- v ii i? v? C L1M5_orf2#LIN 2782 T-TCCCCACTGAATTG----CNTTGGCACCTTTGTCAAAAATCAANTGNC 2738 chr2ptel1M 75760 TATAGTTAT-TGA--CTATTTTGTTCTGTGAAC---CTGACCTATTCCAC 75803 i vv i - i-- i------ i --- ivi i i C L1M5_orf2#LIN 2737 CATATATGTGTGGGTCTATTTC------TGGACTCTCTATTCTGTTCCAT 2694 chr2ptel1M 75804 TGATCAATTAGTCCATTTCTTA-GCTAATACCACATGGTTTTGATGACTG 75852 v v i i- - i iv i v C L1M5_orf2#LIN 2693 TGATCTATTTGTCTATC-CTTACGCCAATACCACACTGTCTTGATTACTG 2645 chr2ptel1M 75853 TTGCTTTATAATATAGTTTT-AGATCAGATACAGCTAGGCCATGC----T 75897 v - i - ? ? i vv - i i v v ---- C L1M5_orf2#LIN 2644 TAGCTTTATAATA-AGTCTTGANATCNGGTAGTG-TAAGTCCTCCAACTT 2597 chr2ptel1M 75898 TATT-TGATTTTTAAAAATTTCATTAGTTCCCTTGAAATTCTTGACCTTT 75946 i - vv v i viv i i -------- ? ii i C L1M5_orf2#LIN 2596 TGTTCTTCTTTTTCAAGATTGTTTTGGCT--------ATTCTNGGTCCTT 2555 chr2ptel1M 75947 TGTTCTTGCAAATGAATTTTG--------TTGTTATTTTTTCTAGATCAT 75988 ivi v v i i-------- i v i vi i vv - C L1M5_orf2#LIN 2554 TGCATTTCCATATAAATTTTAGAATCAGCTTGTCAATTTCTACAAAAAA- 2506 chr2ptel1M 75989 TAGTTCTTGGGAGTCTGATTAGTATAGGACTAAATAAATAGATTAGTTTA 76038 - vi vi v i i v v v i i vv i i i C L1M5_orf2#LIN 2505 -ACCTGCTGGGATTTTGATTGGGATTGCATTGAATCTATAGATCAATTTG 2457 chr2ptel1M 76039 GGTAGTATTC-CATCTTTAATATATTTGCTAAAACTATCCATATATTTGT 76087 v v v- ? vv ----i iv - --- iii C L1M5_orf2#LIN 2456 GGGAGAATTGACATCTTNACAATATT----GAGTCT-TCCA---ATCCAT 2415 chr2ptel1M 76088 GGATCCACTTAATATTTTTCCAATTGTTTAGATCTGACTTTATTTGTGTG 76137 i -- ivvv i i v i i vvi v v v v C L1M5_orf2#LIN 2414 GAA--CATGGTATATCTCTCCATTTATTTAGGTCTTCTTTAATTTCTCTC 2367 chr2ptel1M 76138 GAAAGTGTTTTGAAGTTTTGCTCATATAGTTCCTGACTTTCCCTTGGTAG 76187 iiv i v vvvii ? v i vviv ?ii v C L1M5_orf2#LIN 2366 AGCAATGTTTTGTAGTTTTCAGTGTANAGGTCTTGCACATNTTTTGTTAG 2317 chr2ptel1M 76188 ATATAGATTCCCAAATATTTTATATTATCAACAGTTATTTTAAATGGAAT 76237 v -- i i ? i v ivivv i v v C L1M5_orf2#LIN 2316 ATTTA--TTCCTAAGTATTTNATGTTTTTTGATGCTATTGTAAATGGTAT 2269 chr2ptel1M 76238 TTCTCTTTGTAT---GTGTTGCTGTTGTATTTTGTAGTGATGTATAAAAA 76284 vi i ?iv ---i v v vi v v i-- ii i i C L1M5_orf2#LIN 2268 TGTTTTTNAAATTTCATTTTCCAATTGTTTGTTGC--TAGTATATAGAAA 2221 chr2ptel1M 76285 TCCTGAGGATTTATGTGGATTTATTTTGTATCCTGCAACTTTGCTAAAGT 76334 v vivv v iv v ii ? i i v C L1M5_orf2#LIN 2220 TACAATTGATTTTTGTATATTGACCTTGTATCCNGCGACCTTGCTAAATT 2171 chr2ptel1M 76335 TATGGATTATTTCTAATAGCTTTTTAGTAGAATCTCTGAGGTTCTTTAAG 76384 i ivv v i i ? v v i ?i i i i v C L1M5_orf2#LIN 2170 CACTTATTAGTTCTAGTAGTTTNTTTGTAGATTCTTTNGGATTTTCTACG 2121 chr2ptel1M 76385 TATACCATCATAACATCTGTGAAAAGCTATAATTTGGTTCCT-CATTACC 76433 ? v iv i v i?v i i vi i - v v C L1M5_orf2#LIN 2120 TANACAATCATGTCATCTGCGAATAANGACAGTTTTATTTCTTCCTTTCC 2071 chr2ptel1M 76434 TACTCTAATTCCTTTAATTTCTTTTTCATCTCTTATTGCAGAAGCTAACA 76483 v iii v v v v vi vvi iv C L1M5_orf2#LIN 2070 AATCTTTATGCCTTTTATTTCTTTTTCTTGCCTTATTGCACTGGCTAGGA 2021 chr2ptel1M 76484 TTTCTAATACAATACTGAATAGTAATGGTGATAGTGGGCCACCTTGTTTC 76533 ii i i ii v i ? i i vv i i C L1M5_orf2#LIN 2020 CCTCCAGTACAATGTTGAATAGAAGTGGTGANAGCGGACATCCTTGTCTT 1971 chr2ptel1M 76534 ACTCCTGATTTTATTGGGAATAATTCCAGTTTATCACCATTACACATGAT 76583 ii i i vv viv? i ? v vii C L1M5_orf2#LIN 1970 GTTCCCGATCTTAGGGGGAAAGCNTTCAGTNTTTCACCATTAAGTATGAT 1921 chr2ptel1M 76584 GCTTACTGATGGTTTTAAATAGATGCTACTGACTATTTTAAGGAAAAGTC 76633 i ?i vv vvi ivi v ii vv i ivvi C L1M5_orf2#LIN 1920 GTTNGCTGTAGGTTTTTCGTAGATGCCCTTTATCAGGTTGAGGAAGTTCC 1871 chr2ptel1M 76634 CATTTATTTCTATAATCT-CT-AGTGTTTTTAATAGGAATGGTTGTTGGA 76681 v i i --i i - - v vi v v i C L1M5_orf2#LIN 1870 CTTCTATTCCTA--GTTTGCTGAGAGTTTTTATCATGAATGGGTGTTGAA 1823 chr2ptel1M 76682 GTTTATCAAATGCTTTTTCTGTATATATTGAGGTGGTCATATGACTTTTG 76731 v i i v i i i v C L1M5_orf2#LIN 1822 TTTTGTCAAATGCTTTTTCTGCATCTATTGAGATGATCATATGATTTTTC 1773 chr2ptel1M 76732 T---TAATTTGGTTATTGTTATAGTCAATTATGTTAATAGTTTCCCCAAT 76778 --- v iv v --- i v ii i v v ii v C L1M5_orf2#LIN 1772 TCCTTTATTCTGTTAAT---ATGGTGAATTACATTGATTGATTTTCGAAT 1726 chr2ptel1M 76779 ATTGAACCACCCCTGCATTCCTGGTATAAATCCTACTTGGTCATGGTGTA 76828 i i v i v i i i C L1M5_orf2#LIN 1725 GTTAAACCAACCTTGCATTCCTGGGATAAACCCCACTTGGTCATGATGTA 1676 chr2ptel1M 76829 TTATCCTGGGGATGATTTTCTTTAAACATTTTGCCAATG-TTTATCTAAG 76877 vvvv ivv v vv vv iv i i- i i? i C L1M5_orf2#LIN 1675 TTATCCTTTTTATATATTGCTGGATTCGATTTGCTAATATTTTGTTNAGG 1626 chr2ptel1M 76878 ATTTTTGCATCACTATTAATTAAGGAGATTGGGCTATAATTTTCTTTCTG 76927 vv i v v i v v i - v C L1M5_orf2#LIN 1625 ATTTTTGCATCTATGTTCATGAGGGATATTGGTCTGTAATTTTCTTT-TC 1577 chr2ptel1M 76928 TTTTCAT---TCTACCTGGTTTAGGTATCAGTATCATGAT-ACC---TAA 76970 v v --- i ii ? v vi ? v -i --- C L1M5_orf2#LIN 1576 TTGTAATGTCTTTGTCNGGTTTTGGTATCAGGGTNATGCTGGCCTCATAA 1527 chr2ptel1M 76971 AAGGAATTTGGTAAAACTTCTTCAATCCCTATTTTTCCAAATAGTTTATA 77020 v i v v ivii i i vv ii iivi v i i C L1M5_orf2#LIN 1526 AATGAGTTGGGAAGTGTTCCCTCTTTTTCTATTTTCTGGAAGAGTTTGTG 1477 chr2ptel1M 77021 TAGGATTGGAGTTAATTGTTCTTTGAATTTTTGGTAGAATTCACATTAAA 77070 i vi v v i i v ---v i C L1M5_orf2#LIN 1476 TAAGATTGGTATTATTTCTTCCTTAAATGTTTGGTAGAATTCAC---CAG 1430 chr2ptel1M 77071 TAAACCCATCTGGTCCTGGGATTTTTTTCTGAGGGA--GTTGACTAATAG 77118 i v v ii i - v -- v-i vi C L1M5_orf2#LIN 1429 TGAAGCCATCTGGGCCTGGAGTTTTCTT-TGTGGGAAGGTTT-TTAATTA 1382 chr2ptel1M 77119 CTTGTTCTATTTCTTTTTTTTAAA-ATGGTACTATTTAACCAATTTACTT 77167 vvi v -- vv i - i vi i ivivv i i C L1M5_orf2#LIN 1381 CAAATTCAATTTC--TTTAATAGATATAGGGCTATTCAGATTTTCTATTT 1334 chr2ptel1M 77168 CTTCCTCTGTTAATCTGGCTAATGTATATTTTTGAAGGTATTCATCCATT 77217 i v? i i i v v ?v i i v v ii C L1M5_orf2#LIN 1333 CTTCTTGNGTCAGTTTTGGTAANTTGTGTTTTTCAAGGAATTTGTCCATT 1284 chr2ptel1M 77218 TCATTTAGGTTATCAAATTTATTGGCATAAAGTTAGCCAAAGTA-ACTCT 77266 i i ? ivi v i -v C L1M5_orf2#LIN 1283 TCATCTAAGTTNTCAAATTTATTGGCATAAAGTTGTTCATAATATTCTCT 1234 chr2ptel1M 77267 GAATTATTGCTCTGATTT------GCTCTTCATTGATGGAAAGTTCTCCC 77310 v- ivi i i v ------ v vi v ------ i C L1M5_orf2#LIN 1233 T-ATTATCCTTTTAATGTCTGTAGGATCTGTAGTGATG------TCTCCT 1191 chr2ptel1M 77311 TTTTCATTTTTGAGACTAACAATTTG-------------ATTTTCCTAAT 77347 ii v i iii -------------v i i C L1M5_orf2#LIN 1190 TTTTCATTCCTGATATTGGTAATTTGTGTCTTCTCTCTTTTTTTCTTGAT 1141 chr2ptel1M 77348 CAAATTAACAAAAGGCTTA-----------GCTATT 77372 ivi ?i v i i ----------- v v C L1M5_orf2#LIN 1140 CAGTCTNGCTAGAGGTTTATCAATTTTATTGATCTT 1105 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.69 CpG sites = 460, Kimura (unadjusted) = 39.27 Transitions / transversions = 1.19 (310/261) Gap_init rate = 0.05 (107 / 2037), avg. gap size = 1.57 (168 / 107) 28 0.00 0.00 0.00 chr2ptel1M 77373 77398 (922602) (TTG)n#Simple_repeat 1 26 (0) c_b57s251i0 2065 chr2ptel1M 77373 TTGTTGTTGTTGTTGTTGTTGTTGTT 77398 (TTG)n#Simple 1 TTGTTGTTGTTGTTGTTGTTGTTGTT 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 3777 29.60 5.02 3.32 chr2ptel1M 77399 78409 (921591) C L1M5_orf2#LINE/L1 (2190) 1104 72 m_b57s551i3 2064 chr2ptel1M 77399 TTATAAAACCAACTCTTAGTTTTATTTATTAATTCAATTTTTTTTTTTTA 77448 i v i i i i i ii v -- vv v v ? ? i C L1M5_orf2#LIN 1104 TCAAAGAACCAGCTTTTGGCTTCGTTGATT--TTCTCTATTGTNTNTTTG 1057 chr2ptel1M 77449 CTTTCCAATTTATTAAAC----CTTTTATTTTTAGAATTTCAAGTTTGGT 77494 i i v i i vi---- i i vv vvvii vv C L1M5_orf2#LIN 1056 TTTTCTATTTCATTGATTTCTGCTCTTATCTTTATTATTTCCTTCCTTCT 1007 chr2ptel1M 77495 AATTGACTGGGGTTTTAAATTTGC---TCTTTTTCTAACTTTTTTATTTG 77541 v ?vi v -- --- i i v vv C L1M5_orf2#LIN 1006 ACTTNCTTTGGGTTT--AATTTGCTCTTCTTTTTCTAGCTTCTTAAGGTG 959 chr2ptel1M 77542 CAAGTCCAACTGATTGATCTT--TTCTTTC-TCTATTTTATGCAAGTAAG 77588 v iii iv v i --vi - v i --- vi ? C L1M5_orf2#LIN 958 GAAGCTTAGATCATTGATTTTAAGCCTTTCTTCTTTTCTA---ATATANG 912 chr2ptel1M 77589 TATTTAGTGATATAAAATTTCCCCTTATTACTGCTTTGGCTGCATTCCTC 77638 i i? v v i i v vi i i v C L1M5_orf2#LIN 911 CATTTAANGCTATAAATTTCCCTCTAAGCACTGCTTTAGCTGCATCCCAC 862 chr2ptel1M 77639 AAATTTTTGTTTGTTTTCTCATTATTGTCATTCTCTTGAATGAAATTATT 77688 vi v v v iv i ? vv v viv v vi C L1M5_orf2#LIN 861 AAATTTTGATATGTTGTATTTTCATTNTCATTCAGTTCAAAATATTTTCT 812 chr2ptel1M 77689 AATTGTGTCTATGATTTGGTGTTTCACCC-TTTATTCTTTAGGA-TGAGA 77736 viv?i i vv v v - vvi v i - v - C L1M5_orf2#LIN 811 AATTTCCNTTGTGATTTCTTCTTTGACCCATGGGTTATTTAGAAGTGTG- 763 chr2ptel1M 77737 TTATTTAGTTTCCAATTTCTTTTGGTCCATTTTCCCCTGGC------TTT 77780 i i v vi vv --- --- i ?------ C L1M5_orf2#LIN 762 TTGTTTAATTTCCAAATATTTGGGG---ATTTT---CTAGNTATCTTTTT 719 chr2ptel1M 77781 G-TATTGAATGTAATTTTTATTGCATTGTGATCTGAAAAGGATGCATT-T 77828 - v viv v v v i v i -v i vi - C L1M5_orf2#LIN 718 GTTATTGATTTCTAATTTAATTCCATTGTGGTCAGAGAA-CATACTCTGT 670 chr2ptel1M 77829 ACTATTTCTGCCTTTCTGCATTTGAATTTAAG----GTCTTTATGTGCTA 77874 iv vii i i?iv i--- i ---- - vv i C L1M5_orf2#LIN 669 ATGATTTCAATCCTTTNAAATTTA---TTGAGACTTGT-TTTATGGCCCA 624 chr2ptel1M 77875 TTATATGGTCAGTTTTTGTATAAGTTCCATGAACTACCAAGAAGAGAGTG 77924 v? vi i v v v vi vviii i iv C L1M5_orf2#LIN 623 GNATATGGTCTATCTTGGTAAATGTTCCATGTGCACTTGAAAAGAATGTG 574 chr2ptel1M 77925 TACTTCTTTC--TGTCTCCATTTAGTTTTCTCCTAAGCTCTATCATACCT 77972 - vi?-- - vvi v? v viv vv v i vii v C L1M5_orf2#LIN 573 TA-TTCTGCNGTTGT-TGGGTGNAGTGTTCTATAAATGTCAATTAGGTCA 526 chr2ptel1M 77973 AACT--TTTCTAGTGTTCTATTTACCTCTTCAAC-TTCTTTCTTATTTGT 78019 ii -- vv -- i i vv v i- i v v -- C L1M5_orf2#LIN 525 AGTTGGTTGATAGTGT--TGTTCAAATCTTCTATATCCTTACTGATT--T 480 chr2ptel1M 78020 TTTGTGGTTTTATT-TATCTAGTTCTGAGAGTACAAGGTTGAGATCTCCC 78068 vvvi i - v v v viv?iv i i ? C L1M5_orf2#LIN 479 TTTGTCTACTTGTTCTATCAATTACTGAGAGAGGNGTGTTAAAATCTCCN 430 chr2ptel1M 78069 ACTATTACAATTTTG---CTGTCTGTTTCTTCTTGCAGCTCTCTTGACTT 78115 --- v ---i i i vi i v iiii C L1M5_orf2#LIN 429 ACTAT---AATTGTGGATTTGTCTATTTCTCCTTTTAGTTCTGTCAGTTT 383 chr2ptel1M 78116 CT--TTCG-GAATTTAGATGCTATACCACTTGGTACATATATGTTTAGTA 78162 i -- i- v v v v iii i v i i ii v C L1M5_orf2#LIN 382 TTGCTTCATGTATTTTGAAGCTCTGTTATTAGGTGCATACACATTTAGGA 333 chr2ptel1M 78163 TTGATATTGCTTCATTGTCTA--TGCTACTTTTAGCAAGATATAGTGCCC 78210 v vv - viv -- viv v vv iv i i C L1M5_orf2#LIN 332 TTGTTATGTCTTC-TTGATGAATTGACCCTTTTATCATTATGAAATGTCC 284 chr2ptel1M 78211 TTCCTTATCTCTTTTAAT-----TTAA--TCAATTTTGCTTTTGCTTGAT 78253 i i vv ----- iv-- v v i i - ii C L1M5_orf2#LIN 283 CTCTTTATCTCTGGTAATATTTCTTGCCTTGAAGTCTAC-TTTGTCTGAT 235 chr2ptel1M 78254 -CTAA---GGCTCCCCCTGCTTT-TTTAACTT--CACTTGAAACATAGTA 78296 -i ---i iv ? v - vi? --iii --- i C L1M5_orf2#LIN 234 ATTAATATAGCCACNCCAGCTTTCTTTTGNTTAGTGTTTG---CATGGTA 188 chr2ptel1M 78297 GATTCTGCTCCAGCCTTTTACCTTTACTCTGTAGGTATTATGCTGCTTCA 78346 v ii vi v i i vi ? vv i iv vv ii v C L1M5_orf2#LIN 187 TATCTTTTTCCATCCTTTTACTTTCAACCTNTCTGTGTCTTTATATTTAA 138 chr2ptel1M 78347 AGTGTGTTTCTTATAAACAACATATTATAGGATTCTGACTTTTAATCCAG 78396 i i i i i vi v i ii vi v C L1M5_orf2#LIN 137 AGTGCGTCTCTTGTAGACAGCATATAGTTGGGTCTTGTTTTTTTATCCAG 88 chr2ptel1M 78397 TCTGCTA---TCTGCC 78409 vi --- C L1M5_orf2#LIN 87 TCTGACAATCTCTGCC 72 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.69 CpG sites = 460, Kimura (unadjusted) = 39.27 Transitions / transversions = 0.99 (150/152) Gap_init rate = 0.06 (58 / 1010), avg. gap size = 1.52 (88 / 58) 26 0.00 0.00 0.00 chr2ptel1M 79787 79811 (920189) (TGTC)n#Simple_repeat 1 25 (0) c_b57s251i1 2066 chr2ptel1M 79787 TGTCTGTCTGTCTGTCTGTCTGTCT 79811 (TGTC)n#Simpl 1 TGTCTGTCTGTCTGTCTGTCTGTCT 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 14 9.31 2.50 7.89 chr2ptel1M 80931 80970 (919030) (CTTGACT)n#Simple_repeat 1 38 (0) m_b57s252i1 2067 chr2ptel1M 80931 CTT-ACTCTTGACTTGTCACTTCTTGTGACTCTTGACTCTT 80970 - iv v - - - (CTTGACT)n#Si 1 CTTGACTCTTGACTCTTGAC-TC-T-TGACTCTTGACTCTT 38 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.10 (4 / 39), avg. gap size = 1.00 (4 / 4) 331 25.83 2.48 0.81 chr2ptel1M 81175 81295 (918705) L1ME3A_3end#LINE/L1 430 552 (368) m_b57s551i4 2068 chr2ptel1M 81175 ATATGTGTAA-AATGTTTGTGGCAGCCCTCGTTGTAGTGGCTAGAAACTG 81223 i ii - ii i v vv i i i i?? L1ME3A_3end#L 430 ACATGTACAAGAATGTTCATAGCAGCACTATTCGTAATAGCCNNAAACTG 479 chr2ptel1M 81224 GAAATTA-GTGGATGCCCATCAATTGGAGAATGC-TGAATAAATTGTGGT 81271 i? -viii i iv v v- i L1ME3A_3end#L 480 GAAACNACCCAAATGTCCATCAACAGTAGAATGGATAAATAAATTGTGGT 529 chr2ptel1M 81272 ATATGAATGTTTATGGAATATTAT 81295 vv ii-iv i L1ME3A_3end#L 530 ATATTCACA-CAATGGAATACTAT 552 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.71 CpG sites = 21, Kimura (unadjusted) = 34.08 Transitions / transversions = 2.10 (21/10) Gap_init rate = 0.03 (4 / 120), avg. gap size = 1.00 (4 / 4) 268 33.70 2.14 1.60 chr2ptel1M 81185 81371 (918629) L1MD2_3end#LINE/L1 441 628 (478) m_b57s551i5 2068 chr2ptel1M 81185 AATGTTTGTGGCAGCCCTCGTTGTAGTGGCTAGAAACTGGAAATTA-GTG 81233 ii i ii vv i i i i i iv -vii L1MD2_3end#LI 441 AATGTTCATAGCAGCTTTATTCGTAATAGCCAAAAACTGGAAACAACCCA 490 chr2ptel1M 81234 GATGCCCATCAATTGGAGAAT-GCTGAATAAATTGTGGTATATGAATGTT 81282 i i v iv v - i i i i i vv i-i L1MD2_3end#LI 491 AATGTCCTTCAACGGGTGAATGGTTAAACAAACTGTGGTACATCCATA-C 539 chr2ptel1M 81283 TATGGAATATTATTGTTCTGTAAAAAATGACCAGCCGGAAGAT-TTCAGA 81331 i i i vvv vi ivi v i iiv-v -iv iv L1MD2_3end#LI 540 CATGGAATACTACTCAGCAATAAAAAGGAACGAACTAT-TGATACACGCA 588 chr2ptel1M 81332 AAGGCTTGGAAAGA-CTTACGTGAACTGATGCTGAGTGAAA 81371 vii vi - i v v i - L1MD2_3end#LI 589 ACAACTTGGATGGATCTCAAGGGAATT-ATGCTGAGTGAAA 628 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.85 CpG sites = 39, Kimura (unadjusted) = 47.00 Transitions / transversions = 1.70 (39/23) Gap_init rate = 0.04 (7 / 186), avg. gap size = 1.00 (7 / 7) 16 10.73 6.67 0.00 chr2ptel1M 81611 81640 (918360) (TA)n#Simple_repeat 1 32 (0) m_b57s252i2 2069 chr2ptel1M 81611 TATATATCCATATAT-TATATTTA-ATATATA 81640 vi - v - (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATA 32 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.07 (2 / 29), avg. gap size = 1.00 (2 / 2) 13 16.94 3.03 0.00 chr2ptel1M 81769 81801 (918199) (TAAA)n#Simple_repeat 1 34 (0) m_b57s252i3 2070 chr2ptel1M 81769 TAAATAAGGCTAT-AATAAATAAATAAACAAATA 81801 ivvv - i (TAAA)n#Simpl 1 TAAATAAATAAATAAATAAATAAATAAATAAATA 34 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 15 27.53 0.00 1.89 chr2ptel1M 82228 82281 (917719) (AAAAAGA)n#Simple_repeat 1 53 (0) m_b57s252i4 2071 chr2ptel1M 82228 AATAATAAAAAAGAAAAGAAGAAAAAGCATACTTGAGAAACAAACAAAGA 82277 v v - iv v vvv i vi v (AAAAAGA)n#Si 1 AAAAAGAAAAAAGAAAA-AAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGA 49 chr2ptel1M 82278 AAAA 82281 (AAAAAGA)n#Si 50 AAAA 53 Matrix = Unknown Transitions / transversions = 0.33 (3/9) Gap_init rate = 0.02 (1 / 53), avg. gap size = 1.00 (1 / 1) 181 37.78 1.44 1.24 chr2ptel1M 83136 84104 (915896) (TC)n#Simple_repeat 1 971 (0) m_b57s252i5 2072 chr2ptel1M 83136 TCTCTCTCTCACTCT-TCTCTACTC-CTCTCTGTTTTTCTCTTTTTCTGA 83183 v - - - v i i i i vv (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTCT 49 chr2ptel1M 83184 CTGTCT-TTTTTCACTCACTGTTTTTTGCTTGCTCTCTCTTTTTCTTTCT 83232 v - i i v v v i i iv iv i i i (TC)n#Simple_ 50 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 99 chr2ptel1M 83233 GACTGTTCCTCTCTCT-TCTCTTTCATTTCGCTCTCACTGTTTCTTTCTC 83281 vv v ii - i - i v v v i i (TC)n#Simple_ 100 CTCTCTCTCTCTCTCTCTCTCTCTC-TCTCTCTCTCTCTCTCTCTCTCTC 148 chr2ptel1M 83282 TCTTTTCCTCTCTCACTCCGTCTCTCTCTCTATCTTTCTGACATTGTATC 83331 i ii v iv v i vv vi v v (TC)n#Simple_ 149 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 198 chr2ptel1M 83332 TGGCTCTGTCTTTTTTGATATCTGTGACTGTCCCTCTTTGCTGTCCCTTG 83381 vv v i i ivv v v vv v i i - v i iv (TC)n#Simple_ 199 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT-CTCTCTCTCT 247 chr2ptel1M 83382 GAATCACT-TTTTTTTTTCTTTCTCACTCTCAATTTC-CTCATCTGTTGG 83429 vvv v - i i i i i v vv i - - v ivv (TC)n#Simple_ 248 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TCTCTCTC 296 chr2ptel1M 83430 TGT-TTTCTTTCTCTATCCCTCTTTTTGTTTCTCTCTTTTGTTCTCTATT 83478 v - i i v i i i v i i ivi v i (TC)n#Simple_ 297 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 346 chr2ptel1M 83479 TCTTTCTACCTCTCTCTGTTTCTTTCTCTCTTTCTCACCCTTTTTTTCTC 83528 i vi v i i i v i i i i (TC)n#Simple_ 347 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 396 chr2ptel1M 83529 ACTATCTGGGTGGACCCAGATTTCAGATTCTTTCTCACTTTCTGTCTGTC 83578 v v vvv -vv i -vv i vvvi i v i v v (TC)n#Simple_ 397 TCTCTCTCTCT-CTCTC-TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 444 chr2ptel1M 83579 TATTGGTCTCTTTCTCTTTTTGTCTCAGACCCTTTCTATTACTCTTTCCC 83628 v ivv i i i v vvv i i v iv i i (TC)n#Simple_ 445 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 494 chr2ptel1M 83629 TCATTTTCTGTTTCTCTAACTCTCTCTTCCTATCTTTTTCACTCTTACTC 83678 vi i v i vv ii v i i v iv (TC)n#Simple_ 495 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 544 chr2ptel1M 83679 TCTGACAATCTTTGCCTATCTCTTTCTGATTCTGTTCCTTTCTCTCCTTT 83728 vv vv i vi v i vvi v ii i ii i (TC)n#Simple_ 545 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 594 chr2ptel1M 83729 TCTTTTTCTCTCTCACCTTCTCTATTTC-CTTTTATTCTCTCTCTCTCTC 83777 i i v ii v i - i ivi (TC)n#Simple_ 595 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 644 chr2ptel1M 83778 TGTCTCTCTCTGTCTGTCTCTTTGTCTCTCTGTCTCTCTGTCTCTTTCCC 83827 v v v i v v v i i (TC)n#Simple_ 645 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 694 chr2ptel1M 83828 TCCCTCTCT-TCT-TCCCTTTCTCCTTCCCTCTCTCTCCCCCCCCCATCC 83875 i - - i i ii i i i i i - i (TC)n#Simple_ 695 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TCT 743 chr2ptel1M 83876 CTACTTTCTGGATCTCTTTTTCTCTCTCTGGTACTTTGTTTCTATCCTTC 83925 - i vvv i i -v - i v i v ii (TC)n#Simple_ 744 CT-CTCTCTCTCTCTCTCTCTCTCTCTCT-CT-CTCTCTCTCTCTCTCTC 790 chr2ptel1M 83926 TCTCTTGCT-TCACTCTCTCTATCTCTACCTTGGTTTGCGTGTGTCTCAG 83974 iv - v v vi ivv i - - v v vv (TC)n#Simple_ 791 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT-C-TCTCTCTCTC 838 chr2ptel1M 83975 TCTCTCTTTTTC-CTTTCACTCTCACTGTTTCTTTATTTCTCTTATTCTC 84023 i i - i v v v i i v i ivi (TC)n#Simple_ 839 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 888 chr2ptel1M 84024 TGGCTTCCCCTGTTTCTGTTCCTGTCTGTCTTTTTC-CTCTGACTCT-TC 84071 vv ii i v i v ii v v i i - vv - (TC)n#Simple_ 889 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 938 chr2ptel1M 84072 TTTTACTCTCTCTTTCTCTTTTTCTTTCTCTCT 84104 i iv i i i i (TC)n#Simple_ 939 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 971 Matrix = Unknown Transitions / transversions = 1.09 (145/133) Gap_init rate = 0.03 (26 / 968), avg. gap size = 1.00 (26 / 26) 21 16.01 0.00 0.00 chr2ptel1M 84112 84146 (915854) (T)n#Simple_repeat 1 35 (0) m_b57s252i6 2073 chr2ptel1M 84112 TTGTTTCTTTTTTTTTTTTTTTTTTTGTCTTTCTT 84146 v i v i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 35 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 47 2.26 0.00 0.00 chr2ptel1M 84398 84442 (915558) (TC)n#Simple_repeat 1 45 (0) c_b57s251i2 2074 chr2ptel1M 84398 TCTCTCTCTCTCTCTATCTCTCTCTCTCTCTCTCTCTCTCTCTCT 84442 v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 45 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 664 32.46 4.96 2.78 chr2ptel1M 84678 85241 (914759) C L1MA10_3end#LINE/L1 (448) 633 58 m_b57s551i6 2075 chr2ptel1M 84678 GCTCACTTCACTCAGCATAAGGTCATGTAAGTCTTGCCAGGCCTCTCTGA 84727 i i i v v vi i iivv v i- v vv C L1MA10_3end#L 633 GCTTATTTCACTTAGCATAATGTCCTCCAGGTTCATCCATGT-TGTCGCA 585 chr2ptel1M 84728 AATCATCCTGCTGG------TTCGTTTTTACAGAAT-AATAATATTCCAT 84770 v----- v ------ v - iv - C L1MA10_3end#L 584 AATG-----GCAGGATTTCCTTCTTTTTTA-AGGCTGAATAATATTCCAT 541 chr2ptel1M 84771 AACATCCATATACCATAGTTTATTCAGCCGTTCTCCAGTTGATGGGCATC 84820 vii vi i v v i v i vi v i i i C L1MA10_3end#L 540 TGTATGTATATACCACATTTTCTTTATCCATTCATCCGTCGATGGACATT 491 chr2ptel1M 84821 CACTCAGTTTCGGTTTCTTGAC-ACTACAAAGAGGGCTGCCACAAACATT 84869 i vviv vi v i - i iii v iv v ii v C L1MA10_3end#L 490 TAGGTTGTTTCCATATCTTGGCTATTGTGAATAATGCTGCAATGAACATG 441 chr2ptel1M 84870 T---TGCACATGTGGATCACTTT----TCCTCTTTTACATCTCTTTGGGG 84912 v--- v ---- v i---- vv - vi v i C L1MA10_3end#L 440 GGAGTGCAGAT----ATCTCTTCGAGATCCTGATTT-CAATTCTTTTGGA 396 chr2ptel1M 84913 TAGAAAC-----------ACTGCTGGATCAAAGGGT-GTGCATGGCTTGA 84950 v v ----------- i v v - v - ivi -- C L1MA10_3end#L 395 TATATACCCAGAAGTGGGATTGCTGGATCATATGGTAGTTC-TATTTT-- 349 chr2ptel1M 84951 TAATGCTTTGGGTATAGTTCTACATTTCTCTCCAGATTCTTTGGATCAGT 85000 vi i v - vi i i i vi i v v vvi v i ? C L1MA10_3end#L 348 TAATTTTTTGAGGA-ACCTCCATACTGTTTTCCATAGTGGCTGCACCANT 300 chr2ptel1M 85001 TTTCAACTCCACCAACAATGTATTAGTGTCCCAATTTTCCCATATCCCCT 85050 v vii i iv v i ?? ii i i v C L1MA10_3end#L 299 TTACATTCCCACCAACAGTGTACAAGGGTTCCNNTTTCTCCACATCCTCG 250 chr2ptel1M 85051 CCAACATTTGTCATTATCTTTTCCTGTCATCTCAGTCAAACTGAGAGGTG 85100 i i iv i v ii v v vvi i vv i v C L1MA10_3end#L 249 CCAACACTTGTTATCTTTTGTTTTTTTGATAATAGCCATCCTAACAGGTG 200 chr2ptel1M 85101 TGTAGTGATAGCTAAGAGTTGTCTTAATTGGTATTTCTCTGATCAATAGT 85150 vi v v vv v i i v i i v v C L1MA10_3end#L 199 TGAGGTGATATCTCATTGTGGTTTTGATTTGCATTTCCCTGATGATTAGT 150 chr2ptel1M 85151 GATTTAGAGCTTCTTTTCATTTGACTAGAAATGGTTTTAATTTCTTTATT 85200 v v vi v iv ivviiivi vv v iv C L1MA10_3end#L 149 GATGTTGAGCACCTTTTCATATACCTGTTGGCCATTTGTATGTCTTCTTT 100 chr2ptel1M 85201 TGCAAATTGCTTGTTCATAT-CTTTGGTCATTTATCAGTTGG 85241 v vi v ii i vi - vi v i i i C L1MA10_3end#L 99 GGAGAAATGTCTATTCAGGTCCTTTGCCCATTTTTTAATCGG 58 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 42.47 CpG sites = 86, Kimura (unadjusted) = 43.42 Transitions / transversions = 0.93 (86/92) Gap_init rate = 0.04 (24 / 563), avg. gap size = 1.83 (44 / 24) 1022 30.34 5.43 3.11 chr2ptel1M 84759 85292 (914708) C L1ME5_3end#LINE/L1 (389) 552 7 m_b57s551i7 2075 chr2ptel1M 84759 ATAATATTCCATAACATCCATATACCATAGTTTATTCAGCCGTTCTCCAG 84808 i i iiii v vi i v iii v ii vi C L1ME5_3end#LI 552 ATAGTACTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCA 503 chr2ptel1M 84809 TTGATGGGCATCCAC-TCAGTTTCGGTTTCTTGACACTACAAAGAGGGCT 84857 v i i v- iivi i iii i ii v i v iv C L1ME5_3end#LI 502 GTGATGGACACCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCT 453 chr2ptel1M 84858 GCCACAAACATTTT-GCACATGTGGATCACTTTT---CCTCTTTTACA-T 84902 v ii ii - i ---i v v --- v v v v - C L1ME5_3end#LI 452 GCAATGAACATCCTCGTACATGT---CCCCTTATGGACCTGTGTGAGAAT 406 chr2ptel1M 84903 CTCTTTGGGGTA--------GAAAC---ACTGCTGGATCAAAGGGTGTGC 84941 i i -------- i i --- i i v i C L1ME5_3end#LI 405 TTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATGC 356 chr2ptel1M 84942 ATG-GCTTGATAATGCTTTGGGTATAGTTCTAC---ATTTCTCTCCAGAT 84987 i i-i i ------ iv - v i --- v v C L1ME5_3end#LI 355 GTATACTTAAT------TTGACTA-AGTACTGCCAGATTGCTCTCCAGAA 313 chr2ptel1M 84988 TCTTTGGATCAGTTTTCAACTCCACCAACAATGTATTAGTGTCCCAATTT 85037 vvi v i i v vii i i i v v i v ? C L1ME5_3end#LI 312 TGGCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATNT 263 chr2ptel1M 85038 TCCCATATCCCCTCCAACATTTGTCATTATCT---TTTCCTGTCATCTCA 85084 i i i v i v i--- --- v i iv C L1ME5_3end#LI 262 CCCCACATCCTCGCCAACACTTGGCATTATCCAGCTTTC---TAATTTTT 216 chr2ptel1M 85085 GTCAAACTGAGAGGTGTGTAGTGATAGCTAAGAGTTGTCTTAATTGGTAT 85134 i iv i v iv v v vv i v i C L1ME5_3end#LI 215 GCCAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCAT 166 chr2ptel1M 85135 TTCTCTGATCAATAGTGATTTAGAGCTTCTTTTCATTTGACTAGAAATGG 85184 i v i v v v i v vi ivv iivv C L1ME5_3end#LI 165 TTCTCTGATTACTAATGAGTTTGAGCATCTCTTCATATGCTTGTTAGCCT 116 chr2ptel1M 85185 TTTTAATTTCTTTATTTGCAAATTGCTTGTTCATAT-CTTTGGTCATTTA 85233 ivii i iv i i i - vi v C L1ME5_3end#LI 115 TTCGGGTTTCCTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCCATTTT 66 chr2ptel1M 85234 TCAGTTGGAG--AATGGCTTCAGTTCTTATTAATCTG-AGTCGA-TTTTT 85279 vi i --?vi v i-- i i i - -- - ii C L1ME5_3end#LI 65 TCTATTGGGGTTNCCGTCTTT--TTCTTGTTGATTTGCAG--GAGTTCCT 20 chr2ptel1M 85280 TATATATTTGAGA 85292 i iv C L1ME5_3end#LI 19 TGTATATTCTAGA 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.19 CpG sites = 96, Kimura (unadjusted) = 40.55 Transitions / transversions = 1.57 (96/61) Gap_init rate = 0.06 (30 / 533), avg. gap size = 1.53 (46 / 30) 280 32.45 6.72 1.60 chr2ptel1M 85614 85732 (914268) MIR3#SINE/MIR 27 151 (57) m_b57s601i1 2076 chr2ptel1M 85614 CATTGACTATTGGAGTCAAGAATCCTGAGTTCTGGTCCAAGCTCAGCTGT 85663 iv i-- i iv i i vi v iii MIR3#SINE/MIR 27 CACGGACTG--GGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCAC 74 chr2ptel1M 85664 TAGATA-------GACATTCACCAAGTCATGTCCCCTTAAAAGGCAT-AG 85705 iv ?------- v viv iv v ivvvi v - MIR3#SINE/MIR 75 TAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAG 124 chr2ptel1M 85706 TTCCCTCATTGATTAATGGAAGGAGTT 85732 i ivi v vv i i MIR3#SINE/MIR 125 TTTCCTCATCTGTAAAATGAGGGGGTT 151 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.94 CpG sites = 20, Kimura (unadjusted) = 43.95 Transitions / transversions = 1.11 (20/18) Gap_init rate = 0.03 (4 / 118), avg. gap size = 2.50 (10 / 4) 526 26.34 4.00 1.30 chr2ptel1M 85773 85922 (914078) C MIR3#SINE/MIR (1) 207 54 m_b57s601i2 2077 chr2ptel1M 85773 AGTTATATCATCAGAGGATCATGGAATTGAAGAGGATTGTAGAGGTAATC 85822 i i vv v i vvii ii i ii iiv i v C MIR3#SINE/MIR 207 AATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATC 158 chr2ptel1M 85823 TGCTTTAACCCC-TCATTTTAAACATGAGGAAACTGAGTCCTGTAGAGA- 85870 iv ii - v v v iiv i- C MIR3#SINE/MIR 157 TAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGT 108 chr2ptel1M 85871 GAAGTGACTTGTCCAAGGTCACATGTAAC-AGGTAGTAGC---CCCGGGA 85916 i --i i - v i ---v C MIR3#SINE/MIR 107 GAAGTGACTTGCCCAAGGTCACA--CAGCNAGTTAGTGGCAGAGCCGGGA 60 chr2ptel1M 85917 TTTGAA 85922 i v C MIR3#SINE/MIR 59 CTAGAA 54 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.39 CpG sites = 24, Kimura (unadjusted) = 33.39 Transitions / transversions = 1.60 (24/15) Gap_init rate = 0.04 (6 / 149), avg. gap size = 1.33 (8 / 6) 445 20.27 11.36 2.80 chr2ptel1M 85833 85964 (914036) C MIRc#SINE/MIR (119) 149 7 m_b57s601i3 2077 chr2ptel1M 85833 CCTCATTTTAAACATGAGGAAACTGAGTCCTGTAGAGAG---AAGTGACT 85879 i v v v i--i --- C MIRc#SINE/MIR 149 CCCCATTTTACAGATGAGGAAACTGAGGCT--CAGAGAGGTTAAGTGACT 102 chr2ptel1M 85880 TGTCCAAGGTCACATG--TAACAGGTAGTAGCCCCGGGATTTGAAATTCC 85927 i ii-- ii i i i vv i i --i C MIRc#SINE/MIR 101 TGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAA--CCC 54 chr2ptel1M 85928 AA---TTCCTCA-TCTA----CA-TGCT-TTCCCATTGTACCACCCT 85964 i--- v - i ---- - - i i i v C MIRc#SINE/MIR 53 AGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACT 7 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 23.48 CpG sites = 19, Kimura (unadjusted) = 24.56 Transitions / transversions = 2.71 (19/7) Gap_init rate = 0.08 (11 / 131), avg. gap size = 1.73 (19 / 11) 434 31.34 9.38 1.94 chr2ptel1M 86012 86203 (913797) MIRb#SINE/MIR 7 212 (56) m_b57s601i4 2078 chr2ptel1M 86012 GGAAGCAGTGGGACAG--AAAATATCTTTAACTTTTCATCCAGGAAGACC 86059 v - vi --i v v vivii vv vi iv MIRb#SINE/MIR 7 GGCAGC-GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACC 55 chr2ptel1M 86060 TATGTCCTAATCCCACCTCAGGAACTTATT-----------TTTG--CAA 86096 iv i v iv v vv i -----------i -- MIRb#SINE/MIR 56 TGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 105 chr2ptel1M 86097 TGTACTCAATTCCTC--AACTAATTTGGCTTCCTCATATGTAAAATGGGT 86144 vv i iii -- i i--- ii i v v MIRb#SINE/MIR 106 GTTACTTAACCTCTCTGAGCC---TCAGTTTCCTCATCTGTAAAATGGGG 152 chr2ptel1M 86145 ATCA-ACTAACTACCTCATAAGGTGGTTGTAGAGATCAGATGAAATAACA 86193 v - v v ii i v iii i i i ii MIRb#SINE/MIR 153 ATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATG 202 chr2ptel1M 86194 TATGCAAAAC 86203 i i i MIRb#SINE/MIR 203 CATGTAAAGC 212 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.23 CpG sites = 35, Kimura (unadjusted) = 42.03 Transitions / transversions = 1.46 (35/24) Gap_init rate = 0.05 (9 / 191), avg. gap size = 2.44 (22 / 9) 13 24.13 0.00 0.00 chr2ptel1M 87090 87128 (912872) (AAAAAGA)n#Simple_repeat 1 39 (0) m_b57s252i7 2079 chr2ptel1M 87090 AAAAAGAAAAATGGGTAAAGGAGAAATTAAAAAGAAAAA 87128 v iiv i i vv (AAAAAGA)n#Si 1 AAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAA 39 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 200 38.64 1.14 0.00 chr2ptel1M 90538 90625 (909375) C MIR3#SINE/MIR (60) 148 60 m_b57s601i5 2080 chr2ptel1M 90538 CTTCTCACTCTAATAATGAAGAAACT-ATGTCCATAAAAGTCAGGTGATT 90586 ii i i vvi i - v i v i i v i i C MIR3#SINE/MIR 148 CCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACT 99 chr2ptel1M 90587 CATGCATCACCACATAGAAACTTAAAGGCCGGTCTAGGA 90625 iiiv vvii i v? v iv v iv ii C MIR3#SINE/MIR 98 TGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGA 60 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 55.85 CpG sites = 21, Kimura (unadjusted) = 58.88 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.01 (1 / 87), avg. gap size = 1.00 (1 / 1) 241 31.68 7.69 4.48 chr2ptel1M 90622 90816 (909184) L3#LINE/CR1 3893 4093 (6) m_b57s601i6 2081 chr2ptel1M 90622 AGGAAAATCTTTGTAACAATTAGAGATATGCTTAGGTGGAA-------CT 90664 i v v i v i v vv ii ------- i L3#LINE/CR1 3893 AGGAAGAACTTTCTAACAATCAGAGCTGTCCAAAAATGGAATGGGCTGCC 3942 chr2ptel1M 90665 TGGAGAAGTAGT-AGCATGCCACTGCCTAAAAGTAGTAGCATCAGAGTAG 90713 v ? i - - v vv vv ii i - vvv v vvv L3#LINE/CR1 3943 TCGNGAGGTAGTGAGC-TCCCCGTCACTGGAGGT-GTTCAAGCAGAGGCT 3990 chr2ptel1M 90714 AGATGACAATTTGTCAAGTATATAATGTCTATGTCATTATT--ATTC--T 90759 i v i i v i -- vv v vv vi -- v-- L3#LINE/CR1 3991 GGATGACCACTTGTCAGGGATGT--TGTAGAAGGGATTCCTGCATTGGAT 4038 chr2ptel1M 90760 AATATTCTGGATTAGATAG---TTGAGGTCATCTAATCTCTGATTCTGAG 90806 iiv vvi i ii---i i -i ---- ii i L3#LINE/CR1 4039 GGGAGGTTGGACTAGATGACCTCTAAGGTC-CCT----TCCAACTCTGAG 4083 chr2ptel1M 90807 ATTTTGTGAT 90816 i L3#LINE/CR1 4084 ATTCTGTGAT 4093 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.97 CpG sites = 28, Kimura (unadjusted) = 41.97 Transitions / transversions = 0.90 (28/31) Gap_init rate = 0.07 (14 / 194), avg. gap size = 1.71 (24 / 14) 369 34.74 2.14 6.11 chr2ptel1M 91070 91256 (908744) C MIRc#SINE/MIR (87) 181 2 m_b57s601i7 2082 chr2ptel1M 91070 CCCTGGAAGGTGGTTGTAACAGTTGTTCTTATTCCCAGGTTATAG-TTAG 91118 vi i viivii v i v i vv i - v C MIRc#SINE/MIR 181 CCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAG 132 chr2ptel1M 91119 GAAACTGAGAATGAGAGCCATCAACTATCTCATTGAAGAATTAAACATTA 91168 iv v vvi i v iv iiiiv -i i v --i C MIRc#SINE/MIR 131 GAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAG-GTCACACA--G 85 chr2ptel1M 91169 CTCACTGAAGAAATATCAGGAACAGGATTTGAATCCAGGCTTCACTGACT 91218 ----- iv i iv iiv i i i i ii iv C MIRc#SINE/MIR 84 CT-----AGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACT 40 chr2ptel1M 91219 CTAGGACTTCTAG-GCTA--TCCACTACTCTTCTCTGCCTC 91256 i i --- i - v-- i v iv v C MIRc#SINE/MIR 39 CCAAG---TCCAGTGCTCTTTCCACTGCACCACACTGCCTC 2 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 46.39 CpG sites = 37, Kimura (unadjusted) = 48.65 Transitions / transversions = 1.54 (37/24) Gap_init rate = 0.08 (14 / 186), avg. gap size = 1.07 (15 / 14) 262 33.08 3.45 6.19 chr2ptel1M 91269 91384 (908616) MIRc#SINE/MIR 2 114 (154) m_b57s601i8 2083 chr2ptel1M 91269 GAGGCAGTAAGATTCAATGAAAAGAGCTTTGCATTCAGAATCCAAGGAA- 91317 iv i v i i vi v i ii i -- - MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTC--AGGAAG 49 chr2ptel1M 91318 --CTTGACTTGATTCCCAGCTCCTCCCTGAGATTT-CCACTTTTGTGACT 91364 -- v ii i v i iv ----- i - i vi v i MIRc#SINE/MIR 50 ACCTGGGTTCGAGTCCCGGCTCTGCC-----ACTTACTAGCTGTGTGACC 94 chr2ptel1M 91365 AGAGGCAAAGGGCCTAATCT 91384 vvi ivvi i i MIRc#SINE/MIR 95 TTGGGCAAGTCACTTAACCT 114 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.30 CpG sites = 23, Kimura (unadjusted) = 45.78 Transitions / transversions = 1.77 (23/13) Gap_init rate = 0.09 (10 / 115), avg. gap size = 1.10 (11 / 10) 228 13.59 5.08 12.73 chr2ptel1M 91624 91682 (908318) MER63C#DNA/hAT-Tip100 876 930 (0) m_b57s502i0 2084 chr2ptel1M 91624 CATACATTTTTTTCCCTTAAATTTGGAGAGCCAATT---AAACATTTACC 91670 i-------i ii --- MER63C#DNA/hA 876 CATACATTTTTTTCCCC-------AGAGAGCCGGTTGTTAAACATTTACC 918 chr2ptel1M 91671 CCCATACCACTG 91682 vv i MER63C#DNA/hA 919 AGCACACCACTG 930 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 12.92 CpG sites = 5, Kimura (unadjusted) = 15.12 Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.14 (8 / 58), avg. gap size = 1.25 (10 / 8) 213 24.37 7.95 6.74 chr2ptel1M 91900 91987 (908013) L2a_3end#LINE/L2 390 478 (39) m_b57s601i9 2085 chr2ptel1M 91900 CCCATTATACAGGAATAGAAATTCCCTGAAGG-AGGGATTGTTTG---GT 91945 i ----- iv ii v i - i - --- L2a_3end#LINE 390 CCCACTA-----GAATGTAAGCTCCATGAGGGCAGGGACT-TTTGTCTGT 433 chr2ptel1M 91946 TTTGGTC---TTTTTATCCCTAGTCTCTAGCAGCGCGCCTGGCAC 91987 v ---vi v i ivi v vv i L2a_3end#LINE 434 TTTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCAC 478 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.21 CpG sites = 11, Kimura (unadjusted) = 29.94 Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.10 (9 / 87), avg. gap size = 1.44 (13 / 9) 245 28.86 2.02 2.02 chr2ptel1M 92944 93042 (906958) C MIRc#SINE/MIR (4) 264 166 m_b57s601i10 2086 chr2ptel1M 92944 ATACTAATAGCTAGTATGTCTA-AGCTATTTAAGTTTTGCAAAAGTACTT 92992 v i?v vii v v - vv viv i - ii C MIRc#SINE/MIR 264 ATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAA-GCGCTT 216 chr2ptel1M 92993 T-ACAGATGTTAATTCATTTGATCCTCACAAACAAATCTAGAAAGTAGGT 93041 - v ii vi - vi ivi i i C MIRc#SINE/MIR 215 TCACATACATTATCTCATTTGATCCTCAC-AACAACCCTGTGAGGTAGGC 167 chr2ptel1M 93042 A 93042 C MIRc#SINE/MIR 166 A 166 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.75 CpG sites = 15, Kimura (unadjusted) = 37.60 Transitions / transversions = 1.15 (15/13) Gap_init rate = 0.04 (4 / 98), avg. gap size = 1.00 (4 / 4) 321 22.74 0.00 1.52 chr2ptel1M 92985 93051 (906949) C MIR#SINE/MIR (50) 212 147 m_b57s601i11 2086 chr2ptel1M 92985 AAGTACTTTACAGATGTTAATTCATTTGATCCTCACAAACAAATCTAGAA 93034 ii vi i i i - vi vi C MIR#SINE/MIR 212 AAGCGCTTTACATGTATTAACTCATTTAATCCTCAC-AACAACCCTATGA 164 chr2ptel1M 93035 AGTAGGTATTATTGCTA 93051 i i ii C MIR#SINE/MIR 163 GGTAGGTACTATTATTA 147 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.19 CpG sites = 12, Kimura (unadjusted) = 28.69 Transitions / transversions = 4.00 (12/3) Gap_init rate = 0.02 (1 / 66), avg. gap size = 1.00 (1 / 1) 872 29.95 3.12 4.34 chr2ptel1M 93937 94449 (905551) C L1MC3_3end#LINE/L1 (1899) 633 127 m_b57s551i8 2087 chr2ptel1M 93937 GCTCATTTCACTCAGTATCTGTTCATGTAAGTCTC-TCCAGGCCTTTCTG 93985 iv i i -v i v v vi - v i ii C L1MC3_3end#LI 633 GCTTCTTTCACTTAGCA-ATATGCATTTAAGATTCATCCATGTCTTTTCG 585 chr2ptel1M 93986 AAATCCTTCTGCTGG-TCATTTCTT---ATAGAACAATAATATTCCATAA 94031 vii-- -- v i - --- v vvv vi C L1MC3_3end#LI 584 TGG--CTT--GATAGCTCATTTCTTTTTATCGCTGAATAATATTCCATTG 539 chr2ptel1M 94032 CATTCATATACCACAATTTATTCAGCCATTCTCCAATTAATGGGCATACA 94081 i vv i i i i v v v i v i --- C L1MC3_3end#LI 538 TATGGATGTACCACAGTTTGTTTATCCATTCACCTATTGAAGGACAT--- 492 chr2ptel1M 94082 CTCAGTT---TCCAGTTTCTGGCCATTACAAAAAAGGCTGCCACAAACAT 94128 ii --- i v ii v i i i C L1MC3_3end#LI 491 CTTGGTTGCTTCCAGTTTTTGGCGATTATGAATAAAGCTGCTATAAACAT 442 chr2ptel1M 94129 TCTTGCACATACAGGTCCCTTTCC---CTT---CTTTAAAATCTCTTTGG 94172 ----i i i iii v vi--- v ---i v vv v C L1MC3_3end#LI 441 TC----GCGTGCAGGTTTTTGTGTGGACATAAGTTTTCAAATCAGTTGGG 396 chr2ptel1M 94173 GAGATAAGCCCAGTAGTAACACTGCTGGATCAAA-GGTATGCACA-GTTT 94220 v i -- i v iivv i iv - v vvi - C L1MC3_3end#LI 395 TAAATA--CCTAGGAGCGCGATTGCTGGATCGTATGGTAAGACTATGTTT 348 chr2ptel1M 94221 GATAACTTTTTGAGCATAGTTCCAAATCGCTCTCCAGAATGGCTGGATGT 94270 --- i v i v - v v ii iii i i v ivv C L1MC3_3end#LI 347 ---AGCTTTGTAAGAA-ACTGCCAAACTGTCTTCCAAAGTGGCTGTACCA 302 chr2ptel1M 94271 ATTCACAATTCTACCAACAATGTATCAGTTTCCCAGTTTTCTCACATCCC 94320 v ii v i i i v v vv i v viii i i C L1MC3_3end#LI 301 TTTTGCATTCCCACCAGCAATGAATGAGAGTTCCTGTTGCTCCGCATCCT 252 chr2ptel1M 94321 CTCCAACATTCTGCATTATCTTTCCCTATCATTCTAGCTAGTCTGACTGA 94370 v i ? iv i i vv iii vvv i i v i i--- C L1MC3_3end#LI 251 CGCCAGCANTTGGTATTGTCAGTTTTTTGGATTTTAGCCATTCTAAT--- 205 chr2ptel1M 94371 CAGGTGTGTAGTGGTATCTCAAAGTTGTCTTAATGTGCATTTCTCTGATT 94420 - vv i v v i i v C L1MC3_3end#LI 204 -AGGTGTGTAGTGGTATCTCATTGTTGTTTTAATTTGCAATTCCCTAATG 156 chr2ptel1M 94421 AATAATTACTTGGAGCATCTTTTCATATG 94449 vv v iv v C L1MC3_3end#LI 155 ACAAATGATGTTGAGCATCTTTTCATATG 127 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.97 CpG sites = 78, Kimura (unadjusted) = 39.00 Transitions / transversions = 1.13 (78/69) Gap_init rate = 0.06 (30 / 512), avg. gap size = 1.27 (38 / 30) 1267 26.43 0.69 2.11 chr2ptel1M 94018 94450 (905550) C L1ME3G_3end#LINE/L1 (376) 548 122 m_b57s551i9 2087 chr2ptel1M 94018 ATAATATTCCATAACATTCATATACCACAATTTATTCAGCCATTCTCCAA 94067 i ii vv i i i i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr2ptel1M 94068 TTAATGGGCATACACTCAGTTTCCAGTTTCTGGCCATTACAAAAAAGGCT 94117 i i vi vviv i i v i v v C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr2ptel1M 94118 GCCACAAACATTCTTGCACATACAGGTCCCTTTCC-CTTCTTTAAA-ATC 94165 v ii i i i ?-- i v v - v v vii i- i C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATT 401 chr2ptel1M 94166 TCTTTGGGAGATAAGCCCAGTAGTAACACTGCTGGATCAAAGG-TATGCA 94214 ? i v v v? ? v iiv i i - i C L1ME3G_3end#L 400 TCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCG 351 chr2ptel1M 94215 CAGTTTGATAACTTTTTGAGCATAGTTCCAAATCGCTCTCCAGAATGGCT 94264 v i -- i vvv - v v i i i ? C L1ME3G_3end#L 350 CATTTTAA--ATTTTAATAG-ATACTGCCAAATTGCCCTCCAAAANGGCT 304 chr2ptel1M 94265 GGATGTATTCACAATTCTACCAACAATGTATCAGTTTCCCAGTTTTCTCA 94314 v ivv i v i i i i v vv v v i i C L1ME3G_3end#L 303 GTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCA 254 chr2ptel1M 94315 CATCCCCTCCAACATTCTGCATTATCTTTCCCTATCATTCTAGCTAGTCT 94364 i i v i ?vii vv? ii vvv i v i i C L1ME3G_3end#L 253 CACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATCT 204 chr2ptel1M 94365 GACTGACAGGTGTGTAGTGGTATCTCAAAGTTGTCTTAATGTGCATTTCT 94414 - --- viv i vv i v i C L1ME3G_3end#L 203 GA-TG---GGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCC 158 chr2ptel1M 94415 CTGATTAATAATTACTTGGAGCATCTTTTCATATGT 94450 v i v vv v C L1ME3G_3end#L 157 CTGATTACTAGTGAGGTTGAGCATCTTTTCATATGT 122 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.92 CpG sites = 58, Kimura (unadjusted) = 33.68 Transitions / transversions = 1.07 (58/54) Gap_init rate = 0.03 (12 / 432), avg. gap size = 1.00 (12 / 12) 192 29.96 12.50 1.18 chr2ptel1M 94523 94674 (905326) L2a_3end#LINE/L2 339 507 (10) m_b57s601i12 2088 chr2ptel1M 94523 ATCTGGTCCATAGTGGAT-TTCTACCTAGTTGCTTGTGTATTGTGTG--- 94568 i-- v iv - i i v ii v v --- L2a_3end#LINE 339 ATCTGA--CATACTATATATTTTACTTATTTATTTGTTTATTGTCTGTCT 386 chr2ptel1M 94569 -AGCTTAC-GGTCTGTGACCTCCATGAAAGCCAGGA----TGT---TTTT 94609 -vv ii -i vv i v ii vi ---- --- L2a_3end#LINE 387 CCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTCTGTTTT 436 chr2ptel1M 94610 GCTCTCTTTAGT-TCCC--GTGCTTAGCCCATGGTGTGGCATATAACAGG 94656 i v viv - -- i i vv vv iv i ii L2a_3end#LINE 437 GTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGG 486 chr2ptel1M 94657 CACTG---AAGTGTTTGCTGA 94674 i v--- i i i L2a_3end#LINE 487 CGCTCAATAAATATTTGTTGA 507 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.98 CpG sites = 25, Kimura (unadjusted) = 39.18 Transitions / transversions = 1.25 (25/20) Gap_init rate = 0.07 (11 / 151), avg. gap size = 1.91 (21 / 11) 215 29.17 12.50 0.00 chr2ptel1M 94579 94674 (905326) L2b_3end#LINE/L2 349 456 (10) m_b57s601i13 2088 chr2ptel1M 94579 CTGTGACCTCCATGAAAGCCAGGA---TGT---TTTTGCT---CTCTTTA 94619 v i ii vi ---? --- i i --- v v L2b_3end#LINE 349 CTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTGTA 398 chr2ptel1M 94620 GTTCCCGTGCTTAGCCCATGGTGTGGCATATAACAGGCACT--G-AAGTG 94666 vii v i i v v? iv i i ii i -- - i i L2b_3end#LINE 399 TCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATA 448 chr2ptel1M 94667 TTTGCTGA 94674 i L2b_3end#LINE 449 TTTGTTGA 456 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.53 CpG sites = 19, Kimura (unadjusted) = 39.97 Transitions / transversions = 2.11 (19/9) Gap_init rate = 0.05 (5 / 95), avg. gap size = 2.40 (12 / 5) 294 25.00 0.00 0.89 chr2ptel1M 98134 98246 (901754) C L1ME4c_3end#LINE/L1 (707) 123 12 m_b57s551i10 2089 chr2ptel1M 98134 GTTTTGTGGTTTTAATTTCTCTATTTGAAAATTGCCTTTTCATATCCTTT 98183 vv i? v v i - ? vi i v i C L1ME4c_3end#L 123 GTTTACTANTTGTATTTCCTCT-TNTGTGAATTGTCTGTTCATGTCCTTT 75 chr2ptel1M 98184 GACCATTTATCAATTGGAGAGTGGCTTCAATTCTTATAAATCTGAATCAA 98233 v v i vv v v ?ivv v i v i C L1ME4c_3end#L 74 GCCCATTTATCTATTGGGGTCTTGATNTTTTTCTTATCAATTTGAATGAG 25 chr2ptel1M 98234 TTTTCTATATATT 98246 i i i ? C L1ME4c_3end#L 24 CTCTTTATATANT 12 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 31.92 CpG sites = 12, Kimura (unadjusted) = 31.92 Transitions / transversions = 0.75 (12/16) Gap_init rate = 0.01 (1 / 112), avg. gap size = 1.00 (1 / 1) 1455 30.92 1.11 1.43 chr2ptel1M 98800 99429 (900571) C L1ME4c_3end#LINE/L1 (191) 639 12 m_b57s551i11 2090 chr2ptel1M 98800 TTCTGCTCATTTCACTTAGCATCAGTTCATGTAAGTTCTCTCCAAGCCTC 98849 iv i i vv -- iivi i v iiv C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCAT--AAACATTTTCCATGTTGC 592 chr2ptel1M 98850 TCTGTATTCATCCTGCTGTTCATTTCTTACAGAACAATAATATTGCATAA 98899 vii v v v iv vv i v ii vvvv v vi C L1ME4c_3end#L 591 TACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCG 542 chr2ptel1M 98900 CATTCATATACCACAATTTACCCAACCATTCTCCAATTGATGGTTATCCA 98949 vi ?v i i ii i v v vi ii C L1ME4c_3end#L 541 AGTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTA 492 chr2ptel1M 98950 TTCATTTTCCAGTTTCTAGCCACTACAAACAGGACTGCCACAAACATTTT 98999 vvivv i i v i i i i ivi v ii i C L1ME4c_3end#L 491 GGTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTT 442 chr2ptel1M 99000 GGCACATACAGAGCCCTTTCCCTTCTTTAG---TATCTCTTTGAGGTATA 99046 v ii i --- i i v --- i i ii i v C L1ME4c_3end#L 441 CGTGCATATAG---CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAA 395 chr2ptel1M 99047 AGCCCAGTAGTAGCACTGCTAGATCAAAGGCTATGCACAGTTTGATAACT 99096 vv v i v i i i i v v v v ii C L1ME4c_3end#L 394 TTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCT 345 chr2ptel1M 99097 TTTGGGGCATAATTCCAGATTGCTCTCCAGAATGGTTGGATTCATTCACA 99146 i ivi i v v i i i v v iiv i C L1ME4c_3end#L 344 CTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACA 295 chr2ptel1M 99147 ACTCCACCAACAGTGCATCAGTGTCCCAATTTTCCCTCATCCCCTCCAAC 99196 ?iv i i i v ? v i iv v ? i v i C L1ME4c_3end#L 294 NTGCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGC 245 chr2ptel1M 99197 ATTCGTCATTATTTTTTCCTGTCATCTTAGTCAATCTGACAGGTGTGTAG 99246 v vi ivv ii vvv i v ii i i i i iv i C L1ME4c_3end#L 244 ATTGGGTATTATCAATTTTTTAAATTTTTGCTAATTTAATAGGCGTAAAA 195 chr2ptel1M 99247 TGGTATCTCAGAATTGTCTTAATTTGCATTTCTCTGAACAATAGTGATTT 99296 vvi ii i vi v i vv C L1ME4c_3end#L 194 TGGTATCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACTAGCGAGGT 145 chr2ptel1M 99297 GGAACACTCTTTAATATGAGTGGTAATAGTTTCAATTTCATCATCTGAAA 99346 v i i iv i vv v v ivi? vv v v ? vi C L1ME4c_3end#L 144 TGAACATTTTTCCATGTGTTTGTTTACTANTTGTATTTCCTCTTNTGTGA 95 chr2ptel1M 99347 ATTGTCTGTTCATATCCTTTAACCATTTATCAATTGGAGAATGTCTTGA- 99395 i iv v i---- - C L1ME4c_3end#L 94 ATTGTCTGTTCATGTCCTTTGCCCATTTATCTATTGGG----GTCTTGAT 49 chr2ptel1M 99396 ---TTTCTTATAAATTAGAGTCAATTCTCTATATATT 99429 --- v v i v ii i ? C L1ME4c_3end#L 48 NTTTTTCTTATCAATTTGAATGAGCTCTTTATATANT 12 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.99 CpG sites = 105, Kimura (unadjusted) = 41.39 Transitions / transversions = 1.21 (105/87) Gap_init rate = 0.02 (12 / 629), avg. gap size = 1.33 (16 / 12) 375 32.85 1.07 1.43 chr2ptel1M 99291 99571 (900429) C L1M2_orf2#LINE/L1 (0) 3291 3012 m_b57s551i12 2090 chr2ptel1M 99291 TGATTTGGAACACTCTTTAATATGAGTGGTAATAGTTTCAATTTCATCAT 99340 v v i i i v ivv v iiivi vv v v v C L1M2_orf2#LIN 3291 TGATGTTGAGCATTTTTTCATATACCTGTTGGCCATTTGTATGTCTTCTT 3242 chr2ptel1M 99341 CTGAAAATTGTCTGTTCATATCCTTTAACCATTTATCAATTGGAGAATGT 99390 i i v i vi iv v ? i vv v C L1M2_orf2#LIN 3241 TTGAGAAATGTCTATTCAGGTCCTTTGCCCATTTTTNAATCGGATTATTT 3192 chr2ptel1M 99391 CTTGATTTCTTATAAATTAGAGTCAATTCTCTATATATTTTGGAAATGAG 99440 v vv vi i vi v v vv v i ii i v v i C L1M2_orf2#LIN 3191 GTTTTTTTGCTGTTGAGTTGTTTGAGTTCCTTATATATTCTGGATATTAA 3142 chr2ptel1M 99441 GCCTTTATCACAACCTTTGACTGTGAAGATGTTTTCCCAGTTTGTTGCTT 99490 v i i v vv?v v vi ii v v i v i v v C L1M2_orf2#LIN 3141 TCCCTTGTCAGATGNATAGTTTGCAAATATTTTCTCCCATTCTGTAGGTT 3092 chr2ptel1M 99491 CCCTTCTAATCTTGTTTGCATTAGTTTTATTTG---TACAAAGGCTTTTT 99537 vi ii v iii - - - iv --- i i i C L1M2_orf2#LIN 3091 GTCTCTTCACTCTGTT-G-ATT-GTTTCCTTTGCTGTGCAGAAGCTTTTT 3045 chr2ptel1M 99538 AATTTGATATAATCAAAATTTTCTATTTTGTGCT 99571 i i vv v v - C L1M2_orf2#LIN 3044 AGTTTGATGTAATCCCATTTGTCTATTTT-TGCT 3012 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.37 CpG sites = 41, Kimura (unadjusted) = 44.00 Transitions / transversions = 0.82 (41/50) Gap_init rate = 0.02 (5 / 280), avg. gap size = 1.40 (7 / 5) 399 29.82 3.62 3.62 chr2ptel1M 99326 99739 (900261) C L1M5_orf2#LINE/L1 (35) 3259 2846 m_b57s551i13 2090 chr2ptel1M 99326 TTTCAATTTCATCATCTGAAAATTGTCTGTTCATATCCTTTAACCATTTA 99375 v? v v v i vi v vi i iv v C L1M5_orf2#LIN 3259 TTTGNATATCTTCTTTTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTT 3210 chr2ptel1M 99376 TCAATTGGA--GAATGTCTTGATTTCTTA-TAAATTAGAGTCAATTCTCT 99422 ?v i-- vv -- ? - i ? iv -v i i C L1M5_orf2#LIN 3209 TNTATTGGGTTGTTTGTCTT--TTTNTTATTGANTTGTAG-GAGTTCTTT 3163 chr2ptel1M 99423 ATATATTTTGGAAATGAGGCCTTTATCACAACCTTTG-ACTGTGAAGATG 99471 i v i v i -i iv v -?i ii v v C L1M5_orf2#LIN 3162 ATATATTCTGGATACGAGTCCTTTGTCA-GATATATGTNTTGCAAATATT 3114 chr2ptel1M 99472 TTTTCCCAGTTTGTTGCTTCCCTTCTAATCTTGTTTGCATTAGTTTTATT 99521 i ? i v v i v i v vi iv ivi vvv C L1M5_orf2#LIN 3113 TTCTCCCANTCTGTGGCTTGCCTTTTCATTTTCTTAACGGTGTCTTTTGA 3064 chr2ptel1M 99522 TGTACAAAGGCTTTTTAATTTGATATAATCAAAATTTTCTATTTTGTGCT 99571 ? vi i i i v v i? i v v v v - v C L1M5_orf2#LIN 3063 NGAGCAGAAGTTTTTAATTTTGATGNAGTCCAATTTATCAATTTT-TTCT 3015 chr2ptel1M 99572 CAGTAATGGTCTCTAGTTCATTTTTG-ATC-------ACAAATTTCTTCC 99613 i-- v --- ? v - -i ------- v i i v C L1M5_orf2#LIN 3014 T--TTATGGT---TNGTGC-TTTTTGTGTCCTGTTTAAGAAATCTTTGCC 2971 chr2ptel1M 99614 TCCTCCACAAGTCTGAGAAATAAACTATCCTATG--TTCCTCTAATTTAT 99661 v?i - i -- vi v v i v -- i ivvvv C L1M5_orf2#LIN 2970 TANCCCA-AGGTC--ACGAAGATATTCTCCTATGTTTTCTTCTAGAAGTT 2924 chr2ptel1M 99662 TTATAATCTGGTTCTTTATGCCAAAATC-ATGGACCCATTTTGATCTTAT 99710 i i vi?ii iiiiv ii - - i i ? vi v C L1M5_orf2#LIN 2923 TTATAGTTTTANCTTTTACATTTAGGTCTAT-GATCCATCTNGAATTAAT 2875 chr2ptel1M 99711 CTTGGTATATGGTGTTAAGTGTGGGTTGA 99739 i v i v i iv i C L1M5_orf2#LIN 2874 TTTTGTGTATGGTGTGAGGTAGGGGTCGA 2846 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.48 CpG sites = 61, Kimura (unadjusted) = 40.19 Transitions / transversions = 1.05 (61/58) Gap_init rate = 0.05 (22 / 413), avg. gap size = 1.36 (30 / 22) 528 32.78 4.51 5.19 chr2ptel1M 100217 100837 (899163) L1M2_orf2#LINE/L1 16 632 (2659) m_b57s551i14 2091 chr2ptel1M 100217 CCCCACCTAGATTTAGTAATTTAAACTATGAATGTGAATAGGATGAACTC 100266 ii --- i i --- iv i i iv i i L1M2_orf2#LIN 16 CCTTACCTA---TCAATAAT---AACCTTGAATGTAAATGGATTAAATTC 59 chr2ptel1M 100267 CCCCAT---AAAACAGAAATGGGTAGAAGACTTTGGGTTAAAAGCCGGAA 100313 i v --- i v i ?v iv ----- i v iv iii L1M2_orf2#LIN 60 TCCAATTAAAAGACATAGANTGGCTGAA-----TGGATAAAAAAACAAGA 104 chr2ptel1M 100314 TCCTACAATTTGTTGTTTACAAGAAATTCATTTAAAGCAGAACGACACAT 100363 i v v v i ii i i v vviiv v i L1M2_orf2#LIN 105 CCCAACTATATGCTGCCTACAAGAAACTCACTTCACCTGTAAAGACACAC 154 chr2ptel1M 100364 ACAGAGTAAAGGTACAGGGCTAGAGTACAAACTATT--ATGCTTCAAGTG 100411 i v i i iv v i -- v iv -- --- ii L1M2_orf2#LIN 155 ATAGACTGAAAGTGAAGGGATGGA--AAAAGATATTCCATGC---AAACG 199 chr2ptel1M 100412 --AATTAAGAAA-AGCAGGAGTAGCCATCCTGATCTCAGATCAAGCAA-- 100456 -- ii i i?- i v v v v ii i-- L1M2_orf2#LIN 200 GAAACCAAAAGNGAGCAGGAGTAGCTATACTTATATCAGATAAAATAGAC 249 chr2ptel1M 100457 ---AAG-CAAAAATAGATCTAATTAAAAGTGACAAGGAAGAAAAGTACAT 100502 --- - ----- -i v v i ivv v i L1M2_orf2#LIN 250 TTTAAGTCAAAAA-----CT-GTAAAAAGAGACAAAGAAGGTCATTATAT 293 chr2ptel1M 100503 CCTACTAAAAAGTACCAT------AGAGAATAAAGTAATGTCAATACCAA 100546 vv iv ii vv v ------ i --- --- v?i L1M2_orf2#LIN 294 AATGATAAAGGGGTCAATTCAGCAAGAGGATA---TAA---CAATTNTAA 337 chr2ptel1M 100547 ATACATATGTACCAAGTGGCATAGCATCCAAATTCCTAGAGGAGACGTTG 100596 i i v iiiv iv i i viv i v i ii i L1M2_orf2#LIN 338 ATATATATGCACCCAACACCGGAGCACCCAGATATATAAAGCAAATATTA 387 chr2ptel1M 100597 AGAGAGCTGCAAGAAGAATTAGACAGCAGAACTGTACTAGTCGGGGATCT 100646 ?v v iv i i iv v? iv vi v ? ii L1M2_orf2#LIN 388 NTAGATCTAAAGGGAGAGATAGACTNCAATACAATAATAGTNGGGGACTT 437 chr2ptel1M 100647 TA--ACCTTGATCTCAGAACTAAATAAATTGAACCACAAAATAAATTAG- 100693 i -- iiiv v ? ii i i i- v v v iv i i- L1M2_orf2#LIN 438 CAACACCCCACTCTCAGCANTGGACAGATC-ATCCAGACAGAAAATCAAC 486 chr2ptel1M 100694 AAAGAAGTTAAGGAGGTAAATAGAATTCTAGAAAAGTTAGCTCTGATAGA 100743 iivvv vv iv v i ? vv iv i vi i i L1M2_orf2#LIN 487 AAAGAAACATCGGACTTAAACTGCACTNTAGACCAAATGGACCTAACAGA 536 chr2ptel1M 100744 TCTTTGGAGAAAA----AT-GAATGGAGACAGAAAGCACTATGTTTTTCT 100788 iv iv v ---- -v ii vvi vi ---i i L1M2_orf2#LIN 537 CATTTACAGAACATTTCATCCAACAGCTGCAGAATACAC---ATTCTTCT 583 chr2ptel1M 100789 CAGCAGTACATAGAACTATTACAAAAATTGACCATATATTAGGACATAA 100837 v i i vv iv v ii v i v i L1M2_orf2#LIN 584 CATCAGCACATGGAACATTCTCCAGGATAGACCATATGTTAGGCCACAA 632 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 44.68 CpG sites = 111, Kimura (unadjusted) = 45.33 Transitions / transversions = 1.35 (111/82) Gap_init rate = 0.07 (43 / 620), avg. gap size = 1.40 (60 / 43) 234 21.82 0.00 0.00 chr2ptel1M 100895 100949 (899051) DNM1r#Unknown 2495 2549 (2113) m_b57s502i1 2092 chr2ptel1M 100895 TGTGTATATATCCATATAAATATATGTATATGTGTATATATACATATATA 100944 i vii i vi i i i i ? DNM1r#Unknown 2495 TGTGTGTATATGTGTGTATGTGTGTATATATGTGTATATATACGTATNTA 2544 chr2ptel1M 100945 CAGAA 100949 i DNM1r#Unknown 2545 TAGAA 2549 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 25.35 CpG sites = 10, Kimura (unadjusted) = 28.09 Transitions / transversions = 5.00 (10/2) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 260 31.08 2.70 0.00 chr2ptel1M 100950 101023 (898977) C MIRc#SINE/MIR (161) 107 32 m_b57s601i14 2093 chr2ptel1M 100950 GTGAGTTGTCCAGGATCACAAAGCTAGTCAATATTTGAGGCAG--TTGGA 100997 v i i i v v i iviv v i --i v C MIRc#SINE/MIR 107 GTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGA 58 chr2ptel1M 100998 ATCCAGTTTTTCCTGATTCTGTGTTC 101023 i v i i iiv i C MIRc#SINE/MIR 57 ACCCAGGTCTTCCTGACTCCAAGTCC 32 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.25 CpG sites = 14, Kimura (unadjusted) = 41.63 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.01 (1 / 73), avg. gap size = 2.00 (2 / 1) 541 18.54 3.15 2.34 chr2ptel1M 101047 101173 (898827) C MER63D#DNA/hAT-Tip100 (590) 471 344 m_b57s502i2 2094 chr2ptel1M 101047 CACAACAGGCTTTAAAATTTTAATTTACAATGTTA---TTTTCTTCATCA 101093 i vi v i - i i v i --- i C MER63D#DNA/hA 471 CACGACACACTTTTAAGTTT-AATCTGCATTATTAACATTTTCTCCATCA 423 chr2ptel1M 101094 CTTTCTTCAGTCTAGACAATCATCAAAACAGTGGATCAAGTCCTG-TTGA 101142 v v i ii i - -- C MER63D#DNA/hA 422 CTTTCTTAAGTCTAGACAATCAACAAAACAATAAATCAAGCCCTGATT-- 375 chr2ptel1M 101143 TGTAGCATTTGTCTCTTTCAGAGGTGTAGAT 101173 i i vv v v i C MER63D#DNA/hA 374 TGTAGCGTTTGCCGATTTCCGTGGTGTAAAT 344 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 19.61 CpG sites = 14, Kimura (unadjusted) = 21.64 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.04 (5 / 126), avg. gap size = 1.40 (7 / 5) 414 34.83 1.07 3.28 chr2ptel1M 101442 101628 (898372) MIR3#SINE/MIR 23 205 (3) m_b57s601i15 2095 chr2ptel1M 101442 AGATTACTGCATTTGAAATTAGGAAAACCTGTCTTTAAGTTGTTCCTTAG 101491 vi v - i v i i i i - vv iv ivivv iv MIR3#SINE/MIR 23 AGAGCACGG-ACTGGGAGTCAGGAGA-CCTGGGTTCTAGTCCCGGCTCTG 70 chr2ptel1M 101492 ACATTTCCTATTTTTGTGATACTGAAGAAGTCATTTAATTCTTATAGGCC 101541 v i vv ?vi v ivi iiv i v iiii v i MIR3#SINE/MIR 71 CCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCC 120 chr2ptel1M 101542 TCACTTCCCTCATCATCTCTAGAATGAGGGACCCAGATTGAGTGACCTCT 101591 v i --- v i iviii i iii i MIR3#SINE/MIR 121 TCAGTTTCCTCATC---TGTAAAATGAGGGGGTTGGACTAGATGATCTCT 167 chr2ptel1M 101592 AAGGTGCCTTTTCACTCT-ACA-CCTGTAGGTTCTATGA 101628 v iivi - -i i - i MIR3#SINE/MIR 168 AAGGTCCCTTCCAGCTCTGACATTCTAT-GATTCTATGA 205 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 48.43 CpG sites = 39, Kimura (unadjusted) = 49.57 Transitions / transversions = 1.62 (39/24) Gap_init rate = 0.04 (8 / 186), avg. gap size = 1.00 (8 / 8) 12 29.85 3.17 1.56 chr2ptel1M 101987 102049 (897951) (TCTT)n#Simple_repeat 1 64 (0) m_b57s252i8 2096 chr2ptel1M 101987 TCTCTCTGTTTTTATTTGCTTGCATTGTGT-TTTCTTTCTCAGTTTTTCT 102035 i v i v - v v v v - ivv i i (TCTT)n#Simpl 1 TCTTTCTTTCTTTCTTT-CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT 49 chr2ptel1M 102036 TTTTC-TTCCTTCTT 102049 i - i (TCTT)n#Simpl 50 CTTTCTTTCTTTCTT 64 Matrix = Unknown Transitions / transversions = 0.88 (7/8) Gap_init rate = 0.05 (3 / 62), avg. gap size = 1.00 (3 / 3) 14 4.33 0.00 7.69 chr2ptel1M 102782 102809 (897191) (TTCT)n#Simple_repeat 1 26 (0) m_b57s252i9 2097 chr2ptel1M 102782 TTCTTTCTTTCTTTTCTTTTTTTGCTTT 102809 - i - (TTCT)n#Simpl 1 TTCTTTCTTTC-TTTCTTTCTTT-CTTT 26 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.07 (2 / 27), avg. gap size = 1.00 (2 / 2) 69 6.15 1.18 0.00 chr2ptel1M 103967 104051 (895949) (CT)n#Simple_repeat 1 86 (0) c_b57s251i3 2098 chr2ptel1M 103967 CTCTCCCTCCCTCCCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 104016 i i i (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chr2ptel1M 104017 CTCTCTCTCTCTCTCTCT-TCTCTGGCTCTCTCTCT 104051 - vv (CT)n#Simple_ 51 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 86 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.01 (1 / 84), avg. gap size = 1.00 (1 / 1) 15 24.94 0.00 0.00 chr2ptel1M 104675 104713 (895287) (TTT)n#Simple_repeat 1 39 (0) m_b57s252i11 2099 chr2ptel1M 104675 TTTCTTTCTTCTTTCTCAATCTTTTTTTTTTTTTTTTTT 104713 i i i i ivv i (TTT)n#Simple 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 39 Matrix = Unknown Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 256 22.86 3.31 3.31 chr2ptel1M 104910 105090 (894910) C HERVIP10FH#LTR/ERV1 (4104) 998 818 m_b57s701i0 2100 chr2ptel1M 104910 TCTTTCTCTCTCATTCTGTGTTTATTTAATTTTCTTTTTCTTCCTCACTT 104959 v v v v i v i i v i ii v i C HERVIP10FH#LT 998 TCTATCTCTCTCTTTCTTTCTCTCTTTGACTTTCTGTCTCTCTCTCTCTC 949 chr2ptel1M 104960 TCTCACTCTCTGGCTCTCTGTTTTACTGTCTCTGCCTGTCTTTCTTTCTC 105009 v i ---- i i iv v v i vii C HERVIP10FH#LT 948 TCTGACTCCCT----CTTTGTCTCTCTGTCTCTTCCTCTCTCTGCCTCTC 903 chr2ptel1M 105010 TTTCTATCTGACTC------TGTTCCTTTCTCTCTCTCTCTTTCTCTGTT 105053 i v i ------ ii i i i v i C HERVIP10FH#LT 902 TCTCTCTTTGACTCCCTCTTTGTCTCTCTCTCTCCCTCTCTCTCTCTTTC 853 chr2ptel1M 105054 TCTCTGACTTTCTCTTTCTCTGTCTCTCTCTCTCTTT 105090 -- i i v i C HERVIP10FH#LT 852 TCTCT--CTCTCTCTTCCTCTCTCTCTCTCTCTCTCT 818 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 27.92 CpG sites = 25, Kimura (unadjusted) = 27.92 Transitions / transversions = 1.67 (25/15) Gap_init rate = 0.04 (7 / 180), avg. gap size = 1.71 (12 / 7) 23 33.41 1.38 4.26 chr2ptel1M 105163 105307 (894693) (TTTC)n#Simple_repeat 1 141 (0) m_b57s252i12 2101 chr2ptel1M 105163 TTCCTTTGCTCCTCTCTTTCTTTTTATAACTTTCTGGCTCTCACTTTCTT 105212 i vi i i i - -v --i iv (TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTTTCT-T-TCTTTCT--TTCTTTCTTTCTT 46 chr2ptel1M 105213 GC-TCCTACACTTTCTTTCTCTCCTTCTCTCTTGC-TTCAGTTTGTGTGG 105260 v - i -iv i i i v - vv i v v vv (TTTC)n#Simpl 47 TCTTTCT-TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT 95 chr2ptel1M 105261 CTTGATCTCTCTGTTTCTGTCTCTTCTATTTCTGTTTCTTTGTTTCT 105307 vv i i v v - v i i v v (TTTC)n#Simpl 96 CTTTCTTTCTTTCTTTCTTTCT-TTCTTTCTTTCTTTCTTTCTTTCT 141 Matrix = Unknown Transitions / transversions = 0.89 (17/19) Gap_init rate = 0.06 (8 / 144), avg. gap size = 1.00 (8 / 8) 73 0.00 0.00 0.00 chr2ptel1M 105321 105382 (894618) (TC)n#Simple_repeat 1 62 (0) c_b57s251i4 2102 chr2ptel1M 105321 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 105370 (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr2ptel1M 105371 TCTCTCTCTCTC 105382 (TC)n#Simple_ 51 TCTCTCTCTCTC 62 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0) 14 4.00 7.69 0.00 chr2ptel1M 105383 105408 (894592) (CCTC)n#Simple_repeat 1 28 (0) m_b57s252i14 2103 chr2ptel1M 105383 CCTCCCTCCCTCCCT-CC-CCCTCCTTC 105408 - - i (CCTC)n#Simpl 1 CCTCCCTCCCTCCCTCCCTCCCTCCCTC 28 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.08 (2 / 25), avg. gap size = 1.00 (2 / 2) 397 22.90 2.44 7.69 chr2ptel1M 106040 106162 (893838) MIRc#SINE/MIR 32 148 (120) m_b57s601i16 2104 chr2ptel1M 106040 GGCCTTG-AG-CAGGAAGACTTCTATCTGTGAGTTCAGATCTGGCCCCAG 106087 v - - i -------- i iii iv v i v MIRc#SINE/MIR 32 GGACTTGGAGTCAGGAAGACCT--------GGGTTCGAGTCCCGGCTCTG 73 chr2ptel1M 106088 CCACTTAACTACCTGTGTAACCCTAGCCAAGTCACTTAACC-CTGTTTTC 106136 - v i i i v - v vvv MIRc#SINE/MIR 74 CCACTTA-CTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGC 122 chr2ptel1M 106137 CTCAGTTTTGTCAATTATAAAATGAG 106162 iv vi i i MIRc#SINE/MIR 123 CTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.31 CpG sites = 14, Kimura (unadjusted) = 27.52 Transitions / transversions = 1.17 (14/12) Gap_init rate = 0.10 (12 / 122), avg. gap size = 1.00 (12 / 12) 19 17.49 0.00 0.00 chr2ptel1M 106488 106520 (893480) (A)n#Simple_repeat 1 33 (0) m_b57s252i15 2105 chr2ptel1M 106488 AAAAAAAAAAAGAAAGAGAAAAAAAAAGAATAA 106520 i i i i v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 33 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 33 5.62 0.00 0.00 chr2ptel1M 106631 106667 (893333) (AC)n#Simple_repeat 1 37 (0) c_b57s251i5 2106 chr2ptel1M 106631 ACACATACAAACACACACACACACACACACACACACA 106667 i v (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACA 37 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 24 27.70 4.21 0.00 chr2ptel1M 107319 107413 (892587) (TCTGTC)n#Simple_repeat 1 99 (0) m_b57s252i16 2107 chr2ptel1M 107319 TCTGTCTCTGCCTCTTTGGCTGTCTCCCTCTCTCTTTCTGGC-CCAT-TC 107366 i v vv iv v i v - ii - (TCTGTC)n#Sim 1 TCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTC 50 chr2ptel1M 107367 AGTCTCTCCTTCTCTCTCTAGCT-TG-CTCTGGCTCATTCTCTGACTCT 107413 v vii v iv - - v vv v (TCTGTC)n#Sim 51 TGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCT 99 Matrix = Unknown Transitions / transversions = 0.57 (8/14) Gap_init rate = 0.04 (4 / 94), avg. gap size = 1.00 (4 / 4) 263 19.54 7.29 4.04 chr2ptel1M 108458 108553 (891447) Charlie7a#DNA/hAT-Charlie 173 271 (1) m_b57s502i3 2108 chr2ptel1M 108458 ATATAATTTATAAATAA------GCACACACATTAAAGGTGCATGTATAA 108501 ------ii i i iii i- v Charlie7a#DNA 173 ATATAATTTATAAATAAATAAATATACATATATTGGGGGTGCATGC-TCA 221 chr2ptel1M 108502 AAAAGGTTTTACTT-TAGAGGTGAATTTGACCAAAACAAGTTAGGAGAGT 108550 vv v- i v -- i - v vi Charlie7a#DNA 222 AAAATTTTTTACTGATAGGGGTGCA--TGATCAAAA-AAGTTTGGAGACC 268 chr2ptel1M 108551 ACT 108553 Charlie7a#DNA 269 ACT 271 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 23.06 CpG sites = 11, Kimura (unadjusted) = 23.06 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.06 (6 / 95), avg. gap size = 1.83 (11 / 6) 338 31.57 5.03 6.37 chr2ptel1M 108555 108713 (891287) C MIR3#SINE/MIR (37) 171 15 m_b57s601i17 2109 chr2ptel1M 108555 CCTTCCGGATCATCTATTCTACCCTCCTCCACACTTTCCAGATGAGAAAA 108604 vvi v i v i --- i v i C MIR3#SINE/MIR 171 CCTTAGAGATCATCTAGTCCAACCCCCTC---ATTTTACAGATGAGGAAA 125 chr2ptel1M 108605 CACAGAACCAAGAAGGTTAACTTAATTTACCAAAGATCACTCAG------ 108648 vv iv iii v -v i i i v i v ------ C MIR3#SINE/MIR 124 CTGAGGCCCAGAGAGGTGAA-GTGACTTGCCCAAGGTCACACAGCNAGTT 76 chr2ptel1M 108649 -GCTGCAGAATTAGGATCTAGACTGCATTGGGTCCTCTGG-TCCCAAAGC 108696 - iv iiii - viv --- ii i- -- i C MIR3#SINE/MIR 75 AGTGGCAGAGCCGGGA-CTAGAACCCA---GGTCTCCTGACTCCC--AGT 32 chr2ptel1M 108697 TAGTATTTTTTTCACTC 108713 iv ii i i iii C MIR3#SINE/MIR 31 CCGTGCTCTCTCTGCTC 15 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.72 CpG sites = 31, Kimura (unadjusted) = 43.11 Transitions / transversions = 1.94 (31/16) Gap_init rate = 0.08 (13 / 158), avg. gap size = 1.38 (18 / 13) 360 30.92 6.11 3.73 chr2ptel1M 108582 108712 (891288) C MIRb#SINE/MIR (115) 153 20 m_b57s601i18 2109 chr2ptel1M 108582 TCCACACTTTCCAGATGAGAAAACACAGAACCAAGAAGGTTAACTTAATT 108631 v i v i vv ivi iii -v i C MIRb#SINE/MIR 153 TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAA-GTAACT 105 chr2ptel1M 108632 TACCAAAGATCACTCAG-------GCTGCAGAATTAGGATCTAGACTGCA 108674 i v i v ------- iv iiii iiii i- C MIRb#SINE/MIR 104 TGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACC-CA 56 chr2ptel1M 108675 TTGGGTCC-TCTGGTCCCAAAGCTAGTATTTTTTTCACT 108712 --- i- iii iv ii i i C MIRb#SINE/MIR 55 ---GGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACT 20 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.78 CpG sites = 29, Kimura (unadjusted) = 43.11 Transitions / transversions = 2.90 (29/10) Gap_init rate = 0.05 (7 / 130), avg. gap size = 1.86 (13 / 7) 319 25.85 9.17 6.50 chr2ptel1M 108812 108931 (891069) C MIRc#SINE/MIR (120) 148 26 m_b57s601i19 2110 chr2ptel1M 108812 CTCATTTCACACAGGAGGAAAT--AG---------GGTTAGTTGATTTAC 108850 i i v v i-- --------- iv i i C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr2ptel1M 108851 CCAAAGTAACACAGCTACTGAGTGTCTGAGATCAGATTTGGACTAATGAA 108900 i v v i v -- v v ---- --i C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGC--AGAGCCG----GGACT--CGAA 57 chr2ptel1M 108901 CATTAGTCTTCCCTGTTCCAAACCTAATGCT 108931 vivi ivii ii i i C MIRc#SINE/MIR 56 CCCAGGTCTTCCTGACTCCAAGTCCAGTGCT 26 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.31 CpG sites = 18, Kimura (unadjusted) = 32.67 Transitions / transversions = 1.64 (18/11) Gap_init rate = 0.08 (10 / 119), avg. gap size = 1.90 (19 / 10) 180 26.14 4.35 4.35 chr2ptel1M 108994 109085 (890915) C MIR#SINE/MIR (0) 262 171 m_b57s601i20 2111 chr2ptel1M 108994 AATAATAGCTAACATCTAAT-AGTGATTAATGTGGGCTAAGCCCT-TTAC 109041 i v - i v v i v i i v - vi C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCT 213 chr2ptel1M 109042 AATTACAATTTACAACATGCTAACCC-TTTAA-CATCATAGTCAAC 109085 --i iv - ii ii i - - v i i- C MIR#SINE/MIR 212 AA--GCGCTTTAC-ATGTATTAACTCATTTAATCCTCACAA-CAAC 171 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.81 CpG sites = 15, Kimura (unadjusted) = 33.28 Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.09 (8 / 91), avg. gap size = 1.00 (8 / 8) 16 0.00 0.00 0.00 chr2ptel1M 112043 112060 (887940) (T)n#Simple_repeat 1 18 (0) m_b58s252i0 2112 chr2ptel1M 112043 TTTTTTTTTTTTTTTTTT 112060 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTT 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 17 26.89 1.52 3.08 chr2ptel1M 113181 113246 (886754) (AGAA)n#Simple_repeat 1 65 (0) m_b58s252i1 2113 chr2ptel1M 113181 AGAAAGAAAGAAA-AAATATGAGAAGGAAAACAAAAATGCAAGTAAACAA 113229 - v -i i iv i v v - v (AGAA)n#Simpl 1 AGAAAGAAAGAAAGAAAGA-AAGAAAGAAAGAAAGAAAGAAAG-AAAGAA 48 chr2ptel1M 113230 TAATAGAAAGAGAGGAA 113246 vi v i i (AGAA)n#Simpl 49 AGAAAGAAAGAAAGAAA 65 Matrix = Unknown Transitions / transversions = 1.00 (7/7) Gap_init rate = 0.05 (3 / 65), avg. gap size = 1.00 (3 / 3) 566 31.83 4.62 4.29 chr2ptel1M 113277 113601 (886399) C L3#LINE/CR1 (150) 3949 3624 m_b58s601i0 2114 chr2ptel1M 113277 CTCTGGGTGGAGCTGATTCCATTTTGCATCAACTCTAAGTGCTGAGAAG- 113325 ?v iv v iv vviv i i v i iii - C L3#LINE/CR1 3949 CTCNCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGATTGTTAGAAAGT 3900 chr2ptel1M 113326 -CTTTCTCTTATTG----GAAACCTGTCTCTCCA-AACACCCACCAGCTG 113369 - i iv ---- i i i ii- vi vii C L3#LINE/CR1 3899 TCTTCCTTATATTGAGCCGAAATCTGCCTCCCTGTAACTTCCACCCATTG 3850 chr2ptel1M 113370 CTCTTGCTTCTGCCCAGTGAA---ACACAGAAACACACTCCTGAATCTTT 113416 v i iv vv i --- vv vv ---- ii C L3#LINE/CR1 3849 GTCCTAGTTCTGCCCTCTGGAGCCACACAGAATAAGTCT----AATCCCT 3804 chr2ptel1M 113417 CTTT-ATGTGAATGGAGTCCTTCATATCCTCAGAGACAGCTATTATCTCT 113465 i- ii v--- i v vi iii i v C L3#LINE/CR1 3803 CTTCCACATGAC---AGCCCTTCAAATATTTGAAGACAGCTATCATGTCT 3757 chr2ptel1M 113466 CCTATCAAGTGTCATCTTTTCTTTCTCT--GCTAAACTTTCCCAATGAAT 113513 v - ----- i - i-- v i i vvv C L3#LINE/CR1 3756 CCTCT-AAGT-----CTTCTCTT-CTCCAGGCTAAACATCCCCAGTTCCT 3714 chr2ptel1M 113514 GCAGGCATTCCTCCTAAGCCATCATTCTCACTCCTCTTCCCCTCCTGGCT 113563 v iv i v v v vi ii vv ii iv v ii C L3#LINE/CR1 3713 TCAACCGTTCCTCATATGACATGGTTTCCAGACCCTTCACCATCCTGGTC 3664 chr2ptel1M 113564 GAACTTCTCTAGATGCACCCAAGCTCCTC--TGGCCTTTT 113601 vv i i i i i v i iv -- v i i C L3#LINE/CR1 3663 GCTCTCCTCTGGACGCGCTCCAGTTTGTCAATGTCCCTCT 3624 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.51 CpG sites = 56, Kimura (unadjusted) = 42.78 Transitions / transversions = 1.30 (56/43) Gap_init rate = 0.07 (22 / 324), avg. gap size = 1.32 (29 / 22) 328 31.88 0.00 6.73 chr2ptel1M 113629 113739 (886261) C MIRc#SINE/MIR (153) 115 12 m_b58s601i1 2115 chr2ptel1M 113629 GGGGTTAAGTGGCTTGCTTAGAGACTCATAGGCACTAAATGTCAAGTATG 113678 i i ii ii v v i vi v i v ------ C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCA------ 72 chr2ptel1M 113679 TGAGGCCAGATTTGACCTCAGGTTCCCCTGATTCCAGGGTTAGTACTCTA 113728 - v vi i i v i iii i i vii i v C MIRc#SINE/MIR 71 -GAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTT 23 chr2ptel1M 113729 TGCACTGCCCC 113739 v v C MIRc#SINE/MIR 22 TCCACTGCACC 12 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.41 CpG sites = 21, Kimura (unadjusted) = 43.18 Transitions / transversions = 1.75 (21/12) Gap_init rate = 0.06 (7 / 110), avg. gap size = 1.00 (7 / 7) 243 21.73 4.23 2.78 chr2ptel1M 113778 113848 (886152) C L2a_3end#LINE/L2 (66) 451 380 m_b58s601i2 2116 chr2ptel1M 113778 GATACAAGCAGTCAGCAAATGTAGA-ATAAGTACTTTCCCTCAAGGGGCT 113826 - v i -ii - v v i v v i C L2a_3end#LINE 451 GATACA-GCAGTGAACAAA-ACAGACAAAAGTCCCTGCCCTCATGGAGCT 404 chr2ptel1M 113827 TACATCCTA--AAGGGGAAACAAA 113848 i --ii i i C L2a_3end#LINE 403 TACATTCTAGTGGGGGGAGACAGA 380 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.41 CpG sites = 10, Kimura (unadjusted) = 26.41 Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.06 (4 / 70), avg. gap size = 1.25 (5 / 4) 196 30.30 6.06 0.00 chr2ptel1M 113795 113860 (886140) C L2d_3end#LINE/L2 (82) 434 365 m_b58s601i3 2116 chr2ptel1M 113795 AATGTAGAATA-AGTACTTTCCCTCAAGGGGCTTACATCCTAA-AGGGGA 113842 i i ii i -i v i v i vi i-v C L2d_3end#LINE 434 AGTATAAGACATGGTCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGGA 385 chr2ptel1M 113843 AACAAAAT--ACCTATATGA 113860 i i i-- vi i C L2d_3end#LINE 384 GACAAGACTAACACACATGA 365 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.89 CpG sites = 15, Kimura (unadjusted) = 41.89 Transitions / transversions = 3.00 (15/5) Gap_init rate = 0.05 (3 / 65), avg. gap size = 1.33 (4 / 3) 407 32.34 12.94 2.95 chr2ptel1M 113888 114196 (885804) C L2b_3end#LINE/L2 (10) 456 118 m_b58s601i4 2117 chr2ptel1M 113888 TCAACAAATAATCAGTGAACATTTATTATGTGCC--------TACTAATT 113929 v i v i iii i i -------- i ivi C L2b_3end#LINE 456 TCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGC 407 chr2ptel1M 113930 GCCAGTTGTACAGAGGC--------CAAA-TCAGTCCCTACATACAAGAA 113970 ii vvi v i-------- i -? i i viv v i C L2b_3end#LINE 406 GCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGGA 357 chr2ptel1M 113971 GCTCAATTTGCAATGGGAGAGGCA-ACATGCAAACAG----TTATGTCCA 114015 vvv vi i i i - i ? ---- ? iv v C L2b_3end#LINE 356 GCTCACAGTCTAGTGGGGGAGACAGACATGTAANCAGACAATNATAACCC 307 chr2ptel1M 114016 AGTAAGACACATAAATAGTA-TGGGGA-----AAGGGAGA---CCT---T 114053 viv i ---iii v - i----- ii i--- ---i C L2b_3end#LINE 306 AGAGTGGCA---GGGTAGGACTGGGGGGGCCCAGAGGAGGGCGCCTGACC 260 chr2ptel1M 114054 CAGCATGTGGAAAGATAAGGAAGGACTTCTGATGAAAGAAGTTAC--TTC 114101 i v v --- i v i i i--i i i i v -- v C L2b_3end#LINE 259 CGGCCTGGGG---GGTCAGGGAGGGCTTCC--CGGAGGAGGTGACATTTG 215 chr2ptel1M 114102 AGCTGAGCCTTGAAGGAAGAAGAG-ATTTGAAGAAGCAGAGAAAAGGGAT 114150 v i v iv - v ivv i ii iiv i- C L2b_3end#LINE 214 AGCTGAGACCTGAAGGATGAGTAGGAGTTGGCCAGGCGAAGAGGTGGGG- 166 chr2ptel1M 114151 GAGAAGATTCCAGGCATGAGGG---AGTAAGATCAAAGGTATGGAGATG 114196 i iivi - --- i ? vv iviv ii C L2b_3end#LINE 165 AAGGGCGTTCCAGGCA-GAGGGAACAGCANGTGCAAAGGCCCTGAGGCG 118 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.46 CpG sites = 62, Kimura (unadjusted) = 45.49 Transitions / transversions = 1.77 (62/35) Gap_init rate = 0.07 (22 / 308), avg. gap size = 2.27 (50 / 22) 13 26.07 4.00 0.00 chr2ptel1M 114406 114455 (885545) (TATA)n#Simple_repeat 1 52 (0) m_b58s252i3 2118 chr2ptel1M 114406 TATAAATATGTATATATATCT-TGGATTTA-ATATCTATTTAAACATATT 114453 v i v - iv v - v v v i v (TATA)n#Simpl 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr2ptel1M 114454 TA 114455 (TATA)n#Simpl 51 TA 52 Matrix = Unknown Transitions / transversions = 0.38 (3/8) Gap_init rate = 0.04 (2 / 49), avg. gap size = 1.00 (2 / 2) 251 31.11 5.41 7.34 chr2ptel1M 115596 115706 (884294) MIRc#SINE/MIR 40 148 (120) m_b58s601i5 2119 chr2ptel1M 115596 AATCAGGAAAACTCAACTCCCTGTATTTAAATCCTGTCTCAG------AT 115639 i i -------- vi ii i i v v ------ i MIRc#SINE/MIR 40 AGTCAGGAAGAC--------CTGGGTTCGAGTCCCGGCTCTGCCACTTAC 81 chr2ptel1M 115640 TAGGTGTGTCATCCCAGTAACCTCACTGAAACCCTGTTTGCCTGAGTTTC 115689 v v i iii vv vv v v i v vv v MIRc#SINE/MIR 82 TAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTC 131 chr2ptel1M 115690 TTCCTCTATAAAATGAG 115706 i v i i MIRc#SINE/MIR 132 CTCATCTGTAAAATGGG 148 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.33 CpG sites = 16, Kimura (unadjusted) = 40.67 Transitions / transversions = 1.00 (16/16) Gap_init rate = 0.08 (9 / 110), avg. gap size = 1.56 (14 / 9) 265 31.25 6.25 0.00 chr2ptel1M 115611 115706 (884294) MIR#SINE/MIR 43 144 (118) m_b58s601i6 2119 chr2ptel1M 115611 ACTCCCTGTATTTAAATCCTGTCTCAG------ATTAGGTGTGTCATCCC 115654 v vi ii i v v ------ i v v i ii MIR#SINE/MIR 43 ACTGCCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTT 92 chr2ptel1M 115655 AGTAACCTCACTGAAACCCTGTTTGCCTGAGTTTCTTCCTCTATAAAATG 115704 i vv vv i v v i v v v i v i MIR#SINE/MIR 93 GGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATG 142 chr2ptel1M 115705 AG 115706 i MIR#SINE/MIR 143 GG 144 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.27 CpG sites = 14, Kimura (unadjusted) = 40.79 Transitions / transversions = 0.88 (14/16) Gap_init rate = 0.01 (1 / 95), avg. gap size = 6.00 (6 / 1) 363 25.86 12.39 0.79 chr2ptel1M 118025 118137 (881863) C MIRc#SINE/MIR (140) 128 3 m_b58s601i7 2120 chr2ptel1M 118025 ACTGAATTCCAGTCAAATTAAATTACTTTCCCAAG----CCCAG------ 118064 ivii vv ii i v v ---- v ------ C MIRc#SINE/MIR 128 ACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTA 79 chr2ptel1M 118065 AGTTGCAGAACCAGAATTTCAACCCATGG----CCTAACTCCAAATATAG 118110 v i i i i iv - ---- i i vi C MIRc#SINE/MIR 78 AGTGGCAGAGCCGGGACTCGAACCCA-GGTCTTCCTGACTCCAAGTCCAG 30 chr2ptel1M 118111 TGATCTTTCCATTTTGCCACACTGTCT 118137 v i vii i C MIRc#SINE/MIR 29 TGCTCTTTCCACTGCACCACACTGCCT 3 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.98 CpG sites = 18, Kimura (unadjusted) = 32.67 Transitions / transversions = 1.64 (18/11) Gap_init rate = 0.04 (4 / 112), avg. gap size = 3.75 (15 / 4) 12 24.08 0.00 0.00 chr2ptel1M 120504 120537 (879463) (AAGA)n#Simple_repeat 1 34 (0) m_b58s252i4 2121 chr2ptel1M 120504 AAAAAAGAAAGAAATTAAATAACAAACAAAGAAA 120537 i vv iv v v (AAGA)n#Simpl 1 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 34 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 48 0.00 0.00 0.00 chr2ptel1M 120556 120596 (879404) (TA)n#Simple_repeat 1 41 (0) c_b58s251i0 2122 chr2ptel1M 120556 TATATATATATATATATATATATATATATATATATATATAT 120596 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATAT 41 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 438 22.53 5.93 5.93 chr2ptel1M 121269 121386 (878614) MIRc#SINE/MIR 10 127 (141) m_b58s601i8 2123 chr2ptel1M 121269 GTGGTGCAGTGGATAGAGTACTGAA------GTCAGGAGGACCCAAGTTC 121312 v i i ------ i iii MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr2ptel1M 121313 AAATATGGTATCAGACACTTAACACTTCCTGGTTGTGTGATTCTGGGCAA 121362 i i viv vv v v ------- i i iii MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTGACCTTGGGCAA 102 chr2ptel1M 121363 GTCACTTAACCCCAATT-GCCTCAG 121386 i vv v- MIRc#SINE/MIR 103 GTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.06 CpG sites = 15, Kimura (unadjusted) = 27.31 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.08 (9 / 117), avg. gap size = 1.56 (14 / 9) 265 31.45 11.11 6.38 chr2ptel1M 122505 122684 (877316) MIRb#SINE/MIR 17 204 (64) m_b58s601i9 2124 chr2ptel1M 122505 TACAGTGGATAGAAAATGAATAGAGCCTTG-ATTCATGAAACCCAGGGTT 122553 i v iv i i----- i - v viv iv v MIRb#SINE/MIR 17 TGCAGTGGAAAGAGCACGG-----GCTTTGGAGTCAGACAGACCTGGGTT 61 chr2ptel1M 122554 TTAATCCCACCTCAGAAATTTGCTAGT--------------AAAGTTATA 122589 iv iv v vv i i i--------------v iv MIRb#SINE/MIR 62 CGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACT 111 chr2ptel1M 122590 GGACCTCTGTTAGATTCAGTTTTTTTTTTTTTAATCTGTCAAATGGGCCT 122639 vi v v vi ii i------- v vv MIRb#SINE/MIR 112 TAACCTCTCTGAGCCTCAGTTTCCTC-------ATCTGTAAAATGGGGAT 154 chr2ptel1M 122640 AA-----GCTAAGTTCTTGGATTCTCATTAGGATAAAATAAGATAATGCA 122684 -----v vv iviv i v ii v v i MIRb#SINE/MIR 155 AATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCA 204 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.43 CpG sites = 24, Kimura (unadjusted) = 41.24 Transitions / transversions = 0.83 (24/29) Gap_init rate = 0.08 (15 / 179), avg. gap size = 2.13 (32 / 15) 608 25.91 5.76 1.00 chr2ptel1M 123655 123845 (876155) MIRc#SINE/MIR 10 209 (59) m_b58s601i10 2125 chr2ptel1M 123655 GTAGTTCAGTGGA--GAGTCCTGGACATAGAGTCAAGTATACCTGAGTTT 123702 i v -- iv v i i v v i i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr2ptel1M 123703 GAAGTG--AGCTTTGGACAATTACTAACTATGCATCTCTGGGCAAGTCAA 123750 - v--i i v- v i i iiv ii v MIRc#SINE/MIR 60 GA-GTCCCGGCTCTGC-CACTTACTAGCTGTGTGACCTTGGGCAAGTCAC 107 chr2ptel1M 123751 TTAAACTCTGTTTTCCTCAGTTTCCTCAACTCTTAAATGGGGACA--AAT 123798 v v vvv v v v i -- MIRc#SINE/MIR 108 TTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAAT 157 chr2ptel1M 123799 ATC-ACCGTA---ACTTGGCA-GGTTAAGATGAGGATAAAGTGACACAAT 123843 i -i v i--- i vi - ivvi v i v i MIRc#SINE/MIR 158 ACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAAT 207 chr2ptel1M 123844 AT 123845 i MIRc#SINE/MIR 208 GT 209 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.62 CpG sites = 25, Kimura (unadjusted) = 32.17 Transitions / transversions = 1.04 (25/24) Gap_init rate = 0.04 (8 / 190), avg. gap size = 1.62 (13 / 8) 288 23.19 11.94 3.45 chr2ptel1M 125441 125574 (874426) C MIR3#SINE/MIR (2) 206 62 m_b58s601i11 2126 chr2ptel1M 125441 ATCA-AAAGTCATAAGATGT-GGAGCTGAAAG--ACCGTCAGAAGTAG-- 125484 - i i ii -i i -- - i ii vi-- C MIR3#SINE/MIR 206 ATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACC-TTAGAGATCATC 158 chr2ptel1M 125485 -AATCCAACCCCCTTCAATTTATAG--GAGGAAACTGAAACTCAGAGCAG 125531 - i - v i -- ii i - C MIR3#SINE/MIR 157 TAGTCCAACCCCCT-CATTTTACAGATGAGGAAACTGAGGCCCAGAG-AG 110 chr2ptel1M 125532 G------GATTTGTGCAAAGGTAATA-AGCTTTCTCAGAGACAGGGTCAG 125574 ------ i i- v v i - -?vv i v i i i i C MIR3#SINE/MIR 109 GTGAAGTGACTTGC-CCAAGGTCACACAGC-NAGTTAGTGGCAGAGCCGG 62 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.44 CpG sites = 23, Kimura (unadjusted) = 29.62 Transitions / transversions = 3.29 (23/7) Gap_init rate = 0.10 (13 / 133), avg. gap size = 1.62 (21 / 13) 17 14.42 0.00 5.00 chr2ptel1M 129167 129208 (870792) (TGTGTA)n#Simple_repeat 1 40 (0) m_b58s252i5 2127 chr2ptel1M 129167 TGTGTTTGTGTATGTGTCAATGTGTGAGTGTTTGTGAATGTG 129208 v -- iv v v (TGTGTA)n#Sim 1 TGTGTATGTGTATGTGT--ATGTGTATGTGTATGTGTATGTG 40 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.05 (2 / 41), avg. gap size = 1.00 (2 / 2) 40 2.31 0.00 2.22 chr2ptel1M 129214 129259 (870741) (ATATAC)n#Simple_repeat 1 45 (0) c_b58s251i1 2128 chr2ptel1M 129214 ATATACATATACATTATACATAAACATATACATATACATATACATA 129259 - v (ATATAC)n#Sim 1 ATATACATATACA-TATACATATACATATACATATACATATACATA 45 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1) 30 0.00 0.00 0.00 chr2ptel1M 129540 129565 (870435) (GT)n#Simple_repeat 1 26 (0) c_b58s251i2 2129 chr2ptel1M 129540 GTGTGTGTGTGTGTGTGTGTGTGTGT 129565 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGT 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 447 22.19 0.83 6.14 chr2ptel1M 130342 130461 (869539) MIRc#SINE/MIR 2 115 (153) m_b58s601i12 2130 chr2ptel1M 130342 GGGGCAGCTGGTGTTGCAGTGGATAGAGCACCAGCCCTGAATTTAGGAGG 130391 i i-- v v ii v i i v i i MIRc#SINE/MIR 2 GAGGCAGT--GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAG 49 chr2ptel1M 130392 ACCAGAATTCAAATCA-GACACCTAACACCTTAACTCTGGCTGTGTGACC 130440 v ii i i v- i -i iv - --- i MIRc#SINE/MIR 50 ACCTGGGTTCGAGTCCCGGC-TCTGCCAC-TTA---CTAGCTGTGTGACC 94 chr2ptel1M 130441 CTGGGCAAGTCACTTAACCCC 130461 i i MIRc#SINE/MIR 95 TTGGGCAAGTCACTTAACCTC 115 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.98 CpG sites = 18, Kimura (unadjusted) = 27.25 Transitions / transversions = 2.57 (18/7) Gap_init rate = 0.07 (8 / 119), avg. gap size = 1.00 (8 / 8) 22 0.00 0.00 0.00 chr2ptel1M 132073 132096 (867904) (C)n#Simple_repeat 1 24 (0) m_b58s252i6 2131 chr2ptel1M 132073 CCCCCCCCCCCCCCCCCCCCCCCC 132096 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCC 24 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 254 32.88 3.87 1.90 chr2ptel1M 132504 132658 (867342) L2b_3end#LINE/L2 286 443 (23) m_b58s601i13 2132 chr2ptel1M 132504 CCAGTT-TATCCAGTGCACAGTGGGTTTCTATCTCATTGTTGATGTGT-T 132551 i- i v i- vv vi? - vvi ? v ii - L2b_3end#LINE 286 CCAGTCCTACCCTGC-CACTCTGGGTTATNAT-TGTCTGNTTACATGTCT 333 chr2ptel1M 132552 GTCCGCCCCACCAGTCTGTGACCTCAGTGACACCAGGGG--AAGTC--CC 132597 iv i v v v viv i--i? --i L2b_3end#LINE 334 GTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTC 383 chr2ptel1M 132598 TCAAACCTCCTTTTGCTCCTGGTGCTTAGCCCAGAGTCTGACATGTAGCA 132647 iivv vi vi v iii ii i i v ? i i iii i L2b_3end#LINE 384 TTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTA 433 chr2ptel1M 132648 GGCCCTTCAGT 132658 v - L2b_3end#LINE 434 GGCGC-TCAGT 443 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.18 CpG sites = 30, Kimura (unadjusted) = 46.76 Transitions / transversions = 1.50 (30/20) Gap_init rate = 0.05 (7 / 154), avg. gap size = 1.29 (9 / 7) 268 29.27 3.66 0.00 chr2ptel1M 132757 132838 (867162) C MIR3#SINE/MIR (3) 205 121 m_b58s601i14 2133 chr2ptel1M 132757 TTATAGGATCCTACATGATCA---CTGGAAGGGACTTACCAGGCCATAAA 132803 i i v v vvi --- i vvv ii vv C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTA 156 chr2ptel1M 132804 GTGCAGCCTCTTTATTTTACAGACAGGGAAACAGA 132838 v i i i i iii v C MIR3#SINE/MIR 155 GTCCAACCCCCTCATTTTACAGATGAGGAAACTGA 121 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.81 CpG sites = 13, Kimura (unadjusted) = 37.81 Transitions / transversions = 1.18 (13/11) Gap_init rate = 0.01 (1 / 81), avg. gap size = 3.00 (3 / 1) 427 30.19 8.70 1.01 chr2ptel1M 133918 134101 (865899) MIRb#SINE/MIR 4 201 (67) m_b58s601i15 2134 chr2ptel1M 133918 AAGGGGAGCTGGTGGTACAATAAAGAGACC-TGGGCAT-AGAGTCAGAAG 133965 i v -- i i ii i v -i v -i vi MIRb#SINE/MIR 4 AGGGGCAGC--GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACA 51 chr2ptel1M 133966 TTCCTGAGCTTAAACCAAGCTTCAGGAAGTTCCTAGCTCTGTTCCCCTTG 134015 vv i i ii i vv vi v vv v v v vv i v MIRb#SINE/MIR 52 GACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 101 chr2ptel1M 134016 CCAAGTT-CTTAAACTCTGTTTGCCTCAGTTTCCTTAATTCTTAAGTGGG 134064 v - v v vv i vi v v i MIRb#SINE/MIR 102 GCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 151 chr2ptel1M 134065 GAGAA-------------AGAAGGTTGTTTTGAAGATAAGGTGACATAAT 134101 v -------------iv i v i v ii v MIRb#SINE/MIR 152 GATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAAT 201 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.23 CpG sites = 24, Kimura (unadjusted) = 38.88 Transitions / transversions = 0.77 (24/31) Gap_init rate = 0.03 (6 / 183), avg. gap size = 3.00 (18 / 6) 16 0.00 0.00 0.00 chr2ptel1M 134413 134429 (865571) (A)n#Simple_repeat 1 17 (0) m_b58s252i7 2135 chr2ptel1M 134413 AAAAAAAAAAAAAAAAA 134429 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 260 22.69 19.10 0.95 chr2ptel1M 135176 135264 (864736) C MIR3#SINE/MIR (12) 196 92 m_b58s601i16 2136 chr2ptel1M 135176 CATGAGATGT-AGAGCTGAAAGATGTTTCAGA------CT---CCAACCT 135215 iii - i iviii i ------ --- i C MIR3#SINE/MIR 196 CATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCC 147 chr2ptel1M 135216 TCTTCAATATACAG--GAAGATACTGAAGCTCAGA-----GAAGTGATTT 135258 i - v v -- i v i i ----- i C MIR3#SINE/MIR 146 CCT-CATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTT 98 chr2ptel1M 135259 GCTCAA 135264 i C MIR3#SINE/MIR 97 GCCCAA 92 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.69 CpG sites = 16, Kimura (unadjusted) = 28.69 Transitions / transversions = 4.00 (16/4) Gap_init rate = 0.07 (6 / 88), avg. gap size = 3.00 (18 / 6) 214 22.93 10.53 2.44 chr2ptel1M 135216 135291 (864709) C MIRc#SINE/MIR (118) 150 69 m_b58s601i17 2136 chr2ptel1M 135216 TCTTCAATATACAG--GAAGATACTGAAGCTCAGAG-----AAGTGATTT 135258 ii v v -- i v i ----- i C MIRc#SINE/MIR 150 TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTT 101 chr2ptel1M 135259 GCTCAACTGTCATTGCATTTA-TGTGTGTCAGAG 135291 i -v -ii vi - iv v C MIRc#SINE/MIR 100 GCCCAA-GGTCA-CACAGCTAGTAAGTGGCAGAG 69 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.94 CpG sites = 10, Kimura (unadjusted) = 27.94 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.07 (5 / 75), avg. gap size = 2.00 (10 / 5) 646 30.12 1.20 0.00 chr2ptel1M 136850 137015 (862985) C MIR3#SINE/MIR (5) 203 36 m_b58s601i18 2137 chr2ptel1M 136850 ATCAAATCATGGA--TTTAGAGCTTCCAGGGGCCTTAGAAATCATCTTGT 136897 vi i --v i vvv i i v C MIR3#SINE/MIR 203 ATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGT 154 chr2ptel1M 136898 CCACTCCACTCATTTTAAAGATGAAAGATCTAAGACCCAATGAGGTTAAA 136947 vi v v iii v i i iv v i C MIR3#SINE/MIR 153 CCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAG 104 chr2ptel1M 136948 TGACTTGCTGAACATCCCATAGATACCAGGTGACAAAGCTAAGATTAAAA 136997 iv vi v i v? vivi i i iii i i C MIR3#SINE/MIR 103 TGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAA 54 chr2ptel1M 136998 CTCGGGTTCTCTGTCTTC 137015 i i iii v i C MIR3#SINE/MIR 53 CCCAGGTCTCCTGACTCC 36 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.12 CpG sites = 31, Kimura (unadjusted) = 40.30 Transitions / transversions = 1.63 (31/19) Gap_init rate = 0.01 (1 / 165), avg. gap size = 2.00 (2 / 1) 424 33.58 2.24 0.00 chr2ptel1M 136906 137039 (862961) C MIRc#SINE/MIR (120) 148 12 m_b58s601i19 2137 chr2ptel1M 136906 CTCATTTTAAAGATGAAAGATCTAAGACCCAATGAGGTTAAATGACTTGC 136955 i v iii v i i i iv i C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr2ptel1M 136956 TGAACATCCCATAGATACCAGGTGACAAAGCTAAGATTAAAACTCGGGT- 137004 iv vi v i v vi i i i iii i vi i i - C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTC 49 chr2ptel1M 137005 TCTCTGTCTTCAGAT-AAGCACTG-TTCCATACCACC 137039 ii v i ii -v ii v- ivv C MIRc#SINE/MIR 48 TTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACC 12 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.56 CpG sites = 31, Kimura (unadjusted) = 47.73 Transitions / transversions = 2.21 (31/14) Gap_init rate = 0.02 (3 / 133), avg. gap size = 1.00 (3 / 3) 268 32.84 0.00 0.00 chr2ptel1M 137137 137203 (862797) L2d2_3end#LINE/L2 481 547 (8) m_b58s601i20 2138 chr2ptel1M 137137 TGCAGCCCCTCTGGTGCCTAATACAGTGCCTGGAATAAAACAAGCACTTA 137186 i v ivii i ii v v i v ii i i i L2d2_3end#LIN 481 TGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAGTAGGCGCTCA 530 chr2ptel1M 137187 ATAAGTGTTTATAGATT 137203 i i i v L2d2_3end#LIN 531 ATAAATATTTGTTGATT 547 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.95 CpG sites = 16, Kimura (unadjusted) = 46.80 Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.0 (0 / 0) 21 18.56 2.99 4.55 chr2ptel1M 137327 137393 (862607) (AGAGGG)n#Simple_repeat 1 66 (0) m_b58s252i8 2139 chr2ptel1M 137327 AGAGACAGAGACAGAGGGGAGAGGGACAGGGAG-GGGAGGGGGAAGGATG 137375 iv iv - v - i - - v (AGAGGG)n#Sim 1 AGAGGGAGAGGGAGA-GGGAGAGGGAGAGGGAGAGGGAGAGGG-A-GAGG 47 chr2ptel1M 137376 GAGGAGGAG-GAGAGAGGG 137393 ii - i (AGAGGG)n#Sim 48 GAGAGGGAGAGGGAGAGGG 66 Matrix = Unknown Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.08 (5 / 66), avg. gap size = 1.00 (5 / 5) 16 19.22 0.00 0.00 chr2ptel1M 137963 137998 (862002) (GGAG)n#Simple_repeat 1 36 (0) m_b58s252i9 2140 chr2ptel1M 137963 GGAAGGAGCCAGGGAGGGAGGGAAGAAAGGAGGGAG 137998 i vv i i i (GGAG)n#Simpl 1 GGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAG 36 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 388 24.56 9.23 2.90 chr2ptel1M 138720 138849 (861151) MIRc#SINE/MIR 11 148 (120) m_b58s601i21 2141 chr2ptel1M 138720 TAGCACAGTAGAGAG-GC------CTTAAA--CAGGAACACTCCTATTTG 138760 i ii i i - ------ ii -- v -- ivv v MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC--CTGGGTT 58 chr2ptel1M 138761 TGAG-CTCAAATCTGGCCATTTATTAGCTGTGTGACCCTGGCCAAGTCAC 138809 i - i iiv - i i i v MIRc#SINE/MIR 59 CGAGTCCCGGCTCTG-CCACTTACTAGCTGTGTGACCTTGGGCAAGTCAC 107 chr2ptel1M 138810 TTAATCCTGTTT--TCCTCAGCTTTGTGAATTGTAAAATGAG 138849 - v i --v i iv v vi i MIRc#SINE/MIR 108 TTAA-CCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.39 CpG sites = 20, Kimura (unadjusted) = 30.74 Transitions / transversions = 1.82 (20/11) Gap_init rate = 0.07 (9 / 129), avg. gap size = 1.78 (16 / 9) 342 29.95 0.83 3.39 chr2ptel1M 138765 138885 (861115) MIR3#SINE/MIR 61 178 (30) m_b58s601i22 2141 chr2ptel1M 138765 CTCAAATCTGGCCATTTATTAGCTGTGTGACCCTGGCCAAGTCACTTAAT 138814 i iiv - i v i ? i v v i MIR3#SINE/MIR 61 CCCGGCTCTG-CCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCAC 109 chr2ptel1M 138815 C-CTGTTTTCCTCAGCTTTGTGAATTGTAAAATGAGCTGGAGGTAGAAAT 138863 - v vvv i iv v vi --- i v i v MIR3#SINE/MIR 110 CTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGA---GGGGGTTGGACT 156 chr2ptel1M 138864 GGCTAACCACTCCAGTATCTTC 138885 i v i i v vvi vi MIR3#SINE/MIR 157 AGATGATCTCTAAGGTCCCTTC 178 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.64 CpG sites = 17, Kimura (unadjusted) = 39.02 Transitions / transversions = 0.94 (17/18) Gap_init rate = 0.04 (5 / 120), avg. gap size = 1.00 (5 / 5) 230 23.89 2.17 4.44 chr2ptel1M 139085 139176 (860824) L1MC5a_3end#LINE/L1 493 582 (2195) m_b58s551i0 2142 chr2ptel1M 139085 TGCCCATTCATTGGGGACTGGCTGAATAAGTTATGATACATGGTGCTGAA 139134 i iv v i ii i -vii vv L1MC5a_3end#L 493 TGTCCATCAATAGGGGACTGGTTGAATAAACTATGGTACAT-CCACACAA 541 chr2ptel1M 139135 -GGAATACTACTGT-GCTGTAAGAAATGATGAGCTCAGGATCTC 139176 - i - i- i ivi --v i L1MC5a_3end#L 542 TGGAGTACTA-TGCAGCTGTAAAAAGGAATGAG--GAAGATCTC 582 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 29.68 CpG sites = 14, Kimura (unadjusted) = 29.68 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.07 (6 / 91), avg. gap size = 1.00 (6 / 6) 44 7.71 0.00 0.00 chr2ptel1M 139407 139462 (860538) (AT)n#Simple_repeat 1 56 (0) c_b58s251i3 2143 chr2ptel1M 139407 ATATACATATATGTGTATATATATATGTATATATATATATATATATATAT 139456 i i i i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr2ptel1M 139457 ATATAT 139462 (AT)n#Simple_ 51 ATATAT 56 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0) 32 16.65 0.00 2.90 chr2ptel1M 139927 139997 (860003) (CTCTC)n#Simple_repeat 1 69 (0) m_b58s252i10 2144 chr2ptel1M 139927 CTCTCTCTCTCCTCTCCTCTCCTTTCCTCTCCTTTTCTATTGTCTGCTCT 139976 - i i i v iv v (CTCTC)n#Simp 1 CTCTC-CTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCT 49 chr2ptel1M 139977 GCTCTCCTCTCTACTTCCTCT 139997 v iv - (CTCTC)n#Simp 50 CCTCTCCTCTCCTC-TCCTCT 69 Matrix = Unknown Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.03 (2 / 70), avg. gap size = 1.00 (2 / 2) 15 18.53 4.65 0.00 chr2ptel1M 141779 141821 (858179) (TCTGTC)n#Simple_repeat 1 45 (0) m_b58s252i11 2145 chr2ptel1M 141779 TCTGTCTCT-T-TCTGCTTCTTTTTCTTTCTCAATCTCTGTCTCT 141821 - - ii v i v vi (TCTGTC)n#Sim 1 TCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCT 45 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.00 (2 / 2) 362 32.97 2.17 2.73 chr2ptel1M 142334 142517 (857483) C L1ME5_3end#LINE/L1 (389) 552 370 m_b58s551i1 2146 chr2ptel1M 142334 ATAATATTCCATAACATTCATATAACCACAATTTACTCAACCATTCTCCA 142383 i i iiii v vi - v ii v i v C L1ME5_3end#LI 552 ATAGTACTCCATGGTGTGCATCCA-CCACATTTTACCTATCCACTCTCCC 504 chr2ptel1M 142384 ATTGATGGGCATCCATTCATTTTCCAGCTTCTAGGCACTACAAACAAGGT 142433 v i i vvivvii i i iv v i v i C L1ME5_3end#LI 503 AGTGATGGACACCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGC 454 chr2ptel1M 142434 TGCCACAAACATTTTGGCACATTCAGGTCCCTTT----CCCTTCTTTAGT 142479 v ii ii v i ---- i ----v viv v v C L1ME5_3end#LI 453 TGCAATGAACATCCTCGTACAT----GTCCCCTTATGGACCTGTGTGAGA 408 chr2ptel1M 142480 ATCTCTTTGGAGTATAAGCCCGGTAGAAACACTGCTGG 142517 i ii vi i v viiv i C L1ME5_3end#LI 407 ATTTCTTTGGGATATATACCCAGGAGCGGAATTGCTGG 370 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 43.99 CpG sites = 35, Kimura (unadjusted) = 45.04 Transitions / transversions = 1.46 (35/24) Gap_init rate = 0.03 (6 / 183), avg. gap size = 1.50 (9 / 6) 139 38.35 1.39 1.27 chr2ptel1M 143512 144300 (855700) (TC)n#Simple_repeat 1 790 (0) m_b58s252i12 2147 chr2ptel1M 143512 TCTGTCTCTGTTTCTCTCTTTTGCTTTCTGTCTATTTCTTGCCGCCTCTC 143561 v v i i iv i v v i iv ivi (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr2ptel1M 143562 TATTTTTCTCTCTCACT-TTTTTATTTTTAACTATCTGGCTCCCTATGGT 143610 v i i v - i i v i i vv v vv i v -v (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT-CT 99 chr2ptel1M 143611 AT-TCTCTCTCACTTTTTGTCTCTCAGTCTTTTTCTCAAACCCTTTTTAT 143659 v - v i i v vv i i vvv i i i v (TC)n#Simple_ 100 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 149 chr2ptel1M 143660 TCCTCTCTCTCAATCTGTTTCTCTCTTTCTTCCTATCTTTTTCACTCTTA 143709 ii vv v i i ii v i i v iv (TC)n#Simple_ 150 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 199 chr2ptel1M 143710 CTCTCTGACTACTATGCCTGTCTATCTCTCCCTTTTTCTAACCCTGTTCC 143759 vv - v vi v v i i i vv i v ii (TC)n#Simple_ 200 CTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 248 chr2ptel1M 143760 TTTTTCTCTTATTCACTCTTTCTCTCCTTCTTTCTGGATCTCTTTCTCCC 143809 i i ivi v i ii i vvv i i (TC)n#Simple_ 249 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 298 chr2ptel1M 143810 TCTGGCACT-TTTTTCTCTCCTTTTTTCTATCTCTGATTTGCTCTCTCTG 143858 vv v - i i ii i i v -v i - v (TC)n#Simple_ 299 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT-CTCT-CTCTCTCTC 346 chr2ptel1M 143859 ACTCTTTGTCTGGTCTTTTTTTCTCTTTTTGTCTCCCAGTGGCTCTTTTT 143908 v i v -v i i i i i v i vv vv i i (TC)n#Simple_ 347 TCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 395 chr2ptel1M 143909 CTAAATCTCTCTCACTCTGGCTC-CCCTCTCTATTTCTTTGTCTTTCTCT 143957 vvv v vv - i v i i v i (TC)n#Simple_ 396 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 445 chr2ptel1M 143958 GTCTCTTTTTCTATTTCTCACTCTCTGGCACTCTCTCT-TCATCTCTCCC 144006 v i i v i v vv v - - i (TC)n#Simple_ 446 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TCTCTCTC 494 chr2ptel1M 144007 ACAGTCATAT-TCACTCTCTTCCTCTCACTCTGATTTACTCTAGCTTTTT 144055 v vv - v - v ii v -v i - vv i i (TC)n#Simple_ 495 TCTCTC-TCTCTCTCTCTCTCTCTCTCTCTCT-CTCT-CTCTCTCTCTCT 541 chr2ptel1M 144056 TTCTCTCCCTCTCTCTGTTTCATTCTCTTTCTCTC-CTCTACTCTCTGAC 144104 i i v i vi i - - vv (TC)n#Simple_ 542 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT-CTCTCTCTC 590 chr2ptel1M 144105 TCTCTTGCT-TATGT-TCTGTCTTTTGTTTTCTCTTTATCTTTCT-TATA 144151 iv - v v - v i ivi i i v i - v v (TC)n#Simple_ 591 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 640 chr2ptel1M 144152 TGT-TATCTCATTCTCTCCCTACCTTCCTCTCTCTCTGAAGTTCTCTTTT 144200 v - v vi i vi ii vvvvi i i (TC)n#Simple_ 641 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 690 chr2ptel1M 144201 TATTTCTTACTTGCTTGCTCTTTCACTCTCTGGCTCTCTCTCTTCCTCTG 144250 v i iv iv iv i v vv ii v (TC)n#Simple_ 691 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 740 chr2ptel1M 144251 ACACTTTCTCTCCTTCTGTCTCGCTATCTTTGACTCTATCTGTTGCTCTC 144300 v v i ii v v v i vv v v iv (TC)n#Simple_ 741 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 790 Matrix = Unknown Transitions / transversions = 0.90 (109/121) Gap_init rate = 0.03 (21 / 788), avg. gap size = 1.00 (21 / 21) 26 26.21 4.21 0.00 chr2ptel1M 144550 144644 (855356) (TCTGTC)n#Simple_repeat 1 99 (0) m_b58s252i13 2148 chr2ptel1M 144550 TCTGTCTCTGTCTCAGTCTCTTTGACTGTCTCTCTTTGTGGC-CCAT-TC 144597 v v vv v i v v - ii - (TCTGTC)n#Sim 1 TCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTC 50 chr2ptel1M 144598 AGTCTCTCCTTCTCTCTCTAGCT-TG-CTCTGGCTCATTCTCTGTATCT 144644 v vii v iv - - v vv v (TCTGTC)n#Sim 51 TGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCT 99 Matrix = Unknown Transitions / transversions = 0.40 (6/15) Gap_init rate = 0.04 (4 / 94), avg. gap size = 1.00 (4 / 4) 322 24.02 4.35 7.26 chr2ptel1M 145443 145530 (854470) Charlie7#DNA/hAT-Charlie 2436 2518 (97) m_b58s502i0 2149 chr2ptel1M 145443 TTCCATGTTGATCTCCTCCCTTCAGGATTTCAAATTTGGAGTAAGCTTCA 145492 i v v v i i ii v v v v v i i Charlie7#DNA/ 2436 TTTCATCTTTATCTCATCCTTTTAAAATTTCTATTTTTGTGTATGTTTTA 2485 chr2ptel1M 145493 TAATAGGTTCCATTCT-TAACAGGGATACACACATGCAT 145530 i--- v vv - vi --- vvvi i Charlie7#DNA/ 2486 TAATG---TACATAATATATTAG---TACAGTAGTACAT 2518 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 27.82 CpG sites = 22, Kimura (unadjusted) = 29.47 Transitions / transversions = 0.73 (11/15) Gap_init rate = 0.08 (7 / 87), avg. gap size = 1.00 (7 / 7) 47 4.26 0.00 0.00 chr2ptel1M 145531 145579 (854421) (AC)n#Simple_repeat 1 49 (0) c_b58s251i4 2150 chr2ptel1M 145531 ACACACACACACACACACACACACATACACACACACACATACACACACA 145579 i i (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACA 49 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 322 24.02 4.35 7.26 chr2ptel1M 145580 145674 (854326) Charlie7#DNA/hAT-Charlie 2519 2613 (2) m_b58s502i0 2149 chr2ptel1M 145580 TATATATAAAATTTATAAATAA--GCACACACATTAGAGGTTCA-----A 145622 ---- --ii i i i i v ----- Charlie7#DNA/ 2519 TATATA----ATTTATAAATAAATATACATATATTGGGGGTGCATGCTCA 2564 chr2ptel1M 145623 AAATGTTTTACTGATAGAGTTGAATGTGATCAAAACAAGTTAGGAGACTA 145672 v i i v --i i - v i Charlie7#DNA/ 2565 AAATTTTTTACTGATGGGGATG--CGCGATCAAAA-AAGTTTGGAGACCA 2611 chr2ptel1M 145673 CT 145674 Charlie7#DNA/ 2612 CT 2613 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 27.82 CpG sites = 22, Kimura (unadjusted) = 29.47 Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.10 (9 / 94), avg. gap size = 1.56 (14 / 9) 459 33.37 0.62 3.82 chr2ptel1M 145676 145837 (854163) C MIR3#SINE/MIR (37) 171 15 m_b58s601i23 2151 chr2ptel1M 145676 CCTTTGAGATCATCTATTCTATCCTCCTTCTCACTTTCCAGATGAGAAAA 145725 v v i v i --- i v i C MIR3#SINE/MIR 171 CCTTAGAGATCATCTAGTCCAACCCCCT---CATTTTACAGATGAGGAAA 125 chr2ptel1M 145726 CATAGACCCAAGAAGGTTAACTTAATTTACTCAAGATCACTCAGGTAATA 145775 vv i iii v -v i i i i i v v? i v C MIR3#SINE/MIR 124 CTGAGGCCCAGAGAGGTGAA-GTGACTTGCCCAAGGTCACACAGCNAGTT 76 chr2ptel1M 145776 GGCAGCTGAGTTAGGATCCAGATTCACGTCCTCTGG-TCCCAAAGCCAGT 145824 i ii v iii iivii ii v ii i- -- i v C MIR3#SINE/MIR 75 AGTGGCAGAGCCGGGACTAGAACCCAGGTCTCCTGACTCCC--AGTCCGT 28 chr2ptel1M 145825 ATTTGTTCCACTC 145837 ii ivi ii C MIR3#SINE/MIR 27 GCTCTCTCTGCTC 15 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 46.25 CpG sites = 36, Kimura (unadjusted) = 47.72 Transitions / transversions = 2.25 (36/16) Gap_init rate = 0.04 (7 / 161), avg. gap size = 1.00 (7 / 7) 513 31.58 0.75 0.75 chr2ptel1M 145703 145836 (854164) C MIRb#SINE/MIR (115) 153 20 m_b58s601i24 2151 chr2ptel1M 145703 TTCTCACTTTCCAGATGAGAAAACATAGACCCAAGAAGGTTAACTTAATT 145752 i i i v i vv i i iii v - i C MIRb#SINE/MIR 153 TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGT-AACT 105 chr2ptel1M 145753 TACTCAAGATCACTCAGGTAATAGGCAGCTGAGTTAGGATCCAGATTCAC 145802 i i i v v i i ii v iii i ii ii v C MIRb#SINE/MIR 104 TGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAG 55 chr2ptel1M 145803 GTCC-TCTGGTCCCAAAGCCAGTATTTGTTCCACT 145836 i- iii v ii iv C MIRb#SINE/MIR 54 GTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACT 20 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.59 CpG sites = 32, Kimura (unadjusted) = 44.71 Transitions / transversions = 3.20 (32/10) Gap_init rate = 0.02 (2 / 133), avg. gap size = 1.00 (2 / 2) 394 23.85 9.09 6.45 chr2ptel1M 145937 146057 (853943) C MIRc#SINE/MIR (120) 148 25 m_b58s601i25 2152 chr2ptel1M 145937 CTCATTTCACAGAGGAGGAAGC----------AGAG-TTAAGTGGCTTAC 145975 i i v i ---------- - i i C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr2ptel1M 145976 CCAAAGTAACACAGCTACTGAGTGTATGAGATCAGATTTGGACCAATGAA 146025 i v v i vvv vivi i i i ------ C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACC------ 55 chr2ptel1M 146026 CATGAGTCTTCCTTGTTCCAAATCTAATGCTC 146057 --i vii i i i C MIRc#SINE/MIR 54 CA--GGTCTTCCTGACTCCAAGTCCAGTGCTC 25 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.15 CpG sites = 18, Kimura (unadjusted) = 29.73 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.08 (10 / 120), avg. gap size = 1.90 (19 / 10) 691 22.11 12.11 0.00 chr2ptel1M 146118 146307 (853693) C MIR#SINE/MIR (0) 262 50 m_b58s601i26 2153 chr2ptel1M 146118 AATAATAGCTAACATCAAAT-AGTGATTAATGTATGC------------T 146154 iv v - i v v i i ------------ C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCT 213 chr2ptel1M 146155 AAGCACTTTACA---ATTATCTCATTTGATCCTCACAACTATCCTGGGTG 146201 i --- v i v i iv v C MIR#SINE/MIR 212 AAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAG 163 chr2ptel1M 146202 ATAGATGCTATTGTTACCCCCATCTCACCACTGAGGAAACTGAGG--CAA 146249 i i i i i i i viv -- i C MIR#SINE/MIR 162 GTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAG 113 chr2ptel1M 146250 ATAGATTAACTGACTTACCCAGGGTCAC-C--CTGATAGGT-CCAGGGCT 146295 v i v i i i - -- ii i -v i i C MIR#SINE/MIR 112 AGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCC 63 chr2ptel1M 146296 GTG-TTTGAACTC 146307 v - i i C MIR#SINE/MIR 62 GGGATTCGAACCC 50 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.05 CpG sites = 28, Kimura (unadjusted) = 26.96 Transitions / transversions = 2.00 (28/14) Gap_init rate = 0.04 (8 / 189), avg. gap size = 2.88 (23 / 8) 257 37.10 0.79 1.60 chr2ptel1M 147281 147406 (852594) MIR3#SINE/MIR 27 151 (57) m_b58s601i27 2154 chr2ptel1M 147281 CATTGACTATTGGAGTCAAGAATCCTGAGTTTTGGCCCAACCTCAACTGT 147330 iv i-- i iv i i i i viv vi iii MIR3#SINE/MIR 27 CACGGACTG--GGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCAC 74 chr2ptel1M 147331 TAGATAGTAGTGAGACATTCCCAAAGCCATGTCCCCTTAAAGGGCAT-AG 147379 iv ? iv v v vvvv i iv v ivvv v - MIR3#SINE/MIR 75 TAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAG 124 chr2ptel1M 147380 TTCCCTCATTGATTAATGGAAGGAGTT 147406 i ivi v vv i i MIR3#SINE/MIR 125 TTTCCTCATCTGTAAAATGAGGGGGTT 151 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 49.64 CpG sites = 23, Kimura (unadjusted) = 52.87 Transitions / transversions = 1.00 (23/23) Gap_init rate = 0.02 (3 / 125), avg. gap size = 1.00 (3 / 3) 535 28.83 8.29 2.96 chr2ptel1M 147447 147639 (852361) C MIR3#SINE/MIR (1) 207 5 m_b58s601i28 2155 chr2ptel1M 147447 AGTTATATCATCATGGGATCATGGAATTGAAAAGGATTGTGGATGTGATC 147496 i i vv i i vvii ii i i iiv i vi v C MIR3#SINE/MIR 207 AATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATC 158 chr2ptel1M 147497 TGCTTTAGCCCC-TCATTTTAAAGATGAGGAAACTGAGTCCTGTAGAGA- 147544 iv ii i - v v iiv i- C MIR3#SINE/MIR 157 TAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGT 108 chr2ptel1M 147545 GAAGTGACTTGTCCAAAGTCACATGTAAC-AGGTAGTAGC---TCCGGGA 147590 i i --i i - v i ---v C MIR3#SINE/MIR 107 GAAGTGACTTGCCCAAGGTCACA--CAGCNAGTTAGTGGCAGAGCCGGGA 60 chr2ptel1M 147591 TTTGAA-------ATTCCAATTCCTCATCTACATGCTTTCCCATTGC--- 147630 i v -------v i ii i ivi -- i i i -- --- C MIR3#SINE/MIR 59 CTAGAACCCAGGTCTCCTGACTCCCAGTC--CGTGCTCTCTC--TGCTCA 14 chr2ptel1M 147631 ACCACCCTG 147639 i i C MIR3#SINE/MIR 13 GCCACTCTG 5 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.62 CpG sites = 38, Kimura (unadjusted) = 38.55 Transitions / transversions = 2.38 (38/16) Gap_init rate = 0.06 (12 / 192), avg. gap size = 1.83 (22 / 12) 446 27.45 12.02 0.49 chr2ptel1M 147707 147889 (852111) MIRb#SINE/MIR 7 210 (58) m_b58s601i29 2156 chr2ptel1M 147707 GGAAGCAGTGGGACAG--AAAATATCTTTAACTTTGCATCCGGGAAGACC 147754 v - vi --i v v vivii v vi i iv MIRb#SINE/MIR 7 GGCAGC-GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACC 55 chr2ptel1M 147755 TATGTCCTAATCCCACCTCAGA-ATTTATTTGCTGAAAGTACT----CAA 147799 iv i v iv v v- i i v viv vv ---- MIRb#SINE/MIR 56 TGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 105 chr2ptel1M 147800 -TTCCTTAACTAATTTG-------GCTTTCTCATCTGTAAAATGGGTAT- 147840 - v ivv i ------- i i v - MIRb#SINE/MIR 106 GTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATA 155 chr2ptel1M 147841 ----TAACTACCACATAGGGTGGTTGTGGAGATCAAATGAAATAA--CAT 147884 ---- v v ii v ii i i -- MIRb#SINE/MIR 156 ATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCAT 205 chr2ptel1M 147885 GTAAA 147889 MIRb#SINE/MIR 206 GTAAA 210 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.07 CpG sites = 24, Kimura (unadjusted) = 34.51 Transitions / transversions = 0.92 (24/26) Gap_init rate = 0.04 (8 / 182), avg. gap size = 2.88 (23 / 8) 445 26.96 17.65 0.00 chr2ptel1M 147708 147911 (852089) MIRc#SINE/MIR 2 241 (27) m_b58s601i30 2156 chr2ptel1M 147708 GAAGCAGTG-GG-ACAG--AAAATATCTTTAACTTTGCATCCGGGAAGAC 147753 i - -i --i v v vi iivi v vi i MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr2ptel1M 147754 CTATGTCCTAATCCCACCTCAGA-ATTTATTTGCTGAAAGTACT----CA 147798 iv i v i iv v v- i i v viv vv ---- MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 101 chr2ptel1M 147799 ATTC-CTTAACTAATTTG-------GCTTTCTCATCTGTAAAATGGGTAT 147840 v - ivv i ------- i i v MIRc#SINE/MIR 102 AGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGAT 151 chr2ptel1M 147841 --TAA------------CTACCACATAGGGTGGTTGTGGAGATCAAATGA 147876 -- ------------ v i v ii MIRc#SINE/MIR 152 AATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGA 201 chr2ptel1M 147877 AATAA--CATGTAAAA---TTTTGCAAACCTTCCAATGCT 147911 i --i i ---i i iv vv i MIRc#SINE/MIR 202 GATAATGTATGTGAAAGCGCTTTGTAAACTGTAAAGTGCT 241 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.23 CpG sites = 30, Kimura (unadjusted) = 33.98 Transitions / transversions = 1.20 (30/25) Gap_init rate = 0.05 (11 / 203), avg. gap size = 3.27 (36 / 11) 15 13.87 0.00 0.00 chr2ptel1M 148071 148094 (851906) (T)n#Simple_repeat 1 24 (0) m_b58s252i14 2157 chr2ptel1M 148071 TTTTATTTTTATTTTTTTATTTTT 148094 v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTT 24 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 13 16.42 0.00 5.56 chr2ptel1M 148809 148846 (851154) (AAAAAG)n#Simple_repeat 1 36 (0) m_b58s252i15 2158 chr2ptel1M 148809 AAAGAGAAATGGGTAAAAGAAAAATTAAAAAGAAAAAG 148846 i -ii v -v (AAAAAG)n#Sim 1 AAAAAGAAA-AAGAAAAAGAAAAA-GAAAAAGAAAAAG 36 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 16 16.41 0.00 0.00 chr2ptel1M 149869 149902 (850098) (AAAAAT)n#Simple_repeat 1 34 (0) m_b59s252i2 2159 chr2ptel1M 149869 AATAAAAAAAGTTATAATAAAAATAAAAATAAAA 149902 v v i v v (AAAAAT)n#Sim 1 AAAAATAAAAATAAAAATAAAAATAAAAATAAAA 34 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 13 10.85 9.52 2.22 chr2ptel1M 149909 149950 (850050) (AGGGATGG)n#Simple_repeat 1 45 (0) m_b59s252i3 2160 chr2ptel1M 149909 AGGGA-GGAGGGATGGATGGAT-GAGGAAGTAAAGGG-T-GAGGGA 149950 - v - i - ii - - (AGGGATGG)n#S 1 AGGGATGGAGGGATGGAGGGATGGAGGGA-TGGAGGGATGGAGGGA 45 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.12 (5 / 41), avg. gap size = 1.00 (5 / 5) 15 27.33 0.00 3.85 chr2ptel1M 150067 150120 (849880) (GTAT)n#Simple_repeat 1 52 (0) m_b59s252i4 2161 chr2ptel1M 150067 GTATGTGTATGTGCAAGTAGGTGTATGTATGTATATATCTACATATGCAT 150116 i i i i v -- i v ii i (GTAT)n#Simpl 1 GTATGTATGTATGTATGTA--TGTATGTATGTATGTATGTATGTATGTAT 48 chr2ptel1M 150117 ATAT 150120 i (GTAT)n#Simpl 49 GTAT 52 Matrix = Unknown Transitions / transversions = 4.50 (9/2) Gap_init rate = 0.04 (2 / 53), avg. gap size = 1.00 (2 / 2) 16 21.76 0.00 0.00 chr2ptel1M 150090 150127 (849873) (TATA)n#Simple_repeat 1 38 (0) m_b59s252i6 2161 chr2ptel1M 150090 TATGTATGTATATATCTACATATGCATATATAAATATA 150127 i i v i ii v (TATA)n#Simpl 1 TATATATATATATATATATATATATATATATATATATA 38 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 12 30.81 3.33 0.00 chr2ptel1M 150485 150544 (849456) (ATATAG)n#Simple_repeat 1 62 (0) m_b59s252i7 2162 chr2ptel1M 150485 ATATGGATATAGATATGGATGTATGTATATAAACGGAT-TTCAAATAAAT 150533 i i i vi v v ii - vv v i (ATATAG)n#Sim 1 ATATAGATATAGATATAGATATAGATATAGATATAGATATAGATATAGAT 50 chr2ptel1M 150534 A-AGATTTGGAT 150544 - v i (ATATAG)n#Sim 51 ATAGATATAGAT 62 Matrix = Unknown Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.03 (2 / 59), avg. gap size = 1.00 (2 / 2) 16 0.00 0.00 0.00 chr2ptel1M 150842 150858 (849142) (T)n#Simple_repeat 1 17 (0) m_b59s252i8 2163 chr2ptel1M 150842 TTTTTTTTTTTTTTTTT 150858 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTT 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 16 15.95 0.00 2.78 chr2ptel1M 152021 152057 (847943) (TTTC)n#Simple_repeat 1 36 (0) m_b59s252i9 2164 chr2ptel1M 152021 TTTCTTTCTTTCTTTTTTTTTTTCTCTTGTATTTTTC 152057 i i - v v i (TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTTTCT-TTCTTTCTTTC 36 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 90 33.52 2.08 1.85 chr2ptel1M 152244 152675 (847325) (GAGAAA)n#Simple_repeat 1 433 (0) m_b59s252i10 2165 chr2ptel1M 152244 GAAAAAGAGAGTGAGAAAAAG-GACAAAAACAGAAACAGACAGCAACAGT 152292 i iv i -i v i v v v vi v v (GAGAAA)n#Sim 1 GAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGA 50 chr2ptel1M 152293 GAGAGAGAGAAAGAAAGA-AAAGA-AATGATTAAAAGAAATAAAGTGAAA 152340 i i i - - v vv i v i iv i (GAGAAA)n#Sim 51 GAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGA 100 chr2ptel1M 152341 AAGAGAGAGAGAACCAGAGCCAGAGAGAACAAGACAGAGTGAACAAGAAA 152390 i vv ivv i iv v i v vi (GAGAAA)n#Sim 101 AAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAA 150 chr2ptel1M 152391 GAGAAAGGAGAGAAAGGAAGTGCCAGTTGGAGAAGGAGAGAGAGAGAGAG 152440 - i i i v vv vvii iii i i (GAGAAA)n#Sim 151 GAGAAA-GAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAG 199 chr2ptel1M 152441 TGACAGAGACAAAGAAAGAGACATTGAGAGAGAGAAAGAGACAGAATCAG 152490 v v v i - -v i v ivv (GAGAAA)n#Sim 200 AGAAAGAGAAAGAGAAAGAGA-A-AGAGAAAGAGAAAGAGAAAGAGAAAG 247 chr2ptel1M 152491 AGCTAGAG--AGAGCAAGACAGAGTGAACAAGAAAGAGAAAG-GAAGTGT 152537 vv -- v v i v vi - -v - (GAGAAA)n#Sim 248 AGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAA-AG- 295 chr2ptel1M 152538 CAGATGGAGAAAGAG--AGAGGGGGAG-AAGTGCAACAAGGGGGAGAGAA 152584 - vi -- iii - v - vi iii i i (GAGAAA)n#Sim 296 -AGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAG-AAAGAGAAAGAGAAAG 343 chr2ptel1M 152585 AGACAGAGAAAGAAAGAGACCGAGAGAGACAGAATCAGAGTCATAGAGAG 152634 v i i vvi i v vv ivv v i (GAGAAA)n#Sim 344 AGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAG 393 chr2ptel1M 152635 CAAGGTAGAGTGAACAAGAAAGAGAAATGAGAGAAAGGAAG 152675 v iv i v vi - i i i (GAGAAA)n#Sim 394 AAAGAGAAAGAGAAAGAGAAAGAGAAA-GAGAAAGAGAAAG 433 Matrix = Unknown Transitions / transversions = 1.00 (56/56) Gap_init rate = 0.03 (15 / 431), avg. gap size = 1.13 (17 / 15) 62 0.00 0.00 0.00 chr2ptel1M 152689 152741 (847259) (AG)n#Simple_repeat 1 53 (0) c_b59s251i0 2166 chr2ptel1M 152689 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 152738 (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr2ptel1M 152739 AGA 152741 (AG)n#Simple_ 51 AGA 53 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 360 16.90 1.25 3.85 chr2ptel1M 153706 153785 (846215) MIR1_Amn#SINE/MIR 87 164 (66) m_b59s601i1 2167 chr2ptel1M 153706 CTGTGTGACCCTGGGCAAGACACCCAGTC-CTGTTTGCCTCAGTTTCCTC 153754 ? i v ii?ii - v v? MIR1_Amn#SINE 87 CTGNGTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTC 136 chr2ptel1M 153755 ATCTGTAAAATGAGCTGGAGAAAGAAATTGA 153785 i--- v v v i MIR1_Amn#SINE 137 ATCTGTAAAATGG---GGATAATGATACTGA 164 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 20.18 CpG sites = 7, Kimura (unadjusted) = 20.18 Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.05 (4 / 79), avg. gap size = 1.00 (4 / 4) 343 22.53 5.71 2.78 chr2ptel1M 153818 153922 (846078) EuthAT-N1#DNA/hAT-Tip100 114 221 (114) m_b59s502i0 2168 chr2ptel1M 153818 TACATTTAGATGGTGCTGACAGCTTTTGCTTTCTTTCAGTAAACTAGAAA 153867 v ---i viv vi i i ivv EuthAT-N1#DNA 114 TACATTTACATG---TTGACAGCACATGCACTCCTTCAGCAGCGTAGAAA 160 chr2ptel1M 153868 CAAC--AATTTAATGCCTAGTTAGTAAGAA----TAGTTAAAACTGATAG 153911 -- ii iii i ---- iv iv EuthAT-N1#DNA 161 CAACTGAGCTTAGCACCTAGTTAGCAAGAATAATTAGTTAAAATAGGAAG 210 chr2ptel1M 153912 GTACCAGATGG 153922 v EuthAT-N1#DNA 211 CTACCAGATGG 221 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 27.38 CpG sites = 14, Kimura (unadjusted) = 27.38 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.05 (5 / 104), avg. gap size = 1.80 (9 / 5) 16 3.69 0.00 9.68 chr2ptel1M 154513 154546 (845454) (TCTTT)n#Simple_repeat 1 31 (0) m_b59s252i11 2169 chr2ptel1M 154513 TCTTTTCTGTTTCTTGTTCATTTTCTTTCCTTTT 154546 - - - i (TCTTT)n#Simp 1 TCTTTTCT-TTTCTT-TTC-TTTTCTTTTCTTTT 31 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.09 (3 / 33), avg. gap size = 1.00 (3 / 3) 364 28.09 3.28 0.80 chr2ptel1M 155002 155123 (844877) MIRc#SINE/MIR 24 148 (120) m_b59s601i2 2170 chr2ptel1M 155002 AGAGCCCTGGATTAGAAATCAGCAATTCACGTGTTTCAATCCTGCCTCAG 155051 v i v i i v vv vi v iv i i v v MIRc#SINE/MIR 24 AGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTG 73 chr2ptel1M 155052 ATACTTA-TAGGTGTATTAGCCTGTGCATGTTACTCCAACCTG-CTG--C 155097 vi - v i v v i v v i i- v- -- MIRc#SINE/MIR 74 CCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTT-AACCTCTCTGAGC 122 chr2ptel1M 155098 CTCACTTTCCCCATGTATAAAATGAG 155123 v i v i i MIRc#SINE/MIR 123 CTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.94 CpG sites = 15, Kimura (unadjusted) = 35.38 Transitions / transversions = 0.79 (15/19) Gap_init rate = 0.03 (4 / 121), avg. gap size = 1.25 (5 / 4) 18 26.43 1.41 2.86 chr2ptel1M 158602 158672 (841328) (TTATTTT)n#Simple_repeat 1 70 (0) m_b59s252i12 2171 chr2ptel1M 158602 TTTTTTTTTAGTTTTTTCTTTTTGA-TTAAAGCTTTTTATTTTCTATTTT 158650 v - v v - vvvii i - (TTATTTT)n#Si 1 TTATTTTTTA-TTTTTTATTTTTTATTTTTTATTTTTTATTTTTTA-TTT 48 chr2ptel1M 158651 TTTAATTGAAGCTTTTTATTTT 158672 v vvvii (TTATTTT)n#Si 49 TTTATTTTTTATTTTTTATTTT 70 Matrix = Unknown Transitions / transversions = 0.50 (5/10) Gap_init rate = 0.04 (3 / 70), avg. gap size = 1.00 (3 / 3) 294 30.21 0.61 3.12 chr2ptel1M 159072 159235 (840765) C L1MC4a_3end#LINE/L1 (2029) 600 441 m_b59s551i0 2172 chr2ptel1M 159072 TCACTCAGCATCAGTTCCTATAAGTCTTTCCACGATGATTGTTCTT-ACA 159120 vii v v ii i ----- v v i - C L1MC4a_3end#L 600 TCACTCCATATCAGTTCATAGAGATCTTCC-----TCATTCTTTTTTACA 556 chr2ptel1M 159121 GAACAATAATGTTCCATAAGTTTCATACACCATAACTTATTCAGCCATTC 159170 vvvv i ii vivv vv ii ii i ? C L1MC4a_3end#L 555 GCTGCATAGTACTCCATTGTGTGGATGTACCATAGTTTATTCAACCANTC 506 chr2ptel1M 159171 TCCAGCTGATGGGCATCCACTCAGTTTCCAGTTTTTTGCCCTTACCAAAA 159220 vii?? ii vviv i v vv v v C L1MC4a_3end#L 505 TCCTATNNATGGGCATTTAGGTTGTTTCCAATATTTTGCAATTACAAACA 456 chr2ptel1M 159221 GGGCTGCCATAAATA 159235 iv v i C L1MC4a_3end#L 455 ATGCTGCAATGAATA 441 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.02 CpG sites = 23, Kimura (unadjusted) = 40.02 Transitions / transversions = 0.92 (23/25) Gap_init rate = 0.04 (6 / 163), avg. gap size = 1.00 (6 / 6) 549 31.68 9.15 2.48 chr2ptel1M 159145 159636 (840364) C L1ME3C_3end#LINE/L1 (340) 530 7 m_b59s551i1 2172 chr2ptel1M 159145 ATACACCATAACTTATTCAGCCATTCTCCAGCTGATGGGCATCCACTCAG 159194 i i i i v v i i ii vviv C L1ME3C_3end#L 530 ATATACCACAATTTATTTATCCATTCTCCTGTTGATGGACATTTAGGTTG 481 chr2ptel1M 159195 TTTCCAGTTTTTTGCCCTTACCAAAAGGGCTGCCATAAATATTTATGTAC 159244 i i iv v v iv v i i iv C L1ME3C_3end#L 480 TTTCCAATTTTTCGCTATTACAAACAATGCTGCAATGAACATTCTTGTAC 431 chr2ptel1M 159245 TTCTGGATCCTTTTCC-CTCCTTTAAG-GTCTCTCTGGGATATGGGCCCA 159292 --v vv v v - v v vii - i i i ivi i C L1ME3C_3end#L 430 --ATGTCTCCTTGTGCACACGTGCGAGAGTTTCTCTAGGGTATATACCTA 383 chr2ptel1M 159293 ATAGAAACACTGCTGAATTAGAGGTTAAGAACAGTTTGATAACCCT-TTG 159341 iv viiv i ii iiv v v vi vi --i ii -i i C L1ME3C_3end#L 382 GGAGTGGAATTGCTGGGTCGTAGGGTATGCGCATCTT--CAACTTTACTA 335 chr2ptel1M 159342 GGCAAAGTTCCAAATTGTTCTTCAGAATGGATGGATCAGTTCACAACTCC 159391 -- v v v i i i i v v i i i vii C L1ME3C_3end#L 334 G--ATATTGCCAAATTGCTCTCCAAAGTGGTTGTACCAATTTACACTCCC 287 chr2ptel1M 159392 AACAATAGT---------TTC--------CCACATACCCTATAACATGTC 159424 v ii --------- -------- v i vvi ---- C L1ME3C_3end#L 286 ACCAGCAGTGTATGAGAGTTCCCGTTGCTCCACATCCTCGCCAACA---- 241 chr2ptel1M 159425 CTTAACTTTTTCTGTC------ATTTTAGCCAATATGAGAAGTGTGTAGT 159468 iiiv v v v ------ v v vii v i C L1ME3C_3end#L 240 CTTGGTATTGTCAGACTTTTAAATTTTTGCCAATCTGATGGGTGTGAAAT 191 chr2ptel1M 159469 GGTAATGCAGACTTATCTTAGCTTGCATTTCTCTCATCAGTAGTGATTTA 159518 viv vvv ?i i ii i v i v vv v C L1ME3C_3end#L 190 GGTATCTCATTGTNGTTTTAATTTGCATTTCCCTGATTACTAGTGAGGTT 141 chr2ptel1M 159519 GAGCACCTTTTCATG-----ACTAGAAAT---GGTTTCCACTT------- 159553 i i----- i i vv ---? v ------- C L1ME3C_3end#L 140 GAGCATCTTTTCATATGTTTATTGGCCATTCGNGTTTCCTCTTCTGTGAA 91 chr2ptel1M 159554 ----CTATTCATATCCTTTCACCATTTATCAATTGGAGCAAGGCTTGAAT 159599 ---- i i vv v v ivi--- ii vv C L1ME3C_3end#L 90 TTGCCTGTTCATATCTTTTGCCCATTTTTCTATTGGGTT---GTCTGTTT 44 chr2ptel1M 159600 TTTTATAAATTTGAGTCAATTCTCTATATATTTTAGA 159636 i vi vivv i i i i C L1ME3C_3end#L 43 TCTTATTGATTTGTAGGAGTTCTTTATATATTCTGGA 7 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.87 CpG sites = 82, Kimura (unadjusted) = 42.41 Transitions / transversions = 1.17 (82/70) Gap_init rate = 0.05 (23 / 491), avg. gap size = 2.52 (58 / 23) 239 27.86 3.45 3.45 chr2ptel1M 159553 159697 (840303) C L1MD_orf2#LINE/L1 (60) 3234 3090 m_b59s551i3 2172 chr2ptel1M 159553 TCTATTCATATCCTTTCACCATTTATCAATTGGAGCAAGGCTTGAATTTT 159602 ? i i vv vii vi--- i vv C L1MD_orf2#LIN 3234 TCTNTTCATGTCTTTTGCCCATTTTCTAATTGGATT---GTTTGTTTTTT 3188 chr2ptel1M 159603 TA----TAAATTT-GAGTCAATTCTCTATATATTTTAGAAATGAGGCCTT 159647 ---- i i - -- i i i v i? v C L1MD_orf2#LIN 3187 TACTGTTGAGTTTTGAG--AGTTCTTTATATATTCTAGATACNAGTCCTT 3140 chr2ptel1M 159648 TATCAGAGCTTTTGAATGTAAAAAAGTTTTCCTAGTTTATTGCTTCCCTT 159697 i i vv v v vv i v vv i i i i v vi C L1MD_orf2#LIN 3139 TGTCGGATATGTGGTTTGCAAATATTTTCTCCCAGTCTGTAGCTTGTCTT 3090 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.82 CpG sites = 20, Kimura (unadjusted) = 35.94 Transitions / transversions = 1.05 (20/19) Gap_init rate = 0.05 (7 / 144), avg. gap size = 1.43 (10 / 7) 246 21.65 4.90 4.90 chr2ptel1M 159553 159654 (840346) C L1M4_orf2#LINE/L1 (60) 3234 3133 m_b59s551i2 2172 chr2ptel1M 159553 TCTATTCATATCCTTTCACCATTTATCAATTGGAGCAAGGCTTGAATTTT 159602 v vv v ? ivi ---i vv C L1M4_orf2#LIN 3234 TCTATTCAAATCCTTTGCCCATTTTTNAATTGGGTTA---TTTGTCTTTT 3188 chr2ptel1M 159603 TATAAATTTGAGTC-----AATTCTCTATATATTTTAGAAATGAGGCCTT 159647 vi-- i----- i i i i v i? v i C L1M4_orf2#LIN 3187 TATTG--TTGAGTTGTAAGAGTTCTTTATATATTCTGGATACNAGTCCCT 3140 chr2ptel1M 159648 TATCAGA 159654 C L1M4_orf2#LIN 3139 TATCAGA 3133 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 26.45 CpG sites = 11, Kimura (unadjusted) = 26.45 Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.06 (6 / 101), avg. gap size = 1.67 (10 / 6) 240 32.56 9.62 2.65 chr2ptel1M 159766 160295 (839705) C L1P1_orf2#LINE/L1 (357) 2937 2372 m_b59s551i4 2172 chr2ptel1M 159766 TTCTTCT--GATTTGCTTGTAATATTACTTTTTATGTCTACATCTTGAAC 159813 -- i -- i ii v vv i v i i vi v i C L1P1_orf2#LIN 2937 TTCTTCTAGGGTTT--TTATGGTTTTAGGTCTAACGTTTAAGTCTTTAAT 2890 chr2ptel1M 159814 TCATTTTGACCTTATCTTGGTATACGGTATTAGATGTGGATC-AGTACCT 159862 i i vi v i v v i v iviv - vi v C L1P1_orf2#LIN 2889 CCATCTTGAATTAATTTTTGTATAAGGTGTAAGGAAGGGATCCAGTTTCA 2840 chr2ptel1M 159863 AGTTTC-ACAT-------------TTTCCAAGCAGTTATTGTCAAATAGA 159898 iv - ------------- v vivv i i i C L1P1_orf2#LIN 2839 GCTTTCTACATATGGCTAGCCAGTTTTCCCAGCACCATTTATTAAATAGG 2790 chr2ptel1M 159899 GTATACTTATCCCAAAAGCTGGGGTCTTT-GGGTTTGTCAAATCCTACAT 159947 v v - v vv v vv i i -i vvii v C L1P1_orf2#LIN 2789 GAATCCTT-TCCCCATTGCTTGTTTTTCTCAGGTTTGTCAAAGATCAGAT 2741 chr2ptel1M 159948 TACTATAGTCATTTGAC--TATTTTGTCCTGTGAAC-CTACCCTATTCCA 159994 vii i vi vi i -- ---- v ii - iii i C L1P1_orf2#LIN 2740 AGTTGTAGATATGCGGCGTTATTT----CTGAGGGCTCTGTTCTGTTCCA 2695 chr2ptel1M 159995 CTGATCAATTACTCTATTTCTTAG--CCAGCATCAAATTGTTTTGATGAC 160042 i v vv i -- i -- i i vii i v C L1P1_orf2#LIN 2694 TTGATCTATATCTCTGTTT--TGGTACCAGTACCATGCTGTTTTGGTTAC 2647 chr2ptel1M 160043 CACTGCTTTATAATATAGTTTTAGGTCGG--ACCAAGCCACCTTCA--TT 160088 iiiv i i i v i i -- v iv vii i -- C L1P1_orf2#LIN 2646 TGTAGCCTTGTAGTATAGTTTGAAGTCAGGTAGCGTGATGCCTCCAGCTT 2597 chr2ptel1M 160089 TGAATTTTTTCATTA--ATTACCTTG-------AAATTCTTTACCTTTTG 160129 vvi vvv -- iv -------iiii ---- C L1P1_orf2#LIN 2596 TGTTCTTTTGGCTTAGGATTGACTTGGCGATGCGGGCTCTT----TTTTG 2551 chr2ptel1M 160130 GAATTCCAGATGAACCTT--GTTACTTTTTTCTAGATCTCTAAAATAATT 160177 -- v i --iv v i iv v i iv v C L1P1_orf2#LIN 2550 G--TTCCATATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGT 2503 chr2ptel1M 160178 TCTAGGGAGTTTGAATGGTATGGTACTAAA---GTAGAT----TTAGGTA 160220 iv v v i vv v i i i ---i i ---- i i C L1P1_orf2#LIN 2502 CATTGGTAGCTTGATGGGGATGGCATTGAATCTATAAATTACCTTGGGCA 2453 chr2ptel1M 160221 G-AT-----TTTTTATTACATTCACTTGGCCTACCCATGAGCACTTGATA 160264 - ----- i iv i v i ivv ivvi i C L1P1_orf2#LIN 2452 GTATGGCCATTTTCACGATATTGATTCTTCCTACCCATGAGCATGGAATG 2403 chr2ptel1M 160265 TATTTTCAATTGATTAGATCTGATTTTATTT 160295 vi i v v iv ivv C L1P1_orf2#LIN 2402 TTCTTCCATTTGTTTGTATCCTCTTTTATTT 2372 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 42.15 CpG sites = 92, Kimura (unadjusted) = 43.89 Transitions / transversions = 1.21 (92/76) Gap_init rate = 0.06 (32 / 529), avg. gap size = 2.06 (66 / 32) 283 33.33 7.23 0.27 chr2ptel1M 159982 160327 (839673) C L1MC_orf2#LINE/L1 (587) 2707 2338 m_b59s551i5 2172 chr2ptel1M 159982 CTACCCTATTCCACTGATCAATTACTCTATTTCTTAGCCAGCATCAAATT 160031 ii i i v vv ii v ii i v i C L1MC_orf2#LIN 2707 CTATTCTGTTCCATTGATCTATTTGTCTATTCTTTCGCCAATACCACACT 2658 chr2ptel1M 160032 GTTTTGATGACCACTGCTTTATAATATAGTTTT-AGGTCGGACCAAGCCA 160080 i v iiiv i - i - i iiviv i C L1MC_orf2#LIN 2657 GTCTTGATTACTGTAGCTTTATAGTA-AGTCTTGAAGTCGGGTAGTGTCA 2609 chr2ptel1M 160081 --CCTTCA--TTTGAATTTTTTCATTA--ATTACCTTGAA-ATTCTTTAC 160123 -- i i-- vvi i i v i -- iiv iv- vvii C L1MC_orf2#LIN 2608 GTCCTCCGACTTTGTTCTTCTCCTTCAATATTGTGTTGGCTATTCTGGGT 2559 chr2ptel1M 160124 CTTTTGGAATTCCAGATGAACCTTGTTACT--TTTTTCTAGATCTCTAAA 160171 vvvi v i i ivv ii-- v v v ivi C L1MC_orf2#LIN 2558 CTTTTGCCTCTCCATATAAACTTTAGAATCAGTTTGTCGATATCCACAAA 2509 chr2ptel1M 160172 ATAATTTCTAGGGAGTTTGAATGGTATGGTACTAAA---GTAGAT----T 160214 i viv v v v v i i i ---i ---- C L1MC_orf2#LIN 2508 ATAACTTGCTGGGATTTTGATTGGGATTGCATTGAATCTATAGATCAAGT 2459 chr2ptel1M 160215 TAGGTAGA--T----TTTTTATTACATTCACTTGGCCTACCCATGAGCAC 160258 i v -- ---- i v iv i v v ivv i i i C L1MC_orf2#LIN 2458 TGGGAAGAACTGACATCTTGACAATATTGAGTCTTCCTATCCATGAACAT 2409 chr2ptel1M 160259 TTGATATATTTTCAATTGATTAGATCTGATTTTATTTGTGTGG--AAACT 160306 vvi v i i v iv ? vv v v v vi-- i v C L1MC_orf2#LIN 2408 GGAATATCTCTCCATTTATTTAGNTCTTCTTTGATTTCTTTCATCAGAGT 2359 chr2ptel1M 160307 TTTGCAGTTGTGTTCATATAG 160327 i v vi C L1MC_orf2#LIN 2358 TTTGTAGTTTTCCTCATATAG 2338 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 44.81 CpG sites = 62, Kimura (unadjusted) = 45.34 Transitions / transversions = 1.17 (62/53) Gap_init rate = 0.03 (12 / 345), avg. gap size = 2.17 (26 / 12) 16 21.15 0.00 0.00 chr2ptel1M 162787 162824 (837176) (AAGA)n#Simple_repeat 1 38 (0) m_b59s252i13 2173 chr2ptel1M 162787 AAAAAAGAAAGAAAGAAAACAACAAACAATTAAAGAAA 162824 i iv v v vv (AAGA)n#Simpl 1 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 38 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 435 24.39 0.00 6.80 chr2ptel1M 163527 163636 (836364) MIRc#SINE/MIR 10 112 (156) m_b59s601i3 2174 chr2ptel1M 163527 GTGGCACAGTGGATAGAGCACCAGTCCTGAAGTTAGGAGGACCTGAGTTC 163576 ii v ii v i i i i i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr2ptel1M 163577 AAATGTGGTCACAGATACTTAACACTTCCTGCCTGTGCGATCCTGGGCAA 163626 i ----- v i v --i iv v iv i i i MIRc#SINE/MIR 60 GA-----GTCCCGGCT--CTGCCACTTACTAGCTGTGTGACCTTGGGCAA 102 chr2ptel1M 163627 GTCTCTTAAC 163636 v MIRc#SINE/MIR 103 GTCACTTAAC 112 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.55 CpG sites = 17, Kimura (unadjusted) = 30.41 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.06 (7 / 109), avg. gap size = 1.00 (7 / 7) 303 29.67 1.63 6.84 chr2ptel1M 163528 163650 (836350) MIR#SINE/MIR 7 123 (139) m_b59s601i4 2174 chr2ptel1M 163528 TGGCACAGTGGATA-GAGCACCAGTCCTGAAGTTAGGAGGACCTGAGTTC 163576 i i v - vi ii i ii - vvi i MIR#SINE/MIR 7 TAGCATAGTGGTTAAGAGCACGGGCTCTGGAGCCAG-ACTGCCTGGGTTC 55 chr2ptel1M 163577 AAATGTGGTCACAGATACTTAACACTTCCTGCCTGTGCGATCCTGGGCAA 163626 i ----- v i v --i iv v iv i i i MIR#SINE/MIR 56 GAAT-----CCCGGCT--CTGCCACTTACTAGCTGTGTGACCTTGGGCAA 98 chr2ptel1M 163627 GTCTCTTAACACCCAT-TGCCTGAG 163650 iv vi iv - v MIR#SINE/MIR 99 GTTACTTAACCTCTCTGTGCCTCAG 123 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.02 CpG sites = 21, Kimura (unadjusted) = 38.94 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.08 (10 / 122), avg. gap size = 1.00 (10 / 10) 20 0.00 0.00 0.00 chr2ptel1M 164622 164643 (835357) (T)n#Simple_repeat 1 22 (0) m_b59s252i14 2175 chr2ptel1M 164622 TTTTTTTTTTTTTTTTTTTTTT 164643 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTT 22 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 237 27.91 12.21 4.26 chr2ptel1M 164789 164919 (835081) MIR1_Amn#SINE/MIR 20 160 (70) m_b59s601i5 2176 chr2ptel1M 164789 AGTGGATAGAATG-TGAATAGGGCCTTGAATCTGGAAACGGAGGGTTTTA 164837 iii- i iv v i ----- i vv- i? MIR1_Amn#SINE 20 AGTGGATAGAGCACTGGACTGGGACTCG-----GGAGACCT-GGGTTCNA 63 chr2ptel1M 164838 ATTTCACTTCAGAAATTTGC--------------TGGTCAAGTTA-TAGA 164872 ? ii ivi v vv i ? -------------- v i - v? MIR1_Amn#SINE 64 NTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGTCACTTNA 113 chr2ptel1M 164873 CCTCGGTTAGATTCAGTTTTTTTATCTGTCAAATGGGCATAATAATA 164919 vv v? vi ii i v v i MIR1_Amn#SINE 114 CCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATGATA 160 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.99 CpG sites = 19, Kimura (unadjusted) = 37.65 Transitions / transversions = 1.19 (19/16) Gap_init rate = 0.07 (9 / 130), avg. gap size = 2.44 (22 / 9) 363 25.73 0.93 2.83 chr2ptel1M 164858 164965 (835035) MIRb#SINE/MIR 99 204 (64) m_b59s601i6 2176 chr2ptel1M 164858 TGGTCAAGTTA-TAGACCTCGGTTAGATTCAGTTTTTTTATCTGTCAAAT 164906 v - vi vv v vi ii i v MIRb#SINE/MIR 99 TGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAAT 148 chr2ptel1M 164907 GGGCATAATAATAACAGTTAAGTCCTTGGAGTCTCGTGAGGACAAAATAA 164956 v v --- vv viv iv v i iv i MIRb#SINE/MIR 149 GGGGATAATAATACC---TACCTCGCAGGGTTGTTGTGAGGATTAAATGA 195 chr2ptel1M 164957 GACAATGCA 164965 i MIRb#SINE/MIR 196 GATAATGCA 204 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.55 CpG sites = 11, Kimura (unadjusted) = 31.55 Transitions / transversions = 0.69 (11/16) Gap_init rate = 0.04 (4 / 107), avg. gap size = 1.00 (4 / 4) 234 26.83 4.88 0.00 chr2ptel1M 165350 165431 (834569) C MIR3#SINE/MIR (3) 205 120 m_b59s601i7 2177 chr2ptel1M 165350 TTACAGTATCATAGA-TG--AGCACTGGAAGGGCCCTACAGGGCCACGGA 165396 i i v - -- vi v vvii ii ivv C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTA 156 chr2ptel1M 165397 GCGCAGCCCACTCATTTTGTAGATG-GGAAACCGAG 165431 iv i v ii - i C MIR3#SINE/MIR 155 GTCCAACCCCCTCATTTTACAGATGAGGAAACTGAG 120 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.02 CpG sites = 13, Kimura (unadjusted) = 34.02 Transitions / transversions = 1.44 (13/9) Gap_init rate = 0.04 (3 / 81), avg. gap size = 1.33 (4 / 3) 585 31.61 3.63 0.00 chr2ptel1M 166088 166280 (833720) MIRc#SINE/MIR 10 209 (59) m_b59s601i8 2178 chr2ptel1M 166088 GTAGTTCAGTGGA--GAGTCCTGGACATAGAGTCAAGTGTACCTGAGTTT 166135 i v -- iv v i i viv i i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr2ptel1M 166136 GAAGTGAGCCTTGGACAATTACTAACTGTGCACCTCTGGGCAAGTCAATT 166185 ivivv v iv v v i iiv ii v MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTT 109 chr2ptel1M 166186 AAACTCTGTTTTCCTCAGTTTCTTCAATTCTCAAATGGAGATAACAGTAT 166235 v v vvv i vi v v i i i i MIRc#SINE/MIR 110 AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAC 159 chr2ptel1M 166236 C-AC----CCTAACTTGGAAACTTAAGATGAGAATAAAGTGACAAAATAT 166280 -i ---- v iiv iiv ivvi i v i v v i MIRc#SINE/MIR 160 CTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGT 209 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.80 CpG sites = 31, Kimura (unadjusted) = 41.69 Transitions / transversions = 1.03 (31/30) Gap_init rate = 0.02 (3 / 192), avg. gap size = 2.33 (7 / 3) 17 29.56 2.63 1.30 chr2ptel1M 166470 166545 (833455) (CATATA)n#Simple_repeat 1 77 (0) m_b59s252i15 2179 chr2ptel1M 166470 CAT-TACAAAGAAATTTATTATATACATAGATAAATA-ATAGACATGTAA 166517 - v v v v -i v i v - v i v (CATATA)n#Sim 1 CATATACATATACATATA-CATATACATATACATATACATATACATATAC 49 chr2ptel1M 166518 ATATATATGCATACACACATATACTTAT 166545 i ii i i i v (CATATA)n#Sim 50 ATATACATATACATATACATATACATAT 77 Matrix = Unknown Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.04 (3 / 75), avg. gap size = 1.00 (3 / 3) 13 30.51 0.00 2.00 chr2ptel1M 166488 166538 (833462) (TACA)n#Simple_repeat 1 50 (0) m_b59s252i16 2180 chr2ptel1M 166488 TATATACATAGATAAATAATAGACATGTAAATATATATGCATACACACAT 166537 i v v - i v ii v i i i i (TACA)n#Simpl 1 TACATACATACATACAT-ACATACATACATACATACATACATACATACAT 49 chr2ptel1M 166538 A 166538 (TACA)n#Simpl 50 A 50 Matrix = Unknown Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.02 (1 / 50), avg. gap size = 1.00 (1 / 1) 17 29.56 2.63 1.30 chr2ptel1M 166470 166545 (833455) (CATATA)n#Simple_repeat 1 77 (0) m_b59s252i15 2179 chr2ptel1M 166470 CAT-TACAAAGAAATTTATTATATACATAGATAAATA-ATAGACATGTAA 166517 - v v v v -i v i v - v i v (CATATA)n#Sim 1 CATATACATATACATATA-CATATACATATACATATACATATACATATAC 49 chr2ptel1M 166518 ATATATATGCATACACACATATACTTAT 166545 i ii i i i v (CATATA)n#Sim 50 ATATACATATACATATACATATACATAT 77 Matrix = Unknown Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.04 (3 / 75), avg. gap size = 1.00 (3 / 3) 12 16.57 0.00 0.00 chr2ptel1M 166757 166783 (833217) (TTCCC)n#Simple_repeat 1 27 (0) m_b59s252i17 2181 chr2ptel1M 166757 TTCCCTTCCATTCCTTTCCCTCCACTT 166783 v i i v (TTCCC)n#Simp 1 TTCCCTTCCCTTCCCTTCCCTTCCCTT 27 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 16 9.78 0.00 0.00 chr2ptel1M 166928 166949 (833051) (A)n#Simple_repeat 1 22 (0) m_b59s252i18 2182 chr2ptel1M 166928 AACAAAAAAAATAAAAAAAAAA 166949 v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAA 22 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 243 23.69 20.39 1.64 chr2ptel1M 167424 167526 (832474) C MIR3#SINE/MIR (2) 206 85 m_b59s601i9 2183 chr2ptel1M 167424 ATCA-AAAGTCATGATATG---GAGCTGAAAGACACTTCAGAAATAG--- 167466 - i i iiv --- i iv i i i vi--- C MIR3#SINE/MIR 206 ATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCT 157 chr2ptel1M 167467 AGTCCAAACTCCTCCAATTTACTG--GAGAAAGCTGAAACTCA------- 167507 v i - v v -- i i ii i ------- C MIR3#SINE/MIR 156 AGTCCAACCCCCT-CATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGT 108 chr2ptel1M 167508 -----GATTTGCCCAAAGGTCATA 167526 ----- i - i C MIR3#SINE/MIR 107 GAAGTGACTTGCCC-AAGGTCACA 85 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.04 CpG sites = 18, Kimura (unadjusted) = 30.04 Transitions / transversions = 3.00 (18/6) Gap_init rate = 0.08 (8 / 102), avg. gap size = 2.88 (23 / 8) 12 9.30 0.00 4.17 chr2ptel1M 169672 169696 (830304) (AAGG)n#Simple_repeat 1 24 (0) m_b59s252i19 2184 chr2ptel1M 169672 AAGGAAATGAAGGAAGCAAGGAAGG 169696 - v v (AAGG)n#Simpl 1 AAGG-AAGGAAGGAAGGAAGGAAGG 24 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 314 31.21 3.97 2.86 chr2ptel1M 170478 170754 (829246) L1M1_orf2#LINE/L1 1555 1834 (1460) m_b59s551i6 2185 chr2ptel1M 170478 AAACCAAGGAAAGTCCAAACAGAGAAAGGAAATTACAAATCAAAG----- 170522 iiv v vv v i i i i iii vi----- L1M1_orf2#LIN 1555 AAACCAGACAAAGACACATCAAAAAAAGAAAACTACAGGCCAATATCTCT 1604 chr2ptel1M 170523 AATGAATATTGTTTTTTTTCTCCAATTTTAAACAAAATCCTATCAAAGCA 170572 i v v----- vvv ii v v v v i L1M1_orf2#LIN 1605 GATGAATATTGATG-----CAAAAATCCTCAACAAAATACTAGCAAACCG 1649 chr2ptel1M 170573 AGCACTGTTAAAT-CATCCAAGAAACCATTCATTATGAGCAAGTGGGATT 170621 iiv vii-- - iv i i i i v L1M1_orf2#LIN 1650 AATTCAAC--AATACATTAAAAAGATCATTCATCATGACCAAGTGGGATT 1697 chr2ptel1M 170622 TCTACCAGGGATGGAAAGATATTTCAACATTAGGAAAGCAATGAACATAA 170671 v v ? v i iv vv v v v ii i L1M1_orf2#LIN 1698 TATCCCNGGGATGCAAGGATGGTTCAACATACGCAAATCAATCAATGTGA 1747 chr2ptel1M 170672 TCACATTCTA-AAACAAAAC----ATCTAAAATCACACAGTCAATTCAAT 170716 - iv -v i i----iv v i i iii v L1M1_orf2#LIN 1748 T-ACATCATATCAACAGAATGAAGGACAAAAACCATATGATCATTTCAAT 1796 chr2ptel1M 170717 AGATAAAGAGAATGCTTTGGACAAAGTACAACACTCTT 170754 v ivv i v v v i i v ii i L1M1_orf2#LIN 1797 TGATGCTGAAAAAGCATTTGATAAAATTCAACATCCCT 1834 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.69 CpG sites = 44, Kimura (unadjusted) = 41.33 Transitions / transversions = 1.10 (44/40) Gap_init rate = 0.04 (12 / 276), avg. gap size = 1.58 (19 / 12) 406 27.57 4.31 2.83 chr2ptel1M 170546 170754 (829246) L1M3_orf2#LINE/L1 1617 1828 (1460) m_b59s551i7 2185 chr2ptel1M 170546 AATTTTAAACAAAATCCTATCAAAGCAAGCACTGTTAAAT----CATCCA 170591 ii v v v v i i----- v i---- iv L1M3_orf2#LIN 1617 AATCCTCAACAAAATACTAGCAAACCGAA-----TTCAACAGCACATTAA 1661 chr2ptel1M 170592 AGAAACCATTCATTATGAGCAAGTGGGATTTCTACCAGGGATGGAAAGAT 170641 iii i v ii v v v v v i L1M3_orf2#LIN 1662 AAGGATCATACACCATGACCAAGTGGGATTTATCCCTGGGATGCAAGGAT 1711 chr2ptel1M 170642 ATTTCAACATTAGGAAAGCAATGAACATAAT----CACATT-CTAAAACA 170686 iv vv ? v ? ii i ---- -vi i ii L1M3_orf2#LIN 1712 GGTTCAACATACGNAAATCAATNAATGTGATACACCACATTAACAGAATG 1761 chr2ptel1M 170687 AAACATCTAAAATCACACAGTCAATTCAATAGATAAAGAGAATGCTTTGG 170736 iv v- iii vi iv i v v v L1M3_orf2#LIN 1762 AAGGATA-AAAATCACATGATCATCTCAATAGATGCAGAAAAAGCATTTG 1810 chr2ptel1M 170737 ACAAAGTACAACACTCTT 170754 i v ii L1M3_orf2#LIN 1811 ACAAAATTCAACATCCTT 1828 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.72 CpG sites = 31, Kimura (unadjusted) = 35.51 Transitions / transversions = 1.24 (31/25) Gap_init rate = 0.04 (9 / 208), avg. gap size = 1.67 (15 / 9) 23 9.69 0.00 0.00 chr2ptel1M 172658 172690 (827310) (TG)n#Simple_repeat 1 33 (0) m_b59s252i20 2186 chr2ptel1M 172658 TGTGTGTGTGTGAGAGTGTGTGTATGTGTGTGT 172690 v v i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 33 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 18 7.02 0.00 3.23 chr2ptel1M 173232 173263 (826737) (ATTTT)n#Simple_repeat 1 31 (0) m_b59s252i21 2187 chr2ptel1M 173232 ATATTAATTTATTTTTATTTTATTTTATTTTA 173263 v v - (ATTTT)n#Simp 1 ATTTTATTTTA-TTTTATTTTATTTTATTTTA 31 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 16 0.00 0.00 0.00 chr2ptel1M 173714 173731 (826269) (GT)n#Simple_repeat 1 18 (0) m_b59s252i22 2188 chr2ptel1M 173714 GTGTGTGTGTGTGTGTGT 173731 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGT 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 190 23.68 10.71 4.49 chr2ptel1M 174526 174609 (825391) MIR3#SINE/MIR 17 105 (103) m_b59s601i10 2189 chr2ptel1M 174526 GCAGTGGGAGACACCAGCCGGAATTCAGGAGGCCC-------AGTCCAAA 174568 v i - vii i i v i i------- vii MIR3#SINE/MIR 17 GCAGAGAGAG-CACGGACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCGG 65 chr2ptel1M 174569 TT--AACACCTTAACCCTGCTGTGTGACCCTGGGAAAGTCACT 174609 i --iv -- i?- i v MIR3#SINE/MIR 66 CTCTGCCAC--TAACTN-GCTGTGTGACCTTGGGCAAGTCACT 105 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.20 CpG sites = 13, Kimura (unadjusted) = 30.08 Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.07 (6 / 83), avg. gap size = 2.17 (13 / 6) 181 16.67 4.76 0.00 chr2ptel1M 174585 174626 (825374) MIR#SINE/MIR 80 123 (139) m_b59s601i11 2189 chr2ptel1M 174585 GCTGTGTGACCCTGGGAAAGTCAC-TAACCCCAAT-TGCCTAAG 174626 i v i - i vv - v MIR#SINE/MIR 80 GCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAG 123 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 18.88 CpG sites = 3, Kimura (unadjusted) = 18.88 Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.05 (2 / 41), avg. gap size = 1.00 (2 / 2) 13 16.42 0.00 5.56 chr2ptel1M 174690 174727 (825273) (CTCCTCC)n#Simple_repeat 1 36 (0) m_b59s252i23 2190 chr2ptel1M 174690 CTCCTCCATCTTTTACTCCTCTCTCCTCCCTCCCTCCC 174727 v -i iv i - (CTCCTCC)n#Si 1 CTCCTCCCTC-CTCCCTCCTCCCTCCTCCCT-CCTCCC 36 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 598 30.38 3.16 0.00 chr2ptel1M 177880 178037 (821963) C MIR3#SINE/MIR (21) 187 25 m_b59s601i12 2191 chr2ptel1M 177880 TTAGAGCTGGCAGGCGCCTTAGAAATCACCTTGTCCA-----CTTATTTT 177924 i v vi i i v ----- i C MIR3#SINE/MIR 187 TCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTT 138 chr2ptel1M 177925 AAGGATGAAAGATCTGAGACCCAATGAGGTTAGATGACTTGCTGAACATC 177974 vi iii v i iv v ii iv vi C MIR3#SINE/MIR 137 ACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTC 88 chr2ptel1M 177975 CCACAGATACCAAGTGACAGAGCTAAGATTAAAACTCGGGTTGTCTGCCT 178024 v v? viv i iii i i i i ivi v C MIR3#SINE/MIR 87 ACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGTCTCCTGACT 38 chr2ptel1M 178025 TCAGATCAGCACT 178037 i vii v ii C MIR3#SINE/MIR 37 CCCAGTCCGTGCT 25 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.81 CpG sites = 31, Kimura (unadjusted) = 41.08 Transitions / transversions = 1.82 (31/17) Gap_init rate = 0.01 (1 / 157), avg. gap size = 5.00 (5 / 1) 501 33.33 1.39 0.00 chr2ptel1M 177917 178060 (821940) C MIRc#SINE/MIR (120) 148 3 m_b59s601i13 2191 chr2ptel1M 177917 CTTATTTTAAGGATGAAAGATCTGAGACCCAATGAGGTTAGATGACTTGC 177966 ii vi iii v i i iv ii C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr2ptel1M 177967 TGAACATCCCACAGATACCAAGTGACAGAGCTAAGATTAAAACTCGGGT- 178015 iv vi v v vi i iii i vi i i - C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTC 49 chr2ptel1M 178016 TGTCTGCCTTCAGAT-CAGCACTGATTACATTGTTCCATACCACCT 178060 vi v i ii - ii vv v i iv i ii C MIRc#SINE/MIR 48 TTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTGCCT 3 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.25 CpG sites = 33, Kimura (unadjusted) = 47.17 Transitions / transversions = 2.20 (33/15) Gap_init rate = 0.01 (2 / 143), avg. gap size = 1.00 (2 / 2) 268 31.94 0.00 0.00 chr2ptel1M 178155 178226 (821774) L2a_3end#LINE/L2 440 511 (6) m_b59s601i14 2192 chr2ptel1M 178155 CAGTGCAGTCCCTCTGGTGCCTAATACAGTGCCTGGAACAAAACAGACAC 178204 v v vi i ii i iv v v ii i i L2a_3end#LINE 440 CACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGGCGC 489 chr2ptel1M 178205 TTAATAAGTGCTTATAGATTGA 178226 i i ii i v v L2a_3end#LINE 490 TCAATAAATATTTGTTGAATGA 511 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.77 CpG sites = 15, Kimura (unadjusted) = 43.80 Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.00 (0 / 71), avg. gap size = 0.0 (0 / 0) 24 17.24 3.64 1.79 chr2ptel1M 178353 178407 (821593) (AG)n#Simple_repeat 1 56 (0) m_b59s252i25 2193 chr2ptel1M 178353 AGATGAGAGAGAGAAAAAGAGAGAGAGAGAGAAAGCGGGATGGAG-GAG- 178400 - i i i v i vi - - (AG)n#Simple_ 1 AGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 49 chr2ptel1M 178401 GGGAGAG 178407 i (AG)n#Simple_ 50 GAGAGAG 56 Matrix = Unknown Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.06 (3 / 54), avg. gap size = 1.00 (3 / 3) 425 22.07 6.80 7.53 chr2ptel1M 179089 179235 (820765) MIRb#SINE/MIR 6 151 (117) m_b59s601i15 2194 chr2ptel1M 179089 GGGCAGCTAGGTGCCACAGTAGAGAG-------GCTTTG-AG-CACGAAG 179129 vv --- i i ------- - - viv MIRb#SINE/MIR 6 GGGCAGCGTGGTGC---AGTGGAAAGAGCACGGGCTTTGGAGTCAGACAG 52 chr2ptel1M 179130 ACTCCTATTTCTGAGCTCAAATGTGGCCCCAGCCACCTACTACCTGTGTA 179179 -------- i i i viv v i v i v i MIRb#SINE/MIR 53 AC--------CTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTG 94 chr2ptel1M 179180 ACCTTGGCCAAGTCACTTAACC-CTGTTTACCTCAGCTTCATCAATTGTA 179228 v i - v vvi i v vi MIRb#SINE/MIR 95 ACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTA 144 chr2ptel1M 179229 AAATGAG 179235 i MIRb#SINE/MIR 145 AAATGGG 151 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.34 CpG sites = 15, Kimura (unadjusted) = 26.32 Transitions / transversions = 1.00 (15/15) Gap_init rate = 0.10 (15 / 146), avg. gap size = 1.40 (21 / 15) 431 22.89 1.64 6.90 chr2ptel1M 179114 179235 (820765) MIRc#SINE/MIR 33 148 (120) m_b59s601i16 2194 chr2ptel1M 179114 GGCTTTGAG-CACGAAGACTCCTATTTCTGAGCTCAAATGTGGCCCCAGC 179162 i v - v -------- i i i i viv v i v MIRc#SINE/MIR 33 GACTTGGAGTCAGGAAGAC--------CTGGGTTCGAGTCCCGGCTCTGC 74 chr2ptel1M 179163 CACCTACTACCTGTGTAACCTTGGCCAAGTCACTTAACC-CTGTTTACCT 179211 i v i v - v vvi MIRc#SINE/MIR 75 CACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCT 124 chr2ptel1M 179212 CAGCTTCATCAATTGTAAAATGAG 179235 i v vi i MIRc#SINE/MIR 125 CAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.22 CpG sites = 13, Kimura (unadjusted) = 27.41 Transitions / transversions = 1.00 (13/13) Gap_init rate = 0.08 (10 / 121), avg. gap size = 1.00 (10 / 10) 438 22.92 1.04 0.00 chr2ptel1M 179140 179235 (820765) MIR#SINE/MIR 48 144 (118) m_b59s601i17 2194 chr2ptel1M 179140 CTGAGCTCAAATGTGGCCCCAGCCACCTACTACCTGTGTAACCTTGGCCA 179189 i i i viv v i v i v i v MIR#SINE/MIR 48 CTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 97 chr2ptel1M 179190 AGTCACTTAACC-CTGTTTACCTCAGCTTCATCAATTGTAAAATGAG 179235 i - v v i i v vi i MIR#SINE/MIR 98 AGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGG 144 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.27 CpG sites = 12, Kimura (unadjusted) = 27.70 Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.01 (1 / 95), avg. gap size = 1.00 (1 / 1) 13 4.76 0.00 4.35 chr2ptel1M 179866 179889 (820111) (GGGA)n#Simple_repeat 1 23 (0) m_b59s252i26 2195 chr2ptel1M 179866 GGGAGGTGGGGGAGGGAGGGAGGG 179889 - i (GGGA)n#Simpl 1 GGGAGG-GAGGGAGGGAGGGAGGG 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 18 4.77 0.00 0.00 chr2ptel1M 179966 179987 (820013) (A)n#Simple_repeat 1 22 (0) m_b59s252i27 2196 chr2ptel1M 179966 AAAAAAAAAAAAAAAAAAAGAA 179987 i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAA 22 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 37 4.82 0.00 0.00 chr2ptel1M 180037 180079 (819921) (TGTCTC)n#Simple_repeat 1 43 (0) c_b59s251i1 2197 chr2ptel1M 180037 TGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTCTCTCTCTCTCT 180079 v v (TGTCTC)n#Sim 1 TGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCT 43 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 20 8.02 0.00 0.00 chr2ptel1M 180083 180109 (819891) (TA)n#Simple_repeat 1 27 (0) m_b59s252i28 2198 chr2ptel1M 180083 TATATATATATATATATACACATATAT 180109 i i (TA)n#Simple_ 1 TATATATATATATATATATATATATAT 27 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 15 21.76 2.33 0.00 chr2ptel1M 180369 180411 (819589) (TCTCC)n#Simple_repeat 1 44 (0) m_b59s252i29 2199 chr2ptel1M 180369 TCCCCCCT-CTCTCCTCTCCTCTTCTATTCTGTGCTCTCCTTTC 180411 i i - i v i v v i (TCTCC)n#Simp 1 TCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTC 44 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.02 (1 / 42), avg. gap size = 1.00 (1 / 1) 26 22.80 2.94 5.00 chr2ptel1M 181901 182002 (817998) (TCTTT)n#Simple_repeat 1 100 (0) m_b59s252i30 2200 chr2ptel1M 181901 TCTGTTTCTTTT-TCTCCTATTC-ATTCTCTTTCTTACTACCTGGCACTT 181948 - - i i v -v - -- v i vv -i (TCTTT)n#Simp 1 TCT-TTTCTTTTCTTTTCTTTTCTTTTCT-TTTCTT--TTCTTTTC-TTT 45 chr2ptel1M 181949 TCTTTTTTTTCCTTTTCTTTTCTTCT-TCTTCTTTTTTTTTTTTTTTTTA 181997 i i i - i i i i v (TCTTT)n#Simp 46 TCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTT 95 chr2ptel1M 181998 GCTTT 182002 v (TCTTT)n#Simp 96 TCTTT 100 Matrix = Unknown Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.08 (8 / 101), avg. gap size = 1.00 (8 / 8) 28 19.28 0.00 0.00 chr2ptel1M 181947 181996 (818004) (T)n#Simple_repeat 1 50 (0) m_b59s252i31 2201 chr2ptel1M 181947 TTTCTTTTTTTTCCTTTTCTTTTCTTCTTCTTCTTTTTTTTTTTTTTTTT 181996 i ii i i i i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 Matrix = Unknown Transitions / transversions = 1.00 (8/0) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 26 22.80 2.94 5.00 chr2ptel1M 181901 182002 (817998) (TCTTT)n#Simple_repeat 1 100 (0) m_b59s252i30 2200 chr2ptel1M 181901 TCTGTTTCTTTT-TCTCCTATTC-ATTCTCTTTCTTACTACCTGGCACTT 181948 - - i i v -v - -- v i vv -i (TCTTT)n#Simp 1 TCT-TTTCTTTTCTTTTCTTTTCTTTTCT-TTTCTT--TTCTTTTC-TTT 45 chr2ptel1M 181949 TCTTTTTTTTCCTTTTCTTTTCTTCT-TCTTCTTTTTTTTTTTTTTTTTA 181997 i i i - i i i i v (TCTTT)n#Simp 46 TCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTT 95 chr2ptel1M 181998 GCTTT 182002 v (TCTTT)n#Simp 96 TCTTT 100 Matrix = Unknown Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.08 (8 / 101), avg. gap size = 1.00 (8 / 8) 18 13.86 4.76 6.45 chr2ptel1M 183550 183612 (816388) (TTGCAT)n#Simple_repeat 1 62 (0) m_b59s252i32 2202 chr2ptel1M 183550 TTGCATTTGGCATGTTGAATTTTTTATTTGC-TTTTC-TTGGCA-TGCCA 183596 - - v - vi - v - v - vv (TTGCAT)n#Sim 1 TTGCATTT-GCAT-TTGCA-TTTGCATTTGCATTTGCATTTGCATTTGCA 47 chr2ptel1M 183597 TTTGCATGTTGCATTT 183612 - (TTGCAT)n#Sim 48 TTTGCAT-TTGCATTT 62 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.11 (7 / 62), avg. gap size = 1.00 (7 / 7) 19 14.17 0.00 0.00 chr2ptel1M 184193 184223 (815777) (A)n#Simple_repeat 1 31 (0) m_b59s252i33 2203 chr2ptel1M 184193 AAGAAAAACAAAAACAAAAAACAAAAAAAAA 184223 i v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 31 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 12 22.01 4.76 0.00 chr2ptel1M 184516 184557 (815443) (ATATGT)n#Simple_repeat 1 44 (0) m_b59s252i34 2204 chr2ptel1M 184516 ATATGTTAAAGTATTTGT-TAAATA-CTATATATGTATATGTAT 184557 vv v v - vi -v i (ATATGT)n#Sim 1 ATATGTATATGTATATGTATATGTATATGTATATGTATATGTAT 44 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.05 (2 / 41), avg. gap size = 1.00 (2 / 2) 324 30.97 13.27 0.00 chr2ptel1M 185104 185216 (814784) C MIRc#SINE/MIR (140) 128 1 m_b59s601i18 2205 chr2ptel1M 185104 ACTAAGACCCAGTTAAGTTAAATTATTTTCTCAAGACCACA--------- 185144 i i i vv i i v i v i ii --------- C MIRc#SINE/MIR 128 ACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTA 79 chr2ptel1M 185145 ----GCAGTACTAGAATTTCAACCCATGTCTT-CTGAGTCCAAATGTAGG 185189 ---- vi ii i i iv v - v i vi v C MIRc#SINE/MIR 78 AGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGT 29 chr2ptel1M 185190 GATC-TTCCATTATACCTTGCTGCCTTG 185216 v - i ii vii i C MIRc#SINE/MIR 28 GCTCTTTCCACTGCACCACACTGCCTCG 1 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.12 CpG sites = 23, Kimura (unadjusted) = 41.97 Transitions / transversions = 1.92 (23/12) Gap_init rate = 0.04 (4 / 112), avg. gap size = 3.75 (15 / 4) 219 32.61 5.48 3.36 chr2ptel1M 187243 187388 (812612) C MIRc#SINE/MIR (37) 231 83 m_b60s601i1 2206 chr2ptel1M 187243 AATTTCTAATGAGCTTCC---TGCATAAATACATTAGATCGTTACAGTAA 187289 i vi v v i --- i v viv v v i ii C MIRc#SINE/MIR 231 AGTTTACAAAGCGCTTTCACATACATTATCTCATTTGATCCTCACAACAA 182 chr2ptel1M 187290 ACCTGTGACAATAGGGAAAGT--GCATTCATTCTCACTATGTGCACAACT 187337 v -ii v ii i-- i - v v i - vi iv C MIRc#SINE/MIR 181 CCCTGTGA-GGTAGGCAGGGCAGGTATT-ATTATCCCCAT-TTTACAGAT 135 chr2ptel1M 187338 CAGG---CCAAGAGCTCAGAATATTTGAGTGAGTTGAACCAAATCCCAGC 187384 v --- ii - iviv i v vv v ii v - C MIRc#SINE/MIR 134 GAGGAAACTGAG-GCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACA-C 87 chr2ptel1M 187385 AGCT 187388 C MIRc#SINE/MIR 86 AGCT 83 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.66 CpG sites = 24, Kimura (unadjusted) = 43.66 Transitions / transversions = 1.09 (24/22) Gap_init rate = 0.06 (8 / 145), avg. gap size = 1.62 (13 / 8) 16 16.12 0.00 0.00 chr2ptel1M 187567 187594 (812406) (T)n#Simple_repeat 1 28 (0) m_b60s252i0 2207 chr2ptel1M 187567 TTTTTTGTGTTTTTTTTTTTTGTATTTT 187594 v v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 28 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 290 33.09 1.49 3.03 chr2ptel1M 189432 189565 (810435) MIR3#SINE/MIR 15 146 (62) m_b60s601i2 2208 chr2ptel1M 189432 GAGCTGATAGTACAGTACAGA-TAGACATT-GTATACCTGAGTTTAAATT 189479 v v --- i i - i ivi i- v v i iv i i MIR3#SINE/MIR 15 GAGCAGAGAG---AGCACGGACTGGGAGTCAGGAGACCTGGGTTCTAGTC 61 chr2ptel1M 189480 AAGCCTCGGACAATTACTAACTGTATACCCTTTGGTAACTCAATTAAAAC 189529 vv v v v v v ?i i iv v i v v v v- MIR3#SINE/MIR 62 CCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCAC-C 110 chr2ptel1M 189530 TTTGTTTGCCTTAGTTTCCTCACCTCTTAAGTGGGG 189565 i v vv i i v v i i MIR3#SINE/MIR 111 TCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGG 146 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.06 CpG sites = 19, Kimura (unadjusted) = 44.39 Transitions / transversions = 0.79 (19/24) Gap_init rate = 0.05 (6 / 133), avg. gap size = 1.00 (6 / 6) 481 29.87 0.69 0.69 chr2ptel1M 189464 189608 (810392) MIR#SINE/MIR 45 189 (73) m_b60s601i3 2208 chr2ptel1M 189464 TACCTGAGTTTAAATTAAGCCTCGGACAATTACTAACTGTATACCCTTTG 189513 i i ii ivv v v v v i i iv v MIR#SINE/MIR 45 TGCCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 94 chr2ptel1M 189514 GTAACTCAATTAAAACTTTGTTTGCCTTAGTTTCCTCACCTCTTAAGTGG 189563 i v i v v- i v v i i v v i MIR#SINE/MIR 95 GCAAGTTACTTAAC-CTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGG 143 chr2ptel1M 189564 GGATAACAGTATCACCTAACTTGGAAGGTTAATATTA-CATTAAAT 189608 i i vi v iiv i iv i v -v MIR#SINE/MIR 144 GGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGGATTAAAT 189 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.39 CpG sites = 22, Kimura (unadjusted) = 38.64 Transitions / transversions = 1.05 (22/21) Gap_init rate = 0.01 (2 / 144), avg. gap size = 1.00 (2 / 2) 276 17.34 0.00 2.67 chr2ptel1M 189790 189866 (810134) C DNM1r#Unknown (2110) 2552 2478 m_b60s502i0 2209 chr2ptel1M 189790 CTATTACATGCATACATATATACACACATTTATACACACATATACATATA 189839 i vi i? i i v i i C DNM1r#Unknown 2552 CTGTTCTATANATACGTATATATACACATATATACACACATACACACATA 2503 chr2ptel1M 189840 CACAAATTCATATATCCACACATATAC 189866 i v -- v i C DNM1r#Unknown 2502 TACACA--CATATATACACACATACAC 2478 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 18.80 CpG sites = 9, Kimura (unadjusted) = 20.50 Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.03 (2 / 76), avg. gap size = 1.00 (2 / 2) 239 25.33 0.00 0.00 chr2ptel1M 189808 189882 (810118) C DNM1r#Unknown (2116) 2546 2472 m_b60s502i1 2209 chr2ptel1M 189808 TATACACACATTTATACACACATATACATATACACAAATTCATATATCCA 189857 ? i i v i i i i i v iv iv C DNM1r#Unknown 2546 TATANATACGTATATATACACATATATACACACATACACACATATACACA 2497 chr2ptel1M 189858 CACATATACAGACATAGATATAGCC 189882 i v v ii i C DNM1r#Unknown 2496 CATATATACACACATACACGTGGCC 2472 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 28.41 CpG sites = 13, Kimura (unadjusted) = 32.74 Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.00 (0 / 74), avg. gap size = 0.0 (0 / 0) 227 19.78 0.00 5.63 chr2ptel1M 189818 189892 (810108) C DNM1r#Unknown (2114) 2548 2478 m_b60s502i2 2209 chr2ptel1M 189818 TTTATACACACATATACATATACACAAATTCATATATCCACACATATACA 189867 i ? i i i i i v v i i v C DNM1r#Unknown 2548 TCTATANATACGTATATATACACATATATACACACATACACACATATACA 2499 chr2ptel1M 189868 GACATAGATATAGCCATACATACAC 189892 v v ---- i C DNM1r#Unknown 2498 CACATATATA----CACACATACAC 2478 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 21.89 CpG sites = 9, Kimura (unadjusted) = 23.77 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.05 (4 / 74), avg. gap size = 1.00 (4 / 4) 243 20.61 0.00 2.94 chr2ptel1M 189852 189921 (810079) C DNM1r#Unknown (2116) 2546 2479 m_b60s502i3 2209 chr2ptel1M 189852 TATCCACACATATACAGACATAGATATAGCCATACATACACACATATATG 189901 v? i i i v i v -- i ii C DNM1r#Unknown 2546 TATANATACGTATATATACACATATATA--CACACATACACACATATACA 2499 chr2ptel1M 189902 TACATAGAAACACACATGCA 189921 i v v i C DNM1r#Unknown 2498 CACATATATACACACATACA 2479 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 23.06 CpG sites = 9, Kimura (unadjusted) = 25.07 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.03 (2 / 69), avg. gap size = 1.00 (2 / 2) 228 22.56 0.00 2.82 chr2ptel1M 189862 189934 (810066) C DNM1r#Unknown (2116) 2546 2476 m_b60s502i4 2209 chr2ptel1M 189862 TATACAGACATAGATATAGCCATACATACACACATATATGTACATAGAAA 189911 ? v i v vv i i --i v v C DNM1r#Unknown 2546 TATANATACGTATATATACACATATATACACACATACA--CACATATACA 2499 chr2ptel1M 189912 CACACATGCATACATATACACAT 189934 i ii i i i C DNM1r#Unknown 2498 CACATATATACACACATACACGT 2476 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 23.98 CpG sites = 10, Kimura (unadjusted) = 27.92 Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.03 (2 / 72), avg. gap size = 1.00 (2 / 2) 263 23.53 0.00 0.00 chr2ptel1M 189884 189951 (810049) C DNM1r#Unknown (2116) 2546 2479 m_b60s502i5 2209 chr2ptel1M 189884 TACATACACACATATATGTACATAGAAACACACATGCATACATATACACA 189933 i ? i ii ii v v i i C DNM1r#Unknown 2546 TATANATACGTATATATACACATATATACACACATACACACATATACACA 2497 chr2ptel1M 189934 TATACATTCGTATATACA 189951 i i v ii i C DNM1r#Unknown 2496 CATATATACACACATACA 2479 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 28.39 CpG sites = 13, Kimura (unadjusted) = 30.70 Transitions / transversions = 4.33 (13/3) Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0) 247 30.56 0.00 0.00 chr2ptel1M 190278 190349 (809651) L3#LINE/CR1 3868 3939 (160) m_b60s601i4 2210 chr2ptel1M 190278 GGGATACAAATTGATGCTCATTACAAAGAAGAATATTCCAAATGTTAGAA 190327 vi i vvv v i i iv i vvi i i L3#LINE/CR1 3868 GGGAGGCAGATTTCGGCTCAATATAAGGAAGAACTTTCTAACAATCAGAG 3917 chr2ptel1M 190328 CCATCCCAAAAAGGAATGGGTT 190349 ii v v i L3#LINE/CR1 3918 CTGTCCAAAAATGGAATGGGCT 3939 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.09 CpG sites = 12, Kimura (unadjusted) = 40.09 Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.00 (0 / 71), avg. gap size = 0.0 (0 / 0) 218 24.07 9.26 0.00 chr2ptel1M 191050 191103 (808897) L3#LINE/CR1 4041 4099 (0) m_b60s601i5 2210 chr2ptel1M 191050 GAGGTGAAACAAAATAACCTCTGAGATTACTTCCATGTCTGAGATCC--- 191096 vii v i i i i iv vv i --- L3#LINE/CR1 4041 GAGGTTGGACTAGATGACCTCTAAGGTCCCTTCCAACTCTGAGATTCTGT 4090 chr2ptel1M 191097 --TTCTATC 191103 -- L3#LINE/CR1 4091 GATTCTATC 4099 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.74 CpG sites = 8, Kimura (unadjusted) = 29.74 Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.04 (2 / 53), avg. gap size = 2.50 (5 / 2) 304 28.10 7.69 1.45 chr2ptel1M 191478 191607 (808393) C MIR3#SINE/MIR (7) 201 64 m_b60s601i6 2211 chr2ptel1M 191478 AAAATCATGAGATGT-AGCGCTGTTAGTCCCTTCAGAT-TCAGG-AATCC 191524 i iii - v vv vvv i i v- vv- i C MIR3#SINE/MIR 201 AGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCC 152 chr2ptel1M 191525 AACCCTCTTCAATTTCCA--TAAGGAAACTGAAGCATAGA-----GAAGG 191567 i - v v -- i i vi ----- v C MIR3#SINE/MIR 151 AACCCCCT-CATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGT 103 chr2ptel1M 191568 GATTTGCTTAAAGGTCATACCATTTTTGAGTGTCAGAGTC 191607 i ii- i vii?vv v v i C MIR3#SINE/MIR 102 GACTTGCCC-AAGGTCACACAGCNAGTTAGTGGCAGAGCC 64 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.02 CpG sites = 18, Kimura (unadjusted) = 36.02 Transitions / transversions = 1.00 (18/18) Gap_init rate = 0.05 (7 / 129), avg. gap size = 1.71 (12 / 7) 260 30.58 9.09 0.93 chr2ptel1M 191530 191628 (808372) C MIR#SINE/MIR (116) 146 40 m_b60s601i7 2211 chr2ptel1M 191530 TCTTCAATTTCCA--TAAGGAAACTGAAGCATAGAG-----AAGGGATTT 191572 ii v v -- i i i ----- vi i C MIR#SINE/MIR 146 TCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTT 97 chr2ptel1M 191573 GCTTAAAGGTCATACCATTTTTGAGTGTCAGAGTCATCTTCTGGAACCA- 191621 ii- i vii vv i v i ivvv ii i v - C MIR#SINE/MIR 96 GCCC-AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAG 48 chr2ptel1M 191622 -TAGTCTG 191628 -i C MIR#SINE/MIR 47 GCAGTCTG 40 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.47 CpG sites = 19, Kimura (unadjusted) = 41.01 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.05 (5 / 98), avg. gap size = 2.00 (10 / 5) 837 26.45 5.85 4.46 chr2ptel1M 195382 195757 (804243) C L1ME3F_3end#LINE/L1 (336) 654 274 m_b60s551i0 2212 chr2ptel1M 195382 GTATATAATGATCTCCTG-GCCCTGCTCGTTTCACTCAGCATCA-GTTCA 195429 i i --- i - v i iv ii i - -- C L1ME3F_3end#L 654 GTATGTAGT---CTTCTGNGACTTGCTTTTTTCACTCAATATTATGTT-- 610 chr2ptel1M 195430 TGTAAGTCTC-TCCAGGCTTTT-C-TGAAATCATCCTGTTGGTCATT--- 195473 v vi - v i v - - v i----- v v --- C L1ME3F_3end#L 609 TCTAAGATTCATCCATGTTGTTGCGTGTAG-----CTGTAGTTCATTCAT 565 chr2ptel1M 195474 TCTCACTGAACAATAATATTCCATAATATTCATATACCACAATTTTTTTA 195523 i vvvv vi i vv v C L1ME3F_3end#L 564 TTTCACTGCTGTATAATATTCCATTGTGTGAATATACCACAATTTATTTA 515 chr2ptel1M 195524 GCCATTCTCCAAATTGATGGGCATCTACTCAGTTTCCAGTTTCTGGCCAC 195573 v vi- i i i ivviv i v i i C L1ME3F_3end#L 514 TCCATTCTCCTG-TCGATGGACATTTGGGTTGTTTCCAGTTTTTTGCTAT 466 chr2ptel1M 195574 TACAAAGAGGGCTGCCACAAACATTCATGCACATACAGTTCTTTATG--- 195620 i v v i ii v i ii--i i vi --- C L1ME3F_3end#L 465 TACGAACAGTGCTGCTATGAACATTCTTGTACATGT--CTCCTGGTGCAC 418 chr2ptel1M 195621 ----------ATCTCTTTGGGGTATAAGCCCAGTAGTAGCACTGCTGGAT 195660 ----------i i i v vi i v i v i i C L1ME3F_3end#L 417 ATGTGCAAGAGTTTCTCTTGGGTATATACCTAGGAGTGGAATTGCTGGGT 368 chr2ptel1M 195661 CAAAGGGTATGCACA-GTTTGATAACTTTTTGAGCATAGTTCCAAATTGC 195709 iv iv - ---i vi - i v i C L1ME3F_3end#L 367 CGTAGGGTATGCGAATGTT---CAACTTTACGAG-ATAATGCCAAATTGT 322 chr2ptel1M 195710 TCTCCAGAATGGTTGGATATATTCACAATTCCACCAACAATGTATTAG 195757 i i i v ivv i v i i i v C L1ME3F_3end#L 321 TTTCCAAAGTGGTTGTACCAATTTACACTCCCACCAGCAGTGTATAAG 274 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 31.24 CpG sites = 55, Kimura (unadjusted) = 33.35 Transitions / transversions = 1.38 (55/40) Gap_init rate = 0.07 (26 / 375), avg. gap size = 1.50 (39 / 26) 902 24.05 4.78 2.15 chr2ptel1M 195486 195757 (804243) C L1ME3G_3end#LINE/L1 (376) 548 270 m_b60s551i1 2212 chr2ptel1M 195486 ATAATATTCCATAATATTCATATACCACAATTTTTTTAGCCATTCTCCAA 195535 i i vv i v i i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr2ptel1M 195536 ATTGATGGGCATCTACTCAGTTTCCAGTTTCTGGCCACTACAAAGAGGGC 195585 - i i vviv i i v i i v iv C L1ME3G_3end#L 498 -TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGC 450 chr2ptel1M 195586 TGCCACAAACATTCATGCACATACAGTTCTTTATG-------------AT 195622 v ii i v i i ?-- i i ------------- C L1ME3G_3end#L 449 TGCAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTAT 402 chr2ptel1M 195623 CTCTTTGGGGTATAAGCCCAGTAGTAGCACTGCTGGATCAAAGGGTATGC 195672 i ? i i v v? ? v i v i i C L1ME3G_3end#L 401 TTCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGC 352 chr2ptel1M 195673 ACAGTTTGATAACTTTTTGAGCATAGTTCCAAATTGCTCTCCAGAATGGT 195722 i v i -- i vvv - v v i i ? i C L1ME3G_3end#L 351 GCATTTTAA--ATTTTAATAG-ATACTGCCAAATTGCCCTCCAAAANGGC 305 chr2ptel1M 195723 TGGATATATTCACAATTCCACCAACAATGTATTAG 195757 v ivv i v i i i v C L1ME3G_3end#L 304 TGTACCAATTTACACTCCCACCAGCAGTGTATGAG 270 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 29.70 CpG sites = 37, Kimura (unadjusted) = 30.26 Transitions / transversions = 1.37 (37/27) Gap_init rate = 0.03 (7 / 271), avg. gap size = 2.71 (19 / 7) 460 27.79 3.76 2.60 chr2ptel1M 195861 196126 (803874) L1M3_orf2#LINE/L1 3013 3281 (7) m_b60s551i2 2213 chr2ptel1M 195861 AAAATAGAAAATTTCGATTATACCAAACTGAAAAGTTTTTGTACA---AA 195907 v v vv i i i i i i i --- L1M3_orf2#LIN 3013 AAAATAGACAAGTGGGACTACATCAAACTAAAAAGCTTCTGCACAGCAAA 3062 chr2ptel1M 195908 CAAAACTAATGCAGACAAGATTAGAAGG-AAGCAATAAACTGGGAAAATA 195956 vi - - - iii v i - v v iii v i v L1M3_orf2#LIN 3063 GGAAAC-AAT-CA-ACAGAGTGAAAAGGCAACCTACGGAATGGGAGAAAA 3109 chr2ptel1M 195957 TTTTTACAGTCAAAGGTTCTGATAAAGGCCTCATTTCCAAAATATATGAG 196006 v i iv v vivv i vi v v i L1M3_orf2#LIN 3110 TATTTGCAAACCATATATCTGATAAGGGGTTAATATCCAAAATATATAAG 3159 chr2ptel1M 196007 -AATT-----AACTCTAATTTATAAAAATCAAGCCATTCTCCAATTGAAA 196050 - i ----- - vvvv v --- vvi i ? L1M3_orf2#LIN 3160 GAACTCNTACAACTC-AATAGCAAAAAAACAA---ATAACCCGATTNAAA 3205 chr2ptel1M 196051 AATGGTCAAAGGATATGAACAGACAATTCTCAGATGAAGAAATTGAAACT 196100 v iv i v vi v v vv iv L1M3_orf2#LIN 3206 AATGGGCAAAGGACCTGAATAGACATTTCTCCAAAGAAGACATACAAATG 3255 chr2ptel1M 196101 ATTTCTAGTCATATGAAAAGATGCTC 196126 iiivvi vi L1M3_orf2#LIN 3256 GCCAACAGGTATATGAAAAGATGCTC 3281 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.94 CpG sites = 34, Kimura (unadjusted) = 35.18 Transitions / transversions = 0.89 (34/38) Gap_init rate = 0.04 (11 / 265), avg. gap size = 1.55 (17 / 11) 1454 26.78 1.28 2.03 chr2ptel1M 195992 196536 (803464) L1ME3G_3end#LINE/L1 7 547 (377) m_b60s551i3 2213 chr2ptel1M 195992 TCCAAAATATATGA-GAATTAACTCTAATTTATAAAAATCAAGCCATTCT 196040 i i - i vviv v iv i -v v --vi L1ME3G_3end#L 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAA-AAAGACA--AC 53 chr2ptel1M 196041 CCAATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGAAGA 196090 v v i v v i L1ME3G_3end#L 54 CCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGGA 103 chr2ptel1M 196091 AATTGAAACTATTTCTAGTCATATGAAAAGATGCTCCAAGTCATTATTAA 196140 vv iviiivv iv v vv i v L1ME3G_3end#L 104 AATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTAA 153 chr2ptel1M 196141 TCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACACCTGTC 196190 i i vv i i viv ii L1ME3G_3end#L 154 TCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCATC 203 chr2ptel1M 196191 AGATTGGCTAAGATGAGAGGAAAAAATAATGATGATTATTG--GAGGGT- 196237 v i vvi iii?vvi ivi? v i -- - L1ME3G_3end#L 204 AGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGTG 253 chr2ptel1M 196238 TGCGGAAAACTGGGACATTGATGCATTGTTGGTGGAGTTGTGAACGAATC 196287 - i v v vi v i i i iiv i ivii v L1ME3G_3end#L 254 TG-GGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTA 302 chr2ptel1M 196288 CAACCATTTTGGAGAGTAGTTTGA-ACTATGCTCAAAAAGTTATCAAACT 196336 i ? i i i i- v - vvv i -- i v L1ME3G_3end#L 303 CAGCCNTTTTGGAGGGCAATTTGGCAGTAT-CTATTAAAAT--TTAAAAT 349 chr2ptel1M 196337 GTGCATACCCTTTGATCCAGCAGATGTTACTACTGGGATTATATCCCAAA 196386 i i - vii v ? ?v v i ? L1ME3G_3end#L 350 GCGCATACCCTTTGACCCAGCA-ATTCCACTTCTNGGNATCTATCCTANA 398 chr2ptel1M 196387 GAGATTATAAAAGAAG-GGAAAGGGACCTGTATGTGCACGAATGTTTG-T 196434 i vv viv v v - v v i --? i i v i ii- L1ME3G_3end#L 399 GAAATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTCATT 446 chr2ptel1M 196435 GCATGCCCCTTTTGTAGTAGCTAAAAACTGGAAACTGAATGGATGTCCAT 196484 - viiv i v i vivv ii L1ME3G_3end#L 447 GCA-GCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCAT 495 chr2ptel1M 196485 CAGTTGGAGAATGGTTGAATAAATTGTGGTATATGAAAATTATGGAATAT 196534 i v i i i vv v i i L1ME3G_3end#L 496 CAATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATAC 545 chr2ptel1M 196535 TA 196536 L1ME3G_3end#L 546 TA 547 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.58 CpG sites = 75, Kimura (unadjusted) = 34.16 Transitions / transversions = 1.10 (75/68) Gap_init rate = 0.03 (17 / 544), avg. gap size = 1.06 (18 / 17) 1356 27.58 3.42 3.78 chr2ptel1M 196039 196622 (803378) L1ME5_3end#LINE/L1 56 637 (304) m_b60s551i4 2213 chr2ptel1M 196039 CTCCAATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGAA 196088 i v v i iv v i L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chr2ptel1M 196089 GAAA-TTGAAA--CTATTTCTAGTCATATGAAAAGATGCTCCAAGTCATT 196135 -ii -- --v v - i v v L1ME5_3end#LI 106 GAAACCCGAAAGGCTA--ACAAG-CATATGAAGAGATGCTCAAACTCATT 152 chr2ptel1M 196136 ATTAATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACAC 196185 v i vv i i vi L1ME5_3end#LI 153 AGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACAC 202 chr2ptel1M 196186 CTGTCAGATTGGCTAAGATGAGAGGAAAAAATAATGATGATTATTGGAG- 196234 i i i v i v iiivvii vii v i v - L1ME5_3end#LI 203 CTATTAGACTGGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTGGCGA 252 chr2ptel1M 196235 GGTTGCGGAAAACT-GGGACATTGATGCATTGTTGGTGGAGTTGTGAACG 196283 v i ii ?v - i vi v i i iiv ii v L1ME5_3end#LI 253 GGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACT 302 chr2ptel1M 196284 AATCCAACCATTTTGGAGAGTAGTTTGA----ACTATGCTCAAA--AAGT 196327 ii v i i i i i i---- - iv -- - L1ME5_3end#LI 303 GGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACT-TAGTCAAATTAAG- 350 chr2ptel1M 196328 TATCAAACTGTGCATACCCTTTGATCCAGCAGATGTTACTACTGGGATTA 196377 --- --- v i - viii v vv L1ME5_3end#LI 351 TAT---AC---GCATACCCTATGACCCAGCA-ATTCCGCTCCTGGGTATA 393 chr2ptel1M 196378 TATCCCAAAGAGATTATAAAAGAAG---GGAAAGGGACCTGTATGTGCAC 196424 i v v v v i ---iv i ---- i iv L1ME5_3end#LI 394 TATCCCAAAGAAATTCTCACACAGGTCCATAAGGGGAC----ATGTACGA 439 chr2ptel1M 196425 GAATGTTTG-TGCATGCCCCTTTTGTAGTAGCTAAAAACTGGAAACTGAA 196473 i ii- - viiv i i viii ii ii vivv L1ME5_3end#LI 440 GGATGTTCATTGCA-GCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACC 488 chr2ptel1M 196474 TGGATGTCCATCAGTTGGAGAATGGTTGAATAAATTGTGGTATATGAAAA 196523 i v v i v iii v iv v v L1ME5_3end#LI 489 TGGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACA 538 chr2ptel1M 196524 TTATGGAATATTACTGT-TCTGTAAGAAATGACCAACAGGATAATTTCAG 196572 ii i i - i-v v v iii vi vi i-- v v L1ME5_3end#LI 539 CCATGGAGTACTA-TGCAGCAGTTAGAAGCAACGGACTAGATG--TACAC 585 chr2ptel1M 196573 AAAG--GCCTGGAGAGA-CTTACATGAAC-TGATGCTGAGTGAAATGAGC 196618 v --i v vi - v -- - ii vi i L1ME5_3end#LI 586 ATAGCAACATGGATGGATCTTAAA--AACATAGTGCTGAGTGAAAAAAGT 633 chr2ptel1M 196619 AGGA 196622 i L1ME5_3end#LI 634 AAGA 637 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.49 CpG sites = 92, Kimura (unadjusted) = 35.38 Transitions / transversions = 1.46 (92/63) Gap_init rate = 0.06 (34 / 583), avg. gap size = 1.24 (42 / 34) 25 26.36 0.00 0.00 chr2ptel1M 197080 197142 (802858) (AA)n#Simple_repeat 1 63 (0) m_b60s252i2 2214 chr2ptel1M 197080 AAAAAAAAAAATAATGCATATCAGACATTAAAAAAAAAAAAAAAAAAAAA 197129 v viv v vv i v vv (AA)n#Simple_ 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr2ptel1M 197130 AAAAGAAGAAGAA 197142 i i i (AA)n#Simple_ 51 AAAAAAAAAAAAA 63 Matrix = Unknown Transitions / transversions = 0.56 (5/9) Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0) 273 22.22 0.00 0.00 chr2ptel1M 199359 199412 (800588) HERVIP10F#LTR/ERV1 6914 6967 (770) m_b60s701i0 2215 chr2ptel1M 199359 GGTACCTGTGCAGCAACACAATTGGCTATTCCTTTTACCCTGGCATTTGA 199408 i i vvi iiv i i v HERVIP10F#LTR 6914 GGCACTTGTGCTCTAGTCCAATTGGCTATCCCTTTCACCCTGGCATTTCA 6963 chr2ptel1M 199409 TGAA 199412 v HERVIP10F#LTR 6964 TCAA 6967 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 26.80 CpG sites = 7, Kimura (unadjusted) = 26.80 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 333 27.95 0.00 3.49 chr2ptel1M 200184 200272 (799728) C MIRc#SINE/MIR (181) 87 2 m_b60s601i8 2216 chr2ptel1M 200184 CAAGTATTAAATGTCTGAGGCCAGATTTGAACTTAGGTCCTCCTGACTTC 200233 iv v i v v v vi i i ii i i C MIRc#SINE/MIR 87 CAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCC 38 chr2ptel1M 200234 AGGGCTGGTGTTCTGTCCACTGTACTAACTAGCTGCCTC 200272 i v ii i v i i --i - C MIRc#SINE/MIR 37 AAGTCCAGTGCTCTTTCCACTGCACCA--CA-CTGCCTC 2 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.51 CpG sites = 16, Kimura (unadjusted) = 36.43 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.03 (3 / 88), avg. gap size = 1.00 (3 / 3) 16 10.47 3.23 0.00 chr2ptel1M 202989 203019 (796981) (AATTT)n#Simple_repeat 1 32 (0) m_b60s252i3 2217 chr2ptel1M 202989 AATTT-TTTTATTTTAATTTAATTTCATTTAA 203019 -v v v (AATTT)n#Simp 1 AATTTAATTTAATTTAATTTAATTTAATTTAA 32 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.03 (1 / 30), avg. gap size = 1.00 (1 / 1) 23 18.09 3.57 0.00 chr2ptel1M 203390 203445 (796555) (AAAAC)n#Simple_repeat 1 58 (0) m_b60s252i4 2218 chr2ptel1M 203390 AAAAGAAAAACAAACAAAAAAAAACATGAGAAAGC--AACAAAACAAAAC 203437 v vv v vi v i -- (AAAAC)n#Simp 1 AAAACAAAACAAAACAAAACAAAACAAAACAAAACAAAACAAAACAAAAC 50 chr2ptel1M 203438 AAGACAAA 203445 i (AAAAC)n#Simp 51 AAAACAAA 58 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.02 (1 / 55), avg. gap size = 2.00 (2 / 1) 18 0.00 0.00 0.00 chr2ptel1M 203969 203988 (796012) (T)n#Simple_repeat 1 20 (0) m_b60s252i5 2219 chr2ptel1M 203969 TTTTTTTTTTTTTTTTTTTT 203988 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTT 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 394 27.32 5.67 1.36 chr2ptel1M 204689 204829 (795171) MIRc#SINE/MIR 4 150 (118) m_b60s601i9 2220 chr2ptel1M 204689 GGCGG-GTGCCACAGTGCCCAGAGTCCTGGATTTGGAATTAGGAATACTC 204737 i - vii vvv iv i i i v ii MIRc#SINE/MIR 4 GGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCT 53 chr2ptel1M 204738 AACTTCAGAGTGCC---TCAGACACTTATCATATGTGTCAGCCTGGCCAA 204784 iiv - v --- v v ii vv v v i v MIRc#SINE/MIR 54 GGGTTC-GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 102 chr2ptel1M 204785 TTCCCTCAGGCCTGTTTG--CCT--GTTTCCTCATCTATAAAATGAGAA 204829 v v i i- v i -- -- i i i MIRc#SINE/MIR 103 GTCACTTAA-CCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGA 150 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.49 CpG sites = 20, Kimura (unadjusted) = 34.49 Transitions / transversions = 1.11 (20/18) Gap_init rate = 0.04 (6 / 140), avg. gap size = 1.67 (10 / 6) 348 30.70 8.77 0.00 chr2ptel1M 205616 205729 (794271) C MIRc#SINE/MIR (142) 126 3 m_b60s601i10 2221 chr2ptel1M 205616 TGAGACCCAGTTAATTGAAATTATTTGCCCAAGACCAGAGAG---GTA-- 205660 i i vv iv v i v i ii v v --- -- C MIRc#SINE/MIR 126 TGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAG 77 chr2ptel1M 205661 ---CAGAATTAGGATTTCTACCATGATCT--CTGATTCAAAATCTAGTGA 205705 --- iiii i ivv vv i -- i v i i v C MIRc#SINE/MIR 76 TGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGC 27 chr2ptel1M 205706 TCTTTCCATTCCACCATATTGTCT 205729 i v i i i C MIRc#SINE/MIR 26 TCTTTCCACTGCACCACACTGCCT 3 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.66 CpG sites = 21, Kimura (unadjusted) = 40.83 Transitions / transversions = 1.50 (21/14) Gap_init rate = 0.04 (4 / 113), avg. gap size = 2.50 (10 / 4) 21 36.64 0.00 0.00 chr2ptel1M 206141 206223 (793777) (AA)n#Simple_repeat 1 83 (0) m_b60s252i6 2222 chr2ptel1M 206141 AAGAAAAATCAAATCAAACCAGTAAAAAAAAGAGAGAGAGAAGCAAAAAA 206190 i vv vv vv iv i i i i i iv (AA)n#Simple_ 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr2ptel1M 206191 AAAAAAAAAAATGCAAGCAAACAACAACAAAAA 206223 viv iv v v v (AA)n#Simple_ 51 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 83 Matrix = Unknown Transitions / transversions = 0.71 (10/14) Gap_init rate = 0.00 (0 / 82), avg. gap size = 0.0 (0 / 0) 526 23.51 15.45 5.08 chr2ptel1M 206967 207199 (792801) MIRb#SINE/MIR 13 268 (0) m_b60s601i11 2223 chr2ptel1M 206967 GTGGTACAATGAATTGCATGGGGATAGAGCTTTG-AGTCAGGAAGACCTG 207015 i i i ---- v i v ii - - iv MIRb#SINE/MIR 13 GTGGTGCAGTGGA----AAGAGCACGG-GCTTTGGAGTCAGACAGACCTG 57 chr2ptel1M 207016 AGTTTTAATCCCATGTCAGAAACTTGCTAGT--------------CAAG- 207050 i iv ivv v vv i i-------------- - MIRb#SINE/MIR 58 GGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGT 107 chr2ptel1M 207051 -ATTTAGGACCTCTGTTTCCCTCAGTTTCTCCATCTGTAAAATGGATATA 207099 - i -- v vvv ii iv MIRb#SINE/MIR 108 TACTTA--ACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATA 155 chr2ptel1M 207100 ATAATAGCATAGAAGTCCT----GTGTTGTCTTGTGGATAAAATGAGATA 207145 - v ----- ---- v iv v v MIRb#SINE/MIR 156 ATAATA-CCTA-----CCTCGCAGGGTTGTTGTGAGGATTAAATGAGATA 199 chr2ptel1M 207146 --------------TTTA-TATGGTGCATGATACATAGTAGGTACTATGT 207180 --------------i -i ii v ii i ii vvi MIRb#SINE/MIR 200 ATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAAT 249 chr2ptel1M 207181 AAATGCTAGCTATTTTATT 207199 v v v MIRb#SINE/MIR 250 AAATGGTAGCTCTATTATT 268 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.06 CpG sites = 27, Kimura (unadjusted) = 28.69 Transitions / transversions = 1.08 (27/25) Gap_init rate = 0.09 (20 / 232), avg. gap size = 2.45 (49 / 20) 295 26.45 8.74 0.90 chr2ptel1M 207351 207453 (792547) L2b_3end#LINE/L2 346 456 (10) m_b60s601i12 2224 chr2ptel1M 207351 AGTCTGTGACCTTCATGAGAGCAGGGGATGT-TC---CTTG--CATCTCT 207394 v v i i i ivi ?- --- -- i v L2b_3end#LINE 346 AGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCT 395 chr2ptel1M 207395 TTAACTCCTGGTGCTTAGCCCATGGTCTGGCATATCACAGGCACT---TA 207441 v v i -i i i v v? i i ivii i --- L2b_3end#LINE 396 GTATCCCC-AGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTA 444 chr2ptel1M 207442 AATGTTTGCTGA 207453 i i L2b_3end#LINE 445 AATATTTGTTGA 456 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.70 CpG sites = 18, Kimura (unadjusted) = 34.85 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.05 (5 / 102), avg. gap size = 2.00 (10 / 5) 275 28.56 4.30 2.11 chr2ptel1M 207535 207627 (792373) C MIR3#SINE/MIR (0) 208 114 m_b60s601i13 2225 chr2ptel1M 207535 GAATCTTATAGGGTCATAGATGATCAG---TAGAAGGTACCTACAAGGCC 207581 -- ii vvi --- i v vvi ii C MIR3#SINE/MIR 208 GAATC--ATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATC 161 chr2ptel1M 207582 ATGGAGTGCA-CCCTCTTATTTTCTAGATGGGGAAACTTGGATTTAG 207627 vv v - i i vi i vi iiii C MIR3#SINE/MIR 160 ATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAG 114 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.16 CpG sites = 16, Kimura (unadjusted) = 37.16 Transitions / transversions = 1.60 (16/10) Gap_init rate = 0.04 (4 / 92), avg. gap size = 1.50 (6 / 4) 240 26.79 12.50 0.00 chr2ptel1M 210891 211002 (788998) C MIRc#SINE/MIR (140) 128 3 m_b60s601i14 2226 chr2ptel1M 210891 ACTGATACCCAGTAAATTTAACTTACTT-TCCAAG---AC-CAG-TGGTA 210934 vi i vi iv v v -i --- - - i C MIRc#SINE/MIR 128 ACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTA 79 chr2ptel1M 210935 -----CAGAAAGAGAAATTCAACTCA--TCT-CCTCACTCCAATTCGAGT 210976 ----- ivvi i v iv i -- - v v v C MIRc#SINE/MIR 78 AGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGT 29 chr2ptel1M 210977 GAACTTTCTACTCCACCATGTTGCCT 211002 vv i v iii C MIRc#SINE/MIR 28 GCTCTTTCCACTGCACCACACTGCCT 3 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 30.87 CpG sites = 15, Kimura (unadjusted) = 33.48 Transitions / transversions = 1.00 (15/15) Gap_init rate = 0.06 (7 / 111), avg. gap size = 2.00 (14 / 7) 15 20.03 0.00 0.00 chr2ptel1M 211395 211423 (788577) (T)n#Simple_repeat 1 29 (0) m_b60s252i7 2227 chr2ptel1M 211395 TTTTGTTTATAAGTTTTTTTTTTTTTTTT 211423 v v vvv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 18 0.00 0.00 0.00 chr2ptel1M 211580 211599 (788401) (T)n#Simple_repeat 1 20 (0) m_b60s252i8 2228 chr2ptel1M 211580 TTTTTTTTTTTTTTTTTTTT 211599 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTT 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 22 15.37 0.00 0.00 chr2ptel1M 213741 213776 (786224) (A)n#Simple_repeat 1 36 (0) m_b60s252i9 2229 chr2ptel1M 213741 AAAAAAAAAAAAAAAAAGAAACAAAGAAAACAATAA 213776 i v i v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 36 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 227 32.00 14.00 0.00 chr2ptel1M 215453 215552 (784448) MIRc#SINE/MIR 32 145 (123) m_b60s601i15 2230 chr2ptel1M 215453 GGACCTTGAATCAGGAAGGCAGTGGTTTTAATCCCACCTCAGAAACTTGC 215502 i v i i vvv iv i iv v vv i MIRc#SINE/MIR 32 GGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTAC 81 chr2ptel1M 215503 TAGT--------------CAAGTTATAGGACCTCTGTTTGATTCATTTTC 215538 i-------------- i ivvi v vv vi v MIRc#SINE/MIR 82 TAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTC 131 chr2ptel1M 215539 TATGTCTGTAAAAT 215552 ivii MIRc#SINE/MIR 132 CTCATCTGTAAAAT 145 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.85 CpG sites = 15, Kimura (unadjusted) = 42.13 Transitions / transversions = 0.88 (15/17) Gap_init rate = 0.01 (1 / 99), avg. gap size = 14.00 (14 / 1) 248 29.83 6.57 2.10 chr2ptel1M 215742 215878 (784122) L2b_3end#LINE/L2 301 443 (23) m_b60s601i16 2231 chr2ptel1M 215742 CACAGTGGGCTTCTCAATAGTTGCTGGTATAT-TGTCTTCCCCACCACTC 215790 vv - v ? v ivi ? vii i - i i vv L2b_3end#LINE 301 CACTCTGGG-TTATNATTGTCTGNTTACATGTCTGTCTCCCCCACTAGAC 349 chr2ptel1M 215791 TGTGACCTTCATGAGAGCAGGGG--ATGTC--CCTTA--CATCTCTTTAT 215834 v i i i i--i? --i i-- i v v - L2b_3end#LINE 350 TGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTGTA- 398 chr2ptel1M 215835 GTTCCCGGTGCTCTGCCCAGGG-CTGCCATGTAG-AGGTGCTTAAT 215878 - i i i iiv v ? - v iii - i i i L2b_3end#LINE 399 -TCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGT 443 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.17 CpG sites = 26, Kimura (unadjusted) = 41.50 Transitions / transversions = 1.86 (26/14) Gap_init rate = 0.07 (9 / 136), avg. gap size = 1.33 (12 / 9) 250 30.02 3.48 10.19 chr2ptel1M 215774 215888 (784112) L2c_3end#LINE/L2 361 468 (10) m_b60s601i17 2231 chr2ptel1M 215774 TGTCTTCCCCACCACTCTGTGACCTTCATGAGAGCAGGGGATGTCCCTTA 215823 i i i vv v i v i ivi vi L2c_3end#LINE 361 TGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTA 410 chr2ptel1M 215824 CATCTCTTTATGTTCCCGGTGCTCTGCCCAGGGCTGCCATGTAG-AGGTG 215872 iviv i i i i i ----------- v ii - i L2c_3end#LINE 411 TTCATCTTTGTATCCCCAGCGC-----------CTGGCACATAGTAGGCG 449 chr2ptel1M 215873 CTTAAT---TGTTTACCGA 215888 i --- iii L2c_3end#LINE 450 CTCAATAAATGTTTGTTGA 468 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.35 CpG sites = 22, Kimura (unadjusted) = 40.38 Transitions / transversions = 2.44 (22/9) Gap_init rate = 0.11 (13 / 114), avg. gap size = 1.15 (15 / 13) 320 25.29 4.60 0.00 chr2ptel1M 215989 216075 (783925) C MIR3#SINE/MIR (3) 205 115 m_b60s601i18 2232 chr2ptel1M 215989 TTATAGGATCACA-AATG--AGCACTGAAGGGGACCTACAGGGCCATAGA 216035 i i i - -- vi i i vvii ii vv C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTA 156 chr2ptel1M 216036 GTGCAACCCTCTCCTTTTATAGATG-GGAAGCTGAGATCCA 216075 v i v i - i ii C MIR3#SINE/MIR 155 GTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCA 115 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.08 CpG sites = 15, Kimura (unadjusted) = 32.08 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.03 (3 / 86), avg. gap size = 1.33 (4 / 3) 577 25.26 5.00 5.00 chr2ptel1M 217050 217249 (782751) MIRb#SINE/MIR 2 201 (67) m_b60s601i19 2233 chr2ptel1M 217050 AAAGGGG-AGCTGGTAGTACAGTGGA----GTCCTGGGTATGTAGTCAGG 217094 i - -- i i ---- iv v v v v i MIRb#SINE/MIR 2 AGAGGGGCAGC--GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGA 49 chr2ptel1M 217095 TATACCCAAGTTTGAATTAAGCCTTGGACAGTTACTGCCT-----ACCTC 217139 i v iii i ivv v iv v v iv ----- - MIRb#SINE/MIR 50 CAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCT- 98 chr2ptel1M 217140 TGGGCAAGTCAATTAAACTCTGTTAGTTTGCCTCAGTTTCCTCAACTCTT 217189 i v v v v ---- v v v MIRb#SINE/MIR 99 TGGGCAAGTTACTTAACCTCTCTGAG----CCTCAGTTTCCTCATCTGTA 144 chr2ptel1M 217190 AAATGGGGATAACAATATGACCTAACTTGGAAAGTTAAAATGAAGATAAA 217239 i --- v i v ii ivvi i v MIRb#SINE/MIR 145 AAATGGGGATAATAAT---ACCTACCTCGCAGGGTTGTTGTGAGGATTAA 191 chr2ptel1M 217240 GTGACATAAT 217249 i v MIRb#SINE/MIR 192 ATGAGATAAT 201 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.49 CpG sites = 22, Kimura (unadjusted) = 30.97 Transitions / transversions = 0.85 (22/26) Gap_init rate = 0.07 (13 / 199), avg. gap size = 1.54 (20 / 13) 14 24.17 2.27 0.00 chr2ptel1M 217425 217468 (782532) (TACA)n#Simple_repeat 1 45 (0) m_b60s252i10 2234 chr2ptel1M 217425 TATATAGAAATATATATACATACATAAATA-ATAAACACACACAT 217468 i v v i i v - v i i (TACA)n#Simpl 1 TACATACATACATACATACATACATACATACATACATACATACAT 45 Matrix = Unknown Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.02 (1 / 43), avg. gap size = 1.00 (1 / 1) 248 28.00 8.26 1.72 chr2ptel1M 218241 218349 (781651) C MIR3#SINE/MIR (1) 207 92 m_b60s601i20 2235 chr2ptel1M 218241 AATCATCAAAAGCCCTAAGATGT-GGAGCTGAAAGACTCTTCAGA-ATTA 218288 -- i ii v ii -i i ivv i i - i C MIR3#SINE/MIR 207 AATCAT--AGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCA 160 chr2ptel1M 218289 AAGAGTCCAACCCCTTCAATTTATTG--GAGGAAACTCAAACAC--TGAG 218334 vvv i v iv -- v ii v --v C MIR3#SINE/MIR 159 TCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAG 110 chr2ptel1M 218335 GCAA---GATTTGCCAAA 218349 ii --- i v C MIR3#SINE/MIR 109 GTGAAGTGACTTGCCCAA 92 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.11 CpG sites = 18, Kimura (unadjusted) = 36.11 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.06 (7 / 108), avg. gap size = 1.57 (11 / 7) 12 30.74 0.00 4.84 chr2ptel1M 218519 218583 (781417) (TCCTCT)n#Simple_repeat 1 62 (0) m_b60s252i11 2236 chr2ptel1M 218519 TCCTAATGCTCTCCCAACTCCACTTTCTACTTCCCATTCCTCTTCCTTTT 218568 vv v i vvi v i - iv i (TCCTCT)n#Sim 1 TCCTCTTCCTCTTCCTCTTCCTCTTCCT-CTTCCTCTTCCTCTTCCTCTT 49 chr2ptel1M 218569 ATCTATAACCTCTTC 218583 -i v -v (TCCTCT)n#Sim 50 -CCTCT-TCCTCTTC 62 Matrix = Unknown Transitions / transversions = 0.67 (6/9) Gap_init rate = 0.05 (3 / 64), avg. gap size = 1.00 (3 / 3) 297 30.01 4.99 5.54 chr2ptel1M 219922 220302 (779698) L1M4_orf2#LINE/L1 844 1222 (2072) m_b60s551i5 2237 chr2ptel1M 219922 ATAATATCCCCAAATTTCTGGGGTTGAGTTAAAGCAGTCCTCAGAGGGAG 219971 i i v v i v i vv i? v i i L1M4_orf2#LIN 844 ACAACATACCAAAACTTATGGGATGCAGCNAAAGCAGTGCTTAGAGGGAA 893 chr2ptel1M 219972 AAATATAGACTTACCAT-CATACATTAAGAGAAAAGAAAACGAGATTAAC 220020 vv viv v- - v i i i i -- vv i v L1M4_orf2#LIN 894 ATTTATAGCTGTAA-ATGCCTATATTAAAAAAGAAGAAA--GATCTCAAA 940 chr2ptel1M 220021 TGAATA---------TGCATTATAAAAAAATTAGAAAAATAAATG--AAC 220059 v --------- v iiv i -i v iv -- L1M4_orf2#LIN 941 TCAATAACCTAACCTTCCACCTTAAGAAA-CTAGAAAAAGAAGAGCAAAC 989 chr2ptel1M 220060 -AAATCCAAAATAAGTACAAAAGACAAGATATACAAAAGACAAGATAGTA 220108 - i ii -- i iv i v ----------- -- L1M4_orf2#LIN 990 TAAACCCAAAGCAAG--CAGAAGGAAGGAAATA-----------ATA--A 1024 chr2ptel1M 220109 AAATTAGAAGGAAAACAGATAAATTGGA-AATAAAAAA----TAAAAATG 220153 i iv i i i i v i - i ---- i i vi L1M4_orf2#LIN 1025 AGATTAGAGCGGAAATAAATGAAATAGAGAATAGAAAAACAATAGAGAAA 1074 chr2ptel1M 220154 ACAAACAGAACTAAAAATGGCTTCTTTGAAATGACTTATAAAGTGGAGAA 220203 iv ii i i v v v iiv i i v v L1M4_orf2#LIN 1075 ATCAACGAAACCAAAAGTTGGTTCTTTGAAAAGATCAACAAAATTGACAA 1124 chr2ptel1M 220204 ATGCCTTT-GCTAATCTGATCAAAAGGAAGAGAGCACAAAATCCAGTCAT 220252 -- - iv i i ii i viv i v v i i i L1M4_orf2#LIN 1125 A--CCTTTAGCTAGACTGACCAAGAAAAAAAGAGAGAAGACTCAAATTAC 1172 chr2ptel1M 220253 TGAAATAACAAATGGCAAAGGTGAAATTACAAGAAAACTAAAAGAAATAA 220302 i v vi iv i v v v vvi v v v L1M4_orf2#LIN 1173 TAAAATCAGGAATGAAAGAGGGGACATTACTACCGACCTTACAGAAATAA 1222 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.40 CpG sites = 60, Kimura (unadjusted) = 39.33 Transitions / transversions = 1.25 (60/48) Gap_init rate = 0.07 (28 / 380), avg. gap size = 1.43 (40 / 28) 284 24.73 3.12 3.12 chr2ptel1M 220582 220677 (779323) L1M1_orf2#LINE/L1 1623 1718 (1576) m_b60s551i6 2238 chr2ptel1M 220582 AATTTTAAACAAAGTCCTATCAAAACA---TCCACAATAAATTATCCAAG 220628 ii v i v v v i--- v v --- i L1M1_orf2#LIN 1623 AATCCTCAACAAAATACTAGCAAACCGAATTCAACAATACATTA---AAA 1669 chr2ptel1M 220629 AAACCATGCATTATAATTAAATGGGATTTTTACCAGGAATGGAAGGATG 220677 i i v i i ii i v v ? i v L1M1_orf2#LIN 1670 AGATCATTCATCATGACCAAGTGGGATTTATCCCNGGGATGCAAGGATG 1718 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 29.37 CpG sites = 13, Kimura (unadjusted) = 30.95 Transitions / transversions = 1.30 (13/10) Gap_init rate = 0.04 (4 / 95), avg. gap size = 1.50 (6 / 4) 375 24.63 3.10 5.56 chr2ptel1M 223139 223267 (776733) MIRb#SINE/MIR 143 268 (0) m_b61s601i0 2239 chr2ptel1M 223139 TAAAATAGGGATAATAATATCTACTTTCCAGGGTTTGTTATGAGGAC--- 223185 i i i iv - i i--- MIRb#SINE/MIR 143 TAAAATGGGGATAATAATACCTACCTCGCAGGG-TTGTTGTGAGGATTAA 191 chr2ptel1M 223186 ATGGGGTGCTTGTCCTGATAAGGTGCTTTAAACA-TGTCTGGCACTTAGT 223234 i i iv- - v - i i viv - i v MIRb#SINE/MIR 192 ATGAGATAA-TG-CATG-TAAAGCGCTTAGCACAGTGCCTGGCACATAGT 238 chr2ptel1M 223235 AGATGCCTTATAATAAATGCCAGGTTTCTTCTT 223267 iii i---i vi v i v v MIRb#SINE/MIR 239 AAGCGCT---CAATAAATGGTAGCTCTATTATT 268 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.23 CpG sites = 20, Kimura (unadjusted) = 30.84 Transitions / transversions = 2.00 (20/10) Gap_init rate = 0.07 (9 / 128), avg. gap size = 1.22 (11 / 9) 378 27.06 6.16 1.31 chr2ptel1M 226863 227008 (772992) L2b_3end#LINE/L2 313 465 (1) m_b61s601i1 2240 chr2ptel1M 226863 TTATTGT-TGATGTAT-TGTCTATCTACCCCACCAATCTGTGACCTCCAT 226910 ? - ? - i- i v i iv v i L2b_3end#LINE 313 TNATTGTCTGNT-TACATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGT 361 chr2ptel1M 226911 GAGAGGAAGGG--GTGTC--ACTTGCACCTCCTTTTGATCCTGGTGCTTA 226956 i v i i-- ? --v iv vi vi v ivi ii i i L2b_3end#LINE 362 GAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTGTATCCCCAGCGCCTA 411 chr2ptel1M 226957 GCCCAGGGCCTGGCATTTCCTGGGCACT---TAAATGTTTGATGACTTGA 227003 v ? ivivv i i --- i v v- L2b_3end#LINE 412 GCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTTGTTGAA-TGA 460 chr2ptel1M 227004 ATAAA 227008 i L2b_3end#LINE 461 ATGAA 465 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.39 CpG sites = 23, Kimura (unadjusted) = 35.73 Transitions / transversions = 1.44 (23/16) Gap_init rate = 0.05 (7 / 145), avg. gap size = 1.57 (11 / 7) 439 25.72 7.93 4.66 chr2ptel1M 227336 227751 (772249) C HERVK14C#LTR/ERVK (2326) 5108 4680 m_b61s701i0 2241 chr2ptel1M 227336 TGGCTTCCCCTTTCT----TTTGTTTTTGGAG--GAGCGTCTTAATGTCT 227379 i i i ---- v i-- -? i v - C HERVK14C#LTR/ 5108 TGGTTCCCCCCTTCTGTCTTTTGTTTTTGTAATTGAG-NTTTTAAGGT-T 5061 chr2ptel1M 227380 CAGTT-TCTCTTCTCTACTATTGCCTGTCCTTGAGGATTAAAGGGTATTC 227428 ii -v v - v v v i ? i v v ? C HERVK14C#LTR/ 5060 CGATTAGCTCGT-TCAACAATGGCTTGNCCTTGAGAATTATAGGGGATNC 5012 chr2ptel1M 227429 CAGTAGTGTGTAAAATCTTATAACG-TGCACAAAAGTGTGCAAAATGTTT 227477 ? vv v ?vi vi - v vi v i? ?i i-? C HERVK14C#LTR/ 5011 CAGTANTGTGTTTAATGTNCCATTGTTGAAGGAACGCNTNTAAAG-NTTT 4963 chr2ptel1M 227478 AGAAGGACATGCAGGTCCAATAACTGTTTTTATTTCTTGTGGCACACCCA 227527 vv ??ii vv v v v iv ? v ? i v ii C HERVK14C#LTR/ 4962 ACTANNGTAGCCTGGGCCATTGTCNGTTTTAATNTTTTGTGGAATGCCCA 4913 chr2ptel1M 227528 TAATTGCAAATGCTTGTATAAGGAATTCAGTG------ACCACTAGGA-C 227570 i i? i ------- i i i viv i ------ v v v - C HERVK14C#LTR/ 4912 TGACNGCGAA-------ACAGGAAAGCAAATGTCTTTTAACACGAGCAGC 4870 chr2ptel1M 227571 TGTCTCTTTTGCTGCTGGCA--TTGC-----AAAAGTGAATCCTGAAAAA 227613 ? i ?ii i -- -- ? -----v i ----- i C HERVK14C#LTR/ 4869 NGCCTCNCCTGTT--TGGCAAGTNGCCCANACAAAATGA-----GAAAAG 4827 chr2ptel1M 227614 GTGTCTACCACCACATGAATAAAAGACAGACAACCAAA-ATATTTATAAT 227662 i vii? i iiv ? ? vivv -i? vv i- C HERVK14C#LTR/ 4826 GTATCTACAGTNACATGGACGTANGANAGTTTCCCAAATGNAGGTAC-AT 4778 chr2ptel1M 227663 GGGTCACATCTATTTGCCAAATTTCATTGGGTCTCAAATCATGAAGGTT- 227711 ? i i ? viv? i ?vi vi vi ?i - C HERVK14C#LTR/ 4777 GGGTNACGTCCATTTGCCANAGCGNATTAGGNGCCAATCCTCGNGGGTTA 4728 chr2ptel1M 227712 -CT----TCCCTTGA---GGCAG-TGTAGGAGCATGGAAAGGAAGGCAA 227751 - ?---- --- - v - v v v?? i C HERVK14C#LTR/ 4727 ACNCCAGTCCCTTGATGTGGCAGTTGTAGCA-CCTGGCACNNAGGGCAA 4680 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 32.56 CpG sites = 53, Kimura (unadjusted) = 35.08 Transitions / transversions = 1.08 (53/49) Gap_init rate = 0.08 (34 / 415), avg. gap size = 1.56 (53 / 34) 1007 30.62 2.86 4.11 chr2ptel1M 228760 229597 (770403) C HERVK14C#LTR/ERVK (3762) 3672 2845 m_b61s701i1 2241 chr2ptel1M 228760 ATAGGTAGTGAAGCCTAACACTGGTCACATCCATTGGATTATCTCCTACC 228809 vi v viiv iv v vi - i vi C HERVK14C#LTR/ 3672 ATAGGTAGGAATGCCTAAAGTAGGTCGAATCCAATTAAT-ATCCCCTAAT 3624 chr2ptel1M 228810 AATTTCTGAAAGTCATTTATGGTGTTTAGTTTCTCTGTTCTTAAGGAAAG 228859 i i vi v i vvvv v vv vvvi v C HERVK14C#LTR/ 3623 AATTTTTGAAAATCATTTAAAGTTTTCAGAGAGTCTTTTCGAATTTGAAC 3574 chr2ptel1M 228860 TTTTTGTACTGTAAGCACCTTAGGGTATACTT-CATATCCTAAATATTGA 228908 i ?iviv vii i vvvv iv i - - i i C HERVK14C#LTR/ 3573 CTTTTGNGGCTTAATTGCCCTTTCCTGAACCTGCAT-TCCCAAATATTGG 3525 chr2ptel1M 228909 AAAGGTTCATGTCTTTGAATTTTTTTCTGGAGCTATGTGCAATTTGTATT 228958 vvi v?iv v - ? ? v? ------- C HERVK14C#LTR/ 3524 AAAGGAGTAGNCGTTTGAATTTTAT-CNGGNGCTATGANCAAT------- 3483 chr2ptel1M 228959 TCCTTAGTGTTT-TTATGGTCTTTTGTAGACATGCTTCTAACA------- 229000 - -- i iv-i? iv i i i ii v--v ------- C HERVK14C#LTR/ 3482 -CC--AGCGTCGGCNACCGCCTTCTGTAAATGTGA--ATAACACTGGATA 3438 chr2ptel1M 229001 --TTTGTTCCG-----CAGGTGCACAATCAATAGATTATCCATGTAATGC 229043 -- v ii ----- i vi ?-- vi i i - C HERVK14C#LTR/ 3437 AGTTGGTCTCGAGTTTCGGCCGCACAN--AATATGTCATCCATATAATG- 3391 chr2ptel1M 229044 AATAACAT-TACTTTTGGAAATGGTTTTCTTACTGGAATAAGAGCAGCAG 229092 i i -?ivv i iv v i ? v vvv v vv?vv C HERVK14C#LTR/ 3390 AATGATATANGAATCTGGAAACTGATCTCTNACAGGTTGAATAGCCTNCC 3341 chr2ptel1M 229093 CAACATACATTTGACACATAGTAGGGCTGTTTTTCATTCCCTGTGGCAAA 229142 v ? vi v ? ? i i ivv v i ? C HERVK14C#LTR/ 3340 CCACANAAGTTTGACAAATNGTNGGACTATTCAACATGCCCTGCGGCAAN 3291 chr2ptel1M 229143 ACTGTCCATTCATATCTTTTATAAGGCTCAGCTAA--GTTAACACTGGGC 229190 v v v ? vvivvv? i -- vi-- v i vii v C HERVK14C#LTR/ 3290 ACTTTCCAATGATANCTGGCTGCNGGTTC--CTTGTTGTTCATAGCAGGA 3243 chr2ptel1M 229191 ACTGAAAGGGCAAATCTTTTCATATCCTCCTTATCTAAAGGGATAGAATA 229240 iv v ii i iv v ?vv ivv i i v v C HERVK14C#LTR/ 3242 ATAGTAAAAGCAAATTTTTCAAAATCNGGCTCTGCTAGAGGAATAGTAAA 3193 chr2ptel1M 229241 GAAACAATTCTTAATGTCTATAACCCAAAGAGGCCATTTTCTAGGCAACT 229290 i i i v vi ivvv i? v i v v v C HERVK14C#LTR/ 3192 GAAGCAGTCCTTCAAATCTATAACTATTAANGGCCAGTCTCTAGGAATCA 3143 chr2ptel1M 229291 GAGTAGGAGATGGAAGTCCAGACTGAAGAGTTCCCATAGTTTCTATCTAT 229340 vi ii i ? v i v i v ? ii ? v v? vvv C HERVK14C#LTR/ 3142 TGGCGGGGGANGGCAGCCCTGGCTGCAGNGCCCCCATNGGTTGNATGACT 3093 chr2ptel1M 229341 TCATTTACCTTTTCTAAATCAGTCAACATCCTCCATTTTTCAGATTTCTT 229390 v v vvi iv i i i i ? v i vi i i C HERVK14C#LTR/ 3092 GCATTGACGGCTCGTAAGTCGGTTAGCATNCGCCATCTGCCGGATTTTTT 3043 chr2ptel1M 229391 TTTTACAACAAATACTGGGGAATTCCAAGGATTTAGAGAA----GGTTGT 229436 i ? iv i ? ? ---- i ---- i v? C HERVK14C#LTR/ 3042 CTTNATTACAAACACTGGNGAATTCCANGGA----GAAAATGTGGGCTCN 2997 chr2ptel1M 229437 AAGTGTCCTTGGTCAAGTTGCTCCTGCACTATATCTAATAAAGCCTGAAT 229486 v v? v i i i vv vv ivi i ivv v C HERVK14C#LTR/ 2996 ATGTGTCCTTTNTCTAATTGTTCTTTGACTAATTCCTGTAAGGCCCCCAG 2947 chr2ptel1M 229487 TTTATTACTACCTAAG-GGCCACTGTTTTACCCACACTGGTGTATTAGTT 229535 - v ivv?? - ? i? v ? ?v v vi i C HERVK14C#LTR/ 2946 TTT-TTCCTGAGNNAGCGGCCACTGNTCNACCCAAACNGGNTTTTGGGTC 2898 chr2ptel1M 229536 TTCCATTGGATAGGAACAGGTGAAAATGTTGCCAGGCCTTCAACAGCAGC 229585 ? vv vi i -----? v v -- -- ii C HERVK14C#LTR/ 2897 NTCCATTTTAAGGGAATAGG-----NTCTGG--AGGC--TCAACAGTGGC 2857 chr2ptel1M 229586 CCTGCCTAAAAA 229597 viv C HERVK14C#LTR/ 2856 CGCCCCTAAAAA 2845 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.71 CpG sites = 111, Kimura (unadjusted) = 42.09 Transitions / transversions = 0.82 (111/135) Gap_init rate = 0.05 (42 / 837), avg. gap size = 1.38 (58 / 42) 355 30.82 3.89 1.52 chr2ptel1M 231524 231780 (768220) C L1M3_orf2#LINE/L1 (625) 2663 2401 m_b61s551i0 2242 chr2ptel1M 231524 CAGTACCAAATGGTTTTGATGACCAC-TCTTTTTAATATACTTTTAAGTC 231572 v iv v iii-v v i v i C L1M3_orf2#LIN 2663 CAGTACCATACTGTTTTGATTACTGTAGCTTTGTAATATATTTTGAAATC 2614 chr2ptel1M 231573 TGGCACAACTAGGTCAACTTCA--TTTGCATTTTTTTCATTAA--TCCCC 231618 v --- v iv viiv i -- ivi i - i -- iv i C L1M3_orf2#LIN 2613 AGG---AAGTGTGATGCCTCCAGCTTTGTTCTTCTTTC-TCAAGATTGCT 2568 chr2ptel1M 231619 TTGAA-ATGCTTGACCTTTTGTTCTTCCAAATGAACTTTA---TTATTTT 231664 iv- v vv ii vv v i --- i C L1M3_orf2#LIN 2567 TTGGCTATTCGGGGTCTTTTGTGGTTCCATATGAATTTTAGGATTGTTTT 2518 chr2ptel1M 231665 T-CTAGTTCTGTAAAATAAATTTTTGGGAGTTTGATTGGTGTGGCACTGA 231713 - v v viiiv v v vi v i C L1M3_orf2#LIN 2517 TTCTATTTCTGTAAAAAATGCCATTGGGATTTTGATAGGGATTGCATTGA 2468 chr2ptel1M 231714 ATAAGTAGATTAACTTAAATAATATTGTCATTTTTATTATATTCGCTCAA 231763 vv iivi iii i v v v iv vii vv C L1M3_orf2#LIN 2467 ATCTGTAGATCGCTTTGGGTAGTATGGACATTTTAACAATATTAATTCTT 2418 chr2ptel1M 231764 CTAACCCACGAACACAG 231780 i i i i C L1M3_orf2#LIN 2417 CCAATCCATGAACACGG 2401 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.95 CpG sites = 40, Kimura (unadjusted) = 40.34 Transitions / transversions = 1.05 (40/38) Gap_init rate = 0.04 (10 / 256), avg. gap size = 1.40 (14 / 10) 848 27.49 1.78 1.78 chr2ptel1M 231787 232123 (767877) C L1ME3Cz_3end#LINE/L1 (654) 343 7 m_b61s551i1 2243 chr2ptel1M 231787 AACTTTTTGAGCATAGTTCCAAATTGCTCTCCAGAATGGTTGGATGTATT 231836 viv - v v i i v ivv C L1ME3Cz_3end# 343 AACTTTACTAG-ATATTGCCAAATTGCTCTCCAAAGTGGTTGTACCAATT 295 chr2ptel1M 231837 CACAATTCCATCAACAATGTATTAGTGTCCTTGTTTTCCCACATCCCCTC 231886 i v i i i i v v i ii ii i v C L1ME3Cz_3end# 294 TACACTCCCACCAGCAGTGTATGAGAGTTCCCGTTTCTCCACATCCTCGC 245 chr2ptel1M 231887 CAACATTCCCCATTATCTTTCCCTGTCATTCTAATCAGTCTGACAGGTGT 231936 i ivvi i vvv ii vvv i vii i ii C L1ME3Cz_3end# 244 CAACACTTGGTATTGTCAGACTTTTAAATTTTTGCCAATCTGATGGGTGT 195 chr2ptel1M 231937 GTAGTGGTATCTCAGAGTTGTCTTAATTTGCATTTCTCTGATTAATAATG 231986 v i vv ? i i v i C L1ME3Cz_3end# 194 GAAATGGTATCTCATTGTNGTTTTAATTTGCATTTCCCTGATTACTAGTG 145 chr2ptel1M 231987 ACTAGGATCATCTTTTCATATGTCTAAAAATAGTTTCAATTTCTTCATCT 232036 vvvv v i vviiivi ivii i v C L1ME3Cz_3end# 144 AGGTTGAGCATCTTTTCATATGTTTATTGGCCATTCGGGTTTCCTCTTCT 95 chr2ptel1M 232037 GAGAATTGTCTGTTCAGATCCTTTGACC-TTTATCAATTCGGAAAATGGA 232085 v i v v - v v v ---v vv C L1ME3Cz_3end# 94 GTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGGG---TTGTC 48 chr2ptel1M 232086 TTGATTGCTTATAGAGTC-----AATTCTATATATATTTTGGA 232123 -- v v v i----- i v i C L1ME3Cz_3end# 47 TT--TTTCTTATTGATTTGTAGGAGTTCTTTATATATTCTGGA 7 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 33.77 CpG sites = 44, Kimura (unadjusted) = 34.69 Transitions / transversions = 0.94 (44/47) Gap_init rate = 0.02 (8 / 336), avg. gap size = 1.50 (12 / 8) 894 27.47 0.37 0.00 chr2ptel1M 231805 232077 (767923) C L1ME5_3end#LINE/L1 (611) 330 57 m_b61s551i2 2243 chr2ptel1M 231805 CCAAATTGCTCTCCAGAATGGTTGGATGTATTCACAATTCCATCAACAAT 231854 i i v ivvi ii v i i i i C L1ME5_3end#LI 330 CCAGATTGCTCTCCAGAATGGCTGCACCAGTCTACACTCCCACCAGCAGT 281 chr2ptel1M 231855 GTATTAGTGTCCTTGTTTTCCCACATCCCCTCCAACATTCCCCATTATCT 231904 i v v i i i ? i i v i ivv i C L1ME5_3end#LI 280 GCATGAGGGTTCCTATNTCCCCACATCCTCGCCAACACTTGGCATTATCC 231 chr2ptel1M 231905 TTCCCTGTCATTCTAATCAGTCTGACAGGTGTGTAGTGGTATCTCAGAGT 231954 vv ii v v i vii i i iv i vv C L1ME5_3end#LI 230 AGCTTTCTAATTTTTGCCAGTCTAATAGGTGTAAAGTGATATCTCATTGT 181 chr2ptel1M 231955 TGTCTTAATTTGCATTTCTCTGATTAATAATGACTAGGATCATCTTTTCA 232004 i v v vv v i C L1ME5_3end#LI 180 TGTTTTAATTTGCATTTCTCTGATTACTAATGAGTTTGAGCATCTCTTCA 131 chr2ptel1M 232005 TATGTCTAAAAATAGTTTCAATTTCTTCATCTGAGAATTGTCTGTTCAGA 232054 ii ivv iivv ivii i v vi i v C L1ME5_3end#LI 130 TATGCTTGTTAGCCTTTCGGGTTTCCTCTTCTGTAAATTGCCTGTTCATA 81 chr2ptel1M 232055 TCCTTTGACC-TTTATCAATTCGG 232077 v - v v v C L1ME5_3end#LI 80 TCCTTTGCCCATTTTTCTATTGGG 57 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.42 CpG sites = 41, Kimura (unadjusted) = 34.99 Transitions / transversions = 1.21 (41/34) Gap_init rate = 0.00 (1 / 272), avg. gap size = 1.00 (1 / 1) 440 31.27 4.88 3.82 chr2ptel1M 231992 232483 (767517) C L1M5_orf2#LINE/L1 (7) 3287 2791 m_b61s551i3 2243 chr2ptel1M 231992 GATCATCTTTTCATATGTCTAAAAATAGTTTCAATTTCTTCATCTGAGAA 232041 v i ii vviiivi v? v v i v C L1M5_orf2#LIN 3287 GAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTTTTGTGAA 3238 chr2ptel1M 232042 TTGTCTGTTCAGATCCTTTGACC-TTTATCAATTCGGAAAATGGATTGAT 232090 v ii i v - v ?v -------- i v C L1M5_orf2#LIN 3237 GTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATT--------GGGTTGTT 3196 chr2ptel1M 232091 TG-------CTTATAGAGTC-----AATTCTATATATATTTTGGAAATGA 232128 -------? v ? i----- i v i v i C L1M5_orf2#LIN 3195 TGTCTTTTTNTTATTGANTTGTAGGAGTTCTTTATATATTCTGGATACGA 3146 chr2ptel1M 232129 GGCCTTTATCAGA-ACCTTTGACTGTAAAAATATTTTCCCAGTTTATTGC 232177 v i - iv v ?-i i v v i ? i i v C L1M5_orf2#LIN 3145 GTCCTTTGTCAGATATATGTN-TTGCAAATATTTTCTCCCANTCTGTGGC 3097 chr2ptel1M 232178 TTCCCTTCTAATTTTGTCTGCATTAGTTTTGTTTGTACAAAAACTTTTCA 232227 v i v v ivi iv ivi vvv? vi i ii v C L1M5_orf2#LIN 3096 TTGCCTTTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTTTAA 3047 chr2ptel1M 232228 GTTTGGTATAATCAAA-------ATTTTCTATTTTGTGACCAGTAATGAT 232270 v i i? i v ------- i v i ii--- ?i v C L1M5_orf2#LIN 3046 TTTTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGGT---TNGTGCT 3000 chr2ptel1M 232271 TTCTAGTTCTTCTTTGGTCATAAATTCCTTCCTCTTCCACAGGTCTGAGA 232320 i ivv i v i--- v iii v v?i - vvii C L1M5_orf2#LIN 2999 TTTTGTGTCCTGTTTA---AGAAATCTTTGCCTANCCCA-AGGTCACGAA 2954 chr2ptel1M 232321 GGTAAACTATCCTGTGTT--CTTCTAATTTATTTATAATCTCATTCTTTA 232368 i --i v i -- ivvvv i i i ?ii C L1M5_orf2#LIN 2953 GATA--TTCTCCTATGTTTTCTTCTAGAAGTTTTATAGTTTTANCTTTTA 2906 chr2ptel1M 232369 TGCCTAGGTC-ATGAACCCATTTTGACCTTATCTTGGTGTACGGTGTTAA 232417 iiii - - i i ? vi v i v i v i C L1M5_orf2#LIN 2905 CATTTAGGTCTATG-ATCCATCTNGAATTAATTTTTGTGTATGGTGTGAG 2857 chr2ptel1M 232418 GTGTGGATCAATGCCTGGTTTCTGCCATATTAGTTTCCAATTTTCCCAGC 232467 iv i i v?iiiiv i v vii v v i C L1M5_orf2#LIN 2856 GTAGGGGTCGAGNTTCATTTTTTTCCATATGGATATCCAATTGTTCCAGC 2807 chr2ptel1M 232468 AATTTTTGTCAAACAG 232483 viv ii v C L1M5_orf2#LIN 2806 ACCATTTGTTGAAAAG 2791 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.69 CpG sites = 84, Kimura (unadjusted) = 43.25 Transitions / transversions = 1.31 (84/64) Gap_init rate = 0.05 (26 / 491), avg. gap size = 1.65 (43 / 26) 1699 32.50 4.93 2.04 chr2ptel1M 232510 234274 (765726) C L1M4_orf2#LINE/L1 (867) 2427 613 m_b61s551i5 2243 chr2ptel1M 232510 TTTTGTAACCCACGAACACTTAATATTTTTCCAATTGATTAGATCTGATT 232559 i vi i i ivvi i i v iv i vv C L1M4_orf2#LIN 2427 TCTTCCAATCCATGAACATGGGATGTCTTTCCATTTATTTAGGTCTTCTT 2378 chr2ptel1M 232560 TTATTTGTGTGGAAAATGTTTTGTAATTGTGTTCA---TATAGTTGTTG- 232605 v v v vi v i --- --- i iv v - C L1M4_orf2#LIN 2377 TAATTTCTTTCAACAATGTTTTGTAGTT---TTCAGTGTACAAGTCTTGC 2331 chr2ptel1M 232606 ACTTTACCTTGGCAGGTAGGATCCCAAATATTTTAT-------------A 232642 i-ii vi ii vviv i i ------------- C L1M4_orf2#LIN 2330 ACTTC-TTTTGTTAAATTTATTCCTAAGTATTTTATTCTTTTTGATGCTA 2282 chr2ptel1M 232643 TT-----TGCAATT--TATATTCATATC-TCTTCATATTGAACTTTGTTG 232684 ----- v -- v v v v - i iv --- ii C L1M4_orf2#LIN 2281 TTGTAAATGGAATTGTTTTCTTAATTTCATTTTCGGATTG---TTCATTG 2235 chr2ptel1M 232685 GAAATATATAAAAATGCTGATGATTTCTGTGGATTTATTTTGTATCCTGC 232734 vv i i i i viv i iv v i C L1M4_orf2#LIN 2234 CTAGTGTATAGAAATACAATTGATTTTTGTATATTGATCTTGTATCCTGC 2185 chr2ptel1M 232735 AACTTTGATAAAGTTGTGAATTGTTTCTATTAGTTTTTCTATTGAATCTC 232784 i v i v i vv iv v i?i v v ii C L1M4_orf2#LIN 2184 AACCTTGCTGAACTCGTTTATTAGTTCTAATAGTTTTTTNGTGGATTCCT 2135 chr2ptel1M 232785 CAGGGTTCTCTAAGTATACCATCATATCATCTTCAGATAGTGACAACATG 232834 i i i vi i vv i v ii v i iiv v C L1M4_orf2#LIN 2134 TAGGATTTTCTATATACAAGATCATGTCATCTGCGAATAGAGATAGTTTT 2085 chr2ptel1M 232835 GTTTCCTCATTACCTCC--TCTG-ATTTCTTTAATCTTCTTTTCCTTTGT 232881 ii i v --- -- - vi v - i vvi C L1M4_orf2#LIN 2084 ACTTCTTCCTT---TCCAATCTGGATGCCTTTTAT-TTCTTTTTCTTGCC 2039 chr2ptel1M 232882 TA-TTGCTAAAGCTAATATTTCTAATACAATATTGAACAGTATTGGTGGT 232930 - ivvi iv ii i i i i v v i iv C L1M4_orf2#LIN 2038 TAATTGCCCTGGCTAGAACCTCCAGTACAATGTTGAATAGAAGTGGCGAG 1989 chr2ptel1M 232931 AGCAGACAATCTTGTTGCTT-TCCCTGATCTTATTGGAAATG-GTTCTAT 232978 i vi -- - i vv i v -? vi C L1M4_orf2#LIN 1988 AGCGGACATCCTTGT--CTTGTTCCTGATCTTAGGGGGAAAGCNTTCAGT 1941 chr2ptel1M 232979 TTATCCCCATTACATATGATGCTTGCTGACTGTTTTAAATAGATACTATT 233028 i v v vi i v vvv vvi i iv C L1M4_orf2#LIN 1940 CTTTCACCATTAAGTATGATGTTAGCTGTGGGTTTTTCGTAGATGCCCTT 1891 chr2ptel1M 233029 GATCATTTTAAGGAAAACTCCATTTAGTCTTATAGTCTCT--AGTATTTT 233076 v vv i ivii v i v i -- i v -- i C L1M4_orf2#LIN 1890 TATCAGGTTGAGGAAGTTCCCTTCTATTCCTA--GTTTGTTGAGTGTTTT 1843 chr2ptel1M 233077 TAATAGTAATGGGTGTTGGATTTTGTCAAATGC-CTTTCTGTATCTATTG 233125 vi vv v -i ii C L1M4_orf2#LIN 1842 TATCATGAAAGGGTGTTGGATTTTGTCAAATGCTTTTTCTGCGTCTATTG 1793 chr2ptel1M 233126 AGATCATTATATAACTTTCATTAGCTTGG--CTATTGATAAAATCAAGTA 233173 v i i iii ii i-- vi-- i vii vv v C L1M4_orf2#LIN 1792 AGATGATCATGTGGTTTTTGTC--CTTTATTCTATTAATATGGTGTATTA 1745 chr2ptel1M 233174 TGCTAACAGTTTTCTTAAGATTGAACCAGCCCTGCATTTCTGGTATATAT 233223 iii i iv v iiv? vi i i i v v C L1M4_orf2#LIN 1744 CATTGATTGATTTTCGNATGTTGAACCAACCTTGCATTCCTGGGATAAAT 1695 chr2ptel1M 233224 CCTGCTTGGTCATGGTGTATTTTCCTGGACATGACATT-CAGTAATCTCT 233272 ii vv vvvi - ii - v v v vv C L1M4_orf2#LIN 1694 CCCACTTGGTCATGGTGTATAATCCTTTTTAT-ATGTTGCTGGATTCGGT 1646 chr2ptel1M 233273 TTGCTAATATTTTATGTAAGATTTTTACATCAATATTCATTAGGGAAATT 233322 i i vv i i v v v C L1M4_orf2#LIN 1645 TTGCTAGTATTTTGTTGAGGATTTTTGCATCTATATTCATAAGGGATATT 1596 chr2ptel1M 233323 GATCTATAATTTTCTTCCTCTGT--TTTCATCCTACCTGATTTAGGTATC 233370 i i i iiii -- v v -- ii i v C L1M4_orf2#LIN 1595 GGTCTGTAGTTTTCTTTTCTTGTGATGTCTT--TGTCTGGTTTTGGTATC 1548 chr2ptel1M 233371 AGCTCTATAGCTGTGTCATAAAAGGAATTTGGTAGGACTTCTTAACGTTT 233420 vviv viv iv i v i v v vii i i vviv i C L1M4_orf2#LIN 1547 AGGGTAATACTGGCCTCATAGAATGAGTTGGGAAGTGTTCCCTCCTCTTC 1498 chr2ptel1M 233421 --TTTTTTCAGATAGTTTGCATAATATTGCAGTAAATTGTTCTTTAAATG 233468 -- vii v iiv iv vv v v C L1M4_orf2#LIN 1497 TATTTTTTGGAAGAGTTTGTGAAGGATTGGTGTTAATTCTTCTTTAAATG 1448 chr2ptel1M 233469 TTTGATAGAATTCACGTGCAAATCTATCTGGTCCTGGAGATTTTTTCTTA 233518 i vv ii v i ? ivv i iv i C L1M4_orf2#LIN 1447 TTTGGTAGAATTCACCAGTGAAGCCATCTGGNCCTGGGCTTTTCTTTGTG 1398 chr2ptel1M 233519 CAGAGATGGTTAATAGTTTGTTTTATTTCTTTTTCTAAAATGGGACTATT 233568 vii v vv i vii vi iv i vii ivv i v C L1M4_orf2#LIN 1397 GGAAGTTTTTTGATTACTAATTCAATCTCTTTACTTGTTATAGGTCTATT 1348 chr2ptel1M 233569 TAAGTAATTGATTTCCTTTTTTGTTAATCTGGGCAAACTATATTTTTTGT 233618 i ii vv iv i i vv i i i v i ivi i i i i- C L1M4_orf2#LIN 1347 CAGATTTTCTATTTCTTCTTGAGTCAGTTTCGGTAGTTTGTGTCTTTC-T 1299 chr2ptel1M 233619 AGGTATTCCTCCATTTTACTTAGATTAACAAACTTATTGGCATAC--TTG 233666 v iv i ii i v v i i -- C L1M4_orf2#LIN 1298 AGGAATTTGTCCATTTCATCTAGGTTATCTAATTTGTTGGCATACAATTG 1249 chr2ptel1M 233667 ATCAAAAAAACTCCTAATTATGGCTCTGATTTCC------TC-------- 233702 v v iv vii v v vvi i v i------ -------- C L1M4_orf2#LIN 1248 TTCATAGTATTCCCTTATAATCCTTTTTATTTCTGTAAGGTCGGTAGTAA 1199 chr2ptel1M 233703 TTTTTCCCTTTTCAGCTTTAAGAATAACAATTTGAATTTCTTCTTTCATT 233752 v ii ii viii i vvv ii i i ii i iv C L1M4_orf2#LIN 1198 TGTCCCCTCTTTCATTCCTGATTTTAGTAATTTGAGTCTTCTCTCTTTTT 1149 chr2ptel1M 233753 TTTCTAATCA----AACTAACAGTTTATTTATCATGTAGGTATTTTAATA 233798 ii ii ---- i vi i iv iv v i v v v C L1M4_orf2#LIN 1148 TTCTTGGTCAGTCTAGCTAAAGGTTTGTCAATTTTGTTGATCTTTTCAAA 1099 chr2ptel1M 233799 AGAC--ACTCTTAGTTTTATTTATTAATTCAATAATTTTCTTACTTTCAA 233846 ii -- i i ii v vvi v vi ii i i v C L1M4_orf2#LIN 1098 GAACCAACTTTTGGTTTCGTTGATTTTCTCTATTGTTTTTCTATTCTCTA 1049 chr2ptel1M 233847 TTTTGTTAATCTCTCCTTCTTTTTTCAGTAATTCAAATTTGGTATTTAAT 233896 ii v i iv iivv i i v v vvvii vv ii iv C L1M4_orf2#LIN 1048 TTTCATTTATTTCCGCTCTAATCTTTATTATTTCCTTCCTTCTGCTTGCT 999 chr2ptel1M 233897 TGGGGGTTTTTAATTTG---TTTTGTTTCTAGTTTTTTTAGTTAC-AGGC 233942 v --- i --- i v i v v iv- i C L1M4_orf2#LIN 998 TTGGG---TTTAGTTTGCTCTTCTTTTTCTAGTTTCTTAAGGTGGAAGGT 952 chr2ptel1M 233943 CA-GTCATTAATCTTCACTTTCTCTATTTTGTTCATGTGGGCATCTAGAT 233991 i - i i i vviv i i vi v v i i i v v C L1M4_orf2#LIN 951 TAGGTTATTGATTTGAGATCTTTCTTCTTTTTTAATATAGGCATTTACAG 902 chr2ptel1M 233992 GTATAAAATTTCCTCTAATAACCACTTTGATTGCATTCCACAAATTTTGG 234041 v v i vv ii ?ii i i i C L1M4_orf2#LIN 901 CTATAAATTTCCCTCTAAGCACTGCTTTNGCTGCATCCCATAAGTTTTGG 852 chr2ptel1M 234042 TATGTTGTCTCCTTATTGTTATTC-TCTCGGATGAAATTATTGTGT---- 234086 v ii ii v i - ----- v v v ---- C L1M4_orf2#LIN 851 TATGTTGTGTTTTCGTTTTCATTCATCTC-----AAAGTATTTTCTAATT 807 chr2ptel1M 234087 ----CTATGATTTGTTGTTTTACCCACTCAATCTTTAGGATTAGATTACT 234132 ----i i v v v i viv v v ivi ii C L1M4_orf2#LIN 806 TCCCTTGTGATTTCTTCTTTGACCCATTGGTTATTTAGGAGTGTGTTGTT 757 chr2ptel1M 234133 TACTTTTCAATTAATTTTTTATCTC-----TTTTCCACTGGCCTTTATTG 234177 v i vv v v vv i ----- i iv ---- C L1M4_orf2#LIN 756 TAATTTCCACATATTTGTGAATTTCCCAAATTTCCTTCTG----TTATTG 711 chr2ptel1M 234178 TATGCAATTTTTATTGCATCATGCTCTGAGAAAAATGCATTCAAT-ATTT 234226 vv v v v i v ii v v - v i v vv - C L1M4_orf2#LIN 710 ATTTCTAATTTCATTCCATTGTGGTCGGAG-AACATACTTTGTATGATTT 662 chr2ptel1M 234227 TTGCCTTTCTGCATTTGATTTTGAA----GTTTTATGTTCTACTATATGG 234272 ivii i i iv i--- i---- vi vi C L1M4_orf2#LIN 661 CAATCCTTTTAAATTTA---TTGAGACTTGTTTTATGGCCTAACATATGG 615 chr2ptel1M 234273 TC 234274 C L1M4_orf2#LIN 614 TC 613 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 42.69 CpG sites = 307, Kimura (unadjusted) = 43.87 Transitions / transversions = 1.20 (307/255) Gap_init rate = 0.04 (68 / 1764), avg. gap size = 1.82 (124 / 68) 2054 30.58 4.50 1.62 chr2ptel1M 232510 234065 (765935) C L1M5_orf2#LINE/L1 (867) 2427 828 m_b61s551i4 2243 chr2ptel1M 232510 TTTTGTAACCCACGAACACTTAATATTTTTCCAATTGATTAGATCTGATT 232559 i vi i i ivvv i i v iv i vv C L1M5_orf2#LIN 2427 TCTTCCAATCCATGAACATGGTATATCTCTCCATTTATTTAGGTCTTCTT 2378 chr2ptel1M 232560 TTATTTGTGTGGAAAATGTTTTGTAATTGTGTTCA---TATAGTTGTTGA 232606 v v v viiv i --- --- ? v v v C L1M5_orf2#LIN 2377 TAATTTCTCTCAGCAATGTTTTGTAGTT---TTCAGTGTANAGGTCTTGC 2331 chr2ptel1M 232607 CTTTACCTTGGCAGGTAGGATCCCAAATATTTTATATTT------GCAAT 232650 viv ?ii vi i vviv i i ? i ------ v C L1M5_orf2#LIN 2330 ACATNTTTTGTTAGATTTATTCCTAAGTATTTNATGTTTTTTGATGCTAT 2281 chr2ptel1M 232651 T-TA-----TATT------CATATCTC---TTCATATTGAACTTTGTTGG 232685 - ----- ------? v i --- vv --- v C L1M5_orf2#LIN 2280 TGTAAATGGTATTGTTTTTNAAATTTCATTTTCCAATTG---TTTGTTGC 2234 chr2ptel1M 232686 AAATATATAAAAATGCTGATGATTTCTGTGGATTTATTTTGTATCCTGCA 232735 v i i i viv i iv v ii ? i C L1M5_orf2#LIN 2233 TAGTATATAGAAATACAATTGATTTTTGTATATTGACCTTGTATCCNGCG 2184 chr2ptel1M 232736 ACTTTGATAAAGTTGTGAATTGTTTCTATTAGTTTTTCTATTGAATCTCC 232785 i v v iiivv iv v ? i i v v ii C L1M5_orf2#LIN 2183 ACCTTGCTAAATTCACTTATTAGTTCTAGTAGTTTNTTTGTAGATTCTTT 2134 chr2ptel1M 232786 AGGGTTCTCTAAGTATACCATCATATCATCTTCAGATAGTGACAACATGG 232835 ? i i v ? v i v ii i? iiv vi C L1M5_orf2#LIN 2133 NGGATTTTCTACGTANACAATCATGTCATCTGCGAATAANGACAGTTTTA 2084 chr2ptel1M 232836 TTTCCTCATTACCTCCTCTGATTTCTTTAATCTTCTTTTCCTTTGTTATT 232885 i v v vviii v vi v i ii i viv C L1M5_orf2#LIN 2083 TTTCTTCCTTTCCAATCTTTATGCCTTTTATTTCTTTTTCTTGCCTTATT 2034 chr2ptel1M 232886 GCTAAAGCTAATATTTCTAATACAATATTGAACAGTATTGGTGGTAGCAG 232935 vvvi iv ii i i i i v v i? i C L1M5_orf2#LIN 2033 GCACTGGCTAGGACCTCCAGTACAATGTTGAATAGAAGTGGTGANAGCGG 1984 chr2ptel1M 232936 ACAATCTTGTTGCTT-TCCCTGATCTTATTGGAAATG-GTTCTATTTATC 232983 vi -- - i i vv i v -? vi ? v C L1M5_orf2#LIN 1983 ACATCCTTGT--CTTGTTCCCGATCTTAGGGGGAAAGCNTTCAGTNTTTC 1936 chr2ptel1M 232984 CCCATTACATATGATGCTTGCTGACTGTTTTAAATAGATACTATTGATCA 233033 v vi i ? vvv vvi i iv v C L1M5_orf2#LIN 1935 ACCATTAAGTATGATGTTNGCTGTAGGTTTTTCGTAGATGCCCTTTATCA 1886 chr2ptel1M 233034 TTTTAAGGAAAACTCCATTTAGTCTTATAGTCT-CT-AGTATTTTTAATA 233081 vv i ivii v i v i -- i - - vi vi C L1M5_orf2#LIN 1885 GGTTGAGGAAGTTCCCTTCTATTCCTA--GTTTGCTGAGAGTTTTTATCA 1838 chr2ptel1M 233082 GTAATGGGTGTTGGATTTTGTCAAATGC-CTTTCTGTATCTATTGAGATC 233130 vv i -i i v C L1M5_orf2#LIN 1837 TGAATGGGTGTTGAATTTTGTCAAATGCTTTTTCTGCATCTATTGAGATG 1788 chr2ptel1M 233131 ATTATATAACTTT----CATTAGCTTGGCTATTGATAAAATCAAGTATGC 233176 i i i ---- v -- -- i i vii v v iii C L1M5_orf2#LIN 1787 ATCATATGATTTTTCTCCTTTA--TT--CTGTTAATATGGTGAATTACAT 1742 chr2ptel1M 233177 TAACAGTTTTCTTAAGATTGAACCAGCCCTGCATTTCTGGTATATATCCT 233226 i iv v iiv vi i i i i v v i i C L1M5_orf2#LIN 1741 TGATTGATTTTCGAATGTTAAACCAACCTTGCATTCCTGGGATAAACCCC 1692 chr2ptel1M 233227 GCTTGGTCATGGTGTATTTTCCTGGACATGACATT-CAGTAATCTCTTTG 233275 i i v vvvi - i - v v v vv C L1M5_orf2#LIN 1691 ACTTGGTCATGATGTATTATCCTTTTTAT-ATATTGCTGGATTCGATTTG 1643 chr2ptel1M 233276 CTAATATTTTATGTAAGATTTTTACATCAATATTCATTAGGGAAATTGAT 233325 i v? i i v i v v i C L1M5_orf2#LIN 1642 CTAATATTTTGTTNAGGATTTTTGCATCTATGTTCATGAGGGATATTGGT 1593 chr2ptel1M 233326 CTATAATTTTCTTCCTCTGT--TTTCATCCTACCTGATTTAGGTATCAGC 233373 i iiii -- v v -- ii ? i v v C L1M5_orf2#LIN 1592 CTGTAATTTTCTTTTCTTGTAATGTCTT--TGTCNGGTTTTGGTATCAGG 1545 chr2ptel1M 233374 TCTATAGCT-GTGTCATAAAAGGAATTTGGTAGGACTTCTTAACGTTTTT 233422 vi? - - iv v i v v vii i i -- v i C L1M5_orf2#LIN 1544 GTNAT-GCTGGCCTCATAAAATGAGTTGGGAAGTGTTCCCT--CTTTTTC 1498 chr2ptel1M 233423 --TTTTCAG--ATAGTTTGCATAATATTGCAGTA--AATTGTTCTTTAAA 233466 -- v -- v ii v -- -- v v i C L1M5_orf2#LIN 1497 TATTTTCTGGAAGAGTTTGTGTAAGATTG--GTATTATTTCTTCCTTAAA 1450 chr2ptel1M 233467 TGTTTGATAGAATTCACGTGCAAATCTATCTGGTCCTGGAGATTTTTTCT 233516 i vv ii v i v v i iv C L1M5_orf2#LIN 1449 TGTTTGGTAGAATTCACCAGTGAAGCCATCTGGGCCTGGAGTTTTCTTTG 1400 chr2ptel1M 233517 TACAGAGATGGTTAATAGTTTGTTTTATTTCTTTTTCTAAAATGGGACTA 233566 ivii i vv viivvi iv vvivi v i i C L1M5_orf2#LIN 1399 TGGGAAGGTTTTTAATTACAAATTCAATTTCTTTAATAGATATAGGGCTA 1350 chr2ptel1M 233567 TTTAAGTAATTGATTTCCTTTTTTGTTAATCTGGGCAAACTATATTTTTT 233616 i ii vv iv i i v? i i i v i ?i i i i C L1M5_orf2#LIN 1349 TTCAGATTTTCTATTTCTTCTTGNGTCAGTTTTGGTAANTTGTGTTTTTC 1300 chr2ptel1M 233617 GTAGGTATTCCTCCATTTTACTTAGATTAACAAACTTATTGGCAT--ACT 233664 i- v iv i ii ii ?v i -- v C L1M5_orf2#LIN 1299 A-AGGAATTTGTCCATTTCATCTAAGTTNTCAAATTTATTGGCATAAAGT 1251 chr2ptel1M 233665 TGATCAAAAAAACTCCTAATTATGGCTCTGATTTCC------TC------ 233702 v v v viii v vvi i i v i------ ------ C L1M5_orf2#LIN 1250 TGTTCATAATATTCTCTTATTATCCTTTTAATGTCTGTAGGATCTGTAGT 1201 chr2ptel1M 233703 --TTTTTCCCTTTTCAGCTTTAAGAATAACAATTTGAATTTCTTCTTTCA 233750 -- v i i viii i v v iii vi i ii i iv C L1M5_orf2#LIN 1200 GATGTCTCCTTTTTCATTCCTGATATTGGTAATTTGTGTCTTCTCTCTTT 1151 chr2ptel1M 233751 TTTTTCTAATCA----AACTAACAGTTTATTTATCATGTAGGTATTTTAA 233796 ii i ----?i ivi iv iv i v i v v C L1M5_orf2#LIN 1150 TTTTCTTGATCAGTCTNGCTAGAGGTTTATCAATTTTATTGATCTTTTCA 1101 chr2ptel1M 233797 TAAGAC--ACTCTTAGTTTTATTTATTAATTCAATAATTTTCTTACTTTC 233844 v ii --i i i i ii v vvi v vi ? ?i ii C L1M5_orf2#LIN 1100 AAGAACCAGCTTTTGGCTTCGTTGATTTTCTCTATTGTNTNTTTGTTTTC 1051 chr2ptel1M 233845 AATTTTGTTAATCTCTCCTTCTTTTTTCAGTAATTCAAATTTGGTATTTA 233894 v ii i i v ii v i i v v vvvii vv i ? C L1M5_orf2#LIN 1050 TATTTCATTGATTTCTGCTCTTATCTTTATTATTTCCTTCCTTCTACTTN 1001 chr2ptel1M 233895 ATTGGGGGTTTTTAATTTG---TTTTGTTTCTAGTTTTTTTAGTTACAGG 233941 v v --- --- i v i i v v iv i C L1M5_orf2#LIN 1000 CTTTGGG---TTTAATTTGCTCTTCTTTTTCTAGCTTCTTAAGGTGGAAG 954 chr2ptel1M 233942 C-CAG-TCATTAATCTTCACTTTCTCTATTTTGTTCATGTGGGCATCTAG 233989 -i - i i v vii i vi vi v i i? i i C L1M5_orf2#LIN 953 CTTAGATCATTGATTTTAAGCCTTTCTTCTTTTCTAATATANGCATTTAA 904 chr2ptel1M 233990 ATGTATAAAATTTCCTCTAATAACCACTTTGATTGCATTCCACAAATTTT 234039 ?vv v i vv ii iii i C L1M5_orf2#LIN 903 NGCTATAAATTTCCCTCTAAGCACTGCTTTAGCTGCATCCCACAAATTTT 854 chr2ptel1M 234040 GGTATGTTGTCTCCTTATTGTTATTC 234065 i v ii i ? i C L1M5_orf2#LIN 853 GATATGTTGTATTTTCATTNTCATTC 828 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.45 CpG sites = 265, Kimura (unadjusted) = 41.28 Transitions / transversions = 1.31 (265/203) Gap_init rate = 0.03 (53 / 1555), avg. gap size = 1.81 (96 / 53) 1572 33.01 5.21 2.91 chr2ptel1M 232519 234802 (765198) C L1MC_orf2#LINE/L1 (876) 2418 84 m_b61s551i6 2243 chr2ptel1M 232519 CCACGAACACTTAATATTTTTCCAATTGATTAGATCTGATTTTATTTGTG 232568 i ivv i i v iv ? vv v v v C L1MC_orf2#LIN 2418 CCATGAACATGGAATATCTCTCCATTTATTTAGNTCTTCTTTGATTTCTT 2369 chr2ptel1M 232569 TGGAAAATGTTTTGTAATTGTGTTCATATAGTTGTTGACTTTACCTTGGC 232618 vivv iv i v vi v v vviv ii vi C L1MC_orf2#LIN 2368 TCATCAGAGTTTTGTAGTTTTCCTCATATAGATCTTGTACATATTTTGTT 2319 chr2ptel1M 232619 AGGTAGGATCCCAAATATTTTATATTTG-------CAATTTATAT----T 232657 i vvivv i i i v -------i v v ---- C L1MC_orf2#LIN 2318 AGATTTATACCTAAGTATTTCATTTTTGGGGGTGCTAATGTAAATGGTAT 2269 chr2ptel1M 232658 CATATCTCT----TCATATTGAACTT------TGTTGGAAATATATAAAA 232697 ii i i i ---- v vv ? ------ i --- ii C L1MC_orf2#LIN 2268 TGTGTTTTTAATTTCAAATTCCANTTGTTCATTGCTGG---TATATAGGA 2222 chr2ptel1M 232698 ATGCTGATGATTTCTGTGGATTTATTTTGTATCCTGCAACTTTGATAAAG 232747 v viv i i iv v ii i v v i C L1MC_orf2#LIN 2221 AAGCGATTGACTTTTGTATATTAACCTTGTATCCTGCAACCTTGCTATAA 2172 chr2ptel1M 232748 TTGTGAATTGTTTCTATTAGTTTTTCTATTGAATCTCCAGGGTTCTCTAA 232797 i ivv iv i vv i i i v iiv i i v C L1MC_orf2#LIN 2171 TCGCTTATTAGTTCCAGGAGTTTTTTTGTCGATTCTTTCGGATTTTCTAC 2122 chr2ptel1M 232798 GTATACCATCATATCATCTTCAGATAGTGACAACATGGTTTCCTCATTAC 232847 i v v i v ii i iv iiv vi i v - C L1MC_orf2#LIN 2121 ATAGACAATCATGTCATCTGCGAACAAAGACAGTTTTATTTCTTCCTT-C 2073 chr2ptel1M 232848 CTCCTCTG-ATTTCTTTAATCTTCTTTTCCTTTGTTATTGCTAAAGCTAA 232896 ivv - vi v i i i v v vvv i C L1MC_orf2#LIN 2072 CCAATCTGTATACCTTTTATTTCCTTTTCTTGTCTTATTGCATTAGCTAG 2023 chr2ptel1M 232897 TATTTCTAATACAATATTGAACAGTATTGGTGGTAGCAGACAATCTTGTT 232946 v i i i i i v v v iv vi vi i- C L1MC_orf2#LIN 2022 GACTTCCAGTACGATGTTGAAAAGGAGTGGTGAGAGGGGACATCCTTGC- 1974 chr2ptel1M 232947 GCTT-TCCCTGATCTTATTGGAAATGGTTCTA-TTTATCCCCATTACATA 232994 - - i vi i v v ? - v v vi C L1MC_orf2#LIN 1973 -CTTGTTCCTGATCTTAGCGGGAAAGCTTCNAGTTTCTCACCATTAAGTA 1925 chr2ptel1M 232995 TGATGCTTGCTGACTGTTTTAAATAGATACTATTGATCATTTTAAGGAAA 233044 i v vvv vvi ii v v vv i i C L1MC_orf2#LIN 1924 TGATGTTAGCTGTAGGTTTTTTGTAGATGTTCTTTATCAAGTTGAGGAAG 1875 chr2ptel1M 233045 ACTCCATTTAGTCTTATAGTCT-CT-AGTATTTTTAATAGTAATGGGTGT 233092 vii v i v i -- i - - vi vi vv C L1MC_orf2#LIN 1874 TTCCCCTCTATTCCTA--GTTTGCTGAGAGTTTTTATCATGAATGGGTGT 1827 chr2ptel1M 233093 TGGATTTTGTCAAATGC-CTTTCTGTATCTATTGAGATCATTATATAACT 233141 -i i v v i i i i C L1MC_orf2#LIN 1826 TGGATTTTGTCAAATGCTTTTTCTGCATCTATTGATATGATCATGTGATT 1777 chr2ptel1M 233142 TTCATTAGCTTGGCTATTGATAAAATCAAGTATGCTAACAGTTTTCTTAA 233191 iv vvi v v i ivi vi v iii iv v iiv C L1MC_orf2#LIN 1776 TTTCTTCTTTAGCCTGTTGATGTGATGGATTACATTAATTGATTTTCGAA 1727 chr2ptel1M 233192 GATTGAACCAGCCCTGCATTTCTGGTATATATCCTGCTTGGTCATGGTGT 233241 vi i vi v v ii i C L1MC_orf2#LIN 1726 TGTTGAACCAGCCTTGCATACCTGGGATAAATCCCACTTGGTCGTGGTGT 1677 chr2ptel1M 233242 ATTTTCCTGGACATGACATT-CAGTAATCTCTTTGCTAATATTTTATGTA 233290 vv i vvvi - -iv v v vv i vv C L1MC_orf2#LIN 1676 ATAATTCTTTTTAT-ACATTGTTGGATTCGATTTGCTAATATTTTGTTGA 1628 chr2ptel1M 233291 AGATTTTTACATCAATATTCATTAGGGAAATTGATCTATAATTTTCTTCC 233340 i i v i v i v i i i ii C L1MC_orf2#LIN 1627 GGATTTTTGCATCTATGTTCATGAGAGATATTGGTCTGTAGTTTTCTTTT 1578 chr2ptel1M 233341 TCTGT--TTTCATCCTACCTGATTTAGGTATCAGCTCTATAGCT-GTGTC 233387 ii -- v v -- ii i v i vviv - - iv C L1MC_orf2#LIN 1577 CTTGTAATGTCTT--TGTCTGGTTTTGGTATTAGGGTAAT-GCTGGCCTC 1531 chr2ptel1M 233388 ATAAAAGGAATTTGGTAGGACTTCTTAACGTTTTTTTTTCAG--ATAGTT 233435 i v i v v v i i i vvvv i v i v -- v v C L1MC_orf2#LIN 1530 ATAGAATGAGTTAGGAAGTATTCCCTCTGCTTCTATCTTCTGGAAGAGAT 1481 chr2ptel1M 233436 TGCATAATATTGCAGTAAATTGTTCTTTAAATGTTTGATAGAATTCACGT 233485 i v iv vvi v v i i vv C L1MC_orf2#LIN 1480 TGTAGAGAATTGGTATAATTTCTTCCTTAAATGTTTGGTAGAATTCACCA 1431 chr2ptel1M 233486 GCAAATCTATCTGGTCCTGGAGATTTTTTCTTACAGAGATGGTTAATAGT 233535 ii i i v v v i vi vvii i vi vi C L1MC_orf2#LIN 1430 GTGAACCCATCTGGGCCTGGTGCTTTCTGTTTTGGAAGGTTATTAATTAT 1381 chr2ptel1M 233536 TTGTTTTATTTCTTTTTCTAAAATGGGACTATTTAAGTAATTGATTTCCT 233585 vi iv vvivi v i v i ii vi iv i C L1MC_orf2#LIN 1380 TGATTCAATTTCTTTAATAGATATAGGCCTATTCAGATTGTCTATTTCTT 1331 chr2ptel1M 233586 TTTTTGTTAATCTGGGCAAACTATATTTTTTGTAGGTATTCCTCCATTTT 233635 i v v i i v i i i i i ii- v vv i C L1MC_orf2#LIN 1330 CTTGTGTGAGTTTTGGCAGATTGTGTCTTTCA-AGGAATTGGTCCATTTC 1282 chr2ptel1M 233636 ACTTAGATTAACAAACTTATTGGCAT--ACTTGATCAAAAAAACTCCTAA 233683 ii i v i i v -- v v v iv vii i v C L1MC_orf2#LIN 1281 ATCTAGGTTATCAAATTTGTGGGCATAGAGTTGTTCATAGTATTCCTTTA 1232 chr2ptel1M 233684 TTATGGCTCTGATTTCC------TCT-------TTTTCCCT-TTTCAGCT 233719 vvi i i v ------ ?------- v i - vi C L1MC_orf2#LIN 1231 TTATCCTTTTAATGTCCATGGGATCNGTAGTGATGTCCCCTCTTTCATTT 1182 chr2ptel1M 233720 TTAAGAATAACAATTTGAATTTCTTCTTTCATTTTT------CTAATCAA 233763 i i v v ii -- v i v ------i ii vi C L1MC_orf2#LIN 1181 CTGATATTAGTAATTTG--TGTCTTCTCTCTTTTTTTCTTAGTTAGCCTG 1134 chr2ptel1M 233764 ACTAACAGTTTATTTATCATGTAGGTATTTTAATAAGAC--ACTCTTAGT 233811 i ivi i iv iv i v i v v v ii --i i i C L1MC_orf2#LIN 1133 GCTAGAGGCTTATCAATTTTATTGATCTTTTCAAAGAACCAGCTTTTGGT 1084 chr2ptel1M 233812 TTTATTTATTAATTCAATAATTTTCTTACTTTCAATTTTGTTAATCTCTC 233861 ii v vvi v viv i ii ii i i v C L1MC_orf2#LIN 1083 TTCGTTGATTTTCTCTATTGATTTCCTGTTTTCAATTTCATTGATTTCTG 1034 chr2ptel1M 233862 CTTCTTTTTTCAGTAATTCAAATTTGGTATTTAATTGGGGGTTTTTAATT 233911 iivv i v v vvv i vv ii v v i--- C L1MC_orf2#LIN 1033 CTCTAATTTTTATTATTTCTTTTCTTCTGCTTACTTTGGA---TTTAATT 987 chr2ptel1M 233912 TG---TTTTGTTTCTAGTTTTTTTAGTTACAGGC-CAG-TCATTAATCTT 233956 --- i v ii v v iv i -i - i i i C L1MC_orf2#LIN 986 TGCTCTTCTTTTTCTAGTTTCCTAAGGTGGAAGCTTAGATTATTGATTTT 937 chr2ptel1M 233957 CACTTTCTCTATTTTGTTCATGTGGGCATCTAGATG-TATAAAATTTCCT 234005 viv i i vi vi v i iv ii - - v i C L1MC_orf2#LIN 936 AGATCTTTCTTCTTTTCTAATATATGCATTCA-ATGCTATAAATTTCCCT 888 chr2ptel1M 234006 CTAATAACCACTTTGATTGCATTCCACAAATTTTGGTATGTTGTCTCCTT 234055 vv ii vii i i v v ii i C L1MC_orf2#LIN 887 CTAAGCACTGCTTTCGCTGCATCCCACAAATTTTGATAAGTTGTATTTTC 838 chr2ptel1M 234056 ATTGTTATTCTCTCGGATGAAATTATT-----GTGTCTAT---GATTTGT 234097 v i ---- ii v v v -----i v v --- v C L1MC_orf2#LIN 837 ATTTTCAT----TTAGTTCAAAATATTTTTAAATTTCTCTTGAGATTTCT 792 chr2ptel1M 234098 TGTTTTACCCACTCAATCTTTAGGATTAGATTACTTACTTTTCAATTA-- 234145 v v iviiv v i v ivi ii v i i v -- C L1MC_orf2#LIN 791 TCTTTGACCCATGTGTTATTTAGAAGTGTGTTGTTTAATCTCCAAGTATT 742 chr2ptel1M 234146 -----ATTTTTTATCTCTTTTCCACTGGCCTTTATTGTATGCAATTTTTA 234190 ----- ii v v i i-- ---- vv v v v v C L1MC_orf2#LIN 741 TTGGGATTTTCCAGCTATCTTT--CTG----TTATTGATTTCTAGTTTAA 698 chr2ptel1M 234191 TTGCATCATGCTCTGAGAAAAATGCATTCAAT-ATTTTTGCCTTTCTGCA 234239 v ii v - iv ?i ? vv - i iiii i iv C L1MC_orf2#LIN 697 TTCCATTGTGGTCTGAG-AGCANACNTTGTATGATTTCTATTCTTTTAAA 649 chr2ptel1M 234240 TTTGATTTTGAA----GTTTTATGTTCTACTATATGGTC-GTTTTTGTAT 234284 --- i i---- vi i vv i -i i v iv C L1MC_orf2#LIN 648 TTTG---TTAAGGTGTGTTTTATGGCCCAGAATGTGGTCTATCTTGGTGA 602 chr2ptel1M 234285 AGGTTTTATGTATTGCTGAGGAAAAAAAAAACTATTCCTTTCTTTCTCCA 234334 v ii i-v --v i i vivv ivi v vi vv C L1MC_orf2#LIN 601 ATGTTCCATGTG-AGCT--TGAGAAGAATGTGTATTCTGCTGTTGTTGGA 555 chr2ptel1M 234335 TTCAGTTTTCTCCAAAGGTCTGT--CATCCGTAACTTTTTGAGGATTCTA 234382 vv v? vi i v vi --? -- ii vv v i v i C L1MC_orf2#LIN 554 TGAAGTANTCTATAGATGTCAATTANATCC--AGTTGATTGATGGTGCTG 507 chr2ptel1M 234383 TTTACCTCTTTAGCTTCTTTCTTACTAATTTTGTG---GATCGAATAATC 234429 ? ---v i i viv i i v --- v v vivi C L1MC_orf2#LIN 506 TTNA---GTTCAACTATGTCCTTACTGATTTTCTGCCTGCTGGATCTGTC 460 chr2ptel1M 234430 TAGTTCTGAAAGAGCAAGGTTGAGATCCCCCAAAAGTATAGTTGTGCA-- 234477 ? v ? v viiv ii i --- v i v v -- C L1MC_orf2#LIN 459 NATTNCTGATAGAGGGGTGTTGAAGTCTCC---AACTATAATAGTGGATT 413 chr2ptel1M 234478 -ATCTAATTCTTCTTGAAACTTTCTGAA---------CAC---------- 234507 -i v i v ii i v v i--------- ---------- C L1MC_orf2#LIN 412 CGTCTATTTCTCCTTGCAGTTCTATCAGTTTTTGCCTCACGTATTTTGAC 363 chr2ptel1M 234508 -CTCTTCTACTTGGTGCATATATGTTTAGAATTGATATATCATATTAT-T 234555 - vi ii v i i i v i v i v v iv-v C L1MC_orf2#LIN 362 GCTCTGTTGTTAGGCGCATACACGTTAAGGATTGTTATGTCTTCTTGGAG 313 chr2ptel1M 234556 CATGGAACCTTTAAGCAGGTTGCAGTTTCCTTCCTTATCTCTTTTGATTA 234605 v v v i v v vvv i i vi i i i --- v C L1MC_orf2#LIN 312 AATTGACCCCTTTATCATTATGTAATGCCCCTCTTTATCCC---TGATAA 266 chr2ptel1M 234606 GTTCTATTTTTGCT------TTTGCTTGATCTGAGATTAGGATTTCTACC 234649 v --- ii ------ i ivi i iv vv i C L1MC_orf2#LIN 265 CTT---TCCTTGCTCTGAAGTCTGCTCTGTCTGAAATTAATATAGCTACT 219 chr2ptel1M 234650 CTGGTTTTTGTTTCATTTTGTTTTGTTTTAATTTCAGCTGAAATATAATA 234699 i? i i------ v v v ------ ------ ii C L1MC_orf2#LIN 218 CCNGCTTTC------TTTTGATTAGTGTT------AGC------ATGGTA 187 chr2ptel1M 234700 GATTCTGCTTCAGGATTTTGCTTTTAGTTTGTATGTATCACTCTGCTTTA 234749 v ii v i vvv? i i i i i vi v ii v C L1MC_orf2#LIN 186 TATCTTTCTCCATCCNTTTACTTTTAATCTATATGTGTCTTTATATTTAA 137 chr2ptel1M 234750 AATAAGTTTCTTATAAATAACAAATTGGAGGTTTCTGACTTTTAATCTAG 234799 i ii i i i v v vv v ii vi i i v C L1MC_orf2#LIN 136 AGTGGGTTTCTTGTAGACAACATATAGTTGGGTCTTGTTTTTTGATCCAC 87 chr2ptel1M 234800 TCT 234802 C L1MC_orf2#LIN 86 TCT 84 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 43.81 CpG sites = 383, Kimura (unadjusted) = 44.80 Transitions / transversions = 1.10 (383/349) Gap_init rate = 0.05 (107 / 2283), avg. gap size = 1.75 (187 / 107) 307 26.61 1.83 0.00 chr2ptel1M 234736 234844 (765156) C L1MEj_5end#LINE/L1 (0) 2160 2050 m_b61s551i7 2243 chr2ptel1M 234736 ATCACTCTGCTTTAAATAAGTTTCTTATAAATAACAAATTGGAGGTTTCT 234785 i i i iv i i i v v vv v i C L1MEj_5end#LI 2160 ATCACTTTGTTTTAAGTGTGTTTCTTGTAAACAGCATATAGCTGGGTTTT 2111 chr2ptel1M 234786 GACTTTTAATCTAGTCTTGTATCCACT-TGTTTTA-TGGGAGAGTTCATT 234833 vi i i i vii vi v - v - i v C L1MEj_5end#LI 2110 GTTTTTTAACCCAATCTGACAGTCTCTGTCTTTTAATGGGAGAATTCAGT 2061 chr2ptel1M 234834 CTATTCACATT 234844 i C L1MEj_5end#LI 2060 CCATTCACATT 2050 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 33.63 CpG sites = 17, Kimura (unadjusted) = 33.63 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.02 (2 / 108), avg. gap size = 1.00 (2 / 2) 20 0.00 0.00 0.00 chr2ptel1M 235424 235445 (764555) (T)n#Simple_repeat 1 22 (0) m_b61s252i0 2244 chr2ptel1M 235424 TTTTTTTTTTTTTTTTTTTTTT 235445 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTT 22 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 15 13.86 0.00 0.00 chr2ptel1M 235576 235599 (764401) (T)n#Simple_repeat 1 24 (0) m_b61s252i1 2245 chr2ptel1M 235576 TTCTTTTTGCTTTTTTTTTTTTTT 235599 i vi (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTT 24 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 15 3.45 10.00 0.00 chr2ptel1M 235597 235626 (764374) (TTTAAG)n#Simple_repeat 1 33 (0) m_b61s252i2 2246 chr2ptel1M 235597 TTTAAGTTTGAGTTT---TTTAAGTTTAAGTTT 235626 i --- (TTTAAG)n#Sim 1 TTTAAGTTTAAGTTTAAGTTTAAGTTTAAGTTT 33 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.03 (1 / 29), avg. gap size = 3.00 (3 / 1) 279 33.96 1.87 0.93 chr2ptel1M 236103 236209 (763791) C MIRc#SINE/MIR (158) 110 3 m_b61s601i2 2247 chr2ptel1M 236103 TAAATTACTTTTTCAAGACAACAAGACAAGACAAGTA-CAGAATCAGAAT 236151 i v vii iiv vii v -i i- ii i i i C MIRc#SINE/MIR 110 TAAGTGACTTGCCCAAGGTCACACAGCTAG-TAAGTGGCAGAGCCGGGAC 62 chr2ptel1M 236152 TTCAACTCATGTCCTC-TAACTCCAAATCTACTTAATTTTCCACTATACC 236200 iv i v i - i i i v vvvi ii C MIRc#SINE/MIR 61 TCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACC 12 chr2ptel1M 236201 ACATTGTCT 236209 i i C MIRc#SINE/MIR 11 ACACTGCCT 3 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.81 CpG sites = 25, Kimura (unadjusted) = 48.65 Transitions / transversions = 2.27 (25/11) Gap_init rate = 0.03 (3 / 106), avg. gap size = 1.00 (3 / 3) 18 0.00 0.00 0.00 chr2ptel1M 236433 236452 (763548) (T)n#Simple_repeat 1 20 (0) m_b61s252i3 2248 chr2ptel1M 236433 TTTTTTTTTTTTTTTTTTTT 236452 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTT 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 13 11.28 7.14 4.65 chr2ptel1M 236625 236666 (763334) (TTTAA)n#Simple_repeat 1 43 (0) m_b61s252i4 2249 chr2ptel1M 236625 TTTAATTTAATTCAATTTTTAATTT-TTTTAAGCT--TTTAATTT 236666 i -- -v vi -- (TTTAA)n#Simp 1 TTTAATTTAATTTAA--TTTAATTTAATTTAATTTAATTTAATTT 43 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.10 (4 / 41), avg. gap size = 1.25 (5 / 4) 387 28.90 11.67 1.01 chr2ptel1M 237078 237437 (762563) C L1ME4c_3end#LINE/L1 (192) 638 241 m_b61s551i8 2250 chr2ptel1M 237078 TCTCCTCATTTTACTTGGCATCAGTTCTTGTAACTCTCTCCAGGTCTCTC 237127 v iv i ii i vv v i- vi i v iv v C L1ME4c_3end#L 638 TCTGCTTTTTTCACTTAACATTATATCATA-AACATTTTCCATGTTGCTA 590 chr2ptel1M 237128 CAAAATCATCCTGCTGATCTTTTTTTATAGAACAATAATATCCCATAACA 237177 v i v v iv v v v i vvvv i vivi C L1ME4c_3end#L 589 CATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCGAG 540 chr2ptel1M 237178 TTCATATATCATAATTTCTTCAGCCATTCCTCAACTGATGGGCATCCATT 237227 ?v i i vi i i i v i v i ii vv C L1ME4c_3end#L 539 TNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAGG 490 chr2ptel1M 237228 CACTTTCCAGTTT----CTTTT-------------CA-----CAT----G 237251 ivv i ---- v ------------- ----- ---- C L1ME4c_3end#L 489 TTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTCG 440 chr2ptel1M 237252 TGAAT----CCTTTTCCCTTTTTT--ATGATCTCTTTGGGATACAAGGCC 237295 v ---- i i i -- v i i i v vvv C L1ME4c_3end#L 439 TGCATATAGCTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAATTCCC 390 chr2ptel1M 237296 AGTAGAAATATTGCTGGATCAAAGGGTACGCACATTTTGATGGCCCTT-- 237343 v viiv i i i v v i -- C L1ME4c_3end#L 389 AGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTCTTGA 340 chr2ptel1M 237344 TGAGTATAGTTCCATATTGCTTTCCAGA--------ATCACTTCACAACT 237385 iv -- v v i -------- i v i ?iv C L1ME4c_3end#L 339 TACGTAT--TGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACANTG 292 chr2ptel1M 237386 CCATCAACAATGGATTTGTATCCCAGTTTTCCCCACATCCCCTCCAACAT 237435 i i v vv ?i v - v i ? i v i C L1ME4c_3end#L 291 CCACCAGCAATGTATGAGNGTACCAG-TTTCACCGCANCCTCGCCAGCAT 243 chr2ptel1M 237436 TG 237437 C L1ME4c_3end#L 242 TG 241 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.58 CpG sites = 50, Kimura (unadjusted) = 37.47 Transitions / transversions = 0.94 (50/53) Gap_init rate = 0.03 (12 / 359), avg. gap size = 3.83 (46 / 12) 240 28.04 4.02 4.02 chr2ptel1M 237612 237860 (762140) C L1M3_orf2#LINE/L1 (595) 2693 2445 m_b61s551i9 2251 chr2ptel1M 237612 TTCCACTAATCAACTAT-TCTTTTTTTA-GCCTGTACCGAATGGTTTTGA 237659 i ii v - - v - v iv iv C L1M3_orf2#LIN 2693 TTCCATTGGTCTA-TATGTCTGTTTTTATGCCAGTACCATACTGTTTTGA 2645 chr2ptel1M 237660 TGACCACTGCTTTATAATATAGTTTT--AGTCTGGCACAGCTAGGCTATC 237707 v iiiv i - -- i v --- iv iv v ii C L1M3_orf2#LIN 2644 TTACTGTAGCTTTGTAATATA-TTTTGAAATCAGG---AAGTGTGATGCC 2599 chr2ptel1M 237708 TTC--CTTTGCATTTATTTTTTCATTAA--TTGCCTTGAA-ATTCTTGAC 237752 i -- --- v i - i -- i iv- vv ii C L1M3_orf2#LIN 2598 TCCAGCTTTG---TTCTTCTTTC-TCAAGATTGCTTTGGCTATTCGGGGT 2553 chr2ptel1M 237753 TTTTTGTTCTTCCAGATAAACTTTGTTATTATCTTTTATAGATCTGTAAA 237802 i vv v i i ivv i i v vv C L1M3_orf2#LIN 2552 CTTTTGTGGTTCCATATGAATTTTAGGATTGTTTTTTCTATTTCTGTAAA 2503 chr2ptel1M 237803 ATAATTTT-TTGGGAGTTTTGTTGGTATGGTACTGAATAAGTAGATTTAT 237851 - vii- v vi v v v i i vv ivv C L1M3_orf2#LIN 2502 A-AATGCCATTGGGATTTTGATAGGGATTGCATTGAATCTGTAGATCGCT 2454 chr2ptel1M 237852 TTAGGTAGT 237860 i C L1M3_orf2#LIN 2453 TTGGGTAGT 2445 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.89 CpG sites = 34, Kimura (unadjusted) = 35.54 Transitions / transversions = 1.03 (34/33) Gap_init rate = 0.07 (17 / 248), avg. gap size = 1.18 (20 / 17) 18 15.45 5.77 1.85 chr2ptel1M 237863 237914 (762086) (TATTA)n#Simple_repeat 1 54 (0) m_b61s252i5 2252 chr2ptel1M 237863 TATTATATT-CACTATA-TA-ATTATATTAAATAAAAATATAATATAATT 237909 -i i - - v v v v v - (TATTA)n#Simp 1 TATTATATTATATTATATTATATTATATTATATTATATTATATTAT-ATT 49 chr2ptel1M 237910 ATATT 237914 (TATTA)n#Simp 50 ATATT 54 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.08 (4 / 51), avg. gap size = 1.00 (4 / 4) 228 25.32 0.00 0.00 chr2ptel1M 239096 239174 (760826) C L1ME4a_3end#LINE/L1 (298) 573 495 m_b61s551i10 2253 chr2ptel1M 239096 ATCATTTCCTATAGAAGAATCATATTCCATAATATCCATATATCATAAAT 239145 ? iiv i vv v v v? vv i i v C L1ME4a_3end#L 573 ATNATTTTTAATGGCTGCATAATATTCCATTNTATGGATGTACCATAATT 524 chr2ptel1M 239146 TATTCAGCCATTCTCCAACTGTTGGGCAT 239174 i i ? i v i i C L1ME4a_3end#L 523 TATTTAACCANTCCCCTATTGTTGGACAT 495 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 32.74 CpG sites = 10, Kimura (unadjusted) = 32.74 Transitions / transversions = 1.00 (10/10) Gap_init rate = 0.00 (0 / 78), avg. gap size = 0.0 (0 / 0) 242 21.05 0.00 0.00 chr2ptel1M 239118 239174 (760826) C L1ME3G_3end#LINE/L1 (380) 544 488 m_b61s551i11 2253 chr2ptel1M 239118 TATTCCATAATATCCATATATCATAAATTATTCAGCCATTCTCCAACTGT 239167 i vv i v i i i v i v C L1ME3G_3end#L 544 TATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTATTGA 495 chr2ptel1M 239168 TGGGCAT 239174 i C L1ME3G_3end#L 494 TGGACAT 488 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 25.10 CpG sites = 7, Kimura (unadjusted) = 25.10 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0) 15 3.95 0.00 7.14 chr2ptel1M 240726 240755 (759245) (AAAAG)n#Simple_repeat 1 28 (0) m_b61s252i6 2254 chr2ptel1M 240726 AAAAGAAAAGAAAAGGAACAAGAAAACAAA 240755 - - v (AAAAG)n#Simp 1 AAAAGAAAAGAAAA-GAA-AAGAAAAGAAA 28 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.07 (2 / 29), avg. gap size = 1.00 (2 / 2) 12 13.87 0.00 0.00 chr2ptel1M 240773 240796 (759204) (CACA)n#Simple_repeat 1 24 (0) m_b61s252i7 2255 chr2ptel1M 240773 CACAAACAGACACACCCACACACA 240796 v v v (CACA)n#Simpl 1 CACACACACACACACACACACACA 24 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 61 23.07 1.46 0.00 chr2ptel1M 240798 240934 (759066) (TA)n#Simple_repeat 1 139 (0) m_b61s252i8 2256 chr2ptel1M 240798 TATAAATATATAAATACATATATTTATGTATGTATACATATATACATGCA 240847 v v i v i i i i ii (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr2ptel1M 240848 TATAGATGCATGTATATATATGTGTGTGTATA-ATATATATATATATATA 240896 v ii i i i i i - (TA)n#Simple_ 51 TATATATATATATATATATATATATATATATATATATATATATATATATA 100 chr2ptel1M 240897 TAT-TATACACACACACATATATATATATGCACATATAT 240934 - i i i i i ii i (TA)n#Simple_ 101 TATATATATATATATATATATATATATATATATATATAT 139 Matrix = Unknown Transitions / transversions = 5.50 (22/4) Gap_init rate = 0.01 (2 / 136), avg. gap size = 1.00 (2 / 2) 12 12.46 0.00 12.50 chr2ptel1M 241126 241170 (758830) (TTCACT)n#Simple_repeat 1 40 (0) m_b61s252i9 2257 chr2ptel1M 241126 TTCACTCTCAATTTTTCCCTTTCACTTTCATTATCTGCACTTTCA 241170 i - -i v i - - - (TTCACT)n#Sim 1 TTCACTTTC-A-CTTTCACTTTCACTTTCACT-T-T-CACTTTCA 40 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.11 (5 / 44), avg. gap size = 1.00 (5 / 5) 16 0.00 0.00 0.00 chr2ptel1M 241405 241422 (758578) (T)n#Simple_repeat 1 18 (0) m_b61s252i10 2258 chr2ptel1M 241405 TTTTTTTTTTTTTTTTTT 241422 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTT 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 358 25.22 19.77 1.44 chr2ptel1M 242800 242976 (757024) MIRc#SINE/MIR 6 214 (54) m_b61s601i3 2259 chr2ptel1M 242800 CAGTGCA-TACACTGTGGATAGAGC------CTTAAA-TCAGAAAGACCG 242841 ii- i -- v ------ ii - i v MIRc#SINE/MIR 6 CAGTGTGGTGCA--GTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCT 53 chr2ptel1M 242842 GGGTTTTAATCCCATCTCAGAAGGCTGCTAGTAG---GACCTT------- 242881 iv i iv v vvivi i iv --- ------- MIRc#SINE/MIR 54 GGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAG 103 chr2ptel1M 242882 -CGTTTGAT-----TAAGC-----TTTCTTTATCTGTAAAATGGGCTTAA 242920 - ii i i----- i ----- i i vv MIRc#SINE/MIR 104 TCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAA 153 chr2ptel1M 242921 TAATATAAGAAAAGTCT---TCA---GGTTGTCATGAGGATAAAATAAGA 242964 ivv vvvv i --- --- ii v i MIRc#SINE/MIR 154 TAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGA 203 chr2ptel1M 242965 CAATGCTATGTG 242976 i - MIRc#SINE/MIR 204 TAATG-TATGTG 214 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.83 CpG sites = 26, Kimura (unadjusted) = 31.53 Transitions / transversions = 1.44 (26/18) Gap_init rate = 0.07 (13 / 176), avg. gap size = 2.92 (38 / 13) 268 29.71 4.42 1.72 chr2ptel1M 242877 242989 (757011) MIR#SINE/MIR 107 222 (40) m_b61s601i4 2259 chr2ptel1M 242877 ACCTTCGTTTGATTAAGCTTTCTTTATCTGTAAAATGGGCTTAATAATAT 242926 iiv v vi v - i i vv v MIR#SINE/MIR 107 ACCTCTCTGTGCCTCAG-TTTCCTCATCTGTAAAATGGGGATAATAATAG 155 chr2ptel1M 242927 AAGAAAAGTCTTCAGGTTGTCATGAGGATAAAATAAGACAATGCTATGTG 242976 v vvv vv v vi ii v i vi i - i MIR#SINE/MIR 156 TACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATAC-ATGTA 204 chr2ptel1M 242977 TGACAC-----ACAGTGC 242989 vii i ----- MIR#SINE/MIR 205 AAGCGCTTAGAACAGTGC 222 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.71 CpG sites = 15, Kimura (unadjusted) = 38.12 Transitions / transversions = 0.83 (15/18) Gap_init rate = 0.03 (3 / 112), avg. gap size = 2.33 (7 / 3) 242 32.31 9.23 0.00 chr2ptel1M 243116 243245 (756755) L2d_3end#LINE/L2 352 493 (23) m_b61s601i5 2260 chr2ptel1M 243116 TTCTCCA-TCGTTTCTGGGGTATTG----TGTGTCCC--ACCATGCTGTG 243158 i - i vv v i i---- v -- i vii i L2d_3end#LINE 352 TTCTCTAATTGTTTCATGTGTGTTAGTCTTGTCTCCCCAACTAGATTGTA 401 chr2ptel1M 243159 ATCTCCATGAGAACAGGGGATGTCCCTCACATCACTTTAT-ATTCCT--- 243204 v v ii ivii vi i i ii?i ? -i i--- L2d_3end#LINE 402 AGCTCCTTGAGGGCAGGGACCATGTCTTATACTNTTTTNTCGTTCCCCAC 451 chr2ptel1M 243205 GGTGCTCAGCCCAGGGCTG-TCACATACCAGACACTTAATAA 243245 i i ii v v -v vi i i i L2d_3end#LINE 452 AGCGCCTAGCACAGTGCTGAGCACATAGTAGGCGCTCAATAA 493 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.60 CpG sites = 29, Kimura (unadjusted) = 46.13 Transitions / transversions = 2.23 (29/13) Gap_init rate = 0.05 (6 / 129), avg. gap size = 2.00 (12 / 6) 309 32.41 4.63 0.00 chr2ptel1M 243138 243245 (756755) L2b_3end#LINE/L2 333 445 (21) m_b61s601i6 2260 chr2ptel1M 243138 TGTGTGTCCCACCATGCTGTGATCTCCATGAGAACAGGGG--ATGTCCCT 243185 v vi i vi v i ii i--i? iv L2b_3end#LINE 333 TGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGT 382 chr2ptel1M 243186 CACA-TCACT-TTATATTCCTGGTGCTCAGCCCAGGG-CTGTCACATACC 243232 vii- i-i i i ii i ii v ? - v i vi L2b_3end#LINE 383 CTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGT 432 chr2ptel1M 243233 AGACACTTAATAA 243245 i i i i L2b_3end#LINE 433 AGGCGCTCAGTAA 445 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.38 CpG sites = 26, Kimura (unadjusted) = 47.49 Transitions / transversions = 2.89 (26/9) Gap_init rate = 0.04 (4 / 107), avg. gap size = 1.25 (5 / 4) 285 29.03 4.30 0.00 chr2ptel1M 243320 243412 (756588) C MIR3#SINE/MIR (5) 203 107 m_b61s601i7 2261 chr2ptel1M 243320 ATAAGATCACAGATGATCA---CTGGAAGGGATGTACAGGGCCATGGAGT 243366 ii i vvi --- iv vvii ii vv C MIR3#SINE/MIR 203 ATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGT 154 chr2ptel1M 243367 GTGACCCACTCATTTTATAGATG-GGAAACCAAGGTCCACCTAGGTG 243412 vii v i - ii i vvv C MIR3#SINE/MIR 153 CCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTG 107 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.50 CpG sites = 15, Kimura (unadjusted) = 37.50 Transitions / transversions = 1.25 (15/12) Gap_init rate = 0.02 (2 / 92), avg. gap size = 2.00 (4 / 2) 393 31.96 4.90 3.38 chr2ptel1M 244048 244251 (755749) MIRc#SINE/MIR 3 209 (59) m_b61s601i8 2262 chr2ptel1M 244048 AGGGAGTCAGTAGTACAGTGGA--GAGTCCTGGGCAT--AGTCAGGTCTA 244093 v -- i i -- iv i v -- vvv MIRc#SINE/MIR 3 AGGCAGT--GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA 50 chr2ptel1M 244094 CTCTGAGTTTCAAAGAAACCTTGAAGATTGGCTAAGTGTGTACACCTGAG 244143 - i iv ivvvviv ivivv i vi iv ivv i i MIRc#SINE/MIR 51 C-CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGG 99 chr2ptel1M 244144 CAAGTCAAGTACACTCTGCATGTTAGCCTCAGTTTTTTCATCTCTCAAAT 244193 vv vv - - -- ii v v MIRc#SINE/MIR 100 CAAGTCACTTAACCTCT-C-TG--AGCCTCAGTTTCCTCATCTGTAAAAT 145 chr2ptel1M 244194 GGGGATAACTATATCT------CTTAACTTGGAAAGTTAAGATGAGGTTA 244237 iv i ------ i v iiv ii ivvi v v MIRc#SINE/MIR 146 GGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATC 195 chr2ptel1M 244238 AAGTGACACAATAT 244251 i v i i MIRc#SINE/MIR 196 AAATGAGATAATGT 209 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.44 CpG sites = 30, Kimura (unadjusted) = 42.14 Transitions / transversions = 0.91 (30/33) Gap_init rate = 0.05 (10 / 203), avg. gap size = 1.70 (17 / 10) 20 28.36 4.00 0.00 chr2ptel1M 244429 244503 (755497) (TACA)n#Simple_repeat 1 78 (0) m_b61s252i11 2263 chr2ptel1M 244429 TACATAGA-A-ATATATATATACATAAATA-ATAAACACATGCATGTATG 244475 v - - i i v - v i i ii i (TACA)n#Simpl 1 TACATACATACATACATACATACATACATACATACATACATACATACATA 50 chr2ptel1M 244476 CACATATACACACACACACGCATAGATA 244503 i i i i ii v (TACA)n#Simpl 51 CATACATACATACATACATACATACATA 78 Matrix = Unknown Transitions / transversions = 3.25 (13/4) Gap_init rate = 0.04 (3 / 74), avg. gap size = 1.00 (3 / 3) 482 28.16 6.20 9.16 chr2ptel1M 244616 244873 (755127) MIRb#SINE/MIR 4 254 (14) m_b61s601i9 2264 chr2ptel1M 244616 AGGGGCAGCTAGGTGGCACAGTGGTTAGAGCACCAGTCCTGAAGTCAGGA 244665 --- ii vv vi iii i iv MIRb#SINE/MIR 4 AGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGAC 50 chr2ptel1M 244666 GGACCTGAATACAAATCTGACCTCAGACACTTAACATTGCCTAGCTGTGT 244715 i ii v i iviv v v ------- MIRb#SINE/MIR 51 AGACCTGGGTTCGAATCCCGGCTCTGCCACTTA-------CTAGCTGTGT 93 chr2ptel1M 244716 GACCCTGGGCAAATCACTTA---------AACC-CAATTGCCTCAGGGGA 244755 i i i --------- i - i v vvv - MIRb#SINE/MIR 94 GACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTG- 142 chr2ptel1M 244756 AAAAAAGAGGATACTCAAAATAATGTATTTA-CTGG--AAGTTGTTCTTA 244802 v v i ------ -- ii - v --ii v v MIRb#SINE/MIR 143 TAAAATGGGGAT------AATAA--TACCTACCTCGCAGGGTTGTTGTGA 184 chr2ptel1M 244803 AACAATATT-ATTACTATATTGTAAAGAAAGCATATGGCACAGAACTTGG 244851 ii---- - v ivv v i viv iiv i vi i MIRb#SINE/MIR 185 GG----ATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGG 230 chr2ptel1M 244852 CAAATAGCAAAAA--AAATAAATG 244873 v i ivi--v MIRb#SINE/MIR 231 CACATAGTAAGCGCTCAATAAATG 254 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.27 CpG sites = 37, Kimura (unadjusted) = 35.93 Transitions / transversions = 1.28 (37/29) Gap_init rate = 0.11 (29 / 257), avg. gap size = 1.34 (39 / 29) 364 26.30 7.41 1.40 chr2ptel1M 245479 245613 (754387) C MIR3#SINE/MIR (2) 206 64 m_b61s601i10 2265 chr2ptel1M 245479 ATCA-AAAGTCATAAAATGT-GGAGCTGAAAGAACTTTCAGA-ATGAAAG 245525 - i i i -i i iivii i - v vvv C MIR3#SINE/MIR 206 ATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCT 157 chr2ptel1M 245526 AGTCCCACCCACTTCAATTTATTG--GAGGAACCTGAAACCCAAA----- 245568 v - i v iv -- v ii i ----- C MIR3#SINE/MIR 156 AGTCCAACCC-CCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGT 108 chr2ptel1M 245569 GAAGGGATTTGCCCAAAGGTCACAGTCTTTATGAGTGTCAGAGTC 245613 v i - vvvi?vi v v i C MIR3#SINE/MIR 107 GAAGTGACTTGCCC-AAGGTCACACAGCNAGTTAGTGGCAGAGCC 64 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.25 CpG sites = 19, Kimura (unadjusted) = 33.25 Transitions / transversions = 1.19 (19/16) Gap_init rate = 0.05 (7 / 134), avg. gap size = 1.71 (12 / 7) 233 31.88 7.29 1.98 chr2ptel1M 245537 245632 (754368) C MIRc#SINE/MIR (119) 149 49 m_b61s601i11 2265 chr2ptel1M 245537 CTTCAATTTATTG--GAGGAACCTGAAACCCAAAG-----AAGGGATTTG 245579 ii v iv -- v ii i i ----- v i C MIRc#SINE/MIR 149 CCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTG 100 chr2ptel1M 245580 CCCAAAGGTCACAGTCTTTATGAGTGTCAGAGTCAATCCTTGAGTCTGTG 245629 - vvvi vi i v i iivv i ii ii- C MIRc#SINE/MIR 99 CCC-AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCA-G 52 chr2ptel1M 245630 GTC 245632 C MIRc#SINE/MIR 51 GTC 49 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.65 CpG sites = 19, Kimura (unadjusted) = 43.50 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.04 (4 / 95), avg. gap size = 2.25 (9 / 4) 231 24.07 0.00 0.00 chr2ptel1M 247408 247461 (752539) DNM1r#Unknown 2484 2537 (2125) m_b61s502i0 2266 chr2ptel1M 247408 GTATGTGTGTGTGTGTGTGTATGTGTATATGTGTGTACATGTACATATAC 247457 i i i i i i i i iii i DNM1r#Unknown 2484 GTGTGTATATATGTGTGTATATGTGTGTATGTGTGTATATATGTGTATAT 2533 chr2ptel1M 247458 ACAC 247461 i DNM1r#Unknown 2534 ATAC 2537 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 32.84 CpG sites = 13, Kimura (unadjusted) = 32.84 Transitions / transversions = 1.00 (13/0) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 33 0.00 0.00 0.00 chr2ptel1M 247739 247766 (752234) (GT)n#Simple_repeat 1 28 (0) c_b61s251i0 2267 chr2ptel1M 247739 GTGTGTGTGTGTGTGTGTGTGTGTGTGT 247766 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGT 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 328 31.33 5.75 2.79 chr2ptel1M 250551 250724 (749276) L2b_3end#LINE/L2 287 465 (1) m_b61s601i12 2268 chr2ptel1M 250551 CAGTT-TATCCAGTCTACAATGGGTT-TC--TATCTCATTGGTGTGTTGA 250596 i- i v i - vv - ?-- i v? i-ii ivi L2b_3end#LINE 287 CAGTCCTACCCTGCC-ACTCTGGGTTATNATTGTCTGNTTA-CATGTCTG 334 chr2ptel1M 250597 TTACCCCAACT-GTCTGTGACCTCCATGAGAGCAGGGGATATCCCTTGCA 250645 iv v - v v i i --- i v?v vii L2b_3end#LINE 335 TCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGG---ACCGNGTCTG 381 chr2ptel1M 250646 CCTTCTT--TTACTCAATTTTGAGTGCTTAGCCCAGAGATTGGCATATAG 250693 i v --iii vv iiiv i i v ? vi i i L2b_3end#LINE 382 TCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAG 431 chr2ptel1M 250694 AGGGCACT---TAAATGTTTGCTGACTTAAAGAA 250724 vi i --- i i v v v L2b_3end#LINE 432 TAGGCGCTCAGTAAATATTTGTTGAATGAATGAA 465 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.96 CpG sites = 31, Kimura (unadjusted) = 43.33 Transitions / transversions = 1.41 (31/22) Gap_init rate = 0.06 (11 / 173), avg. gap size = 1.36 (15 / 11) 245 32.93 3.66 0.00 chr2ptel1M 250805 250886 (749114) C MIR3#SINE/MIR (3) 205 121 m_b61s601i13 2269 chr2ptel1M 250805 TTATAGGATCCTAGATGATCA---CTAAAAGGAACCTACCAGGCCATAGA 250851 i i v vvi --- ii i vvv ii vv C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTA 156 chr2ptel1M 250852 GTGCAGCCTCTTTATTTTATAGACAGGGAAATAGA 250886 v i i i i i iii iv C MIR3#SINE/MIR 155 GTCCAACCCCCTCATTTTACAGATGAGGAAACTGA 121 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.45 CpG sites = 17, Kimura (unadjusted) = 45.45 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.01 (1 / 81), avg. gap size = 3.00 (3 / 1) 13 16.42 0.00 5.56 chr2ptel1M 251544 251581 (748419) (AACAAAC)n#Simple_repeat 1 36 (0) m_b61s252i13 2270 chr2ptel1M 251544 AATAAAGCAAGCAGACAATAATAAACAAACAACAAACA 251581 i - - i i vv (AACAAAC)n#Si 1 AACAAA-CAA-CAAACAACAAACAACAAACAACAAACA 36 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 15 19.61 0.00 0.00 chr2ptel1M 252409 252437 (747563) (T)n#Simple_repeat 1 29 (0) m_b61s252i14 2271 chr2ptel1M 252409 TTTTTGTGTTTTTTTTTTTTCTCATTTTT 252437 v v i iv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 28 28.34 1.19 1.19 chr2ptel1M 252593 252676 (747324) (TC)n#Simple_repeat 1 84 (0) m_b61s252i15 2272 chr2ptel1M 252593 TCTCTTTGTCTCTCTCTTTGTCTCTCTCTCTTTTTCTTTCTCCCTTTTTT 252642 i v i v i i i i i i i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr2ptel1M 252643 ATTCTCTCTCATTCTATGTCTACT-TCATTCTCTC 252676 vi vi v v - - vi (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCT-CTCTCTCTCTCTC 84 Matrix = Unknown Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.02 (2 / 83), avg. gap size = 1.00 (2 / 2) 24 42.06 1.92 0.00 chr2ptel1M 252707 252862 (747138) (AG)n#Simple_repeat 1 159 (0) m_b61s252i16 2273 chr2ptel1M 252707 AGAGTCAGAAAAACAGATATAAACAGAAAAAAAAAAAAAGAGAGTAAGAG 252756 vv i i v v v i v i i i i i i vi (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr2ptel1M 252757 -GAAGGAGATAGAGAAAGAGACAGAGAGAAAAAGAGAACAAGACA-AAAG 252804 - ii v i v i i ivi v - i (AG)n#Simple_ 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 100 chr2ptel1M 252805 AGTAAAAAAGAGAATTTGAAAGAGTGAAATAAACAGAGAATCAAAGA-AA 252853 vi i i ivvv i v i v i v ivv i - i (AG)n#Simple_ 101 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 150 chr2ptel1M 252854 AAAGAGAGA 252862 i (AG)n#Simple_ 151 AGAGAGAGA 159 Matrix = Unknown Transitions / transversions = 1.45 (29/20) Gap_init rate = 0.02 (3 / 155), avg. gap size = 1.00 (3 / 3) 17 22.52 0.00 0.00 chr2ptel1M 253670 253705 (746295) (T)n#Simple_repeat 1 36 (0) m_b61s252i17 2274 chr2ptel1M 253670 TTTTATTTTATTTTTTTGTTTGTTTGTTTCTTCTTT 253705 v v v v v i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 36 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 12 26.11 1.67 5.17 chr2ptel1M 253891 253950 (746050) (AGAGTG)n#Simple_repeat 1 58 (0) m_b61s252i18 2275 chr2ptel1M 253891 AGAGTGAGCGTGAGTGAGAAAGAGAATGAGTAATAGAGAGAGCTCA-AAA 253939 v v v i v - - i v v - v - iv (AGAGTG)n#Sim 1 AGAGTGAGAGTGAGAGTGAGAGTG-A-GAGTGAGAGTGAGAG-TGAGAGT 47 chr2ptel1M 253940 GATAGTGAGAG 253950 v (AGAGTG)n#Sim 48 GAGAGTGAGAG 58 Matrix = Unknown Transitions / transversions = 0.33 (3/9) Gap_init rate = 0.07 (4 / 59), avg. gap size = 1.00 (4 / 4) 13 22.91 0.00 8.00 chr2ptel1M 254009 254062 (745938) (AGAC)n#Simple_repeat 1 50 (0) m_b61s252i19 2276 chr2ptel1M 254009 AGAGAGACATTCAGAGGGAGACAGACAGAAAGATCGATCCAGACAGAAAG 254058 v vv --v v - - vv v (AGAC)n#Simpl 1 AGACAGACAGACAGA--CAGACAGACAGACAGA-C-AGACAGACAGACAG 46 chr2ptel1M 254059 AGAG 254062 v (AGAC)n#Simpl 47 ACAG 50 Matrix = Unknown Transitions / transversions = 0.00 (0/9) Gap_init rate = 0.08 (4 / 53), avg. gap size = 1.00 (4 / 4) 14 25.04 1.79 3.64 chr2ptel1M 254870 254925 (745075) (TTTG)n#Simple_repeat 1 55 (0) m_b61s252i20 2277 chr2ptel1M 254870 TTTGTTTGTTCTGGTTGTGTTTTTGTTT-TAGGTTTTTTTTTTAATTTAG 254918 - v v v - vv v v vi - (TTTG)n#Simpl 1 TTTGTTTGTT-TGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTT-G 48 chr2ptel1M 254919 GTTTTTT 254925 v v (TTTG)n#Simpl 49 TTTGTTT 55 Matrix = Unknown Transitions / transversions = 0.10 (1/10) Gap_init rate = 0.05 (3 / 55), avg. gap size = 1.00 (3 / 3) 714 32.53 4.72 1.04 chr2ptel1M 255385 255850 (744150) C L1ME4c_3end#LINE/L1 (191) 639 157 m_b61s551i12 2278 chr2ptel1M 255385 TTCTGCTCATTTCACTTAGCATCTGT-TCATGTAAATCTCTCCAAGGTCT 255433 iv i - i - -- iv i i v v iv C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACAT-TATATCAT--AAACATTTTCCATGTTG 593 chr2ptel1M 255434 CTCTGGAATCATCTTGCTGGTCATTTCTTATAGAACAATAATATTCCATA 255483 viiv i v v iv vi i v i vvvv v C L1ME4c_3end#L 592 CTACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATC 543 chr2ptel1M 255484 GCATTAATTTACTATAACTTATTCAGCTATTCTCCAGCTGATGGGCAAGC 255533 vi ?i v i i i i i i i vii v i vvi C L1ME4c_3end#L 542 GAGTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTT 493 chr2ptel1M 255534 ACTCAATTTCCAGTTTCTTGCTA---------------CAA---ACATTT 255565 vvivi i i i --------------- --- i C L1ME4c_3end#L 492 AGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCT 443 chr2ptel1M 255566 TTTCATATGTAGGTCCCTTTCTCTCCTTTAAG--ATCTCTTTGAGATATA 255613 iviii i -- ii ii i i i-- i i ii v C L1ME4c_3end#L 442 TCGTGCATATAG--CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAA 395 chr2ptel1M 255614 AGCCCAGTAGAAACACTGCTGGATCAAAGGGTCTGCACAGTATGATAACT 255663 vv v viiv i i i v v v v v ii C L1ME4c_3end#L 394 TTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCT 345 chr2ptel1M 255664 TTTGAGA-ATACTTCCAAAATGCTCTCCAGAAGGGTTGTATCACTTCATA 255712 i v -i i v v i i i v i i C L1ME4c_3end#L 344 CTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACA 295 chr2ptel1M 255713 ACTCCATCATGAATGTATCAGTGTCCCAGTTTTCCCACATCCCCTCCAGA 255762 ?iv i vv v ? v iv i ? i v v C L1ME4c_3end#L 294 NTGCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGC 245 chr2ptel1M 255763 AGTGGTCATTATCTTTTCCTGTCATCTTAGCCAATCTGAGAAGTGTGTAA 255812 v vi vv ii vvv i v i i i v i i iv C L1ME4c_3end#L 244 ATTGGGTATTATCAATTTTTTAAATTTTTGCTAATTTAATAGGCGTAAAA 195 chr2ptel1M 255813 GGATACCTCAGCATGGTCTTAATTTGCATTTCTCTTAT 255850 v i i vii v ii i v C L1ME4c_3end#L 194 TGGTATCTCATTGTTGCTTTAATTTGCATTTCTTTGAT 157 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 42.55 CpG sites = 86, Kimura (unadjusted) = 44.54 Transitions / transversions = 1.34 (86/64) Gap_init rate = 0.02 (10 / 465), avg. gap size = 2.70 (27 / 10) 719 30.29 5.00 0.96 chr2ptel1M 255471 255870 (744130) C L1ME3G_3end#LINE/L1 (376) 548 133 m_b61s551i13 2278 chr2ptel1M 255471 ATAATATTCCATAGCATTAATTTACTATAACTTATTCAGCTATTCTCCAG 255520 i i vi v i i i i i i vi C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr2ptel1M 255521 CTGATGGGCAAGCACTCAATTTCCAGTTTCTTGCTA---CAAACATTTTT 255567 i i vvi vvivi i i i --- v vi C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr2ptel1M 255568 TCATATGTAGGTCCCTTT----CTCTCCTT-----------TAAG-ATCT 255601 v - v vi i v ----vi? -----------ii - i C L1ME3G_3end#L 448 GCA-ATGAACATCCTTGTACATGCNTCCTTGTGCACATGTGCGAGTATTT 400 chr2ptel1M 255602 CTTTGAGATATAAGCCCAGTAGAAACACTGCTGGATCAAAGGGTCTGCAC 255651 ? ii v v? ? v viiv i i v i C L1ME3G_3end#L 399 CTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGC 350 chr2ptel1M 255652 AGTATGATAACTTTTGAGA-ATACTTCCAAAATGCTCTCCAGAAGGGTTG 255700 v - -- v i v - v v i i ? i C L1ME3G_3end#L 349 ATT-T--TAAATTTTAATAGATACTGCCAAATTGCCCTCCAAAANGGCTG 303 chr2ptel1M 255701 TATCACTTCATAACTCCATCATGAATGTATCAGTGTCCCAGTTTTCCCAC 255750 i v i i vii i vv i v v v v i C L1ME3G_3end#L 302 TACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCAC 253 chr2ptel1M 255751 ATCCCCTCCAGAAGTGGTCATTATCTTTTCCTGTCATCTTAGCCAATCTG 255800 i i v iv v ? vi vv?iii vvv i v C L1ME3G_3end#L 252 ACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATCTG 203 chr2ptel1M 255801 AGAAGTGTGTAAGGATACCTCAGCATGGTCTTAATTTGCATTTCTCTTAT 255850 vii viv v i i vii v i i v C L1ME3G_3end#L 202 ATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGAT 153 chr2ptel1M 255851 CCACGGTGATTTAGAGCATC 255870 ivvii vv v C L1ME3G_3end#L 152 TACTAGTGAGGTTGAGCATC 133 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.17 CpG sites = 64, Kimura (unadjusted) = 40.52 Transitions / transversions = 1.14 (64/56) Gap_init rate = 0.02 (9 / 399), avg. gap size = 2.67 (24 / 9) 18 19.46 0.00 0.00 chr2ptel1M 257875 257909 (742091) (A)n#Simple_repeat 1 35 (0) m_b61s252i21 2279 chr2ptel1M 257875 AAAACGAAAAAAAAAAGAAAAAATAATAAAACAAA 257909 vi i v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 35 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 19 10.01 0.00 0.00 chr2ptel1M 257930 257961 (742039) (TTAT)n#Simple_repeat 1 32 (0) m_b61s252i22 2280 chr2ptel1M 257930 TTATTTATATATTTCTTTGTTTATTTATTTAT 257961 v v i (TTAT)n#Simpl 1 TTATTTATTTATTTATTTATTTATTTATTTAT 32 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 413 28.83 11.35 2.49 chr2ptel1M 259708 259892 (740108) MIRc#SINE/MIR 14 214 (54) m_b61s601i14 2281 chr2ptel1M 259708 TACAGTGGATAGACTATGGGTAGGGCCTTGATTCAGGAAAACCAGACTTT 259757 i v vi iv ----i i v v i v iv i MIRc#SINE/MIR 14 TGCAGTGGAAAGAGCACTGG----ACTTGGAGTCAGGAAGACCTGGGTTC 59 chr2ptel1M 259758 TAATCCTACCTCAGAAGCTTGCTA----------CT----CAAGTTATAG 259793 v i iiv v vvi i ---------- ---- i ivv MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTT 109 chr2ptel1M 259794 GACCTCTGTTTGATTCAGTTTTCTTTATCTGTAAAATGGGCTTAATAATA 259843 i v vv vi i i- vv MIRc#SINE/MIR 110 AACCTCTCTGAGCCTCAGTTTCCTC-ATCTGTAAAATGGGGATAATAATA 158 chr2ptel1M 259844 TCAGCAAAGT---CCTCA---GGTTGCCATGAGGATAAAATAAGACAATG 259887 i v vvv i--- --- iii v i i MIRc#SINE/MIR 159 CCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATG 208 chr2ptel1M 259888 C-TGTG 259892 i- MIRc#SINE/MIR 209 TATGTG 214 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.18 CpG sites = 27, Kimura (unadjusted) = 37.03 Transitions / transversions = 1.08 (27/25) Gap_init rate = 0.05 (10 / 184), avg. gap size = 2.60 (26 / 10) 357 24.77 14.86 1.80 chr2ptel1M 259784 259931 (740069) MIR#SINE/MIR 96 262 (0) m_b62s601i1 2281 chr2ptel1M 259784 CAAGTTATAGGACCTCTGTTTGATTCAGTTTTCTTTATCTGTAAAATGGG 259833 ivvi v v vi i i- MIR#SINE/MIR 96 CAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTC-ATCTGTAAAATGGG 144 chr2ptel1M 259834 CTTAATAATATCAGCAAAGTCCTCAGGTTGCCATGAGGATAAAATAAGAC 259883 vv vi v v vv v vi iii v i vi MIR#SINE/MIR 145 GATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTT 194 chr2ptel1M 259884 AAT-----------GCT-------GTGCATGACACACAGT----GCTGTA 259911 ----------- ------- v i i ---- vv MIR#SINE/MIR 195 AATACATGTAAAGCGCTTAGAACAGTGCCTGGCACATAGTAAGCGCTCAA 244 chr2ptel1M 259912 TAAGTACTAGCTACTTTATT 259931 i ii -- MIR#SINE/MIR 245 TAAATGTTAGCTA--TTATT 262 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.34 CpG sites = 17, Kimura (unadjusted) = 30.34 Transitions / transversions = 0.89 (17/19) Gap_init rate = 0.04 (6 / 147), avg. gap size = 4.17 (25 / 6) 186 0.00 0.00 0.00 chr2ptel1M 260012 260033 (739967) OldhAT1#DNA/hAT-Ac 2491 2512 (330) m_b62s601i2 2282 chr2ptel1M 260012 ACTAAATTTATTCACAGTGGGT 260033 OldhAT1#DNA/h 2491 ACTAAATTTATTCACAGTGGGT 2512 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 0.00 CpG sites = 0, Kimura (unadjusted) = 0.00 Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 269 33.05 7.20 0.75 chr2ptel1M 260056 260180 (739820) L2b_3end#LINE/L2 333 465 (1) m_b62s601i3 2283 chr2ptel1M 260056 TGTCTGCCCCACCATTCTGTGACCTCCATGAGAGCAGAGG--ATGTC--C 260101 v i vv v i i i i--i? --i L2b_3end#LINE 333 TGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGT 382 chr2ptel1M 260102 CTTACGTCACT-TTATGTTCCTGGTGCTCAGCCCAGGG-CTGCCATGTAC 260149 ii- i-i i i i ii i ii v ? - v iii v L2b_3end#LINE 383 CTTGT-TCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAG 431 chr2ptel1M 260150 AAAGCCCTTAAT---TGTTTACTGACTAGAAGAA 260180 v i v i i --- i ii v ii v L2b_3end#LINE 432 TAGGCGCTCAGTAAATATTTGTTGAATGAATGAA 465 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 41.98 CpG sites = 30, Kimura (unadjusted) = 48.58 Transitions / transversions = 2.73 (30/11) Gap_init rate = 0.05 (6 / 124), avg. gap size = 1.67 (10 / 6) 258 29.67 4.40 0.00 chr2ptel1M 260242 260332 (739668) C MIR3#SINE/MIR (5) 203 109 m_b62s601i4 2284 chr2ptel1M 260242 ATAGGATCACAGATGATCA---CTGGAAGGGATGTACAGGGCCATGGAGT 260288 i i vvi --- iv vvii ii vv C MIR3#SINE/MIR 203 ATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGT 154 chr2ptel1M 260289 GTGAACCACTCATTTTATAGATG-GGAAACCAAGGTTCACTGAGG 260332 vii v v i - ii ii vv C MIR3#SINE/MIR 153 CCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGG 109 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.61 CpG sites = 15, Kimura (unadjusted) = 38.61 Transitions / transversions = 1.25 (15/12) Gap_init rate = 0.02 (2 / 90), avg. gap size = 2.00 (4 / 2) 596 29.23 4.10 0.00 chr2ptel1M 260987 261181 (738819) MIRc#SINE/MIR 10 212 (56) m_b62s601i5 2285 chr2ptel1M 260987 GTAGTACAGTGGA--GAGTCCTGGGCATAGAGTCATGTGTACCTGAGTTT 261034 i i -- iv i v i v viv i i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr2ptel1M 261035 GAATTAAGCCTTGGACAATTACTAACTGTCT-ACCTCTGGCAAGTCAGTT 261083 i ivv v iv v v i v - iv v MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTT 109 chr2ptel1M 261084 AAACACTGTTTGCCTCAGTTTCCTCAACTCTCAAATGGGGATAAAAATA- 261132 v v v vv v v v v - MIRc#SINE/MIR 110 AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAC 159 chr2ptel1M 261133 ----TCAGCCTAACTTGGAAAGGTAAGATGGGAATAAAGTGACACAATAT 261178 ----i v v iiv ii v ivvi i i v i v i i MIRc#SINE/MIR 160 CTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGT 209 chr2ptel1M 261179 TTG 261181 v MIRc#SINE/MIR 210 ATG 212 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.44 CpG sites = 25, Kimura (unadjusted) = 37.23 Transitions / transversions = 0.78 (25/32) Gap_init rate = 0.02 (4 / 194), avg. gap size = 2.00 (8 / 4) 233 24.41 0.00 7.14 chr2ptel1M 261361 261435 (738565) C DNM1r#Unknown (2118) 2544 2475 m_b62s502i0 2286 chr2ptel1M 261361 TATATAGAAATATATATATATATATACACACATACATAGATTAATAATAA 261410 ? viv i i i v ----- v C DNM1r#Unknown 2544 TANATACGTATATATACACATATATACACACATACACACAT-----ATAC 2500 chr2ptel1M 261411 ACACATGCACGCATGCATATATATG 261435 ii ii ii i ii C DNM1r#Unknown 2499 ACACATATATACACACATACACGTG 2475 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 26.96 CpG sites = 13, Kimura (unadjusted) = 31.61 Transitions / transversions = 3.25 (13/4) Gap_init rate = 0.07 (5 / 74), avg. gap size = 1.00 (5 / 5) 34 3.03 0.00 0.00 chr2ptel1M 264198 264231 (735769) (TA)n#Simple_repeat 1 34 (0) c_b62s251i0 2287 chr2ptel1M 264198 TATATATATATATATATATATATATATACATATA 264231 i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATA 34 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 314 30.25 8.50 0.61 chr2ptel1M 267618 267770 (732230) L2a_3end#LINE/L2 353 517 (0) m_b62s601i6 2288 chr2ptel1M 267618 ATTTTCTACCTCATTGTTGATGTATTGTCTGTC-----CCACCAGTGTGT 267662 v i i vv i vi v ----- i vi L2a_3end#LINE 353 ATATTTTACTTATTTATTTGTTTATTGTCTGTCTCCCCCCACTAGAATGT 402 chr2ptel1M 267663 GACCTCCATGAGAGCAGGG---TATGTTCTTTGTACTTCCTTTTG--CTC 267707 i v i --- v iiv v ii iv vi --ii L2a_3end#LINE 403 AAGCTCCATGAGGGCAGGGACTTTTGTCTGTTTTGTTCACTGCTGTATCC 452 chr2ptel1M 267708 CTGGTGCTTAGTCCAGGGCCTGGCATGTTGCAGGCACT---TCACTGTTT 267754 ii i i vv v ii v i i --- v v i L2a_3end#LINE 453 CCAGCGCCTAGAACAGTGCCTGGCACATAGTAGGCGCTCAATAAATATTT 502 chr2ptel1M 267755 GCTGACTTGAAGGAAT 267770 i v- v L2a_3end#LINE 503 GTTGAA-TGAATGAAT 517 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.53 CpG sites = 26, Kimura (unadjusted) = 39.73 Transitions / transversions = 1.30 (26/20) Gap_init rate = 0.03 (5 / 152), avg. gap size = 2.80 (14 / 5) 314 29.75 6.02 1.44 chr2ptel1M 267632 267764 (732236) L2d2_3end#LINE/L2 412 550 (5) m_b62s601i7 2288 chr2ptel1M 267632 TGTTGATGTATTGTCTGTCCCACCAGTGTGTGACCTCCATGAGAGCAGGG 267681 v v vi v i vv i v v i L2d2_3end#LIN 412 TGTTTATGTCTTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGG 461 chr2ptel1M 267682 --TATGTTCTTTGTACTTCCTTTTGCTCC---TGGTGCTTAGTCCAGGGC 267726 --i --i i i v iii ---ii i i iv v L2d2_3end#LIN 462 ACCATGT--CTTATACTTCTTTGTATCCCCCACAGCGCCTAGCACAGTGC 509 chr2ptel1M 267727 CTGGCATGTTGCAGGCACT---TCACTGTTTGCTGACTTGA 267764 v iiiv i i --- v v i i i L2d2_3end#LIN 510 CTTGCACACAGTAGGCGCTCAATAAATATTTGTTGATTTGA 550 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.71 CpG sites = 24, Kimura (unadjusted) = 39.29 Transitions / transversions = 1.60 (24/15) Gap_init rate = 0.04 (5 / 132), avg. gap size = 2.00 (10 / 5) 274 23.36 14.75 5.26 chr2ptel1M 270315 270436 (729564) C MIR3#SINE/MIR (7) 201 69 m_b62s601i8 2289 chr2ptel1M 270315 AAAGTCATGAGATGT-AGAGCTGAAAGACACTTCAGAG---------TCC 270354 i i iii - i iv i i --------- C MIR3#SINE/MIR 201 AGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCC 152 chr2ptel1M 270355 AAGGTTTTTCAATTTT---GATAGTGAAACTGAAGCTCAGA-----GAAG 270396 v-iiii - --- iiv i i ----- C MIR3#SINE/MIR 151 AAC-CCCCTCA-TTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAG 104 chr2ptel1M 270397 TGATTTGCTCAAAGGTCAGAGTACTGGTGTGTTAGAGGCA 270436 i i - ---i -i i?v v C MIR3#SINE/MIR 103 TGACTTGCCC-AAGGTCA---CAC-AGCNAGTTAGTGGCA 69 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.39 CpG sites = 22, Kimura (unadjusted) = 30.39 Transitions / transversions = 4.40 (22/5) Gap_init rate = 0.09 (11 / 121), avg. gap size = 2.27 (25 / 11) 22 6.33 0.00 0.00 chr2ptel1M 271177 271209 (728791) (TAACCC)n#Simple_repeat 1 33 (0) m_b62s252i0 2290 chr2ptel1M 271177 TAACTCTAAGCCTAACCCTAACCCTAACCCTAA 271209 i v (TAACCC)n#Sim 1 TAACCCTAACCCTAACCCTAACCCTAACCCTAA 33 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 74 7.71 1.02 0.00 chr2ptel1M 273101 273198 (726802) (AT)n#Simple_repeat 1 99 (0) c_b62s251i1 2291 chr2ptel1M 273101 ATATATATATATATATATATATATATATATATATATATATATATA-ACAC 273149 - i i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr2ptel1M 273150 ACACACACACATATATATATATATATATATATATATATATATATATATA 273198 i i i i i (AT)n#Simple_ 51 ATATATATATATATATATATATATATATATATATATATATATATATATA 99 Matrix = Unknown Transitions / transversions = 1.00 (7/0) Gap_init rate = 0.01 (1 / 97), avg. gap size = 1.00 (1 / 1) 15 19.61 0.00 0.00 chr2ptel1M 273247 273275 (726725) (A)n#Simple_repeat 1 29 (0) m_b62s252i1 2292 chr2ptel1M 273247 AAAAAGAAACAAAAATGAAAAAAACAAAA 273275 i v vi v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA 29 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 12 17.15 4.88 2.38 chr2ptel1M 273843 273883 (726117) (TTAACA)n#Simple_repeat 1 42 (0) m_b62s252i2 2293 chr2ptel1M 273843 TTAACATTAACTTTAGCTAGTGAC--TAACAGTAACAATAACA 273883 v i - v i -- v v (TTAACA)n#Sim 1 TTAACATTAACATTAAC-ATTAACATTAACATTAACATTAACA 42 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.50 (3 / 2) 263 28.75 6.25 0.00 chr2ptel1M 275676 275755 (724245) MIRb#SINE/MIR 3 87 (181) m_b62s601i9 2294 chr2ptel1M 275676 GAAAGGCAGCATGGCAGAATGGAAAGAAGACTATATTTGGAGTCAGGC-- 275723 ii i iiv i iv vivv i -- MIRb#SINE/MIR 3 GAGGGGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAG 52 chr2ptel1M 275724 -CATGTGTTGAAATTCTGATTCTG-CACCT-CTAG 275755 - v v vi i i ii - i - MIRb#SINE/MIR 53 ACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAG 87 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.75 CpG sites = 15, Kimura (unadjusted) = 37.80 Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.05 (4 / 79), avg. gap size = 1.25 (5 / 4) 230 19.05 9.52 0.00 chr2ptel1M 278425 278487 (721513) C DNM1r#Unknown (2111) 2551 2483 m_b62s502i1 2295 chr2ptel1M 278425 TGTTAAATACA-ATGGGTGTATATATATATATACACACACACACAC---- 278469 vv ? - i vi i i i i ---- C DNM1r#Unknown 2551 TGTTCTATANATACGTATATATACACATATATACACACATACACACATAT 2502 chr2ptel1M 278470 -CACACACATGTCCACACA 278487 - i i v C DNM1r#Unknown 2501 ACACACATATATACACACA 2483 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 20.83 CpG sites = 8, Kimura (unadjusted) = 22.93 Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.05 (3 / 62), avg. gap size = 2.00 (6 / 3) 239 29.96 8.07 5.70 chr2ptel1M 279289 279511 (720489) C L1ME3B_3end#LINE/L1 (332) 657 430 m_b62s551i0 2296 chr2ptel1M 279289 ACCGTATGTAATGATCTCTTG-GTCCTGCTCATTTCACTCAGCATCA-GT 279336 ? - -- i - i iv i i i - C L1ME3B_3end#L 657 ACNGTATGTA-T--TCTTTTGTGTCTTGCTTCTTTCGCTCAACATTATGT 611 chr2ptel1M 279337 TCCTGTAAGTCTC-TCCAGGCCTTT--------CTGAAATCATCCTGCTG 279377 -- i vi - v iiv -------- v i -- v v -- C L1ME3B_3end#L 610 T--TGTGAGATTCATCCATGTTGTTGCGTGTAGCTGTAGT--TCGTTC-- 567 chr2ptel1M 279378 GATATTTCTTACAGAACAATCATATTCCATATCATTCATAAACCAGAACT 279427 - v iv i v v i i --- vvi vv v v i C L1ME3B_3end#L 566 -ATTTTCATTGCTGTATAGT---ATTCCATTGTATGAATATACCACAATT 521 chr2ptel1M 279428 TATTCAGCCATTGTCCAACTGATGGGCATCCA-------CTCAGTTTCTA 279470 i v v v vii i iii-------ii i?i C L1ME3B_3end#L 520 TATTTATCCATTCTACTGTTGATGGACATTTGGGTTGTTTCCAGTTTTNG 471 chr2ptel1M 279471 GCCACTACAAAGAGGGCTGCCACAAACATTTTGACACATAT 279511 i i i v iv i ii i vii i C L1ME3B_3end#L 470 GCTATTACGAACAATGCTGCTATGAACATTCTTGTACATGT 430 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.59 CpG sites = 39, Kimura (unadjusted) = 40.26 Transitions / transversions = 1.62 (39/24) Gap_init rate = 0.08 (18 / 222), avg. gap size = 1.72 (31 / 18) 236 33.32 5.30 2.21 chr2ptel1M 279396 279527 (720473) C L1ME4c_3end#LINE/L1 (275) 555 420 m_b62s551i1 2296 chr2ptel1M 279396 ATCATATTCCATATCATTCATAAACCAGAACTTATTCAGCCATTGTCCAA 279445 v vvvi ?v iv v i i i i vi v C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chr2ptel1M 279446 CTGATGGGCATCCA-------CTCAGTTTCTAGCCACTACAAAGAGGGCT 279488 i v i ii -------ii i i v i i i v iv C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCT 456 chr2ptel1M 279489 GCCACAAACATTTTGACACATATGGATCCCTTTCCCTTC 279527 v ii i viii i --- i i C L1ME4c_3end#L 455 GCAATGAACATCTTCGTGCATATAG---CTTTTTCCTTC 420 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 45.57 CpG sites = 28, Kimura (unadjusted) = 47.13 Transitions / transversions = 1.87 (28/15) Gap_init rate = 0.03 (4 / 131), avg. gap size = 2.50 (10 / 4) 285 30.91 6.36 0.00 chr2ptel1M 279400 279509 (720491) C L1ME3G_3end#LINE/L1 (380) 544 428 m_b62s551i2 2296 chr2ptel1M 279400 TATTCCATATCATTCATAAACCAGAACTTATTCAGCCATTGTCCAACTGA 279449 vi vv v v i i i vi v i C L1ME3G_3end#L 544 TATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTATTGA 495 chr2ptel1M 279450 TGGGCATCCA-------CTCAGTTTCTAGCCACTACAAAGAGGGCTGCCA 279492 i ii -------ii i i v i i v iv v C L1ME3G_3end#L 494 TGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCTGCAA 445 chr2ptel1M 279493 CAAACATTTTGACACAT 279509 ii ii vii C L1ME3G_3end#L 444 TGAACATCCTTGTACAT 428 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.73 CpG sites = 22, Kimura (unadjusted) = 41.73 Transitions / transversions = 1.83 (22/12) Gap_init rate = 0.01 (1 / 109), avg. gap size = 7.00 (7 / 1) 11 11.13 6.90 0.00 chr2ptel1M 281070 281098 (718902) (GAGACA)n#Simple_repeat 1 31 (0) m_b62s252i3 2297 chr2ptel1M 281070 GAGAGAGAAACAGAGAC--AGACAGACACAG 281098 v i -- v (GAGACA)n#Sim 1 GAGACAGAGACAGAGACAGAGACAGAGACAG 31 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.04 (1 / 28), avg. gap size = 2.00 (2 / 1) 11 16.38 5.88 0.00 chr2ptel1M 281441 281474 (718526) (TAAAAA)n#Simple_repeat 1 36 (0) m_b62s252i4 2298 chr2ptel1M 281441 TAAAGA-AAAAATCAAAATGAATTTAAAAA-AAAAA 281474 i - v i vv - (TAAAAA)n#Sim 1 TAAAAATAAAAATAAAAATAAAAATAAAAATAAAAA 36 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2) 206 30.53 5.45 1.75 chr2ptel1M 281934 282043 (717957) C L3#LINE/CR1 (480) 3619 3506 m_b62s601i10 2299 chr2ptel1M 281934 ATGTTTTGCCCATGAC--AACATCATGC-CCAGA-GTGACCTTAGGCACT 281979 vvi vi -- iiv i - - ii v v- vi C L3#LINE/CR1 3619 ATGTGGCGCCCAGAACTGAACGCAATACTCCAGATGTGGTCTGAC-CAGC 3571 chr2ptel1M 281980 ACATAGAATAACAGATAATAGTACTTCACTTGG-ATGGAAACTGT-CTTC 282027 i v v i i i i- v v i v ?-v v i - C L3#LINE/CR1 3570 GCAGAGTACAGCGGG-ACTATTACCTCCCTTGNTCTGGACACTATACTTC 3522 chr2ptel1M 282028 TATCAGTACAGTCTAA 282043 i i i i C L3#LINE/CR1 3521 TATTAATGCAGCCTAA 3506 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.55 CpG sites = 19, Kimura (unadjusted) = 40.86 Transitions / transversions = 1.36 (19/14) Gap_init rate = 0.06 (7 / 109), avg. gap size = 1.14 (8 / 7) 260 23.45 16.19 2.52 chr2ptel1M 282468 282572 (717428) MIR3#SINE/MIR 83 201 (7) m_b62s601i11 2300 chr2ptel1M 282468 TGTGATGACCCTTGAGAAAATCACTTC-----TCTGTGTTTCAGTATCTT 282512 - - i v i ----- v ii v i MIR3#SINE/MIR 83 TGTG-TGACC-TTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCT 130 chr2ptel1M 282513 C--CTGTATATTGAAAAAGGTTGGA---------CTCTGAAATGTCTTTC 282551 -- v v - iii --------- i ii vi i MIR3#SINE/MIR 131 CATCTGTAAAATG-AGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCC 179 chr2ptel1M 282552 AGCTCT-ACAACTCATGATTTT 282572 - viii i MIR3#SINE/MIR 180 AGCTCTGACATTCTATGATTCT 201 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.40 CpG sites = 17, Kimura (unadjusted) = 29.40 Transitions / transversions = 2.43 (17/7) Gap_init rate = 0.07 (7 / 104), avg. gap size = 2.86 (20 / 7) 17 12.69 0.00 0.00 chr2ptel1M 283292 283317 (716683) (T)n#Simple_repeat 1 26 (0) m_b62s252i5 2301 chr2ptel1M 283292 TTTGTTTTTGTTTTTGTTTTTTTTTT 283317 v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 507 30.26 2.50 2.50 chr2ptel1M 283620 283819 (716181) C MIRb#SINE/MIR (67) 201 2 m_b62s601i12 2302 chr2ptel1M 283620 ATTAATTCACCTTATCTTCAAAATAACCTTGCAAGTTAGGTGATTTTATT 283669 vi ii v i v i i i v i--- C MIRb#SINE/MIR 201 ATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTA---TTATT 155 chr2ptel1M 283670 CTCCCCCATTTAAGAGTTGAGGAAACTGAGG--TAAAGAGTTTAAGT-GC 283716 v - v v v --i i v -i C MIRb#SINE/MIR 154 ATCCCC-ATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAAC 106 chr2ptel1M 283717 TTGTTAAGGGGCACAGAGCTAGGAACTGTCTTAAGCTTGATTTAAGCTCA 283766 iiv i v v v v v vv iv vv ii i i C MIRb#SINE/MIR 105 TTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCA 56 chr2ptel1M 283767 GGAACTTATGATTCT-ATGCCCAGGTCTCTTTTAATTATTCTAC-CAGCT 283814 vviv v i i- v iv - iv i iiv i - v i C MIRb#SINE/MIR 55 GGTCTGTCTGACTCCAAAGCCCGTG-CTCTTTCCACTGCACCACGCTGCC 7 chr2ptel1M 283815 CCCCT 283819 i C MIRb#SINE/MIR 6 CCTCT 2 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.73 CpG sites = 30, Kimura (unadjusted) = 39.30 Transitions / transversions = 1.03 (30/29) Gap_init rate = 0.05 (9 / 199), avg. gap size = 1.11 (10 / 9) 259 28.57 4.76 0.00 chr2ptel1M 284918 285001 (714999) MIR3#SINE/MIR 115 202 (6) m_b62s601i13 2303 chr2ptel1M 284918 TGAATCTATGTTTCCCTGTCTGTAAAATGAGGAGG-TGCACTCTATGGCC 284966 iii vv iii i - v vv ii MIR3#SINE/MIR 115 TGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATC 164 chr2ptel1M 284967 TGGTAGGTTCCTTCCAG---TGATCCTCTGGGATCCTA 285001 vvv i --- ivi iv i MIR3#SINE/MIR 165 TCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTA 202 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.91 CpG sites = 14, Kimura (unadjusted) = 36.91 Transitions / transversions = 1.40 (14/10) Gap_init rate = 0.02 (2 / 83), avg. gap size = 2.00 (4 / 2) 182 30.17 5.88 2.53 chr2ptel1M 285103 285255 (714745) C L2b_3end#LINE/L2 (23) 443 286 m_b62s601i14 2304 chr2ptel1M 285103 ACTGAAGGGCCTGCAA-ATGCCAGGCTCTGGGCTAAGCACCAGGAGCAAA 285151 - v i vi-i ? v i i ii iii v C L2b_3end#LINE 443 ACTGA-GCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGGGATACA 395 chr2ptel1M 285152 AGGAGGTTTGAGG-AACCTC---CCCTGGTGTCACGGAGGTCACGGACT- 285196 iv iv vvii i- iv ? --- viv v i v - C L2b_3end#LINE 394 GCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGGAGCTCACAGTCTA 345 chr2ptel1M 285197 GTGGGGCAGACA-ACACATCAACAATGA-GATAGAAACGCGCTGTGCACA 285244 v - ii v ? -- -i ?iv v ivv -i C L2b_3end#LINE 344 GTGGGGGAGACAGACATGTAANCA--GACAATNATAACCCAGAGTG-GCA 298 chr2ptel1M 285245 GGATA-AACTGG 285255 i -i C L2b_3end#LINE 297 GGGTAGGACTGG 286 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 40.03 CpG sites = 26, Kimura (unadjusted) = 41.23 Transitions / transversions = 1.37 (26/19) Gap_init rate = 0.07 (11 / 152), avg. gap size = 1.18 (13 / 11) 20 20.33 3.45 1.69 chr2ptel1M 285692 285749 (714251) (AGG)n#Simple_repeat 1 59 (0) m_b62s252i6 2305 chr2ptel1M 285692 AGGAGGAGGAGGTGAGTGTGGGAGG-GGAGGAAGTGAAGGAGGCCGCGG- 285739 v - v vi - i v i vv v - (AGG)n#Simple 1 AGGAGGAGGAGGAG-GAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA 49 chr2ptel1M 285740 GGAGGAGGAG 285749 (AGG)n#Simple 50 GGAGGAGGAG 59 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.05 (3 / 57), avg. gap size = 1.00 (3 / 3) 15 20.27 2.27 4.65 chr2ptel1M 288210 288253 (711747) (GA)n#Simple_repeat 1 43 (0) m_b62s252i7 2306 chr2ptel1M 288210 GAGAGAGAGGGAACAAGA-AGAGATGATATGAGAGAAAAAGAGAG 288253 i ivi - - v - i i (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGA-GAGA-GAGAGAGAGAGAGAG 43 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.07 (3 / 43), avg. gap size = 1.00 (3 / 3) 434 30.65 5.43 2.64 chr2ptel1M 290260 290517 (709483) HERVP71A#LTR/ERV1 4834 5098 (2492) m_b62s701i0 2307 chr2ptel1M 290260 AGAACAAATTATTCC--GATATGGAATAGTGGAAGAAAT-ACCTCGGATC 290306 i i v -- v vv i i v -ivi i iv HERVP71A#LTR/ 4834 AGAACAGATTGTACCTAGATTTGGCCTGGTGGAAAATATTGATTCAGACA 4883 chr2ptel1M 290307 A-GGGAAACATTTTTCTGCCCAAG--TATT---GAGAATCTGATTAGGGC 290350 - iv i v -- i -- i --- i i-- viii v HERVP71A#LTR/ 4884 ATGGGAGCCACTTTAC--CTCAAGGGTGTTAAGGGGAATT--ATGGAAGG 4929 chr2ptel1M 290351 CTTAGAAATCACATGGGATT--C-CAACCCTTGGCATCCTCCCTCTTCTG 290397 i v i v -- - v i i i HERVP71A#LTR/ 4930 TTTACAAATTAGATGGGATTATCACACCCCTTGGCATCCCCCTTCCTCTG 4979 chr2ptel1M 290398 AGAAAATAGAAAAGATGAATCAAGAAATAAAAAGGCA-ACCAACTAAATT 290446 ii ii ii ivvv v i - i - i i HERVP71A#LTR/ 4980 GAAAGGTAGAAAGAATGAATCAAACTCTCAAAAAGCATATC-ACCAAACT 5028 chr2ptel1M 290447 -GTTTTCGAGACCCAACTATCTAAGACTAAATATCTTTCTTTTGCTGTAG 290495 -i i v i iv v ii vi i i ii vv v vv vv HERVP71A#LTR/ 5029 AATCTTAGAAACTAAAATGCCTTGGACCAAATGTCTCCCAATAGCACTCC 5078 chr2ptel1M 290496 TTAGAATCAGAACCAAGCCACA 290517 i i i -- v HERVP71A#LTR/ 5079 TTAGGATTAGGAC--AGCCCCA 5098 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.89 CpG sites = 47, Kimura (unadjusted) = 40.89 Transitions / transversions = 1.57 (47/30) Gap_init rate = 0.06 (16 / 257), avg. gap size = 1.31 (21 / 16) 13 22.62 5.00 3.28 chr2ptel1M 292487 292546 (707454) (AAATTTA)n#Simple_repeat 1 61 (0) m_b62s252i8 2308 chr2ptel1M 292487 AAATTTGTAAATTTAAAA-TTAATATTTGTTGTATAAAGATTAAAA-AT- 292533 -v - v ivvi v iv -v - (AAATTTA)n#Si 1 AAATTT-AAAATTTAAAATTTAAAATTTAAAATTTAAAATTTAAAATTTA 49 chr2ptel1M 292534 AAATTAAAACATT 292546 v - (AAATTTA)n#Si 50 AAATTTAAA-ATT 61 Matrix = Unknown Transitions / transversions = 0.38 (3/8) Gap_init rate = 0.08 (5 / 59), avg. gap size = 1.00 (5 / 5) 342 22.38 1.68 6.14 chr2ptel1M 294502 294620 (705380) C MIRc#SINE/MIR (153) 115 2 m_b62s601i15 2309 chr2ptel1M 294502 GGGGTTAAGTGACTTGCCCAGGGTCACACAGCCAGGGTTAAGGTGTTAGG 294551 i i i --- - vi i C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG---TAA-GTGGCAGA 70 chr2ptel1M 294552 TGCC-TGATTTGTACTCGGGGCCTCCTGAATTCCGGT-TGGTGCTCTACC 294599 - -v i i v i i v i v i vi -ii vi C MIRc#SINE/MIR 69 -GCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTC 21 chr2ptel1M 294600 CACTGCTACCCCTAGTGCCCC 294620 - v - v i C MIRc#SINE/MIR 20 CACTGC-ACCAC-ACTGCCTC 2 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 25.92 CpG sites = 16, Kimura (unadjusted) = 27.17 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.08 (9 / 118), avg. gap size = 1.00 (9 / 9) 19 26.81 3.57 2.35 chr2ptel1M 295333 295416 (704584) (ATTTTTT)n#Simple_repeat 1 85 (0) m_b62s252i9 2310 chr2ptel1M 295333 ATTTTTTATTTCCAAATTTGTCTTGTCTTTTGTATTTATTTGGGATTTGT 295382 iiv v v v - - vv v vvv v (ATTTTTT)n#Si 1 ATTTTTTATTTTTTATTTTTTATT-T-TTTATTTTTTATTTTTTATTTTT 48 chr2ptel1M 295383 TCATTTAT-TTTTCTAGTTTTT-TTTTTT-TTTTTTA 295416 vv v - i v - - (ATTTTTT)n#Si 49 TATTTTTTATTTTTTATTTTTTATTTTTTATTTTTTA 85 Matrix = Unknown Transitions / transversions = 0.20 (3/15) Gap_init rate = 0.06 (5 / 83), avg. gap size = 1.00 (5 / 5) 216 22.03 9.76 5.88 chr2ptel1M 296786 296867 (703133) MIRc#SINE/MIR 67 151 (117) m_b63s601i0 2311 chr2ptel1M 296786 GACCCTGACTCTCAGAAAGTCTATGACCTTTGGGCAAATC------CCTG 296829 i i v v i vv iv v i - i ------ - MIRc#SINE/MIR 67 GGCTCTGCCACTTACTAGCTGTGTGACCTT-GGGCAAGTCACTTAACCT- 114 chr2ptel1M 296830 CTCTGAGTTTCATTTTCCTC--CTATAAATTGAAGGGGAT 296867 ii v -- i --- v MIRc#SINE/MIR 115 CTCTGAGCCTCAGTTTCCTCATCTGTAAA---ATGGGGAT 151 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.42 CpG sites = 9, Kimura (unadjusted) = 26.42 Transitions / transversions = 1.12 (9/8) Gap_init rate = 0.09 (7 / 81), avg. gap size = 1.86 (13 / 7) 320 22.88 11.61 2.46 chr2ptel1M 296807 296918 (703082) MIR3#SINE/MIR 85 206 (2) m_b63s601i1 2311 chr2ptel1M 296807 TATGACCTTTGGGCAAATC------CCTGCTCTGAGTTTCATTTTCCTC- 296849 i - i ------ - i ii v - MIR3#SINE/MIR 85 TGTGACCTT-GGGCAAGTCACTTCACCT-CTCTGGGCCTCAGTTTCCTCA 132 chr2ptel1M 296850 -CTATAAATTGAAGGGGATTGGATT---CTACTTCTGAAGTGTCTTTCAG 296895 - i v - i i ---iv ii i i vi i MIR3#SINE/MIR 133 TCTGTAAAATG-AGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAG 181 chr2ptel1M 296896 CTCC-ACATCTTCTGACTTT-TGAT 296918 i- ii v i i - MIR3#SINE/MIR 182 CTCTGACATTCTATGATTCTATGAT 206 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.03 CpG sites = 20, Kimura (unadjusted) = 29.03 Transitions / transversions = 4.00 (20/5) Gap_init rate = 0.08 (9 / 111), avg. gap size = 1.78 (16 / 9) 19 38.29 0.00 0.00 chr2ptel1M 299385 299458 (700542) (TA)n#Simple_repeat 1 74 (0) m_b63s252i0 2312 chr2ptel1M 299385 TACATAAGTATATGTGTGTGTGTATATATATATGCATGTATATTTACATG 299434 i vi i i i i i ii i v i i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr2ptel1M 299435 TCTGTGTATATTTCTGTATGTATA 299458 v i i v v i i (TA)n#Simple_ 51 TATATATATATATATATATATATA 74 Matrix = Unknown Transitions / transversions = 3.20 (16/5) Gap_init rate = 0.00 (0 / 73), avg. gap size = 0.0 (0 / 0) 598 29.32 4.71 0.00 chr2ptel1M 299656 299846 (700154) C MIRc#SINE/MIR (59) 209 10 m_b63s601i2 2313 chr2ptel1M 299656 ATATTGTATCACTTTATCCTCATCTTAACTTTCTAACTTAGG----GT-G 299700 i i v i v ivvi ii v i vv ---- i- C MIRc#SINE/MIR 209 ACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAG 160 chr2ptel1M 299701 ATAATGTTATCCCCATTTAAGAGTTGAGGAAACTGAGGAAAACAGAGTTT 299750 i v i v v v vvv v v C MIRc#SINE/MIR 159 GTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTT 110 chr2ptel1M 299751 AATTGACTTACCCAGAGATGCACAGTTAGTAAATGTCCAAGGCTCACTTC 299800 v i ii vii i i v vi v vvivi C MIRc#SINE/MIR 109 AAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTC 60 chr2ptel1M 299801 AAACTCAGGTACACTTGACT--ATGTCCAGGACTC--TCCACTGAACTAC 299846 i i viv i -- v vi -- v i C MIRc#SINE/MIR 59 GAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.73 CpG sites = 27, Kimura (unadjusted) = 37.56 Transitions / transversions = 0.93 (27/29) Gap_init rate = 0.02 (4 / 190), avg. gap size = 2.25 (9 / 4) 265 28.57 6.59 0.00 chr2ptel1M 300498 300588 (699412) MIR3#SINE/MIR 109 205 (3) m_b63s601i3 2314 chr2ptel1M 300498 CCTCAGTGAACCTCAGTTTCC-CATTTACAAAATGAGTGGATCACGCC-- 300544 vv ii - i ii v i iivi i-- MIR3#SINE/MIR 109 CCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAG 158 chr2ptel1M 300545 ATGGCCCTGAAGGGCCCTTCCAGTGCT--CA-TCTGTGATCCCATAA 300588 ii iiv v iv -- - i i i i MIR3#SINE/MIR 159 ATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTATGA 205 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.29 CpG sites = 19, Kimura (unadjusted) = 38.29 Transitions / transversions = 2.71 (19/7) Gap_init rate = 0.04 (4 / 90), avg. gap size = 1.50 (6 / 4) 407 32.05 10.00 1.46 chr2ptel1M 300773 300962 (699038) C MIRb#SINE/MIR (29) 239 34 m_b63s601i4 2315 chr2ptel1M 300773 TAGTATGTGTACAGCCCTGTGTGCCATGCTCT----GCATTGTCTTATTT 300818 v ivvi v ivvvii i ---- i i C MIRb#SINE/MIR 239 TACTATGTGCCAGGCACTGTGCTAAGCGCTTTACATGCATTATCTCATTT 190 chr2ptel1M 300819 TATCCTCATGAGAATCTGAGGACTTAACTGCTATTATTATACCCATTTGA 300868 v ii v i iviv vv --- v v v C MIRb#SINE/MIR 189 AATCCTCACAACAACCCTGCGAGGTA---GGTATTATTATCCCCATTTTA 143 chr2ptel1M 300869 CAGATTAAAAAACTGAATCTAACAGAGGTCCTATAATTTGACC------- 300911 v ii iv v v ivvi i v ------- C MIRb#SINE/MIR 142 CAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCA 93 chr2ptel1M 300912 -------AGCAAATTTTTGAAGTGGGATTAAAACCCTGGGATTCCTGA-T 300953 ------- i i vviv ivi vi v vv vi - C MIRb#SINE/MIR 92 CACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACT 43 chr2ptel1M 300954 TCAAGGCCC 300962 i i C MIRb#SINE/MIR 42 CCAAAGCCC 34 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.62 CpG sites = 28, Kimura (unadjusted) = 42.27 Transitions / transversions = 0.88 (28/32) Gap_init rate = 0.04 (7 / 189), avg. gap size = 3.14 (22 / 7) 385 31.58 11.05 2.03 chr2ptel1M 300804 300984 (699016) C MIRc#SINE/MIR (58) 210 14 m_b63s601i5 2315 chr2ptel1M 300804 TGCATTGTCTTATTTTATCCTCATGAGAATC---TGAGG---ACTTAACT 300847 i i i v ii v i --- ---i vvii v C MIRc#SINE/MIR 210 TACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCA 161 chr2ptel1M 300848 GCTATTATTATACCCATTTGACAGATTAAAAAACTGAATCTAACAGAGGT 300897 v v v v ii iv v v C MIRc#SINE/MIR 160 GGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGT 111 chr2ptel1M 300898 CCTATAATTTGACC--------------AGCAAATTTTTGAAGTGGGATT 300933 ivvi i i v -------------- i i vviv ivi i C MIRc#SINE/MIR 110 TAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACT 61 chr2ptel1M 300934 AAAACCCTGGGATTCCTGATTCAAGGCCCTATCCACATTCTATCCAATGT 300983 vi v vv i v i i vi v ---- v v i C MIRc#SINE/MIR 60 CGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGC----TCTTTCCACTGC 15 chr2ptel1M 300984 A 300984 C MIRc#SINE/MIR 14 A 14 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.79 CpG sites = 28, Kimura (unadjusted) = 41.69 Transitions / transversions = 1.00 (28/28) Gap_init rate = 0.04 (7 / 180), avg. gap size = 3.43 (24 / 7) 16 0.00 0.00 0.00 chr2ptel1M 301131 301148 (698852) (A)n#Simple_repeat 1 18 (0) m_b63s252i1 2316 chr2ptel1M 301131 AAAAAAAAAAAAAAAAAA 301148 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAA 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 435 19.30 7.32 7.32 chr2ptel1M 302027 302149 (697851) C MIRc#SINE/MIR (141) 127 5 m_b63s601i6 2317 chr2ptel1M 302027 CTGAGGC-AATTGGGGTTAAGTGACTTGCCCAGGATCACACAGCCAGGAA 302075 -v vv i i i i --- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG--- 81 chr2ptel1M 302076 GTATTAAGTGTCTGAGAGC--AGATCTGAACTTGGGTCCTCCTGACTTCA 302123 ---- v -- --i iii iii i i C MIRc#SINE/MIR 80 ----TAAGTGGC--AGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCA 37 chr2ptel1M 302124 GG------ACTCTATCCACTGCACCACCCAGC 302149 i ------i v v v C MIRc#SINE/MIR 36 AGTCCAGTGCTCTTTCCACTGCACCACACTGC 5 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 21.74 CpG sites = 15, Kimura (unadjusted) = 22.90 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.10 (12 / 122), avg. gap size = 1.50 (18 / 12) 318 27.81 12.07 0.78 chr2ptel1M 305007 305122 (694878) MIRb#SINE/MIR 3 131 (137) m_b63s601i7 2318 chr2ptel1M 305007 GAAAGGCAGCAGGACGGAATGGAAAGATCACTATATTTGGACTCAGGACA 305056 ii iv ii v i v vivv v - MIRb#SINE/MIR 3 GAGGGGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCA-GACA 51 chr2ptel1M 305057 GA----GGTTGAAATTCTGGTTCTGCAACT------CTGGG----CTTGG 305092 ---- vi i i i v ------ v ---- MIRb#SINE/MIR 52 GACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 101 chr2ptel1M 305093 CAAGGTAATTTAATTTCACTGGAGCTCAGT 305122 vv i v i ii v iiv MIRb#SINE/MIR 102 GCAAGTTACTTAACCTCTCTGAGCCTCAGT 131 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.39 CpG sites = 17, Kimura (unadjusted) = 35.32 Transitions / transversions = 1.13 (17/15) Gap_init rate = 0.03 (4 / 115), avg. gap size = 3.75 (15 / 4) 13 8.14 0.00 7.14 chr2ptel1M 305720 305749 (694251) (TTTG)n#Simple_repeat 1 28 (0) m_b63s252i2 2319 chr2ptel1M 305720 TTTGTTTGTTTGTTTTAGTTTGGTTTTTTG 305749 - - v v (TTTG)n#Simpl 1 TTTGTTTGTTTG-TTT-GTTTGTTTGTTTG 28 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.07 (2 / 29), avg. gap size = 1.00 (2 / 2) 238 28.72 7.34 7.34 chr2ptel1M 307488 307596 (692404) C MIRc#SINE/MIR (120) 148 40 m_b63s601i8 2320 chr2ptel1M 307488 CTCATTTTATAGAGGATGAAACTCGGGCAAACAG-GGTTCAGTGAAGTGG 307536 i i v v vi vv v - v vv v C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr2ptel1M 307537 CTG-GGCTACACACCTAAT------CTGAGACAAGATTTAAATACAGGGA 307579 ii- ii v i ------ v v ii i ii iv -- C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGG-- 51 chr2ptel1M 307580 GTTGAGTCTTCCTGATT 307596 ------ i C MIRc#SINE/MIR 50 ------TCTTCCTGACT 40 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.49 CpG sites = 15, Kimura (unadjusted) = 36.72 Transitions / transversions = 1.07 (15/14) Gap_init rate = 0.10 (11 / 108), avg. gap size = 1.45 (16 / 11) 240 29.79 8.51 0.00 chr2ptel1M 307488 307581 (692419) C MIR#SINE/MIR (118) 144 43 m_b63s601i9 2320 chr2ptel1M 307488 CTCATTTTATAGAGGATGAAACTCGGGCAAACAG-GGTTCAGTGAAGTGG 307536 i i v v vi v v - v i vv v C MIR#SINE/MIR 144 CCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGC 95 chr2ptel1M 307537 CT-GGGCTACACACCTAAT------CTGAGACAAGATTTAAATACAGGGA 307579 i-i ii v i ------ v v ii ii iv v C MIR#SINE/MIR 94 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGCA 45 chr2ptel1M 307580 GT 307581 C MIR#SINE/MIR 44 GT 43 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.92 CpG sites = 14, Kimura (unadjusted) = 38.44 Transitions / transversions = 1.00 (14/14) Gap_init rate = 0.03 (3 / 93), avg. gap size = 2.67 (8 / 3) 18 18.13 0.00 0.00 chr2ptel1M 308812 308843 (691157) (A)n#Simple_repeat 1 32 (0) m_b63s252i3 2321 chr2ptel1M 308812 AACAAAAAGAAAGAAAGAAAAGAAAAAAAAAA 308843 v i i i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 32 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 435 23.97 0.79 11.30 chr2ptel1M 309108 309234 (690766) MIRc#SINE/MIR 1 115 (153) m_b63s601i10 2322 chr2ptel1M 309108 CAGGGCAGTTAAAAGTGGCATAGTGAATAGAGGACCAGCCCTGAAGTTAG 309157 ii ----- iii i v v ii v i i i MIRc#SINE/MIR 1 CGAGGCAGT-----GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAG 45 chr2ptel1M 309158 GAGGACCTGCGTTCAAATTTGGCCCCAGAAACT-TAACACTTCCTAGCTG 309206 i v i i ----- i --- - iv v MIRc#SINE/MIR 46 GAAGACCTGGGTTCGAGT-----CCCGG---CTCTGCCACTTACTAGCTG 87 chr2ptel1M 309207 CATGACCCTGGGTAAGTCACTTAACCCC 309234 ii i i i MIRc#SINE/MIR 88 TGTGACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.18 CpG sites = 21, Kimura (unadjusted) = 30.11 Transitions / transversions = 3.50 (21/6) Gap_init rate = 0.11 (14 / 126), avg. gap size = 1.00 (14 / 14) 362 29.20 11.50 0.00 chr2ptel1M 310369 310481 (689519) MIRc#SINE/MIR 3 128 (140) m_b63s601i11 2323 chr2ptel1M 310369 AGGCAACATGGCAGAATGGAAAGATCACTATATTTGGAGTCAG---GACA 310415 iii iiv i v iv i --- v MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chr2ptel1M 310416 TGGGTTGAAATTCTGGTTCTGCAACTC----------TGGTCTTGGGAAA 310455 vi i i i i v i---------- ii v MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 102 chr2ptel1M 310456 GTAATTTAATTTGACGGGAGCTCAGT 310481 v i ii vv v iiv MIRc#SINE/MIR 103 GTCACTTAACCTCTCTGAGCCTCAGT 128 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.50 CpG sites = 21, Kimura (unadjusted) = 38.46 Transitions / transversions = 1.75 (21/12) Gap_init rate = 0.02 (2 / 112), avg. gap size = 6.50 (13 / 2) 27 18.56 0.00 0.00 chr2ptel1M 311293 311341 (688659) (A)n#Simple_repeat 1 49 (0) m_b63s252i4 2324 chr2ptel1M 311293 AAAAAGCAAAAAACAAAACAAAACAAAAAAAAAAAAAAACCAAAAACAA 311341 iv v v v vv v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 49 Matrix = Unknown Transitions / transversions = 0.14 (1/7) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 223 28.00 8.26 8.26 chr2ptel1M 313435 313543 (686457) C MIRc#SINE/MIR (120) 148 40 m_b63s601i12 2325 chr2ptel1M 313435 CTCATTTTATAGAGGATGAAACTCGGGC--AAACAGGCTTCAATGAGGTG 313482 i i v v vi -- i v - v i vv C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGG-TTAAGTGACTTG 100 chr2ptel1M 313483 ACCAGGCTT-CACACCTAAT------CTGAGACAGGATTTAAATACAAGG 313525 v i v i- v i ------ v v i i ii iv i - C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGG- 51 chr2ptel1M 313526 AGTTGAGTCTTCCTGATT 313543 ------- i C MIRc#SINE/MIR 50 -------TCTTCCTGACT 40 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.41 CpG sites = 15, Kimura (unadjusted) = 35.63 Transitions / transversions = 1.15 (15/13) Gap_init rate = 0.11 (12 / 108), avg. gap size = 1.50 (18 / 12) 449 21.50 3.31 7.76 chr2ptel1M 315394 315514 (684486) MIRc#SINE/MIR 12 127 (141) m_b63s601i13 2326 chr2ptel1M 315394 GGTACAGTGAATAGAGCACCAGCCCTGAAGTCGGGAGGACCAGAGTTCAA 315443 i i v ii v i i i i v i i MIRc#SINE/MIR 12 GGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGA 61 chr2ptel1M 315444 ATATGGTCTTAGACACTTAACAGGAACTAGCTGTGTGACCCT-GGCAAGT 315492 i viv v iv v ------- i - MIRc#SINE/MIR 62 GTCCCGGCTCTGCCACTT-------ACTAGCTGTGTGACCTTGGGCAAGT 104 chr2ptel1M 315493 CACTTAA---CTCCAATTGCCTCAG 315514 --- ii -- MIRc#SINE/MIR 105 CACTTAACCTCTCTGA--GCCTCAG 127 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.71 CpG sites = 16, Kimura (unadjusted) = 25.95 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.09 (11 / 120), avg. gap size = 1.18 (13 / 11) 16 0.00 0.00 0.00 chr2ptel1M 315516 315532 (684468) (A)n#Simple_repeat 1 17 (0) m_b63s252i5 2327 chr2ptel1M 315516 AAAAAAAAAAAAAAAAA 315532 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 18 4.71 0.00 0.00 chr2ptel1M 315911 315932 (684068) (T)n#Simple_repeat 1 22 (0) m_b63s252i6 2328 chr2ptel1M 315911 TTGTTTTTTTTTTTTTTTTTTT 315932 v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTT 22 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 974 30.68 4.57 3.91 chr2ptel1M 320044 320830 (679170) HERVK14#LTR/ERVK 2631 3422 (2674) m_b63s701i0 2329 chr2ptel1M 320044 CCTGTTCCTATTCAGTGGAAAACTGATATACCAGTGTAGATTGAACAGTG 320093 ii v vvv vv vi v i v i i v i i HERVK14#LTR/E 2631 CCCATTCCTCTTGTTTGGCTAACTGCCAAACCGGTTTGGGTGGAGCAATG 2680 chr2ptel1M 320094 GCCCTTAAGAAGCAGTAAAA--TTCAGGCCTTAGTAGATATAGTGCAAAA 320141 vi -- i v -- vv i iv vv i ii HERVK14#LTR/E 2681 GCCGCT--GAAACAGGAAAAACTGGAGGCTTTAAAAGAACTGGTGCAGGA 2728 chr2ptel1M 320142 GCAACTTGACCAAGGACACTTACAAACTGCTCTAAGTCCTTGGAATTCCC 320191 i i vv vv i iv v iv i i vvvi i HERVK14#LTR/E 2729 ACAATTGCAAAAGGGACATATAGAGCCTACTTTCTCCCCTTGGAATTCTC 2778 chr2ptel1M 320192 CAGTATTTGTT-----GAAAGAAACCTGGAAAATGGAGGATGTTGACTGA 320236 v i----- - i v i i i v HERVK14#LTR/E 2779 CTGTATTTGTCATTAAGAAA-AAATCAGGGAAATGGAGAATGTTAACAGA 2827 chr2ptel1M 320237 TTTAAGAAGAGTAAATGAACAGATGGAAACTATGGGAACTCTTCATTCTG 320286 iivv v vvvv vv v i vi v v vi v HERVK14#LTR/E 2828 TTTAAGGGCTGTTAATGCTGTGATTCAACCCATGGGTGCACTGCAACCAG 2877 chr2ptel1M 320287 GACTTCCATCTTCTACTCAAT--TGCCAAGAGAATGGCCTCTTTGGGTTA 320334 i v v ii v -- -- v i v v ivvi v HERVK14#LTR/E 2878 GGCTGCCCTCCCCAA--CAATGATCCCAAAATACTGGCCTCTCATAGTGA 2925 chr2ptel1M 320335 TAGACATTAAGGATTGTTTCTATTCTATCCCTCTAGATAAGGAGGA-TAT 320383 iv v i i v v i i i v ivvv i - HERVK14#LTR/E 2926 TAGATCTAAAGGATTGCTTTTTTACCATTCCTTTAGCTGCCCAAGATTAT 2975 chr2ptel1M 320384 GAGAAAGTTTGTCTTTTCAGTGCTCAGCGTTACT--TTAGCTGAGCCTTA 320431 - i ii v v v i iv i v v -- v i-- i vvv HERVK14#LTR/E 2976 GA-AAAATTTGCTTTTACTGTTCCCGCCATAAATAATAAA--GAACCAGC 3022 chr2ptel1M 320432 TAAAAGATATGAATGGACAGTTTTGCCACAGGGAATGAAAAATAGCCCAA 320481 vi v iv v v vi i i v vv i HERVK14#LTR/E 3023 GGACAGATACCATTGGAAAGTACTACCACAAGGCATGCTAAATAGCCCGA 3072 chr2ptel1M 320482 CTATGTGCCAAAATATATGTTGCTGCTGCTCTTACTCCAGTAAGAAGAGC 320531 v i v - i vvivv v vv v - i HERVK14#LTR/E 3073 CTATTTGTCAAACT-TATGTCGGGAAAGCTATTAAGCCAGTTAG-AGAAC 3120 chr2ptel1M 320532 ATCTCCAAAA--GTAATATTATTATATTATATGGATGATATCTTGGGGTG 320579 vi iv -- v i-i i ii --- HERVK14#LTR/E 3121 AGTTTAAAAAATGTTATATTATC-CATTACATGGATGATATTCT---GTG 3166 chr2ptel1M 320580 TGCACCTGAA------GAACAA--------ATGTTAGAAGCATGGTTACA 320615 v ------ v --------i i v i -- v HERVK14#LTR/E 3167 TGCAGCTGAAACTAGGGAAGAATTGATGTTGTGCTACAAACA--GTTAGA 3214 chr2ptel1M 320616 AAAGACCATAGAAATACTAAGGAACTACAAATTGCACATATCTCCAGAAA 320665 i ii -- i vivi iii --- ---- v i v v HERVK14#LTR/E 3215 AAAGGCTGT--AAATGCGGCAGGGTT---AATT----ATAGCCCCCGATA 3255 chr2ptel1M 320666 AATTTCAAAGACATGCTTCTTTTCAATATTTAGGATATGAAGTATATCTC 320715 v i vviv i i i i - -i vvv HERVK14#LTR/E 3256 AAATCCAAACTTCTACTCCCTTTCAATATCTAGGA-ATGAAG-GTAGAAC 3303 chr2ptel1M 320716 AAGGCAC--TTAGAGTACAAAATCTT----TTCTTAAGAACAGATG--CT 320757 i ii -- iiviv vv ---- ---- v i--i HERVK14#LTR/E 3304 AAAGTGCTATTAAGCCTCAAAAGGTTCAAATTC----GAAGAGATAATTT 3349 chr2ptel1M 320758 AAACACTTTAAATGATTTCCAAAAATTAATAGGAGATATCCAATGGATGT 320807 v i v i iv v vi HERVK14#LTR/E 3350 AAAAACCTTAAATGATTTCCAAAAATTATTAGGAGACATTAATTGGATTC 3399 chr2ptel1M 320808 GTCCAGTGTTAGACTTAACTACC 320830 iiv i v vv HERVK14#LTR/E 3400 GTCCAACTTTAGGCATTCCTACC 3422 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.74 CpG sites = 108, Kimura (unadjusted) = 39.81 Transitions / transversions = 0.87 (108/124) Gap_init rate = 0.05 (42 / 786), avg. gap size = 1.60 (67 / 42) 442 30.65 0.00 1.16 chr2ptel1M 320738 320912 (679088) HERVK3#LTR/ERVK 3384 3556 (3646) m_b63s701i1 2329 chr2ptel1M 320738 TTTTCTTAAGAACAGATGCTAAACACTTTAAATGATTTCCAAAAATTAAT 320787 i i v ii i -- v v i v v HERVK3#LTR/ER 3384 TCTCCGTAAAGACAGGT--TACAGACTTTAAATGATTTTCAACAATTATT 3431 chr2ptel1M 320788 AGGAGATATCCAATGGATGTGTCCAGTGTTAGACTTAACTACCAATCAAT 320837 i iv v v i i ii i iiv vi v i HERVK3#LTR/ER 3432 AGGGGATATTAATTGGCTGCGCCCGATGCTAGGTATTGCTACCTATCAAC 3481 chr2ptel1M 320838 TGCAACCTCTATATTAAATTTTAAGTGGAGACACTGCTTTAAACTCACCA 320887 vvv v v ii iii iviv iv v ? i v i HERVK3#LTR/ER 3482 TTACACATCTTTACCAAACCCTGCAAGGAGATTCTTCNTTAAATTCCCCG 3531 chr2ptel1M 320888 CGCCAGCTTACAAAAGAAGCACAAG 320912 v i ? v i v HERVK3#LTR/ER 3532 CGGCAACTNACTAAAGAGGCAGAAG 3556 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.94 CpG sites = 29, Kimura (unadjusted) = 40.89 Transitions / transversions = 1.21 (29/24) Gap_init rate = 0.01 (2 / 174), avg. gap size = 1.00 (2 / 2) 29 14.20 0.00 0.00 chr2ptel1M 321340 321386 (678614) (T)n#Simple_repeat 1 47 (0) m_b63s252i7 2330 chr2ptel1M 321340 TTTTTTTTTTTTTTTTTTGTTTGTTTGTTTGTTTGTTTTTTTTATTT 321386 v v v v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 47 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 1059 27.73 2.93 3.65 chr2ptel1M 321851 322430 (677570) C L1MC4a_3end#LINE/L1 (1997) 632 57 m_b63s551i0 2331 chr2ptel1M 321851 TGCTCATTTCACTCAGCATCAGTTCGTGTAAGTCTCTCCAGGCC--TTTC 321898 iv i i vi vv v v i v vii -- iv C L1MC4a_3end#L 632 TGCTTTTTTCACTTAACAATATATCCTGGAAATCACTCCATATCAGTTCA 583 chr2ptel1M 321899 T-GAAATCATCCTGTTGGTCATTTCTTACAGA-ACAGTAATATTCCATAA 321946 - i v vv -- - i v-i - i i vi C L1MC4a_3end#L 582 TAGAGATCTTCCTCAT--TC-TTTTTTACAGCTGCA-TAGTACTCCATTG 537 chr2ptel1M 321947 TATTCATATACCATAATTTATTCAGCCATTCTCCAACTGATGGACATCCA 321996 i vv i i i ? v i?? i ii C L1MC4a_3end#L 536 TGTGGATGTACCATAGTTTATTCAACCANTCTCCTATNNATGGGCATTTA 487 chr2ptel1M 321997 TTCAGTTTCCAGTTTCTAGCCACTACAAAGAGGGCTGCCACAAACATTCA 322046 vviv i v i v v i v iv v ii i vi v C L1MC4a_3end#L 486 GGTTGTTTCCAATATTTTGCAATTACAAACAATGCTGCAATGAATAACCT 437 chr2ptel1M 322047 TGCACATACAGGTCCCTTTCC-CTTCTT-----TATAATCTCTTTGGGAT 322090 ii i-- ?vi vi- v v ----- i --- ii i C L1MC4a_3end#L 436 TGTGCATAT--GTNATTTTGTACATGTTGGAGGTGTA---TCTTCAGGGT 392 chr2ptel1M 322091 ATAAGCCCAGTAGTAACACTGCTGGATCAAAGGGTA--TGCACAGTTTGA 322138 v vv i v iiv i i -- i --- - C L1MC4a_3end#L 391 AAATTCCTAGAAGTGGGATTGCTGGGTCAAAGGGTAAATGCATA---TG- 346 chr2ptel1M 322139 TAACTTTTTGAGCATAGTTCCAAACTACTCTCCAAAATGGTTGGATTCGT 322188 ii v v - v v i v i ? v v iiv? C L1MC4a_3end#L 345 TAGTTTTGTTAG-ATATTGCCAAATTCCCCTCCANAAGGGTTGTACCANT 297 chr2ptel1M 322189 TCACAACTCCACCAACAATGAATCAATGTCCCAGTTTTCCCACATCCCCT 322238 ii vii i v v iv v v i v i v C L1MC4a_3end#L 296 TTGCATTCCCACCAGCAATGTATGAGAGTGCCTGTTTCCCCACAGCCTCG 247 chr2ptel1M 322239 CCAACAATCATCATTATTTTTTC---CTGTC--ATCTTAGCCAATCTGAC 322283 i----- v i v v --- v i-- i v i C L1MC4a_3end#L 246 CCAACAG-----AGTGTGTTGTCAAACTTTTGAATTTTTGCCAATCTGAT 202 chr2ptel1M 322284 AGGTGTGTAGTGGTATCTTAGAGTTGTCTTAATTTGCATTTCTCTGATTA 322333 v v i i v v i v C L1MC4a_3end#L 201 AGGTGAGAAATGGTATCTCAGTGTAGTTTTAATTTGCATTTCTCTTATTA 152 chr2ptel1M 322334 ATAATGACTTGGAGCATCTTTTCATATGACTAGAAATAGTTTCAATTTCT 322383 vv i vv v i vi iiiiivi ?v ? C L1MC4a_3end#L 151 TGAGTGAGGTTGAACATCTTTTCATATGTTTAAGGGCCATTTNTATNTCT 102 chr2ptel1M 322384 TCATCTGAGAATTGTCTGTTCATATCCTTTGACCATTTTTCAATTGG 322430 -- i v i i v v i C L1MC4a_3end#L 101 T--TTTGTGAATTGTCTGTTCATGTCTTTTGCCCATTTTTCTATCGG 57 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.49 CpG sites = 81, Kimura (unadjusted) = 35.78 Transitions / transversions = 1.09 (81/74) Gap_init rate = 0.05 (29 / 579), avg. gap size = 1.31 (38 / 29) 1521 26.91 0.36 1.66 chr2ptel1M 321934 322481 (677519) C L1ME3G_3end#LINE/L1 (377) 547 7 m_b63s551i1 2331 chr2ptel1M 321934 TAATATTCCATAATATTCATATACCATAATTTATTCAGCCATTCTCCAAC 321983 i i vv i i i v i C L1ME3G_3end#L 547 TAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTAT 498 chr2ptel1M 321984 TGATGGACATCCATTCAGTTTCCAGTTTCTAGCCACTACAAAGAGGGCTG 322033 ii vviv i i v i i v iv C L1ME3G_3end#L 497 TGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCTG 448 chr2ptel1M 322034 CCACAAACATTCATGCACATACAGGTCCCTTTCC-CTTCTTT-ATAATCT 322081 v ii i v i i ?-- i v v - v v vi- vv i C L1ME3G_3end#L 447 CAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATTT 400 chr2ptel1M 322082 CTTTGGGATATAAGCCCAGTAGTAACACTGCTGGATCAAAGGGTATGCAC 322131 ? i v v? ? v iiv i i i C L1ME3G_3end#L 399 CTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGC 350 chr2ptel1M 322132 AGTTTGATAACTTTTTGAGCATAGTTCCAAACTACTCTCCAAAATGGTTG 322181 v i -- i vvv - v v i i i ? i C L1ME3G_3end#L 349 ATTTTAA--ATTTTAATAG-ATACTGCCAAATTGCCCTCCAAAANGGCTG 303 chr2ptel1M 322182 GATTCGTTCACAACTCCACCAACAATGAATCAATGTCCCAGTTTTCCCAC 322231 v iivi i vii i i v v iv v v i C L1ME3G_3end#L 302 TACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCAC 253 chr2ptel1M 322232 ATCCCCTCCAACAATCATCATTATTTTTTCCTGTCATCTTAGCCAATCTG 322281 i i v v ?ivi ivv?iii vvv i v C L1ME3G_3end#L 252 ACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATCTG 203 chr2ptel1M 322282 ACAGGTGTGTAGTGGTATCTTAGAGTTGTCTTAATTTGCATTTCTCTGAT 322331 ii viv i i vv i i C L1ME3G_3end#L 202 ATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGAT 153 chr2ptel1M 322332 TAATAATGACTTGGAGCATCTTTTCATATGACTAGAAATAGTTTCAATTT 322381 v i vv v vi vviiivi vv C L1ME3G_3end#L 152 TACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGTATTT 103 chr2ptel1M 322382 CTTCATCTGAGAATTGTCTGTTCATATCCTTTGACCATTTTTCAATTGGA 322431 i v v i v v i C L1ME3G_3end#L 102 CCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGGG 53 chr2ptel1M 322432 GAATGGCTTGATTTTTTATAAATTAGAGTTAATTCTCTATATATTTTGGA 322481 v-- v -- i vi v vivv i i i C L1ME3G_3end#L 52 T--TGTCTT--TTTCTTATTGATTTGTAGGAGTTCTTTATATATTCTGGA 7 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 33.74 CpG sites = 75, Kimura (unadjusted) = 34.32 Transitions / transversions = 1.07 (75/70) Gap_init rate = 0.02 (11 / 547), avg. gap size = 1.00 (11 / 11) 402 23.90 1.85 1.85 chr2ptel1M 322338 322499 (677501) C L1M5_orf2#LINE/L1 (0) 3294 3133 m_b63s551i2 2331 chr2ptel1M 322338 TGACTTGGAGCATCTTTTCATATGACTAGAAATAGTTTCAATTTCTTCAT 322387 ?v v i vi vviiivi v? v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr2ptel1M 322388 CTGAGAATTGTCTGTTCATATCCTTTGACCATTTTTCAATTGGA--GAAT 322435 i v v vi i v ?v i-- vv C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTT 3195 chr2ptel1M 322436 GGCTTGATTTTTTA-TAAATTAGAGTTAATTCTCTATATATTTTGGAAAT 322484 v -- ? - i ? iv -v i i i v i C L1M5_orf2#LIN 3194 GTCTT--TTTNTTATTGANTTGTAG-GAGTTCTTTATATATTCTGGATAC 3148 chr2ptel1M 322485 GAGGCCTTTATCAGA 322499 v i C L1M5_orf2#LIN 3147 GAGTCCTTTGTCAGA 3133 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 29.15 CpG sites = 17, Kimura (unadjusted) = 30.05 Transitions / transversions = 0.81 (17/21) Gap_init rate = 0.03 (5 / 161), avg. gap size = 1.20 (6 / 5) 12 9.24 0.00 4.17 chr2ptel1M 323003 323027 (676973) (GGGA)n#Simple_repeat 1 24 (0) m_b63s252i8 2332 chr2ptel1M 323003 GGGAGGGGGTGGAGGGTGGGAGGGA 323027 i - v (GGGA)n#Simpl 1 GGGAGGGAG-GGAGGGAGGGAGGGA 24 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 295 30.24 1.15 1.15 chr2ptel1M 323135 323221 (676779) C L2d2_3end#LINE/L2 (263) 292 206 m_b63s601i14 2333 chr2ptel1M 323135 AGAAATTTTGAGGATGGAAAAAACTGATTTTAGCTGGGG-AATCAAGAAA 323183 i i iv - i i i iiiv ?ivi i -ii i i C L2d2_3end#LIN 292 AGGAGTTCAGAGGA-GGGAGAGATCACTNCGGGCTGGAGTGGTCAGGGAA 244 chr2ptel1M 323184 AGCTTCAAGGAGGAAGTGGCATTTCAGCTAAGCATTGA 323221 i v i ? v ii v C L2d2_3end#LIN 243 GGCTTCACGGAGGAGGTGGNATTTGAGCTGGGCCTTGA 206 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.20 CpG sites = 20, Kimura (unadjusted) = 43.52 Transitions / transversions = 3.33 (20/6) Gap_init rate = 0.02 (2 / 86), avg. gap size = 1.00 (2 / 2) 20 4.35 0.00 0.00 chr2ptel1M 323298 323321 (676679) (A)n#Simple_repeat 1 24 (0) m_b63s252i9 2334 chr2ptel1M 323298 AAAAAAAAAAAAAAAAAAAAGAAA 323321 i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAA 24 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 20 19.43 3.77 0.00 chr2ptel1M 323920 323972 (676028) (TTTTCT)n#Simple_repeat 1 55 (0) m_b63s252i10 2335 chr2ptel1M 323920 TTTTCTTCCATTTTTTC-TTTT-TTTTTCTTTTTTTTTTTTTTTTGGTTT 323967 iivi - - i i vv (TTTTCT)n#Sim 1 TTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTT 50 chr2ptel1M 323968 TGCTT 323972 v (TTTTCT)n#Sim 51 TTCTT 55 Matrix = Unknown Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.00 (2 / 2) 27 11.06 0.00 0.00 chr2ptel1M 323930 323968 (676032) (T)n#Simple_repeat 1 39 (0) m_b63s252i11 2336 chr2ptel1M 323930 TTTTTTCTTTTTTTTTCTTTTTTTTTTTTTTTTGGTTTT 323968 i i vv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 39 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 12 11.05 0.00 9.38 chr2ptel1M 325029 325063 (674937) (TCTGCC)n#Simple_repeat 1 32 (0) m_b63s252i12 2337 chr2ptel1M 325029 TCTGCTCTCTGCCATCTTGGCTCTGCCCCTGGCTC 325063 - - - v i v (TCTGCC)n#Sim 1 TCTGC-CTCTGCC-TC-TGCCTCTGCCTCTGCCTC 32 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.09 (3 / 34), avg. gap size = 1.00 (3 / 3) 741 31.84 4.84 1.68 chr2ptel1M 325116 325693 (674307) L1ME4c_3end#LINE/L1 56 651 (179) m_b63s551i4 2338 chr2ptel1M 325116 CCCCAACTGATAAAAAGTCAAGCAATATGAACAGGCAGTTT---TTAGAT 325162 iv vi v ivi i i i i---?v v L1ME4c_3end#L 56 CCCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAG 105 chr2ptel1M 325163 GAAATTTAAACTATAGT---------CATATAAAAATGCTCTAAATCACT 325203 vi ?--- --------- iv i v vv i L1ME4c_3end#L 106 GAAATACAAN---TAGTAAACAAACACATGGAAAAATGTTCAACCTCGCT 152 chr2ptel1M 325204 ATTGAGTAGAAAAATGCAAATTAAAACAAC--TGAGGGAACATCTCACAC 325251 v i vi i i i -- iv v i i i L1ME4c_3end#L 153 AGTAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGC 202 chr2ptel1M 325252 CTATCAAATTGGCTCACATACAGAAAAA-GAAAATAATAAATACTGGAGA 325300 i i vv v vi i v- v viv i v L1ME4c_3end#L 203 CTATTAAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGCTGGCGA 252 chr2ptel1M 325301 AGATGTGGGAAAATTGAGACATTAATGAACTGTTTGTTAAGTTGTGAACT 325350 i ? i vi i iv ?i v iv i i v vivi? i i L1ME4c_3end#L 253 GGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATT 302 chr2ptel1M 325351 GATCTAAGCATTCTGGAGGACAATTTGGAACTA--TACCCAAATGGCAAT 325398 i vi v v i iii v v -- i v i -- v L1ME4c_3end#L 303 GGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGA--GCCAT 350 chr2ptel1M 325399 AAAACTG--CATACCTTTTGATCCACCAATACCACT---AGGTCTGTGTC 325443 v -- i i vi v ---i vv v i L1ME4c_3end#L 351 AAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATC 400 chr2ptel1M 325444 CCAAA-AAATCATTAAAAAGGAGGAAAGGGCCCACATATAGG-----GTC 325487 i i- v v i ii i- i ii v ----- i L1ME4c_3end#L 401 CTAAGGAAATAATTCAAAAGAAGGAAAAAGCT-ATATGCACGAAGATGTT 449 chr2ptel1M 325488 CCCTGTAGCAGCTCTTTCTGTGTTGCAAAGAATTGGAGATAAAGGGGGTG 325537 vi i - i v v i-i v i i i i vvviii L1ME4c_3end#L 450 CATTGCAGC-GTTATTTATA-ATAGCGAAAAATTGGAAACAACCTAAATG 497 chr2ptel1M 325538 CCCATCAATTGGGGAATGAGTGAACAAGTTGTGGTATATGAATGTAATGG 325587 i v v iv i ii i i i v? ivii L1ME4c_3end#L 498 TCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGG 547 chr2ptel1M 325588 AATTCTATTTTTCTATAAGAAATGATGAGCAGGCAAATTTTAGAAAAACC 325637 vi vivv i v i i vi v v i i v iv iv v L1ME4c_3end#L 548 AATATTATGCAGCCATTAAAAATGATAATTATGAAGACTATGTAGCAACA 597 chr2ptel1M 325638 TGGAAAGATTTACATGAACTCATGTTGAATGAAGTGAGCAGAACCAGAAC 325687 - v vi vv v i i ivi -i v v L1ME4c_3end#L 598 TGGAAA-ATGTTTATGATATAATGTTAAGTGAAAAAAGCAGAA-TACAAA 645 chr2ptel1M 325688 ATTGTA 325693 L1ME4c_3end#L 646 ATTGTA 651 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.64 CpG sites = 102, Kimura (unadjusted) = 43.27 Transitions / transversions = 1.29 (102/79) Gap_init rate = 0.03 (19 / 577), avg. gap size = 2.00 (38 / 19) 798 31.42 4.79 1.21 chr2ptel1M 325116 325595 (674405) L1ME5_3end#LINE/L1 56 552 (389) m_b63s551i3 2338 chr2ptel1M 325116 CCCCAACTGATAAAAAGTCAAGCAATATGAACAGGCAGTTTTTAGA---T 325162 iv v vi v ivi i vi ---v L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chr2ptel1M 325163 GAAATTTAAA---CTA-TAGTCATATAAAAA--TGCTCTAAATCACTATT 325206 iiii --- -i iv i i -- v v i v L1ME5_3end#LI 106 GAAACCCGAAAGGCTAACAAGCATATGAAGAGATGCTCAAACTCATTAGT 155 chr2ptel1M 325207 GAGTAGAAAAATGCAAATTAAAACAAC--TGAGGGAACATCTCACACCTA 325254 i vi i -- iv v ii i L1ME5_3end#LI 156 AATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCTA 205 chr2ptel1M 325255 TCAAATTGGCTCACATACAGAAAA--AGAAAATAATAAATACTGGAGAAG 325302 i i i vv v -i i--i v ivi i ii v i L1ME5_3end#LI 206 TTAGACTGGCAAAAAT-TAGAAAGCTGGATAATGCCAAGTGTTGGCGAGG 254 chr2ptel1M 325303 ATGTGGGAAAATTGAGACATTAATGAACTGTTTGTTAAGTTGTGAACTGA 325352 i ? v ii vi v v i v viiiv ii i L1ME5_3end#LI 255 ATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACTGG 304 chr2ptel1M 325353 TCTAAGCATTCTGGAGGACAATTTGGAACTA--TACCCAAATGGCAATAA 325400 vi iv ii i v v -- vi --i vv L1ME5_3end#LI 305 TGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAAT--TAAGTA 352 chr2ptel1M 325401 AACTGCATACCTTTTGATCCACCAATACCA---CTAGGTCTGTGTCCCAA 325447 v - i v i v v i--- i v i i L1ME5_3end#LI 353 TAC-GCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATATCCCAA 401 chr2ptel1M 325448 A-AAATCATTAAAAAGGAGGA-AAGGGCCCACATAT-AGG--GTCCCCTG 325492 - iv i v v vvv - vv ii i- -- i vi L1ME5_3end#LI 402 AGAAATTCTCACACAGGTCCATAAGGGGACATGTACGAGGATGTTCATTG 451 chr2ptel1M 325493 TAGCAGCTCTTTCTGTGTTGCAAAGAATTGGAGATAAAGGGGGTGCCCAT 325542 i - i v v - v iii i ii vvv i L1ME5_3end#LI 452 CAGC-GTTGTTTGTG-GTGGCGGGGAGTTGGAGGCAACCTGGGTGTCCAT 499 chr2ptel1M 325543 CAATTGGGGAATGAGTGAACAAGTTGTGGTATATGAATGTAATGGAATTC 325592 v v i i ii iiii iv iv v iiiv i v L1ME5_3end#LI 500 CACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACACCATGGAGTAC 549 chr2ptel1M 325593 TAT 325595 L1ME5_3end#LI 550 TAT 552 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.68 CpG sites = 88, Kimura (unadjusted) = 42.22 Transitions / transversions = 1.44 (88/61) Gap_init rate = 0.04 (18 / 479), avg. gap size = 1.61 (29 / 18) 13 17.64 0.00 7.32 chr2ptel1M 326079 326122 (673878) (AAAAG)n#Simple_repeat 1 41 (0) m_b63s252i13 2339 chr2ptel1M 326079 AAAAGTAAAGATCATGAATGTAGAAAAAAAAAGAAAAGAAATGA 326122 v -v v --v i v (AAAAG)n#Simp 1 AAAAGAAAAGA-AAAGAA--AAGAAAAGAAAAGAAAAGAAAAGA 41 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.07 (3 / 43), avg. gap size = 1.00 (3 / 3) 15 24.25 5.17 0.00 chr2ptel1M 326547 326604 (673396) (AAAATGT)n#Simple_repeat 1 61 (0) m_b63s252i14 2340 chr2ptel1M 326547 AAAATG-GAAAT-CAAAATCTCAAAAGT-AAATGTTGAATGTAATTAGAA 326593 -i -i v v v - vi vvv v (AAAATGT)n#Si 1 AAAATGTAAAATGTAAAATGTAAAATGTAAAATGTAAAATGTAAAATGTA 50 chr2ptel1M 326594 AAAAGTAAAAT 326604 v (AAAATGT)n#Si 51 AAATGTAAAAT 61 Matrix = Unknown Transitions / transversions = 0.33 (3/9) Gap_init rate = 0.05 (3 / 57), avg. gap size = 1.00 (3 / 3) 13 22.05 0.00 7.84 chr2ptel1M 326548 326602 (673398) (AAATGT)n#Simple_repeat 1 51 (0) m_b63s252i15 2340 chr2ptel1M 326548 AAATGGAAATCAAAATCTCAAAAGTAAATGTTGAATGTAATTAGAAAAAA 326597 v vv v - v - i v - -v v (AAATGT)n#Sim 1 AAATGTAAATGTAAATGT-AAATGTAAATG-TAAATGTAAAT-G-TAAAT 46 chr2ptel1M 326598 GTAAA 326602 (AAATGT)n#Sim 47 GTAAA 51 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.07 (4 / 54), avg. gap size = 1.00 (4 / 4) 16 20.98 1.89 3.85 chr2ptel1M 331453 331505 (668495) (GAGG)n#Simple_repeat 1 52 (0) m_b63s252i16 2341 chr2ptel1M 331453 GAGGGGGTGGAGTGAGTCTGGGAGGGAGGGA-GGATGGAAGAAGGAATGG 331501 i - v vvv - v i i i - (GAGG)n#Simpl 1 GAGGGAG-GGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGA-GG 48 chr2ptel1M 331502 GAGG 331505 (GAGG)n#Simpl 49 GAGG 52 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.06 (3 / 52), avg. gap size = 1.00 (3 / 3) 15 17.73 2.63 0.00 chr2ptel1M 331699 331736 (668264) (CAGAGG)n#Simple_repeat 1 39 (0) m_b63s252i17 2342 chr2ptel1M 331699 CAGACGCAGAGG-ATAGACTGAGGCAGGGGCAGAGTCAG 331736 v - v i v i v (CAGAGG)n#Sim 1 CAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAG 39 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 203 28.25 9.17 2.59 chr2ptel1M 332668 332776 (667224) MIRc#SINE/MIR 116 231 (37) m_b63s601i15 2343 chr2ptel1M 332668 TTTGAGTTCTAAT---CTCACCTAGTAGAATTTGGAT--TAAGTCACTCA 332712 i iiii i --- i - i vv -- --i iii MIRc#SINE/MIR 116 TCTGAGCCTCAGTTTCCTCATCT-GTAAAATGGGGATAATAA--TACCTG 162 chr2ptel1M 332713 ACCAGTGTA--TCACAGTTTTCTTGTGAAGATACAATGTAAT--TGTGTG 332758 v v iv -- vv v i vv vi -- i MIRc#SINE/MIR 163 CCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATG 212 chr2ptel1M 332759 TG-AAGCTTTTTGTAAATT 332776 - vi i MIRc#SINE/MIR 213 TGAAAGCGCTTTGTAAACT 231 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.57 CpG sites = 18, Kimura (unadjusted) = 36.57 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.07 (8 / 108), avg. gap size = 1.62 (13 / 8) 52 15.45 0.00 0.00 chr2ptel1M 334291 334376 (665624) (A)n#Simple_repeat 1 86 (0) m_b64s252i0 2344 chr2ptel1M 334291 AACAAATACAAAAAGAAGTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 334340 v v v i iv (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr2ptel1M 334341 AAAAAAAAAAAAAAAAAAAGTAAATGAAGAAAATAA 334376 iv vi i v (A)n#Simple_r 51 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 86 Matrix = Unknown Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.00 (0 / 85), avg. gap size = 0.0 (0 / 0) 237 18.28 7.23 1.14 chr2ptel1M 334677 334759 (665241) L1MEc_5end#LINE/L1 1404 1491 (1036) m_b64s551i0 2345 chr2ptel1M 334677 AAAACT---CCAAGGAATATCATAGTTAAATT--TCAGAACTATTCGACC 334721 --- v i i i -- ? i i v - iv L1MEc_5end#LI 1404 AAAACTACACCAAGGCACATCATAATCAAATTGCTNAAAACCAGT-GATA 1452 chr2ptel1M 334722 AAGA-AAAAATATTACAAGCAGCCAGGAAAAAAAAAATA 334759 - v v ii i i L1MEc_5end#LI 1453 AAGAGAAAAATCTTAAAAGCAGCCAGAGAAAAAAAGACA 1491 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 21.75 CpG sites = 10, Kimura (unadjusted) = 21.75 Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.05 (4 / 82), avg. gap size = 1.75 (7 / 4) 16 23.27 0.00 0.00 chr2ptel1M 336068 336102 (663898) (A)n#Simple_repeat 1 35 (0) m_b64s252i1 2346 chr2ptel1M 336068 AAGAACAAACAAAAAAAAAAATGACAAACAAAAAA 336102 i v v vi v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 35 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 12 23.32 2.33 2.33 chr2ptel1M 336906 336948 (663052) (AGAAA)n#Simple_repeat 1 43 (0) m_b64s252i2 2347 chr2ptel1M 336906 AGAAAAGGAAAAGAAAAGATAA-TAAGGGAAGGAAGGGGAAAGA 336948 - v -v i i i ii i (AGAAA)n#Simp 1 AGAAAA-GAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGA 43 Matrix = Unknown Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.00 (2 / 2) 14 22.94 4.35 0.00 chr2ptel1M 337444 337489 (662511) (AACA)n#Simple_repeat 1 48 (0) m_b64s252i3 2348 chr2ptel1M 337444 AACAAACAAACCACAAAACAAA-TAAGAAAGAAATTAA-AAAGAAACA 337489 v vv -v v v iv - v (AACA)n#Simpl 1 AACAAACAAACAAACAAACAAACAAACAAACAAACAAACAAACAAACA 48 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.04 (2 / 45), avg. gap size = 1.00 (2 / 2) 276 24.94 18.29 2.19 chr2ptel1M 337582 338647 (661353) L1M4_orf2#LINE/L1 617 1850 (1444) m_b64s551i1 2345 chr2ptel1M 337582 ATATATT--GACATAAAAC----CTTAAATTAAATGAAAAAGCA--GAAA 337623 i -- v ---- i -- vv v -- L1M4_orf2#LIN 617 ATATGTTAGGCCATAAAACAAGTCTCAA--TAAATTTAAAAGGATTGAAA 664 chr2ptel1M 337624 T---ATAAA-TGCTTTTTTCGATCATGATGCAATAAAA---ACATTCAAC 337666 --- i - iiv i i i ii v i ---iv v i L1M4_orf2#LIN 665 TCATACAAAGTATGTTCTCCGACCACAATGGAATGAAATTAGAAATCAAT 714 chr2ptel1M 337667 AA-------AAATTGGGGAAAT-GACAAAAAGTTTGAAAT-AAAC--TCT 337705 ------- v -v v vv v - --ivi L1M4_orf2#LIN 715 AACAGAAGGAAATTTGGGAAATTCACAAATATGTGGAAATTAAACAACAC 764 chr2ptel1M 337706 ATT--TAAAGAATGATTGGG----GAAAGAAATTA---GATAAATTA--- 337743 i -- v iv v ----ii i --- iv --- L1M4_orf2#LIN 765 ACTCCTAAATAACCAATGGGTCAAAGAAGAAATCACAAGGGAAATTAGAA 814 chr2ptel1M 337744 -ATAATTTACCAAGA--AATGAAAATGGA----CATCA-ACCAAAATTT- 337784 - v i--- -- i i ---- v - i - L1M4_orf2#LIN 815 AATACTTTG---AGATGAATGAAAACGAAAACACAACATACCAAAACTTA 861 chr2ptel1M 337785 TGGGATGCAGCCAAAG-GGTAATAAGAGGGAATTTTATATCC-TAGAGGC 337832 ? -i iv v v v i- i v L1M4_orf2#LIN 862 TGGGATGCAGCNAAAGCAGTGCTTAGAGGGAAATTTATAGCTGTAAATGC 911 chr2ptel1M 337833 TTACTTGAATAAAAAGAAAAGA----AAA--GAT----TAATTTTTAAAA 337872 i iv v v i ii ---- --i ---- ii iv vv L1M4_orf2#LIN 912 CTATATTAAAAAAGAAGAAAGATCTCAAATCAATAACCTAACCTTCCACC 961 chr2ptel1M 337873 CTAAAAAACTAAAAA-----GACCAAAAAAACCCCCAATCAAATA-AATA 337916 i i i ----- v vv v v v ii - vi L1M4_orf2#LIN 962 TTAAGAAACTAGAAAAAGAAGAGCAAACTAAACCCAAAGCAAGCAGAAGG 1011 chr2ptel1M 337917 AATTGGAAAT--TTAAAATTAAAAGGAGAAATTAA--AAATATTGGA-AA 337961 -- -- v i i iv - v -- vv i - i L1M4_orf2#LIN 1012 AA--GGAAATAATAAAGATTAGAGCG-GAAATAAATGAAATAGAGAATAG 1058 chr2ptel1M 337962 AAAATCATTTGA--AAATT--TAAAAC---AGATTGGTTCAT-GAAAAAG 338003 v v v -- i--ii --- ii v - ii L1M4_orf2#LIN 1059 AAAAACAATAGAGAAAATCAACGAAACCAAAAGTTGGTTCTTTGAAAAGA 1108 chr2ptel1M 338004 CCAA-AAAACAGATAG-CCTTTGGTAAATCTGATTAGAAAAAGGAG-GAG 338050 i - iv i i- i iv iv ii ii ii - L1M4_orf2#LIN 1109 TCAACAAAATTGACAAACCTTTAGCTAGACTGACCAAGAAAAAAAGAGAG 1158 chr2ptel1M 338051 GAAAATGAAATTAGTAG--TCAA-AATGAAAAAGA-------ACTTTC-- 338088 i i v v v i-- i- i i------- vi -- L1M4_orf2#LIN 1159 AAGACTCAAATTACTAAAATCAGGAATGAAAGAGGGGACATTACTACCGA 1208 chr2ptel1M 338089 CCCAAGGGAAAGAAATTAGAGAATAAGAGT-TATTTTC--TAACTTTATG 338135 iv vi v vvi vv i v- i v v--i i v L1M4_orf2#LIN 1209 CCTTACAGAAATAAAAAGGATTATAAGGGAATACTATGAACAATTGTATG 1258 chr2ptel1M 338136 --AATAAATTTAA--ACCTA-AGGAAATGGATGACTACCC-CAAAAATAT 338179 -- i vi -- - v ii v v i-v i i i L1M4_orf2#LIN 1259 CCAACAAATTAGATAACCTAGATGAAATGGACAAATTCCTAGAAAGACAC 1308 chr2ptel1M 338180 AGACTTCCA-----GATTAAAGAGGAGGAAGTAAATTTTTGAATGTATTT 338224 i v i----- i v i iiv v i -- iv ii L1M4_orf2#LIN 1309 AAACTACCGAAACTGACTCAAGAAGAAATAGAAAATCT--GAATAGACCT 1356 chr2ptel1M 338225 ----CA-GAAAAGAAATAGAAC-AGGAATTAAAA-----CCCCTAAGAAA 338263 ---- - v i v i- v i ----- vi ii L1M4_orf2#LIN 1357 ATAACAAGTAAAGAGATTGAATTAGTAATCAAAAAACTTCCCACAAAGAA 1406 chr2ptel1M 338264 AATCCCAGGACCAGATGGA---ACATGG--AATTTTACCAAACATTTAAA 338308 v ? v--- - -- i L1M4_orf2#LIN 1407 AAGCCCAGGNCCAGATGGCTTCAC-TGGTGAATTCTACCAAACATTTAAA 1455 chr2ptel1M 338309 GAA-AATT--C-CCAATTAT--ATAAATTATT-TGAAAAATAGGGAAGAA 338351 - -- - iv -- i i v -ii iii i L1M4_orf2#LIN 1456 GAAGAATTAACACCAATCCTTCACAAACTCTTCCAAAAAATAGAAGAGGA 1505 chr2ptel1M 338352 AGTCCCA---CCAAATTCCTTCTATGA--CCAAACAGGTATGATACCCT- 338395 i vvv --- v i v -- ----- -- - L1M4_orf2#LIN 1506 GGGAACACTTCCCAACTCATTCTATGAGGCCA-----GTAT--TACCCTG 1548 chr2ptel1M 338396 ------AAACCAGGTAGGGA----AAAAG-AAAGAAAATTATAA--TAAT 338432 ------ ii ii ---- v - i i i--i L1M4_orf2#LIN 1549 ATACCAAAACCAGACAAAGACATCACAAGAAAAGAAAACTACAGACCAAT 1598 chr2ptel1M 338433 CT-CCTAATGAATATTG-TCTAAA---CTTAAATAAGATATTAGAAAAAG 338477 v - v v - vi --- i v i i i v --- L1M4_orf2#LIN 1599 ATCCCTTATGAATATAGATGCAAAAATCCTCAACAAAATACTAGCAA--- 1645 chr2ptel1M 338478 ACTGAA------AAT-CATCCCAAG--TTACAC----TAGTCAAATGGT- 338513 i ------ i-i vvv -- i ---- iii i v- L1M4_orf2#LIN 1646 ACCGAATCCAGCAACATATAAAAAGGATTATACACCATGACCAAGTGGGA 1695 chr2ptel1M 338514 TTTA---AAGGAATG--GGGTT-TTTCAATATTAGGAAAACTTATAATTG 338557 ---v --i -v i ?v i v ---- i- L1M4_orf2#LIN 1696 TTTATCCCAGGAATGCAAGGTTGGTTCAACATNCGAAAATC----AATC- 1740 chr2ptel1M 338558 GATTTAATA-ACCAAATTAA-------------AAAA---ATATG-TCAT 338589 i v - v ------------- --- i - L1M4_orf2#LIN 1741 AATGTAATACACCATATTAATAGAATAAAGGACAAAAACCACATGATCAT 1790 chr2ptel1M 338590 CTCAATAGATG-AG-AAAAGCATTTG-TAAAATCCAACATCCATTCCCTA 338636 i - - -i i - i v i L1M4_orf2#LIN 1791 CTCAATAGACGCAGAAAAAGCATTTGACAAAATCCAACACCC-TTTCATG 1839 chr2ptel1M 338637 TTAAAAACATT 338647 v i L1M4_orf2#LIN 1840 ATAAAAACACT 1850 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 30.46 CpG sites = 152, Kimura (unadjusted) = 31.19 Transitions / transversions = 1.41 (152/108) Gap_init rate = 0.10 (109 / 1065), avg. gap size = 2.04 (222 / 109) 442 25.48 15.22 0.89 chr2ptel1M 337758 338644 (661356) L1M5_orf2#LINE/L1 835 1847 (1447) m_b64s551i2 2345 chr2ptel1M 337758 AATGAAAATGGACATCA-ACCAAAATTT-TGGGATGCAGCCAAAG-GGTA 337804 -- v - i - i -i i L1M5_orf2#LIN 835 AATGAAAAT--ACAACATATCAAAATTTGTGGGATGCAGCTAAAGCAGTG 882 chr2ptel1M 337805 ATAAGAGGGAATTTTATATCCT-AGAGGCTTAC-TTGAATAAAAAGAAAA 337852 v v v v ? - i v ? i- ii v i i L1M5_orf2#LIN 883 CTTAGAGGGAAATTTATAGCNTTAAATGCNTATATTAGAAAAGAAGAAAG 932 chr2ptel1M 337853 G---AAAA-----GAT-TAATTTTTAAAACTAAAAAACTAAAAA-----G 337888 --- ----- - vi iv vvi i i i ----- L1M5_orf2#LIN 933 GCTTAAAATCAATGATCTAAGCTTCCACCTTAAGAAGCTAGAAAAAGAAG 982 chr2ptel1M 337889 ACCAAAAAAACCCCCAATCAAATA-AATAAATTGGAAATT-TAAAATTAA 337936 v vv v v v? i - vi -- v- iv L1M5_orf2#LIN 983 AGCAAATTAAACCCAAAGNAAGTAGAAGGAA--GGAAATAATAAAGATAA 1030 chr2ptel1M 337937 AAGGAGAAATTAAAAATATTGGAAAAAAAT---CATTTGA--AAATT--T 337979 i v i vi v v i v ?--- v v -- i--i L1M5_orf2#LIN 1031 GAGCAGAAATCAATGAAATAGAAAACAAANANACAATAGAGAAAATCAAC 1080 chr2ptel1M 337980 AAAAC---AGATTGGTTCAT-GAAAAAGCCAA-AAAACAGATAG-CCTTT 338023 i i --- iii v - iii - iv i- i L1M5_orf2#LIN 1081 GAAGCCAAAAGCTGGTTCTTTGAAAAGATCAATAAAATTGATAAACCTCT 1130 chr2ptel1M 338024 GGTAAATCTGATTAGAAAAAGGAGGAGGAAAATG-AAATTAGTAGT--CA 338070 i i? iv i ii ii iii i ii- vi i -- L1M5_orf2#LIN 1131 AGCNAGACTGATCAAGAAAAAAAGAGAGAAGACACAAATTACCAATATCA 1180 chr2ptel1M 338071 A-AATGAAAAAGAACTT-TCCCCAAGGG----AAAGAAATTA----GAGA 338110 i- i vvi- v i vi i---- v v ---- v L1M5_orf2#LIN 1181 GGAATGAAAAAGGAGACATCACTACAGATCCTACAGACATTAAAAGGATA 1230 chr2ptel1M 338111 ATAAGAGT-TATTTTC--TAACTTTATG--AATAAATTT--AAACCTA-A 338152 v- v v--i -- --? i - L1M5_orf2#LIN 1231 ATAAGAGAATATTATGAACAACTTTATGCCAATAAATTTGANAACTTAGA 1280 chr2ptel1M 338153 GGAAATGGATGACTACCCC-AAAAATATAGACTTCCA-----GATTAAAG 338196 v ii v v ii- i i i?i v ----- i?v L1M5_orf2#LIN 1281 TGAAATGGACAAATTCCTTGAAAAACACAANTTACCAAAACTGACNCAAG 1330 chr2ptel1M 338197 AGGAGGAAGTAAATTTTTGAATG----TATTTC-AGAAAAGAAATAGAAC 338241 i iiv v i -- i---- v - vv v i L1M5_orf2#LIN 1331 AAGAAATAGAAAATCT--GAATAGCCCTATATCTATTAAAGAAATTGAAT 1378 chr2ptel1M 338242 AGG-AATTAAAA-----CCCCTAAGAAAAATCCCAGGACCAGATGGA--- 338282 vv - ----- vi ii ii v v--- L1M5_orf2#LIN 1379 TTGTAATTAAAAACCTTCCCACAAAGAAAACTCCAGGCCCAGATGGCTTC 1428 chr2ptel1M 338283 ACATGG--AATTTTACCAAACATTTAAAGA--AAAT--TCCCAA--TTAT 338324 - -- i i -- -- v -- i L1M5_orf2#LIN 1429 AC-TGGTGAATTCTACCAAACATTTAAGGAAGAAATAATACCAATCTTAC 1477 chr2ptel1M 338325 ATAAATTATTTGA-AAAATAGGGAAGAAAGTCCCA---CCAAATTCCTTC 338370 i i v iv - ii ii i vvv --- v i v i L1M5_orf2#LIN 1478 ACAAACTCTTCCAGAAAATAGAAAAAGAGGGAACACTTCCCAACTCATTT 1527 chr2ptel1M 338371 TATGA--CCAA-ACAGGTATGATACCCTAAACCAGGTAGGGA----AAAA 338413 -- i- i?iviv v- ? ii ii ---- v L1M5_orf2#LIN 1528 TATGAGGCCAGCATNACCCTGATACCA-AAACCNGACAAAGACATTACAA 1576 chr2ptel1M 338414 G-AAAGAAAATTATAA--TAATCT-CCTAATGAATATTG-TCTAAA---C 338455 - i i--i v - v i v - vi --- L1M5_orf2#LIN 1577 GAAAAGAAAATTACAGACCAATATCCCTCATGAACATAGATGCAAAAATC 1626 chr2ptel1M 338456 TTAAATAAGATATTAGAAAA---AGACTGAAAAT-CATCCCAAGT----T 338497 i ? i i v --- iv iiiv -i vvv v---- L1M5_orf2#LIN 1627 CTNAACAAAATATTAGCAAATCGAATCCAGCAATATATAAAAAGGATAAT 1676 chr2ptel1M 338498 ACAC--TAGTCAAAT-GGTTTTA---AAGGAATG--GGGTT-TTTCAATA 338538 i-- iii i - v ---v --i -v i i L1M5_orf2#LIN 1677 ACATCATGACCAAGTGGGGTTTATCCCAGGAATGCAAGGTTGGTTTAACA 1726 chr2ptel1M 338539 TTAGGAAAAC--T---TATAATTGGATTTAATAACCAAATTAA----AAA 338579 v i v -- --- i viviv v vi v ---- L1M5_orf2#LIN 1727 TTCGAAAATCAATCAATGTAATTCACCATATTAACAGAATAAAGGAGAAA 1776 chr2ptel1M 338580 A---ATATG-TCATCTCAATAGATG-AG-AAAAGCATTTG-TAAAATCCA 338622 --- - - - -i i L1M5_orf2#LIN 1777 AATCATATGATCATCTCAATAGATGCAGAAAAAGCATTTGACAAAATTCA 1826 chr2ptel1M 338623 ACATCCATTCCCTATTAAAAAC 338644 i - v iv L1M5_orf2#LIN 1827 ACACCCATT-CATGATAAAAAC 1847 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.18 CpG sites = 131, Kimura (unadjusted) = 32.37 Transitions / transversions = 1.41 (131/93) Gap_init rate = 0.08 (75 / 886), avg. gap size = 1.92 (144 / 75) 398 24.81 15.65 2.20 chr2ptel1M 339803 340243 (659757) L1ME4a_3end#LINE/L1 56 554 (317) m_b64s551i3 2345 chr2ptel1M 339803 CTCCAATTGAAAA--TGGTAAAGGA-ATGAA-AGA-AACTCG----ATAA 339843 i v --v i - - - i i---- v L1ME4a_3end#L 56 CCCCAATAGAAAAATGGGCAAAGGACATGAACAGACAATTCACAAAAGAA 105 chr2ptel1M 339844 GAAATTGAAACTATTTCTAGTCA-ATGAAAAGATCTCCAAGTTTATTAAT 339892 vv iviiivv iv - ? v i vi i i i L1ME4a_3end#L 106 GAAATACAAATGGCCAATAAACATATGAAAANATGTTCAACCTCACTAGT 155 chr2ptel1M 339893 A------GAAATGCAAATTAAGAAACCAA---GATACCCTTTACACACCT 339933 ------ i v v --- v vi- L1ME4a_3end#L 156 AATCAAAGAAATGCAAATTAAAACAACAATGAGATACCATTTTT-CACCT 204 chr2ptel1M 339934 GT-AGATTGG--AAGATGACAGGAAAAAATAATGATGAT------TGTTG 339974 i - i -- v----v i -- i ------ L1ME4a_3end#L 205 ATCAAATTGGCAAAGATT----TAAAAGAT--TGATAATACCCAGTGTTG 248 chr2ptel1M 339975 G--AGGG----GTAAAACTGGAATTG--ATTCATTGTTGGTGG-AGTTTG 340015 -- ---- ?i v v i v-- v i i - v i L1ME4a_3end#L 249 GCGAGGGTGTGGNGAAACGGGCACTCTCATACACTGCTGGTGGGAGTGTA 298 chr2ptel1M 340016 AAG-AATCCAACCATTTTGGAAG--AGTTTGA------ATATTAAAAGTT 340056 v-ii v v i i -- i i------i i ii L1ME4a_3end#L 299 AATTGGTACAACCTTTCTGGAGGGCAATTTGGCAATATGTATCAAAAGCC 348 chr2ptel1M 340057 TCAAACTTG--CATACCCTTTGATCCCCAGTG--TTAACT-----GGCTT 340097 i vv -- -- i-- iv ----- iv L1ME4a_3end#L 349 TTAAAAATGTNCATACCCTTTGA--CCCAGTAATTCCACTTCTAGGAATT 396 chr2ptel1M 340098 TATCCCAAAGGATTA--TAAAGAAG-GGAAAGGGACCTTAT-TGCACGAA 340143 i i i v --i i v - ? v ii -i - i v i L1ME4a_3end#L 397 TATCCTAAGGAAATAATCAGAGATGTGNACAAAGA-TTTATGTACAAGGA 445 chr2ptel1M 340144 TGTTTG-GGCAGCCCT-TTTGTAGTGGT-AGAAACTGAAA-----CTGAA 340185 ii-v vi - i i i i- i i i ----- i L1ME4a_3end#L 446 TGTTCATCGCAGCATTATTTATAATAGCGAAAAATTGGAAACAACCTAAA 495 chr2ptel1M 340186 TGGACCATCAGTTGGAGAA-GGCTGAATAAATT-TGGTATATGAAAATTA 340233 v- v i v i ?- i i - i vv v ?v L1ME4a_3end#L 496 TGT-CCAACAATAGGGGANTGGTTAAATAAATTATGGTACATCCATANAA 544 chr2ptel1M 340234 TGGAATATTA 340243 L1ME4a_3end#L 545 TGGAATATTA 554 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 31.09 CpG sites = 65, Kimura (unadjusted) = 31.44 Transitions / transversions = 1.55 (65/42) Gap_init rate = 0.09 (41 / 440), avg. gap size = 1.95 (80 / 41) 343 27.37 5.47 5.47 chr2ptel1M 342043 342243 (657757) C L1MC1_3end#LINE/L1 (447) 633 433 m_b64s551i4 2349 chr2ptel1M 342043 GCTCATTTCCCTCAGTATCAGTTCATGTAAGTCTC-TCCAGGCCTTTCTG 342091 iv v i vi - v v i - v i --- C L1MC1_3end#LI 633 GCTTCTTTCACTTAGTAATA-TGCATTTAAGTTTCCTCCATGTCTTT--- 588 chr2ptel1M 342092 AAATCAT--CCTACTGG-TCATTTCTTACCCAAC----AATAATATTCTA 342134 --- -- i iv i - -iii i ---- i C L1MC1_3end#LI 587 ---TCATGGCTTGATAGCTCATTTCTT-TTTAGCGCTGAATAATATTCCA 542 chr2ptel1M 342135 TAATATTCATATAGCACAATTTATTCAGCCATTCTCCAATTGATGGGCAT 342184 vi v vv i v i i v v v i v i C L1MC1_3end#LI 541 TTGTCTGGATGTACCACAGTTTATTTATCCATTCACCTACTGAAGGACAT 492 chr2ptel1M 342185 CCACTTAGT---TTCCAGTTCCTGGCCACTACAAAGAGGGCTGCCACAAA 342231 --- i --- iv ii v i ii v ii i i C L1MC1_3end#LI 491 ---CTTGGTTGCTTCCAAGTTTTGGCAATTATGAATAAAGCTGCTATAAA 445 chr2ptel1M 342232 CATTCGTGCACA 342243 i ii C L1MC1_3end#LI 444 CATCCGTGTGCA 433 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.23 CpG sites = 33, Kimura (unadjusted) = 35.23 Transitions / transversions = 1.74 (33/19) Gap_init rate = 0.08 (16 / 200), avg. gap size = 1.38 (22 / 16) 607 26.99 2.96 1.46 chr2ptel1M 342124 342326 (657674) C L1ME3G_3end#LINE/L1 (376) 548 343 m_b64s551i5 2349 chr2ptel1M 342124 ATAATATTCTATAATATTCATATAGCACAATTTATTCAGCCATTCTCCAA 342173 i i i vv v i i i i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr2ptel1M 342174 TTGATGGGCATCCACTTAGTTTCCAGTTCCTGGCCACTACAAAGAGGGCT 342223 i ii vv v i ii v i i v iv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr2ptel1M 342224 GCCACAAACATTCGTGCACATACAGGCCCCTTTCCC-----TTCAAG-AT 342267 v ii i v i i ---?i viv ----- v i - C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACATGC---NTCCTTGTGCACATGTGCGAGTAT 402 chr2ptel1M 342268 TTTTTGGGGATATAAGCCCAGTAGAAACACTGCTAGATCAAAGGGTATGC 342317 i ?vi v v? ? v viiv i i i C L1ME3G_3end#L 401 TTCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGC 352 chr2ptel1M 342318 ACAGTTTAA 342326 i v C L1ME3G_3end#L 351 GCATTTTAA 343 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.63 CpG sites = 32, Kimura (unadjusted) = 35.24 Transitions / transversions = 1.45 (32/22) Gap_init rate = 0.02 (5 / 202), avg. gap size = 1.80 (9 / 5) 274 21.33 5.98 7.83 chr2ptel1M 343280 343396 (656604) L1PB4_3end#LINE/L1 75 189 (714) m_b64s551i6 2350 chr2ptel1M 343280 AAAAGTTATGAATAGCCAGTTTTCAGATGAAGAAGGCA---AAGCAATCT 343326 i vi i v v i --- i --- iii v L1PB4_3end#LI 75 AAAGGACATGAACAGACATTTTTCAAA---AGAAGACATACAAGCGGCCA 121 chr2ptel1M 343327 ATAGACGTATTTGAAAAAATTCTTTCAATCACTA----TTAGAGAAATGC 343372 i i i -- v ivvv ---- i L1PB4_3end#LI 122 ACAAACATAT--GAAAAAATGCTCAACATCACTAATCATCAGAGAAATGC 169 chr2ptel1M 343373 ACATTAAAACAACTGATAATGAGA 343396 v v ---- L1PB4_3end#LI 170 AAATTAAAACCAC----AATGAGA 189 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 24.16 CpG sites = 13, Kimura (unadjusted) = 25.39 Transitions / transversions = 1.30 (13/10) Gap_init rate = 0.09 (11 / 116), avg. gap size = 1.45 (16 / 11) 458 30.44 4.46 2.43 chr2ptel1M 343747 343948 (656052) L1PA5_3end#LINE/L1 196 401 (500) m_b64s551i7 2351 chr2ptel1M 343747 CTCATACTA-TCAGACTGGC------TAAGAAGACAGGAAAAGATAAATG 343789 i i - i v ------ i v vi i ii L1PA5_3end#LI 196 CTCACACCAGTTAGAATGGCGATCATTAAAAAGTCAGGAAACAACAGGTG 245 chr2ptel1M 343790 TTGTAAGGGATTTGGGAAAATGAGA-CAGTATTGCATTGTTGGTGGAATT 343838 i v ii v ii ii - v v i i i i L1PA5_3end#LI 246 CTGGAGAGGATGTGGAGAAATAGGAACACTTTTACACTGTTGGTGGGACT 295 chr2ptel1M 343839 GTGAAATGATCCTGCCATTCTGGAGAACAATTTGGATCTATGCC-CAAAA 343887 i v ii i vi v ii i v -- v v - ii L1PA5_3end#LI 296 GTAAACTAGTTCAACCATTGTGGAAGACAGTGTGG--CGATTCCTCAAGG 343 chr2ptel1M 343888 AGCTATGAAACTGTGCATACCCTTTGATCCAGCAGTGTCACTACTGACTC 343937 v --i iviv v i vi vi i iv v L1PA5_3end#LI 344 ATCTA--GAACTAGAAATACCATTTGACCCAGCCATCCCATTACTGGGTA 391 chr2ptel1M 343938 TGTATGCCAAA 343948 i i- L1PA5_3end#LI 392 TATAC-CCAAA 401 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.91 CpG sites = 39, Kimura (unadjusted) = 40.91 Transitions / transversions = 1.86 (39/21) Gap_init rate = 0.04 (9 / 201), avg. gap size = 1.56 (14 / 9) 462 28.66 0.53 2.69 chr2ptel1M 343770 343959 (656041) L1MA1_3end#LINE/L1 226 411 (638) m_b64s551i8 2351 chr2ptel1M 343770 AAGACAGGAAAAGATAAATGTTGTAAGGGATTTGG-GAAAATGAGACAGT 343818 v vi i i vvii v - v ii vv L1MA1_3end#LI 226 AAGACAGGCAATAACAAATGCTGGCGAGGATGTGGAGAAAAGGGAACCCT 275 chr2ptel1M 343819 ATTGCATTGTTGGTGGAATTGTGAAATGATCCTGCCATTCTGGAGAACAA 343868 vv i i i v i v ii v vi i v i L1MA1_3end#LI 276 TGTACACTGTTGGTGGGAATGTAAATTAGTACAACCACTATGGAGAACAG 325 chr2ptel1M 343869 TTTGGATCTATGCCCAAAAAGCTATGAAACTGTGCATACCCTTTGATCCA 343918 vv - v i i -i i v - v v L1MA1_3end#LI 326 TTTGGAGGT-TCCTCAAAAAACTA-AAAATTGAGC-TACCATATGATCCA 372 chr2ptel1M 343919 GCAGTGTCACTACTGACTCTGTATGCCAAATAGAGAATAAA 343959 i vi i iv v i i- - i iv L1MA1_3end#LI 373 GCAATCCCACTGCTGGGTATATAC-CCAAA-AGAAAGGAAA 411 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.82 CpG sites = 28, Kimura (unadjusted) = 36.68 Transitions / transversions = 1.12 (28/25) Gap_init rate = 0.03 (6 / 189), avg. gap size = 1.00 (6 / 6) 24 6.68 0.00 0.00 chr2ptel1M 345538 345569 (654431) (CT)n#Simple_repeat 1 32 (0) m_b64s252i4 2352 chr2ptel1M 345538 CTCTCTCTCTCTCTTTCTCTCTCTCTTTCTCT 345569 i i (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 32 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 18 24.87 0.00 0.00 chr2ptel1M 345585 345627 (654373) (AG)n#Simple_repeat 1 43 (0) m_b64s252i5 2353 chr2ptel1M 345585 AGAGAGACACACAGAAAGACAGAGACAGACACACAGAGAGAGA 345627 v v v i v v v v v (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 43 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 chr2ptel1M 346767 346784 (653216) (A)n#Simple_repeat 1 18 (0) m_b64s252i6 2354 chr2ptel1M 346767 AAAAAAAAAAAAAAAAAA 346784 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAA 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 585 28.21 11.57 2.17 chr2ptel1M 347734 348070 (651930) C L1ME5_3end#LINE/L1 (565) 376 9 m_b64s551i9 2355 chr2ptel1M 347734 TTACTGGGTCAAAAAGTACATGTA-GTTTAATAATTCTTTGGC---GTAA 347779 i v ii iii -ii ------ i --- v C L1ME5_3end#LI 376 TTGCTGGGTCATAGGGTATGCGTATACTTAAT------TTGACTAAGTAC 333 chr2ptel1M 347780 TTTTAGATTGCCCTCCAAAATGGTTGGATCAGTTCACAATTCCACCAACA 347829 vii i i i v i ii v i i C L1ME5_3end#LI 332 TGCCAGATTGCTCTCCAGAATGGCTGCACCAGTCTACACTCCCACCAGCA 283 chr2ptel1M 347830 ATG-ATT----TTTTTTTTTTACCATAACCCCTCCAACATTTATCACTTT 347874 i - v---- ii v ? iv i v i v i iv i v C L1ME5_3end#LI 282 GTGCATGAGGGTTCCTATNTCCCCACATCCTCGCCAACACTTGGCATTAT 233 chr2ptel1M 347875 CC--CCTTCTATCACTTTAATCAATCTGATAGGTATGA---CATATTTCA 347919 -- i -- i vii i i i i ---v i C L1ME5_3end#LI 232 CCAGCTTTCTA--ATTTTTGCCAGTCTAATAGGTGTAAAGTGATATCTCA 185 chr2ptel1M 347920 TGATTATTTTAATTTGCAGTTCTCTAATCAATGGTGATTTAGAACA--TT 347967 vi i v i i v ii v v i -- i C L1ME5_3end#LI 184 TTGTTGTTTTAATTTGCATTTCTCTGATTACTAATGAGTTTGAGCATCTC 135 chr2ptel1M 347968 TTCAAATG------AGTATAT----TTTTTTCTTC-----AT----TATT 347998 v ------ iv v ---- ii ----- ---- i C L1ME5_3end#LI 134 TTCATATGCTTGTTAGCCTTTCGGGTTTCCTCTTCTGTAAATTGCCTGTT 85 chr2ptel1M 347999 CTTATCCTTTGACCATTTATCACTTGAAG----AATTTGATTCTTATAGA 348044 v v v vv ii ----vi i vv i v C L1ME5_3end#LI 84 CATATCCTTTGCCCATTTTTCTATTGGGGTTNCCGTCTTTTTCTTGTTGA 35 chr2ptel1M 348045 TTTGACAAAGTTCTTTATGTATTTTA 348070 vvii i i i i C L1ME5_3end#LI 34 TTTGCAGGAGTTCCTTGTATATTCTA 9 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.01 CpG sites = 60, Kimura (unadjusted) = 37.03 Transitions / transversions = 1.82 (60/33) Gap_init rate = 0.06 (20 / 336), avg. gap size = 2.35 (47 / 20) 32 3.23 0.00 0.00 chr2ptel1M 351240 351271 (648729) (TG)n#Simple_repeat 1 32 (0) c_b64s251i0 2356 chr2ptel1M 351240 TGTGTGTGTATGTGTGTGTGTGTGTGTGTGTG 351271 i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 32 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 350 28.60 0.00 3.06 chr2ptel1M 351924 352024 (647976) Tigger9b#DNA/TcMar-Tigger 312 409 (215) m_b64s502i0 2357 chr2ptel1M 351924 CCACTTCCCAGTGACCCCTGAACTGCTACCCTCATTCCAGTGCCTATGTC 351973 v i i i vii i v --- iii i iv Tigger9b#DNA/ 312 CCACTTCACAATAACTCACAAGCTGCAACCCT---TCCGACGCCCACTTC 358 chr2ptel1M 351974 TACAAGCAAACTCCCGGTCTTTGCTAGAGTAAAGCACCATGTTTATCATA 352023 i i v vii ii ii i ii Tigger9b#DNA/ 359 CACAAGCAAACTTCAGGTCTTTTTCAAGGTAAAGTGCCATATTTATTGTA 408 chr2ptel1M 352024 G 352024 Tigger9b#DNA/ 409 G 409 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.34 CpG sites = 22, Kimura (unadjusted) = 38.95 Transitions / transversions = 3.67 (22/6) Gap_init rate = 0.03 (3 / 100), avg. gap size = 1.00 (3 / 3) 305 20.31 26.45 1.55 chr2ptel1M 352216 352370 (647630) Tigger9b#DNA/TcMar-Tigger 432 624 (0) m_b64s502i1 2358 chr2ptel1M 352216 TTAGCATG----AGACTGTACTGCCATGGTTTTGATTTGGTTCCTTTTAT 352261 i ---- i i i --- v v v iv Tigger9b#DNA/ 432 TTAACATGTGTAAAACTGTGCTACC---GTTTTTATTAGGTTCCTATCTT 478 chr2ptel1M 352262 TTTTTTTAA--TGTCACTGGCCAGA---TTGCGTGCTGTGCTCCCA---- 352302 ? -- i v ii--- v i i i ---- Tigger9b#DNA/ 479 TTTTTTTNATGTGTCACTGACGAAGTTTTTGAGTGTTGTGCCCCTAACCC 528 chr2ptel1M 352303 -----TCC-------CTCTGTGACTTTCATTGTGTGATTTTGTGTAGC-- 352338 ----- ------- i ii i i i ii -- Tigger9b#DNA/ 529 CATTTTCCCCATAAGCCCTGTGGTTTTTATTGCGCGATTTTGCATAGCGC 578 chr2ptel1M 352339 ---------CAGGAATG----TTTC-TGTTACAGCAGAACAGACTG 352370 ---------i i ---- v -i i v Tigger9b#DNA/ 579 GGTGATTTTTAGGAACGCATATGTCGCGTTATAGCAGAACTGACTG 624 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 21.35 CpG sites = 23, Kimura (unadjusted) = 24.93 Transitions / transversions = 2.88 (23/8) Gap_init rate = 0.08 (12 / 154), avg. gap size = 3.67 (44 / 12) 35 29.97 0.00 0.00 chr2ptel1M 354561 354666 (645334) (ATCC)n#Simple_repeat 1 106 (0) m_b64s252i7 2359 chr2ptel1M 354561 ATTCATCCATCCATTTATGAAACCATCCATCTACTCATCGATCCATGCTT 354610 i ii vv v i ii v v v (ATCC)n#Simpl 1 ATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCAT 50 chr2ptel1M 354611 CTTTCCATCTATCTGTGTTTCTTTCCTTCCATCCATCCTTCTATCCATCC 354660 iv i ii viv iv v v i (ATCC)n#Simpl 51 CCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCC 100 chr2ptel1M 354661 ATCGAT 354666 v (ATCC)n#Simpl 101 ATCCAT 106 Matrix = Unknown Transitions / transversions = 1.00 (13/13) Gap_init rate = 0.00 (0 / 105), avg. gap size = 0.0 (0 / 0) 23 10.03 0.00 0.00 chr2ptel1M 355203 355235 (644765) (AC)n#Simple_repeat 1 33 (0) m_b64s252i8 2360 chr2ptel1M 355203 ACACACACACACACGCACACGCACACACATACA 355235 i i i (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACA 33 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 15 25.53 0.00 3.77 chr2ptel1M 355447 355501 (644499) (TTTTCCT)n#Simple_repeat 1 53 (0) m_b64s252i9 2361 chr2ptel1M 355447 TTTTCATATTTTTCTTGTTTGCTTGGTTTTTTTTTCTTTCTCATTTTTCC 355496 v - i - v vv ii i i v (TTTTCCT)n#Si 1 TTTTCCT-TTTTCCTT-TTTCCTTTTTCCTTTTTCCTTTTTCCTTTTTCC 48 chr2ptel1M 355497 CTTTT 355501 i (TTTTCCT)n#Si 49 TTTTT 53 Matrix = Unknown Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.04 (2 / 54), avg. gap size = 1.00 (2 / 2) 468 22.54 0.00 9.82 chr2ptel1M 355690 355812 (644188) MIRc#SINE/MIR 4 115 (153) m_b64s601i1 2362 chr2ptel1M 355690 GGCAGCTAGGTGATGCAGCGGATAGAGCACCAGGTCTGAATTCAGGAGGA 355739 i--- i i v ii iii i v i MIRc#SINE/MIR 4 GGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA 50 chr2ptel1M 355740 CCTGAGTTCAAATCTGGTCTCAGACACTTAACACTTCCTAGCTTTGTGAC 355789 i i i iv v v v ------- v - MIRc#SINE/MIR 51 CCTGGGTTCGAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTGA- 92 chr2ptel1M 355790 CCCTGAGCAAGTCACTTAATCCC 355812 i i i i MIRc#SINE/MIR 93 CCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.27 CpG sites = 18, Kimura (unadjusted) = 27.56 Transitions / transversions = 2.57 (18/7) Gap_init rate = 0.09 (11 / 122), avg. gap size = 1.00 (11 / 11) 28 14.38 2.08 0.00 chr2ptel1M 355826 355873 (644127) (AT)n#Simple_repeat 1 49 (0) m_b64s252i10 2363 chr2ptel1M 355826 ATATACATACATATATATATATATATA-ATATATATACACACACATATA 355873 i i - i i i i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATA 49 Matrix = Unknown Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.02 (1 / 47), avg. gap size = 1.00 (1 / 1) 180 19.80 0.00 10.87 chr2ptel1M 357112 357162 (642838) L3#LINE/CR1 867 912 (3187) m_b64s601i2 2364 chr2ptel1M 357112 TCTTCTTTTCTTTCTTCCAGTTGGAGATACTGAAGCCCTTTGGAAGGAAA 357161 i v i - i i vv ---- ii L3#LINE/CR1 867 TTTTCATCTCTT-CTTCCAGTTGAAGGTCGTGA----CTTTGGAAGAGAA 911 chr2ptel1M 357162 A 357162 L3#LINE/CR1 912 A 912 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 23.23 CpG sites = 6, Kimura (unadjusted) = 23.23 Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.10 (5 / 50), avg. gap size = 1.00 (5 / 5) 195 18.75 0.00 0.00 chr2ptel1M 357455 357486 (642514) C L2c_3end#LINE/L2 (12) 466 435 m_b64s601i3 2365 chr2ptel1M 357455 AATAAGCATTTATAGAATGCCTACTGTGTGCC 357486 i i v ii i C L2c_3end#LINE 466 AACAAACATTTATTGAGCGCCTACTATGTGCC 435 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 18.56 CpG sites = 5, Kimura (unadjusted) = 22.67 Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 404 30.91 4.08 6.25 chr2ptel1M 357459 357703 (642297) C MIR#SINE/MIR (10) 252 13 m_b64s601i4 2366 chr2ptel1M 357459 AGCATTTATAGAATGCCTACTGTGTGCCTCAATGC-CTGTGTTACATCAA 357507 i v ii i i --- v - vi ----- C MIR#SINE/MIR 252 AACATTTATTGAGCGCTTACTATGTGCC---AGGCACTGTTCTA-----A 211 chr2ptel1M 357508 GTGATTTTC--GTAAGAGCCC-TACAAAGTTAATATTAACCTTCATAA-- 357552 i v v -- vv i i - vi vvi v i vi i - i -- C MIR#SINE/MIR 210 GCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCT-ATGAGG 162 chr2ptel1M 357553 TACTTATTATGCTGTTACCTCCACTTTACAGTTGAGAACATGGAAGCAAA 357602 vv i -- i i i i v i v iv i v C MIR#SINE/MIR 161 TAGGTACTAT--TATTATCCCCATTTTACAGATGAGGAAACTGAGGCACA 114 chr2ptel1M 357603 TAGAGGTTGAATGATTTGCCCAGGCTTCCACATCTAGAAAGTGTC-TTGC 357651 v i i i i i v iv v v v -vv C MIR#SINE/MIR 113 GAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGC 64 chr2ptel1M 357652 CTTCTTCCTGAATCTAGGCCCAGT---GCTCTAGCTACTATGCCACTTAG 357698 vvvv i - i i -- --- i vvv ii i- i C MIR#SINE/MIR 63 CGGGATTC-GAACCCAGG--CAGTCTGGCTCCAGAGCCCGTGCT-CTTAA 18 chr2ptel1M 357699 TCACT 357703 i C MIR#SINE/MIR 17 CCACT 13 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.31 CpG sites = 38, Kimura (unadjusted) = 40.57 Transitions / transversions = 1.15 (38/33) Gap_init rate = 0.09 (21 / 244), avg. gap size = 1.19 (25 / 21) 415 26.92 12.31 0.00 chr2ptel1M 357565 357694 (642306) C MIRc#SINE/MIR (113) 155 10 m_b64s601i5 2366 chr2ptel1M 357565 TGTTACCTCCACTTTACAGTTGAGAACATGGAAGCAAATAGAGGTTGAAT 357614 i i i i v i v iv i vv v i i C MIRc#SINE/MIR 155 TATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGT 106 chr2ptel1M 357615 GATTTGCCCAGGCTTCCACATCTAGAAAGTGT-----------CTTG--C 357651 i i v iv v v v----------- i -- C MIRc#SINE/MIR 105 GACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAAC 56 chr2ptel1M 357652 CT---TCTTCCTGAATCTAGGCCCAGTGCTCTAGCTACTATGCCAC 357694 i--- v i i i vv i iii C MIRc#SINE/MIR 55 CCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.04 CpG sites = 21, Kimura (unadjusted) = 34.24 Transitions / transversions = 1.50 (21/14) Gap_init rate = 0.02 (3 / 129), avg. gap size = 5.33 (16 / 3) 285 33.34 0.59 2.41 chr2ptel1M 359601 359769 (640231) C L1ME4b_3end#LINE/L1 (234) 658 493 m_b64s551i10 2367 chr2ptel1M 359601 TATTGTGTACACTGTATTCCTG-ATTTTGCTTGTTTCGCTCAGCATCAGT 359649 i i ii ---i - ii v i i i vi vv C L1ME4b_3end#L 658 TACTATACACACTGT---TCTGCACCTTGCTTTTTTCACTTAACAATATA 612 chr2ptel1M 359650 TCATGTAAATCTCTCCAGGCCTTTCTATAATCAGCTTCTACATCATTTTT 359699 v v i ?i vii vv vi ?vv iv iv C L1ME4b_3end#L 611 TCTTGGAGATCNTTCCATATCAGTACATANAGAGCTTCCTCATTCTTTTT 562 chr2ptel1M 359700 TAAAAGAACAATAACATTCCATTACCTTCATGTACCACAGCTTGTTCGGC 359749 viivvi - ii iiv vv i ii i iii C L1ME4b_3end#L 561 TACGGCTGCA-TAGTATTCCATTGTATGGATGTACCATAATTTATTTAAC 513 chr2ptel1M 359750 CATTCCCCAATTGATGGGCA 359769 v v i C L1ME4b_3end#L 512 CAGTCCCCTATTGATGGACA 493 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 45.49 CpG sites = 33, Kimura (unadjusted) = 46.68 Transitions / transversions = 1.50 (33/22) Gap_init rate = 0.03 (5 / 168), avg. gap size = 1.00 (5 / 5) 300 32.19 0.00 0.68 chr2ptel1M 359623 359769 (640231) C L1MC4a_3end#LINE/L1 (1993) 636 491 m_b64s551i11 2367 chr2ptel1M 359623 ATTTTGCTTGTTTCGCTCAGCATCAGTTCATGTAAATCTCTCCAGGCCTT 359672 i v i i i vi vv v v v vii vv C L1MC4a_3end#L 636 ACTTTGCTTTTTTCACTTAACAATATATCCTGGAAATCACTCCATATCAG 587 chr2ptel1M 359673 TCTATAATCAGCTTCTACATCATTTTTTAAAAGAACAATAACATTCCATT 359722 ii ivv v iv iv v ivvi - ii i C L1MC4a_3end#L 586 TTCATAGAGATCTTCCTCATTCTTTTTTACAGCTGCA-TAGTACTCCATT 538 chr2ptel1M 359723 ACCTTCATGTACCACAGCTTGTTCGGCCATTCCCCAATTGATGGGCA 359769 iiv vv i i i ii ? i v ?? C L1MC4a_3end#L 537 GTGTGGATGTACCATAGTTTATTCAACCANTCTCCTATNNATGGGCA 491 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 44.20 CpG sites = 25, Kimura (unadjusted) = 44.20 Transitions / transversions = 1.14 (25/22) Gap_init rate = 0.01 (1 / 146), avg. gap size = 1.00 (1 / 1) 14 20.54 0.00 0.00 chr2ptel1M 361115 361148 (638852) (TTAAGG)n#Simple_repeat 1 34 (0) m_b64s252i11 2368 chr2ptel1M 361115 TTAGGGTTAGGGTTAGGGTTAAGATTAACCTTAA 361148 i i i i vv (TTAAGG)n#Sim 1 TTAAGGTTAAGGTTAAGGTTAAGGTTAAGGTTAA 34 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 23 0.00 0.00 0.00 chr2ptel1M 361888 361912 (638088) (A)n#Simple_repeat 1 25 (0) m_b64s252i12 2369 chr2ptel1M 361888 AAAAAAAAAAAAAAAAAAAAAAAAA 361912 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAA 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 22 17.84 6.06 1.45 chr2ptel1M 365260 365325 (634675) (GAAAGA)n#Simple_repeat 1 69 (0) m_b64s252i13 2370 chr2ptel1M 365260 GAAAGAAAAAGAGAAATAGAAAGA-AGAGA-AAAG-GATGTGAAAAAAAT 365306 i v - i - - -iv i i v (GAAAGA)n#Sim 1 GAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGA-AAGAGAAAGAG 49 chr2ptel1M 365307 AAAGGGAAAGGGAAAG-GAA 365325 i i - (GAAAGA)n#Sim 50 AAAGAGAAAGAGAAAGAGAA 69 Matrix = Unknown Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.08 (5 / 65), avg. gap size = 1.00 (5 / 5) 36 0.00 0.00 0.00 chr2ptel1M 366134 366164 (633836) (AC)n#Simple_repeat 1 31 (0) c_b64s251i1 2371 chr2ptel1M 366134 ACACACACACACACACACACACACACACACA 366164 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACA 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 229 22.64 3.77 0.00 chr2ptel1M 367758 367810 (632190) C MIR3#SINE/MIR (0) 208 154 m_b64s601i6 2372 chr2ptel1M 367758 GAATCACAGTATCATAGA--TTTAGAACTGAATGAGACTTTAGAGTTTAG 367805 i v --v i i i v i i v i v C MIR3#SINE/MIR 208 GAATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCAT 159 chr2ptel1M 367806 CTAGT 367810 C MIR3#SINE/MIR 158 CTAGT 154 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 27.42 CpG sites = 7, Kimura (unadjusted) = 27.42 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.02 (1 / 52), avg. gap size = 2.00 (2 / 1) 16 0.00 0.00 0.00 chr2ptel1M 368100 368116 (631884) (G)n#Simple_repeat 1 17 (0) m_b64s252i14 2373 chr2ptel1M 368100 GGGGGGGGGGGGGGGGG 368116 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGG 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 198 20.00 0.00 0.00 chr2ptel1M 369152 369191 (630809) L2d_3end#LINE/L2 471 510 (6) m_b64s601i7 2374 chr2ptel1M 369152 AGAACATAATAGATGCTCAATAAATGCTTTTTCATTCATT 369191 v i ii i v v v L2d_3end#LINE 471 AGCACATAGTAGGCGCTCAATAAATACTTGTTGATTGATT 510 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 20.30 CpG sites = 4, Kimura (unadjusted) = 23.41 Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 239 30.14 0.00 0.00 chr2ptel1M 369345 369417 (630583) C MIR3#SINE/MIR (2) 206 134 m_b64s601i8 2375 chr2ptel1M 369345 ATCTTAGAGCCCTAGAATGTTTGAGCTGGAAGAGAGCGGAGAGGTCAACT 369394 v ii v iv i v vv i v C MIR3#SINE/MIR 206 ATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCT 157 chr2ptel1M 369395 GCTTTAAGCCTCACATTCAGCAG 369417 iv ii v i v ivi C MIR3#SINE/MIR 156 AGTCCAACCCCCTCATTTTACAG 134 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.04 CpG sites = 11, Kimura (unadjusted) = 39.04 Transitions / transversions = 1.00 (11/11) Gap_init rate = 0.00 (0 / 72), avg. gap size = 0.0 (0 / 0) 301 22.42 1.03 12.64 chr2ptel1M 369618 369714 (630286) C MIRc#SINE/MIR (171) 97 11 m_b64s601i9 2376 chr2ptel1M 369618 CAGGGTCACACAGCTAGGAAGAGTCTTAAGGCCAG-ATTTGAACTCAGAA 369666 i v v v -- ii i - i i i -- C MIRc#SINE/MIR 97 CAAGGTCACACAGCTAGTAAGTGGC--AGAGCCGGGACTCGAACCCAG-- 52 chr2ptel1M 369667 AGAAATGTCTTTCCTGTCTTCATGCTTATTGCTCTATCCACTGTACCA 369714 ------ - v i v iii v v i C MIRc#SINE/MIR 51 ------GTCTT-CCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCA 11 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 23.62 CpG sites = 12, Kimura (unadjusted) = 26.79 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.12 (12 / 96), avg. gap size = 1.00 (12 / 12) 12 12.63 0.00 3.70 chr2ptel1M 370376 370403 (629597) (TAAA)n#Simple_repeat 1 27 (0) m_b64s252i15 2377 chr2ptel1M 370376 TAAATAGATAAATAATTAGATCAAATAA 370403 i v i - (TAAA)n#Simpl 1 TAAATAAATAAATAAATAAAT-AAATAA 27 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 14 21.26 0.00 4.44 chr2ptel1M 371145 371191 (628809) (GAGATAG)n#Simple_repeat 1 45 (0) m_b65s252i1 2378 chr2ptel1M 371145 GAGATAAGGAGATAGGAGAAAGAAGCTCAGGAAAGTGGAGAGTGGAG 371191 - v i v - i vv vv (GAGATAG)n#Si 1 GAGAT-AGGAGATAGGAGATAGGAGAT-AGGAGATAGGAGATAGGAG 45 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.04 (2 / 46), avg. gap size = 1.00 (2 / 2) 239 22.00 0.00 0.00 chr2ptel1M 371621 371670 (628330) C MIR#SINE/MIR (140) 122 73 m_b65s601i1 2375 chr2ptel1M 371621 TAAGGCAAACATAAATGAAGTGAATTGCCCAGGATCACACAGCTAGTAAG 371670 i v v v ii v i v i i C MIR#SINE/MIR 122 TGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAG 73 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 26.35 CpG sites = 6, Kimura (unadjusted) = 26.35 Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 334 18.75 7.81 0.00 chr2ptel1M 371751 371814 (628186) C L2d_3end#LINE/L2 (0) 516 448 m_b65s601i2 2379 chr2ptel1M 371751 TCATTCAATCAATCAATAAACATTTATTAAGCACCTGCTATGT-----AC 371795 v i ii i i i -----i C L2d_3end#LINE 516 TCAATCAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGC 467 chr2ptel1M 371796 ACTGTGCTAAGTTCTGGGG 371814 i iv v C L2d_3end#LINE 466 ACTGTGCTAGGCGCTGTGG 448 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 18.33 CpG sites = 9, Kimura (unadjusted) = 22.35 Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.02 (1 / 63), avg. gap size = 5.00 (5 / 1) 410 27.47 6.06 0.72 chr2ptel1M 373436 373567 (626433) MIRc#SINE/MIR 10 148 (120) m_b65s601i3 2380 chr2ptel1M 373436 GTGTCACAGTGGACAGAAAGCTGGGGTTGG------GAGGCCCCGAACTC 373479 vii v ivi iv ------ i v i iii MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr2ptel1M 373480 AAAACTGGCCTCAGGACGCT-ACTAGCCATGTGACGCTGGGCAAGTCACT 373528 i iv iv v -v v i - ii vi MIRc#SINE/MIR 60 GAGTCCCGGCTC-TGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACT 108 chr2ptel1M 373529 TCACC-CTGTTTGTCTCAGTTTCCTCACCTATAAAATGAG 373567 v - v vv i i i i MIRc#SINE/MIR 109 TAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.86 CpG sites = 21, Kimura (unadjusted) = 35.06 Transitions / transversions = 1.40 (21/15) Gap_init rate = 0.03 (4 / 131), avg. gap size = 2.25 (9 / 4) 14 14.33 0.00 9.52 chr2ptel1M 374378 374423 (625577) (GGAAGTG)n#Simple_repeat 1 42 (0) m_b65s252i2 2381 chr2ptel1M 374378 GGAACTGGGAAGAGAGAAGGTAGGAAGTGGGAGAGTTTGGCAAGTG 374423 v v i - i - -- v (GGAAGTG)n#Si 1 GGAAGTGGGAAGTGGGAA-GTGGGAAGTGGGA-AG--TGGGAAGTG 42 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.09 (4 / 45), avg. gap size = 1.00 (4 / 4) 187 30.43 5.80 0.00 chr2ptel1M 374760 374828 (625172) C MIR3#SINE/MIR (2) 206 134 m_b65s601i4 2382 chr2ptel1M 374760 ATCCTGGAATCCTAGAATGACAGAGTGAGAAGAAGCC----AAGTGTTGT 374805 v i v v ivi iii ---- ii vv v C MIR3#SINE/MIR 206 ATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCT 157 chr2ptel1M 374806 GGTTCACACCCCACATTTGACAG 374828 i i vv v v C MIR3#SINE/MIR 156 AGTCCAACCCCCTCATTTTACAG 134 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.42 CpG sites = 10, Kimura (unadjusted) = 39.42 Transitions / transversions = 0.91 (10/11) Gap_init rate = 0.01 (1 / 68), avg. gap size = 4.00 (4 / 1) 20 0.00 0.00 0.00 chr2ptel1M 378269 378290 (621710) (A)n#Simple_repeat 1 22 (0) m_b65s252i3 2383 chr2ptel1M 378269 AAAAAAAAAAAAAAAAAAAAAA 378290 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAA 22 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 1376 19.37 1.19 0.00 chr2ptel1M 379750 380002 (619998) Tigger1#DNA/TcMar-Tigger 34 289 (2129) m_b65s502i0 2384 chr2ptel1M 379750 TTGCATTTGGCAAATGTTGCATTTTTTATAGACAGAAGGTTTGTGGCAAC 379799 ii v i i i i i iv Tigger1#DNA/T 34 TTGCGCTTCGCAGATATTGCGTTTTTTACAAATTGAAGGTTTGTGGCAAC 83 chr2ptel1M 379800 AGCTCTTCTAGCAAGTTGATTGGTGCCATTTTTCCAACAGCACATGCTCA 379849 vviv v v iv i i ii Tigger1#DNA/T 84 CCTGCGTCGAGCAAGTCTATCGGCGCCATTTTTCCAACAGCATGTGCTCA 133 chr2ptel1M 379850 CATCCTGTCTCTGTGTCACATCCTGGTAATTTTAACAATATTTCAAGCTT 379899 v v ii i vi i Tigger1#DNA/T 134 CTTCGTGTCTCTGTGTCACATTTTGGTAATTCTCGCAATATTTCAAACTT 183 chr2ptel1M 379900 TTTCATTATTATTACTTGTGTT---GTGACCTGTGATTAGAGATCTTTGA 379946 iv v --- i i v Tigger1#DNA/T 184 TTTCATTATTATTATATCTGTTATGGTGATCTGTGATCAGTGATCTTTGA 233 chr2ptel1M 379947 TATTATTATTGTAAGTGTTTTGGGGTTCCATGAAGAGCATCAATATAAGA 379996 i i v iv i vv ii v Tigger1#DNA/T 234 TGTTACTATTGTAATTGTTTTGGGGCGCCACGAACCGCGCCCATATAAGA 283 chr2ptel1M 379997 TGGCAA 380002 i i Tigger1#DNA/T 284 CGGCGA 289 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 17.86 CpG sites = 30, Kimura (unadjusted) = 22.79 Transitions / transversions = 1.58 (30/19) Gap_init rate = 0.00 (1 / 252), avg. gap size = 3.00 (3 / 1) 1305 16.47 9.16 0.35 chr2ptel1M 380060 380321 (619679) Tigger1#DNA/TcMar-Tigger 2126 2410 (8) m_b65s502i1 2385 chr2ptel1M 380060 AGTCAACAGTCAACACCACCAAGACAAGACCCTATACTGGCAAAAGGATT 380109 i i v v i i i vi ii i Tigger1#DNA/T 2126 AGTCAGCAGCCATCAACATCGAGGCAAGACCCTCCACCAGCAAAAAGATT 2175 chr2ptel1M 380110 ATGATTCCCTGAAGGTTCTGGTGAT-GCTAGCGTTTTTTAGCAATAAAAT 380158 i i v i v i - i i i Tigger1#DNA/T 2176 ACGACTCGCTGAAGGCTCAGATGATCGTTAGCATTTTTTAGCAATAAAGT 2225 chr2ptel1M 380159 ATTTTTTAATTAAGGTTTGTACAATGTTTTT-ATACATAATACTATTGCA 380207 v v v - v i Tigger1#DNA/T 2226 ATTTTTAAATTAAGGTATGTACATTGTTTTTTAGACATAATGCTATTGCA 2275 chr2ptel1M 380208 CACTTAATAGACTATAGTTATATTAT-AACATAACTTTTATAAGAACTGG 380256 i - v i - v v Tigger1#DNA/T 2276 CACTTAATAGACTACAG-TATAGTGTAAACATAACTTTTATATGCACTGG 2324 chr2ptel1M 380257 GAAACCAAAAAATTCCTGTGACT--------------------TTTTTTG 380286 v -------------------- v Tigger1#DNA/T 2325 GAAACCAAAAAATTCGTGTGACTCGCTTTATTGCGATATTCGCTTTATTG 2374 chr2ptel1M 380287 CAATGGTTGGAAAAAGAACCCAC-ATATCTTCAAGG 380321 ii iv i vv i - i i Tigger1#DNA/T 2375 CGGTGGTCTGGAACCGAACCCGCAATATCTCCGAGG 2410 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 16.55 CpG sites = 26, Kimura (unadjusted) = 18.84 Transitions / transversions = 1.53 (26/17) Gap_init rate = 0.02 (6 / 261), avg. gap size = 4.17 (25 / 6) 26 13.98 0.00 0.00 chr2ptel1M 382151 382191 (617809) (A)n#Simple_repeat 1 41 (0) m_b65s252i4 2386 chr2ptel1M 382151 AAAAAAAAAAAAAAAAGAAAGAAAGAAAGAAAAAGAAAAAA 382191 i i i i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 41 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 194 26.83 0.00 0.00 chr2ptel1M 382404 382444 (617556) C MIR1_Amn#SINE/MIR (184) 46 6 m_b65s601i5 2387 chr2ptel1M 382404 GAGATTCAATTCATTGTTCTGTCCATTATACCATACTGCCT 382444 vii i i v i i i v i C MIR1_Amn#SINE 46 GAGTCCCAGTCCAGTGCTCTATCCACTAGACCACACTGCCT 6 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.08 CpG sites = 8, Kimura (unadjusted) = 35.08 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 14 9.12 0.00 0.00 chr2ptel1M 383548 383571 (616429) (GGAG)n#Simple_repeat 1 24 (0) m_b65s252i5 2388 chr2ptel1M 383548 GGGGGGGGGGAGGGAGGGAGGGAG 383571 i i (GGAG)n#Simpl 1 GGAGGGAGGGAGGGAGGGAGGGAG 24 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 17 12.68 0.00 0.00 chr2ptel1M 385688 385713 (614287) (C)n#Simple_repeat 1 26 (0) m_b65s252i6 2389 chr2ptel1M 385688 CCCCCCCCCCCCCCCCGCTCCCTCCC 385713 v i i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCC 26 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 208 33.33 1.56 1.56 chr2ptel1M 389513 389576 (610424) C MIR3#SINE/MIR (7) 201 138 m_b65s601i6 2390 chr2ptel1M 389513 AGGATCACAAGCCGCCAGGAGTCAGAAGAGATCCTA-AGATTATCTAGTT 389561 i i iivi i - iii i i i - i i C MIR3#SINE/MIR 201 AGAATCATAGAATGTCAG-AGCTGGAAGGGACCTTAGAGATCATCTAGTC 153 chr2ptel1M 389562 TAACCATTTTCTTTT 389576 i vii iv C MIR3#SINE/MIR 152 CAACCCCCTCATTTT 138 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 50.76 CpG sites = 18, Kimura (unadjusted) = 50.76 Transitions / transversions = 6.00 (18/3) Gap_init rate = 0.03 (2 / 63), avg. gap size = 1.00 (2 / 2) 464 26.76 8.33 1.81 chr2ptel1M 389602 389757 (610243) MIRc#SINE/MIR 2 167 (101) m_b65s601i7 2391 chr2ptel1M 389602 GGGGCAGCTGGGTGGTGCAGTG-ATAGAGCACCAGCCCTGAAGTCAGGAG 389650 i i--- - v ii v i i i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr2ptel1M 389651 GGTCTGACTCCAA-TCTGACCTCAGATACTTGCTGGCTATGTGACCCTGG 389699 ii iv i i - iviv v vi i i i i MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 98 chr2ptel1M 389700 GCAAGTCACTTAAC--------AC--CAGTTGCCTCAGCCAAAAAAAAGG 389739 --------i -- v v iiv vi MIRc#SINE/MIR 99 GCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 chr2ptel1M 389740 TATTG-AGTACCTACTATG 389757 v vi- i i iv MIRc#SINE/MIR 149 GATAATAATACCTGCCCTG 167 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.37 CpG sites = 27, Kimura (unadjusted) = 34.44 Transitions / transversions = 1.93 (27/14) Gap_init rate = 0.05 (8 / 155), avg. gap size = 2.00 (16 / 8) 219 22.22 0.00 0.00 chr2ptel1M 389724 389768 (610232) C L2a_3end#LINE/L2 (6) 511 467 m_b65s601i8 2392 chr2ptel1M 389724 TCAGCCAAAAAAAAGGTATTGAGTACCTACTATGTATCAGGCACT 389768 vi v v vv ii ii C L2a_3end#LINE 511 TCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACT 467 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 23.33 CpG sites = 5, Kimura (unadjusted) = 26.56 Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 199 23.53 0.00 0.00 chr2ptel1M 389740 389773 (610227) C MIRb#SINE/MIR (18) 250 217 m_b65s601i9 2393 chr2ptel1M 389740 TATTGAGTACCTACTATGTATCAGGCACTAGACT 389773 ii i ii ivi C MIRb#SINE/MIR 250 TATTGAGCGCTTACTATGTGCCAGGCACTGTGCT 217 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 25.61 CpG sites = 7, Kimura (unadjusted) = 30.61 Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 18 8.72 0.00 0.00 chr2ptel1M 389871 389895 (610105) (TA)n#Simple_repeat 1 25 (0) m_b65s252i7 2394 chr2ptel1M 389871 TATATGTGTATATATATATATATAT 389895 i i (TA)n#Simple_ 1 TATATATATATATATATATATATAT 25 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 13 12.16 3.70 0.00 chr2ptel1M 390741 390767 (609233) (GGA)n#Simple_repeat 1 28 (0) m_b65s252i8 2395 chr2ptel1M 390741 GGGGGTGGGGGAGGAGGAGGAGG-GGAG 390767 i v i - (GGA)n#Simple 1 GGAGGAGGAGGAGGAGGAGGAGGAGGAG 28 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.04 (1 / 26), avg. gap size = 1.00 (1 / 1) 16 11.26 0.00 0.00 chr2ptel1M 392697 392725 (607275) (TGTTT)n#Simple_repeat 1 29 (0) m_b65s252i9 2396 chr2ptel1M 392697 TGTTTTGTTTTGTTTTGTTTTTTGTTTTT 392725 v v v (TGTTT)n#Simp 1 TGTTTTGTTTTGTTTTGTTTTGTTTTGTT 29 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 702 33.08 4.36 3.98 chr2ptel1M 393204 393754 (606246) C L1PB1_3end#LINE/L1 (333) 565 13 m_b65s551i0 2397 chr2ptel1M 393204 TTCTTATGG---AATGATATTTTGTAACATTAACATAACATCACTTATTC 393250 i --- i ii iii iii vv i v iv?i v i C L1PB1_3end#LI 565 TTTTTATGGCTGAGTAGTATTCCATGGTATATATATACCACANTTTCTTT 516 chr2ptel1M 393251 AGCCATTCCCTGATTTACTGGAATCCACTCAGTTTCCAGTTTCTTGCCAT 393300 v i vi v iv v iiivv v v vv i v C L1PB1_3end#LI 515 ATCCACTCGTTGATTGATGGGCATTTGGGCTGGTTCCATATTTTTGCAAT 466 chr2ptel1M 393301 TACAAAGAGGGCTGCCTTAAAGATCTTTGCACATGTGGGTCTCTTTTCCT 393350 i i vv v iv v ---- iii iii v -- C L1PB1_3end#LI 465 TGCGAATTGTGCTGCTATAAACAT----GCGTGTGCAAGTATCTTTT--T 422 chr2ptel1M 393351 CCTGTAA-GATCTCTTTG-----GGATATAAACCCAGTGGAAACACTACT 393394 v i - ii v----- i v v i viiv i i C L1PB1_3end#LI 421 CGTATAATGACTTCTTTTCCTCTGGGTAGATACCCAGTAGTGGGATTGCT 372 chr2ptel1M 393395 GGGTCAAAGAGTATGCACAGTTTGATAGCCCTT--GGGCATAGTTCCAAA 393442 i vi vvivi v -- ii --i v --i v C L1PB1_3end#LI 371 GGATCAAATGGTAGTTCTACTTT--TAGTTCTTTAAGGAAT--CTCCACA 326 chr2ptel1M 393443 TTGCTCTCCAGAATGGCTGGATCAGTTCACAACTCCACCAGCCAGGCATT 393492 i i i v i i v ii i vii viv i vv C L1PB1_3end#LI 325 CTGTTTTCCATAGTGGTTGTACTAGTTTACATTCCCACCAGCAGTGTAGA 276 chr2ptel1M 393493 GGTGTCCCAATTTTTCCACATCCCCTCCAATATTTGTTCTTGTAT--TTT 393540 i i vv iv i v v i i i v v v -- C L1PB1_3end#LI 275 AGTGTTCCCTTTTCACCGCATCCACGCCAACATCTATTATTTTTTGATTT 226 chr2ptel1M 393541 CCTGTCATCTTAGCCAATCTGAGAGGTGTGTAGTGGTACCTCAGAGTTGT 393590 ii -- iv i v viv v ivi i v vv v C L1PB1_3end#LI 225 TTTG--ATTATGGCCATTCTTGCAGGAGTAAGGTGGTATCGCATTGTGGT 178 chr2ptel1M 393591 CTTAGTTTGCATTTCCCTAATCAACAATTAT----AGCA-TTTTTAATAC 393635 i ii i vi i v ---- - v i C L1PB1_3end#LI 177 TTTGATTTGCATTTCCCTGATCATTAGTGATGTTGAGCATTTTTTCATAT 128 chr2ptel1M 393636 ATCTAGAAATGGTTTTAATTTCTTCATCTGAAAATTATTTGTTCATATCC 393685 i i ivviiivi vv v v i i i i i i C L1PB1_3end#LI 127 GTTTGTTGGCCATTTGTATATCTTCTTTTGAGAATTGTCTATTCATGTCC 78 chr2ptel1M 393686 TTTG---ACTGTTTGCCAAATGGGGAATGCATCTGTTCTTCTCTTAGCTG 393732 v --- v ---- - v -- i i i - C L1PB1_3end#LI 77 TTAGCCCACTTTTTG----AT-GGGATTG--TTTGTTTTTTTCTT-GCTG 36 chr2ptel1M 393733 ---TGGTGGAATCCAGTTTGTAGAT 393754 --- v v i i --? C L1PB1_3end#LI 35 ATTTGTTTGAGTTC--NTTGTAGAT 13 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 44.14 CpG sites = 99, Kimura (unadjusted) = 45.20 Transitions / transversions = 1.30 (99/76) Gap_init rate = 0.06 (31 / 550), avg. gap size = 1.48 (46 / 31) 1160 29.25 4.26 3.63 chr2ptel1M 393214 393706 (606294) C L1ME3Cz_3end#LINE/L1 (449) 548 53 m_b65s551i1 2397 chr2ptel1M 393214 ATGATATTTTGTAACATTAACATAACATCACTTATTCAGCCATTCCCTGA 393263 ii iii vii v i v iv i i v iv C L1ME3Cz_3end# 548 ATAGTATTCCATTGTATGAATATACCACAATTTATTTATCCATTCCCCTA 499 chr2ptel1M 393264 TTTACTGGAATCCACTCAG----TTTCCAGTTTCTTGCCATTACAAAGAG 393309 v - --- i i ---- i i i i v i C L1ME3Cz_3end# 498 TTGA-TGGA---CATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAA 453 chr2ptel1M 393310 GGCTGCCTTAAAGATCTTTGCACATGTGGGTCTCTTT-TCCTCCTGTAAG 393358 v vv i v i i ---- i - v v v iv C L1ME3Cz_3end# 452 TGCTGCAATGAACATCCTTGTACATGT----CTCCTTGTGCACATGTGCG 407 chr2ptel1M 393359 A---TCTCTTTGGGATATAAACCCAG---TGGAAACACTACTGGGTCAAA 393402 --- i i i i v i --- ---i i iv C L1ME3Cz_3end# 406 AGAGTTTCTCTAGGGTATATACCTAGAAGTGGAA---TTGCTGGGTCGTA 360 chr2ptel1M 393403 GAGTATGCACAGTTTGATAGCCCT--TGGGCATAGTTCCAAATTGCTCTC 393450 i i vi --i i ii -- i -- v v C L1ME3Cz_3end# 359 GGGTATGCGCATCTT--CAACTTTACTAG--ATATTGCCAAATTGCTCTC 314 chr2ptel1M 393451 CAGAATGGCTGGATCAGTTCACAACTCCACCAGCCAGGCATTGGTGTCCC 393500 i i i v i i i vii viv i vi v i C L1ME3Cz_3end# 313 CAAAGTGGTTGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTTCC 264 chr2ptel1M 393501 AATTTTTCCACATCCCCTCCAATATTTGTTCTTGT---ATTTTCCTGTCA 393547 vi i i v i i v v --- i iv---v C L1ME3Cz_3end# 263 CGTTTCTCCACATCCTCGCCAACACTTGGTATTGTCAGACTTTTA---AA 217 chr2ptel1M 393548 TCTTAGCCAATCTGAGAGGTGTGTAGTGGTACCTCAGAGTTGTCTTAGTT 393597 i v vi v i i vv ? i i C L1ME3Cz_3end# 216 TTTTTGCCAATCTGATGGGTGTGAAATGGTATCTCATTGTNGTTTTAATT 167 chr2ptel1M 393598 TGCATTTCCCTAATCAACAATTA----TAGCAT-TTTTAATACATCTAGA 393642 i i vi i v ----v - v ii i vv C L1ME3Cz_3end# 166 TGCATTTCCCTGATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATT 117 chr2ptel1M 393643 AATGGTTTTAATTTCTTCATCTGAAAATTATTTGTTCATATCCTTTGACT 393692 iiivi ivii i v vi iii v i C L1ME3Cz_3end# 116 GGCCATTCGGGTTTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCC 67 chr2ptel1M 393693 GTTTGCCAAATGGG 393706 i vi v v C L1ME3Cz_3end# 66 ATTTTTCTATTGGG 53 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.80 CpG sites = 87, Kimura (unadjusted) = 38.58 Transitions / transversions = 1.67 (87/52) Gap_init rate = 0.05 (26 / 492), avg. gap size = 1.50 (39 / 26) 405 33.55 7.42 3.38 chr2ptel1M 395247 395502 (604498) L2b_3end#LINE/L2 163 428 (38) m_b65s601i10 2398 chr2ptel1M 395247 CTTCTCC--CTTTTCATCT--TCATCTCCTGGTT-TCCTTTAAGTTCTGC 395291 i -- i ii --i v iv i- i i iiiiv L2b_3end#LINE 163 CTTCCCCACCTCTTCGCCTGGCCAACTCCTACTCATCCTTCAGGTCTCAG 212 chr2ptel1M 395292 CTAAGATCTTACCTCCTATAGGAAGCATTGTCCTAGCCCCTC---TTAAT 395338 v i v i vii vi -i ii i ---iiiiv L2b_3end#LINE 213 CTCAAATGTCACCTCCTCCGGGAAGCCCT-CCCTGACCCCCCAGGCCGGG 261 chr2ptel1M 395339 TCTAGTGCCTTCCCTCTTTTAGCAATCTCAAATTTAACCTG------TGT 395382 vi i i --- i vi vvi i ivii v ------ v L2b_3end#LINE 262 TCAGGCGCCCTCC---TCTGGGCCCCCCCAGTCCTACCCTGCCACTCTGG 308 chr2ptel1M 395383 GTATCTCATTTGTATGTTTGCTTATC-GTGTCCCCCACTGTTAGACTGTG 395431 - v ? - v ? i v i - v --- L2b_3end#LINE 309 GT-TATNATT-GTCTGNTTACATGTCTGTCTCCCCCACT---AGACTGTG 353 chr2ptel1M 395432 ATCTTCTCAAGGGCAGGAACTACCTTTGAC-CATTCTTTGTT---TCCTC 395477 v i vii i ii?v i v -ii vii i --- i L2b_3end#LINE 354 AGCTCCGTGAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTGTATCCCC 403 chr2ptel1M 395478 AGTGCTTAATACAATGTCTGTCATA 395502 i i ii i? i v i L2b_3end#LINE 404 AGCGCCTAGCACAGNGCCTGGCACA 428 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 43.08 CpG sites = 58, Kimura (unadjusted) = 49.16 Transitions / transversions = 2.32 (58/25) Gap_init rate = 0.07 (17 / 255), avg. gap size = 1.65 (28 / 17) 299 28.69 9.55 2.09 chr2ptel1M 395356 395533 (604467) L2d_3end#LINE/L2 320 510 (6) m_b65s601i11 2398 chr2ptel1M 395356 TTTAGCAATCTCAAATTTAACCTGTGT-GTAT----CTC-ATTTGT---A 395396 -- i v v vv v - ---- - v --- L2d_3end#LINE 320 TTTAGCA--CTTAATTATATACTGTCTTGTATTGTTCTCTAATTGTTTCA 367 chr2ptel1M 395397 TGTTTGCTTATCGTGTCCCCCACTGTTAGACTGTGATCTTCTCAAGGGCA 395446 v i vi v i - vii i i v i ii L2d_3end#LINE 368 TGTGTGTTAGTCTTGTCTCCC-CAACTAGATTGTAAGCTCCTTGAGGGCA 416 chr2ptel1M 395447 GGAAC--TACCTTTGACCATTCTTT-GTTTCCT-CAGTGCTTAATACAAT 395492 i -- ii vv i? i ? - i i- i i ii i L2d_3end#LINE 417 GGGACCATGTCTTATACTNTTTTNTCGTTCCCCACAGCGCCTAGCACAGT 466 chr2ptel1M 395493 GTCTG---TCATAACAAATGCTTTA-AAATGCTTTCTGACTAACT 395533 - ---v ii iii iv - i vi i i i L2d_3end#LINE 467 G-CTGAGCACATAGTAGGCGCTCAATAAATACTTGTTGATTGATT 510 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.65 CpG sites = 34, Kimura (unadjusted) = 38.65 Transitions / transversions = 2.12 (34/16) Gap_init rate = 0.07 (13 / 177), avg. gap size = 1.62 (21 / 13) 314 33.51 8.55 1.85 chr2ptel1M 395380 395531 (604469) L2a_3end#LINE/L2 350 511 (6) m_b65s601i12 2398 chr2ptel1M 395380 TGTGTATCTCATTTGTATGTTTGCTTATCGT--GTCCCCCACTGTTAGAC 395427 i i i i i i v i i i -- i v iii v L2a_3end#LINE 350 TATATATTTTACTTATTTATTTGTTTATTGTCTGTCTCCCCCCACTAGAA 399 chr2ptel1M 395428 TGTGATCTTCTCAAGGGCAGGAACTACCTTTGACCATTCT--------TT 395469 i v i vii i --- v ii i --------i L2a_3end#LINE 400 TGTAAGCTCCATGAGGGCAGGGACT---TTTGTCTGTTTTGTTCACTGCT 446 chr2ptel1M 395470 GTTTCCTCAGTGCTTAATACAATGTCTGT--CATAACAAATGCTTTA-AA 395516 v i i i iv i i v-- ii iii iv - L2a_3end#LINE 447 GTATCCCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGGCGCTCAATAA 496 chr2ptel1M 395517 ATGCTTTCTGACTAA 395531 ii vi v i L2a_3end#LINE 497 ATATTTGTTGAATGA 511 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 46.18 CpG sites = 38, Kimura (unadjusted) = 49.04 Transitions / transversions = 3.17 (38/12) Gap_init rate = 0.05 (7 / 151), avg. gap size = 2.29 (16 / 7) 503 22.81 0.78 4.84 chr2ptel1M 395602 395730 (604270) C MIRc#SINE/MIR (141) 127 4 m_b65s601i13 2399 chr2ptel1M 395602 CTGAGGC-AATTGGGGTTAAGTGACTTGCCCAGGGTCACACAGGAAGTGT 395650 -v vv i i vv -- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGT-- 80 chr2ptel1M 395651 TAAGTGTCTGAGACTAGATTTGAACACAGGTCCTCCCGACTTCAGGGCTG 395700 - v v v vi i i v i i i i v ii C MIRc#SINE/MIR 79 -AAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCA 31 chr2ptel1M 395701 ATGCTCTATCGACTGTACCATCTAGCTGCC 395730 i v v i i---i C MIRc#SINE/MIR 30 GTGCTCTTTCCACTGCACCAC---ACTGCC 4 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 26.33 CpG sites = 15, Kimura (unadjusted) = 27.44 Transitions / transversions = 1.15 (15/13) Gap_init rate = 0.05 (7 / 128), avg. gap size = 1.00 (7 / 7) 203 23.90 0.00 8.47 chr2ptel1M 398862 398925 (601075) C L2c_3end#LINE/L2 (59) 419 361 m_b65s601i14 2400 chr2ptel1M 398862 AAAGACATAAATAGCTGAAACTATCTTTACCCTCAAGAATTTGACAGTCT 398911 -- i i-- v vi ii i i vi v C L2c_3end#LINE 419 AAAGA--TGAATAA--GACACGGTCCCTGCCCTCAAGGAGCTCACAGTCT 374 chr2ptel1M 398912 TGTGGGGGGAGACA 398925 v - i C L2c_3end#LINE 373 AGT-GGAGGAGACA 361 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.34 CpG sites = 9, Kimura (unadjusted) = 29.34 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.08 (5 / 63), avg. gap size = 1.00 (5 / 5) 206 30.02 0.00 6.19 chr2ptel1M 398870 398972 (601028) C L2a_3end#LINE/L2 (82) 435 339 m_b65s601i15 2400 chr2ptel1M 398870 AAATAGCTGAAACTATCTTTACCCTCAAGAATTTGACAGTCTTGTGGGGG 398919 i vii --i ii i v i vi v v v C L2a_3end#LINE 435 AAACAGACAAAA--GTCCCTGCCCTCATGGAGCTTACATTCTAGTGGGGG 388 chr2ptel1M 398920 GAGACAATGTGTGTATGTAATAGCAATTATGTAGCATCTATTGTATGTCA 398969 ivvvi iv ii- -- - v iv v v C L2a_3end#LINE 387 GAGACAGACAATAAACA-AATA--AA-TAAGTAAAATATATAGTATGTCA 342 chr2ptel1M 398970 GAT 398972 C L2a_3end#LINE 341 GAT 339 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.74 CpG sites = 15, Kimura (unadjusted) = 38.74 Transitions / transversions = 1.07 (15/14) Gap_init rate = 0.06 (6 / 102), avg. gap size = 1.00 (6 / 6) 546 26.20 15.94 0.42 chr2ptel1M 398940 399146 (600854) C MIRb#SINE/MIR (11) 257 19 m_b65s601i16 2401 chr2ptel1M 398940 TAGCAATTATGTAGCATCTATTGTATGTCAGATATTCTACTATGCACTTT 398989 v v vv iii i i i i ii i v i v i C MIRb#SINE/MIR 257 TACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTT 208 chr2ptel1M 398990 GCA---GTTATCTCATTTGAATTCT-------ATCGTG------------ 399017 i ---i - i ------- i v ------------ C MIRb#SINE/MIR 207 ACATGCATTATCTCATTT-AATCCTCACAACAACCCTGCGAGGTAGGTAT 159 chr2ptel1M 399018 ----ATCTCCATTTTACAATCCAGGAAAC--AGGC--AAACAGTTTGTGT 399059 ---- i iviv -- -- i v v iv C MIRb#SINE/MIR 158 TATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGT 109 chr2ptel1M 399060 --CTTGCCCAAGATCACACA-CTAGGAAGTTTCTGAAGCTAGATTTAAAC 399106 -- i - v vv v iv vi ii C MIRb#SINE/MIR 108 AACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAAC 59 chr2ptel1M 399107 TCAGATCTTACTGACTCTAGGCCCAGTGCTCTATCCACTG 399146 i i vv i iiv v v C MIRb#SINE/MIR 58 CCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTG 19 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.66 CpG sites = 31, Kimura (unadjusted) = 32.92 Transitions / transversions = 1.35 (31/23) Gap_init rate = 0.04 (9 / 206), avg. gap size = 3.78 (34 / 9) 559 22.79 5.15 0.00 chr2ptel1M 399011 399146 (600854) C MIRc#SINE/MIR (110) 158 16 m_b65s601i17 2401 chr2ptel1M 399011 TATCGTGATCTCCATTTTACAATCCAGGAAAC--AGGC--AAACAGTTT- 399055 ii v i iviv -- -- i v v - C MIRc#SINE/MIR 158 TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTA 109 chr2ptel1M 399056 -GTGTCTTGCCCAAGATCACACA-CTAGGAAGTTTCTGAAGCTAGATTTA 399103 - v i - v vv v iv vi i ii C MIRc#SINE/MIR 108 AGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCG 59 chr2ptel1M 399104 AACTCAGATCTTACTGACTCTAGGCCCAGTGCTCTATCCACTG 399146 i i v i i i v C MIRc#SINE/MIR 58 AACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTG 16 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 26.41 CpG sites = 17, Kimura (unadjusted) = 27.53 Transitions / transversions = 1.21 (17/14) Gap_init rate = 0.04 (5 / 135), avg. gap size = 1.40 (7 / 5) 307 24.39 7.32 0.00 chr2ptel1M 400727 400808 (599192) MIR3#SINE/MIR 118 205 (3) m_b65s601i18 2402 chr2ptel1M 400727 GCCTCAAATTCCCCATCTATAAAATGAGACAATTGGACTCCATGATTT-- 400774 iv i i ivii vv i -- MIR3#SINE/MIR 118 GCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCT 167 chr2ptel1M 400775 -AGCTCCCTTCCAGGTTAAA---TCTATGCTCCTGTAA 400808 - v v ivi --- v i i i MIR3#SINE/MIR 168 AAGGTCCCTTCCAGCTCTGACATTCTATGATTCTATGA 205 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.16 CpG sites = 12, Kimura (unadjusted) = 30.16 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.04 (3 / 81), avg. gap size = 2.00 (6 / 3) 19 0.00 0.00 0.00 chr2ptel1M 400852 400872 (599128) (A)n#Simple_repeat 1 21 (0) m_b65s252i11 2403 chr2ptel1M 400852 AAAAAAAAAAAAAAAAAAAAA 400872 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAA 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 245 15.56 6.67 0.00 chr2ptel1M 400909 400953 (599047) C L2d2_3end#LINE/L2 (5) 550 503 m_b65s601i19 2404 chr2ptel1M 400909 TCAAGTCAACAAACATTTA---AGTGCCTGCTGTGTACTAGGCTCTGT 400953 i i --- i i i v v C L2d2_3end#LIN 550 TCAAATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGT 503 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 15.18 CpG sites = 5, Kimura (unadjusted) = 17.84 Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.02 (1 / 44), avg. gap size = 3.00 (3 / 1) 433 34.24 6.90 2.31 chr2ptel1M 401664 401953 (598047) C L2#LINE/L2 (938) 2144 1842 m_b65s601i20 2400 chr2ptel1M 401664 GGAGAGAGTGCTTTCACTAAATCCTAGAGGAGAA----TATCAAGAAAAA 401709 v v v vivi v v v i ---- v ii C L2#LINE/L2 2144 GGAGAGTGTGGTGTCCTGGAAGCCAAGTGAAGAAAGTGTTTCAAGAAGGA 2095 chr2ptel1M 401710 ATG-GTAATTGACAATGTTAAA-GCT-TTCAAAG---AAGTA---TGAGG 401750 iv - i ii vi i - -i v ? --- --- C L2#LINE/L2 2094 GGGAGTGATCAACTGTGTCAAATGCTGCTGANAGGTCAAGTAAGATGAGG 2045 chr2ptel1M 401751 A-TGAGGATGAATGGCCACTGAATTTAGTAATTTAAAGATTATTGGTAAT 401799 - i --- i i i i iv ii i i i i C L2#LINE/L2 2044 ACTGAGAAT---TGACCATTGGATTTAGCAACGTGGAGGTCATTGGTGAC 1998 chr2ptel1M 401800 TTTAGAGAAAGAAGTTTCAGTTGAGTAAT-GAAATTAGAGCTAGACTATG 401848 i iivi i v i v ii - ii iv i iv i ivi C L2#LINE/L2 1997 CTTGACAAGAGCAGTTTCGGTGGAGTGGTGGGGACGAAAGCCTGATTGGA 1948 chr2ptel1M 401849 GAAAGTTTCAAAGAAAGCAAG-GAAAAGGAGTTGGAGACATCAGTTATAA 401897 vii iv i i iiii - i i i v iiv i C L2#LINE/L2 1947 GTGGGTTCAAGAGAGAATGGGAGGAGAGGAATTGGAGACAGCGAGTATAG 1898 chr2ptel1M 401898 ATTGTCAGCTC--TCAAT--GTTTAACCCTAAAAAGAAGGAAAGATATTT 401943 ---- i -- i v-- vi iv ii i v i v vv C L2#LINE/L2 1897 A----CAACTCTTTCGAGGAGTTTTGCTGTAAAGGGGAGCAGAGAAATGG 1852 chr2ptel1M 401944 AACAGTATCT 401953 ii i v C L2#LINE/L2 1851 GGCGGTAGCT 1842 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 45.00 CpG sites = 66, Kimura (unadjusted) = 49.35 Transitions / transversions = 2.13 (66/31) Gap_init rate = 0.06 (18 / 289), avg. gap size = 1.50 (27 / 18) 16 13.25 0.00 0.00 chr2ptel1M 402215 402239 (597761) (T)n#Simple_repeat 1 25 (0) m_b65s252i12 2405 chr2ptel1M 402215 TTTTTTGTTTTTGTTTTTGTTTTTT 402239 v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 22 0.00 0.00 0.00 chr2ptel1M 403710 403733 (596267) (A)n#Simple_repeat 1 24 (0) m_b65s252i13 2406 chr2ptel1M 403710 AAAAAAAAAAAAAAAAAAAAAAAA 403733 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAA 24 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 16 9.71 0.00 0.00 chr2ptel1M 404814 404835 (595165) (T)n#Simple_repeat 1 22 (0) m_b65s252i14 2407 chr2ptel1M 404814 TTTTTTTTTTTTTTTTACTTTT 404835 vi (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTT 22 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 1705 28.92 2.33 2.65 chr2ptel1M 405521 406163 (593837) C L1ME5_3end#LINE/L1 (297) 644 4 m_b65s551i2 2408 chr2ptel1M 405521 TCCTGGTTCT-GCTCATTTCGCTCAGCATCA-GTTCATGTAAGTCTCGCC 405568 i v -i iv i ii - -- v vii ii C L1ME5_3end#LI 644 TTCTGTTTCTTACTTTTTTCACTCAGCACTATGTT--TTTAAGATCCATC 597 chr2ptel1M 405569 AATCCT-CTCTGTATTCGTCCTATTGGTCATTTCTTACAGAACAATAATA 405617 v vi - v i v i ivi iv iii v v vvvv i C L1ME5_3end#LI 596 CATGTTGCTATGTGTACATCTAGTCCGTTGCTTCTAACTGCTGCATAGTA 547 chr2ptel1M 405618 TTCCATAACATTCATATACCACAATTTACTCAACCATTCTCCAATTGATG 405667 i iiii v vi v ii v i v v C L1ME5_3end#LI 546 CTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCAGTGATG 497 chr2ptel1M 405668 GGCATCCATTCATT--TTCCAGCTTCTGGCCACTACAAACAGGGCTGCCA 405715 i i --vi --i i i iv i iv v C L1ME5_3end#LI 496 GACACCCA--GGTTGCCTCCAACTCCCCGCCACCACAAACAACGCTGCAA 449 chr2ptel1M 405716 CAAACATTTTGGCACATACAGGTCCCTTTC----CCTTTTTTAGTATCTC 405761 ii ii ---- i v i v---- v v v v i C L1ME5_3end#LI 448 TGAACATCCT----CGTACATGTCCCCTTATGGACCTGTGTGAGAATTTC 403 chr2ptel1M 405762 TTTGGGGTATAAGCCCAGTAGAGACACTGCTGGATCAAAGGGTATGCACA 405811 i vi v v iv i i v --- C L1ME5_3end#LI 402 TTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATGC--- 356 chr2ptel1M 405812 GTTTGATAACTT--TTTGGGCA--TAGTTCCAAATTGCTCTCCAGAATGG 405857 --- - -- ivi -- v v i C L1ME5_3end#LI 355 GT---ATA-CTTAATTTGACTAAGTACTGCCAGATTGCTCTCCAGAATGG 310 chr2ptel1M 405858 CTGGATGTATTCACAATTCCACCAACAATGTATCAGTGTCCCTGTTTTCC 405907 v ivvi ii v i i i i v v i i ? i C L1ME5_3end#LI 309 CTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATNTCCC 260 chr2ptel1M 405908 CACATCCCCTCCAACATTCTGCATTATCTTTCCCTGTCATTCTGGCCAAT 405957 i v i iv ivv ii v v i v i C L1ME5_3end#LI 259 CACATCCTCGCCAACACTTGGCATTATCCAGCTTTCTAATTTTTGCCAGT 210 chr2ptel1M 405958 CTGACAGGTATATAGTGGTATCTCAGAGTTGTCTTAATTTGCATTTCTCT 406007 i i i v i vv i C L1ME5_3end#LI 209 CTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATTTCTCT 160 chr2ptel1M 406008 GATCAATAGTGATTTGGAACACTCTTTCATATGAGTAGTAATAGTTTTAA 406057 i v i v v i iiii vv iv iivv ivii C L1ME5_3end#LI 159 GATTACTAATGAGTTTGAGCATCTCTTCATATGCTTGTTAGCCTTTCGGG 110 chr2ptel1M 406058 TTTCATCATCTGAAAATTGTCTGTTCATATCCTTTGACCATTTATCAATT 406107 v v v i v v v C L1ME5_3end#LI 109 TTTCCTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATT 60 chr2ptel1M 406108 GGAG--AATGGCTTGATTTCTTATAAATTAGAGTCAATTCTCTATATATT 406155 i --?vi v -- i vi v vivv i ii i C L1ME5_3end#LI 59 GGGGTTNCCGTCTT--TTTCTTGTTGATTTGCAGGAGTTCCTTGTATATT 12 chr2ptel1M 406156 TTGGAAAT 406163 i i v C L1ME5_3end#LI 11 CTAGATAT 4 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.73 CpG sites = 102, Kimura (unadjusted) = 37.51 Transitions / transversions = 1.29 (102/79) Gap_init rate = 0.04 (25 / 642), avg. gap size = 1.28 (32 / 25) 1799 25.43 1.09 2.39 chr2ptel1M 405612 406163 (593837) C L1ME3G_3end#LINE/L1 (376) 548 4 m_b65s551i3 2408 chr2ptel1M 405612 ATAATATTCCATAACATTCATATACCACAATTTACTCAACCATTCTCCAA 405661 i ii vv i i i i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr2ptel1M 405662 TTGATGGGCATCCA--TTCATTTTCCAGCTTCTGGCCACTACAAACAGGG 405709 i ii -- v-- ii i v i i iv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTG--TTTCCAATTTTTCGCTATTACAAACAATG 451 chr2ptel1M 405710 CTGCCACAAACATTTTGGCACATACAGGTCCCTTTCC-C-TTTTTTAGTA 405757 v ii ii v i i ?-- i v v - - v viv C L1ME3G_3end#L 450 CTGCAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTA 403 chr2ptel1M 405758 TCTCTTTGGGGTATAAGCCCAGTAGAGACACTGCTGGATCAAAGGGTATG 405807 i ? i i v v? ? v v iv i i C L1ME3G_3end#L 402 TTTCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATG 353 chr2ptel1M 405808 CACAGTTTGATAACTTTT--TGGGCATAGTTCCAAATTGCTCTCCAGAAT 405855 i v --- v -- i -- v v i i ? C L1ME3G_3end#L 352 CGCATTTT---AAATTTTAATAG--ATACTGCCAAATTGCCCTCCAAAAN 308 chr2ptel1M 405856 GGCTGGATGTATTCACAATTCCACCAACAATGTATCAGTGTCCCTGTTTT 405905 v ivv i v i i i v v v i i C L1ME3G_3end#L 307 GGCTGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTC 258 chr2ptel1M 405906 CCCACATCCCCTCCAACATTCTGCATTATCTTTCCCTGTCATTCTGGCCA 405955 i i v i ?vii vv? ii vvv i v C L1ME3G_3end#L 257 CCCACACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCA 208 chr2ptel1M 405956 ATCTGACAGGTATATAGTGGTATCTCAGAGTTGTCTTAATTTGCATTTCT 406005 ii iv v i vv i i C L1ME3G_3end#L 207 ATCTGATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCC 158 chr2ptel1M 406006 CTGATCAATAGTGATTTGGAACACTCTTTCATATGAGTAGTAATAGTTTT 406055 i v vv v i iii vv v iiivi v C L1ME3G_3end#L 157 CTGATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTG 108 chr2ptel1M 406056 AATTTCATCATCTGAAAATTGTCTGTTCATATCCTTTGACCATTTATCAA 406105 v v v vi i v v v C L1ME3G_3end#L 107 TATTTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTA 58 chr2ptel1M 406106 TTGGAGAATGGCTTGATTTCTTATAAATTAGAGTCAATTCTCTATATATT 406155 iv-- v -- vi v vivv i i C L1ME3G_3end#L 57 TTGGGT--TGTCTT--TTTCTTATTGATTTGTAGGAGTTCTTTATATATT 12 chr2ptel1M 406156 TTGGAAAT 406163 i v C L1ME3G_3end#L 11 CTGGATAT 4 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 31.13 CpG sites = 72, Kimura (unadjusted) = 31.95 Transitions / transversions = 1.11 (72/65) Gap_init rate = 0.03 (17 / 551), avg. gap size = 1.12 (19 / 17) 5601 29.39 1.99 1.91 chr2ptel1M 406017 408576 (591424) C L1M5_orf2#LINE/L1 (0) 3294 733 m_b65s551i4 2408 chr2ptel1M 406017 TGATTTGGAACACTCTTTCATATGAGTAGTAATAGTTTTAATTTCATCAT 406066 ?v v i iii i vv v iiivi v? v v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr2ptel1M 406067 CTGAAAATTGTCTGTTCATATCCTTTGACCATTTATCAATTGGA--GAAT 406114 i vi v vi i v v ?v i-- vv C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTT 3195 chr2ptel1M 406115 GGCTTGATTTCTTAT-AAATTAGAGTCAATTCTCTATATATTTTGGAAAT 406163 v -- ? -i ? iv -v i i i v i C L1M5_orf2#LIN 3194 GTCTT--TTTNTTATTGANTTGTAG-GAGTTCTTTATATATTCTGGATAC 3148 chr2ptel1M 406164 GAGTCCTTTATCAGA---ACCTTTGACTGTAAAAATGTTTTCCCAGTTTA 406210 i --- iv ? --- i v v i ? i i C L1M5_orf2#LIN 3147 GAGTCCTTTGTCAGATATATGTNT---TGCAAATATTTTCTCCCANTCTG 3101 chr2ptel1M 406211 TTGTTTCCCTTCTAAT---CTTGCCTGCATTAGTTTTGTTTGTACAAAAA 406257 v i v i v --- iv v ii i-- v?- vi i i C L1M5_orf2#LIN 3100 TGGCTTGCCTTTTCATTTTCTTAACGGTGTC--TTTTGAN-GAGCAGAAG 3054 chr2ptel1M 406258 CTTTTCAATTTGATATAATCAAAATTTTCAATTTT-------GTAGTCAG 406300 i v v i? i v v v -------i i --- C L1M5_orf2#LIN 3053 TTTTTAATTTTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGGT--- 3007 chr2ptel1M 406301 TAGTGATCTCTAGTTCTTCTTTGGTCATAAATTCCTTCCTCTTCCACAGG 406350 ? v i i ivv i v i--- v iii v v?i - C L1M5_orf2#LIN 3006 TNGTGCTTTTTGTGTCCTGTTTA---AGAAATCTTTGCCTANCCCA-AGG 2961 chr2ptel1M 406351 TCTGAGAGGTAAACTATCCTATGCT--CTTCCA--ATTTATTTATGATCT 406396 vvii i --i v i -- i -- v -- ii i C L1M5_orf2#LIN 2960 TCACGAAGATA--TTCTCCTATGTTTTCTTCTAGAAGTT--TTATAGTTT 2915 chr2ptel1M 406397 CATTCTTTATGCCTAGATC-ATGAACCCATTTTGACCTTATCTTGGTGTA 406445 i ?ii iiii i - -i i ? vi v i v C L1M5_orf2#LIN 2914 TANCTTTTACATTTAGGTCTATGA-TCCATCTNGAATTAATTTTTGTGTA 2866 chr2ptel1M 406446 TGGTGTTAAGTGTGGGTCAATGCCTAGTTTCTGCCATACTAATTTCCAAT 406495 v i iv i v?iii v i v ivi v C L1M5_orf2#LIN 2865 TGGTGTGAGGTAGGGGTCGAGNTTCATTTTTTTCCATATGGATATCCAAT 2816 chr2ptel1M 406496 TTTCCCAGCAATTTTTGTCAAATAATGCATTCTTATCCCA--AAACTGGG 406543 v i viv ii v ivvi i vi --i i -- C L1M5_orf2#LIN 2815 TGTTCCAGCACCATTTGTTGAAAAGACTATCCTTTCCCCACTGAATTG-- 2768 chr2ptel1M 406544 GTCTTTGGG---TTTGTCAAACACTAGATAATTA-AGGT-TATTGG-CTA 406587 -- ? v--- v ii i? i?ii - vi - i v - C L1M5_orf2#LIN 2767 --CNTTGGCACCTTTGTCAAAAATCAANTGNCCATATATGTGTGGGTCTA 2720 chr2ptel1M 406588 TTT-TGTCCTTTGAACCTAACCTATTCCATTGATCAACTAGTCTATTTCT 406636 - vv i ---- vi i v i v i- C L1M5_orf2#LIN 2719 TTTCTGGACTCT----CTATTCTGTTCCATTGATCTATTTGTCTATC-CT 2675 chr2ptel1M 406637 TA-GCCAATACCAGATAGTTTTAGTAACCACTGCTTTATAATATAATTTT 406685 - v iv i ii v iiiv - i i C L1M5_orf2#LIN 2674 TACGCCAATACCACACTGTCTTGATTACTGTAGCTTTATAATA-AGTCTT 2626 chr2ptel1M 406686 -AGATCTGGTACAGCTAGG----CCACCTTCATTTGATTTTTTTTCATTA 406730 - ? ? vv - i ---- v ii i-- i v-i C L1M5_orf2#LIN 2625 GANATCNGGTAGTG-TAAGTCCTCCAACTTTGTTC--TTCTTTTTCAA-G 2580 chr2ptel1M 406731 ATTCCCTTGAA-ATTCTTGACCTTTTGTTTTTCCATATGAACTTTGTTGT 406779 vii iv- ? ii i iv i i ivvi C L1M5_orf2#LIN 2579 ATTGTTTTGGCTATTCTNGGTCCTTTGCATTTCCATATAAATTTTAGAAT 2530 chr2ptel1M 406780 TATTTTTTCTAGGTCATCAAAATAGTTTTTGGGAAGTCTGATTGGTATAG 406829 i vi v v vv vv v iii viv i v i v v C L1M5_orf2#LIN 2529 CAGCTTGTCAATTTCTACAAAAAAACCTGCTGGGATTTTGATTGGGATTG 2480 chr2ptel1M 406830 CGCTAAATAAATAGATTAGTTTAGGTAGTATTGTCATCTTTATTATATTT 406879 ii i vv i i i v v v ? iv v C L1M5_orf2#LIN 2479 CATTGAATCTATAGATCAATTTGGGGAGAATTGACATCTTNACAATATTG 2430 chr2ptel1M 406880 GCTCGCCCAATCCAAGAGCATTTAATATTTTTCCAGTTAGTTAGATCAGA 406929 iv vi v i vvv i i v v i vvv C L1M5_orf2#LIN 2429 AGTCTTCCAATCCATGAACATGGTATATCTCTCCATTTATTTAGGTCTTC 2380 chr2ptel1M 406930 CTTAATTTGTGTGGAAAGTGTTTTGTAGTTTTTCTCATAAAGTTTCTG-- 406977 i v v viiv i ivvii ? v ii -- C L1M5_orf2#LIN 2379 TTTAATTTCTCTCAGCAATGTTTTGTAGTTTTCAGTGTANAGGTCTTGCA 2330 chr2ptel1M 406978 -ATTTTCCCTTGGCAGATAGATTCCTAAATATTTTATACTATCAGTAGTT 407026 - ? --- vi vv i ? ii v iv vv i C L1M5_orf2#LIN 2329 CATNTT---TTGTTAGATTTATTCCTAAGTATTTNATGTTTTTTGATGCT 2283 chr2ptel1M 407027 ACTTTAAATGGAATTTCTCTTTGTAACTCTGACTGTTGGATT--TTGTTA 407074 i v v vi i ?-- v i v i v ivi -- i C L1M5_orf2#LIN 2282 ATTGTAAATGGTATTGTTTTTN--AAATTTCATTTTCCAATTGTTTGTTG 2235 chr2ptel1M 407075 GTGATATATAAGAATGCTGATGACTTATGTGGGTTTATTTTATAACCAGC 407124 v ii ii i viv i v ivi v ii i v ? C L1M5_orf2#LIN 2234 CTAGTATATAGAAATACAATTGATTTTTGTATATTGACCTTGTATCCNGC 2185 chr2ptel1M 407125 AACTTTGCTAAAGTTGTGGATTATTTCTAATAACTTTTTAGTAGAATCTC 407174 i i v iiivv v i ii ? v v i C L1M5_orf2#LIN 2184 GACCTTGCTAAATTCACTTATTAGTTCTAGTAGTTTNTTTGTAGATTCTT 2135 chr2ptel1M 407175 TGGGGTTCTCTAAGTATACCATCATATCATCAGCAAAGAGTGATAATTTG 407224 ? i i v ? v i v i v i? i i v C L1M5_orf2#LIN 2134 TNGGATTTTCTACGTANACAATCATGTCATCTGCGAATAANGACAGTTTT 2085 chr2ptel1M 407225 GTTTCCTCATTGCCTATTCTTATTCCTTTAATATCTTTCTCAGCTCTTAT 407274 i i v v v ii v v v i vvvi C L1M5_orf2#LIN 2084 ATTTCTTCCTTTCCAATCTTTATGCCTTTTATTTCTTTTTCTTGCCTTAT 2035 chr2ptel1M 407275 TGCCATAGCTAGCATTTCTAATACAATATTAAATAGTAATGGTGATAGTG 407324 vv i v ii i i i i v i ? i C L1M5_orf2#LIN 2034 TGCACTGGCTAGGACCTCCAGTACAATGTTGAATAGAAGTGGTGANAGCG 1985 chr2ptel1M 407325 GGCAACCTTGTTTCACTCCTGATCTTATTGGGAATGGTTGCAGTTTGTCC 407374 i v i iii i vv v v? v ? v v C L1M5_orf2#LIN 1984 GACATCCTTGTCTTGTTCCCGATCTTAGGGGGAAAGCNTTCAGTNTTTCA 1935 chr2ptel1M 407375 CCATTACATATGATGCTTACTGCTGGTTTTAAATAGATGCTGCTGATTAT 407424 vi i ?i iv vvi ivi v i v C L1M5_orf2#LIN 1934 CCATTAAGTATGATGTTNGCTGTAGGTTTTTCGTAGATGCCCTTTATCAG 1885 chr2ptel1M 407425 TTTAAGGAAAAGTCCATTTATTCCTATACTCTCAAGTGTTTTTAATAGGA 407474 v i ivvi v i vvi viii v vi v C L1M5_orf2#LIN 1884 GTTGAGGAAGTTCCCTTCTATTCCTAGTTTGCTGAGAGTTTTTATCATGA 1835 chr2ptel1M 407475 ATGGATGTTGGATTTTATCAAATGCTTTTTCTGCATCTATTGAGATGATC 407524 i i i C L1M5_orf2#LIN 1834 ATGGGTGTTGAATTTTGTCAAATGCTTTTTCTGCATCTATTGAGATGATC 1785 chr2ptel1M 407525 ATATGGTTTTTGTTAGTTTGGT-TATTAATATGGCCAATTATGCTGATAG 407573 i v i-v iv - i iv iii v C L1M5_orf2#LIN 1784 ATATGATTTTTCTC-CTTTATTCTGTTAATATGGTGAATTACATTGATTG 1736 chr2ptel1M 407574 TTTTCCTAATATTGAACCAGCCCTGCATTCCTGGTATAAATCCTACTTGA 407623 v i v i i i i v i i i C L1M5_orf2#LIN 1735 ATTTTCGAATGTTAAACCAACCTTGCATTCCTGGGATAAACCCCACTTGG 1686 chr2ptel1M 407624 TCATGGTGAATTATCCTGGGGATGATTTTCTGTAGTCTTTTTGCTAATAT 407673 i v vvvv ivv v v v vv C L1M5_orf2#LIN 1685 TCATGATGTATTATCCTTTTTATATATTGCTGGATTCGATTTGCTAATAT 1636 chr2ptel1M 407674 TTTATTTAAGATTTTAGCATCAATATTCATTAGGGAGATTGGTCTATAGT 407723 i ? i v v i v v i i C L1M5_orf2#LIN 1635 TTTGTTNAGGATTTTTGCATCTATGTTCATGAGGGATATTGGTCTGTAAT 1586 chr2ptel1M 407724 TTTCTTTCTCTGT--TTTCAACCTACCTGGTTTAGGTATCAGTACCATGT 407771 iii -- v --ii ii ? v vii? i C L1M5_orf2#LIN 1585 TTTCTTTTCTTGTAATGTC--TTTGTCNGGTTTTGGTATCAGGGTNATGC 1538 chr2ptel1M 407772 CTGTGTCATAGAAGGAATTTGGTAGGACTCCTTCATTCCCTATTTTATCA 407821 iv iv i v i v v vii i v ii v vi C L1M5_orf2#LIN 1537 TGGCCTCATAAAATGAGTTGGGAAGTGTTCCCTCTTTTTCTATTTTCTGG 1488 chr2ptel1M 407822 AATAATTTATATAGCATTGGGGCCAATTGTTCTTTAAATGTTTGGTAGAA 407871 v i i i iv viii v v i C L1M5_orf2#LIN 1487 AAGAGTTTGTGTAAGATTGGTATTATTTCTTCCTTAAATGTTTGGTAGAA 1438 chr2ptel1M 407872 TTCACATGTAAATCCATCTGGTCCTGGGGATTTTTTCTTAGGGAGTTGTT 407921 vv i v v i v i iv i i v v C L1M5_orf2#LIN 1437 TTCACCAGTGAAGCCATCTGGGCCTGGAGTTTTCTTTGTGGGAAGGTTTT 1388 chr2ptel1M 407922 TAATTGCCTGTTCTATTTCTTTTTCTGAAATGGGACTATTCAAGCAATTT 407971 i vvi v vviv v i i iiivv i C L1M5_orf2#LIN 1387 TAATTACAAATTCAATTTCTTTAATAGATATAGGGCTATTCAGATTTTCT 1338 chr2ptel1M 407972 ACTTCCTCCTCTGTTAGTCTGGGAAGTCTATATTTTTGGAGGTAGTCATC 408021 i i i v? i i v v i?i i i vi v v ii C L1M5_orf2#LIN 1337 ATTTCTTCTTGNGTCAGTTTTGGTAANTTGTGTTTTTCAAGGAATTTGTC 1288 chr2ptel1M 408022 CATTTCACTTAGGTTATCAAATTTATTGGCGTAAAGTTGAGCAAAATAAC 408071 ii i ? i vv v vi C L1M5_orf2#LIN 1287 CATTTCATCTAAGTTNTCAAATTTATTGGCATAAAGTTGTTCATAATATT 1238 chr2ptel1M 408072 TCCTTATTATTTCTCTAATTTCCTCTTCATTGGTGGAAAGTTCTCCCTTT 408121 ii iii i v ivivvv iv i vi vv i C L1M5_orf2#LIN 1237 CTCTTATTATCCTTTTAATGTCTGTAGGATCTGTAGTGATGTCTCCTTTT 1188 chr2ptel1M 408122 TCATTTTTAAGACTACTAATTTCATTTTCCTCCCTCCTTTTTCTAATCAG 408171 ii i v i iv vvv i i i ii ii i C L1M5_orf2#LIN 1187 TCATTCCTGATATTGGTAATTTGTGTCTTCTCTCTTTTTTTCTTGATCAG 1138 chr2ptel1M 408172 ATTTACCAAAGGTTTATCAATTTTATTGGTTTTTTCATAAAACCAACTCT 408221 vi ?i i i i i v i i i C L1M5_orf2#LIN 1137 TCTNGCTAGAGGTTTATCAATTTTATTGATCTTTTCAAAGAACCAGCTTT 1088 chr2ptel1M 408222 TAGTTTTATTTATTAGTTCAATAGTTTTTTTAGTTTCAATATTATTAATT 408271 i i ii v vvi v v ? ? iv v v i i C L1M5_orf2#LIN 1087 TGGCTTCGTTGATTTTCTCTATTGTNTNTTTGTTTTCTATTTCATTGATT 1038 chr2ptel1M 408272 TCTCCTTTTAATTTTAGAATTTCAAGTTTAGTAATTGATTGGGGGTTTTT 408321 v i vi vv vvvii vv v ?v v --- C L1M5_orf2#LIN 1037 TCTGCTCTTATCTTTATTATTTCCTTCCTTCTACTTNCTTTGGG---TTT 991 chr2ptel1M 408322 AATTTGGTCTT---TTTCTAGCTTTTTAAGTTGCAAGCCCAATTCATTGA 408368 v --- i v v ii iv C L1M5_orf2#LIN 990 AATTTGCTCTTCTTTTTCTAGCTTCTTAAGGTGGAAGCTTAGATCATTGA 941 chr2ptel1M 408369 CCTT--CTCTTTCTCTATTTTGTTCAAATAAGCCTCTAAGGATATAAAGT 408416 ii --vi - v -i v v ? v i ? v v C L1M5_orf2#LIN 940 TTTTAAGCCTTTCT-TCTTTT-CTAATATANGCATTTAANGCTATAAATT 893 chr2ptel1M 408417 TTCCCCTTATTACCGCTTTGGCTGCATCCCACAAATTTTGGTATGATGTC 408466 i i v vi i i i v v C L1M5_orf2#LIN 892 TCCCTCTAAGCACTGCTTTAGCTGCATCCCACAAATTTTGATATGTTGTA 843 chr2ptel1M 408467 TCACCATTGTCATTATCTTGAGTGAAGTTATTAATTGTGTCTATAATTTG 408516 ivi ? vvv v iviv v vi viv?i i i v C L1M5_orf2#LIN 842 TTTTCATTNTCATTCAGTTCAAAATATTTTCTAATTTCCNTTGTGATTTC 793 chr2ptel1M 408517 CTGTTTCACCCAATCATTCTTTA-AGATGAGATTATTTAGTTTCCAATTA 408565 i v v vvvi v - ii v - i i v C L1M5_orf2#LIN 792 TTCTTTGACCCATGGGTTATTTAGAAGTGTG-TTGTTTAATTTCCAAATA 744 chr2ptel1M 408566 CTTTTTGATTT 408576 i vvv C L1M5_orf2#LIN 743 TTTGGGGATTT 733 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.41 CpG sites = 401, Kimura (unadjusted) = 39.03 Transitions / transversions = 1.19 (401/337) Gap_init rate = 0.03 (75 / 2559), avg. gap size = 1.33 (100 / 75) 5200 29.84 2.10 1.87 chr2ptel1M 406603 409266 (590734) C L1M5_orf2#LINE/L1 (587) 2707 38 m_b66s551i0 2408 chr2ptel1M 406603 CTAACCTATTCCATTGATCAACTAGTCTATTTCTTA-GCCAATACCAGAT 406651 vi i v i v i- - v i C L1M5_orf2#LIN 2707 CTATTCTGTTCCATTGATCTATTTGTCTATC-CTTACGCCAATACCACAC 2659 chr2ptel1M 406652 AGTTTTAGTAACCACTGCTTTATAATATAATTTT-AGATCTGGTACAGCT 406700 v i ii v iiiv - i i - ? ? vv - C L1M5_orf2#LIN 2658 TGTCTTGATTACTGTAGCTTTATAATA-AGTCTTGANATCNGGTAGTG-T 2611 chr2ptel1M 406701 AGG----CCACCTTCATTTGATTTTTTTTCATTAATTCCCTTGAA-ATTC 406745 i ---- v ii i-- i v-i vii iv- C L1M5_orf2#LIN 2610 AAGTCCTCCAACTTTGTTC--TTCTTTTTCAA-GATTGTTTTGGCTATTC 2564 chr2ptel1M 406746 TTGACCTTTTGTTTTTCCATATGAACTTTGTTGTTATTTTTTCTAGGTCA 406795 ? ii i iv i i ivvi i vi v v vv v C L1M5_orf2#LIN 2563 TNGGTCCTTTGCATTTCCATATAAATTTTAGAATCAGCTTGTCAATTTCT 2514 chr2ptel1M 406796 TCAAAATAGTTTTTGGGAAGTCTGATTGGTATAGCGCTAAATAAATAGAT 406845 v v iii viv i v i v v ii i vv C L1M5_orf2#LIN 2513 ACAAAAAAACCTGCTGGGATTTTGATTGGGATTGCATTGAATCTATAGAT 2464 chr2ptel1M 406846 TAGTTTAGGTAGTATTGTCATCTTTATTATATTTGCTCGCCCAATCCAAG 406895 i i i v v v ? iv viv vi v C L1M5_orf2#LIN 2463 CAATTTGGGGAGAATTGACATCTTNACAATATTGAGTCTTCCAATCCATG 2414 chr2ptel1M 406896 AGCATTTAATATTTTTCCAGTTAGTTAGATCAGACTTAATTTGTGTGGAA 406945 i vvv i i v v i vvvi v v viiv C L1M5_orf2#LIN 2413 AACATGGTATATCTCTCCATTTATTTAGGTCTTCTTTAATTTCTCTCAGC 2364 chr2ptel1M 406946 AGTGTTTTGTAGTTTTTCTCATAAAGTTTCTG---ATTTTCCCTTGGCAG 406992 i ivvii ? v ii --- ? --- vi C L1M5_orf2#LIN 2363 AATGTTTTGTAGTTTTCAGTGTANAGGTCTTGCACATNTT---TTGTTAG 2317 chr2ptel1M 406993 ATAGATTCCTAAATATTTTATACTATCAGTAGTTACTTTAAATGGAATTT 407042 vv i ? ii v iv vv i i v v v C L1M5_orf2#LIN 2316 ATTTATTCCTAAGTATTTNATGTTTTTTGATGCTATTGTAAATGGTATTG 2267 chr2ptel1M 407043 CTCTTTGTAACTCTGACTGTTGGATT--TTGTTAGTGATATATAAGAATG 407090 i i ?-- v i v i v ivi -- iv ii ii i C L1M5_orf2#LIN 2266 TTTTTN--AAATTTCATTTTCCAATTGTTTGTTGCTAGTATATAGAAATA 2219 chr2ptel1M 407091 CTGATGACTTATGTGGGTTTATTTTATAACCAGCAACTTTGCTAAAGTTG 407140 viv i v ivi v ii i v ? i i v ii C L1M5_orf2#LIN 2218 CAATTGATTTTTGTATATTGACCTTGTATCCNGCGACCTTGCTAAATTCA 2169 chr2ptel1M 407141 TGGATTATTTCTAATAACTTTTTAGTAGAATCTCTGGGGTTCTCTAAGTA 407190 ivv v i ii ? v v i ? i i v C L1M5_orf2#LIN 2168 CTTATTAGTTCTAGTAGTTTNTTTGTAGATTCTTTNGGATTTTCTACGTA 2119 chr2ptel1M 407191 TACCATCATATCATCAGCAAAGAGTGATAATTTGGTTTCCTCATTGCCTA 407240 ? v i v i v i? i i vi i v v v C L1M5_orf2#LIN 2118 NACAATCATGTCATCTGCGAATAANGACAGTTTTATTTCTTCCTTTCCAA 2069 chr2ptel1M 407241 TTCTTATTCCTTTAATATCTTTCTCAGCTCTTATTGCCATAGCTAGCATT 407290 ii v v v i vvvi vv i v ii C L1M5_orf2#LIN 2068 TCTTTATGCCTTTTATTTCTTTTTCTTGCCTTATTGCACTGGCTAGGACC 2019 chr2ptel1M 407291 TCTAATACAATATTAAATAGTAATGGTGATAGTGGGCAACCTTGTTTCAC 407340 i i i i v i ? i i v i iii C L1M5_orf2#LIN 2018 TCCAGTACAATGTTGAATAGAAGTGGTGANAGCGGACATCCTTGTCTTGT 1969 chr2ptel1M 407341 TCCTGATCTTATTGGGAATGGTTGCAGTTTGTCCCCATTACATATGATGC 407390 i vv v v? v ? v v vi i C L1M5_orf2#LIN 1968 TCCCGATCTTAGGGGGAAAGCNTTCAGTNTTTCACCATTAAGTATGATGT 1919 chr2ptel1M 407391 TTACTGCTGGTTTTAAATAGATGCTGCTGATTATTTTAAGGAAAAGTCCA 407440 ?i iv vvi ivi v i vv i ivvi v C L1M5_orf2#LIN 1918 TNGCTGTAGGTTTTTCGTAGATGCCCTTTATCAGGTTGAGGAAGTTCCCT 1869 chr2ptel1M 407441 TTTATTCCTATACTCTCAAGTGTTTTTAATAGGAATGGATGTTGGATTTT 407490 i vvi viii v vi v i i C L1M5_orf2#LIN 1868 TCTATTCCTAGTTTGCTGAGAGTTTTTATCATGAATGGGTGTTGAATTTT 1819 chr2ptel1M 407491 ATCAAATGCTTTTTCTGCATCTATTGAGATGATCATATGGTTTTTGTTAG 407540 i i v ivv C L1M5_orf2#LIN 1818 GTCAAATGCTTTTTCTGCATCTATTGAGATGATCATATGATTTTTCTCCT 1769 chr2ptel1M 407541 TTTGGTTATTAATATGGCCAATTATGCTGATAGTTTTCCTAATATTGAAC 407590 vvvi i iv iii v v i v i i C L1M5_orf2#LIN 1768 TTATTCTGTTAATATGGTGAATTACATTGATTGATTTTCGAATGTTAAAC 1719 chr2ptel1M 407591 CAGCCCTGCATTCCTGGTATAAATCCTACTTGATCATGGTGAATTATCCT 407640 i i v i i i i v C L1M5_orf2#LIN 1718 CAACCTTGCATTCCTGGGATAAACCCCACTTGGTCATGATGTATTATCCT 1669 chr2ptel1M 407641 GGGGATGATTTTCTGTAGTCTTTTTGCTAATATTTTATTTAAGATTTTAG 407690 vvvv ivv v v v vv i ? i v C L1M5_orf2#LIN 1668 TTTTATATATTGCTGGATTCGATTTGCTAATATTTTGTTNAGGATTTTTG 1619 chr2ptel1M 407691 CATCAATATTCATTAGGGAGATTGGTCTATAGTTTTCTTTCTCTGT--TT 407738 v i v v i i iii -- v C L1M5_orf2#LIN 1618 CATCTATGTTCATGAGGGATATTGGTCTGTAATTTTCTTTTCTTGTAATG 1569 chr2ptel1M 407739 TCAACCTACCTGGTTTAGGTATCAGTACCATGTCTGTGTCATAGAAGGAA 407788 --ii ii ? v vii? iiv iv i v i C L1M5_orf2#LIN 1568 TC--TTTGTCNGGTTTTGGTATCAGGGTNATGCTGGCCTCATAAAATGAG 1521 chr2ptel1M 407789 TTTGGTAGGACTCCTTCATTCCCTATTTTATCAAATAATTTATATAGCAT 407838 v v vii i v ii v vi v i i i iv C L1M5_orf2#LIN 1520 TTGGGAAGTGTTCCCTCTTTTTCTATTTTCTGGAAGAGTTTGTGTAAGAT 1471 chr2ptel1M 407839 TGGGGCCAATTGTTCTTTAAATGTTTGGTAGAATTCACATGTAAATCCAT 407888 viii v v i vv i v C L1M5_orf2#LIN 1470 TGGTATTATTTCTTCCTTAAATGTTTGGTAGAATTCACCAGTGAAGCCAT 1421 chr2ptel1M 407889 CTGGTCCTGGGGATTTTTTCTTAGGGAGTTGTTTAATTGCCTGTTCTATT 407938 v i v i iv i i v v i vvi v C L1M5_orf2#LIN 1420 CTGGGCCTGGAGTTTTCTTTGTGGGAAGGTTTTTAATTACAAATTCAATT 1371 chr2ptel1M 407939 TCTTTTTCTGAAATGGGACTATTCAAGCAATTTACTTCCTCCTCTGTTAG 407988 vviv v i i iiivv i i i i v? i C L1M5_orf2#LIN 1370 TCTTTAATAGATATAGGGCTATTCAGATTTTCTATTTCTTCTTGNGTCAG 1321 chr2ptel1M 407989 TCTGGGAAGTCTATATTTTTGGAGGTAGTCATCCATTTCACTTAGGTTAT 408038 i v v i?i i i vi v v ii ii i ? C L1M5_orf2#LIN 1320 TTTTGGTAANTTGTGTTTTTCAAGGAATTTGTCCATTTCATCTAAGTTNT 1271 chr2ptel1M 408039 CAAATTTATTGGCGTAAAGTTGAGCAAAATAACTCCTTATTATTTCTCTA 408088 i vv v viii iii i C L1M5_orf2#LIN 1270 CAAATTTATTGGCATAAAGTTGTTCATAATATTCTCTTATTATCCTTTTA 1221 chr2ptel1M 408089 ATTTCCTCTTCATTGGTGGAAAGTTCTCCCTTTTCATTTTTAAGACTACT 408138 v ivivvv iv i vi vv i ii i v i iv C L1M5_orf2#LIN 1220 ATGTCTGTAGGATCTGTAGTGATGTCTCCTTTTTCATTCCTGATATTGGT 1171 chr2ptel1M 408139 AATTTCATTTTCCTCCCTCCTTTTTCTAATCAGATTTACCAAAGGTTTAT 408188 vvv i i i ii ii i vi ?i i i C L1M5_orf2#LIN 1170 AATTTGTGTCTTCTCTCTTTTTTTCTTGATCAGTCTNGCTAGAGGTTTAT 1121 chr2ptel1M 408189 CAATTTTATTGGTTTTTTCATAAAACCAACTCTTAGTTTTATTTATTAGT 408238 i i v i i i i i ii v vvi C L1M5_orf2#LIN 1120 CAATTTTATTGATCTTTTCAAAGAACCAGCTTTTGGCTTCGTTGATTTTC 1071 chr2ptel1M 408239 TCAATAGTTTTTTTAGTTTCAATATTATTAATTTCTCCTTTTAATTTTAG 408288 v v ? ? iv v v i i v i vi v C L1M5_orf2#LIN 1070 TCTATTGTNTNTTTGTTTTCTATTTCATTGATTTCTGCTCTTATCTTTAT 1021 chr2ptel1M 408289 AATTTCAAGTTTAGTAATTGATTGGGGGTTTTTAATTTGGTCTT---TTT 408335 v vvvii vv v ?v v --- v --- C L1M5_orf2#LIN 1020 TATTTCCTTCCTTCTACTTNCTTTGGG---TTTAATTTGCTCTTCTTTTT 974 chr2ptel1M 408336 CTAGCTTTTTAAGTTGCAAGCCCAATTCATTGACCTT--CTCTTTCTCTA 408383 i v v ii iv ii --vi - v C L1M5_orf2#LIN 973 CTAGCTTCTTAAGGTGGAAGCTTAGATCATTGATTTTAAGCCTTTCT-TC 925 chr2ptel1M 408384 TTTTGTTCAAATAAGCCTCTAAGGATATAAAGTTTCCCCTTATTACCGCT 408433 -i v v ? v i ? v v i i v vi i C L1M5_orf2#LIN 924 TTTT-CTAATATANGCATTTAANGCTATAAATTTCCCTCTAAGCACTGCT 876 chr2ptel1M 408434 TTGGCTGCATCCCACAAATTTTGGTATGATGTCTCACCATTGTCATTATC 408483 i i v v ivi ? vvv C L1M5_orf2#LIN 875 TTAGCTGCATCCCACAAATTTTGATATGTTGTATTTTCATTNTCATTCAG 826 chr2ptel1M 408484 TTGAGTGAAGTTATTAATTGTGTCTATAATTTGCTGTTTCACCCAATCAT 408533 v iviv v vi viv?i i i vi v v vvvi C L1M5_orf2#LIN 825 TTCAAAATATTTTCTAATTTCCNTTGTGATTTCTTCTTTGACCCATGGGT 776 chr2ptel1M 408534 TCTTTA-AGATGAGATTATTTAGTTTCCAATTACTTTTTGATTTATTTAC 408582 v - ii v - i i v i vvv - i -- C L1M5_orf2#LIN 775 TATTTAGAAGTGTG-TTGTTTAATTTCCAAATATTTGGGGATTT-TCT-- 730 chr2ptel1M 408583 ACCTAACTTTT--TTGTTGAATGTAGTTTTTATTGCATTGTGATCTGAAA 408630 v? v -- i v viviv v v i v i C L1M5_orf2#LIN 729 AGNTATCTTTTTGTTATTGATTTCTAATTTAATTCCATTGTGGTCAGAGA 680 chr2ptel1M 408631 AGAAAGCATTTACTATTTCTGCCTTCCTGCATTTAATTTTGAG----GTC 408676 v v viv v iv vii i ii?iv --- ---- - C L1M5_orf2#LIN 679 ACATACTCTGTATGATTTCAATCCTTTNAAATTTA---TTGAGACTTGT- 634 chr2ptel1M 408677 TTTATGTCCTAATATATGGTCAATTTTTGTGTAGGTTCCATGAGCTGCTG 408726 v i i? v i v iv v v vvi C L1M5_orf2#LIN 633 TTTATGGCCCAGNATATGGTCTATCTTGGTAAATGTTCCATGTGCACTTG 584 chr2ptel1M 408727 AGAAGAAAGTATACTCCTTTCTATCACCATT-----CAGTTTTCTCCAGA 408771 i v i ----- ii?iiii -----? v vi i C L1M5_orf2#LIN 583 AAAAGAATGTGTA-----TTCTGCNGTTGTTGGGTGNAGTGTTCTATAAA 539 chr2ptel1M 408772 GATCTATCATACCTAGTC--TTTCTAATATTCTATTTACTTCTTTAAT-T 408818 vi v i vii v i-- vv i i -- i i vv iv - C L1M5_orf2#LIN 538 TGTCAATTAGGTCAAGTTGGTTGATAGTGT--TGTTCAAATCTTCTATAT 491 chr2ptel1M 408819 TCTTTCTTATTTGTTTTGTG-ATTTGATTTATCTAAAT--CTGAGAGTGC 408865 i v v -- v- i v i -- -- v v C L1M5_orf2#LIN 490 CCTTACTGATT--TTTTGTCTACTTGTTCTATC--AATTACTGAGAGAGG 445 chr2ptel1M 408866 AAGATTGAGGTCTCCCACT---ATTATAGTTTTGCTGTCTATTTCTTCTT 408912 ?ivi i ii ? --- i i v --- i C L1M5_orf2#LIN 444 NGTGTTAAAATCTCCNACTATAATTGTGGATT---TGTCTATTTCTCCTT 398 chr2ptel1M 408913 GCAACTCTCTTAACTTCTCCTTTAGGAAGTTAGATGCTATACCACTTGGT 408962 vi ii v i ii i v i v v v v v v iii i v C L1M5_orf2#LIN 397 TTAGTTCTGTCAGTTTTTGCTTCATGTATTTTGAAGCTCTGTTATTAGGT 348 chr2ptel1M 408963 GCATATATGTTTAATACTGATATTGCTTCATTGTCTATAGTACCTTTTAG 409012 i ii iv i v vv v vi vv v vv v C L1M5_orf2#LIN 347 GCATACACATTTAGGATTGTTATGTCTTCTTGATGAATTGACCCTTTTAT 298 chr2ptel1M 409013 CAAGATATAGTTTCCTTCCTTATCTCTTTTTAATTAGATCAATTTTTGCT 409062 vv iv i v i i - vv --- --- i i C L1M5_orf2#LIN 297 CATTATGAAATGTCCCTCTTTATCTC-TGGTAAT---AT---TTCTTGCC 255 chr2ptel1M 409063 TT------TACTTGATCTGGAGATAAGGATGGCTACTCT--TTTTGACTT 409104 ------ vi - v v iv i i ? i--i -- C L1M5_orf2#LIN 254 TTGAAGTCTACTTTGTCT-GATATTAATATAGCCACNCCAGCTTT--CTT 208 chr2ptel1M 409105 CACCTGAA-----GCATAATAGAT-TCTGCTCAGCCTTTTACCTTTACTC 409148 ivv? v i----- ii v - i vii v i i vi C L1M5_orf2#LIN 207 TTGNTTAGTGTTTGCATGGTATATCTTTTTCCATCCTTTTACTTTCAACC 158 chr2ptel1M 409149 TGTATGTATCTCCCTGTTTTAAATGTGTTTCTTGTAAACAACATATTGTA 409198 ? v i iiv i v i i i i i v v C L1M5_orf2#LIN 157 TNTCTGTGTCTTTATATTTAAAGTGCGTCTCTTGTAGACAGCATATAGTT 108 chr2ptel1M 409199 GGGTTCTGACTTTTGATCCAGTCTGCTATCCGCCTCCTCTTTA-TGGGGA 409247 ii vi v vi vi v iv i v - i v C L1M5_orf2#LIN 107 GGGTCTTGTTTTTTTATCCAGTCTGACAATCTCTGCCTTTTAATTGGAGT 58 chr2ptel1M 409248 GGTCATCCCATTC-CATTTA 409266 v i v? i- C L1M5_orf2#LIN 57 GTTTAGNCCATTTACATTTA 38 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.10 CpG sites = 412, Kimura (unadjusted) = 39.56 Transitions / transversions = 1.12 (412/368) Gap_init rate = 0.03 (74 / 2663), avg. gap size = 1.43 (106 / 74) 354 28.48 1.30 1.96 chr2ptel1M 409130 409283 (590717) C L1MEc_5end#LINE/L1 (67) 2460 2308 m_b66s551i1 2408 chr2ptel1M 409130 CAGCCTTTTACCTTTACTCTGTATGTATCTCCCTGTTTTAAATGTGTTTC 409179 v i vi i v i iiv i v i ? C L1MEc_5end#LI 2460 CATCCTTTTACTTTTAACCTATTTGTGTCTTTATATTTAAAGTGNGTTTC 2411 chr2ptel1M 409180 TTGTAAACAACATATTGTAGGGTTCTGACTTTTGATCCAGTCTGCTATCC 409229 ii i v v ii vi v i vi vi C L1MEc_5end#LI 2410 TTGTAGGCAGCATATAGTTGGGTCTTGCTTTTTTATCCAATCTGACAATC 2361 chr2ptel1M 409230 GCCTCCTCTTTA-TGGGGAGGTCATCCCATTC-CATTTACGGTTAAGATT 409277 v iv i v - v v i vv i- vv --- C L1MEc_5end#LI 2360 TCTGCCTTTTAATTGGGGTGTTTAGACCATTTACATTTAATGT---GATT 2314 chr2ptel1M 409278 ACTAAT 409283 i i C L1MEc_5end#LI 2313 ATTGAT 2308 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.74 CpG sites = 23, Kimura (unadjusted) = 36.74 Transitions / transversions = 1.15 (23/20) Gap_init rate = 0.03 (5 / 153), avg. gap size = 1.00 (5 / 5) 286 28.24 8.91 1.85 chr2ptel1M 409153 409354 (590646) C L1MEi_5end#LINE/L1 (5) 2207 1992 m_b66s551i2 2408 chr2ptel1M 409153 TGTATCTCCCTGTTTTAAATGTGTTTCTTGTAAACAACATATTGTAGGGT 409202 i viii ii i i v iv i C L1MEi_5end#LI 2207 TGTGTCGTTTTGTTTTAGGTGTGTCTCTTGTAAACAGCATATAGCTGGAT 2158 chr2ptel1M 409203 TCTGACTTTTGATCCAGTCTGCTATCCGCCTCCTCTTTATGGG-GAGGTC 409251 i vvi i i v vi v ivi i v i - v i C L1MEi_5end#LI 2157 TTTTTTTTTTAATCCAATCTGATAATCTCTGTCTTTTAATAGGTGAGTTT 2108 chr2ptel1M 409252 ATCCCATTC-CATTTACGGTTAAGATTACTAAT---TCTG----TATTTC 409293 vi i- iv --- i --- i ---- - C L1MEi_5end#LI 2107 AATCCATTTACATTTATTGT---GATTACTGATATATTTGGACTTATTT- 2062 chr2ptel1M 409294 CTGCCATCCTA----ATATCCCCAG---ATTATGCTTTTCTTTTTC--TT 409334 i i ----i i iii v --- i ? ii ? -- C L1MEi_5end#LI 2061 CTACCATCTTATTTTGTGTTTTCTGTTTATCATNCTTTTTCTTTNCTTTT 2012 chr2ptel1M 409335 GCCCTCCTTCCCCACTTCCT 409354 v i i ii i i C L1MEi_5end#LI 2011 TCTCTCCTTTCCTGCCTTCT 1992 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.30 CpG sites = 41, Kimura (unadjusted) = 38.30 Transitions / transversions = 2.73 (41/15) Gap_init rate = 0.05 (11 / 201), avg. gap size = 2.00 (22 / 11) 367 24.13 4.11 0.66 chr2ptel1M 409163 409308 (590692) C L1MEh_5end#LINE/L1 (7) 2228 2078 m_b66s551i3 2408 chr2ptel1M 409163 TGTTTTAAATGTGTTTCTTGTAAACAACATATTGTAGGGTTCTGACTTTT 409212 i i i i v i i vi ? C L1MEh_5end#LI 2228 TGTTTTAAGTGTGTCTCTTGTAGACAGCATATTGTTGGATTTTGTTTTTN 2179 chr2ptel1M 409213 GATCCAGTCTGCTATCCGCCTCCTCTTTA-TGGGGAGGTCATCCCATTC- 409260 i i v? vi v ivi i v - v v i v i- C L1MEh_5end#LI 2178 AATCCAATCTGANAATCTCTGTCTTTTAATTGGTGAGTTTAACCCATTTA 2129 chr2ptel1M 409261 CATTTACGGTTAAGATTACTA-ATTCTG---TATTTCCTGCCATCCTAAT 409306 iv v vv i i? - ?v --- - i v C L1MEh_5end#LI 2128 CATTTATTGTAATTACTGNTATATTNGGACTTATTT-CTGCCATCTTATT 2080 chr2ptel1M 409307 AT 409308 C L1MEh_5end#LI 2079 AT 2078 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 30.58 CpG sites = 19, Kimura (unadjusted) = 30.58 Transitions / transversions = 1.19 (19/16) Gap_init rate = 0.03 (5 / 145), avg. gap size = 1.40 (7 / 5) 20 23.75 0.00 3.45 chr2ptel1M 409429 409488 (590512) (TCCCTT)n#Simple_repeat 1 58 (0) m_b66s252i0 2409 chr2ptel1M 409429 TCCCTTTCCCTTTCTTGTACCCTTCCCTTATTACTCTTTTCCTTTTCCTT 409478 iiv v i i - - i i i (TCCCTT)n#Sim 1 TCCCTTTCCCTTTCCCTTTCCCTTTCCCT-TT-CCCTTTCCCTTTCCCTT 48 chr2ptel1M 409479 TTCCTCTCCC 409488 i i (TCCCTT)n#Sim 49 TCCCTTTCCC 58 Matrix = Unknown Transitions / transversions = 4.50 (9/2) Gap_init rate = 0.03 (2 / 59), avg. gap size = 1.00 (2 / 2) 33 0.00 0.00 0.00 chr2ptel1M 410032 410062 (589938) (CATA)n#Simple_repeat 1 31 (0) c_b66s251i0 2410 chr2ptel1M 410032 CATACATACATACATACATACATACATACAT 410062 (CATA)n#Simpl 1 CATACATACATACATACATACATACATACAT 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 235 30.78 4.02 10.37 chr2ptel1M 412391 412564 (587436) LTR10A#LTR/ERV1 335 498 (111) m_b66s502i0 2411 chr2ptel1M 412391 AGTTTAGAATGTAAGATCC----TCAGCCAATAAGGAAGAGGGTCAGTGG 412436 i v iv i ----ii i i iv ivv ii LTR10A#LTR/ER 335 AGCTTAGACTGTGCGGTCCAACCCTAGCCAATAGGGGAACGACACAGCAG 384 chr2ptel1M 412437 TGGGAGGGGGTATTTGCGTTAGGGATAAAAAGTGTTGACCCTGCCCCCTA 412486 --- v ii i i i vivi vv -- i i LTR10A#LTR/ER 385 T---AGGGGCTACCTGCGTCAGGAATAAGAACCCCTTCCCCT--CCCTTG 429 chr2ptel1M 412487 T---GGTGCTTCCTCCCTTTGATTGTCTGCTCCATGGGTGGGACACCCGA 412533 --- ivii v i--- ---- vv i i ? i v vv LTR10A#LTR/ER 430 TCCAGGTGTGCTCTCGCC---AT----TGCTCCATCCGCGAGNCGCACCC 472 chr2ptel1M 412534 TTCTCCAGAAAGTATAATAAACTGCTTTGCT 412564 vi - ---- i i LTR10A#LTR/ER 473 TTCTATAG-AAGTA----AAATTGCCTTGCT 498 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.96 CpG sites = 30, Kimura (unadjusted) = 41.22 Transitions / transversions = 1.67 (30/18) Gap_init rate = 0.11 (19 / 173), avg. gap size = 1.26 (24 / 19) 12 15.30 3.45 0.00 chr2ptel1M 413299 413327 (586673) (AGAGG)n#Simple_repeat 1 30 (0) m_b66s252i1 2412 chr2ptel1M 413299 AGAGGAGAGGAGACTA-AGGAGAGAGGAGG 413327 vv - ii (AGAGG)n#Simp 1 AGAGGAGAGGAGAGGAGAGGAGAGGAGAGG 30 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1) 1160 33.66 2.34 2.06 chr2ptel1M 415603 416327 (583673) HERVIP10B3#LTR/ERV1 4568 5294 (2309) m_b66s701i0 2413 chr2ptel1M 415603 TAGGAGC--AGTTGGGAACTCGGAAAGACGATGGCTCTTACCTGATGGCA 415650 -- -- ii i i ii vii v v v iv v HERVIP10B3#LT 4568 TAGGAGCTAAG--GAAAACCCAGAGGGAAAGTGGGTATTACCAGACCGAA 4615 chr2ptel1M 415651 GAGAGGTACTGACCAAAGCAAGTATGAGGCAGGTCCTTCAGCATTTGCAC 415700 i ii ii v v vvvi v ii v viv? vi ? i HERVIP10B3#LT 4616 GGGAAATGTTGTCCAAACCCCTCATGAGGGAAATACTGTCNCAGCTNCAT 4665 chr2ptel1M 415701 CAGGGCAGTCACTGGGATGTCCAAAACCTGTGTGATGCTGTGCTGACAAA 415750 i v v i?vii iviv v v -- i HERVIP10B3#LT 4666 CAAGGAACTCACTGGGGNCCTCAAGCTATGTGTGATGCAGTCCT--CAGA 4713 chr2ptel1M 415751 G--TATGTTTCCCCTGGCCTATATACTATGCCCTGACAACTGGTGGACGA 415798 -- vv viviv vv ? iv ?v ?v i v v i iii HERVIP10B3#LT 4714 GTCTATGGGTGTATAGGAATNTATACCCTNGCNAGGCAAGTTGCGGATAG 4763 chr2ptel1M 415799 CTGTCTCATTTGTTGAAGGACTAACAAG---GCTGCTCAACA--CCAGAT 415843 i i? vi v iv ii i ---i i- v v -- ? vv HERVIP10B3#LT 4764 TTGCNTAGTGTGCAGAAAAACTAATAAGCAAACC-CTAAAGAAGCNACCT 4812 chr2ptel1M 415844 CCCAAAAGAGGAACGAGCTCTGGGAATCAGACCATTCTAAAGCATCCAGG 415893 ---i i vi i i v -v v i i i ii i- HERVIP10B3#LT 4813 CCC---GGGGGAAGAAACCCAGGG-TTAAGGCCGTTCCAAAGTGTCCAA- 4857 chr2ptel1M 415894 TGTGGGCTTCACTGAGCTGCCACCAGTGGGTCGCCTCAAATACTTGCTGG 415943 - v i v i iv v i i i ? i i i i HERVIP10B3#LT 4858 -GTTGACTACACCGAAATGCCCCCAATAGGCCGCCTNAAGTATTTACTAG 4906 chr2ptel1M 415944 TCATAGTGGACCATCTGACATCA-TGGGTGGAGGCATTCCTCTCAGCCCG 415992 v i i v -i - i i vv i i-- i HERVIP10B3#LT 4907 TAATAGTAGACCACCTCAC-CCACTGGGTAGAAGCCATCCCCTT--CCCA 4953 chr2ptel1M 415993 A--GCAACTGCCTCTA---CAGT-AAAGTCTTATTAGAACAAATTATTCC 416036 -- ? vv ---i - ivi i i ? v i v HERVIP10B3#LT 4954 AGCGCAACNGCCAGTAATGTAGTCAAAGCACTGTTGGAANATATCATACC 5003 chr2ptel1M 416037 TAGATATGGAATAGTGGAGAGGATACACTCGGATCAGGGAACACATTTTT 416086 i i v v i i i iv vv i i iv v i v i iv HERVIP10B3#LT 5004 CAGGTTTGGACTAATAGAAAACATTGATTCAGACAATGGGACCCACTTCA 5053 chr2ptel1M 416087 CTGCCCAAGT-ATTGCAGAATCTGATTGGGGCCTTAGAAATCACTTGGGA 416135 v v - i- iiv iiiivii vi ? v vv HERVIP10B3#LT 5054 CTGCACACGTCATTA-AGGGGCTAGCCCAAGCACTAGANATAAAATGGGA 5102 chr2ptel1M 416136 TCTCCACACCCCTTGGCATCCTCCCTCTTCTGGGAAAGTAGAAAGGATGA 416185 viv i i i v v v i i HERVIP10B3#LT 5103 ATACCATACCCCCTGGCACCCACCCTCATCAGGGAGAGTAGAAAGAATGA 5152 chr2ptel1M 416186 ATCAAGAAATAAAACGGCAACTGACTAAATTGTCTTTCGAGACCCAACTA 416235 iivvv viv v i i ivii v i iii HERVIP10B3#LT 5153 ATCAGACTCTAAAAAACCACCTAACCAAATTAATCTTAGAAACCCGGTTA 5202 chr2ptel1M 416236 TCTAAGACTAAATATCTTCCTCTTGCTGTAGTTAGAATCAGAACCAAGCC 416285 i vvi ? ii iv iv iv v v iivv HERVIP10B3#LT 5203 CCATGGACNAAATGCCTTCCCATTGCCTTGCTAAGAATCCGAACTGCCCC 5252 chr2ptel1M 416286 ACATAGAGATGGAGGGCTTTCACCTTATGAATTATTGTACGG 416327 v iv i vv v v v v ii ? i HERVIP10B3#LT 5253 TCGGAAAGATGTCGGCCTATCCCCTTATGAAATGCTNTATGG 5294 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 45.67 CpG sites = 133, Kimura (unadjusted) = 47.31 Transitions / transversions = 1.25 (133/106) Gap_init rate = 0.03 (24 / 724), avg. gap size = 1.33 (32 / 24) 781 29.18 4.89 0.55 chr2ptel1M 417307 417654 (582346) HERV1_I#LTR/ERV1 8133 8495 (306) m_b66s701i1 2414 chr2ptel1M 417307 TGGCCTCCAGAGAGAATAGTTAGA--GTATGGGCCAGTCACTTGGGCTCA 417354 v i vi i i --v ii ? ? HERV1_I#LTR/E 8133 TGGCCTCCTGAAAGAATTATCAAATACTATGGGCCAGCTACNTGGGCNCA 8182 chr2ptel1M 417355 AGATGGAAGTTGGGGATATAGAACCCCAATATATATGTTGAACAGAATTA 417404 ivvv ? iv v i v v i i v i HERV1_I#LTR/E 8183 AGATGGGTCATGGGGNTACCGTACTCCTATTTACATGTTAAACCGAATCA 8232 chr2ptel1M 417405 TTAAGCTT-CAAGCAGTTGTAGAGATTATGGC---TGAGGCA-CTAGATC 417449 - v - vv i i i i--- ii - iv v HERV1_I#LTR/E 8233 -TAAGATTGCAAGCAGTACTAGAAATCATAGTCAATGAAACAGCCCGAGC 8281 chr2ptel1M 417450 TTTTG----GCTGAC----CAAGCTAATCAAATCAGAGAGGCTGTTTA-C 417490 i v ---- ii ---- i ? vi i v v ii v - HERV1_I#LTR/E 8282 CTTGGATTTGCTAGCCATACAGGCNACCCAGATGAGAGATGCCATATATC 8331 chr2ptel1M 417491 AACATAGACTTGTGCTGGATTATTTGTTGGTCGAGTAAGGGGGAGTTTGT 417540 v i v iii i i i vi i i vviv i HERV1_I#LTR/E 8332 AAAATAGGCTAGCATTAGACTATCTCCTAGCCTCAGAAGGAGGAGTTTGT 8381 chr2ptel1M 417541 GCAAAACTAAATGTGTATATTTGTTGTATAAAGATTGATGACAATGGAA- 417589 v? v v vv? vi i iv v i i - HERV1_I#LTR/E 8382 GGNAAACTTAATTTGACNAACTGCTGCTTACAAATCGATGACAATGGAAG 8431 chr2ptel1M 417590 ATCTAGTAAAAGAAATCATTAAGAACATTAGGAAACTTGCTCATCTTCCT 417639 v - v vi i ivv iv vv ii v i v i v HERV1_I#LTR/E 8432 AGCT-GTCATGGAAATCACTGCCAGGATGCGGAAGTTAGCCCATGTCCCG 8480 chr2ptel1M 417640 GTACAGAACTGGACC 417654 v v v HERV1_I#LTR/E 8481 GTCCAGACCTGGTCC 8495 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.91 CpG sites = 52, Kimura (unadjusted) = 38.39 Transitions / transversions = 1.06 (52/49) Gap_init rate = 0.03 (10 / 347), avg. gap size = 1.90 (19 / 10) 21 20.20 6.33 3.70 chr2ptel1M 418047 418125 (581875) (AT)n#Simple_repeat 1 81 (0) m_b66s252i2 2415 chr2ptel1M 418047 ATATATATAGATATATTTATA-ACATGTATATAT-TTTATTGCTAT-TAT 418093 v v - i i - v vvv - (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr2ptel1M 418094 ATCTCTACTAGTTTA-ACATA-ATATACTAAATA 418125 v v - - v - i - - v (AT)n#Simple_ 51 ATATATA-TA-TATATATATATATATA-TATATA 81 Matrix = Unknown Transitions / transversions = 0.30 (3/10) Gap_init rate = 0.10 (8 / 78), avg. gap size = 1.00 (8 / 8) 462 29.26 8.29 3.63 chr2ptel1M 419248 419669 (580331) C L1MA8_3end#LINE/L1 (591) 447 7 m_b66s551i4 2416 chr2ptel1M 419248 GAAGATGGCAATTCAAATCTGTCTCAGACAC-TTAAC--CATTCCCCAAT 419294 v v i v i v v iv i-i i i-- i i-- C L1MA8_3end#LI 447 GAACATGGGAGTGCAGATATCTCTTCGACATACTGATTTCATTTCCT--T 400 chr2ptel1M 419295 TGTTGGTACAGATCCAGTAGTAGCACTGCTGGGCCA-ATGGATATGCACA 419343 -- i i v i i v i ii - vvi v -i C L1MA8_3end#LI 399 TG--GATATATACCCAGTAGTGGGATTGCTGGATCATATGGTAGTTC-TA 353 chr2ptel1M 419344 GTTTGATAGCTCTTTAGGCATATTTTCAAAGTTACTTTCCAGAATGATTG 419393 v -- ii i ii v - ii i v -i ii v ii C L1MA8_3end#LI 352 TTTT--TAATTTTTTGAGGA-ACCTCCATA-CTGTTTTCCATAATGGCTG 307 chr2ptel1M 419394 -GCTCATTTCACAATTTCTCCAATAATG--CAAA--------TTTCTCCA 419432 -i v - v ii v i i -- i-------- C L1MA8_3end#LI 306 TACTAATTT-ACATTCCCACCAACAGTGTGCAAGGGTTCCCTTTTCTCCA 258 chr2ptel1M 419433 CTA-------CAACATTTATTATCTTT--TCCTGTC-ATCTTAGTCATTT 419472 - ------- i i -- i v i- vv i i C L1MA8_3end#LI 257 C-ATCCTCGCCAACACTTGTTATCTTTCGTCTTTTTGATAATAGCCATTC 209 chr2ptel1M 419473 TGAGAGATGTGAGGTAGTATCTCAAAGCTTTTTTAAATTTGTATTTCTCT 419522 i v i ii vv ivv - i i C L1MA8_3end#LI 208 TAACAGGTGTGAGGTGATATCTCATTGTGGTTTT-AATTTGCATTTCCCT 160 chr2ptel1M 419523 AATCAATAGTGATTTACAGCATTCTTTTATAGACCTAGAGATGGC--TTT 419570 i v v v vv i i v --- v -- C L1MA8_3end#LI 159 GATGATTAGTGATGTTGAGCATTTTTTCATATACCT---GTTGGCCATTT 113 chr2ptel1M 419571 A-ATTTCTTCATCTGAAAATTGTTCATATTGAGTC-----ACCATTTCTC 419614 i- v v i i v ii - iii -----v i ? C L1MA8_3end#LI 112 GTATGTCTTCTTTTGAGAAATGTCTAT-TCAGGTCCTTTGCCCATTTTTN 64 chr2ptel1M 419615 ATTTGGGGAATGACTTTTATTCTCATAAATTTGACTCGGTTCTT--TATA 419662 v i vv vvv v vii vi v vi vi i -- C L1MA8_3end#LI 63 AATCGGGTTATTTGTTTTCTTGCTATTGAGTTGTTTGAGTTCCTTATATA 14 chr2ptel1M 419663 TTTTAGA 419669 i C L1MA8_3end#LI 13 TTTTGGA 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.94 CpG sites = 70, Kimura (unadjusted) = 38.36 Transitions / transversions = 1.43 (70/49) Gap_init rate = 0.07 (29 / 421), avg. gap size = 1.76 (51 / 29) 509 29.06 7.69 2.62 chr2ptel1M 419299 419662 (580338) C L1PREC2_3end#LINE/L1 (510) 397 16 m_b66s551i5 2416 chr2ptel1M 419299 GGTACAGATCCAGTAGTAGCACTGCTGGGCC-AATGGATATGCACAGTTT 419347 i v i i i v i i - - - iv v C L1PREC2_3end# 397 GGTATATACCCAGTAATGGGATTGCTGGGTCGAATGG-TA-GTTCTGTTT 350 chr2ptel1M 419348 GATAGCTCTTTAGGCATATTTTCAAAGTTACTTTCCAGAATGATTGG-CT 419396 v- ii v - ivi v -i i v i i- C L1PREC2_3end# 349 T-TAGCTCTTTGAGGA-ATCGCCACA-CTGCTTTCCACAATGGTTGAACT 303 chr2ptel1M 419397 CATTTCACAATTTCTCCAATAATGCA-AA---------TTTCTCCACTAC 419436 v - v ii v i i i - --------- i v C L1PREC2_3end# 302 AATTT-ACACTCCCACCAACAGTGTATAAGCGTTCCCTTTTCTCCGCAAC 254 chr2ptel1M 419437 ------AACATTTATTATCTTTT--CCTGTCA-TCTTAGTCATTTTGAGA 419477 ------ i i i i -- i v i - vv i i vv C L1PREC2_3end# 253 CTCGCCAGCATCTGTTATTTTTTGACTTTTTAATAATAGCCATTCTGACT 204 chr2ptel1M 419478 GATGTGAGGTAGTATCTCAAAGCTTTTTTAAATTTGTATTTCTCTAATCA 419527 i i i vv ivv i - i v C L1PREC2_3end# 203 GGTGTGAGATGGTATCTCATTGTGGTTTTGA-TTTGCATTTCTCTAATGA 155 chr2ptel1M 419528 ATAGTGATTTACAGCATTCTTTTATAGACCTAGAGATGGCTTTA---ATT 419574 vi v vv v i i vi i --- v ivi --- v C L1PREC2_3end# 154 TCAGTGATATTGAGCTTTTTTTCATATGCTT---GTTGGCCGCATGTATG 108 chr2ptel1M 419575 TCTTCATCTGAAAA----TTGTTCATATTGAGTCACCATTTCTCATTTGG 419620 v i ----i i ivvv vv i i i v v C L1PREC2_3end# 107 TCTTCTTTTGAAAAGTGTCTGTTCATGTCCTTTGCCCACTTTTTAATGGG 58 chr2ptel1M 419621 GGAATGACTTTTATTCTCATAAATTTGACTCGGTTCTTTATA 419662 vvi vvv v ii vi vi i C L1PREC2_3end# 57 GTTGTTTGTTTTTTTCTTGTAAATTTGTTTAAGTTCCTTATA 16 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.11 CpG sites = 55, Kimura (unadjusted) = 37.47 Transitions / transversions = 1.15 (55/48) Gap_init rate = 0.05 (19 / 363), avg. gap size = 2.00 (38 / 19) 231 25.33 1.32 1.32 chr2ptel1M 419895 419970 (580030) C L1MD_orf2#LINE/L1 (371) 2923 2848 m_b66s551i6 2417 chr2ptel1M 419895 TTATAGTATCACCCTTTATGCCTAAATCATAT-ACCCATTTTGACCTTAT 419943 v i vi iiii i - - i vi v C L1MD_orf2#LIN 2923 TTATAGTTTTACGTTTTACATTTAAGTC-TATGATCCATTTTGAGTTAAT 2875 chr2ptel1M 419944 TTGGGTATGGGGTGTGAGATGTAGGTC 419970 vv ii i v C L1MD_orf2#LIN 2874 TTTTGTATAAGGTGTGAGGTTTAGGTC 2848 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 31.83 CpG sites = 12, Kimura (unadjusted) = 31.83 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.03 (2 / 75), avg. gap size = 1.00 (2 / 2) 12 18.27 5.41 0.00 chr2ptel1M 420162 420198 (579802) (ATAAGT)n#Simple_repeat 1 39 (0) m_b66s252i3 2418 chr2ptel1M 420162 ATATGTTAAAGTATAAGT-TAAATACAA-TATATGTATA 420198 v vv - i i - v (ATAAGT)n#Sim 1 ATAAGTATAAGTATAAGTATAAGTATAAGTATAAGTATA 39 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 1620 28.69 6.58 2.13 chr2ptel1M 420512 421590 (578410) C L1M5_orf2#LINE/L1 (623) 2671 1546 m_b66s551i7 2419 chr2ptel1M 420512 GCCAGTACCATATGGTTTTGATGATTGCTGCTTTATATTAAGTCT---GC 420558 i i iv i v i iv v ---?v C L1M5_orf2#LIN 2671 GCCAATACCACACTGTCTTGATTACTGTAGCTTTATAATAAGTCTTGANA 2622 chr2ptel1M 420559 TTGGACACTGT-------CCA---TTGTATTTGTTTTATTAA--TTTCCC 420596 i? ii v ------- --- vi v - i -- viii C L1M5_orf2#LIN 2621 TCNGGTAGTGTAAGTCCTCCAACTTTGTTCTTCTTTT-TCAAGATTGTTT 2573 chr2ptel1M 420597 TGA-TATTCTTG--CCTTCTTTTCTTCAGATGAATTTAGTTGTTATTTTT 420643 i- ? -- iviv i i v i vivvi i vi v C L1M5_orf2#LIN 2572 TGGCTATTCTNGGTCCTTTGCATTTCCATATAAATTTTAGAATCAGCTTG 2523 chr2ptel1M 420644 TCTAATTTTATAAAATAATTTTTTGGCAGTTTAATTGCTATGTCACTGAA 420693 v v i i v ii vi v v i vv vv i C L1M5_orf2#LIN 2522 TCAATTTCTACAAAAAAACCTGCTGGGATTTTGATTGGGATTGCATTGAA 2473 chr2ptel1M 420694 CAAGCAGACTAATTTAGGTAGAATTAGCATTTTTATTATACTACAGTCT- 420742 ivvii ii i v ii i ? iv i i- - C L1M5_orf2#LIN 2472 TCTATAGATCAATTTGGGGAGAATTGACATCTTNACAATATTG-AGTCTT 2424 chr2ptel1M 420743 ---ACCCTTGAGAAATTGATTTCTCTTTCTCAATTGTTTAGATCTGATTT 420789 --- i v iv -- i v v i - v i i vv C L1M5_orf2#LIN 2423 CCAATCCATGAACA--TGGTATATCTCTC-CATTTATTTAGGTCTTCTTT 2377 chr2ptel1M 420790 TATTTGTGTTTAAAGTATTTTGTAATTATGTTC---GTATAGTTTCTGGA 420836 v v v iviv i i i --- --- ? v ii v C L1M5_orf2#LIN 2376 AATTTCTCTCAGCAATGTTTTGTAGTT---TTCAGTGTANAGGTCTTGCA 2330 chr2ptel1M 420837 TTTGTCTTGGTAGTTAGACTCCCAAATATTTT-TATTTTGTCGGAAGTTA 420885 iv ? i v v vv i i i ?- i v -- v i C L1M5_orf2#LIN 2329 CATNTTTTGTTAGATTTATTCCTAAGTATTTNATGTTTTTT--GATGCTA 2282 chr2ptel1M 420886 TTTTAAATGGTATC-TCTCTG-----TCTTTTGCTGCTAGGTT-TTGTTA 420928 v i- i i ?----- v v iiv v v - i C L1M5_orf2#LIN 2281 TTGTAAATGGTATTGTTTTTNAAATTTCATTTTCCAATTGTTTGTTGCTA 2232 chr2ptel1M 420929 GTAACATAGAAATGCTGGTTATTTGTGTGGGTTTATTTTGTATTCTGC-A 420977 -i i viv v v ivi v ii i ? - C L1M5_orf2#LIN 2231 GTA-TATAGAAATACAATTGATTTTTGTATATTGACCTTGTATCCNGCGA 2183 chr2ptel1M 420978 TTTTCCTAAA---GCT-ATTTTTTCAAGTAGATTTTTGGGTGATTCTCTG 421023 ii v ---i - vv v v ? v vv i ? C L1M5_orf2#LIN 2182 CCTTGCTAAATTCACTTATTAGTTCTAGTAGTTTNTTTGTAGATTCTTTN 2133 chr2ptel1M 421024 GGATTCTTTAATTGTACCATCATATCATCTACAAAAAAGGGTGATAGTTT 421073 i i vv i? v i i i v ? --- i C L1M5_orf2#LIN 2132 GGATTTTCTACGTANACAATCATGTCATCTGCGAATAANG---ACAGTTT 2086 chr2ptel1M 421074 TATCTTCTCCTTGC-----TTTAGTTCCTTGAAAAAGAAATTTCACTTTC 421118 i ii v ----- - v vv ------- vi C L1M5_orf2#LIN 2085 TATTTCTTCCTTTCCAATCTTTA-TGCCTTTTA-------TTTCTTTTTC 2044 chr2ptel1M 421119 TTA--TTACTAAA---GCCAACATTTCTAGTACAATATTGAATAACAGTG 421163 i-- i iv --- i iv ii i i iv C L1M5_orf2#LIN 2043 TTGCCTTATTGCACTGGCTAGGACCTCCAGTACAATGTTGAATAGAAGTG 1994 chr2ptel1M 421164 GTGACAGTGATCATCTTTGTTTCAC-CCTGATCTTATTGGAAATGTGTCT 421212 ? i iv i i iii- i vv i v i? ii C L1M5_orf2#LIN 1993 GTGANAGCGGACATCCTTGTCTTGTTCCCGATCTTAGGGGGAAAGCNTTC 1944 chr2ptel1M 421213 AACTTCTCCCCATTACAAATAATGCTTACTGTTAGTTTTAGACAGATACT 421262 ii? i v viv i i ?i vi vvii i i C L1M5_orf2#LIN 1943 AGTNTTTCACCATTAAGTATGATGTTNGCTGTAGGTTTTTCGTAGATGCC 1894 chr2ptel1M 421263 GTTTATCATTTGAAGGACAATTCCATT-TATTTCCATGCTCTCT-AGTGT 421310 v vv vi - i v - i i - i iv - v C L1M5_orf2#LIN 1893 CTTTATCAGGTTGAGGA-AGTTCCCTTCTATTCCTA-GTTTGCTGAGAGT 1846 chr2ptel1M 421311 TTTTAATAGAAATGGGTGCTGTGTCTTGTCAAAAGTTTTTTCTGCATCTA 421360 vi vi i vi i v i C L1M5_orf2#LIN 1845 TTTTATCATGAATGGGTGTTGAATTTTGTCAAATGCTTTTTCTGCATCTA 1796 chr2ptel1M 421361 TTGAGAGTATTATATGATTTCTGTTGGTTTTGTTATTGATATGGTCAAT- 421409 vv i i v ivv v vi i i v - C L1M5_orf2#LIN 1795 TTGAGATGATCATATGATTTTTCTCCTTTATTCTGTTAATATGGTGAATT 1746 chr2ptel1M 421410 -------TTCCTTTTC-----CTGAACCAGCCCTGCATTCCTGATATAAA 421447 ------- vv -----i i i i iv C L1M5_orf2#LIN 1745 ACATTGATTGATTTTCGAATGTTAAACCAACCTTGCATTCCTGGGATAAA 1696 chr2ptel1M 421448 TCCTTCTTGGTCATAGTCTATTATCATGCTGATAAGTTGTTATAATCTCT 421497 i iv ii v v vi v vi i iv v vv C L1M5_orf2#LIN 1695 CCCCACTTGGTCATGATGTATTATCCTTTTTATATATTGCTGGATTCGAT 1646 chr2ptel1M 421498 TTGGTAATATTTTATTTAAATTTTTTGTATCAATATTCATTTGGAAGATT 421547 v i ? iiv i v i vv i v C L1M5_orf2#LIN 1645 TTGCTAATATTTTGTTNAGGATTTTTGCATCTATGTTCATGAGGGATATT 1596 chr2ptel1M 421548 GATCTGTAGTTTTCTTTT-------TGTCTCTTCCTGGTTCGGATATCAG 421590 i i ------- i vi ? iv i C L1M5_orf2#LIN 1595 GGTCTGTAATTTTCTTTTCTTGTAATGTCTTTGTCNGGTTTTGGTATCAG 1546 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.25 CpG sites = 169, Kimura (unadjusted) = 37.89 Transitions / transversions = 1.26 (169/134) Gap_init rate = 0.05 (50 / 1078), avg. gap size = 1.90 (95 / 50) 45 30.00 2.41 0.59 chr2ptel1M 422003 422168 (577832) (TATA)n#Simple_repeat 1 169 (0) m_b66s252i4 2420 chr2ptel1M 422003 TATAATTATGTACATGTA-ACAGACATATATATATATCTATATTTATATC 422051 vv i i i - i v i v v v (TATA)n#Simpl 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr2ptel1M 422052 TATATAGATATATGTAGATATACACACACATACATATACATAGATATCTA 422101 v i v i i i i i i v v (TATA)n#Simpl 51 TATATATATATATATATATATATATATATATATATATATATATATATATA 100 chr2ptel1M 422102 -ATCATTCACACACACACACATATATATATATTCATATGTATTCATAGTT 422150 - - vi i i i i i i vi i vi vv (TATA)n#Simpl 101 TAT-ATATATATATATATATATATATATATATATATATATATATATATAT 149 chr2ptel1M 422151 ATTTATGTA-AGAT-TATAT 422168 v i - v - (TATA)n#Simpl 150 ATATATATATATATATATAT 169 Matrix = Unknown Transitions / transversions = 1.35 (23/17) Gap_init rate = 0.03 (5 / 165), avg. gap size = 1.00 (5 / 5) 35 30.25 2.90 0.71 chr2ptel1M 422010 422147 (577853) (ATATAC)n#Simple_repeat 1 141 (0) m_b66s252i5 2421 chr2ptel1M 422010 ATGTACATGTA-ACAGACATATATATATATCTATATTTATATCTATATAG 422058 i i - i v i iv iv iv i v (ATATAC)n#Sim 1 ATATACATATACATATACATATACATATACATATACATATACATATACAT 50 chr2ptel1M 422059 ATATATGTAGATATAC--ACACACATACATATACATAGATATCTA-ATCA 422105 i i v -- i i v i v - - (ATATAC)n#Sim 51 ATACATATACATATACATATACATATACATATACATATACATATACAT-A 99 chr2ptel1M 422106 TTCACACACACACACATATATATATATTCATATGTATTCATA 422147 v i i i i i ivi ii v (ATATAC)n#Sim 100 TACATATACATATACATATACATATACATATACATATACATA 141 Matrix = Unknown Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.03 (4 / 137), avg. gap size = 1.25 (5 / 4) 45 30.00 2.41 0.59 chr2ptel1M 422003 422168 (577832) (TATA)n#Simple_repeat 1 169 (0) m_b66s252i4 2420 chr2ptel1M 422003 TATAATTATGTACATGTA-ACAGACATATATATATATCTATATTTATATC 422051 vv i i i - i v i v v v (TATA)n#Simpl 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr2ptel1M 422052 TATATAGATATATGTAGATATACACACACATACATATACATAGATATCTA 422101 v i v i i i i i i v v (TATA)n#Simpl 51 TATATATATATATATATATATATATATATATATATATATATATATATATA 100 chr2ptel1M 422102 -ATCATTCACACACACACACATATATATATATTCATATGTATTCATAGTT 422150 - - vi i i i i i i vi i vi vv (TATA)n#Simpl 101 TAT-ATATATATATATATATATATATATATATATATATATATATATATAT 149 chr2ptel1M 422151 ATTTATGTA-AGAT-TATAT 422168 v i - v - (TATA)n#Simpl 150 ATATATATATATATATATAT 169 Matrix = Unknown Transitions / transversions = 1.35 (23/17) Gap_init rate = 0.03 (5 / 165), avg. gap size = 1.00 (5 / 5) 354 29.93 4.82 7.41 chr2ptel1M 422171 422336 (577664) MIRc#SINE/MIR 2 163 (105) m_b66s601i0 2422 chr2ptel1M 422171 GGGGCAGCTAGGTAGCTCAGTGAATAGCACACCAACCCTGAAGTCAGGAG 422220 i i--- i iv i v vi iiiv i i i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr2ptel1M 422221 GACCTGAGTTCAAATCTGACCCCAGACACGTAAGACTTCCTAGCTGTGTG 422270 i i i iviv i v v ------- v MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCC-------ACTTACTAGCTGTGTG 91 chr2ptel1M 422271 ACCATGTGA----CCCTGAACAAGTCTCTTAACCCCAATTGCCTCA---G 422313 v v v---- v v --v v i i i v --- MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAAC--CTCTCTGAGCCTCAGTTTCCTCATCTG 139 chr2ptel1M 422314 GAAAA-AAAAATTATAATATTTGC 422336 v -iiii v ii MIRc#SINE/MIR 140 TAAAATGGGGATAATAATACCTGC 163 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.03 CpG sites = 27, Kimura (unadjusted) = 39.21 Transitions / transversions = 1.42 (27/19) Gap_init rate = 0.09 (15 / 165), avg. gap size = 1.33 (20 / 15) 298 29.67 8.33 2.63 chr2ptel1M 422437 422616 (577384) L1MC3_3end#LINE/L1 439 628 (1904) m_b66s551i9 2423 chr2ptel1M 422437 CAAATGTTTGTGGCAGCCCTGTTTATAGTGGCTAGAAAATGAATG----- 422481 i i i ii i i i v i i v i v ----- L1MC3_3end#LI 439 CGAATGTTTATAGCAGCTTTATTCATAATCGCCAAAAACTGGAAGCAACC 488 chr2ptel1M 422482 --GATGCCCATCCATTGGAGAATGGTTGGGTAAATTGTGGCATATGAATG 422529 -- i v v v v v iiii i i i vv i L1MC3_3end#LI 489 AAGATGTCCTTCAATAGGTGAATGGATAAACAAACTGTGGTACATCCATA 538 chr2ptel1M 422530 TTATGGAATATTATTCTGT------AAGAAATGA-CCAGCAGGATAAATA 422572 iv v i------ - i v ---- ivi L1MC3_3end#LI 539 CAATGGAATATTATTCAGCGATAAAAAGAAATGAGCTATCA----AGCCA 584 chr2ptel1M 422573 CAGAGAAGCTTGGA-GAGACTTACATGAACTGATGCTGAGTGAAA 422616 ii i ii v - iv v v - iv i L1MC3_3end#LI 585 CGAAAAGACATGGATGAATCTTAAATGCA-TATTGCTAAGTGAAA 628 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.46 CpG sites = 33, Kimura (unadjusted) = 39.37 Transitions / transversions = 1.74 (33/19) Gap_init rate = 0.06 (10 / 179), avg. gap size = 2.00 (20 / 10) 312 30.51 5.93 0.00 chr2ptel1M 422437 422554 (577446) L1MB8_3end#LINE/L1 439 563 (362) m_b66s551i8 2423 chr2ptel1M 422437 CAAATGTTTGTGGCAGCCCTGTTTATAGTGGCTAGAAAATGAA------- 422479 i ii i vi i i i i i i i i ------- L1MB8_3end#LI 439 CGAATGTTCATAGCAGCATTATTCATAATAGCCAAAAAGTGGAAACAACC 488 chr2ptel1M 422480 TGGATGCCCATCCATTGGAGAATGGTTGGGTAAATTGTGGCATATGAATG 422529 iii i v i iv v iii v i vv i L1MB8_3end#LI 489 CAAATGTCCATCAACTGATGAATGGATAAATAAAATGTGGTATATCCATA 538 chr2ptel1M 422530 TTATGGAATATTATTCTGTAAGAAA 422554 iv v i v L1MB8_3end#LI 539 CAATGGAATATTATTCGGCAATAAA 563 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.33 CpG sites = 26, Kimura (unadjusted) = 41.91 Transitions / transversions = 2.60 (26/10) Gap_init rate = 0.01 (1 / 117), avg. gap size = 7.00 (7 / 1) 318 26.92 6.73 0.00 chr2ptel1M 422440 422543 (577457) L1ME3G_3end#LINE/L1 438 548 (376) m_b66s551i10 2423 chr2ptel1M 422440 ATGTTTGTGGCAGCCCTGTTTATAGTGGCTAGAAAATGAA-------TGG 422482 ii v vi i i i v i v i ------- ii L1ME3G_3end#L 438 ATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAA 487 chr2ptel1M 422483 ATGCCCATCCATTGGAGAATGGTTGGGTAAATTGTGGCATATGAATGTTA 422532 i v v i iii i i vv ii L1ME3G_3end#L 488 ATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTA 537 chr2ptel1M 422533 TGGAATATTAT 422543 i L1ME3G_3end#L 538 TGGAATACTAT 548 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.13 CpG sites = 20, Kimura (unadjusted) = 35.13 Transitions / transversions = 2.50 (20/8) Gap_init rate = 0.01 (1 / 103), avg. gap size = 7.00 (7 / 1) 12 13.05 0.00 3.70 chr2ptel1M 422941 422968 (577032) (GGGA)n#Simple_repeat 1 27 (0) m_b66s252i6 2424 chr2ptel1M 422941 GGGAGGGGGTGGAGGGAAGGAAGGAGGG 422968 i - i i (GGGA)n#Simpl 1 GGGAGGGAG-GGAGGGAGGGAGGGAGGG 27 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 14 13.01 9.09 2.13 chr2ptel1M 423204 423247 (576753) (AAT)n#Simple_repeat 1 47 (0) m_b66s252i8 2425 chr2ptel1M 423204 AATAATAGT-ATGATAA-AATAA-AAGAAGTGAAAATAATAA-AATAA 423247 i - i - - v - i v - (AAT)n#Simple 1 AATAATAATAATAATAATAATAATAATAA-TAATAATAATAATAATAA 47 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.12 (5 / 43), avg. gap size = 1.00 (5 / 5) 489 26.19 0.65 7.69 chr2ptel1M 423819 423971 (576029) C MIRc#SINE/MIR (123) 145 3 m_b66s601i1 2426 chr2ptel1M 423819 ATTTTATAGGTGATGAAACTGAGACAAACAGTATTAAATAAATGGCTTGC 423868 i i v i vv v viv --- i i C MIRc#SINE/MIR 145 ATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGT---TAAGTGACTTGC 99 chr2ptel1M 423869 CCACAGTCACACAGCTGATAAGTCTCTGAGGCCATATGTGAACTCATCAA 423918 vi ii vv v - i----- i i-- C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAG-CCG-----GGACTCG--AA 57 chr2ptel1M 423919 CATGAGTGTTCCTGATTCCAAGCCCAGTGCTCTATCCACCA-ACCATGTA 423967 viii v i i v ii- iiiv C MIRc#SINE/MIR 56 CCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACT 7 chr2ptel1M 423968 GCTT 423971 i C MIRc#SINE/MIR 6 GCCT 3 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 30.80 CpG sites = 23, Kimura (unadjusted) = 32.95 Transitions / transversions = 1.64 (23/14) Gap_init rate = 0.08 (12 / 152), avg. gap size = 1.00 (12 / 12) 289 25.65 8.04 2.54 chr2ptel1M 424502 424613 (575387) MIR3#SINE/MIR 90 207 (1) m_b66s601i2 2427 chr2ptel1M 424502 CTTTGGACAA---ACTCC--TTTTCTGTGCTTTAGGTTCCTA--CTATAA 424544 i i --- i --i i v i i v v-- i MIR3#SINE/MIR 90 CCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAA 139 chr2ptel1M 424545 ATTGATGCGGGTTGGATTATGTAA-CATGAAAGTGTCTTTCAGCTCTT-C 424592 v v - i vi i - viv i vi i v- MIR3#SINE/MIR 140 AATGAGG-GGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGAC 188 chr2ptel1M 424593 ATCCTATGACTTTTGATGATT 424613 i i i -- MIR3#SINE/MIR 189 ATTCTATGATTCT--ATGATT 207 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.48 CpG sites = 18, Kimura (unadjusted) = 32.48 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.07 (8 / 111), avg. gap size = 1.50 (12 / 8) 703 26.31 6.87 3.75 chr2ptel1M 425255 425487 (574513) C MIRb#SINE/MIR (25) 243 4 m_b66s601i3 2428 chr2ptel1M 425255 CACCTGCCATTTGCCAGGTGCTGTGCCAAGTGCTTTCTATATAACATGAT 425304 i i i i v ii i i vi i--- v C MIRb#SINE/MIR 243 CGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACATG---CATTAT 197 chr2ptel1M 425305 ATCACTTTATC---ATAGTAACCTTCCAAATTCAGT-GATATCATTATCC 425350 v i v --- i ii i v i i---- - i i C MIRb#SINE/MIR 196 CTCATTTAATCCTCACAACAACCCTGCGAG----GTAGGTATTATTATCC 151 chr2ptel1M 425351 CCTTTTGACAGCTGAGGCAACTGAGACCAACAGAGGGTAAGTGACTTGTT 425400 v v v v i iv v v i ii C MIRb#SINE/MIR 150 CCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCC 101 chr2ptel1M 425401 C-AGATCACACAGCTAGTACCTGTCTGAAGCCAGATTTAAACCTAGCTTT 425449 - i vv v v iv vi ii i v i C MIRb#SINE/MIR 100 CAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCT 51 chr2ptel1M 425450 TCCTG--TC---------TACTCTTCCCACTGTACAACCAACTGCCTCT 425487 vi -- --------- i i i v --i i C MIRb#SINE/MIR 50 GTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCACCAC--GCTGCCCCT 4 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.98 CpG sites = 37, Kimura (unadjusted) = 33.45 Transitions / transversions = 1.68 (37/22) Gap_init rate = 0.06 (14 / 232), avg. gap size = 1.79 (25 / 14) 25 0.00 0.00 0.00 chr2ptel1M 425751 425777 (574223) (A)n#Simple_repeat 1 27 (0) m_b66s252i9 2429 chr2ptel1M 425751 AAAAAAAAAAAAAAAAAAAAAAAAAAA 425777 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAA 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 237 37.04 10.07 2.62 chr2ptel1M 426980 427406 (572594) C MamRTE1#LINE/RTE-BovB (217) 3595 3138 m_b66s601i4 2430 chr2ptel1M 426980 CTTTGCTCAGCA-----CAGCCCTTCTTTGATAAAGGCATGCTGGGC-AG 427023 iv ----- v v iii vivv ii -i C MamRTE1#LINE/ 3595 CTTTGCTCAAAAAGAGCCACCCCGTTCCTGATTGCTGCATGCCAGGCTGG 3546 chr2ptel1M 427024 TC---CTGG-GCCAGTGTCTCC--GCTATCCCACAATCGAATCCGAAGTT 427067 --- v- iiv i -- vi - i- v vv v v v C MamRTE1#LINE/ 3545 TCTGTCTGCTGCTGTTGTTTCCCAGCAGTCC-ACAG-CTATGCCGCATTG 3498 chr2ptel1M 427068 CTTAAGAAGATACTTTGAGAGTGTCCTTGCATCCCTTCTTTTAAGTACTT 427117 i i iivvi i i- v ?i iv v vi i -- iv i C MamRTE1#LINE/ 3497 TTTGAAGCTGTGCTTC-AGTGNATCCTTAAAGCGTTTCTTCT--GCCCTC 3451 chr2ptel1M 427118 TGTGAGCTTG----TGCCCTGTGTGAGTTCTCCAAAAAAATATTCTTTTA 427163 iv -- ---- iiiv v i v iv v i-i viivi i C MamRTE1#LINE/ 3450 CCTG--CTTGCGGTTGCCCCACTTCAGCTCACCGTACAG-CAGCTGCTTG 3404 chr2ptel1M 427164 GGCAAGCGTAC-ATTAGGCATTT---GAACATGATCTGTCTAGCAGAGCT 427209 i -v v i -i i vv i--- v vi v i i i C MamRTE1#LINE/ 3403 GGTA-TCCTGCTGTCATCCATTCTCCGCACATGTCCAGCCCAGCGGAGCT 3355 chr2ptel1M 427210 G---TGC--------TCTCTGCAATGCTTGGCAGATTAATT-CAAGAAAG 427247 --- -------- v v i - i i iii - ivvvv C MamRTE1#LINE/ 3354 GCGTTGCGGCGAGCATCGCTTCAGTGCT-GGTAGACTGGCTGCGTTCCAG 3306 chr2ptel1M 427248 GACCTCATTGTCTGGT-ACCTTATCTCACTAGGTGATCTT--------CC 427288 i - - i i i ii i vv i v -------- i C MamRTE1#LINE/ 3305 GACCTCGTTGT-TGGTGATCCTGTCTTGCCATTTAATGTTAAGTATGGCT 3257 chr2ptel1M 427289 TG-AAACAATTCAAATGGAAGCGATTCAGTTTCCTGGCATGGCGCTGGTA 427337 i - iiii iv vi i vi v iv vvv v iii i iiv i C MamRTE1#LINE/ 3256 CGTAGGTGACGCTGATGAAACTGCTCAAGAAGCCGGATGTGACGTCTGTG 3207 chr2ptel1M 427338 GACTGTCCAGATTTCACTGGCATACAGCAA-TGGGATCAGCCCAAGGGCT 427386 vvv i i v v i ? v i- v - ? v v vv C MamRTE1#LINE/ 3206 GCAGGTCCAGGTCTCACAGCCGTANAGAAGGTTGGA-CANCGCTATCGCT 3158 chr2ptel1M 427387 CTGTAGATCTTCACTTTGGT 427406 i i v C MamRTE1#LINE/ 3157 CTGTAGACCTTTAGTTTGGT 3138 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 50.16 CpG sites = 86, Kimura (unadjusted) = 53.69 Transitions / transversions = 1.26 (86/68) Gap_init rate = 0.06 (27 / 426), avg. gap size = 2.04 (55 / 27) 265 37.99 1.52 2.29 chr2ptel1M 428011 428142 (571858) C MamRTE1#LINE/RTE-BovB (1180) 2632 2502 m_b66s601i5 2430 chr2ptel1M 428011 ACACAATCTTGTTTTACTACATTGGTGATTGGGAA--AGCACAAGAGAAT 428058 i i i i v v --i ivvi v i - C MamRTE1#LINE/ 2632 ACGCAATCCTGCTTCACTCCATTGGTGATGGGGAATGGGTCGGACAGGA- 2584 chr2ptel1M 428059 CATCTTTTATTCAGAGCCCAGGCAAACATGCCATCATGAAACTGATGTAC 428108 ii v iv i v - v iiv iiv i i iiv viv v C MamRTE1#LINE/ 2583 CGCCGTCAACTCTGA-CGCGACCGGCCATACCATCATGGAGTAGCCTTAG 2535 chr2ptel1M 428109 AATACTGATGATTTTTTTCTAGACAACCCAATTT 428142 i vi i -vi i vi i i v i C MamRTE1#LINE/ 2534 GATCTTGGTGA-ACTTCTCAGGGCAGCCAAACTT 2502 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 49.39 CpG sites = 30, Kimura (unadjusted) = 56.11 Transitions / transversions = 1.58 (30/19) Gap_init rate = 0.03 (4 / 131), avg. gap size = 1.25 (5 / 4) 302 39.15 4.41 3.01 chr2ptel1M 428315 428609 (571391) C MamRTE1#LINE/RTE-BovB (1513) 2299 2001 m_b66s601i6 2430 chr2ptel1M 428315 AGTCTGTTGAGGGGCACTCTAACAAGGATCTTGCTAAAAAATGA---CTG 428361 i vi iv ii v ii v i iv vv --- v C MamRTE1#LINE/ 2299 AGCCGATCCAGAAGGACTCTGGCCAGGATCTTGCCAGCAATGGAGAGCAG 2250 chr2ptel1M 428362 AGAGACCCTACTATGATTGTCACAA--AACTATCAATTCCCTTTACCTTT 428409 ? iv ii v ii i i i-- i v -- iv viii C MamRTE1#LINE/ 2249 NGAGATGCCGCGATAGTTGCCGCAGTCAGCTTTC--TCGCCTTTCTTCTT 2202 chr2ptel1M 428410 AAAGA-GATGGAAAATGGAAGCATCCTTGAACTCCTG-GGTATAACCTTC 428457 i - i - vi i vi i v - i vv iv C MamRTE1#LINE/ 2201 GAAGATGGT-GATGATAGTGGCATCTTTGAAATCCTGCGGCATTTCCTCG 2153 chr2ptel1M 428458 TCTTGCCATAAACCCCAGAAAATCTCAATTAC---CTTTTGTAGGAGCAA 428504 viviv vi ivv v ii -- i --- v i ----i i C MamRTE1#LINE/ 2152 GTACTCCATATGCTGAAGAAAAGCCTA--TGCAGACGTCT----AAGCAG 2109 chr2ptel1M 428505 TGGACTCCATAC---CTTGCAGATCTCAGCTGGAATAGAAGCAGTACCAG 428551 i vvii v v --- v i v v ivv v vv ii C MamRTE1#LINE/ 2108 CGTCTCCCCTTCCTGCTTGAAAATCTCAGCAGGTATGCCATCAGGTCCGA 2059 chr2ptel1M 428552 ATTCTTTGCCACATTAAAGGGGCTCAATAGCACTGAAAATTTCTTCTTGA 428601 ivv i ivi vv v viiii i iv ?vi i vvi C MamRTE1#LINE/ 2058 GAGCTTTACCATTCTTCATGGCTCTGACAGCGGTGNTGACTTCTTCAAAA 2009 chr2ptel1M 428602 ATTGGAAC 428609 i i C MamRTE1#LINE/ 2008 GTTGGAGC 2001 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 52.77 CpG sites = 62, Kimura (unadjusted) = 58.28 Transitions / transversions = 1.24 (62/50) Gap_init rate = 0.05 (15 / 294), avg. gap size = 1.47 (22 / 15) 408 21.34 4.72 2.78 chr2ptel1M 428730 428835 (571165) C MIRc#SINE/MIR (141) 127 20 m_b66s601i7 2431 chr2ptel1M 428730 CTGAGGC-AATTGGGTTTAAGTGACTTGCTCATGGTCACACAGCTAGGAA 428778 -v vv i v i v v C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAA 78 chr2ptel1M 428779 ATGTTTGA----GGACATATTGAACTCGGGTCCTCCTGACTTCAGGGCTG 428824 i viv ---- --- i i i i i i v ii C MIRc#SINE/MIR 77 GTGGCAGAGCCGGGAC---TCGAACCCAGGTCTTCCTGACTCCAAGTCCA 31 chr2ptel1M 428825 GTGCTCTATCC 428835 v C MIRc#SINE/MIR 30 GTGCTCTTTCC 20 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 24.14 CpG sites = 12, Kimura (unadjusted) = 25.43 Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.05 (5 / 105), avg. gap size = 1.60 (8 / 5) 181 28.88 7.81 5.34 chr2ptel1M 429465 429592 (570408) C MamRTE1#LINE/RTE-BovB (3309) 503 373 m_b66s601i8 2430 chr2ptel1M 429465 CCCACCTGCCACAGTAA----GAAGGCCAAGGTTGAGT------AAGCAG 429504 v v i ii ---- vii i?v ? ------ i C MamRTE1#LINE/ 503 CCCACCAGACGCGATAATCTGGTGAGCCAGNTTTGANTTTGGCGAGGCAG 454 chr2ptel1M 429505 ACAATCTTTAGGGCACCTTCTTTTATTCTTCTTCACAACAGAAGGTGAGC 429554 i iv - i v? iii i v viv i - C MamRTE1#LINE/ 453 GCAACGTTTAGGGCACCTT-TTCTAGNCCCTTCCCCATTCGGA-GTGAGC 406 chr2ptel1M 429555 TGTGGCCTACTATCAGCAAGGGCCCCAGTCAGAGTCCC 429592 v i vv? v -- i - iv -- vv C MamRTE1#LINE/ 405 AGCGCGNTCCTA--AAC-AGGGCTGC--TCAGACACCC 373 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.53 CpG sites = 19, Kimura (unadjusted) = 38.94 Transitions / transversions = 1.19 (19/16) Gap_init rate = 0.07 (9 / 127), avg. gap size = 1.89 (17 / 9) 276 34.31 4.90 0.00 chr2ptel1M 429601 429702 (570298) C L2d2_3end#LINE/L2 (17) 538 432 m_b66s601i9 2432 chr2ptel1M 429601 ACATTGATTGAACATCTTCTGTTTT--GGACACTGTGTTAAGTCCTG--- 429645 i v i ii v v v--i i i i iv --- C L2d2_3end#LIN 538 ATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGTGG 489 chr2ptel1M 429646 AGTATGCAAAGGAAGGCAAAAAATAGTGTCTGTTGTCACAGAGCTCAGAA 429695 i v i i ivii i v i vi iiv vi i v C L2d2_3end#LIN 488 GGGATACAAAGAAGTATAAGACATGGTCCCTGCCCTCAAGGAGCTTACAA 439 chr2ptel1M 429696 TCTACTT 429702 v C L2d2_3end#LIN 438 TCTAGTT 432 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 44.42 CpG sites = 22, Kimura (unadjusted) = 48.27 Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.02 (2 / 101), avg. gap size = 2.50 (5 / 2) 393 32.87 2.72 0.67 chr2ptel1M 429738 429884 (570116) C MIRc#SINE/MIR (113) 155 6 m_b66s601i10 2433 chr2ptel1M 429738 TATTATACTATATTTTAGTGATAGAGAAACTGATGC--AGAGACCCTA-- 429783 v i-i vv iii v -- vvi -- C MIRc#SINE/MIR 155 TATTATCCC-CATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAG 107 chr2ptel1M 429784 TTACTTGCCTACAGTCAGAGTACTCAAAAGTTTTTGAGGTAGGAACAGAA 429833 v i vi v vvi viv vviv vii viv C MIRc#SINE/MIR 106 TGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAA 57 chr2ptel1M 429834 TTCAGGTCTTCCTGACTCAAGGCACAGCATTCTAACCACTGCACTATCTT 429883 ii v i iv iii vv i ivi C MIRc#SINE/MIR 56 CCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACT 7 chr2ptel1M 429884 G 429884 C MIRc#SINE/MIR 6 G 6 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.61 CpG sites = 24, Kimura (unadjusted) = 43.94 Transitions / transversions = 1.00 (24/24) Gap_init rate = 0.02 (3 / 146), avg. gap size = 1.67 (5 / 3) 22 13.37 8.16 0.00 chr2ptel1M 429985 430033 (569967) (GT)n#Simple_repeat 1 53 (0) m_b66s252i10 2434 chr2ptel1M 429985 GTGTTTG-GTTTG-GTTTG-GTGTGTGTGTGTGTGTGTGTAT-TGTATGT 430030 v - v - v - i - i (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50 chr2ptel1M 430031 TTG 430033 v (GT)n#Simple_ 51 GTG 53 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.08 (4 / 48), avg. gap size = 1.00 (4 / 4) 293 32.32 5.97 0.71 chr2ptel1M 431523 431656 (568344) MIRc#SINE/MIR 91 231 (37) m_b66s601i11 2435 chr2ptel1M 431523 GATTTAGGTCAAGTCACTTAGCCATTCTGAG-TTCA-TGGCCTGAGTTGT 431570 ii v v i vi -i - vv v vi MIRc#SINE/MIR 91 GACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGT 140 chr2ptel1M 431571 GAATAT---GACAAGAATGCTGACCTTGTTTGTGCCGGAGGTTTGTTATG 431617 i - --- i v i ivi i ii iivi iv v i MIRc#SINE/MIR 141 AAA-ATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTG 189 chr2ptel1M 431618 AGAATAAAATATGGTCATGTGTG---GAGCTTTTTATAAATT 431656 i v iv i v i ---i vi i i MIRc#SINE/MIR 190 AGGATCAAATGAGATAATGTATGTGAAAGCGCTTTGTAAACT 231 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 44.24 CpG sites = 27, Kimura (unadjusted) = 44.24 Transitions / transversions = 1.69 (27/16) Gap_init rate = 0.04 (5 / 133), avg. gap size = 1.80 (9 / 5) 14 21.12 2.90 7.58 chr2ptel1M 431789 431857 (568143) (TTGT)n#Simple_repeat 1 66 (0) m_b66s252i11 2436 chr2ptel1M 431789 TTGTGTGTATTTTTGTGGGTGGTGTCTGTATATATTTG-TT-TTTATTTG 431836 v v v vv -v i - - i - - i (TTGT)n#Simpl 1 TTGTTTGTTTGTTTGTTTGT-TTGTTTGT-T-TGTTTGTTTGTTTGTTTG 47 chr2ptel1M 431837 TTTGTATATATTTGTTTCTTT 431857 - - i v (TTGT)n#Simpl 48 TTTGT-T-TGTTTGTTTGTTT 66 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.10 (7 / 68), avg. gap size = 1.00 (7 / 7) 18 0.00 0.00 0.00 chr2ptel1M 433958 433977 (566023) (A)n#Simple_repeat 1 20 (0) m_b66s252i12 2437 chr2ptel1M 433958 AAAAAAAAAAAAAAAAAAAA 433977 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAA 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 204 26.96 0.00 8.45 chr2ptel1M 435744 435820 (564180) L3#LINE/CR1 895 965 (3134) m_b66s601i12 2438 chr2ptel1M 435744 GTTATTTTGGAAGAGACAATAAAGTATTGGAATTTAACAGCTGGCTGCAT 435793 v i v iv iii v v v i i L3#LINE/CR1 895 GTGACTTTGGAAGAGAAAGGAGGATATGGGAAGTGAACAGCTGGCTACGT 944 chr2ptel1M 435794 TTGAGGTGATTATTGAACTGAACTGAA 435820 --- i i- i i -- v i L3#LINE/CR1 945 ---AGATGG-TGTCGAA--GAACAGGA 965 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.87 CpG sites = 12, Kimura (unadjusted) = 34.18 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.08 (6 / 76), avg. gap size = 1.00 (6 / 6) 259 31.02 0.85 4.39 chr2ptel1M 437116 437233 (562767) L1ME3F_3end#LINE/L1 439 552 (438) m_b66s551i11 2439 chr2ptel1M 437116 AGAATGTGTATACATAAGCATCCCTTTTTGCAGTGGCAAGGAACTGGAAA 437165 vi ----- v v v i i i i ii L1ME3F_3end#L 439 AGAATGTTCATA-----GCAGCACTGTTCGTAATAGCAAAAAACTGGAAA 483 chr2ptel1M 437166 CTGAATGGATGTCCATCAGTTGGGAAATGGCT-GATAAGTTATGATATAT 437214 vivviii iiiv ii v -i i i i L1ME3F_3end#L 484 CAACCCAAATGTCCATCGACAGGAGAATGGATAAATAAATTGTGGTATAT 533 chr2ptel1M 437215 GAATGTTATGGAATATTAT 437233 vv iiiv L1ME3F_3end#L 534 TCACACAATGGAATATTAT 552 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.80 CpG sites = 23, Kimura (unadjusted) = 41.97 Transitions / transversions = 1.92 (23/12) Gap_init rate = 0.05 (6 / 117), avg. gap size = 1.00 (6 / 6) 229 31.85 5.19 0.00 chr2ptel1M 437142 437276 (562724) L1MC5a_3end#LINE/L1 460 601 (2176) m_b66s551i13 2439 chr2ptel1M 437142 TTTGCAGTGGCAAGGAACTGGAAACTGAATGGATGTCCATCAGTTGGGAA 437191 i i i iii vivviii i v i L1MC5a_3end#L 460 TTTGTAATAGCAAAAGACTGGAAACAACCCAAATGTCCATCAATAGGGGA 509 chr2ptel1M 437192 ATGGCTG-ATAAGTTATGATATATGAATGTTATGGAATATTATTGTTCTA 437240 v i - ii i i vv iiiv i i vvvv i L1MC5a_3end#L 510 CTGGTTGAATAAACTATGGTACATCCACACAATGGAGTACTATGCAGCTG 559 chr2ptel1M 437241 TAA----GAATCAGCAGGAT-TTTAGA-ACTGATGCTGAGTG 437276 ---- v v i - i v - ? iiv L1MC5a_3end#L 560 TAAAAAGGAATGAGGAAGATCTCTATATACTGNTATGGAGTG 601 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.77 CpG sites = 27, Kimura (unadjusted) = 43.77 Transitions / transversions = 1.69 (27/16) Gap_init rate = 0.03 (4 / 134), avg. gap size = 1.75 (7 / 4) 304 27.17 1.09 0.00 chr2ptel1M 437142 437233 (562767) L1ME3G_3end#LINE/L1 456 548 (376) m_b66s551i12 2439 chr2ptel1M 437142 TTTGCAGTGGCAAGGAACTGGAAACTGAATGGATGTCCATCAGTTGGGAA 437191 i i i i ii i vivv ii i v i L1ME3G_3end#L 456 TTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCAATAGGGGA 505 chr2ptel1M 437192 ATGGCT-GATAAGTTATGATATATGAATGTTATGGAATATTAT 437233 i -i i i vv ii i L1ME3G_3end#L 506 ATGGTTAAATAAATTATGGTATATCCATACTATGGAATACTAT 548 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.18 CpG sites = 19, Kimura (unadjusted) = 36.02 Transitions / transversions = 3.17 (19/6) Gap_init rate = 0.01 (1 / 91), avg. gap size = 1.00 (1 / 1) 17 0.00 0.00 0.00 chr2ptel1M 437517 437535 (562465) (TG)n#Simple_repeat 1 19 (0) m_b66s252i13 2440 chr2ptel1M 437517 TGTGTGTGTGTGTGTGTGT 437535 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGT 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 13 17.11 3.03 0.00 chr2ptel1M 438724 438756 (561244) (AAAG)n#Simple_repeat 1 34 (0) m_b66s252i14 2441 chr2ptel1M 438724 AAAGAAAGAAAAAAACTGGGAAAG-AAGAAAGAA 438756 i vvii - (AAAG)n#Simpl 1 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAA 34 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 2036 29.21 5.43 1.39 chr2ptel1M 438897 440000 (560000) L1M5_orf2#LINE/L1 1053 2200 (1094) m_b66s551i14 2442 chr2ptel1M 438897 AAATAAGAAAACTATTGAGCTAATAAATAAAACTAAGAGTTGGTTTTATG 438946 i i? ? v v vv v ii i i i i i v L1M5_orf2#LIN 1053 AAACAAANANACAATAGAGAAAATCAACGAAGCCAAAAGCTGGTTCTTTG 1102 chr2ptel1M 438947 AAAAATAAACAATAAAATAGATAAACCTTTGGTTAATTTGATTAAAAAAA 438996 i-- v v i i i? ivi i i L1M5_orf2#LIN 1103 AAAAG--ATCAATAAAATTGATAAACCTCTAGCNAGACTGATCAAGAAAA 1150 chr2ptel1M 438997 GGAAAGAAGAAAAC-CAAATTACCAGAATCAAAAGTGAAAAGGGTAAACA 439045 ii i - i - iv ii i i - i L1M5_orf2#LIN 1151 AAAGAGA-GAAGACACAAATTACCAATATCAGGAATGAAAAAGG-AGACA 1198 chr2ptel1M 439046 TCACTAACAGA------GGAAATTAAAGCAACAATTTGGAGCTATTTTGC 439089 - ------i v ivi i vv iiiv v v L1M5_orf2#LIN 1199 TCACTA-CAGATCCTACAGACATTAAAAGGATAATAAGAGAATATTATGA 1247 chr2ptel1M 439090 CTAATTGTACGCAGATAAATCTGATAATCTAAGCAAAATGGATGTTTGCA 439139 vi i v i vi i ? ii iiii iivv v v L1M5_orf2#LIN 1248 ACAACTTTATGCCAATAAATTTGANAACTTAGATGAAATGGACAAATTCC 1297 chr2ptel1M 439140 TACAAAAATATGGATTACTCAGATTAACAGATGAGGAAATAAATTACTTA 439189 vv i iii? iv i i i ?v v i i vv ii i L1M5_orf2#LIN 1298 TTGAAAAACACAANTTACCAAAACTGACNCAAGAAGAAATAGAAAATCTG 1347 chr2ptel1M 439190 AATAGTCCCCC--CCAAAAAAGAAATTGAGCAAGCCATTAATGAACTTCT 439237 i ivi-- i vv iivv iv vi v i L1M5_orf2#LIN 1348 AATAGCCCTATATCTATTAAAGAAATTGAATTTGTAATTAAAAACCTTCC 1397 chr2ptel1M 439238 AAGAAAAAAATCTTCAGGGCCAGATAGATTTATAAGTGAATTCTACCAAT 439287 v v i v i v i v i ivi v L1M5_orf2#LIN 1398 CACAAAGAAAACTCCAGGCCCAGATGGCTTCACTGGTGAATTCTACCAAA 1447 chr2ptel1M 439288 CATTTAA--AAGA--CAATTACAATACTATATAAACT--TCAGAAAAATA 439331 -- --i vv vi i i -- vii L1M5_orf2#LIN 1448 CATTTAAGGAAGAAATAATACCAATCTTACACAAACTCTTCCAGAAAATA 1497 chr2ptel1M 439332 GATTTTAAAAAA---AAC-CTACCAAATTACATTTTATGACACAAATATG 439377 ---- i --- - v v i - vi v ii ? L1M5_orf2#LIN 1498 GA----AAAAGAGGGAACACTTCCCAACT-CATTTTATGAGGCCAGCATN 1542 chr2ptel1M 439378 GCACCAATATCTAAACCAGGAAAGGACA----AAACAAAAAAAATTATAA 439423 i v ii i v ? iv i ---- iv i i i L1M5_orf2#LIN 1543 ACCCTGATACCAAAACCNGACAAAGACATTACAAGAAAAGAAAATTACAG 1592 chr2ptel1M 439424 GCTGATTTTCCTAAATGAATATTGTTGCAAAAATCTTAAATAAATTACCA 439473 i ii v i v - i v v i ? i v ii L1M5_orf2#LIN 1593 ACCAATATCCCTCA-TGAACATAGATGCAAAAATCCTNAACAAAATATTA 1641 chr2ptel1M 439474 GCAAA-GAAATCACAGTAAGTTACTATCAGGATAATATGCTATGACCACG 439522 -vi - i vv iv vv iiii v L1M5_orf2#LIN 1642 GCAAATCGAATC-CAGCAATATATAAAAAGGATAATACATCATGACCAAG 1690 chr2ptel1M 439523 TGGAATTTATACTAAAAATTCAGGAATGGTTCAGTATTAGGAAAACTATC 439572 ii v i ii v i iv i ii v i v v L1M5_orf2#LIN 1691 TGGGGTTTATCCCAGGAATGCAAGGTTGGTTTAACATTCGAAAATCAATC 1740 chr2ptel1M 439573 AGCATAATTGGCCATATTGATA--ATCAAATTAATAGAAATCGTGTGATT 439620 iii vi i i -- v i--i v i i i i L1M5_orf2#LIN 1741 AATGTAATTCACCATATTAACAGAATAAAG--GAGAAAAATCATATGATC 1788 chr2ptel1M 439621 ATATCAATAGATGCAGAAAAACCATTTGACAAAATACAATACCTGTTTCT 439670 v v v i ii iv L1M5_orf2#LIN 1789 ATCTCAATAGATGCAGAAAAAGCATTTGACAAAATTCAACACCCATTCAT 1838 chr2ptel1M 439671 -ATTTAAACACTAGAGAAGAC-AAAAATAATTGGAGTTTTCCTTAAAATA 439718 - vv v v- v i - ii ivv iivi i vv i L1M5_orf2#LIN 1839 GATAAAAACTCTC-AGCAAACTAGGAATAGAAGGGAACTTCCTCAACCTG 1887 chr2ptel1M 439719 ATAAATAGAATCTATCTAAAACTATTAGCAAGCATTATGTGTAATGAGGA 439768 vi v ivv ivvi ? i i iiv iv L1M5_orf2#LIN 1888 ATAAAGGGCATCTACGAAAAACCTACAGCNAACATCATACTTAATGGTGA 1937 chr2ptel1M 439769 TAAGCTAGAAGCATTTCCAATAAGATCAGGGATGAAACAAGGTTCCCCAT 439818 v ?i ii ? v i vv i i ii i v vi ii L1M5_orf2#LIN 1938 AANACTGAANGCTTTCCCCCTAAGATCGGGAACAAGACAAGGATGTCCGC 1987 chr2ptel1M 439819 TATCACCACTATTATTCAATATTATACTAGGAATGTTAGTTTTATTAATA 439868 ? vi i i i iii vi iivvvvi L1M5_orf2#LIN 1988 TNTCACCACTTCTATTCAACATTGTACTGGAGGTCCTAGCCAGTGCAATA 2037 chr2ptel1M 439869 AGGGAAGAAAAAGAAAT--------TAA-----GGGAATGAAGAAACAA- 439904 v -------- ----- i v i - L1M5_orf2#LIN 2038 AGGCAAGAAAAAGAAATAAAAGGCATAAAGATTGGAAAGGAAGAAATAAA 2087 chr2ptel1M 439905 --TGGTATCATTCTGCAAGTGA--TGATGATATATTTAGAGAATC----A 439946 -- vi? i - ii -- vi ? iv i ---- L1M5_orf2#LIN 2088 ACTGTCNTTATTC-GCAGATGACATGATTGTNTACGTAGAAAATCCNAAA 2136 chr2ptel1M 439947 G---CTAAAAAAAAAGTACTAGAAACAATG-------TTAGCCAAGTTGC 439986 --- v ? v vi i------- v i i L1M5_orf2#LIN 2137 GAATCTACAAANAAACTACTAGAACTAATAAGTGAATTTAGCAAGGTCGC 2186 chr2ptel1M 439987 AAGATAAAATGTCA 440000 ?i v v L1M5_orf2#LIN 2187 NGGATACAAGGTCA 2200 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.96 CpG sites = 194, Kimura (unadjusted) = 39.09 Transitions / transversions = 1.56 (194/124) Gap_init rate = 0.03 (37 / 1103), avg. gap size = 2.05 (76 / 37) 253 30.86 3.76 3.76 chr2ptel1M 441919 442184 (557816) L1M4a2_5end#LINE/L1 1661 1926 (730) m_b66s551i15 2443 chr2ptel1M 441919 CACAGAGATCCTTTCCCATAGAAATATTATTGCCAAATT-TTGAATTGTC 441967 v viv -- v i i v i i - v- i L1M4a2_5end#L 1661 CAAAGAGATCCACACC--TAGACACATCATAGTCAAACTGTTGAAA-GCC 1707 chr2ptel1M 441968 AG-GTCAAAGAGAAAATTTTGCAAGAAACAAGGGAAAAA-AATTCA-CAT 442014 i- v i v v i i -i i - i L1M4a2_5end#L 1708 AAAGACAAAGAGAAAATCTTGAAAGCAGCAAGAGAAAAACGACTCATCAC 1757 chr2ptel1M 442015 TTTCTTTTGAACTACAATTAG---AATTGCACAGTACTTATCAGAAGCCA 442061 v v vvvv ?? v --- iv vv v v i --- L1M4a2_5end#L 1758 GTACAGGGGAACNNCAATAAGATTAACGGCTGACTTCTCATCAGAA---A 1804 chr2ptel1M 442062 TAATAAAAGAAACTAGGTCCTAGAATCCTATCTATTGACAAT--CAAATG 442109 i ii i vv vv ivv i i --v iv v v i --ii v L1M4a2_5end#L 1805 CAATGGAGGCCAGAAGGCAGTGGGAT--GACATATTCAAAGTGCTGAAAG 1852 chr2ptel1M 442110 AACTAGGCCAGCAGCCAAAAATATCATATCCAACAAAATTAT-CTGTAAT 442158 vv ii iiv i i vii i i - vi v L1M4a2_5end#L 1853 AAAAAAACTGTCAACCAAGAATTCTATATCCAGCAAAACTATCCTTCAAA 1902 chr2ptel1M 442159 ATTGAATGAGAAAAAAATGGACATTC 442184 v v v v -- L1M4a2_5end#L 1903 AATGAAGGCGAAATAAA--GACATTC 1926 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.62 CpG sites = 37, Kimura (unadjusted) = 40.54 Transitions / transversions = 0.88 (37/42) Gap_init rate = 0.06 (17 / 265), avg. gap size = 1.18 (20 / 17) 36 0.00 0.00 0.00 chr2ptel1M 442540 442570 (557430) (AC)n#Simple_repeat 1 31 (0) c_b66s251i1 2444 chr2ptel1M 442540 ACACACACACACACACACACACACACACACA 442570 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACA 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 32 3.23 0.00 0.00 chr2ptel1M 442970 443001 (556999) (AT)n#Simple_repeat 1 32 (0) c_b66s251i2 2445 chr2ptel1M 442970 ATATATATATATATATATATATATATGTATAT 443001 i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATAT 32 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 25 6.68 0.00 0.00 chr2ptel1M 443209 443240 (556760) (A)n#Simple_repeat 1 32 (0) m_b66s252i15 2446 chr2ptel1M 443209 AAAAAAAAAAAAAAAAAAAAAAAAGGAAAAAA 443240 ii (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 32 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 18 17.33 4.35 0.00 chr2ptel1M 443476 443521 (556479) (AATTT)n#Simple_repeat 1 48 (0) m_b66s252i16 2447 chr2ptel1M 443476 AATTAAATTTAA-TT-AGTTAATTAAAGGTAATTAAATTTAAGTTAAT 443521 v - - v v vv v v (AATTT)n#Simp 1 AATTTAATTTAATTTAATTTAATTTAATTTAATTTAATTTAATTTAAT 48 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.04 (2 / 45), avg. gap size = 1.00 (2 / 2) 350 33.90 5.37 0.70 chr2ptel1M 443522 443931 (556069) L1M4_orf2#LINE/L1 1022 1450 (1844) m_b66s551i16 2443 chr2ptel1M 443522 TAAAAATTAAAGATGAGATTAATACAACTGAGTTTTTAAAAGTCATTGAA 443571 i i vv i v iv iv vv vv iiv v i L1M4_orf2#LIN 1022 TAAAGATTAGAGCGGAAATAAATGAAATAGAGAATAGAAAAACAATAGAG 1071 chr2ptel1M 443572 TTAATAAATAAAGCTAAAAGTTACTTCTATGAAAAAA-----AATATTAA 443616 vv v ii i i iv v i ----- v i L1M4_orf2#LIN 1072 AAAATCAACGAAACCAAAAGTTGGTTCTTTGAAAAGATCAACAAAATTGA 1121 chr2ptel1M 443617 CCATTGTTTAATAATTTTAA--AAGAGACAAAG---GAAAGC-CAAATCA 443660 v viv iiv vvi i -- i v --- ii - i L1M4_orf2#LIN 1122 CAAACCTTTAGCTAGACTGACCAAGAAAAAAAGAGAGAAGACTCAAATTA 1171 chr2ptel1M 443661 ATAGAATTAAAAATGAAAAGGGTGA--TTA-TGTCAGTAGTAAAGATTAG 443707 v i i ii ii v -- - ii iiivv v ---i L1M4_orf2#LIN 1172 CTAAAATCAGGAATGAAAGAGGGGACATTACTACCGACCTTACAGA---A 1218 chr2ptel1M 443708 ATCAAAATAATTAAAAGGAGTTATCTTGCCCAATTATATGCCAGTAAATT 443757 v vi v iiv iiv vv i ii L1M4_orf2#LIN 1219 ATAAAAAGGATTATAAGGGAATACTATGAACAATTGTATGCCAACAAATT 1268 chr2ptel1M 443758 TAATAATATAAGGGAAATAGAAGAATATTT-GCAAGATATAAACTGCCTA 443806 vi iv iiv i vi vii - v i i i v L1M4_orf2#LIN 1269 AGATAACCTAGATGAAATGGACAAATTCCTAGAAAGACACAAACTACCGA 1318 chr2ptel1M 443807 GATTAACAGAAGAGGAAATAGAATATCTAAATAAATCTATTTTAGAAAAA 443856 i i i vv i v i i i vvi iiv L1M4_orf2#LIN 1319 AACTGACTCAAGAAGAAATAGAAAATCTGAATAGACCTATAACAAGTAAA 1368 chr2ptel1M 443857 GAAATTGAAGAGGCTATAAATGAGCTTCCT----AGAAAAA---AGTATC 443899 i vvi iv v vi i i---- i--- v?i L1M4_orf2#LIN 1369 GAGATTGAATTAGTAATCAAAAAACTTCCCACAAAGAAAAGCCCAGGNCC 1418 chr2ptel1M 443900 AGATGGATTTGAAAGTGATTTCTGCCTCACAT 443931 v iivvi v i vv L1M4_orf2#LIN 1419 AGATGGCTTCACTGGTGAATTCTACCAAACAT 1450 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 45.65 CpG sites = 77, Kimura (unadjusted) = 46.64 Transitions / transversions = 1.26 (77/61) Gap_init rate = 0.03 (12 / 409), avg. gap size = 2.08 (25 / 12) 16 0.00 0.00 0.00 chr2ptel1M 444264 444281 (555719) (TC)n#Simple_repeat 1 18 (0) m_b66s252i17 2448 chr2ptel1M 444264 TCTCTCTCTCTCTCTCTC 444281 (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTC 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 33 0.00 0.00 0.00 chr2ptel1M 444282 444312 (555688) (T)n#Simple_repeat 1 31 (0) c_b66s251i3 2449 chr2ptel1M 444282 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 444312 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 47 0.00 0.00 0.00 chr2ptel1M 445067 445106 (554894) (AC)n#Simple_repeat 1 40 (0) c_b67s251i1 2450 chr2ptel1M 445067 ACACACACACACACACACACACACACACACACACACACAC 445106 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACAC 40 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 239 28.35 6.67 0.70 chr2ptel1M 445193 445327 (554673) L1ME4a_3end#LINE/L1 391 533 (338) m_b67s551i1 2443 chr2ptel1M 445193 GGTATCTATCCTAAGCCAAACAA-----GATCT-AACTAAAA---ATGAA 445233 v i v- i ----- v -? v i --- v L1ME4a_3end#L 391 GGAATTTATCCTAAGG-AAATAATCAGAGATGTGNACAAAGATTTATGTA 439 chr2ptel1M 445234 CAATAATATTGATAGCAGCCTTTTTTATGGTGCCAAAAAATTGGAAATCA 445283 vi i v v v v ii iv i iv L1ME4a_3end#L 440 CAAGGATGTTCATCGCAGCATTATTTATAATAGCGAAAAATTGGAAACAA 489 chr2ptel1M 445284 AGGAACTTTTTACCAATTAAGAAATGGCTAAACCAATTATGATA 445327 vvv v v ii v vii i ? i iv i L1ME4a_3end#L 490 CCTAAATGTCCAACAATAGGGGANTGGTTAAATAAATTATGGTA 533 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.46 CpG sites = 18, Kimura (unadjusted) = 36.63 Transitions / transversions = 0.90 (18/20) Gap_init rate = 0.03 (4 / 134), avg. gap size = 2.50 (10 / 4) 258 32.00 0.00 0.00 chr2ptel1M 445229 445328 (554672) L1ME3G_3end#LINE/L1 428 527 (397) m_b67s551i2 2443 chr2ptel1M 445229 ATGAACAATAATATTGATAGCAGCCTTTTTTATGGTGCCAAAAAATTGGA 445278 v vi i v v v v i ii iv i L1ME3G_3end#L 428 ATGTACAAGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGA 477 chr2ptel1M 445279 AATCAAGGAACTTTTTACCAATTAAGAAATGGCTAAACCAATTATGATAT 445328 iv vvv v v ii i vii i i iv i L1ME3G_3end#L 478 AACAACCTAAATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGTAT 527 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 40.85 CpG sites = 17, Kimura (unadjusted) = 42.58 Transitions / transversions = 1.13 (17/15) Gap_init rate = 0.00 (0 / 99), avg. gap size = 0.0 (0 / 0) 17 4.94 0.00 0.00 chr2ptel1M 446116 446136 (553864) (C)n#Simple_repeat 1 21 (0) m_b67s252i1 2451 chr2ptel1M 446116 CCCCCCCCCCCGCCCCCCCCC 446136 v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCC 21 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 191 34.11 2.38 3.13 chr2ptel1M 446325 447161 (552839) (AGGG)n#Simple_repeat 1 824 (134) m_b67s252i2 2452 chr2ptel1M 446325 AGGGAGAGAAGTGGAGGAGAAAAAAAGAGGAGAGGG-GATAGAGAGGTTG 446373 - i - - iii ii - - iv i vv (AGGG)n#Simpl 1 AGGGAG-GGAG-GGAGG-GAGGGAGGGAGG-GAGGGAGGGAGGGAGGGAG 46 chr2ptel1M 446374 AGGAGAGAGGGACAAGAGGGGAGGGAAGGA-GAAAGAAAGAAGGAAGAGA 446422 - i -ii - i - i i i i i i i (AGGG)n#Simpl 47 -GGAGGGAGGGA-GGGA-GGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGA 93 chr2ptel1M 446423 GAGGAGGGGGAAGAGGAAGAAAGATAAGAAAGAGAAGGAGAAAGTGGGAA 446472 - i -i i ii -vi ii i i ii - iii (AGGG)n#Simpl 94 G-GGAGGGAG-GGAGGGAGGGAG-GGAGGGAGGGAGGGAGGGAG-GGAGG 139 chr2ptel1M 446473 GAGAGATTGAGGGACAGAGAAAGACAGAGTGAGTGAGAGAGAAAGAGAGA 446522 i vv vi ii iv i v i v i i ii i (AGGG)n#Simpl 140 GAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGA 189 chr2ptel1M 446523 CAGAGAGAGCGAGAGAGAGAGAGAGAGAGAGAGAGAGAGACAAAGACAGA 446572 vi i v i i i i i i i vii iv i (AGGG)n#Simpl 190 GGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGG 239 chr2ptel1M 446573 CAGAGAAGGGGGGA-GGAGGAGAAGGAGGGAGGGAGAGAGGGAGGAAAGG 446621 v i i i - - i i i i (AGGG)n#Simpl 240 GAGGGAGGGAGGGAGGGAGG-GAGGGAGGGAGGGAGGGAGGGAGGGAGGG 288 chr2ptel1M 446622 TAGGAGAGAGAGA-GAAGGAGAGAAAGGGAGAG-GGGAGAAAGAGAGGG- 446668 vi i i - i - ii i - ii i - (AGGG)n#Simpl 289 AGGGAGGGAGGGAGGGAGG-GAGGGAGGGAGGGAGGGAGGGAGGGAGGGA 337 chr2ptel1M 446669 GGAAGGGAGGGAGGGAGAGAGACAAAGACAGAGAGACAGAGACAGACAGA 446718 i i iv ii vi i vi iv iv - (AGGG)n#Simpl 338 GGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAG- 386 chr2ptel1M 446719 GGGGAGAGGAAGGAAAGGAGAGAGAGAGGGAGGGAAGAAGAGGGAAGGAA 446768 i i i i i i i - -i i i (AGGG)n#Simpl 387 GGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGG-AG-GGAGGGAGGGAG 434 chr2ptel1M 446769 GGAAGGAAAGAGAGGAGGGGAAGGA-AGAGGGAAGGAGGGA-GGAAGGA- 446815 i ii - - i -i i - i - (AGGG)n#Simpl 435 GGAGGGAGGGAG-GGA-GGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAG 482 chr2ptel1M 446816 GGAAGGAGAGAGGGA--GAGGGAGAGGGGGAGAACCAGAAGGGGAGAGAG 446863 i i -- i i iivvi i i i i (AGGG)n#Simpl 483 GGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGG 532 chr2ptel1M 446864 AGACAGAGACAGAGAGACACAGAGAGAGAGACAGACAGAGACAGAGAGAC 446913 iv i vi i viv i i iv iv i vi i v (AGGG)n#Simpl 533 AGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAG 582 chr2ptel1M 446914 ACAGAGAGACAGAGAGGAAGGGGAAGGA-GGAAAGAGGAAAGGAAGGAGG 446962 iv i iv i i - i - ii i i i (AGGG)n#Simpl 583 GGAGGGAGGGAGGGAGGGA-GGGAGGGAGGGAGGGAGGGAGGGAGGGAGG 631 chr2ptel1M 446963 GACAGAAAGGGAGGGA-GGAGGAAGAAGAGAAAGGGAGGGAGGAAAGAGA 447011 -- ii - i -i ii -i i (AGGG)n#Simpl 632 G--AGGGAGGGAGGGAGGGAGGGAG-GGAGGGAGGGAGGGAGG-GAGGGA 677 chr2ptel1M 447012 GACAGAGAAGGTGAAGCAGGGAGGGA-AAAGAGAAGGAGAGAGAGACAGA 447060 iv - i - i v -ii i i i i vi (AGGG)n#Simpl 678 GGGAG-GGAGG-GAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGA 725 chr2ptel1M 447061 GACAGAGAGACTGAGAGACAGGGGGAGGA-AGAAGGAGAGAGGGAGGGAA 447109 iv i ivv i iv i - -i i i -- (AGGG)n#Simpl 726 GGGAGGGAGGGAGGGAGGGAGGGAG-GGAGGGAGGGAGGGAGGGAGGG-- 772 chr2ptel1M 447110 AGGGAGGGAAGGAAGGAGGGAAAGTGGGGGAGGG-GGGA-AGAGGAAAGG 447157 i i -- v i - -i i i (AGGG)n#Simpl 773 AGGGAGGGAGGGAGGGAGGG--AGGGAGGGAGGGAGGGAGGGAGGGAGGG 820 chr2ptel1M 447158 AGGG 447161 (AGGG)n#Simpl 821 AGGG 824 Matrix = Unknown Transitions / transversions = 4.15 (170/41) Gap_init rate = 0.06 (46 / 836), avg. gap size = 1.02 (47 / 46) 27 2.76 5.41 0.00 chr2ptel1M 447162 447198 (552802) (AGAGAC)n#Simple_repeat 1 39 (0) c_b67s251i2 2453 chr2ptel1M 447162 AGAGACAGAGACAGAGAC--ACACAGAGACAGAGACAGA 447198 -- v (AGAGAC)n#Sim 1 AGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGA 39 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.03 (1 / 36), avg. gap size = 2.00 (2 / 1) 191 34.11 2.38 3.13 chr2ptel1M 447199 447325 (552675) (AGGG)n#Simple_repeat 825 957 (1) m_b67s252i2 2454 chr2ptel1M 447199 CCGAGAGCCAGAGAGAGCG-GGGAAGAAGGGAAGGAGGGAGGGAGGAAGA 447247 vv i vvi i v - i i i i i (AGGG)n#Simpl 825 GGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGG 874 chr2ptel1M 447248 AAGAGAGGAAGGGAGGGA-GGAGAGAGAAAGAGAGAGAGGGA--GAGGGA 447294 i i i - i ii i i -- (AGGG)n#Simpl 875 GAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGA 924 chr2ptel1M 447295 AAGAGAGGGGGAGGGAGGGAGGGA--GAGGGAG 447325 ii i i -- (AGGG)n#Simpl 925 GGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAG 957 Matrix = Unknown Transitions / transversions = 4.00 (20/5) Gap_init rate = 0.03 (4 / 126), avg. gap size = 1.50 (6 / 4) 20 20.52 0.00 0.00 chr2ptel1M 447907 447945 (552055) (C)n#Simple_repeat 1 39 (0) m_b67s252i3 2455 chr2ptel1M 447907 CCCCGCCCCCACCCCCTCCACCCCTCGCCCCCCACCCCC 447945 v v i v i v v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 39 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 14 16.38 2.94 0.00 chr2ptel1M 448147 448180 (551820) (TGGGGG)n#Simple_repeat 1 35 (0) m_b67s252i4 2456 chr2ptel1M 448147 TGGGGGTGGGGG-GCGGTAGGAGATGGGGGTGGGG 448180 - v vv i i (TGGGGG)n#Sim 1 TGGGGGTGGGGGTGGGGGTGGGGGTGGGGGTGGGG 35 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 17 5.00 0.00 0.00 chr2ptel1M 450746 450766 (549234) (TA)n#Simple_repeat 1 21 (0) m_b67s252i5 2457 chr2ptel1M 450746 TATACATATATATATATATAT 450766 i (TA)n#Simple_ 1 TATATATATATATATATATAT 21 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 16 4.50 0.00 0.00 chr2ptel1M 455117 455139 (544861) (TGC)n#Simple_repeat 1 23 (0) m_b67s252i6 2458 chr2ptel1M 455117 TGCTGCTGCTGCTGCTGCTGGTG 455139 v (TGC)n#Simple 1 TGCTGCTGCTGCTGCTGCTGCTG 23 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 188 24.62 3.08 0.00 chr2ptel1M 458050 458114 (541886) MIRc#SINE/MIR 202 268 (0) m_b67s601i0 2459 chr2ptel1M 458050 GATGATG-GTGT-AAAGCCCTTTGCAAGTCTTAAAGGGACATAGAAATGT 458097 i -i - v i iiiv v vi v MIRc#SINE/MIR 202 GATAATGTATGTGAAAGCGCTTTGTAAACTGTAAAGTGCTATACAAATGT 251 chr2ptel1M 458098 CAGTTATTATTATCATT 458114 v v?i i MIRc#SINE/MIR 252 AAGGNGTTATTATTATT 268 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 30.94 CpG sites = 9, Kimura (unadjusted) = 30.94 Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.03 (2 / 64), avg. gap size = 1.00 (2 / 2) 449 26.18 5.51 0.75 chr2ptel1M 458151 458277 (541723) MIRc#SINE/MIR 14 146 (122) m_b67s601i1 2460 chr2ptel1M 458151 TATAATGCACAGAGTGCCACATGTGGAGTGAGGAAGACCTAAGCTCAATG 458200 ii i v v ii iiv iv v ii i i - MIRc#SINE/MIR 14 TGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGA-G 62 chr2ptel1M 458201 TAAC--TTCAGATACTTATTAGCTACATGACCCTGGGCAAGTCATTTAA- 458247 vv --i v vi i iii i i - MIRc#SINE/MIR 63 TCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAAC 112 chr2ptel1M 458248 CTCT----ACCTCAGTTTTGTCATCTGCAAAATG 458277 ----i iv i MIRc#SINE/MIR 113 CTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATG 146 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 32.44 CpG sites = 23, Kimura (unadjusted) = 33.71 Transitions / transversions = 2.30 (23/10) Gap_init rate = 0.03 (4 / 126), avg. gap size = 2.00 (8 / 4) 49 39.67 2.19 1.91 chr2ptel1M 462493 462858 (537142) (TCTA)n#Simple_repeat 1 367 (0) m_b67s252i7 2461 chr2ptel1M 462493 TCTATCTTTCTATCTTCCTCCCTGACTGGCTGGCTGGCT-GCTATCTGCC 462541 v vi vi iv iv iv iv -v ii (TCTA)n#Simpl 1 TCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATC 50 chr2ptel1M 462542 T-GCCATTCATCCATCCATCCTCCCT-CCTATCCATCT-CCCATCCCTCC 462588 -v i ii i i - vi -i i -i i iv i (TCTA)n#Simpl 51 TATCTATCTATCTATCTAT-CTATCTATCTATCTATCTATCTATCTATCT 99 chr2ptel1M 462589 ATCTGTCAGTGTAAGCT-TCTTTCTATTCATCCAGCCAGCCATTTATCTG 462637 i vi v - v - v ii i v i v i i i (TCTA)n#Simpl 100 ATCTATCTATCT-ATCTATCTATCTATCTATCTATCTATCTATCTATCTA 148 chr2ptel1M 462638 CCAATCAATCTACTCCCTCTTTCTATTTATCCAACCAGCCATCTATCCAA 462687 i v v - iv v i i v i v i - v (TCTA)n#Simpl 149 TCTATCTATCTA-TCTATCTATCTATCTATCTATCTATCTATCTAT-CTA 196 chr2ptel1M 462688 TCAGTCTATCTACTTCTCTTTCTTTTTATCCAATTATTCATCCATCCAGC 462737 vi ii v v v i i vi ii i i v (TCTA)n#Simpl 197 TCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATC 246 chr2ptel1M 462738 TACTTGTCAATCTGTCCCTCTTTCTGTTCATCCAACTGGTC-ATCTATCC 462786 ii i v i iv v i ii i v -i - i (TCTA)n#Simpl 247 TATCTATCTATCTATCTATCTATCTATCTATCTATCT-ATCTATCTATCT 295 chr2ptel1M 462787 AGTC-AACCATCTATCCATCTATCTA-CTCCTCTTTCTAATTATCCAATT 462834 - - v i i - -v v vi i vi (TCTA)n#Simpl 296 A-TCTATCTATCTATCTATCTATCTATCT-ATCTATCTATCTATCTATCT 343 chr2ptel1M 462835 ATTCATCCTTCCATCCATCTATCT 462858 ii iv i i (TCTA)n#Simpl 344 ATCTATCTATCTATCTATCTATCT 367 Matrix = Unknown Transitions / transversions = 1.65 (66/40) Gap_init rate = 0.04 (15 / 365), avg. gap size = 1.00 (15 / 15) 241 31.34 1.49 0.00 chr2ptel1M 463162 463228 (536772) MIRc#SINE/MIR 113 180 (88) m_b67s601i2 2462 chr2ptel1M 463162 CTCTCTGAGCCTTGGTTTCTTTATCTG-AGAATGGAGACAATGGTCTTTG 463210 ii i i - i i i ii vii MIRc#SINE/MIR 113 CTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTG 162 chr2ptel1M 463211 TACAATCCATCCCAGAGG 463228 iv vii i i i v MIRc#SINE/MIR 163 CCCTGCCTACCTCACAGG 180 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 45.05 CpG sites = 17, Kimura (unadjusted) = 45.05 Transitions / transversions = 4.25 (17/4) Gap_init rate = 0.02 (1 / 66), avg. gap size = 1.00 (1 / 1) 21 33.56 0.00 0.00 chr2ptel1M 463746 463816 (536184) (TT)n#Simple_repeat 1 71 (0) m_b67s252i8 2463 chr2ptel1M 463746 TTTTTCTTTTGGGTTTTTTTTTTTTTTTTATTTCTCTCTCTCATGGTTTT 463795 i vvv v i i i i iv vv (TT)n#Simple_ 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr2ptel1M 463796 TCCCTTTTGTTCTATTTTTTT 463816 iii v i v (TT)n#Simple_ 51 TTTTTTTTTTTTTTTTTTTTT 71 Matrix = Unknown Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0) 192 20.93 0.00 0.00 chr2ptel1M 464235 464277 (535723) C MIR#SINE/MIR (192) 70 28 m_b67s601i3 2464 chr2ptel1M 464235 GCAGGGCTGGGATTCCAGCCCAAGCCTTCTGACTGCAGAGCCC 464277 i i v i i vv i v C MIR#SINE/MIR 70 GCAGAGCCGGGATTCGAACCCAGGCAGTCTGGCTCCAGAGCCC 28 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 21.83 CpG sites = 5, Kimura (unadjusted) = 24.84 Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 199 23.20 1.41 2.86 chr2ptel1M 466969 467039 (532961) C L3b_3end#LINE/CR1 (300) 906 837 m_b67s601i4 2465 chr2ptel1M 466969 TCCTTTTCATAACAACCCTACAAATACGTGAAGCCAGAC-TTAAGTGGAG 467017 i v i i v v v v ? vi- v?vv C L3b_3end#LINE 906 TCCTCTACGTAATAACCCTTCATATACTTGAAGACNGTTATTAAGTCNCC 857 chr2ptel1M 467018 CTTCCGAGTCTTCCCTTCTCCA 467039 i -- i i C L3b_3end#LINE 856 CCTC--AGCCTTCTCTTCTCCA 837 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 26.84 CpG sites = 7, Kimura (unadjusted) = 28.85 Transitions / transversions = 0.78 (7/9) Gap_init rate = 0.04 (3 / 70), avg. gap size = 1.00 (3 / 3) 209 26.15 6.15 0.00 chr2ptel1M 467053 467117 (532883) MIRb#SINE/MIR 19 87 (181) m_b67s601i5 2466 chr2ptel1M 467053 CAGTGGAGAGATT-TGAGAT---GAGTCAGAAAGACCTGAGTTCAAATCC 467098 i vi-i i v --- v i i MIRb#SINE/MIR 19 CAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCGAATCC 68 chr2ptel1M 467099 AAGCCCCCACACTTTCTGG 467117 vi i ivv v i MIRb#SINE/MIR 69 CGGCTCTGCCACTTACTAG 87 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 26.26 CpG sites = 10, Kimura (unadjusted) = 32.90 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.03 (2 / 64), avg. gap size = 2.00 (4 / 2) 412 16.46 6.33 0.00 chr2ptel1M 467142 467220 (532780) MIRb#SINE/MIR 171 254 (14) m_b67s601i6 2466 chr2ptel1M 467142 CAGTGTTGTTGTGAGGATCA-----GATAACATTTGTCAAGTGCTTAGCA 467186 v i ----- iiiv v i MIRb#SINE/MIR 171 CAGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGCA 220 chr2ptel1M 467187 CAGTGCCTGGCACACAGTAGATGCTCTATAAATG 467220 i iii v MIRb#SINE/MIR 221 CAGTGCCTGGCACATAGTAAGCGCTCAATAAATG 254 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 15.93 CpG sites = 9, Kimura (unadjusted) = 18.99 Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.01 (1 / 78), avg. gap size = 5.00 (5 / 1) 13 18.40 0.00 7.50 chr2ptel1M 467224 467266 (532734) (CTTCC)n#Simple_repeat 1 40 (0) m_b67s252i9 2467 chr2ptel1M 467224 CTTCCCTTTCTCTCCCTTCCCATCCCCAGGCCCTTCCCTATCC 467266 i ii - i -vv - (CTTCC)n#Simp 1 CTTCCCTTCCCTTCCCTTCCC-TTCCC-TTCCCTTCCCT-TCC 40 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.07 (3 / 42), avg. gap size = 1.00 (3 / 3) 16 32.57 0.00 0.00 chr2ptel1M 467794 467846 (532154) (TT)n#Simple_repeat 1 53 (0) m_b67s252i11 2468 chr2ptel1M 467794 TTTTTTTTTTTTTTTTGTACTCTGCTGTGCAGTTTTTTATTCTTTTTATT 467843 v vi i vi v vivv v i v (TT)n#Simple_ 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr2ptel1M 467844 TTT 467846 (TT)n#Simple_ 51 TTT 53 Matrix = Unknown Transitions / transversions = 0.56 (5/9) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 266 31.22 0.00 3.90 chr2ptel1M 467871 467950 (532050) MIRc#SINE/MIR 2 78 (190) m_b67s601i7 2469 chr2ptel1M 467871 GAGGCAGTAAGGCGGCACAGTTGATGGAGCATCAGACTTGAAGTCAAAAA 467920 --- i ii v vi iii i ii MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr2ptel1M 467921 GCCTTGAGTTCACATTCTGTCTCAAACACT 467950 v i i ivi i i v viv MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCCACT 78 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 38.27 CpG sites = 17, Kimura (unadjusted) = 43.03 Transitions / transversions = 2.43 (17/7) Gap_init rate = 0.04 (3 / 79), avg. gap size = 1.00 (3 / 3) 12 4.75 0.00 8.33 chr2ptel1M 468568 468593 (531407) (TCCC)n#Simple_repeat 1 24 (0) m_b67s252i12 2470 chr2ptel1M 468568 TCCACTCCCTCCCTCCACCCCCTCCC 468593 - - i (TCCC)n#Simpl 1 TCC-CTCCCTCCCTCC-CTCCCTCCC 24 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.08 (2 / 25), avg. gap size = 1.00 (2 / 2) 263 28.08 3.31 3.31 chr2ptel1M 468918 469068 (530932) C L1ME3G_3end#LINE/L1 (300) 624 474 m_b67s551i3 2471 chr2ptel1M 468918 TTTCACTCAGCATCAGTTCATGTAAGTCTCTCCAAGCCTCTCTGTATTCA 468967 i vi vv v v ii i v i vv vii vv C L1ME3G_3end#L 624 TTTCACTCAACAATATGTCTTGGAGATCTTTCCATGTCAGTACATATAGA 575 chr2ptel1M 468968 TCCTGCTGCTCATTTCTT---ACAGAACAATAATATTCCATAACATTCAT 469014 - i -- ii --- ? vvvv i ii vv C L1ME3G_3end#L 574 TC-TAC--CTCATTCTTTTTAACNGCTGCATAGTATTCCATAGTATGGAT 528 chr2ptel1M 469015 ATACCATAATTTACCCAAACATTCTCCAACTGATGGGCATCCA--TTCAG 469062 iii v i v i i ii -- -- C L1ME3G_3end#L 527 ATACCATAATTTATTTAACCATTCCCCTATTGATGGACATTTAGGTT--G 480 chr2ptel1M 469063 TTTCCA 469068 C L1ME3G_3end#L 479 TTTCCA 474 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 36.10 CpG sites = 22, Kimura (unadjusted) = 36.10 Transitions / transversions = 1.16 (22/19) Gap_init rate = 0.05 (7 / 150), avg. gap size = 1.43 (10 / 7) 86 30.65 2.91 3.18 chr2ptel1M 469423 469800 (530200) (AAG)n#Simple_repeat 1 377 (0) m_b67s252i13 2472 chr2ptel1M 469423 AAGGAGAGGAAAGAGAGAAGAACACAAAG-AGGAGAAGGAGGAAGAAAAA 469471 i i - - v vi - i - i i (AAG)n#Simple 1 AAGAAGAAG-AAGA-AGAAGAAGAAGAAGAAGAAGAA-GAAGAAGAAGAA 47 chr2ptel1M 469472 GAAGAGCAAAAGGAGGAAGAAAAAGAGGAAAAAGAAAAAAGAGAA-AAG- 469519 iv i i i i i i i ii - - (AAG)n#Simple 48 GAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA 97 chr2ptel1M 469520 GGATGAAAAACAAAAATCAGGAGAAGAAAACAAAGGGGAGGAAAGTGTAG 469569 i v i v i vv i i vi ii i iiv v (AAG)n#Simple 98 AGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAG 147 chr2ptel1M 469570 AGGAGGAAAAAG-AGGAGATGAGGGAAGGGAGAGGGAGAGGGATGAA-AA 469617 i i i - i v -i - i i i -i v - (AAG)n#Simple 148 AAGAAGAAGAAGAAGAAGAAGA-AGAA-GAAGAAGAAGA-AGAAGAAGAA 194 chr2ptel1M 469618 GGAGAAGAAG-AGAGGGAATAAAGGAGTAAAAGAGGAAGAAGAA-AAGAA 469665 i - -i -i i v i i - (AAG)n#Simple 195 GAAGAAGAAGAAGA-AGAA-GAAGAAGAAGAAGAAGAAGAAGAAGAAGAA 242 chr2ptel1M 469666 GGAAGAGAAAAAAGGAGAGGAAGTAAAAGGAAGAAG-AGAAGGAGGAGAA 469714 - ii i i i - i i - i i (AAG)n#Simple 243 -GAAGAAGAAGAAGAAGAAGAAG-AAGAAGAAGAAGAAGAAGAAGAAGAA 290 chr2ptel1M 469715 AGAGAAGAAAGAAAATGGGGAGGAA-AAGGAGGGAAAGAAGAAG-AGGAG 469762 ii - i v ii i - i iii - i (AAG)n#Simple 291 GAAGAAG-AAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAG 339 chr2ptel1M 469763 GAGAAAAAGAAAAAGGAGATGGAGGGGGCAG-AGAAGAA 469800 i i i i -i i ii v - (AAG)n#Simple 340 AAGAAGAAGAAGAAGAAGA-AGAAGAAGAAGAAGAAGAA 377 Matrix = Unknown Transitions / transversions = 4.67 (70/15) Gap_init rate = 0.06 (23 / 377), avg. gap size = 1.00 (23 / 23) 241 30.53 5.00 5.00 chr2ptel1M 470663 470762 (529238) L3#LINE/CR1 3901 4000 (99) m_b67s601i8 2473 chr2ptel1M 470663 CTTTATAGCACCTGGAGCTATTAAAAAATAG-----GTTCCGTCAGAAGG 470707 v i viii i iv i ----- i v v i?i L3#LINE/CR1 3901 CTTTCTAACAATCAGAGCTGTCCAAAAATGGAATGGGCTGCCTCGNGAGG 3950 chr2ptel1M 470708 GAGTGGGTGTTCCTTCCCTTCACTGGAGGCCTTCAAGCAAGAGCAGAAGG 470757 v i ----- i v iv iii v i v L3#LINE/CR1 3951 TAGTGAG-----CTCCCCGTCACTGGAGGTGTTCAAGCAGAGGCTGGATG 3995 chr2ptel1M 470758 ATCGC 470762 i i L3#LINE/CR1 3996 ACCAC 4000 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 39.79 CpG sites = 19, Kimura (unadjusted) = 41.71 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.06 (6 / 99), avg. gap size = 1.67 (10 / 6) 35 17.68 5.94 1.90 chr2ptel1M 471214 471314 (528686) (CCCTAA)n#Simple_repeat 1 105 (0) m_b67s252i14 2474 chr2ptel1M 471214 CCCTGACTCTAACCCTAACCCTAAATGCCT--CCC-GACTCTAACCCTAA 471260 i i - -v -- -i i (CCCTAA)n#Sim 1 CCCTAACCCTAACCCTAACCCT-AA-CCCTAACCCTAACCCTAACCCTAA 48 chr2ptel1M 471261 CCCTAA-ATTCGCTCTAACTC-AACCCTAA-CCTGACTCTAACTCTAACC 471307 -vi vi i i - - i i i (CCCTAA)n#Sim 49 CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC 98 chr2ptel1M 471308 CTAAACC 471314 v (CCCTAA)n#Sim 99 CTAACCC 105 Matrix = Unknown Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.07 (7 / 100), avg. gap size = 1.14 (8 / 7) 251 30.58 6.45 1.54 chr2ptel1M 471634 471819 (528181) L2#LINE/L2 2363 2557 (525) m_b67s601i9 2475 chr2ptel1M 471634 CTTCTCGGCTGACCTCTAGTCTCACATCTCCA-CTGCCTGGCAGACACCT 471682 i vv v i v ii v - iviv i L2#LINE/L2 2363 CCTCTCCCCTGAACTCCAGACTCGTATATCCAACTGCCTACTCGACATCT 2412 chr2ptel1M 471683 GGAACTGGATGTTCCAGAGACATCTTAAAGTGAATGTAACCCCAAATGAA 471732 vv vi iiv v i i v v ii iv vv v L2#LINE/L2 2413 CCACTTGGATGTCTAATAGGCATCTCAAACTTAACATGTCCAAAACTGAA 2462 chr2ptel1M 471733 CTCTC--TCTTTCCCC-CATCTCTGCCCCCACCGCTCAGATCTTCCAGAC 471779 ii-- i - vvi i iv -- - vv i L2#LINE/L2 2463 CTCCTGATCTTCCCCCTCAAACCTGCTCCTCCCG--CAG-TCTTCCCCAT 2509 chr2ptel1M 471780 TCCAGCTTCT-GC-ACTCTATCCT---AGCTGC---AGTCAAAGAACT 471819 ii i?vv - - i --- i ---i i i v L2#LINE/L2 2510 CTCAGTNAATGGCAACTCCATCCTTCCAGTTGCTCAGGCCAAAAACCT 2557 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 39.47 CpG sites = 30, Kimura (unadjusted) = 40.39 Transitions / transversions = 1.15 (30/26) Gap_init rate = 0.05 (10 / 185), avg. gap size = 1.50 (15 / 10) 30 18.46 0.00 0.00 chr2ptel1M 471908 471962 (528038) (A)n#Simple_repeat 1 55 (0) m_b67s252i15 2476 chr2ptel1M 471908 AAAAAAAAAAAAGGAAACTAAATTAAAAATAATGAAAAAAAAAAAAAAAA 471957 ii vv vv v vi (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr2ptel1M 471958 AAAAA 471962 (A)n#Simple_r 51 AAAAA 55 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 570 23.13 1.48 0.74 chr2ptel1M 472114 472248 (527752) C MIRc#SINE/MIR (122) 146 11 m_b67s601i10 2477 chr2ptel1M 472114 CATTTTATAGATAAGAAAATGGAAGTGAACAG-GGTTAAGTGACTTGCCC 472162 i i i iv i ivv v - C MIRc#SINE/MIR 146 CATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCC 97 chr2ptel1M 472163 AGGATCACACAGCTAAGCAGTGTCTGCAGCTAG-ATTTGCACTCAGGTCT 472211 i i ivv v v - ii - i i v i C MIRc#SINE/MIR 96 AAGGTCACACAGCTAGTAAGTGGCAG-AGCCGGGACTCGAACCCAGGTCT 48 chr2ptel1M 472212 TCCTGACTCTGGTTGGAGTGCTCTATCCACTGCATCA 472248 iiiv vv v i C MIRc#SINE/MIR 47 TCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCA 11 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 25.97 CpG sites = 18, Kimura (unadjusted) = 28.15 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.02 (3 / 134), avg. gap size = 1.00 (3 / 3) 380 27.15 1.21 15.17 chr2ptel1M 472299 472463 (527537) MIRc#SINE/MIR 2 146 (122) m_b67s601i11 2478 chr2ptel1M 472299 GAAGCTAAGTGGAACTGTGGTTAGAGCACCCAGCATGGAGTCAGGAAGAC 472348 i viv vi v vv ivii v MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr2ptel1M 472349 TCAATTTTTTAAAAAAATCCTCAAATTAAATTCCAACCTCAAGACATTTC 472398 ------------------- viiv ii i i ii iii-- v i v MIRc#SINE/MIR 52 -------------------CTGGGTTCGAGTCCCGGCTCT--GCCACTTA 80 chr2ptel1M 472399 CTAGCTGTGTGATCCTGGGCAAGTCACTTAATCCTGTTT--CCCTCACTT 472446 i i - v i --v v MIRc#SINE/MIR 81 CTAGCTGTGTGACCTTGGGCAAGTCACTTAA-CCTCTCTGAGCCTCAGTT 129 chr2ptel1M 472447 CCCTTATCTGTAAAATG 472463 i i MIRc#SINE/MIR 130 TCCTCATCTGTAAAATG 146 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 31.43 CpG sites = 23, Kimura (unadjusted) = 33.69 Transitions / transversions = 1.53 (23/15) Gap_init rate = 0.14 (23 / 164), avg. gap size = 1.04 (24 / 23) 1129 30.58 7.57 4.04 chr2ptel1M 473804 475071 (524929) C L1MC_orf2#LINE/L1 (1957) 1337 27 m_b67s551i4 2479 chr2ptel1M 473804 ATTTCCTCTTCTGTTAACCTGGGCAGTTTATATTTTTGTAAATATTCTTT 473853 i v v iii v v i i i vv iiv vv i C L1MC_orf2#LIN 1337 ATTTCTTCTTGTGTGAGTTTTGGCAGATTGTGTCTTTCAAGGAATTGGTC 1288 chr2ptel1M 473854 CATTTCTGTTAGATTGTCATACTTGCTGCCATAGAGTTGGGCAAAATATC 473903 vvi i i v i iv v vv v i i C L1MC_orf2#LIN 1287 CATTTCATCTAGGTTATCAAATTTGTGGGCATAGAGTTGTTCATAGTATT 1238 chr2ptel1M 473904 TCCTAATTGTTGCTTTAATTTCTTTTTCATTGGTGGTAAGCTTCGCCCTT 473953 i i v i ivi v iv vvv i? i i vv i v i C L1MC_orf2#LIN 1237 CCTTTATTATCCTTTTAATGTCCATGGGATCNGTAGTGATGTCCCCTCTT 1188 chr2ptel1M 473954 TCATTTTTGATGCTAGTGATT----CCCCCCCCCTTTTTTTTTTTATCAA 473999 i ii i ----i ii i i i vi i i C L1MC_orf2#LIN 1187 TCATTTCTGATATTAGTAATTTGTGTCTTCTCTCTTTTTTTCTTAGTTAG 1138 chr2ptel1M 474000 ATTAACCAAAGGTTTATTTATTTTATTAGTTTTTTCATAAAACCAACTCT 474049 vi ii i i i iv ii i v i i i C L1MC_orf2#LIN 1137 CCTGGCTAGAGGCTTATCAATTTTATTGATCTTTTCAAAGAACCAGCTTT 1088 chr2ptel1M 474050 TTGTTTTGTTTATTAGTTC-AATAATTTTTTGGTTTCTATTTTATTAATC 474098 v i v vvi - v i ii v v i i i C L1MC_orf2#LIN 1087 TGGTTTCGTTGATTTTCTCTATTGATTTCCTGTTTTCAATTTCATTGATT 1038 chr2ptel1M 474099 TTTGAGTTTCAAAATTTTCTGATTTGGTCT-------TTAATTGGGGAGT 474141 i ---i v v v v vv i ------- v v i--- C L1MC_orf2#LIN 1037 TCTG---CTCTAATTTTTATTATTTCTTTTCTTCTGCTTACTTTGGA--- 994 chr2ptel1M 474142 TTTAATTTG---TCCTTTTCCTAACTTTTTTAGTTGCATGCCTAATTCAT 474188 --- i i ii ii v v v v i iv i C L1MC_orf2#LIN 993 TTTAATTTGCTCTTCTTTTTCTAGTTTCCTAAGGTGGAAGCTTAGATTAT 944 chr2ptel1M 474189 TGATTT--ACTCTTTC-TCTATTTT-ATTTATGTCGCTATTTAGATA-TA 474233 --iv - v i - v ----i i - i- C L1MC_orf2#LIN 943 TGATTTTAGATCTTTCTTCTTTTCTAATATATG----CATTCA-ATGCTA 899 chr2ptel1M 474234 TAAAATTTCCCCTAAGAACTGCTTTGGCTGAATCCCA------------- 474270 v i i v v v ------------- C L1MC_orf2#LIN 898 TAAATTTCCCTCTAAGCACTGCTTTCGCTGCATCCCACAAATTTTGATAA 849 chr2ptel1M 474271 ----TATTATAATTTTC--TTGGATGAAATTAT-----GACTTGTTTCAG 474309 ---- v v -- i v v v -----i i v i i- C L1MC_orf2#LIN 848 GTTGTATTTTCATTTTCATTTAGTTCAAAATATTTTTAAATTTCTCTT-G 800 chr2ptel1M 474310 TGATTTGTTGTTTGACCCACTTGTC-CTTAGAATTAGATTATTTAATTTC 474358 v v v iv i-i v ivi i i C L1MC_orf2#LIN 799 AGATTTCTTCTTTGACCCATGTGTTATTTAGAAGTGTGTTGTTTAATCTC 750 chr2ptel1M 474359 CAATTGGTTTTTAGTCTATTTTTCCCTAGTCCTTTATCAGATA-TGATTT 474407 v i-- i --v --- i iiv i v v v - C L1MC_orf2#LIN 749 CAAGTA--TTTTGG--GATTTT---CCAGCTATCTTTCTGTTATTGATTT 707 chr2ptel1M 474408 TT------ATTGCACTATGGTCTGAAAAGGAAGCATT-TACTCTTTCTCT 474450 i ------ v i i - i v ?i ? - ivv v C L1MC_orf2#LIN 706 CTAGTTTAATTCCATTGTGGTCTG-AGAGCANACNTTGTATGATTTCTAT 658 chr2ptel1M 474451 CTTTTTGCATTTGTGAA-----GTTTTAATGCCCTAATACACGGTCACTT 474495 ii iv v ----- - v i iv iii vv i C L1MC_orf2#LIN 657 TCTTTTAAATTTGTTAAGGTGTGTTTT-ATGGCCCAGAATGTGGTCTATC 609 chr2ptel1M 474496 TTTGTGTAGGTGCCATGTACTGCCAAGAAAAAAGTATGTTCCTTTCTGTC 474545 v v v v ivvviii i v i i -- v i C L1MC_orf2#LIN 608 TTGGTGAATGTTCCATGTGAGCTTGAGAAGAATGTGTATTC--TGCTGTT 561 chr2ptel1M 474546 CCT--ATTCAATTTTCTCCAGAAGTCTGTCATATCTAGGT--TTTCTAGC 474591 vi -- vv i v? vi v vi i ? i v -- vv i - C L1MC_orf2#LIN 560 GTTGGATGAAGTANTCTATAGATGTCAATTANATCCAGTTGATTGATGG- 512 chr2ptel1M 474592 ATCCTATTAGCCTCCCTAGCTTCTTTCTTGTTTATTTTATG---ACTAGA 474638 - v i ?ivi --- i viv i ii v v ---i i C L1MC_orf2#LIN 511 -TGCTGTTNAGTTC---AACTATGTCCTTACTGATTTTCTGCCTGCTGGA 466 chr2ptel1M 474639 TTTGTCTGATTCCAAGAGGGGAAGGTTG-AGTTTCCTCACTAGAATAGT- 474686 i ?iv ? ii v i iiv - i -v v - C L1MC_orf2#LIN 465 TCTGTCNATTNCTGATAGAGGGGTGTTGAAGTCTCC-AACTATAATAGTG 417 chr2ptel1M 474687 --TTTGCTCTCCATTTCTTCCTGTAACTGGCT-TAAAATCCTCTCT-AGG 474732 -- i --- i i i i ii -- - v iv ii vi - v C L1MC_orf2#LIN 416 GATTCG---TCTATTTCTCCTTGCAGTT--CTATCAGTTTTTGCCTCACG 372 chr2ptel1M 474733 AATTTTCCTGCTCTACCACTTGATGCTTACACATTTAGTATTGTTAATTA 474782 v vvi iiiii v ii v i v v - vv C L1MC_orf2#LIN 371 TATTTTGACGCTCTGTTGTTAGGCGCATACACGTTAAGGATTGTT-ATGT 323 chr2ptel1M 474783 CTTCATT-----ATTTACAGTACCTTTTATCCAGATGTACTTTCCCATCT 474827 - ----- v ---- i vvv v vi vii C L1MC_orf2#LIN 322 CTTC-TTGGAGAATTGAC----CCCTTTATCATTATGTAATGCCCCTCTT 278 chr2ptel1M 474828 TATCTCTTTTGATAAGATCTATTTTTACT------TTTGCTTTATGTGAG 474871 i --- --- v ii i ------ i i i v i C L1MC_orf2#LIN 277 TATCCC---TGATAA---CTTTCCTTGCTCTGAAGTCTGCTCTGTCTGAA 234 chr2ptel1M 474872 ATCAGAATTGCTACCCCTGTTTTTTTTTTTTTTAACTTCAGCCGAAGCAT 474921 i iv v i ? i i vv vivv ------- C L1MC_orf2#LIN 233 ATTAATATAGCTACTCCNGCTTTCTTTTGATTAGTGTT-------AGCAT 191 chr2ptel1M 474922 AATAAATTCTGGTCCAGCCTTTTATCTTTACTCTGTATGTCTCTCTATGT 474971 ii v ii vv v ? ii v i v i i C L1MC_orf2#LIN 190 GGTATATCTTTCTCCATCCNTTTACTTTTAATCTATATGTGTCTTTATAT 141 chr2ptel1M 474972 CAAAGGT--GTTTCTTGTAAACAACATATTGTAGGATTCTGTTTTTTAAT 475019 iv i -- i v v i ii i C L1MC_orf2#LIN 140 TTAAAGTGGGTTTCTTGTAGACAACATATAGTTGGGTCTTGTTTTTTGAT 91 chr2ptel1M 475020 CCACT---------TCTGTTTT---GTGGGAGAGTCCATCTCATTCACAT 475057 --------- i ---i v v vi ii vvi ? C L1MC_orf2#LIN 90 CCACTCTGACAATCTCTGTCTTTTAATTGGTGTATTTAGACCATTNACAT 41 chr2ptel1M 475058 TCAGAGTAATGATT 475071 i i i v C L1MC_orf2#LIN 40 TTAAAGTGATTATT 27 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 40.16 CpG sites = 211, Kimura (unadjusted) = 40.88 Transitions / transversions = 1.31 (211/161) Gap_init rate = 0.07 (83 / 1267), avg. gap size = 1.80 (149 / 83) 244 28.79 11.98 0.47 chr2ptel1M 474952 475143 (524857) C L1MEi_5end#LINE/L1 (0) 2212 1999 m_b67s551i5 2479 chr2ptel1M 474952 CTCTGTATGTCTCTCTATGTCAAAGGTGTTTCTTGTAAACAACATATTGT 475001 i v i vi i i v i iiv i i v i C L1MEi_5end#LI 2212 CTTTCTGTGTCGTTTTGTTTTAGGTGTGTCTCTTGTAAACAGCATATAGC 2163 chr2ptel1M 475002 AGGATTCTGTTTTTTAATCCA--CT-------TCTGTTTT---GTGGGAG 475039 v i v -- ------- i ---i i v C L1MEi_5end#LI 2162 TGGATTTTTTTTTTTAATCCAATCTGATAATCTCTGTCTTTTAATAGGTG 2113 chr2ptel1M 475040 AGTCCATCTCATTCACATTCAGAGTAATGATTATCAGCTTTG----TATT 475085 ii vii i i vv i v i ivi vv ---- C L1MEi_5end#LI 2112 AGTTTAATCCATTTACATTTATTGTGATTACTGATATATTTGGACTTATT 2063 chr2ptel1M 475086 TCCCTCGATCCTATTTT---TCCCCTG--TAT-ATACTTTTGTTCTCC-C 475128 ivi - i --- iii -- - ? vi i ? -i C L1MEi_5end#LI 2062 TCTACC-ATCTTATTTTGTGTTTTCTGTTTATCATNCTTTTTCTTTNCTT 2014 chr2ptel1M 475129 TTTCTACCCTGTCTT 475143 vi v i C L1MEi_5end#LI 2013 TTTCTCTCCTTTCCT 1999 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 38.45 CpG sites = 36, Kimura (unadjusted) = 38.45 Transitions / transversions = 1.89 (36/19) Gap_init rate = 0.05 (9 / 191), avg. gap size = 2.67 (24 / 9) 398 24.65 10.56 0.00 chr2ptel1M 474961 475102 (524898) C L1MEj_5end#LINE/L1 (1) 2159 2003 m_b67s551i6 2479 chr2ptel1M 474961 TCTCTCTATGTCAAAGGTGTTTCTTGTAAACAACATATTGTAGGATTCTG 475010 v i i v i iv i v iv i i C L1MEj_5end#LI 2159 TCACTTTGTTTTAAGTGTGTTTCTTGTAAACAGCATATAGCTGGGTTTTG 2110 chr2ptel1M 475011 TTTTTTAATCCA--CT-------TCTGTTTT---GTGGGAGAGTCCATCT 475048 i -- ------- i ---i i i vii C L1MEj_5end#LI 2109 TTTTTTAACCCAATCTGACAGTCTCTGTCTTTTAATGGGAGAATTCAGTC 2060 chr2ptel1M 475049 CATTCACATTCAGAGTAATGATT-ATCAGCTTTGTAT--TTCCCTCGATC 475095 i v i i - vvi vi v -- i v C L1MEj_5end#LI 2059 CATTCACATTTAGTGTAACGACTGATATACTTGATTTTATTCCTTCCATC 2010 chr2ptel1M 475096 CTATTTT 475102 i i C L1MEj_5end#LI 2009 TTACTTT 2003 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 29.82 CpG sites = 23, Kimura (unadjusted) = 30.88 Transitions / transversions = 1.92 (23/12) Gap_init rate = 0.04 (5 / 141), avg. gap size = 3.00 (15 / 5) 19 22.38 3.51 0.00 chr2ptel1M 477328 477384 (522616) (TTTTTC)n#Simple_repeat 1 59 (0) m_b67s252i16 2480 chr2ptel1M 477328 TTTTTCTGTTTCTTGCTCATTTTC--TTTCCTTTTCTTTTGGTATTTCCT 477375 v vi v -- i vv v i (TTTTTC)n#Sim 1 TTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTT 50 chr2ptel1M 477376 CTTTTTTTT 477384 i i (TTTTTC)n#Sim 51 TTTCTTTTT 59 Matrix = Unknown Transitions / transversions = 0.83 (5/6) Gap_init rate = 0.02 (1 / 56), avg. gap size = 2.00 (2 / 1) 295 30.56 9.86 4.97 chr2ptel1M 478588 478952 (521048) L2#LINE/L2 2563 2944 (138) m_b67s601i12 2481 chr2ptel1M 478588 TCCTCCTC-ATTCCTCACTGTCTCTCACCATTACCCT-CACCAAAACAAG 478635 v i- i v v ---- i- i ---- v L2#LINE/L2 2563 TCATCCTTGACTCCTCTCTTTCTCTCAC----ACCCCACATC----CAAT 2604 chr2ptel1M 478636 CTATTGCCAAACCCTGTGTAAGAGTTAATAACCTC------TCTCCCAAA 478679 i iiv i v----i i v- v i ------ v vi L2#LINE/L2 2605 CCATCAGCAAATCCTGTC----GGCTC-TACCTTCAAAATATATCCAGAA 2649 chr2ptel1M 478680 CCCCCCTACTTCCCTCTGATC----CTGCCATCCCACTGGTGCACACCCT 478725 i vv i i v i- i ---- i v v v vi vi L2#LINE/L2 2650 TCCGACCACTTCTCACC-ACCTCCACTGCCACCACCCTGGTCCAAGCCAC 2698 chr2ptel1M 478726 CATCACCTTATACCTGGACT--TGCAATAAA-----AATTGGGGATCTGC 478768 i ivii i -- iv----- i --- - L2#LINE/L2 2699 CATCATCTCTCGCCTGGATTACTGCAATAGCCTCCTAACTGG---TCT-C 2744 chr2ptel1M 478769 CCGGCGTGGTCTCT--CTCCATTCCATTTCATTCTCCACTTAGCCACCAA 478816 v v vvv i -- i vi ? v ii v vi vi i L2#LINE/L2 2745 CCTGCTTCCACCCTTGCCCCCCTNCAGTCTATTCTCAACACAGCAGCCAG 2794 chr2ptel1M 478817 AG-----------AAG---AGGTCTGGCCATCCCACCCACCTACTCAATA 478852 ----------- i--- i v ii vi i vi i v L2#LINE/L2 2795 AGTGATCCTTTTAAAACGTAAGTCAGATCATGTCACTCCTCTGCTCAAAA 2844 chr2ptel1M 478853 ACCTCCAGTGGCTTCCCACTGCCCTCAGGATCAAATACAAAGTCCTCTAC 478902 v i iiv v ii v vv - L2#LINE/L2 2845 CCCTCCAATGGCTTCCCATCTCACTCAGAGTAAAAGCCAAAGTCCT-TAC 2893 chr2ptel1M 478903 -TTAAATTGCAAAGTCCTTCATAATCTGGTCTCCTCCTGCCTTTCTGGTC 478951 -v iivi i i i v i i ivi i i ii L2#LINE/L2 2894 AATGGCCTACAAGGCCCTACATGATCTGGTCCCCCGTTACCTCTCTGACC 2943 chr2ptel1M 478952 T 478952 L2#LINE/L2 2944 T 2944 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 39.17 CpG sites = 62, Kimura (unadjusted) = 40.73 Transitions / transversions = 1.41 (62/44) Gap_init rate = 0.08 (29 / 364), avg. gap size = 1.90 (55 / 29) 12 18.29 0.00 3.12 chr2ptel1M 479020 479052 (520948) (CTCTGG)n#Simple_repeat 1 32 (0) m_b67s252i17 2482 chr2ptel1M 479020 CTCCGGCTCTGGCTCTGGACATTTGCTCTGACT 479052 i - vi v i (CTCTGG)n#Sim 1 CTCTGGCTCTGGCTCTGG-CTCTGGCTCTGGCT 32 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 215 28.17 5.22 4.31 chr2ptel1M 479695 479809 (520191) C L2d_3end#LINE/L2 (40) 476 361 m_b67s601i14 2483 chr2ptel1M 479695 TGCGCCAGGCACCGTGATAAGCACTG--GAGAAAGATACTCAAAGGAAAA 479742 i ivi i v i i -- i v ? ---- i? iv C L2d_3end#LINE 476 TGTGCTCAGCACTGTGCTAGGCGCTGTGGGGAACGANA----AAANAGTA 431 chr2ptel1M 479743 GGAAAAAGAATCCCTGTCCTCAAGAAGCTTACTTTCTACTGGGGG----A 479788 vi i v vii i i vv v v ---- C L2d_3end#LINE 430 TAAGACATGGTCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGGAGACA 381 chr2ptel1M 479789 AAACTACACATAAAGGGAACA 479809 i - i v v i C L2d_3end#LINE 380 AGACTA-ACACACATGAAACA 361 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 35.61 CpG sites = 18, Kimura (unadjusted) = 37.11 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.06 (7 / 114), avg. gap size = 1.57 (11 / 7) 311 26.05 1.02 2.06 chr2ptel1M 479695 479792 (520208) C L2a_3end#LINE/L2 (38) 479 383 m_b67s601i13 2483 chr2ptel1M 479695 TGCGCCAGGCACCGTGATAAGCACTGGAGAAAGA-TACTCAAAGGAAAAG 479743 i i vv i i i v v -i v v vii v C L2a_3end#LINE 479 TGTGCCAGGCACTGTTCTAGGCGCTGGGGATACAGCAGTGAACAAAACAG 430 chr2ptel1M 479744 GAAAAAGAATCCCTGTCCTCAAGAAGCTTACTTTCTACTGGGGGAAAAC 479792 iv -- i v i v v i i C L2a_3end#LINE 429 ACAAAAG--TCCCTGCCCTCATGGAGCTTACATTCTAGTGGGGGGAGAC 383 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 30.86 CpG sites = 13, Kimura (unadjusted) = 32.39 Transitions / transversions = 1.08 (13/12) Gap_init rate = 0.03 (3 / 97), avg. gap size = 1.00 (3 / 3) 260 36.36 1.00 1.00 chr2ptel1M 480054 480153 (519847) C L3#LINE/CR1 (3797) 302 203 m_b67s601i15 2484 chr2ptel1M 480054 TTCTGTTTTCTTTGGAAACATTTCATTGTTCCCAACAATCTGGAGCATGG 480103 ii ii ? i i i vi iv ii i i v i i i C L3#LINE/CR1 302 TTCCATCCTNTCTAGGAACCCTTCATCCTCTCTAATAAGCCGGAGCGTAG 253 chr2ptel1M 480104 GAAAGCAGAACCTGAAGTTCTCT-ATCTTCTCTTCTAGGAGAATGGTCAG 480152 ii i - vv v ii i - i i v iiv ii C L3#LINE/CR1 252 AGAGGC-GTTCCTCAAGCCCTTTCACCTTCTCCTCTAGCAGGGAGACCAG 204 chr2ptel1M 480153 C 480153 C L3#LINE/CR1 203 C 203 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 52.35 CpG sites = 28, Kimura (unadjusted) = 57.39 Transitions / transversions = 3.50 (28/8) Gap_init rate = 0.02 (2 / 99), avg. gap size = 1.00 (2 / 2) 210 33.68 7.78 1.04 chr2ptel1M 480805 480984 (519016) C L3#LINE/CR1 (1565) 2534 2343 m_b67s601i16 2485 chr2ptel1M 480805 TTTCTCTCTTCTCACCCAT-TCATAC--CAACTCTCCTTTACCCATTTTT 480851 v v i i - iivi -- i i ii v v v C L3#LINE/CR1 2534 TTACTATCTCCTCACCTATCTTGGGCTTCAATTCCCTCTTAACGATGTTT 2485 chr2ptel1M 480852 GTCCTCCCATTTCTGCCTCAAAGGTTGTTTTCCTTG-----GGAGATAGA 480896 i v v iiviiii i ii i ----- i ii C L3#LINE/CR1 2484 GTTCTACCCTTTCCAGTCTGAAGATCATTCTCCTTGATAGAGAAGACGGA 2435 chr2ptel1M 480897 GCTGAAAGAGGAA-AGAATA-TTCTTCTCTCTAT-TGCCAGGGGTCAATA 480943 ivii v i-v i - v i v - i vvv i i C L3#LINE/CR1 2434 AGCAAAATAGGAGTTGAGTAGTTCTGCTTTCTCTCTGTCATCTGTTAACA 2385 chr2ptel1M 480944 TC-TG--ATTTGTCCTAAAGCAGTGGTCCTTGATCCTTCCCTTT 480984 i-i -- i i i- i v - vi? i i C L3#LINE/CR1 2384 TTACGCCATCTGCCCC-AAGCAGCGGGCC-TGTCNCTTTCTTTT 2343 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 44.76 CpG sites = 41, Kimura (unadjusted) = 48.31 Transitions / transversions = 2.16 (41/19) Gap_init rate = 0.06 (10 / 179), avg. gap size = 1.60 (16 / 10) 360 17.95 13.68 0.00 chr2ptel1M 481704 481820 (518180) MIR1_Amn#SINE/MIR 18 150 (80) m_b68s601i1 2486 chr2ptel1M 481704 CTAGTGCAGAGAGCACTGAACC----TTC---AGCCCTGAGACCAAAT-G 481745 v v i i----i --- v i vi ? ? -v MIR1_Amn#SINE 18 CTAGTGGATAGAGCACTGGACTGGGACTCGGGAGACCTGGGTTCNANTCC 67 chr2ptel1M 481746 CAGCTC-------GGACAGCTGTGTGACCCTGCACAAGTCACTTTACC-C 481787 i -------? v ? ? i vi ? - MIR1_Amn#SINE 68 CGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGTCACTTNACCTC 117 chr2ptel1M 481788 TGTCTGCCTCAGTTTCCTCATCAGCAAAAAGAG 481820 v v? v i v i MIR1_Amn#SINE 118 TCTGNGCCTCAGTTTCCTCATCTGTAAAATGGG 150 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 21.00 CpG sites = 10, Kimura (unadjusted) = 22.13 Transitions / transversions = 0.91 (10/11) Gap_init rate = 0.04 (5 / 116), avg. gap size = 3.20 (16 / 5) 243 27.87 6.36 5.41 chr2ptel1M 481904 482013 (517987) L2a_3end#LINE/L2 368 478 (39) m_b68s601i2 2481 chr2ptel1M 481904 ATATGTCTATTTTATGTGTTTTCTCACACTATATATTGTAAACTCACTGA 481953 v i v v v iii i ---- v v i vv L2a_3end#LINE 368 ATTTGTTTATTGTCTGTCTCCCCCCAC----TAGAATGTAAGCTCCATGA 413 chr2ptel1M 481954 AAACAGGGATCATTTCAT-TGTTGTGT------CTGTATTTCCTGTGTCC 481996 iii i-- ii - v ------ ii v i i i L2a_3end#LINE 414 GGGCAGGGAC--TTTTGTCTGTTTTGTTCACTGCTGTATCCCCAGCGCCT 461 chr2ptel1M 481997 AGAACAGTGCCAGTCAC 482013 v v L2a_3end#LINE 462 AGAACAGTGCCTGGCAC 478 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 34.23 CpG sites = 17, Kimura (unadjusted) = 35.76 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.07 (8 / 109), avg. gap size = 1.62 (13 / 8) 207 34.64 7.87 2.24 chr2ptel1M 481907 482033 (517967) L2c_3end#LINE/L2 345 478 (0) m_b68s601i3 2481 chr2ptel1M 481907 TGTCTATTT---TATGTGTTTTCTCACACTATATATTGTAAACTCACTGA 481953 i --- i v i i - v i-- i i vi L2c_3end#LINE 345 TGTCTGTTTACNTGTCTGTCTCCTC-CACTAGAC--TGTGAGCTCCTTGA 391 chr2ptel1M 481954 AAACAGGGATCATTTCATTGTTGTGTCTGTATTTCCTGTGTCCAGAACA- 482002 iii i i v v vv ii v i ii v i i ii v - L2c_3end#LINE 392 GGGCAGGGACCGTGTCTTATTCATCTTTGTATCCCCAGCGCCTGGCACAT 441 chr2ptel1M 482003 -----GTGC-CAGTCACTGACTGATGGATAGAAGAAT 482033 ----- i - i v v vi v i ii v L2c_3end#LINE 442 AGTAGGCGCTCAATAAATGTTTGTTGAATGAATGAAT 478 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 44.57 CpG sites = 28, Kimura (unadjusted) = 49.42 Transitions / transversions = 1.87 (28/15) Gap_init rate = 0.06 (7 / 126), avg. gap size = 1.86 (13 / 7) 12 6.13 14.71 0.00 chr2ptel1M 482035 482068 (517932) (GGAT)n#Simple_repeat 1 39 (0) m_b68s252i0 2487 chr2ptel1M 482035 GGA-GGATGGAT-AATGG-GGGATGGATGGA--GATGGA 482068 - -i -v -- (GGAT)n#Simpl 1 GGATGGATGGATGGATGGATGGATGGATGGATGGATGGA 39 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.12 (4 / 33), avg. gap size = 1.25 (5 / 4) 202 30.66 14.60 0.00 chr2ptel1M 482772 482908 (517092) C L3#LINE/CR1 (340) 3759 3603 m_b68s601i4 2488 chr2ptel1M 482772 TCTCCTC-----CTTTCTTCCCCCCGGCTCCTCTTCCCAAG--CCTCCAG 482814 ----- iii i i v vvv v v -- i i C L3#LINE/CR1 3759 TCTCCTCTAAGTCTTCTCTTCTCCAGGCTAAACATCCCCAGTTCCTTCAA 3710 chr2ptel1M 482815 CC--TTCT--GATGGCACAGACACAGGACCCTTCCCCAGCCTAGTCAC-C 482859 -- i --v i ii viv vi v v i i - C L3#LINE/CR1 3709 CCGTTCCTCATATGACATGGTTTCCAGACCCTTCACCATCCTGGTCGCTC 3660 chr2ptel1M 482860 ACCTGTGG--------TGACTTATCAATGTCCTGTCTAGAATAAGGTGCC 482901 v v --------iiii i ivii i iv i C L3#LINE/CR1 3659 TCCTCTGGACGCGCTCCAGTTTGTCAATGTCCCTCTTAAAATGTGGCGCC 3610 chr2ptel1M 482902 CAGAACT 482908 C L3#LINE/CR1 3609 CAGAACT 3603 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 38.40 CpG sites = 26, Kimura (unadjusted) = 40.94 Transitions / transversions = 1.62 (26/16) Gap_init rate = 0.04 (6 / 136), avg. gap size = 3.33 (20 / 6) 12 16.52 0.00 0.00 chr2ptel1M 483314 483340 (516660) (CCCAT)n#Simple_repeat 1 27 (0) m_b68s252i1 2489 chr2ptel1M 483314 CCCATCCCAACCGATGCCATTCCATCC 483340 v v v i (CCCAT)n#Simp 1 CCCATCCCATCCCATCCCATCCCATCC 27 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 340 35.50 3.99 1.50 chr2ptel1M 483372 483697 (516303) L2#LINE/L2 1207 1540 (1542) m_b68s601i5 2490 chr2ptel1M 483372 GCTTTGCCAAACCCCAAATCTGGATTGCTTCTGCCATCCGGCCCTCTCC- 483420 i v v ? vi v viv i vi iv - iv - L2#LINE/L2 1207 GCCTGGCAAAACCNCAACCCTGGTTAAATCCAACTCTCCG-CCTACTCCG 1255 chr2ptel1M 483421 CTCCTA-GTGTATGCTGCTGAACAAAGCTAGAGAAAGTTATGGAACTGCA 483469 v i-iivii? v ivi i ivi iiv iiii L2#LINE/L2 1256 CGCCTGCACCCGNGCAGCTGAACGTGGCTGGAGAAAAACACACAACCATG 1305 chr2ptel1M 483470 CTGAATAGGCACATTATAAATTTAACTTA-CATC-ATCTCAATTGGGTTC 483517 v i v v i v i -- v - i?- i v ii L2#LINE/L2 1306 CTGACTGGTCTCACTTTAAATTCA--TGACCACNAACCTCAAGTGGGCCC 1353 chr2ptel1M 483518 TCCTTGCAACAAGGCAATCCTTTGACACCTCCCTAATCAATTAGATATCC 483567 ivv vi vv ? viv ii i v viv v L2#LINE/L2 1354 TTAATGCTGCCCGGCAATCNTACTACATTTCCCTAGTCCATTCACTCTCC 1403 chr2ptel1M 483568 TTCTCACTACAATGAATATTCCAAAGCTTTTCATCCCT-TTCATTACTC- 483615 iv v ivvi i v i v v i v i -i vvv - L2#LINE/L2 1404 CACTCTCCTAGACGACTATTTCACACCTTCTCCTCTCTCCTCAAACCTCC 1453 chr2ptel1M 483616 --TATCTCTTCCCCAA--CT---TCCCAACTGGATACAATGCCTCATATT 483658 --i i i v -- --- i i ivv vv i v L2#LINE/L2 1454 AACACCTCCTCCCCTATCCTCACTCTCAGCTGATGACCTTGCTTCCTATT 1503 chr2ptel1M 483659 TCATCTCTAAAATTAATATCATTTTCCAAGAGCACTTTC 483697 - vvi v iv v -v ivv v i L2#LINE/L2 1504 TCA-CTGAGAAAATAGAAGCA-ATCAGAAGAGAACTTCC 1540 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 47.94 CpG sites = 56, Kimura (unadjusted) = 49.81 Transitions / transversions = 0.97 (56/58) Gap_init rate = 0.04 (14 / 325), avg. gap size = 1.29 (18 / 14) 16 0.00 0.00 0.00 chr2ptel1M 483880 483896 (516104) (T)n#Simple_repeat 1 17 (0) m_b68s252i2 2491 chr2ptel1M 483880 TTTTTTTTTTTTTTTTT 483896 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTT 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 15 5.56 0.00 0.00 chr2ptel1M 484954 484972 (515028) (A)n#Simple_repeat 1 19 (0) m_b68s252i3 2492 chr2ptel1M 484954 AAAAAAAAAAAAAAAAGAA 484972 i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAA 19 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 17 15.51 5.56 0.00 chr2ptel1M 486862 486897 (513103) (TA)n#Simple_repeat 1 38 (0) m_b68s252i4 2493 chr2ptel1M 486862 TATATACCTATAT-TATGTATATATATA-AAATACATA 486897 iv - i - v i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATA 38 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 331 3.87 1.86 0.69 chr2ptel1M 487825 488254 (511746) (GA)n#Simple_repeat 1 435 (0) m_b68s252i5 2494 chr2ptel1M 487825 GAGAGAGAGAGAGACAGACAGAG-GAGAGAG-GAGAGAG-GAGAGAGAGA 487871 v v - - - (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr2ptel1M 487872 GACAGAGAGAGAGAGAGAGAGAGAGAGAGAGCAGAGACAGAGAGACAGAG 487921 v - v v (GA)n#Simple_ 51 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG-AGAGAGAGAGAGAGAGAG 99 chr2ptel1M 487922 -GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 487970 - (GA)n#Simple_ 100 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 149 chr2ptel1M 487971 AGAGAGA-AGAGAGAGAGAGAGAGAGA-AGAGAGAGAGAGAGAGAGAGAG 488018 - - (GA)n#Simple_ 150 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 199 chr2ptel1M 488019 AGAGAGAGAGAGAGGCAGAGACAGGGAGACGAGAGAGAGAGAGAGAGAGA 488068 iv v i - (GA)n#Simple_ 200 AGAGAGAGAGAGAGAGAGAGAGAGAGAGA-GAGAGAGAGAGAGAGAGAGA 248 chr2ptel1M 488069 GAGAGAGAGAGAGAGAGAGAGAGAGAGCAGAGACAGAGAGACAGAGAG-G 488117 - v v - (GA)n#Simple_ 249 GAGAGAGAGAGAGAGAGAGAGAGAGAG-AGAGAGAGAGAGAGAGAGAGAG 297 chr2ptel1M 488118 AGACAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA-AGAGAGAG 488166 v - (GA)n#Simple_ 298 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 347 chr2ptel1M 488167 AGAGAGAGAGAGAGAGAGAGAGAGGCAGAGACAGGGAGAGAGAGAGAGAG 488216 iv v i (GA)n#Simple_ 348 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 397 chr2ptel1M 488217 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 488254 (GA)n#Simple_ 398 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 435 Matrix = Unknown Transitions / transversions = 0.33 (4/12) Gap_init rate = 0.03 (11 / 429), avg. gap size = 1.00 (11 / 11) 30 0.00 0.00 0.00 chr2ptel1M 489430 489457 (510543) (G)n#Simple_repeat 1 28 (0) c_b68s251i0 2495 chr2ptel1M 489430 GGGGGGGGGGGGGGGGGGGGGGGGGGGG 489457 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGG 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 182 29.34 0.00 3.45 chr2ptel1M 489786 489845 (510155) L3#LINE/CR1 3043 3100 (999) m_b68s601i6 2496 chr2ptel1M 489786 GTTGATCTGTGGCTGGCTGAATGAAGCCATACTCAAAGATAATTTATTAA 489835 v ii i i i -- i i iivvi v L3#LINE/CR1 3043 GTGGATTCGTAGCTGGTTGAACGA--CTATACCCAAAAGGTGTTGATTAA 3090 chr2ptel1M 489836 TGTATGGGTG 489845 v v i L3#LINE/CR1 3091 TGGATCGATG 3100 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 33.09 CpG sites = 11, Kimura (unadjusted) = 38.76 Transitions / transversions = 1.83 (11/6) Gap_init rate = 0.03 (2 / 59), avg. gap size = 1.00 (2 / 2) 14 15.91 0.00 0.00 chr2ptel1M 491236 491263 (508737) (TCA)n#Simple_repeat 1 28 (0) m_b68s252i6 2497 chr2ptel1M 491236 TCATCATCATTAACATCATCAACATTAT 491263 i v v i (TCA)n#Simple 1 TCATCATCATCATCATCATCATCATCAT 28 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 316 24.98 10.09 0.84 chr2ptel1M 492525 492633 (507367) C MIR#SINE/MIR (5) 257 139 m_b68s601i7 2498 chr2ptel1M 492525 TAACAAGCAATTACTAAGTGCCCACCATGTGCCAGATGCTGGGCTAAG-- 492572 i v i v i i i ii i iii vv -- C MIR#SINE/MIR 257 TAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGCG 208 chr2ptel1M 492573 ---TACAAACATCATAGTC-TTT-GTCCTC---ACAACCCTG-GGGGTAA 492613 --- vii i - v - -i --- i- i i C MIR#SINE/MIR 207 CTTTACATGTATTA-ACTCATTTAATCCTCACAACAACCCTATGAGGTAG 159 chr2ptel1M 492614 GTGCTATTATTATCCACCTT 492633 i v v C MIR#SINE/MIR 158 GTACTATTATTATCCCCATT 139 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 30.33 CpG sites = 19, Kimura (unadjusted) = 31.76 Transitions / transversions = 2.38 (19/8) Gap_init rate = 0.06 (7 / 108), avg. gap size = 1.71 (12 / 7) 199 40.52 3.92 0.00 chr2ptel1M 492632 492784 (507216) C L3#LINE/CR1 (3019) 1080 922 m_b68s601i8 2499 chr2ptel1M 492632 TTAAGTCTGTAAGAC--CAAGCCAATGCAGTCTTGCGAGCTTGTGTCAGT 492679 i i v ii v -- ?i? v ii iv v vi ii vi v v C L3#LINE/CR1 1080 TCAGGTCGGCGAGTCTCCNGNCAAACACGTTCTTCCCGGTCTTCGTGAGA 1031 chr2ptel1M 492680 CACATTCCATCCTAAATGTGAAGCTTGTCTTCCTA-CATTTCAAATAA-A 492727 ii i i iv?iivv i iii v i i-i i?i iiv -i C L3#LINE/CR1 1030 TGCACTCCGTCCCTNGCCAGGAGCCCATCGTTCTGGTATCNTAAGCCATG 981 chr2ptel1M 492728 GTCCAAAACCCCAAATCCCACTCTC--ATGCCATCTTCTTATGCAGGCGT 492775 i vv iii i-- ii v v vv vi C L3#LINE/CR1 980 GTCCAGAAAACCAAATCCTGTTCTTCGACACCATCTACGTAGCCAGCTGT 931 chr2ptel1M 492776 TTGCTTCCC 492784 ii C L3#LINE/CR1 930 TCACTTCCC 922 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 57.93 CpG sites = 41, Kimura (unadjusted) = 67.04 Transitions / transversions = 1.95 (41/21) Gap_init rate = 0.03 (4 / 152), avg. gap size = 1.50 (6 / 4) 217 34.48 8.28 0.00 chr2ptel1M 492870 493014 (506986) C L3#LINE/CR1 (3337) 762 606 m_b68s601i9 2499 chr2ptel1M 492870 TCAGCA----CGGGTAGAAGTCTTCTGTTTGGACAAGTCTCGGGAGGAG- 492914 ----i vi vv v v v ii i v vv- C L3#LINE/CR1 762 TCAGCAGGAGTGGGTAGCGGTCGGCGGGTTTGATGAGTCTTGGCAGGCTC 713 chr2ptel1M 492915 TCTATTATGTCTTGGATGGGTGCCCCGGGAGGACAATAGAGCTCT--GTT 492962 ii i i i ivii i i i ii v v i--i C L3#LINE/CR1 712 TCCGTCACGTCTCGGATACACGCTCCAGGAAGACAGCACACCTCCCGATT 663 chr2ptel1M 492963 -GT--TGTCCGTTATGAATA--GCAGCTTCATTGCTCCAGAGCCGGGAGT 493007 - i--i v v v v -- v i vv iii vv v C L3#LINE/CR1 662 AGCCACGTCAGGTCTGCATACGGCCGCCTCCGTATCCCTCAGCGGGGAGT 613 chr2ptel1M 493008 TCCCAAC 493014 iv C L3#LINE/CR1 612 CACCAAC 606 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 39.90 CpG sites = 27, Kimura (unadjusted) = 47.40 Transitions / transversions = 1.17 (27/23) Gap_init rate = 0.04 (6 / 144), avg. gap size = 2.00 (12 / 6) 15 21.59 3.51 3.51 chr2ptel1M 494858 494914 (505086) (AATTC)n#Simple_repeat 1 57 (0) m_b68s252i7 2500 chr2ptel1M 494858 AATTCCAACCCTATTCAATT-AAAGAAAATC-ATTCAATTCTATTCAAAT 494905 - ii v - vvv v - v - (AATTC)n#Simp 1 AATT-CAATTCAATTCAATTCAATTCAATTCAATTCAATTCAATTC-AAT 48 chr2ptel1M 494906 TCACCTCAA 494914 vi (AATTC)n#Simp 49 TCAATTCAA 57 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.07 (4 / 56), avg. gap size = 1.00 (4 / 4) 290 29.47 6.77 4.59 chr2ptel1M 496094 496285 (503715) C L3#LINE/CR1 (3766) 333 138 m_b68s601i10 2499 chr2ptel1M 496094 TTCCTTTCTGCTT--CTT--TGGATT-TTTAAATTTGATTTTTTTAATGA 496138 i ? -- -- - --v iv ii ? iv v C L3#LINE/CR1 333 TTTCTTTCTGNTTTCCTTCCTGGATTATTT--CTTCCATCCTNTCTAGGA 286 chr2ptel1M 496139 AGGACTTCCATAATCTTCCCAAACCTGGAGTGTGGAAAGATGGTCCTTGA 496188 --v i i vv iivvv v i i i i ii v ii C L3#LINE/CR1 285 A--CCCTTCATCCTCTCTAATAAGCCGGAGCGTAGAGAGGCGTTCCTCAA 238 chr2ptel1M 496189 AACACTTCACTATCTCCCTATAGGAGGGAG-CCACCTTGTAATTAG---- 496233 iv vi iv - v v - v i v v---- C L3#LINE/CR1 237 GCCCTTTCACCTTCT-CCTCTAGCAGGGAGACCAGCTTGCATTTATAGCA 189 chr2ptel1M 496234 -ACATAACCTGCAGTCTTTTGTCTCTGGCAGAAATACAAATAT-GC-TAT 496280 - iiv iii? ---- i v i v i - -i C L3#LINE/CR1 188 CACATAATTGGTGANC----GCCTCAGGCAGGAAGACAAACATAGCACAT 143 chr2ptel1M 496281 ACTCT 496285 i C L3#LINE/CR1 142 ACCCT 138 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 36.57 CpG sites = 31, Kimura (unadjusted) = 39.33 Transitions / transversions = 1.35 (31/23) Gap_init rate = 0.09 (17 / 191), avg. gap size = 1.29 (22 / 17) 272 19.69 4.48 1.45 chr2ptel1M 496304 496370 (503630) C MIRc#SINE/MIR (32) 236 168 m_b68s601i11 2501 chr2ptel1M 496304 TTTATATATCACAAGAG---TTTTACAAATATTACCTCATTTGATTCTTA 496350 i vv i - --- i v i i i i C MIRc#SINE/MIR 236 TTTACAGTTTACAA-AGCGCTTTCACATACATTATCTCATTTGATCCTCA 188 chr2ptel1M 496351 CAACAAGTCTGGGAGGTAGG 496370 vi v C MIRc#SINE/MIR 187 CAACAACCCTGTGAGGTAGG 168 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 23.26 CpG sites = 8, Kimura (unadjusted) = 23.26 Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.03 (2 / 66), avg. gap size = 2.00 (4 / 2) 335 22.39 0.00 0.00 chr2ptel1M 496316 496382 (503618) C MIRb#SINE/MIR (52) 216 150 m_b68s601i12 2501 chr2ptel1M 496316 AAGAGTTTTACAAATATTACCTCATTTGATTCTTACAACAAGTCTGGGAG 496365 v i vii i i i i vi v C MIRb#SINE/MIR 216 AAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAG 167 chr2ptel1M 496366 GTAGGTGCTATTATGCC 496382 ii v C MIRb#SINE/MIR 166 GTAGGTATTATTATCCC 150 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 27.39 CpG sites = 10, Kimura (unadjusted) = 27.39 Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.0 (0 / 0) 345 23.80 12.40 6.25 chr2ptel1M 496467 496587 (503413) C MIRc#SINE/MIR (120) 148 21 m_b68s601i13 2501 chr2ptel1M 496467 CTCATTTTCTAGATGAGGAAACTTA--------------AAGTGATTTAG 496502 i vi v -------------- i iv C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr2ptel1M 496503 TCAAGACCACATAGCTAGTAAGTGTCTGAGGCCAGATTTGAACTCAGGAA 496552 i ii i v v v vi i i i --- C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAG--- 52 chr2ptel1M 496553 GGTGAGTTTTCCTGACACAGAGACTGG-GCTCTGTC 496587 ----- i v vi v ii - v C MIRc#SINE/MIR 51 -----GTCTTCCTGACTCCAAGTCCAGTGCTCTTTC 21 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 28.09 CpG sites = 16, Kimura (unadjusted) = 29.36 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.08 (10 / 120), avg. gap size = 2.30 (23 / 10) 13 24.04 1.69 5.26 chr2ptel1M 496841 496899 (503101) (TTTCCT)n#Simple_repeat 1 57 (0) m_b68s252i8 2502 chr2ptel1M 496841 TTACCTTTTCC-TTCCCTTTAAGTCTTTTCCTTCTTCAACTGACTATTCC 496889 v - i --vi - vvi vv v (TTTCCT)n#Sim 1 TTTCCTTTTCCTTTTCCTTT--TCCTTTTCCTT-TTCCTTTTCCTTTTCC 47 chr2ptel1M 496890 TTCTCCTTTT 496899 i (TTTCCT)n#Sim 48 TTTTCCTTTT 57 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.07 (4 / 58), avg. gap size = 1.00 (4 / 4) 19 22.23 1.47 4.55 chr2ptel1M 497861 497928 (502072) (AAAATTT)n#Simple_repeat 1 66 (0) m_b68s252i9 2503 chr2ptel1M 497861 AAGATTCTGAAATTT-AAAGAAAAACTAAACAAATTTAAACATTTAAAGA 497909 i - i - vvv v vv - - iv (AAAATTT)n#Si 1 AAAATT-TAAAATTTAAAATTTAAAATTTA-AAATTTAAA-ATTTAAAAT 47 chr2ptel1M 497910 TTAAATTTAAAAATTTAAA 497928 v v (AAAATTT)n#Si 48 TTAAAATTTAAAATTTAAA 66 Matrix = Unknown Transitions / transversions = 0.33 (3/9) Gap_init rate = 0.06 (4 / 67), avg. gap size = 1.00 (4 / 4) 229 31.78 2.61 1.29 chr2ptel1M 498200 498352 (501648) L1MC1_3end#LINE/L1 491 645 (435) m_b68s551i0 2504 chr2ptel1M 498200 GATGCTCATCAATTGGGGAATGGCTGAATAAGTTATGGTATATAAAAGTA 498249 ii v i v v v i ii i i vv iii L1MC1_3end#LI 491 GATGTCCTTCAGTAGGTGAATGGATAAATAAACTGTGGTACATCCAGACA 540 chr2ptel1M 498250 ATGGAATGTTACT--GTGC-AATAAGAAATGAAGAGGCAGATTTTAGAAA 498296 i i -- i - v ivviv iiiiv ii L1MC1_3end#LI 541 ATGGAATATTATTCAGCGCTAAAAAGAAATGAGCTATCAAGCCATGAAAA 590 chr2ptel1M 498297 ATCCTGGA-AAGACTTAAATGAATTGCTGCAAAGTGAAATGAACAGAATC 498345 iv v -i i v - ii i v - vvv L1MC1_3end#LI 591 GACATGGAGGAAACTTAAATGCA-TATTACTAAGTGAAA-GAAGCCAATC 638 chr2ptel1M 498346 AGGAAAG 498352 v i L1MC1_3end#LI 639 TGAAAAG 645 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 41.71 CpG sites = 29, Kimura (unadjusted) = 42.91 Transitions / transversions = 1.53 (29/19) Gap_init rate = 0.03 (5 / 152), avg. gap size = 1.20 (6 / 5) 233 25.28 3.33 3.33 chr2ptel1M 498201 498290 (501710) L1ME3Cz_3end#LINE/L1 488 577 (420) m_b68s551i2 2504 chr2ptel1M 498201 ATGCTCATCAATTGGGGAATGGCTGAATAAGTTATGGTATATAAAAGTAA 498250 ii v v i i i vv vii L1ME3Cz_3end# 488 ATGTCCATCAATAGGGGAATGGATAAATAAATTGTGGTATATTCATACAA 537 chr2ptel1M 498251 TGGAATGTTACTGTGCAATAA--GAAATGAA-GAGGCAGATTT 498290 --- i i ii i--i - ivi i L1ME3Cz_3end# 538 TGGAA---TACTATACAGCAGTTAAAATGAATGAACTAGATCT 577 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 32.41 CpG sites = 16, Kimura (unadjusted) = 32.41 Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.06 (5 / 89), avg. gap size = 1.20 (6 / 5) 266 25.68 0.00 0.00 chr2ptel1M 498201 498274 (501726) L1ME1_3end#LINE/L1 492 565 (361) m_b68s551i1 2504 chr2ptel1M 498201 ATGCTCATCAATTGGGGAATGGCTGAATAAGTTATGGTATATAAAAGTAA 498250 ii i? v v i i i i vv vii L1ME1_3end#LI 492 ATGTCCATCAACNGGTGAATGGATAAACAAATTGTGGTATATCCATACAA 541 chr2ptel1M 498251 TGGAATGTTACTGTGCAATAAGAA 498274 ii vv i L1ME1_3end#LI 542 TGGAATACTACTCAGCAATAAAAA 565 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 32.96 CpG sites = 12, Kimura (unadjusted) = 32.96 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.00 (0 / 73), avg. gap size = 0.0 (0 / 0) 12 36.77 0.00 0.00 chr2ptel1M 498516 498577 (501423) (TTTT)n#Simple_repeat 1 62 (0) m_b68s252i10 2505 chr2ptel1M 498516 TTTTTTCACTTTATTATTTCTTGTGGTTTATTATTTTTTTTCTTTTGATC 498565 ivi v v i v vv v v i vv i (TTTT)n#Simpl 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr2ptel1M 498566 TGTTTCTTCTTT 498577 v i i (TTTT)n#Simpl 51 TTTTTTTTTTTT 62 Matrix = Unknown Transitions / transversions = 0.64 (7/11) Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0) 273 31.83 11.04 1.69 chr2ptel1M 499040 499202 (500798) C L2a_3end#LINE/L2 (8) 509 332 m_b68s601i14 2506 chr2ptel1M 499040 ATTTAA-AAATGCATTGATTAAGCATCTTCT--------GGCATTGTGCT 499080 i - -- v i ii v -------- i v C L2a_3end#LINE 509 ATTCAACAAAT--ATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCT 462 chr2ptel1M 499081 AAGTACTGGGT---TGGGGTTAGGCAAAA--GACAGA---CCTTGCCTTC 499122 i ii v---ii viv iii -- i --- i i C L2a_3end#LINE 461 AGGCGCTGGGGATACAGCAGTGAACAAAACAGACAAAAGTCCCTGCCCTC 412 chr2ptel1M 499123 AAAAAGCTTACTTTTTAATGGAGGAGGGCA-ACATACAAACAACTATGTA 499171 vii v i i i ii i - - i v vi C L2a_3end#LINE 411 ATGGAGCTTACATTCTAGTGGGGGGAGACAGACA-ATAAACAAATAAATA 363 chr2ptel1M 499172 TACAAGATGTAGACTATAATAAAGGGAGCTA 499202 vii i i v v ivi i v v v C L2a_3end#LINE 362 AGTAAAATATATAGTATGTCAGATGGTGATA 332 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 41.39 CpG sites = 34, Kimura (unadjusted) = 43.86 Transitions / transversions = 2.00 (34/17) Gap_init rate = 0.06 (9 / 162), avg. gap size = 2.33 (21 / 9) 56 0.00 0.00 0.00 chr2ptel1M 499308 499355 (500645) (AC)n#Simple_repeat 1 48 (0) c_b68s251i1 2507 chr2ptel1M 499308 ACACACACACACACACACACACACACACACACACACACACACACACAC 499355 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACAC 48 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 464 31.15 10.93 0.00 chr2ptel1M 499446 499628 (500372) MIRb#SINE/MIR 14 216 (52) m_b68s601i15 2508 chr2ptel1M 499446 TGACACAGTGGATGGAACACAGGAATTGGGGTCTTCCAGAC-TGAGTTCA 499494 iii vi i i vv i vvv - i i MIRb#SINE/MIR 14 TGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCG 63 chr2ptel1M 499495 AAT----GTTTTGAATCCTACC-----TCAGACACTAACTAAATTATTTA 499535 ---- i i vvv i i----- vv vi iivi i i MIRb#SINE/MIR 64 AATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTA 113 chr2ptel1M 499536 GCTTCTCTATGGTCCAGTTCCCTTATGTGTAAAATAGGGATAATAACATA 499585 i i iv vii i i v i i iv MIRb#SINE/MIR 114 ACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACC 163 chr2ptel1M 499586 GACTTCCCAAAGATGCTGAGGGGATCAAATG----------TGTAAAGGG 499625 v i v ii v i v i i ---------- v MIRb#SINE/MIR 164 TACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCG 213 chr2ptel1M 499626 CTT 499628 MIRb#SINE/MIR 214 CTT 216 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 39.87 CpG sites = 35, Kimura (unadjusted) = 41.81 Transitions / transversions = 1.59 (35/22) Gap_init rate = 0.02 (4 / 182), avg. gap size = 5.00 (20 / 4) 21 14.49 5.45 1.75 chr2ptel1M 500595 500649 (499351) (TTTTG)n#Simple_repeat 1 57 (0) m_b68s252i11 2509 chr2ptel1M 500595 TTTTG-TTTGTTTTATGTTGTATTTCTTTTCTTTTCTTTT-TTCAGTTTT 500642 - i v - v v v - iv (TTTTG)n#Simp 1 TTTTGTTTTGTTTTGTTTTGT-TTTGTTTTGTTTTGTTTTGTTTTGTTTT 49 chr2ptel1M 500643 -TTTTGTT 500649 - (TTTTG)n#Simp 50 GTTTTGTT 57 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.07 (4 / 54), avg. gap size = 1.00 (4 / 4) 43 0.00 0.00 0.00 chr2ptel1M 500720 500756 (499244) (GT)n#Simple_repeat 1 37 (0) c_b68s251i2 2510 chr2ptel1M 500720 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 500756 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 37 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 280 21.05 0.00 0.00 chr2ptel1M 500778 500834 (499166) C MER63D#DNA/hAT-Tip100 (649) 412 356 m_b68s502i0 2511 chr2ptel1M 500778 TCTAGACAGTAAACAAAACAATAAGTCAAACTCTGGTTTCTACTTTTTGC 500827 i v i i i i v viv C MER63D#DNA/hA 412 TCTAGACAATCAACAAAACAATAAATCAAGCCCTGATTTGTAGCGTTTGC 363 chr2ptel1M 500828 CAGTTTC 500834 ii C MER63D#DNA/hA 362 CGATTTC 356 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 20.74 CpG sites = 8, Kimura (unadjusted) = 25.39 Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0) 240 30.26 1.32 0.00 chr2ptel1M 501114 501189 (498811) C L2#LINE/L2 (236) 2846 2770 m_b68s601i16 2506 chr2ptel1M 501114 GGTATTGCTTAGAGTAGTAGCAGGCTCAGACTTGTGCTTTGGGAA-ATCA 501162 v vvi v ii v v v ii i iii i- C L2#LINE/L2 2846 GGTTTTGAGCAGAGGAGTGACATGATCTGACTTACGTTTTAAAAGGATCA 2797 chr2ptel1M 501163 CTTTGGCAGCTGTGTAGAGAATGAATT 501189 i v v ii i C L2#LINE/L2 2796 CTCTGGCTGCTGTGTTGAGAATAGACT 2770 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 37.86 CpG sites = 14, Kimura (unadjusted) = 40.12 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.01 (1 / 75), avg. gap size = 1.00 (1 / 1) 205 16.98 7.55 0.00 chr2ptel1M 503235 503287 (496713) C L3#LINE/CR1 (9) 4090 4034 m_b68s601i17 2512 chr2ptel1M 503235 ACAGA--TTCAGAGATGGGAGG-ACCTCAGAGGTCAGCTAGT-GACCCTT 503280 --i v i - i v -v v i C L3#LINE/CR1 4090 ACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCAACCTC 4041 chr2ptel1M 503281 CCCTCCA 503287 v C L3#LINE/CR1 4040 CCATCCA 4034 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 19.30 CpG sites = 4, Kimura (unadjusted) = 19.30 Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.06 (3 / 52), avg. gap size = 1.33 (4 / 3) 236 32.17 6.96 0.00 chr2ptel1M 503316 503430 (496570) C L3#LINE/CR1 (139) 3960 3838 m_b68s601i18 2513 chr2ptel1M 503316 GAACTCACTCCC-----AGGCAGTGTTTTCTGCCTGGGGAAAACTCTAAT 503360 i v ----- iviv iiii vv v i i C L3#LINE/CR1 3960 GAGCTCACTACCTCNCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGAT 3911 chr2ptel1M 503361 T-CTCGAGA-TTTGTCCTAACACCAAGCCCAAATCCAGCCCTCGGAAACA 503408 -i v i - iv v i iii v iiv i i v v v C L3#LINE/CR1 3910 TGTTAGAAAGTTCTTCCTTATATTGAGCCGAAATCTGCCTCCCTGTAACT 3861 chr2ptel1M 503409 -CCTCCCATTGCTCCTGGTTCTG 503430 - v v i C L3#LINE/CR1 3860 TCCACCCATTGGTCCTAGTTCTG 3838 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 43.25 CpG sites = 21, Kimura (unadjusted) = 43.25 Transitions / transversions = 1.31 (21/16) Gap_init rate = 0.04 (4 / 114), avg. gap size = 2.00 (8 / 4) 201 32.11 9.15 1.31 chr2ptel1M 503444 503585 (496415) L3b_3end#LINE/CR1 311 463 (743) m_b68s601i19 2514 chr2ptel1M 503444 TTATCCAATCTGAGGAAGGAAGACAGCCAGGAAGGGTGGCCCACACGTTG 503493 v i v?iiv v - ii iv ii iv i L3b_3end#LINE 311 TTATCAAATTTGCNAGTGGCAGA-AGCTGGGAGCGACGGCTAATACGTTG 359 chr2ptel1M 503494 GCTGCAAACCGCAGGAT--GAAAGAAGCTT--CGGATT--------GGGC 503531 v vi- --i vi v i-- i i -------- L3b_3end#LINE 360 GATGCAAAAT-CAGGATCCAAAACGATCTCGACAGACTAGAACGNCGGGC 408 chr2ptel1M 503532 TGAAGCTCCTCTGATGAAATGAAATGGGGATCAGGGTAGAAGCCTG-GCA 503580 i ? ivvivv vv ii v iv i iv -i v L3b_3end#LINE 409 CGAANCCAACAAGATGAAATTCAACAGGGATAAACGTAAAGTCCTGCACT 458 chr2ptel1M 503581 TGGGT 503585 L3b_3end#LINE 459 TGGGT 463 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 38.91 CpG sites = 25, Kimura (unadjusted) = 43.94 Transitions / transversions = 1.25 (25/20) Gap_init rate = 0.04 (6 / 141), avg. gap size = 2.50 (15 / 6) 32 39.09 2.68 1.77 chr2ptel1M 504806 505029 (494971) (GAA)n#Simple_repeat 1 226 (0) m_b68s252i12 2515 chr2ptel1M 504806 GAGGAGGAAGAAGAGGATCAGGAAGAGGAGGAGGGGAAAGATGAGAGGAG 504855 i i i vv i i i i iii v - i (GAA)n#Simple 1 GAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA-AGAAG 49 chr2ptel1M 504856 GTGGGGGAGAAAAAG-AGGAGTCGGGGAAAGAGGGGAA-AA-AAGAAAAG 504902 iv ii i i - i vv ii ii ii - - i i (GAA)n#Simple 50 AAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAA 99 chr2ptel1M 504903 GAAGAAG-AGAAGGAGCAGTAGGAGCAGCTGGAGGAGTGTCAGGAAGAAG 504951 - i v v i v vv i i -ivv i (GAA)n#Simple 100 GAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAG-AAGAAGAAGAAG 148 chr2ptel1M 504952 AAGAGGACAAGGAGGAACAGGAGGGGGAAGAAGGAG-GGAAGGAGGAGGA 505000 i vi i i v i i ii i -i - i i (GAA)n#Simple 149 AAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAA-GAAGAAGA 197 chr2ptel1M 505001 GGTAG-AGCAGCAGGAGGAAGAAGAAGAAG 505029 i v - v - i i (GAA)n#Simple 198 AGAAGAAGAAG-AAGAAGAAGAAGAAGAAG 226 Matrix = Unknown Transitions / transversions = 2.71 (46/17) Gap_init rate = 0.04 (10 / 223), avg. gap size = 1.00 (10 / 10) 18 24.37 3.45 0.00 chr2ptel1M 505975 506032 (493968) (GGAGG)n#Simple_repeat 1 60 (0) m_b68s252i13 2516 chr2ptel1M 505975 GGAGGAAAGCAGAGTTGGGGGGAGGGTTGGAG-GGGGAGGGG-GGGGAGG 506022 ii vi vv i vv i - - (GGAGG)n#Simp 1 GGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGG 50 chr2ptel1M 506023 GGAGACGAGG 506032 iv (GGAGG)n#Simp 51 GGAGGGGAGG 60 Matrix = Unknown Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.04 (2 / 57), avg. gap size = 1.00 (2 / 2) 17 20.54 0.00 0.00 chr2ptel1M 505991 506024 (493976) (G)n#Simple_repeat 1 34 (0) m_b68s252i14 2517 chr2ptel1M 505991 GGGGGGAGGGTTGGAGGGGGAGGGGGGGGAGGGG 506024 i vv i i i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 34 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 18 0.00 0.00 0.00 chr2ptel1M 507042 507064 (492936) (GATT)n#Simple_repeat 1 23 (0) m_b68s252i15 2518 chr2ptel1M 507042 GATTGATTGATTGATTGATTGAT 507064 (GATT)n#Simpl 1 GATTGATTGATTGATTGATTGAT 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 15 4.17 4.00 0.00 chr2ptel1M 507486 507510 (492490) (TCCC)n#Simple_repeat 1 26 (0) m_b68s252i16 2519 chr2ptel1M 507486 TCCCTCCCT-CCTCCCTCCCTCCTTC 507510 - i (TCCC)n#Simpl 1 TCCCTCCCTCCCTCCCTCCCTCCCTC 26 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 254 35.78 4.69 1.01 chr2ptel1M 510004 510195 (489805) C L2c_3end#LINE/L2 (4) 474 276 m_b68s601i20 2520 chr2ptel1M 510004 ATCCAATCAACCA-CAGTTGATAAGCATCTGCTCTGAGTAAGCCAGAGGG 510052 i v v - v iv i ii i v v iv v ivv C L2c_3end#LINE 474 ATTCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGG 425 chr2ptel1M 510053 GATAAAAAGACAAA-ATGACCCCGCAGTTGTCCTCAAGGAGCTTGCATTC 510101 v ii - v v v ivvi i ii v C L2c_3end#LINE 424 GATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTC 375 chr2ptel1M 510102 TACTGGGGGCTGT-GGCACCCAGACAAGTCACTGTAAGATAGGGTA--GA 510148 v i vvii- i ?vi i iiiv i ii v i i v -- C L2c_3end#LINE 374 TAGTGGAGGAGACAGACANGTAAACAGACAATTACAATACAAGTTAATGA 325 chr2ptel1M 510149 TAGAAG---TAAGGAGA-TGTCAGAAAAAGTGCTCCTGGAAAATCAGAGA 510194 iiv --- v i - i - v ii -v i ivv i C L2c_3end#LINE 324 TAAGTGCTATAATGGGAGTAT-AGACAGGGTGCT-ATGGGAGCACAGAGG 277 chr2ptel1M 510195 A 510195 C L2c_3end#LINE 276 A 276 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 48.57 CpG sites = 38, Kimura (unadjusted) = 50.69 Transitions / transversions = 1.27 (38/30) Gap_init rate = 0.04 (8 / 191), avg. gap size = 1.38 (11 / 8) 26 24.56 2.70 5.56 chr2ptel1M 510492 510602 (489398) (AGAAGG)n#Simple_repeat 1 108 (0) m_b68s252i17 2521 chr2ptel1M 510492 AGCAGGAGCACAGGGGAAGGAGGAGGAGAAAGAAGAGGAAAAGCAGAAAA 510541 v - - i i i ii i -- i (AGAAGG)n#Sim 1 AGAAGGAG-A-AGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAG--GAGAA 46 chr2ptel1M 510542 GGAAAAGG-G-AGGAAAAGGAAAAAAGGCAAGAAGATGGAAAATGGAGGG 510589 i - - i - i i iv i v i - ii (AGAAGG)n#Sim 47 GGAGAAGGAGAAGGAGAAGG-AGAAGGAGAAGGAGAAGGAGAA-GGAGAA 94 chr2ptel1M 510590 GGAG-AGGAGGAGG 510602 - i (AGAAGG)n#Sim 95 GGAGAAGGAGAAGG 108 Matrix = Unknown Transitions / transversions = 5.67 (17/3) Gap_init rate = 0.08 (9 / 110), avg. gap size = 1.00 (9 / 9) 14 24.15 7.00 4.90 chr2ptel1M 510505 510604 (489396) (GGGAAGA)n#Simple_repeat 1 102 (0) m_b68s252i18 2521 chr2ptel1M 510505 GGGAAGGAGGAGGAGAAAGAAGA-GGAAAAGCAGAAAAGGAAAAGGGAGG 510553 - - i ii - i -i i -i i - (GGGAAGA)n#Si 1 GGGAA-GAGG-GAAGAGGGAAGAGGGAAGAG-GGAAGAGG-GAAGAG-GG 45 chr2ptel1M 510554 AAAAGGAAAAAAGGCA-A--GAAGATGGAAAATGG-AG-GGGGAGA-GGA 510597 i i i i v - -- v i v - - i - (GGGAAGA)n#Si 46 AAGAGGGAAGAGGGAAGAGGGAAGAGGGAAGAGGGAAGAGGGAAGAGGGA 95 chr2ptel1M 510598 GGAGGGA 510604 i (GGGAAGA)n#Si 96 AGAGGGA 102 Matrix = Unknown Transitions / transversions = 5.00 (15/3) Gap_init rate = 0.11 (11 / 99), avg. gap size = 1.09 (12 / 11) 99 8.20 2.55 0.62 chr2ptel1M 510974 511130 (488870) (TC)n#Simple_repeat 1 160 (0) c_b68s251i3 2522 chr2ptel1M 510974 TCTCCCTCT-TCTGTCTCTGTCTCTGTCTCTGTCTGTCTCTGTCTCTGTC 511022 i - v v v v v v v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr2ptel1M 511023 TCTCT-TC-CTCTCTGTCTCTCTCTCTGTCTCTCTGTCTCTCTCTCTCTC 511070 - - v v v (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chr2ptel1M 511071 TCTGTCTC-CTCTCTCTCTGCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 511119 v - - (TC)n#Simple_ 101 TCTCTCTCTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 149 chr2ptel1M 511120 CTCTCTCTCTC 511130 (TC)n#Simple_ 150 CTCTCTCTCTC 160 Matrix = Unknown Transitions / transversions = 0.09 (1/11) Gap_init rate = 0.03 (5 / 156), avg. gap size = 1.00 (5 / 5) 40 0.00 0.00 0.00 chr2ptel1M 511131 511174 (488826) (AC)n#Simple_repeat 1 44 (0) m_b68s252i19 2523 chr2ptel1M 511131 ACACACACACACACACACACACACACACACACACACACACACAC 511174 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACAC 44 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 13 19.39 0.00 2.78 chr2ptel1M 512450 512486 (487514) (GCGGGG)n#Simple_repeat 1 36 (0) m_b68s252i20 2524 chr2ptel1M 512450 GCGGGTGTCGGGGCGGGGGCGGGGCCGTCGGGCAGGG 512486 v iv v -v i (GCGGGG)n#Sim 1 GCGGGGGCGGGGGCGGGGGCGGGGGCG-GGGGCGGGG 36 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 16 8.78 2.38 7.50 chr2ptel1M 512662 512703 (487297) (CGGGGC)n#Simple_repeat 1 40 (0) m_b68s252i21 2525 chr2ptel1M 512662 CGGGTGTCGGGGCGGGGGCC-GGGCCGGGGCCGTCGGGCAGGG 512703 - i v - -- v (CGGGGC)n#Sim 1 CGGG-GCCGGGGCCGGGGCCGGGGCCGGGGCCG--GGGCCGGG 40 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.10 (4 / 41), avg. gap size = 1.00 (4 / 4) 19 8.13 0.00 0.00 chr2ptel1M 513353 513378 (486622) (G)n#Simple_repeat 1 26 (0) m_b68s252i22 2526 chr2ptel1M 513353 GGGGCGGGGGGGGGGGGGGGGGGAGG 513378 v i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGG 26 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 14 6.64 8.82 2.78 chr2ptel1M 513679 513712 (486288) (CCT)n#Simple_repeat 1 36 (0) m_b68s252i23 2527 chr2ptel1M 513679 CCCCCT-CTCC-CTTCCTCCTCCTCCT-CTCGCTCCT 513712 i - - i - - (CCT)n#Simple 1 CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC-CTCCT 36 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.12 (4 / 33), avg. gap size = 1.00 (4 / 4) 31 11.34 1.72 0.00 chr2ptel1M 514788 514808 (485192) (GAGTCGG)n#Simple_repeat 1 21 (38) m_b68s252i24 2528 chr2ptel1M 514788 GAGTCGGGAGGCGGGAGGCAT 514808 v v iv (GAGTCGG)n#Si 1 GAGTCGGGAGTCGGGAGTCGG 21 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 30 0.00 0.00 0.00 chr2ptel1M 514809 514836 (485164) (TTAGGG)n#Simple_repeat 1 28 (0) c_b68s251i4 2529 chr2ptel1M 514809 TTAGGGTTAGGGTTAGGGTTAGGGTTAG 514836 (TTAGGG)n#Sim 1 TTAGGGTTAGGGTTAGGGTTAGGGTTAG 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 31 11.34 1.72 0.00 chr2ptel1M 514837 514872 (485128) (GAGTCGG)n#Simple_repeat 22 58 (1) m_b68s252i24 2530 chr2ptel1M 514837 AGTCGGGAGTCGGGAGTCGGGAGGC-AGAGTCGGGAG 514872 v -i (GAGTCGG)n#Si 22 AGTCGGGAGTCGGGAGTCGGGAGTCGGGAGTCGGGAG 58 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) 200 18.52 3.70 0.00 chr2ptel1M 515341 515394 (484606) C L3b_3end#LINE/CR1 (473) 733 678 m_b68s601i21 2531 chr2ptel1M 515341 GTCCTTGTTAAGCCTTGGTGGCCAGAACTTGAC-CAGCACTCCAGAC-TG 515388 i v i?iv ? v vi - i ?i-? C L3b_3end#LINE 733 GTCCCTTTTAAANTGTGGNGCCCAGAACTGAACGCAGTACTCCAGNTGNG 684 chr2ptel1M 515389 GCCTGA 515394 C L3b_3end#LINE 683 GCCTGA 678 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 23.64 CpG sites = 6, Kimura (unadjusted) = 23.64 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.04 (2 / 53), avg. gap size = 1.00 (2 / 2) 326 30.85 17.18 0.89 chr2ptel1M 519838 520128 (479872) L2#LINE/L2 2154 2491 (591) m_b69s601i0 2532 chr2ptel1M 519838 TTCTCCCTCTCTGACCGCCCCCTCTC--TCTCCT-----GGCTCCTCATC 519880 i v v i i i -- ----- i v L2#LINE/L2 2154 TCCTACCTCACTGGCCGCTCCTTCTCAGTCTCCTTTGCTGGTTCCTCCTC 2203 chr2ptel1M 519881 ACCTCAG-GCCCTCTAAGTCAAGCCGTGCAGCAG--CCCAGTCCTGGGCA 519927 i vv- v ? iivvv vv vv -- i v vv L2#LINE/L2 2204 ATCTCCCCGACCTCTNAACGTTGGAGTGCCCCAGGGCTCAGTCCTTGGAC 2253 chr2ptel1M 519928 TTCTGGGGCTTCTCCCCAGCT--------TCCCCTGGCAAGTCCCTCATT 519969 i v--- ii i i v -------- i? ii vii v vvv L2#LINE/L2 2254 CTCTT---CTCTTCTCTATCTACACTCACTCCCTNGGTGATCTCATCCAG 2300 chr2ptel1M 519970 TCCCAAGGATTCAGCAACCATCTCTCTGCTGGTGATTCC----------T 520009 i v v i ivv v v i i ---------- L2#LINE/L2 2301 TCTCATGGCTTTAAATACCATCTATATGCTGATGACTCCCAAATTTATAT 2350 chr2ptel1M 520010 TTCCTGCCTCGGTCTCGCTGCCGACCTCCGGTCCCATGTCTCCA------ 520053 i v iv ii v iv i v i v i i i v ------ L2#LINE/L2 2351 CTCCAGCCCGGACCTCTCCCCTGAACTCCAGACTCGTATATCCAACTGCC 2400 chr2ptel1M 520054 -----GAC----------GGAGGTCCAGCAGACATCTGAACCTCAGCATG 520088 ----- ---------- v i ii i v v i i L2#LINE/L2 2401 TACTCGACATCTCCACTTGGATGTCTAATAGGCATCTCAAACTTAACATG 2450 chr2ptel1M 520089 TCCAATACAGAGCTCGGGAACTTCCCCCA-AATCCTTCCCC 520128 v v i vv v v- v v i L2#LINE/L2 2451 TCCAAAACTGAACTCCTGATCTTCCCCCTCAAACCTGCTCC 2491 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.88 CpG sites = 42, Kimura (unadjusted) = 40.59 Transitions / transversions = 0.89 (42/47) Gap_init rate = 0.04 (13 / 290), avg. gap size = 4.08 (53 / 13) 35 16.60 3.16 4.26 chr2ptel1M 521314 521408 (478592) (GGA)n#Simple_repeat 1 94 (0) m_b69s252i0 2533 chr2ptel1M 521314 GGAGGAAGAGGAGGAAAGGGAGGAGGGGGA-GAGCAGG-GGAGCCGGTGG 521361 i iii i - v - vv v (GGA)n#Simple 1 GGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGG 50 chr2ptel1M 521362 AGCAGGGGGAAGGA-GAGGAGGGAGCAGGGAGGAGGGAGCAGGAGGAG 521408 v i - - - v - - v (GGA)n#Simple 51 AGGAGGAGG-AGGAGGAGGA-GGAGGA-GGAGGA-GGAGGAGGAGGAG 94 Matrix = Unknown Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.07 (7 / 94), avg. gap size = 1.00 (7 / 7) 11 20.84 0.00 2.94 chr2ptel1M 521828 521862 (478138) (CCCGCC)n#Simple_repeat 1 34 (0) m_b69s252i1 2534 chr2ptel1M 521828 CCCACCCCTCCCCCGGTCCCAGCCCCCCGCCCCCG 521862 i iv v i v - (CCCGCC)n#Sim 1 CCCGCCCCCGCCCCCGCCCCCG-CCCCCGCCCCCG 34 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 14 22.02 4.00 1.96 chr2ptel1M 522305 522354 (477646) (CCTCC)n#Simple_repeat 1 51 (0) m_b69s252i2 2535 chr2ptel1M 522305 CCTCCAGTCACCCGGCCC-CCCCTCCCCGCCCCAGGCCTGCCC-CCCCTC 522352 vv - vv - v vvv v - (CCTCC)n#Simp 1 CCTCCCCTC-CCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTC 49 chr2ptel1M 522353 CC 522354 (CCTCC)n#Simp 50 CC 51 Matrix = Unknown Transitions / transversions = 0.00 (0/9) Gap_init rate = 0.06 (3 / 49), avg. gap size = 1.00 (3 / 3) 42 2.37 0.00 0.00 chr2ptel1M 523156 523198 (476802) (C)n#Simple_repeat 1 43 (0) c_b69s251i0 2536 chr2ptel1M 523156 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCC 523198 v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 43 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 126 27.11 2.76 0.74 chr2ptel1M 524154 524552 (475448) (TCTCTC)n#Simple_repeat 1 407 (0) m_b69s252i3 2537 chr2ptel1M 524154 TCTGTCTTTCCCTCCCT-TCTCTCGCTGTCTCT-TCCCTTCCTC-CTCCT 524200 v i i i - v v - i ii - ii (TCTCTC)n#Sim 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr2ptel1M 524201 TCCCCCTCTCTCTCTC-CTTCCCCCCTC-CTCT-TGTCT-TCTTTCTCTT 524246 i i - ii i i - - v - i i (TCTCTC)n#Sim 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chr2ptel1M 524247 TTTCATCTC-CTCTCT-TGTCTCTGTCTCTCTCTCTGCCTGTCTCAGAAT 524294 i - - - v v vi v vvvv (TCTCTC)n#Sim 101 TCTC-TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 149 chr2ptel1M 524295 TTCTCTTTTTCTCTGTATCTCACCCTCT-TGTCTCTTTCTCTCTTTCTCT 524343 i i i v v v i - v i i (TCTCTC)n#Sim 150 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 199 chr2ptel1M 524344 GTATCTCCGTCTCTCTCTTTCTCTCTTTTTCTTTCTTCCTCTGCCTTTTT 524393 v v iv i i i i ii vi i i (TCTCTC)n#Sim 200 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 249 chr2ptel1M 524394 CTCTGTATCTTTCCCTCTGTCTCCTTTTCTCTTTCTCTCTTTTTCTCTGT 524443 v v i i v ii i i i i v (TCTCTC)n#Sim 250 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 299 chr2ptel1M 524444 ATCTTTCTCTTTCTCTCTGTCTCTCTCTTTCTTTCTCTGTGTCTTTCTCT 524493 v i i v i i v v i (TCTCTC)n#Sim 300 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 349 chr2ptel1M 524494 TTCTCTGTATCTTTCTTTTTCTCTGTAACTGTCT-TTTTTCTCTGCATCT 524542 i v v i i i v vv v - i i - - (TCTCTC)n#Sim 350 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT-C-TCT 397 chr2ptel1M 524543 CTTTCTCTCT 524552 i (TCTCTC)n#Sim 398 CTCTCTCTCT 407 Matrix = Unknown Transitions / transversions = 1.59 (54/34) Gap_init rate = 0.04 (14 / 398), avg. gap size = 1.00 (14 / 14) 21 17.74 7.46 1.41 chr2ptel1M 524162 524228 (475772) (TCCC)n#Simple_repeat 1 71 (0) m_b69s252i4 2538 chr2ptel1M 524162 TCCCTCCCTTCTCTCGCTGTCT-CTTCCCTTCCT-CCT-CCTTCC-CCCT 524207 - i v vi - i i - - i - (TCCC)n#Simpl 1 TCCCTCCC-TCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCT 49 chr2ptel1M 524208 CTCTCTCTCCTTCCC-CCCTCC 524228 i i i - (TCCC)n#Simpl 50 CCCTCCCTCCCTCCCTCCCTCC 71 Matrix = Unknown Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.09 (6 / 66), avg. gap size = 1.00 (6 / 6) 126 27.11 2.76 0.74 chr2ptel1M 524154 524552 (475448) (TCTCTC)n#Simple_repeat 1 407 (0) m_b69s252i3 2537 chr2ptel1M 524154 TCTGTCTTTCCCTCCCT-TCTCTCGCTGTCTCT-TCCCTTCCTC-CTCCT 524200 v i i i - v v - i ii - ii (TCTCTC)n#Sim 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr2ptel1M 524201 TCCCCCTCTCTCTCTC-CTTCCCCCCTC-CTCT-TGTCT-TCTTTCTCTT 524246 i i - ii i i - - v - i i (TCTCTC)n#Sim 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chr2ptel1M 524247 TTTCATCTC-CTCTCT-TGTCTCTGTCTCTCTCTCTGCCTGTCTCAGAAT 524294 i - - - v v vi v vvvv (TCTCTC)n#Sim 101 TCTC-TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 149 chr2ptel1M 524295 TTCTCTTTTTCTCTGTATCTCACCCTCT-TGTCTCTTTCTCTCTTTCTCT 524343 i i i v v v i - v i i (TCTCTC)n#Sim 150 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 199 chr2ptel1M 524344 GTATCTCCGTCTCTCTCTTTCTCTCTTTTTCTTTCTTCCTCTGCCTTTTT 524393 v v iv i i i i ii vi i i (TCTCTC)n#Sim 200 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 249 chr2ptel1M 524394 CTCTGTATCTTTCCCTCTGTCTCCTTTTCTCTTTCTCTCTTTTTCTCTGT 524443 v v i i v ii i i i i v (TCTCTC)n#Sim 250 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 299 chr2ptel1M 524444 ATCTTTCTCTTTCTCTCTGTCTCTCTCTTTCTTTCTCTGTGTCTTTCTCT 524493 v i i v i i v v i (TCTCTC)n#Sim 300 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 349 chr2ptel1M 524494 TTCTCTGTATCTTTCTTTTTCTCTGTAACTGTCT-TTTTTCTCTGCATCT 524542 i v v i i i v vv v - i i - - (TCTCTC)n#Sim 350 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT-C-TCT 397 chr2ptel1M 524543 CTTTCTCTCT 524552 i (TCTCTC)n#Sim 398 CTCTCTCTCT 407 Matrix = Unknown Transitions / transversions = 1.59 (54/34) Gap_init rate = 0.04 (14 / 398), avg. gap size = 1.00 (14 / 14) 382 33.47 10.10 2.96 chr2ptel1M 524560 525064 (474936) L2#LINE/L2 2245 2784 (298) m_b69s601i1 2539 chr2ptel1M 524560 TCTTTG--TCTCTTTTTCTCTGTATCC-CTGTCTCTCTCTCTGT-ATCTC 524605 i --i i ii v i- vv v i ?v - L2#LINE/L2 2245 TCCTTGGACCTCTTCTCTTCTCTATCTACACTCACTCCCTNGGTGATCTC 2294 chr2ptel1M 524606 TTTCTGTCTC-TCTCTCT---TTTTCTCTGTAT-CT-----CTCTC---T 524642 v i v - vv i --- viiv i - ----- i --- L2#LINE/L2 2295 ATCCAGTCTCATGGCTTTAAATACCATCTATATGCTGATGACTCCCAAAT 2344 chr2ptel1M 524643 CTCTCCCTCCAACCC----CCCCCCCCCG-----------CCCATAACCA 524677 i v vi i ---- i i i ----------- vi v L2#LINE/L2 2345 TTATATCTCCAGCCCGGACCTCTCCCCTGAACTCCAGACTCGTATATCCA 2394 chr2ptel1M 524678 ACTGCTTGTTAGACAA------GTGGATCTGTCTTATAGACATTTTAAAC 524721 i ii v v------v -- v i i i L2#LINE/L2 2395 ACTGCCTACTCGACATCTCCACTTGGA--TGTCTAATAGGCATCTCAAAC 2442 chr2ptel1M 524722 TGAATAAGTCTAAAGTAGAATTAACTATCTTTTTCTGCAAACTCAGCCCT 524771 v i v i iiv i vviv iii iv iiivi L2#LINE/L2 2443 TTAACATGTCCAAAACTGAACTCCTGATCTTCCCCCTCAAACCTGCTCCT 2492 chr2ptel1M 524772 GCTCCAG-CTTCTCCAGTGCTATGGAGGTGTA---TCATCCTTCCAGCAA 524817 v iv - i viv vi ?i v - i ---i ivi L2#LINE/L2 2493 CCCGCAGTCTTCCCCATCTCAGTNAATG-GCAACTCCATCCTTCCAGTTG 2541 chr2ptel1M 524818 CCCAAGTTCAAGGTAGACAGTGAGAGTGTTGGCCTTGACTTCCCCTCCTC 524867 i i -i --- i vv - vv -- i i iiii L2#LINE/L2 2542 CTCAGG-CCAA---AAACCTTG-GAGTCAT--CCTTGACTCCTCTCTTTC 2584 chr2ptel1M 524868 CCTCTGCCCTCCCACCTGCCCTAAGACCAAGACTTGTCAGTTCCATC-TC 524916 i vvv i v i iivi i vv v iv i i i i i - L2#LINE/L2 2585 TCTCACACCCCACATCCAATCCATCAGCAAATCCTGTCGGCTCTACCTTC 2634 chr2ptel1M 524917 AAACT-TCTCTCCCATCCATCCTCTCCTCTC--CCTCACACAGCTTCTGC 524963 v - v ivvv iv v i v -- - v iv ii L2#LINE/L2 2635 AAAATATATCCAGAATCCGACCACTTCTCACCACCTC-CACTGCCACCAC 2683 chr2ptel1M 524964 CCTAGCTCAGGTC-CCATCCCTTCTCACTTGGATTATGGCCAAGGCCTCC 525012 i ii i i - vii i i iv v vi L2#LINE/L2 2684 CCTGGTCCAAGCCACCATCATCTCTCGCCTGGATTACTGCAATAGCCTCC 2733 chr2ptel1M 525013 --AGT-GTCTCTCC-TTTCCAATCCCATTAACCTTCCTAAGGATCTGCTC 525058 -- v - i i-i --- v iv ii i?v -- ii L2#LINE/L2 2734 TAACTGGTCTCCCTGCTTCCA---CCCTTGCCCCCCTNCAG--TCTATTC 2778 chr2ptel1M 525059 TCGACA 525064 i L2#LINE/L2 2779 TCAACA 2784 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.14 CpG sites = 99, Kimura (unadjusted) = 46.73 Transitions / transversions = 1.52 (99/65) Gap_init rate = 0.07 (36 / 504), avg. gap size = 1.86 (67 / 36) 194 13.79 0.00 0.00 chr2ptel1M 525723 525751 (474249) L2c_3end#LINE/L2 375 403 (75) m_b69s601i2 2540 chr2ptel1M 525723 GACTGTAAGCTCCCTGAGGGCAGGAACTG 525751 i i i i L2c_3end#LINE 375 GACTGTGAGCTCCTTGAGGGCAGGGACCG 403 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 12.03 CpG sites = 4, Kimura (unadjusted) = 16.14 Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 37 2.38 4.65 0.00 chr2ptel1M 527239 527281 (472719) (CT)n#Simple_repeat 1 45 (0) c_b69s251i1 2541 chr2ptel1M 527239 CTCTCCCTCTCTCTCTCTCTC-CTC-CTCTCTCTCTCTCTCTCTC 527281 i - - (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 45 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.00 (2 / 2) 19 20.48 6.49 2.50 chr2ptel1M 527379 527455 (472545) (CAAGAAA)n#Simple_repeat 1 80 (0) m_b69s252i5 2542 chr2ptel1M 527379 CAAGGAAATTAGAAAACAGCAACAAGAATACAAGAAA-AACAAA-AACCA 527426 - iv vv v - - v - vv (CAAGAAA)n#Si 1 CAA-GAAACAAGAAACAAGAAACAAGAA-ACAAGAAACAAGAAACAAGAA 48 chr2ptel1M 527427 AC-CTAACCAAGCAA-AAGAAACAA-CAACAA 527455 -vv v v - -v (CAAGAAA)n#Si 49 ACAAGAAACAAGAAACAAGAAACAAGAAACAA 80 Matrix = Unknown Transitions / transversions = 0.08 (1/12) Gap_init rate = 0.09 (7 / 76), avg. gap size = 1.00 (7 / 7) 16 13.42 5.45 5.45 chr2ptel1M 527414 527468 (472532) (AAACCAAC)n#Simple_repeat 1 55 (0) m_b69s252i6 2542 chr2ptel1M 527414 AAAACAA-AAACCAACCTAACCAAGCAAAAGAA-ACAACAACAAACC-AC 527460 v - - v - vv - v v - (AAACCAAC)n#S 1 AAACCAACAAACCAA-CAAACCAA-CAAACCAACAAACCAACAAACCAAC 48 chr2ptel1M 527461 AATACCAA 527468 - (AAACCAAC)n#S 49 AA-ACCAA 55 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.11 (6 / 54), avg. gap size = 1.00 (6 / 6) 18 17.92 2.70 8.57 chr2ptel1M 527863 527936 (472064) (AAAAT)n#Simple_repeat 1 70 (0) m_b69s252i8 2543 chr2ptel1M 527863 AAAATAATCTAATGAATAAAAATAAGAAATGAATAAAATGAAAAATAAAG 527912 vv -- - - vvi -- i (AAAAT)n#Simp 1 AAAATAAAATAA--AAT-AAAATAA-AATAAAATAAAAT--AAAATAAAA 44 chr2ptel1M 527913 T-AAA-AGAATAAAATGTAATACAAT 527936 - - i iv v (AAAAT)n#Simp 45 TAAAATAAAATAAAATAAAATAAAAT 70 Matrix = Unknown Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.11 (8 / 73), avg. gap size = 1.00 (8 / 8) 13 21.17 0.00 6.52 chr2ptel1M 531840 531888 (468112) (CCCGCC)n#Simple_repeat 1 46 (0) m_b69s252i9 2544 chr2ptel1M 531840 CCCTCCTCCGTCTCCGCCTCGGGGCCGCGCCCCGCGCCCCCGCCCGCCG 531888 v i i i - vv v v - - (CCCGCC)n#Sim 1 CCCGCCCCCGCCCCCGCC-CCCGCCCCCGCCCC-CGCCCCCGCCC-CCG 46 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.06 (3 / 48), avg. gap size = 1.00 (3 / 3) 14 20.77 2.17 2.17 chr2ptel1M 532264 532309 (467691) (GGGGGCG)n#Simple_repeat 1 46 (0) m_b69s252i10 2545 chr2ptel1M 532264 GGGTGCGTGGGGGAGGGGCGCGGGGGG-AGGGGAATGGGGGAGGGGG 532309 v - v v -i ivv v (GGGGGCG)n#Si 1 GGGGGCG-GGGGGCGGGGGGCGGGGGGCGGGGGGCGGGGGGCGGGGG 46 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.04 (2 / 45), avg. gap size = 1.00 (2 / 2) 16 9.32 0.00 0.00 chr2ptel1M 533445 533467 (466533) (C)n#Simple_repeat 1 23 (0) m_b69s252i11 2546 chr2ptel1M 533445 CCCCCCCCCCCCCCCCGGCCCCC 533467 vv (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCC 23 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 12 14.96 6.78 6.78 chr2ptel1M 534101 534159 (465841) (CCCCAG)n#Simple_repeat 1 59 (0) m_b69s252i12 2547 chr2ptel1M 534101 CCCCAGCCCCAGGACCCCCATCCTC-CCCCCTGCCCACAG--CCAG-CCC 534146 - -- v i -v v - -- - (CCCCAG)n#Sim 1 CCCCAGCCCCA-G--CCCCAGCCCCAGCCCCAGCCC-CAGCCCCAGCCCC 46 chr2ptel1M 534147 TGCCCCCACCCCA 534159 v vi (CCCCAG)n#Sim 47 AGCCCCAGCCCCA 59 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.12 (7 / 58), avg. gap size = 1.14 (8 / 7) 20 33.55 0.00 2.60 chr2ptel1M 534231 534309 (465691) (GT)n#Simple_repeat 1 77 (0) m_b69s252i13 2548 chr2ptel1M 534231 GTGCGTGTGTCTGCACGTGTGTGCGGGACGGATGCGTGTGTGTGTGCACG 534280 i v iii i v -i vi i iii (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTG-TGTGTGTGTGTGTGTGTGTGTG 49 chr2ptel1M 534281 TGTGGGGCCGTGTGTGTGTGCACTGTGTG 534309 v vvi -vv (GT)n#Simple_ 50 TGTGTGTGTGTGTGTGTGTG-TGTGTGTG 77 Matrix = Unknown Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.03 (2 / 78), avg. gap size = 1.00 (2 / 2) 183 18.18 4.55 0.00 chr2ptel1M 537108 537151 (462849) MIR3#SINE/MIR 98 143 (65) m_b69s601i3 2549 chr2ptel1M 537108 AGGTCACTGCACTTCTCTTGG-CTCA-TTTCCTCAGGGGTAAAGTG 537151 i v i v - - vvv i MIR3#SINE/MIR 98 AAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATG 143 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 20.83 CpG sites = 3, Kimura (unadjusted) = 20.83 Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2) 253 37.80 0.00 0.00 chr2ptel1M 537393 537474 (462526) C L2b_3end#LINE/L2 (2) 464 383 m_b69s601i4 2550 chr2ptel1M 537393 TCAAGCAGTCAGTAAATACTGATTAGGCACCTATGATATGTCAGGTGGTG 537442 vv v ii i v i ii i ivi i i i?v C L2b_3end#LINE 464 TCATTCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTG 415 chr2ptel1M 537443 TGTGAAGCACTGAGGATACCATGAGAGGCAAG 537474 iv i i i vii iviii C L2b_3end#LINE 414 TGCTAGGCGCTGGGGATACAGCGGTGAACAAG 383 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 50.58 CpG sites = 22, Kimura (unadjusted) = 59.40 Transitions / transversions = 2.44 (22/9) Gap_init rate = 0.00 (0 / 81), avg. gap size = 0.0 (0 / 0) 293 38.19 5.21 5.21 chr2ptel1M 537685 538068 (461932) C L2#LINE/L2 (145) 2937 2554 m_b69s601i5 2550 chr2ptel1M 537685 AAACGTAGCAGGGG-CTAAGCTACAAAAGGCCTTGGAGGCCTAGCG-GAG 537732 i v i i - i iiii iiv i v - vi -i C L2#LINE/L2 2937 AGAGGTAACGGGGGACCAGATCATGTAGGGCCTTGTAGGCC-ATTGTAAG 2889 chr2ptel1M 537733 CATTTTGTGTTTGACGCTGGAGGCAATAGGA-GTCATT--CAGGTTTACT 537779 v i vv v v iiv vi i - i --vi -- C L2#LINE/L2 2888 GACTTTGGCTTTTACTCTGAGTGAGATGGGAAGCCATTGGAGGGTTT--T 2841 chr2ptel1M 537780 GAGGAGGGGGTGTGACATGATCAGATCAGTGCTTTAGGAAGATTAATTTG 537829 v i i- v iivii i ii i i v i C L2#LINE/L2 2840 GAGCAGAGGA-GTGACATGATCTGACTTACGTTTTAAAAGGATCACTCTG 2792 chr2ptel1M 537830 GTATCTGGATGAAGGATGGAACACAGGGGAGAGAAACTGGAAACAGATAC 537879 ivv vi vi i i vii? i vi iiv i iv - C L2#LINE/L2 2791 GCTGCTGTGTTGAGAATAGACTGNAGGGGGGCAAGGGTGGAAGCAGGGA- 2743 chr2ptel1M 537880 TTCTCAACCCCCTGCCAGCAGCTGCTGCCATAGTCCA---GAG---TGAA 537923 -----i vvi i--i vi ii vi i --- --- v C L2#LINE/L2 2742 -----GACCAGTTA--GGAGGCTATTGCAGTAATCCAGGCGAGAGATGAT 2700 chr2ptel1M 537924 GG------AGAGAAGGGGGAT-GTGGAAGAGGTGCTGCAGAGGTGAAACA 537966 ------i vv v i - ii vi v - i -iv i C L2#LINE/L2 2699 GGTGGCTTGGACCAGGGTGGTGGCAGTGGAGGTGGTG-AGAAGTG-GTCG 2652 chr2ptel1M 537967 GA--CCAGAGATGTTGCAGAGATGAAACGGACCAGAGATGTTGCAGAGAT 538014 -- ii v i viii i ii i v vi vv i ----- C L2#LINE/L2 2651 GATTCTGGATATATTTTGAAGGTAGAGCCGACAGGATTTGCT-----GAT 2607 chr2ptel1M 538015 GAAACGGACCAGAGATGTTGCAGAGATGAAACGGACCAGAGATGCTGCAG 538064 i vi ivv i i viv i - i v iii ii viv vi C L2#LINE/L2 2606 GGATTGGATGTGGGGTGTGAGAGAAA-GAGAGGAGTCAAGGATGACTCCA 2558 chr2ptel1M 538065 AGGT 538068 C L2#LINE/L2 2557 AGGT 2554 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 55.55 CpG sites = 89, Kimura (unadjusted) = 57.51 Transitions / transversions = 1.78 (89/50) Gap_init rate = 0.08 (29 / 383), avg. gap size = 1.38 (40 / 29) 370 34.85 3.33 2.76 chr2ptel1M 539150 539329 (460671) C L3#LINE/CR1 (219) 3880 3700 m_b69s601i6 2551 chr2ptel1M 539150 AAGGCTGGTATCCAGCACCTCCTCTCCCAGTACTCCTGGTTCTAGTCTCT 539199 iv vivi v i v i - v v iv i ivi C L3#LINE/CR1 3880 AAATCTGCCTCCCTGTAACTTC-CACCCATTGGTCCTAGTTCTGCCCTCT 3832 chr2ptel1M 539200 GGGGTCAAGCAGACCAAGAATGATCATTTGTCC-CATGGTAGCTCTTCAG 539248 i i vi vi vv i vi iv - ii i i C L3#LINE/CR1 3831 GGAGCCACACAGAATAAGTCTAATCCCTCTTCCACATGACAGCCCTTCAA 3782 chr2ptel1M 539249 GTTCAGATTCAGAG---GATTCCACCT-TTCTCAGAGCCTCTTCTCCTGC 539294 i ---- iii --- v vi iv - i vi i ii i v C L3#LINE/CR1 3781 AT----ATTTGAAGACAGCTATCATGTCTCCTCTAAGTCTTCTCTTCTCC 3736 chr2ptel1M 539295 AAGCTCAGCATCCCCA-TTCCTATGGCTGATCCTCA 539329 i v i - viii i v C L3#LINE/CR1 3735 AGGCTAAACATCCCCAGTTCCTTCAACCGTTCCTCA 3700 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 48.16 CpG sites = 38, Kimura (unadjusted) = 49.33 Transitions / transversions = 1.65 (38/23) Gap_init rate = 0.05 (9 / 179), avg. gap size = 1.22 (11 / 9) 201 19.33 11.11 1.45 chr2ptel1M 540346 540408 (459592) L3#LINE/CR1 3528 3596 (503) m_b69s601i7 2552 chr2ptel1M 540346 TAGAATTCAGAGCAAGG-AGGCAGCAGTCCCCTTGGAC-CTG----GATC 540389 vi i ? - i ii vi v - ---- i L3#LINE/CR1 3528 TAGTGTCCAGANCAAGGGAGGTAATAGTCCCGCTGTACTCTGCGCTGGTC 3577 chr2ptel1M 540390 AGATCAC-TCTGAGGGTATT 540408 i - - i L3#LINE/CR1 3578 AGACCACATCTG-GAGTATT 3596 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 23.69 CpG sites = 9, Kimura (unadjusted) = 23.69 Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.08 (5 / 62), avg. gap size = 1.60 (8 / 5) 344 33.84 4.00 4.38 chr2ptel1M 541513 541787 (458213) C L2d_3end#LINE/L2 (2) 514 241 m_b69s601i8 2553 chr2ptel1M 541513 AAGTAATCAATGAATCAATATTTA---AACATCCATTATATGCCAGGCAT 541559 vi v iv i --- i ii i i i ivi i C L2d_3end#LINE 514 AATCAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCAC 465 chr2ptel1M 541560 TGTGTTAAATGCCA-GGGTCAT-AAAAAGAAGCAAAAGATA--GTTCTTG 541605 i iii ii- vv i- ? i? i v i -- i i C L2d_3end#LINE 464 TGTGCTAGGCGCTGTGGGGAACGANAAAANAGTATAAGACATGGTCCCTG 415 chr2ptel1M 541606 CTTTCAAGAAGTTTATAATCTAATGGGGGAAATAACAAGCAAACACATAC 541655 ii i i i i v i i v vvv v i- C L2d_3end#LINE 414 CCCTCAAGGAGCTTACAATCTAGTTGGGGAGACAAGACTAACACACATG- 366 chr2ptel1M 541656 AGACAGCTATTG-ACAAGATAA-CTAGGAAATAATGAAGA--CAAATTGG 541701 i ii vv - v i -vi v v v v--i -- C L2d_3end#LINE 365 AAACAATTAGAGAACAATACAAGACAGTATATAATTAAGTGCTAAATT-- 318 chr2ptel1M 541702 AGGCTTCCTGTAGGAGATGGGATTTTATTTGGAATTTAAGGAAGAATTCA 541751 -- v vv ii ivv ii - vi - v i i ii ii--- C L2d_3end#LINE 317 --GCGTGGTACAGACTATAAG-TGCTA-TAGGAGTTCAGAGAAGGG---A 275 chr2ptel1M 541752 GAGATCAGCAGTTAGAATGGAGGAGGGAGAGAAGGC 541787 ii-- i iv vi vv i C L2d_3end#LINE 274 GAGATCAGTG--TGGGCTGGAGTGGTCAGGGAAGGC 241 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.72 CpG sites = 57, Kimura (unadjusted) = 48.01 Transitions / transversions = 1.78 (57/32) Gap_init rate = 0.07 (19 / 274), avg. gap size = 1.21 (23 / 19) 307 38.51 11.33 1.00 chr2ptel1M 541519 541880 (458120) C L2b_3end#LINE/L2 (6) 460 62 m_b69s601i9 2553 chr2ptel1M 541519 TCAATGAATCAATATTTA---AACATCCATTATATGCCAGGCATTGTGTT 541565 v v iv --- i ii i i i i ?i i C L2b_3end#LINE 460 TCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCT 411 chr2ptel1M 541566 AAATGCCAGGGTCATAA----AAAGAAGCAAAAGATAGTTCTTGCTTTCA 541611 iii ii vi i i----i v vv i v?ii i i ii C L2b_3end#LINE 410 AGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCA 361 chr2ptel1M 541612 AGAAGTTTATAATCTAATGGGGGAAATA-ACAAGCAAACACATACAGACA 541660 v i i i i i i i i - v i ? v i vv? i C L2b_3end#LINE 360 CGGAGCTCACAGTCTAGTGGGGGAGACAGACATGTAANCAGACAATNATA 311 chr2ptel1M 541661 GCT---ATTGACAAGATA--ACTAGGAAA---TAATGAAGA--------- 541693 i i--- v i i i -- i iii---i iv i i--------- C L2b_3end#LINE 310 ACCCAGAGTGGCAGGGTAGGACTGGGGGGGCCCAGAGGAGGGCGCCTGAC 261 chr2ptel1M 541694 -CAAATTGGAG-----------GCTTCCTGTAGGAGATGGGATTTTATTT 541731 - iivi i ----------- i v i iv v vi C L2b_3end#LINE 260 CCGGCCTGGGGGGTCAGGGAGGGCTTCCCGGAGGAGGTGACATTTGAGCT 211 chr2ptel1M 541732 GGAATTTAAGGAAGAATTCAGAGATCAGCAGTT--AGA-ATGGAGGAGGG 541778 ii ii i i i vi v vi v viv vi-- -i i i C L2b_3end#LINE 210 GAGACCTGAAGGATGAGTAGGAGTTGGCCAGGCGAAGAGGTGGGGAAGGG 161 chr2ptel1M 541779 AGAG-AAGGCATGGGGTACAGCCAGACAAAATACTCAGAATTGGAAAGAG 541827 v vv-v vi v v? vvv vi i v ivi i i?ii C L2b_3end#LINE 160 CGTTCCAGGCAGAGGGAACAGCANGTGCAAAGGCCCTGAGGCGGGAGNGA 111 chr2ptel1M 541828 ATGGGGGGGTCTTGTTCATAGGACAGTCAGGAGGCCAATGGCACTAGATC 541877 ii?v ---- v ivi i iv i vvi i v C L2b_3end#LINE 110 GCNTGG----CGTGTTCGAGGAACAGCAAGGAGGCCAGTGTGGCTGGAGC 65 chr2ptel1M 541878 AAA 541880 i C L2b_3end#LINE 64 AGA 62 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 54.98 CpG sites = 91, Kimura (unadjusted) = 60.63 Transitions / transversions = 1.94 (91/47) Gap_init rate = 0.04 (16 / 361), avg. gap size = 2.81 (45 / 16) 217 38.14 3.59 3.59 chr2ptel1M 541700 541922 (458078) C L2d_3end#LINE/L2 (270) 246 24 m_b69s601i10 2553 chr2ptel1M 541700 GGAGGCTTCCTGTAGGAGATGGGATTTTATTTGGAATTTAAGGAAGAATT 541749 i v v i i v vi ivi i i i viiv C L2d_3end#LINE 246 GAAGGCTTCGTGGAGGAGGTGGGACTTGAGCTGGGCCTTGAAGGATGGGT 197 chr2ptel1M 541750 CAGAGATCAGCAGTTAGAATGGAGGAGGGAGAG-----AAGGCATGGGGT 541794 vi vv viii vv iv i i i i -----v iv v C L2d_3end#LINE 196 AGGATTTGGATAGAGAGAGAGGAAGGGGAAGGGCATTCCAGGCGGGGGGA 147 chr2ptel1M 541795 ACAGCCAGACAAAATACTCAGAATTGGAAAGAGATGGGGGGGTCTTGTTC 541844 i vv vv vi v ivi i ---- v vii v v C L2d_3end#LINE 146 ACGGCGTGAGCAAAGGCGCAGAGGCGGGA----ATGCGCAAGGCGTGTTC 101 chr2ptel1M 541845 ATAGGACAGTCAGGAGGCCAATGGCACTAGATCAAAAACTACCTTTGTGG 541894 ivi v i i iiivvv i v ii ii----v i v C L2d_3end#LINE 100 GGGGGACAGTGAAGAGACCGGCCTGACTGGAGCGGAGG----GTTCGTGC 55 chr2ptel1M 541895 T-GGGAGTATTGTAAG--AAGACTGGAAAAG 541922 - v vi -- i ? i C L2d_3end#LINE 54 TGGGGAGTAGTGGGAGATAAGGCTGGANAGG 24 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 48.71 CpG sites = 44, Kimura (unadjusted) = 55.40 Transitions / transversions = 1.16 (44/38) Gap_init rate = 0.05 (11 / 222), avg. gap size = 1.45 (16 / 11) 39 31.08 6.69 2.57 chr2ptel1M 542157 542455 (457545) (ACATAC)n#Simple_repeat 1 311 (0) m_b69s252i14 2554 chr2ptel1M 542157 ACATACACAATACATTATATGCACACGTCTTCCAAATATATATACATCAC 542206 - -i ii i -v v v v i i - i (ACATAC)n#Sim 1 ACATACAC-ATACA-CATACACATAC-ACATACACATACACATACA-CAT 46 chr2ptel1M 542207 ACACGTGTATACTACACA-A-ATATGCCCTCACATATACAAATAC-CGTA 542253 i ii i - - - i i v vi i v - i (ACATAC)n#Sim 47 ACACATACACA-TACACATACACATACACATACACATACACATACACATA 95 chr2ptel1M 542254 CACATACATA-ACACGTGCTGCAT--ACTTACAC-CACACATACATATGT 542299 i - i i -i -- v -i i ii (ACATAC)n#Sim 96 CACATACACATACACATAC-ACATACACATACACATACACATACACATAC 144 chr2ptel1M 542300 GCACA-AC-T-CACACACAGCCCACACATTCACATATA-AGCCCCATGCA 542345 i i - - - i - vi v i - vv v i (ACATAC)n#Sim 145 ACATACACATACACATACA-CATACACATACACATACACATACACATACA 193 chr2ptel1M 542346 TGTGTGTATAAATTATACACATATTCATAAACATTTACAAGCA-ATACA- 542393 ii iiii v -i iv v vi vi - - (ACATAC)n#Sim 194 CATACACATACA-CATACACATACACATACACATACACATACACATACAC 242 chr2ptel1M 542394 ATATGTGCACATATACAC-TTCATATACACATATACA-A-A-TTACACAT 542439 iiiii i - v i i - - -v (ACATAC)n#Sim 243 ATACACATACACATACACATACACATACACATACACATACACATACACAT 292 chr2ptel1M 542440 GCAC--ACATATAC-CATA 542455 i -- i - (ACATAC)n#Sim 293 ACACATACACATACACATA 311 Matrix = Unknown Transitions / transversions = 2.50 (50/20) Gap_init rate = 0.09 (26 / 298), avg. gap size = 1.08 (28 / 26) 15 39.63 3.05 3.05 chr2ptel1M 542200 542330 (457670) (AC)n#Simple_repeat 1 131 (0) m_b69s252i15 2555 chr2ptel1M 542200 ACATCACACACGTGTATACTACACAAATATGCCCTCACATATACAAATAC 542249 - iiii i - v i ii v v i i v i (AC)n#Simple_ 1 ACA-CACACACACACACAC-ACACACACACACACACACACACACACACAC 48 chr2ptel1M 542250 -CGTACACATACATA-ACACGTGCTGCATACTTACAC-CACACATACATA 542296 - ii i i - iii -i i vi - i i (AC)n#Simple_ 49 ACACACACACACACACACACACAC-ACACACACACACACACACACACACA 97 chr2ptel1M 542297 TGTGCACA-ACTCACACACAGCCCACACATTCACA 542330 iiii - v - v iv (AC)n#Simple_ 98 CACACACACACACACACACA-CACACACACACACA 131 Matrix = Unknown Transitions / transversions = 3.50 (28/8) Gap_init rate = 0.06 (8 / 130), avg. gap size = 1.00 (8 / 8) 39 31.08 6.69 2.57 chr2ptel1M 542157 542455 (457545) (ACATAC)n#Simple_repeat 1 311 (0) m_b69s252i14 2554 chr2ptel1M 542157 ACATACACAATACATTATATGCACACGTCTTCCAAATATATATACATCAC 542206 - -i ii i -v v v v i i - i (ACATAC)n#Sim 1 ACATACAC-ATACA-CATACACATAC-ACATACACATACACATACA-CAT 46 chr2ptel1M 542207 ACACGTGTATACTACACA-A-ATATGCCCTCACATATACAAATAC-CGTA 542253 i ii i - - - i i v vi i v - i (ACATAC)n#Sim 47 ACACATACACA-TACACATACACATACACATACACATACACATACACATA 95 chr2ptel1M 542254 CACATACATA-ACACGTGCTGCAT--ACTTACAC-CACACATACATATGT 542299 i - i i -i -- v -i i ii (ACATAC)n#Sim 96 CACATACACATACACATAC-ACATACACATACACATACACATACACATAC 144 chr2ptel1M 542300 GCACA-AC-T-CACACACAGCCCACACATTCACATATA-AGCCCCATGCA 542345 i i - - - i - vi v i - vv v i (ACATAC)n#Sim 145 ACATACACATACACATACA-CATACACATACACATACACATACACATACA 193 chr2ptel1M 542346 TGTGTGTATAAATTATACACATATTCATAAACATTTACAAGCA-ATACA- 542393 ii iiii v -i iv v vi vi - - (ACATAC)n#Sim 194 CATACACATACA-CATACACATACACATACACATACACATACACATACAC 242 chr2ptel1M 542394 ATATGTGCACATATACAC-TTCATATACACATATACA-A-A-TTACACAT 542439 iiiii i - v i i - - -v (ACATAC)n#Sim 243 ATACACATACACATACACATACACATACACATACACATACACATACACAT 292 chr2ptel1M 542440 GCAC--ACATATAC-CATA 542455 i -- i - (ACATAC)n#Sim 293 ACACATACACATACACATA 311 Matrix = Unknown Transitions / transversions = 2.50 (50/20) Gap_init rate = 0.09 (26 / 298), avg. gap size = 1.08 (28 / 26) 12 16.57 0.00 0.00 chr2ptel1M 543506 543532 (456468) (TCCC)n#Simple_repeat 1 27 (0) m_b69s252i16 2556 chr2ptel1M 543506 TCTCTCCCTCCCTCCATCCTTCACTCC 543532 i v i v (TCCC)n#Simpl 1 TCCCTCCCTCCCTCCCTCCCTCCCTCC 27 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 13 18.85 2.78 0.00 chr2ptel1M 545410 545445 (454555) (CCTGCC)n#Simple_repeat 1 37 (0) m_b69s252i17 2557 chr2ptel1M 545410 CCGGCCCCTCCGCCT-CCCCTGCTTCTGCCCCTGGCC 545445 v v v - ii v (CCTGCC)n#Sim 1 CCTGCCCCTGCCCCTGCCCCTGCCCCTGCCCCTGCCC 37 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) 16 0.00 0.00 0.00 chr2ptel1M 545596 545613 (454387) (C)n#Simple_repeat 1 18 (0) m_b69s252i18 2558 chr2ptel1M 545596 CCCCCCCCCCCCCCCCCC 545613 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCC 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 13 29.74 1.54 3.12 chr2ptel1M 546842 546906 (453094) (CGCCCC)n#Simple_repeat 1 64 (0) m_b69s252i19 2559 chr2ptel1M 546842 CGCCCCCGGACCAGGGCCCGCTTCCTCCCGGCCGCCCCAGACAGAGCCCG 546891 vv v vv ii v -- v v vvv v (CGCCCC)n#Sim 1 CGCCCCCGCCCCCGCCCCCGCCCCCGCCC--CCGCCCCCGCCCCCGCCCC 48 chr2ptel1M 546892 TG-CCCCGCCCCCGCC 546906 i - (CGCCCC)n#Sim 49 CGCCCCCGCCCCCGCC 64 Matrix = Unknown Transitions / transversions = 0.25 (3/12) Gap_init rate = 0.05 (3 / 64), avg. gap size = 1.00 (3 / 3) 15 20.83 4.55 0.00 chr2ptel1M 547105 547148 (452852) (GCC)n#Simple_repeat 1 46 (0) m_b69s252i20 2560 chr2ptel1M 547105 GCCGCTGCAGCC-CCGCCGCCGCCCCCAGGGCC-CCCCCGCTGCCG 547148 i v - v ivv - v i (GCC)n#Simple 1 GCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCG 46 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2) 14 13.72 3.12 0.00 chr2ptel1M 547255 547286 (452714) (GGGTTA)n#Simple_repeat 1 33 (0) m_b69s252i21 2561 chr2ptel1M 547255 GGGTTAGGGTTAGAGTTAGAG-TCTGGTTAGGG 547286 i i - vv (GGGTTA)n#Sim 1 GGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGG 33 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 16 24.78 1.92 1.92 chr2ptel1M 547967 548018 (451982) (TCGGAG)n#Simple_repeat 1 52 (0) m_b69s252i22 2562 chr2ptel1M 547967 TCGGAG-CTGGGCCTGGGGTCAGAGTCGGGGTCAGAGCTGGAGCCGGAGT 548015 - v i i - i i i i ii i (TCGGAG)n#Sim 1 TCGGAGTCGGAGTC-GGAGTCGGAGTCGGAGTCGGAGTCGGAGTCGGAGT 49 chr2ptel1M 548016 CGG 548018 (TCGGAG)n#Sim 50 CGG 52 Matrix = Unknown Transitions / transversions = 9.00 (9/1) Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.00 (2 / 2) 19 23.14 0.00 7.14 chr2ptel1M 548151 548225 (451775) (GGCCC)n#Simple_repeat 1 70 (0) m_b69s252i23 2563 chr2ptel1M 548151 GGCCCGCGCCCTGCCCGGCCCCGCCCTCGACTCCGCCCCCGCCCCGCCCC 548200 - v - v - i - v v v v (GGCCC)n#Simp 1 GGCCCG-GCCCGGCCCGG-CCCGGCC-CGGC-CCGGCCCGGCCCGGCCCG 46 chr2ptel1M 548201 GCCTTCCCGGGCCTGGGCCCCGCCC 548225 ivv v -v v (GGCCC)n#Simp 47 GCCCGGCCCGGCC-CGGCCCGGCCC 70 Matrix = Unknown Transitions / transversions = 0.18 (2/11) Gap_init rate = 0.07 (5 / 74), avg. gap size = 1.00 (5 / 5) 25 23.66 4.58 5.38 chr2ptel1M 548153 548283 (451717) (CCCGGC)n#Simple_repeat 1 130 (0) m_b69s252i24 2563 chr2ptel1M 548153 CCCGCGCCCTG-CCCGGCCCCGCCCTCGACTCC-GCCCCCGCCCC-GCCC 548199 vv v - v i i i - v - (CCCGGC)n#Sim 1 CCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCC 50 chr2ptel1M 548200 CGCCTTCCCGGGCCTGGGCCCCGCCCCCGTGCACCTCCGCCCCTGGCCAA 548249 v -- - iv v - - - v - vv (CCCGGC)n#Sim 51 CGGC--CCC-GGCCCCGGCCCCGGCCCCG-GC-CC-CGGCCCC-GGCCCC 93 chr2ptel1M 548250 GG--GTGGAGACGGCTCC-GCCCCGCCTCCGGCTCCG 548283 --vi vvv i - v i i (CCCGGC)n#Sim 94 GGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCG 130 Matrix = Unknown Transitions / transversions = 0.50 (8/16) Gap_init rate = 0.09 (12 / 130), avg. gap size = 1.08 (13 / 12) 626 30.20 1.83 2.78 chr2ptel1M 548806 549023 (450977) MIRb#SINE/MIR 27 242 (26) m_b69s601i11 2564 chr2ptel1M 548806 AGAGCACTGGGTTTAGGGTTGGGAAAGCCCGATTTCAAATCCAGTCTCAA 548855 v v i i ii iv ii i iv i v v v- MIRb#SINE/MIR 27 AGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTCT- 75 chr2ptel1M 548856 GACTGTTCGTAGCTGTGAGACCCCAG-CAAGTCACTTAGCCTGTCC-CGC 548903 v vv vv v iii - i i v i-v MIRb#SINE/MIR 76 GCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGC 125 chr2ptel1M 548904 CTCAGTGTCCTTAATTGTGAAGTGGGATGACAGGAAGAGCCGCAACCTCC 548953 v i vi i i -- i iv v v i--- v MIRb#SINE/MIR 126 CTCAGTTTCCTCATCTGTAAAATGGG--GATAATAATACCT---ACCTCG 170 chr2ptel1M 548954 GAGGGCTGCTGTGAGGATGAG--GAGGTGATAGTTGTGAAGCCCTTGGCC 549001 v i i v i-- i i ivv i v i v MIRb#SINE/MIR 171 CAGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGCA 220 chr2ptel1M 549002 TGGTGCTTGGCACATGATAGGC 549023 ii i ii i MIRb#SINE/MIR 221 CAGTGCCTGGCACATAGTAAGC 242 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.90 CpG sites = 37, Kimura (unadjusted) = 39.70 Transitions / transversions = 1.37 (37/27) Gap_init rate = 0.04 (9 / 217), avg. gap size = 1.11 (10 / 9) 265 31.20 17.60 0.00 chr2ptel1M 549303 549427 (450573) C MIR#SINE/MIR (20) 242 96 m_b69s601i12 2565 chr2ptel1M 549303 GAGTGTGGACTATGTGCCAGGCACTGTATTCAACCCTCTACAGATAGCA- 549351 i ivv vi v i v i vi vi - C MIR#SINE/MIR 242 GAGCGCTTACTATGTGCCAGGCACTGTTCTAAGCGCTTTACATGTATTAA 193 chr2ptel1M 549352 ---------------------CGTTGGGAGGGAGGGGCTAATATAGACTC 549380 --------------------- vi iv v vi v viv i C MIR#SINE/MIR 192 CTCATTTAATCCTCACAACAACCCTATGAGGTAGGTACTATTATTATCCC 143 chr2ptel1M 549381 CATTTTGTAGTTGGGGAAACTGAGGCAGAGATGGGGAGGGGGACTTG 549427 ii v i v vi vvii vi C MIR#SINE/MIR 142 CATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTG 96 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.50 CpG sites = 19, Kimura (unadjusted) = 40.82 Transitions / transversions = 0.95 (19/20) Gap_init rate = 0.02 (2 / 124), avg. gap size = 11.00 (22 / 2) 277 31.54 10.98 1.05 chr2ptel1M 549503 549675 (450325) C L2#LINE/L2 (567) 2515 2326 m_b69s601i13 2566 chr2ptel1M 549503 ACTAAGA--GGGAAGGGAGTGAGAGG-GAGGGTTTG-GGGCAAAGGTCAT 549548 i -- ivv i i - vi - vi i v C L2#LINE/L2 2515 ACTGAGATGGGGAAGACTGCGGGAGGAGCAGGTTTGAGGGGGAAGATCAG 2466 chr2ptel1M 549549 ACGTCCTGTTTGGGACACGCTGACTGTTTGAAATGTC-------CAGCCA 549591 iv i v v i i i -- i i ------- v C L2#LINE/L2 2465 GAGTTCAGTTTTGGACATGTTAA--GTTTGAGATGCCTATTAGACATCCA 2418 chr2ptel1M 549592 GTTCAAGAAGTTTGAAAGGCAGGTGGAGATGCAAAGTTGGACGTCAGCAG 549641 iv vi v iviiv v v i i ivi vv vi C L2#LINE/L2 2417 AGTGGAGATGTCGAGTAGGCAGTTGGATATACGAGTCTGGAGTTCAGGGG 2368 chr2ptel1M 549642 A---GTTTAG--TGCAG---TAAAGGTAGACGTCGTCAGCAT 549675 --- iii -- v --- vv i iv i C L2#LINE/L2 2367 AGAGGTCCGGGCTGGAGATATAAATTTGGGAGTCATCAGCAT 2326 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.94 CpG sites = 30, Kimura (unadjusted) = 42.02 Transitions / transversions = 1.25 (30/24) Gap_init rate = 0.05 (9 / 172), avg. gap size = 2.33 (21 / 9) 271 26.14 10.23 0.00 chr2ptel1M 549718 549805 (450195) C MIR1_Amn#SINE/MIR (38) 192 96 m_b69s601i14 2567 chr2ptel1M 549718 TGGATACCACAGCAATTTGCCA------TCGCCTTCTCTAGCTCC-TTGT 549760 i vi v v i v ------ iviv vi v i - v C MIR1_Amn#SINE 192 TAGATCTCAAAGCACTTTACAAAGGAGGTCAGTATCATTATCCCCATTTT 143 chr2ptel1M 549761 ACAGATGAGGAAATTGAGG--TAAAAAGGTTAAGTGACTTCCCTAGG 549805 i --i i i ? v i i C MIR1_Amn#SINE 142 ACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGCCCAAG 96 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.23 CpG sites = 13, Kimura (unadjusted) = 33.23 Transitions / transversions = 1.30 (13/10) Gap_init rate = 0.03 (3 / 87), avg. gap size = 3.00 (9 / 3) 295 28.57 15.13 0.00 chr2ptel1M 549753 549871 (450129) C MIRc#SINE/MIR (120) 148 12 m_b69s601i15 2567 chr2ptel1M 549753 CTCCTTGTACAGATGAGGAAATTGAGG--TAAAAAGGTTAAGTGACTTCC 549800 i v v i --i i i v C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr2ptel1M 549801 --------------CTAGGAAGTGCCTGGGGCCAGATTTGAACTCAGAAA 549836 -------------- v v v i v vi i i i ivv C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTC 49 chr2ptel1M 549837 GACAACATTCTAA--CCACTGTACCATCTACTGCACC 549871 vv vvv i i -- v iv iv i C MIRc#SINE/MIR 48 TTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACC 12 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.97 CpG sites = 16, Kimura (unadjusted) = 36.26 Transitions / transversions = 0.89 (16/18) Gap_init rate = 0.03 (3 / 118), avg. gap size = 6.00 (18 / 3) 246 31.04 0.84 2.56 chr2ptel1M 550482 550600 (449400) C L2#LINE/L2 (785) 2297 2181 m_b69s601i16 2566 chr2ptel1M 550482 GATGAAATCACCAAAGGAAGTAGTATAGAGGGAAGAGCACAGGACAGGAT 550531 i ? i ivv i vi ii --- i v vi C L2#LINE/L2 2297 GATGAGATCACCNAGGGAGTGAGTGTAGATAGAGAAG---AGAAGAGGTC 2251 chr2ptel1M 550532 CCAGGACAGATCCCTGAAG-ACACCGAAGGTCAGAAGGTATGACCTGGAG 550580 v v v ii - v i v v ? i viiv ivvvv C L2#LINE/L2 2250 CAAGGACTGAGCCCTGGGGCACTCCAACGTTNAGAGGTCGGGGAGATGAG 2201 chr2ptel1M 550581 GAGGATCCGGCAAAGAAGAC 550600 v i i C L2#LINE/L2 2200 GAGGAACCAGCAAAGGAGAC 2181 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.94 CpG sites = 18, Kimura (unadjusted) = 41.58 Transitions / transversions = 1.00 (18/18) Gap_init rate = 0.03 (4 / 118), avg. gap size = 1.00 (4 / 4) 270 34.47 15.75 1.68 chr2ptel1M 550713 551131 (448869) C L2#LINE/L2 (1132) 1950 1474 m_b69s601i17 2566 chr2ptel1M 550713 GGAAAGGGTTAAGGAGAGAGTTGGAGGAGAGAGTGTGAAGGCTGCTAGTG 550762 iv v i i v iivv i i v v i C L2#LINE/L2 1950 GGAGTGGGTTCAAGAGAGAATGGGAGGAGAGGAATTGGAGACAGCGAGTA 1901 chr2ptel1M 550763 TAGATGGCCTCCTTGGGGAGTTT-ACTAGAAAGAG-AGAAGAGAAAGAGG 550810 iii iiii i i -i iv i - v vi C L2#LINE/L2 1900 TAGACAACTCTTTCGAGGAGTTTTGCTGTAAAGGGGAGCAGAGAAATGGG 1851 chr2ptel1M 550811 ATGATATTTAGCAGGG-ATGCAGTAGTCAAAAGAGCATT-------TTTC 550852 ii i vi i vi - ? ii -i ii v ------- v C L2#LINE/L2 1850 GCGGTAGCTGGAGGGGGANGTGG-GGTCAAGGGAGAATTTTTGTTTTTTA 1802 chr2ptel1M 550853 AGGATTAAGGAGCCGGGGGCCTGTG-----------GGGAAGGAGCCAGT 550891 i viii ivi?ivi v v----------- v v C L2#LINE/L2 1801 AAGATGGGAGAAATNACAGCATGTTTGTATGCTGATGGGAATGATCCAGT 1752 chr2ptel1M 550892 GGAGAAGG--------------------ATAGAGTGAAGATT--CTAGTA 550919 i i -------------------- v v i v -- i vi C L2#LINE/L2 1751 AGAGAGGGAAAAATTGATGATGCAGGAGAGAGAGGGGAGAATTGCTGGAG 1702 chr2ptel1M 550920 GGA----CTGGATTCAGC---ACAGAATGGCCTCTCGTGCATGAG--GAA 550960 v ---- v v vi --- vi i vv v ii -- i C L2#LINE/L2 1701 CGATGTCCTTGAGTAGGCGAGAGGGGATGGGATCTAGTGCACAAGTGGAG 1652 chr2ptel1M 550961 AGGTTTGCTTTGGTAAAAAGTA--GTCATTTCTTCTCATGAGGCACAGGA 551008 i v i i vv ii i -- v v v - i - vv C L2#LINE/L2 1651 GGGTTGGCCTTAGATAGGAGCACGGACAGTTCATC-CGT-AGTAACAGGA 1604 chr2ptel1M 551009 GAAAGGACAGAA-----GGCCCCTGAATGCTATGAGATGAGGAGGAGAGG 551053 ii i i i----- v v v - vivv i i v iv v C L2#LINE/L2 1603 GGGAAGGCAGAGTATGTGGGCACAG-ATGCAGGTAGGTGGGTAGATGTGG 1555 chr2ptel1M 551054 AGGAAAAGGAGCTCTCTTGAAGTGCCTTTTT------TTTTTTCTCCCCT 551097 v --vi -?? v v v ii i ------ i v i i i v C L2#LINE/L2 1554 TGG--TGGGAG-NNTGTGGAAGTTCTCTTCTGATTGCTTCTATTTTCTCA 1508 chr2ptel1M 551098 GTAAAATAGG-GGCAAGCTTTTTGGGCAGAAGGTG 551131 i -i v iv i-i v ii C L2#LINE/L2 1507 GTGAAATAGGAAGCAAGGTCATC-AGCTGAGAGTG 1474 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 47.25 CpG sites = 82, Kimura (unadjusted) = 48.70 Transitions / transversions = 1.37 (82/60) Gap_init rate = 0.05 (22 / 418), avg. gap size = 3.36 (74 / 22) 322 26.79 23.04 1.21 chr2ptel1M 551230 551433 (448567) MIRb#SINE/MIR 13 260 (8) m_b69s601i18 2568 chr2ptel1M 551230 GTGCTACAGTAGATGAGATGCAAAAG---TGGAGCTTGGCAGAGTTGAGT 551276 v i i -i - vii --- iiv i vi i MIRb#SINE/MIR 13 GTGGTGCAGTGGA-AAGA-GCACGGGCTTTGGAGTCAGACAGACCTGGGT 60 chr2ptel1M 551277 TGAGGTGCT--CTCAGACATTGACCAGTTGTGTGAC--TGAGCAAGTTAG 551322 viii v i-- v v i v i i -- i v MIRb#SINE/MIR 61 TCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTAC 110 chr2ptel1M 551323 TAAAC-----TG-------GTTTCC----CTATAAACCAGGTCATAACTG 551356 v ----- ------- ---- i vii v- ivi MIRb#SINE/MIR 111 TTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGG-ATAATAA 159 chr2ptel1M 551357 TGACTACCTCTCATGGTC-------------------ATAAT---TGTAA 551384 iv v v i------------------- --- MIRb#SINE/MIR 160 TACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAA 209 chr2ptel1M 551385 AGTGGTTAGCA--GTGTCTGGCACAGAGCAGGCATTTAATAAATGCTTGT 551432 i v -- i v i i ii i v v i MIRb#SINE/MIR 210 AGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAAATGGTAGC 259 chr2ptel1M 551433 T 551433 MIRb#SINE/MIR 260 T 260 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.42 CpG sites = 33, Kimura (unadjusted) = 34.22 Transitions / transversions = 1.57 (33/21) Gap_init rate = 0.06 (12 / 203), avg. gap size = 4.17 (50 / 12) 220 27.12 3.39 0.00 chr2ptel1M 551385 551443 (448557) L2d2_3end#LINE/L2 493 553 (2) m_b69s601i19 2569 chr2ptel1M 551385 AGTGGTTAGCA--GTGTCTGGCACAGAGCAGGCATTTAATAAATGCTTGT 551432 i vi -- i v v i ii i ii L2d2_3end#LIN 493 AGCGCCTAGCACAGTGCCTTGCACACAGTAGGCGCTCAATAAATATTTGT 542 chr2ptel1M 551433 TTACTTCCTTT 551443 v i vv L2d2_3end#LIN 543 TGATTTGATTT 553 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.56 CpG sites = 10, Kimura (unadjusted) = 34.74 Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.02 (1 / 58), avg. gap size = 2.00 (2 / 1) 15 5.56 0.00 0.00 chr2ptel1M 553287 553305 (446695) (C)n#Simple_repeat 1 19 (0) m_b69s252i25 2570 chr2ptel1M 553287 CCTCCCCCCCCCCCCCCCC 553305 i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCC 19 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 16 16.97 2.38 2.38 chr2ptel1M 554507 554548 (445452) (CCGCC)n#Simple_repeat 1 42 (0) m_b69s252i26 2571 chr2ptel1M 554507 CCGACCCGGCCCCGCCCCTCCCGGGCAGGCCCCG-CCCGCCCC 554548 - v v v v vv - (CCGCC)n#Simp 1 CCG-CCCCGCCCCGCCCCGCCCCGCCCCGCCCCGCCCCGCCCC 42 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.05 (2 / 41), avg. gap size = 1.00 (2 / 2) 26 29.92 1.74 2.63 chr2ptel1M 555183 555297 (444703) (GGAGGC)n#Simple_repeat 1 114 (0) m_b69s252i27 2572 chr2ptel1M 555183 GGCGGCCGAGGAAGCAGCGGAGGCGGAAGCGGAGGCAGAGGCGACGGGCG 555232 v v vi vi i i -vi (GGAGGC)n#Sim 1 GGAGGCGGAGGCGGAGGCGGAGGCGGAGGCGGAGGCGGAGGCG-GAGGCG 49 chr2ptel1M 555233 GCTGCAGGTGGGGGCGCGCGGGGGGGGACGCGGGGGCGCACG-GAAGCCG 555281 vv - v v v - i v v i v v - i v (GGAGGC)n#Sim 50 GAGGC-GGAGGCGGAG-GCGGAGGCGGAGGCGGAGGCGGAGGCGGAGGCG 97 chr2ptel1M 555282 GAAGCAG-GAAGGAGGC 555297 i i - iv (GGAGGC)n#Sim 98 GAGGCGGAGGCGGAGGC 114 Matrix = Unknown Transitions / transversions = 0.69 (11/16) Gap_init rate = 0.04 (5 / 114), avg. gap size = 1.00 (5 / 5) 16 20.67 0.00 0.00 chr2ptel1M 555321 555359 (444641) (GGCGGC)n#Simple_repeat 1 39 (0) m_b69s252i28 2573 chr2ptel1M 555321 GGCCGCGGCGGGGACGGGGGAGGCGGGGGCGGCGGCCGC 555359 v v i v v v v (GGCGGC)n#Sim 1 GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC 39 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 16 13.04 2.94 0.00 chr2ptel1M 555752 555785 (444215) (GCGGGG)n#Simple_repeat 1 35 (0) m_b70s252i4 2574 chr2ptel1M 555752 GCGGGGGC-GGGGCGGGGGCGGGGACAGGAGAGGG 555785 - i i i v (GCGGGG)n#Sim 1 GCGGGGGCGGGGGCGGGGGCGGGGGCGGGGGCGGG 35 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 183 37.85 0.88 2.68 chr2ptel1M 557145 557258 (442742) C MamTip2b#DNA/hAT-Tip100 (286) 163 52 m_b70s601i0 2575 chr2ptel1M 557145 GAGACAATCCCTTGGGCTACTGGGATGACCCAGAGTGGTCGGGATC-CAG 557193 v iiv i vv i i -v i v i i- C MamTip2b#DNA/ 163 GAGACAATGCCTTAACCCAAAGGAATGACTC-TAATGGTGGGAATTTCAG 115 chr2ptel1M 557194 AGGCCATTGGAGTGTTCCAGGAGAGATTGGCGGGGGCAGGGGGTCATCTT 557243 ivi iiv v vvivvii i vvviv --ii C MamTip2b#DNA/ 114 GCACCGCGGCAGGCCGGTGGGGGAGATATTTTGGGGCAGGGGG--GCCTT 67 chr2ptel1M 557244 CCTACCTCCCTCCAA 557258 i vi vi v C MamTip2b#DNA/ 66 TCGGCGCCCCTCAAA 52 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 48.70 CpG sites = 22, Kimura (unadjusted) = 54.14 Transitions / transversions = 1.10 (22/20) Gap_init rate = 0.04 (4 / 113), avg. gap size = 1.00 (4 / 4) 15 5.48 0.00 0.00 chr2ptel1M 559834 559852 (440148) (G)n#Simple_repeat 1 19 (0) m_b70s252i5 2576 chr2ptel1M 559834 GGGGGCGGGGGGGGGGGGG 559852 v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGG 19 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 17 5.00 0.00 0.00 chr2ptel1M 564285 564305 (435695) (C)n#Simple_repeat 1 21 (0) m_b70s252i6 2577 chr2ptel1M 564285 CCCCTCCCCCCCCCCCCCCCC 564305 i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCC 21 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 208 26.68 2.56 3.90 chr2ptel1M 564317 564394 (435606) Tigger19a#DNA/TcMar-Tigger 117 193 (130) m_b70s601i1 2578 chr2ptel1M 564317 CCTGCCATCAGTT-GTGTGTATGCA-GGCATGCAGAGCTCATTTCCTTGT 564364 i - iiv - v - i v ivv i Tigger19a#DNA 117 CCCGCCATCAGTTGGTGTGTGCTCAGGGAATGCA-AACTAATTTTAATAT 165 chr2ptel1M 564365 TAGCCGCGTCAGAAAAGAAATCCAAGAAGG 564394 vviv i v v v -- i Tigger19a#DNA 166 TAGCCTAAGCAAAACATAATT--AGGAAGG 193 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.20 CpG sites = 9, Kimura (unadjusted) = 33.12 Transitions / transversions = 0.82 (9/11) Gap_init rate = 0.06 (5 / 77), avg. gap size = 1.00 (5 / 5) 546 31.92 7.89 3.42 chr2ptel1M 564794 565325 (434675) C L1ME4b_3end#LINE/L1 (337) 555 1 m_b70s551i0 2579 chr2ptel1M 564794 TGCAGTAGT-TTCCATTTCAGTATTGCAGTCATATTCTAGCTTATTTAGC 564842 - - --- ---i vii iiv ii i C L1ME4b_3end#L 555 TGCA-TAGTATTCCATT---GTAT---GGATGTACCATAATTTATTTAAC 513 chr2ptel1M 564843 CATTCCCCAGTTAATGGGCATCTCTTTGATTTCTGATTCTTTGCCACCAC 564892 v vi i i i vvv vi ii ii i ii C L1ME4b_3end#L 512 CAGTCCCCTATTGATGGACATTTAGGTTGTTTCCAATCTTTTGCTATTAC 463 chr2ptel1M 564893 AAA--ATTCTGCTGTCTATATTTTTGTACAGATGTGTCCTTTCCCTCCTT 564940 -- v vi vv vii -- ii v v v v v C L1ME4b_3end#L 462 AAACAATGCTGCAATGAATAACCTTGTACA--TACGTCATTTCGCACATG 415 chr2ptel1M 564941 TG----GATGTTTTTGGGATCCAAACCTAGCAGAAGTTGTGCTGGATCAA 564986 ----v i i v i vv vv v vi vvv i C L1ME4b_3end#L 414 TGCGAGTATATCTGTAGGATAAATTCCTAGAAGTGGAATTGCTGGGTCAA 365 chr2ptel1M 564987 AGCATATGCTGT-TTTGCAGCCCTTTGGCC-ATAGTTCCAAATTGCTCTC 565034 vi - i- i ii-- iiv- v v i C L1ME4b_3end#L 364 AGGGTATG-TGCATTTGTAAT--TTTGATAGATATTGCCAAATTGCCCTC 318 chr2ptel1M 565035 CAT-----TTCAATCAGTTGACAGTTCCATTAACAATGCCTGCAGGCAT- 565078 ----- vv i i v v i ii i iv vii iii- C L1ME4b_3end#L 317 CATAGAGGTTGTACCAATTTACACTCCCACCAGCAATGTATGAGAGTGCC 268 chr2ptel1M 565079 TGTTTTCCCACAT----------GCAGC----TTTC---CTTTTT--TGT 565109 i i----------i i---- v --- -- v C L1ME4b_3end#L 267 TGTTTCCCCACACCCTCGCCAACACAGTGTGTTATCAAACTTTTTGATCT 218 chr2ptel1M 565110 T-----ATCTGATGGATGTGTGGCAGCCTCTCAGAGTTGTTTGAATTTGC 565154 ----- i i viviiii iv v v v C L1ME4b_3end#L 217 TTGCCAATCTGATAGGTGAAAAATGGTATCTCAGTGTAGTTTTAATTTGC 168 chr2ptel1M 565155 ATTTCTCTCACTAAGGGTAATTTAGAGCATTTTTCCACAGGACTGCAGAT 565204 i i v i i vv v i i i v vi iviiii C L1ME4b_3end#L 167 ATTTCTCTTATTATGAGTGAGGTTGAGCATCTTTTCATATGTTTAAGAGC 118 chr2ptel1M 565205 AGTTTTAATTTCC---TCTGAAAACGGCCCGGTCCCTATCCTTTGACTAT 565251 vi vv --- vi v i i- i v v i C L1ME4b_3end#L 117 CATTTGTATTTCCTTTTCTGTGAACTGTCT-GTTCATATCCTTTGCCCAT 69 chr2ptel1M 565252 TTATCAGCTGGGGAATTTTTATGAATTGTATTTTTATAAATTTGACTCAG 565301 v vii ------ i vii iv v i vi vvvv C L1ME4b_3end#L 68 TTTTCTATTGGG------TTGTTGGTCTTTTTCTTATTGATTTGTAGGAG 25 chr2ptel1M 565302 TTCTTTATATATTGGAGAAATGAG 565325 i i i v C L1ME4b_3end#L 24 CTCTTTATATATTAGGGAAATTAG 1 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 42.45 CpG sites = 92, Kimura (unadjusted) = 42.80 Transitions / transversions = 1.28 (92/72) Gap_init rate = 0.06 (32 / 531), avg. gap size = 1.91 (61 / 32) 19 0.00 0.00 0.00 chr2ptel1M 565413 565433 (434567) (GT)n#Simple_repeat 1 21 (0) m_b70s252i7 2580 chr2ptel1M 565413 GTGTGTGTGTGTGTGTGTGTG 565433 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTG 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 15 10.03 0.00 0.00 chr2ptel1M 565433 565454 (434546) (GC)n#Simple_repeat 1 22 (0) m_b70s252i8 2581 chr2ptel1M 565433 GCGCGCGCGCGTGCGCGCGTGC 565454 i i (GC)n#Simple_ 1 GCGCGCGCGCGCGCGCGCGCGC 22 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 chr2ptel1M 566298 566315 (433685) (TG)n#Simple_repeat 1 18 (0) m_b70s252i9 2582 chr2ptel1M 566298 TGTGTGTGTGTGTGTGTG 566315 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTG 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 chr2ptel1M 566315 566331 (433669) (G)n#Simple_repeat 1 17 (0) m_b70s252i10 2583 chr2ptel1M 566315 GGGGGGGGGGGGGGGGG 566331 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGG 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 197 30.85 6.38 0.00 chr2ptel1M 566710 566803 (433197) MIR3#SINE/MIR 34 133 (75) m_b70s601i2 2584 chr2ptel1M 566710 TGGCCGTCTGCAGGATGGGGTTTAAACCCTGCTTCTCCCACGGCGT--CT 566757 vv v v iviv iv ii i vi v vivv -- MIR3#SINE/MIR 34 TGGGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCT 83 chr2ptel1M 566758 CTGCGACCTCAGGCAC-TGAC---GCCTCCCTGGGCCTCAGTTTCCCCAT 566803 v i ii v- v ---i i i MIR3#SINE/MIR 84 GTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCAT 133 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.45 CpG sites = 14, Kimura (unadjusted) = 40.18 Transitions / transversions = 0.93 (14/15) Gap_init rate = 0.03 (3 / 93), avg. gap size = 2.00 (6 / 3) 203 22.08 7.79 0.00 chr2ptel1M 566727 566803 (433197) MIR1_Amn#SINE/MIR 56 138 (92) m_b70s601i3 2584 chr2ptel1M 566727 GGGTTTAAACCCTGCTTCTCCCAC--GGCGTCTCTGCGACCTCAGGCAC- 566773 i? ?i i vi v -- v ?v v? i ii v- MIR1_Amn#SINE 56 GGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAG 105 chr2ptel1M 566774 TGAC---GCCTCCCTGGGCCTCAGTTTCCCCAT 566803 v ---i i ? i MIR1_Amn#SINE 106 TCACTTNACCTCTCTGNGCCTCAGTTTCCTCAT 138 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.94 CpG sites = 10, Kimura (unadjusted) = 28.91 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.04 (3 / 76), avg. gap size = 2.00 (6 / 3) 12 14.73 3.33 0.00 chr2ptel1M 567052 567081 (432919) (CCCCCT)n#Simple_repeat 1 31 (0) m_b70s252i11 2585 chr2ptel1M 567052 CCCCCTTGCCCTCTCCC-ACCCCTCCCCCTC 567081 iv i -v (CCCCCT)n#Sim 1 CCCCCTCCCCCTCCCCCTCCCCCTCCCCCTC 31 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 14 31.63 1.61 0.00 chr2ptel1M 567311 567372 (432628) (CCCCCA)n#Simple_repeat 1 63 (0) m_b70s252i12 2586 chr2ptel1M 567311 CCCACACCCGGAGCCTGA-CCCCACCCCCTTCCTCTTCTCCCCCCCCCCC 567359 v vv v iv - vi i vi i v v (CCCCCA)n#Sim 1 CCCCCACCCCCACCCCCACCCCCACCCCCACCCCCACCCCCACCCCCACC 50 chr2ptel1M 567360 CCCAGCCCCTCCC 567372 v v (CCCCCA)n#Sim 51 CCCACCCCCACCC 63 Matrix = Unknown Transitions / transversions = 0.45 (5/11) Gap_init rate = 0.02 (1 / 61), avg. gap size = 1.00 (1 / 1) 26 0.00 0.00 0.00 chr2ptel1M 567637 567661 (432339) (GAGG)n#Simple_repeat 1 25 (0) c_b70s251i0 2587 chr2ptel1M 567637 GAGGGAGGGAGGGAGGGAGGGAGGG 567661 (GAGG)n#Simpl 1 GAGGGAGGGAGGGAGGGAGGGAGGG 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 18 14.00 0.00 4.88 chr2ptel1M 567882 567924 (432076) (GGGGGCG)n#Simple_repeat 1 41 (0) m_b70s252i13 2588 chr2ptel1M 567882 GGGGGTGTGGGGCGGGGGGCACAGGGGGGGCGGGGCGGGGGGC 567924 i v -- i v v (GGGGGCG)n#Si 1 GGGGGCGGGGGGCGGGGGG--CGGGGGGCGGGGGGCGGGGGGC 41 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.00 (2 / 2) 198 13.51 2.70 0.00 chr2ptel1M 568620 568656 (431344) C L2c_3end#LINE/L2 (17) 461 424 m_b70s601i4 2589 chr2ptel1M 568620 ACATGTATGAAGCGCCTCCTGTGTGCCAGGC-CTGGGG 568656 v vi v i - C L2c_3end#LINE 461 ACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGG 424 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 14.91 CpG sites = 2, Kimura (unadjusted) = 14.91 Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 17 24.99 0.00 6.15 chr2ptel1M 568950 569018 (430982) (GGGGC)n#Simple_repeat 1 65 (0) m_b70s252i14 2590 chr2ptel1M 568950 GGGGCTGGGCTGGGCGGCGCTGCCCGGCGCGGGGATGGCGGCGGTGGAGG 568999 v v v v vv v -i - - v (GGGGC)n#Simp 1 GGGGCGGGGCGGGGCGGGGCGGGGCGGGGCGGGG-CGG-GGCGG-GGCGG 47 chr2ptel1M 569000 GGGGGGCCCTGGGCAGGGC 569018 v -v v i (GGGGC)n#Simp 48 GGCGGG-GCGGGGCGGGGC 65 Matrix = Unknown Transitions / transversions = 0.18 (2/11) Gap_init rate = 0.06 (4 / 68), avg. gap size = 1.00 (4 / 4) 17 7.01 0.00 6.25 chr2ptel1M 569058 569091 (430909) (GTGGGG)n#Simple_repeat 1 32 (0) m_b70s252i15 2591 chr2ptel1M 569058 GTGGGGGTGGCTGGAGGGGGTGGGGGGTGGGGGT 569091 -v v - (GTGGGG)n#Sim 1 GTGGGGGTGG-GGGTGGGGGT-GGGGGTGGGGGT 32 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2) 11 21.64 7.27 1.72 chr2ptel1M 569952 570006 (429994) (CCCTCCT)n#Simple_repeat 1 58 (0) m_b70s252i16 2592 chr2ptel1M 569952 CCCTCCTCCC-CCT-CCTCC-CTCTCCGCAGGCCGCATGCGCCCCCTCCT 569998 - - - i v vvv v viv - i (CCCTCCT)n#Si 1 CCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTC-CTCCCTCCT 49 chr2ptel1M 569999 CCCT-CTCC 570006 - (CCCTCCT)n#Si 50 CCCTCCTCC 58 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.09 (5 / 54), avg. gap size = 1.00 (5 / 5) 17 22.70 0.00 0.00 chr2ptel1M 570088 570123 (429877) (G)n#Simple_repeat 1 36 (0) m_b70s252i17 2593 chr2ptel1M 570088 GGGGGGGGGGGGGCCCACCCGGGGGGGGGGGGGGGG 570123 vvvivvv (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 36 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 14 11.19 0.00 6.45 chr2ptel1M 571119 571151 (428849) (CCTC)n#Simple_repeat 1 31 (0) m_b70s252i18 2594 chr2ptel1M 571119 CCTCCCGGCCCTCCGTCACGTCCCTCCCTCCCT 571151 -v v - v (CCTC)n#Simpl 1 CCTCCC-TCCCTCCCTC-CCTCCCTCCCTCCCT 31 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.06 (2 / 32), avg. gap size = 1.00 (2 / 2) 656 28.49 5.71 1.37 chr2ptel1M 575750 575959 (424041) C MIRb#SINE/MIR (35) 233 15 m_b70s601i5 2595 chr2ptel1M 575750 GTGTAAGAAGCTGGGCTAAGC---TGACAAAGACACTTTCGTTT----CT 575792 iv ivi v --- v viv ivv i i ---- C MIRb#SINE/MIR 233 GTGCCAGGCACTGTGCTAAGCGCTTTACATGCATTATCTCATTTAATCCT 184 chr2ptel1M 575793 CGCCACAACCCTGTGAGGAAGGCGCTGTCCCTGTCCCCATTTTACAGCTG 575842 i v i v iii i --- i v C MIRb#SINE/MIR 183 CACAACAACCCTGCGAGGTAGGTATTAT---TATCCCCATTTTACAGATG 137 chr2ptel1M 575843 AGGAAACTGAGGC----AGAGGCAAAATGACTGGCACAGGGTCCCATAGC 575888 ---- iv i i v v i v i C MIRb#SINE/MIR 136 AGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGC 87 chr2ptel1M 575889 TGGCAGATCTCTGGGGCAGGATCAGAATTCAGG-CTTCCTAACCCCAAGG 575937 i i ii vv v i v i iv ii - vi i i i C MIRb#SINE/MIR 86 TAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAG 37 chr2ptel1M 575938 GCAGCGCTCTGTGCCCTGCACC 575959 v v i v v v C MIRb#SINE/MIR 36 CCCGTGCTCTTTCCACTGCACC 15 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.08 CpG sites = 33, Kimura (unadjusted) = 36.62 Transitions / transversions = 1.27 (33/26) Gap_init rate = 0.03 (7 / 209), avg. gap size = 2.14 (15 / 7) 681 25.00 6.25 0.00 chr2ptel1M 575784 575959 (424041) C MIRc#SINE/MIR (70) 198 12 m_b70s601i6 2595 chr2ptel1M 575784 TTCGTTTCTCGCCACAACCCTGTGAGGAAGGC------GCTGTCCCTGTC 575827 i v i i v v ------ v i ivi i C MIRc#SINE/MIR 198 TTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATC 149 chr2ptel1M 575828 CCCATTTTACAGCTGAGGAAACTGAGGC----AGAGGCAAAATGACTGGC 575873 v ---- iv i v C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr2ptel1M 575874 ACAGGGTCCCATAGCTGGCAGATCTCTGGGGCAGGATCAGAATTCAGG-C 575922 v i v i i i ii vv v i v i iiv ii - C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTC 49 chr2ptel1M 575923 TTCCTAACCCCAAGGGCAGCGCTCTGTGCCCTGCACC 575959 i i vv i v v v C MIRc#SINE/MIR 48 TTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACC 12 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.04 CpG sites = 24, Kimura (unadjusted) = 30.86 Transitions / transversions = 1.20 (24/20) Gap_init rate = 0.02 (3 / 175), avg. gap size = 3.67 (11 / 3) 189 21.04 0.00 6.98 chr2ptel1M 577693 577738 (422262) C L3#LINE/CR1 (2029) 2070 2028 m_b70s601i7 2596 chr2ptel1M 577693 GTCAGGACTTCATTTTTGAGAGGGGCCCCTCACCCGTTTTGAGACA 577738 i i i --- ii i ? v i v C L3#LINE/CR1 2070 GTCAGAATTTCATTTTTAAGA---GCTTCCCANCCCTCTTGAGCCA 2028 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.48 CpG sites = 7, Kimura (unadjusted) = 26.48 Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.07 (3 / 45), avg. gap size = 1.00 (3 / 3) 11 17.89 8.06 4.69 chr2ptel1M 577804 577865 (422135) (CTCTGT)n#Simple_repeat 1 64 (0) m_b70s252i19 2597 chr2ptel1M 577804 CTCTTGTCTC-CT-TCTGTCTCTGCCTCTGTGGCTTTCCCT-CCACGTGT 577850 - -v - i vv v i -i v - (CTCTGT)n#Sim 1 CTC-TGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTC-TGT 48 chr2ptel1M 577851 -TCTTTC-CTGATCTCT 577865 - v - - (CTCTGT)n#Sim 49 CTCTGTCTCTG-TCTCT 64 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.13 (8 / 61), avg. gap size = 1.00 (8 / 8) 218 34.37 0.00 5.56 chr2ptel1M 578809 578922 (421078) C MIRb#SINE/MIR (143) 125 18 m_b70s601i8 2598 chr2ptel1M 578809 GCCCGGAGAGGTTTAGGCACTTGCCCAGGCTCCCTCAGCCGGGATGAAGC 578858 i i v vv i v v v ii v v vi C MIRb#SINE/MIR 125 GCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGC 76 chr2ptel1M 578859 CAAGACAGAAGAACCCGAGCCCCGGCGTGTCTCGTGGTGTGAAAGCCAGA 578908 vi v ---i i ii i v iv --- iiviv v v C MIRb#SINE/MIR 75 AGAGCC---GGGATTCGAACCCAGGTCTGTC---TGACTCCAAAGCCCGT 32 chr2ptel1M 578909 TCTCCACCCACTGC 578922 v ivi C MIRb#SINE/MIR 31 GCTCTTTCCACTGC 18 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.76 CpG sites = 18, Kimura (unadjusted) = 46.43 Transitions / transversions = 0.95 (18/19) Gap_init rate = 0.05 (6 / 113), avg. gap size = 1.00 (6 / 6) 308 33.15 7.25 6.73 chr2ptel1M 579410 579616 (420384) L2#LINE/L2 2655 2862 (220) m_b70s601i9 2599 chr2ptel1M 579410 CCCCTTTTGCCCTCTGACACTGCTCCCACCCTGGTACAGACCTTCATCCT 579459 v i vv v ivv iv v ii vi v L2#LINE/L2 2655 CCACTTCTCACCACCTCCACTGCCACCACCCTGGTCCAAGCCACCATCAT 2704 chr2ptel1M 579460 GTCATGCCTGGACTATGGCAGTAGCTGCTGGGGAAGACTGGCGGGGTCAG 579509 v vi i iv i iv iv-----i --------- L2#LINE/L2 2705 CTCTCGCCTGGATTACTGCAATAGCCTCCT-----AACTG---------G 2740 chr2ptel1M 579510 TCTGCCTGCCTCAAGTCTGTCCTGACTCTAGTTGATATTCTACCCC---- 579555 v i v vi vv ivv ?i iv vi v v v---- L2#LINE/L2 2741 TCTCCCTGCTTCCACCCTTGCCCCCCTNCAGTCTATTCTCAACACAGCAG 2790 chr2ptel1M 579556 CCAAAGTGA--CT--------GCAAGTCCAACTATGTCA-TCCCCTGTGC 579594 i -- -------- i vi ii - i iv L2#LINE/L2 2791 CCAGAGTGATCCTTTTAAAACGTAAGTCAGATCATGTCACTCCTCTGCTC 2840 chr2ptel1M 579595 AAAAAATCCCAGCGGTTTCTTA 579616 vvii ii i ii L2#LINE/L2 2841 AAAACCCTCCAATGGCTTCCCA 2862 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.99 CpG sites = 33, Kimura (unadjusted) = 44.93 Transitions / transversions = 1.06 (33/31) Gap_init rate = 0.09 (18 / 206), avg. gap size = 1.61 (29 / 18) 230 31.10 4.38 1.42 chr2ptel1M 580157 580293 (419707) C L2#LINE/L2 (697) 2385 2245 m_b70s601i10 2600 chr2ptel1M 580157 GGGTGTGCTGGTCAGCAGAGAGATTGGGGCAGGAAAGGAA-----GGAGA 580201 i v vv v vi i iv v i viv ----- iii C L2#LINE/L2 2385 GAGTCTGGAGTTCAGGGGAGAGGTCCGGGCTGGAGATATAAATTTGGGAG 2336 chr2ptel1M 580202 TCATCAGCAAAGGGGTGATCATTAAATCCATGGGAAGTGATGAGCTTCAC 580251 v vi i i vv v i vvv v - C L2#LINE/L2 2335 TCATCAGCATATAGATGGTATTTAAAGCCATGAGACTGGATGAGAT-CAC 2287 chr2ptel1M 580252 CCTGGGAACCAGGATGGA-GGAGAAGAGAGAGGGGCCAAAGGA 580293 ?v iiv vi i -i - i i v C L2#LINE/L2 2286 CNAGGGAGTGAGTGTAGATAGAGAAGAGA-AGAGGTCCAAGGA 2245 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.01 CpG sites = 20, Kimura (unadjusted) = 41.01 Transitions / transversions = 0.91 (20/22) Gap_init rate = 0.03 (4 / 136), avg. gap size = 2.00 (8 / 4) 217 22.86 12.39 3.25 chr2ptel1M 580427 580539 (419461) L2c_3end#LINE/L2 333 455 (23) m_b70s601i11 2601 chr2ptel1M 580427 TTCTGTTGTTTATTACCTCTTGTTAC-TATTTCTATCTTCCTC-AGACCG 580474 v i v- ii v -- - i i v v i v - i L2c_3end#LINE 333 TTGTATTGTA-ATTGTCTGTT--TACNTGTCTGTCTCCTCCACTAGACTG 379 chr2ptel1M 580475 TGAGCTTCTCCAGGGCAGGGGC--TGTCTTTCTCA---GTGTACCGCTCA 580519 i iv i -- vi ---v i - i L2c_3end#LINE 380 TGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTATC-CCCA 428 chr2ptel1M 580520 GCACC-----CAT--TAGGTGCTCAGT 580539 i ----- -- i i L2c_3end#LINE 429 GCGCCTGGCACATAGTAGGCGCTCAAT 455 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 25.52 CpG sites = 16, Kimura (unadjusted) = 28.10 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.09 (10 / 112), avg. gap size = 1.80 (18 / 10) 25 19.04 3.12 1.54 chr2ptel1M 582162 582225 (417775) (GAAG)n#Simple_repeat 1 65 (0) m_b70s252i20 2602 chr2ptel1M 582162 GAAAGAAGAAAGG-AGGGAGGACAG-AGGGAGGAAGGAAGGAAGGAAAGG 582209 i i - i vi - i i i (GAAG)n#Simpl 1 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 50 chr2ptel1M 582210 AGGGAGGAGAGGGAGG 582225 i - i (GAAG)n#Simpl 51 AGGAAGGA-AGGAAGG 65 Matrix = Unknown Transitions / transversions = 9.00 (9/1) Gap_init rate = 0.05 (3 / 63), avg. gap size = 1.00 (3 / 3) 364 30.23 0.00 3.77 chr2ptel1M 582253 582362 (417638) MIRc#SINE/MIR 77 182 (86) m_b70s601i12 2603 chr2ptel1M 582253 CTCACTCGCTTTGTGGCCCTGGATGAATCCATAGACTTGTCGGGGCCTCA 582302 i v v i i iii i vv vi i v v i MIRc#SINE/MIR 77 CTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCA 126 chr2ptel1M 582303 GTTTCCTCCTCTCTAAAATGGGGGTGAGACCAGCACCTGCCTCACAGCAC 582352 v v i i ---i ii iii -vi MIRc#SINE/MIR 127 GTTTCCTCATCTGTAAAATGGGGATAA---TAATACCTGCCCTGC-CTAC 172 chr2ptel1M 582353 CTGACAAAGT 582362 v ii MIRc#SINE/MIR 173 CTCACAGGGT 182 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.47 CpG sites = 21, Kimura (unadjusted) = 40.47 Transitions / transversions = 1.91 (21/11) Gap_init rate = 0.04 (4 / 109), avg. gap size = 1.00 (4 / 4) 395 28.87 0.00 0.00 chr2ptel1M 582253 582349 (417651) MIR#SINE/MIR 73 169 (93) m_b70s601i13 2603 chr2ptel1M 582253 CTCACTCGCTTTGTGGCCCTGGATGAATCCATAGACTTGTCGGGGCCTCA 582302 i v v i i iii i ivv vi i v v v MIR#SINE/MIR 73 CTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCA 122 chr2ptel1M 582303 GTTTCCTCCTCTCTAAAATGGGGGTGAGACCAGCACCTGCCTCACAG 582349 v v i i v vi i i i MIR#SINE/MIR 123 GTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTCATAG 169 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.33 CpG sites = 16, Kimura (unadjusted) = 37.33 Transitions / transversions = 1.33 (16/12) Gap_init rate = 0.00 (0 / 96), avg. gap size = 0.0 (0 / 0) 246 34.62 0.00 0.00 chr2ptel1M 582505 582582 (417418) L2a_3end#LINE/L2 428 505 (12) m_b70s601i14 2599 chr2ptel1M 582505 GTTTGTCCTGACCCTTCTTGTATCTCCAGGACCTCGTATGGCCTGTGGCA 582554 i ii vi vi vi i vi v v ii iviv L2a_3end#LINE 428 GTCTGTTTTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCA 477 chr2ptel1M 582555 CATTGTAGGTGCTTAATAAATGCTCCTT 582582 v i i ii iv L2a_3end#LINE 478 CATAGTAGGCGCTCAATAAATATTTGTT 505 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.89 CpG sites = 17, Kimura (unadjusted) = 48.92 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.00 (0 / 77), avg. gap size = 0.0 (0 / 0) 324 25.00 0.00 0.00 chr2ptel1M 582606 582673 (417327) C MIRc#SINE/MIR (157) 111 44 m_b70s601i15 2604 chr2ptel1M 582606 TTAAGTGACTTTCCCAGGGTCATGTAGCTAGTGAGTGTCTAAGGCTGGAC 582655 v i iii i v vi v v C MIRc#SINE/MIR 111 TTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGAC 62 chr2ptel1M 582656 TTGAACTCAGAGCTCTCT 582673 i i iv ii C MIRc#SINE/MIR 61 TCGAACCCAGGTCTTCCT 44 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.18 CpG sites = 11, Kimura (unadjusted) = 31.39 Transitions / transversions = 1.83 (11/6) Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0) 226 23.53 1.96 0.00 chr2ptel1M 582775 582825 (417175) C MIR#SINE/MIR (10) 252 201 m_b70s601i16 2605 chr2ptel1M 582775 AGCATTTATAGAGCACCCTCTGTGTGCCAGGCACTGGTCT-GGCTCCCTA 582823 i v i iiv i v -i v ii C MIR#SINE/MIR 252 AACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGCGCTTTA 203 chr2ptel1M 582824 CA 582825 C MIR#SINE/MIR 202 CA 201 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.34 CpG sites = 8, Kimura (unadjusted) = 29.16 Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.02 (1 / 50), avg. gap size = 1.00 (1 / 1) 397 24.66 19.86 0.00 chr2ptel1M 585922 586067 (413933) C MIRb#SINE/MIR (12) 256 82 m_b70s601i17 2606 chr2ptel1M 585922 ACCATTTA--GAACATCTCTTGAGTTCCAGGCATCATGCAGAGCCTTTTA 585969 -- i iii vi iv v iii vi vi C MIRb#SINE/MIR 256 ACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTA 207 chr2ptel1M 585970 CAGACATCACCTCATTTGTTCCTC---ATAACTCTGGGAGG--GGT---- 586010 vi i i iv --- i i v -- ---- C MIRb#SINE/MIR 206 CATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTA 157 chr2ptel1M 586011 TGATCCCCATCTTACAG-TGGGACAATTG--------------TAGG--- 586042 v i - i iv i -------------- i --- C MIRb#SINE/MIR 156 TTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAA 107 chr2ptel1M 586043 CTTGCCCAAGGGCACACTGCTTGCA 586067 v v v i C MIRb#SINE/MIR 106 CTTGCCCAAGGTCACACAGCTAGTA 82 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.76 CpG sites = 23, Kimura (unadjusted) = 30.79 Transitions / transversions = 1.77 (23/13) Gap_init rate = 0.05 (7 / 145), avg. gap size = 4.14 (29 / 7) 869 33.93 5.23 2.71 chr2ptel1M 586445 587056 (412944) C L1ME4a_3end#LINE/L1 (233) 638 12 m_b70s551i1 2607 chr2ptel1M 586445 CTACTCACTTCATTTAGCATCAGTTCATGTGAGTCTCTCCAGGCCTCTCT 586494 i ivi i i i vv v vi i ii v i vi -- C L1ME4a_3end#L 638 CTGCTTTTTTCACTTAACATTATATCATGAGCATTTTCCCATGTCATT-- 591 chr2ptel1M 586495 GAAATCATTCTCCTGA----TGGTTTCTTATAGAACAATAATATTCCACA 586540 - - i vi ---- ?i i v i vvvv iv C L1ME4a_3end#L 590 -AAAT-ATTCTTCGAAAACATNATTTTTAATGGCTGCATAATATTCCATT 543 chr2ptel1M 586541 ACATTCATATACCAGGACTTATTCAGCCCTTCTCCAACT----------- 586579 ?i vv i vi i i i v? i v i ----------- C L1ME4a_3end#L 542 NTATGGATGTACCATAATTTATTTAACCANTCCCCTATTGTTGGACATTT 493 chr2ptel1M 586580 ----------CAGTTTCCTGCCACTACAAAGAGGGCTGCCACAAACATTT 586619 ---------- i iii i i i v iv v ii ii C L1ME4a_3end#L 492 AGGTTGTTTCCAATTTTTCGCTATTATAAATAATGCTGCGATGAACATCC 443 chr2ptel1M 586620 TTGCACATGGGGTTCCCTTTACCTCCTTTAAGATCTCTTTGGAACATAAG 586669 i iiivi iiv ?i v ii v vv i i i i i v vv C L1ME4a_3end#L 442 TTGTACATAAATCTTTGTNCACATCTCTGATTATTTCCTTAGGATAAATT 393 chr2ptel1M 586670 CCCAGTGGAAACACTGCTGGGTCAAAGGGTGTGCACAGTTTTATAGCCTT 586719 i vi viiv i i i ? v vi i C L1ME4a_3end#L 392 CCTAGAAGTGGAATTACTGGGTCAAAGGGTATGNACATTTTTAAGGCTTT 343 chr2ptel1M 586720 TTGGGCATAGTTACAAACTGCTCTTCAGAATGATTGGATTTGTTCACAAT 586769 vivi v vv i i i v i v iivi i v C L1ME4a_3end#L 342 TGATACATATTGCCAAATTGCCCTCCAGAAAGGTTGTACCAATTTACACT 293 chr2ptel1M 586770 TCCACCAACAATGCATCAGTGTTCCAGTTTTCCCCTCCAATCAATCCCCT 586819 i i i i v v v v i? vi------- i i v C L1ME4a_3end#L 292 CCCACCAGCAGTGTATGAGAGTGCCCGTTTCNCCAC-------ACCCTCG 250 chr2ptel1M 586820 CCGATCAATAGTCATCGTT-ATCTTTTCCTGTCTCTTAGCCAGTCTGACT 586868 i - v i vi ii i- --- ivv v i i iv C L1ME4a_3end#L 249 CCAA-CACTGGGTATTATCAATCTTT---TAAATCTTTGCCAATTTGATA 204 chr2ptel1M 586869 GGTGTGTGGTGGTATCTCAGAATGGTCTTAATTTGCATTTCTCTGATCAA 586918 vivii vvi v i i i v C L1ME4a_3end#L 203 GGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCTTTGATTAC 154 chr2ptel1M 586919 TAGTGATTTGGAGCACCTTTTCATATAAGTAGAAATGGTTTTAATTTCTT 586968 vv v i i? ivv vviiivi vv C L1ME4a_3end#L 153 TAGTGAGGTTGAACATNTTTTCATATGTTTATTGGCCATTTGTATTTCTT 104 chr2ptel1M 586969 TATCTGAAAAT----TGTTCATAACTTTTGACCATCTGCCAATTGGAGAA 587014 iv i vi ---- iv i v i vi v i vi C L1ME4a_3end#L 103 CTTTTGTGAATTGTCTGTTCATGTCCTTTGCCCATTTTTCTATTGGGGTG 54 chr2ptel1M 587015 T--GGCTTGGTTTCTTATAAATTTGAGTCAATTCTTTATATATT 587056 -- v -- vi vivv ii C L1ME4a_3end#L 53 TTCGTCTT--TTTCTTATTGATTTGTAAGAGCTCTTTATATATT 12 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 47.30 CpG sites = 117, Kimura (unadjusted) = 47.63 Transitions / transversions = 1.38 (117/85) Gap_init rate = 0.04 (23 / 611), avg. gap size = 2.13 (49 / 23) 915 32.15 5.06 3.31 chr2ptel1M 586528 587061 (412939) C L1ME3C_3end#LINE/L1 (321) 549 7 m_b70s551i2 2607 chr2ptel1M 586528 ATAATATTCCACAACATTCATATACCAGGACTTATTCAGCCCTTCTCCAA 586577 i ivii vv vi i i v v vi C L1ME3C_3end#L 549 ATAGTATTCCATTGTATGAATATACCACAATTTATTTATCCATTCTCCTG 500 chr2ptel1M 586578 CT---------------------CAGTTTCCTGCCACTACAAAGAGGGCT 586606 i --------------------- i iii i i v iv C L1ME3C_3end#L 499 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 450 chr2ptel1M 586607 GCCACAAACATTTTTGCACATGGGGTTCCCTTTAC-CTCCTTTAAGA-TC 586654 v ii i i v--i i v i - v v vii - i C L1ME3C_3end#L 449 GCAATGAACATTCTTGTACATGT--CTCCTTGTGCACACGTGCGAGAGTT 402 chr2ptel1M 586655 TCTTTGGAACATAAGCCCAGTGGAAACACTGCTGGGTCAAAGGGTGTGCA 586704 i i iii vi i vi viiv i iv i i C L1ME3C_3end#L 401 TCTCTAGGGTATATACCTAGGAGTGGAATTGCTGGGTCGTAGGGTATGCG 352 chr2ptel1M 586705 CAGTTTTATAGCCTTTTGGGCATAGTTACAAACTGCTCTTCAGAATGATT 586754 vi i - vii vi i ii v i-- i i i i i C L1ME3C_3end#L 351 CATCTTCA-ACTTTACTAGATATTGC--CAAATTGCTCTCCAAAGTGGTT 305 chr2ptel1M 586755 GGATTTGTTCACAATTCCACCAACAATGCATCAGTGTTCCAGTTTTCCCC 586804 v iivi i v i i i i v v v v---- C L1ME3C_3end#L 304 GTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTTCCCGTTG----C 259 chr2ptel1M 586805 TCCAATCAATCCCCTCCGATCAATAGTCATCGTTATCTTTTCCTGTCTCT 586854 v--- i v i - v v vi i i vvi -- ivv i C L1ME3C_3end#L 258 TCCAC---ATCCTCGCCAA-CACTTGGTATTGTCAGACTTT--TAAATTT 215 chr2ptel1M 586855 TAGCCAGTCTGACTGGTGTGTGGTGGTATCTCAGAATGGTCTTAATTTGC 586904 v i iv vii vvi ? i C L1ME3C_3end#L 214 TTGCCAATCTGATGGGTGTGAAATGGTATCTCATTGTNGTTTTAATTTGC 165 chr2ptel1M 586905 ATTTCTCTGATCAATAGTGATTTGGAGCACCTTTTCATATAAGTAGAAAT 586954 i i v vv v i ivv vviii C L1ME3C_3end#L 164 ATTTCCCTGATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGC 115 chr2ptel1M 586955 GGTTTTAATTTCTTTATCTGAAAAT----TGTTCATAACTTTTGACCATC 587000 vi iv?i i iv vi ---- v v i C L1ME3C_3end#L 114 CATTCGNGTTTCCTCTTCTGTGAATTGCCTGTTCATATCTTTTGCCCATT 65 chr2ptel1M 587001 TGCCAATTGGAGAATGGCTTGGTTTCTTATAAATTTGAGTCAATTCTTTA 587050 vi v ---i v ii v vi vivv i C L1ME3C_3end#L 64 TTTCTATTGG---GTTGTCTGTTTTCTTATTGATTTGTAGGAGTTCTTTA 18 chr2ptel1M 587051 TATATTTTAGA 587061 i i C L1ME3C_3end#L 17 TATATTCTGGA 7 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 41.98 CpG sites = 99, Kimura (unadjusted) = 43.79 Transitions / transversions = 1.48 (99/67) Gap_init rate = 0.04 (22 / 533), avg. gap size = 2.05 (45 / 22) 262 31.49 6.17 4.03 chr2ptel1M 586922 587553 (412447) C L1M5_orf2#LINE/L1 (0) 3294 2650 m_b70s551i3 2607 chr2ptel1M 586922 TGATTTGGAGCACCTTTTCATATAAGTAGAAATGGTTTTAATTTCTTTAT 586971 ?v v i i ivv vviiivi v? v iv C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr2ptel1M 586972 CTGAAAA----TTGTTCATAACTTTTGACCATCTGCCAATTGGA--GAAT 587015 i vi ----i viv v i vi?v i-- vv C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTT 3195 chr2ptel1M 587016 GGCTTGGTTTCTTATAAATTTGAGTCAATTCTTTATATATTTTAGAAATG 587065 v -- ? vi ? vivv i i i v i C L1M5_orf2#LIN 3194 GTCTT--TTTNTTATTGANTTGTAGGAGTTCTTTATATATTCTGGATACG 3147 chr2ptel1M 587066 AGGCCTTTATCAGAACCCTTGAATGTG----AAATTTTTTC-CCCAGTTA 587110 v i ----- iv ?---- v - ? iv C L1M5_orf2#LIN 3146 AGTCCTTTGTCAGA-----TATATGTNTTGCAAATATTTTCTCCCANTCT 3102 chr2ptel1M 587111 GTTCCTTCCCTTCTAACTTGTCT--ACATTGGTTAAGTTTGTACA--AAA 587156 vv v i v i - -- iv vi --- v?v -- i C L1M5_orf2#LIN 3101 GTGGCTTGCCTTTTCATTT-TCTTAACGGTGTCT---TTTGANGAGCAGA 3056 chr2ptel1M 587157 ACTTTATAACTT-AATATAATCAAAATTATCTGGTGAT-CAATAATGATC 587204 v v i -i i? i v v viv vv - vv v i - C L1M5_orf2#LIN 3055 AGTTTTTAATTTTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGGT- 3007 chr2ptel1M 587205 TTTAGTTCTTCTTAGGTC-------ACAAATTCCTTCCTCCTCCACAGGT 587247 -- ? v i iv ------- v iii v v?i - C L1M5_orf2#LIN 3006 --TNGTGCTTTTTGTGTCCTGTTTAAGAAATCTTTGCCTANCCCA-AGGT 2960 chr2ptel1M 587248 CTGAGAGGTCAGCTATCCTATGTT--CTTCTAATTTGTTTAGAATCTCAT 587295 vvii i --ii v -- ivvvv v i i i ? C L1M5_orf2#LIN 2959 CACGAAGAT--ATTCTCCTATGTTTTCTTCTAGAAGTTTTATAGTTTTAN 2912 chr2ptel1M 587296 TCTTTCTGTCTAGATC-ATGAACCCATTTTGACTTTATCTTGGTGTACGA 587344 ii vii i i - - i i ? v v i v i i C L1M5_orf2#LIN 2911 CTTTTACATTTAGGTCTATG-ATCCATCTNGAATTAATTTTTGTGTATGG 2863 chr2ptel1M 587345 TGTTAAGTGTGTATCAATGCCTACTTTCTGCCATACTGGTTTCCAATTTT 587394 v i iv vi i v?iii i i v iv i v v C L1M5_orf2#LIN 2862 TGTGAGGTAGGGGTCGAGNTTCATTTTTTTCCATATGGATATCCAATTGT 2813 chr2ptel1M 587395 CCCAGCAGTTTTTGTC--AGTGA--ATTCTTATCCCAAAAGCTGGGGT-C 587439 i viv i-- iv -- i vi ---- iiv - C L1M5_orf2#LIN 2812 TCCAGCACCATTTGTTGAAAAGACTATCCTTTCCCCA----CTGAATTGC 2767 chr2ptel1M 587440 TTTGG---GTTTGTCAAACACTAGACTACTATAGTCAT-TGACGATTTTG 587485 ? ---v v ii i?iv? i --i - vv i i vv C L1M5_orf2#LIN 2766 NTTGGCACCTTTGTCAAAAATCAANTGNCCATA--TATGTGTGGGTCTAT 2719 chr2ptel1M 587486 TCCTGTGAATCTC--ACCTGTCCCTCTGATGGACTGCTCTATTTCTTA-G 587532 i - v --vi i vi vv i vv - i - C L1M5_orf2#LIN 2718 TTCTG-GACTCTCTATTCTGTTCCATTGATCTATTTGTCTA-TCCTTACG 2671 chr2ptel1M 587533 CCAGAACCAAATGGTTTTGAT 587553 iv v iv i C L1M5_orf2#LIN 2670 CCAATACCACACTGTCTTGAT 2650 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 42.00 CpG sites = 97, Kimura (unadjusted) = 43.18 Transitions / transversions = 1.03 (97/94) Gap_init rate = 0.07 (44 / 631), avg. gap size = 1.48 (65 / 44) 354 36.85 5.80 1.28 chr2ptel1M 588068 588515 (411485) C L1PREC2_orf2#LINE/L1 (652) 2642 2175 m_b70s551i4 2608 chr2ptel1M 588068 GCTCTGTAATACAGTTTTAGATCAGGTACAGGGAGGCCACCTTCCTTGAC 588117 i i i v ii i vv v v v vv i -- C L1PREC2_orf2# 2642 GCCCTGTAGTATAGTTTGAAGTCGGGTAGCGTGATGCCTCCAGCTTTG-- 2595 chr2ptel1M 588118 GGTTTTTTCCATTAG--TTCCCTTGA-AATTCTTGACCTTTTTTTCTACC 588164 -v i ivv -- v i-v vv vi vv v C L1PREC2_orf2# 2594 -TTCTTTTTGCTTAGGATTGCCTTGGCTATTCGGGCTCTTTTTTGGTTCC 2546 chr2ptel1M 588165 GAGTGAATT----AGCATTTTTTTCTAGCTCTGTGGCATCATTTC-TTGG 588209 ivi ---- ii v i i- vv v - C L1PREC2_orf2# 2545 ATATGAATTTTAAAATAGTTTTTTCTAGTTCTGTGA-AGAATGTCATTGG 2497 chr2ptel1M 588210 GAGTTTGATTGGTTCAGCCGTGAATAAGAAGATTGATAAAAGTGACAATT 588259 v v vvi vv vv v i v vvii iiii vvv C L1PREC2_orf2# 2496 TAGTTTGATAGGAATAGCATTGAATCTGTAAATTGCTTTGGGCAGTATGG 2447 chr2ptel1M 588260 CTACCTTAATCATATTCCTTTGGCCTACCCATGAGCACTCGATATTCTTC 588309 i ii iv vv ivv i ivvi i i C L1PREC2_orf2# 2446 CCATTTTAACGATATTGATTCTTCCTATCCATGAGCATGGAATGTTTTTC 2397 chr2ptel1M 588310 CACTT-----TATCAGACCCGACTTTGTGTGGAAAGCCTTTTGTAGTTGT 588354 i ----- i vvi i - v v iiv iv i v C L1PREC2_orf2# 2396 CATTTGTTTGTGTCATCTCTGA-TTTCTTTGAGCAGTGTTTTGTAATTCT 2348 chr2ptel1M 588355 -GTTCCGGTGCTTCCTGACTTTGTCTTGGCAGGGAGACTCCCAAATATTC 588403 -i vii v v iii v i i-i v vi vviv i i ii i C L1PREC2_orf2# 2347 CATTGTAGAGATCTTTCACCTC-CCTGGTTAGCTGTATTCCTAGGTATTT 2299 chr2ptel1M 588404 CATATTACCCACAGTCATTGTGAGTGGAATTTC--TCTTG-------CCA 588444 i vi viiiiii iv i i v -- i -------i v C L1PREC2_orf2# 2298 TATTCTTTTTGTGGCAATTGTGAATGGGATTGCGTTCCTGATTTGGCTCT 2249 chr2ptel1M 588445 CGG---GGCTGTCAGTAATATGGAGAAATGCTGGAGATTTCTGTGGACTC 588491 --- iiv ii i iv i i v i iv i v C L1PREC2_orf2# 2248 CGGCTTGGCTGTTGTTGGTGTATAGGAATGCTAGTGATTTTTGTACATTG 2199 chr2ptel1M 588492 TGTCTGTGTCCCGCCACCTTGCTG 588515 vv i i i vv i C L1PREC2_orf2# 2198 ATTTTGTATCCTGAAACTTTGCTG 2175 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 51.30 CpG sites = 87, Kimura (unadjusted) = 52.23 Transitions / transversions = 1.14 (87/76) Gap_init rate = 0.03 (15 / 447), avg. gap size = 2.13 (32 / 15) 186 32.56 0.00 0.00 chr2ptel1M 589516 589558 (410442) C MIR3#SINE/MIR (55) 153 111 m_b70s601i18 2609 chr2ptel1M 589516 CCTGCTCCCCTGCTTTATAGATGAGAAAACTGAAGGTCAAGGA 589558 vi i iiii i i i vi ii C MIR3#SINE/MIR 153 CCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGA 111 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 48.84 CpG sites = 12, Kimura (unadjusted) = 48.84 Transitions / transversions = 6.00 (12/2) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 56 21.72 0.00 7.06 chr2ptel1M 590446 590627 (409373) (GTGAGT)n#Simple_repeat 1 170 (0) m_b70s252i21 2610 chr2ptel1M 590446 GTGAGGGGGAGTGTGATTGTGTGAGTGTGCGTGCATGTGTGTGAGTGTGT 590495 v v -- v -- v v (GTGAGT)n#Sim 1 GTGAGTGTGAGTGTGA--GTGTGAGTGTGAGTG--TGAGTGTGAGTGTGA 46 chr2ptel1M 590496 GTGTGTGTGCATATGTGCATGTGTGTATGTGATTGCCTGCATGTGAGTGT 590545 v iivi - - vi v -- vi (GTGAGT)n#Sim 47 GTGTGAGTGTGAGTGTG-A-GTGTGAGTGTGAGTG--TGAGTGTGAGTGT 92 chr2ptel1M 590546 GAGTGTGTATGTGAGTGTGATTGTGTGCATGTGTGCATATGTGCGTGTGT 590595 vi -- - - vi i v i v (GTGAGT)n#Sim 93 GAGTGTGAGTGTGAGTGTGA--GTGTG-A-GTGTGAGTGTGAGTGTGAGT 138 chr2ptel1M 590596 GTGAGTGCATATGTGAGTGTGTGCATGAGTGT 590627 iivi v ii (GTGAGT)n#Sim 139 GTGAGTGTGAGTGTGAGTGTGAGTGTGAGTGT 170 Matrix = Unknown Transitions / transversions = 0.88 (14/16) Gap_init rate = 0.07 (12 / 181), avg. gap size = 1.00 (12 / 12) 258 17.18 3.08 1.52 chr2ptel1M 590634 590698 (409302) HSAT5v1#Satellite 5212 5277 (621) m_b70s502i0 2611 chr2ptel1M 590634 GTGCATGCACATGTGTGTGTGC--GCACGTGTATGAGTATGTGTGTGTGC 590681 - -- i iii v i ? HSAT5v1#Satel 5212 GTGCATGCA-ATGTGTGTGTGCACGCGCGTGCGCGCGTGTGTGTGTGTGN 5260 chr2ptel1M 590682 ATGCAAGTGTGTGTGTG 590698 i iv i i HSAT5v1#Satel 5261 ACGCGTGTGTGCGCGTG 5277 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 7.71 CpG sites = 9, Kimura (unadjusted) = 20.74 Transitions / transversions = 4.50 (9/2) Gap_init rate = 0.03 (2 / 64), avg. gap size = 1.50 (3 / 2) 14 12.44 5.71 0.00 chr2ptel1M 591073 591107 (408893) (GGCCCCT)n#Simple_repeat 1 37 (0) m_b70s252i22 2612 chr2ptel1M 591073 GGCCCCCGGCCCCTGGCCCC-CACCCCT-GCCCCAGG 591107 i -vi - v (GGCCCCT)n#Si 1 GGCCCCTGGCCCCTGGCCCCTGGCCCCTGGCCCCTGG 37 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 11 21.48 6.00 1.92 chr2ptel1M 591283 591332 (408668) (GCGGAG)n#Simple_repeat 1 52 (0) m_b70s252i23 2613 chr2ptel1M 591283 GCGGAGGC-G-GGCTGAGGCGG-CCCAGAAGAAGAGGCTGGAGGAGGAGG 591329 - - v -vv i i vi - v (GCGGAG)n#Sim 1 GCGGAGGCGGAGGCGGAGGCGGAGGCGGAGGCGGAGGC-GGAGGCGGAGG 49 chr2ptel1M 591330 AGG 591332 v (GCGGAG)n#Sim 50 CGG 52 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.08 (4 / 49), avg. gap size = 1.00 (4 / 4) 14 26.06 0.00 0.00 chr2ptel1M 592082 592122 (407878) (AGG)n#Simple_repeat 1 41 (0) m_b70s252i24 2614 chr2ptel1M 592082 AGGAGGAGGAGGAGAAGCAGAAGCGGCTGGTGGAGGAGAAG 592122 i v i vi vv v i (AGG)n#Simple 1 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG 41 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 17 0.00 0.00 0.00 chr2ptel1M 592814 592832 (407168) (C)n#Simple_repeat 1 19 (0) m_b71s252i1 2615 chr2ptel1M 592814 CCCCCCCCCCCCCCCCCCC 592832 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCC 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 13 33.69 1.59 0.00 chr2ptel1M 594188 594250 (405750) (AGGA)n#Simple_repeat 1 64 (0) m_b71s252i2 2616 chr2ptel1M 594188 AGGAAGGGGAGAA-GAAGGAATAAAGGAATAAAGGAATGAACAAACGACT 594236 iii - vi vi v vi v vv (AGGA)n#Simpl 1 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG 50 chr2ptel1M 594237 GAGTGAATAAAGGA 594250 iv vi (AGGA)n#Simpl 51 GAAGGAAGGAAGGA 64 Matrix = Unknown Transitions / transversions = 0.89 (8/9) Gap_init rate = 0.02 (1 / 62), avg. gap size = 1.00 (1 / 1) 44 45.08 0.38 0.38 chr2ptel1M 594206 594467 (405533) (AATA)n#Simple_repeat 1 262 (0) m_b71s252i3 2616 chr2ptel1M 594206 AATAAAGGAATAAAGGAATGAACAAACGACTGAGTGAATAAAGGACTAAG 594255 vi vi i i ii v i i i vi v i (AATA)n#Simpl 1 AATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAA 50 chr2ptel1M 594256 TGAGCAGATAATCGAGCAAAGGAATAAAGGAATGAATGAATGAGTGAGTG 594305 i ii i vii ii vi vi i i i i i i i (AATA)n#Simpl 51 TAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATA 100 chr2ptel1M 594306 AACAGATAAACAAGCAAAGGAATAAAGGAATGAATAAATGGCTGAGTGAA 594355 i i i ii vi vi i iiv i i i (AATA)n#Simpl 101 AATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAA 150 chr2ptel1M 594356 TAAATGATTGAATGAGCAAGTGAACTAAA-GATTGAATTAATAAACTAAC 594404 i v i i ii i - v -i v i v iv i (AATA)n#Simpl 151 TAAATAAATAAATAAATAAAT-AAATAAATAAATAAATAAATAAATAAAT 199 chr2ptel1M 594405 AAATGATTGAATAAATGAATGAGTGAACAGATGAATAAATGAGTAAATAA 594454 i v i i i i i i i i i i (AATA)n#Simpl 200 AAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAA 249 chr2ptel1M 594455 ATGAATGAACAAA 594467 i i i (AATA)n#Simpl 250 ATAAATAAATAAA 262 Matrix = Unknown Transitions / transversions = 3.82 (65/17) Gap_init rate = 0.01 (2 / 261), avg. gap size = 1.00 (2 / 2) 411 29.06 6.84 0.00 chr2ptel1M 595006 595122 (404878) MIR#SINE/MIR 116 240 (22) m_b71s601i0 2617 chr2ptel1M 595006 TGCCTCAGTTTTCTCATCTGTAGAAT-GGGATCATAGCAGCACCCATCTC 595054 i i - v ii i i i MIR#SINE/MIR 116 TGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTC 165 chr2ptel1M 595055 CCAGGGCAGTCACCAGGACCAAACTAGACAAGATTTGGA-------TGGC 595097 vi iv iiiv ii iv vi v iv v ------- i v MIR#SINE/MIR 166 ATAGGGTTGTTGTGAGGATTAAATGAGTTAATACATGTAAAGCGCTTAGA 215 chr2ptel1M 595098 ACAGTGCCCGGCACCGAGTGGGTGC 595122 i vv ii i MIR#SINE/MIR 216 ACAGTGCCTGGCACATAGTAAGCGC 240 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.85 CpG sites = 22, Kimura (unadjusted) = 38.30 Transitions / transversions = 1.83 (22/12) Gap_init rate = 0.02 (2 / 116), avg. gap size = 4.00 (8 / 2) 216 29.85 6.74 2.15 chr2ptel1M 595490 595578 (404422) MamTip2#DNA/hAT-Tip100 197 289 (16) m_b71s601i1 2618 chr2ptel1M 595490 TGCCTTTGGGAG----CACACTT--AGCTAGTGTCAGCTGCTGCCATCCA 595533 i ii ----v i -- i v i ivii v -- MamTip2#DNA/h 197 TACCCCTGGGAGGGGTAACACCTTAAGCCATTATCAGCTAACACCTT--A 244 chr2ptel1M 595534 TCGGGCATTAATTAGGCGCCATCTGGGTGCCAGGCCCTCAGGGAA 595578 v v i iivv i v i v v v? MamTip2#DNA/h 245 GCGGGGATTAGTTGACAGCTAGCTGAGAGCAAGGCCCTGNGGGAA 289 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.47 CpG sites = 14, Kimura (unadjusted) = 39.47 Transitions / transversions = 1.17 (14/12) Gap_init rate = 0.05 (4 / 88), avg. gap size = 2.00 (8 / 4) 18 0.00 0.00 0.00 chr2ptel1M 595624 595643 (404357) (G)n#Simple_repeat 1 20 (0) m_b71s252i4 2619 chr2ptel1M 595624 GGGGGGGGGGGGGGGGGGGG 595643 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGG 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 14 12.57 5.41 2.63 chr2ptel1M 597470 597506 (402494) (GGAG)n#Simple_repeat 1 38 (0) m_b71s252i5 2620 chr2ptel1M 597470 GGAGAGGAAGGAGGGGGAGAGGG-GCG-GGGAGGGAGGG 597506 - i i i - v - (GGAG)n#Simpl 1 GGAG-GGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGG 38 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.08 (3 / 36), avg. gap size = 1.00 (3 / 3) 33 0.00 0.00 0.00 chr2ptel1M 598753 598783 (401217) (C)n#Simple_repeat 1 31 (0) c_b71s251i0 2621 chr2ptel1M 598753 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 598783 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 12 6.98 0.00 14.29 chr2ptel1M 600449 600488 (399512) (CCCTGC)n#Simple_repeat 1 35 (0) m_b71s252i6 2622 chr2ptel1M 600449 CCCTGCCCTTGTGCCCCAGCCCCTCAGGCCCCTGCCCCTG 600488 --v v --- (CCCTGC)n#Sim 1 CCCTGCCC--CTGCCCCTGCCCCT---GCCCCTGCCCCTG 35 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.13 (5 / 39), avg. gap size = 1.00 (5 / 5) 19 8.13 0.00 0.00 chr2ptel1M 601207 601232 (398768) (C)n#Simple_repeat 1 26 (0) m_b71s252i7 2623 chr2ptel1M 601207 CCCCCCCCCCCCCCCCCCCGCCCTCC 601232 v i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCC 26 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 31 0.00 0.00 0.00 chr2ptel1M 602887 602913 (397087) (AG)n#Simple_repeat 1 27 (0) c_b71s251i1 2624 chr2ptel1M 602887 AGAGAGAGAGAGAGAGAGAGAGAGAGA 602913 (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGA 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 32 14.46 6.25 2.41 chr2ptel1M 603285 603364 (396636) (AT)n#Simple_repeat 1 83 (0) m_b71s252i8 2625 chr2ptel1M 603285 ATATATA-ATACATGTGAGTATATATATATATATATATATA-AAATGT-T 603331 - i i - - - v i - (AT)n#Simple_ 1 ATATATATATATATAT-A-TATATATATATATATATATATATATATATAT 48 chr2ptel1M 603332 ACAT-TATATATTAATAT-TATATATAAGAATATA 603364 i - vv - viv (AT)n#Simple_ 49 ATATATATATATATATATATATATATATATATATA 83 Matrix = Unknown Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.09 (7 / 79), avg. gap size = 1.00 (7 / 7) 487 28.27 11.30 2.07 chr2ptel1M 603624 603800 (396200) MIRb#SINE/MIR 41 233 (35) m_b71s601i2 2626 chr2ptel1M 603624 GGGGTGAGGAGGACCCAAGTTTCAAATCCAGCCTCAAACATTTCCTACCT 603673 i v ivi iii - i v v viv i v v MIRb#SINE/MIR 41 GGAGTCAGACAGACCTGGGTT-CGAATCCCGGCTCTGCCACTTACTAGCT 89 chr2ptel1M 603674 GGGCGACCATGGGCA-------------------GCCTCAGTTTCCTCAC 603704 v i v ------------------- i MIRb#SINE/MIR 90 GTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCAT 139 chr2ptel1M 603705 CTGGAAAGTGGGAGTAGTCATAGCACCAGCCCTCCGCGGTTGTGGTGAGG 603754 v i ii --- ii vi iiv iv v MIRb#SINE/MIR 140 CTGTAAAATGGGGATA---ATAATACCTACCTCGCAGGGTTGTTGTGAGG 186 chr2ptel1M 603755 GTCAAATGAGCTCATGTTTGTAAATTGTGCAGC-CACTGCCTCGCGC 603800 i i v v iv vi ivi - v v i MIRb#SINE/MIR 187 ATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCAC 233 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.56 CpG sites = 27, Kimura (unadjusted) = 36.27 Transitions / transversions = 1.23 (27/22) Gap_init rate = 0.03 (6 / 176), avg. gap size = 4.00 (24 / 6) 11 25.38 0.00 6.12 chr2ptel1M 605767 605818 (394182) (GGAGGG)n#Simple_repeat 1 49 (0) m_b71s252i9 2627 chr2ptel1M 605767 GGAGGGGGCAGGCAGAGCTGGAGGGCTGTGGGTTGGGAGGGAGGGGGCGG 605816 - vi vv -v v -v i i v (GGAGGG)n#Sim 1 GGAGGGGG-AGGGGGAGGGGGAGGG-GGAGGG-GGAGGGGGAGGGGGAGG 47 chr2ptel1M 605817 GG 605818 (GGAGGG)n#Sim 48 GG 49 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.00 (3 / 3) 18 30.48 2.86 3.85 chr2ptel1M 607163 607267 (392733) (CCAT)n#Simple_repeat 1 104 (0) m_b71s252i10 2628 chr2ptel1M 607163 CCGTCCTTCCATTCGTTGATCCCTCCGACTCTGTCTACCCATCCCTCCAT 607212 i v i i iv v - - ii i i v (CCAT)n#Simpl 1 CCATCCATCCATCCATCCATCCATCC-A-TCCATCCATCCATCCATCCAT 48 chr2ptel1M 607213 CCGTCTGTCCAT-C-TCCATCCA-CAAGGTGTGGCTCTCCGTCCATCCCT 607259 i ii - - - v -- viiv iv i v (CCAT)n#Simpl 49 CCATCCATCCATCCATCCATCCATCCA--TCCATCCATCCATCCATCCAT 96 chr2ptel1M 607260 CCATCCAT 607267 (CCAT)n#Simpl 97 CCATCCAT 104 Matrix = Unknown Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.07 (7 / 104), avg. gap size = 1.00 (7 / 7) 12 28.68 0.00 3.85 chr2ptel1M 607246 607299 (392701) (CTCC)n#Simple_repeat 1 52 (0) m_b71s252i11 2629 chr2ptel1M 607246 CTCCGTCCATCCCTCCATCCATATGTCCGTCTCTGCTCATCTCTCCCTCT 607295 v v v v viv v i - - v i i (CTCC)n#Simpl 1 CTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCT-C-CCTCCCTCCCTCC 48 chr2ptel1M 607296 CTCC 607299 (CTCC)n#Simpl 49 CTCC 52 Matrix = Unknown Transitions / transversions = 0.50 (4/8) Gap_init rate = 0.04 (2 / 53), avg. gap size = 1.00 (2 / 2) 369 24.22 19.53 0.00 chr2ptel1M 607402 607529 (392471) MIR#SINE/MIR 103 255 (7) m_b71s601i3 2630 chr2ptel1M 607402 CTTCACCTCTTTCTGCCTCAGTTTTTCCATCTGTCCGATGGGGACCATAC 607451 v i v iii vvi iv v MIR#SINE/MIR 103 CTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAA 152 chr2ptel1M 607452 TACTCTCTGTTTCCCAGG--TGCTGTG----TTAAGTG----------TG 607485 v vi iii vi -- i ---- i ---------- MIR#SINE/MIR 153 TAGTACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATACATG 202 chr2ptel1M 607486 TGATG---------CAGTGCCCGGCACACAGTAGGCGCTGCATAAATGCT 607526 i v --------- i i i vv i MIR#SINE/MIR 203 TAAAGCGCTTAGAACAGTGCCTGGCACATAGTAAGCGCTCAATAAATGTT 252 chr2ptel1M 607527 TGC 607529 v MIR#SINE/MIR 253 AGC 255 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.81 CpG sites = 18, Kimura (unadjusted) = 29.81 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.03 (4 / 127), avg. gap size = 6.25 (25 / 4) 18 0.00 0.00 0.00 chr2ptel1M 608530 608552 (391448) (CCA)n#Simple_repeat 1 23 (0) m_b71s252i12 2631 chr2ptel1M 608530 CCACCACCACCACCACCACCACC 608552 (CCA)n#Simple 1 CCACCACCACCACCACCACCACC 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 12 21.28 0.00 8.51 chr2ptel1M 609609 609659 (390341) (GGGCCCC)n#Simple_repeat 1 47 (0) m_b71s252i13 2632 chr2ptel1M 609609 GGGCCCCGGGCCCCTCTGGGGGGGCGGCCGGCGGGCCCCGGGCTCCCGGC 609658 - - -- vvv v vv i v (GGGCCCC)n#Si 1 GGGCCCCGGG-CCC-C--GGGCCCCGGGCCCCGGGCCCCGGGCCCCGGGC 46 chr2ptel1M 609659 C 609659 (GGGCCCC)n#Si 47 C 47 Matrix = Unknown Transitions / transversions = 0.14 (1/7) Gap_init rate = 0.08 (4 / 50), avg. gap size = 1.00 (4 / 4) 20 14.25 2.00 4.08 chr2ptel1M 609855 609904 (390096) (GGCGGG)n#Simple_repeat 1 49 (0) m_b71s252i14 2633 chr2ptel1M 609855 GGTGGGCGGGGCGGCGGGGGCGGGGGCGGGGCCTCGGGGGC-GGGACGGG 609903 i v v v --v - i (GGCGGG)n#Sim 1 GGCGGGGGCGGGGGCGGGGGCGGGGGCGGGG--GCGGGGGCGGGGGCGGG 48 chr2ptel1M 609904 G 609904 (GGCGGG)n#Sim 49 G 49 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.06 (3 / 49), avg. gap size = 1.00 (3 / 3) 15 19.10 0.00 7.84 chr2ptel1M 614133 614187 (385813) (TTGGGGG)n#Simple_repeat 1 51 (0) m_b71s252i15 2634 chr2ptel1M 614133 TTGGGGTTTGGCTGGATAGGGAGGTTTAGGGTTGGGGGTGGGGCGGCTGG 614182 v -- i v - vi v - i (TTGGGGG)n#Si 1 TTGGGGGTTGG--GGGTTGGG-GGTTGGGGGTTGGGGGTTGGG-GGTTGG 46 chr2ptel1M 614183 GCGTT 614187 v (TTGGGGG)n#Si 47 GGGTT 51 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.07 (4 / 54), avg. gap size = 1.00 (4 / 4) 33 3.26 5.33 8.22 chr2ptel1M 614724 614798 (385202) (CTC)n#Simple_repeat 1 73 (0) m_b71s252i16 2635 chr2ptel1M 614724 CTCCTTCCTTCCT-CTCCTCCTTCTTTCTCCTCCCTCCT-CTCCTCCTTC 614771 - - - - i i - - - (CTC)n#Simple 1 CTCC-TCC-TCCTCCTCCTCC-TCCTCCTCCT-CCTCCTCCTCCTCC-TC 45 chr2ptel1M 614772 CTCCTCTCTCCTCCTCCTCC-CC-CCTCC 614798 - - - (CTC)n#Simple 46 CTCCTC-CTCCTCCTCCTCCTCCTCCTCC 73 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.14 (10 / 74), avg. gap size = 1.00 (10 / 10) 14 12.53 6.12 6.12 chr2ptel1M 617331 617379 (382621) (TGAT)n#Simple_repeat 1 49 (0) m_b71s252i17 2636 chr2ptel1M 617331 TGA-TGA-TG-TTGATGGATTTAGTTGATGGATTGATCCGAGTTGATGGA 617377 - - - v v - v -i - v (TGAT)n#Simpl 1 TGATTGATTGATTGATTGATTGA-TTGATTGATTGAT-TGA-TTGATTGA 47 chr2ptel1M 617378 TT 617379 (TGAT)n#Simpl 48 TT 49 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.12 (6 / 48), avg. gap size = 1.00 (6 / 6) 676 31.76 4.72 0.00 chr2ptel1M 618435 618667 (381333) C MIRb#SINE/MIR (0) 268 25 m_b71s601i4 2637 chr2ptel1M 618435 AAGAAGGAAATAAGCATTTATTAAGCACCAACCATGGTCCAGGAGCTGTG 618484 v vii iiv v i i iv i vv vi C MIRb#SINE/MIR 268 AATAATAGAGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTG 219 chr2ptel1M 618485 TTAGGCTATTTACAAATGTGATCCCATTTGGTCTTCACAACCTCTCTGTG 618534 i i vv viii v i ii i vv i i C MIRb#SINE/MIR 218 CTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCG 169 chr2ptel1M 618535 GAGAAGG---TACTAACCCAATTTTACTGTTGAGTAAACTAAG---CAGG 618578 ii v --- i v v v v v i --- i C MIRb#SINE/MIR 168 AGGTAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGA 119 chr2ptel1M 618579 AAG--CAGTTGATTTGTTCAGACTCACAGATCTAGTAAGTATCTGAAGCT 618626 i --i iv i i ii iiv v v iv v iv v C MIRb#SINE/MIR 118 GAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 69 chr2ptel1M 618627 GGGTTTGAACTCAGGTCTTTCTGACCTGACA---CTTGCTCTCT 618667 i i i v iiv v --- v i C MIRb#SINE/MIR 68 GGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTT 25 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.22 CpG sites = 42, Kimura (unadjusted) = 42.47 Transitions / transversions = 1.31 (42/32) Gap_init rate = 0.02 (4 / 232), avg. gap size = 2.75 (11 / 4) 228 31.32 11.55 3.32 chr2ptel1M 618822 619072 (380928) L2d_3end#LINE/L2 232 502 (14) m_b71s601i5 2638 chr2ptel1M 618822 CTCTATG--GCCATCCCT--CCTCTGCTTTTTACTACTGATCTCCCTGGC 618867 i i -- v -- v v vviii - i i-- L2d_3end#LINE 232 CTCCACGAAGCCTTCCCTGACCACTCCAGCCCAC-ACTGATCTCTCC--C 278 chr2ptel1M 618868 TTCTACAGGAAGCCTTGCACAATCCCTCTTAATTCCA-GCACCTT--CCC 618914 - v i vv vvvi v ivivv ivi v - vi -- v L2d_3end#LINE 279 TTCT-CTGAACTCCTATAGCACTTATAGTCTGTACCACGCAATTTAGCAC 327 chr2ptel1M 618915 TTATTTATTCTTCATCCTTTATAGAGCTCACTTTGTATTCAGCTTGTCTA 618964 v viviii i v v vv vvv - --- v i L2d_3end#LINE 328 TTAATTATATACTGTCTTGTATTGTTCTCTAATTGT-TTCA---TGTGTG 373 chr2ptel1M 618965 TTTGT--TGTCCCCTCCATTAGATCGTAAGCTCTTTGAGGACAAGAAC-- 619010 v -- i i v i i i i i i -- L2d_3end#LINE 374 TTAGTCTTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCA 423 chr2ptel1M 619011 TGT---------TTTTTTC--------CAGTGCTTAGCACAAGACCTGAC 619043 --------- ? -------- i i ivi ivii L2d_3end#LINE 424 TGTCTTATACTNTTTTNTCGTTCCCCACAGCGCCTAGCACAGTGCTGAGC 473 chr2ptel1M 619044 ACACAGGA-GTGCAAAATAAACGCTCTGTT 619072 i v - i vv ii - L2d_3end#LINE 474 ACATAGTAGGCGCTCAATAAATACT-TGTT 502 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.50 CpG sites = 39, Kimura (unadjusted) = 41.60 Transitions / transversions = 1.05 (39/37) Gap_init rate = 0.07 (18 / 250), avg. gap size = 2.11 (38 / 18) 282 28.75 20.43 0.90 chr2ptel1M 618887 619072 (380928) L2a_3end#LINE/L2 284 505 (12) m_b71s601i6 2638 chr2ptel1M 618887 CAATCCCTCTTAATTCCAGCACCTTCCCTTATTTATTCTTCAT--CCTTT 618934 ?iv ii i vii vvi i v i - i -- vi L2a_3end#LINE 284 CANCACTCCCTATCCCCCTTACCCTGCTTTATTT-TTCTCCATAGCACTT 332 chr2ptel1M 618935 ATAG--AGCT----CACTTTGTATTCAGCTTGTCTATTTGTT-------- 618970 vi-- v ----i v i ivi i i -------- L2a_3end#LINE 333 ATCACCATCTGACATACTATATATTTTACTTATTTATTTGTTTATTGTCT 382 chr2ptel1M 618971 GTC-CCCTCCATTAGATCGTAAGCTCTTTGAGGACAAGAA-------CTG 619012 - i i vi iv i i i ------- L2a_3end#LINE 383 GTCTCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTCTG 432 chr2ptel1M 619013 TTTTTTT-------------CCAGTGCTTAGCACAAGACCTGACACACAG 619049 v ------------- i i v ivi i i L2a_3end#LINE 433 TTTTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACATAG 482 chr2ptel1M 619050 GA-GTGCAAAATAAACGCTCTGTT 619072 v - i vv ii- i L2a_3end#LINE 483 TAGGCGCTCAATAAATA-TTTGTT 505 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.40 CpG sites = 35, Kimura (unadjusted) = 38.26 Transitions / transversions = 1.94 (35/18) Gap_init rate = 0.05 (10 / 185), avg. gap size = 4.00 (40 / 10) 336 27.52 9.38 2.34 chr2ptel1M 618913 619072 (380928) L2c_3end#LINE/L2 296 466 (12) m_b71s601i7 2638 chr2ptel1M 618913 CCTTATTTATTCTTCATCCTTTATAGAGCT---CACT---TTGTATTCAG 618956 i i i v i --- v vi --- i --- vvi L2c_3end#LINE 296 CCCTGTCTATACTCC---CATTATAGCACTTATCATTAACTTGTATTGTA 342 chr2ptel1M 618957 CTTGTCTATTT----GT-TGTCCCCTCCATTAGATCGTAAGCTCTTTGAG 619001 v i ---- - i i ii i i L2c_3end#LINE 343 ATTGTCTGTTTACNTGTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGAG 392 chr2ptel1M 619002 GACAAGAACTGT-TTTTTTCCAGTGCT-TAGCACAAG-ACCTGACACACA 619048 i i i i - i v i vivi - v v v -i i i L2c_3end#LINE 393 GGCAGGGACCGTGTCTTATTCATCTTTGTATCCCCAGCGCCTGGCACATA 442 chr2ptel1M 619049 GGA-GTGCAAAATAAACGCTCTGTT 619072 v - i vv i - i L2c_3end#LINE 443 GTAGGCGCTCAATAAATG-TTTGTT 466 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.62 CpG sites = 28, Kimura (unadjusted) = 35.70 Transitions / transversions = 1.87 (28/15) Gap_init rate = 0.08 (12 / 159), avg. gap size = 1.58 (19 / 12) 277 33.68 1.85 13.40 chr2ptel1M 619172 619387 (380613) MamRTE1#LINE/RTE-BovB 1131 1324 (2488) m_b71s601i8 2639 chr2ptel1M 619172 CACCTTCTCATCACCAACCCTAAACTTTTCCATTTACCTAGCCACAATAA 619221 v iv v v i --- i iii v --- i v i MamRTE1#LINE/ 1131 CAGCTCGTAATCACCAACACCA---TCTTCCGCCTACCGA---ATAAGAG 1174 chr2ptel1M 619222 ATAAAACATTGTGGTAAAATGTTTTACCCTCACAGCAACCCTCGCAGCAA 619271 - i ii ---- ----- v i vi i---- ------ MamRTE1#LINE/ 1175 A-AAGACATCATGG----ATG-----CACCCAAGGT----CT------AA 1204 chr2ptel1M 619272 ACACTGGCATTTAATAGGCTATGTGAACGTAAGGAGAGGAGACAGGCAGG 619321 i v i v v ii i v v vv iviiv i vv v MamRTE1#LINE/ 1205 GCAGTGGCATCTCATTGATTATATCATCGTTCGACAGCGGGACCTGAAGG 1254 chr2ptel1M 619322 ATG---GAGTGGCCAAGGCCA-GCGTGGCGCAGAGTGCTGGACTGACCAT 619367 ---iii vi iivi i - v i MamRTE1#LINE/ 1255 ATGTTTAGATTACTGCAGCTATGCGTGGCGCCGAGTGCTGGACCGACCAT 1304 chr2ptel1M 619368 AGACTTATCCTCTCTGAGCT 619387 v v v v v ii i MamRTE1#LINE/ 1305 CGCCTGATACGCTCCAAACT 1324 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.14 CpG sites = 35, Kimura (unadjusted) = 44.99 Transitions / transversions = 1.25 (35/28) Gap_init rate = 0.13 (28 / 215), avg. gap size = 1.07 (30 / 28) 252 36.49 5.49 2.13 chr2ptel1M 619788 619969 (380031) MamRTE1#LINE/RTE-BovB 2503 2690 (1122) m_b71s601i9 2639 chr2ptel1M 619788 AGTTTGGCTGCCCAGAGAAATCCATCAGGACGGTACCTC-AGTTTGTGCT 619836 v i i i i ivv vvv - v iii v MamRTE1#LINE/ 2503 AGTTTGGCTGCCCTGAGAAGTTCACCAAGATCCTAAGGCTACTCCATGAT 2552 chr2ptel1M 619837 GGCGTGCTTGCCGGG-GTGCTGGACAAGG-GGCGATGCTCCCCAGCT--T 619882 ii --- v- i iii vvv i- - v vi ii i-- MamRTE1#LINE/ 2553 GGTATG---GCCGGTCGCGTCAGAGTTGACGGCG-TCCTGTCCGACCCAT 2598 chr2ptel1M 619883 TCCTGGTCACCAGTGGAGTGAAATGAGACCGTGTGCTCACTGCCCTGTT- 619931 ivi i iiii ii i iv viv v vv v - MamRTE1#LINE/ 2599 TCCCCATCACCAATGGAGTGAAGCAGGATTGCGTAATAGGTCCAGTCTTA 2648 chr2ptel1M 619932 TGTAGCACGTTTT---CAGTCATCCATGAGGAAG-AACAAGG 619969 vi iivii --- i v vi v - MamRTE1#LINE/ 2649 TTCAATCTATTTTATGCAGCCATGCTCGAGGATGCAACAAGG 2690 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 47.67 CpG sites = 38, Kimura (unadjusted) = 52.25 Transitions / transversions = 1.41 (38/27) Gap_init rate = 0.06 (11 / 181), avg. gap size = 1.27 (14 / 11) 530 24.40 1.59 2.40 chr2ptel1M 621067 621192 (378808) MIRb#SINE/MIR 6 130 (138) m_b71s601i10 2640 chr2ptel1M 621067 GGACAGCTAGGCAATACAATGGATAGAGCACCGGCCCTGAAGTCAGGAGG 621116 i --- iii i i v v ii i ivi MIRb#SINE/MIR 6 GGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAG 52 chr2ptel1M 621117 ACCCGAGTTCAAATCT-GGCCTTAACATTTTCTAGCTGTGTGACCCTGGG 621165 i i i i- ii iv i v i MIRb#SINE/MIR 53 ACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGG 102 chr2ptel1M 621166 CAAGTCACTTAACCCCAAT-CGCCTCAG 621192 i i vv -v MIRb#SINE/MIR 103 CAAGTTACTTAACCTCTCTGAGCCTCAG 130 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.71 CpG sites = 22, Kimura (unadjusted) = 30.96 Transitions / transversions = 2.75 (22/8) Gap_init rate = 0.04 (5 / 125), avg. gap size = 1.00 (5 / 5) 560 21.43 1.79 0.00 chr2ptel1M 621081 621192 (378808) MIRc#SINE/MIR 14 127 (141) m_b71s601i11 2640 chr2ptel1M 621081 TACAATGGATAGAGCACCGGCCCTGAAGTCAGGAGGACCCGAGTTCAAAT 621130 i i v i v i i i i i i i MIRc#SINE/MIR 14 TGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGT 63 chr2ptel1M 621131 CT-GGCCTTAACATTTTCTAGCTGTGTGACCCTGGGCAAGTCACTTAACC 621179 i- ii iv i v i MIRc#SINE/MIR 64 CCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACC 113 chr2ptel1M 621180 CCAAT-CGCCTCAG 621192 i vv -v MIRc#SINE/MIR 114 TCTCTGAGCCTCAG 127 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 24.88 CpG sites = 17, Kimura (unadjusted) = 26.13 Transitions / transversions = 2.43 (17/7) Gap_init rate = 0.02 (2 / 111), avg. gap size = 1.00 (2 / 2) 63 26.40 2.06 2.59 chr2ptel1M 622712 622905 (377095) (GGAG)n#Simple_repeat 1 193 (0) m_b71s252i18 2641 chr2ptel1M 622712 GGAAGAAAGGA-GGAGGGAAAGAAAAAGGGA-AAAGGAAGGAAGGGAGGG 622759 i i i - ii iii -ii i i (GGAG)n#Simpl 1 GGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGG 50 chr2ptel1M 622760 -GGGAGGGAAGGAAGGAGGG-GAGGGGGAGGGAGGGAAGAAGGAAGGAAG 622807 - i i - i i i i i i - (GGAG)n#Simpl 51 AGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGA- 99 chr2ptel1M 622808 GGGAAGAAGGAAGGAAGGGAAGGGAAGGAAGGAAGGAAGGAAGGAAGGAA 622857 i i i i - - i i i i i i (GGAG)n#Simpl 100 GGGAGGGAGGGAGGGAGGG-AGGG-AGGGAGGGAGGGAGGGAGGGAGGGA 147 chr2ptel1M 622858 GGAAGGAAAAGGAAGGAGGGAAGGAAGGGAGGAGGGGAAGGAGGGAGG 622905 i -i i i - i ii i (GGAG)n#Simpl 148 GGGAGG-GAGGGAGGGAGGG-AGGGAGGGAGGGAGGGAGGGAGGGAGG 193 Matrix = Unknown Transitions / transversions = 1.00 (38/0) Gap_init rate = 0.05 (9 / 193), avg. gap size = 1.00 (9 / 9) 28 23.88 4.10 9.73 chr2ptel1M 622717 622911 (377089) (AAAGGA)n#Simple_repeat 1 185 (0) m_b71s252i19 2641 chr2ptel1M 622717 AAAGGAGGAGGGAAAGAAAAAGGGAAAAGGAAGGAAGG-GAGGGGGGAGG 622765 ii i i - -- -i i iii (AAAGGA)n#Sim 1 AAAGGAAAAGGAAAAGGAAAA-GGAAAAGGAA--AAGGAAAAGGAAAAGG 47 chr2ptel1M 622766 -GAAGGAAGGAGG-GGAGGGGGAGG-GAGGGAAGAAGG--AAGGAAGGGG 622810 -i -i -ii iii -i i - -- ii (AAAGGA)n#Sim 48 AAAAGGAA-AAGGAAAAGGAAAAGGAAAAGGAA-AAGGAAAAGGAAAAGG 95 chr2ptel1M 622811 AAGAAGGAAGGAAGGGAAGGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 622860 - -- i i -- -- -- -- (AAAGGA)n#Sim 96 AA-AAGGAA--AAGGAAAAGGAA--AAGGAA--AAGGAA--AAGGAA--A 134 chr2ptel1M 622861 AGGAAAAGGAAGGAGG-GAAGG-AAGGGAGGAGGGGAAGGAGGGAGGAAA 622908 -i -i - i ii ii -ii (AAAGGA)n#Sim 135 AGGAAAAGGAA-AAGGAAAAGGAAAAGGAAAAGGAAAAGGA-AAAGGAAA 182 chr2ptel1M 622909 AGG 622911 (AAAGGA)n#Sim 183 AGG 185 Matrix = Unknown Transitions / transversions = 1.00 (31/0) Gap_init rate = 0.13 (25 / 194), avg. gap size = 1.04 (26 / 25) 235 35.79 1.05 0.00 chr2ptel1M 623527 623621 (376379) L2b_3end#LINE/L2 368 463 (3) m_b71s601i12 2642 chr2ptel1M 623527 AGGGGCGGGCGCTGTTTCCAGCGTCGC-GCATTCTTCCGGCTGAGCAAAC 623575 i v ?vv i ivvv ii - i i iivvv iv v v L2b_3end#LINE 368 AGGGACCGNGTCTGTCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAG 417 chr2ptel1M 623576 CGCCTGGTACACAGTAGGCACCTATTAAATGCTCGTTGGCTTAGTG 623621 ? i i ii v ii i iv v i L2b_3end#LINE 418 NGCCTGGCACACAGTAGGCGCTCAGTAAATATTTGTTGAATGAATG 463 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 49.72 CpG sites = 19, Kimura (unadjusted) = 51.92 Transitions / transversions = 1.27 (19/15) Gap_init rate = 0.01 (1 / 94), avg. gap size = 1.00 (1 / 1) 58 29.59 3.08 3.44 chr2ptel1M 624195 624486 (375514) (GGGAGGG)n#Simple_repeat 1 291 (0) m_b71s252i20 2643 chr2ptel1M 624195 GGGAGGAAGGA-GCGGGAGGGGAGGAGCGGGG-GGACCG-GGGGGGCGGC 624241 ii - v - v - ivv - v - (GGGAGGG)n#Si 1 GGGAGGGGGGAGGGGGGAGGGG-GGAGGGGGGAGGGGGGAGGGGGGAGG- 48 chr2ptel1M 624242 GGGAACGGGGGGGGGGGGAGGAGGGCGCGGGACAGGAGGGCGGCGGGAGC 624291 i v i i v - iv i v v - (GGGAGGG)n#Si 49 GGGGAGGGGGGAGGGGGGAGGGGGGAG-GGGGGAGGGGGGAGGGGGGAG- 96 chr2ptel1M 624292 AAGGGA-GGGCG-GCCGGGAGGCGGGA-CCGGGAGGCGGGGAGCACGGGA 624338 ii - v - vv v -vv - -iv (GGGAGGG)n#Si 97 GGGGGAGGGGGGAGGGGGGAGGGGGGAGGGGGGAGG-GGGGAG-GGGGGA 144 chr2ptel1M 624339 GGAGGG-CGGGGGACGGGGGCCGGGAG-CCGGGGAGGGGGGGGGAAGGGA 624386 i -v v vv i -vv i -i (GGGAGGG)n#Si 145 GGGGGGAGGGGGGAGGGGGGAGGGGGGAGGGGGGAGGGGGGAGG-GGGGA 193 chr2ptel1M 624387 GGGGGGGGGAGCCCGGGAGGAGGGGGACCCGGGGGGCAGGGGCG-GGGAC 624435 i i vvv i --vv - v - iv (GGGAGGG)n#Si 194 GGGGGGAGGGGGGAGGGGGGAGGGGG--GAGGGGGG-AGGGGGGAGGGGG 240 chr2ptel1M 624436 CCAGCGGGCGAGGGGTTGGGCCCGGTTGGCGGGGTGGGGGGTGAGGGGTG 624485 vvi v v i vv vvv vv v v i v v (GGGAGGG)n#Si 241 GAGGGGGGAGGGGGGAGGGGGGAGGGGGGAGGGGGGAGGGGGGAGGGGGG 290 chr2ptel1M 624486 A 624486 (GGGAGGG)n#Si 291 A 291 Matrix = Unknown Transitions / transversions = 0.49 (22/45) Gap_init rate = 0.07 (19 / 291), avg. gap size = 1.00 (19 / 19) 254 24.70 6.45 2.06 chr2ptel1M 626234 626419 (373581) C PABL_B-int#LTR/ERV1 (2898) 4224 4031 m_b71s701i0 2644 chr2ptel1M 626234 TTCTCTGGG--TTTTGGGACAGCCTGTAGCAGCTGTAGTTTTTTTCCTGC 626281 i ? --i --- v v i ?vvi i?v ii?i? C PABL_B-int#LT 4224 TCCTNTGGGGCCTTT---ACTGCCTCTAGTAGNGCCAANATTTCCNTNGC 4178 chr2ptel1M 626282 ATATTTAATAGGTTTCTTTGCTGTCG--AAAAGTCCCCTCTCTTTCCACA 626329 i i vvv?? v ?v ? ???-- i? i i v C PABL_B-int#LT 4177 GTGTTTAATTTCNNTATTNTCNGNNNTTAGNAGCCCCCTTTCTTTCCAGA 4128 chr2ptel1M 626330 TAGCCCCGTGAGCG-GCCCCAACATGGAAGGCACATTTGGGGGC------ 626372 ? ? i- ?v i v -? ? i i i v ------ C PABL_B-int#LT 4127 TNGCCCCGTGNGCATGNACTACCA-NGAANGCATACTTGGAGTCAGTGTA 4079 chr2ptel1M 626373 CCTGTTCCTCTTCTTCCCTT-CCCCAGTGCCAAAGCTCCGGGCAGGGC 626419 vv ?vi?i ? -vvv vv? i i v? C PABL_B-int#LT 4078 AATGTTNGCNCTCTTNCCTTGGGACAGTTGNAAGGCTCTGGTNAGGGC 4031 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 34.92 CpG sites = 22, Kimura (unadjusted) = 35.89 Transitions / transversions = 0.96 (22/23) Gap_init rate = 0.05 (9 / 185), avg. gap size = 1.78 (16 / 9) 236 24.66 2.74 0.00 chr2ptel1M 627982 628054 (371946) C MIR1_Amn#SINE/MIR (81) 149 75 m_b71s601i13 2645 chr2ptel1M 627982 CCATTTGTCCGATGGGGAAACTGAGCCCCGGAGAGG--AGCTGCCTTGTG 628029 vv v i v ? i -- iv v iv C MIR1_Amn#SINE 149 CCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGCC 100 chr2ptel1M 628030 CAAGGCCCAGTAGCCACCCTGTGGC 628054 i vv?i ?iv ?v C MIR1_Amn#SINE 99 CAAGGTCACNCAGCNGGCNAGTGGC 75 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.09 CpG sites = 7, Kimura (unadjusted) = 32.09 Transitions / transversions = 0.64 (7/11) Gap_init rate = 0.01 (1 / 72), avg. gap size = 2.00 (2 / 1) 393 27.65 0.82 5.13 chr2ptel1M 632652 632773 (367227) C MIRc#SINE/MIR (141) 127 11 m_b72s601i0 2646 chr2ptel1M 632652 CTGAGGC-AATTGGGATTAAGTGACTTGCCCAGAGTCATACAGCTACAAG 632700 -v vv i i ii i ---- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTA---- 82 chr2ptel1M 632701 TGTTAAGTGTCTGAAGTCAAATTTTAACTCAGATCCTCCTGACTTCAGGG 632750 - - v v ivivii i iv i i i i i v C MIRc#SINE/MIR 81 -GT-AAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGT 34 chr2ptel1M 632751 CTGGTGCGCTATCCATTGTGCCA 632773 ii v v i ii C MIRc#SINE/MIR 33 CCAGTGCTCTTTCCACTGCACCA 11 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.00 CpG sites = 21, Kimura (unadjusted) = 35.78 Transitions / transversions = 1.91 (21/11) Gap_init rate = 0.06 (7 / 121), avg. gap size = 1.00 (7 / 7) 1235 27.26 6.19 0.89 chr2ptel1M 632834 633366 (366634) C L1ME3G_3end#LINE/L1 (294) 630 70 m_b72s551i0 2647 chr2ptel1M 632834 TGCTTGTTTC-CTCAACATTAGTTCATGTAAATCTTTCCAGGCC------ 632876 v - v vv v v i v i ------ C L1ME3G_3end#L 630 TGCTTTTTTCACTCAACAATATGTCTTGGAGATCTTTCCATGTCAGTACA 581 chr2ptel1M 632877 T-T---TCTTGGTCATCATTTTTAATAGAACAATAAGATTCCATAACATT 632922 - --- vvv iv i? vvvv iv ii v C L1ME3G_3end#L 580 TATAGATCTACCTCATTCTTTTTAACNGCTGCATAGTATTCCATAGTATG 531 chr2ptel1M 632923 CACATACCATATCTTATTCAGCCATTCCCCAACTGATGGGCATGCA---- 632968 v i vi i i v i i vi ---- C L1ME3G_3end#L 530 GATATACCATAATTTATTTAACCATTCCCCTATTGATGGACATTTAGGTT 481 chr2ptel1M 632969 ---CTCAATTCTG-GCCACTACAAACAGGGCTGCCACAAACATTTTGGCA 633014 ---ii i v- i i iv v ii ii v i C L1ME3G_3end#L 480 GTTTCCAATTTTTCGCTATTACAAACAATGCTGCAATGAACATCCTTGTA 431 chr2ptel1M 633015 CATACAGGTCCCTATCC-CTTCTTT-AGTATCTCTTTGGGGTATAAGCCC 633062 i ?-- i i v - v v vi- i ? i i v v? ? C L1ME3G_3end#L 430 CATGCN--TCCTTGTGCACATGTGCGAGTATTTCTNTAGGATAGATNCCN 383 chr2ptel1M 633063 AGTAGTAACACCGCTGGATCAAAGGGGATGCGCAGTTTGATAACTTTTTG 633112 v iiv ii i v v i -- i vvv C L1ME3G_3end#L 382 AGAAGTGGAATTGCTGGGTCAAAGGGTATGCGCATTTTAA--ATTTTAAT 335 chr2ptel1M 633113 AGCATAGTTCCAAACTACTCTCCAGAATGGCTGGATGTGTTCACAATTCC 633162 - v v i i i i ? v ivvi i v i C L1ME3G_3end#L 334 AG-ATACTGCCAAATTGCCCTCCAAAANGGCTGTACCAATTTACACTCCC 286 chr2ptel1M 633163 ACCAACAATGTATCAGTGTCCCAGTTTTCCCACATCCCCTCCAACATTTG 633212 i i v v v v i i i v i ? C L1ME3G_3end#L 285 ACCAGCAGTGTATGAGAGTACCCGTTTCCCCACACCCTCGCCAACACTNG 236 chr2ptel1M 633213 ---TCATCTTTTCTTGCCATCTTAGCCAATCTGAGAGATGTGAGGTGCTA 633259 --- i vv?ii vvv i v vi i vi ii v C L1ME3G_3end#L 235 ATATTATCAANCTTTTAAATTTTTGCCAATCTGATGGGTGAAAAATGGTA 186 chr2ptel1M 633260 CCTCAGAGCTGCTTT-ATTTGCATTTCTCTGATCAATAGTGATTTCAAGC 633308 i vv i i - i i v vv ii C L1ME3G_3end#L 185 TCTCATTGTTGTTTTAATTTGCATTTCCCTGATTACTAGTGAGGTTGAGC 136 chr2ptel1M 633309 AT-TTTTC--ATGTCTATAGATGACTTTAATTTCATCATC--TGAAGT-- 633351 - -- i v iiv i vv v v -- v -- C L1ME3G_3end#L 135 ATCTTTTCATATGTTTATTGGCCATTTGTATTTCCTCTTCTGTGAATTGC 86 chr2ptel1M 633352 -TGTTCAGATCCTTTG 633366 - v C L1ME3G_3end#L 85 CTGTTCATATCCTTTG 70 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 34.68 CpG sites = 73, Kimura (unadjusted) = 34.98 Transitions / transversions = 1.03 (73/71) Gap_init rate = 0.04 (21 / 532), avg. gap size = 1.81 (38 / 21) 344 33.48 4.15 2.26 chr2ptel1M 633991 634207 (365793) C MamRTE2#LINE/RTE-BovB (1325) 227 7 m_b72s551i1 2648 chr2ptel1M 633991 CTTCATCACTGACAGAATCAAAGGCCTTGGTCAGAGCTCCAG--ATATTG 634038 iv i --i v ?v v -- viiii C MamRTE2#LINE/ 227 CTTCACGACTGACAGAGTCAAAGGCCTT--CCTGANGTCGAGGAAGGCCA 180 chr2ptel1M 634039 TGTACAGACCTCTGCCCTGCTGCTGGTATTTCTCCTGGAGCTGTCAGGTA 634088 i v vv i iivi i vi i i ? v ii i C MamRTE2#LINE/ 179 TATAAAGAGGTTTATGTTGTTCTTGGCATTTTTCCTGNAGCTGGCGAGCA 130 chr2ptel1M 634089 GCAAGCACCATCAGCAACTGTTCCTCGGCCCACTCTGAAGCCACACT--G 634136 ii iv i - v ii iv v?vvii i v i -- C MamRTE2#LINE/ 129 GTGAAGACCGT-ATCAGTTGCGCCTCTNGATGCTCTAAACCCACGCTGAG 81 chr2ptel1M 634137 GCTCTGGATGA---TCTTC--CAGGTGCAGGATTAGCCTGTTAAGAATGA 634181 ii i iv --- -- i -- vv i v v i v C MamRTE2#LINE/ 80 ATTCCGGGAGAAGCTCTTCAGCAAGTG--GGAGGAGTCGGTTCAGGAGGA 33 chr2ptel1M 634182 CTCTGACAAAACTCTTGCCAGCAGCG 634207 i vi viv v i i i C MamRTE2#LINE/ 32 TTCTTGCAATGATCTTTCCGGCGGTG 7 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 40.16 CpG sites = 43, Kimura (unadjusted) = 47.22 Transitions / transversions = 1.54 (43/28) Gap_init rate = 0.04 (9 / 216), avg. gap size = 1.56 (14 / 9) 38 0.00 0.00 0.00 chr2ptel1M 635838 635870 (364130) (AT)n#Simple_repeat 1 33 (0) c_b72s251i0 2649 chr2ptel1M 635838 ATATATATATATATATATATATATATATATATA 635870 (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATA 33 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 19 34.85 0.00 0.00 chr2ptel1M 635878 635938 (364062) (AT)n#Simple_repeat 1 61 (0) m_b72s252i0 2649 chr2ptel1M 635878 ATATATATATGTGTGTGTATATATATATACACATCCACATCCACATAGAT 635927 i i i i i i vi i vi i v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr2ptel1M 635928 GTATGTGTATA 635938 i i i (AT)n#Simple_ 51 ATATATATATA 61 Matrix = Unknown Transitions / transversions = 4.33 (13/3) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 238 17.74 0.00 12.70 chr2ptel1M 635984 636034 (363966) DNM1r#Unknown 2470 2514 (2148) m_b72s502i0 2650 chr2ptel1M 635984 TCAGCTCTGTATTTATATGTATATATGTATGTATACATACATGTGTGTGT 636033 i ivi i v i i i ------ i DNM1r#Unknown 2470 TCGGCCACGTGTATGTGTGTATATATGTGTGTATA------TGTGTGTAT 2513 chr2ptel1M 636034 G 636034 DNM1r#Unknown 2514 G 2514 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 17.03 CpG sites = 9, Kimura (unadjusted) = 21.14 Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.12 (6 / 50), avg. gap size = 1.00 (6 / 6) 31 0.00 0.00 0.00 chr2ptel1M 636035 636061 (363939) (TA)n#Simple_repeat 1 27 (0) c_b72s251i1 2651 chr2ptel1M 636035 TATATATATATATATATATATATATAT 636061 (TA)n#Simple_ 1 TATATATATATATATATATATATATAT 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 238 17.74 0.00 12.70 chr2ptel1M 636062 636080 (363920) DNM1r#Unknown 2515 2531 (2131) m_b72s502i0 2650 chr2ptel1M 636062 GTAGGTACATATGTGTATA 636080 -- i DNM1r#Unknown 2515 GT--GTATATATGTGTATA 2531 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 17.03 CpG sites = 9, Kimura (unadjusted) = 21.14 Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.11 (2 / 18), avg. gap size = 1.00 (2 / 2) 17 18.43 3.92 1.92 chr2ptel1M 636176 636226 (363774) (TTTGTTA)n#Simple_repeat 1 52 (0) m_b72s252i1 2652 chr2ptel1M 636176 TTTGTTGTTTGTT-GTTATTATATG-TATTAAATTATTTGTTAATTATTA 636223 i -v i v - -vi v i (TTTGTTA)n#Si 1 TTTGTTATTTGTTATTTGTTATTTGTTATT-TGTTATTTGTTATTTGTTA 49 chr2ptel1M 636224 TTT 636226 (TTTGTTA)n#Si 50 TTT 52 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.06 (3 / 50), avg. gap size = 1.00 (3 / 3) 13 14.03 4.44 6.82 chr2ptel1M 636184 636228 (363772) (TTA)n#Simple_repeat 1 44 (0) m_b72s252i2 2652 chr2ptel1M 636184 TTGTTGTTATTA-TATGTATTA-AATTATTTGTTAATTATTATTTTT 636228 i i - - -v - i - v (TTA)n#Simple 1 TTATTATTATTATTAT-TATTATTATTA-TTATT-ATTATTATTATT 44 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.11 (5 / 44), avg. gap size = 1.00 (5 / 5) 16 28.38 0.00 1.79 chr2ptel1M 639050 639106 (360894) (GAAAT)n#Simple_repeat 1 56 (0) m_b72s252i3 2653 chr2ptel1M 639050 GAACTGAAATTAAGTGAGCTGGAATTGAATTGGAATTCATTGAAATTAAA 639099 v v i iv - v v i vv v v (GAAAT)n#Simp 1 GAAATGAAATGAAATGAAAT-GAAATGAAATGAAATGAAATGAAATGAAA 49 chr2ptel1M 639100 TGATATG 639106 v (GAAAT)n#Simp 50 TGAAATG 56 Matrix = Unknown Transitions / transversions = 0.30 (3/10) Gap_init rate = 0.02 (1 / 56), avg. gap size = 1.00 (1 / 1) 457 24.21 0.81 5.98 chr2ptel1M 639119 639241 (360759) MIRc#SINE/MIR 11 127 (141) m_b72s601i1 2654 chr2ptel1M 639119 TGGTGTAGTGGATAGAGCACCAGCCCTGAAGTCAGGAGGACCTGAGTTCA 639168 i v ii v i i i i i MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr2ptel1M 639169 AAGTTGACCTCAGACATTTAATGCTCCCTGGTTATGTGACCCTGGGCAAG 639218 iviiviv v v i ------- i i i i MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTGACCTTGGGCAAG 103 chr2ptel1M 639219 TCACTTAACCCCAATT-GCCTCAG 639241 i vv v- MIRc#SINE/MIR 104 TCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 27.48 CpG sites = 18, Kimura (unadjusted) = 29.99 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.07 (8 / 122), avg. gap size = 1.00 (8 / 8) 27 3.45 0.00 0.00 chr2ptel1M 639786 639815 (360185) (CCCTAA)n#Simple_repeat 1 30 (0) c_b72s251i2 2655 chr2ptel1M 639786 CCCTAACCCTAACCCTAACCCTAATCCTAA 639815 i (CCCTAA)n#Sim 1 CCCTAACCCTAACCCTAACCCTAACCCTAA 30 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 12 20.15 0.00 2.86 chr2ptel1M 639918 639953 (360047) (ATTTTG)n#Simple_repeat 1 35 (0) m_b72s252i4 2656 chr2ptel1M 639918 ATTTAGCTTTTGATTTTTCAGTTTGTTTTTGACTTT 639953 v v - v v v i (ATTTTG)n#Sim 1 ATTTTGATTTTGA-TTTTGATTTTGATTTTGATTTT 35 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) 243 18.64 1.69 0.00 chr2ptel1M 641664 641722 (358278) C L3#LINE/CR1 (2328) 1771 1712 m_b72s601i2 2657 chr2ptel1M 641664 GATGAAGTTCTCCCCAAGGCCAATCCAGAATT-ATGACCTGCTCTGCTTT 641712 i v vv v i v - v vv C L3#LINE/CR1 1771 GATGAAATTGTCAGCAAGGCAAGTCAAGAATTTATCAGATGCTCTGCTTT 1722 chr2ptel1M 641713 TGGCCGAATG 641722 i ? C L3#LINE/CR1 1721 TAGCNGAATG 1712 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 21.88 CpG sites = 3, Kimura (unadjusted) = 21.88 Transitions / transversions = 0.38 (3/8) Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1) 12 19.62 1.85 7.84 chr2ptel1M 641725 641778 (358222) (CTGGGCC)n#Simple_repeat 1 51 (0) m_b72s252i5 2658 chr2ptel1M 641725 CTGGGCCCTCTGCCCCGGCTCTCCTGCCTGCCCCAGG-CTTGGGCCCTGG 641773 vv i -v - --v ii - i (CTGGGCC)n#Si 1 CTGGGCCCTGGGCCCTGG-GC-CCTG--GGCCCTGGGCCCTGGGCCCTGG 46 chr2ptel1M 641774 GCCCT 641778 (CTGGGCC)n#Si 47 GCCCT 51 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.09 (5 / 53), avg. gap size = 1.00 (5 / 5) 16 19.19 1.96 4.00 chr2ptel1M 642080 642130 (357870) (CCCTG)n#Simple_repeat 1 50 (0) m_b72s252i6 2659 chr2ptel1M 642080 CCCTGCTCAGACGTGGCCCT-CCCTGCTCTGCCCTCCCCAAGCCCTGCTC 642128 i v v v - - i v -v i (CCCTG)n#Simp 1 CCCTGCCCTGCCCT-GCCCTGCCCTGCCCTGCCCTGCCC-TGCCCTGCCC 48 chr2ptel1M 642129 TG 642130 (CCCTG)n#Simp 49 TG 50 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.06 (3 / 50), avg. gap size = 1.00 (3 / 3) 15 14.16 0.00 3.12 chr2ptel1M 645498 645530 (354470) (AAC)n#Simple_repeat 1 32 (0) m_b72s252i7 2660 chr2ptel1M 645498 AAAAACAACAGCAATAACAACAACAATCATCAA 645530 v i i - v (AAC)n#Simple 1 AACAACAACAACAACAACAACAACAA-CAACAA 32 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 257 20.00 0.00 0.00 chr2ptel1M 646109 646153 (353847) C MIR3#SINE/MIR (40) 168 124 m_b72s601i3 2661 chr2ptel1M 646109 TGGAAATCATCCAGTCCAACTCCTTTATTTTATTGATGAGGGAAC 646153 i i i i i i iv i C MIR3#SINE/MIR 168 TAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAAC 124 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 24.86 CpG sites = 8, Kimura (unadjusted) = 24.86 Transitions / transversions = 8.00 (8/1) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 25 11.71 0.00 0.00 chr2ptel1M 646441 646477 (353523) (A)n#Simple_repeat 1 37 (0) m_b72s252i8 2662 chr2ptel1M 646441 AAAAAAAAAAAAAAAAAAAACGAAAAATAAAAGAAAA 646477 vi v i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 37 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 28 0.00 0.00 0.00 chr2ptel1M 647379 647404 (352596) (TTG)n#Simple_repeat 1 26 (0) c_b72s251i3 2663 chr2ptel1M 647379 TTGTTGTTGTTGTTGTTGTTGTTGTT 647404 (TTG)n#Simple 1 TTGTTGTTGTTGTTGTTGTTGTTGTT 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 376 29.73 9.17 2.29 chr2ptel1M 647481 647807 (352193) C L1ME3G_3end#LINE/L1 (445) 479 131 m_b72s551i2 2664 chr2ptel1M 647481 TTTTCAATTCTTTTTCACCACAAAAAGAACTGCTATAAATATTTTTGTAT 647530 i i ivii ii v ivi v i i ii i C L1ME3G_3end#L 479 TTTCCAATTTTTCGCTATTACAAACAATGCTGCAATGAACATCCTTGTAC 430 chr2ptel1M 647531 ATAAACATCCTTTT---CTTCTTCCTTTGATCTCTTTGAGATACAGACAC 647577 i-- ? v --- v v v vvv - i ? ii v v? v? C L1ME3G_3end#L 429 ATG--CNTCCTTGTGCACATGTGCGAGT-ATTTCTNTAGGATAGATNCCN 383 chr2ptel1M 647578 AGTAGGAGTATTACTACATGAAAGGGTATGCCC--TTTAAAC----ATAG 647621 v vi v i ivi v v -- i---- C L1ME3G_3end#L 382 AGAAGTGGAATTGCTGGGTCAAAGGGTATGCGCATTTTAAATTTTAATAG 333 chr2ptel1M 647622 ---CT-TTAAATTGCTCTCCAGAATAGTTGGCTCAGTT------------ 647655 --- -ii i i ?i i vvi i ------------ C L1ME3G_3end#L 332 ATACTGCCAAATTGCCCTCCAAAANGGCTGTACCAATTTACACTCCCACC 283 chr2ptel1M 647656 --CAATGCATTACTGTATCATTTTTTTTAAACACCTGCCCAACATTTGTC 647703 -- i i v vv i vv iiii v - vv i ? vi C L1ME3G_3end#L 282 AGCAGTGTATGAGAGTACCCGTTTCCCCACAC-CCTCGCCAACACTNGAT 234 chr2ptel1M 647704 ATT-TC--TCTTTTCTATCACATTAGCCAATCTGATGAGTGTGTAATGGT 647750 - --? vv i--- v i viv C L1ME3G_3end#L 233 ATTATCAANCTTTTAAATT---TTTGCCAATCTGATGGGTGAAAAATGGT 187 chr2ptel1M 647751 AACTCAAGAGTTATTTTAATTTGCATTTCTGTAAACAATAATTATGTGTA 647800 v vv- i iv i vi v i v v vv C L1ME3G_3end#L 186 ATCTCATT-GTTGTTTTAATTTGCATTTCCCTGATTACTAGTGAGGTTGA 138 chr2ptel1M 647801 GCATTTT 647807 i C L1ME3G_3end#L 137 GCATCTT 131 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 39.15 CpG sites = 49, Kimura (unadjusted) = 39.69 Transitions / transversions = 1.07 (49/46) Gap_init rate = 0.05 (16 / 326), avg. gap size = 2.38 (38 / 16) 307 29.99 2.65 0.65 chr2ptel1M 647676 647826 (352174) C L1MA7_3end#LINE/L1 (772) 266 113 m_b72s551i3 2664 chr2ptel1M 647676 TTTTTTAAACA-CCTGCCCAACATTTGTCATTTCTCTTTTCTATCACATT 647724 i vv - vv i i i i v i i v v i v C L1MA7_3end#LI 266 TTTTCTCCACATCCTCGCCAACACTTGTTATCTTTCGTCTTTTTGATAAT 217 chr2ptel1M 647725 AGCCAATCTGATGAGTGTGTAATGGTAACTCAAGAGTTATTTTAATTTGC 647774 v i iii vii i v vv- vi C L1MA7_3end#LI 216 AGCCATTCTAACAGGTGTGAGGTGATATCTCATT-GTGGTTTTAATTTGC 168 chr2ptel1M 647775 ATTTCTGTAAACAATAATTATGTGTAGCATTTT---AAAAATCCTTTGAC 647821 iv i vv v i v vv --- v v iv i C L1MA7_3end#LI 167 ATTTCCCTGATGATTAGTGATGTTGAGCATTTTTTCATATATCTGTTGGC 118 chr2ptel1M 647822 CATTT 647826 C L1MA7_3end#LI 117 CATTT 113 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 38.63 CpG sites = 21, Kimura (unadjusted) = 38.63 Transitions / transversions = 0.88 (21/24) Gap_init rate = 0.02 (3 / 150), avg. gap size = 1.67 (5 / 3) 329 22.89 4.44 2.92 chr2ptel1M 647692 647826 (352174) C L1ME3_3end#LINE/L1 (660) 249 113 m_b72s551i4 2664 chr2ptel1M 647692 CCAACATTTGTCATT-TC--TCTTTTCTATCACATTAGCCAATCTGATGA 647738 i vi - -- iv i--- v i i C L1ME3_3end#LI 249 CCAACACTTGGTATTGTCAGTCTTTTTAATT---TTAGCCATTCTGGTGG 203 chr2ptel1M 647739 GTGTGTAATGGTAACTCAAGAGTTATTTTAATTTGCATTTCTGTAAACAA 647788 i v vv- vi iv i vv v C L1ME3_3end#LI 202 GTGTGTAGTGGTATCTCATT-GTGGTTTTAATTTGCATTTCCCTGATGAC 154 chr2ptel1M 647789 TAATTATGTGTAGCA-TTTTAAAAATCCT--TTGACCATTT 647826 v vv -i vv v v -- i C L1ME3_3end#LI 153 TAATGATGTTGAGCACCTTTTCATATGCTTATTGGCCATTT 113 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 27.36 CpG sites = 12, Kimura (unadjusted) = 27.36 Transitions / transversions = 0.67 (12/18) Gap_init rate = 0.06 (8 / 134), avg. gap size = 1.25 (10 / 8) 1458 29.27 7.90 3.10 chr2ptel1M 647999 649137 (350863) C L1M5_orf2#LINE/L1 (1089) 2205 1014 m_b72s551i5 2664 chr2ptel1M 647999 TATAT--GCTTTATATGCTGCAATTTTGCTAAAGT----TATTATTTCAA 648042 --i i i v ? i ii v ---- v v C L1M5_orf2#LIN 2205 TATATTGACCTTGTATCCNGCGACCTTGCTAAATTCACTTATTAGTTCTA 2156 chr2ptel1M 648043 GTAGGTTTCTTTTAGTTGGTTTTCTAGGATTCTCTTAAGCATACCATCAA 648092 - ? -- v i i i ? i - v i ? v v C L1M5_orf2#LIN 2155 GTAG-TTTNTTT--GTAGATTCTTTNGGATTTTCT-ACGTANACAATCAT 2110 chr2ptel1M 648093 ATTATCTATAAAGAATAA--ATTGTGTTTCCTCACTGCCTATTCTAATTC 648140 i i iii v ?i --i v i i vi v v ii v v C L1M5_orf2#LIN 2109 GTCATCTGCGAATAANGACAGTTTTATTTCTTCCTTTCCAATCTTTATGC 2060 chr2ptel1M 648141 AATTTATTTTCTTCACTTAACT-ATTA---TTGCTAGCATTTCTAAGACA 648186 vv ii iv iv - i--- v v ii i iv C L1M5_orf2#LIN 2059 CTTTTATTTCTTTTTCTTGCCTTATTGCACTGGCTAGGACCTCCAGTACA 2010 chr2ptel1M 648187 ATATTGAATAATAGTGATGTTAGTAGGCATCCTTGATTTACTATTCATCT 648236 i iv i v? ii i vi ii viiv C L1M5_orf2#LIN 2009 ATGTTGAATAGAAGTGGTGANAGCGGACATCCTTGTCTTGTTCCCGATCT 1960 chr2ptel1M 648237 TACTGGGAAGATTTCTATTTTATCTTCATTATAGATGATGCTTG--GTAA 648284 vv iii? ii v ? v vi viv i ? -- i C L1M5_orf2#LIN 1959 TAGGGGGAAAGCNTTCAGTNTTTCACCATTAAGTATGATGTTNGCTGTAG 1910 chr2ptel1M 648285 TTGTTTTAGATAGATACTAATTATCATTTTAAGAAAAGTTCCATTTATTT 648334 -- vvi i ivv vv i i iv i v i i C L1M5_orf2#LIN 1909 --GTTTTTCGTAGATGCCCTTTATCAGGTTGAGGAAGTTCCCTTCTATTC 1862 chr2ptel1M 648335 CTATACTTTCCAGTGTTTATTTTTTAAATCAGGAATAA-TGATGTATGTT 648383 v-- v v v --- v -- v ii- v v v C L1M5_orf2#LIN 1861 CTAG--TTTGCTGAG---AGTTTTTA--TCATGAATGGGTGTTGAATTTT 1819 chr2ptel1M 648384 GTCAAA------------AGCTATTGAGATAATCGTGTGGTTT----CTG 648417 ------------ v i i i i ---- iv C L1M5_orf2#LIN 1818 GTCAAATGCTTTTTCTGCATCTATTGAGATGATCATATGATTTTTCTCCT 1769 chr2ptel1M 648418 TTAGTTTTGATTTGATATGGTCAGTTATGCTGATTGTTTTCCTAATATTG 648467 - i -- i v i iii v i v i i C L1M5_orf2#LIN 1768 TTA-TTCTG--TTAATATGGTGAATTACATTGATTGATTTTCGAATGTTA 1722 chr2ptel1M 648468 AGCTACCCCTGCATTCCTGGTATAAATTCCATCTGGTCAT-ATG----AT 648512 i i v i v ii ii - ---- C L1M5_orf2#LIN 1721 AACCAACCTTGCATTCCTGGGATAAACCCCACTTGGTCATGATGTATTAT 1672 chr2ptel1M 648513 CTTTGTGATATATGGCTGCAATTTCCTTACTAGTACTTCTAAAAAAGTTT 648562 i v v v v v ivvi i i i - ivv? i v C L1M5_orf2#LIN 1671 CCTTTTTATATATTGCTGGATTCGATTTGCTAATATTT-TGTTNAGGATT 1623 chr2ptel1M 648563 TTTGCATCAATATTCATTAGGGAAATTGGTCAATACTTTTC-TTCCCTGT 648611 v i v v vi v - i i C L1M5_orf2#LIN 1622 TTTGCATCTATGTTCATGAGGGATATTGGTCTGTAATTTTCTTTTCTTGT 1573 chr2ptel1M 648612 ATTTGCTCTTCCTGGCTTAGGTACCAGCAATCATATTTTGG--TCATAAA 648659 v vv i vi ? i v i -ii ? i--i -- C L1M5_orf2#LIN 1572 AATGTCTTTGTCNGGTTTTGGTATCAG-GGTNATG--CTGGCCTCATAAA 1526 chr2ptel1M 648660 AGGAATTTGGGAGGACTCTTTTTTTGACTATTTTTCCAAATAGTTTATAT 648709 v i v i vii ii i vv iivi v i i C L1M5_orf2#LIN 1525 ATGAGTTGGGAAGTGTTCCCTCTTTTTCTATTTTCTGGAAGAGTTTGTGT 1476 chr2ptel1M 648710 AATACTGTAATTAATTATCCTTTAAATAATTGATATAATTCAATTATGAA 648759 v i vv v v i i iv i v vivi C L1M5_orf2#LIN 1475 AAGATTGGTATTATTTCTTCCTTAAATGTTTGGTAGAATTCACCAGTGAA 1426 chr2ptel1M 648760 TCCATCTGGCTCTGAGGATTTTTTTTCTTAG--GGCATTAACTTATGGCC 648807 v vi - ii i v vi -- iv v v ----- C L1M5_orf2#LIN 1425 GCCATCTGGGCCTG-GAGTTTTCTTTGTGGGAAGGTTTTTAATTA----- 1382 chr2ptel1M 648808 TGCTCAACTT--ATTTTTCTA--AGAT---GAGGTACTTTAAGCATTCTA 648850 ---- v -- i i -- --- i v - i iiiv C L1M5_orf2#LIN 1381 ----CAAATTCAATTTCTTTAATAGATATAGGGCTA-TTCAGATTTTCTA 1337 chr2ptel1M 648851 TTTCCTTTTCTGTTAATCTCAGCAATTTATGTTTTTC-------TAATCC 648893 i i v? i i i ii i ? i ------- vi C L1M5_orf2#LIN 1336 TTTCTTCTTGNGTCAGTTTTGGTAANTTGTGTTTTTCAAGGAATTTGTCC 1287 chr2ptel1M 648894 ATTTCATTTGGATTGTCATA-TAATTGTCCTA----TGGGCAAAATAGTT 648938 i iii ? v - v v v ---- vv v v i C L1M5_orf2#LIN 1286 ATTTCATCTAAGTTNTCAAATTTATTGGCATAAAGTTGTTCATAATATTC 1237 chr2ptel1M 648939 TCTAATAATTGCTTTA--GTT--TAAAATCT---------TCACC----- 648970 v v ivi -- i-- ii --------- v ----- C L1M5_orf2#LIN 1236 TCTTATTATCCTTTTAATGTCTGTAGGATCTGTAGTGATGTCTCCTTTTT 1187 chr2ptel1M 648971 CATTTTTAGTATTGGGAATTT-TGTTTTCTC------TTTTTAAGTCAAA 649013 ii ii v - i ------ i vii iv C L1M5_orf2#LIN 1186 CATTCCTGATATTGGTAATTTGTGTCTTCTCTCTTTTTTTCTTGATCAGT 1137 chr2ptel1M 649014 TTAACCAAGTGACTTATCTA-TTTATTGTCCTCCCCCTCCCATAAAACCA 649062 i ?i i- v ii v - vi ----- ii v i C L1M5_orf2#LIN 1136 CTNGCT-AGAGGTTTATCAATTTTATTGATCT-----TTTCAAAGAACCA 1093 chr2ptel1M 649063 GCTTCTAGTTTTATTAAT----TCAATGGTTTTCTTACTTTCAGTTTTAT 649108 i i i ii i ---- v v ? ?i ii vi i C L1M5_orf2#LIN 1092 GCTTTTGGCTTCGTTGATTTTCTCTATTGTNTNTTTGTTTTCTATTTCAT 1043 chr2ptel1M 649109 TCATCTCTTCTTTGATTTTCAGGGTTTCC 649137 v i v i v i i vvi C L1M5_orf2#LIN 1042 TGATTTCTGCTCTTATCTTTATTATTTCC 1014 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 37.95 CpG sites = 190, Kimura (unadjusted) = 39.09 Transitions / transversions = 1.43 (190/133) Gap_init rate = 0.06 (65 / 1138), avg. gap size = 1.95 (127 / 65) 247 18.00 2.00 0.00 chr2ptel1M 649182 649231 (350769) C MIR#SINE/MIR (140) 122 72 m_b72s601i4 2661 chr2ptel1M 649182 TGAGGCA-ATTGAGGTGAAGTGATTTGCCCAGAGTCACACAACTAGCAAG 649230 - vv v i i ii i i C MIR#SINE/MIR 122 TGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAG 73 chr2ptel1M 649231 T 649231 C MIR#SINE/MIR 72 T 72 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 21.03 CpG sites = 6, Kimura (unadjusted) = 21.03 Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.02 (1 / 49), avg. gap size = 1.00 (1 / 1) 250 15.00 0.00 0.00 chr2ptel1M 649192 649231 (350769) C MIRc#SINE/MIR (153) 115 76 m_b72s601i5 2661 chr2ptel1M 649192 GAGGTGAAGTGATTTGCCCAGAGTCACACAACTAGCAAGT 649231 v i ii i i C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGT 76 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 17.36 CpG sites = 5, Kimura (unadjusted) = 17.36 Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 18 31.92 0.00 0.00 chr2ptel1M 650301 650358 (349642) (AA)n#Simple_repeat 1 58 (0) m_b72s252i9 2665 chr2ptel1M 650301 AAAAATCAGAACAAAAGGGAAAAACTACAAGAGAAAAAAAAAAACACAAG 650350 vv i v iii vv v i i v v i (AA)n#Simple_ 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr2ptel1M 650351 AAAAAAAA 650358 (AA)n#Simple_ 51 AAAAAAAA 58 Matrix = Unknown Transitions / transversions = 0.88 (7/8) Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0) 757 27.81 3.16 10.97 chr2ptel1M 650521 650932 (349068) C L1ME3D_3end#LINE/L1 (551) 438 56 m_b72s551i6 2666 chr2ptel1M 650521 TTGTACACTGTATTCCTGGTTGCACATGTGGATCCTTTTCTCTTCTTTAC 650570 i- -i - v ---------------- v C L1ME3D_3end#L 438 TTGTACG-TGT-CTCCTGGT-GCACATGTGCA----------------AG 408 chr2ptel1M 650571 AATTTCCTTGGGATACAGACCCAGTAATGGCACTGTTGGGTCAAAGGGTA 650620 i ii i i i v i v i v i i iv C L1ME3D_3end#L 407 AGTTTCTCTAGGGTATATACCTAGGAGTGGAATTGCTGGGTCGTAGGGTA 358 chr2ptel1M 650621 TGCA---GTTTGATAGTGCTTTGGGCACCGTTCCAAATTTCTCTCCAGAA 650667 i--- ii ivv i --i i vi -- vi i i i C L1ME3D_3end#L 357 TGCGCATGTTCAACTTTACT--AGGTAATG--CCAAATTGTTTTCCAAAG 312 chr2ptel1M 650668 TGGTTGGATGAGTTCACAACTCCACCAACAATGCATTAGTGTCCCAGTT- 650716 v iv i i vii i i i v v i v - C L1ME3D_3end#L 311 TGGTTGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTTCCCGTTG 262 chr2ptel1M 650717 -TTCAC---CCCTACAACATTTATTATCTTTT--CCTGTCATCTTAGCCA 650760 - i --- i vv i iv iv iv-- i v v i v C L1ME3D_3end#L 261 CTCCACATCCTCGCCAACACTTGGTATTGTCAGACTTTTAATTTTTGCCA 212 chr2ptel1M 650761 ATCTGAGAGGTATGAGCCAATCTGAGCAGTACCTCAGAGTTGTTTTAATT 650810 ivi i --- ------i i vv v C L1ME3D_3end#L 211 ATCTGGTGGGTGTGA---AAT------GGTATCTCATTGTGGTTTTAATT 171 chr2ptel1M 650811 TGCATTTCTCTAATCAATAAT--GGCCAAGCATTTTTTTCATATGCTTAT 650858 i i i v -- iii - i i C L1ME3D_3end#L 170 TGCATTTCCCTGATTACTAATGAGGTTGAGCA-TCTTTTCATATGTTTAT 122 chr2ptel1M 650859 AGATGGCT-TAAATGGCTTTAATACTTCATCTGAAAATTGTCTGTTCATA 650907 --- i- vvi -- ---- i v vi v i i C L1ME3D_3end#L 121 ---TGGCCATTCGTG--TTT----CCTCTTCTGTGAAATGCCTGTTCATG 81 chr2ptel1M 650908 TTCTTTGACTATTTATCAATTGAGT 650932 ii v i v v i C L1ME3D_3end#L 80 TCTTTTGCCCATTTTTCTATTGGGT 56 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 33.85 CpG sites = 65, Kimura (unadjusted) = 35.59 Transitions / transversions = 1.76 (65/37) Gap_init rate = 0.12 (49 / 411), avg. gap size = 1.12 (55 / 49) 946 24.16 4.08 7.09 chr2ptel1M 650566 650957 (349043) C L1PREC2_3end#LINE/L1 (496) 411 31 m_b72s551i7 2666 chr2ptel1M 650566 TTTACAATTTCCTTGGGATACAGACCCAGTAATGGCACTGTTGGGTCAAA 650615 i -- v i i v v i i i C L1PREC2_3end# 411 TTTATA--TTCCTTTGGGTATATACCCAGTAATGGGATTGCTGGGTCGAA 364 chr2ptel1M 650616 GGGTA-TGCAGTTTGATAGTGCTTTG-GGCACCGTTCCAAATTTCTCTCC 650663 v - v v v- iv - v i -- v i v i C L1PREC2_3end# 363 TGGTAGTTCTGTTTT-TAGCTCTTTGAGGAATCG--CCACACTGCTTTCC 317 chr2ptel1M 650664 AGAATGGTTGGATGAGTTCACAACTCCACCAACAATGCATTAGTGTCCCA 650713 v i iv i i vii i i v i i v C L1PREC2_3end# 316 ACAATGGTTGAACTAATTTACACTCCCACCAACAGTGTATAAGCGTTCCC 267 chr2ptel1M 650714 GTTTTC------ACCCCTACAACATTTATTATCTTTT--CCTGTCA-TCT 650754 - ------ i vv i i i i -- i v i - vv C L1PREC2_3end# 266 -TTTTCTCCGCAACCTCGCCAGCATCTGTTATTTTTTGACTTTTTAATAA 218 chr2ptel1M 650755 TAGCCAATCTGAGAGGTATGAGCCAATCTGAGCAGTACCTCAGAGTTGTT 650804 v vv i --- ------i i vv v C L1PREC2_3end# 217 TAGCCATTCTGACTGGTGTGAG---AT------GGTATCTCATTGTGGTT 177 chr2ptel1M 650805 TTAATTTGCATTTCTCTAAT---CAATAATGGCCAAGCATTTTTTTCATA 650851 i --- i i i-iii - C L1PREC2_3end# 176 TTGATTTGCATTTCTCTAATGATCAGTGATA-TTGAGC-TTTTTTTCATA 129 chr2ptel1M 650852 TGCTTATAGATGGCTTAAATGGCTTTAATACTTCATCTGAAAATTGTCTG 650901 i v iiv v iv v ----- i--- v C L1PREC2_3end# 128 TGCTTGTTGGCCGCATGTATGTCTT-----CTTT---TGAAAAGTGTCTG 87 chr2ptel1M 650902 TTCATATTCTTTGACTATTTATCAATTGAGTAAT--GATTAATATTCTTG 650949 i i v i i v i v i vi -- v -- v C L1PREC2_3end# 86 TTCATGTCCTTTGCCCACTTTTTAATGGGGTTGTTTGTTT--TTTTCTTG 39 chr2ptel1M 650950 TAAATTTG 650957 C L1PREC2_3end# 38 TAAATTTG 31 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 28.75 CpG sites = 49, Kimura (unadjusted) = 29.54 Transitions / transversions = 1.26 (49/39) Gap_init rate = 0.09 (34 / 391), avg. gap size = 1.26 (43 / 34) 2725 30.15 7.80 2.92 chr2ptel1M 650837 653767 (346233) C L1M5_orf2#LINE/L1 (8) 3286 214 m_b72s551i8 2666 chr2ptel1M 650837 AGCATTTTTTTCATATGCTTATAGATGGCTTAAATGGCTTTAATA-CTTC 650885 i - i --- i--- --- v? - C L1M5_orf2#LIN 3286 AGCATCTTTT-CATGTGCTTAT---TGGCC---AT---TTGNATATCTTC 3247 chr2ptel1M 650886 ATCTGAAAATTGTCTGTTCATATTCTTTGACTATTTATCAATTGAGT--- 650932 v i vi v vi ii v i v ?v i --- C L1M5_orf2#LIN 3246 TTTTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGT 3197 chr2ptel1M 650933 -------------AATGATTAATA----TTCTT-GTAAATT-TGAAT--G 650961 ------------- v ? vi ---- -i v - i -- C L1M5_orf2#LIN 3196 TTGTCTTTTTNTTATTGANTTGTAGGAGTTCTTTATATATTCTGGATACG 3147 chr2ptel1M 650962 AACCCTTCCTT---TAGCTGTA----GAAAATTTTCCCCAGCTTTGTA-C 651003 ii iv i--- vv ?----i v i vi? i i- C L1M5_orf2#LIN 3146 AGTCCTTTGTCAGATATATGTNTTGCAAATATTTTCTCCCANTCTGTGGC 3097 chr2ptel1M 651004 TT--CTTTT-ATTCT--------TGTTTGT------GCAAAATCTTTTTA 651036 -- - i -------- i v ------ i vi v C L1M5_orf2#LIN 3096 TTGCCTTTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTTTAA 3047 chr2ptel1M 651037 ATTTAATGTAAGCAAAGTTGTCCATTCTGCATTTCATAAT--GTTCTCTA 651084 v i ? iv v v i v i viv i ii -- v i - C L1M5_orf2#LIN 3046 TTTTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGGTTNGTGCTTT- 2998 chr2ptel1M 651085 GTTCTTCTTTGGTCATAAATTCCTTTCTT-CCCCAAGATCT----GATAG 651129 - v viii v i vi v i v i -? i v---- - C L1M5_orf2#LIN 2997 -TTGTGTCCTGTTTAAGAAATCTTTGCCTANCCCAAGGTCACGAAGATA- 2950 chr2ptel1M 651130 TTATC--ACTTTCTCTCTTA--ATTTGCTTATGGTATCACTCTTTATGCC 651175 v -- iv i ii -- v -- i v i ?ii iiii C L1M5_orf2#LIN 2949 TTCTCCTATGTTTTCTTCTAGAAGTT--TTATAGTTTTANCTTTTACATT 2902 chr2ptel1M 651176 CATATC-ATGTACCCATTTTGATCTTATTTTGGTATGCGGTGTGAGATGT 651224 i vi - - i i ? vi v v i ii i iv C L1M5_orf2#LIN 2901 TAGGTCTATG-ATCCATCTNGAATTAATTTTTGTGTATGGTGTGAGGTAG 2853 chr2ptel1M 651225 AGGTCTATGCCAACTTTCTGACATTT-----TCCAGTATTCCCAGCAATT 651269 i v v?iiv i i vv v ----- i vv i viv C L1M5_orf2#LIN 2852 GGGTCGAGNTTCATTTTTTTCCATATGGATATCCAATTGTTCCAGCACCA 2803 chr2ptel1M 651270 TTTGTGAAATAGTGAATTCTTATCCCCAAAGATTGAGTTTGGGAG-TTTA 651318 vi v vvv i - vv v viv? v v- i C L1M5_orf2#LIN 2802 TTTGTTGAAAAGACTATCCTT-TCCCCACTGAATTGCNTTGGCACCTTTG 2754 chr2ptel1M 651319 TCAAATGCTAGACTCCTATA-AT-CATTGAT-TATTGTGTCATGTATATC 651365 viii i?iv? i - -ii v i - --- - v i- C L1M5_orf2#LIN 2753 TCAAAAATCAANTGNCCATATATGTGTGGGTCTATT---TC-TGGAC-TC 2709 chr2ptel1M 651366 T-TACT-TATTCCACTAATCCACCACTCTATTCATAGGA-GGTACCAAAT 651412 - i - i i i i iivv i v v v-ii v i C L1M5_orf2#LIN 2708 TCTATTCTGTTCCATTGATCTATTTGTCTATCCTTACGCCAATACCACAC 2659 chr2ptel1M 651413 GTTTTTGATGACTGCTACTTTATAATA-GTTTT-AGGTCTGACACTGCTA 651460 vv i v ivi - i - ?i ? ii v iv C L1M5_orf2#LIN 2658 TGTCTTGATTACTGTAGCTTTATAATAAGTCTTGANATCNGGTAGTGTAA 2609 chr2ptel1M 651461 GACCACTGTCTTTTTTATTTATTTTTTCA---TTAATTCCCTAGATATTA 651507 v v iiv v v i-- --- iv --- i v - C L1M5_orf2#LIN 2608 GTCCTCCAACTTTGTTCTTC--TTTTTCAAGATTGTTT---TGGCTATT- 2565 chr2ptel1M 651508 TTTAG--CTTT---TTTTCAGATGAATTTTGTTATT--TTTTTCTATCTC 651550 i ?i -- --- i v i ivv i--i v v i C L1M5_orf2#LIN 2564 CTNGGTCCTTTGCATTTCCATATAAATTTTAGAATCAGCTTGTCAATTTC 2515 chr2ptel1M 651551 TATAAAATTTTTTTTTTGGCAGTTTGATTGGTATGGCACTGAACAAGTAG 651600 i vvvii vi v - v v v i ivvi C L1M5_orf2#LIN 2514 TACAAAAAAACCTGCTGGG-ATTTTGATTGGGATTGCATTGAATCTATAG 2466 chr2ptel1M 651601 ATCAATTTAGGTAGAATTGTCATTTTTATTACATT-AG-CTTGGCCTA-C 651647 i v v i ? iv i - - -- v - C L1M5_orf2#LIN 2465 ATCAATTTGGGGAGAATTGACATCTTNACAATATTGAGTCTT--CCAATC 2418 chr2ptel1M 651648 CATGACCAATTG--ACATTTTCCCAATTGTTTATGTCTGATTT--TGTGT 651693 v -- -- i i ii v i v vv -- v v C L1M5_orf2#LIN 2417 CATGAACA--TGGTATATCTCTCCATTTATTTAGGTCTTCTTTAATTTCT 2370 chr2ptel1M 651694 TTAA--AGTGTTTTGTTATAGTGTTCA---TATAATTCCTGGAT-TTTCT 651737 i v -- i --- v --- ? iv i v i- ? i C L1M5_orf2#LIN 2369 CTCAGCAATGTTTTGT---AGTTTTCAGTGTANAGGTCTTGCACATNTTT 2323 chr2ptel1M 651738 TGACAGGTAGACACCCAAATATTTGATTTTGTCTATAGTTATCTTAAATG 651787 vi i vv iv i i ? v v i ivv i iv C L1M5_orf2#LIN 2322 TGTTAGATTTATTCCTAAGTATTTNATGTTTTTTGATGCTATTGTAAATG 2273 chr2ptel1M 651788 AAAATTGTCTTTCTA-TCTC--TTGCTGCTGGGCTTTGTTAGTAATATGT 651834 iv - i ?v - i -- v iiv v -- iv i i C L1M5_orf2#LIN 2272 GTA-TTGTTTTTNAAATTTCATTTTCCAATTG--TTTGTTGCTAGTATAT 2226 chr2ptel1M 651835 AAAAATGC---TGATGTTTGTGT---GAGTTTATTATCCTGCAATTTTGT 651878 i i --- v i --- vi i - ? i ii i C L1M5_orf2#LIN 2225 AGAAATACAATTGATTTTTGTATATTGACCTTGT-ATCCNGCGACCTTGC 2177 chr2ptel1M 651879 TAAAGCTGTTAATTGTTTCAAGTGGGTTTTTGGATCATTCTATAGGATTC 651928 viiii v iv v i v ? v vvv v ? i C L1M5_orf2#LIN 2176 TAAATTCACTTATTAGTTCTAGTAGTTTNTTTGTAGATTCTTTNGGATTT 2127 chr2ptel1M 651929 TCTAAGTACACCATCATATTATCTTCAAAGAGTGATAATTTTATCTC--- 651975 v ? v i i v i v i? i i i --- C L1M5_orf2#LIN 2126 TCTACGTANACAATCATGTCATCTGCGAATAANGACAGTTTTATTTCTTC 2077 chr2ptel1M 651976 ATTGCCTATTCTGATTCCTTT-ATTTTTTTT-----CCTTATTGCTAAAG 652019 v v v ii v v - i ----- vvvi C L1M5_orf2#LIN 2076 CTTTCCAATCTTTATGCCTTTTATTTCTTTTTCTTGCCTTATTGCACTGG 2027 chr2ptel1M 652020 TCAACATTTCTAGTACAATATTGAATAACAATGGTGATA-TGGGCATCCT 652068 ii iv ii i i iv i ? -i i C L1M5_orf2#LIN 2026 CTAGGACCTCCAGTACAATGTTGAATAGAAGTGGTGANAGCGGACATCCT 1977 chr2ptel1M 652069 AGTTTCATCCTTGATCTTATTACCAATGTGTCCAGCTTCTCCTCCTTATT 652118 v i ii i ii vvivv v i? i i? i vi v vv C L1M5_orf2#LIN 1976 TGTCTTGTTCCCGATCTTAGGGGGAAAGCNTTCAGTNTTTCACCATTAAG 1927 chr2ptel1M 652119 AATAATGCTGACTGATGGGTGTAGATAGATGCTGCTTATCA--------- 652159 v i i ?i vv v v vvi ivi --------- C L1M5_orf2#LIN 1926 TATGATGTTNGCTGTAGGTTTTTCGTAGATGCCCTTTATCAGGTTGAGGA 1877 chr2ptel1M 652160 AGTTC--------TCC------GGTG-------TTAATAGGATTAGGTAC 652188 -------- ------ v ------- vi v v i ii C L1M5_orf2#LIN 1876 AGTTCCCTTCTATTCCTAGTTTGCTGAGAGTTTTTATCATGAATGGGTGT 1827 chr2ptel1M 652189 TGTATTTTGTCAAGAACTTTTTCTGCATCTATTGAGATTATCATGTGAAT 652238 v ivi v i v C L1M5_orf2#LIN 1826 TGAATTTTGTCAAATGCTTTTTCTGCATCTATTGAGATGATCATATGATT 1777 chr2ptel1M 652239 TCTGTTAGCTTTG--CCATTGATATGGTTAATTGTGACAATAGATTTCCT 652286 i v i-- i-- ii i v iiivii v i v C L1M5_orf2#LIN 1776 TTTCTC--CTTTATTCTGTTAATATGGTGAATTACATTGATTGATTTTCG 1729 chr2ptel1M 652287 GATACTGAACCAGCCCTGCATTCCTCATATAAATCCCCCTTGATTATAGT 652336 i ii i i i viv i v i i ii C L1M5_orf2#LIN 1728 AATGTTAAACCAACCTTGCATTCCTGGGATAAACCCCACTTGGTCATGAT 1679 chr2ptel1M 652337 ATATTATCATGCTGATAAGTTGTTA---------TGC-AACA----ACTT 652372 i v vi v vi i i--------- - i ----ii ? C L1M5_orf2#LIN 1678 GTATTATCCTTTTTATATATTGCTGGATTCGATTTGCTAATATTTTGTTN 1629 chr2ptel1M 652373 AACATTTTTGCATCAATCACTCATTAGGGAGATTGGTCTGTAATTTTCTT 652422 iv v -ii v v C L1M5_orf2#LIN 1628 AGGATTTTTGCATCTAT-GTTCATGAGGGATATTGGTCTGTAATTTTCTT 1580 chr2ptel1M 652423 TCTCTGTTTTTGGATCTT--CCTGGTTTAGGTATCAACACCATATATGTG 652470 iii vv ---i --i ? v ivii? iivv iv C L1M5_orf2#LIN 1579 TTCTTGTAAT---GTCTTTGTCNGGTTTTGGTATCAGGGTNATGCTGGCC 1533 chr2ptel1M 652471 TCATCGAAGGAATTTGTCAAGACTCCTTCTTTATCTGTTTTTCCAAATAA 652520 vi v i v vv ivii i v i iivi v i C L1M5_orf2#LIN 1532 TCATAAAATGAGTTGGGAAGTGTTCCCTCTTTTTCTATTTTCTGGAAGAG 1483 chr2ptel1M 652521 TTTACATAATATTGGAATTAATTGTTCTTTAAATGTTTGGTAGAATTCAC 652570 iii v v v v i C L1M5_orf2#LIN 1482 TTTGTGTAAGATTGGTATTATTTCTTCCTTAAATGTTTGGTAGAATTCAC 1433 chr2ptel1M 652571 TTGGAAATCCATTTGACCAGGGAGATTTTTTCTTAGGGAGTTCATTGATG 652620 iv vi v i iv vv v i iv i i v iv i v C L1M5_orf2#LIN 1432 CAGTGAAGCCATCTGGGCCTGGAGTTTTCTTTGTGGGAAGGTTTTTAATT 1383 chr2ptel1M 652621 ATTTGTTCAATTTCTTTTTTAAAAATGGAATTATTTAAATAATTTATTTC 652670 ivvi vv i v i iii i i vv i C L1M5_orf2#LIN 1382 ACAAATTCAATTTCTTTAATAGATATAGGGCTATTCAGATTTTCTATTTC 1333 chr2ptel1M 652671 CTCTTCTGTTAATCTGGGCAATTTATATTTTTTATAGATATTCATCCATT 652720 i v? i i i v i ? i i i - iv ii C L1M5_orf2#LIN 1332 TTCTTGNGTCAGTTTTGGTAANTTGTGTTTTTCA-AGGAATTTGTCCATT 1284 chr2ptel1M 652721 TCAATGAGATTGTCAGATTTGTTGGCATACAACTGGGTAAAATAGCTCCT 652770 viv ii ? i i v ii vvi v viii C L1M5_orf2#LIN 1283 TCATCTAAGTTNTCAAATTTATTGGCATAAAGTTGTTCATAATATTCTCT 1234 chr2ptel1M 652771 AATTATTGCTTTAATTTCTTCTTCATTGGTAGTAAATTCATCCCTTTTTG 652820 v ivi v vivvv iv i vv - i ii C L1M5_orf2#LIN 1233 TATTATCCTTTTAATGTCTGTAGGATCTGTAGTGATGTC-TCCTTTTTCA 1185 chr2ptel1M 652821 TTTTTGATTCTGGTAATGTATTTTTTTCCTTTTCTTTTTCTAAT-----T 652865 ii vi v i v i ii i i ii i ----- C L1M5_orf2#LIN 1184 TTCCTGATATTGGTAATTTGTGTCTTCTCTCTTTTTTTCTTGATCAGTCT 1135 chr2ptel1M 652866 AGCCAAAGGTTTATCTATTTTGTTGATTTTTTCATAAAGACAACTCTTAG 652915 ? i i v i i v i iv i i i C L1M5_orf2#LIN 1134 NGCTAGAGGTTTATCAATTTTATTGATCTTTTCAAAGAACCAGCTTTTGG 1085 chr2ptel1M 652916 TTTTATTAG--TTCAATAT--TTTTTTAAATTTCAATTTTATTAATCTCT 652961 i ii ii-- vv -- ? ? viv v i i i C L1M5_orf2#LIN 1084 CTTCGTTGATTTTCTCTATTGTNTNTTTGTTTTCTATTTCATTGATTTCT 1035 chr2ptel1M 652962 CCTTTGAGTTTCA-GAATTCCTAATTTGGTATATAATTGGGATTTTTAAT 653010 v i v vi i -v v vvi -v iv ?v v i-- C L1M5_orf2#LIN 1034 GCTCTTATCTTTATTATTTCCTTCCTT-CTACTTNCTTTGGG--TTTAAT 988 chr2ptel1M 653011 TTGTTC-TCTTTTTTTAGCTTTTTTAGTTGCATGTCAAATTCATTGATTT 653059 i - i i v v v v iiv iv C L1M5_orf2#LIN 987 TTGCTCTTCTTTTTCTAGCTTCTTAAGGTGGAAGCTTAGATCATTGATTT 938 chr2ptel1M 653060 T-----TCTC-TATTTTATACATATAACTATTTAAAGATATAAAATTTCC 653103 ----- i - v v - ?vi ? v - C L1M5_orf2#LIN 937 TAAGCCTTTCTTCTTTTCTA-ATATANGCATTTAANGCTAT-AAATTTCC 890 chr2ptel1M 653104 CT-TAAGAACTGCTTTGCCTGCATCTCATAGGTTTTG-TATGTTGTCTTA 653151 - v iv i i ii - v v C L1M5_orf2#LIN 889 CTCTAAGCACTGCTTTAGCTGCATCCCACAAATTTTGATATGTTGTATTT 840 chr2ptel1M 653152 TTATTTTCATTCTCTTAGATGAAATTATT-----GTTTTCATC---ATTT 653193 i ? ---- v v v -----i i ? i--- C L1M5_orf2#LIN 839 TCATTNTCATTC----AGTTCAAAATATTTTCTAATTTCCNTTGTGATTT 794 chr2ptel1M 653194 GTTTTTTGATCCATTCATTCATTAGAATTAGGTCATTTAATTTCCAG--- 653240 v i i vvi vv v iv ii i--- C L1M5_orf2#LIN 793 CTTCTTTGACCCATGGGTTATTTAGAAGTGTGTTGTTTAATTTCCAAATA 744 chr2ptel1M 653241 -TTGG---TTTTTAATCTATTTTCTCTGGCCCTTTATTTA-ATGTAGTTT 653285 - --- iv v? i - i ----- v -v v i C L1M5_orf2#LIN 743 TTTGGGGATTTTCTAGNTATCTT-TTTG-----TTATTGATTTCTAATTT 700 chr2ptel1M 653286 TATTGCATCATGATCTGAAAA-AGAAGCAATTATAAGTTCTGCCCTTCTG 653334 v v ii i v i - v vv vi- i v vii i?i C L1M5_orf2#LIN 699 AATTCCATTGTGGTCAGAGAACATACTCTG-TATGATTTCAATCCTTTNA 651 chr2ptel1M 653335 CATTTGATTATGAAGTG-TTTATGCCCTAATAATTACATGGTCAATTTTT 653383 v - iv vv - v i i----? i v i - C L1M5_orf2#LIN 650 AATTT-ATTGAGACTTGTTTTATGGCCCAG----NATATGGTCTATCTT- 607 chr2ptel1M 653384 TGGGTAGGTG--CCAGATGCTGCTGAGAAAAAGATATATTCCTTTCTGTT 653431 -- ii -- vi vvi i i vi i -- v ? C L1M5_orf2#LIN 606 --GGTAAATGTTCCATGTGCACTTGAAAAGAATGTGTATTC--TGCNGTT 561 chr2ptel1M 653432 CCT--ATTCAGTTTTCTCCAAAGGTC--TTA--TCA---TATTTAA---- 653468 vi --i v? v vi v -- -- --- iv i ---- C L1M5_orf2#LIN 560 GTTGGGTGNAGTGTTCTATAAATGTCAATTAGGTCAAGTTGGTTGATAGT 511 chr2ptel1M 653469 -TTTTTTAAAGATTCTATTAACCTCCTTAAGTTTCTTTGTTTATTTTGTG 653517 - v i vv - v ivi i -- i i -i - C L1M5_orf2#LIN 510 GTTGTTCAAATCTTCTA-TATCCTTACTGA--TTTTTTGTCTA-CTTGT- 466 chr2ptel1M 653518 GTTACATTTATCTAATT-CTGAGTGGGGGAGATTGAGGTCCCCCACTAGT 653566 ------ i - - v i ?ivi i ii i ? --- C L1M5_orf2#LIN 465 ------TCTATC-AATTACTGAGAGAGGNGTGTTAAAATCTCCNAC---T 426 chr2ptel1M 653567 ATAATTTTG---CTATTGATTTCTTCCTGTAATTGGCTTAACTTTT-CTA 653612 v ---i i iv i i v i vvv i ii - v C L1M5_orf2#LIN 425 ATAATTGTGGATTTGTCTATTTCTCCTTTTAGTTCTGTCAGTTTTTGCTT 376 chr2ptel1M 653613 AA---AGTTGGATGCAC---CATTTGGTGTATATATATATA-TATAACCA 653655 v --- v v v v ---i v i i i v -v viii C L1M5_orf2#LIN 375 CATGTATTTTGAAGCTCTGTTATTAGGTGCATACACATTTAGGATTGTTA 326 chr2ptel1M 653656 CTACTTCATTGTCTATGGCACCATTTAATAAGATGTCATTTCCTTCCTTA 653705 ivv v vi vv v vv v vi vv vv v i i C L1M5_orf2#LIN 325 TGTCTTCTTGATGAATTGACCCTTTTATCATTATGAAATGTCCCTCTTTA 276 chr2ptel1M 653706 TTTCTTTTAATTAGATATATTTTTACTTT------TGCTTTATCTGAAAT 653749 i vv --- --- i i i ------ i i v C L1M5_orf2#LIN 275 TCTCTGGTAAT---AT---TTCTTGCCTTGAAGTCTACTTTGTCTGATAT 232 chr2ptel1M 653750 CAGAATTGCTACCCCTGC 653767 i iv v i ? v C L1M5_orf2#LIN 231 TAATATAGCCACNCCAGC 214 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 40.11 CpG sites = 501, Kimura (unadjusted) = 40.52 Transitions / transversions = 1.23 (469/381) Gap_init rate = 0.06 (185 / 2930), avg. gap size = 1.79 (332 / 185) 2985 31.73 6.10 2.35 chr2ptel1M 651186 653767 (346233) C L1M4_orf2#LINE/L1 (403) 2891 214 m_b72s551i9 2666 chr2ptel1M 651186 ACCCATTTTGATCTTATTTTGGTATGCGGTGTGAGATGTAGGTCTATGCC 651235 i vi v v ii i ivi i vvii C L1M4_orf2#LIN 2891 ATCCATTTTGAGTTAATTTTTGTATATGGTGTGAGGTAGGGGTCCAACTT 2842 chr2ptel1M 651236 AACTTTCTGACATTT-----TCCAGTATTCCCAGCAATTTTTGTGAAATA 651280 v i i i vi v ----- vv viv vi v C L1M4_orf2#LIN 2841 CATTCTTTTGCATGTGGATATCCAGTTGTCCCAGCACCATTTGTTGAAAA 2792 chr2ptel1M 651281 GTGAATTCTTATCCCCAAAGATTGAGTTTGGGAGT-TTATCAAATGCTAG 651329 vvv - vv v ?ivi v vi- i i ------ C L1M4_orf2#LIN 2791 GACTATTCTT-TCCCCATTGAATNGTCTTGGCACCCTTGTCGAA------ 2749 chr2ptel1M 651330 ACTCCTATAATCATTGAT-TATTGTGTCATGTATA---TCTTACTT--AT 651373 v vvv i i vi - ?v vv i v v i--- i v -- C L1M4_orf2#LIN 2748 AATCAATTGACCATAAATGTANGGGTTTATTTCTGGACTCTCAATTCTAT 2699 chr2ptel1M 651374 TCCACTAATCCACCACTCTATTCATAGGA-GGTACCAAATGTTTTTGATG 651422 i i i ivvv i v v v-i v ivv i v C L1M4_orf2#LIN 2698 TCCATTGATCTATATGTCTATCCTTATGCCAGTACCACACTGTCTTGATT 2649 chr2ptel1M 651423 ACTGCTACTTTATAATA-GTTTT-AGGTCTGACACTGCTAGACCACTGTC 651470 ivi i i - - ii v iv v iv v v iiv C L1M4_orf2#LIN 2648 ACTGTAGCTTTGTAGTAAGTTTTGAAATCGGGAAGTGTGAGTCCTCCAAC 2599 chr2ptel1M 651471 TTTTTTATTTATTTTTTCA---TTAATTCCCTAGATATTATTTAG---CT 651514 v v i-- --- iv --- i v --i i --- i C L1M4_orf2#LIN 2598 TTTGTTCTTC--TTTTTCAAGATTGTTT---TGGCTATT--CTGGGTCCC 2556 chr2ptel1M 651515 TT---TTTTCAGATGAATTTTGTTATT--TTTTTCTATCTCTATAAAATT 651559 --- i v ivv i--i v v i ii vv C L1M4_orf2#LIN 2555 TTGCATTTCCATATGAATTTTAGGATCAGCTTGTCAATTTCTGCAAAAAA 2506 chr2ptel1M 651560 TTTTTTTTGGCAGTTTGATTGGTATGGCACTGAACAAGTAGATCAATTTA 651609 v?ivvi v - v v v v ii ivv i C L1M4_orf2#LIN 2505 GNCAGCTGGG-ATTTTGATAGGGATTGCGTTGAATCTGTAGATCAATTTG 2457 chr2ptel1M 651610 GGTAGAATTGTCATTTTTATTACATTAGCTTGGCCTA-CCATGACCAATT 651658 v v i i v iv i iv ivv v - v vvv C L1M4_orf2#LIN 2456 GGGAGTATTGCCATCTTAACAATATTAAGTCTTCCAATCCATGAACATGG 2407 chr2ptel1M 651659 GACATTTTCCCAATTGTTTATGTCTGATTT--TGTGTTTAAA--GTGTTT 651704 ii i i v i v vv -- v v v --i C L1M4_orf2#LIN 2406 GATGTCTTTCCATTTATTTAGGTCTTCTTTAATTTCTTTCAACAATGTTT 2357 chr2ptel1M 651705 TGTTATAGTGTTCA---TATAATTCCTGGATTT-TCTTGACAGGTAGACA 651750 --- v --- i v i v i - i vi ii vv iv C L1M4_orf2#LIN 2356 TGT---AGTTTTCAGTGTACAAGTCTTGCACTTCTTTTGTTAAATTTATT 2310 chr2ptel1M 651751 CCCAAATATTTGATTTTGTCTATAGTTATCTTAAATGAAAATTGTCTTTC 651800 i i v i v i ivv i iv i - - C L1M4_orf2#LIN 2309 CCTAAGTATTTTATTCTTTTTGATGCTATTGTAAATGGAA-TTGT-TTTC 2262 chr2ptel1M 651801 T--ATCTC--TTGCTGCTGGGCTTTGTTAGTAATATGTAAAAATGC---T 651843 -- i -- v v v v -- ii iv i i i i i --- C L1M4_orf2#LIN 2261 TTAATTTCATTTTCGGATTG--TTCATTGCTAGTGTATAGAAATACAATT 2214 chr2ptel1M 651844 GATGTTTGTGT---GAGTTTATTATCCTGCAATTTTGTTAAAGCTGTTAA 651890 v i --- vi i - ii i i vii v C L1M4_orf2#LIN 2213 GATTTTTGTATATTGATCTTGT-ATCCTGCAACCTTGCTGAACTCGTTTA 2165 chr2ptel1M 651891 TTGTTTCAAGTGGGTTTTTGGATCATTCTATAGGATTCTCTAAGTACACC 651940 iv v i i v ? vvv iv i vi vv C L1M4_orf2#LIN 2164 TTAGTTCTAATAGTTTTTTNGTGGATTCCTTAGGATTTTCTATATACAAG 2115 chr2ptel1M 651941 ATCATATTATCTTCAAAGAGTGATAATTTTA--TCT-CATTGCCTATTCT 651987 i i v i v v i -- - v v v iiv C L1M4_orf2#LIN 2114 ATCATGTCATCTGCGAATAGAGATAGTTTTACTTCTTCCTTTCCAATCTG 2065 chr2ptel1M 651988 GATTCCTTT-ATTTTTTTTCCTT-----ATTGCTAAAGTCAACATTTCTA 652031 v - i i ----- ivvi ii iv ii i C L1M4_orf2#LIN 2064 GATGCCTTTTATTTCTTTTTCTTGCCTAATTGCCCTGGCTAGAACCTCCA 2015 chr2ptel1M 652032 GTACAATATTGAATAACAATGGTGATA-TGGGCATCCTAGTTTCATCCTT 652080 i iv i i v -i i v i ii i i C L1M4_orf2#LIN 2014 GTACAATGTTGAATAGAAGTGGCGAGAGCGGACATCCTTGTCTTGTTCCT 1965 chr2ptel1M 652081 GATCTTATTACCAATGTGTCCAGCTTCTCCTCCTTATTAATAATGCTGAC 652130 vvivv v i? i ii i vi v vvv i i ii C L1M4_orf2#LIN 1964 GATCTTAGGGGGAAAGCNTTCAGTCTTTCACCATTAAGTATGATGTTAGC 1915 chr2ptel1M 652131 TGATGGGTGTAG-ATAGATGCTGCTTATCA---------AGTTC------ 652164 - v vv-i ivi --------- ------ C L1M4_orf2#LIN 1914 TG-TGGGTTTTTCGTAGATGCCCTTTATCAGGTTGAGGAAGTTCCCTTCT 1866 chr2ptel1M 652165 --TCC----------GGTGTTAATAGGATTA---GGTACTGTATTTTGTC 652199 -- ----------i vv vv v --- ii v C L1M4_orf2#LIN 1865 ATTCCTAGTTTGTTGAGTGTTTTTATCATGAAAGGGTGTTGGATTTTGTC 1816 chr2ptel1M 652200 AAGAACTTTTTCTGCATCTATTGAGATTATCATGTGAATTCTGTTAGCTT 652249 ivi i v iv i i-- C L1M4_orf2#LIN 1815 AAATGCTTTTTCTGCGTCTATTGAGATGATCATGTGGTTTTTGTC--CTT 1768 chr2ptel1M 652250 TG--CCATTGATATGGTTAATTGTGACAATAGATTTCCTGATACTGAACC 652297 i-- i i vv iiivii v i v? ii C L1M4_orf2#LIN 1767 TATTCTATTAATATGGTGTATTACATTGATTGATTTTCGNATGTTGAACC 1718 chr2ptel1M 652298 AGCCCTGCATTCCTCATATAAATCCCCCTTGATTATAGTATATTATCATG 652347 i i viv v i i i i v v v C L1M4_orf2#LIN 1717 AACCTTGCATTCCTGGGATAAATCCCACTTGGTCATGGTGTATAATCCTT 1668 chr2ptel1M 652348 CTGATAAGTTGTTA---------TGCAACAACTT-----AACATTTTTGC 652383 i v v i i--------- v vv i ----- iv C L1M4_orf2#LIN 1667 TTTATATGTTGCTGGATTCGGTTTGCTAGTATTTTGTTGAGGATTTTTGC 1618 chr2ptel1M 652384 ATCAATCACTCATTAGGGAGATTGGTCTGTAATTTTCTTTCTCTGTTTTT 652433 v - i v v i iii vv - C L1M4_orf2#LIN 1617 ATCTAT-ATTCATAAGGGATATTGGTCTGTAGTTTTCTTTTCTTGTGAT- 1570 chr2ptel1M 652434 GGATCTTC--CTGGTTTAGGTATCAACACCATATATGTGTCATCGAAGGA 652481 --i i-- v iviiv ivv iv v v C L1M4_orf2#LIN 1569 --GTCTTTGTCTGGTTTTGGTATCAGGGTAATACTGGCCTCATAGAATGA 1522 chr2ptel1M 652482 ATTTGTCAAGACTCCTTCTTTATCTGTTTTTCCAAATAATTTACATAATA 652531 i v vv ivii i i iv i ivi v i iiiv iv C L1M4_orf2#LIN 1521 GTTGGGAAGTGTTCCCTCCTCTTCTATTTTTTGGAAGAGTTTGTGAAGGA 1472 chr2ptel1M 652532 TTGGAATTAATTGTTCTTTAAATGTTTGGTAGAATTCACTTGGAAATCCA 652581 vi v iv vi v C L1M4_orf2#LIN 1471 TTGGTGTTAATTCTTCTTTAAATGTTTGGTAGAATTCACCAGTGAAGCCA 1422 chr2ptel1M 652582 TTTGACCAGGGAGATTTTTTCTTAGGGAGTTCATTGATGATTTGTTCAAT 652631 i i? vv ivv i iv i i iv v i vi C L1M4_orf2#LIN 1421 TCTGGNCCTGGGCTTTTCTTTGTGGGAAGTTTTTTGATTACTAATTCAAT 1372 chr2ptel1M 652632 TTCTTTTTTAAAAATGGAATTATTTAAATAATTTATTTCCTCTTCTGTTA 652681 i vi vivv i ivi i i vv i i vv i C L1M4_orf2#LIN 1371 CTCTTTACTTGTTATAGGTCTATTCAGATTTTCTATTTCTTCTTGAGTCA 1322 chr2ptel1M 652682 ATCTGGGCAATTTATATTTTTTATAGATATTCATCCATTTCAATGAGATT 652731 i i v i i i i i i- iv ii viv i C L1M4_orf2#LIN 1321 GTTTCGGTAGTTTGTGTCTTTC-TAGGAATTTGTCCATTTCATCTAGGTT 1273 chr2ptel1M 652732 GTCAGATTTGTTGGCATACAACTGGGTAAAATAGCTCCTAATTATTGCTT 652781 i vi i vvi v i vii v v ivi C L1M4_orf2#LIN 1272 ATCTAATTTGTTGGCATACAATTGTTCATAGTATTCCCTTATAATCCTTT 1223 chr2ptel1M 652782 TAATTTCTTCTTCATTGGTAGTAAATTCATCCCTTTTTGTTTTTGATTCT 652831 v vivvvi i vv -i ii ii ii i C L1M4_orf2#LIN 1222 TTATTTCTGTAAGGTCGGTAGTAATGTC-CCCTCTTTCATTCCTGATTTT 1174 chr2ptel1M 652832 GGTAATGT--ATTTTTTTCCTTTTCTTTTT--CTAAT-TAGCCAAAGGTT 652876 i v --i i i ii i i --ii i - i C L1M4_orf2#LIN 1173 AGTAATTTGAGTCTTCTCTCTTTTTTTCTTGGTCAGTCTAGCTAAAGGTT 1124 chr2ptel1M 652877 TATCTATTTTGTTGATTTTTTCATAAAGACAACTCTTAGTTTTATTAG-- 652924 i v i v i iv i i ii ii-- C L1M4_orf2#LIN 1123 TGTCAATTTTGTTGATCTTTTCAAAGAACCAACTTTTGGTTTCGTTGATT 1074 chr2ptel1M 652925 TTCAATATT-TTTTTAAATT-TCAATTTTATTAATCTCTCCTTTGAGTTT 652972 vv - vv - v i v i iv i i vi C L1M4_orf2#LIN 1073 TTCTCTATTGTTTTTCTATTCTCTATTTCATTTATTTCCGCTCTAATCTT 1024 chr2ptel1M 652973 CAGAATT--CCTAATTTGGTATATAATTGGGATTTTTAATTTGTTC-TCT 653019 i vv -- i vv iv iv ii-v --- i i - C L1M4_orf2#LIN 1023 TATTATTTCCTTCCTTCTGCTTGC-TTTGGG---TTTAGTTTGCTCTTCT 978 chr2ptel1M 653020 TTTTTTAGCTTTTTTA-GTTGCATGTCAAATTCATTGATT-------TTT 653061 i i i v - v v v i ii - ------- C L1M4_orf2#LIN 977 TTTTCTAGTTTCTTAAGGTGGAAGGTTAGGTT-ATTGATTTGAGATCTTT 929 chr2ptel1M 653062 C-TCTATTTTATACATATAACTATTTAAAGATATAAAATTTCCCT-TAAG 653109 - v --- ivi v v - - C L1M4_orf2#LIN 928 CTTCTTTTTTA---ATATAGGCATTTACAGCTAT-AAATTTCCCTCTAAG 883 chr2ptel1M 653110 AACTGCTTTGCCTGCATCTCATAGGTTTT-GTATGTTGTCTTATTATTTT 653158 v ?v i i - v v ii C L1M4_orf2#LIN 882 CACTGCTTTNGCTGCATCCCATAAGTTTTGGTATGTTGTGTTTTCGTTTT 833 chr2ptel1M 653159 CATTC-TCTTAGATGAAATT----ATTGTTTTCATCATTTGTTTTTTGAT 653203 - i i - v v ---- viii ii v v i i C L1M4_orf2#LIN 832 CATTCATCTCAAA-GTATTTTCTAATTTCCCTTGTGATTTCTTCTTTGAC 784 chr2ptel1M 653204 CCATTCATTCATTAGAATTAGGTCATTTAATTTCCAGTTGGTTTTTAATC 653253 vi vv i v iv ii vv iv v v i C L1M4_orf2#LIN 783 CCATTGGTTATTTAGGAGTGTGTTGTTTAATTTCCACATATTTGTGAATT 734 chr2ptel1M 653254 T-----ATTTTCTCTGGCCCTTTATTTAATGTAGTTTTATTGCATCATGA 653298 ----- i iiv iiv v --- v i i v ii i C L1M4_orf2#LIN 733 TCCCAAATTTCCTTCTGTTATTGATT---TCTAATTTCATTCCATTGTGG 687 chr2ptel1M 653299 TCTGAAAAAGAAGCAAT-TATAAGTTCTGCCCTTCTGCATTTGATTATGA 653347 - i i v vi vv - i v vii i iv - iv C L1M4_orf2#LIN 686 TC-GGAGAACATACTTTGTATGATTTCAATCCTTTTAAATTT-ATTGAGA 639 chr2ptel1M 653348 AGTG-TTTATGCCCTAATAATTACATGGTCAATTTTTTGGGTAGGTGCCA 653396 vv - v ----i i v - ii v i v v v C L1M4_orf2#LIN 638 CTTGTTTTATGGCCTAA----CATATGGTCTA-TCCTGGAGAATGTTCCA 594 chr2ptel1M 653397 GATGCTGCTGAGAAAAAGATATATTCCTTTCTGTTCCT--ATTCAGTTTT 653444 vi vvi i vi i -- v vi --i vv v C L1M4_orf2#LIN 593 TGTGCACTTGAGAAGAATGTGTATTC--TGCTGTTGTTGGGTGGAGTGTT 546 chr2ptel1M 653445 CTCCAAAGGTCTTATCATATTTAATT-TTTTAAAGATTCTATTAACCTCC 653493 vi i v - i i vi i i -v v - vi i v vv i C L1M4_orf2#LIN 545 CTATAGATGTC-TGTTAGGTCTAGTTGGTTTATAG-TGTTGTTCAAGTCT 498 chr2ptel1M 653494 TTAAGTTTCTTTGTTTATTTTGTG----GTTACATTTATCTAATTCTGAG 653539 iv - i v i v ---- ii- i i v vi i C L1M4_orf2#LIN 497 TCTA-TTTCCTTGTTGATCTTCTGTCTAGTTGT-TCTATCCATTATTGAA 450 chr2ptel1M 653540 TGGGGGAGATTGAGGTCCCCCACTAGTATAATTTTGCTATTGATTTCTTC 653589 v v iv i i v v vi vvii i iv i C L1M4_orf2#LIN 449 AGTGGGGTATTGAAGTCTCCAACTATTATTGTTGAATTGTCTATTTCTCC 400 chr2ptel1M 653590 CTGTAATTGGCTTAACTTTT-CTAAAAG----TTGGATGCACCAT--TTG 653632 vi vvv i ii - vv v ---- i- v ii -- i C L1M4_orf2#LIN 399 CTTCAATTCTGTCAGTTTTTGCTTCATGTATTTTGGG-GCTCTGTTGTTA 351 chr2ptel1M 653633 GTGTATATATATATATATAACCACTA---CTTC-------ATTGTCTATG 653672 - ii i v iiii --- ------- v iv v C L1M4_orf2#LIN 350 G-GTGCATATATGTTTATAATTGTTATATCTTCCTGATGGATTGACCCTT 302 chr2ptel1M 653673 GCACCATTTAATAAGATGTCATTTCCTTCCTTATTTCTTTTAATTAGATA 653722 vi i -- i ----- i i i vv iv?vv v C L1M4_orf2#LIN 301 TTATCATT--ATAAAATG-----TCCTTCTTTGTCTCTAGTAACANTTTT 259 chr2ptel1M 653723 TATTTTTACTTTTGCTTTATCTGAAATCAGAATTGCTACCCCTGC 653767 i i v vv i ii i v i v v i i v C L1M4_orf2#LIN 258 TGTCTTAAAGTCTATTTTGTCTGATATTAGTATAGCCACTCCAGC 214 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 41.62 CpG sites = 459, Kimura (unadjusted) = 42.42 Transitions / transversions = 1.17 (428/366) Gap_init rate = 0.05 (129 / 2581), avg. gap size = 1.78 (230 / 129) 40 0.00 0.00 0.00 chr2ptel1M 653768 653804 (346196) (T)n#Simple_repeat 1 37 (0) c_b72s251i4 2667 chr2ptel1M 653768 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 653804 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 37 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 2985 31.73 6.10 2.35 chr2ptel1M 653805 653974 (346026) C L1M4_orf2#LINE/L1 (3081) 213 39 m_b72s551i9 2666 chr2ptel1M 653805 GGCTTCAGCTGAA-----GCATAACCAGTTCTGCTCCAGTCTTCTACCCT 653849 vv iv v v v----- iiivvi ii vi vi i ii C L1M4_orf2#LIN 213 CTCTTTTGGTTACTGTTTGCATGGTATATCTTTTTCCATCCTTTTACTTT 164 chr2ptel1M 653850 TACTCTATATCTATCTCTCTGTTTTATATATGTTTCTTGTAAACAACACA 653899 i vi v v i i vvi i v vi i i i i i C L1M4_orf2#LIN 163 CAACCTATTTGTGTCTTTGAATCTAAAGTGTGTCTCTTGTAGACAGCATA 114 chr2ptel1M 653900 TTATAGGATTTTGTTTTTTAATCCATTCTGCTATTCACTTCCTTTCTATG 653949 vi v iv v i v v v iv v C L1M4_orf2#LIN 113 TAGTTGGATCATGTTTTTTTATCCATTCTGCCAATCTCTGCCTTTTGATT 64 chr2ptel1M 653950 GGAGAGTTCATCCCATTCACATTTA 653974 v i vi i C L1M4_orf2#LIN 63 GGAGTGTTTAATCCATTTACATTTA 39 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 41.62 CpG sites = 459, Kimura (unadjusted) = 42.42 Transitions / transversions = 1.11 (31/28) Gap_init rate = 0.01 (1 / 169), avg. gap size = 5.00 (5 / 1) 481 24.72 2.20 2.20 chr2ptel1M 653862 654043 (345957) C L1MEj_5end#LINE/L1 (0) 2160 1979 m_b72s551i10 2666 chr2ptel1M 653862 ATCTCTCTGTTTTATATATGTTTCTTGTAAACAACACATTATAGGATTTT 653911 v i vi i i i viiv i C L1MEj_5end#LI 2160 ATCACTTTGTTTTAAGTGTGTTTCTTGTAAACAGCATATAGCTGGGTTTT 2111 chr2ptel1M 653912 GTTTTTTAATCCATTCTGCTATTCACTTCCTTTCTATGGGAGAGTTCATC 653961 i v vi v v vi iv i vi C L1MEj_5end#LI 2110 GTTTTTTAACCCAATCTGACAGTCTCTGTCTTTTAATGGGAGAATTCAGT 2061 chr2ptel1M 653962 CCATTCACATTTACAGTTATGAT---TACCCCTGTATATT-TCCCCTCCA 654007 vv v i i--- iv i - v - i i C L1MEj_5end#LI 2060 CCATTCACATTTAGTGTAACGACTGATATACTTG-ATTTTATTCCTTCCA 2012 chr2ptel1M 654008 TCCTATTTTCTCCCCTATATATACTTTTGTTGTTTT 654043 i i v i?ii v --- v C L1MEj_5end#LI 2011 TCTTACTTTATTNTTTATTTA---TTTTGTTTTTTT 1979 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 29.92 CpG sites = 25, Kimura (unadjusted) = 30.74 Transitions / transversions = 1.32 (25/19) Gap_init rate = 0.03 (6 / 181), avg. gap size = 1.33 (8 / 6) 16 0.00 0.00 0.00 chr2ptel1M 654627 654644 (345356) (T)n#Simple_repeat 1 18 (0) m_b72s252i10 2668 chr2ptel1M 654627 TTTTTTTTTTTTTTTTTT 654644 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTT 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 271 23.60 8.99 7.18 chr2ptel1M 654703 654880 (345120) C L1M4a2_5end#LINE/L1 (756) 1900 1720 m_b72s551i11 2666 chr2ptel1M 654703 TGATGGTCAATCTCGCTGGGTAGTTAATTCTTGGTTGTTACTCCAAGTCC 654752 v vi i i i i vvv -- ---- ii C L1M4a2_5end#L 1900 TGAAGGATAGTTTTGCTGGATATAGAATTCTTGGTTG--AC----AGTTT 1857 chr2ptel1M 654753 TTTGCCTTC--CA----GAATATGGTATTCCA-GGCCCTCTGA--TCCTT 654793 v i -- ---- vi i -v i i-- v C L1M4a2_5end#L 1856 TTTTCTTTCAGCACTTTGAATATGTCATCCCACTGCCTTCTGGCCTCCAT 1807 chr2ptel1M 654794 TATT----ATAAACACTGCCAGATCCTGTGTAATCCTTACTGTAGTTCCT 654839 i ---- i iv -- i --- i - - i ?? i C L1M4a2_5end#L 1806 TGTTTCTGATGAGAA--GTCAG---CCGT-TAAT-CTTATTGNNGTTCCC 1764 chr2ptel1M 654840 CAATACT---TGAATTGTTTTTGTCTGACTGCTTGCAATATTTT 654880 vi v--- i i v vi v v C L1M4a2_5end#L 1763 CTGTACGTGATGAGTCGTTTTTCTCTTGCTGCTTTCAAGATTTT 1720 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 27.64 CpG sites = 23, Kimura (unadjusted) = 29.40 Transitions / transversions = 1.44 (23/16) Gap_init rate = 0.11 (19 / 177), avg. gap size = 1.53 (29 / 19) 17 15.49 0.00 0.00 chr2ptel1M 655266 655294 (344706) (T)n#Simple_repeat 1 29 (0) m_b72s252i11 2669 chr2ptel1M 655266 TTTTTTTTAGTGTATTTTTTTTTTTTTTT 655294 vv v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 16 16.42 1.82 7.69 chr2ptel1M 655579 655633 (344367) (TTATT)n#Simple_repeat 1 52 (0) m_b72s252i12 2670 chr2ptel1M 655579 TTATTTTATCTTTCTTGTTCATTTTCTTTT-TTTTTTTTTCTTCTTTTCC 655627 - v - - v - v v - v ii (TTATT)n#Simp 1 TTATTTTAT-TTTATT-TT-ATTTTATTTTATTTTATTTTATT-TTATTT 46 chr2ptel1M 655628 TATTTT 655633 (TTATT)n#Simp 47 TATTTT 52 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.09 (5 / 54), avg. gap size = 1.00 (5 / 5) 12 8.85 4.17 0.00 chr2ptel1M 657401 657424 (342576) (AAAC)n#Simple_repeat 1 25 (0) m_b72s252i13 2671 chr2ptel1M 657401 AAACAAACAAACAAA-AGAAAAACA 657424 - i v (AAAC)n#Simpl 1 AAACAAACAAACAAACAAACAAACA 25 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 236 31.61 11.25 1.14 chr2ptel1M 658777 658936 (341064) L1MB4_3end#LINE/L1 396 571 (356) m_b72s551i12 2672 chr2ptel1M 658777 CCCAGAAAGAA----AGGAAGGGACCCA--CA------TGTGCAAAAATG 658814 - ---- i v i -- ------ i vv L1MB4_3end#LI 396 CCCA-AAAGAATTGAAAGCAGGGACTCAAACAGATACTTGTACACCAATG 444 chr2ptel1M 658815 TTTGTGGCAGCCCTGTTTGTAGTGGCTAGAAACTGGAGACTGAGTGGATG 658864 ii i vi i iii i i i i iv i vivviiii L1MB4_3end#LI 445 TTCATAGCAGCATTATTCACAATAGCCAAAAGGTGGAAACAACCCAAGTG 494 chr2ptel1M 658865 CCCATCAGCTGGGGAATGGCTGAATAAGTTATGGTGTATGAATGTTATGG 658914 i - i v iv v i i iv i i iv iiv L1MB4_3end#LI 495 TCCAT-AACAGATGAATGGATAAACAAAATGTGGTATATACATACAATGG 543 chr2ptel1M 658915 AATATTGTTCTGC------AAGAAATGA 658936 i v ------ i L1MB4_3end#LI 544 AATATTATTCAGCCNTAAAAAGGAATGA 571 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 43.87 CpG sites = 35, Kimura (unadjusted) = 43.87 Transitions / transversions = 2.33 (35/15) Gap_init rate = 0.04 (6 / 159), avg. gap size = 3.33 (20 / 6) 355 33.10 0.00 1.44 chr2ptel1M 658782 658922 (341078) L1ME4c_3end#LINE/L1 417 555 (275) m_b72s551i13 2672 chr2ptel1M 658782 AAAGAAAGGAAGGGACCCACATGTGCAAAAATGTTTGTGGCAGCCCTGTT 658831 i i ii -- i i ii i i ii v vi i L1ME4c_3end#L 417 AAAGAAGGAAAAAG--CTATATGCACGAAGATGTTCATTGCAGCGTTATT 464 chr2ptel1M 658832 TGTAGTGGCTAGAAACTGGAGACTGAGTGGATGCCCATCAGCTGGGGAAT 658881 i i i v i i i vivv ii i v iiv L1ME4c_3end#L 465 TATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAAT 514 chr2ptel1M 658882 GGCTGAATAAGTTATGGTGTATGAATGTTATGGAATATTGT 658922 i i i i ii v? iviv i L1ME4c_3end#L 515 GGTTAAGTAAATTATGGTACATCNACTCGATGGAATATTAT 555 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 45.49 CpG sites = 35, Kimura (unadjusted) = 48.55 Transitions / transversions = 3.18 (35/11) Gap_init rate = 0.01 (2 / 140), avg. gap size = 1.00 (2 / 2) 451 29.20 1.46 0.00 chr2ptel1M 658800 658936 (341064) L1ME3F_3end#LINE/L1 430 568 (422) m_b72s551i14 2672 chr2ptel1M 658800 ACATGTGCAAAAATGTTTGTGGCAGCCCTGTTTGTAGTGGCTAGAAACTG 658849 i i ii i v i i i v i L1ME3F_3end#L 430 ACATGTACAAGAATGTTCATAGCAGCACTGTTCGTAATAGCAAAAAACTG 479 chr2ptel1M 658850 GAGACTGAGTGGATGCCCATCAGCTGGGGAATGGCTGAATAAGTTATGGT 658899 i vivviii i ii v i v i i i L1ME3F_3end#L 480 GAAACAACCCAAATGTCCATCGACAGGAGAATGGATAAATAAATTGTGGT 529 chr2ptel1M 658900 GTATGAATGTTATGGAATATTGTTCTGCA--AGAAATGA 658936 i vv iiiv i v v --ii L1ME3F_3end#L 530 ATATTCACACAATGGAATATTATACAGCAGTGAAAATGA 568 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 36.57 CpG sites = 28, Kimura (unadjusted) = 39.11 Transitions / transversions = 2.33 (28/12) Gap_init rate = 0.01 (1 / 136), avg. gap size = 2.00 (2 / 1) 459 27.87 0.00 0.00 chr2ptel1M 658801 658922 (341078) L1ME3G_3end#LINE/L1 427 548 (376) m_b72s551i15 2672 chr2ptel1M 658801 CATGTGCAAAAATGTTTGTGGCAGCCCTGTTTGTAGTGGCTAGAAACTGG 658850 i ii ii v vi i i v i i L1ME3G_3end#L 427 CATGTACAAGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGG 476 chr2ptel1M 658851 AGACTGAGTGGATGCCCATCAGCTGGGGAATGGCTGAATAAGTTATGGTG 658900 i vivv ii i iiv i i i i L1ME3G_3end#L 477 AAACAACCTAAATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGTA 526 chr2ptel1M 658901 TATGAATGTTATGGAATATTGT 658922 vv ii i i L1ME3G_3end#L 527 TATCCATACTATGGAATACTAT 548 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 37.04 CpG sites = 25, Kimura (unadjusted) = 37.04 Transitions / transversions = 2.78 (25/9) Gap_init rate = 0.00 (0 / 121), avg. gap size = 0.0 (0 / 0) 12 23.14 6.90 1.64 chr2ptel1M 659276 659333 (340667) (TATA)n#Simple_repeat 1 61 (0) m_b72s252i14 2673 chr2ptel1M 659276 TATAAATATGTATACATATAT-TGTATTTA-ACATATACTTTA-ACATAT 659322 v i i - i v - i - v - i (TATA)n#Simpl 1 TATATATATATATATATATATATATATATATATATATA-TATATATATAT 49 chr2ptel1M 659323 TTA-ACATGTAT 659333 v - i i (TATA)n#Simpl 50 ATATATATATAT 61 Matrix = Unknown Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.09 (5 / 57), avg. gap size = 1.00 (5 / 5) 264 23.93 4.17 1.35 chr2ptel1M 659455 659526 (340474) MIRb#SINE/MIR 189 262 (6) m_b72s601i6 2674 chr2ptel1M 659455 TAATTAAAATAA---AAATAAAATGCTTCCCAAAGTGCTTGGCACACAGT 659501 v i i --- vi ii vv v i i MIRb#SINE/MIR 189 TAAATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGT 238 chr2ptel1M 659502 AGGTGCTTAATAAGTGGTTAGCCCT 659526 i i i i - i MIRb#SINE/MIR 239 AAGCGCTCAATAAATGG-TAGCTCT 262 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 25.93 CpG sites = 12, Kimura (unadjusted) = 30.05 Transitions / transversions = 2.40 (12/5) Gap_init rate = 0.03 (2 / 71), avg. gap size = 2.00 (4 / 2) 180 30.00 0.00 0.00 chr2ptel1M 660269 660318 (339682) C L2c_3end#LINE/L2 (6) 472 423 m_b72s601i8 2675 chr2ptel1M 660269 TCATTCAGGAAGTATTTCCAAAGCACCCACTGTGTGCCGGGCCCCAGGGA 660318 iv ii vivi i i i i v ii C L2c_3end#LINE 472 TCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGA 423 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 37.44 CpG sites = 11, Kimura (unadjusted) = 41.06 Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 208 20.45 0.00 0.00 chr2ptel1M 660269 660312 (339688) C L2b_3end#LINE/L2 (6) 460 417 m_b72s601i7 2675 chr2ptel1M 660269 TCATTCAGGAAGTATTTCCAAAGCACCCACTGTGTGCCGGGCCC 660312 iv i v vi i i i ? C L2b_3end#LINE 460 TCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNC 417 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 22.09 CpG sites = 6, Kimura (unadjusted) = 25.21 Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 187 24.44 2.22 0.00 chr2ptel1M 662012 662056 (337944) L2d_3end#LINE/L2 461 506 (10) m_b72s601i9 2676 chr2ptel1M 662012 CACATCACT-AGCATGTGGTAGGAGTTTAATAAATATTTGTTGACT 662056 vii - ii i v i i i i L2d_3end#LINE 461 CACAGTGCTGAGCACATAGTAGGCGCTCAATAAATACTTGTTGATT 506 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 31.72 CpG sites = 9, Kimura (unadjusted) = 31.72 Transitions / transversions = 4.50 (9/2) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 20 8.80 0.00 5.26 chr2ptel1M 662906 662945 (337055) (AGAGAC)n#Simple_repeat 1 38 (0) m_b72s252i15 2677 chr2ptel1M 662906 AGAGACAGAGACAGAAACAGACACAGAGAGGCAGAGAAAG 662945 i v -- v (AGAGAC)n#Sim 1 AGAGACAGAGACAGAGACAGAGACAGAGA--CAGAGACAG 38 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 29 0.00 0.00 0.00 chr2ptel1M 663193 663217 (336783) (TG)n#Simple_repeat 1 25 (0) c_b72s251i5 2678 chr2ptel1M 663193 TGTGTGTGTGTGTGTGTGTGTGTGT 663217 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGT 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 262 21.95 0.00 9.78 chr2ptel1M 663576 663676 (336324) MIR3#SINE/MIR 21 112 (96) m_b72s601i10 2679 chr2ptel1M 663576 AGAGACCTACAGCCCTGAAGTCAGGAGGACCCAAGTTCAAATCTGGCCAC 663625 v - i v iv i - iii v i iv v v MIR3#SINE/MIR 21 AGAGAGC-ACGGACTGGGAGTCAGGAG-ACCTGGGTTCTAGTCCCGGCTC 68 chr2ptel1M 663626 AGACACTTAACATTTCTTAGCTGTGTGACCCTGGGCAAGTCACTTAACCC 663675 v v - ------ ? i v i MIR3#SINE/MIR 69 TGCCACT-AAC------TNGCTGTGTGACCTTGGGCAAGTCACTTCACCT 111 chr2ptel1M 663676 C 663676 MIR3#SINE/MIR 112 C 112 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 24.75 CpG sites = 10, Kimura (unadjusted) = 26.20 Transitions / transversions = 1.00 (10/10) Gap_init rate = 0.09 (9 / 100), avg. gap size = 1.00 (9 / 9) 356 19.89 2.02 8.60 chr2ptel1M 663589 663687 (336313) MIRc#SINE/MIR 35 127 (141) m_b72s601i11 2679 chr2ptel1M 663589 CCTGAAGTCAGGAGGACCCAAGTTCAAATCTGGCCACAGACACTTAACAT 663638 i i i iii i i iv v v v v ---- MIRc#SINE/MIR 35 CTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTA---- 80 chr2ptel1M 663639 TTCTTAGCTGTGTGACCCTGGGCAAGTCACTTAACCCCAACTGA--CTCA 663686 ---i i i -v -- MIRc#SINE/MIR 81 ---CTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC-TCTGAGCCTCA 126 chr2ptel1M 663687 G 663687 MIRc#SINE/MIR 127 G 127 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 22.08 CpG sites = 12, Kimura (unadjusted) = 23.53 Transitions / transversions = 2.00 (12/6) Gap_init rate = 0.09 (9 / 98), avg. gap size = 1.11 (10 / 9) 310 22.29 9.29 0.66 chr2ptel1M 666338 666477 (333523) PABL_B-int#LTR/ERV1 4035 4186 (2936) m_b73s701i0 2680 chr2ptel1M 666338 TGATCAGAGCTTTAGAATTGGGGAAAGGAATGAGAGTGAACATCTGCACT 666387 ? i i ?v i vvvv ? v ? i? i i PABL_B-int#LT 4035 TNACCAGAGCCTTNCAACTGTCCCAAGGNAAGAGNGCNAACATTTACACT 4084 chr2ptel1M 666388 GACTCC----ATGTTT---------TGCATGTCTCATGGGGCTGCAGGGA 666424 ---- i? --------- ? - ? i ?iivv PABL_B-int#LT 4085 GACTCCAAGTATGCNTTCNTGGTAGTNCATG-CNCACGGGGCNATCTGGA 4133 chr2ptel1M 666425 AAGAAAGGGGATTTTTAACAGCTAAACATTCCCCCATTAAGTACGAAGGG 666474 ii ?i ??? ?i ?v v??vvv ii v?i? PABL_B-int#LT 4134 AAGAAAGGGGGCTNCTAANNNCNGANAATANNGAAATTAAACACGCNANG 4183 chr2ptel1M 666475 GAA 666477 PABL_B-int#LT 4184 GAA 4186 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 30.95 CpG sites = 17, Kimura (unadjusted) = 32.18 Transitions / transversions = 1.21 (17/14) Gap_init rate = 0.02 (3 / 139), avg. gap size = 4.67 (14 / 3) 351 28.22 22.49 1.47 chr2ptel1M 670962 671130 (328870) C MIRb#SINE/MIR (19) 249 46 m_b73s601i0 2681 chr2ptel1M 670962 ATTAAGTATTTACTTAGCACCTGGCACCAGGCTCAGCAATTT----GTTT 671007 i iii vv ii v iiv v iv ---- iv C MIRb#SINE/MIR 249 ATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACATGCAT 200 chr2ptel1M 671008 TATC------AATCTTCCTCACAACCTTTTGAAATAAGTGCTGTTATTAT 671051 ------ i viv i vi ii i i--- C MIRb#SINE/MIR 199 TATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTA---TTATTAT 153 chr2ptel1M 671052 TCCC---TT-----TGAGGAAACTGAGGCAAAGAGAAGTGAAGCTACT-- 671091 i --- ----- vv i v iv -- C MIRb#SINE/MIR 152 CCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTG 103 chr2ptel1M 671092 ------------------GTAAATGTCTGAGGCCAGATTTGAACTCGGGC 671123 ------------------ i v v v vi i i i i C MIRb#SINE/MIR 102 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGT 53 chr2ptel1M 671124 TTTTCTG 671130 i v C MIRb#SINE/MIR 52 CTGTCTG 46 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 32.65 CpG sites = 28, Kimura (unadjusted) = 36.56 Transitions / transversions = 1.47 (28/19) Gap_init rate = 0.05 (9 / 168), avg. gap size = 4.56 (41 / 9) 406 27.38 12.24 3.12 chr2ptel1M 670962 671108 (328892) C MIR#SINE/MIR (17) 245 86 m_b73s601i1 2681 chr2ptel1M 670962 ATTAAGTATTTACTTAGCACCTGGCACCAGGCTCAGCAATTT----GTTT 671007 i iii vv ii v iivv v iv ---- v C MIR#SINE/MIR 245 ATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGCGCTTTACATGTAT 196 chr2ptel1M 671008 TA------TCAATCTTCCTCACAACCTTTTGAAATAAGTGCTGTTATTAT 671051 ------ i i viv i v ii i i i C MIR#SINE/MIR 195 TAACTCATTTAATCCTCACAACAACCCTATGAGGTAGGTACTATTATTAT 146 chr2ptel1M 671052 TCCC-TT-------TGAGGAAACTGAGGCAAAGAGAAGTGAAGCTACTGT 671093 i - ------- v i v iv -- C MIR#SINE/MIR 145 CCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACT-- 98 chr2ptel1M 671094 AAATGTCTGAGGCCA 671108 --- i ii i C MIR#SINE/MIR 97 ---TGCCCAAGGTCA 86 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 33.07 CpG sites = 25, Kimura (unadjusted) = 35.45 Transitions / transversions = 1.79 (25/14) Gap_init rate = 0.06 (9 / 146), avg. gap size = 2.56 (23 / 9) 378 18.99 3.80 0.00 chr2ptel1M 673076 673154 (326846) C MIR#SINE/MIR (118) 144 63 m_b73s601i2 2682 chr2ptel1M 673076 CTCATTTTACAGATGAGGAAACTGAGGTAAACAG-GGTGGAGTGACT--C 673122 i i v v - vi i -- C MIR#SINE/MIR 144 CCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGC 95 chr2ptel1M 673123 CCGGGGCCACATAGCTAGGAAGGGGCCGAGTC 673154 ii i i v v v i C MIR#SINE/MIR 94 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCC 63 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 22.22 CpG sites = 9, Kimura (unadjusted) = 22.22 Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.03 (2 / 78), avg. gap size = 1.50 (3 / 2) 386 30.05 10.47 2.68 chr2ptel1M 673401 673677 (326323) L1PB1_3end#LINE/L1 268 565 (333) m_b73s551i0 2683 chr2ptel1M 673401 GGAACAATCCCACCATGTAATTGGGAATG------AATCCAACCATTCTG 673444 v i i vv iviv ------ i v i v L1PB1_3end#LI 268 GGAACACTTCTACACTGCTGGTGGGAATGTAAACTAGTACAACCACTATG 317 chr2ptel1M 673445 GAGAGCAATTTGGAACTATGCCTT------------TTGGGGCTATCA-- 673480 i i i v i-- v ------------v i ii i -- L1PB1_3end#LI 318 GAAAACAGTGTGGAG--ATTCCTTAAAGAACTAAAAGTAGAACTACCATT 365 chr2ptel1M 673481 --ATACAGCAGTGTCTCTACTGGGCTTATATCCCAAAG----AGATGTTA 673524 -- v i vi v iv v - i ---- v i L1PB1_3end#LI 366 TGATCCAGCAATCCCACTACTGGGTATCTA-CCCAGAGGAAAAGAAGTCA 414 chr2ptel1M 673525 A-AGAAGAAAAGGGACCCGTATGTGCACAA--ATGTTTGTGGCAGCCCTT 673571 v- v v i i----- iv v-- i i v vv L1PB1_3end#LI 415 TTATACGAAAAAGA-----TACTTGCACACGCATGTTTATAGCAGCACAA 459 chr2ptel1M 673572 TTTGTAGTGGCAAGAAACTGGAACCTGAGTAGATGCCCATCATTTGGAGA 673621 i i i v i vv v vvi i v iiiv L1PB1_3end#LI 460 TTCGCAATTGCAAAAATATGGAACCAGCCCAAATGCCCATCAATCAACGA 509 chr2ptel1M 673622 ATGGCTGAATAAATTGTGGTATATGAATGTTATGGAATATTATTATTCTA 673671 i v i v ? iv iii i i vvv i L1PB1_3end#LI 510 GTGGATAAAGAAANTGTGGTATATATATACCATGGAATACTACTCAGCCA 559 chr2ptel1M 673672 TAAGAA 673677 i L1PB1_3end#LI 560 TAAAAA 565 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 38.77 CpG sites = 43, Kimura (unadjusted) = 39.40 Transitions / transversions = 1.13 (43/38) Gap_init rate = 0.05 (15 / 276), avg. gap size = 2.47 (37 / 15) 332 31.33 9.94 3.87 chr2ptel1M 673426 673767 (326233) L1MA1_3end#LINE/L1 299 660 (389) m_b73s551i1 2683 chr2ptel1M 673426 AATGAATCCAACCATTCTGGAGAGCAATTTGGAACTATGCCTT------- 673468 v i v i v i i i--i v i------- L1MA1_3end#LI 299 AATTAGTACAACCACTATGGAGAACAGTTTGGAG--GTTCCTCAAAAAAC 346 chr2ptel1M 673469 ------TTGGGGCTATCA----ATACAGCAGTGTCTCTACTGGGCTTATA 673508 ------ i - i ---- v i vi v i iv L1MA1_3end#LI 347 TAAAAATTGAG-CTACCATATGATCCAGCAATCCCACTGCTGGGTATATA 395 chr2ptel1M 673509 TCCCAAAGAGATGTTAAAGAAGAA-----AAGGGACCCGTATGTGCACAA 673553 i v i v -- vv v ----- i ---- v vv L1MA1_3end#LI 396 CCCAAAAGAAAGG--AAATCAGTATATCGAAGAGA----TATCTGCACTC 439 chr2ptel1M 673554 --ATGTTTGTGGCAGCCCTTTTTGTAGTGGCAAGAAACTGGAACCTGAGT 673601 -- v v v ii i i v ii vi v vivv L1MA1_3end#LI 440 CTATGTTTGTTGCAGCACTGTTTACAATAGCTAAGATTTGGAAGCAACCT 489 chr2ptel1M 673602 AGATGCCCATCATTTGGAGAATGGCTGAATAAATTGTGGTATATGAATGT 673651 ii i viv iv v i v v i iv iii L1MA1_3end#LI 490 AAGTGTCCATCAACAGATGAATGGATAAAGAAAATGTGGTACATATACAC 539 chr2ptel1M 673652 TATGGAATATTATTATTCTATAAGAAACGATCAG---CAGGCAGAGTTCA 673698 v i i vvv i i vi v --- v --- ii L1MA1_3end#LI 540 AATGGAGTACTATTCAGCCATAAAAAAGAATGAGATCCAGTCA---TTTG 586 chr2ptel1M 673699 GAAAAACCTGGAAAGA--CAGACATGAGCTGATACTGAGTGAAATGAGCA 673746 v v v vi --ii v v -- v ii i i v L1MA1_3end#LI 587 CAACAACATGGATGGAACTGGAGATCA--TTATGTTAAGTGAAATAAGCC 634 chr2ptel1M 673747 GAACCTGGAGAG-----CATCGCATG 673767 iii vii i ----- L1MA1_3end#LI 635 AGGCACAGAAAGACAAACATCGCATG 660 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 41.52 CpG sites = 55, Kimura (unadjusted) = 41.52 Transitions / transversions = 1.15 (55/48) Gap_init rate = 0.06 (22 / 341), avg. gap size = 2.18 (48 / 22) 484 28.80 7.36 0.81 chr2ptel1M 673434 673664 (326336) L1ME3G_3end#LINE/L1 303 548 (376) m_b73s551i2 2683 chr2ptel1M 673434 CAACCATTCTGGAGAGCAATTTGGAACTATGCCTT-----TTG----GGG 673474 i ? i i v v viv ----- i---- v L1ME3G_3end#L 303 CAGCCNTTTTGGAGGGCAATTTGGCAGTATCTATTAAAATTTAAAATGCG 352 chr2ptel1M 673475 C-TATC----AATACAGCAGTGTCTCTACTGGGCTTATATCCCAAAGAGA 673519 - i ----i iv i vi v v ? ?v v i ? i L1ME3G_3end#L 353 CATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAGAAA 402 chr2ptel1M 673520 TGTT---AAAGAAGAAAAGGGACCCGTATGTGCACAAATGTTTGTGGCAG 673566 ii --- v viv v v i ?-- i i vii ii v L1ME3G_3end#L 403 TACTCGCACATGTGCACAAGGAN--GCATGTACAAGGATGTTCATTGCAG 450 chr2ptel1M 673567 CCCTTTTTGTAGTGGCAAGAAACTGGAACCTGAGTAGATGCCCATCATTT 673616 vi v i i i i i v vivv i i v v L1ME3G_3end#L 451 CATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCAATA 500 chr2ptel1M 673617 GGAGAATGGCTGAATAAATTGTGGTATATGAATGTTATGGAATATTAT 673664 i i i i vv ii i L1ME3G_3end#L 501 GGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACTAT 548 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 37.66 CpG sites = 38, Kimura (unadjusted) = 38.40 Transitions / transversions = 1.36 (38/28) Gap_init rate = 0.03 (7 / 230), avg. gap size = 2.71 (19 / 7) 467 34.22 1.13 1.13 chr2ptel1M 673484 673749 (326251) L1ME4c_3end#LINE/L1 374 639 (191) m_b73s551i3 2683 chr2ptel1M 673484 CAGCAGTGTCTCTACTGGGCTTATATCCCAAAGAGATG-TT--AAAGAAG 673530 i i vi v v vv v i i i i- -- L1ME4c_3end#L 374 CAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAAGAAG 423 chr2ptel1M 673531 AAAAGGGACCCGTATGTGCACAAATGTTTGTGGCAGCCCTTTTTGTAGTG 673580 i ii -- ii ii iv i ii v vi v i i i L1ME4c_3end#L 424 GAAAAAG--CTATATGCACGAAGATGTTCATTGCAGCGTTATTTATAATA 471 chr2ptel1M 673581 GCAAGAAACTGGAACCTGAGTAGATGCCCATCATTTGGAGAATGGCTGAA 673630 i i i v vivv i i v v v i i i i L1ME4c_3end#L 472 GCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAATGGTTAAG 521 chr2ptel1M 673631 TAAATTGTGGTATATGAATGTTATGGAATATTATTATTCTATAAGAAACG 673680 i i v? iviv vvvv i v i i L1ME4c_3end#L 522 TAAATTATGGTACATCNACTCGATGGAATATTATGCAGCCATTAAAAATG 571 chr2ptel1M 673681 ATCAGCAGGCAGAGTTCAGAAAAACCTGGAAAGACAGACATGAGCTGATA 673730 v vi v v v viiv iv v - iivvi vv i i L1ME4c_3end#L 572 ATAATTATGAAGACTATGTAGCAACATGGAAA-ATGTTTATGATATAATG 620 chr2ptel1M 673731 CTGAGTGAAATGAGCAGAA 673749 i i vi L1ME4c_3end#L 621 TTAAGTGAAAAAAGCAGAA 639 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 45.28 CpG sites = 51, Kimura (unadjusted) = 47.46 Transitions / transversions = 1.31 (51/39) Gap_init rate = 0.02 (5 / 265), avg. gap size = 1.20 (6 / 5) 22 0.00 0.00 0.00 chr2ptel1M 675135 675158 (324842) (A)n#Simple_repeat 1 24 (0) m_b73s252i0 2684 chr2ptel1M 675135 AAAAAAAAAAAAAAAAAAAAAAAA 675158 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAA 24 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 17 20.11 4.92 3.23 chr2ptel1M 675315 675375 (324625) (TATA)n#Simple_repeat 1 62 (0) m_b73s252i1 2685 chr2ptel1M 675315 TATACATGT-TAAATATGT-TAAAGTATATGT-TAAATACTATATATATA 675361 i i - v i - v - i - v - (TATA)n#Simpl 1 TATATATATATATATATATATATA-TATATATATATATA-TATATATATA 48 chr2ptel1M 675362 TGTACATATTTATA 675375 i i v (TATA)n#Simpl 49 TATATATATATATA 62 Matrix = Unknown Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.08 (5 / 60), avg. gap size = 1.00 (5 / 5) 13 24.03 0.00 0.00 chr2ptel1M 676401 676435 (323565) (TTTC)n#Simple_repeat 1 35 (0) m_b73s252i3 2686 chr2ptel1M 676401 TTTCTCTGTGTCTCTCTTTCCTTCCCTCTTTCTTT 676435 i v v i i ii (TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT 35 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 486 24.14 0.74 7.94 chr2ptel1M 679163 679297 (320703) MIRc#SINE/MIR 2 127 (141) m_b73s601i3 2687 chr2ptel1M 679163 GAGGCAGCTAGTTGGCATAGTGTATAGAGCATCAGCCCTGAAGTCATGAG 679212 - i-- iii v v iii v i i v i MIRc#SINE/MIR 2 GAGGCAG-TG--TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr2ptel1M 679213 GACCTGAGTTCAAATCTGGCCTCAGATACTTAATACTTCCTGGATGTGTG 679262 i i i iv v v vi ------- i v MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTG 91 chr2ptel1M 679263 ACCTTGGGCAAGTCATTTAACCCCAATT-GCCTCAG 679297 i i vv v- MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 28.40 CpG sites = 18, Kimura (unadjusted) = 29.56 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.08 (11 / 134), avg. gap size = 1.00 (11 / 11) 316 24.83 7.39 1.61 chr2ptel1M 679311 679486 (320514) L1M4_orf2#LINE/L1 748 933 (2361) m_b73s551i4 2688 chr2ptel1M 679311 TGGAAACCAAGTAATATA-----AAACTAAAGAATGGG-CAAAGAACAAA 679354 ii ii i i ----- - vv - v L1M4_orf2#LIN 748 TGGAAATTAAACAACACACTCCTAAA-TAACCAATGGGTCAAAGAAGAAA 796 chr2ptel1M 679355 TCATAGAACCAATT------TCATTAAAGA-GAATGAAAACAATGAGATA 679397 i iiivv ------ vv vi - i vi v i L1M4_orf2#LIN 797 TCACAAGGGAAATTAGAAAATACTTTGAGATGAATGAAAACGAAAACACA 846 chr2ptel1M 679398 ACATAACAAAATTCATGGGATGAAGCCAAAGCAGTATGTACAGGAAATTT 679447 v i i v ? iiv v i v L1M4_orf2#LIN 847 ACATACCAAAACTTATGGGATGCAGCNAAAGCAGTGCTTAGAGGGAAATT 896 chr2ptel1M 679448 TATATTTCTAAATGTTTACATCAATATAATGGAGAAAGA 679486 vi v ii i i - - v i L1M4_orf2#LIN 897 TATAGCTGTAAATGCCTATATTAA-A-AAAGAAGAAAGA 933 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 30.17 CpG sites = 25, Kimura (unadjusted) = 31.03 Transitions / transversions = 1.39 (25/18) Gap_init rate = 0.04 (7 / 175), avg. gap size = 2.29 (16 / 7) 337 23.81 0.00 4.10 chr2ptel1M 679345 679471 (320529) L1P4_orf2#LINE/L1 799 920 (2374) m_b73s551i5 2688 chr2ptel1M 679345 AAAGAACAAATCATAGAACCAATTTCATTAAAGAGAATGAAAACAATGAG 679394 i v v v i ----- v i iv? iv v L1P4_orf2#LIN 799 AAGGCAGAAATCAAAAAA-----TTCTTTGAAATNAATGAAAACAGAGAC 843 chr2ptel1M 679395 ATAACATAACAAAATTCATGGGATGAAGCCAAAGCAGTATGTACAGGAAA 679444 i v iiv v ? i vv v L1P4_orf2#LIN 844 ACAACATACCAAAATCTCTGGGATGCAGCNAAAGCAGTGTTAAGAGGAAA 893 chr2ptel1M 679445 TTTTATATTTCTAAATGTTTACATCAA 679471 v viv i ii L1P4_orf2#LIN 894 GTTTATAGCGCTAAACGCCTACATCAA 920 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 27.04 CpG sites = 13, Kimura (unadjusted) = 29.29 Transitions / transversions = 0.81 (13/16) Gap_init rate = 0.04 (5 / 126), avg. gap size = 1.00 (5 / 5) 13 19.49 0.00 2.78 chr2ptel1M 679790 679826 (320174) (AAAAC)n#Simple_repeat 1 36 (0) m_b73s252i4 2689 chr2ptel1M 679790 AAAATAATACTTAAAAATACAAAAACAAAACAAAACA 679826 i v vv v v - (AAAAC)n#Simp 1 AAAACAAAACAAAACAAAAC-AAAACAAAACAAAACA 36 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 259 28.09 0.00 0.00 chr2ptel1M 679871 679959 (320041) L1MD_orf2#LINE/L1 1396 1484 (1810) m_b73s551i6 2690 chr2ptel1M 679871 CCTAAGAAAAAATATTTAGGACTAGATGGATTTACAGGGGAATTTTACAA 679920 i i i v ii v i v i v i i v L1MD_orf2#LIN 1396 CCCAAAAAGAAATCTCCAGGCCCAGATGGTTTCACTGGAGAATTCTACCA 1445 chr2ptel1M 679921 AACATTTAAAGAACAATTCATTCTAAAACTATATAAACT 679959 i v v iv i vv i i v L1MD_orf2#LIN 1446 AACGTTTAAAGAAGAATTAACACCAATTCTACACAATCT 1484 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 34.16 CpG sites = 14, Kimura (unadjusted) = 35.93 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.00 (0 / 88), avg. gap size = 0.0 (0 / 0) 309 23.68 0.00 0.00 chr2ptel1M 680246 680321 (319679) C L1M3_orf2#LINE/L1 (586) 2702 2627 m_b73s551i7 2691 chr2ptel1M 680246 TCTCCTCTGTTCCACTGATCTGTATTTCTATTTCTTAGCTAGTACCATAT 680295 vi i i i v i i vv i i C L1M3_orf2#LIN 2702 TCTATTCTGTTCCATTGGTCTATATGTCTGTTTTTATGCCAGTACCATAC 2653 chr2ptel1M 680296 GGTTTTGATAATTATAGCTTTACAAT 680321 v v i i ii C L1M3_orf2#LIN 2652 TGTTTTGATTACTGTAGCTTTGTAAT 2627 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 29.40 CpG sites = 12, Kimura (unadjusted) = 29.40 Transitions / transversions = 2.00 (12/6) Gap_init rate = 0.00 (0 / 75), avg. gap size = 0.0 (0 / 0) 662 22.22 1.98 1.98 chr2ptel1M 680395 680596 (319404) C L1M5_orf2#LINE/L1 (1444) 1850 1649 m_b73s551i8 2692 chr2ptel1M 680395 AGTGTTTTTAATAAGAATGAGTATTGAATTTTGTCAAAAGCTTTTTTTGC 680444 v vi v i i v i C L1M5_orf2#LIN 1850 AGAGTTTTTATCATGAATGGGTGTTGAATTTTGTCAAATGCTTTTTCTGC 1801 chr2ptel1M 680445 ATCTATAGCCATGATCATAGAATTTTTGTTACTTTTAT--TGCTGATATA 680492 v vv vi v -- i -- i i i C L1M5_orf2#LIN 1800 ATCTATTGAGATGATCATATGATTTTTCT--CCTTTATTCTGTTAATATG 1753 chr2ptel1M 680493 ATCAATCATATT--CTGAGTTTTCCTTTTGTTAAACCATCCTTGCATTCC 680540 i v i i --i -- i vvv v C L1M5_orf2#LIN 1752 GTGAATTACATTGATTGA--TTTTCGAATGTTAAACCAACCTTGCATTCC 1705 chr2ptel1M 680541 TTGTAGAAATCCCACTTGATCACAATGTACAGTCTTTATAATATATTATT 680590 v v v i i ii ivi i v v ii C L1M5_orf2#LIN 1704 TGGGATAAACCCCACTTGGTCATGATGTATTATCCTTTTTATATATTGCT 1655 chr2ptel1M 680591 GGAATC 680596 v C L1M5_orf2#LIN 1654 GGATTC 1649 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 26.61 CpG sites = 23, Kimura (unadjusted) = 26.61 Transitions / transversions = 1.10 (23/21) Gap_init rate = 0.03 (6 / 201), avg. gap size = 1.33 (8 / 6) 542 32.15 8.43 0.54 chr2ptel1M 680717 681060 (318940) L1ME4c_3end#LINE/L1 185 555 (275) m_b73s551i9 2693 chr2ptel1M 680717 TGAGACGCCACCCCACACCTCTCAGATGGGCTAAAATGACAGGAAAAGAT 680766 ii iiii i v i i vi v vvv ii vv L1ME4c_3end#L 185 TGAGATACCATTTTACGCCTATTAAATTAGCAAAAATTTAAAAAATTGAT 234 chr2ptel1M 680767 AATGATAAATGTTGGAGGGGATGTGGGAAAACTGGAACACTAATGCATTC 680816 iviv i v i ? i vi v ? v i v L1ME4c_3end#L 235 AATACCCAATGCTGGCGAGGNTGCGGTGAAACTGGTACNCTCATACATTG 284 chr2ptel1M 680817 TTGGTGGAGTTCTGAAAT----CATCCATTCTGGAAA--AGTTTGGAACT 680860 i vi? v i v ---- v v i -- i v v L1ME4c_3end#L 285 CTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGGCAAT 334 chr2ptel1M 680861 ATGCCCAAAGAGGTATAAAACTGTGCATACCCTTTGATCCAGCAG-TCTT 680909 i iviv vi v v i i i- iv L1ME4c_3end#L 335 ACGTATCAAGAGCCATAAAAATGTTCATACCCTTTGACCCAGTAATTCCA 384 chr2ptel1M 680910 CTTATTGGTGTTATATCCCAAAGAGATCATAGAAAAGAGAGAAGGACCCA 680959 v v vi - i i i v vv ii ii v i L1ME4c_3end#L 385 CTTCTGGGAATT-TATCCTAAGGAAATAATTCAAAAGAAGGAAAAAGCTA 433 chr2ptel1M 680960 ----CACA------------GCAGC------CCTAATGGCAAGGAAGTGG 680987 ---- i------------ ------iv i i ii v L1ME4c_3end#L 434 TATGCACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGG 483 chr2ptel1M 680988 AAACTGAGTGGACACCCATCAGCTGAAAAATAGCTGAATTAAGTTATGGT 681037 vivv ii iii v iiv iii i i - v i L1ME4c_3end#L 484 AAACAACCTAAATGTCCAACAATAGGGGAATGGTT-AAGTAAATTATGGT 532 chr2ptel1M 681038 ACATGAATGTTATAGAATATTAT 681060 v? iviv i L1ME4c_3end#L 533 ACATCNACTCGATGGAATATTAT 555 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 40.91 CpG sites = 64, Kimura (unadjusted) = 44.10 Transitions / transversions = 1.39 (64/46) Gap_init rate = 0.02 (8 / 343), avg. gap size = 3.88 (31 / 8) 22 11.68 4.08 2.00 chr2ptel1M 681310 681358 (318642) (TCCTTTT)n#Simple_repeat 1 50 (0) m_b73s252i5 2694 chr2ptel1M 681310 TCTTTTTTCCTTTTTCCTTTTTTTCTTTTT--TTTCTCGTTTTTCCCTTT 681357 i - i -- i v i (TCCTTTT)n#Si 1 TCCTTTTTCCTTTTTCC-TTTTTCCTTTTTCCTTTTTCCTTTTTCCTTTT 49 chr2ptel1M 681358 T 681358 (TCCTTTT)n#Si 50 T 50 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.04 (2 / 48), avg. gap size = 1.50 (3 / 2) 273 35.89 5.76 5.44 chr2ptel1M 682710 683039 (316961) C MamRTE1#LINE/RTE-BovB (506) 3306 2976 m_b73s601i4 2695 chr2ptel1M 682710 GGACCCCAGTGTCTGGT-ACCTTATCCTGCCAAGAAATCTTCAGAATCTT 682758 i iv - - i i i i vvv v v v vvi C MamRTE1#LINE/ 3306 GGACCTCGTTGT-TGGTGATCCTGTCTTGCCATTTAATGTTAAGTATGGC 3258 chr2ptel1M 682759 CCCAAGACAACTCAAATGGAAGCAATTCGGGTTCCTGGCCTGGTGCTGCG 682808 i vv iii v vi i - vii ii v----i v i ivi C MamRTE1#LINE/ 3257 TCGTAGGTGACGCTGATGAAA-CTGCTCAAGA----AGCCGGATGTGACG 3213 chr2ptel1M 682809 ATCATAGCAGATTTCCCAGGTAT-ACAACCATG----AGGT----CAGCA 682849 viii i i --- v - i i i---- ---- ? i C MamRTE1#LINE/ 3212 TCTGTGGCAGGT---CCAGGTCTCACAGCCGTANAGAAGGTTGGACANCG 3166 chr2ptel1M 682850 CAATGACTCTGCGGACCTCCAGTTGGGTGGTCAGTCCGAGATTTCT-CCT 682898 v vi ii ii --- v --- v vv - v C MamRTE1#LINE/ 3165 CTATCGCTCTGTAGACCTTTAGTT---TGGTCTG---GAGCTTGATGCCA 3122 chr2ptel1M 682899 C-TT----CCACACTTT-TCTTCAGAGCCTCCCAAACACTGAGCTAGCTC 682942 - ---- i - v v- viviiv i ii C MamRTE1#LINE/ 3121 CGTTGGCGCCACACTCTGTCTGCC-AGCCTCCCAAAGGACATGCTGGCCT 3073 chr2ptel1M 682943 TGACTATGTGGAGGCCAACCTCCTTATCAGTGTGCACATCCCTGGAAAGT 682992 vviv vi vvvi v i i i ?i vv ii vi v i C MamRTE1#LINE/ 3072 TCTTGATTCGGTTTTCTACTTCTTTGTCNATCAGTGCATCATTGGACAGC 3023 chr2ptel1M 682993 GTCCCACTGAGG--GGAGAGCTGATCCACAGCTTTCAACCTTCTCCATT 683039 v ii iv -- v ii viviv i -- vi C MamRTE1#LINE/ 3022 GTGCTGCCTAGGTAGCAGAATTCGGTGACAGCTTTCAGC--TCTGTATT 2976 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 46.50 CpG sites = 62, Kimura (unadjusted) = 50.93 Transitions / transversions = 1.24 (62/50) Gap_init rate = 0.08 (27 / 329), avg. gap size = 1.37 (37 / 27) 221 30.25 9.88 0.00 chr2ptel1M 684477 684638 (315362) L2b_3end#LINE/L2 288 465 (1) m_b73s601i5 2696 chr2ptel1M 684477 AACCCT-CCCTTCCATACTGTGGAAAGCTTGTTTGG--ACAGGTCT---- 684519 ii - v iv v vv v?v i ?-- v ---- L2b_3end#LINE 288 AGTCCTACCCTGCCACTCTGGGTTATNATTGTCTGNTTACATGTCTGTCT 337 chr2ptel1M 684520 CCCCCTTTACACTGGGAGATTC-TGGGGG-AGGGGTC----CTG-CTT-T 684561 vi v v v i - i - ii ---- - - L2b_3end#LINE 338 CCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCTTGT 387 chr2ptel1M 684562 TCCCCTCCCTTTCTATGGAGTTT-GAACAGTGTCTGGCACAGAGTAGGGT 684610 v v iv v ivii v ii - v ? i v vv L2b_3end#LINE 388 TCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCG 437 chr2ptel1M 684611 TTTTCTGATTTCTTGTTGATTTAAAGAA 684638 i ivv i v vi v v v L2b_3end#LINE 438 CTCAGTAAATATTTGTTGAATGAATGAA 465 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 39.80 CpG sites = 20, Kimura (unadjusted) = 39.80 Transitions / transversions = 0.69 (20/29) Gap_init rate = 0.06 (9 / 161), avg. gap size = 1.78 (16 / 9) 347 29.91 4.87 2.26 chr2ptel1M 686107 686537 (313463) L1M5_orf2#LINE/L1 2853 3294 (0) m_b73s551i10 2697 chr2ptel1M 686107 CCACCTAACACCATCTACCAAGATAAGGTCGAAGTGG-TCAT-GATCTAG 686154 i v vi v i v iv ? ii - - i i L1M5_orf2#LIN 2853 CTACCTCACACCATACACAAAAATTAATTCNAGATGGATCATAGACCTAA 2902 chr2ptel1M 686155 ACATAAAGAATGACATTCTAAACAAATTAGAAGAA--CATAGGATAGTTG 686202 ii ii? i v i v vvvvi -- v i -- L1M5_orf2#LIN 2903 ATGTAAAAGNTAAAACTATAAAACTTCTAGAAGAAAACATAGGAGAAT-- 2950 chr2ptel1M 686203 ACCTCTCAGATCTGTAGAGTAGG-AAGGAATTTGTGACCAAAGAACAACT 686251 i iivv i - i i? - i v iv i v iiiv vv L1M5_orf2#LIN 2951 ATCTTCGTGACCT-TGGGNTAGGCAAAGATTTCTTAAACAGGACACAAAA 2999 chr2ptel1M 686252 AG---AGATCATCATTAATATAAAATAGATAATTTTGATTATATTAAA-T 686297 ---?i i v -- v v v v v i ?i i - L1M5_orf2#LIN 3000 AGCACNAACCATAA--AAGAAAAAATTGATAAATTGGACTNCATCAAAAT 3047 chr2ptel1M 686298 TAAAAAAAATTGT--ATAAATAAAACTAATGTAGACAATATTAGAAGGGA 686345 vvvi i--? v - i - vi vi v v v i v L1M5_orf2#LIN 3048 TAAAAACTTCTGCTCNTCAA-AAGAC-ACCGTTAAGAAAATGAAAAGGCA 3095 chr2ptel1M 686346 AGCAATAAACTGGGAAAACATTTTTACAGTCAAAGGT-TCTGATAAAGGC 686394 v i i ? i v v i i?- v vi - i v L1M5_orf2#LIN 3096 AGCCACAGANTGGGAGAAAATATTTGCAAN-ACATATATCTGACAAAGGA 3144 chr2ptel1M 686395 CTCATTTCCAAAATATATAAAGAATT-----GACTCTACAAGAATTCAAG 686439 i v i i -----i ? v i ? --v L1M5_orf2#LIN 3145 CTCGTATCCAGAATATATAAAGAACTCCTACAANTCAATAANAA--AAAG 3192 chr2ptel1M 686440 CCATTC--TCCAATTGATAAATGGTCAAAGAATATGAAGAGGCAATTTTC 686487 v vv --i v? v v ii iv v i v iv L1M5_orf2#LIN 3193 ACAAACAACCCAATANAAAAATGGGCAAAAGACTTGAACAGACACTTCAC 3242 chr2ptel1M 686488 AGATGAAGAAACTGAAACTTTC--TAGTCATATGAAAAGATGCTCCAAAT 686535 i v v i?v ivvi -- iv i v v? L1M5_orf2#LIN 3243 AAAAGAAGATATNCAAATGGCCAATAAGCACATGAAAAGATGCTCAACNT 3292 chr2ptel1M 686536 CA 686537 L1M5_orf2#LIN 3293 CA 3294 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 39.13 CpG sites = 63, Kimura (unadjusted) = 40.34 Transitions / transversions = 1.00 (63/63) Gap_init rate = 0.05 (21 / 430), avg. gap size = 1.48 (31 / 21) 1043 27.05 5.15 5.54 chr2ptel1M 686401 686944 (313056) L1ME3Cz_3end#LINE/L1 7 548 (449) m_b73s551i11 2697 chr2ptel1M 686401 TCCAAAATATATAAAGAATT-----GACTCTACAAGAATTCAAGCCATTC 686445 i i -----i v v i --v v --v L1ME3Cz_3end# 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAA--AAAGACA--A 52 chr2ptel1M 686446 TCCAATTGATAAATGGTCAAAGAATATGAAGAGGCAATTTTCAGATGAAG 686495 i v v v i v iv v i L1ME3Cz_3end# 53 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chr2ptel1M 686496 AAACTGAAACTTTC--TAGTCATATGAAAAGATGCTCCAAATCACTATTG 686543 ivi ivvi -- iv v vv v i L1ME3Cz_3end# 103 AAACCCGAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTA 152 chr2ptel1M 686544 ATCAGGAAAATGCCAATTAAGACAAGTCTGAAATACCACTACACATTC-T 686592 i v i ? vvv i i v ii - L1ME3Cz_3end# 153 ATCAGGGAAATGCAAATTAAAACNACAATGAGATACCATTTCACACCCAT 202 chr2ptel1M 686593 CAGATTGGA-------TAAGA----GACAGGAAAAGATAATGATGAAAGT 686631 v------- i ---- iv vv ii iv ii iii L1ME3Cz_3end# 203 CAGATTGGCAAAAATTTAAAAGTCTGACAATACCAAGTGTTGGCGAGGAT 252 chr2ptel1M 686632 -TGGAGGAAAACTGGGACACTGATATATTGTTGGTGGAGTTGTGAATTCC 686680 - -- v i v v i i i iiv i -- L1ME3Cz_3end# 253 GTGGAG--AAACGGGAACTCTCATACACTGCTGGTGGGAGTGTAAATT-- 298 chr2ptel1M 686681 ACCAATCTGTAATCCAACCATTCTGGAGAGAGATTTGGAACTATGCTCAA 686730 -------v --- i i vi v v - viv L1ME3Cz_3end# 299 -------GGTA---CAACCACTTTGGAGAGCAATTTGGCAATAT-CTAGT 337 chr2ptel1M 686731 AAAGTTATCAAACTGTGCAGACCCTTTGATCCAGCAGTGGATCCAGCAAC 686780 i-- iv i v vi i i --- - vv L1ME3Cz_3end# 338 AAAGTTG--AAGATGCGCATACCCTACGACCCAGCAAT---TCCA-CTTC 381 chr2ptel1M 686781 TGGGCTTATATCTCAAAGAGA---TCTTAAAGGAGGGAAAGGGACCCACA 686827 i iv i ii i i --- vi v v v viv ii--- L1ME3Cz_3end# 382 TAGGTATATACCCTAGAGAAACTCTCGCACATGTGCACAAGGAG---ACA 428 chr2ptel1M 686828 TGTGTAAAAATGTTTGTGGCAGCCCTTGTTGTAATGGCAAGAAACTGAAA 686877 ii ii ii v vi vv i i i i i L1ME3Cz_3end# 429 TGTACAAGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAA 478 chr2ptel1M 686878 A----CTGAGTGGACCCATCAGTTGGGGAATGACTGAATAAATT-TCGTA 686922 ---- i i --i i v iv i - v L1ME3Cz_3end# 479 ACAACCTAAATG--TCCATCAATAGGGGAATGGATAAATAAATTGTGGTA 526 chr2ptel1M 686923 TATGAATATTATGGAATATTAT 686944 vv iv i L1ME3Cz_3end# 527 TATTCATACAATGGAATACTAT 548 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 32.79 CpG sites = 78, Kimura (unadjusted) = 34.29 Transitions / transversions = 1.28 (78/61) Gap_init rate = 0.07 (39 / 543), avg. gap size = 1.49 (58 / 39) 278 29.03 3.64 3.95 chr2ptel1M 688653 688982 (311018) C L1PREC2_orf2#LINE/L1 (616) 2678 2350 m_b73s551i12 2698 chr2ptel1M 688653 TTTTCTTAGCCAGTATCATATGGTATTAATGATT--AGCCCCTTATATAT 688700 iv - i iiv v ii v i -- iv -i C L1PREC2_orf2# 2678 TTTTTGTA-CCAGTACCATGCTGTTTTGGTTACTGTAGCCCTGTA-GTAT 2631 chr2ptel1M 688701 AGTGTGAGCTCTGGTAGTGTAAAGCCACCTTCCTTTGTATTTTTTTTTCA 688750 v iv v i i v v vv - vi vi i C L1PREC2_orf2# 2630 AGTTTGAAGTCGGGTAGCGTGATGCCTCCAGC-TTTGTTCTTTTTGCTTA 2582 chr2ptel1M 688751 TTAATTCCTTTGATATTCTTGACCTTTTGTTCTTTCAGATGAATTTTATT 688800 vv v v v v vv vi v vv i v vv C L1PREC2_orf2# 2581 GGATTGCCTTGGCTATTCGGGCTCTTTTTTGGTTCCATATGAATTTTAAA 2532 chr2ptel1M 688801 ATGTTTTTTTTTTCTGGTTTTATAAAATAATTTTTTTGCTAGTTTGATTG 688850 iv --- i i i i i- v iv v v C L1PREC2_orf2# 2531 ATAGTTTTTT---CTAGTTCTGTGAAG-AATGTCATTGGTAGTTTGATAG 2486 chr2ptel1M 688851 ATATGGCACTTAATAAGTAAATTCATTTAGACAGT-----CATTTTTTAT 688895 iv i i v vv vv i i ----- - v i C L1PREC2_orf2# 2485 GAATAGCATTGAATCTGTAAATTGCTTTGGGCAGTATGGCCA-TTTTAAC 2437 chr2ptel1M 688896 TATATTGCCTTGGCCTACCCATGAGCAATTACTTTTTTCTCCAATTGTTT 688945 v vi ivv i vvv v v - v C L1PREC2_orf2# 2436 GATATTGATTCTTCCTATCCATGAGCATGGAATGTTTT-TCCATTTGTTT 2388 chr2ptel1M 688946 -----AAATTTGACTTTATCTTGCAAGAACTGTTTTGTAATT 688982 ----- vv i i --- -ii v v C L1PREC2_orf2# 2387 GTGTCATCTCTGATT---TCTT-TGAGCAGTGTTTTGTAATT 2350 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 35.83 CpG sites = 37, Kimura (unadjusted) = 36.78 Transitions / transversions = 0.67 (37/55) Gap_init rate = 0.05 (16 / 329), avg. gap size = 1.56 (25 / 16) 915 29.25 3.56 0.93 chr2ptel1M 689046 689466 (310534) C L1M4_orf2#LINE/L1 (1057) 2237 1806 m_b73s551i13 2699 chr2ptel1M 689046 TTGGTTATATATAGAAATGCTGGTGATTTATCTGGGCTTATTTTATAGCA 689095 v vi i i viv v v ivii v i i v v C L1M4_orf2#LIN 2237 TTGCTAGTGTATAGAAATACAATTGATTTTTGTATATTGATCTTGTATCC 2188 chr2ptel1M 689096 TGCAACTTTACTAAAGTTGTTAATTATTTTGAGTAGTTTTGTAGTTGATT 689145 i i i v i v v iv i v ? v C L1M4_orf2#LIN 2187 TGCAACCTTGCTGAACTCGTTTATTAGTTCTAATAGTTTTTTNGTGGATT 2138 chr2ptel1M 689146 CTCTAAG----TATACCCACTATATCATATCATACTGCCAAGAGCAATAG 689191 ii i ---- v ivi v v i - v v vi C L1M4_orf2#LIN 2137 CCTTAGGATTTTCTATATACAAGATCATGTCAT-CTGCGAATAGAGATAG 2089 chr2ptel1M 689192 TTTTGTTTCCTCATGATCCATTCTC-ATTCCTTCAATTTCTTTTCCCTCT 689240 ii i v v- v v- v iv i i vi C L1M4_orf2#LIN 2088 TTTTACTTCTTCCTT-TCCAATCTGGATGCCTTTTATTTCTTTTTCTTGC 2040 chr2ptel1M 689241 CTTATTGCTATAGCTAGCATTTTTTGTACAACATGGAATAACAGTGGTGA 689290 v iv i v ii iiv ii v iv i C L1M4_orf2#LIN 2039 CTAATTGCCCTGGCTAGAACCTCCAGTACAATGTTGAATAGAAGTGGCGA 1990 chr2ptel1M 689291 CAATGGGCATCCTTGTTTTGCTCCTGATCTTATTGGGAAGGCTTCTAG-- 689338 v ii i i i vv i ? ii -- C L1M4_orf2#LIN 1989 GAGCGGACATCCTTGTCTTGTTCCTGATCTTAGGGGGAAAGCNTTCAGTC 1940 chr2ptel1M 689339 -------ATTACGGATAATGCTTGTTGGTGGTTTTAGATAGATATTAATT 689381 ------- v v i i v i vv vvi iiivv C L1M4_orf2#LIN 1939 TTTCACCATTAAGTATGATGTTAGCTGTGGGTTTTTCGTAGATGCCCTTT 1890 chr2ptel1M 689382 ATCATTTTAAGGAATGCTTCCTT-TATTCCTGTGCTCTCCAGTGTTTTTT 689430 vv i - i i - ivvi v iv - C L1M4_orf2#LIN 1889 ATCAGGTTGAGGAA-GTTCCCTTCTATTCCTAGTTTGTTGAGTG-TTTTT 1842 chr2ptel1M 689431 ATTAGGAATGGTTGCTGTATTTTGTCAAAAGCTTCT 689466 i v v v i v v i C L1M4_orf2#LIN 1841 ATCATGAAAGGGTGTTGGATTTTGTCAAATGCTTTT 1806 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 36.33 CpG sites = 63, Kimura (unadjusted) = 37.87 Transitions / transversions = 1.07 (63/59) Gap_init rate = 0.02 (9 / 420), avg. gap size = 2.11 (19 / 9) 18 0.00 0.00 0.00 chr2ptel1M 690468 690487 (309513) (T)n#Simple_repeat 1 20 (0) m_b73s252i6 2700 chr2ptel1M 690468 TTTTTTTTTTTTTTTTTTTT 690487 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTT 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 226 21.57 3.92 0.00 chr2ptel1M 690488 690538 (309462) C MIR#SINE/MIR (139) 123 71 m_b73s601i6 2701 chr2ptel1M 690488 CTAAAGCA-ATTGGAGTTAAGTGACTTGCCCT-GATCACACAGCTAGGAA 690535 i i - vv ii i v- i v C MIR#SINE/MIR 123 CTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAA 74 chr2ptel1M 690536 ATG 690538 i C MIR#SINE/MIR 73 GTG 71 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 26.03 CpG sites = 7, Kimura (unadjusted) = 26.03 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.04 (2 / 50), avg. gap size = 1.00 (2 / 2) 238 15.00 2.50 0.00 chr2ptel1M 690499 690538 (309462) C MIRc#SINE/MIR (153) 115 75 m_b73s601i7 2701 chr2ptel1M 690499 GGAGTTAAGTGACTTGCCC-TGATCACACAGCTAGGAAATG 690538 ii -v i v i C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTG 75 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 17.02 CpG sites = 4, Kimura (unadjusted) = 17.02 Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1) 247 26.98 23.02 0.00 chr2ptel1M 691529 691654 (308346) L3#LINE/CR1 3251 3405 (694) m_b73s601i8 2702 chr2ptel1M 691529 ATGTTGGATAACAG--TCAGAATCCACAAAGACCTTG------------- 691563 i ? i -- ii i v ? i i ------------- L3#LINE/CR1 3251 ACGNTGGATGACAGAATCAAGATTCAAAANGATCTCGACAGGCTGGAACG 3300 chr2ptel1M 691564 ----GCCAAATCCAATAAGGTGAAGCTTAAAATGGGTAACTGTCAAGTTA 691609 ---- i v i i ii v v i v v iv L3#LINE/CR1 3301 ATGGGCCGAAACCAACAAGATGAAATTTAACAGGGATAAATGTAAAGTCC 3350 chr2ptel1M 691610 -AAATTTAGATTTTAAAAATC--TT-------TACAAAATCAAGAAGGTA 691649 -iv i iv --i ------- ii vi i i v L3#LINE/CR1 3351 TGCATTTAGGTTCAAAAAATCAACTGCACAAGTACAGGATGGAGAGGATC 3400 chr2ptel1M 691650 TGGCT 691654 L3#LINE/CR1 3401 TGGCT 3405 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 31.79 CpG sites = 23, Kimura (unadjusted) = 35.66 Transitions / transversions = 2.09 (23/11) Gap_init rate = 0.05 (6 / 125), avg. gap size = 4.83 (29 / 6) 241 27.69 0.00 0.00 chr2ptel1M 692118 692182 (307818) MamRTE1#LINE/RTE-BovB 3138 3202 (610) m_b73s601i9 2703 chr2ptel1M 692118 ACCAAACTGAAGGTCTGCAAAGCCTTTGTGCTGGCCCTATTGTTGTGTGC 692167 i i i vv v i ? v vvvi vi ? ii v MamRTE1#LINE/ 3138 ACCAAACTAAAGGTCTACAGAGCGATAGCGNTGTCCAACCTTCTNTACGG 3187 chr2ptel1M 692168 CTGTGGGACCTGGAC 692182 i MamRTE1#LINE/ 3188 CTGTGAGACCTGGAC 3202 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 31.63 CpG sites = 9, Kimura (unadjusted) = 36.39 Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0) 12 4.75 0.00 8.33 chr2ptel1M 692529 692554 (307446) (GGGA)n#Simple_repeat 1 24 (0) m_b73s252i7 2704 chr2ptel1M 692529 GGGAGGGGGTGGAGGGAGGGAAGGGA 692554 i - - (GGGA)n#Simpl 1 GGGAGGGAG-GGAGGGAGGG-AGGGA 24 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.08 (2 / 25), avg. gap size = 1.00 (2 / 2) 20 12.24 0.00 0.00 chr2ptel1M 693553 693588 (306412) (AGACTCC)n#Simple_repeat 1 36 (0) m_b73s252i8 2705 chr2ptel1M 693553 AGACTCGAGGCTCCAGATTCCAGACTCCGGACTCCA 693588 v i i i (AGACTCC)n#Si 1 AGACTCCAGACTCCAGACTCCAGACTCCAGACTCCA 36 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 314 26.75 2.27 2.27 chr2ptel1M 695267 695354 (304646) L2c_3end#LINE/L2 379 466 (12) m_b73s601i10 2706 chr2ptel1M 695267 GTGAGACCCCTGACAGCAGGGTCTGTG--CTGCTCCTCCCTCTGTATCTC 695314 vi i vi v i --i ii v -- i i L2c_3end#LINE 379 GTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCAT--CTTTGTATCCC 426 chr2ptel1M 695315 TAGCACTTTGCACACAGTAGGTGCTCACTCAGTGTTTTTT 695354 i i i v i i v v i v L2c_3end#LINE 427 CAGCGCCTGGCACATAGTAGGCGCTCAATAAATGTTTGTT 466 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 28.97 CpG sites = 15, Kimura (unadjusted) = 34.30 Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.03 (3 / 87), avg. gap size = 1.33 (4 / 3) 365 29.67 1.10 0.00 chr2ptel1M 695725 695815 (304185) MIRb#SINE/MIR 163 254 (14) m_b73s601i11 2707 chr2ptel1M 695725 CTGTCCCAC-GGGCTGTTGTGAGGCTCAAATGAGGTTATATCTATAGAGT 695773 ii i i - i v i i v iiv i i i MIRb#SINE/MIR 163 CTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGC 212 chr2ptel1M 695774 CCTTAGCCTGGAGCCTGGCACGTAGTAGGCGTTTCACAGATG 695815 v vii v i i i iv i i MIRb#SINE/MIR 213 GCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAAATG 254 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 36.58 CpG sites = 20, Kimura (unadjusted) = 40.51 Transitions / transversions = 2.86 (20/7) Gap_init rate = 0.01 (1 / 90), avg. gap size = 1.00 (1 / 1) 22 7.25 0.00 0.00 chr2ptel1M 696469 696497 (303503) (T)n#Simple_repeat 1 29 (0) m_b73s252i9 2708 chr2ptel1M 696469 TTGTTTTTTTTTTTTTTTTTTTTTTCTTT 696497 v i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 17 5.76 4.76 7.32 chr2ptel1M 696696 696737 (303263) (GGA)n#Simple_repeat 1 41 (0) m_b73s252i10 2709 chr2ptel1M 696696 GGAGGGAGGA-GAGCAGGAGGGAGGA-GAGCAGGAGGGAGGAGG 696737 - - v - - v - (GGA)n#Simple 1 GGA-GGAGGAGGAGGAGGA-GGAGGAGGAGGAGGA-GGAGGAGG 41 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.12 (5 / 41), avg. gap size = 1.00 (5 / 5) 471 28.54 10.86 2.92 chr2ptel1M 696824 697173 (302827) C L2#LINE/L2 (562) 2520 2144 m_b73s601i12 2710 chr2ptel1M 696824 CAGTAACAGGGAGTTAGGAAGAC--CAGAGGGAGTGGGTT--AGGG---- 696865 v ? v i - vi -- i ii ii -- ---- C L2#LINE/L2 2520 CATTNACTGAGA-TGGGGAAGACTGCGGGAGGAGCAGGTTTGAGGGGGAA 2472 chr2ptel1M 696866 --TCGGGAGCTCTGCTTTGGCTGCCTTGGGTTCCAGATGTCTGTGGGGCG 696913 -- i i v i viiiv ii iv i i vi i i C L2#LINE/L2 2471 GATCAGGAGTTCAGTTTTGGACATGTTAAGTTTGAGATGCCTATTAGACA 2422 chr2ptel1M 696914 TCCAGCTGGAGATGG---------------------GAGGTTGGAGGTCA 696942 iv v--------------------- vi v C L2#LINE/L2 2421 TCCAAGTGGAGATGTCGAGTAGGCAGTTGGATATACGAGTCTGGAGTTCA 2372 chr2ptel1M 696943 GCAGA-AGGTCGGGGCAGGAAACACAGGGCTGAGAACCATCAGCAAAAAC 696991 vi - v v i i i iivi i ii v v v C L2#LINE/L2 2371 GGGGAGAGGTCCGGGCTGGAGATATAAATTTGGGAGTCATCAGCATATAG 2322 chr2ptel1M 696992 ATGGCCATTACCTCCATGGGAGCTGG-TGAGATCACCAAGGGAGCAGGC- 697039 ivv vvv i - - ? iii i- C L2#LINE/L2 2321 ATGGTATTTAAAGCCATGAGA-CTGGATGAGATCACCNAGGGAGTGAGTG 2273 chr2ptel1M 697040 TAGAGGAAGAGGAGAAGAGGGTCCAA-GACAGAGCCCTGAGGGGTAC-CC 697087 vii i - - v -- i - C L2#LINE/L2 2272 TAGATAGAGAAGAGAAGA-GGTCCAAGGACTGAGCCCT--GGGGCACTCC 2226 chr2ptel1M 697088 AA-GGTCAGAATTCTAGTCAAGGAGATGGGGGAGGAGAGAGAGAGAGAGA 697136 - v ? -----i ii - i ivv vi ii C L2#LINE/L2 2225 AACGTTNAGA-----GGTCGGGGAGAT-GAGGAGGAACCAGCAAAGGAGA 2182 chr2ptel1M 697137 GAGAGAGAGAG-AGAGAGAGAGACAGAGACACAAACAG 697173 vv ii -i vv v ii iiiv v v C L2#LINE/L2 2181 CTGAGAAGGAGCGGCCAGTGAGGTAGGAGGAAAACCAG 2144 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 36.14 CpG sites = 59, Kimura (unadjusted) = 37.62 Transitions / transversions = 1.55 (59/38) Gap_init rate = 0.07 (23 / 349), avg. gap size = 2.13 (49 / 23) 132 20.80 0.72 0.00 chr2ptel1M 697174 697449 (302551) (AGAG)n#Simple_repeat 1 278 (0) m_b73s252i12 2711 chr2ptel1M 697174 AGACAGAGAGATAGAGAAACAGAGACAAAGACAGAGAGATAGACAGGGAC 697223 v v i v v i v v v i v (AGAG)n#Simpl 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr2ptel1M 697224 AGATAGAGACAGAGAGAGAGAGACAGAGAGAGAGACAGAGACAGAGAAAG 697273 v v v v v i (AGAG)n#Simpl 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 100 chr2ptel1M 697274 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAG-GAGAGAGAGAGAGA-AGGG 697321 - - i (AGAG)n#Simpl 101 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 150 chr2ptel1M 697322 AGGGAGAGACAGAGAAAGAAAAAAAAGGAGGGAGAGAGAGAAGGAGAGGG 697371 i v i i i i ii i ii i (AGAG)n#Simpl 151 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 200 chr2ptel1M 697372 AGGGAGGGGAAGAGACAAAGACAGAGTGACAGAGACAGACAGACAGAGAG 697421 i i ii v i v v v v v v (AGAG)n#Simpl 201 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 250 chr2ptel1M 697422 AGAATCACACGGAGAGACAGAGACAGAG 697449 ivv v vi v v (AGAG)n#Simpl 251 AGAGAGAGAGAGAGAGAGAGAGAGAGAG 278 Matrix = Unknown Transitions / transversions = 0.85 (23/27) Gap_init rate = 0.01 (2 / 275), avg. gap size = 1.00 (2 / 2) 248 32.00 9.52 1.77 chr2ptel1M 697621 697725 (302275) C MIRb#SINE/MIR (7) 261 149 m_b73s601i13 2712 chr2ptel1M 697621 GAACAAGCACTGATTAAGCACCTGCTGTGTGCCCAGCACT---------- 697660 i v v i v i i i i i vi ---------- C MIRb#SINE/MIR 261 GAGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCG 212 chr2ptel1M 697661 TTTTACCAAAAGTTCTCTCCTTCCATCTTCCTGAAGGCCCTGGGGAGGTA 697710 i - vivi v v iv i vii vii v - C MIRb#SINE/MIR 211 CTTTAC-ATGCATTATCTCATTTAATCCTCACAACAACCCTGCG-AGGTA 164 chr2ptel1M 697711 AGTGCTATTATTCCC 697725 i ii i C MIRb#SINE/MIR 163 GGTATTATTATCCCC 149 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 41.97 CpG sites = 21, Kimura (unadjusted) = 43.78 Transitions / transversions = 1.75 (21/12) Gap_init rate = 0.03 (3 / 104), avg. gap size = 4.00 (12 / 3) 13 5.48 15.79 0.00 chr2ptel1M 698295 698332 (301668) (CTCGGC)n#Simple_repeat 1 44 (0) m_b73s252i13 2713 chr2ptel1M 698295 CTCGG-C-CGGCC-CGGCCTCGGCGTCGG-CTC--CCTCGGGCT 698332 - - - v - -- v (CTCGGC)n#Sim 1 CTCGGCCTCGGCCTCGGCCTCGGCCTCGGCCTCGGCCTCGGCCT 44 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.14 (5 / 37), avg. gap size = 1.20 (6 / 5) 39 4.59 0.00 0.00 chr2ptel1M 699459 699503 (300497) (C)n#Simple_repeat 1 45 (0) c_b73s251i0 2714 chr2ptel1M 699459 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCTCCCCCCCGCCCCC 699503 i v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 45 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 17 12.37 1.82 9.80 chr2ptel1M 701082 701136 (298864) (GGGCTG)n#Simple_repeat 1 51 (0) m_b73s252i14 2715 chr2ptel1M 701082 GGGCTCGGGGCCGGGACTGGGG-TGGACAGCTGGGGGTTCGGGGCTGGGA 701130 - i i - --i - i - i (GGGCTG)n#Sim 1 GGGCT-GGGGCTGGGGCTGGGGCTGG--GGCT-GGGGCT-GGGGCTGGGG 45 chr2ptel1M 701131 CTGGGG 701136 (GGGCTG)n#Sim 46 CTGGGG 51 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.11 (6 / 54), avg. gap size = 1.00 (6 / 6) 19 6.07 5.71 0.00 chr2ptel1M 701650 701684 (298316) (CCTCTCT)n#Simple_repeat 1 37 (0) m_b73s252i16 2716 chr2ptel1M 701650 CCTCTCCCCTCTCTCCT-T-TCCCCTCTCCTCTCTCC 701684 i - - i (CCTCTCT)n#Si 1 CCTCTCTCCTCTCTCCTCTCTCCTCTCTCCTCTCTCC 37 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 13 11.21 3.23 3.23 chr2ptel1M 701875 701905 (298095) (CCTC)n#Simple_repeat 1 31 (0) m_b73s252i17 2717 chr2ptel1M 701875 CCTGCCCTCCCTCCCACCC-ACCTCCCTCGCT 701905 - v -v v (CCTC)n#Simpl 1 CCT-CCCTCCCTCCCTCCCTCCCTCCCTCCCT 31 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2) 199 17.95 0.00 0.00 chr2ptel1M 702632 702670 (297330) L3#LINE/CR1 3712 3750 (349) m_b73s601i14 2718 chr2ptel1M 702632 GGAGGCCCAGGAGATGTTTACCCTGGAGAAGAGAAGGCT 702670 i vv v i v i L3#LINE/CR1 3712 GAAGGAACTGGGGATGTTTAGCCTGGAGAAGAGAAGACT 3750 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 20.55 CpG sites = 3, Kimura (unadjusted) = 20.55 Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 185 28.57 3.17 0.00 chr2ptel1M 702914 702976 (297024) MIR3#SINE/MIR 111 175 (33) m_b73s601i15 2719 chr2ptel1M 702914 TCTCTGAGGCTCGGTTTCCT-GGCTGTACAG-GAGATGACTGGACTCCAT 702961 i v i -iv v i- iv ii vv MIR3#SINE/MIR 111 TCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGAT 160 chr2ptel1M 702962 GACCCCCGAGCTCCC 702976 i i ii v MIR3#SINE/MIR 161 GATCTCTAAGGTCCC 175 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 37.12 CpG sites = 11, Kimura (unadjusted) = 37.12 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.03 (2 / 62), avg. gap size = 1.00 (2 / 2) 192 32.61 5.10 3.00 chr2ptel1M 703158 703255 (296745) L2#LINE/L2 2394 2493 (589) m_b73s601i16 2720 chr2ptel1M 703158 AATTGCCGGCTTTTAGAACTTTCCAACTGGAAGCCCTGTAGGCATTTCAG 703207 i vi i--- vv i vi v i ivi i i L2#LINE/L2 2394 AACTGCCTACTC---GACATCTCCACTTGGATGTCTAATAGGCATCTCAA 2440 chr2ptel1M 703208 GCTCTA---GTCCATAAGCGATCTCATGACCTTTCCCTCGGAACC--CTC 703252 i iv --- v vi v v i i iivi -- L2#LINE/L2 2441 ACTTAACATGTCCAAAACTGAACTCCTGATCTTCCCCCTCAAACCTGCTC 2490 chr2ptel1M 703253 CCC 703255 i L2#LINE/L2 2491 CTC 2493 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 42.68 CpG sites = 19, Kimura (unadjusted) = 44.64 Transitions / transversions = 1.58 (19/12) Gap_init rate = 0.05 (5 / 97), avg. gap size = 1.60 (8 / 5) 363 34.04 5.63 5.63 chr2ptel1M 706991 707292 (292708) C L3b_3end#LINE/CR1 (358) 848 547 m_b74s601i3 2721 chr2ptel1M 706991 TTCCCCTCTCACAGGTGAAGCAATTGCCATCAGTCTTCTCCAGACTAAAC 707040 i i - ivi ii i----i - i ------ v C L3b_3end#LINE 848 TTCTCTTCTC-CAGGCTGAATAATC----CCAGT-TCCT------TTAAC 811 chr2ptel1M 707041 CTTGCC-CGCTGCTCCCACTTAAC-GTCATATAACATGATTTCTGTCTTC 707088 v - iiv v i vv - i v v -- v i - v C L3b_3end#LINE 810 CTTTCCTCATAGGTCCCATTTTCCAGCCCTTTA--ATCATTTTTGT-TGC 764 chr2ptel1M 707089 TGCACTTCGGGTCTTTTTCTCGATCTTCAAGGCCTCCAT--AGCTGTGTT 707136 - v i v iv i i ivi? ii v v i i iv -- i? v? C L3b_3end#LINE 763 T-CTCCTCTGAACTCTCTCCAANTTCTCCACGTCCCTTTTAAANTGTGGN 715 chr2ptel1M 707137 GTCCAGAGCTACACCCAGTGCTCCCGGTGTGGCCGAGCCAGGGCAGCAGG 707186 i i iv v i v ? ? vii v - v C L3b_3end#LINE 714 GCCCAGAACTGAACGCAGTACTCCAGNTGNGGCCTGACCAGCGCAG-AGT 666 chr2ptel1M 707187 CATGGGGGCCGTGCGCTTCCCT-------------GTTCCTCTCTAGCTA 707223 viv v v??vv i i -------------i ? i v viv i C L3b_3end#LINE 665 AGAGCGGGANNATCACCTCCCTTGNTCTGTCGGCGATNCTTCTGTTAATG 616 chr2ptel1M 707224 CACCCCAGGAGCCTACAAGGTGGCTGGGGCGCCGCATCAGATTGCTGATT 707273 v i v vi iv v vvi v vv i iv i i C L3b_3end#LINE 615 CAGCCCAAGATCGCATTAGCTTTTTTGGCAGCCGCGTCGCACTGCTGACT 566 chr2ptel1M 707274 CATCCTGAGTTTGCAATCA 707292 vi i ii C L3b_3end#LINE 565 CATATTGAGCTTGCGGTCA 547 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.25 CpG sites = 51, Kimura (unadjusted) = 48.30 Transitions / transversions = 1.11 (51/46) Gap_init rate = 0.07 (21 / 301), avg. gap size = 1.62 (34 / 21) 431 36.80 11.15 0.00 chr2ptel1M 707024 707292 (292708) C L3#LINE/CR1 (356) 3743 3445 m_b74s601i4 2721 chr2ptel1M 707024 TCTTCTCCAGACTAAACCTTGCCCGCTGCTCCCACTTAACGTCATATAAC 707073 i v iv v i v i v ivvv v i C L3#LINE/CR1 3743 TCTTCTCCAGGCTAAACATCCCCAGTTCCTTCAACCGTTCCTCATATGAC 3694 chr2ptel1M 707074 ATGATTTCTGTCTTCTGCAC--TTCGGGTC---TTTTTCTCGAT---CT- 707114 i iivvii v -- i v ---i ii v i--- - C L3#LINE/CR1 3693 ATGGTTTCCAGACCCTTCACCATCCTGGTCGCTCTCCTCTGGACGCGCTC 3644 chr2ptel1M 707115 -------TCAAGG--CCTCCATAGCTGTGTTGTCCAGAGCTACACCCAGT 707155 ------- v -- ivv iv vi i i iv v i C L3#LINE/CR1 3643 CAGTTTGTCAATGTCCCTCTTAAAATGTGGCGCCCAGAACTGAACGCAAT 3594 chr2ptel1M 707156 GCTCCCGGTGTGGCCGAGCCAGGGCAGCAGGCATGGGGGCCGTGCGCTTC 707205 i v i i vii v vivi vv i ii vvv i C L3#LINE/CR1 3593 ACTCCAGATGTGGTCTGACCAGCGCAGAGTACAGCGGGACTATTACCTCC 3544 chr2ptel1M 707206 CCTGTT------------CCTCTCTAGCTACACCCCAGGAGCCTACAAGG 707243 i ? ------------ i v viv i v i i vivi iv v C L3#LINE/CR1 3543 CTTGNTCTGGACACTATACTTCTATTAATGCAGCCTAAGATTGCATTAGC 3494 chr2ptel1M 707244 TGGCTGGGGCGCCGCATCAGATTGCTGATTCATCCTGAGTTTGCAATCA 707292 vvi v vv i v i i ii vi i ii C L3#LINE/CR1 3493 TTTTTTGGCAGCCACATCACACTGTTGGCTCATATTGAGCTTGCGGTCA 3445 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 49.37 CpG sites = 53, Kimura (unadjusted) = 52.38 Transitions / transversions = 1.15 (53/46) Gap_init rate = 0.03 (7 / 268), avg. gap size = 4.29 (30 / 7) 184 20.89 6.33 9.09 chr2ptel1M 708217 708295 (291705) X9_LINE#LINE/L1 91 167 (769) m_b74s601i5 2722 chr2ptel1M 708217 TCCCCAGCATCC-CTAGCTGGGATACCTGATCTGGGCCTCT-TGCT--CA 708262 v v - i v ------- v - -- i X9_LINE#LINE/ 91 TCCCAAGCTTCCGCTAGCCGGGAGAC-------GGGCCTGTCTGCTTTCG 133 chr2ptel1M 708263 CCTTCCCATCACTGGGAGGCTCAGATTC-ACTTA 708295 vi v i ii iv i- X9_LINE#LINE/ 134 GTTTCACACCATCGGGAGGTACAGATTTGACTTA 167 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 19.42 CpG sites = 8, Kimura (unadjusted) = 24.65 Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.14 (11 / 78), avg. gap size = 1.09 (12 / 11) 325 29.67 1.10 0.00 chr2ptel1M 709926 710016 (289984) MIRb#SINE/MIR 18 109 (159) m_b74s601i6 2723 chr2ptel1M 709926 GCTGGAGATAGTGCAGTGGCTCTGGAGACAGA-AAACCCCAGTTCAAATC 709974 v vi v v vv i v - i ivi i MIRb#SINE/MIR 18 GCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCGAATC 67 chr2ptel1M 709975 CAGTTTCAGACATTTCCTAATTGTGTGGCCCTGGACAAGTCA 710016 v vi v v i v ii i i i i MIRb#SINE/MIR 68 CCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTA 109 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.59 CpG sites = 14, Kimura (unadjusted) = 38.35 Transitions / transversions = 1.08 (14/13) Gap_init rate = 0.01 (1 / 90), avg. gap size = 1.00 (1 / 1) 28 7.37 0.00 2.27 chr2ptel1M 712291 712335 (287665) (AAGTGATACA)n#Simple_repeat 1 44 (0) c_b74s251i0 2724 chr2ptel1M 712291 AAGTGGATACAAAGTGATACAAAGAGATAGAAAGAGATACAAAGT 712335 - v v v (AAGTGATACA)n 1 AAGT-GATACAAAGTGATACAAAGTGATACAAAGTGATACAAAGT 44 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 36 29.90 1.78 3.61 chr2ptel1M 713232 713400 (286600) (GGCGG)n#Simple_repeat 1 166 (0) m_b74s252i0 2725 chr2ptel1M 713232 GGAGGGGAGGGG-AGGGCGGGGCTGGCGGCCGGGGAAGGAGGGGCCGGGG 713280 v v -i - - v vii v v v (GGCGG)n#Simp 1 GGCGGGGCGGGGCGGGGCGGGGC-GG-GGCGGGGCGGGGCGGGGCGGGGC 48 chr2ptel1M 713281 AGGGCGGGGCTGGCGGCCGGGGAAGGAGGGGCCGAGGAGGGCGGGGC-TG 713329 i - - v vii v v i vi -v (GGCGG)n#Simp 49 GGGGCGGGGC-GG-GGCGGGGCGGGGCGGGGCGGGGCGGGGCGGGGCGGG 96 chr2ptel1M 713330 G-TGGGCGGGGAAGGAGCCGAGGAAGGCGGGGCGGGGCGGCCACCGGCTG 713378 -v -v i v i vii vvvvv v (GGCGG)n#Simp 97 GCGGGGCGGGG-CGGGGCGGGGCGGGGCGGGGCGGGGCGGGGCGGGGCGG 145 chr2ptel1M 713379 CTCTGGGCGGGGCCGGGGTGGG 713400 vv v - i (GGCGG)n#Simp 146 GGCGGGGCGGGG-CGGGGCGGG 166 Matrix = Unknown Transitions / transversions = 0.50 (13/26) Gap_init rate = 0.05 (9 / 168), avg. gap size = 1.00 (9 / 9) 13 33.38 0.00 0.00 chr2ptel1M 713793 713844 (286156) (AGA)n#Simple_repeat 1 52 (0) m_b74s252i1 2726 chr2ptel1M 713793 AGAAGATGGACACGAAGAAGAAGGAGGAGCAGCTGAAGCTGCTGAAGGAG 713842 v i v v i i v vv vv vv i (AGA)n#Simple 1 AGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAG 50 chr2ptel1M 713843 AA 713844 (AGA)n#Simple 51 AA 52 Matrix = Unknown Transitions / transversions = 0.40 (4/10) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 431 36.22 4.27 1.85 chr2ptel1M 716868 717078 (282922) C MIRb#SINE/MIR (14) 254 39 m_b74s601i7 2727 chr2ptel1M 716868 CACTTATGTTGTGCCTGCTGTGTGCTAGGTCCCGGGCTAAGTGCTGTACA 716917 i vvv i i i i i iv i v i v C MIRb#SINE/MIR 254 CATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACA 205 chr2ptel1M 716918 CAGAGAATCTCATTTGACCCTCAGGAGCAGCACGGGAGGTCAGCGAGGGT 716967 iiv vv i i vi vv v vi v vi iivviv C MIRb#SINE/MIR 204 TGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATT 155 chr2ptel1M 716968 GTCCACGTTGTACAGCGGAGGAAGCTGAAGCAGCCGCAGCGAGG------ 717011 i v i v vv i i ---- v v ------ C MIRb#SINE/MIR 154 ATCCCCATTTTACAGATGAGGAAACTGAGG----CTCAGAGAGGTTAAGT 109 chr2ptel1M 717012 GGCTTGCCTGGGGTCACACC-CGAGCAGCTTCTGAGGTT--GCTTTGAGT 717058 ii iii v- v i iv vviiii ii-- v i ii C MIRb#SINE/MIR 108 AACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAAC 59 chr2ptel1M 717059 CCCGCTCTTCCTGGCTCCAA 717078 v v vi i C MIRb#SINE/MIR 58 CCAGGTCTGTCTGACTCCAA 39 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 47.24 CpG sites = 41, Kimura (unadjusted) = 51.05 Transitions / transversions = 1.21 (41/34) Gap_init rate = 0.03 (7 / 210), avg. gap size = 1.86 (13 / 7) 209 33.99 9.18 0.94 chr2ptel1M 717570 717667 (282333) L2c_3end#LINE/L2 369 474 (4) m_b74s601i8 2728 chr2ptel1M 717570 CCACTGG---GTGAATTTCTTGAGGGCAGGAGACTGTGTGTCCAGCA-CT 717615 i --- ii i - i v ivvv - L2c_3end#LINE 369 CCACTAGACTGTGAGCTCCTTGAGGGCAGG-GACCGTGTCTTATTCATCT 417 chr2ptel1M 717616 CAGAAC-----GTGCCCAGCATGTGGTCAGTGCTTAGGAAATGCCTAGTG 717660 iv v i----- i ii ii i vi i i iv ii iv L2c_3end#LINE 418 TTGTATCCCCAGCGCCTGGCACATAGTAGGCGCTCAATAAATGTTTGTTG 467 chr2ptel1M 717661 GTTGGAT 717667 iv i L2c_3end#LINE 468 AATGAAT 474 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.64 CpG sites = 23, Kimura (unadjusted) = 48.83 Transitions / transversions = 2.30 (23/10) Gap_init rate = 0.04 (4 / 97), avg. gap size = 2.50 (10 / 4) 15 21.31 0.00 0.00 chr2ptel1M 718013 718050 (281950) (GGTGGG)n#Simple_repeat 1 38 (0) m_b74s252i2 2729 chr2ptel1M 718013 GGTGGTGGTGGTGGGGGGGGGCGGGGCGGGGCTGGGGG 718050 v v v vv i v (GGTGGG)n#Sim 1 GGTGGGGGTGGGGGTGGGGGTGGGGGTGGGGGTGGGGG 38 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 364 29.00 6.82 0.71 chr2ptel1M 719941 720072 (279928) L3#LINE/CR1 3409 3548 (551) m_b74s601i9 2730 chr2ptel1M 719941 CAATAGTT-ATCTGAAGAGGATCTGTGGGTCTGTGTAGAC-GCAAGCTCG 719988 ii - iv i i i iv i vv v - i L3#LINE/CR1 3409 CAGCAGTTCACGTGAAAAAGACCTAGGGGTTTTAGTTGACCGCAAGCTCA 3458 chr2ptel1M 719989 ------GGTAGCAATGTGATTTGGCAGCCAAAAGA-CAAATGCCATCTGT 720031 ------ vi i i v v i - v v vv L3#LINE/CR1 3459 ATATGAGCCAACAGTGTGATGTGGCTGCCAAAAAAGCTAATGCAATCTTA 3508 chr2ptel1M 720032 GGCTGCCTTAACAGATAGTGTTGCGCCCGGGGCGGAGAAAG 720072 v i - i v i i i i? iii i i L3#LINE/CR1 3509 GGCTGCATTAATAGA-AGTATAGTGTCCAGANCAAGGGAGG 3548 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.16 CpG sites = 24, Kimura (unadjusted) = 38.47 Transitions / transversions = 1.71 (24/14) Gap_init rate = 0.04 (5 / 131), avg. gap size = 2.00 (10 / 5) 12 22.45 0.00 2.70 chr2ptel1M 722179 722216 (277784) (CCCTTC)n#Simple_repeat 1 37 (0) m_b74s252i4 2731 chr2ptel1M 722179 CCCTCGCCCTCCTCCCCTCGCCAGCCCCTTCCCCTTCC 722216 iv i - i v vv (CCCTTC)n#Sim 1 CCCTTCCCCTTC-CCCTTCCCCTTCCCCTTCCCCTTCC 37 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 18 16.89 6.12 1.96 chr2ptel1M 723005 723053 (276947) (CT)n#Simple_repeat 1 51 (0) m_b74s252i5 2732 chr2ptel1M 723005 CTCGTCTCTGTC-CTC-CTTGCTCCCT-TCTCTCTCTCTCTCCCTCCCCC 723051 - v - - iv i - i i i (CT)n#Simple_ 1 CTC-TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 49 chr2ptel1M 723052 TC 723053 (CT)n#Simple_ 50 TC 51 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.08 (4 / 48), avg. gap size = 1.00 (4 / 4) 29 27.37 2.54 3.42 chr2ptel1M 723015 723132 (276868) (TCC)n#Simple_repeat 1 117 (0) m_b74s252i6 2732 chr2ptel1M 723015 TCCTCCTTGCTCCCTTCTCTCTCTCTCTCCCTCCCCCTCC-CAGCCT-TT 723062 - v - i - - ii i - vv -i (TCC)n#Simple 1 TCCTCC-TCCT-CCTCCTC-CTC-CTCCTCCTCCTCCTCCTCCTCCTCCT 46 chr2ptel1M 723063 CCCCCTCCTCCCGGACCTCCTCCAGC-CCTCCTCCTCTGTCTCCTCTTCC 723111 i ivvv vv - ivi i (TCC)n#Simple 47 CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC 96 chr2ptel1M 723112 CCCCCCCCTTTCTCCTGCTCC 723132 i i i i i v (TCC)n#Simple 97 TCCTCCTCCTCCTCCTCCTCC 117 Matrix = Unknown Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.06 (7 / 117), avg. gap size = 1.00 (7 / 7) 16 10.03 0.00 0.00 chr2ptel1M 723352 723373 (276627) (C)n#Simple_repeat 1 22 (0) m_b74s252i7 2733 chr2ptel1M 723352 CCCTCCTCCCCCCCCCCCCCCC 723373 i i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCC 22 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 14 10.11 6.25 0.00 chr2ptel1M 723393 723424 (276576) (GGGGCT)n#Simple_repeat 1 34 (0) m_b74s252i8 2734 chr2ptel1M 723393 GGGACT-GGGC-AGGGCTGGGGGTGGGGCTGGGG 723424 i - -i v (GGGGCT)n#Sim 1 GGGGCTGGGGCTGGGGCTGGGGCTGGGGCTGGGG 34 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.06 (2 / 31), avg. gap size = 1.00 (2 / 2) 276 31.00 4.00 0.00 chr2ptel1M 723731 723830 (276170) MIRb#SINE/MIR 83 186 (82) m_b74s601i10 2735 chr2ptel1M 723731 ACCGGCTCTGT--CCCTGGG-AGGCCCCTTAGCTTCAGTCTGCCTCAGTC 723777 ii v -- i - i iiv i i vv vv i MIRb#SINE/MIR 83 ACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTT 132 chr2ptel1M 723778 TCCTCACCTGTGAAATGGGAACCACAG-ACCTCCTCCCCAGGTTAGGTGG 723826 i i i iv i i- v ii v v v v v MIRb#SINE/MIR 133 TCCTCATCTGTAAAATGGGGATAATAATACCTACCTCGCAGGGTTGTTGT 182 chr2ptel1M 723827 GAAG 723830 i MIRb#SINE/MIR 183 GAGG 186 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.19 CpG sites = 18, Kimura (unadjusted) = 41.19 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.03 (3 / 99), avg. gap size = 1.33 (4 / 3) 42 23.83 1.82 1.82 chr2ptel1M 724262 724371 (275629) (CA)n#Simple_repeat 1 110 (0) m_b74s252i9 2736 chr2ptel1M 724262 CACACAGACACAGAGCACACACACACACATGTACACACACACAC-CATGT 724310 v v - iii - iii (CA)n#Simple_ 1 CACACACACACACA-CACACACACACACACACACACACACACACACACAC 49 chr2ptel1M 724311 GCACACACAGAGCACACACACATGCTCACAGACACGTACACGCAC-CACG 724359 i v - ii v v ii i - i (CA)n#Simple_ 50 ACACACACACA-CACACACACACACACACACACACACACACACACACACA 98 chr2ptel1M 724360 TGCACACACGCA 724371 ii i (CA)n#Simple_ 99 CACACACACACA 110 Matrix = Unknown Transitions / transversions = 3.20 (16/5) Gap_init rate = 0.04 (4 / 109), avg. gap size = 1.00 (4 / 4) 256 25.12 14.66 3.91 chr2ptel1M 724707 724822 (275178) C L2d2_3end#LINE/L2 (5) 550 423 m_b74s601i11 2737 chr2ptel1M 724707 TCCAATCAACAGGCAGCATTGATTAAACAGCTCTCATGGGCA-GGCCCTG 724755 v --- ii v i i iv viii v - v C L2d2_3end#LIN 550 TCAAATCAACA---AATATTTATTGAGCGCCTACTGTGTGCAAGGCACTG 504 chr2ptel1M 724756 TGCTGGGTGC--TAGGGGAT-CGAAGACAAATGCTGAACA----CTCTGC 724798 i i -- i - i -- i iivii ---- i C L2d2_3end#LIN 503 TGCTAGGCGCTGTGGGGGATACAAAG--AAGTATAAGACATGGTCCCTGC 456 chr2ptel1M 724799 TCTC--GGAGCTTCCA-------TGGGGCGACA 724822 i -- v ------- v C L2d2_3end#LIN 455 CCTCAAGGAGCTTACAATCTAGTTGGGGAGACA 423 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.22 CpG sites = 19, Kimura (unadjusted) = 31.96 Transitions / transversions = 2.11 (19/9) Gap_init rate = 0.10 (11 / 115), avg. gap size = 2.00 (22 / 11) 35 21.82 2.02 2.02 chr2ptel1M 724991 725089 (274911) (CTCTCA)n#Simple_repeat 1 99 (0) m_b74s252i10 2738 chr2ptel1M 724991 CTCTCATTCTCACTATCCCTGTCTCTCTCACTGTCTCTCTCACTATCCCT 725040 i v v v v v v v v (CTCTCA)n#Sim 1 CTCTCACTCTCACTCTCACTCTCACTCTCACTCTCACTCTCACTCTCACT 50 chr2ptel1M 725041 CTCTTACTCTCCCTGTCTCTCTCGCT-T-ACTCTCTTGTTCTCTCTCACT 725088 -- v v v i - - vivi v (CTCTCA)n#Sim 51 CTC--ACTCTCACTCTCACTCTCACTCTCACTCTCACTCTCACTCTCACT 98 chr2ptel1M 725089 C 725089 (CTCTCA)n#Sim 99 C 99 Matrix = Unknown Transitions / transversions = 0.29 (4/14) Gap_init rate = 0.04 (4 / 98), avg. gap size = 1.00 (4 / 4) 30 19.45 2.78 1.37 chr2ptel1M 726245 726316 (273684) (AG)n#Simple_repeat 1 73 (0) m_b74s252i11 2739 chr2ptel1M 726245 AGAGAGAGACAGAGACAGAGACAAAGAGAGAGA-AGAGA-AGAGAAGGAG 726292 v v v i - - ii (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr2ptel1M 726293 AAAGACAGGGAGCGCCGAGAGCGA 726316 i v i v -v v (AG)n#Simple_ 51 AGAGAGAGAGAGAG-AGAGAGAGA 73 Matrix = Unknown Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.04 (3 / 71), avg. gap size = 1.00 (3 / 3) 236 41.59 0.58 2.99 chr2ptel1M 726332 726502 (273498) L3#LINE/CR1 3380 3546 (553) m_b74s601i12 2740 chr2ptel1M 726332 AAGTACAAGGCAATGAGGAAGTGGCCAGGTTGCATTTTGTCTGAAAAA-T 726380 i iiiiv vv ivi iv v iiiv -v L3#LINE/CR1 3380 AAGTACAGGATGGAGAGGATCTGGCTTAGCAGCAGTTCACGTGAAAAAGA 3429 chr2ptel1M 726381 TTGAGCAGTCTTGGTGGGCCTTGAGTGTGGATTGAGTCCACAGTGGGATA 726430 iiv vi i i v i vii iviiivv i v v i L3#LINE/CR1 3430 CCTAGGGGTTTTAGTTGACCGCAAGCTCAATATGAGCCAACAGTGTGATG 3479 chr2ptel1M 726431 CAGCAGGGAAGAAAGCCAGAAGAATCTGGCGTTAGATGAAGCTTCCAGGA 726480 ii v vv i i iviv viv i iv v -----i i L3#LINE/CR1 3480 TGGCTGCCAAAAAAGCTAATGCAATCTTAGGCTGCATTAA-----TAGAA 3524 chr2ptel1M 726481 ATATAATGTCGGGAGCCAGAAA 726502 i i vi ? v ii L3#LINE/CR1 3525 GTATAGTGTCCAGANCAAGGGA 3546 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 63.69 CpG sites = 41, Kimura (unadjusted) = 65.30 Transitions / transversions = 1.46 (41/28) Gap_init rate = 0.04 (6 / 170), avg. gap size = 1.00 (6 / 6) 219 32.81 7.59 3.31 chr2ptel1M 726444 726588 (273412) L3#LINE/CR1 785 935 (3164) m_b74s601i13 2740 chr2ptel1M 726444 AGCCAGAAGAA-TCTGGCGTTAGATGAAGCTTCCAGGAATATAATGTCGG 726492 i -i -----i v v iiviv v v i v vv L3#LINE/CR1 785 AGTCAGAAGAAACCTGG-----AATGCATCTCTAGTGACTTTGAAGTCCT 829 chr2ptel1M 726493 GAGCCAGAAACCGGAGACCACAGGAGCACGGGAGGTGTTTTAAT-TGTTC 726541 i vi i i iv vii i i v v - v L3#LINE/CR1 830 GGGCAGGAAACTGAAGGACTTGGGGGCACAGGTGGTGTTTTCATCTCTTC 879 chr2ptel1M 726542 -----GTTGAAGA-CAAGCCCC---AAGAGAAAATTTCATCTGAGAAATA 726582 ----- i- iv v ii--- ivvvv v i i i L3#LINE/CR1 880 TTCCAGTTGAAGGTCGTGACTTTGGAAGAGAAAGGAGGATATGGGAAGTG 929 chr2ptel1M 726583 AACAGC 726588 L3#LINE/CR1 930 AACAGC 935 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.82 CpG sites = 24, Kimura (unadjusted) = 44.09 Transitions / transversions = 1.09 (24/22) Gap_init rate = 0.07 (10 / 144), avg. gap size = 1.60 (16 / 10) 264 33.57 4.76 6.02 chr2ptel1M 726585 726752 (273248) C L2c_3end#LINE/L2 (3) 475 310 m_b74s601i14 2741 chr2ptel1M 726585 CAGCCAATCAGACAGCCTTAATTAA-CACCTTCTGTTTGCCAGACACC-G 726632 vi v ivv i v v i - i v i v i i i- C L2c_3end#LINE 475 CATTCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGG 426 chr2ptel1M 726633 TGCTATACGGA-GAAAAGGA----GTCCCTGCCCTGGGGGAGCCGGCGCT 726677 v v i vi - v i ---- vii i---- v C L2c_3end#LINE 425 GGATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCT----CA 380 chr2ptel1M 726678 CAGCCTGACAGAGGAGACT-ACATGCAGATTGGGAGACACCGATACGGGA 726726 i iiii v- ? i i i---- vi-- iiv C L2c_3end#LINE 379 CAGTCTAGTGGAGGAGACAGACANGTAAAC----AGACAAT--TACAATA 336 chr2ptel1M 726727 TAAATTGAGGATAATCACTACAGGGG 726752 i i i v vii i iv C L2c_3end#LINE 335 CAAGTTAATGATAAGTGCTATAATGG 310 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.56 CpG sites = 33, Kimura (unadjusted) = 47.03 Transitions / transversions = 1.65 (33/20) Gap_init rate = 0.09 (15 / 167), avg. gap size = 1.20 (18 / 15) 17 23.12 0.00 2.13 chr2ptel1M 727525 727572 (272428) (CCCCCT)n#Simple_repeat 1 47 (0) m_b74s252i12 2742 chr2ptel1M 727525 CCCCCTCCACCCCCCCTGTCCCCTTCCCCGTCCCCCCCTACCCCCCCC 727572 - i iv i v i iv i (CCCCCT)n#Sim 1 CCCCCTCC-CCCTCCCCCTCCCCCTCCCCCTCCCCCTCCCCCTCCCCC 47 Matrix = Unknown Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.02 (1 / 47), avg. gap size = 1.00 (1 / 1) 208 32.02 3.79 3.01 chr2ptel1M 728004 728135 (271865) L2c_3end#LINE/L2 130 262 (216) m_b74s601i15 2743 chr2ptel1M 728004 CCTTTAGACGCAGGCTGTGCTAG-TGCCTCGGA-GCCCTTCTTTCTCACC 728051 i-- i v v ivv- v i - i iii - v L2c_3end#LINE 130 CCTTTG--CACATGCTGTTCCCTCTGCCTGGAATGCTCTTCCCCC-CTCC 176 chr2ptel1M 728052 CTGCTCTTGG--AACCCCTAATTCTC-TTCAAGGCTTAGCTCAAGGACCC 728098 i v v i -- i v iv - ? i iivii v L2c_3end#LINE 177 TTCCACCTGGCTAACTCCTACTCATCCTTCAAGNCTCAGCTCAGATGTCA 226 chr2ptel1M 728099 CCTCTTCCAGGAGGTCTTTTTCCCCCTCTCCAATTCT 728135 i i i - i ii ivv i i v? L2c_3end#LINE 227 CCTCCTCCGGGAAG-CCTTCCCTGACCCCCCAAGNCT 262 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.23 CpG sites = 26, Kimura (unadjusted) = 44.74 Transitions / transversions = 1.73 (26/15) Gap_init rate = 0.06 (8 / 131), avg. gap size = 1.12 (9 / 8) 222 26.42 5.56 3.26 chr2ptel1M 728027 728116 (271884) L2b_3end#LINE/L2 150 241 (225) m_b74s601i16 2743 chr2ptel1M 728027 TGCCTCGGA-GCCCTTCTTTCTCACC-CTGCTCTTGG--AACCCCTAATT 728072 v i - --- i - v v i -- i v i L2b_3end#LINE 150 TGCCTGGAACGCCCTTC---CCCACCTCTTCGCCTGGCCAACTCCTACTC 196 chr2ptel1M 728073 CTC-TTCAAGGCTTAGCTCAAGGACCCCCTCTTCCAGGAGGTCTT 728116 v - i v i ivii v i i i i i L2b_3end#LINE 197 ATCCTTCAGGTCTCAGCTCAAATGTCACCTCCTCCGGGAAGCCCT 241 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.98 CpG sites = 15, Kimura (unadjusted) = 33.79 Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.08 (7 / 89), avg. gap size = 1.14 (8 / 7) 189 37.58 4.03 0.00 chr2ptel1M 728028 728176 (271824) L2d_3end#LINE/L2 154 308 (208) m_b74s601i17 2743 chr2ptel1M 728028 GCCTCGGA-GCCCTTCTTTCTCACCCTGCTCT-TGGAACCCCTAATTCTC 728075 v i - iiii vi iiv - vv vi viiv L2d_3end#LINE 154 GCCTGGAATGCCCTTCCCCTTCCTCTCTCTCTATCCAAATCCTACCCATC 203 chr2ptel1M 728076 -TTCAAGGCTTAGCTCAAGGACCCCCTCTTCCAGGAGGTCTTTTTCCCCC 728124 - ii vv v i v i i iiiivv L2d_3end#LINE 204 CTTCAAGGCCCAGCTCAAGTCCCACCTCCTCCACGAAGCCTTCCCTGACC 253 chr2ptel1M 728125 TCTCCAATTCTCTGTGATTTTTTGTTTTTAT--TTTCCTTTAA-GCTGAT 728171 v iii v vv i i ivi i v --vi v i-i v L2d_3end#LINE 254 ACTCCAGCCCACACTGATCTCTCCCTTCTCTGAACTCCTATAGCACTTAT 303 chr2ptel1M 728172 AATTT 728176 i i L2d_3end#LINE 304 AGTCT 308 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 54.71 CpG sites = 33, Kimura (unadjusted) = 54.71 Transitions / transversions = 1.43 (33/23) Gap_init rate = 0.03 (5 / 148), avg. gap size = 1.20 (6 / 5) 1573 29.37 2.07 0.94 chr2ptel1M 729040 729668 (270332) C L1ME4a_3end#LINE/L1 (232) 639 4 m_b74s551i0 2744 chr2ptel1M 729040 CCTGCTTGTTTCACTTAGCATCAGTTCATGTAAGTCTCTCCAGGCCTTTC 729089 v i i vv vivi i ii v i v - C L1ME4a_3end#L 639 CCTGCTTTTTTCACTTAACATTATATCATGAGCATTTTCCCATGTCATT- 591 chr2ptel1M 729090 TGAAATCTTCCTGTTGG-----TCATTTCTTACAG-AACAGTAATATTCC 729133 -- v i --i i----- ? i v ii -vi - C L1ME4a_3end#L 590 --AAATATTCTT--CGAAAACATNATTTTTAATGGCTGCA-TAATATTCC 546 chr2ptel1M 729134 ATAATATTCATATACCACAATTTATTCAGCCATTCTCCAACTGATGGACA 729183 v? vv i i i i ? i v i v C L1ME4a_3end#L 545 ATTNTATGGATGTACCATAATTTATTTAACCANTCCCCTATTGTTGGACA 496 chr2ptel1M 729184 TCCATTCAGTTTCCAGTTTCTAGCCACTACAAAGAGGGCTGCCACAAACA 729233 ii vviv i i v i i i v iv v ii C L1ME4a_3end#L 495 TTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAATGCTGCGATGAACA 446 chr2ptel1M 729234 TTCGTGCACATACAGGTTCCTTTCCCTTCTTTATAATCTCTTTGGGATAT 729283 i v i v vv iv ?iv v iii v v i i i v C L1ME4a_3end#L 445 TCCTTGTACATAAATCTTTGTNCACATCTCTGATTATTTCCTTAGGATAA 396 chr2ptel1M 729284 AAGCCCAGTAGTAACACTGCTGGATCAAAGGGTATGTACAGTTTGATAAC 729333 vv i v iiv i i i ? v v vii C L1ME4a_3end#L 395 ATTCCTAGAAGTGGAATTACTGGGTCAAAGGGTATGNACATTTTTAAGGC 346 chr2ptel1M 729334 TTTTTGAGCCTAGTTCCAAACTACTCTCCAGAATGGTTGGATGTATTCAC 729383 vivi v v v i i i v v ivv i C L1ME4a_3end#L 345 TTTTGATACATATTGCCAAATTGCCCTCCAGAAAGGTTGTACCAATTTAC 296 chr2ptel1M 729384 AGTTCCACCAATAATGTATTAGTGTCCCTGTTTTCCCACATCCCCTCCAA 729433 v i ii i v v v i i? i i v C L1ME4a_3end#L 295 ACTCCCACCAGCAGTGTATGAGAGTGCCCGTTTCNCCACACCCTCGCCAA 246 chr2ptel1M 729434 CATTCCGCATTATCTTTCCCTGTCATTCTAGCCAATCTGACAGGTGTGTA 729483 i vv i vv ii vvv ii v i i viv C L1ME4a_3end#L 245 CACTGGGTATTATCAATCTTTTAAATCTTTGCCAATTTGATAGGTGAAAA 196 chr2ptel1M 729484 GTGGTATCTCAGAGTTGTCTTAATTTGCATTTCTCTGATTAATAATGACT 729533 i vv i i v i vv C L1ME4a_3end#L 195 ATGGTATCTCATTGTTGTTTTAATTTGCATTTCTTTGATTACTAGTGAGG 146 chr2ptel1M 729534 TGGAGCATCTTTTCATATGACTAGAAATAGTTTCAGTTTCTTCATCTGAG 729583 v i ? vi vviiivi vvi v i v C L1ME4a_3end#L 145 TTGAACATNTTTTCATATGTTTATTGGCCATTTGTATTTCTTCTTTTGTG 96 chr2ptel1M 729584 AATTGTCTGTTCATATCCTTTGACCATTTATCAATTGGAGAAT--GGCTT 729631 i v v v i vi -- v C L1ME4a_3end#L 95 AATTGTCTGTTCATGTCCTTTGCCCATTTTTCTATTGGGGTGTTCGTCTT 46 chr2ptel1M 729632 GATTTTTTTGAGTC-----AATTCTCTATATATTTTGGAGAT 729668 vv i v v i----- ii i vv v C L1ME4a_3end#L 45 TTTCTTATTGATTTGTAAGAGCTCTTTATATATTAAGGATAT 4 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 37.86 CpG sites = 94, Kimura (unadjusted) = 38.39 Transitions / transversions = 1.06 (94/89) Gap_init rate = 0.02 (10 / 628), avg. gap size = 1.90 (19 / 10) 1588 27.77 1.48 1.48 chr2ptel1M 729125 729665 (270335) C L1ME3Cz_3end#LINE/L1 (450) 547 7 m_b74s551i1 2744 chr2ptel1M 729125 TAATATTCCATAATATTCATATACCACAATTTATTCAGCCATTCTCCAAC 729174 i vi vv i v i v i C L1ME3Cz_3end# 547 TAGTATTCCATTGTATGAATATACCACAATTTATTTATCCATTCCCCTAT 498 chr2ptel1M 729175 TGATGGACATCCATTCAGTTTCCAGTTTCTAGCCACTACAAAGAGGGCTG 729224 ii vviv i i v i i v iv C L1ME3Cz_3end# 497 TGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCTG 448 chr2ptel1M 729225 CCACAAACATTCGTGCACATACAGGTTCCTTTCCCTTCTTT---ATAATC 729271 v ii i v i --- vi viv viv v --- v i i C L1ME3Cz_3end# 447 CAATGAACATCCTTGTACAT---GTCTCCTTGTGCACATGTGCGAGAGTT 401 chr2ptel1M 729272 TCTTTGGGATATAAGCCCAGTAGTAACACTGCTGGATCAAAGGGTATGTA 729321 i i i vi i v iiv i i iv ii C L1ME3Cz_3end# 400 TCTCTAGGGTATATACCTAGAAGTGGAATTGCTGGGTCGTAGGGTATGCG 351 chr2ptel1M 729322 CAGTTTGATAACTTTTTGAGCCTAGTTCCAAACTACTCTCCAGAATGGTT 729371 vi --i viv v- v v i i i i C L1ME3Cz_3end# 350 CATCTT--CAACTTTACTAGA-TATTGCCAAATTGCTCTCCAAAGTGGTT 304 chr2ptel1M 729372 GGATGTATTCACAGTTCCACCAATAATGTATTAGTGTCCCTGTTTTCCCA 729421 v ivv i v i ii i v v i i ii C L1ME3Cz_3end# 303 GTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTTCCCGTTTCTCCA 254 chr2ptel1M 729422 CATCCCCTCCAACATTCCGCATTATCTTTCCCTGTCATTCTAGCCAATCT 729471 i v i iv i i vvv ii vvv i v C L1ME3Cz_3end# 253 CATCCTCGCCAACACTTGGTATTGTCAGACTTTTAAATTTTTGCCAATCT 204 chr2ptel1M 729472 GACAGGTGTGTAGTGGTATCTCAGAGTTGTCTTAATTTGCATTTCTCTGA 729521 ii v i vv ? i i C L1ME3Cz_3end# 203 GATGGGTGTGAAATGGTATCTCATTGTNGTTTTAATTTGCATTTCCCTGA 154 chr2ptel1M 729522 TTAATAATGACTTGGAGCATCTTTTCATATGACTAGAAATAGTTTCAGTT 729571 v i vv v vi vviiivi ivi C L1ME3Cz_3end# 153 TTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTCGGGTT 104 chr2ptel1M 729572 TCTTCATCTGAGAATTGTCTGTTCATATCCTTTGACCATTTATCAATTGG 729621 i v v i v v v C L1ME3Cz_3end# 103 TCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGG 54 chr2ptel1M 729622 AGAATGGCTTGATTTTTTTGAGTC-----AATTCTCTATATATTTTGGA 729665 iv-- v vv i v v i----- i i i C L1ME3Cz_3end# 53 GT--TGTCTTTTTCTTATTGATTTGTAGGAGTTCTTTATATATTCTGGA 7 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 34.16 CpG sites = 80, Kimura (unadjusted) = 35.36 Transitions / transversions = 1.18 (80/68) Gap_init rate = 0.02 (10 / 540), avg. gap size = 1.60 (16 / 10) 389 31.47 2.79 0.00 chr2ptel1M 729529 729779 (270221) C L1M5_orf2#LINE/L1 (0) 3294 3037 m_b74s551i2 2744 chr2ptel1M 729529 TGACTTGGAGCATCTTTTCATATGACTAGAAATAGTTTCAGTTTCTTCAT 729578 ?v v i vi vviiivi v?i v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr2ptel1M 729579 CTGAGAATTGTCTGTTCATATCCTTTGACCATTTATCAATTGGA--GAAT 729626 i v v vi i v v ?v i-- vv C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTT 3195 chr2ptel1M 729627 GGCTTGATTTTTTTGAGTC-----AATTCTCTATATATTTTGGAGATGAG 729671 v vv ? v ? i----- i i i v i C L1M5_orf2#LIN 3194 GTCTTTTTNTTATTGANTTGTAGGAGTTCTTTATATATTCTGGATACGAG 3145 chr2ptel1M 729672 GCCTTTATCAGAACCTTTGACTGTAAAAATATTTTCCCAGTTTATTGCTT 729721 v i vviv vv?i i v v i ? i i v C L1M5_orf2#LIN 3144 TCCTTTGTCAGATATATGTNTTGCAAATATTTTCTCCCANTCTGTGGCTT 3095 chr2ptel1M 729722 CCCTTCTAATCTTGTCTGCATTAGTTTTGTTTGTACAAAAACTTTTCAGT 729771 v i v i v ivi iv ivi vvv? vi i ii v v C L1M5_orf2#LIN 3094 GCCTTTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTTTAATT 3045 chr2ptel1M 729772 TTGGTATA 729779 i i? C L1M5_orf2#LIN 3044 TTGATGNA 3037 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 41.82 CpG sites = 36, Kimura (unadjusted) = 43.21 Transitions / transversions = 0.84 (36/43) Gap_init rate = 0.01 (2 / 250), avg. gap size = 3.50 (7 / 2) 254 33.02 4.37 2.14 chr2ptel1M 729942 730170 (269830) C L1ME4c_3end#LINE/L1 (179) 651 418 m_b74s551i3 2745 chr2ptel1M 729942 TATTACTTTGTACACAGTACCTTTCATTTTGCATGGGCTCATTGGGCACT 729991 iv i iv v ivii i vi vivv -iii i C L1ME4c_3end#L 651 TACAATTTTGTATTCTGCTTTTTTCACTTAACATTATATCAT-AAACATT 603 chr2ptel1M 729992 TTCTAGGTT-TTACTGAGAGCATGC-TGCTCATCATTTCTTATAGAACAA 730039 i v -i -- v iv v - iv i i v i vvvv C L1ME4c_3end#L 602 TTCCATGTTGCTAC--ATAGTCTTCATAATTATCATTTTTAATGGCTGCA 555 chr2ptel1M 730040 TAGTATTCCAT--AATC-CCATACCACAATTTATTCAACTGTTCCCCAAT 730086 i -- i ?-vii i i i ii v C L1ME4c_3end#L 554 TAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTAT 505 chr2ptel1M 730087 TGATGGGCATCCCCTCAATGTCCAATTCTTTGCCTTGAGAAATGA-GCTG 730135 v i iivvvivi v i i iv v v i - C L1ME4c_3end#L 504 TGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCTG 455 chr2ptel1M 730136 CTATTAA----TTTGTACAAATAGATCCTTTTCCTTCCT 730170 v v ---- i i v -- i i C L1ME4c_3end#L 454 CAATGAACATCTTCGTGCATATAG--CTTTTTCCTTCTT 418 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 43.52 CpG sites = 42, Kimura (unadjusted) = 45.17 Transitions / transversions = 1.31 (42/32) Gap_init rate = 0.05 (11 / 228), avg. gap size = 1.36 (15 / 11) 288 26.79 7.14 0.00 chr2ptel1M 730039 730150 (269850) C L1ME3G_3end#LINE/L1 (376) 548 429 m_b74s551i4 2745 chr2ptel1M 730039 ATAGTATTCCATAATCC---CATACCACAATTTATTCAACTGTTCCCCAA 730085 i vi---i i i ii v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr2ptel1M 730086 TTGATGGGCATCCCCTCAATGTCCAATTCTTTGCCTTGAGAAATGA-GCT 730134 i iivvvivi v i i iv v v ii - C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr2ptel1M 730135 GCTATTAA----TTTGTACA 730150 v v ----i C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACA 429 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 32.62 CpG sites = 18, Kimura (unadjusted) = 34.01 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.03 (3 / 111), avg. gap size = 2.67 (8 / 3) 347 34.31 2.39 2.39 chr2ptel1M 731895 732103 (267897) L1ME4c_3end#LINE/L1 431 639 (191) m_b74s551i5 2746 chr2ptel1M 731895 CTCTGTGCA-AAAAATGTTTGTGGCAGTCCTTTTTCTAGTGGCAAGAAAC 731943 v i -i i ii v ivi v v i i i i i L1ME4c_3end#L 431 CTATATGCACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAAT 480 chr2ptel1M 731944 TGGAA----CCTGAGAGGATGCCCATCAGCTGGGGAATGGCTGAATAAAT 731989 ---- i ---- i v iiv i i i L1ME4c_3end#L 481 TGGAAACAACCTAA----ATGTCCAACAATAGGGGAATGGTTAAGTAAAT 526 chr2ptel1M 731990 TATGGCATATGAATGTTATGGAATATTATTGTTCTATAAGAAACAATTAA 732039 i i v? iviv vvvv i v i ii v v L1ME4c_3end#L 527 TATGGTACATCNACTCGATGGAATATTATGCAGCCATTAAAAATGATAAT 576 chr2ptel1M 732040 CACGATGATTTCAGAGAGACCTGGAGAGACTTATGTGAGCTGATACTGAG 732089 i i v i viiv vi v - i iv v i vv i ii i L1ME4c_3end#L 577 TATGAAGACTATGTAGCAACATGGA-AAATGTTTATGATATAATGTTAAG 625 chr2ptel1M 732090 TGAAAGGATCAGGA 732103 ii v i L1ME4c_3end#L 626 TGAAAAAAGCAGAA 639 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 44.55 CpG sites = 43, Kimura (unadjusted) = 48.40 Transitions / transversions = 1.59 (43/27) Gap_init rate = 0.03 (7 / 208), avg. gap size = 1.43 (10 / 7) 378 25.23 3.48 3.48 chr2ptel1M 731904 732018 (267982) L1ME3G_3end#LINE/L1 434 548 (376) m_b74s551i6 2746 chr2ptel1M 731904 AAAAATGTTTGTGGCAGTCCTTTTTCTAGTGGCAAGAAACTGGAA----C 731949 ii ii v ivi v v i i i i i ---- L1ME3G_3end#L 434 AAGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAAC 483 chr2ptel1M 731950 CTGAGAGGATGCCCATCAGCTGGGGAATGGCTGAATAAATTATGGCATAT 731999 i ---- i iiv i i i L1ME3G_3end#L 484 CTAA----ATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGTATAT 529 chr2ptel1M 732000 GAATGTTATGGAATATTAT 732018 vv ii i L1ME3G_3end#L 530 CCATACTATGGAATACTAT 548 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 31.06 CpG sites = 21, Kimura (unadjusted) = 32.49 Transitions / transversions = 3.00 (21/7) Gap_init rate = 0.04 (5 / 114), avg. gap size = 1.60 (8 / 5) 26 6.42 8.16 0.00 chr2ptel1M 732280 732328 (267672) (TGTT)n#Simple_repeat 1 53 (0) m_b74s252i13 2747 chr2ptel1M 732280 TGTTTG-TTG-TTGTTTGCTTGCTT-TTTGTTT-TTTTTTTGTTTGTTTG 732325 - - i i - - v (TGTT)n#Simpl 1 TGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTG 50 chr2ptel1M 732326 TTT 732328 (TGTT)n#Simpl 51 TTT 53 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.08 (4 / 48), avg. gap size = 1.00 (4 / 4) 185 28.00 2.00 0.00 chr2ptel1M 733572 733621 (266379) C MIR#SINE/MIR (5) 257 207 m_b74s601i18 2748 chr2ptel1M 733572 TGGCCAACAAGCATTGGGTGCTC-CTAGGTGCCAGGCTCTGCTCTGGGTG 733620 i i vvi i i i- v v i ii i C MIR#SINE/MIR 257 TAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGCG 208 chr2ptel1M 733621 C 733621 C MIR#SINE/MIR 207 C 207 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.57 CpG sites = 10, Kimura (unadjusted) = 37.06 Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.02 (1 / 49), avg. gap size = 1.00 (1 / 1) 188 24.82 2.38 8.86 chr2ptel1M 733816 733899 (266101) AmnL2-1#LINE/L2 2142 2220 (393) m_b74s601i19 2749 chr2ptel1M 733816 GTGACCATGTCACCCCCACTCAGTAAAAACTCCAGTGGCTTCC--TTCCT 733863 i ii ii vvv v v i -- v AmnL2-1#LINE/ 2142 GCGACCACATCACCCCCATCCTCAAACAACTCCACTGGCTCCCCATTCAT 2191 chr2ptel1M 733864 GTTTGGCCTTCAGAACCTTTCACAACCTGCCTTCCT 733899 - ii vv i ----- - vi AmnL2-1#LINE/ 2192 -TTCAGGATCCAG-----TTCA-AAATTGCCTTCCT 2220 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.45 CpG sites = 10, Kimura (unadjusted) = 30.29 Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.10 (8 / 83), avg. gap size = 1.12 (9 / 8) 259 17.86 7.14 0.00 chr2ptel1M 734929 734984 (265016) MIR#SINE/MIR 63 122 (140) m_b74s601i20 2750 chr2ptel1M 734929 GACTCTATCG---ACTAGCTCTGTGACCCTGGGCAAGTCACTTAATCTCA 734975 i ii i--- v i i i v MIR#SINE/MIR 63 GGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCT 112 chr2ptel1M 734976 AT-TGCCTCA 734984 v - MIR#SINE/MIR 113 CTGTGCCTCA 122 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 20.92 CpG sites = 7, Kimura (unadjusted) = 20.92 Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.04 (2 / 55), avg. gap size = 2.00 (4 / 2) 18 0.00 0.00 0.00 chr2ptel1M 734991 735010 (264990) (A)n#Simple_repeat 1 20 (0) m_b74s252i14 2751 chr2ptel1M 734991 AAAAAAAAAAAAAAAAAAAA 735010 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAA 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 506 24.64 8.80 9.81 chr2ptel1M 735047 735262 (264738) C MIRb#SINE/MIR (21) 247 34 m_b74s601i21 2752 chr2ptel1M 735047 TGAGCACTTA---TATGCTACCGACTGTTGCTGAG------ACAT---TT 735084 i --- i i vvv - i ------ --- C MIRb#SINE/MIR 247 TGAGCGCTTACTATGTGCCAGGCACTGT-GCTAAGCGCTTTACATGCATT 199 chr2ptel1M 735085 AT------TAGACCTCACAAAAACCCTGGGAGGGAGGTACTCTTATACTC 735128 ------ iv v v v i v --- C MIRb#SINE/MIR 198 ATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATTAT---C 152 chr2ptel1M 735129 CCTGTTTGACAAGCAAGTCAAACACACAAACAAGCAAGTTGAGGCACACA 735178 ii -----------------i i ii v ii v v C MIRb#SINE/MIR 151 CCCATTT-----------------TACAGATGAGGAAACTGAGGCTCAGA 119 chr2ptel1M 735179 GAAGTGAAATAACATGTCCAGGATCACCCAGCTTGAAAGCTTCTGAGGCG 735228 i v i v i i i v v v ivv v v C MIRb#SINE/MIR 118 GAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 69 chr2ptel1M 735229 GGATTTGAATTCAGTTCTTCCTGACTCT-AGGCCC 735262 i ii v vi i- i C MIRb#SINE/MIR 68 GGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCC 34 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.79 CpG sites = 26, Kimura (unadjusted) = 30.25 Transitions / transversions = 1.18 (26/22) Gap_init rate = 0.12 (26 / 215), avg. gap size = 1.54 (40 / 26) 401 28.80 0.00 2.88 chr2ptel1M 735154 735296 (264704) C MIR1_Amn#SINE/MIR (88) 142 4 m_b74s601i22 2752 chr2ptel1M 735154 ACAAACAAGCAAGTTGAGGCACACAGAAGTGAAATAACATGTCCAGGATC 735203 i ii v ii ? v i ? i i v i i i C MIR1_Amn#SINE 142 ACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGCCCAAGGTC 93 chr2ptel1M 735204 ACCCAGCTTGAAAGCTTCTGAGGCGGGATTTGAATTCAGTTCTTCCTGAC 735253 ? ?v v? ivv v v ? ? ii v - i v C MIR1_Amn#SINE 92 ACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAACCCAGGTC-TCCCGAG 44 chr2ptel1M 735254 TCTAGGCCCAGAGGCCTGTGCCATGTGAGACCACCCAGCTGCC 735296 ivi i v vi i - --iv v v iv C MIR1_Amn#SINE 43 TCCCAGTCCAGTGCTCTAT-CCA--CTAGACCACACTGCCTCC 4 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.41 CpG sites = 22, Kimura (unadjusted) = 39.68 Transitions / transversions = 1.22 (22/18) Gap_init rate = 0.03 (4 / 142), avg. gap size = 1.00 (4 / 4) 18 17.73 0.00 0.00 chr2ptel1M 737108 737145 (262855) (CCT)n#Simple_repeat 1 38 (0) m_b74s252i15 2753 chr2ptel1M 737108 CCTCCTCCTCCTCCTCCGCGTCCGTCTCCTCTTCGTCC 737145 v v vi i v (CCT)n#Simple 1 CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC 38 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 chr2ptel1M 738718 738734 (261266) (T)n#Simple_repeat 1 17 (0) m_b74s252i16 2754 chr2ptel1M 738718 TTTTTTTTTTTTTTTTT 738734 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTT 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 196 14.30 0.00 2.86 chr2ptel1M 739630 739665 (260335) C L2c_3end#LINE/L2 (23) 455 421 m_b74s601i23 2755 chr2ptel1M 739630 ATTAAGCACCTGCTGTGTGCCTGGCGCTGTGGGATA 739665 i i i i v - C L2c_3end#LINE 455 ATTGAGCGCCTACTATGTGCCAGGCGCTG-GGGATA 421 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 12.99 CpG sites = 4, Kimura (unadjusted) = 16.33 Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) 736 31.38 7.37 1.39 chr2ptel1M 741757 742299 (257701) L1ME3G_3end#LINE/L1 56 630 (294) m_b75s551i0 2756 chr2ptel1M 741757 AATTGATAAATGGACAAAGGATATGAACAGGCAATTTTTGGATCAAGAAA 741806 v v i ivii vv i L1ME3G_3end#L 56 AATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGGAAA 105 chr2ptel1M 741807 TCAAAGCTGTTTATAGTCACAT--AAAAATGCTTTA---TATTATTGATT 741851 vv iiv iiv iv i -- i iv ---i i v i i L1ME3G_3end#L 106 TACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTAATC 155 chr2ptel1M 741852 AGAGAAATGCAGATTAAAACAACTCTGAAACACCATCTC-------TCAG 741894 i i vv i i i i------- L1ME3G_3end#L 156 AGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCATCAG 205 chr2ptel1M 741895 ATTGGCTAAAATCATAGAATGGAAAAAATGACAAATGTTGG-AAGAGTTT 741943 v i- i v?vvi v iv ? i -i i v L1ME3G_3end#L 206 ATTGGCAAAAATT-TAAAAGNTTGATAATATCNAGTGTTGGCGAGGGTGT 254 chr2ptel1M 741944 GAAAAAAACTGAGACAT---TACACTGTTGGTGGAACCATGAACTGATCC 741990 -iii v iv vi--- i i vii i i i v L1ME3G_3end#L 255 G-GGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTAC 303 chr2ptel1M 741991 AACCA-TTTGGAGAGCAATCTGGAATTATGCCCAGAGAGTTATAAAACTG 742039 i ?- i i v v -- i vvi iv v - L1ME3G_3end#L 304 AGCCNTTTTGGAGGGCAATTTGGCAGTAT--CTATTAAAATTTAAAA-TG 350 chr2ptel1M 742040 TCTATCCCCTTTGACCCAGCTATACCAATATTAGGTCTGTTTCCT---GA 742086 ivi v v v v vi ? ?v v v --- L1ME3G_3end#L 351 CGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAGA 400 chr2ptel1M 742087 AATGTTCA---AGGAAAAAGAGAACCTATGTTCTAAAATGTTTATAGAGA 742133 ii i--- v viv vi i ?vi v v ii i v vii L1ME3G_3end#L 401 AATACTCGCACATGTGCACAAGGANGCATGTACAAGGATGTTCATTGCAG 450 chr2ptel1M 742134 TTCTCTTTGTGGTGGCAAAGAACTGGAAA----TTGGAGGTTGCCCATCA 742179 ivi v ii i i i i ----i ii --- i L1ME3G_3end#L 451 CATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAA---TGTCCATCA 497 chr2ptel1M 742180 GATGGGGATTGGCTGAACAAATTATG------TCGTGTGATTGACTACTG 742223 ivv v i i i ------i i iiv v v i L1ME3G_3end#L 498 ATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACTA 547 chr2ptel1M 742224 T---GCTATAAGAAAGGATGAGCTCGGTGGTCTTAGAGAGACATGGATAG 742270 --- ?i v i i v v i vvviv iv vv v L1ME3G_3end#L 548 TGCAGCNGTTAAAAAGAATGAGGTAGATCTATATGTACTGACATGGAAAG 597 chr2ptel1M 742271 ACTTGCGTGAAATA----AGAGTGAAATGAGCA 742299 ii v iv v ----v vi L1ME3G_3end#L 598 ATCTCCAAGACATATTGTTGAGTGAAAAAAGCA 630 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 41.17 CpG sites = 94, Kimura (unadjusted) = 42.50 Transitions / transversions = 1.27 (94/74) Gap_init rate = 0.04 (20 / 542), avg. gap size = 2.40 (48 / 20) 201 40.83 3.33 0.00 chr2ptel1M 742493 742612 (257388) C L2#LINE/L2 (593) 2489 2366 m_b75s601i1 2757 chr2ptel1M 742493 AGCAAGCCTGGAAGAGAGAAACATTATTT--GTATGGGGCATGTTGCATT 742540 i ii iii i ii v vv v -- v v i ivi C L2#LINE/L2 2489 AGCAGGTTTGAGGGGGAAGATCAGGAGTTCAGTTTTGGACATGTTAAGTT 2440 chr2ptel1M 742541 TGAATGGCCCCGTGGCTTGTCA--TCGGAATGTCCCATAGGCACTTGGTG 742588 ivv ivv i vivvi -- v ii vvi v vv C L2#LINE/L2 2439 TGAGATGCCTATTAGACATCCAAGTGGAGATGTCGAGTAGGCAGTTGGAT 2390 chr2ptel1M 742589 ATTGGGGATAGAAGCTCGGGGGAG 742612 vv i viv i i i C L2#LINE/L2 2389 ATACGAGTCTGGAGTTCAGGGGAG 2366 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 60.71 CpG sites = 25, Kimura (unadjusted) = 60.71 Transitions / transversions = 1.04 (25/24) Gap_init rate = 0.02 (2 / 119), avg. gap size = 2.00 (4 / 2) 759 29.91 6.89 0.52 chr2ptel1M 742644 743006 (256994) C L2#LINE/L2 (788) 2294 1909 m_b75s601i2 2757 chr2ptel1M 742644 GAGGTCACCAGGAGAG-AAG---AGAGGAAGAAGAGACCGGAGGGCTCGA 742689 i ?i i -i --- vii --i v ivii C L2#LINE/L2 2294 GAGATCACCNAGGGAGTGAGTGTAGATAGAGAAGAGA--AGAGGTCCAAG 2247 chr2ptel1M 742690 GACCTAACCCTGGGGGACACCTGTGGTTAGGGCATG---AGCTAGAGAGG 742736 iv i v v vii v ? i vvi --- v iii C L2#LINE/L2 2246 GACTGAGCCCTGGGGCACTCCAACGTTNAGAGGTCGGGGAGATGAGGAGG 2197 chr2ptel1M 742737 ATCCAGCCAAGTAGACAGAGGAGGAGTGGGCAGAGAGGGAGGAGGAAAGT 742786 v v v v i i v v v ii C L2#LINE/L2 2196 AACCAGCAAAGGAGACTGAGAAGGAGCGGCCAGTGAGGTAGGAGGAAAAC 2147 chr2ptel1M 742787 CAGGAGAAGGT-----CCTAGAAACCAAGAGAA--AAGGGTTTCTAGAAG 742829 iv ----- i i v -- v v C L2#LINE/L2 2146 CAGGAGAGTGTGGTGTCCTGGAAGCCAAGTGAAGAAAGTGTTTCAAGAAG 2097 chr2ptel1M 742830 GAGAGGGCGACCAGTAGGATCAAAAGCTGCAGGGAGGTCTGGGAGAATGA 742879 i i i i iiv vi v v i? vi v ii C L2#LINE/L2 2096 GAGGGAGTGATCAACTGTGTCAAATGCTGCTGANAGGTCAAGTAAGATGA 2047 chr2ptel1M 742880 GGATGGAGAGAGGGCCTCAGGATCTGGACACTAAGACGTCACCGGTCGCT 742929 iv ivv i viv i i vv vvi v ii vi i C L2#LINE/L2 2046 GGACTGAGAATTGACCATTGGATTTAGCAACGTGGAGGTCATTGGTGACC 1997 chr2ptel1M 742930 TTGGAGAGGGCAGTTTTGGTGGAAGGATCAGGTTGGAAGCCAGAT----- 742974 ivi i i iv i vi vi i v ----- C L2#LINE/L2 1996 TTGACAAGAGCAGTTTCGGTGGAGTGGTGGGGACGAAAGCCTGATTGGAG 1947 chr2ptel1M 742975 --GGCTTAAGA-AGA---GCAGGAGAAGAAGCGGAGGC 743006 -- i i - --- v i vi i C L2#LINE/L2 1946 TGGGTTCAAGAGAGAATGGGAGGAGAGGAATTGGAGAC 1909 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.29 CpG sites = 62, Kimura (unadjusted) = 39.63 Transitions / transversions = 1.35 (62/46) Gap_init rate = 0.03 (11 / 362), avg. gap size = 2.45 (27 / 11) 33 8.66 0.00 0.00 chr2ptel1M 744028 744076 (255924) (CGGCAG)n#Simple_repeat 1 49 (0) c_b75s251i0 2758 chr2ptel1M 744028 CGGCAGCGGCAGTGGCAGCGCCAGCGGCAACGGCAGCGGCAGCTGCAGC 744076 i v i v (CGGCAG)n#Sim 1 CGGCAGCGGCAGCGGCAGCGGCAGCGGCAGCGGCAGCGGCAGCGGCAGC 49 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 19 17.36 0.00 0.00 chr2ptel1M 744080 744119 (255881) (AGCGCC)n#Simple_repeat 1 40 (0) m_b75s252i0 2759 chr2ptel1M 744080 AGCACCAGTGCCAGTGCCAGCGCCAACGGCAGCGCCAACG 744119 i i i i v i (AGCGCC)n#Sim 1 AGCGCCAGCGCCAGCGCCAGCGCCAGCGCCAGCGCCAGCG 40 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 250 27.87 16.53 2.17 chr2ptel1M 744401 744521 (255479) MIRb#SINE/MIR 105 242 (26) m_b75s601i3 2760 chr2ptel1M 744401 AGTCAC--GACCCCTGCCCGCCTCGGCTTCCTCACCTGTAAAATGGCCCT 744448 i --i i vivv i i i vvv MIRb#SINE/MIR 105 AGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGAT 154 chr2ptel1M 744449 CGCCACGACCCTCCCTGCCGGGCTGGTTTGTGAGG--------------- 744483 viiv i- iv ii v i -- --------------- MIRb#SINE/MIR 155 AATAAT-ACCTACCTCGCAGGGTTG--TTGTGAGGATTAAATGAGATAAT 201 chr2ptel1M 744484 --ATGTAAAA-GCTTATCCCAGTACCTGGTACGCAATAGGC 744521 -- i- v v i i ii i i MIRb#SINE/MIR 202 GCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGC 242 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.89 CpG sites = 21, Kimura (unadjusted) = 36.27 Transitions / transversions = 1.75 (21/12) Gap_init rate = 0.06 (7 / 120), avg. gap size = 3.29 (23 / 7) 184 27.42 4.97 1.23 chr2ptel1M 745194 745897 (254103) (GGAA)n#Simple_repeat 1 730 (0) m_b75s252i1 2761 chr2ptel1M 745194 GGGAGGACAGG-AGG-AGG-AGGAAGGAGGGGAAGGAAGG-AGGGAGAAT 745239 i - - - - -i - i i v (GGAA)n#Simpl 1 GGAAGGA-AGGAAGGAAGGAAGGAAGGA-AGGAAGGAAGGAAGGAAGGAA 48 chr2ptel1M 745240 AGAAGGAA-AAAGGGAAGAAGG-AGCAGGGGA-GAATAGAGGAAGG-AGA 745285 i -i i i - v i i - vii - i (GGAA)n#Simpl 49 GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG 98 chr2ptel1M 745286 GAGGAAGGAAGGGAGGAAAG-AGGGAGAATAGAAAGAAGGAAGG-AGAAT 745333 i i i - i i vi i - i v (GGAA)n#Simpl 99 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 148 chr2ptel1M 745334 AGAAGGAA-AAAGGGAAGAAAGAA-GAAGGGAGAATAGCA-GAAGG-AGG 745379 i -i i i i - i i vi v - - (GGAA)n#Simpl 149 GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG 198 chr2ptel1M 745380 TAGAATAGAA-AAAGGAAAGAATAGAAGGAAAGAAGGAA-GAA-GATGCA 745426 v i vi -i i -i i - - v v (GGAA)n#Simpl 199 AAGGAAGGAAGGAAGGAAGGAA-GGAAGGAAGGAAGGAAGGAAGGAAGGA 247 chr2ptel1M 745427 GGGGA-GACTAGAGGAAGG-AGAAAGGAAGGAAGGAAGG-AGAAAGACAA 745473 i i - vvii - i - i -v (GGAA)n#Simpl 248 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG-GAA 296 chr2ptel1M 745474 CGAATAGAGGAAGG-AGAGAGGCTAAAAGGAGAGGAGAGAA-GATGGAAG 745521 v vii - ii vvii - ii - v (GGAA)n#Simpl 297 GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA-AGGAAGGAAGGAAGGAAG 345 chr2ptel1M 745522 GAAGGGAGGATAGAAGGAAGGAATGAGAGTA-GAAGGAAGGAAGAAGGGA 745570 i vi v ii v - i i (GGAA)n#Simpl 346 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 395 chr2ptel1M 745571 TAGATGGAAAGAGGGGAGGATAGAGGGGAGGAAGGGAGATAGG-AGGAAG 745619 vi v i i i vi i i i iv - (GGAA)n#Simpl 396 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG 445 chr2ptel1M 745620 AAAAGAATAAAGGAAGG-AGAGAGGCTAAAAGGAAGGAAAGGAGAGAA-G 745667 i i vi - ii vvii - ii - (GGAA)n#Simpl 446 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG-AAGGAAGGAAGG 494 chr2ptel1M 745668 ATGGAAGGAAGAAAGGATAAAAGGAAGGAAGAAGGGATAGAGGGAAGGAA 745717 v i vii i i vi i (GGAA)n#Simpl 495 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 544 chr2ptel1M 745718 AGGAGAATAGAAAGCGGGAAGACGAAGGAGGGGAAAATGGAGAGAA-GAT 745766 i i i vi i vi -- i i ii v ii - v (GGAA)n#Simpl 545 GGAAGGAAGGAAGGAAGGAAG--GAAGGAAGGAAGGAAGGAAGGAAGGAA 592 chr2ptel1M 745767 GGAAGAAAGAAAGGAAAGAATAGAAGGAAGGAGGGAAGG-AGCAGGGAA- 745814 i i i -i i - v i - (GGAA)n#Simpl 593 GGAAGGAAGGAAGGAAGGAA-GGAAGGAAGGAAGGAAGGAAGGAAGGAAG 641 chr2ptel1M 745815 G-AGGGAGGAGAGAATAGAGGAAGAAAGTCTGGAAGGATGGAAAGGA-GA 745862 - i ii vii i vvv v i i - (GGAA)n#Simpl 642 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 691 chr2ptel1M 745863 AGGGAGGAA-GAAGG--GGTAGAAAGG-AGGGAGGAGGG 745897 i - -- v i - i i (GGAA)n#Simpl 692 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG 730 Matrix = Unknown Transitions / transversions = 2.56 (110/43) Gap_init rate = 0.06 (43 / 703), avg. gap size = 1.02 (44 / 43) 484 30.87 9.38 1.66 chr2ptel1M 747635 747858 (252142) C L2b_3end#LINE/L2 (2) 464 224 m_b75s601i4 2762 chr2ptel1M 747635 TTACTCAATCCATCGGTAAACATTAAGTGCTTTTTGTTTGCCAGGGACTG 747684 i i v v ivii vvi i i i i vi v v? C L2b_3end#LINE 464 TCATTCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTG 415 chr2ptel1M 747685 TGCTAAGAGCTAGAGATATAAAGGCAAA--AGGCAG------TCCCTGCC 747726 i v i i i iv ii -- i ------ C L2b_3end#LINE 414 TGCTAGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCC 365 chr2ptel1M 747727 TTCAAGGAACTTACAGTCTAATGGGGGAGACA-ACAT--------ACACA 747767 i v i i i - -------- vv C L2b_3end#LINE 364 CTCACGGAGCTCACAGTCTAGTGGGGGAGACAGACATGTAANCAGACAAT 315 chr2ptel1M 747768 CATAACACAGTAAGGTAGATGTAGGGACATGGGACACGAGAAGCAAGGC- 747816 ? v viv i i- iviiv ivv v i - i - C L2b_3end#LINE 314 NATAACCCAGAGTGGCAGG-GTAGGACTGGGGGGGCCCAGAGG-AGGGCG 267 chr2ptel1M 747817 TCTGGATTGA---AGGGGGCTGGGGAAGGCTGCCTTTAGAGCAGG 747858 i ivii i---i iii i v --ii v C L2b_3end#LINE 266 CCTGACCCGGCCTGGGGGGTCAGGGAGGGCTTCC--CGGAGGAGG 224 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.70 CpG sites = 44, Kimura (unadjusted) = 42.27 Transitions / transversions = 1.83 (44/24) Gap_init rate = 0.04 (10 / 223), avg. gap size = 2.50 (25 / 10) 497 25.17 6.25 0.66 chr2ptel1M 747641 747784 (252216) C L2d2_3end#LINE/L2 (8) 547 396 m_b75s601i5 2762 chr2ptel1M 747641 AATCCATCGGTAAACATTAAGTGCTTTTTGTTTGCCAGGGACTGTGCTAA 747690 v ivii vvi i i i vi v v v i C L2d2_3end#LIN 547 AATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAG 498 chr2ptel1M 747691 GAGCTA---GAGATATAAAG--GCAAAAGGCA--GTCCCTGCCTTCAAGG 747733 v i--- i i -- i v i -- i C L2d2_3end#LIN 497 GCGCTGTGGGGGATACAAAGAAGTATAAGACATGGTCCCTGCCCTCAAGG 448 chr2ptel1M 747734 AACTTACAGTCTAATGGGGGAGACA--ACATACACACATAACACAGTAAG 747781 i i i v -- v i i - v v i C L2d2_3end#LIN 447 AGCTTACAATCTAGTTGGGGAGACAAGACATAAACACGTGA-AAAGTTAA 399 chr2ptel1M 747782 GTA 747784 i C L2d2_3end#LIN 398 ATA 396 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.38 CpG sites = 22, Kimura (unadjusted) = 31.46 Transitions / transversions = 1.57 (22/14) Gap_init rate = 0.03 (5 / 143), avg. gap size = 2.00 (10 / 5) 261 29.41 2.35 0.00 chr2ptel1M 748116 748200 (251800) MIR3#SINE/MIR 116 202 (6) m_b75s601i6 2763 chr2ptel1M 748116 GGGGCTCAGTTTTCTACTCTTTAAAATTAAGGGAGGGGGCTAGATGCCTT 748165 v i vv v v i ivv i vii MIR3#SINE/MIR 116 GGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCT 165 chr2ptel1M 748166 TTGAGAACCTTTTCAGC-CTTAGA-TCTGGGATACTA 748200 i i iv i i - v v - iv v MIR3#SINE/MIR 166 CTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTA 202 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.70 CpG sites = 12, Kimura (unadjusted) = 37.70 Transitions / transversions = 0.92 (12/13) Gap_init rate = 0.02 (2 / 84), avg. gap size = 1.00 (2 / 2) 456 30.59 2.38 12.42 chr2ptel1M 748906 749241 (250759) C L2c_3end#LINE/L2 (0) 478 173 m_b75s601i7 2764 chr2ptel1M 748906 ATTCAGTCAATCAACAAACATGCATTGAGCACTTACTGTGTGCCAGCCAT 748955 v v vi i i i ---- C L2c_3end#LINE 478 ATTCATTCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAG---- 433 chr2ptel1M 748956 GTGCTAAGAGCTGGAAATGCAAGGACAGGCAAAA-ACAGTCCTTGCCTTC 749004 ------- v ii i i iiiii i - i i i C L2c_3end#LINE 432 -------GCGCTGGGGATACAAAGATGAATAAGACACGGTCCCTGCCCTC 390 chr2ptel1M 749005 AAGGAGCAGCTAGTATCTGATGGTGGAAACAG-CATGAAAAC-GACTGTG 749052 vvvi -- ii v i - ? v - vi - C L2c_3end#LINE 389 AAGGAGCTCACAG--TCTAGTGGAGGAGACAGACANGTAAACAGACAAT- 343 chr2ptel1M 749053 TACAA-ACAAGATACATGAAGAATTAAACGACATAATCTCAGAGGGGAGA 749101 - v - ----- ii vi -- vi viv C L2c_3end#LINE 342 TACAATACAAGTTA-ATGA-----TAAGTGCTATAA--TGGGAGTATAGA 301 chr2ptel1M 749102 CACTAGCACTGAGGG-GAATCGGGAAAAACTTTTGGATTAGAAAGGAAGG 749150 -vi ii iv - v iv i i iii vii i i ?vvv ---- C L2c_3end#LINE 300 CA-GGGTGCTATGGGAGCACAGAGGAGGGCACCTAGACTAGNCTTG---- 256 chr2ptel1M 749151 AGGAGGTCAAGTAATGGAGGGCTTTAACATGGAGGATGTTGTATTTGTCC 749200 - i i----- i --- vi v vii i vv C L2c_3end#LINE 255 -GGGGGTCAG-----GGAAGGCTT---CCCGGAGGAGGTGACATCTGAGC 215 chr2ptel1M 749201 TGGATACCATG-GGAATCCACTGGAGTTTGTCGAGT--AAGGAG 749241 i--i? v -i i vviiv v i ii -- C L2c_3end#LINE 214 TGA--GNCTTGAAGGATGAGTAGGAGTTAGCCAGGTGGAAGGAG 173 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.03 CpG sites = 57, Kimura (unadjusted) = 40.82 Transitions / transversions = 1.73 (57/33) Gap_init rate = 0.13 (45 / 335), avg. gap size = 1.02 (46 / 45) 493 23.18 5.00 1.38 chr2ptel1M 748906 749045 (250955) C L2b_3end#LINE/L2 (0) 466 322 m_b75s601i8 2764 chr2ptel1M 748906 ATTCAGTCAATCAACAAACATGCATTGAGCACTTACTGTGTGCCA-GCCA 748954 v v i vi i i i - ?v C L2b_3end#LINE 466 ATTCATTCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNC 417 chr2ptel1M 748955 TGTGCTAAGAGCTGGAAATGCAA----GGAC-AGGCAAAAACAGTCCTTG 748999 i v ii i i---- i - i i v? i i C L2b_3end#LINE 416 TGTGCTAGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTG 367 chr2ptel1M 749000 CCTTCAAGGAGCAGCTAGTATCTGATGGTGGAAACAG-CATGAAAAC 749045 i v vvvi -- ii v i - v ? C L2b_3end#LINE 366 CCCTCACGGAGCTCACAG--TCTAGTGGGGGAGACAGACATGTAANC 322 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.09 CpG sites = 20, Kimura (unadjusted) = 29.22 Transitions / transversions = 1.67 (20/12) Gap_init rate = 0.04 (6 / 139), avg. gap size = 1.50 (9 / 6) 432 38.97 5.74 1.84 chr2ptel1M 749136 749501 (250499) C L2#LINE/L2 (139) 2943 2564 m_b75s601i9 2764 chr2ptel1M 749136 GATTAGAAAGGAAGGAGGAGGTCAAGTAATGGAGGGCTTTAA----CATG 749181 i i i v ivi i ii ii v v i iv---- v C L2#LINE/L2 2943 GGTCAGAGAGGTAACGGGGGACCAGATCATGTAGGGCCTTGTAGGCCATT 2894 chr2ptel1M 749182 G--AGGATGTTG-TATTTGTCCTGGATACCATGGGAATCCACTGGAGTTT 749228 -- iv -iv iii ii ivv v i vv C L2#LINE/L2 2893 GTAAGGACTTTGGCTTTTACTCTGAGTGAGATGGGAAGCCATTGGAGGGT 2844 chr2ptel1M 749229 GTCGAGTA-AGGAGTGACATGGTTAGACCTGTGCTTTCAGAAAATCACTT 749277 v i i - i iv i ii i v i ii i C L2#LINE/L2 2843 TTTGAGCAGAGGAGTGACATGATCTGACTTACGTTTTAAAAGGATCACTC 2794 chr2ptel1M 749278 TGGTAGCTGAATGGAG-ATGGACTGGAGTGGGTAAAAACTTGAGG-ACAG 749325 iv vi v - i ? v vv iiv v i - vi C L2#LINE/L2 2793 TGGCTGCTGTGTTGAGAATAGACTGNAGGGGGGCAAGGGTGGAAGCAGGG 2744 chr2ptel1M 749326 CGATCCCCCAGCA-ACTGTTGCAACAGCCTGGGCATTTGGTGATTAGACT 749374 v i vvii v -i i ii ii ii ivvv i vivivi C L2#LINE/L2 2743 AGACCAGTTAGGAGGCTATTGCAGTAATCCAGGCGAGAGATGATGGTGGC 2694 chr2ptel1M 749375 CCGCACCAGGGGGAGGGAAGGGACAGAGGAGAGAA----------TCTGA 749414 ii v v iv v v ivi v v ---------- - C L2#LINE/L2 2693 TTGGACCAGGGTGGTGGCAGTGGAGGTGGTGAGAAGTGGTCGGATTCTG- 2645 chr2ptel1M 749415 GAGATGCAGCAGAGGTGAAATGGACCAGAGATGCTATAGAGGTGAAATGG 749464 v iivviii ii iiv vi vv ----- i i v C L2#LINE/L2 2644 GATATATTTTGAAGGTAGAGCCGACAGGATTTGCT-----GATGGATTGG 2600 chr2ptel1M 749465 ATCAGAGATGTTGCAGAGGTGAAATGGATCAGAAATG 749501 vv i i viv ii- i v ii iii C L2#LINE/L2 2599 ATGTGGGGTGTGAGAGAAA-GAGAGGAGTCAAGGATG 2564 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 56.54 CpG sites = 84, Kimura (unadjusted) = 58.51 Transitions / transversions = 1.50 (84/56) Gap_init rate = 0.04 (15 / 365), avg. gap size = 1.87 (28 / 15) 289 34.36 4.29 0.00 chr2ptel1M 750417 750579 (249421) L2b_3end#LINE/L2 281 450 (16) m_b75s601i10 2765 chr2ptel1M 750417 CTTCCCCAG--CTGCCTTGACTTCCTTGGGTACCCTCA-CTCTTCCCCT- 750462 ii -- i i v vii v v i?v ii- v? iv v - L2b_3end#LINE 281 CCCCCCCAGTCCTACCCTGCCACTCTGGGTTATNATTGTCTGNTTACATG 330 chr2ptel1M 750463 TCCCTCCCCCTTTCCAG-CTTTTTGCTTCCTGAGGGCAGGAACCG--TCT 750509 iv i iiv i - v vv i v i -- L2b_3end#LINE 331 TCTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCT 380 chr2ptel1M 750510 TGTTTGCTTGTCTTTGTTTCCCCTGCACTCAGCACCATACCTGGCACACA 750559 vvi i iii vi v v i ii vi?i L2b_3end#LINE 381 GTCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACA 430 chr2ptel1M 750560 GTAAGCTTTTAACAAATGCT 750579 i vi i ii ii L2b_3end#LINE 431 GTAGGCGCTCAGTAAATATT 450 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 48.38 CpG sites = 35, Kimura (unadjusted) = 49.67 Transitions / transversions = 1.67 (35/21) Gap_init rate = 0.03 (5 / 162), avg. gap size = 1.40 (7 / 5) 329 29.72 3.54 1.74 chr2ptel1M 750467 750579 (249421) L2d2_3end#LINE/L2 425 539 (16) m_b75s601i11 2765 chr2ptel1M 750467 TCCCCCTTTCCAGCTT-TTTGCTTCCTGAGGGCAGGAACCGTCTTGTTTG 750515 i ivv i v - vv i i i i v iv v i L2d2_3end#LIN 425 TCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATA 474 chr2ptel1M 750516 CTTGTCTTTGTTTCCCCT---GCACTCAGCACCATACCTGGCACACAGTA 750562 -- v i--- i ii vi i v L2d2_3end#LIN 475 CTT--CTTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAGTA 522 chr2ptel1M 750563 AGCTTTTAACAAATGCT 750579 i vi i i ii L2d2_3end#LIN 523 GGCGCTCAATAAATATT 539 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.86 CpG sites = 21, Kimura (unadjusted) = 39.41 Transitions / transversions = 1.75 (21/12) Gap_init rate = 0.04 (4 / 112), avg. gap size = 1.50 (6 / 4) 427 27.85 22.97 0.55 chr2ptel1M 751737 752032 (247968) C L2b_3end#LINE/L2 (6) 460 99 m_b75s601i14 2766 chr2ptel1M 751737 TCACTCAATAAACATTTATGAAGCACCTGCTGTGTTCCAGGCGCTG---- 751782 i i i ivi i i v ? ---- C L2b_3end#LINE 460 TCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCT 411 chr2ptel1M 751783 ---------AGATACAA-----------AAAGACCCAGTCCCTGACCTTG 751812 ---------i i----------- v ? i v ii C L2b_3end#LINE 410 AGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCA 361 chr2ptel1M 751813 AGGAGCTTACAATCTAGTTGGGGG--TGGGGGTG---GGGGACGACAATA 751857 v i i v i--ii ivi ---?vi i i? C L2b_3end#LINE 360 CGGAGCTCACAGTCTAGTGGGGGAGACAGACATGTAANCAGACAATNATA 311 chr2ptel1M 751858 TGCCAA----GCAAGTTA--ACGGGAAAGAC--AGA--------CATGA- 751890 vv i---- i v -- v iii i -- -------- v - C L2b_3end#LINE 310 ACCCAGAGTGGCAGGGTAGGACTGGGGGGGCCCAGAGGAGGGCGCCTGAC 261 chr2ptel1M 751891 ------AGAAGGGTTAGGGAGGGGCTTCCTGGAGAAGGGGGCTTTTGGAG 751934 ------v ii i - i i v i v - C L2b_3end#LINE 260 CCGGCCTGGGGGGTCAGGGAGGG-CTTCCCGGAGGAGGTGACATTT-GAG 213 chr2ptel1M 751935 TCGGGGCTTAAAGGAAGCAGAGGAATGGG------GAA-------GGGAG 751971 ii i i i i v viv i v ------ ------- i C L2b_3end#LINE 212 CTGAGACCTGAAGGATGAGTAGGAGTTGGCCAGGCGAAGAGGTGGGGAAG 163 chr2ptel1M 751972 AGTGTTCCAGGCCTGGGGGACACCA-GCGAGAATACCCAGAGCTGAGAGA 752020 i i vvi i v - i vi vi v vi i ? C L2b_3end#LINE 162 GGCGTTCCAGGCAGAGGGAACAGCANGTGCAAAGGCCCTGAGGCGGGAGN 113 chr2ptel1M 752021 GGG--GGGCTTGTT 752032 i --v v C L2b_3end#LINE 112 GAGCNTGGCGTGTT 99 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.23 CpG sites = 53, Kimura (unadjusted) = 37.07 Transitions / transversions = 1.83 (53/29) Gap_init rate = 0.06 (17 / 295), avg. gap size = 4.12 (70 / 17) 517 24.81 7.04 0.66 chr2ptel1M 751737 751878 (248122) C L2c_3end#LINE/L2 (6) 472 322 m_b75s601i13 2766 chr2ptel1M 751737 TCACTCAATAAACATTTATGAAGCACCTGCTGTGTTCCAGGCGCT-GAGA 751785 i i vi i i i v - i C L2c_3end#LINE 472 TCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGA 423 chr2ptel1M 751786 TACAAA-------AAGACCCAGTCCCTGACCTTGAGGAGCTTACAATCTA 751828 ------- v i v ii i i C L2c_3end#LINE 422 TACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTA 373 chr2ptel1M 751829 GTTGGGGGTGGGGGTGGG-GGAC-GACAATATGCCAAGCAAGTTAACGGG 751876 v i ivivi iii? -ii - - i v vi i iv C L2c_3end#LINE 372 GTGGAGGAGACAGACANGTAAACAGACAAT-TACAATACAAGTTAATGAT 324 chr2ptel1M 751877 AA 751878 C L2c_3end#LINE 323 AA 322 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.63 CpG sites = 25, Kimura (unadjusted) = 31.83 Transitions / transversions = 2.50 (25/10) Gap_init rate = 0.04 (5 / 141), avg. gap size = 2.20 (11 / 5) 202 36.10 10.72 3.47 chr2ptel1M 751964 752448 (247552) C L2#LINE/L2 (0) 3082 2564 m_b75s601i15 2766 chr2ptel1M 751964 GAAGGGAGAGTGTTCCAGGCCTGGGGGACA-CCAGCGAGAATACCCAGAG 752012 ii i i vvi i - v i vi vi v C L2#LINE/L2 3082 GGGGGAAGAGCGTTCCAGGCAGAGGGAACAGCAAGTGCAAAGGCCCTGAG 3033 chr2ptel1M 752013 CTGAGAGAGGG--GGGCTTGTT----------------GGCTGGGGTCAC 752044 vi i v v --v v ---------------- ii v vi C L2#LINE/L2 3032 GCGGGAGCGTGCCTGGCGTGTTCGAGGAACAGCAAGGAGGCCAGTGTGGC 2983 chr2ptel1M 752045 AGGACCAGAGCATACGTTGGGGTG-----TAGG----GAG-TCTGAAAGG 752084 v v i iivi vv v ----- ---- - v i C L2#LINE/L2 2982 TGGAGCGGAGTGAGCGAGGGGGAGAGTGGTAGGAGATGAGGTCAGAGAGG 2933 chr2ptel1M 752085 -AAGGAGGGGTTACATCGGG-AGGGCGCTGGAGGCCAA-GCAGAGCATTT 752131 - v i iii v iv - vi v v- i ii vv C L2#LINE/L2 2932 TAACGGGGGACCAGATCATGTAGGGCCTTGTAGGCCATTGTAAGGACTTT 2883 chr2ptel1M 752132 TGTATTTATTCTTGAGGGTGATAGGGAGCCATTGGA---TTTGACTGAGC 752178 v iv i - v v i i --- --- C L2#LINE/L2 2882 GGCTTTTACTCT-GAGTGAGATGGGAAGCCATTGGAGGGTTT---TGAGC 2837 chr2ptel1M 752179 AG-GAGGTGACAGGGAGAGGTCTCTGCTTTGGAAAAATCACTTGAGTGGC 752227 - ii v ivvv iii vi i ii ii ivi iv C L2#LINE/L2 2836 AGAGGAGTGACATGATCTGACTTACGTTTTAAAAGGATCACTCTGGCTGC 2787 chr2ptel1M 752228 CGGATGGAGGGTGGACCGGGGTAGGGTCACTCCTGAGGCCGGTGGAGCTC 752277 i vi v ii i i ?i vi iv vvviv i v vi v vv C L2#LINE/L2 2786 TGTGTTGAGAATAGACTGNAGGGGGGCAAGGGTGGAAGCAGGGAGACCAG 2737 chr2ptel1M 752278 CCA-GAAGCCACTG--------CAGGTGGGAG--GATGAGAGTCTGCCCC 752316 ii - i i i -------- i i -- ivi ii vv C L2#LINE/L2 2736 TTAGGAGGCTATTGCAGTAATCCAGGCGAGAGATGATGGTGGCTTGGACC 2687 chr2ptel1M 752317 AGGGCAG-GGCAGGTTCAGAGGGGGCATCTGAGAGGCA--CGGGCCTTGG 752363 ii - ---ii v ---- i ii-- iiii C L2#LINE/L2 2686 AGGGTGGTGGCAG---TGGAGGTGG----TGAGAAGTGGTCGGATTCTGG 2644 chr2ptel1M 752364 TGCCATATTGGATAAGCCACTGGGGGGAGGCAGGAAGAGTTCATGAA--G 752411 vvvi v --- vi ---- i vv i vvv i v i -- C L2#LINE/L2 2643 ATATATTTTG---AAGGTA----GAGCCGACAGGATTTGCTGATGGATTG 2601 chr2ptel1M 752412 GATCCAGGGTGACTGTGGAAGTGGGAGGTGGAGGCTG 752448 vii vvv v i v i ii vi v C L2#LINE/L2 2600 GATGTGGGGTGTGAGAGAAAGAGAGGAGTCAAGGATG 2564 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 49.09 CpG sites = 94, Kimura (unadjusted) = 51.26 Transitions / transversions = 1.25 (94/75) Gap_init rate = 0.07 (35 / 484), avg. gap size = 2.00 (70 / 35) 12 13.05 0.00 3.70 chr2ptel1M 752454 752481 (247519) (GGAGG)n#Simple_repeat 1 27 (0) m_b75s252i2 2767 chr2ptel1M 752454 GGAGGGAAGGGGGGGTGGAGGGGAAGGG 752481 i i - i (GGAGG)n#Simp 1 GGAGGGGAGGGGAGG-GGAGGGGAGGGG 27 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 13 13.74 0.00 8.57 chr2ptel1M 753445 753482 (246518) (CCT)n#Simple_repeat 1 35 (0) m_b75s252i3 2768 chr2ptel1M 753445 CCGCCTCCTTGATCCTCCCTCTGTCCTCCTCCTCCTCC 753482 v - vv - -v (CCT)n#Simple 1 CCTCCTCC-TCCTCCT-CCTC-CTCCTCCTCCTCCTCC 35 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.08 (3 / 37), avg. gap size = 1.00 (3 / 3) 13 23.45 2.44 0.00 chr2ptel1M 754027 754067 (245933) (GGGGGGC)n#Simple_repeat 1 42 (0) m_b75s252i4 2769 chr2ptel1M 754027 GGGAGACGGGCACCGGGGAG-GGAGGGCGGGGGGCAGGGGGC 754067 i i viv i - i i (GGGGGGC)n#Si 1 GGGGGGCGGGGGGCGGGGGGCGGGGGGCGGGGGGCGGGGGGC 42 Matrix = Unknown Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 17 22.79 0.00 0.00 chr2ptel1M 755684 755719 (244281) (C)n#Simple_repeat 1 36 (0) m_b75s252i5 2770 chr2ptel1M 755684 CCCCCCCCTGCCCCTGCTCCCCCCCCTCACCCCCCC 755719 iv iv i i v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 36 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 15 13.67 0.00 0.00 chr2ptel1M 756234 756257 (243743) (C)n#Simple_repeat 1 24 (0) m_b75s252i6 2771 chr2ptel1M 756234 CCCGCCCCCGCCCCCTCCCCCCCC 756257 v v i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCC 24 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 245 28.74 9.20 0.00 chr2ptel1M 756532 756618 (243382) L2c_3end#LINE/L2 384 478 (0) m_b75s601i16 2772 chr2ptel1M 756532 CTCCCCGAGAAC-GGGA---TGTCTTCTGC--CTTTGGTTCT--AGTGCT 756573 ii ii - --- v v -- vv i-- i i L2c_3end#LINE 384 CTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTATCCCCAGCGCC 433 chr2ptel1M 756574 TGGCACACAGTAGGCACTTAATAGTTGCTCCTCGAGTTAGGGAGT 756618 i i i iv i iv i i v iv i L2c_3end#LINE 434 TGGCACATAGTAGGCGCTCAATAAATGTTTGTTGAATGAATGAAT 478 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.19 CpG sites = 17, Kimura (unadjusted) = 38.04 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.05 (4 / 86), avg. gap size = 2.00 (8 / 4) 19 4.50 0.00 0.00 chr2ptel1M 756775 756797 (243203) (C)n#Simple_repeat 1 23 (0) m_b75s252i7 2773 chr2ptel1M 756775 CCCGCCCCCCCCCCCCCCCCCCC 756797 v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCC 23 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 15 16.01 1.72 9.26 chr2ptel1M 758439 758496 (241504) (CCCGCC)n#Simple_repeat 1 54 (0) m_b75s252i8 2774 chr2ptel1M 758439 CCCG-CCCGGCCCCCGCCGCTCTTCCTCCCGACGCTGACCCCCGCCCCGG 758487 - v - - iv - v v i - v (CCCGCC)n#Sim 1 CCCGCCCCCGCCCCCGCC-C-CCGCC-CCCGCCCCCG-CCCCCGCCCCCG 46 chr2ptel1M 758488 CCCCCTGCC 758496 - (CCCGCC)n#Sim 47 CCCCC-GCC 54 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.11 (6 / 57), avg. gap size = 1.00 (6 / 6) 12 19.85 0.00 0.00 chr2ptel1M 758637 758665 (241335) (CGGGG)n#Simple_repeat 1 29 (0) m_b75s252i9 2775 chr2ptel1M 758637 CGGGGCGGGGCTGGAGAGGGCGGGGCAGG 758665 v ivi i (CGGGG)n#Simp 1 CGGGGCGGGGCGGGGCGGGGCGGGGCGGG 29 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 15 0.00 0.00 0.00 chr2ptel1M 759462 759478 (240522) (TG)n#Simple_repeat 1 17 (0) m_b75s252i10 2776 chr2ptel1M 759462 TGTGTGTGTGTGTGTGT 759478 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGT 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 32 22.50 0.00 1.37 chr2ptel1M 759611 759684 (240316) (CA)n#Simple_repeat 1 73 (0) m_b75s252i11 2777 chr2ptel1M 759611 CACACACATATTTTACACACACACACACACACACACTGACATTCACTCAC 759660 i -ivi vv iv v (CA)n#Simple_ 1 CACACACACA-CACACACACACACACACACACACACACACACACACACAC 49 chr2ptel1M 759661 ACACTCACACATTCATACACAGAC 759684 v iv i v (CA)n#Simple_ 50 ACACACACACACACACACACACAC 73 Matrix = Unknown Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.01 (1 / 73), avg. gap size = 1.00 (1 / 1) 12 8.44 0.00 7.41 chr2ptel1M 761313 761341 (238659) (CCCTC)n#Simple_repeat 1 27 (0) m_b75s252i12 2778 chr2ptel1M 761313 CCCTCCCCTTCCCCCCACCCTCCCCACCC 761341 - i - v (CCCTC)n#Simp 1 CCCTCCCC-TCCCCTC-CCCTCCCCTCCC 27 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.07 (2 / 28), avg. gap size = 1.00 (2 / 2) 15 25.32 0.00 0.00 chr2ptel1M 762937 762978 (237022) (CCT)n#Simple_repeat 1 42 (0) m_b75s252i13 2779 chr2ptel1M 762937 CCTCCTTCTTCTTGTCCTCCACCTTCACATCCACCTCCTCCT 762978 i i iv v i v v v (CCT)n#Simple 1 CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT 42 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 181 22.27 1.63 8.70 chr2ptel1M 763321 763443 (236557) L2d_3end#LINE/L2 144 258 (258) m_b75s601i17 2780 chr2ptel1M 763321 CATCCTCCCCTCCTGGACTCCTCTGCTGACCATCCTCTCTC-CTGTCCCA 763369 i i i v v v i v i-- v - i v L2d_3end#LINE 144 CGTTCCCCCCGCCTGGAATGCCCTTCC--CCTTCCTCTCTCTCTATCCAA 191 chr2ptel1M 763370 GCACTGGCCTCCCTGGCTTCCTTTATGTCCCAGC-CAAGTCCCCCCTCCT 763418 ii----- v --- v i v v - v L2d_3end#LINE 192 AT-----CCTACC---CATCCTTCAAGGCCCAGCTCAAGTCCCACCTCCT 233 chr2ptel1M 763419 ACAGGAAGCCTTCCCCGGCCCCTCC 763443 v v i i v L2d_3end#LINE 234 CCACGAAGCCTTCCCTGACCACTCC 258 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 25.14 CpG sites = 11, Kimura (unadjusted) = 26.30 Transitions / transversions = 0.79 (11/14) Gap_init rate = 0.10 (12 / 122), avg. gap size = 1.00 (12 / 12) 209 24.94 10.83 3.10 chr2ptel1M 765733 765852 (234148) MIR3#SINE/MIR 18 146 (62) m_b75s601i18 2781 chr2ptel1M 765733 CAGAGACAGCTGCTGGTGCAGGGGGT--GGAATGCTGGGCGTCGAGTCA- 765779 v --vi -i v i -- ivv i- v v- MIR3#SINE/MIR 18 CAGAGAGAGC--ACGG-ACTGGGAGTCAGGAGACCTGGGT-TCTAGTCCC 63 chr2ptel1M 765780 GCCTTAGACACTTCCTAGCTGTGAGTC--TGGGAAAGTCACTG------T 765821 v iv v vv ? v v -- v v------ MIR3#SINE/MIR 64 GGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCT 113 chr2ptel1M 765822 CTA--CCTCGGTTTTATCAATTGTAAAATGGGG 765852 i-- i iv vi i MIR3#SINE/MIR 114 CTGGGCCTCAGTTTCCTCATCTGTAAAATGAGG 146 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.57 CpG sites = 11, Kimura (unadjusted) = 30.76 Transitions / transversions = 0.61 (11/18) Gap_init rate = 0.08 (9 / 119), avg. gap size = 1.89 (17 / 9) 492 28.18 9.64 0.93 chr2ptel1M 765747 765943 (234057) MIR#SINE/MIR 29 242 (20) m_b75s601i19 2781 chr2ptel1M 765747 GGTGCAGGGGGTGGAATGCTGGGCGTCGAGTCA-GCCTTAGACACTTCCT 765795 iv v i vii v iv vv i v- v iv v v MIR#SINE/MIR 29 GGCTCTGGAGCCAGACTGCCTGGGTTCGAATCCCGGCTCTGCCACTTACT 78 chr2ptel1M 765796 AGCTGTGAGTC--TGGGAAAGTCACTG--------TCTACCTCGGTTTTA 765835 v v -- v i v-------- v i i iv MIR#SINE/MIR 79 AGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCC 128 chr2ptel1M 765836 TCAATTGTAAAATGGGGATCATTAACAGCACCTGTTTCTCAGGTTTGTTG 765885 vi v - i i iii vi v MIR#SINE/MIR 129 TCATCTGTAAAATGGGGATAAT-AATAGTACCTACCTCATAGGGTTGTTG 177 chr2ptel1M 765886 TGAGGATCGAA--AAT--ATAACTGTAAAGAGCGCTAGCACA----TCGG 765927 ii -- i -- vv v -i v ----ii MIR#SINE/MIR 178 TGAGGATTAAATGAGTTAATACATGTAAAGCGC-TTAGAACAGTGCCTGG 226 chr2ptel1M 765928 CGCACAGCAGGGGCTC 765943 i i i i v MIR#SINE/MIR 227 CACATAGTAAGCGCTC 242 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.83 CpG sites = 28, Kimura (unadjusted) = 35.83 Transitions / transversions = 1.04 (28/27) Gap_init rate = 0.04 (8 / 196), avg. gap size = 2.62 (21 / 8) 246 39.17 0.99 5.67 chr2ptel1M 768218 768420 (231580) C MIRb#SINE/MIR (72) 196 3 m_b75s601i20 2782 chr2ptel1M 768218 CTAATGAAACCCTTTGCATTATCTTGGGAGTTAGGGGTATCATTAATCCT 768267 v vv i ivvv iv i i v v -- i - i C MIRb#SINE/MIR 196 CTCATTTAATCCTCACAACAACCCTGCGAGGTAGG--TATTATTA-TCCC 150 chr2ptel1M 768268 CTCTGTTCCAGAAGAGGGAACTTAGGCCTAATGGCCTAAGAGGTTTAATG 768317 vi - v v i v ii i------- v i i C MIRb#SINE/MIR 149 CATT-TTACAGATGAGGAAACTGAGGCTCAG-------AGAGGTTAAGTA 108 chr2ptel1M 768318 GCCTGTCCATTGTCATTTGGCATAAGAGTGACTATGGCCATATT-GAACT 768366 i i i vv ivii vvivi i viv v viv - i C MIRb#SINE/MIR 107 ACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACC 58 chr2ptel1M 768367 TAAGACT-TCTGGGCTCAAGCCTAGAGTTCTAACCACAGCCTCATGTGGC 768415 i i v - ivii iv iv v i vv v vi i iv C MIRb#SINE/MIR 57 CAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCACCACGCTGC 8 chr2ptel1M 768416 TATTC 768420 ivi C MIRb#SINE/MIR 7 CCCTC 3 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 55.65 CpG sites = 39, Kimura (unadjusted) = 56.79 Transitions / transversions = 1.08 (39/36) Gap_init rate = 0.06 (13 / 202), avg. gap size = 1.00 (13 / 13) 298 33.34 5.81 5.81 chr2ptel1M 768238 768409 (231591) C MIRc#SINE/MIR (86) 182 11 m_b75s601i21 2782 chr2ptel1M 768238 ATCTTGGGAGTTAGG-------GGTATCATTAATCCTCTCTGTTCCAGAA 768280 i i v v ------- i - i vi - v v C MIRc#SINE/MIR 182 ACCCTGTGAGGTAGGCAGGGCAGGTATTATTA-TCCCCATT-TTACAGAT 135 chr2ptel1M 768281 GAGGGAACTTAGGCCTAATGGCCTAAGAGGTTTAATGGCCTGTCCATTGT 768330 i v ii i------- v i i i i vv C MIRc#SINE/MIR 134 GAGGAAACTGAGGCTCAG-------AGAGGTTAAGTGACTTGCCCAAGGT 92 chr2ptel1M 768331 CATTTGGCATAAGAGTGACTATGGCCATA--TTGAACTTAAGACTTCTGG 768378 ivii vvivi i - vi ivi-- i ii i v iv C MIRc#SINE/MIR 91 CACACAGCTAGTAAGTGGC-AGAGCCGGGACTCGAACCCAGGTCTTCCTG 43 chr2ptel1M 768379 GCT-CAAGCCTAGAGTTCTAACCACAGCCTCA 768409 i - i i v i vv v vi C MIRc#SINE/MIR 42 ACTCCAAGTCCAGTGCTCTTTCCACTGCACCA 11 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.45 CpG sites = 32, Kimura (unadjusted) = 45.77 Transitions / transversions = 1.45 (32/22) Gap_init rate = 0.08 (13 / 171), avg. gap size = 1.54 (20 / 13) 314 30.34 1.34 7.09 chr2ptel1M 768254 768402 (231598) C MIR1_Amn#SINE/MIR (69) 161 21 m_b75s601i22 2782 chr2ptel1M 768254 GTATCATTAATCCTCTCTGTTCCAGAAGAGGGAACTTAGGCCTAATGGCC 768303 - i vi - v v i v ?i i----- C MIR1_Amn#SINE 161 GTATCATTA-TCCCCATT-TTACAGATGAGGAAACTGAGGCNCAG----- 119 chr2ptel1M 768304 TAAGAGGTTTAATGGCCTGTCCATTGTCATTTGGCATAAGAGTGACTATG 768353 -- ?v i i i i vv i?ii ?viv? i - vi C MIR1_Amn#SINE 118 --AGAGGTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNAGTGGC-AGA 72 chr2ptel1M 768354 GCCA--TATTGAACTTAAGACTTCTGGGCTCAAGCCTAGAGTTCTAACCA 768401 i--v? ? ii i v i i i ii v i i v i v C MIR1_Amn#SINE 71 GCCGGGANTNGAACCCAGGTCTCCCGAGTCCCAGTCCAGTGCTCTATCCA 22 chr2ptel1M 768402 C 768402 C MIR1_Amn#SINE 21 C 21 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.65 CpG sites = 27, Kimura (unadjusted) = 43.43 Transitions / transversions = 1.80 (27/15) Gap_init rate = 0.07 (11 / 148), avg. gap size = 1.09 (12 / 11) 218 27.83 4.94 2.41 chr2ptel1M 768416 768496 (231504) C L2c_3end#LINE/L2 (22) 456 374 m_b75s601i23 2783 chr2ptel1M 768416 TATTCAGGTCCCATGATGC-CCAGGCCCTGGGAATGCAA--ATGCACAAG 768462 v vv i iv i- v i i -- v i - C L2c_3end#LINE 456 TATTGAGCGCCTACTATGTGCCAGGCGCTGGGGATACAAAGATGAATAA- 408 chr2ptel1M 768463 CGGGACAAGTTCTG-CCTCAAGGAGCTTCCATTCT 768496 - iv iivii - iv v C L2c_3end#LINE 407 -GACACGGTCCCTGCCCTCAAGGAGCTCACAGTCT 374 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.48 CpG sites = 12, Kimura (unadjusted) = 35.44 Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.06 (5 / 80), avg. gap size = 1.20 (6 / 5) 20 14.05 0.00 7.84 chr2ptel1M 768655 768709 (231291) (AGGCAGG)n#Simple_repeat 1 51 (0) m_b75s252i14 2784 chr2ptel1M 768655 AGGCAGGAGCCAGGTGGGCCAGGAGGCAGGAGCCGGGTGGGCCAGGGGGC 768704 v -i - v i -i - i (AGGCAGG)n#Si 1 AGGCAGGAGGCAGG-AGG-CAGGAGGCAGGAGGCAGG-AGG-CAGGAGGC 46 chr2ptel1M 768705 AGGAG 768709 (AGGCAGG)n#Si 47 AGGAG 51 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.07 (4 / 54), avg. gap size = 1.00 (4 / 4) 184 32.14 7.14 0.00 chr2ptel1M 768930 769013 (230987) MIRc#SINE/MIR 143 232 (36) m_b75s601i24 2785 chr2ptel1M 768930 AACTGGGCTAATAATAGCA--TTTACCT---TCACAGGACTGGGATGAGG 768974 iv v v v--ii i --- ii vvi MIRc#SINE/MIR 143 AATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGG 192 chr2ptel1M 768975 AGCAAGTGAGAGGA-GGAGATGAAAGCTTCTGGCAGGCTG 769013 v i vi - v vi vii v i ii MIRc#SINE/MIR 193 ATCAAATGAGATAATGTATGTGAAAGCGCTTTGTAAACTG 232 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.07 CpG sites = 15, Kimura (unadjusted) = 43.07 Transitions / transversions = 1.25 (15/12) Gap_init rate = 0.04 (3 / 83), avg. gap size = 2.00 (6 / 3) 206 27.78 0.00 1.85 chr2ptel1M 768930 768984 (231016) MIR#SINE/MIR 139 192 (70) m_b75s601i25 2785 chr2ptel1M 768930 AACTGGGCTAATAATAGCATTTACCTTCACAGGACTGGGATGAGGAGCAA 768979 iv v i ii - i ii vvi vi MIR#SINE/MIR 139 AATGGGGATAATAATAGTACCTACC-TCATAGGGTTGTTGTGAGGATTAA 187 chr2ptel1M 768980 GTGAG 768984 i MIR#SINE/MIR 188 ATGAG 192 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.20 CpG sites = 10, Kimura (unadjusted) = 36.20 Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1) 41 22.66 4.72 1.53 chr2ptel1M 769113 769239 (230761) (GAG)n#Simple_repeat 1 131 (0) m_b75s252i15 2786 chr2ptel1M 769113 GAGGAGGAGCAGGAAGAGGAGG-GGAAAAAGAGGGGGGAGAAGAGGAAAA 769161 v i - ii i i ii i ii (GAG)n#Simple 1 GAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA 50 chr2ptel1M 769162 GG-GGAGGAGGAAGAAGAAGGAGGGAGAGGAAGAGG-GGTGGGTGA-GAG 769208 - - i i ii i - v iv - (GAG)n#Simple 51 GGAGGAGGAGG-AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG 99 chr2ptel1M 769209 CAAGGA-GAGGAGAAGG-GGAAGAGGAGGAAGA 769239 -i - i - i i (GAG)n#Simple 100 -GAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA 131 Matrix = Unknown Transitions / transversions = 6.67 (20/3) Gap_init rate = 0.06 (8 / 126), avg. gap size = 1.00 (8 / 8) 35 17.96 5.88 4.13 chr2ptel1M 769116 769234 (230766) (GAGGA)n#Simple_repeat 1 121 (0) m_b75s252i16 2786 chr2ptel1M 769116 GAGGAGCAGGAAGAGGAGGGGAAAAAGAGGGGGGAGAAGAGGAAAAGGGG 769165 - - i - i i i i i - i i (GAGGA)n#Simp 1 GAGGAG-AGG-AGAGGAGAGG-AGAGGAGAGGAGAGGAGAGG-AGAGGAG 46 chr2ptel1M 769166 AGGAG-GAAGAAGA-AGGAG-GGAGAGGAAGAGGGGTGG-G-TGAGAGCA 769210 - i i - - - i v - -v v (GAGGA)n#Simp 47 AGGAGAGGAGAGGAGAGGAGAGGAGAGG-AGAGGAGAGGAGAGGAGAGGA 95 chr2ptel1M 769211 -AGGAGAGGAGAAG-GGGAAGAGGAG 769234 - i - i i (GAGGA)n#Simp 96 GAGGAGAGGAGAGGAGAGGAGAGGAG 121 Matrix = Unknown Transitions / transversions = 4.67 (14/3) Gap_init rate = 0.10 (12 / 118), avg. gap size = 1.00 (12 / 12) 20 0.00 0.00 0.00 chr2ptel1M 769607 769628 (230372) (C)n#Simple_repeat 1 22 (0) m_b75s252i17 2787 chr2ptel1M 769607 CCCCCCCCCCCCCCCCCCCCCC 769628 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCC 22 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 30 18.23 1.59 0.00 chr2ptel1M 770137 770199 (229801) (AGG)n#Simple_repeat 1 64 (0) m_b75s252i18 2788 chr2ptel1M 770137 AGGAGGAGGAGGAGGAAGGGGAGAAGGATGAAGAGG-GGAAAAGGGGGAG 770185 i i i v i - ii i (AGG)n#Simple 1 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG 50 chr2ptel1M 770186 GAGCAGGAGGACGA 770199 v v (AGG)n#Simple 51 GAGGAGGAGGAGGA 64 Matrix = Unknown Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.02 (1 / 62), avg. gap size = 1.00 (1 / 1) 427 28.83 2.41 1.80 chr2ptel1M 771173 771338 (228662) C MIR1_Amn#SINE/MIR (17) 213 47 m_b75s601i26 2789 chr2ptel1M 771173 TTGTGTTCAACTTTTCATGACCCATTTGCAGAG-ATTCTGCAATGATCTG 771221 i vvv v viviv iv i - i i i v ivvvv C MIR1_Amn#SINE 213 TTATGTAGCACTTTTCATCAGTAGATCTCAAAGCACTTTACAAAGGAGGT 164 chr2ptel1M 771222 CCATTTCCTTCTCCAGCTCACTGTACAGATGAAGAAACTGAG--TCAGAC 771269 vi v v v ---i i v i --? v C MIR1_Amn#SINE 163 CAGTATCATTATCC---CCATTTTACAGATGAGGAAACTGAGGCNCAGAG 117 chr2ptel1M 771270 AGGGGGAGTGACTTGCCCAGGACCA-ACAGCTCCTTAGTGTCTGAGACTG 771318 v?i i ii -? ?vvi? v v v v C MIR1_Amn#SINE 116 AGGTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNAGTGGCAGAGCCGG 67 chr2ptel1M 771319 GATTTGAACTCAGGGCTTCC 771338 ? ? i v i C MIR1_Amn#SINE 66 GANTNGAACCCAGGTCTCCC 47 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.68 CpG sites = 20, Kimura (unadjusted) = 38.68 Transitions / transversions = 0.74 (20/27) Gap_init rate = 0.04 (6 / 165), avg. gap size = 1.17 (7 / 6) 496 23.85 6.15 0.00 chr2ptel1M 771238 771367 (228633) C MIRc#SINE/MIR (120) 148 11 m_b75s601i27 2789 chr2ptel1M 771238 CTCACTGTACAGATGAAGAAACTGAG--TCAGACAGGGGGAGTGACTTGC 771285 i i v i -- v vvi C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr2ptel1M 771286 CCAGGACCA-ACAGCTCCTTAGTGTCTGAGACTGGATTTGAACTCAGGGC 771334 i ii - vv v v v v v i i i v C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTC 49 chr2ptel1M 771335 TTCCCAACT----GTGCTG-GTATCTTCTACTGCACCA 771367 ii ---- v v - ivii i C MIRc#SINE/MIR 48 TTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCA 11 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.92 CpG sites = 16, Kimura (unadjusted) = 28.99 Transitions / transversions = 1.07 (16/15) Gap_init rate = 0.03 (4 / 129), avg. gap size = 2.00 (8 / 4) 227 34.08 7.80 4.44 chr2ptel1M 771351 771568 (228432) L2#LINE/L2 2774 2998 (84) m_b75s601i28 2790 chr2ptel1M 771351 TATCTTC--TACTGCA-CCA-AGTGATTTTCCTAAC-TGAAGGTCTGACC 771395 ii --i v - - ii ii v-i v i v i L2#LINE/L2 2774 TATTCTCAACACAGCAGCCAGAGTGATCCTTTTAAAACGTAAGTCAGATC 2823 chr2ptel1M 771396 ACGTCATTGCCCTGCACATAAAACCAGCCTAGGGCTTCCC---------- 771435 i i v i v -- vv v v ---------- L2#LINE/L2 2824 ATGTCACTCCTCTGCTCA--AAACCCTCCAATGGCTTCCCATCTCACTCA 2871 chr2ptel1M 771436 GGACCAAATATAAAGTGCTC-TGTGGGCATCCAAAGGCCCTCAGGACTTC 771484 iiiv vvi v i-iivv v v i v iv v ii v L2#LINE/L2 2872 GAGTAAAAGCCAAAGTCCTTACAATGGCCTACAAGGCCCTACATGATCTG 2921 chr2ptel1M 771485 CCTTCCCGTTCTTCATTGCTCTGACCACTCCCCATGCCTGAAACTCTTCC 771534 viii ---- iiv v vi i v i -- vv ii L2#LINE/L2 2922 GTCCCCCGTT----ACCTCTCTGACCTCATCTCCTACC--ACTCTCCCCC 2965 chr2ptel1M 771535 TC-CTCACTCTGCTTCCCGGCTTCTCCGGCTCCCT 771568 - i -- i iv v i ii L2#LINE/L2 2966 TCGCTCACTCCGCT--CCAGCCACACTGGCCTCCT 2998 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.17 CpG sites = 40, Kimura (unadjusted) = 46.99 Transitions / transversions = 1.29 (40/31) Gap_init rate = 0.08 (17 / 217), avg. gap size = 1.59 (27 / 17) 234 25.30 10.96 2.53 chr2ptel1M 772823 772968 (227032) C MamRTE2#LINE/RTE-BovB (1388) 164 7 m_b75s551i1 2791 chr2ptel1M 772823 GCTGTTCCTGACGTTTCTCCTGGAGTTGTCGGGCAGCAAACCCC----CA 772868 i i i i i ? i v i ii vv ---- C MamRTE2#LINE/ 164 GTTGTTCTTGGCATTTTTCCTGNAGCTGGCGAGCAGTGAAGACCGTATCA 115 chr2ptel1M 772869 -TTG-ACCTC------CTCTGAAGCCACGCTG-GCTCCCGGCGAGATGAC 772909 - -i ------ i v - v i - v vi C MamRTE2#LINE/ 114 GTTGCGCCTCTNGATGCTCTAAACCCACGCTGAGATTCCGG-GAGAAGCT 66 chr2ptel1M 772910 CTTCTTCCAGATGCAGGA-TCAGCCACTGAAGAGGA--CTGGCAAGAATC 772956 vv v vv v - i ---i v i -- v vi C MamRTE2#LINE/ 65 CTTCAGCAAGTGGGAGGAGTCGG---TTCAGGAGGATTCTTGCAATGATC 19 chr2ptel1M 772957 TTGCCAGCGATG 772968 v i i C MamRTE2#LINE/ 18 TTTCCGGCGGTG 7 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 28.57 CpG sites = 19, Kimura (unadjusted) = 31.62 Transitions / transversions = 1.12 (19/17) Gap_init rate = 0.08 (11 / 145), avg. gap size = 1.82 (20 / 11) 200 27.16 0.00 10.45 chr2ptel1M 774649 774722 (225278) C MamRTE1#LINE/RTE-BovB (3365) 447 381 m_b75s601i29 2792 chr2ptel1M 774649 TTTAGGGTCCCTTTTCCAGGCCCTTCTTCACACTGTGAGGCGAGCAGCAG 774698 iv i ? ii --- vi ii i iv C MamRTE1#LINE/ 447 TTTAGGGCACCTTTTCTAGNCCCTTCCCCA---TTCGGAGTGAGCAGCGC 401 chr2ptel1M 774699 CTGCTCAGACCCCGGGGGCTGCTC 774722 v?v ii i ----i C MamRTE1#LINE/ 400 GNTCCTAAAC----AGGGCTGCTC 381 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.55 CpG sites = 13, Kimura (unadjusted) = 36.58 Transitions / transversions = 2.60 (13/5) Gap_init rate = 0.10 (7 / 73), avg. gap size = 1.00 (7 / 7) 371 33.09 1.55 3.97 chr2ptel1M 775328 775456 (224544) L2c_3end#LINE/L2 346 471 (7) m_b75s601i30 2793 chr2ptel1M 775328 GCCTGTTTGTTTGCCGGGCTCCTCCATGAAGCTGAGGGTTCTCTGGAGAT 775377 i ii? i v v iv ii v i i ii ii ii L2c_3end#LINE 346 GTCTGTTTACNTGTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGC 395 chr2ptel1M 775378 AGGGGC--TGTCTGTGTCCCTAGCACTTAGCACACACAGTGTCTGGCACA 775425 i -- - i i v ---- v i iv v i i L2c_3end#LINE 396 AGGGACCGTGTCT-TATTCAT----CTTTGTATCCCCAGCGCCTGGCACA 440 chr2ptel1M 775426 TAGTAGGTACCTACCAAATGCTTCCCGAGTG 775456 ii ii vi i vii i L2c_3end#LINE 441 TAGTAGGCGCTCAATAAATGTTTGTTGAATG 471 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.86 CpG sites = 31, Kimura (unadjusted) = 48.45 Transitions / transversions = 3.10 (31/10) Gap_init rate = 0.05 (6 / 128), avg. gap size = 1.17 (7 / 6) 12 15.26 3.45 0.00 chr2ptel1M 776614 776642 (223358) (AGG)n#Simple_repeat 1 30 (0) m_b75s252i19 2794 chr2ptel1M 776614 AGGAGGA-GACGAGGAGGAGTTGGGGGAGG 776642 - v vv i (AGG)n#Simple 1 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGG 30 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1) 13 20.67 2.08 4.26 chr2ptel1M 777064 777111 (222889) (TCCCC)n#Simple_repeat 1 47 (0) m_b75s252i20 2795 chr2ptel1M 777064 TCCCCTCCCCTCCCCCCGCCGCTCGGCCCCT-TCCTCACCCGCCCGCTC 777111 i v v i vv -i - v - (TCCCC)n#Simp 1 TCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTC-CCCTCCC-CTC 47 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.06 (3 / 47), avg. gap size = 1.00 (3 / 3) 188 24.49 6.12 0.00 chr2ptel1M 777798 777846 (222154) MIRb#SINE/MIR 55 106 (162) m_b76s601i0 2796 chr2ptel1M 777798 CCGAGCTCAAATTCAGCCTCTGACAC---CGAGCTGTGCGGCCCTGGGCA 777844 i i i i i v v v --- v i i i MIRb#SINE/MIR 55 CTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 104 chr2ptel1M 777845 AG 777846 MIRb#SINE/MIR 105 AG 106 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.67 CpG sites = 8, Kimura (unadjusted) = 30.68 Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.02 (1 / 48), avg. gap size = 3.00 (3 / 1) 19 14.69 0.00 0.00 chr2ptel1M 778567 778602 (221398) (ACGC)n#Simple_repeat 1 36 (3) m_b76s252i2 2797 chr2ptel1M 778567 ACGCACGCACGCCCGCACGCACGCCCGCCCCCAGGC 778602 v v v v v (ACGC)n#Simpl 1 ACGCACGCACGCACGCACGCACGCACGCACGCACGC 36 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 26 0.00 0.00 0.00 chr2ptel1M 778603 778627 (221373) (TCCCG)n#Simple_repeat 1 25 (0) c_b76s251i0 2798 chr2ptel1M 778603 TCCCGTCCCGTCCCGTCCCGTCCCG 778627 (TCCCG)n#Simp 1 TCCCGTCCCGTCCCGTCCCGTCCCG 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 30 16.86 0.00 0.00 chr2ptel1M 783132 783184 (216816) (C)n#Simple_repeat 1 53 (0) m_b76s252i3 2799 chr2ptel1M 783132 CCCCCCCCCCCCCCCCGCCCCGGGTCCTCCTCCCCCCCCCCCCCCCCCGC 783181 v vvvi i i v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 50 chr2ptel1M 783182 CCC 783184 (C)n#Simple_r 51 CCC 53 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 282 26.79 3.70 6.67 chr2ptel1M 783571 783678 (216322) MIR3#SINE/MIR 76 180 (28) m_b76s601i1 2800 chr2ptel1M 783571 AGCTAGCTGCGTGACCCTGGAGAAG-CGCTT-GTCCCTCTTCCCCCAAGT 783618 i ? i i iv - i -ii i vvv iv MIR3#SINE/MIR 76 AACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGT 125 chr2ptel1M 783619 TTTCTCACCTGTAAAGTGAGACGTGGAAGGGCTGGGCCA-ACCAT-TCCA 783666 i i i -------i i i i - iv - i MIR3#SINE/MIR 126 TTCCTCATCTGTAAAATGAG-------GGGGTTGGACTAGATGATCTCTA 168 chr2ptel1M 783667 AGCTCTCTCCCA 783678 v i i MIR3#SINE/MIR 169 AGGTCCCTTCCA 180 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.51 CpG sites = 20, Kimura (unadjusted) = 35.51 Transitions / transversions = 2.86 (20/7) Gap_init rate = 0.10 (11 / 107), avg. gap size = 1.00 (11 / 11) 300 26.95 18.11 0.67 chr2ptel1M 786082 786208 (213792) C MIR#SINE/MIR (107) 155 7 m_b76s601i2 2801 chr2ptel1M 786082 CTAGCACTGTCTTT-TTTTA-AGCTGAGGAAATTGGGG----------TT 786119 vi i i iii- - v i i ---------- C MIR#SINE/MIR 155 CTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTT 106 chr2ptel1M 786120 AAGTGAGTTGCCCAGGGTCCCAGAA--AGT--GTGTCTGAGGCAGGATTT 786165 i v i v v i-- -- v v v i i C MIR#SINE/MIR 105 AAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTC 56 chr2ptel1M 786166 GAACTCGGATCCTCCTGACTTCAGGGCTC-------TAACTACTGTGCCA 786208 i i iivv - i i i i ------- i i i C MIR#SINE/MIR 55 GAACCCAGGCAGT-CTGGCTCCAGAGCCCGTGCTCTTAACCACTATGCTA 7 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.58 CpG sites = 24, Kimura (unadjusted) = 35.16 Transitions / transversions = 2.40 (24/10) Gap_init rate = 0.06 (7 / 126), avg. gap size = 3.43 (24 / 7) 377 22.06 16.80 2.10 chr2ptel1M 786096 786220 (213780) C MIRc#SINE/MIR (124) 144 2 m_b76s601i3 2801 chr2ptel1M 786096 TTTTA-AGCTGAGGAAATTGGGG----------TTAAGTGAGTTGCCCAG 786134 - v i i ---------- v i C MIRc#SINE/MIR 144 TTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAA 95 chr2ptel1M 786135 GGTCCCAGAA--AGT--GTGTCTGAGGCAGGATTTGAACTCGGATCCTCC 786180 v v i-- -- v v v i i i i i i i C MIRc#SINE/MIR 94 GGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCC 45 chr2ptel1M 786181 TGACTTCAGG------GCTCTAACTACTGTGCCACCTAGCTGCCCC 786220 i i ------ vv i ii ---i i C MIRc#SINE/MIR 44 TGACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC---ACTGCCTC 2 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 24.72 CpG sites = 18, Kimura (unadjusted) = 27.00 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.06 (8 / 124), avg. gap size = 3.00 (24 / 8) 371 24.15 2.65 8.41 chr2ptel1M 790649 790761 (209239) MIRc#SINE/MIR 20 126 (142) m_b76s601i4 2802 chr2ptel1M 790649 GGACAGAGCCCCAGCCCCGAAGTCAGGAGGACCCGAGTTCAAATGTGGCC 790698 v v ii v ii i i i i i i viv v MIRc#SINE/MIR 20 GGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGC 69 chr2ptel1M 790699 TCAGACACATAACACTTCCCAGCTGTGGGACTCTGGGCAAGTCACTTAGC 790748 ------- iv v i v ii i MIRc#SINE/MIR 70 TC-------TGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAAC 112 chr2ptel1M 790749 C---CTGATTGCCTCA 790761 --- -- MIRc#SINE/MIR 113 CTCTCTGA--GCCTCA 126 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.41 CpG sites = 16, Kimura (unadjusted) = 29.81 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.09 (10 / 112), avg. gap size = 1.20 (12 / 10) 243 29.49 7.63 6.82 chr2ptel1M 790650 790780 (209220) MIR3#SINE/MIR 20 151 (57) m_b76s601i5 2802 chr2ptel1M 790650 GACAGAGCCCCAGCCCCGAAGTCAGGAGGACCCGAGTTCAAATGTGGCCT 790699 v v -i v iv i - i i v i viv v MIR3#SINE/MIR 20 GAGAGAGCAC-GGACTGGGAGTCAGGAG-ACCTGGGTTCTAGTCCCGGCT 67 chr2ptel1M 790700 CAGACACATAACACTTCCCAGCTGTGGGACTCTGGGCAAGTCACTT---- 790745 v v - ------i? v ii ---- MIR3#SINE/MIR 68 CTGCCAC-TAAC------TNGCTGTGTGACCTTGGGCAAGTCACTTCACC 110 chr2ptel1M 790746 ------AGCCCTGATTGCCTCAACAGGAAAAAAAAAAAGTT 790780 ------i iiii v v v v vi iiii MIR3#SINE/MIR 111 TCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTT 151 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.38 CpG sites = 20, Kimura (unadjusted) = 38.75 Transitions / transversions = 1.25 (20/16) Gap_init rate = 0.08 (11 / 130), avg. gap size = 1.73 (19 / 11) 15 28.06 0.00 0.00 chr2ptel1M 794749 794795 (205205) (AGG)n#Simple_repeat 1 47 (0) m_b76s252i4 2803 chr2ptel1M 794749 AGGAGGAGGACGGCGACATGGAGGTGGAGGAGGCTGAAGGGGAGGAG 794795 v iv viv v vv i i (AGG)n#Simple 1 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG 47 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 17 4.94 0.00 0.00 chr2ptel1M 795189 795209 (204791) (G)n#Simple_repeat 1 21 (0) m_b76s252i5 2804 chr2ptel1M 795189 GGTGGGGGGGGGGGGGGGGGG 795209 v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGG 21 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 17 0.00 0.00 0.00 chr2ptel1M 795238 795256 (204744) (G)n#Simple_repeat 1 19 (0) m_b76s252i6 2804 chr2ptel1M 795238 GGGGGGGGGGGGGGGGGGG 795256 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGG 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 217 26.09 10.14 0.00 chr2ptel1M 795568 795636 (204364) L2c_3end#LINE/L2 382 457 (21) m_b76s601i6 2805 chr2ptel1M 795568 AGCTCCTCAAGGGCAAGAA--GTGTC---CCCAGTGTT-TAGCCCC-GTG 795610 ii i i -- ---ii viv - v - i L2c_3end#LINE 382 AGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTATCCCCAGCG 431 chr2ptel1M 795611 TCTGGTACACAGTTGGGGTTTAATAA 795636 i i i v v i i L2c_3end#LINE 432 CCTGGCACATAGTAGGCGCTCAATAA 457 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.43 CpG sites = 13, Kimura (unadjusted) = 33.74 Transitions / transversions = 2.60 (13/5) Gap_init rate = 0.06 (4 / 68), avg. gap size = 1.75 (7 / 4) 229 26.00 0.00 0.00 chr2ptel1M 795587 795636 (204364) L2b_3end#LINE/L2 396 445 (21) m_b76s601i7 2805 chr2ptel1M 795587 GTGTCCCCAGTGTTTAGCCCCGTGTCTGGTACACAGTTGGGGTTTAATAA 795636 i i ii v v ? i i v v i i i L2b_3end#LINE 396 GTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAA 445 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.03 CpG sites = 9, Kimura (unadjusted) = 34.26 Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 13 29.98 1.41 4.35 chr2ptel1M 796063 796133 (203867) (CCCTGCC)n#Simple_repeat 1 69 (0) m_b76s252i7 2806 chr2ptel1M 796063 CCCGGGCCCCTGCCCCCCGGCCTCTGTCCCACTGACCTCCAGCCTCTCGG 796112 v v i v i - v - i v - i v (CCCTGCC)n#Si 1 CCCTGCCCCCTGCCCCCTGCCCCCTG-CCCCCTG-CCCCCTGCC-CCCTG 47 chr2ptel1M 796113 CTTCTTG-TCCTTGCCGCCTGC 796133 ii i -i i v (CCCTGCC)n#Si 48 CCCCCTGCCCCCTGCCCCCTGC 69 Matrix = Unknown Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.06 (4 / 70), avg. gap size = 1.00 (4 / 4) 15 15.84 0.00 2.78 chr2ptel1M 796494 796530 (203470) (GGGGGCC)n#Simple_repeat 1 36 (0) m_b76s252i8 2807 chr2ptel1M 796494 GGGGGGCGGGGGCTGGGGATCCGGGGGACTGGGGCCG 796530 v i -v v v (GGGGGCC)n#Si 1 GGGGGCCGGGGGCCGGGG-GCCGGGGGCCGGGGGCCG 36 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 18 12.57 0.00 0.00 chr2ptel1M 798165 798191 (201809) (A)n#Simple_repeat 1 27 (0) m_b76s252i9 2808 chr2ptel1M 798165 AAAAAAAAAAAAGAAAGGAAAAAAAAA 798191 i ii (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAA 27 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 768 29.36 0.00 1.37 chr2ptel1M 798353 798649 (201351) C L1ME3G_3end#LINE/L1 (628) 296 4 m_b76s551i0 2809 chr2ptel1M 798353 TTCACAACTCCACCAACAATGCATCAGCATCCCGGTTTTCCCACATCCCC 798402 i vii i i i v vi v v i i i C L1ME3G_3end#L 296 TTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCACACCCTC 247 chr2ptel1M 798403 TCCAACATTCATCATTATCTATTCTTGTCATCTTAGCCAATCTGACAGGT 798452 v i ?ivi v ?ii vvv i v ii C L1ME3G_3end#L 246 GCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATCTGATGGGT 197 chr2ptel1M 798453 GTGTAGTGGTACCTTAGAGTCGTCTTAATTTGCATTTCTCTGATCAGTAG 798502 viv i i i vv i i i i v C L1ME3G_3end#L 196 GAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGATTACTAG 147 chr2ptel1M 798503 TGATCTGGAACACTCTTTCATATGAGTAGAAATAATTTCAATTTCTTCAT 798552 vv v i iii vv vviiiv vv i v C L1ME3G_3end#L 146 TGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGTATTTCCTCTT 97 chr2ptel1M 798553 CTGAAAATTGTCTCTTCATATCCTTTGACCATTTCTCAATTGCAGAATGA 798602 vi i v v i v -- iv v C L1ME3G_3end#L 96 CTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTG--GGTTGT 49 chr2ptel1M 798603 TTTAAATTCTTTTAGATTTGAGTCAATTCTCTATATATTTTAAAAAT 798649 i --v v v vivv i i i ii v C L1ME3G_3end#L 48 CTT--TTTCTTATTGATTTGTAGGAGTTCTTTATATATTCTGGATAT 4 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 38.18 CpG sites = 45, Kimura (unadjusted) = 38.18 Transitions / transversions = 1.10 (45/41) Gap_init rate = 0.01 (4 / 296), avg. gap size = 1.00 (4 / 4) 17 9.12 0.00 0.00 chr2ptel1M 798975 798998 (201002) (T)n#Simple_repeat 1 24 (0) m_b76s252i10 2810 chr2ptel1M 798975 TTTTCTTTTCTTTTTTTTTTTTTT 798998 i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTT 24 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 16 9.78 0.00 0.00 chr2ptel1M 799093 799114 (200886) (A)n#Simple_repeat 1 22 (0) m_b76s252i11 2811 chr2ptel1M 799093 AAAAAAAAAAAAAATAATAAAA 799114 v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAA 22 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 307 37.51 4.10 2.11 chr2ptel1M 799295 799806 (200194) C L1ME4a_3end#LINE/L1 (338) 533 12 m_b76s551i1 2812 chr2ptel1M 799295 TACTATAACCTCATTCAGCAGGTCCCCAGTTGAGGGATGTCCCTTCAGTT 799344 i ii - i i vi? vi vv ii --- vi C L1ME4a_3end#L 533 TACCATAATTT-ATTTAACCANTCCCCTATTGTTGGACAT---TTAGGTT 488 chr2ptel1M 799345 G---CCAGTAGT---CTATTACCAAAAAGAGCTGCTCTGGATGTTTTGGT 799388 --- i vv --- i- v iv vv i ii ii v C L1ME4a_3end#L 487 GTTTCCAATTTTTCGCTATTAT-AAATAATGCTGCGATGAACATCCTTGT 439 chr2ptel1M 799389 ACCTGTTAGTCCTCCTCC---TTTTTCATTGACCTCTTGGGAAATAGATG 799435 v i-- i i iv ? --- i i v iviii i v v vviv C L1ME4a_3end#L 438 ACATA--AATCTTTGTNCACATCTCTGATTATTTCCTTAGGATAAATTCC 391 chr2ptel1M 799436 AAGCAGTGATATTGATGGCTCCA-GGTTGTGGACAGTTTTCTTGCTCTTT 799484 v v iv iv v v - v i ? v vvv i v C L1ME4a_3end#L 390 TAGAAGTGGAATTACTGGGTCAAAGGGTATGNACATTTTTAAGGCTTTTG 341 chr2ptel1M 799485 GGACATAGCTCCAAGTTGCTCTCCGGAATAGATGGACTCGTCGTCAGCTC 799534 iv viv i i i vi v v ivi ivv vii C L1ME4a_3end#L 340 ATACATATTGCCAAATTGCCCTCCAGAAAGGTTGTACCAATTTACACTCC 291 chr2ptel1M 799535 TACCAGTGATGTGTTAGAATCCCTGTTTTTCTGCAGACTT-----TACGG 799579 i iii i v i v i i? ii vv i-----i v C L1ME4a_3end#L 290 CACCAGCAGTGTATGAGAGTGCCCGTTTCNCCACACCCTCGCCAACACTG 241 chr2ptel1M 799580 AGTTTTGTCATTTTCCT---TTTCTGTCACCTTAAATGCATTTGAGGTGC 799626 i v i v i ii --- i i i vi i - ivi vvi ii v C L1ME4a_3end#L 240 GGTATTATCAATCTTTTAAATCTTTGCCAATTTGA-TAGGTGAAAAATGG 192 chr2ptel1M 799627 TA-CT-ATCTCTGTTTTGGCTTGCGTTTTCTCTGGTTTTTAGCAAGGTGG 799674 - - ivi iii i - i i vi ii v C L1ME4a_3end#L 191 TATCTCATTGTTGTTTTAATTTGCATTT-CTTTGATTACTAGTGAGGTTG 143 chr2ptel1M 799675 AGTGTTAGTTTTTAAATAACTATTGATAGCTTG-ATTTCTTCCTCTGAAA 799723 iii ?-- i v ivi iivii - i i vi C L1ME4a_3end#L 142 AACATN--TTTTCATATGTTTATTGGCCATTTGTATTTCTTCTTTTGTGA 95 chr2ptel1M 799724 ACTACCTTTTCATATCTGTTGACCATTTATCAATTAGGAAATGGCTGTTA 799773 i ii v i iv v v v i ivi vvv v v C L1ME4a_3end#L 94 ATTGTCTGTTCATGTCCTTTGCCCATTTTTCTATTGGGGTGTTCGTCTTT 45 chr2ptel1M 799774 TTCTTATGCATTTGGTTCAGTTCCCAGTATATT 799806 vv vvvv i iivi C L1ME4a_3end#L 44 TTCTTATTGATTTGTAAGAGCTCTTTATATATT 12 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 54.26 CpG sites = 108, Kimura (unadjusted) = 55.15 Transitions / transversions = 1.35 (108/80) Gap_init rate = 0.04 (20 / 511), avg. gap size = 1.60 (32 / 20) 427 35.89 3.25 1.49 chr2ptel1M 799354 799814 (200186) C L1ME4c_3end#LINE/L1 (358) 472 4 m_b76s551i2 2812 chr2ptel1M 799354 CTATTACCAAAAAGAGCTGCTCTGGATGTTTTGGTACCTGTTAG--TCCT 799401 i- v iv vv i ii i v i v i - -- ii C L1ME4c_3end#L 472 CTATTAT-AAATAACGCTGCAATGAACATCTTCGTGCATAT-AGCTTTTT 425 chr2ptel1M 799402 CCTCCTTTTTCATTGACCTCTTGGGAAATAGATGAAGCAGTGATATTGAT 799451 i vv iviii i v v vvivv v iv iv C L1ME4c_3end#L 424 CCTTCTTTTGAATTATTTCCTTAGGATAAATTCCCAGAAGTGGAATTACT 375 chr2ptel1M 799452 GGCTCCA-GGTTGTGGACAGTTTTCTTGCTCTTTGGACATAGCTCCAAGT 799500 v v - v i i v v v viv i viv i C L1ME4c_3end#L 374 GGGTCAAAGGGTATGAACATTTTTATGGCTCTTGATACGTATTGCCAAAT 325 chr2ptel1M 799501 TGCTCTCCGGAATAGATGGACTCGTCGTCAGCTCTACCAGTGATGTGTTA 799550 i ii vi v v ivi ivv ?iv i ii i v C L1ME4c_3end#L 324 TGCTTTCCAAAAGGGTTGTACCAATTTACANTGCCACCAGCAATGTATGA 275 chr2ptel1M 799551 GAATCCCTGTTTTTCTGCAGACTT-----TACGGAGTTTTGTCATTTTCC 799595 ?i v v iv i ?v i-----i iv i v i v ii C L1ME4c_3end#L 274 GNGTACCAGTTTCACCGCANCCTCGCCAGCATTGGGTATTATCAATTTTT 225 chr2ptel1M 799596 T---TTTCTGTCACCTTAA-ATGCATTTGAGGTGCTA-CT-ATCTCTGTT 799639 --- i ii vi - v i --i ii v - - ivi i C L1ME4c_3end#L 224 TAAATTTTTGCTAATTTAATAGGCGT--AAAATGGTATCTCATTGTTGCT 177 chr2ptel1M 799640 TTGGCTTGCGTTTTCTCTGGTTTTTAGCAAGGTGGAGTGTTAGTTTTTAA 799689 iii i - i i vi i v iii -- ii v C L1ME4c_3end#L 176 TTAATTTGCATTT-CTTTGATTACTAGCGAGGTTGAACATT--TTTCCAT 130 chr2ptel1M 799690 ATAACTATTGATAGCTTG-ATTTCTTCCTCTGAAAACTACCTTTTCATAT 799738 i ivi i v ivi? - i i ? vi i ii v i C L1ME4c_3end#L 129 GTGTTTGTTTACTANTTGTATTTCCTCTTNTGTGAATTGTCTGTTCATGT 80 chr2ptel1M 799739 CTGTTGACCATTTATCAATTAGGAAATGGCTGTTATTCTTATGCATTTGG 799788 iv v v i ivv v v ? v vv i C L1ME4c_3end#L 79 CCTTTGCCCATTTATCTATTGGGGTCTTGATNTTTTTCTTATCAATTTGA 30 chr2ptel1M 799789 TTCAGTTCCCAGTATATTTGAAAAAT 799814 v v i iivi ? v? i v C L1ME4c_3end#L 29 ATGAGCTCTTTATATANTANAGATAT 4 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 49.77 CpG sites = 93, Kimura (unadjusted) = 52.08 Transitions / transversions = 1.33 (93/70) Gap_init rate = 0.03 (15 / 460), avg. gap size = 1.47 (22 / 15) 17 12.53 0.00 0.00 chr2ptel1M 800212 800237 (199763) (T)n#Simple_repeat 1 26 (0) m_b76s252i12 2813 chr2ptel1M 800212 TTTCTTTTTTTTTTTTTTAATTTTTT 800237 i vv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 1512 31.07 1.10 0.63 chr2ptel1M 800666 801300 (198700) C L1ME4c_3end#LINE/L1 (191) 639 2 m_b76s551i3 2814 chr2ptel1M 800666 TTCTGCTCATTTCACTCAGCATCAGTTCATGTAATTCTCTCCAAGCCTCT 800715 iv i i i vv i- ivi i v iiv C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATA-AACATTTTCCATGTTGCT 591 chr2ptel1M 800716 GTAT--TCATCCTGCTGGTCATTTCTTACAGAACAATAATATTCCATAAC 800763 ii -- v v iv vi i v ii vvvv viv C L1ME4c_3end#L 590 ACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCGA 541 chr2ptel1M 800764 ATTCATATACCACAATTTACCCAACCATTTTCCAGTGGATGGGCATCCAC 800813 i ?v i i ii ii vi v v i ii v C L1ME4c_3end#L 540 GTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAG 491 chr2ptel1M 800814 TCAGTTTCCAGTTTCTGGCCACGACAAACAGGGCCGCCACAAACATTTTG 800863 viv i i v i iv i i iv i v ii i v C L1ME4c_3end#L 490 GTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTC 441 chr2ptel1M 800864 GCCCATACAGGTCCCTTTCCCTTCTTC---AGTATCTCTTTGGGGTATAA 800910 iv i --- i i i--- v i i i i v v C L1ME4c_3end#L 440 GTGCATATAG---CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAAT 394 chr2ptel1M 800911 GCCCAGTAGTAATACTGCTGGATCAAAGGGTATGCACAGTTTGATAACTT 800960 v v iiv i i i v v v ii i C L1ME4c_3end#L 393 TCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTC 344 chr2ptel1M 800961 TTTGGGCATAATTACAGATTGCTCTCCAGAATGGCTGGATATGTTCACAA 801010 vivi i v vv i i i v i v ivvi i ? C L1ME4c_3end#L 343 TTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACAN 294 chr2ptel1M 801011 CTCCACCAACAATGCATCAGTGTCCCAGTTTTCCCACATTCCCTCCAACA 801060 iv i i v ? v iv i ?i i v i C L1ME4c_3end#L 293 TGCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGCA 244 chr2ptel1M 801061 TTCATCATTATTTTTTCCTGTCATCTTAGCCAATCTGACAGGTGTATAGT 801110 vivi ivv ii vvv i v i i i i i v i C L1ME4c_3end#L 243 TTGGGTATTATCAATTTTTTAAATTTTTGCTAATTTAATAGGCGTAAAAT 194 chr2ptel1M 801111 GGTATCTCAGAGTTGTCTTAATTTGCATTTCTCTGATTAATAGTGATTTG 801160 vv ii i v i vv v C L1ME4c_3end#L 193 GGTATCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACTAGCGAGGTT 144 chr2ptel1M 801161 GAACACTTT--CATATGAGTGAAAATAGTTTCAATTTCATCATCTGAAAA 801208 i -- i vv vvv ivi? vv v v ? vi C L1ME4c_3end#L 143 GAACATTTTTCCATGTGTTTGTTTACTANTTGTATTTCCTCTTNTGTGAA 94 chr2ptel1M 801209 TTGTCTGTTCATATCCTTTGACCATTTATCAATTGGAGAATGGCTTGATT 801258 i v v i vv v v ?vv C L1ME4c_3end#L 93 TTGTCTGTTCATGTCCTTTGCCCATTTATCTATTGGGGTCTTGATNTTTT 44 chr2ptel1M 801259 TCTTATAAATTAGAGTCAATTCTCTATATATTTTGGAAATTA 801300 v v i v ii i ? v?i v C L1ME4c_3end#L 43 TCTTATCAATTTGAATGAGCTCTTTATATANTANAGATATTA 2 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 40.31 CpG sites = 104, Kimura (unadjusted) = 41.69 Transitions / transversions = 1.13 (104/92) Gap_init rate = 0.01 (7 / 634), avg. gap size = 1.57 (11 / 7) 288 33.82 1.46 0.72 chr2ptel1M 801154 801427 (198573) C L1M3_orf2#LINE/L1 (0) 3288 3013 m_b76s551i4 2814 chr2ptel1M 801154 TGATTTGGAACAC--TTTCATATGAGTGAAAATAGTTTCAATTTCATCAT 801201 v v i i-- ivv vviiivi vv v v v C L1M3_orf2#LIN 3288 TGATGTTGAGCATCTTTTCATATACCTGTTGGCCATTTGTATGTCTTCTT 3239 chr2ptel1M 801202 CTGAAAATTGTCTGTTCATATCCTTTGACCATTTATCAATTGGAGAATGG 801251 iv i v i vi v v ? i ivv vv C L1M3_orf2#LIN 3238 TGGAGAAATGTCTATTCAGGTCCTTTGCCCATTTTTNAATCGGGTTATTT 3189 chr2ptel1M 801252 CTTGATTTCTTATAAATTAGAGTCAATTCTCTATATATTTTGGAAATTAG 801301 v vv vi vi v v vi?v i ii v i C L1M3_orf2#LIN 3188 GTTTTTTTGCTATTGAGTTGTANGAGTTCCTTATATATTTTGGATATTAA 3139 chr2ptel1M 801302 GCCTTTATCAGAACCTTTAACTGTGAAGATATTTTCCCAGTTTTTTGCTT 801351 v i vviv vivi ii v v i v iiv v v C L1M3_orf2#LIN 3138 CCCCTTATCAGATATATGGTTTGCAAATATTTTCTCCCATTCCGTAGGTT 3089 chr2ptel1M 801352 CCCTTCTAATCTTGTTTGCATTAGTTTTGTT--TGTATAGAAGCTTTTTA 801399 v i v iii --v iv iiv -- ii C L1M3_orf2#LIN 3088 GCCTTTTCACTCTGTT--GATTGTTTCCTTTGCTGTGCAGAAGCTTTTTA 3041 chr2ptel1M 801400 ATTTGATGTAATCAAAATTTTCTATTTT 801427 i i vv v v C L1M3_orf2#LIN 3040 GTTTGATGTAGTCCCACTTGTCTATTTT 3013 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 44.43 CpG sites = 40, Kimura (unadjusted) = 45.72 Transitions / transversions = 0.77 (40/52) Gap_init rate = 0.01 (4 / 273), avg. gap size = 1.50 (6 / 4) 308 32.19 1.27 1.27 chr2ptel1M 801192 801427 (198573) C L1PREC2_orf2#LINE/L1 (40) 3254 3019 m_b76s551i5 2814 chr2ptel1M 801192 ATTTCATCATCTGAAAATTGTCTGTTCATATCCTTTGACCATTTATCAAT 801241 v v v i v i v i v i C L1PREC2_orf2# 3254 ATGTCTTCTTTTGAAAAGTGTCTGTTCATGTCCTTTGCCCACTTTTTAAT 3205 chr2ptel1M 801242 TGGAGAATGGCTTGATTTCTTATAAATTAGAGTCAATTCTCTATATATTT 801291 v ivvi vvv vv i v vv v i ii v vi C L1PREC2_orf2# 3204 GGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTAAGTTCCTTATAGATGC 3155 chr2ptel1M 801292 TGGAAATTAGGCCTTTATCAGAACCTTTAACTGTGAAGATATTTTCCCAG 801341 v i i vv v vivi ii ? v i v C L1PREC2_orf2# 3154 TGGATATTAGACCTTTGTCAGATGCATAGTTTGCAAANATTTTCTCCCAT 3105 chr2ptel1M 801342 TTTTTTGCTTCCCTTCTAATCTTGTTTGCATTAGTTTTGTT---TGTATA 801388 i v v v vi vi v iii ---iv iv --- ii C L1PREC2_orf2# 3104 TCTGTAGGTTGTCTGTTTACTCTGTT---GATAGTTTCTTTTGCTGTGCA 3058 chr2ptel1M 801389 GAAGCTTTTTAATTTGATGTAATCAAAATTTTCTATTTT 801427 i i i vvi vv v v v C L1PREC2_orf2# 3057 GAAGCTCTTTAGTTTAATTAGATCCCATTTGTCAATTTT 3019 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 42.50 CpG sites = 32, Kimura (unadjusted) = 42.50 Transitions / transversions = 0.74 (32/43) Gap_init rate = 0.02 (4 / 235), avg. gap size = 1.50 (6 / 4) 60 0.00 0.00 0.00 chr2ptel1M 801530 801583 (198417) (T)n#Simple_repeat 1 54 (0) c_b76s251i1 2815 chr2ptel1M 801530 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 801579 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr2ptel1M 801580 TTTT 801583 (T)n#Simple_r 51 TTTT 54 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 406 24.98 5.41 2.63 chr2ptel1M 801603 801713 (198287) C MIRc#SINE/MIR (153) 115 2 m_b76s601i8 2816 chr2ptel1M 801603 GGGGTCAAGTGACTTGCCCAGGCTAA------TTTTAAGTGTCTGAGGCC 801646 i i i v v ------ vv v v v v C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 66 chr2ptel1M 801647 ACATTTGAACTCGGGTCCTCCTGACTTCAGGGCTGATACTCTATCCACTG 801696 iv i i i i i i i v iii i v C MIRc#SINE/MIR 65 GGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTG 16 chr2ptel1M 801697 CACCACCTAGCTGCCTC 801713 ---i C MIRc#SINE/MIR 15 CACCAC---ACTGCCTC 2 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.72 CpG sites = 16, Kimura (unadjusted) = 31.08 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.04 (4 / 110), avg. gap size = 2.25 (9 / 4) 469 33.62 4.88 2.31 chr2ptel1M 801723 802398 (197602) C L1M5_orf2#LINE/L1 (726) 2568 1876 m_b76s551i6 2814 chr2ptel1M 801723 TATTCTTGACCTTTTATTCTTCCAGATGAATTTTATTATT--TTTTTCTT 801770 ? ii i iivi v i vv i--i v vv C L1M5_orf2#LIN 2568 TATTCTNGGTCCTTTGCATTTCCATATAAATTTTAGAATCAGCTTGTCAA 2519 chr2ptel1M 801771 GTTCTAAAAAGTAATTGTTTGCTAGTTTGAT----ATTACACTCACTAAG 801816 v v iv iivvi vv v ---- i i v v vvi C L1M5_orf2#LIN 2518 TTTCTACAAAAAAACCTGCTGGGATTTTGATTGGGATTGCATTGAATCTA 2469 chr2ptel1M 801817 TAATTTAATTTAGGTAGCATTGTCATTTTTTTTATATTGAGTTAGCCCAC 801866 iv i i v v v i ?viv ivv v i C L1M5_orf2#LIN 2468 TAGATCAATTTGGGGAGAATTGACATCTTNACAATATTGAGTCTTCCAAT 2419 chr2ptel1M 801867 CCATGAGCA-ATTACCATTTCTCCAGCTATTTAAATCTGTCTTTATTTGT 801915 i -iv -i i vi ii vii v v C L1M5_orf2#LIN 2418 CCATGAACATGGTA-TATCTCTCCATTTATTTAGGTCTTCTTTAATTTCT 2370 chr2ptel1M 801916 GT-AG-AGTGTTTTGTAGTTGT--GTTCAAACGCTACTTGTGTGTGTCTT 801961 v - - i v -- vi ? v i-- iiii ? i C L1M5_orf2#LIN 2369 CTCAGCAATGTTTTGTAGTTTTCAGTGTANAGGT--CTTGCACATNTTTT 2322 chr2ptel1M 801962 GGCAGGTAGACTTCCTAAGCTCTGGGAACAGTTTACAGTTGTTTTCGATG 802011 vi i vv - ivi v?iviivv ivv i i v vi C L1M5_orf2#LIN 2321 GTTAGATTTA-TTCCTAAGTATTTNATGTTTTTTGATGCTATTGTAAATG 2273 chr2ptel1M 802012 GGGTTTCTCTTTCAATCTCTTCCTTCTGATT-TTTGTTGTTGTTTTCTGT 802060 vi vi i ?v i v -i ii - i--------- C L1M5_orf2#LIN 2272 GTATTGTTTTTNAAATTTCAT-TTTCCAATTGTTTGTTGC---------T 2233 chr2ptel1M 802061 GATGTGTAGAAATCTTGACGATTTGTATGGGTTTATTTGATATCTTGCAA 802110 ii i i vivivi v i ivi v ii vi i? i C L1M5_orf2#LIN 2232 AGTATATAGAAATACAATTGATTTTTGTATATTGACCTTGTATCCNGCGA 2183 chr2ptel1M 802111 CTTTGCTAG---TGTTCATTGCTTTCAGTAGTTTTTTTACTTGACTCTTT 802157 i i---iii i iv ii ? i- v i C L1M5_orf2#LIN 2182 CCTTGCTAAATTCACTTATTAGTTCTAGTAGTTTNTTTG-TAGATTCTTT 2134 chr2ptel1M 802158 AGGATGTTGC---TAAATAAACATATTATTTAC-----AAGA-AGCCTGC 802198 ? v vi--- ? i v i i i i ----- ? - ii vv C L1M5_orf2#LIN 2133 NGGATTTTCTACGTANACAATCATGTCATCTGCGAATAANGACAGTTTTA 2084 chr2ptel1M 802199 TTTCTTCATCACCTCTGCTTATTCCCTCAATTT-TCTTTC-TGTCTAATT 802246 v iv vv vi v i iv - i - i v C L1M5_orf2#LIN 2083 TTTCTTCCTTTCCAATCTTTATGCCTTTTATTTCTTTTTCTTGCCTTATT 2034 chr2ptel1M 802247 GCCATCGCTAGTATTTCTAGTGCATTATCGAATGATCATGGTGAT----- 802291 vv v v ii i i v i i iivvi ?----- C L1M5_orf2#LIN 2033 GCACTGGCTAGGACCTCCAGTACAATGTTGAATAGAAGTGGTGANAGCGG 1984 chr2ptel1M 802292 -CATTCTTGTTTCATTCTTGATCTTACTGGAAAGGCTTCTAGGATATCCC 802340 - i i ii ii vv i i ? ii v? v v C L1M5_orf2#LIN 1983 ACATCCTTGTCTTGTTCCCGATCTTAGGGGGAAAGCNTTCAGTNTTTCAC 1934 chr2ptel1M 802341 CGTTATAGGA-AATGAGCGCTTTTGGTTTTAGATAGATACTACTTATCAT 802389 i - v -i vv? v v vvi i ivi v C L1M5_orf2#LIN 1933 CATTA-AGTATGATGTTNGCTGTAGGTTTTTCGTAGATGCCCTTTATCAG 1885 chr2ptel1M 802390 TTTAAGGAA 802398 v i C L1M5_orf2#LIN 1884 GTTGAGGAA 1876 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 46.65 CpG sites = 125, Kimura (unadjusted) = 47.55 Transitions / transversions = 1.29 (125/97) Gap_init rate = 0.05 (32 / 675), avg. gap size = 1.53 (49 / 32) 182 27.97 7.58 5.19 chr2ptel1M 803536 803667 (196333) MamRTE1#LINE/RTE-BovB 2048 2182 (1630) m_b76s601i9 2817 chr2ptel1M 803536 TGGCAAAGTACCTGGTGTAGATC-TATCCCAGCTGAGATTTACA---AGG 803581 i iv ii vviv v-i v v v --- MamRTE1#LINE/ 2048 TGGTAAAGCTCTCGGACCTGATGGCATACCTGCTGAGATTTTCAAGCAGG 2097 chr2ptel1M 803582 TGGGGGGTCCACTGCTCCTACAGAAG-CTGACTGGGATCTCC--CAGCTT 803628 vi ivv i ----i v - vv i v i i -- -- MamRTE1#LINE/ 2098 AAGGGGAGACGCTGCT----TAGACGTCTGCATAGGCTTTTCTTCAGC-- 2141 chr2ptel1M 803629 ATATGGCAGGA--GAGGCTCTGCC-CAGGAGGTCAAGGATGC 803667 - v -- vvv - vv i MamRTE1#LINE/ 2142 ATATGG-AGTACCGAGGAAATGCCGCAGGATTTCAAAGATGC 2182 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.80 CpG sites = 14, Kimura (unadjusted) = 35.12 Transitions / transversions = 0.67 (14/21) Gap_init rate = 0.10 (13 / 131), avg. gap size = 1.31 (17 / 13) 183 19.35 0.00 0.00 chr2ptel1M 803927 803957 (196043) MamRTE1#LINE/RTE-BovB 2503 2533 (1279) m_b76s601i10 2817 chr2ptel1M 803927 AGTTCAGCTGCCCAGAGAAGTCCATCAGGAT 803957 ii v i i i MamRTE1#LINE/ 2503 AGTTTGGCTGCCCTGAGAAGTTCACCAAGAT 2533 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 23.58 CpG sites = 5, Kimura (unadjusted) = 23.58 Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 16 15.91 0.00 0.00 chr2ptel1M 806638 806665 (193335) (A)n#Simple_repeat 1 28 (0) m_b76s252i13 2818 chr2ptel1M 806638 AATAAAAATGAAAAAAAAAAAAGAAAAA 806665 v vi i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA 28 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 23 23.60 3.33 0.00 chr2ptel1M 808599 808658 (191342) (TG)n#Simple_repeat 1 62 (0) m_b76s252i14 2819 chr2ptel1M 808599 TGCGTGTGTGCATGGGTGTCAGTATGTATGTGTGCATCTGTGTGT-TCTG 808647 i ii v vv i i ii v - v (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr2ptel1M 808648 TGTGTGT-TGTG 808658 - (TG)n#Simple_ 51 TGTGTGTGTGTG 62 Matrix = Unknown Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.03 (2 / 59), avg. gap size = 1.00 (2 / 2) 270 31.20 2.04 12.78 chr2ptel1M 809839 809985 (190015) C MIRc#SINE/MIR (45) 223 91 m_b76s601i11 2820 chr2ptel1M 809839 AGGCACCTTC-TGCATTTTGCCTGATTTGATCTTCACAAGAATCCTGGCA 809887 i i i -iii iv ii v i v i v-- C MIRc#SINE/MIR 223 AAGCGCTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGT-- 176 chr2ptel1M 809888 ATTGGGGGAGGGGGGAAGGGGGGAGAGTTAGGTGCTATCATAAC-AGTGT 809936 ------- vi v --------i ii i vv - v v C MIRc#SINE/MIR 175 -------GAGGTAGGCAGGG--------CAGGTATTATTATCCCCATTTT 141 chr2ptel1M 809937 GTAGCTGAGTAGGCTGAGGCAGGCAGAGGCCAGGCGACTTGCCC-AGGTC 809985 ii v v ii vviv ii i i - C MIRc#SINE/MIR 140 ACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTC 91 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.85 CpG sites = 25, Kimura (unadjusted) = 41.22 Transitions / transversions = 1.67 (25/15) Gap_init rate = 0.14 (20 / 146), avg. gap size = 1.00 (20 / 20) 226 20.57 10.68 0.88 chr2ptel1M 810421 810523 (189477) L1PB_orf2#LINE/L1 2023 2135 (1159) m_b76s551i7 2821 chr2ptel1M 810421 CTAGCAATCGCAATCA-ACAAGAGAAAAAATTAAAGG-CTTAAAGATAGG 810468 v vv - i v - v vv i v L1PB_orf2#LIN 2023 CTAGCCAGAGCAATCAGACAAGAGAAAGAAATAAAGGGCATCCAAATCGG 2072 chr2ptel1M 810469 TAAAGGAGAGAATT---CTGTCCCAATTTGCTGATGATTTGA------AC 810509 ii - i i--- v vi v ------ L1PB_orf2#LIN 2073 TAAAGAGGA-AGTCAAACTGTCGCTGTTTGCTGATGATATGATCGTNTAC 2121 chr2ptel1M 810510 ATAGGAAATCCTAA 810523 v i i L1PB_orf2#LIN 2122 CTAGAAAACCCTAA 2135 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 24.12 CpG sites = 9, Kimura (unadjusted) = 24.12 Transitions / transversions = 0.75 (9/12) Gap_init rate = 0.05 (5 / 102), avg. gap size = 2.40 (12 / 5) 546 19.03 1.61 6.78 chr2ptel1M 811645 811768 (188232) C MIRc#SINE/MIR (141) 127 10 m_b76s601i12 2822 chr2ptel1M 811645 CTGAGGC--AGTTGTGGTTAAGTGACTTGCCCAGGATCGCACAACTAGAA 811692 -- v- v i i i i v C MIRc#SINE/MIR 127 CTGAGGCTCAGA-GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTA 79 chr2ptel1M 811693 AGTGGTAAGTGTCTGAGACCAGATTTGAACTCAAGTCTTCCTGAATTCAG 811742 i ------- v vi i i i i v i i C MIRc#SINE/MIR 78 AGTGGCA-------GAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAA 36 chr2ptel1M 811743 GGCTAGTGCTCTGTCTACTGCACCAC 811768 v i v i C MIRc#SINE/MIR 35 GTCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 21.18 CpG sites = 14, Kimura (unadjusted) = 22.29 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.07 (9 / 123), avg. gap size = 1.11 (10 / 9) 12 21.56 2.13 4.35 chr2ptel1M 812205 812251 (187749) (GAAGGG)n#Simple_repeat 1 46 (0) m_b76s252i15 2823 chr2ptel1M 812205 GAAGGAG-AGGAGAAAAGGAATGCAATAGGGCAATGGGGAAGGGGAAG 812251 i - i ii v vi - v - (GAAGGG)n#Sim 1 GAAGGGGAAGGGGAAGGGGAAGGGGA-AGGGGAA-GGGGAAGGGGAAG 46 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.07 (3 / 46), avg. gap size = 1.00 (3 / 3) 231 27.87 4.10 0.00 chr2ptel1M 812502 812623 (187377) L1MEh_5end#LINE/L1 2108 2234 (1) m_b76s551i8 2824 chr2ptel1M 812502 TAGCAGTCCTAAC--TAGATGTAAATGAGGGGAAATCGCCTATGAAATGG 812549 ? vv v -- i i vvi v i v v v i L1MEh_5end#LI 2108 TANCAGTAATTACAATAAATGTAAATGGGTTAAACTCACCAATTAAAAGA 2157 chr2ptel1M 812550 AAAAGGATAGCATAAGGGATTAGAAATCAGAATGCAACAATA---TGTTT 812596 v i iv ?v v vv ?i v i v --- i L1MEh_5end#LI 2158 CAGAGATTNTCAGATTGGATTNAAAAACAAAATCCAACAATATGCTGTCT 2207 chr2ptel1M 812597 ATAAGAAACACGCTTGAAATAGAAAAA 812623 i i i i i ? ii L1MEh_5end#LI 2208 ACAAGAGACACACTTAAAACANAAGGA 2234 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 36.80 CpG sites = 17, Kimura (unadjusted) = 36.80 Transitions / transversions = 1.00 (17/17) Gap_init rate = 0.02 (2 / 121), avg. gap size = 2.50 (5 / 2) 17 23.26 5.00 0.00 chr2ptel1M 813280 813339 (186661) (AATTA)n#Simple_repeat 1 63 (0) m_b76s252i16 2825 chr2ptel1M 813280 AATTATATTCAATAAGATTCAATTAGATTCAATAAGATTAAA--AAA-TA 813326 v v v i v i v v i -- - (AATTA)n#Simp 1 AATTAAATTAAATTAAATTAAATTAAATTAAATTAAATTAAATTAAATTA 50 chr2ptel1M 813327 ATTTCAACTAAAT 813339 v v i (AATTA)n#Simp 51 AATTAAATTAAAT 63 Matrix = Unknown Transitions / transversions = 0.50 (4/8) Gap_init rate = 0.03 (2 / 59), avg. gap size = 1.50 (3 / 2) 12 14.61 8.16 3.92 chr2ptel1M 814822 814870 (185130) (CCAGCAGC)n#Simple_repeat 1 51 (0) m_b77s252i1 2826 chr2ptel1M 814822 CCAGGAGCCC-CCAGCCC-TC-GCCGAGCAGGCCCAACAG-CCAGGATGC 814867 v -v -v - v - i - v - (CCAGCAGC)n#S 1 CCAGCAGCCCAGCAGCCCAGCAGCCCAGCA-GCCCAGCAGCCCAGCA-GC 48 chr2ptel1M 814868 CCA 814870 (CCAGCAGC)n#S 49 CCA 51 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.12 (6 / 48), avg. gap size = 1.00 (6 / 6) 13 18.55 8.77 1.64 chr2ptel1M 818608 818664 (181336) (GGGCGCTC)n#Simple_repeat 1 61 (0) m_b77s252i2 2827 chr2ptel1M 818608 GGGCTCTCGGGCGCTCGGG-GC-AGGAAGGTCGGTGC-CAGGGGC-CGCG 818653 v - -v iv v - - vv - v (GGGCGCTC)n#S 1 GGGCGCTCGGGCGCTCGGGCGCTCGGGCGCTCGG-GCGCTCGGGCGCTCG 49 chr2ptel1M 818654 GTC-CTCGGGCG 818664 v - (GGGCGCTC)n#S 50 GGCGCTCGGGCG 61 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.11 (6 / 56), avg. gap size = 1.00 (6 / 6) 214 28.81 1.09 5.68 chr2ptel1M 818866 818957 (181043) MIR1_Amn#SINE/MIR 96 183 (47) m_b77s601i1 2828 chr2ptel1M 818866 CCTGGGCAGGTTCCTCAGCCT-TGGGTGCCTCAGTTTGCTGTTCTGTACA 818914 i i iv i?i - vv ? v vv v MIR1_Amn#SINE 96 CTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAA 145 chr2ptel1M 818915 GTGGGGGCAAGAAGAGCACCTGCCTCCCAGGGGGAAAGTGCTT 818957 i ii vi ---i ivi i--vv v MIR1_Amn#SINE 146 ATGGGGATAATGA---TACTGACCTCCT--TTGTAAAGTGCTT 183 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.92 CpG sites = 13, Kimura (unadjusted) = 37.92 Transitions / transversions = 1.08 (13/12) Gap_init rate = 0.07 (6 / 91), avg. gap size = 1.00 (6 / 6) 326 24.69 1.23 0.00 chr2ptel1M 818866 818946 (181054) MIR#SINE/MIR 90 171 (91) m_b77s601i0 2828 chr2ptel1M 818866 CCTGGGCAGGTTCCTCAGCCT-TGGGTGCCTCAGTTTGCTGTTCTGTACA 818914 i i v i i - vv v vv v MIR#SINE/MIR 90 CTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAA 139 chr2ptel1M 818915 GTGGGGGCAAGAAGAGCACCTGCCTCCCAGGG 818946 i ii v v i i vi MIR#SINE/MIR 140 ATGGGGATAATAATAGTACCTACCTCATAGGG 171 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.22 CpG sites = 10, Kimura (unadjusted) = 30.22 Transitions / transversions = 1.00 (10/10) Gap_init rate = 0.01 (1 / 80), avg. gap size = 1.00 (1 / 1) 36 7.03 1.52 4.69 chr2ptel1M 819220 819285 (180715) (CCTC)n#Simple_repeat 1 64 (0) m_b77s252i3 2829 chr2ptel1M 819220 CCTCCCTCCCTTCCTCCTCTCCCTCCCTCCCTTCCGTCCCCTTCC-CCCT 819268 i - - v - i - (CCTC)n#Simpl 1 CCTCCCTCCCTCCCTCC-CTCCCTCCCTCCC-TCCCT-CCCTCCCTCCCT 47 chr2ptel1M 819269 CCCTCCCTCCCTCTCTC 819285 i (CCTC)n#Simpl 48 CCCTCCCTCCCTCCCTC 64 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.06 (4 / 65), avg. gap size = 1.00 (4 / 4) 12 23.11 0.00 4.76 chr2ptel1M 822164 822207 (177793) (CTTCCC)n#Simple_repeat 1 42 (0) m_b77s252i4 2830 chr2ptel1M 822164 CTGCCCCTTGCCCAGCCCCTCCAGCCTTTCCCCTTCGGCTTCCC 822207 v v vv i -- i vv (CTTCCC)n#Sim 1 CTTCCCCTTCCCCTTCCCCTTC--CCCTTCCCCTTCCCCTTCCC 42 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2) 366 38.15 13.37 1.19 chr2ptel1M 822524 822897 (177103) L2#LINE/L2 2171 2589 (493) m_b77s601i2 2831 chr2ptel1M 822524 CTCCCTCTCCGTCTGCTGGGCTACATCCTCCTCCACATTGTGCCCTCTGG 822573 i v v vv ivv vv viivi v ?i L2#LINE/L2 2171 CTCCTTCTCAGTCTCCTTTGCTGGTTCCTCCTCATCTCCCCGACCTCTNA 2220 chr2ptel1M 822574 ACGTAGGGAT--CCCCGGGCCCTGTCCCTGGCC----------------- 822604 v ii -- v i v i v ----------------- L2#LINE/L2 2221 ACGTTGGAGTGCCCCAGGGCTCAGTCCTTGGACCTCTTCTCTTCTCTATC 2270 chr2ptel1M 822605 ----CTCATG---GAGGGGCTCTCATCAGTTCCCATGGACTCCATGCCCA 822647 ---- iv---v? v v viv i vi iv vvv L2#LINE/L2 2271 TACACTCACTCCCTNGGTGATCTCATCCAGTCTCATGGCTTTAAATACCA 2320 chr2ptel1M 822648 TCTGAAAGCTGGTGATGGTCTGATTGGCGTTTCCTGCTCCAGTCTCCCTG 822697 iv v i ivvi vi viii i v i viii i iv L2#LINE/L2 2321 TCTATATGCTGATGACTCCCAAATTTATATCTCCAGCCCGGACCTCTCCC 2370 chr2ptel1M 822698 CCAACCTGCAGGACTGGATGTCCAACTG---------------------G 822726 ii v v ivii v i --------------------- L2#LINE/L2 2371 CTGAACTCCAGACTCGTATATCCAACTGCCTACTCGACATCTCCACTTGG 2420 chr2ptel1M 822727 ACGTCTAGGAGATACCCCAGACTCCAGGGATCCAACAGTGACCTTGTGCT 822776 i iv ii i i i iv vivi v v v iv v L2#LINE/L2 2421 ATGTCTAATAGGCATCTCAAACTTAACATGTCCAAAACTGAACTCCTGAT 2470 chr2ptel1M 822777 CTCCCCCCTCCCCCCAAACCCACTACCCTGGCTATCTCCGTTGCTGCTCT 822826 i ----- ii v i iv vi i viiiiiv vv L2#LINE/L2 2471 CTTCCCCCT-----CAAACCTGCTCCTCCCGCAGTCTTCCCCATCTCAGT 2515 chr2ptel1M 822827 AGAGGGT-GCCCCCTCTTCCCGGTAGTCCAGGCT-CCAGCTTTGGAGTCA 822874 ?i v i-i i v i i i v ii i-vv i i L2#LINE/L2 2516 NAATGGCAACTCCATCCTTCCAGTTGCTCAGGCCAAAAACCTTGGAGTCA 2565 chr2ptel1M 822875 TTCTC-ATTGCTCCCCCATTTTCA 822897 i i- i v i iivi i L2#LINE/L2 2566 TCCTTGACTCCTCTCTTTCTCTCA 2589 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 55.08 CpG sites = 79, Kimura (unadjusted) = 56.29 Transitions / transversions = 1.27 (79/62) Gap_init rate = 0.03 (13 / 373), avg. gap size = 4.23 (55 / 13) 208 33.02 6.19 0.84 chr2ptel1M 825934 826046 (173954) L3#LINE/CR1 3873 3991 (108) m_b77s601i3 2832 chr2ptel1M 825934 GCAGAGCTCGGCA----GTCAGGAAACACTTCCTGCCCCTGAGAGGTGGC 825979 vi v----i v iv i iv vv v v v L3#LINE/CR1 3873 GCAGATTTCGGCTCAATATAAGGAAGAACTTTCTAACAATCAGAGCTGTC 3922 chr2ptel1M 825980 CCATGGCTGAATGGGCTGCCCC---AGGCTGGCGGCTTGCCACTTCTGGG 826026 v viiiv i --- iv vvi iv iiiv - L3#LINE/CR1 3923 CAAAAATGGAATGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGTCACT-GG 3971 chr2ptel1M 826027 AGGGCTTCAGGAAGAGGCTG 826046 vv i v L3#LINE/CR1 3972 AGGTGTTCAAGCAGAGGCTG 3991 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.30 CpG sites = 16, Kimura (unadjusted) = 43.80 Transitions / transversions = 0.76 (16/21) Gap_init rate = 0.03 (3 / 112), avg. gap size = 2.67 (8 / 3) 15 30.42 1.92 0.00 chr2ptel1M 827013 827064 (172936) (GT)n#Simple_repeat 1 53 (0) m_b77s252i5 2833 chr2ptel1M 827013 GTGTTTAT-TGTCTCTGTGTGTTGGGGGGAGTGTGTGCGCGTGCGTTTGT 827061 v i - v v vv v v v i i i v (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50 chr2ptel1M 827062 GTG 827064 (GT)n#Simple_ 51 GTG 53 Matrix = Unknown Transitions / transversions = 0.44 (4/9) Gap_init rate = 0.02 (1 / 51), avg. gap size = 1.00 (1 / 1) 192 22.10 1.85 7.84 chr2ptel1M 827101 827154 (172846) C OldhAT1#DNA/hAT-Ac (2680) 162 112 m_b77s601i4 2834 chr2ptel1M 827101 GAAATTTTCCATTTGGACTTTTCCGGAGTGACTTT-AAGCACAGCTTTTA 827149 ---- i i -i iiiii v v C OldhAT1#DNA/h 162 GAAATTTTC----TGGACTTTTCCAGGGTGACTTTGGAATGTGGCTTATC 117 chr2ptel1M 827150 TCCTG 827154 i C OldhAT1#DNA/h 116 CCCTG 112 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.63 CpG sites = 9, Kimura (unadjusted) = 27.63 Transitions / transversions = 4.50 (9/2) Gap_init rate = 0.09 (5 / 53), avg. gap size = 1.00 (5 / 5) 16 17.55 5.36 3.51 chr2ptel1M 827248 827303 (172697) (TCCCT)n#Simple_repeat 1 57 (0) m_b77s252i6 2835 chr2ptel1M 827248 TCCCCTGCC-TCCCTGTCCC-TCTCTTCCC-TCCCCTCCTTTCCTCGCCC 827294 i v - - - i - i i - vi (TCCCT)n#Simp 1 TCCCTTCCCTTCCCT-TCCCTTCCCTTCCCTTCCCTTCCCTTCC-CTTCC 48 chr2ptel1M 827295 CTTCCCCTC 827303 i (TCCCT)n#Simp 49 CTTCCCTTC 57 Matrix = Unknown Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.09 (5 / 55), avg. gap size = 1.00 (5 / 5) 27 9.23 4.17 2.04 chr2ptel1M 831524 831571 (168429) (TA)n#Simple_repeat 1 49 (0) m_b77s252i7 2836 chr2ptel1M 831524 TATAT-TATATGGTATAAATATATATATATTTATATA-ATATAAATATAT 831571 - -i v v - v (TA)n#Simple_ 1 TATATATATAT-ATATATATATATATATATATATATATATATATATATAT 49 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.06 (3 / 47), avg. gap size = 1.00 (3 / 3) 438 33.10 4.49 4.15 chr2ptel1M 831725 832036 (167964) C Charlie7#DNA/hAT-Charlie (1968) 647 335 m_b77s502i0 2837 chr2ptel1M 831725 GAGGCTGGCCATTAATGACCGGGTGGAA--AAATCCATATTCCACAGAAG 831772 i vii i i i--i v-- i v v iv C Charlie7#DNA/ 647 GAGGTTCATCGTTAACGAT--AGTGGATGTAAATCCATATTTCAAATAGT 600 chr2ptel1M 831773 CT-CGCGAGCATTTCCCAAGGTTTCTTTGGCCCCATCGTTATCCAGGCTG 831821 - vi vv ---iii i vvv iv i viiv C Charlie7#DNA/ 599 CTTCTTGATAATTTC---GAATTTTTTTGGCCGACTTCTTGTCAGATCTG 553 chr2ptel1M 831822 ACT----CATGTTTGTTTTCAGTTTGTAAGGTGGCGGCGTCCACGAGCTC 831867 i ---- i vv i vi i v --i v v v C Charlie7#DNA/ 552 ATTAGATCGTCATTGTTTTTACCTCGTAATGTGGC--TGACGAAGAGCTC 505 chr2ptel1M 831868 CTCCCGGCGGCAGCAGGAGGAGCGTGGGCTGGGCTGTTTTCTTGTGGTTT 831917 v v i------ v v i i vi vv ii v i C Charlie7#DNA/ 504 GTACT------AGGAGTAGAAGTGTCAGCTCTGCCATTTTCTTGTTGTTC 461 chr2ptel1M 831918 GCTTGGGCTTGCCCAGGTAATCCTGTCTTCCCAGGGGAGTTTCCTTGCAG 831967 v viviv i vi i vvvvv vi i C Charlie7#DNA/ 460 GCTTGTGCTTGCATTATTAGTATTATCTTCAATCCGCGGTTTCTTTGCAG 411 chr2ptel1M 831968 TCATC--TCCAAGTTGCCTG-----TTTCCAAGGGTTAGTTTAGTTCAAA 832010 vv -- ii iii i ----- vii v C Charlie7#DNA/ 410 GAATCTTTTTAAGCCACTTGTCCATTTTGTGAGGGTTAGTTTAGTTAAAA 361 chr2ptel1M 832011 TGAAGTCGGATCATCGGTAAATCCAC 832036 iv ii viv v v C Charlie7#DNA/ 360 CTAGATAATATAATCCGTAAATCCAC 335 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 40.39 CpG sites = 50, Kimura (unadjusted) = 44.42 Transitions / transversions = 1.02 (50/49) Gap_init rate = 0.06 (18 / 311), avg. gap size = 1.50 (27 / 18) 17 0.00 0.00 0.00 chr2ptel1M 834612 834630 (165370) (C)n#Simple_repeat 1 19 (0) m_b77s252i8 2838 chr2ptel1M 834612 CCCCCCCCCCCCCCCCCCC 834630 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCC 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 190 31.35 1.45 2.94 chr2ptel1M 836414 836482 (163518) C MIR3#SINE/MIR (59) 149 82 m_b77s601i5 2839 chr2ptel1M 836414 CTTCCTCCTTGTACAGATGAGGAAACAGAGGGTTGGGGGGAGGGGCGCTG 836463 ii v v v vii--i i v viv C MIR3#SINE/MIR 149 CCCCCTCATTTTACAGATGAGGAAACTGAGGCCC--AGAGAGGTGAAGTG 102 chr2ptel1M 836464 ACTTA-ATGAGGCCACATGG 836482 i-vii i ii C MIR3#SINE/MIR 101 ACTTGCCCAAGGTCACACAG 82 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.23 CpG sites = 13, Kimura (unadjusted) = 42.23 Transitions / transversions = 1.62 (13/8) Gap_init rate = 0.04 (3 / 68), avg. gap size = 1.00 (3 / 3) 17 19.96 0.00 0.00 chr2ptel1M 839204 839243 (160757) (GTTT)n#Simple_repeat 1 40 (0) m_b77s252i9 2840 chr2ptel1M 839204 GTTTCTTTGTTTCTCTGTTCGTTATTTCGTTTGTTTGTTT 839243 v v i i vv i (GTTT)n#Simpl 1 GTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTT 40 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 14 24.32 2.00 2.00 chr2ptel1M 840416 840465 (159535) (GCGGCA)n#Simple_repeat 1 50 (0) m_b77s252i10 2841 chr2ptel1M 840416 GCGGCCGGGGGAGGGGGGGTCGGCGGTGGCAGGGGCAG-GGCTGCGGCAG 840464 v v v v vi - i i v - v (GCGGCA)n#Sim 1 GCGGCAGCGGCAGCGGCAG-CGGCAGCGGCAGCGGCAGCGGCAGCGGCAG 49 chr2ptel1M 840465 C 840465 (GCGGCA)n#Sim 50 C 50 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.04 (2 / 49), avg. gap size = 1.00 (2 / 2) 228 20.49 6.25 2.41 chr2ptel1M 840495 840574 (159426) C MIRc#SINE/MIR (145) 123 41 m_b77s601i6 2842 chr2ptel1M 840495 GGATCGGGCAGGCAAAGGCACTTGCC--GGGTCACAGAGCT-GTAAGTGT 840541 v i iv iv vv --i v - v C MIRc#SINE/MIR 123 GGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGG 74 chr2ptel1M 840542 CCAAG--GGCACCTCTGAACCCGGGTCTCCCTGAC 840574 vi -- v - - i i C MIRc#SINE/MIR 73 CAGAGCCGGGA-CTC-GAACCCAGGTCTTCCTGAC 41 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 24.03 CpG sites = 7, Kimura (unadjusted) = 24.03 Transitions / transversions = 0.78 (7/9) Gap_init rate = 0.06 (5 / 79), avg. gap size = 1.40 (7 / 5) 183 24.37 5.88 3.45 chr2ptel1M 840504 840588 (159412) C MIR3#SINE/MIR (97) 111 25 m_b77s601i7 2842 chr2ptel1M 840504 AGGCAAAGGCACTTGCC--GGGTCACAGAGCT-GTAAGTGTCCAAG--GG 840548 ii vv --i v ?- v v vi -- C MIR3#SINE/MIR 111 AGGTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGG 62 chr2ptel1M 840549 CACCTCTGAACCCGGGTCTCCCTGACCGCCTCTCCATCCT 840588 v iv-- i - iv vv i v C MIR3#SINE/MIR 61 GACTA--GAACCCAGGTCT-CCTGACTCCCAGTCCGTGCT 25 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.32 CpG sites = 8, Kimura (unadjusted) = 29.99 Transitions / transversions = 0.67 (8/12) Gap_init rate = 0.07 (6 / 84), avg. gap size = 1.33 (8 / 6) 16 23.34 5.00 3.28 chr2ptel1M 840973 841032 (158968) (TC)n#Simple_repeat 1 61 (0) m_b77s252i11 2843 chr2ptel1M 840973 TCTC-CCCTACTGTGTCTTTCTGCTC-CCCCCACTCCCTCT-TCTCTCTC 841019 - i - v v i - - i i v i - (TC)n#Simple_ 1 TCTCTCTCT-CTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTC 48 chr2ptel1M 841020 CCCCTCCCTCTCT 841032 i i i (TC)n#Simple_ 49 TCTCTCTCTCTCT 61 Matrix = Unknown Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.08 (5 / 59), avg. gap size = 1.00 (5 / 5) 14 29.19 2.41 4.94 chr2ptel1M 840995 841077 (158923) (CTCC)n#Simple_repeat 1 81 (0) m_b77s252i12 2843 chr2ptel1M 840995 CTCCCCCCACTCCCT-CTTCTCTCTCCCCCTCCCTCTCTGGAACATCTTC 841043 i - - i i i i i vvvv -i i (CTCC)n#Simpl 1 CTCCCTCC-CTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTC-CCTCC 48 chr2ptel1M 841044 CTCTCCTTCCTGCCTTCGGCTCCT-CCTCCCCCCC 841077 - i v i vv - - i (CTCC)n#Simpl 49 CTC-CCTCCCTCCCTCCCTC-CCTCCCTCCCTCCC 81 Matrix = Unknown Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.07 (6 / 82), avg. gap size = 1.00 (6 / 6) 375 28.26 8.33 5.20 chr2ptel1M 843887 844054 (155946) C MIR3#SINE/MIR (32) 176 4 m_b77s601i8 2844 chr2ptel1M 843887 AGGGTTTTCCAAGAGCTTCCTGTTCATCCTTTTCATTTTCC---TGAGGC 843933 vii ivi v v iv i v iii v --- v C MIR3#SINE/MIR 176 AGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGA 127 chr2ptel1M 843934 AATTGGGG----------TTAAATGACTTGCCC-AGGTCACACAACCAGG 843972 i i ---------- v i - i ? - C MIR3#SINE/MIR 126 AACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGCNAG- 78 chr2ptel1M 843973 AAGTGTTAAGTGTCTGAGGCCGGATTTGAACTCGGGTCCTCCTGACTTCA 844022 ------ v v v v v i v i i - i v C MIR3#SINE/MIR 77 ------TTAGTGGCAGAGCCGGGACTAGAACCCAGGT-CTCCTGACTCCC 35 chr2ptel1M 844023 GGGCTGGGGCTCTATCCACTGCACCACCCAGC 844054 i v i- v v ii vvi i v C MIR3#SINE/MIR 34 AGTCC-GTGCTCTCTCTGCTCAGCCACTCTGC 4 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.31 CpG sites = 23, Kimura (unadjusted) = 36.30 Transitions / transversions = 1.05 (23/22) Gap_init rate = 0.07 (12 / 167), avg. gap size = 1.92 (23 / 12) 517 20.71 1.56 5.69 chr2ptel1M 843927 844054 (155946) C MIRc#SINE/MIR (141) 127 5 m_b77s601i9 2844 chr2ptel1M 843927 CTGAGGCA-ATTGGGGTTAAATGACTTGCCCA-GGTCACACAACCAGGAA 843974 v- vv i i - i i --- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG--- 81 chr2ptel1M 843975 GTGTTAAGTGTCTGAGGCCGGATTTGAACTCGGGTCCTCCTGACTTCAGG 844024 ---- v v v v i i i i i i i C MIRc#SINE/MIR 80 ----TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr2ptel1M 844025 GCTGGGGCTCTATCCACTGCACCACCCAGC 844054 v ii v v v v C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTGCACCACACTGC 5 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 23.30 CpG sites = 13, Kimura (unadjusted) = 24.37 Transitions / transversions = 1.08 (13/12) Gap_init rate = 0.07 (9 / 127), avg. gap size = 1.00 (9 / 9) 13 18.80 4.55 2.22 chr2ptel1M 844370 844413 (155587) (CACCCTC)n#Simple_repeat 1 45 (0) m_b77s252i13 2845 chr2ptel1M 844370 CACTCTACACCCACCGCCCCTCCAGCCTCC-CTCT-CATCCTCCAC 844413 i v v -v v - i - i (CACCCTC)n#Si 1 CACCCTCCACCCTCC-ACCCTCCACCCTCCACCCTCCACCCTCCAC 45 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.07 (3 / 43), avg. gap size = 1.00 (3 / 3) 81 33.84 2.61 0.00 chr2ptel1M 846271 846576 (153424) (TGCC)n#Simple_repeat 1 314 (0) m_b77s252i14 2846 chr2ptel1M 846271 TGCCTGCCCATCTGCCTGCCTACCCACTTACCCACCTGCCTGCCGGCCAA 846320 iii i ii i i ii v vi (TGCC)n#Simpl 1 TGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTG 50 chr2ptel1M 846321 CCTGTCTGCCTACCT-CCTACCTTCTTGTTTGTCTGCTTACC-ACCTATG 846368 i i - i v i ii i i i -i iiv (TGCC)n#Simpl 51 CCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCC 100 chr2ptel1M 846369 TACCTCCCCACCTGCCTACCT-CCTGTCCGCCCGCTTGCCTACCTGCCTG 846417 i v ii i - i i i i i (TGCC)n#Simpl 101 TGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTG 150 chr2ptel1M 846418 CCTACTCACCGGCCTGTCTGCCT-CTTACCTGCCTGCTTGCCTACTTG-C 846465 i iii v i - i i i i i - (TGCC)n#Simpl 151 CCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCC 200 chr2ptel1M 846466 TGCCTACATACCCACCCACCTGCCCACCT-CTTCCCTGCCCACTTCCCTA 846514 i v i ii ii ii - i v ii i v i (TGCC)n#Simpl 201 TGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTG 250 chr2ptel1M 846515 CCTGCTGGCCTACTCACCGGCCTGTCTGCTTGCCTACCCGGCTGCC-GCC 846563 iv i iii v i i i i v - (TGCC)n#Simpl 251 CCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCC 300 chr2ptel1M 846564 T-CTTGTCTGCCTG 846576 - i i (TGCC)n#Simpl 301 TGCCTGCCTGCCTG 314 Matrix = Unknown Transitions / transversions = 5.50 (66/12) Gap_init rate = 0.03 (8 / 305), avg. gap size = 1.00 (8 / 8) 182 33.82 4.41 0.00 chr2ptel1M 846843 846910 (153090) C L2a_3end#LINE/L2 (15) 502 432 m_b77s601i10 2847 chr2ptel1M 846843 AAGCATCTATGAAGTGCTGACTTGGAGCAAAGCGCTGCCCCAAGTCCTGG 846892 ii i vi i iv vv v v i i ii i i iv C L2a_3end#LINE 502 AAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGCGCTGG 453 chr2ptel1M 846893 GGGTGCAG--GTGGA-AAAAC 846910 i i -- i - C L2a_3end#LINE 452 GGATACAGCAGTGAACAAAAC 432 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.52 CpG sites = 16, Kimura (unadjusted) = 48.37 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.03 (2 / 67), avg. gap size = 1.50 (3 / 2) 561 32.74 8.70 0.40 chr2ptel1M 846976 847205 (152795) MIRb#SINE/MIR 5 253 (15) m_b77s601i11 2848 chr2ptel1M 846976 GGGGCACCACGACGCAG-----AGTTCACTGGGCTGGGATGCA-AGAGGA 847019 v ii ii ----- vv v vi v vv - v iv MIRb#SINE/MIR 5 GGGGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGAC 54 chr2ptel1M 847020 TTGAGTTCAAATCTCATCTCCCCTAGATGGCCGTTTGTGTGCCC--GAGA 847067 i i i i iv iv i v- vi iivi v -- i v MIRb#SINE/MIR 55 CTGGGTTCGAATCCCGGCTCTGCCAC-TTACTAGCTGTGTGACCTTGGGC 103 chr2ptel1M 847068 AAGC-ACTTAACTT------GCCTCAGTCTCCTCACCTGTAAAATGGAAA 847110 i- i ------ i i ii MIRb#SINE/MIR 104 AAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGA 153 chr2ptel1M 847111 T--CAGCATCTGCCTCCCAGGGTTAT---GAAGACCAGCTGAGGTAGCAA 847155 --i ii i i v i --- i ii iv i iiiv MIRb#SINE/MIR 154 TAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGC 203 chr2ptel1M 847156 TTACAAAGCACTCAGCACAGTGCAGGGCTTAGTGTAGGCATTTCATAGAT 847205 v ii i i vv vi vv i ii iv i MIRb#SINE/MIR 204 ATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAAAT 253 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.16 CpG sites = 48, Kimura (unadjusted) = 45.24 Transitions / transversions = 1.78 (48/27) Gap_init rate = 0.03 (8 / 229), avg. gap size = 2.62 (21 / 8) 223 29.63 0.00 0.00 chr2ptel1M 847159 847212 (152788) L2d_3end#LINE/L2 449 502 (14) m_b77s601i12 2849 chr2ptel1M 847159 CAAAGCACTCAGCACAGTGCAGGGCTTAGTGTAGGCATTTCATAGATACT 847208 v i ii v i vi vv ii iv i L2d_3end#LINE 449 CACAGCGCCTAGCACAGTGCTGAGCACATAGTAGGCGCTCAATAAATACT 498 chr2ptel1M 847209 TATT 847212 i L2d_3end#LINE 499 TGTT 502 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.07 CpG sites = 10, Kimura (unadjusted) = 39.12 Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 312 22.06 0.00 0.00 chr2ptel1M 848330 848397 (151603) C DNM1r#Unknown (2114) 2548 2481 m_b77s502i1 2850 chr2ptel1M 848330 TCTATGAATACTCGGGCATACACATATGTGTACACACATACATATGTACA 848379 i? viivii i ii i i i i C DNM1r#Unknown 2548 TCTATANATACGTATATATACACATATATACACACATACACACATATACA 2499 chr2ptel1M 848380 CACATATGTACACACATA 848397 i C DNM1r#Unknown 2498 CACATATATACACACATA 2481 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 28.60 CpG sites = 13, Kimura (unadjusted) = 28.60 Transitions / transversions = 6.50 (13/2) Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0) 278 22.22 0.00 0.00 chr2ptel1M 848347 848409 (151591) C DNM1r#Unknown (2119) 2543 2481 m_b77s502i2 2850 chr2ptel1M 848347 ATACACATATGTGTACACACATACATATGTACACACATATGTACACACAT 848396 ? i i i i i i i iii i i i C DNM1r#Unknown 2543 ANATACGTATATATACACATATATACACACATACACACATATACACACAT 2494 chr2ptel1M 848397 ATGTACACACATA 848409 i C DNM1r#Unknown 2493 ATATACACACATA 2481 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 27.46 CpG sites = 14, Kimura (unadjusted) = 30.04 Transitions / transversions = 1.00 (14/0) Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0) 227 23.97 0.00 5.97 chr2ptel1M 848351 848421 (151579) C DNM1r#Unknown (2117) 2545 2479 m_b77s502i3 2850 chr2ptel1M 848351 ACATATGTGTACACACATACATATGTACACACATATGTACACACATATGT 848400 i ? ii i i i i i ---- ii C DNM1r#Unknown 2545 ATANATACGTATATATACACATATATACACACATA----CACACATATAC 2500 chr2ptel1M 848401 ACACACATATGAATGTATACA 848421 i iv iii C DNM1r#Unknown 2499 ACACATATATACACACATACA 2479 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 29.98 CpG sites = 15, Kimura (unadjusted) = 32.48 Transitions / transversions = 15.00 (15/1) Gap_init rate = 0.06 (4 / 70), avg. gap size = 1.00 (4 / 4) 237 26.47 0.00 0.00 chr2ptel1M 848363 848430 (151570) C DNM1r#Unknown (2117) 2545 2478 m_b77s502i4 2850 chr2ptel1M 848363 ACACATACATATGTACACACATATGTACACACATATGTACACACATATGA 848412 i ? i i i i iii i i i iiv C DNM1r#Unknown 2545 ATANATACGTATATATACACATATATACACACATACACACATATACACAC 2496 chr2ptel1M 848413 ATGTATACATTCATTCAC 848430 i iv v C DNM1r#Unknown 2495 ATATATACACACATACAC 2478 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 33.68 CpG sites = 15, Kimura (unadjusted) = 36.26 Transitions / transversions = 5.00 (15/3) Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0) 13 25.07 7.79 1.22 chr2ptel1M 848583 848659 (151341) (ATAGTT)n#Simple_repeat 1 82 (0) m_b77s252i15 2851 chr2ptel1M 848583 ATAATTCTAGATTAGATATATAGTTATAGGAATA--TATAATTAT-G-TA 848628 i v - v vv vv -- i - - (ATAGTT)n#Sim 1 ATAGTTATAG-TTATAGTTATAGTTATAGTTATAGTTATAGTTATAGTTA 49 chr2ptel1M 848629 TA--CATACGTACATGTATACATATAGTTATAG 848659 --i vv i vv vv (ATAGTT)n#Sim 50 TAGTTATAGTTATAGTTATAGTTATAGTTATAG 82 Matrix = Unknown Transitions / transversions = 0.33 (4/12) Gap_init rate = 0.07 (5 / 76), avg. gap size = 1.40 (7 / 5) 21 14.43 0.00 0.00 chr2ptel1M 849763 849801 (150199) (CTCTCT)n#Simple_repeat 1 39 (0) m_b77s252i16 2852 chr2ptel1M 849763 CTCTCCTTCTCCCTCTCTCCCTCTCTGTCTCTCTCTCTC 849801 ii i i v (CTCTCT)n#Sim 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 39 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 15 0.00 0.00 0.00 chr2ptel1M 850524 850542 (149458) (GTT)n#Simple_repeat 1 19 (0) m_b77s252i17 2853 chr2ptel1M 850524 GTTGTTGTTGTTGTTGTTG 850542 (GTT)n#Simple 1 GTTGTTGTTGTTGTTGTTG 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 353 27.30 13.48 1.27 chr2ptel1M 850964 851104 (148896) MIR1_Amn#SINE/MIR 7 164 (66) m_b77s601i13 2854 chr2ptel1M 850964 GGCTATGTGGCCCAGTGGGTGGAG-----GGCTGAGCCCCGAGTCAGACC 851008 vi i i i i ----- i i v i i -- MIR1_Amn#SINE 7 GGCAGTGTGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGG--AGACC 54 chr2ptel1M 851009 TGAGCTCAAACCTGGCCTCGGATGCTTCCCAGCTGGGTGACTTTG---CT 851055 i i ? ?i iv v v vii ?v ? ? i ---vv MIR1_Amn#SINE 55 TGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAA 104 chr2ptel1M 851056 GCTACTT-----------GCTTCGGTTTCCTCACCTGTAAAGTGAGGAGG 851094 ii ----------- i i i i i vi MIR1_Amn#SINE 105 GTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGGATA 154 chr2ptel1M 851095 AGCACAGTGA 851104 vv i v MIR1_Amn#SINE 155 ATGATACTGA 164 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.15 CpG sites = 25, Kimura (unadjusted) = 37.15 Transitions / transversions = 1.92 (25/13) Gap_init rate = 0.04 (5 / 140), avg. gap size = 4.20 (21 / 5) 266 28.16 16.50 0.00 chr2ptel1M 851849 851951 (148049) C L3#LINE/CR1 (197) 3902 3783 m_b78s601i1 2855 chr2ptel1M 851849 AGCTTTTCCTGATATCCAGCCTAAGCATTCC--CCTGTA-CT-------- 851887 i i v iv v iiv v -- - -------- C L3#LINE/CR1 3902 AGTTCTTCCTTATATTGAGCCGAAATCTGCCTCCCTGTAACTTCCACCCA 3853 chr2ptel1M 851888 ------CTTGTTTTGCCCTTTGGGACCAAGGAGGGCAAGTCTCATTCCTC 851931 ------ v i i ii viv iii v i C L3#LINE/CR1 3852 TTGGTCCTAGTTCTGCCCTCTGGAGCCACACAGAATAAGTCTAATCCCTC 3803 chr2ptel1M 851932 CTCCATAGGATGGTCCTTCA 851951 i i v ii i C L3#LINE/CR1 3802 TTCCACATGACAGCCCTTCA 3783 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.77 CpG sites = 19, Kimura (unadjusted) = 36.77 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.04 (4 / 102), avg. gap size = 4.25 (17 / 4) 12 16.52 0.00 0.00 chr2ptel1M 852194 852220 (147780) (TTGCA)n#Simple_repeat 1 27 (0) m_b78s252i1 2856 chr2ptel1M 852194 TTGCAGTGCTCTGCATTGCATTTCATT 852220 v vi v (TTGCA)n#Simp 1 TTGCATTGCATTGCATTGCATTGCATT 27 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 474 23.91 0.00 9.65 chr2ptel1M 852450 852574 (147426) C L2d2_3end#LINE/L2 (18) 537 424 m_b78s601i2 2857 chr2ptel1M 852450 TATTTAGTAAGTGCCTACTGTGTGCCAGGTGCTGGGTGCCAGATGCTGTG 852499 v i i v ii -- i ii C L2d2_3end#LIN 537 TATTTATTGAGCGCCTACTGTGTGCAAGGCACTG--TGCTAGGCGCTGTG 490 chr2ptel1M 852500 CTAAGTGCTGGAGATACAAGTAAGTGAAAGAAACAGTCCTTGCCCTCAAG 852549 --------- i iv iv v ii i C L2d2_3end#LIN 489 ---------GGGGATACAAAGAAGTATAAGACATGGTCCCTGCCCTCAAG 449 chr2ptel1M 852550 GAGCCTCCAGGCTCATGGAGGAGGC 852574 i v iv vi v i i C L2d2_3end#LIN 448 GAGCTTACAATCTAGTTGGGGAGAC 424 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.86 CpG sites = 18, Kimura (unadjusted) = 29.40 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.09 (11 / 124), avg. gap size = 1.00 (11 / 11) 225 31.82 6.36 0.00 chr2ptel1M 852829 852938 (147062) MIRc#SINE/MIR 3 119 (149) m_b78s601i3 2858 chr2ptel1M 852829 AGGCAG---GGCGT-GTGGCCAGAGCCCGGGGGCTGGACTCAGGAAGCCC 852874 --- i i- vv v v ivi v v MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chr2ptel1M 852875 CAAATGCAAATCCAGCCTCGGACACTTCCGAGCGAGCTGATC-TGGGCAG 852923 iiii v i i v v v v v v vivv i - i MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 102 chr2ptel1M 852924 GCTAC--GGCCCCTCTG 852938 ii --ii i MIRc#SINE/MIR 103 GTCACTTAACCTCTCTG 119 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.56 CpG sites = 18, Kimura (unadjusted) = 42.12 Transitions / transversions = 1.06 (18/17) Gap_init rate = 0.04 (4 / 109), avg. gap size = 1.75 (7 / 4) 20 17.78 0.00 2.17 chr2ptel1M 857717 857763 (142237) (CCCCTT)n#Simple_repeat 1 46 (0) m_b78s252i2 2859 chr2ptel1M 857717 CCCCTTCCCCTTCCCCTTCCTCTTCCCACCATCTCTTCCTCATCCCC 857763 i - ivi i i v (CCCCTT)n#Sim 1 CCCCTTCCCCTTCCCCTTCCCCTTCCC-CTTCCCCTTCCCCTTCCCC 46 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.02 (1 / 46), avg. gap size = 1.00 (1 / 1) 194 33.45 5.95 9.50 chr2ptel1M 859551 859735 (140265) L3#LINE/CR1 2309 2487 (1612) m_b78s601i4 2860 chr2ptel1M 859551 AGGGCTTTTTGAACAAGAAGCGATAATGGGAGGAAGAGGAGGATCCAGGA 859600 i ---- -- v iv v v ii ii --- i L3#LINE/CR1 2309 AAGGCTTTT----CAA--AGCTATGTTCGGAGCAGAAGGAAAA---AGAA 2349 chr2ptel1M 859601 AGGGATGAGACGAGGCCACGGAGGCTGGGGGTCGATGG-ACACTGCCGCC 859649 ? i------ v-- vv v iv -ii v iiiv L3#LINE/CR1 2350 AGNGAC------AGGCCC--GCTGCTTGGGGCAGATGGCGTAATGTTAAC 2391 chr2ptel1M 859650 GGACAGCAGGACGA--GCGG-----CGCAACTTGGACTTTGCTTCTTTTT 859692 i iii iiv -- i ----- v ivv i iv i L3#LINE/CR1 2392 AGATGACAGAGAGAAAGCAGAACTACTCAACTCCTATTTTGCTTCCGTCT 2441 chr2ptel1M 859693 TCTCCAGCAAGGCCATTG---TTTGGCCTAAAAAGGAAGGAGCAGA 859735 i v vv v --- ii v ii ivi i i L3#LINE/CR1 2442 TCTCTATCAAGGAGAATGATCTTCAGACTGGAAAGGGTAGAACAAA 2487 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.07 CpG sites = 34, Kimura (unadjusted) = 46.35 Transitions / transversions = 1.55 (34/22) Gap_init rate = 0.11 (21 / 184), avg. gap size = 1.33 (28 / 21) 18 31.06 2.94 0.00 chr2ptel1M 862909 862976 (137024) (AG)n#Simple_repeat 1 70 (0) m_b78s252i3 2861 chr2ptel1M 862909 AGAGTGTGAGAGACAGAGAGGAAGGCAGGGAGAGACA-ACGGAG-GAGAG 862956 v v v ii iv i v - vi - (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr2ptel1M 862957 AGGGCAAGAGAAAGGGGGAG 862976 i vi i i i (AG)n#Simple_ 51 AGAGAGAGAGAGAGAGAGAG 70 Matrix = Unknown Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.03 (2 / 67), avg. gap size = 1.00 (2 / 2) 186 35.89 7.58 2.90 chr2ptel1M 863879 864010 (135990) C L2d_3end#LINE/L2 (1) 515 378 m_b78s601i5 2862 chr2ptel1M 863879 CACTCACTCACTCACCCAGCACTTGCCAACTGCCTCCTGGCCACTTGAC- 863927 v v v v v i i iiii vi v ivvii iii - C L2d_3end#LINE 515 CAATCAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCA 466 chr2ptel1M 863928 CTGGGGTGGTCATTGTACTTGGTGGA-GAGAAACAAATG-AAG---TAAC 863972 v v i v ii ---- v i - ? v? i i- --- iii C L2d_3end#LINE 465 CTGTGCTAGGCGCTGT----GGGGAACGANAAAANAGTATAAGACATGGT 420 chr2ptel1M 863973 CTCTGTCCTCAAAGGGTTTTCA--TTA--TGGGGAGGCTGGA 864010 i i i i i v --i -- i vi C L2d_3end#LINE 419 CCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGGAGACAAGA 378 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 50.06 CpG sites = 30, Kimura (unadjusted) = 53.54 Transitions / transversions = 1.88 (30/16) Gap_init rate = 0.08 (10 / 131), avg. gap size = 1.40 (14 / 10) 248 31.47 4.83 6.37 chr2ptel1M 864471 864677 (135323) L2a_3end#LINE/L2 35 238 (279) m_b78s601i6 2863 chr2ptel1M 864471 TCCTCTCACGCCTCACTCCTGCTCCCTTACCCT--TCCA--CCCAGTGAC 864516 v vii v v iv v i i i-- -- v v i L2a_3end#LINE 35 TCATCTCCTACCACTCTCCCCCTCGCTCACTCCGCTCCAGCCACACTGGC 84 chr2ptel1M 864517 CTCCTGACTGTCCCATGAACAAGAGCCTCCAC-CTCCTGCCTCCACGCCT 864565 vi i vi v -v vvv - i viv L2a_3end#LINE 85 CTCCTTGCTGTTCCTCGAACACG-CCAGGCACGCTCCCGCCTCAGGGCCT 133 chr2ptel1M 864566 TGGCACCAGGCTGTCTCCTGTGCCTGGAGGATCCTTCCTCCTCAAATAAC 864615 v i-v ii v iviii -- i i v L2a_3end#LINE 134 TTGCACT-TGCTGTTCCCTCTGCCTGGAACGCTCTTC--CCCCAGATATC 180 chr2ptel1M 864616 TA-AAAGCTCCTGGGCTACCAGGCTTCCCTCTGCTTTAGTCTTGGCTTAC 864664 ii- vi ---- v vvi i i v ----- v i v L2a_3end#LINE 181 CGCATGGCTC----GCTCCCTCACCTCCTTCAG-----GTCTTTGCTCAA 221 chr2ptel1M 864665 A----GCTTTTTCAAGG 864677 ----i i i i? L2a_3end#LINE 222 ATGTCACCTTCTCAGNG 238 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.41 CpG sites = 32, Kimura (unadjusted) = 41.81 Transitions / transversions = 1.10 (32/29) Gap_init rate = 0.09 (18 / 206), avg. gap size = 1.28 (23 / 18) 490 37.70 5.93 4.69 chr2ptel1M 864746 865335 (134665) C MamRTE1#LINE/RTE-BovB (1138) 2674 2078 m_b78s601i7 2864 chr2ptel1M 864746 AACATGGCTGGAAAAATCATGAT--AAAAGCACAGGAGCAAATACACAGC 864793 i v v vi - -- v iv v v v v i ii C MamRTE1#LINE/ 2674 AGCATGGCTGCATAAAATA-GATTGAATAAGACTGGACCTATTACGCAAT 2626 chr2ptel1M 864794 CCTGCTGCA------TGGCAATCGGGAAAGTGCTGGAGCATCCTCCGTCA 864837 v ------ ii v v v ii vvivv v C MamRTE1#LINE/ 2625 CCTGCTTCACTCCATTGGTGATGGGGAATGGGTCGGACAGGACGCCGTCA 2576 chr2ptel1M 864838 TCCAGAACCTGTGCAAGCTTGCTGTTGTGAGACTGGCGTATGAGGCCAAC 864887 v ivvi vi vv iiv v i ii ii iiiiv v v v vviiiii C MamRTE1#LINE/ 2575 ACTCTGACGCGACCGGCCATACCATCATGGAGTAGCCTTAGGATCTTGGT 2526 chr2ptel1M 864888 -AACTTCTCTGGGCAACCAAATCCTGCCTAG-ATCTTCCT---------T 864926 - v i - i i - v v v--------- C MamRTE1#LINE/ 2525 GAACTTCTCAGGGCAGCCAAA-CTTGCTTAGTAGCTGCCAGAGCCCAGGT 2477 chr2ptel1M 864927 CTTCTGGATAGTATCAAAGGTCTTATGCA----TGATGAATGCAGTGCTC 864972 v - i ii v - v i ----i i vv C MamRTE1#LINE/ 2476 CTACTG-ATGGCGTCAAATG-CTTTTGTAAGGTCGATGAATACAGTGCAG 2429 chr2ptel1M 864973 GGACCTCATTCCAAAAATGCTCCTGGCAACTCTCCTGGAA-TGATCGGTG 865021 i ii iiv -----iv i iv ivi i v v- ivv i? C MamRTE1#LINE/ 2428 AGGTCTTGAT-----GTTGTTCCCTGCGCTTTTCCTGTATCTGACATGCN 2384 chr2ptel1M 865022 AGCAAACACAACATCAACTATTTCTTGGCCCTTTCTGAAGCCCTACTG-G 865070 - v iv i vi ? vi vi viv vvi i vi i - C MamRTE1#LINE/ 2383 -GCAAAGATCACGTCCGCTNTACCGCGCTGCGGCCTAAAGCCACATTGCG 2335 chr2ptel1M 865071 CTGTCAGG------TGGATAGCCATCTTCTAAGTGAAGGGTCGGCCCAAT 865114 v vi i ------i v ii v v v --- v ivi i ii i- C MamRTE1#LINE/ 2334 ATTCCGGGAGCGCACGGTTGACGATGTTGT---TCAGTAGCCGATCCAG- 2289 chr2ptel1M 865115 AAGGAGATCTGTGGCAAGAATCTTGCCAGCGATAACTAAGAGAGAGACCT 865164 --- v v i i iivv iv ? -- C MamRTE1#LINE/ 2288 AAGGA---CTCTGGCCAGGATCTTGCCAGCAATGGAGAGCAGNGAGA--T 2244 chr2ptel1M 865165 GCCCTCCCATCACTGTCACAGGACAATCTATTTCCTTGACCTTAACAGAG 865214 --v v vii i i vvviv i v iv --i vviii C MamRTE1#LINE/ 2243 GCC--GCGATAGTTGCCGCAGTCAGCTTTCTCGCCTT--TCTTCTTGAAG 2198 chr2ptel1M 865215 ATGGTCA--ATGGAGGCATCCTTGAACTCCTGGGGAATTGAATTACCCCC 865262 v -- i v i v v v vvv iiviv i C MamRTE1#LINE/ 2197 ATGGTGATGATAGTGGCATCTTTGAAATCCTGCGGCATTTCCTCGGTACT 2148 chr2ptel1M 865263 TTCTCAGCTAACCCAGAATA-TTTGTGACAACTTTTTAATGAGCGG-TGT 865310 iiv vv i --- v -ii i - iviv i vv v- vi C MamRTE1#LINE/ 2147 CCATATGCTGA---AGAAAAGCCTATG-CAGACGTCTAAGCAGCGTCTCC 2102 chr2ptel1M 865311 ACTCCTTGCCTTGCAAATCTCAGCA 865335 v i i - v C MamRTE1#LINE/ 2101 CCTTCCTG-CTTGAAAATCTCAGCA 2078 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 48.31 CpG sites = 107, Kimura (unadjusted) = 54.05 Transitions / transversions = 1.02 (107/105) Gap_init rate = 0.07 (40 / 589), avg. gap size = 1.57 (63 / 40) 279 18.52 0.00 0.00 chr2ptel1M 867153 867206 (132794) C L2d2_3end#LINE/L2 (0) 555 502 m_b78s601i8 2865 chr2ptel1M 867153 TCAGTTCAACTCAAAAAACATTTATTAAGCACCTACTGTGTGCTACACAC 867202 iv v v i i i v vi C L2d2_3end#LIN 555 TCAAATCAAATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCAC 506 chr2ptel1M 867203 TGTG 867206 C L2d2_3end#LIN 505 TGTG 502 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 19.13 CpG sites = 5, Kimura (unadjusted) = 21.39 Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 220 30.58 11.27 3.27 chr2ptel1M 869413 869554 (130446) MIR1_Amn#SINE/MIR 17 169 (61) m_b78s601i9 2866 chr2ptel1M 869413 TTTAGTAAAGGAAGCAGTGAGCTGAG-CTCTGCCCCTGCGGCCTGG---- 869457 i ii vii v ii i - v ----- v i ---- MIR1_Amn#SINE 17 TCTAGTGGATAGAGCACTGGACTGGGACTCGG-----GAGACCTGGGTTC 61 chr2ptel1M 869458 -AGTCCTGG-ACACCCATC--CTTGCTG-GTGGCCTTAGCCAAGTCCCAT 869502 - ? i -v vv ii-- i? - i i v v v MIR1_Amn#SINE 62 NANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGTCACTT 111 chr2ptel1M 869503 TAATGTT----GCCT--GTGTCCTCTTTTGGAAAATGGAGACATCTGCAC 869546 ? vivi ---- -- v v i v i i vivii MIR1_Amn#SINE 112 NACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATGATAC 161 chr2ptel1M 869547 TAACTTCC 869554 i i MIR1_Amn#SINE 162 TGACCTCC 169 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.65 CpG sites = 25, Kimura (unadjusted) = 41.97 Transitions / transversions = 1.47 (25/17) Gap_init rate = 0.09 (13 / 141), avg. gap size = 1.62 (21 / 13) 308 25.61 22.29 0.52 chr2ptel1M 869457 869613 (130387) MIRc#SINE/MIR 60 250 (18) m_b78s601i10 2866 chr2ptel1M 869457 GAGTCCTGG-ACACCCA--TCCTTGCTG-GTGGCCTTAGCCAAGTCCCAT 869502 i -v vv -- v v - i i v v - MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCAC-T 108 chr2ptel1M 869503 TAATGTT-----GCCT--GTGTCCTCTTTTGGAAAATGGAGACA------ 869539 iv i----- -- v v i v i i ------ MIRc#SINE/MIR 109 TAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATA 158 chr2ptel1M 869540 TCTGCACTA---ACTTCCCAGGGT--------------GCCGAGGCGATA 869572 i v i--- i v --------------ivi iii i MIRc#SINE/MIR 159 CCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATG 208 chr2ptel1M 869573 TTTG-GAAAGCACTTTGTAGACTTCAGAGTGCTGCATAAATG 869613 v - i i vi i ii i MIRc#SINE/MIR 209 TATGTGAAAGCGCTTTGTAAACTGTAAAGTGCTATACAAATG 250 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.22 CpG sites = 24, Kimura (unadjusted) = 32.14 Transitions / transversions = 1.50 (24/16) Gap_init rate = 0.06 (10 / 156), avg. gap size = 3.60 (36 / 10) 12 9.43 8.33 2.63 chr2ptel1M 873805 873840 (126160) (CCCAAA)n#Simple_repeat 1 38 (0) m_b78s252i4 2867 chr2ptel1M 873805 CCCAAACCC--ACCC-TTCCCAAACCCAAAACCCAATCC 873840 -- -vv - v (CCCAAA)n#Sim 1 CCCAAACCCAAACCCAAACCCAAACCC-AAACCCAAACC 38 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.09 (3 / 35), avg. gap size = 1.33 (4 / 3) 38 6.53 0.00 0.00 chr2ptel1M 874007 874055 (125945) (C)n#Simple_repeat 1 49 (0) c_b78s251i0 2868 chr2ptel1M 874007 CCCCCCCCCCCCCCCCCTTTCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 874055 iii (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 49 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 17 16.74 2.27 2.27 chr2ptel1M 875778 875821 (124179) (CCTTTCC)n#Simple_repeat 1 44 (0) m_b78s252i5 2869 chr2ptel1M 875778 CCTTTCCCCTTTCCCCATTTTTCCTTTTTCC-CCCCCCTTTCCCC 875821 - ii ii -ii (CCTTTCC)n#Si 1 CCTTTCCCCTTTCCCC-TTTCCCCTTTCCCCTTTCCCCTTTCCCC 44 Matrix = Unknown Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2) 235 28.21 8.97 0.00 chr2ptel1M 875872 875949 (124051) C MIRc#SINE/MIR (159) 109 25 m_b78s601i11 2870 chr2ptel1M 875872 AAGCGACTTG------GTCCTTCAGCTAGTGAGTGTCTGAGCTGAATCT- 875914 i ------ viv i v v i iiv - C MIRc#SINE/MIR 109 AAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTC 60 chr2ptel1M 875915 GAATTCAGCTCCTCCTGCGTCCAGGGCTGGGGCTC 875949 ii v i vv i v ii v C MIRc#SINE/MIR 59 GAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTC 25 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.03 CpG sites = 12, Kimura (unadjusted) = 36.03 Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.03 (2 / 77), avg. gap size = 3.50 (7 / 2) 264 37.50 1.77 0.88 chr2ptel1M 876345 876457 (123543) C MIRc#SINE/MIR (144) 124 11 m_b78s601i12 2871 chr2ptel1M 876345 AGGTTCAGGGATGGCCAATGATTTACTTAAGGTCACACAGGGAGCCACCC 876394 i i v viv i i i ii vv iv viv C MIRc#SINE/MIR 124 AGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTG 75 chr2ptel1M 876395 TCGGGGGAGGGGTCTGGACCCCAGCC--CCCAGCTCCAAAGCCAGGCCTC 876442 v i i vv iiii i vi i -- iii iv vv C MIRc#SINE/MIR 74 GCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTC 25 chr2ptel1M 876443 TTTGTGGCTGCATCA 876457 -ivi i C MIRc#SINE/MIR 24 TTT-CCACTGCACCA 11 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 53.12 CpG sites = 26, Kimura (unadjusted) = 55.13 Transitions / transversions = 1.62 (26/16) Gap_init rate = 0.02 (2 / 112), avg. gap size = 1.50 (3 / 2) 13 9.98 5.88 2.86 chr2ptel1M 877076 877109 (122891) (AAAAGG)n#Simple_repeat 1 35 (0) m_b78s252i6 2872 chr2ptel1M 877076 AAAAAGAAAA--ACAAGGAAATGGATAAAGGAAAAG 877109 i -- v v - (AAAAGG)n#Sim 1 AAAAGGAAAAGGAAAAGGAAAAGGA-AAAGGAAAAG 35 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.50 (3 / 2) 248 37.00 6.50 2.43 chr2ptel1M 877583 877859 (122141) L2c_3end#LINE/L2 147 434 (44) m_b78s601i13 2873 chr2ptel1M 877583 CCTCCCACCCGCCAGGCTCTCCCTTCTTGTCTCCTGCTGTCGGAATTCCT 877632 ii ii i vv v i ii i vii vv v v- i L2c_3end#LINE 147 CCCTCTGCCTGGAATGCTCTTCCCCCCTCCTTCCACCTGGCT-AACTCCT 195 chr2ptel1M 877633 AGTC-TCACTGACGCTTCATCACAGGCATCCCTTCGTGCAGGAGGCTCTC 877681 v - vi v v ?i v v iii v i v v i i ii L2c_3end#LINE 196 ACTCATCCTTCAAGNCTCAGCTCAGATGTCACCTCCTCCGGGAAGCCTTC 245 chr2ptel1M 877682 CCGGGCCGACCAA--CT-GCC--GGCAACTTCCCGGGGGCTCTCCTT-TA 877725 v i vv -- - i -- iiv i ivv v i v v-i L2c_3end#LINE 246 CCTGACCCCCCAAGNCTAGTCTAGGTGCCCTCCTCTGTGCTCCCATAGCA 295 chr2ptel1M 877726 TCTGTTTTATACTGGTCTAT----GCCCTT--CATTGG--TGTAGACAAG 877767 i ivv i --i i ---- v -- ii-- vvvv i L2c_3end#LINE 296 CCCTGTCTATACT--CCCATTATAGCACTTATCATTAACTTGTATTGTAA 343 chr2ptel1M 877768 CCATTACTTTAGGCATG-CTGTCTCCCTCATTAGGATCTGAACTCCTCGA 877816 iii ivv -- ? - ii i iv v i i L2c_3end#LINE 344 TTGTCTGTTTA--CNTGTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGA 391 chr2ptel1M 877817 GAGCTAAGA--ATGTCTGGACTTGGTCTTGCTATCTCAAGCAGCT 877859 i vii --i vi-- vi vv i v iv L2c_3end#LINE 392 GGGCAGGGACCGTGTCTTA--TTCATCTTTGTATCCCCAGCGCCT 434 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 51.22 CpG sites = 56, Kimura (unadjusted) = 53.58 Transitions / transversions = 1.27 (56/44) Gap_init rate = 0.06 (17 / 276), avg. gap size = 1.47 (25 / 17) 182 32.41 5.33 1.28 chr2ptel1M 880077 880151 (119849) Penelope1_Vert#LINE/Penelope 836 913 (166) m_b78s601i14 2874 chr2ptel1M 880077 ATTAAGACCCGACGTTCTGGGCAAGAGCCCGAGGTTCTGGCC-CAGAGGT 880125 i i i v v ii i vvvi iv v - i Penelope1_Ver 836 ATCAAAACCTGAAGATCTGGATAAAAGAAAAAACTTCTGGACGCAGAGGC 885 chr2ptel1M 880126 TT---TTTCTGGTTCCCCTGAGGTCCAGA 880151 ---vi i i - v ii i Penelope1_Ver 886 TTAAAACTCTAGCT-CCCTGTGGTTTAAA 913 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.40 CpG sites = 15, Kimura (unadjusted) = 44.40 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.04 (3 / 74), avg. gap size = 1.67 (5 / 3) 12 13.59 2.78 5.71 chr2ptel1M 883391 883426 (116574) (GGC)n#Simple_repeat 1 35 (0) m_b78s252i7 2875 chr2ptel1M 883391 GGCGGCCGCAGGC-ACGGAGGGAGGCGGCGGCGGCGG 883426 v - -i -v v (GGC)n#Simple 1 GGCGGCGGC-GGCGGCGG-CGGCGGCGGCGGCGGCGG 35 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.09 (3 / 35), avg. gap size = 1.00 (3 / 3) 12 12.34 5.13 5.13 chr2ptel1M 884622 884660 (115340) (AGGGAAG)n#Simple_repeat 1 39 (0) m_b78s252i8 2876 chr2ptel1M 884622 AGGG-AGGGGGTGCAGGGAAG-GGGAAGAGGGACCAGAGGG 884660 - i viv - -- (AGGGAAG)n#Si 1 AGGGAAGAGGGAAGAGGGAAGAGGGAAGAGGGA--AGAGGG 39 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.11 (4 / 38), avg. gap size = 1.00 (4 / 4) 205 27.38 2.41 7.59 chr2ptel1M 885208 885290 (114710) MIR3#SINE/MIR 101 179 (29) m_b78s601i15 2877 chr2ptel1M 885208 TCGCTGCCCCGCCTTG--CCTCAGTTTCCTCATCTGTACAATGAGCCGGA 885255 i v v v ii -- v -- i MIR3#SINE/MIR 101 TCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAG--GGG 148 chr2ptel1M 885256 GAAGCTTGGCTGAGAAAGCCCCCAACGCCCCCCCC 885290 ---- viv viii i i v i ii MIR3#SINE/MIR 149 G----TTGGACTAGATGATCTCTAAGGTCCCTTCC 179 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.95 CpG sites = 13, Kimura (unadjusted) = 34.95 Transitions / transversions = 1.62 (13/8) Gap_init rate = 0.09 (7 / 82), avg. gap size = 1.14 (8 / 7) 12 21.49 4.44 2.17 chr2ptel1M 885526 885570 (114430) (CGCC)n#Simple_repeat 1 46 (0) m_b78s252i9 2878 chr2ptel1M 885526 CGCCCTCCCTGCCC-CCCCCCCCCCAGCCC-CGCAAGCGCCCGCCCG 885570 v - - v v v - v ivv (CGCC)n#Simpl 1 CGCCCGCCC-GCCCGCCCGCCCGCCCGCCCGCCCGCCCGCCCGCCCG 46 Matrix = Unknown Transitions / transversions = 0.14 (1/7) Gap_init rate = 0.07 (3 / 44), avg. gap size = 1.00 (3 / 3) 15 14.38 0.00 0.00 chr2ptel1M 885687 885710 (114290) (C)n#Simple_repeat 1 24 (0) m_b78s252i10 2879 chr2ptel1M 885687 CCCCTCCCCCTCCCCCCTCCCCCC 885710 i i i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCC 24 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 19 37.02 0.00 0.00 chr2ptel1M 885961 886029 (113971) (CC)n#Simple_repeat 1 69 (0) m_b78s252i11 2880 chr2ptel1M 885961 CCCCTCCCCCTCTTCTCGCCCCCCCTCCCCTCAGCCCCCCTTCCCCCCTC 886010 i i ii i v i i vv ii i (CC)n#Simple_ 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 50 chr2ptel1M 886011 TTCTCATTCCCCCCCCCCC 886029 ii i vii (CC)n#Simple_ 51 CCCCCCCCCCCCCCCCCCC 69 Matrix = Unknown Transitions / transversions = 3.75 (15/4) Gap_init rate = 0.00 (0 / 68), avg. gap size = 0.0 (0 / 0) 14 23.41 4.00 0.00 chr2ptel1M 888346 888395 (111605) (CTCTCGC)n#Simple_repeat 1 52 (0) m_b79s252i0 2881 chr2ptel1M 888346 CTCTGGCCTC-CGTCTCTCAGCTCCGGCCTC-CGTCTCTCAGCTCTGGCC 888393 v - i iv iv - i iv v (CTCTCGC)n#Si 1 CTCTCGCCTCTCGCCTCTCGCCTCTCGCCTCTCGCCTCTCGCCTCTCGCC 50 chr2ptel1M 888394 TC 888395 (CTCTCGC)n#Si 51 TC 52 Matrix = Unknown Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.04 (2 / 49), avg. gap size = 1.00 (2 / 2) 204 27.54 4.35 0.00 chr2ptel1M 890164 890232 (109768) MIRc#SINE/MIR 16 87 (181) m_b79s601i0 2882 chr2ptel1M 890164 CAGGGCACAGAGCCGGGGGCTT--AGGCAGGAAGACCTGAATGCCAATTC 890211 v v v vvv i -- v ii v v i i MIRc#SINE/MIR 16 CAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCC 65 chr2ptel1M 890212 AGCCTCCA-CACTTCCTAGCTG 890232 v v ii- v MIRc#SINE/MIR 66 CGGCTCTGCCACTTACTAGCTG 87 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.33 CpG sites = 7, Kimura (unadjusted) = 34.33 Transitions / transversions = 0.58 (7/12) Gap_init rate = 0.03 (2 / 68), avg. gap size = 1.50 (3 / 2) 257 35.98 11.92 0.60 chr2ptel1M 893528 893678 (106322) C MIRc#SINE/MIR (85) 183 16 m_b79s601i1 2883 chr2ptel1M 893528 AGTCCCGTGAGGGAGGGACTGCAATGATTGCCACTCCCACT----AGAGA 893573 ii i v v vv ivv iii ii i ---- vi C MIRc#SINE/MIR 183 AACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATG 134 chr2ptel1M 893574 AGGAAACTGAGACTTGGGGATG----GGGATCAGCCT----TTGCACGGC 893615 i ii i v ---- v iiv i---- ii i C MIRc#SINE/MIR 133 AGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGC 84 chr2ptel1M 893616 CCCCATATGTTATGAGCTAGAGCTTAAAACC-GGT----CTGATTCCAAA 893660 ivvi vi vi - ii ii ii v - ---- i i C MIRc#SINE/MIR 83 TAGTAAGTGGCA-GAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr2ptel1M 893661 TCCAG-GCCTTCCCTTCTG 893678 - ii ii iv C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTG 16 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 50.17 CpG sites = 38, Kimura (unadjusted) = 53.51 Transitions / transversions = 2.38 (38/16) Gap_init rate = 0.05 (7 / 150), avg. gap size = 2.71 (19 / 7) 180 30.00 0.00 0.00 chr2ptel1M 894551 894600 (105400) C X17_LINE#LINE/CR1 (166) 130 81 m_b79s601i2 2884 chr2ptel1M 894551 CACTGTGGGACAGATCTCGCTCTTGGGGATCCCTTCCTGCCATCCAGCCT 894600 v vvi i v i i viii vi i C X17_LINE#LINE 130 CACAGTCTAATAGATCTCGCTGTTAGGAAATTTTTCCTGATATTCAGCCT 81 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.56 CpG sites = 9, Kimura (unadjusted) = 39.56 Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 331 32.01 20.39 1.41 chr2ptel1M 894681 895038 (104962) C L3#LINE/CR1 (348) 3751 3327 m_b79s601i3 2885 chr2ptel1M 894681 AGGCCTTCCCTTGTCCAGGGTGAACACCTCCAGCTCCG------GGTC-- 894722 i i i v v i i i i v------ v -- C L3#LINE/CR1 3751 AAGTCTTCTCTTCTCCAGGCTAAACATCCCCAGTTCCTTCAACCGTTCCT 3702 chr2ptel1M 894723 --TAGAACAGG--TTGCAGACCTTGCCCCACACTG---GCTCTTCTCCCC 894765 -- vi v -- v i v v iv --- i ivv C L3#LINE/CR1 3701 CATATGACATGGTTTCCAGACCCTTCACCATCCTGGTCGCTCTCCTCTGG 3652 chr2ptel1M 894766 GCCTGCTCTTTCTCCCCACTTGTTCTTCTCAAGCCAAATAT---ATCTAG 894812 i vi ivvi ivi v- i i i ---- i ---ii i C L3#LINE/CR1 3651 ACGCGCTCCAGTTTGTCAA-TGTCCCTCTTA----AAATGTGGCGCCCAG 3607 chr2ptel1M 894813 AAC--AACCCCGTGTTCCGGCTGTGCTGTGATCAGAGCAGGG-ACAGCAG 894859 -- v vi ii i v v v i v i - i C L3#LINE/CR1 3606 AACTGAACGCAATACTCCAGATGTGGTCTGACCAGCGCAGAGTACAGCGG 3557 chr2ptel1M 894860 GATTCTGGGCTTAGTAGTTCCGAA-AATGT-TTCCCCTTTCTGGGG---A 894904 i v viv ivv v ? i i - v i -i i iv vv vi --- C L3#LINE/CR1 3556 GACTATTACCTCCCTTGNTCTGGACACTATACTTCTATTAATGCAGCCTA 3507 chr2ptel1M 894905 AGA------------TTTTGGCTGCTG-GTCACA-------CTTATAGTG 894934 ------------ v ii-i ------- i v C L3#LINE/CR1 3506 AGATTGCATTAGCTTTTTTGGCAGCCACATCACACTGTTGGCTCATATTG 3457 chr2ptel1M 894935 AACCTGTGGTCCACCATGGGCCCCTCATCGTTTT----TG---------- 894970 i i i v i viiv ivvi v ---- ---------- C L3#LINE/CR1 3456 AGCTTGCGGTCAACTAAAACCCCTAGGTCTTTTTCACGTGAACTGCTGCT 3407 chr2ptel1M 894971 --------TCTCCCTCAAGGTGTCCTTGTGAAGTTGTGTTTTTGAACCAA 895012 -------- ii ii vvv v v vv v C L3#LINE/CR1 3406 AAGCCAGATCCTCTCCATCCTGTACTTGTGCAGTTGATTTTTTGAACCTA 3357 chr2ptel1M 895013 CTT-----ACTTTATGTTTATCCGCTGTCAA 895038 vv ----- ii - i C L3#LINE/CR1 3356 AATGCAGGACTTTACATTTATCC-CTGTTAA 3327 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.02 CpG sites = 61, Kimura (unadjusted) = 43.02 Transitions / transversions = 1.17 (61/52) Gap_init rate = 0.07 (24 / 357), avg. gap size = 3.29 (79 / 24) 13 16.80 2.78 2.78 chr2ptel1M 895096 895131 (104869) (AAG)n#Simple_repeat 1 36 (0) m_b79s252i2 2886 chr2ptel1M 895096 AAGAAGAAAGAGGAAGAAG-AGAAAAGGTAGGAGAAG 895131 - i - i i v i (AAG)n#Simple 1 AAGAAG-AAGAAGAAGAAGAAGAAGAAGAAGAAGAAG 36 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 204 31.43 2.86 0.00 chr2ptel1M 895679 895748 (104252) MIRb#SINE/MIR 6 77 (191) m_b79s601i4 2887 chr2ptel1M 895679 GGGCAAGATGGTACAGTGGGCAGAACACAGCC--TGGAGTGAAAAGGAGC 895726 ivi i iv i i v -- v i vi v MIRb#SINE/MIR 6 GGGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACC 55 chr2ptel1M 895727 CGACTTCAAATATGGCCTCTGC 895748 i iv i viv v MIRb#SINE/MIR 56 TGGGTTCGAATCCCGGCTCTGC 77 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.67 CpG sites = 12, Kimura (unadjusted) = 41.66 Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.01 (1 / 69), avg. gap size = 2.00 (2 / 1) 217 15.79 0.00 0.00 chr2ptel1M 895739 895776 (104224) MIR#SINE/MIR 105 142 (120) m_b79s601i5 2887 chr2ptel1M 895739 TGGCCTCTGCTTGCCTCAGTTCCCTCATCTGTAAAATG 895776 ii viv i MIR#SINE/MIR 105 TAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATG 142 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 18.05 CpG sites = 4, Kimura (unadjusted) = 18.05 Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 27 0.00 0.00 0.00 chr2ptel1M 895934 895959 (104041) (G)n#Simple_repeat 1 26 (0) c_b79s251i0 2888 chr2ptel1M 895934 GGGGGGGGGGGGGGGGGGGGGGGGGG 895959 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGG 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 28 30.55 1.82 0.90 chr2ptel1M 896996 897105 (102895) (GGCAG)n#Simple_repeat 1 111 (0) m_b79s252i3 2889 chr2ptel1M 896996 GGAAGGACA-GGCCGGGCGGGGGGAGGCCTGGGCAGGACAGGGGAGGGCA 897044 v i - v -i v v v i v (GGCAG)n#Simp 1 GGCAGGGCAGGGCAGGGC-AGGGCAGGGCAGGGCAGGGCAGGGCAGGGCA 49 chr2ptel1M 897045 GAGCTGGCTGGGGCTGGGCA-GGCTAAGTAGGACAGAGCTAAGCTGGGCA 897093 i v vii v - vii i i i vii v (GGCAG)n#Simp 50 GGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCA 99 chr2ptel1M 897094 GGGCTGGGCTGG 897105 v v (GGCAG)n#Simp 100 GGGCAGGGCAGG 111 Matrix = Unknown Transitions / transversions = 0.93 (13/14) Gap_init rate = 0.03 (3 / 109), avg. gap size = 1.00 (3 / 3) 78 15.88 0.00 0.00 chr2ptel1M 897164 897296 (102704) (TG)n#Simple_repeat 1 133 (0) m_b79s252i4 2890 chr2ptel1M 897164 TGTGTGTGTGAGTGCGAGTGTGTGTGTGTCTGGTTGTGTATGTGTGAGTA 897213 v i v v vv i v i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr2ptel1M 897214 TGTGTGATTATGTGTGTGTGAGTGTGTGTCTGGTTGTGTGAGTGATTGTG 897263 vv i v v vv v vv (TG)n#Simple_ 51 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 100 chr2ptel1M 897264 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 897296 (TG)n#Simple_ 101 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 133 Matrix = Unknown Transitions / transversions = 0.27 (4/15) Gap_init rate = 0.00 (0 / 132), avg. gap size = 0.0 (0 / 0) 202 32.91 3.80 0.00 chr2ptel1M 898483 898561 (101439) C L3#LINE/CR1 (98) 4001 3920 m_b79s601i6 2891 chr2ptel1M 898483 AGTGATTGTTCTGCTCCCGCCTGGA-GCCCCCAAGGAGGGGGAGCCCAGT 898531 i ii i v ii i i i -i i iv v i v C L3#LINE/CR1 4001 AGTGGTCATCCAGCCTCTGCTTGAACACCTCCAGTGACGGGGAGCTCACT 3952 chr2ptel1M 898532 -CTTTGTGAGA-AGCCCCTTCCCCTTCGGGAC 898561 - i i?i i- v vi iv C L3#LINE/CR1 3951 ACCTCNCGAGGCAGCCCATTCCATTTTTGGAC 3920 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.30 CpG sites = 19, Kimura (unadjusted) = 47.96 Transitions / transversions = 2.71 (19/7) Gap_init rate = 0.04 (3 / 78), avg. gap size = 1.00 (3 / 3) 203 31.34 1.49 0.00 chr2ptel1M 898714 898780 (101220) C L3#LINE/CR1 (416) 3683 3616 m_b79s601i7 2891 chr2ptel1M 898714 GACCCTTCGACAGCCCGCTCGC-CTCCCTGGGAGGGTTTGAAGTTCATTA 898762 iv v i v - iiv v vvi vv ii i C L3#LINE/CR1 3683 GACCCTTCACCATCCTGGTCGCTCTCCTCTGGACGCGCTCCAGTTTGTCA 3634 chr2ptel1M 898763 ATCGCCTTCTTAAAATAT 898780 vv i i C L3#LINE/CR1 3633 ATGTCCCTCTTAAAATGT 3616 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.01 CpG sites = 10, Kimura (unadjusted) = 41.01 Transitions / transversions = 0.91 (10/11) Gap_init rate = 0.02 (1 / 66), avg. gap size = 1.00 (1 / 1) 12 12.17 3.70 0.00 chr2ptel1M 899887 899913 (100087) (GGGCT)n#Simple_repeat 1 28 (0) m_b79s252i5 2892 chr2ptel1M 899887 GGGCTGGGCT-CCCTGGGCTGGGCAGGG 899913 -vv v (GGGCT)n#Simp 1 GGGCTGGGCTGGGCTGGGCTGGGCTGGG 28 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.04 (1 / 26), avg. gap size = 1.00 (1 / 1) 241 17.44 7.79 10.67 chr2ptel1M 900145 900221 (99779) MIR3#SINE/MIR 71 145 (63) m_b79s601i8 2893 chr2ptel1M 900145 CCGCTAACTTGGAGTATCTTCAAAGACCCTGGGCAAATCA----ACCTCT 900190 i ? vv i ------- i i ---- MIR3#SINE/MIR 71 CCACTAACTNGCTGTGT-------GACCTTGGGCAAGTCACTTCACCTCT 113 chr2ptel1M 900191 GCTG--CCTTAGTTTCCCTGTCAGTAAAATGGG 900221 - -- i iii v i MIR3#SINE/MIR 114 -CTGGGCCTCAGTTTCCTCATCTGTAAAATGAG 145 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 20.78 CpG sites = 9, Kimura (unadjusted) = 20.78 Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.13 (10 / 76), avg. gap size = 1.40 (14 / 10) 427 29.71 9.42 0.00 chr2ptel1M 900169 900306 (99694) MIR#SINE/MIR 87 237 (25) m_b79s601i9 2893 chr2ptel1M 900169 GACCCTGGGCAAATCA----ACCTCTGC-TGCCTTAGTTTCCCTGTCAGT 900213 i i i ---- vi- i iii v MIR#SINE/MIR 87 GACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGT 136 chr2ptel1M 900214 AAAATGGGTTTAAATACAGCCCCAACCCCGGAGAGTCATTGTGACCATCA 900263 vv vv i iv v i iv i ii vv i MIR#SINE/MIR 137 AAAATGGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGGATTA 186 chr2ptel1M 900264 AGTG--------TCTATAAAGCCCTCAGCATAGGGCCTGGCCTGCAGTAG 900305 i --------iv i v i v i v viii i MIR#SINE/MIR 187 AATGAGTTAATACATGTAAAGCGCTTAGAACAGTGCCTGGCACATAGTAA 236 chr2ptel1M 900306 G 900306 MIR#SINE/MIR 237 G 237 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.12 CpG sites = 25, Kimura (unadjusted) = 39.12 Transitions / transversions = 1.56 (25/16) Gap_init rate = 0.02 (3 / 137), avg. gap size = 4.33 (13 / 3) 215 29.87 1.27 2.56 chr2ptel1M 900357 900435 (99565) C MIRc#SINE/MIR (153) 115 38 m_b79s601i10 2894 chr2ptel1M 900357 GAAGTTA-GTGACTCAGCCAAGGCCACACAGTCAGTCTGTGTCTGAGGCA 900405 i - iiv i ii vv v v v i C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 66 chr2ptel1M 900406 GGACCTCCGAGGCCATCTCACTCTCCCTCC 900435 --i iv vv vii vv C MIRc#SINE/MIR 65 GGAC--TCGAACCCAGGTCTTCCTGACTCC 38 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.42 CpG sites = 11, Kimura (unadjusted) = 38.47 Transitions / transversions = 0.92 (11/12) Gap_init rate = 0.04 (3 / 78), avg. gap size = 1.00 (3 / 3) 208 34.02 3.09 0.00 chr2ptel1M 900363 900459 (99541) C MIR3#SINE/MIR (103) 105 6 m_b79s601i11 2894 chr2ptel1M 900363 AGTGACTCAGCCAAGGCCACACAGTCAGTCTGTGTCTGAGGCAGGACC-- 900410 iiv i i? iv v v v i i-- C MIR3#SINE/MIR 105 AGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAG 56 chr2ptel1M 900411 -TCCGAGGCCATCTCACTCTCCCTCCCTCCCTCCTTCTCTTTGTCTCTCT 900459 -v v i vi v i vv v v iii iiv iv i v C MIR3#SINE/MIR 55 AACCCAGGTCTCCTGACTCCCAGTCCGTGCTCTCTCTGCTCAGCCACTCT 6 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.00 CpG sites = 17, Kimura (unadjusted) = 46.92 Transitions / transversions = 1.06 (17/16) Gap_init rate = 0.02 (2 / 96), avg. gap size = 1.50 (3 / 2) 21 13.42 2.44 0.00 chr2ptel1M 900466 900506 (99494) (TCCC)n#Simple_repeat 1 42 (0) m_b79s252i6 2895 chr2ptel1M 900466 TCCCTCCTTCCCTCTCTCCCTCCC-CCCTCTCTCAGTCCCTC 900506 i i - i vv (TCCC)n#Simpl 1 TCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTC 42 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 241 31.91 2.13 0.00 chr2ptel1M 900525 900665 (99335) L1M1_orf2#LINE/L1 1620 1763 (1531) m_b79s551i0 2896 chr2ptel1M 900525 AAAAATGCTAAATGAAAGTCTGGCAAACACGCCACGACAATATATCCAAA 900574 v v ii vv i vviviv i i iv L1M1_orf2#LIN 1620 AAAAATCCTCAACAAAATACTAGCAAACCGAATTCAACAATACATTAAAA 1669 chr2ptel1M 900575 ACATGATTCACAACAA--AAGTTGGATTTATATCCTG-ATACGGGGATGG 900621 v v iv ii -- v vi ?v - i ii L1M1_orf2#LIN 1670 AGATCATTCATCATGACCAAGTGGGATTTATCCCNGGGATGCAAGGATGG 1719 chr2ptel1M 900622 TTCAACATGAGGAAAACCAGCAGCATAATTAATCACATTAAAAG 900665 iv v v v v iii i vv i i v L1M1_orf2#LIN 1720 TTCAACATACGCAAATCAATCAATGTGATACATCATATCAACAG 1763 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 42.52 CpG sites = 22, Kimura (unadjusted) = 42.52 Transitions / transversions = 0.96 (22/23) Gap_init rate = 0.01 (2 / 140), avg. gap size = 1.50 (3 / 2) 14 17.74 2.50 2.50 chr2ptel1M 901010 901049 (98951) (AGCCC)n#Simple_repeat 1 40 (0) m_b79s252i7 2897 chr2ptel1M 901010 AGCCCCGTCCTGCACA-CACAGGGCCAGCCCAGCCCAGCCC 901049 v i v v - v - v (AGCCC)n#Simp 1 AGCCCAGCCCAGCCCAGCCCA-GCCCAGCCCAGCCCAGCCC 40 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 472 35.92 4.43 1.43 chr2ptel1M 903872 904481 (95519) L1ME4a_3end#LINE/L1 4 631 (240) m_b79s551i1 2898 chr2ptel1M 903872 ATTTTTTAAACATATAGAGAACCGAGTCAAATTTATAAAGATAAGAGCTA 903921 v ii v i i i ivvvv iv ii v vvv L1ME4a_3end#L 4 ATATCCTTAATATATAAAGAGCTCTTACAAATCAATAAGAAAAAGACGAA 53 chr2ptel1M 903922 TTTCTGAATTGATAGATAATCAAAATATATGGATGG----TTTTCAATTG 903967 ivi iv v v i iiv iv i i ii ---- iv vv L1ME4a_3end#L 54 CACCCCAATAGAAAAATGGGCAAAGGACATGAACAGACAATTCACAAAAG 103 chr2ptel1M 903968 AAGTAAC-CAAAGCTAGCTG-TAGTCATATGAAAAACTGTTCTGACCCAC 904015 v i- -- i ii- iv ?v viv i L1ME4a_3end#L 104 AAGAAATACAAA--TGGCCAATAAACATATGAAAANATGTTCAACCTCAC 151 chr2ptel1M 904016 TATTGATTGGAGAAATTCAAATTAAAACAATTCTGAGGTACCAACACATA 904065 v i iii v ivv i vivivi L1ME4a_3end#L 152 TAGTAATCAAAGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCA 201 chr2ptel1M 904066 TCTATTAGGTTGGCTAATAGTACAGAAAAGGAAAATAACAATTGGTGAAA 904115 i i ii v v v vv i i vv v v v v v ivi L1ME4a_3end#L 202 CCTATCAAATTGGCAAAGATTTAAAAGATTGATAATACCCAGTGTTGGCG 251 chr2ptel1M 904116 GAGATGTGGAAAAAAATGAAACATTAATGTACGGGGGGTAGAGTTTTGAA 904165 ii i ?i vi- iv vi v ii v vv i iiv v i L1ME4a_3end#L 252 AGGGTGTGGNGAAACG-GGCACTCTCATACACTGCTGGTGGGAGTGTAAA 300 chr2ptel1M 904166 CCGATCTAACCATTCTGTAGAGCAATTTGGAACTATG-GCCAAATGATTA 904214 ii i vi v v i v v -ii v vi - L1ME4a_3end#L 301 TTGGTACAACCTTTCTGGAGGGCAATTTGGCAATATGTATCAAAAGCCT- 349 chr2ptel1M 904215 TAAAATCATGCATACCCTTTGATCTAGCAATACCACTACTAGGTCTGTAT 904264 vii ? i i i v v vv v L1ME4a_3end#L 350 TAAAAATGTNCATACCCTTTGACCCAGTAATTCCACTTCTAGGAATTTAT 399 chr2ptel1M 904265 CCCAAG---------AGAGGTGAAAACCAAAA---AAGGACAAAAATATT 904302 i --------- i vi? v i --- v v ii i L1ME4a_3end#L 400 CCTAAGGAAATAATCAGAGATGTGNACAAAGATTTATGTACAAGGATGTT 449 chr2ptel1M 904303 TATACCCTCCCT-TTTCTGGTGGCAAAGAACTGGAAATTGAGGGGGTACC 904351 i vv vv vi - v ii i i i i ivivvviii ii L1ME4a_3end#L 450 CATCGCAGCATTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTC 499 chr2ptel1M 904352 CATTAACTAGAAAATGGCTGAAGAAAT--TGGTATATGATTGTGATAGTA 904399 vi ivi ii ? i i v -- i vvv i?i i v L1ME4a_3end#L 500 CAACAATAGGGGANTGGTTAAATAAATTATGGTACATCCATANAATGGAA 549 chr2ptel1M 904400 TACTATTGTGCTATAAGAAATGATAA----GCAGGATGCTCTCAGAAAAA 904445 i vvv i v i ? iv---- v i ii i---- vi L1ME4a_3end#L 550 TATTATGCAGCCATTAAAAATNATGTTTTCGAAGAATATTT----AATGA 595 chr2ptel1M 904446 CCT-GGAAAGTGCTCCATGAGCTGATTCAAAGTGAAA 904481 v - i - vv i viv L1ME4a_3end#L 596 CATGGGAAAATGCT-CATGATATAATGTTAAGTGAAA 631 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 50.17 CpG sites = 116, Kimura (unadjusted) = 51.19 Transitions / transversions = 1.16 (116/100) Gap_init rate = 0.03 (19 / 609), avg. gap size = 1.89 (36 / 19) 489 34.68 4.75 2.42 chr2ptel1M 903880 904405 (95595) L1ME3C_3end#LINE/L1 12 549 (321) m_b79s551i2 2898 chr2ptel1M 903880 AACATATAGAGAACCGAGTCAAATTTATAAAGATAAGAGCTATTTCTGAA 903929 i i ivvvv iv - v v vi vii -- L1ME3C_3end#L 12 AATATATAAAGAACTCCTACAAATCAATAA-GAAAACAGACAACCC--AA 58 chr2ptel1M 903930 TTGATAGATAATCAAAATATATGGATGG----TTTTCAATTGAAGTAAC- 903974 v v i iiv v i ii ---- iv ivv i v - L1ME3C_3end#L 59 TAGAAAAATGGGCAAAAGATATGAACAGGCAATTCACAGAAGAGGAAACN 108 chr2ptel1M 903975 CAAAGCTAGCTG-TAGTCATATGAAAAACTGTTCTGACCCACTATTGATT 904023 i -- i ii- iv iv i viv i v i i L1ME3C_3end#L 109 CGAA--TGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTAATC 156 chr2ptel1M 904024 GGAGAAATTCAAATTAAAACAATTCTGAGGTACCAACACATATCTATTAG 904073 i i v ? ivv i viv i i i i L1ME3C_3end#L 157 AGGGAAATGCAAATTAAAACNACAATGAGATACCATTTCACACCCATCAG 206 chr2ptel1M 904074 GTTGGCTAATAGTACAGAAAAG---GAAAATAACAATTGGTGAAAGAGAT 904120 i v v v ---v --- v v v v iviii L1ME3C_3end#L 207 ATTGGCAAAAATT---TAAAAGTCTGACAATACCAAGTGTTGGCGAGGAT 253 chr2ptel1M 904121 GTGGAAAAAAATGAAACATTAATGTACGGGGGGTAGAGTTTTGAACCGAT 904170 iv vi- i vi v ii v vv i iiv v i ii i L1ME3C_3end#L 254 GTGGAGCAACG-GGAACTCTCATACACTGCTGGTGGGAGTGTAAATTGGT 302 chr2ptel1M 904171 CTAACCATTCTGTAGAGCAATTTGGAACTATGGCCAAATGATTATAAAAT 904220 vi i i v v v --- v i i vvv i iv L1ME3C_3end#L 303 ACAACCACTTTGGAGAGCAATTTGGCAATAT---CTAGTAAAGTTGAAGA 349 chr2ptel1M 904221 CATGCATACCCTTTGATCTAGCAATACCACTACTAGGTCTGTATCCCAAG 904270 iii vi i i v v v i - v L1ME3C_3end#L 350 TGCGCATACCCTACGACCCAGCAATTCCACTCCTAGGTATATA-CCCTAG 398 chr2ptel1M 904271 AGAG----------GTGAAAACCAAAAAA---GGACAAAAATATTTATAC 904307 i---------- viv v ii i --- v i i i vv L1ME3C_3end#L 399 AGAAACTCTCGCACGTGTGCACAAGGAGACATGTACAAGAATGTTCATTG 448 chr2ptel1M 904308 CCTCCCT-TTTCTGGTGGCAAAGAACTGGAAATTGAGGGGGTACCCATTA 904356 vv vi - v ii i i i i ivivvviii ii i L1ME3C_3end#L 449 CAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCA 498 chr2ptel1M 904357 ACTAGAAAATGGCTGAAGAAAT--TGGTATATGATTGTGATAGTATACTA 904404 vi i v i v -- vvv iii i v L1ME3C_3end#L 499 ACAGGAGAATGGATAAATAAATTGTGGTATATTCATACAATGGAATACTA 548 chr2ptel1M 904405 T 904405 L1ME3C_3end#L 549 T 549 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 45.85 CpG sites = 98, Kimura (unadjusted) = 48.09 Transitions / transversions = 1.23 (98/80) Gap_init rate = 0.04 (21 / 525), avg. gap size = 1.81 (38 / 21) 559 33.55 5.14 2.51 chr2ptel1M 903991 904418 (95582) L1ME1_3end#LINE/L1 127 565 (361) m_b79s551i3 2898 chr2ptel1M 903991 CATATGAAAAACTGTTCTGACCCACTATTGATTGGAGAAATTCAAATTAA 904040 i iv i vivvi i v v i i v L1ME1_3end#LI 127 CACATGAAAAGATGCTCAACATCATTAGTCATTAGGGAAATGCAAATTAA 176 chr2ptel1M 904041 AACAATTCTGAGGTACCAACACATATCTATTAGGTTGGCTAATAGTACAG 904090 v ivv i vi i i iv v v v i L1ME1_3end#LI 177 AACCACAATGAGATACCACTACACACCTATTAGAATGGCTAAAATTAAAA 226 chr2ptel1M 904091 AAAAGGAAAATAACAATTGGTGAAAGAGATGTGGAAAAAAATGAAACATT 904140 i vv v v v v iviii - iv v i vi L1ME1_3end#LI 227 AGACTGACAATACCAAGTGTTGGCGAGGATGTGG-AGCAACTGGAACTCT 275 chr2ptel1M 904141 AATGTACGGGGGGTAGAGTTTTGAACCGATCTAACCATTCTGTAGAGCAA 904190 v ii iv vv i iiv vii vi i vi i i i v i i i L1ME1_3end#LI 276 CATACATTGCTGGTGGGAATGCAAAATGGTACAGCCACTTTGGAAAACAG 325 chr2ptel1M 904191 TTTGGAACTATGGCCAAATGATTATAAAATCATGCATACCCTT------T 904234 --------- iv vv ? i i vi v ------ L1ME1_3end#LI 326 TTTGG---------CAGTTTCTTANAAAGTTAAACATACACTTACCATAT 366 chr2ptel1M 904235 GATCTAGCAATACCACTACTAGGTCTGTATCCCAAGAGAGGTGAAAAC-- 904282 i i v v v v - ii -- L1ME1_3end#LI 367 GACCCAGCAATTCCACTCCTAGGTATTTA-CCCAAGAGAAATGAAAACAT 415 chr2ptel1M 904283 ---------CAAAAA--AGGACAAAAATATTTATACCCTCCCTTTTC-TG 904320 --------- i --v v vi i i v vv ii v - i L1ME1_3end#LI 416 ATGTCCACACAAAGACTTGTACACGAATGTTCATAGCAGCTTTATTCGTA 465 chr2ptel1M 904321 GTGGCAAAGAACTGGAAATTGAGGGGGTACCCATTAACTAGAAAATGGCT 904370 i i v i ivivvviii ii i ?i vi v L1ME1_3end#LI 466 ATAGCCAAAAACTGGAAACAACCCAAATGTCCATCAACNGGTGAATGGAT 515 chr2ptel1M 904371 GAAGAAAT--TGGTATATGATTGTGATAGTATACTATTGTGCTATAAGAA 904418 i v -- vvv iii i v i vv v i L1ME1_3end#LI 516 AAACAAATTGTGGTATATCCATACAATGGAATACTACTCAGCAATAAAAA 565 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 45.00 CpG sites = 75, Kimura (unadjusted) = 45.89 Transitions / transversions = 1.15 (75/65) Gap_init rate = 0.04 (17 / 427), avg. gap size = 1.94 (33 / 17) 12 16.52 0.00 0.00 chr2ptel1M 904879 904905 (95095) (AAAT)n#Simple_repeat 1 27 (0) m_b79s252i8 2899 chr2ptel1M 904879 AAATAAACTACTAAATAAATAAAAAAA 904905 iv v v (AAAT)n#Simpl 1 AAATAAATAAATAAATAAATAAATAAA 27 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 344 30.59 10.34 1.36 chr2ptel1M 904914 905387 (94613) L1M2_orf2#LINE/L1 1770 2285 (1006) m_b79s551i4 2900 chr2ptel1M 904914 CACATACCATATGATTATATCACAAGATACAGAAAAAGCCTTTGGCAAAG 904963 v v i v vv i v ii i L1M2_orf2#LIN 1770 CAAAAACCATATGATCATCTCAATAGATGCAGAAAAAGCATTTGATAAAA 1819 chr2ptel1M 904964 CACAGCTCTCATTTA--------ACTTATGAGGCAG-AGGTAGAGAAGGA 905004 iv i vii v i -------- ivii viv v- v L1M2_orf2#LIN 1820 TTCAACATCCCTTCATGATAAAAACTCTCAACAAATTAGGTATAGAAGGA 1869 chr2ptel1M 905005 TCTT--CTTAA-ATGATAAAAA--AAAAAAGAGCTAAAACCTAAAATTAT 905049 v v -- i - ii ii-- v v v v--- i v ii v L1M2_orf2#LIN 1870 ACGTACCTCAACACAATAAAGGCCATATATGAC---AAACCCACAGCTAA 1916 chr2ptel1M 905050 CATTTTAAACAGTGGGGAAACATGGGAAGTGTTTCC---AAGAGTTAAAA 905096 iv vvv i vi v i iv --- ?i ii L1M2_orf2#LIN 1917 CATCATACTGAATGGGGAAAAGTTGAAAGCCTTTCCTCTAAGANCTGGAA 1966 chr2ptel1M 905097 CAAGGCCA--TCTCCCCCTTTCCCTGCTGTTGTTTGATATCATTCTAGAA 905144 i v --viv v v ii vi i ii i vi v i L1M2_orf2#LIN 1967 CAAGACAAGGATGCCCACTTTCACCACTTCTATTCAACATAGTACTGGAA 2016 chr2ptel1M 905145 ACACTGTCCATAGTAATAAGGCAA----AAGAGATAAAAC-CATAGATAT 905189 iiv iv v i v ---- i v- vv v L1M2_orf2#LIN 2017 GTCCTAGCCAGAGCAATTAGGCAAGAGAAAGAAATAAAAGGCATCCAAAT 2066 chr2ptel1M 905190 AGTCAAAGAAGAGGTAAAATGGGCGCTGA----AGGCCACCT-ATTTC-- 905232 v vv i i i v v v v v---- iiv v - i i-- L1M2_orf2#LIN 2067 TGGAAAGGAGGAAGTCAAATTGTCCCTGTTTGCAGATGACATGATCTTAT 2116 chr2ptel1M 905233 -TGTAGAAAACCCAAGAGAATCAG--AAAAAA-----AGAAGTAATAGC- 905273 - ? ? v i v vi-- ----- v i iv- L1M2_orf2#LIN 2117 ATNTAGAAAANCCTAAAGACTCCACCAAAAAACTNTTAGAACTGATAAAC 2166 chr2ptel1M 905274 ---TTCAGTAAAATGACAGGATATGAAATAAATACACCAAAAATTAACAG 905320 --- i vi ii v i i - i ii L1M2_orf2#LIN 2167 GAATTCAGTAAAGTTGCAGGATACAAAATCAACATA-CAAAAATCAGTAG 2215 chr2ptel1M 905321 CATTTCTATATA--GACAACAAA--ATC--AAGGGAAAATGATAGAAAGG 905364 ii--i i -- -- iiii v - - L1M2_orf2#LIN 2216 CATTTCTATACGCCAACAACGAACTATCTGAAAAAGAAATCA-AGAAA-G 2263 chr2ptel1M 905365 CACATCCTACTCCAAATAACTAC 905387 - i i ivv i L1M2_orf2#LIN 2264 CA-ATCCCATTTACAATAGCTAC 2285 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 39.78 CpG sites = 78, Kimura (unadjusted) = 40.56 Transitions / transversions = 1.20 (78/65) Gap_init rate = 0.05 (26 / 473), avg. gap size = 2.15 (56 / 26) 376 30.59 10.87 1.32 chr2ptel1M 904919 905332 (94668) L1MD_orf2#LINE/L1 1778 2230 (1064) m_b79s551i5 2900 chr2ptel1M 904919 ACCATATGATTATATCACAAGATACAGAAAAAGCCTTTGGCAAAGCACAG 904968 i i i vvv i v i iiv i L1MD_orf2#LIN 1778 ATCACATGATCATATCAATTGATGCAGAAAAAGCATTTGACAAAATTCAA 1827 chr2ptel1M 904969 CTCTCATT-----TAA-----CTTATGAGGC-AGAGGTAGAGAAGGATCT 905007 v i ----- ----- i v? ii - iii ii i ii L1MD_orf2#LIN 1828 CACCCATTCATGATAAAAACTCTCAGNAAACTAGGAATAGAGGGGAACTT 1877 chr2ptel1M 905008 TCTTAA-ATGATAAAAAAAA---AAAGAGCTAAAACCTAAAATTATCATT 905053 i i -v i iv --- v i---- v ii v i L1MD_orf2#LIN 1878 CCTCAACTTGATAAAGAGCATCTACAA----AAAACCTACAGCTAACATC 1923 chr2ptel1M 905054 TTAAACAGTGGGGAAACATGGGAAGTGTTTCC---AAGAGTTAAAACAAG 905100 v vvi i v v iv i v iv i --- vivii L1MD_orf2#LIN 1924 ATACTTAATGGTGAAAGACTGAATGCTTTCCCCCTAAGATCGGGAACAAG 1973 chr2ptel1M 905101 GCC---ATCTCCCCCTTTCCCTGCTGTTGTTTGATATCATTCTAGAAACA 905147 v--- v - v i v ii v i ii i vi v i iiv L1MD_orf2#LIN 1974 GCAAGGATGT-CCGCTCTCACCACTCTTATTCAACATAGTACTGGAAGTT 2022 chr2ptel1M 905148 CTGTCCATAGTAATAAGGC----AAAAGAGATAAAA-CCATAGATATAGT 905192 iv vv i ---- i i -v v v v v L1MD_orf2#LIN 2023 CTAGCCAGTGCAATAAGGCAAGAAAAGGAAATAAAAGGCATACAGATTGG 2072 chr2ptel1M 905193 CAAAGAAGAGGTAAAATGGGCGC----TGAAGGCCACCT-ATT-TCT--G 905234 v i ii iv v v ---- v iiv v - - -- L1MD_orf2#LIN 2073 AAAGGAAGAAATAAAACTGTCCCTATTTGCAGATGACATGATTGTCTACG 2122 chr2ptel1M 905235 TAGAAAACCCAAGAGAATC-AGAAAAAA------AGAAGTAATA----GC 905273 i v ii - v ------ v ----iv L1MD_orf2#LIN 2123 TAGAAAATCCCAAGGAATCTACAAAAAAACTCCTAGAACTAATAAGTGAG 2172 chr2ptel1M 905274 TTCAGTAAAATGACAGGATATGAAATAAATACACCAAAAATTAACAGCAT 905323 i ii vi ii i ? i i - i iv i L1MD_orf2#LIN 2173 TTCAGCAAGGTCGCAGGATACAAGATNAACATA-CAAAAATCAATTGTAT 2221 chr2ptel1M 905324 TTCTATATA 905332 L1MD_orf2#LIN 2222 TTCTATATA 2230 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 40.05 CpG sites = 74, Kimura (unadjusted) = 40.91 Transitions / transversions = 1.45 (74/51) Gap_init rate = 0.05 (22 / 413), avg. gap size = 2.32 (51 / 22) 97 15.45 2.71 3.18 chr2ptel1M 907831 908051 (91949) (GACAGA)n#Simple_repeat 1 220 (0) m_b79s252i9 2901 chr2ptel1M 907831 GATAGAGACAGAGAGGAGGGAGCGAGACTGAGAGAGAAAGACAGAGAAAG 907880 i -v i vv -- v i v (GACAGA)n#Sim 1 GACAGAGACAGAGA-CAGAGACAGAGAC--AGAGACAGAGACAGAGACAG 47 chr2ptel1M 907881 AGAGAGAGACAGAGA-AG-GACAGAGAGGAGAGACAGAGACAAAGAGACA 907928 v - - -v -- (GACAGA)n#Sim 48 AGACAGAGACAGAGACAGAGACAGAGA-CAGAGACAGAGAC--AGAGACA 94 chr2ptel1M 907929 CAGAGAGAAACAGAGAGACAGACAGAAACAGAAACAGAGAGAGAGACATA 907978 v v i v v i i v v (GACAGA)n#Sim 95 GAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGA 144 chr2ptel1M 907979 GACACAGACACACACAGAGACAGAGACAGACA-AGAGAGACAGAGAGGGA 908027 v v v v - v v v i (GACAGA)n#Sim 145 GACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGA 194 chr2ptel1M 908028 CAGAGAGCA-AGCCAG-GAGAGA-ACA 908051 - - v - v - (GACAGA)n#Sim 195 CAGAGA-CAGAGACAGAGACAGAGACA 220 Matrix = Unknown Transitions / transversions = 0.32 (7/22) Gap_init rate = 0.06 (13 / 220), avg. gap size = 1.00 (13 / 13) 18 4.71 0.00 0.00 chr2ptel1M 908312 908333 (91667) (C)n#Simple_repeat 1 22 (0) m_b79s252i11 2902 chr2ptel1M 908312 CCCCGCCCCCCCCCCCCCCCCC 908333 v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCC 22 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 191 34.04 9.82 1.65 chr2ptel1M 908611 908834 (91166) AmnL2-1#LINE/L2 2099 2340 (273) m_b79s601i12 2903 chr2ptel1M 908611 GTGCAG--TGAGACCGGCCCCCTCCTCATCATCTGCA-----GTCTGACC 908653 -- vvi i v v i - iv i ----- ivi AmnL2-1#LINE/ 2099 GTGCAGAATGCTGCTGCCCGCCTTCTCA-CACGTACAAAGAAGCGCGACC 2147 chr2ptel1M 908654 ATGTCGCCTCCCCCCCCCC----CCCCAATGAA--CTCATTGCCTCCAGA 908697 ii i i vi i vv---- i v iv-- i vvi i i AmnL2-1#LINE/ 2148 ACATCACCCCCATCCTCAAACAACTCCACTGGCTCCCCATTCATTTCAGG 2197 chr2ptel1M 908698 ATCAAATACAAAAC-GCCCTGCTGGTGTTCAAGGCCCTTCA-GGATCAGC 908745 v i v i- i v v v i ii i - iiv AmnL2-1#LINE/ 2198 ATCCAGTTCAAAATTGCCTTCCTTGTTTTTAAAACCCTCCATGGACTTGC 2247 chr2ptel1M 908746 CCCCAACTCCTTCCTG--CCTCCTTCCACTTGACTCCCCTCCACATTGTC 908793 i viv v i vi -- iv ii v iv v ii vi AmnL2-1#LINE/ 2248 TCCAGCCTACCTCACGGACCTTGTCTCTCTCTACTCCCCTCCCCGCTCCC 2297 chr2ptel1M 908794 TCC---CACCTAGTGACATCGGCCT-CTAGCTGCTCCTCC-CACAA 908834 --- ii --- i - vv ii i - AmnL2-1#LINE/ 2298 TCCGCTCGTCTAG---CACCGGCCTCCTCTCTGTCCCTTCACACAA 2340 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.26 CpG sites = 45, Kimura (unadjusted) = 47.38 Transitions / transversions = 1.50 (45/30) Gap_init rate = 0.06 (14 / 223), avg. gap size = 1.86 (26 / 14) 293 33.45 6.69 1.19 chr2ptel1M 908645 908883 (91117) L2#LINE/L2 2815 3066 (16) m_b79s601i13 2903 chr2ptel1M 908645 AGTCTGACCATGTCGCCTCCCCCCCC----CCCCCCAATGA--ACTCATT 908688 v i i ii i iv i ---- i i--v i i L2#LINE/L2 2815 AGTCAGATCATGTCACTCCTCTGCTCAAAACCCTCCAATGGCTTCCCATC 2864 chr2ptel1M 908689 GCCTCCAGAATCAAATACAAAACGCCCTGC--TGGTGTTCAAGGCCCTTC 908736 v vii i v vv ii- i i -- iv v v L2#LINE/L2 2865 TCACTCAGAGTAAAAGCCAAAGT-CCTTACAATGGCCTACAAGGCCCTAC 2913 chr2ptel1M 908737 AGGATCAG--CCCCCAACTCCTTCCTG-CCTC--CTTCCACTTGACTCCC 908781 v v -- iviv ii - -- i i i-- i L2#LINE/L2 2914 ATGATCTGGTCCCCCGTTACCTCTCTGACCTCATCTCCTACC--ACTCTC 2961 chr2ptel1M 908782 CTCCACATTGTCTCCCACCTAGTGACATCGGCCT-CTAGCTGCTCCTCCC 908830 i v ii vv vvi i iv ii - v i vv L2#LINE/L2 2962 CCCCTCGCTCACTCCGCTCCAGCCACACTGGCCTCCTTGCTGTTCCTCGA 3011 chr2ptel1M 908831 ACAAGAT-GCTCCGCGTCCTCCCCA-GGCCTTTGCGTTAGCAGCACCTCG 908878 v vi- viv vi v i - ii v v iv iiv L2#LINE/L2 3012 ACACGCCAGGCACGCTCCCGCCTCAGGGCCTTTGCACTTGCTGTTCCCTC 3061 chr2ptel1M 908879 TGCCT 908883 L2#LINE/L2 3062 TGCCT 3066 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.18 CpG sites = 45, Kimura (unadjusted) = 45.76 Transitions / transversions = 1.32 (45/34) Gap_init rate = 0.05 (12 / 238), avg. gap size = 1.58 (19 / 12) 184 35.80 3.70 0.00 chr2ptel1M 909441 909521 (90479) C MIRc#SINE/MIR (126) 142 59 m_b79s601i14 2904 chr2ptel1M 909441 TTATACAGGGAGAATTTGGGGCTCAGAGAGGGTAGGC-CCTGGCCTACTG 909489 i v v ii vi i v i i-v v i vv C MIRc#SINE/MIR 142 TTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGG 93 chr2ptel1M 909490 TCACCCCGGCCATGAGCAGCGGG--CAGGACTTG 909521 v v vivi i ii i i-- i i C MIRc#SINE/MIR 92 TCACACAGCTAGTAAGTGGCAGAGCCGGGACTCG 59 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.84 CpG sites = 17, Kimura (unadjusted) = 50.74 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.03 (2 / 80), avg. gap size = 1.50 (3 / 2) 29 19.02 0.00 0.00 chr2ptel1M 910191 910244 (89756) (A)n#Simple_repeat 1 54 (0) m_b79s252i12 2905 chr2ptel1M 910191 AAAAAATAAAATAAAATAAAAAACAAAACAAAACAAACAAACAAAAAAAA 910240 v v v v v v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr2ptel1M 910241 GAAA 910244 i (A)n#Simple_r 51 AAAA 54 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 221 23.54 0.00 1.96 chr2ptel1M 910438 910489 (89511) L2a_3end#LINE/L2 386 436 (81) m_b79s601i15 2903 chr2ptel1M 910438 TCCTCCAGTTAAAATGGGAGCTCAATGAGGGAAGGGACTGTCTCTCTGTT 910487 i vii i vi v v - i v L2a_3end#LINE 386 TCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGACT-TTTGTCTGTT 434 chr2ptel1M 910488 CT 910489 i L2a_3end#LINE 435 TT 436 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.76 CpG sites = 7, Kimura (unadjusted) = 28.76 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.02 (1 / 51), avg. gap size = 1.00 (1 / 1) 388 40.30 4.48 0.00 chr2ptel1M 910632 910899 (89101) C L2#LINE/L2 (192) 2890 2611 m_b79s601i16 2906 chr2ptel1M 910632 AGGATTTCAG--TCAGCTGTCAGGGTCATAGGGAGCCAATAGAGTTTACT 910679 i ii -- ivi v v v vv i i v i vv vi C L2#LINE/L2 2890 AGGACTTTGGCTTTTACTCTGAGTGAGATGGGAAGCCATTGGAGGGTTTT 2841 chr2ptel1M 910680 GAGTAGGGG-GTGACACAATTGGACCTGTGCTTTAGGAAAATCATTTGAG 910728 i i - ii iv i ii i ii ii i ivi C L2#LINE/L2 2840 GAGCAGAGGAGTGACATGATCTGACTTACGTTTTAAAAGGATCACTCTGG 2791 chr2ptel1M 910729 TGGCTGAATGAAAGAGAAACGGGAGTGGGACAAGAATAGGGGCAAGCAGA 910778 iv vi vi ii v i v ? v i ii i ii i v C L2#LINE/L2 2790 CTGCTGTGTTGAGAATAGACTGNAGGGGGGCAAGGGTGGAAGCAGGGAGA 2741 chr2ptel1M 910779 ACCCCCAGTAG------CCAATAGTCCAGGTGTGAGGAGATGAGGGTCTG 910822 v vvii v ------v i i i v iv iv ii C L2#LINE/L2 2740 CCAGTTAGGAGGCTATTGCAGTAATCCAGGCGAGAGATGATGGTGGCTTG 2691 chr2ptel1M 910823 CACCA-GGTGACGGCACTGTCAGGGCAGAGGAGGGGATGTAG--CAGAGA 910869 v - ii v vvi v vv i v vi v v--ii v C L2#LINE/L2 2690 GACCAGGGTGGTGGCAGTGGAGGTGGTGAGAAGTGGTCGGATTCTGGATA 2641 chr2ptel1M 910870 TGCTGCAATGGAGAAATCAACAAGAGATGC 910899 ii vii v vii ii i i vv C L2#LINE/L2 2640 TATTTTGAAGGTAGAGCCGACAGGATTTGC 2611 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 58.01 CpG sites = 64, Kimura (unadjusted) = 61.67 Transitions / transversions = 1.45 (64/44) Gap_init rate = 0.02 (5 / 267), avg. gap size = 2.40 (12 / 5) 456 34.08 5.82 4.09 chr2ptel1M 910946 911306 (88694) C L2#LINE/L2 (413) 2669 2303 m_b79s601i17 2907 chr2ptel1M 910946 GATGGTGCAGCAGAGGTGAAATCAGCCAGAGATGCTTCATAAGTGAAATC 910995 i - v v vii i-- ii v ii iiv i - i v C L2#LINE/L2 2669 GGTGGTG-AGAAGTGGTCGGATT--CTGGATATATTTTGAAGGT-AGAGC 2624 chr2ptel1M 910996 CACACAAGATGCAGCAGAGGCCTTGGTGCCATATTGGATGGCAGC-AATG 911044 i- i vi- v v vv ---- i v i vv v- v C L2#LINE/L2 2623 CG-ACAGGATTT-GCTGATGGATTGG----ATGTGGGGTGTGAGAGAAAG 2580 chr2ptel1M 911045 AAAGAA-------ATAATTTCTAGGTAGGGAGCCTGAGGGATTGGGAGGA 911087 i i ------- i i i v vvvvi vi i i C L2#LINE/L2 2579 AGAGGAGTCAAGGATGACTCCAAGGTTTTTGGCCTGAGCAACTGGAAGGA 2530 chr2ptel1M 911088 GTGTGTTGACCT---CAGAGGTTTGGAAA---GAGGGAAG----GATTTG 911127 vv v v v --- v i vv i--- v i ---- i C L2#LINE/L2 2529 TGGAGTTGCCATTNACTGAGATGGGGAAGACTGCGGGAGGAGCAGGTTTG 2480 chr2ptel1M 911128 GGAGTAAAGATCACGAGGTCTGCTT-GGACAGATAGAGTTTAAGATGTCT 911176 i i vi v v v i - vi vi i i C L2#LINE/L2 2479 AGGGGGAAGATCAGGAGTTCAGTTTTGGACATGTTAAGTTTGAGATGCCT 2430 chr2ptel1M 911177 CCTGGACCTTCAGTTCAAAGTATTTG--AGGCAGTTGGAAAAATGAGCCT 911224 vi i v i iv vi ii i ivi-- v v i i C L2#LINE/L2 2429 ATTAGACATCCAAGTGGAGATGTCGAGTAGGCAGTTGGATATACGAGTCT 2380 chr2ptel1M 911225 GTATGTAAGGAGAGAGGTTAGGGCTCTAGCTAAGTAGATTTGAGATTCAT 911274 v vv v i iv vv v -- i i v C L2#LINE/L2 2379 GGAGTTCAGGGGAGAGGTCCGGGCTGGAGATA--TAAATTTGGGAGTCAT 2332 chr2ptel1M 911275 CAGCTTCCCTTAGATACCGATGAAAATCCTGA 911306 v v--- iviiv v ii v C L2#LINE/L2 2331 CAGCATA---TAGATGGTATTTAAAGCCATGA 2303 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.17 CpG sites = 59, Kimura (unadjusted) = 46.25 Transitions / transversions = 1.00 (59/59) Gap_init rate = 0.06 (22 / 360), avg. gap size = 1.64 (36 / 22) 212 39.67 5.91 0.75 chr2ptel1M 911280 911533 (88467) L2b_3end#LINE/L2 198 464 (2) m_b79s601i18 2908 chr2ptel1M 911280 TCCCTTAGATACCGATGAAAATCCTGACTTTTACAGGGAGCTTTCCCCCA 911329 i i i vi iiivv viiiv ii v i i ii iv L2b_3end#LINE 198 TCCTTCAGGTCTCAGCTCAAATGTCACCTCCTCCGGGAAGCCCTCCCTGA 247 chr2ptel1M 911330 CCCCTCCATTCTAGT---GT-CTTTCCTCTG---TTAATCATTTCTCATT 911372 i vivi vi --- i- ii ---iivvi v i vvii L2b_3end#LINE 248 CCCCCCAGGCCGGGTCAGGCGCCCTCCTCTGGGCCCCCCCAGTCCTACCC 297 chr2ptel1M 911373 TA--ACTTTGATGTACT-TTGCTT--CTACATTTTGGTTTCCTTGTTTCC 911417 i-- i ivv i?- ii --i v iv i iivvi vv L2b_3end#LINE 298 TGCCACTCTGGGTTATNATTGTCTGNTTACATGTCTGTCTCCCCCACTAG 347 chr2ptel1M 911418 CTCATGAGATTCCTTCAGAGAAGAGTCAGATTTTTGTCTTTTTT--TG-T 911464 viii -i v v i v i v v ?v i - v i--i - L2b_3end#LINE 348 ACTGTGAG-CTCCGTGAGGGCAGGGACCGNGTCT-GTCTTGTTCACCGCT 395 chr2ptel1M 911465 GTGTCCCCAGTACTTAGCACAGTGCTTGTCACTTAGTCGGCATTTAGTAA 911514 i ii i ? i v vi v ii i L2b_3end#LINE 396 GTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAA 445 chr2ptel1M 911515 ATGTTTATTAACTGCTTGA 911533 i i i v vv L2b_3end#LINE 446 ATATTTGTTGAATGAATGA 464 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 56.89 CpG sites = 63, Kimura (unadjusted) = 61.97 Transitions / transversions = 1.70 (63/37) Gap_init rate = 0.04 (10 / 253), avg. gap size = 1.70 (17 / 10) 287 30.89 9.72 2.60 chr2ptel1M 911318 911533 (88467) L2a_3end#LINE/L2 285 515 (2) m_b79s601i19 2908 chr2ptel1M 911318 AGCTTTCCCCCACCCCTCCATTCTAGTGT-CTTTCCTCTGTTAATCATTT 911366 ? vi ivv iii ii iv v -i i ii -- v i L2a_3end#LINE 285 ANCACTCCCTATCCCCCTTACCCTGCTTTATTTTTCTCCAT--AGCACTT 332 chr2ptel1M 911367 CTCA---TTTAACTT-TGATGTACTTTGCTTCTACATTTTGGTTTCCT-- 911410 v --- i i v -iv i i i v vi -- vi -- L2a_3end#LINE 333 ATCACCATCTGACATACTATATATTTTACTTATTTATTT--GTTTATTGT 380 chr2ptel1M 911411 -TGTTTCCCTC-ATGAGATTC----CTTCA-GAGAAGAGTCAGATTTTTG 911453 - i i - iv v v---- i - iiv --i i L2a_3end#LINE 381 CTGTCTCCCCCCACTAGAATGTAAGCTCCATGAGGGCAG--GGACTTTTG 428 chr2ptel1M 911454 TCTTTTTT------TG-TGTGTCCCCAGTACTTAGCACAGTGCTTGTCAC 911496 v ------ - i ii i v i v L2a_3end#LINE 429 TCTGTTTTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCAC 478 chr2ptel1M 911497 TTAGTCGGCATTTAGTAAATGTTTATTAACTGCTTGA 911533 v v ii i i i i i v vv L2a_3end#LINE 479 ATAGTAGGCGCTCAATAAATATTTGTTGAATGAATGA 515 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.09 CpG sites = 41, Kimura (unadjusted) = 41.90 Transitions / transversions = 1.71 (41/24) Gap_init rate = 0.07 (16 / 215), avg. gap size = 1.69 (27 / 16) 849 33.31 14.91 0.43 chr2ptel1M 911537 912341 (87659) C L2#LINE/L2 (755) 2327 1407 m_b79s601i20 2907 chr2ptel1M 911537 ACACAAATAGTCATGAAATCCAT-AGACGTTGATGAGATCAC----AAAG 911581 i i i i vv v v - - v ----ii C L2#LINE/L2 2327 ATATAGATGGTATTTAAAGCCATGAGAC-TGGATGAGATCACCNAGGGAG 2279 chr2ptel1M 911582 TG-GTACAGAGAGAAAAGAGATGAGGGCCCAGGAT-----CTTGAGGGTC 911625 - ii v i v v v i----- i i vv C L2#LINE/L2 2278 TGAGTGTAGATAGAGAAGAGAAGAGGTCCAAGGACTGAGCCCTGGGGCAC 2229 chr2ptel1M 911626 ACCTGCAGTTAGAGGGTGTAAACTGGAGGACGATCCAGCAAGTGAGACAG 911675 v vi iv ? vi vii vvv v v iv v C L2#LINE/L2 2228 TCCAACGTTNAGAGGTCGGGGAGATGAGGAGGAACCAGCAAAGGAGACTG 2179 chr2ptel1M 911676 AGAAAGAAACAGCAGAAAAGTCGGAGGAGGGCCGGGA-----------TC 911714 i ivviv vi i v iii i -----------i C L2#LINE/L2 2178 AGAAGGAGCGGCCAGTGAGGTAGGAGGAAAACCAGGAGAGTGTGGTGTCC 2129 chr2ptel1M 911715 TAGA--------GAAGAGAGGAT--CCGGGAGGAGAGAGTGACCAGCAGT 911754 i -------- i vi -- vi i i i i v C L2#LINE/L2 2128 TGGAAGCCAAGTGAAGAAAGTGTTTCAAGAAGGAGGGAGTGATCAACTGT 2079 chr2ptel1M 911755 GTCAGAGGCTGCAGAGAGGTCAAG---------------------GCCAT 911783 i v v ? ---------------------i C L2#LINE/L2 2078 GTCAAATGCTGCTGANAGGTCAAGTAAGATGAGGACTGAGAATTGACCAT 2029 chr2ptel1M 911784 TGGATCTGGCCACTAAGAGATCCCTGGTCACCCGGGAATGGGCGGTGTGA 911833 i i v vvi i vi v iv iv v i i v vi C L2#LINE/L2 2028 TGGATTTAGCAACGTGGAGGTCATTGGTGACCTTGACAAGAGCAGTTTCG 1979 chr2ptel1M 911834 ATGGAATGATAAAGTCAGATGTCAGAC---AGCAGAGTTAAG-GAGAAT- 911878 i i i iii v ii v i v i--- ii iv i - - C L2#LINE/L2 1978 GTGGAGTGGTGGGGACGAAAGCCTGATTGGAGTGGGTTCAAGAGAGAATG 1929 chr2ptel1M 911879 ----------AATTG-------------CAGATGACTTTTTTAAGGAGTT 911905 ---------- -------------i ii i ii C L2#LINE/L2 1928 GGAGGAGAGGAATTGGAGACAGCGAGTATAGACAACTCTTTCGAGGAGTT 1879 chr2ptel1M 911906 TGGCTGGAAAGGGGAGGAGAGATAAAGAACAATAATTAGCAGGGATGGAT 911955 v v v v vi ii ii ii i vi iv? vv C L2#LINE/L2 1878 TTGCTGTAAAGGGGAGCAGAGAAATGGGGCGGTAGCTGGAGGGGGANGTG 1829 chr2ptel1M 911956 GGATCAAG----------TCTTTTTGGAGGAGGGGGGAAACC-TGGGATG 911994 i ---------- v vi i v i i?-ii v C L2#LINE/L2 1828 GGGTCAAGGGAGAATTTTTGTTTTTTAAAGATGGGAGAAATNACAGCATG 1779 chr2ptel1M 911995 TCTGTGGGCAGCGGGGAAGGTGCCAGTAGAGAGGGAGAA---GA-----C 912036 i iv v vv v vv i --- ----- C L2#LINE/L2 1778 TTTGTATGCTGATGGGAATGATCCAGTAGAGAGGGAAAAATTGATGATGC 1729 chr2ptel1M 912037 AAATGAGAGAGGGG-GTGCCGGGGGAGCATTCTGTCGGAGGAGATGGGTT 912085 iiv - viii vv iv v viiv v ii i vv C L2#LINE/L2 1728 AGGAGAGAGAGGGGAGAATTGCTGGAGCGATGTCCTTGAGTAGGCGAGAG 1679 chr2ptel1M 912086 GGGATGGGAGCTCCTGAGCA--------GGTTGGCCTTGGTTGGGAGTAA 912127 v vv vi -------- i v i i v C L2#LINE/L2 1678 GGGATGGGATCTAGTGCACAAGTGGAGGGGTTGGCCTTAGATAGGAGCAC 1629 chr2ptel1M 912128 GGTCACCTCA-CCATGGGAGATTCAGATGAAGGAAGAGAAGGGCTGAAGA 912176 v vi - i i v - ivviiiv v v v -- iiv C L2#LINE/L2 1628 GGACAGTTCATCCGTAGTA-ACAGGAGGGAAGGCAGAGTATG--TGGGCA 1582 chr2ptel1M 912177 CAACTG--GGTA-ATGAG-GGATGAGG-GAGAGGAGAG-AAGGGAGCTCG 912220 iv -- -i i -i v - ivi ??-iv i i v C L2#LINE/L2 1581 CAGATGCAGGTAGGTGGGTAGATGTGGTGGTGGGAGNNTGTGGAAGTTCT 1532 chr2ptel1M 912221 TGACAAACAGC--CTGCGGTTTAGGTAAAATATGAAATGAGGGTCCGGCC 912268 ivv vi iv -- iivv i vi i v iii viviviv C L2#LINE/L2 1531 CTTCTGATTGCTTCTATTTTCTCAGTGAAATAGGAAGCAAGGTCATCAGC 1482 chr2ptel1M 912269 TGAGAGTGGGGAC--GGGGGGAACTATAGGAGGCTTGAGGGGGGATGAGA 912316 i i-- i iv i v i i i v C L2#LINE/L2 1481 TGAGAGTGAGGATAGGGGAGGAGGTGTTGGAGGTTTGAGGAGAGAGGAGA 1432 chr2ptel1M 912317 GGGTCTGGGAGAGTCACTGTGGAGA 912341 i v ii v iiivv C L2#LINE/L2 1431 AGGTGTGAAATAGTCGTCTAGGAGA 1407 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.50 CpG sites = 149, Kimura (unadjusted) = 45.85 Transitions / transversions = 1.26 (149/118) Gap_init rate = 0.04 (31 / 804), avg. gap size = 4.00 (124 / 31) 12 26.07 0.00 0.00 chr2ptel1M 913337 913373 (86627) (AGGGGGG)n#Simple_repeat 1 37 (0) m_b79s252i13 2909 chr2ptel1M 913337 AGGGTGGAGGTGGGGCAGGGAAGGGGGAAAGGGGGAG 913373 v v ivi i i i (AGGGGGG)n#Si 1 AGGGGGGAGGGGGGAGGGGGGAGGGGGGAGGGGGGAG 37 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 192 29.05 8.05 1.08 chr2ptel1M 917065 917151 (82849) MIRb#SINE/MIR 4 96 (172) m_b79s601i21 2910 chr2ptel1M 917065 AGAAGCAGCAGTGGCTCAG-GGCATGAGAGCCGGTGTACGAGCCAGTGAG 917113 ii - iv - v v vi v iv vv i vv MIRb#SINE/MIR 4 AGGGGCAGC-GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAG 52 chr2ptel1M 917114 AGCTGAATTCGAATC------CTGACACATCCCATCTGTGCGAC 917151 v ii ------ v v v i v i MIRb#SINE/MIR 53 ACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGAC 96 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.85 CpG sites = 10, Kimura (unadjusted) = 36.85 Transitions / transversions = 0.67 (10/15) Gap_init rate = 0.03 (3 / 86), avg. gap size = 2.67 (8 / 3) 533 28.89 8.86 3.61 chr2ptel1M 918187 918423 (81577) MIRc#SINE/MIR 2 250 (18) m_b79s601i22 2911 chr2ptel1M 918187 GAGGCAGAGGCAGCGCAGGGAATACAGTGACAGGCCTGGAGTCGGGAAG- 918235 -v ii i v i v v iivii i i i - MIRc#SINE/MIR 2 GAGGCAG-TGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA 50 chr2ptel1M 918236 --------CAAGTCCGGCCTCAGACATTTG---GATGGACGACCCAGG-- 918272 -------- i v v v v i i--- v vii iv -- MIRc#SINE/MIR 51 CCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGC 100 chr2ptel1M 918273 AAGTCACTTCTCCACTGTTTGCTTTAGTTTCCTCATGTGTAAAATGGGGA 918322 vv v v vv i i v MIRc#SINE/MIR 101 AAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGA 150 chr2ptel1M 918323 GAGTAATATC------ACCTCTCTCCCAGGGTTGTGATAAGCAGCAAATA 918366 v i i ------i vi v vi i v v i MIRc#SINE/MIR 151 TAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATG 200 chr2ptel1M 918367 AAATAATTATACGGTGTTTAGCTCAGCGGTCGGCACGCAG-GAAGTGCAG 918415 i -i --- vv ---- v iv i vi v -i vi MIRc#SINE/MIR 201 AGATAAT-GTA---TGTGAA----AGCGCTTTGTAAACTGTAAAGTGCTA 242 chr2ptel1M 918416 TATAAATG 918423 i MIRc#SINE/MIR 243 TACAAATG 250 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.40 CpG sites = 34, Kimura (unadjusted) = 37.10 Transitions / transversions = 1.06 (34/32) Gap_init rate = 0.06 (14 / 236), avg. gap size = 2.14 (30 / 14) 611 27.51 3.81 4.81 chr2ptel1M 918215 918424 (81576) MIRb#SINE/MIR 48 255 (13) m_b79s601i23 2911 chr2ptel1M 918215 GACAGGCCTGGAGTCGGGAAGCAAGTCCGGCCTCAGACATTTG---GATG 918261 i iv ------ vi - v v i i--- v MIRb#SINE/MIR 48 GACAGACCTGGGTTCG------AATCCCGGC-TCTGCCACTTACTAGCTG 90 chr2ptel1M 918262 GACGACCCAGG--AAGTCACTTCTCCACTGTTTGCTTTAGTTTCCTCATG 918309 vii iv -- i vv v v vv i i v MIRb#SINE/MIR 91 TGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATC 140 chr2ptel1M 918310 TGTAAAATGGGGAGAGTAATATCACCTCTCTCCCAGGGTTGTGATAAGCA 918359 v i --- vi v vi i v MIRb#SINE/MIR 141 TGTAAAATGGGGATAATAAT---ACCTACCTCGCAGGGTTGTTGTGAGGA 187 chr2ptel1M 918360 GCAAATAAAATAAT---TATACGGTGTTTAGCTCAGCGGTCGGCACGCAG 918406 vi i i --- i vi i i v i vii ii MIRb#SINE/MIR 188 TTAAATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAG 237 chr2ptel1M 918407 GAAGTGCAGTATAAATGG 918424 v i vvv MIRb#SINE/MIR 238 TAAGCGCTCAATAAATGG 255 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.16 CpG sites = 28, Kimura (unadjusted) = 34.67 Transitions / transversions = 1.04 (28/27) Gap_init rate = 0.06 (13 / 209), avg. gap size = 1.38 (18 / 13) 72 19.28 0.72 0.00 chr2ptel1M 919502 919639 (80361) (GT)n#Simple_repeat 1 139 (0) m_b79s252i14 2912 chr2ptel1M 919502 GTGTGTG-GTGTGTGTGTGAGTGTGTGTGCACATGTGTGTGAATGTGTGC 919550 - v iiii vi i (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50 chr2ptel1M 919551 ATGTGCGTGTGTGTTCATGTGTGAGTGTGTATGTGTGTGTGAGTGTGTGT 919600 i i vii v i v (GT)n#Simple_ 51 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 100 chr2ptel1M 919601 ATGTGAGTGTGTGTATGCATGTATGTGAGTGTGTGTGTG 919639 i v i ii i v (GT)n#Simple_ 101 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 139 Matrix = Unknown Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.01 (1 / 137), avg. gap size = 1.00 (1 / 1) 450 35.33 15.20 2.17 chr2ptel1M 919681 920088 (79912) L3#LINE/CR1 2922 3381 (718) m_b79s601i24 2913 chr2ptel1M 919681 TGGATTGGAGACGTCTTGTAGACAAAGGGCCCATCACTGTTGGCAGAGCA 919730 i ii i ivi vii ? v iviv viv v ii ii L3#LINE/CR1 2922 TAGATCAGGGGAATGCCGTAGACANAGTGTATCTGGATTTCAGCAAGGCA 2971 chr2ptel1M 919731 CGGGTCTGAGCTGC-------AGCCTCGTGCGTGGGATGGAAAGATACGG 919773 ivv v vi iiv ------- v i viiii i i i L3#LINE/CR1 2972 TTTGACAAAGTCTCTCATGATATCCTTGTGGACAAGATGGAGAAATATGG 3021 chr2ptel1M 919774 CCTG-ATTAGAAT-CAATGGTGTAGATATGGAACTGGTTAAAAAAAAAAT 919821 v - v v i - i viv i vi v i i vi vv v- L3#LINE/CR1 3022 GCTGGATGATAGTACAGTTAGGTGGATTCGTAGCTGGTTGAACGACTAT- 3070 chr2ptel1M 919822 AAAGAAACCAAGAAACATCAGGACTTTGTGACCCGATGTCAATCTGGCAG 919871 ----- v i iiii i-- - vi ivi i vi L3#LINE/CR1 3071 -----ACCCAAAAGGTGTT--GA-TTAATGGATCGATGTCAACCTGGAGG 3112 chr2ptel1M 919872 GAGATCTCCAGT----------CGAGCTCC--CCTTGGATCTGGGATCTT 919909 i i ----------v i i-- vi vvv v L3#LINE/CR1 3113 GAGGTCTCTAGTGGCGTGCCACAGGGCTCTGTCCTTGGCCCTGTCCTGTT 3162 chr2ptel1M 919910 AGACGGTTTTGTCAACGATTTGGAGAAAAATA-----GGCGT-------- 919946 vi iv i i i vi i i ----- i -------- L3#LINE/CR1 3163 CAACATTTTTATCAATGACTTGGATGAAGACATAGAAGGCATGCTTATCA 3212 chr2ptel1M 919947 ---------ATGACATGAAGCTG------ACATCTTC--------ATCAC 919973 --------- ii ------ i v vv-------- v L3#LINE/CR1 3213 AATTTGCAGATGACACAAAGCTGGGAGGGATAGCTAATACGNTGGATGAC 3262 chr2ptel1M 919974 AAACCTTAGGATCCCCCCAAATCGTCACAGCTTGGAACGCTGGGT-AAAT 920022 i v- i i i vvvv?i viv vi v i-i v L3#LINE/CR1 3263 AGAA-TCAAGATTCAAAANGATCTCGACAGGCTGGAACGATGGGCCGAAA 3311 chr2ptel1M 920023 CGAATAAGA--AACTTTATTATG-ATGAATACAAAATCCTATGTTT-GGT 920068 v i -- v vi v - i ii i iii - L3#LINE/CR1 3312 CCAACAAGATGAAATTTAACAGGGATAAATGTAAAGTCCTGCATTTAGGT 3361 chr2ptel1M 920069 TTAAAAAATCAACTTCACGA 920088 i v i L3#LINE/CR1 3362 TCAAAAAATCAACTGCACAA 3381 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 47.81 CpG sites = 83, Kimura (unadjusted) = 50.36 Transitions / transversions = 1.43 (83/58) Gap_init rate = 0.06 (24 / 407), avg. gap size = 3.00 (72 / 24) 322 17.30 18.42 1.12 chr2ptel1M 921591 921666 (78334) MIR#SINE/MIR 56 144 (118) m_b79s601i25 2914 chr2ptel1M 921591 GAAACCTGGCCTCGGACACTCACTAGTTGTGCGATCCTAGGCCAGTT--- 921637 v i - v v i i i i i i v --- MIR#SINE/MIR 56 GAATCCCGGC-TCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACT 104 chr2ptel1M 921638 -----------TGCCTCAGTTTCCTTATCTGTAAAATGAG 921666 ----------- i i MIR#SINE/MIR 105 TAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGG 144 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 18.51 CpG sites = 9, Kimura (unadjusted) = 20.18 Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.04 (3 / 75), avg. gap size = 5.00 (15 / 3) 15 0.00 0.00 0.00 chr2ptel1M 923595 923611 (76389) (GT)n#Simple_repeat 1 17 (0) m_b79s252i15 2915 chr2ptel1M 923595 GTGTGTGTGTGTGTGTG 923611 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTG 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 38 2.78 0.00 0.00 chr2ptel1M 923612 923648 (76352) (TA)n#Simple_repeat 1 37 (0) c_b79s251i1 2916 chr2ptel1M 923612 TATATATGTATATATATATATATATATATATATATAT 923648 i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATAT 37 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 79 30.26 2.70 0.66 chr2ptel1M 923654 923949 (76051) (TCTA)n#Simple_repeat 1 302 (0) m_b79s252i16 2917 chr2ptel1M 923654 TCTATCTCTCTATCCATCTATCTGAT-TATATTTTCATTTATC-ATCTTT 923701 v i - - v v ii i - v (TCTA)n#Simpl 1 TCTATCTATCTATCTATCTATCT-ATCTATCTATCTATCTATCTATCTAT 49 chr2ptel1M 923702 CT-T-TACCTATAGTTTGATGTATCCATCCATCCATCTATATTTCCACCT 923749 - - i vvv iv v i i i v v i i (TCTA)n#Simpl 50 CTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCT 99 chr2ptel1M 923750 ATCCACCCATCTATCAATCTA--TATTTATCACCTCTAACTATATTTCCA 923797 i i i v -- i -iv v v v i (TCTA)n#Simpl 100 ATCTATCTATCTATCTATCTATCTATCTATC-TATCTATCTATCTATCTA 148 chr2ptel1M 923798 TCCATCCATCCATCTATCAATCTATATTTTCAGTTAGC-ATCTCTCTTTC 923846 i i i v v v ii vi v - v v (TCTA)n#Simpl 149 TCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATC 198 chr2ptel1M 923847 TCTCCATATTTCCACCTATCCATCCATCTGTCTGTCCATCTATCTATCTA 923896 v i v v i i i i i i i (TCTA)n#Simpl 199 TATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTA 248 chr2ptel1M 923897 TCTATCCACCTATCTCTTCATTTATC-ATCTGCCTCTGTCTCTGTGTCTC 923945 i i v ii i - ii v v v i v v (TCTA)n#Simpl 249 TCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATC 298 chr2ptel1M 923946 TCTC 923949 v (TCTA)n#Simpl 299 TATC 302 Matrix = Unknown Transitions / transversions = 1.18 (39/33) Gap_init rate = 0.03 (9 / 295), avg. gap size = 1.11 (10 / 9) 11 13.83 2.78 5.71 chr2ptel1M 924551 924586 (75414) (CCTCCT)n#Simple_repeat 1 35 (0) m_b79s252i17 2918 chr2ptel1M 924551 CCTCATTCTCCCTCCTCCTCCTTCCCCCT-CTCTTCC 924586 v i - - i - i (CCTCCT)n#Sim 1 CCTCCTCCT-CCTCCTCCTCC-TCCTCCTCCTCCTCC 35 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.09 (3 / 35), avg. gap size = 1.00 (3 / 3) 295 29.80 2.86 0.93 chr2ptel1M 926253 926357 (73643) L2b_3end#LINE/L2 350 456 (10) m_b80s601i0 2919 chr2ptel1M 926253 TATGTGCCCTCTGGGGG--GGGGCAGGGCCCTTTCTTGCCTTTGTCTGTA 926300 i v i iv i -- i v ? i - v iiivivv L2b_3end#LINE 350 TGTGAGCTCCGTGAGGGCAGGGACCGNGTC-TGTCTTGTTCACCGCTGTA 398 chr2ptel1M 926301 TTCCCAGAAC-TAGCCCAGTGCCGGGCACACAGTAGGTGCTTCAGAAGTG 926349 i vi - v ? v i iviv i i L2b_3end#LINE 399 TCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATA 448 chr2ptel1M 926350 CTTGCTGA 926357 i i L2b_3end#LINE 449 TTTGTTGA 456 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.45 CpG sites = 19, Kimura (unadjusted) = 40.39 Transitions / transversions = 1.58 (19/12) Gap_init rate = 0.03 (3 / 104), avg. gap size = 1.33 (4 / 3) 352 24.47 5.32 0.00 chr2ptel1M 926269 926362 (73638) L2d2_3end#LINE/L2 452 550 (5) m_b80s601i1 2919 chr2ptel1M 926269 GGGGGCAGGGCCCTT-TCTTGCCTTTGTCTGTATTCCC-AGAAC---TAG 926313 i v v - iivi v i i - v i --- L2d2_3end#LIN 452 GAGGGCAGGGACCATGTCTTATACTTCTTTGTATCCCCCACAGCGCCTAG 501 chr2ptel1M 926314 CCCAGTGCCGGGCACACAGTAGGTGCTTCAGAAGTGCTTGCTGATTTGA 926362 v vv i iv v i ii i L2d2_3end#LIN 502 CACAGTGCCTTGCACACAGTAGGCGCTCAATAAATATTTGTTGATTTGA 550 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.60 CpG sites = 13, Kimura (unadjusted) = 30.12 Transitions / transversions = 1.30 (13/10) Gap_init rate = 0.03 (3 / 93), avg. gap size = 1.67 (5 / 3) 287 38.37 0.81 3.31 chr2ptel1M 926318 926441 (73559) C MIRb#SINE/MIR (35) 233 113 m_b80s601i2 2920 chr2ptel1M 926318 GTGCCGGGCAC-ACAGTAGGTGCTTCAGAAGTGCTTGCTGATTTGAAGAT 926366 i -iiiv i i i v v iii vv v i vvv C MIRb#SINE/MIR 233 GTGCCAGGCACTGTGCTAAGCGCTTTACATGCATTATCTCATTTAATCCT 184 chr2ptel1M 926367 CATGACAGTGCTATGATCTTAGCAGGGACCCCCCCCCCCATTTAATAGAT 926416 ii iiv ii ----i i v iiviivi v i C MIRb#SINE/MIR 183 CACAACAACCCTGCGA----GGTAGGTATTATTATCCCCATTTTACAGAT 138 chr2ptel1M 926417 AAGAAAAGTGAGGTTTAAAGAGGCT 926441 i i v i i i i C MIRb#SINE/MIR 137 GAGGAAACTGAGGCTCAGAGAGGTT 113 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 54.49 CpG sites = 31, Kimura (unadjusted) = 58.51 Transitions / transversions = 2.07 (31/15) Gap_init rate = 0.04 (5 / 123), avg. gap size = 1.00 (5 / 5) 218 31.31 10.10 0.00 chr2ptel1M 926722 926820 (73180) C MIRc#SINE/MIR (141) 127 19 m_b80s601i3 2921 chr2ptel1M 926722 CTGAGGCTCCAGCAGG--GGGTGTCTGGCTCAAGGTGACACT-----TCG 926764 viiv --ii v v i v v----- vi C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAA 78 chr2ptel1M 926765 GGGGAAGAGCAGGGACTC---CCCCACCTGTGCTGGGTCCAAGTTCACTA 926811 v v v --- viviiv v iv i v i C MIRc#SINE/MIR 77 GTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTG 28 chr2ptel1M 926812 TTTTCTCCA 926820 i i i C MIRc#SINE/MIR 27 CTCTTTCCA 19 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.00 CpG sites = 15, Kimura (unadjusted) = 41.00 Transitions / transversions = 0.94 (15/16) Gap_init rate = 0.03 (3 / 98), avg. gap size = 3.33 (10 / 3) 349 19.10 2.20 2.20 chr2ptel1M 926817 926907 (73093) L2d2_3end#LINE/L2 187 277 (278) m_b80s601i4 2922 chr2ptel1M 926817 TCCAGATCTTTCCCAGCCTTCAAGGCCTAGTTCAAGTGCTGCC-CCTCTG 926865 i i v v i i i ? ii - i L2d2_3end#LIN 187 TCCAAATCCTACCCATCCTTCAAGGCCCAGCTCAAATNCCACCTCCTCCG 236 chr2ptel1M 926866 GGAAGCCTTCCCCGACCA-GCCGGCGCCACAGGGACCCTCTCC 926907 v i -v i - i? v -i L2d2_3end#LIN 237 TGAAGCCTTCCCTGACCACTCCAGC-CCGNAGTGA-TCTCTCC 277 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 20.31 CpG sites = 12, Kimura (unadjusted) = 23.33 Transitions / transversions = 2.40 (12/5) Gap_init rate = 0.04 (4 / 90), avg. gap size = 1.00 (4 / 4) 311 33.50 6.04 1.58 chr2ptel1M 927794 927975 (72025) L3b_3end#LINE/CR1 900 1089 (117) m_b80s601i5 2923 chr2ptel1M 927794 TGGGGGGGGGTGAGCACTCACTGCCCTTGTCC-CAGAGCTCTGAACCAG- 927841 i i iv v viiii vi v v - v vv v v - L3b_3end#LINE 900 TAGAGGACGGTGACCAGCTGTTCTCCATCTCCACTGAGGACAGAACAAGA 949 chr2ptel1M 927842 -GAAACTGGCTTGGATTGCAGAGAGGGAGATTTAGGTCAGATA-AAGAAA 927889 - iv ii i viv i i i - i L3b_3end#LINE 950 GGAAATGGGCTTAAACTGCAGCATGAGGGATTTAGGTTAGATATAAGGAA 999 chr2ptel1M 927890 AAGCTT------GGGGAGAATCAGGAGCCACTGGGGCAGGGGTGAGGGGG 927933 i i ------i v i iivv iv i-- v v vv i L3b_3end#LINE 1000 GAACTTCCTGACAGTGAGAGTTGTTAAACACTGGA--ATGGGTTACCGAG 1047 chr2ptel1M 927934 GGTGGGGGTGCGAATTTCCTTCCCCAGAGC-CCTTTGGAAACA 927975 v vv i - i i ii v-? ii i L3b_3end#LINE 1048 GGAGGTTGCG-GAATCTCCTTCTCTGGAGAGNCTTTAAAAATA 1089 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.13 CpG sites = 34, Kimura (unadjusted) = 46.19 Transitions / transversions = 1.31 (34/26) Gap_init rate = 0.05 (9 / 181), avg. gap size = 1.56 (14 / 9) 44 22.81 2.16 3.65 chr2ptel1M 928035 928173 (71827) (GGGGA)n#Simple_repeat 1 137 (0) m_b80s252i1 2924 chr2ptel1M 928035 GGGGAGGTTGGGGGAGGGGAGGGGAGGAGGGAGAGATAAGAAGGGGAGGG 928084 vvi - - i ivii i (GGGGA)n#Simp 1 GGGGAGGGGAGGGGAGGGGAGGGGA-G-GGGAGGGGAGGGGAGGGGAGGG 48 chr2ptel1M 928085 GA-GGAAGGGAAGGGGAAAGGA-GGGA-GAGATGGGAGGGGGGAAGAGGG 928131 - i i ii - - i v i ii (GGGGA)n#Simp 49 GAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGG 98 chr2ptel1M 928132 GAAGAGGAAGGGAGAGGTGGGGGGAGAGCAGGGCAGGGCAGG 928173 - - i - v i i v v v (GGGGA)n#Simp 99 G-AG-GGGAGGG-GAGGGGAGGGGAGGGGAGGGGAGGGGAGG 137 Matrix = Unknown Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.06 (8 / 138), avg. gap size = 1.00 (8 / 8) 14 14.13 0.00 3.12 chr2ptel1M 928508 928540 (71460) (CGGCC)n#Simple_repeat 1 32 (0) m_b80s252i2 2925 chr2ptel1M 928508 CGGCCCAGCCCGGCCCTGAGCGGCCCGGCTCCG 928540 i v vv - (CGGCC)n#Simp 1 CGGCCCGGCCCGGCCCGGCCCGGCCCGGC-CCG 32 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 408 27.54 13.38 0.56 chr2ptel1M 929804 929960 (70040) L2b_3end#LINE/L2 282 458 (8) m_b80s601i6 2922 chr2ptel1M 929804 CCCCCGGGTCTTCCCCTGCCCCC-----TTCTAGTTCCTTATATATACA- 929847 vi i v v i----- v ?i vii i?v i ii- L2b_3end#LINE 282 CCCCCCAGTCCTACCCTGCCACTCTGGGTTATNATTGTCTGNTTACATGT 331 chr2ptel1M 929848 CTGCCTTTCCCCATGAAAGTATAAGCTCCTTGAGGACAGGAGCTGTCTTT 929897 i i- iv i v i i v i ii i ?v i L2b_3end#LINE 332 CTGTCTC-CCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCT 380 chr2ptel1M 929898 TTCTTATT------TGTATTCCCGGT--CT-------TGCCTGGCACACA 929932 v i ------ i i i-- -------? L2b_3end#LINE 381 GTCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACA 430 chr2ptel1M 929933 GCAGGTACTTAATAAATGTTTGCTGAAT 929960 i ii i i i i L2b_3end#LINE 431 GTAGGCGCTCAGTAAATATTTGTTGAAT 458 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.40 CpG sites = 32, Kimura (unadjusted) = 37.91 Transitions / transversions = 2.91 (32/11) Gap_init rate = 0.04 (6 / 156), avg. gap size = 3.67 (22 / 6) 480 26.16 2.24 3.01 chr2ptel1M 929827 929960 (70040) L2c_3end#LINE/L2 338 470 (8) m_b80s601i7 2922 chr2ptel1M 929827 TTCTAGTTCCTTATATATACA-CTGCCTTTCCCCATGAAAGTATAAGCTC 929875 v i vii i v i?ii- i i- i iv i v i i L2c_3end#LINE 338 TTGTAATTGTCTGTTTACNTGTCTGTCTC-CTCCACTAGACTGTGAGCTC 386 chr2ptel1M 929876 CTTGAGGACAGGAGC--TGTCTTTTTCTTATTTGTATTCCCGGTCTTGCC 929923 i ii -- v v v i i i--- L2c_3end#LINE 387 CTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTATCCCCAGC---GCC 433 chr2ptel1M 929924 TGGCACACAGCAGGTACTTAATAAATGTTTGCTGAAT 929960 i i ii i i L2c_3end#LINE 434 TGGCACATAGTAGGCGCTCAATAAATGTTTGTTGAAT 470 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.92 CpG sites = 26, Kimura (unadjusted) = 34.60 Transitions / transversions = 3.25 (26/8) Gap_init rate = 0.05 (6 / 133), avg. gap size = 1.17 (7 / 6) 262 33.52 12.17 4.03 chr2ptel1M 930087 930316 (69684) C L2b_3end#LINE/L2 (15) 451 204 m_b80s601i8 2926 chr2ptel1M 930087 AAAAATTAACTGATTATTTCCCATGTGTCAGATATAGTG-TAAACACTAG 930135 v v viiii v ii i ii?iv - ii i i C L2b_3end#LINE 451 AAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGG 402 chr2ptel1M 930136 GGAAACAAAAAAGGCAAACCGCCCAGGAACAGCCTCG-TCCCTGTTCTCA 930184 v iv--- ii ----- i - v ? - ii C L2b_3end#LINE 401 GGATACAGC---GGTGAAC-----AAGA-CAGACNCGGTCCCTGCCCTCA 361 chr2ptel1M 930185 AGGAGTTTGGGGTCTGATGGGAGAAAGAG-CATG----CGAAGAATTGTA 930229 v i iivi ii i i v - ---- ii v ?i C L2b_3end#LINE 360 CGGAGCTCACAGTCTAGTGGGGGAGACAGACATGTAANCAGACAATNATA 311 chr2ptel1M 930230 TACAA---------------ACT----AGGCCCAAACGGGAGAGCCTGG- 930259 vv v --------------- ----i i v i i v i- C L2b_3end#LINE 310 ACCCAGAGTGGCAGGGTAGGACTGGGGGGGCCCAGAGGAGGGCGCCTGAC 261 chr2ptel1M 930260 -TGACGAAGGGGGAGCAGGAAAGTCTCCTGGTGGAAGGTGGGATTGTAGC 930308 -i i vvi vvvi ii ii i v - iv vv C L2b_3end#LINE 260 CCGGCCTGGGGGGTCAGGGAGGGCTTCCCGGAGG-AGGTGACATTTGAGC 212 chr2ptel1M 930309 TGGGATCT 930316 i i C L2b_3end#LINE 211 TGAGACCT 204 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.40 CpG sites = 48, Kimura (unadjusted) = 48.15 Transitions / transversions = 1.85 (48/26) Gap_init rate = 0.08 (18 / 229), avg. gap size = 2.11 (38 / 18) 310 43.10 1.72 0.00 chr2ptel1M 930376 930607 (69393) C L2#LINE/L2 (74) 3008 2773 m_b80s601i9 2926 chr2ptel1M 930376 AGGAACAGCAAGGAGGTCAGTACCCATGAGTCACAGGGCACAAGGAGAGC 930425 i iivvv iiv iv v vi i i iiv C L2#LINE/L2 3008 AGGAACAGCAAGGAGGCCAGTGTGGCTGGAGCGGAGTGAGCGAGGGGGAG 2959 chr2ptel1M 930426 AAAAGTATAAGA--AAACCAGGAAAGTGAGCAACAGCCAATTTAAGAGGG 930473 ivi vi -- iii ii i i vviivii iv i v vi C L2#LINE/L2 2958 AGTGGTAGGAGATGAGGTCAGAGAGGTAACGGGGGACCAGATCATGTAGG 2909 chr2ptel1M 930474 GCTTGACACACCACACAGTAGACTTTGCATTTCATCCTGGAGGAAAGAGG 930523 i vii vi ivvvivi vv i ii iiv i vi C L2#LINE/L2 2908 GCCTTGTAGGCCATTGTAAGGACTTTGGCTTTTACTCTGAGTGAGATGGG 2859 chr2ptel1M 930524 AAGCCACTGGAGATTACTGAAT-GGGGAATGACCTGGGCAGAGCCATCCT 930572 i iv vi ii- i i v iv v vii ivi C L2#LINE/L2 2858 AAGCCATTGGAGGGTTTTGAGCAGAGGAGTGACATGATCTGACTTACGTT 2809 chr2ptel1M 930573 ACAAAAAGACCAATCTGAC-ACTGGAGCGGGAAAAG 930607 vi i i v i -i vivi i v C L2#LINE/L2 2808 TTAAAAGGATCACTCTGGCTGCTGTGTTGAGAATAG 2773 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 66.12 CpG sites = 62, Kimura (unadjusted) = 69.83 Transitions / transversions = 1.63 (62/38) Gap_init rate = 0.01 (3 / 231), avg. gap size = 1.33 (4 / 3) 241 35.48 5.66 2.28 chr2ptel1M 930620 931043 (68957) L1MD_orf2#LINE/L1 1777 2214 (1080) m_b80s551i0 2927 chr2ptel1M 930620 AACCAGACGATGATGGCAATTGGC-CAGGAAAA-CTCTTGACCAAATACA 930667 i v i v iv ii- i - vi v v L1MD_orf2#LIN 1777 AATCACATGATCATATCAATTGATGCAGAAAAAGCATTTGACAAAATTCA 1826 chr2ptel1M 930668 ACACCCATTTTCAGTAAAAAC-CACAACACACTGAAAACAGCAAAAAACC 930716 iviii - v i? v iii i viiii - L1MD_orf2#LIN 1827 ACACCCATTCATGATAAAAACTCTCAGNAAACTAGGAATAGAGGGGAAC- 1875 chr2ptel1M 930717 TGACTTTTCTTTAAGATGGCAACTGGTATCTACCTAAAATCAAGAGCCAG 930766 ------ i i vv ii vvi i vv i v v i i L1MD_orf2#LIN 1876 ------TTCCTCAACTTGATAAAGAGCATCTACAAAAAACCTACAGCTAA 1919 chr2ptel1M 930767 AATTATATGTAATGGAGAAACATTATAGATATTTCCAATAAGACCAGGGG 930816 v i iv v v i iv viiv i vv i i ii L1MD_orf2#LIN 1920 CATCATACTTAATGGTGAAAGACTGAATGCTTTCCCCCTAAGATCGGGAA 1969 chr2ptel1M 930817 TAAAGCAAGGACATCCATTAGCACCACTATTAATTGGTA-AGTTTAC-AG 930864 i i ii ii vv v v iiii - -- -i L1MD_orf2#LIN 1970 CAAGGCAAGGATGTCCGCTCTCACCACTCTTATTCAACATAG--TACTGG 2017 chr2ptel1M 930865 AAATGCTAGATGGTACAGTAGG--AAAACAAAAAAAT-CAAGGCA----- 930906 i v vii i i i -- i v ii -v ----- L1MD_orf2#LIN 2018 AAGTTCTAGCCAGTGCAATAAGGCAAGAAAAGGAAATAAAAGGCATACAG 2067 chr2ptel1M 930907 ATAAGCAAG--AGGAGTAAA--TATCACTTATTACTGAAGATATTG-GGT 930951 vi v -- i i -- i v vv i v v i vi-v L1MD_orf2#LIN 2068 ATTGGAAAGGAAGAAATAAAACTGTCCCTATTTGCAGATGACATGATTGT 2117 chr2ptel1M 930952 CTACTTAAAGAACATTGAGGATTTGACTAAAA------TTAAATGAAACA 930995 v i i iviii v iv v ------ vi iv vv L1MD_orf2#LIN 2118 CTACGTAGAAAATCCCAAGGAATCTACAAAAAAACTCCTAGAACTAATAA 2167 chr2ptel1M 930996 ATAATTTAAATAAAAGAAACAGGACATAAAGTAAACCCACACAAGTCA 931043 i i v v ii- i vvi i i ii ? vi v i L1MD_orf2#LIN 2168 GTGAGTTCAGC-AAGGTCGCAGGATACAAGATNAACATACAAAAATCA 2214 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 49.18 CpG sites = 88, Kimura (unadjusted) = 50.68 Transitions / transversions = 1.49 (88/59) Gap_init rate = 0.05 (22 / 423), avg. gap size = 1.55 (34 / 22) 492 25.00 7.03 0.00 chr2ptel1M 931629 931756 (68244) C MIRc#SINE/MIR (122) 146 10 m_b80s601i10 2928 chr2ptel1M 931629 CACTTTGCAGATGAGGAGAC--AGGCACATAG-GGTGAAGGGACTTGTTC 931675 i i i -- v v - v v ii C MIRc#SINE/MIR 146 CATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCC 97 chr2ptel1M 931676 AAGGTCACACGGGTTGT------CTGAGGCTGGATTTGCCCTTAGGTTCT 931719 i v v ------ v v v i i vv ii ii C MIRc#SINE/MIR 96 AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTT 47 chr2ptel1M 931720 CCTGACTCTAAGCATGGCGCTCTATCTATTGCACCAC 931756 i ivii i v i i C MIRc#SINE/MIR 46 CCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.93 CpG sites = 19, Kimura (unadjusted) = 31.09 Transitions / transversions = 1.46 (19/13) Gap_init rate = 0.02 (3 / 127), avg. gap size = 3.00 (9 / 3) 383 24.75 11.88 0.00 chr2ptel1M 932635 932735 (67265) C MIRc#SINE/MIR (124) 144 32 m_b80s601i11 2929 chr2ptel1M 932635 TTTTACAGGTGAGGAAACTGAGG--CAGACAGG------GGTTTGCTCAG 932676 i -- v ------ ii i i C MIRc#SINE/MIR 144 TTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAA 95 chr2ptel1M 932677 GGGCAGATAGCTGGTGTAT----GAAGCAAGATTCAAACTCACGTTTTCC 932722 v v i i ivi ---- iv ii i i i v i C MIRc#SINE/MIR 94 GGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCC 45 chr2ptel1M 932723 CAACTCCAAGCCC 932735 ii i C MIRc#SINE/MIR 44 TGACTCCAAGTCC 32 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.70 CpG sites = 19, Kimura (unadjusted) = 31.77 Transitions / transversions = 3.17 (19/6) Gap_init rate = 0.03 (3 / 100), avg. gap size = 4.00 (12 / 3) 393 23.35 27.41 0.00 chr2ptel1M 932742 932938 (67062) C MIRc#SINE/MIR (3) 265 15 m_b80s601i12 2930 chr2ptel1M 932742 AGTAACAACAGACGGCATTTATATAGCACCT--------ACTATGTGCTT 932783 i i ?vvivi i i -------- v v i C MIRc#SINE/MIR 265 AATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCGCTT 216 chr2ptel1M 932784 T-ACAGCCATTATCTCACCTGAGCCTCCCAGC--CCCTGAGA-GTGGGT- 932828 - vv ii v v i -- v - i i- C MIRc#SINE/MIR 215 TCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCA 166 chr2ptel1M 932829 -----GCTCTCATTTCTCCCATTTTACA---GAGGACACTGAGGCAAAGA 932870 ----- v v i vii --- v vv C MIRc#SINE/MIR 165 GGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGA 116 chr2ptel1M 932871 GA----------------CAA----ACATAGCTAGGAAGTGTCTGA---- 932896 ---------------- ---- i v v v ---- C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 66 chr2ptel1M 932897 --ACTCGA-------TGTCCCCAACCCCAGGCCCAGAGCTCCACCCACTG 932937 -- ------- v i ii i i i v ivi C MIRc#SINE/MIR 65 GGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTG 16 chr2ptel1M 932938 C 932938 C MIRc#SINE/MIR 15 C 15 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.74 CpG sites = 24, Kimura (unadjusted) = 28.45 Transitions / transversions = 1.09 (24/22) Gap_init rate = 0.06 (12 / 196), avg. gap size = 4.50 (54 / 12) 64 25.05 1.55 3.16 chr2ptel1M 934721 934913 (65087) (AGG)n#Simple_repeat 1 190 (0) m_b80s252i3 2931 chr2ptel1M 934721 AGGACAAAGAGGAGGAGGAGGGAAGACAGAGG-GGAGGAGGAGGAGGGAA 934769 vi i - i -i - - i (AGG)n#Simple 1 AGGAGGAGGAGGAGGAGGA-GGAGGA-GGAGGAGGAGGAGGAGGA-GGAG 47 chr2ptel1M 934770 GATG-GGAGGAAGAAGAGGAAGAGGAGGAAGAGAAAGAGGAGGGGGAAGG 934818 v - i i i i i i i - (AGG)n#Simple 48 GAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGG-AGG 96 chr2ptel1M 934819 AAGAAGAGGAGGAAAGATGAAGGGGAGGAAGAGGAAGAAGAAGAGGGAGA 934868 i i - i v i i i i i i ii (AGG)n#Simple 97 AGGAGGAGGAGG-AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA 145 chr2ptel1M 934869 GGGGCAGGGGGAGG-GAAGAAGGAAAGATGGGGAGAGGGATGAGGA 934913 i v i - i i - i v i ii v (AGG)n#Simple 146 GGAGGAGGAGGAGGAGGAGGAGG-AGGAGGAGGAGGAGGAGGAGGA 190 Matrix = Unknown Transitions / transversions = 5.17 (31/6) Gap_init rate = 0.05 (9 / 192), avg. gap size = 1.00 (9 / 9) 418 27.72 0.99 0.00 chr2ptel1M 935879 935979 (64021) C MIRc#SINE/MIR (99) 169 68 m_b80s601i13 2932 chr2ptel1M 935879 GACAGGGCCC-TCCTATTATGCCCATTTTATAGATAAGAAGACTGAGTCT 935927 i vv- vi v i i i i v C MIRc#SINE/MIR 169 GGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCT 120 chr2ptel1M 935928 CTGGACACTGAAATGACTTGGCCAGAGTCATACAGCTAATAAGTATCGGG 935977 v iiviv v i v ii i i iv i i C MIRc#SINE/MIR 119 CAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGA 70 chr2ptel1M 935978 GC 935979 C MIRc#SINE/MIR 69 GC 68 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.63 CpG sites = 17, Kimura (unadjusted) = 35.63 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.01 (1 / 100), avg. gap size = 1.00 (1 / 1) 14 11.25 3.45 0.00 chr2ptel1M 936102 936130 (63870) (CTTC)n#Simple_repeat 1 30 (0) m_b80s252i4 2933 chr2ptel1M 936102 CTTCCTTCCTTCCTTCC-TCCCCACTTCCT 936130 - iiv (CTTC)n#Simpl 1 CTTCCTTCCTTCCTTCCTTCCTTCCTTCCT 30 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1) 265 28.19 8.51 0.00 chr2ptel1M 937950 938137 (61863) L1MEi_5end#LINE/L1 2004 2207 (5) m_b80s551i1 2934 chr2ptel1M 937950 AGAAGGGATAGGATAAAAGGAGAGAAGGTTAAGCAGGAGG---AAAATAG 937996 i i v iii? iii i ? v v i i ii--- i L1MEi_5end#LI 2004 AGGAGAGAAAAAGNAAAGAAAAAGNATGATAAACAGAAAACACAAAATAA 2053 chr2ptel1M 937997 GAAGG-AGAAA--AATACACA---GTTAGTAATCA---TAACTGTGGATG 938037 v - -- i v v ---i i --- v ii L1MEi_5end#LI 2054 GATGGTAGAAATAAGTCCAAATATATCAGTAATCACAATAAATGTAAATG 2103 chr2ptel1M 938038 TGATGAGCTCACCC-TTAAAA--CGGAAAC-AGTAGAATGGATGAGAAAC 938083 viv i i i- -- i i i- vi v v i v L1MEi_5end#LI 2104 GATTAAACTCACCTATTAAAAGACAGAGATTATCAGATTGGATTAAAAAA 2153 chr2ptel1M 938084 CAGAATCCGACTATATGTTGTTTACAAGAGAGACACGGGAAACTAAAAGA 938133 v i ii i v vvi v v L1MEi_5end#LI 2154 AAAAATCCAGCTATATGCTGTTTACAAGAGACACACCTAAAACAAAACGA 2203 chr2ptel1M 938134 CATA 938137 i L1MEi_5end#LI 2204 CACA 2207 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 37.24 CpG sites = 34, Kimura (unadjusted) = 37.24 Transitions / transversions = 1.79 (34/19) Gap_init rate = 0.04 (8 / 187), avg. gap size = 2.00 (16 / 8) 236 35.07 4.80 1.07 chr2ptel1M 938016 938286 (61714) L1MC_orf2#LINE/L1 25 305 (2989) m_b80s551i3 2934 chr2ptel1M 938016 TTAGTAATCA---TAACTGTGGATGTGATGAGCTCACCC-TTAAAA--CG 938059 i i --- v ?i vvv i iiv v- -- i L1MC_orf2#LIN 25 TCAATAATCACTTTAAATGTNAATGGTCTAAATACACCAATTAAAAGACA 74 chr2ptel1M 938060 GAAACAGT-AGAATGGATGAGAAACCAGAATCCGACTATATGTTGTTTAC 938108 i iv - i v i v ii i i i L1MC_orf2#LIN 75 GAGATTGTCAGAGTGGATCAAAAAACAAGACCCAACTATATGTTGTCTAC 124 chr2ptel1M 938109 AAGAGAGACACGGGAAACTAAAAGACATACATAGATTCAAAATAAGGATA 938158 i vv vvv ivv i i v i i?iv L1MC_orf2#LIN 125 AAGAAACCCACTTTAAATATAAAGACACATATAGATTAAAAGTAAANGGA 174 chr2ptel1M 938159 TAAAGCAGAACTGAATATGCTTCAACTGAAGTAAAAAAGGCAGAGGGAGA 938208 ii v ii ivv vi vvv i vvv i i ? ii v v L1MC_orf2#LIN 175 TGGAGAAAGATATACCATGCTAACACTAATCAAAAGAAAGCNGGAGTAGC 224 chr2ptel1M 938209 AACCATGATTTTGAACAAAGTA------AAAGCAAAAACATCTAATTAAA 938252 v ivv i iii i i ------ i ii v vi vi--- L1MC_orf2#LIN 225 TATATTAATTTCAGACAGAGCAGACTTCAGAGCAAGGAAAGTTATC---A 271 chr2ptel1M 938253 GAGATCACCAGGGAAACAGCATTATGCTAAAAGG 938286 i v vv iv ivi v v i L1MC_orf2#LIN 272 GGGATAAAGAGGGGCATTACATAATGATAAAGGG 305 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 49.42 CpG sites = 51, Kimura (unadjusted) = 49.42 Transitions / transversions = 1.19 (51/43) Gap_init rate = 0.03 (8 / 270), avg. gap size = 2.00 (16 / 8) 319 27.89 6.12 0.00 chr2ptel1M 938016 938162 (61838) L1M4_orf2#LINE/L1 25 180 (3114) m_b80s551i2 2934 chr2ptel1M 938016 TTAGTAATCA---TAACTGTGGATGTGATGAGCTCACCC-TTAAAA--CG 938059 i i --- v ii viv i i v v v- i -- i L1M4_orf2#LIN 25 TCAGTAATTACATTAAATGTAAATGGATTAAACACTCCAATCAAAAGGCA 74 chr2ptel1M 938060 GAAAC-AGTAGAATGGATGAGAAACCAGAATCCGACTATATGTTGTTTAC 938108 i i-i i i i v vi i i i L1M4_orf2#LIN 75 GAGATTGGCAGAATGGATAAAAAAACATGATCCAACTATATGCTGTCTAC 124 chr2ptel1M 938109 AAGAGAGACACGGGAAACTAAAAGACATACATAGATTCAAAAT--AAGGA 938156 v vvv i i v i v i v i -- L1M4_orf2#LIN 125 AAGAGACACACTTTAGATTCAAAGACACAAATAGGTTGAAAGTAAAAGGA 174 chr2ptel1M 938157 TATAAA 938162 iv L1M4_orf2#LIN 175 TGGAAA 180 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 35.94 CpG sites = 25, Kimura (unadjusted) = 35.94 Transitions / transversions = 1.56 (25/16) Gap_init rate = 0.03 (5 / 146), avg. gap size = 1.80 (9 / 5) 479 33.69 6.95 1.73 chr2ptel1M 938354 938957 (61043) L1ME4c_3end#LINE/L1 6 640 (190) m_b80s551i4 2934 chr2ptel1M 938354 ATATATATTGAATATTGAACTGATCCGATTT-ATAAAAATAAAAATCAT- 938401 v ? ? iv vv i v i i v - i - ? v- L1ME4c_3end#L 6 ATCTNTANTATATAAAGAGCTCATTCAAATTGATAAGAA-AAANATCAAG 54 chr2ptel1M 938402 CCCACAAATGATAAATGGTCAAAAGATATGAAGAGGAAATTTTCAGAAGA 938451 v v vv v i i v iv iv ? L1ME4c_3end#L 55 ACCCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGA 104 chr2ptel1M 938452 AATCAAAGCTATCGATAGGATATTTTTTCTT--AAAAATGCACTAAATCA 938499 ii-- -- ivi? v v ivvviv v -- iv v vv i L1ME4c_3end#L 105 GG--AAA--TACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCG 150 chr2ptel1M 938500 CTAATGATTAGGGAAATGCAAATTAAAGAAAAAATCTAAGATACCACTTC 938549 i i i ii v v --i i i L1ME4c_3end#L 151 CTAGTAATCAAAGAAATGCAAATTAAAGCAACAAT--GAGATACCATTTT 198 chr2ptel1M 938550 ACACCTGTTAGA------------------------AATGAGCAGTCCTG 938575 i i i ------------------------ ivv i v L1ME4c_3end#L 199 ACGCCTATTAAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGCTG 248 chr2ptel1M 938576 AAGGGGATCCGG-GAAATGGGCACATTAATTAATTGTTGATGGAATAGTG 938624 iv i ? v - iv i ?i v vv i i v ?v i L1ME4c_3end#L 249 GCGAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTA 298 chr2ptel1M 938625 AACTGATTCAAACATTCTGGAGAACAATTTGGATTTATTCACAAAGGGCT 938674 i i v v v i i i vvv ivi iv i i L1ME4c_3end#L 299 AATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCC 348 chr2ptel1M 938675 ATACAACTCTGCCATACCCTTTGATCCCCTAATATCATTACTG------T 938718 v v v -i i vv vi i v ------ L1ME4c_3end#L 349 ATAAAAATGT-TCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTT 397 chr2ptel1M 938719 GCCTCAAAGTGATA----AAAAGAGAAAAAGACCTGTGTGGAGAAAAATA 938764 ii ii i vi ---- iii i v i i v vi i i L1ME4c_3end#L 398 ATCCTAAGGAAATAATTCAAAAGAAGGAAAAAGCTATATGCACGAAGATG 447 chr2ptel1M 938765 TTTACAGTAGCTCTTTTTGTTGTTGGCAAAGAACTGAAAATCGAGGGCAT 938814 i iv i vi v i- iv i i i i i ivivvviv L1ME4c_3end#L 448 TTCATTGCAGCGTTATTTA-TAATAGCGAAAAATTGGAAACAACCTAAAT 496 chr2ptel1M 938815 GCCCATCAGC-GGGGGGTGGCTGAATAAGTTGTG--ACATGATTGTGATG 938861 i v ii- ii i i i i i -- v?vivi L1ME4c_3end#L 497 GTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATG 546 chr2ptel1M 938862 GAGGTACTATTACGCTATAAGAAATGACAAAGAGGATGACTCCAGAAAAA 938911 -i i vvv i v i i vv v v viiv iv L1ME4c_3end#L 547 GA-ATATTATGCAGCCATTAAAAATGATAATTATGAAGACTATGTAGCAA 595 chr2ptel1M 938912 TATGACAAGATCCATATGAACTAATTGAAAGTGAAGTGGGAAGAAT 938957 i i- i viv vv vvv ivii v L1ME4c_3end#L 596 CATGG-AAAATGTTTATGATATAATGTTAAGTGAAAAAAGCAGAAT 640 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 45.02 CpG sites = 108, Kimura (unadjusted) = 46.94 Transitions / transversions = 1.17 (108/92) Gap_init rate = 0.03 (20 / 603), avg. gap size = 2.65 (53 / 20) 186 37.40 3.23 0.79 chr2ptel1M 939496 939619 (60381) L2d_3end#LINE/L2 177 303 (213) m_b80s601i14 2935 chr2ptel1M 939496 TCTCT-TCTCTCTCGGGCCTGCTCTTTTGTCTAGGTCTCAGGCAAGTCCC 939544 - v iviiv i i v iiv v i ivivv L2d_3end#LINE 177 TCTCTCTCTATCCAAATCCTACCCATCCTTCAAGGCCCAGCTCAAGTCCC 226 chr2ptel1M 939545 TCCCCTTCTGGGAAGTTTTCCCTGACCATCCTAAGAACACAACAACATCC 939594 v i i iiv ii ii i- vv vii iv i L2d_3end#LINE 227 ACCTCCTCCACGAAGCCTTCCCTGACCACTCC-AGCCCACACTGATCTCT 275 chr2ptel1M 939595 CCCAT---TGATTTCCCGTCCCTCTTAT 939619 v --- vi ii vv v L2d_3end#LINE 276 CCCTTCTCTGAACTCCTATAGCACTTAT 303 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 53.85 CpG sites = 26, Kimura (unadjusted) = 53.85 Transitions / transversions = 1.30 (26/20) Gap_init rate = 0.02 (3 / 123), avg. gap size = 1.67 (5 / 3) 193 31.45 10.09 0.84 chr2ptel1M 939510 939618 (60382) L2a_3end#LINE/L2 186 304 (213) m_b80s601i15 2935 chr2ptel1M 939510 GGCCTGCTCTTTTGTCT-----AGGTCTCAG-GCAAGTCCCTCCCCTTCT 939553 ii ii iii ----- iv -v i vi v iii v L2a_3end#LINE 186 GGCTCGCTCCCTCACCTCCTTCAGGTCTTTGCTCAAATGTCACCTTCTCA 235 chr2ptel1M 939554 GGGAAGTTTTCCCTGACCATCCTA---AGAACACAACAACAT--CCCCCA 939598 ? i ii i --- i i?vv v v -- L2a_3end#LINE 236 GNGAGGCCTTCCCTGACCACCCTATTTAAAATNGCACACCCTCNCCCCCA 285 chr2ptel1M 939599 TTGATTTCCCGTCCCTCTTA 939618 ?i- i i ii i L2a_3end#LINE 286 NC-ACTCCCTATCCCCCTTA 304 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.05 CpG sites = 25, Kimura (unadjusted) = 45.97 Transitions / transversions = 2.78 (25/9) Gap_init rate = 0.05 (5 / 108), avg. gap size = 2.40 (12 / 5) 14 17.66 2.50 2.50 chr2ptel1M 940641 940680 (59320) (ACCTCC)n#Simple_repeat 1 40 (0) m_b80s252i5 2936 chr2ptel1M 940641 ACCCCCAGCTCCACCGCCACCTCGCCGCTCC-CCTCTACCT 940680 i v v - vv - i (ACCTCC)n#Sim 1 ACCTCCACCTCCACCTCCACCTC-CACCTCCACCTCCACCT 40 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 42 22.17 0.97 0.97 chr2ptel1M 942090 942192 (57808) (ACCA)n#Simple_repeat 1 103 (0) m_b80s252i6 2937 chr2ptel1M 942090 ACCAAAC-AGCAACCCACCAACCAGTCAATCAAGCAACCAGCCGACCGAC 942138 v - v v ii i v i i i (ACCA)n#Simpl 1 ACCAACCAACCAACCAACCAACCAACCAACCAACCAACCAACCAACCAAC 50 chr2ptel1M 942139 AAATCAGCCAACCAACCAACCAGCCAACTGACAAACCAGCCGACCAACCA 942188 v i i i ii v i i (ACCA)n#Simpl 51 CAACCAACCAACCAACCAACCAACCAACCAACCAACCAACCAACCAACCA 100 chr2ptel1M 942189 GACC 942192 - (ACCA)n#Simpl 101 -ACC 103 Matrix = Unknown Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.02 (2 / 102), avg. gap size = 1.00 (2 / 2) 230 21.57 5.88 0.00 chr2ptel1M 942396 942497 (57503) SVA_F#Retroposon/SVA 1 108 (1267) m_b80s502i0 2938 chr2ptel1M 942396 CTCTCCTTCTCCTTCTCC---TCCCTCTCCCTCTCCTTCTCCCTCTCCTT 942442 i i --- i ii SVA_F#Retropo 1 CTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCC 50 chr2ptel1M 942443 CCCTCCCTCTGTCTCTCTCTCATG-GAAGTAGGGTGTGGGCTGCCCTAC- 942490 i i i v v i - i iv iivv i iv i - SVA_F#Retropo 51 TCTTTCCACGGTCTCCCTCTCATGCGGAGCCGAAGCTGGACTGTACTGCT 100 chr2ptel1M 942491 -CCATCTC 942497 - SVA_F#Retropo 101 GCCATCTC 108 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 26.43 CpG sites = 16, Kimura (unadjusted) = 26.43 Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.04 (4 / 101), avg. gap size = 1.50 (6 / 4) 184 34.88 9.90 1.44 chr2ptel1M 942971 943162 (56838) L2b_3end#LINE/L2 47 254 (212) m_b80s601i16 2939 chr2ptel1M 942971 TTTCCACTTGCTGGGTCCCTTGTTCC--CCTTACTGCCCTC-----AGCC 943013 i v ---iv ii i -- vi v -----v ii L2b_3end#LINE 47 TCTCCCCTTGCT---CACTCTGCTCCAGCCACACTGGCCTCCTTGCTGTT 93 chr2ptel1M 943014 CCT---GCATGGCTGGCTTTTCTCAGCCCCTGG--CTTTGCCCAGACTGT 943058 ---i i v v? i?iii v i v -- v ?vi L2b_3end#LINE 94 CCTCGAACACGCCANGCTCNCTCCCGCCTCAGGGCCTTTGCACNTGCTGT 143 chr2ptel1M 943059 CCCTCCTGCCGGGAATGCCCTCC----CCTCATCATTT--CTGCCTCCCA 943102 i ii v i i ---- v iii -- iiv i L2b_3end#LINE 144 TCCCTCTGCCTGGAACGCCCTTCCCCACCTCTTCGCCTGGCCAACTCCTA 193 chr2ptel1M 943103 GAC-TCCTTTAAGATTCAGCTCAGCCACTATGACCTCCACAAGACCTCCC 943151 vv - i i vi iviiii ivv ivi ii ii L2b_3end#LINE 194 CTCATCCTTCAGGTCTCAGCTCAAATGTCACCTCCTCCGGGAAGCCCTCC 243 chr2ptel1M 943152 CCGAGTCCCCA 943162 i vi L2b_3end#LINE 244 CTGACCCCCCA 254 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.97 CpG sites = 44, Kimura (unadjusted) = 51.50 Transitions / transversions = 2.00 (44/22) Gap_init rate = 0.05 (10 / 191), avg. gap size = 2.20 (22 / 10) 270 33.09 6.67 2.92 chr2ptel1M 942991 943155 (56845) L2d2_3end#LINE/L2 81 251 (304) m_b80s601i17 2939 chr2ptel1M 942991 TGTTCCCCTTACTGCCCTCAGCCCCTGCATGGCTGGCTTTTCTCAGCCCC 943040 v iv i i ---- vvi i v v vi? ii v i L2d2_3end#LIN 81 TGGTCTACTCACTGTCC----CCCGAACACGCCTTGCGCNTTCCCGCCTC 126 chr2ptel1M 943041 TGG--CTTTGCCCAGACTGTCCCTCCTGCCGGGAATGCCCTCCCCTCATC 943088 v-- i vi i i i i v i - v L2d2_3end#LIN 127 TGCGCCTTTGCTCACGCCGTTCCCCCCGCCTGGAATGCCCTTCCC-CTTC 175 chr2ptel1M 943089 ATTTCTGCCT-CCCAGAC--------TCCTTTAAGATTCAGCTCAGCCAC 943129 v i ii -i i i-------- i iii ivi? L2d2_3end#LIN 176 CTCTCCACCTATCCAAATCCTACCCATCCTTCAAGGCCCAGCTCAAATNC 225 chr2ptel1M 943130 TATGACCTCCACAAGACCTCCCCCGA 943155 i ivv iii ii i i L2d2_3end#LIN 226 CACCTCCTCCGTGAAGCCTTCCCTGA 251 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.60 CpG sites = 37, Kimura (unadjusted) = 47.81 Transitions / transversions = 2.31 (37/16) Gap_init rate = 0.05 (8 / 164), avg. gap size = 2.00 (16 / 8) 314 31.88 7.25 0.00 chr2ptel1M 943026 943163 (56837) L2c_3end#LINE/L2 111 258 (220) m_b80s601i18 2939 chr2ptel1M 943026 GCTTTTCTCAGCCCCTGG--CTTTGCCCAGACTGTCCCTCCTGCCGGGAA 943073 i i ii v i i ?-- v vi i ii v L2c_3end#LINE 111 GTTCTTTCCTGCCTCCGNGCCTTTGCACATGCTGTTCCCTCTGCCTGGAA 160 chr2ptel1M 943074 TGCCCTCCCCTCATCATTT-------CTGCCTCCCAGAC-TCCTTTAAGA 943115 i i i v v i------- iv i vv - i ? L2c_3end#LINE 161 TGCTCTTCCCCCCTCCTTCCACCTGGCTAACTCCTACTCATCCTTCAAGN 210 chr2ptel1M 943116 TTCAGCTCAGCCACTATGACCTCCACAAGACCTCCCCCGAGTCCCCAA 943163 i viiii ivv ivi ii i i vi L2c_3end#LINE 211 CTCAGCTCAGATGTCACCTCCTCCGGGAAGCCTTCCCTGACCCCCCAA 258 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.22 CpG sites = 30, Kimura (unadjusted) = 45.04 Transitions / transversions = 2.14 (30/14) Gap_init rate = 0.02 (3 / 137), avg. gap size = 3.33 (10 / 3) 829 27.23 1.84 1.84 chr2ptel1M 945118 945334 (54666) C MIRb#SINE/MIR (8) 260 44 m_b80s601i19 2940 chr2ptel1M 945118 AACCAGCATTTATATAGTACCTGCTGTGTACCAGGCGCCGTGCCAAACGC 945167 i i v vv ii i i i i i i i i C MIRb#SINE/MIR 260 AGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGC 211 chr2ptel1M 945168 TTTGC-TAAATCTGTCTCATGCGATCCTCCCAACAACTCTGGGAGGCTGG 945216 i - iv - i vii v i v iv C MIRb#SINE/MIR 210 TTTACATGCAT-TATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGG 162 chr2ptel1M 945217 CAATATCATTATACCCCTTTTACAGATGAGGGACCTGAGGCAAACAGAGG 945266 --- i v v i v vv v C MIRb#SINE/MIR 161 ---TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGG 115 chr2ptel1M 945267 TAAAGTGACTCACCCATGGTCACATGG---GCAAGTGCCCAAGGCTGGAT 945313 v i ii v ii --- i v vi v v C MIRb#SINE/MIR 114 TTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGAT 65 chr2ptel1M 945314 CTGAGCTTGGGTTTTCCTGGC 945334 ii i iii i vi i C MIRb#SINE/MIR 64 TCGAACCCAGGTCTGTCTGAC 44 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.44 CpG sites = 37, Kimura (unadjusted) = 35.02 Transitions / transversions = 1.76 (37/21) Gap_init rate = 0.03 (6 / 216), avg. gap size = 1.33 (8 / 6) 42 28.11 0.75 2.27 chr2ptel1M 945575 945708 (54292) (AC)n#Simple_repeat 1 132 (0) m_b80s252i7 2941 chr2ptel1M 945575 ACACACTCACACACATGACACATTCATACCCATACACACTCACAGGACAT 945624 v -v iv i v i v -v - (AC)n#Simple_ 1 ACACACACACACACA-CACACACACACACACACACACACACACA-CACA- 47 chr2ptel1M 945625 CATACACATGTTCTCACACTCACACCCACA-AGACATTCATACATATACA 945673 i iiiv v v v - v iv i i i (AC)n#Simple_ 48 CACACACACACACACACACACACACACACACACACACACACACACACACA 97 chr2ptel1M 945674 CGCATGCACACACACACACACAGTCTCACACTCAC 945708 i ii vv v v (AC)n#Simple_ 98 CACACACACACACACACACACACACACACACACAC 132 Matrix = Unknown Transitions / transversions = 0.88 (14/16) Gap_init rate = 0.03 (4 / 133), avg. gap size = 1.00 (4 / 4) 353 26.32 0.00 0.00 chr2ptel1M 946838 946913 (53087) C MIRb#SINE/MIR (21) 247 172 m_b80s601i20 2942 chr2ptel1M 946838 TAAGTGCCTACTGTATGTGAGGGACAGTGCAAAGCATTTTACAAACACGA 946887 i i i i i iv v v v ii vi iv C MIRb#SINE/MIR 247 TGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACATGCATTA 198 chr2ptel1M 946888 TCTCATTCAGTCTTCACAATAACCCT 946913 i i i i C MIRb#SINE/MIR 197 TCTCATTTAATCCTCACAACAACCCT 172 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.84 CpG sites = 14, Kimura (unadjusted) = 33.95 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.00 (0 / 75), avg. gap size = 0.0 (0 / 0) 273 37.62 7.39 2.92 chr2ptel1M 947946 948175 (51825) C L2c_3end#LINE/L2 (1) 477 238 m_b80s601i21 2943 chr2ptel1M 947946 TTTGATCAGACAACAAGGATTTGTTGCATGGAGCCCCACTGGGAACCGTG 947995 iiv vv iv i vii ---- i iv vi iv C L2c_3end#LINE 477 TTCATTCATTCAACAAACATTTATTGAGCG----CCTACTATGTGCCAGG 432 chr2ptel1M 947996 TTCTGCCCCGAATATGCAGA---AGAAGAC-CAGTCCC--CCCTCGGGGA 948039 iv v--- i iiv --- v - i -- ii C L2c_3end#LINE 431 CGCTGG---GGATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGA 385 chr2ptel1M 948040 GCTCATGTTTTAGT--AGGAGCCACACACATATAGAGGGAGACACAGACC 948087 iiv i -- v v ?i v v iv ivi ivv C L2c_3end#LINE 384 GCTCACAGTCTAGTGGAGGAGACAGACANGTAAACAGACAATTACAATAC 335 chr2ptel1M 948088 AGATAGACGCAAGGCACTCTGGGAGGGGCA-GCACTAGCTATTGTGGG-- 948134 ii vi i vv i ii v iivi i i -iv vi v ii i -- C L2c_3end#LINE 334 AAGTTAATGATAAGTGCTATAATGGGAGTATAGACAGGGTGCTATGGGAG 285 chr2ptel1M 948135 --CAGATGAAGGCGTCCAG--TA--CGTGGGATCTCAGGAAAAGTCT 948175 -- v i ii i -- -- v ivv i i ii C L2c_3end#LINE 284 CACAGAGGAGGGCACCTAGACTAGNCTTGGGGGGTCAGGGAAGGCTT 238 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 52.65 CpG sites = 51, Kimura (unadjusted) = 55.66 Transitions / transversions = 1.55 (51/33) Gap_init rate = 0.07 (16 / 229), avg. gap size = 1.50 (24 / 16) 218 29.11 2.02 9.78 chr2ptel1M 948173 948271 (51729) C L3#LINE/CR1 (779) 3320 3229 m_b80s601i22 2944 chr2ptel1M 948173 TCTTGGCGTTCTCGCTGCCCA--GTTTCATCTTTGATTTAGCCGAGATCT 948220 vi v i -- -- i v i ------- i ? C L3#LINE/CR1 3320 TCTTGTTGGTTTCG--GCCCATCGTTCCAGCCT-------GTCGAGATCN 3280 chr2ptel1M 948221 TCTTGGGTTGTGATTTTATCATTCAACACGTCAGCTCCTCTTTCCAGCAT 948270 i ii iv i i i ? iii i vii i i v C L3#LINE/CR1 3279 TTTTGAATCTTGATTCTGTCATCCANCGTATTAGCTATCCCTCCCAGCTT 3230 chr2ptel1M 948271 T 948271 C L3#LINE/CR1 3229 T 3229 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.55 CpG sites = 20, Kimura (unadjusted) = 40.65 Transitions / transversions = 3.33 (20/6) Gap_init rate = 0.10 (10 / 98), avg. gap size = 1.10 (11 / 10) 392 25.23 3.20 4.88 chr2ptel1M 948417 948541 (51459) C L3#LINE/CR1 (1111) 2988 2866 m_b80s601i23 2944 chr2ptel1M 948417 TGAGAGACTTTGCCGGATGATTTGCTAAAATCTCAG---CAACTTATCT- 948462 i ii vi i - --- vi? i - C L3#LINE/CR1 2988 TGAGAGACTTTGTCAAATGCCTTGCTGAAATC-CAGATACACTNTGTCTA 2940 chr2ptel1M 948463 CGCCGTTTCTCTGATCTAGCAGGCTTCCGACCTTGTTAAAATTGAAAAGA 948512 v i i i v v vvii i i i ---- i C L3#LINE/CR1 2939 CGGCATTCCCCTGATCTACCAGTCTAGTAACCCTATCAAA----AAAGGA 2894 chr2ptel1M 948513 AAGGTGCTCAGATTGGCACGATCTTGCTC 948541 v v v i v i - i C L3#LINE/CR1 2893 AATGAGGTTAGTTTGGCATGA-CTTGTTC 2866 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.99 CpG sites = 19, Kimura (unadjusted) = 31.99 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.06 (8 / 124), avg. gap size = 1.25 (10 / 8) 270 36.77 3.23 0.00 chr2ptel1M 948596 948750 (51250) C Plat_L3#LINE/CR1 (1299) 2274 2115 m_b80s551i5 2945 chr2ptel1M 948596 GTTTACTAAAGTGCTCTAGCAGCTAGCTGGGAATGGAAATGAAGCTGATT 948645 iv i vv i i v vv ii v v vi v ii C Plat_L3#LINE/ 2274 GTTTGATGATTTGTTCTAGTATCTTCCCAGGTATCGATGTTAAGCTGACC 2225 chr2ptel1M 948646 GACCCGGCACTTCCAGACTC-TGCTCTTCCCCGTTTGGGAAACTGAG-GT 948693 ii i vv i v iv - v i i v vvi iv i -ii C Plat_L3#LINE/ 2224 GGTCTGTAATTACCAGGGTCGTCCTTTTTCCCTTTTTTAAAGATGGGCAC 2175 chr2ptel1M 948694 GGCCCCTGCCCTTTCCCAGGCCTTTGAGACATCT---GTCCTCCAGGAGC 948740 ii vii i iv iv i v --- iv i C Plat_L3#LINE/ 2174 AACGTTTGCCCTTTTCCAATCCTCAGGGACTTCTCCCGTCCTCCGCGAGT 2125 chr2ptel1M 948741 TTTCAAAGAT 948750 i i C Plat_L3#LINE/ 2124 TCTCAAAAAT 2115 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 50.02 CpG sites = 33, Kimura (unadjusted) = 52.72 Transitions / transversions = 1.38 (33/24) Gap_init rate = 0.02 (3 / 154), avg. gap size = 1.67 (5 / 3) 27 29.74 3.28 6.78 chr2ptel1M 948753 948935 (51065) (TTCCCC)n#Simple_repeat 1 177 (0) m_b80s252i8 2946 chr2ptel1M 948753 TTCTCCCTCCCCCACTTTTCC-TCTCCTCTCCCTTCCCCTCTCTCTTCCC 948801 - -i - ii - i ii ii i (TTCCCC)n#Sim 1 TTC-CCCT-TCCC-CTTCCCCTTCCCCTTCCCCTTCCCCTTCCCCTTCCC 47 chr2ptel1M 948802 CTCTCCCATTCCTC-T-CTCTT-CTCTTCCCCTTTCTTTTCCCTCCTTCA 948848 - v i - - i - i i ii - - v (TTCCCC)n#Sim 48 CT-TCCCCTTCCCCTTCCCCTTCCCCTTCCCCTTCCCCTT-CC-CCTTCC 94 chr2ptel1M 948849 TTTTCTTCCTT--CCTTCCCTTTCTTTCATTCTCCCTTCTTCTTCTTCTT 948896 ii -i -- i --i v - ii ii (TTCCCC)n#Sim 95 CCTTC-CCCTTCCCCTTCCCCTTC--CCCTTC-CCCTTCCCCTTCCCCTT 140 chr2ptel1M 948897 CTTCCTCCTCCTCCTCCTCCTCCTCCCTCTGTCCCTTTC 948935 -i i i i i i i i i - i (TTCCCC)n#Sim 141 C-CCCTTCCCCTTCCCCTTCCCCTTCCCCT-TCCCCTTC 177 Matrix = Unknown Transitions / transversions = 11.33 (34/3) Gap_init rate = 0.09 (17 / 182), avg. gap size = 1.06 (18 / 17) 30 24.45 3.29 7.53 chr2ptel1M 948810 948961 (51039) (TTC)n#Simple_repeat 1 146 (0) m_b80s252i9 2946 chr2ptel1M 948810 TTCCTCTCTCTTC-TCTTCCCCTTTCTT-TTC-CCTCCTTCATTTTCTTC 948856 i - - ii - - -i i v i - (TTC)n#Simple 1 TTCTTCT-TCTTCTTCTTCTTC-TTCTTCTTCTTCTTCTTCTTCTTCTT- 47 chr2ptel1M 948857 CTTCCTTCCCTTTCTTTCATTCTCCCTTCTTCTTCTTCTTCTTCCTCCTC 948906 - iii - - -i - i i (TTC)n#Simple 48 CTT-CTTCTTCTTC-TTC-TTCT-TCTTCTTCTTCTTCTTCTT-CTTCTT 92 chr2ptel1M 948907 CTCCTCCTCCTCCTCCCTCTGTC-CCTTTCTCTTGTCTCTACCTTCCT-T 948954 i i i i i i - -i ii v - -i i - (TTC)n#Simple 93 CTTCTTCTTCTTCTTCTTCT-TCTTCTTCTTCTTCT-TCT-TCTTCTTCT 139 chr2ptel1M 948955 TCTCCTT 948961 i (TTC)n#Simple 140 TCTTCTT 146 Matrix = Unknown Transitions / transversions = 12.00 (24/2) Gap_init rate = 0.11 (16 / 151), avg. gap size = 1.00 (16 / 16) 416 22.01 6.36 0.86 chr2ptel1M 949155 949264 (50736) C MIRc#SINE/MIR (39) 229 114 m_b80s601i24 2947 chr2ptel1M 949155 TTTTCAGACTGCTTTTACACAC-----CTTATTTGAGCCTCCCAAACCAC 949199 v i vi i i ----- i v v - v C MIRc#SINE/MIR 229 TTTACAAAGCGCTTTCACATACATTATCTCATTTGATCCTCACAA-CAAC 181 chr2ptel1M 949200 TGTGTGAAGGAGGCACCAGAGGCCTTATTATACCCATTTTCCAGATGAGG 949249 iv i v vviv iv v v C MIRc#SINE/MIR 180 CCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGG 131 chr2ptel1M 949250 AATCTGA--CTCCGAGA 949264 v -- v C MIRc#SINE/MIR 130 AAACTGAGGCTCAGAGA 114 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 24.91 CpG sites = 9, Kimura (unadjusted) = 26.08 Transitions / transversions = 0.60 (9/15) Gap_init rate = 0.03 (3 / 109), avg. gap size = 2.67 (8 / 3) 206 32.48 2.50 3.80 chr2ptel1M 949660 949739 (50261) MIRc#SINE/MIR 4 82 (186) m_b80s601i25 2948 chr2ptel1M 949660 GGCTCTGAGGGGCACTGTCAGGAAGACCACTGCGCCCGGGCTCCAGAGAG 949709 vv v v v --- i v vi ii iv vi iii MIRc#SINE/MIR 4 GGCAGTGTGGTGCAGTG---GAAAGAGCACTGGACTTGGAGTCAGGAAGA 50 chr2ptel1M 949710 C--AGATTCGAATCCCAGTTTTGCCGCTTACT 949739 --i i i i i i i MIRc#SINE/MIR 51 CCTGGGTTCGAGTCCCGGCTCTGCCACTTACT 82 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.23 CpG sites = 16, Kimura (unadjusted) = 44.67 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.05 (4 / 79), avg. gap size = 1.25 (5 / 4) 15 16.48 0.00 2.86 chr2ptel1M 951643 951678 (48322) (GGCG)n#Simple_repeat 1 35 (0) m_b80s252i10 2949 chr2ptel1M 951643 GGCTGGGGAGGCTGGCGGGTGGGCGGGCAGGCGGGC 951678 - vi v i i (GGCG)n#Simpl 1 GGC-GGGCGGGCGGGCGGGCGGGCGGGCGGGCGGGC 35 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) 184 30.47 6.67 8.11 chr2ptel1M 952376 952525 (47475) MIRb#SINE/MIR 4 151 (117) m_b80s601i26 2950 chr2ptel1M 952376 AGGGGCCCCATGGCACTTAGTGGCCAACCCAAAGGCCT---AGCCTGCCA 952422 vv i ii -- vv ivv vi i --- i v -- MIRb#SINE/MIR 4 AGGGGCAGCGTGGTGC--AGTGGAAAGAGCACGGGCTTTGGAGTCAG--A 49 chr2ptel1M 952423 CAGGCCTGGCCTCG--CCCCTAAAGGGGCCCTGAATCACTTCTGAGCTGT 952470 i vi --i ------ i --i viv MIRb#SINE/MIR 50 CAGACCTGGGTTCGAATCCC------GGCTCTG--CCACTTACTAGCTGT 91 chr2ptel1M 952471 GTGACTCTAAGCCAAC--CTCTGCCCCCCGAAG--TCAGTGCCCTCCTCA 952516 ii ii v ii-- ivi i i vi -- vi v v MIRb#SINE/MIR 92 GTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCT 141 chr2ptel1M 952517 GT-AAATGGG 952525 - MIRb#SINE/MIR 142 GTAAAATGGG 151 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.83 CpG sites = 25, Kimura (unadjusted) = 40.30 Transitions / transversions = 1.47 (25/17) Gap_init rate = 0.11 (17 / 149), avg. gap size = 1.29 (22 / 17) 199 34.67 6.00 1.92 chr2ptel1M 952447 952546 (47454) MIRc#SINE/MIR 67 170 (98) m_b80s601i27 2950 chr2ptel1M 952447 GGCCCTGAATCACTTCTGAGCTGTGTGACTCTAAGCCAACCTCT--GCCC 952494 i --i viv ii ii v ii v --i i MIRc#SINE/MIR 67 GGCTCTG--CCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCT 114 chr2ptel1M 952495 CCCGAAG--TCAGTGCCCTCCTCAGTAAAT--GGGATGACTGTCCCCAAT 952540 i vi -- vi v v v-- i ivi v iivi MIRc#SINE/MIR 115 CTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCC 164 chr2ptel1M 952541 CTGTTT 952546 ii MIRc#SINE/MIR 165 CTGCCT 170 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 49.39 CpG sites = 22, Kimura (unadjusted) = 49.39 Transitions / transversions = 1.83 (22/12) Gap_init rate = 0.05 (5 / 99), avg. gap size = 1.60 (8 / 5) 16 12.38 0.00 5.41 chr2ptel1M 954163 954201 (45799) (CCCTCCC)n#Simple_repeat 1 37 (0) m_b80s252i11 2951 chr2ptel1M 954163 CCCTCCAACCTCCCACCCTCCCTCCTCTCCCCCTTCCCC 954201 vv - i - i (CCCTCCC)n#Si 1 CCCTCCCCCCTCCC-CCCTCCCCCCTC-CCCCCTCCCCC 37 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2) 15 15.05 6.52 2.08 chr2ptel1M 954561 954606 (45394) (GCCCA)n#Simple_repeat 1 48 (0) m_b80s252i12 2952 chr2ptel1M 954561 GCCCAGGCCAGCCACTGCCCAGGCCAG-TC-GCCCA-CCCACGCCAGCC 954606 v - v v -i - - vv (GCCCA)n#Simp 1 GCCCAGCCCAGCC-CAGCCCAGCCCAGCCCAGCCCAGCCCAGCCCAGCC 48 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.09 (4 / 45), avg. gap size = 1.00 (4 / 4) 15 13.69 3.12 0.00 chr2ptel1M 955227 955258 (44742) (GGGA)n#Simple_repeat 1 33 (0) m_b80s252i13 2953 chr2ptel1M 955227 GGGA-GGTGGGCGGGAGAGAGGGAGGGAGGCAG 955258 - v v i v (GGGA)n#Simpl 1 GGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAG 33 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 34 11.79 0.00 0.00 chr2ptel1M 955319 955373 (44627) (TGTG)n#Simple_repeat 1 55 (0) m_b80s252i14 2954 chr2ptel1M 955319 TGTGTGTGTGCATGTGAGTGAGTGTGTGTGTGTGAGTGAGTGTGTGTGTG 955368 ii v v v v (TGTG)n#Simpl 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr2ptel1M 955369 TGTGT 955373 (TGTG)n#Simpl 51 TGTGT 55 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 36 17.34 11.54 1.75 chr2ptel1M 955875 956030 (43970) (CAGGGG)n#Simple_repeat 1 171 (0) m_b80s252i15 2955 chr2ptel1M 955875 CAGAGGGAGGGGTAGGGGCA--GG-AGGGGCA-GGG--GGGGCAGAGGGA 955918 i v i -- - - -- i v (CAGGGG)n#Sim 1 CAGGGGCAGGGGCAGGGGCAGGGGCAGGGGCAGGGGCAGGGGCAGGGGCA 50 chr2ptel1M 955919 GGGGCAGGGAGAAAGGGCACAGGCA-GAG--GGGGCAGGGGCA--GG-AG 955962 - v i vi - i -- -- - (CAGGGG)n#Sim 51 GGGGCAGGG-GCAGGGGCAGGGGCAGGGGCAGGGGCAGGGGCAGGGGCAG 99 chr2ptel1M 955963 GGGCA-GGG--GGGACAGAGAGAAATGTCACAGGCA-GAG--GGGGCAGG 956006 - -- i - i v iv v vi - i -- (CAGGGG)n#Sim 100 GGGCAGGGGCAGGGGCAG-GGGCAGGGGCAGGGGCAGGGGCAGGGGCAGG 148 chr2ptel1M 956007 GGCAGGGACAGAAAGCAGGAGCAG 956030 i -ii i (CAGGGG)n#Sim 149 GGCAGGGGCAG-GGGCAGGGGCAG 171 Matrix = Unknown Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.10 (15 / 155), avg. gap size = 1.40 (21 / 15) 17 19.95 4.21 8.79 chr2ptel1M 956377 956471 (43529) (AGCCCG)n#Simple_repeat 1 91 (0) m_b80s252i16 2956 chr2ptel1M 956377 AGCCCAGGCCTGAGCCC-A-CTGGCGCCAGAGGCCCAGGTAGGCTGGGCC 956424 ii i - - iv v v - -- - v i i (AGCCCG)n#Sim 1 AGCCCGAGCCCGAGCCCGAGCCCGAGCCCGA-GCCC--G-AGCCCGAGCC 46 chr2ptel1M 956425 CGAGCCC-A-CCAATGCCAGAGCCCCGGGTAGCCCGAGCCCGAGCCCGA 956471 - - viv v - -- - (AGCCCG)n#Sim 47 CGAGCCCGAGCCCGAGCCCGAG-CCC--G-AGCCCGAGCCCGAGCCCGA 91 Matrix = Unknown Transitions / transversions = 1.00 (7/7) Gap_init rate = 0.13 (12 / 94), avg. gap size = 1.00 (12 / 12) 273 29.41 2.86 2.86 chr2ptel1M 957814 957918 (42082) L3#LINE/CR1 3339 3443 (656) m_b80s601i28 2957 chr2ptel1M 957814 AATATAAAGGCTTGCACTTGGGTTCAAACAATCAATGGCCCAGTCACCCA 957863 i v i i i v iv v ivi -- L3#LINE/CR1 3339 AATGTAAAGTCCTGCATTTAGGTTCAAAAAATCAACTGCACAAGTA--CA 3386 chr2ptel1M 957864 GGACACGGGGGCTCC--CTTAGAAAGA-TCCAAGAGGAAAAGATCTGAGA 957910 iivi i v i-- v iv - i v v i i - i L3#LINE/CR1 3387 GGATGGAGAGGATCTGGCTTAGCAGCAGTTCACGTGAAAAAGACCT-AGG 3435 chr2ptel1M 957911 GGGTTGAG 957918 v v L3#LINE/CR1 3436 GGTTTTAG 3443 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.24 CpG sites = 17, Kimura (unadjusted) = 38.24 Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.05 (5 / 104), avg. gap size = 1.20 (6 / 5) 510 22.65 3.82 2.26 chr2ptel1M 959530 959660 (40340) C MIR3#SINE/MIR (28) 180 48 m_b80s601i29 2958 chr2ptel1M 959530 TGGCAAAGATCTTTCGGGGGATGGCCTTCTCCAGC----TCATTTTACAG 959575 v ii i ---i i vii vv i ---- C MIR3#SINE/MIR 180 TGGAAGGGACCTT---AGAGATCATCTAGTCCAACCCCCTCATTTTACAG 134 chr2ptel1M 959576 ATGAAGAAACTGAGGCAATTAG-GGTAAAGTGACTTGCCCAAGGTCACAC 959624 i vvvv - i C MIR3#SINE/MIR 133 ATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACAC 84 chr2ptel1M 959625 AGCCAGTCCATGTCTGAGGCCAGATTTGAACTCAGG 959660 ? ivi v v v vi i v i C MIR3#SINE/MIR 83 AGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGG 48 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.49 CpG sites = 15, Kimura (unadjusted) = 27.49 Transitions / transversions = 1.07 (15/14) Gap_init rate = 0.04 (5 / 130), avg. gap size = 1.60 (8 / 5) 315 29.91 3.02 12.64 chr2ptel1M 959671 959869 (40131) L2c_3end#LINE/L2 291 472 (6) m_b80s601i30 2959 chr2ptel1M 959671 TGGCATTCTGTGAGCTCTGGCGCCCATTCTGCTGCTAATTATGTCCTATT 959720 i ii --- v i- v v ivii v i ---iv i L2c_3end#LINE 291 TAGCACCCTGT---CTATA-CTCCCATTATAGCACTTATCAT---TAACT 333 chr2ptel1M 959721 TATCCCGTATCTAGTTTGGTTTGTGTGTTTGTTTGC---ATTAG--TGTA 959765 i vii vi - i - ii? i i v --- i -- i L2c_3end#LINE 334 TGTATTGTAATT-GTCTG-TTTACNTGTCTGTCTCCTCCACTAGACTGTG 381 chr2ptel1M 959766 AACTCCTTGAGGGCCAGGGCC-TGTCTTCTGCCTCTTTTTGTACCTCTAG 959814 i vi i - v v v -- i i i L2c_3end#LINE 382 AGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTT--GTATCCCCAG 429 chr2ptel1M 959815 CACTTAGCTCAGGGTCTGGCACACAGTAAGACCTTAATAAGCGTGTACTG 959864 i ------------ i i vv i ii v ii L2c_3end#LINE 430 CGC------------CTGGCACATAGTAGGCGCTCAATAAATGTTTGTTG 467 chr2ptel1M 959865 ATTGA 959869 v L2c_3end#LINE 468 AATGA 472 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.76 CpG sites = 35, Kimura (unadjusted) = 39.77 Transitions / transversions = 2.06 (35/17) Gap_init rate = 0.13 (26 / 198), avg. gap size = 1.12 (29 / 26) 405 27.29 8.43 2.86 chr2ptel1M 959702 959867 (40133) L2d2_3end#LINE/L2 373 547 (8) m_b80s601i31 2959 chr2ptel1M 959702 CTGCTAATTATGTCCTAT-TTATCCCGTATCTAGTTTG------GTTTGT 959744 i v vi i i - i ---- i ii v------ i L2d2_3end#LIN 373 CTGTTATTTAAATCTTGTATTGT----TATTTAACTTTTCACGTGTTTAT 418 chr2ptel1M 959745 GTGTTTGTTTGC---ATTAG--TGTAAACTCCTTGAGGGCCAGGGCC-TG 959788 -i i v --- i -- i vi i - L2d2_3end#LIN 419 GT-CTTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATG 467 chr2ptel1M 959789 TCTTCTGCCTCTTTTTGTACCTC-TAGCACTTAGCTCAGGGTCTGGCACA 959837 v i i v i v i -i i i v v i v L2d2_3end#LIN 468 TCTTATACTTCTTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCACA 517 chr2ptel1M 959838 CAGTAAGACCTTAATAAGCGTGTACTGATT 959867 i vv i iii v ii L2d2_3end#LIN 518 CAGTAGGCGCTCAATAAATATTTGTTGATT 547 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.53 CpG sites = 30, Kimura (unadjusted) = 35.55 Transitions / transversions = 2.14 (30/14) Gap_init rate = 0.07 (11 / 165), avg. gap size = 1.73 (19 / 11) 196 31.23 10.00 3.94 chr2ptel1M 960676 960795 (39205) L2c_3end#LINE/L2 351 477 (1) m_b80s601i32 2960 chr2ptel1M 960676 TTCTCGTGTC---CTGCCCGGCCAGCCCCTGAGCTCCCCGAAGTCCAGAG 960722 iv ? --- v i vi i v iv ii i v - i L2c_3end#LINE 351 TTTACNTGTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGC-AGGG 399 chr2ptel1M 960723 CCTGCCTTTTAGCTACACTCAGTCAGATTCTCTGCTCATGA-----AGTA 960767 v i iv i vii i- iv --- i i v v v i----- L2c_3end#LINE 400 ACCGTGTCTTATTCAT-CTTTGT---ATCCCCAGCGCCTGGCACATAGTA 445 chr2ptel1M 960768 GGCGCTTAATAGA----TGCTGAATGAATCAA 960795 i i ---- i v L2c_3end#LINE 446 GGCGCTCAATAAATGTTTGTTGAATGAATGAA 477 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.01 CpG sites = 22, Kimura (unadjusted) = 42.59 Transitions / transversions = 1.57 (22/14) Gap_init rate = 0.07 (8 / 119), avg. gap size = 2.12 (17 / 8) 354 27.12 7.63 0.00 chr2ptel1M 961190 961307 (38693) MER63D#DNA/hAT-Tip100 337 463 (598) m_b80s502i1 2961 chr2ptel1M 961190 TGGGAACATTTATCCTTC--AAATCAGCAAATGCTACAAATCAGAAGTCG 961237 ii iv iv -- i i iiv i MER63D#DNA/hA 337 TGGGAGTATTTACACCACGGAAATCGGCAAACGCTACAAATCAGGGCTTG 386 chr2ptel1M 961238 CTTT---GTTCTGCTGGTCACCGTGACTTAAG----TGGTGGAGAAAGTA 961280 v --- i i i iii vv ---- i i i MER63D#DNA/hA 387 ATTTATTGTTTTGTTGATTGTCTAGACTTAAGAAAGTGATGGAGAAAATG 436 chr2ptel1M 961281 TTCCTAGGAAAGATTAAACTTGAAAAT 961307 vv iviv i i MER63D#DNA/hA 437 TTAATAATGCAGATTAAACTTAAAAGT 463 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 32.50 CpG sites = 22, Kimura (unadjusted) = 35.23 Transitions / transversions = 2.20 (22/10) Gap_init rate = 0.03 (3 / 117), avg. gap size = 3.00 (9 / 3) 257 31.18 2.15 0.00 chr2ptel1M 961459 961551 (38449) C L3#LINE/CR1 (84) 4015 3921 m_b80s601i33 2962 chr2ptel1M 961459 CAACATCGCTGAAAAGTGGGTGTGTAGCCTGTGCCAGAAGGCCCCCAA-G 961507 v v vii vi v iv vi i i- C L3#LINE/CR1 4015 CAACATCCCTGACAAGTGGTCATCCAGCCTCTGCTTGAACACCTCCAGTG 3966 chr2ptel1M 961508 AAAGGAGGCCCACTGCCTCTGGGTGCAGGCC-CTCAACTTCAGGA 961551 vi ii i i ?v iv v -i v i iv C L3#LINE/CR1 3965 ACGGGGAGCTCACTACCTCNCGAGGCAGCCCATTCCATTTTTGGA 3921 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.01 CpG sites = 16, Kimura (unadjusted) = 41.89 Transitions / transversions = 1.23 (16/13) Gap_init rate = 0.02 (2 / 92), avg. gap size = 1.00 (2 / 2) 220 33.97 2.33 6.45 chr2ptel1M 961656 961784 (38216) C L3#LINE/CR1 (373) 3726 3603 m_b80s601i34 2962 chr2ptel1M 961656 ATCCTCACCTCCCCC--CTGCCCCCCACAGGATGAGCCCTTTCTGGTCCT 961703 i vi ii -- i ii i i v iiv v-- ii v i C L3#LINE/CR1 3726 ATCCCCAGTTCCTTCAACCGTTCCTCATATGACATGG--TTTCCAGACCC 3679 chr2ptel1M 961704 TTAATAAGCTGGGCTGGGCTTGATCTCCCACGGACACTTTCTCGTCTGTC 961753 v iv v ---- -- i v ivi i vi iv i C L3#LINE/CR1 3678 TTCACCATC----CTGG--TCGCTCTCCTCTGGACGCGCTCCAGTTTGTC 3635 chr2ptel1M 961754 AATGTCCTACTTAAATCATGGC-TTCAGAACT 961784 iv vii -ii C L3#LINE/CR1 3634 AATGTCCCTCTTAAAATGTGGCGCCCAGAACT 3603 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.00 CpG sites = 27, Kimura (unadjusted) = 47.85 Transitions / transversions = 1.93 (27/14) Gap_init rate = 0.08 (10 / 128), avg. gap size = 1.10 (11 / 10) 238 31.91 13.18 2.82 chr2ptel1M 962209 962337 (37663) C L3#LINE/CR1 (11) 4088 3947 m_b81s601i2 2963 chr2ptel1M 962209 AGAATCTCA-TGCTAGAAGATTCCTCGGAGACCCTC--------CCTCCA 962249 -v i i ivv ii ii v -------- v C L3#LINE/CR1 4088 AGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCAACCTCCC 4039 chr2ptel1M 962250 TTACGCACACAAGCGTTCCCTCTGTCA--------ATAAGTGCTTATTAC 962291 v v i- ii i vi i i iiv -------- i v i iv- C L3#LINE/CR1 4038 ATCCA-ATGCAGGAATCCCTTCTACAACATCCCTGACAAGTGGTCATCC- 3991 chr2ptel1M 962292 GGAGTCTCTGCTTGAATGCCCCCACTGATGGGTAACTCATTACCCC 962337 -- i ii i v i v i i i C L3#LINE/CR1 3990 --AGCCTCTGCTTGAACACCTCCAGTGACGGGGAGCTCACTACCTC 3947 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.70 CpG sites = 27, Kimura (unadjusted) = 44.22 Transitions / transversions = 2.08 (27/13) Gap_init rate = 0.05 (7 / 128), avg. gap size = 3.00 (21 / 7) 194 35.00 9.17 0.00 chr2ptel1M 963513 963632 (36368) MIR3#SINE/MIR 72 202 (6) m_b81s601i3 2964 chr2ptel1M 963513 CACTGACTTGATGGGCAGCCATGGGCACAGCCCTTGCCCTCTCTGGGCCT 963562 i ? v v iii v viv v vv MIR3#SINE/MIR 72 CACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCT 121 chr2ptel1M 963563 C----------TCTGCACAAGGAGTGCCGAGGTCTTGG-GAGCCCCGGAG 963601 ---------- i v v v vvvv v v i- v i iiii MIR3#SINE/MIR 122 CAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGG 171 chr2ptel1M 963602 TCAGTCCTGCCTCAGACACTGAGTGATCCTA 963632 vv i iiv v i vvi i MIR3#SINE/MIR 172 TCCCTTCCAGCTCTGACATTCTATGATTCTA 202 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 47.99 CpG sites = 18, Kimura (unadjusted) = 47.99 Transitions / transversions = 0.75 (18/24) Gap_init rate = 0.02 (2 / 119), avg. gap size = 5.50 (11 / 2) 208 37.11 7.04 1.33 chr2ptel1M 964874 965015 (34985) L3#LINE/CR1 3934 4083 (16) m_b81s601i4 2965 chr2ptel1M 964874 TGGGGCCCCATGGGAGGCACTGAACTCTCTGCCACTGGAAGCCTCCAAAC 964923 viv vi ? i v i i i i i iv i i L3#LINE/CR1 3934 TGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGTCACTGGAGGTGTTCAAGC 3983 chr2ptel1M 964924 CCATGAGCCCCCTGGCCA----TCAGG----CGGCGGAGGACACACTTGT 964965 -- vii ivvv i ---- ----iv ii i iv iv i i L3#LINE/CR1 3984 --AGAGGCTGGATGACCACTTGTCAGGGATGTTGTAGAAGGGATTCCTGC 4031 chr2ptel1M 964966 -TCGGGCGGGCT-TCGGCCTAGGTGCCCGCTTAGATTCCTTCCGGCTTCG 965013 - i ii vv- i v i v v v i i ii ii L3#LINE/CR1 4032 ATTGGATGGGAGGTTGGACTAGATGACCTCTAAGGTCCCTTCCAACTCTG 4081 chr2ptel1M 965014 AG 965015 L3#LINE/CR1 4082 AG 4083 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 52.42 CpG sites = 34, Kimura (unadjusted) = 55.70 Transitions / transversions = 1.89 (34/18) Gap_init rate = 0.04 (6 / 141), avg. gap size = 2.00 (12 / 6) 42 21.45 1.83 1.83 chr2ptel1M 966425 966533 (33467) (GAGG)n#Simple_repeat 1 109 (0) m_b81s252i0 2966 chr2ptel1M 966425 GAGGGA-GGTGGGAAGGAGGGAGAGAGGGTGGGA-GAAGGGAGGGAAAAA 966472 - v i i v - i iii (GAGG)n#Simpl 1 GAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGA 50 chr2ptel1M 966473 GGAAGGAAGGGAGGGCAAGAGGGAGGGAGAAAGACAGAGGGAGAAAGGGA 966522 i i vii --i vi ii (GAGG)n#Simpl 51 GGGAGGGAGGGAGGGAGGGAGGGAGGGAG--GGAGGGAGGGAGGGAGGGA 98 chr2ptel1M 966523 GGAAGGGAGGG 966533 i (GAGG)n#Simpl 99 GGGAGGGAGGG 109 Matrix = Unknown Transitions / transversions = 3.75 (15/4) Gap_init rate = 0.04 (4 / 108), avg. gap size = 1.00 (4 / 4) 15 16.74 5.00 0.00 chr2ptel1M 966660 966699 (33301) (GGAG)n#Simple_repeat 1 42 (0) m_b81s252i1 2967 chr2ptel1M 966660 GGAGGGAGGGAGGGAGCTAGCAAGGGA-GTAGGG-GAGAGGG 966699 vv vi - v - i (GGAG)n#Simpl 1 GGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGG 42 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 100 6.50 0.00 1.53 chr2ptel1M 967901 968033 (31967) (CCTTC)n#Simple_repeat 1 131 (0) c_b81s251i0 2968 chr2ptel1M 967901 CCTTCCCTTCCCTTCCCTTTCCTTGCCTTTCCTTTCCTTCCCTTCCCCTT 967950 i v i i - - (CCTTC)n#Simp 1 CCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTT-CCC-T 48 chr2ptel1M 967951 TCCCTTCCCTTCCCTTCCCTTCCCTTCCTTTCCCTTCCCTTCCCTTCCCT 968000 i (CCTTC)n#Simp 49 TCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCT 98 chr2ptel1M 968001 TCCCTTCCCCTGCCTTCCCTTCCCTTGCCTTCC 968033 i v v (CCTTC)n#Simp 99 TCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCC 131 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.02 (2 / 132), avg. gap size = 1.00 (2 / 2) 17 13.23 0.00 2.94 chr2ptel1M 968084 968118 (31882) (CGG)n#Simple_repeat 1 34 (0) m_b81s252i2 2969 chr2ptel1M 968084 CGGCAGCGAGAGGCGGCAGCGGCGGCGGCGGCTGC 968118 i - v i v (CGG)n#Simple 1 CGGCGGCG-GCGGCGGCGGCGGCGGCGGCGGCGGC 34 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 13 4.70 0.00 4.35 chr2ptel1M 968259 968282 (31718) (CCGG)n#Simple_repeat 1 23 (0) m_b81s252i3 2970 chr2ptel1M 968259 CCGGCCTGGCCGCCCGGCCGGCCG 968282 - v (CCGG)n#Simpl 1 CCGGCC-GGCCGGCCGGCCGGCCG 23 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 14 7.25 6.90 0.00 chr2ptel1M 968346 968374 (31626) (GCGG)n#Simple_repeat 1 31 (0) m_b81s252i4 2971 chr2ptel1M 968346 GCGGGCGGGC--GCGGGCCGGCGGGCGAGCG 968374 -- v i (GCGG)n#Simpl 1 GCGGGCGGGCGGGCGGGCGGGCGGGCGGGCG 31 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 28), avg. gap size = 2.00 (2 / 1) 19 13.42 0.00 4.65 chr2ptel1M 968658 968702 (31298) (AGCCCGG)n#Simple_repeat 1 43 (0) m_b81s252i5 2972 chr2ptel1M 968658 AGCCGGGAGCCCGGAGCCCCGCAGCCCGCAGCCCCGGCGCCCCGA 968702 v - v v - v v (AGCCCGG)n#Si 1 AGCCCGGAGCCCGGAG-CCCGGAGCCCGGAG-CCCGGAGCCCGGA 43 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.05 (2 / 44), avg. gap size = 1.00 (2 / 2) 17 6.54 6.25 0.00 chr2ptel1M 968863 968894 (31106) (GGCCAC)n#Simple_repeat 1 34 (0) m_b81s252i6 2973 chr2ptel1M 968863 GGCCA-GCCCACGGCCGC-GCCACGGCCACGGCC 968894 - v i - (GGCCAC)n#Sim 1 GGCCACGGCCACGGCCACGGCCACGGCCACGGCC 34 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.06 (2 / 31), avg. gap size = 1.00 (2 / 2) 25 35.82 0.00 0.00 chr2ptel1M 969193 969285 (30715) (CA)n#Simple_repeat 1 93 (0) m_b81s252i7 2974 chr2ptel1M 969193 CACACACGCACACACACGTAGACACGCGCGGACGCGGGCACGGACACACA 969242 i ii v i i iv i ivi iv (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 chr2ptel1M 969243 CACAGACACACACCCCGGCACTCGGGCGCGCACACACACTCAC 969285 v v vvi v ivi i i v (CA)n#Simple_ 51 CACACACACACACACACACACACACACACACACACACACACAC 93 Matrix = Unknown Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.00 (0 / 92), avg. gap size = 0.0 (0 / 0) 16 9.26 0.00 0.00 chr2ptel1M 969322 969344 (30656) (GC)n#Simple_repeat 1 23 (0) m_b81s252i8 2975 chr2ptel1M 969322 GCGAGCACGCGCGCGCGCGCGCG 969344 v i (GC)n#Simple_ 1 GCGCGCGCGCGCGCGCGCGCGCG 23 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 40 0.00 0.00 0.00 chr2ptel1M 969348 969381 (30619) (AC)n#Simple_repeat 1 34 (0) c_b81s251i1 2976 chr2ptel1M 969348 ACACACACACACACACACACACACACACACACAC 969381 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACAC 34 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 13 29.48 2.00 0.00 chr2ptel1M 969406 969455 (30545) (CAG)n#Simple_repeat 1 51 (0) m_b81s252i9 2977 chr2ptel1M 969406 CATCATCAGCAGCAGCCGCGGCGGTGGCGGCGGCGGCAGC-GCAGGCGCA 969454 v v v i i ii i i i - vv (CAG)n#Simple 1 CAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA 50 chr2ptel1M 969455 G 969455 (CAG)n#Simple 51 G 51 Matrix = Unknown Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.02 (1 / 49), avg. gap size = 1.00 (1 / 1) 16 20.74 0.00 0.00 chr2ptel1M 969414 969452 (30548) (GCGGCG)n#Simple_repeat 1 39 (0) m_b81s252i10 2978 chr2ptel1M 969414 GCAGCAGCCGCGGCGGTGGCGGCGGCGGCAGCGCAGGCG 969452 i i v i i vv (GCGGCG)n#Sim 1 GCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCG 39 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 21 6.91 0.00 0.00 chr2ptel1M 969557 969587 (30413) (CTC)n#Simple_repeat 1 31 (0) m_b81s252i11 2979 chr2ptel1M 969557 CTCCTCTTCCTCCTCCTCCTCCTCTTCCTCC 969587 i i (CTC)n#Simple 1 CTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC 31 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 14 22.11 2.38 0.00 chr2ptel1M 969721 969762 (30238) (CGGCGG)n#Simple_repeat 1 43 (0) m_b81s252i12 2980 chr2ptel1M 969721 CGG-GGCGGTGGCGGCGGCAGCGGCAGCCCGGGCAGCGGCCGC 969762 - i i i vvv i v (CGGCGG)n#Sim 1 CGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC 43 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.02 (1 / 41), avg. gap size = 1.00 (1 / 1) 15 31.98 1.41 1.41 chr2ptel1M 970378 970448 (29552) (CCGCCA)n#Simple_repeat 1 71 (0) m_b81s252i13 2981 chr2ptel1M 970378 CCGTCACCGCCGCCGCCAGCGCCTCCCCCACCTGCTCCCTCC-CCTCCTC 970426 i i v v v - iv v - v v (CCGCCA)n#Sim 1 CCGCCACCGCCACCGCCACCGCCACCGCCACC-GCCACCGCCACCGCCAC 49 chr2ptel1M 970427 TGCTCCCCCCTCCTCCTCCCCC 970448 i iv v v v v v (CCGCCA)n#Sim 50 CGCCACCGCCACCGCCACCGCC 71 Matrix = Unknown Transitions / transversions = 0.38 (5/13) Gap_init rate = 0.03 (2 / 70), avg. gap size = 1.00 (2 / 2) 126 15.64 3.30 2.17 chr2ptel1M 970399 970671 (29329) (CCT)n#Simple_repeat 1 276 (0) m_b81s252i14 2981 chr2ptel1M 970399 CCTCCCCCACCTGCTCCCTCC-CCTCCT-CTGCTCC-CC-CCTCCTCCTC 970444 i v v - - - v - - (CCT)n#Simple 1 CCTCCTCCTCCTCCT-CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC 49 chr2ptel1M 970445 CCCCTTTTCCTTCTCCTCCTCCTCCTTCTCCTCCCCCT-TTTCTCCTCCT 970493 i ii i i i -i i (CCT)n#Simple 50 CTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT 99 chr2ptel1M 970494 CC-CCTCTTGCTCCTCCTCCTCCTCCTTCTCCTCCTCCCCTTTTTCCACC 970542 - i v i i i ii v (CCT)n#Simple 100 CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC 149 chr2ptel1M 970543 TCCTCC-CCTCCTCCTCCTCTTCCCTCTTCTCCCTCCTCTCCCTTCTTC- 970590 - i - i ii ii i i - (CCT)n#Simple 150 TCCTCCTCCTCCTCCTCCTCCT-CCTCCTCCTCCTCCTCCTCCTCCTCCT 198 chr2ptel1M 970591 CCTCCTCCTCCTCCTCCTTCTCTCTCCCTCCCTCCTCCTTGTCACCTTCC 970640 i - - - iv vi i (CCT)n#Simple 199 CCTCCTCCTCCTCCTCCTCCTC-CT-CCT-CCTCCTCCTCCTCCTCCTCC 245 chr2ptel1M 970641 TCCTCTTCCTCCTCC-CCTCTTCCTCCTTCCT 970671 i - i - (CCT)n#Simple 246 TCCTCCTCCTCCTCCTCCTCCTCCTCC-TCCT 276 Matrix = Unknown Transitions / transversions = 4.14 (29/7) Gap_init rate = 0.06 (15 / 272), avg. gap size = 1.00 (15 / 15) 14 4.35 4.17 0.00 chr2ptel1M 971347 971370 (28630) (GGGA)n#Simple_repeat 1 25 (0) m_b81s252i16 2982 chr2ptel1M 971347 GGGAGAG-GGGAGGGAGGGAGGGAG 971370 i - (GGGA)n#Simpl 1 GGGAGGGAGGGAGGGAGGGAGGGAG 25 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 12 16.21 6.98 2.22 chr2ptel1M 971346 971388 (28612) (GGGGAGAG)n#Simple_repeat 1 45 (0) m_b81s252i15 2983 chr2ptel1M 971346 GGGGAGA-GGGGAG-GGAGG-GAGGGAGATTGGGGGTGACTGGGGA 971388 - - i - i vv v -v (GGGGAGAG)n#S 1 GGGGAGAGGGGGAGAGGGGGAGAGGGGGAGAGGGGGAGA-GGGGGA 45 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.10 (4 / 42), avg. gap size = 1.00 (4 / 4) 203 25.42 3.39 0.00 chr2ptel1M 973948 974006 (25994) C L3#LINE/CR1 (178) 3921 3861 m_b81s601i5 2984 chr2ptel1M 973948 ATAGCTTT--TAGTTGGAAAGTTGGTCCTAACATTCAGCCTAAATTTTCC 973995 i i -- v i vv v i v v i v C L3#LINE/CR1 3921 ACAGCTCTGATTGTTAGAAAGTTCTTCCTTATATTGAGCCGAAATCTGCC 3872 chr2ptel1M 973996 TCTTTGGAACT 974006 ii v C L3#LINE/CR1 3871 TCCCTGTAACT 3861 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.24 CpG sites = 7, Kimura (unadjusted) = 31.24 Transitions / transversions = 0.88 (7/8) Gap_init rate = 0.02 (1 / 58), avg. gap size = 2.00 (2 / 1) 218 23.53 3.92 0.00 chr2ptel1M 973948 973998 (26002) C X17_LINE#LINE/CR1 (175) 121 69 m_b81s601i6 2984 chr2ptel1M 973948 ATAGCTTTTA--GTTGGAAAGTTGGTCCTAACATTCAGCCTAAATTTTCC 973995 v i ii-- i i i vv i i C X17_LINE#LINE 121 ATAGATCTCGCTGTTAGGAAATTTTTCCTGATATTCAGCCTAAATTTTCC 72 chr2ptel1M 973996 TCT 973998 i C X17_LINE#LINE 71 TTT 69 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.43 CpG sites = 9, Kimura (unadjusted) = 29.66 Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.02 (1 / 50), avg. gap size = 2.00 (2 / 1) 412 34.22 7.34 1.83 chr2ptel1M 974574 974832 (25168) C L3#LINE/CR1 (209) 3890 3618 m_b81s601i7 2985 chr2ptel1M 974574 TATTGAGAAAAACATTTTCTATTTTTCCACTTCC--CCATTGCTCTTGGC 974621 vvi - i v iviii viv -- v i i i C L3#LINE/CR1 3890 TATTGAGCCGAA-ATCTGCCTCCCTGTAACTTCCACCCATTGGTCCTAGT 3842 chr2ptel1M 974622 CCTGCCCTTTGAGGCCAATC----TGGGACTATACTATACACCATAGAAT 974667 i i ii vv ---- ii v vv iv viv i vi i C L3#LINE/CR1 3841 TCTGCCCTCTGGAGCCACACAGAATAAGTCTAATCCCTCTTCCACATGAC 3792 chr2ptel1M 974668 AATTCTTCACCTCTT---AGTTCCCTTTTATGTTAGCTCTTAGTCGTTTT 974714 iii vv v --- vivv v i ivv v - i C L3#LINE/CR1 3791 AGCCCTTCAAATATTTGAAGACAGCTATCATGTCTCCTCTAAGTC-TTCT 3743 chr2ptel1M 974715 TTTCTCCAAGCTGTACTTCC---------TCAACCCATCCTCACATCATG 974755 i i iv v --------- vv i v ii C L3#LINE/CR1 3742 CTTCTCCAGGCTAAACATCCCCAGTTCCTTCAACCGTTCCTCATATGACA 3693 chr2ptel1M 974756 TGGACTCCAGAGCCTTTCTTTCTACCTTGGATGCCTTCCTCTGGATACCT 974805 vi v iv--- i i i vi ii ii vi C L3#LINE/CR1 3692 TGGTTTCCAGACCCTTCA---CCATCCTGGTCGCTCTCCTCTGGACGCGC 3646 chr2ptel1M 974806 TCCAGGTTATCAGTGT-CCTTTGAAAGT 974832 v i i - i v i C L3#LINE/CR1 3645 TCCAGTTTGTCAATGTCCCTCTTAAAAT 3618 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.90 CpG sites = 49, Kimura (unadjusted) = 47.22 Transitions / transversions = 1.29 (49/38) Gap_init rate = 0.04 (10 / 258), avg. gap size = 2.40 (24 / 10) 407 34.44 2.36 1.40 chr2ptel1M 974842 975053 (24947) C L3#LINE/CR1 (562) 3537 3324 m_b81s601i8 2985 chr2ptel1M 974842 CTGGGAGCTCTACCACTCTCAATGCTTTCCAGTATCCCAGCAGCTCCTTT 974891 ivi v iv v i vvi i iv iv vi ii C L3#LINE/CR1 3537 CTGGACACTATACTTCTATTAATGCAGCCTAAGATTGCATTAGCTTTTTT 3488 chr2ptel1M 974892 GGT-GCCCCATCTCACTGCTT-TTCATTGGGATCTTGCAGTCTATTCAAA 974939 i- v v i v-i vvv v i v i v C L3#LINE/CR1 3487 GGCAGCCACATCACACTGTTGGCTCATATTGAGCTTGCGGTCAACTAAAA 3438 chr2ptel1M 974940 CCCCCAGATCTTTTCCTAGAACAGCCACTATCTAAACTTGTTTC-CTCTG 974988 i i i - vivv i ii i- i iv v i - ii C L3#LINE/CR1 3437 CCCCTAGGTCTTTTTC-ACGTGAACTGCTG-CTAAGCCAGATCCTCTCCA 3390 chr2ptel1M 974989 CCTTGTAATGATGGAGTTGATTTTTGTATACCT-ACTGTGAGACTTGGTG 975037 i i v vi v - iv - v iii viii C L3#LINE/CR1 3389 TCCTGTACTTGTGCAGTTGATTTTT-TGAACCTAAATGCAGGACTTTACA 3341 chr2ptel1M 975038 TTTATTCTT-TTATACT 975053 i i - v i C L3#LINE/CR1 3340 TTTATCCCTGTTAAATT 3324 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.02 CpG sites = 42, Kimura (unadjusted) = 47.88 Transitions / transversions = 1.40 (42/30) Gap_init rate = 0.04 (8 / 211), avg. gap size = 1.00 (8 / 8) 45 8.69 0.00 0.00 chr2ptel1M 975075 975135 (24865) (GT)n#Simple_repeat 1 61 (0) c_b81s251i2 2986 chr2ptel1M 975075 GTGTGTGTGTGTGTGTCTGTGTGTCTGTGTGTGTGTCTGTGTGTCTGTGT 975124 v v v v (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50 chr2ptel1M 975125 GTGTATGTGTG 975135 i (GT)n#Simple_ 51 GTGTGTGTGTG 61 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 242 11.01 4.84 12.07 chr2ptel1M 975136 975186 (24814) C Charlie4a#DNA/hAT-Charlie (22) 486 440 m_b81s502i1 2987 chr2ptel1M 975136 ---ATGGACCCCTTTGACAGGTGACAGTCTGGGGAAGCTTATGGATCCCT 975182 --- i ------- v i i C Charlie4a#DNA 486 GCCATGGACCCCTTTGGCAG-------TCTGGTGAAGCCTATGGACCCCT 444 chr2ptel1M 975183 GCTT 975186 v i C Charlie4a#DNA 443 TCTC 440 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 12.42 CpG sites = 4, Kimura (unadjusted) = 12.42 Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.16 (8 / 50), avg. gap size = 1.25 (10 / 8) 40 0.00 0.00 0.00 chr2ptel1M 975187 975220 (24780) (TG)n#Simple_repeat 1 34 (0) c_b81s251i3 2988 chr2ptel1M 975187 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 975220 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 34 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 1041 34.83 7.61 2.36 chr2ptel1M 975513 976156 (23844) C L3#LINE/CR1 (731) 3368 2692 m_b81s601i9 2985 chr2ptel1M 975513 TTTTTCTATTCAAGTTCACAGACCTCTATAAATTTATC---AATAGACCT 975559 vv iii i --i iv i i -- ---iv i ii C L3#LINE/CR1 3368 TTTTTGAACCTAAAT--GCAGGACTTTACA--TTTATCCCTGTTAAATTT 3323 chr2ptel1M 975560 CATGCATTGTAAGTTAAGTGTGGAATCCACAGTTCTAGCCTATTAGGATC 975609 v-- vi vv ------ii iv i i iii C L3#LINE/CR1 3322 CATC--TTGTTGGTTTCG------GCCCATCGTTCCAGCCTGTCGAGATC 3281 chr2ptel1M 975610 TGCTTGGTTCCCAAATCTGTCCTTCAGCGTGTT--CTCCTCACCCCATTT 975657 ?vi iv iii v v i ? i -- vii vi vi C L3#LINE/CR1 3280 NTTTTGAATCTTGATTCTGTCATCCANCGTATTAGCTATCCCTCCCAGCT 3231 chr2ptel1M 975658 TGGGGTTTTCTGAACATCTAATTAACGTGACAATTTGATCTTTTTCTAAG 975707 v v iv v v i i v i i v vvi vvi iv i C L3#LINE/CR1 3230 TTGTGTCATCTGCAAATTTGATAAGCATGCCTTCTATGTCTTCATCCAAG 3181 chr2ptel1M 975708 TCATTGGTTAAAA-----AAAAAGAC-----TAAGTACAGATCCTCAAGG 975747 i v ----- v i -----i v v iiiv C L3#LINE/CR1 3180 TCATTGATAAAAATGTTGAACAGGACAGGGCCAAGGACAGAGCCCTGTGG 3131 chr2ptel1M 975748 CACTCCACTGGAGACCT---GCCAAGCCAGCATTGGACCATTCATTATTT 975794 v i ---v i iiii i iv v i viv C L3#LINE/CR1 3130 CACGCCACTAGAGACCTCCCTCCAGGTTGACATCGATCCATTAATCAACA 3081 chr2ptel1M 975795 CCCTTTGGATTTAGTCATTCCTCCAGCTTTTAGGCCTTCTATTTGAGCTG 975844 i i v i vv viv iv vi vi vi i C L3#LINE/CR1 3080 CCTTTTGGGTATAGTCGTTCAACCAGCTACGAATCCACCTAACTGTACTA 3031 chr2ptel1M 975845 CTATCCATCCC-TACCCCTTTCTCC--CTTTTCCACAAGAAAAGCTTGAG 975891 ii v - ---- -- v i v v v C L3#LINE/CR1 3030 TCATCCAGCCCATA----TTTCTCCATCTTGTCCACAAGGATATCATGAG 2985 chr2ptel1M 975892 AACCCTTGTCCAGTGAGTTCCTACAATCTAGGTAAATGACATTTAC-CCC 975940 iv i v i vv v iv i i v iv?ii i -v v C L3#LINE/CR1 2984 AGACTTTGTCAAATGCCTTGCTGAAATCCAGATACACTNTGTCTACGGCA 2935 chr2ptel1M 975941 TTTCTCTGAGCAATCAGGTTAAAAACTC-ATCAAGAT---ATACAAGGTC 975986 i i v v i vi iv i - i v--- v ii i C L3#LINE/CR1 2934 TTCCCCTGATCTACCAGTCTAGTAACCCTATCAAAAAAGGAAATGAGGTT 2885 chr2ptel1M 975987 TGTTTAGGA--------------GGAATCCAAGATGGTCCTTCATGAGGA 976022 v i v --------------v i v v ii i vi vv C L3#LINE/CR1 2884 AGTTTGGCATGACTTGTTCTTAGTGAACCCATGCTGGCTCCTAGTGATCA 2835 chr2ptel1M 976023 TCA-TGC--TTTCTGC---CTTGTGAATCCTCTCTCCAATGAACCACTCT 976066 i i- v -- iv--- iiii i v v ii i v ii C L3#LINE/CR1 2834 CCGCTTCCTTTTCTAAGTGCTCACAAACCATCTGTTTAATAATCCGTTCT 2785 chr2ptel1M 976067 AGATTCTTCCCAGGAACCAAAGGCAAGTTCACTGG-CTGGAGTTTGCAAA 976115 v i v i i i i v v i i i - v ? i C L3#LINE/CR1 2784 AGAATTTTGCCGGGGATCGACGTCAAGCTTACCGGTCTGTAGTTTNCAGA 2735 chr2ptel1M 976116 CTCCATTCCTTACCCAGCTTGGAAA--AGGTGCACAATGTGCC 976156 v iii vi vvi vi -- ?i ?vv v C L3#LINE/CR1 2734 ATCCATCTTTTTTCCCTTTTTAAAANTAGGNACNACATTTGCC 2692 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.34 CpG sites = 124, Kimura (unadjusted) = 49.20 Transitions / transversions = 1.31 (124/95) Gap_init rate = 0.05 (32 / 643), avg. gap size = 2.03 (65 / 32) 512 33.33 8.70 0.00 chr2ptel1M 976160 976366 (23634) C L3#LINE/CR1 (3041) 1058 834 m_b81s601i10 2985 chr2ptel1M 976160 AAACGCATTCTTCCCAGACTTTTTTGGGTGTACTCCATCCCTGGCCGGGA 976209 i i i v iv vi i i i ? i C L3#LINE/CR1 1058 AAACACGTTCTTCCCGGTCTTCGTGAGATGCACTCCGTCCCTNGCCAGGA 1009 chr2ptel1M 976210 ATCTGTCATTCCTACATTGTAAACTTTGGTCCAGAAATCTAAATCCTGAT 976259 ii ii i ivii i? i iv v i v C L3#LINE/CR1 1008 GCCCATCGTTCTGGTATCNTAAGCCATGGTCCAGAAAACCAAATCCTGTT 959 chr2ptel1M 976260 CT----CA----------GGCCGGTTG-TCACTTCTCATATGTGTTTTTT 976294 ---- ----------i i i - i vivii i C L3#LINE/CR1 958 CTTCGACACCATCTACGTAGCCAGCTGTTCACTTCCCATATCCTCCTTTC 909 chr2ptel1M 976295 GTTTCT---GTATCCATCTTCAGTGGGCAACAGTGATAAAAAGAGTACTT 976341 vi i--- vv v i iiv v iv v i v vi i C L3#LINE/CR1 908 TCTTCCAAAGTCACGACCTTCAACTGGAAGAAGAGATGAAAACACCACCT 859 chr2ptel1M 976342 TTGTCTTTGTGAGCTCCAGTCTCTT 976366 v i iiiiv vv i i i C L3#LINE/CR1 858 GTGCCCCCAAGTCCTTCAGTTTCCT 834 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.75 CpG sites = 46, Kimura (unadjusted) = 47.51 Transitions / transversions = 2.00 (46/23) Gap_init rate = 0.02 (4 / 206), avg. gap size = 4.50 (18 / 4) 287 31.51 14.12 1.04 chr2ptel1M 976367 976536 (23464) MIRc#SINE/MIR 31 222 (46) m_b81s601i11 2989 chr2ptel1M 976367 TGGACTTAGATTCAGGAAGATATGAGTTCAAATTCAGCTTCAGATA---- 976412 i v iv i i i i v vi v vi ---- MIRc#SINE/MIR 31 TGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTA 80 chr2ptel1M 976413 -TAGCTA---GACT------AAATCACTTTAC--------ACTTTAGTTT 976444 - i--- i------ i v --------i i i MIRc#SINE/MIR 81 CTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTT 130 chr2ptel1M 976445 CCTCATCTGTAAAATGAGCTGCAGAAGGAATGGCCAGCCCCTCTGGTATC 976494 i vvvv v vivv v v ivi vii vv MIRc#SINE/MIR 131 CCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAGG 180 chr2ptel1M 976495 TTTGCCAAGAAGACTCCAAATGAGTTCATGGC--TGAAAGGGCT 976536 v iiiv i --i v v vv-- v MIRc#SINE/MIR 181 GTTGTTGTGAGGA--TCAAATGAGATAATGTATGTGAAAGCGCT 222 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.35 CpG sites = 25, Kimura (unadjusted) = 41.34 Transitions / transversions = 0.89 (25/28) Gap_init rate = 0.05 (8 / 169), avg. gap size = 3.25 (26 / 8) 510 27.63 0.58 11.61 chr2ptel1M 976549 976720 (23280) MIR#SINE/MIR 105 259 (3) m_b81s601i12 2990 chr2ptel1M 976549 TACCCCCGCT-TCCCTCAATGCCTTCATTGGTAACATGGAAATTATGATA 976597 v i v - v i vi i iv v ii v i MIR#SINE/MIR 105 TAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATA 154 chr2ptel1M 976598 GCATCTCTTCCCCCCCCCTTTCCCCCCGCCTAGGGCTGTTGTGAAGACTA 976647 i i v------------------ v v i i i MIR#SINE/MIR 155 GTACCTA------------------CCTCATAGGGTTGTTGTGAGGATTA 186 chr2ptel1M 976648 AATGAAGTCCTAGTTGTAAAGGGTTCAGCACAGTGGCTGGCACACAGTAG 976697 iv vv vv v i i v v i i MIR#SINE/MIR 187 AATGAGTTAATACATGTAAAGCGCTTAGAACAGTGCCTGGCACATAGTAA 236 chr2ptel1M 976698 GTGCTATATAAGTGGTAGCTGTT 976720 i vv i v i MIR#SINE/MIR 237 GCGCTCAATAAATGTTAGCTATT 259 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.29 CpG sites = 21, Kimura (unadjusted) = 34.27 Transitions / transversions = 1.00 (21/21) Gap_init rate = 0.11 (19 / 171), avg. gap size = 1.00 (19 / 19) 215 29.51 0.00 0.00 chr2ptel1M 976667 976727 (23273) L2d2_3end#LINE/L2 493 553 (2) m_b81s601i13 2991 chr2ptel1M 976667 AGGGTTCAGCACAGTGGCTGGCACACAGTAGGTGCTATATAAGTGGTAGC 976716 v iii v v i vv i iv v i L2d2_3end#LIN 493 AGCGCCTAGCACAGTGCCTTGCACACAGTAGGCGCTCAATAAATATTTGT 542 chr2ptel1M 976717 TGTTGGGATCT 976727 v vv i L2d2_3end#LIN 543 TGATTTGATTT 553 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.20 CpG sites = 8, Kimura (unadjusted) = 37.71 Transitions / transversions = 0.80 (8/10) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 184 33.61 5.17 2.52 chr2ptel1M 976734 976849 (23151) C L3#LINE/CR1 (3291) 808 690 m_b81s601i14 2985 chr2ptel1M 976734 ATGCTTTCTGGCTTGCCAC---CTGTGTCATCGGAGCCCAAGTGACTTA- 976779 v ii v v iv --- iv vv v v i - C L3#LINE/CR1 808 ATGCATTCCAGGTTTCTTCTGACTGTGTCATTCGTTCCCACGTGAATCAG 759 chr2ptel1M 976780 TAGAGATGATTTAGGAGTCAGC--TTTTTTTGAGTGTTGATGGGATCTCT 976827 i iii i-v vi i --v vv v iii -- C L3#LINE/CR1 758 CAGGAGTGG-GTAGCGGTCGGCGGGTTTGATGAGTCTTGGCAGG--CTCT 712 chr2ptel1M 976828 CTGGCTCTTCTCAGATATGTGC 976849 i v v v i iii C L3#LINE/CR1 711 CCGTCACGTCTCGGATACACGC 690 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.01 CpG sites = 20, Kimura (unadjusted) = 45.59 Transitions / transversions = 1.11 (20/18) Gap_init rate = 0.05 (6 / 115), avg. gap size = 1.50 (9 / 6) 512 31.73 7.69 0.00 chr2ptel1M 977147 977354 (22646) MIRc#SINE/MIR 37 260 (8) m_b81s601i15 2992 chr2ptel1M 977147 TAGAAACACAAAGAGGCAAATATAAATCCAGCCTCAAACACGTCCTTGCT 977196 i iv vi vviiii vii i v v viv v v v MIRc#SINE/MIR 37 TGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCT 86 chr2ptel1M 977197 -TGTCACCCCTAGCAAGTCATATAACCTTGGTTTGCCTCAGTTCCCTCAA 977245 - v iivi iv ivv vv i v MIRc#SINE/MIR 87 GTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCAT 136 chr2ptel1M 977246 CCCTAAAATGGGAGTGAT-GTA---GCC---CCTCCTTCCCAGAGTGGTT 977288 iv ii i -i --- --- v i v i v MIRc#SINE/MIR 137 CTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTT 186 chr2ptel1M 977289 GTGAGGATCAAGTGAGATGTTATTTATAAATGTGC--------CTGACAA 977330 i iv i v i i v i -------- vv MIRc#SINE/MIR 187 GTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTTTGTAAACTGTAAA 236 chr2ptel1M 977331 GTTCTTGACACATAGAAGGGGCTA 977354 v vv v iv ? i MIRc#SINE/MIR 237 GTGCTATACAAATGTAAGGNGTTA 260 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.31 CpG sites = 32, Kimura (unadjusted) = 42.02 Transitions / transversions = 0.94 (32/34) Gap_init rate = 0.02 (5 / 207), avg. gap size = 3.20 (16 / 5) 626 29.70 1.46 1.46 chr2ptel1M 977171 977375 (22625) MIR#SINE/MIR 57 261 (1) m_b81s601i16 2992 chr2ptel1M 977171 AATCCAGCCTCAAACACGTCCTTGCT-TGTCACCCCTAGCAAGTCATATA 977219 v v viv v v v - v iivi i iv MIR#SINE/MIR 57 AATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTA 106 chr2ptel1M 977220 ACCTTGGTTTGCCTCAGTTCCCTCAACCCTAAAATGGGAGTGATG-TAGC 977268 ivv v i v iv ii i i- i MIR#SINE/MIR 107 ACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGT 156 chr2ptel1M 977269 CCCTCCTTCCCAGAGTGGTTGTGAGGATCAAGTGAGATGTTATTTATAAA 977318 v v i vi i v i i v iv iv i MIR#SINE/MIR 157 ACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATACATGTAAA 206 chr2ptel1M 977319 TGTGCCT-GACAAGTTCTTGACACATAGAAGGGGCTACACAACTACTAGC 977367 - i i - vv v i i v i v vv i v ii MIR#SINE/MIR 207 -GCGCTTAGAACAGTGCCTGGCACATAGTAAGCGCTCAATAAATGTTAGC 255 chr2ptel1M 977368 TACATTAT 977375 -- MIR#SINE/MIR 256 T--ATTAT 261 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.50 CpG sites = 30, Kimura (unadjusted) = 38.30 Transitions / transversions = 1.00 (30/30) Gap_init rate = 0.03 (6 / 204), avg. gap size = 1.00 (6 / 6) 15 12.24 5.56 0.00 chr2ptel1M 977604 977639 (22361) (ATCTCCA)n#Simple_repeat 1 38 (0) m_b81s252i17 2993 chr2ptel1M 977604 ATCTCCAATCTTTCATCCCCAA--TCCAATCTCCAATC 977639 iiv i -- (ATCTCCA)n#Si 1 ATCTCCAATCTCCAATCTCCAATCTCCAATCTCCAATC 38 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.03 (1 / 35), avg. gap size = 2.00 (2 / 1) 264 40.50 2.52 0.62 chr2ptel1M 977781 977939 (22061) C MIR3#SINE/MIR (15) 193 32 m_b81s601i17 2994 chr2ptel1M 977781 AGAAAATCCATGTGGGGAGTTGCCCTTAAGATCACTGA--CTAAGGCCTT 977828 vi viv iv i vvi i vi iiv -- i vv i C MIR3#SINE/MIR 193 AGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCT 144 chr2ptel1M 977829 CATGATTCAGAGATGGAAACTGAGGTCTAGGAAGGTGAA--CACTTTTTC 977876 vv v viv i i ii --v vii C MIR3#SINE/MIR 143 CATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCC 94 chr2ptel1M 977877 TGGGCTCCAGAGGGAGCTGAGCAGAGGACTTAAAACTCTCACCCACCTCT 977926 vi iiv v v? i - ii vi viiiii vvv vv C MIR3#SINE/MIR 93 AAGGTCACACAGCNAGTT-AGTGGCAGAGCCGGGACTAGAACCCAGGTCT 45 chr2ptel1M 977927 TCAGCCTCTCGAT 977939 i v v i ii C MIR3#SINE/MIR 44 CCTGACTCCCAGT 32 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 59.31 CpG sites = 34, Kimura (unadjusted) = 60.97 Transitions / transversions = 1.13 (34/30) Gap_init rate = 0.02 (3 / 158), avg. gap size = 1.67 (5 / 3) 875 35.96 12.39 1.97 chr2ptel1M 979228 980010 (19990) L3#LINE/CR1 2645 3507 (592) m_b81s601i18 2995 chr2ptel1M 979228 TTGGAGAGGTTGTGGCAAAAGGGATGGGGTCTCT----ACTTCGGAGAAG 979273 v ii iii - i v v i vi v---- -- v L3#LINE/CR1 2645 TTTGAGAAATCACGG-AGAACGGAAGAGGTGCCAGAAGACT--GGAGACG 2691 chr2ptel1M 979274 GGCACGTGTT---TCTGGTTTTAAAAGGGGAAGATGG-CAAAGTTTACAG 979319 vi ?---i i? i i vi -iii v i i? i L3#LINE/CR1 2692 GGCAAATGTNGTNCCTANTTTTAAAAAGGGAAAAAAGATGGATTCTGNAA 2741 chr2ptel1M 979320 ATGAGTGGCCAGTGAGCTTGACTTTAATTCTTGGGGAATCTCCA-ATGGG 979368 iv vv i i i v ii i ii vi vi i - vv L3#LINE/CR1 2742 ACTACAGACCGGTAAGCTTGACGTCGATCCCCGGCAAAATTCTAGAACGG 2791 chr2ptel1M 979369 ACCATTGAAGAGAGGCTTGGTCAACACC-AGAGAAGAGATTGGCGATTAC 979417 ii i v v v v v i i- i ii vi i i L3#LINE/CR1 2792 ATTATTAAACAGATGGTTTGTGAGCACTTAGAAAAGGAAGCGGTGATCAC 2841 chr2ptel1M 979418 C--GAGCCA--------------AGAGCAGGTCACGGCCAACCAGCCCCA 979451 i-- -------------- i i i v v i i i L3#LINE/CR1 2842 TAGGAGCCAGCATGGGTTCACTAAGAACAAGTCATGCCAAACTAACCTCA 2891 chr2ptel1M 979452 TTTCCTTCGT-GAGGGGGTTACCAGCCTAGCAAATCTGGGCAACATGGTA 979500 iv - vi i v i i i v v iiiv L3#LINE/CR1 2892 TTTCCTTTTTTGATAGGGTTACTAGACTGGTAGATCAGGGGAATGCCGTA 2941 chr2ptel1M 979501 GAGATAACTGACTTAAATCGACTAAATTTTAGCAAATCTGTTGATAA--T 979548 v ? i------ iv --- ii i iv vv i -- L3#LINE/CR1 2942 GACANAG------TGTAT---CTGGATTTCAGCAAGGCATTTGACAAAGT 2982 chr2ptel1M 979549 ATATCATAATGTCTTCTCCTAGAGAAGTGAGAGGGATGGAGACCTAA--A 979596 v v i i -- iv i v vvi ii ivi i ivi -- L3#LINE/CR1 2983 CTCTCATGATATC--CTTGTGGACAAGATGGAGAAATATGGGCTGGATGA 3030 chr2ptel1M 979597 CAATATGATTA-ATGACTTGGGAACTGGGCAAA-AAAGATGCTCCAAGGG 979644 i i iii -i iv v v i vii -i vv i i v i L3#LINE/CR1 3031 TAGTACAGTTAGGTGGATTCGTAGCTGGTTGAACGACTATACCCAAAAGG 3080 chr2ptel1M 979645 CGTCCCTGAACAG-TCAGCA-CAGCCAGCAGG-----CTCCAGGGGAGTG 979687 i ivv v ii - iiii- i v v ----- i v v L3#LINE/CR1 3081 TGTTGATTAATGGATCGATGTCAACCTGGAGGGAGGTCTCTAGTGGCGTG 3130 chr2ptel1M 979688 ACCCGGGATGC-GTGCTTGGCTCTGAACTAGTCAACATTTGAATC----- 979731 v v i iiv - v i vv iv vv ----- L3#LINE/CR1 3131 CCACAGGGCTCTGTCCTTGGCCCTGTCCTGTTCAACATTTTTATCAATGA 3180 chr2ptel1M 979732 ---------GGGCCCAGAGGGCACGTGGGTCCCATTTCCCCACGCCCCAA 979772 ---------i i vi i i ivvi vv v vv i v v L3#LINE/CR1 3181 CTTGGATGAAGACATAGAAGGCATGCTTATCAAATTTGCAGATGACACAA 3230 chr2ptel1M 979773 AGCTTGGAGGAGTTGCCCACGTAGGGGATGAT--GATCGGGATCCCGAGA 979820 v ii v iv iiii?v i--i ii i vi i? L3#LINE/CR1 3231 AGCTGGGAGGGATAGCTAATACGNTGGATGACAGAATCAAGATTCAAAAN 3280 chr2ptel1M 979821 GATTTTTGGCAGGC-AGAGCATTGGGATGAACTCAAGAACACAACAGTC- 979868 - i i i -i i iv vi vi v v ii v v i- L3#LINE/CR1 3281 GA-TCTCGACAGGCTGGAACGATGGGCCGAAACCAACAAGATGAAATTTA 3329 chr2ptel1M 979869 ----GGATAAGTG------CCT---------TCC------CCAGTT-CCC 979892 ---- i ------ --------- i ------i ii - v L3#LINE/CR1 3330 ACAGGGATAAATGTAAAGTCCTGCATTTAGGTTCAAAAAATCAACTGCAC 3379 chr2ptel1M 979893 CAGTTTAGGACTGGGGAGA----GACAT--CAGTGGGTC---TGAAAAAG 979933 v vi - i i---- i v -- ii v --- L3#LINE/CR1 3380 AAGTACAGGA-TGGAGAGGATCTGGCTTAGCAGCAGTTCACGTGAAAAAG 3428 chr2ptel1M 979934 AGCTGTTAGTTTGGATGGGTTGTAAGGTCAGAGAGAGCCAGCCAAGGAGG 979983 v ivvi vii v iii i v iviv i- iv v i L3#LINE/CR1 3429 ACCTAGGGGTTTTAGTTGACCGCAAGCTCAATATGAGCCAA-CAGTGTGA 3477 chr2ptel1M 979984 GGCAGCTACCAACA---CTAAGGAAATATT 980010 v ii i v --- v v v L3#LINE/CR1 3478 TGTGGCTGCCAAAAAAGCTAATGCAATCTT 3507 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 48.82 CpG sites = 167, Kimura (unadjusted) = 52.17 Transitions / transversions = 1.53 (167/109) Gap_init rate = 0.06 (47 / 782), avg. gap size = 2.43 (114 / 47) 361 23.25 8.06 6.35 chr2ptel1M 980019 980142 (19858) MIRc#SINE/MIR 2 127 (141) m_b81s601i19 2996 chr2ptel1M 980019 GGGGCAGCTTGGGGGCACAGTGGGTAGAGAATCAGCCCTGAAGTCAGGAG 980068 i iv v --- iv v iii v i i i MIRc#SINE/MIR 2 GAGGCAGTGTGGTG---CAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr2ptel1M 980069 GACCTGAGTTCAAATCTTCTGGTCTTAGACACTTAATACTT-------CC 980111 i i i -- i - iv v v vi ------- i MIRc#SINE/MIR 49 GACCTGGGTTCGAGTC--CCGG-CTCTGCCACTTACTAGCTGTGTGACCT 95 chr2ptel1M 980112 TGGGCAAATCACTTAACC---CTAATTGCCTCAG 980142 i --- i -- MIRc#SINE/MIR 96 TGGGCAAGTCACTTAACCTCTCTGA--GCCTCAG 127 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.29 CpG sites = 18, Kimura (unadjusted) = 28.76 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.08 (10 / 123), avg. gap size = 1.80 (18 / 10) 431 34.57 3.62 3.15 chr2ptel1M 980169 980389 (19611) L3#LINE/CR1 3514 3735 (364) m_b81s601i20 2995 chr2ptel1M 980169 CATTAAAGAAGGCAGAGGATCCCAATGTAAGGAAAGGATTGTCCCCCCGG 980218 vii i i v vi vi ?vv i iivi v v i v L3#LINE/CR1 3514 CATTAATAGAAGTATAGTGTCCAGANCAAGGGAGGTAATAGTCCCGCTGT 3563 chr2ptel1M 980219 CCTCTGCCCTTAGCAG--CATAGTGGGCAG----GTGCTCATTTCTGGAT 980262 v v viv -- i viv - ---- i i v ii L3#LINE/CR1 3564 ACTCTGCGCTGGTCAGACCACATCTGG-AGTATTGCGTTCAGTTCTGGGC 3612 chr2ptel1M 980263 GCCACAGCATTGGAAGGACATTGCTGGACT-CAGGATGTCCAGAGAAAAG 980311 viv vi i viii -v vii i i L3#LINE/CR1 3613 GCCACATTTTAAGAGGGACATTGACAAACTGGAGCGCGTCCAGAGGAGAG 3662 chr2ptel1M 980312 CAGCTCCAAGAGAGGGAGGAGTCTGGCTTCCATGTCCCAAGGGGATAACA 980361 ii-- i vi v i i vvv vi v i ---- L3#LINE/CR1 3663 CGA--CCAGGATGGTGAAGGGTCTGGAAACCATGTCATATGAGGA----A 3706 chr2ptel1M 980362 TGGCAGAATCAGCTGGGCCTGTTT-GCCT 980389 i iv vv i vv - L3#LINE/CR1 3707 CGGTTGAAGGAACTGGGGATGTTTAGCCT 3735 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.64 CpG sites = 39, Kimura (unadjusted) = 47.77 Transitions / transversions = 1.11 (39/35) Gap_init rate = 0.05 (11 / 220), avg. gap size = 1.36 (15 / 11) 232 24.14 0.00 0.00 chr2ptel1M 980380 980437 (19563) MIR#SINE/MIR 81 138 (124) m_b81s601i21 2997 chr2ptel1M 980380 CTGTTTGCCTTTCGGTGAGTGTCTCCACCTCTCTGTGCCCCAGTTTCCTC 980429 v v i v ii vv iv i MIR#SINE/MIR 81 CTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTC 130 chr2ptel1M 980430 AGTGGTAA 980437 viv MIR#SINE/MIR 131 ATCTGTAA 138 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.21 CpG sites = 6, Kimura (unadjusted) = 29.21 Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0) 41 26.50 3.33 2.65 chr2ptel1M 980631 980780 (19220) (TCCT)n#Simple_repeat 1 151 (0) m_b81s252i18 2998 chr2ptel1M 980631 TCCCTCCCTCTTTCCTTCCCTCCCTCCCTCTCCCCTTTC-TCTCTCTTTC 980679 i i i i i i iii i - ii i (TCCT)n#Simpl 1 TCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC 50 chr2ptel1M 980680 TTTTCTTCCTACCTTCCTCGCTCCCTCCCTT-CTTCCTTTCCCTCCTTGC 980728 i i v iv i i - - i - (TCCT)n#Simpl 51 CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC-TTCCTTCCTT-C 98 chr2ptel1M 980729 CTT-CTTCCTTTCTTTCCCCCCATCTTTTC-CCCTTCC-TCCTCCCTCTC 980775 - - i ii v i i -i - i - (TCCT)n#Simpl 99 CTTCCTTCC-TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT-TC 146 chr2ptel1M 980776 TTTCC 980780 i (TCCT)n#Simpl 147 CTTCC 151 Matrix = Unknown Transitions / transversions = 9.00 (27/3) Gap_init rate = 0.06 (9 / 149), avg. gap size = 1.00 (9 / 9) 211 21.05 0.00 0.00 chr2ptel1M 980891 980928 (19072) L2d_3end#LINE/L2 470 507 (9) m_b81s601i22 2999 chr2ptel1M 980891 GAGCACATAGGAGGCACTTAACAAGTGTTTATTGATTG 980928 v i i i i ii i L2d_3end#LINE 470 GAGCACATAGTAGGCGCTCAATAAATACTTGTTGATTG 507 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 22.69 CpG sites = 7, Kimura (unadjusted) = 26.46 Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 550 38.97 7.98 1.34 chr2ptel1M 981051 981539 (18461) C L3#LINE/CR1 (1260) 2839 2319 m_b81s601i23 3000 chr2ptel1M 981051 GACTCCTGGTTCCCTTTCTAGGT--TGATA-----TTTCTTTTATGCCGC 981093 iiv i v i i -- v i ----- i v v iviv C L3#LINE/CR1 2839 GATCACCGCTTCCTTTTCTAAGTGCTCACAAACCATCTGTTTAATAATCC 2790 chr2ptel1M 981094 ATCCTAAAATTTGGCCCGGATGCAGAGTCAGGTTCCTTAGTTCACTGTTT 981143 i i i v v ivv iiv i i iviii iiiiv C L3#LINE/CR1 2789 GTTCTAGAATTTTGCCGGGGATCGACGTCAAGCTTACCGGTCTGTAGTTT 2740 chr2ptel1M 981144 CCAGACTTTGTTCTCTTCCCTTTTGGGCAAGTAGGGACAGCACTTTTTCC 981193 ? v iii ii i i i vviv ? ? ?i - vi C L3#LINE/CR1 2739 NCAGAATCCATCTTTTTTCCCTTTTTAAAANTAGGNACNACA-TTTGCCC 2691 chr2ptel1M 981194 CACTCCTATTGTGGGTTTCTTCCTCCCTTTTCCCAGCGTCTTTCACATGT 981243 vv vi iv vv viv i i v i vv -i i i v vi C L3#LINE/CR1 2690 GTCTCCAGTCTTCTGGCACCTCTTCCGTTCTCCGTG-ATTTCTCAAAGAT 2642 chr2ptel1M 981244 CACCGACGATGGTTCAGCCATCTTCTATTACTCTGGGTCTGTCAGGACCC 981293 i iii v v viv v v--- vi v v v C L3#LINE/CR1 2641 TACCGACAGCGGTTCCGCGATCACATCTG---CAAGTTCTTTCAGTACCC 2595 chr2ptel1M 981294 CAGACT-CGGCTCATCCAGGCCTGGGGCATGTGGACT------------- 981329 ii iv -iiii i ii i - iv i ------------- C L3#LINE/CR1 2594 TGGGATGTAATTCGTCTGGGCCTGGAG-ACTTGAACTCATTTAAAGCGGC 2546 chr2ptel1M 981330 ----TGCTCT--TGCTACCTCCTCACTTGTGTTGGGGATCCACTTTTGAG 981373 ---- -- i i i i v vv v i iiivvv C L3#LINE/CR1 2545 TAGGTGCTCTCTTACTATCTCCTCACCTATCTTGGGCTTCAATTCCCTCT 2496 chr2ptel1M 981374 GAACCATTTTCCTTCTGTCCTTTCCATGGCCAAGGTCACTGTTCCAGGCA 981423 v v v iv ii vvviv i i v i iv ii C L3#LINE/CR1 2495 TAACGATGTTTGTTCTACCCTTTCCAGTCTGAAGATCATTCTCCTTGATA 2446 chr2ptel1M 981424 GAGAACATACAAATAAAGT-----TCAGAGAGCTCTGCCG--GCTCTGTT 981466 v iiv ii i ----- iiiiv i iv--v i C L3#LINE/CR1 2445 GAGAAGACGGAAGCAAAATAGGAGTTGAGTAGTTCTGCTTTCTCTCTGTC 2396 chr2ptel1M 981467 GTCTGTT---ATCCCG-GGTCTGTCCAACATGAGC-GGCCATTCCCTTCC 981511 i --- iv -vi i v vii- - vv ? i C L3#LINE/CR1 2395 ATCTGTTAACATTACGCCATCTGCCCCAAGC-AGCGGGCCTGTCNCTTTC 2347 chr2ptel1M 981512 GCCTTTGATCTTTCCCAAGTAGAGTTTT 981539 vii ivv vii i ii v i C L3#LINE/CR1 2346 TTTTTCCTTCTGCTCCGAACATAGCTTT 2319 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 55.04 CpG sites = 111, Kimura (unadjusted) = 59.03 Transitions / transversions = 1.44 (111/77) Gap_init rate = 0.04 (18 / 488), avg. gap size = 2.56 (46 / 18) 43 0.00 0.00 0.00 chr2ptel1M 981865 981901 (18099) (TG)n#Simple_repeat 1 37 (0) c_b81s251i4 3001 chr2ptel1M 981865 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 981901 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 37 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 68 0.00 0.00 0.00 chr2ptel1M 983372 983429 (16571) (TC)n#Simple_repeat 1 58 (0) c_b81s251i5 3002 chr2ptel1M 983372 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 983421 (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr2ptel1M 983422 TCTCTCTC 983429 (TC)n#Simple_ 51 TCTCTCTC 58 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0) 22 29.44 0.97 6.12 chr2ptel1M 983433 983535 (16465) (TCCC)n#Simple_repeat 1 98 (0) m_b81s252i19 3003 chr2ptel1M 983433 TCCCTTCCCTTCTTCTCTCCCTCCTTCTCCCTCTCTTTCCATCTTCCTCC 983482 - i i i -- i ii ivi i (TCCC)n#Simpl 1 TCCC-TCCCTCCCTCCCTCCCTCC--CTCCCTCCCTCCCTCCCTCCCTCC 47 chr2ptel1M 983483 CTTTCTTCCTCCTTCTCCCTCCCT-TCTTTTTTCCTCCTTCCCACCTCTC 983531 ii i -- -i iii i i v - (TCCC)n#Simpl 48 CTCCCTCCCTCC--CTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCC-CTC 94 chr2ptel1M 983532 TCTC 983535 i (TCCC)n#Simpl 95 CCTC 98 Matrix = Unknown Transitions / transversions = 9.50 (19/2) Gap_init rate = 0.07 (7 / 102), avg. gap size = 1.00 (7 / 7) 217 37.48 4.72 1.83 chr2ptel1M 984667 984772 (15228) C L2#LINE/L2 (184) 2898 2790 m_b81s601i24 3004 chr2ptel1M 984667 CCACTGTGCTGACAATTTGG---TGCCTCTAGGCAATAGGGACATCC--T 984711 i ivv -- --- vv ii ii v v iv v -- C L2#LINE/L2 2898 CCATTGTAAGGAC--TTTGGCTTTTACTCTGAGTGAGATGGGAAGCCATT 2851 chr2ptel1M 984712 GAAGATTCTTGGGTAAGGGAGTGACATGGTCATATTTGCGCTTCGGCAAG 984761 i iv i i i ii i vv i i i iiiv i C L2#LINE/L2 2850 GGAGGGTTTTGAGCAGAGGAGTGACATGATCTGACTTACGTTTTAAAAGG 2801 chr2ptel1M 984762 GTTATTTTAGC 984772 i i i i i C L2#LINE/L2 2800 ATCACTCTGGC 2790 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 56.90 CpG sites = 27, Kimura (unadjusted) = 56.90 Transitions / transversions = 2.25 (27/12) Gap_init rate = 0.04 (4 / 105), avg. gap size = 1.75 (7 / 4) 57 0.00 0.00 0.00 chr2ptel1M 985344 985392 (14608) (TG)n#Simple_repeat 1 49 (0) c_b81s251i6 3005 chr2ptel1M 985344 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 985392 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 49 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 486 33.88 1.08 1.08 chr2ptel1M 986143 986327 (13673) L1ME4c_3end#LINE/L1 352 536 (294) m_b81s551i0 3006 chr2ptel1M 986143 AAACTGCCCATACCCTTTGACCCAGCGGTATTCCTACTGCGCTTGTATCC 986192 v ii iii viiv v v vv v L1ME4c_3end#L 352 AAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCC 401 chr2ptel1M 986193 CAAAGAGAT--TTTAAAGGAGGGAAAGGGACCTATATGTGAAAGAATGTT 986240 i i i -- i i i ii -- iivi ii L1ME4c_3end#L 402 TAAGGAAATAATTCAAAAGAAGGAAAAAG--CTATATGCACGAAGATGTT 449 chr2ptel1M 986241 TGTAGCAGCCCTCTTTGTAGTGACCAGAAACTGGAAACTGAGTGCACGCC 986290 ii v vi v i i ii v i i vivv iv i i L1ME4c_3end#L 450 CATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTC 499 chr2ptel1M 986291 CATCAGTGGGAGAATAGCTGAATAAATTACAGGATAT 986327 v i i i i i i i ii v i L1ME4c_3end#L 500 CAACAATAGGGGAATGGTTAAGTAAATTATGGTACAT 536 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 47.32 CpG sites = 43, Kimura (unadjusted) = 48.46 Transitions / transversions = 2.26 (43/19) Gap_init rate = 0.02 (3 / 184), avg. gap size = 1.33 (4 / 3) 202 27.56 9.09 1.05 chr2ptel1M 986352 986439 (13561) C L3#LINE/CR1 (251) 3848 3754 m_b81s601i25 3007 chr2ptel1M 986352 TCTTAAGTTTGCTTGCTGGGGACAAACAGAA-AAGTTGGATC----TTTC 986396 i iv i iiv i v v - ivi ---- i C L3#LINE/CR1 3848 TCCTAGTTCTGCCCTCTGGAGCCACACAGAATAAGTCTAATCCCTCTTCC 3799 chr2ptel1M 986397 A-AGGGTAGCT-TTGAGATATTTGAAGATCAGC-ATCATAATCCCT 986439 - v ii i- v i - - ivii C L3#LINE/CR1 3798 ACATGACAGCCCTTCAAATATTTGAAGA-CAGCTATCATGTCTCCT 3754 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.87 CpG sites = 16, Kimura (unadjusted) = 35.87 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.07 (6 / 87), avg. gap size = 1.50 (9 / 6) 437 26.32 6.14 0.00 chr2ptel1M 986759 986872 (13128) C L2d2_3end#LINE/L2 (0) 555 435 m_b81s601i26 3008 chr2ptel1M 986759 TTAAGTCAG-TCAATAAACATTTATCAAGTGCTTTCTGTGTGCCAAACAC 986807 i i i- i i ii i i v v ii C L2d2_3end#LIN 555 TCAAATCAAATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCAC 506 chr2ptel1M 986808 TGTGCTAAAGGCTG-GGGCTACACAGAGAGGGAAAA-----AGTCTCTGC 986851 iiv - vv i i i v v -----i i C L2d2_3end#LIN 505 TGTGCTAGGCGCTGTGGGGGATACAAAGAAGTATAAGACATGGTCCCTGC 456 chr2ptel1M 986852 TCTTAAGGAGTTCACAATGTA 986872 i i i i v C L2d2_3end#LIN 455 CCTCAAGGAGCTTACAATCTA 435 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.80 CpG sites = 22, Kimura (unadjusted) = 34.23 Transitions / transversions = 2.75 (22/8) Gap_init rate = 0.03 (3 / 113), avg. gap size = 2.33 (7 / 3) 186 37.26 6.67 4.21 chr2ptel1M 986766 987020 (12980) C L2d_3end#LINE/L2 (172) 344 84 m_b81s601i27 3008 chr2ptel1M 986766 AGTCAATAAACATTTATCAAGTGCTTT-CTGTGTGCCAAACACTGTGCTA 986814 v i v i --- i vv-i i vi v v i --- C L2d_3end#LINE 344 AGACAGTATATA---ATTAAGTGCTAAATTGCGTGGTACAGACTAT---A 301 chr2ptel1M 986815 AAGGCTGGGGCTACACAGAGAGGGAAAAAGTC--TCTGCTCTTAAGGAGT 986862 iv ivi vviiv i i i ii -- v vv vi vi C L2d_3end#LINE 300 AGTGCTATAGGAGTTCAGAGAAGGGAGAGATCAGTGTGGGCTGGAGTGGT 251 chr2ptel1M 986863 TCACAATGTAACGACTTCTGGAAGAAGGTGGGATTTTCTCTGGGACTCAA 986912 --- iv -- v i vv i i i vvv v ii C L2d_3end#LINE 250 ---CAGGG--AAGGCTTCGTGGAGGAGGTGGGACTTGAGCTGGGCCTTGA 206 chr2ptel1M 986913 AGGA--AGTCAGTTCT---CAGA-ATAGAGAAGGGAGAA---CGTTCTGG 986953 --i vi v i ---i - v i i i --- i ii C L2d_3end#LINE 205 AGGATGGGTAGGATTTGGATAGAGAGAGAGGAAGGGGAAGGGCATTCCAG 156 chr2ptel1M 986954 GCATGGGGGAC-CCAAGAGAACAAGCCCAGAGCTGAG-ACACGGAGGG-- 986999 iv i -v iv v v i v vi i - ii v i -- C L2d_3end#LINE 155 GCGGGGGGAACGGCGTGAGCAAAGGCGCAGAGGCGGGAATGCGCAAGGCG 106 chr2ptel1M 987000 -ATTTGGAAGAAAAGGGAAGGA 987020 -i i ii v iv i ii C L2d_3end#LINE 105 TGTTCGGGGGACAGTGAAGAGA 84 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 49.62 CpG sites = 53, Kimura (unadjusted) = 53.93 Transitions / transversions = 1.39 (53/38) Gap_init rate = 0.08 (21 / 254), avg. gap size = 1.33 (28 / 21) 390 33.34 2.78 3.35 chr2ptel1M 987014 987193 (12807) C MIR3#SINE/MIR (29) 179 1 m_b81s601i28 3009 chr2ptel1M 987014 GGAAGGAAACTTAGAGGCAGTTTAGTGCCAACTCTCTCCTTTTACAAATG 987063 i v iivi i - i i v i C MIR3#SINE/MIR 179 GGAAGGGACCTTAGAGATCATCTAGT-CCAACCCCCTCATTTTACAGATG 131 chr2ptel1M 987064 AAGGACTTGAATGTCAGAGAACTTCACTGAC---CTCAAGGTCCCAGAGG 987110 i i vi ivvi iv vv v --- i v v v C MIR3#SINE/MIR 130 AGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGC 81 chr2ptel1M 987111 TTCTAAGT--CAGATCTAGAATTCCAACCCAGAACCTCTGACCTCAAATC 987158 ?vv v -- v ii i i vv iv ii ii v i C MIR3#SINE/MIR 80 NAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGTCTCCTGACTCCCAGTC 31 chr2ptel1M 987159 TCCTTCCATTTCCACATATTCAGTTCCTCTTCTAG 987193 - v v iv i ---- ii iiv v i C MIR3#SINE/MIR 30 -CGTGCTCTCTC----TGCTCAGCCACTCTGCCAG 1 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.47 CpG sites = 32, Kimura (unadjusted) = 45.66 Transitions / transversions = 1.23 (32/26) Gap_init rate = 0.04 (8 / 179), avg. gap size = 1.38 (11 / 8) 248 38.58 1.56 0.78 chr2ptel1M 987327 987454 (12546) C MIRc#SINE/MIR (13) 255 127 m_b81s601i29 3010 chr2ptel1M 987327 CCTCAAATCCCTGAAGCCTCGCACCATTTGAGAAGCTCTTTC-TACCCAT 987375 i v iiv iv viivi vi ivi v -i iv C MIRc#SINE/MIR 255 CCTTACATTTGTATAGCACTTTACAGTTTACAAAGCGCTTTCACATACAT 206 chr2ptel1M 987376 TGCTTCCATTAAAGCTTCATAATGACCATGAAGGGTAAATAGAACTCCTA 987425 iii - vi v i i ii v vii iii ii vvv C MIRc#SINE/MIR 205 TATCTC-ATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTA 157 chr2ptel1M 987426 ATATTATCCCT-TTTGACAAATAAGGAAGC 987454 v i- v i i i C MIRc#SINE/MIR 156 TTATTATCCCCATTTTACAGATGAGGAAAC 127 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 58.04 CpG sites = 31, Kimura (unadjusted) = 58.04 Transitions / transversions = 1.72 (31/18) Gap_init rate = 0.02 (3 / 127), avg. gap size = 1.00 (3 / 3) 12 18.14 0.00 3.12 chr2ptel1M 988329 988361 (11639) (CCTGC)n#Simple_repeat 1 32 (0) m_b81s252i20 3011 chr2ptel1M 988329 CCAGCCCTGCCCTTGGCCGGCCCTGCCTTGGCC 988361 v - v v i v (CCTGC)n#Simp 1 CCTGCCCTGCCC-TGCCCTGCCCTGCCCTGCCC 32 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 539 31.07 7.79 2.47 chr2ptel1M 988837 989067 (10933) C MIRc#SINE/MIR (1) 267 25 m_b81s601i30 3012 chr2ptel1M 988837 ATAGGAATAA----TTAGTGTTTACACAGAACTCTGAGACCGGCCAAGT- 988881 iv ---- -ii ii i v i iviiiivi v i- C MIRc#SINE/MIR 267 ATAATAATAACNCCTTA-CATTTGTATAGCACTTTACAGTTTACAAAGCG 219 chr2ptel1M 988882 CCTTCACAAATATTATCTCGCCCGATTTGGAGCCCACAACCATCCCGGGA 988931 i v i ----- ivv i v i i v C MIRc#SINE/MIR 218 CTTTCACATACATTATCTC-----ATTTGATCCTCACAACAACCCTGTGA 174 chr2ptel1M 988932 GGTCG--ATGTCA--TTATATTAACCCCATTTTACAGCTGAGGAAACTGA 988977 v -- v v -- vv v v C MIRc#SINE/MIR 173 GGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGA 124 chr2ptel1M 988978 GGTAAACAGAGACTATATGGCTTGCCCA---------AGCTAGTGAGTAT 989018 ivv v ii vi i --------- i iv C MIRc#SINE/MIR 123 GGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGG 74 chr2ptel1M 989019 CTGAGGTTGAATTGGAACTCAGCTCCTTGTACCTCTGGGGCAAGGACTC 989067 v viv i i v i v i iv iv iii v v vi C MIRc#SINE/MIR 73 CAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTC 25 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.55 CpG sites = 38, Kimura (unadjusted) = 41.06 Transitions / transversions = 1.19 (38/32) Gap_init rate = 0.05 (11 / 230), avg. gap size = 2.18 (24 / 11) 544 29.15 4.86 5.43 chr2ptel1M 988875 989059 (10941) C MIRb#SINE/MIR (49) 219 36 m_b81s601i31 3012 chr2ptel1M 988875 GCCAAGTCCTTCACAAATATTATCTCGCCCGATTTGGAGCCCACAACCAT 988924 i iv i vii ----- iivv i v i C MIRb#SINE/MIR 219 GCTAAGCGCTTTACATGCATTATCTC-----ATTTAATCCTCACAACAAC 175 chr2ptel1M 988925 CCCGGGAGGTCGATGTCATTATATTAACCCCATTTTACAGCTGAGGAAAC 988974 i v v i i i ----- v C MIRb#SINE/MIR 174 CCTGCGAGGTAGGTATTATTAT-----CCCCATTTTACAGATGAGGAAAC 130 chr2ptel1M 988975 TGAGGTAAACAGAGACTATATGGCTTGCCCA---------AGCTAGTGAG 989015 ivv v ii vi ii --------- i C MIRb#SINE/MIR 129 TGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAG 80 chr2ptel1M 989016 TATCTGAGGTTGAATTGGAACTCAGCTCCTTGTACCTCTGGGGC 989059 iv v viv i v i v iv v iv iiii C MIRb#SINE/MIR 79 TGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGC 36 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.06 CpG sites = 30, Kimura (unadjusted) = 37.94 Transitions / transversions = 1.43 (30/21) Gap_init rate = 0.06 (11 / 184), avg. gap size = 1.73 (19 / 11) 283 30.54 1.80 5.61 chr2ptel1M 990350 990460 (9540) MIRb#SINE/MIR 4 110 (158) m_b81s601i32 3013 chr2ptel1M 990350 AGGGGCAGCTAGAAGGGGCAGTGAATAAAATCTCAGCCCTGGAATCAGGA 990399 ---iv v i v i iivivi ii i iv MIRb#SINE/MIR 4 AGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGAC 50 chr2ptel1M 990400 GGACCCGAGTTCAAATCAGGCCTCAGACACTTCACACTCATTA-GTGA-C 990447 i i i i vv v v v --- vii i- - MIRb#SINE/MIR 51 AGACCTGGGTTCGAATCCCGGCTCTGCCACTT---ACTAGCTGTGTGACC 97 chr2ptel1M 990448 TTGGGTAAGTCAC 990460 i i MIRb#SINE/MIR 98 TTGGGCAAGTTAC 110 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.82 CpG sites = 20, Kimura (unadjusted) = 40.67 Transitions / transversions = 1.67 (20/12) Gap_init rate = 0.07 (8 / 110), avg. gap size = 1.00 (8 / 8) 303 29.80 2.06 3.12 chr2ptel1M 990364 990460 (9540) MIRc#SINE/MIR 12 107 (161) m_b81s601i33 3013 chr2ptel1M 990364 GGGGCAGTGAATAAAATCTCAGCCCTGGAATCAGGAGGACCCGAGTTCAA 990413 v i v i iiviii v i i i i i i MIRc#SINE/MIR 12 GGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGA 61 chr2ptel1M 990414 ATCAGGCCTCAGACACTTCACACTCATTA-GTGA-CTTGGGTAAGTCAC 990460 i vv v v v --- vii i- - i MIRc#SINE/MIR 62 GTCCCGGCTCTGCCACTT---ACTAGCTGTGTGACCTTGGGCAAGTCAC 107 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.74 CpG sites = 18, Kimura (unadjusted) = 39.59 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.05 (5 / 96), avg. gap size = 1.00 (5 / 5) 654 31.85 2.18 5.24 chr2ptel1M 990601 990875 (9125) MIRc#SINE/MIR 2 268 (0) m_b81s601i34 3014 chr2ptel1M 990601 GAGGTGATATAGTATA-TGGCTAAAGTGCTGGACTTGGAGTCAGAAGGAC 990649 iii i i ii - vv i ii i i MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr2ptel1M 990650 ATGAGTTCAAATCCTAGTACAGATATTCACTGGCAGTGTGACCCTGGGCA 990699 v i i i ii iv v vi i i i v i MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 101 chr2ptel1M 990700 GACCATTTTAC----TTGAGCCTTTTTCAGTTTCTTCCTATGTAACATGT 990745 iii i v ----i ---- i v v v v MIRc#SINE/MIR 102 AGTCACTTAACCTCTCTGAGCC----TCAGTTTCCTCATCTGTAAAATGG 147 chr2ptel1M 990746 GGATAATCATATCTATAGTACCTACCTCCTAGGACCATTGGAAAAATCCC 990795 v i iivv i vi iiii vi ii --- MIRc#SINE/MIR 148 GGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGAT--- 194 chr2ptel1M 990796 CCAAATTACACGTGTGTTTTATGAAAACATTTTA-AGGTTTCCAAATGTT 990844 - v v ii-i - v i i ii i- iii viv i i MIRc#SINE/MIR 195 -CAAATGAGATA-ATG-TATGTGAAAGCGCTTTGTAAACTGTAAAGTGCT 241 chr2ptel1M 990845 AAAGAATCATGTAATATCCTTTGTTATTATT 990875 v v -- vi--?v i MIRc#SINE/MIR 242 ATACAA--ATGTAAGG--NGTTATTATTATT 268 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.96 CpG sites = 57, Kimura (unadjusted) = 44.24 Transitions / transversions = 2.19 (57/26) Gap_init rate = 0.06 (17 / 274), avg. gap size = 1.18 (20 / 17) 353 25.15 8.13 8.65 chr2ptel1M 990909 991117 (8883) MIR1_Amn#SINE/MIR 6 213 (17) m_b81s601i36 3015 chr2ptel1M 990909 AGGTAGTGC--TGTGGTGGATAAAGTGCTGGGACAGGCTAGAGTCAGGAA 990956 i i-- v i i ii - v --- v i i MIR1_Amn#SINE 6 AGGCAGTGTGGTCTAGTGGATAGAGCACTGG-ACTGG---GACTCGGGAG 51 chr2ptel1M 990957 GAGTCATCTTTGTGAGCTCAAACCTGGCCTCGG--ACT------CTGTGT 990998 ----- i ---- i i ? ?i iv v v -- ------ ? MIR1_Amn#SINE 52 -----ACCT----GGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGT 92 chr2ptel1M 990999 AATCCAGGGCAAGTCACTTAACC-CTGTTTGCCTCAGTTT-CTCATCTGT 991046 i i iv ? - v v? - MIR1_Amn#SINE 93 GACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGT 142 chr2ptel1M 991047 AAAATGAGCTGGAGAAGGATGTAGTGAACCACTCCAGGATCTCTAATGAG 991096 i--- v v -- v v iv iiivi vv vivv MIR1_Amn#SINE 143 AAAATGG---GGATAATGA--TACTGACCTCCTTTGTAAAGTGCTTTGAG 187 chr2ptel1M 991097 GTC-----GTGAAAAGTCAGACATAA 991117 i -----i vvv MIR1_Amn#SINE 188 ATCTACTGATGAAAAGTGCTACATAA 213 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.23 CpG sites = 25, Kimura (unadjusted) = 32.02 Transitions / transversions = 1.09 (25/23) Gap_init rate = 0.12 (24 / 208), avg. gap size = 1.46 (35 / 24) 448 25.00 4.11 4.11 chr2ptel1M 990909 991054 (8946) MIRc#SINE/MIR 3 148 (120) m_b81s601i35 3015 chr2ptel1M 990909 AGGTAGTGCTGTG--GTGGATAAAGTGCTGGGACAGGCTAGAGTCAGGAA 990956 i iv -- v i ii - ---i i MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGG-AC---TTGGAGTCAGGAA 48 chr2ptel1M 990957 GAGTCATCTTTGTGAGCTCAAACCTGGCCTCGGACT--CTGTGTAATCCA 991004 viiivv i -- ii vii iiv v vv -- i i iv MIRc#SINE/MIR 49 GACCTGGGTTCG--AGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTT 96 chr2ptel1M 991005 GGGCAAGTCACTTAACC-CTGTTTGCCTCAGTTT-CTCATCTGTAAAATG 991052 - v vv - MIRc#SINE/MIR 97 GGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATG 146 chr2ptel1M 991053 AG 991054 i MIRc#SINE/MIR 147 GG 148 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.02 CpG sites = 21, Kimura (unadjusted) = 31.12 Transitions / transversions = 1.50 (21/14) Gap_init rate = 0.07 (10 / 145), avg. gap size = 1.20 (12 / 10) 18 13.82 0.00 3.03 chr2ptel1M 991213 991246 (8754) (GT)n#Simple_repeat 1 33 (0) m_b81s252i21 3016 chr2ptel1M 991213 GTGTAGTCTTTGTGTGTGTGTTTGTGTTTGTGTG 991246 - v v v v (GT)n#Simple_ 1 GTGT-GTGTGTGTGTGTGTGTGTGTGTGTGTGTG 33 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 21 31.54 2.11 1.04 chr2ptel1M 991218 991312 (8688) (GTGTTT)n#Simple_repeat 1 96 (0) m_b81s252i22 3016 chr2ptel1M 991218 GTCTTTGTGTGTGTGTTTGTGTTTGTG--TGACCTTCTACCTTTGTTTTT 991265 v v -- vvi v iii v v (GTGTTT)n#Sim 1 GTGTTTGTGTTTGTGTTTGTGTTTGTGTTTGTGTTTGTGTTTGTGTTTGT 50 chr2ptel1M 991266 GTTAATTTTTTTGTTGGTGTTTGAATATGTTCTTCTTGTTCTTGTTT 991312 vi v v v vi v - v iv iv (GTGTTT)n#Sim 51 GTTTGTGTTTGTGTTTGTGTTTGTGTTTG-TGTTTGTGTTTGTGTTT 96 Matrix = Unknown Transitions / transversions = 0.50 (8/16) Gap_init rate = 0.02 (2 / 94), avg. gap size = 1.50 (3 / 2) 23 26.89 1.39 1.39 chr2ptel1M 991295 991366 (8634) (TTCTCC)n#Simple_repeat 1 72 (0) m_b81s252i23 3017 chr2ptel1M 991295 TTCTTCTTGTTCTTGTTTTTCTTCTCCCCCTTTCCCTTCTCCTTCTCCTC 991344 i v i v ii i i i ii i (TTCTCC)n#Sim 1 TTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTT 50 chr2ptel1M 991345 CTCACCT-TCCTCCTCCTTCCCC 991366 - i - i i (TTCTCC)n#Sim 51 CTC-CTTCTCCTTCTCCTTCTCC 72 Matrix = Unknown Transitions / transversions = 6.50 (13/2) Gap_init rate = 0.03 (2 / 71), avg. gap size = 1.00 (2 / 2) 294 20.90 0.00 0.00 chr2ptel1M 991960 992026 (7974) C X30_DNA#DNA (165) 233 167 m_b81s502i2 3018 chr2ptel1M 991960 TTTGTTGATTCTTTCAAGGTGATAAATTGCCATTGTGTTCACCCTTTTGT 992009 vi vv i ivv i i C X30_DNA#DNA 233 TTTGTTGAGCCTGGCAAAGTGATAAATTGTGCTTGTGTTTACTCTTTTGT 184 chr2ptel1M 992010 TCCCAGGGTTAACTGCT 992026 i i i i C X30_DNA#DNA 183 TCCCAAGGCTAATTGTT 167 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 25.07 CpG sites = 9, Kimura (unadjusted) = 25.07 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.0 (0 / 0) 15 30.57 2.33 3.53 chr2ptel1M 992923 993008 (6992) (TCCTC)n#Simple_repeat 1 85 (0) m_b81s252i25 3019 chr2ptel1M 992923 TCCTC-CCCCTCCTCTGTTCTCCCTTCCCTTTCAGC-CCTCCTCTCTCCT 992970 - i vi - ii i vv - ii (TCCTC)n#Simp 1 TCCTCTCCTCTCCTCTCCTCT-CCTCTCCTCTCCTCTCCTCTCCTCTCCT 49 chr2ptel1M 992971 TCCCTCGCCCCACCTTGTCCTCCCCACATGCTCTACTC 993008 ii v i v - v i v - v v (TCCTC)n#Simp 50 CTCCTCTCCTCTCC-TCTCCTCTCCTC-TCCTCTCCTC 85 Matrix = Unknown Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.06 (5 / 85), avg. gap size = 1.00 (5 / 5) 11 16.10 4.26 6.52 chr2ptel1M 993853 993899 (6101) (TTCCTCT)n#Simple_repeat 1 46 (0) m_b81s252i26 3020 chr2ptel1M 993853 TTCCTCTGTCC-CTTCTGGATC-TTCCTCCCTCCTCATTTCCACTTTCC 993899 v - - -vv - ii - v (TTCCTCT)n#Si 1 TTCCTCTTTCCTCTT-T-CCTCTTTCCTCTTTCCTC-TTTCCTCTTTCC 46 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.11 (5 / 46), avg. gap size = 1.00 (5 / 5) 31 0.00 0.00 0.00 chr2ptel1M 994055 994083 (5917) (GGA)n#Simple_repeat 1 29 (0) c_b81s251i7 3021 chr2ptel1M 994055 GGAGGAGGAGGAGGAGGAGGAGGAGGAGG 994083 (GGA)n#Simple 1 GGAGGAGGAGGAGGAGGAGGAGGAGGAGG 29 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 192 27.21 16.07 1.56 chr2ptel1M 997990 998101 (1899) L2c_3end#LINE/L2 339 466 (12) m_b81s601i37 3022 chr2ptel1M 997990 TGTACCCGGCTGTTTGCTTGT-GGTCTCTCCCAGT-GCCTCCG---TCC- 998033 vii v i ? -v ii v - v vi --- - L2c_3end#LINE 339 TGTAATTGTCTGTTTACNTGTCTGTCTCCTCCACTAGACTGTGAGCTCCT 388 chr2ptel1M 998034 -GAGGAGAGGGATACCCTGCCTTCTT-----TTGCATCCCCAGTGCTTAG 998077 - iv -- v i v ----- i i i i L2c_3end#LINE 389 TGAGGGCAGGGA--CCGTGTCTTATTCATCTTTGTATCCCCAGCGCCTGG 436 chr2ptel1M 998078 CCT------GGTACCTAATGAATGCTTGCT 998101 vi------ ii ii i i i L2c_3end#LINE 437 CACATAGTAGGCGCTCAATAAATGTTTGTT 466 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.64 CpG sites = 20, Kimura (unadjusted) = 35.76 Transitions / transversions = 2.00 (20/10) Gap_init rate = 0.08 (9 / 111), avg. gap size = 2.22 (20 / 9) 251 23.53 0.00 0.00 chr2ptel1M 998346 998396 (1604) L2b_3end#LINE/L2 410 460 (6) m_b81s601i38 3023 chr2ptel1M 998346 TAGTGCAGCGGCCGGCACACAGGAAGCGCTTATTAAATGCTTGTTGACCG 998395 ii ? v i v i i v ii vi L2b_3end#LINE 410 TAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTTGTTGAATG 459 chr2ptel1M 998396 A 998396 L2b_3end#LINE 460 A 460 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.90 CpG sites = 8, Kimura (unadjusted) = 29.90 Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 184 34.84 9.17 2.59 chr2ptel1M 999567 999675 (325) MIRb#SINE/MIR 37 152 (116) m_b81s601i39 3024 chr2ptel1M 999567 CTTTGGGAAACCAGCCTGGTCTCACATTTGCTTCTGGTCCCCATCACTGA 999616 -- ii v v ii vi-i i vv iv v i iii v MIRb#SINE/MIR 37 CTTTGG--AGTCAGACAGACCTGG-GTTCGAATCCCGGCTCTGCCACTTA 83 chr2ptel1M 999617 CCAACTGTGTGG--------AAGTCATTCCCAGGCTCTGGGCT--AGTTA 999656 i i i-------- i i ivvvvv i i-- v MIRb#SINE/MIR 84 CTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTT 133 chr2ptel1M 999657 TCTCTTCTGTAAAATGGAG 999675 i v i MIRb#SINE/MIR 134 CCTCATCTGTAAAATGGGG 152 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 47.10 CpG sites = 22, Kimura (unadjusted) = 48.98 Transitions / transversions = 1.47 (22/15) Gap_init rate = 0.05 (5 / 108), avg. gap size = 2.60 (13 / 5) 274 27.64 18.70 0.00 chr2ptel1M 999598 999720 (280) MIR3#SINE/MIR 54 199 (9) m_b81s601i40 3024 chr2ptel1M 999598 TTCTGGTCCC-----CATCACTGACCAACTGTGTGG--------AAGTCA 999634 i -----iii i i?i i-------- MIR3#SINE/MIR 54 TTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCA 103 chr2ptel1M 999635 TTCCCAGGCTCTGGGCT--AGTTATCTCTTCTGTAAAATG---GAGCTG- 999678 i i vvvv i-- vi v --- i i - MIR3#SINE/MIR 104 CTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGG 153 chr2ptel1M 999679 --TGGGTA--CCCCAAAGCAGCTTCCAGTTCTAAGATTCTTTGCTT 999720 -- i i i-- i i i ivv i i v v v MIR3#SINE/MIR 154 ACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATT 199 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.45 CpG sites = 23, Kimura (unadjusted) = 36.45 Transitions / transversions = 2.09 (23/11) Gap_init rate = 0.06 (7 / 122), avg. gap size = 3.29 (23 / 7) 184 33.44 8.10 4.61 chr2ptel1M 999770 999979 (21) L3b_3end#LINE/CR1 864 1080 (126) m_b81s601i41 3025 chr2ptel1M 999770 TAGAACCCGTCC-CAAGCTTCTGAAAGGTCCAGACGTGGAGAA--GGGAT 999816 iv v ? i- iv v i ivvv i i -- v i L3b_3end#LINE 864 TAATAACNGTCTTCAAGTATATGAAGGGTTATTACGTAGAGGACGGTGAC 913 chr2ptel1M 999817 CGGCTGATTCCCGTCCGGCCCCAGAAGGCCGAGCCAGGAATGACGGA-GG 999865 i v ii i i-- v v i i v i v iiivi i i-vv L3b_3end#LINE 914 CAGCTGTTCTCCATCT--CCACTGAGGACAGAACAAGAGGAAATGGGCTT 961 chr2ptel1M 999866 AAGCTGCAG----AGGCAGATTTCGGCAGGAGAGGCTGGGAAGTTCT-CC 999910 i ---- -- v ivi v vi--i vv - L3b_3end#LINE 962 AAACTGCAGCATGAGG--GATTTAGGTTAGATATA--AGGAAGAACTTCC 1007 chr2ptel1M 999911 TGACTGGGAGGGTTGGCTCAGAGCCGAGTGGG----CAGGGGACGGGTTC 999956 v v i vivv v viv i ---- ii -- v L3b_3end#LINE 1008 TGACAGTGAGAGTTGTTAAACACTGGAATGGGTTACCGAGGGA--GGTTG 1055 chr2ptel1M 999957 T----TCATCTTCTCTGGGCAGAGGCT 999979 i---- vi -- ? L3b_3end#LINE 1056 CGGAATCTCCTTCTCTGG--AGAGNCT 1080 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.12 CpG sites = 35, Kimura (unadjusted) = 45.96 Transitions / transversions = 1.09 (35/32) Gap_init rate = 0.08 (17 / 209), avg. gap size = 1.59 (27 / 17) 316 29.24 3.74 0.91 chr2ptel1M 999782 999888 (112) L3#LINE/CR1 3775 3884 (215) m_b81s601i42 3025 chr2ptel1M 999782 CAAGCTTCTGAAAGGTCCAGACGTGGAGAAGGGATC-GGCTGATTCCCGT 999830 iiv i i iivvv i ii i- i v - i L3#LINE/CR1 3775 CAAATATTTGAAGGGCTGTCATGTGGAAGAGGGATTAGACTTATT-CTGT 3823 chr2ptel1M 999831 CCGGCCCCAGAAGGCCGAGCCAGGAATGACGGA-GGAAGCTGCA--GAGG 999877 vi i i v i i vii i i- i i -- L3#LINE/CR1 3824 GTGGCTCCAGAGGGCAGAACTAGGACCAATGGGTGGAAGTTACAGGGAGG 3873 chr2ptel1M 999878 CAGATTTCGGC 999888 L3#LINE/CR1 3874 CAGATTTCGGC 3884 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.70 CpG sites = 23, Kimura (unadjusted) = 39.70 Transitions / transversions = 2.88 (23/8) Gap_init rate = 0.04 (4 / 106), avg. gap size = 1.25 (5 / 4) 214 14.58 0.00 14.29 chr2qtel1M 3 58 (999942) MIR1_Amn#SINE/MIR 123 171 (59) m_b82s601i0 3026 chr2qtel1M 3 GCCTCAGTTTCCTCATCTGTTAAATGAGCTGGAGAAGGAAATATTATAAC 52 v i--- v v -- i-- i MIR1_Amn#SINE 123 GCCTCAGTTTCCTCATCTGTAAAATGG---GGATAATG--ATAC--TGAC 165 chr2qtel1M 53 TTCCTT 58 i MIR1_Amn#SINE 166 CTCCTT 171 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 15.98 CpG sites = 4, Kimura (unadjusted) = 15.98 Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.13 (7 / 55), avg. gap size = 1.00 (7 / 7) 218 3.57 0.00 0.00 chr2qtel1M 3 30 (999970) MIR3#SINE/MIR 118 145 (63) m_b82s601i1 3026 chr2qtel1M 3 GCCTCAGTTTCCTCATCTGTTAAATGAG 30 v MIR3#SINE/MIR 118 GCCTCAGTTTCCTCATCTGTAAAATGAG 145 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 3.67 CpG sites = 0, Kimura (unadjusted) = 3.67 Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 234 30.77 10.58 0.00 chr2qtel1M 455 558 (999442) MIR3#SINE/MIR 91 205 (3) m_b82s601i2 3027 chr2qtel1M 455 CTCAGATCAGTCCTTTAACTTTTCTGGGTCTCA------TAAACC---AC 495 ii iiv vi v i i i ------ v v i--- v MIR3#SINE/MIR 91 CTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAA 140 chr2qtel1M 496 ATAAGGCAGTTGGTCTGGAGGATGCTTAAGGTTCCTTCCTGCTCCAA-AG 544 i vi v i v vii i v ii - v MIR3#SINE/MIR 141 ATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACAT 190 chr2qtel1M 545 TCTGTCA-TCTACGA 558 i v - i MIR3#SINE/MIR 191 TCTATGATTCTATGA 205 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.90 CpG sites = 19, Kimura (unadjusted) = 40.90 Transitions / transversions = 1.46 (19/13) Gap_init rate = 0.04 (4 / 103), avg. gap size = 2.75 (11 / 4) 18 36.68 0.00 0.00 chr2qtel1M 622 691 (999309) (TA)n#Simple_repeat 1 70 (0) m_b82s252i0 3028 chr2qtel1M 622 TATATGTTTCAATATCAATATATATAGACACGCATAGACATATTTAAGTA 671 i v vv vv v i iii v i v vi (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr2qtel1M 672 TACATGCATATATATGTATA 691 i ii i (TA)n#Simple_ 51 TATATATATATATATATATA 70 Matrix = Unknown Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0) 13 13.52 2.00 10.87 chr2qtel1M 3817 3866 (996134) (TTA)n#Simple_repeat 1 46 (0) m_b82s252i1 3029 chr2qtel1M 3817 TTATTTATTATTATTATTAGGTGATTGCTTATTTATTACTA-GATAATTA 3865 - -- v -v - i -v v (TTA)n#Simple 1 TTA-TTATTATTATTATTA--TTATT-ATTA-TTATTATTATTATTATTA 45 chr2qtel1M 3866 T 3866 (TTA)n#Simple 46 T 46 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.12 (6 / 49), avg. gap size = 1.00 (6 / 6) 12 16.57 0.00 0.00 chr2qtel1M 4142 4168 (995832) (ACAT)n#Simple_repeat 1 27 (0) m_b82s252i2 3030 chr2qtel1M 4142 ACATCTATGCATACATACATTCATACA 4168 vi i v (ACAT)n#Simpl 1 ACATACATACATACATACATACATACA 27 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 21 0.00 0.00 0.00 chr2qtel1M 4250 4272 (995728) (T)n#Simple_repeat 1 23 (0) m_b82s252i3 3031 chr2qtel1M 4250 TTTTTTTTTTTTTTTTTTTTTTT 4272 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTT 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 477 21.83 2.42 7.63 chr2qtel1M 4275 4398 (995602) C MIRc#SINE/MIR (141) 127 10 m_b82s601i3 3032 chr2qtel1M 4275 CTGAGGCAATTGGAG---TCAAATGACTTGCCCAGGGTCACACAGCTGGG 4321 -- ii --- i i i i - C MIRc#SINE/MIR 127 CTGAGGC--TCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG- 81 chr2qtel1M 4322 AAGTGTTAAGTGTCTGAGGCTAGATTTGAACTCAGGTCCTCCTGACTTCA 4371 ------ v v v vi i i i i i C MIRc#SINE/MIR 80 ------TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCA 37 chr2qtel1M 4372 GGGCTGGTGCTCTATTCACTGTGCAAC 4398 i v ii v i ii v C MIRc#SINE/MIR 36 AGTCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 25.42 CpG sites = 18, Kimura (unadjusted) = 26.66 Transitions / transversions = 2.57 (18/7) Gap_init rate = 0.08 (10 / 123), avg. gap size = 1.20 (12 / 10) 260 25.34 8.96 2.82 chr2qtel1M 4477 4610 (995390) L1PREC2_orf2#LINE/L1 3110 3251 (43) m_b82s551i0 3033 chr2qtel1M 4477 AAAAAATACT-GCAAG---TACCTCTGACAAAGGCCTGATTTTTCAAATA 4522 i ?i - i--- i v i i v iiviv v L1PREC2_orf2# 3110 AGAAAATNTTTGCAAACTATGCATCTGACAAAGGTCTAATATCCAGCATC 3159 chr2qtel1M 4523 TATTAAGGAGC-----CAAATTTGTAAGAATA---CAAATCATTCCCCAA 4564 - i ----- ii v --- iv -- - L1PREC2_orf2# 3160 TAT-AAGGAACTTAAACAAATTTACAAGAAAAAAACAAACAA--CCCCA- 3205 chr2qtel1M 4565 TTGACAAATGGTCAAAGGATATGCATGAGCAGTTTTCAAACAAAGA 4610 i v i v i v iiii v vi L1PREC2_orf2# 3206 TTAAAAAGTGGGCAAAGGACATGAACAGACACTTTTCAAAAGAAGA 3251 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.26 CpG sites = 21, Kimura (unadjusted) = 32.26 Transitions / transversions = 1.75 (21/12) Gap_init rate = 0.06 (8 / 133), avg. gap size = 2.00 (16 / 8) 264 24.98 7.38 1.55 chr2qtel1M 4508 4629 (995371) L1ME4b_3end#LINE/L1 1 129 (763) m_b82s551i1 3033 chr2qtel1M 4508 CTGATTTTTCAAATATATTAAGGAGC-----CAAATTTGTAAGAATACAA 4552 i ii v - i ----- ivi - v i L1ME4b_3end#L 1 CTAATTTCCCTAATATAT-AAAGAGCTCCTACAAATCAATAAGAA-AAAG 48 chr2qtel1M 4553 ATCATTC-CCCAATTGACAAATGGTCAAAGGATATGCATGAGCAGTTTTC 4601 i viv- v v v v iiii iv L1ME4b_3end#L 49 ACCAACAACCCAATAGAAAAATGGGCAAAGGATATGAACAGACAGTTCAC 98 chr2qtel1M 4602 AAACAAAGAAAC-CAAAAG--TCTTACACAT 4629 i v i i- v -- v L1ME4b_3end#L 99 AGAAAAGGAAATACAAATGGCTCTTAAACAT 129 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 30.96 CpG sites = 17, Kimura (unadjusted) = 30.96 Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.05 (6 / 121), avg. gap size = 1.83 (11 / 6) 24 14.86 3.85 0.00 chr2qtel1M 4981 5032 (994968) (ATGT)n#Simple_repeat 1 54 (0) m_b82s252i4 3034 chr2qtel1M 4981 ATATATGCATTTATCTA--TATCTATGTATGTATGTATGCATGTATGTAT 5028 i i v v -- v i (ATGT)n#Simpl 1 ATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTAT 50 chr2qtel1M 5029 CTAT 5032 v (ATGT)n#Simpl 51 GTAT 54 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.02 (1 / 51), avg. gap size = 2.00 (2 / 1) 602 34.21 4.73 2.22 chr2qtel1M 5186 5756 (994244) C L1ME4c_3end#LINE/L1 (190) 640 56 m_b82s551i2 3035 chr2qtel1M 5186 ATTCTGCTCATTTTGCTCTCCATTATTTTGTGCAAATCTTTCCATGTTTT 5235 iv ii ivv v ii iv v - vi C L1ME4c_3end#L 640 ATTCTGCTTTTTTCACTTAACATTATATCATAAACAT-TTTCCATGTTGC 592 chr2qtel1M 5236 TCTAAAATCATCAAGCTCATCATTTCTTATATCAGAGTAGTATTTCATCA 5285 vi v i v viv i i v iv v vi i i i C L1ME4c_3end#L 591 TACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCG 542 chr2qtel1M 5286 TGAACATATGCCACAACTT---TAA-----------TTGATTGACATCTC 5321 v v?v i i i i --- ----------- v v i v C L1ME4c_3end#L 541 AGTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTA 492 chr2qtel1M 5322 CTCAATTTCTAATTCTTTGTCACCACTAAGAAAGATGC--TAGACATTTT 5369 vvivi i i i ii ii iv v v v -- ii i C L1ME4c_3end#L 491 GGTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTT 442 chr2qtel1M 5370 TGAACACATAGGTTTTTTTTTCCTTCTGTTTCCTCTAATCAT---CTTGG 5416 i vi i ----i v v----- i --- i C L1ME4c_3end#L 441 CGTGCATATAG----CTTTTTCCTTCTTTTG-----AATTATTTCCTTAG 401 chr2qtel1M 5417 AAAACAGATCTAATGGTGATAGTATTGGAATAAAGGGTATAGACAGCTTA 5466 i v v vvi i ivi iv v i ivi ii vi v C L1ME4c_3end#L 400 GATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTT 351 chr2qtel1M 5467 ATAACATTTTGG-GCATAATTCCAAATCATTCTATAAAATAGTTTGGTCA 5515 ii - i i-i i v v iii i vi vi vvii C L1ME4c_3end#L 350 ATGGC-TCTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCA 302 chr2qtel1M 5516 GCTCACAGATCCACCAACAATGAATCAGTGTCCCAATTTTCCCCCATCCC 5565 ii i ?vv i v v ? v i iv v ? i C L1ME4c_3end#L 301 ATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCT 252 chr2qtel1M 5566 CTTCATTATTTGTTGCTTTC---CTTTCAACTATTTTAGCCAATCTCATA 5612 vi vi v v ii v ---i i -- v i i v C L1ME4c_3end#L 251 CGCCAGCATTGGGTATTATCAATTTTTTAA--ATTTTTGCTAATTTAATA 204 chr2qtel1M 5613 ACTGTAAAA---TATTTCAAGTTTGTTTTAATTTGTATTTCTCTAATTAT 5659 ivi --- i vvv i i i i i C L1ME4c_3end#L 203 GGCGTAAAATGGTATCTCATTGTTGCTTTAATTTGCATTTCTTTGATTAC 154 chr2qtel1M 5660 TAATGATTTAGAACATTTTT-CATATGCCTATAAATTATTTTGATTCCTT 5708 ii vv v - i ii i vv i ? vv i i C L1ME4c_3end#L 153 TAGCGAGGTTGAACATTTTTCCATGTGTTTGTTTACTANTTGTATTTCCT 104 chr2qtel1M 5709 CATCAAAAAACTGCCTCTTCATAGCTTTTCAGCATTCCTTAATTGGGG 5756 v ?vivi i i v iv i vvv iv iv C L1ME4c_3end#L 103 CTTNTGTGAATTGTCTGTTCATGTCCTTTGCCCATTTATCTATTGGGG 56 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 45.86 CpG sites = 108, Kimura (unadjusted) = 47.95 Transitions / transversions = 1.30 (108/83) Gap_init rate = 0.04 (21 / 570), avg. gap size = 1.90 (40 / 21) 591 32.17 2.28 2.57 chr2qtel1M 5450 5800 (994200) C L1ME3C_3end#LINE/L1 (509) 361 12 m_b82s551i3 3035 chr2qtel1M 5450 AGGGTATAGACAGCTTAATAACATT-TTGGGCATAATTCCAAATCATTCT 5498 ivi v --i v -i i -- v v iii C L1ME3C_3end#L 361 AGGGTATGCGCATCTT--CAACTTTACTAG--ATATTGCCAAATTGCTCT 316 chr2qtel1M 5499 ATAAAATAGTTTGGTCAGCTCACAGATCCACCAACAATGAATCAGTGTCC 5548 vi i i vvii ii i vvi i i v v v i C L1ME3C_3end#L 315 CCAAAGTGGTTGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTTC 266 chr2qtel1M 5549 CAATTTTCCCCCATCCCCTTCATTATTTGTTGCTTTC---CTTTCAACTA 5595 vi vii v i vi vi i v ii v --- i -- C L1ME3C_3end#L 265 CCGTTGCTCCACATCCTCGCCAACACTTGGTATTGTCAGACTTTTAA--A 218 chr2qtel1M 5596 TTTTAGCCAATCTCATAACTGTAAAAT---ATTTCAAGTTTGTTTTAATT 5642 v v iiv i --- i vvv ? C L1ME3C_3end#L 217 TTTTTGCCAATCTGATGGGTGTGAAATGGTATCTCATTGTNGTTTTAATT 168 chr2qtel1M 5643 TGTATTTCTCTAATTATTAATGATTTAGAACAT-TTTTCATATGCCTATA 5691 i i i i i vv v i - ii v C L1ME3C_3end#L 167 TGCATTTCCCTGATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATT 118 chr2qtel1M 5692 AATTATTTTGATTCCTTCATCAAAAAACTGCCTCTTCATAGCTTTTCAGC 5741 iiii iv?i i i v vivi i v v vvv C L1ME3C_3end#L 117 GGCCATTCGNGTTTCCTCTTCTGTGAATTGCCTGTTCATATCTTTTGCCC 68 chr2qtel1M 5742 ATTCCTTAATTGGGGAACAATCCATCTTTTTAAAGATTTGACATAGTTCT 5791 ii iv ---ivi ii i i vv vviv C L1ME3C_3end#L 67 ATTTTTCTATTGGG---TTGTCTGTTTTCTTATTGATTTGTAGGAGTTCT 21 chr2qtel1M 5792 TAATATATT 5800 v C L1ME3C_3end#L 20 TTATATATT 12 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 42.05 CpG sites = 63, Kimura (unadjusted) = 43.64 Transitions / transversions = 1.34 (63/47) Gap_init rate = 0.04 (13 / 350), avg. gap size = 1.31 (17 / 13) 633 31.54 3.11 1.53 chr2qtel1M 5487 5808 (994192) C L1ME5_3end#LINE/L1 (611) 330 4 m_b82s551i4 3035 chr2qtel1M 5487 CCAAATCATTCTATAAAATAGTTTGGTCAGCTCACAGATCCACCAACAAT 5536 i iii vi i i i vvii iii vvi i i C L1ME5_3end#LI 330 CCAGATTGCTCTCCAGAATGGCTGCACCAGTCTACACTCCCACCAGCAGT 281 chr2qtel1M 5537 GAATCAGTGTCCCAATTTTCCCCCATCCCCTTCATTATTTGTTGCTTTCC 5586 v v v i v ? i v i vi vi i viii v C L1ME5_3end#LI 280 GCATGAGGGTTCCTATNTCCCCACATCCTCGCCAACACTTGGCATTATCC 231 chr2qtel1M 5587 ---TTTCAACTATTTTAGCCAATCTCATAACTGTAAA---ATATTTCAAG 5630 --- v -- v i v iv --- i vv C L1ME5_3end#LI 230 AGCTTTCTA--ATTTTTGCCAGTCTAATAGGTGTAAAGTGATATCTCATT 183 chr2qtel1M 5631 TTTGTTTTAATTTGTATTTCTCTAATTATTAATGATTTAGAACAT-TTTT 5679 v i i i v v i - i C L1ME5_3end#LI 182 GTTGTTTTAATTTGCATTTCTCTGATTACTAATGAGTTTGAGCATCTCTT 133 chr2qtel1M 5680 CATATGCCTATAAATTATTTTGATTCCTTCATCAAAAAACTGCCTCTTCA 5729 i i v iiiv iv i i i v viv i v C L1ME5_3end#LI 132 CATATGCTTGTTAGCCTTTCGGGTTTCCTCTTCTGTAAATTGCCTGTTCA 83 chr2qtel1M 5730 TAGCTTTTCAGCATTCCTTAATTGGGGAACAATCCATCTTT---TTAAAG 5776 v i vvv ii iv ---vv? i --- ivv C L1ME5_3end#LI 82 TATCCTTTGCCCATTTTTCTATTGGGG---TTNCCGTCTTTTTCTTGTTG 36 chr2qtel1M 5777 ATTTGACATAGTTCTTAATATATTTGAGGCAT 5808 vviv i vi iv ii C L1ME5_3end#LI 35 ATTTGCAGGAGTTCCTTGTATATTCTAGATAT 4 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.25 CpG sites = 56, Kimura (unadjusted) = 42.37 Transitions / transversions = 1.27 (56/44) Gap_init rate = 0.03 (9 / 321), avg. gap size = 1.67 (15 / 9) 230 33.90 4.14 2.37 chr2qtel1M 6050 6339 (993661) C L1MC_orf2#LINE/L1 (384) 2910 2616 m_b82s551i5 3036 chr2qtel1M 6050 TTTCATGTCTAGGTC-ATGTACCCATTTTGACTTGG-----GTAAATGGT 6093 i ii i - - i v ii----- i v C L1MC_orf2#LIN 2910 TTTTACATTTAGGTCTATG-ATCCATTTTGAGTTAATTTTTGTGAAGGGT 2862 chr2qtel1M 6094 GTAAGACATTGGTCTATGTTTAATTTCTTTCAGACTGCTTTTCCATTTCC 6143 iiv vv vi i v i v vi- vv v v vi C L1MC_orf2#LIN 2861 GTAAGGTCTGTGTCTAGATTCATTTTTTTGCATG-TGGATGTCCAGTTGT 2813 chr2qtel1M 6144 CCCA-CAACTTTTACTAAATA-ATGAATTCTTGACC--TGAAAGGTTACA 6189 i - v v ii i v - iv vi i vv -- ? --- i - C L1MC_orf2#LIN 2812 TCCAGCACCATTTGTTGAAAAGACTATCTTTTCTCCATTGNA---TTGC- 2767 chr2qtel1M 6190 TCTTTACACAT--ATCAAACACTAGATTACTATATTCATTTGCTGCTGTA 6237 - i v v --i v ii v v i v vvv i v C L1MC_orf2#LIN 2766 -CTTTGCTCCTTTGTCAAAGATCAGTTGACTATATTTATGTGGGTCTATT 2718 chr2qtel1M 6238 AATTGTATGTCTATTCTGTCCCACTGAAGTACTTTTCTATTTCTTTGCAT 6287 vv v vv v i i vv i v ii i vv C L1MC_orf2#LIN 2717 TCTGGGCTCTCTATTCTGTTCCATTGATCTATTTGTCTATTCTTTCGCCA 2668 chr2qtel1M 6288 GTACCAGGCAGTTTTGATAATCATTGCCTTATAATATGTTTTAAGATCTA 6337 i vi v i v iii v i i v i i ii vi C L1MC_orf2#LIN 2667 ATACCACACTGTCTTGATTACTGTAGCTTTATAGTAAGTCTTGAAGTCGG 2618 chr2qtel1M 6338 GT 6339 C L1MC_orf2#LIN 2617 GT 2616 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 45.49 CpG sites = 48, Kimura (unadjusted) = 46.14 Transitions / transversions = 1.00 (48/48) Gap_init rate = 0.04 (13 / 289), avg. gap size = 1.46 (19 / 13) 269 26.74 1.16 0.00 chr2qtel1M 6247 6332 (993668) C L1PB_orf2#LINE/L1 (586) 2708 2622 m_b82s551i6 3036 chr2qtel1M 6247 TCTATTCTGTCCCACTGAAGTACTTTTCTATTTCTTTGCATGTACCAGGC 6296 i i ivv iv vi i v i vv v C L1PB_orf2#LIN 2708 TCTATTCTGTTCCATTGGTCTATGTGCCTATTTTTATACCAGTACCATGC 2659 chr2qtel1M 6297 AGTTTTGATAATCATTGCCTTATAATAT-GTTTTAAG 6332 v i i ii v i - v C L1PB_orf2#LIN 2658 TGTTTTGGTGACTATGGCCTTATAGTATAGTTTGAAG 2622 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.51 CpG sites = 12, Kimura (unadjusted) = 33.51 Transitions / transversions = 1.09 (12/11) Gap_init rate = 0.01 (1 / 85), avg. gap size = 1.00 (1 / 1) 17 14.77 0.00 5.00 chr2qtel1M 6415 6456 (993544) (ATATCT)n#Simple_repeat 1 40 (0) m_b82s252i5 3037 chr2qtel1M 6415 ATATTTATACCCATATCTATCTTTCTATACCTATATCTATAT 6456 i i i -- v i (ATATCT)n#Sim 1 ATATCTATATCTATATCTA--TATCTATATCTATATCTATAT 40 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.05 (2 / 41), avg. gap size = 1.00 (2 / 2) 257 31.37 3.61 4.69 chr2qtel1M 6471 6664 (993336) C L1MC_orf2#LINE/L1 (807) 2487 2296 m_b82s551i7 3036 chr2qtel1M 6471 TGGAATGGCATTGTATATATAGATCAACTTAGGTGAAATTATTGTTTGTA 6520 i v v v v i vii i ivii i vv C L1MC_orf2#LIN 2487 TGGGATTGCATTGAATCTATAGATCAAGTTGGGAAGAACTGACATCTTGA 2438 chr2qtel1M 6521 TTAAAATGGCTCTACCTACCCATTAAGAATGAATGTTTATCCATTTATTT 6570 iv v v iv v i v v vv i i v C L1MC_orf2#LIN 2437 CAATATTGAGTCTTCCTATCCATGAACATGGAATATCTCTCCATTTATTT 2388 chr2qtel1M 6571 AAATC-----TGACTTTATCTATACAAAATTTAAAAAAATAATTTTGTTC 6615 i? ----- i iv ii - i i -----vi i vi C L1MC_orf2#LIN 2387 AGNTCTTCTTTGATTTCTTTCAT-CAGAGTTT-----TGTAGTTTTCCTC 2344 chr2qtel1M 6616 ACATAGTTCCTGGGTTTGTTTTGGCAG--TTATACTTCACAGGTATTTTA 6663 i v i viiv i vi -- i --- i i C L1MC_orf2#LIN 2343 ATATAGATCTTGTACATATTTTGTTAGATTTATACCT---AAGTATTTCA 2297 chr2qtel1M 6664 T 6664 C L1MC_orf2#LIN 2296 T 2296 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 42.04 CpG sites = 33, Kimura (unadjusted) = 42.04 Transitions / transversions = 1.32 (33/25) Gap_init rate = 0.06 (11 / 193), avg. gap size = 1.45 (16 / 11) 258 31.07 0.96 0.96 chr2qtel1M 6472 6575 (993425) C L1P1_orf2#LINE/L1 (808) 2486 2383 m_b82s551i8 3036 chr2qtel1M 6472 GGAATGGCATTGTATATATAGATCAACTTAGGTGAAATTATTGTTTGTAT 6521 i v v i i v i iiiv viiii vi i C L1P1_orf2#LIN 2486 GGGATGGCATTGAATCTATAAATTACCTTGGGCAGTATGGCCATTTTCAC 2437 chr2qtel1M 6522 TAAAATGGCTCTACCTACCCATTAAGAAT-GAATGTTTATCCATTTATTT 6570 v v v ii v - i v - iv i C L1P1_orf2#LIN 2436 GATATTGATTCTTCCTACCCA-TGAGCATGGAATGTTCTTCCATTTGTTT 2388 chr2qtel1M 6571 AAATC 6575 iv C L1P1_orf2#LIN 2387 GTATC 2383 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.75 CpG sites = 19, Kimura (unadjusted) = 41.45 Transitions / transversions = 1.46 (19/13) Gap_init rate = 0.02 (2 / 103), avg. gap size = 1.00 (2 / 2) 446 24.35 1.48 8.73 chr2qtel1M 6697 6831 (993169) C MIRc#SINE/MIR (141) 127 2 m_b82s601i4 3038 chr2qtel1M 6697 CTGAGGC-AATTGGGGTTAAATGACTTGTCCAGGATCAC-CAGCTAGGAG 6744 -v vv i i i i i - --- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG--- 81 chr2qtel1M 6745 GTGTTAAGTGTTTGAGGTCAAATTTGAACTCAGATCCTCCTGACTTCAGG 6794 ---- viv vivii i i i i i i i C MIRc#SINE/MIR 80 ----TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr2qtel1M 6795 GCTGGTGCTCTATTCCAGTGCACCATCTAGCTGCCCC 6831 v ii - v i---i i C MIRc#SINE/MIR 34 TCCAGTGCTCT-TTCCACTGCACCAC---ACTGCCTC 2 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.01 CpG sites = 21, Kimura (unadjusted) = 30.41 Transitions / transversions = 2.33 (21/9) Gap_init rate = 0.10 (13 / 134), avg. gap size = 1.00 (13 / 13) 1116 29.41 3.87 0.90 chr2qtel1M 6917 7458 (992542) C L1M5_orf2#LINE/L1 (1269) 2025 1468 m_b82s551i9 3035 chr2qtel1M 6917 TAAGATCTCCAATATAACATTAAATAATATTAGTGACAGTGGACATCCTT 6966 i i i i ii i iv v i ? i C L1M5_orf2#LIN 2025 TAGGACCTCCAGTACAATGTTGAATAGAAGTGGTGANAGCGGACATCCTT 1976 chr2qtel1M 6967 GTTTCATATCTAATCTCACTGAGAAGTCTTCTAGCTTATTCCTATTACAA 7016 i ii vi ii i vv i iv ? ii i? v iv i -- C L1M5_orf2#LIN 1975 GTCTTGTTCCCGATCTTAGGGGGAAAGCNTTCAGTNTTTCACCATTA--A 1928 chr2qtel1M 7017 AAATGGTGTTAG--GTAAATATTTCTTAA---CAATTTA--AGG--GAAA 7057 iv i ? -- ii v v i--- vv -- -- ii C L1M5_orf2#LIN 1927 GTATGATGTTNGCTGTAGGTTTTTCGTAGATGCCCTTTATCAGGTTGAGG 1878 chr2qtel1M 7058 AAAATCCATT-TGTATCTAATCTTTTAAGTGTTTTTAATAGAAATTAGTG 7106 iv v - i vi i i vi i v vi vi vi C L1M5_orf2#LIN 1877 AAGTTCCCTTCTATTCCTAGTTTGCTGAGAGTTTTTATCATGAATGGGTG 1828 chr2qtel1M 7107 TTGTACTTTATCAAATGCTTTTTCTGCATCTATTGAAATAATCATATGAT 7156 v i i i i C L1M5_orf2#LIN 1827 TTGAATTTTGTCAAATGCTTTTTCTGCATCTATTGAGATGATCATATGAT 1778 chr2qtel1M 7157 TTTTGTTACTTTTATTATTGTT-ATA-GTTGGA-TATGTTAATGGTTTTC 7203 v -- i -i - - v i - ii i v v i C L1M5_orf2#LIN 1777 TTTTCT--CCTTTATT-CTGTTAATATGGTGAATTACATTGATTGATTTT 1731 chr2qtel1M 7204 TTTATGCTAAATCATCCCTGCGTTCGTGGTATGAA--TCATTTGGTCATG 7251 ivv i i v i i v v i --i i C L1M5_orf2#LIN 1730 CGAATGTTAAACCAACCTTGCATTCCTGGGATAAACCCCACTTGGTCATG 1681 chr2qtel1M 7252 GTGTGCAATCTTTGTAATATATTGT--AATCT--TTAAGTAGTATTTTAT 7297 i iiv i v v i--i ii-- viv i i C L1M5_orf2#LIN 1680 ATGTATTATCCTTTTTATATATTGCTGGATTCGATTTGCTAATATTTTGT 1631 chr2qtel1M 7298 TTAGAATTTTTGCATCTATATTCATTAATTAAATTGGTTTATAATTTTCT 7347 ? i i v ivv v i i C L1M5_orf2#LIN 1630 TNAGGATTTTTGCATCTATGTTCATGAGGGATATTGGTCTGTAATTTTCT 1581 chr2qtel1M 7348 TTCTCTGTTTTTACTTTTACTTGTTT--ACATCAATGTTACATTTGTTTC 7395 iii vv vv vv ?v --ii iv ? iii v ii C L1M5_orf2#LIN 1580 TTTCTTGTAATGTCTTTGTCNGGTTTTGGTATCAGGGTNATGCTGGCCTC 1531 chr2qtel1M 7396 ATAAAAGAAGTTTGGTAGAACTCCTTCTTTGCCAATTATTCAAAATAATT 7445 vi v v vii i vi v v iiii v i C L1M5_orf2#LIN 1530 ATAAAATGAGTTGGGAAGTGTTCCCTCTTTTTCTATTTTCTGGAAGAGTT 1481 chr2qtel1M 7446 TATTTAATGTTGG 7458 i v vi C L1M5_orf2#LIN 1480 TGTGTAAGATTGG 1468 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.13 CpG sites = 99, Kimura (unadjusted) = 39.47 Transitions / transversions = 1.68 (99/59) Gap_init rate = 0.03 (17 / 541), avg. gap size = 1.53 (26 / 17) 289 29.62 6.86 1.63 chr2qtel1M 7964 8138 (991862) C L1ME3G_3end#LINE/L1 (397) 527 344 m_b82s551i10 3039 chr2qtel1M 7964 ATACTATAGTTTATTCAGCCATTCCCCAATTGATGGGTATCCTCTCAATT 8013 i i i i v ii iivvvivi C L1ME3G_3end#L 527 ATACCATAATTTATTTAACCATTCCCCTATTGATGGACATTTAGGTTGTT 478 chr2qtel1M 8014 TCCCATTCTCTGCCCTGAGAAAAGA-GCTGTTAT--ACA----TATAGAT 8056 v i ii iv v v vi - iv -- ---- i v C L1ME3G_3end#L 477 TCCAATTTTTCGCTATTACAAACAATGCTGCAATGAACATCCTTGTACAT 428 chr2qtel1M 8057 TCTTTCCCTTAAAAAAA----CAAA-ATTCTTTTGGGATTCATGCCTAGT 8101 v ? -- iviv v ---- i i- ii ? i vv ? ? v C L1ME3G_3end#L 427 GCNT--CCTTGTGCACATGTGCGAGTATTTCTNTAGGATAGATNCCNAGA 380 chr2qtel1M 8102 AGGGGTATTGTTAGGTCAAAGGATATGTATGATTTTA 8138 v v i i i iii- C L1ME3G_3end#L 379 AGTGGAATTGCTGGGTCAAAGGGTATGCGC-ATTTTA 344 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.98 CpG sites = 30, Kimura (unadjusted) = 40.09 Transitions / transversions = 1.43 (30/21) Gap_init rate = 0.05 (8 / 174), avg. gap size = 1.88 (15 / 8) 14 15.86 2.86 0.00 chr2qtel1M 9184 9218 (990782) (GAGGACA)n#Simple_repeat 1 36 (0) m_b82s252i6 3040 chr2qtel1M 9184 GAGG-CAGAGGGAAGAGGAGAGAGGTCAGAGAACAG 9218 - iv v v i (GAGGACA)n#Si 1 GAGGACAGAGGACAGAGGACAGAGGACAGAGGACAG 36 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 66 0.00 0.00 4.35 chr2qtel1M 9242 9313 (990687) (ATC)n#Simple_repeat 1 69 (0) c_b82s251i0 3041 chr2qtel1M 9242 ATCATCATCAATCATCATCATCATCATCATCATCATCAATCATCATCATC 9291 - - (ATC)n#Simple 1 ATCATCATC-ATCATCATCATCATCATCATCATCATC-ATCATCATCATC 48 chr2qtel1M 9292 ATCATCATCATCATCAATCATC 9313 - (ATC)n#Simple 49 ATCATCATCATCATC-ATCATC 69 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.04 (3 / 71), avg. gap size = 1.00 (3 / 3) 12 9.26 0.00 0.00 chr2qtel1M 9314 9328 (990672) (CTC)n#Simple_repeat 9 23 (1) m_b82s252i7 3042 chr2qtel1M 9314 CTCCTCCTCCTCCTC 9328 (CTC)n#Simple 9 CTCCTCCTCCTCCTC 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 14), avg. gap size = 0.0 (0 / 0) 15 0.00 5.26 0.00 chr2qtel1M 11711 11729 (988271) (AT)n#Simple_repeat 1 20 (0) m_b82s252i8 3043 chr2qtel1M 11711 ATATATATATATATAT-TAT 11729 - (AT)n#Simple_ 1 ATATATATATATATATATAT 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.06 (1 / 18), avg. gap size = 1.00 (1 / 1) 428 31.81 1.87 3.80 chr2qtel1M 11981 12248 (987752) C L1ME4a_3end#LINE/L1 (316) 555 293 m_b82s551i11 3044 chr2qtel1M 11981 ATAATATTCCATTATATTCATATACCATAATTTATTCGGCTATTTCTCAA 12030 ? vv i iii i ? i i v C L1ME4a_3end#L 555 ATAATATTCCATTNTATGGATGTACCATAATTTATTTAACCANTCCCCTA 506 chr2qtel1M 12031 TCAATGTGCATCCACTCAATTTCTAATTCCTTGCCACTACAAAAAGAAGT 12080 iiv vi ii vvivi i ii i i i i v i--- C L1ME4a_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAA---T 459 chr2qtel1M 12081 GCTCC----AACCTTTTTTTGCACGTTACCCTTCCCTCCCCCCCTCCTTT 12126 v ---- v ii -- i i v vi iv- ? v vi ivv C L1ME4a_3end#L 458 GCTGCGATGAACATCCTT--GTACATAAATCTTTG-TNCACATCTCTGAT 412 chr2qtel1M 12127 TATGAACTTTTTGGGATACAGACCCAGGAGAGACATTGTTGGATCAAAGG 12176 ---i ii i v vv i i v iv ii i C L1ME4a_3end#L 411 TAT---TTCCTTAGGATAAATTCCTAGAAGTGGAATTACTGGGTCAAAGG 365 chr2qtel1M 12177 GTGTGTACAATTTTATAGCCCTTTGG-GCACAGTTCCAGATTTCTCTGCA 12225 i ? v - v i i-i i v v i v i v C L1ME4a_3end#L 364 GTATGNACATTTTTA-AGGCTTTTGATACATATTGCCAAATTGCCCTCCA 316 chr2qtel1M 12226 GAATGGCTAGATCAATTCACACT 12248 v i iv i i C L1ME4a_3end#L 315 GAAAGGTTGTACCAATTTACACT 293 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.33 CpG sites = 51, Kimura (unadjusted) = 44.07 Transitions / transversions = 1.65 (51/31) Gap_init rate = 0.04 (12 / 267), avg. gap size = 1.25 (15 / 12) 16 0.00 0.00 0.00 chr2qtel1M 12536 12553 (987447) (A)n#Simple_repeat 1 18 (0) m_b82s252i9 3045 chr2qtel1M 12536 AAAAAAAAAAAAAAAAAA 12553 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAA 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 13 31.00 0.00 3.28 chr2qtel1M 13221 13283 (986717) (TTTAA)n#Simple_repeat 1 61 (0) m_b82s252i10 3046 chr2qtel1M 13221 TTCAATTGTATTTAAAGTAGTAGCATTTTGTATATTATATATTTAATTTA 13270 i vv vv i vvv vi v v v - (TTTAA)n#Simp 1 TTTAATTTAATTTAATTTAATTTAATTTAATTTAATTTA-ATTTAATTTA 49 chr2qtel1M 13271 TATTTAATATAAT 13283 - v (TTTAA)n#Simp 50 -ATTTAATTTAAT 61 Matrix = Unknown Transitions / transversions = 0.25 (3/12) Gap_init rate = 0.03 (2 / 62), avg. gap size = 1.00 (2 / 2) 55 6.57 0.00 0.00 chr2qtel1M 13535 13599 (986401) (CA)n#Simple_repeat 1 65 (0) c_b82s251i1 3047 chr2qtel1M 13535 CACACACACACACATACACACACACACACATACACACACACACACACACA 13584 i i (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 chr2qtel1M 13585 CACATACATACACAC 13599 i i (CA)n#Simple_ 51 CACACACACACACAC 65 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0) 16 14.95 0.00 5.13 chr2qtel1M 15395 15435 (984565) (TCTTCTT)n#Simple_repeat 1 39 (0) m_b82s252i11 3048 chr2qtel1M 15395 TCTTCCTTCTCCTTTTTCTCTTTCATATTTCTTGCTTTCTT 15435 i i i - v v - (TCTTCTT)n#Si 1 TCTTCTTTCTTCTTTCT-TCTTTCTTCTTTCTT-CTTTCTT 39 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 201 33.40 9.62 5.56 chr2qtel1M 16040 16299 (983701) C MamRTE1#LINE/RTE-BovB (2882) 930 661 m_b82s601i5 3049 chr2qtel1M 16040 CAGAATTCATCATGGGAGCAACATGTGCACTGAT---GGTGTTGTAGTGC 16086 i v i vi vii i i --- vii? i C MamRTE1#LINE/ 930 CGGTATTCGTCATGGTGGGGGCATATGCGCTGATGACGGTGGCANAGCGC 881 chr2qtel1M 16087 CTTC-CTGC-GAGG--GGCG-ATTGTCATGAGCCTGTTGCTCACTCCTTT 16131 i i-i v - ? -- - vv v v v ii ? iv i C MamRTE1#LINE/ 880 TTTTGTTTCAGANGTAGGCGTAGGGTCATCAGACGGTCACTNATGCCTCT 831 chr2qtel1M 16132 TGG-AGACATACAAGCTT--ATTTAGGAGATTATTTTTGATTGCAAAACT 16178 v - i iv ivi ?i -- vvi i v i i-- i i C MamRTE1#LINE/ 830 GGGCAAATTTGGGAGNCTTGAGACAAGTGACTG--TCTGATTGCAAAGCT 783 chr2qtel1M 16179 CATGGAAGCTTCATGGTGCTCCCCATCCCTGCTG-----------CTACT 16217 ---- v i v vi ------ i v - ----------- iv C MamRTE1#LINE/ 782 ----GACGCCTGAGAG------CCGTCGCT-CTGAAGAGGGAAGACCTCT 744 chr2qtel1M 16218 CCACAAAAATGTGTTTCCAG--CTTGAACTTTGAGAAACTGGCCTTTATT 16265 v i v i v? i -- i -v ii v - i v i i C MamRTE1#LINE/ 743 CCAGAAGAAGGCGTANCCGGCACCTG-TCTCCGTG-AGCTGTCCTTCATC 696 chr2qtel1M 16266 TACCAGCCTTGTTCCACTCGGT-CTGTGATTTAGA 16299 vivv i v i i i - v i v v C MamRTE1#LINE/ 695 AGGAAGTCTGGTTTCGCTCAGTGCGGCGATGTCGA 661 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.66 CpG sites = 47, Kimura (unadjusted) = 47.18 Transitions / transversions = 1.34 (47/35) Gap_init rate = 0.10 (25 / 259), avg. gap size = 1.60 (40 / 25) 21 10.47 0.00 0.00 chr2qtel1M 16425 16455 (983545) (TG)n#Simple_repeat 1 31 (0) m_b82s252i12 3050 chr2qtel1M 16425 TGTGTGTGTCTGTGTGTCTGTGTGTCTGTGT 16455 v v v (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 31 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 312 29.03 9.14 1.60 chr2qtel1M 16489 16663 (983337) C MamRTE1#LINE/RTE-BovB (3330) 482 295 m_b82s601i6 3049 chr2qtel1M 16489 GTGAGC-AGGCCAGGGGTGAGTGAAGCTGACAATTTTCAGGGAAGCTTTT 16537 - ?iiv i?v vi i i v i iv i v v C MamRTE1#LINE/ 482 GTGAGCCAGNTTTGANTTTGGCGAGGCAGGCAACGTTTAGGGCACCTTTT 433 chr2qtel1M 16538 CCAGTCCCTTCCCCATGTCAGGAAGTGGACA-C-TGGTCCTTAAGAAGGC 16585 i ? - -- i ii - -i ? v v i C MamRTE1#LINE/ 432 CTAGNCCCTTCCCCAT-TC--GGAGTGAGCAGCGCGNTCCTAAACAGGGC 386 chr2qtel1M 16586 TTCCTAGGTGCCCAAGG-GCTGCTGAATCCCACTCCTCCTTC--CAGGGA 16632 v ii iii i ?- i ivvii v v i -- v C MamRTE1#LINE/ 385 TGCTCAGACACCCAGGNCGCTGCCGAACGGTGCTGCTGCCTCNTCAGCGA 336 chr2qtel1M 16633 GAAGACAGC------CCTGGGCCACGT----GTATAGGACT 16663 vv ii ii ------ i v ---- i ? C MamRTE1#LINE/ 335 CTAAGCGACCAATATCCTGGGCCGCCTACTCGCANAGGACT 295 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.18 CpG sites = 32, Kimura (unadjusted) = 40.17 Transitions / transversions = 1.78 (32/18) Gap_init rate = 0.06 (10 / 174), avg. gap size = 1.90 (19 / 10) 203 24.50 0.00 2.04 chr2qtel1M 17283 17332 (982668) C L3#LINE/CR1 (1241) 2858 2810 m_b82s601i7 3051 chr2qtel1M 17283 ACTCCTGTGGGCTCTTGGTGATCACAGCTTCCCTTTTCTACACATTCACA 17332 i v iv i i v - viiii C L3#LINE/CR1 2858 ACCCATGCTGGCTCCTAGTGATCACCGCTT-CCTTTTCTAAGTGCTCACA 2810 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 30.68 CpG sites = 8, Kimura (unadjusted) = 30.68 Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.02 (1 / 49), avg. gap size = 1.00 (1 / 1) 305 34.35 1.32 5.52 chr2qtel1M 17578 17728 (982272) MIR#SINE/MIR 43 187 (75) m_b82s601i8 3052 chr2qtel1M 17578 ATTGTATGATTCCAAAGCCCTAAGTCTGG-ACTAATCTGGTTGTA-GACA 17625 i iv iv i i v -iiv v- v - i i i- - MIR#SINE/MIR 43 ACTGCCTGGGTTCGAATCCC-GGCTCTGCCACTTA-CTAGCTGTGTGAC- 89 chr2qtel1M 17626 CTTAGTACCCACAGGTGACTTGACCCCAATTTGCTTCCATTTCCTCACTA 17675 i -----i i v i i vv v i vi iiv MIR#SINE/MIR 90 CTTGG-----GCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCT 134 chr2qtel1M 17676 GTAAAATGGAGATGACGATAGCACCGTCTCTGTGGGGTTATCCTGAAGAC 17725 i i ii i vv iiii i i iv i i MIR#SINE/MIR 135 GTAAAATGGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGGAT 184 chr2qtel1M 17726 CAA 17728 i MIR#SINE/MIR 185 TAA 187 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 46.40 CpG sites = 34, Kimura (unadjusted) = 49.31 Transitions / transversions = 2.27 (34/15) Gap_init rate = 0.07 (10 / 150), avg. gap size = 1.00 (10 / 10) 242 31.48 10.45 2.78 chr2qtel1M 17637 17770 (982230) MIRb#SINE/MIR 103 246 (22) m_b82s601i9 3052 chr2qtel1M 17637 CAGGTGACTTGACCCCAATTTGCTTCCATTTCCTCACTAGTAAAATGGAG 17686 i v i i vv vv i vi iiv i MIRb#SINE/MIR 103 CAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGG 152 chr2qtel1M 17687 ATGACGATAGCACCGTCTCTGTGGGGTTATCCTGAAGACCAAGCC---TA 17733 ---i ii vv iii ii i iv i ii iiv--- MIRb#SINE/MIR 153 AT---AATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATA 199 chr2qtel1M 17734 --GCAT----AGCACCTGGCACAG-----AGCAGGTAGTAAAGCGTTC 17770 -- ---- i i i -----i vi - i MIRb#SINE/MIR 200 ATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGT-AAGCGCTC 246 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.85 CpG sites = 29, Kimura (unadjusted) = 43.76 Transitions / transversions = 2.42 (29/12) Gap_init rate = 0.06 (8 / 133), avg. gap size = 2.25 (18 / 8) 65 25.17 2.67 3.12 chr2qtel1M 17965 18189 (981811) (AAG)n#Simple_repeat 1 224 (0) m_b82s252i13 3053 chr2qtel1M 17965 AAGAAGAATGACAATAATGAGAAGAATAAGAACAAAAAGAGGAGGAGGAG 18014 vi v v vi v v i i i i i (AAG)n#Simple 1 AAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAA 50 chr2qtel1M 18015 GAAGAACGAGAGGAAGAA-AAGAAGGATCAACAAGAAGAGGAAG-AGAAG 18062 vi i - - vv v i - - (AAG)n#Simple 51 GAAGAAGAAGAAGAAGAAGAAGAA-GAAGAAGAAGAAGAAGAAGAAGAA- 98 chr2qtel1M 18063 GAAAAAG-AGAAGGAGGAAGAACCAG-AGAAAAAGGAGGAGGAAGAAGAG 18110 i - - i vv - i - i i i (AAG)n#Simple 99 GAAGAAGAAGAA-GAAGAAGAAGAAGAAGAAGAA-GAAGAAGAAGAAGAA 146 chr2qtel1M 18111 GAAG-AGAAGGAATAGGAACAAGAAG-GGGAGAAGAAACAACTAGATGAG 18158 - - v i v -i i - v vv v i (AAG)n#Simple 147 GAAGAAGAA-GAAGAAGAAGAAGAAGAAGAAGAAG-AAGAAGAAGAAGAA 194 chr2qtel1M 18159 GAAAAGGAGGAACAAGAGGAAAGATGCAGAA 18189 i i i v i - v v (AAG)n#Simple 195 GAAGAAGAAGAAGAAGAAG-AAGAAGAAGAA 224 Matrix = Unknown Transitions / transversions = 1.14 (24/21) Gap_init rate = 0.06 (13 / 224), avg. gap size = 1.00 (13 / 13) 82 26.87 2.59 0.00 chr2qtel1M 18893 19124 (980876) (GA)n#Simple_repeat 1 238 (0) m_b82s252i14 3054 chr2qtel1M 18893 GAGAGAGAAACAGAGAGAGAGAAATGGGGGGAG-GGGGGAGACAAAGACA 18941 i v i vi i i - i i v i v (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr2qtel1M 18942 GAGACA-AAAGAGAAAGACAGAGAGAGACA-AGAGA-AGGGGGGGGGGGA 18988 v - i i v v - - i i i i i (GA)n#Simple_ 51 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 100 chr2qtel1M 18989 GAGACAAAGAGAAACAGAGACAGAGACAAAGGGAG-GAGAGAGAGACAGA 19037 v i i v v v i i - v (GA)n#Simple_ 101 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 150 chr2qtel1M 19038 GAGAGAGAG-GGGAGAGACAGAGACAAAGTGGGGGAGAGAGGGGGGAAAA 19086 - i v v i v i i i i ii i (GA)n#Simple_ 151 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 200 chr2qtel1M 19087 GAGGGAGGGAGGGAGAAGGAAAGAGGGAGACAGAGAGA 19124 i i i ii i i v (GA)n#Simple_ 201 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 238 Matrix = Unknown Transitions / transversions = 2.19 (35/16) Gap_init rate = 0.03 (6 / 231), avg. gap size = 1.00 (6 / 6) 268 30.83 0.00 4.40 chr2qtel1M 19130 19224 (980776) C MIR3#SINE/MIR (10) 198 108 m_b82s601i10 3055 chr2qtel1M 19130 ATTATAGAGGACAAGTTCTGGGAAGGATCTTTGGAGGTCACCTTGTTCAA 19179 i iviiv vv i i i -i i i v i C MIR3#SINE/MIR 198 ATCATAGAATGTCAGAGCTGGAAGGGACCTT-AGAGATCATCTAGTCCAA 150 chr2qtel1M 19180 CCCAGTTATCATTTTGGAAAGCAAGAAAATGAGCCCCAGAAGGGT 19224 ---iv iv i vv i v v ii C MIR3#SINE/MIR 149 CCC---CCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGT 108 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.03 CpG sites = 17, Kimura (unadjusted) = 41.03 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.04 (4 / 94), avg. gap size = 1.00 (4 / 4) 37 15.51 0.00 0.00 chr2qtel1M 19487 19546 (980454) (T)n#Simple_repeat 1 60 (0) m_b82s252i15 3056 chr2qtel1M 19487 TTTCTTTCTTTCTTTCTTTTTCTTTTCTTTTCTTTTCTTTTTTTTTTTTT 19536 i i i i i i i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr2qtel1M 19537 TTTTTTTTTT 19546 (T)n#Simple_r 51 TTTTTTTTTT 60 Matrix = Unknown Transitions / transversions = 1.00 (8/0) Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0) 242 36.56 9.52 6.98 chr2qtel1M 20977 21270 (978730) C L3#LINE/CR1 (8) 4091 3791 m_b82s601i11 3057 chr2qtel1M 20977 CATAGATTCTGAGAAAGAGAAGAAGCCTTTAGAGGCTG-CTACTCTTACC 21025 i v v ivvi iii - iii- v iv C L3#LINE/CR1 4091 CACAGAATCTCAGAGTTGGAAGGGACCTT-AGAGGTCATCTAGTCCAACC 4043 chr2qtel1M 21026 TCCCATGGAATATAAAACCAAACCAACCAAACCATTGTTCCCAACATCTT 21075 vv ii ii ------------ v v v --v ii C L3#LINE/CR1 4042 TCCCATCCAATGCAGGA------------ATCCCTTCT--ACAACATCCC 4007 chr2qtel1M 21076 TTAGAAA--G--ATCCAACTACTACCAAAAAATAGCTGCTGATAGGAAGG 21121 v v i-- -- i iv i ivi v ivv iiv ii i v C L3#LINE/CR1 4006 TGACAAGTGGTCATCCAGCCTCTGCTTGAACACCTCCAGTGACGGGGAGC 3957 chr2qtel1M 21122 AAGCCAGTGCCTTGGAATATCGCCCATTCTGTCATTGGATGGAATTAACT 21171 ---i v i i?vi viiv ii iv ii vvi i i C L3#LINE/CR1 3956 ---TCACTACCTCNCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGATT 3910 chr2qtel1M 21172 TTTAGAG-GTT---------------------TCTGTTTCATTGGAAACA 21199 v i- --------------------- ii vi v - v C L3#LINE/CR1 3909 GTTAGAAAGTTCTTCCTTATATTGAGCCGAAATCTGCCTCCCTGTAA-CT 3861 chr2qtel1M 21200 TTAACCCATTGATCCTTTTCCCATCCTCTAGCGCTAAACAGAAACTTACC 21249 iv i vv i iii i v i v -- v vi C L3#LINE/CR1 3860 TCCACCCATTGGTCCTAGTTCTGCCCTCTGGAGCCACACAGAA--TAAGT 3813 chr2qtel1M 21250 TTAGT-CTTCCCCCCCATGACA 21270 i i - i ii v C L3#LINE/CR1 3812 CTAATCCCTCTTCCACATGACA 3791 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 51.40 CpG sites = 60, Kimura (unadjusted) = 53.07 Transitions / transversions = 1.50 (60/40) Gap_init rate = 0.09 (27 / 293), avg. gap size = 1.81 (49 / 27) 230 35.09 1.75 0.00 chr2qtel1M 21374 21487 (978513) C L3#LINE/CR1 (798) 3301 3186 m_b82s601i12 3057 chr2qtel1M 21374 TTATTCCAACATTTTGAGATGTCTTGGACTCAGTATTCTGTCATAATATG 21423 ii i v v i v?i v v vvv vvv?i C L3#LINE/CR1 3301 TCGTTCCAGCCTGTCGAGATCNTTTTGAATCTTGATTCTGTCATCCANCG 3252 chr2qtel1M 21424 TGCTTGTGATCTCTTT--GTTTTAGGGCATCAACAACTCTGAAGAGTATT 21471 ii v iv i ii-- i iv v vi v i vi i v C L3#LINE/CR1 3251 TATTAGCTATCCCTCCCAGCTTTGTGTCATCTGCAAATTTGATAAGCATG 3202 chr2qtel1M 21472 CATTCTATCCCTTCAT 21487 v vi C L3#LINE/CR1 3201 CCTTCTATGTCTTCAT 3186 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 44.14 CpG sites = 19, Kimura (unadjusted) = 49.16 Transitions / transversions = 0.90 (19/21) Gap_init rate = 0.01 (1 / 113), avg. gap size = 2.00 (2 / 1) 231 25.49 0.00 0.00 chr2qtel1M 21913 21963 (978037) HSAT5v1#Satellite 5221 5271 (627) m_b82s502i0 3058 chr2qtel1M 21913 ATATGTGTGTGTGAGTATGTGCACATGTGTATGTGTGTGCACATGTGTGT 21962 i iiv iii i ii i ? ii HSAT5v1#Satel 5221 ATGTGTGTGTGCACGCGCGTGCGCGCGTGTGTGTGTGTGNACGCGTGTGT 5270 chr2qtel1M 21963 G 21963 HSAT5v1#Satel 5271 G 5271 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 15.01 CpG sites = 12, Kimura (unadjusted) = 35.68 Transitions / transversions = 12.00 (12/1) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 16 14.95 0.00 5.13 chr2qtel1M 22198 22238 (977762) (TCTTCTT)n#Simple_repeat 1 39 (0) m_b82s252i16 3059 chr2qtel1M 22198 TCTTCCTTCTCCTTTTTCTCTTTCATATTTCTTGCTTTCTT 22238 i i i - v v - (TCTTCTT)n#Si 1 TCTTCTTTCTTCTTTCT-TCTTTCTTCTTTCTT-CTTTCTT 39 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 14 30.68 0.00 0.00 chr2qtel1M 22336 22384 (977616) (TTTT)n#Simple_repeat 1 49 (0) m_b82s252i17 3060 chr2qtel1M 22336 TTCTTTCTTCTATTTTTCATTTCCCTCTTGGTTTTTTTTTTTTTTTTTT 22384 i i i v iv iii i vv (TTTT)n#Simpl 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 49 Matrix = Unknown Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 285 15.69 0.00 1.96 chr2qtel1M 24416 24467 (975533) MIR3#SINE/MIR 118 168 (40) m_b82s601i13 3061 chr2qtel1M 24416 GCCTCAGTTTCCTTATCTAAAAATTGAGGGAGTAGGACTAGAATGATACC 24465 i iv v i v - vi MIR3#SINE/MIR 118 GCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAG-ATGATCTC 166 chr2qtel1M 24466 TA 24467 MIR3#SINE/MIR 167 TA 168 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 17.68 CpG sites = 4, Kimura (unadjusted) = 17.68 Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.02 (1 / 51), avg. gap size = 1.00 (1 / 1) 32 0.00 3.23 0.00 chr2qtel1M 25367 25397 (974603) (TG)n#Simple_repeat 1 32 (0) c_b82s251i2 3062 chr2qtel1M 25367 TGTGTG-GTGTGTGTGTGTGTGTGTGTGTGTG 25397 - (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 32 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.03 (1 / 30), avg. gap size = 1.00 (1 / 1) 78 15.22 3.43 2.26 chr2qtel1M 25398 25572 (974428) (AGACAG)n#Simple_repeat 1 177 (0) m_b82s252i19 3063 chr2qtel1M 25398 AGAGAGAGAGAGAGACAGACAGACAGATACAGACAGACAGAGAC--AGAC 25445 v v -- v -- -- (AGACAG)n#Sim 1 AGACAGAGACAGAGACAG--AGACAGAGACAG--AGACAGAGACAGAGAC 46 chr2qtel1M 25446 -GAGACAGAGAGACAGAC-GAGACAGAGAGACAGAGAGACACAGTGACAC 25493 - v v - v v v v v v (AGACAG)n#Sim 47 AGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAG 96 chr2qtel1M 25494 A-A-TGACACAGAGACAGAGAAAGAGACACACACAAAGGCAGAGACAGAG 25541 - -v v v v v i i (AGACAG)n#Sim 97 AGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAG 146 chr2qtel1M 25542 AAAGAGACACACACAAAGGCAGAGACAGAGA 25572 v v v i i (AGACAG)n#Sim 147 ACAGAGACAGAGACAGAGACAGAGACAGAGA 177 Matrix = Unknown Transitions / transversions = 0.21 (4/19) Gap_init rate = 0.05 (9 / 174), avg. gap size = 1.11 (10 / 9) 18 19.81 2.17 0.00 chr2qtel1M 25734 25779 (974221) (AAAAAT)n#Simple_repeat 1 47 (0) m_b82s252i21 3064 chr2qtel1M 25734 AAAACTAAAAA-AAAAAAAAATAAAAAAATAATAATAATGGTAAAAA 25779 v - v v v v vii (AAAAAT)n#Sim 1 AAAAATAAAAATAAAAATAAAAATAAAAATAAAAATAAAAATAAAAA 47 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1) 14 22.64 2.44 0.00 chr2qtel1M 25739 25779 (974221) (TAA)n#Simple_repeat 1 42 (0) m_b82s252i22 3064 chr2qtel1M 25739 TAAAAAAAAAAAAAATAA-AAAAATAATAATAATGGTAAAAA 25779 v v v v - v ii v (TAA)n#Simple 1 TAATAATAATAATAATAATAATAATAATAATAATAATAATAA 42 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 20 18.65 0.00 0.00 chr2qtel1M 25734 25770 (974230) (A)n#Simple_repeat 1 37 (0) m_b82s252i20 3064 chr2qtel1M 25734 AAAACTAAAAAAAAAAAAAATAAAAAAATAATAATAA 25770 vv v v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 37 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 3142 29.57 2.16 2.10 chr2qtel1M 26635 28254 (971746) L1M5_orf2#LINE/L1 1674 3294 (0) m_b82s551i12 3065 chr2qtel1M 26635 AATTCAT-ATGATCAAGTAGGATTTATACCAGGAATGCAGGGCTGGTTCA 26683 v - i i i v i i i L1M5_orf2#LIN 1674 AATACATCATGACCAAGTGGGGTTTATCCCAGGAATGCAAGGTTGGTTTA 1723 chr2qtel1M 26684 ATATTAGGAAAACTATCAATATAATTGGCCATGTTAATA-ACCAAATTAA 26732 i v i v v i vi i i - vi -vi L1M5_orf2#LIN 1724 ACATTCGAAAATCAATCAATGTAATTCACCATATTAACAGAATAAA-GGA 1772 chr2qtel1M 26733 CAAAAACCATATGATCATCTCAACAGATGCAGAAAAAGCATTTGATAAAA 26782 v i i i L1M5_orf2#LIN 1773 GAAAAATCATATGATCATCTCAATAGATGCAGAAAAAGCATTTGACAAAA 1822 chr2qtel1M 26783 TCCAACATCCATTCCTATTAAAAACACTTGAGAGTATAGGAATAAATGGA 26832 i i v iv v iiiv ivv i v i L1M5_orf2#LIN 1823 TTCAACACCCATTCATGATAAAAACTCTCAGCAAACTAGGAATAGAAGGG 1872 chr2qtel1M 26833 CTTTTCCTTAAAATAATCAGCAGCATCTATTTAAAACCATCAGTAAGCAT 26882 vvi i vv i v ivi ivv vv i? i L1M5_orf2#LIN 1873 AACTTCCTCAACCTGATAAAGGGCATCTACGAAAAACCTACAGCNAACAT 1922 chr2qtel1M 26883 CATATGTAATGGAGACAAACTGCAACCATTCCCAATAAGATCTGGAGTGA 26932 iv v v ? v ?v v vv v iii L1M5_orf2#LIN 1923 CATACTTAATGGTGAAANACTGAANGCTTTCCCCCTAAGATCGGGAACAA 1972 chr2qtel1M 26933 AACAAGGTTGCCCACTATCACCGTTACTATTTAATATTGTATTAGAAACG 26982 i v i i ? ii v i i i i iiiv L1M5_orf2#LIN 1973 GACAAGGATGTCCGCTNTCACCACTTCTATTCAACATTGTACTGGAGGTC 2022 chr2qtel1M 26983 CTAGCTATAGCAATAAGAGCTGAGAAAGAGATTAAAGGAATAAGAATAGG 27032 i vv ivvv i i v v ii v L1M5_orf2#LIN 2023 CTAGCCAGTGCAATAAGGCAAGAAAAAGAAATAAAAGGCATAAAGATTGG 2072 chr2qtel1M 27033 CAATGAGGAAGCCAAATTATCACTCTTTGCCGATGACATGATGGTATACT 27082 v v i iiv i i ?i v i v v ? v L1M5_orf2#LIN 2073 AAAGGAAGAAATAAAACTGTCNTTATTCGCAGATGACATGATTGTNTACG 2122 chr2qtel1M 27083 TAGAGAACCCCAGAGATTCTGCTAAAAAGTTATTAGAAATAATCCACAAC 27132 i i ? i v i v ? ii i v vviii v L1M5_orf2#LIN 2123 TAGAAAATCCNAAAGAATCTACAAANAAACTACTAGAACTAATAAGTGAA 2172 chr2qtel1M 27133 TTTAGCAAAGTTGCTGGTTATAAAATAAACCCACATAAGTCATCAGCATT 27182 i i ? v i ii v ivi v i viv i L1M5_orf2#LIN 2173 TTTAGCAAGGTCGCNGGATACAAGGTCAATATACAAAAATCAATTGTATT 2222 chr2qtel1M 27183 CTTATATATCACTAACAA--AATCCAACAGTCAGAGTTACAAAGAGAAAT 27230 ii ii vi -- ivi v i v i v --? i iv L1M5_orf2#LIN 2223 TCTATATACTAGCAACAAACAATTGGAAAATGAAATTT--NAAAAACAAT 2270 chr2qtel1M 27231 TCCATTTAAAGTAACTACTGATAATATAAAATATTTAGGAATCTATCTGC 27280 v v i i vv vi v i ? i vv iv L1M5_orf2#LIN 2271 ACCATTTACAATAGCATCAAAAAACATNAAATACTTAGGAATAAATCTAA 2320 chr2qtel1M 27281 CAAGGGAAAAT---CAGAAACTTTATGAGCAAAATTACAGACCACTTTTC 27327 --- ? --- ii v ? iivvv i i v i vi v L1M5_orf2#LIN 2321 CAA---AANATGTGCAAGACCTNTACACTGAAAACTACAAAACATTGCTG 2367 chr2qtel1M 27328 ACACAAATTAAGTCTGATCTAACCAATTGGAAAAATATTAAATGCTCTTG 27377 v v ivvv i vi v i i vvv i v L1M5_orf2#LIN 2368 AGAGAAATTAAAGAAGACCTAAATAAATGGAGAGATATACCATGTTCATG 2417 chr2qtel1M 27378 GATAGGGCGAGCAAATATAATAAAGATGACAATATTACCTAAACTAATCT 27427 v iv viv vi ? v vi v i i i L1M5_orf2#LIN 2418 GATTGGAAGACTCAATATTGTNAAGATGTCAATTCTCCCCAAATTGATCT 2467 chr2qtel1M 27428 ATTTATTTAGCGCTATACCAATCAGACTCCCAAAAAACTATTTTAATGAC 27477 vv i ii v v i v iv iii v ivv v L1M5_orf2#LIN 2468 ATAGATTCAATGCAATCCCAATCAAAATCCCAGCAGGTTTTTTTGTAGAA 2517 chr2qtel1M 27478 CTAGAAAAAATAACAACAAAGTTCATATGGAAAAACAAAAGGTCAAGAAT 27527 v v v iv i ivvi i i vi i ii ? L1M5_orf2#LIN 2518 ATTGACAAGCTGATTCTAAAATTTATATGGAAATGCAAAGGACCNAGAAT 2567 chr2qtel1M 27528 -TTCAAGGGAATTAATGAAAAA-AAAATCAAATGATGGTGG-CTTAGCTG 27574 -vi iiv i-v - i v - v v - - vv L1M5_orf2#LIN 2568 AGCCAAAACAATC-TTGAAAAAGAAGAACAAA-GTTGGAGGACTTA-CAC 2614 chr2qtel1M 27575 TACCAGATCT-AAAATTATATTATAGAGCAGCAGTTACCAAAACTATTTG 27623 ? ? - i i - i vi v i i vi v L1M5_orf2#LIN 2615 TACCNGATNTCAAGACT-TATTATAAAGCTACAGTAATCAAGACAGTGTG 2663 chr2qtel1M 27624 GTATTGGC-TAAGGAATAGATTAGTTGATCAGTGGAATAGATTAG---GT 27669 - - iv i v i i v --- L1M5_orf2#LIN 2664 GTATTGGCGTAAGG-ATAGACAAATAGATCAATGGAACAGAATAGAGAGT 2712 chr2qtel1M 27670 TCAAGGGATAAAACAGTCA-ACAAATATAGCAACCTAGTCTTTGACAAA- 27717 i - ii i v --- - v i ?v ?i ii i - L1M5_orf2#LIN 2713 CC-AGAAATAGACC---CACACATATATGGNCANTTGATTTTTGACAAAG 2758 chr2qtel1M 27718 --CCCAAAG-ATCCCAGCTTTTGGGATAAGAACTTACTGTTTGATAAAAA 27764 --v ? - vii ---- iv i ivvv v ii i vi L1M5_orf2#LIN 2759 GTGCCAANGCAATTCAG----TGGGGAAAGGATAGTCTTTTCAACAAATG 2804 chr2qtel1M 27765 TTGCTGGGAAAATTGGAAACTAATATGGCAGAAACTAGGCATTGATCCAT 27814 v i v v iiv v i v iii?v i i v L1M5_orf2#LIN 2805 GTGCTGGAACAATTGGATATCCATATGGAAAAAAATGAANCTCGACCCCT 2854 chr2qtel1M 27815 ACTTAACGCCGTACACCAAGATAAGGTCAAAATGGGTTCAT-GACCTAGG 27863 i v i i v i v iv ? i i- - ii L1M5_orf2#LIN 2855 ACCTCACACCATACACAAAAATTAATTCNAGATGGA-TCATAGACCTAAA 2903 chr2qtel1M 27864 CATAAAGAATGAAATTATTAATAAATTAGAGG--AACATAGGATAGTTTA 27911 ii ii? i i v vvvvi i -- v i-- L1M5_orf2#LIN 2904 TGTAAAAGNTAAAACTATAAAACTTCTAGAAGAAAACATAGGAGAA--TA 2951 chr2qtel1M 27912 CCTCTCAGACCTGTGGA-AGGGGAAGGTCTTTATGACCAAAGCAGAACTA 27960 i iivv vv ?- vi i i i - i v iii v -- L1M5_orf2#LIN 2952 TCTTCGTGACCTTGGGNTAGGCAAAGATTTCT-TAAACAGGACACAA--A 2998 chr2qtel1M 27961 GAGATCATTACTGATCACAAAATAGAAAAT-------TTCGATTATACCA 28003 i -----i ?i i i v i ------- v i ?i i L1M5_orf2#LIN 2999 AAG-----CACNAACCATAAAAGAAAAAATTGATAAATTGGACTNCATCA 3043 chr2qtel1M 28004 AACTGAAAAGTTTTTGTACAAACAAAACTAATGCAGACAAGATTAGAAGG 28053 v v ii i iv ?vvv ivi vi ivi v i v i L1M5_orf2#LIN 3044 AAATTAAAAACTTCTGCTCNTCAAAAGACACCGTTAAGAAAATGAAAAGG 3093 chr2qtel1M 28054 GAAGCAATAAACTGGGAAAATATTTTTACAGT-CAAAGGTTCTGATAAAG 28102 v v i i ? i v v i i?- v vi- i L1M5_orf2#LIN 3094 CAAGCCACAGANTGGGAGAAAATATTTGCAANACATATA-TCTGACAAAG 3142 chr2qtel1M 28103 GCCTCATTTCCAAAATATATAGAGAATTAACTCTAATTT-ATAAAAAATC 28151 v i v i i i -v vi ? i- ? -- L1M5_orf2#LIN 3143 GACTCGTATCCAGAATATATAAAGAACT-CCTACAANTCAATAANAAA-- 3189 chr2qtel1M 28152 AAGCCATTC--TCCAATTGAAAAATGGTCAAAGGATATGAACAGACAATT 28199 v vv --i v? v i iv v L1M5_orf2#LIN 3190 AAGACAAACAACCCAATANAAAAATGGGCAAAAGACTTGAACAGACACTT 3239 chr2qtel1M 28200 CTCAGATGAAGAAATTGAAACTATTTCTAGTCATATGAAAAGATGCTCCA 28249 v i v v ?v iviiivv iv i v L1M5_orf2#LIN 3240 CACAAAAGAAGATATNCAAATGGCCAATAAGCACATGAAAAGATGCTCAA 3289 chr2qtel1M 28250 AGTCA 28254 v? L1M5_orf2#LIN 3290 CNTCA 3294 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.62 CpG sites = 255, Kimura (unadjusted) = 39.48 Transitions / transversions = 1.19 (255/214) Gap_init rate = 0.03 (55 / 1619), avg. gap size = 1.25 (69 / 55) 1576 27.06 3.31 3.80 chr2qtel1M 28111 28744 (971256) L1ME5_3end#LINE/L1 7 637 (304) m_b82s551i14 3065 chr2qtel1M 28111 TCCAAAATATATAGAGAATTAACTCTAATTTATAAAAAATCAAGCCATT- 28159 i i i ii i vviv v iv i i -- v iv?- L1ME5_3end#LI 7 TCTAGAATATACAAGGAACTCCTGCAAATCAACAAGAAA--AAGACGGNA 54 chr2qtel1M 28160 -CTCCAATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGA 28208 - i v v i iv v L1ME5_3end#LI 55 ACCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGA 104 chr2qtel1M 28209 AGAAA-TTGAAA--CTATTTCTAGTCATATGAAAAGATGCTCCAAGTCAT 28255 i -ii -- --v v - i v v L1ME5_3end#LI 105 GGAAACCCGAAAGGCTA--ACAAG-CATATGAAGAGATGCTCAAACTCAT 151 chr2qtel1M 28256 TATTAATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACA 28305 v i vv i i vi L1ME5_3end#LI 152 TAGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACA 201 chr2qtel1M 28306 CCTGTCAGATTGGCTAAGATGACAGGAAA---AAATAATGATGATTGTTG 28352 i i i v i v --- ---ii vii v L1ME5_3end#LI 202 CCTATTAGACTGGCAAAAATTA---GAAAGCTGGATAATGCCAAGTGTTG 248 chr2qtel1M 28353 GAGGGGATGTGGGAAAACTGGGACATTGATTCATTGTTGGTGGAGTTGTG 28402 v i i ? iv i vi v v i i iiv i L1ME5_3end#LI 249 GCGAGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTA 298 chr2qtel1M 28403 AACGAATCCAACCATTTTGGAGAGTAGTTTGGAACTA--TGCTCAAA--A 28448 i vii v i i i i i v v -- iv -- L1ME5_3end#LI 299 GACTGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTA 348 chr2qtel1M 28449 AGTTATCAAACTGTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGAT 28498 - --- --- v i i viii v vv L1ME5_3end#LI 349 AG-TAT---AC---GCATACCCTATGACCCAGCAATTCCGCTCCTGGGTA 391 chr2qtel1M 28499 TATATCCCAAAGAGATTATAAAGAAGG----GAAAGGGACCTGTATGTGC 28544 i v v viv ----v i ---- i L1ME5_3end#LI 392 TATATCCCAAAGAAATTCTCACACAGGTCCATAAGGGGAC----ATGTAC 437 chr2qtel1M 28545 ACGAATGTTTGTGGCAGCCCTTTTTGTAGTGGCTAGAAACTGGAAACTGA 28594 iv i ii v vi v i vi i ii ii viv L1ME5_3end#LI 438 GAGGATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAAC 487 chr2qtel1M 28595 ATGGATGTCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATATGAAA 28644 v i v v i v iii v iv v v L1ME5_3end#LI 488 CTGGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCAC 537 chr2qtel1M 28645 ATTATGGAATATTACTGT-TCTGTAAGAAATGACCAACAGGATGATTTCA 28693 ii i i - i-v v v iii vi vi -- v L1ME5_3end#LI 538 ACCATGGAGTACTA-TGCAGCAGTTAGAAGCAACGGACTAGATG--TACA 584 chr2qtel1M 28694 GAAAG--GCCTGGAGAGA-CTTACACGAAC-TGATGCTGAGTGAAATGAG 28739 v v --i v vi - v -- - ii vi L1ME5_3end#LI 585 CATAGCAACATGGATGGATCTTAAA--AACATAGTGCTGAGTGAAAAAAG 632 chr2qtel1M 28740 CAGGA 28744 i i L1ME5_3end#LI 633 TAAGA 637 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.36 CpG sites = 94, Kimura (unadjusted) = 34.40 Transitions / transversions = 1.32 (94/71) Gap_init rate = 0.06 (36 / 633), avg. gap size = 1.25 (45 / 36) 1620 27.27 0.36 1.66 chr2qtel1M 28111 28658 (971342) L1ME3G_3end#LINE/L1 7 547 (377) m_b82s551i13 3065 chr2qtel1M 28111 TCCAAAATATATAGAGAATTAACTCTAATTTATAAAAAATCAAGCCATTC 28160 i i i vviv v iv i -- v --v L1ME3G_3end#L 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAA--AAGACA--A 52 chr2qtel1M 28161 TCCAATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGAAG 28210 i v v i v v i L1ME3G_3end#L 53 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chr2qtel1M 28211 AAATTGAAACTATTTCTAGTCATATGAAAAGATGCTCCAAGTCATTATTA 28260 vv iviiivv iv v vv i v L1ME3G_3end#L 103 AAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTA 152 chr2qtel1M 28261 ATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACACCTGT 28310 i i vv i i viv ii L1ME3G_3end#L 153 ATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCAT 202 chr2qtel1M 28311 CAGATTGGCTAAGATGACAGGAAAAAATAATGATGATTGTTGGAGGGGAT 28360 v i vvv iii?vvi ivi? v v i i L1ME3G_3end#L 203 CAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGT 252 chr2qtel1M 28361 GTGGGAAAACTGGGACATTGATTCATTGTTGGTGGAGTTGTGAACGAATC 28410 i v v vi v v i i iiv i ivii v L1ME3G_3end#L 253 GTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTA 302 chr2qtel1M 28411 CAACCATTTTGGAGAGTAGTTTGGAACTATGCTCAAAAAGTTATCAAACT 28460 i ? i i i v v - vvv i -- i v L1ME3G_3end#L 303 CAGCCNTTTTGGAGGGCAATTTGGCAGTAT-CTATTAAAAT--TTAAAAT 349 chr2qtel1M 28461 GTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGATTATATCCCAAAG 28510 i i i vii v ? ?v v i ? L1ME3G_3end#L 350 GCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAG 399 chr2qtel1M 28511 AGATTAT-AAAGAAG-GGAAAGGGACCTGTATGTGCACGAATGTTTGTGG 28558 i vv -iv v v - v v i --? i i v i ii v L1ME3G_3end#L 400 AAATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTCATTG 447 chr2qtel1M 28559 CAGCCCTTTTTGTAGTGGCTAGAAACTGGAAACTGAATGGATGTCCATCA 28608 vi v i i v i i vivv ii L1ME3G_3end#L 448 CAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCA 497 chr2qtel1M 28609 GTTGGAGAATGGCTGAATAAATTGTGGTATATGAAAATTATGGAATATTA 28658 i v i i i i vv v i i L1ME3G_3end#L 498 ATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACTA 547 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.35 CpG sites = 76, Kimura (unadjusted) = 34.93 Transitions / transversions = 1.07 (76/71) Gap_init rate = 0.02 (11 / 547), avg. gap size = 1.00 (11 / 11) 19 11.70 0.00 0.00 chr2qtel1M 29201 29228 (970772) (A)n#Simple_repeat 1 28 (0) m_b82s252i23 3066 chr2qtel1M 29201 AAATAAAAAAAAAAAATAAAAATAAAAA 29228 v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA 28 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 18 30.38 2.44 1.20 chr2qtel1M 29417 29498 (970502) (ATAT)n#Simple_repeat 1 83 (0) m_b82s252i24 3067 chr2qtel1M 29417 ATCTATATGAATATAAAT-TCTATATCTATATCTATATGAATATGAATGA 29465 v iv v - v v v iv iv - (ATAT)n#Simpl 1 ATATATATATATATATATATATATATATATATATATATATATATATAT-A 49 chr2qtel1M 29466 AATATCTATATGAAAATAAAT-TTTATACAAATA 29498 v v iv v v - v i v (ATAT)n#Simpl 50 TATATATATATATATATATATATATATATATATA 83 Matrix = Unknown Transitions / transversions = 0.33 (5/15) Gap_init rate = 0.04 (3 / 81), avg. gap size = 1.00 (3 / 3) 22 25.76 3.85 0.00 chr2qtel1M 29421 29498 (970502) (ATATAA)n#Simple_repeat 1 81 (0) m_b82s252i25 3067 chr2qtel1M 29421 ATATGAATATAAAT-TCTATATCTATATCTATATGAATATGAAT-GAAAT 29468 i - vv vv vv i i -v (ATATAA)n#Sim 1 ATATAAATATAAATATAAATATAAATATAAATATAAATATAAATATAAAT 50 chr2qtel1M 29469 ATCTATATGAAAATAAAT-TTTATACAAATA 29498 vv i v - vv i (ATATAA)n#Sim 51 ATAAATATAAATATAAATATAAATATAAATA 81 Matrix = Unknown Transitions / transversions = 0.42 (5/12) Gap_init rate = 0.04 (3 / 77), avg. gap size = 1.00 (3 / 3) 296 15.39 0.00 1.92 chr2qtel1M 30274 30326 (969674) C MIR3#SINE/MIR (40) 168 117 m_b82s601i14 3068 chr2qtel1M 30274 TAGATATCATTCTAGTCCTACTCCCTCATTTTTAAGATAGGGAAATTGAG 30323 v - v i vv ii i C MIR3#SINE/MIR 168 TAGAGATCAT-CTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAG 120 chr2qtel1M 30324 GCC 30326 C MIR3#SINE/MIR 119 GCC 117 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 17.29 CpG sites = 4, Kimura (unadjusted) = 17.29 Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.02 (1 / 52), avg. gap size = 1.00 (1 / 1) 53 17.35 2.94 3.70 chr2qtel1M 32038 32173 (967827) (TTCC)n#Simple_repeat 1 135 (0) m_b82s252i26 3069 chr2qtel1M 32038 TTTCTTCCTTACTTCCTTCCCTCCCTTTC-TCCCTCCCTCCTTCCCTTCC 32086 i v - i i - i i - (TTCC)n#Simpl 1 TTCCTTCCTTCCTTCCTT-CCTTCCTTCCTTCCTTCCTTCCTT-CCTTCC 48 chr2qtel1M 32087 TTCCTTCCTTCTTTCCTTCCTTTCCCTCCCTTCCTTCCTCCCTCTCTTCC 32136 i - - i i ii (TTCC)n#Simpl 49 TTCCTTCCTTCCTTCCTTCC-TT-CCTTCCTTCCTTCCTTCCTTCCTTCC 96 chr2qtel1M 32137 -ACC-CCCTTTCTCTCCTTCCTT-TTTTCATCTTTCTTTC 32173 -v -i i - -i i v i i (TTCC)n#Simpl 97 TTCCTTCCTTCCT-TCCTTCCTTCCTTCCTTCCTTCCTTC 135 Matrix = Unknown Transitions / transversions = 5.33 (16/3) Gap_init rate = 0.07 (9 / 135), avg. gap size = 1.00 (9 / 9) 208 34.51 1.11 3.41 chr2qtel1M 32353 32442 (967558) L2a_3end#LINE/L2 428 515 (2) m_b82s601i15 3070 chr2qtel1M 32353 GCCTCTTTCTTTC-TTTTTGTATATTCAGGGTTCAATATAATAATATCTG 32401 i v iv -i vi vii v ii--- v i i ii L2a_3end#LINE 428 GTCTGTTTTGTTCACTGCTGTATCCCCAGCGCC---TAGAACAGTGCCTG 474 chr2qtel1M 32402 GCCCACAGACAGCGCTGAATAAAAGCTTGCTGACTGAGTGA 32442 v i vvi v vii i v i L2a_3end#LINE 475 GCACATAGTAGGCGCTCAATAAATATTTGTTGAATGAATGA 515 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 48.19 CpG sites = 18, Kimura (unadjusted) = 48.19 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.04 (4 / 89), avg. gap size = 1.00 (4 / 4) 342 27.05 5.43 5.43 chr2qtel1M 32540 32668 (967332) MIRc#SINE/MIR 4 132 (136) m_b82s601i16 3071 chr2qtel1M 32540 GGCAATGGAATGTATTTGAAAGAACACTGATTCTGGAGTCA-GAAGATCA 32588 i vii i v v i ivii - i v MIRc#SINE/MIR 4 GGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCT 53 chr2qtel1M 32589 GGCTTTGAACCCCAGCTCTGACTCTTGCTTGAGCTTCCATGTCCTTGTCG 32638 v i ii i v v i -- - vii v -- MIRc#SINE/MIR 54 GGGTTCGAGTCCCGGCTCTGCCACTTACT--AGC-TGTGTGACCTTG--G 98 chr2qtel1M 32639 ATATGAGTCAT----CCCCTCTGGGACT--ATTTCC 32668 ii -- i---- i i v --i MIRc#SINE/MIR 99 GCA--AGTCACTTAACCTCTCTGAGCCTCAGTTTCC 132 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.32 CpG sites = 22, Kimura (unadjusted) = 34.94 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.08 (10 / 128), avg. gap size = 1.40 (14 / 10) 16 15.95 0.00 2.78 chr2qtel1M 32837 32873 (967127) (AAAACA)n#Simple_repeat 1 36 (0) m_b82s252i27 3072 chr2qtel1M 32837 AAGACAAGAAAGGGAAAAAAAAACAAAAACAAAAACA 32873 i - vii v (AAAACA)n#Sim 1 AAAACAA-AAACAAAAACAAAAACAAAAACAAAAACA 36 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 229 24.14 1.72 0.00 chr2qtel1M 33893 33950 (966050) L1ME5_3end#LINE/L1 56 114 (827) m_b82s551i15 3073 chr2qtel1M 33893 CCTCAAT-GAAAAATGGTCAAATAGTAGAAATAGACAGTTTTCAAAAGAA 33941 i - v vii vi i i i v i i L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chr2qtel1M 33942 GAAATCCGA 33950 i L1ME5_3end#LI 106 GAAACCCGA 114 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 30.41 CpG sites = 10, Kimura (unadjusted) = 30.41 Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.02 (1 / 57), avg. gap size = 1.00 (1 / 1) 205 29.94 5.88 6.67 chr2qtel1M 33979 34114 (965886) C L2#LINE/L2 (659) 2423 2289 m_b82s601i17 3074 chr2qtel1M 33979 CATCAAATTGGCAAAGATGACAA------AGTGAGA-ATATGAGTTTTGT 34021 v v --- v i ------ vi - i i v v C L2#LINE/L2 2423 CATCCAAGTGG---AGATGTCGAGTAGGCAGTTGGATATACGAGTCTGGA 2377 chr2qtel1M 34022 GTTAATGCATTCTTGGAGATTAGGGCTGGATAAGTAGATAAGAGGATCAT 34071 v v vi-----i i iv v vi i vv i ii C L2#LINE/L2 2376 GTTCAGGGG-----AGAGGTCCGGGCTGGAGATATAAATTTGGGAGTCAT 2332 chr2qtel1M 34072 TAGTCTCCAGGTGGTAATTAAATCCACAGAAGCTG-ATGAGATC 34114 i iv vi i v v i- ii - C L2#LINE/L2 2331 CAGCATATAGATGGTATTTAAAGCCAT-GAGACTGGATGAGATC 2289 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.29 CpG sites = 20, Kimura (unadjusted) = 38.84 Transitions / transversions = 1.11 (20/18) Gap_init rate = 0.09 (12 / 135), avg. gap size = 1.42 (17 / 12) 652 19.25 4.17 4.17 chr2qtel1M 34668 34835 (965165) Charlie4a#DNA/hAT-Charlie 341 508 (0) m_b82s502i1 3075 chr2qtel1M 34668 AACTTGATTTTTTTAACATATATTAATAATTCCATTTCAATATAATTCAT 34717 i ? ---v v i i vi vi Charlie4a#DNA 341 AATTTGNTTTTTT---AATATTTTGATAACTGTATTTCAATATAATTGGT 387 chr2qtel1M 34718 TTCCTTTGGGATCCT-----CTTTATTTCACGCACTTAAAAGCATAATTC 34762 vi -----i i i i i v Charlie4a#DNA 388 TTCCTTTGTAATCCTATGTATTTTATTTTATGCATTTAAAAACATTATTC 437 chr2qtel1M 34763 TGAGAAGGTGTCCATAGGTTTGGCCAGAATGTCATCAAAGGCTTCTGTGA 34812 v i vi v ---i vv ii i Charlie4a#DNA 438 TGAGAAGGGGTCCATAGGCTTCACCAGACTG---CCAAAGGGGTCCATGG 484 chr2qtel1M 34813 TGCAAGAAAAGGT--AGAACCTCTG 34835 ii - -- i Charlie4a#DNA 485 CACAA-AAAAGGTTAAGAACCCCTG 508 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 22.89 CpG sites = 20, Kimura (unadjusted) = 22.89 Transitions / transversions = 1.82 (20/11) Gap_init rate = 0.05 (9 / 167), avg. gap size = 1.56 (14 / 9) 421 21.67 7.27 3.51 chr2qtel1M 35363 35472 (964528) C MIRc#SINE/MIR (153) 115 2 m_b82s601i18 3076 chr2qtel1M 35363 GGGGTTAAGTGACTTGCCCAGGATCACACTGGCTAGGAAGTGTTA----- 35407 i i i -i v vi ----- C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACAC-AGCTAGTAAGTGGCAGAGCC 67 chr2qtel1M 35408 ---ATTTTAACTCAGATCCTCCTGACTTCAGGGCTGGTGCTCTATCCACT 35454 --- i iv i i i i i v ii v C MIRc#SINE/MIR 66 GGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACT 17 chr2qtel1M 35455 GAGCCACCTAGCTGCCCC 35472 vi ---i i C MIRc#SINE/MIR 16 GCACCAC---ACTGCCTC 2 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 25.35 CpG sites = 17, Kimura (unadjusted) = 26.69 Transitions / transversions = 2.83 (17/6) Gap_init rate = 0.06 (6 / 109), avg. gap size = 2.00 (12 / 6) 12 19.85 0.00 0.00 chr2qtel1M 36834 36862 (963138) (ATGT)n#Simple_repeat 1 29 (0) m_b82s252i28 3077 chr2qtel1M 36834 ATGTATGTGTGTATACCTTTATGTATGTA 36862 i iiv v (ATGT)n#Simpl 1 ATGTATGTATGTATGTATGTATGTATGTA 29 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 352 28.12 0.88 9.52 chr2qtel1M 36981 37094 (962906) C MIRc#SINE/MIR (154) 114 10 m_b82s601i19 3078 chr2qtel1M 36981 AGATTTAGTGACTTGCTCAGGGTTATACAGCTAGTAAGTGTATGAGCTTG 37030 i v i i i i vvv iv C MIRc#SINE/MIR 114 AGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGG 65 chr2qtel1M 37031 GATTTTAACTCAGCAATACATAAGCATTCCTGACTCAAGGTTTGGTA-TA 37079 i iv i ---------- iv v i iii i- v C MIRc#SINE/MIR 64 GACTCGAACCCAG----------GTCTTCCTGACTCCAAGTCCAGTGCTC 25 chr2qtel1M 37080 TATCCATTGTGGCAC 37094 v i iiv C MIRc#SINE/MIR 24 TTTCCACTGCACCAC 10 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.95 CpG sites = 18, Kimura (unadjusted) = 36.01 Transitions / transversions = 1.64 (18/11) Gap_init rate = 0.10 (11 / 113), avg. gap size = 1.00 (11 / 11) 17 8.52 0.00 11.90 chr2qtel1M 37118 37164 (962836) (CACATA)n#Simple_repeat 1 42 (0) m_b82s252i29 3079 chr2qtel1M 37118 CAGATACACACTACAATGATACATATACACATGCACACATACACATA 37164 v - - -v i -- (CACATA)n#Sim 1 CACATACACA-TAC-A-CATACACATACACAT--ACACATACACATA 42 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.11 (5 / 46), avg. gap size = 1.00 (5 / 5) 32 27.61 5.51 1.52 chr2qtel1M 37136 37262 (962738) (AT)n#Simple_repeat 1 132 (0) m_b82s252i30 3079 chr2qtel1M 37136 ATACATATACACATGCACACATACACATATTTATGTATGCAGAGATA-AT 37184 i i i ii i i i i v i ii v v - (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr2qtel1M 37185 ACACATGTATGT-TAT-TATATGTATACTGTATATATAGACATA-ATGTA 37231 i i i i - - i - i v i - i (AT)n#Simple_ 51 ATATATATATATATATATATATATATA-TATATATATATATATATATATA 99 chr2qtel1M 37232 TATAT-TACATGTATA-ATATGTAGTATAT-TAT 37262 - i i - i - - (AT)n#Simple_ 100 TATATATATATATATATATATATA-TATATATAT 132 Matrix = Unknown Transitions / transversions = 5.75 (23/4) Gap_init rate = 0.07 (9 / 126), avg. gap size = 1.00 (9 / 9) 234 25.87 12.05 2.20 chr2qtel1M 38202 38284 (961716) MIRc#SINE/MIR 66 156 (112) m_b83s601i1 3080 chr2qtel1M 38202 CAGCTGGTTGGCACTTTCTAGCTGTGTGACCGGAAGCAAGCCACTTAA-- 38249 i --i v v vvii i -- MIRc#SINE/MIR 66 CGGCT--CTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACC 113 chr2qtel1M 38250 --------CCCCAATTGCCTCATCAAAAAAAGAAAGAAAACAA 38284 -------- i i v viv viii v i MIRc#SINE/MIR 114 TCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAA 156 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.60 CpG sites = 12, Kimura (unadjusted) = 32.45 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.05 (4 / 82), avg. gap size = 3.00 (12 / 4) 238 21.68 1.61 3.28 chr2qtel1M 38202 38263 (961737) MIR#SINE/MIR 62 122 (140) m_b83s601i2 3080 chr2qtel1M 38202 CAGCTGGTTGGCACTTTCTAGCTGTGTGACCGGAAGCAAGCCACTTAACC 38251 i --i v v vvii ii MIR#SINE/MIR 62 CGGCT--CTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACC 109 chr2qtel1M 38252 CCAAT-TGCCTCA 38263 i vv - MIR#SINE/MIR 110 TCTCTGTGCCTCA 122 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 23.65 CpG sites = 7, Kimura (unadjusted) = 25.85 Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.05 (3 / 61), avg. gap size = 1.00 (3 / 3) 339 33.15 0.00 4.62 chr2qtel1M 39160 39295 (960705) C MIR1_Amn#SINE/MIR (100) 130 1 m_b83s601i3 3081 chr2qtel1M 39160 ATTGGCACACAAAAACAGGATGAAGTGACTTGTCTAGGGTCACAGAGCTA 39209 i ivi ? i i --- i ? i i i ?v ?i C MIR1_Amn#SINE 130 ACTGAGGCNCAGAGA---GGTNAAGTGACTTGCCCAAGGTCACNCAGCNG 84 chr2qtel1M 39210 CAAAGCGTCTGAGGCCACGTTTGAACTCGGGTCTTCCTGACTTAGGTTTG 39259 vv? i v v v vivi? ? i i i viiiiivi iii C MIR1_Amn#SINE 83 GCNAGTGGCAGAGCCGGGANTNGAACCCAGGTCTCCCGAGTCCCAGTCCA 34 chr2qtel1M 39260 GTGTTCTATCCACTGTGACGGCACCTCGCTTCCCCA 39295 i i- -- vii i i C MIR1_Amn#SINE 33 GTGCTCTATCCACTA-GAC--CACACTGCCTCCCTA 1 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 51.44 CpG sites = 31, Kimura (unadjusted) = 51.44 Transitions / transversions = 2.58 (31/12) Gap_init rate = 0.04 (6 / 135), avg. gap size = 1.00 (6 / 6) 390 27.84 1.03 0.00 chr2qtel1M 39178 39274 (960726) C MIRc#SINE/MIR (155) 113 16 m_b83s601i4 3081 chr2qtel1M 39178 GATGAAGTGACTTGTCTAGGGTCACAGAGCTACAAAGCGTCTGAGGCCAC 39227 i v i i i v vv i v v v viv C MIRc#SINE/MIR 113 GGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGG 64 chr2qtel1M 39228 GTTTGAACTCGGGTCTTCCTGACT-TAGGTTTGGTGTTCTATCCACTG 39274 ii i i i -i i iii i v C MIRc#SINE/MIR 63 ACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTG 16 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.32 CpG sites = 17, Kimura (unadjusted) = 35.99 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.01 (1 / 96), avg. gap size = 1.00 (1 / 1) 278 34.48 5.98 6.40 chr2qtel1M 43457 43707 (956293) C L3#LINE/CR1 (1583) 2516 2267 m_b83s601i5 3082 chr2qtel1M 43457 TCTTGAGTTTCCATTTGCCATTTTGA--------GCTCT--CTTGCCCAG 43496 i i v -- v i i -------- i -- i vi C L3#LINE/CR1 2516 TCTTGGGCTTCAATT--CCCTCTTAACGATGTTTGTTCTACCCTTTCCAG 2469 chr2qtel1M 43497 TTCAAATACCATTCTCCTAGGTAGGTATAAGAGAAGCAAAGTAAGAACCG 43546 iii v i v i iv vi vi i i iii C L3#LINE/CR1 2468 TCTGAAGATCATTCTCCTTGATAGAGAAGACGGAAGCAAAATAGGAGTTG 2419 chr2qtel1M 43547 AGAAACTGCGTGTATTTTCTTTCTGTATTCATATACTTACATATCATGAG 43596 v ii - --- ii i --- v ii v vv iiv v C L3#LINE/CR1 2418 AGTAGTT-C---TGCTTTCTCTCTG---TCATCTGTTAACATTACGCCAT 2376 chr2qtel1M 43597 CAGCACTTTAAGCAGC---CTCATCAGCTTTCTGATCCTTCTCTTTTACA 43643 v v --i --- iii -? vv i i - vi v i C L3#LINE/CR1 2375 CTGCCC--CAAGCAGCGGGCCTGTC-NCTTTCTTTTTCCT-TCTGCTCCG 2330 chr2qtel1M 43644 AATATTACCTCAGAGAAAGAAAACTTTCTGGTTATCTTTGAC--TTTCTC 43691 i vi i i--- iivvvi? i v i i ii -- i i C L3#LINE/CR1 2329 AACATAGCTTT---GAAAAGCCTTNTTTTTGTTGTCCTTAGCATTTTTTT 2283 chr2qtel1M 43692 TTGCCAGCTCCATCTC 43707 v ii v C L3#LINE/CR1 2282 TTGCAAGCCTCAGCTC 2267 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 47.01 CpG sites = 53, Kimura (unadjusted) = 49.67 Transitions / transversions = 1.89 (53/28) Gap_init rate = 0.08 (20 / 250), avg. gap size = 1.55 (31 / 20) 14 4.11 3.70 3.70 chr2qtel1M 47362 47388 (952612) (TTGT)n#Simple_repeat 1 27 (0) m_b83s252i2 3083 chr2qtel1M 47362 TTGTTT-TTTGTTTGTTTTGTTTTTTTG 47388 - - v (TTGT)n#Simpl 1 TTGTTTGTTTGTTTG-TTTGTTTGTTTG 27 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.08 (2 / 26), avg. gap size = 1.00 (2 / 2) 282 20.33 3.33 1.64 chr2qtel1M 47457 47516 (952484) C L2d_3end#LINE/L2 (3) 513 453 m_b83s601i6 3084 chr2qtel1M 47457 ATCAATTAATCAACAAACATTTATTAAA-ATCTGCTATGTG-TCAGATAC 47504 i ii i i-ii i - -i C L2d_3end#LINE 513 ATCAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAG-CAC 465 chr2qtel1M 47505 TGTGTTAAGTGC 47516 i i i C L2d_3end#LINE 464 TGTGCTAGGCGC 453 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 21.21 CpG sites = 12, Kimura (unadjusted) = 26.11 Transitions / transversions = 1.00 (12/0) Gap_init rate = 0.05 (3 / 59), avg. gap size = 1.00 (3 / 3) 14 33.92 1.23 2.50 chr2qtel1M 47653 47733 (952267) (AATAAT)n#Simple_repeat 1 80 (0) m_b83s252i3 3085 chr2qtel1M 47653 AACAATCATCATGACTACAATGCTAATAGAAACAACATAAATAACAA-AA 47701 i v v i iv i iv iv i i vv i - (AATAAT)n#Sim 1 AATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAA 50 chr2qtel1M 47702 TAAAAATGAATATTGTGTAATTATAATAATAA 47733 v - v -vi v (AATAAT)n#Sim 51 TAATAAT-AATAAT-AATAATAATAATAATAA 80 Matrix = Unknown Transitions / transversions = 0.91 (10/11) Gap_init rate = 0.04 (3 / 80), avg. gap size = 1.00 (3 / 3) 195 28.80 1.32 4.05 chr2qtel1M 48448 48523 (951477) MIRc#SINE/MIR 78 151 (117) m_b83s601i7 3086 chr2qtel1M 48448 TTACTAGGAGCATTACTTAGAGAGAGAATCACACAACCTCT-TGAGACTT 48496 vv ii v i v i vi -- vi - - i MIRc#SINE/MIR 78 TTACTAGCTGTGTGACCTTGGGCAAG--TCACTTAACCTCTCTGAG-CCT 124 chr2qtel1M 48497 CTCTTTCTTCCCTTGTATAATGAGGAT 48523 vv i vii v i MIRc#SINE/MIR 125 CAGTTTCCTCATCTGTAAAATGGGGAT 151 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.85 CpG sites = 11, Kimura (unadjusted) = 36.85 Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.05 (4 / 75), avg. gap size = 1.00 (4 / 4) 251 32.93 2.44 0.00 chr2qtel1M 48474 48555 (951445) MIR3#SINE/MIR 99 182 (26) m_b83s601i8 3086 chr2qtel1M 48474 AATCACACAACCTCTTGAGACTTCTCTTTCTTCCCTTGTATAATGAGGA- 48522 i viv ivi i i vv i vii v i- MIR3#SINE/MIR 99 AGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGG 148 chr2qtel1M 48523 -TTTAACTAAAGGACTTCTAAGAACTCTCCCAGC 48555 - vi i v ii iv i i MIR3#SINE/MIR 149 GTTGGACTAGATGATCTCTAAGGTCCCTTCCAGC 182 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.45 CpG sites = 17, Kimura (unadjusted) = 45.45 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.02 (2 / 81), avg. gap size = 1.00 (2 / 2) 15 25.92 1.59 3.23 chr2qtel1M 48622 48684 (951316) (AAGCAGG)n#Simple_repeat 1 62 (0) m_b83s252i4 3087 chr2qtel1M 48622 AAG-AGGAAGCAGAAAAAAGTAAGCAGAGTTCACCACAGCAAGGAAGGAG 48670 - i iv v iivv vv - - v (AAGCAGG)n#Si 1 AAGCAGGAAGCAGGAAGCAGGAAGCAGGAAGCAGGA-AGC-AGGAAGCAG 48 chr2qtel1M 48671 GAAGCAGGCAGAAG 48684 v v (AAGCAGG)n#Si 49 GAAGCAGGAAGCAG 62 Matrix = Unknown Transitions / transversions = 0.44 (4/9) Gap_init rate = 0.05 (3 / 62), avg. gap size = 1.00 (3 / 3) 455 28.12 2.96 7.41 chr2qtel1M 51563 51731 (948269) C MIR3#SINE/MIR (23) 185 24 m_b83s601i9 3088 chr2qtel1M 51563 AGACTTGGCAGAGTTCTTTGACAGCTTGTCTAGTCTGACC---TCATTTT 51609 vi v i vi -- v v ii ii --- C MIR3#SINE/MIR 185 AGAGCTGGAAGGGACCTT--AGAGATCATCTAGTCCAACCCCCTCATTTT 138 chr2qtel1M 51610 AAGAATGAAGAAACTGAAATGAAAGAAAGATTAAGTGACTTGCTCAAGCA 51659 vii i iiivv - i i v i vv C MIR3#SINE/MIR 137 ACAGATGAGGAAACTGAGGCCCA-GAGAGGTGAAGTGACTTGCCCAAGGT 89 chr2qtel1M 51660 CACTTGGTTAGGTCATATAGAGTAGAGCCAGGATTGGAATCCAGGTCCAA 51709 vii i? v vi i---- i i i i i --- C MIR3#SINE/MIR 88 CACACAGCNAGTTAGTG----GCAGAGCCGGGACTAGAACCCAGGTC--- 46 chr2qtel1M 51710 ATCC--ACTGTCCTTTCAGTGCTC 51731 - -- -i vv v C MIR3#SINE/MIR 45 -TCCTGACT-CCCAGTCCGTGCTC 24 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.46 CpG sites = 27, Kimura (unadjusted) = 36.51 Transitions / transversions = 1.59 (27/17) Gap_init rate = 0.08 (14 / 168), avg. gap size = 1.21 (17 / 14) 17 29.34 1.69 0.00 chr2qtel1M 51897 51955 (948045) (TCA)n#Simple_repeat 1 60 (0) m_b83s252i5 3089 chr2qtel1M 51897 TCATCATCATCATCTTCACAATCATTGCCACAATCACCAAAACTATCACC 51946 v iv iii iv i vv ii i (TCA)n#Simple 1 TCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATC 50 chr2qtel1M 51947 A-CATCATCA 51955 - (TCA)n#Simple 51 ATCATCATCA 60 Matrix = Unknown Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1) 18 26.64 1.69 0.00 chr2qtel1M 51898 51956 (948044) (CATCAC)n#Simple_repeat 1 60 (0) m_b83s252i6 3089 chr2qtel1M 51898 CATCATCATCATCTTCACAATCATTGCCACAATCACCAAAACTATCACCA 51947 i i v v iiii v vv i (CATCAC)n#Sim 1 CATCACCATCACCATCACCATCACCATCACCATCACCATCACCATCACCA 50 chr2qtel1M 51948 -CATCATCAC 51956 - i (CATCAC)n#Sim 51 TCACCATCAC 60 Matrix = Unknown Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1) 258 32.88 4.11 0.00 chr2qtel1M 52375 52520 (947480) C L1ME2z_3end#LINE/L1 (610) 581 430 m_b83s551i0 3090 chr2qtel1M 52375 ATCAGTTGTTCATCATGTTTTATAAAACAATGATATTCCATTACCTTCAT 52424 v i iviv vivvv i ii iiv vv C L1ME2z_3end#L 581 ATCAGTAGTTCGTTCCTTTTTATTGCTGAGTAGTATTCCATTGTATGAAT 532 chr2qtel1M 52425 ATACCACTACTTGTTCAT-CATTCCCCAACTGATGGGTATCTACTCATTT 52473 vii i - i vii ii i ivv vv C L1ME2z_3end#L 531 ATACCACAGTTTGTTTATCCATTCTCCTGTTGATGGACACCTGGGCTGTT 482 chr2qtel1M 52474 TCCCGTT-----CTATCACAAAAAGAGCTGCTGCAAACATTTTTGCATAT 52518 v ----- i ii v i iii i i i v C L1ME2z_3end#L 481 TCCAGTTTTTGGCTATTATGAATAAAGCTGCTATGAACATTCTTGTACAA 432 chr2qtel1M 52519 GT 52520 C L1ME2z_3end#L 431 GT 430 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 43.72 CpG sites = 29, Kimura (unadjusted) = 45.01 Transitions / transversions = 1.53 (29/19) Gap_init rate = 0.01 (2 / 145), avg. gap size = 3.00 (6 / 2) 260 29.91 5.13 0.00 chr2qtel1M 52404 52520 (947480) C L1ME3F_3end#LINE/L1 (438) 552 430 m_b83s551i1 3090 chr2qtel1M 52404 ATGATATTCCATTACCTTCATATACCACTACTTGTTCAT-CATTCCCCAA 52452 i iiv vv v i i i - i vi C L1ME3F_3end#L 552 ATAATATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTCCTG 503 chr2qtel1M 52453 CTGATGGGTATCTACTCATTTTCCCGTT-----CTATCACAAAAAGAGCT 52497 ii ii i ivvivv v ----- i i v v C L1ME3F_3end#L 502 TCGATGGACATTTGGGTTGTTTCCAGTTTTTTGCTATTACGAACAGTGCT 453 chr2qtel1M 52498 GCTGCAAACATTTTTGCATATGT 52520 iii i i i C L1ME3F_3end#L 452 GCTATGAACATTCTTGTACATGT 430 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.01 CpG sites = 23, Kimura (unadjusted) = 39.97 Transitions / transversions = 1.92 (23/12) Gap_init rate = 0.02 (2 / 116), avg. gap size = 3.00 (6 / 2) 298 27.62 1.45 2.94 chr2qtel1M 52615 52752 (947248) L1ME3F_3end#LINE/L1 439 574 (416) m_b83s551i2 3091 chr2qtel1M 52615 AAAATATTGATACCAGCACTTTTTGTGATAGCAAAGAATTGGAAGCAA-A 52663 i i v v v i i i i i -v L1ME3F_3end#L 439 AGAATGTTCATAGCAGCACTGTTCGTAATAGCAAAAAACTGGAAACAACC 488 chr2qtel1M 52664 GAGATGTCCCTCAATTGAGGAATGGTTAAAT-GCTTCTAATACATGACTG 52712 v i v i iv ii v -iv v ii i vvvii L1ME3F_3end#L 489 CAAATGTCCATCGACAGGAGAATGGATAAATAAATTGTGGTATATTCACA 538 chr2qtel1M 52713 TAATGGAATATTAACTGTGGAAATGATAAATGAGATGAAC 52752 i -- iii v i - - L1ME3F_3end#L 539 CAATGGAATATTA--TACAGCAGTGA-AAATGA-ATGAAC 574 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 33.17 CpG sites = 23, Kimura (unadjusted) = 35.55 Transitions / transversions = 1.64 (23/14) Gap_init rate = 0.04 (6 / 137), avg. gap size = 1.00 (6 / 6) 323 25.23 1.87 0.00 chr2qtel1M 52619 52725 (947275) L1ME4b_3end#LINE/L1 443 551 (341) m_b83s551i3 3091 chr2qtel1M 52619 TATTGATACCAGCACTTTTTGTGATAGCAAAGAATTGGAAGCAAAG-AGA 52667 v vv i v i ii i vv- i L1ME4b_3end#L 443 TATTCATTGCAGCATTGTTTGTAATAGCAAAAGATTGGAAACAACCTAAA 492 chr2qtel1M 52668 TGTCCCTCAATTGAGGAATGGTTAAAT-GCTTCTAATACATGACTGTAAT 52716 v v i v -iv v ii vvv ii L1ME4b_3end#L 493 TGTCCATCAATAGGGGACTGGTTAAATAAATTATGGTACATCCATACAAT 542 chr2qtel1M 52717 GGAATATTA 52725 i L1ME4b_3end#L 543 GGAATACTA 551 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 30.99 CpG sites = 13, Kimura (unadjusted) = 30.99 Transitions / transversions = 0.93 (13/14) Gap_init rate = 0.02 (2 / 106), avg. gap size = 1.00 (2 / 2) 282 26.21 6.21 0.00 chr2qtel1M 52628 52772 (947228) L1ME3Cz_3end#LINE/L1 448 601 (396) m_b83s551i4 3091 chr2qtel1M 52628 CAGCACTTTTTGTGATAGCAAAGAATTGGAAGCAAAG-AGATGTCCCTCA 52676 i v i i i i vv- i v L1ME3Cz_3end# 448 CAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCA 497 chr2qtel1M 52677 ATTGAGGAATGGTTAAAT-GCTTCTAATACATGACTGTAATGGAATATTA 52725 v i v -iv v ii i vvv ii i L1ME3Cz_3end# 498 ATAGGGGAATGGATAAATAAATTGTGGTATATTCATACAATGGAATACTA 547 chr2qtel1M 52726 -ACTGTGG---AAATG-ATAAATGAGATGAACAGGAA--AACATGGAAGG 52768 - v ii --- - i iv vv v v -- vii L1ME3Cz_3end# 548 TACAGCAGTTAAAATGAATGAACTAGATCTACATGTATCAACATGGATAA 597 chr2qtel1M 52769 ATCT 52772 L1ME3Cz_3end# 598 ATCT 601 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 31.65 CpG sites = 20, Kimura (unadjusted) = 32.68 Transitions / transversions = 1.11 (20/18) Gap_init rate = 0.04 (6 / 144), avg. gap size = 1.50 (9 / 6) 20 16.66 0.00 0.00 chr2qtel1M 52948 52981 (947019) (T)n#Simple_repeat 1 34 (0) m_b83s252i7 3092 chr2qtel1M 52948 TTTTTTTTTTTTTTTTTTTTGGTTGTTGTTGTTT 52981 vv v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 34 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 15 20.30 4.44 0.00 chr2qtel1M 52949 52993 (947007) (TTTG)n#Simple_repeat 1 47 (0) m_b83s252i8 3092 chr2qtel1M 52949 TTTTTTTTTTTTTTTTTTTGGTTG-TTG-TTGTTTGCTTGCTTGCTT 52993 v v v v v - - i i i (TTTG)n#Simpl 1 TTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTT 47 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.05 (2 / 44), avg. gap size = 1.00 (2 / 2) 13 20.98 2.44 2.44 chr2qtel1M 53374 53414 (946586) (TTC)n#Simple_repeat 1 41 (0) m_b83s252i9 3093 chr2qtel1M 53374 TTTTTCCTCCTCTTCTTCCTCTTTCTCCTTCTT-TTGGTCTT 53414 i i i i - i - vv (TTC)n#Simple 1 TTCTTCTTCTTCTTCTTCTTC-TTCTTCTTCTTCTTCTTCTT 41 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 13 4.53 0.00 8.00 chr2qtel1M 54437 54463 (945537) (GGGA)n#Simple_repeat 1 25 (0) m_b83s252i10 3094 chr2qtel1M 54437 GGGAGGGAGAGAGGGAGAGGAAGGGAG 54463 i - - (GGGA)n#Simpl 1 GGGAGGGAGGGAGGGAG-GG-AGGGAG 25 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.08 (2 / 26), avg. gap size = 1.00 (2 / 2) 16 21.33 0.00 0.00 chr2qtel1M 54980 55012 (944988) (A)n#Simple_repeat 1 33 (0) m_b83s252i12 3095 chr2qtel1M 54980 AAAACAACAACAACAACAACAAAAAAAAAAAAA 55012 v v v v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 33 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 20 16.12 2.38 0.00 chr2qtel1M 54979 55020 (944980) (CAA)n#Simple_repeat 1 43 (0) m_b83s252i11 3096 chr2qtel1M 54979 CAA-AACAACAACAACAACAACAAAAAAAAAAAAACCCACAAC 55020 - v v v v v v (CAA)n#Simple 1 CAACAACAACAACAACAACAACAACAACAACAACAACAACAAC 43 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.02 (1 / 41), avg. gap size = 1.00 (1 / 1) 14 17.04 5.00 0.00 chr2qtel1M 54982 55021 (944979) (AACAACC)n#Simple_repeat 1 42 (0) m_b83s252i13 3096 chr2qtel1M 54982 AACAA-CAACAA-CAACAACAAAAAAAAAAAAACCCACAACC 55021 - - v v vv v v (AACAACC)n#Si 1 AACAACCAACAACCAACAACCAACAACCAACAACCAACAACC 42 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 405 30.18 1.74 1.74 chr2qtel1M 57830 58001 (941999) L1ME4c_3end#LINE/L1 384 555 (275) m_b83s551i5 3097 chr2qtel1M 57830 ACTACTGGACTTATATCCCAAAGAGATCAT---AAAGAAGGGAAAGGGAC 57876 v ivv v i i i v --- i i --- L1ME4c_3end#L 384 ACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAAGAAGGAAAAAG--- 430 chr2qtel1M 57877 CTGTATGTACAAGAATGTTTGTGGCAGCCCTCTTTGTAGTGGCCAGAAGC 57926 i i i ii ii v vi v i i i v i ii L1ME4c_3end#L 431 CTATATGCACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAAT 480 chr2qtel1M 57927 TGGAAACTGAGTGGATGCCCATTAATTGCAGAATGGCTGAATAAATTGTG 57976 vivv ii i vi v vi i i i i L1ME4c_3end#L 481 TGGAAACAACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATG 530 chr2qtel1M 57977 GTATATGAATATTATGGAATATTAT 58001 i v? iviv L1ME4c_3end#L 531 GTACATCNACTCGATGGAATATTAT 555 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.59 CpG sites = 33, Kimura (unadjusted) = 40.69 Transitions / transversions = 1.83 (33/18) Gap_init rate = 0.02 (4 / 171), avg. gap size = 1.50 (6 / 4) 405 33.73 2.35 2.35 chr2qtel1M 57831 58085 (941915) L1ME5_3end#LINE/L1 382 636 (305) m_b83s551i6 3097 chr2qtel1M 57831 CTACTGGACTTATATCCCAAAGAGATCATAAAGAAGG----GAAAGGGAC 57876 v iiv i iv v viv ----v i L1ME5_3end#LI 382 CTCCTGGGTATATATCCCAAAGAAATTCTCACACAGGTCCATAAGGGGAC 431 chr2qtel1M 57877 CTGTATGTACAAGAATGTTTGTGGCAGCCCTCTTTGTAGTGGCCAGAAGC 57926 ---- i i ii v vi v i vi i i L1ME5_3end#LI 432 ----ATGTACGAGGATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGT 477 chr2qtel1M 57927 TGGAAACTGAGTGGATGCCCATTAATTGCAGAATGGCTGAATAAATTGTG 57976 ii vivv i i i v v v i v iii v L1ME5_3end#LI 478 TGGAGGCAACCTGGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTG 527 chr2qtel1M 57977 GTATATGAATATTATGGAATATTATTGTTTGGTAAGAAATGACCAACAGG 58026 iv v i ii i i vvvvii v iii vi vi L1ME5_3end#LI 528 GTGGATGCACACCATGGAGTACTATGCAGCAGTTAGAAGCAACGGACTAG 577 chr2qtel1M 58027 ATGATTTCAGAAAAGCCTGGAGAGA-CTTACACAAAC-TGATGCTGAATG 58074 vviv v iv i v vi - -- v - ii i L1ME5_3end#LI 578 ATGTACACATAGCAACATGGATGGATCTT--AAAAACATAGTGCTGAGTG 625 chr2qtel1M 58075 AAACAAGCAGG 58085 v i i L1ME5_3end#LI 626 AAAAAAGTAAG 636 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 45.40 CpG sites = 47, Kimura (unadjusted) = 46.16 Transitions / transversions = 1.27 (47/37) Gap_init rate = 0.04 (9 / 254), avg. gap size = 1.33 (12 / 9) 498 23.14 0.00 0.00 chr2qtel1M 57881 58001 (941999) L1ME3A_3end#LINE/L1 432 552 (368) m_b83s551i7 3097 chr2qtel1M 57881 ATGTACAAGAATGTTTGTGGCAGCCCTCTTTGTAGTGGCCAGAAGCTGGA 57930 ii i v v i i i ?? i L1ME3A_3end#L 432 ATGTACAAGAATGTTCATAGCAGCACTATTCGTAATAGCCNNAAACTGGA 481 chr2qtel1M 57931 AACTGAGTGGATGCCCATTAATTGCAGAATGGCTGAATAAATTGTGGTAT 57980 ?ivviii i i iv i v i L1ME3A_3end#L 482 AACNACCCAAATGTCCATCAACAGTAGAATGGATAAATAAATTGTGGTAT 531 chr2qtel1M 57981 ATGAATATTATGGAATATTAT 58001 vv i iv i L1ME3A_3end#L 532 ATTCACACAATGGAATACTAT 552 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 28.29 CpG sites = 19, Kimura (unadjusted) = 29.54 Transitions / transversions = 2.11 (19/9) Gap_init rate = 0.00 (0 / 120), avg. gap size = 0.0 (0 / 0) 418 33.50 0.50 0.50 chr2qtel1M 57882 58082 (941918) L1MD1_3end#LINE/L1 433 633 (356) m_b83s551i8 3097 chr2qtel1M 57882 TGTACAAGAATGTTTGTGGCAGCCCTCTTTGTAGTGGCCAGAAGCTGGAA 57931 v i i ii v i i i i i L1MD1_3end#LI 433 TGTACACGAATGTTTATAGCAGCTTTATTCGTAATAGCCAAAAACTGGAA 482 chr2qtel1M 57932 ACTGAGTGGATGCCCATTAATTGCAGAATGGCTGAATAAATTGTGGTATA 57981 vivvii i v i iv vv i i i i i L1MD1_3end#LI 483 ACAACCCAGATGTCCTTCAACGGGTGAATGGTTAAACAAACTGTGGTACA 532 chr2qtel1M 57982 TGAATATTATGGAATATTATTGTTTGGTAAGAAATGACCAACAGGATGAT 58031 vv ii i i vvviii i ivi v -viv L1MD1_3end#LI 533 TCCATACCATGGAATACTACTCAGCAATAAAAAGGAACGAAC-TATTGAT 581 chr2qtel1M 58032 -TTCAGAAAAGCCTGGAGAGACTTACACAAACTGATGCTGAATGAAACAA 58080 -iv iv v i vii ii v v i v v i v L1MD1_3end#LI 582 ACACGCAACAACCTGGATGAATCTCCAGAGAATTATGCTGAGTGAAAAAA 631 chr2qtel1M 58081 GC 58082 L1MD1_3end#LI 632 GC 633 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 43.33 CpG sites = 40, Kimura (unadjusted) = 46.15 Transitions / transversions = 1.48 (40/27) Gap_init rate = 0.01 (2 / 200), avg. gap size = 1.00 (2 / 2) 12 3.81 11.11 0.00 chr2qtel1M 58423 58449 (941551) (GGGGA)n#Simple_repeat 1 30 (0) m_b83s252i14 3098 chr2qtel1M 58423 GGGGA-GGG-GGGGAGGGGA-TGGAGGGGA 58449 - - -v (GGGGA)n#Simp 1 GGGGAGGGGAGGGGAGGGGAGGGGAGGGGA 30 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.12 (3 / 26), avg. gap size = 1.00 (3 / 3) 252 28.13 5.88 1.69 chr2qtel1M 58538 58707 (941293) L1ME3Cz_3end#LINE/L1 156 332 (665) m_b83s551i9 3099 chr2qtel1M 58538 AGAAAGATGCAGATGAAAAATAACCTTGATATA-----TTACAACTACCA 58582 ii i i v -i? vv v ----- i v i i L1ME3Cz_3end# 156 AGGGAAATGCAAATTAAAA-CNACAATGAGATACCATTTCACACCCATCA 204 chr2qtel1M 58583 GATTGGCTAAAAAGATAGAAAG--GGAAAGTGACAAATGTTGAAGAGGGT 58630 - vv - --v v i iv i iv i L1ME3Cz_3end# 205 GATTGGC-AAAAATTTA-AAAGTCTGACAATACCAAGTGTTGGCGAGGAT 252 chr2qtel1M 58631 GTGCAAAAATTGGGGCATTAATTCA---CTGGTACAATTGTAAAATGAAA 58677 v i iv ii vi v v --- ivi v v iv L1ME3Cz_3end# 253 GTGGAGAAACGGGAACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTA 302 chr2qtel1M 58678 CAACTATTTTAGAGAGAAATTTGGAATTAT 58707 i i i v v v L1ME3Cz_3end# 303 CAACCACTTTGGAGAGCAATTTGGCAATAT 332 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.08 CpG sites = 24, Kimura (unadjusted) = 36.02 Transitions / transversions = 1.04 (24/23) Gap_init rate = 0.04 (6 / 169), avg. gap size = 2.17 (13 / 6) 253 29.12 3.88 1.52 chr2qtel1M 58573 58701 (941299) L1ME2_3end#LINE/L1 199 330 (581) m_b83s551i10 3099 chr2qtel1M 58573 ACAACTACCAGATTGGCTAAAAAGATAGAAAGG--GAAAGTGACAAATGT 58620 v i i v --v i i-- v i iv L1ME2_3end#LI 199 ACACCCACTAGAATGGCTAAAA--TTAAAAAGACTGACAATACCAAATGT 246 chr2qtel1M 58621 TGAAGAGGGTGTGCAAAAATTGGGGCATTAATTCA---CTGGTACAATTG 58667 iv i v iv i ii vi v v --- ivi v L1ME2_3end#LI 247 TGGCGAGGATGTGGAGCAACTGGAACTCTCATACATTGCTGGTGGGAGTG 296 chr2qtel1M 58668 TAAAATGAAACAACTATTTTAGAGAGAAATTTGG 58701 iv i i i i iv?i L1ME2_3end#LI 297 TAAAATGGTACAACCACTTTGGAAAACNGTTTGG 330 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.38 CpG sites = 22, Kimura (unadjusted) = 38.38 Transitions / transversions = 1.47 (22/15) Gap_init rate = 0.03 (4 / 128), avg. gap size = 1.75 (7 / 4) 319 24.64 0.00 28.70 chr2qtel1M 58761 58908 (941092) MIRb#SINE/MIR 4 118 (150) m_b83s601i10 3100 chr2qtel1M 58761 AGGGGCAACTAGGTAGTACAATGGATAGAGCACCAGCCCTGAAGTTAGGA 58810 i --- i i i v vi ii i ------ MIRb#SINE/MIR 4 AGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAG------ 44 chr2qtel1M 58811 GGGTTAGAGTCAGGAGTTGGGTTAGAGTCAGGTTAGAATCTGGTTTCAAA 58860 --- i -- - vi v i ---------- i i i---- MIRb#SINE/MIR 45 ---TCAGA--CAG-ACCTGGGTTCGAATC----------CCGGCTC---- 74 chr2qtel1M 58861 CATTTAACACTTCTTAGCTGTGTGGCCCTGGGCAAGTTATTTAACCCC 58908 ---- iv vi i i i i MIRb#SINE/MIR 75 ----TGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTC 118 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.01 CpG sites = 20, Kimura (unadjusted) = 28.30 Transitions / transversions = 3.33 (20/6) Gap_init rate = 0.22 (33 / 147), avg. gap size = 1.00 (33 / 33) 237 28.90 5.88 2.27 chr2qtel1M 58835 58919 (941081) MIR3#SINE/MIR 37 124 (84) m_b83s601i11 3100 chr2qtel1M 58835 GAGTCAGG----TTAGAATCTGGTTTCAAACATTTAACACTTCTTAGCTG 58880 ----i i iv i ii ii- - i iv vvi ? MIR3#SINE/MIR 37 GAGTCAGGAGACCTGGGTTCTAGTCCCGG-C-TCTGCCACTAACTNGCTG 84 chr2qtel1M 58881 TGTGGCCCTGGGCAAGTTATTTAACCCCAATTGG-CTCAG 58919 i i i i v i vv v - MIR3#SINE/MIR 85 TGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAG 124 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.78 CpG sites = 16, Kimura (unadjusted) = 38.88 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.05 (4 / 84), avg. gap size = 1.75 (7 / 4) 252 31.45 3.31 1.63 chr2qtel1M 58937 59117 (940883) L1ME3G_3end#LINE/L1 441 624 (300) m_b83s551i11 3099 chr2qtel1M 58937 TTTATAGCAGCTTTCTTTGTGATGACAAAGAATGAGAAATGGAAGAGATT 58986 i v v v i ii i i vi iiivvv i v L1ME3G_3end#L 441 TTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATG 490 chr2qtel1M 58987 CCCATCAATTGGGGAATGGCTGAACAAATTGTGGTATATG---ATTGTGA 59033 i v i i i i v--- i i i L1ME3G_3end#L 491 TCCATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGG 540 chr2qtel1M 59034 CAGA--ATAAAACTGCTACAAGAAATGATG-AGCTCAAGATTTTAGAAAA 59080 v v -- iv i ? i v ii v - v v v v --- vvi L1ME3G_3end#L 541 AATACTATGCAGCNGTTAAAAAGAATGAGGTAGATCTATATGT---ACTG 587 chr2qtel1M 59081 ACACAGAAAGATTTGCACAAAATACTGAAGAGTGAAA 59117 ii i v vi v i vv L1ME3G_3end#L 588 ACATGGAAAGATCTCCAAGACATATTGTTGAGTGAAA 624 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.98 CpG sites = 30, Kimura (unadjusted) = 41.96 Transitions / transversions = 1.15 (30/26) Gap_init rate = 0.03 (6 / 180), avg. gap size = 1.50 (9 / 6) 308 26.97 0.00 0.00 chr2qtel1M 58937 59025 (940975) L1ME1_3end#LINE/L1 445 533 (393) m_b83s551i12 3099 chr2qtel1M 58937 TTTATAGCAGCTTTCTTTGTGATGACAAAGAATGAGAAATGGAAGAGATT 58986 i v i i ii v i ivi iiivvv i v L1ME1_3end#LI 445 TTCATAGCAGCTTTATTCGTAATAGCCAAAAACTGGAAACAACCCAAATG 494 chr2qtel1M 58987 CCCATCAATTGGGGAATGGCTGAACAAATTGTGGTATAT 59025 i i? v v i L1ME1_3end#LI 495 TCCATCAACNGGTGAATGGATAAACAAATTGTGGTATAT 533 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 33.19 CpG sites = 15, Kimura (unadjusted) = 35.00 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.00 (0 / 88), avg. gap size = 0.0 (0 / 0) 15 15.47 0.00 10.42 chr2qtel1M 60028 60080 (939920) (GGAGAA)n#Simple_repeat 1 48 (0) m_b83s252i15 3101 chr2qtel1M 60028 GGAAAAGGCAGAAGGAAAAAGGAAAAGGGGAAGGCAGAAGATGAGATGGA 60077 i - - i i i - -- v (GGAGAA)n#Sim 1 GGAGAAGG-AGAAGG-AGAAGGAGAAGGAGAAGG-AGAAG--GAGAAGGA 45 chr2qtel1M 60078 TAA 60080 v (GGAGAA)n#Sim 46 GAA 48 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.10 (5 / 52), avg. gap size = 1.00 (5 / 5) 232 26.50 7.00 1.90 chr2qtel1M 60960 61059 (938941) L3#LINE/CR1 3523 3627 (472) m_b83s601i12 3102 chr2qtel1M 60960 AAATATAG-GTCAAG-GCAACTGAGG--ATGCTCCCCGCTCCCTTTCTAC 61005 i - v -? vv -- iv - vivi - i L3#LINE/CR1 3523 AAGTATAGTGTCCAGANCAAGGGAGGTAATAGTCCC-GCTGTACT-CTGC 3570 chr2qtel1M 61006 -CT--TCAGATCACATCTGAACTATCATGTTCATCTCTAGGCACTGGAGT 61052 - -- i i v iii vi i i iiv v L3#LINE/CR1 3571 GCTGGTCAGACCACATCTGGAGTATTGCGTTCAGTTCTGGGCGCCACATT 3620 chr2qtel1M 61053 TTATGAG 61059 v L3#LINE/CR1 3621 TTAAGAG 3627 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.78 CpG sites = 15, Kimura (unadjusted) = 33.90 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.07 (7 / 99), avg. gap size = 1.29 (9 / 7) 525 26.49 2.58 2.58 chr2qtel1M 61066 61220 (938780) C L2d2_3end#LINE/L2 (10) 545 391 m_b83s601i13 3103 chr2qtel1M 61066 TTAACAAGCCTTTATTAAGCACATACTGTTTTCTAGGCAATGAGCTAAGC 61115 i iiv i i v v v v v v i C L2d2_3end#LIN 545 TCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGC 496 chr2qtel1M 61116 ATTG---GGGACACAAAGAATGGCAAAAGAAAGTCCCTGCTCTGAAGGAG 61162 ii --- i vvii i v vi i v C L2d2_3end#LIN 495 GCTGTGGGGGATACAAAGAAGTATAAGACATGGTCCCTGCCCTCAAGGAG 446 chr2qtel1M 61163 CTCACAATCTAATGGAGGAGACAACAAGGAAATGAATTTG-GAAAAATAA 61211 i i v i ---- v i ivi - i v C L2d2_3end#LIN 445 CTTACAATCTAGTTGGGGAGACAA----GACATAAACACGTGAAAAGTTA 400 chr2qtel1M 61212 GGTAACTAT 61220 ii v C L2d2_3end#LIN 399 AATAACAAT 391 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.40 CpG sites = 23, Kimura (unadjusted) = 33.37 Transitions / transversions = 1.35 (23/17) Gap_init rate = 0.04 (6 / 154), avg. gap size = 1.33 (8 / 6) 661 34.34 5.39 0.97 chr2qtel1M 61240 61536 (938464) L3#LINE/CR1 3613 3922 (177) m_b83s601i14 3102 chr2qtel1M 61240 GCTATAATCAAGAAGAGACATTGACAAATTGGAATAGGCCCAAAGAATGG 61289 i i v iv ii i i iiiv i i i vi L3#LINE/CR1 3613 GCCACATTTTAAGAGGGACATTGACAAACTGGAGCGCGTCCAGAGGAGAG 3662 chr2qtel1M 61290 CTATGAATATAA---------TGGAGACCA-GCCAAATGAAGAGAAATGG 61329 v iv iv ii--------- i - i v i ivii v L3#LINE/CR1 3663 CGACCAGGATGGTGAAGGGTCTGGAAACCATGTCATATGAGGAACGGTTG 3712 chr2qtel1M 61330 AAAGATCTGAGGTTACTTATCCTGAAAAAGAGAAAAC-TAGGGGAGCAAG 61378 i v i v ii v i i i - i -- v L3#LINE/CR1 3713 AAGGAACTGGGGATGTTTAGCCTGGAGAAGAGAAGACTTAGAGGAG--AC 3760 chr2qtel1M 61379 ATGAAATACTG--TTCAAATATCTGAAAGGTCGTCATGTTTAGGATGTAT 61426 v -i -- i i ii vv i v v L3#LINE/CR1 3761 ATGATA-GCTGTCTTCAAATATTTGAAGGGCTGTCATGTGGAAGAGGGAT 3809 chr2qtel1M 61427 CACACTCATTGTGCTTGATCCCAGAGGCAATATCTGGGATCTACAAGAAC 61476 i v i v iv iii vv v v i i v iii viv L3#LINE/CR1 3810 TAGACTTATTCTGTGTGGCTCCAGAGGGCAGAACTAGGACCAATGGGTGG 3859 chr2qtel1M 61477 AAGATGC-CAGAGGTAGATTTCAGTTGGATGTGATGAACAGTATCTTAAT 61525 v i -vi i i i vi i i v v iiv ii i L3#LINE/CR1 3860 AAGTTACAGGGAGGCAGATTTCGGCTCAATATAAGGAAGAACTTTCTAAC 3909 chr2qtel1M 61526 AAT--GGACTGCC 61536 -- ii i L3#LINE/CR1 3910 AATCAGAGCTGTC 3922 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 46.61 CpG sites = 66, Kimura (unadjusted) = 48.77 Transitions / transversions = 1.89 (66/35) Gap_init rate = 0.03 (9 / 296), avg. gap size = 2.11 (19 / 9) 17 19.64 0.00 6.12 chr2qtel1M 62782 62833 (937167) (AAAC)n#Simple_repeat 1 49 (0) m_b83s252i16 3104 chr2qtel1M 62782 AAACAAATAAACAATATAACACATACAGATCACACACACACACAAACACA 62831 i - i - v - v v v v v (AAAC)n#Simpl 1 AAACAAACAAACAA-ACAA-ACAAACA-AACAAACAAACAAACAAACAAA 47 chr2qtel1M 62832 CA 62833 (AAAC)n#Simpl 48 CA 49 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.00 (3 / 3) 22 26.83 0.00 1.69 chr2qtel1M 62800 62859 (937141) (AC)n#Simple_repeat 1 59 (0) m_b83s252i17 3104 chr2qtel1M 62800 ACACATACAGATCACACACACACACAAACACACAGAGATGAATACATACA 62849 i v - v v v iiv i i (AC)n#Simple_ 1 ACACACACACA-CACACACACACACACACACACACACACACACACACACA 49 chr2qtel1M 62850 CCCATGCACA 62859 v ii (AC)n#Simple_ 50 CACACACACA 59 Matrix = Unknown Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.02 (1 / 59), avg. gap size = 1.00 (1 / 1) 282 26.11 8.96 2.82 chr2qtel1M 62993 63126 (936874) C MIRc#SINE/MIR (39) 229 88 m_b83s601i15 3105 chr2qtel1M 62993 TTTACCAAGAGCTTT---ACCCATGATGACAATTGATTCTCACTAG---T 63036 v v --- iv v vv v i v v---i C MIRc#SINE/MIR 229 TTTACAAAGCGCTTTCACATACATTATCTCATTTGATCCTCACAACAACC 180 chr2qtel1M 63037 CTGTGACATAGGCAGGAC---CATCATTCTCATCACATTCACAACTCAGG 63083 vi i ---i i v vi i- i iv v C MIRc#SINE/MIR 179 CTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCAT-TTTACAGATGAGG 131 chr2qtel1M 63084 ---CTGTGAGCTAAAAATGGTTGAGGGACTTGACCCAAATATCACA 63126 --- v - v i iv i v - i-i C MIRc#SINE/MIR 130 AAACTGAG-GCTCAGAGAGGTTAAGTGACTTG-CCCAAG-GTCACA 88 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.38 CpG sites = 16, Kimura (unadjusted) = 32.38 Transitions / transversions = 0.89 (16/18) Gap_init rate = 0.06 (8 / 133), avg. gap size = 2.00 (16 / 8) 37 0.00 0.00 0.00 chr2qtel1M 63494 63527 (936473) (T)n#Simple_repeat 1 34 (0) c_b83s251i0 3106 chr2qtel1M 63494 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 63527 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 34 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 16 10.03 0.00 0.00 chr2qtel1M 64318 64339 (935661) (A)n#Simple_repeat 1 22 (0) m_b83s252i18 3107 chr2qtel1M 64318 AAAAAAAGAAAAAAAAAGAAAA 64339 i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAA 22 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 440 28.39 15.38 1.19 chr2qtel1M 65483 65703 (934297) MIRb#SINE/MIR 9 260 (8) m_b83s601i16 3108 chr2qtel1M 65483 CAG-GTGATGCACTGGATAAAACACTGAGTCTCAAATCACAAAGAACTGA 65531 - i v v i i v iv i vi i v v v i MIRb#SINE/MIR 9 CAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGG 58 chr2qtel1M 65532 GTTTTAATCCC---TCT--------TTAGAAAGG-------AGGCAAGTC 65563 iv --- --------i vviv -------i i MIRb#SINE/MIR 59 GTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTT 108 chr2qtel1M 65564 ACAAGACCTCTATT-TCCTT-GTTTCTTTATCTGT-AAATAGGTATAATA 65610 vvi v v-v i- i i - i v MIRb#SINE/MIR 109 ACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATA 158 chr2qtel1M 65611 ATAACACCTAACTCTTAGGGTTTTGATGAGGACAAAATAAGACAAT--AT 65658 --- v vi v vi iv i i -- MIRb#SINE/MIR 159 AT---ACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCAT 205 chr2qtel1M 65659 TTA----------CACCGGACATGACGTATAGTAGGTACAGTATAAATGC 65698 v ---------- v vi v i ii i ii vvv v MIRb#SINE/MIR 206 GTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAAATGG 255 chr2qtel1M 65699 TAGTT 65703 i MIRb#SINE/MIR 256 TAGCT 260 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.68 CpG sites = 31, Kimura (unadjusted) = 36.18 Transitions / transversions = 1.00 (31/31) Gap_init rate = 0.05 (12 / 220), avg. gap size = 3.08 (37 / 12) 446 27.27 9.74 0.00 chr2qtel1M 65556 65709 (934291) MIR#SINE/MIR 94 262 (0) m_b83s601i17 3108 chr2qtel1M 65556 GGCAAGTCACAAGACCTCTATTT-CCTT-GTTTCTTTATCTGTAAA-TAG 65602 i vvi v v - i- i i - i MIR#SINE/MIR 94 GGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGG 143 chr2qtel1M 65603 GTATAATAATAACACCTAACTCTTAGGGTTTTGATGAGGACAAAATAAGA 65652 v ii v v v vi iv i v MIR#SINE/MIR 144 GGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGT 193 chr2qtel1M 65653 CAATAT-----------TTACACCGG-ACATGACGTATAGTAGGTACAGT 65690 i i----------- v v i -i v i ii i ii vvv MIR#SINE/MIR 194 TAATACATGTAAAGCGCTTAGAACAGTGCCTGGCACATAGTAAGCGCTCA 243 chr2qtel1M 65691 ATAAATGCTAGTTATCACT 65709 i i i i MIR#SINE/MIR 244 ATAAATGTTAGCTATTATT 262 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.65 CpG sites = 25, Kimura (unadjusted) = 34.79 Transitions / transversions = 1.47 (25/17) Gap_init rate = 0.03 (5 / 153), avg. gap size = 3.00 (15 / 5) 236 35.16 8.79 1.54 chr2qtel1M 65781 65962 (934038) L2d2_3end#LINE/L2 353 547 (8) m_b83s601i18 3109 chr2qtel1M 65781 TCTTTTATTTCCCTGCTGAATTAATTTATTTCTATTCCAAAACATTCTTT 65830 i viiv vi i i-- vv iiiiv vii v L2d2_3end#LIN 353 TCTTCTATTGTTGTCTTGAACTG--TTATTTAAATCTTGTATTGTTATTT 400 chr2qtel1M 65831 ---TTTTCCCAGTTTCAGATCTCATTTGTCTA-TAAGATTTTGAGTTTCC 65876 --- v ivv i vi ii i vi i -iv v i i i i L2d2_3end#LIN 401 AACTTTTCACGTGTTTATGTCTTGTCTCCCCAACTAGATTGTAAGCTCCT 450 chr2qtel1M 65877 TGACAGCAGAGACT--------TACTCTCCTTGCAATCTTCATGGC--TT 65916 vi i i-------- - i i vi ii ii --i L2d2_3end#LIN 451 TGAGGGCAGGGACCATGTCTTATACT-TCTTTGTATCCCCCACAGCGCCT 499 chr2qtel1M 65917 AGCCCAGTGCCT--AAAACAGAAGGTGCTCCATCAGTACTTCTTGATT 65962 v --v v v i v v i i v L2d2_3end#LIN 500 AGCACAGTGCCTTGCACACAGTAGGCGCTCAATAAATATTTGTTGATT 547 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 47.70 CpG sites = 39, Kimura (unadjusted) = 49.98 Transitions / transversions = 1.62 (39/24) Gap_init rate = 0.04 (8 / 181), avg. gap size = 2.38 (19 / 8) 257 29.70 11.88 0.00 chr2qtel1M 65862 65962 (934038) L2d_3end#LINE/L2 394 506 (10) m_b83s601i19 3109 chr2qtel1M 65862 AGATTTTGAGTTTCCTGACAGCAGAGACT--------TACTCTCCTTGCA 65903 v i i i i vi i i-------- ? ii ?v i L2d_3end#LINE 394 AGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACTNTTTTNTCG 443 chr2qtel1M 65904 ATCTTCATGGC--TTAGCCCAGTGCCTAAAACAGA--AGGTGCTCCATCA 65949 v ii ii --i v iv iv v -- i v v L2d_3end#LINE 444 TTCCCCACAGCGCCTAGCACAGTGCTGAGCACATAGTAGGCGCTCAATAA 493 chr2qtel1M 65950 GTACTTCTTGATT 65962 i v L2d_3end#LINE 494 ATACTTGTTGATT 506 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.96 CpG sites = 19, Kimura (unadjusted) = 40.44 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.03 (3 / 100), avg. gap size = 4.00 (12 / 3) 612 29.70 0.60 1.20 chr2qtel1M 67389 67555 (932445) MIRc#SINE/MIR 2 167 (101) m_b83s601i20 3110 chr2qtel1M 67389 GAAGCAACTGATAGTGTAGCGTAAAGAACCCTGGATCTAGAGTCAGGAAT 67438 i i- - i i i v i v ii i v MIRc#SINE/MIR 2 GAGGCAG-TG-TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAG 49 chr2qtel1M 67439 GCTAGGGTCTAAATCTAGCCTCAGACAGTTATGAACTTTGTGTTCCTGGA 67488 i iv iii i iv v v v v iv i v vi i i MIRc#SINE/MIR 50 ACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGG 99 chr2qtel1M 67489 AAAATCACTTAACTTTCATTTGTCTCAGTTTCCTCAACTGTCAAATGGGT 67538 v i i iiv vv i v v v MIRc#SINE/MIR 100 CAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGG 149 chr2qtel1M 67539 ATAATACTATC-ACCTTG 67555 v i -i i MIRc#SINE/MIR 150 ATAATAATACCTGCCCTG 167 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.81 CpG sites = 29, Kimura (unadjusted) = 38.94 Transitions / transversions = 1.45 (29/20) Gap_init rate = 0.02 (3 / 166), avg. gap size = 1.00 (3 / 3) 218 26.39 5.15 6.25 chr2qtel1M 68048 68144 (931856) MIR#SINE/MIR 157 252 (10) m_b83s601i21 3110 chr2qtel1M 68048 ACCTAACCAAGAAGATTGCTATG-GGATGAAGTGACATAATA-ATGTAAA 68095 v iv v i i i i - v i vv - MIR#SINE/MIR 157 ACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATACATGTAAA 206 chr2qtel1M 68096 GAAACTACTTGGCACAGCATCTGGCAAAAAGTA---GTTCAAAACAAATG 68142 ----ii i v iii v v --- i -- i MIR#SINE/MIR 207 G----CGCTTAGAACAGTGCCTGGCACATAGTAAGCGCTC--AATAAATG 250 chr2qtel1M 68143 CT 68144 i MIR#SINE/MIR 251 TT 252 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.60 CpG sites = 15, Kimura (unadjusted) = 33.49 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.09 (9 / 96), avg. gap size = 1.22 (11 / 9) 268 28.29 8.70 1.63 chr2qtel1M 68803 68917 (931083) C MIR3#SINE/MIR (2) 206 84 m_b83s601i22 3111 chr2qtel1M 68803 ATCA-AAAGTTATACGGT-TTAGAGCTGAAAGACACTTCAGAT-TTAAAT 68849 - i i i vii - i i iv i i v- i vv C MIR3#SINE/MIR 206 ATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCT 157 chr2qtel1M 68850 AATCCAACCGTCATTAATTTACAGA--ACAAAACTGAAATACAGA----- 68892 i vi - i v -- vi iiiv ----- C MIR3#SINE/MIR 156 AGTCCAACCCCC-TCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGT 108 chr2qtel1M 68893 AAAGGGATTTGCCCAAAAGTCATAC 68917 i v i - i i C MIR3#SINE/MIR 107 GAAGTGACTTGCCC-AAGGTCACAC 84 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.36 CpG sites = 22, Kimura (unadjusted) = 37.36 Transitions / transversions = 2.20 (22/10) Gap_init rate = 0.06 (7 / 114), avg. gap size = 1.71 (12 / 7) 26 10.05 2.22 2.22 chr2qtel1M 69309 69353 (930647) (AT)n#Simple_repeat 1 45 (0) m_b83s252i19 3112 chr2qtel1M 69309 ATTTATAT-TATATATATATATATATATCACATACATATATACATA 69353 v - - i i i (AT)n#Simple_ 1 ATATATATATATATATATATATATATAT-ATATATATATATATATA 45 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.05 (2 / 44), avg. gap size = 1.00 (2 / 2) 19 22.40 1.61 3.28 chr2qtel1M 69318 69379 (930621) (ATATAC)n#Simple_repeat 1 61 (0) m_b83s252i20 3112 chr2qtel1M 69318 ATATATATATATATATATCACATACATATATACATAAACACACAT-CACA 69366 i i - i i i v i i -i (ATATAC)n#Sim 1 ATATACATATACATATA-CATATACATATACATATACATATACATATACA 49 chr2qtel1M 69367 CTCTACATATTCA 69379 - v v (ATATAC)n#Sim 50 -TATACATATACA 61 Matrix = Unknown Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.05 (3 / 61), avg. gap size = 1.00 (3 / 3) 584 24.70 1.33 5.56 chr2qtel1M 70536 70685 (929315) MIRc#SINE/MIR 1 144 (124) m_b83s601i23 3113 chr2qtel1M 70536 CAAGCTAG-GTGCCACAATGGATAGCGCACTGAACTTGCAATCAGGAAGA 70584 i vi - vii i v v i v i MIRc#SINE/MIR 1 CGAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA 50 chr2qtel1M 70585 CTTATCTTCATGAGTTCAAATCTGGGCTCTGAAAATTACTAGCTGTGTGA 70634 i -------- i i i iv vv v MIRc#SINE/MIR 51 CCT--------GGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGA 92 chr2qtel1M 70635 ACCTGAATAATACAATTAAACTCCTTTA-CCTCAGTTTCCTCATTTGTAA 70683 v i iii vv v v ii v - i MIRc#SINE/MIR 93 CCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAA 142 chr2qtel1M 70684 GA 70685 i MIRc#SINE/MIR 143 AA 144 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.40 CpG sites = 20, Kimura (unadjusted) = 30.43 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.07 (10 / 149), avg. gap size = 1.00 (10 / 10) 994 28.33 4.90 0.70 chr2qtel1M 71885 72435 (927565) C L1M5_orf2#LINE/L1 (1138) 2156 1583 m_b83s551i13 3114 chr2qtel1M 71885 AGTAGTTTTTTATTTGATTTTCTAGAATTCTCTAAGTATACCATCATATC 71934 ? vv v i i ? i i v ? v i C L1M5_orf2#LIN 2156 AGTAGTTTNTTTGTAGATTCTTTNGGATTTTCTACGTANACAATCATGTC 2107 chr2qtel1M 71935 ATCAGCAAAGAGTGA--GTTTTGTTTTTTCATTGCCTATTCCAATTCCTT 71982 v i v i? -- i i v v v iiiv v C L1M5_orf2#LIN 2106 ATCTGCGAATAANGACAGTTTTATTTCTTCCTTTCCAATCTTTATGCCTT 2057 chr2qtel1M 71983 CAATATCTTTGTCTTCTCTTATTGCTAGGGCTAATGTTTCTAGTACAATG 72032 iv v v vi vvv iviii i C L1M5_orf2#LIN 2056 TTATTTCTTTTTCTTGCCTTATTGCACTGGCTAGGACCTCCAGTACAATG 2007 chr2qtel1M 72033 TTGAAT---AATGGTGATAATGGCCATGCTCGTTTCA-CCCCAATCTTAT 72078 --- i ? ii v v i i ii-i i - C L1M5_orf2#LIN 2006 TTGAATAGAAGTGGTGANAGCGGACATCCTTGTCTTGTTCCCGATCTTA- 1958 chr2qtel1M 72079 TTGTGAATGTATCTAGCTTATCCCCATTATCTATAATGCTTACTAATGGT 72128 vv v v i? ii i? v v vv i i ?i ivv C L1M5_orf2#LIN 1957 GGGGGAAAGCNTTCAGTNTTTCACCATTAAGTATGATGTTNGCTGTAGGT 1908 chr2qtel1M 72129 TTTAGATAGACACTGCTTTTCATTTAAATAAAAATTTCATTTATTACTA- 72177 vvi ii ivi v vv vi vi iv ii v i v - C L1M5_orf2#LIN 1907 TTTTCGTAGATGCCCTTTATCAGGTTGAGGAAGTTCCCTTCTATTCCTAG 1858 chr2qtel1M 72178 -TAGCTTCTAGTGTTTTTCATAGGAATGAGTGCTACATTTTCTCAAAGGC 72226 - v vvv v v -- i i iv v v C L1M5_orf2#LIN 1857 TTTGCTGAGAGTTTTTATCAT--GAATGGGTGTTGAATTTTGTCAAATGC 1810 chr2qtel1M 72227 TTTTTCTGC--CT-TGGAAATAAT-ATATGATTTGTTAGTTTTGT--TAT 72270 -- - v i i - v ivvi i -- i C L1M5_orf2#LIN 1809 TTTTTCTGCATCTATTGAGATGATCATATGATTTTTCTCCTTTATTCTGT 1760 chr2qtel1M 72271 TGACATGTTCAATTATGTTGATAGTTTTCCTAATAATGAACCAGTCTTCC 72320 i i v v ii v v i v iv i ii v C L1M5_orf2#LIN 1759 TAATATGGTGAATTACATTGATTGATTTTCGAATGTTAAACCAACCTTGC 1710 chr2qtel1M 72321 ATTCCAGGTATAAATCGTACCTGCTCATAGTGTACTAT--------TACA 72362 v v i vi i v ii i -------- i C L1M5_orf2#LIN 1709 ATTCCTGGGATAAACCCCACTTGGTCATGATGTATTATCCTTTTTATATA 1660 chr2qtel1M 72363 GT----GATCTG-TGTGCTAATATTTTTATTTTAAAATTTTGAATCAATA 72407 v ---- ii - v - i ?vii v v v i C L1M5_orf2#LIN 1659 TTGCTGGATTCGATTTGCTAATA-TTTTGTTNAGGATTTTTGCATCTATG 1611 chr2qtel1M 72408 TTCATTAGGGAAATTGGTCTATACTTTT 72435 v v i v C L1M5_orf2#LIN 1610 TTCATGAGGGATATTGGTCTGTAATTTT 1583 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.38 CpG sites = 79, Kimura (unadjusted) = 36.84 Transitions / transversions = 1.04 (79/76) Gap_init rate = 0.03 (16 / 550), avg. gap size = 1.94 (31 / 16) 27 0.00 0.00 0.00 chr2qtel1M 72709 72734 (927266) (T)n#Simple_repeat 1 26 (0) c_b83s251i1 3115 chr2qtel1M 72709 TTTTTTTTTTTTTTTTTTTTTTTTTT 72734 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 273 29.68 4.27 7.55 chr2qtel1M 76263 76426 (923574) C L2d2_3end#LINE/L2 (17) 538 380 m_b84s601i0 3116 chr2qtel1M 76263 ACATTTATTAAACACCTATTGAGTGCCAGTCACAATGATAAAAATTGAGG 76312 i i i i i v v v vi v iivii v C L2d2_3end#LIN 538 ATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGTGG 489 chr2qtel1M 76313 ATTTAAAAAAAAAAGAGGCAAAAGACA--ATTACT----TCAAGGAATAT 76356 i----ii v v i i v --i iv ---- iiv C L2d2_3end#LIN 488 G----GGATACAAAGAAGTATAAGACATGGTCCCTGCCCTCAAGGAGCTT 443 chr2qtel1M 76357 ACAATCCAATGTGGGAAACAATACACAAATATGGACAAAGTAAGCTAAAT 76406 i i vv i v i i i viv ---- C L2d2_3end#LIN 442 ACAATCTAGTTGGGGAGACAAGACATAAACACGTGAAAAGT----TAAAT 397 chr2qtel1M 76407 CCAGAACAA-ATAGGATTTAA 76426 ---- - i i C L2d2_3end#LIN 396 ----AACAATACAAGATTTAA 380 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.75 CpG sites = 28, Kimura (unadjusted) = 39.05 Transitions / transversions = 1.65 (28/17) Gap_init rate = 0.09 (15 / 163), avg. gap size = 1.27 (19 / 15) 16 0.00 0.00 0.00 chr2qtel1M 76699 76715 (923285) (A)n#Simple_repeat 1 17 (0) m_b84s252i0 3117 chr2qtel1M 76699 AAAAAAAAAAAAAAAAA 76715 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 15 23.74 1.96 1.96 chr2qtel1M 76751 76801 (923199) (AAAAT)n#Simple_repeat 1 51 (0) m_b84s252i1 3118 chr2qtel1M 76751 AAATTAAATACAAAATAAAAGAAAA-AAAATTAGAAAAAGGAAAAAACAA 76799 v - i v - v i v iv v v (AAAAT)n#Simp 1 AAAATAAA-ATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAA 49 chr2qtel1M 76800 TA 76801 (AAAAT)n#Simp 50 TA 51 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.04 (2 / 50), avg. gap size = 1.00 (2 / 2) 50 22.77 0.00 0.00 chr2qtel1M 76908 77014 (922986) (T)n#Simple_repeat 1 107 (0) m_b84s252i2 3119 chr2qtel1M 76908 TTTTTTTTTTTTTTTTTTTTTTTAAAATATATTTTTTTTTTTTTATTTAT 76957 vvvv v v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr2qtel1M 76958 ATCTCTTCCTTTTTTTTTTTTTTTTTTTTTGTTTCCTTGTAGGTTTTTTT 77007 v i i ii v ii v vvv (T)n#Simple_r 51 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 100 chr2qtel1M 77008 TTTTGTT 77014 v (T)n#Simple_r 101 TTTTTTT 107 Matrix = Unknown Transitions / transversions = 0.40 (6/15) Gap_init rate = 0.00 (0 / 106), avg. gap size = 0.0 (0 / 0) 21 33.81 1.22 1.22 chr2qtel1M 77086 77167 (922833) (AT)n#Simple_repeat 1 82 (0) m_b84s252i3 3120 chr2qtel1M 77086 ATATATTTATGTAAACATACATTTATATAGACACACACACACATATATAT 77135 v i v i i v v i i i i i i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr2qtel1M 77136 ACACAAATATA-ATGATACAGATACACATACAT 77167 i i v - - i v i i i (AT)n#Simple_ 51 ATATATATATATAT-ATATATATATATATATAT 82 Matrix = Unknown Transitions / transversions = 2.50 (15/6) Gap_init rate = 0.02 (2 / 81), avg. gap size = 1.00 (2 / 2) 36 0.00 0.00 0.00 chr2qtel1M 77444 77474 (922526) (AC)n#Simple_repeat 1 31 (0) c_b84s251i0 3121 chr2qtel1M 77444 ACACACACACACACACACACACACACACACA 77474 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACA 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 398 25.46 0.00 9.57 chr2qtel1M 77629 77754 (922246) C MIRb#SINE/MIR (152) 116 2 m_b84s601i1 3122 chr2qtel1M 77629 GGTCAAGTGCCTTGCCCCGGGTCACACAGCTAGGAAGTGTTAAGTGTCTG 77678 i iv vi ------- v v C MIRb#SINE/MIR 116 GGTTAAGTAACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGCAG 74 chr2qtel1M 77679 AGACCAAATTTGAACACCTAGTCCTCTTGACTTCAGGGTTGGCACTCTAT 77728 v vii i - vi ivii i ii iiv ii v C MIRb#SINE/MIR 73 AGCCGGGATTCGAAC-CCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTT 25 chr2qtel1M 77729 CCACTGAACCATCTAGCTGCCCCTCT 77754 v i--- C MIRb#SINE/MIR 24 CCACTGCACCAC---GCTGCCCCTCT 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.00 CpG sites = 18, Kimura (unadjusted) = 31.58 Transitions / transversions = 1.64 (18/11) Gap_init rate = 0.09 (11 / 125), avg. gap size = 1.00 (11 / 11) 12 29.60 1.82 1.82 chr2qtel1M 78275 78329 (921671) (ATTTT)n#Simple_repeat 1 55 (0) m_b84s252i4 3123 chr2qtel1M 78275 ATTTTATTTCTTTCTTGTCATATTATACTAGATTTTATTTT-TTTGATCA 78323 - v i i iv v i vv - v iv (ATTTT)n#Simp 1 ATTTTATTT-TATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTT 49 chr2qtel1M 78324 TAGTTT 78329 v (ATTTT)n#Simp 50 TATTTT 55 Matrix = Unknown Transitions / transversions = 0.62 (5/8) Gap_init rate = 0.04 (2 / 54), avg. gap size = 1.00 (2 / 2) 206 32.35 4.26 3.52 chr2qtel1M 79350 79490 (920510) C L2#LINE/L2 (217) 2865 2724 m_b84s601i2 3124 chr2qtel1M 79350 AAATGGGAAGGCACTTCAATTTATTGAGTAGGGCAGTGACAGGATAAGAA 79399 i v i vv ivv v i i v v vv v C L2#LINE/L2 2865 AGATGGGAAGCCATTGGAGGGTTTTGAGCAGAGGAGTGACATGATCTGAC 2816 chr2qtel1M 79400 CTGCATTGTAGGA-AATCACTCTACTGGCTGACTGGGT----AATGGCTT 79444 i i i v ii -i --- - v ---- i vi C L2#LINE/L2 2815 TTACGTTTTAAAAGGATCACT---CTGGCTG-CTGTGTTGAGAATAGACT 2770 chr2qtel1M 79445 AGAGGAAAGAGAGCTTTGAGGGAGGCAGATGTAG-CAGTAGACTATT 79490 i? iii vi vv v i v v i-i -i v i C L2#LINE/L2 2769 GNAGGGGGGCAAGGGTGGAAGCAGGGAGAC-CAGTTAGGAGGCTATT 2724 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.30 CpG sites = 23, Kimura (unadjusted) = 43.61 Transitions / transversions = 1.10 (23/21) Gap_init rate = 0.06 (8 / 140), avg. gap size = 1.38 (11 / 8) 708 32.60 4.53 1.73 chr2qtel1M 79821 80438 (919562) C L1ME4c_3end#LINE/L1 (178) 652 18 m_b84s551i0 3125 chr2qtel1M 79821 ATACAATGTTCTCCTGATTCTGTTCACTTCACTTAGCATTAGTTCATTTA 79870 v v ---- i ivi i vv v- C L1ME4c_3end#L 652 ATACAATTTTGT----ATTCTGCTTTTTTCACTTAACATTATATCATA-A 608 chr2qtel1M 79871 AGGTTTCCCAGACTTTTCTGAAATCAGCTTGTTCATCATTTCTTAGAGAC 79920 vi i vii vi viiv i vv v iv i - iv i C L1ME4c_3end#L 607 ACATTTTCCATGTTGCTACATAGTCTTCATAATTATCATTT-TTAATGGC 559 chr2qtel1M 79921 CAAA-AATATTCTTTTATTTTCATATAACACAATTTATTTGACCATTCTC 79969 iiv - iv iivv ?v i v i i i i C L1ME4c_3end#L 558 TGCATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCC 509 chr2qtel1M 79970 CAAGTTATGGGCATCTACTCAATTTACAATTCCTTGCCAGTACAAA--AT 80017 v v vv i i vvivi v ii i i v i -- i C L1ME4c_3end#L 508 CTATTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAAC 459 chr2qtel1M 80018 GCT-------ACATTTTTCCACATGTGGATC---CTTTATCATGTCCTAT 80057 ------- i ivii i i v i--- i v iv vvi C L1ME4c_3end#L 458 GCTGCAATGAACATCTTCGTGCATATAGCTTTTTCCTTCTTTTGAATTAT 409 chr2qtel1M 80058 CTCTTTGGAACCTAGA--CCCAGTGGTGAGATTGTTGGA-CAAAGAATAT 80104 i i i i -- i -- vi ii ii i- ii C L1ME4c_3end#L 408 TTCCTTAGGA--TAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTAT 361 chr2qtel1M 80105 GCACAATTTTATAGTCCTTTGGGCACAGTTCCAAATTACTCTTCAGAATG 80154 v v i ii vivi ii v v i i i i v C L1ME4c_3end#L 360 GAACATTTTTATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAGG 311 chr2qtel1M 80155 GTTGGATAAATTCACAATTCCAGCAACAATACATTAGTGTCACAGTTTCT 80204 v iv i ? v v i ii v ? vv v C L1ME4c_3end#L 310 GTTGTACCAATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCA 261 chr2qtel1M 80205 CCACATCCCTTCCAACATTTGTCATTATC--TTTTGTGTCATCTTGGCCA 80252 i ? iiv i v vi -- v i-v i v i C L1ME4c_3end#L 260 CCGCANCCTCGCCAGCATTGGGTATTATCAATTTTTTA-AATTTTTGCTA 212 chr2qtel1M 80253 ATCTGAGAGGTATGAAGTGGTACCTCAGTGTTATCTTAATTTGCATTT-- 80300 i i v ii i i i v iii -- C L1ME4c_3end#L 211 ATTTAATAGGCGTAAAATGGTATCTCATTGTTGCTTTAATTTGCATTTCT 162 chr2qtel1M 80301 -------ATAATGATTTAGAGCATTTTTTTCATGCTATTAGAAATGGCTT 80343 -------v ii vv v i - i ivv ivvv ivi? C L1ME4c_3end#L 161 TTGATTACTAGCGAGGTTGAACA-TTTTTCCATGTGTTTGTTTACTANTT 113 chr2qtel1M 80344 TAATTTCTTTATCTGATAAGTGTCTGTTCATAACGTTTGACCATTTATCA 80393 vv i iv ? vv v iv v v v C L1ME4c_3end#L 112 GTATTTCCTCTTNTGTGAATTGTCTGTTCATGTCCTTTGCCCATTTATCT 63 chr2qtel1M 80394 ATTGAAG-AATGACTTGTATTGTTATAAATTTGACTCACTTCTCTA 80438 ii -vv i? v - v v v v vi i C L1ME4c_3end#L 62 ATTGGGGTCTTGATNTTT-TTCTTATCAATTTGAATGAGCTCTTTA 18 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.88 CpG sites = 109, Kimura (unadjusted) = 44.64 Transitions / transversions = 1.22 (109/89) Gap_init rate = 0.03 (21 / 617), avg. gap size = 1.86 (39 / 21) 858 26.84 7.02 2.74 chr2qtel1M 79942 80397 (919603) C L1ME3G_3end#LINE/L1 (395) 529 55 m_b84s551i1 3125 chr2qtel1M 79942 ATATAACACAATTTATTTGACCATTCTCCAAGTTATGGGCATCTACTCAA 79991 v i i i v v v i i vvivi C L1ME3G_3end#L 529 ATATACCATAATTTATTTAACCATTCCCCTATTGATGGACATTTAGGTTG 480 chr2qtel1M 79992 TTTACAATTCCTTGCCAGTACAAA--ATGCT-------ACATTTTTCCAC 80032 v ii i i v -- ------- ii vi C L1ME3G_3end#L 479 TTTCCAATTTTTCGCTATTACAAACAATGCTGCAATGAACATCCTTGTAC 430 chr2qtel1M 80033 ATGTGGATCCTT-TAT-CATGTCC---TATCTCTTTGGAACCTAGA--CC 80075 i?-- - ii- v --- i ? i i -- -- C L1ME3G_3end#L 429 ATGCN--TCCTTGTGCACATGTGCGAGTATTTCTNTAGGA--TAGATNCC 384 chr2qtel1M 80076 CAGTGGTGAGATTGTTGGA-CAAAGAATATGCACAATTTTATAGTCCTTT 80124 ? vi ii i i- ii i - v v iivv C L1ME3G_3end#L 383 NAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGCA-TTTTAAATTTTAAT 335 chr2qtel1M 80125 GGGCACAGTTCCAAATTACTCTTCAGAATGGTTGGATAAATTCACAATTC 80174 i ii -- v i i i i ? i v iv i v i C L1ME3G_3end#L 334 AGATAC--TGCCAAATTGCCCTCCAAAANGGCTGTACCAATTTACACTCC 287 chr2qtel1M 80175 CAGCAACAATACATTAGTGTCACAGTTTCTCCACATCCCTTCCAACATTT 80224 v i i ii v v vv v i i iiv i ? C L1ME3G_3end#L 286 CACCAGCAGTGTATGAGAGTACCCGTTTCCCCACACCCTCGCCAACACTN 237 chr2qtel1M 80225 GTCATTATC----TTTTGTGTCATCTTGGCCAATCTGAGAGGTATGAAGT 80270 vi ---- i---v i v vi ivi i C L1ME3G_3end#L 236 GATATTATCAANCTTTTA---AATTTTTGCCAATCTGATGGGTGAAAAAT 190 chr2qtel1M 80271 GGTACCTCAGTGTTATCTTAATTTGCATTT---------ATAATGATTTA 80311 i v i i ---------v i vv v C L1ME3G_3end#L 189 GGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGATTACTAGTGAGGTT 140 chr2qtel1M 80312 GAGCATTTTTTT-CATG-CTATTAGAAATGGCTTTAATTTCTTTATCTGA 80359 i i-i -i i vv --- vv i iv v C L1ME3G_3end#L 139 GAGCATCTTTTCATATGTTTATTGGCCAT---TTGTATTTCCTCTTCTGT 93 chr2qtel1M 80360 TAAGTGTCTGTTCATAACGTTTGACCATTTATCAATTG 80397 v v i v v v v v C L1ME3G_3end#L 92 GAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTG 55 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 33.45 CpG sites = 69, Kimura (unadjusted) = 34.52 Transitions / transversions = 1.38 (69/50) Gap_init rate = 0.05 (24 / 455), avg. gap size = 1.88 (45 / 24) 235 29.56 4.76 3.36 chr2qtel1M 80345 80491 (919509) C L1P3_orf2#LINE/L1 (39) 3255 3107 m_b84s551i2 3125 chr2qtel1M 80345 AATTTCTTTATCTGATAAGTGTCTGTTCATAACGTTTGACCATTTATCAA 80394 v iv i v v v i v i v ii C L1P3_orf2#LIN 3255 AATGTCTTCTTTTGAGAAGTGTCTGTTCATATCCTTCGCCCACTTTTTGA 3206 chr2qtel1M 80395 TTGAAGAATGACTTG---TATTGTTATAAATTTGACTCACTTCTCTAGAA 80441 ---i ii vii --- v v i vi v v ii iv i C L1P3_orf2#LIN 3205 T---GGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTAAGTTCCTTGTAG 3159 chr2qtel1M 80442 ATTTTAGAAATGAGGCCTTTATC--ATAAATACTGGCTG--AAAATTTTT 80487 i i v v v i -- ii -- ii -- i C L1P3_orf2#LIN 3158 ATTCTGGATATTAGCCCTTTGTCAGATGGATA--GATTGCAAAAATTTTC 3111 chr2qtel1M 80488 TCCC 80491 C L1P3_orf2#LIN 3110 TCCC 3107 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.57 CpG sites = 25, Kimura (unadjusted) = 38.76 Transitions / transversions = 1.47 (25/17) Gap_init rate = 0.05 (8 / 146), avg. gap size = 1.50 (12 / 8) 320 33.48 8.88 1.77 chr2qtel1M 80764 81292 (918708) C L1MD_orf2#LINE/L1 (778) 2516 1951 m_b84s551i3 3126 chr2qtel1M 80764 TCTACAAAGTAATTTCTTGGCAGTTTGATTGGTATGGCACTGAATAAGTA 80813 iv vi vi v v v v v ii i ivv C L1MD_orf2#LIN 2516 TCTACAAAAAATCTTGCTGGGATTTTGATAGGAATTGCGTTAAACCTGTA 2467 chr2qtel1M 80814 GACTGATTTTAGATAGAATTATTGTTTTTATTATACACGTTGGCT----- 80858 ? iii vi i- ivii i i ---- iv ----- C L1MD_orf2#LIN 2466 NATCAATTTGGGG-AGAATTGACATCTTTACTAT----GTTGAGTCTTCC 2422 chr2qtel1M 80859 -ACCCATGAGCACTTGACACTCTTCCAATTTCTTATATATAATTTTATTT 80907 - i i vvv iiiiii v vi v v vv v C L1MD_orf2#LIN 2421 AATCCATGAACACGGTATGTCTCTCCATTTATTTAGATCTTCTTTGATTT 2372 chr2qtel1M 80908 CTGTGAAAAGAGTTTTTTAATTGTGTGGATATAATTCCTGGATTTGTCTT 80957 v v vv v v i v vv v i v v iv i C L1MD_orf2#LIN 2371 CTTTCATCAGCGTTTTGTAGTTTTCAGCATACAAGTCCTGTACATGTTTT 2322 chr2qtel1M 80958 GGCAGGGAGACACCCAAATATTTTATATTGTCTCCAGGAATTTTGAATGG 81007 vi ivvv i i i i v v i iv vi v i C L1MD_orf2#LIN 2321 GTTAGATTTATACCTAAGTATTTCATTTTTTTTTGAGCGATTGTAAATGG 2272 chr2qtel1M 81008 ------------GATTTCTCTTTCTA---GTTC-TTTCTGCT-----GA- 81035 ------------i vv i --- - v iv ----- - C L1MD_orf2#LIN 2271 TATTGTATTTTTAATTTCGGTTTCCACGTGTTCATTGCTAGTATATAGAA 2222 chr2qtel1M 81036 -------TGATTTATATCAGTTTATTTTATGTCCTTCCATTTTGCTAAAG 81078 ------- v i vv ? i i i v v ii i v C L1MD_orf2#LIN 2221 ATACAATTGATTTTTGTATGTTNATCTTGTATCCTGCGACCTTGCTGAAC 2172 chr2qtel1M 81079 TTGTTAAGTGTTTGTTTCTTGAGGTTTTTCCGTTGATTCTCTAGAATTCT 81128 iii v ---- iv v ii ii v ii i i i C L1MD_orf2#LIN 2171 TCACTTA----TTAGTTCTAGGAGTTTTTTTGTAGATTCCTTGGGATTTT 2126 chr2qtel1M 81129 GTATGT---CAG-CATATCATCTGCAAAGCATGGTAGTTTTGTTTCCTAG 81174 v i --- i- i vviv ii i i vv C L1MD_orf2#LIN 2125 CTACGTAGACAATCATGTCATCTGCAAATAGGGACAGTTTTATTTCTTCC 2076 chr2qtel1M 81175 TTGTTTACTCTAATTAC--TTCAGTTTCTTTTCTT--TTTACTAAA---G 81217 - ii v ivv i -- i v i --i i iv --- C L1MD_orf2#LIN 2075 TT-TCCAATCTGTATGCCTTTTATTTCCTTTTCTTGCCTTATTGCACTGG 2027 chr2qtel1M 81218 CTAACATTTCTAGTACAATGTTGCATTATAGTGATGAAAATGG-CAACAT 81266 iv i i v v v v i i ii - v v C L1MD_orf2#LIN 2026 CTAGAACTTCCAGTACTATGTTGAATAAGAGTGGTGAGAGCGGACATCCT 1977 chr2qtel1M 81267 TGTTTCACCCCTGATCTTACTGGGAA 81292 ii iiii i vv C L1MD_orf2#LIN 1976 TGCCTTGTTCCCGATCTTAGGGGGAA 1951 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 44.07 CpG sites = 95, Kimura (unadjusted) = 45.85 Transitions / transversions = 1.20 (95/79) Gap_init rate = 0.04 (23 / 528), avg. gap size = 2.48 (57 / 23) 322 29.91 4.76 3.25 chr2qtel1M 81030 81302 (918698) C L1M1_orf2#LINE/L1 (1074) 2220 1944 m_b84s551i4 3126 chr2qtel1M 81030 TGCTGATGATTTATATCAGTTTATTTTATGTCCTTCCATTTTGCTAAAGT 81079 iv v i vv v i i v v i i i v C L1M1_orf2#LIN 2220 TGCTACTGATTTTTGTATGTTGATTTTGTATCCTGCAACTTTACTGAATT 2171 chr2qtel1M 81080 TGTTAAGTGTTTGTTTCTTGAGGTTTTTCCGTTGATTCTCTAGAATTCTG 81129 v ---- iiv vivi i? v v i iv i v C L1M1_orf2#LIN 2170 TGTTTA----TCAGTTCTAATAGTTTTTTNGTGGAGTCTTTAGGTTTTTC 2125 chr2qtel1M 81130 TA--TGTCAG--CATATCATCTGCAAAGCATGGTAGT--------TTTGT 81167 i -- i v -- vv v i i -------- iv C L1M1_orf2#LIN 2124 CAAATATAAGATCATATCATCTGCAAACAAGGATAATTTGACTTCTTCCT 2075 chr2qtel1M 81168 TTCCTAGTTGTTTACTCTAATTACTTCAGTTTCTTTTCTTTTTACTAAAG 81217 v v vv i i -- i vv i v vv i vv C L1M1_orf2#LIN 2074 TTCCAATTTGGATGCCCT--TTATTTCTTTCTCTTGTCTGATTGCTCTAG 2027 chr2qtel1M 81218 CTAACATTTCTAGTACAATGTTGCATTATAGTGATGAAAAT-GGCAACAT 81266 iv i i v v v i i i - v v C L1M1_orf2#LIN 2026 CTAGGACTTCCAGTACTATGTTGAATAACAGTGGTGAAAGTGGGCATCCT 1977 chr2qtel1M 81267 TGTTTCACCCCTGATCTTACTGGGAATTAGGCTCTC 81302 iviiii v -vi -- i C L1M1_orf2#LIN 1976 TGTCGTGTTCCAGATCTTA-GAGGAA--AGGCTTTC 1944 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.16 CpG sites = 38, Kimura (unadjusted) = 38.77 Transitions / transversions = 0.93 (38/41) Gap_init rate = 0.05 (13 / 272), avg. gap size = 1.69 (22 / 13) 727 33.06 4.09 3.29 chr2qtel1M 81796 82308 (917692) C L2#LINE/L2 (535) 2547 2031 m_b84s601i3 3124 chr2qtel1M 81796 CTTGAAGAAATGGGAAGATAGTGATGCCTCTTCAATAATAGGGAGAGTGT 81845 i iv v i i i v v -v ? v i v v i i--- C L2#LINE/L2 2547 CCTGAGCAACTGGAAGGATGGAGTTGCC-ATTNACTGAGATGGGGAA--- 2502 chr2qtel1M 81846 GAGTGTGTATGTATGAGAATATCTGGGGTAGAA-ATAATAAGTTCTGTTC 81894 v i --- v v v vi i i vi - v vi v i C L2#LINE/L2 2501 GACTGCG---GGAGGAGCAGGTTTGAGGGGGAAGATCAGGAGTTCAGTTT 2455 chr2qtel1M 81895 TG-ATGTATTGAATTTGCGTTTCTAGACTACTGGATATTCAATGTG-AGA 81942 - ii i i i v v v ---- i i i i - - C L2#LINE/L2 2454 TGGACATGTTAAGTTTGAGATGC----CTATTAGACATCCAA-GTGGAGA 2410 chr2qtel1M 81943 CATCTATAAGGAAATTGAAGATATAAAACTAGAGGTCAGCAGAGAAATT- 81991 ii v vv v i i v ii iv i v vi ii i- C L2#LINE/L2 2409 TGTCGAGTAGGCAGTTGGATATACGAGTCTGGAGTTCAGGGGAGAGGTCC 2360 chr2qtel1M 81992 GGGCACAAAAGGGACATTTGAAAATCATCAAAATATAGATAGCAATTAAA 82041 vvi i viv v ii i iv i i v C L2#LINE/L2 2359 GGGCTGGAGATATAAATTTGGGAGTCATCAGCATATAGATGGTATTTAAA 2310 chr2qtel1M 82042 TCCATGGTAGTTGATGAAATCACCAAGAAAAGAAATAATGAGGGAAAAGA 82091 v iv v v i ? ii ivi i ivv vi i C L2#LINE/L2 2309 GCCATGAGACTGGATGAGATCACCNAGGGAGTGAGTGTAGATAGAGAAGA 2260 chr2qtel1M 82092 GAAGAGGAACAAGGATAGAACACAAGGG-ACCCATATGGCTGGAAGTTTT 82140 vv iv i v vi - i vv i vi?i i ivv C L2#LINE/L2 2259 GAAGAGGTCCAAGGACTGAGCCCTGGGGCACTCCAACGTTNAGAGGTCGG 2210 chr2qtel1M 82141 G-ATCTCAGGAATATCCA--AAAAGATA--GAAAAGAAGTGGTCAGAGAA 82185 - vv v iv v -- i v -- i i i i v - C L2#LINE/L2 2209 GGAGATGAGGAGGAACCAGCAAAGGAGACTGAGAAGGAGCGGCCAGTGA- 2161 chr2qtel1M 82186 TAGGAAGAAGGGAAATCAAGAGAGAG-GGTGTCCTAAAATCCTAGAGAAC 82234 -- v i i i i v - ii v v v v C L2#LINE/L2 2160 --GGTAGGAGGAAAACCAGGAGAGTGTGGTGTCCTGGAAGCCAAGTGAAG 2113 chr2qtel1M 82235 AGAGAGGATCATAAAGGGAAGAGTA----------TCAAAGCCTGAATAA 82274 i v vv vi iii i---------- vv vvv ? C L2#LINE/L2 2112 AAAGTGTTTCAAGAAGGAGGGAGTGATCAACTGTGTCAAATGCTGCTGAN 2063 chr2qtel1M 82275 AAGTCAAAGGAGAATGAGGATGGAGAAAGTGACC 82308 i ivi - iv - v C L2#LINE/L2 2062 AGGTCAAGTAAGA-TGAGGACTGAG-AATTGACC 2031 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.15 CpG sites = 86, Kimura (unadjusted) = 45.01 Transitions / transversions = 1.10 (86/78) Gap_init rate = 0.05 (27 / 512), avg. gap size = 1.41 (38 / 27) 27 0.00 4.76 4.76 chr2qtel1M 82774 82815 (917185) (AATGA)n#Simple_repeat 1 42 (0) c_b84s251i1 3127 chr2qtel1M 82774 AATGAAATGAAAAATGAAATGAAATG-AATG-AATGAAATGAAA 82815 -- - - (AATGA)n#Simp 1 AATGAAATG--AAATGAAATGAAATGAAATGAAATGAAATGAAA 42 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.10 (4 / 41), avg. gap size = 1.00 (4 / 4) 19 7.28 0.00 0.00 chr2qtel1M 83260 83288 (916712) (ACAA)n#Simple_repeat 1 29 (0) m_b84s252i5 3128 chr2qtel1M 83260 ACCAAGAAACAAACAAACAAACAAACAAA 83288 v v (ACAA)n#Simpl 1 ACAAACAAACAAACAAACAAACAAACAAA 29 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 19 12.06 0.00 0.00 chr2qtel1M 83779 83806 (916194) (A)n#Simple_repeat 1 28 (0) m_b84s252i6 3129 chr2qtel1M 83779 AAAAAAAAAAAAAAAGAAAGAAAAGAAA 83806 i i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA 28 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 23 14.69 0.00 0.00 chr2qtel1M 84050 84087 (915913) (T)n#Simple_repeat 1 38 (0) m_b84s252i7 3130 chr2qtel1M 84050 TTTTTTTTTAATTTTTTTTAATTTTTTTTTTTTTATTT 84087 vv vv v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 38 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 245 21.54 3.08 0.00 chr2qtel1M 84228 84292 (915708) MIR3#SINE/MIR 78 144 (64) m_b84s601i4 3131 chr2qtel1M 84228 CCAGCTGTG-GACCG-GAGAAAGCCACTCCAGCCCTTTTGTCCCCAGTGT 84275 i? - v- i v i i v i i v v i v MIR3#SINE/MIR 78 CTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTT 127 chr2qtel1M 84276 CCTCATCTGGAAAATGA 84292 v MIR3#SINE/MIR 128 CCTCATCTGTAAAATGA 144 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.06 CpG sites = 7, Kimura (unadjusted) = 26.06 Transitions / transversions = 1.00 (7/7) Gap_init rate = 0.03 (2 / 64), avg. gap size = 1.00 (2 / 2) 180 3.37 0.00 10.00 chr2qtel1M 87385 87417 (912583) C L3#LINE/CR1 (1116) 2983 2954 m_b84s601i5 3132 chr2qtel1M 87385 GACTTTGTGCAACTCTGCCTTGCTGAAATCCAG 87417 - v -- C L3#LINE/CR1 2983 GACTTTGT-CAAAT--GCCTTGCTGAAATCCAG 2954 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 3.42 CpG sites = 0, Kimura (unadjusted) = 3.42 Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.09 (3 / 32), avg. gap size = 1.00 (3 / 3) 208 32.84 16.67 0.60 chr2qtel1M 87566 87709 (912291) MamRTE1#LINE/RTE-BovB 336 502 (3310) m_b84s601i6 3133 chr2qtel1M 87566 TCACTG--GACACAGCGGTGGGATCTAGCAGCCCCTTAGATGTATGAGC- 87612 i -- vi i iivvi iii v? i i i v - MamRTE1#LINE/ 336 TCGCTGANGAGGCAGCAGCACCGTTCGGCAGCGNCCTGGGTGTCTGAGCA 385 chr2qtel1M 87613 --TCTGAAAAAAAAAA------TCCCCCTGGTATGAGGAAGAGACCAGAA 87654 --i vvv ii ?vi------ v i i i- i i ? i MamRTE1#LINE/ 386 GCCCTGTTTAGGANCGCGCTGCTCACTCCGA-ATGGGGAAGGGNCTAGAA 434 chr2qtel1M 87655 AAGGTGCACTAAAAAT---CTGCTT------AATCAGCCCTGGCCTGTC- 87694 v vi --- i ------ ? iv? iiii - MamRTE1#LINE/ 435 AAGGTGCCCTAAACGTTGCCTGCCTCGCCAAANTCAAANCTGGCTCACCA 484 chr2qtel1M 87695 ---TACCATGGTTGGTGG 87709 --- i ii vi MamRTE1#LINE/ 485 GATTATCGCGTCTGGTGG 502 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.78 CpG sites = 33, Kimura (unadjusted) = 49.01 Transitions / transversions = 2.36 (33/14) Gap_init rate = 0.06 (9 / 143), avg. gap size = 2.78 (25 / 9) 22 14.94 0.00 0.00 chr2qtel1M 87722 87758 (912242) (AC)n#Simple_repeat 1 37 (0) m_b84s252i8 3134 chr2qtel1M 87722 ACAGAAATACAGACACACACAAACACACACACACACA 87758 v v i v v (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACA 37 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 258 33.29 9.33 1.86 chr2qtel1M 88037 88186 (911814) MamRTE1#LINE/RTE-BovB 1140 1300 (2512) m_b84s601i7 3133 chr2qtel1M 88037 ATCACCAACGCGGTCTTCTGCTAACTTAA-AAGCAACAGAACTTCATGGG 88085 i vi i iv iv - vi v - v i MamRTE1#LINE/ 1140 ATCACCAACACCATCTTCCGCCTACCGAATAAGAGAAAG-ACATCATGGA 1188 chr2qtel1M 88086 TGCACTTTTACAG--CAAACACTGTCATTTAGTAGACTATATAATTATAA 88133 --ii vi --i i v v i vi v i v ii vv MamRTE1#LINE/ 1189 TGCAC--CCAAGGTCTAAGCAGTGGCATCTCATTGATTATATCATCGTTC 1236 chr2qtel1M 88134 GA-AACAGGA--TAGAGAATG--------ACAAAGGCCATATGTGAGGCA 88172 - i i -- ii i -------- vivi i ii iv v MamRTE1#LINE/ 1237 GACAGCGGGACCTGAAGGATGTTTAGATTACTGCAGCTATGCGTGGCGCC 1286 chr2qtel1M 88173 GAATGATGGACTGA 88186 i v i MamRTE1#LINE/ 1287 GAGTGCTGGACCGA 1300 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.53 CpG sites = 30, Kimura (unadjusted) = 46.02 Transitions / transversions = 1.58 (30/19) Gap_init rate = 0.05 (8 / 149), avg. gap size = 2.12 (17 / 8) 569 31.73 4.96 3.51 chr2qtel1M 89947 90733 (909267) L1M5_orf2#LINE/L1 828 1625 (1669) m_b84s551i5 3135 chr2qtel1M 89947 GAATGACAATAATGACACA-TATAACAAAACTTACGGAATACA-CTAAAG 89994 ? i vi i -i v i ii i i - L1M5_orf2#LIN 828 GAATGANAATGAAAATACAACATATCAAAATTTGTGGGATGCAGCTAAAG 877 chr2qtel1M 89995 -------TAGAAGAAATTTTACACCTCTGAATATTTACAT----AAATAA 90033 ------- i i v i v ?i i ii? i ---- v L1M5_orf2#LIN 878 CAGTGCTTAGAGGGAAATTTATAGCNTTAAATGCNTATATTAGAAAAGAA 927 chr2qtel1M 90034 AATAG-----AGATCAATGAATTGATTATACAACTAAAAAAGCTAGAAAA 90078 i v ----- i vi i viv v v v i L1M5_orf2#LIN 928 GAAAGGCTTAAAATCAATGATCTAAGCTTCCACCTTAAGAAGCTAGAAAA 977 chr2qtel1M 90079 G--AGAACAAATTTTTTAAAATCCCAATTAAATAGTAAATTAGATATTTT 90126 i-- i ----- i v v? i v iivvi v vv L1M5_orf2#LIN 978 AGAAGAGCAAATT-----AAACCCAAAGNAAGTAGAAGGAAGGAAATAAT 1022 chr2qtel1M 90127 AAAAATCTAAGAAGGGATAAATTCTCTTCTTCCTTTGAAGAAAATGGAAA 90176 i -- -- v v i-------------- vi i L1M5_orf2#LIN 1023 AAAGAT--AAGA--GCAGAAATC--------------AATGAAATAGAAA 1054 chr2qtel1M 90177 GTAAGGAAACTATTAAACTAATAAGTAAAATTAAAACTTGATTATG-AAA 90225 ii i? ? v vi ivv v iii iii vi i v v-i L1M5_orf2#LIN 1055 ACAAANANACAATAGAGAAAATCAACGAAGCCAAAAGCTGGTTCTTTGAA 1104 chr2qtel1M 90226 AAAATTAATAAAGCAGATGAAGTTTTGGTTAATTTGATTA-GAAAAAAGA 90274 i i iiv i vi i i i? ivi i - ii L1M5_orf2#LIN 1105 AAGATCAATAAAATTGATAAACCTCTAGCNAGACTGATCAAGAAAAAAAG 1154 chr2qtel1M 90275 AGGAAAG---CAAATTACTAGTATCAAAAATGAAAAGGGTAAAGTTACCA 90321 ii --- i i ii i vi vi i i L1M5_orf2#LIN 1155 AGAGAAGACACAAATTACCAATATCAGGAATGAAAAAGGAGACATCACTA 1204 chr2qtel1M 90322 GCAATGAAGAAGAAATTAAA-GCATGA-AGTAGGACCTATTTTGCTCAAC 90369 vvi vvviv v - v i - iv i -- v vv L1M5_orf2#LIN 1205 CAGATCCTACAGACATTAAAAGGATAATAAGAGAA--TATTATGAACAAC 1252 chr2qtel1M 90370 TGTTTGCCAACAAATCAGACCATTTAATTGAAATGGATGAATATTTGCAG 90419 v v i iv ?v i iv ii vii vv i L1M5_orf2#LIN 1253 TTTATGCCAATAAATTTGANAACTTAGATGAAATGGACAAATTCCTTGAA 1302 chr2qtel1M 90420 AAACATAAATTGCCCATATTAACAGAAGAAAAAGTAAAATGCTAAAATAA 90469 i ? i v v i i ?v i i i viiivi i L1M5_orf2#LIN 1303 AAACACAANTTACCAAAACTGACNCAAGAAGAAATAGAAAATCTGAATAG 1352 chr2qtel1M 90470 CCCCAT-TTTAAAAATAGAAATTAAACAAGTCAATGAA----TTCCCAAA 90514 i - i vv - i ivv v v i ---- v L1M5_orf2#LIN 1353 CCCTATATCTATTAA-AGAAATTGAATTTGTAATTAAAAACCTTCCCACA 1401 chr2qtel1M 90515 GAAAAAAATCTCCAGGGTGAGATGAATTTGCAAGGACATTCTACCAAATA 90564 i i -- viv iv ii vi viv i L1M5_orf2#LIN 1402 AAGAAAA--CTCCAGGCCCAGATGGCTTCACTGGTGAATTCTACCAAACA 1449 chr2qtel1M 90565 TTTAGGGAACAATTAATTCTGATATAATGTAAACTACTTGAAAAGATAGG 90614 i v v v ii v v iii vi iv i i i L1M5_orf2#LIN 1450 TTTAAGGAAGAAATAATACCAATCTTACACAAACTCTTCCAGAAAATAGA 1499 chr2qtel1M 90615 TGAAGAATGATTGCTAGCTAATTCATTTTATGACACAAATATGGTGCTAG 90664 vi iv vii vv i i vi v ii ?iiv ii L1M5_orf2#LIN 1500 AAAAGAGGGAACACTTCCCAACTCATTTTATGAGGCCAGCATNACCCTGA 1549 chr2qtel1M 90665 ----AAAATAGGA-AGAGCTAAAACA--GAAAGAAAATTATAGACCAATT 90707 ---- iv? - i vi vv --i i v L1M5_orf2#LIN 1550 TACCAAAACCNGACAAAGACATTACAAGAAAAGAAAATTACAGACCAATA 1599 chr2qtel1M 90708 TCCCTAATAAATATTGATGCAAAGAT 90733 v i i v i L1M5_orf2#LIN 1600 TCCCTCATGAACATAGATGCAAAAAT 1625 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 43.51 CpG sites = 145, Kimura (unadjusted) = 43.79 Transitions / transversions = 1.51 (145/96) Gap_init rate = 0.06 (44 / 786), avg. gap size = 1.52 (67 / 44) 346 28.50 17.19 1.35 chr2qtel1M 90762 90953 (909047) MIRb#SINE/MIR 13 234 (34) m_b84s601i9 3136 chr2qtel1M 90762 GTGGCGCAGTGGATAGAGCACCAGACCTGAAGTCAAGAAGACCTGAGTTC 90811 i v vi vii i iiv i MIRb#SINE/MIR 13 GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTC 62 chr2qtel1M 90812 AAATATGGCCTCAGACACTTAACA-CT------TCCTGGGCAAGTCACTT 90854 i viv v v v vi - ------i i i MIRb#SINE/MIR 63 GAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTT 112 chr2qtel1M 90855 AA----------CCCCAATTTCCTCA--AAAAAAAAAAGAATAATAAAA- 90891 ---------- i i --viv vii i v - MIRb#SINE/MIR 113 AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAC 162 chr2qtel1M 90892 -------AGAAGACTATCAAGGGGGTT-AATGAAAACTAATGCA---AAA 90930 -------iv i ii i iiv i i - i -- --- MIRb#SINE/MIR 163 CTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGA--TAATGCATGTAAA 210 chr2qtel1M 90931 ATAGCCTA--ACAATACCAGACATA 90953 ii- i -- i i v i i MIRb#SINE/MIR 211 GC-GCTTAGCACAGTGCCTGGCACA 234 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.12 CpG sites = 37, Kimura (unadjusted) = 37.80 Transitions / transversions = 2.18 (37/17) Gap_init rate = 0.06 (12 / 191), avg. gap size = 3.00 (36 / 12) 452 22.66 14.84 0.00 chr2qtel1M 90762 90889 (909111) MIRc#SINE/MIR 10 156 (112) m_b84s601i8 3136 chr2qtel1M 90762 GTGGCGCAGTGGATAGAGCACCAGACCTGAAGTCAAGAAGACCTGAGTTC 90811 i v ii i i i i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr2qtel1M 90812 AAATATGGCCTCAGACACTTAACA-CT------TCCTGGGCAAGTCACTT 90854 i i viv v v v vi - ------i i MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTT 109 chr2qtel1M 90855 AA----------CCCCAATTTCCTCA--AAAAAAAAAAGAATAATAA 90889 ---------- i i --viv vii i MIRc#SINE/MIR 110 AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAA 156 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.64 CpG sites = 19, Kimura (unadjusted) = 27.75 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.03 (4 / 127), avg. gap size = 4.75 (19 / 4) 180 34.56 5.88 2.13 chr2qtel1M 92011 92146 (907854) C AmnL2-1#LINE/L2 (371) 2242 2102 m_b84s601i10 3137 chr2qtel1M 92011 TCCATTAAGTTTTTCAATGGCAAACAAGAGGACTTTGAATCTGA-CCTCA 92059 vi vv i vii iv ivi i iiv - v C AmnL2-1#LINE/ 2242 TCCATGGAGGGTTTTAAAAACAAGGAAGGCAATTTTGAACTGGATCCTGA 2193 chr2qtel1M 92060 GAGGCAACAGAGAGTTATTGGAG-TGACTGAGGAGGGGACTGACAT--TT 92106 i v - ii i ii v - vi v iv ii -- i C AmnL2-1#LINE/ 2192 AATG-AATGGGGAGCCAGTGGAGTTGTTTGAGGATGGGGGTGATGTGGTC 2144 chr2qtel1M 92107 G---TTC-TTATATGGAAGGGAATACCGGTGTGGCAGCTTCCTG 92146 --- - i i viv i -iv - ii v i C AmnL2-1#LINE/ 2143 GCGCTTCTTTGTACGTGTGAGAA-GGCGG-GCAGCAGCATTCTG 2102 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.87 CpG sites = 29, Kimura (unadjusted) = 48.88 Transitions / transversions = 1.71 (29/17) Gap_init rate = 0.06 (8 / 135), avg. gap size = 1.38 (11 / 8) 254 39.91 4.37 0.42 chr2qtel1M 92270 92498 (907502) C L2#LINE/L2 (460) 2622 2385 m_b84s601i11 3138 chr2qtel1M 92270 GGCAAAATTGGGCAATCGATTCCACTTGAGAATTGAGAGA--TAATGCAG 92317 i ii v vii v vv iv i ivv --v iv v C L2#LINE/L2 2622 GACAGGATTTGCTGATGGATTGGATGTGGGGTGTGAGAGAAAGAGAGGAG 2573 chr2qtel1M 92318 TTAAGAATAAAATTGGGATTATTAATATTGGTGACTGGAGGAGTGATGGT 92367 i i i vviiii i v iiiv vi ii i ii iv v C L2#LINE/L2 2572 TCAAGGATGACTCCAAGGTTTTTGGCCTGAGCAACTGGAAGGATGGAGTT 2523 chr2qtel1M 92368 ACC-----CTCAAGGAAGGAAATATG-GAGAGGGGGATGATCTG--GGGA 92409 i ----- v iivii ivv - i i v - i i -- i C L2#LINE/L2 2522 GCCATTNACTGAGATGGGGAAGACTGCGGGAGGAGCA-GGTTTGAGGGGG 2474 chr2qtel1M 92410 AAGGTAATAGGTTTTGTTGTGGATATGGTGAGTTGGAGATGCCCGTTAGC 92459 i v vii iv v i v i v ii v C L2#LINE/L2 2473 AAGATCAGGAGTTCAGTTTTGGACATGTTAAGTTTGAGATGCCTATTAGA 2424 chr2qtel1M 92460 TATGTAATTCAAAATGTCTGGTAGCTATTTGGATGTGTG 92498 i vi v vi i vi vi v i ii C L2#LINE/L2 2423 CATCCAAGTGGAGATGTCGAGTAGGCAGTTGGATATACG 2385 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 59.53 CpG sites = 55, Kimura (unadjusted) = 60.62 Transitions / transversions = 1.53 (55/36) Gap_init rate = 0.02 (5 / 228), avg. gap size = 2.20 (11 / 5) 34 0.00 0.00 0.00 chr2qtel1M 96985 97013 (902987) (CA)n#Simple_repeat 1 29 (0) c_b84s251i2 3139 chr2qtel1M 96985 CACACACACACACACACACACACACACAC 97013 (CA)n#Simple_ 1 CACACACACACACACACACACACACACAC 29 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 1352 27.99 2.20 2.82 chr2qtel1M 98833 99332 (900668) L1ME5_3end#LINE/L1 56 552 (389) m_b84s551i6 3140 chr2qtel1M 98833 CTCTAATTGATAAATGGTCAAAGGATATGAACAGACAATTTTCAGATGAT 98882 i i v v v i v v v L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chr2qtel1M 98883 GAAATTGAAACTATTACCACTCATATGAAAGAGTGTTCCAAATCACTATT 98932 iivi vvii v vv iiii i v v i v L1ME5_3end#LI 106 GAAACCCGAAAGGCTAACAAGCATATGAAGAGATGCTCAAACTCATTAGT 155 chr2qtel1M 98933 AATCAGAGAAATACAAATTAAGACAACTCTGAGATACCACTACCCACCTG 98982 i i vv i viv i L1ME5_3end#LI 156 AATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCTA 205 chr2qtel1M 98983 TCAGATTGACTAGAATGACAGGAAA---AAATAACGACGAATGTTGGAGG 99029 i i i v i v --- ---ii i v i i v i L1ME5_3end#LI 206 TTAGACTGGCAAAAATTA---GAAAGCTGGATAATGCCAAGTGTTGGCGA 252 chr2qtel1M 99030 GGATGTGGGAGAACTGGGACACTGATGCCTTGTTGGTGGAGTTGTGAACG 99079 ii? iv i v v vi i iiv ii v L1ME5_3end#LI 253 GGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACT 302 chr2qtel1M 99080 AATCCAATCATTCTGGAGAGAAATCTGGAATTA--TGCCCAAA--AAGTT 99125 ii v ii v v v -- ivi -- - L1ME5_3end#LI 303 GGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTAAG-T 351 chr2qtel1M 99126 ATCAAACTGTGCATACCCTTTGACCCAGCAGTACTACTACTGGGCTTATA 99175 --- --- v i v ii v iv L1ME5_3end#LI 352 AT---AC---GCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATA 395 chr2qtel1M 99176 CCCCAAAGAGATACTAAAGAAGG----GAAAGGGACCAGTATGTGCCAAA 99221 i i v v viv ----v i ---- i v ii L1ME5_3end#LI 396 TCCCAAAGAAATTCTCACACAGGTCCATAAGGGGAC----ATGTACGAGG 441 chr2qtel1M 99222 ATGTTTGTGGCAGCCCTGTTTGTAGTAGCTAGAAACTGGAAAATGAATGG 99271 ii v vi i i vi i ii iivvivv L1ME5_3end#LI 442 ATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGG 491 chr2qtel1M 99272 ATGTCCATCAATTGGAGAATGGTTGGGTAAATTGTGGTATATGAATGTTA 99321 i v v i v i v iv v iiii L1ME5_3end#LI 492 GTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACACCA 541 chr2qtel1M 99322 TGGAATGTTAT 99332 i ii L1ME5_3end#LI 542 TGGAGTACTAT 552 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.29 CpG sites = 79, Kimura (unadjusted) = 35.99 Transitions / transversions = 1.39 (79/57) Gap_init rate = 0.04 (18 / 499), avg. gap size = 1.39 (25 / 18) 45 9.47 0.00 0.00 chr2qtel1M 99607 99674 (900326) (T)n#Simple_repeat 1 68 (0) c_b84s251i3 3141 chr2qtel1M 99607 TTTTTATTTTTATTTTTTTTTTTTTATTTTTTTATTTTTTTTTTTTTTTT 99656 v v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr2qtel1M 99657 GTTGTTTTTTTTTTTTTT 99674 v v (T)n#Simple_r 51 TTTTTTTTTTTTTTTTTT 68 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0) 278 25.54 8.09 5.00 chr2qtel1M 101619 101754 (898246) C MIR3#SINE/MIR (1) 207 68 m_b84s601i12 3142 chr2qtel1M 101619 AAGCATCAAAGTCATGAGACAT-AGAGCTGAAAGTCACTTCAGAATTCAA 101667 v - i i iii ii - i vv i i iv -- C MIR3#SINE/MIR 207 AATCAT-AGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATC-- 161 chr2qtel1M 101668 GAATCCAA-CCAACCCTCCCCAATTTACAG--GAGGAAAGTCAAG--CAG 101712 -- i i- - i v -- v v i -- C MIR3#SINE/MIR 160 --ATCTAGTCCAACCC-CCTCATTTTACAGATGAGGAAACTGAGGCCCAG 114 chr2qtel1M 101713 AGA----AAG-GATTTGCTCAAAGCTCATGCCATTTGTGAGTGTCAG 101754 ---- - i i i - ii vii?v v v C MIR3#SINE/MIR 113 AGAGGTGAAGTGACTTGCCCAAGG-TCACACAGCNAGTTAGTGGCAG 68 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.79 CpG sites = 22, Kimura (unadjusted) = 32.79 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.10 (13 / 135), avg. gap size = 1.38 (18 / 13) 12 19.17 2.13 6.67 chr2qtel1M 105299 105345 (894655) (TTCTT)n#Simple_repeat 1 45 (0) m_b84s252i9 3143 chr2qtel1M 105299 TTCATTTTCTTTTCTCTTTTTTTTCCCTTTATGATC-TGACTTTTCTT 105345 - - i - i v vv - vv (TTCTT)n#Simp 1 TTC-TTTTCTTTTCT-TTTCTTTT-CTTTTCTTTTCTTTTCTTTTCTT 45 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.09 (4 / 46), avg. gap size = 1.00 (4 / 4) 13 29.24 1.61 3.28 chr2qtel1M 105392 105453 (894547) (TTTAT)n#Simple_repeat 1 61 (0) m_b84s252i10 3144 chr2qtel1M 105392 TTTATTTTATTTAATATT-TGCAATAATATTTGCAAAAATATTTTATTTT 105440 v v - viv vv --v vvv (TTTAT)n#Simp 1 TTTATTTTATTTTATTTTATTTTATTTTATTT--TATTTTATTTTATTTT 48 chr2qtel1M 105441 ATTTAGGTTTATT 105453 viv (TTTAT)n#Simp 49 ATTTTATTTTATT 61 Matrix = Unknown Transitions / transversions = 0.17 (2/12) Gap_init rate = 0.05 (3 / 61), avg. gap size = 1.00 (3 / 3) 364 27.03 0.90 6.67 chr2qtel1M 105651 105761 (894239) C MIRc#SINE/MIR (141) 127 23 m_b84s601i13 3145 chr2qtel1M 105651 CTGAGGC-AATTGGGGTTAAGGGACTTGCCTAGGGTTACACAGATAAGAA 105699 -v vv i v i i i v i--- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG--- 81 chr2qtel1M 105700 GTGTTAAGTGTCTGAGGTCAGATTTGAACTCAGGTCCTCCTGACTTCAGG 105749 ---- v v vivi i i i i i i C MIRc#SINE/MIR 80 ----TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr2qtel1M 105750 GATGGTGATTTT 105761 vvii v i C MIRc#SINE/MIR 34 TCCAGTGCTCTT 23 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.15 CpG sites = 16, Kimura (unadjusted) = 34.06 Transitions / transversions = 1.33 (16/12) Gap_init rate = 0.07 (8 / 110), avg. gap size = 1.00 (8 / 8) 12 8.85 4.17 0.00 chr2qtel1M 106441 106464 (893536) (CTC)n#Simple_repeat 1 25 (0) m_b84s252i11 3146 chr2qtel1M 106441 CTCCTCCTTC-CCTCCACCTCCTCC 106464 i - v (CTC)n#Simple 1 CTCCTCCTCCTCCTCCTCCTCCTCC 25 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 16 10.03 0.00 0.00 chr2qtel1M 107010 107031 (892969) (A)n#Simple_repeat 1 22 (0) m_b84s252i12 3147 chr2qtel1M 107010 AAAAAAAAAAAAAAAGAAGAAA 107031 i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAA 22 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 319 18.85 6.15 6.15 chr2qtel1M 107794 107923 (892077) C HERVK14#LTR/ERVK (2921) 3175 3046 m_b84s701i0 3148 chr2qtel1M 107794 TCAG-TGCACACCTCAAGATATCATCCATGAAATGTAATAATATTAC-TT 107841 - --- ii v -i v - C HERVK14#LTR/E 3175 TCAGCTGCACAC---AGAATATCATCCATGTAATG-GATAATATAACATT 3130 chr2qtel1M 107842 TTGGAAATGCTTTTCTTACTAGAATAATAG------CGAATCATAAACAT 107885 vv ivv i v i vv ------ -- --i C HERVK14#LTR/E 3129 TTTTAAACTGTTCTCTAACTGGCTTAATAGCTTTCCCGA--CATAA--GT 3084 chr2qtel1M 107886 TTGACACATAGTAGGACTATTTTTCATTCCCTGTGGTA 107923 v v i vv v i C HERVK14#LTR/E 3083 TTGACAAATAGTCGGGCTATTTAGCATGCCTTGTGGTA 3046 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 21.73 CpG sites = 9, Kimura (unadjusted) = 21.73 Transitions / transversions = 0.64 (9/14) Gap_init rate = 0.09 (11 / 129), avg. gap size = 1.45 (16 / 11) 267 26.62 10.34 5.32 chr2qtel1M 107806 108182 (891818) C HERVK11D#LTR/ERVK (4156) 3596 3202 m_b84s701i1 3148 chr2qtel1M 107806 TCAAGATATCATCCATGAAATGTAATAAT---ATTACTTTTGGAAATGCT 107852 iv iv - v --- i -- v ii C HERVK11D#LTR/ 3596 TCAGTATATCATCCATATAATG-AAGAATGTAATTATTTTT--AAAAGTC 3550 chr2qtel1M 107853 TTTCTTACTAGA--ATAATAGCGAATC-ATAAACATTTGACACATAGTAG 107899 v vv - i--i i vv v i - i vi v C HERVK11D#LTR/ 3549 TGTCGGA-TAGGTTGTAACACAGTACCGACAAACAACTGACAAATAGTAG 3501 chr2qtel1M 107900 GACTATTTTTCATTCCCTGTGGTAAAAC--ACTATTCATATCTTTTATAA 107947 i vv i v --v i v ------- C HERVK11D#LTR/ 3500 GACTGTTAATCATTCCTTGAGGTAAAACTTTCCATTGATATCT------- 3458 chr2qtel1M 107948 AGCT----CAGCTAAA---CTAATG------ACACTAAAAGTCAAACCTT 107984 ----v i ---i ------ i v i - -i C HERVK11D#LTR/ 3457 AGCTGCGGGAGCTGAATTGTTAATGGAAGGTATAGTGAAAG-CAAA-TTT 3410 chr2qtel1M 107985 TTCATATCCTT-CTTAACTAGAGG-ATAGAATGGAAACAATC--TAATTG 108030 i vi v- iv i - vi vii i i -- -v C HERVK11D#LTR/ 3409 TTCACAGTCTGACTTGTCTAAAGGAATATGAAAAAAGCAGTCCTTAA-GG 3361 chr2qtel1M 108031 TGTATTACCCAA--AGAGGCCATTCTCTAGCAACT------GAGTAGGGC 108072 vv v --i -- i ii v ii------ i v C HERVK11D#LTR/ 3360 TCAATGA--TAATTAAAGGCCATTCCTTAGGAATCATGGAGGGGGAGGGC 3313 chr2qtel1M 108073 ATGGAATCTAG-TAAAATGTTCCTATTATTTCCAT--CTGTTCATTTGCT 108119 --- i vi - iv i ii i viv iv -- -- vi v C HERVK11D#LTR/ 3312 AT---ACCGGGTTGTAACGCCCCCATAGGTTTAATAACTG--CATTAACA 3268 chr2qtel1M 108120 TTTCTCAAATCAG-TACCATCCTCCA-TTTCCAGATTTCTTTT-TATAGC 108166 vi i i v - - v i i - i i C HERVK11D#LTR/ 3267 GCTCTTAAGTCTGTTACCATCCTCCATTTTCCTGACTTTTTTTGTACAAC 3218 chr2qtel1M 108167 AAATACAGGAGAATTC 108182 i v i C HERVK11D#LTR/ 3217 AAACACAGGCGAGTTC 3202 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 33.22 CpG sites = 54, Kimura (unadjusted) = 33.66 Transitions / transversions = 1.32 (54/41) Gap_init rate = 0.10 (38 / 376), avg. gap size = 1.58 (60 / 38) 300 20.53 7.21 3.48 chr2qtel1M 108123 108233 (891767) C HERVK14#LTR/ERVK (3263) 2833 2719 m_b84s701i2 3148 chr2qtel1M 108123 CTCAAATCAGT-ACCATCCTCCATTTCCA-GATTTCTTTTTA-TAGCAAA 108169 i v - v i v- i i - ii C HERVK14#LTR/E 2833 CTTAAATCTGTTAACATTCTCCATTTCCCTGATTTTTTCTTAATGACAAA 2784 chr2qtel1M 108170 TACAGGAGAATTCGAAGACTTAGGAGAATGT----TGTA-AGGACCTTGC 108214 v ----i v ---- v - v v i vi C HERVK14#LTR/E 2783 TACAGGAGAATTCCAAG----GGGAGAAAGTAGGCTCTATATGTCCCTTT 2738 chr2qtel1M 108215 TGAAGTTGTTCCTGTACTA 108233 v i i i C HERVK14#LTR/E 2737 TGCAATTGTTCCTGCACCA 2719 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 24.29 CpG sites = 12, Kimura (unadjusted) = 24.29 Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.08 (9 / 110), avg. gap size = 1.33 (12 / 9) 496 37.07 9.20 3.61 chr2qtel1M 108839 109784 (890216) C MamRTE1#LINE/RTE-BovB (2501) 1311 315 m_b84s601i14 3149 chr2qtel1M 108839 TCAGTCTATGATCATTCCAGCATTCTGCATCACATATGGCCTTTGTCACT 108888 v v i iv i v ii ii i iviv v - C MamRTE1#LINE/ 1311 TCAGGCGATGGTCGGTCCAGCACTCGGCGCCACGCATAGCTGCAGTAA-T 1263 chr2qtel1M 108889 CTC--TATCTT---GTTTCTTCCCTT--ACAATTATACAGTCTACTAAAT 108931 v--i i --- v i iv iv i-- i v i i v iv i C MamRTE1#LINE/ 1262 CTAAACATCCTTCAGGTCCCGCTGTCGAACGATGATATAATCAATGAGAT 1213 chr2qtel1M 108932 GACAATGTTTG--CTGTAAATGTGCATGCATGAAATTTTGTT-------- 108971 v v i i-- iv ii-- v vi i vi -------- C MamRTE1#LINE/ 1212 GCCACTGCTTAGACCTTGG--GTGCATCCATGATGTCTTTCTCTTATTCG 1165 chr2qtel1M 108972 ----GCG----ACAGTGTTGGTGAT-AGGGTCTTCAGATGCACAA-ATCT 109011 ---- ---- ii - v iv --- viii- iv C MamRTE1#LINE/ 1164 GTAGGCGGAAGATGGTGTTGGTGATTACGAGCT---GATGCTTGGCACAT 1118 chr2qtel1M 109012 TCACTAAT----AACTGACCAGTGCTGTTGCTGTTTTCAA-CCTATTCCA 109056 i i v---- iiv v ?vvv i - ii v?vi C MamRTE1#LINE/ 1117 TCGCTGAGCAGGAGTAGACCATTGCTGTTNAGCTTTCCAATCCCGTGNGG 1068 chr2qtel1M 109057 CCCAAAGACATTCC--CTTGTCTGAGCCTAGT-----ATA---ACCTTAA 109096 i i v v i -- vi i vi v v i----- i ---i v i C MamRTE1#LINE/ 1067 TCCGATGACTTTTCTCCACGTTTCGGCATCGCTGCCGACACGTGCGTTGA 1018 chr2qtel1M 109097 AATTAGCCAGGATTAGATAAGCTTGTCCTCTTTTGGCAA-ATTGAGGATG 109145 ivv iv i-- v vvv v i v-ii v - C MamRTE1#LINE/ 1017 AATCTCCCGTGAC--GATCAGCTTGTCAGATGTTGGTACCGCTGCG-ATG 971 chr2qtel1M 109146 AGCATCTCTAG-TCTTCTGAAAATTTTCCTTTGACCTCATCAAGGTTCCT 109194 iv v i - i ivv i i i vv iivi v C MamRTE1#LINE/ 970 AGTCTGTCCAGATCCTTGTAGAATCTTTCTTTCTCCTCATCGGTATTCGT 921 chr2qtel1M 109195 CATGGTGGGAAGATAGTCACTGATCATGTAACCATGGCA-TTTTCCTACA 109243 iiv vv i v i vviv ?i i- vi v C MamRTE1#LINE/ 920 CATGGTGGGGGCATATGCGCTGATGACGGTGGCANAGCGCTTTTGTTTCA 871 chr2qtel1M 109244 GGTGCCAAGGGCATTGTTATAAGCCTGACATTAAGTCTTTTTGGCAGACA 109293 i? -i i v i vv i v v v v i ? vv i i v i iv C MamRTE1#LINE/ 870 GANG-TAGGCGTAGGGTCATCAGACGGTCACTNATGCCTCTGGGCAAATT 822 chr2qtel1M 109294 TACAGGGTTGCTGATTTG-AACTGGTTCATTGCTAACCTATACCAACTTC 109342 ivii ?i vvv ivv -i vi v v v i- --i i v C MamRTE1#LINE/ 821 TGGGAGNCTTGAGACAAGTGACTGTCTGATTGCAAAGCTG-AC--GCCTG 775 chr2qtel1M 109343 ACAATGCTCCCTCC----ACTGCACTCC-CTGCAGAAAACCTTGTATGTA 109387 v iivv v i---- vv v vv - v i vvvi ?vii C MamRTE1#LINE/ 774 AGAGCCGTCGCTCTGAAGAGGGAAGACCTCTCCAGAAGAAGGCGTANCCG 725 chr2qtel1M 109388 GCTCCGACTTCAGTAAGGTGGCCTTTATTTGCCAGCCTTGTTTCACTCAG 109437 v viii v i v v i iv vv i v i C MamRTE1#LINE/ 724 GCACCTGTCTCCGTGAGCTGTCCTTCATCAGGAAGTCTGGTTTCGCTCAG 675 chr2qtel1M 109438 GGCTGCCTTTTGGATG-AGACACC-TA-CTG---AATTCTCTGGCCACTA 109481 v v ------ -v v - - --- i v vv v v C MamRTE1#LINE/ 674 TGCGGC------GATGTCGACTCCGTATCTGGACAGTTCACGTGCGACGA 631 chr2qtel1M 109482 GAGCTGTCCATCTTTCAGGTTTGCTGCATTATCCATAATGGTGACACATT 109531 v i i v v vivi vv vii i v ----- i v C MamRTE1#LINE/ 630 GTGCCGTTCTTCTTTCTGGACGACTGCTGTTCTCGTCAT-----CGCATA 586 chr2qtel1M 109532 CCAAGGACTGATGGTGAATGAAATCTTTGTACAAGT--TTTTATATGTAT 109579 v -- vv v vv ------i i vvi -- v v ?? C MamRTE1#LINE/ 585 GC--GTCCTGATGTTCCATGA------CGCAATGGTTATTTTCTTTGTNN 544 chr2qtel1M 109580 CTGTTTGTGTGTGTGTGTCTGTATTTCTATCACAGGA-TGGGGTCCACCA 109628 i? v v --- v v i i ?v vi i i i - iiiii C MamRTE1#LINE/ 543 TNGGTAGT---TTTCTATTTGNTTTTGCACCGCAAGANTAAAACCCACCA 497 chr2qtel1M 109629 ACCATGGTAGAC-----AGCCAGGGCTGATT------AAGCAGAT----T 109663 iv ii i iv ----- ?vi ? ------ i ii---- C MamRTE1#LINE/ 496 GACGCGATAATCTGGTGAGCCAGNTTTGANTTTGGCGAGGCAGGCAACGT 447 chr2qtel1M 109664 TTATTGTACCTTTTCTGGTCCCTTCCTCAT--AAAGGGGG--ATTTTTTT 109709 vv i i ? i --ii v i --iiviv? i C MamRTE1#LINE/ 446 TTAGGGCACCTTTTCTAGNCCCTTCCCCATTCGGAGTGAGCAGCGCGNTC 397 chr2qtel1M 109710 TTA---AGA---GCTCATACATCTAGGGAACTGCTACATCTCACTGCTGT 109753 i --- i--- v i i ?vi iiv ivvii i C MamRTE1#LINE/ 396 CTAAACAGGGCTGCTCAGACACCCAGGNCGCTGCCGAACGGTGCTGCTGC 347 chr2qtel1M 109754 GTC--CAGTGAGAAGATGGCTGCATAGCTTGGG 109784 v -- i vv iii i ii- v i C MamRTE1#LINE/ 346 CTCNTCAGCGACTAAGCGACCA-ATATCCTGGG 315 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.66 CpG sites = 175, Kimura (unadjusted) = 53.98 Transitions / transversions = 1.07 (175/163) Gap_init rate = 0.07 (70 / 945), avg. gap size = 1.76 (123 / 70) 17 12.81 2.94 0.00 chr2qtel1M 110263 110296 (889704) (TTTC)n#Simple_repeat 1 35 (0) m_b84s252i14 3150 chr2qtel1M 110263 TTTCTTTCTTTCTTTCTGTCTTT-TATTTTTATTT 110296 v - v i v (TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT 35 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 17 22.67 1.89 1.89 chr2qtel1M 110261 110313 (889687) (TATTTT)n#Simple_repeat 1 53 (0) m_b84s252i13 3151 chr2qtel1M 110261 TATTTCTTTCTTTCTTTCTGTCTTTTATTTTTATTTTTA-ATAGCTTTTT 110309 i v i v i i - -v vvv (TATTTT)n#Sim 1 TATTTTTATTTTTATTTTTAT-TTTTATTTTTATTTTTATTTTTATTTTT 49 chr2qtel1M 110310 ATTT 110313 (TATTTT)n#Sim 50 ATTT 53 Matrix = Unknown Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.00 (2 / 2) 12 9.12 4.17 0.00 chr2qtel1M 110376 110399 (889601) (TCCC)n#Simple_repeat 1 25 (0) m_b84s252i15 3152 chr2qtel1M 110376 TCCCTTCCT-TCTCCCTCCCTCCCT 110399 i -i (TCCC)n#Simpl 1 TCCCTCCCTCCCTCCCTCCCTCCCT 25 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 274 32.24 6.35 1.52 chr2qtel1M 111001 111252 (888748) L1M4_orf2#LINE/L1 1951 2214 (1080) m_b84s551i7 3153 chr2qtel1M 111001 TTCCCAGTAAGATCAGGG-TGAAACAATGGTG-CCATTTTCATCACTATA 111048 vv i-ii i v i - ii i ii viv L1M4_orf2#LIN 1951 TTCCCCCTAAGATCAGGAACAAGACAAGGATGTCCGCTCTCGCCACTTCT 2000 chr2qtel1M 111049 ATGCAACATTGTACTAAAAATGATAGCTTTAGTAA------AAAGAAAAG 111092 v ii ii vv ivvi i ------ ii L1M4_orf2#LIN 2001 ATTCAACATTGTACTGGAGGTTCTAGCCAGGGCAATTAGGCAAGAAAAAG 2050 chr2qtel1M 111093 AAATTGAAGTAATT-AGA---GAAAACAACTAGGAAACAAAACTACCATG 111138 vi vv i- --- iv ---- ii i viv L1M4_orf2#LIN 2051 AAATAAAAGGCATCCAGATTGGAAAGGAA----GAAGTAAAACTATCTCT 2096 chr2qtel1M 111139 CTTTGAAGATGATATG--CTGACCTACAGAA--TTCTAGAGAATCAACTG 111184 v i v i -- viiv i -- i ii v ?i L1M4_orf2#LIN 2097 ATTCGCAGATGACATGATCTTGTATATAGAAAATCCTAAGGAATCCACNA 2146 chr2qtel1M 111185 AAAAACTACAAGAAACACTTAACAACTTTAGCATAATGGAAGGACATAAA 111234 iv vi v v i v i vii v v i i i L1M4_orf2#LIN 2147 AAAAACTATTAGAACTAATAAACGAGTTCAGCAAGGTTGCAGGATACAAG 2196 chr2qtel1M 111235 ATAAACCGATATAAATCA 111252 v ivv i v L1M4_orf2#LIN 2197 ATCAATATACAAAAATCA 2214 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.95 CpG sites = 47, Kimura (unadjusted) = 43.87 Transitions / transversions = 1.42 (47/33) Gap_init rate = 0.04 (11 / 251), avg. gap size = 1.82 (20 / 11) 277 34.39 1.76 0.70 chr2qtel1M 111272 111555 (888445) L1P1_orf2#LINE/L1 2263 2549 (745) m_b84s551i8 3154 chr2qtel1M 111272 AGAGAAATCCCATTCAAAATTCCTGGAGACAATATAAAATATTTGGGTGT 111321 v v v v vv i v iv ii i vi L1P1_orf2#LIN 2263 AGTGAACTCCCATTCACAATTGCTTCAAAGAGAATAAAATACCTAGGAAT 2312 chr2qtel1M 111322 CTCCCTGCCAAGACAAATCCAGGAATTATATCCAC-ACAATTAAAAAATA 111370 ivv vv iv vi vv vi v - v v- v i v vi L1P1_orf2#LIN 2313 CCAACTTACAAGGGATGTGAAGGACCTCT-TCAAGGAGAACTACAAACCA 2361 chr2qtel1M 111371 CTTTTCACAGAAATATAATTATATATAAG-AAATTGAAGAGTGTCAAGTG 111419 vi v? v vviv i i- v iii ivvi L1P1_orf2#LIN 2362 CTGCTCAANGAAATAAAAGAGGATACAAACAAATGGAAGAACATTCCATG 2411 chr2qtel1M 111420 TTCATGGGTAGCCAACAT--GTATAATAAAAACAATAATTCTATCCAAAA 111467 i vv iv --i vi i iiiiv v ii ii L1P1_orf2#LIN 2412 CTCATGGGTAGGAAGAATCAATATCGTGAAAATGGCCATACTGCCCAAGG 2461 chr2qtel1M 111468 TCAATCTACTTATTCAGTGCCATACCAATCAAACTGCCAAGAAATTACTT 111517 - i ivv i v v i i vi v v L1P1_orf2#LIN 2462 T-AATTTATAGATTCAATGCCATCCCCATCAAGCTACCAATGACTTTCTT 2510 chr2qtel1M 111518 TATAGAGATGAAAAATA-TACAACAAAATTCATCTGGAA 111555 i i iv i v - vvi i v L1P1_orf2#LIN 2511 CACAGAATTGGAAAAAACTACTTTAAAGTTCATATGGAA 2549 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 46.18 CpG sites = 46, Kimura (unadjusted) = 46.83 Transitions / transversions = 0.90 (46/51) Gap_init rate = 0.02 (6 / 283), avg. gap size = 1.17 (7 / 6) 13 20.44 2.44 2.44 chr2qtel1M 111970 112010 (887990) (ATTAA)n#Simple_repeat 1 41 (0) m_b85s252i0 3155 chr2qtel1M 111970 ATGAAATGCAAAATAGA-TAATTTTAATTATATTAAATTAAA 112010 v -i v i - v v v (ATTAA)n#Simp 1 ATTAAAT-TAAATTAAATTAAATTAAATTAAATTAAATTAAA 41 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 1014 31.16 3.15 2.96 chr2qtel1M 112109 112647 (887353) L1ME3Cz_3end#LINE/L1 7 546 (451) m_b85s551i3 3153 chr2qtel1M 112109 TCTAAAATATGTAGAGAAGCGAGTTAAATTTATAAGAATGCAAGTCATTC 112158 i i i i vivvvvi iv --v v --v L1ME3Cz_3end# 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAA--AAAGACA--A 52 chr2qtel1M 112159 CTCAGTTGATAAATGATCAAAGGATATAAACAGACACTTTTCCGATAAAG 112208 i i v v iv i i v iv v vi i L1ME3Cz_3end# 53 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chr2qtel1M 112209 AAATTAAAGCATTTCTAATAT---TATGACAAAAATGCTCTAAATCATTA 112255 iivi -- vv i v--- - i v vv i L1ME3Cz_3end# 103 AAACCCGA--ATGGCCAATAAACATATGA-AAAGATGCTCAACCTCACTA 149 chr2qtel1M 112256 TTGATCAGAGAAAAGCAAATTAAGACAACTCTGAGGTACCACCTCACACC 112305 v i i v i ? vv i ii L1ME3Cz_3end# 150 GTAATCAGGGAAATGCAAATTAAAACNACAATGAGATACCATTTCACACC 199 chr2qtel1M 112306 TCCTCAGATTGGCCAAGATGACAGGAACAGATAATGACAAATTTTGGAAG 112355 - v v i vvv iiiv v i iv i v vii L1ME3Cz_3end# 200 -CATCAGATTGGCAAAAATTTAAAAGTCTGACAATACCAAGTGTTGGCGA 248 chr2qtel1M 112356 GGATGTGGGAAAACTGGGACACTAATGCAGTGTTGGTAGAATTGTGAATT 112405 ii v i v v i v i i i v i L1ME3Cz_3end# 249 GGATGTGGAGAAACGGGAACTCTCATACACTGCTGGTGGGAGTGTAAATT 298 chr2qtel1M 112406 TATCCAAACATTCTCAAGAGTAATTTGGAACTGTGCT--CAAAGGACTAT 112453 vi v v i i vi i v v i - --i v---- L1ME3Cz_3end# 299 GGTACAACCACTTTGGAGAGCAATTTGGCAATAT-CTAGTAAAGT----T 343 chr2qtel1M 112454 AAAATTGTGCATACCCTTAGTTCCAACATTCTCATTACTGGGTCTAGATT 112503 i iv i vv vi i v ii i v i v v ii L1ME3Cz_3end# 344 GAAGATGCGCATACCCTACGACCCAGCAATTCCACTTCTAGGTATATACC 393 chr2qtel1M 112504 CCAAAGAGATAGTAGGACATG---ATAAAGAATCCACATGTGGGAAAATG 112550 i i i ivv v v --- i i i--- ivi ii L1ME3Cz_3end# 394 CTAGAGAAACTCTCGCACATGTGCACAAGGAG---ACATGTACAAGGATG 440 chr2qtel1M 112551 T-------AGCAT--TTTGTACTGGCAAGGAACTGGAAATTGAGTAGATG 112591 ------- -- v i i ii i ivivv i L1ME3Cz_3end# 441 TTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATG 490 chr2qtel1M 112592 CCCATCACTTAGAAAATGGCCAAATAAATTGTGTTATATGAAAGTAAAGG 112641 i v vi ii vi v vv vii v L1ME3Cz_3end# 491 TCCATCAATAGGGGAATGGATAAATAAATTGTGGTATATTCATACAATGG 540 chr2qtel1M 112642 AATATT 112647 i L1ME3Cz_3end# 541 AATACT 546 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.98 CpG sites = 89, Kimura (unadjusted) = 41.30 Transitions / transversions = 1.20 (89/74) Gap_init rate = 0.04 (21 / 538), avg. gap size = 1.57 (33 / 21) 1046 31.67 3.16 2.09 chr2qtel1M 112158 112631 (887369) L1ME5_3end#LINE/L1 56 534 (407) m_b85s551i4 3153 chr2qtel1M 112158 CCTCAGTTGATAAATGATCAAAGGATATAAACAGACACTTTTCCGATAAA 112207 i i v v iv i i v v v vi i L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chr2qtel1M 112208 GAAATT--AAAGCATTTCTAATATTATGACAAAAATGCTCTAAATCATTA 112255 ii-- vv vv v ii - - i i v v L1ME5_3end#LI 106 GAAACCCGAAAGGCTAACAAGCAT-ATGA-AGAGATGCTCAAACTCATTA 153 chr2qtel1M 112256 TTGATCAGAGAAAAGCAAATTAAGACAACTCTGAGGTACCACCTCACACC 112305 v i v i vv i i i i L1ME5_3end#LI 154 GTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACC 203 chr2qtel1M 112306 TCCTCAGATTGGCCAAGATGACAGGAACAGATAATGACAAATTTTGGAAG 112355 vi - i v i v v iiivii v i v vii L1ME5_3end#LI 204 TATT-AGACTGGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTGGCGA 252 chr2qtel1M 112356 GGATGTGGGAAAACTGGGACACTAATGCAGTGTTGGTAGAATTGTGAATT 112405 i ? iv i v v v i i i v ii i L1ME5_3end#LI 253 GGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACT 302 chr2qtel1M 112406 TATCCAAACATTCTCAAGAGTAATTTGGAACTGTGCTCAAAGGACTATAA 112455 vi v iv vi i i -- v i i ivvi -- v L1ME5_3end#LI 303 GGTGCAGCCATTCTGGAGAGCAATCTGG--CAGTACTTAGTCAA--ATTA 348 chr2qtel1M 112456 AAT-TGTGCATACCCTTAGTTCCAACATTCTCATTACTGGGTCTAGATTC 112504 i - ii vv vi i v ii ii v v v i L1ME5_3end#LI 349 AGTATACGCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATATCC 398 chr2qtel1M 112505 CAAAGAGATAGTAGGACATG---ATAAAGAATCCACATGTGGGAAAATGT 112551 i vv viv v --- i ii--- iv ii L1ME5_3end#LI 399 CAAAGAAATTCTCACACAGGTCCATAAGGGG---ACATGTACGAGGATGT 445 chr2qtel1M 112552 -------AGCAT--TTTGTACTGGCAAGGAACTGGAAATTGAGTAGATGC 112592 ------- i -- iv ii ii iiivivv i i i L1ME5_3end#LI 446 TCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGGGTGT 495 chr2qtel1M 112593 CCATCACTTAGAAAATGGCCAAATAAATTGTGTTATATG 112631 vi i i vi ii v v iv L1ME5_3end#LI 496 CCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATG 534 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.71 CpG sites = 86, Kimura (unadjusted) = 42.63 Transitions / transversions = 1.41 (86/61) Gap_init rate = 0.03 (15 / 473), avg. gap size = 1.67 (25 / 15) 11 11.25 6.90 0.00 chr2qtel1M 113125 113153 (886847) (TATACT)n#Simple_repeat 1 31 (0) m_b85s252i1 3156 chr2qtel1M 113125 TATACATATA-TTGTATTTA-ACTTATACTT 113153 v - i i - (TATACT)n#Sim 1 TATACTTATACTTATACTTATACTTATACTT 31 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.07 (2 / 28), avg. gap size = 1.00 (2 / 2) 13 28.45 0.00 2.08 chr2qtel1M 113291 113339 (886661) (AAAAAAC)n#Simple_repeat 1 48 (0) m_b85s252i2 3157 chr2qtel1M 113291 AAAAAAGCACAAAGAAATAACAAATCTATAAAAATCTAAAAAAAAAAAA 113339 vv v v v -vv i v v v (AAAAAAC)n#Si 1 AAAAAACAAAAAACAAAAAACAAA-AAACAAAAAACAAAAAACAAAAAA 48 Matrix = Unknown Transitions / transversions = 0.10 (1/10) Gap_init rate = 0.02 (1 / 48), avg. gap size = 1.00 (1 / 1) 19 10.01 0.00 0.00 chr2qtel1M 114075 114106 (885894) (ATTTTT)n#Simple_repeat 1 32 (0) m_b85s252i3 3158 chr2qtel1M 114075 ATTTTTATTTTTATTTTTACTTATATTTATAT 114106 i v v (ATTTTT)n#Sim 1 ATTTTTATTTTTATTTTTATTTTTATTTTTAT 32 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 47 4.91 6.67 3.23 chr2qtel1M 116063 116152 (883848) (AGAA)n#Simple_repeat 1 93 (0) m_b85s252i4 3159 chr2qtel1M 116063 AGAAAGAAA-AACAAAAGAAAGAAAAGAAAAGAAAACAAGAAAGAAAGAA 116111 - vi - - iv (AGAA)n#Simpl 1 AGAAAGAAAGAAAGAAAGAAAG-AAAG-AAAGAAAGAAAGAAAGAAAGAA 48 chr2qtel1M 116112 AGAAAAGAAA-AAAG-AAG-AAGAAAGAAAG-AA-AAAGAAAGAAA 116152 - - - - - - (AGAA)n#Simpl 49 AG-AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 93 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.10 (9 / 89), avg. gap size = 1.00 (9 / 9) 803 26.22 5.65 1.55 chr2qtel1M 117839 118086 (881914) MIRc#SINE/MIR 11 268 (0) m_b85s601i0 3160 chr2qtel1M 117839 TGGTGTAGTGAATAGAA-ACAGAACT-AAAATCAGTGAGATTTGAGTTCA 117886 i i v i- v i -ii i vi ii i i MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr2qtel1M 117887 AATTTTTCTTCAAACACTTAATAGCTATGTGATCCTGGGCAAATCACTTA 117936 i iiivvi viv v i i i i MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTA 110 chr2qtel1M 117937 ATCTCTC----CCTCAATTTCCTCATCTGTAAAAATGGGAATAATAAATA 117982 i ---- i - i - MIRc#SINE/MIR 111 ACCTCTCTGAGCCTCAGTTTCCTCATCTGT-AAAATGGGGATAAT-AATA 158 chr2qtel1M 117983 ---GC---ACTTACCTCCCAAAGTTGTTGTTAGGATCAAAAGAGGCAAAC 118026 --- ---i i v ii v v ii vv MIRc#SINE/MIR 159 CCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATG 208 chr2qtel1M 118027 AATGTG-GTGTTCTTCATTAAGTCTG-AAAACACCAAATAATTGGCAGTT 118074 v -iv iv ii v -- - iii i v i v vv v? MIRc#SINE/MIR 209 TATGTGAAAGCGCTTTGTAAA--CTGTAAAGTGCTATACAAATGTAAGGN 256 chr2qtel1M 118075 TTAATTATTATT 118086 v v MIRc#SINE/MIR 257 GTTATTATTATT 268 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.53 CpG sites = 40, Kimura (unadjusted) = 33.43 Transitions / transversions = 1.67 (40/24) Gap_init rate = 0.04 (11 / 247), avg. gap size = 1.64 (18 / 11) 638 18.36 7.14 2.74 chr2qtel1M 119229 119368 (880632) MIRc#SINE/MIR 3 148 (120) m_b85s601i1 3161 chr2qtel1M 119229 AGGCAGCTGGTTGGTTCAGTGGTTAGAGAACTTGACTTGGCATCAGGAAG 119278 - -- v vv v v vi MIRc#SINE/MIR 3 AGGCAG-TG--TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAG 49 chr2qtel1M 119279 ACTTGAGTTCAAGTCCAATCTCAGATATTTACTAGTTGTATGATCCAGAG 119328 i i i viv v vi i i i i iv i MIRc#SINE/MIR 50 ACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGG 99 chr2qtel1M 119329 CAAGTCGCTTAA----------CCTCAGTTTCCTCATCTGTACAAATGAG 119368 i ---------- - i MIRc#SINE/MIR 100 CAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTA-AAATGGG 148 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 19.49 CpG sites = 14, Kimura (unadjusted) = 21.31 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.04 (5 / 139), avg. gap size = 2.80 (14 / 5) 429 30.35 4.42 0.85 chr2qtel1M 119872 119984 (880016) L2b_3end#LINE/L2 335 451 (15) m_b85s601i2 3162 chr2qtel1M 119872 TCTTTTCAATTAAATTATGAGCTTCTTAAGAGCAGGGATTGAGTTTTGCC 119921 iii v i i i i i v i i ii ? i - i L2b_3end#LINE 335 TCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCT-GTC 383 chr2qtel1M 119922 TTGCTC-----TGTAACTCCAACACTTAGCACAGTGCCTGCTGTATAATA 119966 i ----- v i i i i ? viii i i L2b_3end#LINE 384 TTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTA 433 chr2qtel1M 119967 GGTTCTTAATCATTATTT 119984 iv i i v v L2b_3end#LINE 434 GGCGCTCAGTAAATATTT 451 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.61 CpG sites = 27, Kimura (unadjusted) = 43.84 Transitions / transversions = 3.86 (27/7) Gap_init rate = 0.02 (2 / 112), avg. gap size = 3.00 (6 / 2) 372 21.49 9.35 6.29 chr2qtel1M 119986 120124 (879876) MIRb#SINE/MIR 6 148 (120) m_b85s601i3 3163 chr2qtel1M 119986 GGGCAGC-TAGT-CA-CAAAAATAGC-CAGACTT-GAAGTCAGGAAGACT 120030 - i - -iii v - i i - i iv - MIRb#SINE/MIR 6 GGGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGAC- 54 chr2qtel1M 120031 CATTTTCCTAAGTTCAAATTTAGCCTCAG------ACTAACTGGGT-ACC 120073 ------- ii i iiv v v ------ i v - MIRb#SINE/MIR 55 -------CTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACC 97 chr2qtel1M 120074 TGTGGGCAAATCACTTCACCT-TGTATGCCTCAGTTTCCTAATCTGTATA 120122 - i i v - v iv v v MIRb#SINE/MIR 98 T-TGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAA 146 chr2qtel1M 120123 AT 120124 MIRb#SINE/MIR 147 AT 148 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 23.81 CpG sites = 17, Kimura (unadjusted) = 25.88 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.12 (17 / 138), avg. gap size = 1.29 (22 / 17) 434 24.57 1.71 2.59 chr2qtel1M 120008 120124 (879876) MIRc#SINE/MIR 30 145 (123) m_b85s601i4 3163 chr2qtel1M 120008 CCAGACTTGAAGTCAGGAAGACTCATTTTCCTAAGTTCAAATTTAGCCTC 120057 ii i iiivv --i i viii iv v MIRc#SINE/MIR 30 CTGGACTTGGAGTCAGGAAGACCTGGGTTC--GAGTCCCGGCTCTGCCAC 77 chr2qtel1M 120058 AGACTAACTGGGT-ACCTGTGGGCAAATCACTTCACCT-TGTATGCCTCA 120105 vv i v - - i v - v iv MIRc#SINE/MIR 78 TTACTAGCTGTGTGACCT-TGGGCAAGTCACTTAACCTCTCTGAGCCTCA 126 chr2qtel1M 120106 GTTTCCTAATCTGTATAAT 120124 v v MIRc#SINE/MIR 127 GTTTCCTCATCTGTAAAAT 145 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 27.67 CpG sites = 15, Kimura (unadjusted) = 30.15 Transitions / transversions = 1.15 (15/13) Gap_init rate = 0.04 (5 / 116), avg. gap size = 1.00 (5 / 5) 216 31.48 4.42 4.42 chr2qtel1M 120326 120438 (879562) L2d_3end#LINE/L2 148 260 (256) m_b85s601i5 3164 chr2qtel1M 120326 CTCCCAGACTG---TGCCCCATGACTCCTTAATCTCTGGTTCT-TTCAAT 120371 i v v --- i- -- i vv --i - i v L2d_3end#LINE 148 CCCCCCGCCTGGAATGCCCT-T--CCCCTTCCTCTCT--CTCTATCCAAA 192 chr2qtel1M 120372 GCTTATCT-TACTTCAAGATTCAGTTTAGGAATGACTTCTTTCACAAAGC 120420 v i i i- v iii i i i vviv i i i i L2d_3end#LINE 193 TCCTACCCATCCTTCAAGGCCCAGCTCAAGTCCCACCTCCTCCACGAAGC 242 chr2qtel1M 120421 CTTCCTTGATCTTCCCAG 120438 i i vii L2d_3end#LINE 243 CTTCCCTGACCACTCCAG 260 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.48 CpG sites = 23, Kimura (unadjusted) = 43.21 Transitions / transversions = 2.09 (23/11) Gap_init rate = 0.07 (8 / 112), avg. gap size = 1.25 (10 / 8) 246 33.84 0.00 5.81 chr2qtel1M 120371 120461 (879539) L2c_3end#LINE/L2 195 280 (198) m_b85s601i6 3164 chr2qtel1M 120371 TGCTTATCTTACTTCAAGATTCAGTTTAGGAATGACTTCTTTCACAAAGC 120420 i i --- ?i i i ivi v i i i ivi L2c_3end#LINE 195 TACTCATC---CTTCAAGNCTCAGCTCAGATGTCACCTCCTCCGGGAAGC 241 chr2qtel1M 120421 CTTCCTTGATCTTCCCAGTTGTTAGTTTACATTTTCTTTTC 120461 i i ii v --?i i vi vii ii L2c_3end#LINE 242 CTTCCCTGACCCCCCAAG--NCTAGTCTAGGTGCCCTCCTC 280 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 49.37 CpG sites = 23, Kimura (unadjusted) = 52.11 Transitions / transversions = 3.83 (23/6) Gap_init rate = 0.06 (5 / 90), avg. gap size = 1.00 (5 / 5) 276 24.77 12.98 1.37 chr2qtel1M 120464 120594 (879406) L2c_3end#LINE/L2 327 472 (6) m_b85s601i7 3164 chr2qtel1M 120464 ATCACCTTGTATTTT--TTGTCTGTGTATTTGT---TCTCC--CATCA-- 120504 i v v -- v i? --- -- ii -- L2c_3end#LINE 327 ATTAACTTGTATTGTAATTGTCTGTTTACNTGTCTGTCTCCTCCACTAGA 376 chr2qtel1M 120505 TGGTGAGCTCTTTGAGGG-----ACCAT--TTTGTTTTTCATTCTATTGC 120547 iv i ----- i --i i iv v v iv L2c_3end#LINE 377 CTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTATCCC 426 chr2qtel1M 120548 AAACTCCAATGTC-CAGAATTGATGCTTAATAAACTTTTGTTGAATAA 120594 v i v -- v - v i v ii i iv i L2c_3end#LINE 427 CAGCGCC--TGGCACATAGTAGGCGCTCAATAAATGTTTGTTGAATGA 472 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.68 CpG sites = 18, Kimura (unadjusted) = 30.94 Transitions / transversions = 1.29 (18/14) Gap_init rate = 0.07 (9 / 130), avg. gap size = 2.11 (19 / 9) 12 8.15 3.57 3.57 chr2qtel1M 120849 120876 (879124) (GTCT)n#Simple_repeat 1 28 (0) m_b85s252i5 3165 chr2qtel1M 120849 GTCTGTCT-TCTGTCTGACTTTCTGATCT 120876 - v v - (GTCT)n#Simpl 1 GTCTGTCTGTCTGTCTGTCTGTCTG-TCT 28 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.07 (2 / 27), avg. gap size = 1.00 (2 / 2) 19 25.21 2.94 1.45 chr2qtel1M 120946 121013 (878987) (ACAC)n#Simple_repeat 1 69 (0) m_b85s252i6 3166 chr2qtel1M 120946 ACACCCATATCCACACCCATACACTCACACAAACATACACACACATAGAC 120995 v i iv v i v v i i v (ACAC)n#Simpl 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50 chr2qtel1M 120996 ATATA-ACAGCA-ATACACA 121013 i i - - - i (ACAC)n#Simpl 51 ACACACACA-CACACACACA 69 Matrix = Unknown Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.04 (3 / 67), avg. gap size = 1.00 (3 / 3) 278 22.81 1.75 0.00 chr2qtel1M 121154 121210 (878790) MIRc#SINE/MIR 2 59 (209) m_b85s601i8 3167 chr2qtel1M 121154 GAGGCAAT-TAGTGCAATGGATAGAGCATTAGATCAGGAGTCATAGAGAC 121202 i - i i v i i iiv vii MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr2qtel1M 121203 CTGAGTTC 121210 i MIRc#SINE/MIR 52 CTGGGTTC 59 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.62 CpG sites = 10, Kimura (unadjusted) = 28.62 Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.02 (1 / 56), avg. gap size = 1.00 (1 / 1) 16 15.86 0.00 0.00 chr2qtel1M 121535 121562 (878438) (A)n#Simple_repeat 1 28 (0) m_b85s252i8 3168 chr2qtel1M 121535 AAAAATTAAAAAATAAAAGAAAAAAAAA 121562 vv v i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA 28 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 14 23.72 0.00 0.00 chr2qtel1M 122165 122204 (877796) (CCTCCCC)n#Simple_repeat 1 40 (0) m_b85s252i9 3169 chr2qtel1M 122165 CCTCCCCTTTCCCCCGTCCCTCCCCCCCAATCCCCTCTCC 122204 ii v i i vv i (CCTCCCC)n#Si 1 CCTCCCCCCTCCCCCCTCCCCCCTCCCCCCTCCCCCCTCC 40 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 14 22.19 2.38 0.00 chr2qtel1M 123570 123611 (876389) (AAAATAA)n#Simple_repeat 1 43 (0) m_b85s252i11 3170 chr2qtel1M 123570 AAAAT-AAAAAGGAAAATTCAAACTTTAAAAAAAAAAAATAAA 123611 - vi v v vv v v (AAAATAA)n#Si 1 AAAATAAAAAATAAAAAATAAAAAATAAAAAATAAAAAATAAA 43 Matrix = Unknown Transitions / transversions = 0.14 (1/7) Gap_init rate = 0.02 (1 / 41), avg. gap size = 1.00 (1 / 1) 19 0.00 0.00 0.00 chr2qtel1M 126559 126579 (873421) (A)n#Simple_repeat 1 21 (0) m_b85s252i13 3171 chr2qtel1M 126559 AAAAAAAAAAAAAAAAAAAAA 126579 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAA 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 12 26.53 0.00 4.26 chr2qtel1M 127682 127730 (872270) (TTAAAT)n#Simple_repeat 1 47 (0) m_b85s252i14 3172 chr2qtel1M 127682 TTAAATTCAAAATTAAAATTTCAATGTTAATGAAAAGTTTTGCTTTAAA 127730 -v v v v v vv - viv (TTAAAT)n#Sim 1 TTAAATT-TAAATTTAAATTTAAATTTAAATTTAAA-TTTAAATTTAAA 47 Matrix = Unknown Transitions / transversions = 0.11 (1/9) Gap_init rate = 0.04 (2 / 48), avg. gap size = 1.00 (2 / 2) 228 24.98 6.32 3.35 chr2qtel1M 129511 129684 (870316) L1M4_orf2#LINE/L1 3109 3287 (7) m_b85s551i5 3173 chr2qtel1M 129511 GGGAAAATATTTTTACAGTCAAAGGTTCAATAAAGGCCTCATTTCAAAAA 129560 i vi - i v vi iii i v ?i v v i L1M4_orf2#LIN 3109 GAGAAAATATTTGCA-AATCATATATCTGATAAGGGACTNGTATCCAGAA 3157 chr2qtel1M 129561 TATAGAAATTAACTCTAAT--TTTAAAAATCAA--GCCATTT--CCCAAT 129604 v v- v i--i i v v -- v vv -- L1M4_orf2#LIN 3158 TATATAAAG-AACTCTTACAACTCAACAATAAAAAGACAAATAACCCAAT 3206 chr2qtel1M 129605 TGAAAAAATGGTCAAAAGGATATGAAC-GACAATTCTCAGATGAAAAT-T 129652 ? - v - v i- v vi v i - L1M4_orf2#LIN 3207 TNAAAAA-TGGGCAAA-GGATTTGAATAGACATTTCTCCAAAGAAGATAT 3254 chr2qtel1M 129653 GAAACTATTTCTAGT---CATATGAAAAGATGCTC 129684 iv -- vv i i --- i L1M4_orf2#LIN 3255 ACAA--ATGGCCAATAAGCACATGAAAAGATGCTC 3287 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 31.08 CpG sites = 20, Kimura (unadjusted) = 31.08 Transitions / transversions = 0.91 (20/22) Gap_init rate = 0.07 (12 / 173), avg. gap size = 1.42 (17 / 12) 628 26.37 11.56 1.41 chr2qtel1M 129599 130048 (869952) L1ME3G_3end#LINE/L1 53 547 (377) m_b85s551i6 3173 chr2qtel1M 129599 CCCAATTGAAAAAATGGTCAAAAGGATATGAAC-GACAATTCTCAGATGA 129647 v - v - - i v v L1ME3G_3end#L 53 CCCAATAGAAAAA-TGGGCAAA-GGATATGAACAGGCAATTCACAGAAGA 100 chr2qtel1M 129648 --AAATTGAAACTATTTCTAGTCATATGAAAAGATGCTCCAAGTCATTAT 129695 -- vv iviiivv iv v vv i v L1ME3G_3end#L 101 GGAAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAG 150 chr2qtel1M 129696 TAATAAG--AAATG-AAATTAAGACAACTCTAAAATACC---------CT 129733 v -- - i vv i i --------- i L1ME3G_3end#L 151 TAATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCC 200 chr2qtel1M 129734 GTCAGATTGGCTAAAAT---GACGGGAAAAAATAATGATT-TTGGAGGGG 129779 i v ---i v ?vvi v vi? v - v i L1ME3G_3end#L 201 ATCAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGG 250 chr2qtel1M 129780 ATGCGGGAAAACGGG-ACATTGATGCATTTTT--TGGGTTTGAAGA---A 129823 i i i - vi v i i vi -- vv v i ---i L1ME3G_3end#L 251 GTGTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGG 300 chr2qtel1M 129824 TCCAACCATTTTGGGAAAGTATTTGAACTATGTCAA--AAAGTTATCAAA 129871 v i ? - ii i v vii vi i v -- i --i L1ME3G_3end#L 301 TACAGCCNTTTTGG-AGGGCAATTTGGCAGTATCTATTAAAATT--TAAA 347 chr2qtel1M 129872 CTGTGCATACCCTTTGATCCAACAGTGTTA---CTAGGGAT-TAT-ATAA 129916 v i i i i vii --- ? ? - -v ? L1ME3G_3end#L 348 ATGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTAN 397 chr2qtel1M 129917 AGA-----TTATAAAGAAGGAAAAGGGACCTTGT-CACGAA-GTT--TTG 129957 ----- iii v viv v v i?v v - v i - -- L1ME3G_3end#L 398 AGAAATACTCGCACATGTGCACAAGGANGCATGTACAAGGATGTTCATTG 447 chr2qtel1M 129958 -GGCCCTTTTTG---TGGCTAGAAACTGGCTGAA-----TGGATGTCCAT 129998 -i vi v --- i v i i --i ----- ii L1ME3G_3end#L 448 CAGCATTGTTTGTAATAGCGAAAAATTGG--AAACAACCTAAATGTCCAT 495 chr2qtel1M 129999 CAGTTGGAGAATAGCTGAATAAATTGTGG--TATTAAAATTATGGAATAT 130046 i v i i i i i -- iv v i i L1ME3G_3end#L 496 CAATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATAC 545 chr2qtel1M 130047 TA 130048 L1ME3G_3end#L 546 TA 547 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.04 CpG sites = 64, Kimura (unadjusted) = 33.78 Transitions / transversions = 1.21 (64/53) Gap_init rate = 0.06 (29 / 449), avg. gap size = 2.03 (59 / 29) 46 17.93 0.00 0.00 chr2qtel1M 130542 130624 (869376) (A)n#Simple_repeat 1 83 (0) m_b85s252i15 3174 chr2qtel1M 130542 AAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAGA 130591 v i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr2qtel1M 130592 AAAAATGAGTGGAAGGGTAAAAAAAAAAAAAAA 130624 vi ivii iiiv (A)n#Simple_r 51 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 83 Matrix = Unknown Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.00 (0 / 82), avg. gap size = 0.0 (0 / 0) 17 4.94 0.00 0.00 chr2qtel1M 131015 131035 (868965) (A)n#Simple_repeat 1 21 (0) m_b85s252i16 3175 chr2qtel1M 131015 AATAAAAAAAAAAAAAAAAAA 131035 v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAA 21 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 15 29.76 3.53 2.33 chr2qtel1M 131230 131314 (868686) (TTATAAT)n#Simple_repeat 1 86 (0) m_b85s252i17 3176 chr2qtel1M 131230 TTATATTTTAAAATTT-TAGTTT-TTATTTAAAATTTACGCCCAAAAATT 131277 v v - i - v v iiviiv v (TTATAAT)n#Si 1 TTATAATTTATAATTTATAATTTATAATTTATAATTTATAATTTATAATT 50 chr2qtel1M 131278 TTTAATTTCTGTAATTT-TAATAAATTTTTTTTGATTT 131314 v - - i - vv vv v i (TTATAAT)n#Si 51 TATAA-TT-TATAATTTATAATTTATAATTTATAATTT 86 Matrix = Unknown Transitions / transversions = 0.54 (7/13) Gap_init rate = 0.06 (5 / 84), avg. gap size = 1.00 (5 / 5) 18 30.38 2.44 1.20 chr2qtel1M 136728 136809 (863191) (ATAT)n#Simple_repeat 1 83 (0) m_b85s252i18 3177 chr2qtel1M 136728 ATCTATATGAATATAAAT-TCTATATCTATATCTATATGAATATGAATGA 136776 v iv v - v v v iv iv - (ATAT)n#Simpl 1 ATATATATATATATATATATATATATATATATATATATATATATATAT-A 49 chr2qtel1M 136777 AATATCTATATGAAAATAAAT-TTTATACAAATA 136809 v v iv v v - v i v (ATAT)n#Simpl 50 TATATATATATATATATATATATATATATATATA 83 Matrix = Unknown Transitions / transversions = 0.33 (5/15) Gap_init rate = 0.04 (3 / 81), avg. gap size = 1.00 (3 / 3) 22 25.76 3.85 0.00 chr2qtel1M 136732 136809 (863191) (ATATAA)n#Simple_repeat 1 81 (0) m_b85s252i19 3177 chr2qtel1M 136732 ATATGAATATAAAT-TCTATATCTATATCTATATGAATATGAAT-GAAAT 136779 i - vv vv vv i i -v (ATATAA)n#Sim 1 ATATAAATATAAATATAAATATAAATATAAATATAAATATAAATATAAAT 50 chr2qtel1M 136780 ATCTATATGAAAATAAAT-TTTATACAAATA 136809 vv i v - vv i (ATATAA)n#Sim 51 ATAAATATAAATATAAATATAAATATAAATA 81 Matrix = Unknown Transitions / transversions = 0.42 (5/12) Gap_init rate = 0.04 (3 / 77), avg. gap size = 1.00 (3 / 3) 296 15.39 0.00 1.92 chr2qtel1M 137585 137637 (862363) C MIR3#SINE/MIR (40) 168 117 m_b85s601i9 3178 chr2qtel1M 137585 TAGATATCATTCTAGTCCTACTCCCTCATTTTTAAGATAGGGAAATTGAG 137634 v - v i vv ii i C MIR3#SINE/MIR 168 TAGAGATCAT-CTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAG 120 chr2qtel1M 137635 GCC 137637 C MIR3#SINE/MIR 119 GCC 117 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 17.29 CpG sites = 4, Kimura (unadjusted) = 17.29 Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.02 (1 / 52), avg. gap size = 1.00 (1 / 1) 56 18.28 2.21 2.96 chr2qtel1M 139349 139484 (860516) (TTCC)n#Simple_repeat 1 135 (0) m_b85s252i20 3179 chr2qtel1M 139349 TTTCTTCCTTACTTCCTTCCCTCCCTTTC-TCCCTCCCTCCTTCCCTTCC 139397 i v - i i - i i - (TTCC)n#Simpl 1 TTCCTTCCTTCCTTCCTT-CCTTCCTTCCTTCCTTCCTTCCTT-CCTTCC 48 chr2qtel1M 139398 TTCCTTCCTTCTTTCCTTCCTTTCCCTCCCTTCCTTCCTCCCTCTCTTCC 139447 i - - i i ii (TTCC)n#Simpl 49 TTCCTTCCTTCCTTCCTTCC-TT-CCTTCCTTCCTTCCTTCCTTCCTTCC 96 chr2qtel1M 139448 -CCCCCCCTTCCCTCCTTCCTT-TTTTCATCTTTCTTTC 139484 -i ii i -i i v i i (TTCC)n#Simpl 97 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC 135 Matrix = Unknown Transitions / transversions = 9.00 (18/2) Gap_init rate = 0.05 (7 / 135), avg. gap size = 1.00 (7 / 7) 208 34.51 1.11 3.41 chr2qtel1M 139664 139753 (860247) L2a_3end#LINE/L2 428 515 (2) m_b85s601i10 3180 chr2qtel1M 139664 GCCTCTTTCTTTC-TTTTTGTATATTCAGGGTTCAATATAATAATATCTG 139712 i v iv -i vi vii v ii--- v i i ii L2a_3end#LINE 428 GTCTGTTTTGTTCACTGCTGTATCCCCAGCGCC---TAGAACAGTGCCTG 474 chr2qtel1M 139713 GCCCACAGACAGCGCTGAATAAAAGCTTGCTGACTGAGTGA 139753 v i vvi v vii i v i L2a_3end#LINE 475 GCACATAGTAGGCGCTCAATAAATATTTGTTGAATGAATGA 515 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 48.19 CpG sites = 18, Kimura (unadjusted) = 48.19 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.04 (4 / 89), avg. gap size = 1.00 (4 / 4) 342 27.05 5.43 5.43 chr2qtel1M 139851 139979 (860021) MIRc#SINE/MIR 4 132 (136) m_b85s601i11 3181 chr2qtel1M 139851 GGCAATGGAATGTATTTGAAAGAACACTGATTCTGGAGTCA-GAAGATCA 139899 i vii i v v i ivii - i v MIRc#SINE/MIR 4 GGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCT 53 chr2qtel1M 139900 GGCTTTGAACCCCAGCTCTGACTCTTGCTTGAGCTTCCATGTCCTTGTCG 139949 v i ii i v v i -- - vii v -- MIRc#SINE/MIR 54 GGGTTCGAGTCCCGGCTCTGCCACTTACT--AGC-TGTGTGACCTTG--G 98 chr2qtel1M 139950 ATATGAGTCAT----CCCCTCTGGGACT--ATTTCC 139979 ii -- i---- i i v --i MIRc#SINE/MIR 99 GCA--AGTCACTTAACCTCTCTGAGCCTCAGTTTCC 132 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.32 CpG sites = 22, Kimura (unadjusted) = 34.94 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.08 (10 / 128), avg. gap size = 1.40 (14 / 10) 16 9.32 0.00 0.00 chr2qtel1M 140166 140188 (859812) (A)n#Simple_repeat 1 23 (0) m_b85s252i21 3182 chr2qtel1M 140166 AAAAAAAAAAACAAAAACAAAAA 140188 v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAA 23 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 229 24.14 1.72 0.00 chr2qtel1M 141210 141267 (858733) L1ME5_3end#LINE/L1 56 114 (827) m_b85s551i7 3183 chr2qtel1M 141210 CCTCAAT-GAAAAATGGTCAAATAGTAGAAATAGACAGTTTTCAAAAGAA 141258 i - v vii vi i i i v i i L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chr2qtel1M 141259 GAAATCCGA 141267 i L1ME5_3end#LI 106 GAAACCCGA 114 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 30.41 CpG sites = 10, Kimura (unadjusted) = 30.41 Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.02 (1 / 57), avg. gap size = 1.00 (1 / 1) 220 29.87 1.28 1.28 chr2qtel1M 141355 141432 (858568) C L2#LINE/L2 (716) 2366 2289 m_b85s601i12 3184 chr2qtel1M 141355 GAGATTAGGGCTGGATAAGTAGATAAGAGGATCATTAGTCTCCAGGTGGT 141404 i iv v vi i vv i ii i iv vi i C L2#LINE/L2 2366 GAGGTCCGGGCTGGAGATATAAATTTGGGAGTCATCAGCATATAGATGGT 2317 chr2qtel1M 141405 AATTAAATCCACAGAAGCTG-ATGAGATC 141432 v v i- ii - C L2#LINE/L2 2316 ATTTAAAGCCAT-GAGACTGGATGAGATC 2289 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.40 CpG sites = 14, Kimura (unadjusted) = 39.40 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.03 (2 / 77), avg. gap size = 1.00 (2 / 2) 650 19.10 4.32 3.05 chr2qtel1M 141995 142156 (857844) Charlie4#DNA/hAT-Charlie 3215 3378 (0) m_b85s502i0 3185 chr2qtel1M 141995 TTTTTTTTAACATATATTAATAATTCCATTTCAATATAATTCATTTCCTT 142044 v - v i i vi vi Charlie4#DNA/ 3215 TTGTTTTTAA-ATATTTTGATAACTATATTTCAATATAATTGGTTTCCTT 3263 chr2qtel1M 142045 TGGGATCCT-----CTTTATTTCACGCACTTAAAAGCATAATTCTGAGAA 142089 vi -----i i i i i v Charlie4#DNA/ 3264 TGTAATCCTATGTATTTTATTTTATGCATTTAAAAACATTATTCTGAGAA 3313 chr2qtel1M 142090 GGTGTCCATAGGTTTGGCCAGAATGTCATCAAAGGCTTCTGTGATGCAAG 142139 v i vi v ---i vv ii iii - Charlie4#DNA/ 3314 GGGGTCCATAGGCTTCACCAGACTG---CCAAAGGGGTCCATGGCACAA- 3359 chr2qtel1M 142140 AAAAGGT--AGAACCTCTG 142156 -- i Charlie4#DNA/ 3360 AAAAGGTTAAGAACCCCTG 3378 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 22.48 CpG sites = 19, Kimura (unadjusted) = 22.48 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.04 (7 / 161), avg. gap size = 1.71 (12 / 7) 404 23.34 6.31 3.51 chr2qtel1M 142687 142797 (857203) C MIRc#SINE/MIR (153) 115 2 m_b85s601i13 3186 chr2qtel1M 142687 GGGGTTAAGTGACTTGCCCAGGATCACACTGGCTAGGAAGTGTTAAT--- 142733 i i i -i v vi iv--- C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACAC-AGCTAGTAAGTGGCAGAGCC 67 chr2qtel1M 142734 ----TTTTAACTCAGATCCTCCTGACTTCAGGGCTGGTGCTCTATCCACT 142779 ----i iv i i i i i v ii v C MIRc#SINE/MIR 66 GGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACT 17 chr2qtel1M 142780 GAGCCACCTAGCTGCCCC 142797 vi ---i i C MIRc#SINE/MIR 16 GCACCAC---ACTGCCTC 2 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 27.82 CpG sites = 18, Kimura (unadjusted) = 29.20 Transitions / transversions = 2.57 (18/7) Gap_init rate = 0.05 (6 / 110), avg. gap size = 1.83 (11 / 6) 16 16.52 0.00 0.00 chr2qtel1M 143925 143951 (856049) (A)n#Simple_repeat 1 27 (0) m_b85s252i22 3187 chr2qtel1M 143925 AAAAAACAAAAGAAAACAAACAAAAAA 143951 v i v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAA 27 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 12 19.85 0.00 0.00 chr2qtel1M 144162 144190 (855810) (ATGT)n#Simple_repeat 1 29 (0) m_b85s252i23 3188 chr2qtel1M 144162 ATGTATGTGTGTATACCTTTATGTATGTA 144190 i iiv v (ATGT)n#Simpl 1 ATGTATGTATGTATGTATGTATGTATGTA 29 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 352 28.12 0.88 9.52 chr2qtel1M 144310 144423 (855577) C MIRc#SINE/MIR (154) 114 10 m_b85s601i14 3189 chr2qtel1M 144310 AGATTTAGTGACTTGCTCAGGGTTATACAGCTAGTAAGTGTATGAGCTTG 144359 i v i i i i vvv iv C MIRc#SINE/MIR 114 AGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGG 65 chr2qtel1M 144360 GATTTTAACTCAGCAATACATAAGCATTCCTGACTCAAGGTTTGGTA-TA 144408 i iv i ---------- iv v i iii i- v C MIRc#SINE/MIR 64 GACTCGAACCCAG----------GTCTTCCTGACTCCAAGTCCAGTGCTC 25 chr2qtel1M 144409 TATCCATTGTGGCAC 144423 v i iiv C MIRc#SINE/MIR 24 TTTCCACTGCACCAC 10 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.95 CpG sites = 18, Kimura (unadjusted) = 36.01 Transitions / transversions = 1.64 (18/11) Gap_init rate = 0.10 (11 / 113), avg. gap size = 1.00 (11 / 11) 17 8.52 0.00 11.90 chr2qtel1M 144448 144494 (855506) (CACATA)n#Simple_repeat 1 42 (0) m_b85s252i24 3190 chr2qtel1M 144448 CAGATACACACTACAATGATACATATACACATGCACACATACACATA 144494 v - - -v i -- (CACATA)n#Sim 1 CACATACACA-TAC-A-CATACACATACACAT--ACACATACACATA 42 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.11 (5 / 46), avg. gap size = 1.00 (5 / 5) 32 27.61 5.51 1.52 chr2qtel1M 144466 144592 (855408) (AT)n#Simple_repeat 1 132 (0) m_b85s252i25 3190 chr2qtel1M 144466 ATACATATACACATGCACACATACACATATTTATGTATGCAGAGATA-AT 144514 i i i ii i i i i v i ii v v - (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr2qtel1M 144515 ACACATGTATGT-TAT-TATATGTATACTGTATATATAGACATA-ATGTA 144561 i i i i - - i - i v i - i (AT)n#Simple_ 51 ATATATATATATATATATATATATATA-TATATATATATATATATATATA 99 chr2qtel1M 144562 TATAT-TACATGTATA-ATATGTAGTATAT-TAT 144592 - i i - i - - (AT)n#Simple_ 100 TATATATATATATATATATATATA-TATATATAT 132 Matrix = Unknown Transitions / transversions = 5.75 (23/4) Gap_init rate = 0.07 (9 / 126), avg. gap size = 1.00 (9 / 9) 232 21.68 1.61 3.28 chr2qtel1M 145538 145599 (854401) MIR#SINE/MIR 62 122 (140) m_b85s601i15 3191 chr2qtel1M 145538 CAGCTGGTTGGCACTTTCTAGCTGTGTGACCGGAAGCAAGCCACTTAACC 145587 i --i v v vvii ii MIR#SINE/MIR 62 CGGCT--CTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACC 109 chr2qtel1M 145588 CCAAT-TGCCTCA 145599 i vv - MIR#SINE/MIR 110 TCTCTGTGCCTCA 122 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 23.65 CpG sites = 7, Kimura (unadjusted) = 25.85 Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.05 (3 / 61), avg. gap size = 1.00 (3 / 3) 16 13.24 0.00 0.00 chr2qtel1M 145602 145626 (854374) (A)n#Simple_repeat 1 25 (0) m_b85s252i26 3192 chr2qtel1M 145602 AAAAAAAAAGAAAAAAGAAAACAAA 145626 i i v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAA 25 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 328 33.15 0.00 4.62 chr2qtel1M 146512 146647 (853353) C MIR1_Amn#SINE/MIR (100) 130 1 m_b85s601i16 3193 chr2qtel1M 146512 ATTGGCACACAAAAACAGGATGAAGTGACTTGTCTAGGGTCACAGAGCTA 146561 i ivi ? i i --- i ? i i i ?v ?i C MIR1_Amn#SINE 130 ACTGAGGCNCAGAGA---GGTNAAGTGACTTGCCCAAGGTCACNCAGCNG 84 chr2qtel1M 146562 CAAAGCGTCTGAGGCCACGTTTGAACTCGGGTCTTCCTGACTTAGGTTTG 146611 vv? i v v v vivi? ? i i i viiiiivi iii C MIR1_Amn#SINE 83 GCNAGTGGCAGAGCCGGGANTNGAACCCAGGTCTCCCGAGTCCCAGTCCA 34 chr2qtel1M 146612 GTGTTCTATCCACTGTGACGGCACCTCGCTTCCCCA 146647 i i- -- vii i i C MIR1_Amn#SINE 33 GTGCTCTATCCACTA-GAC--CACACTGCCTCCCTA 1 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 51.44 CpG sites = 31, Kimura (unadjusted) = 51.44 Transitions / transversions = 2.58 (31/12) Gap_init rate = 0.04 (6 / 135), avg. gap size = 1.00 (6 / 6) 382 27.84 1.03 0.00 chr2qtel1M 146530 146626 (853374) C MIRc#SINE/MIR (155) 113 16 m_b85s601i17 3193 chr2qtel1M 146530 GATGAAGTGACTTGTCTAGGGTCACAGAGCTACAAAGCGTCTGAGGCCAC 146579 i v i i i v vv i v v v viv C MIRc#SINE/MIR 113 GGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGG 64 chr2qtel1M 146580 GTTTGAACTCGGGTCTTCCTGACT-TAGGTTTGGTGTTCTATCCACTG 146626 ii i i i -i i iii i v C MIRc#SINE/MIR 63 ACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTG 16 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.32 CpG sites = 17, Kimura (unadjusted) = 35.99 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.01 (1 / 96), avg. gap size = 1.00 (1 / 1) 268 34.91 5.95 6.80 chr2qtel1M 150717 150968 (849032) C L3#LINE/CR1 (1583) 2516 2267 m_b86s601i0 3194 chr2qtel1M 150717 TCTTGAGTTTCCATTTGCCATTTTGA--------GCTCT--CTTGCCCAG 150756 i i v -- v i i -------- i -- i vi C L3#LINE/CR1 2516 TCTTGGGCTTCAATT--CCCTCTTAACGATGTTTGTTCTACCCTTTCCAG 2469 chr2qtel1M 150757 TTCAAATACCATTCTCCTAGGTAGGTATAAGAGAAGCAAAGTAAGAACCG 150806 iii v i v i iv vi vi i i iii C L3#LINE/CR1 2468 TCTGAAGATCATTCTCCTTGATAGAGAAGACGGAAGCAAAATAGGAGTTG 2419 chr2qtel1M 150807 AGAAACTGCGTGTATTTTCTTTCTGTATTCATATACTTACATATCATGAG 150856 v ii - --- ii i --- v ii v vv iiv v C L3#LINE/CR1 2418 AGTAGTT-C---TGCTTTCTCTCTG---TCATCTGTTAACATTACGCCAT 2376 chr2qtel1M 150857 CAGCACTTTAAGCAGC---CTCATCAGCTTTCTGATCCTTCTCTTTTTAC 150903 v v --i --- iii -? -- ii i ii vi v C L3#LINE/CR1 2375 CTGCCC--CAAGCAGCGGGCCTGTC-NCTTTCT--TTTTCCTTCTGCTCC 2331 chr2qtel1M 150904 AAATATTACCTCAGAGAAAGAAAACTTTCTGGTTATCTTTGAC--TTTCT 150951 i i vi i i--- iivvvi? i v i i ii -- i C L3#LINE/CR1 2330 GAACATAGCTTT---GAAAAGCCTTNTTTTTGTTGTCCTTAGCATTTTTT 2284 chr2qtel1M 150952 CTTGCCAGCTCCATCTC 150968 i v ii v C L3#LINE/CR1 2283 TTTGCAAGCCTCAGCTC 2267 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 48.41 CpG sites = 56, Kimura (unadjusted) = 51.17 Transitions / transversions = 2.15 (56/26) Gap_init rate = 0.08 (21 / 251), avg. gap size = 1.52 (32 / 21) 17 15.49 0.00 0.00 chr2qtel1M 154651 154679 (845321) (T)n#Simple_repeat 1 29 (0) m_b86s252i0 3195 chr2qtel1M 154651 TTGTTTTTTTGTTTGTTTTTGTTTTTTTT 154679 v v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 286 20.33 3.33 1.64 chr2qtel1M 154749 154808 (845192) C L2d_3end#LINE/L2 (3) 513 453 m_b86s601i1 3196 chr2qtel1M 154749 ATCAATTAATCAACAAACATTTATTAAA-ATCTGCTATGTG-TCAGATAC 154796 i ii i i-ii i - -i C L2d_3end#LINE 513 ATCAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAG-CAC 465 chr2qtel1M 154797 TGTGTTAAGTGC 154808 i i i C L2d_3end#LINE 464 TGTGCTAGGCGC 453 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 21.21 CpG sites = 12, Kimura (unadjusted) = 26.11 Transitions / transversions = 1.00 (12/0) Gap_init rate = 0.05 (3 / 59), avg. gap size = 1.00 (3 / 3) 12 14.15 3.03 3.03 chr2qtel1M 154974 155006 (844994) (AAAT)n#Simple_repeat 1 33 (0) m_b86s252i1 3197 chr2qtel1M 154974 AAACAACATAAATAACAAAATAAA-AAATGAATA 155006 i - vv - i (AAAT)n#Simpl 1 AAATAA-ATAAATAAATAAATAAATAAATAAATA 33 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.06 (2 / 32), avg. gap size = 1.00 (2 / 2) 194 28.80 1.32 4.05 chr2qtel1M 155746 155821 (844179) MIRc#SINE/MIR 78 151 (117) m_b86s601i2 3198 chr2qtel1M 155746 TTACTAGGAGCATTACTTAGAGAGAGAATCACACAACCTCT-TGAGACTT 155794 vv ii v i v i vi -- vi - - i MIRc#SINE/MIR 78 TTACTAGCTGTGTGACCTTGGGCAAG--TCACTTAACCTCTCTGAG-CCT 124 chr2qtel1M 155795 CTCTTTCTTCCCTTGTATAATGAGGAT 155821 vv i vii v i MIRc#SINE/MIR 125 CAGTTTCCTCATCTGTAAAATGGGGAT 151 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.85 CpG sites = 11, Kimura (unadjusted) = 36.85 Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.05 (4 / 75), avg. gap size = 1.00 (4 / 4) 251 32.93 2.44 0.00 chr2qtel1M 155772 155853 (844147) MIR3#SINE/MIR 99 182 (26) m_b86s601i3 3198 chr2qtel1M 155772 AATCACACAACCTCTTGAGACTTCTCTTTCTTCCCTTGTATAATGAGGA- 155820 i viv ivi i i vv i vii v i- MIR3#SINE/MIR 99 AGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGG 148 chr2qtel1M 155821 -TTTAACTAAAGGACTTCTAAGAACTCTCCCAGC 155853 - vi i v ii iv i i MIR3#SINE/MIR 149 GTTGGACTAGATGATCTCTAAGGTCCCTTCCAGC 182 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 45.45 CpG sites = 17, Kimura (unadjusted) = 45.45 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.02 (2 / 81), avg. gap size = 1.00 (2 / 2) 15 25.92 1.59 3.23 chr2qtel1M 155920 155982 (844018) (AAGCAGG)n#Simple_repeat 1 62 (0) m_b86s252i2 3199 chr2qtel1M 155920 AAG-AGGAAGCAGAAAAAAGTAAGCAGAGTTCACCACAGCAAGGAAGGAG 155968 - i iv v iivv vv - - v (AAGCAGG)n#Si 1 AAGCAGGAAGCAGGAAGCAGGAAGCAGGAAGCAGGA-AGC-AGGAAGCAG 48 chr2qtel1M 155969 GAAGCAGGCAGAAG 155982 v v (AAGCAGG)n#Si 49 GAAGCAGGAAGCAG 62 Matrix = Unknown Transitions / transversions = 0.44 (4/9) Gap_init rate = 0.05 (3 / 62), avg. gap size = 1.00 (3 / 3) 451 28.12 2.96 7.41 chr2qtel1M 158861 159029 (840971) C MIR3#SINE/MIR (23) 185 24 m_b86s601i4 3200 chr2qtel1M 158861 AGACTTGGCAGAGTTCTTTGACAGCTTGTCTAGTCTGACC---TCATTTT 158907 vi v i vi -- v v ii ii --- C MIR3#SINE/MIR 185 AGAGCTGGAAGGGACCTT--AGAGATCATCTAGTCCAACCCCCTCATTTT 138 chr2qtel1M 158908 AAGAATGAAGAAACTGAAATGAAAGAAAGATTAAGTGACTTGCTCAAGCA 158957 vii i iiivv - i i v i vv C MIR3#SINE/MIR 137 ACAGATGAGGAAACTGAGGCCCA-GAGAGGTGAAGTGACTTGCCCAAGGT 89 chr2qtel1M 158958 CACTTGGTTAGGTCATATAGAGTAGAGCCAGGATTGGAATCCAGGTCCAA 159007 vii i? v vi i---- i i i i i --- C MIR3#SINE/MIR 88 CACACAGCNAGTTAGTG----GCAGAGCCGGGACTAGAACCCAGGTC--- 46 chr2qtel1M 159008 ATCC--ACTGTCCTTTCAGTGCTC 159029 - -- -i vv v C MIR3#SINE/MIR 45 -TCCTGACT-CCCAGTCCGTGCTC 24 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.46 CpG sites = 27, Kimura (unadjusted) = 36.51 Transitions / transversions = 1.59 (27/17) Gap_init rate = 0.08 (14 / 168), avg. gap size = 1.21 (17 / 14) 17 29.34 1.69 0.00 chr2qtel1M 159194 159252 (840748) (TCA)n#Simple_repeat 1 60 (0) m_b86s252i3 3201 chr2qtel1M 159194 TCATCATCATCATCTTCACAATCATTGCCACAATCACCAAAACTATCACC 159243 v iv iii iv i vv ii i (TCA)n#Simple 1 TCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATC 50 chr2qtel1M 159244 A-CATCATCA 159252 - (TCA)n#Simple 51 ATCATCATCA 60 Matrix = Unknown Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1) 18 26.64 1.69 0.00 chr2qtel1M 159195 159253 (840747) (CATCAC)n#Simple_repeat 1 60 (0) m_b86s252i4 3201 chr2qtel1M 159195 CATCATCATCATCTTCACAATCATTGCCACAATCACCAAAACTATCACCA 159244 i i v v iiii v vv i (CATCAC)n#Sim 1 CATCACCATCACCATCACCATCACCATCACCATCACCATCACCATCACCA 50 chr2qtel1M 159245 -CATCATCAC 159253 - i (CATCAC)n#Sim 51 TCACCATCAC 60 Matrix = Unknown Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1) 261 30.91 5.05 1.96 chr2qtel1M 159614 159811 (840189) C L1ME3_3end#LINE/L1 (276) 633 430 m_b86s551i0 3202 chr2qtel1M 159614 GCTTGTTTTGCTCAACATCG-GTTCGTGTAAATCTTTTCCA-GACCTTTC 159661 v i ?i- ii - i - iv - viv v C L1ME3_3end#LI 633 GCTTCTTTCGCTCAACATNATGTCTGTG-AGAT-TCATCCATGTTGTTGC 586 chr2qtel1M 159662 TAAAATCAGTTGTTCATCATGTTTTATAAAACAATG--ATATTCCATTAC 159709 vviv ? v i iv v vi-- vi --i ii C L1ME3_3end#LI 585 GTGTANCAGTAGTTCGTTCTTTTTTATTG--CTGTGTAGTATTCCATTGT 538 chr2qtel1M 159710 CTTCATATACCACTACTTGTTCAT-CATTCCCCAACTGATGGGTATCTAC 159758 v vv v i i i - i? vii ii i iv C L1ME3_3end#LI 537 ATGAATATACCACAATTTATTTATCCATTCTNCTGTTGATGGACATTTGG 488 chr2qtel1M 159759 TCATTTTCCCGTT-----CTATCACAAAAAGAGCTGCTGCAAACATTTTT 159803 vivv v ----- i ii v i iii i C L1ME3_3end#LI 487 GTTGTTTCCAGTTTTNGGCTATTATGAATAAAGCTGCTATGAACATTCTT 438 chr2qtel1M 159804 GCATATGT 159811 i i C L1ME3_3end#LI 437 GTACATGT 430 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.30 CpG sites = 36, Kimura (unadjusted) = 42.16 Transitions / transversions = 1.50 (36/24) Gap_init rate = 0.05 (9 / 197), avg. gap size = 1.56 (14 / 9) 294 32.88 4.11 0.00 chr2qtel1M 159666 159811 (840189) C L1ME2z_3end#LINE/L1 (610) 581 430 m_b86s551i1 3202 chr2qtel1M 159666 ATCAGTTGTTCATCATGTTTTATAAAACAATGATATTCCATTACCTTCAT 159715 v i iviv vivvv i ii iiv vv C L1ME2z_3end#L 581 ATCAGTAGTTCGTTCCTTTTTATTGCTGAGTAGTATTCCATTGTATGAAT 532 chr2qtel1M 159716 ATACCACTACTTGTTCAT-CATTCCCCAACTGATGGGTATCTACTCATTT 159764 vii i - i vii ii i ivv vv C L1ME2z_3end#L 531 ATACCACAGTTTGTTTATCCATTCTCCTGTTGATGGACACCTGGGCTGTT 482 chr2qtel1M 159765 TCCCGTT-----CTATCACAAAAAGAGCTGCTGCAAACATTTTTGCATAT 159809 v ----- i ii v i iii i i i v C L1ME2z_3end#L 481 TCCAGTTTTTGGCTATTATGAATAAAGCTGCTATGAACATTCTTGTACAA 432 chr2qtel1M 159810 GT 159811 C L1ME2z_3end#L 431 GT 430 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.72 CpG sites = 29, Kimura (unadjusted) = 45.01 Transitions / transversions = 1.53 (29/19) Gap_init rate = 0.01 (2 / 145), avg. gap size = 3.00 (6 / 2) 273 28.13 5.85 2.26 chr2qtel1M 159893 160063 (839937) L1MC2_3end#LINE/L1 429 605 (486) m_b86s551i2 3203 chr2qtel1M 159893 AACC-GCATACAATAAAATATTGATACCAGCACTTTTTGTGATAGCAAAG 159941 - i i ---- i v v vi v ii i v v i L1MC2_3end#LI 429 AACCTGCACACGA----ATGTTTATAGCAGCTTTATTCATAATTGCCAAA 474 chr2qtel1M 159942 AATTGGAAGCAAA-GAGATGTCCCTCAATTGAGGAATGGTTAAAT-GCTT 159989 v v-i i v iv v i-ivi L1MC2_3end#LI 475 ACTTGGAAGCAACCAAGATGTCCTTCAATAGGTGAATGGATAAACAAACT 524 chr2qtel1M 159990 CTAATACATGACTGTAATGGAATATTA-ACTGTGGAAATGATAAATGAG- 160037 v ii vvv ii -v v i iv vi v - L1MC2_3end#LI 525 GTGGTACATCCATACAATGGAATATTATTCAGCGATAAAAAGAAATGAGC 574 chr2qtel1M 160038 -ATGAA--CAGGAAA--ACATGGAAGGATCT 160063 - v -- v -- i i i L1MC2_3end#LI 575 TATCAAGCCACGAAAAGACATGGAGGAACCT 605 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.90 CpG sites = 24, Kimura (unadjusted) = 35.74 Transitions / transversions = 1.04 (24/23) Gap_init rate = 0.07 (12 / 170), avg. gap size = 1.17 (14 / 12) 332 24.72 1.12 0.00 chr2qtel1M 159897 159985 (840015) L1ME3G_3end#LINE/L1 426 515 (409) m_b86s551i3 3203 chr2qtel1M 159897 GCATACAATAAAATATTGATACCAGCACTTTTTGTGATAGCAAAGAATTG 159946 ii vv ii i v vv i v i i i L1ME3G_3end#L 426 GCATGTACAAGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTG 475 chr2qtel1M 159947 GAAGCAAAG-AGATGTCCCTCAATTGAGGAATGGTTAAAT 159985 i vv- i v v i L1ME3G_3end#L 476 GAAACAACCTAAATGTCCATCAATAGGGGAATGGTTAAAT 515 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 28.82 CpG sites = 12, Kimura (unadjusted) = 30.43 Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.01 (1 / 88), avg. gap size = 1.00 (1 / 1) 327 27.62 1.45 2.94 chr2qtel1M 159906 160043 (839957) L1ME3F_3end#LINE/L1 439 574 (416) m_b86s551i4 3203 chr2qtel1M 159906 AAAATATTGATACCAGCACTTTTTGTGATAGCAAAGAATTGGAAGCAA-A 159954 i i v v v i i i i i -v L1ME3F_3end#L 439 AGAATGTTCATAGCAGCACTGTTCGTAATAGCAAAAAACTGGAAACAACC 488 chr2qtel1M 159955 GAGATGTCCCTCAATTGAGGAATGGTTAAAT-GCTTCTAATACATGACTG 160003 v i v i iv ii v -iv v ii i vvvii L1ME3F_3end#L 489 CAAATGTCCATCGACAGGAGAATGGATAAATAAATTGTGGTATATTCACA 538 chr2qtel1M 160004 TAATGGAATATTAACTGTGGAAATGATAAATGAGATGAAC 160043 i -- iii v i - - L1ME3F_3end#L 539 CAATGGAATATTA--TACAGCAGTGA-AAATGA-ATGAAC 574 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.17 CpG sites = 23, Kimura (unadjusted) = 35.55 Transitions / transversions = 1.64 (23/14) Gap_init rate = 0.04 (6 / 137), avg. gap size = 1.00 (6 / 6) 246 29.28 7.30 2.14 chr2qtel1M 159908 160085 (839915) L1MD2_3end#LINE/L1 441 627 (479) m_b86s551i5 3203 chr2qtel1M 159908 AATATTGATACCAGCACTTTTTGTGATAGCAAAGAATTGGAAGCAAAG-A 159956 i v v vi v i i v i i i vv- L1MD2_3end#LI 441 AATGTTCATAGCAGCTTTATTCGTAATAGCCAAAAACTGGAAACAACCCA 490 chr2qtel1M 159957 GATGTCCCTCAATTGAGGAATGGTTAAAT-GCTTCTAATACATGACTGTA 160005 i i iv iv i-ivi v ii -- ii L1MD2_3end#LI 491 AATGTCCTTCAACGGGTGAATGGTTAAACAAACTGTGGTACAT--CCATA 538 chr2qtel1M 160006 --ATGGAATATTAACTGTGGAAATGATA---AATGA------GATGAACA 160044 -- i - -ii v i v --- i ------ iv i L1MD2_3end#LI 539 CCATGGAATACT-ACT-CAGCAATAAAAAGGAACGAACTATTGATACACG 586 chr2qtel1M 160045 GGAAAACATGGAAGGATCTGTATGGACTGATGCAGAGTAAA 160085 vi v v v vv v v v v i L1MD2_3end#LI 587 CAACAACTTGGATGGATCTCAAGGGAATTATGCTGAGTGAA 627 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.19 CpG sites = 27, Kimura (unadjusted) = 37.80 Transitions / transversions = 1.12 (27/24) Gap_init rate = 0.05 (9 / 177), avg. gap size = 1.89 (17 / 9) 348 25.23 1.87 0.00 chr2qtel1M 159910 160016 (839984) L1ME4b_3end#LINE/L1 443 551 (341) m_b86s551i6 3203 chr2qtel1M 159910 TATTGATACCAGCACTTTTTGTGATAGCAAAGAATTGGAAGCAAAG-AGA 159958 v vv i v i ii i vv- i L1ME4b_3end#L 443 TATTCATTGCAGCATTGTTTGTAATAGCAAAAGATTGGAAACAACCTAAA 492 chr2qtel1M 159959 TGTCCCTCAATTGAGGAATGGTTAAAT-GCTTCTAATACATGACTGTAAT 160007 v v i v -iv v ii vvv ii L1ME4b_3end#L 493 TGTCCATCAATAGGGGACTGGTTAAATAAATTATGGTACATCCATACAAT 542 chr2qtel1M 160008 GGAATATTA 160016 i L1ME4b_3end#L 543 GGAATACTA 551 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 30.99 CpG sites = 13, Kimura (unadjusted) = 30.99 Transitions / transversions = 0.93 (13/14) Gap_init rate = 0.02 (2 / 106), avg. gap size = 1.00 (2 / 2) 316 26.21 6.21 0.00 chr2qtel1M 159919 160063 (839937) L1ME3Cz_3end#LINE/L1 448 601 (396) m_b86s551i7 3203 chr2qtel1M 159919 CAGCACTTTTTGTGATAGCAAAGAATTGGAAGCAAAG-AGATGTCCCTCA 159967 i v i i i i vv- i v L1ME3Cz_3end# 448 CAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCA 497 chr2qtel1M 159968 ATTGAGGAATGGTTAAAT-GCTTCTAATACATGACTGTAATGGAATATTA 160016 v i v -iv v ii i vvv ii i L1ME3Cz_3end# 498 ATAGGGGAATGGATAAATAAATTGTGGTATATTCATACAATGGAATACTA 547 chr2qtel1M 160017 -ACTGTGG---AAATG-ATAAATGAGATGAACAGGAA--AACATGGAAGG 160059 - v ii --- - i iv vv v v -- vii L1ME3Cz_3end# 548 TACAGCAGTTAAAATGAATGAACTAGATCTACATGTATCAACATGGATAA 597 chr2qtel1M 160060 ATCT 160063 L1ME3Cz_3end# 598 ATCT 601 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 31.65 CpG sites = 20, Kimura (unadjusted) = 32.68 Transitions / transversions = 1.11 (20/18) Gap_init rate = 0.04 (6 / 144), avg. gap size = 1.50 (9 / 6) 18 17.86 0.00 0.00 chr2qtel1M 160238 160269 (839731) (T)n#Simple_repeat 1 32 (0) m_b86s252i6 3204 chr2qtel1M 160238 TTTTTTTTTTTTTTTTTTGGTTGTTGTTGTTT 160269 vv v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 32 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 14 20.83 4.55 0.00 chr2qtel1M 160238 160281 (839719) (TTGT)n#Simple_repeat 1 46 (0) m_b86s252i5 3205 chr2qtel1M 160238 TTTTTTTTTTTTTTTTTTGGTTG-TTG-TTGTTTGCTTGCTTGCTT 160281 v v v v v - - i i i (TTGT)n#Simpl 1 TTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTT 46 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2) 15 21.66 2.22 2.22 chr2qtel1M 160652 160696 (839304) (CTT)n#Simple_repeat 1 45 (0) m_b86s252i7 3206 chr2qtel1M 160652 CTTATTTTTCCTCCTCTTCTTCCTCTTTCTCCTTCTT-TTGGTCTT 160696 v i i i i - i - vv (CTT)n#Simple 1 CTTCTTCTTCTTCTTCTTCTTCTTC-TTCTTCTTCTTCTTCTTCTT 45 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.05 (2 / 44), avg. gap size = 1.00 (2 / 2) 14 4.33 0.00 7.69 chr2qtel1M 161714 161741 (838259) (AGGG)n#Simple_repeat 1 26 (0) m_b86s252i8 3207 chr2qtel1M 161714 AGGGAGGGAGAGAGGGAGAGGAAGGGAG 161741 i - - (AGGG)n#Simpl 1 AGGGAGGGAGGGAGGGAG-GG-AGGGAG 26 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.07 (2 / 27), avg. gap size = 1.00 (2 / 2) 16 21.33 0.00 0.00 chr2qtel1M 162253 162285 (837715) (A)n#Simple_repeat 1 33 (0) m_b86s252i10 3208 chr2qtel1M 162253 AAAACAACAACAACAACAACAAAAAAAAAAAAA 162285 v v v v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 33 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 20 16.12 2.38 0.00 chr2qtel1M 162252 162293 (837707) (CAA)n#Simple_repeat 1 43 (0) m_b86s252i9 3209 chr2qtel1M 162252 CAA-AACAACAACAACAACAACAAAAAAAAAAAAACCCACAAC 162293 - v v v v v v (CAA)n#Simple 1 CAACAACAACAACAACAACAACAACAACAACAACAACAACAAC 43 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.02 (1 / 41), avg. gap size = 1.00 (1 / 1) 14 17.04 5.00 0.00 chr2qtel1M 162255 162294 (837706) (AACAACC)n#Simple_repeat 1 42 (0) m_b86s252i11 3209 chr2qtel1M 162255 AACAA-CAACAA-CAACAACAAAAAAAAAAAAACCCACAACC 162294 - - v v vv v v (AACAACC)n#Si 1 AACAACCAACAACCAACAACCAACAACCAACAACCAACAACC 42 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 439 33.87 2.76 2.35 chr2qtel1M 165092 165345 (834655) L1ME5_3end#LINE/L1 382 636 (305) m_b86s551i8 3210 chr2qtel1M 165092 CTACTGGACTTATATCCCAAAGAGATCATAAAGAAGG----GAAAGGGAC 165137 v iiv i iv v viv ----v i L1ME5_3end#LI 382 CTCCTGGGTATATATCCCAAAGAAATTCTCACACAGGTCCATAAGGGGAC 431 chr2qtel1M 165138 CTGTATGTACAAGAATGTTTGTGGCAGCCCT-CTTGTAGTGGCCAGAAGC 165186 ---- i i ii v vi -i i vi i i L1ME5_3end#LI 432 ----ATGTACGAGGATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGT 477 chr2qtel1M 165187 TGGAAACTGAGTGGATGCCCATTAATTGCAGAATGGCTGAATAAATTGTG 165236 ii vivv i i i v v v i v iii v L1ME5_3end#LI 478 TGGAGGCAACCTGGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTG 527 chr2qtel1M 165237 GTATATGAATATTATGGAATATTATTGTTTGGTAAGAAATGACCAACAGG 165286 iv v i ii i i vvvvii v iii vi vi L1ME5_3end#LI 528 GTGGATGCACACCATGGAGTACTATGCAGCAGTTAGAAGCAACGGACTAG 577 chr2qtel1M 165287 ATGATTTCAGAAAAGCCTGGAGAGA-CTTACACAAAC-TGATGCTGAATG 165334 vviv v iv i v vi - -- v - ii i L1ME5_3end#LI 578 ATGTACACATAGCAACATGGATGGATCTT--AAAAACATAGTGCTGAGTG 625 chr2qtel1M 165335 AAACAAGCAGG 165345 v i i L1ME5_3end#LI 626 AAAAAAGTAAG 636 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 45.80 CpG sites = 48, Kimura (unadjusted) = 46.57 Transitions / transversions = 1.33 (48/36) Gap_init rate = 0.04 (10 / 253), avg. gap size = 1.30 (13 / 10) 501 22.50 0.83 0.00 chr2qtel1M 165142 165261 (834739) L1ME3A_3end#LINE/L1 432 552 (368) m_b86s551i9 3210 chr2qtel1M 165142 ATGTACAAGAATGTTTGTGGCAGCCCTCTT-GTAGTGGCCAGAAGCTGGA 165190 ii i v v - i i ?? i L1ME3A_3end#L 432 ATGTACAAGAATGTTCATAGCAGCACTATTCGTAATAGCCNNAAACTGGA 481 chr2qtel1M 165191 AACTGAGTGGATGCCCATTAATTGCAGAATGGCTGAATAAATTGTGGTAT 165240 ?ivviii i i iv i v i L1ME3A_3end#L 482 AACNACCCAAATGTCCATCAACAGTAGAATGGATAAATAAATTGTGGTAT 531 chr2qtel1M 165241 ATGAATATTATGGAATATTAT 165261 vv i iv i L1ME3A_3end#L 532 ATTCACACAATGGAATACTAT 552 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 28.45 CpG sites = 18, Kimura (unadjusted) = 28.45 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.01 (1 / 119), avg. gap size = 1.00 (1 / 1) 306 31.90 5.52 0.00 chr2qtel1M 165787 165949 (834051) L1MD1_3end#LINE/L1 159 330 (659) m_b86s551i10 3211 chr2qtel1M 165787 TAGAAAGATGCAGATGAAAATAACCTTGATATATTAC-----AACTACCA 165831 ii i i v iv vv v i ----- v i L1MD1_3end#LI 159 TAGGGAAATGCAAATTAAAACCACAATGAGATATCACTACACACCTATCA 208 chr2qtel1M 165832 GATTGGCTAAAAAGATAGAAAGGGAAAGTGACAAATGTTGAAGAGG-TGT 165880 v vi v i v v v iiiv i iv - i L1MD1_3end#LI 209 GAATGGCTAAAATAAAAAATAGTGACAACACCAAATGCTGGCGAGGATGC 258 chr2qtel1M 165881 GCAAAAATTGGGGCATTAATTCA---CTGGTACAATTGTAAAATGAAACA 165927 v i i iv i v v --- ivi v iv L1MD1_3end#LI 259 GGAGAAACTGGATCACTCATACATTGCTGGTGGGAATGTAAAATGGTACA 308 chr2qtel1M 165928 ACTATTTTAGAGAGAAATTTGG 165949 i i i i i i iv i L1MD1_3end#LI 309 GCCACTCTGGAAAACAGTTTGG 330 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.73 CpG sites = 30, Kimura (unadjusted) = 42.83 Transitions / transversions = 1.36 (30/22) Gap_init rate = 0.02 (3 / 162), avg. gap size = 3.00 (9 / 3) 311 24.64 0.00 28.70 chr2qtel1M 166009 166156 (833844) MIRb#SINE/MIR 4 118 (150) m_b86s601i5 3212 chr2qtel1M 166009 AGGGGCAACTAGGTAGTACAATGGATAGAGCACCAGCCCTGAAGTTAGGA 166058 i --- i i i v vi ii i ------ MIRb#SINE/MIR 4 AGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAG------ 44 chr2qtel1M 166059 GGGTTAGAGTCAGGAGTTGGGTTAGAGTCAGGTTAGAATCTGGTTTCAAA 166108 --- i -- - vi v i ---------- i i i---- MIRb#SINE/MIR 45 ---TCAGA--CAG-ACCTGGGTTCGAATC----------CCGGCTC---- 74 chr2qtel1M 166109 CATTTAACACTTCTTAGCTGTGTGGCCCTGGGCAAGTTATTTAACCCC 166156 ---- iv vi i i i i MIRb#SINE/MIR 75 ----TGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTC 118 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 27.01 CpG sites = 20, Kimura (unadjusted) = 28.30 Transitions / transversions = 3.33 (20/6) Gap_init rate = 0.22 (33 / 147), avg. gap size = 1.00 (33 / 33) 233 28.90 5.88 2.27 chr2qtel1M 166083 166167 (833833) MIR3#SINE/MIR 37 124 (84) m_b86s601i6 3212 chr2qtel1M 166083 GAGTCAGG----TTAGAATCTGGTTTCAAACATTTAACACTTCTTAGCTG 166128 ----i i iv i ii ii- - i iv vvi ? MIR3#SINE/MIR 37 GAGTCAGGAGACCTGGGTTCTAGTCCCGG-C-TCTGCCACTAACTNGCTG 84 chr2qtel1M 166129 TGTGGCCCTGGGCAAGTTATTTAACCCCAATTGG-CTCAG 166167 i i i i v i vv v - MIR3#SINE/MIR 85 TGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAG 124 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.78 CpG sites = 16, Kimura (unadjusted) = 38.88 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.05 (4 / 84), avg. gap size = 1.75 (7 / 4) 257 31.63 3.89 1.63 chr2qtel1M 166180 166359 (833641) L1ME3G_3end#LINE/L1 441 624 (300) m_b86s551i11 3211 chr2qtel1M 166180 TTTATAGCAGCTTTCTTTGTGATGACAAAGAATGAGAAATGGAAGAGATT 166229 i v v v i ii i i vi iiivvv i v L1ME3G_3end#L 441 TTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATG 490 chr2qtel1M 166230 CCCATCAAT-TGGGAATGGCTGAACAAATTGTGGTATATG---ATTGTGA 166275 i -v i i i i v--- i i i L1ME3G_3end#L 491 TCCATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGG 540 chr2qtel1M 166276 CAGA--ATAAAACTGCTACAAGAAATGATG-AGCTCAAGATTTTAGAAAA 166322 v v -- iv i ? i v ii v - v v v v --- vvi L1ME3G_3end#L 541 AATACTATGCAGCNGTTAAAAAGAATGAGGTAGATCTATATGT---ACTG 587 chr2qtel1M 166323 ACACAGAAAGATTTGCACAAAATACTGAAGAGTGAAA 166359 ii i v vi v i vv L1ME3G_3end#L 588 ACATGGAAAGATCTCCAAGACATATTGTTGAGTGAAA 624 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.30 CpG sites = 30, Kimura (unadjusted) = 42.29 Transitions / transversions = 1.15 (30/26) Gap_init rate = 0.04 (7 / 179), avg. gap size = 1.43 (10 / 7) 315 26.14 1.14 0.00 chr2qtel1M 166180 166267 (833733) L1ME1_3end#LINE/L1 445 533 (393) m_b86s551i12 3211 chr2qtel1M 166180 TTTATAGCAGCTTTCTTTGTGATGACAAAGAATGAGAAATGGAAGAGATT 166229 i v i i ii v i ivi iiivvv i v L1ME1_3end#LI 445 TTCATAGCAGCTTTATTCGTAATAGCCAAAAACTGGAAACAACCCAAATG 494 chr2qtel1M 166230 CCCATCAATTGG-GAATGGCTGAACAAATTGTGGTATAT 166267 i i? - v i L1ME1_3end#LI 495 TCCATCAACNGGTGAATGGATAAACAAATTGTGGTATAT 533 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 31.98 CpG sites = 15, Kimura (unadjusted) = 33.79 Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.01 (1 / 87), avg. gap size = 1.00 (1 / 1) 14 12.89 1.92 10.42 chr2qtel1M 167260 167311 (832689) (GGAGAA)n#Simple_repeat 1 48 (0) m_b86s252i12 3213 chr2qtel1M 167260 GGAAAAGGCAGAAGGAAAAAGGAAAAGG-GAAGGCAGAAGATGAGATGGA 167308 i - - i i - - -- v (GGAGAA)n#Sim 1 GGAGAAGG-AGAAGG-AGAAGGAGAAGGAGAAGG-AGAAG--GAGAAGGA 45 chr2qtel1M 167309 TAA 167311 v (GGAGAA)n#Sim 46 GAA 48 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.12 (6 / 51), avg. gap size = 1.00 (6 / 6) 227 26.50 7.00 1.90 chr2qtel1M 168191 168290 (831710) L3#LINE/CR1 3523 3627 (472) m_b86s601i7 3214 chr2qtel1M 168191 AAATATAG-GTCAAG-GCAACTGAGG--ATGCTCCCCGCTCCCTTTCTAC 168236 i - v -? vv -- iv - vivi - i L3#LINE/CR1 3523 AAGTATAGTGTCCAGANCAAGGGAGGTAATAGTCCC-GCTGTACT-CTGC 3570 chr2qtel1M 168237 -CT--TCAGATCACATCTGAACTATCATGTTCATCTCTAGGCACTGGAGT 168283 - -- i i v iii vi i i iiv v L3#LINE/CR1 3571 GCTGGTCAGACCACATCTGGAGTATTGCGTTCAGTTCTGGGCGCCACATT 3620 chr2qtel1M 168284 TTATGAG 168290 v L3#LINE/CR1 3621 TTAAGAG 3627 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 30.78 CpG sites = 15, Kimura (unadjusted) = 33.90 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.07 (7 / 99), avg. gap size = 1.29 (9 / 7) 525 26.49 2.58 2.58 chr2qtel1M 168297 168451 (831549) C L2d2_3end#LINE/L2 (10) 545 391 m_b86s601i8 3215 chr2qtel1M 168297 TTAACAAGCCTTTATTAAGCACATACTGTTTTCTAGGCAATGAGCTAAGC 168346 i iiv i i v v v v v v i C L2d2_3end#LIN 545 TCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGC 496 chr2qtel1M 168347 ATTG---GGGACACAAAGAATGGCAAAAGAAAGTCCCTGCTCTGAAGGAG 168393 ii --- i vvii i v vi i v C L2d2_3end#LIN 495 GCTGTGGGGGATACAAAGAAGTATAAGACATGGTCCCTGCCCTCAAGGAG 446 chr2qtel1M 168394 CTCACAATCTAATGGAGGAGACAACAAGGAAATGAATTTG-GAAAAATAA 168442 i i v i ---- v i ivi - i v C L2d2_3end#LIN 445 CTTACAATCTAGTTGGGGAGACAA----GACATAAACACGTGAAAAGTTA 400 chr2qtel1M 168443 GGTAACTAT 168451 ii v C L2d2_3end#LIN 399 AATAACAAT 391 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 30.40 CpG sites = 23, Kimura (unadjusted) = 33.37 Transitions / transversions = 1.35 (23/17) Gap_init rate = 0.04 (6 / 154), avg. gap size = 1.33 (8 / 6) 659 34.34 5.39 0.97 chr2qtel1M 168471 168767 (831233) L3#LINE/CR1 3613 3922 (177) m_b86s601i9 3214 chr2qtel1M 168471 GCTATAATCAAGAAGAGACATTGACAAATTGGAATAGGCCCAAAGAATGG 168520 i i v iv ii i i iiiv i i i vi L3#LINE/CR1 3613 GCCACATTTTAAGAGGGACATTGACAAACTGGAGCGCGTCCAGAGGAGAG 3662 chr2qtel1M 168521 CTATGAATATAA---------TGGAGACCA-GCCAAATGAAGAGAAATGG 168560 v iv iv ii--------- i - i v i ivii v L3#LINE/CR1 3663 CGACCAGGATGGTGAAGGGTCTGGAAACCATGTCATATGAGGAACGGTTG 3712 chr2qtel1M 168561 AAAGATCTGAGGTTACTTATCCTGAAAAAGAGAAAAC-TAGGGGAGCAAG 168609 i v i v ii v i i i - i -- v L3#LINE/CR1 3713 AAGGAACTGGGGATGTTTAGCCTGGAGAAGAGAAGACTTAGAGGAG--AC 3760 chr2qtel1M 168610 ATGAAATACTG--TTCAAATATCTGAAAGGTCGTCATGTTTAGGATGTAT 168657 v -i -- i i ii vv i v v L3#LINE/CR1 3761 ATGATA-GCTGTCTTCAAATATTTGAAGGGCTGTCATGTGGAAGAGGGAT 3809 chr2qtel1M 168658 CACACTCATTGTGCTTGATCCCAGAGGCAATATCTGGGATCTACAAGAAC 168707 i v i v iv iii vv v v i i v iii viv L3#LINE/CR1 3810 TAGACTTATTCTGTGTGGCTCCAGAGGGCAGAACTAGGACCAATGGGTGG 3859 chr2qtel1M 168708 AAGATGC-CAGAGGTAGATTTCAGTTGGATGTGATGAACAGTATCTTAAT 168756 v i -vi i i i vi i i v v iiv ii i L3#LINE/CR1 3860 AAGTTACAGGGAGGCAGATTTCGGCTCAATATAAGGAAGAACTTTCTAAC 3909 chr2qtel1M 168757 AAT--GGACTGCC 168767 -- ii i L3#LINE/CR1 3910 AATCAGAGCTGTC 3922 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 46.61 CpG sites = 66, Kimura (unadjusted) = 48.77 Transitions / transversions = 1.89 (66/35) Gap_init rate = 0.03 (9 / 296), avg. gap size = 2.11 (19 / 9) 17 19.64 0.00 6.12 chr2qtel1M 170013 170064 (829936) (AAAC)n#Simple_repeat 1 49 (0) m_b86s252i13 3216 chr2qtel1M 170013 AAACAAATAAACAATATAACACATACAGATCACACACACACACAAACACA 170062 i - i - v - v v v v v (AAAC)n#Simpl 1 AAACAAACAAACAA-ACAA-ACAAACA-AACAAACAAACAAACAAACAAA 47 chr2qtel1M 170063 CA 170064 (AAAC)n#Simpl 48 CA 49 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.00 (3 / 3) 22 26.83 0.00 1.69 chr2qtel1M 170031 170090 (829910) (AC)n#Simple_repeat 1 59 (0) m_b86s252i14 3216 chr2qtel1M 170031 ACACATACAGATCACACACACACACAAACACACAGAGATGAATACATACA 170080 i v - v v v iiv i i (AC)n#Simple_ 1 ACACACACACA-CACACACACACACACACACACACACACACACACACACA 49 chr2qtel1M 170081 CCCATGCACA 170090 v ii (AC)n#Simple_ 50 CACACACACA 59 Matrix = Unknown Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.02 (1 / 59), avg. gap size = 1.00 (1 / 1) 278 26.11 8.96 2.82 chr2qtel1M 170224 170357 (829643) C MIRc#SINE/MIR (39) 229 88 m_b86s601i10 3217 chr2qtel1M 170224 TTTACCAAGAGCTTT---ACCCATGATGACAATTGATTCTCACTAG---T 170267 v v --- iv v vv v i v v---i C MIRc#SINE/MIR 229 TTTACAAAGCGCTTTCACATACATTATCTCATTTGATCCTCACAACAACC 180 chr2qtel1M 170268 CTGTGACATAGGCAGGAC---CATCATTCTCATCACATTCACAACTCAGG 170314 vi i ---i i v vi i- i iv v C MIRc#SINE/MIR 179 CTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCAT-TTTACAGATGAGG 131 chr2qtel1M 170315 ---CTGTGAGCTAAAAATGGTTGAGGGACTTGACCCAAATATCACA 170357 --- v - v i iv i v - i-i C MIRc#SINE/MIR 130 AAACTGAG-GCTCAGAGAGGTTAAGTGACTTG-CCCAAG-GTCACA 88 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.38 CpG sites = 16, Kimura (unadjusted) = 32.38 Transitions / transversions = 0.89 (16/18) Gap_init rate = 0.06 (8 / 133), avg. gap size = 2.00 (16 / 8) 21 10.84 0.00 0.00 chr2qtel1M 170725 170754 (829246) (T)n#Simple_repeat 1 30 (0) m_b86s252i15 3218 chr2qtel1M 170725 TTCTTTTTTTCTGTTTTTTTTTTTTTTTTT 170754 i i v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 30 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 16 10.03 0.00 0.00 chr2qtel1M 171545 171566 (828434) (A)n#Simple_repeat 1 22 (0) m_b86s252i16 3219 chr2qtel1M 171545 AAAAAAAGAAAAAAAAAGAAAA 171566 i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAA 22 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 444 28.39 15.38 1.19 chr2qtel1M 172711 172931 (827069) MIRb#SINE/MIR 9 260 (8) m_b86s601i11 3220 chr2qtel1M 172711 CAG-GTGATGCACTGGATAAAACACTGAGTCTCAAATCACAAAGAACTGA 172759 - i v v i i v iv i vi i v v v i MIRb#SINE/MIR 9 CAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGG 58 chr2qtel1M 172760 GTTTTAATCCC---TCT--------TTAGAAAGG-------AGGCAAGTC 172791 iv --- --------i vviv -------i i MIRb#SINE/MIR 59 GTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTT 108 chr2qtel1M 172792 ACAAGACCTCTATT-TCCTT-GTTTCTTTATCTGT-AAATAGGTATAATA 172838 vvi v v-v i- i i - i v MIRb#SINE/MIR 109 ACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATA 158 chr2qtel1M 172839 ATAACACCTAACTCTTAGGGTTTTGATGAGGACAAAATAAGACAAT--AT 172886 --- v vi v vi iv i i -- MIRb#SINE/MIR 159 AT---ACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCAT 205 chr2qtel1M 172887 TTA----------CACCGGACATGACGTATAGTAGGTACAGTATAAATGC 172926 v ---------- v vi v i ii i ii vvv v MIRb#SINE/MIR 206 GTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAAATGG 255 chr2qtel1M 172927 TAGTT 172931 i MIRb#SINE/MIR 256 TAGCT 260 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.68 CpG sites = 31, Kimura (unadjusted) = 36.18 Transitions / transversions = 1.00 (31/31) Gap_init rate = 0.05 (12 / 220), avg. gap size = 3.08 (37 / 12) 451 27.27 9.74 0.00 chr2qtel1M 172784 172937 (827063) MIR#SINE/MIR 94 262 (0) m_b86s601i12 3220 chr2qtel1M 172784 GGCAAGTCACAAGACCTCTATTT-CCTT-GTTTCTTTATCTGTAAA-TAG 172830 i vvi v v - i- i i - i MIR#SINE/MIR 94 GGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGG 143 chr2qtel1M 172831 GTATAATAATAACACCTAACTCTTAGGGTTTTGATGAGGACAAAATAAGA 172880 v ii v v v vi iv i v MIR#SINE/MIR 144 GGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGT 193 chr2qtel1M 172881 CAATAT-----------TTACACCGG-ACATGACGTATAGTAGGTACAGT 172918 i i----------- v v i -i v i ii i ii vvv MIR#SINE/MIR 194 TAATACATGTAAAGCGCTTAGAACAGTGCCTGGCACATAGTAAGCGCTCA 243 chr2qtel1M 172919 ATAAATGCTAGTTATCACT 172937 i i i i MIR#SINE/MIR 244 ATAAATGTTAGCTATTATT 262 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.65 CpG sites = 25, Kimura (unadjusted) = 34.79 Transitions / transversions = 1.47 (25/17) Gap_init rate = 0.03 (5 / 153), avg. gap size = 3.00 (15 / 5) 238 35.16 8.79 1.54 chr2qtel1M 173009 173190 (826810) L2d2_3end#LINE/L2 353 547 (8) m_b86s601i13 3221 chr2qtel1M 173009 TCTTTTATTTCCCTGCTGAATTAATTTATTTCTATTCCAAAACATTCTTT 173058 i viiv vi i i-- vv iiiiv vii v L2d2_3end#LIN 353 TCTTCTATTGTTGTCTTGAACTG--TTATTTAAATCTTGTATTGTTATTT 400 chr2qtel1M 173059 ---TTTTCCCAGTTTCAGATCTCATTTGTCTA-TAAGATTTTGAGTTTCC 173104 --- v ivv i vi ii i vi i -iv v i i i i L2d2_3end#LIN 401 AACTTTTCACGTGTTTATGTCTTGTCTCCCCAACTAGATTGTAAGCTCCT 450 chr2qtel1M 173105 TGACAGCAGAGACT--------TACTCTCCTTGCAATCTTCATGGC--TT 173144 vi i i-------- - i i vi ii ii --i L2d2_3end#LIN 451 TGAGGGCAGGGACCATGTCTTATACT-TCTTTGTATCCCCCACAGCGCCT 499 chr2qtel1M 173145 AGCCCAGTGCCT--AAAACAGAAGGTGCTCCATCAGTACTTCTTGATT 173190 v --v v v i v v i i v L2d2_3end#LIN 500 AGCACAGTGCCTTGCACACAGTAGGCGCTCAATAAATATTTGTTGATT 547 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 47.70 CpG sites = 39, Kimura (unadjusted) = 49.98 Transitions / transversions = 1.62 (39/24) Gap_init rate = 0.04 (8 / 181), avg. gap size = 2.38 (19 / 8) 253 29.70 11.88 0.00 chr2qtel1M 173090 173190 (826810) L2d_3end#LINE/L2 394 506 (10) m_b86s601i14 3221 chr2qtel1M 173090 AGATTTTGAGTTTCCTGACAGCAGAGACT--------TACTCTCCTTGCA 173131 v i i i i vi i i-------- ? ii ?v i L2d_3end#LINE 394 AGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACTNTTTTNTCG 443 chr2qtel1M 173132 ATCTTCATGGC--TTAGCCCAGTGCCTAAAACAGA--AGGTGCTCCATCA 173177 v ii ii --i v iv iv v -- i v v L2d_3end#LINE 444 TTCCCCACAGCGCCTAGCACAGTGCTGAGCACATAGTAGGCGCTCAATAA 493 chr2qtel1M 173178 GTACTTCTTGATT 173190 i v L2d_3end#LINE 494 ATACTTGTTGATT 506 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.96 CpG sites = 19, Kimura (unadjusted) = 40.44 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.03 (3 / 100), avg. gap size = 4.00 (12 / 3) 611 29.70 0.60 1.20 chr2qtel1M 174617 174783 (825217) MIRc#SINE/MIR 2 167 (101) m_b86s601i15 3222 chr2qtel1M 174617 GAAGCAACTGATAGTGTAGCGTAAAGAACCCTGGATCTAGAGTCAGGAAT 174666 i i- - i i i v i v ii i v MIRc#SINE/MIR 2 GAGGCAG-TG-TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAG 49 chr2qtel1M 174667 GCTAGGGTCTAAATCTAGCCTCAGACAGTTATGAACTTTGTGTTCCTGGA 174716 i iv iii i iv v v v v iv i v vi i i MIRc#SINE/MIR 50 ACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGG 99 chr2qtel1M 174717 AAAATCACTTAACTTTCATTTGTCTCAGTTTCCTCAACTGTCAAATGGGT 174766 v i i iiv vv i v v v MIRc#SINE/MIR 100 CAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGG 149 chr2qtel1M 174767 ATAATACTATC-ACCTTG 174783 v i -i i MIRc#SINE/MIR 150 ATAATAATACCTGCCCTG 167 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.81 CpG sites = 29, Kimura (unadjusted) = 38.94 Transitions / transversions = 1.45 (29/20) Gap_init rate = 0.02 (3 / 166), avg. gap size = 1.00 (3 / 3) 218 26.39 5.15 6.25 chr2qtel1M 175278 175374 (824626) MIR#SINE/MIR 157 252 (10) m_b86s601i16 3222 chr2qtel1M 175278 ACCTAACCAAGAAGATTGCTATG-GGATGAAGTGACATAATA-ATGTAAA 175325 v iv v i i i i - v i vv - MIR#SINE/MIR 157 ACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATACATGTAAA 206 chr2qtel1M 175326 GAAACTACTTGGCACAGCATCTGGCAAAAAGTA---GTTCAAAACAAATG 175372 ----ii i v iii v v --- i -- i MIR#SINE/MIR 207 G----CGCTTAGAACAGTGCCTGGCACATAGTAAGCGCTC--AATAAATG 250 chr2qtel1M 175373 CT 175374 i MIR#SINE/MIR 251 TT 252 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.60 CpG sites = 15, Kimura (unadjusted) = 33.49 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.09 (9 / 96), avg. gap size = 1.22 (11 / 9) 272 28.29 8.70 1.63 chr2qtel1M 176037 176151 (823849) C MIR3#SINE/MIR (2) 206 84 m_b86s601i17 3223 chr2qtel1M 176037 ATCA-AAAGTTATACGGT-TTAGAGCTGAAAGACACTTCAGAT-TTAAAT 176083 - i i i vii - i i iv i i v- i vv C MIR3#SINE/MIR 206 ATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCT 157 chr2qtel1M 176084 AATCCAACCGTCATTAATTTACAGA--ACAAAACTGAAATACAGA----- 176126 i vi - i v -- vi iiiv ----- C MIR3#SINE/MIR 156 AGTCCAACCCCC-TCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGT 108 chr2qtel1M 176127 AAAGGGATTTGCCCAAAAGTCATAC 176151 i v i - i i C MIR3#SINE/MIR 107 GAAGTGACTTGCCC-AAGGTCACAC 84 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.36 CpG sites = 22, Kimura (unadjusted) = 37.36 Transitions / transversions = 2.20 (22/10) Gap_init rate = 0.06 (7 / 114), avg. gap size = 1.71 (12 / 7) 26 12.61 2.27 0.00 chr2qtel1M 176546 176589 (823411) (AT)n#Simple_repeat 1 45 (0) m_b86s252i17 3224 chr2qtel1M 176546 ATTTATAT-TATATATATATATATATACACATACATATATACATA 176589 v - i i i i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATA 45 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.02 (1 / 43), avg. gap size = 1.00 (1 / 1) 22 22.03 1.64 1.64 chr2qtel1M 176555 176615 (823385) (ATATAC)n#Simple_repeat 1 61 (0) m_b86s252i18 3224 chr2qtel1M 176555 ATATATATATATATATACACATACATATATACATAAACACACAT-CACAC 176603 i i i i i v i i -i - (ATATAC)n#Sim 1 ATATACATATACATATACATATACATATACATATACATATACATATACA- 49 chr2qtel1M 176604 TCTACATATTCA 176615 v v (ATATAC)n#Sim 50 TATACATATACA 61 Matrix = Unknown Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.03 (2 / 60), avg. gap size = 1.00 (2 / 2) 16 13.25 0.00 0.00 chr2qtel1M 176965 176989 (823011) (T)n#Simple_repeat 1 25 (0) m_b86s252i19 3225 chr2qtel1M 176965 TTTTTTTTGTTTTGTTTTTTTTGTT 176989 v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 582 24.70 1.33 5.56 chr2qtel1M 177778 177927 (822073) MIRc#SINE/MIR 1 144 (124) m_b86s601i18 3226 chr2qtel1M 177778 CAAGCTAG-GTGCCACAATGGATAGCGCACTGAACTTGCAATCAGGAAGA 177826 i vi - vii i v v i v i MIRc#SINE/MIR 1 CGAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA 50 chr2qtel1M 177827 CTTATCTTCATGAGTTCAAATCTGGGCTCTGAAAATTACTAGCTGTGTGA 177876 i -------- i i i iv vv v MIRc#SINE/MIR 51 CCT--------GGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGA 92 chr2qtel1M 177877 ACCTGAATAATACAATTAAACTCCTTTA-CCTCAGTTTCCTCATTTGTAA 177925 v i iii vv v v ii v - i MIRc#SINE/MIR 93 CCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAA 142 chr2qtel1M 177926 GA 177927 i MIRc#SINE/MIR 143 AA 144 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.40 CpG sites = 20, Kimura (unadjusted) = 30.43 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.07 (10 / 149), avg. gap size = 1.00 (10 / 10) 1178 28.85 2.65 1.22 chr2qtel1M 179127 179691 (820309) C L1M5_orf2#LINE/L1 (1138) 2156 1584 m_b86s551i13 3227 chr2qtel1M 179127 AGTAGTTTTTTATTTGATTTTCTAGGATTCTCTATGTATACCATTATATC 179176 ? vv v i i ? i i ? v i i C L1M5_orf2#LIN 2156 AGTAGTTTNTTTGTAGATTCTTTNGGATTTTCTACGTANACAATCATGTC 2107 chr2qtel1M 179177 ATCAGCAAAGAGTGA--GTTTGGTTTTTTCATTGCCTATTCCAATTCCTT 179224 v i v i? -- vi i v v v iiiv v C L1M5_orf2#LIN 2106 ATCTGCGAATAANGACAGTTTTATTTCTTCCTTTCCAATCTTTATGCCTT 2057 chr2qtel1M 179225 CAATATGTTTCTCTTCTCTTATTGCCAGGGCTAACGTTTCTAGTACAATG 179274 iv v v i vi vvv iviii i C L1M5_orf2#LIN 2056 TTATTTCTTTTTCTTGCCTTATTGCACTGGCTAGGACCTCCAGTACAATG 2007 chr2qtel1M 179275 TTGAATAA---TGGTGATAATGGCCATGCTCGTTTCAC-CCCAATCTTAT 179320 i--- ? ii v v i i iii- i v C L1M5_orf2#LIN 2006 TTGAATAGAAGTGGTGANAGCGGACATCCTTGTCTTGTTCCCGATCTTAG 1957 chr2qtel1M 179321 TTATGAATGTGTCTAGTTTATCCCCATTACATATAATGCTTATTCATGGT 179370 vvi- v i? ii ? v v vi i i ?ii vvv C L1M5_orf2#LIN 1956 GGG-GAAAGCNTTCAGTNTTTCACCATTAAGTATGATGTTNGCTGTAGGT 1908 chr2qtel1M 179371 TTTAGATAGATACTGCTTCTCATTTAAATGAAAATTTCATTTACTACTAT 179420 vvi i ivi v vv vi v iv ii v i i v - C L1M5_orf2#LIN 1907 TTTTCGTAGATGCCCTTTATCAGGTTGAGGAAGTTCCCTTCTATTCCTA- 1859 chr2qtel1M 179421 GGCTT-CT-AGTGTTTTTCCTAGGAATGAGTGCTACATTTTCTCAAAGGC 179468 - i - - v vii v i i iv v v C L1M5_orf2#LIN 1858 -GTTTGCTGAGAGTTTTTATCATGAATGGGTGTTGAATTTTGTCAAATGC 1810 chr2qtel1M 179469 TTTTTCTGCCT-TGT--AAATAAT-ATATGATTTCTGTTAGTTTTATT-- 179512 v - i -- i i - i v i--i -- C L1M5_orf2#LIN 1809 TTTTTCTGCATCTATTGAGATGATCATATGATTTTTCTC--CTTTATTCT 1762 chr2qtel1M 179513 ATTGACATGTTCAATTATGTTGATAGTTTTCCTAATAATGAACCAGTCTT 179562 i i i v v ii v v i v iv i ii C L1M5_orf2#LIN 1761 GTTAATATGGTGAATTACATTGATTGATTTTCGAATGTTAAACCAACCTT 1712 chr2qtel1M 179563 CCATTTCTGGTATTAATCCTACCTGCTCATAGTGTACTATTCTGGTGATA 179612 v i v v i i i v ii i i vv v C L1M5_orf2#LIN 1711 GCATTCCTGGGATAAACCCCACTTGGTCATGATGTATTATCCTTTTTATA 1662 chr2qtel1M 179613 AATTACAGTGATAT-ATTTGCTAATGTTTTTATTTTAAAATTTTGCATCA 179661 v i v - vi- i- i ?vii v v C L1M5_orf2#LIN 1661 TATTGCTG-GATTCGATTTGCTAATA-TTTTGTTNAGGATTTTTGCATCT 1614 chr2qtel1M 179662 ATATTCATTCGGGAAATTGGTCTATACTTT 179691 i vv v i v C L1M5_orf2#LIN 1613 ATGTTCATGAGGGATATTGGTCTGTAATTT 1584 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.14 CpG sites = 87, Kimura (unadjusted) = 37.90 Transitions / transversions = 1.18 (87/74) Gap_init rate = 0.03 (17 / 564), avg. gap size = 1.29 (22 / 17) 236 25.83 0.00 3.23 chr2qtel1M 179937 180032 (819968) C L1PA15-16_5end#LINE/L1 (670) 2292 2200 m_b86s551i14 3228 chr2qtel1M 179937 AGGGAAGTTTTCCTTGATTATTTCTTGAAAGATGTTGGCTAGGCTTTTTT 179986 vi i i v v vv i i i ? v C L1PA15-16_5en 2292 AGGGAAGTTTTCCTGAATTATTCCCTCAAATATGTTTTCCAAGTTNTTTA 2243 chr2qtel1M 179987 TTTTTATATACTCATGTCTTTCAAGTAATCCAATAATTCTTAAATT 180032 i - v v -- v i i v vv v ii C L1PA15-16_5en 2242 CTTTT-TCTCCT--TCTCTCTCAGGAACGCCAATAATTCGTAGGTT 2200 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.24 CpG sites = 11, Kimura (unadjusted) = 32.24 Transitions / transversions = 0.85 (11/13) Gap_init rate = 0.03 (3 / 95), avg. gap size = 1.00 (3 / 3) 14 3.65 2.94 9.38 chr2qtel1M 180468 180501 (819499) (AAC)n#Simple_repeat 1 32 (0) m_b86s252i20 3229 chr2qtel1M 180468 AACAA-AACAAAATACAAGCAAACAACAACAACAA 180501 - v - - - (AAC)n#Simple 1 AACAACAACAACA-ACAA-C-AACAACAACAACAA 32 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.12 (4 / 33), avg. gap size = 1.00 (4 / 4) 226 22.35 5.13 2.50 chr2qtel1M 181580 181657 (818343) L1P4_orf2#LINE/L1 841 920 (2374) m_b86s551i15 3230 chr2qtel1M 181580 GAAACAACATATTAAAAAC-CTGAGAAATACAATAAAAGCAGTG---AGA 181625 v ii v - i -- i ii? --- L1P4_orf2#LIN 841 GACACAACATACCAAAATCTCTGGGA--TGCAGCNAAAGCAGTGTTAAGA 888 chr2qtel1M 181626 GGAAAATTTCTCTCTCTCAAGGCTTAGATCAA 181657 i v vv v v v i v L1P4_orf2#LIN 889 GGAAAGTTTATAGCGCTAAACGCCTACATCAA 920 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 27.13 CpG sites = 8, Kimura (unadjusted) = 27.13 Transitions / transversions = 0.89 (8/9) Gap_init rate = 0.05 (4 / 77), avg. gap size = 1.50 (6 / 4) 282 29.68 4.27 7.55 chr2qtel1M 183530 183693 (816307) C L2d2_3end#LINE/L2 (17) 538 380 m_b86s601i19 3231 chr2qtel1M 183530 ACATTTATTAAACACCTATTGAGTGCCAGTCACAATGATAAAAATTGAGG 183579 i i i i i v v v vi v iivii v C L2d2_3end#LIN 538 ATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGTGG 489 chr2qtel1M 183580 ATTTAAAAAAAAAAGAGGCAAAAGACA--ATTACT----TCAAGGAATAT 183623 i----ii v v i i v --i iv ---- iiv C L2d2_3end#LIN 488 G----GGATACAAAGAAGTATAAGACATGGTCCCTGCCCTCAAGGAGCTT 443 chr2qtel1M 183624 ACAATCCAATGTGGGAAACAATACACAAATATGGACAAAGTAAGCTAAAT 183673 i i vv i v i i i viv ---- C L2d2_3end#LIN 442 ACAATCTAGTTGGGGAGACAAGACATAAACACGTGAAAAGT----TAAAT 397 chr2qtel1M 183674 CCAGAACAA-ATAGGATTTAA 183693 ---- - i i C L2d2_3end#LIN 396 ----AACAATACAAGATTTAA 380 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.75 CpG sites = 28, Kimura (unadjusted) = 39.05 Transitions / transversions = 1.65 (28/17) Gap_init rate = 0.09 (15 / 163), avg. gap size = 1.27 (19 / 15) 16 0.00 0.00 0.00 chr2qtel1M 183966 183983 (816017) (A)n#Simple_repeat 1 18 (0) m_b86s252i21 3232 chr2qtel1M 183966 AAAAAAAAAAAAAAAAAA 183983 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAA 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 15 23.74 1.96 1.96 chr2qtel1M 184019 184069 (815931) (AAAAT)n#Simple_repeat 1 51 (0) m_b86s252i22 3233 chr2qtel1M 184019 AAATTAAATACAAAATAAAAGAAAA-AAAATTAGAAAAAGGAAAAAACAA 184067 v - i v - v i v iv v v (AAAAT)n#Simp 1 AAAATAAA-ATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAA 49 chr2qtel1M 184068 TA 184069 (AAAAT)n#Simp 50 TA 51 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.04 (2 / 50), avg. gap size = 1.00 (2 / 2) 50 22.77 0.00 0.00 chr2qtel1M 184176 184282 (815718) (T)n#Simple_repeat 1 107 (0) m_b86s252i23 3234 chr2qtel1M 184176 TTTTTTTTTTTTTTTTTTTTTTTAAAATATATTTTTTTTTTTTTATTTAT 184225 vvvv v v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr2qtel1M 184226 ATCTCTTCCTTTTTTTTTTTTTTTTTTTTTGTTTCCTTGTAGGTTTTTTT 184275 v i i ii v ii v vvv (T)n#Simple_r 51 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 100 chr2qtel1M 184276 TTTTGTT 184282 v (T)n#Simple_r 101 TTTTTTT 107 Matrix = Unknown Transitions / transversions = 0.40 (6/15) Gap_init rate = 0.00 (0 / 106), avg. gap size = 0.0 (0 / 0) 21 33.81 1.22 1.22 chr2qtel1M 184354 184435 (815565) (AT)n#Simple_repeat 1 82 (0) m_b86s252i24 3235 chr2qtel1M 184354 ATATATTTATGTAAACATACATTTATATAGACACACACACACATATATAT 184403 v i v i i v v i i i i i i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr2qtel1M 184404 ACACAAATATA-ATGATACAGATACACATACAT 184435 i i v - - i v i i i (AT)n#Simple_ 51 ATATATATATATAT-ATATATATATATATATAT 82 Matrix = Unknown Transitions / transversions = 2.50 (15/6) Gap_init rate = 0.02 (2 / 81), avg. gap size = 1.00 (2 / 2) 36 0.00 0.00 0.00 chr2qtel1M 184712 184742 (815258) (AC)n#Simple_repeat 1 31 (0) c_b86s251i0 3236 chr2qtel1M 184712 ACACACACACACACACACACACACACACACA 184742 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACA 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 385 25.46 0.00 9.57 chr2qtel1M 184897 185022 (814978) C MIRb#SINE/MIR (152) 116 2 m_b86s601i20 3237 chr2qtel1M 184897 GGTCAAGTGCCTTGCCCCGGGTCACACAGCTAGGAAGTGTTAAGTGTCTG 184946 i iv vi ------- v v C MIRb#SINE/MIR 116 GGTTAAGTAACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGCAG 74 chr2qtel1M 184947 AGACCAAATTTGAACACCTAGTCCTCTTGACTTCAGGGTTGGCACTCTAT 184996 v vii i - vi ivii i ii iiv ii v C MIRb#SINE/MIR 73 AGCCGGGATTCGAAC-CCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTT 25 chr2qtel1M 184997 CCACTGAACCATCTAGCTGCCCCTCT 185022 v i--- C MIRb#SINE/MIR 24 CCACTGCACCAC---GCTGCCCCTCT 2 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.00 CpG sites = 18, Kimura (unadjusted) = 31.58 Transitions / transversions = 1.64 (18/11) Gap_init rate = 0.09 (11 / 125), avg. gap size = 1.00 (11 / 11) 12 29.60 1.82 1.82 chr2qtel1M 185543 185597 (814403) (ATTTT)n#Simple_repeat 1 55 (0) m_b86s252i25 3238 chr2qtel1M 185543 ATTTTATTTCTTTCTTGTCATATTATACTAGATTTTATTTT-TTTGATCA 185591 - v i i iv v i vv - v iv (ATTTT)n#Simp 1 ATTTTATTT-TATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTT 49 chr2qtel1M 185592 TAGTTT 185597 v (ATTTT)n#Simp 50 TATTTT 55 Matrix = Unknown Transitions / transversions = 0.62 (5/8) Gap_init rate = 0.04 (2 / 54), avg. gap size = 1.00 (2 / 2) 206 32.35 4.26 3.52 chr2qtel1M 186618 186758 (813242) C L2#LINE/L2 (217) 2865 2724 m_b87s601i1 3239 chr2qtel1M 186618 AAATGGGAAGGCACTTCAATTTATTGAGTAGGGCAGTGACAGGATAAGAA 186667 i v i vv ivv v i i v v vv v C L2#LINE/L2 2865 AGATGGGAAGCCATTGGAGGGTTTTGAGCAGAGGAGTGACATGATCTGAC 2816 chr2qtel1M 186668 CTGCATTGTAGGA-AATCACTCTACTGGCTGACTGGGT----AATGGCTT 186712 i i i v ii -i --- - v ---- i vi C L2#LINE/L2 2815 TTACGTTTTAAAAGGATCACT---CTGGCTG-CTGTGTTGAGAATAGACT 2770 chr2qtel1M 186713 AGAGGAAAGAGAGCTTTGAGGGAGGCAGATGTAG-CAGTAGACTATT 186758 i? iii vi vv v i v v i-i -i v i C L2#LINE/L2 2769 GNAGGGGGGCAAGGGTGGAAGCAGGGAGAC-CAGTTAGGAGGCTATT 2724 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.30 CpG sites = 23, Kimura (unadjusted) = 43.61 Transitions / transversions = 1.10 (23/21) Gap_init rate = 0.06 (8 / 140), avg. gap size = 1.38 (11 / 8) 704 32.99 4.20 1.57 chr2qtel1M 187089 187707 (812293) C L1ME4c_3end#LINE/L1 (178) 652 18 m_b87s551i0 3240 chr2qtel1M 187089 ATACAATGTTCTCCTGATTCTGTTCACTTCACTTAGCATTAGTTCATTTA 187138 v v ---- i ivi i vv v- C L1ME4c_3end#L 652 ATACAATTTTGT----ATTCTGCTTTTTTCACTTAACATTATATCATA-A 608 chr2qtel1M 187139 AGGTTTCCCAGACTTTTCTGAAATCAGCTTGTTCATCATTTCTTAGAGAC 187188 vi i vii vi viiv i vv v iv i - iv i C L1ME4c_3end#L 607 ACATTTTCCATGTTGCTACATAGTCTTCATAATTATCATTT-TTAATGGC 559 chr2qtel1M 187189 CAAA-AATATTCTTTTATTTTCATATAACACAATTTATTTGACCATTCTC 187237 iiv - iv iivv ?v i v i i i i C L1ME4c_3end#L 558 TGCATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCC 509 chr2qtel1M 187238 CAAGTTATGGGCATCTACTCAATTTACAATTCCTTGCCAGTACAAA--AT 187285 v v vv i i vvivi v ii i i v i -- i C L1ME4c_3end#L 508 CTATTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAAC 459 chr2qtel1M 187286 GCT-------ACATTTTTCCACATGTGGATC---CTTTATCATGTCCTAT 187325 ------- i ivii i i v i--- i v iv vvi C L1ME4c_3end#L 458 GCTGCAATGAACATCTTCGTGCATATAGCTTTTTCCTTCTTTTGAATTAT 409 chr2qtel1M 187326 CTCTTTGGAACCTAGA--CCCAGTGGTGAGATTGTTGGA-CAAAGAATAT 187372 i i i i -- i -- vi ii ii i- ii C L1ME4c_3end#L 408 TTCCTTAGGA--TAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTAT 361 chr2qtel1M 187373 GCACAATTTTATAGTCCTTTGGGCACAGTTCCAAATTACTCTTCAGAATG 187422 v v i ii vivi ii v v i i i i v C L1ME4c_3end#L 360 GAACATTTTTATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAGG 311 chr2qtel1M 187423 GTTGGATAAATTCACAATTCCAGCAACAATACATTAGTGTCACAGTTTCT 187472 v iv i ? v v i ii v ? vv v C L1ME4c_3end#L 310 GTTGTACCAATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCA 261 chr2qtel1M 187473 CCACATCCCTTCCAACATTTGTCATTATCTTTTTGTGTCATCTTGGCCAA 187522 i ? iiv i v vi vv v vvv i v i C L1ME4c_3end#L 260 CCGCANCCTCGCCAGCATTGGGTATTATCAATTTTTTAAATTTTTGCTAA 211 chr2qtel1M 187523 TCTGAGAGGTATGAAGTGGTACCTCAGTGTTATCTTAATTTGCATTT--- 187569 i i v ii i i i v iii --- C L1ME4c_3end#L 210 TTTAATAGGCGTAAAATGGTATCTCATTGTTGCTTTAATTTGCATTTCTT 161 chr2qtel1M 187570 ------ATAATGATTTAGAGCATTTTTTTCATGCTATTAGAAATGGCTTT 187613 ------v ii vv v i - i ivv ivvv ivi? v C L1ME4c_3end#L 160 TGATTACTAGCGAGGTTGAACA-TTTTTCCATGTGTTTGTTTACTANTTG 112 chr2qtel1M 187614 AATTTCTTTATCTGATAAGTGTCTGTTCATAACGTTTGACCATTTATCAA 187663 v i iv ? vv v iv v v v C L1ME4c_3end#L 111 TATTTCCTCTTNTGTGAATTGTCTGTTCATGTCCTTTGCCCATTTATCTA 62 chr2qtel1M 187664 TTGAAG-AATGACTTGTATTGTTATAAATTTGACTCACTTCTCTA 187707 ii -vv i? v - v v v v vi i C L1ME4c_3end#L 61 TTGGGGTCTTGATNTTT-TTCTTATCAATTTGAATGAGCTCTTTA 18 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 42.49 CpG sites = 108, Kimura (unadjusted) = 45.24 Transitions / transversions = 1.16 (108/93) Gap_init rate = 0.03 (19 / 618), avg. gap size = 1.89 (36 / 19) 858 27.00 6.78 2.74 chr2qtel1M 187210 187666 (812334) C L1ME3G_3end#LINE/L1 (395) 529 55 m_b87s551i1 3240 chr2qtel1M 187210 ATATAACACAATTTATTTGACCATTCTCCAAGTTATGGGCATCTACTCAA 187259 v i i i v v v i i vvivi C L1ME3G_3end#L 529 ATATACCATAATTTATTTAACCATTCCCCTATTGATGGACATTTAGGTTG 480 chr2qtel1M 187260 TTTACAATTCCTTGCCAGTACAAA--ATGCT-------ACATTTTTCCAC 187300 v ii i i v -- ------- ii vi C L1ME3G_3end#L 479 TTTCCAATTTTTCGCTATTACAAACAATGCTGCAATGAACATCCTTGTAC 430 chr2qtel1M 187301 ATGTGGATCCTT-TAT-CATGTCC---TATCTCTTTGGAACCTAGA--CC 187343 i?-- - ii- v --- i ? i i -- -- C L1ME3G_3end#L 429 ATGCN--TCCTTGTGCACATGTGCGAGTATTTCTNTAGGA--TAGATNCC 384 chr2qtel1M 187344 CAGTGGTGAGATTGTTGGA-CAAAGAATATGCACAATTTTATAGTCCTTT 187392 ? vi ii i i- ii i - v v iivv C L1ME3G_3end#L 383 NAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGCA-TTTTAAATTTTAAT 335 chr2qtel1M 187393 GGGCACAGTTCCAAATTACTCTTCAGAATGGTTGGATAAATTCACAATTC 187442 i ii -- v i i i i ? i v iv i v i C L1ME3G_3end#L 334 AGATAC--TGCCAAATTGCCCTCCAAAANGGCTGTACCAATTTACACTCC 287 chr2qtel1M 187443 CAGCAACAATACATTAGTGTCACAGTTTCTCCACATCCCTTCCAACATTT 187492 v i i ii v v vv v i i iiv i ? C L1ME3G_3end#L 286 CACCAGCAGTGTATGAGAGTACCCGTTTCCCCACACCCTCGCCAACACTN 237 chr2qtel1M 187493 GTCATTATC---TTTTTGTGTCATCTTGGCCAATCTGAGAGGTATGAAGT 187539 vi ---i i---v i v vi ivi i C L1ME3G_3end#L 236 GATATTATCAANCTTTTA---AATTTTTGCCAATCTGATGGGTGAAAAAT 190 chr2qtel1M 187540 GGTACCTCAGTGTTATCTTAATTTGCATTT---------ATAATGATTTA 187580 i v i i ---------v i vv v C L1ME3G_3end#L 189 GGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGATTACTAGTGAGGTT 140 chr2qtel1M 187581 GAGCATTTTTTT-CATG-CTATTAGAAATGGCTTTAATTTCTTTATCTGA 187628 i i-i -i i vv --- vv i iv v C L1ME3G_3end#L 139 GAGCATCTTTTCATATGTTTATTGGCCAT---TTGTATTTCCTCTTCTGT 93 chr2qtel1M 187629 TAAGTGTCTGTTCATAACGTTTGACCATTTATCAATTG 187666 v v i v v v v v C L1ME3G_3end#L 92 GAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTG 55 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 33.74 CpG sites = 70, Kimura (unadjusted) = 34.81 Transitions / transversions = 1.40 (70/50) Gap_init rate = 0.05 (24 / 456), avg. gap size = 1.83 (44 / 24) 235 29.56 4.76 3.36 chr2qtel1M 187614 187760 (812240) C L1P3_orf2#LINE/L1 (39) 3255 3107 m_b87s551i2 3240 chr2qtel1M 187614 AATTTCTTTATCTGATAAGTGTCTGTTCATAACGTTTGACCATTTATCAA 187663 v iv i v v v i v i v ii C L1P3_orf2#LIN 3255 AATGTCTTCTTTTGAGAAGTGTCTGTTCATATCCTTCGCCCACTTTTTGA 3206 chr2qtel1M 187664 TTGAAGAATGACTTG---TATTGTTATAAATTTGACTCACTTCTCTAGAA 187710 ---i ii vii --- v v i vi v v ii iv i C L1P3_orf2#LIN 3205 T---GGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTAAGTTCCTTGTAG 3159 chr2qtel1M 187711 ATTTTAGAAATGAGGCCTTTATC--ATAAATACTGGCTG--AAAATTTTT 187756 i i v v v i -- ii -- ii -- i C L1P3_orf2#LIN 3158 ATTCTGGATATTAGCCCTTTGTCAGATGGATA--GATTGCAAAAATTTTC 3111 chr2qtel1M 187757 TCCC 187760 C L1P3_orf2#LIN 3110 TCCC 3107 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.57 CpG sites = 25, Kimura (unadjusted) = 38.76 Transitions / transversions = 1.47 (25/17) Gap_init rate = 0.05 (8 / 146), avg. gap size = 1.50 (12 / 8) 302 33.66 8.45 1.65 chr2qtel1M 187996 188563 (811437) C L1MD_orf2#LINE/L1 (738) 2556 1951 m_b87s551i3 3241 chr2qtel1M 187996 TTTGTTTTTCCAGGTGAATTTTGTTAGTATTTTTTCAAC-TCTACAAAGT 188044 ii vi i ivv vv ?i v v i- iv C L1MD_orf2#LIN 2556 TTTGCCTTTCCATATAAATTTTAGAATAANCTTGTCTATATCTACAAAAA 2507 chr2qtel1M 188045 AATTTCTTGGCAGTTTGATTGGTATGGCACTGAATAAGTAGACTGATTTT 188094 vi vi v v v v v ii i ivv ? iii v C L1MD_orf2#LIN 2506 ATCTTGCTGGGATTTTGATAGGAATTGCGTTAAACCTGTANATCAATTTG 2457 chr2qtel1M 188095 AGATAGAATTATTGTTTTTATTATACACGTTGGCT------ACCCATGAG 188138 i i- ivii i i ---- iv ------ i i C L1MD_orf2#LIN 2456 GGG-AGAATTGACATCTTTACTAT----GTTGAGTCTTCCAATCCATGAA 2412 chr2qtel1M 188139 CACTTGACACTCTTCCAATTTCTTATATATAATTTTATTTCTGTGAAAAG 188188 vvv iiiiii v vi v v vv v v v vv C L1MD_orf2#LIN 2411 CACGGTATGTCTCTCCATTTATTTAGATCTTCTTTGATTTCTTTCATCAG 2362 chr2qtel1M 188189 AGTTTTTTAATTGTGTGGATATAATTCCTGGATTTGTCTTGGCAGGGAGA 188238 v v i v vv v i v v iv i vi ivvv C L1MD_orf2#LIN 2361 CGTTTTGTAGTTTTCAGCATACAAGTCCTGTACATGTTTTGTTAGATTTA 2312 chr2qtel1M 188239 CACCCAAATATTTTATATTGTCTCCAGGAATTTTGAATGG---------- 188278 i i i i v v i iv vi v i ---------- C L1MD_orf2#LIN 2311 TACCTAAGTATTTCATTTTTTTTTGAGCGATTGTAAATGGTATTGTATTT 2262 chr2qtel1M 188279 --GATTTCTCTTTCTA---GTTC-TTTCTGCT-----GA--------TGA 188309 --i vv i --- - v iv ----- -------- C L1MD_orf2#LIN 2261 TTAATTTCGGTTTCCACGTGTTCATTGCTAGTATATAGAAATACAATTGA 2212 chr2qtel1M 188310 TTTATATCAGTTTATTTTATGTCCTTCCATTTTGCTAAAGTTGTTAAGTG 188359 v i vv ? i i i v v ii i v iii v --- C L1MD_orf2#LIN 2211 TTTTTGTATGTTNATCTTGTATCCTGCGACCTTGCTGAACTCACTTA--- 2165 chr2qtel1M 188360 TTTGTTTCTTGAGGTTTTTCCGTTGATTCTCTAGAATTCTGTATGT---C 188406 - iv v ii ii v ii i i i v i --- C L1MD_orf2#LIN 2164 -TTAGTTCTAGGAGTTTTTTTGTAGATTCCTTGGGATTTTCTACGTAGAC 2116 chr2qtel1M 188407 AG-CATATCATCTGCAAAGCATGGTAGTTTTGTTTCCTAGTTGTTTACTC 188455 i- i vviv ii i i vv - ii v C L1MD_orf2#LIN 2115 AATCATGTCATCTGCAAATAGGGACAGTTTTATTTCTTCCTT-TCCAATC 2067 chr2qtel1M 188456 TAATTAC--TTCAGTTTCTTTTCTT--TTTACTAAA---GCTAACATTTC 188498 ivv i -- i v i --i i iv --- iv i C L1MD_orf2#LIN 2066 TGTATGCCTTTTATTTCCTTTTCTTGCCTTATTGCACTGGCTAGAACTTC 2017 chr2qtel1M 188499 TAGTACAATGTTGCATTATAGTGATGAAAATGG-CAACATTGTTTCACCC 188547 i v v v v i i ii - v v ii iiii C L1MD_orf2#LIN 2016 CAGTACTATGTTGAATAAGAGTGGTGAGAGCGGACATCCTTGCCTTGTTC 1967 chr2qtel1M 188548 CTGATCTTACTGGGAA 188563 i vv C L1MD_orf2#LIN 1966 CCGATCTTAGGGGGAA 1951 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 44.57 CpG sites = 102, Kimura (unadjusted) = 46.24 Transitions / transversions = 1.19 (102/86) Gap_init rate = 0.04 (24 / 567), avg. gap size = 2.42 (58 / 24) 322 29.91 4.76 3.25 chr2qtel1M 188301 188573 (811427) C L1M1_orf2#LINE/L1 (1074) 2220 1944 m_b87s551i4 3241 chr2qtel1M 188301 TGCTGATGATTTATATCAGTTTATTTTATGTCCTTCCATTTTGCTAAAGT 188350 iv v i vv v i i v v i i i v C L1M1_orf2#LIN 2220 TGCTACTGATTTTTGTATGTTGATTTTGTATCCTGCAACTTTACTGAATT 2171 chr2qtel1M 188351 TGTTAAGTGTTTGTTTCTTGAGGTTTTTCCGTTGATTCTCTAGAATTCTG 188400 v ---- iiv vivi i? v v i iv i v C L1M1_orf2#LIN 2170 TGTTTA----TCAGTTCTAATAGTTTTTTNGTGGAGTCTTTAGGTTTTTC 2125 chr2qtel1M 188401 TA--TGTCAG--CATATCATCTGCAAAGCATGGTAGT--------TTTGT 188438 i -- i v -- vv v i i -------- iv C L1M1_orf2#LIN 2124 CAAATATAAGATCATATCATCTGCAAACAAGGATAATTTGACTTCTTCCT 2075 chr2qtel1M 188439 TTCCTAGTTGTTTACTCTAATTACTTCAGTTTCTTTTCTTTTTACTAAAG 188488 v v vv i i -- i vv i v vv i vv C L1M1_orf2#LIN 2074 TTCCAATTTGGATGCCCT--TTATTTCTTTCTCTTGTCTGATTGCTCTAG 2027 chr2qtel1M 188489 CTAACATTTCTAGTACAATGTTGCATTATAGTGATGAAAAT-GGCAACAT 188537 iv i i v v v i i i - v v C L1M1_orf2#LIN 2026 CTAGGACTTCCAGTACTATGTTGAATAACAGTGGTGAAAGTGGGCATCCT 1977 chr2qtel1M 188538 TGTTTCACCCCTGATCTTACTGGGAATTAGGCTCTC 188573 iviiii v -vi -- i C L1M1_orf2#LIN 1976 TGTCGTGTTCCAGATCTTA-GAGGAA--AGGCTTTC 1944 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.16 CpG sites = 38, Kimura (unadjusted) = 38.77 Transitions / transversions = 0.93 (38/41) Gap_init rate = 0.05 (13 / 272), avg. gap size = 1.69 (22 / 13) 764 33.86 3.49 3.29 chr2qtel1M 189068 189583 (810417) C L2#LINE/L2 (535) 2547 2031 m_b87s601i2 3239 chr2qtel1M 189068 CTTGAAGAAATGGGAAGATAGTGATGCCTCTTCAATAATAGGGAGAGTGT 189117 i iv v i i i v v -v ? v i v v i i--- C L2#LINE/L2 2547 CCTGAGCAACTGGAAGGATGGAGTTGCC-ATTNACTGAGATGGGGAA--- 2502 chr2qtel1M 189118 GAGTGTGTATGTATGAGAATATCTGGGGTAGAA-ATAATAAGTTCTGTTC 189166 v i --- v v v vi i i vi - v vi v i C L2#LINE/L2 2501 GACTGCG---GGAGGAGCAGGTTTGAGGGGGAAGATCAGGAGTTCAGTTT 2455 chr2qtel1M 189167 TG-ATGTATTGAATTTGCGTTTCTAGACTACTGGATATTCAATGTG-AGA 189214 - ii i i i v v v ---- i i i i - - C L2#LINE/L2 2454 TGGACATGTTAAGTTTGAGATGC----CTATTAGACATCCAA-GTGGAGA 2410 chr2qtel1M 189215 CATCTATAAGGAAATTGAAGATATAAAACTAGAGGTCAGCAGAGAAATT- 189263 ii v vv v i i v ii iv i v vi ii i- C L2#LINE/L2 2409 TGTCGAGTAGGCAGTTGGATATACGAGTCTGGAGTTCAGGGGAGAGGTCC 2360 chr2qtel1M 189264 GGGCACAAAAGGGACATTTGAAAATCATCAAAATATAGATAGCAATTAAA 189313 vvi i viv v ii i iv i i v C L2#LINE/L2 2359 GGGCTGGAGATATAAATTTGGGAGTCATCAGCATATAGATGGTATTTAAA 2310 chr2qtel1M 189314 TCCATGGTAGTTGATGAAATCACCAAGAAAAGAAATAATGAGGGAAAAGA 189363 v iv v v i ? ii ivi i ivv vi i C L2#LINE/L2 2309 GCCATGAGACTGGATGAGATCACCNAGGGAGTGAGTGTAGATAGAGAAGA 2260 chr2qtel1M 189364 GAAGAGGAACAAGGATAGAACACCAAGGGACCCATATGGCTGGAAGTT-T 189412 vv iv i v iii v i vv i vi?i i i-v C L2#LINE/L2 2259 GAAGAGGTCCAAGGACTGAGCCCTGGGGCACTCCAACGTTNAGAGGTCGG 2210 chr2qtel1M 189413 TGATCTCAGGAATATC---CAAAAAAGATAGAAAAGAAGTGGTCAGAGAA 189459 v vv v iv v --- ii iv i i i i v -- C L2#LINE/L2 2209 GGAGATGAGGAGGAACCAGCAAAGGAGACTGAGAAGGAGCGGCCAGTG-- 2162 chr2qtel1M 189460 TAGGAAGAAGGGAAATCAAGAGAGAGGGGTGTCCTAAAATCCTAGAGAAC 189509 - v i i i i v v ii v v v v C L2#LINE/L2 2161 -AGGTAGGAGGAAAACCAGGAGAGTGTGGTGTCCTGGAAGCCAAGTGAAG 2113 chr2qtel1M 189510 AGAGAGGATCATAAAGGGAAGA----------GTATCAAAGCCTGAATAA 189549 i v vv vi iii ---------- i vv vvv ? C L2#LINE/L2 2112 AAAGTGTTTCAAGAAGGAGGGAGTGATCAACTGTGTCAAATGCTGCTGAN 2063 chr2qtel1M 189550 AAGTCAAAGGAGAATGAGGATGGAGAAAGTGACC 189583 i - v ii iv - v C L2#LINE/L2 2062 AGGTC-AAGTAAGATGAGGACTGAG-AATTGACC 2031 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.74 CpG sites = 90, Kimura (unadjusted) = 46.65 Transitions / transversions = 1.14 (90/79) Gap_init rate = 0.05 (24 / 515), avg. gap size = 1.46 (35 / 24) 27 0.00 4.76 4.76 chr2qtel1M 190054 190095 (809905) (AATGA)n#Simple_repeat 1 42 (0) c_b87s251i0 3242 chr2qtel1M 190054 AATGAAATGAAAAATGAAATGAAATG-AATG-AATGAAATGAAA 190095 -- - - (AATGA)n#Simp 1 AATGAAATG--AAATGAAATGAAATGAAATGAAATGAAATGAAA 42 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.10 (4 / 41), avg. gap size = 1.00 (4 / 4) 19 10.11 0.00 0.00 chr2qtel1M 190547 190578 (809422) (ACAA)n#Simple_repeat 1 32 (0) m_b87s252i1 3243 chr2qtel1M 190547 ACCAAGAAACAAACAAACAAACAAACAAAAAA 190578 v v v (ACAA)n#Simpl 1 ACAAACAAACAAACAAACAAACAAACAAACAA 32 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 22 10.38 0.00 0.00 chr2qtel1M 191069 191100 (808900) (A)n#Simple_repeat 1 32 (0) m_b87s252i2 3244 chr2qtel1M 191069 AAAAAAAAAAAAAAAAAAAGAAAGAAAAGAAA 191100 i i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 32 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 34 8.53 0.00 0.00 chr2qtel1M 191347 191396 (808604) (T)n#Simple_repeat 1 50 (0) c_b87s251i1 3245 chr2qtel1M 191347 TTTTTTTTTTTTTTTAATTTTTTTTTAATTTTTTTTTTTTTTTTTTTTTT 191396 vv vv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 300 22.39 0.00 0.00 chr2qtel1M 191545 191611 (808389) MIR3#SINE/MIR 78 144 (64) m_b87s601i3 3246 chr2qtel1M 191545 CCAGCTGTGTGACCCGGAGAAAGCCACTCCAGCCCTTTTGTCCCCAGTGT 191594 i? iv i v i i v i i v v i v MIR3#SINE/MIR 78 CTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTT 127 chr2qtel1M 191595 CCTCATCTGGAAAATGA 191611 v MIR3#SINE/MIR 128 CCTCATCTGTAAAATGA 144 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.38 CpG sites = 8, Kimura (unadjusted) = 27.38 Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.0 (0 / 0) 13 7.86 7.41 0.00 chr2qtel1M 194067 194093 (805907) (CCT)n#Simple_repeat 1 29 (0) m_b87s252i3 3247 chr2qtel1M 194067 CCGCCTCC-CATCC-CCTCCTCCTCCTCC 194093 v - v - (CCT)n#Simple 1 CCTCCTCCTCCTCCTCCTCCTCCTCCTCC 29 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.08 (2 / 26), avg. gap size = 1.00 (2 / 2) 180 3.37 0.00 10.00 chr2qtel1M 194739 194771 (805229) C L3#LINE/CR1 (1116) 2983 2954 m_b87s601i4 3248 chr2qtel1M 194739 GACTTTGTGCAACTCTGCCTTGCTGAAATCCAG 194771 - v -- C L3#LINE/CR1 2983 GACTTTGT-CAAAT--GCCTTGCTGAAATCCAG 2954 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 3.42 CpG sites = 0, Kimura (unadjusted) = 3.42 Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.09 (3 / 32), avg. gap size = 1.00 (3 / 3) 208 32.84 16.67 0.60 chr2qtel1M 194920 195063 (804937) MamRTE1#LINE/RTE-BovB 336 502 (3310) m_b87s601i5 3249 chr2qtel1M 194920 TCACTG--GACACAGCGGTGGGATCTAGCAGCCCCTTAGATGTATGAGC- 194966 i -- vi i iivvi iii v? i i i v - MamRTE1#LINE/ 336 TCGCTGANGAGGCAGCAGCACCGTTCGGCAGCGNCCTGGGTGTCTGAGCA 385 chr2qtel1M 194967 --TCTGAAAAAAAAAA------TCCCCCTGGTATGAGGAAGAGACCAGAA 195008 --i vvv ii ?vi------ v i i i- i i ? i MamRTE1#LINE/ 386 GCCCTGTTTAGGANCGCGCTGCTCACTCCGA-ATGGGGAAGGGNCTAGAA 434 chr2qtel1M 195009 AAGGTGCACTAAAAAT---CTGCTT------AATCAGCCCTGGCCTGTC- 195048 v vi --- i ------ ? iv? iiii - MamRTE1#LINE/ 435 AAGGTGCCCTAAACGTTGCCTGCCTCGCCAAANTCAAANCTGGCTCACCA 484 chr2qtel1M 195049 ---TACCATGGTTGGTGG 195063 --- i ii vi MamRTE1#LINE/ 485 GATTATCGCGTCTGGTGG 502 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.78 CpG sites = 33, Kimura (unadjusted) = 49.01 Transitions / transversions = 2.36 (33/14) Gap_init rate = 0.06 (9 / 143), avg. gap size = 2.78 (25 / 9) 22 14.94 0.00 0.00 chr2qtel1M 195076 195112 (804888) (AC)n#Simple_repeat 1 37 (0) m_b87s252i4 3250 chr2qtel1M 195076 ACAGAAATACAGACACACACAAACACACACACACACA 195112 v v i v v (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACA 37 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 258 33.29 9.33 1.86 chr2qtel1M 195391 195540 (804460) MamRTE1#LINE/RTE-BovB 1140 1300 (2512) m_b87s601i6 3249 chr2qtel1M 195391 ATCACCAACGCGGTCTTCTGCTAACTTAA-AAGCAACAGAACTTCATGGG 195439 i vi i iv iv - vi v - v i MamRTE1#LINE/ 1140 ATCACCAACACCATCTTCCGCCTACCGAATAAGAGAAAG-ACATCATGGA 1188 chr2qtel1M 195440 TGCACTTTTACAG--CAAACACTGTCATTTAGTAGACTATATAATTATAA 195487 --ii vi --i i v v i vi v i v ii vv MamRTE1#LINE/ 1189 TGCAC--CCAAGGTCTAAGCAGTGGCATCTCATTGATTATATCATCGTTC 1236 chr2qtel1M 195488 GA-AACAGGA--TAGAGAATG--------ACAAAGGCCATATGTGAGGCA 195526 - i i -- ii i -------- vivi i ii iv v MamRTE1#LINE/ 1237 GACAGCGGGACCTGAAGGATGTTTAGATTACTGCAGCTATGCGTGGCGCC 1286 chr2qtel1M 195527 GAATGATGGACTGA 195540 i v i MamRTE1#LINE/ 1287 GAGTGCTGGACCGA 1300 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.53 CpG sites = 30, Kimura (unadjusted) = 46.02 Transitions / transversions = 1.58 (30/19) Gap_init rate = 0.05 (8 / 149), avg. gap size = 2.12 (17 / 8) 408 31.13 6.03 3.51 chr2qtel1M 197301 198079 (801921) L1M5_orf2#LINE/L1 828 1625 (1669) m_b87s551i5 3251 chr2qtel1M 197301 GAATGACAATAATGACACA-TATAACAAAAACTTACGGAATACA-CTAAA 197348 ? i vi i -i v -i ii i i - L1M5_orf2#LIN 828 GAATGANAATGAAAATACAACATATCAAAA-TTTGTGGGATGCAGCTAAA 876 chr2qtel1M 197349 G-------TAGAAGAAATTTTACACCTCTGAATATTTACAT----AAATA 197387 ------- i i v i v ?i i ii? i ---- v L1M5_orf2#LIN 877 GCAGTGCTTAGAGGGAAATTTATAGCNTTAAATGCNTATATTAGAAAAGA 926 chr2qtel1M 197388 AAATAG-----AGATCAATGAATTGATTATACAACT-AAAAAGCTAGAAA 197431 i v ----- i vi i viv v v - i L1M5_orf2#LIN 927 AGAAAGGCTTAAAATCAATGATCTAAGCTTCCACCTTAAGAAGCTAGAAA 976 chr2qtel1M 197432 AG--AGAACAAATTTTTAAAATCCCAATTAAATAGTAAATTAGATATTTT 197479 i-- i ---- i v v? i v iivvi v vv L1M5_orf2#LIN 977 AAGAAGAGCAAATT----AAACCCAAAGNAAGTAGAAGGAAGGAAATAAT 1022 chr2qtel1M 197480 AAAAATCTAAGAAGGGATAAATTCTCTTCTTCCTTTGAAGAAAATGGAAA 197529 i -- -- v v i-------------- vi i L1M5_orf2#LIN 1023 AAAGAT--AAGA--GCAGAAATC--------------AATGAAATAGAAA 1054 chr2qtel1M 197530 GTAAGGAAACTATTAAACTAATAAGTAAAATTAAAACTTGATTAT--GAA 197577 ii i? ? v vi ivv v iii iii vi i v -- L1M5_orf2#LIN 1055 ACAAANANACAATAGAGAAAATCAACGAAGCCAAAAGCTGGTTCTTTGAA 1104 chr2qtel1M 197578 AA-ATTAATAAAGCAGATGAAGTTTT---TAATTTGATTAGAAAAAGAAG 197623 - i iiv i vi i ---? ivi i ii i L1M5_orf2#LIN 1105 AAGATCAATAAAATTGATAAACCTCTAGCNAGACTGATCAAGAAAAAAAG 1154 chr2qtel1M 197624 -GA-AAG---CAAATTACTAGTATCAA-AATGAAAAGGGTAAAGTTACCA 197667 - - --- i i i- i vi vi i i L1M5_orf2#LIN 1155 AGAGAAGACACAAATTACCAATATCAGGAATGAAAAAGGAGACATCACTA 1204 chr2qtel1M 197668 GCAATGAAGAAGAAATTAAA-GCATGA-AGTAGGACCTATTTTGCTCAAC 197715 vvi vvviv v - v i - iv i -- v vv L1M5_orf2#LIN 1205 CAGATCCTACAGACATTAAAAGGATAATAAGAGAA--TATTATGAACAAC 1252 chr2qtel1M 197716 TGTTTGCCAACAAATCAGACCATTTAATTGAAATGGATGAATATTTGCAG 197765 v v i iv ?v i iv ii vii vv i L1M5_orf2#LIN 1253 TTTATGCCAATAAATTTGANAACTTAGATGAAATGGACAAATTCCTTGAA 1302 chr2qtel1M 197766 AAACATAAATTGCCCATATTAACAGAAGAAAAAGTAAAATGCTAAAATAA 197815 i ? i v v i i ?v i i i viiivi i L1M5_orf2#LIN 1303 AAACACAANTTACCAAAACTGACNCAAGAAGAAATAGAAAATCTGAATAG 1352 chr2qtel1M 197816 CCCCAT-TTTAAAAATAGAAATTAAACAAGTCAATGAA----TTCCCAAA 197860 i - i vv - i ivv v v i ---- v L1M5_orf2#LIN 1353 CCCTATATCTATTAA-AGAAATTGAATTTGTAATTAAAAACCTTCCCACA 1401 chr2qtel1M 197861 GAAAAAATCTCCAGGGTGAGATGAATTTGCAAGGACATTCTACCAAATAT 197910 i i - viv iv ii vi viv i L1M5_orf2#LIN 1402 AAGAAAA-CTCCAGGCCCAGATGGCTTCACTGGTGAATTCTACCAAACAT 1450 chr2qtel1M 197911 TTAGGGAACAATTAATTCTGGATATAATGTAAACTACTTGAAAAGATAGG 197960 i v v v i-i v v iii vi iv i i i L1M5_orf2#LIN 1451 TTAAGGAAGAAATAATACC-AATCTTACACAAACTCTTCCAGAAAATAGA 1499 chr2qtel1M 197961 TGAAGAATGATTGTTAGCTAATTCATTTTATGACACAAATATGGTGCTAG 198010 vi iv viii vv i i vi v ii ?iiv ii L1M5_orf2#LIN 1500 AAAAGAGGGAACACTTCCCAACTCATTTTATGAGGCCAGCATNACCCTGA 1549 chr2qtel1M 198011 ----AAAATAGGA-AGAGCTAAAACA--GAAAGAAAATTATAGACCAATT 198053 ---- iv? - i vi vv --i i v L1M5_orf2#LIN 1550 TACCAAAACCNGACAAAGACATTACAAGAAAAGAAAATTACAGACCAATA 1599 chr2qtel1M 198054 TCCCTAATAAATATTGATGCAAAGAT 198079 v i i v i L1M5_orf2#LIN 1600 TCCCTCATGAACATAGATGCAAAAAT 1625 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 42.34 CpG sites = 140, Kimura (unadjusted) = 42.61 Transitions / transversions = 1.49 (140/94) Gap_init rate = 0.06 (49 / 778), avg. gap size = 1.53 (75 / 49) 428 21.20 7.00 0.94 chr2qtel1M 198108 198207 (801793) MIRc#SINE/MIR 10 115 (153) m_b87s601i7 3252 chr2qtel1M 198108 GTGGCGCAGTGGATAGAGCACCAGACCTGAAGTCAAGAAGACCTGAGTTC 198157 i v ii i i i i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr2qtel1M 198158 AAATATGGCCTCCAGACACTTAACA-CT------TCCTGGGCAAGTCACT 198200 i i viv v i- v vi - ------i i MIRc#SINE/MIR 60 GAGTCCCGGCTCT-GCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACT 108 chr2qtel1M 198201 TAACCCC 198207 i MIRc#SINE/MIR 109 TAACCTC 115 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.42 CpG sites = 15, Kimura (unadjusted) = 25.83 Transitions / transversions = 2.50 (15/6) Gap_init rate = 0.03 (3 / 99), avg. gap size = 2.67 (8 / 3) 215 39.24 4.28 0.52 chr2qtel1M 199633 199819 (800181) C L2#LINE/L2 (496) 2586 2393 m_b87s601i8 3253 chr2qtel1M 199633 GAGAGATAATGCAGTTAAGAATAAAATTGGGATTATTAATATTGGTGACT 199682 i v iv v i i i vviiii i v iiiv vi ii C L2#LINE/L2 2586 GAGAAAGAGAGGAGTCAAGGATGACTCCAAGGTTTTTGGCCTGAGCAACT 2537 chr2qtel1M 199683 GGAGGAGTGATGGTACC-----CTCAAGGAAGGAAATATG-GAGAGGGGG 199726 i ii iv v i ----- v iivii ivv - i i v C L2#LINE/L2 2536 GGAAGGATGGAGTTGCCATTNACTGAGATGGGGAAGACTGCGGGAGGAGC 2487 chr2qtel1M 199727 ATGATCTG--GGGAAAGGTAATAGGTTTTGTTGTGGATATGGTGAGTTGG 199774 - i i -- i i v vii iv v i v i v C L2#LINE/L2 2486 A-GGTTTGAGGGGGAAGATCAGGAGTTCAGTTTTGGACATGTTAAGTTTG 2438 chr2qtel1M 199775 AGATGCCCGTTAGCTATGTAATTCAAAATGTCTGGTAGCTATTTG 199819 ii vi vi v vi i vi vi v C L2#LINE/L2 2437 AGATGCCTATTAGACATCCAAGTGGAGATGTCGAGTAGGCAGTTG 2393 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 59.27 CpG sites = 45, Kimura (unadjusted) = 59.27 Transitions / transversions = 1.61 (45/28) Gap_init rate = 0.02 (4 / 186), avg. gap size = 2.25 (9 / 4) 12 10.03 0.00 0.00 chr2qtel1M 204281 204302 (795698) (ACAT)n#Simple_repeat 1 22 (0) m_b87s252i5 3254 chr2qtel1M 204281 ACATACATACATACACACACAC 204302 i i (ACAT)n#Simpl 1 ACATACATACATACATACATAC 22 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 1225 29.53 0.81 0.81 chr2qtel1M 206116 206610 (793390) L1ME3G_3end#LINE/L1 54 548 (376) m_b87s551i6 3255 chr2qtel1M 206116 CTAATTGATAAATGGTCAAAGGATATGAACAGACAATTTTCAGATGATGA 206165 i v v v i iv v v L1ME3G_3end#L 54 CCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGGA 103 chr2qtel1M 206166 AATTGAAACTATTACCACTCATATGAAAGAGTGTTCCAAATCACTATTAA 206215 vv iviii vi vv iii i v vv v L1ME3G_3end#L 104 AATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTAA 153 chr2qtel1M 206216 TCAGAGAAATACAAATTAAGACAACTCTGAGATACCACTACCCACCTGTC 206265 i i i vv i vii ii L1ME3G_3end#L 154 TCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCATC 203 chr2qtel1M 206266 AGATTGACTAGAA-TGACAGGAAAAATAACGACGAATGTTGGAG-GGATG 206313 i v i - v v i ?vvi iiv ? i v - i L1ME3G_3end#L 204 AGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGTG 253 chr2qtel1M 206314 TGGGAGAACTGGGACACTGATGCCTTGTTGGTGGAGTTGTGAACGAATCC 206363 ii v v v v i vi i iiv i ivii v L1ME3G_3end#L 254 TGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTAC 303 chr2qtel1M 206364 AATCATTCTGGAGAGAAATCTGGAATTATGCCCAAAAGTTATCAAACTGT 206413 ii ? i i v i v v viviv i -- i v i L1ME3G_3end#L 304 AGCCNTTTTGGAGGGCAATTTGGCAGTATCTATTAAAAT--TTAAAATGC 351 chr2qtel1M 206414 GCATACCCTTTGACCCAGCAGTACTACTACTGGGCTTATA-CCCAAAGAG 206462 i v i v ? ?v v - i ? i L1ME3G_3end#L 352 GCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAGAA 401 chr2qtel1M 206463 ATACCAATAGAAG-GGAAAGGGACCCGTATGTGCCAAAATGTTTGTGGCA 206511 ivii v v - v v i --? i i v ii ii v L1ME3G_3end#L 402 ATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTCATTGCA 449 chr2qtel1M 206512 GCCCTGTTTGTAGTAGCTAGAAACTGGAAACTGAAGGGATGCCCATCCAT 206561 vi i v i i vivvvii i v L1ME3G_3end#L 450 GCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCAAT 499 chr2qtel1M 206562 TGGAGAATGCTTGGGCAAATTGTGGTATATGAATGTTAAGGAATGTTAT 206610 v i v iiii i vv ii v ii L1ME3G_3end#L 500 AGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACTAT 548 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.44 CpG sites = 81, Kimura (unadjusted) = 39.14 Transitions / transversions = 1.27 (81/64) Gap_init rate = 0.02 (8 / 494), avg. gap size = 1.00 (8 / 8) 38 15.83 0.00 0.00 chr2qtel1M 206884 206947 (793053) (T)n#Simple_repeat 1 64 (0) m_b87s252i6 3256 chr2qtel1M 206884 TTTTTATTTTTATTTTTTTTTTTTAATTTTTTATTTATTTTTTTTTGTTG 206933 v v vv v v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr2qtel1M 206934 TTGTTTTTTTTTTT 206947 v (T)n#Simple_r 51 TTTTTTTTTTTTTT 64 Matrix = Unknown Transitions / transversions = 0.00 (0/9) Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0) 278 25.54 8.09 5.00 chr2qtel1M 208875 209010 (790990) C MIR3#SINE/MIR (1) 207 68 m_b87s601i9 3257 chr2qtel1M 208875 AAGCATCAAAGTCATGAGACAT-AGAGCTGAAAGTCACTTCAGAATTCAA 208923 v - i i iii ii - i vv i i iv -- C MIR3#SINE/MIR 207 AATCAT-AGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATC-- 161 chr2qtel1M 208924 GAATCCAA-CCAACCCTCCCCAATTTACAG--GAGGAAAGTCAAG--CAG 208968 -- i i- - i v -- v v i -- C MIR3#SINE/MIR 160 --ATCTAGTCCAACCC-CCTCATTTTACAGATGAGGAAACTGAGGCCCAG 114 chr2qtel1M 208969 AGA----AAG-GATTTGCTCAAAGCTCATGCCATTTGTGAGTGTCAG 209010 ---- - i i i - ii vii?v v v C MIR3#SINE/MIR 113 AGAGGTGAAGTGACTTGCCCAAGG-TCACACAGCNAGTTAGTGGCAG 68 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.79 CpG sites = 22, Kimura (unadjusted) = 32.79 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.10 (13 / 135), avg. gap size = 1.38 (18 / 13) 12 19.17 2.13 6.67 chr2qtel1M 212525 212571 (787429) (TTCTT)n#Simple_repeat 1 45 (0) m_b87s252i7 3258 chr2qtel1M 212525 TTCATTTTCTTTTCTCTTTTTTTTCCCTTTATGATC-TGACTTTTCTT 212571 - - i - i v vv - vv (TTCTT)n#Simp 1 TTC-TTTTCTTTTCT-TTTCTTTT-CTTTTCTTTTCTTTTCTTTTCTT 45 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.09 (4 / 46), avg. gap size = 1.00 (4 / 4) 13 29.24 1.61 3.28 chr2qtel1M 212618 212679 (787321) (TTTAT)n#Simple_repeat 1 61 (0) m_b87s252i8 3259 chr2qtel1M 212618 TTTATTTTATTTAATATT-TGCAATAATATTTGCAAAAATATTTTATTTT 212666 v v - viv vv --v vvv (TTTAT)n#Simp 1 TTTATTTTATTTTATTTTATTTTATTTTATTT--TATTTTATTTTATTTT 48 chr2qtel1M 212667 ATTTAGGTTTATT 212679 viv (TTTAT)n#Simp 49 ATTTTATTTTATT 61 Matrix = Unknown Transitions / transversions = 0.17 (2/12) Gap_init rate = 0.05 (3 / 61), avg. gap size = 1.00 (3 / 3) 364 27.03 0.90 6.67 chr2qtel1M 212876 212986 (787014) C MIRc#SINE/MIR (141) 127 23 m_b87s601i10 3260 chr2qtel1M 212876 CTGAGGC-AATTGGGGTTAAGGGACTTGCCTAGGGTTACACAGATAAGAA 212924 -v vv i v i i i v i--- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG--- 81 chr2qtel1M 212925 GTGTTAAGTGTCTGAGGTCAGATTTGAACTCAGGTCCTCCTGACTTCAGG 212974 ---- v v vivi i i i i i i C MIRc#SINE/MIR 80 ----TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr2qtel1M 212975 GATGGTGATTTT 212986 vvii v i C MIRc#SINE/MIR 34 TCCAGTGCTCTT 23 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.15 CpG sites = 16, Kimura (unadjusted) = 34.06 Transitions / transversions = 1.33 (16/12) Gap_init rate = 0.07 (8 / 110), avg. gap size = 1.00 (8 / 8) 12 8.85 4.17 0.00 chr2qtel1M 213676 213699 (786301) (CTC)n#Simple_repeat 1 25 (0) m_b87s252i9 3261 chr2qtel1M 213676 CTCCTCCTTC-CCTCCACCTCCTCC 213699 i - v (CTC)n#Simple 1 CTCCTCCTCCTCCTCCTCCTCCTCC 25 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 12 24.48 0.00 8.77 chr2qtel1M 214488 214549 (785451) (CTCTGA)n#Simple_repeat 1 57 (0) m_b87s252i10 3262 chr2qtel1M 214488 CTCTGAATCCTGGCTCTGAATCTCCCAACTGATTTCTGGCTCTCAATCTC 214537 v - i v vv -v -i i v v v (CTCTGA)n#Sim 1 CTCTGACT-CTGACTCTGACTCTGAC-TCTGA-CTCTGACTCTGACTCTG 47 chr2qtel1M 214538 ATCTACTGACTC 214549 - - (CTCTGA)n#Sim 48 A-CT-CTGACTC 57 Matrix = Unknown Transitions / transversions = 0.38 (3/8) Gap_init rate = 0.08 (5 / 61), avg. gap size = 1.00 (5 / 5) 352 29.04 4.00 4.64 chr2qtel1M 214992 215316 (784684) L1MC4a_3end#LINE/L1 310 632 (1997) m_b87s551i8 3263 chr2qtel1M 214992 TTTTGGAGAGTAGTTTGGAACTATGCTCAAAAAGTTATCAAACTGTGCAT 215041 ? i v i v v - v v ii - --- i L1MC4a_3end#L 310 TTNTGGAGGGGAATTTGGCAATAT-CTAACAAAACTA-CA---TATGCAT 354 chr2qtel1M 215042 --ACCCTTTGATCCAGCAGTGTTACTACTGGGATTATATCCCAAAGAGAT 215089 -- i i vii v i v v i ii --- L1MC4a_3end#L 355 TTACCCTTTGACCCAGCAATCCCACTTCTAGGAATTTACCCTGAAGA--- 401 chr2qtel1M 215090 TATA-----AAGAAG-GGAAAGGGACCTGTATGTGCACGAATGTTTGTGG 215133 i ----- v v -iv iv? --i ii v iv i ii v L1MC4a_3end#L 402 TACACCTCCAACATGTACAAAATNAC--ATATGCACAAGGTTATTCATTG 449 chr2qtel1M 215134 CAGCCCTCTTTGTAGTGGCTAGAAACTGGAAACTGAATGGATGCCCATCA 215183 vi v i v v i v i vivv ii ?? L1MC4a_3end#L 450 CAGCATTGTTTGTAATTGCAAAATATTGGAAACAACCTAAATGCCCATNN 499 chr2qtel1M 215184 GTTGGAGAATGGCTGAATAAATTGTGGTATATGAAAATTATGGAATAT-- 215231 i v ? i i i i vv v iv i i-- L1MC4a_3end#L 500 ATAGGAGANTGGTTGAATAAACTATGGTACATCCACACAATGGAGTACTA 549 chr2qtel1M 215232 TGCTGTTCTGTAAGAAATGACCAACAGGATGATTTC-AGAAA--GGCCTG 215278 v -- i - -- vv v i - vi -- iiv L1MC4a_3end#L 550 TGCAG--CTGTAAAAAA-GA--ATGAGGAAGATCTCTATGAACTGATATG 594 chr2qtel1M 215279 GAGAGACTTACACGAACTGATGCTGAGTGAAATGAGCA 215316 v i v v vv iv i i vi L1MC4a_3end#L 595 GAGTGATTTCCAGGATATATTGTTAAGTGAAAAAAGCA 632 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.17 CpG sites = 48, Kimura (unadjusted) = 38.17 Transitions / transversions = 1.14 (48/42) Gap_init rate = 0.06 (21 / 324), avg. gap size = 1.33 (28 / 21) 636 27.97 2.07 2.07 chr2qtel1M 214992 215232 (784768) L1ME4c_3end#LINE/L1 313 553 (277) m_b87s551i7 3263 chr2qtel1M 214992 TTTTGGAGAGTAGTTTGGAACTATGCTCAAAAAGTTATCAAACTGTGCAT 215041 i i i v v i iviv i ii v v v L1ME4c_3end#L 313 TTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAAAATGTTCAT 362 chr2qtel1M 215042 ACCCTTTGATCCAGCAGTGTTACTACTGGGATTATATCCCAAAGAGATTA 215091 i i i vii v v v i i i v L1ME4c_3end#L 363 ACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAA 412 chr2qtel1M 215092 T---AAAGAAGGGAAAGGGACCTGTATGTGCACGA--ATGTTTGTGGCAG 215136 --- i i -----v i -- ii v L1ME4c_3end#L 413 TTCAAAAGAAGGAAAAAG-----CTATATGCACGAAGATGTTCATTGCAG 457 chr2qtel1M 215137 CCCTCTTTGTAGTGGCTAGAAACTGGAAACTGAATGGATGCCCATCAGTT 215186 vi v i i i v i i vivv ii i v i v L1ME4c_3end#L 458 CGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAATA 507 chr2qtel1M 215187 GGAGAATGGCTGAATAAATTGTGGTATATGAAAATTATGGAATATT 215232 i i i i i i v? vviv L1ME4c_3end#L 508 GGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATATT 553 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.86 CpG sites = 40, Kimura (unadjusted) = 36.24 Transitions / transversions = 1.54 (40/26) Gap_init rate = 0.03 (7 / 240), avg. gap size = 1.43 (10 / 7) 17 4.94 0.00 0.00 chr2qtel1M 215772 215792 (784208) (A)n#Simple_repeat 1 21 (0) m_b87s252i11 3264 chr2qtel1M 215772 AAATAAAAAAAAAAAAAAAAA 215792 v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAA 21 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 256 32.11 5.18 0.76 chr2qtel1M 215793 216043 (783957) L1M1_orf2#LINE/L1 1959 2220 (1074) m_b87s551i9 3265 chr2qtel1M 215793 AAGATCAGGGGTGAAACAATGTTGCC-ATTTTCATCACTATAATGCAACA 215841 v iiiivi v v - i i i v v L1M1_orf2#LIN 1959 AAGATCTGGAACACGACAAGGATGCCCACTTTCACCACTGTTATTCAACA 2008 chr2qtel1M 215842 TTGTACTAAAAATGATAGCTTTAGTAAAAAGAAAAGAAATTGAAGTAATT 215891 v ii i vv vv i vv v i vv i -- L1M1_orf2#LIN 2009 TAGTACTGGAAGTCCTAGCTAGAGCAATCAGACAAGAGAAAGAAATAA-- 2056 chr2qtel1M 215892 AGAGAAAACAACTAGGAAACAAA--------ACTACCATGCTTTGAAGAT 215933 i v vv v v vi -------- i i v vv v L1M1_orf2#LIN 2057 AGGGCATCCAAATTGGAAAGGAAGAAGTCAAATTATCCTTGTTTGCAGAT 2106 chr2qtel1M 215934 GATATGCTG----ACCTACAGAATTCTAGAGAATCAACTGAAAAACTACA 215979 v v---- ii iv i vi i v v ?i iv L1M1_orf2#LIN 2107 GATATGATCTTATATTTGGAAAAACCTAAAGACTCCACNAAAAAACTATT 2156 chr2qtel1M 215980 AGAAACACTTAACAACTTTAGCATAATGGAAGGACATAAAATAAACCGAT 216029 viiv v v i i v i v v i i v vv i L1M1_orf2#LIN 2157 AGAACTGATAAACAAATTCAGTAAAGTTGCAGGATACAAAATCAACATAC 2206 chr2qtel1M 216030 ATAAATCATCAGCA 216043 v vi L1M1_orf2#LIN 2207 AAAAATCAGTAGCA 2220 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.75 CpG sites = 35, Kimura (unadjusted) = 42.42 Transitions / transversions = 0.78 (35/45) Gap_init rate = 0.02 (5 / 250), avg. gap size = 3.00 (15 / 5) 267 33.16 2.02 1.00 chr2qtel1M 216143 216340 (783660) L1P1_orf2#LINE/L1 2350 2549 (745) m_b87s551i10 3266 chr2qtel1M 216143 AATTAAAAAATACTTTTCACAGAAATATAATTATATATAAGAAATTGGAA 216192 i v vi vi v? v vviv i iv v L1P1_orf2#LIN 2350 AACTACAAACCACTGCTCAANGAAATAAAAGAGGATACAAACAAATGGAA 2399 chr2qtel1M 216193 GAGTGTCAAGTGCTCATGGGTAGCCAACGT--GTATAATAAAAACAATAA 216240 iii ivvi vv ivi --i vi i iiiiv L1P1_orf2#LIN 2400 GAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAATGGCCA 2449 chr2qtel1M 216241 TTCTATCTAAAATCAATCTACTTATTCAGTGCCATACCAATCAAACTGCC 216290 v ii i ii - i ivv i v v i i L1P1_orf2#LIN 2450 TACTGCCCAAGGT-AATTTATAGATTCAATGCCATCCCCATCAAGCTACC 2498 chr2qtel1M 216291 AAGAAATTACTTTATAGAGATGAAAAAATACTAA--CAAAATTCATCTGG 216338 vi v v i i iv i - v--i i v L1P1_orf2#LIN 2499 AATGACTTTCTTCACAGAATTGGAAAAA-ACTACTTTAAAGTTCATATGG 2547 chr2qtel1M 216339 AA 216340 L1P1_orf2#LIN 2548 AA 2549 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 44.52 CpG sites = 37, Kimura (unadjusted) = 45.48 Transitions / transversions = 1.32 (37/28) Gap_init rate = 0.02 (4 / 197), avg. gap size = 1.50 (6 / 4) 236 28.27 2.03 2.03 chr2qtel1M 216243 216390 (783610) L1M3_orf2#LINE/L1 2446 2593 (695) m_b87s551i11 3266 chr2qtel1M 216243 CTATCTAAAATCAATCTACTTATTCAGTGCCATACCAATCAAACTGCCAA 216292 i i i- i vv i v v v v v L1M3_orf2#LIN 2446 CTACCCAAAG-CGATCTACAGATTCAATGCAATCCCTATCAAAATCCCAA 2494 chr2qtel1M 216293 -GAAATTACTTTATAGAGAT-GAAAAAATACTAACAAAATTCATCTGGAA 216340 - iv -i i i - i v vvi v L1M3_orf2#LIN 2495 TGGCATT-TTTTACAGAAATAGAAAAAACAATCCTAAAATTCATATGGAA 2543 chr2qtel1M 216341 GAACGAAAAGTCACAAATA-TCAAGGGAATTAATGAAAAAAAAATGCAAA 216389 vv i iii v i -i i v i-v i i ivi L1M3_orf2#LIN 2544 CCACAAAAGACCCCGAATAGCCAAAGCAATC-TTGAGAAAGAAGAACAAA 2592 chr2qtel1M 216390 G 216390 L1M3_orf2#LIN 2593 G 2593 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.07 CpG sites = 23, Kimura (unadjusted) = 36.25 Transitions / transversions = 1.28 (23/18) Gap_init rate = 0.04 (6 / 147), avg. gap size = 1.00 (6 / 6) 13 20.44 2.44 2.44 chr2qtel1M 216765 216805 (783195) (ATTAA)n#Simple_repeat 1 41 (0) m_b87s252i12 3267 chr2qtel1M 216765 ATGAAATGCAAAATAGA-TAATTTTAATTATATTAAATTAAA 216805 v -i v i - v v v (ATTAA)n#Simp 1 ATTAAAT-TAAATTAAATTAAATTAAATTAAATTAAATTAAA 41 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 787 33.12 2.33 1.86 chr2qtel1M 216908 217550 (782450) L1ME4c_3end#LINE/L1 7 652 (178) m_b87s551i12 3268 chr2qtel1M 216908 TCTAAAATATGTAGAGAAGCGAGTTAAATTTATAAGAATGCAAGTCATT- 216956 ?v ? i i iviv v i v -iv ?i vv- L1ME4c_3end#L 7 TCTNTANTATATAAAGAGCTCATTCAAATTGATAAGAA-AAANATCAAGA 55 chr2qtel1M 216957 CCTCAGTTGATAAATGATCAAAGGATATAAACAGACACTTTTCCGATAAA 217006 i i v iv i i v iv v? vi i L1ME4c_3end#L 56 CCCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAG 105 chr2qtel1M 217007 GAAATTAAAGCATTT--CTAATATTATGACAAAAAATGCTCTAAATCATT 217054 vv ?i v v-- v i i- i-- i v vv ii L1ME4c_3end#L 106 GAAATACAANTAGTAAACAAACAC-ATGG--AAAAATGTTCAACCTCGCT 152 chr2qtel1M 217055 ATTGATCAGAGAAAAGCAAATTAAGACAACTCTGAGGTACCACCTCACAC 217104 v i i v ii vv i ii i i L1ME4c_3end#L 153 AGTAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGC 202 chr2qtel1M 217105 CTCTCAGATTGGCCAAGATGACAGGAACAGATAATGACAAATTTTGGAAG 217154 v i i i v i vvv ii iv iv v vi vii L1ME4c_3end#L 203 CTATTAAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGCTGGCGA 252 chr2qtel1M 217155 GGATGTGGGAAAACTGGGACACTAATGCAGTGTTGGTAGAATTGTGAATT 217204 ? i vi v ? v i v i i v ? i L1ME4c_3end#L 253 GGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATT 302 chr2qtel1M 217205 TATCCAAACATTCTCAAGAGTAATTTGGAACTGTGCTCAAAGGACTATAA 217254 vi v v v i vi i i v v ii iviv ii i L1ME4c_3end#L 303 GGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAA 352 chr2qtel1M 217255 AATTGTGCATACCCTTAGTTCCAACATTCTCATTACTGGGTCTAGATTCC 217304 v v v vi ii v ii i v vv vv i i L1ME4c_3end#L 353 AAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCT 402 chr2qtel1M 217305 AAAGAGATAGTAGGACATGATAAAGAATCCACATGTGGGAAAATGT---- 217350 i i i vvi v vi vi i v i i iiv i ---- L1ME4c_3end#L 403 AAGGAAATAATTCAAAAGAAGGAAAAAGCTATATGCACGAAGATGTTCAT 452 chr2qtel1M 217351 ---AGCAT--TTTGTACTGGCAAGGAACTGGAAATTGAGTAGATGCCCAT 217395 --- i -- i v i i ii i ivivv i i v L1ME4c_3end#L 453 TGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAA 502 chr2qtel1M 217396 CACTTAGAAAATGGCCAAATAAATTGTGTTATATGAAAGTAAAGGAATAT 217445 v vi ii ii i i v i v? vvii v L1ME4c_3end#L 503 CAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATAT 552 chr2qtel1M 217446 TTTTGGTCTATAAGAAATGATGA--A-GAAGATGATTTCAGAAAAGTCTG 217492 v vviv i v i i -- - iv v - v --iv L1ME4c_3end#L 553 TATGCAGCCATTAAAAATGATAATTATGAAGACTATGT-AGCAA--CATG 599 chr2qtel1M 217493 GGAAACCTTAAATGAACTGATGCTAAGTGAAGTGAACAGAATCAGGAGAA 217542 i iv -v vv i i ivi i ---- v L1ME4c_3end#L 600 GAAAATGTT-TATGATATAATGTTAAGTGAAAAAAGCAGAAT----ACAA 644 chr2qtel1M 217543 CATTGTAT 217550 v L1ME4c_3end#L 645 AATTGTAT 652 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 43.35 CpG sites = 114, Kimura (unadjusted) = 45.74 Transitions / transversions = 1.20 (114/95) Gap_init rate = 0.03 (19 / 642), avg. gap size = 1.42 (27 / 19) 856 32.06 3.15 2.77 chr2qtel1M 216908 217446 (782554) L1ME3C_3end#LINE/L1 7 547 (323) m_b87s551i13 3268 chr2qtel1M 216908 TCTAAAATATGTAGAGAAGCGAGTTAAATTTATAAGAATGCAAGTCATTC 216957 i i i i vivvvvi iv vi iiiv --- L1ME3C_3end#L 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAAACAGACAA--- 53 chr2qtel1M 216958 CTCAGTTGATAAATGATCAAAGGATATAAACAGACACTTTTCCGATAAAG 217007 i i v v iv i i i v iv v vi i L1ME3C_3end#L 54 CCCAATAGAAAAATGGGCAAAAGATATGAACAGGCAATTCACAGAAGAGG 103 chr2qtel1M 217008 AAATTAAAGCATTTCTAATAT---TATGACAAAAAATGCTCTAAATCATT 217054 i?vi -- vv i v--- -- i v vv i L1ME3C_3end#L 104 AAACNCGA--ATGGCCAATAAACATATGA--AAAGATGCTCAACCTCACT 149 chr2qtel1M 217055 ATTGATCAGAGAAAAGCAAATTAAGACAACTCTGAGGTACCACCTCACAC 217104 v i i v i ? vv i ii L1ME3C_3end#L 150 AGTAATCAGGGAAATGCAAATTAAAACNACAATGAGATACCATTTCACAC 199 chr2qtel1M 217105 CTCTCAGATTGGCCAAGATGACAGGAACAGATAATGACAAATTTTGGAAG 217154 iv v i vvv iiiv v i iv i v vii L1ME3C_3end#L 200 CCATCAGATTGGCAAAAATTTAAAAGTCTGACAATACCAAGTGTTGGCGA 249 chr2qtel1M 217155 GGATGTGGGAAAACTGGGACACTAATGCAGTGTTGGTAGAATTGTGAATT 217204 iiv v i v v i v i i i v i L1ME3C_3end#L 250 GGATGTGGAGCAACGGGAACTCTCATACACTGCTGGTGGGAGTGTAAATT 299 chr2qtel1M 217205 TATCCAAACATTCTCAAGAGTAATTTGGAACTGTGCT--CAAAGGACTAT 217252 vi v v i i vi i v v i - --i v---- L1ME3C_3end#L 300 GGTACAACCACTTTGGAGAGCAATTTGGCAATAT-CTAGTAAAGT----T 344 chr2qtel1M 217253 AAAATTGTGCATACCCTTAGTTCCAACATTCTCATTACTGGGTCTAGATT 217302 i iv i vv vi i v ii i v i v v ii L1ME3C_3end#L 345 GAAGATGCGCATACCCTACGACCCAGCAATTCCACTCCTAGGTATATACC 394 chr2qtel1M 217303 CCAAAGAGATAGTAGGACATG---ATAAAGAATCCACATGTGGGAAAATG 217349 i i i ivv v v i --- i i i--- ivi i L1ME3C_3end#L 395 CTAGAGAAACTCTCGCACGTGTGCACAAGGAG---ACATGTACAAGAATG 441 chr2qtel1M 217350 T-------AGCAT--TTTGTACTGGCAAGGAACTGGAAATTGAGTAGATG 217390 ------- -- v i i ii i ivivv i L1ME3C_3end#L 442 TTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATG 491 chr2qtel1M 217391 CCCATCACTTAGAAAATGGCCAAATAAATTGTGTTATATGAAAGTAAAGG 217440 i vivi i vi v vv vii v L1ME3C_3end#L 492 TCCATCAACAGGAGAATGGATAAATAAATTGTGGTATATTCATACAATGG 541 chr2qtel1M 217441 AATATT 217446 i L1ME3C_3end#L 542 AATACT 547 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.48 CpG sites = 94, Kimura (unadjusted) = 43.18 Transitions / transversions = 1.27 (94/74) Gap_init rate = 0.04 (20 / 538), avg. gap size = 1.60 (32 / 20) 932 31.67 3.16 2.09 chr2qtel1M 216957 217430 (782570) L1ME5_3end#LINE/L1 56 534 (407) m_b87s551i14 3268 chr2qtel1M 216957 CCTCAGTTGATAAATGATCAAAGGATATAAACAGACACTTTTCCGATAAA 217006 i i v v iv i i v v v vi i L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chr2qtel1M 217007 GAAATT--AAAGCATTTCTAATATTATGACAAAAAATGCTCTAAATCATT 217054 ii-- vv vv v ii - -- i i v v L1ME5_3end#LI 106 GAAACCCGAAAGGCTAACAAGCAT-ATGA--AGAGATGCTCAAACTCATT 152 chr2qtel1M 217055 ATTGATCAGAGAAAAGCAAATTAAGACAACTCTGAGGTACCACCTCACAC 217104 v i v i vv i i i i L1ME5_3end#LI 153 AGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACAC 202 chr2qtel1M 217105 CTCTCAGATTGGCCAAGATGACAGGAACAGATAATGACAAATTTTGGAAG 217154 v i i v i v v iiivii v i v vii L1ME5_3end#LI 203 CTATTAGACTGGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTGGCGA 252 chr2qtel1M 217155 GGATGTGGGAAAACTGGGACACTAATGCAGTGTTGGTAGAATTGTGAATT 217204 i ? iv i v v v i i i v ii i L1ME5_3end#LI 253 GGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACT 302 chr2qtel1M 217205 TATCCAAACATTCTCAAGAGTAATTTGGAACTGTGCTCAAAGGACTATAA 217254 vi v iv vi i i v -- i i ivvi -- v L1ME5_3end#LI 303 GGTGCAGCCATTCTGGAGAGCAATCTGGCA--GTACTTAGTCAA--ATTA 348 chr2qtel1M 217255 AAT-TGTGCATACCCTTAGTTCCAACATTCTCATTACTGGGTCTAGATTC 217303 i - ii vv vi i v ii ii v v v i L1ME5_3end#LI 349 AGTATACGCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATATCC 398 chr2qtel1M 217304 CAAAGAGATAGTAGGACATG---ATAAAGAATCCACATGTGGGAAAATGT 217350 i vv viv v --- i ii--- iv ii L1ME5_3end#LI 399 CAAAGAAATTCTCACACAGGTCCATAAGGGG---ACATGTACGAGGATGT 445 chr2qtel1M 217351 -------AGCAT--TTTGTACTGGCAAGGAACTGGAAATTGAGTAGATGC 217391 ------- i -- iv ii ii iiivivv i i i L1ME5_3end#LI 446 TCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGGGTGT 495 chr2qtel1M 217392 CCATCACTTAGAAAATGGCCAAATAAATTGTGTTATATG 217430 vi i i vi ii v v iv L1ME5_3end#LI 496 CCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATG 534 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.71 CpG sites = 86, Kimura (unadjusted) = 42.63 Transitions / transversions = 1.41 (86/61) Gap_init rate = 0.03 (15 / 473), avg. gap size = 1.67 (25 / 15) 17 18.17 0.00 0.00 chr2qtel1M 217705 217735 (782265) (T)n#Simple_repeat 1 31 (0) m_b87s252i13 3269 chr2qtel1M 217705 TTTTTACTGTTTTGTTTCTTTTTTTTTTTTT 217735 vi v v i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 31 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 11 11.25 6.90 0.00 chr2qtel1M 217946 217974 (782026) (TATACT)n#Simple_repeat 1 31 (0) m_b87s252i14 3270 chr2qtel1M 217946 TATACATATA-TTGTATTTA-ACTTATACTT 217974 v - i i - (TATACT)n#Sim 1 TATACTTATACTTATACTTATACTTATACTT 31 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.07 (2 / 28), avg. gap size = 1.00 (2 / 2) 19 11.70 0.00 0.00 chr2qtel1M 218155 218182 (781818) (A)n#Simple_repeat 1 28 (0) m_b87s252i15 3271 chr2qtel1M 218155 AAAAATCTAAAAAAAAAAAAAAAAAAAA 218182 vvv (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA 28 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 215 35.76 3.55 2.82 chr2qtel1M 218344 218484 (781516) L2#LINE/L2 2724 2865 (217) m_b87s601i11 3272 chr2qtel1M 218344 AATAGTTTACTGGTACATCTGCCTCCCTCAAAGCTCTCTTTCCTCTAAGC 218393 ii v iiivvi v v i v vv iv iii ?i iv L2#LINE/L2 2724 AATAGCCTCCTAACTGGTCTCCCTGCTTCCACCCTTGCCCCCCTNCAGTC 2773 chr2qtel1M 218394 CATT----ACCCAGTCAGCCAGTAGAGTGATT-TCCTACAATACAGTTCT 218438 i ---- v - --- i- ii v iii iv v L2#LINE/L2 2774 TATTCTCAACACAG-CAGCCAG---AGTGATCCTTTTAAAACGTAAGTCA 2819 chr2qtel1M 218439 TATCATGTCACTGCCCTACTCAATGAATTCTAGTGCCTTCCCGTTT 218484 v v i i vivvi i i v i i L2#LINE/L2 2820 GATCATGTCACTCCTCTGCTCAAAACCCTCCAATGGCTTCCCATCT 2865 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 49.62 CpG sites = 29, Kimura (unadjusted) = 51.32 Transitions / transversions = 1.45 (29/20) Gap_init rate = 0.04 (6 / 140), avg. gap size = 1.50 (9 / 6) 1105 31.22 5.05 3.94 chr2qtel1M 218815 220221 (779779) L1M5_orf2#LINE/L1 1078 2499 (795) m_b87s551i16 3273 chr2qtel1M 218815 AATAAAATTAAAACTTGATGTTAAGAAAAAAT-AATAAAGCAGATGAAGT 218863 ii iii vi i vi vv i - iiv i vi L1M5_orf2#LIN 1078 AACGAAGCCAAAAGCTGGTTCTTTGAAAAGATCAATAAAATTGATAAACC 1127 chr2qtel1M 218864 TTTGGCTAATTTGATTA-GAAAAAAGGAAAGGA-ATGCAAATTACTAGTA 218911 i i ? ivi i - i i i - ii i i L1M5_orf2#LIN 1128 TCTAGCNAGACTGATCAAGAAAAAAAGAGAGAAGACACAAATTACCAATA 1177 chr2qtel1M 218912 TCAAAAATGAAAAAGAGTGAAGTTACCAGCAATGAAGAAGAAATTAAAGC 218961 ii - v vi i i vvi vvviv v iv L1M5_orf2#LIN 1178 TCAGGAATGAAAAAG-GAGACATCACTACAGATCCTACAGACATTAAAAG 1226 chr2qtel1M 218962 AACAAATAGGACCTATT-TTACTAACTGTTTGCTAACAAATCAGACCATT 219010 i i vv iivv - v vi v v i i iv ?v i L1M5_orf2#LIN 1227 GATAATAAGAGAATATTATGAACAACTTTATGCCAATAAATTTGANAACT 1276 chr2qtel1M 219011 TAATTGAAATGGATGAATATTTGCAGAAACATAAATTGTCCATATTAACA 219060 iv ii vii vv i i ? ii v v i i ? L1M5_orf2#LIN 1277 TAGATGAAATGGACAAATTCCTTGAAAAACACAANTTACCAAAACTGACN 1326 chr2qtel1M 219061 GAAGAA--AATATAAATGCTGAAATAACTC---ATTTA--AAAGTAGAAC 219103 v -- v vv - i i --- i -- --- v L1M5_orf2#LIN 1327 CAAGAAGAAATAGAAAATCTGAA-TAGCCCTATATCTATTAAAG---AAA 1372 chr2qtel1M 219104 TTAAACAAGTCATCAATGAA--TTCCCAAAGAAAAAAAAAAAAATCTCCA 219151 i ivv v i -i -- v i i -------- L1M5_orf2#LIN 1373 TTGAATTTGTAATTAA-AAACCTTCCCACAAAGAAAA--------CTCCA 1413 chr2qtel1M 219152 GGGCAAGATGAATTGCAAGGAT--ATTCTACCAAATATTTAAAGAA---- 219195 v v iv - vv i -- i i ---- L1M5_orf2#LIN 1414 GGCCCAGATGGCTT-CACTGGTGAATTCTACCAAACATTTAAGGAAGAAA 1462 chr2qtel1M 219196 ---CACCAATTTTGGATACAATGTAAAACTACTTGAAAAAAAAAAAAATG 219242 ---i i -- i ------ vi iv i v i v L1M5_orf2#LIN 1463 TAATACCAATCTT--ACACAA------ACTCTTCCAGAAAATAGAAAAAG 1504 chr2qtel1M 219243 GGTGAAAAATGATTGTTACCCACCAC-TTTTGTGACACAAATATGGGGGT 219291 i v v -------i v v v - i vi v ii ?ivvv L1M5_orf2#LIN 1505 AGGGAACA-------CTTCCCAACTCATTTTATGAGGCCAGCATNACCCT 1547 chr2qtel1M 219292 AACATTTAAAATAGGAAGAGCTAAAACAG--AAAGAAAATTATAGACCAC 219339 i i iiv vi? iv i vi vv i-- i v L1M5_orf2#LIN 1548 GATACCAAAACCNGACAAAGACATTACAAGAAAAGAAAATTACAGACCAA 1597 chr2qtel1M 219340 CTCCCCTAATGAATACTGATGCAAAAATATATAAATAAAACAATAGTAAA 219389 ivi v i iv -iv ? i i v i L1M5_orf2#LIN 1598 TATCCCTCATGAACATAGATGCAAAAAT-CCTNAACAAAATATTAGCAAA 1646 chr2qtel1M 219390 -CAAAT-TAGATCAATGTATAAACAGGACAATAATATAGTATAACCAAAT 219437 - i -i -- i v --- i vi i i L1M5_orf2#LIN 1647 TCGAATCCAG--CAATATATAAAAAGG---ATAATACATCATGACCAAGT 1691 chr2qtel1M 219438 AAGATCTATACCAGGAATGCAGAACTGATTCAATGTCAGGGAAAGTATCA 219487 ii i i v iiii i i ii iv ii vvv L1M5_orf2#LIN 1692 GGGGTTTATCCCAGGAATGCAAGGTTGGTTTAACATTCGAAAATCAATCA 1741 chr2qtel1M 219488 GCATAAT----CATATCA--AGAATAAAACTAACAGAAACCATCTGATTA 219531 iii ---- i -- i--i v i i v i L1M5_orf2#LIN 1742 ATGTAATTCACCATATTAACAGAATAAAG--GAGAAAAATCATATGATCA 1789 chr2qtel1M 219532 TATCAATAGATAAAGAAAAAGATTTTGAGAAAATACAGTACCCACTCCTA 219581 v iv vv v v ii i v i L1M5_orf2#LIN 1790 TCTCAATAGATGCAGAAAAAGCATTTGACAAAATTCAACACCCATTCATG 1839 chr2qtel1M 219582 TTAAAAA-TATTAGAGAGCATGGGAATAAATGGAGTTTTCCTCAAAATGG 219630 v - v i vi i - i i v iivi vv i L1M5_orf2#LIN 1840 ATAAAAACTCTCAGCAAAC-TAGGAATAGAAGGGAACTTCCTCAACCTGA 1888 chr2qtel1M 219631 CAAATAATATCTATCCAAAACCATCAGTATGCATTATATGAAATGGCTAT 219680 i viii ivv vv i?vi i ivv iv v L1M5_orf2#LIN 1889 TAAAGGGCATCTACGAAAAACCTACAGCNAACATCATACTTAATGGTGAA 1938 chr2qtel1M 219681 AAACTAGGTACATTCACAATAAGTTCGGGGGTTGAAACAAAGATACCTAC 219730 ? iii?i v v vv v ii-ii i i ii ii L1M5_orf2#LIN 1939 ANACTGAANGCTTTCCCCCTAAGATCGGGAA-CAAGACAAGGATGTCCGC 1987 chr2qtel1M 219731 TATCACTACTATTGTTCAACATTGTATTAGAAATGTTGGCTTTAGCAATA 219780 ? i vi i i i ii vi i ivvv L1M5_orf2#LIN 1988 TNTCACCACTTCTATTCAACATTGTACTGGAGGTCCTAGCCAGTGCAATA 2037 chr2qtel1M 219781 AGAAAAG-AAAAGAAACAGAAGGAATTAGAGTAGGCAATGAGGAAACAGA 219829 iv - i i v v iii v v v i i i L1M5_orf2#LIN 2038 AGGCAAGAAAAAGAAATAAAAGGCATAAAGATTGGAAAGGAAGAAATAAA 2087 chr2qtel1M 219830 ACTATCCCTATTTTCAGATGGTATAATGGTAGATCTAGAGAGTACTAAAG 219879 i ?i iv ii i v ?v iv i i v ? L1M5_orf2#LIN 2088 ACTGTCNTTATTCGCAGATGACATGATTGTNTACGTAGAAAATCCNAAAG 2137 chr2qtel1M 219880 AATCAAACAAAAAA------AAAACTATT---TGA----AACAAAAGCTT 219916 -v ? ------ i v --- ---- i ii--- L1M5_orf2#LIN 2138 AATC-TACAAANAAACTACTAGAACTAATAAGTGAATTTAGCAAGG---T 2183 chr2qtel1M 219917 TGCAGGATACAAAATAAACCCACATAAATCAACAGCATTATTACCATGAA 219966 i ? ii v ivi v iv --- v i iv L1M5_orf2#LIN 2184 CGCNGGATACAAGGTCAATATACAAAAATCAATTG---TATTTCTATATA 2230 chr2qtel1M 219967 ACCCAGCAGCAAGAGA-TAGAAAAAGAAATT------------CCATTTA 220003 -- i i ivi - i v ------------ L1M5_orf2#LIN 2231 --CTAGCAACAAACAATTGGAAAATGAAATTTNAAAAACAATACCATTTA 2278 chr2qtel1M 220004 AAATAACTGTAGACTATATAAAATATCTAACAGTCTCCCTCCCAAGACAA 220053 v i vvi i vv i ? ii iv i vvvi vv i ? - L1M5_orf2#LIN 2279 CAATAGCATCAAAAAACATNAAATACTTAGGAATAAATCTAACAAAANA- 2327 chr2qtel1M 220054 ACTCTGAAA-----TTATATTCATACCATTAAAAAACAATTCT--TATAA 220096 -- v v -----? i i v v -- i v v v --v v L1M5_orf2#LIN 2328 --TGTGCAAGACCTNTACACTGAAA--ACTACAAAACATTGCTGAGAGAA 2373 chr2qtel1M 220097 ATAAATTCAGACAGAAACAACTGGAAAAA-AAATTGTGTTTATGGGTTGG 220145 v vvv vv i v i i - v iii i i L1M5_orf2#LIN 2374 ATTAAAGAAGACCTAAATAAATGGAGAGATATACCATGTTCATGGATTGG 2423 chr2qtel1M 220146 CCAAGG--TAATATAATAAAAATCACAATTCTAGTTAAATTAGTCTGCTT 220193 -- i--i vi ? i vv vvii ii iivv L1M5_orf2#LIN 2424 --AAGACTCAATATTGTNAAGATGTCAATTCTCCCCAAATTGATCTATAG 2471 chr2qtel1M 220194 ATTCAGTGCCCCACCAATCAAATTGCCA 220221 i vviv v v L1M5_orf2#LIN 2472 ATTCAATGCAATCCCAATCAAAATCCCA 2499 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.53 CpG sites = 245, Kimura (unadjusted) = 42.50 Transitions / transversions = 1.38 (245/177) Gap_init rate = 0.06 (84 / 1406), avg. gap size = 1.51 (127 / 84) 1143 32.16 4.35 3.31 chr2qtel1M 218815 220010 (779990) L1M4_orf2#LINE/L1 1078 2285 (1009) m_b87s551i15 3273 chr2qtel1M 218815 AATAAAATTAAAACTTGATGTTAAGAAAAAAT-AATAAAGCAGATGAAGT 218863 ii ii v i vi vv i - i iiv ii vi L1M4_orf2#LIN 1078 AACGAAACCAAAAGTTGGTTCTTTGAAAAGATCAACAAAATTGACAAACC 1127 chr2qtel1M 218864 TTTGGCTAATTTGATTA-GAAAAAAGGAAAGGA-ATGCAAATTACTAGTA 218911 i ivi ii - i i i - iv iv L1M4_orf2#LIN 1128 TTTAGCTAGACTGACCAAGAAAAAAAGAGAGAAGACTCAAATTACTAAAA 1177 chr2qtel1M 218912 TCAAAAATGAAAAAGAGTGAAGTTACCAGCAATGAAGAAGAAATTAAAGC 218961 ii i i - vi i v i ivvviv v iv L1M4_orf2#LIN 1178 TCAGGAATGAAAGAGGG-GACATTACTACCGACCTTACAGAAATAAAAAG 1226 chr2qtel1M 218962 AACAAATAGGACCTATT-TTACTAACTGTTTGCTAACAAATCAGACCATT 219010 i iv vv ivv i - v vi i v i i iv ii L1M4_orf2#LIN 1227 GATTATAAGGGAATACTATGAACAATTGTATGCCAACAAATTAGATAACC 1276 chr2qtel1M 219011 TAATTGAAATGGATGAATATTTGCAGAAACATAAATTGTCCATATTAAC- 219059 iv ii vii iv i i i i ii v v i i - L1M4_orf2#LIN 1277 TAGATGAAATGGACAAATTCCTAGAAAGACACAAACTACCGAAACTGACT 1326 chr2qtel1M 219060 --AGAAGAAAATATAAATGCTGAAATAACTCATTTAA-AAGTA--GAACT 219104 -- - v vv vvi ii -- - -- iv L1M4_orf2#LIN 1327 CAAGAAGAAA-TAGAAAATCTGAATAGACCTAT--AACAAGTAAAGAGAT 1373 chr2qtel1M 219105 TAAACAAGTCATCAATGAA-TTCCCAAAGAAAAAAAAAAAAATCTCCAGG 219153 i iv v vi - v i i i--------i L1M4_orf2#LIN 1374 TGAATTAGTAATCAAAAAACTTCCCACAAAGAAAAG--------CCCAGG 1415 chr2qtel1M 219154 GCAAGATGAATTGCAAGGAT--ATTCTACCAAATATTTAAAGAA------ 219195 ? v iv - vv i -- i ------ L1M4_orf2#LIN 1416 NCCAGATGGCTT-CACTGGTGAATTCTACCAAACATTTAAAGAAGAATTA 1464 chr2qtel1M 219196 -CACCAATTTTGGATACAATGTAAAACTACTTGAAAAAAAAAAAAATGGG 219244 - ii vv i -------- vi iv v i i v i L1M4_orf2#LIN 1465 ACACCAATCCTTCACA--------AACTCTTCCAAAAAATAGAAGAGGAG 1506 chr2qtel1M 219245 TGAAAAATGATTGTTACCCACCAC-TTTTGTGACACAAATATGGGGGTAA 219293 v v -------i v v v - i i vi v i vivvv i L1M4_orf2#LIN 1507 GGAACA-------CTTCCCAACTCATTCTATGAGGCCAGTATTACCCTGA 1549 chr2qtel1M 219294 CATTTAAAATAGGAAGAGCTAAAACAG--AAAGAAAATTATAGACCACCT 219341 i iiv vi iv i vi vv i-- i i viv L1M4_orf2#LIN 1550 TACCAAAACCAGACAAAGACATCACAAGAAAAGAAAACTACAGACCAATA 1599 chr2qtel1M 219342 CCCCTAATGAATACTGATGCAAAAATATATAAATAAAACAATAGTAAACA 219391 i v iv -iv v i i v i v L1M4_orf2#LIN 1600 TCCCTTATGAATATAGATGCAAAAAT-CCTCAACAAAATACTAGCAAACC 1648 chr2qtel1M 219392 AATTAGATCAATGTATAAACAGGACAATAATATAGTATAACCAAATAAGA 219441 i v vv v ii v --- v i vi i i ii L1M4_orf2#LIN 1649 GAATCCAGCAACATATAAAAAGG---ATTATACACCATGACCAAGTGGGA 1695 chr2qtel1M 219442 TCTATACCAGGAATGCAGAACTGATTCAATGTCAGGGAAAGTATCAGCAT 219491 i v iiii i ii ?v ii vvv iii L1M4_orf2#LIN 1696 TTTATCCCAGGAATGCAAGGTTGGTTCAACATNCGAAAATCAATCAATGT 1745 chr2qtel1M 219492 AAT----CATATCA--AGAATAAAACTAACAGAAACCATCTGATTATATC 219535 ---- i -- i--i i iv i v L1M4_orf2#LIN 1746 AATACACCATATTAATAGAATAAAG--GACAAAAACCACATGATCATCTC 1793 chr2qtel1M 219536 AATAGATAAAGAAAAAGATTTTGAGAAAATACAGTACCCACTCCTATTAA 219585 iiv vv v v ii vi v iv L1M4_orf2#LIN 1794 AATAGACGCAGAAAAAGCATTTGACAAAATCCAACACCCTTTCATGATAA 1843 chr2qtel1M 219586 AAATATTAGAGAGCATGGGAATAAATGGAGTTTTCCTCAAAATGGCAAAT 219635 i i vi v ivv i i v iivi vv ii v L1M4_orf2#LIN 1844 AAACACTCAACAAACTAGGAATAGAAGGGAACTTCCTCAACCTGATAAAG 1893 chr2qtel1M 219636 AATATCTATCCAAAACCATCAGTATGCATTATATGAAATGGCTATAAACT 219685 iii ivv vv ivvi i ivv iv v i L1M4_orf2#LIN 1894 GGCATCTACGAAAAACCCACAGCTAACATCATACTTAATGGTGAAAGACT 1943 chr2qtel1M 219686 AGGTACATTCACAATAAGTTCGGGGGTTGAAACAAAGATACCTACTATCA 219735 iii?i v v vv v i ii-ii i i ii ii v i L1M4_orf2#LIN 1944 GAANGCTTTCCCCCTAAGATCAGGAA-CAAGACAAGGATGTCCGCTCTCG 1992 chr2qtel1M 219736 CTACTATTGTTCAACATTGTATTAGAAATGTTGGCTTTAGCAATAAGAAA 219785 i vi i i i ii vi i ivvi v iv L1M4_orf2#LIN 1993 CCACTTCTATTCAACATTGTACTGGAGGTTCTAGCCAGGGCAATTAGGCA 2042 chr2qtel1M 219786 AG-AAAAGAAACAGAAGGAAT-TAGAGTAGGCAATGAGGAAACAGAACTA 219833 - i i v -i v - v v i ii i L1M4_orf2#LIN 2043 AGAAAAAGAAATAAAAGGCATCCAGATT-GGAAAGGAAGAAGTAAAACTA 2091 chr2qtel1M 219834 TCCCTATTTTCAGATGGTATAATGGTAGATCTAGAGAGTACTAAAGAATC 219883 i iv ii i vv iv v i i v i L1M4_orf2#LIN 2092 TCTCTATTCGCAGATGACATGATCTTGTATATAGAAAATCCTAAGGAATC 2141 chr2qtel1M 219884 AAACAAAAAA-----AAAACTATTTGAAACAAA---AGC---TTTGCAGG 219922 v v? ----- i v -- i i--- ---v L1M4_orf2#LIN 2142 CACNAAAAAACTATTAGAACTAAT--AAACGAGTTCAGCAAGGTTGCAGG 2189 chr2qtel1M 219923 ATACAAAATAAACCCACATAAATCAACAGCATT-------ATTACC-ATG 219964 i v ivi v iv i ------- i v - L1M4_orf2#LIN 2190 ATACAAGATCAATATACAAAAATCAATTGTATTTCTATACACTAGCAATG 2239 chr2qtel1M 219965 AAACCCAGCAGCAA--GAGATAGAAAAAGAAATTCCATTTAAAATAAC 220010 -- v v v v -- i vi i iv v i L1M4_orf2#LIN 2240 AA--CAATCCGAAAATGAAATTAAGAAAACAATTCCATTTACAATAGC 2285 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 42.17 CpG sites = 217, Kimura (unadjusted) = 43.64 Transitions / transversions = 1.40 (217/155) Gap_init rate = 0.05 (64 / 1195), avg. gap size = 1.44 (92 / 64) 290 23.10 26.56 1.89 chr2qtel1M 220301 220428 (779572) MIRb#SINE/MIR 3 161 (107) m_b87s601i12 3274 chr2qtel1M 220301 GGGAGGCAGCTAGGTGGCACAGTGGATAGAGCAC---------------- 220334 i i --- ii v ---------------- MIRb#SINE/MIR 3 GAGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGA 49 chr2qtel1M 220335 CAGACCTGAGTTCAAATATGGCCTCAGACACTTAACA-CT------TCCT 220377 i i viv v v v vi - ------i i MIRb#SINE/MIR 50 CAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTT 99 chr2qtel1M 220378 GGGTAAGTCACTTAA----------CCCCAATTTCCTCATA-AAAAAATA 220416 i i ---------- i i v-iv i MIRb#SINE/MIR 100 GGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATG 149 chr2qtel1M 220417 AAAAGAATAATA 220428 iii v MIRb#SINE/MIR 150 GGGATAATAATA 161 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.43 CpG sites = 19, Kimura (unadjusted) = 28.58 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.06 (8 / 127), avg. gap size = 4.62 (37 / 8) 318 26.70 4.98 4.98 chr2qtel1M 222205 222405 (777595) C L1MC1_3end#LINE/L1 (447) 633 433 m_b87s551i17 3275 chr2qtel1M 222205 GCTCATTTCACTCAGCATCAGTTCATATAAGTCTC-TCCAGGCCTTTCTG 222253 iv i i vi - v v i - v i --- C L1MC1_3end#LI 633 GCTTCTTTCACTTAGTAATA-TGCATTTAAGTTTCCTCCATGTCTTT--- 588 chr2qtel1M 222254 AAATCAT--CCTGTTGG-TCATTTCTTAC-AGAAC--AATAATATTCCAT 222297 --- -- i v i - vi- vi -- C L1MC1_3end#LI 587 ---TCATGGCTTGATAGCTCATTTCTTTTTAGCGCTGAATAATATTCCAT 541 chr2qtel1M 222298 AATATTCATATACCACAATTTATTCTGCCATTCTCCAACTGATGGGCATC 222347 vi v vv i i ivv v v v i - C L1MC1_3end#LI 540 TGTCTGGATGTACCACAGTTTATTTATCCATTCACCTACTGAAGGACAT- 492 chr2qtel1M 222348 CACTCAGT---TTCCAGTTTCTAGCCACTACAAAGAGGGCTGCCACAAAC 222394 -- ii --- iv i i v i ii v ii i i C L1MC1_3end#LI 491 --CTTGGTTGCTTCCAAGTTTTGGCAATTATGAATAAAGCTGCTATAAAC 444 chr2qtel1M 222395 ATTCATGCACA 222405 i i ii C L1MC1_3end#LI 443 ATCCGTGTGCA 433 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 32.30 CpG sites = 31, Kimura (unadjusted) = 33.92 Transitions / transversions = 1.55 (31/20) Gap_init rate = 0.08 (16 / 200), avg. gap size = 1.25 (20 / 16) 332 31.41 1.89 1.89 chr2qtel1M 222286 222444 (777556) C L1ME4c_3end#LINE/L1 (275) 555 397 m_b87s551i19 3275 chr2qtel1M 222286 ATAATATTCCATAATATTCATATACCACAATTTATTCTGCCATTCTCCAA 222335 vivi ?v i i i ivi i v C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chr2qtel1M 222336 CTGATGGGCATCCACTCAGTTTCCAGTTTCTAGCCACTACAAAGAGGGCT 222385 i v i ii vviv i i v i i i v iv C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCT 456 chr2qtel1M 222386 GCCACAAACATTCATGCACATACAGGTCCCTTTCTCTTCTTT---ATGAT 222432 v ii iivi ii i --- i ii --- v C L1ME4c_3end#L 455 GCAATGAACATCTTCGTGCATATAG---CTTTTTCCTTCTTTTGAATTAT 409 chr2qtel1M 222433 CTCTTGGGGATA 222444 i i vi C L1ME4c_3end#L 408 TTCCTTAGGATA 397 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.02 CpG sites = 33, Kimura (unadjusted) = 43.43 Transitions / transversions = 2.06 (33/16) Gap_init rate = 0.03 (4 / 158), avg. gap size = 1.50 (6 / 4) 418 26.83 0.00 0.00 chr2qtel1M 222286 222408 (777592) C L1ME3G_3end#LINE/L1 (376) 548 426 m_b87s551i18 3275 chr2qtel1M 222286 ATAATATTCCATAATATTCATATACCACAATTTATTCTGCCATTCTCCAA 222335 i i vv i ivi i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr2qtel1M 222336 CTGATGGGCATCCACTCAGTTTCCAGTTTCTAGCCACTACAAAGAGGGCT 222385 i i ii vviv i i v i i v iv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr2qtel1M 222386 GCCACAAACATTCATGCACATAC 222408 v ii i v i i C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACATGC 426 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.33 CpG sites = 21, Kimura (unadjusted) = 34.33 Transitions / transversions = 1.75 (21/12) Gap_init rate = 0.00 (0 / 122), avg. gap size = 0.0 (0 / 0) 223 38.24 5.42 2.34 chr2qtel1M 222595 222760 (777240) C L2#LINE/L2 (495) 2587 2417 m_b87s601i13 3276 chr2qtel1M 222595 AGAGACAGTAGAGAATTATGAATAAATCTCAGGTTATGAATTTGGGTGAC 222644 v viii i i v i i v iv v viiii i ii C L2#LINE/L2 2587 AGAGAAAGAGAGGAGTCAAGGATGACTCCAAGGTTTTTGGCCTGAGCAAC 2538 chr2qtel1M 222645 TAAAGGAATGATGGTATC-----CTCAGGTA---AAGACATTTGGAAGAA 222686 ii i i iv v ii ----- v i i--- - vi i i C L2#LINE/L2 2537 TGGAAGGATGGAGTTGCCATTNACTGAGATGGGGAAGAC-TGCGGGAGGA 2489 chr2qtel1M 222687 TCATAACATTTG-GGGGTAACATAGTAAGTTTTGTTGTGGATATGGTGAG 222735 v vi--- - v v vivi iv v i v i C L2#LINE/L2 2488 GCAGG---TTTGAGGGGGAAGATCAGGAGTTCAGTTTTGGACATGTTAAG 2442 chr2qtel1M 222736 TTTGCCAGGCCCACTGGCTATCTAA 222760 vv v i i i vi i C L2#LINE/L2 2441 TTTGAGATGCCTATTAGACATCCAA 2417 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 55.38 CpG sites = 38, Kimura (unadjusted) = 56.81 Transitions / transversions = 1.58 (38/24) Gap_init rate = 0.04 (7 / 165), avg. gap size = 1.86 (13 / 7) 342 34.64 3.90 1.27 chr2qtel1M 222890 223120 (776880) HERVP71A#LTR/ERV1 2437 2673 (4917) m_b88s701i0 3277 chr2qtel1M 222890 CAGGGAGTGTTTAAAAATTCC-CCATT-TAAACTGAATCTGACAAACA-- 222935 iiv v iv - v -i i i - i -- -- HERVP71A#LTR/ 2437 CAGGGGAGGGTTAAAAATCACACCCTTACAGATTGAA-CTAA--AACAAC 2483 chr2qtel1M 222936 CAGAGGATGTGGTGTGTGCTAAACAGTATCTTATATC-ATGGAGGGAAAA 222984 ii v i v iivv i ii v - v i i i HERVP71A#LTR/ 2484 CAGGAGAAGTAGTTTGCAGAAAACAATATCCCATTTCCATTGAAGGGAGA 2533 chr2qtel1M 222985 ATAAGATTGCAATTACTAATAAAGAGACTTGTGAACGATGGACTATTATG 223034 v i vi v iiiv i i i vi v v vi HERVP71A#LTR/ 2534 AAAGGTCTCCAACCGGTAATAGAGGGATTGATTAAAGATGGACTATTAGA 2583 chr2qtel1M 223035 --TTTGTATGCCCCCTTTCAATATCCCTATTGTGCTCATTAAGAAATCAG 223082 --ii i i v v v ii v v v ivi i ii v HERVP71A#LTR/ 2584 ACCCTGCATGTCACCATACAATACTCCAATTCTCCCAGTCAAGAAGCCTG 2633 chr2qtel1M 223083 ATGAAAC--ATGGATTAATACAAAACCTTGGAGGAATAAA 223120 iiv -- i ii i i i vi i vv HERVP71A#LTR/ 2634 ATGGGTCGTATAGATTGGTGCAAGATCTAAGGGCTATAAA 2673 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 47.85 CpG sites = 49, Kimura (unadjusted) = 48.84 Transitions / transversions = 1.63 (49/30) Gap_init rate = 0.04 (9 / 230), avg. gap size = 1.33 (12 / 9) 407 29.67 2.21 3.35 chr2qtel1M 223927 224198 (775802) L1M3_orf2#LINE/L1 3013 3281 (7) m_b88s551i3 3278 chr2qtel1M 223927 AAAATAGAAAATTTCGATTATACCAAACTGAAAAGTTTTTGCACAAACAA 223976 v v vv i i i i i i i- L1M3_orf2#LIN 3013 AAAATAGACAAGTGGGACTACATCAAACTAAAAAGCTTCTGCACAG-CAA 3061 chr2qtel1M 223977 AGCTAATG--CAGACAAGATTAGAAGGGAAGCAATAAACTGGGAAAATAT 224024 vv ii-- - iii v i v v v iii v i v L1M3_orf2#LIN 3062 AGGAAACAATCA-ACAGAGTGAAAAGGCAACCTACGGAATGGGAGAAAAT 3110 chr2qtel1M 224025 TTTTACAGTCAAAGGTTCTGGATAAAAGGCCCTCATTTCCAAAAATATAT 224074 v i iv v vivv - ii i-- v v - L1M3_orf2#LIN 3111 ATTTGCAAACCATATATCTG-ATAAGGGGT--TAATATCCAAAA-TATAT 3156 chr2qtel1M 224075 AGAGAATTAACCTAATTT-ATA--AAAAAATCAAGCCATTCTCCAATTGA 224121 ii i v?ivi i i- -- v --- vvi i ? L1M3_orf2#LIN 3157 AAGGAACTCNTACAACTCAATAGCAAAAAAACAA---ATAACCCGATTNA 3203 chr2qtel1M 224122 AAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGAAGAAATTGAAA 224171 v iv i v vi v v vv L1M3_orf2#LIN 3204 AAAATGGGCAAAGGACCTGAATAGACATTTCTCCAAAGAAGACATACAAA 3253 chr2qtel1M 224172 CTATTTCTAGTCATATG-AAAGATGCTC 224198 iviiivvi vi - L1M3_orf2#LIN 3254 TGGCCAACAGGTATATGAAAAGATGCTC 3281 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.45 CpG sites = 41, Kimura (unadjusted) = 38.77 Transitions / transversions = 1.11 (41/37) Gap_init rate = 0.05 (13 / 271), avg. gap size = 1.15 (15 / 13) 1017 29.75 4.17 3.61 chr2qtel1M 224066 224616 (775384) L1MB8_3end#LINE/L1 10 563 (362) m_b88s551i4 3278 chr2qtel1M 224066 AAAATATATAGAGAATT-----AACCTAATTTATAAAAAAATCAAGCCAT 224110 i i i ----- ii v- i - --- L1MB8_3end#LI 10 AGAATATATAAAGAACTCTTACAACTCAATA-ATAAAAAGA-CAA---AT 54 chr2qtel1M 224111 TCTCCAATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGA 224160 vvi ? v v i v vi v L1MB8_3end#LI 55 AACCCAATTNAAAAATGGGCAAAGGATCTGAATAGACATTTCTCCAAAGA 104 chr2qtel1M 224161 AGAAATTGAAACTATTTCTAGTCATATGAAA-GATGCTCCAAGTCATTAT 224209 v vv iviiivv iv i - v vi v L1MB8_3end#LI 105 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCATTAG 154 chr2qtel1M 224210 TAATCAGGAGAAATGCAAATTAAGACAACTCTAAGATACCACTCACACAC 224259 v - i i v vv i i- L1MB8_3end#LI 155 TCATCAGG-GAAATGCAAATCAAAACCACAATGAGATACCACTT-CACAC 202 chr2qtel1M 224260 CTGTCA----GATTACAAATGACAGGAAAAATAATGATGATTGTTGA-GG 224304 iiii ---- ii i vii v i v i i ii v i- i L1MB8_3end#LI 203 CCACTAGGATGGCTATAATCAAAAAGACAGATAATAACAAGTGTTGGCGA 252 chr2qtel1M 224305 GGATGTGGGAAAACTGGGACATTGATGCATTGTT-ATGGAGTTGTGAACG 224353 ii i i vi v i i i -i iiv i vv L1MB8_3end#LI 253 GGATGTGGAGAAATTGGAACCCTCATACACTGCTGGTGGGAATGTAAAAT 302 chr2qtel1M 224354 AATCCAACCATTTTGGAGAGTAGTTTGGAACTATGTCAAAAAGTT----A 224399 ii v i ii i ii i v v viv i ---- L1MB8_3end#LI 303 GGTGCAGCCGCTTTGGAAAACAGTCTGGCAGTTCCTCAAAAGGTTAAACA 352 chr2qtel1M 224400 TCAAATCAGCATACTTTGATCCAGCAGTGTTACTACTGGGATTATATATC 224449 vi i i v --- i i vii v i -- i L1MB8_3end#LI 353 TAGAGTTACCATA---TGACCCAGCAATTCCACTCCTAGG--TATATACC 397 chr2qtel1M 224450 CCAAAGAGATTATAAAGAAGG-----AAAGGGACCTGTATGTGCACGAAT 224494 v i i v v viv v ----- v iii i ---- L1MB8_3end#LI 398 CAAGAGAAATGAAAACATATGTCCACACAAAAACTTGTA----CACGAAT 443 chr2qtel1M 224495 GCTTGTGGCAGCCCT-TTTGTAGTGGTTAGAAACT-GAAACTGAATGGAT 224542 i ii i vi - ii i i ii i v - vivviii L1MB8_3end#LI 444 GTTCATAGCAGCATTATTCATAATAGCCAAAAAGTGGAAACAACCCAAAT 493 chr2qtel1M 224543 GTCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATATGAAAAATTAT 224592 ii iv v i v -vv v iv L1MB8_3end#LI 494 GTCCATCAACTGATGAATGGATAAATAAAATGTGGTATAT-CCATACAAT 542 chr2qtel1M 224593 GGAATATTACCGTTCTGTAAGAAA 224616 --- v i v L1MB8_3end#LI 543 GGAATATTA---TTCGGCAATAAA 563 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.02 CpG sites = 97, Kimura (unadjusted) = 39.35 Transitions / transversions = 1.59 (97/61) Gap_init rate = 0.05 (29 / 550), avg. gap size = 1.48 (43 / 29) 807 31.52 4.23 3.36 chr2qtel1M 224096 224686 (775314) L1PB1_3end#LINE/L1 43 638 (260) m_b88s551i5 3278 chr2qtel1M 224096 AAAAAATCAAGCCATTCTCCAATTGAAAAATGGTCAAAGGATATGAACAG 224145 v i v --- v ii i v v i i L1PB1_3end#LI 43 AAAAAAACAAACAAT---CCCATCAAAAAGTGGGCTAAGGACATGAATAG 89 chr2qtel1M 224146 ACAATTCTCAGATGAAGAAATTGAAACTATTTCTAGTCATATG-AAAGAT 224194 i v v vv iviiivvi iv - i L1PB1_3end#LI 90 ACAATTCTCAAAAGAAGATATACAAATGGCCAACAAACATATGAAAAAAT 139 chr2qtel1M 224195 GCTCCAAGTCATTATTAATCAGGAGAAATGCAAATTAAGACAACTCTAAG 224244 v vi i v i - i i v vv iv L1PB1_3end#LI 140 GCTCAACATCACTAATGATCAGG-GAAATGCAAATCAAAACCACAATGCG 188 chr2qtel1M 224245 ATACCACTCACACACCTGTCAGATTACAAATGA-CAGGAA---AAATAAT 224290 - vi v iv v ivvv i - ii --- v L1PB1_3end#LI 189 ATACCAC-CTTACTCCTGCAAGAATGGCCATAATCAAAAAATCAAAAAAT 237 chr2qtel1M 224291 GATGATTGTTGAGG-GGATGTGGGAAAACTGGGACATTGATGCATTGTT- 224338 i iiv iv - i vi vv i i vv i i i - L1PB1_3end#LI 238 AATAGATGTTGGCGTGGATGCGGTGAAAAGGGAACACTTCTACACTGCTG 287 chr2qtel1M 224339 ATGGAGTTGTGAACGAATCCAACCATTTTGGAGAGTAGTTTGGAACTATG 224388 i iiv i v i v i v i ii v iv viv L1PB1_3end#LI 288 GTGGGAATGTAAACTAGTACAACCACTATGGAAAACAGTGTGGAGATTCC 337 chr2qtel1M 224389 TCAAAAAGTTATCAAATCAGCA-TAC--TTTGATCCAGCAGTGTTACTAC 224435 i i ii -- vi v - -- i vii L1PB1_3end#LI 338 TTAAAGAACTA--AAAGTAGAACTACCATTTGATCCAGCAATCCCACTAC 385 chr2qtel1M 224436 TGGGATTATATATCCCAAAGAGATTATAAAGAAG---------GAAAGGG 224476 -- v - i - ---- --------- ii L1PB1_3end#LI 386 TGGG--TATCTA-CCCAGAG-GA----AAAGAAGTCATTATACGAAAAAG 427 chr2qtel1M 224477 ACCTGTATGTGCACGAATGCTTGTGGCAGC-CCTTTTGTAGTGGTTAGAA 224525 -- iiv ii v i i i - vv i i i v iv i L1PB1_3end#LI 428 A--TACTTGCACACGCATGTTTATAGCAGCACAATTCGCAATTGCAAAAA 475 chr2qtel1M 224526 ACTGAAACT-GAATGGATGTCCATCAGTTGGAGAATGGCTGAATAAATTG 224574 vv i i- vviii i i iiiv i v i v ? L1PB1_3end#LI 476 TATGGAACCAGCCCAAATGCCCATCAATCAACGAGTGGATAAAGAAANTG 525 chr2qtel1M 224575 TGGTATATGAAAAATTATGGAATATTACCGTTCTGTAAGAAATGACCAAC 224624 - v v ii i ivvv ii i ivi iv ? L1PB1_3end#LI 526 TGGTATAT-ATATACCATGGAATACTACTCAGCCATAAAAAGGAATGAAN 574 chr2qtel1M 224625 AGATGAT-TTCAGAAAGGCCTGGAGAGACTTACACGAACTG-GATGCTAA 224672 vi ii- iv iv i vi v iv --i i-v v L1PB1_3end#LI 575 TAATGGCATTCGCAGCGACCTGGATGGAATTGGA--GACTATTATTCTAA 622 chr2qtel1M 224673 GTGAAATGA--CAGGA 224686 i i -- L1PB1_3end#LI 623 GTGAAGTAACTCAGGA 638 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.45 CpG sites = 105, Kimura (unadjusted) = 42.40 Transitions / transversions = 1.40 (105/75) Gap_init rate = 0.06 (33 / 590), avg. gap size = 1.36 (45 / 33) 1271 26.26 4.90 3.63 chr2qtel1M 224112 224601 (775399) L1ME5_3end#LINE/L1 56 551 (390) m_b88s551i6 3278 chr2qtel1M 224112 CTCCAATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGAA 224161 i v v i iv v i L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chr2qtel1M 224162 GAAA-TTGAAA--CTATTTCTAGTCATATGAA-AGATGCTCCAAGTCATT 224207 -ii -- --v v - - v v L1ME5_3end#LI 106 GAAACCCGAAAGGCTA--ACAAG-CATATGAAGAGATGCTCAAACTCATT 152 chr2qtel1M 224208 ATTAATCAGGAGAAATGCAAATTAAGACAACTCTAAGATACCACTCACAC 224257 v - i vv i i i-i L1ME5_3end#LI 153 AGTAATCA-GAGAAATGCAAATTAAAACAACAATGAGATATCACTT-TAC 200 chr2qtel1M 224258 ACCTGTCAGATT-ACAAATGACAGGAA---AAATAATGATGATTGTTGA- 224302 i i i -i vivi i ---ii vii v i- L1ME5_3end#LI 201 ACCTATTAGACTGGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTGGC 250 chr2qtel1M 224303 GGGGATGTGGGAAAACTGGGACATTGATGCATTGTT-ATGGAGTTGTGAA 224351 i i ? iv i vi v i i -i iiv ii L1ME5_3end#LI 251 GAGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGA 300 chr2qtel1M 224352 CGAATCCAACCATTTTGGAGAGTAGTTTGGAACTAT---GTCAAA--AAG 224396 vii v i i i i i v v i--- -- L1ME5_3end#LI 301 CTGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTAAG 350 chr2qtel1M 224397 TTATCAAATCAGCATACTT--TGATCCAGCAGTGTTACTACTGGGATTAT 224444 ------ vv ii-- i i viii v -- L1ME5_3end#LI 351 T------ATACGCATACCCTATGACCCAGCAATTCCGCTCCTGGG--TAT 392 chr2qtel1M 224445 ATATCCCAAAGAGATTATAAAGAAGG-----AAAGGGACCTGTATGTGCA 224489 i v v viv ----- i ---- i i L1ME5_3end#LI 393 ATATCCCAAAGAAATTCTCACACAGGTCCATAAGGGGAC----ATGTACG 438 chr2qtel1M 224490 CGAATGCTTGTGGCAGCCCT-TTTGTAGTGGTTAGAAACTGAAACTGA-A 224537 v i i ii v vi - i ivi i ii i ivii -v L1ME5_3end#LI 439 AGGATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACC 488 chr2qtel1M 224538 TGGATGTCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATATGAAAA 224587 i v v i v iii v iv -v v L1ME5_3end#LI 489 TGGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATG-CAC 537 chr2qtel1M 224588 ATTATGGAATATTA 224601 ii i i L1ME5_3end#LI 538 ACCATGGAGTACTA 551 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.18 CpG sites = 80, Kimura (unadjusted) = 33.55 Transitions / transversions = 1.82 (80/44) Gap_init rate = 0.06 (31 / 489), avg. gap size = 1.35 (42 / 31) 42 23.80 0.00 0.00 chr2qtel1M 225136 225234 (774766) (AAA)n#Simple_repeat 1 99 (0) m_b88s252i0 3279 chr2qtel1M 225136 AAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAATCACATGGAAT 225185 v i vv v vii v (AAA)n#Simple 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr2qtel1M 225186 AAAATGAAGTGGAGGAGTAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAA 225234 vi ivii ii iv i (AAA)n#Simple 51 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 99 Matrix = Unknown Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.00 (0 / 98), avg. gap size = 0.0 (0 / 0) 16 9.26 0.00 0.00 chr2qtel1M 225764 225786 (774214) (A)n#Simple_repeat 1 23 (0) m_b88s252i2 3280 chr2qtel1M 225764 AACAAAAAAAAAAAAAAAAAGAA 225786 v i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAA 23 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 1629 31.67 3.54 3.46 chr2qtel1M 234976 236303 (763697) L1M5_orf2#LINE/L1 832 2160 (1134) m_b88s551i7 3281 chr2qtel1M 234976 GAAAATAATAACACA-TATAACAAAATTTATGGAATACA-CTAAAG---- 235019 ? i v i -i v i i i - ---- L1M5_orf2#LIN 832 GANAATGAAAATACAACATATCAAAATTTGTGGGATGCAGCTAAAGCAGT 881 chr2qtel1M 235020 ---TAGAAGAAATTTTATATGTCTAAATATGTACAT--GAATAAAATAGA 235064 --- i i v vv?i ii? i -- v i v i L1M5_orf2#LIN 882 GCTTAGAGGGAAATTTATAGCNTTAAATGCNTATATTAGAAAAGAAGAAA 931 chr2qtel1M 235065 G-------ATCAATGAATTGGTTTTACAGCTAAAAAAGCTAGAAAAA--A 235105 ------- vi iivi v v v i -- L1M5_orf2#LIN 932 GGCTTAAAATCAATGATCTAAGCTTCCACCTTAAGAAGCTAGAAAAAGAA 981 chr2qtel1M 235106 GAATAAATTTTTAAAATCCTAATTAAGTACTAAATTAGATATTTTAAAAA 235155 ii ---- i v v? vv iivvi v vv i L1M5_orf2#LIN 982 GAGCAAATT----AAACCCAAAGNAAGTAGAAGGAAGGAAATAATAAAGA 1027 chr2qtel1M 235156 TCTAAGGAGGGATAAATTCTTTTCTTCCTTTCAACAAAATGGAAAGTAAG 235205 vvi v ---- -------------- ii i ii i L1M5_orf2#LIN 1028 TAAGAGCAG----AAAT--------------CAATGAAATAGAAAACAAA 1059 chr2qtel1M 235206 AAAACTTTTAAACTAGTAAATAAAATTAAAACTTGATGTTAAGAAAAAAT 235255 ? ? vv vi ivv i v ii iii vi i vi vv i L1M5_orf2#LIN 1060 NANACAATAGAGAAAATCAACGAAGCCAAAAGCTGGTTCTTTGAAAAGAT 1109 chr2qtel1M 235256 -AATAAAGCAGATGAAGTTTTGGCTAATTTGATTAG---AAAAAGGAAGG 235301 - iiv i vi i i ? ivi i i--- ii i L1M5_orf2#LIN 1110 CAATAAAATTGATAAACCTCTAGCNAGACTGATCAAGAAAAAAAGAGAGA 1159 chr2qtel1M 235302 A-ATGCAAATTACTAGTATCAAAAATGAAAAGAGTGAAGTTACCAGCAAT 235350 - ii i i ii ii v vi i i vvi L1M5_orf2#LIN 1160 AGACACAAATTACCAATATCAGGAATGAAAAAGGAGACATCACTACAGAT 1209 chr2qtel1M 235351 GAAGAAGAAATTAAAGCAATAAATAGGACCTATTTTGCTCAACTGTTTGC 235400 vvviv v ivi vv iivv v vv v v L1M5_orf2#LIN 1210 CCTACAGACATTAAAAGGATAATAAGAGAATATTATGAACAACTTTATGC 1259 chr2qtel1M 235401 TAACAAATCAGACCATTTAATTGAAATGGATGAATATTTGCAGAAACATA 235450 i i iv ?v i iv ii vii vv i i L1M5_orf2#LIN 1260 CAATAAATTTGANAACTTAGATGAAATGGACAAATTCCTTGAAAAACACA 1309 chr2qtel1M 235451 AATTGTCCATATTAACAGAAGAA--AATATAAAATGCTGAAATAACCCCA 235498 ? ii v v i i ?v -- v - - i i L1M5_orf2#LIN 1310 ANTTACCAAAACTGACNCAAGAAGAAATAGAAAAT-CTGAA-TAGCCCTA 1357 chr2qtel1M 235499 T-TTTA--AAAGTAGAACTTAAACAAGTCATCAATGAA--TTCCCAAAGA 235543 - i -- --- v i ivv v i -i -- v i L1M5_orf2#LIN 1358 TATCTATTAAAG---AAATTGAATTTGTAATTAA-AAACCTTCCCACAAA 1403 chr2qtel1M 235544 AAAAAAATCTCCAGGGCAAGATGAATTTGCAAGGATATTCTACCAAATAT 235593 i --- v v iv ii vi viv i L1M5_orf2#LIN 1404 GAAAA---CTCCAGGCCCAGATGGCTTCACTGGTGAATTCTACCAAACAT 1450 chr2qtel1M 235594 TTAAAGAACAATTAATTTTGATACAATGTAAACTACTTGAAAAAATGGGT 235643 i v v viii viv iii vi iv i i iv L1M5_orf2#LIN 1451 TTAAGGAAGAAATAATACCAATCTTACACAAACTCTTCCAGAAAATAGAA 1500 chr2qtel1M 235644 GAAAAATGATTGCTACCTAATTAATTTTGTGACACAAATATGGGGGTAAC 235693 i i iv vii v i i v i vi v ii ?ivvv i i L1M5_orf2#LIN 1501 AAAGAGGGAACACTTCCCAACTCATTTTATGAGGCCAGCATNACCCTGAT 1550 chr2qtel1M 235694 ATTTAAAATAGGAAGAGCTAAAACAG--AAAGAAAATTATAGACCAATTT 235741 iiv vi? iv i vi vv i-- i v L1M5_orf2#LIN 1551 ACCAAAACCNGACAAAGACATTACAAGAAAAGAAAATTACAGACCAATAT 1600 chr2qtel1M 235742 CCCTAATGAATACTGATGCAAAAATATATAAATAAAACAATAGTAAA-CA 235790 v i iv -iv ? i i v i - i L1M5_orf2#LIN 1601 CCCTCATGAACATAGATGCAAAAAT-CCTNAACAAAATATTAGCAAATCG 1649 chr2qtel1M 235791 AAT-TAGATCAATGTATAAACAGGACAATAATATAGTATAACCAAATAAG 235839 -i -- i v --- i vi i i ii L1M5_orf2#LIN 1650 AATCCAG--CAATATATAAAAAGG---ATAATACATCATGACCAAGTGGG 1694 chr2qtel1M 235840 ATCTATACCAGGAATGCAGAACTGATTCAATGTCAGGGAAAGTATCAGCA 235889 i i v iiii i i ii iv ii vvv iii L1M5_orf2#LIN 1695 GTTTATCCCAGGAATGCAAGGTTGGTTTAACATTCGAAAATCAATCAATG 1744 chr2qtel1M 235890 TAAT----CATATCA--AGAATAAAACTAACAGAAACCATCTGATTATAT 235933 ---- i -- i--i v i i v i v L1M5_orf2#LIN 1745 TAATTCACCATATTAACAGAATAAAG--GAGAAAAATCATATGATCATCT 1792 chr2qtel1M 235934 CAATAGATAAAGAAAAAGATTTTGAGAAAATACAGTACCCACTCCTATTA 235983 iv vv v v ii i v iv L1M5_orf2#LIN 1793 CAATAGATGCAGAAAAAGCATTTGACAAAATTCAACACCCATTCATGATA 1842 chr2qtel1M 235984 AAAA-TATTAGAGAGCATGGGAATAAATGGAGTTTTCCTCAAAATGGCAA 236032 - v i vi i - i i v iivi vv ii L1M5_orf2#LIN 1843 AAAACTCTCAGCAAAC-TAGGAATAGAAGGGAACTTCCTCAACCTGATAA 1891 chr2qtel1M 236033 ATAATATCTATCCAAAACCATCAGTATGCATTATATGAAATGGCTATAAA 236082 viii ivv vv i?vi i ivv iv v ? L1M5_orf2#LIN 1892 AGGGCATCTACGAAAAACCTACAGCNAACATCATACTTAATGGTGAAANA 1941 chr2qtel1M 236083 CTAGGTACATTCACAATAAGTTCGGGGGTTGAAACAAAGATACCTACTAT 236132 iii?i v v vv v ii-ii i i ii ii ? L1M5_orf2#LIN 1942 CTGAANGCTTTCCCCCTAAGATCGGGAA-CAAGACAAGGATGTCCGCTNT 1990 chr2qtel1M 236133 CACTACTATTGTTCAACATTGTATTAGAAATGTTGGC---TTTAGCAAGA 236179 i vi i i i ii vi i --- vi ii i L1M5_orf2#LIN 1991 CACCACTTCTATTCAACATTGTACTGGAGGTCCTAGCCAGTGCAATAAGG 2040 chr2qtel1M 236180 AAAG-AAAAGAAACAGAAGGGAATTAGGAGTAGGCAATGAGGAAACAGAA 236228 v - i i v -- iiii v v v i i i L1M5_orf2#LIN 2041 CAAGAAAAAGAAATAAAAGGCA--TAAAGATTGGAAAGGAAGAAATAAAA 2088 chr2qtel1M 236229 CTATCCCTATTTTCAGATGGTATAATGGTAGATCTAGAGAGTACTAAAGA 236278 i ?i iv ii i v ?v iv i i v ? L1M5_orf2#LIN 2089 CTGTCNTTATTCGCAGATGACATGATTGTNTACGTAGAAAATCCNAAAGA 2138 chr2qtel1M 236279 ATCAAACAAAAAAAAACTATTTGAA 236303 ---i v ? i v L1M5_orf2#LIN 2139 ATC---TACAAANAAACTACTAGAA 2160 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 42.85 CpG sites = 248, Kimura (unadjusted) = 43.77 Transitions / transversions = 1.57 (248/158) Gap_init rate = 0.05 (68 / 1327), avg. gap size = 1.37 (93 / 68) 245 21.46 23.81 2.36 chr2qtel1M 236690 236794 (763206) MIRb#SINE/MIR 3 129 (139) m_b88s601i1 3282 chr2qtel1M 236690 GGGAGGCAGCTAGGTGGCACAGTGGATAGAGCAC---------------- 236723 i i --- ii v ---------------- MIRb#SINE/MIR 3 GAGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGA 49 chr2qtel1M 236724 CAGACCTGAGTTCAAATATGGCCTCAGACACTTAACA-CT------TCCT 236766 i i viv v v v vi - ------i i MIRb#SINE/MIR 50 CAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTT 99 chr2qtel1M 236767 GGGTAAGTCACTTAACCCCACT--TCCTCA 236794 i i i v --v MIRb#SINE/MIR 100 GGGCAAGTTACTTAACCTCTCTGAGCCTCA 129 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 24.54 CpG sites = 13, Kimura (unadjusted) = 25.87 Transitions / transversions = 1.44 (13/9) Gap_init rate = 0.07 (7 / 104), avg. gap size = 4.00 (28 / 7) 395 30.43 4.98 4.55 chr2qtel1M 238587 238827 (761173) C L1ME5_3end#LINE/L1 (313) 628 387 m_b88s551i8 3283 chr2qtel1M 238587 TTTCACTCAGCATCA-GTTCATATAAGTCTCTTCCAGGC--CTTTCTGGA 238633 ii - -- v vii v v i-- v v v C L1ME5_3end#LI 628 TTTCACTCAGCACTATGTT--TTTAAGATCCATCCATGTTGCTATGTGTA 581 chr2qtel1M 238634 AATCATCCTGTTGGTCATTTCTTACAGAACAATAATATTCCATAATATTC 238683 --- iv iv iii v v vvvv i i ii i v C L1ME5_3end#LI 580 ---CATCTAGTCCGTTGCTTCTAACTGCTGCATAGTACTCCATGGTGTGC 534 chr2qtel1M 238684 ATATAACACAATTTATTCTGCCATTCTCCAACTGATGGGCATCCACCTGA 238733 vi v v iiivv i v v i i vv v- C L1ME5_3end#LI 533 ATCCACCACATTTTACCTATCCACTCTCCCAGTGATGGACACCCAGGTT- 485 chr2qtel1M 238734 AGCCTCCAGTTTCTAGCCACCACAAAGAGGGCTGCCACAAACATTCATGC 238783 - ii i iv v iv v ii i vi i C L1ME5_3end#LI 484 -GCCTCCAACTCCCCGCCACCACAAACAACGCTGCAATGAACATCCTCGT 436 chr2qtel1M 238784 ACATACAGGTCCCTTT------CTTTATG---ATCTCTTGGGGATATAAG 238824 ---- i ------ v i --- i v vi C L1ME5_3end#LI 435 ACAT----GTCCCCTTATGGACCTGTGTGAGAATTTCTTTGGGATATATA 390 chr2qtel1M 238825 CCC 238827 C L1ME5_3end#LI 389 CCC 387 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.93 CpG sites = 36, Kimura (unadjusted) = 39.65 Transitions / transversions = 1.06 (36/34) Gap_init rate = 0.06 (15 / 240), avg. gap size = 1.53 (23 / 15) 391 29.83 2.18 3.69 chr2qtel1M 240303 240577 (759423) L1M3_orf2#LINE/L1 3011 3281 (7) m_b88s551i9 3284 chr2qtel1M 240303 CAAAAATAGAAAATTTTGATTATACCAAACTGAAAAGCTCTTGCACAAAC 240352 v v vv i i i i ii i- L1M3_orf2#LIN 3011 CAAAAATAGACAAGTGGGACTACATCAAACTAAAAAGCTTCTGCACAG-C 3059 chr2qtel1M 240353 AAAGCTAATGCAGACAA--GATTAGAAGGGAAGTGAATAAACTGGGAAAA 240400 vv -- iv -- v ii i v iivv iii v i L1M3_orf2#LIN 3060 AAAGGAAA--CAATCAACAGAGTGAAAAGGCAACCTACGGAATGGGAGAA 3107 chr2qtel1M 240401 TATTTTTACAGTCAAAGGTTCTGGATAAAAGGCCCTCATTTCCAAAAATA 240450 v v i iv v vivv - ii i-- v v - L1M3_orf2#LIN 3108 AATATTTGCAAACCATATATCTG-ATAAGGGGT--TAATATCCAAAA-TA 3153 chr2qtel1M 240451 TATAGAGAATTAACCTAATTT-ATA--AAAAAATCAAGCCATTCTCCAAT 240497 ii i v?ivi i i- -- v --- vvi i L1M3_orf2#LIN 3154 TATAAGGAACTCNTACAACTCAATAGCAAAAAAACAA---ATAACCCGAT 3200 chr2qtel1M 240498 TGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGAAGAAATTG 240547 ? v iv i v vi v v vv L1M3_orf2#LIN 3201 TNAAAAATGGGCAAAGGACCTGAATAGACATTTCTCCAAAGAAGACATAC 3250 chr2qtel1M 240548 AAACTATTTCTAGTCATATG-AAAGATGCTC 240577 iviiivvi vi - L1M3_orf2#LIN 3251 AAATGGCCAACAGGTATATGAAAAGATGCTC 3281 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.68 CpG sites = 41, Kimura (unadjusted) = 38.99 Transitions / transversions = 1.08 (41/38) Gap_init rate = 0.05 (14 / 274), avg. gap size = 1.14 (16 / 14) 1017 29.75 4.17 3.61 chr2qtel1M 240445 240995 (759005) L1MB8_3end#LINE/L1 10 563 (362) m_b88s551i10 3284 chr2qtel1M 240445 AAAATATATAGAGAATT-----AACCTAATTTATAAAAAAATCAAGCCAT 240489 i i i ----- ii v- i - --- L1MB8_3end#LI 10 AGAATATATAAAGAACTCTTACAACTCAATA-ATAAAAAGA-CAA---AT 54 chr2qtel1M 240490 TCTCCAATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGA 240539 vvi ? v v i v vi v L1MB8_3end#LI 55 AACCCAATTNAAAAATGGGCAAAGGATCTGAATAGACATTTCTCCAAAGA 104 chr2qtel1M 240540 AGAAATTGAAACTATTTCTAGTCATATGAAA-GATGCTCCAAGTCATTAT 240588 v vv iviiivv iv i - v vi v L1MB8_3end#LI 105 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCATTAG 154 chr2qtel1M 240589 TAATCAGGAGAAATGCAAATTAAGACAACTCTAAGATACCACTCACACAC 240638 v - i i v vv i i- L1MB8_3end#LI 155 TCATCAGG-GAAATGCAAATCAAAACCACAATGAGATACCACTT-CACAC 202 chr2qtel1M 240639 CTGTCA----GATTACAAATGACAGGAAAAATAATGATGATTGTTGA-GG 240683 iiii ---- ii i vii v i v i i ii v i- i L1MB8_3end#LI 203 CCACTAGGATGGCTATAATCAAAAAGACAGATAATAACAAGTGTTGGCGA 252 chr2qtel1M 240684 GGATGTGGGAAAACTGGGACATTGATGCATTGTT-ATGGAGTTGTGAACG 240732 ii i i vi v i i i -i iiv i vv L1MB8_3end#LI 253 GGATGTGGAGAAATTGGAACCCTCATACACTGCTGGTGGGAATGTAAAAT 302 chr2qtel1M 240733 AATCCAACCATTTTGGAGAGTAGTTTGGAACTATGTCAAAAAGTT----A 240778 ii v i ii i ii i v v viv i ---- L1MB8_3end#LI 303 GGTGCAGCCGCTTTGGAAAACAGTCTGGCAGTTCCTCAAAAGGTTAAACA 352 chr2qtel1M 240779 TCAAATCAGCATACTTTGATCCAGCAGTGTTACTACTGGGATTATATATC 240828 vi i i v --- i i vii v i -- i L1MB8_3end#LI 353 TAGAGTTACCATA---TGACCCAGCAATTCCACTCCTAGG--TATATACC 397 chr2qtel1M 240829 CCAAAGAGATTATAAAGAAGG-----AAAGGGACCTGTATGTGCACGAAT 240873 v i i v v viv v ----- v iii i ---- L1MB8_3end#LI 398 CAAGAGAAATGAAAACATATGTCCACACAAAAACTTGTA----CACGAAT 443 chr2qtel1M 240874 GCTTGTGGCAGCCCT-TTTGTAGTGGTTAGAAACT-GAAACTGAATGGAT 240921 i ii i vi - ii i i ii i v - vivviii L1MB8_3end#LI 444 GTTCATAGCAGCATTATTCATAATAGCCAAAAAGTGGAAACAACCCAAAT 493 chr2qtel1M 240922 GTCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATATGAAAAATTAT 240971 ii iv v i v -vv v iv L1MB8_3end#LI 494 GTCCATCAACTGATGAATGGATAAATAAAATGTGGTATAT-CCATACAAT 542 chr2qtel1M 240972 GGAATATTACCGTTCTGTAAGAAA 240995 --- v i v L1MB8_3end#LI 543 GGAATATTA---TTCGGCAATAAA 563 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.02 CpG sites = 97, Kimura (unadjusted) = 39.35 Transitions / transversions = 1.59 (97/61) Gap_init rate = 0.05 (29 / 550), avg. gap size = 1.48 (43 / 29) 807 31.52 4.23 3.36 chr2qtel1M 240475 241065 (758935) L1PB1_3end#LINE/L1 43 638 (260) m_b88s551i11 3284 chr2qtel1M 240475 AAAAAATCAAGCCATTCTCCAATTGAAAAATGGTCAAAGGATATGAACAG 240524 v i v --- v ii i v v i i L1PB1_3end#LI 43 AAAAAAACAAACAAT---CCCATCAAAAAGTGGGCTAAGGACATGAATAG 89 chr2qtel1M 240525 ACAATTCTCAGATGAAGAAATTGAAACTATTTCTAGTCATATG-AAAGAT 240573 i v v vv iviiivvi iv - i L1PB1_3end#LI 90 ACAATTCTCAAAAGAAGATATACAAATGGCCAACAAACATATGAAAAAAT 139 chr2qtel1M 240574 GCTCCAAGTCATTATTAATCAGGAGAAATGCAAATTAAGACAACTCTAAG 240623 v vi i v i - i i v vv iv L1PB1_3end#LI 140 GCTCAACATCACTAATGATCAGG-GAAATGCAAATCAAAACCACAATGCG 188 chr2qtel1M 240624 ATACCACTCACACACCTGTCAGATTACAAATGA-CAGGAA---AAATAAT 240669 - vi v iv v ivvv i - ii --- v L1PB1_3end#LI 189 ATACCAC-CTTACTCCTGCAAGAATGGCCATAATCAAAAAATCAAAAAAT 237 chr2qtel1M 240670 GATGATTGTTGAGG-GGATGTGGGAAAACTGGGACATTGATGCATTGTT- 240717 i iiv iv - i vi vv i i vv i i i - L1PB1_3end#LI 238 AATAGATGTTGGCGTGGATGCGGTGAAAAGGGAACACTTCTACACTGCTG 287 chr2qtel1M 240718 ATGGAGTTGTGAACGAATCCAACCATTTTGGAGAGTAGTTTGGAACTATG 240767 i iiv i v i v i v i ii v iv viv L1PB1_3end#LI 288 GTGGGAATGTAAACTAGTACAACCACTATGGAAAACAGTGTGGAGATTCC 337 chr2qtel1M 240768 TCAAAAAGTTATCAAATCAGCA-TAC--TTTGATCCAGCAGTGTTACTAC 240814 i i ii -- vi v - -- i vii L1PB1_3end#LI 338 TTAAAGAACTA--AAAGTAGAACTACCATTTGATCCAGCAATCCCACTAC 385 chr2qtel1M 240815 TGGGATTATATATCCCAAAGAGATTATAAAGAAG---------GAAAGGG 240855 -- v - i - ---- --------- ii L1PB1_3end#LI 386 TGGG--TATCTA-CCCAGAG-GA----AAAGAAGTCATTATACGAAAAAG 427 chr2qtel1M 240856 ACCTGTATGTGCACGAATGCTTGTGGCAGC-CCTTTTGTAGTGGTTAGAA 240904 -- iiv ii v i i i - vv i i i v iv i L1PB1_3end#LI 428 A--TACTTGCACACGCATGTTTATAGCAGCACAATTCGCAATTGCAAAAA 475 chr2qtel1M 240905 ACTGAAACT-GAATGGATGTCCATCAGTTGGAGAATGGCTGAATAAATTG 240953 vv i i- vviii i i iiiv i v i v ? L1PB1_3end#LI 476 TATGGAACCAGCCCAAATGCCCATCAATCAACGAGTGGATAAAGAAANTG 525 chr2qtel1M 240954 TGGTATATGAAAAATTATGGAATATTACCGTTCTGTAAGAAATGACCAAC 241003 - v v ii i ivvv ii i ivi iv ? L1PB1_3end#LI 526 TGGTATAT-ATATACCATGGAATACTACTCAGCCATAAAAAGGAATGAAN 574 chr2qtel1M 241004 AGATGAT-TTCAGAAAGGCCTGGAGAGACTTACACGAACTG-GATGCTAA 241051 vi ii- iv iv i vi v iv --i i-v v L1PB1_3end#LI 575 TAATGGCATTCGCAGCGACCTGGATGGAATTGGA--GACTATTATTCTAA 622 chr2qtel1M 241052 GTGAAATGA--CAGGA 241065 i i -- L1PB1_3end#LI 623 GTGAAGTAACTCAGGA 638 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.45 CpG sites = 105, Kimura (unadjusted) = 42.40 Transitions / transversions = 1.40 (105/75) Gap_init rate = 0.06 (33 / 590), avg. gap size = 1.36 (45 / 33) 1271 26.26 4.90 3.63 chr2qtel1M 240491 240980 (759020) L1ME5_3end#LINE/L1 56 551 (390) m_b88s551i12 3284 chr2qtel1M 240491 CTCCAATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGAA 240540 i v v i iv v i L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chr2qtel1M 240541 GAAA-TTGAAA--CTATTTCTAGTCATATGAA-AGATGCTCCAAGTCATT 240586 -ii -- --v v - - v v L1ME5_3end#LI 106 GAAACCCGAAAGGCTA--ACAAG-CATATGAAGAGATGCTCAAACTCATT 152 chr2qtel1M 240587 ATTAATCAGGAGAAATGCAAATTAAGACAACTCTAAGATACCACTCACAC 240636 v - i vv i i i-i L1ME5_3end#LI 153 AGTAATCA-GAGAAATGCAAATTAAAACAACAATGAGATATCACTT-TAC 200 chr2qtel1M 240637 ACCTGTCAGATT-ACAAATGACAGGAA---AAATAATGATGATTGTTGA- 240681 i i i -i vivi i ---ii vii v i- L1ME5_3end#LI 201 ACCTATTAGACTGGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTGGC 250 chr2qtel1M 240682 GGGGATGTGGGAAAACTGGGACATTGATGCATTGTT-ATGGAGTTGTGAA 240730 i i ? iv i vi v i i -i iiv ii L1ME5_3end#LI 251 GAGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGA 300 chr2qtel1M 240731 CGAATCCAACCATTTTGGAGAGTAGTTTGGAACTAT---GTCAAA--AAG 240775 vii v i i i i i v v i--- -- L1ME5_3end#LI 301 CTGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTAAG 350 chr2qtel1M 240776 TTATCAAATCAGCATACTT--TGATCCAGCAGTGTTACTACTGGGATTAT 240823 ------ vv ii-- i i viii v -- L1ME5_3end#LI 351 T------ATACGCATACCCTATGACCCAGCAATTCCGCTCCTGGG--TAT 392 chr2qtel1M 240824 ATATCCCAAAGAGATTATAAAGAAGG-----AAAGGGACCTGTATGTGCA 240868 i v v viv ----- i ---- i i L1ME5_3end#LI 393 ATATCCCAAAGAAATTCTCACACAGGTCCATAAGGGGAC----ATGTACG 438 chr2qtel1M 240869 CGAATGCTTGTGGCAGCCCT-TTTGTAGTGGTTAGAAACTGAAACTGA-A 240916 v i i ii v vi - i ivi i ii i ivii -v L1ME5_3end#LI 439 AGGATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACC 488 chr2qtel1M 240917 TGGATGTCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATATGAAAA 240966 i v v i v iii v iv -v v L1ME5_3end#LI 489 TGGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATG-CAC 537 chr2qtel1M 240967 ATTATGGAATATTA 240980 ii i i L1ME5_3end#LI 538 ACCATGGAGTACTA 551 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.18 CpG sites = 80, Kimura (unadjusted) = 33.55 Transitions / transversions = 1.82 (80/44) Gap_init rate = 0.06 (31 / 489), avg. gap size = 1.35 (42 / 31) 42 23.80 0.00 0.00 chr2qtel1M 241515 241613 (758387) (AAA)n#Simple_repeat 1 99 (0) m_b88s252i3 3285 chr2qtel1M 241515 AAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAATCACATGGAAT 241564 v i vv v vii v (AAA)n#Simple 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr2qtel1M 241565 AAAATGAAGTGGAGGAGTAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAA 241613 vi ivii ii iv i (AAA)n#Simple 51 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 99 Matrix = Unknown Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.00 (0 / 98), avg. gap size = 0.0 (0 / 0) 22 7.25 0.00 0.00 chr2qtel1M 242138 242166 (757834) (A)n#Simple_repeat 1 29 (0) m_b88s252i5 3286 chr2qtel1M 242138 AATAAAAAAAAAAAAAAAAAAAAAAAGAA 242166 v i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA 29 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 12 10.03 0.00 0.00 chr2qtel1M 246301 246322 (753678) (ACAT)n#Simple_repeat 1 22 (0) m_b88s252i6 3287 chr2qtel1M 246301 ACATACATACATACACACACAC 246322 i i (ACAT)n#Simpl 1 ACATACATACATACATACATAC 22 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 218 27.98 9.65 5.93 chr2qtel1M 249130 249243 (750757) C MIR3#SINE/MIR (23) 185 68 m_b88s601i2 3288 chr2qtel1M 249130 AGAGCTGAAAGTCACTTCAGAATTCAAGAATACAACCAATCCTCCCCAAT 249179 i vv i i iv ---- vi ii v v i i v C MIR3#SINE/MIR 185 AGAGCTGGAAGGGACCTTAGAGATC----ATCTAGTCCAACCCCCTCATT 140 chr2qtel1M 249180 TTACAA--GAGGAAACTCAAGC-------AGTGAACTAATTGGCTCAAAG 249220 i-- v i -------i v i i v i i C MIR3#SINE/MIR 139 TTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGG 90 chr2qtel1M 249221 TT-CAT-GCCATTTCTGTGTGGCAG 249243 i- i- ? v v--- C MIR3#SINE/MIR 89 TCACACAGCNAGTTA---GTGGCAG 68 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.57 CpG sites = 18, Kimura (unadjusted) = 36.57 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.10 (11 / 113), avg. gap size = 1.64 (18 / 11) 13 18.66 2.08 6.52 chr2qtel1M 250347 250394 (749606) (TTTCT)n#Simple_repeat 1 46 (0) m_b88s252i7 3289 chr2qtel1M 250347 TTTCATTTTCTTTTCTCTTTTTTTTCCCTTTATGATC-TGACTTTTCTT 250394 - - i - i v vv - vv (TTTCT)n#Simp 1 TTTC-TTTTCTTTTCT-TTTCTTTT-CTTTTCTTTTCTTTTCTTTTCTT 46 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.09 (4 / 47), avg. gap size = 1.00 (4 / 4) 344 23.48 3.03 9.68 chr2qtel1M 250613 250711 (749289) C MIRc#SINE/MIR (141) 127 35 m_b88s601i3 3290 chr2qtel1M 250613 CTGAGGCAATTGGAG---TTAAGTGACTTGCCTATGATTACACACATAAG 250659 -- ii --- i v i i vv i- C MIRc#SINE/MIR 127 CTGAGGC--TCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG- 81 chr2qtel1M 250660 AAGTATTAAGTGTCTGAGGTCAGATTTGAACTCAGGTCCTCCTGACTTCA 250709 ------ v v vivi i i i i i C MIRc#SINE/MIR 80 ------TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCA 37 chr2qtel1M 250710 GG 250711 i C MIRc#SINE/MIR 36 AG 35 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 25.68 CpG sites = 14, Kimura (unadjusted) = 28.85 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.10 (10 / 98), avg. gap size = 1.20 (12 / 10) 13 7.81 7.41 0.00 chr2qtel1M 251406 251432 (748568) (CTC)n#Simple_repeat 1 29 (0) m_b88s252i9 3291 chr2qtel1M 251406 CTCCTCCTTC-CCTCCACCTCCTCC-CCT 251432 i - v - (CTC)n#Simple 1 CTCCTCCTCCTCCTCCTCCTCCTCCTCCT 29 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.08 (2 / 26), avg. gap size = 1.00 (2 / 2) 17 9.12 0.00 0.00 chr2qtel1M 251996 252019 (747981) (A)n#Simple_repeat 1 24 (0) m_b88s252i10 3292 chr2qtel1M 251996 AAAAAAAAAAAAAAAAAGAAGAAA 252019 i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAA 24 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 12 24.48 0.00 8.77 chr2qtel1M 252328 252389 (747611) (CTCTGA)n#Simple_repeat 1 57 (0) m_b88s252i11 3293 chr2qtel1M 252328 CTCTGAATCCTGGCTCTGAATCTCCCAACTGATTTCTGGCTCTCAATCTC 252377 v - i v vv -v -i i v v v (CTCTGA)n#Sim 1 CTCTGACT-CTGACTCTGACTCTGAC-TCTGA-CTCTGACTCTGACTCTG 47 chr2qtel1M 252378 ATCTACTGACTC 252389 - - (CTCTGA)n#Sim 48 A-CT-CTGACTC 57 Matrix = Unknown Transitions / transversions = 0.38 (3/8) Gap_init rate = 0.08 (5 / 61), avg. gap size = 1.00 (5 / 5) 618 30.97 3.23 5.02 chr2qtel1M 252811 253398 (746602) C HERVK14C#LTR/ERVK (4012) 3422 2845 m_b88s701i2 3294 chr2qtel1M 252811 TCAGGTGCACACCTCAAGATATCATCCATGAAATGTAATAATAT-TACTT 252859 i vi ?--- v i iv - i -?ivv C HERVK14C#LTR/ 3422 TCGGCCGCACAN---AATATGTCATCCATATAATG-AATGATATANGAAT 3377 chr2qtel1M 252860 TTGGAAATGCTTTTCTTACTAGAAT-AATAGCAGCAATCATAAACATTTG 252908 i ivvv i ? - iv - vv?vvi i ? vi C HERVK14C#LTR/ 3376 CTGGAAACTGATCTCTNAC-AGGTTGAATAGCCTNCCCCACANAAGTTTG 3328 chr2qtel1M 252909 ACACATAGTAGGACTATTTTTCATTCCCTGTGGTAAAACTACCTATTCAT 252958 v ? ? ivv v i i ? vi i v v C HERVK14C#LTR/ 3327 ACAAATNGTNGGACTATTCAACATGCCCTGCGGCAANACTTTCCAATGAT 3278 chr2qtel1M 252959 ATCTTTTATAAAGCTCAGCTAA--ACTAATGCCAG--ACACTAAAAAGTC 253004 ? vvivvv?i i -- vi--ii v iv -- i v i-- C HERVK14C#LTR/ 3277 ANCTGGCTGCNGGTTC--CTTGTTGTTCATAGCAGGAATAGTAAAAG--C 3232 chr2qtel1M 253005 AAACCTTTTCATATCCTTCTTAACTAGAGGGATAGAATGGAAACAATACT 253054 ii iv v ?vv ivi i v vi i i v C HERVK14C#LTR/ 3231 AAATTTTTCAAAATCNGGCTCTGCTAGAGGAATAGTAAAGAAGCAGTCCT 3182 chr2qtel1M 253055 T--AATTGTGTATTACCCAAAGAGGCCATTCTCTAGGCAACTGAGTAGGG 253102 -- i--- v ivvv i? v v v vvi ii C HERVK14C#LTR/ 3181 TCAAATC---TATAACTATTAANGGCCAGTCTCTAGGAATCATGGCGGGG 3135 chr2qtel1M 253103 CATGGAAGTC-TAGCTAAAATGTTCCTATTATTTCCAT--CTGTTCATTT 253149 v ? v i - i iv i? ii i ?iv v? -- -- v C HERVK14C#LTR/ 3134 GANGGCAGCCCTGGCTGCAGNGCCCCCATNGGTTGNATGACTG--CATTG 3087 chr2qtel1M 253150 GCTTTTCTCAAATCAGT-ACCATCCTCCATTTTCCAGATTTCTTTTTTAT 253198 i vvi vi i i - v ? v i v i i i ? C HERVK14C#LTR/ 3086 ACGGCTCGTAAGTCGGTTAGCATNCGCCATCTGCCGGATTTTTTCTTNAT 3037 chr2qtel1M 253199 AGCAAATACAGGAGAATTCCGAAGACTTAGAGAATGTTG----TAAACGA 253244 vi i v ? i?i ---- i v ----? vii v C HERVK14C#LTR/ 3036 TACAAACACTGGNGAATTCCANGG----AGAAAATGTGGGCTCNATGTGT 2991 chr2qtel1M 253245 CCTTGCTGAAGTTGTTCCTGTACTA---CATCTAATCATTCTTGAATTTT 253291 v? vv i i vv --- v v --ivi iiv i C HERVK14C#LTR/ 2990 CCTTTNTCTAATTGTTCTTTGACTAATTCCTGTAA--GGCCCCCAGTTTT 2943 chr2qtel1M 253292 TGACTAGTCAAGGGCCACTGTTCTACCAACACTGTTGTATTAGTTTTACA 253341 vviv ?? iv ? ? v v ? v?v v vi i? v C HERVK14C#LTR/ 2942 TCCTGAGNNAGCGGCCACTGNTCNACCCAAACNGGNTTTTGGGTCNTCCA 2893 chr2qtel1M 253342 TTGAATGGGAACAGGTCAGAGCACAGGCAGGCCTTCAACAGCAGCTCTGC 253391 vv v i ?i------ v - -- ii iviv C HERVK14C#LTR/ 2892 TTTTAAGGGAATAGGNT------CTGG-AGGC--TCAACAGTGGCCGCCC 2852 chr2qtel1M 253392 CTAAAAA 253398 C HERVK14C#LTR/ 2851 CTAAAAA 2845 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.18 CpG sites = 83, Kimura (unadjusted) = 43.47 Transitions / transversions = 0.92 (83/90) Gap_init rate = 0.07 (39 / 587), avg. gap size = 1.23 (48 / 39) 635 32.20 3.30 3.50 chr2qtel1M 252811 253325 (746675) C HERVK14#LTR/ERVK (2921) 3175 2662 m_b88s701i1 3294 chr2qtel1M 252811 TCAGGTGCACACCTCAAGATATCATCCATGAAATGTAATAATATTAC--T 252858 v --- ii v -i v -- C HERVK14#LTR/E 3175 TCAGCTGCACAC---AGAATATCATCCATGTAATG-GATAATATAACATT 3130 chr2qtel1M 252859 TTTGGAAATGCTTTTCTTACTAGAATAATAGC---AGCAATCATAAACAT 252905 vi v - i v i vv ---vv i - i-- C HERVK14#LTR/E 3129 TTTTAAACTG-TTCTCTAACTGGCTTAATAGCTTTCCCGA-CATAAG--T 3084 chr2qtel1M 252906 TTGACACATAGTAGGACTATTTTTCATTCCCTGTGGTAAAACTACCTATT 252955 v v i vv v i iv vi i v C HERVK14#LTR/E 3083 TTGACAAATAGTCGGGCTATTTAGCATGCCTTGTGGTAGTACTTTCCAAT 3034 chr2qtel1M 252956 CATATCTTTTATAAAGCTCAGCTAA--ACTAATGCCAG--ACACTAAAAA 253001 vi v ivvvvi i --i v -- i v v i -- v i C HERVK14#LTR/E 3033 GGTATCTGTCCGCTGGTTC--TTTATTATTTATGGCGGGAACAGTAAAAG 2986 chr2qtel1M 253002 GTCAAACCTTTTCATA-TCCTTCTTAACTAGAGGGATAGAATGGAAACAA 253050 -- i- - i vvvi i i i i v vii i C HERVK14#LTR/E 2985 --CAAAT-TTTTCATAATCTTGGGCAGCTAAAGGAATGGTAAAAAAGCAA 2939 chr2qtel1M 253051 TACTTAATTGTGTATTACCCAAAGAGGCCATTCTCTAGGCAACTGAGTAG 253100 v v v-i v i ivvi v v i v v v vvv v C HERVK14#LTR/E 2938 TCCTTTAG-ATCTATCACTATGAGAGGCCAGTATTTTGGGATCATTGTTG 2890 chr2qtel1M 253101 GGCATGGAAGTC-TAGCTAAAATGTTCCTATTATTTCCATCTGTTCATTT 253149 v v v i - i i iv i iv i viv vv vvvv v C HERVK14#LTR/E 2889 GGGAGGGCAGCCCTGGTTGCAGTGCACCCATGGGTTGAATCACAGCATTA 2840 chr2qtel1M 253150 GCTTTTCTCAAATCAGT-ACCATCCTCCATTTTCCAGATTTCTTTTTTAT 253198 i vvii i v - v i i v i i v C HERVK14#LTR/E 2839 ACAGCCCTTAAATCTGTTAACATTCTCCATTTCCCTGATTTTTTCTTAAT 2790 chr2qtel1M 253199 AGCAAATACAGGAGAATTCCGAAGACTTAGAGAATGTTGTAAACGACCTT 253248 ii i i ivvv i v v i v v i v i C HERVK14#LTR/E 2789 GACAAATACAGGAGAATTCCAAGGGGAGAAAGTAGGCTCTATATGTCCCT 2740 chr2qtel1M 253249 GCTGAAGTTGTTCCTGTACTA---CATCTAATCATTCTTGAATTTTTGAC 253295 vi v i i i --- v i -- vi iv i -- C HERVK14#LTR/E 2739 TTTGCAATTGTTCCTGCACCAGTTCTTTTAA--AGCCTCCAGTTTTT--C 2694 chr2qtel1M 253296 TAG--TCAAGGGCCACTGTTCTACCAACACTG 253325 iv -- iv i i i v v i C HERVK14#LTR/E 2693 CTGTTTCAGCGGCCATTGCTCCACCCAAACCG 2662 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.46 CpG sites = 75, Kimura (unadjusted) = 42.48 Transitions / transversions = 0.88 (75/85) Gap_init rate = 0.05 (27 / 514), avg. gap size = 1.30 (35 / 27) 468 37.07 9.20 3.61 chr2qtel1M 253893 254838 (745162) C MamRTE1#LINE/RTE-BovB (2501) 1311 315 m_b88s601i4 3295 chr2qtel1M 253893 TCAGTCTATGATCATTCCAGCATTCTGCATCACATATGGCCTTTGTCACT 253942 v v i iv i v ii ii i iviv v - C MamRTE1#LINE/ 1311 TCAGGCGATGGTCGGTCCAGCACTCGGCGCCACGCATAGCTGCAGTAA-T 1263 chr2qtel1M 253943 CTC--TATCTT---GTTTCTTCCCTT--ACAATTATACAGTCTACTAAAT 253985 v--i i --- v i iv iv i-- i v i i v iv i C MamRTE1#LINE/ 1262 CTAAACATCCTTCAGGTCCCGCTGTCGAACGATGATATAATCAATGAGAT 1213 chr2qtel1M 253986 GACAATGTTTG--CTGTAAATGTGCATGCATGAAATTTTGTT-------- 254025 v v i i-- iv ii-- v vi i vi -------- C MamRTE1#LINE/ 1212 GCCACTGCTTAGACCTTGG--GTGCATCCATGATGTCTTTCTCTTATTCG 1165 chr2qtel1M 254026 ----GCG----ACAGTGTTGGTGAT-AGGGTCTTCAGATGCACAA-ATCT 254065 ---- ---- ii - v iv --- viii- iv C MamRTE1#LINE/ 1164 GTAGGCGGAAGATGGTGTTGGTGATTACGAGCT---GATGCTTGGCACAT 1118 chr2qtel1M 254066 TCACTAAT----AACTGACCAGTGCTGTTGCTGTTTTCAA-CCTATTCCA 254110 i i v---- iiv v ?vvv i - ii v?vi C MamRTE1#LINE/ 1117 TCGCTGAGCAGGAGTAGACCATTGCTGTTNAGCTTTCCAATCCCGTGNGG 1068 chr2qtel1M 254111 CCCAAAGACATTCC--CTTGTCTGAGCCTAGT-----ATA---ACCTTAA 254150 i i v v i -- vi i vi v v i----- i ---i v i C MamRTE1#LINE/ 1067 TCCGATGACTTTTCTCCACGTTTCGGCATCGCTGCCGACACGTGCGTTGA 1018 chr2qtel1M 254151 AATTAGCCAGGATTAGATAAGCTTGTCCTCTTTTGGCAA-ATTGAGGATG 254199 ivv iv i-- v vvv v i v-ii v - C MamRTE1#LINE/ 1017 AATCTCCCGTGAC--GATCAGCTTGTCAGATGTTGGTACCGCTGCG-ATG 971 chr2qtel1M 254200 AGCATCTCTAG-TCTTCTGAAAATTTTCCTTTGACCTCATCAAGGTTCCT 254248 iv v i - i ivv i i i vv iivi v C MamRTE1#LINE/ 970 AGTCTGTCCAGATCCTTGTAGAATCTTTCTTTCTCCTCATCGGTATTCGT 921 chr2qtel1M 254249 CATGGTGGGAAGATAGTCACTGATCATGTAACCATGGCA-TTTTCCTACA 254297 iiv vv i v i vviv ?i i- vi v C MamRTE1#LINE/ 920 CATGGTGGGGGCATATGCGCTGATGACGGTGGCANAGCGCTTTTGTTTCA 871 chr2qtel1M 254298 GGTGCCAAGGGCATTGTTATAAGCCTGACATTAAGTCTTTTTGGCAGACA 254347 i? -i i v i vv i v v v v i ? vv i i v i iv C MamRTE1#LINE/ 870 GANG-TAGGCGTAGGGTCATCAGACGGTCACTNATGCCTCTGGGCAAATT 822 chr2qtel1M 254348 TACAGGGTTGCTGATTTG-AACTGGTTCATTGCTAACCTATACCAACTTC 254396 ivii ?i vvv ivv -i vi v v v i- --i i v C MamRTE1#LINE/ 821 TGGGAGNCTTGAGACAAGTGACTGTCTGATTGCAAAGCTG-AC--GCCTG 775 chr2qtel1M 254397 ACAATGCTCCCTCC----ACTGCACTCC-CTGCAGAAAACCTTGTATGTA 254441 v iivv v i---- vv v vv - v i vvvi ?vii C MamRTE1#LINE/ 774 AGAGCCGTCGCTCTGAAGAGGGAAGACCTCTCCAGAAGAAGGCGTANCCG 725 chr2qtel1M 254442 GCTCCGACTTCAGTAAGGTGGCCTTTATTTGCCAGCCTTGTTTCACTCAG 254491 v viii v i v v i iv vv i v i C MamRTE1#LINE/ 724 GCACCTGTCTCCGTGAGCTGTCCTTCATCAGGAAGTCTGGTTTCGCTCAG 675 chr2qtel1M 254492 GGCTGCCTTTTGGATG-AGACACC-TA-CTG---AATTCTCTGGCCACTA 254535 v v ------ -v v - - --- i v vv v v C MamRTE1#LINE/ 674 TGCGGC------GATGTCGACTCCGTATCTGGACAGTTCACGTGCGACGA 631 chr2qtel1M 254536 GAGCTGTCCATCTTTCAGGTTTGCTGCATTATCCATAATGGTGACACATT 254585 v i i v v vivi vv vii i v ----- i v C MamRTE1#LINE/ 630 GTGCCGTTCTTCTTTCTGGACGACTGCTGTTCTCGTCAT-----CGCATA 586 chr2qtel1M 254586 CCAAGGACTGATGGTGAATGAAATCTTTGTACAAGT--TTTTATATGTAT 254633 v -- vv v vv ------i i vvi -- v v ?? C MamRTE1#LINE/ 585 GC--GTCCTGATGTTCCATGA------CGCAATGGTTATTTTCTTTGTNN 544 chr2qtel1M 254634 CTGTTTGTGTGTGTGTGTCTGTATTTCTATCACAGGA-TGGGGTCCACCA 254682 i? v v --- v v i i ?v vi i i i - iiiii C MamRTE1#LINE/ 543 TNGGTAGT---TTTCTATTTGNTTTTGCACCGCAAGANTAAAACCCACCA 497 chr2qtel1M 254683 ACCATGGTAGAC-----AGCCAGGGCTGATT------AAGCAGAT----T 254717 iv ii i iv ----- ?vi ? ------ i ii---- C MamRTE1#LINE/ 496 GACGCGATAATCTGGTGAGCCAGNTTTGANTTTGGCGAGGCAGGCAACGT 447 chr2qtel1M 254718 TTATTGTACCTTTTCTGGTCCCTTCCTCAT--AAAGGGGG--ATTTTTTT 254763 vv i i ? i --ii v i --iiviv? i C MamRTE1#LINE/ 446 TTAGGGCACCTTTTCTAGNCCCTTCCCCATTCGGAGTGAGCAGCGCGNTC 397 chr2qtel1M 254764 TTA---AGA---GCTCATACATCTAGGGAACTGCTACATCTCACTGCTGT 254807 i --- i--- v i i ?vi iiv ivvii i C MamRTE1#LINE/ 396 CTAAACAGGGCTGCTCAGACACCCAGGNCGCTGCCGAACGGTGCTGCTGC 347 chr2qtel1M 254808 GTC--CAGTGAGAAGATGGCTGCATAGCTTGGG 254838 v -- i vv iii i ii- v i C MamRTE1#LINE/ 346 CTCNTCAGCGACTAAGCGACCA-ATATCCTGGG 315 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 45.66 CpG sites = 175, Kimura (unadjusted) = 53.98 Transitions / transversions = 1.07 (175/163) Gap_init rate = 0.07 (70 / 945), avg. gap size = 1.76 (123 / 70) 17 12.81 2.94 0.00 chr2qtel1M 255317 255350 (744650) (TTTC)n#Simple_repeat 1 35 (0) m_b88s252i13 3296 chr2qtel1M 255317 TTTCTTTCTTTCTTTCTGTCTTT-TATTTTTATTT 255350 v - v i v (TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT 35 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 17 22.67 1.89 1.89 chr2qtel1M 255315 255367 (744633) (TATTTT)n#Simple_repeat 1 53 (0) m_b88s252i12 3297 chr2qtel1M 255315 TATTTCTTTCTTTCTTTCTGTCTTTTATTTTTATTTTTA-ATAGCTTTTT 255363 i v i v i i - -v vvv (TATTTT)n#Sim 1 TATTTTTATTTTTATTTTTAT-TTTTATTTTTATTTTTATTTTTATTTTT 49 chr2qtel1M 255364 ATTT 255367 (TATTTT)n#Sim 50 ATTT 53 Matrix = Unknown Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.00 (2 / 2) 12 9.12 4.17 0.00 chr2qtel1M 255430 255453 (744547) (TCCC)n#Simple_repeat 1 25 (0) m_b88s252i14 3298 chr2qtel1M 255430 TCCCTTCCT-TCTCCCTCCCTCCCT 255453 i -i (TCCC)n#Simpl 1 TCCCTCCCTCCCTCCCTCCCTCCCT 25 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 390 32.95 9.11 0.83 chr2qtel1M 256055 256614 (743386) L1MD_orf2#LINE/L1 1951 2556 (738) m_b88s551i13 3299 chr2qtel1M 256055 TTCCCAGTAAGATCAGGG-TGAAACAATGGTG-CCATTTTCATCACTATA 256102 vv i i-ii ii v i - ii i i v v L1MD_orf2#LIN 1951 TTCCCCCTAAGATCGGGAACAAGGCAAGGATGTCCGCTCTCACCACTCTT 2000 chr2qtel1M 256103 ATGCAACATTGTACTAGAAATGTTAGC---TTTAGTAAA--AAGAAAAG- 256146 v v i i vi --- vi i i-- - L1MD_orf2#LIN 2001 ATTCAACATAGTACTGGAAGTTCTAGCCAGTGCAATAAGGCAAGAAAAGG 2050 chr2qtel1M 256147 AAATTGAAGTAAT-TAGAGTAAACAACTAGGAAACAAAACTACCATGCTT 256195 vi vv -i v ii - vv i i ii vivv L1MD_orf2#LIN 2051 AAATAAAAGGCATACAGATTGGA-AAGGAAGAAATAAAACTGTCCCTATT 2099 chr2qtel1M 256196 TGAAGATGATATGCTGACCTAC----AGAATTCTAGAGAATCAACTGAAA 256241 v i v vii ---- i i i ii v vi L1MD_orf2#LIN 2100 TGCAGATGACATGATTGTCTACGTAGAAAATCCCAAGGAATCTACAAAAA 2149 chr2qtel1M 256242 A-CTACAAGAAACACTTAACAACTTTAGCAAAATGGAAGGACATAAAATA 256290 - v v vi v v iii v i ii v v i i i ? L1MD_orf2#LIN 2150 AACTCCTAGAACTAATAAGTGAGTTCAGCAAGGTCGCAGGATACAAGATN 2199 chr2qtel1M 256291 AACCGATATAAATCA--------TC-----AGCAGAAA-GAAC---TAGA 256323 vv i v -------- ----- vi v - --- i L1MD_orf2#LIN 2200 AACATACAAAAATCAATTGTATTTCTATATACTAGCAATGAACACGTGGA 2249 chr2qtel1M 256324 AAGAGAAAT-------------CCATTCAAAATTCCTGGAGACAATATAA 256360 vv ------------- i v iv vi i v v i L1MD_orf2#LIN 2250 AACCGAAATTAAAAATACAATACCATTTACAATCGCTCAAAAAAAAATGA 2299 chr2qtel1M 256361 AATATTTGGGTGTCTCCCTGCCAAGACAAATCCAGGAATTATATCCACAC 256410 i i i vvvi iv i vi v v i v vv v L1MD_orf2#LIN 2300 AATACTTAGGTATAAATCTAACAAAACATGTACAGGACTTGTATGCTGAA 2349 chr2qtel1M 256411 AATTAAAAAATACTTTTCACAGAAATATAATTATATATAAGAAATTGGA- 256459 i v ii vv v v vv vv v v iv v - L1MD_orf2#LIN 2350 AACTACAAAACGCTGATGAAAGAAATCAAAGAAGATCTAAATAAATGGAG 2399 chr2qtel1M 256460 AGA-GTGTCAAGTGTTCATGGGT----AGCTACATGTATAATAAAAACAA 256504 -i ii -- i ---- viv -ii i i iiv L1MD_orf2#LIN 2400 AGACATACC--GTGTTCATGGATTGGAAGACTCA-ACATAGTAAAGATGT 2446 chr2qtel1M 256505 TAATTCTATCCAAAATCAATCTACTTATTCAGTGCCATACCAATCAAACT 256554 i -i v ii ? vvi i ii v v v v L1MD_orf2#LIN 2447 CAATTCT-CCCCAAATTGATNTACAGGTTTAACGCAATTCCTATCAAAAT 2495 chr2qtel1M 256555 GCCAAGAAATTACTTTATAGAGAT-GAAAAAATACTAACAAAATTCATCT 256603 v iv iv vi i v - v i? vv vvi i v L1MD_orf2#LIN 2496 CCCAGCAAGATTTTTTGTAGATATAGACAAGNTTATTCTAAAATTTATAT 2545 chr2qtel1M 256604 GGAAGAACGAA 256614 iii i L1MD_orf2#LIN 2546 GGAAAGGCAAA 2556 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 42.97 CpG sites = 95, Kimura (unadjusted) = 44.62 Transitions / transversions = 1.08 (95/88) Gap_init rate = 0.04 (22 / 559), avg. gap size = 2.55 (56 / 22) 228 25.52 4.83 2.70 chr2qtel1M 256510 256654 (743346) L1P4_orf2#LINE/L1 2452 2599 (695) m_b88s551i14 3299 chr2qtel1M 256510 CTATCCAAAATCAATCTACTTATTCAGTGCCATACCAATCAAACTGCCAA 256559 ii i- vv ii i v v i L1P4_orf2#LIN 2452 CTGCCCAAAG-CAATCTACAGATTCAACGCTATTCCTATCAAACTACCAA 2500 chr2qtel1M 256560 -GAAATTACTTTATAGAGATGAAAAAATACTA--ACAAAATTCATCTGGA 256606 - vv -i i i - v i v --vi v L1P4_orf2#LIN 2501 CGTCATT-TTTCACAGA-ATTAGAAAAAACTATTCTAAAATTCATATGGA 2548 chr2qtel1M 256607 A-GAACGAAAAGTCACAAAT-GTCAAGGGAAT--TAATGAAAAAATGCAA 256652 -v vi i i - i - i i v -- vv ivi L1P4_orf2#LIN 2549 ACCAAAAAAGAGCC-CGAATAGCCAAAGCAATCCTAAGCAAAAAGAACAA 2597 chr2qtel1M 256653 AG 256654 L1P4_orf2#LIN 2598 AG 2599 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 29.67 CpG sites = 20, Kimura (unadjusted) = 31.74 Transitions / transversions = 1.25 (20/16) Gap_init rate = 0.06 (9 / 144), avg. gap size = 1.22 (11 / 9) 869 27.62 3.10 2.61 chr2qtel1M 257165 257584 (742416) L1ME3G_3end#LINE/L1 7 428 (496) m_b88s551i15 3300 chr2qtel1M 257165 TCTAAAATATGTAGAGAAGTGAGTA-AAATCTATAAGACTGCAAGTCATT 257213 i i i i v vv- - v --iv v -- L1ME3G_3end#L 7 TCCAGAATATATAAAGAACTCC-TACAAATCAATAAGA--AAAAGACA-- 51 chr2qtel1M 257214 CCTCAGTTGATAAATGATCAA-GGATATGAACAGATACTTTTTAGATAAA 257262 v i i v v iv - ii v ivi vi i L1ME3G_3end#L 52 ACCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAG 101 chr2qtel1M 257263 GAAAT-TAAA--GCCATTTCTAATATGACAAAAAATGCTCTAAATCATTA 257309 -i -- v vvvv -- i v vv i L1ME3G_3end#L 102 GAAATACAAATGGCCAATAAACATATGA--AAAGATGCTCAACCTCACTA 149 chr2qtel1M 257310 TTGATCAGAGAAAAGCAAATTAAGACAACTCTGAGGTACCAT-----ACC 257354 v i i v i vv i ----- L1ME3G_3end#L 150 GTAATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACC 199 chr2qtel1M 257355 TCTCAGATTGG-ACAAGGTGACACGAACAGATAATGACAAATGTTGGAAG 257403 iv - v iv v v v -?iv iv ? i vii L1ME3G_3end#L 200 CATCAGATTGGCAAAAATTTAAAAG-NTTGATAATATCNAGTGTTGGCGA 248 chr2qtel1M 257404 GGATGTGAGAAAACTGGGACACTAATGCATTGTTGGTGGAAATGTGAATT 257453 i i i v v v v i i i i i i L1ME3G_3end#L 249 GGGTGTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATT 298 chr2qtel1M 257454 TATCCAACCATTCTGAAGAGTAATTTGGAACTGTGCCCAAAGGACTATAA 257503 vi v i ? i i i i -- v ii i vvii v v L1ME3G_3end#L 299 GGTACAGCCNTTTTGGAGGGCAATTTGG--CAGTATCTATTAAAATTTAA 346 chr2qtel1M 257504 AATTGTGCATACCCTTAGTTCCAACAGTCTCACTACTGGGTCTAGATTCC 257553 - i v vi i i ii v ? ?v vv i i L1ME3G_3end#L 347 AA-TGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCT 395 chr2qtel1M 257554 AAAGAAATAGTAGGAAATG-GTA-AAGGATCCA 257584 ? v v v v - i - ?v L1ME3G_3end#L 396 ANAGAAATACTCGCACATGTGCACAAGGANGCA 428 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.88 CpG sites = 57, Kimura (unadjusted) = 35.65 Transitions / transversions = 1.02 (57/56) Gap_init rate = 0.05 (19 / 419), avg. gap size = 1.26 (24 / 19) 912 30.11 2.87 1.70 chr2qtel1M 257214 257561 (742439) L1ME5_3end#LINE/L1 56 407 (534) m_b88s551i16 3300 chr2qtel1M 257214 CCTCAGTTGATAAATGATCAA-GGATATGAACAGATACTTTTTAGATAAA 257262 i i v v iv - ii v vi vi i L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chr2qtel1M 257263 GAAATT---AAAGCCATTTCTAATATGACAAAAAATGCTCTAAATCATTA 257309 ii--- i i vivvvv -- i i v v L1ME5_3end#LI 106 GAAACCCGAAAGGCTAACAAGCATATGA--AGAGATGCTCAAACTCATTA 153 chr2qtel1M 257310 TTGATCAGAGAAAAGCAAATTAAGACAACTCTGAGGTACCAT-----ACC 257354 v i v i vv i i i----- L1ME5_3end#LI 154 GTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACC 203 chr2qtel1M 257355 TCTCAGATTGGACAAGGTGACACGAACAGATAATGACAAATGTTGGAAGG 257404 v i i vv ii v v viivii v i vii L1ME5_3end#LI 204 TATTAGACTGGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTGGCGAG 253 chr2qtel1M 257405 GATGTGAGAAAACTGGGACACTAATGCATTGTTGGTGGAAATGTGAATTT 257454 i i ? iv i v v i i i i ii i v L1ME5_3end#LI 254 GATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACTG 303 chr2qtel1M 257455 ATCCAACCATTCTGAAGAGTAATTTGGAACTGTGCCCAAAGGACTATAAA 257504 i v i i i i -- v i ii ivvi -- v L1ME5_3end#LI 304 GTGCAGCCATTCTGGAGAGCAATCTGG--CAGTACTTAGTCAA--ATTAA 349 chr2qtel1M 257505 AT-TGTGCATACCCTTAGTTCCAACAGTCTCACTACTGGGTCTAGATTCC 257553 i - ii vv vi i i ii i v v v i L1ME5_3end#LI 350 GTATACGCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATATCCC 399 chr2qtel1M 257554 AAAGAAAT 257561 L1ME5_3end#LI 400 AAAGAAAT 407 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.44 CpG sites = 62, Kimura (unadjusted) = 39.95 Transitions / transversions = 1.51 (62/41) Gap_init rate = 0.03 (10 / 347), avg. gap size = 1.60 (16 / 10) 250 25.35 2.82 0.00 chr2qtel1M 258201 258271 (741729) L1ME3Cz_3end#LINE/L1 457 529 (468) m_b88s551i17 3300 chr2qtel1M 258201 TTCTAACAGTAAGGAATTGGAAAT--TGAAGATGCCCATCACTTGGAGAA 258248 v i ii ii i--ivv i i v v i L1ME3Cz_3end# 457 TTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCAATAGGGGAA 506 chr2qtel1M 258249 TGGCCAAATAAATTGTGTTATAT 258271 vi v L1ME3Cz_3end# 507 TGGATAAATAAATTGTGGTATAT 529 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 29.42 CpG sites = 11, Kimura (unadjusted) = 31.74 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.01 (1 / 70), avg. gap size = 2.00 (2 / 1) 249 37.59 0.71 0.00 chr2qtel1M 259148 259288 (740712) L2#LINE/L2 2724 2865 (217) m_b88s601i5 3301 chr2qtel1M 259148 AATAGTCTATTGGTACATCTGCCTCTCTCAAAGCTCTCCTTCCTCCAAAC 259197 i vi iiivvi v vii v vv iv ii ? iv L2#LINE/L2 2724 AATAGCCTCCTAACTGGTCTCCCTGCTTCCACCCTTGCCCCCCTNCAGTC 2773 chr2qtel1M 259198 CCTTATCCAGTCAGCTAGTAGAGTGATT-TCCTACAATGCAGTTCTTATC 259246 iv v v vv vivi i- ii v i i iv vv L2#LINE/L2 2774 TATTCTCAACACAGCAGCCAGAGTGATCCTTTTAAAACGTAAGTCAGATC 2823 chr2qtel1M 259247 ATGTCACTGTCCTACTCAATAAATTCCAGTGCCTTCCCATTT 259288 vii i v vvi i v i L2#LINE/L2 2824 ATGTCACTCCTCTGCTCAAAACCCTCCAATGGCTTCCCATCT 2865 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 52.49 CpG sites = 27, Kimura (unadjusted) = 53.97 Transitions / transversions = 1.04 (27/26) Gap_init rate = 0.01 (1 / 140), avg. gap size = 1.00 (1 / 1) 13 18.89 4.55 2.22 chr2qtel1M 260124 260167 (739833) (AAAAGA)n#Simple_repeat 1 45 (0) m_b89s252i0 3302 chr2qtel1M 260124 AAAAGCAATAATAATAATAAAAA-AAAAAGATAGTG-AAAAGAAAA 260167 - v v v v - v iv - (AAAAGA)n#Sim 1 AAAAG-AAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAA 45 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.07 (3 / 43), avg. gap size = 1.00 (3 / 3) 436 22.96 2.21 10.32 chr2qtel1M 260970 261105 (738895) MIRc#SINE/MIR 2 127 (141) m_b89s601i1 3303 chr2qtel1M 260970 GGGGCAGCTAGGTGGTTCAGTGGATAGAGTGCCAACCCTGAAGTCAAGAG 261019 i i--- v v ii iiiv i i i i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr2qtel1M 261020 GACTTGGAGTTCAAATTTGGTCTCAGACACTTAACACTTCCTACCTGTGG 261069 i - i i iiv v v v ------- v v MIRc#SINE/MIR 49 GACCTGG-GTTCGAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGT 90 chr2qtel1M 261070 GACCCTGGGCAAGTCACTTAACC---CTAATTGCCCCAG 261105 i --- i -- i MIRc#SINE/MIR 91 GACCTTGGGCAAGTCACTTAACCTCTCTGA--GCCTCAG 127 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.86 CpG sites = 19, Kimura (unadjusted) = 28.03 Transitions / transversions = 2.11 (19/9) Gap_init rate = 0.10 (14 / 135), avg. gap size = 1.14 (16 / 14) 22 35.33 0.00 3.54 chr2qtel1M 261220 261336 (738664) (TATATG)n#Simple_repeat 1 113 (0) m_b89s252i1 3304 chr2qtel1M 261220 TACATGTATATGTATACATACACTATGTATATGTATTGGTGAGTGTGTGT 261269 i -- ii - vv ivi i i (TATATG)n#Sim 1 TATATGTATATGTAT--ATGTA-TATGTATATGTATATGTATATGTATAT 47 chr2qtel1M 261270 GTGTGGTTGTGTGTGTGTGTATATCATATCTAGATAGGTATGTATGTATC 261319 i ivv i i i i -i v iv v i i i v (TATATG)n#Sim 48 GTATATGTATATGTATATGTATAT-GTATATGTATATGTATATGTATATG 96 chr2qtel1M 261320 TATATGTATGTATCTAT 261336 i i v (TATATG)n#Sim 97 TATATGTATATGTATAT 113 Matrix = Unknown Transitions / transversions = 2.00 (20/10) Gap_init rate = 0.03 (4 / 116), avg. gap size = 1.00 (4 / 4) 23 23.98 4.26 3.16 chr2qtel1M 261243 261336 (738664) (TATG)n#Simple_repeat 1 95 (0) m_b89s252i2 3304 chr2qtel1M 261243 TATGTA--TATGTATTGGTGAGTGTGTGTGTGTGGTTGTGTGTGTGTGTA 261290 -- - - iv i i i vv i i i i (TATG)n#Simpl 1 TATGTATGTATGTA-T-GTATGTATGTATGTATGTATGTATGTATGTATG 48 chr2qtel1M 261291 TATCATATCTAGATAGGTATGTATGTATCTA--TATGTATGTATCTAT 261336 -i v vi v v -- v (TATG)n#Simpl 49 TAT-GTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTAT 95 Matrix = Unknown Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.05 (5 / 93), avg. gap size = 1.40 (7 / 5) 23 20.30 0.00 0.00 chr2qtel1M 261245 261289 (738711) (TG)n#Simple_repeat 1 45 (0) m_b89s252i3 3305 chr2qtel1M 261245 TGTATATGTATTGGTGAGTGTGTGTGTGTGGTTGTGTGTGTGTGT 261289 i i i vv v vv (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 45 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 22 35.33 0.00 3.54 chr2qtel1M 261220 261336 (738664) (TATATG)n#Simple_repeat 1 113 (0) m_b89s252i1 3304 chr2qtel1M 261220 TACATGTATATGTATACATACACTATGTATATGTATTGGTGAGTGTGTGT 261269 i -- ii - vv ivi i i (TATATG)n#Sim 1 TATATGTATATGTAT--ATGTA-TATGTATATGTATATGTATATGTATAT 47 chr2qtel1M 261270 GTGTGGTTGTGTGTGTGTGTATATCATATCTAGATAGGTATGTATGTATC 261319 i ivv i i i i -i v iv v i i i v (TATATG)n#Sim 48 GTATATGTATATGTATATGTATAT-GTATATGTATATGTATATGTATATG 96 chr2qtel1M 261320 TATATGTATGTATCTAT 261336 i i v (TATATG)n#Sim 97 TATATGTATATGTATAT 113 Matrix = Unknown Transitions / transversions = 2.00 (20/10) Gap_init rate = 0.03 (4 / 116), avg. gap size = 1.00 (4 / 4) 23 23.98 4.26 3.16 chr2qtel1M 261243 261336 (738664) (TATG)n#Simple_repeat 1 95 (0) m_b89s252i2 3304 chr2qtel1M 261243 TATGTA--TATGTATTGGTGAGTGTGTGTGTGTGGTTGTGTGTGTGTGTA 261290 -- - - iv i i i vv i i i i (TATG)n#Simpl 1 TATGTATGTATGTA-T-GTATGTATGTATGTATGTATGTATGTATGTATG 48 chr2qtel1M 261291 TATCATATCTAGATAGGTATGTATGTATCTA--TATGTATGTATCTAT 261336 -i v vi v v -- v (TATG)n#Simpl 49 TAT-GTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTAT 95 Matrix = Unknown Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.05 (5 / 93), avg. gap size = 1.40 (7 / 5) 20 26.94 0.00 0.00 chr2qtel1M 262015 262072 (737928) (TGTATG)n#Simple_repeat 1 58 (0) m_b89s252i5 3306 chr2qtel1M 262015 TGTATGTGTATCTGCATCTATTTGTATTTGTATATGTGTGTGTATAAATG 262064 v i v i v i v i i i vi (TGTATG)n#Sim 1 TGTATGTGTATGTGTATGTGTATGTGTATGTGTATGTGTATGTGTATGTG 50 chr2qtel1M 262065 TATGTTTA 262072 v (TGTATG)n#Sim 51 TATGTGTA 58 Matrix = Unknown Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0) 13 40.24 0.00 0.00 chr2qtel1M 262014 262083 (737917) (ATAT)n#Simple_repeat 1 70 (0) m_b89s252i4 3307 chr2qtel1M 262014 ATGTATGTGTATCTGCATCTATTTGTATTTGTATATGTGTGTGTATAAAT 262063 i i i v ii v v i v i i i i i v (ATAT)n#Simpl 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr2qtel1M 262064 GTATGTTTACATAAATATAT 262083 i i v i v (ATAT)n#Simpl 51 ATATATATATATATATATAT 70 Matrix = Unknown Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0) 14 6.98 0.00 11.76 chr2qtel1M 262297 262334 (737666) (TTTTC)n#Simple_repeat 1 34 (0) m_b89s252i6 3308 chr2qtel1M 262297 TTTTCTAATTTCTTTTCTTTTATTTTGTATTTACTTTT 262334 -- v v - - (TTTTC)n#Simp 1 TTTTCT--TTTCTTTTCTTTTCTTTTCT-TTT-CTTTT 34 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.11 (4 / 37), avg. gap size = 1.00 (4 / 4) 270 36.75 5.57 3.45 chr2qtel1M 262489 262829 (737171) L2c_3end#LINE/L2 124 471 (7) m_b89s601i2 3309 chr2qtel1M 262489 TCCAGGCATTTTCA-ATGGCTATTCCTTATTCCTGTAATAGTTTTCCCTT 262537 i? v v - - i i v v v iv i ii L2c_3end#LINE 124 TCCGNGCCTTTGCACATG-CTGTTCCCTCTGCCTGGAATGCTCTTCCCCC 172 chr2qtel1M 262538 GAAGTTTAGACTGCCAACCTCATTATTT-TCCTTTATGACCCAACTGAAA 262586 vvvv iviv v v v -i i i- i v ? i i v i L2c_3end#LINE 173 CTCCTTCCACCTGGCTAACTC-CTACTCATCCTTCAAGNCTCAGCTCAGA 221 chr2qtel1M 262587 -ACTAAAACCTACAGCAAGTATTCACTAATCCCTCTTAATTCTTGTTC-- 262633 -iii vvv v i v iv v i i i -- v? v ii-- L2c_3end#LINE 222 TGTCACCTCCTCCGGGAAGCCTTCCCTGACCCCCC--AAGNCTAGTCTAG 269 chr2qtel1M 262634 CTTCCCTCTTCTAATTAAGTCTAATTAAGTCCTAATTA-AGTCC-GTTCT 262681 v v i i-- iv- iv vivii ivi - v -i v L2c_3end#LINE 270 GTGCCCTCCTCTG--TGC-TCCCATAGCACCCTGTCTATACTCCCATTAT 316 chr2qtel1M 262682 GG-----AT--TTAGCTTGCTTTGTACACATTTGTATAT-----TATTTC 262719 i ----- -- i iv vvii i v i----- i i L2c_3end#LINE 317 AGCACTTATCATTAACTTGTATTGTAATTGTCTGTTTACNTGTCTGTCTC 366 chr2qtel1M 262720 CTACAATGTATTGTACATTACTTGAAGGAATTGTCTTTGCCTCCTAATTA 262769 v v iv i ivii v i v vv v iv i -- v i L2c_3end#LINE 367 CTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCT--TATTCA 414 chr2qtel1M 262770 TTTTTTTTAATCCTCAGTGCTTATCATTGTGGCTGGCACTCAATAGGTGT 262819 i v -- i i i iv i-i i iv i ii L2c_3end#LINE 415 TCTTTGT--ATCCCCAGCGCCTGGCAC-ATAGTAGGCGCTCAATAAATGT 461 chr2qtel1M 262820 TTGATAAATG 262829 v i L2c_3end#LINE 462 TTGTTGAATG 471 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 49.88 CpG sites = 67, Kimura (unadjusted) = 53.04 Transitions / transversions = 1.24 (67/54) Gap_init rate = 0.06 (20 / 340), avg. gap size = 1.55 (31 / 20) 426 30.17 3.64 5.07 chr2qtel1M 263697 263916 (736084) L1ME5_3end#LINE/L1 268 484 (457) m_b89s551i0 3310 chr2qtel1M 263697 GGGACACTGATACTTCGTTGATGGAATTGTGAATGCATCCAGCCATTCTG 263746 i v v i vii i i i v ii ivvi v L1ME5_3end#LI 268 GGAACCCTCATGCACTGCTGGTGGGAGTGTAGACTGGTGCAGCCATTCTG 317 chr2qtel1M 263747 AAGAGCGATTTGGAACTA--TACTCAAA--AAGCTATCAAACTGTGCATA 263792 i i i v v -- v -- - --- --- L1ME5_3end#LI 318 GAGAGCAATCTGGCAGTACTTAGTCAAATTAAG-TAT---AC---GCATA 360 chr2qtel1M 263793 TCCTTTGATCCAGCAGTGTTTCTACTGGGCTTATATCCCAAAGAGA-TCT 263841 i v i i viiv v iv i - L1ME5_3end#LI 361 CCCTATGACCCAGCAATTCCGCTCCTGGGTATATATCCCAAAGAAATTCT 410 chr2qtel1M 263842 TAAAGAAG---GGAAAGGAACCTCTATGTGCCAACATGTTTGTGGCAGCC 263888 i v v i ---iv i i ---- i v iv ii v v L1ME5_3end#LI 411 CACACAGGTCCATAAGGGGAC----ATGTACGAGGATGTTCATTGCAGCG 456 chr2qtel1M 263889 CTTTTTGTAGTGGCCAGAAACTGAAAAC 263916 i v i vi i ii i ii L1ME5_3end#LI 457 TTGTTTGTGGTGGCGGGGAGTTGGAGGC 484 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.16 CpG sites = 39, Kimura (unadjusted) = 40.00 Transitions / transversions = 1.62 (39/24) Gap_init rate = 0.07 (15 / 219), avg. gap size = 1.27 (19 / 15) 278 23.94 0.00 0.00 chr2qtel1M 264595 264665 (735335) L1ME3E_3end#LINE/L1 481 551 (438) m_b89s551i1 3310 chr2qtel1M 264595 AACACCACAGATGCTCATCAACTGGAGAAGGGCTGAATAAATTGTGGCAT 264644 v v i ii i v v v i i L1ME3E_3end#L 481 AACAACCCAAATGTCCATCGACAGGAGAATGGATAAATAAATTGTGGTAT 530 chr2qtel1M 264645 ATGAATGTTATGGAATATTAT 264665 vv iiv i L1ME3E_3end#L 531 ATTCATACAATGGAATACTAT 551 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 27.22 CpG sites = 9, Kimura (unadjusted) = 29.18 Transitions / transversions = 1.12 (9/8) Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0) 607 28.15 6.18 2.60 chr2qtel1M 265585 265956 (734044) L1ME3Cz_3end#LINE/L1 7 391 (606) m_b89s551i2 3311 chr2qtel1M 265585 TCTAAAATATATGGAGAACAGT--CAAATTTTTAAGAATGTAAGTCATTC 265632 i i ii vvi-- ivv v-- v vi L1ME3Cz_3end# 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAA--AAGACAACC 54 chr2qtel1M 265633 TTCAATTGATAAATGGTCAAAAGATATGAACAGTT--TTCAAATAAATTA 265680 -- v v v i vi-- v v ivvi L1ME3Cz_3end# 55 --CAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chr2qtel1M 265681 AAGCT------ATTTATAACCATATGAAAA--TTCTTTACTTTACTTGAT 265722 i i------iiiv v -- v iv i i v - L1ME3Cz_3end# 103 AAACCCGAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAG-T 151 chr2qtel1M 265723 GATTAGG-AAATGCAATTTAAAATAACCCTGAGGTGCCAACTCACACCTA 265771 i i - v i? vv i i vi i L1ME3Cz_3end# 152 AATCAGGGAAATGCAAATTAAAACNACAATGAGATACCATTTCACACCCA 201 chr2qtel1M 265772 TCAGATTGGATAATATGACAAAAA---GAAAATGATAAATGGT------G 265812 vv v v-i i--- v ivi i v ------ L1ME3Cz_3end# 202 TCAGATTGGCAAAAATT-TAAAAGTCTGACAATACCAAGTGTTGGCGAGG 250 chr2qtel1M 265813 ATGTGGGAAAACTGGGACACTAATGCATTGTTGGTTGAGTTGTGAACTGA 265862 ii v i v v i i i v iiv i i i L1ME3Cz_3end# 251 ATGTGGAGAAACGGGAACTCTCATACACTGCTGGTGGGAGTGTAAATTGG 300 chr2qtel1M 265863 TCCAAGCATTCTAGAGAGCACTTTGGAACAAAGCCCAA-AAGGCTGTAAT 265911 v v i i i v -- vii i i- i i - v L1ME3Cz_3end# 301 TACAACCACTTTGGAGAGCAATTTGG--CAATATCTAGTAAAGTTG-AAG 347 chr2qtel1M 265912 ACTGAGCATATCCTTTGATCCAACAATACCACTAGTAGGTCTATA 265956 - v i vi i i v vv v L1ME3Cz_3end# 348 A-TGCGCATACCCTACGACCCAGCAATTCCACTTCTAGGTATATA 391 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.64 CpG sites = 55, Kimura (unadjusted) = 36.08 Transitions / transversions = 1.17 (55/47) Gap_init rate = 0.05 (18 / 371), avg. gap size = 1.83 (33 / 18) 13 15.42 0.00 3.33 chr2qtel1M 266067 266097 (733903) (AATA)n#Simple_repeat 1 30 (0) m_b89s252i7 3312 chr2qtel1M 266067 AATAAATAAATCAATTTAAAAATAAAATAAA 266097 v vv v - (AATA)n#Simpl 1 AATAAATAAATAAATAAATAAAT-AAATAAA 30 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.03 (1 / 30), avg. gap size = 1.00 (1 / 1) 15 9.71 0.00 0.00 chr2qtel1M 270925 270946 (729054) (AC)n#Simple_repeat 1 22 (0) m_b89s252i8 3313 chr2qtel1M 270925 ACCCATACACACACACACACAC 270946 v i (AC)n#Simple_ 1 ACACACACACACACACACACAC 22 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 12 12.79 13.21 1.69 chr2qtel1M 272310 272362 (727638) (CTCCTT)n#Simple_repeat 1 59 (0) m_b89s252i9 3314 chr2qtel1M 272310 CTCCTTCCCAGTCTTCCTAC-CC--CTCATTC-CCTTCTCC-T-TCC-TC 272352 i vv - v - -- v - - - - (CTCCTT)n#Sim 1 CTCCTTCTCCTTC-TCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTC 49 chr2qtel1M 272353 TCCATCTCCT 272362 v (CTCCTT)n#Sim 50 TCCTTCTCCT 59 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.13 (7 / 52), avg. gap size = 1.14 (8 / 7) 17 17.11 6.52 0.00 chr2qtel1M 272939 272984 (727016) (CTC)n#Simple_repeat 1 49 (0) m_b89s252i10 3315 chr2qtel1M 272939 CTCCTCCTTC-CCAAAGCCGCCTCC-CATCC-CCTCCTCCTCCTCCTCC 272984 i - vvvv v - v - (CTC)n#Simple 1 CTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC 49 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.07 (3 / 45), avg. gap size = 1.00 (3 / 3) 192 6.12 0.00 9.09 chr2qtel1M 273627 273662 (726338) C L3#LINE/CR1 (1113) 2986 2954 m_b89s601i3 3316 chr2qtel1M 273627 AGGGACTTTGTGCAACTCTGCCTTGCTGAAATCCAG 273662 i - v -- C L3#LINE/CR1 2986 AGAGACTTTGT-CAAAT--GCCTTGCTGAAATCCAG 2954 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 6.33 CpG sites = 1, Kimura (unadjusted) = 6.33 Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.09 (3 / 35), avg. gap size = 1.00 (3 / 3) 215 36.07 6.43 4.93 chr2qtel1M 273811 273950 (726050) MamRTE1#LINE/RTE-BovB 336 477 (3335) m_b89s601i4 3317 chr2qtel1M 273811 TCACTG--GACACAGCGGTGGGATCTAGCAGCCCCTTAGATGTATGAGC- 273857 i -- vi i iivvi iii v? i i i v - MamRTE1#LINE/ 336 TCGCTGANGAGGCAGCAGCACCGTTCGGCAGCGNCCTGGGTGTCTGAGCA 385 chr2qtel1M 273858 --TCTG----AAAAAAAAATCCCCCCCTTGTGTGAAGAAGGGATCAGAAA 273901 --i ----ii ?viviv v i v iii vi ii ?ii MamRTE1#LINE/ 386 GCCCTGTTTAGGANCGCGCTGCTCACTCCGAATGGGGAAGGGNCTAGAAA 435 chr2qtel1M 273902 AGGTGCACTAAAAATCTGCTTATCTAATCCTGGCTAATGTTAAGGCTAG 273950 v vi - i i------ v i v? i i? i MamRTE1#LINE/ 436 AGGTGCCCTAAACGT-TGCCTG------CCTCGCCAAANTCAAANCTGG 477 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.73 CpG sites = 33, Kimura (unadjusted) = 56.77 Transitions / transversions = 2.20 (33/15) Gap_init rate = 0.08 (11 / 139), avg. gap size = 1.45 (16 / 11) 369 34.49 6.52 2.94 chr2qtel1M 273985 274214 (725786) MamRTE1#LINE/RTE-BovB 1072 1309 (2503) m_b89s601i5 3317 chr2qtel1M 273985 ATAGGGTTGAAAAGAGCAACAGCTCTGGTC----ACTAATAAGTGAAGAT 274030 ii i i vv? vv ----v iv v i vi MamRTE1#LINE/ 1072 ACGGGATTGGAAAGCTNAACAGCAATGGTCTACTCCTGCTCAGCGAATGT 1121 chr2qtel1M 274031 -TTGTGCATCTGAAGACTCC--ATCACCAACACTGTCTTCTGCTCACCTA 274077 -iiiv --- - v-- ii i ii v MamRTE1#LINE/ 1122 GCCAAGCATC---AG-CTCGTAATCACCAACACCATCTTCCGCCTACCGA 1167 chr2qtel1M 274078 A-AAGCAACAGAACTTCATGCGTGCATTTTTACAG--CAAACATTGTCAT 274124 - vi v - v vi --iii vi --i i v v MamRTE1#LINE/ 1168 ATAAGAGAAAG-ACATCATGGATGCA--CCCAAGGTCTAAGCAGTGGCAT 1214 chr2qtel1M 274125 TTAGTAGACTATATAATTGTAAGGAGAAGAAACATGATAGA-----GAAT 274169 i vi v i v i vv iviiv ii v vi -----ii MamRTE1#LINE/ 1215 CTCATTGATTATATCATCGTTCGACAGCGGGACCTGAAGGATGTTTAGAT 1264 chr2qtel1M 274170 GACAAAGGCCATGTGTGATGCAGAATGCTGGACTGATCATGGACT 274214 v vivi i i ii v i i i v v MamRTE1#LINE/ 1265 TACTGCAGCTATGCGTGGCGCCGAGTGCTGGACCGACCATCGCCT 1309 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.23 CpG sites = 44, Kimura (unadjusted) = 48.20 Transitions / transversions = 1.33 (44/33) Gap_init rate = 0.06 (13 / 229), avg. gap size = 1.69 (22 / 13) 235 22.00 0.00 0.00 chr2qtel1M 275771 275820 (724180) L1P3_orf2#LINE/L1 568 617 (2677) m_b89s551i3 3318 chr2qtel1M 275771 GAATATATATTTTTCTTAGTGGTACATGGCGCTTACACAAAAATTGACCA 275820 i i i i vi v i iv v L1P3_orf2#LIN 568 GAATATACATTCTTCTCAGCGCCACATCGCACTTATTCTAAAATTGACCA 617 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 23.94 CpG sites = 7, Kimura (unadjusted) = 26.67 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 1534 31.76 1.99 1.81 chr2qtel1M 276205 277307 (722693) L1M5_orf2#LINE/L1 1040 2144 (1150) m_b89s551i4 3319 chr2qtel1M 276205 TCAACAAAATGGAAAGTAAGGAAAGTATTAAACTAGTAAATAAAAAAAAA 276254 ii i ii i? ? -i v i --- v v vi iv L1M5_orf2#LIN 1040 TCAATGAAATAGAAAACAAANANA-CAATAGA---GAAAATCAACGAAGC 1085 chr2qtel1M 276255 AAACACTTGATTTGATGAAAAAACAAATAAAGCAGATGAAATTTTCGCTA 276304 v v vi i ivv i iv iiv i vi i v ? L1M5_orf2#LIN 1086 CAAAAGCTGGTTCTTTGAAAAGATCAATAAAATTGATAAACCTCTAGCNA 1135 chr2qtel1M 276305 ATTTGATTA-GAAAAAAGGAAA------ACAAATTATTAGTATCAAAAAT 276347 ivi i - i i ------ ii i ii L1M5_orf2#LIN 1136 GACTGATCAAGAAAAAAAGAGAGAAGACACAAATTACCAATATCAGGAAT 1185 chr2qtel1M 276348 GAAAAGGGTGAAGTTACCAGCAATGAAGAAGAAATTAAAGCAAGAAGTAG 276397 i v vi i i vvi vvviv v ivi v vv L1M5_orf2#LIN 1186 GAAAAAGGAGACATCACTACAGATCCTACAGACATTAAAAGGATAATAAG 1235 chr2qtel1M 276398 GACCTATTTTGCTCAACTGTTTGCCAACAAATCAGACCATTTAATTGAAA 276447 iivv v vv v v i iv ?v i iv L1M5_orf2#LIN 1236 AGAATATTATGAACAACTTTATGCCAATAAATTTGANAACTTAGATGAAA 1285 chr2qtel1M 276448 TGGATGAATATTTGCAAAAACGTAAATTGCCCATATTAACAGAAGAAAAA 276497 ii vii vv ii ? i v v i i ?v i L1M5_orf2#LIN 1286 TGGACAAATTCCTTGAAAAACACAANTTACCAAAACTGACNCAAGAAGAA 1335 chr2qtel1M 276498 ATAAAATGCTCAGATTACCCCAT-TTTAAAAATAGAAATTAAACAAGTCA 276546 i viiiiii vi i - i vv - i ivv v L1M5_orf2#LIN 1336 ATAGAAAATCTGAATAGCCCTATATCTATTAA-AGAAATTGAATTTGTAA 1384 chr2qtel1M 276547 TCAATGAA--TTCAAGGAAAAAAAAAATCTTCAGGCTGAGATGAATTTGC 276594 i -i -- vviv i --- i iv iv ii L1M5_orf2#LIN 1385 TTAA-AAACCTTCCCACAAAGAAAA---CTCCAGGCCCAGATGGCTTCAC 1430 chr2qtel1M 276595 AAGGACATTCTACCAAATATTTAGAGAACAATTAATTCAGATACAATGTA 276644 vi viv i ii v v v vi viv iii L1M5_orf2#LIN 1431 TGGTGAATTCTACCAAACATTTAAGGAAGAAATAATACCAATCTTACACA 1480 chr2qtel1M 276645 AACTATTTGAAAAAATAGGTGAAGAATGATTGCTACCTAATTCATTTTAT 276694 v iv i ivi iv vii v i i L1M5_orf2#LIN 1481 AACTCTTCCAGAAAATAGAAAAAGAGGGAACACTTCCCAACTCATTTTAT 1530 chr2qtel1M 276695 GACACAAATATGATGCTAATACTTAAAATAGGAAGAGCTAAAACAG--AA 276742 vi v ii ? iv i iv vi? iv i vi vv i-- L1M5_orf2#LIN 1531 GAGGCCAGCATNACCCTGATACCAAAACCNGACAAAGACATTACAAGAAA 1580 chr2qtel1M 276743 AGAAAATTATAGACCAATTTCCCTAATAAATATTGATGCAAAAATAAATA 276792 i v v i i v vv- ? L1M5_orf2#LIN 1581 AGAAAATTACAGACCAATATCCCTCATGAACATAGATGCAAAAATCC-TN 1629 chr2qtel1M 276793 AATAAAAAAACATTAGCAAACAGATTATGTCAATTTATCAACAAGACAAT 276842 i ---i iv v viiv v v v i i L1M5_orf2#LIN 1630 AACAAAA---TATTAGCAAATCGAATCCAGCAATATATAAAAAGGATAAT 1676 chr2qtel1M 276843 AACACAGTATGAGCAAATAAGATCTATACCAGGAATGCAGGGCTGATTCA 276892 --- vi v i ii i i v i i i i L1M5_orf2#LIN 1677 A---CATCATGACCAAGTGGGGTTTATCCCAGGAATGCAAGGTTGGTTTA 1723 chr2qtel1M 276893 ATATCAGGCAAACTATCAGCATAAT----CATATCAA--GAATAAAACTA 276936 i iv iv v v iii ---- i -- i--i L1M5_orf2#LIN 1724 ACATTCGAAAATCAATCAATGTAATTCACCATATTAACAGAATAAAG--G 1771 chr2qtel1M 276937 ACAGAAATCATCCTATTATATCAA-AAATGCAGAAAAAGATTTTGAGAAA 276985 v i viv i v - i vv v L1M5_orf2#LIN 1772 AGAAAAATCATATGATCATCTCAATAGATGCAGAAAAAGCATTTGACAAA 1821 chr2qtel1M 276986 ATACAGTACCCATTCCTATTTACAAACATTAGAGCACA-TGGGAATAAAT 277034 v ii v iv - v vi v- v - i i v L1M5_orf2#LIN 1822 ATTCAACACCCATTCATGAT-AAAAACTCTC-AGCAAACTAGGAATAGAA 1869 chr2qtel1M 277035 GGAATTTCCCTCAAAATGGCAAATAACATCTATCCAAAACCATCAGTATG 277084 i vi i vv ii vii ivv vv i?vi L1M5_orf2#LIN 1870 GGGAACTTCCTCAACCTGATAAAGGGCATCTACGAAAAACCTACAGCNAA 1919 chr2qtel1M 277085 CATTATATGAAATGGCTATAAACTAGATACATTCACAATAAGATCGGGGA 277134 i ivv iv v ? ii ?i v v vv i L1M5_orf2#LIN 1920 CATCATACTTAATGGTGAAANACTGAANGCTTTCCCCCTAAGATCGGGAA 1969 chr2qtel1M 277135 TGAACCAAGAATGCCTATTATCACTACTATTGTTCAACATTGTATTAGAA 277184 ii iv i i iii ? i vi i i i i L1M5_orf2#LIN 1970 CAAGACAAGGATGTCCGCTNTCACCACTTCTATTCAACATTGTACTGGAG 2019 chr2qtel1M 277185 ATCTTGGCTTTAGCAATAAGAAAAG-AAAAGAAACAGAAGGAATTAGAGT 277233 i i i ivvv iv - i i v v iii L1M5_orf2#LIN 2020 GTCCTAGCCAGTGCAATAAGGCAAGAAAAAGAAATAAAAGGCATAAAGAT 2069 chr2qtel1M 277234 AGGCAATGAGGAAACAGAACTATCGCTCTTTGCAGATG-TATGATGCTGG 277282 v v v i i i i ?i v i -i vv ?v L1M5_orf2#LIN 2070 TGGAAAGGAAGAAATAAAACTGTCNTTATTCGCAGATGACATGATTGTNT 2119 chr2qtel1M 277283 ATATAGAGAATACTAGAGAATCAAC 277307 ii i v ? i v L1M5_orf2#LIN 2120 ACGTAGAAAATCCNAAAGAATCTAC 2144 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 42.51 CpG sites = 196, Kimura (unadjusted) = 43.39 Transitions / transversions = 1.32 (196/148) Gap_init rate = 0.03 (31 / 1102), avg. gap size = 1.35 (42 / 31) 1392 32.57 3.58 3.16 chr2qtel1M 276207 277658 (722342) L1M4_orf2#LINE/L1 1042 2499 (795) m_b89s551i5 3319 chr2qtel1M 276207 AACAAAATGGAAAGTAAGGAAAGTATTAAACTAGTAAATAAAAAAAAAAA 276256 ii i i i - i ii v i --- v v vi vv L1M4_orf2#LIN 1042 AATGAAATAGAGAATA-GAAAAACAATAGA---GAAAATCAACGAAACCA 1087 chr2qtel1M 276257 ACACTTGATTTGATGAAAAAACAAATAAAGCAGATGAAATTTTCGCTAAT 276306 v v i ivv i iv i iiv ii vi v iv L1M4_orf2#LIN 1088 AAAGTTGGTTCTTTGAAAAGATCAACAAAATTGACAAACCTTTAGCTAGA 1137 chr2qtel1M 276307 TTGATTA-GAAAAAAGGAAAA------CAAATTATTAGTATCAAAAATGA 276349 i ii - i i i------ i iv ii L1M4_orf2#LIN 1138 CTGACCAAGAAAAAAAGAGAGAAGACTCAAATTACTAAAATCAGGAATGA 1187 chr2qtel1M 276350 AAAGGGTGAAGTTACCAGCAATGAAGAAGAAATTAAAGCAAGAAGTA--- 276396 ii v vi i v i ivvviv - -- i v --- L1M4_orf2#LIN 1188 AAGAGGGGACATTACTACCGACCTTACAGAAAT-AAA--AAGGATTATAA 1234 chr2qtel1M 276397 GGACCTATTTTGCTCAACTGTTTGCCAACAAATCAGACCATTTAATTGAA 276446 ivv i v vv i v i iv ii iv L1M4_orf2#LIN 1235 GGGAATACTATGAACAATTGTATGCCAACAAATTAGATAACCTAGATGAA 1284 chr2qtel1M 276447 ATGGATGAATATTTGCAAAAACGTAAATTGCCCATATTAACAGAAGAAAA 276496 ii vii iv i ii i i v v i i vv i L1M4_orf2#LIN 1285 ATGGACAAATTCCTAGAAAGACACAAACTACCGAAACTGACTCAAGAAGA 1334 chr2qtel1M 276497 AATAAAATGCTCAGATTACCCCATTTTAAAAATAGAAATTAAACAAGTCA 276546 i viiiiii viv i vvi iv v i i iv v L1M4_orf2#LIN 1335 AATAGAAAATCTGAATAGACCTATAACAAGTAAAGAGATTGAATTAGTAA 1384 chr2qtel1M 276547 TCAATGAATTCAAGGAAAAAAAAAATCTTCAGGCTGAGATGAATTTGCAA 276596 vi i ivvviv i ii -- ?iv iv ii vi L1M4_orf2#LIN 1385 TCAAAAAACTTCCCACAAAGAAAAGCC--CAGGNCCAGATGGCTTCACTG 1432 chr2qtel1M 276597 GGACATTCTACCAAATATTTAGAGAACAATTAATTCAGATACAATGTAAA 276646 viv i i v iv vi v vviii L1M4_orf2#LIN 1433 GTGAATTCTACCAAACATTTAAAGAAGAATTAACACCAATCCTTCACAAA 1482 chr2qtel1M 276647 CTATTTGAAAAAATAGGTGAAGAATGATTGCTACCTAATTCATTTTATGA 276696 v iv iv i iv vii v i i i L1M4_orf2#LIN 1483 CTCTTCCAAAAAATAGAAGAGGAGGGAACACTTCCCAACTCATTCTATGA 1532 chr2qtel1M 276697 CACAAATATGATGCTAATACTTAAAATAGGAAGAGCTAAAACAG--AAAG 276744 vi v i v iv i iv vi iv i vi vv i-- L1M4_orf2#LIN 1533 GGCCAGTATTACCCTGATACCAAAACCAGACAAAGACATCACAAGAAAAG 1582 chr2qtel1M 276745 AAAATTATAGACCAATTTCCCTAATAAATATTGATGCAAAAATAAATAAA 276794 i i v v i v vv- v L1M4_orf2#LIN 1583 AAAACTACAGACCAATATCCCTTATGAATATAGATGCAAAAATCC-TCAA 1631 chr2qtel1M 276795 TAAAAAAACATTAGCAAACAGATTATGTCAATTTATCAACAAGACAATAA 276844 i ---i i v v viiv iv v v i iv - L1M4_orf2#LIN 1632 CAAAA---TACTAGCAAACCGAATCCAGCAACATATAAAAAGGATTATA- 1677 chr2qtel1M 276845 CACAGTATGAGCAAATAAGATCTATACCAGGAATGCAGGGCTGATTCAAT 276894 -- vi v i ii i v i i i i L1M4_orf2#LIN 1678 --CACCATGACCAAGTGGGATTTATCCCAGGAATGCAAGGTTGGTTCAAC 1725 chr2qtel1M 276895 ATCAGGCAAACTATCAGCATAAT----CATATCAA--GAATAAAACTAAC 276938 ?v iv v v iii ---- i -- i--i L1M4_orf2#LIN 1726 ATNCGAAAATCAATCAATGTAATACACCATATTAATAGAATAAAG--GAC 1773 chr2qtel1M 276939 AGAAATCATCCTATTATATCAA-AAATGCAGAAAAAGATTTTGAGAAAAT 276987 i i iviv i v - i i vv v L1M4_orf2#LIN 1774 AAAAACCACATGATCATCTCAATAGACGCAGAAAAAGCATTTGACAAAAT 1823 chr2qtel1M 276988 ACAGTACCCATTCCTATTTACAAACATTAGAGCACA-TGGGAATAAATGG 277036 v ii v v iv - v i vi - v - i i v L1M4_orf2#LIN 1824 CCAACACCCTTTCATGAT-AAAAACACTCAA-CAAACTAGGAATAGAAGG 1871 chr2qtel1M 277037 AATTTCCCTCAAAATGGCAAATAACATCTATCCAAAACCATCAGTATGCA 277086 i vi i vv ii vii ivv vv ivvi L1M4_orf2#LIN 1872 GAACTTCCTCAACCTGATAAAGGGCATCTACGAAAAACCCACAGCTAACA 1921 chr2qtel1M 277087 TTATATGAAATGGCTATAAACTAGATACATTCACAATAAGATCGGGGATG 277136 i ivv iv v i ii ?i v v vv i i ii L1M4_orf2#LIN 1922 TCATACTTAATGGTGAAAGACTGAANGCTTTCCCCCTAAGATCAGGAACA 1971 chr2qtel1M 277137 AACCAAGAATGCCTATTATCACTACTATTGTTCAACATTGTATTAGAAAT 277186 iv i i iii v i i vi i i i ii L1M4_orf2#LIN 1972 AGACAAGGATGTCCGCTCTCGCCACTTCTATTCAACATTGTACTGGAGGT 2021 chr2qtel1M 277187 CTTGGCTTTAGCAATAAGAAAAG-AAAAGAAACAGAAGGAAT-TAGAGTA 277234 ii i ivvi v iv - i i v -i v - L1M4_orf2#LIN 2022 TCTAGCCAGGGCAATTAGGCAAGAAAAAGAAATAAAAGGCATCCAGATT- 2070 chr2qtel1M 277235 GGCAATGAGGAAACAGAACTATCGCTCTTTGCAGATG-TATGATGCTGGA 277283 v v i ii i v v i -i vi v L1M4_orf2#LIN 2071 GGAAAGGAAGAAGTAAAACTATCTCTATTCGCAGATGACATGATCTTGTA 2120 chr2qtel1M 277284 TATAGAGAATACTAGAGAATCAACCCCCCCCAAAAAAA-----AAAACTC 277328 i v ii ------- v ? ----- i v L1M4_orf2#LIN 2121 TATAGAAAATCCTAAGGAAT-------CCACNAAAAAACTATTAGAACTA 2163 chr2qtel1M 277329 TTTGAAACAA---CAGC---TTTGCAGGATACAAAATAAACCCACATAAA 277372 v -- i --- ---v i v ivi v L1M4_orf2#LIN 2164 AT--AAACGAGTTCAGCAAGGTTGCAGGATACAAGATCAATATACAAAAA 2211 chr2qtel1M 277373 TCATCAGCATT-------ATTACCAATGAAACCCAGCAGCAA--GAGATA 277413 viv i ------- i v -- v v v v -- i v L1M4_orf2#LIN 2212 TCAATTGTATTTCTATACACTAGCAATGAA--CAATCCGAAAATGAAATT 2259 chr2qtel1M 277414 GAAAAAGAAATTCCATTTAAAATAACTGTAGACTATATAAAATATCTAGC 277463 i i iv v i vvi i vviv ii v L1M4_orf2#LIN 2260 AAGAAAACAATTCCATTTACAATAGCATCAAAAAGAATAAAATACTTAGG 2309 chr2qtel1M 277464 AGT---TTTACCTCCCAAGACAAACTCAGAAACTATATTTACACC----A 277506 i --- ----v i v iiv - i --- v i---- L1M4_orf2#LIN 2310 AATAAATTTA----ACAAAAGAAGTGCA-AGACT---TGTACACTGAAAA 2351 chr2qtel1M 277507 TTACAAAACA--ATTCATACAAATAAATTCAGATACAAACAATTGGAAAA 277554 i --i v v v v vvv ivi i v - L1M4_orf2#LIN 2352 CTACAAAACATTGTTGAAAGAAATTAAAGAAGACCTAAATAAATGG-AAA 2400 chr2qtel1M 277555 AAAATATTGTGTTTATTATTATATTAGCTTGCCTAATATAATAAAAATCA 277604 i v viii i ---- iv i vvvi i vi v i vi L1M4_orf2#LIN 2401 GACATCCCATGTTCA----TGGATTGGAAGACTTAATATTGTTAAGATGG 2446 chr2qtel1M 277605 CAGTTCTCCGTTAAATAAGTCTACTTATTCAGTGCCATACCAATCAAATT 277654 i v -ii vii vv ii v v v v L1M4_orf2#LIN 2447 CAATACTCC-CCAAATTGATCTACAGATTCAACGCAATCCCTATCAAAAT 2495 chr2qtel1M 277655 GCCA 277658 v L1M4_orf2#LIN 2496 CCCA 2499 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 42.91 CpG sites = 256, Kimura (unadjusted) = 44.09 Transitions / transversions = 1.27 (256/202) Gap_init rate = 0.04 (65 / 1451), avg. gap size = 1.51 (98 / 65) 198 31.65 6.33 0.00 chr2qtel1M 279109 279187 (720813) L3#LINE/CR1 3535 3618 (481) m_b89s601i6 3320 chr2qtel1M 279109 CAGGAAAAAGCAGGGCATGATCCCACTGAGCTCTT-----GTCAAACACC 279153 i?v i v vv ii i vi v----- i vv L3#LINE/CR1 3535 CAGANCAAGGGAGGTAATAGTCCCGCTGTACTCTGCGCTGGTCAGACCAC 3584 chr2qtel1M 279154 ATCTACATTATTGCACTCCATCCTGGGCACCTCA 279187 iv v ii vi i i v L3#LINE/CR1 3585 ATCTGGAGTATTGCGTTCAGTTCTGGGCGCCACA 3618 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.25 CpG sites = 13, Kimura (unadjusted) = 42.58 Transitions / transversions = 1.08 (13/12) Gap_init rate = 0.01 (1 / 78), avg. gap size = 5.00 (5 / 1) 248 36.02 5.65 2.75 chr2qtel1M 279263 279439 (720561) C L2#LINE/L2 (484) 2598 2417 m_b89s601i7 3321 chr2qtel1M 279263 TATGAGAACTGAGAGACAGTAGAGAATTATGAATAAATCTGGAGTTATGA 279312 i i ivv v viii i i v i i v iiii v vi C L2#LINE/L2 2598 TGTGGGGTGTGAGAGAAAGAGAGGAGTCAAGGATGACTCCAAGGTTTTTG 2549 chr2qtel1M 279313 ATTTGGGTGACTAGA-GGAGGGAGGGTACC-----CTCAGGTA---AAGA 279353 iii i ii i - v v- i ----- v i i--- C L2#LINE/L2 2548 GCCTGAGCAACTGGAAGGATGGAGT-TGCCATTNACTGAGATGGGGAAGA 2500 chr2qtel1M 279354 CATTTGGAAGAATCATAAGATTTG-GGGGCAACATAGTAAGTTTTGTTGT 279402 - vi i i v --- i - v v vivi iv v C L2#LINE/L2 2499 C-TGCGGGAGGAGCA---GGTTTGAGGGGGAAGATCAGGAGTTCAGTTTT 2454 chr2qtel1M 279403 GGATATGGTGAGTTTGACAGGCCCACTGGCTATCTAA 279439 i v i v v i i i vi i C L2#LINE/L2 2453 GGACATGTTAAGTTTGAGATGCCTATTAGACATCCAA 2417 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 50.77 CpG sites = 39, Kimura (unadjusted) = 52.02 Transitions / transversions = 1.70 (39/23) Gap_init rate = 0.05 (9 / 176), avg. gap size = 1.67 (15 / 9) 21 0.00 0.00 0.00 chr2qtel1M 279492 279514 (720486) (T)n#Simple_repeat 1 23 (0) m_b89s252i11 3322 chr2qtel1M 279492 TTTTTTTTTTTTTTTTTTTTTTT 279514 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTT 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 392 31.18 3.17 1.33 chr2qtel1M 281975 282195 (717805) HERVP71A#LTR/ERV1 2437 2661 (4929) m_b89s701i0 3323 chr2qtel1M 281975 CAGGGAGTGTTTAAAAATTCC-CCATT-TAAATTGAATCTGAAA-AACAC 282021 iiv v iv - v -i i - i - - HERVP71A#LTR/ 2437 CAGGGGAGGGTTAAAAATCACACCCTTACAGATTGAA-CTAAAACAAC-C 2484 chr2qtel1M 282022 AGAAGATGTGGTGTGTGCTAAACAGTATCTTATATC-ATGGAGGGAAAAA 282070 i v i v iivv i ii v - v i i i HERVP71A#LTR/ 2485 AGGAGAAGTAGTTTGCAGAAAACAATATCCCATTTCCATTGAAGGGAGAA 2534 chr2qtel1M 282071 TAAGATTGCAATTACTAATAAAGGGACTTGTGAACGATGGACTATTATAA 282120 v i vi v iiiv i i vi v v v HERVP71A#LTR/ 2535 AAGGTCTCCAACCGGTAATAGAGGGATTGATTAAAGATGGACTATTAGAA 2584 chr2qtel1M 282121 GTTTGTATGCC-CCCTATCAATATCCCTATTGTGCTCATTAAGAAATCAG 282169 vii i i - v - ii v v v ivi i ii v HERVP71A#LTR/ 2585 CCCTGCATGTCACCATA-CAATACTCCAATTCTCCCAGTCAAGAAGCCTG 2633 chr2qtel1M 282170 ATGAAAC--ATGGATTAATACAAGACCT 282195 iiv -- i ii i i HERVP71A#LTR/ 2634 ATGGGTCGTATAGATTGGTGCAAGATCT 2661 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.01 CpG sites = 42, Kimura (unadjusted) = 41.93 Transitions / transversions = 1.62 (42/26) Gap_init rate = 0.04 (9 / 220), avg. gap size = 1.11 (10 / 9) 192 30.41 9.49 6.38 chr2qtel1M 282793 282929 (717071) C AmnL2-1#LINE/L2 (371) 2242 2102 m_b89s601i8 3324 chr2qtel1M 282793 TCCATTAAGTGTTTTCAATGGCAAAAAAGAGGACTTTGAATCTGA-CCTC 282841 vi v v -ii ii ivi i iiv - v C AmnL2-1#LINE/ 2242 TCCATGGAGGGTTTTAAA-AACAAGGAAGGCAATTTTGAACTGGATCCTG 2194 chr2qtel1M 282842 AGAGGCAACAGAGAGTTATTGGAG-TGACTGAGGAGAGGACTGA------ 282884 i v - ii i ii v - vi vi iv ------ C AmnL2-1#LINE/ 2193 AAATG-AATGGGGAGCCAGTGGAGTTGTTTGAGGATGGGGGTGATGTGGT 2145 chr2qtel1M 282885 --CATTTGTTTTTACATG---GAAGGGAATATCGGTGTGGCAGCTTCCTG 282929 -- ii v v i --- ------ - ii v i C AmnL2-1#LINE/ 2144 CGCGCTTCTTTGTACGTGTGAGAAGG------CGG-GCAGCAGCATTCTG 2102 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.09 CpG sites = 25, Kimura (unadjusted) = 40.83 Transitions / transversions = 1.79 (25/14) Gap_init rate = 0.10 (14 / 136), avg. gap size = 1.57 (22 / 14) 321 36.55 4.78 1.26 chr2qtel1M 283053 283282 (716718) C L2#LINE/L2 (460) 2622 2385 m_b89s601i9 3325 chr2qtel1M 283053 GACAGAATTGGGCAATTGATTCCACATGTGAGT-TGAGAGATAATGCAGA 283101 i v vii v vv ii - i - v iv vi C L2#LINE/L2 2622 GACAGGATTTGCTGATGGATTGGATGTG-GGGTGTGAGAGAAAGAGAGGA 2574 chr2qtel1M 283102 GTTAATAA-AATT--GGGATTATTAATATTGGTGACTGGAGGAGTGATGG 283148 i vi -i i --ii i v iiiv vi ii i ii i-i C L2#LINE/L2 2573 GTCAAGGATGACTCCAAGGTTTTTGGCCTGAGCAACTGGAAGGATGG-AG 2525 chr2qtel1M 283149 GTACC-----CTCAAGGAAGGAAATATG-GAGAGGGGCATGATCTG-GGG 283191 v i ----- v iivii ivv - i i - i i - C L2#LINE/L2 2524 TTGCCATTNACTGAGATGGGGAAGACTGCGGGAGGAGCA-GGTTTGAGGG 2476 chr2qtel1M 283192 GAAAGGTAATAGGTTTTGTTGTGGATATGGTGAGTTGGAGATGCCCATTA 283241 i i v vii iv v i v i v i C L2#LINE/L2 2475 GGAAGATCAGGAGTTCAGTTTTGGACATGTTAAGTTTGAGATGCCTATTA 2426 chr2qtel1M 283242 ACTATCTAATTCAAAATGTCTGGTAGCTATTTGGATGTGTG 283282 ivi i v vi i vi vi v i ii C L2#LINE/L2 2425 GACATCCAAGTGGAGATGTCGAGTAGGCAGTTGGATATACG 2385 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 52.64 CpG sites = 54, Kimura (unadjusted) = 53.63 Transitions / transversions = 1.86 (54/29) Gap_init rate = 0.04 (9 / 229), avg. gap size = 1.56 (14 / 9) 19 8.13 0.00 0.00 chr2qtel1M 287341 287366 (712634) (AC)n#Simple_repeat 1 26 (0) m_b89s252i12 3326 chr2qtel1M 287341 ACCCATACACACACACACACACACAC 287366 v i (AC)n#Simple_ 1 ACACACACACACACACACACACACAC 26 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 181 31.38 8.11 8.70 chr2qtel1M 287896 288080 (711920) C MIR#SINE/MIR (46) 216 33 m_b89s601i10 3327 chr2qtel1M 287896 TTCTAATGGGCTTCAAACACA--AATATATTGAATCCTCACAATAAACCT 287943 - v i v iii -- ivi v i v C MIR#SINE/MIR 216 TTCTAA-GCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCT 168 chr2qtel1M 287944 GTGACAACAGAGAATACTTCCATTGTCACTACTTTCACAATTCAGGCCAC 287993 i -iii ---i vii i v i - i iv v vv C MIR#SINE/MIR 167 ATGA-GGTAG---GTACTATTATTATCCCCA-TTTTACAGATGAGGAAAC 123 chr2qtel1M 287994 C--AGTTCAAAG-GACAGAGGGACTTGAGCCAAAGCCCTGTAGCTA---- 288036 i--i iv i - iivi vi -v i i viii ---- C MIR#SINE/MIR 122 TGAGGCACAGAGAGGTTAAGTAACTTG-CCCAAGGTCACACAGCTAGTAA 74 chr2qtel1M 288037 -----AGA-CAGGAATTCACACCCAGTGAATGGGCAGGCTCTGCCTTCAG 288080 ----- - v i iv ------- -- v i C MIR#SINE/MIR 73 GTGGCAGAGCCGGGATTCGAACCCA-------GGCAG--TCTGGCTCCAG 33 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.44 CpG sites = 34, Kimura (unadjusted) = 42.53 Transitions / transversions = 1.79 (34/19) Gap_init rate = 0.12 (22 / 184), avg. gap size = 1.41 (31 / 22) 30 0.00 0.00 0.00 chr2qtel1M 288534 288559 (711441) (AT)n#Simple_repeat 1 26 (0) c_b89s251i0 3328 chr2qtel1M 288534 ATATATATATATATATATATATATAT 288559 (AT)n#Simple_ 1 ATATATATATATATATATATATATAT 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 206 26.79 9.65 5.04 chr2qtel1M 290663 290776 (709224) C MIR3#SINE/MIR (1) 207 89 m_b89s601i11 3329 chr2qtel1M 290663 AAGCATCAAAGTCATGAGACAT-AGAGCTGAAAGTCACTTCAGAATTCAA 290711 v - i i iii ii - i vv i i iv -- C MIR3#SINE/MIR 207 AATCAT-AGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATC-- 161 chr2qtel1M 290712 GAATCCAA-CCAACCGTCCCCAATTTACAGTC--GGAAACTCAAG--CAG 290756 -- i i- -i i v vi-- v i -- C MIR3#SINE/MIR 160 --ATCTAGTCCAACC-CCCTCATTTTACAGATGAGGAAACTGAGGCCCAG 114 chr2qtel1M 290757 A-----GAAGGGATTGGCTCAAAGT 290776 ----- v i v i i C MIR3#SINE/MIR 113 AGAGGTGAAGTGACTTGCCCAAGGT 89 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.79 CpG sites = 20, Kimura (unadjusted) = 34.79 Transitions / transversions = 2.22 (20/9) Gap_init rate = 0.10 (11 / 113), avg. gap size = 1.55 (17 / 11) 324 33.09 0.00 0.00 chr2qtel1M 292759 292894 (707106) L1MC5_3end#LINE/L1 430 565 (2129) m_b89s551i6 3330 chr2qtel1M 292759 GTATGTGCCAAAATGTTTGTGGCAGCCCTGTTTGCAGTGGCCAGAAGCTG 292808 ii v iiv i ii v v i i i i v i ii L1MC5_3end#LI 430 GTATGCACAAGGCTATTCATTGCAGCACTATTTGTAATAGCAAAAGACTG 479 chr2qtel1M 292809 GAAAATGAATGGATGCCCATCAATTGGAGAATGGTTGAGTAAATTGTGGT 292858 vvivviii i v i v i i i L1MC5_3end#LI 480 GAAACAACCCAAATGTCCATCAATAGGGGACTGGTTGAATAAACTATGGT 529 chr2qtel1M 292859 ACATGAACATTATGGAATATTATTGTTCTGTAAGAA 292894 vv iv i i vvvv i L1MC5_3end#LI 530 ACATCCACACAATGGAGTACTATGCAGCTGTAAAAA 565 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 45.38 CpG sites = 27, Kimura (unadjusted) = 45.38 Transitions / transversions = 1.50 (27/18) Gap_init rate = 0.00 (0 / 135), avg. gap size = 0.0 (0 / 0) 401 28.10 0.00 0.00 chr2qtel1M 292761 292881 (707119) L1ME3F_3end#LINE/L1 432 552 (438) m_b89s551i7 3330 chr2qtel1M 292761 ATGTGCCAAAATGTTTGTGGCAGCCCTGTTTGCAGTGGCCAGAAGCTGGA 292810 i v i ii i v i i i i v i i L1ME3F_3end#L 432 ATGTACAAGAATGTTCATAGCAGCACTGTTCGTAATAGCAAAAAACTGGA 481 chr2qtel1M 292811 AAATGAATGGATGCCCATCAATTGGAGAATGGTTGAGTAAATTGTGGTAC 292860 vvivviii i i iv v i i i L1ME3F_3end#L 482 AACAACCCAAATGTCCATCGACAGGAGAATGGATAAATAAATTGTGGTAT 531 chr2qtel1M 292861 ATGAACATTATGGAATATTAT 292881 vv iv L1ME3F_3end#L 532 ATTCACACAATGGAATATTAT 552 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 33.90 CpG sites = 22, Kimura (unadjusted) = 36.60 Transitions / transversions = 1.83 (22/12) Gap_init rate = 0.00 (0 / 120), avg. gap size = 0.0 (0 / 0) 325 27.59 0.00 0.00 chr2qtel1M 292780 292895 (707105) L1MC4a_3end#LINE/L1 449 564 (2065) m_b89s551i8 3330 chr2qtel1M 292780 GCAGCCCTGTTTGCAGTGGCCAGAAGCTGGAAAATGAATGGATGCCCATC 292829 vi i i v v i vii vvivv ii ? L1MC4a_3end#L 449 GCAGCATTGTTTGTAATTGCAAAATATTGGAAACAACCTAAATGCCCATN 498 chr2qtel1M 292830 AATTGGAGAATGGTTGAGTAAATTGTGGTACATGAACATTATGGAATATT 292879 ? v ? i i i vv iv i i L1MC4a_3end#L 499 NATAGGAGANTGGTTGAATAAACTATGGTACATCCACACAATGGAGTACT 548 chr2qtel1M 292880 ATTGTTCTGTAAGAAA 292895 vvvv i L1MC4a_3end#L 549 ATGCAGCTGTAAAAAA 564 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.97 CpG sites = 16, Kimura (unadjusted) = 35.97 Transitions / transversions = 1.00 (16/16) Gap_init rate = 0.00 (0 / 115), avg. gap size = 0.0 (0 / 0) 13 4.76 0.00 4.35 chr2qtel1M 293292 293315 (706685) (GGGA)n#Simple_repeat 1 23 (0) m_b89s252i13 3331 chr2qtel1M 293292 GGGAGGGGGTGGAGGGAGGGAGGG 293315 i - (GGGA)n#Simpl 1 GGGAGGGAG-GGAGGGAGGGAGGG 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 236 33.64 0.00 2.59 chr2qtel1M 294350 294468 (705532) L1MC5_3end#LINE/L1 418 533 (2161) m_b89s551i9 3332 chr2qtel1M 294350 ATATTAAAAGATGCCATATGTGCAAAAATGTTTGTGGCAGCCCTTTTTGT 294399 iv i --- ii iiv i ii v v v L1MC5_3end#LI 418 ATACGAAAAGACG---TATGCACAAGGCTATTCATTGCAGCACTATTTGT 464 chr2qtel1M 294400 AGTGAGAAGAAACTGGGAACTGAGGGGATGTCCATCAATTGGAGAACAGC 294449 i iiv i i i vivvvii v i vii i L1MC5_3end#LI 465 AATAGCAAAAGACTGGAAACAACCCAAATGTCCATCAATAGGGGACTGGT 514 chr2qtel1M 294450 TGGACAAGTAATGGTACAT 294468 i i iiv L1MC5_3end#LI 515 TGAATAAACTATGGTACAT 533 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 44.02 CpG sites = 26, Kimura (unadjusted) = 47.43 Transitions / transversions = 2.00 (26/13) Gap_init rate = 0.03 (3 / 118), avg. gap size = 1.00 (3 / 3) 257 33.65 0.00 0.00 chr2qtel1M 294365 294468 (705532) L1ME3F_3end#LINE/L1 430 533 (457) m_b89s551i10 3332 chr2qtel1M 294365 ATATGTGCAAAAATGTTTGTGGCAGCCCTTTTTGTAGTGAGAAGAAACTG 294414 i i i ii i v v i i iiv i L1ME3F_3end#L 430 ACATGTACAAGAATGTTCATAGCAGCACTGTTCGTAATAGCAAAAAACTG 479 chr2qtel1M 294415 GGAACTGAGGGGATGTCCATCAATTGGAGAACAGCTGGACAAGTAATGGT 294464 i vivvvii i iv ii v ii i i vi L1ME3F_3end#L 480 GAAACAACCCAAATGTCCATCGACAGGAGAATGGATAAATAAATTGTGGT 529 chr2qtel1M 294465 ACAT 294468 i L1ME3F_3end#L 530 ATAT 533 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 44.42 CpG sites = 25, Kimura (unadjusted) = 48.35 Transitions / transversions = 2.50 (25/10) Gap_init rate = 0.00 (0 / 103), avg. gap size = 0.0 (0 / 0) 12 27.69 0.00 0.00 chr2qtel1M 294753 294791 (705209) (TTT)n#Simple_repeat 1 39 (0) m_b89s252i14 3333 chr2qtel1M 294753 TTTTTTTGTGTTTGTTTGAATTTCATTTTCTTTTTTTTT 294791 v v v vvv iv i (TTT)n#Simple 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 39 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 16 20.32 2.44 0.00 chr2qtel1M 295016 295056 (704944) (CATA)n#Simple_repeat 1 42 (0) m_b89s252i15 3334 chr2qtel1M 295016 CATACATATGTATGTATGTACATACATACATA-ATCCATACA 295056 ii ii ii - v (CATA)n#Simpl 1 CATACATACATACATACATACATACATACATACATACATACA 42 Matrix = Unknown Transitions / transversions = 6.00 (6/1) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 25 9.18 0.00 0.00 chr2qtel1M 295569 295603 (704397) (A)n#Simple_repeat 1 35 (0) m_b89s252i16 3335 chr2qtel1M 295569 AAATAAAAAAAAGAAAAAAAAAAAAAAAAAAAGAA 295603 v i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 35 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 581 30.31 2.58 4.01 chr2qtel1M 296840 297420 (702580) C HERVK14C#LTR/ERVK (4017) 3417 2845 m_b90s701i0 3336 chr2qtel1M 296840 CACACACCAAGATATCATCCATGAAATGTAATAATAT-TACTTTTGGAAA 296888 i ?- v i iv - i -?ivv i C HERVK14C#LTR/ 3417 CGCACAN-AATATGTCATCCATATAATG-AATGATATANGAATCTGGAAA 3370 chr2qtel1M 296889 TGCTTTTCTTACTAGAGT-AATAGCAGCAGTCACATGCATTTGACACATA 296937 ivvv i ? - iv - vv?vvi ?ivi v ? C HERVK14C#LTR/ 3369 CTGATCTCTNAC-AGGTTGAATAGCCTNCCCCACANAAGTTTGACAAATN 3321 chr2qtel1M 296938 GTAGGACTATTTTTCATTCCCTGTGGCAAAACTATCTATTCTTATCTTTT 296987 ? ivv v i ? v i v vv ? vvi C HERVK14C#LTR/ 3320 GTNGGACTATTCAACATGCCCTGCGGCAANACTTTCCAATGATANCTGGC 3271 chr2qtel1M 296988 ATAAAGGTCAGCTA-AATTAATGCCAGG--CACTAAGAAGTCAAACCTTT 297034 - iv? ivvi i-vi v iv --i v - - ii C HERVK14C#LTR/ 3270 -TGCNGGTTCCTTGTTGTTCATAGCAGGAATAGTAA-AAG-CAAATTTTT 3224 chr2qtel1M 297035 TCATATCCTCCTTAACTAGAAGAATAGAATAGAAATAATTCTTAATGTCT 297084 iv v ?vv ivi i v v ii i i v vi C HERVK14C#LTR/ 3223 CAAAATCNGGCTCTGCTAGAGGAATAGTAAAGAAGCAGTCCTTCAAATCT 3174 chr2qtel1M 297085 ATAAC--CCAACGAGGCCATTCT-TAGGCAACTGAGTAGGACATGGAAGT 297131 --ii --? v - v v vvi ii iv ? v i C HERVK14C#LTR/ 3173 ATAACTATTAA--NGGCCAGTCTCTAGGAATCATGGCGGGGGANGGCAGC 3126 chr2qtel1M 297132 CTAGGCTGAAAAGTTCCTATGATTTCCAT--CTGCTCATTTGCTTTTCTC 297179 iv v i? ii i ?iv v? -- -- vi vvi vi C HERVK14C#LTR/ 3125 CCTGGCTGCAGNGCCCCCATNGGTTGNATGACTG--CATTGACGGCTCGT 3078 chr2qtel1M 297180 AAATCAG-TACCATTCTCCATTTTCCAGATTTCTCTTTTATAGCAAATAC 297228 i i - v ? v i v i i ii ? vi i C HERVK14C#LTR/ 3077 AAGTCGGTTAGCATNCGCCATCTGCCGGATTTTTTCTTNATTACAAACAC 3028 chr2qtel1M 297229 AGGGGAATTTCAAGGACTTAGAGAATGT----TATAAAAGACCTTGGTGA 297274 v ? i ? ---- i ---- v? viv v v? vv C HERVK14C#LTR/ 3027 TGGNGAATTCCANGG----AGAAAATGTGGGCTCNATGTGTCCTTTNTCT 2982 chr2qtel1M 297275 AGTTATTCCTGTACTATATCTAATCATTCTTGAATTTTTTGATTAGCTAG 297324 i i i vv vv ivi v vv iivv v vv v ?? C HERVK14C#LTR/ 2981 AATTGTTCTTTGACTAATTCCTGTAAGGCCCCCAGTTTTTCCTGAGNNAG 2932 chr2qtel1M 297325 GGGCCACTGTTCTTCCAACACGGGTATATTAGTTTTCCATTGAATGGGAA 297374 v ? ?v v v ? ?v v vi i? vv v C HERVK14C#LTR/ 2931 CGGCCACTGNTCNACCCAAACNGGNTTTTGGGTCNTCCATTTTAAGGGAA 2882 chr2qtel1M 297375 CAGGTCAGAGTACTGGCAGGCCTTCAATAGCAGCCCTGCCTAAAAA 297420 i ?i------ - -- i ii viv C HERVK14C#LTR/ 2881 TAGGNT------CTGG-AGGC--TCAACAGTGGCCGCCCCTAAAAA 2845 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.47 CpG sites = 77, Kimura (unadjusted) = 42.07 Transitions / transversions = 0.84 (77/92) Gap_init rate = 0.06 (32 / 580), avg. gap size = 1.19 (38 / 32) 644 36.09 8.19 4.20 chr2qtel1M 297923 298862 (701138) C MamRTE1#LINE/RTE-BovB (2501) 1311 336 m_b90s601i0 3337 chr2qtel1M 297923 TCAGTCTATGATCATTCCAGCATTCTGCATCACATATGGCCTTTGTCACT 297972 v v i iv i v ii ii i iviv v ii C MamRTE1#LINE/ 1311 TCAGGCGATGGTCGGTCCAGCACTCGGCGCCACGCATAGCTGCAGTAATC 1262 chr2qtel1M 297973 C-----TCTATCGTGTTTCTTCTCCTTACAATTATATAGTCTACTAAATG 298017 i----- iv iv ii viivi vv i v i v iv i C MamRTE1#LINE/ 1261 TAAACATCCTTCAGGTCCCGCTGTCGAACGATGATATAATCAATGAGATG 1212 chr2qtel1M 298018 ACAATATTTG--CTGTAAATGTGCATGCATGAAGTTTTGTTGCTTTTAGG 298065 v v ii i-- iv ii-- v v i vi vi v v C MamRTE1#LINE/ 1211 CCACTGCTTAGACCTTGG--GTGCATCCATGATGTCTTTCTCTTATTCGG 1164 chr2qtel1M 298066 TTAGTAAAAGACAGTGT-GGTGATGGGGTCTTGA-GAT--GCACAAATCT 298111 vi iii ii - viv vvi - v -- ---- C MamRTE1#LINE/ 1163 TAGGCGGAAGATGGTGTTGGTGATTACGAGCTGATGCTTGGCACA----T 1118 chr2qtel1M 298112 TCACTAAT---AAGT-GACCAGTGCTATTGCTGTTTTCAACCTTATTCCT 298157 i i v---i - v i ?vvv i i iii v?vv C MamRTE1#LINE/ 1117 TCGCTGAGCAGGAGTAGACCATTGCTGTTNAGCTTTCCAATCCCGTGNGG 1068 chr2qtel1M 298158 TCCAAGGACATTCC-CTA-ATCTGAGC----CTAGTCTA-----GCCTTA 298196 i v v i - i -i i vi ---- - i v ----- v i C MamRTE1#LINE/ 1067 TCCGATGACTTTTCTCCACGTTTCGGCATCGCT-GCCGACACGTGCGTTG 1019 chr2qtel1M 298197 AAATCAGCCAGGATTAGATAAGTTTGTCCTCTTTTGGCAA-ACTGAGGAT 298245 vv iv i-- v i vvv v i v-i v - C MamRTE1#LINE/ 1018 AAATCTCCCGTGAC--GATCAGCTTGTCAGATGTTGGTACCGCTGCG-AT 972 chr2qtel1M 298246 GAGCATCTCTAG-TCTTCATAAAAT-TTCCCTTGAACTTATCAAGGTTTG 298293 iv v i - i ii i - i i vvv i iivi i C MamRTE1#LINE/ 971 GAGTCTGTCCAGATCCTTGTAGAATCTTTCTTTCTCCTCATCGGTATTCG 922 chr2qtel1M 298294 GCATGGTGGAAGGATAGTCACTGATGATGGTACCATGGCA-TTTTACTAT 298342 v ii v vv i i iv ?i i- ii vi C MamRTE1#LINE/ 921 TCATGGTGGGGGCATATGCGCTGATGACGGTGGCANAGCGCTTTTGTTTC 872 chr2qtel1M 298343 AGGTGATAAAGGCATTGTCATGAGTCTGTCATTCAGTCTTTTTGGCAGAC 298392 i? - iiv i vv v v v i ? vv i i v i i C MamRTE1#LINE/ 871 AGANG-TAGGCGTAGGGTCATCAGACGGTCACTNATGCCTCTGGGCAAAT 823 chr2qtel1M 298393 ATATAAGATTGCTGAT--TTGATTCGGTTTGATTGCTAACCTATACCAAC 298440 v ivi ?i vvv i--v i -- i v v i- --i C MamRTE1#LINE/ 822 TTGGGAGNCTTGAGACAAGTGACT--GTCTGATTGCAAAGCTG-AC--GC 778 chr2qtel1M 298441 TTCACAATGCTC-CTCTCCACTG----CACTCCCTGCAGAAAACCTTGGA 298485 i v v iivv - vv vv ----v - i v i vvvi v C MamRTE1#LINE/ 777 CTGAGAGCCGTCGCTCTGAAGAGGGAAGAC-CTCTCCAGAAGAAGGCGTA 729 chr2qtel1M 298486 TGTAGCTCCGACTTCAGTAAGGTGGCTTTTATTTGCCAGCCTTGTTTCAC 298535 ?vii v viii v i v v i i iv vv i v i C MamRTE1#LINE/ 728 NCCGGCACCTGTCTCCGTGAGCTGTCCTTCATCAGGAAGTCTGGTTTCGC 679 chr2qtel1M 298536 TCAGGGCTGCCTTTTGGATG-AGACACC-TA-CTG---AATTCTCTGGCC 298579 v v ------ -v v - - --- i v vv v C MamRTE1#LINE/ 678 TCAGTGCGGC------GATGTCGACTCCGTATCTGGACAGTTCACGTGCG 635 chr2qtel1M 298580 ACTAGAGCTGTCCATCTTTC---AGGTTTGCTG----CATTATC-CATAA 298621 v v i i v --- v vi ---- i i - i C MamRTE1#LINE/ 634 ACGAGTGCCGTTCTTCTTTCTGGACGACTGCTGTTCTCGTCATCGCATAG 585 chr2qtel1M 298622 TGGTGCACACATTCCAAGGACTGATGGTGAATGACATCTTTGTAGAAGTT 298671 i- v vv ii v ivvii v v v--- ??v? v C MamRTE1#LINE/ 584 C-GTCCTGATGTTCCATGACGCAATGGTTATTT---TCTTTGTNNTNGGT 539 chr2qtel1M 298672 TTTATAAGTGTCTGTGTGTGTGTCTGTATTTCTATCACTGGCT-GGGTCC 298720 ------ - i v i v ?v i i iiv v ----- i? -iiii C MamRTE1#LINE/ 538 ------AGT-TTTCTATTTGNTTTTGCACCGCAA-----GANTAAAACCC 501 chr2qtel1M 298721 ACCAACCATGGTA----GACAGACCAGGGCTGATT------AAGCAG--- 298757 iv ii i ---- iiiii ?vi ? ------ i --- C MamRTE1#LINE/ 500 ACCAGACGCGATAATCTGGTGAGCCAGNTTTGANTTTGGCGAGGCAGGCA 451 chr2qtel1M 298758 ATTTTTAGTGCACCTTTTCTGGTCTCTTCTTCATACCAGGAGGGA----T 298803 iv v i ? i ii v -- v ----i C MamRTE1#LINE/ 450 ACGTTTAGGGCACCTTTTCTAGNCCCTTCCCCATTC--GGAGTGAGCAGC 403 chr2qtel1M 298804 TTTTTTTTA---AGA---GCTCATACATCTAGGGAACTGCTACATCCCAC 298847 viv? ii --- i--- v i i ?vi iiv ivvii C MamRTE1#LINE/ 402 GCGNTCCTAAACAGGGCTGCTCAGACACCCAGGNCGCTGCCGAACGGTGC 353 chr2qtel1M 298848 TGCTGTGTC--CAGTGA 298862 iv -- i C MamRTE1#LINE/ 352 TGCTGCCTCNTCAGCGA 336 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.51 CpG sites = 175, Kimura (unadjusted) = 52.23 Transitions / transversions = 1.17 (175/150) Gap_init rate = 0.08 (74 / 939), avg. gap size = 1.59 (118 / 74) 295 29.39 10.17 1.96 chr2qtel1M 300117 300352 (699648) L1M4_orf2#LINE/L1 1951 2205 (1089) m_b90s551i0 3338 chr2qtel1M 300117 TTCCCAGTAAGATGAGGAGTGAAACAATGTTG-CCATTTTCATCACTATA 300165 vv v iii i v v - ii i ii viv L1M4_orf2#LIN 1951 TTCCCCCTAAGATCAGGAACAAGACAAGGATGTCCGCTCTCGCCACTTCT 2000 chr2qtel1M 300166 ATGCAATATTGTACTAGAAATGTTAGCTTTAGCAA------AAAGAAAAG 300209 v i i ii vi ivvi ------ ii L1M4_orf2#LIN 2001 ATTCAACATTGTACTGGAGGTTCTAGCCAGGGCAATTAGGCAAGAAAAAG 2050 chr2qtel1M 300210 AAATTGAA-GCAATTAGAGTACACAATGAGGAAACAAAACTAC------- 300251 vi - vii v iv - v i ii i------- L1M4_orf2#LIN 2051 AAATAAAAGGCATCCAGATTGGA-AAGGAAGAAGTAAAACTATCTCTATT 2099 chr2qtel1M 300252 --CATATGATATG--CTGACATACAG--AATTCTAGAGAATCAACT-GAA 300294 -- v i -- vii i -- i ii v ?-i L1M4_orf2#LIN 2100 CGCAGATGACATGATCTTGTATATAGAAAATCCTAAGGAATCCACNAAAA 2149 chr2qtel1M 300295 AACTACAAAAA--AGTTAACAACTTTAGCAAAATTGAAGGACATAAAATA 300342 iv i -- i v i v i ii v i i i - L1M4_orf2#LIN 2150 AACTATTAGAACTAATAAACGAGTTCAGCAAGGTTGCAGGATACAAGAT- 2198 chr2qtel1M 300343 AAACAATATA 300352 --- L1M4_orf2#LIN 2199 ---CAATATA 2205 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.12 CpG sites = 45, Kimura (unadjusted) = 39.37 Transitions / transversions = 1.96 (45/23) Gap_init rate = 0.06 (14 / 235), avg. gap size = 2.07 (29 / 14) 822 33.52 3.77 3.38 chr2qtel1M 302131 302661 (697339) C L2#LINE/L2 (519) 2563 2031 m_b90s601i1 3339 chr2qtel1M 302131 ACTCCT-GATTTTTGATCCTGAAGAAATGGGAACATAGTGATGCCCTCTT 302179 v- i i- iv v i iv i v v v i?v C L2#LINE/L2 2563 ACTCCAAGGTTTTTGG-CCTGAGCAACTGGAAGGATGGAGTTGCCATTNA 2515 chr2qtel1M 302180 CAGTAATAGGGAA-AGTGTGAG-GGTGTGTGTATGAGAATATGTGGGATA 302227 v vi i - v i i - v iiv v i------ -- C L2#LINE/L2 2514 CTGAGATGGGGAAGACTGCGGGAGGAGCAGGTTTGAGG------GGGA-- 2473 chr2qtel1M 302228 GAAATAATAAGTTCTGTTTTGAACATATTGAATTTGAGATTCTGGTCTAT 302277 - i v vi v i i i i ---- i C L2#LINE/L2 2472 -AGATCAGGAGTTCAGTTTTGGACATGTTAAGTTTGAGAT----GCCTAT 2428 chr2qtel1M 302278 TGGCCATTCAATTTGAGCCATCTATAAGGAAATTGAAGATATAAA-ATGG 302326 i v i v v vii v vv v i i v ii i-v C L2#LINE/L2 2427 TAGACATCCAAGTGGAGATGTCGAGTAGGCAGTTGGATATACGAGTCTGG 2378 chr2qtel1M 302327 AGGTCAGCAGAGAGATTGGGGCATGAAAAGGATATTTGAAAATCATAA-- 302374 v vi i iv vv i viv v ii i v -- C L2#LINE/L2 2377 AGTTCAGGGGAGAGGTCCGGGCTGGAGATATAAATTTGGGAGTCATCAGC 2328 chr2qtel1M 302375 AAATAGTTAGAAATTAAATTCATGGTAGCTGATAAAATCACCAAAAAAAG 302424 v v i v v vi iv viv i i ? iii iv C L2#LINE/L2 2327 ATATAGATGGTATTTAAAGCCATGAGACTGGATGAGATCACCNAGGGAGT 2278 chr2qtel1M 302425 TAATAATGAGGCAAAAGAGAAGAGGATCAAAGATAGAACGCCAAGGAACC 302474 v i ivv viv i vi i iv i v iii v i C L2#LINE/L2 2277 GAGTGTAGATAGAGAAGAGAAGAGGTCCAAGGACTGAGCCCTGGGGCACT 2228 chr2qtel1M 302475 CATATGGTTGGAGGTT-TCAATCTCAGGAATATC---CAAAAAAGATAGA 302520 vv i v ?i i-vvi vv v iv v --- ii iv C L2#LINE/L2 2227 CCAACGTTNAGAGGTCGGGGAGATGAGGAGGAACCAGCAAAGGAGACTGA 2178 chr2qtel1M 302521 AAAGAAGTGGTCAGAGAATAGGAAGAAGGGAAATCAGGAGAGAGGGGTGT 302570 i i i i v --- v i i i v v C L2#LINE/L2 2177 GAAGGAGCGGCCAGTG---AGGTAGGAGGAAAACCAGGAGAGTGTGGTGT 2131 chr2qtel1M 302571 CCTAAAATCCTAGAGAACAGAGAGGATCGTGATGGGAAGA---------- 302610 ii v v v v i v vv iv v iii ---------- C L2#LINE/L2 2130 CCTGGAAGCCAAGTGAAGAAAGTGTTTCAAGAAGGAGGGAGTGATCAACT 2081 chr2qtel1M 302611 GTATCAAAGCCTGAAGAGAAGTCAAGGATAATGAGGATGGAGAAGGTGAC 302660 i vv vv ? i v vi iv -v C L2#LINE/L2 2080 GTGTCAAATGCTGCTGANAGGTCAAGTAAGATGAGGACTGAGAA-TTGAC 2032 chr2qtel1M 302661 C 302661 C L2#LINE/L2 2031 C 2031 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.86 CpG sites = 86, Kimura (unadjusted) = 45.66 Transitions / transversions = 1.00 (86/86) Gap_init rate = 0.05 (26 / 530), avg. gap size = 1.46 (38 / 26) 55 0.00 0.00 0.00 chr2qtel1M 304293 304339 (695661) (TA)n#Simple_repeat 1 47 (0) c_b90s251i0 3340 chr2qtel1M 304293 TATATATATATATATATATATATATATATATATATATATATATATAT 304339 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATAT 47 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 399 22.69 0.84 11.11 chr2qtel1M 304398 304516 (695484) MIRb#SINE/MIR 7 114 (154) m_b90s601i2 3341 chr2qtel1M 304398 GGTAGCTAGATGGCACATCAGATACAGCACCTGTGCTCTGAAGTTCAAAA 304447 i ---i ii vii v v -- v i i ivi v MIRb#SINE/MIR 7 GGCAGC---GTGGTGCAGTGGAAAGAGCAC--GGGCTTTGGAGTCAGACA 51 chr2qtel1M 304448 GACCTGGGTTCAAATCG-GGCTCAAACACTTAGTACTTCCTAGCTGTGTG 304496 i v- viv ------- MIRb#SINE/MIR 52 GACCTGGGTTCGAATCCCGGCTCTGCCACTTA-------CTAGCTGTGTG 94 chr2qtel1M 304497 ACCCTGGGCAAGTCACTTGA 304516 i i i MIRb#SINE/MIR 95 ACCTTGGGCAAGTTACTTAA 114 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.69 CpG sites = 15, Kimura (unadjusted) = 27.27 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.11 (13 / 118), avg. gap size = 1.00 (13 / 13) 372 21.95 1.80 9.71 chr2qtel1M 304423 304533 (695467) MIR#SINE/MIR 23 125 (137) m_b90s601i3 3341 chr2qtel1M 304423 AGCACCTGTGCTCTGAAGTTCAAAAGACCTGGGTTCAAATCG-GGCTCAA 304471 -- v i i- i vvi i v- vi MIR#SINE/MIR 23 AGCAC--GGGCTCTGGAGC-CAGACTGCCTGGGTTCGAATCCCGGCTCTG 69 chr2qtel1M 304472 ACACTTAGTACTTCCTAGCTGTGTGACCCTGGGCAAGTCACTTGATTCCA 304521 v ------- i i i iii v MIR#SINE/MIR 70 CCACTTA-------CTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCT 112 chr2qtel1M 304522 AT-TGTCTCAGCT 304533 v - i i MIR#SINE/MIR 113 CTGTGCCTCAGTT 125 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.98 CpG sites = 14, Kimura (unadjusted) = 26.35 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.11 (12 / 110), avg. gap size = 1.00 (12 / 12) 16 21.24 3.45 3.45 chr2qtel1M 304534 304591 (695409) (AAAAG)n#Simple_repeat 1 58 (0) m_b90s252i1 3342 chr2qtel1M 304534 AAAAAAAAAG-AAAGAAAAGAAAGAGAAAA-ATATAAAATTAAGAGGTGA 304581 i - - - v vi vv - i vi (AAAAG)n#Simp 1 AAAAGAAAAGAAAAGAAAAGAAA-AGAAAAGAAAAGAAAAGAA-AAGAAA 48 chr2qtel1M 304582 GGAAAAGAAA 304591 i (AAAAG)n#Simp 49 AGAAAAGAAA 58 Matrix = Unknown Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.07 (4 / 57), avg. gap size = 1.00 (4 / 4) 17 30.88 3.75 0.00 chr2qtel1M 304538 304617 (695383) (AAAGAG)n#Simple_repeat 1 83 (0) m_b90s252i2 3342 chr2qtel1M 304538 AAAAAGAAAGA-AAAGAAAGAGAAAAATATAAA-ATTAAGAG-GTGAGGA 304584 i - i i i v v - vv -iv i (AAAGAG)n#Sim 1 AAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAA 50 chr2qtel1M 304585 AAAGAAATGTCTAGAGAAAGGGAAAGGGAGAGA 304617 i vivvv i i i (AAAGAG)n#Sim 51 AGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGA 83 Matrix = Unknown Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.04 (3 / 79), avg. gap size = 1.00 (3 / 3) 18 22.46 0.00 0.00 chr2qtel1M 304534 304570 (695430) (A)n#Simple_repeat 1 37 (0) m_b90s252i0 3342 chr2qtel1M 304534 AAAAAAAAAGAAAGAAAAGAAAGAGAAAAATATAAAA 304570 i i i i i v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 37 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 444 23.91 0.87 5.45 chr2qtel1M 304824 304938 (695062) MIRc#SINE/MIR 19 128 (140) m_b90s601i4 3343 chr2qtel1M 304824 TGGATGGAGCACCGGCCCTGAAGTCAGGAGGATCTGAGTTCAAATGTGAC 304873 vi i v i i i i i i i ----- MIRc#SINE/MIR 19 TGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGT----- 63 chr2qtel1M 304874 CTCAGCAGTTAACACTTCCTAGTAGTGTGACCATGGGCAAGTCACTTAAC 304923 i i -vi iv v iv v MIRc#SINE/MIR 64 CCCGGC-TCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAAC 112 chr2qtel1M 304924 CCCAATT-GCTTCAGT 304938 i vv v- i MIRc#SINE/MIR 113 CTCTCTGAGCCTCAGT 128 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.78 CpG sites = 16, Kimura (unadjusted) = 29.40 Transitions / transversions = 1.60 (16/10) Gap_init rate = 0.06 (7 / 114), avg. gap size = 1.00 (7 / 7) 36 0.00 0.00 0.00 chr2qtel1M 304947 304977 (695023) (AG)n#Simple_repeat 1 31 (0) c_b90s251i1 3344 chr2qtel1M 304947 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 304977 (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 534 30.85 4.35 3.82 chr2qtel1M 305149 305539 (694461) L1PA5_3end#LINE/L1 12 404 (497) m_b90s551i1 3345 chr2qtel1M 305149 AATATACAGATAAATGAGTCAAATTTATAAAAATAAGAAC---CATTTGC 305195 v i v v v iv i i - i --- vi-- L1PA5_3end#LI 12 AATCTACAAAGAACTCAAACAAATTTACAAGAA-AAAAACAAACAAC--C 58 chr2qtel1M 305196 CCATTGAAAATGATAAAAAAAAAATAGGAAGAGTCAGTTTTCAGATGAAT 305245 ii --i iiivi ii v v v v i i v v L1PA5_3end#LI 59 CCATCAAAAA--GTGGGCGAAGGATATGAACAGACACTTCTCAAAAGAAG 106 chr2qtel1M 305246 TAATTT--GAAGTTATCTGTAGCCATATGAA-----GC-CAT-ATGACTA 305286 vv -- v ii v --- v i ----- - - v i L1PA5_3end#LI 107 ACATTTATGCAGCCAAC---AGACACATGAAAAAATGCTCATCATCACTG 153 chr2qtel1M 305287 TCAGTTGGAGAAATGCTAATTAAAACAATTCTGAGCTACTACCTTACTTC 305336 v vi ii v i v ivv v i i i vi L1PA5_3end#LI 154 GCCATCAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTCACACC 203 chr2qtel1M 305337 TGTTAGATTGGCTATTAGAAAAGAAAATAA--AAATGACAAGTATTGGAG 305384 v v v i vv -- i v -- ii i ii L1PA5_3end#LI 204 AGTTAGAATGGCGATCATTAA--AAAGTCAGGAAACAACAGGTGCTGGAG 251 chr2qtel1M 305385 GGGATGTGGGAAAACTGAGACAC--ATACGCTTTTGCTGAAATTGTATAC 305432 i ii iv ii --v i v v ii i v L1PA5_3end#LI 252 AGGATGTGGAGAAATAGGAACACTTTTACACTGTTGGTGGGACTGTAAAC 301 chr2qtel1M 305433 TGATTCAACCATTCTGTAAAGCAAT-TGGGAACTAGGCCCACAAGGTTTA 305481 ii v v ii i - vi i ---- v v i- L1PA5_3end#LI 302 TAGTTCAACCATTGTGGAAGACAGTGTGGCGATT----CCTCAAGGATC- 346 chr2qtel1M 305482 TAAAACCACATACACCCTTTGACCTAGCAATTCCACTAGTAAATGTGTAT 305531 i i v v i v i v i i v iii i i i L1PA5_3end#LI 347 TAGAACTAGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATATAC 396 chr2qtel1M 305532 CCAAAAGA 305539 i L1PA5_3end#LI 397 CCAAAGGA 404 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.05 CpG sites = 68, Kimura (unadjusted) = 40.97 Transitions / transversions = 1.42 (68/48) Gap_init rate = 0.06 (23 / 390), avg. gap size = 1.39 (32 / 23) 596 25.75 4.02 4.86 chr2qtel1M 305294 305542 (694458) L1ME5_3end#LINE/L1 161 407 (534) m_b90s551i2 3345 chr2qtel1M 305294 GAGAAATGCTAATTAAAACAATTCTGAGCTACTACCTTACTTCTGTTAGA 305343 v ivv v ii i vi i L1ME5_3end#LI 161 GAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCTATTAGA 210 chr2qtel1M 305344 TTGGC---TATTAGAAAAGAAAATAAAAATGACAAGTATTGGAGGGGATG 305390 i ---v ivvii --- v i v i L1ME5_3end#LI 211 CTGGCAAAAATTAGAAAGCTGGAT---AATGCCAAGTGTTGGCGAGGATG 257 chr2qtel1M 305391 TGGGAAAACTGAGACA--CATACGCTTTTGCTGAAATTGTATACTGATTC 305438 i ? iv ii v-- i i vi v ii v v i v L1ME5_3end#LI 258 TGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACTGGTGC 307 chr2qtel1M 305439 AACCATTCTGTAAAGCAAT-TGGGA--ACTAGGCCCA--CAAGGTTTATA 305483 i v i - v -- vi i v --i --- L1ME5_3end#LI 308 AGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTAAG---TATA 354 chr2qtel1M 305484 AAACCACATACACCCTTTGACCTAGCAATTCCACTAGTAAATGTGTATCC 305533 ---- i -- v i i vv iii i i L1ME5_3end#LI 355 ----CGCAT--ACCCTATGACCCAGCAATTCCGCTCCTGGGTATATATCC 398 chr2qtel1M 305534 AAAAGAGAT 305542 v i L1ME5_3end#LI 399 CAAAGAAAT 407 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 31.14 CpG sites = 36, Kimura (unadjusted) = 32.42 Transitions / transversions = 1.44 (36/25) Gap_init rate = 0.07 (17 / 248), avg. gap size = 1.29 (22 / 17) 512 31.21 2.08 2.43 chr2qtel1M 305295 305583 (694417) L1ME4c_3end#LINE/L1 162 449 (381) m_b90s551i3 3345 chr2qtel1M 305295 AGAAATGCTAATTAAAACAATTCTGAGCTACTACCTTACTTCTGTTAGAT 305344 v i ivv v i ii vi i i L1ME4c_3end#L 162 AGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCTATTAAAT 211 chr2qtel1M 305345 TGGCTATTAGAAA---AGAAAA-TAAAAATGACAAGTATTGGAGGGGATG 305390 i ---- i --- i - i v iv v i ii v i ? L1ME4c_3end#L 212 TAGC----AAAAATTTAAAAAATTGATAATACCCAATGCTGGCGAGGNTG 257 chr2qtel1M 305391 TGGGAAAACTGAGACA--CATACGCTTTTGCTGAAATTGTATACTGATTC 305438 i vi iv ?-- ii vi v iv ? v i i v L1ME4c_3end#L 258 CGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGTAC 307 chr2qtel1M 305439 AACCATTCTGTAAAGCAATTGGGAACTAGGCCCACAAGGTTTATAAAACC 305488 v i v v v v v ivi- ivii vi L1ME4c_3end#L 308 AACCCTTTTGGAAAGCAATTTGGCAATACGTAT-CAAGAGCCATAAAAAT 356 chr2qtel1M 305489 ACATACACCCTTTGACCTAGCAATTCCACTAGTAAATGTGTATCCAAAAG 305538 iivi i i i vv iiivi v v i L1ME4c_3end#L 357 GTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGG 406 chr2qtel1M 305539 AGATGAAAAACAAAAAGGAAAATGACCTATATATACAAAAATATT 305583 i i vvv v i -- v ii i i i L1ME4c_3end#L 407 AAATAATTCAAAAGAAGGAAAA--AGCTATATGCACGAAGATGTT 449 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.02 CpG sites = 52, Kimura (unadjusted) = 42.30 Transitions / transversions = 1.44 (52/36) Gap_init rate = 0.03 (10 / 288), avg. gap size = 1.30 (13 / 10) 13 20.23 4.26 2.08 chr2qtel1M 305746 305792 (694208) (AAATAT)n#Simple_repeat 1 48 (0) m_b90s252i3 3346 chr2qtel1M 305746 AAATCATAAGT-TAAATA-CAATATATGTATACATATTTATATAATTAT 305792 - i - -v vi v vv v (AAATAT)n#Sim 1 AAAT-ATAAATATAAATATAAATATAAATATAAATATAAATATAAATAT 48 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.07 (3 / 46), avg. gap size = 1.00 (3 / 3) 12 12.79 13.21 1.69 chr2qtel1M 306979 307031 (692969) (CTCCTT)n#Simple_repeat 1 59 (0) m_b90s252i4 3347 chr2qtel1M 306979 CTCCTTCCCAGTCTTCCTAC-CC--CTCATTC-CCTTCTCC-T-TCC-TC 307021 i vv - v - -- v - - - - (CTCCTT)n#Sim 1 CTCCTTCTCCTTC-TCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTC 49 chr2qtel1M 307022 TCCATCTCCT 307031 v (CTCCTT)n#Sim 50 TCCTTCTCCT 59 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.13 (7 / 52), avg. gap size = 1.14 (8 / 7) 16 16.18 2.22 4.55 chr2qtel1M 307621 307665 (692335) (CCT)n#Simple_repeat 1 44 (0) m_b90s252i5 3348 chr2qtel1M 307621 CCTCCACCACCTCC-CCCCCTCCCACTTAGCTCCTCCTCCTCCTCC 307665 v v - i - v i -v (CCT)n#Simple 1 CCTCCTCCTCCTCCTCCTCCT-CCTCCT-CCTCCTCCTCCTCCTCC 44 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.07 (3 / 44), avg. gap size = 1.00 (3 / 3) 549 35.38 6.69 3.65 chr2qtel1M 307845 308457 (691543) MamRTE1#LINE/RTE-BovB 604 1234 (2578) m_b90s601i5 3349 chr2qtel1M 307845 GCAGCAAACCTGAAAGATGGACAGCTCTAGTGGCCAGAGAATTCAGCAGG 307894 iviv v v i i v v v vv v i vvv i MamRTE1#LINE/ 604 GCAGTCGTCCAGAAAGAAGAACGGCACTCGTCGCACGTGAACTGTCCAGA 653 chr2qtel1M 307895 TGTCACATCCCAATGGCAGCCCTGAGTGAAATAAGGCTGGCAAATGAAAG 307944 iivivi vvv v v v i iv i vv vi i MamRTE1#LINE/ 654 TACGGAGTCGACATCGCCGCACTGAGCGAAACCAGACTTCCTGATGAAGG 703 chr2qtel1M 307945 CCACCTTACTGAAGTTGGAGCCACGTACAAGGTTTTCTGCAGGGAGGGCA 307994 v v i v iiiv v iv? ivvv i -- i v v MamRTE1#LINE/ 704 ACAGCTCACGGAGACAGGTGCCGGNTACGCCTTCTTCTG--GAGAGGTCT 751 chr2qtel1M 307995 GT-------GGAGGGAGCATTGTGAAGTTGGCAT-AGGTTAGCAATCAAA 308036 vi-------i v vvii v v ---- i - v v i MamRTE1#LINE/ 752 TCCCTCTTCAGAGCGACGGCTCTCA----GGCGTCAGCTTTGCAATCAGA 797 chr2qtel1M 308037 CCGAATCAA--GTCAGCAACCTTGTATGTCTGCCAAAAAGACTGAATGGC 308084 -- i v-- vvv i? ivi vi i v i i vv ? i i MamRTE1#LINE/ 798 C--AGTCACTTGTCTCAAGNCTCCCAAATTTGCCCAGAGGCATNAGTGAC 845 chr2qtel1M 308085 AGGTTCATGACA--ATGCCATGGGCACCTGTAGGAAAA-TGCCATGGCAC 308131 v vi v v-- i ---vi ?i v iv -i i? v MamRTE1#LINE/ 846 CGTCTGATGACCCTACGCC---TACNTCTGAAACAAAAGCGCTNTGCCAC 892 chr2qtel1M 308132 CATCATCAGTGACTATCTTCCCACCATGAGGAACCTTGATGAGGTCAAAG 308181 i i vv vii v ivii vv MamRTE1#LINE/ 893 CGTCATCAGCGCATATGCCCCCACCATGACGAATACCGATGAGGAGAAAG 942 chr2qtel1M 308182 AAA-ATTTGATGAAGA-CTAGAGATGCTCATCCTCAAT-TTGCCAAAAGA 308228 - iv ii i - i v vi - v ii-v i v vv MamRTE1#LINE/ 943 AAAGATTCTACAAGGATCTGGACAGACTCAT-CGCAGCGGTACCAACATC 991 chr2qtel1M 308229 GGACAAGCTTATCTAATCCTGGCTGATTTTAAGGC-----TAGACTAG-- 308271 v v --i vi vv i v ----- v i - -- MamRTE1#LINE/ 992 TGACAAGCTGATC--GTCACGGGAGATTTCAACGCACGTGTCGGC-AGCG 1038 chr2qtel1M 308272 --GCTCAGAC---AAGGGATATCCTTGGGAGGAATAAGGTTGAAACAGC- 308315 -- iv i ---i ii vi v i ivv?v iii i i - - MamRTE1#LINE/ 1039 ATGCCGAAACGTGGAGAAAAGTCATCGGACCNCACGGGATTGGAA-AGCT 1087 chr2qtel1M 308316 -AACAGCACTGGTC-ACTT---ATTAGTGAAGATTTGTGC--ATCCTAAG 308358 - v - i---v i i ---- -- v v v MamRTE1#LINE/ 1088 NAACAGCAATGGTCTACTCCTGCTCAGCGAA----TGTGCCAAGCATCAG 1133 chr2qtel1M 308359 ACCCC-ATCACCAACATTGTCTTCTGCTAACCTAA-AAGCAACAGAACTT 308406 vi vi- iii i iv v - vi v - v MamRTE1#LINE/ 1134 CTCGTAATCACCAACACCATCTTCCGCCTACCGAATAAGAGAAAG-ACAT 1182 chr2qtel1M 308407 CACACATGCACTTTTACAG--CAAACATTGCCAT-TTGTAGACTATATAA 308453 iiv --ii vi --i i v v - ii v i v MamRTE1#LINE/ 1183 CATGGATGCAC--CCAAGGTCTAAGCAGTGGCATCTCATTGATTATATCA 1230 chr2qtel1M 308454 TTAT 308457 ii MamRTE1#LINE/ 1231 TCGT 1234 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.88 CpG sites = 102, Kimura (unadjusted) = 49.43 Transitions / transversions = 0.95 (102/107) Gap_init rate = 0.07 (43 / 612), avg. gap size = 1.49 (64 / 43) 16 24.35 4.23 2.78 chr2qtel1M 308853 308923 (691077) (GAATGAA)n#Simple_repeat 1 72 (0) m_b90s252i6 3350 chr2qtel1M 308853 GAAT-ATGAATGACAGAATG-AGAATCTAGATAAAATAAAAAACAA-GAA 308899 - v - - vv vvi v vi v - (GAATGAA)n#Si 1 GAATGAAGAATGA-AGAATGAAGAATGAAGAATGAAGAATGAAGAATGAA 49 chr2qtel1M 308900 ATATGGAGAATGAAGAGAGGAAGA 308923 iv i - v (GAATGAA)n#Si 50 GAATGAAGAATGAAGA-ATGAAGA 72 Matrix = Unknown Transitions / transversions = 0.40 (4/10) Gap_init rate = 0.07 (5 / 70), avg. gap size = 1.00 (5 / 5) 1702 32.76 2.04 1.95 chr2qtel1M 310246 311372 (688628) L1M4_orf2#LINE/L1 1087 2214 (1080) m_b90s551i4 3351 chr2qtel1M 310246 AAAACTTGATTTTATGAAAAAACTAATAAAGCAGATGATATTTTCGCTAA 310295 v i i v i ii i iiv ii vvi v i L1M4_orf2#LIN 1087 AAAAGTTGGTTCTTTGAAAAGATCAACAAAATTGACAAACCTTTAGCTAG 1136 chr2qtel1M 310296 TTTGATTA-GAAAAAAGGAAAG------CAAATTACTGGTATCAAAAATG 310338 vi ii - i i ------ iiv ii L1M4_orf2#LIN 1137 ACTGACCAAGAAAAAAAGAGAGAAGACTCAAATTACTAAAATCAGGAATG 1186 chr2qtel1M 310339 AAAAGGGTGAAGTTACCAGCAATGAAGAAGAAATTAAAGCAATAAGTAGG 310388 ii v vi i v i ivvviv v ivi v vv L1M4_orf2#LIN 1187 AAAGAGGGGACATTACTACCGACCTTACAGAAATAAAAAGGATTATAAGG 1236 chr2qtel1M 310389 ACCTATTTTGCTCAACTGTTTGCCAACAAATCAGACCATTTAATTGAAAT 310438 ivv i v vv i v i iv ii iv L1M4_orf2#LIN 1237 GAATACTATGAACAATTGTATGCCAACAAATTAGATAACCTAGATGAAAT 1286 chr2qtel1M 310439 GGATGAATATTTGCAAAAACGTAAATTGCCCATATTAACAGAAGAAAAAA 310488 ii vii iv i ii i i v v i i vv i L1M4_orf2#LIN 1287 GGACAAATTCCTAGAAAGACACAAACTACCGAAACTGACTCAAGAAGAAA 1336 chr2qtel1M 310489 TAAAATGCTCAAATAAACCCATTTTAAAAAGAGAAATTAAACAAGTCATC 310538 i viiiii i i vvi iv i i i iv v L1M4_orf2#LIN 1337 TAGAAAATCTGAATAGACCTATAACAAGTAAAGAGATTGAATTAGTAATC 1386 chr2qtel1M 310539 AATGAATTCCCAAGGAAAAAAATCTCCAGGCTGAGATGAATTTGCAAGGG 310588 vi i i v vi i v - ?iv iv ii vi v L1M4_orf2#LIN 1387 AAAAAACTTCCCACAAAGAAAAGC-CCAGGNCCAGATGGCTTCACTGGTG 1435 chr2qtel1M 310589 CATTCTACCAAATAGTTAGAGAACAATTAATTCTGATACAATGTAAACTA 310638 v i v i v iv ii v vviii v L1M4_orf2#LIN 1436 AATTCTACCAAACATTTAAAGAAGAATTAACACCAATCCTTCACAAACTC 1485 chr2qtel1M 310639 CTTGAAAAAATAGGTGAAGAATGATTGCTACCTAATTCATTTTATGATAC 310688 i iv iv i iv vii v i i i vi L1M4_orf2#LIN 1486 TTCCAAAAAATAGAAGAGGAGGGAACACTTCCCAACTCATTCTATGAGGC 1535 chr2qtel1M 310689 AAATATGGGGGTAATACTTAAAATAGGAAGAGCTA----AAACAAAGAAA 310734 v i vivvv i iv vi iv i vi ---- iv L1M4_orf2#LIN 1536 CAGTATTACCCTGATACCAAAACCAGACAAAGACATCACAAGAAAAGAAA 1585 chr2qtel1M 310735 ATTATAGACCAATTTCCCTAATGAATACTGATGCAAAAATAAATAAATAA 310784 i i v v iv ---------v L1M4_orf2#LIN 1586 ACTACAGACCAATATCCCTTATGAATATAGATGCAAAAAT---------C 1626 chr2qtel1M 310785 ATAAATGAAACATTAGCAAACAGATTAGATCAATTTATCAACAGGACAAT 310834 v v ii i i v v vv v iv v v --- L1M4_orf2#LIN 1627 CTCAACAAAATACTAGCAAACCGAATCCAGCAACATATAAAAAGG---AT 1673 chr2qtel1M 310835 AATACAGTATGAGCAAATAAGATCTATACCAGGAATGTAGGGATGATTCA 310884 v vi v i ii i v i i v i L1M4_orf2#LIN 1674 TATACACCATGACCAAGTGGGATTTATCCCAGGAATGCAAGGTTGGTTCA 1723 chr2qtel1M 310885 ATATAGGAAA--CTATCAGCATAAT----CATATCA--AGAACAAAACTA 310926 i ?v -- v iii ---- i -- i i--i L1M4_orf2#LIN 1724 ACATNCGAAAATCAATCAATGTAATACACCATATTAATAGAATAAAG--G 1771 chr2qtel1M 310927 ACAGAAATCATCCTATTATATCAATAGATGCAGAAAAAGATTTTGAGAAA 310976 i i iviv i v i vv v L1M4_orf2#LIN 1772 ACAAAAACCACATGATCATCTCAATAGACGCAGAAAAAGCATTTGACAAA 1821 chr2qtel1M 310977 ATACAGTACCCATTCCTATTTACAAACATTAGAGAGCATGGGAATAAATG 311026 v ii v v i-v v i vi v ivv i i v L1M4_orf2#LIN 1822 ATCCAACACCCTTTCATG-ATAAAAACACTCAACAAACTAGGAATAGAAG 1870 chr2qtel1M 311027 GAGTTTTCCTCAAAATGGCAAATAACATCTATCCAAAACCATCAGTATGC 311076 iivi vv ii vii ivv vv ivvi L1M4_orf2#LIN 1871 GGAACTTCCTCAACCTGATAAAGGGCATCTACGAAAAACCCACAGCTAAC 1920 chr2qtel1M 311077 ATTATATGAAATGGCAATAAGCTAGATATATTCACAATAAGATCAGGGGA 311126 i ivv ii v ii ii ?iiv v vv - i L1M4_orf2#LIN 1921 ATCATACTTAATGGTGAAAGACTGAANGCTTTCCCCCTAAGATCA-GGAA 1969 chr2qtel1M 311127 TGAAACAAGGATGCCTATTATCACTACTATTGTTCAACATTGTATTAAAA 311176 ii i i iii v i i vi i i ii i L1M4_orf2#LIN 1970 CAAGACAAGGATGTCCGCTCTCGCCACTTCTATTCAACATTGTACTGGAG 2019 chr2qtel1M 311177 ATGTTGGCTTTAGCAATAAGAAAAG-AAAAGAAACAGAAGGAAT-TAGAG 311224 i vi i ivvi v iv - i i v -i v L1M4_orf2#LIN 2020 GTTCTAGCCAGGGCAATTAGGCAAGAAAAAGAAATAAAAGGCATCCAGAT 2069 chr2qtel1M 311225 TAGGCAATAAGGTAACAGAACTATCCCTCTTTGCAGATCGTATGATGGTA 311274 - v vi i v ii i i v i vii vv i L1M4_orf2#LIN 2070 T-GGAAAGGAAGAAGTAAAACTATCTCTATTCGCAGATGACATGATCTTG 2118 chr2qtel1M 311275 TCTCTAGAGAATACTAGAGAATCAACCAAAAAAAAA--AAAACTATTTGA 311322 v v i v ii v ? vv -- i v -- L1M4_orf2#LIN 2119 TATATAGAAAATCCTAAGGAATCCACNAAAAAACTATTAGAACTAAT--A 2166 chr2qtel1M 311323 AACAACAGCCTTACAAAGTTGCAAGATACAAAATAAATCCACACAAATCA 311372 i-- iiivi i i i v vi v L1M4_orf2#LIN 2167 AACG--AGTTCAGCAAGGTTGCAGGATACAAGATCAATATACAAAAATCA 2214 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 43.50 CpG sites = 209, Kimura (unadjusted) = 44.70 Transitions / transversions = 1.37 (209/153) Gap_init rate = 0.03 (31 / 1126), avg. gap size = 1.45 (45 / 31) 337 31.15 0.00 7.00 chr2qtel1M 311507 311613 (688387) C MIRc#SINE/MIR (141) 127 28 m_b90s601i6 3352 chr2qtel1M 311507 CTGAGGTTAATTGGTATTAAGTGACTTATCCAGGGTTCCACAAATAAGAA 311556 i v vv ivi ii i iv iv i--- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG--- 81 chr2qtel1M 311557 GTGTTAAGTGTCTGAGGTCACATTTGAACTCAGGTCCTCCTGACTTCAGG 311606 ---- v v viviv i i i i i i C MIRc#SINE/MIR 80 ----TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr2qtel1M 311607 GCTGGTG 311613 v ii C MIRc#SINE/MIR 34 TCCAGTG 28 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.04 CpG sites = 19, Kimura (unadjusted) = 41.52 Transitions / transversions = 1.58 (19/12) Gap_init rate = 0.07 (7 / 106), avg. gap size = 1.00 (7 / 7) 12 31.65 3.23 0.00 chr2qtel1M 312665 312726 (687274) (CAGAGA)n#Simple_repeat 1 64 (0) m_b90s252i7 3353 chr2qtel1M 312665 CAGGGCCAGGAACAGAAGCCCAGACAGAGACACAGA-AG-CCCACTCTCA 312712 i v ii ii vv v - -vv vvvv (CAGAGA)n#Sim 1 CAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACA 50 chr2qtel1M 312713 GAGGCAGAGACAGA 312726 i (CAGAGA)n#Sim 51 GAGACAGAGACAGA 64 Matrix = Unknown Transitions / transversions = 0.60 (6/10) Gap_init rate = 0.03 (2 / 61), avg. gap size = 1.00 (2 / 2) 210 31.02 1.13 12.58 chr2qtel1M 313535 313711 (686289) L2d2_3end#LINE/L2 380 538 (17) m_b90s601i7 3354 chr2qtel1M 313535 TTAAGTCCTAT-TTGTTCTGGATTTAGCTTGCTTTGTATATATTTGTGTA 313583 i i i - ---- i ---- vi ii i i v L2d2_3end#LIN 380 TTAAATCTTGTATTGTT----ATTTAACTT----TTCACGTGTTTATGTC 421 chr2qtel1M 313584 TTGTTTCCCACATTGGATTGTACATTACTTGAAGGAATTGTCTTTTGTCT 313633 i vv i i vii v i v vv v -iv - L2d2_3end#LIN 422 TTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGAC-CATGTC- 469 chr2qtel1M 313634 CTTTATTTTATTTTATTTTATTTTTTAATTCTCAGTGCTTATCATTGTGG 313683 -- --- i iv v iiiii ----- i i v iv v L2d2_3end#LIN 470 --TTA---TACTTCTTTGTATCCCCCA-----CAGCGCCTAGCACAGTGC 509 chr2qtel1M 313684 CTGGCACTCA-TAGGTGTTTAATAAATGT 313711 v v - i i i i L2d2_3end#LIN 510 CTTGCACACAGTAGGCGCTCAATAAATAT 538 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.43 CpG sites = 30, Kimura (unadjusted) = 40.85 Transitions / transversions = 1.67 (30/18) Gap_init rate = 0.12 (22 / 176), avg. gap size = 1.00 (22 / 22) 238 30.37 4.23 7.25 chr2qtel1M 313570 313711 (686289) L2a_3end#LINE/L2 363 500 (17) m_b90s601i8 3354 chr2qtel1M 313570 TATATATTTGTGTATTGTTT-----CCCACATTGGATTGTACATTACTTG 313614 v v i ----- v i i v vii v v L2a_3end#LINE 363 TATTTATTTGTTTATTGTCTGTCTCCCCCCACTAGAATGTAAGCTCCATG 412 chr2qtel1M 313615 AAGGAATTGTCTTTTGTCTCTTTATTTTATTTTATTTTATTTTTTAATTC 313664 i v vv v ---- i i------ i i vi vv i L2a_3end#LINE 413 AGGGCAGGGACTTTTGTC----TGTTTTG------TTCACTGCTGTATCC 452 chr2qtel1M 313665 TCAGTGCTTATCATTGTGGCTGGCAC-TCATAGGTGTTTAATAAATGT 313711 i i i vv iv v - vi i i i i L2a_3end#LINE 453 CCAGCGCCTAGAACAGTGCCTGGCACATAGTAGGCGCTCAATAAATAT 500 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.02 CpG sites = 21, Kimura (unadjusted) = 39.49 Transitions / transversions = 1.11 (21/19) Gap_init rate = 0.09 (12 / 141), avg. gap size = 1.33 (16 / 12) 229 28.70 4.65 2.74 chr2qtel1M 314317 314531 (685469) C L1M5_orf2#LINE/L1 (2246) 1048 830 m_b90s551i5 3355 chr2qtel1M 314317 TTTTATTAACCTTACCTTTAATTTTTATAATTTCCAATTTAGTGTTCAAT 314366 i i ii ivv i v i v vvii vv ii i?v C L1M5_orf2#LIN 1048 TTTCATTGATTTCTGCTCTTATCTTTATTATTTCCTTCCTTCTACTTNCT 999 chr2qtel1M 314367 TAGGGATTTTAATTT--TTTTCTTTTTACAGCTTTTTAAGGTGTATACCC 314414 v -- -- i vi i v vi ii C L1M5_orf2#LIN 998 TTGGG--TTTAATTTGCTCTTCTTTTTCTAGCTTCTTAAGGTGGAAGCTT 951 chr2qtel1M 314415 AATTCATTAACCT--GTTCTTTTCTCTGTTTTATTGATCTAAGCATTTAG 314462 iv i ii --ivi ii v i --- v ? i C L1M5_orf2#LIN 950 AGATCATTGATTTTAAGCCTTTCTTCTTTTCTA---ATATANGCATTTAA 904 chr2qtel1M 314463 AGAGATAAATTTTTCTTT---CACTGCTTTTATTGGATTTCTCAGATTTT 314509 ? vv ii i --- vii v ii v i - C L1M5_orf2#LIN 903 NGCTATAAATTTCCCTCTAAGCACTGCTTTAGCTGCATCCCACAAA-TTT 855 chr2qtel1M 314510 TAATATGTTG---TTTCAATTTCAT 314531 i --- v ? C L1M5_orf2#LIN 854 TGATATGTTGTATTTTCATTNTCAT 830 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.40 CpG sites = 37, Kimura (unadjusted) = 38.40 Transitions / transversions = 1.61 (37/23) Gap_init rate = 0.05 (10 / 214), avg. gap size = 1.60 (16 / 10) 12 32.75 0.00 0.00 chr2qtel1M 315270 315318 (684682) (TTT)n#Simple_repeat 1 49 (0) m_b90s252i8 3356 chr2qtel1M 315270 TTTTGTTGTTTTAATTTTATTCTATCTTTTTTCATTATTATTCTTTTTT 315318 v v vv v i v i iv v v i (TTT)n#Simple 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 49 Matrix = Unknown Transitions / transversions = 0.44 (4/9) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 663 27.22 3.07 5.33 chr2qtel1M 319987 320312 (679688) HERVK11D#LTR/ERVK 3201 3519 (4233) m_b90s701i1 3357 chr2qtel1M 319987 GGAATTCCCCTGTATTTGTTGTTAAAAAAAAAAAAAAATCTGGAAAATGG 320036 i v i ------ v i v HERVK11D#LTR/ 3201 GGAACTCGCCTGTGTTTGTTGT------ACAAAAAAAGTCAGGAAAATGG 3244 chr2qtel1M 320037 AGGATGTTGACTAATTTAAGAAAAGTAAATGAACAG--ATGGAAACTATG 320084 v i vi i ivv v -- -- vi v HERVK11D#LTR/ 3245 AGGATGGTAACAGACTTAAGAGCTGTTAATG--CAGTTATTAAACCTATG 3292 chr2qtel1M 320085 GGGACTCTTCAGACTGGACTTCCATCTCTTACC-CAATTGCCTAGAGAAT 320133 i vi v iv i vv v v i iiv -ii - ii HERVK11D#LTR/ 3293 GGGGCGTTACAACCCGGTATGCCCTCCCCCTCCATGATT-CCTAAGGAAT 3341 chr2qtel1M 320134 GGCCTCT--TTGGATTATAGACATTAAGGATTATTTCTATTCTATCCCTT 320181 i -- -- i v v i ii i v iv i HERVK11D#LTR/ 3342 GGCCTTTAATT--ATCATTGACCTTAAGGACTGCTTTTTTCATATTCCTT 3389 chr2qtel1M 320182 TGGATAAG-GAGGATATGAAAAGATTCACCTTTTCAGTGCTCAGCATTAA 320230 i i -v iv i - ii i iv vi i iivv HERVK11D#LTR/ 3390 TAGACAAGTCAGACTGTGAAAA-ATTTGCTTTCACTATACCTTCCATTAA 3438 chr2qtel1M 320231 C---TTAGCTGAGCCTTATAAA-AGATATCAATGGACAGTTTTGCCACAG 320276 --- i ---- iiii iv- v i v i HERVK11D#LTR/ 3439 CAATTCAGCT----CCCGCAGCTAGATATCAATGGAAAGTTTTACCTCAA 3484 chr2qtel1M 320277 GGAATGAAAAACAGCCCTACTATATGTAATGTTATT 320312 vv i v v - i HERVK11D#LTR/ 3485 GGAATGATTAACAGTCCTACTATTTGTCA-GTTGTT 3519 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 33.50 CpG sites = 49, Kimura (unadjusted) = 34.56 Transitions / transversions = 1.40 (49/35) Gap_init rate = 0.07 (23 / 325), avg. gap size = 1.17 (27 / 23) 395 26.79 7.48 4.07 chr2qtel1M 321613 322040 (677960) HERVK14C#LTR/ERVK 4670 5111 (2323) m_b90s701i2 3357 chr2qtel1M 321613 TTGTACAGC-TTGCCTTCCTTTCCATGCTCCTACA-CTGTC---TCTAGG 321657 ? i - i ??v v v - v - i --- v HERVK14C#LTR/ 4670 TTGTNCAACATTGCCCTNNGTGCCAGG-TGCTACAACTGCCACATCAAGG 4718 chr2qtel1M 321658 GA----AG--AACCCTCATGATTTGAGACCTAATGAAATTTGGCAACTGG 321701 ----? -- ? iv iv iv? ?viv ? v HERVK14C#LTR/ 4719 GACTGGNGTTAACCCNCGAGGATTGGCNCCTAATNCGCTNTGGCAAATGG 4768 chr2qtel1M 321702 ATGTGACCCATTATAAATGT-TTTGGTTGTGTGTCTTTTATCCACGTTGT 321750 i ? -i vv ?i- vvivv ? ? vii i ?ii HERVK14C#LTR/ 4769 ACGTNACCCAT-GTACCTNCATTTGGGAAACTNTCNTACGTCCATGTNAC 4817 chr2qtel1M 321751 GGTAGACACCTTTTCAGGATTCACTTT---TGCAATACCAGCAGCAAAAG 321797 v i ----- i --- viv? iv viv v i HERVK14C#LTR/ 4818 TGTAGATACCTTTTC-----TCATTTTGTNTGGGCNACTTGCCAAACAGG 4862 chr2qtel1M 321798 AGAGA-----GCCCGAGT----AGTCACTGAATTCCTTATACAAGCATTT 321838 ? i----- i v ---- v i viv i i i ------- i HERVK14C#LTR/ 4863 NGAGGCNGCTGCTCGTGTTAAAAGACATTTGCTTTCCTGT-------TTC 4905 chr2qtel1M 321839 GCAATTATGGGTGTGCCACAAGCAATAAAAACAGATAATGGACCTGCATA 321888 ?i i ii v iv? v ? i v v vv HERVK14C#LTR/ 4906 GCNGTCATGGGCATTCCACAAAANATTAAAACNGACAATGGCCCAGGCTA 4955 chr2qtel1M 321889 GACTTCCAAACATTTTGCACACTTTTGTGCA-CAGTATAAGATTTTACAC 321937 v?? vvi ?-i i? ?i v iv v - i iv? v vv HERVK14C#LTR/ 4956 CNNTAGTAAAN-CTTTANANGCGTTCCTTCAACAATGGNACATTAAACAC 5004 chr2qtel1M 321938 ACCACCGGCATACCTTTTAATCCTCAAGGACAGGCAATAGTAGAGAAGAG 321987 ?i i ? v i v i ? i v v v - v HERVK14C#LTR/ 5005 ANTACTGGNATCCCCTATAATTCTCAAGGNCAAGCCATTGTTGA-ACGAG 5053 chr2qtel1M 321988 A-AACAGAGACACTAAGACGCTCCAT--CAAAAACAAA----AGAAAGGG 322030 v- iv - vi i ?- v -- ---- i HERVK14C#LTR/ 5054 CTAATCGA-ACCTTAAAAN-CTCAATTACAAAAACAAAAGACAGAAGGGG 5101 chr2qtel1M 322031 GGAGCCACAG 322040 i v HERVK14C#LTR/ 5102 GGAACCAGAG 5111 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.62 CpG sites = 53, Kimura (unadjusted) = 36.68 Transitions / transversions = 0.93 (53/57) Gap_init rate = 0.07 (31 / 427), avg. gap size = 1.61 (50 / 31) 350 31.74 7.25 2.90 chr2qtel1M 322913 323243 (676757) HERVK#LTR/ERVK 4856 5200 (2336) m_b90s701i3 3358 chr2qtel1M 322913 TATGGTAGATAGATGTTACACAT--------ATGGGGAAAA----CATGC 322950 i i i i i -------- vv i ---- ?i HERVK#LTR/ERV 4856 TATGGCAAATGGATGTCACGCATGTACCTTCATTTGGAAGATTGTCATNT 4905 chr2qtel1M 322951 GTTCATGTTACAGTTGACACACATTTGGGCTTTGTAGCTGCATCCTTTCA 323000 i v i vi iivii ii vvv v vi HERVK#LTR/ERV 4906 GTCCATGTAACAGTTGATACTTATTCACATTTCATATGGGCAACCTGCCA 4955 chr2qtel1M 323001 ATGAAGGGAAGCTGC--CTCATGTGATCAATCACTCATTTCACTGTTTTG 323048 ivv i i iv i -- i v vv v i i vivi HERVK#LTR/ERV 4956 GACAGGAGAAAGTACTTCCCATGTTAAAAAACATTTATTATCTTGTTTTG 5005 chr2qtel1M 323049 CCTCTACGGGTATCACACACACCATCAAGACTGACAATGGACCCTCATAC 323098 ivii i vi iv v v vv i i i vvv HERVK#LTR/ERV 5006 CTGTCATGGGAGTTCCAGAAAAAATTAAAACTGACAATGGGCCAGGATAC 5055 chr2qtel1M 323099 ATCTCA-AAAATATTAAAACAATTCTTA---CAG--GAATTCTCCATATG 323142 - v vi- ii? vv v --- -- vvi v i i HERVK#LTR/ERV 5056 -TGTAGTAAAGCNTTCCAAAAATTCTTAAATCAGTGGAAAATTACACATA 5104 chr2qtel1M 323143 TCATATTTTTGGAATTCCTTACAACCCCACAGGACAGGCCACTGTAGAAA 323192 iv i ----- i ii vv iv v HERVK#LTR/ERV 5105 CAACA-----GGAATTCCTTATAATTCCCAAGGACAGGCCATAGTTGAAA 5149 chr2qtel1M 323193 GGACTAATCAGACCCTGAAGAG----ATTCATCAAAAATCAGAAAGAGGG 323238 i vii v v - ---- vi i --- i i HERVK#LTR/ERV 5150 GAACTAATAGAACACTCAA-AGCTCAATTGGTTAAA---CAAAAAGAAGG 5195 chr2qtel1M 323239 AGGAG 323243 i HERVK#LTR/ERV 5196 GGGAG 5200 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 42.14 CpG sites = 56, Kimura (unadjusted) = 42.70 Transitions / transversions = 1.22 (56/46) Gap_init rate = 0.05 (17 / 330), avg. gap size = 2.00 (34 / 17) 1007 29.81 4.01 3.44 chr2qtel1M 323405 323953 (676047) L1ME5_3end#LINE/L1 77 628 (313) m_b90s551i7 3359 chr2qtel1M 323405 AAGATATGAACAGACAATTTTCAGATGATGAAATT-GAAAGTATTTCCAC 323453 i i v v v ii- -ii vv v L1ME5_3end#LI 77 AGGATATGAACAGGCAATTTACAGAAGAGGAAACCCGAAAG-GCTAACAA 125 chr2qtel1M 323454 TGGTATGAAAGAGTGTTCCAAATCACTGTTGATCAGAAAAATGCAAA--- 323500 vvi iiii i v v i iv i i --- L1ME5_3end#LI 126 GCATATGAAGAGATGCTCAAACTCATTAGTAATCAGAGAAATGCAAATTA 175 chr2qtel1M 323501 -GACAACTCTGAGATACCACTACACACCTGTCAAATTGGCTAAGATGACA 323549 -i vv i vi i i i i v i v -- L1ME5_3end#LI 176 AAACAACAATGAGATATCACTTTACACCTATTAGACTGGCAAAAATTA-- 223 chr2qtel1M 323550 GGAAAAAGTT--ATGATG---AATGTTGGAGGGGATGTGGGAAAACTGGG 323594 ---i i -- i --- i v i i ? iv i L1ME5_3end#LI 224 ---GAAAGCTGGATAATGCCAAGTGTTGGCGAGGATGTGGGGANATAGGA 270 chr2qtel1M 323595 ACACTGATGCATTGTTGATGGAGTTGTGAATGAATCCAACCATTCTGGAG 323644 v v i i i iiv ii ivii v i L1ME5_3end#LI 271 ACCCTCATGCACTGCTGGTGGGAGTGTAGACTGGTGCAGCCATTCTGGAG 320 chr2qtel1M 323645 AGCAATCTGGAATTA--TGCCCAAA--AAGTTATCAAACTGTGCAAACCC 323690 v v -- ivi -- - --- --- v L1ME5_3end#LI 321 AGCAATCTGGCAGTACTTAGTCAAATTAAG-TAT---AC---GCATACCC 363 chr2qtel1M 323691 TTTGATCCAGCACTGTTACTACTGGGCTTAAACCCCAAAGAGATACTAAA 323740 v i v viii v iv v i i v v v L1ME5_3end#LI 364 TATGACCCAGCAATTCCGCTCCTGGGTATATATCCCAAAGAAATTCTCAC 413 chr2qtel1M 323741 GAAGG----GAAAGGGCCCTGTATGTGCCAAAATGTTTGTGGCAGCCCTG 323786 iv ----v i v v i ---- ii ii v vi L1ME5_3end#LI 414 ACAGGTCCATAAGGGGACATGTACG----AGGATGTTCATTGCAGCGTTG 459 chr2qtel1M 323787 TTTGTAGTGGCTAGAAACTGGAAAATGAATGGATGCCCATCAATTGGAGA 323836 i vi i ii iivvivv i i v v L1ME5_3end#LI 460 TTTGTGGTGGCGGGGAGTTGGAGGCAACCTGGGTGTCCATCACTGGGAGA 509 chr2qtel1M 323837 ATGGTTGGGTAAATTGTGGTATATG--AATTATGGAATATTATTGTTCTG 323884 i v i v iv --v ii i i vvvv v L1ME5_3end#LI 510 GTGGATAGGTAAAATGTGGTGGATGCACACCATGGAGTACTATGCAGCAG 559 chr2qtel1M 323885 TAAGAAATGACCAGCAGGATGAATACAGAGAGGCTTGGAGAGA-CTTACA 323933 v iii vii vi v i v vii v vi - v L1ME5_3end#LI 560 TTAGAAGCAACGGACTAGATGTACACATAGCAACATGGATGGATCTTAAA 609 chr2qtel1M 323934 TGAAC-TGATGCTAAATGAAA 323953 -- - ii i i L1ME5_3end#LI 610 --AACATAGTGCTGAGTGAAA 628 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.44 CpG sites = 91, Kimura (unadjusted) = 39.11 Transitions / transversions = 1.36 (91/67) Gap_init rate = 0.05 (30 / 548), avg. gap size = 1.37 (41 / 30) 1067 28.66 3.17 1.88 chr2qtel1M 323405 323877 (676123) L1ME4c_3end#LINE/L1 77 555 (275) m_b90s551i6 3359 chr2qtel1M 323405 AAGATATGAACAGACAATTTTCAGATGATGAAATTGAA--AGTATTTCCA 323452 i i iv ? v v vv -- vvivv L1ME4c_3end#L 77 AGGACATGAACAGACAATTCACANAAGAGGAAATACAANTAGTAAACAAA 126 chr2qtel1M 323453 CTGGTATGAAAGAGTGTTCCAAATCACTGTTGATCAGAAAAATGCAAA-- 323500 --ii i i i v vv i iv i i i -- L1ME4c_3end#L 127 C--ACATGGAAAAATGTTCAACCTCGCTAGTAATCAAAGAAATGCAAATT 174 chr2qtel1M 323501 --GACAACTCTGAGATACCACTACACACCTGTCAAATTGGCTAAGATGAC 323548 --ii vv i vi i i i i v i --- L1ME4c_3end#L 175 AAAGCAACAATGAGATACCATTTTACGCCTATTAAATTAGCAAAAAT--- 221 chr2qtel1M 323549 AGGAAAAAGTT-ATGATG---AATGTTGGAGGGGATGTGGGAAAACTGGG 323594 -vv i - i i--- i v i ? i vi v L1ME4c_3end#L 222 -TTAAAAAATTGATAATACCCAATGCTGGCGAGGNTGCGGTGAAACTGGT 270 chr2qtel1M 323595 ACACTGATGCATTGTTGATGGAGTTGTGAATGAATCCAACCATTCTGGAG 323644 ? v i i i vi? i vii v v i i L1ME4c_3end#L 271 ACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAA 320 chr2qtel1M 323645 AGCAATCTGGAATTATGCCCAAAAAGTTATCAAACTGTGCAAACCCTTTG 323694 i v v i iviv i ii v v v v L1ME4c_3end#L 321 AGCAATTTGGCAATACGTATCAAGAGCCATAAAAATGTTCATACCCTTTG 370 chr2qtel1M 323695 ATCCAGCACTGTTACTACTGGGCTTAAACCCCAAAGAGATA---CTAAAG 323741 i i v vii v vv vv i i i i --- v L1ME4c_3end#L 371 ACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAAG 420 chr2qtel1M 323742 AAGGGAAAGGGCCCTGTATGTGCCAAAATGTTTGTGGCAGCCCTGTTTGT 323791 i i --- i ii v i ii v vi i i L1ME4c_3end#L 421 AAGGAAAAAG---CTATATGCACGAAGATGTTCATTGCAGCGTTATTTAT 467 chr2qtel1M 323792 AGTGGCTAGAAACTGGAAAATGAATGGATGCCCATCAATTGGAGAATGGT 323841 i i v i i vvivv ii i v v i L1ME4c_3end#L 468 AATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAATGGT 517 chr2qtel1M 323842 TGGGTAAATTGTGGTATATGAATT--ATGGAATATTAT 323877 ii i i v? i -- L1ME4c_3end#L 518 TAAGTAAATTATGGTACATCNACTCGATGGAATATTAT 555 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.25 CpG sites = 79, Kimura (unadjusted) = 37.69 Transitions / transversions = 1.46 (79/54) Gap_init rate = 0.03 (16 / 472), avg. gap size = 1.50 (24 / 16) 291 33.49 1.50 3.83 chr2qtel1M 327298 327564 (672436) L1MC_orf2#LINE/L1 2447 2707 (587) m_b90s551i8 3360 chr2qtel1M 327298 CAATACTACCTAAATTAATCTACTTATTCAGTGCCATACCAATCAAACTC 327347 i v v i v i ivv i v v v L1MC_orf2#LIN 2447 CAGTTCTTCCCAACTTGATCTATAGATTCAATGCAATCCCAATCAAAATC 2496 chr2qtel1M 327348 CCAAGAAGTTATTTAACAGATCTAGAAAAA--AATAACAAAATTCATCTG 327395 iv viii v v v --i vvi i i v L1MC_orf2#LIN 2497 CCAGCAAGTTATTTTGTGGATATCGACAAACTGATTCTAAAGTTTATATG 2546 chr2qtel1M 327396 GCAGAACATAAGATCAAGAAT-TTCAAGGGAATTAATGAAAAAAAAAAAA 327444 viiii v i v -vi viv - v ii i i v L1MC_orf2#LIN 2547 GAGAGGCAAAAGACCCAGAATAGCCAACACAA-TATTGAAGGAGAAGAAC 2595 chr2qtel1M 327445 AATGCCAGCGAAGGGGGTCTAGCAGTGGCAGA-TCTAAAACTATATTATA 327493 v i ------ i v ii v iv v - ii i - i L1MC_orf2#LIN 2596 AAAGTC------GGAGGACTGACACTACCCGACTTCAAGACT-TACTATA 2638 chr2qtel1M 327494 AAGCAGCAGTTCATCAAAGCTGTTTGTTACTGGCAAAGAAATGAGGTAGC 327543 vi - v ii v v v i i ii - ii iv L1MC_orf2#LIN 2639 AAGCTACAG-TAATCAAGACAGTGTGGTATTGGCGAAAGAAT-AGACAAA 2686 chr2qtel1M 327544 CGGATCTGTGAAATAGGTTAG 327564 ii vi i i iv L1MC_orf2#LIN 2687 TAGATCAATGGAACAGAATAG 2707 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 45.01 CpG sites = 49, Kimura (unadjusted) = 45.74 Transitions / transversions = 1.32 (49/37) Gap_init rate = 0.05 (13 / 266), avg. gap size = 1.08 (14 / 13) 268 33.36 3.18 4.61 chr2qtel1M 327300 327739 (672261) L1PREC2_orf2#LINE/L1 2449 2882 (412) m_b90s551i10 3360 chr2qtel1M 327300 ATACTACCTAAATTAATCTACTTATTCAGTGCCATACCAATCAAACTCCC 327349 i i vi i vv i i v v v L1PREC2_orf2# 2449 ATACTGCCCAAAGCAATTTACAGATTCAATGCTATTCCTATCAAACTACC 2498 chr2qtel1M 327350 AA-GAAGTTATTTAACAGATCTAGAAAAAAATA--ACAAAATTCATCTGG 327396 - vi v i - v v --vi v L1PREC2_orf2# 2499 AATGACATTCTTCA-CAGAACTAGAAAAAACTATTTTAAAATTCATATGG 2547 chr2qtel1M 327397 CAGAACATAAGATCAAGAAT-TTCAAGGGAAT--TAATGAAAAAAAAAAA 327443 v vv v v v vv -vi v -- vv i v L1PREC2_orf2# 2548 AACCAAAAAAGAGCCCGAATAGCCAAGGCAATCCTAAGCAAAAAGAACAA 2597 chr2qtel1M 327444 AAATGCCAGCGAAGGGGGTCTAGCAGTGGCAGATCTAAAACTATATTATA 327493 iv --------- i iv vi iv iv v ii v i i L1PREC2_orf2# 2598 AGCT---------GGAGGCATCACGCTACCCGACTTCAAACTATACTACA 2638 chr2qtel1M 327494 AAGCAGCAGTTCATCAAAGCTGTTTGTTACTGGCAAAGAAATGAGGTAGC 327543 ii vi - v i i v iv v i v i i- ii vv L1PREC2_orf2# 2639 GGGCTACAG-TAACCAAAACAGCATGGTACTGGTACAAAAAC-AGACACA 2686 chr2qtel1M 327544 CGGATCTGTGAAATAGGTTAGTCTCATGGGGC---AAAATA--GTCA-AT 327587 ii i vi i i iv ------i i ---i -- i i- i L1PREC2_orf2# 2687 TAGACCAATGGAACAGAATAG------AGAGCCCAGAAATAAGGCCGCAC 2730 chr2qtel1M 327588 TACTATAATAATCTAGTGTTTGACAAAGCCC-TAAACCCCAGCTTTTAGG 327636 vv i iv ii v i iv-i vv v vv vi L1PREC2_orf2# 2731 ACCTACAACCATCTGATCTTCGACAAAGCTGACAAAAACAAGCAATGGGG 2780 chr2qtel1M 327637 ATAAAAACTCACCATTTGAGAAAAACTGCTGGGAAAATTGGAAAGTAGCA 327686 - ii v i ii v viv v i vv ivii L1PREC2_orf2# 2781 A-AAGGACTCCCTATTCAATAAATGGTGCTGGGATAACTGGCTAGCCATA 2829 chr2qtel1M 327687 TGGCAGAAACTAGGTACT-GACCCACAGCTAACACCCCATACCAACATAA 327735 - iv v iv - vivv v vi v v v L1PREC2_orf2# 2830 T-GCAGAAGATTGAAACTGGACCCCTTCCTTACACCATATACAAAAATCA 2878 chr2qtel1M 327736 AGTC 327739 v L1PREC2_orf2# 2879 ACTC 2882 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 43.37 CpG sites = 67, Kimura (unadjusted) = 44.63 Transitions / transversions = 0.92 (67/73) Gap_init rate = 0.07 (29 / 439), avg. gap size = 1.17 (34 / 29) 374 27.45 1.70 3.91 chr2qtel1M 327300 327534 (672466) L1M3_orf2#LINE/L1 2443 2672 (616) m_b90s551i9 3360 chr2qtel1M 327300 ATACTACCTAAATTAATCTACTTATTCAGTGCCATACCAATCAAACTCCC 327349 i vii vv i v v v v L1M3_orf2#LIN 2443 ATACTACCCAAAGCGATCTACAGATTCAATGCAATCCCTATCAAAATCCC 2492 chr2qtel1M 327350 AA-GAAGTTATTTAACAGATCTAGAAAAA--AATAACAAAATTCATCTGG 327396 - ivi v - vv -- vvi v L1M3_orf2#LIN 2493 AATGGCATTTTTTA-CAGAAATAGAAAAAACAATCCTAAAATTCATATGG 2541 chr2qtel1M 327397 CAGAACATAAGATCAAGAAT-TTCAAGGGAATTAATGAAAAAAAAAAAAA 327445 v vv v i vv -vi i v i-v i i i v L1M3_orf2#LIN 2542 AACCACAAAAGACCCCGAATAGCCAAAGCAATC-TTGAGAAAGAAGAACA 2590 chr2qtel1M 327446 ATGCCAGCGAAGGGGGTCTAGCAGTGGCAGATCTAAAACTATATTATAAA 327495 v i------ i iv vi v vv v i v v i L1M3_orf2#LIN 2591 AAGCT------GGAGGCATCACACTTCCTGATTTCAAAATATATTACAAA 2634 chr2qtel1M 327496 GCAGCAGTTCATCAAAGCTGTTTGTTACTGGCAAAGAAA 327534 vi - v i v v v v i L1M3_orf2#LIN 2635 GCTACAG-TAATCAAAACAGTATGGTACTGGCATAAAAA 2672 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 33.47 CpG sites = 23, Kimura (unadjusted) = 34.17 Transitions / transversions = 0.59 (23/39) Gap_init rate = 0.05 (12 / 234), avg. gap size = 1.08 (13 / 12) 334 28.54 0.81 5.98 chr2qtel1M 327790 327912 (672088) MIRc#SINE/MIR 11 127 (141) m_b90s601i9 3361 chr2qtel1M 327790 TGGTGTAGTAGATAGAGCACCGGCCCTGCAGTCACTAGGAGCCAAGTTCA 327839 i i v i v i v vv i v iii i MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr2qtel1M 327840 AATTTGGCCTCAAACACTTCACACTTCCTGGGTAGGTGACCCTTGGCAAG 327889 i iiv v ------ v - v i v iv i v MIRc#SINE/MIR 61 AGTCCCGGCT------CTGC-CACTTACTAGCTGTGTGACCTTGGGCAAG 103 chr2qtel1M 327890 TCACTTAGCCCCAATT-GCCTCAG 327912 i i vv v- MIRc#SINE/MIR 104 TCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.92 CpG sites = 17, Kimura (unadjusted) = 36.27 Transitions / transversions = 1.06 (17/16) Gap_init rate = 0.07 (8 / 122), avg. gap size = 1.00 (8 / 8) 16 0.00 0.00 0.00 chr2qtel1M 330036 330053 (669947) (T)n#Simple_repeat 1 18 (0) m_b90s252i9 3362 chr2qtel1M 330036 TTTTTTTTTTTTTTTTTT 330053 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTT 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 340 28.85 0.76 4.76 chr2qtel1M 330546 330676 (669324) C MIRc#SINE/MIR (141) 127 2 m_b90s601i10 3363 chr2qtel1M 330546 CTGAGG-TAATTGGGGTTAATTGACTTGTTTGGGGTCACAGGGCTAGGAA 330594 - v vv i v iiiii vi v C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAA 78 chr2qtel1M 330595 GTGTTGTCTGAGTGCAGATTTGAACTCAGGGCCTCCTCTCTTCAGGGCTA 330644 -- - v ivvi i i i v i vv i i v i C MIRc#SINE/MIR 77 GTG--G-CAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCA 31 chr2qtel1M 330645 GTGCTCTGGTCACTGTGCCACCTAGCTGCCCC 330676 vvi ii ---i i C MIRc#SINE/MIR 30 GTGCTCTTTCCACTGCACCAC---ACTGCCTC 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.99 CpG sites = 21, Kimura (unadjusted) = 37.30 Transitions / transversions = 1.40 (21/15) Gap_init rate = 0.05 (7 / 130), avg. gap size = 1.00 (7 / 7) 12 14.12 3.03 3.03 chr2qtel1M 330743 330775 (669225) (TTTAA)n#Simple_repeat 1 33 (0) m_b90s252i10 3364 chr2qtel1M 330743 TTTAATTTAAGTTTTATTT-CTTCAATTAAATTT 330775 - v -v i v (TTTAA)n#Simp 1 TTTAATTTAA-TTTAATTTAATTTAATTTAATTT 33 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.06 (2 / 32), avg. gap size = 1.00 (2 / 2) 449 23.92 0.74 7.09 chr2qtel1M 331216 331350 (668650) MIRc#SINE/MIR 1 127 (141) m_b90s601i11 3365 chr2qtel1M 331216 CAGGACAGTTAGATGGCACAGTGGATAGAGCACCAGCCCTGAAGTCAGGC 331265 ii i ---i ii v ii v i i v MIRc#SINE/MIR 1 CGAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGA 47 chr2qtel1M 331266 AGACTGAGGGAAAATCTGTCCTCAGACTCTGAATACTTCCTAGCTGTGTG 331315 ivi vvvi --- i-- i v-i v MIRc#SINE/MIR 48 AGACCTGGGTTCGA---GTCCC--GGCTCTGC-CACTTACTAGCTGTGTG 91 chr2qtel1M 331316 ACCCTGGGCAAGTCACTTAACCCCAATT-GCCTCAG 331350 i i vv v- MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.91 CpG sites = 18, Kimura (unadjusted) = 29.26 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.07 (10 / 134), avg. gap size = 1.00 (10 / 10) 245 10.95 0.00 8.70 chr2qtel1M 331401 331450 (668550) C L2a_3end#LINE/L2 (88) 429 384 m_b90s601i12 3366 chr2qtel1M 331401 ACAAAAGTCAGGCCGTGCCCCCAAGGAGCTTACATTCTTTTGGGGGAAGA 331450 --- - i v vv i C L2a_3end#LINE 429 ACAAAAGTC---CC-TGCCCTCATGGAGCTTACATTCTAGTGGGGGGAGA 384 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 11.75 CpG sites = 2, Kimura (unadjusted) = 11.75 Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.08 (4 / 49), avg. gap size = 1.00 (4 / 4) 199 22.22 1.85 0.00 chr2qtel1M 331413 331466 (668534) C L2d_3end#LINE/L2 (97) 419 365 m_b90s601i13 3366 chr2qtel1M 331413 CCGTGCCCCCAAGGAGCTTACATTCT-TTTGGGGGAAGATGACTTTCACC 331461 v i v -v ii v v vv v C L2d_3end#LINE 419 CCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGGAGACAAGACTAACACA 370 chr2qtel1M 331462 CTTGA 331466 v C L2d_3end#LINE 369 CATGA 365 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.41 CpG sites = 3, Kimura (unadjusted) = 26.41 Transitions / transversions = 0.33 (3/9) Gap_init rate = 0.02 (1 / 53), avg. gap size = 1.00 (1 / 1) 11 14.79 4.88 4.88 chr2qtel1M 333317 333357 (666643) (TGGGAT)n#Simple_repeat 1 41 (0) m_b90s252i11 3367 chr2qtel1M 333317 TGGTGATTGGGA-TGTGA-TGAAAATGGTGATTGGGATTTGGA 333357 - - v - ii v - v (TGGGAT)n#Sim 1 TGG-GATTGGGATTGGGATTGGGATTGG-GATTGGGATTGGGA 41 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.10 (4 / 40), avg. gap size = 1.00 (4 / 4) 18 25.24 0.00 0.00 chr2qtel1M 333621 333662 (666338) (TC)n#Simple_repeat 1 42 (0) m_b90s252i12 3368 chr2qtel1M 333621 TCTTTCTTACTGTGTTTCTCTGTCTCTGTCTCTGTCTCTCTC 333662 i iv v v i v v v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 42 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 18 4.50 0.00 0.00 chr2qtel1M 333662 333684 (666316) (CA)n#Simple_repeat 1 23 (0) m_b91s252i2 3369 chr2qtel1M 333662 CACAGACACACACACACACACAC 333684 v (CA)n#Simple_ 1 CACACACACACACACACACACAC 23 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 193 30.56 4.17 0.00 chr2qtel1M 334046 334117 (665883) MIR#SINE/MIR 186 260 (2) m_b91s601i1 3365 chr2qtel1M 334046 AAATGAGAAAATATTTGCAAAGTACTTAGAA---TACTTGCCATATAGTT 334092 vv iv i ii --- i i v i v MIR#SINE/MIR 186 AAATGAGTTAATACATGTAAAGCGCTTAGAACAGTGCCTGGCACATAGTA 235 chr2qtel1M 334093 AATGCTACATAAAATCCAATTATTA 334117 ii vv vvii ii MIR#SINE/MIR 236 AGCGCTCAATAAATGTTAGCTATTA 260 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.59 CpG sites = 13, Kimura (unadjusted) = 40.48 Transitions / transversions = 1.44 (13/9) Gap_init rate = 0.01 (1 / 71), avg. gap size = 3.00 (3 / 1) 198 28.33 5.00 0.00 chr2qtel1M 334046 334105 (665895) MIRb#SINE/MIR 190 252 (16) m_b91s601i0 3365 chr2qtel1M 334046 AAATGAGAAAATATTTGCAAAGTACTTAG---AATACTTGCCATATAGTT 334092 v iiv i ii --- i i i v i v MIRb#SINE/MIR 190 AAATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTA 239 chr2qtel1M 334093 AATGCTACATAAA 334105 ii vv MIRb#SINE/MIR 240 AGCGCTCAATAAA 252 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.40 CpG sites = 11, Kimura (unadjusted) = 37.01 Transitions / transversions = 1.83 (11/6) Gap_init rate = 0.02 (1 / 59), avg. gap size = 3.00 (3 / 1) 17 2.94 11.43 0.00 chr2qtel1M 334689 334723 (665277) (ACATAT)n#Simple_repeat 1 39 (0) m_b91s252i3 3370 chr2qtel1M 334689 ACATATA-A-AT-CATACACATATACATATACATA-ACA 334723 - - - i - (ACATAT)n#Sim 1 ACATATACATATACATATACATATACATATACATATACA 39 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.12 (4 / 34), avg. gap size = 1.00 (4 / 4) 207 12.12 3.03 0.00 chr2qtel1M 336234 336266 (663734) L3#LINE/CR1 536 569 (3530) m_b91s601i2 3371 chr2qtel1M 336234 GGATTCGCAGGCACTA-CAAATGAGAGGAATCTT 336266 - ii v i L3#LINE/CR1 536 GGATTCGCAGGCACTAGCAGGTGCGAGGAATCCT 569 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 13.48 CpG sites = 3, Kimura (unadjusted) = 13.48 Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 15 17.81 2.63 0.00 chr2qtel1M 336520 336557 (663443) (TTTTG)n#Simple_repeat 1 39 (0) m_b91s252i4 3372 chr2qtel1M 336520 TTTTGTTTTGTTTTATTTTCCTTTG-CTTGTATTCTTTT 336557 i vi -i v v (TTTTG)n#Simp 1 TTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTT 39 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 293 22.06 0.00 1.47 chr2qtel1M 337631 337699 (662301) C MIR3#SINE/MIR (63) 145 78 m_b91s601i3 3373 chr2qtel1M 337631 CTTATTTTCCAGATGAGGACACTGGGGAACAAAAGGGCTGGCGTGGCTTG 337680 i v v i vv i ii - iv i C MIR3#SINE/MIR 145 CTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGG-TGAAGTGACTTG 97 chr2qtel1M 337681 CTCAGGGTCACACAGCTGG 337699 i i ?i C MIR3#SINE/MIR 96 CCCAAGGTCACACAGCNAG 78 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 27.39 CpG sites = 10, Kimura (unadjusted) = 27.39 Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.01 (1 / 68), avg. gap size = 1.00 (1 / 1) 552 23.30 4.48 0.72 chr2qtel1M 337883 338016 (661984) C MIRc#SINE/MIR (120) 148 10 m_b91s601i4 3374 chr2qtel1M 337883 CTCATTTTACAAATGAGGAAACTGAGGC--AGGCAGGGTGAAGTGACTTG 337930 i i -- iv v - C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTT-AAGTGACTTG 100 chr2qtel1M 337931 CCCAGGATCACACAGCT----AGTGTCTGAGATAAGATTCAAAGTCAGAT 337976 i i ---- v v viii i i vi i C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGT 50 chr2qtel1M 337977 CCTCTTTAATTCAAGGCCAGCCCTCCATCCACAGGGCCAC 338016 i i v v i v iv iv v vi C MIRc#SINE/MIR 49 CTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.20 CpG sites = 18, Kimura (unadjusted) = 28.41 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.02 (3 / 133), avg. gap size = 2.33 (7 / 3) 12 28.34 1.89 1.89 chr2qtel1M 338804 338856 (661144) (AGGAGA)n#Simple_repeat 1 53 (0) m_b91s252i5 3375 chr2qtel1M 338804 AGGAGATGGAGATGAAGAAGAAG-GGAACGAGGGGTAGGAAGACTGAGAA 338852 v v i i -i i vi i v - vv (AGGAGA)n#Sim 1 AGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGG-AGAAGGAGAA 49 chr2qtel1M 338853 GGAG 338856 (AGGAGA)n#Sim 50 GGAG 53 Matrix = Unknown Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.00 (2 / 2) 458 28.43 9.18 4.87 chr2qtel1M 339699 340112 (659888) C L1ME3G_3end#LINE/L1 (376) 548 118 m_b91s551i0 3376 chr2qtel1M 339699 ATAATATTCCATAACA--AATATAT-ATAGC------AGCTATTACCCAA 339739 i ii --i i- ii------ i i v v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr2qtel1M 339740 CTGATGAGCATCCCCCCAGTTTCCATTTCTTTGTCACCACTAAAAAAAAT 339789 i ii iivvviv v i i --- i i v v C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCG---CTATTACAAACAAT 452 chr2qtel1M 339790 TGCTACAAT----ATTTTTGTACATATAGGCCATTTTCCTTTT-----TG 339830 - i ---- ii ---- ?---- v ----- C L1ME3G_3end#L 451 -GCTGCAATGAACATCCTTGTACAT----GCN----TCCTTGTGCACATG 411 chr2qtel1M 339831 TTTT-TTATCTCTTTGGGATACAGATTTACTAGTGGTATTGCTGGGGCAA 339879 viv-v i ? i v v?ii? vv v v C L1ME3G_3end#L 410 TGCGAGTATTTCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAA 361 chr2qtel1M 339880 AGGGTGTACATGATTTTACAAGCCCTGTGGGCCTAGTTCCAAA-TGCTTT 339928 i i ii- - viiivi i i-- v v - ii C L1ME3G_3end#L 360 AGGGTATGCGC-ATTTTA-AATTTTAATAGA--TACTGCCAAATTGCCCT 315 chr2qtel1M 339929 ACAGAATTGTTGAATCAGTTATACAATCTTGCCAAGAGTGTATTACTTTT 339978 v i ?v i v i i - v iii iv v vvv v C L1ME3G_3end#L 314 CCAAAANGGCTGTACCAATT-TACACTCCCACCAGCAGTGTATGAGAGTA 266 chr2qtel1M 339979 TCAGTTTTCCCACA-TCTCTCCAATATTTGTCATT-TTTATTTTCT---T 340023 i v i -i v i i ? vi - iv ?i i --- C L1ME3G_3end#L 265 CCCGTTTCCCCACACCCTCGCCAACACTNGATATTATCAANCTTTTAAAT 216 chr2qtel1M 340024 TTCTGATAATCAATCTAATTA--GAAAGGTAGTACCTCAGAATTGTTTTA 340071 i ----i i vi-- ii i i vvi C L1ME3G_3end#L 215 TTTTG----CCAATCTGATGGGTGAAAAATGGTATCTCATTGTTGTTTTA 170 chr2qtel1M 340072 ATTAGCATTTTCC-AATTGATAGTGA----------TTTTTCATATGTGT 340110 v i -i iv ----------i v C L1ME3G_3end#L 169 ATTTGCATTTCCCTGATTACTAGTGAGGTTGAGCATCTTTTCATATGTTT 120 chr2qtel1M 340111 AT 340112 C L1ME3G_3end#L 119 AT 118 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.64 CpG sites = 69, Kimura (unadjusted) = 37.94 Transitions / transversions = 1.60 (69/43) Gap_init rate = 0.08 (34 / 413), avg. gap size = 1.74 (59 / 34) 336 29.79 8.53 5.98 chr2qtel1M 339729 340185 (659815) C L1ME3Cz_3end#LINE/L1 (488) 509 42 m_b91s551i1 3376 chr2qtel1M 339729 CTATTACCCAACTGATGAGCATCCCCCCAGTTTCCATTTCTTTGTCACCA 339778 i v v i ii iivvviv v i i --- i C L1ME3Cz_3end# 509 CCATTCCCCTATTGATGGACATTTAGGTTGTTTCCAATTTTTCG---CTA 463 chr2qtel1M 339779 CTAAAAAAAATTGCTACAAT----ATTTTTGTACATATAGGCCATTTTCC 339824 i v v - i ---- ii i --------i C L1ME3Cz_3end# 462 TTACAAACAAT-GCTGCAATGAACATCCTTGTACATGT--------CTCC 422 chr2qtel1M 339825 TTTT-----TGTTTTTTA-TCTCTTTGGGATACAGATTTACTAGTGGTAT 339868 v ----- vivvv - i i i i i v ii vv v C L1ME3Cz_3end# 421 TTGTGCACATGTGCGAGAGTTTCTCTAGGGTATATACCTAGAAGTGGAAT 372 chr2qtel1M 339869 TGCTGGGGCAAAGGGTGTACATGATTTTACAAGCCCTGTGGGCCTAG--- 339915 v iv i i ii- i - --- v i--- --- C L1ME3Cz_3end# 371 TGCTGGGTCGTAGGGTATGCGC-ATCTT-CAA---CTTTA---CTAGATA 330 chr2qtel1M 339916 -TTCCAAA-TGCTTTACAGAATTGTTGAATCAGTTATACAATCTTGCCAA 339963 - v - i v i i v v i i - v iii i C L1ME3Cz_3end# 329 TTGCCAAATTGCTCTCCAAAGTGGTTGTACCAATT-TACACTCCCACCAG 281 chr2qtel1M 339964 GAGTGTATTACTTTTTCAGTTTTCCCACAT-CTCTCCAATATTTGTCATT 340012 v v vvv i v ii - v i i vi C L1ME3Cz_3end# 280 CAGTGTATGAGAGTTCCCGTTTCTCCACATCCTCGCCAACACTTGGTATT 231 chr2qtel1M 340013 TTTA---TTTT-CTTTTCTGATAATCAATCTAATTA----GAAAGGTAGT 340054 v i --- -vv i ----i i vi---- -- i C L1ME3Cz_3end# 230 GTCAGACTTTTAAATTTTTG----CCAATCTGATGGGTGTGAAA--TGGT 187 chr2qtel1M 340055 ACCTCAGAATTGTTTTAATTAGCATTTTCC-AATTGATAGTGA------- 340096 i vvi ? v i -i iv ------- C L1ME3Cz_3end# 186 ATCTCATTGTNGTTTTAATTTGCATTTCCCTGATTACTAGTGAGGTTGAG 137 chr2qtel1M 340097 ---TTTTTCATATGTGTATAGATAACTTCAGATTATTTCATGTGAAAACT 340143 ---i v v iiv - i i vii v v vi i C L1ME3Cz_3end# 136 CATCTTTTCATATGTTTATTGGCCA-TTCGGGTTTCCTCTTCTGTGAATT 88 chr2qtel1M 340144 GACTCTTCCTAATTTTT--TTATTTTTTTTTT--TTTATCATTTTC 340185 v v v vii --ii i v --v i v C L1ME3Cz_3end# 87 GCCTGTTCATATCCTTTGCCCATTTTTCTATTGGGTTGTCTTTTTC 42 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.14 CpG sites = 72, Kimura (unadjusted) = 39.07 Transitions / transversions = 1.29 (72/56) Gap_init rate = 0.09 (43 / 456), avg. gap size = 1.56 (67 / 43) 478 28.30 7.38 8.26 chr2qtel1M 339735 340100 (659900) C L1ME5_3end#LINE/L1 (435) 506 144 m_b91s551i2 3376 chr2qtel1M 339735 CCCAACTGATGAGCATCCCCCCAGTT---TCCATTTCTTTGTCACCACTA 339781 i- ii --- vi --- vi iii i - C L1ME5_3end#LI 506 CCCAG-TGATGGACA---CCCAGGTTGCCTCCAACTCCCCGCCACCAC-A 462 chr2qtel1M 339782 AAAAAAATTGCTAC-AATATTTTTGTACATATAGGCCATTTTCCTTTTTG 339830 v vii v i- i ii i i --- ----- v v C L1ME5_3end#LI 461 AACAACGCTGCAATGAACATCCTCGTACATGT---CC-----CCTTATGG 420 chr2qtel1M 339831 TTTTTT------ATCTCTTTGGGATACAGATTTACTAGTGGTATTGCTGG 339874 vii v ------ i i v iii vv i v C L1ME5_3end#LI 419 ACCTGTGTGAGAATTTCTTTGGGATATATACCCAGGAGCGGAATTGCTGG 370 chr2qtel1M 339875 GGCAAAGGGTGTACA------TGATTTTAC-AAGCCCTGTGGGCCTAGTT 339917 v v i i i------ i v - iv ----------- C L1ME5_3end#LI 369 GTCATAGGGTATGCGTATACTTAATTTGACTAAGTACTG----------- 331 chr2qtel1M 339918 CCAAA-TGCTTTACAGAATTGTTGAATCAGTTATACAATCTTGCCAAGAG 339966 i - i v v i v i i- v iii iv C L1ME5_3end#LI 330 CCAGATTGCTCTCCAGAATGGCTGCACCAGTC-TACACTCCCACCAGCAG 282 chr2qtel1M 339967 TGTATTACTTTTTCAGTTTTCCCACAT-CTCTCCAATATTTGTCATT-TT 340014 i v vvv i vi ? i - v i i v - i C L1ME5_3end#LI 281 TGCATGAGGGTTCCTATNTCCCCACATCCTCGCCAACACTTGGCATTATC 232 chr2qtel1M 340015 TA-TTTTCT--TTTCTGATAATCAATCTAATTAGA---AAGGTAGTACCT 340058 i -i -- i ----i i - i--- i ii i C L1ME5_3end#LI 231 CAGCTTTCTAATTTTTG----CCAGTCTAA-TAGGTGTAAAGTGATATCT 187 chr2qtel1M 340059 CAGAATTGTTTTAATTAGCATTT-TCCAATTGATAGTGATTTT 340100 vvi v - ii iv i v C L1ME5_3end#LI 186 CATTGTTGTTTTAATTTGCATTTCTCTGATTACTAATGAGTTT 144 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.56 CpG sites = 61, Kimura (unadjusted) = 37.01 Transitions / transversions = 1.79 (61/34) Gap_init rate = 0.12 (42 / 365), avg. gap size = 1.36 (57 / 42) 357 29.15 8.16 4.68 chr2qtel1M 339840 340170 (659830) C L1ME3C_3end#LINE/L1 (469) 401 60 m_b91s551i3 3376 chr2qtel1M 339840 TCTTTGGGATACAGATTTACTAGTGGTATTGCTGGGGCAAAGGGTGTACA 339889 i i i i v ii vv v v iv i i i C L1ME3C_3end#L 401 TCTCTAGGGTATATACCTAGGAGTGGAATTGCTGGGTCGTAGGGTATGCG 352 chr2qtel1M 339890 TGATTTTACAAGCCCTGTGGGCCTAG----TTCCAAA-TGCTTTACAGAA 339934 i- i - --- v i--- ---- v - i v i i C L1ME3C_3end#L 351 C-ATCTT-CAA---CTTTA---CTAGATATTGCCAAATTGCTCTCCAAAG 310 chr2qtel1M 339935 TTGTTGAATCAGTTATACAATCTTGCCAAGAGTGTATTACTTTTTCAGTT 339984 v v i i - v iii iv v vvv i v C L1ME3C_3end#L 309 TGGTTGTACCAATT-TACACTCCCACCAGCAGTGTATGAGAGTTCCCGTT 261 chr2qtel1M 339985 TTCCCACAT-CTCTCCAATATTTGTCATTTTTA---TTTT-CTTTTCTGA 340029 vii - v i i vi v i --- -vv i - C L1ME3C_3end#L 260 GCTCCACATCCTCGCCAACACTTGGTATTGTCAGACTTTTAAATTTTTG- 212 chr2qtel1M 340030 TAATCAATCTAATTA----GAAAGGTAGTACCTCAGAATTGTTTTAATTA 340075 ---i i vi---- -- i i vvi ? v C L1ME3C_3end#L 211 ---CCAATCTGATGGGTGTGAAA--TGGTATCTCATTGTNGTTTTAATTT 167 chr2qtel1M 340076 GCATTTTCC-AATTGATAGTGA----------TTTTTCATATGTGTATAG 340114 i -i iv ----------i v v C L1ME3C_3end#L 166 GCATTTCCCTGATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTG 117 chr2qtel1M 340115 ATAACTTCAGATTATTTCATGTGAAAACTGACTCTTCCTAATTTTT--TT 340162 iiv - i?i vii v v vi i v v v vi --ii C L1ME3C_3end#L 116 GCCA-TTCGNGTTTCCTCTTCTGTGAATTGCCTGTTCATATCTTTTGCCC 68 chr2qtel1M 340163 ATTTTTTT 340170 i C L1ME3C_3end#L 67 ATTTTTCT 60 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.62 CpG sites = 52, Kimura (unadjusted) = 38.19 Transitions / transversions = 1.30 (52/40) Gap_init rate = 0.08 (25 / 330), avg. gap size = 1.72 (43 / 25) 15 23.53 2.22 0.00 chr2qtel1M 340411 340455 (659545) (TTCTCT)n#Simple_repeat 1 46 (0) m_b91s252i6 3377 chr2qtel1M 340411 TTCTCTTTCTCTTTCTTGCTCTATTT-TTTTTTTCTTTACATTTCT 340455 ivi v - i i viv (TTCTCT)n#Sim 1 TTCTCTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCTTTCT 46 Matrix = Unknown Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 384 25.87 0.00 6.19 chr2qtel1M 340466 340568 (659432) C MIRc#SINE/MIR (153) 115 19 m_b91s601i5 3378 chr2qtel1M 340466 GGGGTTTAATGACTTGTCCATGGTCACACCGCTAGGAAGTGTTAAGTGCT 340515 i v i i v v v vi- v i C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGC-AGAGCC 67 chr2qtel1M 340516 GAGGTCAAATTTGAACTCAGATCCTCCTGACTTCAGGGCTGGTGTTTTAT 340565 i ----- i i i i i i i v ii i i v C MIRc#SINE/MIR 66 GGG-----ACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTT 22 chr2qtel1M 340566 CCA 340568 C MIRc#SINE/MIR 21 CCA 19 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.71 CpG sites = 17, Kimura (unadjusted) = 32.88 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.06 (6 / 102), avg. gap size = 1.00 (6 / 6) 17 26.04 2.20 6.90 chr2qtel1M 340774 340864 (659136) (TTTTTCC)n#Simple_repeat 1 87 (0) m_b91s252i7 3379 chr2qtel1M 340774 TTTTTCCCTTTTCCTTTTTCCTAGTACATTCCTTTCTCTCACCTCTTAAT 340823 i -- --v i iivii i -v (TTTTTCC)n#Si 1 TTTTTCCTTTTTCCTTTTTCCT--T--TTTCCTTTTTCCTTTTTCCT-TT 45 chr2qtel1M 340824 TTCATATTTTTCTCTTT-C-TTTTCTTTTCTCTTTTTTTCTTT 340864 v - i i - - i i i i (TTTTTCC)n#Si 46 TTCCT-TTTTCCTTTTTCCTTTTTCCTTTTTCCTTTTTCCTTT 87 Matrix = Unknown Transitions / transversions = 3.25 (13/4) Gap_init rate = 0.09 (8 / 90), avg. gap size = 1.00 (8 / 8) 18 25.54 0.00 0.00 chr2qtel1M 340830 340869 (659131) (T)n#Simple_repeat 1 40 (0) m_b91s252i8 3380 chr2qtel1M 340830 TTTTTCTCTTTCTTTTCTTTTCTCTTTTTTTCTTTCTTTT 340869 i i i i i i i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 40 Matrix = Unknown Transitions / transversions = 1.00 (8/0) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 371 25.17 8.33 6.72 chr2qtel1M 340870 341001 (658999) C MIRc#SINE/MIR (124) 144 11 m_b91s601i6 3381 chr2qtel1M 340870 TTTTATAGCTGAGACAATTG---------GAA-TCAAGTGACTTGCCCAG 340909 i v iv i --------- i- i i C MIRc#SINE/MIR 144 TTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAA 95 chr2qtel1M 340910 GGTCACACAGCTAGGAAG-AACTAAGAGTCTGAGCCTATTTTGAACTCAG 340958 v -ii -- i v ii ----- i i C MIRc#SINE/MIR 94 GGTCACACAGCTAGTAAGTGGC--AGAGCCGGGAC-----TCGAACCCAG 52 chr2qtel1M 340959 GTCCTTTTGACTTCAGCGCACAGGTGCTGTATCTACCATGCCA 341001 i ii i i- iv - v v i iiii C MIRc#SINE/MIR 51 GTCTTCCTGACTCCAA-GTCCA-GTGCTCTTTCCACTGCACCA 11 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.35 CpG sites = 24, Kimura (unadjusted) = 32.65 Transitions / transversions = 3.43 (24/7) Gap_init rate = 0.09 (12 / 131), avg. gap size = 1.67 (20 / 12) 14 10.11 6.25 0.00 chr2qtel1M 341725 341756 (658244) (GTTTT)n#Simple_repeat 1 34 (0) m_b91s252i9 3382 chr2qtel1M 341725 GTTTT-TATTTATTTGTTTTGTTTTG-TTTGTTT 341756 - v vv - (GTTTT)n#Simp 1 GTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTT 34 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.06 (2 / 31), avg. gap size = 1.00 (2 / 2) 13 11.61 0.00 6.67 chr2qtel1M 341728 341759 (658241) (TTTG)n#Simple_repeat 1 30 (0) m_b91s252i10 3382 chr2qtel1M 341728 TTTATTTATTTGTTTTGTTTTGTTTGTTTCTT 341759 i i - - v (TTTG)n#Simpl 1 TTTGTTTGTTTG-TTTG-TTTGTTTGTTTGTT 30 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.06 (2 / 31), avg. gap size = 1.00 (2 / 2) 18 0.00 0.00 0.00 chr2qtel1M 342597 342616 (657384) (T)n#Simple_repeat 1 20 (0) m_b91s252i11 3383 chr2qtel1M 342597 TTTTTTTTTTTTTTTTTTTT 342616 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTT 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 818 33.97 3.57 2.61 chr2qtel1M 342733 343264 (656736) L2#LINE/L2 2031 2567 (515) m_b91s601i7 3384 chr2qtel1M 342733 GGTCACCTTCTCCATCCTCATTCTCCTTGACTTCTCTTCAGGCTTTGATA 342782 v- vi ii v i ? vv vv i L2#LINE/L2 2031 GGTCAA-TTCTCAGTCCTCATCTTACTTGACCTNTCAGCAGCATTTGACA 2079 chr2qtel1M 342783 C----------TCTTCCCTTCATGATCCTCTCTGTTCTTTAGGATTTTAG 342822 ---------- iii v vv v i v vi v v ii L2#LINE/L2 2080 CAGTTGATCACTCCCTCCTTCTTGAAACACTTTCTTCACTTGGCTTCCAG 2129 chr2qtel1M 342823 AACACCCCTCTCTCCTGATTTCCCTCCTTCCTATTCTCTGACTACTTCTT 342872 i v v i i v --- v i ii i L2#LINE/L2 2130 GACACCACACTCTCCTGGTTTTCCTCCTACCT---CACTGGCCGCTCCTT 2176 chr2qtel1M 342873 TTCTATCTTTTTTG---GATATTCCTGAGATCAA-AACTTCAAGCCATAT 342918 i vi ii --- v vi v vv vv-i i v?iv i vv L2#LINE/L2 2177 CTCAGTCTCCTTTGCTGGTTCCTCCTCATCTCCCCGACCTCTNAACGTTG 2226 chr2qtel1M 342919 GGGTCCCTTGGTGTTCTATCTTTGATCCTCTTCTCTTTTGCCTCATTATT 342968 i v iii v i vi i iv i viv vvi i L2#LINE/L2 2227 GAGTGCCCCAGGGCTCAGTCCTTGGACCTCTTCTCTTCTCTATCTACACT 2276 chr2qtel1M 342969 ACTTTTCTTGGTGATTTCATCAGCTACCATGAATTTAATTTCTAACTATT 343018 vvi ii ? i viv vi iv v v i v v L2#LINE/L2 2277 CACTCCCTNGGTGATCTCATCCAGTCTCATGGCTTTAAATACCATCTATA 2326 chr2qtel1M 343019 T--TGATGATTTTCAAATATCCCTTTCATGCCCCAATCTCTCTGCTGACC 343066 -- i ii v viv i vv vi i iv v L2#LINE/L2 2327 TGCTGATGACTCCCAAATTTATATCTCCAGCCCGGACCTCTCCCCTGAAC 2376 chr2qtel1M 343067 TCCAT-TTTATATCTTTAATTTCCTTAAAGACATCTCTAATTGAATGGTC 343115 v-i ii v ii i v vvvv i v i vii L2#LINE/L2 2377 TCCAGACTCGTATATCCAACTGCCTACTCGACATCTCCACTTGGATGTCT 2426 chr2qtel1M 343116 AGTAGTCTAGGATCTCAAATTCAATATGTTCAAAACAGAACTTATTAT-T 343164 i ---- v i i i i v iv v - L2#LINE/L2 2427 AATAG----GCATCTCAAACTTAACATGTCCAAAACTGAACTCCTGATCT 2472 chr2qtel1M 343165 TCTACCCCAGATATTCTCATACACACACTCACACTCTCC-TATTATTGAA 343213 iv i i iv v v - v i v ---i i - v i v ? - L2#LINE/L2 2473 TCCCCCTCAAACCTGCTCCT-CCCGCAGTC---TTCCCCATCTCAGTNA- 2517 chr2qtel1M 343214 GAGGGCATCACTATCTTCCCATTTCTTCAGGATCACCATCTAGGAGTTTT 343263 - v v v i i i v vi viv vv i v iv L2#LINE/L2 2518 -ATGGCAACTCCATCCTTCCAGTTGCTCAGGCCAAAAACCTTGGAGTCAT 2566 chr2qtel1M 343264 C 343264 L2#LINE/L2 2567 C 2567 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 44.63 CpG sites = 87, Kimura (unadjusted) = 46.47 Transitions / transversions = 0.98 (87/89) Gap_init rate = 0.04 (21 / 531), avg. gap size = 1.57 (33 / 21) 17 29.60 0.00 0.00 chr2qtel1M 344059 344104 (655896) (AA)n#Simple_repeat 1 46 (0) m_b91s252i12 3385 chr2qtel1M 344059 AAAAAAGAAAAACCATAAGAGAAAAAAAAAACAGAAGGGAAAAAAA 344104 i vv v i i v i iii (AA)n#Simple_ 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 46 Matrix = Unknown Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 352 26.88 16.03 1.10 chr2qtel1M 344522 344758 (655242) C L1ME3G_3end#LINE/L1 (298) 626 355 m_b91s551i4 3386 chr2qtel1M 344522 TTGTTCACTCAGCATCACTTCTTGTAAATCTTTCTAGGCCTTTCTAAAAT 344571 v i vi iv v i i v i vv vi v - C L1ME3G_3end#L 626 TTTTTCACTCAACAATATGTCTTGGAGATCTTTCCATGTCAGTACATA-T 578 chr2qtel1M 344572 CAATCTGTTCCTCATTTTT------------ATAGTATTTCATA-TACC- 344607 vi i-- i ------------ i - iv- C L1ME3G_3end#L 577 AGATCTA--CCTCATTCTTTTTAACNGCTGCATAGTATTCCATAGTATGG 530 chr2qtel1M 344608 ATACACCATAATTTATTCAGCTATTCCCCCACTGATGGGCATCTCA---G 344654 i i i i i i i i vi--- C L1ME3G_3end#L 529 ATATACCATAATTTATTTAACCATTCCCCTATTGATGGACATTTAGGTTG 480 chr2qtel1M 344655 TTTCCCATTCTTTGCTCCCACTGAAA--GCTGCTACAAACTTCCTC---- 344698 v i i vii vi v -- v ii v i---- C L1ME3G_3end#L 479 TTTCCAATTTTTCGCTATTACAAACAATGCTGCAATGAACATCCTTGTAC 430 chr2qtel1M 344699 ---CCTCTTT-----TATG-------ATCTCTTTGGGATACAGATCCAGT 344733 --- ? i -----i ------- i ? i v v?i ? v C L1ME3G_3end#L 429 ATGCNTCCTTGTGCACATGTGCGAGTATTTCTNTAGGATAGATNCCNAGA 380 chr2qtel1M 344734 AGCAGCACTACTGGATCAAAGAATA 344758 ii v i i i ii C L1ME3G_3end#L 379 AGTGGAATTGCTGGGTCAAAGGGTA 355 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.69 CpG sites = 41, Kimura (unadjusted) = 35.40 Transitions / transversions = 1.86 (41/22) Gap_init rate = 0.05 (12 / 236), avg. gap size = 3.42 (41 / 12) 18 27.30 0.00 0.00 chr2qtel1M 344802 344846 (655154) (TA)n#Simple_repeat 1 45 (0) m_b91s252i13 3387 chr2qtel1M 344802 TATATATATGTATGTGTGTGTGTCTATATATCTATATCTATACAT 344846 i i i i i i v v v i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATAT 45 Matrix = Unknown Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 38 0.00 0.00 0.00 chr2qtel1M 346905 346937 (653063) (AC)n#Simple_repeat 1 33 (0) c_b91s251i0 3388 chr2qtel1M 346905 ACACACACACACACACACACACACACACACACA 346937 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACA 33 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 27 0.00 0.00 0.00 chr2qtel1M 348259 348284 (651716) (T)n#Simple_repeat 1 26 (0) c_b91s251i1 3389 chr2qtel1M 348259 TTTTTTTTTTTTTTTTTTTTTTTTTT 348284 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 504 31.51 8.65 0.50 chr2qtel1M 348873 349057 (650943) C MIR3#SINE/MIR (6) 202 3 m_b91s601i8 3390 chr2qtel1M 348873 TAAAATGAAAAGAT-TTAGAGCTGGAAGAGATCTTGGAGATCACTTGGCC 348921 i v v ii - i i i i ii i i C MIR3#SINE/MIR 202 TAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTC 153 chr2qtel1M 348922 TAATATCCT-ATTTTTCAGATGAGGGAACTAAGACCCA-----ATTAAAT 348965 i ivi - v i i i -----i v i C MIR3#SINE/MIR 152 CAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGT 103 chr2qtel1M 348966 TTCTTCATTGAGGCTATAGAGGTAA--------AAAGCCAGAATTTCAAC 349007 vv vviii ii i v v? i-------- i i i i vv C MIR3#SINE/MIR 102 GACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAAC 53 chr2qtel1M 349008 CCATGCCT-CTGACTACAAATCAAATGCTCTTTCCTTTCCACCATGCTGC 349056 v i - v v i -vi i ivi vi iv C MIR3#SINE/MIR 52 CCAGGTCTCCTGACTCCCAGTC-CGTGCTCTCTCTGCTCAGCCACTCTGC 4 chr2qtel1M 349057 C 349057 C MIR3#SINE/MIR 3 C 3 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.32 CpG sites = 38, Kimura (unadjusted) = 43.34 Transitions / transversions = 1.90 (38/20) Gap_init rate = 0.03 (6 / 184), avg. gap size = 2.83 (17 / 6) 217 29.82 3.51 0.00 chr2qtel1M 349532 349588 (650412) C L2b_3end#LINE/L2 (6) 460 402 m_b91s601i9 3391 chr2qtel1M 349532 TCATTT--TAAGCATATATTAAGCACCTACTACGTTCCAGATGCTCAGCT 349579 i--i ii v i i i ii v ii? vv C L2b_3end#LINE 460 TCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCT 411 chr2qtel1M 349580 AAGCACTGG 349588 i i C L2b_3end#LINE 410 AGGCGCTGG 402 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.73 CpG sites = 13, Kimura (unadjusted) = 42.22 Transitions / transversions = 3.25 (13/4) Gap_init rate = 0.02 (1 / 56), avg. gap size = 2.00 (2 / 1) 599 28.52 9.06 3.36 chr2qtel1M 350073 350326 (649674) L3#LINE/CR1 3626 3893 (206) m_b91s601i10 3392 chr2qtel1M 350073 AGAGACACTGACAAGTTGGAAGACATCCCAAGGAGAGCTGTGAATATCAT 350122 i i ii ivi i vi --- ---i - L3#LINE/CR1 3626 AGGGACATTGACAAACTGGAGCGCGTCCAGAGGAGAGC---GA---CCA- 3668 chr2qtel1M 350123 GGAATAGAGAAGGTTCTG-------TGCCAAATGAGGAACAGTTGAAAGA 350165 - i i v v ------- i v i i L3#LINE/CR1 3669 -GGATGGTGAAGGGTCTGGAAACCATGTCATATGAGGAACGGTTGAAGGA 3717 chr2qtel1M 350166 ACTGAGGCTACTTATTCC---AAAGAGAAAACTTGGTGGGTAACATGA-A 350211 i v ii vi i---i i i -i vi - L3#LINE/CR1 3718 ACTGGGGATGTTTAGCCTGGAGAAGAGAAGACTTAG-AGGAGACATGATA 3766 chr2qtel1M 350212 ATAGTAT--AAATATCTGAAAGGTTG---TGTTAAAGATGAATCCCACTT 350256 iiv v -- i i i --- vi v i ivv L3#LINE/CR1 3767 GCTGTCTTCAAATATTTGAAGGGCTGTCATGTGGAAGAGGGATTAGACTT 3816 chr2qtel1M 350257 -TTCCACTTGGCCCCAGAGGGAATCCTGAGGAGTGATGAGGGGA------ 350299 - iiiv i v vvviv vii i v ------ L3#LINE/CR1 3817 ATTCTGTGTGGCTCCAGAGGGCAGAACTAGGACCAATGGGTGGAAGTTAC 3866 chr2qtel1M 350300 AAAGAGGCAGATTTCAGCCTGATGTGA 350326 ii i iii i i L3#LINE/CR1 3867 AGGGAGGCAGATTTCGGCTCAATATAA 3893 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.05 CpG sites = 48, Kimura (unadjusted) = 37.80 Transitions / transversions = 2.18 (48/22) Gap_init rate = 0.06 (15 / 253), avg. gap size = 2.13 (32 / 15) 16 27.70 0.00 1.89 chr2qtel1M 352737 352790 (647210) (AAAT)n#Simple_repeat 1 53 (0) m_b91s252i14 3393 chr2qtel1M 352737 AAAAAAATAAACAATAAAAGAAATATATATACTAAAGAAACATATATATA 352786 v i vv v v - v v i v v (AAAT)n#Simpl 1 AAATAAATAAATAAATAAATAAATAAATA-AATAAATAAATAAATAAATA 49 chr2qtel1M 352787 TATA 352790 v (AAAT)n#Simpl 50 AATA 53 Matrix = Unknown Transitions / transversions = 0.20 (2/10) Gap_init rate = 0.02 (1 / 53), avg. gap size = 1.00 (1 / 1) 18 14.13 0.00 3.12 chr2qtel1M 352759 352791 (647209) (AT)n#Simple_repeat 1 32 (0) m_b91s252i15 3393 chr2qtel1M 352759 ATATATATACTAAAGAAACATATATATATATAT 352791 - v v v i (AT)n#Simple_ 1 ATATATATA-TATATATATATATATATATATAT 32 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 185 36.36 0.00 0.00 chr2qtel1M 354542 354607 (645393) MIRc#SINE/MIR 10 75 (193) m_b91s601i11 3394 chr2qtel1M 354542 GTGGTACAGTGGACAGAACGAAAGGCCCTAAGACATTAAGAACTGGGTTT 354591 i v i ivvi i iivi v vv v i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr2qtel1M 354592 GAACCCCACCTTAGTC 354607 ii iv iv i MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCC 75 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 45.85 CpG sites = 14, Kimura (unadjusted) = 51.90 Transitions / transversions = 1.40 (14/10) Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0) 298 20.93 15.53 2.59 chr2qtel1M 355092 355194 (644806) C MIR3#SINE/MIR (7) 201 86 m_b91s601i12 3395 chr2qtel1M 355092 AGAATCATAGA-TG--ATGACTGGAAGTGACCTAAAAGG-CTTCC--TTC 355135 - -- vii v v i i- v i-- i C MIR3#SINE/MIR 201 AGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCC 152 chr2qtel1M 355136 AACCTTGTCCATTTTACAGTTGGGGAAACTAAGATTC----------AGT 355175 iiv - v i i iii ---------- C MIR3#SINE/MIR 151 AACCCCCTC-ATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGT 103 chr2qtel1M 355176 AACTGGCCCAAGAAGTCAC 355194 i v -- C MIR3#SINE/MIR 102 GACTTGCCCAAG--GTCAC 86 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 25.31 CpG sites = 14, Kimura (unadjusted) = 25.31 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.08 (8 / 102), avg. gap size = 2.38 (19 / 8) 285 30.84 10.28 0.00 chr2qtel1M 355144 355250 (644750) C MIRc#SINE/MIR (121) 147 30 m_b91s601i13 3395 chr2qtel1M 355144 CCATTTTACAGTTGGGGAAACTAAGATTC----------AGTAACTGGCC 355183 v i i ii ---------- i v C MIRc#SINE/MIR 147 CCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCC 98 chr2qtel1M 355184 CAAGAAGTCACTGCTGAGAAATATCTGAAAAAGAATTCCAAGGCTGGTCT 355233 ivvv v iiv i iv v ivvi i i v vv v C MIRc#SINE/MIR 97 CAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCT 48 chr2qtel1M 355234 TTCTC-CCCCAAATCCAG 355250 i v- i i C MIRc#SINE/MIR 47 TCCTGACTCCAAGTCCAG 30 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.82 CpG sites = 17, Kimura (unadjusted) = 40.37 Transitions / transversions = 1.06 (17/16) Gap_init rate = 0.02 (2 / 106), avg. gap size = 5.50 (11 / 2) 312 29.98 5.74 1.57 chr2qtel1M 355793 355914 (644086) MIRc#SINE/MIR 10 136 (132) m_b91s601i14 3396 chr2qtel1M 355793 GTAATG-AATGGAGAGAGAGCTGGGCATAGAGCCAAGAGTGCCTGGGGGG 355841 ii - i i vi i v i i i ivi -- v MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTG--GGT 57 chr2qtel1M 355842 CTGAG--CAAGCC---CCAATTAAGAGCTGTGCATCCCTTGGTAAGT-AT 355885 ii -- vi i--- v vv iiv i v i - i MIRc#SINE/MIR 58 TCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCAC 107 chr2qtel1M 355886 TTAAATTCTGTTTACCTCAGTTTCCTCAT 355914 vi v vvi MIRc#SINE/MIR 108 TTAACCTCTCTGAGCCTCAGTTTCCTCAT 136 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.84 CpG sites = 22, Kimura (unadjusted) = 39.66 Transitions / transversions = 1.57 (22/14) Gap_init rate = 0.05 (6 / 121), avg. gap size = 1.50 (9 / 6) 12 24.45 2.56 0.00 chr2qtel1M 355942 355980 (644020) (CATA)n#Simple_repeat 1 40 (0) m_b91s252i16 3397 chr2qtel1M 355942 CATGCA-ACATACATATATACTTACACAAACACACACCTA 355980 i - i v i v i i v (CATA)n#Simpl 1 CATACATACATACATACATACATACATACATACATACATA 40 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.03 (1 / 38), avg. gap size = 1.00 (1 / 1) 200 29.47 2.22 5.75 chr2qtel1M 360014 360103 (639897) C OldhAT1#DNA/hAT-Ac (48) 2794 2708 m_b91s601i15 3398 chr2qtel1M 360014 ACCAATGGGGAAGATGAAA-GGGAAA-GAACGGTGACTAGGGATGGGAGA 360061 ii ii iv -ii i - ? ---- viii C OldhAT1#DNA/h 2794 ACCAACAGGAGAGGGGAAATAAGAGATGAACGGNG----GGGAAAAAAGA 2749 chr2qtel1M 360062 CACTTTAGAAGCATAGTGGATTCTTTTCCCCGGTCCCCTGCT 360103 ? i ivv iiiv i -ii v C OldhAT1#DNA/h 2748 NACCTTAACTGTGCCGTGGATTCTTTCCCCC-ACCCCCTCCT 2708 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.67 CpG sites = 19, Kimura (unadjusted) = 41.67 Transitions / transversions = 3.17 (19/6) Gap_init rate = 0.08 (7 / 89), avg. gap size = 1.00 (7 / 7) 14 15.04 5.41 0.00 chr2qtel1M 364300 364336 (635664) (AAAAGGA)n#Simple_repeat 1 39 (0) m_b91s252i17 3399 chr2qtel1M 364300 AAAAGAAAAAAGG-GAAA-GAAAAAGGAAATTGGGAAAA 364336 i -i - vv i (AAAAGGA)n#Si 1 AAAAGGAAAAAGGAAAAAGGAAAAAGGAAAAAGGAAAAA 39 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 18 0.00 0.00 0.00 chr2qtel1M 365336 365355 (634645) (A)n#Simple_repeat 1 20 (0) m_b91s252i18 3400 chr2qtel1M 365336 AAAAAAAAAAAAAAAAAAAA 365355 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAA 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 13 32.67 0.00 0.00 chr2qtel1M 366750 366802 (633198) (TTTT)n#Simple_repeat 1 53 (0) m_b91s252i19 3401 chr2qtel1M 366750 TTTTTTTTGTTTTTTTCATTAACCCCTTTAGTTTTTCTTTATTTATTTTT 366799 v iv vviiii vv i v v (TTTT)n#Simpl 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr2qtel1M 366800 TTT 366802 (TTTT)n#Simpl 51 TTT 53 Matrix = Unknown Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 12 30.20 0.00 0.00 chr2qtel1M 367076 367120 (632880) (TTTTTG)n#Simple_repeat 1 45 (0) m_b91s252i20 3402 chr2qtel1M 367076 TTTTTTTTTTTGTTTTTGTAATGGGTTTAAATATAGTTTTGGTTT 367120 v vv v v viv v v v (TTTTTG)n#Sim 1 TTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTT 45 Matrix = Unknown Transitions / transversions = 0.10 (1/10) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 17 21.83 5.75 4.55 chr2qtel1M 367678 367764 (632236) (TTTTCAA)n#Simple_repeat 1 88 (0) m_b91s252i21 3403 chr2qtel1M 367678 TTTTCTGTTTT-AGTCTTCCATTTTAAGATTCTCAATTTTCAAAAATTTT 367726 vi - i i v v - i --- (TTTTCAA)n#Si 1 TTTTCAATTTTCAATTTTCAATTTTCA-ATTTTCAATTTTC---AATTTT 46 chr2qtel1M 367727 CAA---TC-ATTTTTACTTTTTAAAATTTTATTTTTAATTTT 367764 --- - i v i vv iv i (TTTTCAA)n#Si 47 CAATTTTCAATTTTCAATTTTCAATTTTCAATTTTCAATTTT 88 Matrix = Unknown Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.08 (7 / 86), avg. gap size = 1.29 (9 / 7) 15 13.87 0.00 0.00 chr2qtel1M 367937 367960 (632040) (T)n#Simple_repeat 1 24 (0) m_b91s252i22 3404 chr2qtel1M 367937 TTTTTTTTTAATTTTTTTTTATTT 367960 vv v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTT 24 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 18 36.32 0.00 0.00 chr2qtel1M 368552 368624 (631376) (TT)n#Simple_repeat 1 73 (0) m_b91s252i23 3405 chr2qtel1M 368552 TTTTTATTTTTTTCCATTTTTTTTTTTAAATTAGTCCTTTAAATTTTATA 368601 v iiv vvv vv ii vvv v v (TT)n#Simple_ 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr2qtel1M 368602 TCTTCTTTATGTGTTTTTTTTTT 368624 i i v v v (TT)n#Simple_ 51 TTTTTTTTTTTTTTTTTTTTTTT 73 Matrix = Unknown Transitions / transversions = 0.40 (6/15) Gap_init rate = 0.00 (0 / 72), avg. gap size = 0.0 (0 / 0) 15 13.67 0.00 0.00 chr2qtel1M 371299 371322 (628678) (A)n#Simple_repeat 1 24 (0) m_b92s252i0 3406 chr2qtel1M 371299 AAAAAAAAAAAGAAATAAACAAAA 371322 i v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAA 24 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 14 30.74 0.00 1.85 chr2qtel1M 371651 371705 (628295) (TTTTC)n#Simple_repeat 1 54 (0) m_b92s252i1 3407 chr2qtel1M 371651 TTTTTATTTCCCCTCTTTCCCTTTTCTTTACTGGTTTTTTTTTTTTTTTT 371700 iv iii -i v vv i i i (TTTTC)n#Simp 1 TTTTCTTTTCTTTTCTTT-TCTTTTCTTTTCTTTTCTTTTCTTTTCTTTT 49 chr2qtel1M 371701 TTTTT 371705 i (TTTTC)n#Simp 50 CTTTT 54 Matrix = Unknown Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1) 20 16.38 0.00 0.00 chr2qtel1M 371672 371705 (628295) (T)n#Simple_repeat 1 34 (0) m_b92s252i2 3407 chr2qtel1M 371672 TTTTCTTTACTGGTTTTTTTTTTTTTTTTTTTTT 371705 i vi vv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 34 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 25 9.10 0.00 0.00 chr2qtel1M 371879 371913 (628087) (T)n#Simple_repeat 1 35 (0) m_b92s252i3 3408 chr2qtel1M 371879 TTTTTTTTAATTTTTTTTTTTTTTTTTTCTTTTTT 371913 vv i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 35 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 13 20.28 2.38 2.38 chr2qtel1M 371882 371923 (628077) (TTTTTAA)n#Simple_repeat 1 42 (0) m_b92s252i4 3408 chr2qtel1M 371882 TTTTTAATTTTT-TTTTTTTTTTTTTCTTTTTTGAAAATTTAA 371923 -v vv vv - vv (TTTTTAA)n#Si 1 TTTTTAATTTTTAATTTTTAATTTTTAATTTTT-AATTTTTAA 42 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.05 (2 / 41), avg. gap size = 1.00 (2 / 2) 12 21.98 2.70 0.00 chr2qtel1M 372216 372252 (627748) (TTAATT)n#Simple_repeat 1 38 (0) m_b92s252i5 3409 chr2qtel1M 372216 TTAATTTT-TTTTTAATTTTCCTTTTTCTTTCCATTTT 372252 -v vv vv iv (TTAATT)n#Sim 1 TTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTT 38 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 17 21.51 0.00 0.00 chr2qtel1M 372220 372262 (627738) (TTTTCT)n#Simple_repeat 1 43 (0) m_b92s252i6 3409 chr2qtel1M 372220 TTTTTTTTTAATTTTCCTTTTTCTTTCCATTTTTCTTTATCTT 372262 i vv i iiv v (TTTTCT)n#Sim 1 TTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTT 43 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 811 33.39 4.02 3.23 chr2qtel1M 373831 374353 (625647) L2#LINE/L2 2037 2563 (519) m_b92s601i0 3410 chr2qtel1M 373831 TTCTCA-TCCTCATTATCCTTGACTTCTCTTCAGGCTTTGATAC------ 373873 - iv v i ? vv vv i ------ L2#LINE/L2 2037 TTCTCAGTCCTCATCTTACTTGACCTNTCAGCAGCATTTGACACAGTTGA 2086 chr2qtel1M 373874 ----TCTTCCCATCACGATCCTCTCTGTTCTCTAGGATTTTAGGACACCC 373919 ---- iii v vi vv v i v v v v ii v L2#LINE/L2 2087 TCACTCCCTCCTTCTTGAAACACTTTCTTCACTTGGCTTCCAGGACACCA 2136 chr2qtel1M 373920 CTCTCTCCTGATTTCCCTTCTTCCTATTCTCTGACCACTTCTTTTCTATC 373969 v i i i v --- v i i i i vi L2#LINE/L2 2137 CACTCTCCTGGTTTTCCTCCTACCT---CACTGGCCGCTCCTTCTCAGTC 2183 chr2qtel1M 373970 TTTTTTG---GATATTCCTGAGATTGA-AACCTCCAACCATATGGGTTCC 374015 ii --- v vi v vv ivv-i i? v i vv i v L2#LINE/L2 2184 TCCTTTGCTGGTTCCTCCTCATCTCCCCGACCTCTNAACGTTGGAGTGCC 2233 chr2qtel1M 374016 TTGGCGTTCTATCTTTGATCCTCTTCTCTTTTGCCTCATTATTACTTTTT 374065 iii v i vi i iv i viv vvi i vvi iii L2#LINE/L2 2234 CCAGGGCTCAGTCCTTGGACCTCTTCTCTTCTCTATCTACACTCACTCCC 2283 chr2qtel1M 374066 TTGGTGATTTTATCAGCTACCATGAATTTAATTTCTAACTATTT--TTAT 374113 ? i i viv vi iv v v i v v -- v L2#LINE/L2 2284 TNGGTGATCTCATCCAGTCTCATGGCTTTAAATACCATCTATATGCTGAT 2333 chr2qtel1M 374114 GATTTTCAAATATCCTTTTCATGCCCCAATCTCTCTGCTGACCTCCAT-T 374162 i ii v viv i vv vi i iv v v-i L2#LINE/L2 2334 GACTCCCAAATTTATATCTCCAGCCCGGACCTCTCCCCTGAACTCCAGAC 2383 chr2qtel1M 374163 TTATATCTTCAATTTCCTTATAGATGGCTCAAATTGAATGGCCAATAGAC 374212 ii v i i v vv v iiv v v i v i i L2#LINE/L2 2384 TCGTATATCCAACTGCCTACTCGACATCTCCACTTGGATGTCTAATAGGC 2433 chr2qtel1M 374213 CAGAATCTCAAATTCAATATGTTCAAAACAGAACTTATTATTTCTATCCC 374262 ---- i i i i v iv v i --- L2#LINE/L2 2434 ----ATCTCAAACTTAACATGTCCAAAACTGAACTCCTGATCT---TCCC 2476 chr2qtel1M 374263 ACATATTCTCATACACACACC-CTCACACT-TTCCCTATTACTGAAGAGG 374310 ------i v vii v - i i v - i iv v v?i v L2#LINE/L2 2477 ------CCTCAAACCTGCTCCTCCCGCAGTCTTCCCCATCTCAGTNAATG 2520 chr2qtel1M 374311 GCATCACTATGTTCCCATTTCTTCAGGATCAAAAATC-AGGAGT 374353 v v i vi i v vi -i i -v L2#LINE/L2 2521 GCAACTCCATCCTTCCAGTTGCTCAGG-CCAAAAACCTTGGAGT 2563 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.62 CpG sites = 85, Kimura (unadjusted) = 45.45 Transitions / transversions = 1.01 (85/84) Gap_init rate = 0.05 (27 / 522), avg. gap size = 1.41 (38 / 27) 13 11.63 0.00 6.67 chr2qtel1M 375633 375664 (624336) (TTTA)n#Simple_repeat 1 30 (0) m_b92s252i7 3411 chr2qtel1M 375633 TTTATTTTATTTTTTAAATTGATTTATTTATT 375664 - v -v v (TTTA)n#Simpl 1 TTTA-TTTATTTATT-TATTTATTTATTTATT 30 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.06 (2 / 31), avg. gap size = 1.00 (2 / 2) 16 19.56 0.00 0.00 chr2qtel1M 375730 375759 (624241) (A)n#Simple_repeat 1 30 (0) m_b92s252i8 3412 chr2qtel1M 375730 AAAAAAGAGAAAAAAAAACAGAAAAAAGAA 375759 i i v i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 30 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 697 29.02 5.35 2.34 chr2qtel1M 375781 376154 (623846) C L1ME3Cz_3end#LINE/L1 (606) 391 7 m_b92s551i0 3413 chr2qtel1M 375781 TATAGACCTACTAGTGGTATTGTTGGATCAAAGGATATGCTCAGTATTAC 375830 v vv v i i iv i v - v - C L1ME3Cz_3end# 391 TATATACCTAGAAGTGGAATTGCTGGGTCGTAGGGTATGCGCA-TCTT-C 344 chr2qtel1M 375831 AGCCTT-TTGGGCTTTGTTCCAAAGTGCTCTCTAGAATGCTTGGATCAGT 375879 i i -i i iiv -- v i i i v v i i C L1ME3Cz_3end# 343 AACTTTACTAGATATTG--CCAAATTGCTCTCCAAAGTGGTTGTACCAAT 296 chr2qtel1M 375880 TCACAACTCAACCAACAATGCATTAGTGTCCCAGTTTTCCCACATC---- 375925 i vii v i i i v v i v ii ---- C L1ME3Cz_3end# 295 TTACACTCCCACCAGCAGTGTATGAGAGTTCCCGTTTCTCCACATCCTCG 246 chr2qtel1M 375926 --ACCATTTATCATTTTCTTTTTTTGTCATATTATCCAATCTGATAGGTG 375973 -- v i ivi v vvvi vvv v vv i C L1ME3Cz_3end# 245 CCAACACTTGGTATTGTCAGACTTTTAAATTTTTGCCAATCTGATGGGTG 196 chr2qtel1M 375974 TGAGTTGGCACCTCAGGGTTATTTTAAATTGCATTT-CCTAATCATCAAG 376022 iv i i vv ?i v - i i - v C L1ME3Cz_3end# 195 TGAAATGGTATCTCATTGTNGTTTTAATTTGCATTTCCCTGATTA-CTAG 147 chr2qtel1M 376023 TAAAGTAAAGAA--TTTTCATATGGTTATAAAT------AGCTTTAATTT 376064 i i vi v -- v viii------i i ivvi C L1ME3Cz_3end# 146 TGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTCGGGTTTCCTCTT 97 chr2qtel1M 376065 ATTTGAA--AACTGTTCATATCTTTTGACCATTTATCAATTGAAGAATGA 376112 v v --iv i v v v -- iv v C L1ME3Cz_3end# 96 CTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTG--GGTTGT 49 chr2qtel1M 376113 CTTACATTCTTAAAAATTTG--ACTGTTCTCCATATATTTTAGA 376154 --v vvi --ivv ii i i C L1ME3Cz_3end# 48 CTT--TTTCTTATTGATTTGTAGGAGTTCTTTATATATTCTGGA 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.92 CpG sites = 54, Kimura (unadjusted) = 37.36 Transitions / transversions = 1.04 (54/52) Gap_init rate = 0.05 (17 / 373), avg. gap size = 1.71 (29 / 17) 236 30.92 1.94 1.94 chr2qtel1M 376995 377149 (622851) C L1ME3G_3end#LINE/L1 (292) 632 478 m_b92s551i1 3414 chr2qtel1M 376995 CCTGCTCATTTCACTCAGCATCAGTTCATGCAGGTCTCTCCAGGCC--TT 377042 i iv i vi vv v v i i v i -- v C L1ME3G_3end#L 632 CTTGCTTTTTTCACTCAACAATATGTCTTGGAGATCTTTCCATGTCAGTA 583 chr2qtel1M 377043 CCTG-AAATCCTCCTGCTGGTCATTTCTTACAGGACAATAATATTCCATA 377091 v i- i iv vv -- - i v ? vvvv i C L1ME3G_3end#L 582 CATATAGATCTACCTCAT--TC-TTTTTAACNGCTGCATAGTATTCCATA 536 chr2qtel1M 377092 ACATTCATATGCCACAATTTATTCAGCCCTTCTCCAGTTGATGAGCATCT 377141 ii vv i i i i v i vi ii i C L1ME3G_3end#L 535 GTATGGATATACCATAATTTATTTAACCATTCCCCTATTGATGGACATTT 486 chr2qtel1M 377142 GTGGTGTT 377149 iv v C L1ME3G_3end#L 485 AGGTTGTT 478 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.85 CpG sites = 24, Kimura (unadjusted) = 40.85 Transitions / transversions = 1.04 (24/23) Gap_init rate = 0.03 (5 / 154), avg. gap size = 1.20 (6 / 5) 298 23.94 0.00 0.00 chr2qtel1M 377079 377149 (622851) C L1ME3E_3end#LINE/L1 (438) 551 481 m_b92s551i2 3414 chr2qtel1M 377079 ATAATATTCCATAACATTCATATGCCACAATTTATTCAGCCCTTCTCCAG 377128 i vii vv i i v v v C L1ME3E_3end#L 551 ATAGTATTCCATTGTATGAATATACCACAATTTATTTATCCATTCTCCTG 502 chr2qtel1M 377129 TTGATGAGCATCTGTGGTGTT 377149 i ii i v v C L1ME3E_3end#L 501 TCGATGGACATTTGGGTTGTT 481 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 27.22 CpG sites = 9, Kimura (unadjusted) = 29.18 Transitions / transversions = 1.12 (9/8) Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0) 487 28.39 4.09 5.53 chr2qtel1M 377831 378050 (621950) C L1ME5_3end#LINE/L1 (457) 484 268 m_b92s551i3 3414 chr2qtel1M 377831 GTTTTCAGTTTCTGGCCACTACAAAAAGGGCTGCCACAAACATGTTGGCA 377880 ii i ii i iv i v iv v ii vi v i C L1ME5_3end#LI 484 GCCTCCAACTCCCCGCCACCACAAACAACGCTGCAATGAACATCCTCGTA 435 chr2qtel1M 377881 CATAGAGGTTCCTTTCC---CTTCTTTAAGA-TCTCTTTGGGATATAAGC 377926 ---- i i vi--- i v v i - i vi C L1ME5_3end#LI 434 CAT----GTCCCCTTATGGACCTGTGTGAGAATTTCTTTGGGATATATAC 389 chr2qtel1M 377927 CCAGTAGAAACACTGCTGGATCAAAGGATATGCACAGTTTGATAGCTT-- 377974 v viiv i i v i --- --- - -- C L1ME5_3end#LI 388 CCAGGAGCGGAATTGCTGGGTCATAGGGTATGC---GT---ATA-CTTAA 346 chr2qtel1M 377975 TTTGAGTA--TAGTTCCAAATCGCTCTTCAGAATGGCTGGATGCATTC-A 378021 v -- v v i i i v i- v - C L1ME5_3end#LI 345 TTTGACTAAGTACTGCCAGATTGCTCTCCAGAATGGCTGCAC-CAGTCTA 297 chr2qtel1M 378022 CAATTCCATCAACGAAGTATCAGTGTCCC 378050 v i i i iiv i v v i C L1ME5_3end#LI 296 CACTCCCACCAGCAGTGCATGAGGGTTCC 268 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.97 CpG sites = 36, Kimura (unadjusted) = 36.76 Transitions / transversions = 1.57 (36/23) Gap_init rate = 0.08 (17 / 219), avg. gap size = 1.24 (21 / 17) 262 36.96 5.23 4.02 chr2qtel1M 378925 379268 (620732) C L2c_3end#LINE/L2 (7) 471 124 m_b92s601i1 3415 chr2qtel1M 378925 CATTTATCAAACACCTATTGAGTGCCAGCCACAATGATAAGCACTGAGGA 378974 i v ii i vi i i-i vi i i i C L2c_3end#LINE 471 CATTCAACAAACATTTATTGAGCGCCTACTAT-GTGCCAGGCGCTGGGGA 423 chr2qtel1M 378975 TTAAAAAAAAATAATTAGGAGGCAAAAGACAATTCCTTCAAGTAATGTAC 379024 --- v i i v i vi ---i v vv v i v iivi C L2c_3end#LINE 422 T---ACAAAGATGAATAAGACAC---GGTCCCTGCCCTCAAGGAGCTCAC 379 chr2qtel1M 379025 AATACATTGTAGGAAATA-----ATATACAAATGTGTACAAAGCAAGCTA 379069 i vi v v i i -----i v i iivv vi i C L2c_3end#LINE 378 AGTCTAGTGGAGGAGACAGACANGTAAACAGACAATTACAATACAAGTTA 329 chr2qtel1M 379070 A--AT-----CCAGAAC-GGACT-TAATTAGGACTTAATTAGACTTAATT 379110 -- ----- i v i- v - ivi iiviv vi -vi --i C L2c_3end#LINE 328 ATGATAAGTGCTATAATGGGAGTATAGACAGGGTGCTATGGGA-GCA--C 282 chr2qtel1M 379111 AGAAGAGGGAAG--GAACAAGAATTAAGAGGGATTAGTGAATACTTGCTG 379158 i v v--ii v ?v -- i i i v vi v i C L2c_3end#LINE 281 AGAGGAGGGCACCTAGACTAGNCTT--GGGGGGTCAGGGAAGGCTTCCCG 234 chr2qtel1M 379159 TAGGTTTTTAGTTTTCAGTTGGGTCATAAAGGA-AAATAATGAGGTTGGC 379207 v vvv v vv i v i i ? v i -i i i- v v v C L2c_3end#LINE 233 GAGGAGGTGACATCTGAGCTGAGNCTTGAAGGATGAGTAG-GAGTTAGCC 185 chr2qtel1M 379208 AGTCTAAACTTCAAGGGAAAACTATTACAGGAATAAGGAATAGCCAT-TG 379256 vivi vvvvii i vi v v v i i - - C L2c_3end#LINE 184 AGGTGGAAGGAGGGGGGAAGAGCATTCCAGGCAGAGGGAACAG-CATGTG 136 chr2qtel1M 379257 AAAATGCCTGGA 379268 v v ?i C L2c_3end#LINE 135 CAAAGGCNCGGA 124 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 50.02 CpG sites = 65, Kimura (unadjusted) = 53.13 Transitions / transversions = 1.14 (65/57) Gap_init rate = 0.06 (22 / 343), avg. gap size = 1.45 (32 / 22) 13 18.24 0.00 5.13 chr2qtel1M 379422 379462 (620538) (AAAATAG)n#Simple_repeat 1 39 (0) m_b92s252i9 3416 chr2qtel1M 379422 AAAAAAGTAAATACAAAATAAAAGAAAAAGAAATTAGAAAA 379462 v v v - i - v v (AAAATAG)n#Si 1 AAAATAGAAAATAGAAAAT-AGA-AAATAGAAAATAGAAAA 39 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 19 27.92 2.86 0.00 chr2qtel1M 379687 379756 (620244) (ATACAT)n#Simple_repeat 1 72 (0) m_b92s252i11 3417 chr2qtel1M 379687 ATATATTTATGTAAACATACATTTATACACACACATATACAAATACA-A- 379734 i v ii v i iv i i v - - (ATACAT)n#Sim 1 ATACATATACATATACATATACATATACATATACATATACATATACATAT 50 chr2qtel1M 379735 ATAGATGCAGATACACATACAT 379756 i v i v i (ATACAT)n#Sim 51 ACATATACATATACATATACAT 72 Matrix = Unknown Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.03 (2 / 69), avg. gap size = 1.00 (2 / 2) 32 20.26 6.14 2.54 chr2qtel1M 380444 380557 (619443) (ATAC)n#Simple_repeat 1 118 (0) m_b92s252i13 3418 chr2qtel1M 380444 ATAGATACATACAT--ATAGATACATACATACCTATCTAGATATGATATA 380491 v -- v v iv v -v i (ATAC)n#Simpl 1 ATACATACATACATACATACATACATACATACATACATACATA-CATACA 49 chr2qtel1M 380492 CACACACACACA-AC-CACACACACACATACACAAATACAT--ATACATA 380537 i i i - -i i i i v -- (ATAC)n#Simpl 50 TACATACATACATACATACATACATACATACATACATACATACATACATA 99 chr2qtel1M 380538 -ATGTATGCACATATATACAT 380557 - ii -- i (ATAC)n#Simpl 100 CATACAT--ACATACATACAT 118 Matrix = Unknown Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.07 (8 / 113), avg. gap size = 1.25 (10 / 8) 25 17.59 0.00 0.00 chr2qtel1M 380491 380535 (619465) (AC)n#Simple_repeat 1 45 (0) m_b92s252i14 3419 chr2qtel1M 380491 ACACACACACACAACCACACACACACATACACAAATACATATACA 380535 vv i v i i i (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACA 45 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 32 20.26 6.14 2.54 chr2qtel1M 380444 380557 (619443) (ATAC)n#Simple_repeat 1 118 (0) m_b92s252i13 3418 chr2qtel1M 380444 ATAGATACATACAT--ATAGATACATACATACCTATCTAGATATGATATA 380491 v -- v v iv v -v i (ATAC)n#Simpl 1 ATACATACATACATACATACATACATACATACATACATACATA-CATACA 49 chr2qtel1M 380492 CACACACACACA-AC-CACACACACACATACACAAATACAT--ATACATA 380537 i i i - -i i i i v -- (ATAC)n#Simpl 50 TACATACATACATACATACATACATACATACATACATACATACATACATA 99 chr2qtel1M 380538 -ATGTATGCACATATATACAT 380557 - ii -- i (ATAC)n#Simpl 100 CATACAT--ACATACATACAT 118 Matrix = Unknown Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.07 (8 / 113), avg. gap size = 1.25 (10 / 8) 401 28.23 1.51 7.45 chr2qtel1M 380614 380812 (619188) C MIR1_Amn#SINE/MIR (42) 188 1 m_b92s601i2 3420 chr2qtel1M 380614 TCTCAAAGCTCATTTGTATAGCA--TAATTACCATATTTACTATTTCCTA 380661 v - ii v v -- v v i vv iv i ivi C MIR1_Amn#SINE 188 TCTCAAAGCAC-TTTACAAAGGAGGTCAGTATCATTATCCCCATTTTACA 140 chr2qtel1M 380662 GACTGATTGATTGCTGGGGCA-ATTGGGGTTAAGTGACTTGCCCAGGGTC 380710 - vvi --i i ?- vv i ? i C MIR1_Amn#SINE 139 GA-TGAGGAA--ACTGAGGCNCAGAGAGGTNAAGTGACTTGCCCAAGGTC 93 chr2qtel1M 380711 ACACAGGTAGGAAGTGTTAAGTGTCTGAGACCAAATTTGAACTCCAAGTC 380760 ? - i? ------i? v v v vii ? ? - i - C MIR1_Amn#SINE 92 ACNCA-GCNGG------CNAGTGGCAGAGCCGGGANTNGAAC-CCAGGT- 52 chr2qtel1M 380761 CTCTTGACTTCAGGGTTGGCACTCTATCCACTGAACCACCTAGCTGTCCC 380810 ii v i vi viii ii ii viv i- C MIR1_Amn#SINE 51 CTCCCGAGTCCCAGTCCAGTGCTCTATCCACTAGACCACACTGCC-TCCC 3 chr2qtel1M 380811 TA 380812 C MIR1_Amn#SINE 2 TA 1 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.04 CpG sites = 30, Kimura (unadjusted) = 37.97 Transitions / transversions = 1.36 (30/22) Gap_init rate = 0.08 (16 / 198), avg. gap size = 1.06 (17 / 16) 465 22.77 0.00 7.55 chr2qtel1M 380686 380799 (619201) C MIRc#SINE/MIR (153) 115 10 m_b92s601i3 3420 chr2qtel1M 380686 GGGGTTAAGTGACTTGCCCAGGGTCACACAGGTAGGAAGTGTTAAGTGTC 380735 i i v ------- v C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGC 73 chr2qtel1M 380736 TGAGACCAAATTTGAACTCCAAGTCCTCTTGACTTCAGGGTTGGCACTCT 380785 v v vii i i - i i i i i viii ii C MIRc#SINE/MIR 72 AGAGCCGGGACTCGAAC-CCAGGTCTTCCTGACTCCAAGTCCAGTGCTCT 24 chr2qtel1M 380786 ATCCACTGAACCAC 380799 v v C MIRc#SINE/MIR 23 TTCCACTGCACCAC 10 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.43 CpG sites = 16, Kimura (unadjusted) = 27.78 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.07 (8 / 113), avg. gap size = 1.00 (8 / 8) 16 18.91 0.00 0.00 chr2qtel1M 381481 381510 (618490) (T)n#Simple_repeat 1 30 (0) m_b92s252i15 3421 chr2qtel1M 381481 TTTTTTTTCATTTTTTATATTTTGTTTTTT 381510 iv v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 30 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 249 37.59 0.71 0.00 chr2qtel1M 382492 382632 (617368) C L2#LINE/L2 (217) 2865 2724 m_b92s601i4 3422 chr2qtel1M 382492 AAATGGGAAGGCACTGGAATTTATTGAGTAGGACAGTGACATGATAAGAA 382541 i v i ivv v i iiv vv v C L2#LINE/L2 2865 AGATGGGAAGCCATTGGAGGGTTTTGAGCAGAGGAGTGACATGATCTGAC 2816 chr2qtel1M 382542 CTGCATTGTAGGA-AATCACTCTACTAGCTGACTGGATAAGGGTTTGGAG 382590 i i i v ii -i iviv vv v v vi vi ? C L2#LINE/L2 2815 TTACGTTTTAAAAGGATCACTCTGGCTGCTGTGTTGAGAATAGACTGNAG 2766 chr2qtel1M 382591 GAAGGAGAGCTTTGAGAGAGGCAGATGTACCAATAGACTATT 382632 ii vi vv v iiv v ivviii iv i C L2#LINE/L2 2765 GGGGGCAAGGGTGGAAGCAGGGAGACCAGTTAGGAGGCTATT 2724 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 52.49 CpG sites = 27, Kimura (unadjusted) = 53.97 Transitions / transversions = 1.04 (27/26) Gap_init rate = 0.01 (1 / 140), avg. gap size = 1.00 (1 / 1) 250 25.35 2.82 0.00 chr2qtel1M 383526 383596 (616404) C L1ME3C_3end#LINE/L1 (340) 530 458 m_b92s551i4 3423 chr2qtel1M 383526 ATATAACACAATTTATTTGGCCATTCTCCAAGTGATGGGCATCTTCA--A 383573 v iv viv i i vvi--i C L1ME3C_3end#L 530 ATATACCACAATTTATTTATCCATTCTCCTGTTGATGGACATTTAGGTTG 481 chr2qtel1M 383574 TTTCCAATTCCTTACTGTTAGAA 383596 ii ii i v C L1ME3C_3end#L 480 TTTCCAATTTTTCGCTATTACAA 458 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 29.42 CpG sites = 11, Kimura (unadjusted) = 31.74 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.01 (1 / 70), avg. gap size = 2.00 (2 / 1) 869 27.62 3.10 2.61 chr2qtel1M 384213 384632 (615368) C L1ME3G_3end#LINE/L1 (496) 428 7 m_b92s551i5 3423 chr2qtel1M 384213 TGGATCCTT-TAC-CATTTCCTACTATTTCTTTGGAATCTAGACCCAGTA 384260 v? - i - v v v v ? i i vv v? ? v C L1ME3G_3end#L 428 TGCNTCCTTGTGCACATGTGCGAGTATTTCTNTAGGATAGATNCCNAGAA 379 chr2qtel1M 384261 GTGAGACTGTTGGAACTAAGGGTATGCACAATTTTATAGTCCTTTGGGCA 384310 ii i i iv v i - v v iivv i ii C L1ME3G_3end#L 378 GTGGAATTGCTGGGTCAAAGGGTATGCGCA-TTTTAAATTTTAATAGATA 330 chr2qtel1M 384311 CAGTTCCAAATTACTCTTCAGAATGGTTGGATAAATTCACATTTCCACCA 384360 v -- i i i i ? i v iv i i i C L1ME3G_3end#L 329 CTG--CCAAATTGCCCTCCAAAANGGCTGTACCAATTTACACTCCCACCA 282 chr2qtel1M 384361 ACAATGCATTAGTGTCCCAGTTTTCTCACATCCCTTCCAACATTTGTCAT 384410 i i i v v v v i i i iiv i ? vi C L1ME3G_3end#L 281 GCAGTGTATGAGAGTACCCGTTTCCCCACACCCTCGCCAACACTNGATAT 232 chr2qtel1M 384411 TATCTGTTCGTGTCACCTTGT-CCAATCTGAGAGGT-----ATGGTACCT 384454 vi?- v v v vi v - vi ----- i C L1ME3G_3end#L 231 TATCAAN-CTTTTAAATTTTTGCCAATCTGATGGGTGAAAAATGGTATCT 183 chr2qtel1M 384455 CAGAGTTGTCTTAATTTGCTTTTCTCTGATCAATAATGATTTAGAGCATT 384504 vv i v i i v i vv v i C L1ME3G_3end#L 182 CATTGTTGTTTTAATTTGCATTTCCCTGATTACTAGTGAGGTTGAGCATC 133 chr2qtel1M 384505 TTTTGTCATATTAGAAATGGC--TTTA-ATTTCTTTATCTAAAAAGTATC 384551 -- vvvv v -- i- i iv ivi v ii C L1ME3G_3end#L 132 TTT--TCATATGTTTATTGGCCATTTGTATTTCCTCTTCTGTGAATTGCC 85 chr2qtel1M 384552 TGTTCATATCC-TTGATCATTTATCAACTGAGGAATGACTTGCAGTCTTA 384600 - vi v v i i v-- v vi-- C L1ME3G_3end#L 84 TGTTCATATCCTTTGCCCATTTTTCTATTGGGT--TGTCTTTT--TCTTA 39 chr2qtel1M 384601 TAGATTT-TACTCACTTCTCTACATATTTTAGA 384632 v - -vv v i i i i C L1ME3G_3end#L 38 TTGATTTGTA-GGAGTTCTTTATATATTCTGGA 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.88 CpG sites = 57, Kimura (unadjusted) = 35.65 Transitions / transversions = 1.02 (57/56) Gap_init rate = 0.05 (19 / 419), avg. gap size = 1.26 (24 / 19) 912 30.11 2.87 1.70 chr2qtel1M 384236 384583 (615417) C L1ME5_3end#LINE/L1 (534) 407 56 m_b92s551i6 3423 chr2qtel1M 384236 ATTTCTTTGGAATCTAGACCCAGTAGTGAGACTGTTGGAACTAAGGGTAT 384285 i v v v i ii i i iv vv C L1ME5_3end#LI 407 ATTTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTAT 358 chr2qtel1M 384286 GCACA-ATTTTATAGTCCTTTGGGCACAGTTCCAAATTACTCTTCAGAAT 384334 ii - i v -- ivvi ii i v -- i i i C L1ME5_3end#LI 357 GCGTATACTTAAT--TTGACTAAGTACTG--CCAGATTGCTCTCCAGAAT 312 chr2qtel1M 384335 GGTTGGATAAATTCACATTTCCACCAACAATGCATTAGTGTCCCAGTTTT 384384 i v iv i ii i i i i v v i vi ? i C L1ME5_3end#LI 311 GGCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATNTC 262 chr2qtel1M 384385 CTCACATCCCTTCCAACATTTGTCATTATCTGTTCGTGTCACCTTGTCCA 384434 i iiv i v iiviiv v v ii vv C L1ME5_3end#LI 261 CCCACATCCTCGCCAACACTTGGCATTATCCAGCTTTCTAATTTTTGCCA 212 chr2qtel1M 384435 ATCTGAGAGGT-----ATGGTACCTCAGAGTTGTCTTAATTTGCTTTTCT 384479 i i v -----i i i vv i v C L1ME5_3end#LI 211 GTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATTTCT 162 chr2qtel1M 384480 CTGATCAATAATGATTTAGAGCATTTTTTGTCATATTAGAAATGGCTTT- 384528 i v v v i i -- vvvviv i i - C L1ME5_3end#LI 161 CTGATTACTAATGAGTTTGAGCATCTCT--TCATATGCTTGTTAGCCTTT 114 chr2qtel1M 384529 --AATTTCTTTATCTAAAAAGTATCTGTTCATATCC-TTGATCATTTATC 384575 --ii i iv iv v ii - vi v C L1ME5_3end#LI 113 CGGGTTTCCTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCCATTTTTC 64 chr2qtel1M 384576 AACTGAGG 384583 v i i C L1ME5_3end#LI 63 TATTGGGG 56 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.44 CpG sites = 62, Kimura (unadjusted) = 39.95 Transitions / transversions = 1.51 (62/41) Gap_init rate = 0.03 (11 / 347), avg. gap size = 1.45 (16 / 11) 494 31.29 8.72 1.89 chr2qtel1M 385163 385758 (614242) C L1M2_orf2#LINE/L1 (715) 2576 1941 m_b92s551i7 3424 chr2qtel1M 385163 ATTCCCTTGAC-ATTTGTGACTTTTCGTTCTTCCAGATGAATTTTGTTAG 385211 v i i - i v iii i vv v i ivv v C L1M2_orf2#LIN 2576 ATTGCTTTGGCTATTCGGGGTCTTTTGTGGTTCCATACGAATTTTAGGAT 2527 chr2qtel1M 385212 TATTTTTTC-ATCTCTATAAAGTAATTTC-TTGGCAGTTTGATTGGTATG 385259 ? - i i i - v - i v v v v C L1M2_orf2#LIN 2526 TNTTTTTTCTATTTCTGTGAAG-AATGTCATTGGTATTTTGATAGGGATT 2478 chr2qtel1M 385260 GCACTGAATAAGTAGATTGATTTTGGATAGAATTATTGTTTTTATTATAC 385309 i vv i -i i v vi?ii v iv i C L1M2_orf2#LIN 2477 GCATTGAATCTGTAGATCG-CTTTGGGTAGTATGGNCATTTTAACAATAT 2429 chr2qtel1M 385310 --ATGTTGGCTACCCATGAACACTTGACACTCTTCCAATTTCTTATATAT 385357 -- vi vv v i i ivv i iii v ?i i i vi C L1M2_orf2#LIN 2428 TAATTCTTCCAATCCATGAGCATGGGATATCTTTCCATTTNTTTGTGTCC 2379 chr2qtel1M 385358 AATTATATTTCTGTGAAAAGTATTTTTTAATT----GTGTGGATATAATT 385403 vv vv v v vv i v i ----v i v vv C L1M2_orf2#LIN 2378 TCTTCAATTTCTTTCATCAGTGTTTTATAGTTTTCNTTGTAGAGATCTTT 2329 chr2qtel1M 385404 CCTGGATTTGTCTTGG-CAGGGAGACACCCAAATATTTTATATTGTCTCC 385452 ---- ii -i -i iivvv iv i ii v v i vi C L1M2_orf2#LIN 2328 C----ACCT-CCTTGGTTAAATTTATTCCTAGGTATTTTATTTTTTTTGT 2284 chr2qtel1M 385453 AGGAATTTTGAATGG------------GATTTCTCTTTC---TAGTTCTT 385487 vv v i ------------ i --- v C L1M2_orf2#LIN 2283 AGCTATTGTAAATGGGATTGCTTTCTTGATTTCTTTTTCAGATAGTTCGT 2234 chr2qtel1M 385488 T-----C---------TGCTGATGATTTATATCGGTTTATTTTATGTCCT 385523 ----- --------- iv v i vv v i i C L1M2_orf2#LIN 2233 TGTTGGCGTATAGAAATGCTACTGATTTTTGTATGTTGATTTTGTATCCT 2184 chr2qtel1M 385524 TCCATTTTGCTAAAGTTGTTAAGTGTTTCTTGTAGTTTTTCAGTTGATTC 385573 v v i i i v i v viiv vi? ii v v C L1M2_orf2#LIN 2183 GCAACTTTACTGAATTCGTTTATCAGTTCTAANAGTTTTTTGGTGGAGTC 2134 chr2qtel1M 385574 TCTAGAA--TTCTGTAGGTCAG--CATATCATCTTCAAAGCATGG-TAGT 385618 i i?-- i? vi v -- i v - v -i i C L1M2_orf2#LIN 2133 TTTAGGNTTTTCTANATATAAGATCATGTCATCTGCAAA-CAGGGACAAT 2085 chr2qtel1M 385619 TTTGTTTCCTAGTTGTTTACTCTAATTACTTCAATTTCTTTTCTTTTTAC 385668 vii vv viiv i ivi vv iv - i vv C L1M2_orf2#LIN 2084 TTGACTTCCTCCTTTCCAATTTGGATGCCTTTTATTTC-TTTCTCTTGCC 2036 chr2qtel1M 385669 TAA-------AGCTAACATTTCTAGTACAATGTTGCATTATAGTGATGAA 385711 -------i iv i i v v viv i C L1M2_orf2#LIN 2035 TAATTGCTCTGGCTAGGACTTCCAGTACTATGTTGAATAGAAGTGGTGAA 1986 chr2qtel1M 385712 AAT-GGCACCATTGTTTCACCCCTGATCTTACTGGGAATTAGGCTCTC 385758 i - i v i iiii v ? -vi -- i C L1M2_orf2#LIN 1985 AGTGGGCATCCTTGTCTTGTTCCAGNTCTTA-GAGGAA--AGGCTTTC 1941 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.78 CpG sites = 95, Kimura (unadjusted) = 41.97 Transitions / transversions = 1.08 (95/88) Gap_init rate = 0.05 (27 / 595), avg. gap size = 2.37 (64 / 27) 17 22.79 1.89 1.89 chr2qtel1M 386441 386493 (613507) (AAATAA)n#Simple_repeat 1 53 (0) m_b92s252i16 3425 chr2qtel1M 386441 AAATAAAAA-GCTATTAAAAATAAAAATAAAAGACAGAAAGAAAGAAAGA 386489 -ivv v - i i v i v i (AAATAA)n#Sim 1 AAATAAAAATAAAAATAAAAATAAAAATAAAA-ATAAAAATAAAAATAAA 49 chr2qtel1M 386490 AATA 386493 (AAATAA)n#Sim 50 AATA 53 Matrix = Unknown Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.00 (2 / 2) 17 12.81 2.94 0.00 chr2qtel1M 386458 386491 (613509) (AAAG)n#Simple_repeat 1 35 (0) m_b92s252i17 3425 chr2qtel1M 386458 AAATAAA-AATAAAAGACAGAAAGAAAGAAAGAAA 386491 v - vi v (AAAG)n#Simpl 1 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 35 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 398 36.99 8.51 4.91 chr2qtel1M 386970 387933 (612067) MamRTE1#LINE/RTE-BovB 315 1311 (2501) m_b92s601i5 3426 chr2qtel1M 386970 CCCAAGCTATGCAGCCATCTTCTCACTG--GACACAGCAGTGAGATGTAG 387017 i v -ii i iii vv i -- vi iivvi vii MamRTE1#LINE/ 315 CCCAGGATAT-TGGTCGCTTAGTCGCTGANGAGGCAGCAGCACCGTTCGG 363 chr2qtel1M 387018 CAGTTCCCTAGATGTATGAGC--TCTTAAAAAAAAAAAAAATCCCCCCCC 387065 iv? i i v --i i ivvv ii ?viviv v i v i MamRTE1#LINE/ 364 CAGCGNCCTGGGTGTCTGAGCAGCCCTGTTTAGGANCGCGCTGCTCACTC 413 chr2qtel1M 387066 CCCTTTATGAGGAAGGGACCAGAAAAGGTACAATAAAAAT---CTGCTT- 387111 vv--- i ? i i vv vi --- i - MamRTE1#LINE/ 414 CGA---ATGGGGAAGGGNCTAGAAAAGGTGCCCTAAACGTTGCCTGCCTC 460 chr2qtel1M 387112 -----AATCAGCCCTGGCT-----GTCTACCATGGTTGGTGGACCCCA-T 387150 ----- ? iv? ----- vi i ii vi iiiii - MamRTE1#LINE/ 461 GCCAAANTCAAANCTGGCTCACCAGATTATCGCGTCTGGTGGGTTTTANT 510 chr2qtel1M 387151 CCTGTGATAGAAATACAGACACACACACACAAACAGATACATATAAAAAC 387200 i i i iv v? i i v ------- --- v? ?? ---- MamRTE1#LINE/ 511 CTTGCGGTGCAAAANCAAATAGA-------AAAC---TACCNANNA---- 546 chr2qtel1M 387201 TTGTACAAAGATTTCATTCACCATCAGTCCTTGGAATGTGTGCACCATTA 387250 ----- ---v v v iivvi v ii vv v -ii MamRTE1#LINE/ 547 -----CAAAGA---AAATAACCATTGCGTCATGGAACATCAGGAC-GCTA 587 chr2qtel1M 387251 TG-GATAATG----CAGCAAACCT---GAAAGATGGACAGCTCTAGTGGC 387292 - i i ---- iv v --- v i i v v v MamRTE1#LINE/ 588 TGCGATGACGAGAACAGCAGTCGTCCAGAAAGAAGAACGGCACTCGTCGC 637 chr2qtel1M 387293 CAGAGAATT---CAG-TA-GGTGTCT-CATCCAAAAGGCAGCCCTGAGTG 387336 vv v i --- - - v v- ------ v v i MamRTE1#LINE/ 638 ACGTGAACTGTCCAGATACGGAGTCGACATC------GCCGCACTGAGCG 681 chr2qtel1M 387337 AAACAAGGCTGGCAAATAAAGGCCACCTTACTGAAGTCGGAGCTACATAC 387386 v i vv vi i v v i v iiiv v iiv? MamRTE1#LINE/ 682 AAACCAGACTTCCTGATGAAGGACAGCTCACGGAGACAGGTGCCGGNTAC 731 chr2qtel1M 387387 AAGGTTTTCTGCAG-GGAGTGCAGT----GGAGGGGAGCATTGTGAAGTT 387431 ivvv i v - vv v vv ----i v iv -ii v v i i- MamRTE1#LINE/ 732 GCCTTCTTCTGGAGAGGTCTTCCCTCTTCAGAGCGACG-GCTCTCAGGC- 779 chr2qtel1M 387432 GGTATAGGTTAGCAATGAACCAGTT-CAAATCAGCAACCCTGTATGTCTG 387480 - -i v v v iv i- vvi vvv i? iivi vi i MamRTE1#LINE/ 780 -GT-CAGCTTTGCAATCAGACAGTCACTTGTCTCAAGNCTCCCAAATTTG 827 chr2qtel1M 387481 CCAAAAAAGACTTAATGTCAGGCTTATAACAATGCCCTTGGCACCTGTAG 387530 v i iiv - ? i v v v v i vv i v i i- ?i v i MamRTE1#LINE/ 828 CCCAGAGGCA-TNAGTGACCGTCTGATGACCCTACGCCTA-CNTCTGAAA 875 chr2qtel1M 387531 GAAAA-TGCCATGGTTACATGATCAGTGACTATCTTCCCACCATGAGGAA 387579 v -i i? vivv i v i vv vii v MamRTE1#LINE/ 876 CAAAAGCGCTNTGCCACCGTCATCAGCGCATATGCCCCCACCATGACGAA 925 chr2qtel1M 387580 CCTTGATGAGGTCAAAGGAAAATTTTCAGAAGA-CTAGAGATGCTCATCC 387628 ivii vv i i i vvi i - i v vi - MamRTE1#LINE/ 926 TACCGATGAGGAGAAAGAAAGATTCTACAAGGATCTGGACAGACTCAT-C 974 chr2qtel1M 387629 TCAAT-TTGCCAAAAAGAGGACAAGCTTATCTAATCCTGGCTAATTTTAA 387677 v ii-v i - v vvv v --i vi vvi i MamRTE1#LINE/ 975 GCAGCGGTACC-AACATCTGACAAGCTGATC--GTCACGGGAGATTTCAA 1021 chr2qtel1M 387678 GGT---TAT-----ACTAGGCTCAGACAAG--GGAATGTCTTTGGGTGGA 387717 v i--- i -----i v v iv i iv -- i v v i iiv?v MamRTE1#LINE/ 1022 CGCACGTGTCGGCAGCGATGCCGAAACGTGGAGAAAAGTCATCGGACCNC 1071 chr2qtel1M 387718 ATAGGGTTGAAAACAGCAACAGCACTGGTCAGTT----ATTAGTGAAGAT 387763 ii i i vvv? v vii ----v i i vi MamRTE1#LINE/ 1072 ACGGGATTGGAAAGCTNAACAGCAATGGTCTACTCCTGCTCAGCGAATGT 1121 chr2qtel1M 387764 -TTGTGCATCTGAAGACCCT-ATCACCAACACTGT----CGC-------- 387799 -iiiv --- vi v - ii ---- -------- MamRTE1#LINE/ 1122 GCCAAGCATC---AGCTCGTAATCACCAACACCATCTTCCGCCTACCGAA 1168 chr2qtel1M 387800 ----AACAAAATTTCATGCATGCACATTTACAG--CAAACATTGTCATTT 387843 ---- iv i iv v --ii vi --i i v v i MamRTE1#LINE/ 1169 TAAGAGAAAGACATCATGGATGCAC--CCAAGGTCTAAGCAGTGGCATCT 1216 chr2qtel1M 387844 AGTAGACTGTATAATTGTAAGGGGAAGAAAC----AAGATA--GAGAGTG 387887 vi v i i v i vv iviiv ii ---- i i--v - v MamRTE1#LINE/ 1217 CATTGATTATATCATCGTTCGACAGCGGGACCTGAAGGATGTTTAGA-TT 1265 chr2qtel1M 387888 ACAAAGGCCATATGTGATGCAGAATGCTGGAATGATCATAGACTGA 387933 vivi i ii ii v i vi i v v MamRTE1#LINE/ 1266 ACTGCAGCTATGCGTGGCGCCGAGTGCTGGACCGACCATCGCCTGA 1311 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 46.38 CpG sites = 178, Kimura (unadjusted) = 53.88 Transitions / transversions = 1.11 (178/161) Gap_init rate = 0.08 (80 / 963), avg. gap size = 1.64 (131 / 80) 13 14.17 3.23 0.00 chr2qtel1M 388044 388074 (611926) (AATTA)n#Simple_repeat 1 32 (0) m_b92s252i18 3427 chr2qtel1M 388044 AATTAGA-TAATTTTAATTACATTAAATTAAA 388074 i - v v v (AATTA)n#Simp 1 AATTAAATTAAATTAAATTAAATTAAATTAAA 32 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.03 (1 / 30), avg. gap size = 1.00 (1 / 1) 616 30.49 3.40 5.36 chr2qtel1M 388431 389019 (610981) HERVK14C#LTR/ERVK 2845 3422 (4012) m_b92s701i0 3428 chr2qtel1M 388431 TTTTTAGGCAGAGCTGCTGTTGAAGGCCTGCCTGTGCTCTGACCTGTTCC 388480 vivi ii -- - v ------i? i HERVK14C#LTR/ 2845 TTTTTAGGGGCGGCCACTGTTGA--GCCT-CCAG------ANCCTATTCC 2885 chr2qtel1M 388481 CATTCAATGTAAAACTAATACAACAGTGTTGGTAGAACAGTGGCCCTTGA 388530 v vv v ?i iv v v?v ? v v ? ? vi ?? HERVK14C#LTR/ 2886 CTTAAAATGGANGACCCAAAANCCNGTTTGGGTNGANCAGTGGCCGCTNN 2935 chr2qtel1M 388531 CT-AGTCAAAAAATTCAAGAATGATTAGATG---TAGTACAGGAACAACT 388576 - --i i vii ivi-- v v --- vv i i HERVK14C#LTR/ 2936 CTCAG--GAAAAACTGGGGGCC--TTACAGGAATTAGTCAAAGAACAATT 2981 chr2qtel1M 388577 TCAGCAAGGTCGTTTA----CAACATTCTCTAAGTCTTCGGAATTCTCCT 388622 vv ?v v iiv ?---- v i ---- i?i ? v HERVK14C#LTR/ 2982 AGANAAAGGACACATNGAGCCCACATTTTCT----CCNTGGAATTCNCCA 3027 chr2qtel1M 388623 GTATTTGCTATAAAAAAGAAATCTGGAAAATGGAGGATGGT-ACTGATTT 388671 i iv ? i i i v i v ? v - i i HERVK14C#LTR/ 3028 GTGTTTGTAATNAAGAAAAAATCCGGCAGATGGCGNATGCTAACCGACTT 3077 chr2qtel1M 388672 GAGAAAAGCAAATGAACAG--ATGGAAATAATAGGAACATTTTAGCTA-G 388718 iv ivv iv -- -- ?v vi? i ii ?i vi i - HERVK14C#LTR/ 3078 ACGAGCCGTCAATG--CAGTCATNCAACCNATGGGGGCNCTGCAGCCAGG 3125 chr2qtel1M 388719 ACTTCCATGCCCTACTCAGTTGCCTAGAGAATGGCCTCTTTGGGTAATAC 388768 i v ? v ii ivv v v v ?i vvvi v - HERVK14C#LTR/ 3126 GCTGCCNTCCCCCGCCATGATTCCTAGAGACTGGCCNTTAATAGTTATA- 3174 chr2qtel1M 388769 ACAATT--AAGTATTGTTTCCATTCTATCCCTCTAGTTAAGAAGGATATG 388816 --i -- v i i iv v i ivi vv? v v HERVK14C#LTR/ 3175 --GATTTGAAGGACTGCTTCTTTACTATTCCTCTAGCAGAGCCNGATTTT 3222 chr2qtel1M 388817 AAAAGGTTTGACTTTTTAGTGT--CTGGCATTAGT--TTAGCTGAGCTTT 388862 i ii --i v i -- vi v ii--iv -- i i?v HERVK14C#LTR/ 3223 GAAAAATTTG--CTTTTACTATTCCTGCTATGAACAACAAG--GAACCNG 3268 chr2qtel1M 388863 ATAAAAGATATGAATAGGTAGTTTTACCACAGGGAATGAAAAATAGTCCT 388912 vvivv ? v v i iv ? i i v vvi ? HERVK14C#LTR/ 3269 CAGCCAGNTATCATTGGAAAGTNTTGCCGCAGGGCATGTTGAATAGTCCN 3318 chr2qtel1M 388913 ACTATGTGTCAAATGTTTATGATTGCTGCTATT-ATTCTAGTAAGAAAAG 388961 ? v iv ? i ivv?vv - vi - ? i vv HERVK14C#LTR/ 3319 ACNATTTGTCAAACTTNTGTGGGGNAGGCTATTCAACCT-GTNAGAGATC 3367 chr2qtel1M 388962 CATTTCCAAAAGTA-ATATTATTACATTTCATGGATGATATCTTGAGGTG 389010 vi i vvi?- i - vi i v ---? HERVK14C#LTR/ 3368 AGTTTCCAGATTCNTATATCATT-CATTATATGGATGACATATT---NTG 3413 chr2qtel1M 389011 TGCACCTGA 389019 iv i HERVK14C#LTR/ 3414 TGCGGCCGA 3422 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.34 CpG sites = 83, Kimura (unadjusted) = 42.61 Transitions / transversions = 0.95 (83/87) Gap_init rate = 0.07 (42 / 588), avg. gap size = 1.21 (51 / 42) 635 32.33 3.10 3.50 chr2qtel1M 388504 389019 (610981) HERVK14#LTR/ERVK 2662 3175 (2921) m_b92s701i1 3428 chr2qtel1M 388504 CAGTGTTGGTAGAACAGTGGCCCTTGAC-TAGTCAAAAAATTCAAGAATG 388552 i v v i i i vi v-i --i i vi iv - HERVK14#LTR/E 2662 CGGTTTGGGTGGAGCAATGGCCGCTGAAACAG--GAAAAACTGGAGGCT- 2708 chr2qtel1M 388553 ATTAGATG---TAGTACAGGAACAACTTCAGCAAGGTCGTTTACAACATT 388599 - i v --- i i i v iv i v i v v i v v HERVK14#LTR/E 2709 -TTAAAAGAACTGGTGCAGGAACAATTGCAAAAGGGACATATAGAGCCTA 2757 chr2qtel1M 388600 CTCTAAGTCTTCGGAATTCTCCTGTATTTGCTATAAAAAAGAAATCTGGA 388649 i vvvi i i ii v i i v i HERVK14#LTR/E 2758 CTTTCTCCCCTTGGAATTCTCCTGTATTTGTCATTAAGAAAAAATCAGGG 2807 chr2qtel1M 388650 AAATGGAGGATGGT-ACTGATTTGAGAAAAGCAAATGAACAGATGGAAAT 388698 i v - v i iivv iv vvvv vv vi HERVK14#LTR/E 2808 AAATGGAGAATGTTAACAGATTTAAGGGCTGTTAATGCTGTGATTCAACC 2857 chr2qtel1M 388699 AATAGGAACATTTTAGCTA-GACTTCCATGCCCTACTCAGTTGCCTAGAG 388747 v i vi i vi i i - i v v v v vvv v v v i v HERVK14#LTR/E 2858 CATGGGTGCACTGCAACCAGGGCTGCCCTCCCCAACAATGATCCCAAAAT 2907 chr2qtel1M 388748 AATGGCCTCTTTGGGTAATACACAATTAAGTATTGTTTCCATTCTATCCC 388797 v ivvi i v i-v v v i iiv v i i HERVK14#LTR/E 2908 ACTGGCCTCTCATAGTGATAGAT-CTAAAGGATTGCTTTTTTACCATTCC 2956 chr2qtel1M 388798 TCTAGTTAAGAAGGA-TATGAAAAGGTTTGACTTTTTAGTGT--CTGGCA 388844 i i ivvv i - -i --i v -- i v HERVK14#LTR/E 2957 TTTAGCTGCCCAAGATTATGAAAA-ATTTG--CTTTTACTGTTCCCGCCA 3003 chr2qtel1M 388845 TTAGT--TTAGCTGAGCTTTATAAAAGATATGAATAGGTAGTTTTACCAC 388892 v i -- v i-- i ivvvvi v iv v i iv vi HERVK14#LTR/E 3004 TAAATAATAAA--GAACCAGCGGACAGATACCATTGGAAAGTACTACCAC 3051 chr2qtel1M 388893 AGGGAATGAAAAATAGTCCTACTATGTGTCAAATGTTTATGATTGCT--- 388939 i v vv i v v --i - i vv--- HERVK14#LTR/E 3052 AAGGCATGCTAAATAGCCCGACTATTTGTCAAA--CTTATG-TCGGGAAA 3098 chr2qtel1M 388940 GCTATTATTCTAGTAAGAAAAGCATTTCCAAAA--GTAATATTATTACAT 388987 vv i v i - v iv -- v i- HERVK14#LTR/E 3099 GCTATTAAGCCAGTTAGAGAA-CAGTTTAAAAAATGTTATATTATC-CAT 3146 chr2qtel1M 388988 TTCATGGATGATATCTTGAGGTGTGCACCTGA 389019 v ii --- v HERVK14#LTR/E 3147 TACATGGATGATATTCT---GTGTGCAGCTGA 3175 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.72 CpG sites = 76, Kimura (unadjusted) = 42.74 Transitions / transversions = 0.89 (76/85) Gap_init rate = 0.05 (27 / 515), avg. gap size = 1.26 (34 / 27) 12 24.48 0.00 8.77 chr2qtel1M 389442 389503 (610497) (GAGTCA)n#Simple_repeat 1 57 (0) m_b92s252i19 3429 chr2qtel1M 389442 GAGTCAGTAGATGAGATTGAGAGCCAGAAATCAGTTGGGAGATTCAGAGC 389491 - - v v v i - i -v vv v i (GAGTCA)n#Sim 1 GAGTCAG-AG-TCAGAGTCAGAGTCAG-AGTCAG-AGTCAGAGTCAGAGT 46 chr2qtel1M 389492 CAGGATTCAGAG 389503 - v (GAGTCA)n#Sim 47 CA-GAGTCAGAG 57 Matrix = Unknown Transitions / transversions = 0.38 (3/8) Gap_init rate = 0.08 (5 / 61), avg. gap size = 1.00 (5 / 5) 18 8.72 0.00 0.00 chr2qtel1M 389816 389840 (610160) (T)n#Simple_repeat 1 25 (0) m_b92s252i20 3430 chr2qtel1M 389816 TTTCTTCTTTTTTTTTTTTTTTTTT 389840 i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 13 7.81 7.41 0.00 chr2qtel1M 390404 390430 (609570) (AGG)n#Simple_repeat 1 29 (0) m_b92s252i21 3431 chr2qtel1M 390404 AGG-GGAGGAGGTGGAGG-GAAGGAGGAG 390430 - v - i (AGG)n#Simple 1 AGGAGGAGGAGGAGGAGGAGGAGGAGGAG 29 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.08 (2 / 26), avg. gap size = 1.00 (2 / 2) 344 23.48 3.03 9.68 chr2qtel1M 391125 391223 (608777) MIRc#SINE/MIR 35 127 (141) m_b92s601i6 3432 chr2qtel1M 391125 CCTGAAGTCAGGAGGACCTGAGTTCAAATCTGACCTCAGACACTTAATAC 391174 i i i i i i iviv v v ---- MIRc#SINE/MIR 35 CTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTA---- 80 chr2qtel1M 391175 TTCTTATGTGTGTAATCATAGGCAAGTCACTTAA---CTCCAATTGCCTC 391221 ---i vv i i v i --- ii -- MIRc#SINE/MIR 81 ---CTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGA--GCCTC 125 chr2qtel1M 391222 AG 391223 MIRc#SINE/MIR 126 AG 127 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 25.68 CpG sites = 14, Kimura (unadjusted) = 28.85 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.10 (10 / 98), avg. gap size = 1.20 (12 / 10) 13 18.66 2.08 6.52 chr2qtel1M 391433 391480 (608520) (AAGAA)n#Simple_repeat 1 46 (0) m_b92s252i22 3433 chr2qtel1M 391433 AAGAAAAG-TCAGATCATAAAGGGAAAAAAAAGAGAAAAGAAAACGAAA 391480 -vv vv v -i i - - (AAGAA)n#Simp 1 AAGAAAAGAAAAGAAAAGAAA-AGAAAAGAAA-AGAAAAGAAAA-GAAA 46 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.09 (4 / 47), avg. gap size = 1.00 (4 / 4) 218 27.98 9.65 5.93 chr2qtel1M 392582 392695 (607305) MIR3#SINE/MIR 68 185 (23) m_b92s601i7 3434 chr2qtel1M 392582 CTGCCACACAGAAATGGC-ATG-AACTTTGAGCCAATTAGTTCACT---- 392625 ---v v ? -i -i i i v i i v i---- MIR3#SINE/MIR 68 CTGCCAC---TAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTC 114 chr2qtel1M 392626 ---GCTTGAGTTTCCTC--TTGTAAATTGGGGAGGATTGGTTGTATTCTT 392670 --- i v --i v i i v v ii iv ---- MIR3#SINE/MIR 115 TGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGAT---- 160 chr2qtel1M 392671 GAATTCTGAAGTGACTTTCAGCTCT 392695 vi i i vv i MIR3#SINE/MIR 161 GATCTCTAAGGTCCCTTCCAGCTCT 185 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.57 CpG sites = 18, Kimura (unadjusted) = 36.57 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.11 (12 / 113), avg. gap size = 1.50 (18 / 12) 20 8.14 2.33 4.76 chr2qtel1M 393292 393334 (606666) (TTGTT)n#Simple_repeat 1 42 (0) m_b92s252i26 3435 chr2qtel1M 393292 TTGTTTTTGTTTTTGTTTTGTTTTG-TTTGTTTGTTTTTGTATT 393334 - - - vv v (TTGTT)n#Simp 1 TTG-TTTTG-TTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTT 42 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.07 (3 / 42), avg. gap size = 1.00 (3 / 3) 207 22.64 8.62 8.62 chr2qtel1M 396473 396588 (603412) MIR3#SINE/MIR 85 200 (8) m_b92s601i8 3436 chr2qtel1M 396473 TATGGCCTGTGGG-AAATC-CTTG--CTCTCTG--TTTCTGTTTCC--AT 396514 i i - - i - v-- --ii v -- MIR3#SINE/MIR 85 TGTGACCT-TGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCAT 133 chr2qtel1M 396515 CTATAAAGTGGAAGGGATTGGACTCTACTTCTAGAGGGTCTTTCAGCTCC 396564 i i - i i -------- v i i v v MIR3#SINE/MIR 134 CTGTAAAATG-AGGGGGTTGGA--------CTAGATGATCTCTAAGGTCC 174 chr2qtel1M 396565 ATGTC--TTCTGACTTTTGATGCTTC 396588 v vi --i v iv v MIR3#SINE/MIR 175 CTTCCAGCTCTGACATTCTATGATTC 200 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 27.42 CpG sites = 14, Kimura (unadjusted) = 27.42 Transitions / transversions = 1.40 (14/10) Gap_init rate = 0.14 (16 / 115), avg. gap size = 1.25 (20 / 16) 14 22.17 4.26 0.00 chr2qtel1M 397366 397412 (602588) (ATCTCC)n#Simple_repeat 1 49 (0) m_b92s252i27 3437 chr2qtel1M 397366 ATGTCCAACTTC-TCTCCATCTTCATCTCTAACT-GATTTCCATGTCCA 397412 v v i - i i v -v i v (ATCTCC)n#Sim 1 ATCTCCATCTCCATCTCCATCTCCATCTCCATCTCCATCTCCATCTCCA 49 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.04 (2 / 46), avg. gap size = 1.00 (2 / 2) 219 33.33 4.30 0.00 chr2qtel1M 397649 397741 (602259) MIR3#SINE/MIR 109 205 (3) m_b92s601i9 3438 chr2qtel1M 397649 CCTCTGTGAATCTCGATTTCC-CATCTACAAAATGAATAGATCGCCCTCC 397697 v iii ii - ii ivi i i vv vv MIR3#SINE/MIR 109 CCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAG 158 chr2qtel1M 397698 ATGGCCCTGTAGGTCCCTTTCAGTGCT--C-CTCTGCGATCCTATAA 397741 ii iivv i iv -- -i ii i i MIR3#SINE/MIR 159 ATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTATGA 205 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 47.56 CpG sites = 22, Kimura (unadjusted) = 47.56 Transitions / transversions = 2.44 (22/9) Gap_init rate = 0.03 (3 / 92), avg. gap size = 1.33 (4 / 3) 296 29.88 10.05 5.24 chr2qtel1M 398095 398313 (601687) C MIRc#SINE/MIR (26) 242 14 m_b92s601i10 3439 chr2qtel1M 398095 TAGCATTTTTATAGCT--CTGAGTGCCATGCTTTGCAATGTCTTATTTCA 398142 i - i i -- vi i iv vviv i v i i v C MIRc#SINE/MIR 242 TAGCACTTT-ACAGTTTACAAAGCGCTTTCACATACATTATCTCATTTGA 194 chr2qtel1M 398143 TCCTCATAAGAATCC---AA---AGACTTGGCTGCTATTATTATGCCCA- 398185 i v i ---i --- i vv v v v - C MIRc#SINE/MIR 193 TCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCAT 144 chr2qtel1M 398186 TTTACAAGATAAAAAGAAACTATGAATCCAACTTGAAGTT---CTACTTA 398232 - --i i iv iv vi --- i ---iv i C MIRc#SINE/MIR 143 TTTAC-AGAT--GAGGAAACTGAGGCTCAGA---GAGGTTAAGTGACTTG 100 chr2qtel1M 398233 TT-----TCACACCACTAG---GT-TCTGAGGTGGGATTAAAACGCTGGG 398273 ii----- vi --- -v v vi i vi - ii C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAAC-CCAGG 51 chr2qtel1M 398274 CTTTACTGA-TTCAAGCCCTATCCACATTCTATCCACTGTA 398313 ii v - i i vi v ---- v i C MIRc#SINE/MIR 50 TCTTCCTGACTCCAAGTCCAGTGC----TCTTTCCACTGCA 14 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.88 CpG sites = 36, Kimura (unadjusted) = 39.30 Transitions / transversions = 1.38 (36/26) Gap_init rate = 0.10 (21 / 218), avg. gap size = 1.62 (34 / 21) 318 27.17 7.98 7.98 chr2qtel1M 398126 398313 (601687) C MIRb#SINE/MIR (64) 204 17 m_b92s601i11 3439 chr2qtel1M 398126 TGCAATGTCTTATTTCATCCTCATAAGAATCCAAAGACTTGGCTGCTATT 398175 v i i v i v i viv --- iv v C MIRb#SINE/MIR 204 TGCATTATCTCATTTAATCCTCACAACAACCCTGCGA---GGTAGGTATT 158 chr2qtel1M 398176 ATTATGCCCA-TTTACAAGATAAAAAGAAACTATGAATCCAACTTGAAGT 398224 v - - --i i iv iv vi --- i C MIRb#SINE/MIR 157 ATTATCCCCATTTTAC-AGAT--GAGGAAACTGAGGCTCAGA---GAGGT 114 chr2qtel1M 398225 T---CTACTTATT-----TCACACCACTAG---GT-TCTGAGGTGGGATT 398262 ---iv iii----- vi --- -v v vi C MIRb#SINE/MIR 113 TAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATT 64 chr2qtel1M 398263 AAAACGCTGGGCTTTACTGATTC--AAGCCCTATCCACATTCTATCCACT 398310 vi v v v v - i -- ----- iiii v C MIRb#SINE/MIR 63 CGAACCCAGGTCTGT-CTGACTCCAAAGC-----CCGTGCTCTTTCCACT 20 chr2qtel1M 398311 GTA 398313 i C MIRb#SINE/MIR 19 GCA 17 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.64 CpG sites = 25, Kimura (unadjusted) = 34.25 Transitions / transversions = 1.14 (25/22) Gap_init rate = 0.11 (21 / 187), avg. gap size = 1.43 (30 / 21) 25 9.40 0.00 0.00 chr2qtel1M 400097 400131 (599869) (TG)n#Simple_repeat 1 35 (0) m_b92s252i28 3440 chr2qtel1M 400097 TGTGTGTGTGTGTGTGTGTGTGTATGTGCATGTGT 400131 i ii (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 35 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 13 18.28 2.56 2.56 chr2qtel1M 400150 400188 (599812) (TTTC)n#Simple_repeat 1 39 (0) m_b92s252i29 3441 chr2qtel1M 400150 TTTGTTTTATTATTTGCTGT-TTTCTTTCTTTGTTTCTTT 400188 v iv v - v - v (TTTC)n#Simpl 1 TTTCTTTCTTTCTTT-CTTTCTTTCTTTCTTTCTTTCTTT 39 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2) 15 17.52 7.69 0.00 chr2qtel1M 402233 402271 (597729) (AT)n#Simple_repeat 1 42 (0) m_b92s252i30 3442 chr2qtel1M 402233 ATACATAT-TAAATATAT-TAAATGCA-ATATATATATACAT 402271 i - v - v ii - i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATAT 42 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.08 (3 / 38), avg. gap size = 1.00 (3 / 3) 911 26.82 4.73 2.91 chr2qtel1M 402679 403016 (596984) C L1ME5_3end#LINE/L1 (471) 470 127 m_b92s551i8 3443 chr2qtel1M 402679 GCCACTACAAAAAGGGATGCCACAAACATTTTTGCACATAACAGGTCCTT 402728 i v iv v v ii ii i i ----- ii C L1ME5_3end#LI 470 GCCACCACAAACAACGCTGCAATGAACATCCTCGTACAT-----GTCCCC 426 chr2qtel1M 402729 TTC----CCTTCTTTAAAATCTCTTTGGGCTATAAGCCCAGTAGTAACAC 402774 v---- viv v i i v vi v iiiv i C L1ME5_3end#LI 425 TTATGGACCTGTGTGAGAATTTCTTTGGGATATATACCCAGGAGCGGAAT 376 chr2qtel1M 402775 TGCTGGGTATGCACAG--TTTG---ATAGTTT-TTTGAGCA--TAATTCC 402816 --- i -- v --- v v- vi -- v v C L1ME5_3end#LI 375 TGCTGGGT---CATAGGGTATGCGTATACTTAATTTGACTAAGTACTGCC 329 chr2qtel1M 402817 AAATTCCTCTCCAAAATGGCTGGATGTATTCACAATTTCACCAACAATGT 402866 i v i v ivvi ii v ii i i i C L1ME5_3end#LI 328 AGATTGCTCTCCAGAATGGCTGCACCAGTCTACACTCCCACCAGCAGTGC 279 chr2qtel1M 402867 ATCAGTGTCCCAGTTTTCCTTTACCCTT-CCAACATTCTGCATTATCT-- 402913 v v i vi ? i ivi i i- i iv i-- C L1ME5_3end#LI 278 ATGAGGGTTCCTATNTCCCCACATCCTCGCCAACACTTGGCATTATCCAG 229 chr2qtel1M 402914 -TTCCTGTCATTCTAGCTAATCTGACAGGTGTGTAGTGGTATCTCAGAGT 402962 - i i-- i v i i i i iv i vv C L1ME5_3end#LI 228 CTTTCTA--ATTTTTGCCAGTCTAATAGGTGTAAAGTGATATCTCATTGT 181 chr2qtel1M 402963 TGTCTTAATTTGCATTTCTCTGATTAATAATGTCTTGGAGCATCTTTTCA 403012 i v vv v i C L1ME5_3end#LI 180 TGTTTTAATTTGCATTTCTCTGATTACTAATGAGTTTGAGCATCTCTTCA 131 chr2qtel1M 403013 TATG 403016 C L1ME5_3end#LI 130 TATG 127 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.68 CpG sites = 52, Kimura (unadjusted) = 34.16 Transitions / transversions = 1.44 (52/36) Gap_init rate = 0.05 (18 / 337), avg. gap size = 1.44 (26 / 18) 1138 25.86 3.18 6.77 chr2qtel1M 403568 404102 (595898) C L1ME3C_3end#LINE/L1 (347) 523 7 m_b92s551i9 3444 chr2qtel1M 403568 ACAATTTACTTTTACAACCATTCTCCAGTTGATGG-CATC--GATTCATT 403614 -- i-- v - i-- i v--- C L1ME3C_3end#L 523 ACAATTTA--TTTAT--CCATTCTCCTGTTGATGGACATTTAGGTTG--- 481 chr2qtel1M 403615 TTTTCAGTTTCTAGCCACCACAAACAGGGCTGCCACAAACATT-TGGCAC 403663 i i i v i ii iv v ii - v i C L1ME3C_3end#L 480 TTTCCAATTTTTCGCTATTACAAACAATGCTGCAATGAACATTCTTGTAC 431 chr2qtel1M 403664 ATGGAATTCTACTTT--CACACTTCTTTAGTATTGATATCTCTTTTGGAG 403711 ---- v v-- ------- ii- v vi ii i i i C L1ME3C_3end#L 430 ATG----TCTCCTTGTGCACAC-------GTGC-GAGAGTTTCTCTAGGG 393 chr2qtel1M 403712 TATAAGCCCAGTAGTAGCACTGCTGGGTAG--AAATATGCATAGTTTGAT 403759 vi i v i v i v --iii ii vi --i C L1ME3C_3end#L 392 TATATACCTAGGAGTGGAATTGCTGGGTCGTAGGGTATGCGCATCTT--C 345 chr2qtel1M 403760 AACTTT-TTAGGCATAATTCCAGATTGCTCTC-AGAATGGTTGTGGATTT 403807 -i -- v v i - i i -- iiv C L1ME3C_3end#L 344 AACTTTACTAG--ATATTGCCAAATTGCTCTCCAAAGTGGTTGT--ACCA 299 chr2qtel1M 403808 ATTCACAACTCACAACAGAAGTACATCAGTGTCCCAGTTTTCCCACATCC 403857 i - v v v ii v v i v vii C L1ME3C_3end#L 298 ATTTACA-CTCCCACCAGCAGTGTATGAGAGTTCCCGTTGCTCCACATCC 250 chr2qtel1M 403858 CCTCCAACATTCATCATTATT---TTTTCCTGTCTTCTTAGCCAATCTGA 403904 i v i iivi i i---i -- ivv i - C L1ME3C_3end#L 249 TCGCCAACACTTGGTATTGTCAGACTTT--TAAATTTTT-GCCAATCTGA 203 chr2qtel1M 403905 CAGATGTGTAGTGGTATCTCAGAGTTGTGTTA-TTTGCATTTCTCTGATT 403953 ii i v i vv ? v - i C L1ME3C_3end#L 202 TGGGTGTGAAATGGTATCTCATTGTNGTTTTAATTTGCATTTCCCTGATT 153 chr2qtel1M 403954 AATAGTGATTTGGAACACTCTTTCATATG---AATGGTAATAGTTGCAAT 404000 v vv v i iii --- v iv -- i ?i- C L1ME3C_3end#L 152 ACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCAT--TCGNG-T 106 chr2qtel1M 404001 TTCATCATCTGAAAATTGTCTGTTCATATCCTTTGACCATTTATCAATTA 404050 v v vi i i v v v - C L1ME3C_3end#L 105 TTCCTCTTCTGTGAATTGCCTGTTCATATCTTTTGCCCATTTTTCTATT- 57 chr2qtel1M 404051 GAGAGTGGGTTGATTTCTTATAAATTAGAGTCAATTCTCTATATATTTTG 404100 -- i v vi v vi v vivv i i i C L1ME3C_3end#L 56 --GGGTTGTCTGTTTTCTTATTGATTTGTAGGAGTTCTTTATATATTCTG 9 chr2qtel1M 404101 GA 404102 C L1ME3C_3end#L 8 GA 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 31.59 CpG sites = 76, Kimura (unadjusted) = 32.50 Transitions / transversions = 1.43 (76/53) Gap_init rate = 0.08 (45 / 534), avg. gap size = 1.16 (52 / 45) 300 30.63 2.84 5.07 chr2qtel1M 403959 404240 (595760) C L1M3_orf2#LINE/L1 (0) 3288 3013 m_b92s551i10 3444 chr2qtel1M 403959 TGATTTGGAACACTCTTTCATATGAATGGTAAT-AGTTGCAATTTCATCA 404007 v v i iii ivv v iii- v i - v v v C L1M3_orf2#LIN 3288 TGATGTTGAGCATCTTTTCATATACCTGTTGGCCATTTGTA-TGTCTTCT 3240 chr2qtel1M 404008 TCTGAAAATTGTCTGTTCATATCCTTTGACCATTTATCAATTAGAGAGTG 404057 iv i v i vi v v ? ii --- v C L1M3_orf2#LIN 3239 TTGGAGAAATGTCTATTCAGGTCCTTTGCCCATTTTTNAATCGG---GTT 3193 chr2qtel1M 404058 GGTTGATTTCTTA----TAAATTAGAGTCAATTCTCTATATATTTTGGAA 404103 iv v i i---- i i iv ?v- i ii v C L1M3_orf2#LIN 3192 ATTTGTTTTTTTGCTATTGAGTTGTANG-AGTTCCTTATATATTTTGGAT 3144 chr2qtel1M 404104 ATGAAGGCCTTTTATCAGAACCTTTA-ACTGTGAGGGTGTATTTTCCCAA 404152 v -- ii --- v -iv v viii i v i v C L1M3_orf2#LIN 3143 ATTAA--CCCCTTATCAGA---TATATGGTTTGCAAATATTTTCTCCCAT 3099 chr2qtel1M 404153 TTTATTGCTTCCCCTTCTAATCTTGTT--TTGCATTAGTTTTGTTTGTAC 404200 iii v v v i ii v - -- -- vvi -i i C L1M3_orf2#LIN 3098 TCCGTAGGTTGCCTTTTCACTC-TGTTGATTG--TTTCCTTTG-CTGTGC 3053 chr2qtel1M 404201 AAAGGCTTTTTAATTTGATGTAATCAAAATTTTCTATTTT 404240 i i i i vv v v C L1M3_orf2#LIN 3052 AGAAGCTTTTTAGTTTGATGTAGTCCCACTTGTCTATTTT 3013 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.18 CpG sites = 45, Kimura (unadjusted) = 40.60 Transitions / transversions = 1.22 (45/37) Gap_init rate = 0.06 (18 / 281), avg. gap size = 1.22 (22 / 18) 323 29.28 0.00 1.63 chr2qtel1M 403998 404122 (595878) C L1P3_orf2#LINE/L1 (39) 3255 3133 m_b92s551i11 3444 chr2qtel1M 403998 AATTTCATCATCTGAAAATTGTCTGTTCATATCCTTTGACCATTTATCAA 404047 v v v i i v i v i v ii C L1P3_orf2#LIN 3255 AATGTCTTCTTTTGAGAAGTGTCTGTTCATATCCTTCGCCCACTTTTTGA 3206 chr2qtel1M 404048 TTAGAGAGTGGGTTGATTTCTTATAAATTAGAGTCAATTCTCTATATATT 404097 vi ivv vv vv i v vv v i ii i v C L1P3_orf2#LIN 3205 TGGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTAAGTTCCTTGTAGATT 3156 chr2qtel1M 404098 TTGGAAATGAAGGCCTTTTATCAGA 404122 i v v -- i i C L1P3_orf2#LIN 3155 CTGGATATTA--GCCCTTTGTCAGA 3133 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.06 CpG sites = 16, Kimura (unadjusted) = 37.31 Transitions / transversions = 0.80 (16/20) Gap_init rate = 0.02 (2 / 124), avg. gap size = 1.00 (2 / 2) 16 15.86 0.00 0.00 chr2qtel1M 404731 404758 (595242) (A)n#Simple_repeat 1 28 (0) m_b92s252i31 3445 chr2qtel1M 404731 AATAAAAAAAAAAAAGAAATTAAAAAAA 404758 v i vv (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA 28 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 20 8.14 2.33 4.76 chr2qtel1M 409629 409671 (590329) (TTGTT)n#Simple_repeat 1 42 (0) m_b93s252i2 3446 chr2qtel1M 409629 TTGTTTTTGTTTTTGTTTTGTTTTG-TTTGTTTGTTTTTGTATT 409671 - - - vv v (TTGTT)n#Simp 1 TTG-TTTTG-TTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTT 42 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.07 (3 / 42), avg. gap size = 1.00 (3 / 3) 18 4.30 0.00 4.00 chr2qtel1M 412162 412187 (587813) (AT)n#Simple_repeat 1 25 (0) m_b93s252i3 3447 chr2qtel1M 412162 ATATCATATAAATATATATATATATA 412187 - v (AT)n#Simple_ 1 ATAT-ATATATATATATATATATATA 25 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.04 (1 / 25), avg. gap size = 1.00 (1 / 1) 181 20.28 12.31 1.39 chr2qtel1M 412800 412864 (587136) MIR3#SINE/MIR 85 156 (52) m_b93s601i0 3448 chr2qtel1M 412800 TATGGCCT-GTGGAAATC-CTTG--CTCTCTG--TTTCTGTTTCC--ATC 412841 i i - v v i - v-- --ii v -- MIR3#SINE/MIR 85 TGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATC 134 chr2qtel1M 412842 TATAAAGTGGAAGGGATTGGACT 412864 i i - i i MIR3#SINE/MIR 135 TGTAAAATG-AGGGGGTTGGACT 156 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.40 CpG sites = 9, Kimura (unadjusted) = 24.40 Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.09 (6 / 64), avg. gap size = 1.50 (9 / 6) 236 34.04 3.19 0.00 chr2qtel1M 413989 414082 (585918) MIR3#SINE/MIR 109 205 (3) m_b93s601i1 3449 chr2qtel1M 413989 CCTCTGTGAATCTCGATTTCC-CATCTACAAAATGAATAGATCGCCCTCC 414037 v iii ii - ii ivi i i vv vv MIR3#SINE/MIR 109 CCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAG 158 chr2qtel1M 414038 ATGGCCCTGTAGGTCCCTTTCAGTGCT--CCCTCTGCGATCCTATAA 414082 ii iivv i iv -- vi ii i i MIR3#SINE/MIR 159 ATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTATGA 205 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 48.70 CpG sites = 22, Kimura (unadjusted) = 48.70 Transitions / transversions = 2.20 (22/10) Gap_init rate = 0.02 (2 / 93), avg. gap size = 1.50 (3 / 2) 254 29.66 11.01 5.68 chr2qtel1M 414440 414657 (585343) C MIRc#SINE/MIR (26) 242 14 m_b93s601i2 3450 chr2qtel1M 414440 TAGCATTTTATAGCT--CTGAGTGCCATGCTTTGCAATGTCTTATTTCAT 414487 i i i -- vi i iv vviv i v i i v C MIRc#SINE/MIR 242 TAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATCTCATTTGAT 193 chr2qtel1M 414488 CCTCATAAGAATCC----A---AGGCTTGGC-TTTATTATTATGCCCA-T 414528 i v i ---- --- vv -vv v - C MIRc#SINE/MIR 192 CCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATT 143 chr2qtel1M 414529 TTACAAGATAAAAAGAAACTATGAATCCAACTTGAAGTT---CTACTTAT 414575 - --i i iv iv vi --- i ---iv ii C MIRc#SINE/MIR 142 TTAC-AGAT--GAGGAAACTGAGGCTCAGA---GAGGTTAAGTGACTTGC 99 chr2qtel1M 414576 T-----TCACACCACTAG---GT-TCAGGG-TGGGATTAAAACGCTGAAA 414615 i----- vi --- -v i -i i vi v -- ii C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCC--AGG 51 chr2qtel1M 414616 CTTTACTGAAAGTTCAAGCCCTATCCACGTCTATCCACTGTA 414657 ii v -- v i i vi v --- v i C MIRc#SINE/MIR 50 TCTTCCTG--ACTCCAAGTCCAGTGC---TCTTTCCACTGCA 14 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.48 CpG sites = 35, Kimura (unadjusted) = 38.90 Transitions / transversions = 1.35 (35/26) Gap_init rate = 0.11 (23 / 217), avg. gap size = 1.61 (37 / 23) 25 9.40 0.00 0.00 chr2qtel1M 416469 416503 (583497) (TG)n#Simple_repeat 1 35 (0) m_b93s252i4 3451 chr2qtel1M 416469 TGTGTGTGTGTGTGTGTGTGTGTATGTGCATGTGT 416503 i ii (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 35 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 15 17.52 7.69 0.00 chr2qtel1M 418605 418643 (581357) (AT)n#Simple_repeat 1 42 (0) m_b93s252i5 3452 chr2qtel1M 418605 ATACATAT-TAAATATAT-TAAATGCA-ATATATATATACAT 418643 i - v - v ii - i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATAT 42 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.08 (3 / 38), avg. gap size = 1.00 (3 / 3) 748 29.87 3.30 1.47 chr2qtel1M 419053 419385 (580615) C L1ME5_3end#LINE/L1 (471) 470 132 m_b93s551i0 3453 chr2qtel1M 419053 GCCACTACAAAAAGGGATGCCACAAACATTTTTGCACATAACAGGTCCTT 419102 i v iv v v ii ii i i ----- ii C L1ME5_3end#LI 470 GCCACCACAAACAACGCTGCAATGAACATCCTCGTACAT-----GTCCCC 426 chr2qtel1M 419103 TTC----CCTTCTTTAAAATCTCTTTGGGCTATAAGCCCAGTAATGCTAC 419148 v---- viv v i i v vi v ii vv i C L1ME5_3end#LI 425 TTATGGACCTGTGTGAGAATTTCTTTGGGATATATACCCAGGAGCGGAAT 376 chr2qtel1M 419149 TACTGGTATACACAGTTTG---ATAGTTT-TTTGAGCA--TAATTCCAAA 419192 i vvi i vi v --- v v- vi -- v v i C L1ME5_3end#LI 375 TGCTGGGTCATAGGGTATGCGTATACTTAATTTGACTAAGTACTGCCAGA 326 chr2qtel1M 419193 TTCCTCTCCAAAATGGCTGGATGTATTCACAATTTCACCAACAATGTATC 419242 v i v ivvi ii v ii i i i v C L1ME5_3end#LI 325 TTGCTCTCCAGAATGGCTGCACCAGTCTACACTCCCACCAGCAGTGCATG 276 chr2qtel1M 419243 AGTGTCCCAGTTTTCCTTTACCCTT-CCAACATTCTGCATTATCTTTCCC 419291 v i vi ? i ivi i i- i iv ivv ii C L1ME5_3end#LI 275 AGGGTTCCTATNTCCCCACATCCTCGCCAACACTTGGCATTATCCAGCTT 226 chr2qtel1M 419292 TGTCATTCTAGCTAATCTGACAGGTGTGTAGTGGTATCTCAGAGTTGTCT 419341 v v i v i i i i iv i vv i C L1ME5_3end#LI 225 TCTAATTTTTGCCAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTT 176 chr2qtel1M 419342 TAATTTGCATTTCTCTGATTAATAATGTCTTGGAGCATCTTTTC 419385 v vv v i C L1ME5_3end#LI 175 TAATTTGCATTTCTCTGATTACTAATGAGTTTGAGCATCTCTTC 132 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.58 CpG sites = 54, Kimura (unadjusted) = 39.10 Transitions / transversions = 1.23 (54/44) Gap_init rate = 0.03 (10 / 332), avg. gap size = 1.60 (16 / 10) 840 25.72 4.12 7.54 chr2qtel1M 419948 420481 (579519) C L1ME3C_3end#LINE/L1 (347) 523 7 m_b93s551i1 3454 chr2qtel1M 419948 ACAATTTACTTTTACAACCATTCTCCAGTTGATGG-CATC--GATTCATT 419994 -- i-- v - i-- i v--- C L1ME3C_3end#L 523 ACAATTTA--TTTAT--CCATTCTCCTGTTGATGGACATTTAGGTTG--- 481 chr2qtel1M 419995 TTTTCAGTTTCTAGCCACCACAAACAGGGCTGCCACAAACATT-TGGCAC 420043 i i i v i ii iv v ii - v i C L1ME3C_3end#L 480 TTTCCAATTTTTCGCTATTACAAACAATGCTGCAATGAACATTCTTGTAC 431 chr2qtel1M 420044 ATGGAATTCTACTTT--CACACTTCTTTAGTATTGATATCTCTTTTGGAG 420091 ---- v v-- ------- ii- v vi ii i i i C L1ME3C_3end#L 430 ATG----TCTCCTTGTGCACAC-------GTGC-GAGAGTTTCTCTAGGG 393 chr2qtel1M 420092 TATAAGCCCAGTAGTAGCACTGCTGGGTAG--AAATATGCATAGTTTGAT 420139 vi i v i v i v --iii ii vi --i C L1ME3C_3end#L 392 TATATACCTAGGAGTGGAATTGCTGGGTCGTAGGGTATGCGCATCTT--C 345 chr2qtel1M 420140 AACTTT-TTAGGCATAATTCCAGATTGCTCTC-AGAATGGTTGTGGATTT 420187 -i -- v v i - i i -- iiv C L1ME3C_3end#L 344 AACTTTACTAG--ATATTGCCAAATTGCTCTCCAAAGTGGTTGT--ACCA 299 chr2qtel1M 420188 ATTCACAACTCACAACAGAAGTACATCAGTGTCCCAGTT-TTCC-CATCC 420235 i - v v v ii v v i v -i - C L1ME3C_3end#L 298 ATTTACA-CTCCCACCAGCAGTGTATGAGAGTTCCCGTTGCTCCACATCC 250 chr2qtel1M 420236 CCTCCAACATTCATCATTATT---TTTTCCTGTCTTCTTAGCCAATCTGA 420282 i v i iivi i i---i -- ivv i - C L1ME3C_3end#L 249 TCGCCAACACTTGGTATTGTCAGACTTT--TAAATTTTT-GCCAATCTGA 203 chr2qtel1M 420283 CAGATGTGTAGTAGTATCTCAGAGTTGT----ATTTGCATTTCTCTGATT 420328 ii i v i i vv ? ---- i C L1ME3C_3end#L 202 TGGGTGTGAAATGGTATCTCATTGTNGTTTTAATTTGCATTTCCCTGATT 153 chr2qtel1M 420329 AATAGTGATTTGGAACACTCTTTCATATG---AATGGTAATAGTTGCAAT 420375 v vv v i iii --- v iv -- i -?i C L1ME3C_3end#L 152 ACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCAT--TCG-NGT 106 chr2qtel1M 420376 TTCATCATCTGAGAATTGTCTGTTCTTCCTTATCCTTTGACCATTTATCA 420425 v v v i ---- v i v v v C L1ME3C_3end#L 105 TTCCTCTTCTGTGAATTGCCTGTT----CATATCTTTTGCCCATTTTTCT 60 chr2qtel1M 420426 ATTAGAGTGGGTTGATTTCTTATAAATTAGAGTCAATTCTCTATATATAT 420475 - i v vi v vi v vivv i i-- C L1ME3C_3end#L 59 ATT-GGGTTGTCTGTTTTCTTATTGATTTGTAGGAGTTCTT--TATATAT 13 chr2qtel1M 420476 TTTGGA 420481 i C L1ME3C_3end#L 12 TCTGGA 7 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 31.36 CpG sites = 75, Kimura (unadjusted) = 32.28 Transitions / transversions = 1.44 (75/52) Gap_init rate = 0.10 (51 / 533), avg. gap size = 1.20 (61 / 51) 243 22.95 0.00 0.00 chr2qtel1M 420829 420889 (579111) L1ME3G_3end#LINE/L1 488 548 (376) m_b93s551i2 3455 chr2qtel1M 420829 ATGCCTATCAGTTGGAGAATGGTTGAATAAATTGTGGTATATGAATGTTG 420878 i i i v i i i vv ii i L1ME3G_3end#L 488 ATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTA 537 chr2qtel1M 420879 TAGAATATTAT 420889 i i L1ME3G_3end#L 538 TGGAATACTAT 548 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 28.96 CpG sites = 11, Kimura (unadjusted) = 28.96 Transitions / transversions = 3.67 (11/3) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 16 22.14 5.56 1.79 chr2qtel1M 422368 422421 (577579) (AT)n#Simple_repeat 1 56 (0) m_b93s252i6 3456 chr2qtel1M 422368 ATAAATATATATGCATATAT-TAGATTTA-AGATATATTTTTACCATAT- 422414 v ii - v v - v v v -i - (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATA-TATATA 49 chr2qtel1M 422415 TTTATAT 422421 v (AT)n#Simple_ 50 TATATAT 56 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.08 (4 / 53), avg. gap size = 1.00 (4 / 4) 204 40.86 1.60 1.06 chr2qtel1M 423207 423394 (576606) L2#LINE/L2 2387 2575 (507) m_b93s601i3 3457 chr2qtel1M 423207 TACATCCAATTACTTATCATACATTTTCAATTAGGTATTTCTTTGATATC 423256 i i i i iivv i i v i i i i vv v ii L2#LINE/L2 2387 TATATCCAACTGCCTACTCGACATCTCCACTTGGATGTCTAATAGGCATC 2436 chr2qtel1M 423257 TCAAATTCGTCATATCCAAAACAAAACCTATTAACTTCCAGC-CAAATCA 423305 i iiv i vi iiv v v vv - i - L2#LINE/L2 2437 TCAAACTTAACATGTCCAAAACTGAACTCCTGATCTTCCCCCTCAAACC- 2485 chr2qtel1M 423306 TATCCCTCTTCCA-TGATCCATACTCCGGTTCA-GATTACTACCACCTTT 423353 iii iiv - vv vi iii i ?v - iiv - i i L2#LINE/L2 2486 TGCTCCTCCCGCAGTCTTCCCCATCTCAGTNAATGGCAACT-CCATCCTT 2534 chr2qtel1M 423354 CTAATAACCCAAATTTAAAGTCCTGTAACATTTCTCAACTC 423394 i i vi i iiiiv ii i v iivv i ii L2#LINE/L2 2535 CCAGTTGCTCAGGCCAAAAACCTTGGAGTCATCCTTGACTC 2575 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 64.82 CpG sites = 52, Kimura (unadjusted) = 66.37 Transitions / transversions = 2.17 (52/24) Gap_init rate = 0.03 (5 / 187), avg. gap size = 1.00 (5 / 5) 16 9.32 0.00 0.00 chr2qtel1M 424111 424133 (575867) (A)n#Simple_repeat 1 23 (0) m_b93s252i7 3458 chr2qtel1M 424111 AAAAAAAAAAAAAATAAAAATAA 424133 v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAA 23 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 22 12.84 0.00 0.00 chr2qtel1M 426711 426744 (573256) (CA)n#Simple_repeat 1 34 (0) m_b93s252i8 3459 chr2qtel1M 426711 CAAACAGACGCACACACACATACACACACACACA 426744 v v i i (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACA 34 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 38 2.55 0.00 0.00 chr2qtel1M 427294 427333 (572667) (TTTG)n#Simple_repeat 1 40 (0) c_b93s251i0 3460 chr2qtel1M 427294 TTTGTTTTTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTG 427333 v (TTTG)n#Simpl 1 TTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTG 40 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 12 12.17 3.70 0.00 chr2qtel1M 430831 430857 (569143) (TTTAT)n#Simple_repeat 1 28 (0) m_b93s252i9 3461 chr2qtel1M 430831 TTTATTAT-TTTTTTTTTATTGTATTTT 430857 v - v v (TTTAT)n#Simp 1 TTTATTTTATTTTATTTTATTTTATTTT 28 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.04 (1 / 26), avg. gap size = 1.00 (1 / 1) 350 30.57 0.64 0.00 chr2qtel1M 431625 431781 (568219) C L1MC4_3end#LINE/L1 (2191) 598 441 m_b93s551i3 3462 chr2qtel1M 431625 TCCATGTTTTT-CTAAAATCTGGAGCTCATCACTTCTTATAGCACAGTAG 431673 ? - vvi? v v i iv i v vv C L1MC4_3end#LI 598 TCCATGTTNTTGCGTGNATCAGTAGTTCATTCCTTTTTATCGCTGAGTAG 549 chr2qtel1M 431674 TATTCCATCATAATCATGTACCACAACTTATGTGATCGTTCCCCAGGTGA 431723 ii vvv ii i v ivi i v v v C L1MC4_3end#LI 548 TATTCCATTGTATGGATGTACCACAGTTTGTTTATCCATTCACCTGTTGA 499 chr2qtel1M 431724 CAGGCATCTCTGCAATTTCTAATTCTTAGCCACCACAAAGAGTGCAGCTA 431773 vi i ?v ivi i i? i i ? ii ii v iv v C L1MC4_3end#LI 498 AGGACATCTNGGTTGTTTCCAGNTTTTGGCNATTATGAATAAAGCTGCTA 449 chr2qtel1M 431774 TGAACATT 431781 i C L1MC4_3end#LI 448 TAAACATT 441 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.90 CpG sites = 26, Kimura (unadjusted) = 41.90 Transitions / transversions = 1.18 (26/22) Gap_init rate = 0.01 (1 / 156), avg. gap size = 1.00 (1 / 1) 418 31.78 5.86 4.55 chr2qtel1M 431671 432148 (567852) C L1ME3A_3end#LINE/L1 (369) 551 68 m_b93s551i4 3462 chr2qtel1M 431671 TAGTATTCCATCATAATCATGTACCACAACTTATGTGATCGTTCCCCAGG 431720 ii ivvv i i v ivi i iv v v C L1ME3A_3end#L 551 TAGTATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTACTGT 502 chr2qtel1M 431721 TGACAGGCATCTCTGCAATTTCTAATTCTTAGCCACCACAAAGAGTGCAG 431770 ii i i vv i?i i i i??i i ii i v v C L1ME3A_3end#L 501 TGATGGACATTTGGGTNGTTTCCAGTTTNNGGCTATTACGAATAGTGCTG 452 chr2qtel1M 431771 CTATGAACATTTTTA---ATGTATTTT-TCAAACATA---ATG--TTTAG 431811 i i--- v -vii --- i -- vv C L1ME3A_3end#L 451 CTATGAACATTCTTGTACATGTCTTTTGGTGAACATATGTACGCATTTCT 402 chr2qtel1M 431812 AATGAGTTGACA-CTAGGATTCCAACATCGATGTTGGAATCCTAGTGTCA 431860 iv i vv i - v vv i----- i -i v v vv C L1ME3A_3end#L 401 GTTGGGTATATACCTAGGAGTGGAAT-----TGCTGG-GTCATAGGGTAT 358 chr2qtel1M 431861 ACTAGAATGGATCCAGTCTTGGT--ATAC--CCAAAGGACTCTGCAAAAT 431906 i ---- ivi i ii i -- -- viii i v i C L1ME3A_3end#L 357 GC----ATATGTTCAGCTTTAGTAGATACTGCCAAACAGTTTTCCAAAGT 312 chr2qtel1M 431907 GGTTGTTTTATTTTACAATTCCCACCAACAAT------TAATTCTTTCTC 431950 vii v - i i i ------v i ----- C L1ME3A_3end#L 311 GGTTGTACCAATTTAC-ACTCCCACCAGCAGTGTATGAGAGTTC-----C 268 chr2qtel1M 431951 AGTTTTTCCACAAGCTCTTCAACATTTGTCACTTTCT---CCTATCACTT 431997 i vi vv vi i vi i v ---ii v i C L1ME3A_3end#L 267 GGTTGCTCCACATCCTCGCCAACACTTGGTATTGTCTGTCTTTTTCATTT 218 chr2qtel1M 431998 TAGACAATGTGGTAAGAGTAAAATGATGTTTCCAAGTAGTTTTAATATGA 432047 v v v ii v iv i i i i? vvv i v v C L1ME3A_3end#L 217 TAGCCATTCTGGTGGGTGTGTAGTGGTATCNCATTGTGGTTTTAATTTGC 168 chr2qtel1M 432048 ATTTCTCTGAT--CTATTATGATGT--AGAACCTTTTAAAAACATGACTA 432093 i -- -- v -- v ---v i vi C L1ME3A_3end#L 167 ATTTCCCTGATGACTA--ATGAAGTTGAGCACCTTTT---CATATGTTTA 123 chr2qtel1M 432094 TAAATTCTTTTGAAT-TCTTCTTTGAAAAACTGTCCATTCATTTCATTTA 432142 vii-i v i - i vivi v i ii vv v i C L1ME3A_3end#L 122 TTGG-CCATTTGGATATCCTCTTTTGTGAAGTGCCTGTTCAAGTCTTTTG 74 chr2qtel1M 432143 TCCATT 432148 i C L1ME3A_3end#L 73 CCCATT 68 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.99 CpG sites = 84, Kimura (unadjusted) = 43.19 Transitions / transversions = 1.38 (84/61) Gap_init rate = 0.07 (34 / 477), avg. gap size = 1.47 (50 / 34) 13 4.17 8.00 0.00 chr2qtel1M 432574 432598 (567402) (ATAC)n#Simple_repeat 1 27 (0) m_b93s252i10 3463 chr2qtel1M 432574 ATACATACATACAT--ATATATACATA 432598 -- i (ATAC)n#Simpl 1 ATACATACATACATACATACATACATA 27 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 24), avg. gap size = 2.00 (2 / 1) 12 16.12 0.00 0.00 chr2qtel1M 434138 434161 (565839) (GAGA)n#Simple_repeat 1 24 (5) m_b93s252i11 3464 chr2qtel1M 434138 GAGAGAGACAGACAGAGAGTGAGC 434161 v v v v (GAGA)n#Simpl 1 GAGAGAGAGAGAGAGAGAGAGAGA 24 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 26 6.26 0.00 0.00 chr2qtel1M 434162 434195 (565805) (TGA)n#Simple_repeat 1 34 (0) c_b93s251i1 3465 chr2qtel1M 434162 TGATGATGGTGATGATGATGATGATGATAATGAT 434195 i i (TGA)n#Simple 1 TGATGATGATGATGATGATGATGATGATGATGAT 34 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 683 28.34 6.23 2.33 chr2qtel1M 436249 436537 (563463) L1ME5_3end#LINE/L1 156 455 (486) m_b93s551i5 3466 chr2qtel1M 436249 AATCAGAAAAATGCAAATTAAGACAACTTTGAGATACCACTACACATCTG 436298 i i vv i vi i i L1ME5_3end#LI 156 AATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCTA 205 chr2qtel1M 436299 TCAAATTGGCTAGGATGACAGGAAA---AGATACTGCTGAATGTTGGAGG 436345 i i i v ii v --- ---i v ii i v i L1ME5_3end#LI 206 TTAGACTGGCAAAAATTA---GAAAGCTGGATAATGCCAAGTGTTGGCGA 252 chr2qtel1M 436346 GGATGTGGGAAAACTGGGACACTGATACATTGTTGATGGAATTGTGAATA 436395 i ? iv i v v i i i i i v ii iv L1ME5_3end#LI 253 GGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACT 302 chr2qtel1M 436396 CATCCAGCCATT-----GAATGATTTGGAACTATGCTCAAAAAAGTTATC 436440 vi v ----- iii i v v -- i ivv i -- L1ME5_3end#LI 303 GGTGCAGCCATTCTGGAGAGCAATCTGGCAGTA--CTTAGTCAAATTA-- 348 chr2qtel1M 436441 AAACTGTTCATACCCTTTGATCCAGCAGTGTTGCTACTGGGCTTATATCC 436490 ivv iiv v i i vii v iv L1ME5_3end#LI 349 AGTATACGCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATATCC 398 chr2qtel1M 436491 CAAAGAGA-TCTTA---AAG------AAGGGAAATGTGCAAGAATGTTTG 436530 i - i --- i ------ i v i i i ii L1ME5_3end#LI 399 CAAAGAAATTCTCACACAGGTCCATAAGGGGACATGTACGAGGATGTTCA 448 chr2qtel1M 436531 TGGCAAC 436537 v i L1ME5_3end#LI 449 TTGCAGC 455 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.60 CpG sites = 53, Kimura (unadjusted) = 37.39 Transitions / transversions = 1.96 (53/27) Gap_init rate = 0.04 (12 / 288), avg. gap size = 2.08 (25 / 12) 16 37.06 0.00 0.00 chr2qtel1M 437022 437086 (562914) (AA)n#Simple_repeat 1 65 (0) m_b93s252i12 3467 chr2qtel1M 437022 AAAAAAAATAAATCCTTTAAAAGAAAAGTTGACAAAATGAAAAAGGAGAT 437071 v vvvvvv i ivvi v vi ii i v (AA)n#Simple_ 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr2qtel1M 437072 AAAAAAAAAAAAAAA 437086 (AA)n#Simple_ 51 AAAAAAAAAAAAAAA 65 Matrix = Unknown Transitions / transversions = 0.58 (7/12) Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0) 20 0.00 0.00 0.00 chr2qtel1M 437283 437304 (562696) (A)n#Simple_repeat 1 22 (0) m_b93s252i13 3468 chr2qtel1M 437283 AAAAAAAAAAAAAAAAAAAAAA 437304 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAA 22 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 218 32.27 7.03 0.74 chr2qtel1M 441156 441283 (558717) C L2b_3end#LINE/L2 (27) 439 304 m_b93s601i5 3469 chr2qtel1M 441156 AGTGCCTGTTATAAGCCAGGCCCTGGCCTATGCCTCAGGAACATAAAGAG 441205 i ii i iv ? vv v viii i i i iv iv C L2b_3end#LINE 439 AGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGGGATACAGCGGT 390 chr2qtel1M 441206 AGGCAAG--GGACAT--TCTCTG--CTCAC-AAG-TCACAGACTGCTGGG 441247 iii --i ?i-- i -- -i - v iv C L2b_3end#LINE 389 GAACAAGACAGACNCGGTCCCTGCCCTCACGGAGCTCACAGTCTAGTGGG 340 chr2qtel1M 441248 GCAGACA-ATACATCAACAACTATGTAGAAACCCAGA 441283 v - i ii v ? ivi -i ?iv C L2b_3end#LINE 339 GGAGACAGACATGTAANCAGACA-ATNATAACCCAGA 304 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.87 CpG sites = 28, Kimura (unadjusted) = 47.10 Transitions / transversions = 2.15 (28/13) Gap_init rate = 0.06 (7 / 127), avg. gap size = 1.43 (10 / 7) 227 29.34 7.27 0.85 chr2qtel1M 441156 441265 (558735) C L2d2_3end#LINE/L2 (27) 528 412 m_b93s601i4 3469 chr2qtel1M 441156 AGTGCCTGTTATAAGCCAGGCCCTGGCCTATGC-CTCAGGAACATAAAGA 441204 i ii i iv v v vv v - vv iiv v i C L2d2_3end#LIN 528 AGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGTGGGGGATACAAA 479 chr2qtel1M 441205 GAGGCAAGGGACAT--TCTCTGCTCACAAG----TCACAGACT-GCTGGG 441247 i i vii -- i i v ---- i iv - i C L2d2_3end#LIN 478 GAAGTATAAGACATGGTCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGG 429 chr2qtel1M 441248 GCAGACAATACATCAACA 441265 - v v C L2d2_3end#LIN 428 G-AGACAAGACATAAACA 412 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.42 CpG sites = 17, Kimura (unadjusted) = 37.90 Transitions / transversions = 1.13 (17/15) Gap_init rate = 0.05 (5 / 109), avg. gap size = 1.80 (9 / 5) 363 23.54 18.44 0.60 chr2qtel1M 441381 441521 (558479) C MIR#SINE/MIR (1) 261 96 m_b93s601i6 3470 chr2qtel1M 441381 ATAATAACATAGCATTTATACAGTACTTA--ATGTGTCA----------- 441417 i - i vv ii -- i ----------- C MIR#SINE/MIR 261 ATAATAGC-TAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCT 213 chr2qtel1M 441418 ------TTCAC-TATATTGTCTCATTCTATTCTCATGAGAACCTTAGGAC 441460 ------ i - i iv iv i ii v i v v C MIR#SINE/MIR 212 AAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAG 163 chr2qtel1M 441461 TTGGGGGCTATTATTGTGCCCATTTTACAGA-----AAAC-ACGGCAAAC 441504 v i vi i v ----- -iv v v C MIR#SINE/MIR 162 GTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAG 113 chr2qtel1M 441505 AGAGGTCCTGTAACTTG 441521 ivv C MIR#SINE/MIR 112 AGAGGTTAAGTAACTTG 96 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.57 CpG sites = 18, Kimura (unadjusted) = 28.68 Transitions / transversions = 1.20 (18/15) Gap_init rate = 0.05 (7 / 140), avg. gap size = 3.86 (27 / 7) 349 30.77 14.44 0.94 chr2qtel1M 441389 441575 (558425) C MIRc#SINE/MIR (25) 243 32 m_b93s601i7 3470 chr2qtel1M 441389 ATAGCATTTATACAGTACTTAATGTGTCATTCAC-TATATTGTCTCATTC 441437 i - vivi v i - v - i i i C MIRc#SINE/MIR 243 ATAGCACTT-TACAGTTTACAAAGCG-CTTTCACATACATTATCTCATTT 196 chr2qtel1M 441438 TATTCTCATGAGAACCTTAGGACTTGGG---GGC---TATTATTGTGCCC 441481 v i ii v i iv vv i --- --- i v C MIRc#SINE/MIR 195 GATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCC 146 chr2qtel1M 441482 ATTTTACAGA-----AAAC-ACGGCAAACAGAGGTCCTGTAACTTG---- 441521 ----- -iv vv v ivv i ---- C MIRc#SINE/MIR 145 ATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCA 96 chr2qtel1M 441522 ----------ATTAGCAAGTTACTGAAGTGGGATGAATACTCAGCCCTTG 441561 ----------ii i vi v ivi ivviv i vi v C MIRc#SINE/MIR 95 AGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTC 46 chr2qtel1M 441562 TTAATTCAAAACCC 441575 i i i v ii C MIRc#SINE/MIR 45 CTGACTCCAAGTCC 32 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.94 CpG sites = 32, Kimura (unadjusted) = 40.68 Transitions / transversions = 1.28 (32/25) Gap_init rate = 0.05 (9 / 186), avg. gap size = 3.22 (29 / 9) 30 14.24 0.00 0.00 chr2qtel1M 443464 443517 (556483) (GAGAGA)n#Simple_repeat 1 54 (0) m_b93s252i14 3471 chr2qtel1M 443464 GAGAGAGACAGAGACAGAGACAGAGAGACAGAGGGAGAGAGAGAGAGAAT 443513 v v v v i iv (GAGAGA)n#Sim 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr2qtel1M 443514 GAGA 443517 (GAGAGA)n#Sim 51 GAGA 54 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 20 11.44 2.44 2.44 chr2qtel1M 443512 443552 (556448) (ATG)n#Simple_repeat 1 41 (0) m_b93s252i15 3472 chr2qtel1M 443512 ATGA-GATGATGATGGTGATGGTGACGATGATGGTGACTGAT 443552 - i i i i - (ATG)n#Simple 1 ATGATGATGATGATGATGATGATGATGATGATGATGA-TGAT 41 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 24 0.00 0.00 0.00 chr2qtel1M 443898 443923 (556077) (A)n#Simple_repeat 1 26 (0) m_b93s252i16 3473 chr2qtel1M 443898 AAAAAAAAAAAAAAAAAAAAAAAAAA 443923 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAA 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 27 25.99 4.30 0.00 chr2qtel1M 444263 444355 (555645) (ATGT)n#Simple_repeat 1 97 (0) m_b93s252i17 3474 chr2qtel1M 444263 ATGCATGTGTGTATATATGT-T-TGTGTTTGTAAGTATATATGTAGATAT 444310 i i i - - i v v i vi (ATGT)n#Simpl 1 ATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTAT 50 chr2qtel1M 444311 GCATGCATGT-TGT-TCTATGTAGATGTGTATATAGGTTTATATATA 444355 i i - - v vi i i v v i i (ATGT)n#Simpl 51 GTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTA 97 Matrix = Unknown Transitions / transversions = 1.86 (13/7) Gap_init rate = 0.04 (4 / 92), avg. gap size = 1.00 (4 / 4) 1637 30.21 4.85 3.86 chr2qtel1M 444445 445804 (554196) L1M5_orf2#LINE/L1 1922 3294 (0) m_b94s551i0 3475 chr2qtel1M 444445 TCATATGTAATGGGGACAAACTGCAACCATTCCCAATAATTTCAGGAGTT 444494 iv v v ? v ?v v vv vv i iiv L1M5_orf2#LIN 1922 TCATACTTAATGGTGAAANACTGAANGCTTTCCCCCTAAGATCGGGAACA 1971 chr2qtel1M 444495 AAACAAGGTTGCCCACTATCACCGTTGCTATTTAATATTGTATTAGAAAT 444544 i v i i ? ii v i i i i ii L1M5_orf2#LIN 1972 AGACAAGGATGTCCGCTNTCACCACTTCTATTCAACATTGTACTGGAGGT 2021 chr2qtel1M 444545 GCTAGCTTTGGCAATAAGAGCTGAGAAAGAGATTAAAGGAATAAGAATAG 444594 v ivvv ivvv i i v v ii v L1M5_orf2#LIN 2022 CCTAGCCAGTGCAATAAGGCAAGAAAAAGAAATAAAAGGCATAAAGATTG 2071 chr2qtel1M 444595 GCAATGAAGAAACCAAATTATCACTCTTTGCTGATGATATGATGGTATAC 444644 v v iv i i ?i v i v i v ? L1M5_orf2#LIN 2072 GAAAGGAAGAAATAAAACTGTCNTTATTCGCAGATGACATGATTGTNTAC 2121 chr2qtel1M 444645 TTAGAGAACCCCAGAGATTCTACTAAAAAGTTATTAGAAACAATCCACAT 444694 v i i ? i v v ? ii i vi vviiiv L1M5_orf2#LIN 2122 GTAGAAAATCCNAAAGAATCTACAAANAAACTACTAGAACTAATAAGTGA 2171 chr2qtel1M 444695 CTTTAGCAAAGTTGCAGGTTACAAAATAAACCCACAAAAGTCATCAGCAT 444744 v i i ? v ii v ivi i viv i L1M5_orf2#LIN 2172 ATTTAGCAAGGTCGCNGGATACAAGGTCAATATACAAAAATCAATTGTAT 2221 chr2qtel1M 444745 TCTTATACATAACTAACAAAACCCAACAGTTAG-------AGCTACAAAG 444787 ii i--- i --- v i i ------- ii v? i L1M5_orf2#LIN 2222 TTCTATAT---ACTAGCAA---CAAACAATTGGAAAATGAAATTTNAAAA 2265 chr2qtel1M 444788 AGAA----ATTTCTGATTG----------TATAAAATATTTAGGAATCTA 444823 v ---- vii v ----------i ? i vv L1M5_orf2#LIN 2266 ACAATACCATTTACAATAGCATCAAAAAACATNAAATACTTAGGAATAAA 2315 chr2qtel1M 444824 TCTGCCAAGGGAAAACCAGAAACTTTATGAGCAAAACTACAAAATGCTTT 444873 iv ii? vivv ii v ? iivvv iii vi L1M5_orf2#LIN 2316 TCTAACAAAANATGTGCAAGACCTNTACACTGAAAACTACAAAACATTGC 2365 chr2qtel1M 444874 CCACACAAATTAAGTCTGATCTAACCAACTGGAAAAA-ATATTAAATGCT 444922 iv v v ivvv i vi v i i - ii-- i L1M5_orf2#LIN 2366 TGAGAGAAATTAAAGAAGACCTAAATAAATGGAGAGATATACC--ATGTT 2413 chr2qtel1M 444923 CTTGGATTGG-TGAGCAAATATAATAAAGATGACAATACTACCTAAACTA 444971 v -v viv vi ? v v v i i i L1M5_orf2#LIN 2414 CATGGATTGGAAGACTCAATATTGTNAAGATGTCAATTCTCCCCAAATTG 2463 chr2qtel1M 444972 ATCTATTTATTTAGTACTATACCAATCAGATTCCCAAAACTATTTTTATG 445021 vv i i i v v i v iv -vi v L1M5_orf2#LIN 2464 ATCTATAGATTCAATGCAATCCCAATCAAAATCCCAGCA-GGTTTTTTTG 2512 chr2qtel1M 445022 ACCTAGAAAAATAACAAAC-------AAAGTTCATATGGAAA-ACAAAGG 445063 --- - v i i ------- i i -i L1M5_orf2#LIN 2513 ---TAG-AAATTGACAAGCTGATTCTAAAATTTATATGGAAATGCAAAGG 2558 chr2qtel1M 445064 -TCAAGAATTTCAACGGAATTAA---TGAAAAAAAATCAAATGAAGGTGG 445109 -i ? --- i vi vi --- i --i ii v L1M5_orf2#LIN 2559 ACCNAGAAT---AGCCAAAACAATCTTGAAAAAGAA--GAACAAAGTTGG 2603 chr2qtel1M 445110 ----CCTAGCTGTACCAGATCTAAAAGTATATTATAAAGCAGTGGTTACT 445155 ---- i - vv ? ? v iiiv viii v ii L1M5_orf2#LIN 2604 AGGACTTA-CACTACCNGATNTCAAGACTTATTATAAAGCTACAGTAATC 2652 chr2qtel1M 445156 AAAACCATCTGGTATTGGC-TAAGAAATGGACTAGTTGATCAATGGAATA 445204 i vi v - -i i v i v i L1M5_orf2#LIN 2653 AAGACAGTGTGGTATTGGCGTAAG-GATAGACAAATAGATCAATGGAACA 2701 chr2qtel1M 445205 TATTAG---GTTC-GAAGGACAAAACAGCCAATAACTTTAATAATCTAGT 445250 v v --- i - -- i i v vi vv -- v ii?v ?i ii L1M5_orf2#LIN 2702 GAATAGAGAGTCCAGAA--ATAGACCCACACATA--TATGGNCANTTGAT 2747 chr2qtel1M 445251 ATTTGACAAA---CCCAAAGACGCCAGTTT--TTGGGAAAAGAACGCATT 445295 v ---v ? ---- i i-- v i vv iv L1M5_orf2#LIN 2748 TTTTGACAAAGGTGCCAANG----CAATTCAGTGGGGAAAGGATAGTCTT 2793 chr2qtel1M 445296 ATTTGACAAAAACTGCTGGGAAAATTGGAAATTAGCATGGCAGGAACTAA 445345 - ii viv i v v ivii v ii v i L1M5_orf2#LIN 2794 -TTCAACAAATGGTGCTGGAACAATTGGATATCCATATGGAAAAAAATGA 2842 chr2qtel1M 445346 GCATTGACCTACACTTAACACCGTACACCAAGATAAGGCCAAAATGGGTT 445395 i?v i ivi i v i v i v ivi ? i i- L1M5_orf2#LIN 2843 ANCTCGACCCCTACCTCACACCATACACAAAAATTAATTCNAGATGGA-T 2891 chr2qtel1M 445396 CAT-GACCCCTAGGTCACACACAAAGAATGAGATTATAAATAAATT---G 445441 - -------i v iii ii? i i i -- v --- L1M5_orf2#LIN 2892 CATAGACC-------TAAATGTAAAAGNTAAAACTATAA--AACTTCTAG 2932 chr2qtel1M 445442 AA-AGAGCATAGGATAGTTTACCTCTCAT-ACCTAAGGAAGAGGAAGGAA 445489 - i i v i-- i - i - -v i?v v iii L1M5_orf2#LIN 2933 AAGAAAACATAGGAGAA--TATCT-TCGTGACCT-TGGGNTAGGCAAAGA 2978 chr2qtel1M 445490 TTTATGACCAAAGAAGAACTAGAGACCACTATTGATTACAAAATAGAAAA 445539 v ---i v i vvi i i v ? --- ii i v i L1M5_orf2#LIN 2979 TTTCT---TAAACAGGACACAAAAAGCACNA---ACCATAAAAGAAAAAA 3022 chr2qtel1M 445540 T-------TTTGATTATATCAAATTGAAAAGTTTTTGTACAAACAAAACT 445582 ------- v i ?i v v ii i iv ?vvv ivi L1M5_orf2#LIN 3023 TTGATAAATTGGACTNCATCAAAATTAAAAACTTCTGCTCNTCAAAAGAC 3072 chr2qtel1M 445583 AATGCAGACAAGATTAGAAGTGAAACAATAAACTGGGAAAATATTTTTAC 445632 vi ivi v i v i vv i v i i ? i v v i L1M5_orf2#LIN 3073 ACCGTTAAGAAAATGAAAAGGCAAGCCACAGANTGGGAGAAAATATTTGC 3122 chr2qtel1M 445633 AGT-CAAAGGTTCTGATAAAGGCCTCATTTCCAAAATATATAGAGAATTG 445681 i?- v vi- i v i v i i i - L1M5_orf2#LIN 3123 AANACATATA-TCTGACAAAGGACTCGTATCCAGAATATATAAAGAACT- 3170 chr2qtel1M 445682 ACTCTAATTT-ATAAGAAATCAAGCCATTC--TCCAATTGATAAATGGTC 445728 v vi ? i- ? -- v vv --i v? v v L1M5_orf2#LIN 3171 CCTACAANTCAATAANAAA--AAGACAAACAACCCAATANAAAAATGGGC 3218 chr2qtel1M 445729 AAAGGATATGAACACATAATTCTCAAATGAAGAAATTGAAACTATTTCTA 445778 i iv v i v v v v ?v iviiivv L1M5_orf2#LIN 3219 AAAAGACTTGAACAGACACTTCACAAAAGAAGATATNCAAATGGCCAATA 3268 chr2qtel1M 445779 GCCATATGAAAATATGCTCCAAATCA 445804 iv i v v v? L1M5_orf2#LIN 3269 AGCACATGAAAAGATGCTCAACNTCA 3294 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.85 CpG sites = 217, Kimura (unadjusted) = 40.93 Transitions / transversions = 1.22 (217/178) Gap_init rate = 0.06 (76 / 1359), avg. gap size = 1.57 (119 / 76) 1572 28.59 2.80 2.48 chr2qtel1M 445661 446302 (553698) L1ME5_3end#LINE/L1 7 650 (291) m_b94s551i1 3475 chr2qtel1M 445661 TCCAAAATATATAGAGAATTGACTCTAATTTATAAGAAATCAAGCCATT- 445709 i i i ii i vviv v iv i -- v iv?- L1ME5_3end#LI 7 TCTAGAATATACAAGGAACTCCTGCAAATCAACAAGAAA--AAGACGGNA 54 chr2qtel1M 445710 -CTCCAATTGATAAATGGTCAAAGGATATGAACACATAATTCTCAAATGA 445758 - i v v v vii iv i v L1ME5_3end#LI 55 ACCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGA 104 chr2qtel1M 445759 AGAAA-TTGAAA--CTATTTCTAGCCATATGAAAATATGCTCCAAATCAT 445805 i -ii -- --v v - i v v v L1ME5_3end#LI 105 GGAAACCCGAAAGGCTA--ACAAG-CATATGAAGAGATGCTCAAACTCAT 151 chr2qtel1M 445806 TATTAATCAGAGAAATGCAAATTAAGACAACTCCAAGATACCACTACACA 445855 v i vvii i vi L1ME5_3end#LI 152 TAGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACA 201 chr2qtel1M 445856 CCTATCAGATTGGCTAGAATGACAGAGA-AAATAATGCGGAATGTTGGAG 445904 i i v i v v i v-ii vi i v L1ME5_3end#LI 202 CCTATTAGACTGGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTGGCG 251 chr2qtel1M 445905 GAGATGTGGGAAAACAGG-ACACTGATACATTGTTAGTGGAATTGTGAAC 445953 ii i ? i - v v i i i i i v ii L1ME5_3end#LI 252 AGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGAC 301 chr2qtel1M 445954 ACATCCAGTCATTCTGGAGAGCAATTTGGAACTAGGCTCAAAAAAGTTAT 446003 vvi v i i v v -- i ivv i - L1ME5_3end#LI 302 TGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTA--CTTAGTCAAATTA- 348 chr2qtel1M 446004 CAAACTGTGCATACCTTTTGATCCAGCAGTGTTTCTACTGGGCTTATACC 446053 - ivv ii i v i i viiv v iv i L1ME5_3end#LI 349 -AGTATACGCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATATC 397 chr2qtel1M 446054 CCAAAGAGATACTAAAGAAGG----GAAAGGGACCTGGATGTGCCAAAAT 446099 i v v viv ----v i ---- i v ii L1ME5_3end#LI 398 CCAAAGAAATTCTCACACAGGTCCATAAGGGGAC----ATGTACGAGGAT 443 chr2qtel1M 446100 GTTTGTGGCAGCCCTGTTTGTAGTGGCTAGAAGGTGGAAAATGAATGGAT 446149 ii v vi i vi i v iivvivv i L1ME5_3end#LI 444 GTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGGGT 493 chr2qtel1M 446150 GCCCATCAATTGGAGAATGGTTGGGTAAATTGTGGTGTATAAATGTTATG 446199 i v v i v i v v iv iiii L1ME5_3end#LI 494 GTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACACCATG 543 chr2qtel1M 446200 GAATATTATTGTTCCA-TAAGAAATGACCGGCAGGATGAATACAGAGAGG 446248 i i - ivv - v iii v i vi v i v vii L1ME5_3end#LI 544 GAGTACTA-TGCAGCAGTTAGAAGCAACGGACTAGATGTACACATAGCAA 592 chr2qtel1M 446249 CTTGGCAAGA-CTTACATGAAC-TGATGCTAAGTGAAATGAGC-AGAACC 446295 v vvi - v -- - ii i vi i- v L1ME5_3end#LI 593 CATGGATGGATCTTAAA--AACATAGTGCTGAGTGAAAAAAGTAAGAAAC 640 chr2qtel1M 446296 AG---GAGAT 446302 --- L1ME5_3end#LI 641 AGAATGAGAT 650 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.90 CpG sites = 100, Kimura (unadjusted) = 36.93 Transitions / transversions = 1.27 (100/79) Gap_init rate = 0.04 (28 / 641), avg. gap size = 1.21 (34 / 28) 13 4.76 0.00 4.35 chr2qtel1M 446600 446623 (553377) (GGGA)n#Simple_repeat 1 23 (0) m_b94s252i2 3476 chr2qtel1M 446600 GGGAGGGGGTGGAGGGAGGGAGGG 446623 i - (GGGA)n#Simpl 1 GGGAGGGAG-GGAGGGAGGGAGGG 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 22 19.80 0.00 0.00 chr2qtel1M 446831 446871 (553129) (A)n#Simple_repeat 1 41 (0) m_b94s252i3 3477 chr2qtel1M 446831 AACAATAACAACAACAACAACAAAAAAAAAAAAAAAAAAAA 446871 v v v v v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 41 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 75 0.00 1.49 0.00 chr2qtel1M 446911 446977 (553023) (AT)n#Simple_repeat 1 68 (0) c_b94s251i0 3478 chr2qtel1M 446911 ATATATATATATATATATATATATATAT-TATATATATATATATATATAT 446959 - (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr2qtel1M 446960 ATATATATATATATATAT 446977 (AT)n#Simple_ 51 ATATATATATATATATAT 68 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.02 (1 / 66), avg. gap size = 1.00 (1 / 1) 104 0.00 0.00 0.00 chr2qtel1M 447097 447187 (552813) (AAAG)n#Simple_repeat 1 91 (0) c_b94s251i1 3479 chr2qtel1M 447097 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAA 447146 (AAAG)n#Simpl 1 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAA 50 chr2qtel1M 447147 AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 447187 (AAAG)n#Simpl 51 AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 91 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 90), avg. gap size = 0.0 (0 / 0) 15 13.23 4.44 4.44 chr2qtel1M 449396 449440 (550560) (CTTATA)n#Simple_repeat 1 45 (0) m_b94s252i4 3480 chr2qtel1M 449396 CTTATATCTTAGACCTTAGGC-TATACTTAT-TGTATACTTATACTT 449440 - v - vi - -iv (CTTATA)n#Sim 1 CTTATA-CTTATA-CTTATACTTATACTTATACTTATACTTATACTT 45 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4) 373 28.77 0.68 1.36 chr2qtel1M 450814 450961 (549039) L1ME4c_3end#LINE/L1 409 555 (275) m_b94s551i2 3481 chr2qtel1M 450814 ATGATTCAAG-GAGGTAAAGAGACCAAGATGTAGAAAAATGTTTGTGGCA 450862 i i- i v i -- v v i vi i ii v L1ME4c_3end#L 409 ATAATTCAAAAGAAGGAAAAAG--CTATATGCACGAAGATGTTCATTGCA 456 chr2qtel1M 450863 GCCTTTTTTGTAATGGCAAGGAACTGGAAAGTGAGTGGATGCCCATCAAT 450912 v v i i i ii i vvivv ii i v L1ME4c_3end#L 457 GCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAAT 506 chr2qtel1M 450913 TGGAGAATGGCTAAATAAATTATGGTATATGAATGTTATGAAATATTAT 450961 v i i i i v? iviv i L1ME4c_3end#L 507 AGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATATTAT 555 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.49 CpG sites = 26, Kimura (unadjusted) = 37.88 Transitions / transversions = 1.62 (26/16) Gap_init rate = 0.02 (3 / 147), avg. gap size = 1.00 (3 / 3) 473 24.79 0.00 0.00 chr2qtel1M 450841 450961 (549039) L1ME3G_3end#LINE/L1 428 548 (376) m_b94s551i3 3481 chr2qtel1M 450841 ATGTAGAAAAATGTTTGTGGCAGCCTTTTTTGTAATGGCAAGGAACTGGA 450890 v ii ii v v v i i ii i L1ME3G_3end#L 428 ATGTACAAGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGA 477 chr2qtel1M 450891 AAGTGAGTGGATGCCCATCAATTGGAGAATGGCTAAATAAATTATGGTAT 450940 vvivv ii i v i i L1ME3G_3end#L 478 AACAACCTAAATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGTAT 527 chr2qtel1M 450941 ATGAATGTTATGAAATATTAT 450961 vv ii i i L1ME3G_3end#L 528 ATCCATACTATGGAATACTAT 548 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 29.74 CpG sites = 19, Kimura (unadjusted) = 30.97 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.00 (0 / 120), avg. gap size = 0.0 (0 / 0) 326 29.95 3.12 2.59 chr2qtel1M 450850 451041 (548959) L1MC2_3end#LINE/L1 441 633 (458) m_b94s551i4 3481 chr2qtel1M 450850 AATGTTTGTGGCAGCCTTTTTTGTAATGGCAAGGAACTGGAAAGTGAGTG 450899 i i i v ii v v i- v i ii vii L1MC2_3end#LI 441 AATGTTTATAGCAGCTTTATTCATAATTGCCAA-AACTTGGAAGCAACCA 489 chr2qtel1M 450900 -GATGCCCATCAATTGGAGAATGGCTAAATAAATTATGGTATATGAATGT 450948 - i v v v v i i i i vv ii L1MC2_3end#LI 490 AGATGTCCTTCAATAGGTGAATGGATAAACAAACTGTGGTACATCCATAC 539 chr2qtel1M 450949 TATGAAATATTATTGTTCTGT---AAGACATGATC-AACAGGATAATTCA 450994 v i vvv vi --- v v - v i vi --- i L1MC2_3end#LI 540 AATGGAATATTATTCAGCGATAAAAAGAAATGAGCTATCAAGCCA---CG 586 chr2qtel1M 450995 GAGAGCCCTGGAGAGA-CTTACATGAATTGATGCCAAGTGAAATGAGC 451041 i i v v ii - v v - iv i vi L1MC2_3end#LI 587 AAAAGACATGGAGGAACCTTAAATGCA-TATTGCTAAGTGAAAGAAGC 633 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.06 CpG sites = 30, Kimura (unadjusted) = 38.95 Transitions / transversions = 1.15 (30/26) Gap_init rate = 0.05 (9 / 191), avg. gap size = 1.22 (11 / 9) 25 15.25 0.00 2.22 chr2qtel1M 451463 451508 (548492) (AG)n#Simple_repeat 1 45 (0) m_b94s252i5 3482 chr2qtel1M 451463 AGAGAGAGAGAGAGAGAGAGAGACAGATAGATTAGATAGATATAGA 451508 v v -v v v v (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA-GAGAGAGAGAGAGA 45 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1) 979 28.42 2.53 2.75 chr2qtel1M 451731 452204 (547796) C L1ME3G_3end#LINE/L1 (445) 479 7 m_b94s551i5 3483 chr2qtel1M 451731 TTTCCAATGTTTGGTTACCACAAAAAGCTGCTGCAA---ACATCTTTGTA 451777 v v i ii v i- --- i C L1ME3G_3end#L 479 TTTCCAATTTTTCGCTATTACAAACAA-TGCTGCAATGAACATCCTTGTA 431 chr2qtel1M 451778 CATGTGGGTCCTTGTCCTTTTTTTTATG-ATCTCTTTGGGATACAGACCC 451826 i?-- v viv v viiv - i ? i v v? ? C L1ME3G_3end#L 430 CATGCN--TCCTTGTGCACATGTGCGAGTATTTCTNTAGGATAGATNCCN 383 chr2qtel1M 451827 TGTAGAGACACTGCTGA-TCAAAGGGTATGCATAGTTTGATAACCCTTTG 451875 v v v iv i i- ii v --- vii vi C L1ME3G_3end#L 382 AGAAGTGGAATTGCTGGGTCAAAGGGTATGCGCATTTT---AAATTTTAA 336 chr2qtel1M 451876 GACATAGTTCCAAATTGCTCTCTGTAATGGTTGGGTCCTTTCACAATGTC 451925 v v v v i iiv ? i vii vv i v vi C L1ME3G_3end#L 335 TAGATACTGCCAAATTGCCCTCCAAAANGGCTGTACCAATTTACACTCCC 286 chr2qtel1M 451926 CCCAACAGTGCATTAGTGTCCTACTTTTCCTAAATCTTC--CAATATTTA 451973 v i i v v v ivv i i v i i -- i i ?i C L1ME3G_3end#L 285 ACCAGCAGTGTATGAGAGTACCCGTTTCCCCACACCCTCGCCAACACTNG 236 chr2qtel1M 451974 TCATTATCTTTTCCTGAGATCTTAGCCAATCTGAGAGGTGGGAAGTGGTA 452023 vi vv?iii v i i v vi ii i C L1ME3G_3end#L 235 ATATTATCAANCTTTTAAATTTTTGCCAATCTGATGGGTGAAAAATGGTA 186 chr2qtel1M 452024 CCTCAGAGTTGTTTTAATTTGCATTT--GTTATCAATAGTGATTTAGAGC 452071 i vv --v v i v vv v C L1ME3G_3end#L 185 TCTCATTGTTGTTTTAATTTGCATTTCCCTGATTACTAGTGAGGTTGAGC 136 chr2qtel1M 452072 ATTTTTTCTTATGACTCTAATTCGC--TTTA-ATTTCCTCACCTGAAAAT 452118 i v -- i - v -- i- vi vi C L1ME3G_3end#L 135 ATCTTTTCATATG--TTT-ATTGGCCATTTGTATTTCCTCTTCTGTGAAT 89 chr2qtel1M 452119 TGTCTGTTCCTACCCTTTGAGTATGTATCAAGTAATGAATGATTTGTATT 452168 i v i vvi v v --- v ii vi i v - C L1ME3G_3end#L 88 TGCCTGTTCATATCCTTTGCCCATTTTTC---TATTGGGTTGTCTTT-TT 43 chr2qtel1M 452169 TTTATAAATTTGAAACAGTTCTTTATATATCTTAGA 452204 i vi v iv ii i C L1ME3G_3end#L 42 CTTATTGATTTGTAGGAGTTCTTTATATATTCTGGA 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.19 CpG sites = 67, Kimura (unadjusted) = 36.93 Transitions / transversions = 1.05 (67/64) Gap_init rate = 0.04 (20 / 473), avg. gap size = 1.25 (25 / 20) 304 26.25 3.61 3.61 chr2qtel1M 452061 452226 (547774) C L1M4_orf2#LINE/L1 (0) 3294 3129 m_b94s551i6 3483 chr2qtel1M 452061 TGATTTAGAGCATTTTTTCTTATGACTCTAATTCGC--TTTA-ATTTCCT 452107 v v i v i --- v v -- i- v i C L1M4_orf2#LIN 3294 TGATGTTGAGCATCTTTTCATGTG---CTTATTGGCCATTTGTATATCTT 3248 chr2qtel1M 452108 CACCTGAAAATTGTCTGTTCCTACCCTTTGAGTATGTATCAAGTAATGAA 452157 viiv i v i vv i vvi v v ? v --- ii C L1M4_orf2#LIN 3247 CTTTGGAGAAATGTCTATTCAAATCCTTTGCCCATTTTTNAATT---GGG 3201 chr2qtel1M 452158 TGATTTGTATTTTTATAA---ATTTGAAACAGTTCTTTATATATCTTAGA 452204 v v vi--- v v v ii i C L1M4_orf2#LIN 3200 TTATTTGTCTTTTTATTGTTGAGTTGTAAGAGTTCTTTATATATTCTGGA 3151 chr2qtel1M 452205 AATGAGACCTTTATCAGATATA 452226 v i? v i C L1M4_orf2#LIN 3150 TACNAGTCCCTTATCAGATATA 3129 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.93 CpG sites = 18, Kimura (unadjusted) = 32.93 Transitions / transversions = 0.75 (18/24) Gap_init rate = 0.05 (9 / 165), avg. gap size = 1.33 (12 / 9) 21 6.35 0.00 2.94 chr2qtel1M 452239 452273 (547727) (TTTTG)n#Simple_repeat 1 34 (0) m_b94s252i7 3484 chr2qtel1M 452239 TTTTTTTTTGTTGTTTTTTTGTTTTGTTTTGTTTT 452273 v - v (TTTTG)n#Simp 1 TTTTGTTTTGTT-TTGTTTTGTTTTGTTTTGTTTT 34 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 20 31.88 1.74 3.54 chr2qtel1M 452239 452353 (547647) (TTTTA)n#Simple_repeat 1 113 (0) m_b94s252i6 3485 chr2qtel1M 452239 TTTTTTTTTGTTGTTTTTTTGTTTTGTTTTGTTTTCCCAAAACAGATTAT 452288 v i - v i i i --- vvvi vv (TTTTA)n#Simp 1 TTTTATTTTATT-TTATTTTATTTTATTTTATTTT---ATTTTATTTTAT 46 chr2qtel1M 452289 TTTATTTTTTTTTCTGTAATTCCA-AATGTTTT-TTTTTTTTTTTTTTAT 452336 v v v v ii -vv i - v v (TTTTA)n#Simp 47 TTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTAT 96 chr2qtel1M 452337 TTAATAGCCTTTTATTT 452353 v vviv (TTTTA)n#Simp 97 TTTATTTTATTTTATTT 113 Matrix = Unknown Transitions / transversions = 0.47 (9/19) Gap_init rate = 0.05 (6 / 114), avg. gap size = 1.00 (6 / 6) 315 22.23 1.19 8.97 chr2qtel1M 452719 452802 (547198) MIRc#SINE/MIR 38 115 (153) m_b94s601i0 3486 chr2qtel1M 452719 GAAGTCTGGAGGACCTGAATACAA-TCTGGTCTCAGACACTTAATACTTC 452767 i v i ii v i - iv v v v ------- MIRc#SINE/MIR 38 GGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTA------- 80 chr2qtel1M 452768 CTAGCTGTTTAACTCTGGGCAAGTCACTTAACCCC 452802 v i ii i MIRc#SINE/MIR 81 CTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 24.84 CpG sites = 10, Kimura (unadjusted) = 26.61 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.10 (8 / 83), avg. gap size = 1.00 (8 / 8) 251 20.22 8.79 7.61 chr2qtel1M 452723 452813 (547187) MIR#SINE/MIR 32 123 (139) m_b94s601i1 3486 chr2qtel1M 452723 TCTGGAG---GAC---CTGAATAC-AATCTGGTCTCAGACACTTAATACT 452765 --- --- ii v - iv v v v ----- MIR#SINE/MIR 32 TCTGGAGCCAGACTGCCTGGGTTCGAATCCCGGCTCTGCCACTTA----- 76 chr2qtel1M 452766 TCCTAGCTGTTTAACTCTGGGCAAGTCACTTAACCCCAAT-TGCATCAG 452813 -- v i ii i i vv - v MIR#SINE/MIR 77 --CTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAG 123 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 23.69 CpG sites = 8, Kimura (unadjusted) = 23.69 Transitions / transversions = 0.89 (8/9) Gap_init rate = 0.12 (11 / 90), avg. gap size = 1.36 (15 / 11) 340 19.00 3.85 3.85 chr2qtel1M 452847 452950 (547050) C L1ME4c_3end#LINE/L1 (720) 110 7 m_b94s551i7 3487 chr2qtel1M 452847 ATTTTATCATCTGAAAATTATCTGGTCATATCCTTTGACCATTTATCAAC 452896 iv v ? vi i v i v v i C L1ME4c_3end#L 110 ATTTCCTCTTNTGTGAATTGTCTGTTCATGTCCTTTGCCCATTTATCTAT 61 chr2qtel1M 452897 TGAGAAATGTCTTG----TATTCTTATAAATTTGAAACAGTTCTTTATGT 452942 i ---- ---- v v vv i i C L1ME4c_3end#L 60 TGGG----GTCTTGATNTTTTTCTTATCAATTTGAATGAGCTCTTTATAT 15 chr2qtel1M 452943 ATTTTAGA 452950 ? v? C L1ME4c_3end#L 14 ANTANAGA 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 22.74 CpG sites = 8, Kimura (unadjusted) = 22.74 Transitions / transversions = 0.73 (8/11) Gap_init rate = 0.05 (5 / 103), avg. gap size = 1.60 (8 / 5) 410 30.04 3.54 1.30 chr2qtel1M 452859 453084 (546916) C L1M3_orf2#LINE/L1 (52) 3236 3006 m_b94s551i8 3487 chr2qtel1M 452859 GAAAATTATCTGGTCATATCCTTTGACCATTTATCAACTGAGAAATGTCT 452908 i v i iv vi v v ? ii i vv v v C L1M3_orf2#LIN 3236 GAGAAATGTCTATTCAGGTCCTTTGCCCATTTTTNAATCGGGTTATTTGT 3187 chr2qtel1M 452909 TGTATTCTTATAAATTTGAAACAGTTCTTTATGTATTTTAGAAATGAGAC 452958 v v vi vi v v ?v i i i v v iv C L1M3_orf2#LIN 3186 TTTTTTGCTATTGAGTTGTANGAGTTCCTTATATATTTTGGATATTAACC 3137 chr2qtel1M 452959 CTTTAGCAGATATACTGGCCATAAAGATTTTTTGCC---CC--AACTTTC 453003 i v iv viiii v i v --- -- iv v C L1M3_orf2#LIN 3136 CCTTATCAGATATATGGTTTGCAAATATTTTCTCCCATTCCGTAGGTTGC 3087 chr2qtel1M 453004 TTCTTCCCTCTTATAATCTTGGTTTTGTTT--TATGCAAAATCTTTTTAA 453051 i i v vv i i--- iv -- i i v i C L1M3_orf2#LIN 3086 CTTTTCACTCTGTTGATT---GTTTCCTTTGCTGTGCAGAAGCTTTTTAG 3040 chr2qtel1M 453052 TTTAATGTAATCAAAGTTGTCCA-TTTTGCCTTT 453084 i i vv v i - i C L1M3_orf2#LIN 3039 TTTGATGTAGTCCCACTTGTCTATTTTTGCTTTT 3006 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.57 CpG sites = 33, Kimura (unadjusted) = 39.31 Transitions / transversions = 0.97 (33/34) Gap_init rate = 0.03 (7 / 225), avg. gap size = 1.57 (11 / 7) 12 11.68 10.81 0.00 chr2qtel1M 453785 453821 (546179) (CTTTCTG)n#Simple_repeat 1 41 (0) m_b94s252i8 3488 chr2qtel1M 453785 CTTGCAGCTTTGT-CCTT-TGC-TTCTGC-TTCTGCTTTCT 453821 v v v - i - - - (CTTTCTG)n#Si 1 CTTTCTGCTTTCTGCTTTCTGCTTTCTGCTTTCTGCTTTCT 41 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.11 (4 / 36), avg. gap size = 1.00 (4 / 4) 13 6.76 9.68 0.00 chr2qtel1M 453799 453829 (546171) (CTTCTG)n#Simple_repeat 1 34 (0) m_b94s252i9 3488 chr2qtel1M 453799 CTT-TGCTTCTGCTTCTGCTT-T-CTTCAGCCTC 453829 - - - v i (CTTCTG)n#Sim 1 CTTCTGCTTCTGCTTCTGCTTCTGCTTCTGCTTC 34 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.10 (3 / 30), avg. gap size = 1.00 (3 / 3) 2135 32.84 1.87 1.60 chr2qtel1M 454407 455904 (544096) C L1M2_orf2#LINE/L1 (404) 2887 1386 m_b94s551i9 3487 chr2qtel1M 454407 TCTATTTTGACCTTGTTTGGGTATAGAGTGGGAGATGTAGGTCTATACTG 454456 i vi vi vv vi i ivi vvi v C L1M2_orf2#LIN 2887 TCCATTTTGAGTTGATTTTTGTATATGGTGAGAGATAGGGGTCTAGTTTC 2838 chr2qtel1M 454457 AGT-TTCTGACATATTATTGTCT-GTTTCCCC-GCAATTTCTATCACATA 454503 v - - viv i i- i - viv i iiv v C L1M2_orf2#LIN 2837 ATTCTTCTG-CATATGGATATCCAGTTTTCCCAGCACCATTTATTGAAGA 2789 chr2qtel1M 454504 GAGAATTCTTATTCTAGAACCTGGATTTTGGGGG--TTTATCAAATACTA 454551 vvi i vii i ?viiv -- i v v -- i i v ii C L1M2_orf2#LIN 2788 GACTGTCCTTTCCCCANTGTATG--TTCTTGGCGCCTTTGTCGAAAATCA 2741 chr2qtel1M 454552 CATTGCTATGA--GCTTTGATTATTGTGTCCTATGT-ATCTAATCTATTC 454598 vv v i i -- v v -- i - i iv -v v i C L1M2_orf2#LIN 2740 GTTGGCTGTAAATGCGTGGATT--TAT-TTCTGGGTTCTCTATTCTGTTC 2694 chr2qtel1M 454599 CACTGATGCCTCACTCTATTTCTTAGCTAGTACCA-AATGGTTTGATTAT 454647 i i viv vvv i i vv i -iv v i i C L1M2_orf2#LIN 2693 CATTGGTCTATGTGTCTGTTTTTATGCCAGTACCATGCTGTTTTGGTTAC 2644 chr2qtel1M 454648 TGCTGCTTTGTAACATAGTTTTAGGGTTGGTACTATTAAGCTACCATCCT 454697 iiv ii v v i viv v i v v iv v - C L1M2_orf2#LIN 2643 TATAGCTTTGTAGTATATTTTGAAGTCAGGTAGTGTGATGCCTCCAGC-T 2595 chr2qtel1M 454698 TTGTATTTTTTTATTCATTAATCCTTTGA-TATTCTTGACTTTTTGTTCT 454746 - i ii vv v v i- vv iii vv C L1M2_orf2#LIN 2594 TTGT-TCTTTTTGCTCAGGATTGCTTTGGCTATTCGGGGTCTTTTGTGGT 2546 chr2qtel1M 454747 TCTAGATAGCTTTTGCTTTTTTTCTTTCTAGTTCTATAAAATAGTGTT-T 454795 i v iiiv ivvv ? i v i i i- i i- C L1M2_orf2#LIN 2545 TCCATACGAATTTTAGGATTNTTTTTTCTATTTCTGTGAAG-AATGTCAT 2497 chr2qtel1M 454796 TTGCAGTTGGATTGTTATGGCACTGAACAAGTAGACCAATTTAGGCAGAA 454845 v i v v v vv v i ivv i iv i i v C L1M2_orf2#LIN 2496 TGGTATTTTGATAGGGATTGCATTGAATCTGTAGATCGCTTTGGGTAGTA 2447 chr2qtel1M 454846 TTGTGGTTTATATTATATCAGCTCAACCTAGCCATGAACAATTAATATTT 454895 v ?vi vv iv i ii vv v v i vvvi i C L1M2_orf2#LIN 2446 TGGNCATTTTAACAATATTAATTCTTCCAATCCATGAGCATGGGATATCT 2397 chr2qtel1M 454896 TTCCAGTTGTTTAGATCTGATTTTC--TTTGTGTGAGAAGTGTTTTGTAA 454943 v ? ivi i-- i -- v v v vv i i C L1M2_orf2#LIN 2396 TTCCATTTNTTTGTGTCC--TCTTCAATTTCTTTCATCAGTGTTTTATAG 2349 chr2qtel1M 454944 CTGTGTTTATATGGTATTTGGATTTGTCTTGTCAGGTAGACTC--CCCCA 454991 i v v? i vi - i --- iii iv ii v i i i--i i C L1M2_orf2#LIN 2348 TTTTCNTTGTAGAG-ATCT---TTCACCTCCTTGGTTAAATTTATTCCTA 2303 chr2qtel1M 454992 AGTATTTTATTTTGCTTATAGTTGTTTTCAATGGAATT--TTTCTTTGTA 455039 i vi i i i v v i -- vi v C L1M2_orf2#LIN 2302 GGTATTTTATTTTTTTTGTAGCTATTGTAAATGGGATTGCTTTCTTGATT 2253 chr2qtel1M 455040 TGTCTTGCTTATAATCTTTGTCAGTAATATAGAGAAACACTGATGATTTG 455089 v i v vv i -- i iiv iiii v ii iv v C L1M2_orf2#LIN 2252 TCTTTTTCAGATAGT--TCGTTGTTGGCGTATAGAAATGCTACTGATTTT 2205 chr2qtel1M 455090 TGTGAGTTCATTTTATATATTGCAATTTTGCTAGAGCTGTGAATTGTTTC 455139 iv v i vi i i ii vii vv iiv C L1M2_orf2#LIN 2204 TGTATGTTGATTTTGTATCCTGCAACTTTACTGAATTCGTTTATCAGTTC 2155 chr2qtel1M 455140 CAGTAGATTTTTGGATGATTTTCTAGGATTGTCAAAGTATCTCCTCATAT 455189 i i? v vv v i i ? v v ?i vvvv i C L1M2_orf2#LIN 2154 TAANAGTTTTTTGGTGGAGTCTTTAGGNTTTTCTANATATAAGATCATGT 2105 chr2qtel1M 455190 CTTCTCCAAAGAGTGATAGTTTTATTTCCTCATTGCCTATTCTAATTCCT 455239 v v v v i i v i v v v ivi v C L1M2_orf2#LIN 2104 CATCTGCAAACAGGGACAATTTGACTTCCTCCTTTCCAATTTGGATGCCT 2055 chr2qtel1M 455240 TTAATTTCTTTTTCATTTCTTATCAGTGAAGCTAACATTTCTAGAACAAT 455289 v i v vi v iiv vvi iv i i v v C L1M2_orf2#LIN 2054 TTTATTTCTTTCTCTTGCCTAATTGCTCTGGCTAGGACTTCCAGTACTAT 2005 chr2qtel1M 455290 ACTGAATAATAGTAGTGATAATGGATAACCTTGCTTTACCCCTGATTTTA 455339 ii iv i v i ii v ii iii v ? i C L1M2_orf2#LIN 2004 GTTGAATAGAAGTGGTGAAAGTGGGCATCCTTGTCTTGTTCCAGNTCTTA 1955 chr2qtel1M 455340 TTGAGAATGCATCCAGCTTCTCTTCATTACAA-ATAATGCTTCCTATAGG 455388 vv ii v v i i i ii - i- i i vv i i C L1M2_orf2#LIN 1954 GAGGAAAGGCTTTCAACTTTTCCCCATT-CAGTATGATGTTAGCTGTGGG 1906 chr2qtel1M 455389 TTTTAGATAGGTTACTGC--TTATTGTTTTCAGGAAAGTTCCCTTTAT-C 455435 vvv --- iv -- v v v v i i - C L1M2_orf2#LIN 1905 TTTGTCATA---TATGGCCTTTATTGTGTTGAGGTACGTTCCTTCTATAC 1859 chr2qtel1M 455436 CTTATGCCTTCTAGCGTTTATTAATAGGAATGGGTACTGTATTTTGTCAA 455485 v viv v- v - vi v v i ii v i C L1M2_orf2#LIN 1858 CTAATTTGTTG-AGAGTTT-TTATCATGAAGGGATGTTGAATTTTATCAA 1811 chr2qtel1M 455486 --GCTTTTTCTGCATCTATTGGGATTATAATATGATTTTGGTTGGTTTTG 455533 -- i v v i v ivv iv v C L1M2_orf2#LIN 1810 ATGCTTTTTCTGCATCTATTGAGATGATCATATGGTTTTTGTCCTTCATT 1761 chr2qtel1M 455534 TTATTGATATGGTCAATTATGGTAA--GATTTCCTGATACTGAACCAGCC 455581 i i i i vv i i v v -- v vv ii v C L1M2_orf2#LIN 1760 CTGTTGATGTGATGTATCACGTTTATTGATTTGCGTATGTTGAACCATCC 1711 chr2qtel1M 455582 ATGTATTCCTGGTATAAATTCCACTTGCTCATAGTGTATTATCCTGCTGA 455631 v i i v i v i ? ? i vi i C L1M2_orf2#LIN 1710 TTGCATCCCTGGGATAAATCCCACTTGATCATGGTGNATNATCTTTTTAA 1661 chr2qtel1M 455632 TAAATTGCTATAATCTCTTTGGTAACATTTTATTTAGAACTTGAGCATAA 455681 ivii i iv v vv v ii i v i i vv vv C L1M2_orf2#LIN 1660 TGTGCTGTTGAATTCGGTTTGCTAGTATTTTGTTGAGGATTTTTGCATCT 1611 chr2qtel1M 455682 GTATTCAAGAGGGAGATTGGTCTGCAATTTTGTTTCTTTGTTTTAGC--T 455729 i i vv v i i i v i v iv -- C L1M2_orf2#LIN 1610 ATGTTCATCAGGGATATTGGCCTGTAGTTTTCTTTTTTTGTTGTGTCCTT 1561 chr2qtel1M 455730 GTCTTGTTTTAGATTCAGTGCCATAATGGTGTCATACAAGGAATTTGGCA 455779 v i vv v iv iv iv i v v i v C L1M2_orf2#LIN 1560 GTCTGGTTTTGGTATCAGGGTAATGCTGGCCTCGTAGAATGAGTTTGGAA 1511 chr2qtel1M 455780 GTACTCCTTCTTCATCTGTTTTTCCAAATAG-TTGACATAGTACTGGAAT 455828 ? i i i v vi ivi - v - v i v C L1M2_orf2#LIN 1510 GNATTCCCTCCTCTTCAATTTTTTGGAATAGTTTGAGA-AGAATTGGTAT 1462 chr2qtel1M 455829 TAATTGTTCTTTAAATGTTTGGGAGAATTCACTTGTGAATTCAACTGGTC 455878 i v v viv vi v ? C L1M2_orf2#LIN 1461 TAGTTCTTCTTTAAATGTTTGGTAGAATTCAGCAGTGAAGCCATCNGGTC 1412 chr2qtel1M 455879 CTGGAGATTTTTTTCTTAGGGAATTT 455904 ivv i v? i ii i C L1M2_orf2#LIN 1411 CTGGGCTTTTCTTTGNTGGGAGACTT 1386 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.52 CpG sites = 246, Kimura (unadjusted) = 44.52 Transitions / transversions = 1.03 (246/238) Gap_init rate = 0.03 (43 / 1497), avg. gap size = 1.21 (52 / 43) 2508 30.35 1.29 1.29 chr2qtel1M 454587 455901 (544099) C L1M5_orf2#LINE/L1 (586) 2708 1394 m_b94s551i10 3487 chr2qtel1M 454587 TCTAATCTATTCCACTGATGCCTCACTCTATTTCTTA-GCTAGTACCAAA 454635 v i i viv ivv i- - i i v C L1M5_orf2#LIN 2708 TCTATTCTGTTCCATTGATCTATTTGTCTATC-CTTACGCCAATACCACA 2660 chr2qtel1M 454636 TGGT-TTGATTATTGCTGCTTTGTAACATAGTTTTAGGGT-TGGTACTAT 454683 iv - i iv i i - i ii?i -? v i C L1M5_orf2#LIN 2659 CTGTCTTGATTACTGTAGCTTTATAATA-AGTCTTGANATCNGGTAGTGT 2611 chr2qtel1M 454684 TAAGCTACCATCCTTTGTATTTTTTTATTCATTAATCCTTTGA-TATTCT 454732 v iv iv -v vi i - vv v vi i- C L1M5_orf2#LIN 2610 AAGTCCTCCA-ACTTTGTTCTTCTTT-TTCAAGATTGTTTTGGCTATTCT 2563 chr2qtel1M 454733 TGACTTTTTGTTCTTCTAGATAGCTTTTGCTTTTTTTCTTTCTAGTTCTA 454782 ? iiii ivi i v iv ivvv ivvii v v v C L1M5_orf2#LIN 2562 NGGTCCTTTGCATTTCCATATAAATTTTAGAATCAGCTTGTCAATTTCTA 2513 chr2qtel1M 454783 TAAAATAGTGTTTTTGCAGTTGGATTGTTATGGCACTGAACAAGTAGACC 454832 i v iiv vi v v v v vv v i ivvi i C L1M5_orf2#LIN 2512 CAAAAAAACCTGCTGGGATTTTGATTGGGATTGCATTGAATCTATAGATC 2463 chr2qtel1M 454833 AATTTAGGCAGAATTGTGGTTTATATTATATCAGCTCAACCTAGCCATGA 454882 i v vvi i v? iv iiiv vv v v C L1M5_orf2#LIN 2462 AATTTGGGGAGAATTGACATCTTNACAATATTGAGTCTTCCAATCCATGA 2413 chr2qtel1M 454883 ACAATTAATATTTTTCCAGTTGTTTAGATCTGATTTTCTTTGTGTGAGAA 454932 vvvv i i v i i vv vv v v v v C L1M5_orf2#LIN 2412 ACATGGTATATCTCTCCATTTATTTAGGTCTTCTTTAATTTCTCTCAGCA 2363 chr2qtel1M 454933 GTGTTTTGTAACTGT--GTTTATATGGTATTTGGATTTGTCTTGTCAGGT 454980 i ii v -- v ? - -i v iv ? i i i C L1M5_orf2#LIN 2362 ATGTTTTGTAGTTTTCAGTGTANA-GGT-CTTGCACATNTTTTGTTAGAT 2315 chr2qtel1M 454981 AGACTCCCCCAAGTATTTTATTTTGCTTATAGTTGTTTTCAATGGAATTT 455030 vv i i-- ? v vi ivv i i v v v v C L1M5_orf2#LIN 2314 TTATTCCT--AAGTATTTNATGTTTTTTGATGCTATTGTAAATGGTATTG 2267 chr2qtel1M 455031 TTCTTTGTATGTCTTGCTTATAATC-TTTGTCAGTAATATAGAGAAACAC 455079 i ?iv v v -i vi i- iiv i v i C L1M5_orf2#LIN 2266 TTTTTNAAATTTCAT-TTTCCAATTGTTTGTTGCTAGTATATAGAAATAC 2218 chr2qtel1M 455080 TGATGATTTGTGTGAGTTCATTTTATATATTGCAATTTTGCTAGAGCTGT 455129 viv v ivi v ii i vi? i ii i viiii C L1M5_orf2#LIN 2217 AATTGATTTTTGTATATTGACCTTGTATCCNGCGACCTTGCTAAATTCAC 2168 chr2qtel1M 455130 GAATTGTTTCCAGTAGATTTTTGGATGATTTTCTAGGATTGTCAAAGTAT 455179 vv iv i v ? v vv i i ? v v v ? C L1M5_orf2#LIN 2167 TTATTAGTTCTAGTAGTTTNTTTGTAGATTCTTTNGGATTTTCTACGTAN 2118 chr2qtel1M 455180 CTCCTCATATCTTCTCCAAAGAGTGATAGTTTTATTTCCTCATTGCCTAT 455229 vivv i v v i v i? i i v v v C L1M5_orf2#LIN 2117 ACAATCATGTCATCTGCGAATAANGACAGTTTTATTTCTTCCTTTCCAAT 2068 chr2qtel1M 455230 TCTAATTCCTTTAATTTCTTTTTCATTTCTTAT--CAGTGAAGCTAACAT 455277 ii v v v v vi -- v -- iv i C L1M5_orf2#LIN 2067 CTTTATGCCTTTTATTTCTTTTTCTTGCCTTATTGCACTG--GCTAGGAC 2020 chr2qtel1M 455278 TTCTAGAACAATACTGAATAATAGTAGTGATAATGGATAACCTTGCTTTA 455327 i i v ii iv i ? ii i v ii i C L1M5_orf2#LIN 2019 CTCCAGTACAATGTTGAATAGAAGTGGTGANAGCGGACATCCTTGTCTTG 1970 chr2qtel1M 455328 CCCCTGATTTTATTGAGAATGCATCCAGCTTCTCTTCATTACAAATAATG 455377 ii i i vv i v ? i i? i vi viv i C L1M5_orf2#LIN 1969 TTCCCGATCTTAGGGGGAAAGCNTTCAGTNTTTCACCATTAAGTATGATG 1920 chr2qtel1M 455378 CTTCCTATAGGTTTTAGATAGGTTACTGCTTATTGTTTTCAGGAAAGTTC 455427 i ?v i vvi i -i ivi iivv v - C L1M5_orf2#LIN 1919 TTNGCTGTAGGTTTTTCGTAGAT-GCCCTTTATCAGGTTGAGGAA-GTTC 1872 chr2qtel1M 455428 CCTT-TATCCTTATGCCTTCT-AGCGTTTATTAATAGGAATGGGTACTGT 455475 - i i - ii v - v - vi v ii v C L1M5_orf2#LIN 1871 CCTTCTATTCCTA-GTTTGCTGAGAGTTT-TTATCATGAATGGGTGTTGA 1824 chr2qtel1M 455476 ATTTTGTCAA--GCTTTTTCTGCATCTATTGGGATTATAATATGATTTTG 455523 -- i v v v C L1M5_orf2#LIN 1823 ATTTTGTCAAATGCTTTTTCTGCATCTATTGAGATGATCATATGATTTTT 1774 chr2qtel1M 455524 GTTGGTTTTGTTATTGATATGGTCAATTATGGTAA--GATTTCCTGATAC 455571 v ivv v vi i i v iiv i -- i vi ii C L1M5_orf2#LIN 1773 CTCCTTTATTCTGTTAATATGGTGAATTACATTGATTGATTTTCGAATGT 1724 chr2qtel1M 455572 TGAACCAGCCATGTATTCCTGGTATAAATTCCACTTGCTCATAGTGTATT 455621 i i v i v ii v ii C L1M5_orf2#LIN 1723 TAAACCAACCTTGCATTCCTGGGATAAACCCCACTTGGTCATGATGTATT 1674 chr2qtel1M 455622 ATCCTGCTGATAAATTGCTATAATCTCTTTGGTAACATTTTATTTAGAAC 455671 vi v v iv v vv v i i ? i i C L1M5_orf2#LIN 1673 ATCCTTTTTATATATTGCTGGATTCGATTTGCTAATATTTTGTTNAGGAT 1624 chr2qtel1M 455672 TTGAGCATAAGTATTCAAGAGGGAGATTGGTCTGCAATTTTGTTTCTTTG 455721 vv vvi i v v i v ii C L1M5_orf2#LIN 1623 TTTTGCATCTATGTTCATGAGGGATATTGGTCTGTAATTTTCTTTTCTTG 1574 chr2qtel1M 455722 TTTTAGC--TGTCTTGTTTTAGATTCAGTGCCATAATGGTGTCATACAAG 455769 vv iv -- ?v i vv v i? iv iv v v C L1M5_orf2#LIN 1573 TAATGTCTTTGTCNGGTTTTGGTATCAGGGTNATGCTGGCCTCATAAAAT 1524 chr2qtel1M 455770 GAATTTGGCAGTACTCCTTCTTCATCTGTTTTTCCAAATAGTTGACATAG 455819 i v v ii i iv i iivi v viii i C L1M5_orf2#LIN 1523 GAGTTGGGAAGTGTTCCCTCTTTTTCTATTTTCTGGAAGAGTTTGTGTAA 1474 chr2qtel1M 455820 TACTGGAATTAATTGTTCTTTAAATGTTTGGGAGAATTCACTTGTGAATT 455869 v i v v v i v iv vi C L1M5_orf2#LIN 1473 GATTGGTATTATTTCTTCCTTAAATGTTTGGTAGAATTCACCAGTGAAGC 1424 chr2qtel1M 455870 CAACTGGTCCTGGAGATTTTTTTCTTAGGGAA 455901 v v v i v -- C L1M5_orf2#LIN 1423 CATCTGGGCCTGGAGTTTTCTTTGT--GGGAA 1394 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.63 CpG sites = 199, Kimura (unadjusted) = 40.28 Transitions / transversions = 1.02 (199/195) Gap_init rate = 0.02 (29 / 1314), avg. gap size = 1.17 (34 / 29) 1420 28.44 1.58 2.38 chr2qtel1M 456966 457599 (542401) C L1ME3G_3end#LINE/L1 (294) 630 2 m_b94s551i11 3489 chr2qtel1M 456966 TGCTCATTTCACTCAGCATCAGCTCATGTAAGTCTTTCCAAGCCTCTCTG 457015 iv i vi vv v v ii v i vv vii C L1ME3G_3end#L 630 TGCTTTTTTCACTCAACAATATGTCTTGGAGATCTTTCCATGTCAGTACA 581 chr2qtel1M 457016 TATTCATCCTCC-CAGTCATTTCTTAGAGAACAATAATATTCCATAACAT 457064 vv iv - v - i v v? vvvv i ii C L1ME3G_3end#L 580 TATAGATCTACCTCATTC-TTTTTAACNGCTGCATAGTATTCCATAGTAT 532 chr2qtel1M 457065 TCATATACCA-AATTTACCCAAACATTCTCCAATTGATGGGCATCCATTC 457113 vv - iii v i v i ii vvi C L1ME3G_3end#L 531 GGATATACCATAATTTATTTAACCATTCCCCTATTGATGGACATTTAGGT 482 chr2qtel1M 457114 ATTTTCCAGTTTCTAGCCACTACAAA-AAGGGTGCCACAAACATTTTGGC 457162 vv i i v i i - v v v ii ii v i C L1ME3G_3end#L 481 TGTTTCCAATTTTTCGCTATTACAAACAATGCTGCAATGAACATCCTTGT 432 chr2qtel1M 457163 ATACCCAGGTCCCTTT-CTCTTCTTT-AGTATCTCTTTGGGATACAAAGC 457210 i iv ?-- i v - v v v vi- i ? i -i v? C L1ME3G_3end#L 431 ACATGCN--TCCTTGTGCACATGTGCGAGTATTTCTNTAGGATA-GATNC 385 chr2qtel1M 457211 CCAGTAGTAACACTGCTGGATCAAAGG-TATGCACAGTTTGATAACTTTT 457259 ? v iiv i i - i v i -- i v C L1ME3G_3end#L 384 CNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGCATTTTAA--ATTTTA 337 chr2qtel1M 457260 TGAGCATAATTCCAAATTGCTCTCCAGAATGGCTGGATCTGTTCACAATT 457309 vv - v v i i ? v i vi i v i C L1ME3G_3end#L 336 ATAG-ATACTGCCAAATTGCCCTCCAAAANGGCTGTACCAATTTACACTC 288 chr2qtel1M 457310 CCACCAACAATGCATCAGTGTCCCAATTTTCCCACATGCCCTCCAACATT 457359 i i i v v v vi i iv i v i C L1ME3G_3end#L 287 CCACCAGCAGTGTATGAGAGTACCCGTTTCCCCACACCCTCGCCAACACT 238 chr2qtel1M 457360 CATCATTATC----TTTTACTGTCATCTTAGCCAATCTGACAGGTATATA 457405 ?ivi ---- v---- i v ii iv v C L1ME3G_3end#L 237 NGATATTATCAANCTTTTAA----ATTTTTGCCAATCTGATGGGTGAAAA 192 chr2qtel1M 457406 GTGGTATCTCAGAGTTGTCTTAATTTGAATTTCTCTGATCAATAGTGATT 457455 i vv i v i i v vv C L1ME3G_3end#L 191 ATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGATTACTAGTGAGG 142 chr2qtel1M 457456 TGGAACACCCTTTTATATGGGTAAAAATAGTTTCAATTTCATCATCTGAA 457505 v i i i i vv vviiivi vv v v vi C L1ME3G_3end#L 141 TTGAGCATCTTTTCATATGTTTATTGGCCATTTGTATTTCCTCTTCTGTG 92 chr2qtel1M 457506 AATTGTCTGTTCATATCCTTTGACCATTTATCAATTGGAGAATGGCTTGA 457555 i v v v iv-- v -- C L1ME3G_3end#L 91 AATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGGGT--TGTCTT-- 46 chr2qtel1M 457556 TTTCCTATAAATTAGAGTTAATTCTCTATATACTTTGGAAATTA 457599 i vi v vivv i i i i v C L1ME3G_3end#L 45 TTTCTTATTGATTTGTAGGAGTTCTTTATATATTCTGGATATTA 2 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.88 CpG sites = 86, Kimura (unadjusted) = 36.65 Transitions / transversions = 0.96 (86/90) Gap_init rate = 0.03 (22 / 633), avg. gap size = 1.14 (25 / 22) 4179 29.84 3.42 3.01 chr2qtel1M 457451 460166 (539834) C L1M5_orf2#LINE/L1 (0) 3294 568 m_b94s551i12 3489 chr2qtel1M 457451 TGATTTGGAACACCCTTTTATATGGGTAAAAATAGTTTCAATTTCATCAT 457500 ?v v i i i i i vv vviiivi v? v v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr2qtel1M 457501 CTGAAAATTGTCTGTTCATATCCTTTGACCATTTATCAATTGGA--GAAT 457548 i vi v vi i v v ?v i-- vv C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTT 3195 chr2qtel1M 457549 GGCTTGATTTCCTAT-AAATTAGAGTTAATTCTCTATATACTTTGGAAAT 457597 v -- ?i -i ? iv v- i i i i v i C L1M5_orf2#LIN 3194 GTCTT--TTTNTTATTGANTTGTAGG-AGTTCTTTATATATTCTGGATAC 3148 chr2qtel1M 457598 TAGACCTTTATCAGA-ACCTTTAACTGTAAA-ATGTTTTCCCAGTTTATT 457645 v v i - iv v ?-i i - v i ? i i v C L1M5_orf2#LIN 3147 GAGTCCTTTGTCAGATATATGTN-TTGCAAATATTTTCTCCCANTCTGTG 3099 chr2qtel1M 457646 GCTTCCCTTCTGATCTTGTCTGCATTAGTTTTGTTTGTACAAAAACTTTT 457695 v i v i v ivi iv ivi vvv? vi i ii C L1M5_orf2#LIN 3098 GCTTGCCTTTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTTT 3049 chr2qtel1M 457696 TAATTTGATATAATCAAA-------ATTTTCTATTTTGTGATCAATAATG 457738 v v i? i v ------- i v i i --- ?i C L1M5_orf2#LIN 3048 AATTTTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGGT---TNGTG 3002 chr2qtel1M 457739 GTCTCTAGTTCTTCTTTGGTCACAAATTCCTTCCTCCTTCACAGGTCTGA 457788 v i i ivv i v i--- v iii v v?ii - vvi C L1M5_orf2#LIN 3001 CTTTTTGTGTCCTGTTTA---AGAAATCTTTGCCTANCCCA-AGGTCACG 2956 chr2qtel1M 457789 GAGGTAAACTGTCCTGTGTT--CCTCTAATTTATTTATAATTTTGTTCTT 457836 i i --i v i -- i ivvvv i i?ii C L1M5_orf2#LIN 2955 AAGATA--TTCTCCTATGTTTTCTTCTAGAAGTTTTATAGTTTTANCTTT 2908 chr2qtel1M 457837 TATGCCTAAATC-ACGAACCCGTTTTGATCTTATCTTGGTATATAGTGTT 457885 iiii ii - i -i i i ? vi v i v i i v C L1M5_orf2#LIN 2907 TACATTTAGGTCTATGA-TCCATCTNGAATTAATTTTTGTGTATGGTGTG 2859 chr2qtel1M 457886 AAGTGTGAGTCCTTGCCTAGTTTCTGCCATACTAATTTCCACTTTTCCCA 457935 i iv i vvv?iii v i v ivi v v v i C L1M5_orf2#LIN 2858 AGGTAGGGGTCGAGNTTCATTTTTTTCCATATGGATATCCAATTGTTCCA 2809 chr2qtel1M 457936 GCAGTTTTTGTCAAATAGTGAATTCTTATCCCAA-AAGTTGGGATCTTGG 457984 viv ii v vvv i vi v-i i ---i? C L1M5_orf2#LIN 2808 GCACCATTTGTTGAAAAGACTATCCTTTCCCCACTGAATTG---CNTTGG 2762 chr2qtel1M 457985 G---TTTGTCAAAGACTAGATTGCTGTAGTTAT-TGA--CTATTTTATCC 458028 v--- i ii i? v? ii vv i - i-- i---- C L1M5_orf2#LIN 2761 CACCTTTGTCAAAAATCAANTGNCCATATATGTGTGGGTCTATTTC---- 2716 chr2qtel1M 458029 TGTGAAC---CTAACCTATTCCACTGATCAACTAATCTATTTCTTAGGT- 458074 -- i --- vi i i v i vi i- v i- C L1M5_orf2#LIN 2715 --TGGACTCTCTATTCTGTTCCATTGATCTATTTGTCTATC-CTTACGCC 2669 chr2qtel1M 458075 AATACCAAATGGTTTTGGTGACTGCTGCTTTATAATATACTTTCAGATCA 458124 v iv i i v iv viii v ? ? C L1M5_orf2#LIN 2668 AATACCACACTGTCTTGATTACTGTAGCTTTATAATAAGTCTTGANATCN 2619 chr2qtel1M 458125 GGTACAGCTAGGCTGCCTTAA-TTTGATTTT-TTTTTCATTAG-TTCCCT 458171 vv iv v iv -- - v i - -- - vii C L1M5_orf2#LIN 2618 GGTAGTGTAAGTCCTCC--AACTTTGTTCTTCTTTTTCA--AGATTGTTT 2573 chr2qtel1M 458172 TGAA-AGTCTTGACCTTTTGTTCTTTCAGACGAATTTTATTGTTATTTT- 458219 iv- v ? ii i ivi i v ii vvi i vi - C L1M5_orf2#LIN 2572 TGGCTATTCTNGGTCCTTTGCATTTCCATATAAATTTTAGAATCAGCTTG 2523 chr2qtel1M 458220 ----TTTCTAGATCATTAAAATAGTTTCTTCAGAGTCTGATTGGTATAGC 458265 ---- ------i v iii vi vi v i v v C L1M5_orf2#LIN 2522 TCAATTTCTA------CAAAAAAACCTGCTGGGATTTTGATTGGGATTGC 2479 chr2qtel1M 458266 ACTAAATAAATAGATTA-----GGGAATATTGTCATCTTTATTATATTCA 458310 i i vv i ----- iv v ? iv v C L1M5_orf2#LIN 2478 ATTGAATCTATAGATCAATTTGGGGAGAATTGACATCTTNACAATATTGA 2429 chr2qtel1M 458311 CTTGGCCTATCCAAGAGCACTTAATATTTTTTCAATTGTTTAAATCTGAC 458360 v ivv v v i ivvv i i i v i ii vvi C L1M5_orf2#LIN 2428 GTCTTCCAATCCATGAACATGGTATATCTCTCCATTTATTTAGGTCTTCT 2379 chr2qtel1M 458361 TTTATTTGTGTGGAAAGTATTTTGTAGTTTTGCTG-ATATAATTCCTGAC 458409 v v v viiv i i - v -i ? iv i vv C L1M5_orf2#LIN 2378 TTAATTTCTCTCAGCAATGTTTTGTAGTTTT-CAGTGTANAGGTCTTGCA 2330 chr2qtel1M 458410 TTTCCTTTGGCAAATAGATTCCCAAATATTTTATGCTATC-AACACTTAT 458458 iv ?i vi i vv i i ? i v i-i ii - C L1M5_orf2#LIN 2329 CATNTTTTGTTAGATTTATTCCTAAGTATTTNATGTTTTTTGATGCT-AT 2281 chr2qtel1M 458459 TCTAAATGGAATTTCTCTTTGTATCTC---TTGCTGTTGGATTTTGTTGT 458505 v v vi i ?iv i --- v vi --- i C L1M5_orf2#LIN 2280 TGTAAATGGTATTGTTTTTNAAATTTCATTTTCCAATTG---TTTGTTGC 2234 chr2qtel1M 458506 TGATGTATAAAAATGATGAG-GATTTATGTGGCTTTATTTTGTATTTTGC 458554 ii i i - ii v- v ivv v ii ii? C L1M5_orf2#LIN 2233 TAGTATATAGAAAT-ACAATTGATTTTTGTATATTGACCTTGTATCCNGC 2185 chr2qtel1M 458555 AACTTTGCTAAAGTTGTCAATTATTTCTAATATCTTTTTAGTAGAATCTC 458604 i i v iiiiv v i vi ? v v i C L1M5_orf2#LIN 2184 GACCTTGCTAAATTCACTTATTAGTTCTAGTAGTTTNTTTGTAGATTCTT 2135 chr2qtel1M 458605 TGGGGTTCCCTAAGTATACCATCATATCATCTGCAAAGAGTGATAATTTG 458654 ? i ii v ? v i i v i? i i v C L1M5_orf2#LIN 2134 TNGGATTTTCTACGTANACAATCATGTCATCTGCGAATAANGACAGTTTT 2085 chr2qtel1M 458655 GTTTCTTCATTATCTACTCTA-ATTCCTTTAATCTCTTTCTCAACTCTTA 458703 i v - i v v- v v i i vvvi C L1M5_orf2#LIN 2084 ATTTCTTCCTT-TCCAATCTTTATGCCTTTTATTTCTTTTTCTTGCCTTA 2036 chr2qtel1M 458704 TTGCCAAAGCTAGCATTTCTAATACAATATTGAATAATAATGGTGATAGA 458753 vvvi v ii i i i iv i ? v C L1M5_orf2#LIN 2035 TTGCACTGGCTAGGACCTCCAGTACAATGTTGAATAGAAGTGGTGANAGC 1986 chr2qtel1M 458754 GGGCAATCTTGTTTCATTCCTGATCTTACTGGGAATGGTTCCAGTTTATC 458803 i vi i ii i vv v v? i ? v C L1M5_orf2#LIN 1985 GGACATCCTTGTCTTGTTCCCGATCTTAGGGGGAAAGCNTTCAGTNTTTC 1936 chr2qtel1M 458804 CCCATTACGTATGAT---TGCTGATGGTTTTAAATAAATGCTCCTGAGTA 458850 v v ---? vv vvi i i i v vi C L1M5_orf2#LIN 1935 ACCATTAAGTATGATGTTNGCTGTAGGTTTTTCGTAGATGCCCTTTATCA 1886 chr2qtel1M 458851 TTTTACGGAAAAGTCAATTTATTCCTATATTCTCAAGTGTTTTTATTAGG 458900 vv iv ivvi vv i vv viii v i v C L1M5_orf2#LIN 1885 GGTTGAGGAAGTTCCCTTCTATTCCTAGTTTGCTGAGAGTTTTTATCATG 1836 chr2qtel1M 458901 AATGAATGTTGGATTTTATCAAATGCTTTTTCTGCATCTATTGAGATGAT 458950 ii i i C L1M5_orf2#LIN 1835 AATGGGTGTTGAATTTTGTCAAATGCTTTTTCTGCATCTATTGAGATGAT 1786 chr2qtel1M 458951 CATATGGTTTTT---GTTAATTTGGTTATTGATATAGTCAATTATGCTAA 458997 i ---v v iv --- i v iii i C L1M5_orf2#LIN 1785 CATATGATTTTTCTCCTTTATTCTGTTA---ATATGGTGAATTACATTGA 1739 chr2qtel1M 458998 TAGTTTTCCCAATATTGAACCAGCCCTGCATTCCTGGTATAAATCCTACT 459047 v v i v i i i i v i i C L1M5_orf2#LIN 1738 TTGATTTTCGAATGTTAAACCAACCTTGCATTCCTGGGATAAACCCCACT 1689 chr2qtel1M 459048 TGGTCATGGTGTATTATCCTGGGGATGATTTTCTGTAATCTTTTTGCTAA 459097 i vvvv ivv v v v vv C L1M5_orf2#LIN 1688 TGGTCATGATGTATTATCCTTTTTATATATTGCTGGATTCGATTTGCTAA 1639 chr2qtel1M 459098 TACTTTATTTAAGATTTTTGCATCAATGTTCATTAGGGAAATTGGTTTAT 459147 i i ? i v v v i i C L1M5_orf2#LIN 1638 TATTTTGTTNAGGATTTTTGCATCTATGTTCATGAGGGATATTGGTCTGT 1589 chr2qtel1M 459148 AATTTTCTTTCTCTGT--TTTCAGCCTACTCAGTTTAAGTATCAGTACCA 459195 iii -- v --ii iii?i vi vii? C L1M5_orf2#LIN 1588 AATTTTCTTTTCTTGTAATGTC--TTTGTCNGGTTTTGGTATCAGGGTNA 1541 chr2qtel1M 459196 TGTCTGTGTCATAAAAGGAATTTGGTAGGACTCCTTCAATCCCTATTTTT 459245 iiv iv v i v v vii i vv ii i C L1M5_orf2#LIN 1540 TGCTGGCCTCATAAAATGAGTTGGGAAGTGTTCCCTCTTTTTCTATTTTC 1491 chr2qtel1M 459246 TCAAATAATTTATATAGCATTGGAATTAATTGTTCTTTAAATGTTTGGTA 459295 vi v i i i iv v v v i C L1M5_orf2#LIN 1490 TGGAAGAGTTTGTGTAAGATTGGTATTATTTCTTCCTTAAATGTTTGGTA 1441 chr2qtel1M 459296 GGATTCACATTTAAATACATCTGATCCTGGGGATTTTTTCTTAGGCAGTT 459345 i vvv i vv iv i v i iv i v v C L1M5_orf2#LIN 1440 GAATTCACCAGTGAAGCCATCTGGGCCTGGAGTTTTCTTTGTGGGAAGGT 1391 chr2qtel1M 459346 GATTAATAGCTTGTTCTATTTCTTTCCAAG--ATGGGACTGTTTAATGAA 459393 vv vi vvi v vvv -- i i i i -- v C L1M5_orf2#LIN 1390 TTTTAATTACAAATTCAATTTCTTTAATAGATATAGGGCTATTCA--GAT 1343 chr2qtel1M 459394 TT--TACTTCTTCT---GTTAATCTGGGCAAGATATATTTTTGAAAGTAT 459438 -- i --- i i i v i ?v i i v i v C L1M5_orf2#LIN 1342 TTTCTATTTCTTCTTGNGTCAGTTTTGGTAANTTGTGTTTTTCAAGGAAT 1293 chr2qtel1M 459439 TATTCCATTTCATTTAAGTTATTGAATTTATTGGCATAAAGTTGGGCAAA 459488 vv i ? ii vv v C L1M5_orf2#LIN 1292 TTGTCCATTTCATCTAAGTTNTCAAATTTATTGGCATAAAGTTGTTCATA 1243 chr2qtel1M 459489 GTAACTCCTAATTACTGCTTTAATTTCCTCT----TCCTTAGTGGCGAGT 459534 i viii v iivi v - v ---- iv ii --- C L1M5_orf2#LIN 1242 ATATTCTCTTATTATCCTTTTAATGT-CTGTAGGATCTGTAGTGATG--- 1197 chr2qtel1M 459535 TCTCCCTTTTTATTTTTAAGACTAACAATTTG-GTTTTC-CTCTTTCCTT 459582 i i ii i v i iii - i - --- C L1M5_orf2#LIN 1196 TCTCCTTTTTCATTCCTGATATTGGTAATTTGTGTCTTCTCTCTT---TT 1150 chr2qtel1M 459583 TTTTTTCATCAGATTTACTAAGGGTTTATCTATTTTGTTGGT-TTTTCAT 459631 i v vi ?i ii v i i - v C L1M5_orf2#LIN 1149 TTTCTTGATCAGTCTNGCTAGAGGTTTATCAATTTTATTGATCTTTTCAA 1100 chr2qtel1M 459632 AAAACCAAATCTTAGTTTTGTTTATTAATTCAATAGTTTTTTTTTTAACT 459681 i iv i i i i v vvi v v ? ? v ---- C L1M5_orf2#LIN 1099 AGAACCAGCTTTTGGCTTCGTTGATTTTCTCTATTGTNTNTTTGT----T 1054 chr2qtel1M 459682 TTCAATTTTATTAATCTTTCCTTTTATTTTTAGAATTTCAAGTTTAGTGT 459731 v i i i i v i i vv vvvii vv ii C L1M5_orf2#LIN 1053 TTCTATTTCATTGATTTCTGCTCTTATCTTTATTATTTCCTTCCTTCTAC 1004 chr2qtel1M 459732 TTGACTGGAGGTTTTTAATTTGTTC----TTTTCTAGCTTTTTTAGTTGC 459777 ?vi v i --- i ---- i v v v C L1M5_orf2#LIN 1003 TTNCTTTGGG---TTTAATTTGCTCTTCTTTTTCTAGCTTCTTAAGGTGG 957 chr2qtel1M 459778 AAGCCCAATTCACTGACCTT---CTCTTTTTCTATTTTATGCAAGTAGGT 459824 ii iv i ii --- ii i v i --- vi ? i C L1M5_orf2#LIN 956 AAGCTTAGATCATTGATTTTAAGCCTTTCTTCTTTTCTA---ATATANGC 910 chr2qtel1M 459825 CTCTAGAGATATAAAATTTCCCTTT-ATTACCGCTTTGGCTGCATCCCAC 459873 v i i? v - i - vi i i C L1M5_orf2#LIN 909 ATTTAANGCTAT-AAATTTCCCTCTAAGCACTGCTTTAGCTGCATCCCAC 861 chr2qtel1M 459874 ACATGTTGATATGACATCTCATTATTGTCATTTTCGTGGGTGAAGTTAT- 459922 v v vii v iv i ? ----ii v v iv - C L1M5_orf2#LIN 860 AAATTTTGATATGTTGTATTTTCATTNTCATT----CAGTTCAAAATATT 815 chr2qtel1M 459923 ---TAATTATGTCTGTGATCTGCTGTTTCACCCAATCATTCTTTAG-GGT 459968 --- viv?i i vi v v vvvi v -i C L1M5_orf2#LIN 814 TTCTAATTTCCNTTGTGATTTCTTCTTTGACCCATGGGTTATTTAGAAGT 765 chr2qtel1M 459969 GAGATTATTTAGTTTCCAATTACTTTTTGGCCAATTTACCCTGG----CT 460014 v - i i v --- vv v --- i ---- C L1M5_orf2#LIN 764 GTG-TTGTTTAATTTCCAAATA---TTTGGGGATTTT---CTAGNTATCT 722 chr2qtel1M 460015 TTTTG---TTGAATGTAATTTTCATTGCATTGTGATTTGAAAAGGATGCA 460061 --- v viv v v v i iv i -v i v C L1M5_orf2#LIN 721 TTTTGTTATTGATTTCTAATTTAATTCCATTGTGGTCAGAGAA-CATACT 673 chr2qtel1M 460062 TT-TACTATTTCTGCCTTTCTGCATTTGAATTTCAGGT---TTTTATGTA 460107 i - iv vii i i?iv i--- v ii--- -i C L1M5_orf2#LIN 672 CTGTATGATTTCAATCCTTTNAAATTTA---TTGAGACTTGTTTTATG-G 627 chr2qtel1M 460108 CTAATAATATGGTCAATTTTTGTATAGGTTCCATGAACTGCTAAGAAGAA 460157 iv v? v i v v v vi vvi i i C L1M5_orf2#LIN 626 CCCAGNATATGGTCTATCTTGGTAAATGTTCCATGTGCACTTGAAAAGAA 577 chr2qtel1M 460158 ACTGTAGTC 460166 vv v C L1M5_orf2#LIN 576 TGTGTATTC 568 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.29 CpG sites = 428, Kimura (unadjusted) = 39.82 Transitions / transversions = 1.20 (428/358) Gap_init rate = 0.05 (126 / 2715), avg. gap size = 1.39 (175 / 126) 4011 31.38 3.54 3.00 chr2qtel1M 457503 460521 (539479) C L1M4_orf2#LINE/L1 (52) 3242 208 m_b94s551i13 3489 chr2qtel1M 457503 GAAAATTGTCTGTTCATATCCTTTGACCATTTATCAATTGGAGAATGGCT 457552 i v i v v v ? ivv --- C L1M4_orf2#LIN 3242 GAGAAATGTCTATTCAAATCCTTTGCCCATTTTTNAATTGGGTTAT---T 3196 chr2qtel1M 457553 TGATTTCCTATAAATTAGAGTT-----AATTCTCTATATACTTTGGAAAT 457597 vi ii vi- - ----- i i i i v i C L1M4_orf2#LIN 3195 TGTCTTTTTATTG-TT-GAGTTGTAAGAGTTCTTTATATATTCTGGATAC 3148 chr2qtel1M 457598 TAGACCTTTATCAGAACCTTTAACTGTAAA-ATGTTTTCCCAGTTTATTG 457646 ? v i vviv v vi i - v i v i i v C L1M4_orf2#LIN 3147 NAGTCCCTTATCAGATATATGATTTGCAAATATTTTCTCCCATTCTGTGG 3098 chr2qtel1M 457647 CTTCCCTTCTGATCTTGTCTGCATTAGTTTTGTTTG---TACAAAAACTT 457693 v vi i v - - vv - v iv ---i ii C L1M4_orf2#LIN 3097 GTTGTCTTTTCA-CTT-TCTTGAT-AGTGTCCTTTGAAGCACAAAAGTTT 3051 chr2qtel1M 457694 TTTAATTTGATATAATCAAAATTTTCTATTTTGTGATCAATAATGGTCTC 457743 v v iv i v v v v vv ------ v iv C L1M4_orf2#LIN 3050 TTAATTTTGATGAAGTCCAATTTATCTATTTTTTCTT------TTGTTGC 3007 chr2qtel1M 457744 TAGTTCTTCTTTGGTCACA------AATTCCTT-CCTCCTTCACAGGTCT 457786 v v i vvv i ------ vi v - vv i - v C L1M4_orf2#LIN 3006 TTGTGCTTTTGGTGTCATATCTAAGAAACCATTGCCTAATCCA-AGGTCA 2958 chr2qtel1M 457787 GAGAGGTAAACTGTCCTGTGTTCCTCTAATTTATTTATAATTTT-GTTCT 457835 vii i vv ?viiv v i vvvv i - i C L1M4_orf2#LIN 2957 CGAAGATTTACNCCTATGTTTTCTTCTAAGAGTTTTATAGTTTTAGCTCT 2908 chr2qtel1M 457836 TTATGCCTAAATCACGAACCCGTTTTGATCTTATCTTGGTATATAGTGTT 457885 - iiii ii vivi i i vi v i v i v C L1M4_orf2#LIN 2907 T-ACATTTAGGTCTTTGATCCATTTTGAGTTAATTTTTGTATATGGTGTG 2859 chr2qtel1M 457886 AAGTGTGAGTCC--TTGCCTAGTTTCTGCCATACTAATTTCCACTTTTCC 457933 i iv i --i v v vv - - iivi v v v C L1M4_orf2#LIN 2858 AGGTAGGGGTCCAACTTCATTCTTT-TGC-ATGTGGATATCCAGTTGTCC 2811 chr2qtel1M 457934 CAGCAGTTTTTGTCAAATAGTGAATTCTTATCCCAAAAGTTGG--GATCT 457981 viv ii v vvv vi ---- i--?i C L1M4_orf2#LIN 2810 CAGCACCATTTGTTGAAAAGACTATTCTTTCCCCA----TTGAATNGTCT 2765 chr2qtel1M 457982 TGGG---TTTGTCAAAGACTAGATTG-CTGTAGTTATTGACTATTTTATC 458027 v---i i i ii - - ii iv i -- ?viv i C L1M4_orf2#LIN 2764 TGGCACCCTTGTCGAAAATCA-ATTGACCATAAATGT--ANGGGTTTATT 2718 chr2qtel1M 458028 CTGTGAAC-CTAA--CCTATTCCACTGATCAACTAATCTATTTCTTA-GG 458073 - v i - v --i i v ivvi i- - v C L1M4_orf2#LIN 2717 -TCTGGACTCTCAATTCTATTCCATTGATCTATATGTCTATC-CTTATGC 2670 chr2qtel1M 458074 TAATACCAAATGGTTTTGGTGACTGCTGCTTTATAATATACTTTCAGATC 458123 i i v iv i i v iv i i vii v i C L1M4_orf2#LIN 2669 CAGTACCACACTGTCTTGATTACTGTAGCTTTGTAGTAAGTTTTGAAATC 2620 chr2qtel1M 458124 AGGTACAGCTAGGCTGCCTTAA-TTTGATTTT-TTTTTCATTAG-TTCCC 458170 i v vv iv v iv -- - v i - -- - vii C L1M4_orf2#LIN 2619 GGGAAGTGTGAGTCCTCC--AACTTTGTTCTTCTTTTTCA--AGATTGTT 2574 chr2qtel1M 458171 TTGAA-AGTCTTGACCTTTTGTTCTTTCAGACGAATTTTA--------TT 458211 iv- v v ii ii ivi i v i -------- C L1M4_orf2#LIN 2573 TTGGCTATTCTGGGTCCCTTGCATTTCCATATGAATTTTAGGATCAGCTT 2524 chr2qtel1M 458212 GTTATTTTTTTCTAGATCATTAAAATAGTTTCTTCAGAGTCTGATTGGTA 458261 i v i v --------- v ?ivvi vi v i v v C L1M4_orf2#LIN 2523 GTCAATTTCTGC---------AAAAAAGNCAGCTGGGATTTTGATAGGGA 2483 chr2qtel1M 458262 TAGCACTAAATAAATAGATTA-----GGGAATATTGTCATCTTTATTATA 458306 v ii i vvi i ----- i i v iv C L1M4_orf2#LIN 2482 TTGCGTTGAATCTGTAGATCAATTTGGGGAGTATTGCCATCTTAACAATA 2433 chr2qtel1M 458307 TTCACTTGGCCTATCCAAGAGCACTTAATATTTTTTCAATTGTTTAAATC 458356 v v ivv v v i ivvi i i i v i ii C L1M4_orf2#LIN 2432 TTAAGTCTTCCAATCCATGAACATGGGATGTCTTTCCATTTATTTAGGTC 2383 chr2qtel1M 458357 TGACTTTATTTGTGTGGAAAGTATTTTGTAGTTTTGCTG-ATATAATTCC 458405 vvi v v v vi v i i - v -i i v i C L1M4_orf2#LIN 2382 TTCTTTAATTTCTTTCAACAATGTTTTGTAGTTTT-CAGTGTACAAGTCT 2334 chr2qtel1M 458406 TGACTTTCCTTTGGCAAATAGATTCCCAAATATTTTATGCTATC-AACAC 458454 vvi i vi vv i i v v i-i ii C L1M4_orf2#LIN 2333 TGCACTTCTTTTGTTAAATTTATTCCTAAGTATTTTATTCTTTTTGATGC 2284 chr2qtel1M 458455 TTATTCTAAATGGAATTTCTCTTTGTATCTCTTGCTGTTGGATT--TTGT 458502 - v vi i i vv i v -- v i -- ii C L1M4_orf2#LIN 2283 T-ATTGTAAATGGAATTGTTTTCTTAATTTCAT--TTTCGGATTGTTCAT 2237 chr2qtel1M 458503 TGTTGATGTATAAAAATGATGAG-GATTTATGTGGCTTTATTTTGTATTT 458551 i ii i - ii v- v ivv v i ii C L1M4_orf2#LIN 2236 TGCTAGTGTATAGAAAT-ACAATTGATTTTTGTATATTGATCTTGTATCC 2188 chr2qtel1M 458552 TGCAACTTTGCTAAAGTTGTCAATTATTTCTAATATCTTTTTAGTAGAAT 458601 i i v i iv v vi ? i v C L1M4_orf2#LIN 2187 TGCAACCTTGCTGAACTCGTTTATTAGTTCTAATAGTTTTTTNGTGGATT 2138 chr2qtel1M 458602 CTCTGGGGTTCCCTAAGTATACCATCATATCATCTGCAAAGAGTGATAAT 458651 ii i i ii vi i vv i i v v i C L1M4_orf2#LIN 2137 CCTTAGGATTTTCTATATACAAGATCATGTCATCTGCGAATAGAGATAGT 2088 chr2qtel1M 458652 TTGGTTTCTTCATTATCTACTCTA-ATTCCTTTAATCTCTTTCTCAACTC 458700 vii v - i v i- v v i i vvvi C L1M4_orf2#LIN 2087 TTTACTTCTTCCTT-TCCAATCTGGATGCCTTTTATTTCTTTTTCTTGCC 2039 chr2qtel1M 458701 TTATTGCCAAAGCTAGCATTTCTAATACAATATTGAATAATAATGGTGAT 458750 v vvi v ii i i i iv i i v C L1M4_orf2#LIN 2038 TAATTGCCCTGGCTAGAACCTCCAGTACAATGTTGAATAGAAGTGGCGAG 1989 chr2qtel1M 458751 AGAGGGCAATCTTGTTTCATTCCTGATCTTACTGGGAATGGTTCCAGTTT 458800 v i vi i ii vv v v? i i C L1M4_orf2#LIN 1988 AGCGGACATCCTTGTCTTGTTCCTGATCTTAGGGGGAAAGCNTTCAGTCT 1939 chr2qtel1M 458801 ATCCCCATTACGTATGATT---GCTGATGGTTTTAAATAAATGCTCCTGA 458847 v v v v--- vv vvi i i i v C L1M4_orf2#LIN 1938 TTCACCATTAAGTATGATGTTAGCTGTGGGTTTTTCGTAGATGCCCTTTA 1889 chr2qtel1M 458848 GTATTTTACGGAAAAGTCAATTTATTCCTATATTCTCAAGTGTTTTTATT 458897 vi vv iv ivvi vv i vv v ii i C L1M4_orf2#LIN 1888 TCAGGTTGAGGAAGTTCCCTTCTATTCCTAGTTTGTTGAGTGTTTTTATC 1839 chr2qtel1M 458898 AGGAATGAATGTTGGATTTTATCAAATGCTTTTTCTGCATCTATTGAGAT 458947 v v ii i i C L1M4_orf2#LIN 1838 ATGAAAGGGTGTTGGATTTTGTCAAATGCTTTTTCTGCGTCTATTGAGAT 1789 chr2qtel1M 458948 GATCATATGGTTTTTGTTAATTTGGT-TATTGATATAGTCAATTATGCTA 458996 i iv- iv - i i vv iii i C L1M4_orf2#LIN 1788 GATCATGTGGTTTTTGTCC-TTTATTCTATTAATATGGTGTATTACATTG 1740 chr2qtel1M 458997 ATAGTTTTCCCAATATTGAACCAGCCCTGCATTCCTGGTATAAATCCTAC 459046 v v i v? i i i v i C L1M4_orf2#LIN 1739 ATTGATTTTCGNATGTTGAACCAACCTTGCATTCCTGGGATAAATCCCAC 1690 chr2qtel1M 459047 TTGGTCATGGTGTATTATCCTGGGGATGATTTTCTGTAATCTTTTTGCTA 459096 v vvvv ivv v v v vv C L1M4_orf2#LIN 1689 TTGGTCATGGTGTATAATCCTTTTTATATGTTGCTGGATTCGGTTTGCTA 1640 chr2qtel1M 459097 ATACTTTATTTAAGATTTTTGCATCAATGTTCATTAGGGAAATTGGTTTA 459146 i i i v i v i v v i i C L1M4_orf2#LIN 1639 GTATTTTGTTGAGGATTTTTGCATCTATATTCATAAGGGATATTGGTCTG 1590 chr2qtel1M 459147 TAATTTTCTTTCTCTGT----TTTCAGCCTACTCAGTTTAAGTATCAGTA 459192 i iii ---- i iv i i---- vi vi C L1M4_orf2#LIN 1589 TAGTTTTCTTTTCTTGTGATGTCTTTGTCTG----GTTTTGGTATCAGGG 1544 chr2qtel1M 459193 CCATGTCTGTGTCATAAAAGGAATTTGGTAGGACTCCTTCAATCCCTATT 459242 iv iiiv iv i v i v v vii i vviii C L1M4_orf2#LIN 1543 TAATACTGGCCTCATAGAATGAGTTGGGAAGTGTTCCCTCCTCTTCTATT 1494 chr2qtel1M 459243 TTTTCAAATAATTTATATAGCATTGGAATTAATTGTTCTTTAAATGTTTG 459292 vi v i i iv v vi v C L1M4_orf2#LIN 1493 TTTTGGAAGAGTTTGTGAAGGATTGGTGTTAATTCTTCTTTAAATGTTTG 1444 chr2qtel1M 459293 GTAGGATTCACATTTAAATACATCTGATCCTGGGGATTTTTTCTTAGGCA 459342 i vvv i vv i? vv i iv i v C L1M4_orf2#LIN 1443 GTAGAATTCACCAGTGAAGCCATCTGGNCCTGGGCTTTTCTTTGTGGGAA 1394 chr2qtel1M 459343 GTTGATTAATAGCTTGTTCTATTTCTTTCCAAG--ATGGGACTGTTTAAT 459390 vv i vi vi v i v vv -- i v i i -- C L1M4_orf2#LIN 1393 GTTTTTTGATTACTAATTCAATCTCTTTACTTGTTATAGGTCTATTCA-- 1346 chr2qtel1M 459391 GAATT--TACTTCTTCT---GTTAATCTGGGCAAGATATATTTTTGAAAG 459435 v -- i --- i i i v i ivv i i i vv i C L1M4_orf2#LIN 1345 GATTTTCTATTTCTTCTTGAGTCAGTTTCGGTAGTTTGTGTCTTTCTAGG 1296 chr2qtel1M 459436 TATTATTCCATTTCATTTAAGTTATTGAATTTATTGGCATAAAGTTGGGC 459485 v vv i i iv i v i vv C L1M4_orf2#LIN 1295 AATTTGTCCATTTCATCTAGGTTATCTAATTTGTTGGCATACAATTGTTC 1246 chr2qtel1M 459486 AAAGTAACTCCTAATTACTGCTTTAATTTCCTCT----TCCTTAGTGGCG 459531 v vii v v iivi v - v ---- vv iii C L1M4_orf2#LIN 1245 ATAGTATTCCCTTATAATCCTTTTTATTT-CTGTAAGGTCGGTAGTAATG 1197 chr2qtel1M 459532 AGTTCTCCCTTTTTATTTTTAAGACTAACAATTTGGTTTTCCTCTTTCCT 459581 --- i ii i ii i vvi ii iv i i i -i C L1M4_orf2#LIN 1196 ---TCCCCTCTTTCATTCCTGATTTTAGTAATTTGAGTCTTCTCTCT-TT 1151 chr2qtel1M 459582 TTTTTTTCATCAGATTTACTAAGGGTTTATCTATTTTGTTGGT-TTTTCA 459630 i vi vi vi i i v i - C L1M4_orf2#LIN 1150 TTTTCTTGGTCAGTCTAGCTAAAGGTTTGTCAATTTTGTTGATCTTTTCA 1101 chr2qtel1M 459631 TAAAACCAAATCTTAGTTTTGTTTATTAATTCAATAGTTTTTTTTTTAAC 459680 v i v i i i v vvi v v i ---- i C L1M4_orf2#LIN 1100 AAGAACCAACTTTTGGTTTCGTTGATTTTCTCTATTGTTTTTCT----AT 1055 chr2qtel1M 459681 TTTCAATTTTATTAATCTTTCCTTTTATTTTTAGAATTTCAAGTTTAGTG 459730 i v i v i iiv i v i vv vvvii vv C L1M4_orf2#LIN 1054 TCTCTATTTCATTTATTTCCGCTCTAATCTTTATTATTTCCTTCCTTCTG 1005 chr2qtel1M 459731 TTTGACTGGAGGTTTTTAATTTGTTC----TTTTCTAGCTTTTTTAGTTG 459776 i vi v i --- i i ---- i i v v C L1M4_orf2#LIN 1004 CTTGCTTTGGG---TTTAGTTTGCTCTTCTTTTTCTAGTTTCTTAAGGTG 958 chr2qtel1M 459777 CAAGCCCAATTCACTGACCT----TCTCTTTTTCTATTTTATGCAAGTAG 459822 v vii iv i i ii ---- - i v --- vi C L1M4_orf2#LIN 957 GAAGGTTAGGTTATTGATTTGAGATCT-TTCTTCTTTTTTA---ATATAG 912 chr2qtel1M 459823 GTCTCTAGAGATATAAAATTTCCCTTT-ATTACCGCTTTGGCTGCATCCC 459871 iv i v v - i - vi i ? C L1M4_orf2#LIN 911 GCATTTACAGCTAT-AAATTTCCCTCTAAGCACTGCTTTNGCTGCATCCC 863 chr2qtel1M 459872 ACACATGTTGATATGACATCTCATTATTGTCATTTTCGTGGGTGAAGTTA 459921 i vi v i vii v iv ii v iviv viiv v v v C L1M4_orf2#LIN 862 ATAAGTTTTGGTATGTTGTGTTTTCGTTTTCATTCATCTCAAAGTATTTT 813 chr2qtel1M 459922 TTAATTATGTCTGTGATCTGCTGTTTCACCCAATCATTCTTTAGG-GTGA 459970 i vivii i vi v v v vi v - v C L1M4_orf2#LIN 812 CTAATTTCCCTTGTGATTTCTTCTTTGACCCATTGGTTATTTAGGAGTGT 763 chr2qtel1M 459971 GATTATTTAGTTTCCAATTACTTTTTGG-----CCAATTTACCCTGGCTT 460015 - i i vv - v i----- v v i ---i C L1M4_orf2#LIN 762 G-TTGTTTAATTTCCACATA-TTTGTGAATTTCCCAAATTTCCTT---CT 718 chr2qtel1M 460016 TTTGTTGAATGTAATTTTCATTGCATTGTGATTTGAAAAGGATGCATT-T 460064 v i v viv v v i iv i -v i v - C L1M4_orf2#LIN 717 GTTATTGATTTCTAATTTCATTCCATTGTGGTCGGAGAA-CATACTTTGT 669 chr2qtel1M 460065 ACTATTTCTGCCTTTCTGCATTTGAATTTCAGGT---TTTTATGTACTAA 460111 iv vii i i iv i--- v ii--- vv C L1M4_orf2#LIN 668 ATGATTTCAATCCTTTTAAATTTA---TTGAGACTTGTTTTATGGCCTAA 622 chr2qtel1M 460112 TAATATGGTCAATTTTTGTATAGGTTCCATGAACTGCTAAGAAGAAACTG 460161 i- v ii v viv v vi vvi i vv C L1M4_orf2#LIN 621 C-ATATGGTCTATCCTGGAGAATGTTCCATGTGCACTTGAGAAGAATGTG 573 chr2qtel1M 460162 TAGTCCTTCCTGT--CTCCATTTCATTTTCTCCAAAGATCTACCATACCT 460209 v -- v --i vvi vvvi v vi i vi iii vii C L1M4_orf2#LIN 572 TATTC--TGCTGTTGTTGGGTGGAGTGTTCTATAGATGTCTGTTAGGTCT 525 chr2qtel1M 460210 AACT--TTTCTAGTATTCTCT---TTCCCTGGCTTTTTCTTATTTATTTT 460254 ii -- v i v ii--- iii i--- i i v i C L1M4_orf2#LIN 524 AGTTGGTTTATAGTGTTGTTCAAGTCTTCTA---TTTCCTTGTTGATCTT 478 chr2qtel1M 460255 GTGGT---TTGCTTTATCTAATTCTAAGAGTGCAAGGTTGAGATCTCCCA 460301 v vi--- i i i v vi i i viivi ii v C L1M4_orf2#LIN 477 CTGTCTAGTTGTTCTATCCATTATTGAAAGTGGGGTATTGAAGTCTCCAA 428 chr2qtel1M 460302 CTATTATAGTTTTGCTGTCTATTTCTTCTTGTAGCTCTCTTAATTTCTTT 460351 v vvii i i vi ii v i i i vi C L1M4_orf2#LIN 427 CTATTATTGTTGAATTGTCTATTTCTCCCTTCAATTCTGTCAGTTTTTGC 378 chr2qtel1M 460352 TTTAAGAATTTAGATGCTACACCAGTTGATGCATATATGTTTAATATTGA 460401 i v v v iv viiiiiv v i vv v C L1M4_orf2#LIN 377 TTCATGTATTTTGGGGCTCTGTTGTTAGGTGCATATATGTTTATAATTGT 328 chr2qtel1M 460402 TATTGCTTCATTATCTATGGTACCTTTTAGCAAGATAAAGTTCCCTTTCT 460451 vv v v vv v vv v vv i vi ii C L1M4_orf2#LIN 327 TATATCTTCCTGATGGATTGACCCTTTTATCATTATAAAATGTCCTTCTT 278 chr2qtel1M 460452 TTTCTCTTTTAATTAGATCAATTTTTGTTTT------TGCTTGATCTGAG 460495 v vv ------ ? i ------ ii vi v C L1M4_orf2#LIN 277 TGTCTCTAGTAA------CANTTTTTGTCTTAAAGTCTATTTTGTCTGAT 234 chr2qtel1M 460496 ATCAGGATGGCTACCCCTGCTTTTTT 460521 i v i i i v i i C L1M4_orf2#LIN 233 ATTAGTATAGCCACTCCAGCTCTCTT 208 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.81 CpG sites = 481, Kimura (unadjusted) = 41.64 Transitions / transversions = 1.10 (481/438) Gap_init rate = 0.04 (135 / 3018), avg. gap size = 1.47 (198 / 135) 349 25.90 2.13 1.41 chr2qtel1M 461145 461285 (538715) C L1MC_orf2#LINE/L1 (3115) 179 38 m_b94s551i14 3487 chr2qtel1M 461145 CTCCAGCTTTTTACCTTTACTCTGTATGTATCACCCTGCTTTAAATGTGT 461194 v i? i v i i viiv ii v i v C L1MC_orf2#LIN 179 CTCCATCCNTTTACTTTTAATCTATATGTGTCTTTATATTTAAAGTGGGT 130 chr2qtel1M 461195 TTCCTGTAAACAACATATTGTAGGATTCTGGATTTTAATCCAGTCTGCTA 461244 i i v v i ii vv i v vi C L1MC_orf2#LIN 129 TTCTTGTAGACAACATATAGTTGGGTCTTGTTTTTTGATCCACTCTGACA 80 chr2qtel1M 461245 TCCGCT-TCTGCTTTATGTGGGG--TTTACCCCATTCACATTTA 461285 vi v - -- vv v -- vv ? C L1MC_orf2#LIN 79 ATCTCTGTCT--TTTAATTGGTGTATTTAGACCATTNACATTTA 38 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.58 CpG sites = 17, Kimura (unadjusted) = 32.58 Transitions / transversions = 0.89 (17/19) Gap_init rate = 0.03 (4 / 140), avg. gap size = 1.25 (5 / 4) 411 18.44 2.52 4.27 chr2qtel1M 461181 461299 (538701) C L1MEh_5end#LINE/L1 (7) 2228 2112 m_b94s551i15 3487 chr2qtel1M 461181 TGCTTTAAATGTGTTTCCTGTAAACAACATATTGTAGGATTCTGGATTTT 461230 i i i i i i v i vv ? C L1MEh_5end#LI 2228 TGTTTTAAGTGTGTCTCTTGTAGACAGCATATTGTTGGATTTTGTTTTTN 2179 chr2qtel1M 461231 AATCCAGTCTGCTATCCGCT-TCTGCTTTA--TGTGGGGTTTACCCCATT 461277 i v? vi v - -- -- vv i v C L1MEh_5end#LI 2178 AATCCAATCTGANAATCTCTGTCT--TTTAATTGGTGAGTTTAACCCATT 2131 chr2qtel1M 461278 CACATTTATGGTTAAAATTACT 461299 i v --- C L1MEh_5end#LI 2130 TACATTTATTGT---AATTACT 2112 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 21.74 CpG sites = 11, Kimura (unadjusted) = 21.74 Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.06 (7 / 118), avg. gap size = 1.14 (8 / 7) 376 17.84 9.21 7.79 chr2qtel1M 461187 461338 (538662) C L1M4b_5end#LINE/L1 (13) 3224 3071 m_b94s551i16 3487 chr2qtel1M 461187 AAATGTGTTTCCTGTAAACAACATATTGTAGGATTCTGGATTTTAATCCA 461236 i i i i v v ii vv C L1M4b_5end#LI 3224 AAGTGTGTCTCCTGTAGACAGCATATAGTTGGATCTTGTTTTTTAATCCA 3175 chr2qtel1M 461237 GTCTG-CTATCCGCTTCTGCTTTATG--TGGG--GTTTACCCCATTCACA 461281 - v ---- i v -- i-- vi C L1M4b_5end#LI 3174 GTCTGACAATC----TCTGCCTTTTGATTGGATTGTTTAATCCATTCACA 3129 chr2qtel1M 461282 TTTATGGTTAAAATTACTCATTCTGTAGT---------GCTTGCCATCTT 461322 vv --- i v --- i --------- ii -- C L1M4b_5end#LI 3128 TTTAATGTT---ATTATTGA---TATAGTTGGATTTACGTCTGCCA--TT 3087 chr2qtel1M 461323 TTGCTTTTGGTTTTCT 461338 i v C L1M4b_5end#LI 3086 TTACTTTTTGTTTTCT 3071 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 20.60 CpG sites = 14, Kimura (unadjusted) = 20.60 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.11 (16 / 151), avg. gap size = 1.62 (26 / 16) 14 16.53 0.00 5.56 chr2qtel1M 462965 463002 (536998) (CAAA)n#Simple_repeat 1 36 (0) m_b94s252i10 3490 chr2qtel1M 462965 CAAAGAATCAAAGAAAACAACCAAACAAAAAAAGCAAA 463002 v v -v v v - (CAAA)n#Simpl 1 CAAACAAACAAA-CAAACAAACAAACAAACAAA-CAAA 36 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 15 4.71 0.00 0.00 chr2qtel1M 464689 464710 (535290) (ACC)n#Simple_repeat 1 22 (0) m_b94s252i11 3491 chr2qtel1M 464689 ACCCCCACCACCACCACCACCA 464710 v (ACC)n#Simple 1 ACCACCACCACCACCACCACCA 22 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 16 23.21 4.84 1.56 chr2qtel1M 464712 464773 (535227) (AAAATG)n#Simple_repeat 1 64 (0) m_b94s252i12 3492 chr2qtel1M 464712 AAAAT-AAAATAGAATTGAAAATGATCACTTAAAA-GTACA-GACAATGA 464758 - ii v -v v v - v v - v (AAAATG)n#Sim 1 AAAATGAAAATGAAAATGAAAATGA-AAATGAAAATGAAAATGAAAATGA 49 chr2qtel1M 464759 AAGGGAAAAGGAAAA 464773 iv v (AAAATG)n#Sim 50 AAATGAAAATGAAAA 64 Matrix = Unknown Transitions / transversions = 0.33 (3/9) Gap_init rate = 0.07 (4 / 61), avg. gap size = 1.00 (4 / 4) 191 35.64 2.10 5.80 chr2qtel1M 464839 464981 (535019) MIR#SINE/MIR 79 216 (46) m_b94s601i3 3493 chr2qtel1M 464839 AGCTGCTGGGATTTGAGTCAAGTCATTCAATCCCCCTGAGCT--GGTGGC 464886 - v ii vi v i i i i i i v i--i vv MIR#SINE/MIR 79 AGCTG-TGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTC 127 chr2qtel1M 464887 CTGAGTTGTACAAGCAGTGAGAATGAAGGCACTTTCCATGTTGTCCCAGG 464936 v vi - iii v v i vi i i v ------ vi MIR#SINE/MIR 128 CTCATCTGTA-AAATGGGGATAATAATAGTACCTACC------TCATAGG 170 chr2qtel1M 464937 CTTACTGTGAGAATCCAATGTATTTTTGCATG-AAGGTCATTAGAA 464981 v ii i iv vi vv i - i ivv MIR#SINE/MIR 171 GTTGTTGTGAGGATTAAATGAGTTAATACATGTAAAGCGCTTAGAA 216 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 48.67 CpG sites = 28, Kimura (unadjusted) = 50.17 Transitions / transversions = 1.40 (28/20) Gap_init rate = 0.07 (10 / 142), avg. gap size = 1.10 (11 / 10) 224 33.63 4.24 4.24 chr2qtel1M 464839 464956 (535044) MIRc#SINE/MIR 83 200 (68) m_b94s601i2 3493 chr2qtel1M 464839 AGCTGCTGGGATTTGAGTCAAGTCATTCAATCCCCCTGAGC--TGGTGGC 464886 - v ii vi v i i i i i --ii vv MIRc#SINE/MIR 83 AGCTG-TGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTC 131 chr2qtel1M 464887 CTGAGTTGTACAAGCAGTGAGAATGAAGGCACTTTCCATGT---TGTCCC 464933 v vi v ---- i i i viii i v v i---iv v MIRc#SINE/MIR 132 CTCATCTGTAAAA----TGGGGATAATAATACCTGCCCTGCCTACCTCAC 177 chr2qtel1M 464934 AGGCTTACTGTGAGAATCCAATG 464956 v ii i v MIRc#SINE/MIR 178 AGGGTTGTTGTGAGGATCAAATG 200 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 46.52 CpG sites = 23, Kimura (unadjusted) = 46.52 Transitions / transversions = 1.53 (23/15) Gap_init rate = 0.06 (7 / 117), avg. gap size = 1.43 (10 / 7) 824 31.65 2.59 1.64 chr2qtel1M 465057 465480 (534520) L1ME4c_3end#LINE/L1 22 449 (381) m_b94s551i17 3494 chr2qtel1M 465057 GAACTGACTCAAATTTATAATAATGCAAGCCATTTTCCAATTGATAAATG 465106 i v i v v viv? v v vvii v L1ME4c_3end#L 22 GAGCTCATTCAAATTGATAAGAAAAANATCAAGACCCCAATAGATAAATG 71 chr2qtel1M 465107 GTCAAAGGATTTGAATAGACAATTTTCAGATGAAAAAAATAAAAATCATT 465156 v iv i iv ? v ii - v ? vi v L1ME4c_3end#L 72 GGCAAAGGACATGAACAGACAATTCACANAAGAGGAAA-TACAANTAGTA 120 chr2qtel1M 465157 TCTAGTCCTATGAAAAAATATTCTAAATCACTATTAGTCAGAGAAACATA 465206 vvi iv vi i i v vv i v i i iii L1ME4c_3end#L 121 AACAAACACATGGAAAAATGTTCAACCTCGCTAGTAATCAAAGAAATGCA 170 chr2qtel1M 465207 AATTAAGACAACTCTGAGGTACCA-----GATCTTTCAGACTGGCTAAGA 465251 ii vv i -----vii v i i i i v i L1ME4c_3end#L 171 AATTAAAGCAACAATGAGATACCATTTTACGCCTATTAAATTAGCAAAAA 220 chr2qtel1M 465252 TGACAGGGAAAGATAATGATGAATGTTGAAGGGGATGTGGAAAAACTGGG 465301 vvv iii vv iviv i iv i ? i vi v L1ME4c_3end#L 221 TTTAAAAAATTGATAATACCCAATGCTGGCGAGGNTGCGGTGAAACTGGT 270 chr2qtel1M 465302 ACAC--ATACATTGTTGGTGGAGTTGTGAATTGATCCAATCATTCTAGAA 465349 ? -- i vi? i i v i v i i L1ME4c_3end#L 271 ACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAA 320 chr2qtel1M 465350 AGCAATATGGAACTATGCCCAGAGGGCAATCACACTGTGCATACCCTTTG 465399 v v v i ivivi i v v v v v L1ME4c_3end#L 321 AGCAATTTGGCAATACGTATCAAGAGCCATAAAAATGTTCATACCCTTTG 370 chr2qtel1M 465400 ATTGAGCAGTGTCTA-TACTGAACCTGTTTCCCAAAGAGATTAT---AAA 465445 iiv i i - i - v iivv v v i i i v --- L1ME4c_3end#L 371 ACCCAGTAAT-TCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAA 419 chr2qtel1M 465446 GAAGGGAAACGGCCTTCCACATGTGCAAAAATGTT 465480 i v ----- i i ii i i L1ME4c_3end#L 420 GAAGGAAAAAG-----CTATATGCACGAAGATGTT 449 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.74 CpG sites = 71, Kimura (unadjusted) = 42.86 Transitions / transversions = 1.16 (71/61) Gap_init rate = 0.03 (11 / 423), avg. gap size = 1.64 (18 / 11) 825 28.99 2.27 0.32 chr2qtel1M 465093 465400 (534600) L1ME4a_3end#LINE/L1 58 371 (500) m_b94s551i18 3494 chr2qtel1M 465093 CCAATTGATAAATGGTCAAAGGATTTGAATAGACAATTTTCAGATGAAAA 465142 v v v iv i iv i v i L1ME4a_3end#L 58 CCAATAGAAAAATGGGCAAAGGACATGAACAGACAATTCACAAAAGAAGA 107 chr2qtel1M 465143 AAATAAAAATCATTTCTAGTCCTATGAAAAAATATTCTAAATCACTATTA 465192 - v viiivv iv v ? i v vv v L1ME4a_3end#L 108 AA-TACAAATGGCCAATAAACATATGAAAANATGTTCAACCTCACTAGTA 156 chr2qtel1M 465193 GTCAGAGAAACATAAATTAAGACAACTCTGAGGTACCA-----GATCTTT 465237 i i iii i vv i -----v i v L1ME4a_3end#L 157 ATCAAAGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCTAT 206 chr2qtel1M 465238 CAGACTGGCTAAGATGACAGGGAAAGATAATGATGAATGTTGAAGGGGAT 465287 i i v vvv ii vv iviv i iv i i L1ME4a_3end#L 207 CAAATTGGCAAAGATTTAAAAGATTGATAATACCCAGTGTTGGCGAGGGT 256 chr2qtel1M 465288 GTGGAAAAACTGGGACAC--ATACATTGTTGGTGGAGTTGTGAATTGATC 465335 ?i v v v -- i i iiv i i v L1ME4a_3end#L 257 GTGGNGAAACGGGCACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTA 306 chr2qtel1M 465336 CAATCATTCTAGAAAGCAATATGGAACTATGCCCAGAGGGCAATCACACT 465385 i v i ii v v v ivivi ii vv v v v L1ME4a_3end#L 307 CAACCTTTCTGGAGGGCAATTTGGCAATATGTATCAAAAGCCTTAAAAAT 356 chr2qtel1M 465386 GTGCATACCCTTTGA 465400 ? L1ME4a_3end#L 357 GTNCATACCCTTTGA 371 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.54 CpG sites = 44, Kimura (unadjusted) = 37.54 Transitions / transversions = 0.98 (44/45) Gap_init rate = 0.01 (3 / 307), avg. gap size = 2.67 (8 / 3) 17 31.16 0.00 0.00 chr2qtel1M 465552 465602 (534398) (TT)n#Simple_repeat 1 51 (0) m_b94s252i13 3495 chr2qtel1M 465552 TTTTTTTTTTTTTTTTGGTAGTTTGCATTTGGTTTTCTTTCTCATTTTTT 465601 vv vv viv vv i i iv (TT)n#Simple_ 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr2qtel1M 465602 T 465602 (TT)n#Simple_ 51 T 51 Matrix = Unknown Transitions / transversions = 0.44 (4/9) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 22 0.00 0.00 0.00 chr2qtel1M 465781 465804 (534196) (TG)n#Simple_repeat 1 24 (0) m_b94s252i14 3496 chr2qtel1M 465781 TGTGTGTGTGTGTGTGTGTGTGTG 465804 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTG 24 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 35 0.00 0.00 0.00 chr2qtel1M 465805 465834 (534166) (TA)n#Simple_repeat 1 30 (0) c_b94s251i2 3497 chr2qtel1M 465805 TATATATATATATATATATATATATATATA 465834 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATA 30 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 498 22.62 0.71 8.46 chr2qtel1M 465841 465980 (534020) C MIRb#SINE/MIR (138) 130 1 m_b94s601i4 3498 chr2qtel1M 465841 CTGAGGC-AATTGAAGTTAAATGATTTGCTCCAGGGTCACACAGCTAGGA 465889 -v vv i i i i - i -- C MIRb#SINE/MIR 130 CTGAGGCTCAGAGAGGTTAAGTAACTTGC-CCAAGGTCACACAGCTAG-- 84 chr2qtel1M 465890 AATGTTAAGTGTCTAAGACCAGATTTGAACTCAGGTTCTCCTGACTTCAG 465939 ----- v vi v vi i i iivi i i C MIRb#SINE/MIR 83 -----TAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAA 39 chr2qtel1M 465940 GGCTGGTGCTCTATCCACTGTGACACCTAGCTGCCCCTATG 465980 i iv v --- vv v C MIRb#SINE/MIR 38 AGCCCGTGCTCTTTCCACTG---CACCACGCTGCCCCTCTG 1 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.02 CpG sites = 16, Kimura (unadjusted) = 27.08 Transitions / transversions = 1.23 (16/13) Gap_init rate = 0.09 (12 / 139), avg. gap size = 1.00 (12 / 12) 17 5.00 0.00 0.00 chr2qtel1M 467788 467808 (532192) (T)n#Simple_repeat 1 21 (0) m_b94s252i16 3499 chr2qtel1M 467788 TTTCTTTTTTTTTTTTTTTTT 467808 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTT 21 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 15 18.05 0.00 0.00 chr2qtel1M 467783 467815 (532185) (TTCTTT)n#Simple_repeat 1 33 (0) m_b94s252i15 3500 chr2qtel1M 467783 TTCTCTTTCTTTTTTTTTTTTTTTTTCCCTTTC 467815 i i i ii (TTCTTT)n#Sim 1 TTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTC 33 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 17 14.97 0.00 8.33 chr2qtel1M 469401 469452 (530548) (TTTTTTA)n#Simple_repeat 1 48 (0) m_b94s252i17 3501 chr2qtel1M 469401 TTTTGGATTTTTTATTTCCTGTCTATTTTCTCTTTTTTTTTTTTTTTTTT 469450 vv -- - - i v v v (TTTTTTA)n#Si 1 TTTTTTATTTTTTATTT--T-T-TATTTTTTATTTTTTATTTTTTATTTT 46 chr2qtel1M 469451 TT 469452 (TTTTTTA)n#Si 47 TT 48 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.08 (4 / 51), avg. gap size = 1.00 (4 / 4) 23 20.62 0.00 0.00 chr2qtel1M 469408 469452 (530548) (T)n#Simple_repeat 1 45 (0) m_b94s252i18 3501 chr2qtel1M 469408 TTTTTTATTTCCTGTCTATTTTCTCTTTTTTTTTTTTTTTTTTTT 469452 v ii v i v i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 45 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 14 18.24 0.00 5.13 chr2qtel1M 470266 470306 (529694) (TAGATA)n#Simple_repeat 1 39 (0) m_b94s252i19 3502 chr2qtel1M 470266 TAGTTATAGTTAGGTAGATATAGATATAAAGTTAGCTATAG 470306 v v -- i vv v (TAGATA)n#Sim 1 TAGATATAGATA--TAGATATAGATATAGATATAGATATAG 39 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 14 10.81 3.12 3.12 chr2qtel1M 471073 471104 (528896) (AAAT)n#Simple_repeat 1 32 (0) m_b94s252i20 3503 chr2qtel1M 471073 AAATAAATGAAAGCAATAAAT-AATAAAGAAAT 471104 - vv - v (AAAT)n#Simpl 1 AAATAAAT-AAATAAATAAATAAATAAATAAAT 32 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.06 (2 / 31), avg. gap size = 1.00 (2 / 2) 25 11.81 0.00 0.00 chr2qtel1M 471208 471244 (528756) (T)n#Simple_repeat 1 37 (0) m_b94s252i21 3504 chr2qtel1M 471208 TTTTTTTTTTTTTTTTTTTTTATTTATTTATTTATTT 471244 v v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 37 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 244 25.22 9.18 2.88 chr2qtel1M 471707 471804 (528196) MIRc#SINE/MIR 47 150 (118) m_b94s601i5 3505 chr2qtel1M 471707 AGGACCATGGTTGCAGGAGCCGACTTTTAACACTCAAAAATGGCATGAAC 471756 i - v v ii vv i i -iv i vv iiv ii - MIRc#SINE/MIR 47 AAGACC-TGGGTTCGAGTCCCGGCTCT-GCCACTTACTAGCTGTGTGA-C 93 chr2qtel1M 471757 TTTGAGCAAATC-CTT----TCTCTG--CTTCAGTTTCCTC--CTGTAAA 471797 i i i - ---- -- i -- MIRc#SINE/MIR 94 CTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAA 143 chr2qtel1M 471798 TTGGGGA 471804 v MIRc#SINE/MIR 144 ATGGGGA 150 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 30.10 CpG sites = 15, Kimura (unadjusted) = 31.68 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.07 (7 / 97), avg. gap size = 1.71 (12 / 7) 248 24.62 11.39 2.33 chr2qtel1M 471726 471804 (528196) MIR#SINE/MIR 61 146 (116) m_b94s601i6 3505 chr2qtel1M 471726 CCGACTTTTAACACTCAAAAATGGCATGAACTTTGAGCAAAT-------C 471768 i i -iv i vv iiv ii - i i i ------- MIR#SINE/MIR 61 CCGGCTCT-GCCACTTACTAGCTGTGTGA-CCTTGGGCAAGTTACTTAAC 108 chr2qtel1M 471769 CTTTCTCTGCTTCAGTTTCCTC--CTGTAAATTGGGGA 471804 i v i -- v MIR#SINE/MIR 109 CTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGA 146 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.09 CpG sites = 13, Kimura (unadjusted) = 31.09 Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.05 (4 / 78), avg. gap size = 2.75 (11 / 4) 271 21.51 10.28 4.42 chr2qtel1M 471755 471861 (528139) MIR3#SINE/MIR 89 201 (7) m_b94s601i7 3505 chr2qtel1M 471755 ACTTTGAGCAAATC-CTT----TCTCTG--CTTCAGTTTCCTC--CTGTA 471795 i i i - ---- -- i -- MIR3#SINE/MIR 89 ACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTA 138 chr2qtel1M 471796 AATTGGGGAGGGCTGG-TTGGATTCTTGAAGTTTTAAGTGACTTTCAGCT 471844 v i - i -i i ---- vv i v i vv i MIR3#SINE/MIR 139 AAATGAGG-GGGTTGGACTAGA----TGATCTCTAAGGTCCCTTCCAGCT 183 chr2qtel1M 471845 CT-ACATGTCATGACTTT 471861 - vii i i MIR3#SINE/MIR 184 CTGACATTCTATGATTCT 201 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.22 CpG sites = 15, Kimura (unadjusted) = 26.22 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.10 (11 / 106), avg. gap size = 1.45 (16 / 11) 19 0.00 0.00 0.00 chr2qtel1M 472827 472847 (527153) (A)n#Simple_repeat 1 21 (0) m_b94s252i22 3506 chr2qtel1M 472827 AAAAAAAAAAAAAAAAAAAAA 472847 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAA 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 266 21.24 6.17 1.18 chr2qtel1M 473277 473357 (526643) MIR3#SINE/MIR 121 205 (3) m_b94s601i8 3507 chr2qtel1M 473277 TCAGTTTTC-CATCTATCAAATGAGTGGGTTGTCCTCCATGGCCTTGTAG 473325 i - i v v vv vv ii ivv MIR3#SINE/MIR 121 TCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAG 170 chr2qtel1M 473326 GTCCCTTCCAG---TGATCATT-TGGGATCCTATAA 473357 --- - - iv i i MIR3#SINE/MIR 171 GTCCCTTCCAGCTCTGA-CATTCTATGATTCTATGA 205 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 25.11 CpG sites = 8, Kimura (unadjusted) = 25.11 Transitions / transversions = 0.89 (8/9) Gap_init rate = 0.05 (4 / 80), avg. gap size = 1.50 (6 / 4) 232 28.37 4.43 10.74 chr2qtel1M 473448 473605 (526395) C L2c_3end#LINE/L2 (10) 468 320 m_b94s601i10 3508 chr2qtel1M 473448 TCAGCAAACTTTTA---AGTGCCTGCTATAAGCCAGACCCTGGCCTAAGC 473494 i v --- i i iv i v ------- C L2c_3end#LINE 468 TCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGG------- 426 chr2qtel1M 473495 ACCAGGAACATAAAGA-GAGACAGAGACATCCCCTGCTCTCCTGGAGGTC 473543 ----- i i i - ivv v ivi i vv v C L2c_3end#LINE 425 -----GGATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTC 381 chr2qtel1M 473544 AGAGATCGCTGGGGCAGACAGTACACCAGT-AATATACTATGGACCAGAT 473592 v viiiv i v --- v? - i v v -v v v i C L2c_3end#LINE 380 ACAGTCTAGTGGAGGAGACAG---ACANGTAAACAGACAAT-TACAATAC 335 chr2qtel1M 473593 AAGTTG--GATAAAT 473605 i-- i C L2c_3end#LINE 334 AAGTTAATGATAAGT 320 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.88 CpG sites = 20, Kimura (unadjusted) = 36.06 Transitions / transversions = 1.00 (20/20) Gap_init rate = 0.13 (20 / 157), avg. gap size = 1.15 (23 / 20) 301 31.62 6.84 0.00 chr2qtel1M 473448 473564 (526436) C L2b_3end#LINE/L2 (10) 456 332 m_b94s601i9 3508 chr2qtel1M 473448 TCAGCAAACTTTTA---AGTGCCTGCTATAAGCCAGACCCTGGCCTAAGC 473494 i iv --- i i i iv i ? vv i C L2b_3end#LINE 456 TCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGC 407 chr2qtel1M 473495 ACCAGGAACATAAAGA-----GAGACAGAGACATCCCCTGCTCTCCTGGA 473539 i ii i i i iv i-----i v? ivi i vi C L2b_3end#LINE 406 GCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGGA 357 chr2qtel1M 473540 GGTCAGAGATCGCTGGGGCAGACAG 473564 v v viiiv v C L2b_3end#LINE 356 GCTCACAGTCTAGTGGGGGAGACAG 332 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.95 CpG sites = 24, Kimura (unadjusted) = 44.20 Transitions / transversions = 1.85 (24/13) Gap_init rate = 0.02 (2 / 116), avg. gap size = 4.00 (8 / 2) 16 9.78 0.00 0.00 chr2qtel1M 473958 473979 (526021) (A)n#Simple_repeat 1 22 (0) m_b94s252i23 3509 chr2qtel1M 473958 AAAATACAAAAAAAAAAAAAAA 473979 v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAA 22 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 231 36.29 4.24 4.24 chr2qtel1M 474135 474252 (525748) MIRc#SINE/MIR 82 199 (69) m_b94s601i11 3510 chr2qtel1M 474135 TAGCTGCTAGGATTTCAGTCAAGTCACTCAACTCCTCTGAGC--TGATGG 474182 - iv ii ii v i ii --iii vv MIRc#SINE/MIR 82 TAGCTG-TGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTT 130 chr2qtel1M 474183 CTTGAGTTGTGACTACAGCGAGAATGAAAATATTTTTTGTGT---TGTCA 474229 i v vi i ---- ii i i i v ii viiv i---iv MIRc#SINE/MIR 131 CCTCATCTGTAA----AATGGGGATAATAATACCTGCCCTGCCTACCTCA 176 chr2qtel1M 474230 CAGATTTACTGTGAGAATCCAAT 474252 iv ii i v MIRc#SINE/MIR 177 CAGGGTTGTTGTGAGGATCAAAT 199 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 54.28 CpG sites = 29, Kimura (unadjusted) = 54.28 Transitions / transversions = 2.42 (29/12) Gap_init rate = 0.06 (7 / 117), avg. gap size = 1.43 (10 / 7) 677 32.41 4.24 2.19 chr2qtel1M 474354 474801 (525199) L1ME4c_3end#LINE/L1 22 478 (352) m_b94s551i19 3511 chr2qtel1M 474354 GAATTGACTCAAATTTATAAGAATACAAGCCATTCACCAATTGGTATATG 474403 ii v i v v v? v v vv v v i v L1ME4c_3end#L 22 GAGCTCATTCAAATTGATAAGAAAAANATCAAGACCCCAATAGATAAATG 71 chr2qtel1M 474404 GTCAAAGGATTTGAACAGACAATTTTCAGATAAAAAAATAACCATTTCTA 474453 v iv iv ? vi ii - v ? --- L1ME4c_3end#L 72 GGCAAAGGACATGAACAGACAATTCACANAAGAGGAAATA-CAANT---A 117 chr2qtel1M 474454 GT-------CATATGAAAAAATA------CTCGAAATTGGTCAAAGAAAT 474490 ------- i i i------ vv v ii L1ME4c_3end#L 118 GTAAACAAACACATGGAAAAATGTTCAACCTCGCTAGTAATCAAAGAAAT 167 chr2qtel1M 474491 GTAAATTTAGACAGTTCTGAATTACCATTGTATATCTCTCAGCTTGACTA 474540 i v ii iivv iv v iii v i iv ii v L1ME4c_3end#L 168 GCAAATTAAAGCAACAATGAGATACCATTTTACGCCTATTAAATTAGCAA 217 chr2qtel1M 474541 AGATGACAGGAAAAGATAATGATGAATGTTGGAGGGGGTGGGGGAAAAGT 474590 i vvv ii vv iviv i v i ? v vi v L1ME4c_3end#L 218 AAATTTAAAAAATTGATAATACCCAATGCTGGCGAGGNTGCGGTGAAACT 267 chr2qtel1M 474591 GGGAAACTAATATATTGTTGGTAGAGTTGTGAACTGATCCAATCAATCTA 474640 v v? v i i i vi? i i i v i vv i i L1ME4c_3end#L 268 GGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTG 317 chr2qtel1M 474641 GAGAATGCTAT---GCAATTAG-ACCCTTAGGGCTGTCACCCTGTGTATA 474686 i -- v --- vv - i v-- i ii v vvv vi L1ME4c_3end#L 318 GAAA--GCAATTTGGCAATACGTATCA--AGAGCCATAAAAATGTTCATA 363 chr2qtel1M 474687 TGTTTTGATCTAGCAATGTCTCTACTGAACCTGTATCCCAAAGAGATGAT 474736 ivi i i i vi v v iivv v i i i i L1ME4c_3end#L 364 CCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAAT 413 chr2qtel1M 474737 --AAAGGAAGGAAAAAGACCCACATGTGCAAAAATGTTTCTAGCAGCCCT 474784 -- i -- i i ii i i iv v vi L1ME4c_3end#L 414 TCAAAAGAAGGAAAAAG--CTATATGCACGAAGATGTTCATTGCAGCGTT 461 chr2qtel1M 474785 TTCTATAGTGGAGAGAA 474801 v i i i v i L1ME4c_3end#L 462 ATTTATAATAGCGAAAA 478 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.36 CpG sites = 76, Kimura (unadjusted) = 44.24 Transitions / transversions = 1.15 (76/66) Gap_init rate = 0.03 (15 / 447), avg. gap size = 1.93 (29 / 15) 20 32.59 4.27 0.83 chr2qtel1M 478094 478210 (521790) (TGTGTA)n#Simple_repeat 1 121 (0) m_b94s252i24 3512 chr2qtel1M 478094 TGGGTAAATGCATGTGTCTCTATATGTTTATGTGTATAAG-A-GTATATC 478141 v vi i v v i v iv - - i v (TGTGTA)n#Sim 1 TGTGTATGTGTATGTGTATGTGTATGTGTATGTGTATGTGTATGTGTATG 50 chr2qtel1M 478142 TATATATATATATACAT-TTTCCCTCTATGTGTATATGCATATAGCATGT 478190 i i i i ii - v viv v i i i - i (TGTGTA)n#Sim 51 TGTATGTGTATGTGTATGTGTATGTGTATGTGTATGTGTATGT-GTATGT 99 chr2qtel1M 478191 GTCTATG--TCTGTATGTGTAT 478210 v i -- v (TGTGTA)n#Sim 100 GTATGTGTATGTGTATGTGTAT 121 Matrix = Unknown Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.04 (5 / 116), avg. gap size = 1.20 (6 / 5) 20 28.06 2.82 1.39 chr2qtel1M 478114 478184 (521816) (TA)n#Simple_repeat 1 72 (0) m_b94s252i25 3513 chr2qtel1M 478114 TATATGTTTATGTGTATA-AGAGTATATCTATATATATATATACAT-TTT 478161 i v i i - v - v i - v (TA)n#Simple_ 1 TATATATATATATATATATATA-TATATATATATATATATATATATATAT 49 chr2qtel1M 478162 CCCTCTATGTGTATATGCATATA 478184 viv v i i ii (TA)n#Simple_ 50 ATATATATATATATATATATATA 72 Matrix = Unknown Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.04 (3 / 70), avg. gap size = 1.00 (3 / 3) 20 32.59 4.27 0.83 chr2qtel1M 478094 478210 (521790) (TGTGTA)n#Simple_repeat 1 121 (0) m_b94s252i24 3512 chr2qtel1M 478094 TGGGTAAATGCATGTGTCTCTATATGTTTATGTGTATAAG-A-GTATATC 478141 v vi i v v i v iv - - i v (TGTGTA)n#Sim 1 TGTGTATGTGTATGTGTATGTGTATGTGTATGTGTATGTGTATGTGTATG 50 chr2qtel1M 478142 TATATATATATATACAT-TTTCCCTCTATGTGTATATGCATATAGCATGT 478190 i i i i ii - v viv v i i i - i (TGTGTA)n#Sim 51 TGTATGTGTATGTGTATGTGTATGTGTATGTGTATGTGTATGT-GTATGT 99 chr2qtel1M 478191 GTCTATG--TCTGTATGTGTAT 478210 v i -- v (TGTGTA)n#Sim 100 GTATGTGTATGTGTATGTGTAT 121 Matrix = Unknown Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.04 (5 / 116), avg. gap size = 1.20 (6 / 5) 22 19.51 0.00 0.00 chr2qtel1M 478404 478444 (521556) (T)n#Simple_repeat 1 41 (0) m_b94s252i26 3514 chr2qtel1M 478404 TTTTTTGTTGTTTTTCTTTTTTTATGTTTTTATTTTTTATT 478444 v v i v v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 41 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 13 4.76 0.00 4.35 chr2qtel1M 478577 478600 (521400) (GGAA)n#Simple_repeat 1 23 (0) m_b94s252i27 3515 chr2qtel1M 478577 GGAAGGTAAGGAAAGAAGGAAGGA 478600 - i (GGAA)n#Simpl 1 GGAAGG-AAGGAAGGAAGGAAGGA 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 588 28.63 3.20 3.61 chr2qtel1M 480735 480984 (519016) C L1ME4c_3end#LINE/L1 (275) 555 307 m_b94s551i20 3516 chr2qtel1M 480735 ATAATATTCCATACCATTCATATACCATAACTTACTCGGCCTTTCTCCAA 480784 vvvi ?v i i iii v i v C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chr2qtel1M 480785 ATGATGGGCATCCCTTCGGTT---TCCAGATTCTTGCCACCACCAAAAGG 480831 v v i --- v --- iv i i i ii iv v iv C L1ME4c_3end#L 505 TTGTTGGACAT---TTAGGTTGTTTCCAATTTTTCGCTATTATAAATAAC 459 chr2qtel1M 480832 GCTGCCACAAACATTTTTGCACATATGGGTCCCTTTCTTTCCTTTTAAG- 480880 v ii i i ii i -- ii i i v v- C L1ME4c_3end#L 458 GCTGCAATGAACATCTTCGTGCATATAG--CTTTTTCCTTCTTTTGAATT 411 chr2qtel1M 480881 ATCTCCTTGGGATATAAATCT----AGTGGAGACACTGTTGGATCAAAGG 480926 i i - v i---- --- i ii i C L1ME4c_3end#L 410 ATTTCCTTAGGATA-AATTCCCAGAAGTGGA---ATTACTGGGTCAAAGG 365 chr2qtel1M 480927 GCATGCACACTTTGATAACCATTTGGGCATAGTTCCAAATTGCTCTCCAG 480976 i v i v ii iv vivi i v v i i C L1ME4c_3end#L 364 GTATGAACATTTTTATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAA 315 chr2qtel1M 480977 AATGGTTG 480984 v C L1ME4c_3end#L 314 AAGGGTTG 307 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.58 CpG sites = 44, Kimura (unadjusted) = 37.66 Transitions / transversions = 1.76 (44/25) Gap_init rate = 0.05 (12 / 249), avg. gap size = 1.42 (17 / 12) 20 0.00 0.00 0.00 chr2qtel1M 480989 481010 (518990) (T)n#Simple_repeat 1 22 (0) m_b94s252i28 3517 chr2qtel1M 480989 TTTTTTTTTTTTTTTTTTTTTT 481010 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTT 22 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 779 25.07 8.50 2.23 chr2qtel1M 481513 482018 (517982) C L1ME3G_3end#LINE/L1 (381) 543 7 m_b95s551i1 3518 chr2qtel1M 481513 ATTCCATAATATTCATATACCA-AATTTATTCAGCCATTCTCCAAT-GAT 481560 i vv - i i i v - C L1ME3G_3end#L 543 ATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTATTGAT 494 chr2qtel1M 481561 GGACATC---ATTCAGTTTC--ATTTTTC--CACTACAAA-AGGGC--CA 481600 i---i -- -- --i i - iv -- C L1ME3G_3end#L 493 GGACATTTAGGTT--GTTTCCAATTTTTCGCTATTACAAACAATGCTGCA 446 chr2qtel1M 481601 A---ACATTCGTGCACATACAGATCCCTTTCCTTCTTTATAA-----TCT 481642 --- i v i i ?-- i v v viv v iii ----- C L1ME3G_3end#L 445 ATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATTTCT 398 chr2qtel1M 481643 TTGGGATATAATCCCAGTAGTAACACTGCTGGATCAAAGGG-ATGCACAG 481691 ? i v v? ? v iiv i i - i v C L1ME3G_3end#L 397 NTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGCAT 348 chr2qtel1M 481692 TTTGATAACTTTGA-GCATATT-CCAAACTTACTCTTCCAAATGGTTGGA 481739 i -- i i -iv i - - i i i v ? i v C L1ME3G_3end#L 347 TTTAA--ATTTTAATAGATACTGCCAAA-TTGCCCTCCAAAANGGCTGTA 301 chr2qtel1M 481740 T---TCCACAACTCCACCAACAATGCATCAATGTCCCAGTTTTCC-ACAT 481785 i--- ii vii i i i v iv v v i - i C L1ME3G_3end#L 300 CCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCACAC 251 chr2qtel1M 481786 CCTC--CAAAA-TCATCATTATT----TTTCCTGTTCTTACCAA-CTGAC 481827 -- v - ?ivi i---- ivvi i i - i C L1ME3G_3end#L 250 CCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATCTGAT 201 chr2qtel1M 481828 AGGTTGTTAGTGGTATCTTAG-GTTGTCTTTAATTTTGATTTCTCTGATT 481876 i vivv i i v- - vv i C L1ME3G_3end#L 200 GGGTGAAAAATGGTATCTCATTGTTGT-TTTAATTTGCATTTCCCTGATT 152 chr2qtel1M 481877 AATA---AACTTGGAGCATCTTTTCATATGACTAGAAATAGTTTCAATTT 481923 v --- iv - vi vviiivi vv C L1ME3G_3end#L 151 ACTAGTGAGGTTG-AGCATCTTTTCATATGTTTATTGGCCATTTGTATTT 103 chr2qtel1M 481924 CTTCATCTGAGAACTGTC--TTCATATCC-TTGACCATTTTTCAATTGGA 481970 i v v i i -- - v v i C L1ME3G_3end#L 102 CCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGGG 53 chr2qtel1M 481971 GAATGCCGATTT-TTATAAAATTAGAGTTAATTCTTCATATATTTTGGA 482018 v-- i vv - vi v iv -v i i i C L1ME3G_3end#L 52 T--TGTCTTTTTCTTATTGATTTGTAG-GAGTTCTTTATATATTCTGGA 7 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 31.02 CpG sites = 72, Kimura (unadjusted) = 31.67 Transitions / transversions = 1.38 (72/52) Gap_init rate = 0.07 (35 / 505), avg. gap size = 1.57 (55 / 35) 1445 29.04 5.27 1.96 chr2qtel1M 481887 483270 (516730) C L1M5_orf2#LINE/L1 (7) 3287 1859 m_b95s551i2 3518 chr2qtel1M 481887 GAGCATCTTTTCATATGACTAGAAATAGTTTCAATTTCTTCATCTGAGAA 481936 i vi vviiivi v? v v i v C L1M5_orf2#LIN 3287 GAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTTTTGTGAA 3238 chr2qtel1M 481937 CTGTCT--TCATATCCTT-GACCATTTTTCAATTGGA--GAATGCCGATT 481981 v -- vi i - v ?v i-- vv i vv C L1M5_orf2#LIN 3237 GTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTTGTCTTTT 3188 chr2qtel1M 481982 T-TTATAAAATTAGAGTTAATTCTTCATATATTTTGGAAATGAGGCCTTT 482030 - vi ? iv v- i i i v i v C L1M5_orf2#LIN 3187 TNTTATTGANTTGTAGG-AGTTCTTTATATATTCTGGATACGAGTCCTTT 3139 chr2qtel1M 482031 ATCAGA-ACTTGACTATAAAATATTTTC---CAGTTTATT-CTT-CCTTC 482074 i - iv v? vvv --- ? i i v- - i C L1M5_orf2#LIN 3138 GTCAGATATATGTNTTGCAAATATTTTCTCCCANTCTGTGGCTTGCCTTT 3089 chr2qtel1M 482075 TAATCTTGCTGCATTAGTTTTGTTTGTA---CAAAACTTTTCAGTTT-GG 482120 v i vi -- vii v iv v?--- i v i i - i C L1M5_orf2#LIN 3088 TCATTTTCTT--AACGGTGTCTTTTGANGAGCAGAAGTTTTTAATTTTGA 3041 chr2qtel1M 482121 TATAATCGAAATT-TCTATTTTGTGATTATAATGATTC-TGGTTCTTG-- 482166 i? i v v - v v --i v v i ?- v i -- C L1M5_orf2#LIN 3040 TGNAGTCCAATTTATCAATTTTTT--CTTTTATGGTTNGTGCTTTTTGTG 2993 chr2qtel1M 482167 -CTTGGTCATAAG----CCTTCCCT-TCCACAGGTCTGAGAGGTAAACTA 482210 - i v -- ---- i v -? vv vvii i --i v C L1M5_orf2#LIN 2992 TCCTGTT--TAAGAAATCTTTGCCTANCCCAAGGTCACGAAGATA--TTC 2947 chr2qtel1M 482211 TCCT-TGTTCTCT-----AATTTATTAAAATTTCATTCTTTAT-CCTAGG 482253 - i ----- v - v i i ?ii i-ii C L1M5_orf2#LIN 2946 TCCTATGTTTTCTTCTAGAAGTT-TTATAGTTTTANCTTTTACATTTAGG 2898 chr2qtel1M 482254 TC-ATGAACCATTTTGACCTTATCTTGGTGTAT----TTAAGTATGGATC 482298 - v i ? vi v i v ---- v i v i C L1M5_orf2#LIN 2897 TCTATGATCCATCTNGAATTAATTTTTGTGTATGGTGTGAGGTAGGGGTC 2848 chr2qtel1M 482299 AATGCCTAGTTT---CCATATTG-T-TTCAATT-TTCCAGCAAT-TTTAT 482341 i v?iii v --- v - - i - vi- i C L1M5_orf2#LIN 2847 GAGNTTCATTTTTTTCCATATGGATATCCAATTGTTCCAGCACCATTTGT 2798 chr2qtel1M 482342 CAAACAGTAAGTTCTTATCCCAAAAGCTGAGAT-CTTTGGG---TTTGTC 482387 ii v vvvi i vi ---- iv - ? v--- C L1M5_orf2#LIN 2797 TGAAAAGACTATCCTTTCCCCA----CTGAATTGCNTTGGCACCTTTGTC 2752 chr2qtel1M 482388 AAAACT-AGGTTGCTATATTTGT-TGACTGTTTTATCCCTTGAAC---CT 482432 v - i? v? i v - --- v i ii - i --- C L1M5_orf2#LIN 2751 AAAAATCAANTGNCCATATATGTGTG---GGTCTATTTCT-GGACTCTCT 2706 chr2qtel1M 482433 AATCTATTTCCACTGATCAACTAATCTATTCTTAG--CAATACCTAAATA 482480 v i - i v i vi i v-- - v iv C L1M5_orf2#LIN 2705 ATTCTGTT-CCATTGATCTATTTGTCTATCCTTACGCCAATACC-ACACT 2658 chr2qtel1M 482481 GTTTTG-TAACTGCTGCTCTATAATAAATTT--AGATCTGGCAAGCTAAG 482527 i - v iv i i i -- ? ? i ivv C L1M5_orf2#LIN 2657 GTCTTGATTACTGTAGCTTTATAATAAGTCTTGANATCNGGTAGTGTAAG 2608 chr2qtel1M 482528 CCACCTTCA--TTTGATTTT-TTTTTCATTAATTCCTTGAA-ATTCTTGA 482573 i -- i -- v i - vv v vii iv- ? i C L1M5_orf2#LIN 2607 TC--CTCCAACTTTGTTCTTCTTTTTCAAGATTGTTTTGGCTATTCTNGG 2560 chr2qtel1M 482574 CCTTTTGTTTTTCCATATGAACTTTGTTGTTATTTTTTCTAGGTC-ATTA 482622 i i iv i i ivvi i vi v v vv - iv C L1M5_orf2#LIN 2559 TCCTTTGCATTTCCATATAAATTTTAGAATCAGCTTGTCAATTTCTACAA 2510 chr2qtel1M 482623 AAATAGTTTTTGGGACTCTGATTGGTATAGCGCTAAATAAATAGATTAGT 482672 v vi vi i i v v ii i vv i i C L1M5_orf2#LIN 2509 AAAAACCTGCTGGGATTTTGATTGGGATTGCATTGAATCTATAGATCAAT 2460 chr2qtel1M 482673 TTAGGTAATATTGTCATCTTTATTATATTT-GTCGCCCTATCCAAGAGCA 482721 i v iv v ? iv v- vi v v i C L1M5_orf2#LIN 2459 TTGGGGAGAATTGACATCTTNACAATATTGAGTCTTCCAATCCATGAACA 2410 chr2qtel1M 482722 TTTAATATTTTTCCAATTGGTTAGATCAGATTTAATTTGTTGTGAAAAGT 482771 vvv i i v iv i vvv v i- v iv i C L1M5_orf2#LIN 2409 TGGTATATCTCTCCATTTATTTAGGTCTTCTTTAATTTCTC-TCAGCAAT 2361 chr2qtel1M 482772 GGTCT-TAATTTTGCTCATAAAGTTTCTTG---ATTTTCCCTTGGCAGAT 482817 v i - i vvvii ? v - --- ? --- vi C L1M5_orf2#LIN 2360 GTTTTGTAGTTTTCAGTGTANAGGT-CTTGCACATNTT---TTGTTAGAT 2315 chr2qtel1M 482818 AGATTCCTAAATATTTTATATTATCAGTAGTTACTTTAAATGGAATTTCT 482867 vv i ? i v iv vv i i v v vi C L1M5_orf2#LIN 2314 TTATTCCTAAGTATTTNATGTTTTTTGATGCTATTGTAAATGGTATTGTT 2265 chr2qtel1M 482868 TTTGTAACTCTGACTGTTGGATT--TTGTTAGTGATATATAAGAATGCTG 482915 ?- v i v i v ivi -- iv ii ii i vi C L1M5_orf2#LIN 2264 TTTN-AAATTTCATTTTCCAATTGTTTGTTGCTAGTATATAGAAATACAA 2216 chr2qtel1M 482916 ATGACTTATGTGGGTTTATTTTATAACCAGCAACTTTGCTAAAGTTGTGG 482965 v i v ivi v ii i v ? i i v iiivv C L1M5_orf2#LIN 2215 TTGATTTTTGTATATTGACCTTGTATCCNGCGACCTTGCTAAATTCACTT 2166 chr2qtel1M 482966 ATTATTTCTAATAACTT-TTAGCAGAATCTT-AGGGTTCTCTAAGTATAC 483013 v i ii - v i v -? i i v ? C L1M5_orf2#LIN 2165 ATTAGTTCTAGTAGTTTNTTTGTAGATTCTTTNGGATTTTCTACGTANAC 2116 chr2qtel1M 483014 CATCATGTCATCGGCAAAGAGTGATAATTTGGTTTCCTCATTGCCTATTC 483063 v v i v i? i i vi i v v v ii C L1M5_orf2#LIN 2115 AATCATGTCATCTGCGAATAANGACAGTTTTATTTCTTCCTTTCCAATCT 2066 chr2qtel1M 483064 TTATTCCTTTAATCTCTTTCTCAGCTCTTATTGCTAAAGCTAGCATTTCT 483113 v v i i vvvi vvvi v ii i C L1M5_orf2#LIN 2065 TTATGCCTTTTATTTCTTTTTCTTGCCTTATTGCACTGGCTAGGACCTCC 2016 chr2qtel1M 483114 AATACAATATTAAATAGTAACGGTGATAGTGGGCAACCTTGTTTCACTCC 483163 i i i v ii ? i i v i iii C L1M5_orf2#LIN 2015 AGTACAATGTTGAATAGAAGTGGTGANAGCGGACATCCTTGTCTTGTTCC 1966 chr2qtel1M 483164 AGATCTTACTGGGAATGGTTGCAGTTTGTCTCCATTACATATGATGCTTA 483213 v vv v v? v ? v v vi i ?i C L1M5_orf2#LIN 1965 CGATCTTAGGGGGAAAGCNTTCAGTNTTTCACCATTAAGTATGATGTTNG 1916 chr2qtel1M 483214 CTGATGGTTTTAAATAGATGCTGCTGATTATTTTAAGGAAAAGTCCATTT 483263 vv vvi ivi v i vv i ivvi v i C L1M5_orf2#LIN 1915 CTGTAGGTTTTTCGTAGATGCCCTTTATCAGGTTGAGGAAGTTCCCTTCT 1866 chr2qtel1M 483264 ATTCCTA 483270 C L1M5_orf2#LIN 1865 ATTCCTA 1859 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.42 CpG sites = 201, Kimura (unadjusted) = 38.41 Transitions / transversions = 1.04 (201/193) Gap_init rate = 0.05 (72 / 1383), avg. gap size = 1.40 (101 / 72) 2080 28.19 1.41 0.70 chr2qtel1M 483279 484132 (515868) L1M5_orf2#LINE/L1 1123 1982 (1312) m_b95s551i3 3519 chr2qtel1M 483279 AAGCCTTTGGTAAATCTGATTAGAAAAAAGAGGGAGGAAAATGAAATTAG 483328 i i i i? iv i ii i i i i vvv v L1M5_orf2#LIN 1123 AAACCTCTAGCNAGACTGATCAAGAAAAAAAGAGAGAAGACACAAATTAC 1172 chr2qtel1M 483329 TAGTCTTAAAAATGAAAA-GGAGAACTTTCCACCAATGAAGAGGAAATTA 483377 i i v i ii - vv iv i vi vvvivi v L1M5_orf2#LIN 1173 CAATATCAGGAATGAAAAAGGAGACATCACTACAGATCCTACAGACATTA 1222 chr2qtel1M 483378 GAGAAATAATAAGGAGTTATTTTGCTCAACTTTATGCCAATAAATTTGAT 483427 i iii iiiv v vv ? L1M5_orf2#LIN 1223 AAAGGATAATAAGAGAATATTATGAACAACTTTATGCCAATAAATTTGAN 1272 chr2qtel1M 483428 AACCTAAGTGAAATAGATGACTACCTCCAAAAATATAGACTTCCCAGACT 483477 i ii i ii v v iv i i i?i v v i L1M5_orf2#LIN 1273 AACTTAGATGAAATGGACAAATTCCTTGAAAAACACAANTTACCAAAACT 1322 chr2qtel1M 483478 AACAGAGGAGGAAGTAAATTGCTTGAATAGTCCCATTTCAGAAAAAGAAA 483527 i ?v i i i i vviii i i v vivv L1M5_orf2#LIN 1323 GACNCAAGAAGAAATAGAAAATCTGAATAGCCCTATATCTATTAAAGAAA 1372 chr2qtel1M 483528 TAGAACAGGCAATTAAACAACTCCCTAAGAAAAAATCCCTAGGACCAGAT 483577 v ivv i v v i i vi i v i i v L1M5_orf2#LIN 1373 TTGAATTTGTAATTAAAAACCTTCCCACAAAGAAAACTCCAGGCCCAGAT 1422 chr2qtel1M 483578 GGATTTATATGTGAATTTTACCAAACATTTAAAGAACAATTGGTCCCAAT 483627 v i ivv i i v v ii v L1M5_orf2#LIN 1423 GGCTTCACTGGTGAATTCTACCAAACATTTAAGGAAGAAATAATACCAAT 1472 chr2qtel1M 483628 GCTATATAAATTATTTGATAAAATAGGGAATGA-GGAGTCCTACCAAATT 483676 vi i i i v iv v ii v - iiv v v i L1M5_orf2#LIN 1473 CTTACACAAACTCTTCCAGAAAATAGAAAAAGAGGGAACACTTCCCAACT 1522 chr2qtel1M 483677 CCTTCTATGACACAGACATGGTACTGATACCTAAACCAGGTAGGCTAGAA 483726 v i vi vii ?iiv v ? ii i--- v L1M5_orf2#LIN 1523 CATTTTATGAGGCCAGCATNACCCTGATACCAAAACCNGACAA---AGAC 1569 chr2qtel1M 483727 A--ACAGAGAAAAGAAAATT-TAGACCAATCT-CCTAATGAATATTGATG 483772 -- - -i v - v i v L1M5_orf2#LIN 1570 ATTACA-AGAAAAGAAAATTACAGACCAATATCCCTCATGAACATAGATG 1618 chr2qtel1M 483773 CTAAAATCTTAAATAAGATATTAGTAAA-AGACTACAGAAAAATCATCTC 483821 v i ? i i i -v v v v v - vvv L1M5_orf2#LIN 1619 CAAAAATCCTNAACAAAATATTAGCAAATCGAATCCAGCAATAT-ATAAA 1667 chr2qtel1M 483822 CAAGATAATACACTATGATCAAGTAGGATTTATACCAGGAATGCAGGG-T 483870 v i ii i i i v i - L1M5_orf2#LIN 1668 AAGGATAATACATCATGACCAAGTGGGGTTTATCCCAGGAATGCAAGGTT 1717 chr2qtel1M 483871 GGTTCAATATTAGGAAAACTATCAATATAATTGGCCATGTTAAAAAATTA 483920 i i v i v v i vi i v i v L1M5_orf2#LIN 1718 GGTTTAACATTCGAAAATCAATCAATGTAATTCACCATATTAACAGAATA 1767 chr2qtel1M 483921 ----ACAAAAACCATATGATCATTCTCAATAGATGCAGAAAAAGCATTTG 483966 ---- v i - L1M5_orf2#LIN 1768 AAGGAGAAAAATCATATGATCA-TCTCAATAGATGCAGAAAAAGCATTTG 1816 chr2qtel1M 483967 ATAAAATCCAACATCCATTCCTATTAAAAACACTTGAGAGTATAGGAATA 484016 i i i v iv v iiiv ivv L1M5_orf2#LIN 1817 ACAAAATTCAACACCCATTCATGATAAAAACTCTCAGCAAACTAGGAATA 1866 chr2qtel1M 484017 AATGGACTTTTTCTTAAAATAGTCAGGAGCATATATTTAAAACCATCAGT 484066 i v ivvi i i vv ii v i i v ivv vv i L1M5_orf2#LIN 1867 GAAGGGAACTTCCTCAACCTGATAAAGGGCATCTACGAAAAACCTACAGC 1916 chr2qtel1M 484067 AAGCATCATATGTAATGGAGACAAACTGCAACCATTCCCAATAAGATCTG 484116 ? i iv v v ? v ?v v vv v L1M5_orf2#LIN 1917 NAACATCATACTTAATGGTGAAANACTGAANGCTTTCCCCCTAAGATCGG 1966 chr2qtel1M 484117 GAGTGAAACATGGTTG 484132 iii i v v L1M5_orf2#LIN 1967 GAACAAGACAAGGATG 1982 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.39 CpG sites = 131, Kimura (unadjusted) = 36.58 Transitions / transversions = 1.21 (131/108) Gap_init rate = 0.02 (14 / 853), avg. gap size = 1.29 (18 / 14) 421 29.42 5.96 1.76 chr2qtel1M 484126 484343 (515657) C L1ME5_3end#LINE/L1 (628) 313 87 m_b95s551i4 3520 chr2qtel1M 484126 ATGGTTGGATCATTTCACAATGCCACCAACAATGTATTACAATCCCACTT 484175 i v i v ii v v i i i v vii i vv ? C L1ME5_3end#LI 313 ATGGCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATN 264 chr2qtel1M 484176 TTCCCAAATCCACTCCAACATTCACCATTATCT---TTTCCTGTCATCTT 484222 i v v v i iiv i--- --- v i C L1ME5_3end#LI 263 TCCCCACATCCTCGCCAACACTTGGCATTATCCAGCTTTC---TAATTTT 217 chr2qtel1M 484223 GGCCAATCTGAGAGTTGTGTAGTGGAATCTC---------TTAATTTGTA 484263 v i i v v iv iv --------- i C L1ME5_3end#LI 216 TGCCAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCA 167 chr2qtel1M 484264 TTTCTCTAATCAAGAGTGATTTAGAGCACCTTTTCATATTACTAGAAATG 484313 i i vv i v v i i - i v vv vv C L1ME5_3end#LI 166 TTTCTCTGATTACTAATGAGTTTGAGCATCTCTTCATA-TGCTTGTTAGC 118 chr2qtel1M 484314 GTTTCAAGTTT-TTCATCTAAAAATTGTTTG 484343 v ii -i v iv ii C L1ME5_3end#LI 117 CTTTCGGGTTTCCTCTTCTGTAAATTGCCTG 87 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.46 CpG sites = 33, Kimura (unadjusted) = 38.23 Transitions / transversions = 1.10 (33/30) Gap_init rate = 0.03 (7 / 217), avg. gap size = 2.43 (17 / 7) 503 24.70 6.25 1.08 chr2qtel1M 484127 484302 (515698) C L1MC4_3end#LINE/L1 (2477) 312 128 m_b95s551i5 3520 chr2qtel1M 484127 TGGTTGGATCATTTCACAATGCCACCAACAATGTATTACAATCCCACTTT 484176 i v i ii v v i v v i i ?v v C L1MC4_3end#LI 312 TGGCTGTACCATTTTGCATTCCCACCAGCAATGTATGAGAGTTCCNGTTG 263 chr2qtel1M 484177 TCCCAAATCCACTCCAACATTCACCATTATC--TTTTCCTGTCATCTTGG 484224 ii v v v i iivi i -- ? ii -- i i C L1MC4_3end#LI 262 CTCCACATCCTCGCCAGCATTTGGTATTGTCAGTNTTTTTG--ATTTTAG 215 chr2qtel1M 484225 CCAATCTGAGAGTTGTGTAGTGGAATCTC---------TTAATTTGTATT 484265 v i v v v --------- i C L1MC4_3end#LI 214 CCATTCTAATAGGTGTGTAGTGGTATCTCATTGTGGTTTTAATTTGCATT 165 chr2qtel1M 484266 TCTCTAATCAAGAGTGATTTAGAGCACCTTTTCATAT 484302 i v v? i v v i i C L1MC4_3end#LI 164 TCCCTAATGACNAATGATGTTGAGCATCTTTTCATGT 128 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 31.15 CpG sites = 24, Kimura (unadjusted) = 31.15 Transitions / transversions = 1.26 (24/19) Gap_init rate = 0.02 (4 / 175), avg. gap size = 3.25 (13 / 4) 483 21.06 3.70 8.53 chr2qtel1M 484373 484507 (515493) MIRc#SINE/MIR 2 130 (138) m_b95s601i0 3521 chr2qtel1M 484373 GAGGCAGCTGAGTGGTGCAATGGATAGAGCACCAGTCCTGAAGTCAGGAG 484422 i--- i v ii v i i i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr2qtel1M 484423 GACTAGAGTTCAATTCTTGGGTCAGACACTTAACACTTCCTAGCTGTGTG 484472 iv i i v ii v v v ------- MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTG 91 chr2qtel1M 484473 ACCCTGGGTAACTTA---AACCTGCATT--GCCTCAGCTT 484507 i i v i --- - vi -- i MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACCT-CTCTGAGCCTCAGTTT 130 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 23.04 CpG sites = 17, Kimura (unadjusted) = 25.21 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.10 (13 / 134), avg. gap size = 1.23 (16 / 13) 19 14.91 0.00 0.00 chr2qtel1M 484508 484544 (515456) (AAAG)n#Simple_repeat 1 37 (0) m_b95s252i1 3522 chr2qtel1M 484508 AAAAAAAAAAACAAAGAAAGAAAGAAAGAAACTAAGA 484544 i i v vv (AAAG)n#Simpl 1 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA 37 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 466 20.76 1.61 6.78 chr2qtel1M 484623 484746 (515254) C MIRc#SINE/MIR (141) 127 10 m_b95s601i1 3523 chr2qtel1M 484623 CTGAGGC-AACTGGGGTTAAGTGACTTTCCCAGGATCACACAGTTATGAA 484671 -v vv i v i i i vv C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAA 78 chr2qtel1M 484672 GTGTTAAGTATCTGATGCCAG-ATTTGAACACCAGTCCTCCTGACTTCAG 484720 ---- i --- - i - i i v vi i i i C MIRc#SINE/MIR 77 GTG----GCA---GA-GCCGGGACTCGAACCCAGGTCTTCCTGACTCCAA 36 chr2qtel1M 484721 GTCTGGTGCTCTATCCACTGCTCCAC 484746 ii v v C MIRc#SINE/MIR 35 GTCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 22.32 CpG sites = 14, Kimura (unadjusted) = 24.58 Transitions / transversions = 1.40 (14/10) Gap_init rate = 0.08 (10 / 123), avg. gap size = 1.00 (10 / 10) 35 30.14 2.69 3.80 chr2qtel1M 484948 485133 (514867) (ATTTT)n#Simple_repeat 1 184 (0) m_b95s252i3 3524 chr2qtel1M 484948 ATTTTGATTT-TTTTATTTCAATTCA-TCTATTTCCTTTCCCTCTTTAAT 484995 iv - i v i - i iv -iv - v (ATTTT)n#Simp 1 ATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTT-TAT-TTTATT 48 chr2qtel1M 484996 GTTTTGTCATTTATACTTATTTGAGGTTTA-TTCACTTAATTTTCTCAAT 485044 v v v vv -i v -v - i i v v ivvv (ATTTT)n#Simp 49 TTATTTTATTTTAT-TTTATTTTA-TTTTATTTTATTTTATTTTATTTTA 96 chr2qtel1M 485045 TTTTAGATGCAGATTTACTTATTTTTTACTTTATTTATTTTTACTTTATA 485094 -v vi -v - v v i vv i v (ATTTT)n#Simp 97 TTTTA-TTTTA-TTTTA-TTTTATTTTATTTTATTTTATTTTATTTTATT 143 chr2qtel1M 485095 TTA-TTTACTTTATTTTA-TTTACTTTTTTTTACTTTACTT 485133 - i - i v i i (ATTTT)n#Simp 144 TTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTT 184 Matrix = Unknown Transitions / transversions = 0.65 (17/26) Gap_init rate = 0.06 (12 / 185), avg. gap size = 1.00 (12 / 12) 489 31.52 4.56 3.66 chr2qtel1M 486412 486872 (513128) C L1PA17_3end#LINE/L1 (448) 465 1 m_b95s551i6 3525 chr2qtel1M 486412 TGTGAAAAGGGCTGCCACAAACATTTTGCACATACAGGTCCCTTTCCCTT 486461 v v v i ---i ivi i vi iivv C L1PA17_3end#L 465 TGTGAATAGTGCTGCGATAAACAT---ACGAGTGCAGGTGTCTTTTTGGT 419 chr2qtel1M 486462 ----C--TTTAGTATCTCTTTGGGATATAAGCCCAGTAGTAACACTGCTG 486505 ---- -- v v - - vi i iiv i C L1PA17_3end#L 418 AGAACGATTTATTTTC-CTTTGGG-TATATACCCAGTAATGGGATTGCTG 371 chr2qtel1M 486506 CATCAAAGGGTATGCACAATTTGATAACTTTTTGAACGTAGT-TCCAAAT 486554 vi i v - iv v v- ii i -- v i - i C L1PA17_3end#L 370 GGTCGAATGGTA-GTTCTATTTT-TAGTTCTTTGA--GAAATCTCCAAAC 325 chr2qtel1M 486555 TGTTTTCCAGAATGGTTGGATCCATTCACAACTCCACCAACAATGCATCA 486604 i v iv i i iiv i vii i i v C L1PA17_3end#L 324 TGCTTTCCACAGGGGCTGAACTAATTTACATTCCCACCAACAGTGTATAA 275 chr2qtel1M 486605 TTGTCGCAGTTTTCCAACATCGCCTACAAAAATCATCATTGTCTTTTCCT 486654 vi iv vv ii vi ? vi vv ---- -- iv ii C L1PA17_3end#L 274 GCGTTCCCTTTTCTCCGCANCCTCGCCAA----CATC--TGTTATTTTTT 231 chr2qtel1M 486655 GTCATTTTA------TCCAATCTGACAGGTGTGTAGTGGTATCTCAGAAT 486698 v v ------v v v vii vvi C L1PA17_3end#L 230 GACTTTTTAATAATAGCCATTCTGACTGGTGTGAGATGGTATCTCATTGT 181 chr2qtel1M 486699 TGTCTTAATTTACATTTCTCTGATCAATAATGATTTGGAACA----CTCA 486744 v i i i v v i v v i ----i C L1PA17_3end#L 180 GGTTTTGATTTGCATTTCTCTGATGATTAGTGATGTTGAGCATTTTTTCA 131 chr2qtel1M 486745 TACGAGTAGAAATAGTTCCAATTTCATCATCTGA-AAGT-TGTGCTTATA 486792 i vv ivviiiv i ivv v v v i - - v i i i C L1PA17_3end#L 130 TATGTTTGTTGGCCGCTTGTATGTCTTCTTTTGAGAAGTGTCTGTTCATG 81 chr2qtel1M 486793 TCCTTTGACCATTTATCAATTGGAGAA--TGGTTTGATTTCTTATAAATT 486840 v i v i v ivv -- v -- i vi C L1PA17_3end#L 80 TCCTTTGCCCACTTTTTAATGGGGTTATTTGTTTT--TTTCTTGTTGATT 33 chr2qtel1M 486841 AGAGTCAATTCTCAATATATTTTGGAAATGAG 486872 v vv v i iiv v i v v C L1PA17_3end#L 32 TGTTTAAGTTCCTTATAGATTCTGGATATTAG 1 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.10 CpG sites = 70, Kimura (unadjusted) = 41.62 Transitions / transversions = 1.00 (70/70) Gap_init rate = 0.05 (25 / 460), avg. gap size = 1.52 (38 / 25) 853 28.90 4.04 3.00 chr2qtel1M 486422 486817 (513183) C L1ME5_3end#LINE/L1 (486) 455 56 m_b95s551i7 3525 chr2qtel1M 486422 GCTGCCACAAACATTTTGCACATACAGGTCCCTTTC----CCTTCTTTAG 486467 v ii ii --- i v i v---- viv v C L1ME5_3end#LI 455 GCTGCAATGAACATCCT---CGTACATGTCCCCTTATGGACCTGTGTGAG 409 chr2qtel1M 486468 TATCTCTTTGGGATATAAGCCCAGTAGTAACACTGCTGCATCAAAGGGTA 486517 v i vi v iiiv i vi v C L1ME5_3end#LI 408 AATTTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTA 359 chr2qtel1M 486518 TGCACA-ATTTGATAACTTTTTGA--ACGTAGTTCCAAATTGTTTTCCAG 486564 ii - i i ------ -- v v v i i i C L1ME5_3end#LI 358 TGCGTATACTTAAT------TTGACTAAGTACTGCCAGATTGCTCTCCAG 315 chr2qtel1M 486565 AATGGTTGGATCCATTCACAACTCCACCAACAATGCATCATTGTCGCAGT 486614 i v i vi ii vii i i v vv iv vi C L1ME5_3end#LI 314 AATGGCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTAT 265 chr2qtel1M 486615 TTTCCAACATCGCCTACAAAAATCATCATTGTCT---TTTCCTGTCATTT 486661 ? i v vi vv v v iiv i i--- --- v C L1ME5_3end#LI 264 NTCCCCACATCCTCGCCAACACTTGGCATTATCCAGCTTTC---TAATTT 218 chr2qtel1M 486662 TATCCAATCTGACAGGTGTGTAGTGGTATCTCAGAATTGTCTTAATTTAC 486711 vv i i i iv i vvi i i C L1ME5_3end#LI 217 TTGCCAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGC 168 chr2qtel1M 486712 ATTTCTCTGATCAATAATGATTTGGAACA----CTCATACGAGTAGAAAT 486757 i v v v i ----i i vv ivv ii C L1ME5_3end#LI 167 ATTTCTCTGATTACTAATGAGTTTGAGCATCTCTTCATATGCTTGTTAGC 118 chr2qtel1M 486758 AGTTCCAATTTCATCATCTGAAAGTTG--TGCTTATATCCTTTGACCATT 486805 vv vii v v v i -- i i v C L1ME5_3end#LI 117 CTTTCGGGTTTCCTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCCATT 68 chr2qtel1M 486806 TATCAATTGGAG 486817 v v i C L1ME5_3end#LI 67 TTTCTATTGGGG 56 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.96 CpG sites = 59, Kimura (unadjusted) = 37.26 Transitions / transversions = 1.13 (59/52) Gap_init rate = 0.05 (18 / 395), avg. gap size = 1.56 (28 / 18) 761 28.35 2.99 3.25 chr2qtel1M 486466 486866 (513134) C L1ME3G_3end#LINE/L1 (518) 406 7 m_b95s551i8 3525 chr2qtel1M 486466 AGTATCTCTTTGGGATATAAGCCCAGTAGTAACACTGCTGCATCAAAGGG 486515 i ? i v v? ? v iiv i vi C L1ME3G_3end#L 406 AGTATTTCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGG 357 chr2qtel1M 486516 TATGCACAATTTGATAACTTTTTGAACGTAGTTCCAAATTGTTTTCCAGA 486565 i - -- v viv vi v v iii i C L1ME3G_3end#L 356 TATGCGCA-TTT--TAAATTTTAATAGATACTGCCAAATTGCCCTCCAAA 310 chr2qtel1M 486566 ATGGTTGGATCCATTCACAACTCCACCAACAATGCATCATTGTCGCAGTT 486615 ? i v i v i vii i i i v vv vv v C L1ME3G_3end#L 309 ANGGCTGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTT 260 chr2qtel1M 486616 TTCCAACA---TCGCCTACA---AAAATCATCATTGTCTTTTCCTGTCAT 486659 i v --- v ---i v i --i? vv---- C L1ME3G_3end#L 259 TCCCCACACCCTCGCCAACACTNGATATTATCA--ANCTTTTAA----AT 216 chr2qtel1M 486660 TTTATCCAATCTGACAGGTGTGTAGTGGTATCTCAGAATTGTCTTAATTT 486709 vv ii viv i vvi i C L1ME3G_3end#L 215 TTTTGCCAATCTGATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTT 166 chr2qtel1M 486710 ACATTTCTCTGATCAATAATGATTTGGAACA----CTCATACGAGTAGAA 486755 i i i v i vv v i ----i i vv vvi C L1ME3G_3end#L 165 GCATTTCCCTGATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTG 116 chr2qtel1M 486756 ATAGTTCCAATTTCATCATCTGAAAGTTG--TGCTTATATCCTTTGACCA 486803 iivi ivv v v vi i -- i i v C L1ME3G_3end#L 115 GCCATTTGTATTTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCA 66 chr2qtel1M 486804 TTTATCAATTGGAGAATGGTTTGATTTCTTATAAATTAGAGTCAATTCTC 486853 v v iv-- vi -- vi v vivv i i C L1ME3G_3end#L 65 TTTTTCTATTGGGT--TGTCTT--TTTCTTATTGATTTGTAGGAGTTCTT 20 chr2qtel1M 486854 AATATATTTTGGA 486866 v i C L1ME3G_3end#L 19 TATATATTCTGGA 7 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.19 CpG sites = 54, Kimura (unadjusted) = 36.60 Transitions / transversions = 0.96 (54/56) Gap_init rate = 0.04 (17 / 400), avg. gap size = 1.47 (25 / 17) 1176 29.92 2.01 1.81 chr2qtel1M 488209 488705 (511295) C L1ME5_3end#LINE/L1 (304) 637 140 m_b95s551i9 3526 chr2qtel1M 488209 TCCTACTCATTTCACTCAGCATCA-GTTCATGTAAG-TCTTTCCAGGCCT 488256 i iv ii - -- v - iv v iiv C L1ME5_3end#LI 637 TCTTACTTTTTTCACTCAGCACTATGTT--TTTAAGATCCATCCATGTTG 590 chr2qtel1M 488257 TTCTGAAGTCATCCTGTTGGTCATTTCTTACTGAACAATAATATTCCATA 488306 i v vivv iv iv iii v vvvv i i i C L1ME5_3end#LI 589 CTATGTGTACATCTAGTCCGTTGCTTCTAACTGCTGCATAGTACTCCATG 540 chr2qtel1M 488307 ATATTCATATACCACAATTTATTCAGCCATTCTCCAATTGAGGGGTATCC 488356 i i v vi v iii v i v v v ii i C L1ME5_3end#LI 539 GTGTGCATCCACCACATTTTACCTATCCACTCTCCCAGTGATGGACACCC 490 chr2qtel1M 488357 ACTCAGTTTCCAGTTTCTGGCCACTAGAAACAGGGCTGCCACAAACATTC 488406 vviv ii ii i iv i v iv v ii i C L1ME5_3end#LI 489 AGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCTGCAATGAACATCC 440 chr2qtel1M 488407 TTGCACAGGGCCCTTTC----CCTTCTTTAGTATCTCTTTGGGATATAAG 488452 i i v v i v---- viv v v i vi C L1ME5_3end#LI 439 TCGTACATGTCCCCTTATGGACCTGTGTGAGAATTTCTTTGGGATATATA 390 chr2qtel1M 488453 CCCAGTAGTAACACTGCTGGATCAAAGGGTATGCACAGTTTGATAACTT- 488501 v iiiv i i v --- --- - - C L1ME5_3end#LI 389 CCCAGGAGCGGAATTGCTGGGTCATAGGGTATGC---GT---ATA-CTTA 347 chr2qtel1M 488502 -TTTGAGCA--TAGTTCCAAATTGTTCTCCAGAATGGCTGGATGTATTCA 488548 - vi -- v v i i v ivvi ii C L1ME5_3end#LI 346 ATTTGACTAAGTACTGCCAGATTGCTCTCCAGAATGGCTGCACCAGTCTA 297 chr2qtel1M 488549 CAATTCCATCAACAATGGATCAGTGTCCCTGTTTTCCCACATCCCCTCCA 488598 v i i i i v v v i i ? i i v C L1ME5_3end#LI 296 CACTCCCACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATCCTCGCCA 247 chr2qtel1M 488599 ACATTCCACATTATCTTTCCCTGTCATTCTAGCCAATCTGACAGGTGTGT 488648 i ivi ivv ii v v i v i i i iv C L1ME5_3end#LI 246 ACACTTGGCATTATCCAGCTTTCTAATTTTTGCCAGTCTAATAGGTGTAA 197 chr2qtel1M 488649 AGTAGTATCTCAGAGTTGTCTTAATTTGCATTTCTCTAATTAATAATTGT 488698 ii vv i i v viv C L1ME5_3end#LI 196 AGTGATATCTCATTGTTGTTTTAATTTGCATTTCTCTGATTACTAATGAG 147 chr2qtel1M 488699 TGTGAGC 488705 v C L1ME5_3end#LI 146 TTTGAGC 140 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.42 CpG sites = 81, Kimura (unadjusted) = 39.14 Transitions / transversions = 1.25 (81/65) Gap_init rate = 0.03 (15 / 496), avg. gap size = 1.27 (19 / 15) 1203 26.82 1.00 0.74 chr2qtel1M 488294 488695 (511305) C L1ME3G_3end#LINE/L1 (376) 548 146 m_b95s551i10 3526 chr2qtel1M 488294 ATAATATTCCATAATATTCATATACCACAATTTATTCAGCCATTCTCCAA 488343 i i vv i i i i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr2qtel1M 488344 TTGAGGGGTATCCACTCAGTTTCCAGTTTCTGGCCACTAGAAACAGGGCT 488393 v ii ii vviv i i v i i v iv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr2qtel1M 488394 GCCACAAACATTCTTGCACAGGGCCCTTT---CCCTTCTTT-AGTATCTC 488439 v ii i i v v?i i --- v v v vi- i C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACATGCNTCCTTGTGCACATGTGCGAGTATTTC 399 chr2qtel1M 488440 TTTGGGATATAAGCCCAGTAGTAACACTGCTGGATCAAAGGGTATGCACA 488489 ? i v v? ? v iiv i i i C L1ME3G_3end#L 398 TNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGCA 349 chr2qtel1M 488490 GTTTGATAACTTTTTGAGCATAGTTCCAAATTGTTCTCCAGAATGGCTGG 488539 v i -- i vvv - v v ii i ? v C L1ME3G_3end#L 348 TTTTAA--ATTTTAATAG-ATACTGCCAAATTGCCCTCCAAAANGGCTGT 302 chr2qtel1M 488540 ATGTATTCACAATTCCATCAACAATGGATCAGTGTCCCTGTTTTCCCACA 488589 ivv i v i i i i v v v v i i C L1ME3G_3end#L 301 ACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCACA 252 chr2qtel1M 488590 TCCCCTCCAACATTCCACATTATCTTTCCCTGTCATTCTAGCCAATCTGA 488639 i i v i ?v i vv? ii vvv i v C L1ME3G_3end#L 251 CCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATCTGA 202 chr2qtel1M 488640 CAGGTGTGTAGTAGTATCTCAGAGTTGTCTTAATTTGCATTTCTCTAATT 488689 ii viv i i vv i i i C L1ME3G_3end#L 201 TGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGATT 152 chr2qtel1M 488690 AATAAT 488695 v i C L1ME3G_3end#L 151 ACTAGT 146 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 33.38 CpG sites = 59, Kimura (unadjusted) = 34.56 Transitions / transversions = 1.23 (59/48) Gap_init rate = 0.01 (5 / 401), avg. gap size = 1.40 (7 / 5) 12 13.74 2.78 5.71 chr2qtel1M 488947 488982 (511018) (GAGT)n#Simple_repeat 1 35 (0) m_b95s252i4 3527 chr2qtel1M 488947 GAGTCAGTGAG-GATTGAGTGAGTTGGAGGGATTGAG 488982 v - v - - v v (GAGT)n#Simpl 1 GAGTGAGTGAGTGAGTGAGTGAG-T-GAGTGAGTGAG 35 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.09 (3 / 35), avg. gap size = 1.00 (3 / 3) 235 28.10 1.97 4.03 chr2qtel1M 489230 489381 (510619) C L1MC3_3end#LINE/L1 (2377) 155 7 m_b95s551i11 3526 chr2qtel1M 489230 ACAAATAATGACTTGAAGCATTTTTTCATATGGCTAGAAATAGTTTCAAT 489279 i -- - i vi vvviivi i vv C L1MC3_3end#LI 155 ACAAATGATG--TTGA-GCATCTTTTCATATGCTTATTTGCCATCTGTAT 109 chr2qtel1M 489280 TTCTTCATCTGAGAATTGTCTATTCATATCCTTTGACCATTTATCAATTG 489329 v v iv v iv i v i v v i C L1MC3_3end#LI 108 ATCTTCTTTGGTGAGGTGTCTGTTCAGATCTTTTGCCCATTTTTTAATTG 59 chr2qtel1M 489330 GAGAATGGCATGATTTCTTATAAATTAGAGTCAA---TTCTCTATATATT 489376 i--- v iv v viv v vv i --- i i C L1MC3_3end#LI 58 GG---TTGTTTGTTTTCTTATTGTTGAGTTTTAAGAGTTCTTTGTATATT 12 chr2qtel1M 489377 TTGGA 489381 C L1MC3_3end#LI 11 TTGGA 7 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.35 CpG sites = 18, Kimura (unadjusted) = 35.35 Transitions / transversions = 0.78 (18/23) Gap_init rate = 0.05 (7 / 151), avg. gap size = 1.29 (9 / 7) 314 26.80 0.00 0.00 chr2qtel1M 489235 489331 (510669) C L1PB2_3end#LINE/L1 (745) 153 57 m_b95s551i12 3526 chr2qtel1M 489235 TAATGACTTGAAGCATTTTTTCATATGGCTAGAAATAGTTTCAATTTCTT 489284 i iv vi vi ivviiiv vv v C L1PB2_3end#LI 153 TAGTGATGTTGAGCATTTTTTCATATGTTTGTTGGCCGTTTGTATATCTT 104 chr2qtel1M 489285 CATCTGAGAATTGTCTATTCATATCCTTTGACCATTTATCAATTGGA 489331 v i i v i v ii v C L1PB2_3end#LI 103 CTTTTGAGAATTGTCTATTCATGTCCTTTGCCCACTTTTTGATGGGA 57 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 33.51 CpG sites = 13, Kimura (unadjusted) = 33.51 Transitions / transversions = 1.00 (13/13) Gap_init rate = 0.00 (0 / 96), avg. gap size = 0.0 (0 / 0) 385 34.08 3.61 3.61 chr2qtel1M 489246 489799 (510201) C L1P3_orf2#LINE/L1 (8) 3286 2733 m_b95s551i14 3526 chr2qtel1M 489246 AGCATTTTTTCATATGGCTAGAAATAGTTTCAATTTCTTCATCTGAGAAT 489295 v vi ivviiiv iv v v v i v C L1P3_orf2#LIN 3286 AGCTTTTTTTCATATGTTTGTTGGCCGCATAAATGTCTTCTTTTGAGAAG 3237 chr2qtel1M 489296 TGTCTATTCATATCCTTTGACCATTTATCAATTGGAGAATGGCATG---A 489342 i i v i v ii v ---i v iv ---v C L1P3_orf2#LIN 3236 TGTCTGTTCATATCCTTCGCCCACTTTTTGATGGG---GTTGTTTGTTTT 3190 chr2qtel1M 489343 TTTCTTATAAATTAGAGTCAATTCTCTATATATTTTGGAAATGAAGCCTT 489392 i v vv v i ii i v i v v iv C L1P3_orf2#LIN 3189 TTTCTTGTAAATTTGTTTAAGTTCCTTGTAGATTCTGGATATTAGCCCTT 3140 chr2qtel1M 489393 TATCAGAACATTTGACTGTAAAAATGTTTTCCCAATTTATTGCTTCCCTT 489442 i vviv v i i v i v i i v v v v C L1P3_orf2#LIN 3139 TGTCAGATGGATAGATTGCAAAAATTTTCTCCCATTCTGTAGGTTGCCTG 3090 chr2qtel1M 489443 CTAATCTTGTCTGCAT--TAGTTTTGTT---TGTACAAAAACTTTTCAAT 489487 i v i---- - -- iv --- i i i i i i C L1P3_orf2#LIN 3089 TTCAC----TCTG-ATGATAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGT 3045 chr2qtel1M 489488 TTGATATAATCAAAATTTTCTATTCTG-----TGATCAGTAATGATCTCT 489532 i vvi vv v v v i ----- v -- iv viii i C L1P3_orf2#LIN 3044 TTAATTAGATCCCATTTGTCAATTTTGGCTTTTGTT--GCCATTGCTTTT 2997 chr2qtel1M 489533 AGTTTTTCTTTGGTCATAAATTCCTTCCTCTTCCACAGGT-CTGAGAGAT 489581 i v --- i i v i v i v v vi v - iv i C L1P3_orf2#LIN 2996 GGTGT---TTTAGTCATGAAGTCTTTGCCCATGCCTATGTCCTGAATGGT 2950 chr2qtel1M 489582 AAACTATCCTATG--TTCCTCTAATTTATTTATAATCTCATTCTTTATGC 489629 --- vv v -- i ivv v ii i i vvii i i C L1P3_orf2#LIN 2949 A---TTGCCTAGGTTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTTACGT 2903 chr2qtel1M 489630 CTAAACCATGAATCCCTTTTAATCTTATCTTGGTATATGGTATGAATTGT 489679 i ii v v v i i vi v i v v i i ivviv C L1P3_orf2#LIN 2902 TTAAGTCTTTAATCCATCTTGAGTTAATTTTTGTATAAGGTGTAAGGAAG 2853 chr2qtel1M 489680 AGGTCCATGCCTAG-TTTCTGCCATATTAATTTCCAATTTTCCCAGCAGT 489728 i vviii - - viv vv i i vi C L1P3_orf2#LIN 2852 GGGTCCAGTTTCAGTTTTCTG-CATATGGCTAGCCAGTTTTCCCAACACC 2804 chr2qtel1M 489729 TTCTGTCAAGTAGTGAATTCTTATCCCAAAAGTTGGGGTCTTTG---GGT 489775 v i i i i v i vi vviv --- i --- C L1P3_orf2#LIN 2803 ATTTATTAAATAGGGAATCCTTTCCCCATTGCTT---GTTTTTGTCAGGT 2757 chr2qtel1M 489776 TTGTCAGATACTAGATTGCTATAG 489799 i v ii v i i C L1P3_orf2#LIN 2756 TTGTCAAAGATCAGATGGTTGTAG 2733 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 45.73 CpG sites = 95, Kimura (unadjusted) = 46.42 Transitions / transversions = 1.09 (95/87) Gap_init rate = 0.05 (28 / 553), avg. gap size = 1.43 (40 / 28) 394 32.55 2.91 2.91 chr2qtel1M 489246 489726 (510274) C L1M5_orf2#LINE/L1 (8) 3286 2806 m_b95s551i13 3526 chr2qtel1M 489246 AGCATTTTTTCATATGGCTAGAAATAGTTTCAATTTCTTCATCTGAGAAT 489295 i i vi vviiivi v? v v i v v C L1M5_orf2#LIN 3286 AGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTTTTGTGAAG 3237 chr2qtel1M 489296 TGTCTATTCATATCCTTTGACCATTTATCAATTGGA--GAATGGCATGAT 489343 i vi i v v ?v i-- vv v v -- C L1M5_orf2#LIN 3236 TGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTTGTCTT--T 3189 chr2qtel1M 489344 TTCTTAT-AAATTAGAGTCAATTCTCTATATATTTTGGAAATGAAGCCTT 489392 ? -i ? iv v- i i i v i iv C L1M5_orf2#LIN 3188 TTNTTATTGANTTGTAGG-AGTTCTTTATATATTCTGGATACGAGTCCTT 3140 chr2qtel1M 489393 TATCAGA-ACATTTGACTGTAAAAATGTTTTCCCAATTTATTGCTTCCCT 489441 i - i v -?i i v v i ? i i v v C L1M5_orf2#LIN 3139 TGTCAGATATATGT-NTTGCAAATATTTTCTCCCANTCTGTGGCTTGCCT 3091 chr2qtel1M 489442 TCTAATCTTGTCTGCATTAGTTTTGTTTGTACAAAAACTTTTCAATTTGA 489491 i v i v ivi iv ivi vvv? vi i ii v v C L1M5_orf2#LIN 3090 TTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTTTAATTTTGA 3041 chr2qtel1M 489492 TATAATCAA-------AATTTTCTATTCTGTGATCAGTAATGATCTCTAG 489534 i? i v ------- i v i i i --- ?i v i i iv C L1M5_orf2#LIN 3040 TGNAGTCCAATTTATCAATTTTTTCTTTTATGGT---TNGTGCTTTTTGT 2994 chr2qtel1M 489535 TTTTTCTTTGGTCATAAATTCCTTCCTCTTCCACAGGTCTGAGAGATAAA 489584 v ii v i--- v iii v v?i - vvii -- C L1M5_orf2#LIN 2993 GTCCTGTTTA---AGAAATCTTTGCCTANCCCA-AGGTCACGAAGAT--A 2950 chr2qtel1M 489585 CTATCCTATG--TTCCTCTAATTTATTTATAATCTCATTCTTTATGCCTA 489632 i v -- i ivvvv i i i ?ii iiii C L1M5_orf2#LIN 2949 TTCTCCTATGTTTTCTTCTAGAAGTTTTATAGTTTTANCTTTTACATTTA 2900 chr2qtel1M 489633 AA-CCATGAATCCCTTTTAATCTTATCTTGGTATATGGTATGAATTGTAG 489681 ii- i - v i ?i vi v i v i i iv ivi C L1M5_orf2#LIN 2899 GGTCTATG-ATCCATCTNGAATTAATTTTTGTGTATGGTGTGAGGTAGGG 2851 chr2qtel1M 489682 GTCCATGCCTAGTTTCTGCCATATTAATTTCCAATTTTCCCAGCA 489726 v v?iii v i v vi v v i C L1M5_orf2#LIN 2850 GTCGAGNTTCATTTTTTTCCATATGGATATCCAATTGTTCCAGCA 2806 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 44.49 CpG sites = 86, Kimura (unadjusted) = 45.73 Transitions / transversions = 1.30 (86/66) Gap_init rate = 0.04 (20 / 480), avg. gap size = 1.40 (28 / 20) 13 14.87 3.64 9.62 chr2qtel1M 491411 491465 (508535) (CCTT)n#Simple_repeat 1 52 (0) m_b95s252i6 3528 chr2qtel1M 491411 CCTTTCTTCCTCCCCTTCC-TCATTCCCCTCC-CCCTCCCTCTCCCTCTC 491458 i -i - v - i -i i - - - (CCTT)n#Simpl 1 CCTTCCTTCCT-TCCTTCCTTCCTT-CCTTCCTTCCTTCCT-T-CCT-TC 45 chr2qtel1M 491459 CTTCCTT 491465 (CCTT)n#Simpl 46 CTTCCTT 52 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.13 (7 / 54), avg. gap size = 1.00 (7 / 7) 20 16.87 0.00 0.00 chr2qtel1M 491419 491459 (508541) (CCTCCC)n#Simple_repeat 1 41 (0) m_b95s252i7 3529 chr2qtel1M 491419 CCTCCCCTTCCTCATTCCCCTCCCCCTCCCTCTCCCTCTCC 491459 i i v i i i (CCTCCC)n#Sim 1 CCTCCCCCTCCCCCTCCCCCTCCCCCTCCCCCTCCCCCTCC 41 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 13 14.87 3.64 9.62 chr2qtel1M 491411 491465 (508535) (CCTT)n#Simple_repeat 1 52 (0) m_b95s252i6 3528 chr2qtel1M 491411 CCTTTCTTCCTCCCCTTCC-TCATTCCCCTCC-CCCTCCCTCTCCCTCTC 491458 i -i - v - i -i i - - - (CCTT)n#Simpl 1 CCTTCCTTCCT-TCCTTCCTTCCTT-CCTTCCTTCCTTCCT-T-CCT-TC 45 chr2qtel1M 491459 CTTCCTT 491465 (CCTT)n#Simpl 46 CTTCCTT 52 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.13 (7 / 54), avg. gap size = 1.00 (7 / 7) 47 10.52 0.00 0.00 chr2qtel1M 491478 491549 (508451) (TC)n#Simple_repeat 1 72 (0) c_b95s251i0 3530 chr2qtel1M 491478 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTGTGTGTGTC 491527 v v v v v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr2qtel1M 491528 TGTCTCTGTCTCTCTCTCTCTC 491549 v v (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTC 72 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.00 (0 / 71), avg. gap size = 0.0 (0 / 0) 17 0.00 0.00 0.00 chr2qtel1M 492531 492549 (507451) (A)n#Simple_repeat 1 19 (0) m_b95s252i8 3531 chr2qtel1M 492531 AAAAAAAAAAAAAAAAAAA 492549 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAA 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 chr2qtel1M 493033 493049 (506951) (A)n#Simple_repeat 1 17 (0) m_b95s252i9 3532 chr2qtel1M 493033 AAAAAAAAAAAAAAAAA 493049 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 390 28.05 0.00 0.00 chr2qtel1M 493630 493711 (506289) Charlie1b#DNA/hAT-Charlie 1 82 (441) m_b95s502i0 3533 chr2qtel1M 493630 CAATGGTCCTCAAAGTGTAGTCCAAAGAATTGTTGGGGTCTCTGAAACCC 493679 ii i i iii viiv v i i i Charlie1b#DNA 1 CAGCGGTTCTCAAAGTGTGGTCCGGGGACCCCTGGGGGTCCCCGAGACCC 50 chr2qtel1M 493680 TTTCAGAGGGTCTACAAATTCAAAATCATTTT 493711 i ii i iv ii Charlie1b#DNA 51 TTTCAGGGGGTCCGCGAGGTCAAAACTATTTT 82 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 28.11 CpG sites = 19, Kimura (unadjusted) = 38.46 Transitions / transversions = 4.75 (19/4) Gap_init rate = 0.00 (0 / 81), avg. gap size = 0.0 (0 / 0) 435 20.97 2.34 3.15 chr2qtel1M 493705 493832 (506168) Charlie1a#DNA/hAT-Charlie 1329 1455 (0) m_b95s502i1 3534 chr2qtel1M 493705 TCATTTTTTATTTCTAATATAGTAAATAGCTATAAATATAACGCATGTGA 493754 v v i v v i v ii i Charlie1a#DNA 1329 TCAGTTTTAATTTCTAATATGGTAAATATCGATAGATATAACCCACATAA 1378 chr2qtel1M 493755 ACAAAAACTCTTTGAACAGATCCTTGATAGCTTTTTAACAATATGAA--C 493802 i ---i i ii i- v i i i --v Charlie1a#DNA 1379 ACAAAAGCTCTTTG---GGGTCCTCAATAA-TTTTTAAGAGTGTAAAGGG 1424 chr2qtel1M 493803 ATACTAAGAAC-AAAAGTTTGAGAACCACTG 493832 i v i v - i Charlie1a#DNA 1425 GTCCTGAGACCAAAAAGTTTGAGAACCGCTG 1455 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 24.11 CpG sites = 17, Kimura (unadjusted) = 25.21 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.05 (6 / 127), avg. gap size = 1.17 (7 / 6) 18 23.47 0.00 7.25 chr2qtel1M 495682 495755 (504245) (GAGGGG)n#Simple_repeat 1 69 (0) m_b95s252i10 3535 chr2qtel1M 495682 GAGGCGGGAGCAGAGAGGGGGAAAGGGGCGGTGGAGGGAGTGGGGCAGCC 495731 - -i i - i v v i v v -- (GAGGGG)n#Sim 1 GAGG-GGGAG-GGGGAGGGGG-AGGGGGAGGGGGAGGGGGAGGGGGAG-- 45 chr2qtel1M 495732 TGGGAGGAGGTGGAGGTGGGGGAG 495755 v i v i v (GAGGGG)n#Sim 46 GGGGAGGGGGAGGGGGAGGGGGAG 69 Matrix = Unknown Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.07 (5 / 73), avg. gap size = 1.00 (5 / 5) 232 32.69 0.00 0.00 chr2qtel1M 497358 497461 (502539) L1ME3A_3end#LINE/L1 430 533 (387) m_b95s551i15 3536 chr2qtel1M 497358 ACATGTGGAAAAATGTTTGTGGCAGCTCTTTCCATAGAGACATGAAACTG 497407 iv i ii i v v i i ivii v?? L1ME3A_3end#L 430 ACATGTACAAGAATGTTCATAGCAGCACTATTCGTAATAGCCNNAAACTG 479 chr2qtel1M 497408 GCAAATAAGTGGGTGCCCATCAGTAGGGGAATGGCTGAATAAGTTTTGAC 497457 v v? vviiii i ii vi v i i v ii L1ME3A_3end#L 480 GAAACNACCCAAATGTCCATCAACAGTAGAATGGATAAATAAATTGTGGT 529 chr2qtel1M 497458 ATAT 497461 L1ME3A_3end#L 530 ATAT 533 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 45.24 CpG sites = 22, Kimura (unadjusted) = 47.21 Transitions / transversions = 1.83 (22/12) Gap_init rate = 0.00 (0 / 103), avg. gap size = 0.0 (0 / 0) 786 29.39 7.46 1.91 chr2qtel1M 498305 498800 (501200) C L1ME4c_3end#LINE/L1 (294) 536 14 m_b95s551i16 3537 chr2qtel1M 498305 ATGTATCACAACTTGTTCAGCCATTCCCCAGTTGGTGAGCTTCCATTCCT 498354 i i i ii i i vi v ii v ii vviiv C L1ME4c_3end#L 536 ATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAGGTTG 487 chr2qtel1M 498355 TTTCCACTTCTGTGTTACCACAGAAAGAGCTGCTGCAAACATCTTTGCAC 498404 v i vi i ii i i v iv viii i ii C L1ME4c_3end#L 486 TTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTCGTGC 437 chr2qtel1M 498405 ATGTGGGTCCTTTTCC--CTTTTTGATGATGTCTTTGGGATAAAGACCCT 498452 i i -- i -- vi v v i i vv v C L1ME4c_3end#L 436 ATATAG--CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAATTCCCA 389 chr2qtel1M 498453 GTAGAGACACTGCTGGATCCAAGGGTATGCACAGTTTGATAGCCCTTTGA 498502 v v iv i i i v v v v i i viv C L1ME4c_3end#L 388 GAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTCTTGAT 339 chr2qtel1M 498503 GCATAGTTCCAAATTACTCTCCACAATGGTTGGATCATTTCAGAATTCCC 498552 i i v v i i v v v i v i v ? v v C L1ME4c_3end#L 338 ACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACANTGCCA 289 chr2qtel1M 498553 CCTACAATGTATTAGTGTCCCACTTTTCCCACATCCCCTCTAATATTTAT 498602 vi v ? v v iv i ? i v i ii viv C L1ME4c_3end#L 288 CCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGCATTGGG 239 chr2qtel1M 498603 CGTTAT--ATTTTCCTGTGATCTTAGCCAGTCTGAGAGGTGTGAAGTGGT 498650 ii -- -- vvi i v i i i i v i i i C L1ME4c_3end#L 238 TATTATCAATTTT--TTAAATTTTTGCTAATTTAATAGGCGTAAAATGGT 191 chr2qtel1M 498651 ACCTCA----------------GAGTTCTGTGATT--TAG--------AG 498674 i ----------------v v v -- -------- i C L1ME4c_3end#L 190 ATCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACTAGCGAGGTTGAA 141 chr2qtel1M 498675 CATTTTTC-ATATAAC-----ACTAAATGGCTTTAATTTGCTCATCTGAA 498718 - i ivi----- ?v v----- v v ? vi C L1ME4c_3end#L 140 CATTTTTCCATGTGTTTGTTTACTANTTGT-----ATTTCCTCTTNTGTG 96 chr2qtel1M 498719 AATTGTCTGTTCCTATCCTTTGACCATGTATCAAGTAGGG-AATGATTTG 498767 v i v v v v i -vv ? v C L1ME4c_3end#L 95 AATTGTCTGTTCATGTCCTTTGCCCATTTATCTATTGGGGTCTTGATNTT 46 chr2qtel1M 498768 TATTTTTATAAATTTGAAACAGTTCTTTATATA 498800 - i v vv i C L1ME4c_3end#L 45 T-TTCTTATCAATTTGAATGAGCTCTTTATATA 14 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.95 CpG sites = 76, Kimura (unadjusted) = 38.65 Transitions / transversions = 1.13 (76/67) Gap_init rate = 0.04 (18 / 495), avg. gap size = 2.61 (47 / 18) 296 25.37 8.37 4.21 chr2qtel1M 498665 498915 (501085) C L1M3_orf2#LINE/L1 (0) 3288 3028 m_b95s551i18 3537 chr2qtel1M 498665 TGATTTAGAGCAT-TTTTCATATAACACTAAATGGCTTTAATTTGC---T 498710 v v - v vv --- i--- i--- C L1M3_orf2#LIN 3288 TGATGTTGAGCATCTTTTCATATACCTGT---TGGCC---ATTTGTATGT 3245 chr2qtel1M 498711 CATCT---GAAAATTGTCTGTTCCTATCCTTTGACCATGTATCAAGTAGG 498757 v --- i v i vvi v v v ? - v C L1M3_orf2#LIN 3244 CTTCTTTGGAGAAATGTCTATTCAGGTCCTTTGCCCATTTTTNAA-TCGG 3196 chr2qtel1M 498758 GAATGATTTGTATTTT---TATAAATTTGAAACAGTTCTTTATATATCTT 498804 -- v v --- vi v v ?v i i C L1M3_orf2#LIN 3195 G--TTATTTGTTTTTTTGCTATTGAGTTGTANGAGTTCCTTATATATTTT 3148 chr2qtel1M 498805 AGAAATGAGACCTTTAACAGATATACTGGCCATAAAGATTTTTTCCCAGC 498854 i v v iv i v iv viiii v i -- C L1M3_orf2#LIN 3147 GGATATTAACCCCTTATCAGATATATGGTTTGCAAATATTTTCTCCCA-- 3100 chr2qtel1M 498855 TTTC-TA------CTTCCCCCTTTATC--TCATTTCTGGT-TTGTGCAAA 498894 i - ------ ii v i i i-- ii ivv -i i C L1M3_orf2#LIN 3099 TTCCGTAGGTTGCCTTTTCACTCTGTTGATTGTTTCCTTTGCTGTGCAGA 3050 chr2qtel1M 498895 AAC-TTTTAATTTAATGTAATC 498915 i - i i i C L1M3_orf2#LIN 3049 AGCTTTTTAGTTTGATGTAGTC 3028 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 31.76 CpG sites = 32, Kimura (unadjusted) = 31.76 Transitions / transversions = 1.10 (32/29) Gap_init rate = 0.08 (20 / 250), avg. gap size = 1.60 (32 / 20) 332 25.14 5.32 4.76 chr2qtel1M 498665 498852 (501148) C L1M4_orf2#LINE/L1 (0) 3294 3106 m_b95s551i17 3537 chr2qtel1M 498665 TGATTTAGAGCAT-TTTTCATATAACACTAAATGGCTTTAATTTGCTCAT 498713 v v - i i--- v v i--- ivi C L1M4_orf2#LIN 3294 TGATGTTGAGCATCTTTTCATGTG---CTTATTGGCC---ATTTGTATAT 3251 chr2qtel1M 498714 CT------GAAAATTGTCTGTTCCTATCCTTTGACCATGTATCAAGTAGG 498757 ------ i v i vv v v v ? v i C L1M4_orf2#LIN 3250 CTTCTTTGGAGAAATGTCTATTCAAATCCTTTGCCCATTTTTNAATTGGG 3201 chr2qtel1M 498758 GAATGATTTGTATTTTTATAA---ATTTGAAACAGTTCTTTATATATCTT 498804 --- v v vi--- v v v ii C L1M4_orf2#LIN 3200 ---TTATTTGTCTTTTTATTGTTGAGTTGTAAGAGTTCTTTATATATTCT 3154 chr2qtel1M 498805 AGAAATGAGACCTTTAACAGATATACTGGCCATAAAGATTTTTTCCCA 498852 i v i? v i v iviviiii v i C L1M4_orf2#LIN 3153 GGATACNAGTCCCTTATCAGATATATGATTTGCAAATATTTTCTCCCA 3106 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 31.24 CpG sites = 21, Kimura (unadjusted) = 31.24 Transitions / transversions = 0.88 (21/24) Gap_init rate = 0.06 (12 / 187), avg. gap size = 1.58 (19 / 12) 296 33.57 6.22 3.64 chr2qtel1M 499493 500135 (499865) C L1PREC2_orf2#LINE/L1 (641) 2653 1995 m_b95s551i19 3537 chr2qtel1M 499493 TGCTTACTGGTGCTTTGTAACATAGTTCTAGGGTAGGTACTGCTAAGTCA 499542 v vv ii ii iv i vii vi iv v i v C L1PREC2_orf2# 2653 TGGTTACTGTAGCCCTGTAGTATAGTTTGAAGTCGGGTAGCGTGATGCCT 2604 chr2qtel1M 499543 CCATCCTT--TCTGTTTTGTTGTTGTAAATCCCTTGA-TATTCTTGACCT 499589 v i -- - i -- ivi v v i- vv vi C L1PREC2_orf2# 2603 CCAGCTTTGTTCT-TTTTGCT--TAGGATTGCCTTGGCTATTCGGGCTCT 2557 chr2qtel1M 499590 TTTGTTCTTCTAGATAGCTTTTTGT-TGCTTTTTTCTAGTTCTATAAA-- 499636 v vv i v iiv viv- iv i i -- C L1PREC2_orf2# 2556 TTTTTGGTTCCATATGAATTTTAAAATAGTTTTTTCTAGTTCTGTGAAGA 2507 chr2qtel1M 499637 ATGTT-TTTGCAATTTGATTGTTATGGCACTGAAGAAATAGACCAATTTA 499685 i- v i i v vv i i vvvi i iiiv i C L1PREC2_orf2# 2506 ATGTCATTGGTAGTTTGATAGGAATAGCATTGAATCTGTAAATTGCTTTG 2457 chr2qtel1M 499686 GGAAGAATTGTGATTT-----ACATCAGCTCAACTTGGCCAGGAACAATT 499730 v v v iv ----- i iiii vv i iv v i vvv C L1PREC2_orf2# 2456 GGCAGTATGGCCATTTTAACGATATTGATTCTTCCTATCCATGAGCATGG 2407 chr2qtel1M 499731 AATATTTTT------GTTT-----AGATCTGATTTTCTTTGTGTGAGAAG 499769 i ------ ----- vv - ---- v C L1PREC2_orf2# 2406 AATGTTTTTCCATTTGTTTGTGTCATCTCTGATTT-CTTTG----AGCAG 2362 chr2qtel1M 499770 TGTTTTATAATTGTGTTCATATTGTA-----TTTGGGTTTGTCTTAGCAG 499814 i v -----i -----i vviii vi vivi C L1PREC2_orf2# 2361 TGTTTTGTAATTCT-----CATTGTAGAGATCTTTCACCTCCCTGGTTAG 2317 chr2qtel1M 499815 CTTGCTCCCCAGTTATTTTATTTTGTCTATAGATATTTTCAATGGAATTT 499864 vvv i i v i v i i i vv v v i v C L1PREC2_orf2# 2316 CTGTATTCCTAGGTATTTTATTCTTTTTGTGGCAATTGTGAATGGGATTG 2267 chr2qtel1M 499865 C--TCTT--TGTATCTCTTG-CTTATGGGCT-TTATCAATAACATAGAGA 499908 -- i -- v iv i - --- - i iii i--- v i C L1PREC2_orf2# 2266 CGTTCCTGATTTGGCTCTCGGCTT---GGCTGTTGTTGGTG---TATAGG 2223 chr2qtel1M 499909 AATGATGATAATTTGTGTAGCTTCATTTTATATACTGCAATTTTGCTAAA 499958 v ii i v vv v i v v i i C L1PREC2_orf2# 2222 AATGCTAGTGATTTTTGTACATTGATTTTGTATCCTGAAACTTTGCTGAA 2173 chr2qtel1M 499959 ACTGTGATTGTTTTCAGT----AGATATTTTGA--TGATTTTCTAGGATT 500002 ii ----- v i----i vv i--i vvi v i i C L1PREC2_orf2# 2172 GTTGT-----TTATCAGCTNAAGGAGCTTTTGGGCCGAGACTATGGGGTT 2128 chr2qtel1M 500003 CTCCAAGTATCTCATCATATCATCTCCAAAGAGTGATAGTTTTATTTTCT 500052 i i ii vvv i i v v v v i i C L1PREC2_orf2# 2127 TTCTAGATATAGAATCATGTCGTCTGCAAACAGGGATAGTTTGACTTCCT 2078 chr2qtel1M 500053 CGTTGCCTATTCTAATTCCTTTTGTTTCTTTTTCTTTTCTTATCCATGAA 500102 vi v ivi v i i i vi v ivv vvi C L1PREC2_orf2# 2077 CTCTTCCTATTTGGATGCCCTTTATTTCTTTCTCTTGCCTGATTGCTCTG 2028 chr2qtel1M 500103 GCTAACATTTCTAGAATAATGTTGAATAATAGT 500135 i iv i i iv iv iv C L1PREC2_orf2# 2027 GCCAGGACTTCCAATACTATGTTGAATAGGAGT 1995 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 44.02 CpG sites = 109, Kimura (unadjusted) = 45.52 Transitions / transversions = 1.10 (109/99) Gap_init rate = 0.06 (39 / 642), avg. gap size = 1.64 (64 / 39) 477 32.97 3.94 1.05 chr2qtel1M 499578 500135 (499865) C L1M1_orf2#LINE/L1 (726) 2568 1995 m_b95s551i20 3537 chr2qtel1M 499578 TATTCTTGACCTTTTGTTCTTCTAGATAGCTTTTTG--TTGCTTTTTTCT 499625 v ii vv i v iv v -- - C L1M1_orf2#LIN 2568 TATTCTGGGTCTTTTGTGGTTCCATATAAATTTTAGGATTG-TTTTTTCT 2520 chr2qtel1M 499626 AGTTCTATAAA--ATGTT-TTTGCAATTTGATTGTTATGGCACTGAAGAA 499672 v i i -- i- v i v v vv v i vvv C L1M1_orf2#LIN 2519 ATTTCTGTGAAGAATGTCATTGGTATTTTGATAGGGATTGCATTGAATCT 2470 chr2qtel1M 499673 ATAGACCAATTTAGGAAGAATTGTGATTT-----ACATCAGCTCAACTTG 499717 i iiiv i v v v vv ----- i iiii vv ivi C L1M1_orf2#LIN 2469 GTAGATTGCTTTGGGTAGTATGGACATTTTAACAATATTGATTCTTCCAA 2420 chr2qtel1M 499718 GCCAGGAACAATTAATATTTTTG----TTTAGATCTGATTTTC--TTTGT 499761 v v vvv i v---- v i v vv i -- v C L1M1_orf2#LIN 2419 TCCATGAACATGGAATATCTTTCCATTTTTTGGTGTCCTCTTCAATTTCT 2370 chr2qtel1M 499762 GTGAGAAGTGTTTTATAATTGTGTTCATATTGTA-----TTTGGGTTTGT 499806 v v vv i --- -- -----i vvii v C L1M1_orf2#LIN 2369 TTCATCAGTGTTTTATAGTT---TTCAT--TGTAGAGATCTTTCACTTCT 2325 chr2qtel1M 499807 CTTAGCAGCTTGCTCCCCAGTTATTTTATTTTGTCTATAGATATTTTCAA 499856 i vivi iv iv i i v v i i i i v v v C L1M1_orf2#LIN 2324 TTGGTTAAGTTAATTCCTAGGTATTTAATTTTATTTGTGGCTATTGTAAA 2275 chr2qtel1M 499857 TGGAATTTCTCTTTGTATCTCTTGCTTATGGGCTTTATCAATAACATAGA 499906 i v i vv i vi i vivvv i iiiv ii v C L1M1_orf2#LIN 2274 TGGGATTACTTTTTTGATTTCTTTTTCAGATTGTTCACTGTTGGCATATA 2225 chr2qtel1M 499907 GAAATGATGATAATTTGTGTAGCTTCATTTTATATACTGCAATTTTGCTA 499956 v iv i v vv v i v i i i C L1M1_orf2#LIN 2224 GAAATGCTACTGATTTTTGTATGTTGATTTTGTATCCTGCAACTTTACTG 2175 chr2qtel1M 499957 AAACTGTG-ATTGTTTTCAGTAGATATTTTGATGATTTTCTAGGATTCTC 500005 vi v- iiv ii i v v ? vv v i i v i C L1M1_orf2#LIN 2174 AATTTGTTTATCAGTTCTAATAGTTTTTTNGTGGAGTCTTTAGGTTTTTC 2125 chr2qtel1M 500006 CAAGTATCTCATCATATCATCTCCAAAGAGTGATAGTTTTATTTTCTCGT 500055 i vvv v v iv i v i ii v C L1M1_orf2#LIN 2124 CAAATATAAGATCATATCATCTGCAAACAAGGATAATTTGACTTCTTCCT 2075 chr2qtel1M 500056 TGCCTATTCTAATTCCTTTTGTTTCTTTTTCTTTTCTTATCCATGAAGCT 500105 v v ivi v i i i v v ivv vv C L1M1_orf2#LIN 2074 TTCCAATTTGGATGCCCTTTATTTCTTTCTCTTGTCTGATTGCTCTAGCT 2025 chr2qtel1M 500106 AACATTTCTAGAATAATGTTGAATAATAGT 500135 iv i i v iv i C L1M1_orf2#LIN 2024 AGGACTTCCAGTACTATGTTGAATAACAGT 1995 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 43.92 CpG sites = 83, Kimura (unadjusted) = 43.92 Transitions / transversions = 0.84 (83/99) Gap_init rate = 0.03 (14 / 557), avg. gap size = 2.00 (28 / 14) 515 32.58 0.64 0.32 chr2qtel1M 499822 500135 (499865) C L1M2_orf2#LINE/L1 (985) 2306 1992 m_b95s551i21 3537 chr2qtel1M 499822 CCCAGTTATTTTATTTTGTCTATAGATATTTTCAATGGAATTTCTCTTTG 499871 i v v i i v v v i v i i v C L1M2_orf2#LIN 2306 CCTAGGTATTTTATTTTTTTTGTAGCTATTGTAAATGGGATTGCTTTCTT 2257 chr2qtel1M 499872 TATCTCTTGCTTATGGGCTTTATCAATAACATAGAGAAATGATGATAATT 499921 v i vi i viviv ii iiv ii i v v iv i C L1M2_orf2#LIN 2256 GATTTCTTTTTCAGATAGTTCGTTGTTGGCGTATAGAAATGCTACTGATT 2207 chr2qtel1M 499922 TGTGTAGCTTCATTTTATATACTGCAATTTTGCTAAAACTGTG-ATTGTT 499970 v vv v i v i i i vii v- iiv C L1M2_orf2#LIN 2206 TTTGTATGTTGATTTTGTATCCTGCAACTTTACTGAATTCGTTTATCAGT 2157 chr2qtel1M 499971 TTCAGTAGATATTTTGATG-ATTTTCTAGGATTCTCCAAGTATCTCATCA 500019 ii i? v - i - v i i ? i i ?i vvv C L1M2_orf2#LIN 2156 TCTAANAGTT-TTTTGGTGGAGTCTTTAGGNTTTTCTANATATAAGATCA 2108 chr2qtel1M 500020 TATCATCTCCAAAGAGTGATAGTTTTATTTTCTCGTTGCCTATTCTAATT 500069 i v v v i i v i i v v v ivi v C L1M2_orf2#LIN 2107 TGTCATCTGCAAACAGGGACAATTTGACTTCCTCCTTTCCAATTTGGATG 2058 chr2qtel1M 500070 CCTTTTGTTTCTTTTTCTTTTCTTATCCATGAAGCTAACATTTCTAGAAT 500119 i i vi v ivv vvi iv i i v i C L1M2_orf2#LIN 2057 CCTTTTATTTCTTTCTCTTGCCTAATTGCTCTGGCTAGGACTTCCAGTAC 2008 chr2qtel1M 500120 AATGTTGAATAATAGT 500135 v iv C L1M2_orf2#LIN 2007 TATGTTGAATAGAAGT 1992 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 42.46 CpG sites = 54, Kimura (unadjusted) = 44.25 Transitions / transversions = 1.12 (54/48) Gap_init rate = 0.01 (3 / 313), avg. gap size = 1.00 (3 / 3) 1119 30.16 4.76 0.97 chr2qtel1M 500144 500836 (499164) C L1MD_orf2#LINE/L1 (1180) 2114 1396 m_b95s551i22 3538 chr2qtel1M 500144 ATCATATCACCTCCAAAGAGTGATAGTTTTATTTTCTCGTTGCCTATTCT 500193 i i v v v i ii v v v - C L1MD_orf2#LIN 2114 ATCATGTCATCTGCAAATAGGGACAGTTTTATTTCTTCCTTTCCAAT-CT 2066 chr2qtel1M 500194 G-ATAACTTTTGTTTCTTTTTCTTTTCTTATC-CATAAAGCTAACATTTC 500241 - iv i i vi i- ivi- iv i C L1MD_orf2#LIN 2065 GTATGCCTTTTATTTCCTTTTCTTGCCTTATTGCACTG-GCTAGAACTTC 2017 chr2qtel1M 500242 TAGAACAATGTTGAATAATAGTGGTGATAAT-------TTAACC-----C 500279 i v v v v ii-------i vi ----- C L1MD_orf2#LIN 2016 CAGTACTATGTTGAATAAGAGTGGTGAGAGCGGACATCCTTGCCTTGTTC 1967 chr2qtel1M 500280 CTGATTTTACTGGGAATGCATCCAGCTTCTGTCCATGTCATATAATGCTT 500329 i i vv v i ii i vv vvvi i i v C L1MD_orf2#LIN 1966 CCGATCTTAGGGGGAAAGCATTCAGTCTTTCACCATTAAGTATGATGTTA 1917 chr2qtel1M 500330 TCTATAGGTTTTAACAAAGTATTGCTTATTGTTTTAAGGAAAGTTCCCTT 500379 v i vvvv ii ii vi iivv i iv i i C L1MD_orf2#LIN 1916 GCTGTAGGTTTTTTGTAGATGCTCTTTATCAAGTTGAGGAAGTTCCCCTC 1867 chr2qtel1M 500380 TTTACCTATGCCCTCT-AGTGTTTACTTATAA-GAATGGGTACTGTATTT 500427 v v - iii? - v -- v - ii v C L1MD_orf2#LIN 1866 TATTCCTA-GTTTNCTGAGAGTTT--TTATCATGAATGGGTGTTGAATTT 1820 chr2qtel1M 500428 TGTCAAAAGCCTTTTCTGCTTGAATTGGGATTGTGATGTGATTTTGGTTG 500477 v i v v iv vi v vv v C L1MD_orf2#LIN 1819 TGTCAAATGCTTTTTCTGCATCAATTGATATGATCATGTGATTTTTCTTC 1770 chr2qtel1M 500478 GTTTTGT-TATTGATGTGGTCAACTGTAGTAAGT--CTTCCTGATACTGA 500524 - v i- i i i vi i ii v i v --i i vi i C L1MD_orf2#LIN 1769 -TTTAGCCTGTTAATATGGTGGATTACATTGATTGATTTTCGAATATTGA 1721 chr2qtel1M 500525 ACCAGCCATGCATTACTGTTATAAATCCCA-TTGGTTATAGGGTACTATC 500573 v ?v vv i - i i v iv i C L1MD_orf2#LIN 1720 ACCAGCCTTGCATNCCTGGAATAAACCCCACTTGGTCATGGTGTATAATT 1671 chr2qtel1M 500574 TTGCTCGTAAGTTGCTGTAATCTCTTTGCTAATATGTCATTTAGA----- 500618 i vi ii vi v v ?v v ii v i----- C L1MD_orf2#LIN 1670 CTTTTTATATATTGCTGAATTCNATTTGCTAATATTTTGTTGAGGATTTT 1621 chr2qtel1M 500619 -----CAGTATTCAACAGGGATATTGGTCTGTAATTTTTTTTCTCTGTTT 500663 ----- vi i vv i i i i vi C L1MD_orf2#LIN 1620 TGCGTCTATGTTCATGAGGGATATTGGTCTGTAGTTTTCTTTTTTTGTAC 1571 chr2qtel1M 500664 TAGCCCTTCGTGTTTTAGGTAGCAGTGCCATAACTGGG-TCATACAGGAA 500712 iv ii viv v v v v iv - v- v ivi C L1MD_orf2#LIN 1570 TGTCTTTGTCTGGTTTTGGTATCAGGGTAATA-CTGGCCTCATAAAATGA 1522 chr2qtel1M 500713 ATGTGGCAGTACTCCTTCGTGTATT-TTTTCCAAATG-GATGACGTACTA 500760 i vv v ii i v v vi - iii v - vii vv C L1MD_orf2#LIN 1521 GTTGGGAAGTGTTCCCTCCTCTTCTATTTTCTGGAAGAGATTGTGTAGAA 1472 chr2qtel1M 500761 TTGGAAGTAATTGTTCTTTGAACATTTGGGAGAATTCACTTGTGGATCCA 500810 viv v i i v v iv i v C L1MD_orf2#LIN 1471 TTGGTGTTAATTCTTCTTTAAACGTTTGGTAGAATTCTCCAGTGAAACCA 1422 chr2qtel1M 500811 ATTGTCCCTGGAGATTTTTTCTTAGG 500836 vi vv i i i C L1MD_orf2#LIN 1421 TCTGGGCCTGGAGATTTCTTTTTGGG 1396 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.72 CpG sites = 107, Kimura (unadjusted) = 39.45 Transitions / transversions = 1.07 (107/100) Gap_init rate = 0.03 (21 / 692), avg. gap size = 1.90 (40 / 21) 184 34.10 2.13 4.35 chr2qtel1M 501200 501340 (498660) MIR#SINE/MIR 79 216 (46) m_b95s601i3 3539 chr2qtel1M 501200 AGCTGCTGGGATTTGGGTCAAGTCTCTCAATCCCTTTGAGCT--GGTGGC 501247 - v ii v v iv i i i i v i--i vv MIR#SINE/MIR 79 AGCTG-TGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTC 127 chr2qtel1M 501248 CTGAGGTGTACAAATAGTGAGAATGAAGGTTCTTTCTGTTGTCCCAGGTT 501297 v vv - i v v i vi v i v i---- vi v MIR#SINE/MIR 128 CTCATCTGTA-AAATGGGGATAATAATAGTACCTACC----TCATAGGGT 172 chr2qtel1M 501298 GACTGTGAGAATTCAATGTCTTTGTGCATG-AAGGTCATTAGAA 501340 vii i v vv vi i - i ivv MIR#SINE/MIR 173 TGTTGTGAGGATTAAATGAGTTAATACATGTAAAGCGCTTAGAA 216 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.69 CpG sites = 22, Kimura (unadjusted) = 46.01 Transitions / transversions = 0.92 (22/24) Gap_init rate = 0.06 (8 / 140), avg. gap size = 1.12 (9 / 8) 189 33.61 4.31 2.54 chr2qtel1M 501200 501315 (498685) MIRc#SINE/MIR 83 200 (68) m_b95s601i2 3539 chr2qtel1M 501200 AGCTGCTGGGATTTGGGTCAAGTCTCTCAATCCCTTTGAGC--TGGTGGC 501247 - v ii v v v i i i i --ii vv MIRc#SINE/MIR 83 AGCTG-TGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTC 131 chr2qtel1M 501248 CTGAGGTGTACAAATAGTGAGAATGAAG---GTTCTTTCTGTTGTCCCAG 501294 v vv - i v v i vi--- ii vi iii- v MIRc#SINE/MIR 132 CTCATCTGTA-AAATGGGGATAATAATACCTGCCCTGCCTACC-TCACAG 179 chr2qtel1M 501295 GTTGACTGTGAGAATTCAATG 501315 v vii i iv MIRc#SINE/MIR 180 GGTTGTTGTGAGGATCAAATG 200 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.87 CpG sites = 21, Kimura (unadjusted) = 45.87 Transitions / transversions = 1.24 (21/17) Gap_init rate = 0.04 (5 / 115), avg. gap size = 1.60 (8 / 5) 686 32.36 2.16 1.19 chr2qtel1M 501449 501864 (498136) L1ME4a_3end#LINE/L1 56 475 (396) m_b95s551i23 3540 chr2qtel1M 501449 CTTCAATTGATAAATAGTCAAAGGATTTGAACAGACAATTTTCAGATGAA 501498 ii v v i v iv iv i v L1ME4a_3end#L 56 CCCCAATAGAAAAATGGGCAAAGGACATGAACAGACAATTCACAAAAGAA 105 chr2qtel1M 501499 AAAATAAAAATCATTTCTAGTCCTATGAAAAAATGCTTCAA-ATCACTAT 501547 i v viiivv iv v ? - -v v L1ME4a_3end#L 106 GAAATACAAATGGCCAATAAACATATGAAAANATG-TTCAACCTCACTAG 154 chr2qtel1M 501548 TGGTCAGAAAAATGTAAATCAAGACACCTCTGAGATACCA-----GATAT 501592 ii i i i i i v vv -----v iv L1ME4a_3end#L 155 TAATCAAAGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCT 204 chr2qtel1M 501593 TTCAGATTGGCTAAGATGACAGGGAAAGATATTGATGTATGTTGAAGGGA 501642 v i v vvv ii vv v ivivvi iv i i L1ME4a_3end#L 205 ATCAAATTGGCAAAGATTTAAAAGATTGATAATACCCAGTGTTGGCGAGG 254 chr2qtel1M 501643 ATGGGGAAAAAGTGGGACACTAATACATTGTT-GTGGAGTTGTGAATTGA 501691 i v ?i vv v v v i i - iiv i i L1ME4a_3end#L 255 GTGTGGNGAAACGGGCACTCTCATACACTGCTGGTGGGAGTGTAAATTGG 304 chr2qtel1M 501692 TCCAGTCATTCTAGAGAACAATATGGAACTATGCCTGAAGGGCTGTCACA 501741 v ii v i ii v v v iv v ii iv v v L1ME4a_3end#L 305 TACAACCTTTCTGGAGGGCAATTTGGCAATATGTATCAAAAGCCTTAAAA 354 chr2qtel1M 501742 CTGTGGGTACCCTTTGATCTAGCAGTGTCTCTACTGAACCTGTATCCTAA 501791 v ?vi i i i i vi v v iiivv v L1ME4a_3end#L 355 ATGTNCATACCCTTTGACCCAGTAATTCCACTTCTAGGAATTTATCCTAA 404 chr2qtel1M 501792 AGAGATCAT-AAAGAAG-GGAGAAGGCCTTCCACATGTGCAAAAATGTTT 501839 i i v - i v - ? v i vi ---- i ii i L1ME4a_3end#L 405 GGAAATAATCAGAGATGTGNACAAAGATTT----ATGTACAAGGATGTTC 450 chr2qtel1M 501840 CTAACATCCTTTTCTGTAGTGGCGA 501864 v vi v v v i i i i L1ME4a_3end#L 451 ATCGCAGCATTATTTATAATAGCGA 475 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 43.23 CpG sites = 68, Kimura (unadjusted) = 43.67 Transitions / transversions = 1.05 (68/65) Gap_init rate = 0.02 (10 / 415), avg. gap size = 1.40 (14 / 10) 16 9.71 0.00 0.00 chr2qtel1M 502166 502187 (497813) (A)n#Simple_repeat 1 22 (0) m_b95s252i11 3541 chr2qtel1M 502166 AAAAAAAAAAAAAAAGAAACAA 502187 i v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAA 22 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 12 22.17 6.38 0.00 chr2qtel1M 503403 503449 (496551) (CTTTT)n#Simple_repeat 1 50 (0) m_b95s252i12 3542 chr2qtel1M 503403 CTTTTATATT-TTTTTATTTCTTGTCTATTC-CCTCTTCTC-TTTCTTTT 503449 v v - iv v v -ii i - (CTTTT)n#Simp 1 CTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTT 50 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.07 (3 / 46), avg. gap size = 1.00 (3 / 3) 265 18.97 13.79 0.00 chr2qtel1M 507429 507486 (492514) MIR3#SINE/MIR 116 181 (27) m_b95s601i4 3543 chr2qtel1M 507429 GAATCTCAGTTTCCCC-TTTATAAAATGAGTGGGTTAG-------GATCT 507470 iii i - i i v i ------- MIR3#SINE/MIR 116 GGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCT 165 chr2qtel1M 507471 TGTAGGTCCCTTCCAG 507486 ivv MIR3#SINE/MIR 166 CTAAGGTCCCTTCCAG 181 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 22.57 CpG sites = 8, Kimura (unadjusted) = 22.57 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.04 (2 / 57), avg. gap size = 4.00 (8 / 2) 295 30.14 5.43 2.26 chr2qtel1M 507607 507735 (492265) C L2b_3end#LINE/L2 (10) 456 324 m_b95s601i5 3544 chr2qtel1M 507607 TCAGTAAACTTTTA---AGTGCCTGCTATCAGCCAGGCCCTGGGCTGTGC 507653 ii iv --- i i i vv ? v iv C L2b_3end#LINE 456 TCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGC 407 chr2qtel1M 507654 CCCAGGAACATAAAGAGAGACAAG--GGACTT--CCCCTGCTCTCGTGGA 507699 v ii i i i iv ivii --i ?i--i i ii C L2b_3end#LINE 406 GCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGGA 357 chr2qtel1M 507700 GGTCACAGACAGCTGAGGCAGGCAGTACATCAGTAA 507735 v v viv i v i - -- C L2b_3end#LINE 356 GCTCACAGTCTAGTGGGGGAGACAG-ACAT--GTAA 324 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.11 CpG sites = 25, Kimura (unadjusted) = 41.35 Transitions / transversions = 1.92 (25/13) Gap_init rate = 0.05 (6 / 128), avg. gap size = 1.67 (10 / 6) 437 29.70 12.45 3.15 chr2qtel1M 507862 508094 (491906) C MIRb#SINE/MIR (0) 268 15 m_b95s601i6 3545 chr2qtel1M 507862 AATACCATACCTAGCATTTATACCGCACCTGCT--GTGACATGCAGTGTG 507909 vi v v v vvv i i i -- v v v C MIRb#SINE/MIR 268 AATAATAGAGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTG 219 chr2qtel1M 507910 TCA------------GTATTGTCTCATTTTGTCCTCCTGAGAACCCTAGG 507947 ii ------------ i i vi vii v iv C MIRb#SINE/MIR 218 CTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCG 169 chr2qtel1M 507948 ACTCGGGTGCCATTATTGTGCCCTTCTTACAGATAAAGTCACTGAGGCAG 507997 vvii --- i v v i i i vv vv C MIRb#SINE/MIR 168 AGGTAGGT---ATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC 122 chr2qtel1M 507998 ACAGAGGTCTTGTAAGTTGCC--------------TAGCAAGTTGCTGAG 508033 v ivv v -------------- i v v C MIRb#SINE/MIR 121 AGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAG 72 chr2qtel1M 508034 GTGGGATGAACACTCAGGTCTTGCTGA-TTGAAGGCCCTGTTCATACTTT 508082 vi vviv i vv - iv i ----- i i i C MIRb#SINE/MIR 71 CCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCC-----CGTGCTCT 27 chr2qtel1M 508083 TCCCCTTGTACC 508094 i vi i C MIRb#SINE/MIR 26 TTCCACTGCACC 15 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.48 CpG sites = 31, Kimura (unadjusted) = 38.24 Transitions / transversions = 0.86 (31/36) Gap_init rate = 0.05 (12 / 232), avg. gap size = 3.08 (37 / 12) 587 31.53 5.08 0.98 chr2qtel1M 509723 510116 (489884) L1ME4c_3end#LINE/L1 21 430 (400) m_b95s551i24 3546 chr2qtel1M 509723 AGAAGTGACTCAAATTTATAAGAATGCAAACCATTCTTCAATTGATAAAT 509772 iv v i v viv? v v vv ii v L1ME4c_3end#L 21 AGAGCTCATTCAAATTGATAAGAAAAANATCAAGACCCCAATAGATAAAT 70 chr2qtel1M 509773 GGTCAAAGAATTTGAACAGACAGTTATGAGATGAAAAAATAAAAATCATT 509822 v i iv i vvv ? v ii v ? vi v L1ME4c_3end#L 71 GGGCAAAGGACATGAACAGACAATTCACANAAGAGGAAATACAANTAGTA 120 chr2qtel1M 509823 TCTACTCCTATGAAAAAATGCTTTAAGTCACTATTGGTCAGAGAAACGAA 509872 vvi vv vi i i iv vv i v ii i i v L1ME4c_3end#L 121 AACAAACACATGGAAAAATGTTCAACCTCGCTAGTAATCAAAGAAATGCA 170 chr2qtel1M 509873 AATTTAAACAATGCTGAGGTACCAGATATT-------TCAGATTGGCTAA 509915 v i iiv i -- v ------- i i i v L1ME4c_3end#L 171 AATTAAAGCAACAATGAGATACC--ATTTTACGCCTATTAAATTAGCAAA 218 chr2qtel1M 509916 GATAATAGAGAAA--GATAATGATGTATGTTGAAGGAAATGGGGAAATAG 509963 i -- vi i -- ivivv i iv iii? v vi v v L1ME4c_3end#L 219 AAT--TTAAAAAATTGATAATACCCAATGCTGGCGAGGNTGCGGTGAAAC 266 chr2qtel1M 509964 GGGCACCTTAATACATTGTTGGTGGAGTTGTGAATTGATCCAGTCATTCT 510013 v i ?i v i vi? i i v ii v i L1ME4c_3end#L 267 TGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTT 316 chr2qtel1M 510014 AGAGAGCAATATGCCCA--------AACAGCTATCACACTGTGCATACCC 510055 i i v v v -------- v i v v v v L1ME4c_3end#L 317 GGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAAAATGTTCATACCC 366 chr2qtel1M 510056 TTTGATCCAGCAGTATCTCTACTGAACCTGTATCCCAAAGAGATCAT--- 510102 i i i vi v v iivv v i i i v --- L1ME4c_3end#L 367 TTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCA 416 chr2qtel1M 510103 AAAGAAGGGAAAAG 510116 i L1ME4c_3end#L 417 AAAGAAGGAAAAAG 430 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.92 CpG sites = 61, Kimura (unadjusted) = 42.37 Transitions / transversions = 0.98 (61/62) Gap_init rate = 0.02 (8 / 393), avg. gap size = 3.00 (24 / 8) 722 29.25 4.13 1.15 chr2qtel1M 509761 510099 (489901) L1ME3G_3end#LINE/L1 55 403 (521) m_b95s551i25 3546 chr2qtel1M 509761 CAATTGATAAATGGTCAAAGAATTTGAACAGACAGTTATGAGATGAAAAA 509810 v v v i v i i vvv v ii L1ME3G_3end#L 55 CAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGGAA 104 chr2qtel1M 509811 ATAAAAATCATTTCTACTCCTATGAAAAAATGCTTTAAGTCACTATTGGT 509860 v viiivv vv v i iv vv v ii L1ME3G_3end#L 105 ATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTAAT 154 chr2qtel1M 509861 CAGAGAAACGAAAATTTAAACAATGCTGAGGTACCAGATATT-----TCA 509905 i i v v iiv i vv v i----- L1ME3G_3end#L 155 CAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCATCA 204 chr2qtel1M 509906 GATTGGCTAAGATAATAGAGAAAGATAATGATGTATGTTG--AAGGAAAT 509953 v i vvv i ?vv ivi?vi --i ivi L1ME3G_3end#L 205 GATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGTGT 254 chr2qtel1M 509954 GGGGAAATAGGGGCACCTTAATACATTGTTGGTGGAGTTGTGAATTGATC 510003 i-- i ii v i i iiv i i v L1ME3G_3end#L 255 GGGGAAAC--GGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTA 302 chr2qtel1M 510004 CAGTCATTCTAGAGAGCAATATGCCCAAACAGCTA-------TCACACTG 510046 i ? i i i v v -- ii v ------- i v v L1ME3G_3end#L 303 CAGCCNTTTTGGAGGGCAATTTGGC--AGTATCTATTAAAATTTAAAATG 350 chr2qtel1M 510047 TGCATACCCTTTGATCCAGCAGTATCTCTACTGAACCTGTATCCCAAAGA 510096 i i i vi v v ?ii?v v i ? L1ME3G_3end#L 351 CGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAGA 400 chr2qtel1M 510097 GAT 510099 i L1ME3G_3end#L 401 AAT 403 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.09 CpG sites = 51, Kimura (unadjusted) = 38.57 Transitions / transversions = 1.09 (51/47) Gap_init rate = 0.02 (7 / 338), avg. gap size = 2.57 (18 / 7) 18 18.13 0.00 0.00 chr2qtel1M 510452 510483 (489517) (A)n#Simple_repeat 1 32 (0) m_b95s252i13 3547 chr2qtel1M 510452 AAAAAAAAAAAAAGAAAGAAAGAAAGAAACAA 510483 i i i i v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 32 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 17 13.12 0.00 0.00 chr2qtel1M 512786 512811 (487189) (T)n#Simple_repeat 1 26 (0) m_b95s252i15 3548 chr2qtel1M 512786 TTTTCTTTCTTTTTTTTTTTTTCTTT 512811 i i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 314 21.90 16.19 0.00 chr2qtel1M 515907 516011 (483989) C L1ME3G_3end#LINE/L1 (376) 548 427 m_b95s551i26 3549 chr2qtel1M 515907 ATAATATTCCATAACATTCATGTACCATAATTTATTTAGCCATTCTCCAA 515956 i ii vv i i i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr2qtel1M 515957 CTGATGGA----------GTCACTA-------GCCAATACAAAAAAGGCT 515989 i ---------- iv i ------- i v v v C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr2qtel1M 515990 GCCACAAACATTTTTGTACCTG 516011 v ii ii v C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACATG 427 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 26.42 CpG sites = 14, Kimura (unadjusted) = 26.42 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.02 (2 / 104), avg. gap size = 8.50 (17 / 2) 1432 28.37 2.22 2.38 chr2qtel1M 516054 516685 (483315) L1ME5_3end#LINE/L1 7 637 (304) m_b95s551i27 3550 chr2qtel1M 516054 TCCAAAATATAGAGAGAATTGACTCTAATTTATAAGAAATCAAGCCATT- 516102 i i v ii i vviv v iv i -- v iv?- L1ME5_3end#LI 7 TCTAGAATATACAAGGAACTCCTGCAAATCAACAAGAAA--AAGACGGNA 54 chr2qtel1M 516103 -CTCCAGTTGATAAATGGTCAAAGGATATGAACAGACAATTCTGAGATGA 516151 - i i v v v i ivv v L1ME5_3end#LI 55 ACCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGA 104 chr2qtel1M 516152 AGAAA-CTGAAA--CTATTTCTAGTCATATGAAAAGATGCTGCAATTCAT 516198 i - i -- --v v - i vv i L1ME5_3end#LI 105 GGAAACCCGAAAGGCTA--ACAAG-CATATGAAGAGATGCTCAAACTCAT 151 chr2qtel1M 516199 TATTAATCAGAGAAATGCAAATTAAGACAACTCTGAGATACCACTACACA 516248 v i vv i vi L1ME5_3end#LI 152 TAGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACA 201 chr2qtel1M 516249 CCTGTCAGATTGGCTAGAAAGACAGGGAAAGATAATGCGGAATGTTGGAG 516298 i i i v i vv v ii vvi vi i v L1ME5_3end#LI 202 CCTATTAGACTGGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTGGCG 251 chr2qtel1M 516299 GGGATGTGGGAAAACAGGGACACTGATAAATTATTGGTAGAATTGTGAAT 516348 i i ? i i v v iv i ii i i v ii i L1ME5_3end#LI 252 AGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGAC 301 chr2qtel1M 516349 ACATCCAGCCATTCTGGAGAAGAATTTGGAACTA--TGATCAAA--AAGC 516394 vvi v iv i v v -- ii -- - L1ME5_3end#LI 302 TGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTAAG- 350 chr2qtel1M 516395 TATCAAACTGCATACCCTTTGAACCAGCAGTGTCACTACTGGGCTTATAC 516444 --- - v v i vi i v iv i L1ME5_3end#LI 351 TAT---AC-GCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATAT 396 chr2qtel1M 516445 CCCAAAGAGATACTAAAGAAGG---AAAAGGGTCCTGTATGTGCCAAAAT 516491 i v v viv --- v vv --- i v ii L1ME5_3end#LI 397 CCCAAAGAAATTCTCACACAGGTCCATAAGGGGAC---ATGTACGAGGAT 443 chr2qtel1M 516492 ATTTGTGGCAGCCCTGTTTGTAGTGGCTAGAAACTGGAAACTGAGTGGAT 516541 i ii v vi i vi i ii ii vivv i L1ME5_3end#LI 444 GTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGGGT 493 chr2qtel1M 516542 GCCCATCAATTGGAGAATGGTTGGGTAAATTGTGGTATATGAATGTTATG 516591 i v v i v i v iv v iiii L1ME5_3end#LI 494 GTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACACCATG 543 chr2qtel1M 516592 GAATATTATTGTTCTGTAAGAAATGACCAGCAGGATGAATACAGAGAGGC 516641 i i vvvv v v iii vii vi v i v vii L1ME5_3end#LI 544 GAGTACTATGCAGCAGTTAGAAGCAACGGACTAGATGTACACATAGCAAC 593 chr2qtel1M 516642 TTGGAGAGA-CTTACATGAAC-TGATGCTGAGTGAAATGAGCAGGA 516685 v vi - v -- - ii vi i i L1ME5_3end#LI 594 ATGGATGGATCTTAAA--AACATAGTGCTGAGTGAAAAAAGTAAGA 637 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.66 CpG sites = 95, Kimura (unadjusted) = 36.44 Transitions / transversions = 1.19 (95/80) Gap_init rate = 0.04 (24 / 631), avg. gap size = 1.21 (29 / 24) 16 16.22 4.44 4.44 chr2qtel1M 516924 516968 (483032) (AT)n#Simple_repeat 1 45 (0) m_b95s252i17 3551 chr2qtel1M 516924 ATATAT-TGTATCTAGGATATACATGTATCATATTTA-ATATATATA 516968 - i v -v i i - v - (AT)n#Simple_ 1 ATATATATATATATA-TATATATATATAT-ATATATATATATATATA 45 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4) 25 20.63 0.00 0.00 chr2qtel1M 517096 517145 (482855) (A)n#Simple_repeat 1 50 (0) m_b95s252i18 3552 chr2qtel1M 517096 AATAAAAAAAAATAAAATTAAAAAAAAGAGATAAAAAAAAGAAAAAGAAA 517145 v v vv i i v i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 355 30.98 6.24 3.84 chr2qtel1M 517517 517949 (482051) C L1PB_orf2#LINE/L1 (532) 2762 2320 m_b95s551i28 3553 chr2qtel1M 517517 TTTGGTTTGTCCAAGACCAGACCACTA-AAGCCTTTGG--TTATTTT--- 517560 v v i vivi i- iv -- i--- C L1PB_orf2#LIN 2762 TTTGCTTTGTCGAAGATCAGTTGGCTGTAAGTATTTGGGTTTATTTCTGG 2713 chr2qtel1M 517561 GTCCTATGAACCTAACCTTTTCCATTGATCAACTAT-TCTATTTCTTAGT 517609 i ------ vi v i v - i -i i vvii C L1PB_orf2#LIN 2712 GTTCT------CTATTCTGTTCCATTGGTCTA-TGTGCCTATTTTTATAC 2670 chr2qtel1M 517610 CAGTATCTTATGGTTTTGACGTCCACTACGTTTTAATATAGTGTTAGACC 517659 i v iiv ii v i ivi v v i v v iii C L1PB_orf2#LIN 2669 CAGTACCATGCTGTTTTGGTGACTATGGCCTTATAGTATAGTTTGAAGTC 2620 chr2qtel1M 517660 TGGTATACCTAGGGCACCTTC--GTTTGTTTTTTTTTCCCCATTAATCCT 517707 v ---v iv iii i --i i v ---- i i C L1PB_orf2#LIN 2619 GGGTA---ATGTGATGCCTCCAGATTTGTTCTTTTTGC----TTAGTCTT 2577 chr2qtel1M 517708 -CTTGAAAT-TCTTGACTTTTTGTT--TTCCAGATGAATTTT---GTTAT 517750 - viiv - viv i i v -- v ---i i C L1PB_orf2#LIN 2576 GCTTTGGCTATGCGGGCTCTTTTTTGGTTCCATATGAATTTTAGGATTGT 2527 chr2qtel1M 517751 TTTTTCTAAGCCACT--ACAATGGTTTCATGGGAGTTTGATTGGCATGGC 517798 ivi vv -- v i-- vi v v v v v C L1PB_orf2#LIN 2526 TTTTTCTAGTTCTGTGAAGAATGA--TGGTGGTATTTTGATGGGAATTGC 2479 chr2qtel1M 517799 ACTAAA----TAAATTAATTTAGATAGTATTGTCATCTTTATGATATTCA 517844 i i ---- i iv v ii v i i ii v C L1PB_orf2#LIN 2478 ATTGAATTTGTAGATTGCTTTTGGCAGTATGGTCATTTTCACAATATTGA 2429 chr2qtel1M 517845 CTCGACCTATCCAAGAGCACTTGATATTGTTCCAATTATTTAGATCTGAC 517894 i v i v ivv i vv v i ivi - v C L1PB_orf2#LIN 2428 TTCTACCCATCCATGAGCATGGGATGTGTTTCCATTTGTTTGTGTC-GTC 2380 chr2qtel1M 517895 T-TTATTTGTGTGGAAAGTGTTTTGTAGTTTTGCTCGTATAG----TTCA 517939 - v v v viiv v i v ---- C L1PB_orf2#LIN 2379 TATGATTTCTTTCAGCAGTGTTTTGTAGTTTTCCTTGTAGAGGTCTTTCA 2330 chr2qtel1M 517940 TCCTTTTGAT 517949 i iii i C L1PB_orf2#LIN 2329 CCTCCTTGGT 2320 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.53 CpG sites = 71, Kimura (unadjusted) = 40.94 Transitions / transversions = 1.22 (71/58) Gap_init rate = 0.07 (30 / 432), avg. gap size = 1.47 (44 / 30) 389 28.35 5.69 1.36 chr2qtel1M 517720 517930 (482070) C L1P1_orf2#LINE/L1 (732) 2562 2343 m_b95s551i29 3553 chr2qtel1M 517720 GACTTTTTGTT--TTCCAGATGAATTTT---GTTATTTTTTCTAAGCCAC 517764 i i v -- v i --- vi i vi vv C L1P1_orf2#LIN 2562 GGCTCTTTTTTGGTTCCATATGAACTTTAAAGTAGTTTTTTCCAATTCTG 2513 chr2qtel1M 517765 T--ACAATGGTTTCATGGG-AGTTTGATTGGCATGGCACTAAAT----AA 517807 -- v v --- v - i v v i i ---- C L1P1_orf2#LIN 2512 TGAAGAAAG---TCATTGGTAGCTTGATGGGGATGGCATTGAATCTATAA 2466 chr2qtel1M 517808 ATTAATTTAGATAGTATTGTCATCTTTATGATATTCACTCGACCTATCCA 517857 vi i ii v i i i i v i vv i C L1P1_orf2#LIN 2465 ATTACCTTGGGCAGTATGGCCATTTTCACGATATTGATTCTTCCTACCCA 2416 chr2qtel1M 517858 AGAGCACTTGATATTGTTCCAATTATTTAGATCTGACTTTATTTGTGTGG 517907 v ivvi i v v i iv ivvi v?v i C L1P1_orf2#LIN 2415 TGAGCATGGAATGTTCTTCCATTTGTTTGTATCCTCTTTTATTTCNTTGA 2366 chr2qtel1M 517908 AAAGTGTTTTGTAGTTTTGCTCG 517930 iv v i v i C L1P1_orf2#LIN 2365 GCAGTGGTTTGTAGTTCTCCTTG 2343 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.56 CpG sites = 30, Kimura (unadjusted) = 36.32 Transitions / transversions = 1.03 (30/29) Gap_init rate = 0.04 (8 / 210), avg. gap size = 1.88 (15 / 8) 20 20.67 0.00 0.00 chr2qtel1M 519626 519664 (480336) (A)n#Simple_repeat 1 39 (0) m_b96s252i0 3554 chr2qtel1M 519626 AAAAAAAAGCCACCAATTAAAAAAAAAAAAAAAAAAAAA 519664 ivv vv vv (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 39 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 18 23.47 0.00 7.25 chr2qtel1M 522596 522669 (477331) (GAGGGG)n#Simple_repeat 1 69 (0) m_b96s252i1 3555 chr2qtel1M 522596 GAGGAGGGAGCAGAGAGGGGGAAAGGGGCGGTGGAGGGAGTGGGGCAGCC 522645 - -i i - i v v i v v -- (GAGGGG)n#Sim 1 GAGG-GGGAG-GGGGAGGGGG-AGGGGGAGGGGGAGGGGGAGGGGGAG-- 45 chr2qtel1M 522646 TGGGAGGAGGTGGAGGTGGGGGAG 522669 v i v i v (GAGGGG)n#Sim 46 GGGGAGGGGGAGGGGGAGGGGGAG 69 Matrix = Unknown Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.07 (5 / 73), avg. gap size = 1.00 (5 / 5) 225 19.05 0.00 0.00 chr2qtel1M 524230 524271 (475729) L1ME3G_3end#LINE/L1 488 529 (395) m_b96s551i2 3556 chr2qtel1M 524230 ATGCCCATCAGTAGGGGAATGGCTGAATAAGTTATGACGTAT 524271 i i i i i iii L1ME3G_3end#L 488 ATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGTATAT 529 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 23.98 CpG sites = 8, Kimura (unadjusted) = 23.98 Transitions / transversions = 1.00 (8/0) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 27 0.00 0.00 0.00 chr2qtel1M 525215 525240 (474760) (AATGGG)n#Simple_repeat 1 26 (0) c_b96s251i0 3557 chr2qtel1M 525215 AATGGGAATGGGAATGGGAATGGGAA 525240 (AATGGG)n#Sim 1 AATGGGAATGGGAATGGGAATGGGAA 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 16 5.20 0.00 0.00 chr2qtel1M 525249 525268 (474732) (A)n#Simple_repeat 1 20 (0) m_b96s252i2 3558 chr2qtel1M 525249 AAAAAAAAAAAAAAAACAAA 525268 v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAA 20 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 323 27.81 7.92 1.94 chr2qtel1M 525751 526091 (473909) L1ME3G_3end#LINE/L1 10 370 (554) m_b96s551i3 3559 chr2qtel1M 525751 AAAATATATAGAGAATTGACTCAATTTA-TAAGAAATCGTTC-TCCAATT 525798 i i i vviv v i - vv viv-i v L1ME3G_3end#L 10 AGAATATATAAAGAACTCCTACAAATCAATAAGAAAAAGACAACCCAATA 59 chr2qtel1M 525799 GATAAATGGTCAAAGGATATGAA-AGACAATTTTCAT--GATAAAATTGA 525845 v v - i iv v-- vi vv L1ME3G_3end#L 60 GAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGGAAATACA 109 chr2qtel1M 525846 AA---CTATTACCACTGATGAAAGAGTGTTCCAAATCAAT--TGATCAGA 525890 --- i v v- vv iii i v vv v -- i i L1ME3G_3end#L 110 AATGGCCAATAA-ACATATGAAAAGATGCTCAACCTCACTAGTAATCAGG 158 chr2qtel1M 525891 GAAATGC-AATTAAAA-AACTTTAATATACCA----ACACCCTGGGGATT 525934 - - vv i v ----v vvvi L1ME3G_3end#L 159 GAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCATCAGATT 208 chr2qtel1M 525935 GGCTAAGA-TGACAGGAAAAATAATGATGAATGTTG--GAGGGTATGCAG 525981 v i - v v i ?vvi ivi? i -- i -- L1ME3G_3end#L 209 GGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGTGTG--G 256 chr2qtel1M 525982 GAAAACTGGGACT---ATGCCTTGTTGGTGGAGTTGTGAATGAATCAAAC 526028 i v v --- i vi i iiv i vii vv i L1ME3G_3end#L 257 GGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTACAGC 306 chr2qtel1M 526029 CATTCTGG-GAGAAATCTGA-ATTATCCA--AAAAGTTACAAACTGTG-A 526073 ? i - i v i i- v i -- v -- v i - L1ME3G_3end#L 307 CNTTTTGGAGGGCAATTTGGCAGTATCTATTAAAATTT--AAAATGCGCA 354 chr2qtel1M 526074 TATTCTTTGGGATCCAGC 526091 ii -- i L1ME3G_3end#L 355 TACCCTTT--GACCCAGC 370 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.07 CpG sites = 45, Kimura (unadjusted) = 35.53 Transitions / transversions = 0.94 (45/48) Gap_init rate = 0.07 (23 / 340), avg. gap size = 1.48 (34 / 23) 301 27.76 12.68 1.29 chr2qtel1M 525753 526241 (473759) L1ME4c_3end#LINE/L1 12 555 (275) m_b96s551i4 3559 chr2qtel1M 525753 AATATATAGAGAATTGACTCAA-TTTATAAGAAATCGTTC-----TCCAA 525796 ? i ii v i - v vv?v -----i L1ME4c_3end#L 12 ANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAAGACCCCAA 61 chr2qtel1M 525797 TTGATAAATGGTCAAAGGATATGAA-AGACAATTTTCATGATA-AAATTG 525844 v v i - iv ?i v -i v i L1ME4c_3end#L 62 TAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAGGAAATA 111 chr2qtel1M 525845 AAACTATT--AC---CACTGATGAAAGAGTGTTCCAAATCA--ATTGATC 525887 v ? v -- --- -- i i i v vv i-- v i L1ME4c_3end#L 112 CAANTAGTAAACAAACAC--ATGGAAAAATGTTCAACCTCGCTAGTAATC 159 chr2qtel1M 525888 AGAGAAATGC-AATTAAAA-AACTTTAATATACCA----ACACCCTGGGG 525931 i - i- vv i v ---- i ivvvii L1ME4c_3end#L 160 AAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCTATTAA 209 chr2qtel1M 525932 ATTGGCTAAGATGACAGGAAA--AATAATGATGAATGTTGGAGGGTATGC 525979 i v i v-i ii --i iviv i v i v? L1ME4c_3end#L 210 ATTAGCAAAAATT-TAAAAAATTGATAATACCCAATGCTGGCGAGGNTGC 258 chr2qtel1M 525980 AGGAAAACTGGGACT---ATGCCTTGTTGGTGGAGTTGTGAATGAATCAA 526026 i vi v ?--- i v i vi? i vii vv L1ME4c_3end#L 259 GGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACA 308 chr2qtel1M 526027 ACCATTCTGG-GAGAAATCTG--AAT---TATCCAAAAAGTTAC-AAACT 526069 v i -i v i -- --- -- i ii i- v L1ME4c_3end#L 309 ACCCTTTTGGAAAGCAATTTGGCAATACGTATC--AAGAGCCATAAAAAT 356 chr2qtel1M 526070 G-TGATATTCTTTGGGATCCAGCTGTGCTACTAC-GGCAACT----CCAA 526113 - v ii -- i ivi v i v - v i ---- i L1ME4c_3end#L 357 GTTCATACCCTTT--GACCCAGTAATTCCACTTCTGGGAATTTATCCTAA 404 chr2qtel1M 526114 AGAA------TAAAAGAAGGGAAAGGG-ACCGGCTGAAAAATGTTTGTGG 526156 i ------i i i v- ivv vvi i ii v L1ME4c_3end#L 405 GGAAATAATTCAAAAGAAGGAAAAAGCTATATGCACGAAGATGTTCATTG 454 chr2qtel1M 526157 --GCCCTGTT--TGATAG----AAACTGAAAATGA-ATGGATGCCCATCA 526197 -- vi i -- i ---- i i ii -v ii i v L1ME4c_3end#L 455 CAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACA 504 chr2qtel1M 526198 ATTGAGAA--GG-TGGGTAAATTTTGGT--ATGAATT--ATGGAATATTA 526240 v i i -- - ii v -- v? i -- L1ME4c_3end#L 505 ATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATATTA 554 chr2qtel1M 526241 T 526241 L1ME4c_3end#L 555 T 555 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.08 CpG sites = 79, Kimura (unadjusted) = 36.44 Transitions / transversions = 1.44 (79/55) Gap_init rate = 0.07 (36 / 488), avg. gap size = 1.92 (69 / 36) 376 29.23 8.20 1.09 chr2qtel1M 525791 526046 (473954) L1ME5_3end#LINE/L1 56 329 (612) m_b96s551i5 3559 chr2qtel1M 525791 CTCCAATTGATAAATGGTCAAAGGATATGAA-AGACAATTTTCAT--GAT 525837 i v v v - i v v-- v L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chr2qtel1M 525838 AAAATTGAAACTATTACCA--CTGATGAAAGAGTGTTCCAAATCA--ATT 525883 i iivi vvii v -- vv iiii i v v -- v L1ME5_3end#LI 106 GAAACCCGAAAGGCTAACAAGCATATGAAGAGATGCTCAAACTCATTAGT 155 chr2qtel1M 525884 GATCAGAGAAATGC-AATTAAAA-AACTTTAATATACCA----ACACCCT 525927 i - - vv i v i ---- iv L1ME5_3end#LI 156 AATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCTA 205 chr2qtel1M 525928 GGGGATTGGCTAAGATGACAGGAAA----AATAATGATGAATGTTGGAGG 525973 vvi i v i v --- ----i vii i v i L1ME5_3end#LI 206 TTAGACTGGCAAAAATTA---GAAAGCTGGATAATGCCAAGTGTTGGCGA 252 chr2qtel1M 525974 GTATGCAGGAAAACTGGGAC---TATGCCTTGTTGGTGGAGTTGTGAATG 526020 v ii i ? iv i ---i vi i iiv ii iv L1ME5_3end#LI 253 GGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACT 302 chr2qtel1M 526021 AATCAAACCATTCTGG-GAGAAATCTG 526046 ii vv i - v L1ME5_3end#LI 303 GGTGCAGCCATTCTGGAGAGCAATCTG 329 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.41 CpG sites = 41, Kimura (unadjusted) = 38.06 Transitions / transversions = 1.24 (41/33) Gap_init rate = 0.05 (13 / 255), avg. gap size = 1.85 (24 / 13) 18 0.00 0.00 0.00 chr2qtel1M 526742 526761 (473239) (A)n#Simple_repeat 1 20 (0) m_b96s252i3 3560 chr2qtel1M 526742 AAAAAAAAAAAAAAAAAAAA 526761 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAA 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 920 29.46 3.16 2.21 chr2qtel1M 526822 527359 (472641) C L1ME4a_3end#LINE/L1 (316) 555 13 m_b96s551i6 3561 chr2qtel1M 526822 ATAATAGTCCATGATCTTCATGTTTCACAACTTGTTCAGCCATTCCCCAG 526871 v v? v vv vi i i i i i ? vi C L1ME4a_3end#L 555 ATAATATTCCATTNTATGGATGTACCATAATTTATTTAACCANTCCCCTA 506 chr2qtel1M 526872 TTGGTGAGCATCCATTCCATTTCCACTTCTGTGCTACCACAAAAAGAGCT 526921 v ii ii vviii v i vi ii i v iv C L1ME4a_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAATGCT 456 chr2qtel1M 526922 GCTACAATCATCATTGCACATGTGGGTCCTTGTCC-C-TTTTTGATGATG 526969 v ii v v i i--ii i ? - - i i v v C L1ME4a_3end#L 455 GCGATGAACATCCTTGTACATA--AATCTTTGTNCACATCTCTGATTATT 408 chr2qtel1M 526970 TCTTTGGGATAAAGAGCCTGTAGAGACACTTCTGGATCCAAGGGTATGCA 527019 i i vvv iv v v iv i v i v ? C L1ME4a_3end#L 407 TCCTTAGGATAAATTCCTAGAAGTGGAATTACTGGGTCAAAGGGTATGNA 358 chr2qtel1M 527020 CAGTTTGATAGCCCTTTGG-GCATAGTTCCAAATTACTCTCCACAATAGT 527068 v v - v i i-i v v i i v vi C L1ME4a_3end#L 357 CATTTTTA-AGGCTTTTGATACATATTGCCAAATTGCCCTCCAGAAAGGT 309 chr2qtel1M 527069 TGGATCATTTCAGACATCCCCCAACAATGCATTAGTGT-CCCACTTTTCC 527117 v i v i v vi v i i i v v - ii i? C L1ME4a_3end#L 308 TGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTGCCCGTTTCNCC 259 chr2qtel1M 527118 ACATCCCCTTTAATAT------TTATC-ATCTTTTCCTGTGATCTTAACT 527160 i i vii i i------ - v----i vi i C L1ME4a_3end#L 258 ACACCCTCGCCAACACTGGGTATTATCAATCTTTTA----AATCTTTGCC 213 chr2qtel1M 527161 AGTCTGAGAGGTATGATGTGGTAGCTCAGAGTTA-CATAATTTGCATTTT 527209 i i v ivi vi v vv i-iv i C L1ME4a_3end#L 212 AATTTGATAGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTC 163 chr2qtel1M 527210 TCTTATCAATAGTGATTTAGTGCATTTTTTCATATAACTCTAATTGGC-- 527257 i v i v vv v vi ? i-- i - -- C L1ME4a_3end#L 162 TTTGATTACTAGTGAGGTTGAACATNTTTTCATATG--TTT-ATTGGCCA 116 chr2qtel1M 527258 TTTA-ATTTCCTCATCTGAAAATTGTCTGTTCATACCCTTTGACTATGTA 527306 i- i v i vi ii v i v v C L1ME4a_3end#L 115 TTTGTATTTCTTCTTTTGTGAATTGTCTGTTCATGTCCTTTGCCCATTTT 66 chr2qtel1M 527307 TCAATTAAGGAAT--GACTTGCATTCTTATAAATTTATAACTGTTCTTTA 527354 v ii vi -- v v-- vi i vv i C L1ME4a_3end#L 65 TCTATTGGGGTGTTCGTCTTT--TTCTTATTGATTTGTAAGAGCTCTTTA 18 chr2qtel1M 527355 TATAT 527359 C L1ME4a_3end#L 17 TATAT 13 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.15 CpG sites = 85, Kimura (unadjusted) = 38.79 Transitions / transversions = 1.21 (85/70) Gap_init rate = 0.04 (22 / 537), avg. gap size = 1.32 (29 / 22) 377 27.95 4.21 4.58 chr2qtel1M 527222 527506 (472494) C L1M3_orf2#LINE/L1 (0) 3288 3005 m_b96s551i7 3561 chr2qtel1M 527222 TGATTTAGTGCATTTTTTCATATAACTCTAATTGGC--TTTA-ATTTCCT 527268 v v v i v ---i -- i- v i C L1M3_orf2#LIN 3288 TGATGTTGAGCATCTTTTCATATACCT---GTTGGCCATTTGTATGTCTT 3242 chr2qtel1M 527269 CATCTGAAAATTGTCTGTTCATACCCTTTGACTATGTATCAATTAAGGAA 527318 v iv i v i vii v i v v ? iii --- C L1M3_orf2#LIN 3241 CTTTGGAGAAATGTCTATTCAGGTCCTTTGCCCATTTTTNAATCGGG--- 3195 chr2qtel1M 527319 TGACTTGCATTCTT---ATAAATTTATAACTGTTCTTTATATATCTTAGA 527365 v i iv i --- vi v i ?vv i i i C L1M3_orf2#LIN 3194 TTATTTGTTTTTTTGCTATTGAGTTGTANGAGTTCCTTATATATTTTGGA 3145 chr2qtel1M 527366 AATTAAACCTTTATCAGATATACTAGTAGGCCATAAAGATTTTGCCCCAG 527415 v v i - i vv --- v vi v C L1M3_orf2#LIN 3144 TATTAACCCCTTATCAGATATA-TGGTTTGC---AAATATTTTCTCCCAT 3099 chr2qtel1M 527416 CCTTCTACTTCCCTCTTAATCTTGTTTCTGGTGGTTTGTT----TGTGCA 527461 i iviviv v i v iii --- i v vi ---- C L1M3_orf2#LIN 3098 TCCGTAGGTTGCCTTTTCACTCTGT---TGATTGTTTCCTTTGCTGTGCA 3052 chr2qtel1M 527462 AAAAC-TTTTAATTTATTGTAATCAAAGTTGTCTA-TTTTGCCTTTG 527506 i i - i iv i vv v - i C L1M3_orf2#LIN 3051 GAAGCTTTTTAGTTTGATGTAGTCCCACTTGTCTATTTTTGCTTTTG 3005 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.61 CpG sites = 40, Kimura (unadjusted) = 35.83 Transitions / transversions = 1.11 (40/36) Gap_init rate = 0.07 (19 / 284), avg. gap size = 1.32 (25 / 19) 905 32.32 4.25 2.47 chr2qtel1M 527813 528729 (471271) C L1P4_orf2#LINE/L1 (591) 2703 1771 m_b96s551i8 3562 chr2qtel1M 527813 TCTGGTCCACTGATAGCCCATG---CTATTTCTTAGCCAGTACCA-AATG 527858 v i i --- i --- i i vvi -iv C L1P4_orf2#LIN 2703 TCTGTTCCATTGGT---CTATGTGTCTGTTTTTGTACCAGTACCATGCTG 2657 chr2qtel1M 527859 GTTTGCTTACTGCTGCTTTGTAACATAGTTCTAGGGTAGGTACTGCTAAG 527908 v v iv i ii iv i vii v iv v C L1P4_orf2#LIN 2656 TTTTGGTTACTGTAGCCTTGTAGTATAGTTTGAAGTCGGGTAATGTGATG 2607 chr2qtel1M 527909 TCACCATCCTTTCTGTTTTGTTGTGTATATTTTTTTTGTTGTTGATATTC 527958 i v iv i vi v -- iv viv vi ----- v C L1P4_orf2#LIN 2606 CCTCCGGCTTTGTTCTTTT--TGCTTAGGATTGCTTTG-----GCTATTC 2564 chr2qtel1M 527959 TTGACCTTTTGTTCTTCTAGATAGCTTTTGT--TGTTTTTTTCTAGTTCT 528006 vv vi v vv i v iiv iv-- iv i C L1P4_orf2#LIN 2563 GGGCTCTTTTTTGGTTCCATATGAATTTTAGAATAGTTTTTTCTAATTCT 2514 chr2qtel1M 528007 AT--AAAATG-TTTTTGCAGTTTGGTTGTTATGGCATTGAATAAATAGAC 528053 i -- -iv v i i v vv i i vvi i C L1P4_orf2#LIN 2513 GTGAAAAATGACGTTGGTAGTTTGATAGGAATAGCGTTGAATCTGTAGAT 2464 chr2qtel1M 528054 CAATTTAGGCAGAATTGTGATTT-----ATATCAGCTCAACCTAACCATG 528098 iiv i v v iv ----- iiii vv v v C L1P4_orf2#LIN 2463 TGCTTTGGGCAGTATGGCCATTTTAACGATATTGATTCTTCCAATCCATG 2414 chr2qtel1M 528099 AACAATTAATATTTTTCCAGTTGTTTAGATCTAATTTTC--TTTGTGTAA 528146 i vvv i v ivi -- i ?i-- v v v C L1P4_orf2#LIN 2413 AGCATGGAATGTTTTTCCATTTGTTTGTGTC--ATCTNTGATTTCTTTCA 2366 chr2qtel1M 528147 GAAGTGTTTTGTAATTGTGTTCATATGG-TATTTGGGTTTGCCTTGGC-A 528194 v i v vi ii vi - v vivi -- i- C L1P4_orf2#LIN 2365 GCAGTGTTTTGTAGTTCTCCTTGTAGAGATCTTTCACCT--CCTTGGTTA 2318 chr2qtel1M 528195 CTTGC-TCCCCAATTATTTTATTTTGTCTATAGACATTTTCAATGGAATT 528243 vv i- i i iv v i i i vi v v i C L1P4_orf2#LIN 2317 GATGTATTCCTAGGTATTTTATTTTTTTTGTGGCTATTGTAAATGGGATT 2268 chr2qtel1M 528244 TC--TCTT--TGTGTCTCTT-GCTTATGGGCTTTATCAGTAATTTAGAGA 528288 v -- -- v v i- -- ii v ii i--- v C L1P4_orf2#LIN 2267 GCGTTCTTGATTTGGCTCTCAGCT--TGAACGTTATTGGTG---TATAGA 2223 chr2qtel1M 528289 AATACTGATGATTTGTGAGACTTCATTTTATATACCTCAATTTTGCTAAA 528338 i iv v vivv v i v ivv i i i C L1P4_orf2#LIN 2222 AATGCTACTGATTTTTGTACATTGATTTTGTATCCTGAAACTTTACTGAA 2173 chr2qtel1M 528339 GCTGTGAATTGTTTTCAGTAGATATTTTGATGG-TTTTCTAGGATTCTCA 528387 ii vv iiv ii v -iv ii -v i i i i v C L1P4_orf2#LIN 2172 GTCGTTTATCAGTTCTAGGAG-CCTTTTGGCGGAGTCTTTAGGGTTTTCT 2124 chr2qtel1M 528388 AAGTATCTCATCATATCATCTCCAAAGAGTAATAGTTTTATTTCCTCATT 528437 i vvv i vv i vi v i i v C L1P4_orf2#LIN 2123 AGGTATAGAATCATATCGTCAGCGAAGAGAGATAGTTTGACTTCTTCTTT 2074 chr2qtel1M 528438 GCCTATTCCAATTCCTTTTATTTTTTTTTCTTTTCATATCAATGAAGCTG 528487 v ivi v i i vi vv iiv vvi i C L1P4_orf2#LIN 2073 TCCTATTTGGATGCCTTTTATTTCTTTCTCTTGCCTGATTGCTCTGGCTA 2024 chr2qtel1M 528488 ACATTTCTAGAACAGTGTTGAATAATAGTGGTGATAAT--------TTAA 528529 iv i i v vi iv v i -------- iv C L1P4_orf2#LIN 2023 GGACTTCCAGTACTATGTTGAATAGGAGTGGTGAGAGTGGGCATCCTTGT 1974 chr2qtel1M 528530 C----CCCTGATTTTACTAGGAATGCATCCAGCTTCTATCCATTTCATAT 528575 ----i v v i i vvi v i ii i ivi C L1P4_orf2#LIN 1973 CTTGTTCCAGTTCTCAAGGGGAATGCTTCCAGCTTTTGCCCGTTCAGTAT 1924 chr2qtel1M 528576 AATGCTTTCTACGGGTTT-TAATGAAGTATTGCTTATTTTTTTAAGGAAA 528624 i i vv ii - v - ii iviv v i v v C L1P4_orf2#LIN 1923 GATGTTGGCTGTGGGTTTGTCAT-AGATGGCTCTTATTATTTTGAGGTAT 1875 chr2qtel1M 528625 GTTCCCTTTATCCCTATGCCCTTTAGTGTTTATTTA-CAAGAATGGGTAC 528673 i iv v vviiv v v -- - v v i ii C L1P4_orf2#LIN 1874 GTTCCTTCGATGCCTAGTTTGTTGAGGGTT--TTTATCATGAAGGGATGT 1827 chr2qtel1M 528674 TGTATTTTGTCAAAAGCTTTTTCTGCTTGTATTGGGATTATAATATGATT 528723 v i i v v i v v i C L1P4_orf2#LIN 1826 TGGATTTTATCGAAAGCTTTTTCTGCGTCTATTGAGATGATCATATGGTT 1777 chr2qtel1M 528724 TTGGTT 528729 v C L1P4_orf2#LIN 1776 TTTGTT 1771 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.95 CpG sites = 148, Kimura (unadjusted) = 43.09 Transitions / transversions = 1.05 (148/141) Gap_init rate = 0.04 (41 / 916), avg. gap size = 1.51 (62 / 41) 682 30.72 4.43 1.76 chr2qtel1M 528310 528806 (471194) C L1MC_orf2#LINE/L1 (1093) 2201 1692 m_b96s551i9 3562 chr2qtel1M 528310 TTCATTTTATATACCTCAATTTTGCTAAAGCTGTGAATTGTTTTCAGTAG 528359 v ii i v iv ii v iii ivv iv i v C L1MC_orf2#LIN 2201 TTAACCTTGTATCCTGCAACCTTGCTATAATCGCTTATTAGTTCCAGGAG 2152 chr2qtel1M 528360 ATATTTTGATGGTTTTCTAGGATTCTCAAAGTATCTCATCATATCATCTC 528409 v v vi i i i v i v vi vviv i v C L1MC_orf2#LIN 2151 TTTTTTTGTCGATTCTTTCGGATTTTCTACATAGACAATCATGTCATCTG 2102 chr2qtel1M 528410 CAAAGAGTAATAGTTTTATTTCCTCATTGCCTATTCCAATTCCTTTTATT 528459 i v ivi i i v v v iivv v C L1MC_orf2#LIN 2101 CGAACAAAGACAGTTTTATTTCTTCCTTCCCAATCTGTATACCTTTTATT 2052 chr2qtel1M 528460 TTTTTTTCTTTTCATAT--CAATGAAGCTGACATTTCTAGAACAGTGTTG 528507 ii v v -- v -- iiv i i v ii C L1MC_orf2#LIN 2051 TCCTTTTCTTGTCTTATTGCATT--AGCTAGGACTTCCAGTACGATGTTG 2004 chr2qtel1M 528508 AATAATAGTGGTGATAA-------TTTAACC-----CCTGATTTTACTAG 528545 v iv v i-------ii vi ----- i vii C L1MC_orf2#LIN 2003 AAAAGGAGTGGTGAGAGGGGACATCCTTGCCTTGTTCCTGATCTTAGCGG 1954 chr2qtel1M 528546 GAATGCATCCAGCTTCTATCCATTTCATATAATGCTTTCTACGGGTTTTA 528595 v v ? i vv vvi i i vv iii v C L1MC_orf2#LIN 1953 GAAAGCTTCNAGTTTCTCACCATTAAGTATGATGTTAGCTGTAGGTTTTT 1904 chr2qtel1M 528596 ATGAAG-TATTGCTTATTTTTTTAAGGAAAGTTCCCTTTATCCCTA---T 528641 - v - i vi ivvv i iv i i i --- C L1MC_orf2#LIN 1903 -TGTAGATGTTCTTTATCAAGTTGAGGAAGTTCCCCTCTATTCCTAGTTT 1855 chr2qtel1M 528642 GCCCTTTAGTGTTTATTTA-CAAGAATGGGTACTGTATTTTGTCAAAAGC 528690 --- v v -- - v ii v v C L1MC_orf2#LIN 1854 GC---TGAGAGTTT--TTATCATGAATGGGTGTTGGATTTTGTCAAATGC 1810 chr2qtel1M 528691 TTTTTCTGCTTGTATTGGGATTATAATATGATTTTGGTTGGTTTTG-TTA 528739 v v iv v v i vv -v v -i i C L1MC_orf2#LIN 1809 TTTTTCTGCATCTATTGATATGATCATGTGATTTTTCTT-CTTTAGCCTG 1761 chr2qtel1M 528740 TTGATGAGGTCGACTGTAGTAA--GTTTTCCTGAAACTGAAGTAGCCATG 528787 v i v i ii v -- v i vi vii vi v C L1MC_orf2#LIN 1760 TTGATGTGATGGATTACATTAATTGATTTTCGAATGTTGAACCAGCCTTG 1711 chr2qtel1M 528788 CATTACTGGTAAAAATCCC 528806 vv v v C L1MC_orf2#LIN 1710 CATACCTGGGATAAATCCC 1692 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.41 CpG sites = 73, Kimura (unadjusted) = 40.12 Transitions / transversions = 0.95 (73/77) Gap_init rate = 0.03 (17 / 496), avg. gap size = 1.82 (31 / 17) 12 20.33 0.00 7.14 chr2qtel1M 528952 528996 (471004) (GAAACCA)n#Simple_repeat 1 42 (0) m_b96s252i4 3563 chr2qtel1M 528952 GAATCAAGAAGCCAGCCAGACCAGAAACCACCAGACCAGAATCCA 528996 v v i -- i -v i v (GAAACCA)n#Si 1 GAAACCAGAAACCAG--AAACCAGAAACCA-GAAACCAGAAACCA 42 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.07 (3 / 44), avg. gap size = 1.00 (3 / 3) 12 12.45 5.13 5.13 chr2qtel1M 528963 529001 (470999) (CCAGA)n#Simple_repeat 1 39 (0) m_b96s252i5 3563 chr2qtel1M 528963 CCAG-CCAGACCAGAAACCACCAGACCAGAATCCA-ACCAG 529001 - vvvv - - - (CCAGA)n#Simp 1 CCAGACCAGACCAGACCAGACCAGACCAG-A-CCAGACCAG 39 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.11 (4 / 38), avg. gap size = 1.00 (4 / 4) 287 28.06 7.91 4.20 chr2qtel1M 530044 530296 (469704) C HERVK#LTR/ERVK (2273) 5263 5002 m_b96s701i0 3564 chr2qtel1M 530044 AAGAAGTTAATAGTATAAAGAGGTAGATTTAGAAGTTT--TCTAGGG--- 530088 i v - i v v --- v-- i --- C HERVK#LTR/ERV 5263 AAAAATTTAA-AGTATAGAGTGCTAGATT---AAGTTGCATCTGGGGAGT 5218 chr2qtel1M 530089 -TTAC--------CTGTGGCTCCCCCTTTCTTTTGTTTTGGAGA---AGC 530126 -? -------- -- ii vivvi --- C HERVK#LTR/ERV 5217 GNTACACTCCTTACTGT--CTCCCCCTTCTTTTTGTTTAACCAATTGAGC 5170 chr2qtel1M 530127 ATCTTAATATTTCTGTTTCTCCTCTCTACTATTGCCTGTCCTTGAGGATT 530176 - i v i i - i vv i i v v i i C HERVK#LTR/ERV 5169 -TTTGAGTGTT-CTATTAGTTCTTTCAACTATGGCCTGTCCTTGGGAATT 5122 chr2qtel1M 530177 AAAAGGTATGCCCGTGGTGTGTAAAATCTTATACTGTGCACAAAAGTGTG 530226 v v v i v i iv i vi -iivi i i v v C HERVK#LTR/ERV 5121 ATAAGGAATTCCTGTTGTATGTGTAATTTTCCACTG-ATTTAAGAATTTT 5073 chr2qtel1M 530227 CAAAATGTTT---GGAAGTATAAGCAGGAACATTGTCTGTTTTTATTGCT 530273 iii ? i ---viv --v v vv v v vi C HERVK#LTR/ERV 5072 TGGAANGCTTTACTACAGTAT--CCTGGCCCATTGTCAGTTTTAATTTTT 5025 chr2qtel1M 530274 TCCAGCACACCCATAATGGCAAA 530296 ii v v i ii C HERVK#LTR/ERV 5024 TCTGGAACTCCCATGACAGCAAA 5002 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.15 CpG sites = 36, Kimura (unadjusted) = 36.15 Transitions / transversions = 1.12 (36/32) Gap_init rate = 0.07 (17 / 252), avg. gap size = 1.82 (31 / 17) 443 30.75 5.39 3.64 chr2qtel1M 530151 530447 (469553) C HERVK11#LTR/ERVK (2674) 5279 4978 m_b96s701i1 3564 chr2qtel1M 530151 TCTACTATTGCCTGTCCTTGAGGATTAAAAGGTATGCCCGTGGTGTGTAA 530200 i i iv i iv v v v ii i vi C HERVK11#LTR/E 5279 TCCACCACAGCCTGTCCCTGAGGATTGTAAGGGATTCCGGTAATATGGGA 5230 chr2qtel1M 530201 AATCTTATACTGT-GCACAAA--AGTGTGCAAAATGTTTGGAAGTATAAG 530247 iiivi - i -- i --- vvi ivv ii vv C HERVK11#LTR/E 5229 AATTCCCCACTGTTGCATAAATAAAT---CAAAAGCCTTACTAACATATC 5183 chr2qtel1M 530248 CAGGAACATTGTCTGTTTTTATTGCTTCCAGCACACCCATAATGGCAAAT 530297 ii i i vvv vii v vv iv - C HERVK11#LTR/E 5182 CAGGGGCGTTGTCTGTCTTTATTTGATATGGAAGCCCCATAACTGCAAA- 5134 chr2qtel1M 530298 GCTTGTGTGAGGAATTCAG-TGACC----ACTTGGGCTGTCTCTTTTGCT 530342 ------- i v - vii---- v i vi iiv C HERVK11#LTR/E 5133 GC-------AAGAATACAGATGTTTTTTAACATGGGCCGTGCCTTCCCCT 5091 chr2qtel1M 530343 GCT-----GGTATTGCATATA---CCTGAAAAGTTATCTACCACAACGTG 530384 i -----i viv v --- i v viv i C HERVK11#LTR/E 5090 GTTTGGCAAGTAGCCCAGATAAAACCTGAGAAGGTATCTACAGAAACATG 5041 chr2qtel1M 530385 AATAAAAGACAGACGACCAAAAGATTTATAATGGGTCACATCCATTTGCC 530434 v i v v ? v vi i vi vv i C HERVK11#LTR/E 5040 CACATATGANAGTCTGCCAAAGGAGCTAACATGAGTCACATCCATTTGCC 4991 chr2qtel1M 530435 AGATTTCATTGGG 530447 v vv? i C HERVK11#LTR/E 4990 ATAAANCATTAGG 4978 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.42 CpG sites = 45, Kimura (unadjusted) = 40.60 Transitions / transversions = 1.05 (45/43) Gap_init rate = 0.06 (17 / 296), avg. gap size = 1.59 (27 / 17) 313 30.58 1.26 1.26 chr2qtel1M 531449 531607 (468393) C HERVK3#LTR/ERVK (3651) 3551 3393 m_b96s701i2 3565 chr2qtel1M 531449 GCTTCTTTTGTAAGCTGGCGTGGTGAACTTAAAGCACTAGCTCCCCTTAA 531498 i v ? i v i v i ? v vv -- i iv C HERVK3#LTR/ER 3551 GCCTCTTTAGTNAGTTGCCGCGGGGAATTTAANGAAGAA--TCTCCTTGC 3504 chr2qtel1M 531499 AATGTCACACAACGGT-TGTAA-CTGATAGGTAGTCAAGCCTAACACTGG 531546 iv ivvii v i - -i iv vi i ii C HERVK3#LTR/ER 3503 AGGGTTTGGTAAAGATGTGTAAGTTGATAGGTAGCAATACCTAGCATCGG 3454 chr2qtel1M 531547 TCGCATCCATTGGATATCTCCTATCAATTTCTGAAAATCTTTCAATGTGT 531596 v v v vi i vi vi v i v v C HERVK3#LTR/ER 3453 GCGCAGCCAATTAATATCCCCTAATAATTGTTGAAAATCATTTAAAGTCT 3404 chr2qtel1M 531597 TTAGCTTCTCT 531607 v i i v C HERVK3#LTR/ER 3403 GTAACCTGTCT 3393 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.37 CpG sites = 24, Kimura (unadjusted) = 40.49 Transitions / transversions = 1.00 (24/24) Gap_init rate = 0.03 (4 / 158), avg. gap size = 1.00 (4 / 4) 1127 29.17 3.47 4.47 chr2qtel1M 531523 532358 (467642) C HERVK14C#LTR/ERVK (3762) 3672 2845 m_b96s701i3 3565 chr2qtel1M 531523 ATAGGTAGTCAAGCCTAACACTGGTCGCATCCATTGGATATCTCCTATCA 531572 vv v viiv v v vi i vi C HERVK14C#LTR/ 3672 ATAGGTAGGAATGCCTAAAGTAGGTCGAATCCAATTAATATCCCCTAATA 3623 chr2qtel1M 531573 ATTTCTGAAAATCTTTCAATGTGTTTAGCTTCTCTGTTC----TTAAGAA 531618 i v i v v i vvvv v ---- -- C HERVK14C#LTR/ 3622 ATTTTTGAAAATCATTTAAAGTTTTCAGAGAGTCTTTTCGAATTT--GAA 3575 chr2qtel1M 531619 CAGTTTTGTACTGTAAGCACCTTAGGGTATACTT-CATATCCTAAATATT 531667 v- ?iviv vii i vvvv iv i - - i C HERVK14C#LTR/ 3574 CC-TTTTGNGGCTTAATTGCCCTTTCCTGAACCTGCAT-TCCCAAATATT 3527 chr2qtel1M 531668 GAAAAGGAGCATGTCTTTGAATTTTTTCTGGTGCTATGTATAATTAGTAA 531717 i i v?iv v ? ? ------- ?i C HERVK14C#LTR/ 3526 GGAAAGGAGTAGNCGTTTGAATTTTATCNGGNGCTATG-------ANCAA 3484 chr2qtel1M 531718 TTCTTTAGTGTTT-CTATGGTCTTTTGTAGATATGCTTCTAACA-----T 531761 i --- i iv- ? iv i i i i v--v ----- C HERVK14C#LTR/ 3483 TCC---AGCGTCGGCNACCGCCTTCTGTAAATGTGA--ATAACACTGGAT 3439 chr2qtel1M 531762 ATGTT--CCTTGGGT-------GCACATCCCAATATATCATCCATATAAT 531802 v --i i i ------- ?--- i C HERVK14C#LTR/ 3438 AAGTTGGTCTCGAGTTTCGGCCGCACAN---AATATGTCATCCATATAAT 3392 chr2qtel1M 531803 --ATAATAGCATAATTTTTGGAAATGCTTTTCTTACTGGAGCAAGAGCAG 531850 -- i vv?v i -- ivvv i ? v vvv v vv C HERVK14C#LTR/ 3391 GAATGATATANGAATCT--GGAAACTGATCTCTNACAGGTTGAATAGCCT 3344 chr2qtel1M 531851 TAGCAACATACACTTGACACATAGTAGGGCTGTTTTTCATTCCCTGTGGC 531900 ?vv v ? vii v ? ? i i ivv v i C HERVK14C#LTR/ 3343 NCCCCACANAAGTTTGACAAATNGTNGGACTATTCAACATGCCCTGCGGC 3294 chr2qtel1M 531901 AAAACTGTCCATTCATATCTTTTATAATGGTCAGCTAA-GTTAACACTGG 531949 ? v v v ? vvi- iv? ivvi iv- v i vii C HERVK14C#LTR/ 3293 AANACTTTCCAATGATANCTGGC-TGCNGGTTCCTTGTTGTTCATAGCAG 3245 chr2qtel1M 531950 GCACTGAAAAGGCAAATCTTTTCATATCCTCCTTATCCAGAGGGATAGAA 531999 v iv v i i iv v ?vv ivv i i v C HERVK14C#LTR/ 3244 GAATAGTAAAAGCAAATTTTTCAAAATCNGGCTCTGCTAGAGGAATAGTA 3195 chr2qtel1M 532000 TAGAAACAATCCTTAATATCTATGACCCAAAGAGGCCATTCTCTAGGCAA 532049 v i i v v i ivvv i? v v v C HERVK14C#LTR/ 3194 AAGAAGCAGTCCTTCAAATCTATAACTATTAANGGCCAGTCTCTAGGAAT 3145 chr2qtel1M 532050 CTGAGTAGGAGATGGAAGTCCAGGCTGAAGAATTCTCATAG-TTGC-TAT 532097 vvi ii i ? v i v v ?iii i ? - ?- iv C HERVK14C#LTR/ 3144 CATGGCGGGGGANGGCAGCCCTGGCTGCAGNGCCCCCATNGGTTGNATGA 3095 chr2qtel1M 532098 CTGTTCATTCACCTTTCTTAAATTTGTTAACATCCTCCATTTTCCAGATT 532147 -- v vvi v i iv i ? v i v i C HERVK14C#LTR/ 3094 CTG--CATTGACGGCTCGTAAGTCGGTTAGCATNCGCCATCTGCCGGATT 3047 chr2qtel1M 532148 TCTTTTTTACAACAAATACTGGGGAATTCCAAGGACTTAGAGAA----GA 532193 i i ? iv i ? ? ---- i ---- i C HERVK14C#LTR/ 3046 TTTTCTTNATTACAAACACTGGNGAATTCCANGGA----GAAAATGTGGG 3001 chr2qtel1M 532194 TTGTAAGTGTCCTTGGTCAAGCCGCTCCTGTACTATATCTAATAAGGCCT 532243 i v? v v? v iii i i vv vv ivi i C HERVK14C#LTR/ 3000 CTCNATGTGTCCTTTNTCTAATTGTTCTTTGACTAATTCCTGTAAGGCCC 2951 chr2qtel1M 532244 GAATTTTATCGCTACCTAAGGGCCACTGTTCTATCCACACTGGTGTATCA 532293 vv v v viv v?? iv ? ? i v ? ?v v vi C HERVK14C#LTR/ 2950 CCAGTTTTTCCTGAGNNAGCGGCCACTGNTCNACCCAAACNGGNTTTTGG 2901 chr2qtel1M 532294 GTTTTCCATTGGATAGGAACAAGTGAAAGTGTTGGCAGGCCTTCAACAGC 532343 i? vv vi i i -------? iv v -- i C HERVK14C#LTR/ 2900 GTCNTCCATTTTAAGGGAATAGG-------NTCTGGAGGC--TCAACAGT 2860 chr2qtel1M 532344 AGCCCTGCTTAAAAA 532358 i viv i C HERVK14C#LTR/ 2859 GGCCGCCCCTAAAAA 2845 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.80 CpG sites = 106, Kimura (unadjusted) = 39.50 Transitions / transversions = 0.83 (106/127) Gap_init rate = 0.06 (48 / 835), avg. gap size = 1.38 (66 / 48) 21 0.00 0.00 0.00 chr2qtel1M 534812 534834 (465166) (A)n#Simple_repeat 1 23 (0) m_b96s252i6 3566 chr2qtel1M 534812 AAAAAAAAAAAAAAAAAAAAAAA 534834 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAA 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 1064 30.83 1.29 1.29 chr2qtel1M 535346 535966 (464034) C L1M5_orf2#LINE/L1 (1596) 1698 1078 m_b96s551i10 3567 chr2qtel1M 535346 AAATCCCAATTGGTTGTAGTGTACTATCCTGCTCATAAGTTGCTGTAATC 535395 i v ii ii i vi i vi v v C L1M5_orf2#LIN 1698 AAACCCCACTTGGTCATGATGTATTATCCTTTTTATATATTGCTGGATTC 1649 chr2qtel1M 535396 TCTTTGCTAATATGTTATTTAGAATTTGTGCATCAGTATTCAACAGGGAT 535445 vv v i ? i v vi i vv C L1M5_orf2#LIN 1648 GATTTGCTAATATTTTGTTNAGGATTTTTGCATCTATGTTCATGAGGGAT 1599 chr2qtel1M 535446 ATTTGTCTATAATTTTTTTTTCTCTTTTAGCTCT---TCTTGTTTTAGGT 535492 v i i - v v vv --- ?v - C L1M5_orf2#LIN 1598 ATTGGTCTGTAATTTTCTTTTCT-TGTAATGTCTTTGTCNGGTTTT-GGT 1551 chr2qtel1M 535493 AGCAGTGCCATAACTGTGTTGTACAAGGAATATGGCAGTACTCCACCTAT 535542 v v i? iviv iv ii v v i vv v ii vi v C L1M5_orf2#LIN 1550 ATCAGGGTNATGCTGGCCTCATAAAATGAGTTGGGAAGTGTTCCCTCTTT 1501 chr2qtel1M 535543 TT---TTTCC--AAATAGTTGACGTACTATCGGAAGTAATTTGTTCTTTA 535587 --- i --i v vii vv i v v - v i C L1M5_orf2#LIN 1500 TTCTATTTTCTGGAAGAGTTTGTGTAAGATTGGTATT-ATTTCTTCCTTA 1452 chr2qtel1M 535588 AATGTTTGGGAGAATTCACTAGTAGATCCAACTGGCCCTGGAGATTTTTT 535637 v i ii v v v -- i C L1M5_orf2#LIN 1451 AATGTTTGGTAGAATTCACCAGTGAAGCCATCTGGGCCTGGAG--TTTTC 1404 chr2qtel1M 535638 TTTCTTAGAGAGTTCATTAATGATTTGTTCAATTTCTATTTCTGAAATGG 535687 v vi ii i- v ivvi v vviv v i C L1M5_orf2#LIN 1403 TTTGTGGGAAGGTTT-TTAATTACAAATTCAATTTCTTTAATAGATATAG 1355 chr2qtel1M 535688 AACTATTTAAATATTTTATTTCCTCTTCTATTAACCTGGGAAATTTGTAT 535737 ii i i v i i v?i i iii v v ? i- C L1M5_orf2#LIN 1354 GGCTATTCAGATTTTCTATTTCTTCTTGNGTCAGTTTTGGTAANTTGTG- 1306 chr2qtel1M 535738 TTTTTCTAAACATTCTTCCATTTCAGTTAGATTGTCAGAGTCACTGCCAT 535787 v iiv iv vi ii ? i v i i v C L1M5_orf2#LIN 1305 TTTTTCAAGGAATTTGTCCATTTCATCTAAGTTNTCAAATTTATTGGCAT 1256 chr2qtel1M 535788 AGTGTTGGGGGGGAAAGTTCCTAATTTTTGCTTTAATTTCTTTTTCATTG 535837 iv vvvivi v v ii v v ivi v v vvv iv C L1M5_orf2#LIN 1255 AAAGTTGTTCATAATATTCTCTTATTATCCTTTTAATGTCTGTAGGATCT 1206 chr2qtel1M 535838 GTAGTGAATTCATCCCTTTCATCTTTGATGTTGGTGATTTGTTTTTTTTT 535887 vv vi ii iii i i v i i i C L1M5_orf2#LIN 1205 GTAGTGATGTCTCCTTTTTCATTCCTGATATTGGTAATTTGTGTCTTCTC 1156 chr2qtel1M 535888 TCTTTTTCTCATCATCAAATGTGGGCAAAGATTTATTTGTTTTGTTAGTT 535937 i v v - i v ? vi i i ivi i ii i C L1M5_orf2#LIN 1155 TCTTTTTTTCTTGATC-AGTCTNGCTAGAGGTTTATCAATTTTATTGATC 1107 chr2qtel1M 535938 TTTTCATAAAACCGACTCTTAGTTTTATT 535966 v i ii i i i ii C L1M5_orf2#LIN 1106 TTTTCAAAGAACCAGCTTTTGGCTTCGTT 1078 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.86 CpG sites = 102, Kimura (unadjusted) = 41.18 Transitions / transversions = 1.17 (102/87) Gap_init rate = 0.02 (11 / 620), avg. gap size = 1.45 (16 / 11) 218 30.19 6.85 4.70 chr2qtel1M 537262 537407 (462593) MIRc#SINE/MIR 83 231 (37) m_b96s601i0 3568 chr2qtel1M 537262 AGCTGCTGGGATTTGGGTCAAGTCACTCAATCCCTCTGAGC--TGGTGGC 537309 - v ii v v i i i --ii vv MIRc#SINE/MIR 83 AGCTG-TGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTC 131 chr2qtel1M 537310 CTGAGGTGTACAAGAAGTGAGAATGA-AGTTTCT-TTCTGTGTGATCCCA 537357 v vv ---- i i i i - i vi -ii iv - i i MIRc#SINE/MIR 132 CTCATCTGTA----AAATGGGGATAATAATACCTGCCCTGCCT-ACCTCA 176 chr2qtel1M 537358 ---GGTTGACTGTGAGAATCCAATGTATT--TGTGCATGAAGGT-CATTA 537401 --- -i i v viv -- iii i i- v i MIRc#SINE/MIR 177 CAGGGTTG-TTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTTTG 225 chr2qtel1M 537402 GAAACT 537407 v MIRc#SINE/MIR 226 TAAACT 231 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.11 CpG sites = 27, Kimura (unadjusted) = 40.38 Transitions / transversions = 1.80 (27/15) Gap_init rate = 0.09 (13 / 145), avg. gap size = 1.31 (17 / 13) 573 31.48 1.94 1.29 chr2qtel1M 537479 537787 (462213) L1ME3Cz_3end#LINE/L1 22 332 (665) m_b96s551i11 3569 chr2qtel1M 537479 GAACTGCCTCAAATTTATAGGAATGCAAGCCATTCTCCAATTGATAAATG 537528 v iv iv i --v v --vi v v L1ME3Cz_3end# 22 GAACTCCTACAAATCAATAAGAA--AAAGACA--ACCCAATAGAAAAATG 67 chr2qtel1M 537529 GTCAAAGGATTTAAACAGACAAATTTCAGATGAAAAAATAAAAATCATTT 537578 v v i i v iv v ii ivvi viiiv L1ME3Cz_3end# 68 GGCAAAGGATATGAACAGGCAATTCACAGAAGAGGAAACCCGAATGGCCA 117 chr2qtel1M 537579 CTAGTCCTATGAAAAAATGCTCTAAATCACTA-TGGTCAGAGAAATGTAA 537627 v iv v i v vv - ii i i L1ME3Cz_3end# 118 ATAAACATATGAAAAGATGCTCAACCTCACTAGTAATCAGGGAAATGCAA 167 chr2qtel1M 537628 ATTAAGACACCTCTGAGGTACCA---GATATT--TCAGATTGGCTAAGAT 537672 i ?v vv i ---v i ii-- v i L1ME3Cz_3end# 168 ATTAAAACNACAATGAGATACCATTTCACACCCATCAGATTGGCAAAAAT 217 chr2qtel1M 537673 GACAGGGAAAGATAATGATGTATGTTGAAGGGAATGGGGAAAAACTGGGA 537722 vvv ii vvv i iviivi iv i i v i v i L1ME3Cz_3end# 218 TTAAAAGTCTGACAATACCAAGTGTTGGCGAGGATGTGGAGAAACGGGAA 267 chr2qtel1M 537723 CACTAATACATTGTTGGTGGAGTTGTGAATTGATCCAGTAATTCTGGAAA 537772 v v i i iiv i i v iiv i i i L1ME3Cz_3end# 268 CTCTCATACACTGCTGGTGGGAGTGTAAATTGGTACAACCACTTTGGAGA 317 chr2qtel1M 537773 GCAATATGGAACTAT 537787 v v v L1ME3Cz_3end# 318 GCAATTTGGCAATAT 332 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.09 CpG sites = 49, Kimura (unadjusted) = 41.65 Transitions / transversions = 1.04 (49/47) Gap_init rate = 0.02 (7 / 308), avg. gap size = 1.43 (10 / 7) 717 32.52 1.92 0.95 chr2qtel1M 537513 537928 (462072) L1ME4a_3end#LINE/L1 56 475 (396) m_b96s551i12 3569 chr2qtel1M 537513 CTCCAATTGATAAATGGTCAAAGGATTTAAACAGACAAATTTCAGATGAA 537562 i v v v iv i v iv i v L1ME4a_3end#L 56 CCCCAATAGAAAAATGGGCAAAGGACATGAACAGACAATTCACAAAAGAA 105 chr2qtel1M 537563 AAAATAAAAATCATTTCTAGTCCTATGAAAAAATGCTCTAAATCACTA-T 537611 i v viiivv iv v ? i v vv - L1ME4a_3end#L 106 GAAATACAAATGGCCAATAAACATATGAAAANATGTTCAACCTCACTAGT 155 chr2qtel1M 537612 GGTCAGAGAAATGTAAATTAAGACACCTCTGAGGTACCA-----GATATT 537656 ii i i i v vv i -----v iv v L1ME4a_3end#L 156 AATCAAAGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCTA 205 chr2qtel1M 537657 TCAGATTGGCTAAGATGACAGGGAAAGATAATGATGTATGTTGAAGGGAA 537706 i v vvv ii vv ivivvi iv i ii L1ME4a_3end#L 206 TCAAATTGGCAAAGATTTAAAAGATTGATAATACCCAGTGTTGGCGAGGG 255 chr2qtel1M 537707 TGGGGAAAAACTGGGACACTAATACATTGTTGGTGGAGTTGTGAATTGAT 537756 v ?i v v v v i i iiv i i L1ME4a_3end#L 256 TGTGGNGAAACGGGCACTCTCATACACTGCTGGTGGGAGTGTAAATTGGT 305 chr2qtel1M 537757 CCAGTAATTCTGGAAAGCAATATGGAACTATGCCTGAAGGGCTATCACAC 537806 v iivv ii v v v iv v ii iv v v v L1ME4a_3end#L 306 ACAACCTTTCTGGAGGGCAATTTGGCAATATGTATCAAAAGCCTTAAAAA 355 chr2qtel1M 537807 TGTGTATGACCTTTGATCCAGCAGTGTCTCTACTGAACCTGTTTCCCAAA 537856 ?i iv i i i vi v v iiivv v v i i L1ME4a_3end#L 356 TGTNCATACCCTTTGACCCAGTAATTCCACTTCTAGGAATTTATCCTAAG 405 chr2qtel1M 537857 GAGATCAT-AACGA-ATGGAAAAGGACTTCCACATGTGCAAAAATGTTTG 537904 i v - iv -i ? v i i ---- i ii ii L1ME4a_3end#L 406 GAAATAATCAGAGATGTGNACAAAGATTT----ATGTACAAGGATGTTCA 451 chr2qtel1M 537905 TAGCTGCCTTTTCTGTAGTGGAGA 537928 v v v v i i i i v L1ME4a_3end#L 452 TCGCAGCATTATTTATAATAGCGA 475 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 43.94 CpG sites = 68, Kimura (unadjusted) = 43.94 Transitions / transversions = 1.03 (68/66) Gap_init rate = 0.02 (8 / 415), avg. gap size = 1.50 (12 / 8) 12 19.15 2.63 2.63 chr2qtel1M 538182 538219 (461781) (ATGAAT)n#Simple_repeat 1 38 (0) m_b96s252i7 3570 chr2qtel1M 538182 ATGAAATATGAAAATGATTATGCATAT-ATTTTGAAAAT 538219 - v v v - v v v (ATGAAT)n#Sim 1 ATG-AATATGAATATGAATATGAATATGAATATGAATAT 38 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 219 30.23 4.65 0.00 chr2qtel1M 544430 544515 (455485) MIR3#SINE/MIR 116 205 (3) m_b96s601i1 3571 chr2qtel1M 544430 GAATCTCAGTTTCC-CATTTGTACAATGAGTGGGAGGCGCTCCATGGCCT 544478 iii - i v v vv vi vv ii MIR3#SINE/MIR 116 GGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCT 165 chr2qtel1M 544479 TGTAGGTCCCTTCCCG---TGATCATCTGGGATCCTGTAA 544515 ivv v --- ivv iv i i i MIR3#SINE/MIR 166 CTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTATGA 205 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.21 CpG sites = 13, Kimura (unadjusted) = 39.21 Transitions / transversions = 1.00 (13/13) Gap_init rate = 0.02 (2 / 85), avg. gap size = 2.00 (4 / 2) 331 27.59 6.90 0.00 chr2qtel1M 544617 544732 (455268) C L2b_3end#LINE/L2 (11) 455 332 m_b96s601i2 3572 chr2qtel1M 544617 CAGCAAACTTTTA---AGTGCCTGCTATCAGCCAGACCCTGGGCTGTGCC 544663 i iv --- i i i vv i ? v iv v C L2b_3end#LINE 455 CAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCG 406 chr2qtel1M 544664 CCAGGAACATAAAGAGAAACAAGG--GACT---TCCCTGCTCTCATGGAG 544708 ii i i i iv ivi i-- ?--- i i C L2b_3end#LINE 405 CTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGGAG 356 chr2qtel1M 544709 GTCACAGACACCTGGGGCAGACAG 544732 v v vvv v C L2b_3end#LINE 355 CTCACAGTCTAGTGGGGGAGACAG 332 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.18 CpG sites = 18, Kimura (unadjusted) = 35.91 Transitions / transversions = 1.29 (18/14) Gap_init rate = 0.03 (3 / 115), avg. gap size = 2.67 (8 / 3) 453 28.15 13.30 3.94 chr2qtel1M 544870 545102 (454898) C MIRb#SINE/MIR (0) 268 15 m_b96s601i3 3573 chr2qtel1M 544870 AATACCATACCTAGCATTTATACAGCACCTGCT--GTGACATGCAGTGTG 544917 vi v v v vv i i i -- v v v C MIRb#SINE/MIR 268 AATAATAGAGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTG 219 chr2qtel1M 544918 TCA------------GTATTGTCTCATTTTATCCTCATGAGAACCCTAGG 544955 ii ------------ i i v ii v iv C MIRb#SINE/MIR 218 CTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCG 169 chr2qtel1M 544956 ACTCGGGTGCCATTATTGTGCCCTTCTTATAGATAAAGTCACTGAGGCAG 545005 vvii --- i v v i i i i vv vv C MIRb#SINE/MIR 168 AGGTAGGT---ATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC 122 chr2qtel1M 545006 ACAGAGGT-------CTTGT---AAGTTGCGTAGC----AGATTGCTGAG 545041 v ------- i--- i ii ii ---- ii v v C MIRb#SINE/MIR 121 AGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAG 72 chr2qtel1M 545042 GTGGGAT--GAACCCTCAGGTCTTGCTGA-TTGAAGGCCCTGTTCGTACT 545088 vi -- -- vv - iv i ----- i C MIRb#SINE/MIR 71 CCGGGATTCGAACCC--AGGTCTGTCTGACTCCAAAGCC-----CGTGCT 29 chr2qtel1M 545089 TTTCTCCTTGTACC 545102 i ii vi i C MIRb#SINE/MIR 28 CTTTCCACTGCACC 15 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.75 CpG sites = 35, Kimura (unadjusted) = 36.17 Transitions / transversions = 1.25 (35/28) Gap_init rate = 0.07 (17 / 232), avg. gap size = 2.41 (41 / 17) 584 31.84 7.42 1.20 chr2qtel1M 546253 546643 (453357) L1ME5_3end#LINE/L1 59 473 (468) m_b96s551i13 3574 chr2qtel1M 546253 CAGTTGATAAATGGTCAAAGGATTTGAAGTGACAATTTTCAGATGAAAAA 546302 i v v v v vv i v v ii L1ME5_3end#LI 59 CAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAGGAA 108 chr2qtel1M 546303 GCAAAAATCATTTCTAGTCCTATGAAAAAATGCTCTAAATCACTATTGGT 546352 i vvi vvii vvi iv v i i v v i v ii L1ME5_3end#LI 109 ACCCGAAAGGCTAACAAGCATATGAAGAGATGCTCAAACTCATTAGTAAT 158 chr2qtel1M 546353 CAGAAAAACGTAAATTAAAACAACGCTGAGA---------ATACC--TCA 546391 i i i iv --------- i -- i L1ME5_3end#LI 159 CAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCTATTA 208 chr2qtel1M 546392 GAGTGGCTAACATGACAGGGAAAGATAATGATGA-TGT-----ATGTTGA 546435 v v v v v ii vvi vii - ----- v v v L1ME5_3end#LI 209 GACTGGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTGGCGAGGATGT 258 chr2qtel1M 546436 AGGGA-AT-GGGACACTAATCCATTTTTGGTGGAATTGTGAATTGATCTA 546483 i - - i v v v i vi i v ii i i vi L1ME5_3end#LI 259 GGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACTGGTGCA 308 chr2qtel1M 546484 GTCATTCTGGAGAACAGTATGCAACTATGCCTAA--AAGTCTATCACACT 546531 i i i v --i vi i i i-- i iv vi i - L1ME5_3end#LI 309 GCCATTCTGGAGAGCAATCTG--GCAGTACTTAGTCAAATTAAGTATAC- 355 chr2qtel1M 546532 GTGCATAACCTTTGATCCAGCAGTGTCTCTACTGAACCTGTATCCCAAAG 546581 -- v v i i vi v v iiiv i L1ME5_3end#LI 356 --GCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATATCCCAAAG 403 chr2qtel1M 546582 AAA---TGATAAAGATCTTC-----CACATGTGCAAAAATGTTTATAGCC 546623 --- v i v i ivi-----v i i ii i v v L1ME5_3end#LI 404 AAATTCTCACACAGGTCCATAAGGGGACATGTACGAGGATGTTCATTGCA 453 chr2qtel1M 546624 GCCTTTTCTGTAGTGGAGAG 546643 v v i i v i L1ME5_3end#LI 454 GCGTTGTTTGTGGTGGCGGG 473 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.54 CpG sites = 67, Kimura (unadjusted) = 42.45 Transitions / transversions = 1.20 (67/56) Gap_init rate = 0.04 (14 / 390), avg. gap size = 2.43 (34 / 14) 16 5.20 0.00 0.00 chr2qtel1M 546945 546964 (453036) (A)n#Simple_repeat 1 20 (0) m_b96s252i8 3575 chr2qtel1M 546945 AAAAAAAAAAAAAAAAACAA 546964 v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAA 20 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 17 0.00 0.00 0.00 chr2qtel1M 548189 548209 (451791) (TGC)n#Simple_repeat 1 21 (0) m_b96s252i9 3576 chr2qtel1M 548189 TGCTGCTGCTGCTGCTGCTGC 548209 (TGC)n#Simple 1 TGCTGCTGCTGCTGCTGCTGC 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 12 8.87 10.53 2.44 chr2qtel1M 549906 549943 (450057) (CTCTC)n#Simple_repeat 1 41 (0) m_b96s252i10 3577 chr2qtel1M 549906 CTCACCT-TCCT-TTC-CTCCTCTACCCCTCCTCT-CTCTCC 549943 v - - i - - i - (CTCTC)n#Simp 1 CTCTCCTCTCCTCTCCTCTCCTCT-CCTCTCCTCTCCTCTCC 41 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.14 (5 / 37), avg. gap size = 1.00 (5 / 5) 19 11.56 0.00 0.00 chr2qtel1M 551325 551352 (448648) (T)n#Simple_repeat 1 28 (0) m_b96s252i11 3578 chr2qtel1M 551325 TTTATTTGCTTTTTTTTTTTTTTTTTTT 551352 v vi (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 28 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 185 23.36 2.08 15.29 chr2qtel1M 551376 551471 (448529) C OldhAT1#DNA/hAT-Ac (51) 2791 2707 m_b96s601i4 3579 chr2qtel1M 551376 AAAAGGGGAGGG--AAGAAGAGATAGGAAATTGGGGAAAGAGGAACCCCT 551423 v i -- v - i viv? i i ?v i C OldhAT1#DNA/h 2791 AACAGGAGAGGGGAAATAAGAGAT-GAACGGNGGGGAAAAAAGANACCTT 2743 chr2qtel1M 551424 AGTTTCCTGTTCACTTTGCCCTAGGTACTTCTGCCCACCCCCTCTCTC 551471 ----------- v v i i v iiv - C OldhAT1#DNA/h 2742 A-----------ACTGTGCCGTGGATTCTTTCCCCCACCCCCTC-CTC 2707 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.74 CpG sites = 10, Kimura (unadjusted) = 28.44 Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.15 (14 / 95), avg. gap size = 1.07 (15 / 14) 18 0.00 0.00 0.00 chr2qtel1M 551624 551643 (448357) (T)n#Simple_repeat 1 20 (0) m_b96s252i12 3580 chr2qtel1M 551624 TTTTTTTTTTTTTTTTTTTT 551643 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTT 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 273 33.73 5.41 4.37 chr2qtel1M 552566 553064 (446936) HERVS71#LTR/ERV1 6100 6603 (2375) m_b96s701i4 3581 chr2qtel1M 552566 GCTGCCCGCCAATGCCTGACTTGTGCCAAGGTGAATCCT--GCCCGTTCC 552613 v i v ii vii i i v i v i-- vv v HERVS71#LTR/E 6100 GCAGCTCTCCGGTGCACAACCTGCGCCCAGGTAAATGCCAAGCAAGGTCC 6149 chr2qtel1M 552614 CCAACTGTGCCT-GCCCTGCGCCCCCGAGGGCTATCACCCGGGGAACACT 552662 iv ivv i- v vv i i iiivvv i v i v v HERVS71#LTR/E 6150 TAAACCCAGCCCAGGCCACCGTCTCCGAAAAAACTCGCCAGGAGAAAAGT 6199 chr2qtel1M 552663 GGGAAGTTGATTTCACGGACATGGAATT---TCAGGCTCAAGGACATCGT 552709 i i i i vi ii ii---i i - v -vi HERVS71#LTR/E 6200 GGGAAATTGACTTTACAGAAGTAAAACCACACCGGGCT-AAGTACA-AAT 6247 chr2qtel1M 552710 TTTTTCTTGGTGTTTGTTGACACCTTCTCAGGATGGCCTGAAGCCTTTCC 552759 vii -i ii v v v v i v v HERVS71#LTR/E 6248 ACCTTCT-AGTACTAGTAGACACCTTCTCCGGATGGACTGAGGCATTTGC 6296 chr2qtel1M 552760 TGTGAGGTCCGAATCTGCTTTGATCACGACTAAGAAACTTGTAAC----T 552805 iiviiivv v i i--- v i- ivv v v v ---- HERVS71#LTR/E 6297 TACCGAAAACGAAACCGCC---AACACGG-TAGTTAAGTTTTTACTCAAT 6342 chr2qtel1M 552806 GAGATTATTCCCCAGTTTGGGCCCCCCTTCTCCC-TCGGATCTGACAATG 552854 i i i i ii v i - iv v v - v i i HERVS71#LTR/E 6343 GAAATCATCCCTCGATATAGG-CTGCCTGCTGCCATAGGGTCTGATAATG 6391 chr2qtel1M 552855 GCCCGGCCTTCATTTCTAAGGTTGTTCAGTCTCTGGCTAAAGCTCTTGG- 552903 v ii vvvvi v i vv viv i vi vii- HERVS71#LTR/E 6392 GACCGGCCTTCACCTCGCCCATAGCTCAGTCAGTCAGTAAGGCGTTAAAC 6441 chr2qtel1M 552904 GTTCA--GGTTGCGCCTTCACTGTGCTTATCGTCCACAAAGTTCGGGTCA 552951 i -- vv --- i i i v v i i v v HERVS71#LTR/E 6442 ATTCAACGGAAG---CTCCATTGTGCCTATCGACCCCAGAGCTCCGGGCA 6488 chr2qtel1M 552952 GGTAGAAAGGATGAATGGGACACTGAAGGAGCACATTT------CTAAGC 552995 v v iv v v - ii i vi ------i v HERVS71#LTR/E 6489 GGTAGAACGCATGAACCGCACCCT-AAAAAACACTCTTACAAAATTAATC 6537 chr2qtel1M 552996 T------CCGGTTGGACATTGGCATCCCTAGGTGGG-CTTCTTCCCTTTG 553038 ------ - ? v --------- ii - i i v HERVS71#LTR/E 6538 TTAAAAACCGG-TGNAAAT---------TAGGTAAGTCTCCTTCCTTTAG 6577 chr2qtel1M 553039 CCCTCTTTAGGGCCAGGTGTATTCCT 553064 vi i iv i ii HERVS71#LTR/E 6578 CCCTACTTAGAGTAAGGTGCACCCCT 6603 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 43.42 CpG sites = 87, Kimura (unadjusted) = 46.11 Transitions / transversions = 1.18 (87/74) Gap_init rate = 0.06 (32 / 498), avg. gap size = 1.53 (49 / 32) 17 8.91 0.00 0.00 chr2qtel1M 555685 555708 (444292) (T)n#Simple_repeat 1 24 (0) m_b97s252i0 3582 chr2qtel1M 555685 TTTTTTTTTTGTGTTTTTTTTTTT 555708 v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTT 24 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 20 6.76 0.00 0.00 chr2qtel1M 558086 558116 (441884) (GACAGA)n#Simple_repeat 1 31 (0) m_b97s252i2 3583 chr2qtel1M 558086 GAGAGAGACAGGGACAGAGACAGAGACAGAG 558116 v i (GACAGA)n#Sim 1 GACAGAGACAGAGACAGAGACAGAGACAGAG 31 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 12 30.70 0.00 4.84 chr2qtel1M 558081 558145 (441855) (GAGGGA)n#Simple_repeat 1 62 (0) m_b97s252i1 3584 chr2qtel1M 558081 GAGGTGAGAGAGACAGGGACAGAGACAGAGACAGAGGGAGAATAAGATGG 558130 - i v -- iv iv ivi v (GAGGGA)n#Sim 1 GAGG-GAGAGGGAGAGGG--AGAGGGAGAGGGAGAGGGAGAGGGAGAGGG 47 chr2qtel1M 558131 TGATGGTGATGGTGA 558145 v v v v v (GAGGGA)n#Sim 48 AGAGGGAGAGGGAGA 62 Matrix = Unknown Transitions / transversions = 0.50 (5/10) Gap_init rate = 0.05 (3 / 64), avg. gap size = 1.00 (3 / 3) 268 22.83 10.74 2.29 chr2qtel1M 563754 563874 (436126) C HERVK22#LTR/ERVK (2280) 4557 4427 m_b97s701i0 3585 chr2qtel1M 563754 TCCCACTATTGCCTGTCCTTGAGGGTTAAAAGGTATGCCT-TGGTGTATA 563802 i i v i v v v - vi i v C HERVK22#LTR/E 4557 TTCTACTATGGCCTGTCCTTGGGGGTTATACGGGATGCCTGTGGAATGTT 4508 chr2qtel1M 563803 AAAT----CATACTGTG-CAAAAGTGTCAAATGTTTTAA----GTATAAG 563843 ii ---- ii- - v ii -i v i ---- i C HERVK22#LTR/E 4507 GGATGTTCCACG-TGTGACAAAATTGTTGAA-ATTGTGAGCTGGCATAAG 4460 chr2qtel1M 563844 -AGGACCATTGTCTGTTTT--TTGCTTGTGGCCC 563874 -v i v -- -i v C HERVK22#LTR/E 4459 CCGGACCATTATCAGTTTTAATT-TTTGTGGGCC 4427 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 26.50 CpG sites = 16, Kimura (unadjusted) = 27.82 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.07 (9 / 120), avg. gap size = 1.78 (16 / 9) 363 25.16 11.93 4.42 chr2qtel1M 565214 565741 (434259) C HERVK14C#LTR/ERVK (4024) 3410 2845 m_b97s701i1 3585 chr2qtel1M 565214 AAAATGTCATCCATGTAAAGAA-GATAACTT--TTTGGGGA-TGCTTT-T 565258 v i v - vv?v-- i ii - v i - C HERVK14C#LTR/ 3410 AATATGTCATCCATATAATGAATGATATANGAATCTGGAAACTGATCTCT 3361 chr2qtel1M 565259 CACTGGGCAAAGAGCA---GCAACATAA-TTTGACACATAGTAGGGTTGT 565304 ? v vii v v---v v ? - v ? ? ii i C HERVK14C#LTR/ 3360 NACAGGTTGAATAGCCTNCCCCACANAAGTTTGACAAATNGTNGGACTAT 3311 chr2qtel1M 565305 TTT-CATTCCCTTGGGCAA-ACTGTCCATTCATATCTTTTATAAGGCT-C 565351 iv- v vv - v v v ? ------- - C HERVK14C#LTR/ 3310 TCAACATGCCCTGCGGCAANACTTTCCAATGATANCT-------GGCTGC 3268 chr2qtel1M 565352 AGCTAAGTTAATGTT-------GGGACTGAAAAGGAAAATCTTTTCAA-- 565392 ? v vvv iv ------- i iv v i v - -- C HERVK14C#LTR/ 3267 NGGTTCCTTGTTGTTCATAGCAGGAATAGTAAAAGCAAAT-TTTTCAAAA 3219 chr2qtel1M 565393 TCCTCCT-TATCAGAGGGATAGAATAGAA----------AAATCTTAATA 565431 ?vv - iii i v v ---------- -- C HERVK14C#LTR/ 3218 TCNGGCTCTGCTAGAGGAATAGTAAAGAAGCAGTCCTTCAAATCT--ATA 3171 chr2qtel1M 565432 TCTATTTACCCGGGCC-TTCTCTAGGCAACTGAGTAGGAGATGGAATC-- 565478 v v ?--- -v v v vvi ii i ? v v -- C HERVK14C#LTR/ 3170 ACTATTAAN---GGCCAGTCTCTAGGAATCATGGCGGGGGANGGCAGCCC 3124 chr2qtel1M 565479 -AGGTGAAGTTCCC---TAGTTTCCAT--CTGT-TTTCCTTTTCTTAAAT 565521 -i v v ?v --- ? v v? -- i- vv vvi v i C HERVK14C#LTR/ 3123 TGGCTGCAGNGCCCCCATNGGTTGNATGACTGCATTGACGGCTCGTAAGT 3074 chr2qtel1M 565522 CC-TTAACATCTTCCATTTTTCAGATTTCTTTTTTCA--ACAAACACTGG 565568 v- i ?iv i vi i - i ? -- C HERVK14C#LTR/ 3073 CGGTTAGCATNCGCCATCTGCCGGATTT-TTTCTTNATTACAAACACTGG 3025 chr2qtel1M 565569 GGAATTCCAAGGACTTAGAA---GGTTTTAAAGTGTCC--GGTC-AACTG 565612 ? ? v-- i --- vi i? v --v? - i C HERVK14C#LTR/ 3024 NGAATTCCANGGAG--AAAATGTGGGCTCNATGTGTCCTTTNTCTAATTG 2977 chr2qtel1M 565613 CTCCTATAC--ATATCTAATAAGG---CCAATTTTATCTTTACTTAAAGG 565657 i i vv -- - ivi --- i - i v v?? iv C HERVK14C#LTR/ 2976 TTCTTTGACTAAT-TCCTGTAAGGCCCCCAGTTTT-TCCTGAGNNAGCGG 2929 chr2qtel1M 565658 -GACT-CTCTATCC-CACTGGTGTATCAGTTTTCCATTGGATAGGAACAG 565704 -v -? ? i -v ? ?v v vi i? vv vi i C HERVK14C#LTR/ 2928 CCACTGNTCNACCCAAACNGGNTTTTGGGTCNTCCATTTTAAGGGAATAG 2879 chr2qtel1M 565705 GTGAAAGTGTTGGCAGGTTCAACA--AGC--CCCTTAAAAA 565741 -------? iv v i --i -- i C HERVK14C#LTR/ 2878 G-------NTCTGGAGGCTCAACAGTGGCCGCCCCTAAAAA 2845 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 32.13 CpG sites = 53, Kimura (unadjusted) = 33.06 Transitions / transversions = 0.72 (53/74) Gap_init rate = 0.11 (56 / 527), avg. gap size = 1.57 (88 / 56) 398 28.00 10.11 2.08 chr2qtel1M 565276 565720 (434280) C HERVK11#LTR/ERVK (4382) 3571 3092 m_b97s701i2 3585 chr2qtel1M 565276 CAACATAA-TTTGACACATAGTAGGGTTGTTT-TCATTCCCTTGGGCAA- 565322 -vi i v v i i -v vi v i- C HERVK11#LTR/E 3571 CAACATAAAGCTGGCAGATTGTAGGGCTATTTAGCATTCCCTGAGGAAGT 3522 chr2qtel1M 565323 ACTGTCCATTCATATCT-TTTATAAGGCTCAGCTAA--GTTAAT-GTTGG 565368 v v v v-vi ii - -- i --i i - v C HERVK11#LTR/E 3521 ACTTTCCATTGATAACGAGCTGCA-GGCTC--CTGATTATTGATAGATGG 3475 chr2qtel1M 565369 GACTGAAAAGGAAAATCTTTT-CAATCCTCCTTAT-CAGAGGGATA-GAA 565415 v v v i v i i- vvi -i i vi - C HERVK11#LTR/E 3474 TACAGTAAAAGCAAATTTTTCACAATCCGATTTATGTAAAGCAATATGAA 3425 chr2qtel1M 565416 TAGAAAAATCTT-AATATCTAT--TTACCCG-GGCCT-TCTCTAGGCAAC 565460 v i v - v v --i ivv - v- i i i vi C HERVK11#LTR/E 3424 AAAAACAATCTTTAAGATCAATAACTATGAGAGGCCAATTTTTAGGTATT 3375 chr2qtel1M 565461 TGAGTAGGAGATGGAAT--CAGGT--GAAGTTCCC--TAGTTTCCAT--C 565502 vi i i vv v -- i -- v vi -- v iv -- C HERVK11#LTR/E 3374 AAAGCAGGGGCAGGCATGCCGGGTTGGACGGCCCCCATAGGTTTAATTAC 3325 chr2qtel1M 565503 TGTTTTCCTT-TTCTTAAATCC-TTAACATCTTCCATTTTTCAGATTTCT 565550 v iv vv v-ii v- v iv i vi v C HERVK11#LTR/E 3324 AGCATTAATGGCCCTTAAATCGGTTACCATCCGCCACTTGCCTGATTTCT 3275 chr2qtel1M 565551 TTTTT-CAACAAACACTGGGGAATTCCA--AGGACTTAGAAGGTTTTAAA 565597 - v v v i --i vvv ii v C HERVK11#LTR/E 3274 TTTTTACTAGAAACACAGGAGAATTCCAGGGGGAAAGAGAAGGTTCCACA 3225 chr2qtel1M 565598 GTGTCCGGT--CAACTGCTCCTATACATATCTAA-TAAGG---CCAATTT 565641 v vi vi --i i vv v vv iv i- i --- i C HERVK11#LTR/E 3224 TTTCCAAGTTGTAACTGTTCAGAAACCAATTGAGTTAAAGCCTCCAGTTT 3175 chr2qtel1M 565642 TATCTTTACTTAAAGGG---ACT-CTCTATCC-CACTGGTGTATCAGTTT 565686 - v-- v --- - vv -v v i v C HERVK11#LTR/E 3174 T-TCTTTAG--AAAGCGGCCACTGCTGAATCCAAACGGGTGTGTCAGATT 3128 chr2qtel1M 565687 TCCATT------GGATAGGAACAGGTGAAAGTGTTGGCAG 565720 ------ v --- i i - C HERVK11#LTR/E 3127 TCCATTGTAAAGGGATAGGATCAGG---AGGCG-TGGCAG 3092 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 34.25 CpG sites = 53, Kimura (unadjusted) = 35.27 Transitions / transversions = 0.77 (53/69) Gap_init rate = 0.09 (38 / 444), avg. gap size = 1.45 (55 / 38) 415 35.75 3.24 1.41 chr2qtel1M 568829 569106 (430894) HERV1_I#LTR/ERV1 8210 8492 (309) m_b97s701i3 3586 chr2qtel1M 568829 TATATATATATATAACAGATTAATTCAACTGCAAACAGTCTTAGAGGTAA 568878 v i i vv v v v vvi i i vi ii v HERV1_I#LTR/E 8210 TATTTACATGTTAAACCGAATCATAAGATTGCAAGCAGTACTAGAAATCA 8259 chr2qtel1M 568879 CAACTAACCAAACTGCTCAGGCCCTTAATCTATTAGCCAATCAAGCCACC 568928 i iii iv v i ii i vi i ii vv i ? HERV1_I#LTR/E 8260 TAGTCAATGAAACAGCCCGAGCCTTGGATTTGCTAGCCATACAGGCNACC 8309 chr2qtel1M 568929 CAGACAAGAGAAGTAGTTTTATAACCTAGATTGGTTTCAAATTACCTGTT 568978 ii v ivi v vvi vv ii i iv i i i i vi HERV1_I#LTR/E 8310 CAGATGAGAGATGCCATATATCAAAATAGGCTAGCATTAGACTATCTCCT 8359 chr2qtel1M 568979 AGCAGAGGAAGGAGGAG-----GGAAGGGTC--TGTGAGAAACAATGTTG 569021 vvvi ----- ? iiv i-- v v? -- i HERV1_I#LTR/E 8360 AGCCTCAGAAGGAGGAGTTTGTGGNAAACTTAATTTGACNAAC--TGCTG 8407 chr2qtel1M 569022 TATGCAAATTGATGACAATGGACAACCAGTAAAAGAAATTACTA--AGGT 569069 iv i i vi v v v vi i i-- - HERV1_I#LTR/E 8408 CTTACAAATCGATGACAATGGAAGAGCTGTCATGGAAATCACTGCCAGG- 8456 chr2qtel1M 569070 CATTCGCAGGATAGTTCATGTGACTATACAAATTTGG 569106 - v v i v ii vv vi v i ii HERV1_I#LTR/E 8457 -ATGCGGAAGTTAGCCCATGTCCCGGTCCAGACCTGG 8492 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 49.61 CpG sites = 55, Kimura (unadjusted) = 51.12 Transitions / transversions = 1.28 (55/43) Gap_init rate = 0.03 (7 / 277), avg. gap size = 1.86 (13 / 7) 11 26.71 4.08 0.00 chr2qtel1M 571103 571151 (428849) (AGGTGG)n#Simple_repeat 1 51 (0) m_b97s252i3 3587 chr2qtel1M 571103 AGG-GGCGGTGGAGGGAGTGGGGCAGCCTG-GGAGGAGGTGGAGGTGGGG 571150 - v vi v v v viv - v i (AGGTGG)n#Sim 1 AGGTGGAGGTGGAGGTGGAGGTGGAGGTGGAGGTGGAGGTGGAGGTGGAG 50 chr2qtel1M 571151 G 571151 (AGGTGG)n#Sim 51 G 51 Matrix = Unknown Transitions / transversions = 0.38 (3/8) Gap_init rate = 0.04 (2 / 48), avg. gap size = 1.00 (2 / 2) 253 35.76 2.19 3.10 chr2qtel1M 572686 572913 (427087) L1ME4c_3end#LINE/L1 414 639 (191) m_b97s551i0 3588 chr2qtel1M 572686 TTAAAGGAGGGAAAGAG----ACCCACGTTGGAAAAATGTTTGTGGCAGC 572731 i i i i ---- iv ----- i ii v L1ME4c_3end#L 414 TCAAAAGAAGGAAAAAGCTATATGCACG-----AAGATGTTCATTGCAGC 458 chr2qtel1M 572732 TCTTTCCATAGTGACATGAAACTGGCAAATGAG-TGGATGCCCATCAGTG 572780 vi v ii i ii ivi i - ii v- ii i v i i L1ME4c_3end#L 459 GTTATTTATAATAGCGAAAAATTGG-AAACAACCTAAATGTCCAACAATA 507 chr2qtel1M 572781 GGGGAATGGCTGAATAAGTTATGACATATGAATGTCTTGGAATGTTATTG 572830 i i i i ii i v? ivivv i vv L1ME4c_3end#L 508 GGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATATTATGC 557 chr2qtel1M 572831 TTCTATAAGAAATGATCAGCAGGATGATTTCAGAGAGGCCTAGAGAGTCT 572880 vv i v i v vi v v i viiv vii v i i i v L1ME4c_3end#L 558 AGCCATTAAAAATGATAATTATGAAGACTATGTAGCAACATGGAAAATGT 607 chr2qtel1M 572881 TAAATGAACTGAGGCTAAGTGCAATGAGCAGAA 572913 -v vv i v i v vi L1ME4c_3end#L 608 T-TATGATATAATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 49.43 CpG sites = 48, Kimura (unadjusted) = 51.33 Transitions / transversions = 1.55 (48/31) Gap_init rate = 0.04 (9 / 227), avg. gap size = 1.33 (12 / 9) 277 34.21 0.87 0.87 chr2qtel1M 572714 572828 (427172) L1ME3G_3end#LINE/L1 434 548 (376) m_b97s551i1 3588 chr2qtel1M 572714 AAAAATGTTTGTGGCAGCTCTTTCCATAGTGACATGAAACTGGCAAATGA 572763 ii ii v vi v iii i ii ivi i - ii L1ME3G_3end#L 434 AAGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGG-AAACAA 482 chr2qtel1M 572764 G-TGGATGCCCATCAGTGGGGGAATGGCTGAATAAGTTATGACATATGAA 572812 v- ii i i i i i i ii vv L1ME3G_3end#L 483 CCTAAATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCA 532 chr2qtel1M 572813 TGTCTTGGAATGTTAT 572828 iiiv ii L1ME3G_3end#L 533 TACTATGGAATACTAT 548 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 49.38 CpG sites = 31, Kimura (unadjusted) = 51.38 Transitions / transversions = 3.88 (31/8) Gap_init rate = 0.02 (2 / 114), avg. gap size = 1.00 (2 / 2) 13 26.49 5.80 1.39 chr2qtel1M 573084 573152 (426848) (CATTTT)n#Simple_repeat 1 72 (0) m_b97s252i4 3589 chr2qtel1M 573084 CATTTTCA--CTCTTTTTCATATATGTTTACATTTTACTTTGTCATTTT- 573130 --i v v vii v - v v - (CATTTT)n#Sim 1 CATTTTCATTTTCATTTTCATTTTCATTTTCATTTT-CATTTTCATTTTC 49 chr2qtel1M 573131 -TTCTCCTGTTTAATTTGATTTT 573152 - i v v i v v (CATTTT)n#Sim 50 ATTTTCATTTTCATTTTCATTTT 72 Matrix = Unknown Transitions / transversions = 0.50 (5/10) Gap_init rate = 0.06 (4 / 68), avg. gap size = 1.25 (5 / 4) 33 0.00 0.00 0.00 chr2qtel1M 573375 573402 (426598) (CA)n#Simple_repeat 1 28 (0) c_b97s251i0 3590 chr2qtel1M 573375 CACACACACACACACACACACACACACA 573402 (CA)n#Simple_ 1 CACACACACACACACACACACACACACA 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 604 32.89 4.76 2.43 chr2qtel1M 573613 574095 (425905) L1PREC2_orf2#LINE/L1 2431 2924 (370) m_b97s551i2 3591 chr2qtel1M 573613 AATATAATAAAGATGACAATACTCCCTAAACTAATCTATTTATTTAGTGC 573662 vi v i i v v i vi i ivv i i L1PREC2_orf2# 2431 AATATCGTTAAAATGGCCATACTGCCCAAAGCAATTTACAGATTCAATGC 2480 chr2qtel1M 573663 TATACAAATCAGACTCCCAAGAAAATATTTTAATGATCTAGAAAAAATAA 573712 v vv i v vi v vi i vv v iv L1PREC2_orf2# 2481 TATTCCTATCAAACTACCAATGACATTCTTCACAGAACTAGAAAAAACTA 2530 chr2qtel1M 573713 CAATAAAATTCATATGGAAGAACAAAAGGTCGAGAAT-CTCAAGGGAAT- 573760 ivv vv v iv vv -vi v - L1PREC2_orf2# 2531 TTTTAAAATTCATATGGAACCAAAAAAGAGCCCGAATAGCCAAGGCAATC 2580 chr2qtel1M 573761 -TAATGAAAAACAAAAACAAA--TGGAGGTGGC---CTAGCTGTATCTAA 573804 - vv --- i -- iiv --- v i - ii v L1PREC2_orf2# 2581 CTAAGCAAA---AAGAACAAAGCTGGAGGCATCACGCTACCCG-ACTTCA 2626 chr2qtel1M 573805 AACTATATTATAAAGCAGCAGTCACTAAAACCATTTGGTATTGGCTAAGA 573854 i i ii vi v i viiv i ivv i L1PREC2_orf2# 2627 AACTATACTACAGGGCTACAGTAACCAAAACAGCATGGTACTGGTACAAA 2676 chr2qtel1M 573855 AATAGATTAGTTGATCAGTGGAATAGGTTAG---GTTCACAAGACAAAAT 573901 i ivvi v i i i iv --- ii v - i iii L1PREC2_orf2# 2677 AACAGACACATAGACCAATGGAACAGAATAGAGAGCCCAGAA-ATAAGGC 2725 chr2qtel1M 573902 AGT-CAACTATAGCAGTCTAGTGTTTGACAAACC---CAAAGATCCTAAC 573947 v i- v i i vi ii v i v --- i -- v i L1PREC2_orf2# 2726 CGCACACCTACAACCATCTGATCTTCGACAAAGCTGACAAAAA--CAAGC 2773 chr2qtel1M 573948 TTTTGGGATAAGAATTCATTATT---TGGCTAGT-TTGGGAAAACTAGAA 573993 vv v - i i vi --- iiv i -i v i -- L1PREC2_orf2# 2774 AATGGGGA-AAGGACTCCCTATTCAATAAATGGTGCTGGGATAACTGG-- 2820 chr2qtel1M 573994 ATTAG---TATGGCAGAA-ATTAGGCATGGGCCCACACTTAACACTGTAT 574039 -i --- - - iiivv i viv i v ii L1PREC2_orf2# 2821 -CTAGCCATAT-GCAGAAGATTGAAACTGGACCCCTTCCTTACACCATAT 2868 chr2qtel1M 574040 ACCAAGATAAGATCAAAATGGGTCCATGATTTAGGCATAAAGAACGAGAT 574089 v i v iv i i iv v i iiii ivv i i i L1PREC2_orf2# 2869 ACAAAAATCAACTCAAGATGGATTAAAGACTTAAATGTAAAACCCAAAAC 2918 chr2qtel1M 574090 TATAAA 574095 L1PREC2_orf2# 2919 TATAAA 2924 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 43.41 CpG sites = 87, Kimura (unadjusted) = 44.57 Transitions / transversions = 1.28 (87/68) Gap_init rate = 0.05 (24 / 482), avg. gap size = 1.46 (35 / 24) 299 30.25 2.23 3.98 chr2qtel1M 574183 574361 (425639) L1P3_orf2#LINE/L1 3073 3248 (46) m_b97s551i3 3592 chr2qtel1M 574183 ATTAT-ATCAAATTAAATAGAAGGGAAGCAACAAATTGGGAAAACATTTT 574231 i - i v i i --- v v v i v i v L1P3_orf2#LIN 3073 ACTATCATCAGAGTGAACAG---GCAACCTACAGAATGGGAGAAAATTTT 3119 chr2qtel1M 574232 CACAGTTAAAGGTTCTGATAAAGGCCTTATTTCCAAAATATATCAGAGAA 574281 ii i iv vvvv i v v v i v - ii L1P3_orf2#LIN 3120 TGCAATCTATCCATCTGACAAAGGGCTAATATCCAGAATCTA-CAAGGAA 3168 chr2qtel1M 574282 TTCACTCTAATTTATAAGAAAT---CAAGCCATTCTCCAATTGATAAATG 574328 i i vv v i v--- i v -- i - ii v i L1P3_orf2#LIN 3169 CTTAAACAAATTTACAAGAAAAAAACAAACAA--CCCCA-TCAAAAAGTG 3215 chr2qtel1M 574329 GTCAAAGGATATGAATTTACAATTTTCAGATGA 574361 v i ivv v i i v L1P3_orf2#LIN 3216 GGCGAAGGATATGAACAGACACTTCTCAAAAGA 3248 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.26 CpG sites = 26, Kimura (unadjusted) = 39.21 Transitions / transversions = 1.00 (26/26) Gap_init rate = 0.05 (9 / 178), avg. gap size = 1.22 (11 / 9) 314 22.98 5.56 6.29 chr2qtel1M 574200 574343 (425657) L1MC_orf2#LINE/L1 3088 3230 (64) m_b97s551i4 3592 chr2qtel1M 574200 AGAAGGGAAGCAACAAATTGGGAAAACATTTTCACAGTTAAAGGT---TC 574246 i iv v i i i v v ii --- ii--- L1MC_orf2#LIN 3088 AAAAGACAAGCCACAGACTGGGAGAAAATATTTGCA---AAAGACATATC 3134 chr2qtel1M 574247 TGATAAAGGCCTTATTTCCAAAATATATCAGAGAATTC-----ACTCTAA 574291 v vv v - i i ----- - L1MC_orf2#LIN 3135 TGATAAAGGACTGTTATCCAAAATATA-CAAAGAACTCTTAAAACTC-AA 3182 chr2qtel1M 574292 TTTATAAGAAATCAAGCCATTCTCCAATTGATAAATGGTCAAAGGATATG 574341 -iv v i v ---i i ? v v i iv L1MC_orf2#LIN 3183 -CAATAAGAAAACAAACAA---CCCGATTNAAAAATGGGCAAAAGACCTG 3228 chr2qtel1M 574342 AA 574343 L1MC_orf2#LIN 3229 AA 3230 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 27.00 CpG sites = 17, Kimura (unadjusted) = 28.03 Transitions / transversions = 1.21 (17/14) Gap_init rate = 0.08 (11 / 143), avg. gap size = 1.55 (17 / 11) 1047 29.82 4.93 5.10 chr2qtel1M 574257 574885 (425115) L1MD2_3end#LINE/L1 1 628 (478) m_b97s551i5 3592 chr2qtel1M 574257 CTTATTTCCAAAATATATCAGAGAATTC-----ACTCTAATTTATAAGAA 574301 ?i v i i - i i ----- - iv-i i L1MD2_3end#LI 1 CTNGTATCTAGAATATAT-AAAGAACTCTCAAAACTC-AACA-GTAAAAA 47 chr2qtel1M 574302 ATCAAGCCATTCTCCAATTGATAAATGGTCAAAGGATATGAATTTACAAT 574351 v i v --- iiv v i i ivv v L1MD2_3end#LI 48 AACAAACAAT---CCAATTAGAAAATGGGCAAAAGACATGAACAGACATT 94 chr2qtel1M 574352 TTTC---AGATGATA---AAATTGAAACTATTCCACTTATATGAAAG--T 574393 iv --- v --- i v v v vv ----- i i-- L1MD2_3end#LI 95 TCACCGAAGAGGATATACAGATGGCAAATAAGC-----ACATGAAAAGAT 139 chr2qtel1M 574394 GTTTCAAATCACTATTGATCAGGGAAATGCAAATTAAGACAACTCTGAGA 574443 iv v i viv i i v vv L1MD2_3end#LI 140 GTTCAACATCATTAGCCATTAGGGAAATGCAAATTAAAACCACAATGAGA 189 chr2qtel1M 574444 TACCACTACACATCTGTCAGATTGGCTAAGATGACAGGAAAAATTAATGA 574493 i i i v i ------ v i L1MD2_3end#LI 190 TATCACTACACACCTATCAGAATGGCTAAAAT------AAAAAATAGTGA 233 chr2qtel1M 574494 ------TGAATGTTGGAAGGTATGAGGGAAAACTGGGACACTGATGTATT 574537 ------ii i vii v v ii iv v ii L1MD2_3end#LI 234 CAACACCAAATGCTGGCGAGGATGCGGAGAAACTGGATCACTCATACATT 283 chr2qtel1M 574538 GTTGATGGAGTTGT-GAATGAAACCAACCATTCTGGAGAGCAATTTGGAA 574586 i i iiv -i iv - i i i i i v L1MD2_3end#LI 284 GCTGGTGGGAATGTAAAATGGTA-CAGCCACTCTGGAAAACAGTTTGGCA 332 chr2qtel1M 574587 CTATTATCAGAAAGTTATCACACTATGCA--TACCCTTTGATCCAGCAGT 574634 v - v i v ii ---- vi -- v vi i i L1MD2_3end#LI 333 GT-TTCTTATAAAACTA----AACATGCANTTACCATACGACCCAGCAAT 377 chr2qtel1M 574635 GTTACTACTGGGCTTATACCCCAAAGAGAT----ACTAAAGAAGGGAAAG 574680 vvi vi v v i i i ---- v v vvviv v i L1MD2_3end#LI 378 TGCACTCTTGGGCATTTATCCCAGAGAAATGAAAACTTATGTTCACACAA 427 chr2qtel1M 574681 GAACCTGGATGTGCCAAAATGTTTGTGGCACCCCTGTTTGTAGTGGCCAG 574730 i v iii ---- ii i v ii i i i i i L1MD2_3end#LI 428 AAACCTGTACACG----AATGTTCATAGCAGCTTTATTCGTAATAGCCAA 473 chr2qtel1M 574731 AAACTGGAAAATGAA--TGGATGCCCATCAATTGGAGAATGGTTGGGTAA 574778 --v --iii i v iv v iiii L1MD2_3end#LI 474 AAACTGGAAA--CAACCCAAATGTCCTTCAACGGGTGAATGGTTAAACAA 521 chr2qtel1M 574779 ATCGTGGTATATGAATGTTATGGAATATTATTGTTCTGTAACAAATGAAC 574828 ii i vv iii i i vvv vi - v L1MD2_3end#LI 522 ACTGTGGTACATCCATACCATGGAATACTACTCAGCAATAA-AAAGGAAC 570 chr2qtel1M 574829 AGCAGGATGAATACAGAGA--GGCTTGAAGAGA-CTTACATGAACTGATG 574875 - v vv vi viv --ii i vi - i viv i - L1MD2_3end#LI 571 -GAACTATTGATACACGCAACAACTTGGATGGATCTCAAGGGAATT-ATG 618 chr2qtel1M 574876 CTCAGTGAAA 574885 v L1MD2_3end#LI 619 CTGAGTGAAA 628 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.49 CpG sites = 104, Kimura (unadjusted) = 39.18 Transitions / transversions = 1.41 (104/74) Gap_init rate = 0.07 (43 / 628), avg. gap size = 1.47 (63 / 43) 1412 26.47 2.91 3.85 chr2qtel1M 574260 574809 (425191) L1ME3G_3end#LINE/L1 4 548 (376) m_b97s551i6 3592 chr2qtel1M 574260 ATTTCCAAAATATATCAGAGAATTCACTCTAATTTATAAGAAATCAAGCC 574309 v i - i i viv v iv -- v L1ME3G_3end#L 4 ATATCCAGAATATAT-AAAGAACTCCTACAAATCAATAAGAAA--AAGAC 50 chr2qtel1M 574310 ATTCTCCAATTGATAAATGGTCAAAGGATATGAATTTACAATTTTCAGAT 574359 --vi v v v ivvi iv v L1ME3G_3end#L 51 A--ACCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAA 98 chr2qtel1M 574360 GATAAAATTGAAA---CTATTCCACTTATATGAAAG--TGTTTCAAATCA 574404 vi vv --- i v vv -- i-- i iv vv L1ME3G_3end#L 99 GAGGAAATACAAATGGCCAATAAAC--ATATGAAAAGATGCTCAACCTCA 146 chr2qtel1M 574405 CTATTGATCAGGGAAATGCAAATTAAGACAACTCTGAGATACCACTACAC 574454 v i i vv i viv L1ME3G_3end#L 147 CTAGTAATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTC 196 chr2qtel1M 574455 ATCTGTCAGATTGGCTAAGATGACAGGAAAAATTAATGAT---GAATGTT 574501 i ii v i v---vi i? i i ---? i L1ME3G_3end#L 197 ACCCATCAGATTGGCAAAAATT---TAAAAGNTTGATAATATCNAGTGTT 243 chr2qtel1M 574502 G--GAAGGTATGAGGGAAAACTGGGACACTGATGTATTGTTGATGGAGTT 574549 -- i i -- i v v v v ii i i i iiv L1ME3G_3end#L 244 GGCGAGGGTGT--GGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGT 291 chr2qtel1M 574550 GTGAATGAAACCAACCATTCTGGAGAGCAATTTGGAACTAT-TATCAGAA 574598 i viivv i ? i i v v - i - L1ME3G_3end#L 292 GTAAATTGGTACAGCCNTTTTGGAGGGCAATTTGGCAGTATCTATTA-AA 340 chr2qtel1M 574599 AGTTATCACACTATGCATACCCTTTGATCCAGCAGTGTTACTACTGGGCT 574648 v --- v v ii i i vii v ? ?v L1ME3G_3end#L 341 ATTT---AAAATGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNA 387 chr2qtel1M 574649 TATACCCCAAAGAGATACT---AAAGAAGGGAAAGGAACCTGGATGTGCC 574695 v i i ? i --- v viv viv ---? v i v L1ME3G_3end#L 388 TCTATCCTANAGAAATACTCGCACATGTGCACAAGGA---NGCATGTACA 434 chr2qtel1M 574696 AAAATGTTTGTGGCACCCCTGTTTGTAGTGGCCAGAAACTGGAAAATGAA 574745 ii ii v v vi i i v i i --v L1ME3G_3end#L 435 AGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAA--CAA 482 chr2qtel1M 574746 --TGGATGCCCATCAATTGGAGAATGGTTGGGTAAATCGTGGTATATGAA 574793 -- ii i v i iii ii vv L1ME3G_3end#L 483 CCTAAATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCA 532 chr2qtel1M 574794 TGTTATGGAATATTAT 574809 ii i L1ME3G_3end#L 533 TACTATGGAATACTAT 548 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.48 CpG sites = 77, Kimura (unadjusted) = 33.77 Transitions / transversions = 1.22 (77/63) Gap_init rate = 0.05 (28 / 549), avg. gap size = 1.32 (37 / 28) 16 5.27 0.00 0.00 chr2qtel1M 575321 575340 (424660) (A)n#Simple_repeat 1 20 (0) m_b97s252i5 3593 chr2qtel1M 575321 AAAAAAAAAAAAAAAAAGAA 575340 i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAA 20 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 26 0.00 0.00 0.00 chr2qtel1M 575385 575409 (424591) (AAT)n#Simple_repeat 1 25 (0) c_b97s251i1 3594 chr2qtel1M 575385 AATAATAATAATAATAATAATAATA 575409 (AAT)n#Simple 1 AATAATAATAATAATAATAATAATA 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 1103 31.33 2.47 1.89 chr2qtel1M 575423 575949 (424051) C L1ME4c_3end#LINE/L1 (294) 536 7 m_b97s551i7 3595 chr2qtel1M 575423 ATGTTCCACAACTTGTTCAGCCATTCCCCAATTGGCGAGCATCCATTCCA 575472 v i i ii i i v vi ii ii vviii C L1ME4c_3end#L 536 ATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAGGTTG 487 chr2qtel1M 575473 TTTCCACTTCTGTATTACCACAAAAAGAGCTGCTGCAATCATCGTTGCAC 575522 v i viii ii i v iv viii v v i ii C L1ME4c_3end#L 486 TTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTCGTGC 437 chr2qtel1M 575523 ATGTGGGTCCTTGTCTCTTTTTGATGATGTCTTTGGGATAAAGAGCCTGT 575572 i i v ii vii vi v v i i vvv v v C L1ME4c_3end#L 436 ATATAGCTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAATTCCCAGA 387 chr2qtel1M 575573 AGAGACACTTCTGGATCCAAGGGTATGCACAGTTTGATAGCCCTTTGGAC 575622 v iv i v i v v v v i i viv C L1ME4c_3end#L 386 AGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTCTTGATAC 337 chr2qtel1M 575623 ATAGTTCCAAATTATTCTCCACAATGGTTGGATCATTTCAGAATTCCCCC 575672 i v v ii i v v v i v i v ? v v C L1ME4c_3end#L 336 GTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACANTGCCACC 287 chr2qtel1M 575673 AACAATGCATTAGTATCTCACTTTT-CCACAACCACTCTAATATTTATCA 575721 i i v ?i vi v i- i ? v v i ii vivi C L1ME4c_3end#L 286 AGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGCATTGGGTA 237 chr2qtel1M 575722 TTATC--TTTTCCTGATCTTAGCCAATCTGAGAGGTATGAGGTGATAGCT 575769 -- iivi i v i i i v ii i ii i v C L1ME4c_3end#L 236 TTATCAATTTTTTAAATTTTTGCTAATTTAATAGGCGTAAAATGGTATCT 187 chr2qtel1M 575770 CAGAGTTA-TATAATTTGCATTTTTCTTATCAATAGTGATTTAGAGCATT 575818 vv i- v i i v i v i vv v i C L1ME4c_3end#L 186 CATTGTTGCTTTAATTTGCATTTCTTTGATTACTAGCGAGGTTGAACATT 137 chr2qtel1M 575819 TTTTCTTATAATT-----CTAATTGGCTTTAATTTCCTCATCTGAAAATT 575863 i v i iv ----- ? v----- v ? vi C L1ME4c_3end#L 136 TTTCCATGTGTTTGTTTACTANTTGT-----ATTTCCTCTTNTGTGAATT 92 chr2qtel1M 575864 GTCTGTTCCTATCCTTTGACTATATTATCAAGTAATGAA----TGATTTG 575909 v i v i - --- v ii---- ? v C L1ME4c_3end#L 91 GTCTGTTCATGTCCTTTGCCCAT-TTATC---TATTGGGGTCTTGATNTT 46 chr2qtel1M 575910 TAGTCTTATAAATTTGAAATAGTTCTTTATATATCTTAGA 575949 -v v vv i ?iv? C L1ME4c_3end#L 45 T-TTCTTATCAATTTGAATGAGCTCTTTATATANTANAGA 7 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.30 CpG sites = 89, Kimura (unadjusted) = 42.43 Transitions / transversions = 1.22 (89/73) Gap_init rate = 0.03 (15 / 526), avg. gap size = 1.53 (23 / 15) 2596 30.53 4.99 3.33 chr2qtel1M 575805 577990 (422010) C L1M5_orf2#LINE/L1 (0) 3294 1074 m_b97s551i8 3595 chr2qtel1M 575805 TGATTTAGAGCATTTTTTCTTATAATTCTAATTGGC---TTTAATTTCCT 575851 ?v v i v i iv --- --- v? v i C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTT---ATTGGCCATTTGNATATCTT 3248 chr2qtel1M 575852 CATCTGAAAATTGTCTGTTCCTATCCTTTGACTATATTATCAAGTAATGA 575901 v i vi v vvi i v i v - ?--- v i C L1M5_orf2#LIN 3247 CTTTTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTT-TN---TATTGG 3202 chr2qtel1M 575902 ATGATTTGTAGT---CTTATAAATTTGAAATAGTTCTTTATATATCTTAG 575948 i vi vv ---? vi ? v iv ii i C L1M5_orf2#LIN 3201 GTTGTTTGTCTTTTTNTTATTGANTTGTAGGAGTTCTTTATATATTCTGG 3152 chr2qtel1M 575949 AAAAGAAACTTTTATCAGATATACTGGCCATAAATATTTT-TCCCAGCTT 575997 v v iv i i ivv?iiii - ?ii C L1M5_orf2#LIN 3151 ATACGAGTCCTTTGTCAGATATATGTNTTGCAAATATTTTCTCCCANTCT 3102 chr2qtel1M 575998 TTTACTTCCCTCTTAATCTTGTTTTCTGGTGGTTTGTT--TGTGCAGAAA 576045 v vi v i v i v vv - vi - --? v i C L1M5_orf2#LIN 3101 GTGGCTTGCCTTTTCATTTTCTTAAC-GGTGTCTT-TTGANGAGCAGAAG 3054 chr2qtel1M 576046 CTTTTAATTTATG--GTAATCAAAGTTGTCCATTTTGCCTTTGACAATGT 576093 i - -- ? i v v i v vi v ------ C L1M5_orf2#LIN 3053 TTTTTAATTT-TGATGNAGTCCAATTTATCAATTTTTTCTTTTA------ 3011 chr2qtel1M 576094 TGTCTAGTGCTTCCT-TGCCC------ATAAATTCCTCCCTTCTGCAAAG 576136 vi ? ii - i ------ v iii v v?iv i C L1M5_orf2#LIN 3010 TGGTTNGTGCTTTTTGTGTCCTGTTTAAGAAATCTTTGCCTANCCCAAGG 2961 chr2qtel1M 576137 ATGTAATAAATAAATTATTCTTTGTAATC--CTAATTGGTTTATGGTATC 576184 --- v ii v v v i v vv -- ivv v i v i C L1M5_orf2#LIN 2960 ---TCACGAAGATATTCTCCTATGTTTTCTTCTAGAAGTTTTATAGTTTT 2914 chr2qtel1M 576185 ATCCTTTATGCCCAGATC-ATGTCCTATTTTCCCTTTATTTTTGCATAGA 576233 ? i iiiii i - vi i i ?vvv v ii vi C L1M5_orf2#LIN 2913 ANCTTTTACATTTAGGTCTATGATCCATCTNGAATTAATTTTTGTGTATG 2864 chr2qtel1M 576234 GTGTAAGATGTAGATCTATGCTGAGTCTGTGACATACTATTATCCA--TG 576281 i i ivi i v v?i v v i v vv iviv -- C L1M5_orf2#LIN 2863 GTGTGAGGTAGGGGTCGAGNTTCATTTTTTTCCATATGGATATCCAATTG 2814 chr2qtel1M 576282 TTTCCCAGCAATTTCTGTCACACAGAGAATTCTTATTCCATTCCTTGAAT 576331 -- viv i iiv v vv i vii i ---- C L1M5_orf2#LIN 2813 TT--CCAGCACCATTTGTTGAAAAGACTATCCTTTCCCCACT----GAAT 2770 chr2qtel1M 576332 T---TAGGG---TTTATCACATACTACATTGCC---ATAGGCTTTGAT-T 576371 --- v v--- i v v ii - ? ? --- v iv v i - C L1M5_orf2#LIN 2769 TGCNTTGGCACCTTTGTCAAAAATCA-ANTGNCCATATATGTGTGGGTCT 2721 chr2qtel1M 576372 ATTGTGTCCTGTACATATATAATCTGTTCCACTGATGCCCAACTCTATTT 576421 ----i v - v v v i -------- C L1M5_orf2#LIN 2720 ATT----TCTGGAC-TCTCTATTCTGTTCCATTGAT--------CTATTT 2684 chr2qtel1M 576422 -TCTA-------GCCAGTACCAAATGGT-TTGCTTACTGCTGCTTTGTAA 576462 - ------- i v iv - v iv i C L1M5_orf2#LIN 2683 GTCTATCCTTACGCCAATACCACACTGTCTTGATTACTGTAGCTTTATAA 2634 chr2qtel1M 576463 CATAGTTCTAGTGT-AGGTACTGCTAAACCACCATTCTTTATGTTTTGTT 576511 i - ii ii?i -? v iv iv v v- i - i v C L1M5_orf2#LIN 2633 TA-AGTCTTGANATCNGGTAGTGTAAGTCCTCCAA-CTTTGT-TCTTCTT 2587 chr2qtel1M 576512 GTTGTAAATCCCTT--GATATTCTTGATCTTTTGTTCTTCTAGATAGCTT 576559 v vv i ivi -- v ? i i ivi i v iv C L1M5_orf2#LIN 2586 TTTCAAGATTGTTTTGGCTATTCTNGGTCCTTTGCATTTCCATATAAATT 2537 chr2qtel1M 576560 TTTG--TTGTTTTTTT--TTTCTAGTTCTATAAAATGTTTTTGTAGTTTG 576605 v -- iivi v i-- --- v v iv vi v v v C L1M5_orf2#LIN 2536 TTAGAATCAGCTTGTCAATTTCTA---CAAAAAAACCTGCTGGGATTTTG 2490 chr2qtel1M 576606 ATTGTTATGGCACTGAACAAATAGACCAGTTTCGGAAGAATTGTGATTT- 576654 vv v i ivv i i v i vv i - C L1M5_orf2#LIN 2489 ATTGGGATTGCATTGAATCTATAGATCAATTTGGGGAGAATTGACATCTT 2440 chr2qtel1M 576655 ----ATATCAGCTCAACCTAACCATGA-CA----ATATTTTTCCGGTTGT 576695 ---- iiiv vv v v - ---- i i iv i C L1M5_orf2#LIN 2439 NACAATATTGAGTCTTCCAATCCATGAACATGGTATATCTCTCCATTTAT 2390 chr2qtel1M 576696 TTAGATCTGATTTTCTTTGTGTAAGAAGTGTTTTGTAATTCT--GTTCAT 576743 i vv vv v v v v i i i -- vi ? C L1M5_orf2#LIN 2389 TTAGGTCTTCTTTAATTTCTCTCAGCAATGTTTTGTAGTTTTCAGTGTAN 2340 chr2qtel1M 576744 ATGGTATTTCAGTTTGCCTTGGCAGCTTGTTCCCCATTTATTTTAT---- 576789 - v v -iv ?ii vi v vv i i vv ? ---- C L1M5_orf2#LIN 2339 A-GGTCTTGCA-CATNTTTTGTTAGATTTATTCCTAAGTATTTNATGTTT 2292 chr2qtel1M 576790 TTTG--TCTAT-----A-GATATT-TTATTTGTATCTC--TTGCTTATGG 576828 --v ----- - i - v ?iv i -- v iv v C L1M5_orf2#LIN 2291 TTTGATGCTATTGTAAATGGTATTGTTTTTNAAATTTCATTTTCCAATTG 2242 chr2qtel1M 576829 GCTTTATCAGTAATATAGAGAAATACTGATGATTTGTGTAGCTTCATTTT 576878 -- i iiv i v viv v vv v ii C L1M5_orf2#LIN 2241 --TTTGTTGCTAGTATATAGAAATACAATTGATTTTTGTATATTGACCTT 2194 chr2qtel1M 576879 ATATACTGCAATTTTGCTAAAGCTG-TGATTGTTTTCAGTAGATATTTTG 576927 i v ? i ii viii- v iv ii v v? C L1M5_orf2#LIN 2193 GTATCCNGCGACCTTGCTAAATTCACTTATTAGTTCTAGTAGTTTNTTTG 2144 chr2qtel1M 576928 ATGGTTTTCTAGGATTCTCAAAGTAACTCATCATATCACCTCTAAAGAGT 576977 vv i i i ? i v v ?viv i i vii v i? C L1M5_orf2#LIN 2143 TAGATTCTTTNGGATTTTCTACGTANACAATCATGTCATCTGCGAATAAN 2094 chr2qtel1M 576978 AATAGTTTTATTTCCTCATTGCCTATTCTAATTCCTTTTGCTTCTTTTTC 577027 i i i v v v ii v v ii C L1M5_orf2#LIN 2093 GACAGTTTTATTTCTTCCTTTCCAATCTTTATGCCTTTTATTTCTTTTTC 2044 chr2qtel1M 577028 TTTTCTTAT--CAATGAAGCTAACATTTCTAGAACAACATTGAATAATAG 577075 vi -- v -- iv ii i v ii iv C L1M5_orf2#LIN 2043 TTGCCTTATTGCACTG--GCTAGGACCTCCAGTACAATGTTGAATAGAAG 1996 chr2qtel1M 577076 TGGTGTAA-------------TTTAACCCCTGATTTTACTGGGAATGCAT 577112 v? ------------- i viii i i vv v ? C L1M5_orf2#LIN 1995 TGGTGANAGCGGACATCCTTGTCTTGTTCCCGATCTTAGGGGGAAAGCNT 1946 chr2qtel1M 577113 CCAGCTTCTCTTCATTTCATATAATGCTTTCTATAGGTTTTAACAAAGTA 577162 i i? i vi vvi i i ?v i vvvv ii i C L1M5_orf2#LIN 1945 TCAGTNTTTCACCATTAAGTATGATGTTNGCTGTAGGTTTTTCGTAGATG 1896 chr2qtel1M 577163 TTGCTTATTGTTTTAAGGAAAGTTCCCTT-TATCCCT-GTGCCCTCTAGT 577210 iivi iivv i - - i - viv v- v C L1M5_orf2#LIN 1895 CCCTTTATCAGGTTGAGGAA-GTTCCCTTCTATTCCTAGTTTGCTG-AGA 1848 chr2qtel1M 577211 GTTTATTTAT-AGGAATGGGTACTGTATTTTGTCAAAAGCTTTTTCTGCT 577259 -- - v ii v v v C L1M5_orf2#LIN 1847 GTTT--TTATCATGAATGGGTGTTGAATTTTGTCAAATGCTTTTTCTGCA 1800 chr2qtel1M 577260 TGTTTTGGGATTGTAATATGATTCTGTTCGTTT-TGCTATTGATGTGATC 577308 v v i vi v i vi v - v i i i i v C L1M5_orf2#LIN 1799 TCTATTGAGATGATCATATGATTTTTCTCCTTTATTCTGTTAATATGGTG 1750 chr2qtel1M 577309 CACTGGAGTAAGT--TTTCCTGATAACAAACCAGCCATGCATTACTGGTA 577356 v i iv v i v -- i vi ivi i v v v C L1M5_orf2#LIN 1749 AATTACATTGATTGATTTTCGAATGTTAAACCAACCTTGCATTCCTGGGA 1700 chr2qtel1M 577357 TAAATCCCAAATGGTTGTAGTGTACTATCCTGCTCATAAGTTGCTGTAAT 577406 i vv ii ii i vi i vi v v C L1M5_orf2#LIN 1699 TAAACCCCACTTGGTCATGATGTATTATCCTTTTTATATATTGCTGGATT 1650 chr2qtel1M 577407 CTCTTTGCTAATATGTTATTTAGAATTTGTGCATCAGTATTCAACAGGGA 577456 vv v i ? i v vi i vv C L1M5_orf2#LIN 1649 CGATTTGCTAATATTTTGTTNAGGATTTTTGCATCTATGTTCATGAGGGA 1600 chr2qtel1M 577457 TATTGGTCTGTAATTTATTTTTTTTCTCTCTTTTAGCCCTTTGT---GTT 577503 --- i --- v v vvi --- C L1M5_orf2#LIN 1599 TATTGGTCTGTAAT---TTTCTTTTCT---TGTAATGTCTTTGTCNGGTT 1556 chr2qtel1M 577504 TTAGGTAGCAGTGCCATAACTGG-GTCGTAGAGGAAATGTGGCAGTACTC 577552 - v v i? -i -v i i ivi i vv v ii C L1M5_orf2#LIN 1555 TT-GGTATCAGGGTNAT-GCTGGCCTCATAAAATGAGTTGGGAAGTGTTC 1508 chr2qtel1M 577553 CTTC---ACCTATTTTTTCCAAATAGTTGACGTAGTATTAGAAGTAATTG 577599 i ---vi i vv i- vii iv i v v v v C L1M5_orf2#LIN 1507 CCTCTTTTTCTATTTTCTGGAAG-AGTTTGTGTAAGATTGGTATTATTTC 1459 chr2qtel1M 577600 TTCTTTAAATATTTGGGAGAATTCACCGGTGAATGCAACTGGCCCTAGAG 577649 i i v i vv v v i C L1M5_orf2#LIN 1458 TTCCTTAAATGTTTGGTAGAATTCACCAGTGAAGCCATCTGGGCCTGGAG 1409 chr2qtel1M 577650 ATTTTTTCTTAGAGAATTCATTAATGAGTTGTTCAATTTCTGTTTCTGAA 577699 v i iv i ii iv iv v vvvi v vviv v C L1M5_orf2#LIN 1408 TTTTCTTTGTGGGAAGGTTTTTAATTACAAATTCAATTTCTTTAATAGAT 1359 chr2qtel1M 577700 ATGGAACTATTTAAATATTTTATTTCCTCTTCTGTTAACCTGGGAAATTT 577749 i ii i i v i i v? i iii v v ? C L1M5_orf2#LIN 1358 ATAGGGCTATTCAGATTTTCTATTTCTTCTTGNGTCAGTTTTGGTAANTT 1309 chr2qtel1M 577750 GTATTTTTTGTAAACATTCTTCCATTTCAATTAGAGTGTCAGACTTGCTG 577799 i ii- iiv iv vi iiv ? i i ii C L1M5_orf2#LIN 1308 GTGTTTTTCA-AGGAATTTGTCCATTTCATCTAAGTTNTCAAATTTATTG 1260 chr2qtel1M 577800 CCATAGTGTTGGGGA-AAAAAGCTCTTAATTTTTACTTTAATTTCTTT-- 577846 v iv vvv - v vv - v ivi v v -- C L1M5_orf2#LIN 1259 GCATAAAGTTGTTCATAATATTCTCTT-ATTATCCTTTTAATGTCTGTAG 1211 chr2qtel1M 577847 -TTCCTTGGTGGTACATTCACCTCTTTCACTTTTGATGGTGGTGATTTGG 577895 -v iv i i i--- v i i ii iv i - C L1M5_orf2#LIN 1210 GATCTGTAGTGATG---TCTCCTTTTTCATTCCTGATATTGGTAATTT-G 1165 chr2qtel1M 577896 TTTTTTTTCTTTTCTTTTTCTCATCATGAAATGTAGGCAAATATTTATTT 577945 v i i i i ii v ---- i v ? vi i vi iv C L1M5_orf2#LIN 1164 TGTCTTCTCTCTTTTTTTCTTGATC----AGTCTNGCTAGAGGTTTATCA 1119 chr2qtel1M 577946 GTTTTGTTAGTTTTTTCATAAAACCAACTCTTAGTTTTGTTTATT 577990 i i ii i v i i i i i i v C L1M5_orf2#LIN 1118 ATTTTATTGATCTTTTCAAAGAACCAGCTTTTGGCTTCGTTGATT 1074 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.42 CpG sites = 334, Kimura (unadjusted) = 40.85 Transitions / transversions = 1.07 (334/311) Gap_init rate = 0.05 (120 / 2185), avg. gap size = 1.52 (183 / 120) 258 33.04 2.54 2.54 chr2qtel1M 578893 579010 (420990) MIRc#SINE/MIR 83 200 (68) m_b97s601i0 3596 chr2qtel1M 578893 AGCTGCTGGGATTTGGGACAAGTCACTCAATCACTCTGAGCT--GGTGGC 578940 - v ii v i i i v i--i vv MIRc#SINE/MIR 83 AGCTG-TGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTC 131 chr2qtel1M 578941 CTGAATTGTACAAGCAGTGACAATGAAGGTTCTTTCTGTGTGG-TCCCAG 578989 v vi - iii v i - viiiivii iv iv- v MIRc#SINE/MIR 132 CTCATCTGTA-AAATGGGGATAAT-AATACCTGCCCTGCCTACCTCACAG 179 chr2qtel1M 578990 GATTACTGTGAGAATCCAATG 579010 i ii i v MIRc#SINE/MIR 180 GGTTGTTGTGAGGATCAAATG 200 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 45.71 CpG sites = 24, Kimura (unadjusted) = 45.71 Transitions / transversions = 1.71 (24/14) Gap_init rate = 0.04 (5 / 117), avg. gap size = 1.20 (6 / 5) 876 28.96 3.11 3.38 chr2qtel1M 579110 579495 (420505) L1ME3G_3end#LINE/L1 22 406 (518) m_b97s551i9 3597 chr2qtel1M 579110 GAACTGCCTCAGATTTATAAGAACACAAACCATTTTCCAATTGATAAATG 579159 v iv i iv v - i v i--- v v L1ME3G_3end#L 22 GAACTCCTACAAATCAATAAGAAAA-AGACAAC---CCAATAGAAAAATG 67 chr2qtel1M 579160 GTCAAAGGATTTAAACAGACAGTTTTCAGATGAAAAAATAAAAATCATTT 579209 v v i i i iv v ii v viiiv L1ME3G_3end#L 68 GGCAAAGGATATGAACAGGCAATTCACAGAAGAGGAAATACAAATGGCCA 117 chr2qtel1M 579210 CTAGTAC-TATGAAAAAATGCTCTAAATCACTATTGGTCAGAGAAATGCA 579258 v i- - i v vv v ii i L1ME3G_3end#L 118 ATAA-ACATATGAAAAGATGCTCAACCTCACTAGTAATCAGGGAAATGCA 166 chr2qtel1M 579259 AATTAAAACACCTCTGAGGTACCA-----GATACTTCAGATTGGCTAAGA 579303 v vv i -----v iv v v i L1ME3G_3end#L 167 AATTAAAACAACAATGAGATACCATTTTTCACCCATCAGATTGGCAAAAA 216 chr2qtel1M 579304 TGACTGGGAAAGACAATGATGT---ATGTTGAAAAGAATAGGGAAAAACT 579350 --- vii i?vii i i ---i ivi ii iv ii v L1ME3G_3end#L 217 T---TTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGTGTGGGGAAACG 263 chr2qtel1M 579351 GGGACACTAATCCATTGTTGGTGGAGTTGTGAATTGATCCAGTCATTCTG 579400 v v v v i i iiv i i v i ? i L1ME3G_3end#L 264 GGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTACAGCCNTTTTG 313 chr2qtel1M 579401 GA-AACAATATGGAACTGTGCCTA--AAGGGCTATCACACTGTGCATACC 579447 -ii v v -- ii -- iiv--- i v v i L1ME3G_3end#L 314 GAGGGCAATTTGGCA--GTATCTATTAAAAT---TTAAAATGCGCATACC 358 chr2qtel1M 579448 CTTTGATTCAGCAGTGTCTCTACTGAACTTGTATCCTAAAGAGTTACT 579495 ii i vi v v ?ii?v v ? iv L1ME3G_3end#L 359 CTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAGAAATACT 406 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.15 CpG sites = 60, Kimura (unadjusted) = 38.05 Transitions / transversions = 1.25 (60/48) Gap_init rate = 0.05 (18 / 385), avg. gap size = 1.39 (25 / 18) 17 12.68 0.00 0.00 chr2qtel1M 580536 580561 (419439) (A)n#Simple_repeat 1 26 (0) m_b97s252i6 3598 chr2qtel1M 580536 AAAAAAAAAAAAGAAAAGAAACAAAA 580561 i i v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAA 26 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 12 11.71 10.81 0.00 chr2qtel1M 582773 582809 (417191) (TATTCTC)n#Simple_repeat 1 41 (0) m_b97s252i7 3599 chr2qtel1M 582773 TATTTTTTATT-TC-CTT-TCTATTCTCTCTTCTCT-TTCT 582809 i i - -v - v - (TATTCTC)n#Si 1 TATTCTCTATTCTCTATTCTCTATTCTCTATTCTCTATTCT 41 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.11 (4 / 36), avg. gap size = 1.00 (4 / 4) 14 10.39 0.00 8.82 chr2qtel1M 582775 582811 (417189) (TTCT)n#Simple_repeat 1 34 (0) m_b97s252i8 3599 chr2qtel1M 582775 TTTTTTATTTCCTTTCTATTCTCTCTTCTCTTTCTTT 582811 i v - - i - (TTCT)n#Simpl 1 TTCTTTCTTT-CTTTCT-TTCTTTCTT-TCTTTCTTT 34 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.08 (3 / 36), avg. gap size = 1.00 (3 / 3) 12 19.57 2.86 0.00 chr2qtel1M 584047 584081 (415919) (TGAAATC)n#Simple_repeat 1 36 (0) m_b97s252i9 3600 chr2qtel1M 584047 TGAATTCTGATATCTTATA-CTAAACTCTGAAATCT 584081 v v v v - i v (TGAAATC)n#Si 1 TGAAATCTGAAATCTGAAATCTGAAATCTGAAATCT 36 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 228 27.94 4.41 0.00 chr2qtel1M 586285 586352 (413648) MIR3#SINE/MIR 111 181 (27) m_b97s601i1 3601 chr2qtel1M 586285 TCACTGAATCTCAGTTTCCCC-TTTATAAAATGAGTGGGAGGCACTCCGT 586333 v iii i - i i v vv v vvi MIR3#SINE/MIR 111 TCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGAT 160 chr2qtel1M 586334 GGCCTT--GGATCCCTTCCAG 586352 ii i--i i MIR3#SINE/MIR 161 GATCTCTAAGGTCCCTTCCAG 181 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.19 CpG sites = 12, Kimura (unadjusted) = 36.19 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.03 (2 / 67), avg. gap size = 1.50 (3 / 2) 261 32.54 5.22 3.68 chr2qtel1M 586472 586605 (413395) C L2b_3end#LINE/L2 (10) 456 321 m_b97s601i2 3602 chr2qtel1M 586472 TCAGCAAACTTTTA---AATGCCTGCTATCAGCCGGGACCTGGGCTGTGC 586518 i iv --- ii i i vv i v? v iv C L2b_3end#LINE 456 TCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGC 407 chr2qtel1M 586519 CCCAGAAACATAAAGAGAGACAAGG--GACCC--CTCCTGCTCTCGTGGA 586564 v ii ii i i iv ivii i-- ? --ii i ii C L2b_3end#LINE 406 GCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGGA 357 chr2qtel1M 586565 GGTCACAGACAGCTGGGGCAGACAATACACACGTGTAAGTA 586605 v v viv v i----- i ?i C L2b_3end#LINE 356 GCTCACAGTCTAGTGGGGGAGACAG-----ACATGTAANCA 321 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 43.71 CpG sites = 28, Kimura (unadjusted) = 46.83 Transitions / transversions = 2.00 (28/14) Gap_init rate = 0.06 (8 / 133), avg. gap size = 1.50 (12 / 8) 379 32.17 10.65 2.14 chr2qtel1M 586727 586942 (413058) C MIRb#SINE/MIR (7) 261 28 m_b97s601i3 3603 chr2qtel1M 586727 GAAATACCAT--ATCTAGCATTTA-----TACCACACCTGCTGTGACATG 586769 iv -- iv ii ----- i vi --i vi v C MIRb#SINE/MIR 261 GAGCTACCATTTATTGAGCGCTTACTATGTGCCAGGC--ACTGTGCTAAG 214 chr2qtel1M 586770 CAGTGTATCAGTATTGTCTCATTTTATCATCATGAGAACCCTAGGACTCG 586819 iv v ivv i i v v ii v iv vvii C MIRb#SINE/MIR 213 CGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTA 164 chr2qtel1M 586820 GGTGCCATTATTGTGCCCTTTTTATAGATAAAGGAACTGAGACAGACAGA 586869 --- i v v i i i i i vv v C MIRb#SINE/MIR 163 GGT---ATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGA 117 chr2qtel1M 586870 GATCTTGTAAGTTG--------------ACTAGCAAATTGCTGAGTTTGG 586905 i ivv v --------------i i i v v iiv C MIRb#SINE/MIR 116 GGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGG 67 chr2qtel1M 586906 ATGAACACGCAAGTCTTGCTGA-TTGAAGGCCC-TGTTC 586942 vviv v i vv - iv i - i C MIRb#SINE/MIR 66 ATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTC 28 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.64 CpG sites = 35, Kimura (unadjusted) = 42.86 Transitions / transversions = 1.06 (35/33) Gap_init rate = 0.05 (10 / 215), avg. gap size = 2.80 (28 / 10) 392 28.79 10.84 1.66 chr2qtel1M 586780 586945 (413055) C MIR#SINE/MIR (63) 199 19 m_b97s601i4 3603 chr2qtel1M 586780 GTATTGTCTCATTTTATCATCATGAGAACCCTAGGACTCGGGTGCCATTA 586829 iv v v ii v v vvii i i C MIR#SINE/MIR 199 GTATTAACTCATTTAATCCTCACAACAACCCTATGAGGTAGGTACTATTA 150 chr2qtel1M 586830 TTGTGCCCTTTTTATAGATAAAGGAACTGAGACAGACAGAGATCTTGTAA 586879 i v v i i i i i v v i ivv C MIR#SINE/MIR 149 TTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAA 100 chr2qtel1M 586880 GTTG--------------ACTAGCAAATTGCTGAGTTTGGAT--GAACAC 586913 v --------------i i i v v iiv -- v C MIR#SINE/MIR 99 CTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCC 50 chr2qtel1M 586914 --GCAAGTCTTGCTGATTGAAGGCCCTGTTCATA 586945 -- - v --iiii v v i v C MIR#SINE/MIR 49 AGGC-AGTCTGGCT--CCAGAGCCCGTGCTCTTA 19 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.03 CpG sites = 25, Kimura (unadjusted) = 37.01 Transitions / transversions = 1.14 (25/22) Gap_init rate = 0.04 (6 / 165), avg. gap size = 3.50 (21 / 6) 16 23.33 4.84 1.56 chr2qtel1M 588272 588333 (411667) (AAAATG)n#Simple_repeat 1 64 (0) m_b97s252i10 3604 chr2qtel1M 588272 AAAAT-AAAATAAAATTGAAAATGATCACTTAAAA-GTACA-GACAATGA 588318 - i v -v v v - v v - v (AAAATG)n#Sim 1 AAAATGAAAATGAAAATGAAAATGA-AAATGAAAATGAAAATGAAAATGA 49 chr2qtel1M 588319 AAGGGAACAGGAAAA 588333 iv v v (AAAATG)n#Sim 50 AAATGAAAATGAAAA 64 Matrix = Unknown Transitions / transversions = 0.20 (2/10) Gap_init rate = 0.07 (4 / 61), avg. gap size = 1.00 (4 / 4) 900 29.11 2.86 3.40 chr2qtel1M 588610 588993 (411007) L1ME3G_3end#LINE/L1 22 403 (521) m_b97s551i10 3605 chr2qtel1M 588610 GAACTGCCTCAGATTTATAAGAATGCAAGCCATTTGCCAATTGATAAATG 588659 v iv i iv --v v vi-- v v L1ME3G_3end#L 22 GAACTCCTACAAATCAATAAGAA--AAAGACAAC--CCAATAGAAAAATG 67 chr2qtel1M 588660 GTCAGAGGATTTAAACAGACAGTTTTCAGATAAAAAAATTAAAATCATTT 588709 v i v i i i iv vi ii vv viiiv L1ME3G_3end#L 68 GGCAAAGGATATGAACAGGCAATTCACAGAAGAGGAAATACAAATGGCCA 117 chr2qtel1M 588710 CTAGTCCTATGAAAAAATACTCTAAATCTCTATTGGTCAGAGAAATGTAA 588759 v iv v i i v vv v v ii i i L1ME3G_3end#L 118 ATAAACATATGAAAAGATGCTCAACCTCACTAGTAATCAGGGAAATGCAA 167 chr2qtel1M 588760 ATTAAAACAATGCTGAGGTACCA-----GATCTTTCAGATTGTCTAACAT 588804 iiv i -----v i iv v v v L1ME3G_3end#L 168 ATTAAAACAACAATGAGATACCATTTTTCACCCATCAGATTGGCAAAAAT 217 chr2qtel1M 588805 GACAGGAATAGATTG-TGATGT---GTGTTGAAGGGGATGTGGAAAAACT 588850 ----vv v ? - i i --- iv i i ii v L1ME3G_3end#L 218 ----TTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGTGTGGGGAAACG 263 chr2qtel1M 588851 GCGACACTAATACATTGTTGGTGGAGTTGTGAATTGATCCAGTCATTCTG 588900 vv v v i i iiv i i v i ? i L1ME3G_3end#L 264 GGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTACAGCCNTTTTG 313 chr2qtel1M 588901 GAAAACAATATGGAACTATGCCTA--AAAGTCTATCACACTGTGCATACC 588948 iii v v v -- -- i --- i v v i L1ME3G_3end#L 314 GAGGGCAATTTGGCAGTAT--CTATTAAAAT---TTAAAATGCGCATACC 358 chr2qtel1M 588949 CTTTGATCCAGCAGTGTCTCTACTGAACCTGTACCTCAAAGAGAT 588993 i i vi v v ?ii?v v i ii ? i L1ME3G_3end#L 359 CTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAGAAAT 403 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.69 CpG sites = 57, Kimura (unadjusted) = 38.13 Transitions / transversions = 1.12 (57/51) Gap_init rate = 0.04 (17 / 383), avg. gap size = 1.41 (24 / 17) 818 32.87 2.91 2.46 chr2qtel1M 588618 589063 (410937) L1ME4c_3end#LINE/L1 30 477 (353) m_b97s551i11 3605 chr2qtel1M 588618 TCAGATTTATAAGAATGCAAGCCATTTGCCAATTGATAAATGGTCAGAGG 588667 i v viv? v v vviv v v i L1ME4c_3end#L 30 TCAAATTGATAAGAAAAANATCAAGACCCCAATAGATAAATGGGCAAAGG 79 chr2qtel1M 588668 ATTTAAACAGACAGTTTTCAGATAAAAAAATTAAAATCATTTCTAGTCCT 588717 iv i i iv ? vi ii vv ? vi vvvi iv vi L1ME4c_3end#L 80 ACATGAACAGACAATTCACANAAGAGGAAATACAANTAGTAAACAAACAC 129 chr2qtel1M 588718 ATGAAAAAATACTCTAAATCTCTATTGGTCAGAGAAATGTAAATTAAAAC 588767 i ii v vv v v ii i i i L1ME4c_3end#L 130 ATGGAAAAATGTTCAACCTCGCTAGTAATCAAAGAAATGCAAATTAAAGC 179 chr2qtel1M 588768 AATGCTGAGGTACCAGATCTTTCA-GATTGTCTAACATGACAGGAAT--- 588813 iiv i ---- i - vi i - vv ii ii --- L1ME4c_3end#L 180 AACAATGAGATACCA----TTTTACGCCTAT-TAAATTAGCAAAAATTTA 224 chr2qtel1M 588814 --AGATTG-TGATGT---GTGTTGAAGGGGATGTGGAAAAACTGCGACAC 588857 -- i - i ii---i i iv i ? i vi vv ? L1ME4c_3end#L 225 AAAAATTGATAATACCCAATGCTGGCGAGGNTGCGGTGAAACTGGTACNC 274 chr2qtel1M 588858 TAATACATTGTTGGTGGAGTTGTGAATTGATCCAGTCATTCTGGAAAACA 588907 v i vi? i i v ii v i i L1ME4c_3end#L 275 TCATACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGCA 324 chr2qtel1M 588908 ATATGGAACTATGCCTAAAAGTCTATCACACTGTGCATACCCTTTGATCC 588957 v v v i iv v iiv i v v v v i L1ME4c_3end#L 325 ATTTGGCAATACGTATCAAGAGCCATAAAAATGTTCATACCCTTTGACCC 374 chr2qtel1M 588958 AGCAGTGTCTCTACTGAACCTGTACCTCAAAGAGAT--CTTAAAGAAAAG 589005 i i vi v v iivv v i ii i i --i i ii i L1ME4c_3end#L 375 AGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAAGAAGG 424 chr2qtel1M 589006 AAAAGGCCTTTCACATGTGCA-AAAAATGTTTGTAGCCGCCTTTTCTGTA 589054 i ------i i -i i ii v v v v i i L1ME4c_3end#L 425 AAAAAGC------TATATGCACGAAGATGTTCATTGCAGCGTTATTTATA 468 chr2qtel1M 589055 CTGGAGAGA 589063 v i v i L1ME4c_3end#L 469 ATAGCGAAA 477 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 44.30 CpG sites = 83, Kimura (unadjusted) = 45.62 Transitions / transversions = 1.38 (83/60) Gap_init rate = 0.04 (18 / 445), avg. gap size = 1.33 (24 / 18) 13 16.85 0.00 5.71 chr2qtel1M 590604 590640 (409360) (TCATC)n#Simple_repeat 1 35 (0) m_b97s252i11 3606 chr2qtel1M 590604 TCATCTCTTCTGCTCTCATCTCAATCTACATTTCTTC 590640 v vv - - i v (TCATC)n#Simp 1 TCATCTCATCTCATCTCATCTC-ATCT-CATCTCATC 35 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 223 28.65 4.32 3.05 chr2qtel1M 591327 591488 (408512) L2#LINE/L2 2025 2188 (894) m_b97s601i5 3607 chr2qtel1M 591327 TCCAA--GTCCATGGATCTCAATCCCCCATTTT-CTTGATTGTTCTCCAG 591373 -- v --- i i - i - iiv? vv L2#LINE/L2 2025 TCCAATGGTCAAT---TCTCAGTCCTC-ATCTTACTTGACCTNTCAGCAG 2070 chr2qtel1M 591374 CCTTTGACATTCCTGATGACTCTCTCTCCTCCAGGGTC-CTCTCTTCTCA 591422 v ivvi v i - i iv iiv - i v v L2#LINE/L2 2071 CATTTGACACAGTTGATCACTCCCTC-CTTCTTGAAACACTTTCTTCACT 2119 chr2qtel1M 591423 TAGTTTTTAGAACTCTGCTCTCTCCTGCCTTTTCCCCTTCCTATCTGACC 591472 i i ii i v ii v vi i i v vv i L2#LINE/L2 2120 TGGCTTCCAGGACACCACACTCTCCTGGTTTTCCTCCTACCTCACTGGCC 2169 chr2qtel1M 591473 A---CTTCTCTGTCTTCTT 591488 i--- v i L2#LINE/L2 2170 GCTCCTTCTCAGTCTCCTT 2188 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.29 CpG sites = 26, Kimura (unadjusted) = 37.34 Transitions / transversions = 1.37 (26/19) Gap_init rate = 0.06 (9 / 161), avg. gap size = 1.33 (12 / 9) 219 26.27 9.15 6.16 chr2qtel1M 593985 594126 (405874) MIRc#SINE/MIR 84 229 (39) m_b98s601i0 3608 chr2qtel1M 593985 GCTGCTGGGATTTGGGTCAAGTCACTCAACCT-TCTGAGCTGAAGACCCG 594033 - v ii v v i - ------ i - MIRc#SINE/MIR 84 GCTG-TGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGC------CTC- 125 chr2qtel1M 594034 AGTTGTGCCCAT-TGT-----GTGACTGAAAATACTT--TCTGTAT-TGT 594074 - v i - ----- v iv i v i --i iv -iv MIRc#SINE/MIR 126 AGTT-TCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCT 174 chr2qtel1M 594075 CCCAGGTTTACTGTGAGAATCCAATGATTTTGTGCATG---AAGCTCATT 594121 v v ii i v vv vi i --- v v MIRc#SINE/MIR 175 CACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTTT 224 chr2qtel1M 594122 AGAAA 594126 iv MIRc#SINE/MIR 225 GTAAA 229 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.69 CpG sites = 17, Kimura (unadjusted) = 32.69 Transitions / transversions = 0.94 (17/18) Gap_init rate = 0.11 (15 / 141), avg. gap size = 1.47 (22 / 15) 422 22.28 0.81 8.77 chr2qtel1M 594137 594259 (405741) MIRc#SINE/MIR 2 115 (153) m_b98s601i1 3609 chr2qtel1M 594137 GGGGCAGCTCAGTGGTGCAGTGGATAAAGCACCAGCCATGAAGGCAGGAG 594186 i i--- v i ii v v i v i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr2qtel1M 594187 GACTTGAGTTCTAATTTGACCTCAGATGCTTAACACTTCCTAGTTGTGTG 594236 i i v i iiviv --- ---- v i MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTC---TGC----CACTTACTAGCTGTGTG 91 chr2qtel1M 594237 ACC-TGGGCAAGTCCCTTACCCCC 594259 - v v i MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.50 CpG sites = 15, Kimura (unadjusted) = 26.72 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.09 (11 / 122), avg. gap size = 1.00 (11 / 11) 286 26.45 2.54 7.08 chr2qtel1M 594155 594272 (405728) MIR#SINE/MIR 13 125 (137) m_b98s601i2 3609 chr2qtel1M 594155 AGTGGATAA-AGCACCAGCCATGAAGGCAGGAGGACTTGAGTTCTAATTT 594203 v - vi iv i v - vvi i i v ii MIR#SINE/MIR 13 AGTGGTTAAGAGCACGGGCTCTGGAGCCAG-ACTGCCTGGGTTCGAATCC 61 chr2qtel1M 594204 GACCTCAGATGCTTAACACTTCCTAGTTGTGTGACC-TGGGCAAGTCCCT 594252 viv --- ---- v i - iv MIR#SINE/MIR 62 CGGCTC---TGC----CACTTACTAGCTGTGTGACCTTGGGCAAGTTACT 104 chr2qtel1M 594253 T-ACCCCCAAATGGCTCAGCT 594272 - i ivvi v i MIR#SINE/MIR 105 TAACCTCTCTGTGCCTCAGTT 125 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.54 CpG sites = 15, Kimura (unadjusted) = 32.89 Transitions / transversions = 1.07 (15/14) Gap_init rate = 0.09 (11 / 117), avg. gap size = 1.00 (11 / 11) 15 22.59 7.27 1.72 chr2qtel1M 594889 594943 (405057) (AT)n#Simple_repeat 1 58 (0) m_b98s252i0 3610 chr2qtel1M 594889 ATACATGT-TAAATATGT-TAAAGTATATGT-TATATACA-ACACATATA 594934 i i - v i - v - i - i - i i (AT)n#Simple_ 1 ATATATATATATATATATATATA-TATATATATATATATATATATATATA 49 chr2qtel1M 594935 TATACATAT 594943 i (AT)n#Simple_ 50 TATATATAT 58 Matrix = Unknown Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.09 (5 / 54), avg. gap size = 1.00 (5 / 5) 810 29.07 5.09 3.45 chr2qtel1M 595212 595781 (404219) C L1MC5a_3end#LINE/L1 (2141) 636 58 m_b98s551i0 3611 chr2qtel1M 595212 CCTGCTCATTTCACTCAGCATCAGTTCATGTAAATCTCTCCAGGCCTTTC 595261 i iv i i vi vv v v i v vi? vv v C L1MC5a_3end#L 636 CTTGCTTTTTTCACTTAACAATATATCCTGGAGATCACTCCATANCAGTA 587 chr2qtel1M 595262 T---GAAATCCTCCTGCTGGTCATTTCTTATAGAACAATAATATTCCATA 595308 --- i i vv -- v - i vvvv i i v C L1MC5a_3end#L 586 TATAGAGATCTTCCTCAT--TCCTTT-TTACAGCTGCATAGTACTCCATT 540 chr2qtel1M 595309 ACATTCATATACCACAACTTATTCAGCCATTCTCCAGTTGATGGGCATCC 595358 iii vv i i ii i v i vi i ii C L1MC5a_3end#L 539 GTGTGGATGTACCATAGTTTATTCAACCAGTCCCCTATTGATGGACATTT 490 chr2qtel1M 595359 ATTCAATTTCCAGTTTCTGGCCACTACAAAAAGAGCTGC--CGCA-AACC 595405 ivvivi i i v i i v iv --i v - C L1MC5a_3end#L 489 GGGTTGTTTCCAGTCTTTTGCTATTACAAATAATGCTGCAATGAATAACC 440 chr2qtel1M 595406 TTTTGGCACATACAGGTGCCTTTCCCTCCTTT----AAAATCTCTTTGGG 595451 v --- ---- i ? i v vi ---- ivi v i C L1MC5a_3end#L 439 TTGTG---CATAC----GTCNTTTCGTATTTTTGCNAGTGTATCTTCGGG 397 chr2qtel1M 595452 ATA--TTAGCCCAGTAGTAGCACTGCTGGATCAAAGGGTATACACAGTTT 595499 -- -- i v i v i i v ii - v C L1MC5a_3end#L 396 ATAGATT--CCTAGAAGTGGGATTGCTGGGTCAAAGGGTAAATGCA-TAT 350 chr2qtel1M 595500 GATGACTTTTTGAGCAGAGTTCCAAATTCCTCTCCAGAATGGCTGGATGT 595549 - i i viv - v v v i v iv i v ivv C L1MC5a_3end#L 349 G-TAATTTTGCTAG-ATATTGCCAAATTCCCCTCCATAGGGGTTGTACCA 302 chr2qtel1M 595550 ATTCACAATTCCACCAACAATGTATCAA------TGT---CCCACATCCC 595590 v ii v i i v i------ --- v i C L1MC5a_3end#L 301 TTTTGCATTCCCACCAGCAATGTATGAGAGTGCCTGTTTCCCCACAGCCT 252 chr2qtel1M 595591 CTCCAACATTCAGCATTATCTTTTC---CTGTC--ATCCTAGCCAATATG 595635 v v----- v v v --- v i-- ii v v C L1MC5a_3end#L 251 CGCCAACAG-----AGTATGTTGTCAAACTTTTGGATTTTTGCCAATCTG 207 chr2qtel1M 595636 ACAGGTGTGTAGTGGTATCTCAGAGATGTCTTAATTTGCATTGCTCTGAT 595685 i v v i v vv i v v C L1MC5a_3end#L 206 ATAGGTGAGAAATGGTATCTCAGTGTAGTTTTAATTTGCATTTCTCTTAT 157 chr2qtel1M 595686 TA---ATGGCTTGGAGGATCTTTTCATATGGATAGAAATAGTTTCAATTT 595732 ---i ivv v v vv iiiiivi vv C L1MC5a_3end#L 156 TATGAGTGAGGTTGAGCATCTTTTCATATGTTTAAGGGCCATTTGCATTT 107 chr2qtel1M 595733 TTTTATCTGAAAATTCTCTGTTCATATCTTTTGACCATTTATCACTTGG 595781 i v vi i v v v vv C L1MC5a_3end#L 106 CTTTTTCTGTGAACTGTCTGTTCATATCTTTTGCCCATTTTTCTATTGG 58 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.03 CpG sites = 76, Kimura (unadjusted) = 37.32 Transitions / transversions = 0.90 (76/84) Gap_init rate = 0.05 (30 / 569), avg. gap size = 1.63 (49 / 30) 1052 29.73 4.71 2.82 chr2qtel1M 595296 595783 (404217) C L1ME5_3end#LINE/L1 (389) 552 56 m_b98s551i1 3611 chr2qtel1M 595296 ATAATATTCCATAACATTCATATACCACAACTTATTCAGCCATTCTCCAG 595345 i i iiii v vi vi iii v i vi C L1ME5_3end#LI 552 ATAGTACTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCA 503 chr2qtel1M 595346 TTGATGGGCATCCATTCAATTTCCAGTTTCTGGCCACTACAAAAAGAGCT 595395 v i i vviviii ii i iv i v iv C L1ME5_3end#LI 502 GTGATGGACACCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCT 453 chr2qtel1M 595396 GCCGCAAACCTTTTGGCACATACAGGTGCCTTTC----CCTCCTTTAAAA 595441 viii v ii ---- i v v i v---- viv v i C L1ME5_3end#LI 452 GCAATGAACATCCT----CGTACATGTCCCCTTATGGACCTGTGTGAGAA 407 chr2qtel1M 595442 TCTCTTTGGGATATTAGCCCAGTAGTAGCACTGCTGGATCAAAGGGTATA 595491 i vvi v ii v i i v i C L1ME5_3end#LI 406 TTTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATG 357 chr2qtel1M 595492 CACAGTTTGATGACTT--TTTGAGCAG--AGTTCCAAATTCCTCTCCAGA 595537 --- --- - -- vi i-- v v i v C L1ME5_3end#LI 356 C---GT---AT-ACTTAATTTGACTAAGTACTGCCAGATTGCTCTCCAGA 314 chr2qtel1M 595538 ATGGCTGGATGTATTCACAATTCCACCAACAATGTATCAATGT------- 595580 v ivvi ii v i i i i v iv ------- C L1ME5_3end#LI 313 ATGGCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATN 264 chr2qtel1M 595581 --CCCACATCCCCTCCAACATTCAGCATTATCT---TTTCCTGTCATCCT 595625 -- i v i ii i--- --- v ii C L1ME5_3end#LI 263 TCCCCACATCCTCGCCAACACTTGGCATTATCCAGCTTTC---TAATTTT 217 chr2qtel1M 595626 AGCCAATATGACAGGTGTGTAGTGGTATCTCAGAGATGTCTTAATTTGCA 595675 v i v i i iv i vv v i C L1ME5_3end#LI 216 TGCCAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCA 167 chr2qtel1M 595676 TTGCTCTGAT---TAATGGCTTGGAGGATCTTTTCATATGGATAGAAATA 595722 v --- iv v v i vv ivv iiv C L1ME5_3end#LI 166 TTTCTCTGATTACTAATGAGTTTGAGCATCTCTTCATATGCTTGTTAGCC 117 chr2qtel1M 595723 GTTTCAATTTTTTTATCTGAAAATTCTCTGTTCATATCTTTTGACCATTT 595772 v ivii ii iv v vi i v C L1ME5_3end#LI 116 TTTCGGGTTTCCTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCCATTT 67 chr2qtel1M 595773 ATCACTTGGAG 595783 v vv i C L1ME5_3end#LI 66 TTCTATTGGGG 56 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.74 CpG sites = 80, Kimura (unadjusted) = 38.83 Transitions / transversions = 1.31 (80/61) Gap_init rate = 0.04 (21 / 487), avg. gap size = 1.76 (37 / 21) 26 0.00 0.00 0.00 chr2qtel1M 596813 596837 (403163) (T)n#Simple_repeat 1 25 (0) c_b98s251i0 3612 chr2qtel1M 596813 TTTTTTTTTTTTTTTTTTTTTTTTT 596837 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 45 2.38 0.00 0.00 chr2qtel1M 596914 596956 (403044) (TC)n#Simple_repeat 1 43 (0) c_b98s251i1 3613 chr2qtel1M 596914 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTTCTCT 596956 i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 43 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 19 0.00 0.00 0.00 chr2qtel1M 596957 596977 (403023) (T)n#Simple_repeat 1 21 (0) m_b98s252i1 3614 chr2qtel1M 596957 TTTTTTTTTTTTTTTTTTTTT 596977 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTT 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 369 30.65 2.76 10.93 chr2qtel1M 598870 599195 (400805) C HERVK11#LTR/ERVK (2674) 5279 4978 m_b98s701i0 3615 chr2qtel1M 598870 TCTACTATTGCCTATCCTTGAGGATTAAAGAGTATGCCAGTGATATGTAA 598919 i i iv i i iv ii v v i i -ii C HERVK11#LTR/E 5279 TCCACCACAGCCTGTCCCTGAGGATTGTAAGGGATTCCGGTAATATG-GG 5231 chr2qtel1M 598920 AAATTTTATACTGT-GCACAAAAGTATGCAAAATATTTGGAAGTATATGC 598968 iivi - i viv - vvi ivv ii v C HERVK11#LTR/E 5230 AAATTCCCCACTGTTGCATAAATAAAT-CAAAAGCCTTACTAACATATCC 5182 chr2qtel1M 598969 AGGTCCATTGTCTGTTTTTATGGCTTGTGGTTTTATGGCTTTATGGCTAT 599018 vv i i ---------------------- v v C HERVK11#LTR/E 5181 AGGGGCGTTGTCTGTCTTTAT----------------------TTGATAT 5154 chr2qtel1M 599019 GTGTGCACCCATAATTGCAAATGCTTGTATAAGGAATTCA-ATGACC--- 599064 viv - i - ------- i v - vii--- C HERVK11#LTR/E 5153 GGAAGC-CCCATAACTGCAAA-GC-------AAGAATACAGATGTTTTTT 5113 chr2qtel1M 599065 -ACTCGGGCTGTCCTTTTTGCTGCT-GGTA--TTGCAAAAGTGAATCCTG 599110 - vi i v i iiv i - i -- v vv ii i v C HERVK11#LTR/E 5112 AACATGGGCCGTGCCTTCCCCTGTTTGGCAAGTAGCCCAGATAAAACCTG 5063 chr2qtel1M 599111 AAAAAGTGTCTACCACAACATGGATAAAAGACAGACGACTAAAAGATTTA 599160 i i i viv v i v v ? v vi i i vi C HERVK11#LTR/E 5062 AGAAGGTATCTACAGAAACATGCACATATGANAGTCTGCCAAAGGAGCTA 5013 chr2qtel1M 599161 TAATGGGTCACATCCATTTGCCAAATTTCATTGGG 599195 vv i v vv? i C HERVK11#LTR/E 5012 ACATGAGTCACATCCATTTGCCATAAANCATTAGG 4978 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.45 CpG sites = 49, Kimura (unadjusted) = 40.18 Transitions / transversions = 1.23 (49/40) Gap_init rate = 0.12 (39 / 325), avg. gap size = 1.08 (42 / 39) 331 27.75 7.34 6.61 chr2qtel1M 600226 600661 (399339) C HERVK11D#LTR/ERVK (3848) 3904 3466 m_b98s701i1 3615 chr2qtel1M 600226 GTTTAAAGCACTGTCTCCCCT--TAAAATGTCATATA-ATG-GTTGCAAT 600271 v -- v i -- i v v - - v -- C HERVK11D#LTR/ 3904 GTTTAAATC--TGTATCTCCTGATAAAGTGGCAAATAGATGAGAT--AAT 3859 chr2qtel1M 600272 TAATAGGTAGTCAAGCCTAACACTGATCACATCCATTGGATATCTCCTAT 600321 vv i vv v ivii i vv vvi v v i v v C HERVK11D#LTR/ 3858 GCATAAGTAGGGATGCCTAGGGTTGGTCTGAGATAATTGATGTCACCTAG 3809 chr2qtel1M 600322 CAGTTTCTGAAAGTCATTTAAGGTGTTTAACTTTTCAGTTCTTAAGGAAA 600371 i i i i v v v vv ivvii C HERVK11D#LTR/ 3808 TAATTTTTGAAAATCATTTAAGGTGTTTAAATTGTCAGTACGAAGTTGGA 3759 chr2qtel1M 600372 GTTTTTA-----TACTGTGAAC-ACCTTAGGATATACTCCATATCCTAAA 600415 v i----- v - i - v ---v -i v - i C HERVK11D#LTR/ 3758 CTTTTTGGGGCTTAATG-GAGCGAGCTT---CTA-GCTGCAT-TCCTAAG 3715 chr2qtel1M 600416 TATTGAAAAGGAGCATGTTTTTGAATTTTTTCTGGAGCTATGTGCAAT-T 600464 iv iivv v v v v v i -i C HERVK11D#LTR/ 3714 TACAGAAAAGGAGTGGCTTGTTGAATTTTATCAGGAGCGATGTGGAGTCC 3665 chr2qtel1M 600465 TGTAGTATCTTAGTGTATCCATGGTCTTTTGTAGACAGGC-TAACATTT- 600512 i ----- i ----- v ii iivv v i v i-v v- C HERVK11D#LTR/ 3664 TGCA-----TTGG-----CAACAGCTAATTTTAAAGAGGTAAAACATTGA 3625 chr2qtel1M 600513 ----ATTCCTC------GGATGCA-CATCCAAATATATCATCCATGTAAT 600551 ---- v ------ iv - vi - i i C HERVK11D#LTR/ 3624 ATTAATTCATCTTTAGTGGGAGCAGCAATC-AGTATATCATCCATATAAT 3576 chr2qtel1M 600552 AAAATAACATAAC--TTTTGGAAATACTTTCCTTACTGGA------GTAA 600593 i i- ii i-- vi vv v ------ ------ C HERVK11D#LTR/ 3575 GAAG-AATGTAATTATTTTTAAAAGTCTGTC------GGATAGGTTGTAA 3533 chr2qtel1M 600594 GAGTAGCAGCAACATACATTTGACACATAGTAGGACTGTTTTTCATCCCC 600643 v -i i v i v vi v vv i i C HERVK11D#LTR/ 3532 CA-CAGTACCGACAAACAACTGACAAATAGTAGGACTGTTAATCATTCCT 3484 chr2qtel1M 600644 TGTGGCAAAGCTGTCCAT 600661 v i i v C HERVK11D#LTR/ 3483 TGAGGTAAAACTTTCCAT 3466 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.50 CpG sites = 51, Kimura (unadjusted) = 34.87 Transitions / transversions = 0.82 (51/62) Gap_init rate = 0.10 (42 / 435), avg. gap size = 1.45 (61 / 42) 485 27.58 6.20 5.38 chr2qtel1M 600274 600660 (399340) C HERVK14#LTR/ERVK (2671) 3425 3036 m_b98s701i2 3615 chr2qtel1M 600274 ATAGGTAGTCAAGCCTAACACTGATCACATCCATTGGATATCTCCTATCA 600323 vv v vii iv iv v vi i vi C HERVK14#LTR/E 3425 ATAGGTAGGAATGCCTAAAGTTGGACGAATCCAATTAATGTCTCCTAATA 3376 chr2qtel1M 600324 GTTTCTGAAAGTCATTTAAGGTGTTTAACTTTTCAGTTC----TTAAGGA 600369 i i i i v v v vv ---- --- C HERVK14#LTR/E 3375 ATTTTTGGAAATCATTTAAGGTTTTTAAATTATCTCTTCGAATTT---GA 3329 chr2qtel1M 600370 AAGTTTTTATACTGTGA--ACACCTTAGGATATAC-TCCATATCCTAAAT 600416 vv v vi - i --i i -- v v - i - i C HERVK14#LTR/E 3328 ACCTTTTGAGGCT-TAATAGCACTTT--GTTCTACCTTCAT-TCCTAGAT 3283 chr2qtel1M 600417 ATTGAAAAGGAGCATGTTTTTGAATTTTTTCTGGAGCTATGTGCAATTTG 600466 i i vivv i v v i ---- -- C HERVK14#LTR/E 3282 ATTGAAAGGGAGTAGAAGTTTGGATTTTATCGGGGGCTAT----AATT-- 3239 chr2qtel1M 600467 TAGTATCTTAGTGTATCCATGGTCTTTTGTAGACAG------GC-TAACA 600509 - -- i i ivi i ii ii i v - v ------ -i C HERVK14#LTR/E 3238 -A--ACCCTGCCGCATTTACAGCCTTTTCTA-ACTGTTTGTAGCACAACA 3193 chr2qtel1M 600510 T---TTATTCC------TCGGATGCACATCCAAATATATCATCCATGTAA 600550 --- v ------ i v -- i - C HERVK14#LTR/E 3192 TCAATTCTTCCCTAGTTTCAGCTGCACA--CAGA-ATATCATCCATGTAA 3146 chr2qtel1M 600551 TAAAATAACATAAC-TTTTGGAAATACTTTCCTTACTGGAGTAAGAGTAG 600599 -ii i - vv ivv ii v vv v ivv C HERVK14#LTR/E 3145 T-GGATAATATAACATTTTTTAAACTGTTCTCTAACTGGCTTAATAGCTT 3097 chr2qtel1M 600600 CAGCAACATACATTTGACACATAGTAGGACTGTTTTTCATCCCCTGTGGC 600649 ivv i vi v v i i vv v i i C HERVK14#LTR/E 3096 TCCCGACATAAGTTTGACAAATAGTCGGGCTATTTAGCATGCCTTGTGGT 3047 chr2qtel1M 600650 AAAGCTGTCCA 600660 ivi v C HERVK14#LTR/E 3046 AGTACTTTCCA 3036 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 33.57 CpG sites = 51, Kimura (unadjusted) = 34.81 Transitions / transversions = 1.02 (51/50) Gap_init rate = 0.08 (29 / 386), avg. gap size = 1.55 (45 / 29) 27 0.00 3.33 0.00 chr2qtel1M 601399 601428 (398572) (AAAAC)n#Simple_repeat 1 31 (0) c_b98s251i2 3616 chr2qtel1M 601399 AAAACAAAACAAAACAAAACAAAA-AAAACA 601428 - (AAAAC)n#Simp 1 AAAACAAAACAAAACAAAACAAAACAAAACA 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 13 21.28 0.00 0.00 chr2qtel1M 604011 604043 (395957) (AAAAAG)n#Simple_repeat 1 33 (0) m_b98s252i2 3617 chr2qtel1M 604011 AAAAAATACAGGAAAAAAAAAAAGAAGAAGAAA 604043 iv v i i i (AAAAAG)n#Sim 1 AAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAA 33 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 36 10.57 1.64 0.00 chr2qtel1M 604776 604836 (395164) (TA)n#Simple_repeat 1 62 (0) c_b98s251i3 3618 chr2qtel1M 604776 TATATATATTTACATATATATA-ATGTGTATATATATATTTATATTTATA 604824 v i - i i v v (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr2qtel1M 604825 TATATATATATA 604836 (TA)n#Simple_ 51 TATATATATATA 62 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.02 (1 / 60), avg. gap size = 1.00 (1 / 1) 1039 28.01 3.93 2.40 chr2qtel1M 605031 605564 (394436) C L1ME3G_3end#LINE/L1 (376) 548 7 m_b98s551i2 3619 chr2qtel1M 605031 ATAATAATCCATAAGCTTCATGTACCACAACTTGTTCAGCCATTCCCCAG 605080 i v ivv vv i i i i i i vi C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr2qtel1M 605081 TTGATGAACATCCATTCCTTTTCCAATTCTGTGTTACTACAAAAAGAGCT 605130 i ii vviiv i vi i i v iv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr2qtel1M 605131 GCTGCAAATATTATTGCACATGTGGGTCCTTGTCC-C-TTTTTGATGATG 605178 viii i iv i i?-- v - - v vi vv v C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATT 401 chr2qtel1M 605179 TCT-TGGGATAAAGACCCTGTAGAGACACTGCTGGATCCAAGGGTATGCA 605227 - i i v? ?v v v iv i i v i C L1ME3G_3end#L 400 TCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCG 351 chr2qtel1M 605228 CAGTTTGATAGCCCTTTGG-ACATAGTTCCAAATTACTCTCCACAATATT 605276 v i ----vi ii- v v v i i v ?ivi C L1ME3G_3end#L 350 CATTTTAA----ATTTTAATAGATACTGCCAAATTGCCCTCCAAAANGGC 305 chr2qtel1M 605277 TGGATCATTTCAGAAGTCCCCCAACAATGCATTAGTGTCCCACTTTTCCC 605326 v i v i v vvi v i i i v v v vv i C L1ME3G_3end#L 304 TGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCC 255 chr2qtel1M 605327 ACATCCCCTCTAATATT--ATCTTTTC---CTGT--GATCTTAGCCAATC 605369 i i v i i i -- v v --- v --i i v C L1ME3G_3end#L 254 ACACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATC 205 chr2qtel1M 605370 TGAGAGGTGTGAGATGGTACCAGATTGT-GT---AATTTGCATTTCTCTT 605415 vi vi i i vv - --- i v C L1ME3G_3end#L 204 TGATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTG 155 chr2qtel1M 605416 ATCAATAGTGATTTAGAGCATTTTTTCATATAATCCTAATTGGC--TTTA 605463 i v vv v i iv i--- -- i C L1ME3G_3end#L 154 ATTACTAGTGAGGTTGAGCATCTTTTCATATGTTT---ATTGGCCATTTG 108 chr2qtel1M 605464 -ATTTCCTCATCTGAAAATTATCTATTCATATCCTTTGACCATGTATCAA 605512 - v vi ii i v v v v C L1ME3G_3end#L 107 TATTTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTA 58 chr2qtel1M 605513 TTAAGGAATGACTTGCATTCTTATAAATTTAC---AATTCTTTATATATC 605559 -- iv v v-- vi ii--- i i C L1ME3G_3end#L 57 TT--GGGTTGTCTTT--TTCTTATTGATTTGTAGGAGTTCTTTATATATT 12 chr2qtel1M 605560 TTAGA 605564 i i C L1ME3G_3end#L 11 CTGGA 7 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.08 CpG sites = 77, Kimura (unadjusted) = 35.99 Transitions / transversions = 1.12 (77/69) Gap_init rate = 0.05 (25 / 533), avg. gap size = 1.36 (34 / 25) 402 24.80 6.45 4.58 chr2qtel1M 605424 605702 (394298) C L1M2_orf2#LINE/L1 (0) 3291 3008 m_b98s551i3 3619 chr2qtel1M 605424 TGATTTAGAGCATTTTTTCATATAATCCTAATTGGC--TTTA-ATTTCCT 605470 v v -- -i -- i- v i C L1M2_orf2#LIN 3291 TGATGTTGAGCATTTTTTCATATA--CCT-GTTGGCCATTTGTATGTCTT 3245 chr2qtel1M 605471 CATCTGAAAATTATCTATTCATATCCTTTGACCATGTATCAATTAAGGAA 605520 v i i v i vi v v v ? i--- i C L1M2_orf2#LIN 3244 CTTTTGAGAAATGTCTATTCAGGTCCTTTGCCCATTTTTNAATC---GGA 3198 chr2qtel1M 605521 TGACTTGCATTCTTA----TAAAT--TTACAATTCTTTATATATCTTAGA 605564 v i iv i i---- i i -- vv i i ii i C L1M2_orf2#LIN 3197 TTATTTGTTTTTTTGCTGTTGAGTTGTTTGAGTTCCTTATATATTCTGGA 3148 chr2qtel1M 605565 AATGAAACCTTTATCAGATATA---CTTGCCATAAAGATTTTTTCCCAGG 605611 v v v i i i? ---i --- v i -- C L1M2_orf2#LIN 3147 TATTAATCCCTTGTCAGATGNATAGTTTGC---AAATATTTTCTCCCA-- 3103 chr2qtel1M 605612 TTTCTAT---TTCCCTCTTAATCTTGTT-ACTGGTGGTTTTGTTTGTGCA 605657 - i --- vi v iii - i v vvi -i C L1M2_orf2#LIN 3102 -TTCTGTAGGTTGTCTCTTCACTCTGTTGATTGTTTCCTTTG-CTGTGCA 3055 chr2qtel1M 605658 AAAAC-GTTTACTTTATTGTAATCAAAGTTGTCCA-TTTTGCCTTTG 605702 i i -v v iv vv v i - i C L1M2_orf2#LIN 3054 GAAGCTTTTTAGTTTGATGTAATCCCATTTGTCTATTTTTGCTTTTG 3008 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 30.44 CpG sites = 38, Kimura (unadjusted) = 31.00 Transitions / transversions = 1.36 (38/28) Gap_init rate = 0.08 (22 / 278), avg. gap size = 1.41 (31 / 22) 233 30.16 13.19 1.64 chr2qtel1M 606206 606751 (393249) C L1P4_orf2#LINE/L1 (872) 2422 1815 m_b98s551i4 3619 chr2qtel1M 606206 CAACCCA--ACCATGAAATATTTTTCCGTT-GTTTGTCGTGATTTTC--T 606250 i -- v i i i - - v i ?i-- C L1P4_orf2#LIN 2422 CAATCCATGAGCATGGAATGTTTTTCCATTTGTTTGT-GTCATCTNTGAT 2374 chr2qtel1M 606251 TTGTGTAAGAAGTGTTTTGTAATTGTGTTCTTGGTA------TTTAGTTT 606294 v v v v i ---i i v ------ viii C L1P4_orf2#LIN 2373 TTCTTTCAGCAGTGTTTTGTAGTT---CTCCTTGTAGAGATCTTTCACCT 2327 chr2qtel1M 606295 TGCCGGC-AG-CGT-TCCCCATTTATTTTATTTTGTCTATAGATATT--- 606338 ivii i- -i - i i vv v i i i v --- C L1P4_orf2#LIN 2326 CCTTGGTTAGATGTATTCCTAGGTATTTTATTTTTTTTGTGGCTATTGTA 2277 chr2qtel1M 606339 ------------TTCTT--TGTATCTCTTTGCTTGGGCTTTATCAATA-A 606373 ------------ -- v iv iv ii v iii i- C L1P4_orf2#LIN 2276 AATGGGATTGCGTTCTTGATTTGGCTCTCAGCTTGAACGTTATTGGTGTA 2227 chr2qtel1M 606374 TAAGAA-AATACTGATTTTGTTTGGGC-TTCATTTTATATACTGCAATTT 606421 ii -iv --- vi - v i v v i C L1P4_orf2#LIN 2226 TAGAAATGCTACTGATTTT---TGTACATTGATTTTGTATCCTGAAACTT 2180 chr2qtel1M 606422 TGCTAAAGCTGTG-ATTGTTTTCAGTAGATATTTTGATGG--TTTTCTAG 606468 i i ii v- iiv ii v vi- ii -- i ivi C L1P4_orf2#LIN 2179 TACTGAAGTCGTTTATCAGTTCTAGGAGCC-TTTTGGCGGAGTCTTTAGG 2131 chr2qtel1M 606469 GTTCTCAAAGTAACTCATCAT-TCACC--CCAAAAGTAATAGTTTTATTT 606515 i v i vvvv - ii -- v i vi v i C L1P4_orf2#LIN 2130 GTTTTCTAGGTATAGAATCATATCGTCAGCGAAGAGAGATAGTTTGACTT 2081 chr2qtel1M 606516 C--CCTTTCCTATTCTAATTCCTTTTGCTTTTTTCTTTT--CTTATCAA- 606560 -- i ivi v ii i i -- v iiv- C L1P4_orf2#LIN 2080 CTTCTTTTCCTATTTGGATGCCTTTTATTTCTTTCTCTTGCCTGATTGCT 2031 chr2qtel1M 606561 CAAGCTAACATTTCTAGAAC-AAATTGAATAACAGTGGTGTAATTTAACC 606609 vi iv i i v - vi iv vi v vii v C L1P4_orf2#LIN 2030 CTGGCTAGGACTTCCAGTACTATGTTGAATAGGAGTGGTGAGAGTGGGCA 1981 chr2qtel1M 606610 CCCTGAT----------TTCT-----GGAATGCATCCAGCTTCTTTCATT 606644 i vi ---------- ----- v i vi vv C L1P4_orf2#LIN 1980 TCCTTGTCTTGTTCCAGTTCTCAAGGGGAATGCTTCCAGCTTTTGCCCGT 1931 chr2qtel1M 606645 TCA-TATAATGTT--TTATGGTTT-----TAAAAGATTTTTATTGTTTTA 606686 - i --i i v ----- i v ii i i i C L1P4_orf2#LIN 1930 TCAGTATGATGTTGGCTGTGGGTTTGTCATAGATGGCTCTTATTATTTTG 1881 chr2qtel1M 606687 AGGAAAGTTCCCTTTATCCATATGCCTTTTGGTGTTTATTGATAGGAATG 606736 v v i iv v v - ii v iv v v ivi v - C L1P4_orf2#LIN 1880 AGGTATGTTCCTTCGATGCCTA-GTTTGTTGAGGGTTTTTATCATGAA-G 1833 chr2qtel1M 606737 GGATGT---ATTTTGTCG 606751 --- i C L1P4_orf2#LIN 1832 GGATGTTGGATTTTATCG 1815 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.71 CpG sites = 96, Kimura (unadjusted) = 40.00 Transitions / transversions = 1.45 (96/66) Gap_init rate = 0.07 (37 / 545), avg. gap size = 2.22 (82 / 37) 291 27.28 14.97 1.62 chr2qtel1M 606400 607107 (392893) C L1M5_orf2#LINE/L1 (1093) 2201 1401 m_b98s551i5 3619 chr2qtel1M 606400 TTCATTTTATATACTGCAATTTTGCTAAAGCTG-TGATTGTTTTCAGTAG 606448 v ii i v ? i ii viii- v iv ii C L1M5_orf2#LIN 2201 TTGACCTTGTATCCNGCGACCTTGCTAAATTCACTTATTAGTTCTAGTAG 2152 chr2qtel1M 606449 ATATTTTGATGGTTTTCTAGG-TTCTCAAAGTAACTCATCAT-TCACC-- 606494 v v? vv i i i ? - i v v ?viv - i -- C L1M5_orf2#LIN 2151 TTTNTTTGTAGATTCTTTNGGATTTTCTACGTANACAATCATGTCATCTG 2102 chr2qtel1M 606495 CCAAAAGTAATAGTTTTATTTC--CCTTTCCTATTCTAATTCCTTTTGCT 606542 v v i?i i -- v ii v v ii C L1M5_orf2#LIN 2101 CGAATAANGACAGTTTTATTTCTTCCTTTCCAATCTTTATGCCTTTTATT 2052 chr2qtel1M 606543 --TTTTTCTTTTCTTATCA-ACAAGCTAACATTTCTAGAACAA-ATTGAA 606588 -- vi ii- vi iv ii i v -i C L1M5_orf2#LIN 2051 TCTTTTTCTTGCCTTATTGCACTGGCTAGGACCTCCAGTACAATGTTGAA 2002 chr2qtel1M 606589 TAACAGTGGTGTAATTTAAC--CC----------CCTGATTTC---TGGA 606623 iv v? vivi -- ---------- i i i---v C L1M5_orf2#LIN 2001 TAGAAGTGGTGANAGCGGACATCCTTGTCTTGTTCCCGATCTTAGGGGGA 1952 chr2qtel1M 606624 ATGCATCCAGCTTCTT-TCATTTCATATAATGTTT----TATGGTTTTAA 606668 v ? i i? i i-i vvi i ?---- v v vi C L1M5_orf2#LIN 1951 AAGCNTTCAGTNTTTCACCATTAAGTATGATGTTNGCTGTAGGTTTTTCG 1902 chr2qtel1M 606669 AAGAT---TTTTATTGTTTTAAGGAAAGTTCCCTT-TATCCATATGCCTT 606714 v ---i iivv i - - i v - ii v C L1M5_orf2#LIN 1901 TAGATGCCCTTTATCAGGTTGAGG-AAGTTCCCTTCTATTCCTA-GTTTG 1854 chr2qtel1M 606715 TTG---GTGTTTATTGATAGGAATGGGATGT---ATTTTGTC----GTTT 606754 i --- v ---i v - --- ---- i C L1M5_orf2#LIN 1853 CTGAGAGTTTTTAT---CATGAATGGG-TGTTGAATTTTGTCAAATGCTT 1808 chr2qtel1M 606755 TCTCT---TTT-TTGGGATTGTAATA--ATTCTGTTCGTTT----TGTT- 606793 i --- i - i vi v -- i vi v ---- - C L1M5_orf2#LIN 1807 TTTCTGCATCTATTGAGATGATCATATGATTTTTCTCCTTTATTCTGTTA 1758 chr2qtel1M 606794 AT-TGGTGGGCCAATATTAA--GTTTTCCTGATACTGACCCAA-----TA 606835 - iiii- i i -- v i vi ii i v -----i C L1M5_orf2#LIN 1757 ATATGGTGAATT-ACATTGATTGATTTTCGAATGTTAAACCAACCTTGCA 1709 chr2qtel1M 606836 TTTCT-GTATAAATCCCA-TTG-------TGTACTATCCTGCTCATAAGG 606876 i - v i - ------- i vi i viv C L1M5_orf2#LIN 1708 TTCCTGGGATAAACCCCACTTGGTCATGATGTATTATCCTTTTTATATAT 1659 chr2qtel1M 606877 CTTTAAACTC--TTTGCTAAT-TGTTATTTA-AATTTTAAGATT------ 606916 ivi ii i -- - v i ? -i viv i------ C L1M5_orf2#LIN 1658 TGCTGGATTCGATTTGCTAATATTTTGTTNAGGATTTTTGCATCTATGTT 1609 chr2qtel1M 606917 -----GGGATATTGGTCT-TAATTTATTTTTTTTTCTTTTAGC-CCTTTG 606959 ----- - ---- i v ii-i C L1M5_orf2#LIN 1608 CATGAGGGATATTGGTCTGTA----ATTTTCTTTTCTTGTAATGTCTTTG 1563 chr2qtel1M 606960 T----TTTTGGT---AG---AATCCATAATTT--TAAAACAAAAAGGGA- 606996 ---- --- ---? v - iiii -- ii ivv - C L1M5_orf2#LIN 1562 TCNGGTTTTGGTATCAGGGTNATGC-TGGCCTCATAAAATGAGTTGGGAA 1514 chr2qtel1M 606997 -TACTCCTTCCTTATTT-TTTTCC-AAATAGTTGACATAGTATTGGAAGT 607043 - ii i i v i - i-i v viii iv v v C L1M5_orf2#LIN 1513 GTGTTCCCTCTTTTTCTATTTTCTGGAAGAGTTTGTGTAAGATTGGTATT 1464 chr2qtel1M 607044 AATTGTTCTTTAAATGTTTGGGAGAATTCACTTGCAAATCCAAGTGGCCC 607093 v v i v iv ii v vv v C L1M5_orf2#LIN 1463 ATTTCTTCCTTAAATGTTTGGTAGAATTCACCAGTGAAGCCATCTGGGCC 1414 chr2qtel1M 607094 TGGAGATTTTCTTT 607107 - C L1M5_orf2#LIN 1413 TGGAG-TTTTCTTT 1401 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.84 CpG sites = 117, Kimura (unadjusted) = 35.79 Transitions / transversions = 1.60 (117/73) Gap_init rate = 0.08 (57 / 707), avg. gap size = 2.09 (119 / 57) 314 25.71 0.00 2.75 chr2qtel1M 606999 607110 (392890) C L1M1_orf2#LINE/L1 (1788) 1506 1398 m_b98s551i6 3619 chr2qtel1M 606999 CTCCTTCCTTATTTTTTTCCAAATAGTTGACATAGTATTGGAAGTAATTG 607048 i ii -- vi vivi v v v i v C L1M1_orf2#LIN 1506 CTCCTCCTCTATTTTT--CGGAATAGTTTGAGTAGGATTGGTATTAGTTC 1459 chr2qtel1M 607049 TTCTTTAAATGTTTGGGAGAATTCACTTGCAAATCCAAGTGGCCCTGGAG 607098 v viv ii v vvv i i - C L1M1_orf2#LIN 1458 TTCTTTAAATGTTTGGTAGAATTCAGCAGTGAAGCCATCGGGTCCCGG-G 1410 chr2qtel1M 607099 ATTTTCTTTTCT 607110 v v C L1M1_orf2#LIN 1409 CTTTTCTTTACT 1398 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 30.26 CpG sites = 12, Kimura (unadjusted) = 31.55 Transitions / transversions = 0.75 (12/16) Gap_init rate = 0.03 (3 / 111), avg. gap size = 1.00 (3 / 3) 266 31.66 9.38 5.70 chr2qtel1M 608350 608637 (391363) L1PA4_3end#LINE/L1 22 319 (583) m_b98s551i7 3620 chr2qtel1M 608350 GAACTGACAGAAATTTATAA---AAATGCAAGCCATTCTCCAATTGATAA 608396 v v v i --- vi i v i--- v ii v L1PA4_3end#LI 22 GAACTCAAACAAATTTACAAGAAAAAAACAAACAAC---CCCATCAAAAA 68 chr2qtel1M 608397 ATGGTCAAAGAATCTGAACAA----TTTTTAAATGAAAAAA--------- 608433 i v i i v i---- i i v i v --------- L1PA4_3end#LI 69 GTGGGCGAAGGATATGAACAGACACTTCTCAAAAGAAGACATTTATGCAG 118 chr2qtel1M 608434 -CAAAAGTCATTTCTAGTCTTATGAAAAAATGTTCTAAATCACTATGGGT 608482 - v i---------- i vvv ivvvi L1PA4_3end#LI 119 CCAAAAGACAC----------ATGAAAAAATGCTCATCATCACTGGCCAT 158 chr2qtel1M 608483 CAGAGAAATGTAAATTAAGACACCTCTGAGGTAACAGATATTTCAGATTA 608532 i i i vv vv i v ---- i v ii L1PA4_3end#LI 159 CAGAGAAATGCAAATCAAAACCACAATGAGATACCA----TCTCACACCA 204 chr2qtel1M 608533 GCTAAAATGAC-------AGGAA---AGATAATGATGTATGTTGAAGGGA 608572 i i i ------- ii --- iv ii iivi i i i i L1PA4_3end#LI 205 GTTAGAATGGCGATCATTAAAAAGTCAGGAAACAACAGGTGCTGGAGAGG 254 chr2qtel1M 608573 ATGGGGAAAAACTGGGACAGTAATACTTTGTTGGTGGAGTTATGAACTGA 608622 v i iv i v vv vi iii i i ii L1PA4_3end#LI 255 ATGTGGAGAAATAGGAACACTTTTACACTGTTGGTGGGACTGTAAACTAG 304 chr2qtel1M 608623 TCCAGTCATTCTGGA 608637 i ii v L1PA4_3end#LI 305 TTCAACCATTGTGGA 319 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 42.27 CpG sites = 53, Kimura (unadjusted) = 42.94 Transitions / transversions = 1.61 (53/33) Gap_init rate = 0.08 (23 / 287), avg. gap size = 1.91 (44 / 23) 571 31.03 6.62 2.84 chr2qtel1M 608384 608791 (391209) L1ME5_3end#LINE/L1 56 478 (463) m_b98s551i8 3620 chr2qtel1M 608384 CTCCAATTGATAAATGGTCAAAGAATCTGAACA----ATTTTTAAATGAA 608429 i v v v i v ---- vi i v i L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chr2qtel1M 608430 AAAAC--AAAAGTCATTTCTAGTCTTATGAAAAAATGTTCTAAATCACTA 608477 i --i v - vv v - v i i i v v i L1ME5_3end#LI 106 GAAACCCGAAAGGC-TAACAAG-CATATGAAGAGATGCTCAAACTCATTA 153 chr2qtel1M 608478 TGGGTCAGAGAAATGTAAATTAAGACACCTCTGAGGTA-------ACAGA 608520 vvii i i v vv i ------- vv L1ME5_3end#LI 154 GTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACC 203 chr2qtel1M 608521 TATTTCAGATTAGCTAAAATGACAGGAAAG----ATAATGATGTATGTTG 608566 -- i i v v --- ---- viivi L1ME5_3end#LI 204 TATT--AGACTGGCAAAAATTA---GAAAGCTGGATAATGCCAAGTGTTG 248 chr2qtel1M 608567 AAGGGAATGGGGAAAAACTGGGACAGTAATACTTTGTTGGTGGAGTTATG 608616 iv i i v ii ? iv i vv v i vi i iiv i i L1ME5_3end#LI 249 GCGAGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTA 298 chr2qtel1M 608617 AACTGATCCAGTCATTCTGGAGAAAAATATAGAACTAT---GCCTAA--A 608661 i i v i iv v i v v i--- i v -- L1ME5_3end#LI 299 GACTGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTA 348 chr2qtel1M 608662 ATTTTA--CATACTCTTTGATCCAGCAGTATCTCTACTGAACCTGTATCT 608709 v v -- i v i i vi v v iiiv i i L1ME5_3end#LI 349 AGTATACGCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATATCC 398 chr2qtel1M 608710 CAAAGAGATT---ACAGAGAAGCGAAAAGGCCTTCTACATGTGCAGAAAT 608756 i --- v ivv iv i -----v i iiii L1ME5_3end#LI 399 CAAAGAAATTCTCACACAGGTCCATAAGGG-----GACATGTACGAGGAT 443 chr2qtel1M 608757 GTTTGTAACAGCCTTTTCTGTAGTGGAAAGAGGTT 608791 ii vi v v i i vii ii L1ME5_3end#LI 444 GTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTT 478 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.96 CpG sites = 69, Kimura (unadjusted) = 41.27 Transitions / transversions = 1.28 (69/54) Gap_init rate = 0.05 (20 / 407), avg. gap size = 1.95 (39 / 20) 306 31.22 8.77 4.49 chr2qtel1M 613432 613602 (386398) C MIRb#SINE/MIR (76) 192 15 m_b98s601i3 3621 chr2qtel1M 613432 TTTTATCCTCCTGAGAACCCTAGGACCTGGGTGCCATTTTTGGGCCCTTC 613481 v vii v iv vv i iii v i--- v i C MIRb#SINE/MIR 192 TTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATTATC---CCCATT 146 chr2qtel1M 613482 TTATACATAAAGAAACTGAGGCAAACAGAGGCCTTGTAAGTTG------- 613524 i v i i vv v iivv v ------- C MIRb#SINE/MIR 145 TTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGG 96 chr2qtel1M 613525 -------ACTAGCGAGTTGCTGAGGTGGGATGAACACTCAGGTCTTGCTG 613567 -------i ii v v vi vviv i vv C MIRb#SINE/MIR 95 TCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTG 46 chr2qtel1M 613568 A-TTGAAGGCCCTGTTCACACTTTTCCCTCTGTACC 613602 - iv i - ----i i i v i C MIRb#SINE/MIR 45 ACTCCAAAGCCC-GT----GCTCTTTCCACTGCACC 15 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.08 CpG sites = 26, Kimura (unadjusted) = 41.13 Transitions / transversions = 1.04 (26/25) Gap_init rate = 0.06 (11 / 170), avg. gap size = 2.09 (23 / 11) 255 24.39 11.27 10.49 chr2qtel1M 613476 613617 (386383) C MIR3#SINE/MIR (61) 147 5 m_b98s601i4 3621 chr2qtel1M 613476 CCCT--TCTTATACATAAAGAAACTGAGGCAAACAGAGGC-------CTT 613516 -- i i v i i vv v i------- C MIR3#SINE/MIR 147 CCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTT 98 chr2qtel1M 613517 G--TAAGTTGAC-TAGCGAGTT----GCTGAGGTGGGATGAACACTCAGG 613559 --i v v -i ? ---- v vi iv iv i C MIR3#SINE/MIR 97 GCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGG 48 chr2qtel1M 613560 TCTTGCTGATTGAAGGCCCTGTTCACACTTTTCCCTCTGTACCCTCAGTT 613609 i- i ----- v i iii i --- ---- -- C MIR3#SINE/MIR 47 TCTC-CTGACT-----CCCAGTCCGTGCTCT---CTCTG----CTCAG-- 13 chr2qtel1M 613610 CTATTCTG 613617 i i C MIR3#SINE/MIR 12 CCACTCTG 5 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.39 CpG sites = 20, Kimura (unadjusted) = 30.74 Transitions / transversions = 1.82 (20/11) Gap_init rate = 0.14 (20 / 141), avg. gap size = 1.55 (31 / 20) 28 33.46 2.29 3.47 chr2qtel1M 615482 615656 (384344) (CTTTTT)n#Simple_repeat 1 173 (0) m_b98s252i3 3622 chr2qtel1M 615482 CTTTCCCTTTTTCTTTGGATTTCCATTTTTAAACCTTCCTTAAGTTTTGT 615531 ii vvv iiv -vvii i vvv vi (CTTTTT)n#Sim 1 CTTTTTCTTTTTCTTTTTCTTTTTCTTTTT-CTTTTTCTTTTTCTTTTTC 49 chr2qtel1M 615532 TTTTTCATTTTGCCTTTAAATTTCCCATTTCCCTTTAATTCTTTTTCTTT 615581 - -i vvv ii - ii -- (CTTTTT)n#Sim 50 TTTTTC-TTTT-TCTTTTTCTTTTTC-TTTTTCTTT--TTCTTTTTCTTT 94 chr2qtel1M 615582 CCCCATTAATTTTTATTTTTCCTTTTCCAGAT-TTTTTC--TTCCCTTTA 615628 ii iv vv v i ivvv - -- i i v (CTTTTT)n#Sim 95 TTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTT 144 chr2qtel1M 615629 CTTTTT-TTTTTGTTTTCCTTTTTTTTTT 615656 - v i i (CTTTTT)n#Sim 145 CTTTTTCTTTTTCTTTTTCTTTTTCTTTT 173 Matrix = Unknown Transitions / transversions = 1.00 (22/22) Gap_init rate = 0.05 (9 / 174), avg. gap size = 1.11 (10 / 9) 26 24.77 1.45 0.00 chr2qtel1M 617551 617619 (382381) (CTCT)n#Simple_repeat 1 70 (0) m_b98s252i5 3623 chr2qtel1M 617551 CTCTCTCCCTCCCTCCTTTTCTCCTTCCCTCCCTCCCTCTCTCTGTCTCT 617600 i i ii i ii i i i v (CTCT)n#Simpl 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chr2qtel1M 617601 GTCTCTAT-TCTCTCTTTCT 617619 v v - i (CTCT)n#Simpl 51 CTCTCTCTCTCTCTCTCTCT 70 Matrix = Unknown Transitions / transversions = 3.67 (11/3) Gap_init rate = 0.01 (1 / 68), avg. gap size = 1.00 (1 / 1) 13 22.02 4.08 2.00 chr2qtel1M 618373 618421 (381579) (AATTC)n#Simple_repeat 1 50 (0) m_b98s252i6 3624 chr2qtel1M 618373 AATTCCAACTCTGTTGAATT-AAAGAAATTC-ATTCAATTTTATTCAATT 618420 - i vi v - vvv - iv (AATTC)n#Simp 1 AATT-CAATTCAATTCAATTCAATTCAATTCAATTCAATTCAATTCAATT 49 chr2qtel1M 618421 C 618421 (AATTC)n#Simp 50 C 50 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.06 (3 / 48), avg. gap size = 1.00 (3 / 3) 249 31.45 1.39 2.82 chr2qtel1M 621835 621978 (378022) L1ME4c_3end#LINE/L1 414 555 (275) m_b98s551i9 3625 chr2qtel1M 621835 TTAAAGGAGGGAAAGAGACCCACATTGCA-AAAAATGTTTGCGGCAGCTC 621883 i i i i -- i i - -i i iiiv vi L1ME4c_3end#L 414 TCAAAAGAAGGAAAAAG--CTATAT-GCACGAAGATGTTCATTGCAGCGT 460 chr2qtel1M 621884 TTTCTGTAGTGGCAAGAAACTGGTAAATGAG-TGGATGCCCATCAGTGGG 621932 v i i i i i i i - ii v- ii i v i i L1ME4c_3end#L 461 TATTTATAATAGCGAAAAATTGG-AAACAACCTAAATGTCCAACAATAGG 509 chr2qtel1M 621933 GGAATGGCTGAATAAGTTATGACATATGAATGTGTTGGAATGTTAT 621978 i i i i ii i v? ivi v i L1ME4c_3end#L 510 GGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATATTAT 555 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.53 CpG sites = 36, Kimura (unadjusted) = 45.90 Transitions / transversions = 4.50 (36/8) Gap_init rate = 0.04 (6 / 143), avg. gap size = 1.00 (6 / 6) 261 31.57 0.87 0.87 chr2qtel1M 621864 621978 (378022) L1ME3G_3end#LINE/L1 434 548 (376) m_b98s551i10 3625 chr2qtel1M 621864 AAAAATGTTTGCGGCAGCTCTTTCTGTAGTGGCAAGAAACTGGTAAATGA 621913 ii iiiv vi v i i i i i i - ii L1ME3G_3end#L 434 AAGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGG-AAACAA 482 chr2qtel1M 621914 G-TGGATGCCCATCAGTGGGGGAATGGCTGAATAAGTTATGACATATGAA 621962 v- ii i i i i i i ii vv L1ME3G_3end#L 483 CCTAAATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCA 532 chr2qtel1M 621963 TGTGTTGGAATGTTAT 621978 iivv ii L1ME3G_3end#L 533 TACTATGGAATACTAT 548 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 43.22 CpG sites = 28, Kimura (unadjusted) = 44.99 Transitions / transversions = 3.50 (28/8) Gap_init rate = 0.02 (2 / 114), avg. gap size = 1.00 (2 / 2) 23 23.64 0.00 0.00 chr2qtel1M 622508 622557 (377443) (TA)n#Simple_repeat 1 50 (0) m_b98s252i7 3626 chr2qtel1M 622508 TATACATGCATGTGTGTATATATCTATATCTATATATAGATATAGATATA 622557 i ii i i i v v v v (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 Matrix = Unknown Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 887 32.50 2.03 1.21 chr2qtel1M 622751 623242 (376758) C L1ME4c_3end#LINE/L1 (275) 555 60 m_b98s551i11 3627 chr2qtel1M 622751 ATAATAGTCCATAAGCTTCATGTACCACAACTCGTTCAGCCATTCCCCAG 622800 v viiv ?v i i iii i i vi C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chr2qtel1M 622801 TTGGTAAGCATCTATTCCTTTTCCATTTCTGTATTACCACAAAAAGAACT 622850 v iii i vviiv v i viii ii i v ivi C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCT 456 chr2qtel1M 622851 GCTGTAAACATCTTTGAATATGTGGGTCCTTTTCCCTTTTT---ATGATG 622897 vi i i vii i i -- i i i --- v v C L1ME4c_3end#L 455 GCAATGAACATCTTCGTGCATATAG--CTTTTTCCTTCTTTTGAATTATT 408 chr2qtel1M 622898 TCTTTGGGATAAAGATCCTGTAGAGACACTGCTGGATCCAAGGGTATGCA 622947 i i vvi v v v iv i i i v v C L1ME4c_3end#L 407 TCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAA 358 chr2qtel1M 622948 CAGTTTGATAGCCCTTTGGACATAGTTCCAAATTACTCTCCACAATGGTT 622997 v v i i viv i v v i i v v C L1ME4c_3end#L 357 CATTTTTATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTT 308 chr2qtel1M 622998 AGATCATTTCAGAATTCCCCCAACAATGCATTAGTGT-CCACTTTTCTCA 623046 iv i v i v ? v v i i v ? - v ivi i C L1ME4c_3end#L 307 GTACCAATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCACCG 258 chr2qtel1M 623047 CATCCACTTTAATATTAATCATTATCTTTTCCTGTGATCTTAGCCGATCT 623096 ? v vii ii iivi vv ii vvi i v ii i C L1ME4c_3end#L 257 CANCCTCGCCAGCATTGGGTATTATCAATTTTTTAAATTTTTGCTAATTT 208 chr2qtel1M 623097 GAGACGTGTGAGGTGGTACCTCAGAGATA-TGTAATTTGTATTTCTCTTA 623145 i v v i i ii i vv v i- v i i v C L1ME4c_3end#L 207 AATAGGCGTAAAATGGTATCTCATTGTTGCTTTAATTTGCATTTCTTTGA 158 chr2qtel1M 623146 TCAATAGTGATTTAGAGCATTTTTTCATATAACT-----CTAATTGGCTT 623190 i v i vv v i i i ivi ----- ? ---- C L1ME4c_3end#L 157 TTACTAGCGAGGTTGAACATTTTTCCATGTGTTTGTTTACTANTTG---- 112 chr2qtel1M 623191 TAATTTCCCATCTGAAAATTGTCTGTTCATATCCTTTGACCATGTAGCAA 623240 v i i v ? vi i v v v v C L1ME4c_3end#L 111 TATTTCCTCTTNTGTGAATTGTCTGTTCATGTCCTTTGCCCATTTATCTA 62 chr2qtel1M 623241 TT 623242 C L1ME4c_3end#L 61 TT 60 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.63 CpG sites = 90, Kimura (unadjusted) = 44.68 Transitions / transversions = 1.32 (90/68) Gap_init rate = 0.02 (10 / 491), avg. gap size = 1.60 (16 / 10) 19 6.31 2.86 2.86 chr2qtel1M 623358 623392 (376608) (GGA)n#Simple_repeat 1 35 (0) m_b98s252i8 3628 chr2qtel1M 623358 GGTGGAGGGAGAAGGAGGAGGAGGAGGAGGA-GAGG 623392 v - i - (GGA)n#Simple 1 GGAGGA-GGAGGAGGAGGAGGAGGAGGAGGAGGAGG 35 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 28 0.00 0.00 0.00 chr2qtel1M 623461 623490 (376510) (A)n#Simple_repeat 1 30 (0) m_b98s252i9 3629 chr2qtel1M 623461 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 623490 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 30 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 16 16.62 1.54 10.00 chr2qtel1M 627407 627471 (372529) (AGTCCAA)n#Simple_repeat 1 60 (0) m_b98s252i10 3630 chr2qtel1M 627407 AGTCCAAAGTCCAAAATAGTCCAAAATCCATTGTCCATTAGTTC-ATGTT 627455 -- - i vv -v i - v i (AGTCCAA)n#Si 1 AGTCCAAAGTCC--AA-AGTCCAAAGTCCAAAGTCCA-AAGTCCAAAGTC 46 chr2qtel1M 627456 CTAAGTACTCAAAGTC 627471 v - - (AGTCCAA)n#Si 47 CAAAGT-C-CAAAGTC 60 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.11 (7 / 64), avg. gap size = 1.00 (7 / 7) 14 18.95 2.78 0.00 chr2qtel1M 627886 627921 (372079) (TCTC)n#Simple_repeat 1 37 (0) m_b98s252i11 3631 chr2qtel1M 627886 TCTCTCACTCTGTC-CTCTCACTCTTTCTCTGTATCT 627921 v v - v i v v (TCTC)n#Simpl 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 37 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) 1518 31.03 3.49 3.23 chr2qtel1M 630273 631877 (368123) C L1M5_orf2#LINE/L1 (612) 2682 1074 m_b99s551i0 3632 chr2qtel1M 630273 TCTATTTCTTA-GCCAGTACCGAATGGT-TTGATTACTGCTGCTTTGTAA 630320 i- - i iv iv - iv i C L1M5_orf2#LIN 2682 TCTATC-CTTACGCCAATACCACACTGTCTTGATTACTGTAGCTTTATAA 2634 chr2qtel1M 630321 CATAGCTCAAGGATTGGTACTGCTAAACCACCATCCTTTATATTTTGTTG 630370 i viv ii ?ivi? v - i------ ii - i v C L1M5_orf2#LIN 2633 TAAGTCTTGANATCNGGTAGTG-TAAG------TCCTCCA-ACTTTGTTC 2592 chr2qtel1M 630371 TTGTTGTTAA----TCCCTTGA-TATTCTTGACCATTTTTTCTTCTAGAC 630415 v v v ---- vii i- ? ii v vivi i v i C L1M5_orf2#LIN 2591 TTCTTTTTCAAGATTGTTTTGGCTATTCTNGGTCCTTTGCATTTCCATAT 2542 chr2qtel1M 630416 AGTTTTTGTTGTT--TTTTTCTATTTCTACAAAA---TGTTTTTGCAGTT 630460 iv ivvi i--i v v ---iv vi v v v C L1M5_orf2#LIN 2541 AAATTTTAGAATCAGCTTGTCAATTTCTACAAAAAAACCTGCTGGGATTT 2492 chr2qtel1M 630461 TGATTGTTATGGCACTAAACAAATAGACCAATTTAGGCAAAATTGTGAT- 630509 vv v i i ivv i i v i vv - C L1M5_orf2#LIN 2491 TGATTGGGATTGCATTGAATCTATAGATCAATTTGGGGAGAATTGACATC 2442 chr2qtel1M 630510 -TTATA-TATCAGAACAACCTAGCCATGAACAATTAATATTTTTCCAGTT 630557 - ? i - iiiiv vv v v vvvv i i v C L1M5_orf2#LIN 2441 TTNACAATATTGAGTCTTCCAATCCATGAACATGGTATATCTCTCCATTT 2392 chr2qtel1M 630558 GTTTAGATCTGATTTTCTTTGTGTGAGAAGTGTTTTGTAATTGT--GTTC 630605 i i vv vv v v v v i i v -- vi C L1M5_orf2#LIN 2391 ATTTAGGTCTTCTTTAATTTCTCTCAGCAATGTTTTGTAGTTTTCAGTGT 2342 chr2qtel1M 630606 ATATGGTATTTGGGTTTGCCTTGGCAGCTTGATCCCTAATTATTTTATTT 630655 ? - -i viiv ?ii vi v v i v ? v C L1M5_orf2#LIN 2341 ANA-GGT-CTTGCACATNTTTTGTTAGATTTATTCCTAAGTATTTNATGT 2294 chr2qtel1M 630656 TGTGTATAGACATTTTCAATGGAATTTCTCTTTGTATCCC--TTCCTTAT 630703 v v ivv vi v v v vi i ?iv ii -- i iv C L1M5_orf2#LIN 2293 TTTTTGATGCTATTGTAAATGGTATTGTTTTTNAAATTTCATTTTCCAAT 2244 chr2qtel1M 630704 GGGCTTTATCAGTAATATAGAGAAATGCTGATGATTTGTGTGGCTTCATT 630753 v -- i iiv i v i viv v ivv v ii C L1M5_orf2#LIN 2243 TG--TTTGTTGCTAGTATATAGAAATACAATTGATTTTTGTATATTGACC 2196 chr2qtel1M 630754 TTATGTACTGCAATTTTACTGAAGCTGTGAATTGTTTTCAGTAGATATTT 630803 i i v ? i ii i i viiiivv iv ii v v? C L1M5_orf2#LIN 2195 TTGTATCCNGCGACCTTGCTAAATTCACTTATTAGTTCTAGTAGTTTNTT 2146 chr2qtel1M 630804 TGATGATTTTCTAGGATTCTCGAAGTATCTCATCATATCATCTCCAAAGA 630853 vv i i ? i v v ?viv i v i v C L1M5_orf2#LIN 2145 TGTAGATTCTTTNGGATTTTCTACGTANACAATCATGTCATCTGCGAATA 2096 chr2qtel1M 630854 GTGATAGTTTTATTTCTTCATTGCCCATTCTAATTCCATTTGGTTTTTTT 630903 i? i v v v ii v v v i-- i C L1M5_orf2#LIN 2095 ANGACAGTTTTATTTCTTCCTTTCCAATCTTTATGCCTTTTA--TTTCTT 2048 chr2qtel1M 630904 TTTATTTTCTTAT--CAGTAAAACTAACATGTCTAGAACAATATTGAATA 630951 v vi -- v ii-- iv iv i v i C L1M5_orf2#LIN 2047 TTTCTTGCCTTATTGCACTGG--CTAGGACCTCCAGTACAATGTTGAATA 2000 chr2qtel1M 630952 ATAGTGGTGATAA------------TTTAATGCCTGGTTTTACTGGGACT 630989 iv ? i------------ i vi v i i i vv vv C L1M5_orf2#LIN 1999 GAAGTGGTGANAGCGGACATCCTTGTCTTGTTCCCGATCTTAGGGGGAAA 1950 chr2qtel1M 630990 GCATCCAGCTTCTCTTCATTTTATATAATGCTTTCTATAGGTTTTAACAA 631039 ? i i? i vi vvi i i ?v i v- iv C L1M5_orf2#LIN 1949 GCNTTCAGTNTTTCACCATTAAGTATGATGTTNGCTGTAGGTTTTT-CGT 1901 chr2qtel1M 631040 AGTTTTGCTT-ATT-GTTTTAGGGAAAGTTCCCTT-TATCCCTATGCCCT 631086 v viv - i- v v -- - i - iiiv C L1M5_orf2#LIN 1900 AGATGCCCTTTATCAGGTTGAGG--AAGTTCCCTTCTATTCCTA-GTTTG 1854 chr2qtel1M 631087 CT-AGTGTTTATTAATAGCAATGAGTAATTTATTTTGTCAAAAG-TTTTT 631134 - v - vi vv i iv vv v - C L1M5_orf2#LIN 1853 CTGAGAGTTT-TTATCATGAATGGGTGTTGAATTTTGTCAAATGCTTTTT 1805 chr2qtel1M 631135 CTGCTTTTATTGGGATTGTAATATGATTTTGGTTAGTTTTGTTATTGATG 631184 v i i vi v vv ivv v vi i i i C L1M5_orf2#LIN 1804 CTGCATCTATTGAGATGATCATATGATTTTTCTCCTTTATTCTGTTAATA 1755 chr2qtel1M 631185 TGGTTGACTATAGTAAAT--TTTTCTGATACTGAACCAGCCATGCATTAC 631232 vi i i v i v -- vi ii i i v v C L1M5_orf2#LIN 1754 TGGTGAATTACATTGATTGATTTTCGAATGTTAAACCAACCTTGCATTCC 1705 chr2qtel1M 631233 TGGTATATTACTGGTACAACCCAATTGGTTATAGTGTACTATCCTGCTGA 631282 --------- i v v v i ii i vi v C L1M5_orf2#LIN 1704 TGG---------GATAAACCCCACTTGGTCATGATGTATTATCCTTTTTA 1664 chr2qtel1M 631283 TAAGTTGCTGTAACATCTTTGCTAATATGTTATTTACAATTTGTGCATCA 631332 vi v vivvv v i ? vi v v C L1M5_orf2#LIN 1663 TATATTGCTGGATTCGATTTGCTAATATTTTGTTNAGGATTTTTGCATCT 1614 chr2qtel1M 631333 GTATTCAAGTGGGATATTAGTCTATAATCTTTTTTTTCTGTTTTAGTCCT 631382 i i v v i i i i ii vv - i C L1M5_orf2#LIN 1613 ATGTTCATGAGGGATATTGGTCTGTAATTTTCTTTTCTTGTAAT-GTCTT 1565 chr2qtel1M 631383 --TCATGTTTTAGGTAGCACTGCCAAAACTGTACTTTACAAGA--AATTT 631428 -- ?v - v -v vi? vi -i i i i i -- i v C L1M5_orf2#LIN 1564 TGTCNGGTTTT-GGTATCA-GGGTNATGCTG-GCCTCATAAAATGAGTTG 1518 chr2qtel1M 631429 GGCAGTATTCCACCTAATT---TTTTCC-AAAGAATTGACGTAGTATTGG 631474 v i vi vv --- i-i i vii iv C L1M5_orf2#LIN 1517 GGAAGTGTTCCCTCTTTTTCTATTTTCTGGAAGAGTTTGTGTAAGATTGG 1468 chr2qtel1M 631475 AGGCAATTGTTCTTTAAATGTTTGGGAGAATTCACTTGTGGATCCAACTG 631524 vivi v v i v iv i v v C L1M5_orf2#LIN 1467 TATTATTTCTTCCTTAAATGTTTGGTAGAATTCACCAGTGAAGCCATCTG 1418 chr2qtel1M 631525 GTCCTGGAGATTTTTTCTTAGGGAGTTCATTAATGACTTGTTCAATTATT 631574 v v i iv i i v iv v vvi vi C L1M5_orf2#LIN 1417 GGCCTGGAGTTTTCTTTGTGGGAAGGTTTTTAATTACAAATTCAATTTCT 1368 chr2qtel1M 631575 TTTTCTGAAATGGAACTATT-AAATATTTTATTTCCTCTTCTGTTAACCT 631623 vviv v i ii - i v i i v? i iii C L1M5_orf2#LIN 1367 TTAATAGATATAGGGCTATTCAGATTTTCTATTTCTTCTTGNGTCAGTTT 1318 chr2qtel1M 631624 GTGAAATTTGTATTTTTTGTAAACATTCTTCCATTTCAGTTAGATTGTCA 631673 vv v ? i ii- iiv iv vi ii ? C L1M5_orf2#LIN 1317 TGGTAANTTGTGTTTTTCA-AGGAATTTGTCCATTTCATCTAAGTTNTCA 1269 chr2qtel1M 631674 GACATGTTGCCATAG---TGTTCAGGAAAAAAGCTCCTAATTATTGCTTT 631720 i iv i v i--- v-- v vv i - ivi C L1M5_orf2#LIN 1268 AATTTATTGGCATAAAGTTGTTCAT--AATATTCTCTT-ATTATCCTTTT 1222 chr2qtel1M 631721 AATTTCTTT----TTTGTTGGTGATGAATTCACCCCTTTTATTTTCGATA 631766 v v ---- i - i --- v ii i iii C L1M5_orf2#LIN 1221 AATGTCTGTAGGATCTG-TAGTGATG---TCTCCTTTTTCATTCCTGATA 1176 chr2qtel1M 631767 TTGGTGATTGGTTTTTTTTCTTTTCTTTTCTTTTTCTCATCATGAAATGT 631816 i v v i i i i ----- v ---- i v C L1M5_orf2#LIN 1175 TTGGTAATTTGTGTCTTCTCTCTTTTTTTCT-----TGATC----AGTCT 1135 chr2qtel1M 631817 AGGCAAAGATTTGTTTATTTTGTTAATTTTTTCATAAAACTGACTCTTTG 631866 ? vi i i i iv i i i v i iii i v C L1M5_orf2#LIN 1134 NGCTAGAGGTTTATCAATTTTATTGATCTTTTCAAAGAACCAGCTTTTGG 1085 chr2qtel1M 631867 TTTTGTTTATT 631877 i i v C L1M5_orf2#LIN 1084 CTTCGTTGATT 1074 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.10 CpG sites = 253, Kimura (unadjusted) = 41.66 Transitions / transversions = 1.10 (253/229) Gap_init rate = 0.05 (78 / 1604), avg. gap size = 1.38 (108 / 78) 247 32.45 2.56 2.56 chr2qtel1M 632807 632923 (367077) MIRc#SINE/MIR 83 199 (69) m_b99s601i0 3633 chr2qtel1M 632807 AGCTGCTGGGATTTAGGTCAAGTCACTCAATCCCTCTAAGC--TGGTGGC 632854 - v ii v v i i i i --ii vv MIRc#SINE/MIR 83 AGCTG-TGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTC 131 chr2qtel1M 632855 CTGAGTTGTACAAGTGGTAAGAATGAAGGTCATTTCTGTGT-TGTCCCAG 632903 v vi - i vi v - vii vvii iv -iv v MIRc#SINE/MIR 132 CTCATCTGTA-AAATGGGGATAAT-AATACCTGCCCTGCCTACCTCACAG 179 chr2qtel1M 632904 GCTTACTGTGAGAATCGAAT 632923 v ii i i MIRc#SINE/MIR 180 GGTTGTTGTGAGGATCAAAT 199 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.78 CpG sites = 21, Kimura (unadjusted) = 43.78 Transitions / transversions = 1.31 (21/16) Gap_init rate = 0.04 (5 / 116), avg. gap size = 1.20 (6 / 5) 728 32.13 2.66 1.98 chr2qtel1M 633025 633475 (366525) L1ME4c_3end#LINE/L1 22 475 (355) m_b99s551i1 3634 chr2qtel1M 633025 GAACTGACTCAAATTTATAAGGATGCAAGCCATTCTCCAATTGATAAATG 633074 i v i v i viv? v v vv i v L1ME4c_3end#L 22 GAGCTCATTCAAATTGATAAGAAAAANATCAAGACCCCAATAGATAAATG 71 chr2qtel1M 633075 GTCAAAGGATTTGAACAGACAATGTTCAGATGAAAAAATAAAAATCATTT 633124 v iv viv ? v ii v ? vi vv L1ME4c_3end#L 72 GGCAAAGGACATGAACAGACAATTCACANAAGAGGAAATACAANTAGTAA 121 chr2qtel1M 633125 CTAGTCCTATGAAGAAATGCTCTGAATCACTACTAGTCACAGAAATGTTA 633174 vi iv vi i i i vivv i v i v iv L1ME4c_3end#L 122 ACAAACACATGGAAAAATGTTCAACCTCGCTAGTAATCAAAGAAATGCAA 171 chr2qtel1M 633175 ATTAAGACCTC--TGAGGGACCAGATATT-------TCAGATTGGCTAAG 633215 ii vv -- iv -- v ------- i i i v i L1ME4c_3end#L 172 ATTAAAGCAACAATGAGATACCA--TTTTACGCCTATTAAATTAGCAAAA 219 chr2qtel1M 633216 ATGACAGGGAAAGATAATGATGTATGTTGAAGAGAATGAGGGAAAAAACT 633265 vvv iii vv ivivv i iv i? v vi -- L1ME4c_3end#L 220 ATTTAAAAAATTGATAATACCCAATGCTGGCGAGGNTGCGGTGAAA--CT 267 chr2qtel1M 633266 GGGACACTAATACATTGTTGGTGGAGTTTTGAACTGATCTAGTTATTCTG 633315 v ? v i vi? v i i i vi iiiv i L1ME4c_3end#L 268 GGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTG 317 chr2qtel1M 633316 GAGAACAATATGGAACTATGCCCAAAGAGCTATCACACTGTTCATACCCT 633365 i i v v v i iviv i v v v L1ME4c_3end#L 318 GAAAGCAATTTGGCAATACGTATCAAGAGCCATAAAAATGTTCATACCCT 367 chr2qtel1M 633366 GTGATCCAGCAGTGTCTCTACTGAACCTGTATCCCAAAGAGATCAT---A 633412 v i i i vi v v iivv v i i i v --- L1ME4c_3end#L 368 TTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAA 417 chr2qtel1M 633413 AAGAAGGGAAAAGGCCTTCCACATGTGCAAAAATGTTTATAGCAGCCTTT 633462 i ----- i i ii i i i v v v L1ME4c_3end#L 418 AAGAAGGAAAAAG-----CTATATGCACGAAGATGTTCATTGCAGCGTTA 462 chr2qtel1M 633463 TCTGTAGTGGAGA 633475 i i i i v L1ME4c_3end#L 463 TTTATAATAGCGA 475 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 42.28 CpG sites = 73, Kimura (unadjusted) = 43.49 Transitions / transversions = 1.06 (73/69) Gap_init rate = 0.03 (12 / 450), avg. gap size = 1.75 (21 / 12) 13 27.99 0.00 0.00 chr2qtel1M 633869 633911 (366089) (TGTTTGT)n#Simple_repeat 1 43 (0) m_b99s252i0 3635 chr2qtel1M 633869 TGTGTGTAGTATCTATTTTACTGTTTGTTTTTTGTTGTTTTTT 633911 v v v v vv ii v v (TGTTTGT)n#Si 1 TGTTTGTTGTTTGTTGTTTGTTGTTTGTTGTTTGTTGTTTGTT 43 Matrix = Unknown Transitions / transversions = 0.25 (2/8) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 15 5.56 0.00 0.00 chr2qtel1M 635383 635401 (364599) (T)n#Simple_repeat 1 19 (0) m_b99s252i1 3636 chr2qtel1M 635383 TTTCTTTTTTTTTTTTTTT 635401 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 15 10.11 9.38 0.00 chr2qtel1M 635679 635710 (364290) (TC)n#Simple_repeat 1 35 (0) m_b99s252i2 3637 chr2qtel1M 635679 TCTCT-TCTC-CTCACTCTCTCTCT-TCCCTTTCT 635710 - - v - i i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 35 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.10 (3 / 31), avg. gap size = 1.00 (3 / 3) 13 20.99 0.00 5.00 chr2qtel1M 636024 636065 (363935) (TCTTA)n#Simple_repeat 1 40 (0) m_b99s252i3 3638 chr2qtel1M 636024 TCTTATCTTATCTCTTTATTTTCTCTATTATCTCTTATCCTA 636065 - v v v - iv v i (TCTTA)n#Simp 1 TCTTATCTTATCT-TATCTTATCT-TATCTTATCTTATCTTA 40 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.05 (2 / 41), avg. gap size = 1.00 (2 / 2) 195 33.11 6.76 0.00 chr2qtel1M 636395 636542 (363458) L2#LINE/L2 2037 2194 (888) m_b99s601i1 3639 chr2qtel1M 636395 TCCCCAGTCCTCCATTAACTTAACTATTCTCCAGTCTTTGACATTCCTGG 636444 i i vvi v i iv? vv iv ivvi i L2#LINE/L2 2037 TTCTCAGTCCTCATCTTACTTGACCTNTCAGCAGCATTTGACACAGTTGA 2086 chr2qtel1M 636445 TGACT-CCTCC-----AGGGTCCTCTCTTCTCTTAGTTTTTAGGATTCGG 636488 v - -----iiiiiv i v i i ii iv vi L2#LINE/L2 2087 TCACTCCCTCCTTCTTGAAACACTTTCTTCACTTGGCTTCCAGGACACCA 2136 chr2qtel1M 636489 CTCTTTCCTGCCTTTCCCCCTCCCTATCTGACCA---CTTCTCTGTATTC 636535 v i vi i v vv i i--- v v i L2#LINE/L2 2137 CACTCTCCTGGTTTTCCTCCTACCTCACTGGCCGCTCCTTCTCAGTCTCC 2186 chr2qtel1M 636536 -TTACTGG 636542 - i L2#LINE/L2 2187 TTTGCTGG 2194 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.24 CpG sites = 28, Kimura (unadjusted) = 45.51 Transitions / transversions = 1.33 (28/21) Gap_init rate = 0.03 (4 / 147), avg. gap size = 2.50 (10 / 4) 13 21.01 0.00 5.00 chr2qtel1M 637792 637833 (362167) (TAAGA)n#Simple_repeat 1 40 (0) m_b99s252i4 3640 chr2qtel1M 637792 TAGGATAAGAGATAATAGAGAAAATGAAGAGATAAGATAAGA 637833 i v vi - v - vi (TAAGA)n#Simp 1 TAAGATAAGATAAGATA-AGATAA-GATAAGATAAGATAAGA 40 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.05 (2 / 41), avg. gap size = 1.00 (2 / 2) 288 26.81 1.10 5.75 chr2qtel1M 640685 640775 (359225) MIR3#SINE/MIR 111 197 (11) m_b99s601i2 3641 chr2qtel1M 640685 TCACTGAATCTCAGTTTCC-CATTTGTAAAATGAGTGGGAAGCGCTCCAT 640733 v iii - i v vv vi vv MIR3#SINE/MIR 111 TCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGAT 160 chr2qtel1M 640734 GGCCTTGTAGGTCCTTTCCAGCGATCATCTGGAATCCTGTAA 640775 ii ivv i ----- iv i i i MIR3#SINE/MIR 161 GATCTCTAAGGTCCCTTCCAGC-----TCTGACATTCTATGA 197 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.73 CpG sites = 13, Kimura (unadjusted) = 33.73 Transitions / transversions = 1.30 (13/10) Gap_init rate = 0.07 (6 / 90), avg. gap size = 1.00 (6 / 6) 240 33.05 5.93 0.00 chr2qtel1M 640875 640992 (359008) C L2b_3end#LINE/L2 (10) 456 332 m_b99s601i3 3642 chr2qtel1M 640875 TCAGCAAACTTTTA---AGTGCCTGCTATCAGCCGGGCCCTGGACTGTGC 640921 i iv --- i i i vv i ? vi iv C L2b_3end#LINE 456 TCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGC 407 chr2qtel1M 640922 CCCAGGAACATAAAGAGAGACAAGG--GACTT--CCCCTGCTCTCCTGGA 640967 v ii i i i iv ivii i-- ?i--i i vi C L2b_3end#LINE 406 GCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGGA 357 chr2qtel1M 640968 GGTCACGGACAGCTGGGGCAGGCAG 640992 v i v viv v i C L2b_3end#LINE 356 GCTCACAGTCTAGTGGGGGAGACAG 332 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.08 CpG sites = 25, Kimura (unadjusted) = 47.02 Transitions / transversions = 1.79 (25/14) Gap_init rate = 0.03 (3 / 117), avg. gap size = 2.33 (7 / 3) 459 28.11 13.88 1.28 chr2qtel1M 641130 641338 (358662) C MIRb#SINE/MIR (0) 268 34 m_b99s601i4 3643 chr2qtel1M 641130 AATACCATACCTAGCATTTATACCGCACCTGCT--GTGACATGCAGTGTG 641177 vi v v v vvv i i i -- v v v C MIRb#SINE/MIR 268 AATAATAGAGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTG 219 chr2qtel1M 641178 TCA------------GTATTGTCTCATTTTATCCTCAGGAGAACCCTAGG 641215 ii ------------ i i v vi v iv C MIRb#SINE/MIR 218 CTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCG 169 chr2qtel1M 641216 ACTCGGGTGCCATTATTGTGCCCTTTTTATAGATAAAGTCACTGAGGCAG 641265 vvii --- i v v i i i vv vv C MIRb#SINE/MIR 168 AGGTAGGT---ATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC 122 chr2qtel1M 641266 ACAGAGGTCTTGTAAGTTGT--------------CTAGCAAGTTGCTGAG 641301 v ivv v i-------------- i v v C MIRb#SINE/MIR 121 AGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAG 72 chr2qtel1M 641302 GTGGGATGAACACTCAGGTCTTGCTGA-TTCAAGGCCC 641338 vi vviv i vv - i i C MIRb#SINE/MIR 71 CCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCC 34 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.26 CpG sites = 24, Kimura (unadjusted) = 35.40 Transitions / transversions = 0.71 (24/34) Gap_init rate = 0.03 (7 / 208), avg. gap size = 4.57 (32 / 7) 14 23.05 4.11 5.56 chr2qtel1M 641788 641860 (358140) (GAAAAT)n#Simple_repeat 1 72 (0) m_b99s252i5 3644 chr2qtel1M 641788 GAAAAAAAAAATGAAAGTGATAACTTGATAATG--CA-GAAAATGAATGA 641834 vi i - -v v --v - viv (GAAAAT)n#Sim 1 GAAAATGAAAATGAAAATGA-AA-ATGAAAATGAAAATGAAAATGAAAAT 48 chr2qtel1M 641835 GAAAGAGAAAAATTGAGAATGAAGAT 641860 - vi - i i (GAAAAT)n#Sim 49 GAAA-ATGAAAA-TGAAAATGAAAAT 72 Matrix = Unknown Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.08 (6 / 72), avg. gap size = 1.17 (7 / 6) 239 28.10 13.95 0.68 chr2qtel1M 641920 642048 (357952) MIRc#SINE/MIR 84 229 (39) m_b99s601i5 3645 chr2qtel1M 641920 GCTGCTGCGATTTGGGTCAAGTCACTCAACCT-TCTGAGCTGAAG--GCC 641966 - i ii v v i - ivv --v MIRc#SINE/MIR 84 GCTG-TGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCC 132 chr2qtel1M 641967 TGAGTTGT---ATGAA---AATACTTTCTGTGTTG------TCCCAGGTT 642004 v vi --- ii--- v vi ivi ------ v v MIRc#SINE/MIR 133 TCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGT 182 chr2qtel1M 642005 TACTGTGAGAATCCAATGATTTTGTGCATG---AAGCTCATTAGAAA 642048 ii i v vv vi i --- v v iv MIRc#SINE/MIR 183 TGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTTTGTAAA 229 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.53 CpG sites = 17, Kimura (unadjusted) = 35.53 Transitions / transversions = 0.89 (17/19) Gap_init rate = 0.05 (7 / 128), avg. gap size = 2.71 (19 / 7) 489 21.21 0.00 8.77 chr2qtel1M 642059 642182 (357818) MIRc#SINE/MIR 2 115 (153) m_b99s601i6 3646 chr2qtel1M 642059 GGGGCAGCTCAGTGGTGCAGTGGATAAAGCACCAGCCATGAAGGCAGGAG 642108 i i--- v i ii v v i v i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr2qtel1M 642109 GACCCGAGTTCAAATTCGGCCTCAGATGCCTAACACTTCCTAGTTGTGTG 642158 i i i i i v v --- ---- v i MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTC---TGC----CACTTACTAGCTGTGTG 91 chr2qtel1M 642159 ATTCTGGGCAAGTCACTTAACCCC 642182 iii i MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.34 CpG sites = 17, Kimura (unadjusted) = 25.56 Transitions / transversions = 2.43 (17/7) Gap_init rate = 0.08 (10 / 123), avg. gap size = 1.00 (10 / 10) 651 33.14 1.98 0.00 chr2qtel1M 645129 645481 (354519) L1ME4c_3end#LINE/L1 71 430 (400) m_b99s551i3 3647 chr2qtel1M 645129 GGGGAAAGGATTTAAACAGACAATTTTCAGATGAAAAAATAAAAATCATT 645178 v iv i iv ? v ii v ? vi v L1ME4c_3end#L 71 GGGCAAAGGACATGAACAGACAATTCACANAAGAGGAAATACAANTAGTA 120 chr2qtel1M 645179 TCTAGTCCTATGAAAAAATATTCTAAATCACTATTGGTCAGAGAAACGTA 645228 vvi iv vi i i v vv i v ii i i i L1ME4c_3end#L 121 AACAAACACATGGAAAAATGTTCAACCTCGCTAGTAATCAAAGAAATGCA 170 chr2qtel1M 645229 AATTAAGAGAACTCTGACGTACCA----AGATCTTTCAGATTGGCTAAGA 645274 iiv vv vi ---- vii v i i i v i L1ME4c_3end#L 171 AATTAAAGCAACAATGAGATACCATTTTACGCCTATTAAATTAGCAAAAA 220 chr2qtel1M 645275 TGACAGGGAAAGATAATAATGTATGTTGAAGGGAATGGGGAAAAACTAAG 645324 vvv iii vv vivv i iv i i? v vi iiv L1ME4c_3end#L 221 TTTAAAAAATTGATAATACCCAATGCTGGCGAGGNTGCGGTGAAACTGGT 270 chr2qtel1M 645325 ACACTAACACATTGTTGGTGAAGTTGTGAATTGATCCAGTCATTCTGGAG 645374 ? v i i ivi? i i v ii v i i L1ME4c_3end#L 271 ACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAA 320 chr2qtel1M 645375 AACAATATGGAACTATGCCTTAAAAGCTATCACATTGTGCATACCCTTTG 645424 i v v v i iv i i i v v v v L1ME4c_3end#L 321 AGCAATTTGGCAATACGTATCAAGAGCCATAAAAATGTTCATACCCTTTG 370 chr2qtel1M 645425 ATCCAGCAGTGTCTCTACTGAACCTGTATCGCAAAGAGATCAT---AAAG 645471 i i i vi v v iivv v vi i i v --- L1ME4c_3end#L 371 ACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAAG 420 chr2qtel1M 645472 AAGGGAAAAG 645481 i L1ME4c_3end#L 421 AAGGAAAAAG 430 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 44.12 CpG sites = 63, Kimura (unadjusted) = 45.70 Transitions / transversions = 1.17 (63/54) Gap_init rate = 0.01 (2 / 352), avg. gap size = 3.50 (7 / 2) 709 30.79 1.32 0.00 chr2qtel1M 645129 645430 (354570) L1ME4a_3end#LINE/L1 71 376 (495) m_b99s551i2 3647 chr2qtel1M 645129 GGGGAAAGGATTTAAACAGACAATTTTCAGATGAAAAAATAAAAATCATT 645178 v iv i iv i v i v viii L1ME4a_3end#L 71 GGGCAAAGGACATGAACAGACAATTCACAAAAGAAGAAATACAAATGGCC 120 chr2qtel1M 645179 TCTAGTCCTATGAAAAAATATTCTAAATCACTATTGGTCAGAGAAACGTA 645228 vv iv v ? i v vv v ii i i i L1ME4a_3end#L 121 AATAAACATATGAAAANATGTTCAACCTCACTAGTAATCAAAGAAATGCA 170 chr2qtel1M 645229 AATTAAGAGAACTCTGACGTACCAA----GATCTTTCAGATTGGCTAAGA 645274 i v vv vi v----v i v i v L1ME4a_3end#L 171 AATTAAAACAACAATGAGATACCATTTTTCACCTATCAAATTGGCAAAGA 220 chr2qtel1M 645275 TGACAGGGAAAGATAATAATGTATGTTGAAGGGAATGGGGAAAAACTAAG 645324 vvv ii vv vivvi iv i ii v ?i viiv L1ME4a_3end#L 221 TTTAAAAGATTGATAATACCCAGTGTTGGCGAGGGTGTGGNGAAACGGGC 270 chr2qtel1M 645325 ACACTAACACATTGTTGGTGAAGTTGTGAATTGATCCAGTCATTCTGGAG 645374 v v i i i iiiv i i v ii v L1ME4a_3end#L 271 ACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTACAACCTTTCTGGAG 320 chr2qtel1M 645375 AACAATATGGAACTATGCCTTAAAAGCTATCACATTGTGCATACCCTTTG 645424 ii v v v iv i iv v v v ? L1ME4a_3end#L 321 GGCAATTTGGCAATATGTATCAAAAGCCTTAAAAATGTNCATACCCTTTG 370 chr2qtel1M 645425 ATCCAG 645430 i L1ME4a_3end#L 371 ACCCAG 376 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.70 CpG sites = 46, Kimura (unadjusted) = 40.70 Transitions / transversions = 0.98 (46/47) Gap_init rate = 0.00 (1 / 301), avg. gap size = 4.00 (4 / 1) 12 3.78 6.45 6.45 chr2qtel1M 645834 645864 (354136) (TAAG)n#Simple_repeat 1 31 (0) m_b99s252i6 3648 chr2qtel1M 645834 TAAGTACATGTAAGT-AGTAAGT-ACTAAGTAA 645864 - - - - v (TAAG)n#Simpl 1 TAAGTA-A-GTAAGTAAGTAAGTAAGTAAGTAA 31 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.13 (4 / 30), avg. gap size = 1.00 (4 / 4) 293 18.90 4.30 8.99 chr2qtel1M 648907 648999 (351001) MIRc#SINE/MIR 25 113 (155) m_b99s601i7 3649 chr2qtel1M 648907 GAGCTCTGTCCT--GAGGCAG-AAGACCTGAGTTCCAATTTGGCCCCAGA 648953 v vv -- v - i v i ----- i - MIRc#SINE/MIR 25 GAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGT-----CCCGG- 68 chr2qtel1M 648954 AGCT-TAACACTTCCTAGCTGTCTGATCCTGGGCAATTCATTTAACC 648999 -- - iv v v i i v i MIRc#SINE/MIR 69 --CTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACC 113 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 20.29 CpG sites = 7, Kimura (unadjusted) = 21.72 Transitions / transversions = 0.78 (7/9) Gap_init rate = 0.12 (11 / 92), avg. gap size = 1.09 (12 / 11) 33 0.00 0.00 0.00 chr2qtel1M 649029 649056 (350944) (AT)n#Simple_repeat 1 28 (0) c_b99s251i0 3650 chr2qtel1M 649029 ATATATATATATATATATATATATATAT 649056 (AT)n#Simple_ 1 ATATATATATATATATATATATATATAT 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 553 31.30 5.26 2.25 chr2qtel1M 649059 649705 (350295) C L1M2_orf2#LINE/L1 (639) 2652 1987 m_b99s551i4 3651 chr2qtel1M 649059 TTTGATTAATACTGCTTTGTAACATAGTT-----CTAGGTACTGCTAAGG 649103 i v iv ii v -----ii v iv v v C L1M2_orf2#LIN 2652 TTTGGTTACTATAGCTTTGTAGTATATTTTGAAGTCAGGTAGTGTGATGC 2603 chr2qtel1M 649104 CACCATCCTTTGTATTTTGTTGTTGTAGTAAATCCCTTGA-TATTCTTGA 649152 v -v - i v i -i -i v v i i- vv i C L1M2_orf2#LIN 2602 CTCCA-GCTTTGT-TCTTTTTGCT-CAG-GATTGCTTTGGCTATTCGGGG 2557 chr2qtel1M 649153 CCTTTTATTCTTCTAGATAGCTTTT--GTTGTTTTTTTCTAGTTCTATAA 649200 i i vv i v iiiv -- v v? v i i C L1M2_orf2#LIN 2556 TCTTTTGTGGTTCCATACGAATTTTAGGATTNTTTTTTCTATTTCTGTGA 2507 chr2qtel1M 649201 AGTAATGTT-TTTGCAATTAGATTATTATGGCACTGACCAAATAGACCAG 649249 - i- v i v v vivv v i vivvi i iv C L1M2_orf2#LIN 2506 AG-AATGTCATTGGTATTTTGATAGGGATTGCATTGAATCTGTAGATCGC 2458 chr2qtel1M 649250 TTTAGGCAAAATTGTGATTT-----ATATCAGCTCAACCTAGTCATGAAC 649294 i i iv v ?v ----- i ii vv v vi i C L1M2_orf2#LIN 2457 TTTGGGTAGTATGGNCATTTTAACAATATTAATTCTTCCAATCCATGAGC 2408 chr2qtel1M 649295 AATTAATATTTTTCCAGTTGTTTACATCTGATTTTC--TTTGTGTGAGAA 649342 vvvi i v ? iii i-- i -- v v v vv C L1M2_orf2#LIN 2407 ATGGGATATCTTTCCATTTNTTTGTGTCC--TCTTCAATTTCTTTCATCA 2360 chr2qtel1M 649343 GTGTTTTGTAATCGTGTTCATAT-GATATTTGGGTTTGCCTTGG-CAGCT 649390 i i iv v? ii v- v vivi -- -i iv C L1M2_orf2#LIN 2359 GTGTTTTATAGTTTTCNTTGTAGAGATCTTTCACCT--CCTTGGTTAAAT 2312 chr2qtel1M 649391 TGATCCCCAATTATTTTATTTTGTTTATAGATATTTTCAATGGAATTTCT 649440 v i i iv v i v v v i v C L1M2_orf2#LIN 2311 TTATTCCTAGGTATTTTATTTTTTTTGTAGCTATTGTAAATGGGATTGCT 2262 chr2qtel1M 649441 CTTTCTATCTCTTACTTATGGGCCTTATCAGTAATATAGAGAAATGTTGA 649490 i i iv i vi i vivivi ii iiv iiii v i iv C L1M2_orf2#LIN 2261 TTCTTGATTTCTTTTTCAGATAGTTCGTTGTTGGCGTATAGAAATGCTAC 2212 chr2qtel1M 649491 TGATTTGTGTGGCTTCATTTTATATACTTCAATTTTGCTAAAGCTGAATT 649540 v ivv v i v v i ------i C L1M2_orf2#LIN 2211 TGATTTTTGTATGTTGATTTTGTATCCTGCAACTTT------ACTGAATT 2168 chr2qtel1M 649541 -GTTT-TCAGT----AGA-TATTTTAATGG-GTTTCTAGGATTTTCAAAA 649582 - - ---- ? - v ii - i i ? v ? C L1M2_orf2#LIN 2167 CGTTTATCAGTTCTAANAGTTTTTTGGTGGAGTCTTTAGGNTTTTCTANA 2118 chr2qtel1M 649583 T--------ATCTCATCTCCAAAGAGTGATAGTTTTATTTCCTCATTGCC 649624 -------- v v v v i i v i v v C L1M2_orf2#LIN 2117 TATAAGATCATGTCATCTGCAAACAGGGACAATTTGACTTCCTCCTTTCC 2068 chr2qtel1M 649625 TATTCTAATTCCTTTTGTTTCTTTTTCTTTTCTTATCAGTGAAGCTAACA 649674 v ivi v i i vi v iiv vvi iv C L1M2_orf2#LIN 2067 AATTTGGATGCCTTTTATTTCTTTCTCTTGCCTAATTGCTCTGGCTAGGA 2018 chr2qtel1M 649675 TTTCTAGAACAATGTTGAATAATAGTGGTGA 649705 i i v v iv C L1M2_orf2#LIN 2017 CTTCCAGTACTATGTTGAATAGAAGTGGTGA 1987 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.65 CpG sites = 101, Kimura (unadjusted) = 41.83 Transitions / transversions = 1.04 (101/97) Gap_init rate = 0.04 (29 / 646), avg. gap size = 1.69 (49 / 29) 577 30.26 6.31 3.35 chr2qtel1M 649183 649705 (350295) C L1P4_orf2#LINE/L1 (767) 2527 1990 m_b99s551i5 3651 chr2qtel1M 649183 TTTTTTCTAGTTCTAT--AAAGTAATGTTTTTGCAATTAGATTATTATGG 649230 i i -- i i i v-- i i v vivv i C L1P4_orf2#LIN 2527 TTTTTTCTAATTCTGTGAAAAATGACGTTG--GTAGTTTGATAGGAATAG 2480 chr2qtel1M 649231 CACTGACCAAATAGACCAGTTTAGGCAAAATTGTGATTT-----ATATCA 649275 ii vivvi iiiv i iv v iv ----- ii C L1P4_orf2#LIN 2479 CGTTGAATCTGTAGATTGCTTTGGGCAGTATGGCCATTTTAACGATATTG 2430 chr2qtel1M 649276 GCTCAACCTAGTCATGAACAATTAATATTTTTCCAGTTGTTTA---CATC 649322 ii vv v vi i vvv i v i--- C L1P4_orf2#LIN 2429 ATTCTTCCAATCCATGAGCATGGAATGTTTTTCCATTTGTTTGTGTCATC 2380 chr2qtel1M 649323 T--GATTTTCTTTGTGTGAGAAGTGTTTTGTAATCGTGTTCATAT-GATA 649369 -- ii i----- v i iv vi ii v- v C L1P4_orf2#LIN 2379 TNTGATTTCTTTC-----AGCAGTGTTTTGTAGTTCTCCTTGTAGAGATC 2335 chr2qtel1M 649370 TTTGGGTTTGCCTTGGC-AGCTTGATCCCCAATTATTTTATTTTGTTTAT 649418 vivi -- i- v vv i i iv v i C L1P4_orf2#LIN 2334 TTTCACCT--CCTTGGTTAGATGTATTCCTAGGTATTTTATTTTTTTTGT 2287 chr2qtel1M 649419 AGATATTTTCAATGGAATTTC--TCTT--TCTATCTCTTACTTATGGGCC 649464 i v v v i v -- -- i iv i vi - ii v C L1P4_orf2#LIN 2286 GGCTATTGTAAATGGGATTGCGTTCTTGATTTGGCTCTCAGCT-TGAACG 2238 chr2qtel1M 649465 TTATCAGTAATATAGAGAAATGTTGATGATTTGTGTGGCTTCATTTTATA 649514 --- ii i v i iv v ivv v i C L1P4_orf2#LIN 2237 TTAT---TGGTGTATAGAAATGCTACTGATTTTTGTACATTGATTTTGTA 2191 chr2qtel1M 649515 TACTTCAATTTTGCTAAAGCTGAATTGTTT-TCAGT----AGA-TATTTT 649558 v vv i i i ----- i - ----i -iv C L1P4_orf2#LIN 2190 TCCTGAAACTTTACTGAAG-----TCGTTTATCAGTTCTAGGAGCCTTTT 2146 chr2qtel1M 649559 AATGG-GTTTCTAGGATTTTC-------AAAAT-ATCTCATCTCCAAAGA 649599 iii - i i i ------- i - v i vv i C L1P4_orf2#LIN 2145 GGCGGAGTCTTTAGGGTTTTCTAGGTATAGAATCATATCGTCAGCGAAGA 2096 chr2qtel1M 649600 GTGATAGTTTTATTTCCTCATTGCCTATTCTAATTCCTTTTGTTTCTTTT 649649 v v i i v v ivi v i i C L1P4_orf2#LIN 2095 GAGATAGTTTGACTTCTTCTTTTCCTATTTGGATGCCTTTTATTTCTTTC 2046 chr2qtel1M 649650 TCTTTTCTTATCAGTGAAGCTAACATTTCTAGAACAATGTTGAATAATAG 649699 vi v iiv vvi iv i i v v iv C L1P4_orf2#LIN 2045 TCTTGCCTGATTGCTCTGGCTAGGACTTCCAGTACTATGTTGAATAGGAG 1996 chr2qtel1M 649700 TGGTGA 649705 C L1P4_orf2#LIN 1995 TGGTGA 1990 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.77 CpG sites = 86, Kimura (unadjusted) = 39.76 Transitions / transversions = 1.28 (86/67) Gap_init rate = 0.06 (32 / 522), avg. gap size = 1.59 (51 / 32) 1352 30.53 1.83 1.70 chr2qtel1M 649810 650572 (349428) C L1M4_orf2#LINE/L1 (1458) 1836 1073 m_b99s551i6 3652 chr2qtel1M 649810 GAACGGGTACTGTATTTAGTCAAAAGCTTTTTTTGCTTCAATTG-GATTG 649858 v ii v v v i v v - vi C L1M4_orf2#LIN 1836 GAAAGGGTGTTGGATTTTGTCAAATGCTTTTTCTGCGTCTATTGAGATGA 1787 chr2qtel1M 649859 CAATTTGATTTTGGTTGGTTTTGTTATTGGTATGGTTGCCTATAGTAACT 649908 iv v i v ivv v vi ii vvvi i v i i C L1M4_orf2#LIN 1786 TCATGTGGTTTTTGTCCTTTATTCTATTAATATGGTGTATTACATTGATT 1737 chr2qtel1M 649909 --TTTCCTGATACTGAACCAGCCATGCATTACTGATATAAATCCCA-TTG 649955 -- i v? ii i v v iv - C L1M4_orf2#LIN 1736 GATTTTCGNATGTTGAACCAACCTTGCATTCCTGGGATAAATCCCACTTG 1687 chr2qtel1M 649956 GTTGTAGTATAGTATCCTGCGCCTAAGTGGCTGTAATCCCTTTGCTAATA 650005 ii i i vv viviv v v v v vv i C L1M4_orf2#LIN 1686 GTCATGGTGTATAATCCTTTTTATATGTTGCTGGATTCGGTTTGCTAGTA 1637 chr2qtel1M 650006 TATTATTTAGAATTTGTGCATCAGTATTCAACAGGGATACTAGTCTGTAA 650055 v i v i v vi vv i i i C L1M4_orf2#LIN 1636 TTTTGTTGAGGATTTTTGCATCTATATTCATAAGGGATATTGGTCTGTAG 1587 chr2qtel1M 650056 TTTTTTTTTCTATTTTAGCCCTTTGTAT--TTTAGGTAGCAGTGCCATAA 650103 i - v v vvi v -- v v v iv v C L1M4_orf2#LIN 1586 TTTTCTTTTCT-TGTGATGTCTTTGTCTGGTTTTGGTATCAGGGTAATAC 1538 chr2qtel1M 650104 CTGTGGCATTCAAGAAATTTGGCAGTATTCCTTCACCT---ATTTTTTCC 650150 iv ivv vv vi i v v i i vi --- vv C L1M4_orf2#LIN 1537 TGGCCTCATAGAATGAGTTGGGAAGTGTTCCCTCCTCTTCTATTTTTTGG 1488 chr2qtel1M 650151 AAATAGTTGACATAGTATTGGAAGTAATTGTTCTTTAAATGTTTGGGAGA 650200 i- viiiv v viv v v C L1M4_orf2#LIN 1487 AAG-AGTTTGTGAAGGATTGGTGTTAATTCTTCTTTAAATGTTTGGTAGA 1439 chr2qtel1M 650201 ATTCACTGGTGGATCCAACTGGCCCTGGAGATTTTTTCTTAGGGAGTTCA 650250 ii i v v ? ivv i iv i i iv C L1M4_orf2#LIN 1438 ATTCACCAGTGAAGCCATCTGGNCCTGGGCTTTTCTTTGTGGGAAGTTTT 1389 chr2qtel1M 650251 TTAATGACTTGTTCAATTTCTTTTTCTGAAATGGAACTATTTAAATATTT 650300 i v vi i vii vv i iv i i v i C L1M4_orf2#LIN 1388 TTGATTACTAATTCAATCTCTTTACTTGTTATAGGTCTATTCAGATTTTC 1339 chr2qtel1M 650301 TATTTCCTCTTCTGTTAACTTAGGAAATTTGTATTTTTTGTAAACATTCT 650350 i vv i ii v v i i i i- iiv iv C L1M4_orf2#LIN 1338 TATTTCTTCTTGAGTCAGTTTCGGTAGTTTGTGTCTTTC-TAGGAATTTG 1290 chr2qtel1M 650351 TCCACTTCAGTTAGATTGTCAGACTTGCTGCCAT---ATTGTTGGGGAAA 650397 i vi i i vi i i v --- -viv iv C L1M4_orf2#LIN 1289 TCCATTTCATCTAGGTTATCTAATTTGTTGGCATACAATTGTT-CATAGT 1241 chr2qtel1M 650398 AGCTGCTAATTATTGCTTTAATTTCTTTTTCCTTGGTGGTGAATTCACCC 650447 viiv v v ivi v v vvvv i i i vv v i C L1M4_orf2#LIN 1240 ATTCCCTTATAATCCTTTTTATTTCTGTAAGGTCGGTAGTAATGTCCCCT 1191 chr2qtel1M 650448 CTTTCATTTTTGATGTTAGTGATTTGGTTTTTTTTTC--CTTTTCTTTGT 650495 ii v i iv i i i --i v C L1M4_orf2#LIN 1190 CTTTCATTCCTGATTTTAGTAATTTGAGTCTTCTCTCTTTTTTTCTTGGT 1141 chr2qtel1M 650496 CTCATCATCAAATGTAGGCAAAGATTTATTTGTTTTGTTAGTTTTTTCAT 650545 --------- i v vi i i ivi ii i v C L1M4_orf2#LIN 1140 C---------AGTCTAGCTAAAGGTTTGTCAATTTTGTTGATCTTTTCAA 1100 chr2qtel1M 650546 AAAACCAACTCTTAGTTTTGTTTATTT 650572 i i i i v C L1M4_orf2#LIN 1099 AGAACCAACTTTTGGTTTCGTTGATTT 1073 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.45 CpG sites = 115, Kimura (unadjusted) = 39.89 Transitions / transversions = 1.01 (115/114) Gap_init rate = 0.03 (20 / 762), avg. gap size = 1.35 (27 / 20) 12 19.16 0.00 8.89 chr2qtel1M 651534 651582 (348418) (CCCACTG)n#Simple_repeat 1 45 (0) m_b99s252i7 3653 chr2qtel1M 651534 CCCTCTGTCCACTGGACCCTCTGTCCACTGGACCCTCTGTCCAGTGCCC 651582 v i - - v i - - v i v (CCCACTG)n#Si 1 CCCACTGCCCACT-G-CCCACTGCCCACT-G-CCCACTGCCCACTGCCC 45 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.08 (4 / 48), avg. gap size = 1.00 (4 / 4) 827 29.54 8.64 3.05 chr2qtel1M 653966 654555 (345445) C L1ME5_3end#LINE/L1 (313) 628 7 m_b99s551i7 3654 chr2qtel1M 653966 TTTCACTCAGCATCA-GTTCATGTAAG-TCTCTCCAGGTCTCTCTGAAAT 654013 ii - -- v - iv v iv v vivv C L1ME5_3end#LI 628 TTTCACTCAGCACTATGTT--TTTAAGATCCATCCATGTTGCTATGTGTA 581 chr2qtel1M 654014 CATCCTGTTGGTTGTTTCTTACAGAACAATAATATTCCATAACATTAATA 654063 iv iv i v v vvvv i i iiii vv v C L1ME5_3end#LI 580 CATCTAGTCCGTTGCTTCTAACTGCTGCATAGTACTCCATGGTGTGCATC 531 chr2qtel1M 654064 TACCATAACTTATTCAGCCATTCTCCAGTTGATA-ACA--------GTCG 654104 i i vi iii v i viv i- -------- i v C L1ME5_3end#LI 530 CACCACATTTTACCTATCCACTCTCCCAGTGATGGACACCCAGGTTGCCT 481 chr2qtel1M 654105 CTA-------GTCACTTCAAAAAGGGCTGCCACAAGCATTTTTGCACATG 654147 i ------- i iv v iv v ii i ii i i C L1ME5_3end#LI 480 CCAACTCCCCGCCACCACAAACAACGCTGCAATGAACATCCTCGTACATG 431 chr2qtel1M 654148 TGGGTTCCTTTC---CCTCTTTTAAGATGTCTTTGGGATATAAGTCCAGT 654194 ---ii vi--- v v v ii v vii v C L1ME5_3end#LI 430 T---CCCCTTATGGACCTGTGTGAGAATTTCTTTGGGATATATACCCAGG 384 chr2qtel1M 654195 AGAAACAATGCTGGGTCAAATGCTAAGCACAGTTTGATATCTT--TTTGA 654242 viiv v v v v v --- --- - -- C L1ME5_3end#LI 383 AGCGGAATTGCTGGGTCATAGGGTATGC---GT---ATA-CTTAATTTGA 341 chr2qtel1M 654243 GCA--TAGTTCCAAACTGCTCTCCAGAATGATTGAATTTCATTC-ACAAT 654289 vi -- v v i i ii v i-- v - v C L1ME5_3end#LI 340 CTAAGTACTGCCAGATTGCTCTCCAGAATGGCTGCAC--CAGTCTACACT 293 chr2qtel1M 654290 TCCACCAACAATGTATCAGTGTTCCAGTTTTCCCACATCCCCTCCAACAA 654339 i i i i v v vi ? i i v v C L1ME5_3end#LI 292 CCCACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATCCTCGCCAACAC 243 chr2qtel1M 654340 TTGACATTGTCTTATCCTATCATCTTAGCCAGTCTGACAAGTGTG----- 654384 i i iviiii v v i v i i i i----- C L1ME5_3end#LI 242 TTGGCATTATCCAGCTTTCTAATTTTTGCCAGTCTAATAGGTGTAAAGTG 193 chr2qtel1M 654385 ---------------TCTAATTTGCATTTCTCTGATCAATAGTGATTTGA 654419 --------------- i i v i v vi C L1ME5_3end#LI 192 ATATCTCATTGTTGTTTTAATTTGCATTTCTCTGATTACTAATGAGTTTG 143 chr2qtel1M 654420 AGCACCTTTTAATGAGACTAGAAATAG--TTTC-AATTTCTTCATCTGAA 654466 i i v - vi v --v -- -ii i v v C L1ME5_3end#LI 142 AGCATCTCTTCAT-ATGCTTG--TTAGCCTTTCGGGTTTCCTCTTCTGTA 96 chr2qtel1M 654467 AATTGTCTGTTCATATCCTTTGACTATTTATCAGTTGGAG--AATGGCTT 654514 i v i v vi i --?vi v C L1ME5_3end#LI 95 AATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGGGGTTNCCGTCTT 46 chr2qtel1M 654515 GAATTCTTACAAATTTGAGTCAATTCTGTATATATTTTAGA 654555 v-- iivi vivv i iv i i C L1ME5_3end#LI 45 T--TTCTTGTTGATTTGCAGGAGTTCCTTGTATATTCTAGA 7 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.71 CpG sites = 92, Kimura (unadjusted) = 38.58 Transitions / transversions = 1.19 (92/77) Gap_init rate = 0.06 (33 / 589), avg. gap size = 2.12 (70 / 33) 874 30.33 7.59 1.84 chr2qtel1M 654042 654555 (345445) C L1ME3C_3end#LINE/L1 (321) 549 7 m_b99s551i8 3654 chr2qtel1M 654042 ATAATATTCCATAACATTAATATACCATAACTTATTCAGCCATTCTCCAG 654091 i vii v i i i v v C L1ME3C_3end#L 549 ATAGTATTCCATTGTATGAATATACCACAATTTATTTATCCATTCTCCTG 500 chr2qtel1M 654092 TTGATA-ACA-----GTCG---CTA-------GTCACTTCAAAAAGGGCT 654125 i- ----- i --- i ------- ii i v v iv C L1ME3C_3end#L 499 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 450 chr2qtel1M 654126 GCCACAAGCATTTTTGCACATGTGGGTTCCTTT--CCCTCTTTTAAGA-T 654172 v ii i i i ---i v-- v v v vii - C L1ME3C_3end#L 449 GCAATGAACATTCTTGTACATGT---CTCCTTGTGCACACGTGCGAGAGT 403 chr2qtel1M 654173 GTCTTTGGGATATAAGTCCAGTAGAAACAATGCTGGGTCAAATGCTAAGC 654222 v i i i vii i v viiv v iv v v v C L1ME3C_3end#L 402 TTCTCTAGGGTATATACCTAGGAGTGGAATTGCTGGGTCGTAGGGTATGC 353 chr2qtel1M 654223 ACAGTTTGATATCTTTTTGAGCATAGTTCCAAACTGCTCTCCAGAATGAT 654272 i vi --i v viv - v v i i i i C L1ME3C_3end#L 352 GCATCTT--CAACTTTACTAG-ATATTGCCAAATTGCTCTCCAAAGTGGT 306 chr2qtel1M 654273 TGAATTTCATTCACAATTCCACCAACAATGTATCAGTGTTCCAGTTTTCC 654322 v ii-v i v i i i v v v vii C L1ME3C_3end#L 305 TGTACC-AATTTACACTCCCACCAGCAGTGTATGAGAGTTCCCGTTGCTC 257 chr2qtel1M 654323 CACATCCCCTCCAACAATTGACATTGTCTTATCCTATCATCTTAGCCAGT 654372 i v v ii vv iii vvv i v i C L1ME3C_3end#L 256 CACATCCTCGCCAACACTTGGTATTGTCAGACTTTTAAATTTTTGCCAAT 207 chr2qtel1M 654373 CTGACAAGTGTG--------------------TCTAATTTGCATTTCTCT 654402 iii -------------------- i i C L1ME3C_3end#L 206 CTGATGGGTGTGAAATGGTATCTCATTGTNGTTTTAATTTGCATTTCCCT 157 chr2qtel1M 654403 GATCAATAGTGATTTGAAGCACCTTTTAATGAGACTAGAAATAGTTTCAA 654452 i v vv vi i v iv vi vviiivi iv?i C L1ME3C_3end#L 156 GATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTCGNG 107 chr2qtel1M 654453 TTTCTTCATCTGAAAATTGTCTGTTCATATCCTTTGACTATTTATCAGTT 654502 i v vi i i v i v vi C L1ME3C_3end#L 106 TTTCCTCTTCTGTGAATTGCCTGTTCATATCTTTTGCCCATTTTTCTATT 57 chr2qtel1M 654503 GGAGAATGGCTTGAATTCTTACAAATTTGAGTCAATTCTGTATATATTTT 654552 ---i v ii vv ivi vivv i v i C L1ME3C_3end#L 56 GG---GTTGTCTGTTTTCTTATTGATTTGTAGGAGTTCTTTATATATTCT 10 chr2qtel1M 654553 AGA 654555 i C L1ME3C_3end#L 9 GGA 7 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.55 CpG sites = 85, Kimura (unadjusted) = 39.92 Transitions / transversions = 1.25 (85/68) Gap_init rate = 0.03 (17 / 513), avg. gap size = 2.88 (49 / 17) 332 31.78 5.59 4.58 chr2qtel1M 654420 655349 (344651) C L1M5_orf2#LINE/L1 (8) 3286 2348 m_b99s551i9 3654 chr2qtel1M 654420 AGCACCTTTTAATGAGACTAGAAATAGTTTCAATTTCTTCATCTGAAAAT 654469 i v v vi vviiivi v? v v i vi v C L1M5_orf2#LIN 3286 AGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTTTTGTGAAG 3237 chr2qtel1M 654470 TGTCTGTTCATATCCTTTGACTATTTATCAGTTGGA--GAATGGCTTGAA 654517 vi i v i v ?vi i-- vv v v-- C L1M5_orf2#LIN 3236 TGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTTGTCTTT-- 3189 chr2qtel1M 654518 TTCTTACAAATTTGAGTCAATTCTGTATATATTTTAGAAATGAGGCTTTC 654567 ? ivi ? vivv i v i i v i v i i C L1M5_orf2#LIN 3188 TTNTTATTGANTTGTAGGAGTTCTTTATATATTCTGGATACGAGTCCTTT 3139 chr2qtel1M 654568 ATCCAAACCCTTGAAT-GTAAAAAGGTTTTCCCAGTTTATTGTTTCCCTT 654616 i - i iviv v? - i v vv i ? i i v i v C L1M5_orf2#LIN 3138 GTC-AGATATATGTNTTGCAAATATTTTCTCCCANTCTGTGGCTTGCCTT 3090 chr2qtel1M 654617 TTAATCTTGTCTGCATTAGTTTTGTTTGTACAAAA------AACTT-AAT 654659 v i v ivi iv ivi vvv? vi i ------ i -i C L1M5_orf2#LIN 3089 TTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTTTAATTTTGAT 3040 chr2qtel1M 654660 ATAATCAAAATTAT-----TTTTCAGTAATGATCTATAGTTCTTCTT-TG 654703 i? i v v ----- vv v i --- ? v i - C L1M5_orf2#LIN 3039 GNAGTCCAATTTATCAATTTTTTCTTTTATGGT---TNGTGCTTTTTGTG 2993 chr2qtel1M 654704 GAC------AAAAATTCTTCCCTCCTCCACAGATCTGAGAAGTAAACTAT 654747 vv ------ i ii v v?i - i -iv - v i v C L1M5_orf2#LIN 2992 TCCTGTTTAAGAAATCTTTGCCTANCCCA-AGGTC-ACGAAG-ATATTCT 2946 chr2qtel1M 654748 TCTATGTTTT--TCTAACTTATTTATAAA---ATTCTTTATGTCTAGATA 654792 i -- ivvvv iv--- ?ii ii i i v C L1M5_orf2#LIN 2945 CCTATGTTTTCTTCTAGAAGTTTTATAGTTTTANCTTTTACATTTAGGTC 2896 chr2qtel1M 654793 -ATGAACCCATTTCAACCTTATCTTGGCATACGGTGTTAGATGTGGGTCG 654841 - -i i ?i vi v i v ii i v i iv C L1M5_orf2#LIN 2895 TATGA-TCCATCTNGAATTAATTTTTGTGTATGGTGTGAGGTAGGGGTCG 2847 chr2qtel1M 654842 ATGCCAAGTTTCTGCCATACTTGTTTCCAATTTTCCCAGACATT-TTTGT 654890 v?iiv v i v ivvi v v i - ii- C L1M5_orf2#LIN 2846 AGNTTCATTTTTTTCCATATGGATATCCAATTGTTCCAG-CACCATTTGT 2798 chr2qtel1M 654891 CAAATAGTGAATTCTTATCCCAAAAGCTGGGTT-CTTTGGG---TTTGTC 654936 ii v vvv i vi ---- ii - ? v--- C L1M5_orf2#LIN 2797 TGAAAAGACTATCCTTTCCCCA----CTGAATTGCNTTGGCACCTTTGTC 2752 chr2qtel1M 654937 AAACACCAGATCACTATA---GTCTTTGACTATTTTGTCCTGTGAAC--- 654980 v i i? v? i --- v vv v i------ i --- C L1M5_orf2#LIN 2751 AAAAATCAANTGNCCATATATGTGTGGGTCTATTTC------TGGACTCT 2708 chr2qtel1M 654981 CTAACCTTTTCCATTGGTCAACTATTCTATTTTTTAGCCAGTATCTAATG 655030 vi v i v i vv ii vv i i vv iv C L1M5_orf2#LIN 2707 CTATTCTGTTCCATTGATCTATTTGTCTATCCTTACGCCAATACCACACT 2658 chr2qtel1M 655031 GTTTTAATGTCCGCTATGTTT-TAATATAGTGTT-AGACCTGGTACAGCT 655078 i i vv i - vv - - v - ? i ? vv iv C L1M5_orf2#LIN 2657 GTCTTGATTACTG-TAGCTTTATAATA-AGTCTTGANATCNGGTAGTGTA 2610 chr2qtel1M 655079 AGGCCACCTTAATTTGCTTTTTCTTTTTTTAATTCCATTAATTCTCTTGA 655128 v v -- i vv i i- -------i v i i C L1M5_orf2#LIN 2609 AGTCCTCC--AACTTTGTTCTTCTTTTTC-AA-------GATTGTTTTGG 2570 chr2qtel1M 655129 A-ATTTTTGACCTTTTGTTTTTCCAGATGAATTTTG---TTTGTTTGTTT 655174 v- i ? ii i iv v i i--- iv i iv C L1M5_orf2#LIN 2569 CTATTCTNGGTCCTTTGCATTTCCATATAAATTTTAGAATCAGCTTGTCA 2520 chr2qtel1M 655175 GTTTTTTTATTTCAGTAAAATAGTTTCTTGGGAGTTTGATTGGCATAGCA 655224 -------- vii v iii vi v v v C L1M5_orf2#LIN 2519 --------ATTTCTACAAAAAAACCTGCTGGGATTTTGATTGGGATTGCA 2478 chr2qtel1M 655225 CTAAAT----AAATTAATATAGGTAGTATTGCCATCTTTATGATATTCAC 655270 i i ---- i i v i v v v ? ii v v C L1M5_orf2#LIN 2477 TTGAATCTATAGATCAATTTGGGGAGAATTGACATCTTNACAATATTGAG 2428 chr2qtel1M 655271 TCAATCTATCCAAGAGCACTTGATAT---TTTCCAACTGTTTAGATCTGA 655317 vvi v v i -- i --- i vi i i vv C L1M5_orf2#LIN 2427 TCTTCCAATCCATGAACA--TGGTATATCTCTCCATTTATTTAGGTCTTC 2380 chr2qtel1M 655318 CTTTATTTGTGTGGAAAGTGTTTTGTAGTTTT 655349 i v v v viiv i C L1M5_orf2#LIN 2379 TTTAATTTCTCTCAGCAATGTTTTGTAGTTTT 2348 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 42.95 CpG sites = 143, Kimura (unadjusted) = 43.35 Transitions / transversions = 1.03 (143/139) Gap_init rate = 0.07 (64 / 929), avg. gap size = 1.48 (95 / 64) 408 30.70 4.11 5.74 chr2qtel1M 654780 655363 (344637) C L1P3_orf2#LINE/L1 (386) 2908 2334 m_b99s551i10 3654 chr2qtel1M 654780 TTATGTCTAGATAATGAACCCATTTCAACCTTATCTTGGCATACGGTGTT 654829 i i ii vv v i i ii vi v i v i v v C L1P3_orf2#LIN 2908 TTACGTTTAAGTCTTTAATCCATCTTGAGTTAATTTTTGTATAAGGTGTA 2859 chr2qtel1M 654830 AGATGTGGGTCGA-TGCCAAGTTTCTGCCATACTTGTTT--CCAATTTTC 654876 iviv v - vi iv - -- vi -- i C L1P3_orf2#LIN 2858 AGGAAGGGGTCCAGTTTCAGTTTTCTGC-ATA--TGGCTAGCCAGTTTTC 2812 chr2qtel1M 654877 CCAGACATT-TTTGTCAAATAGTGAATTCTTATCCCAAAAGCTGGGTTCT 654925 - ii- i i v i - v vv v v i C L1P3_orf2#LIN 2811 CCA-ACACCATTTATTAAATAGGGAATCCTT-TCCCCATTGCTTGTTTTT 2764 chr2qtel1M 654926 -TTGGGTTTGTCAAACACCAGATCACTATAG-TCTTTGAC--TATTTTGT 654971 - ii v i vii i - v v i -- --- C L1P3_orf2#LIN 2763 GTCAGGTTTGTCAAAGATCAGATGGTTGTAGATGTGTGGCGTTATTT--- 2717 chr2qtel1M 654972 CCTGTGAAC-CTAACCTTTTCCATTGGTCAACTAT-TCTATTTTTTAGCC 655019 - v iv - ivi v v - - i vvvi C L1P3_orf2#LIN 2716 -CTGAGGCCTCTGTTCTGTTCCATTGGTCTA-TATATCTGTTTTGGTACC 2669 chr2qtel1M 655020 AGTATCTAATG--GTTTTAATGTCCGCTATGTTTTAATATAGTGTTAGAC 655067 i -- -- ii vv i iviiv v i v v iii C L1P3_orf2#LIN 2668 AGTACC--ATGCTGTTTTGGTTACTGTAGCCTTGTAGTATAGTTTGAAGT 2621 chr2qtel1M 655068 CTGGTACAGCTAGGCCACCTTAATTTGCTTT-TTCTTTTT--TTAATTCC 655114 v vv iv v v --- --- - -- i---- C L1P3_orf2#LIN 2620 CAGGTAGCGTGATGCCTCC---A---GCTTTGTTCTTTTTGCTTAG---- 2581 chr2qtel1M 655115 ATTAATTCTCTTGAAATTTTTGACCTTTTGTTT--TTCCAGATGAATTTT 655162 ---i v iv- v vi iv i v -- v v C L1P3_orf2#LIN 2580 ---GATTGTCTTGGC-TATACGGGCTCTTTTTTGGTTCCATATGAAATTT 2535 chr2qtel1M 655163 G--TTTGTTTGTTTGTTTTTTTATTTCAGTAAAATAGTTTCTTGGGAGTT 655210 i--v v ------- i v v i iv iv ivv v i C L1P3_orf2#LIN 2534 AAAGTAGTTT-------TTTCTAATTCTGTGAAGAAAGTCAATGGTAGCT 2492 chr2qtel1M 655211 TGATTGGCATAGCACTAAAT----AAATTAATATAGGTAGTATTGCCATC 655256 v v i i ---- v v i i v i C L1P3_orf2#LIN 2491 TGATGGGGATAGCATTGAATCTATAAATTACTTTGGGCAGTATGGCCATT 2442 chr2qtel1M 655257 TTTATGATATTCACTCAATCTATCCAAGAGCACTTGATA-TTTTCCAACT 655305 i i v i vvi v ivvi i- vi C L1P3_orf2#LIN 2441 TTCACGATATTGATTCTTCCTATCCATGAGCATGGAATGTTTTTCCATTT 2392 chr2qtel1M 655306 GTTTAGATCTGACTTTATTTGTGTGGAAAGTGTTTTGTAGTTTTGTTCGT 655355 ivi ivvii viv iiv v i vi i v C L1P3_orf2#LIN 2391 GTTTGTGTCCTCTCTTATTTCCTTGAGCAGTGGTTTGTAGTTCTCCTTGA 2342 chr2qtel1M 655356 ATAGTTCC 655363 v v C L1P3_orf2#LIN 2341 AGAGGTCC 2334 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.06 CpG sites = 84, Kimura (unadjusted) = 39.96 Transitions / transversions = 0.99 (84/85) Gap_init rate = 0.08 (48 / 583), avg. gap size = 1.19 (57 / 48) 279 24.49 0.00 3.19 chr2qtel1M 655475 655571 (344429) L1MB8_3end#LINE/L1 470 563 (362) m_b99s551i11 3655 chr2qtel1M 655475 CTAAAAACTGGAAACTGAATGGATGTCCATCAGTTGGAGAATGGCTGAAT 655524 i v vivviii ii iv v i L1MB8_3end#LI 470 CCAAAAAGTGGAAACAACCCAAATGTCCATCAACTGATGAATGGATAAAT 519 chr2qtel1M 655525 AAATTGTGGTATATGAATATTATGGAATATTACTGTTCTGTAAGAAA 655571 v vv iv --- v i v L1MB8_3end#LI 520 AAAATGTGGTATATCCATACAATGGAATATTA---TTCGGCAATAAA 563 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 29.82 CpG sites = 11, Kimura (unadjusted) = 29.82 Transitions / transversions = 0.92 (11/12) Gap_init rate = 0.03 (3 / 96), avg. gap size = 1.00 (3 / 3) 360 22.62 0.00 0.00 chr2qtel1M 655475 655558 (344442) L1ME2z_3end#LINE/L1 470 553 (638) m_b99s551i12 3655 chr2qtel1M 655475 CTAAAAACTGGAAACTGAATGGATGTCCATCAGTTGGAGAATGGCTGAAT 655524 i v vvii i iiv v i i L1ME2z_3end#L 470 CCAAAAACTGGAAACAGCCCAGGTGTCCATCAACAGGAGAATGGATAAAC 519 chr2qtel1M 655525 AAATTGTGGTATATGAATATTATGGAATATTACT 655558 i vv iv i L1ME2z_3end#L 520 AAACTGTGGTATATTCATACAATGGAATACTACT 553 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 27.37 CpG sites = 11, Kimura (unadjusted) = 27.37 Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.00 (0 / 83), avg. gap size = 0.0 (0 / 0) 18 25.86 0.00 0.00 chr2qtel1M 656071 656121 (343879) (AAATA)n#Simple_repeat 1 51 (0) m_b99s252i8 3656 chr2qtel1M 656071 AAATAAAAGGCTATTAAATAAAAAAAAATTAAATTAAATTAAAAAAAAAA 656120 vivv v v v v v v v (AAATA)n#Simp 1 AAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATA 50 chr2qtel1M 656121 A 656121 (AAATA)n#Simp 51 A 51 Matrix = Unknown Transitions / transversions = 0.10 (1/10) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 348 32.82 3.36 3.36 chr2qtel1M 656797 657272 (342728) C L1PREC2_orf2#LINE/L1 (2787) 507 32 m_b99s551i13 3654 chr2qtel1M 656797 GTTTACTTCCTTAATTTCTTTCTTATTTATTTTGTGGTT---TGATATAT 656843 i vv v v v --- v vi --- v i C L1PREC2_orf2# 507 GTTCAGGTCCTGAATATCTTTGTTA---ATTTTCTGCCTCGATGATCTGT 461 chr2qtel1M 656844 CTAGTTATGAGAGAGCAAAGTTGAA--CTCCCAATAGTATAGTTTTACTT 656891 i vv vv v viiv -- v v v v vivvv C L1PREC2_orf2# 460 CTAATACTGTCAGTGGGGTGTTGAAGTCTCCCACTATTATTGTGTGGGAG 411 chr2qtel1M 656892 TCTATTTCTTGTTGCATCTCTCTTAATTTCTCCTCTAGGAATCTGGGTGC 656941 vv iv ? vv v ivvii v i v C L1PREC2_orf2# 410 TCTAAGTCTCTTTGNAGGTCTCTAAGAACTTGCTTTATGAATCTGGGTGC 361 chr2qtel1M 656942 TATACCCCTTGGTACATATATGTTTAGTAT---T-GATCTTGCTTCATTA 656987 vivvivi v i i v --- - i - -i i C L1PREC2_orf2# 360 TCCTGTGTTGGGTGCATATATATTTAGGATAGTTAGGTCTT-CTT-GTTG 313 chr2qtel1M 656988 TCTTTGGTACTCTTTAGTAAGATATAGTTTCTTTCCTTATCTCTTTTCAT 657037 vv -- v i vi vv i i vi i i i i --- C L1PREC2_orf2# 312 AATT--GAACCCTTTACCATTATGTAATGCCCTTCTTTGTCTTTTTT--- 268 chr2qtel1M 657038 TAGATCTATCTTTGCTT-----TTATTTGATCTGAGATCAGGATTGCTAT 657082 -- v v v i -----i i vi i i v i C L1PREC2_orf2# 267 --GATCTTTGTTGGTTTAAAGTCTGTTTTGTCTGAAATTAGGATTGCAAC 220 chr2qtel1M 657083 CTTTTTTTTTTTTTTTTTAACTTTATCTGCAGTATAACATTCTACTCCAG 657132 ii vi i v --- ii i vvvi i- i v v C L1PREC2_orf2# 219 CCCTGCTTTTTTCTGTTT---TCCATTTGCTTGGTAG-ATTTTTCTCCAT 174 chr2qtel1M 657133 CCCTTTATCTTTACTTTGTATGTATCACTG--TTTTAAATGTGTCTCTTG 657180 i v vii i iv i i -- v v i v C L1PREC2_orf2# 173 CCCTTTATTTTGAGCCTATGGGTGTCATTGCATGTGAGATGGGTCTCTTG 124 chr2qtel1M 657181 TAAATAACATATTGTAGGATTCTGGCTTTTAATCCAGTTTGCTATTCCCT 657230 v i i i iii v i ii vi i v i i i iv C L1PREC2_orf2# 123 AAGACAGCATACCATTGGGTCTTGCTTCTTTATCCAGCTTGCCACTCTGT 74 chr2qtel1M 657231 TCTATTTTATGGGAGAATTCATCTCATTCACATTCACAGTTA 657272 v iv v v i v i v i i vi C L1PREC2_orf2# 73 GCCTTTTAATTGGGGCATTTAGCCCATTTACATTCAAGGTTA 32 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 43.96 CpG sites = 75, Kimura (unadjusted) = 43.96 Transitions / transversions = 0.99 (75/76) Gap_init rate = 0.05 (22 / 475), avg. gap size = 1.45 (32 / 22) 446 27.60 2.06 3.12 chr2qtel1M 656919 657307 (342693) C L1MC4_5end#LINE/L1 (0) 2555 2171 m_b99s551i14 3654 chr2qtel1M 656919 TTCTCCTCTAGGAATCTGGGTGCTATACCCCTTGGTACATATATGTTTAG 656968 i v i vi ?v ? ? iiivi i ? i v C L1MC4_5end#LI 2555 TTTTGCTTTATAAANGTGGNTGCTNTGTTATTTGGTGCATANATATTTAT 2506 chr2qtel1M 656969 TATTGATCTTGCTTCATTATCTTTGGTACTCTTTAGTAAGATATAGTTTC 657018 v v v vv i vvv v ???i ?i vv v i v? C L1MC4_5end#LI 2505 AATTGTTATATCTTCATTGTGAATTGNNNCCTTTANCATTATAAAATGNC 2456 chr2qtel1M 657019 TTTCCTTATCTCTTTTCATTAGATCTATCTTTGCTTTTATTTGATCTGAG 657068 i i i ? v vvvv i i? viv? i i vi v C L1MC4_5end#LI 2455 CTTCTTTGTCTCNTTTAATGCTTTTTGNCTTGAANTCTACTTTGTCTGAT 2406 chr2qtel1M 657069 ATCAGGATTGCTATCTTTTTTTTTTTTTTTTTAACTTTATCTGCAGTATA 657118 ? i? v i i i v ii---v ii -- C L1MC4_5end#LI 2405 ATNAANATTGCAACCCTTCTTTTTTGTTTCC---ATTTGCCTG--GTATA 2361 chr2qtel1M 657119 ACATTCTACTCCAGCCCTTTATCTTTACTTTGTATGTATCACTGTTTT-A 657167 v v ? --- v i i vii v v v v - C L1MC4_5end#LI 2360 TCTTTNT---CCATCCCTTTATTTTCAGCCTTTCTGAATCACTTTTTTTA 2314 chr2qtel1M 657168 AATGTGTCTCTTGTAAATAACATATTGTAGGATTCTGGCTTTTAATCCAG 657217 ii ? i i v v i ii vi ? ? ? i C L1MC4_5end#LI 2313 GGTGTGTCTCTTGTANACAGCATATAGTTGGGTCTTGCTTTNTNANCCAA 2264 chr2qtel1M 657218 TTTGCTATTCCCTTCTATTTT-ATGGGAGAATTCATCTCATTCACATTCA 657266 ? vv v - i ? v - ? v i ? v i i i C L1MC4_5end#LI 2263 NTTGAAAAT-CTTTNTCTTTTAATNGGTGAGTTNAGCCCATTTACATTTA 2215 chr2qtel1M 657267 CAGTTAAAATAACTAA----TTCTGTATT--TCCTGCCATCTTATTT 657307 --- i?v ? i ---- iv v -- i i v C L1MC4_5end#LI 2214 ---TTGNTATNACTGATATGTTTGGTCTTAATTCTGTCATATTATTT 2171 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.09 CpG sites = 53, Kimura (unadjusted) = 38.09 Transitions / transversions = 1.04 (53/51) Gap_init rate = 0.04 (16 / 388), avg. gap size = 1.25 (20 / 16) 389 25.24 5.67 1.99 chr2qtel1M 657156 657349 (342651) C L1MEj_5end#LINE/L1 (0) 2160 1960 m_b99s551i15 3654 chr2qtel1M 657156 ATCACT--GTTTTAAATGTGTCTCTTGTAAATAACATATTGTAGGATTCT 657203 -- i i i i v iv i i C L1MEj_5end#LI 2160 ATCACTTTGTTTTAAGTGTGTTTCTTGTAAACAGCATATAGCTGGGTTTT 2111 chr2qtel1M 657204 GGCTTTTAATCCAGTTTGCTATTCCCT-TCTATTTTATGGGAGAATTCAT 657252 vi i i i vi v i - - v v C L1MEj_5end#LI 2110 GTTTTTTAACCCAATCTGACAGTCTCTGTCT-TTTAATGGGAGAATTCAG 2062 chr2qtel1M 657253 CTCATTCACATTC------ACAGTTAAAATAACTAATTCTGTATTTCCTG 657296 ii i------ iii i v vi i i i--- v C L1MEj_5end#LI 2061 TCCATTCACATTTAGTGTAACGACTGATATACTTGATTTTA---TTCCTT 2015 chr2qtel1M 657297 CCATCTTA-TTTA-CCCTAAATTATGCTTTTTTTTCTTTCCTTTCCCCCT 657344 - -i?i v v vi v i? ii i iii C L1MEj_5end#LI 2014 CCATCTTACTTTATTNTTTATTTATTTTGTTTTTTTNTTTTTTTTCTTTT 1965 chr2qtel1M 657345 TCCTT 657349 C L1MEj_5end#LI 1964 TCCTT 1960 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 31.84 CpG sites = 34, Kimura (unadjusted) = 32.68 Transitions / transversions = 2.43 (34/14) Gap_init rate = 0.05 (9 / 193), avg. gap size = 1.67 (15 / 9) 821 28.80 3.17 3.17 chr2qtel1M 658926 659366 (340634) L1ME4a_3end#LINE/L1 199 639 (232) m_b99s551i17 3657 chr2qtel1M 658926 TCACCTGTCAGATTGGTTAAGATGACAGGAAAAAATAATGATGAT----- 658970 i i iv v----v i -- i ----- L1ME4a_3end#L 199 TCACCTATCAAATTGGCAAAGATT----TAAAAGAT--TGATAATACCCA 242 chr2qtel1M 658971 -TGTTGGAGGGCATGTGGGAAAACTGGGACACTGATACATTGTTGGTGGA 659019 - v i vi ?i v v v v i i i L1ME4a_3end#L 243 GTGTTGGCGAGGGTGTGGNGAAACGGGCACTCTCATACACTGCTGGTGGG 292 chr2qtel1M 659020 GTTGTGACCGAATCCAACCATTCTGGAGAGCAGTTTGGAACTATGCTCAA 659069 iv i vivii v v i i v v iviv L1ME4a_3end#L 293 AGTGTAAATTGGTACAACCTTTCTGGAGGGCAATTTGGCAATATGTATCA 342 chr2qtel1M 659070 AAAGTTATCAAACTGTGCATACCCTTTGATCCAGCAGTGTTACTACTGGG 659119 iiv v v ? i i i vii v i L1ME4a_3end#L 343 AAAGCCTTAAAAATGTNCATACCCTTTGACCCAGTAATTCCACTTCTAGG 392 chr2qtel1M 659120 CTTATATCCCAAAGAGATCAT-AAAGAAG-GGAAAGGGACCTGTATGTGC 659167 vv v i i i v - i v - ? v ii -- v i L1ME4a_3end#L 393 AATTTATCCTAAGGAAATAATCAGAGATGTGNACAAAGA--TTTATGTAC 440 chr2qtel1M 659168 ACGAATGTTTGTGGCAGCCCTCTTTGTAGTGGCTAGAAACTGGAAAATGA 659217 v i ii v vi v i i i v i i vviv L1ME4a_3end#L 441 AAGGATGTTCATCGCAGCATTATTTATAATAGCGAAAAATTGGAAACAAC 490 chr2qtel1M 659218 GTGGATGCCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATATGAAT 659267 v ii i v i v i ? i i i i vv L1ME4a_3end#L 491 CTAAATGTCCAACAATAGGGGANTGGTTAAATAAATTATGGTACATCCAT 540 chr2qtel1M 659268 ATTATGGAATATTATTGTTCTATAAGAAATGA------CCAACAGGAAGA 659311 ?v vvvv i v i ? ------ v --- v L1ME4a_3end#L 541 ANAATGGAATATTATGCAGCCATTAAAAATNATGTTTTCGAA---GAATA 587 chr2qtel1M 659312 TTTCAGAAAGGCCTGGAGAGACTTACATGAACTGATGCTGAGTGAAACAA 659361 --- v i v ii i iviv vv i i i v L1ME4a_3end#L 588 TTT---AATGACATGGGAAAATGCTCATGATATAATGTTAAGTGAAAAAA 634 chr2qtel1M 659362 GCAGG 659366 L1ME4a_3end#L 635 GCAGG 639 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.64 CpG sites = 65, Kimura (unadjusted) = 37.64 Transitions / transversions = 1.12 (65/58) Gap_init rate = 0.04 (19 / 440), avg. gap size = 1.47 (28 / 19) 823 29.83 0.56 1.41 chr2qtel1M 658926 659282 (340718) L1ME3G_3end#LINE/L1 195 548 (376) m_b99s551i16 3657 chr2qtel1M 658926 TCACCTGTCAGATTGGTTAAGATGACAGGAAAAAATAATGATGATTGTTG 658975 ii iv i vvv iii?vvi ivi? v L1ME3G_3end#L 195 TCACCCATCAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTG 244 chr2qtel1M 658976 GAGGGCATGTGGGAAAACTGGGACACTGATACATTGTTGGTGGAGTTGTG 659025 v i vi i v v v v i i iiv i L1ME3G_3end#L 245 GCGAGGGTGTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTA 294 chr2qtel1M 659026 ACCGAATCCAACCATTCTGGAGAGCAGTTTGGAACTATGCTCAAAAAGTT 659075 vivii v i ? i i i v v viviv v L1ME3G_3end#L 295 AATTGGTACAGCCNTTTTGGAGGGCAATTTGGCAGTATCTATTAAAATTT 344 chr2qtel1M 659076 ATCAAACTGTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGCTTATA 659125 --- v i i i vii v ? ?v v L1ME3G_3end#L 345 A---AAATGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTA 391 chr2qtel1M 659126 TCCCAAAGAGAT-CATAAAGAAG-GGAAAGGGACCTGTATGTGCACGAAT 659173 i ? i - viiv v v - v v i --? i i v i L1ME3G_3end#L 392 TCCTANAGAAATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGAT 439 chr2qtel1M 659174 GTTTGTGGCAGCCCTCTTTGTAGTGGCTAGAAACTGGAAAATGAGTGGAT 659223 ii v vi v i i v i i vvivv ii L1ME3G_3end#L 440 GTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAAT 489 chr2qtel1M 659224 GCCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATATGAATATTATG 659273 i i v i i i i vv i L1ME3G_3end#L 490 GTCCATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATG 539 chr2qtel1M 659274 GAATATTAT 659282 i L1ME3G_3end#L 540 GAATACTAT 548 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.90 CpG sites = 58, Kimura (unadjusted) = 39.93 Transitions / transversions = 1.23 (58/47) Gap_init rate = 0.02 (7 / 356), avg. gap size = 1.00 (7 / 7) 16 16.35 4.88 0.00 chr2qtel1M 659810 659850 (340150) (AAATA)n#Simple_repeat 1 43 (0) m_b99s252i10 3658 chr2qtel1M 659810 AAATAAAAGGCTATTAAAT--AATAAAATAAAATAAAAAAAAA 659850 vivv v -- v (AAATA)n#Simp 1 AAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAA 43 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.03 (1 / 40), avg. gap size = 2.00 (2 / 1) 18 17.57 0.00 0.00 chr2qtel1M 659825 659856 (340144) (A)n#Simple_repeat 1 32 (0) m_b99s252i11 3658 chr2qtel1M 659825 AAATAATAAAATAAAATAAAAAAAAAAAGAAA 659856 v v v v i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 32 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 234 34.46 0.00 1.68 chr2qtel1M 665411 665531 (334469) L1ME4c_3end#LINE/L1 414 532 (298) m_b99s551i18 3659 chr2qtel1M 665411 TTAAAGGAGGGAAAGAGACCCACATGTGGAAAAATGTTTGTGGAAGCCCT 665460 i i i i -- i i iivi i ii v v vi L1ME4c_3end#L 414 TCAAAAGAAGGAAAAAG--CTATATGCACGAAGATGTTCATTGCAGCGTT 461 chr2qtel1M 665461 TTCTGTAGTGACAAGAAACTGGAAATTGAGTGGATATCCATCAGTGGGGA 665510 v i i i ii i i i ivivv ii i v i i i L1ME4c_3end#L 462 ATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGG 511 chr2qtel1M 665511 AATGGCTGAGTAAATTCTGGT 665531 i i v L1ME4c_3end#L 512 AATGGTTAAGTAAATTATGGT 532 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 47.36 CpG sites = 31, Kimura (unadjusted) = 51.05 Transitions / transversions = 3.10 (31/10) Gap_init rate = 0.02 (2 / 120), avg. gap size = 1.00 (2 / 2) 251 34.00 0.00 0.00 chr2qtel1M 665432 665531 (334469) L1ME3F_3end#LINE/L1 430 529 (461) m_b99s551i19 3659 chr2qtel1M 665432 ACATGTGGAAAAATGTTTGTGGAAGCCCTTTCTGTAGTGACAAGAAACTG 665481 iv i ii i v v v ii i ii i L1ME3F_3end#L 430 ACATGTACAAGAATGTTCATAGCAGCACTGTTCGTAATAGCAAAAAACTG 479 chr2qtel1M 665482 GAAATTGAGTGGATATCCATCAGTGGGGAAATGGCTGAGTAAATTCTGGT 665531 ivivviii i iiii ii v i i v L1ME3F_3end#L 480 GAAACAACCCAAATGTCCATCGACAGGAGAATGGATAAATAAATTGTGGT 529 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 45.33 CpG sites = 25, Kimura (unadjusted) = 49.54 Transitions / transversions = 2.78 (25/9) Gap_init rate = 0.00 (0 / 99), avg. gap size = 0.0 (0 / 0) 38 0.00 0.00 0.00 chr2qtel1M 665920 665952 (334048) (AT)n#Simple_repeat 1 33 (0) c_b99s251i1 3660 chr2qtel1M 665920 ATATATATATATATATATATATATATATATATA 665952 (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATA 33 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 822 29.06 1.78 2.83 chr2qtel1M 665953 666339 (333661) C L1ME5_3end#LINE/L1 (551) 390 8 m_b99s551i20 3661 chr2qtel1M 665953 CCCAGTAGTAACACTGTTGAATCAAACGATATGCATA-ATTTGATAACTT 666001 v iiiv i i ii v v i i - i i --i v C L1ME5_3end#LI 390 CCCAGGAGCGGAATTGCTGGGTCATAGGGTATGCGTATACTTAAT--TTG 343 chr2qtel1M 666002 TCTGAGCATAGTTCCAAATCATTCTCCAGAATGGCTGGATGTGTTCACAA 666051 v i -- v v i iii v ivv ii v C L1ME5_3end#LI 342 ACTAAG--TACTGCCAGATTGCTCTCCAGAATGGCTGCACCAGTCTACAC 295 chr2qtel1M 666052 ATCCACCAACAATGTATCACTGTCCCAGTTTTCCCACATCTCCTTCAACA 666101 vi i i i v vv i vi ? i ii vi C L1ME5_3end#LI 294 TCCCACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATCCTCGCCAACA 245 chr2qtel1M 666102 TTCCGCATTATCTTTCCCTGTCATTCTAGCCAATCCAACAGGTATATAGT 666151 i iv ivv ii v v i v i i i i v C L1ME5_3end#LI 244 CTTGGCATTATCCAGCTTTCTAATTTTTGCCAGTCTAATAGGTGTAAAGT 195 chr2qtel1M 666152 GATATTTCAGAGCTGTCTTAATTTGCATTTTTCTGA-TAATAATGGCTTG 666200 i vv i i i - v iv v C L1ME5_3end#LI 194 GATATCTCATTGTTGTTTTAATTTGCATTTCTCTGATTACTAATGAGTTT 145 chr2qtel1M 666201 GAGCATCTTTTCATGTGGCTAGAAATAG--TTTC-AATTTCTTCATCTGA 666247 i i - v --v -- -ii i v v C L1ME5_3end#LI 144 GAGCATCTCTTCATAT-GCTTG--TTAGCCTTTCGGGTTTCCTCTTCTGT 98 chr2qtel1M 666248 GAATTTTCTTGTTTATATCCTTTGACCATTTAATCAATTGGAG--AATGA 666295 i - v i i v -v v i --?vi v C L1ME5_3end#LI 97 AAA-TTGCCTGTTCATATCCTTTGCCCATTT-TTCTATTGGGGTTNCCGT 50 chr2qtel1M 666296 CTTGATTTCTTATAAATTAGAGTTAATTCTCTATATATTTTGGA 666339 -- i vi v vivv i ii i i i C L1ME5_3end#LI 49 CTT--TTTCTTGTTGATTTGCAGGAGTTCCTTGTATATTCTAGA 8 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.87 CpG sites = 66, Kimura (unadjusted) = 38.24 Transitions / transversions = 1.42 (64/45) Gap_init rate = 0.04 (16 / 386), avg. gap size = 1.12 (18 / 16) 571 29.09 5.14 4.16 chr2qtel1M 666201 666939 (333061) C L1M5_orf2#LINE/L1 (7) 3287 2542 m_b99s551i21 3661 chr2qtel1M 666201 GAGCATCTTTTCATGTGGCTAGAAATAGTTTCAATTTCTTCATCTGAGAA 666250 vi vviiivi v? v v i v C L1M5_orf2#LIN 3287 GAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTTTTGTGAA 3238 chr2qtel1M 666251 TTTTCTTGTTTATATCCTTTGACCATTTAATCAATTGGA--GAATGACTT 666298 v v - i vi i v v- ?v i-- vv v C L1M5_orf2#LIN 3237 GTGTCT-GTTCAAGTCTTTTGCCCATTTT-TNTATTGGGTTGTTTGTCTT 3190 chr2qtel1M 666299 GATTTCTTAT-AAATTAGAGTTAATTCTCTATATATTTTGGAAATGAGGC 666347 -- ? -i ? iv v- i i i v i v C L1M5_orf2#LIN 3189 --TTTNTTATTGANTTGTAGG-AGTTCTTTATATATTCTGGATACGAGTC 3143 chr2qtel1M 666348 CTTTATCAGAACTTTTGACTGTAAAAATGTTTTCCCAGTTAATCGCTTCC 666397 i vv v vv?i i v v i ? ivi v v C L1M5_orf2#LIN 3142 CTTTGTCAGATATATGTNTTGCAAATATTTTCTCCCANTCTGTGGCTTGC 3093 chr2qtel1M 666398 CTTCTAATATTGTCTGCATTAGTTTTGTTTGTAGA--AAAACTTTTCAAT 666445 i --i v -i vii v iv v? -- i v i C L1M5_orf2#LIN 3092 CTTTT--CATTTTCT-TAACGGTGTCTTTTGANGAGCAGAAGTTTTTAAT 3046 chr2qtel1M 666446 TTC-ATATAATCAGA-------ATTTTCTATTTTGTGATCAATAATGATC 666487 i- i? i vi ------- i v i i --- ?i v i C L1M5_orf2#LIN 3045 TTTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGGT---TNGTGCTT 2999 chr2qtel1M 666488 TTTA-GTTCTTCTTCAGTCATAAATTCCTTCCTCTTCCACAGGTCTGAGA 666536 i- i vi v ---- iii v v?i - vvii C L1M5_orf2#LIN 2998 TTTGTGTCCTGTTTAAG----AAATCTTTGCCTANCCCA-AGGTCACGAA 2954 chr2qtel1M 666537 GGTAAACTATCCTATGTT--CTTCTAATTTGTTTATAAT---ATTTTTTA 666581 i --i v -- ivvvv i --- ?i C L1M5_orf2#LIN 2953 GATA--TTCTCCTATGTTTTCTTCTAGAAGTTTTATAGTTTTANCTTTTA 2906 chr2qtel1M 666582 TGTCTAGGTC-ATGAACCCATTTTGACCTTATCTTGGTGT--TGTGTGAA 666628 ii i - -i i ? vi v i v --v i C L1M5_orf2#LIN 2905 CATTTAGGTCTATGA-TCCATCTNGAATTAATTTTTGTGTATGGTGTGAG 2857 chr2qtel1M 666629 GTGTGGGTCAATGCCTAGTTTCTGCCATACTAATTTCCAATT--TTCAGC 666676 iv i v?iii v i v ivi v -- i C L1M5_orf2#LIN 2856 GTAGGGGTCGAGNTTCATTTTTTTCCATATGGATATCCAATTGTTCCAGC 2807 chr2qtel1M 666677 AGTTTTTGTCAAACAGTGAATTCTTATCCCAAAAGCTGGGGT-CTTTGGG 666725 viv ii v vvv i vi ---- iiv - ? v C L1M5_orf2#LIN 2806 ACCATTTGTTGAAAAGACTATCCTTTCCCCA----CTGAATTGCNTTGGC 2761 chr2qtel1M 666726 ---TTTGTCAAACACTAGATTAT--TAAAGTTATTGAT-TATTT-TGTCC 666768 --- v ii i? v?i-- v vv i v i - - vv C L1M5_orf2#LIN 2760 ACCTTTGTCAAAAATCAANTGNCCATATATGTGTGGGTCTATTTCTGGAC 2711 chr2qtel1M 666769 TTTGAGCCTAACCTATTCCACTGATCAACTAGTCTATTTCTTGGCCAGTA 666818 i ---- vi i i v i v iii vv i C L1M5_orf2#LIN 2710 TCT----CTATTCTGTTCCATTGATCTATTTGTCTATCCTTACGCCAATA 2665 chr2qtel1M 666819 CCAAATGGTTTTGGTTAATGCTGCTTTATAATACAATTTT-AGATCTGGT 666867 v iv i i v iv - i i - ? ? C L1M5_orf2#LIN 2664 CCACACTGTCTTGATTACTGTAGCTTTATAATA-AGTCTTGANATCNGGT 2616 chr2qtel1M 666868 AAAGCTAGG----CCACCTTCATTTGATTTTTTTTCATAGTTCCCTTGAA 666913 iv - i ---- v ii i-- i vii vii iv C L1M5_orf2#LIN 2615 AGTG-TAAGTCCTCCAACTTTGTTC--TTCTTTTTCAAGATTGTTTTGGC 2569 chr2qtel1M 666914 -ATTCTTGACCTTTTGTTTTTCCATAT 666939 - ? ii i iv C L1M5_orf2#LIN 2568 TATTCTNGGTCCTTTGCATTTCCATAT 2542 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.96 CpG sites = 113, Kimura (unadjusted) = 38.95 Transitions / transversions = 1.22 (113/93) Gap_init rate = 0.07 (50 / 738), avg. gap size = 1.38 (69 / 50) 447 30.81 8.63 3.46 chr2qtel1M 666233 667113 (332887) C L1P3_orf2#LINE/L1 (39) 3255 2331 m_b99s551i22 3661 chr2qtel1M 666233 AATTTCTTCATCTGAGAATTTTCTTGTTTATATCCTTTGACCATTTAATC 666282 v v i v v - i i v i v- i C L1P3_orf2#LIN 3255 AATGTCTTCTTTTGAGAAGTGTCT-GTTCATATCCTTCGCCCACTTT-TT 3208 chr2qtel1M 666283 AATTGGA--GAATGACTTGATTTCTTATAAATTAGAGTTAATTCTCTATA 666330 i v i-- vv vi -- i v vv v i ii i C L1P3_orf2#LIN 3207 GATGGGGTTGTTTGTTTT--TTTCTTGTAAATTTGTTTAAGTTCCTTGTA 3160 chr2qtel1M 666331 TATTTTGGAAATGAGGCCTTTATCAGAACTTTTGACTGTAAAAATGTTTT 666380 v i v v v i vvvv v i i v i C L1P3_orf2#LIN 3159 GATTCTGGATATTAGCCCTTTGTCAGATGGATAGATTGCAAAAATTTTCT 3110 chr2qtel1M 666381 CCCAGTTAATCGCTTCCCTTCTAATATTGTCTGCAT--TAGTTTTGTTTG 666428 v ivi v v v vi v i---- - -- iv C L1P3_orf2#LIN 3109 CCCATTCTGTAGGTTGCCTGTTCAC----TCTG-ATGATAGTTTCTTTTG 3065 chr2qtel1M 666429 ---TAGAAAAACTTTTCAATTTCATATAATCAGAATTTTCTATTTTG--- 666472 --- iv i i i i i v vvi vv v v v --- C L1P3_orf2#LIN 3064 CTGTGCAGAAGCTCTTTAGTTTAATTAGATCCCATTTGTCAATTTTGGCT 3015 chr2qtel1M 666473 -TGATCAATAATGATCTTTAGTTCTTCTTCAGTCATAAATTCCTTCCTCT 666521 - vi iivi v -- v v v i -- i v i v i v C L1P3_orf2#LIN 3014 TTTGTTGCCATTG--CTTTTGGTGTTTT--AGTCATGAAGTCTTTGCCCA 2969 chr2qtel1M 666522 TCCACAGGTC-TGAGAGGTAAACTATCCTATGTT--CTTCTAATTTGTTT 666568 v vi v - iv --- vv v -- ivv v C L1P3_orf2#LIN 2968 TGCCTATGTCCTGAATGGTA---TTGCCTAGGTTTTCTTCTAGGGTTTTT 2922 chr2qtel1M 666569 ATAATATT---TTTTATGTCTAGGTCATGAACCCATTTTGACCTTATCTT 666615 ii v --- i i i i v v i i vi v i C L1P3_orf2#LIN 2921 ATGGTTTTAGGTCTTACGTTTAAGTCTTTAATCCATCTTGAGTTAATTTT 2872 chr2qtel1M 666616 GGTGT--TGTGTGAAGTGTGGGTCAATGCCTAGTTT-CTGCCATA---CT 666659 v i --v i i viv v vviii - - --- C L1P3_orf2#LIN 2871 TGTATAAGGTGTAAGGAAGGGGTCCAGTTTCAGTTTTCTGC-ATATGGCT 2823 chr2qtel1M 666660 AATTTCCAATTTTC--AGCAGTTTTTGTCAAACAGTGAATTCTTATCCCA 666707 i--- i -- i viv i i i v i - v C L1P3_orf2#LIN 2822 AG---CCAGTTTTCCCAACACCATTTATTAAATAGGGAATCCTT-TCCCC 2777 chr2qtel1M 666708 AAAGCTGGGGTCTTTG---GGTTTGTCAAACACTAGATTATTAAAGTTAT 666754 vv v -- i --- v ii vi iv v i C L1P3_orf2#LIN 2776 ATTGCTTG--TTTTTGTCAGGTTTGTCAAAGATCAGATGGTTGTAGATGT 2729 chr2qtel1M 666755 -TGA--TTATTTTGTCCTTTGAG---CCTAACCTATTCCACTGATCAACT 666798 - i-- i------ ---i ivi i i i v iv C L1P3_orf2#LIN 2728 GTGGCGTTATTTC------TGAGGCCTCTGTTCTGTTCCATTGGTCTATA 2685 chr2qtel1M 666799 AGTCTATTTCTTGG--CCAGTACCAAATGGTTTTGGTTAATGCTGCTTTA 666846 vi i -- -- viiv v iv i i C L1P3_orf2#LIN 2684 TATCTGTTT--TGGTACCAGTACCATGCTGTTTTGGTTACTGTAGCCTTG 2637 chr2qtel1M 666847 TAATACAATTTTAGATCTGGTAAAGCTAGGCCACCTTCATTTGATTTTTT 666896 i i i v ii v iv iv v v vv - v i C L1P3_orf2#LIN 2636 TAGTATAGTTTGAAGTCAGGTAGCGTGATGCCTCCAGC-TTTGTTCTTTT 2588 chr2qtel1M 666897 TTCATAG--TTCCCTTGAA-ATTCTTGACCTTTTGTTTTTCCATATG--- 666940 v v -- vi iv- v vv vi v vv --- C L1P3_orf2#LIN 2587 TGCTTAGGATTGTCTTGGCTATACGGGCTCTTTTTTGGTTCCATATGAAA 2538 chr2qtel1M 666941 TTT----T-GTTTTTT-------------GGGAGTC--TGGTA------- 666963 ---- - ------------- ii -- ------- C L1P3_orf2#LIN 2537 TTTAAAGTAGTTTTTTCTAATTCTGTGAAGAAAGTCAATGGTAGCTTGAT 2488 chr2qtel1M 666964 -----TAACGCTAAATAAATAGATTACTTTAGGTAGTCTTGTCATCTTTA 667008 ----- i ii i vv i i i v v i i i C L1P3_orf2#LIN 2487 GGGGATAGCATTGAATCTATAAATTACTTTGGGCAGTATGGCCATTTTCA 2438 chr2qtel1M 667009 TGATATTCACTTGACCTATCCAAAAGCACTTGATATTTTTCCAAATGTTT 667058 i v i ivv vi ivvi i vv C L1P3_orf2#LIN 2437 CGATATTGATTCTTCCTATCCATGAGCATGGAATGTTTTTCCATTTGTTT 2388 chr2qtel1M 667059 CGATC--TGCCTATTTATGTGGAAAGTGTTTTGTAGTTTTGCTCATATAG 667106 vvi --iv i viv iiv v i v iiv v C L1P3_orf2#LIN 2387 GTGTCCTCTCTTATTTCCTTGAGCAGTGGTTTGTAGTTCTCCTTGAAGAG 2338 chr2qtel1M 667107 TTCCTCC 667113 v i C L1P3_orf2#LIN 2337 GTCCTTC 2331 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.65 CpG sites = 128, Kimura (unadjusted) = 40.23 Transitions / transversions = 0.96 (128/134) Gap_init rate = 0.07 (58 / 880), avg. gap size = 1.86 (108 / 58) 270 27.34 5.02 3.14 chr2qtel1M 667779 667997 (332003) C L1M3_orf2#LINE/L1 (2796) 492 270 m_b100s551i5 3661 chr2qtel1M 667779 TTTCTTATTCATTTTGTGGTT---TGATTTATCTAGTTATAGAGAGCAAG 667825 i v v vi --- ? i i - i v i iii C L1M3_orf2#LIN 492 TTCCTTATTGATTTTCTGTCTGGATGNTCTATCCA-TTGTTGAAAGTGGG 444 chr2qtel1M 667826 --ATTGAGATCTCCCAGTAGTATAGTTTTACTATCTATTTCTTCTTGCAT 667873 -- ii i v v v v i i i i v v C L1M3_orf2#LIN 443 GTATTGAAGTCTCCTACTATTATTGTATTGCTGTCTATTTCTCCCTTCAG 394 chr2qtel1M 667874 CTCTCTTAACTTCTCCTCTAGGAATTTGGGTGCTATACCA--GTT-GGTG 667920 i v i iv i v i viv i --- i-- - C L1M3_orf2#LIN 393 TTCTGTCAATATTTGCTTTATATATTTAGGTGCT---CCGATGTTGGGTG 347 chr2qtel1M 667921 CATGTATGTTTAGTATTGATATGGCTTCATTGTCTG---TGGTACTCTTT 667967 i i vv v iv - -? --- iiv - C L1M3_orf2#LIN 346 CATATATATTTATAATTGTTATATCTTC-TTG-NTGAATTGACCCT-TTT 300 chr2qtel1M 667968 AGCAAGATAGAGTTTTCTTCCTTATCTCTT 667997 v vv v i v?i i i C L1M3_orf2#LIN 299 ATCATTATATAATGNCCTTCTTTGTCTCTT 270 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.66 CpG sites = 33, Kimura (unadjusted) = 35.42 Transitions / transversions = 1.32 (33/25) Gap_init rate = 0.06 (12 / 218), avg. gap size = 1.50 (18 / 12) 250 29.80 4.89 5.49 chr2qtel1M 667780 668127 (331873) C L1P3_orf2#LINE/L1 (2803) 491 146 m_b100s551i6 3661 chr2qtel1M 667780 TTCTTATTCATTTTGTGGTT---TGATTTATCTAGTTATAGAGAGCAAGA 667826 i i v v vi --- i i i - v v iii i C L1P3_orf2#LIN 491 TCCTTGTTAATTTTCTGTCTCGTTGATCTGTCTAAT-ATTGACAGTGGGG 443 chr2qtel1M 667827 T--TGAGATCTCCCAGTAGTATAGTTTTACTATCTATTTCTTCTTGCATC 667874 -- i ii v v v v vivvi vv ii i vv C L1P3_orf2#LIN 442 TGTTAAAGTCTCCCACTATTATTGTGTGGGAGTCTAAGTCTCTTTGTAGG 393 chr2qtel1M 667875 TCTCT--TAACTTCTCCTCTAGGAATTTGGGTGCTATACCAGTTGGTGCA 667922 --v v-- i v i vivvi v v C L1P3_orf2#LIN 392 TCTCTAAGAACTTG--CTTTATGAATCTGGGTGCTCCTGTATTGGGTGCA 345 chr2qtel1M 667923 TGTATGTTTAGTATTGATATGGCTTCATTGTCTG---TGGTACTCTTTAG 667969 i i v v v vvv - - --- i - i v C L1P3_orf2#LIN 344 TATATATTTAGGATAGTTAGCTCTTC-TTGT-TGCATTGAT-CCCTTTAC 298 chr2qtel1M 667970 CAAGATAGAGTTTTCTTCCTTATCTCTTTTAATTAGATCTATCTTTGCTT 668019 vv iv i vii i i i ----- v v v i C L1P3_orf2#LIN 297 CATTATGTAATGCCCTTCTTTGTCTTTTTT-----GATCTTTGTTGGTTT 253 chr2qtel1M 668020 ----TC-ACTTGATCTCAGACCAGGATTGCTATCCTTCCTTTTTTTTTTT 668064 ---- -ii v vv i v i i v vi C L1P3_orf2#LIN 252 AAAGTCTGTTTTATCAGAGACTAGGATTGCAACCCCTGCTTTTTTTTGCT 203 chr2qtel1M 668065 TTTTACTTCATCTGAAGCATAATAGATTCTACTCCAGCCCTTTATCTTTA 668114 ii i -------- v ii i ?i v v i v C L1P3_orf2#LIN 202 TTCCATTT--------GCTTGGTAAATNTTCCTCCATCCCTTTATTTTGA 161 chr2qtel1M 668115 --CTATGTATGTATT 668127 -- i v C L1P3_orf2#LIN 160 GCCTATGTGTGTCTT 146 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.60 CpG sites = 49, Kimura (unadjusted) = 38.60 Transitions / transversions = 1.00 (49/49) Gap_init rate = 0.07 (26 / 347), avg. gap size = 1.38 (36 / 26) 261 27.74 4.70 6.85 chr2qtel1M 667827 668124 (331876) C L1PREC2_orf2#LINE/L1 (2854) 440 149 m_b100s551i7 3661 chr2qtel1M 667827 TTGAGATCTCCCAGTAGTATAGTTTTACTATCTATTTCTTCTTGCATCTC 667876 ii v v v v vivvi vv ii ? vv C L1PREC2_orf2# 440 TTGAAGTCTCCCACTATTATTGTGTGGGAGTCTAAGTCTCTTTGNAGGTC 391 chr2qtel1M 667877 TCT--TAACTTCTCCTCTAGGAATTTGGGTGCTATACCAGTT---GGTGC 667921 --v v-- i v i --- v v--- C L1PREC2_orf2# 390 TCTAAGAACTTG--CTTTATGAATCTGGGTGCT---CCTGTGTTGGGTGC 346 chr2qtel1M 667922 ATGTATGTTTAGTATTGATATGGCTTCATTGTCTG--TGGTACTCTTTAG 667969 i i v v v v v - - -- v v i v C L1PREC2_orf2# 345 ATATATATTTAGGATAGTTAGGTCTTC-TTGT-TGAATTGAACCCTTTAC 298 chr2qtel1M 667970 CAAGATAGAGTTTTCTTCCTTATCTCTTTTAATTAGATCTATCTTTGCTT 668019 vv iv i vii i i i ----- v v v i C L1PREC2_orf2# 297 CATTATGTAATGCCCTTCTTTGTCTTTTTT-----GATCTTTGTTGGTTT 253 chr2qtel1M 668020 ----TC-ACTTGATCTCAGACCAGGATTGCTATCCTTCCTTTTTTTTTTT 668064 ---- -ii vi v i ii v i i v i v C L1PREC2_orf2# 252 AAAGTCTGTTTTGTCTGAAATTAGGATTGCAACCCCTGCTTTTTTCTGTT 203 chr2qtel1M 668065 TTTTACTTCATCTGAAGCATAATAGATTCTACTCCAGCCCTTTATCTTTA 668114 ii i -------- v ii i v v i v C L1PREC2_orf2# 202 TTCCATTT--------GCTTGGTAGATTTTTCTCCATCCCTTTATTTTGA 161 chr2qtel1M 668115 --CTATGTATGT 668124 -- vi C L1PREC2_orf2# 160 GCCTATGGGTGT 149 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.98 CpG sites = 36, Kimura (unadjusted) = 34.98 Transitions / transversions = 0.88 (36/41) Gap_init rate = 0.09 (26 / 297), avg. gap size = 1.31 (34 / 26) 331 29.61 0.00 5.12 chr2qtel1M 667884 668150 (331850) C L1MC4_5end#LINE/L1 (0) 2555 2302 m_b100s551i8 3661 chr2qtel1M 667884 TTCTCCTCTAGGAATTTGGGTGCTATACCAGTTGGTGCATGTATGTTTAG 667933 i v i vi ?v ? ? iii v i? i v C L1MC4_5end#LI 2555 TTTTGCTTTATAAANGTGGNTGCTNTGTTATTTGGTGCATANATATTTAT 2506 chr2qtel1M 667934 TATTGATATGGCTTCATTGTCTGTGGTACTCTTTAGCAAGATAGAGTTTT 667983 v v iv vvi v ???i ? vv i i v?i C L1MC4_5end#LI 2505 AATTGTTATATCTTCATTGTGAATTGNNNCCTTTANCATTATAAAATGNC 2456 chr2qtel1M 667984 CTTCCTTATCTCTTTTAATTAGATCTATCTTTGCTTTCACTTGATCTCAG 668033 i i ? vvvv i i? viv? ii vi v v C L1MC4_5end#LI 2455 CTTCTTTGTCTCNTTTAATGCTTTTTGNCTTGAANTCTACTTTGTCTGAT 2406 chr2qtel1M 668034 ACCAGGATTGCTATCCTTCCTTTTTTTTTTTTTTTACTTCATCTGAAGCA 668083 i? i? v i ---- v ii i -------- v C L1MC4_5end#LI 2405 ATNAANATTGCAACCCTTC----TTTTTTGTTTCCATTT--------GCC 2368 chr2qtel1M 668084 TAATAGATTCTACTCCAGCCCTTTATCTTTACTATGTATGTATTACTATC 668133 ii v ii v? v i i viv v v v i - i C L1MC4_5end#LI 2367 TGGTATATCTTTNTCCATCCCTTTATTTTCAGCCTTTCTGAATCACT-TT 2319 chr2qtel1M 668134 TTTTAAATGTGTTTTTT 668150 ii i i C L1MC4_5end#LI 2318 TTTTAGGTGTGTCTCTT 2302 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.58 CpG sites = 41, Kimura (unadjusted) = 41.58 Transitions / transversions = 1.21 (41/34) Gap_init rate = 0.05 (13 / 266), avg. gap size = 1.00 (13 / 13) 402 21.50 0.93 0.93 chr2qtel1M 668316 668423 (331577) C L1MEj_5end#LINE/L1 (12) 2148 2041 m_b100s551i9 3662 chr2qtel1M 668316 TAAATGTGTTTCTTTTAAACAACATATTGTAGGGTTCTGACTTTTAATCC 668365 i v i v iv i vi i C L1MEj_5end#LI 2148 TAAGTGTGTTTCTTGTAAACAGCATATAGCTGGGTTTTGTTTTTTAACCC 2099 chr2qtel1M 668366 AATCTGCTATGCTCT-TCTGTTTTATGAGAGAGTTCATCCCATTCACAAT 668414 vi vv - - v i i vi v C L1MEj_5end#LI 2098 AATCTGACAGTCTCTGTCT-TTTAATGGGAGAATTCAGTCCATTCACATT 2050 chr2qtel1M 668415 TAAAATAAC 668423 ivi C L1MEj_5end#LI 2049 TAGTGTAAC 2041 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 25.56 CpG sites = 12, Kimura (unadjusted) = 25.56 Transitions / transversions = 1.09 (12/11) Gap_init rate = 0.02 (2 / 107), avg. gap size = 1.00 (2 / 2) 16 23.31 0.00 0.00 chr2qtel1M 670401 670435 (329565) (T)n#Simple_repeat 1 35 (0) m_b100s252i0 3663 chr2qtel1M 670401 TTTTCTTTTATTTTTTCATTTTTCTGTTTTTGTTT 670435 i v iv i v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 35 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 13 26.86 2.04 0.00 chr2qtel1M 670406 670454 (329546) (TTTTATT)n#Simple_repeat 1 50 (0) m_b100s252i1 3663 chr2qtel1M 670406 TTTTATTTTTTCATTTTTCTGTTTT-TGTTTGATTCTTGAAGTCTTATTT 670454 vv v v - v v i v vv i (TTTTATT)n#Si 1 TTTTATTTTTTATTTTTTATTTTTTATTTTTTATTTTTTATTTTTTATTT 50 Matrix = Unknown Transitions / transversions = 0.22 (2/9) Gap_init rate = 0.02 (1 / 48), avg. gap size = 1.00 (1 / 1) 14 7.79 3.45 3.45 chr2qtel1M 672136 672164 (327836) (GGA)n#Simple_repeat 1 29 (0) m_b100s252i2 3664 chr2qtel1M 672136 GGTGGAGGGAGAAGGAGGAGGAGGA-GAGG 672164 v - i - (GGA)n#Simple 1 GGAGGA-GGAGGAGGAGGAGGAGGAGGAGG 29 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.07 (2 / 28), avg. gap size = 1.00 (2 / 2) 290 26.36 10.91 0.00 chr2qtel1M 674973 675082 (324918) HERVK11D#LTR/ERVK 4931 5052 (2700) m_b100s701i0 3665 chr2qtel1M 674973 CCTAATGATATCTGGCAAATGGATGTTACCCA-----------TTGG-AG 675010 v i i ----------- - i HERVK11D#LTR/ 4931 CCTAATGCTATTTGGCAAATGGATGTTACTCATGTTCCTTCTTTTGGAAA 4980 chr2qtel1M 675011 GTCACAGTGTGTTCATGTAACAGTAGATACTCATTCTAATTTTATAGTAG 675060 i i vvv i v v v i iiv i i vvvi HERVK11D#LTR/ 4981 ATTAGCTTATGTGCATGTCACAGTTGACACCTTTTCCAATTTCATCTGGG 5030 chr2qtel1M 675061 CTACTGTTCAACCTGGAGAGGC 675082 ivv v i i HERVK11D#LTR/ 5031 CTACCTGTCAAACCGGAGAAGC 5052 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 31.54 CpG sites = 15, Kimura (unadjusted) = 32.89 Transitions / transversions = 1.07 (15/14) Gap_init rate = 0.02 (2 / 109), avg. gap size = 6.00 (12 / 2) 342 25.08 6.35 1.90 chr2qtel1M 679778 680029 (319971) HERVK14C#LTR/ERVK 2878 3140 (4294) m_b100s701i1 3666 chr2qtel1M 679778 CCTGTTCCTATCCAATGGAAAAACGATAA-CCAGTGTGGGATACAGCAGT 679826 i iv vv ?i v v v - ? v - ?v ? HERVK14C#LTR/ 2878 CCTATTCCCTTAAAATGGANGACCCAAAANCCNGTTTGGG-TNGANCAGT 2926 chr2qtel1M 679827 GGCC-CTTAATAAAGATAAAAATTCAGGCCTTTTAGA---TATATAAGGA 679872 - ??v v i - v vvi vi i--- vvi i HERVK14C#LTR/ 2927 GGCCGCTNNCTCAGGA-AAAACTGGGGGCCTTACAGGAATTAGTCAAAGA 2975 chr2qtel1M 679873 GCAGCTTGACCAAGGA-AC-TTAAACCCTC--TAAGTCCTTGGAATTCCC 679918 i ii v ?v - - ?i i v -- vvv ? ? HERVK14C#LTR/ 2976 ACAATTAGANAAAGGACACATNGAGCCCACATTTTCTCCNTGGAATTCNC 3025 chr2qtel1M 679919 CA-TGTTTG--GTGAA-AAGAAATCTGGAAAAATGGAGGATGTTAATGGA 679964 - --i ? - i i -v i v ? i iv HERVK14C#LTR/ 3026 CAGTGTTTGTAATNAAGAAAAAATCCGG-CAGATGGCGNATGCTAACCGA 3074 chr2qtel1M 679965 TTTAAGAAAAG-GAATGAACAG--ATGGAAACTATGGGAACTCTTCAGCC 680011 i v ivv -v -- -- ?v v ? ii ? v HERVK14C#LTR/ 3075 CTTACGAGCCGTCAATG--CAGTCATNCAACCNATGGGGGCNCTGCAGCC 3122 chr2qtel1M 680012 TGGACTTCCATCTCCTAC 680029 v i v ? i ii HERVK14C#LTR/ 3123 AGGGCTGCCNTCCCCCGC 3140 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 32.07 CpG sites = 28, Kimura (unadjusted) = 33.40 Transitions / transversions = 0.82 (28/34) Gap_init rate = 0.06 (16 / 251), avg. gap size = 1.31 (21 / 16) 16 0.00 0.00 0.00 chr2qtel1M 690172 690188 (309812) (A)n#Simple_repeat 1 17 (0) m_b100s252i3 3667 chr2qtel1M 690172 AAAAAAAAAAAAAAAAA 690188 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 chr2qtel1M 690192 690208 (309792) (T)n#Simple_repeat 1 17 (0) m_b100s252i4 3668 chr2qtel1M 690192 TTTTTTTTTTTTTTTTT 690208 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTT 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 573 31.79 0.00 0.00 chr2qtel1M 691049 691243 (308757) HERVP71A#LTR/ERV1 3490 3684 (3906) m_b100s701i2 3669 chr2qtel1M 691049 ACCAGTGGCTTTCCTTTCTAAAGTATTAGACCCGGTAGCCAAAGGATGGC 691098 v v iv i i iv vi v i v vv ivii i HERVP71A#LTR/ 3490 ACCTGTTGCTTTTGTCTCCAAGCTTCTCGATCCTGTCTCTCGGGGGTGGC 3539 chr2qtel1M 691099 TGACCTGTGTACAAGCAGTAGCTGCTACCACACTCTTGGCAGAAGAGAGT 691148 ivivv i i vi v vi i i HERVP71A#LTR/ 3540 CCGAATGTGTGCAAGCAGTAGCTGCCACAGCCCTGCTGGTAGAGGAGAGT 3589 chr2qtel1M 691149 AGGAAGCTCACCTTTGGAGGCAGTGTTATAGTAAGTGTCCCACACCAAGT 691198 v i v v viviv v iii i HERVP71A#LTR/ 3590 CGAAAGCTAACCTTTGGCGGGGCCCTAATAGTAAGCACCCCACACCAGGT 3639 chr2qtel1M 691199 AAGAACAATAGTAAATCAGAGGGCTGGGAAATAGCTCACAGATTC 691243 v i vv v i ii i i i i v i HERVP71A#LTR/ 3640 CAGGAATATATTAAATCAAAAAGCCGGGAGATGGTTAACGGATTC 3684 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.85 CpG sites = 34, Kimura (unadjusted) = 42.36 Transitions / transversions = 1.21 (34/28) Gap_init rate = 0.00 (0 / 194), avg. gap size = 0.0 (0 / 0) 1081 31.57 1.47 0.63 chr2qtel1M 691811 692285 (307715) HERVIP10B3#LTR/ERV1 4816 5294 (2309) m_b100s701i3 3669 chr2qtel1M 691811 GGGAGACAAGCTCCGGGAATCAGACCATTCTAAAGCATCCAAGTGGAATT 691860 i vi ivi i iv v i i i ii v v v HERVIP10B3#LT 4816 GGGGGAAGAAACCCAGGGTTAAGGCCGTTCCAAAGTGTCCAAGTTGACTA 4865 chr2qtel1M 691861 CACTGAGCTGCCACCAGTGGGTCGCCTCAAATATTTGCTGGTCATAGTAG 691910 i iv v i i i ? i i i v HERVIP10B3#LT 4866 CACCGAAATGCCCCCAATAGGCCGCCTNAAGTATTTACTAGTAATAGTAG 4915 chr2qtel1M 691911 ACCATCTGACTTCATGGGTGGAGGCATTCCCCTCAGCCCAAGC--AACTG 691958 i v iivv i i vv i-- -- ? HERVIP10B3#LT 4916 ACCACCTCACCCACTGGGTAGAAGCCATCCCCTT--CCCAAGCGCAACNG 4963 chr2qtel1M 691959 CC-TTGAC--AGT-AAGGTCTTATTAGAACAAATTATTCCTAGATATGGA 692004 -v i i-- - i ivi i i ? v i v i i v HERVIP10B3#LT 4964 CCAGTAATGTAGTCAAAGCACTGTTGGAANATATCATACCCAGGTTTGGA 5013 chr2qtel1M 692005 ATAGTGGAAAGGATAGACTTGGCTCAGGGAACACATTTTTCTCCCCAAGT 692054 v i i iv v i ii viv v i v i iv v v v HERVIP10B3#LT 5014 CTAATAGAAAACATTGATTCAGACAATGGGACCCACTTCACTGCACACGT 5063 chr2qtel1M 692055 -ATTGGAAAATCTGATTGGGGCCTTAGAAATCACTTGGGATCTCCACACC 692103 - i- iiiv iiiivii vi ? v vv viv i HERVIP10B3#LT 5064 CATTA-AGGGGCTAGCCCAAGCACTAGANATAAAATGGGAATACCATACC 5112 chr2qtel1M 692104 CCTTGGCATCCTCCCTCTTCTGGGAAAGTAGAAAGGATGAATCAAGAAAT 692153 i i v v v i i iivvv HERVIP10B3#LT 5113 CCCTGGCACCCACCCTCATCAGGGAGAGTAGAAAGAATGAATCAGACTCT 5162 chr2qtel1M 692154 AAAACAGCAACTAACTAAATTATCTTTAGAGACCCCACTACCTTGGACTA 692203 v v v i vii i vii v ? HERVIP10B3#LT 5163 AAAAAACCACCTAACCAAATTAATCTTAGAAACCCGGTTACCATGGACNA 5212 chr2qtel1M 692204 AATGTCTTCCTCATGCTGTGATCAGAATCAGAATCAAGCCACATAGAGAT 692253 i ivv iv v v v iiivv v iv i HERVIP10B3#LT 5213 AATGCCTTCCCATTGCCTTGCTAAGAATCCGAACTGCCCCTCGGAAAGAT 5262 chr2qtel1M 692254 AGAGGGCTTTCACCTTATGAATTATTGTACGG 692285 ivv v v v v ii ? i HERVIP10B3#LT 5263 GTCGGCCTATCCCCTTATGAAATGCTNTATGG 5294 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.57 CpG sites = 82, Kimura (unadjusted) = 42.71 Transitions / transversions = 1.22 (82/67) Gap_init rate = 0.02 (8 / 474), avg. gap size = 1.25 (10 / 8) 510 31.44 6.76 0.83 chr2qtel1M 693769 694108 (305892) HERV1_I#LTR/ERV1 8133 8492 (309) m_b100s701i4 3670 chr2qtel1M 693769 TGGCCTCCAGCAAGAATAGTTAAAGAGTATGAGCCAGCCACTTGGGGTCA 693818 v v vi i v v i i ? v? HERV1_I#LTR/E 8133 TGGCCTCCTGAAAGAATTATCAAATACTATGGGCCAGCTACNTGGGCNCA 8182 chr2qtel1M 693819 AGATGGAAGTTGGGGATATAGAACCCC------------------AAT-A 693849 ivvv ? iv v i ------------------ - HERV1_I#LTR/E 8183 AGATGGGTCATGGGGNTACCGTACTCCTATTTACATGTTAAACCGAATCA 8232 chr2qtel1M 693850 TA-GCTT-CAAGCAGTTGTAGAGATTATCACCAATCAGATGGCTGAGGCA 693897 - v - vv i i vii v i ii ivii v HERV1_I#LTR/E 8233 TAAGATTGCAAGCAGTACTAGAAATCATAGTCAATGAAACAGCCCGAGCC 8282 chr2qtel1M 693898 CTAGATCTTTTGGCTGACCAAGCTACTCAAAACCAGAGAGGCCGTTTTAC 693947 i i i vi i iivv i ? i i -iv v i v vv HERV1_I#LTR/E 8283 TTGGATTTGCTAGCCATACAGGCNACCCAGA-TGAGAGATGCCATATATC 8331 chr2qtel1M 693948 CACATAGACTTGTGCTGGATTATTTGTTGGC-TGAGTAAAGGGGAGTTTG 693996 v v i v iii i i i vi i - v - i i HERV1_I#LTR/E 8332 AAAATAGGCTAGCATTAGACTATCTCCTAGCCTCAG-AAGGAGGAGTTTG 8380 chr2qtel1M 693997 TGCGAAACTAAATTTGTATATTTGTTGTATAAAGATTGATGACAATGGAA 694046 v? v vv? vi i iv v i i HERV1_I#LTR/E 8381 TGGNAAACTTAATTTGACNAACTGCTGCTTACAAATCGATGACAATGGAA 8430 chr2qtel1M 694047 -ATCTAGTAAAATAAGTCATTAAGAACATTAGGGAACTTGCTCATGTTCT 694095 - v - v viv i i ivv iv vv i ii v i i i HERV1_I#LTR/E 8431 GAGCT-GTCATGGAAATCACTGCCAGGATGCGGAAGTTAGCCCATGTCCC 8479 chr2qtel1M 694096 TGTACAGACCTGG 694108 v v HERV1_I#LTR/E 8480 GGTCCAGACCTGG 8492 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.03 CpG sites = 56, Kimura (unadjusted) = 42.60 Transitions / transversions = 1.12 (56/50) Gap_init rate = 0.03 (9 / 339), avg. gap size = 2.89 (26 / 9) 12 17.53 3.12 0.00 chr2qtel1M 695795 695826 (304174) (TTTTC)n#Simple_repeat 1 33 (0) m_b100s252i5 3671 chr2qtel1M 695795 TTTTCCTGTCTATTC-TCTCTTTTGTTTTCTTT 695826 i v v - i v (TTTTC)n#Simp 1 TTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTT 33 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 216 30.23 6.98 0.00 chr2qtel1M 697575 697660 (302340) MIR3#SINE/MIR 114 205 (3) m_b100s601i0 3672 chr2qtel1M 697575 CTGAATCT--GTTTCCT-ATATACAAAATTAGTTGATTGCACTCCATGGC 697621 iii -- - v ii v vv i v vv ii MIR3#SINE/MIR 114 CTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGAT 163 chr2qtel1M 697622 CTTGTAGGTCCCTTCCAA---TGATCATCTGGGATCCTATAA 697660 ivv i--- ivv iv i i MIR3#SINE/MIR 164 CTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTATGA 205 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.47 CpG sites = 14, Kimura (unadjusted) = 39.47 Transitions / transversions = 1.17 (14/12) Gap_init rate = 0.04 (3 / 85), avg. gap size = 2.00 (6 / 3) 350 32.66 4.64 0.64 chr2qtel1M 697762 697912 (302088) C L2b_3end#LINE/L2 (10) 456 300 m_b100s601i1 3673 chr2qtel1M 697762 TCAGCAAACAT---CTCAGTGCCTATTATACGTCAGGCCCTGGGATAAGT 697808 i i --- v i i i ii i ? v v i i C L2b_3end#LINE 456 TCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGC 407 chr2qtel1M 697809 ACCAGGAACATAAAGAGAGACAAGG-GGACAT--CCCCTGCTCTCCTGGA 697855 i ii i i i iv ivii i-i ?i--i i vi C L2b_3end#LINE 406 GCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGGA 357 chr2qtel1M 697856 GGTCACACACTGCTGGGGCAGACAG-TATATCAACAACTATGTAGAAACC 697904 v vv iv v -i i v ? ivi -i ?iv C L2b_3end#LINE 356 GCTCACAGTCTAGTGGGGGAGACAGACATGTAANCAGACA-ATNATAACC 308 chr2qtel1M 697905 CACTGTGG 697912 vv C L2b_3end#LINE 307 CAGAGTGG 300 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.95 CpG sites = 33, Kimura (unadjusted) = 47.42 Transitions / transversions = 2.06 (33/16) Gap_init rate = 0.03 (5 / 150), avg. gap size = 1.60 (8 / 5) 483 24.81 8.97 1.80 chr2qtel1M 698024 698179 (301821) C MIR#SINE/MIR (4) 258 92 m_b100s601i2 3674 chr2qtel1M 698024 ATAGCTTTCATTTGTACAGCACCTACTGTTTGTCATGTACTGT------- 698066 vv i vv i i i v i v i ------- C MIR#SINE/MIR 258 ATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGC 209 chr2qtel1M 698067 -----ATAAGTATTGTCTCATTCTAGCCTCATGAAAACCCTAGGATTTGG 698111 ----- i v iv iv v ii v v vv i C MIR#SINE/MIR 208 GCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGGTAG 159 chr2qtel1M 698112 GTACTTATTATTGTGCCCATTTTTTAGATAAAGACACTGAGGCAAACAGA 698161 - i v vi i i v -- C MIR#SINE/MIR 158 GTACT-ATTATTATCCCCATTTTACAGATGAGGAAACTGAGGC--ACAGA 112 chr2qtel1M 698162 GGGCCTA--TAACTTGATCA 698179 i vi -- vi C MIR#SINE/MIR 111 GAGGTTAAGTAACTTGCCCA 92 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.51 CpG sites = 19, Kimura (unadjusted) = 30.44 Transitions / transversions = 1.00 (19/19) Gap_init rate = 0.04 (6 / 155), avg. gap size = 2.83 (17 / 6) 38 25.81 2.84 2.84 chr2qtel1M 699497 699637 (300363) (TGTA)n#Simple_repeat 1 141 (0) m_b100s252i6 3675 chr2qtel1M 699497 TGTATAGATGTTTATAAGCATTTATGTAGATATGTATGCATGTTACTCTA 699546 iv v i v i v vi i - - v (TGTA)n#Simpl 1 TGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATG-TA-TGTA 48 chr2qtel1M 699547 TGTA-G-ATGTGTATATAGATTTATGTATCTGTGTGTGGGTCTGTGGATG 699594 - - i i iv v v i i vi v i v - (TGTA)n#Simpl 49 TGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTAT- 97 chr2qtel1M 699595 GGTATTAATGTGTGTGTGTGTGTATGTATG--TGTATGTATGTAT 699637 - vv i i i -- (TGTA)n#Simpl 98 -GTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTAT 141 Matrix = Unknown Transitions / transversions = 1.07 (15/14) Gap_init rate = 0.05 (7 / 140), avg. gap size = 1.14 (8 / 7) 23 26.89 0.00 0.00 chr2qtel1M 699569 699635 (300365) (TGTGTG)n#Simple_repeat 1 67 (0) m_b100s252i7 3676 chr2qtel1M 699569 TGTATCTGTGTGTGGGTCTGTGGATGGGTATTAATGTGTGTGTGTGTGTA 699618 i v v v vi v i vvi i (TGTGTG)n#Sim 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr2qtel1M 699619 TGTATGTGTATGTATGT 699635 i i i (TGTGTG)n#Sim 51 TGTGTGTGTGTGTGTGT 67 Matrix = Unknown Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.0 (0 / 0) 265 28.04 0.00 0.00 chr2qtel1M 699657 699763 (300237) L1MC4a_3end#LINE/L1 458 564 (2065) m_b100s551i11 3677 chr2qtel1M 699657 TTTGTAGTGGCTAGAAACTGGAAACTGAGTGGATGCCCATCAATTGGAGA 699706 i v v i v i vivv ii ?? v L1MC4a_3end#L 458 TTTGTAATTGCAAAATATTGGAAACAACCTAAATGCCCATNNATAGGAGA 507 chr2qtel1M 699707 ATGGCTGAATAAATTGTGGTATATGAATATTAGGGAATATTATTGTTCTG 699756 ? i i i i vv i iv v i i vvvv L1MC4a_3end#L 508 NTGGTTGAATAAACTATGGTACATCCACACAATGGAGTACTATGCAGCTG 557 chr2qtel1M 699757 TAAGAAA 699763 i L1MC4a_3end#L 558 TAAAAAA 564 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.85 CpG sites = 15, Kimura (unadjusted) = 36.85 Transitions / transversions = 1.00 (15/15) Gap_init rate = 0.00 (0 / 106), avg. gap size = 0.0 (0 / 0) 351 23.66 0.00 0.00 chr2qtel1M 699657 699749 (300251) L1ME3G_3end#LINE/L1 456 548 (376) m_b100s551i10 3677 chr2qtel1M 699657 TTTGTAGTGGCTAGAAACTGGAAACTGAGTGGATGCCCATCAATTGGAGA 699706 i i v i i vivv ii i v i L1ME3G_3end#L 456 TTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCAATAGGGGA 505 chr2qtel1M 699707 ATGGCTGAATAAATTGTGGTATATGAATATTAGGGAATATTAT 699749 i i i vv i v i L1ME3G_3end#L 506 ATGGTTAAATAAATTATGGTATATCCATACTATGGAATACTAT 548 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 29.20 CpG sites = 14, Kimura (unadjusted) = 29.20 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.00 (0 / 92), avg. gap size = 0.0 (0 / 0) 17 11.98 0.00 5.26 chr2qtel1M 700271 700310 (299690) (AAATAAA)n#Simple_repeat 1 38 (0) m_b100s252i8 3678 chr2qtel1M 700271 AAATAAAAGGCTATTAAATAAAAAATAAAAAAATAAAAAA 700310 -iv vv - (AAATAAA)n#Si 1 AAATAAAA-AATAAAAAATAAAAAAT-AAAAAATAAAAAA 38 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 17 12.69 0.00 0.00 chr2qtel1M 700286 700311 (299689) (A)n#Simple_repeat 1 26 (0) m_b100s252i9 3678 chr2qtel1M 700286 AAATAAAAAATAAAAAAATAAAAAAA 700311 v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAA 26 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 16 24.23 1.82 1.82 chr2qtel1M 700335 700389 (299611) (GAAAAAA)n#Simple_repeat 1 55 (0) m_b100s252i10 3678 chr2qtel1M 700335 GAAAGAAGAAAACAGAACTAAGTAAAAAAGTACACAGCAGAGA-ACAAAA 700383 i v vv - v v v v i i - v (GAAAAAA)n#Si 1 GAAAAAAGAAAAAAGAAAAAAG-AAAAAAGAAAAAAGAAAAAAGAAAAAA 49 chr2qtel1M 700384 GAAAAA 700389 (GAAAAAA)n#Si 50 GAAAAA 55 Matrix = Unknown Transitions / transversions = 0.38 (3/8) Gap_init rate = 0.04 (2 / 54), avg. gap size = 1.00 (2 / 2) 31 7.90 0.00 0.00 chr2qtel1M 701021 701060 (298940) (TA)n#Simple_repeat 1 40 (0) c_b100s251i1 3679 chr2qtel1M 701021 TATATATATATATATATAAATATGTATATTTATATATATA 701060 v i v (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATA 40 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 680 28.67 2.40 2.05 chr2qtel1M 701575 701866 (298134) C L1ME3A_3end#LINE/L1 (627) 293 1 m_b100s551i13 3680 chr2qtel1M 701575 TTCTGCCAACGATGTATCAGTGTCCCAGTTTTCCCACATGCCCTCCAACA 701624 i ii i ii v v i i vii v i v C L1ME3A_3end#L 293 TCCCACCAGCAGTGTATGAGAGTTCCGGTTGCTCCACATCCTCGCCAACA 244 chr2qtel1M 701625 TTCAGCATTATCTTTTCTTGTCATCCTAGCCAATCGGGGACTTCTGTAGT 701674 i ii i i v ii v ii v v vivv v C L1ME3A_3end#L 243 CTTGGTATTGTCTGTCTTTTTCATTTTAGCCATTCTGGTGGGTGTGTAGT 194 chr2qtel1M 701675 GGTATCTCAGAGTTGTCTTAATTTGCATTGCTCTGATTAATAATGACTTT 701724 ? vv v i v i v v vv C L1ME3A_3end#L 193 GGTATCNCATTGTGGTTTTAATTTGCATTTCCCTGATGACTAATGAAGTT 144 chr2qtel1M 701725 GAG-ATCTTTTTATGTGACTAGAAATCGTTTCAATTTCTTCTTCTGAAAA 701773 - i i i vi vviii i vi v i i vi C L1ME3A_3end#L 143 GAGCACCTTTTCATATGTTTATTGGCCATTTGGATATCCTCTTTTGTGAA 94 chr2qtel1M 701774 TTGTCTGTTCATATCCTTTGACCATTTATCAATTGAAGAATGGC--TCGA 701821 v i vi i v v v -- iv v -- vv C L1ME3A_3end#L 93 GTGCCTGTTCAAGTCTTTTGCCCATTTTTCTATTG--GGTTGTCTGTCTT 46 chr2qtel1M 701822 TTTCTTATAAATT----AGAGTTCATTCTCTATATATTTGGGAAATGAG 701866 vi ----i ---- i iv v C L1ME3A_3end#L 45 TTTCTTATTGATTTGTAGGAG----TTCTTTATATATTCTGGATATGAG 1 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.30 CpG sites = 43, Kimura (unadjusted) = 36.86 Transitions / transversions = 1.10 (43/39) Gap_init rate = 0.03 (9 / 291), avg. gap size = 1.44 (13 / 9) 699 29.11 0.42 0.00 chr2qtel1M 701575 701811 (298189) C L1ME5_3end#LINE/L1 (648) 293 56 m_b100s551i12 3680 chr2qtel1M 701575 TTCTGCCAACGATGTATCAGTGTCCCAGTTTTCCCACATGCCCTCCAACA 701624 i ii i ii i v v i vi ? i v i v C L1ME5_3end#LI 293 TCCCACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATCCTCGCCAACA 244 chr2qtel1M 701625 TTCAGCATTATCTTTTCTTGTCATCCTAGCCAATCGGGGACTTCTGTAGT 701674 i ii ivvii v v ii v i viiv vv v iv C L1ME5_3end#LI 243 CTTGGCATTATCCAGCTTTCTAATTTTTGCCAGTCTAATAGGTGTAAAGT 194 chr2qtel1M 701675 GGTATCTCAGAGTTGTCTTAATTTGCATTGCTCTGATTAATAATGACTTT 701724 i vv i v v v C L1ME5_3end#LI 193 GATATCTCATTGTTGTTTTAATTTGCATTTCTCTGATTACTAATGAGTTT 144 chr2qtel1M 701725 GAG-ATCTTTTTATGTGACTAGAAATCGTTTCAATTTCTTCTTCTGAAAA 701773 - i i i vi ivv ii v ivii i v C L1ME5_3end#LI 143 GAGCATCTCTTCATATGCTTGTTAGCCTTTCGGGTTTCCTCTTCTGTAAA 94 chr2qtel1M 701774 TTGTCTGTTCATATCCTTTGACCATTTATCAATTGAAG 701811 i v v v ii C L1ME5_3end#LI 93 TTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGGGG 56 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.23 CpG sites = 39, Kimura (unadjusted) = 37.92 Transitions / transversions = 1.30 (39/30) Gap_init rate = 0.00 (1 / 236), avg. gap size = 1.00 (1 / 1) 316 28.57 2.34 1.86 chr2qtel1M 701718 701931 (298069) C L1M5_orf2#LINE/L1 (0) 3294 3080 m_b100s551i14 3680 chr2qtel1M 701718 TGACTTTGAG-ATCTTTTTATGTGACTAGAAATCGTTTCAATTTCTTCTT 701766 ?v - i vi vviii i v? v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr2qtel1M 701767 CTGAAAATTGTCTGTTCATATCCTTTGACCATTTATCAATTGAA--GAAT 701814 i vi v vi i v v ?v ii-- vv C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTT 3195 chr2qtel1M 701815 GGCTCGATTTCTTA-TAAATTAGAGTTCATTCTCTATATATTTGGGAAAT 701863 v i-- ? - i ? iv -vvi i iv v i C L1M5_orf2#LIN 3194 GTCTT--TTTNTTATTGANTTGTAG-GAGTTCTTTATATATTCTGGATAC 3148 chr2qtel1M 701864 GAGTCGTTTATCAGA-ACCTTTAACTATAAAAATGTTTTTCCAGCTTATT 701912 v i - iv v -?i ii v v i i ?ii i v C L1M5_orf2#LIN 3147 GAGTCCTTTGTCAGATATATGT-NTTGCAAATATTTTCTCCCANTCTGTG 3099 chr2qtel1M 701913 GTTTCCCTTCTAATCTTCT 701931 i v i v i C L1M5_orf2#LIN 3098 GCTTGCCTTTTCATTTTCT 3080 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.45 CpG sites = 32, Kimura (unadjusted) = 38.25 Transitions / transversions = 1.14 (32/28) Gap_init rate = 0.04 (8 / 213), avg. gap size = 1.12 (9 / 8) 254 29.65 8.10 3.65 chr2qtel1M 701756 701965 (298035) C L1P3_orf2#LINE/L1 (39) 3255 3037 m_b100s551i15 3680 chr2qtel1M 701756 AATTTCTTCTTCTGAAAATTGTCTGTTCATATCCTTTGACCATTTATCAA 701805 v i i v i v i v ii C L1P3_orf2#LIN 3255 AATGTCTTCTTTTGAGAAGTGTCTGTTCATATCCTTCGCCCACTTTTTGA 3206 chr2qtel1M 701806 TTGAAGAATGGCTCG---ATTTCTTATAAATTAGAGTTCA--TTCTCTAT 701850 ---i ii v i i ---v i --v i -- ii i C L1P3_orf2#LIN 3205 T---GGGGTTGTTTGTTTTTTTCTTGTAAATT--TGTTTAAGTTCCTTGT 3161 chr2qtel1M 701851 ATATTTGGGAAATGAGTCGTTTATCAGAACCTTTAACTATAAAAATGTTT 701900 v iv v v i v i vvvv vi i ii v i C L1P3_orf2#LIN 3160 AGATTCTGGATATTAGCCCTTTGTCAGATGGATAGATTGCAAAAATTTTC 3111 chr2qtel1M 701901 TTCCAGCTTATTGTTTCCCT------TCTAAT-----CTTC-TCTGCATT 701938 i vii i v v v ------ i -----i - i --- C L1P3_orf2#LIN 3110 TCCCATTCTGTAGGTTGCCTGTTCACTCTGATGATAGTTTCTTTTGC--- 3064 chr2qtel1M 701939 TGTACAAAAGCTTTTTAACTTCATTGG 701965 i i i ii v i C L1P3_orf2#LIN 3063 TGTGCAGAAGCTCTTTAGTTTAATTAG 3037 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.33 CpG sites = 37, Kimura (unadjusted) = 39.18 Transitions / transversions = 1.61 (37/23) Gap_init rate = 0.06 (13 / 209), avg. gap size = 1.92 (25 / 13) 1163 28.42 3.05 2.01 chr2qtel1M 702405 702896 (297104) L1ME5_3end#LINE/L1 56 552 (389) m_b100s551i16 3681 chr2qtel1M 702405 CTCCAATTGATAAATGGTCAAAGGATATGAACAGATAATTTTCAGATGAT 702454 i v v v ii v v v L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chr2qtel1M 702455 GAAATTGAAACTATTTCTACTCATATGAAAGAGTATGC-CAAA-TCACTA 702502 iivi vvii vvi vv - - - - i L1ME5_3end#LI 106 GAAACCCGAAAGGCTAACAAGCATATG-AAGAG-ATGCTCAAACTCATTA 153 chr2qtel1M 702503 TTGAGCAGAGAAATGCAAATTAAGACAACTCTCAGATACCACTACACACC 702552 v i v i vv v i vi L1ME5_3end#LI 154 GTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACC 203 chr2qtel1M 702553 TGTCAGATTGGCTAAGATGACAGGAAA---AAATAATGATGAATGTTGAA 702599 i i i v i v --- ---ii vii i iv L1ME5_3end#LI 204 TATTAGACTGGCAAAAATTA---GAAAGCTGGATAATGCCAAGTGTTGGC 250 chr2qtel1M 702600 GGGGATGCAGGGAAAACTGGGACACTGATGCATTGTTGGTGGAGTTGTGA 702649 i i- i ? iv i v v i i iiv ii L1ME5_3end#LI 251 GAGGATGT-GGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAG 299 chr2qtel1M 702650 ACAAATCCAACCATTCTGGAGAGCAATCATGAATTAT---GCCCAA--AA 702694 vii v i vv v v i--- i v -- L1ME5_3end#LI 300 ACTGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTAA 349 chr2qtel1M 702695 CTGT--CCATACCCTTTGATCCAGCAATGTTACTACTGGGCTTATACCCC 702742 v i --v v i viii v iv i L1ME5_3end#LI 350 GTATACGCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATATCCC 399 chr2qtel1M 702743 AAAGAGATACTAAAAGAAG--GGAAAGGGTTCTGAT-TGTGCCAAAAGGT 702789 i v v v v i --viv ---- i- i v ii v L1ME5_3end#LI 400 AAAGAAATTCTCACACAGGTCCATAAGGG----GACATGTACGAGGATGT 445 chr2qtel1M 702790 TTGTGGCAGCCCTGTTTGTAGTGGCTAGAAACTGGAAAATGAATGGATGC 702839 ii v vi i vi i ii iivvivv i i L1ME5_3end#LI 446 TCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGGGTGT 495 chr2qtel1M 702840 CCATCAATTGGAGATTGGTTGGGTAAATTGTGGTATATGAATGTTATGGA 702889 v v v v i v iv v iiii L1ME5_3end#LI 496 CCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACACCATGGA 545 chr2qtel1M 702890 ATATTAT 702896 i i L1ME5_3end#LI 546 GTACTAT 552 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.81 CpG sites = 75, Kimura (unadjusted) = 36.51 Transitions / transversions = 1.21 (75/62) Gap_init rate = 0.04 (18 / 491), avg. gap size = 1.39 (25 / 18) 239 16.07 3.45 3.45 chr2qtel1M 705841 705898 (294102) L1ME3G_3end#LINE/L1 491 548 (376) m_b101s551i2 3682 chr2qtel1M 705841 TCCATCAGTGGGGGAATGGCTGAATAAGTTATGACATAT-AATCCT-TGG 705888 i i i i i ii -v v - L1ME3G_3end#L 491 TCCATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGG 540 chr2qtel1M 705889 AATTTACTAT 705898 -- L1ME3G_3end#L 541 AA--TACTAT 548 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 18.68 CpG sites = 7, Kimura (unadjusted) = 18.68 Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.07 (4 / 57), avg. gap size = 1.00 (4 / 4) 14 28.99 1.52 3.08 chr2qtel1M 706150 706215 (293785) (TTCTTT)n#Simple_repeat 1 65 (0) m_b101s252i0 3683 chr2qtel1M 706150 TTCTTTTTGTTTATTTGCTTACATTTTACTTTCTC-ATTTCTTCTCCTAT 706198 v - ivi v - v i -v i i v (TTCTTT)n#Sim 1 TTCTTTTTCTTT-TTCTTTTTC-TTTTTCTTTTTCTTTTTCTTTTTCTTT 48 chr2qtel1M 706199 TTAATTTGATTTTTCTT 706215 vv vv (TTCTTT)n#Sim 49 TTCTTTTTCTTTTTCTT 65 Matrix = Unknown Transitions / transversions = 0.50 (5/10) Gap_init rate = 0.05 (3 / 65), avg. gap size = 1.00 (3 / 3) 35 21.57 4.40 0.00 chr2qtel1M 706414 706504 (293496) (AT)n#Simple_repeat 1 95 (0) m_b101s252i1 3684 chr2qtel1M 706414 ATA-ATAATTATACATACATACATGCATATATAGACATATATTTATATTT 706462 - vv i i i ii v i v v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr2qtel1M 706463 GTATATA-ATATAT-TTTATATTAATTTATATATATA-ACATATA 706504 i - - v vv v - i (AT)n#Simple_ 51 ATATATATATATATATATATATATATATATATATATATATATATA 95 Matrix = Unknown Transitions / transversions = 0.89 (8/9) Gap_init rate = 0.04 (4 / 90), avg. gap size = 1.00 (4 / 4) 12 15.98 2.56 5.26 chr2qtel1M 706452 706490 (293510) (TATTT)n#Simple_repeat 1 38 (0) m_b101s252i2 3685 chr2qtel1M 706452 TATTTATATTTGTA-TATAATATATTTTATATTAATTTAT 706490 - - - v v v v v (TATTT)n#Simp 1 TATTT-TATTT-TATTTTATTTTATTTTATTTTATTTTAT 38 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.08 (3 / 38), avg. gap size = 1.00 (3 / 3) 35 21.57 4.40 0.00 chr2qtel1M 706414 706504 (293496) (AT)n#Simple_repeat 1 95 (0) m_b101s252i1 3684 chr2qtel1M 706414 ATA-ATAATTATACATACATACATGCATATATAGACATATATTTATATTT 706462 - vv i i i ii v i v v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr2qtel1M 706463 GTATATA-ATATAT-TTTATATTAATTTATATATATA-ACATATA 706504 i - - v vv v - i (AT)n#Simple_ 51 ATATATATATATATATATATATATATATATATATATATATATATA 95 Matrix = Unknown Transitions / transversions = 0.89 (8/9) Gap_init rate = 0.04 (4 / 90), avg. gap size = 1.00 (4 / 4) 734 29.23 7.88 2.82 chr2qtel1M 706606 707214 (292786) C L1ME4c_3end#LINE/L1 (187) 643 5 m_b101s551i3 3686 chr2qtel1M 706606 TGTATTCCTGGTTGCCTTTTTC-CCCAGCATCAT-TCAAGTAAATGGTTT 706653 ----- i - ii i i - -- iiv C L1ME4c_3end#L 643 TGTATTC-----TGCTTTTTTCACTTAACATTATATCA--TAAACATTTT 601 chr2qtel1M 706654 CC--CTTTCTATAACATTTTCATCATTAT----TTTAG-AGC--AATAAT 706694 --v v i vvi i v ---- i-i --v C L1ME4c_3end#L 600 CCATGTTGCTACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAAT 551 chr2qtel1M 706695 AGTCCGTAAGCTTCATGTACCACAACTTGTTCAGCCATTCCCCAGTTGAT 706744 v i viiv ?v i i ii i i vi v C L1ME4c_3end#L 550 ATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTT 501 chr2qtel1M 706745 GATCATCCATTCCTTTTCCACTTCTGTGTTACCACAAAAAGAGCTGCTGC 706794 iv ii vviiv v i vi i ii i v iv vii C L1ME4c_3end#L 500 GGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAAT 451 chr2qtel1M 706795 AAATATCCTTGCACATGTGGGTCCTTGTCCCTTTTTT--ATGATGTCTTT 706842 i i i i ii i i -- i v i i -- v v i C L1ME4c_3end#L 450 GAACATCTTCGTGCATATAG--CTTTTTCCTTCTTTTGAATTATTTCCTT 403 chr2qtel1M 706843 GGGATAAAGACCCTGTAGAGACACTGCTAGATCCAAGGGTATGCACAGTT 706892 i vv v v v iv i i i i v v v C L1ME4c_3end#L 402 AGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTT 353 chr2qtel1M 706893 TGATAGCCTTTTGGACATCGTTCCAAATTACTCTCCACTGGGATCATTTC 706942 v i ii viv i vv v i i vvi i ii vi C L1ME4c_3end#L 352 TTATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACC 303 chr2qtel1M 706943 AAATT------CC-CCAACAATGCATT-GTATCCTACTTTT-CCACATCC 706983 v ------ - i i v- ?i v i v i- i ? C L1ME4c_3end#L 302 AATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCC 253 chr2qtel1M 706984 C--TTAATATT---TATCATTACCTTTTCCTGTGATCTTAGCCAATC--- 707025 i--ii ii --- i i vi iv---i i v i i--- C L1ME4c_3end#L 252 TCGCCAGCATTGGGTATTATCAATTTTTTA---AATTTTTGCTAATTTAA 206 chr2qtel1M 707026 TAGG----AAATGGGTGTACCTCA-GGTTG--TTAATTTGCATTTCTCTT 707068 ---- --- i -v -- i v C L1ME4c_3end#L 205 TAGGCGTAAAATG---GTATCTCATTGTTGCTTTAATTTGCATTTCTTTG 159 chr2qtel1M 707069 ATCAGTAGTGA-TTTAGACATTTT--CATATACCT-CTAACTGCTTTAAT 707114 i v i -v ii -- i iii -i v i? vv C L1ME4c_3end#L 158 ATTACTAGCGAGGTTGAACATTTTTCCATGTGTTTGTTTACTANTTGTAT 109 chr2qtel1M 707115 TTGCTCATCTGGAAATTCTCT-TTCATATTCTTTGACCTTGTATCAAGTA 707163 v v ? vi v - i i v v v --- C L1ME4c_3end#L 108 TTCCTCTTNTGTGAATTGTCTGTTCATGTCCTTTGCCCATTTATC---TA 62 chr2qtel1M 707164 TTAAGAT-TTG----TATTCTTATCAATTTGAA-ACGTTCTTTATATATT 707207 ii i - ---- v -iv i ? C L1ME4c_3end#L 61 TTGGGGTCTTGATNTTTTTCTTATCAATTTGAATGAGCTCTTTATATANT 12 chr2qtel1M 707208 TTAAATA 707214 v? i C L1ME4c_3end#L 11 ANAGATA 5 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.26 CpG sites = 106, Kimura (unadjusted) = 39.00 Transitions / transversions = 1.58 (106/67) Gap_init rate = 0.07 (42 / 608), avg. gap size = 1.57 (66 / 42) 762 27.36 8.38 4.60 chr2qtel1M 706690 707214 (292786) C L1ME3G_3end#LINE/L1 (376) 548 5 m_b101s551i4 3686 chr2qtel1M 706690 ATAATAGTCCGTAAGCTTCATGTACCACAACTTGTTCAGCCATTCCCCAG 706739 i v i ivv vv i i i i i i vi C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr2qtel1M 706740 TTGATGATCATCCATTCCTTTTCCACTTCTGTGTTACCACAAAAAGAGCT 706789 iv ii vviiv v i vi i ii v iv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr2qtel1M 706790 GCTGCAAATATCCTTGCACATGTGGGTCCTTGTCC-CTTTTTTATG-ATG 706837 viii i i i?-- v - v v viiv - v C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATT 401 chr2qtel1M 706838 TCTTTGGGATAAAGACCCTGTAGAGACACTGCTAGATCCAAGGGTATGCA 706887 ? i i v? ?v v v iv i i i v i C L1ME3G_3end#L 400 TCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCG 351 chr2qtel1M 706888 CAGTTTGATAGCCTTT--TGGACATCGTTCCAAATTACTCTCCA------ 706929 v --- ivi -- i i ii -- i i ------ C L1ME3G_3end#L 350 CATTT---TAAATTTTAATAGATACTG--CCAAATTGCCCTCCAAAANGG 306 chr2qtel1M 706930 CTGGGATCATTTCAAATTCC--CCAACAATGCATT---GTATCCTACTTT 706974 - v i v i v i -- i i i v--- - iii i C L1ME3G_3end#L 305 CT-GTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTA-CCCGTTTC 258 chr2qtel1M 706975 TCCACATCC---------CTTAATATTTATCATTACCTTTTCCTGTGATC 707015 i i --------- ?i - -- ? v----i i C L1ME3G_3end#L 257 CCCACACCCTCGCCAACACTNGATA-TTATCA--ANCTTTTA----AATT 215 chr2qtel1M 707016 TTAGCCAATCTAGGAAATGGGT--------GTACCTCA-GGTTG--TTAA 707054 v ----i -------- i -v -- C L1ME3G_3end#L 214 TTTGCCAATCT----GATGGGTGAAAAATGGTATCTCATTGTTGTTTTAA 169 chr2qtel1M 707055 TTTGCATTTCTCTTATCAGTAGTGA--TTTAG-ACATTTTCATATACCT- 707100 i v i v -- v - iv iii - C L1ME3G_3end#L 168 TTTGCATTTCCCTGATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTA 119 chr2qtel1M 707101 CTAACTGCTTTAATTTGCTCATCTGGAAATTCTCT-TTCATATTCTTTGA 707149 i ii iii vv v v vi vi - i v C L1ME3G_3end#L 118 TTGGCCATTTGTATTTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGC 69 chr2qtel1M 707150 CCTTGTATCAAGTATTAAGATTTGTA---TTCTTATCAATTTG-AAACGT 707195 v v v --- ii -- v--- ii - iiv C L1ME3G_3end#L 68 CCATTTTTC---TATTGGG--TTGTCTTTTTCTTATTGATTTGTAGGAGT 24 chr2qtel1M 707196 TCTTTATATATTTTAAATA 707214 i ii C L1ME3G_3end#L 23 TCTTTATATATTCTGGATA 5 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.37 CpG sites = 85, Kimura (unadjusted) = 35.75 Transitions / transversions = 1.63 (85/52) Gap_init rate = 0.08 (41 / 524), avg. gap size = 1.68 (69 / 41) 13 22.18 5.33 5.33 chr2qtel1M 707707 707781 (292219) (TTTGTTCT)n#Simple_repeat 1 75 (0) m_b101s252i3 3687 chr2qtel1M 707707 TTTG-TATTTTGTTGTTTTAATCCTTGATATTC-TTTGACCTTTTGTTCT 707754 - v v -i i -v i - vi (TTTGTTCT)n#S 1 TTTGTTCTTTTGTTCTTTT-GTTCTT-TTGTTCTTTTGTTCTTTTGTTCT 48 chr2qtel1M 707755 TCTAGATGCTTTT-TTGGTTT-TTCTCTT 707781 - v - v - vv - i (TTTGTTCT)n#S 49 T-TTG-TTCTTTTGTTCTTTTGTTCTTTT 75 Matrix = Unknown Transitions / transversions = 0.62 (5/8) Gap_init rate = 0.11 (8 / 74), avg. gap size = 1.00 (8 / 8) 902 30.57 7.68 1.50 chr2qtel1M 707879 708881 (291119) C L1M4_orf2#LINE/L1 (899) 2395 1332 m_b101s551i5 3686 chr2qtel1M 707879 ATTTTTTTAGATCTGATTTTCTTTGTGTGAGAAGTGTTTTATAATT---- 707924 v i vv vv v v v iv i i i ---- C L1M4_orf2#LIN 2395 ATTTATTTAGGTCTTCTTTAATTTCTTTCAACAATGTTTTGTAGTTTTCA 2346 chr2qtel1M 707925 GTGTTCA--TATTGTATTTGGTTGTCTTAGCAGCTTGCTCCCCAGTTATT 707972 v -- v i i vv - v -- ii ii iv - C L1M4_orf2#LIN 2345 GTGTACAAGTCTTGCACTTCTTT-TGTTA--AATTTATTCCTAAGT-ATT 2300 chr2qtel1M 707973 TTATTTTGTCTATAGATAGTTTCAATGGAATT--TCTCTTTGTATCTCTT 708020 i v i ivv v v v v -- i vi v vi C L1M4_orf2#LIN 2299 TTATTCTTTTTGATGCTATTGTAAATGGAATTGTTTTCTTAATTTCATTT 2250 chr2qtel1M 708021 GCTTATGGGCTTTATCAGTTATATAGAGCAATGCTGATGATTTGTGTGAC 708070 v vv v -- i iiv vi i v v i viv v ivv C L1M4_orf2#LIN 2249 TCGGATTG--TTCATTGCTAGTGTATAGAAATACAATTGATTTTTGTATA 2202 chr2qtel1M 708071 TTCATTTTATATACTGCAATTTTGCTAAAGCTGTGAATTGTTTTCAGTAG 708120 v i i v ii i vii vv iv ii i C L1M4_orf2#LIN 2201 TTGATCTTGTATCCTGCAACCTTGCTGAACTCGTTTATTAGTTCTAATAG 2152 chr2qtel1M 708121 ATATTTTGATGGTTTTCT-AGGATTCTCAAAGTAACTCATCATATCATCT 708169 v - ?i v i - i v vi vvvv i C L1M4_orf2#LIN 2151 TT-TTTTNGTGGATTCCTTAGGATTTTCTATATACAAGATCATGTCATCT 2103 chr2qtel1M 708170 CCAAAGAGTGATAGATTTATTTCTTCATTGCCTATTCTATTTCCTTTTGA 708219 v i v v v i v v v iiviv v iv C L1M4_orf2#LIN 2102 GCGAATAGAGATAGTTTTACTTCTTCCTTTCCAATCTGGATGCCTTTTAT 2053 chr2qtel1M 708220 TTCTTTTTCTTTTCATATCAATGAAGCTGACATTTCTAGAACAACATTGA 708269 vi vv iivivvi iiv ii i v ii C L1M4_orf2#LIN 2052 TTCTTTTTCTTGCCTAATTGCCCTGGCTAGAACCTCCAGTACAATGTTGA 2003 chr2qtel1M 708270 ATAATAGTGGTGAAA--------------TTTAACCCTGATTTTACTGGG 708305 iv i i --------------i ivi i vv C L1M4_orf2#LIN 2002 ATAGAAGTGGCGAGAGCGGACATCCTTGTCTTGTTCCTGATCTTAGGGGG 1953 chr2qtel1M 708306 AATGCATCCAGCTTCTCTTCATTTCATATAATCTT-TCTATAAGGTTTTA 708354 v ? i ii i vi vvi i v -v i -i v C L1M4_orf2#LIN 1952 AAAGCNTTCAGTCTTTCACCATTAAGTATGATGTTAGCTGT-GGGTTTTT 1904 chr2qtel1M 708355 AGAAGTATTGCTTTTTTTAAG----GAAAGTTCCCTT-TATCCATA---T 708396 v v - vv i v i i ---- i - i v --- C L1M4_orf2#LIN 1903 CGTAG-ATGCCCTTTATCAGGTTGAGGAAGTTCCCTTCTATTCCTAGTTT 1855 chr2qtel1M 708397 GGCCTTTAGTTTTATTA--ATAAATGGGTACTTTATTTT-TCAAA-GCTT 708442 --- v v v -- i v ii vv - - C L1M4_orf2#LIN 1854 G---TTGAGTGTTTTTATCATGAAAGGGTGTTGGATTTTGTCAAATGCTT 1808 chr2qtel1M 708443 TTTC----TCTTTTTGGATTGTAATATA--TTCTTTCGTT--TTCTATTG 708484 ---- v vi vi v i i-- i v v -- i C L1M4_orf2#LIN 1807 TTTCTGCGTCTATTGAGATGATCATGTGGTTTTTGTCCTTTATTCTATTA 1758 chr2qtel1M 708485 ATGTGGTCCACTG----GAGTAATTTTCG-ATAACAAACCAAACCC-CAT 708528 i vi i i---- v i - ivii v ii- C L1M4_orf2#LIN 1757 ATATGGTGTATTACATTGATTGATTTTCGNATGTTGAACCAACCTTGCAT 1708 chr2qtel1M 708529 TACTGGTTTTAAATCCCCAAATGGTTGT-TTAAATTATCCTGCTTA-A-G 708575 v -vv - vv ii -v iv v vi - - C L1M4_orf2#LIN 1707 TCCTGG-GATAAAT-CCCACTTGGTCATGGTGTATAATCCTTTTTATATG 1660 chr2qtel1M 708576 TTGCT-AATCT--TTTGCTAATATTTATTTAA--ATTTGTGCATCAGTAT 708620 -i ii-- i vv i -- v vi C L1M4_orf2#LIN 1659 TTGCTGGATTCGGTTTGCTAGTATTTTGTTGAGGATTTTTGCATCTATAT 1610 chr2qtel1M 708621 TCA-ACAGGATATTGGTCTGTAATTTTTCTCTGTTTTAGC-CCTTCGT-- 708666 - vi i ii i v v iii-i i -- C L1M4_orf2#LIN 1609 TCATAAGGGATATTGGTCTGTAGTTTTCTTTTCTTGTGATGTCTTTGTCT 1560 chr2qtel1M 708667 -GTTTC--TAGCAGTCCATAACTGGGTTTTACAGGA--AAT---GTAGTA 708708 - i-- v vvi vv - ii i i i -- i --- v i C L1M4_orf2#LIN 1559 GGTTTTGGTATCAGGGTAATACT-GGCCTCATAGAATGAGTTGGGAAGTG 1511 chr2qtel1M 708709 TTCCTTCACCTATT-TTTTTCCAAATAGTTGACGTAGTATTGGAAGTAAT 708757 i vi vi - ivi v vii v v viv C L1M4_orf2#LIN 1510 TTCCCTCCTCTTCTATTTTTTGGAAGAGTTTGTGAAGGATTGGTGTTAAT 1461 chr2qtel1M 708758 TGTTCTTTAAATGTTTGGGAGAATTCACTGGTGGATCCAACTGGCCCTGG 708807 v v ii i v v ? C L1M4_orf2#LIN 1460 TCTTCTTTAAATGTTTGGTAGAATTCACCAGTGAAGCCATCTGGNCCTGG 1411 chr2qtel1M 708808 AGATTTTCT---TAGAGAATTCATTAATGACTTATTCAATTTCTGTTTCT 708854 - v --- i ii i iv i v v i v vii C L1M4_orf2#LIN 1410 -GCTTTTCTTTGTGGGAAGTTTTTTGATTACTAATTCAATCTCTTTACTT 1362 chr2qtel1M 708855 GAAATAGAACTATTT---TATTTTATTTTT 708881 vv iv i--- v i i C L1M4_orf2#LIN 1361 GTTATAGGTCTATTCAGATTTTCTATTTCT 1332 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.37 CpG sites = 153, Kimura (unadjusted) = 40.05 Transitions / transversions = 1.03 (153/149) Gap_init rate = 0.05 (50 / 1002), avg. gap size = 1.86 (93 / 50) 1070 27.86 8.43 1.56 chr2qtel1M 708040 708881 (291119) C L1M5_orf2#LINE/L1 (1064) 2230 1332 m_b101s551i6 3686 chr2qtel1M 708040 TATATAGAGCAATGCTGATGATTTGTGTGACTTCATTTTATATACTGCAA 708089 -- i viv v ivv v ii i v ? i C L1M5_orf2#LIN 2230 TATATAGA--AATACAATTGATTTTTGTATATTGACCTTGTATCCNGCGA 2183 chr2qtel1M 708090 TTTTGCTAAAGCTGTGAATTGTTTTCAGTAGATATTTTGATGGTTTTCTA 708139 ii viiiivv iv ii v v? vv i i i ? C L1M5_orf2#LIN 2182 CCTTGCTAAATTCACTTATTAGTTCTAGTAGTTTNTTTGTAGATTCTTTN 2133 chr2qtel1M 708140 GGATTCTCAAAGTAACTCATCATATCATCTCCAAAGAGTGATAGATTTAT 708189 i v v ?viv i v i v i? i v C L1M5_orf2#LIN 2132 GGATTTTCTACGTANACAATCATGTCATCTGCGAATAANGACAGTTTTAT 2083 chr2qtel1M 708190 TTCTTCATTGCCTATTCTATTTCCTTTTGATTCTTTTTCTTTTCATAT-- 708237 v v v ii vv v iv vi v -- C L1M5_orf2#LIN 2082 TTCTTCCTTTCCAATCTTTATGCCTTTTATTTCTTTTTCTTGCCTTATTG 2033 chr2qtel1M 708238 CAATGAAGCTGACATTTCTAGAACAACATTGAATAATAGTGGTGAAATTT 708287 v -- iiv ii i v ii iv ? viv C L1M5_orf2#LIN 2032 CACTG--GCTAGGACCTCCAGTACAATGTTGAATAGAAGTGGTGANAGCG 1985 chr2qtel1M 708288 AAC--------------CCTGATTTTACTGGGAATGCATCCAGCTTCTCT 708323 i -------------- i i vv v ? i i? i v C L1M5_orf2#LIN 1984 GACATCCTTGTCTTGTTCCCGATCTTAGGGGGAAAGCNTTCAGTNTTTCA 1935 chr2qtel1M 708324 TCATTTCATATAATCTTT-CTATAAGGTTTTAAGAAGTATTGCTTTTTTT 708372 i vvi i v ?- i - vv v - vv i v i C L1M5_orf2#LIN 1934 CCATTAAGTATGATGTTNGCTGTA-GGTTTTTCGTAG-ATGCCCTTTATC 1887 chr2qtel1M 708373 AAG----GAAAGTTCCCTT-TATCCATA--TGGCCTTTAGTTTTATTAAT 708415 i ---- i - i v -- v ivvv vv v C L1M5_orf2#LIN 1886 AGGTTGAGGAAGTTCCCTTCTATTCCTAGTTTGCTGAGAGTTTTTATCAT 1837 chr2qtel1M 708416 AAATGGGTACTTTATTTT-TCAAA-GCTTTTTCT----CTTTTTGGATTG 708459 i ii vv - - ---- v vi vi C L1M5_orf2#LIN 1836 GAATGGGTGTTGAATTTTGTCAAATGCTTTTTCTGCATCTATTGAGATGA 1787 chr2qtel1M 708460 TAATATA--TTCTTTCGTTT--TCTATTGATGTGGTCCACTG----GAGT 708501 v i-- i i v -- i i i vv i i---- v C L1M5_orf2#LIN 1786 TCATATGATTTTTCTCCTTTATTCTGTTAATATGGTGAATTACATTGATT 1737 chr2qtel1M 708502 AATTTTCGA-TAACAAACCAAACCC-CATTACTGGTTTTAAATCCCCAAA 708549 i - ivi v ii- v vv - - vv C L1M5_orf2#LIN 1736 GATTTTCGAATGTTAAACCAACCTTGCATTCCTGGGAT-AAA-CCCCACT 1689 chr2qtel1M 708550 TGGTTGTT-TAAATTATCCTGCTTA-A-GTTGCTA-ATCT--TTTGCTAA 708593 ii v- iv vi - -i i- ii-- C L1M5_orf2#LIN 1688 TGGTCATGATGTATTATCCTTTTTATATATTGCTGGATTCGATTTGCTAA 1639 chr2qtel1M 708594 TATTTATTTAA--ATTTGTGCATCAGTATTCAACAGG-ATATTGGTCTGT 708640 vv ? -- v vi i vv - C L1M5_orf2#LIN 1638 TATTTTGTTNAGGATTTTTGCATCTATGTTCATGAGGGATATTGGTCTGT 1589 chr2qtel1M 708641 AATTTTTCTCTGTTTTA--GCCCT--TCGTGTTTC--TAGCA-GTCCATA 708683 ii i v v -- i i -- ?v i-- v - vi? - C L1M5_orf2#LIN 1588 AATTTTCTTTTCTTGTAATGTCTTTGTCNGGTTTTGGTATCAGGGTNAT- 1540 chr2qtel1M 708684 ACTGGGTTTTACAGGAAAT--GT-----AGTATTCCTTCACCTATTTTTT 708726 i vi --- vi -- ----- i i vii vi v C L1M5_orf2#LIN 1539 GCTGGCCT---CATAAAATGAGTTGGGAAGTGTTCCCTCTTTTTCTATTT 1493 chr2qtel1M 708727 TCC-AAATAGTTGACGTAGTATTGGAAGTAATTGTTCTTTAAATGTTTGG 708775 i-i v vii iv v v v v i C L1M5_orf2#LIN 1492 TCTGGAAGAGTTTGTGTAAGATTGGTATTATTTCTTCCTTAAATGTTTGG 1443 chr2qtel1M 708776 GAGAATTCACTGGTGGATCCAACTGGCCCTGGAGATTTTCTT----AGAG 708821 v ii i v v v - ----i i C L1M5_orf2#LIN 1442 TAGAATTCACCAGTGAAGCCATCTGGGCCTGGAG-TTTTCTTTGTGGGAA 1394 chr2qtel1M 708822 AATTCATTAATGACTTATTCAATTTCTGTTTCTGAAATAGAACTATTT-- 708869 ii i- v vv v vviv v ii i-- C L1M5_orf2#LIN 1393 GGTTT-TTAATTACAAATTCAATTTCTTTAATAGATATAGGGCTATTCAG 1345 chr2qtel1M 708870 -TATTTTATTTTT 708881 - v i i C L1M5_orf2#LIN 1344 ATTTTCTATTTCT 1332 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.04 CpG sites = 117, Kimura (unadjusted) = 35.99 Transitions / transversions = 1.03 (117/114) Gap_init rate = 0.05 (45 / 841), avg. gap size = 1.89 (85 / 45) 18 6.77 0.00 6.06 chr2qtel1M 708883 708917 (291083) (TATT)n#Simple_repeat 1 33 (0) m_b101s252i4 3688 chr2qtel1M 708883 TATTTATTTATATATATTATATATTATATTTATTT 708917 v - v - (TATT)n#Simpl 1 TATTTATTTATTTAT-TTATTTATT-TATTTATTT 33 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 237 32.01 2.69 2.69 chr2qtel1M 708919 709178 (290822) C L1M1_orf2#LINE/L1 (1957) 1337 1078 m_b101s551i7 3689 chr2qtel1M 708919 ATTTCCTCTAATGGT--AACCTGGGAAATTTGATTTTTTGTAAACATTCT 708966 i -- -- i v v iv vv v v v iiv iv C L1M1_orf2#LIN 1337 ATTTCTTC--ATGGTTCAATCTTGGTAGGTTGTATGTGTCTAGGAATTTG 1290 chr2qtel1M 708967 TCCATTTCAGTTAGATTGTCAGACTTGCTGCCATATTGTTGGGGAAAAAA 709016 vvi v vi i ii v v vvv v iv C L1M1_orf2#LIN 1289 TCCATTTCTTCTAGATTTTCCAATTTATTGGCATATAGTTGCTCATAGTA 1240 chr2qtel1M 709017 GCTGCTAATTATTGCTTTAATTTCTTTTTCCTTGGTGGTGAATTCACCCC 709066 ii v ivi v vivviv ii v i vv v ii C L1M1_orf2#LIN 1239 GCCACTAATGATCCTTTGAATTTCTGCGGTATCAGTTGTAATGTCTCCTT 1190 chr2qtel1M 709067 TTTCATTTTTGATGTTGTTGATTTAGTTTTTTTTTCCTTTTCTTTTTCTC 709116 i i v i v i v i i i i i i ?? i C L1M1_orf2#LIN 1189 TTTCATCTCTGATTTTATTTATTTGGGTCTTCTCTCTTTTTTTCTTNNTT 1140 chr2qtel1M 709117 A-TC--GTCAAATGTAGGCAAAGATTTATTTG--TTTTCATAAAACCAAC 709161 - -- ii v vv iv v- i i-- v C L1M1_orf2#LIN 1139 AGTCTGGCTAAAGGTTTGTCAAT-TTTGTTTANCTTTTCAAAAAACCAAC 1091 chr2qtel1M 709162 TCTTGTTTTTTTTCATT 709178 ---- v C L1M1_orf2#LIN 1090 T----TTTTGTTTCATT 1078 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 42.02 CpG sites = 39, Kimura (unadjusted) = 42.70 Transitions / transversions = 0.93 (39/42) Gap_init rate = 0.04 (11 / 259), avg. gap size = 1.27 (14 / 11) 588 29.59 3.91 1.39 chr2qtel1M 710239 710519 (289481) L1ME3G_3end#LINE/L1 26 313 (611) m_b101s551i8 3690 chr2qtel1M 710239 TCCT-CAAATTTATAAGAATGAAAGCCATTTTCCAGTTAATAAATGGTCA 710287 - iv -- v vi-- i vi v v L1ME3G_3end#L 26 TCCTACAAATCAATAAGAA--AAAGACAAC--CCAATAGAAAAATGGGCA 71 chr2qtel1M 710288 AAGGATTTGAACA--CAATTTTCAGATGAAAAAATAATAATCATTTCTAG 710335 v -- iv v ii vv viiivv i L1ME3G_3end#L 72 AAGGATATGAACAGGCAATTCACAGAAGAGGAAATACAAATGGCCAATAA 121 chr2qtel1M 710336 TCCTATGAAAAAATGCTCTAAGTCACTATTGGTCAGAGAAACGTAAATTA 710385 v v i v vv v ii i i i L1ME3G_3end#L 122 ACATATGAAAAGATGCTCAACCTCACTAGTAATCAGGGAAATGCAAATTA 171 chr2qtel1M 710386 AAATGAAGCTGAGGTACCAGATATT-----TCAGATTGGCTAAGATGACA 710430 ii viv i vv v i----- v i vvv L1ME3G_3end#L 172 AAACAACAATGAGATACCATTTTTCACCCATCAGATTGGCAAAAATTTAA 221 chr2qtel1M 710431 AGGAAAGATAATAT---ATCTTGAAGAGAATGGGGAAAAACTGGGACACT 710477 i ?vv ---i v iv ii v ii v v v L1ME3G_3end#L 222 AAGNTTGATAATATCNAGTGTTGGCGAGGGTGTGGGGAAACGGGTACTCT 271 chr2qtel1M 710478 AATACATCCTTGGTGGAGTTGTGAATTGATCTATTCTTTCTG 710519 v iivi iiv i i vi vi ? i L1ME3G_3end#L 272 CATACACTGCTGGTGGGAGTGTAAATTGGTACAGCCNTTTTG 313 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.43 CpG sites = 40, Kimura (unadjusted) = 38.43 Transitions / transversions = 0.95 (40/42) Gap_init rate = 0.03 (8 / 280), avg. gap size = 1.88 (15 / 8) 16 32.90 0.00 0.00 chr2qtel1M 711811 711863 (288137) (AA)n#Simple_repeat 1 53 (0) m_b101s252i5 3691 chr2qtel1M 711811 AAAAAAATTTTAAAAAAAAAAAGAAAAAATAAGAACCAGGAAGAGGAAAA 711860 vvvv i v i vv ii i ii (AA)n#Simple_ 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr2qtel1M 711861 AAA 711863 (AA)n#Simple_ 51 AAA 53 Matrix = Unknown Transitions / transversions = 1.00 (7/7) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 419 27.17 0.00 2.65 chr2qtel1M 715650 715804 (284196) L1ME3G_3end#LINE/L1 22 172 (752) m_b101s551i9 3692 chr2qtel1M 715650 GAACTGCCTCAGATTTATAAGAATGCAAGCCATTCACCAATTGATAAATA 715699 v iv i iv --v v vi -- v v i L1ME3G_3end#L 22 GAACTCCTACAAATCAATAAGAA--AAAGACAACC--CAATAGAAAAATG 67 chr2qtel1M 715700 GTCAAAGGATTTAAACAGACAATTTTCAGATGAAAAAACAAAAATCATTT 715749 v v i i iv v ii i v viiiv L1ME3G_3end#L 68 GGCAAAGGATATGAACAGGCAATTCACAGAAGAGGAAATACAAATGGCCA 117 chr2qtel1M 715750 CTAGTTATATGAAAAAATGCTCTAAATCACTATTGGTCAGAGAAATGCAA 715799 v ivi i v vv v ii i L1ME3G_3end#L 118 ATAAACATATGAAAAGATGCTCAACCTCACTAGTAATCAGGGAAATGCAA 167 chr2qtel1M 715800 ATTAA 715804 L1ME3G_3end#L 168 ATTAA 172 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.02 CpG sites = 20, Kimura (unadjusted) = 34.02 Transitions / transversions = 0.95 (20/21) Gap_init rate = 0.03 (4 / 154), avg. gap size = 1.00 (4 / 4) 422 25.21 0.00 0.00 chr2qtel1M 715686 715804 (284196) L1MA8_3end#LINE/L1 58 176 (862) m_b101s551i10 3692 chr2qtel1M 715686 CCAATTGATAAATAGTCAAAGGATTTAAACAGACAATTTTCAGATGAAAA 715735 i ? v i v ii i i v i i v i L1MA8_3end#LI 58 CCGATTNAAAAATGGGCAAAGGACCTGAATAGACATTTCTCAAAAGAAGA 107 chr2qtel1M 715736 AACAAAAATCATTTCTAGTTATATGAAAAAATGCTCTAAATCACTATTGG 715785 v i v viiivvi v v v v vi L1MA8_3end#LI 108 CATACAAATGGCCAACAGGTATATGAAAAAATGCTCAACATCACTAATCA 157 chr2qtel1M 715786 TCAGAGAAATGCAAATTAA 715804 i L1MA8_3end#LI 158 TCAGGGAAATGCAAATTAA 176 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 30.24 CpG sites = 16, Kimura (unadjusted) = 31.47 Transitions / transversions = 1.14 (16/14) Gap_init rate = 0.00 (0 / 118), avg. gap size = 0.0 (0 / 0) 485 31.33 1.60 2.70 chr2qtel1M 715860 716046 (283954) L1ME4c_3end#LINE/L1 277 461 (369) m_b101s551i11 3693 chr2qtel1M 715860 ATACATTGTTGATGGAGTCGTGAATTGATCCAGTCATTGTGGAAAGCAAT 715909 i i vi?i i i v ii v v L1ME4c_3end#L 277 ATACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGCAAT 326 chr2qtel1M 715910 ATGGAAGTATGCCTAAAGGGCTATCACAATGTACATAACTTTTGATCCAG 715959 v v i i iv v i i v v v v i i L1ME4c_3end#L 327 TTGGCAATACGTATCAAGAGCCATAAAAATGTTCATACCCTTTGACCCAG 376 chr2qtel1M 715960 CAGTGTCTCTATTGAACCTATATCTCAAAGAGATGAT---AAAGAAGGGG 716006 i i vi v vi iivv v ii i i i --- ii L1ME4c_3end#L 377 TAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAAGAAGGAA 426 chr2qtel1M 716007 AAAGGCCTTCCCCATGTGCAAAAATGTTTATAACAGCTTT 716046 ----- ivi ii i i i vi v L1ME4c_3end#L 427 AAAG-----CTATATGCACGAAGATGTTCATTGCAGCGTT 461 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.65 CpG sites = 36, Kimura (unadjusted) = 42.66 Transitions / transversions = 1.71 (36/21) Gap_init rate = 0.03 (6 / 186), avg. gap size = 1.33 (8 / 6) 17 25.05 3.17 1.56 chr2qtel1M 716429 716491 (283509) (TGTT)n#Simple_repeat 1 64 (0) m_b101s252i6 3694 chr2qtel1M 716429 TGTTTGTGTGTGTGTGTGTGTGTGTGTTGGTGTTATTTTACTATTT-TTT 716477 v v v v v v - i vvi i - (TGTT)n#Simpl 1 TGTTTGTTTGTTTGTTTGTTTGTTTGTTTGT-TTGTTTGTTTGTTTGTTT 49 chr2qtel1M 716478 -TTTGGTTGTTTTTT 716491 - v v (TGTT)n#Simpl 50 GTTTGTTTGTTTGTT 64 Matrix = Unknown Transitions / transversions = 0.30 (3/10) Gap_init rate = 0.05 (3 / 62), avg. gap size = 1.00 (3 / 3) 15 4.16 0.00 7.41 chr2qtel1M 720792 720820 (279180) (TTCT)n#Simple_repeat 1 27 (0) m_b101s252i7 3695 chr2qtel1M 720792 TTCTTTCTTTCTTTTTTTTCTTTTCTTTC 720820 - i - (TTCT)n#Simpl 1 TTCTTTCTTTC-TTTCTTTC-TTTCTTTC 27 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.07 (2 / 28), avg. gap size = 1.00 (2 / 2) 23 6.99 0.00 0.00 chr2qtel1M 721997 722026 (277974) (T)n#Simple_repeat 1 30 (0) m_b101s252i8 3696 chr2qtel1M 721997 TTTTTTTCTTTTTTTTTTTTTTTTTATTTT 722026 i v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 30 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 328 27.27 7.98 0.50 chr2qtel1M 722543 722728 (277272) C L1ME3G_3end#LINE/L1 (376) 548 349 m_b101s551i12 3697 chr2qtel1M 722543 ATAATATTCCCTAATATTCATAT-CCA-AATTTATTCAGCCATTCTCA-A 722589 i v i vv - - i i i v- C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr2qtel1M 722590 TTGATGGGCATCC--CTCGTTT-CAGTTT----CTAATAC---CGG-ACT 722628 i ii--v i - i ---- v --- ii-i C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr2qtel1M 722629 GCCACAAACATTCATGCACATACAGGCCGCTTTCCCTTCTTTATG-ATCT 722677 v ii i v i i -?v viv v v v v viiv - i C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACATGC-NTCCTTGTGCACATGTGCGAGTATTT 400 chr2qtel1M 722678 CTTTGGGGTATAAGCCCAATAGTAACACTGCTGGATCAAAGGGTATGCAC 722727 ? i i v v? ? iv iiv i i i C L1ME3G_3end#L 399 CTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGC 350 chr2qtel1M 722728 A 722728 C L1ME3G_3end#L 349 A 349 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.16 CpG sites = 30, Kimura (unadjusted) = 36.00 Transitions / transversions = 1.43 (30/21) Gap_init rate = 0.05 (10 / 185), avg. gap size = 1.60 (16 / 10) 33 5.20 0.00 0.00 chr2qtel1M 722729 722768 (277232) (GTTT)n#Simple_repeat 1 40 (0) c_b101s251i0 3698 chr2qtel1M 722729 GTTTGTTTGTTTTTTTTTTTGTTTGTTTGTTTGTTTGTTT 722768 v v (GTTT)n#Simpl 1 GTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTT 40 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 367 26.68 7.82 1.58 chr2qtel1M 723273 723451 (276549) C L1ME4c_3end#LINE/L1 (276) 554 365 m_b101s551i14 3699 chr2qtel1M 723273 TAATATTCCAT--AATTTTCTTACCACAATTTATTCAGCCATTCTCA-AC 723319 -- i ?vviv i i i i i v- i C L1ME4c_3end#L 554 TAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTAT 505 chr2qtel1M 723320 TGATGGACATCCATTCAGTTTCCG--TTCTAACCACTACAAA--GGGCTG 723365 v ii vviv i-- i vi i i i --iv C L1ME4c_3end#L 504 TGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCTG 455 chr2qtel1M 723366 CCACAAACAT--TCGTGCACATAAATCCCTTTCCCTTCTTT---ATAATC 723410 v ii -- i i--- i i --- v i C L1ME4c_3end#L 454 CAATGAACATCTTCGTGCATATAG---CTTTTTCCTTCTTTTGAATTATT 408 chr2qtel1M 723411 TCTTTGGGATATAATCCCAGTAGTAACACT--TGGATCAAAGG 723451 i i v v v iiv i -- i C L1ME4c_3end#L 407 TCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGG 365 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.63 CpG sites = 31, Kimura (unadjusted) = 34.55 Transitions / transversions = 1.94 (31/16) Gap_init rate = 0.06 (10 / 178), avg. gap size = 1.70 (17 / 10) 554 29.74 15.33 0.21 chr2qtel1M 723292 723702 (276298) C L1ME3C_3end#LINE/L1 (343) 527 55 m_b101s551i15 3699 chr2qtel1M 723292 TACCACAATTTATTCAGCCATTCTCA-ACTGATGGACATCCATTCAGTTT 723340 i v v-ii ii vviv C L1ME3C_3end#L 527 TACCACAATTTATTTATCCATTCTCCTGTTGATGGACATTTAGGTTGTTT 478 chr2qtel1M 723341 CCG--TTCTAACCACTACAAAGG--GCTGCCACAAACATTCGTGCACATA 723386 i-- i vi i i vi-- v ii v i i C L1ME3C_3end#L 477 CCAATTTTTCGCTATTACAAACAATGCTGCAATGAACATTCTTGTACATG 428 chr2qtel1M 723387 AATCCCTTTCCCTTCTT--TATAATCTCTTTGGGATATAATCCCAGTAGT 723434 vv i v v viv v --v v i i i i i vv i v C L1ME3C_3end#L 427 TCTCCTTGTGCACACGTGCGAGAGTTTCTCTAGGGTATATACCTAGGAGT 378 chr2qtel1M 723435 AACACT--TGGATCA-AAGGTAT-CACGTTTGATAACTTTTTTGGGCAAT 723480 iiv i -- i i- i - i i i v-i vi i ii v C L1ME3C_3end#L 377 GGAATTGCTGGGTCGTAGGGTATGCGCATCTT-CAACTTTACTAGATATT 329 chr2qtel1M 723481 TCCAAACT--TCTCAGAA-------TATAAATTCACAATTCT-CCAATTA 723520 v i -- vi ------- iv i v i i- iivi C L1ME3C_3end#L 328 GCCAAATTGCTCTCCAAAGTGGTTGTACCAATTTACACTCCCACCAGCAG 279 chr2qtel1M 723521 TGTAT--CAGTTCCCTTTACCTT---TCCT------------------TC 723547 --v v i iii--- ------------------ C L1ME3C_3end#L 278 TGTATGAGAGTTCCCGTTGCTCCACATCCTCGCCAACACTTGGTATTGTC 229 chr2qtel1M 723548 A---TTCTAGAT----------CTGATAAATGTG---TGGTATCTCAGAG 723581 --- i i ---------- iii --- vv C L1ME3C_3end#L 228 AGACTTTTAAATTTTTGCCAATCTGATGGGTGTGAAATGGTATCTCATTG 179 chr2qtel1M 723582 TTGTCTTAACTTGTATTTCTCTGATTAATAATGACTTGGAGCATCTTTTC 723631 ? i i i i v i vv v C L1ME3C_3end#L 178 TNGTTTTAATTTGCATTTCCCTGATTACTAGTGAGGTTGAGCATCTTTTC 129 chr2qtel1M 723632 ATATGGCTAGAAATAGTTTCAATTTCTTCATCTGAGAATTATCTG---GT 723678 vi vviiivi iv?i i v v ii ---i C L1ME3C_3end#L 128 ATATGTTTATTGGCCATTCGNGTTTCCTCTTCTGTGAATTGCCTGTTCAT 79 chr2qtel1M 723679 ATTCTTTGACCATTTATCAATTGG 723702 ii v v v C L1ME3C_3end#L 78 ATCTTTTGCCCATTTTTCTATTGG 55 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.77 CpG sites = 74, Kimura (unadjusted) = 39.44 Transitions / transversions = 1.54 (74/48) Gap_init rate = 0.04 (18 / 410), avg. gap size = 3.56 (64 / 18) 294 15.26 1.64 3.33 chr2qtel1M 723749 723809 (276191) C HERV35I#LTR/ERV1 (28) 6890 6831 m_b101s701i0 3700 chr2qtel1M 723749 ATTCTTTTGGA-AAAGGGTCAGAGATCTCAGATCTTCTGTAGCTACTTCC 723797 vv - i ii -- v C HERV35I#LTR/E 6890 ATTCTTAAGGAGAAAGGGCCGAAGATCTCA--TCTTCTGAAGCTACTTCC 6843 chr2qtel1M 723798 TGCTGGAAATGG 723809 i v v C HERV35I#LTR/E 6842 TGCTGAACAGGG 6831 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 15.17 CpG sites = 4, Kimura (unadjusted) = 17.09 Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.05 (3 / 60), avg. gap size = 1.00 (3 / 3) 69 0.00 0.00 0.00 chr2qtel1M 724525 724583 (275417) (TA)n#Simple_repeat 1 59 (0) c_b101s251i1 3701 chr2qtel1M 724525 TATATATATATATATATATATATATATATATATATATATATATATATATA 724574 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr2qtel1M 724575 TATATATAT 724583 (TA)n#Simple_ 51 TATATATAT 59 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.0 (0 / 0) 40 0.00 0.00 0.00 chr2qtel1M 724868 724901 (275099) (AT)n#Simple_repeat 1 34 (0) c_b101s251i2 3702 chr2qtel1M 724868 ATATATATATATATATATATATATATATATATAT 724901 (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATAT 34 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 952 30.35 6.68 2.71 chr2qtel1M 725158 725726 (274274) C L1ME5_3end#LINE/L1 (295) 646 56 m_b101s551i16 3703 chr2qtel1M 725158 CGTTCTTGTTCT-GCTCATTTCACTCAGCATCA-GTTTATATACGTCTCT 725205 i vv -i iv ii - v - vi iv C L1ME5_3end#LI 646 CATTCTGTTTCTTACTTTTTTCACTCAGCACTATGTTTTTA-AGATCCAT 598 chr2qtel1M 725206 CCAGGCCTCTATG---AAATCAAACTGTTGGCCGTTTCT---TACAGAAT 725249 v iiv --- v v --- iv ii i --- i v v C L1ME5_3end#LI 597 CCATGTTGCTATGTGTACATCTA---GTCCGTTGCTTCTAACTGCTGCAT 551 chr2qtel1M 725250 AATATTTCATAACATTTATATACCATAACTTATTCAGCCATTCTCC-ATT 725298 i i i iiii vi vi i vi iii v i - v C L1ME5_3end#LI 550 AGTACTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCAGT 501 chr2qtel1M 725299 GATGGA----------G--TCCA----CTAGTCACTTCAGAAAGGGCTGC 725332 ---------- -- ---- iv i iv i v iv C L1ME5_3end#LI 500 GATGGACACCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCTGC 451 chr2qtel1M 725333 CATAACTATTTTTGCACATGTGTCCCTTTCCATTCT---TCAAGATCTCT 725379 v i vi ii i i -i vivivi --- v ii i C L1ME5_3end#LI 450 AATGAACATCCTCGTACATGT-CCCCTTATGGACCTGTGTGAGAATTTCT 402 chr2qtel1M 725380 TTGGGATATAAGTCCAATAGAAACACTGCTGGGTCAAAGGGTATGCACAA 725429 vii iv viiv i v i--- C L1ME5_3end#LI 401 TTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATGCG--- 355 chr2qtel1M 725430 TTTTATACCTT-TTTGAGCA--TAGTTCCATATTGTTCTCCAGAACGATT 725476 --- i v- vi -- v v v i i ii C L1ME5_3end#LI 354 ---TATACTTAATTTGACTAAGTACTGCCAGATTGCTCTCCAGAATGGCT 308 chr2qtel1M 725477 GAATAACATTC-ATAGCTCCACCAATAATGTATG--TGTTCCAATTTTCC 725523 v i-- v - i vii ii i i --v v ? i C L1ME5_3end#LI 307 GCAC--CAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATNTCCC 260 chr2qtel1M 725524 CACATCCCCTCCTATAATCTTCATTATCT--TTTCCTAGCATCTTAGCCA 725571 i v v i v ivv i--i i -- i v C L1ME5_3end#LI 259 CACATCCTCGCCAACACTTGGCATTATCCAGCTTTCTA--ATTTTTGCCA 212 chr2qtel1M 725572 GTCTGACAAGTATGTACTGGTACCTCAGAGTTGTCT-AATTTGCATTTCT 725620 i i i i iv v i i vv i - C L1ME5_3end#LI 211 GTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATTTCT 162 chr2qtel1M 725621 CTGATCAATAGTGATTTGGAACACCTTTTAATGTGACTAGAAATACTTTC 725670 i v i v v i i i v i - v vv vv C L1ME5_3end#LI 161 CTGATTACTAATGAGTTTGAGCATCTCTTCATATG-CTTGTTAGCCTTTC 113 chr2qtel1M 725671 AA-TTTCTTCATTTGAAAACTGTCTCTTCATATCCTTTAACCCTTTATTA 725719 ii- i v i v i i v iv v v iv C L1ME5_3end#LI 112 GGGTTTCCTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCCATTTTTCT 63 chr2qtel1M 725720 ATTGGAG 725726 i C L1ME5_3end#LI 62 ATTGGGG 56 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.00 CpG sites = 99, Kimura (unadjusted) = 40.24 Transitions / transversions = 1.43 (99/69) Gap_init rate = 0.06 (32 / 568), avg. gap size = 1.69 (54 / 32) 981 29.83 4.92 2.21 chr2qtel1M 725248 725775 (274225) C L1ME3G_3end#LINE/L1 (376) 548 7 m_b101s551i17 3703 chr2qtel1M 725248 ATAATATTTCATAACATTTATATACCATAACTTATTCAGCCATTCTCC-A 725296 i i ii vv i i i i - C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr2qtel1M 725297 TTGATGGA----------GT--CCA----CTAGTCACTTCAGAAAGGGCT 725330 ---------- -- ----i v ii i v i v iv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr2qtel1M 725331 GCCATAACTATTTTTGCACATGTGTCCCTTTCCAT-TCTTCAAG-ATCTC 725378 v i vi ii i i? i v v i- v v i - i C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACATGCNTCCTTGTGCACATGTGCGAGTATTTC 399 chr2qtel1M 725379 TTTGGGATATAAGTCCAATAGAAACACTGCTGGGTCAAAGGGTATGCACA 725428 ? i v v?i ? iv viiv i i C L1ME3G_3end#L 398 TNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGCA 349 chr2qtel1M 725429 ATTTTATACCTTTTTGA-GCATAGTTCCATATTGTTCTCCAGAACGATTG 725477 - v --- i -iv v v v ii i ? ii C L1ME3G_3end#L 348 -TTTTAAA---TTTTAATAGATACTGCCAAATTGCCCTCCAAAANGGCTG 303 chr2qtel1M 725478 AATAACATTCATAGCTCCACCAATAATGTATGTG--TTCCAATTTTCCCA 725525 v iv - i i vii ii i v -- v vi i C L1ME3G_3end#L 302 TACCA-ATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCA 254 chr2qtel1M 725526 CATCCCCTCCTATAATCTTCATTATC---TTTTCCTAGCATCTTAGCCAG 725572 i i v v i v ?vvi ---i -- i- i v i C L1ME3G_3end#L 253 CACCCTCGCCAACACTNGATATTATCAANCTTT--TAA-ATTTTTGCCAA 207 chr2qtel1M 725573 TCTGACAAGTATGTACTGGTACCTCAGAGTTGTCT-AATTTGCATTTCTC 725621 iii iviv v i vv i - i C L1ME3G_3end#L 206 TCTGATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCC 157 chr2qtel1M 725622 TGATCAATAGTGATTTGGAACACCTTTTAATGTGACTAGAAATACTTTCA 725671 i v vv v i i v i vi vviiivv vv C L1ME3G_3end#L 156 TGATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGT 107 chr2qtel1M 725672 ATTTCTTCATTTGAAAACTGTCTCTTCATATCCTTTAACCCTTTATTAAT 725721 i v i vi i i v iv v v iv C L1ME3G_3end#L 106 ATTTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTAT 57 chr2qtel1M 725722 TGGAGAATGGCTTCAAGTCTTATAAATTCGAGTCAATTCTGTATATAGTT 725771 iv-- v i--v vi i vivv i v v i C L1ME3G_3end#L 56 TGGGT--TGTCTTT--TTCTTATTGATTTGTAGGAGTTCTTTATATATTC 11 chr2qtel1M 725772 TAGA 725775 i C L1ME3G_3end#L 10 TGGA 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.61 CpG sites = 87, Kimura (unadjusted) = 39.61 Transitions / transversions = 1.30 (87/67) Gap_init rate = 0.04 (22 / 527), avg. gap size = 1.73 (38 / 22) 240 29.90 4.23 4.23 chr2qtel1M 725632 725844 (274156) C L1MD_orf2#LINE/L1 (0) 3294 3082 m_b101s551i18 3703 chr2qtel1M 725632 TGATTTGGAACACCTTTTAATGTGACTA---GAAATACTTTCAATTTCTT 725678 v v i v vi --- vv - v -- v i C L1MD_orf2#LIN 3294 TGATGTTGAACATCTTTTCATGTGCTTATTTGCCAT-CTGT--ATATCCT 3248 chr2qtel1M 725679 CATTTGAAAACTGTCTCTTCATATCCTTTAACCCTTTATTAATTGGAGAA 725728 v iv vi v ? i i iv v vi --- C L1MD_orf2#LIN 3247 CTTCGGTGAAATGTCTNTTCATGTCTTTTGCCCATTTTCTAATTGG---A 3201 chr2qtel1M 725729 TGGCTTCAAGTCTTATAAAT-TCGAGTC-----AATTCTGTATATAGTTT 725772 v i --- i v v v - i i----- i v v i C L1MD_orf2#LIN 3200 TTGTTT---GTTTTTTTACTGTTGAGTTTTGAGAGTTCTTTATATATTCT 3154 chr2qtel1M 725773 AGAAATGAGGCCTTTATCCAAACCCTTGAATGTAAAAATGTTTTCCCAGT 725822 v i? v i vi vviv v vv i v v i C L1MD_orf2#LIN 3153 AGATACNAGTCCTTTGTCGGATATGTGGTTTGCAAATATTTTCTCCCAGT 3104 chr2qtel1M 725823 TTACTGCTTCCCTTTTAATCTT 725844 i iiv vi v i C L1MD_orf2#LIN 3103 CTGTAGCTTGTCTTTTCATCCT 3082 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.03 CpG sites = 26, Kimura (unadjusted) = 38.80 Transitions / transversions = 0.74 (26/35) Gap_init rate = 0.06 (12 / 212), avg. gap size = 1.50 (18 / 12) 280 32.55 6.91 6.28 chr2qtel1M 725671 726509 (273491) C L1P1_orf2#LINE/L1 (39) 3255 2412 m_b101s551i19 3703 chr2qtel1M 725671 AATTTCTTCATTTGAAAACTGTCTCTTCATATCCTTTAACCCTTTATTAA 725720 v v i v v i iiv vi v i C L1P1_orf2#LIN 3255 AATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGA 3206 chr2qtel1M 725721 TTGGA--GAATGGCTTCAAGTCTTATAAATTCGAGTCAATTCTGTATATA 725768 v i-- vv vi i--v i i vv v i vv i v C L1P1_orf2#LIN 3205 TGGGGTTGTTTGTTTTT--TTCTTGTAAATTTGTTTGAGTTCATTGTAGA 3158 chr2qtel1M 725769 GTTTAGAAATGAGGCCTTTATCCAAACCCTTGAATGTAAAAATGTTTTCC 725818 v i i v v v i vi vvvv v iv ii v i C L1P1_orf2#LIN 3157 TTCTGGATATTAGCCCTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCC 3108 chr2qtel1M 725819 CAGTTTACTGCTTCCCTTTTAATCTTGTCTGCAT--TAGTTTTGTTTG-- 725864 v i iiv v v v v i---- - -- iv -- C L1P1_orf2#LIN 3107 CATTCTGTAGGTTGCCTGTTCAC----TCTG-ATGGTAGTTTCTTTTGCT 3063 chr2qtel1M 725865 -TCCAAAAACT---TGATATAATCAGAATTATCCATTTTTCAATAATGAC 725910 - v i i --- ii v i -- -i v vv i C L1P1_orf2#LIN 3062 GTGCAGAAGCTCTTTAGTTTAATTAGA--T-CCCATTTGTCAATTTTGGC 3016 chr2qtel1M 725911 CT------CTAGTTCTTCT------TTGGACAAAAACTCCTTCCTCCTTC 725948 i ------ i v v i ------ i vi v v i v v C L1P1_orf2#LIN 3015 TTTTGTTGCCATTGCTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATGC 2966 chr2qtel1M 725949 ACA-GATCTGAGAGGTAAACTATCCTATGTT--CTTCTCATTTGTTTATA 725995 vi - vi iv ?-- i- v -- vivv v i C L1P1_orf2#LIN 2965 CTATGTCCTGAATGGTAN--TG-CCTAGGTTTTCTTCTAGGGTTTTTATG 2919 chr2qtel1M 725996 ATATTCTTTAGGTCTGG-------ATCATGAATTCATTTCAACCTTATCT 726038 i ---- ii-------i v v i i ii vi v i C L1P1_orf2#LIN 2918 GT----TTTAGGTCTAACGTTTAAGTCTTTAATCCATCTTGAATTAATTT 2873 chr2qtel1M 726039 TGGTATATGGTGTTAAATGTGGG--CTGATGCCAAGTTTCTGC-CATG-C 726084 v v - iviv -- iii vi iv i -i - C L1P1_orf2#LIN 2872 TTGTATAAGGTGT-AAGGAAGGGATCCAGTTTCAGCTTTCTACATATGGC 2824 chr2qtel1M 726085 TTGTTTCCAATTTTCCCAGACATT-TTTGTCAAATAGTGAATTCTTATCC 726133 v --- i - ii- i i v i - C L1P1_orf2#LIN 2823 TAG---CCAGTTTTCCCAG-CACCATTTATTAAATAGGGAATCCTT-TCC 2779 chr2qtel1M 726134 CAAAAGCT-GAGTTCTTTGGGTTTGTGAAACACCAGACCACTATA-ATCT 726181 v vv - vv ii ii v v i ivii i - v C L1P1_orf2#LIN 2778 CCATTGCTTGTTTTTCTCAGGTTTGTCAAAGATCAGATAGTTGTAGATAT 2729 chr2qtel1M 726182 TTGAC--TATTTTGTCCTGTGAAC-CTAACCTTTTCCATTGATCAATTAT 726228 vi i -- ---- v ii - ivi v v vvi C L1P1_orf2#LIN 2728 GCGGCGTTATTT----CTGAGGGCTCTGTTCTGTTCCATTGATCTATATC 2683 chr2qtel1M 726229 TCTATTTCTTAG--CCAGTATCTAATG--GTTTTAATGTCTCCTACATTT 726274 i -- i -- i -- -- ii vv vivi v v C L1P1_orf2#LIN 2682 TCTGTT--TTGGTACCAGTACC--ATGCTGTTTTGGTTACTGTAGCCTTG 2637 chr2qtel1M 726275 TAATAGAGTGTTAGACCTGGTACACCTAGGCCACCTTC--CTTTATTTTT 726322 i v v v iii v -i v -- vii i -- i i C L1P1_orf2#LIN 2636 TAGTATAGTTTGAAGTCAGGTA-GCGT--GATGCCTCCAGCTTTGTTCTT 2590 chr2qtel1M 726323 TTGTTTTTTTGGGTTTTTTTCCTATTAATTCTCTTGA-AATTCTTGAACT 726371 ---vi i ---------- i ---- i-i v -- ii C L1P1_orf2#LIN 2589 TTG---GCTTAGG----------ATTGA----CTTGGCGATGC--GGGCT 2559 chr2qtel1M 726372 TTTGTT---TTCCAGATGAATTTTGTTGCAATTTTCT-TAGGTCACTAAA 726417 i v --- v i ivv i i i -i iv vv i C L1P1_orf2#LIN 2558 CTTTTTTGGTTCCATATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAA 2509 chr2qtel1M 726418 ATAGTTTCTTGGACGTTTGATTGTCATAGCACTAA----ATAAATTAATT 726463 iv iv iv vv i v vv i i i ---- vi C L1P1_orf2#LIN 2508 GAAAGTCATTGGTAGCTTGATGGGGATGGCATTGAATCTATAAATTACCT 2459 chr2qtel1M 726464 TAGGTAGTATTGTCTTCTTTATGACATTCACTCAACCTATCC-TGAG 726509 i i v i v i i i i v i vv i - C L1P1_orf2#LIN 2458 TGGGCAGTATGGCCATTTTCACGATATTGATTCTTCCTACCCATGAG 2412 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 42.53 CpG sites = 136, Kimura (unadjusted) = 43.72 Transitions / transversions = 1.13 (136/120) Gap_init rate = 0.09 (79 / 838), avg. gap size = 1.41 (111 / 79) 258 23.08 0.00 1.28 chr2qtel1M 726721 726799 (273201) HUERS-P3#LTR/ERV1 3251 3328 (5591) m_b101s701i1 3704 chr2qtel1M 726721 TTGCTGTTTCAGGGACTTATTGTTTCCACATTCCTTTTTAATTATTCCTT 726770 v vvi i -i v v i v v HUERS-P3#LTR/ 3251 TTGCAGTTGGGGGGACCTAT-ATTTACACATGCCTTTTTAATCATGCCTG 3299 chr2qtel1M 726771 CCTGTCCCATTCCTTTATTGGGGTGAGAC 726799 vvv i i vv HUERS-P3#LTR/ 3300 AAAGTCCCACTCCTTTATTAGGTAGAGAC 3328 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 27.58 CpG sites = 6, Kimura (unadjusted) = 27.58 Transitions / transversions = 0.50 (6/12) Gap_init rate = 0.01 (1 / 78), avg. gap size = 1.00 (1 / 1) 922 28.57 6.49 0.00 chr2qtel1M 727009 727316 (272684) HERV4_I#LTR/ERV1 3020 3347 (3192) m_b101s701i2 3705 chr2qtel1M 727009 CAATATCCAATTAAGCAGGCAGAAAGGATAGGGTTA---CTC-TGATTGA 727054 i v v v i v vi --- i - ii HERV4_I#LTR/E 3020 CAATACCCAATTAAGCTGGAAGCAAGAAAAGGCCTAGCACCCATAGTTGA 3069 chr2qtel1M 727055 -------------CAAG--TTCCTAATTCGCTGCCATTCTCCCTGTAACA 727089 ------------- v --i i vv v v i i HERV4_I#LTR/E 3070 GGTATTACTTACCCATGGACTCTTAAAACCCTGCAATTCTCCCTGCAATA 3119 chr2qtel1M 727090 CTCTGATTCCTTCTGTTAGAAAAGCGACCAGAGAATACCGCATGGTACAG 727139 i iv iiivi i vv iv vv vi i v? i HERV4_I#LTR/E 3120 CCCCCATCTTACCCGTTCTAAAGCCTTCGGGGGAATACCGGNTAGTACAG 3169 chr2qtel1M 727140 GATCTCAGGGTGATTAATAAAGCGGTCATTCCGATCCATCCCCTGGTGCC 727189 i ii i i i v i i vi i vi v HERV4_I#LTR/E 3170 GACCTCAGAATAATTAATGAGGCTGTTATCCCCGTCCACCCATTGGTGGC 3219 chr2qtel1M 727190 TAATTCATATAGA-TCCTCACCCAGATGCCTGGGAATACTCAATGGTTCT 727238 vi i vv- vi i i v i i vv HERV4_I#LTR/E 3220 GGATCCATATACCCTCCTGGCTCAGGTGCCAGGGGATGCAAAATGGTTCT 3269 chr2qtel1M 727239 CCCCCCTGGATCTAAAAGATGCCTTTTGCTGCATTCCTTTACCTACAGAC 727288 vvi i i i i v v i iv iv v HERV4_I#LTR/E 3270 CAGTCCTAGACCTAAAAGATGCTTTCTTCTCCATTCCTCTGGCCCCAGAG 3319 chr2qtel1M 727289 TCCCAGTTTCTCTTTGCCTTTGAATGGG 727316 i vi i HERV4_I#LTR/E 3320 TCCCAATACCTTTTTGCCTTTGAATGGG 3347 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.90 CpG sites = 50, Kimura (unadjusted) = 36.96 Transitions / transversions = 1.32 (50/38) Gap_init rate = 0.02 (5 / 307), avg. gap size = 4.00 (20 / 5) 13 26.85 0.00 0.00 chr2qtel1M 729753 729792 (270208) (AATCA)n#Simple_repeat 1 40 (0) m_b101s252i9 3706 chr2qtel1M 729753 AATAAAATAAAATCACTCCCAGTCAAATGAAATCAATTCA 729792 v v vvi v i v v (AATCA)n#Simp 1 AATCAAATCAAATCAAATCAAATCAAATCAAATCAAATCA 40 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 16 16.52 0.00 0.00 chr2qtel1M 731673 731699 (268301) (A)n#Simple_repeat 1 27 (0) m_b101s252i10 3707 chr2qtel1M 731673 AAAAAACAAAAATAAACAAAAAAGAAA 731699 v v v i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAA 27 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 244 33.33 0.97 0.97 chr2qtel1M 731835 731937 (268063) L1MD1_3end#LINE/L1 451 553 (436) m_b101s551i20 3708 chr2qtel1M 731835 GCAGCTTTTTCTGTACTGGCAAGAAACTGGCAAATGA-GTGGATGCCCAT 731883 v ii v i v i - ii -vii i v L1MD1_3end#LI 451 GCAGCTTTATTCGTAATAGCCAAAAACTGG-AAACAACCCAGATGTCCTT 499 chr2qtel1M 731884 CAGTGGGGTAATGGCTGAATAAGTTATGACATATGAATGTCTTGGAATAT 731933 ii vv i i i ii i ii i vv ii v i L1MD1_3end#LI 500 CAACGGGTGAATGGTTAAACAAACTGTGGTACATCCATACCATGGAATAC 549 chr2qtel1M 731934 TATT 731937 i L1MD1_3end#LI 550 TACT 553 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.56 CpG sites = 24, Kimura (unadjusted) = 47.50 Transitions / transversions = 2.40 (24/10) Gap_init rate = 0.02 (2 / 102), avg. gap size = 1.00 (2 / 2) 15 20.03 0.00 0.00 chr2qtel1M 731988 732016 (267984) (T)n#Simple_repeat 1 29 (0) m_b101s252i11 3709 chr2qtel1M 731988 TTTTTTGTTTTTAATGTTTTTTTTATTTT 732016 v vv v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 965 29.85 1.76 6.07 chr2qtel1M 732420 732986 (267014) C L1MC4a_3end#LINE/L1 (2029) 600 57 m_b101s551i21 3710 chr2qtel1M 732420 TCACTCAGCATCAGTTCATGTAAGTCTCTCCAAGCCTCTCTTCATCCTGC 732469 vii iv ii ----------- i i -- C L1MC4a_3end#L 600 TCACTCCATATCAGTTCATAGAGATCT-----------TCCTCATTCT-- 564 chr2qtel1M 732470 TGGTCATTTCTTACAGAACAATAATATTCCATAACATTCATATACCACAA 732519 ------- i vvvv i i viii vv i i i C L1MC4a_3end#L 563 -------TTTTTACAGCTGCATAGTACTCCATTGTGTGGATGTACCATAG 521 chr2qtel1M 732520 TTTACCCAACCATTCTCCAATGCATGGACATCCATTCATTTTCCAGTTTC 732569 ii ? v ?? i ii vvivv i v i C L1MC4a_3end#L 520 TTTATTCAACCANTCTCCTATNNATGGGCATTTAGGTTGTTTCCAATATT 471 chr2qtel1M 732570 TGGCCACTACAAACAGGGCTGCCACAAACA--TTTG-GCACATTCAAGGT 732616 v v i iv v ii i --i - i vi? vv C L1MC4a_3end#L 470 TTGCAATTACAAACAATGCTGCAATGAATAACCTTGTGCATATGTNATTT 421 chr2qtel1M 732617 CCCTATCCCTTCTTTAC-TATCTCTTTGGGGTACAAGCCCAGTAGTAGCA 732665 --- i v v vi vv v- i v ii v vv i v i v C L1MC4a_3end#L 420 ---TGTACATGTTGGAGGTGTATCTTCAGGGTAAATTCCTAGAAGTGGGA 374 chr2qtel1M 732666 CTGCTGGGTCAAAGGGTA--TGCACAATTTGATAACTTTTGGGGCATAAT 732713 i -- i --- - i- vviv v C L1MC4a_3end#L 373 TTGCTGGGTCAAAGGGTAAATGCATA---TG-TAG-TTTTGTTAGATATT 329 chr2qtel1M 732714 TCCAGATTGCTCTCCAGAATGGTTGGATTCGTTCACAACTCCACCAACAA 732763 v i v i ? v v iiv? ii vii i C L1MC4a_3end#L 328 GCCAAATTCCCCTCCANAAGGGTTGTACCANTTTGCATTCCCACCAGCAA 279 chr2qtel1M 732764 GGCATCAGTGTCCCAGTTTTCCCACATCCCCTCCGACA---TTCATCATT 732810 v i v v v v i v i v i --- vii ii i C L1MC4a_3end#L 278 TGTATGAGAGTGCCTGTTTCCCCACAGCCTCGCCAACAGAGTGTGTTGTC 229 chr2qtel1M 732811 ATTTTTTCCTGTCATCTTAGCCAATCTGACAGGTGTGTAGTGGTATCTCA 732860 vvi -- -v i v i v v i C L1MC4a_3end#L 228 AAACTTT--TG-AATTTTTGCCAATCTGATAGGTGAGAAATGGTATCTCA 182 chr2qtel1M 732861 GAGT-TTCTTAATTTGCATTTCTCTGATCAATAGTGATTTGGAACACTCT 732909 v -v i v i vv vv v iii C L1MC4a_3end#L 181 GTGTAGTTTTAATTTGCATTTCTCTTATTATGAGTGAGGTTGAACATCTT 132 chr2qtel1M 732910 TTCATACGAGTGGAAATACTTTCAATTTCATCATCTGAAAATTGTCTGTT 732959 i vv iiiiiivv ?v ? v -- i vi C L1MC4a_3end#L 131 TTCATATGTTTAAGGGCCATTTNTATNTCTT--TTTGTGAATTGTCTGTT 84 chr2qtel1M 732960 CATATCCTTTGACCATTTATCAGTTGG 732986 i i v v vi i C L1MC4a_3end#L 83 CATGTCTTTTGCCCATTTTTCTATCGG 57 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.03 CpG sites = 83, Kimura (unadjusted) = 39.34 Transitions / transversions = 1.09 (83/76) Gap_init rate = 0.07 (39 / 566), avg. gap size = 1.10 (43 / 39) 1428 27.00 3.65 4.03 chr2qtel1M 732490 733037 (266963) C L1ME5_3end#LINE/L1 (389) 552 7 m_b101s551i22 3710 chr2qtel1M 732490 ATAATATTCCATAACATTCATATACCACAATTTACCCAACCATTCTCC-A 732538 i i iiii v vi v i v i - C L1ME5_3end#LI 552 ATAGTACTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCA 503 chr2qtel1M 732539 ATGCATGGACATCCATTCATTTTCCAGTTTCTGGCCACTACAAACAGGGC 732588 i - i vvivvii ii i iv i iv C L1ME5_3end#LI 502 GTG-ATGGACACCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGC 454 chr2qtel1M 732589 TGCCACAAACATT-TGGCACATTCAAGGTCCC--TATC--CCTTCTTTAC 732633 v ii i- v i ----- -- v-- viv v v C L1ME5_3end#LI 453 TGCAATGAACATCCTCGTACAT-----GTCCCCTTATGGACCTGTGTGAG 409 chr2qtel1M 732634 TATCTCTTTGGGGTACAAGCCCAGTAGTAGCACTGCTGGGTCAAAGGGTA 732683 v i i i vi v ii v i v C L1ME5_3end#LI 408 AATTTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTA 359 chr2qtel1M 732684 TGC----AC--AATTTGA-TAACTTTTGGGGCATAATTCCAGATTGCTCT 732726 ---- -- - v vi ---------- C L1ME5_3end#LI 358 TGCGTATACTTAATTTGACTAAGTACTG----------CCAGATTGCTCT 319 chr2qtel1M 732727 CCAGAATGGTTGGATTCGTTCACAACTCCACCAACAAGGCATCAGTGTCC 732776 i v iiv ii vii i iv v v i C L1ME5_3end#LI 318 CCAGAATGGCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTC 269 chr2qtel1M 732777 CAGTTTTCCCACATCCCCTCCGACATTCATCATTATT---TTTTCCTGTC 732823 vi ? i i v i i iiv i---i --- v C L1ME5_3end#LI 268 CTATNTCCCCACATCCTCGCCAACACTTGGCATTATCCAGCTTTC---TA 222 chr2qtel1M 732824 ATCTTAGCCAATCTGACAGGTGTGTAGTGGTATCTCAGAGTT-TCTTAAT 732872 i v i i i iv i vv - i C L1ME5_3end#LI 221 ATTTTTGCCAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAAT 172 chr2qtel1M 732873 TTGCATTTCTCTGATCAATAGTGATTTGGAACACTCTTTCATACGAGTGG 732922 i v i v v i iiii i vv v C L1ME5_3end#LI 171 TTGCATTTCTCTGATTACTAATGAGTTTGAGCATCTCTTCATATGCTTGT 122 chr2qtel1M 732923 AAATACTTTC-AATTTCATCATCTGAAAATTGTCTGTTCATATCCTTTGA 732971 v ii- -ii v v v i v C L1ME5_3end#LI 121 TAGC-CTTTCGGGTTTCCTCTTCTGTAAATTGCCTGTTCATATCCTTTGC 73 chr2qtel1M 732972 CCATTTATCAGTTGGAG--AATGGCTTGATTTCTTATACATTAGAGTTAA 733019 v vi i --?vi v -- i vv v vivv i C L1ME5_3end#LI 72 CCATTTTTCTATTGGGGTTNCCGTCTT--TTTCTTGTTGATTTGCAGGAG 25 chr2qtel1M 733020 TTCTCTATATATTTTGGA 733037 ii i i i C L1ME5_3end#LI 24 TTCCTTGTATATTCTAGA 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.80 CpG sites = 83, Kimura (unadjusted) = 34.43 Transitions / transversions = 1.41 (83/59) Gap_init rate = 0.06 (33 / 547), avg. gap size = 1.27 (42 / 33) 235 31.29 7.96 1.40 chr2qtel1M 732894 733094 (266906) C L1PB_orf2#LINE/L1 (0) 3294 3081 m_b101s551i23 3710 chr2qtel1M 732894 TGATTTGGAACACTCTTTCATACGAGTGGAAATACTTTCAATTTCATCAT 732943 v v i i i i vv vviiivv vv v v v C L1PB_orf2#LIN 3294 TGATGTTGAGCATTTTTTCATATGTTTGTTGGCCATTTGTATATCTTCTT 3245 chr2qtel1M 732944 CTGAAAATTGTCTGTTCATATCCTTTGACCATTTATCAGTTGGAGAATGG 732993 i i i i v v i v iii v --- v C L1PB_orf2#LIN 3244 TTGAGAATTGTCTATTCATGTCCTTAGCCCACTTTTTGATGGG---ATTG 3198 chr2qtel1M 732994 CTTG---ATTTCTTATACATTAGAGTTAATTCTCTATATATTTTGGAAAT 733040 i ---v iivv v vv v i ?i i v i v C L1PB_orf2#LIN 3197 TTTGTTTTTTTCTTGCTGATTTGTTTGAGTTCNTTGTAGATTCTGGATAT 3148 chr2qtel1M 733041 GAGGCCTT--TC----------ACTGTGAAGATGTTTTCCCAGTTTGTTG 733078 v v -- ---------- i v i v i v C L1PB_orf2#LIN 3147 TAGTCCTTTGTCAGATGTATAGATTGTGAAGATTTTCTCCCACTCTGTGG 3098 chr2qtel1M 733079 CTTCCCT-TCTAATCTG 733094 v vi - i v C L1PB_orf2#LIN 3097 GTTGTCTGTTTACTCTG 3081 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.03 CpG sites = 27, Kimura (unadjusted) = 41.03 Transitions / transversions = 0.77 (27/35) Gap_init rate = 0.04 (7 / 200), avg. gap size = 2.71 (19 / 7) 274 22.62 11.49 4.43 chr2qtel1M 732945 733092 (266908) C L1MD_orf2#LINE/L1 (53) 3241 3084 m_b101s551i24 3710 chr2qtel1M 732945 TGAAAATTGTCTGTTCATATCCTTTGACCATTTATCAGTTGGAGAATGGC 732994 -- ? i i v vii i --- v i C L1MD_orf2#LIN 3241 TGAAA--TGTCTNTTCATGTCTTTTGCCCATTTTCTAATTGGA---TTGT 3197 chr2qtel1M 732995 TTGATTTCTTATACATTAGAGTT-----AATTCTCTATATATTTTGGAAA 733039 v i i-ii - ----- i i i i v C L1MD_orf2#LIN 3196 TTGTTTTTTTAC-TGTT-GAGTTTTGAGAGTTCTTTATATATTCTAGATA 3149 chr2qtel1M 733040 TGAGGCCTTTCAC-----TGTG-------AAGATGTTTTCCCAGTTTGTT 733077 i? v vv ----- ------- v v i i v C L1MD_orf2#LIN 3148 CNAGTCCTTTGTCGGATATGTGGTTTGCAAATATTTTCTCCCAGTCTGTA 3099 chr2qtel1M 733078 GCTTCCCTTCTAATC 733092 vi i v C L1MD_orf2#LIN 3098 GCTTGTCTTTTCATC 3084 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 28.03 CpG sites = 19, Kimura (unadjusted) = 28.03 Transitions / transversions = 1.46 (19/13) Gap_init rate = 0.07 (10 / 147), avg. gap size = 2.40 (24 / 10) 15 10.32 0.00 6.06 chr2qtel1M 733324 733358 (266642) (TTTAT)n#Simple_repeat 1 33 (0) m_b101s252i12 3711 chr2qtel1M 733324 TTTATTGTTATTTTCTTACATTTTACTTTTATTTT 733358 - v vi - (TTTAT)n#Simp 1 TTTATT-TTATTTTATTTTATTTTA-TTTTATTTT 33 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 23 21.38 3.64 0.00 chr2qtel1M 733551 733605 (266395) (AT)n#Simple_repeat 1 57 (0) m_b101s252i13 3712 chr2qtel1M 733551 ATA-ATAATTACACATACATACATTCATATATATACACATATAT-TATAT 733598 - vv i i i i vi i i - (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr2qtel1M 733599 ATATATA 733605 (AT)n#Simple_ 51 ATATATA 57 Matrix = Unknown Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.04 (2 / 54), avg. gap size = 1.00 (2 / 2) 1109 27.84 4.34 4.34 chr2qtel1M 733812 734318 (265682) C L1ME5_3end#LINE/L1 (428) 513 7 m_b101s551i25 3713 chr2qtel1M 733812 CCATTC-CCCAGTTGGTGAGCATCCA--TTCCTTTATCAATTCTGTGTTA 733858 i - - i ii i -- v i i-- i ivi ii C L1ME5_3end#LI 513 CCACTCTCCCAGT-GATGGACACCCAGGTTGCCTC--CAACTCCCCGCCA 467 chr2qtel1M 733859 CCACAGAAAGAGCTGCTGCAAACATCTTTGCACATGTGGGTCCTTGTC-- 733906 i v iv viii i i i v--i i v-- C L1ME5_3end#LI 466 CCACAAACAACGCTGCAATGAACATCCTCGTACATGTC--CCCTTATGGA 419 chr2qtel1M 733907 CCTTTTTGATGATGTCTTTGGGATAAAGACCCTGTGGAGACACTGCTGGA 733956 v v vi v v v v vi v iv i i C L1ME5_3end#LI 418 CCTGTGTGAGAATTTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGG 369 chr2qtel1M 733957 TGCA-AGGGTATGCACA-GTTTGATAGCCCTTTGAGCA--TAGTTCCAAA 734002 - - ii -ii i ------ vi -- v v i C L1ME5_3end#LI 368 T-CATAGGGTATGCGTATACTTAAT------TTGACTAAGTACTGCCAGA 326 chr2qtel1M 734003 TTACTCTCCACAATGGTTGGATCATTTCAGAATTCC-CCAACAACGCATT 734051 i v i v i v ii v v i - i ii v C L1ME5_3end#LI 325 TTGCTCTCCAGAATGGCTGCACCAGTCTACACTCCCACCAGCAGTGCATG 276 chr2qtel1M 734052 AGTGTCCCACTTTTCCCACATCCCCTCTAATATTTATCATTATCT---TT 734098 v i vv ? i i v i i i iv i--- C L1ME5_3end#LI 275 AGGGTTCCTATNTCCCCACATCCTCGCCAACACTTGGCATTATCCAGCTT 226 chr2qtel1M 734099 TCTGTGATCTTAGCCAATCTGAGAGGTGTGAGGTGGTACCTCAGAGTTGT 734148 i-- i v i i v i i i i vv C L1ME5_3end#LI 225 TCTA--ATTTTTGCCAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGT 178 chr2qtel1M 734149 GT-AATTTGCATTTCTCTTATCAGTAGTGATTTAGAGCATTTTTTCTTAT 734197 v - v i v i v v i i v C L1ME5_3end#LI 177 TTTAATTTGCATTTCTCTGATTACTAATGAGTTTGAGCATCTCTTCATAT 128 chr2qtel1M 734198 ACCTCTAATTGGCTTT---AATTTGCTCATCTGGAAATTCTCTGTTCATA 734244 i i ---i i i ---ii v v v vi C L1ME5_3end#LI 127 GCTT---GTTAGCCTTTCGGGTTTCCTCTTCTGTAAATTGCCTGTTCATA 81 chr2qtel1M 734245 TTCTTTGACCTTGTATCAAGTAATGAATGATTT--GTA---TTCTTATCA 734289 i v v v v --- v i-- i ?-- v--- i ii C L1ME5_3end#LI 80 TCCTTTGCCCATTTTTC---TATTGG--GGTTNCCGTCTTTTTCTTGTTG 36 chr2qtel1M 734290 ATTTGAAACAGGTCTTTATATATTTTAGA 734318 v iv v i i i C L1ME5_3end#LI 35 ATTTGCAGGAGTTCCTTGTATATTCTAGA 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.96 CpG sites = 81, Kimura (unadjusted) = 35.97 Transitions / transversions = 1.50 (81/54) Gap_init rate = 0.07 (34 / 506), avg. gap size = 1.29 (44 / 34) 271 29.57 5.36 5.03 chr2qtel1M 734175 734491 (265509) C L1PREC2_orf2#LINE/L1 (0) 3294 2977 m_b101s551i27 3713 chr2qtel1M 734175 TGATTTAGAGCATTTTTTCTTATACCTCTAATTGGCTTTA---ATTTGCT 734221 v v v v i i ---i ivi --- v vi C L1PREC2_orf2# 3294 TGATGTTGAGCTTTTTTTCATATGCTT---GTTGGCCGCATGTATGTCTT 3248 chr2qtel1M 734222 CATCTGGAAATTCTCTGTTCATATTCTTTGACCTTGTATCAAGTAAT-GA 734270 v i i v v i i v viv v ---- - i C L1PREC2_orf2# 3247 CTTTTGAAAAGTGTCTGTTCATGTCCTTTGCCCACTTTT----TAATGGG 3202 chr2qtel1M 734271 ATGATTTG---TATTCTTATCAATTTGAAACAGGTCTTTATATATTTTAG 734317 i vi --- v i v vvvv v i v vi i C L1PREC2_orf2# 3201 GTTGTTTGTTTTTTTCTTGTAAATTTGTTTAAGTTCCTTATAGATGCTGG 3152 chr2qtel1M 734318 AAATCAGACTTTTGACAGATATACTGATCATAAAGATTTTTCCCCAGCTT 734367 v i i v ii iv v iii ? ii --- C L1PREC2_orf2# 3151 ATATTAGACCTTTGTCAGATGCATAGTTTGCAAANATTTTCTCCCA---T 3105 chr2qtel1M 734368 TCTAC---TTCCCTCTTAATCTTGTTTCTGGTGGTTTTGTT---TGTGCA 734411 ii--- vi v v iii --- i i iv --- C L1PREC2_orf2# 3104 TCTGTAGGTTGTCTGTTTACTCTGT---TGATAGTTTCTTTTGCTGTGCA 3058 chr2qtel1M 734412 ATAACT-TTTAATTTATTGAAATCAAAGTTGTCCA-TTTTGCCTTTA--G 734457 iv i - i v v i vv v v - i i-- C L1PREC2_orf2# 3057 GAAGCTCTTTAGTTTAATTAGATCCCATTTGTCAATTTTTGCTTTTGTTG 3008 chr2qtel1M 734458 TAATATTCTTTAGTGCTTCCTTGGTCATAAATTC 734491 i - v v - v - v i v C L1PREC2_orf2# 3007 CAAT-TGCTTTTG-GCGT-CTTCGTCATGAAATC 2977 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.73 CpG sites = 45, Kimura (unadjusted) = 38.27 Transitions / transversions = 1.02 (45/44) Gap_init rate = 0.08 (24 / 316), avg. gap size = 1.38 (33 / 24) 321 31.63 2.49 2.13 chr2qtel1M 734175 734455 (265545) C L1M5_orf2#LINE/L1 (0) 3294 3013 m_b101s551i26 3713 chr2qtel1M 734175 TGATTTAGAGCATTTTTTCTTATACCTCTAATTGGC---TTTAATTTGCT 734221 ?v v i v i i i --- --- v? v vi C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTT---ATTGGCCATTTGNATATCTT 3248 chr2qtel1M 734222 CATCTGGAAATTCTCTGTTCATATTCTTTGACCTTGTATCAAGTAATGAA 734271 v i vi v v vi ii v v v v ?--- v ii C L1M5_orf2#LIN 3247 CTTTTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTN---TATTGGG 3201 chr2qtel1M 734272 TGATTTGTATT---CTTATCAATTTGAAACAGGTCTTTATATATTTTAGA 734318 vi v ---? ii ? v iv v i i C L1M5_orf2#LIN 3200 TTGTTTGTCTTTTTNTTATTGANTTGTAGGAGTTCTTTATATATTCTGGA 3151 chr2qtel1M 734319 AATCAGACTTTTGACAGATATACTGATCATAAAGATTTTTCCCCAGCTTT 734368 v iv v i v ivv? iii v ii ?ii v C L1M5_orf2#LIN 3150 TACGAGTCCTTTGTCAGATATATGTNTTGCAAATATTTTCTCCCANTCTG 3101 chr2qtel1M 734369 CTACTTCCCTCTTAATCTTGTTTCTGGTGGTTTTGTTTGTGCAATAACTT 734418 ivi v i v i v vvi vi vvv? v iv ii C L1M5_orf2#LIN 3100 TGGCTTGCCTTTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTT 3051 chr2qtel1M 734419 TTAA-TTTATTGAAATCAAAGTTGTCCATTTTGCCTTT 734455 - iv ? i v v i v vi C L1M5_orf2#LIN 3050 TTAATTTTGATGNAGTCCAATTTATCAATTTTTTCTTT 3013 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 42.14 CpG sites = 41, Kimura (unadjusted) = 43.42 Transitions / transversions = 0.89 (41/46) Gap_init rate = 0.03 (9 / 280), avg. gap size = 1.44 (13 / 9) 2048 28.84 6.28 2.82 chr2qtel1M 734751 736327 (263673) C L1M5_orf2#LINE/L1 (586) 2708 1079 m_b101s551i28 3713 chr2qtel1M 734751 TCTAATCTATTCCACTGATGGCCCAT--G-CTATTTTTTAGCCAGTACCA 734797 v i i --- i -- - ii vv i C L1M5_orf2#LIN 2708 TCTATTCTGTTCCATTGAT---CTATTTGTCTATCCTTACGCCAATACCA 2662 chr2qtel1M 734798 AATGGT-TTGATTACTGCGGCTTTGTAACATAGTTCTAGGGT-AGGTACT 734845 v iv - ii i i - ii ii?i -? v C L1M5_orf2#LIN 2661 CACTGTCTTGATTACTGTAGCTTTATAATA-AGTCTTGANATCNGGTAGT 2613 chr2qtel1M 734846 GCTAAG-CCACCATCCTTTGTATTTTGTTGTT----GTTGTTAATCCCTT 734890 - - v -v - i v v ----i ------ C L1M5_orf2#LIN 2612 G-TAAGTCCTCCA-ACTTTGT-TCTTCTTTTTCAAGATTGTT------TT 2572 chr2qtel1M 734891 GA-TATTGTTGACCTTTTG---TT-------GGTTTT----------TTT 734919 i- v ? ii i --- -------ii ---------- v C L1M5_orf2#LIN 2571 GGCTATTCTNGGTCCTTTGCATTTCCATATAAATTTTAGAATCAGCTTGT 2522 chr2qtel1M 734920 CTAGTTCTATAAAATAATGTTTTTTCAGTTTGATTGTTAGGGCATTAAAC 734969 v v i v iv vi vvv v vv vv i i C L1M5_orf2#LIN 2521 CAATTTCTACAAAAAAACCTGCTGGGATTTTGATTGGGATTGCATTGAAT 2472 chr2qtel1M 734970 AAATAGACTAATTTAGGAAGAATTGTGATCT-----ATAT-GAGCTCAAC 735013 vv ii i i vv ----- - - vv C L1M5_orf2#LIN 2471 CTATAGATCAATTTGGGGAGAATTGACATCTTNACAATATTGAG-TCTTC 2423 chr2qtel1M 735014 CTAGCCATGAACAATTAATATTT------TTGTTTAGATCTGATTTTCTT 735057 v v vvvv i ------ i i vv vv C L1M5_orf2#LIN 2422 CAATCCATGAACATGGTATATCTCTCCATTTATTTAGGTCTTCTTTAATT 2373 chr2qtel1M 735058 TGCGTGAGAAGTGTTTTGTAATTGT--GTTCATATGGTATTTGCGTTTGC 735105 viv v v i i v -- vi ? - -i iiv ?i C L1M5_orf2#LIN 2372 TCTCTCAGCAATGTTTTGTAGTTTTCAGTGTANA-GGT-CTTGCACATNT 2325 chr2qtel1M 735106 CTTGGCAGCTTGATCCCTAATTATTT--TGTCTATAGAC---ATTTTCAA 735150 i vi v v i v -- i v v i--- v v C L1M5_orf2#LIN 2324 TTTGTTAGATTTATTCCTAAGTATTTNATGTTTTTTGATGCTATTGTAAA 2275 chr2qtel1M 735151 TGGAATTTCTCTTTGTATCTC--TTACTTATGGGCT-TTATCAGTTATAT 735197 v vi i ?iv i -- v iv v vi - iii - C L1M5_orf2#LIN 2274 TGGTATTGTTTTTNAAATTTCATTTTCCAATTGTTTGTTGCTAGT-ATAT 2226 chr2qtel1M 735198 AGAGCAATGCTGATGATTTGTGTGATTTCATTTTATATACTGCAATTTTG 735247 -- i viv v ivv v ii i v ? i ii C L1M5_orf2#LIN 2225 AGA--AATACAATTGATTTTTGTATATTGACCTTGTATCCNGCGACCTTG 2178 chr2qtel1M 735248 CTAAAGCTGCG-ATTGTTTTCAGTAGATATTTTGATGGTTTTCAAGGATT 735296 viii v- iv ii v v? vv i i iv? C L1M5_orf2#LIN 2177 CTAAATTCACTTATTAGTTCTAGTAGTTTNTTTGTAGATTCTTTNGGATT 2128 chr2qtel1M 735297 CTCAAAATATCTCATCATATCATCTCCAAAGAGT---AGTTTTATTTCCT 735343 i v vi ?viv i v i v i?--- i C L1M5_orf2#LIN 2127 TTCTACGTANACAATCATGTCATCTGCGAATAANGACAGTTTTATTTCTT 2078 chr2qtel1M 735344 CATTGCCTATTCTAATTCCTTTTGTTTCTTTTTCTTTTCTTAT--CAATG 735391 v v v ii v v i vi -- v C L1M5_orf2#LIN 2077 CCTTTCCAATCTTTATGCCTTTTATTTCTTTTTCTTGCCTTATTGCACTG 2028 chr2qtel1M 735392 AAGCTGATATTTCTAGAACAGTGTTGAATAATAGTGGTGATAA------- 735434 -- iiv ii i v i iv ? i------- C L1M5_orf2#LIN 2027 --GCTAGGACCTCCAGTACAATGTTGAATAGAAGTGGTGANAGCGGACAT 1980 chr2qtel1M 735435 -----TTTAACCCCTGATTTTACTGGGAATGCATCCAGCTTCTGTCCAT- 735478 ----- i viii i i vv v ? i i? i vv - C L1M5_orf2#LIN 1979 CCTTGTCTTGTTCCCGATCTTAGGGGGAAAGCNTTCAGTNTTTCACCATT 1930 chr2qtel1M 735479 ------AATGTTT-CTATAGGTTTTAACGAAGCATTGC---TTATTGTTT 735518 ------i ?- i v- v v-- --- iivv C L1M5_orf2#LIN 1929 AAGTATGATGTTNGCTGTAGGTTTTT-CGTAGA--TGCCCTTTATCAGGT 1883 chr2qtel1M 735519 TCAGGAAAGTTCCCTT-TATCCCTATGCCCTCT-AGTGTTTCTTTATAA- 735565 v - - i - iiiv - v -- v - C L1M5_orf2#LIN 1882 TGAGGAA-GTTCCCTTCTATTCCTA-GTTTGCTGAGAGTTT--TTATCAT 1837 chr2qtel1M 735566 GAATGGGTACTGTATTTTGTCAAAAGCTTTTCCTGCTTGTATTGGGATTG 735615 ii v v i v v i vi C L1M5_orf2#LIN 1836 GAATGGGTGTTGAATTTTGTCAAATGCTTTTTCTGCATCTATTGAGATGA 1787 chr2qtel1M 735616 TAATATGATTTTGGTTGGTTTTGTTATTGATGTGATCGGCTGTAGTTAA- 735664 v vv ivv v vi i i i i viii ii - i - C L1M5_orf2#LIN 1786 TCATATGATTTTTCTCCTTTATTCTGTTAATATGGTGAATTACA-TTGAT 1738 chr2qtel1M 735665 -GTTTTCCTGATACCAAACCAGCCCTGCATTACTGGTATAAATCCC-CTT 735712 - v i vi iii i i v v i - C L1M5_orf2#LIN 1737 TGATTTTCGAATGTTAAACCAACCTTGCATTCCTGGGATAAACCCCACTT 1688 chr2qtel1M 735713 GGTTGTAGTGTACTATCCTGCTCATAAGTTGCTGTAATCTCTTTGCTAAT 735762 ii ii i vi i vi v v vv C L1M5_orf2#LIN 1687 GGTCATGATGTATTATCCTTTTTATATATTGCTGGATTCGATTTGCTAAT 1638 chr2qtel1M 735763 ATGTTATTTAGCATTTGTGCATCAGTATTCAACAGGGATATTGGTCTGTA 735812 v i ? v v vi i vv C L1M5_orf2#LIN 1637 ATTTTGTTNAGGATTTTTGCATCTATGTTCATGAGGGATATTGGTCTGTA 1588 chr2qtel1M 735813 ATTTTTTTTCTCTGTTTTAGCCCT-TCGTGTTTTACGTAGCAGTGCCATA 735861 i iii vv iv ii - ?v i- v v i? - C L1M5_orf2#LIN 1587 ATTTTCTTTTCTTGTAATGTCTTTGTCNGGTTTTG-GTATCAGGGTNAT- 1540 chr2qtel1M 735862 ACTGG-GTCGTACAGGAAATGTGGCAGTACTCCTTC---ACCTATTTTTT 735907 i -v i v ivi i vv v ii i ---vi i C L1M5_orf2#LIN 1539 GCTGGCCTCATAAAATGAGTTGGGAAGTGTTCCCTCTTTTTCTATTTTCT 1490 chr2qtel1M 735908 CCAAATAGTTGACGTAGTATTGGAAGTAATTGTTCTTTAAATGTTTGGGA 735957 -vi v vii iv v v v v i v C L1M5_orf2#LIN 1489 -GGAAGAGTTTGTGTAAGATTGGTATTATTTCTTCCTTAAATGTTTGGTA 1441 chr2qtel1M 735958 GAATTCACTGGTGGATCCAACTGGTGCTGGAGATTTTTTCTTAGG--GGC 736005 ii i v v vv v i iv i -- i C L1M5_orf2#LIN 1440 GAATTCACCAGTGAAGCCATCTGGGCCTGGAGTTTTCTTTGTGGGAAGGT 1391 chr2qtel1M 736006 TTCAGTAATGACTTGTTCAATTTCGTTTTCTGAAATGGAGCTATTTAAAT 736055 i-- v vvi v vviv v i i i i C L1M5_orf2#LIN 1390 TTT--TAATTACAAATTCAATTTCTTTAATAGATATAGGGCTATTCAGAT 1343 chr2qtel1M 736056 ATTGTATTTCCTCTTCTGTTAACCTAGGAAATTTGTATTTTTTGTAAACA 736105 v v i v? i iii v v ? i ii- iiv C L1M5_orf2#LIN 1342 TTTCTATTTCTTCTTGNGTCAGTTTTGGTAANTTGTGTTTTTCA-AGGAA 1294 chr2qtel1M 736106 TTCTTCCATTTCAGTTAGATTGTCAGACTTGTTGCCATAGTGTTGGGAA- 736154 iv vi ii ? i i i v iv vvv - C L1M5_orf2#LIN 1293 TTTGTCCATTTCATCTAAGTTNTCAAATTTATTGGCATAAAGTTGTTCAT 1244 chr2qtel1M 736155 AAAAAGCTCCTAATATTTGCTTTAATTTCTTT---TTCCTTGGTGGTATA 736201 v vv i v ii-i v v ---v iv i i i-- C L1M5_orf2#LIN 1243 AATATTCTCTTATTATCC-TTTTAATGTCTGTAGGATCTGTAGTGATG-- 1197 chr2qtel1M 736202 TTCACCCCTTTCACTTTTGATGTTGGTGATTTGGGCTTTATTTTCTTTTC 736251 - v ii i ii i i ----- i i - i C L1M5_orf2#LIN 1196 -TCTCCTTTTTCATTCCTGATATTGGTAATTTG-----TGTCTTC-TCTC 1154 chr2qtel1M 736252 TTTTTCTCATCATCAAATGTGGGCAAAGATTTATTTGTTTTGTTAGTTTT 736301 i v v - i v ? vi i i ivi i ii i C L1M5_orf2#LIN 1153 TTTTTTTCTTGATC-AGTCTNGCTAGAGGTTTATCAATTTTATTGATCTT 1105 chr2qtel1M 736302 TTTATAAAACCAACTATTAGTTTTGT 736327 i v i i v i i i C L1M5_orf2#LIN 1104 TTCAAAGAACCAGCTTTTGGCTTCGT 1079 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.30 CpG sites = 239, Kimura (unadjusted) = 37.84 Transitions / transversions = 1.18 (239/203) Gap_init rate = 0.05 (83 / 1576), avg. gap size = 1.75 (145 / 83) 476 32.82 6.78 2.47 chr2qtel1M 737478 737905 (262095) L1ME3_3end#LINE/L1 22 467 (442) m_b101s551i30 3714 chr2qtel1M 737478 GAACTGCCTTAAATTTATAAGAA---TGCAAACCATTCTTCAAATGATAA 737524 v ivi iv ---vi v ii --- v i v L1ME3_3end#LI 22 GAACTCCTACAAATCAATAAGAAAAAGACAAACAACCC---AATTAAAAA 68 chr2qtel1M 737525 ATGGTCAAAGGATTTAAACAGAAAATTTTTGGATGAAAAAACAAAAATCA 737574 v i i i iv v iviii v ii v ivv vi L1ME3_3end#LI 69 ATGGGCAAAAGACTTGAACAGGCACTTCACAAAAGAGGATATCCAAATGG 118 chr2qtel1M 737575 TTTCTAGTCCTATGAAAAAATTCTCTAAAACACTGTTGGTCAGATAATTG 737624 iivv iv v ii v v v v i iv vi iv v L1ME3_3end#LI 119 CCAATAAGCATATGAAAAGGTGCTCAACATCATTAGTCATCAGGGAAATG 168 chr2qtel1M 737625 TAAATTATAACAAGGCTGAGATACCAG---ATATTT--CAGATTGGCTAA 737669 i v v viv v--- i iii-- v L1ME3_3end#LI 169 CAAATTAAAACCACAATGAGATACCACTACACACCCACCAGAATGGCTAA 218 chr2qtel1M 737670 GAT--GACAG---GGCAAGATGTA-TGTTGAAGGGAATGGGGAAAAACTG 737713 i --i v --- i v ivv - iv i i v iv L1ME3_3end#LI 219 AATTAAAAAGACTGACAATACCAAGTGTTGGCGAGGATGTGGAGCAACTG 268 chr2qtel1M 737714 GGACACTAATACATTGTTGGTGGAGTTGGGAATTGATCCAGTCATTCTAG 737763 i v v i iiv vi i v ii i i i L1ME3_3end#LI 269 GAACTCTCATACATTGCTGGTGGGAGTGTAAATTGGTACAACCACTTTGG 318 chr2qtel1M 737764 AGAACAATATGGAACTATGC-CTGAGGGGCTATCACACTGTGTATACCCT 737812 i vi v v v vi- i --i -v - ii iv L1ME3_3end#LI 319 AAAACTGTTTGGCAGTATCTACTAA--AGCTA-AACA-TACGCCTACCCT 364 chr2qtel1M 737813 TTGATCCAGCAGTGTCTACTGAACCT--GTAT---CCCAA-AGAGATGA- 737855 v i i - i --- -- --- - i - L1ME3_3end#LI 365 ATGACCCAGCAAT-TCCACT---CCTAGGTATATACCCAAGAGAAATGAG 410 chr2qtel1M 737856 --TAAAGGCCTTCC-----ACATGGGCAAAAATGTTTGTAGCCACCTTTT 737898 --i v v i iv ----- vi i ii vi i v L1ME3_3end#LI 411 TGCATATGTCCACCAAAAGACATGTACAAGAATGTTCATAGCAGCTTTAT 460 chr2qtel1M 737899 CTGTAAT 737905 iii L1ME3_3end#LI 461 TCATAAT 467 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 44.04 CpG sites = 77, Kimura (unadjusted) = 44.48 Transitions / transversions = 1.28 (77/60) Gap_init rate = 0.06 (24 / 427), avg. gap size = 1.67 (40 / 24) 552 33.13 3.38 2.23 chr2qtel1M 737478 737832 (262168) L1ME3C_3end#LINE/L1 22 380 (490) m_b101s551i29 3714 chr2qtel1M 737478 GAACTGCCTTAAATTTATAAGAATGCAAACCATTCTTCAAAT-GATAAAT 737526 v ivi iv vi i v ii ---- - v L1ME3C_3end#L 22 GAACTCCTACAAATCAATAAGAAAACAGACAACCC----AATAGAAAAAT 67 chr2qtel1M 737527 GGTCAAAGGATTTAAACAGAAAATTTTTGGATGAAAAAACAAAAATCATT 737576 v i v i iv ivii v ii ?vi viii L1ME3C_3end#L 68 GGGCAAAAGATATGAACAGGCAATTCACAGAAGAGGAAACNCGAATGGCC 117 chr2qtel1M 737577 TCTAGTCCTATGAAAAAATTCTCTAAAACACTGTTGGTCAGATAATTGTA 737626 vv iv v i v v vvv iv ii iv v i L1ME3C_3end#L 118 AATAAACATATGAAAAGATGCTCAACCTCACTAGTAATCAGGGAAATGCA 167 chr2qtel1M 737627 AATTATAACAAGGCTGAGATACCA---GATATT--TCAGATTGGCTAAGA 737671 v ? viv ---v i ii-- v i L1ME3C_3end#L 168 AATTAAAACNACAATGAGATACCATTTCACACCCATCAGATTGGCAAAAA 217 chr2qtel1M 737672 --TGACAG---GGCAAGATGTA-TGTTGAAGGGAATGGGGAAAAACTGGG 737715 -- i v --- i v ivv - iv i i v iv v i L1ME3C_3end#L 218 TTTAAAAGTCTGACAATACCAAGTGTTGGCGAGGATGTGGAGCAACGGGA 267 chr2qtel1M 737716 ACACTAATACATTGTTGGTGGAGTTGGGAATTGATCCAGTCATTCTAGAG 737765 v v i i iiv vi i v ii i i i L1ME3C_3end#L 268 ACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTACAACCACTTTGGAG 317 chr2qtel1M 737766 AACAATATGGAACTATGCCTGAGGGGCTATCACACTGTGTATACCCTTTG 737815 i v v v - iv viii i i-- viv i i vi L1ME3C_3end#L 318 AGCAATTTGGCAATAT-CTAGTAAAGTTG--AAGATGCGCATACCCTACG 364 chr2qtel1M 737816 ATCCAGCAGTGTCTACT 737832 i i - i L1ME3C_3end#L 365 ACCCAGCAAT-TCCACT 380 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.74 CpG sites = 64, Kimura (unadjusted) = 45.34 Transitions / transversions = 1.25 (64/51) Gap_init rate = 0.04 (14 / 354), avg. gap size = 1.43 (20 / 14) 606 31.72 4.75 0.86 chr2qtel1M 737520 737856 (262144) L1ME4a_3end#LINE/L1 64 413 (458) m_b101s551i31 3714 chr2qtel1M 737520 GATAAATGGTCAAAGGATTTAAACAGAAAATTTTTGGATGAAAAAACAAA 737569 v v iv i v iviii v i i v L1ME4a_3end#L 64 GAAAAATGGGCAAAGGACATGAACAGACAATTCACAAAAGAAGAAATACA 113 chr2qtel1M 737570 AATCATTTCTAGTCCTATGAAAAAATTCTCTAAAACACTGTTGGTCAGAT 737619 viiivv iv v ? vi v vvv iv ii i v L1ME4a_3end#L 114 AATGGCCAATAAACATATGAAAANATGTTCAACCTCACTAGTAATCAAAG 163 chr2qtel1M 737620 AATTGTAAATTATAACAAGGCTGAGATACCA-----GATATTTCAGATTG 737664 v i v viv -----v iv v i L1ME4a_3end#L 164 AAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCTATCAAATTG 213 chr2qtel1M 737665 GCTAAGAT--GACAG---GGCAAGATGTA-TGTTGAAGGGAATGGGGAAA 737708 v --i v --- ii v ivi - iv i ii v ?i L1ME4a_3end#L 214 GCAAAGATTTAAAAGATTGATAATACCCAGTGTTGGCGAGGGTGTGGNGA 263 chr2qtel1M 737709 AACTGGGACACTAATACATTGTTGGTGGAGTTGGGAATTGATCCAGTCAT 737758 v v v v i i iiv vi i v ii v L1ME4a_3end#L 264 AACGGGCACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTACAACCTT 313 chr2qtel1M 737759 TCTAGAGAACAATATGGAACTATGCCTGAGGGGCTATCACACTGTGTATA 737808 i ii v v v iv v iii iv v v v ?i L1ME4a_3end#L 314 TCTGGAGGGCAATTTGGCAATATGTATCAAAAGCCTTAAAAATGTNCATA 363 chr2qtel1M 737809 CCCTTTGATCCAGCAGTGTCTACT-----GAACCTGTATCCCAAAGAGAT 737853 i i i - i ----- -- v i i i L1ME4a_3end#L 364 CCCTTTGACCCAGTAAT-TCCACTTCTAGGAA--TTTATCCTAAGGAAAT 410 chr2qtel1M 737854 GAT 737856 i L1ME4a_3end#L 411 AAT 413 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 42.60 CpG sites = 56, Kimura (unadjusted) = 42.60 Transitions / transversions = 1.12 (56/50) Gap_init rate = 0.02 (8 / 336), avg. gap size = 2.38 (19 / 8) 249 23.75 13.75 0.00 chr2qtel1M 741103 741182 (258818) MIR3#SINE/MIR 115 205 (3) m_b102s601i1 3715 chr2qtel1M 741103 TGACTCTCAGTTTCC-CAATTATAAAATGAGTGGGTTAG-------GATC 741144 ivi - vi i v i ------- MIR3#SINE/MIR 115 TGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATC 164 chr2qtel1M 741145 ACGTAGGTCCCTTCCAG---TGATCATCTGGGAACCTATAA 741182 v vv --- ivv iv vi i MIR3#SINE/MIR 165 TCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTATGA 205 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.73 CpG sites = 9, Kimura (unadjusted) = 28.73 Transitions / transversions = 0.90 (9/10) Gap_init rate = 0.04 (3 / 79), avg. gap size = 3.67 (11 / 3) 268 30.17 6.90 0.00 chr2qtel1M 741283 741398 (258602) C L2b_3end#LINE/L2 (11) 455 332 m_b102s601i2 3716 chr2qtel1M 741283 CAGCAAACTTTTA---AGTGCCTGCTATCAGCCGGGCCCTGAGCTGTGCC 741329 i iv --- i i i vv i ? v iv v C L2b_3end#LINE 455 CAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCG 406 chr2qtel1M 741330 CCAGGAACATATTAGAGA-CAAGG--GACTC--CTCCTGCTCTCGTGGAG 741374 ii i i i vii v - i-- ? --ii i ii C L2b_3end#LINE 405 CTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGGAG 356 chr2qtel1M 741375 GTCACAGACAGCTGGGGCAGGCAG 741398 v v viv v i C L2b_3end#LINE 355 CTCACAGTCTAGTGGGGGAGACAG 332 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.44 CpG sites = 22, Kimura (unadjusted) = 41.13 Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.03 (4 / 115), avg. gap size = 2.00 (8 / 4) 416 28.23 11.91 3.54 chr2qtel1M 741536 741770 (258230) C MIRb#SINE/MIR (0) 268 15 m_b102s601i3 3717 chr2qtel1M 741536 AATACCATACCTAGCATTTATACAGCACCTGTT--GTGACATGCAGTGTG 741583 vi v v v vv i i ii -- v v v C MIRb#SINE/MIR 268 AATAATAGAGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTG 219 chr2qtel1M 741584 T-----GT----CA-GTATTGTCTCATTTTGTCCTCCTGAGAACCCTAGG 741623 i----- i---- - i i vi vii v iv C MIRb#SINE/MIR 218 CTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCG 169 chr2qtel1M 741624 ACTCGGGTGCCATTATTGTGCCCTTCTTACAGATGAAGTCACTGAGGCAG 741673 vvii --- i v v i i vv vv C MIRb#SINE/MIR 168 AGGTAGGT---ATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC 122 chr2qtel1M 741674 ACAGAGGTCTTGTAAGTTG--------------ACTAGCAAGTTGCTGAG 741709 v ivv v --------------i i v v C MIRb#SINE/MIR 121 AGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAG 72 chr2qtel1M 741710 GTGGGATGAACACTCAGGTCTTGCTGA-TTGAAGGTCCTGTTCGTACTTT 741758 vi vviv i vv - iv i i ----- i i C MIRb#SINE/MIR 71 CCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCC-----CGTGCTCT 27 chr2qtel1M 741759 TCTCCA-TGTACC 741770 - - i C MIRb#SINE/MIR 26 T-TCCACTGCACC 15 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.83 CpG sites = 30, Kimura (unadjusted) = 35.84 Transitions / transversions = 0.88 (30/34) Gap_init rate = 0.07 (16 / 234), avg. gap size = 2.31 (37 / 16) 424 27.46 15.03 0.00 chr2qtel1M 741542 741734 (258266) C MIR#SINE/MIR (4) 258 37 m_b102s601i4 3717 chr2qtel1M 741542 ATACCTAGCATTTATACAGCACCTGTT--GTGACATGCAGTGT-----GT 741584 v i vv i i ii -- v v v ----- i C MIR#SINE/MIR 258 ATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGC 209 chr2qtel1M 741585 GT----CA-GTATTGTCTCATTTTGTCCTCCTGAGAACCCTAGGACTCGG 741629 i---- - iv vi vii v v vvii C MIR#SINE/MIR 208 GCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGGTAG 159 chr2qtel1M 741630 GTGCCATTATTGTGCCCTTCTTACAGATGAAGTCACTGAGGCAGACAGAG 741679 i i i v v i i vv v v C MIR#SINE/MIR 158 GTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAG 109 chr2qtel1M 741680 GTCTTGTAAGTTG--------------ACTAGCAAGTTGCTGAGGTGGGA 741715 ivv v --------------i i v v vi C MIR#SINE/MIR 108 GTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGA 59 chr2qtel1M 741716 TGAACACTCAG---GTCTTGCT 741734 vviv i --- v C MIR#SINE/MIR 58 TTCGAACCCAGGCAGTCTGGCT 37 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.38 CpG sites = 24, Kimura (unadjusted) = 34.39 Transitions / transversions = 0.83 (24/29) Gap_init rate = 0.03 (6 / 192), avg. gap size = 4.83 (29 / 6) 252 22.03 11.27 10.49 chr2qtel1M 741644 741785 (258215) C MIR3#SINE/MIR (61) 147 5 m_b102s601i5 3717 chr2qtel1M 741644 CCCT--TCTTACAGATGAAGTCACTGAGGCAGACAGAGGT-------CTT 741684 -- i i vv vv v ------- C MIR3#SINE/MIR 147 CCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTT 98 chr2qtel1M 741685 G--TAAGTTGAC-TAGCAAGTT----GCTGAGGTGGGATGAACACTCAGG 741727 --i v v -i ? ---- v vi iv iv i C MIR3#SINE/MIR 97 GCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGG 48 chr2qtel1M 741728 TCTTGCTGATTGAAGGTCCTGTTCGTACTTTTCTCCATGTACCCTCAGCT 741777 i- i -----i v i i - i -- ---- -- C MIR3#SINE/MIR 47 TCTC-CTGACT-----CCCAGTCCGTGC-TCTCTC--TG----CTCAG-- 13 chr2qtel1M 741778 CTATTCTG 741785 i i C MIR3#SINE/MIR 12 CCACTCTG 5 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 25.68 CpG sites = 16, Kimura (unadjusted) = 26.76 Transitions / transversions = 1.33 (16/12) Gap_init rate = 0.14 (20 / 141), avg. gap size = 1.55 (31 / 20) 182 30.39 5.34 4.55 chr2qtel1M 743033 743163 (256837) MIRc#SINE/MIR 87 218 (50) m_b102s601i6 3718 chr2qtel1M 743033 GTGTGAATTCCAGGCACAGTCACTCAAACCCTCTGAGCT--GGTGACCTC 743080 vi i-i - i v i i--i vv MIRc#SINE/MIR 87 GTGTGACCTT-GGGCA-AGTCACTTAACCTCTCTGAGCCTCAGTTTCCTC 134 chr2qtel1M 743081 AGGTGTACAAGTAGTGAGAACAAAGGTTCTT--TCTGTGTGG-TCCCAGG 743127 vv - i i v v i --- v i --i iv iv- v MIRc#SINE/MIR 135 ATCTGTA-AAATGGGGATAATAA---TACCTGCCCTGCCTACCTCACAGG 180 chr2qtel1M 743128 TTGACTGTGAGAATCTAGTGTATT--TGTGTTTGAAAG 743163 v vii i v i viv -- i v MIRc#SINE/MIR 181 GTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAG 218 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.67 CpG sites = 20, Kimura (unadjusted) = 39.67 Transitions / transversions = 1.11 (20/18) Gap_init rate = 0.08 (10 / 130), avg. gap size = 1.30 (13 / 10) 969 30.60 2.01 2.24 chr2qtel1M 743260 743707 (256293) L1ME4c_3end#LINE/L1 30 476 (354) m_b102s551i0 3719 chr2qtel1M 743260 TCAAATTTATAAGGATGCAAGCCATTCTCCAATTGATAAATGGTCAAAGG 743309 v i viv? v v vv i v v L1ME4c_3end#L 30 TCAAATTGATAAGAAAAANATCAAGACCCCAATAGATAAATGGGCAAAGG 79 chr2qtel1M 743310 ATTTGAACAGATAATTTTCAGATGAAAAAATAAAAATCATTTCTAGTCAT 743359 iv i iv ? v ii v ? vi vvvi iv i L1ME4c_3end#L 80 ACATGAACAGACAATTCACANAAGAGGAAATACAANTAGTAAACAAACAC 129 chr2qtel1M 743360 ATGAAAAAATACTCTAAATCACTATTAGTCACAGAAATGTAAATTAAGAC 743409 i ii v vv i v i v i ii L1ME4c_3end#L 130 ATGGAAAAATGTTCAACCTCGCTAGTAATCAAAGAAATGCAAATTAAAGC 179 chr2qtel1M 743410 ACCTCTGAGGTACCAGATATTACAG--ATTGGCTTAGATGACAGGGAAAG 743457 v vv i -- v iv-- iiv vvi v vvv i L1ME4c_3end#L 180 AACAATGAGATACC--ATTTTACGCCTATTAAATTAGCAAAAATTTAAAA 227 chr2qtel1M 743458 A--TAATGATGTTGAATGATGTTGAAGGGAATGGGGAAAAACTGTGACAC 743505 -- i i iiiv v vi --- i? v vi vv ? L1ME4c_3end#L 228 AATTGATAATACCCAATGCTGGCGA---GGNTGCGGTGAAACTGGTACNC 274 chr2qtel1M 743506 TAATACATTGTTGGTGGAGCTGTGAATTGATCCAGTCATTCTGGAGAACA 743555 v i vi? i i v ii v i i i L1ME4c_3end#L 275 TCATACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGCA 324 chr2qtel1M 743556 ATATGGAACTATGCCTAAAGTGCTATCACACTGTTCCTACCCTTTGATCC 743605 v v v i iv v v i v v v v i L1ME4c_3end#L 325 ATTTGGCAATACGTATCAAGAGCCATAAAAATGTTCATACCCTTTGACCC 374 chr2qtel1M 743606 AGCAGTGTCTCTACTGAACCTTTATCCCAA--ACATTAT---AAAGAAGG 743650 i i vi v v iivv i -- v v --- L1ME4c_3end#L 375 AGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAAGAAGG 424 chr2qtel1M 743651 GGAAAGGCCTTCTACATGGGCAAAAATGATTGTAGCATCCTTTTCTGTAA 743700 ii ----- i vi i i v ii v v v v i i L1ME4c_3end#L 425 AAAAAG-----CTATATGCACGAAGATGTTCATTGCAGCGTTATTTATAA 469 chr2qtel1M 743701 TGGAGAA 743707 i v L1ME4c_3end#L 470 TAGCGAA 476 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.56 CpG sites = 64, Kimura (unadjusted) = 40.45 Transitions / transversions = 0.91 (64/70) Gap_init rate = 0.03 (14 / 447), avg. gap size = 1.36 (19 / 14) 20 0.00 0.00 0.00 chr2qtel1M 747264 747285 (252715) (T)n#Simple_repeat 1 22 (0) m_b102s252i0 3720 chr2qtel1M 747264 TTTTTTTTTTTTTTTTTTTTTT 747285 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTT 22 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 21 3.54 0.00 0.00 chr2qtel1M 748304 748332 (251668) (TTTTG)n#Simple_repeat 1 29 (0) m_b102s252i2 3721 chr2qtel1M 748304 TTTTTTTTTGTTTTGTTTTGTTTTGTTTT 748332 v (TTTTG)n#Simp 1 TTTTGTTTTGTTTTGTTTTGTTTTGTTTT 29 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 17 3.42 6.67 0.00 chr2qtel1M 751937 751966 (248034) (TTTA)n#Simple_repeat 1 32 (0) m_b102s252i3 3722 chr2qtel1M 751937 TTTATTTATTTTTTTATTTA-TT-TTTATTTA 751966 v - - (TTTA)n#Simpl 1 TTTATTTATTTATTTATTTATTTATTTATTTA 32 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.07 (2 / 29), avg. gap size = 1.00 (2 / 2) 1021 29.93 5.43 3.41 chr2qtel1M 752428 752887 (247113) C L1MD1_3end#LINE/L1 (355) 634 166 m_b102s551i1 3723 chr2qtel1M 752428 GGCTCATTTCACTCAGCATCAGTTCATGCAAGTCTCTCCAGGCCTTTCTG 752477 iv v v iiv v ii iiv iiv vi C L1MD1_3end#LI 634 GGCTTTTTTCACTCAGCATAATTCTCTGGAGATTCATCCAGGTTGTTGCG 585 chr2qtel1M 752478 AA-ATCATCCTGTTGGTCATTTCTTACAGAAGAGTAATATTCCATAATAT 752526 vi- viv- v ivi i iv vv i ii C L1MD1_3end#LI 584 TGTATCAATA-GTTCGTTCCTTTTTATTGCTGAGTAGTATTCCATGGTAT 536 chr2qtel1M 752527 TCATATACCACAATTTATCCAAC-----------TGATGGACATCCACTC 752565 vv i i i ii ----------- v iivvi C L1MD1_3end#LI 535 GGATGTACCACAGTTTGTTTAACCATTCACCCGTTGAAGGACATCTGGGT 486 chr2qtel1M 752566 AGTTTCCAGTTTCTAGCCACTACAAAAAGGGCTGCCACAAACATTCGTGC 752615 v i i i i i v ii i i - C L1MD1_3end#LI 485 TGTTTCCAGTTTTTGGCTATTACGAATAAAGCTGCTATAAACATTCGTG- 437 chr2qtel1M 752616 ACATACAGGTCCCTTTC----CCTTCTTTATAATCTCTTTGGGACATAAG 752661 --- iii v v---- v vvv v v i i i v v C L1MD1_3end#LI 436 ---TACAGGTTTTTGTGTGAACATAAGTTTTCATTTCTCTGGGATAAATG 390 chr2qtel1M 752662 CCCAGTAGTAACACTGCTGGATCAAAGGGTA--TGCACAGTTTGATAACT 752709 v ivv i i iv v -- i- ii --- C L1MD1_3end#LI 389 CCCAGGAGTGCAATTGCTGGGTCGTATGGTAGTTGCAT-GTTTAGT---T 344 chr2qtel1M 752710 TTTTGAGCATAGTTCCAAACTACTCTCCAAAATGGTTGGATTCGTTCACA 752759 i v - v v ii i i i i v iivv i C L1MD1_3end#LI 343 TTTTAAGAA-ACTGCCAAACTGTTTTCCAGAGTGGCTGTACCATTTTACA 295 chr2qtel1M 752760 ACTCCACCAACAATGCATCAATGTCCTAGTTTTCCCACATCCCCTCCAAC 752809 vii i i v i vi i ii i i v i C L1MD1_3end#LI 294 TTCCCACCAGCAATGTATGAGTGATCCAGTTTCTCCGCATCCTCGCCAGC 245 chr2qtel1M 752810 A------ATCATCATTATTTTTTCCCATCATCTTAGCCAATC-GACAGGT 752852 ------i ii i ------ i v - i C L1MD1_3end#LI 244 ATTTGGTGTTGTCACTATTTTTT------ATTTTAGCCATTCTGATAGGT 201 chr2qtel1M 752853 ATGTAGTGGTATCTCAGAATTGTCTTAATTTGCAT 752887 i i vvi v i C L1MD1_3end#LI 200 GTGTAGTGATATCTCATTGTGGTTTTAATTTGCAT 166 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.02 CpG sites = 81, Kimura (unadjusted) = 39.56 Transitions / transversions = 1.56 (81/52) Gap_init rate = 0.05 (22 / 459), avg. gap size = 1.86 (41 / 22) 409 28.71 1.98 0.00 chr2qtel1M 753365 753465 (246535) MIRc#SINE/MIR 16 118 (150) m_b102s601i7 3724 chr2qtel1M 753365 CAGTAGGTACAATTCTAGACCTGGAGTCACAAAGAACTGAGTTCAAATTC 753414 i iv v iiv i i vi v i i i i MIRc#SINE/MIR 16 CAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCC 65 chr2qtel1M 753415 AGCCTCAGACATTTACTAGATGTGTGTC--TAGGTAAGTCATTTAATCTT 753462 v v v v i v v -- i i i i i MIRc#SINE/MIR 66 CGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 chr2qtel1M 753463 CCT 753465 i MIRc#SINE/MIR 116 TCT 118 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.81 CpG sites = 18, Kimura (unadjusted) = 37.45 Transitions / transversions = 1.64 (18/11) Gap_init rate = 0.01 (1 / 100), avg. gap size = 2.00 (2 / 1) 255 31.70 3.23 0.79 chr2qtel1M 753631 753754 (246246) C L3#LINE/CR1 (162) 3937 3811 m_b102s601i8 3725 chr2qtel1M 753631 CCCATTCTCCTTTGGGCCAGCTTTCATTGTTGAGCGGTCTTTCCTGACAT 753680 ivi v v i v iiivi ii v i C L3#LINE/CR1 3937 CCCATTCCATTTTTGGACAGCTCTGATTGTTAGAAAGTTCTTCCTTATAT 3888 chr2qtel1M 753681 CAGGCCTAGATCAGTCTC---GTCCCTTCCACTTGAGGCTCCCACCTCTG 753727 iii v i v i --- vv iiivv v i vi C L3#LINE/CR1 3887 TGAGCCGAAATCTGCCTCCCTGTAACTTCCACCCATTGGTCCTAGTTCTG 3838 chr2qtel1M 753728 CCCTC-GGAGGCTCAGCAGGACAAGGCT 753754 - v v - i i v C L3#LINE/CR1 3837 CCCTCTGGAGCCACA-CAGAATAAGTCT 3811 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 42.34 CpG sites = 22, Kimura (unadjusted) = 42.34 Transitions / transversions = 1.29 (22/17) Gap_init rate = 0.02 (3 / 123), avg. gap size = 1.67 (5 / 3) 191 31.80 10.00 5.65 chr2qtel1M 753834 754003 (245997) C L3b_3end#LINE/CR1 (507) 699 523 m_b102s601i9 3726 chr2qtel1M 753834 CAATAATGTAGATGATGTCTAAC-AG----GAGCTCAGAGGGATCATCCC 753878 i v vi ? ?v i i - ---- ivv v ?? v C L3b_3end#LINE 699 CAGTACTCCAGNTGNGGCCTGACCAGCGCAGAGTAGAGCGGGANNATCAC 650 chr2qtel1M 753879 CTGCCCATTCCTGCCT-CAATTCATC-----------CCTCAGATGACAC 753916 v ivv?i i v- i ? v ----------- iv vi i C L3b_3end#LINE 649 CTCCCTTGNTCTGTCGGCGATNCTTCTGTTAATGCAGCCCAAGATCGCAT 600 chr2qtel1M 753917 TAAACTCTTTGACTCCTGCATTCCAATGCCGACTCTCATTAAGCTTGTGG 753966 ivi i i vv i i iv v i vi i i C L3b_3end#LINE 599 TAGCTTTTTTGGCAGCCGCGTCGCACTGCTGACTCATATTGAGCTTGCGG 550 chr2qtel1M 753967 AGGCTCCATTCGAGCCCCAATTCCTTAGTTTTTTTCA 754003 ---- v i vi i v ------i i C L3b_3end#LINE 549 ----TCAACTAAAACCCCCA------GGTCTTTTTCA 523 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.12 CpG sites = 28, Kimura (unadjusted) = 44.84 Transitions / transversions = 1.22 (28/23) Gap_init rate = 0.08 (14 / 169), avg. gap size = 1.93 (27 / 14) 489 28.08 5.82 2.04 chr2qtel1M 754592 754780 (245220) C L3#LINE/CR1 (806) 3293 3098 m_b102s601i10 3725 chr2qtel1M 754592 GCCTGCCAGGATTCTTTATAATCCTGACTCGGTCATCCAAT-TCTT--CT 754638 i ii i? vv i i v ?i- v -- C L3#LINE/CR1 3293 GCCTGTCGAGATCNTTTTGAATCTTGATTCTGTCATCCANCGTATTAGCT 3244 chr2qtel1M 754639 CTTTTCCCCAGCTTTGCTTTGT---CAAATATTGTTGAGTGGGCTTTCTT 754685 v iiii iv ii --- - v i iiv i v C L3#LINE/CR1 3243 ATCCCTCCCAGCTTTGTGTCATCTGCAAAT-TTGATAAGCATGCCTTCTA 3195 chr2qtel1M 754686 TGTCTTCATGCTCAAGCCATTGAC-AAAATATTAAACAGCCCAGGACCAA 754734 --i i i- i i vv i C L3#LINE/CR1 3194 TGTCTTCAT--CCAAGTCATTGATAAAAATGTTGAACAGGACAGGGCCAA 3147 chr2qtel1M 754735 GCACTTAGTCC----ACATCTCTCCCAGAGATCTCTTGGTATGTTGGCAT 754780 v vv i ----i - v iv i i iivvi v i C L3#LINE/CR1 3146 GGACAGAGCCCTGTGGCA-CGCCACTAGAGACCTCCCTCCAGGTTGACAT 3098 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.24 CpG sites = 33, Kimura (unadjusted) = 37.04 Transitions / transversions = 1.74 (33/19) Gap_init rate = 0.05 (9 / 188), avg. gap size = 1.67 (15 / 9) 19 0.00 0.00 0.00 chr2qtel1M 758162 758182 (241818) (AC)n#Simple_repeat 1 21 (0) m_b102s252i5 3727 chr2qtel1M 758162 ACACACACACACACACACACA 758182 (AC)n#Simple_ 1 ACACACACACACACACACACA 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 267 31.35 2.52 0.83 chr2qtel1M 759976 760094 (239906) L1ME3G_3end#LINE/L1 427 547 (377) m_b102s551i2 3728 chr2qtel1M 759976 CATATGGAAAAATGTTTGT-GCAGCTCTTTCTGTAGTGGCATGAAACTGG 760024 i iv ii ii - vi v i i i ivi i L1ME3G_3end#L 427 CATGTACAAGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGG 476 chr2qtel1M 760025 CAAATGAG-TGGATGGCCATCAGT-GGGGAATGGCTGAATAAGTTATGAC 760072 - ii v- ii v i - i i i ii L1ME3G_3end#L 477 -AAACAACCTAAATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGT 525 chr2qtel1M 760073 ATATGAATGTCTTGGAATGTTA 760094 vv iiiv ii L1ME3G_3end#L 526 ATATCCATACTATGGAATACTA 547 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 42.49 CpG sites = 28, Kimura (unadjusted) = 44.16 Transitions / transversions = 3.11 (28/9) Gap_init rate = 0.03 (4 / 118), avg. gap size = 1.00 (4 / 4) 17 18.27 1.82 5.66 chr2qtel1M 760351 760405 (239595) (TTTC)n#Simple_repeat 1 53 (0) m_b102s252i6 3729 chr2qtel1M 760351 TTTCATTCTTTGCTTCATTGTTTGCTTGCATT-TTTCTTTCTTTCTCATT 760399 v vi v v - v v - -- (TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTTT-CTTTCTTTCTTTCTTTCTTTCT--TT 47 chr2qtel1M 760400 TTTTCT 760405 i (TTTC)n#Simpl 48 CTTTCT 53 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.07 (4 / 54), avg. gap size = 1.00 (4 / 4) 1252 31.71 1.11 0.55 chr2qtel1M 760833 761371 (238629) C L1ME4c_3end#LINE/L1 (275) 555 14 m_b102s551i3 3730 chr2qtel1M 760833 ATAATAGTCCATAAGCTTCATATACCATAACTTGTTCAGCCATTCCCCAG 760882 v viiv ?v i i ii i i vi C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chr2qtel1M 760883 TTGATGAGCATCCA--TTCCTTTATCAGTTCTGTGTTACCACAGAAAGAG 760930 v ii ii -- vi i-- i i vi i ii i i v iv C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTGTTTC--CAATTTTTCGCTATTATAAATAACG 458 chr2qtel1M 760931 CTGCTACAAACATCTTTGCACATGTGGGTCCTTGTCCCTTTTTAATGATG 760980 v ii i ii i i v ii viii v v v C L1ME4c_3end#L 457 CTGCAATGAACATCTTCGTGCATATAGCTTTTTCCTTCTTTTGAATTATT 408 chr2qtel1M 760981 GCTTTGGGATAAAGACCCTGTAGAGACACTGGTGGATCCAAGGGTATGCA 761030 v i i vv v v v iv i iv i v v C L1ME4c_3end#L 407 TCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAA 358 chr2qtel1M 761031 CAGTTTGATAGCCCTTTGGACATAGTTCCAAATTACTCTCCACAATGTTT 761080 v v i i viv i v v i i v v v C L1ME4c_3end#L 357 CATTTTTATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTT 308 chr2qtel1M 761081 GGATCATTCCGGAA-GTCCCCAACAATGCATTAGTGTCCCACTTTT-CCA 761128 v i v iiiv ?- i v i i v ? v v i- i C L1ME4c_3end#L 307 GTACCAATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCACCG 258 chr2qtel1M 761129 CATCCCCTCTAATATTTGTCATTATCTTTTCCTGTGATCTTAGCCAATCT 761178 ? i v i ii v vi vv ii vvi i v i i C L1ME4c_3end#L 257 CANCCTCGCCAGCATTGGGTATTATCAATTTTTTAAATTTTTGCTAATTT 208 chr2qtel1M 761179 GAGAGGTGTGAGGTGGTACCTCAGAGGTA-TGTGATTTGCATTTCTATTA 761227 i v i i ii i vv v i- v i v v C L1ME4c_3end#L 207 AATAGGCGTAAAATGGTATCTCATTGTTGCTTTAATTTGCATTTCTTTGA 158 chr2qtel1M 761228 TCAATAGTGATTTAGAGCATTTTTCCATATAACTGTAAATGGTTTTAATT 761277 i v i vv v i i ivi vv ivi? vv C L1ME4c_3end#L 157 TTACTAGCGAGGTTGAACATTTTTCCATGTGTTTGTTTACTANTTGTATT 108 chr2qtel1M 761278 TCCTCATCTGAAAATTGTCTGTTCATATCCTTTGACCATGTATCAAGTAA 761327 v ? vi i v v v v ii C L1ME4c_3end#L 107 TCCTCTTNTGTGAATTGTCTGTTCATGTCCTTTGCCCATTTATCTATTGG 58 chr2qtel1M 761328 GG-AATGACTTGTATTCTTATAAATTTGAAACTGTTCTTTATATA 761371 -vv i? v - v vvv i C L1ME4c_3end#L 57 GGTCTTGATNTTT-TTCTTATCAATTTGAATGAGCTCTTTATATA 14 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.53 CpG sites = 90, Kimura (unadjusted) = 42.82 Transitions / transversions = 1.12 (90/80) Gap_init rate = 0.01 (8 / 538), avg. gap size = 1.12 (9 / 8) 546 28.88 2.47 2.11 chr2qtel1M 761235 761517 (238483) C L1M3_orf2#LINE/L1 (0) 3288 3005 m_b102s551i4 3730 chr2qtel1M 761235 TGATTTAGAGCATTTTTCCATATAACTGTAAATGGTTTTAATTTCCTCAT 761284 v v i i v viiivi vv v i v C L1M3_orf2#LIN 3288 TGATGTTGAGCATCTTTTCATATACCTGTTGGCCATTTGTATGTCTTCTT 3239 chr2qtel1M 761285 CTGAAAATTGTCTGTTCATATCCTTTGACCATGTATCAAGTAAGGAATGA 761334 iv i v i vi v v v ? - vi -- v C L1M3_orf2#LIN 3238 TGGAGAAATGTCTATTCAGGTCCTTTGCCCATTTTTNAA-TCGGG--TTA 3192 chr2qtel1M 761335 CTTGTATTCTT---ATAAATTTGAAACTGTTCTTTATATATCTTAGGAAT 761381 i v i --- vi v v ?vv i i i iv C L1M3_orf2#LIN 3191 TTTGTTTTTTTGCTATTGAGTTGTANGAGTTCCTTATATATTTTGGATAT 3142 chr2qtel1M 761382 GAGACCTTTAACAGATATACTGGCCGTAAAGATTTTTTCCCAGCTTTC-T 761430 v iv i v iv vii i v i -- i - C L1M3_orf2#LIN 3141 TAACCCCTTATCAGATATATGGTTTGCAAATATTTTCTCCCA--TTCCGT 3094 chr2qtel1M 761431 AA-TTCCCTCTTGATCTTGTTT-CTGTTGGTTTTGTTTGTGCAAAAAGTT 761478 i- v i v iii v-i vvi i - i iv C L1M3_orf2#LIN 3093 AGGTTGCCTTTTCACTCTGTTGATTGTTTCCTTTGCT-GTGCAGAAGCTT 3045 chr2qtel1M 761479 TTTAATTTCATGTAATCAAAGTTGTCTA-TTTTGCCTTTG 761517 i v i vv v - i C L1M3_orf2#LIN 3044 TTTAGTTTGATGTAGTCCCACTTGTCTATTTTTGCTTTTG 3005 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.68 CpG sites = 40, Kimura (unadjusted) = 37.26 Transitions / transversions = 1.00 (40/40) Gap_init rate = 0.04 (11 / 282), avg. gap size = 1.18 (13 / 11) 729 32.64 4.29 1.09 chr2qtel1M 761828 762270 (237730) L1ME4c_3end#LINE/L1 22 478 (352) m_b102s551i5 3731 chr2qtel1M 761828 GAATTGACTGAAATTTATAAGAATATAAGCCATTCTCCAATTGATAAATG 761877 ii v i v v v v? v v vv i v L1ME4c_3end#L 22 GAGCTCATTCAAATTGATAAGAAAAANATCAAGACCCCAATAGATAAATG 71 chr2qtel1M 761878 GTCAAAGGATTTGAACAATT--TTCAGTTAA---AAAATAAAAATCATTT 761922 v iv ivi-- vv? ---i v ? vi vv L1ME4c_3end#L 72 GGCAAAGGACATGAACAGACAATTCACANAAGAGGAAATACAANTAGTAA 121 chr2qtel1M 761923 CTAATCCTATGAAAAAATGCCCTAAATCACTATTGCTCAGAGAAATGTAA 761972 vi v vi i ii v vv i v iv i i L1ME4c_3end#L 122 ACAAACACATGGAAAAATGTTCAACCTCGCTAGTAATCAAAGAAATGCAA 171 chr2qtel1M 761973 ATTAAGACAACTCTGAGGTACCCAAGTCTTAC-------AGATTGGCTAA 762015 ii vv i ---i i ------- i i v L1ME4c_3end#L 172 ATTAAAGCAACAATGAGATACC---ATTTTACGCCTATTAAATTAGCAAA 218 chr2qtel1M 762016 GATGACAGGGAAAGATAATGATGAATGTTGAAGGGGATGGGGGAAAACTG 762065 i vvv iii vv iviv i iv i ? v vi L1ME4c_3end#L 219 AATTTAAAAAATTGATAATACCCAATGCTGGCGAGGNTGCGGTGAAACTG 268 chr2qtel1M 762066 GGACCCTAACACAT---TGGTGGAGTTGTGAACTGATCCAATCATTCTGG 762112 v ? v i --- vi? i i i v i v i L1ME4c_3end#L 269 GTACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGG 318 chr2qtel1M 762113 AGAACAATATGGAACTATGCCCAAAGTGCTGTCACAATTTGAATA-CCTT 762161 i i v v v i iviv v ii v v v vv - L1ME4c_3end#L 319 AAAGCAATTTGGCAATACGTATCAAGAGCCATAAAAATGTTCATACCCTT 368 chr2qtel1M 762162 TGA-TCAGCAGTGCCTCTATTGAGCCTGTATCCCAAAGAGAT--TGTAAA 762208 -i i i v v vi i vv v i i i -- vi L1ME4c_3end#L 369 TGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAA 418 chr2qtel1M 762209 GGAGGGAAAAGAACCCACATGTACAGAAATTTTTGGAGCAGCCCTTTCTA 762258 i i -- v i i i ii i v iivv vi v i L1ME4c_3end#L 419 AGAAGGAAA--AAGCTATATGCACGAAGATGTTCATTGCAGCGTTATTTA 466 chr2qtel1M 762259 TAGTGGAGAGAA 762270 i i v i L1ME4c_3end#L 467 TAATAGCGAAAA 478 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 43.21 CpG sites = 73, Kimura (unadjusted) = 44.45 Transitions / transversions = 1.04 (73/70) Gap_init rate = 0.03 (12 / 442), avg. gap size = 2.00 (24 / 12) 741 28.90 5.31 2.00 chr2qtel1M 761863 762201 (237799) L1MA5A_3end#LINE/L1 57 406 (638) m_b102s551i6 3731 chr2qtel1M 761863 TCCAATTGATAAATGGTCAAAGGATTTGAACA---ATTT-TCAGTTAAAA 761908 i ? v v v i --- - ivvi i L1MA5A_3end#L 57 TCCGATTNAAAAATGGGCAAATGATCTGAACAGACATTTCTCAAAAGAAG 106 chr2qtel1M 761909 A-ATAAAAATCATTTCTAATCCTATGAAAAAATGCCCTAAATCACTATTG 761957 - v viiivvi viv i v v v v L1MA5A_3end#L 107 ACATACAAATGGCCAACAAATATATGAAAAAATGCTCAACATCACTAATC 156 chr2qtel1M 761958 CTCAGAGAAATGTAAATTAAGACAACTCTGAGGTACCCAAGTCTTAC--- 762004 v i i i i v vv i ---i i --- L1MA5A_3end#L 157 ATCAGGGAAATGCAAATCAAAACCACAATGAGGTATC---ATCTCACCCC 203 chr2qtel1M 762005 ----AGATTGGCTAAGATGACAGGGAAAGATAATGATGAATGTTGAAGGG 762050 ---- iv vv v v ii v i v i ii i iv i L1MA5A_3end#L 204 AGTTAGGATGGCTATTATCAAAAAGACAAAAAATAACAAATGCTGGCGAG 253 chr2qtel1M 762051 GATGGGGGAAAACTGGGACCCTAACACA---TTGGTGGAGTTGTGAACTG 762097 v ii vv i i v i --- iiv i i L1MA5A_3end#L 254 GATGCGGAGAAAAGGGAACTCTTATACACTGTTGGTGGGAATGTAAACTA 303 chr2qtel1M 762098 ATCCAATCATTCTGGAGAACAATATGGAACTATGCCCAAAGTGCTGTCAC 762147 i v ii i v i iv - v i ivi --- L1MA5A_3end#L 304 GTACAGCCACTATGGAGAACAGTATGGAGGT-TCCTCAAAAAACT---AC 349 chr2qtel1M 762148 AATTTGAA-TACC-TTTGAT-CAGCAGTGCCTCTATTGAGCCTGTATCCC 762194 v v - - v - i v v i i v v v L1MA5A_3end#L 350 AAATAGAACTACCATATGATCCAGCAATCCCACTACTGGGCATTTATCCA 399 chr2qtel1M 762195 AAAGAGA 762201 i i L1MA5A_3end#L 400 AAGGAAA 406 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.81 CpG sites = 51, Kimura (unadjusted) = 37.29 Transitions / transversions = 1.13 (51/45) Gap_init rate = 0.05 (16 / 338), avg. gap size = 1.56 (25 / 16) 12 10.03 0.00 0.00 chr2qtel1M 764352 764373 (235627) (TCTT)n#Simple_repeat 1 22 (0) m_b102s252i7 3732 chr2qtel1M 764352 TCTTTCTTTTTTTTTTTCTTTC 764373 i i (TCTT)n#Simpl 1 TCTTTCTTTCTTTCTTTCTTTC 22 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 15 10.01 9.38 0.00 chr2qtel1M 764651 764682 (235318) (TC)n#Simple_repeat 1 35 (0) m_b102s252i8 3733 chr2qtel1M 764651 TCTCTC-CTC-CTCACTCTCTCTCT-TCCCTATCT 764682 - - v - i v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 35 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.10 (3 / 31), avg. gap size = 1.00 (3 / 3) 12 19.41 0.00 5.41 chr2qtel1M 765656 765694 (234306) (TGGTTT)n#Simple_repeat 1 37 (0) m_b102s252i9 3734 chr2qtel1M 765656 TGGGTTTGGTTTTTGGATCCTGGATTTGAGTTTGGTTTT 765694 v - - ii v iv (TGGTTT)n#Sim 1 TGGTTTTGG-TTTTGG-TTTTGGTTTTGGTTTTGGTTTT 37 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2) 13 15.37 5.56 0.00 chr2qtel1M 765660 765695 (234305) (TTTGGAT)n#Simple_repeat 1 38 (0) m_b102s252i10 3734 chr2qtel1M 765660 TTTGGTTTTTGGATCCTGGA-TTT-GAGTTTGGTTTTT 765695 v ii - - v v (TTTGGAT)n#Si 1 TTTGGATTTTGGATTTTGGATTTTGGATTTTGGATTTT 38 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 30 0.00 0.00 5.56 chr2qtel1M 766901 766938 (233062) (ATTAA)n#Simple_repeat 1 36 (0) c_b102s251i0 3735 chr2qtel1M 766901 ATTAAATTAAACTTAAATTAAATTAAATTAAAATTAAA 766938 - - (ATTAA)n#Simp 1 ATTAAATTAAA-TTAAATTAAATTAAATT-AAATTAAA 36 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 303 27.65 7.89 1.65 chr2qtel1M 767043 767156 (232844) MIR3#SINE/MIR 81 201 (7) m_b102s601i11 3736 chr2qtel1M 767043 GCCATG-AACTTTGAGGAAATAAATCC-CTTCTCTG--CTTCAGTTTCCT 767088 ii -i i i v i v v i - i -- i MIR3#SINE/MIR 81 GCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCT 130 chr2qtel1M 767089 AATTTGCAG---GAGGGTTGGTTGAATTCT-TGAATTCTAAAGTGACTTT 767134 v i i i--- -- i i vv- vi i vv i MIR3#SINE/MIR 131 CATCTGTAAAATGAGGG--GGTTGGACTAGATGATCTCTAAGGTCCCTTC 178 chr2qtel1M 767135 CAGCTCT-ACATCTCATGACTTT 767156 - iii i i MIR3#SINE/MIR 179 CAGCTCTGACATTCTATGATTCT 201 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.43 CpG sites = 22, Kimura (unadjusted) = 36.43 Transitions / transversions = 2.44 (22/9) Gap_init rate = 0.07 (8 / 113), avg. gap size = 1.38 (11 / 8) 274 25.00 1.47 0.00 chr2qtel1M 768198 768265 (231735) MIR3#SINE/MIR 111 179 (29) m_b102s601i12 3737 chr2qtel1M 768198 TCACTGAATCTCAGTTTCC-CATTTATAAAATGAGTGGGAGGCACTCCAT 768246 v iii - i i v vv v vv MIR3#SINE/MIR 111 TCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGAT 160 chr2qtel1M 768247 GGCCTTGTAGGTCCCTTCC 768265 ii ivv MIR3#SINE/MIR 161 GATCTCTAAGGTCCCTTCC 179 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.60 CpG sites = 8, Kimura (unadjusted) = 30.60 Transitions / transversions = 0.89 (8/9) Gap_init rate = 0.01 (1 / 67), avg. gap size = 1.00 (1 / 1) 205 26.78 12.95 3.29 chr2qtel1M 768388 768526 (231474) C L2a_3end#LINE/L2 (10) 507 356 m_b102s601i14 3738 chr2qtel1M 768388 TCAGCAAATTTTTA---AGTGCCTGCTATCAGCCAGGCCCTG-----GGC 768429 i v --- i i vv v ----- C L2a_3end#LINE 507 TCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGC 458 chr2qtel1M 768430 TGCTC----CCCAGCAATATA-AAGAGAGACAAGGGACTTCCCCTGCTTT 768474 - v----iv i iv - i v ii ----i ii C L2a_3end#LINE 457 -GCTGGGGATACAGCAGTGAACAAAACAGACAAAAG----TCCCTGCCCT 413 chr2qtel1M 768475 CCTGGAGGTCACAGAC-AGCTGGGG----CAGGCAGTACACCAGTAAGTC 768519 v v i vv - iv ---- i i v v i i v C L2a_3end#LINE 412 CATGGAGCTTACATTCTAGTGGGGGGAGACAGACAATAAACAAATAAATA 363 chr2qtel1M 768520 TGTAGAA 768526 v i C L2a_3end#LINE 362 AGTAAAA 356 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.61 CpG sites = 19, Kimura (unadjusted) = 33.74 Transitions / transversions = 1.12 (19/17) Gap_init rate = 0.08 (11 / 138), avg. gap size = 2.09 (23 / 11) 281 31.36 5.93 0.00 chr2qtel1M 768388 768505 (231495) C L2b_3end#LINE/L2 (10) 456 332 m_b102s601i13 3738 chr2qtel1M 768388 TCAGCAAATTTTTA---AGTGCCTGCTATCAGCCAGGCCCTGGGCTGCTC 768434 i v --- i i i vv ? v ivv C L2b_3end#LINE 456 TCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGC 407 chr2qtel1M 768435 CCCAGCAATATAAAGAGAGACAAGG--GACTT--CCCCTGCTTTCCTGGA 768480 v ii vi i iv ivii i-- ?i--i ii vi C L2b_3end#LINE 406 GCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGGA 357 chr2qtel1M 768481 GGTCACAGACAGCTGGGGCAGGCAG 768505 v v viv v i C L2b_3end#LINE 356 GCTCACAGTCTAGTGGGGGAGACAG 332 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.28 CpG sites = 21, Kimura (unadjusted) = 42.73 Transitions / transversions = 1.31 (21/16) Gap_init rate = 0.03 (3 / 117), avg. gap size = 2.33 (7 / 3) 437 27.02 15.98 2.01 chr2qtel1M 768643 768861 (231139) C MIRb#SINE/MIR (0) 268 20 m_b102s601i15 3739 chr2qtel1M 768643 AATACCATACCTAGCATTTATACAGCACCTGCT--GTGACACGCAGTGTG 768690 vi v v v vv i i i -- v v v C MIRb#SINE/MIR 268 AATAATAGAGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTG 219 chr2qtel1M 768691 TCA------------GTATTGTCTCATTTTATCCTCATGAGAACCCTAGG 768728 ii ------------ i i v ii v iv C MIRb#SINE/MIR 218 CTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCG 169 chr2qtel1M 768729 ACTCGGGTGCCATTATTGTGCCCTTCTTATAGATAAAGTCACTGAGGCAG 768778 vvii --- i v v i i i i vv vv C MIRb#SINE/MIR 168 AGGTAGGT---ATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC 122 chr2qtel1M 768779 ACAGAGGT-------CTTGT---AAGTTGCGTAGC----AGATTGCTGAG 768814 v ------- i--- i ii ii ---- ii v v C MIRb#SINE/MIR 121 AGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAG 72 chr2qtel1M 768815 GTGGGAT--GAACGCTCAGGTCTTGCTGA-TTCAAGGCC----CTCTTCA 768857 vi -- --i vv - i i ---- iv C MIRb#SINE/MIR 71 CCGGGATTCGAAC--CCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTC 24 chr2qtel1M 768858 CACT 768861 C MIRb#SINE/MIR 23 CACT 20 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.73 CpG sites = 31, Kimura (unadjusted) = 34.15 Transitions / transversions = 1.15 (31/27) Gap_init rate = 0.06 (13 / 218), avg. gap size = 3.08 (40 / 13) 15 5.56 0.00 0.00 chr2qtel1M 769121 769139 (230861) (T)n#Simple_repeat 1 19 (0) m_b102s252i11 3740 chr2qtel1M 769121 TTTTCTTTTTTTTTTTTTT 769139 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 15 13.56 0.00 11.11 chr2qtel1M 770199 770248 (229752) (AAAGTG)n#Simple_repeat 1 45 (0) m_b102s252i12 3741 chr2qtel1M 770199 AAATTGAAAGTGATAAGTTGAAAGTGCAGACAATGAATGGGAAAGGGAAA 770248 v - - - - - i v v v (AAAGTG)n#Sim 1 AAAGTGAAAGTGA-AAG-TGAAAGTG-A-A-AGTGAAAGTGAAAGTGAAA 45 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.10 (5 / 49), avg. gap size = 1.00 (5 / 5) 513 22.01 0.00 6.14 chr2qtel1M 770464 770584 (229416) MIRc#SINE/MIR 2 115 (153) m_b102s601i16 3742 chr2qtel1M 770464 GAAGCATAGTGGTGCAGTAGATAGAGCACCAGCTGTGAAGTCAGGAGTAC 770513 i vv i v ii viv i iv MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr2qtel1M 770514 CTGAGTTCAAATCAGGTCTCAGACACTTAACACTTCCTAGATGTGTGACC 770563 i i i vv v v v ------- v MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTGACC 94 chr2qtel1M 770564 CTGGGCAAGTCACTTACCCCC 770584 i v i MIRc#SINE/MIR 95 TTGGGCAAGTCACTTAACCTC 115 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 24.94 CpG sites = 12, Kimura (unadjusted) = 26.09 Transitions / transversions = 0.92 (12/13) Gap_init rate = 0.06 (7 / 120), avg. gap size = 1.00 (7 / 7) 16 16.12 0.00 0.00 chr2qtel1M 770598 770625 (229375) (A)n#Simple_repeat 1 28 (0) m_b102s252i13 3743 chr2qtel1M 770598 AAAAAAAATAATAAAAAAATAAAATAAA 770625 v v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA 28 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 452 30.40 8.04 4.12 chr2qtel1M 770700 771097 (228903) L1ME4c_3end#LINE/L1 33 445 (385) m_b102s551i7 3744 chr2qtel1M 770700 AATTTATAAGAATACAACCCAT-CTCTAATTCACAAATGGTCATAGGATT 770748 v v v? i v v- i i vv i v v iv L1ME4c_3end#L 33 AATTGATAAGAAAAANATCAAGACCCCAATAGATAAATGGGCAAAGGACA 82 chr2qtel1M 770749 TGAACA----ATTT---TAAGATGAAAAATAA-----AAACCACTTCTAG 770786 ---- i---? v v i ----- ------- i L1ME4c_3end#L 83 TGAACAGACAATTCACANAAGAGGAAATACAANTAGTAAAC-------AA 125 chr2qtel1M 770787 TCCTATGAAAAAATGTTTTAAATCACTATTGGTCAGAGAAATGTGAATTG 770836 v vi i iv vv i v ii i ii i L1ME4c_3end#L 126 ACACATGGAAAAATGTTCAACCTCGCTAGTAATCAAAGAAATGCAAATTA 175 chr2qtel1M 770837 AGACAATTCTGAGTTACCATTGTACATCTCT--GATTGGCTAAGA--CAA 770882 ii ivv v v ii v --i i v i --i L1ME4c_3end#L 176 AAGCAACAATGAGATACCATTTTACGCCTATTAAATTAGCAAAAATTTAA 225 chr2qtel1M 770883 CAGGAAAA--GATAATGATGAATGTTGGATGGGATGGG--AAAATTGGGA 770928 ---- -- iviv i vvi ? v --i i v L1ME4c_3end#L 226 ----AAAATTGATAATACCCAATGCTGGCGAGGNTGCGGTGAAACTGGTA 271 chr2qtel1M 770929 GACTAATACATTGTT--TGG-GTTGTGAACTAATCTAGTCAATTTGGAGA 770975 v? v i -- -i? i i ii vi ii vv i L1ME4c_3end#L 272 CNCTCATACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAAA 321 chr2qtel1M 770976 AAAATATGGAACTAAGCCCAAAAGGCTGTCATCTTGTGTATAGCTTCTAA 771025 iv v v v v iviv ii ii v vvv vi v i i i L1ME4c_3end#L 322 GCAATTTGGCAATACGTATCAAGAGCCATAAAAATGTTCATACCCTTTGA 371 chr2qtel1M 771026 TCCAGCTGTGTCTACTAAATCTG------TATCCTAAAGAGATGAT--AA 771067 i ivi - i --- ------ i i i -- L1ME4c_3end#L 372 CCCAGTAAT-TCCACT---TCTGGGAATTTATCCTAAGGAAATAATTCAA 417 chr2qtel1M 771068 AGGATAGAAAAGGAGCTACATGTATGAAGA 771097 i vi -- i i i L1ME4c_3end#L 418 AAGAAGGAAAA--AGCTATATGCACGAAGA 445 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.44 CpG sites = 66, Kimura (unadjusted) = 40.82 Transitions / transversions = 1.32 (66/50) Gap_init rate = 0.07 (29 / 397), avg. gap size = 1.69 (49 / 29) 21 16.12 0.00 0.00 chr2qtel1M 772797 772831 (227169) (T)n#Simple_repeat 1 35 (0) m_b102s252i14 3745 chr2qtel1M 772797 TTTTTTTTTTTTTTTTTAATTTATTTATTTTTATT 772831 vv v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 35 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 1069 30.57 3.83 6.19 chr2qtel1M 772952 773760 (226240) C HERVK14C#LTR/ERVK (3799) 3635 2845 m_b102s701i0 3746 chr2qtel1M 772952 ATATCTCCTATCAATTTCTGAAAGTGATTTAAAGTGTTTAGCTTCTCTGT 773001 i vi i i v v i vvvv v C HERVK14C#LTR/ 3635 ATATCCCCTAATAATTTTTGAAAATCATTTAAAGTTTTCAGAGAGTCTTT 3586 chr2qtel1M 773002 TC----TTAAAGCTTTTGTACTGTGAGTACCTTAGCATATACTT-CATAT 773046 ---- i v ?iviv i v i i vv v iv i - - C HERVK14C#LTR/ 3585 TCGAATTTGAACCTTTTGNGGCTTAATTGCCCTTTCCTGAACCTGCAT-T 3537 chr2qtel1M 773047 CCTAAATATTGAAAAGGAACATGTCTTTGAATTTTTTCTGTGGCTATGTG 773096 i i ii v?iv v ? v? v? C HERVK14C#LTR/ 3536 CCCAAATATTGGAAAGGAGTAGNCGTTTGAATTTTATCNGGNGCTATGAN 3487 chr2qtel1M 773097 CAATTTGTAGTTCCTTACTGTTTCTATGGTCCTTTGTAGACATGCTT--- 773143 iiivv ivvi? i ii --------- i i ii vv --- C HERVK14C#LTR/ 3486 CAATCCAGCGTCGGCNACCGCCT---------TCTGTAAATGTGAATAAC 3446 chr2qtel1M 773144 -CTA---ACGTTTG-CTC----CTCAGGTGCACACCCCAAGATATCATCC 773184 - i--- v v - ----i i vi ?--- v i C HERVK14C#LTR/ 3445 ACTGGATAAGTTGGTCTCGAGTTTCGGCCGCACAN---AATATGTCATCC 3399 chr2qtel1M 773185 ATGTAATGTAATAACATAACTTTTGGAGTACATGTAATGTAACAACATAA 773234 i - i i ?v--------------- v iiv vv v C HERVK14C#LTR/ 3398 ATATAATG-AATGATATANG---------------AATCTGGAAACTGAT 3365 chr2qtel1M 773235 CTTTTACTGGAGTAAGAGCAGCAGCCACATACATTAGGCACATTGTAGGG 773284 i ? v vvv v vv?vv ? vi v i v ? ? i C HERVK14C#LTR/ 3364 CTCTNACAGGTTGAATAGCCTNCCCCACANAAGTTTGACAAATNGTNGGA 3315 chr2qtel1M 773285 CTATTTTTCATTCTCTGTGGCAAAACTGTCCATTCATGTCC--CTTCTAT 773332 ivv v i i ? v v v i? i-- v ?-- C HERVK14C#LTR/ 3314 CTATTCAACATGCCCTGCGGCAANACTTTCCAATGATANCTGGCTGCN-- 3267 chr2qtel1M 773333 AGGGTTCAGCTAA--GTTAACACTGGACACTGAAAAGGCAAATCTTTTCA 773380 -- -- vi-- v i vii iv iv v i i iv C HERVK14C#LTR/ 3266 --GGTTC--CTTGTTGTTCATAGCAGGAATAGTAAAAGCAAATTTTTCAA 3221 chr2qtel1M 773381 TATCCTTCTTATCTAGAGGGATAGAATAGAAACAATCCTTAATATCTATA 773430 v ?vv ivv i v v i i v v C HERVK14C#LTR/ 3220 AATCNGGCTCTGCTAGAGGAATAGTAAAGAAGCAGTCCTTCAAATCTATA 3171 chr2qtel1M 773431 GCCCAAAATTGCCATTCTCTAGGCAACTGAATAGGAGACAGAAGTCCAGG 773480 i ivvv ?v v v v vviiii i ?i v i v C HERVK14C#LTR/ 3170 ACTATTAANGGCCAGTCTCTAGGAATCATGGCGGGGGANGGCAGCCCTGG 3121 chr2qtel1M 773481 CTGAAAAGTTCCCATAATTTCCATTTGTTCATTTACTTTTCTCAAATCAG 773530 v i? ii ?iv v? vvv v v vvi vi i i C HERVK14C#LTR/ 3120 CTGCAGNGCCCCCATNGGTTGNATGACTGCATTGACGGCTCGTAAGTCGG 3071 chr2qtel1M 773531 TCAATATCCTCCATTTTTCAGATTTCTTTCTTACAACAAATACTGGGGAA 773580 i ii ? v i vi i i ii ? iv i ? C HERVK14C#LTR/ 3070 TTAGCATNCGCCATCTGCCGGATTTTTTCTTNATTACAAACACTGGNGAA 3021 chr2qtel1M 773581 TTCCAAGACTTATAGAA------GGTTATAAGT-TCCTTGGTCAAGTTGC 773623 ? i----- ------ i v? v - v? v i i C HERVK14C#LTR/ 3020 TTCCANGG-----AGAAAATGTGGGCTCNATGTGTCCTTTNTCTAATTGT 2976 chr2qtel1M 773624 TCCTGTAGTATCTCTAATAAGGCCTGAATTTTATCGCTACCCAACGGCCA 773673 i vv v vi ivi ivv v v viv v?? i C HERVK14C#LTR/ 2975 TCTTTGACTAATTCCTGTAAGGCCCCCAGTTTTTCCTGAGNNAGCGGCCA 2926 chr2qtel1M 773674 CTGTTCTATCCACACTGGTGTATCAGTTTTCCATTGGATAGGAACAGGTG 773723 ? ? i v ? ?v v vi i? vv vi i -- C HERVK14C#LTR/ 2925 CTGNTCNACCCAAACNGGNTTTTGGGTCNTCCATTTTAAGGGAATAGG-- 2878 chr2qtel1M 773724 AAAGTATTGGCAGGCCTTCAACA---GCCCTGCCTAAAAA 773760 -----? iv v -- --- viv C HERVK14C#LTR/ 2877 -----NTCTGGAGGC--TCAACAGTGGCCGCCCCTAAAAA 2845 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.10 CpG sites = 108, Kimura (unadjusted) = 42.19 Transitions / transversions = 0.87 (108/124) Gap_init rate = 0.08 (61 / 808), avg. gap size = 1.31 (80 / 61) 16 0.00 0.00 0.00 chr2qtel1M 776600 776617 (223383) (A)n#Simple_repeat 1 18 (0) m_b102s252i15 3747 chr2qtel1M 776600 AAAAAAAAAAAAAAAAAA 776617 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAA 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 13 18.09 8.33 3.17 chr2qtel1M 776805 776864 (223136) (AAACAG)n#Simple_repeat 1 63 (0) m_b102s252i16 3748 chr2qtel1M 776805 AAACAG-TA-AGAAACAGAAAAACAGAAAAAG-AATACAAA-AGAAATTA 776850 -v - -- v - i v - ivi (AAACAG)n#Sim 1 AAACAGAAACAGAAACAG--AAACAGAAACAGAAACAGAAACAGAAACAG 48 chr2qtel1M 776851 AAGCA-AAACAAAAA 776864 i - i (AAACAG)n#Sim 49 AAACAGAAACAGAAA 63 Matrix = Unknown Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.12 (7 / 59), avg. gap size = 1.00 (7 / 7) 12 27.27 0.00 5.45 chr2qtel1M 777683 777740 (222260) (GAAAAT)n#Simple_repeat 1 55 (0) m_b103s252i2 3749 chr2qtel1M 777683 GAAAAAAAAATTTATAAGGAAAACAAAAATGCAAACATCAACAGAAATAA 777732 vi v v v v ii - - v v vi - (GAAAAT)n#Sim 1 GAAAATGAAAATGAAAATGAAAATGAAAATG-AAA-ATGAAAATGAA-AA 47 chr2qtel1M 777733 TGAAAATG 777740 (GAAAAT)n#Sim 48 TGAAAATG 55 Matrix = Unknown Transitions / transversions = 0.50 (4/8) Gap_init rate = 0.05 (3 / 57), avg. gap size = 1.00 (3 / 3) 778 27.86 1.43 5.65 chr2qtel1M 777903 778252 (221748) C L1ME3G_3end#LINE/L1 (518) 406 71 m_b103s551i0 3750 chr2qtel1M 777903 AATATCTCATTGGGATATAAGCCCAGTAGAAACACTGCTGGATCCAAGGG 777952 i i v? i v v? ? v viiv i i v C L1ME3G_3end#L 406 AGTATTTCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGG 357 chr2qtel1M 777953 TATACACAGTTTGATAACATTTTGA-ACATAGTTCCAAATTGCTCTCCAG 778001 i i v i ---- i - v v v i i C L1ME3G_3end#L 356 TATGCGCATTTTAA----ATTTTAATAGATACTGCCAAATTGCCCTCCAA 311 chr2qtel1M 778002 AATGGCTGGCTCTGTTCACAACTCCACCAACAAAATATCAGTCTTCATCA 778051 ? vvi vi i vii i ivi v --------- C L1ME3G_3end#L 310 AANGGCTGTACCAATTTACACTCCCACCAGCAGTGTATGAG--------- 270 chr2qtel1M 778052 ACAAAATACCAGTTTTCTCACATCCCCTC-CCAATATTCGTCATC-TCGT 778099 ---- i v i i -- - i i ? vi i- iv C L1ME3G_3end#L 269 ----AGTACCCGTTTCCCCACA--CCCTCGCCAACACTNGATATTATCAA 226 chr2qtel1M 778100 CCTGCCA--TTTTAGCCAATCTAAGAGGTGTATAGTGGTACCTCAGAGTT 778147 ? vii -- v i vi v v i i vv C L1ME3G_3end#L 225 NCTTTTAAATTTTTGCCAATCTGATGGGTGAAAAATGGTATCTCATTGTT 176 chr2qtel1M 778148 ATGTTAATTTGCATTTTTCTGATCAATAGTGGTTTAGAGCACCTTCTCAT 778197 i v ii i v ivv v i i C L1ME3G_3end#L 175 GTTTTAATTTGCATTTCCCTGATTACTAGTGAGGTTGAGCATCTTTTCAT 126 chr2qtel1M 778198 ATGATTAGAAATAATTTAAATGTCTTTATCTGAAAACTGTCTATTCATAT 778247 v vviiiv iv v i iv vi i i i C L1ME3G_3end#L 125 ATGTTTATTGGCCATTTGTATTTCCTCTTCTGTGAATTGCCTGTTCATAT 76 chr2qtel1M 778248 CCTTT 778252 C L1ME3G_3end#L 75 CCTTT 71 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.84 CpG sites = 52, Kimura (unadjusted) = 36.33 Transitions / transversions = 1.30 (52/40) Gap_init rate = 0.07 (23 / 349), avg. gap size = 1.04 (24 / 23) 1227 26.41 1.86 1.44 chr2qtel1M 778521 779004 (220996) C L1M5_orf2#LINE/L1 (1231) 2063 1578 m_b103s551i1 3750 chr2qtel1M 778521 ATTCCTTTAATCTCTTTTTATTTTCTTATTGATAAAGCTAACATTTCTAC 778570 v v i v vi vvvvi iv ii i v C L1M5_orf2#LIN 2063 ATGCCTTTTATTTCTTTTTCTTGCCTTATTGCACTGGCTAGGACCTCCAG 2014 chr2qtel1M 778571 CACAATATTGAATAGTAATGGTGATAGTGGCCAGCCTTGTTTCATTCCTG 778620 i i v i ? i v v i ii i C L1M5_orf2#LIN 2013 TACAATGTTGAATAGAAGTGGTGANAGCGGACATCCTTGTCTTGTTCCCG 1964 chr2qtel1M 778621 ATCCCAATAAGATCAGGATTGA-TCTGTCCCTATTACATATGATGCTTGC 778669 ii ivii -v v? v - ? v v i vi i ? C L1M5_orf2#LIN 1963 ATCTTAGGGGGA-AAGCNTTCAGTNTTTCACCATTAAGTATGATGTTNGC 1915 chr2qtel1M 778670 TGATGGTTTTAAATAGATGCTACTCGTCATTTTAAGGAAAAGTCCATTTA 778719 vv vvi ivi ii vv i ivvi v i C L1M5_orf2#LIN 1914 TGTAGGTTTTTCGTAGATGCCCTTTATCAGGTTGAGGAAGTTCCCTTCTA 1865 chr2qtel1M 778720 TTCCTA-TACTCTGTAGTGTTTTTTAATAGGAATGGGTTTTGGATTTTAT 778768 - viv - v - vi v v i i C L1M5_orf2#LIN 1864 TTCCTAGTTTGCTG-AGAG-TTTTTATCATGAATGGGTGTTGAATTTTGT 1817 chr2qtel1M 778769 CAAATGCTTTTTTGACATCTATTGAGATAATCACACGATTTTT---GTTA 778815 ivi i i i ---v v C L1M5_orf2#LIN 1816 CAAATGCTTTTTCTGCATCTATTGAGATGATCATATGATTTTTCTCCTTT 1767 chr2qtel1M 778816 GTTTGGTTACTGATATAGTTGATTATGCTGATAG-TTT---AATATTGAA 778861 i iv --- i vi iii v - --- i i C L1M5_orf2#LIN 1766 ATTCTGTTA---ATATGGTGAATTACATTGATTGATTTTCGAATGTTAAA 1720 chr2qtel1M 778862 CCAGCCCTGCATCACTGGTATAAATCCTTCTTAGTCATAGTGTGTTATTC 778911 i i iv v i iv i ii i i C L1M5_orf2#LIN 1719 CCAACCTTGCATTCCTGGGATAAACCCCACTTGGTCATGATGTATTATCC 1670 chr2qtel1M 778912 TAGGCATGGCTTTTTGTAATCTCTTTGCTAATATTTTATTTAAGATTTTT 778961 vvvi ivv vi v v vv i ? i - C L1M5_orf2#LIN 1669 TTTTTATATATTGCTGGATTCGATTTGCTAATATTTTGTTNAGGA-TTTT 1621 chr2qtel1M 778962 TTCATCAATATTCATTAGGGAAATTGGTCTGTAATTTTCTGTT 779004 v v i v v v C L1M5_orf2#LIN 1620 TGCATCTATGTTCATGAGGGATATTGGTCTGTAATTTTCTTTT 1578 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 32.49 CpG sites = 66, Kimura (unadjusted) = 33.44 Transitions / transversions = 1.10 (66/60) Gap_init rate = 0.02 (12 / 483), avg. gap size = 1.33 (16 / 12) 875 30.53 2.63 2.79 chr2qtel1M 779488 780134 (219866) C L1M5_orf2#LINE/L1 (1702) 1592 947 m_b103s551i2 3750 chr2qtel1M 779488 CTACAATTTTCTTTTTCTGT----TTTTATCCTACCCAGTTTAACTATCA 779533 ii ii ---- i ---- ii ?i viv C L1M5_orf2#LIN 1592 CTGTAATTTTCTTTTCTTGTAATGTCTT----TGTCNGGTTTTGGTATCA 1547 chr2qtel1M 779534 GCACCATATCTGTATCATAAAAGGAATTTGGTAGGATTCCTTCTTTCTCT 779583 vii? iiiv iv v i v v vi i i C L1M5_orf2#LIN 1546 GGGTNATGCTGGCCTCATAAAATGAGTTGGGAAGTGTTCCCTCTTTTTCT 1497 chr2qtel1M 779584 ATTTTTTTTTCATATAGTTTATATAGTATTGGAATCAATTGTTCTTTGAA 779633 i v---iv v i i iv v i v v i i C L1M5_orf2#LIN 1496 ATTTTCTG---GAAGAGTTTGTGTAAGATTGGTATTATTTCTTCCTTAAA 1450 chr2qtel1M 779634 TGTTTGGTAGAATTCACATGTAAATCCATCTGGCCCTGGAGATTTTTTCT 779683 vv i v v v i iv C L1M5_orf2#LIN 1449 TGTTTGGTAGAATTCACCAGTGAAGCCATCTGGGCCTGGAGTTTTCTTTG 1400 chr2qtel1M 779684 TAGGGAGTTCCTTAATAGCTTGTTCTACTTCTTTTTCTAAAATTAGGCTG 779733 i i v ii vi vvi v i vvivi v vi i C L1M5_orf2#LIN 1399 TGGGAAGGTTTTTAATTACAAATTCAATTTCTTTAATAGATATAGGGCTA 1350 chr2qtel1M 779734 TTTAAATAATTTATTTCCTCTTCTGTTAACCGGGGCAATCTATATTTTTG 779783 i i vv i i v? i iiivv i ?i i i v C L1M5_orf2#LIN 1349 TTCAGATTTTCTATTTCTTCTTGNGTCAGTTTTGGTAANTTGTGTTTTTC 1300 chr2qtel1M 779784 AAGGTATTCCTCCATTTTATTTAGATTATCAAATTTATTGGTGTATATTT 779833 v iv i i ii ? ii v v C L1M5_orf2#LIN 1299 AAGGAATTTGTCCATTTCATCTAAGTTNTCAAATTTATTGGCATAAAGTT 1250 chr2qtel1M 779834 GGGCAAAGTAACTCCTAATTATTGCTCTAATTTCCTCT----TCCTTGGT 779879 vv v i viii v ivi i v - v ---- iv i C L1M5_orf2#LIN 1249 GTTCATAATATTCTCTTATTATCCTTTTAATGT-CTGTAGGATCTGTAGT 1201 chr2qtel1M 779880 GGAAAGTTCTCCCTTTTCATTTTTGATA-CAACAATTTGATTTTCTTCTT 779928 --- vv i ii -iiii -- v i C L1M5_orf2#LIN 1200 G---ATGTCTCCTTTTTCATTCCTGATATTGGTAATTTG--TGTCTTCTC 1156 chr2qtel1M 779929 TCCTTTTT--CTAATCAAATTAACTAAAGGTTTATCTATTTTGTTTGTTT 779976 i --i i ivi ?i i v i vi i C L1M5_orf2#LIN 1155 TCTTTTTTTCTTGATCAGTCTNGCTAGAGGTTTATCAATTTTATTGATCT 1106 chr2qtel1M 779977 TTTCATAAAA-CAAC--TCAGTTTTATTTATTAATTCAATAGTTTTCTTA 780023 v i - i -- ii i ii v vvi v v ? ?i i C L1M5_orf2#LIN 1105 TTTCAAAGAACCAGCTTTTGGCTTCGTTGATTTTCTCTATTGTNTNTTTG 1056 chr2qtel1M 780024 TTTTCAATTTTACTAACCTACTCTTTTATTTTCAGAATTTCAAATTTGGT 780073 v i i i ii viv i i i vv vvvii vv C L1M5_orf2#LIN 1055 TTTTCTATTTCATTGATTTCTGCTCTTATCTTTATTATTTCCTTCCTTCT 1006 chr2qtel1M 780074 ATTTAATTGAGGGCTTTTTAATTTG---TTCTTTTTCTAGCTTTTTTTAG 780120 i ?v vi ---- --- - i v C L1M5_orf2#LIN 1005 ACTTNCTTTGGG----TTTAATTTGCTCTTCTTTTTCTAGC-TTCTTAAG 961 chr2qtel1M 780121 TTGTAAGCCCAAAT 780134 v v ii i C L1M5_orf2#LIN 960 GTGGAAGCTTAGAT 947 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.94 CpG sites = 114, Kimura (unadjusted) = 41.26 Transitions / transversions = 1.46 (114/78) Gap_init rate = 0.04 (25 / 646), avg. gap size = 1.40 (35 / 25) 18 19.57 0.00 0.00 chr2qtel1M 781338 781378 (218622) (TGTTTT)n#Simple_repeat 1 41 (0) m_b103s252i3 3751 chr2qtel1M 781338 TGTTTTCTTCTATTTTTTCATTTTTGTTTTTGTTTTTGTTT 781378 iv i v v ii (TGTTTT)n#Sim 1 TGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTT 41 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 28 28.91 0.84 4.35 chr2qtel1M 782614 782732 (217268) (TATGTG)n#Simple_repeat 1 115 (0) m_b103s252i4 3752 chr2qtel1M 782614 TATGGGTAACTGCATATGTGTATACATGTTTATGTGTGTGAGTGTATCTA 782663 v vv i i i i ii v i -- v i (TATGTG)n#Sim 1 TATGTGTATGTGTATGTGTATGTGTATGTGTATGTGTAT--GTGTATGTG 48 chr2qtel1M 782664 GATATGTCTGCATTTTGCTCTATGTATATATGTATATAGTATGTGTGTGT 782713 v i v -vv v - v i i i - i (TATGTG)n#Sim 49 TATGTGTATG-TGTATG-TGTATGTGTATGTGTATGT-GTATGTGTATGT 95 chr2qtel1M 782714 -TATGTGCATGTGTGTGTGT 782732 - i i (TATGTG)n#Sim 96 GTATGTGTATGTGTATGTGT 115 Matrix = Unknown Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.05 (6 / 118), avg. gap size = 1.00 (6 / 6) 274 35.22 0.00 1.41 chr2qtel1M 786850 786993 (213007) L1ME4c_3end#LINE/L1 414 555 (275) m_b103s551i3 3753 chr2qtel1M 786850 TTAAAAGAGGGAAAGAGACCCACATGTGGAACAATATTTGTGGCAGCTCT 786899 i i i -- i i iivi vi i ii v vi L1ME4c_3end#L 414 TCAAAAGAAGGAAAAAG--CTATATGCACGAAGATGTTCATTGCAGCGTT 461 chr2qtel1M 786900 TTCTGTAGTGGCAAGGAACTGGAAACTGAGTAGACACCCATCAGTTGGGA 786949 v i i i i i ii i vivv i iii v i v i L1ME4c_3end#L 462 ATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGG 511 chr2qtel1M 786950 AATGACTGAATAAGTTATGATATATGAATGTGTTGGAATATTAT 786993 ii i i i i i v? ivi v L1ME4c_3end#L 512 AATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATATTAT 555 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 48.32 CpG sites = 37, Kimura (unadjusted) = 53.08 Transitions / transversions = 2.85 (37/13) Gap_init rate = 0.01 (2 / 143), avg. gap size = 1.00 (2 / 2) 286 34.96 0.00 0.00 chr2qtel1M 786871 786993 (213007) L1ME3F_3end#LINE/L1 430 552 (438) m_b103s551i4 3753 chr2qtel1M 786871 ACATGTGGAACAATATTTGTGGCAGCTCTTTCTGTAGTGGCAAGGAACTG 786920 iv v i ii i v v ii i i ii L1ME3F_3end#L 430 ACATGTACAAGAATGTTCATAGCAGCACTGTTCGTAATAGCAAAAAACTG 479 chr2qtel1M 786921 GAAACTGAGTAGACACCCATCAGTTGGGAAATGACTGAATAAGTTATGAT 786970 vivvi i iii iiiv ii iv i i i i L1ME3F_3end#L 480 GAAACAACCCAAATGTCCATCGACAGGAGAATGGATAAATAAATTGTGGT 529 chr2qtel1M 786971 ATATGAATGTGTTGGAATATTAT 786993 vv iiiiv L1ME3F_3end#L 530 ATATTCACACAATGGAATATTAT 552 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 47.90 CpG sites = 31, Kimura (unadjusted) = 51.44 Transitions / transversions = 2.58 (31/12) Gap_init rate = 0.00 (0 / 122), avg. gap size = 0.0 (0 / 0) 242 37.23 0.00 0.00 chr2qtel1M 786884 787020 (212980) L1MC5a_3end#LINE/L1 443 579 (2198) m_b103s551i5 3753 chr2qtel1M 786884 TATTTGTGGCAGCTCTTTCTGTAGTGGCAAGGAACTGGAAACTGAGTAGA 786933 ii v vi v i i i iii vivvi i L1MC5a_3end#L 443 TATTCATTGCAGCATTATTTGTAATAGCAAAAGACTGGAAACAACCCAAA 492 chr2qtel1M 786934 CACCCATCAGTTGGGAAATGACTGAATAAGTTATGATATATGAATGTGTT 786983 iii i v i v ii ii i i vv iiiiv L1MC5a_3end#L 493 TGTCCATCAATAGGGGACTGGTTGAATAAACTATGGTACATCCACACAAT 542 chr2qtel1M 786984 GGAATATTATTGTTCTATAAGAAACAATCAGCAGGAT 787020 i i vvvv i i iv v v i L1MC5a_3end#L 543 GGAGTACTATGCAGCTGTAAAAAGGAATGAGGAAGAT 579 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 55.11 CpG sites = 33, Kimura (unadjusted) = 55.11 Transitions / transversions = 1.83 (33/18) Gap_init rate = 0.00 (0 / 136), avg. gap size = 0.0 (0 / 0) 1423 28.44 1.66 2.28 chr2qtel1M 787244 787905 (212095) C L1M5_orf2#LINE/L1 (1145) 2149 1492 m_b103s551i6 3754 chr2qtel1M 787244 TATTTGGATGGTTTTTTAGGATTCTTGAAGTATCTCATCATATCATCTCC 787293 ? v - i i ? i iv v ?viv i v C L1M5_orf2#LIN 2149 TNTTTGTA-GATTCTTTNGGATTTTCTACGTANACAATCATGTCATCTGC 2101 chr2qtel1M 787294 AAAGAGTGATAGTTTTATTTCCTTATCACCCATTCTAATTGCTTTAATTT 787343 i v i? i i iv iv v ii v vv v C L1M5_orf2#LIN 2100 GAATAANGACAGTTTTATTTCTTCCTTTCCAATCTTTATGCCTTTTATTT 2051 chr2qtel1M 787344 CTTTTTCTTTTCTTAT--CAATGAAGCTAACATTTCTAGAACAATGTTGA 787391 vi -- v -- iv ii i v C L1M5_orf2#LIN 2050 CTTTTTCTTGCCTTATTGCACTG--GCTAGGACCTCCAGTACAATGTTGA 2003 chr2qtel1M 787392 ATAATAGTCGTGTTAATGGGCATCCTTGTTTTACCCCTGATTTTATTAGG 787441 iv v v? ii i i iii i i vvi C L1M5_orf2#LIN 2002 ATAGAAGTGGTGANAGCGGACATCCTTGTCTTGTTCCCGATCTTAGGGGG 1953 chr2qtel1M 787442 AATGCGGACAGCTTCTCTTCATTTCAAATAATGCTTCCTATAGATTTTAG 787491 v ?vv i? i vi vviv i i ?v i i vv C L1M5_orf2#LIN 1952 AAAGCNTTCAGTNTTTCACCATTAAGTATGATGTTNGCTGTAGGTTTTTC 1903 chr2qtel1M 787492 ATAAGTACTGCTTATTGTTTTAAGGAAAGTTCCCTTTATCCCTTTATCCC 787541 i ii i ivi iivv i - i------- i C L1M5_orf2#LIN 1902 GTAGATGCCCTTTATCAGGTTGAGGAA-GTTCCCTTC-------TATTCC 1861 chr2qtel1M 787542 TATGCCCTCT-AGTGTTTCTCAATAGGAATGGGTACTGTATTTTGTCAAA 787590 - iiiv - v i - vi v ii v C L1M5_orf2#LIN 1860 TA-GTTTGCTGAGAGTTTTT-ATCATGAATGGGTGTTGAATTTTGTCAAA 1813 chr2qtel1M 787591 AGCCTTTTCTACATCTATTGGGATTATAATATGATTTTATTTGGTTTTGT 787640 v i i i v v vi ivv v vi C L1M5_orf2#LIN 1812 TGCTTTTTCTGCATCTATTGAGATGATCATATGATTTTTCTCCTTTATTC 1763 chr2qtel1M 787641 TATTTATATGATCAATTATAGTAAGT--TTTCCTGATACTTGAACCAGCC 787688 i v i v i v i v -- i vi i- i i C L1M5_orf2#LIN 1762 TGTTAATATGGTGAATTACATTGATTGATTTTCGAATG-TTAAACCAACC 1714 chr2qtel1M 787689 ATGCGTTCTTGATATAAATCCCACTTGGTCATAGTGCATTATCCTGCTGA 787738 v i i iv i ii i vi v C L1M5_orf2#LIN 1713 TTGCATTCCTGGGATAAACCCCACTTGGTCATGATGTATTATCCTTTTTA 1664 chr2qtel1M 787739 TAAGTTGTAGTAATCTCTTTGCTGATATTTTATTTAGAATTTGTGCATCA 787788 vi iv v v vv i i ? i v v C L1M5_orf2#LIN 1663 TATATTGCTGGATTCGATTTGCTAATATTTTGTTNAGGATTTTTGCATCT 1614 chr2qtel1M 787789 GTATTCATCAGGGATATTGGTCTGTAATTGGTCTATTTTA----GCCCT- 787833 i i v vvii v i i---- i i - C L1M5_orf2#LIN 1613 ATGTTCATGAGGGATATTGGTCTGTAATTTTCTTTTCTTGTAATGTCTTT 1564 chr2qtel1M 787834 -TCTTGTTTTAGGGATCAGTGCCATAAGTGTGTTGTAAAAGGAATTTGGC 787882 - ?v - v v i? ivvv iv ii v i v v C L1M5_orf2#LIN 1563 GTCNGGTTTT-GGTATCAGGGTNATGCTGGCCTCATAAAATGAGTTGGGA 1515 chr2qtel1M 787883 AGTACTCCTTCTTCACCTATTTT 787905 ii i ivi C L1M5_orf2#LIN 1514 AGTGTTCCCTCTTTTTCTATTTT 1492 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.34 CpG sites = 103, Kimura (unadjusted) = 37.36 Transitions / transversions = 1.27 (103/81) Gap_init rate = 0.03 (21 / 661), avg. gap size = 1.24 (26 / 21) 319 21.43 0.00 0.00 chr2qtel1M 788276 788345 (211655) C L1PB_orf2#LINE/L1 (1815) 1479 1410 m_b103s551i7 3755 chr2qtel1M 788276 CAATAATATTGGAATTAATTGTTCTTTAAAGGTTTGGGAGAATTCACTTG 788325 iv v ii v i v i v ?vi C L1PB_orf2#LIN 1479 CAATAGGATTGGTACCAATTCTTCTTTGAATGTCTGGTAGAATTCNGCTG 1430 chr2qtel1M 788326 TGAATCTGACTGGCCCTGGA 788345 i v i C L1PB_orf2#LIN 1429 TGAATCCGTCTGGTCCTGGA 1410 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 24.02 CpG sites = 8, Kimura (unadjusted) = 25.94 Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0) 319 24.53 0.94 0.00 chr2qtel1M 788283 788388 (211612) C L1MD_orf2#LINE/L1 (1822) 1472 1366 m_b103s551i8 3755 chr2qtel1M 788283 ATTGGAATTAATTGTTCTTTAAAGGTTTGGGAGAATTCACTTGTGAATCT 788332 vi v v v v iv v i C L1MD_orf2#LIN 1472 ATTGGTGTTAATTCTTCTTTAAACGTTTGGTAGAATTCTCCAGTGAAACC 1423 chr2qtel1M 788333 GACTGGCCCTGGAGATAT-TTCCTAGGGAGTTCATTAATGACTTGTTCAG 788381 iv v v - ii i iv?v v vvi i C L1MD_orf2#LIN 1422 ATCTGGGCCTGGAGATTTCTTTTTGGGGAGTTTTNAAATTACGAATTCAA 1373 chr2qtel1M 788382 TTTCTTT 788388 i C L1MD_orf2#LIN 1372 TTTCCTT 1366 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 30.13 CpG sites = 11, Kimura (unadjusted) = 30.13 Transitions / transversions = 0.73 (11/15) Gap_init rate = 0.01 (1 / 105), avg. gap size = 1.00 (1 / 1) 515 31.19 3.75 5.15 chr2qtel1M 788646 789098 (210902) L1ME4c_3end#LINE/L1 29 475 (355) m_b103s551i9 3756 chr2qtel1M 788646 TTCAAATTTATAAGAATACAAGCCATTCTCCAATTGATTTGAAAGGATTG 788695 v v v? v v vv i v --i v i--- L1ME4c_3end#L 29 TTCAAATTGATAAGAAAAANATCAAGACCCCAATAGAT--AAATGGG--- 73 chr2qtel1M 788696 ATTCTCAAAGGATTTGAACACACAATTTTCAGATGAAAAAAATAAAAATC 788745 ----- iv v iv ? v ii - v ? v L1ME4c_3end#L 74 -----CAAAGGACATGAACAGACAATTCACANAAGAGGAAA-TACAANTA 117 chr2qtel1M 788746 ATTTCTAGTCATATGAAAAAATGCTTTAAATCACTATTGGTCTGAGAAAT 788795 i vvvi iv i i i iv vv i v ii vi L1ME4c_3end#L 118 GTAAACAAACACATGGAAAAATGTTCAACCTCGCTAGTAATCAAAGAAAT 167 chr2qtel1M 788796 GTAAATTAAGAGATACTCTGAGGTACCATATATTTCAGATTGACTAAGAT 788845 i - vv vv i ---- i viiiv i iv L1ME4c_3end#L 168 GCAAATTAA-AGCAACAATGAGATACCAT----TTTACGCCTATTAAATT 212 chr2qtel1M 788846 GACAAGGA-----AAAA---ATAATTAGGAATGTTGAAGGAAATGGGG-A 788886 ii ii ----- --- vvvv i iv iii? v -i L1ME4c_3end#L 213 AGCAAAAATTTAAAAAATTGATAATACCCAATGCTGGCGAGGNTGCGGTG 262 chr2qtel1M 788887 AGACTGGGACACTAATACATTGTTGGAG---TTGTGAACTGATCCAATCA 788933 i v ? v i v ---? i i i v i v L1ME4c_3end#L 263 AAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACAACCC 312 chr2qtel1M 788934 TTCTGGAGAACAGT---ATAATACTGTATCCAAAGGGCTATCACAGTGTA 788980 i i i i ---ii - -- i i v v i v L1ME4c_3end#L 313 TTTTGGAAAGCAATTTGGCAATAC-GTATC--AAGAGCCATAAAAATGTT 359 chr2qtel1M 788981 CGTACCCTTTGATCCAGCAGTGTCTCTAGTGAGCCTGTATCCCAAAGAGA 789030 i i i i vi v vv i vv v i i i L1ME4c_3end#L 360 CATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAA 409 chr2qtel1M 789031 T--TACAAAGAAGGGAAAAGGCCTTGCACATGTGCAAAAATGTTTGTAGC 789078 -- v ii i i ----i i ii i i ii v L1ME4c_3end#L 410 TAATTCAAAAGAAGGAAAAAGC----TATATGCACGAAGATGTTCATTGC 455 chr2qtel1M 789079 ATCCTTTTCTGTAGTGGAGA 789098 v v v i i i i v L1ME4c_3end#L 456 AGCGTTATTTATAATAGCGA 475 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.93 CpG sites = 76, Kimura (unadjusted) = 42.18 Transitions / transversions = 1.31 (76/58) Gap_init rate = 0.06 (29 / 452), avg. gap size = 1.38 (40 / 29) 546 29.41 4.52 3.48 chr2qtel1M 788701 789098 (210902) L1ME4a_3end#LINE/L1 74 475 (396) m_b103s551i10 3756 chr2qtel1M 788701 CAAAGGATTTGAACACACAATTTTCAGATGAAAAAAATAAAAATCATTTC 788750 iv v iv i v i - v viiivv L1ME4a_3end#L 74 CAAAGGACATGAACAGACAATTCACAAAAGAAGAAA-TACAAATGGCCAA 122 chr2qtel1M 788751 TAGTCATATGAAAAAATGCTTTAAATCACTATTGGTCTGAGAAATGTAAA 788800 iv ? i iv vv v ii vi i L1ME4a_3end#L 123 TAAACATATGAAAANATGTTCAACCTCACTAGTAATCAAAGAAATGCAAA 172 chr2qtel1M 788801 TTAAGAGATACTCTGAGGTACCAT-----ATATTTCAGATTGACTAAGAT 788845 i v - vv i ----- iv v i i v L1ME4a_3end#L 173 TTAAAACA-ACAATGAGATACCATTTTTCACCTATCAAATTGGCAAAGAT 221 chr2qtel1M 788846 GACAAGGA--AAAAATAATTAGGAATGTTGA--AGGAAATGGGGAAGACT 788891 vvv i --i v vii --- i-- ivi ? - v L1ME4a_3end#L 222 TTAAAAGATTGATAATACCCAG---TGTTGGCGAGGGTGTGGNGAA-ACG 267 chr2qtel1M 788892 GGGACACTAATACATTGTTGG----AGTTGTGAACTGATCCAATCATTCT 788937 v v v i i ---- - i i i v i v L1ME4a_3end#L 268 GGCACTCTCATACACTGCTGGTGGGAGT-GTAAATTGGTACAACCTTTCT 316 chr2qtel1M 788938 GGAGAACAGT---ATAATACTGTATCCAAAGGGCTATCACAGTGTACGTA 788984 ii i ---ii - v -- iv v v i ? i L1ME4a_3end#L 317 GGAGGGCAATTTGGCAATA-TGTATCAAAAG--CCTTAAAAATGTNCATA 363 chr2qtel1M 788985 CCCTTTGATCCAGCAGTGTCTCTAGTGAGCCTGTATCCCAAAGAGATTA- 789033 i i i vi v vv ii vv v i i i v - L1ME4a_3end#L 364 CCCTTTGACCCAGTAATTCCACTTCTAGGAATTTATCCTAAGGAAATAAT 413 chr2qtel1M 789034 CAAAGAAG-GGAAAAGGCCTTGCACATGTGCAAAAATGTTTGTAGCATCC 789082 i v - ? v i vi ---- i ii ii v v v L1ME4a_3end#L 414 CAGAGATGTGNACAAAGATTT----ATGTACAAGGATGTTCATCGCAGCA 459 chr2qtel1M 789083 TTTTCTGTAGTGGAGA 789098 v i i i i v L1ME4a_3end#L 460 TTATTTATAATAGCGA 475 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.61 CpG sites = 61, Kimura (unadjusted) = 38.61 Transitions / transversions = 1.17 (61/52) Gap_init rate = 0.05 (21 / 397), avg. gap size = 1.52 (32 / 21) 446 24.32 0.00 8.62 chr2qtel1M 789361 789486 (210514) MIRb#SINE/MIR 3 118 (150) m_b103s601i0 3757 chr2qtel1M 789361 GAGGGGCAGCTAGGTGGCGCAGTAGATAGAATACCAGCCCTGAAGTCAGC 789410 --- i i v ii vi ii i v MIRb#SINE/MIR 3 GAGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGA 49 chr2qtel1M 789411 AGGACCCGAGTTCAAATGTGGTCTCAGACACTTAACTCTTCCTAGCTGTG 789460 vi i i i viv v v v ------- MIRb#SINE/MIR 50 CAGACCTGGGTTCGAATCCCGGCTCTGCCACTTA-------CTAGCTGTG 92 chr2qtel1M 789461 TGACGCTGGCCAAGTCACTTAATCCC 789486 vi v i i i MIRb#SINE/MIR 93 TGACCTTGGGCAAGTTACTTAACCTC 118 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.55 CpG sites = 17, Kimura (unadjusted) = 29.80 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.08 (10 / 125), avg. gap size = 1.00 (10 / 10) 15 10.84 3.33 0.00 chr2qtel1M 789496 789525 (210475) (AGAAA)n#Simple_repeat 1 31 (0) m_b103s252i6 3758 chr2qtel1M 789496 AGCAAA-AAAAAAAAGGAAAAGAAAAGAAAA 789525 v - i i (AGAAA)n#Simp 1 AGAAAAGAAAAGAAAAGAAAAGAAAAGAAAA 31 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 16 17.57 0.00 0.00 chr2qtel1M 789499 789525 (210475) (A)n#Simple_repeat 1 27 (0) m_b103s252i7 3758 chr2qtel1M 789499 AAAAAAAAAAAGGAAAAGAAAAGAAAA 789525 ii i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAA 27 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 16 4.00 3.85 0.00 chr2qtel1M 790595 790620 (209380) (TTGTT)n#Simple_repeat 1 27 (0) m_b103s252i8 3759 chr2qtel1M 790595 TTG-TTTGTTTTGTTTCGTTTTGTTTT 790620 - i (TTGTT)n#Simp 1 TTGTTTTGTTTTGTTTTGTTTTGTTTT 27 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 25), avg. gap size = 1.00 (1 / 1) 12 11.05 0.00 9.38 chr2qtel1M 790595 790629 (209371) (TTGT)n#Simple_repeat 1 32 (0) m_b103s252i9 3760 chr2qtel1M 790595 TTGTTTGTTTTGTTTCGTTTTGTTTTTCTGTATGT 790629 - - - v i v (TTGT)n#Simpl 1 TTGTTTG-TTTGTTT-G-TTTGTTTGTTTGTTTGT 32 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.09 (3 / 34), avg. gap size = 1.00 (3 / 3) 15 12.03 5.56 0.00 chr2qtel1M 791209 791244 (208756) (CCTCTTC)n#Simple_repeat 1 38 (0) m_b103s252i10 3761 chr2qtel1M 791209 CCTCTTCACTC-TCCCTCTTCCCT-TTCTGTCTTGCCT 791244 v - - iv v (CCTCTTC)n#Si 1 CCTCTTCCCTCTTCCCTCTTCCCTCTTCCCTCTTCCCT 38 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 228 25.25 13.13 0.00 chr2qtel1M 794533 794631 (205369) MIR3#SINE/MIR 90 201 (7) m_b103s601i1 3762 chr2qtel1M 794533 CTTTGAGCCAATCCCTTC-----TCTG---CTCAGTTTCCTC--CTGTAA 794572 i i v i v ----- --- -- MIR3#SINE/MIR 90 CCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAA 139 chr2qtel1M 794573 ATTG-GTTGGTTGGATTCT-TAAATTCTGAAGTGACTTTCAGCTC-GACA 794619 v - vv i vv- i vi i i vv i - MIR3#SINE/MIR 140 AATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACA 189 chr2qtel1M 794620 TCTCCTGACTTT 794631 iiiv i i MIR3#SINE/MIR 190 TTCTATGATTCT 201 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.32 CpG sites = 14, Kimura (unadjusted) = 31.32 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.06 (6 / 98), avg. gap size = 2.17 (13 / 6) 238 29.36 3.91 1.53 chr2qtel1M 796595 796722 (203278) C L1MC1_3end#LINE/L1 (508) 572 442 m_b103s551i11 3763 chr2qtel1M 796595 TCATTTCTT---AGAGAACAATAATATTCCATAACATTCATATACCACAA 796641 --- v vvv viiv vv i i C L1MC1_3end#LI 572 TCATTTCTTTTTAGCGCTGAATAATATTCCATTGTCTGGATGTACCACAG 523 chr2qtel1M 796642 TTTACCCAACCATTCCCCAACTGATGGGCATCCATTCATT--TTCCAGTT 796689 iii v v v v i -- vi -- iv C L1MC1_3end#LI 522 TTTATTTATCCATTCACCTACTGAAGGACATC--TTGGTTGCTTCCAAGT 475 chr2qtel1M 796690 TCTAGTCACTACAAACAGGGCTGCCACAAATAT 796722 i i iv i ii i ii i i i C L1MC1_3end#LI 474 TTTGGCAATTATGAATAAAGCTGCTATAAACAT 442 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.38 CpG sites = 22, Kimura (unadjusted) = 38.38 Transitions / transversions = 1.47 (22/15) Gap_init rate = 0.03 (4 / 127), avg. gap size = 1.75 (7 / 4) 632 30.26 2.49 4.73 chr2qtel1M 796612 796892 (203108) C L1ME5_3end#LINE/L1 (389) 552 278 m_b103s551i12 3763 chr2qtel1M 796612 ATAATATTCCATAACATTCATATACCACAATTTACCCAACCATTCCCCAA 796661 i i iiii v vi v i v i i v C L1ME5_3end#LI 552 ATAGTACTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCA 503 chr2qtel1M 796662 CTGATGGGCATCCATTCATTTTCCAGTTTCTAGTCACTACAAACAGGGCT 796711 v i i vvivvii ii i iv i i iv C L1ME5_3end#LI 502 GTGATGGACACCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCT 453 chr2qtel1M 796712 GCCACAAATATTTTGGCACATCTGCCAGGTCCCTTTC----CCTTCTTTA 796757 v ii i ii v i ------- i v---- viv v C L1ME5_3end#LI 452 GCAATGAACATCCTCGTACAT-------GTCCCCTTATGGACCTGTGTGA 410 chr2qtel1M 796758 GTATCTCTTTGGGGTTTAAGCCCAGTAGTAACACTGCTGGATCAAAGGGT 796807 v i i v vi v iiiv i i v C L1ME5_3end#LI 409 GAATTTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGT 360 chr2qtel1M 796808 ATGCACAGTTTGCTACCTT-TTTGAGTA--TAGTTCCTAATTGCTCTCCA 796854 ii ------ i v- v -- v v vi C L1ME5_3end#LI 359 ATGCGTA------TACTTAATTTGACTAAGTACTGCCAGATTGCTCTCCA 316 chr2qtel1M 796855 GAATGGCTGGATGTGTTCACAATTCCACCAACAATGCA 796892 v ivv ii v i i i C L1ME5_3end#LI 315 GAATGGCTGCACCAGTCTACACTCCCACCAGCAGTGCA 278 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.55 CpG sites = 48, Kimura (unadjusted) = 39.89 Transitions / transversions = 1.45 (48/33) Gap_init rate = 0.06 (16 / 280), avg. gap size = 1.25 (20 / 16) 270 27.98 1.10 5.75 chr2qtel1M 797005 797095 (202905) MIR3#SINE/MIR 111 197 (11) m_b103s601i2 3764 chr2qtel1M 797005 TCACTGAATCTCAGTTTCC-CATTTGTACAATAAGTGGGAGGCACTCCAT 797053 v iii - i v i v vv v vv MIR3#SINE/MIR 111 TCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGAT 160 chr2qtel1M 797054 GGCCTTGTAGGTCCCTTCCAGTGATCATCTGGAATCCTGTAA 797095 ii ivv i----- iv i i i MIR3#SINE/MIR 161 GATCTCTAAGGTCCCTTCCAGC-----TCTGACATTCTATGA 197 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.51 CpG sites = 13, Kimura (unadjusted) = 35.51 Transitions / transversions = 1.18 (13/11) Gap_init rate = 0.07 (6 / 90), avg. gap size = 1.00 (6 / 6) 257 29.04 6.78 0.80 chr2qtel1M 797192 797309 (202691) C L2b_3end#LINE/L2 (10) 456 332 m_b103s601i3 3765 chr2qtel1M 797192 TCAGCAAACTTTTA---AGTGCCTGCTATCAGCCAGGCCCTGGGCTGTGC 797238 i iv --- i i i vv ? v iv C L2b_3end#LINE 456 TCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGC 407 chr2qtel1M 797239 CCCAGGAACATAAAGAGTG-GCAAG--GGACTT--CCCCTGCTCTCCTGG 797283 v ii i i i iv - -i --i ?i--i i vi C L2b_3end#LINE 406 GCTGGGGATACAGCG-GTGAACAAGACAGACNCGGTCCCTGCCCTCACGG 358 chr2qtel1M 797284 AGGTCACAGACAGCTGGGGCAGGTAG 797309 v v viv v ii C L2b_3end#LINE 357 AGCTCACAGTCTAGTGGGGGAGACAG 332 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.63 CpG sites = 21, Kimura (unadjusted) = 38.94 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.04 (5 / 117), avg. gap size = 1.80 (9 / 5) 433 29.76 18.14 0.38 chr2qtel1M 797447 797672 (202328) C MIRb#SINE/MIR (0) 268 3 m_b103s601i4 3766 chr2qtel1M 797447 AATACCAAACCTAGCATTTATACAGCACCTGCT--GTGACATACAGTGTA 797494 vi i v v vv i i i -- v vi v i C MIRb#SINE/MIR 268 AATAATAGAGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTG 219 chr2qtel1M 797495 TCA------------GTGTTGTCTCATTTTATCCTCATGAGAACCCTAGG 797532 ii ------------ ii i v ii v iv C MIRb#SINE/MIR 218 CTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCG 169 chr2qtel1M 797533 ACTCAGGTG--------CCCTTTTTATAGATAAAGGAACTGAGGCAAACA 797574 vvi i-------- v i i i i vv v C MIRb#SINE/MIR 168 AGGTAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGA 119 chr2qtel1M 797575 GAAGTTTTGTATCTTG--------------ACTAGCAAGTTGCTGATGTG 797610 i vv v --------------i i v v vvi C MIRb#SINE/MIR 118 GAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 69 chr2qtel1M 797611 GGATGAACACTCAGGTCTTGCTGA-TTGAAGGCCC-TGTTC---ACACTT 797655 vviv i vv - iv i - i ---v v C MIRb#SINE/MIR 68 GGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTG 19 chr2qtel1M 797656 TACCCCATTGTACCCTC 797672 i v ii i- C MIRb#SINE/MIR 18 CACCACGCTGC-CCCTC 3 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.65 CpG sites = 34, Kimura (unadjusted) = 38.47 Transitions / transversions = 1.03 (34/33) Gap_init rate = 0.04 (8 / 225), avg. gap size = 5.25 (42 / 8) 17 7.25 3.45 0.00 chr2qtel1M 797988 798016 (201984) (GTT)n#Simple_repeat 1 30 (0) m_b103s252i11 3767 chr2qtel1M 797988 GTT-TTGTTGTTGTTATTGTTGTTGTTTTT 798016 - i v (GTT)n#Simple 1 GTTGTTGTTGTTGTTGTTGTTGTTGTTGTT 30 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1) 217 32.77 4.17 5.93 chr2qtel1M 799123 799242 (200758) MIRc#SINE/MIR 84 201 (67) m_b103s601i5 3768 chr2qtel1M 799123 GCTGCTGGGATTTGGGTCAAATCACTGAACCCTTCTGAGC--TGATGGCC 799170 - v ii v v i v ii --iii vv MIRc#SINE/MIR 84 GCTG-TGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCC 132 chr2qtel1M 799171 TGAGTTGTGCCCATAGTGAAAATGAAAATACTTTCTGTGT---TGTCCCA 799217 v vi ---- v i iii i v i v iv i---iv v MIRc#SINE/MIR 133 TCATCTGT----AAAATGGGGATAATAATACCTGCCCTGCCTACCTCACA 178 chr2qtel1M 799218 GGTTTACTGTGAGAATCGAGGATGA 799242 v ii i i -- MIRc#SINE/MIR 179 GGGTTGTTGTGAGGATCAA--ATGA 201 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.63 CpG sites = 22, Kimura (unadjusted) = 44.63 Transitions / transversions = 1.47 (22/15) Gap_init rate = 0.08 (9 / 119), avg. gap size = 1.33 (12 / 9) 388 27.74 0.00 6.67 chr2qtel1M 799278 799389 (200611) MIRc#SINE/MIR 11 115 (153) m_b103s601i6 3769 chr2qtel1M 799278 TGGCGCAGGCAATAGAGCACAAGCCCTGAAATCGGGATGACTTGAGTTCA 799327 i vvi v vi v i i i i v i i i MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr2qtel1M 799328 AATCTGACCTCAGGCAATTAATAGTTCTTAGCTGTGTGACCCTAGGCAAG 799377 i iviv v v v -------i i i MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTGACCTTGGGCAAG 103 chr2qtel1M 799378 TCACTTACCCCC 799389 v i MIRc#SINE/MIR 104 TCACTTAACCTC 115 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.35 CpG sites = 17, Kimura (unadjusted) = 35.31 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.06 (7 / 111), avg. gap size = 1.00 (7 / 7) 526 33.33 4.34 0.66 chr2qtel1M 799485 799922 (200078) L1ME4c_3end#LINE/L1 22 475 (355) m_b103s551i13 3770 chr2qtel1M 799485 GAATTGATTCAGATTTGTAAGAACACAAGTCATTCTCCAGTTGATAAAAG 799534 ii v i vi v v? viv vv i i v v L1ME4c_3end#L 22 GAGCTCATTCAAATTGATAAGAAAAANATCAAGACCCCAATAGATAAATG 71 chr2qtel1M 799535 GTCAAAGAATTTGAACA----ATTT---TAAGATGGAAAAAAATTTTTT- 799576 v i iv ---- i---? v i v v ? vv v- L1ME4c_3end#L 72 GGCAAAGGACATGAACAGACAATTCACANAAGAGGAAATACAANTAGTAA 121 chr2qtel1M 799577 -CTAATACTATGAAAAAATGTTCTAAATCACTTTTGGTCAGAGAAATGTA 799625 - v i - i v vv i vv ii i i L1ME4c_3end#L 122 ACAAACAC-ATGGAAAAATGTTCAACCTCGCTAGTAATCAAAGAAATGCA 170 chr2qtel1M 799626 AATTAAAGCAATTCTCAGTTACCGTTGTATGTC--TCAGACTGGCTAAGA 799673 ivv v v i v i i -- i i i i v i L1ME4c_3end#L 171 AATTAAAGCAACAATGAGATACCATTTTACGCCTATTAAATTAGCAAAAA 220 chr2qtel1M 799674 TGACAGGAAAAGATAATAACAAATGTTGGATGGGATGTGGGAAAACTGGG 799723 vvv ii vv v v i vvi ? i vi v L1ME4c_3end#L 221 TTTAAAAAATTGATAATACCCAATGCTGGCGAGGNTGCGGTGAAACTGGT 270 chr2qtel1M 799724 AGACTAATACATTATTGATGGAGTTGTAGAGAAGT--AATC----TGGAG 799767 v? v ii i vi? i vvi -- i ---- i L1ME4c_3end#L 271 ACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAA 320 chr2qtel1M 799768 AAAAATATGGAAATAAACCCAAATGACTATCACCCTGTGTATACCTTCTA 799817 iv v v viiviv vii i v vvv vi i i i L1ME4c_3end#L 321 AGCAATTTGGCAATACGTATCAAGAGCCATAAAAATGTTCATACCCTTTG 370 chr2qtel1M 799818 ATCTAGCTGTGTCTCTACTGAACCTTTATCCCAAAGAGATGAT--AAAGG 799865 i i ivi vi v v iivv i i i i -- i L1ME4c_3end#L 371 ACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAAG 420 chr2qtel1M 799866 AGGGAAAAGGAGCCACATGTGCAAAAATGTTTGTAGTAGCCTTTTTTGTA 799915 i -- i i ii i i ii v i v v i L1ME4c_3end#L 421 AAGGAAAA--AGCTATATGCACGAAGATGTTCATTGCAGCGTTATTTATA 468 chr2qtel1M 799916 GTGGAGA 799922 i i v L1ME4c_3end#L 469 ATAGCGA 475 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 43.84 CpG sites = 77, Kimura (unadjusted) = 45.97 Transitions / transversions = 1.13 (77/68) Gap_init rate = 0.03 (11 / 437), avg. gap size = 2.00 (22 / 11) 14 21.98 2.38 0.00 chr2qtel1M 800000 800041 (199959) (TTTTCT)n#Simple_repeat 1 43 (0) m_b103s252i12 3771 chr2qtel1M 800000 TTTTCTTTTTCATTTT-TTTCCCTTTTTGATCTGATTTTTCTT 800041 v - ii vv i vv (TTTTCT)n#Sim 1 TTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTT 43 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.02 (1 / 41), avg. gap size = 1.00 (1 / 1) 12 20.36 0.00 0.00 chr2qtel1M 800119 800147 (199853) (AGGA)n#Simple_repeat 1 29 (0) m_b103s252i13 3772 chr2qtel1M 800119 AGGAAGGAGTGGGGGAAGGAAGGGAGGAA 800147 iv ii i (AGGA)n#Simpl 1 AGGAAGGAAGGAAGGAAGGAAGGAAGGAA 29 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 17 26.80 0.00 5.71 chr2qtel1M 800306 800379 (199621) (TATTTT)n#Simple_repeat 1 70 (0) m_b103s252i14 3773 chr2qtel1M 800306 TATTTATATATGTATATGTGTAATGTCTATCTTTATTGTTTGTTTTTGGT 800355 - - v v - v v v i i - i iv (TATTTT)n#Sim 1 TATTT-T-TATTTTTAT-TTTTATTTTTATTTTTATT-TTTATTTTTATT 46 chr2qtel1M 800356 TGTTTTTTTTTTTTTTTTTTTTTT 800379 v v v v v (TATTTT)n#Sim 47 TTTATTTTTATTTTTATTTTTATT 70 Matrix = Unknown Transitions / transversions = 0.36 (4/11) Gap_init rate = 0.05 (4 / 73), avg. gap size = 1.00 (4 / 4) 26 15.69 0.00 0.00 chr2qtel1M 800337 800379 (199621) (T)n#Simple_repeat 1 43 (0) m_b103s252i15 3773 chr2qtel1M 800337 TTTATTGTTTGTTTTTGGTTGTTTTTTTTTTTTTTTTTTTTTT 800379 v v v vv v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 43 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 352 27.27 0.83 0.00 chr2qtel1M 801485 801605 (198395) L1P3_orf2#LINE/L1 2013 2134 (1160) m_b103s551i14 3774 chr2qtel1M 801485 ATTGGGA-TGCTAGCTTTGGTAATTAGAGTTGAGAAAGAGATTAAAGGAA 801533 i - v i ivv i i ivvv i v i v L1P3_orf2#LIN 2013 ATTGGAAGTTCTGGCCAGGGCAATCAGGCAAGAGAAAGAAATAAAGGGTA 2062 chr2qtel1M 801534 TTAGAGTAGGTGATGAGGAATCCAAATTATCACTCTTTGCAGATGATATG 801583 vi i viiv vi i v v i L1P3_orf2#LIN 2063 TTCAAATAGGAAGAGAGGAAGTCAAATTGTCTCTGTTTGCAGATGACATG 2112 chr2qtel1M 801584 ATGGTAAACTTAGAGAACCCCA 801605 v v i i L1P3_orf2#LIN 2113 ATTGTATATTTAGAAAACCCCA 2134 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.33 CpG sites = 17, Kimura (unadjusted) = 34.33 Transitions / transversions = 1.06 (17/16) Gap_init rate = 0.01 (1 / 120), avg. gap size = 1.00 (1 / 1) 335 28.91 0.78 0.00 chr2qtel1M 801494 801621 (198379) L1PB_orf2#LINE/L1 2023 2151 (1143) m_b103s551i15 3774 chr2qtel1M 801494 CTAGCTTTGGTAATTAGAGTTGAGAAAGAGATTAAAGGAATTAGAGTAGG 801543 ivvi i i vvv i v i v ivi i v L1PB_orf2#LIN 2023 CTAGCCAGAGCAATCAGACAAGAGAAAGAAATAAAGGGCATCCAAATCGG 2072 chr2qtel1M 801544 TGATGAGGAATCCAAATTATCACTCTTTGCAGATGATATGATGGTAAACT 801593 i v vi i i i v v v ?v i L1PB_orf2#LIN 2073 TAAAGAGGAAGTCAAACTGTCGCTGTTTGCTGATGATATGATCGTNTACC 2122 chr2qtel1M 801594 TAGAGAACCCCAGAAA-TAATCCATAAAG 801621 i i i i - vv v L1PB_orf2#LIN 2123 TAGAAAACCCTAAAGACTCCTCCAGAAAG 2151 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.16 CpG sites = 19, Kimura (unadjusted) = 37.41 Transitions / transversions = 1.06 (19/18) Gap_init rate = 0.01 (1 / 127), avg. gap size = 1.00 (1 / 1) 12 12.64 0.00 3.70 chr2qtel1M 801765 801792 (198208) (TTGTT)n#Simple_repeat 1 27 (0) m_b103s252i16 3775 chr2qtel1M 801765 TTTTTTTGTTTTGTTTTTGGTTTGGTTT 801792 v - v v (TTGTT)n#Simp 1 TTGTTTTGTTTTG-TTTTGTTTTGTTTT 27 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 20 16.38 0.00 0.00 chr2qtel1M 802716 802749 (197251) (T)n#Simple_repeat 1 34 (0) m_b103s252i17 3776 chr2qtel1M 802716 TTTTTTCTACTTTTATTTTATTTTTTTTTTTTTT 802749 i vi v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 34 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 290 26.88 6.45 0.00 chr2qtel1M 803193 803285 (196715) MIRc#SINE/MIR 17 115 (153) m_b103s601i7 3777 chr2qtel1M 803193 AATAGATACAGTTCTGGATCTTGAGTCACAAAGAACTGGGTTCTAATTCA 803242 i i v v iv ii v vi v v i i v MIRc#SINE/MIR 17 AGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCC 66 chr2qtel1M 803243 GCCTCAGACATTTAGTAGATGGGTGTC--TGGGTAAG--ACTT--CCTC 803285 v v v i v v v v -- i -- -- MIRc#SINE/MIR 67 GGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.34 CpG sites = 10, Kimura (unadjusted) = 33.34 Transitions / transversions = 0.67 (10/15) Gap_init rate = 0.03 (3 / 92), avg. gap size = 2.00 (6 / 3) 194 37.12 1.01 2.04 chr2qtel1M 803425 803523 (196477) C L3b_3end#LINE/CR1 (131) 1075 978 m_b103s601i8 3778 chr2qtel1M 803425 CTTCAAAGGTTGGAGTCCCCACCACCTGTCAAGGTGACCCATTTCACT-T 803473 i i iv- vii i v vi vv i i v - C L3b_3end#LINE 1075 CTCCAGAGAA-GGAGATTCCGCAACCTCCCTCGGTAACCCATTCCAGTGT 1027 chr2qtel1M 803474 TCAGCCAGTTTTAATTATTAAAATGTCTTTCCTGAGATCAGGCCTAGATC 803523 i i- ii i v i i i ii v ii v v vii i C L3b_3end#LINE 1026 TTAA-CAACTCTCACTGTCAGGAAGTTCTTCCTTATATCTAACCTAAATC 978 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 52.92 CpG sites = 24, Kimura (unadjusted) = 55.30 Transitions / transversions = 2.00 (24/12) Gap_init rate = 0.03 (3 / 98), avg. gap size = 1.00 (3 / 3) 466 33.79 0.00 1.35 chr2qtel1M 803436 803585 (196415) C L3#LINE/CR1 (138) 3961 3814 m_b103s601i9 3778 chr2qtel1M 803436 GGAGTCCCCACCACCTGTCAAGGTGACCCATTTCACTTTCAGCCAGTTTT 803485 -- i i v? i iii i i ii v i i C L3#LINE/CR1 3961 GGAG--CTCACTACCTCNCGAGGCAGCCCATTCCATTTTTGGACAGCTCT 3914 chr2qtel1M 803486 AATTATTAAAATGTCTTTCCTGAGATCAGGCCTAGATCAGTCTCTTTCTT 803535 i i i v ii v v iii v i v i ii v v C L3#LINE/CR1 3913 GATTGTTAGAAAGTTCTTCCTTATATTGAGCCGAAATCTGCCTCCCTGTA 3864 chr2qtel1M 803536 ACTTCCACTAGAGACTCCCAGCTCTGCCCTCTGAGGCTCAGCAGGACAAG 803585 ivivviv i i ii ivvi i i C L3#LINE/CR1 3863 ACTTCCACCCATTGGTCCTAGTTCTGCCCTCTGGAGCCACACAGAATAAG 3814 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 47.44 CpG sites = 35, Kimura (unadjusted) = 48.87 Transitions / transversions = 2.33 (35/15) Gap_init rate = 0.01 (2 / 149), avg. gap size = 1.00 (2 / 2) 207 28.92 9.34 3.11 chr2qtel1M 803664 803845 (196155) C L3b_3end#LINE/CR1 (476) 730 538 m_b103s601i10 3779 chr2qtel1M 803664 CTTTTTCAACTCAGTTGCCTGGAATGGGGGACAATAATGCAGCTGATGTC 803713 i v ? vv v? ii iv iivi i v v ? ?v i C L3b_3end#LINE 730 CCTTTTAAANTGTGGNGCCCAGAACTGAACGCAGTACTCCAGNTGNGGCC 681 chr2qtel1M 803714 TGACAGCAGCTCAGAG-------GGATCATCCCCTGCCT-GTTCC----- 803750 -- v ------- ?? v v - ? i----- C L3b_3end#LINE 680 TGAC--CAGCGCAGAGTAGAGCGGGANNATCACCTCCCTTGNTCTGTCGG 633 chr2qtel1M 803751 ---TGCCTCACTTCATGCCTCCCCAGATGACACTGAGCTGTTTCA-CTTC 803796 --- ? i vv v vv v vi i - v ii- vv C L3b_3end#LINE 632 CGATNCTTCTGTTAATGCAGCCCAAGATCGCATT-AGCTTTTTTGGCAGC 584 chr2qtel1M 803797 TGCCCCCCAGGGCTCACACATGCCGAGCTTGTGCTCAAACCCTAAATCC 803845 i vi v vv v v iii i v --- v C L3b_3end#LINE 583 CGCGTCGCACTGCTGACTCATATTGAGCTTGCGGTCAA---CTAAAACC 538 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.41 CpG sites = 21, Kimura (unadjusted) = 39.03 Transitions / transversions = 0.70 (21/30) Gap_init rate = 0.06 (11 / 181), avg. gap size = 2.09 (23 / 11) 13 24.72 0.00 0.00 chr2qtel1M 804320 804357 (195643) (TTTT)n#Simple_repeat 1 38 (0) m_b103s252i18 3780 chr2qtel1M 804320 TTTTTTTTTCTTTCTTAGTTTTATTTTGATTCTTTTTT 804357 i i vv v vv i (TTTT)n#Simpl 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 38 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 275 33.85 4.28 2.29 chr2qtel1M 804707 804963 (195037) C CR1-3_Croc#LINE/CR1 (1287) 2318 2057 m_b103s551i16 3781 chr2qtel1M 804707 CATATTGAACTTCATCTTATGATATTTGGCCCAGGTCTCT--TCTCTGGA 804754 ii i i v vv i i v i i-- v v C CR1-3_Croc#LI 2318 CGCATTGAACTTCATCCTGTTAGCTCTAGCCCAGCTTTCCAATCTGTCGA 2269 chr2qtel1M 804755 GAACGCTTTATAATCCCGACTCTGTCATCCA----GTTACTCATTCTCTC 804800 v - ivv iv vii?i v ---- - v v ii C CR1-3_Croc#LI 2268 GATC-CTTCTGAATTGCGCTCNCGTCCTCCAACGTGTT-CGCAATCCTTC 2221 chr2qtel1M 804801 CCAGCTTTGCTTTGTCAGAAATATTGTTGAGTAGGCTCTCTTTACCTTCA 804850 i i iv i v v vv i v iv i i v i vv C CR1-3_Croc#LI 2220 CCAGTTTCGTGTCGTCTGCAAACTTGCTCAAGAAGCTTTCTATGCCAGCA 2171 chr2qtel1M 804851 TGCTGAAGCCATTGGCACA-ATCTTAAACAGCCCAGGAGCGAGCACCCAG 804899 v -- ii iii v - iv i v v iv v v -- C CR1-3_Croc#LI 2170 TCC--AAATCATTAATAAACACGTTGAACAGCACCGGGCCCAGGA--CAG 2125 chr2qtel1M 804900 ATCCATGT----CTCTCCCAGAGGCTTCTTGGTATTCTGGCATTGAACAA 804945 i v ---- iv iv ii i i vi i v v vi C CR1-3_Croc#LI 2124 ACCCCTGTGGGACTCCACTCGAAACCTCCTGCCATTCTGACATGGACCCG 2075 chr2qtel1M 804946 TTAAAAACTACTCCTTGC 804963 v i i i C CR1-3_Croc#LI 2074 TTAATAATTACCCTTTGC 2057 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 42.03 CpG sites = 45, Kimura (unadjusted) = 46.34 Transitions / transversions = 1.12 (45/40) Gap_init rate = 0.04 (10 / 256), avg. gap size = 1.70 (17 / 10) 20 18.65 0.00 0.00 chr2qtel1M 806914 806950 (193050) (CA)n#Simple_repeat 1 37 (0) m_b103s252i19 3782 chr2qtel1M 806914 CACACTCACAAAGACACAGACTCAGACACACACACAC 806950 v v v v v v (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACAC 37 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 717 27.82 1.19 1.59 chr2qtel1M 807026 807277 (192723) L1ME3A_3end#LINE/L1 127 377 (543) m_b103s551i17 3783 chr2qtel1M 807026 CATATGAAAAGATGCTCCAAGTCATTATTAATCAGAGAAATGCAAGTTAA 807075 i v vv v v i i L1ME3A_3end#L 127 CATATGAAAAGGTGCTCAACTTCATTAGTCATCAGGGAAATGCAAATTAA 176 chr2qtel1M 807076 GACAACTCTGAGATACCACTACACACCTGTCAGATTGTCTAGAATGACAG 807125 i v vv ? iii v v i v i L1ME3A_3end#L 177 AACCACAATGNGATACCACTACACACCCACCAGAATGGCTAAAATGAAAA 226 chr2qtel1M 807126 GGAAACATAATGCGGAAGACTGAAGGGAATGTGCGAAAACTGGGA--CAC 807173 i v v i i vi ivii iv i i viiv i i -- v L1ME3A_3end#L 227 AGACAGACAATACCAAGTGTTGGCGAGGATGTGGAGCAACCGGAACTCTC 276 chr2qtel1M 807174 GTACATTGTTGGTGGAATTGTGAATGCGTCCAACCATTCTGGAGAGCAAT 807223 i i i i v i vv v i i i i vi L1ME3A_3end#L 277 ATACACTGCTGGTGGGAGTGTAAATTGGTACAACCACTTTGGAAAACTGT 326 chr2qtel1M 807224 CTGGAATTATGCCCCAAAAGTTATCCAAC-TGTGCATACCCTTTGATGCA 807272 i v v - iv v i i--- - i v iv L1ME3A_3end#L 327 TTGGCAGTAT-CTACTAAAGCTG---AACATATGCATACCCTATGACCCA 372 chr2qtel1M 807273 GCAAT 807277 L1ME3A_3end#L 373 GCAAT 377 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.06 CpG sites = 39, Kimura (unadjusted) = 35.70 Transitions / transversions = 1.30 (39/30) Gap_init rate = 0.02 (6 / 251), avg. gap size = 1.17 (7 / 6) 13 4.55 4.35 0.00 chr2qtel1M 807278 807300 (192700) (GTTT)n#Simple_repeat 1 24 (0) m_b103s252i20 3784 chr2qtel1M 807278 GTTT-TTTGTTTATTTGTTTGTTT 807300 - i (GTTT)n#Simpl 1 GTTTGTTTGTTTGTTTGTTTGTTT 24 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.05 (1 / 22), avg. gap size = 1.00 (1 / 1) 392 29.78 1.03 6.52 chr2qtel1M 807831 808024 (191976) C L1ME4c_3end#LINE/L1 (275) 555 372 m_b103s551i19 3785 chr2qtel1M 807831 ATAATATTCCATAATATTCATATACTACAATTTATTCAGCCATTCTCCAA 807880 vivi ?v i i i i i i i v C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chr2qtel1M 807881 CTGATGGGCATCCATTCAGTTTCCAGTTTCTGGCCACTACAAACAGGGCT 807930 i v i ii vviv i i v i i i i iv C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCT 456 chr2qtel1M 807931 GCCACAAACATTCTTGCACATACAGGTCCCTTTCCCTTTTTAAAA--ATG 807978 v ii ii i ii i -- ii i i vi -- v C L1ME4c_3end#L 455 GCAATGAACATCTTCGTGCATATAG--CTTTTTCCTTCTTTTGAATTATT 408 chr2qtel1M 807979 TCTTTGGGATATAAGTCCAGTAGATTCCAGAAGTGTTACTACAGGG 808024 i i - v --------- vv i v C L1ME4c_3end#L 407 TCCTTAGGATA-AATTC---------CCAGAAGTGGAATTACTGGG 372 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.17 CpG sites = 37, Kimura (unadjusted) = 40.14 Transitions / transversions = 2.18 (37/17) Gap_init rate = 0.07 (13 / 193), avg. gap size = 1.08 (14 / 13) 487 29.94 2.34 2.34 chr2qtel1M 807831 808001 (191999) C L1ME5_3end#LINE/L1 (389) 552 382 m_b103s551i18 3785 chr2qtel1M 807831 ATAATATTCCATAATATTCATATACTACAATTTATTCAGCCATTCTCCAA 807880 i i ii i v vi i v iii v i v C L1ME5_3end#LI 552 ATAGTACTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCA 503 chr2qtel1M 807881 CTGATGGGCATCCATTCAGTTTCCAGTTTCTGGCCACTACAAACAGGGCT 807930 v i i vviv ii ii i iv i iv C L1ME5_3end#LI 502 GTGATGGACACCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCT 453 chr2qtel1M 807931 GCCACAAACATTCTTGCACATACAGGTCCCTTTC----CCTTTTTAAAAA 807976 v ii i i i ---- i v---- v v i i C L1ME5_3end#LI 452 GCAATGAACATCCTCGTACAT----GTCCCCTTATGGACCTGTGTGAGAA 407 chr2qtel1M 807977 TGTCTTTGGGATATAAGTCCAGTAG 808001 v vii v C L1ME5_3end#LI 406 TTTCTTTGGGATATATACCCAGGAG 382 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.79 CpG sites = 32, Kimura (unadjusted) = 39.84 Transitions / transversions = 1.78 (32/18) Gap_init rate = 0.03 (5 / 170), avg. gap size = 1.60 (8 / 5) 231 27.47 2.15 2.15 chr2qtel1M 808090 808182 (191818) L1ME1_3end#LINE/L1 441 533 (393) m_b103s551i20 3783 chr2qtel1M 808090 AATGTTTGTGGCAGCTCTTTCCATAG-AGACATGAAACTGGCAAATGAGT 808138 ii i i v i i i- v -i - ii vi L1ME1_3end#LI 441 AATGTTCATAGCAGCTTTATTCGTAATAGCCA-AAAACTGG-AAACAACC 488 chr2qtel1M 808139 -GAATGCCCATCAGTGGGTGAATGGCTGAATAAGTTATGACATAT 808182 -i i ii? v i i i i ii L1ME1_3end#LI 489 CAAATGTCCATCAACNGGTGAATGGATAAACAAATTGTGGTATAT 533 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.10 CpG sites = 21, Kimura (unadjusted) = 38.11 Transitions / transversions = 5.25 (21/4) Gap_init rate = 0.04 (4 / 92), avg. gap size = 1.00 (4 / 4) 322 30.28 5.74 0.45 chr2qtel1M 808560 808768 (191232) C L1MC_orf2#LINE/L1 (1995) 1299 1080 m_b103s551i21 3786 chr2qtel1M 808560 AATGAATTG-TGCATTTCAGTTAGATTGTTAGACTTACTGTCATAGAGTT 808608 v - v vi i i i i i iiv v C L1MC_orf2#LIN 1299 AAGGAATTGGTCCATTTCATCTAGGTTATCAAATTTGTGGGCATAGAGTT 1250 chr2qtel1M 808609 GAGCAAAAGAGCTCCCAATTATTGATTTAATTTCTTTTTCATTGGTGGTG 808658 vv v iv vii iiv ivv v iv vvv i? i C L1MC_orf2#LIN 1249 GTTCATAGTATTCCTTTATTATCCTTTTAATGTCCATGGGATCNGTAGTG 1200 chr2qtel1M 808659 AATTCGCCCCTTTCATTTTTGATGTTGGTGATTT---TTTTCT---TTTT 808702 vv v i i i i i --- i --- C L1MC_orf2#LIN 1199 ATGTCCCCTCTTTCATTTCTGATATTAGTAATTTGTGTCTTCTCTCTTTT 1150 chr2qtel1M 808703 TTTCTCAACTAATC-----AAATATTTATCTGTTTTGTTAGTTTTTTTCA 808747 i ii ii ----- i vii vi i - v i C L1MC_orf2#LIN 1149 TTTCTTAGTTAGCCTGGCTAGAGGCTTATCAATTTTATT-GATCTTTTCA 1101 chr2qtel1M 808748 TAAAACCAGCTCTTAGTTTTG 808768 v i i i i C L1MC_orf2#LIN 1100 AAGAACCAGCTTTTGGTTTCG 1080 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.53 CpG sites = 38, Kimura (unadjusted) = 40.38 Transitions / transversions = 1.52 (38/25) Gap_init rate = 0.02 (5 / 208), avg. gap size = 2.60 (13 / 5) 306 28.94 6.09 0.83 chr2qtel1M 808566 808795 (191205) C L1M5_orf2#LINE/L1 (2002) 1292 1051 m_b103s551i22 3786 chr2qtel1M 808566 TTGTGCATTTCAGTTAGATTGTTAGACTTACTGTCATAGAGTTGAGCAAA 808615 v vi ii ? i i i i v i vv v C L1M5_orf2#LIN 1292 TTGTCCATTTCATCTAAGTTNTCAAATTTATTGGCATAAAGTTGTTCATA 1243 chr2qtel1M 808616 AGAGCTCCCAATTATTGATTTAATTTCTTTTTCATTGGTGGTGAATTCGC 808665 v viii iv ivv v v vvv iv i vv v C L1M5_orf2#LIN 1242 ATATTCTCTTATTATCCTTTTAATGTCTGTAGGATCTGTAGTGATGTCTC 1193 chr2qtel1M 808666 CCCTTTCATTTTTGATGTTGGTGATTT-----TTTTCT-TTTTTTTCTCA 808709 ii ii i i ----- i - ii C L1M5_orf2#LIN 1192 CTTTTTCATTCCTGATATTGGTAATTTGTGTCTTCTCTCTTTTTTTCTTG 1143 chr2qtel1M 808710 ACTAATC-----AAATATTTATCTGTTTTGTTAGTTTTTTTCATAAAACC 808754 ii i ----- i vi vi i - v i v i C L1M5_orf2#LIN 1142 ATCAGTCTNGCTAGAGGTTTATCAATTTTATT-GATCTTTTCAAAGAACC 1094 chr2qtel1M 808755 AGCTCTTAGTT---TTGCTTTACTCAAATTGTATTTGTGGTCTC 808795 i i i --- v v -v ? ? v v i C L1M5_orf2#LIN 1093 AGCTTTTGGCTTCGTTGATTTTCTC-TATTGTNTNTTTGTTTTC 1051 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.06 CpG sites = 37, Kimura (unadjusted) = 38.06 Transitions / transversions = 1.28 (37/29) Gap_init rate = 0.03 (6 / 229), avg. gap size = 2.67 (16 / 6) 580 30.40 8.21 0.00 chr2qtel1M 809938 810266 (189734) L1ME4a_3end#LINE/L1 56 411 (460) m_b103s551i23 3787 chr2qtel1M 809938 CTCCAATTGACAAATGGTCAAAGGATTT-------CAAT--------GAA 809972 i v v v iv ------- -------- L1ME4a_3end#L 56 CCCCAATAGAAAAATGGGCAAAGGACATGAACAGACAATTCACAAAAGAA 105 chr2qtel1M 809973 AAAATAAAAATCATTTCTAGTCACATGAAAAAATGCTCTAAATCACTATT 810022 i v viiivv iv i ? i v vv v L1ME4a_3end#L 106 GAAATACAAATGGCCAATAAACATATGAAAANATGTTCAACCTCACTAGT 155 chr2qtel1M 810023 GGTCAGAGAAATGTAAATGAAGACAATTCTGAGGTACCA-----GATCTT 810067 ii i i v i ivv i -----v i v L1ME4a_3end#L 156 AATCAAAGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCTA 205 chr2qtel1M 810068 TCATATTGGATAAGATAGCAGAGAAAGATAATGATGAGTGTTGAAA---- 810113 v vv vvv i vv iviv ivi---- L1ME4a_3end#L 206 TCAAATTGGCAAAGATTTAAAAGATTGATAATACCCAGTGTTGGCGAGGG 255 chr2qtel1M 810114 ---GGAAAAACTGGGACACTAATACATTGTTGGTGGAATTGTGAACTGAG 810160 --- ?i v v v v i i i v i i iv L1ME4a_3end#L 256 TGTGGNGAAACGGGCACTCTCATACACTGCTGGTGGGAGTGTAAATTGGT 305 chr2qtel1M 810161 TCAGTCATTCTGGAGAATAATATGGAACTATGCCCAAAAAGCTAGCACAG 810210 v ii v iii v v v iviv ivvv v i L1ME4a_3end#L 306 ACAACCTTTCTGGAGGGCAATTTGGCAATATGTATCAAAAGCCTTAAAAA 355 chr2qtel1M 810211 TGTGCATACCCTTTGATCCAGCAGTATCTCTACTGAACCTGTATCCCAAA 810260 ? i i i vi v v iiivv v i i L1ME4a_3end#L 356 TGTNCATACCCTTTGACCCAGTAATTCCACTTCTAGGAATTTATCCTAAG 405 chr2qtel1M 810261 GAGATA 810266 i L1ME4a_3end#L 406 GAAATA 411 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.36 CpG sites = 48, Kimura (unadjusted) = 39.86 Transitions / transversions = 0.92 (48/52) Gap_init rate = 0.02 (5 / 328), avg. gap size = 5.40 (27 / 5) 574 31.26 6.80 1.68 chr2qtel1M 809940 810336 (189664) L1ME3G_3end#LINE/L1 54 470 (454) m_b103s551i24 3787 chr2qtel1M 809940 CCAATTGACAAATGGTCAAAGGATTT-------CAAT--------GAAAA 809974 v v v v ------- -------- ii L1ME3G_3end#L 54 CCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGGA 103 chr2qtel1M 809975 AATAAAAATCATTTCTAGTCACATGAAAAAATGCTCTAAATCACTATTGG 810024 v viiivv iv i i v vv v ii L1ME3G_3end#L 104 AATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTAA 153 chr2qtel1M 810025 TCAGAGAAATGTAAATGAAGACAATTCTGAGGTACCA-----GATCTTTC 810069 i i v i ivv i -----v i iv L1ME3G_3end#L 154 TCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCATC 203 chr2qtel1M 810070 ATATTGGATAAGATAGCAGAGAAAGATAATGATGAGTGTTGAAA------ 810113 v vv i vvv i ?vv ivi? ivi------ L1ME3G_3end#L 204 AGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGTG 253 chr2qtel1M 810114 -GGAAAAACTGGGACACTAATACATTGTTGGTGGAATTGTGAACTGAGTC 810162 - ii v v v v i i i v i i ivv L1ME3G_3end#L 254 TGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTAC 303 chr2qtel1M 810163 AGTCATTCTGGAGAATAATATGGAACTATGCCCAAAAAGCTAGCACAGTG 810212 i ? i iii v v v viviv vi i--- i L1ME3G_3end#L 304 AGCCNTTTTGGAGGGCAATTTGGCAGTATCTATTAAAATTTAA---AATG 350 chr2qtel1M 810213 TGCATACCCTTTGATCCAGCAGTATCTCTACTGAACCTGTATCCCAAAGA 810262 i i i vi v v ?ii?v v i ? L1ME3G_3end#L 351 CGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAGA 400 chr2qtel1M 810263 GATACAGATAAAAAGAGGCTAAAGGACTCACATGTGCAAAAATGTTTGTA 810312 i --viiv v viv vv --?i i ii ii v L1ME3G_3end#L 401 AATAC--TCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTCATT 446 chr2qtel1M 810313 GTAGCTCTTTCTGTAGTGGAGGAA 810336 i vi v i i i v i L1ME3G_3end#L 447 GCAGCATTGTTTGTAATAGCGAAA 470 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.86 CpG sites = 64, Kimura (unadjusted) = 42.26 Transitions / transversions = 1.10 (64/58) Gap_init rate = 0.03 (12 / 396), avg. gap size = 2.83 (34 / 12) 233 31.21 7.89 5.13 chr2qtel1M 814065 814216 (185784) MIR3#SINE/MIR 46 201 (7) m_b103s601i11 3788 chr2qtel1M 814065 GACCATGGTTGTAGGAACTGACCCTAACACTCAGAAATGGC-AT-CAATT 814112 vv v vv- i i i iv --- v ? -i -ii ii MIR3#SINE/MIR 46 GACCTGGGTTCTAGTC-CCGGCTCTGCCACT---AACTNGCTGTGTGACC 91 chr2qtel1M 814113 TTGAGTAAATC-CTT----TCTCTG--CTTGAGTTTCCTC--TTGTAAAT 814153 i i i - ---- -- i v --i v MIR3#SINE/MIR 92 TTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAA 141 chr2qtel1M 814154 TGGAGCAGTTTGGTTGGATTCTTGAATTTTGAAGTGAATTTCAGCTCT-A 814202 ii vi v ii i ---- vi i i i vvv i - MIR3#SINE/MIR 142 TGAGGGGGTTGGACTAGA----TGATCTCTAAGGTCCCTTCCAGCTCTGA 187 chr2qtel1M 814203 CATCTCATGACTTT 814216 iii i i MIR3#SINE/MIR 188 CATTCTATGATTCT 201 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.75 CpG sites = 30, Kimura (unadjusted) = 43.05 Transitions / transversions = 2.00 (30/15) Gap_init rate = 0.10 (15 / 151), avg. gap size = 1.33 (20 / 15) 15 15.89 2.86 0.00 chr2qtel1M 814927 814961 (185039) (TACAA)n#Simple_repeat 1 36 (0) m_b104s252i0 3789 chr2qtel1M 814927 TATAATACATTA-ACAACAATACAATACAAAACAAT 814961 i v - vv v (TACAA)n#Simp 1 TACAATACAATACAATACAATACAATACAATACAAT 36 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 26 18.85 0.00 0.00 chr2qtel1M 815042 815089 (184911) (A)n#Simple_repeat 1 48 (0) m_b104s252i1 3790 chr2qtel1M 815042 AAATAAAAAGCTATAATAAAAAAAAAAAAGAAAAAAAAAAAGAAAAAA 815089 v ivv v v i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 48 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 247 26.74 6.98 0.00 chr2qtel1M 815772 815857 (184143) MIR3#SINE/MIR 111 202 (6) m_b104s601i1 3791 chr2qtel1M 815772 TCCCTGAATCT--GTTTCC-CATTTGTACAATGAGTGGGAGGCACTCCAT 815818 i iii -- - i v v vv v vv MIR3#SINE/MIR 111 TCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGAT 160 chr2qtel1M 815819 GGCCTTGTAGATCCCTTCCAG---TGATTATCTAGGATCCTA 815857 ii ivv i --- ivv v i MIR3#SINE/MIR 161 GATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTA 202 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.34 CpG sites = 11, Kimura (unadjusted) = 33.34 Transitions / transversions = 0.92 (11/12) Gap_init rate = 0.04 (3 / 85), avg. gap size = 2.00 (6 / 3) 276 32.44 6.96 0.82 chr2qtel1M 815958 816072 (183928) C L2d2_3end#LINE/L2 (6) 549 428 m_b104s601i2 3792 chr2qtel1M 815958 CAAATTAGCAAACATTTA---AGTGCCTGCTATAAGCCAGGCCCTGAGTT 816004 i i i --- i i i iv v v v i C L2d2_3end#LIN 549 CAAATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCT 500 chr2qtel1M 816005 ATGCCCCA---GGAACATAAAAAGATGCAAGGGACTTCCCCTGCTCTCCT 816051 v v ii--- i i i i ii ii iv ivvi i vv C L2d2_3end#LIN 499 AGGCGCTGTGGGGGATACAAAGAAGTATAAGACATGGTCCCTGCCCTCAA 450 chr2qtel1M 816052 GCAGTTTACACATC--ACTGGGG 816072 v i - --ii C L2d2_3end#LIN 449 GGAGCTTACA-ATCTAGTTGGGG 428 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 43.46 CpG sites = 25, Kimura (unadjusted) = 45.16 Transitions / transversions = 2.08 (25/12) Gap_init rate = 0.04 (4 / 114), avg. gap size = 2.25 (9 / 4) 270 31.42 7.14 1.50 chr2qtel1M 815962 816087 (183913) C L2b_3end#LINE/L2 (10) 456 324 m_b104s601i3 3792 chr2qtel1M 815962 TTAGCAAACATTTA---AGTGCCTGCTATAAGCCAGGCCCTGAGTTATGC 816008 i i i --- i i i iv ? v i v C L2b_3end#LINE 456 TCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGC 407 chr2qtel1M 816009 CCCAGGAACATAAAAAGATG--CAAG--GGACTT--CCCCTGCTCTCCTG 816052 v ii i-- v iv i -- --i ?i--i i vi C L2b_3end#LINE 406 GCTGGGG--ATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACG 359 chr2qtel1M 816053 CAGTTTACACATCACTGGGGCACATATACCAGTAA 816087 v i i vvii v v v i v vv C L2b_3end#LINE 358 GAGCTCACAGTCTAGTGGGGGAGACAGACATGTAA 324 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.78 CpG sites = 23, Kimura (unadjusted) = 43.09 Transitions / transversions = 1.44 (23/16) Gap_init rate = 0.05 (6 / 125), avg. gap size = 1.83 (11 / 6) 405 27.85 14.76 2.55 chr2qtel1M 816207 816416 (183584) C MIRb#SINE/MIR (0) 268 34 m_b104s601i4 3793 chr2qtel1M 816207 AATACCATACCTAGCATATATACAGCACCTTCTATG--ACATGCAGTGTG 816254 vi v v v v vv i i v --v v v C MIRb#SINE/MIR 268 AATAATAGAGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTG 219 chr2qtel1M 816255 TCA------------GTATTGTCTCATTTTATCCTCATGAGAACCCTAGG 816292 ii ------------ i i v ii v iv C MIRb#SINE/MIR 218 CTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCG 169 chr2qtel1M 816293 ACTTGGGTACTGTTATTGTGTCCTTTTTATACATAAAGAAACTGAGACAA 816342 vv i --- i vi v i v i i i vv C MIRb#SINE/MIR 168 AGGTAGGTA---TTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC 122 chr2qtel1M 816343 ACAGAGGTCTTGTAAGTTG--------------ATTAGCAAGTTGCTGAG 816378 v ivv v --------------ii i v v C MIRb#SINE/MIR 121 AGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAG 72 chr2qtel1M 816379 GTGGGAT--GAACACTCAGTTTATTGCTGACT-TAAGGCCC 816416 vi -- - ivi i i -- -i i C MIRb#SINE/MIR 71 CCGGGATTCGAAC-CCAGGTCTGT--CTGACTCCAAAGCCC 34 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.82 CpG sites = 28, Kimura (unadjusted) = 35.31 Transitions / transversions = 0.97 (28/29) Gap_init rate = 0.05 (11 / 209), avg. gap size = 3.36 (37 / 11) 428 28.63 9.43 1.16 chr2qtel1M 816258 816416 (183584) C MIR#SINE/MIR (63) 199 28 m_b104s601i5 3793 chr2qtel1M 816258 GTATTGTCTCATTTTATCCTCATGAGAACCCTAGGACTTGGGTACTGTTA 816307 iv v ii v v vv i i C MIR#SINE/MIR 199 GTATTAACTCATTTAATCCTCACAACAACCCTATGAGGTAGGTACTATTA 150 chr2qtel1M 816308 TTGTGTCCTTTTTATACATAAAGAAACTGAGACAAACAGAGGTCTTGTAA 816357 i vi v i v i i i v v ivv C MIR#SINE/MIR 149 TTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAA 100 chr2qtel1M 816358 GTTG--------------ATTAGCAAGTTGCTGAGGTGGGATGAACACTC 816393 v --------------ii i v v vi vviv i C MIR#SINE/MIR 99 CTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCC 50 chr2qtel1M 816394 AGTTTATTGCTGACTTAAG-GCCC 816416 vivi -- i iv - C MIR#SINE/MIR 49 AGGCAGT--CTGGCTCCAGAGCCC 28 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.53 CpG sites = 22, Kimura (unadjusted) = 36.49 Transitions / transversions = 0.96 (22/23) Gap_init rate = 0.03 (4 / 158), avg. gap size = 4.25 (17 / 4) 22 4.00 0.00 0.00 chr2qtel1M 819670 819695 (180305) (T)n#Simple_repeat 1 26 (0) m_b104s252i2 3794 chr2qtel1M 819670 TTTTTTTTTTTTTTTTTTTTCTTTTT 819695 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 chr2qtel1M 823061 823078 (176922) (T)n#Simple_repeat 1 18 (0) m_b104s252i3 3795 chr2qtel1M 823061 TTTTTTTTTTTTTTTTTT 823078 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTT 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 417 34.39 1.17 1.56 chr2qtel1M 823489 823745 (176255) C L1ME4c_3end#LINE/L1 (191) 639 384 m_b104s551i0 3796 chr2qtel1M 823489 TTCTGCTCATTTCACTCAGCATCAGTTCATGTCAGTCTCTCCAATCCT-C 823537 iv i i i vv i-- iiv i i v vi - C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATA--AACATTTTCCATGTTGC 592 chr2qtel1M 823538 TCTGTATTCATCCTGCTGGTCATTTCTTACAGAACAACAATATTCCATAA 823587 vii v v v iv vi i v ii vvvv i vi C L1ME4c_3end#L 591 TACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCG 542 chr2qtel1M 823588 CATTCATATACCACAATTTACCCAGGCATTTTCCGATTGATGGGCATCCA 823637 vi ?v i i ii iv ii v v i ii C L1ME4c_3end#L 541 AGTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTA 492 chr2qtel1M 823638 CTCATTTTCCAGTTTCTGGCCACTACAAAAAGAGCTGCCGCAAACATTTT 823687 vvivv i i v i i i v iv viii i C L1ME4c_3end#L 491 GGTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTT 442 chr2qtel1M 823688 GGCACATACAGGTCCTTTTCCTTTCTTT--AGTATCTCTTTGGGATATAG 823735 v ii i -- i ii -- v i i i v v C L1ME4c_3end#L 441 CGTGCATATAG--CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAAT 394 chr2qtel1M 823736 GCCCAGTAGT 823745 v v C L1ME4c_3end#L 393 TCCCAGAAGT 384 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 47.14 CpG sites = 50, Kimura (unadjusted) = 47.92 Transitions / transversions = 1.35 (50/37) Gap_init rate = 0.02 (6 / 256), avg. gap size = 1.17 (7 / 6) 358 27.83 2.26 5.43 chr2qtel1M 824456 824588 (175412) L1ME3Cz_3end#LINE/L1 420 548 (449) m_b104s551i1 3797 chr2qtel1M 824456 AAGGAGACCCACATGTGGAAAAATGTTTGTGGCAGCTCTTTCTGTAGTGG 824505 ---- iv ii ii v vi v i i i L1ME3Cz_3end# 420 AAGGAGAC----ATGTACAAGGATGTTCATTGCAGCATTGTTTGTAATAG 465 chr2qtel1M 824506 CAAGAAATTGT---CAACTGAATGGATGCCCATCAGTGGGGGAATGGCTG 824552 i i v--- iv --- i i i v i L1ME3Cz_3end# 466 CGAAAAATTGGAAACAACCTAA---ATGTCCATCAATAGGGGAATGGATA 512 chr2qtel1M 824553 AATAAGTTATGACATATGAATGTATTGGACTGTTAT 824588 i i ii vv ii v v ii L1ME3Cz_3end# 513 AATAAATTGTGGTATATTCATACAATGGAATACTAT 548 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 35.05 CpG sites = 24, Kimura (unadjusted) = 36.38 Transitions / transversions = 2.18 (24/11) Gap_init rate = 0.06 (8 / 132), avg. gap size = 1.25 (10 / 8) 299 36.41 1.43 1.91 chr2qtel1M 824464 824673 (175327) L1ME4c_3end#LINE/L1 431 639 (191) m_b104s551i2 3797 chr2qtel1M 824464 CCACATGTGGAAAAATGTTTGTGGCAGCTCTTTCTGTAGTGGCAAGAAAT 824513 i i iivi i ii v vi v i i i i i i L1ME4c_3end#L 431 CTATATGCACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAAT 480 chr2qtel1M 824514 TGT---CAACTGAATGGATGCCCATCAGTGGGGGAATGGCTGAATAAGTT 824560 v--- iv --- i v i i i i i i L1ME4c_3end#L 481 TGGAAACAACCTAA---ATGTCCAACAATAGGGGAATGGTTAAGTAAATT 527 chr2qtel1M 824561 ATGACATATGAATGTATTGGACTGTTATTGTTCTATAAGAAATGATCAGC 824610 ii i v? iviiv v i vvvv i v i v vi L1ME4c_3end#L 528 ATGGTACATCNACTCGATGGAATATTATGCAGCCATTAAAAATGATAATT 577 chr2qtel1M 824611 AGGATGATTTCAGAGAGGCCTAGAGAGTCTTACATGAACTGAGGCTAAGT 824660 v v i viiv vii v i i i v -i vv i v i L1ME4c_3end#L 578 ATGAAGACTATGTAGCAACATGGAAAATGTT-TATGATATAATGTTAAGT 626 chr2qtel1M 824661 GCAATGAGCAGAA 824673 v vi L1ME4c_3end#L 627 GAAAAAAGCAGAA 639 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 49.48 CpG sites = 45, Kimura (unadjusted) = 52.67 Transitions / transversions = 1.50 (45/30) Gap_init rate = 0.02 (5 / 209), avg. gap size = 1.40 (7 / 5) 362 26.00 2.91 2.91 chr2qtel1M 824467 824569 (175431) L1ME3G_3end#LINE/L1 427 529 (395) m_b104s551i3 3797 chr2qtel1M 824467 CATGTGGAAAAATGTTTGTGGCAGCTCTTTCTGTAGTGGCAAGAAATTGT 824516 iv ii ii v vi v i i i i i v L1ME3G_3end#L 427 CATGTACAAGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGG 476 chr2qtel1M 824517 ---CAACTGAATGGATGCCCATCAGTGGGGGAATGGCTGAATAAGTTATG 824563 --- iv --- i i i i i i L1ME3G_3end#L 477 AAACAACCTAA---ATGTCCATCAATAGGGGAATGGTTAAATAAATTATG 523 chr2qtel1M 824564 ACATAT 824569 ii L1ME3G_3end#L 524 GTATAT 529 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 32.37 CpG sites = 20, Kimura (unadjusted) = 34.01 Transitions / transversions = 3.33 (20/6) Gap_init rate = 0.04 (4 / 102), avg. gap size = 1.50 (6 / 4) 487 30.54 2.06 1.64 chr2qtel1M 825081 825323 (174677) C L1M5_orf2#LINE/L1 (2000) 1294 1051 m_b104s551i4 3798 chr2qtel1M 825081 ATCTATGCATTTTAGTTAGATTGTCAGACTTGCTGTCATAGAGTTGGGCA 825130 i i v i vi ii ? i i ii v i vv C L1M5_orf2#LIN 1294 ATTTGTCCATTTCATCTAAGTTNTCAAATTTATTGGCATAAAGTTGTTCA 1245 chr2qtel1M 825131 AAAGAGCTCCTAATTATTGATTTAATTTCTTTTTCATTGATAATGAATTC 825180 v v viii v ivv v v vvv ivi i vv C L1M5_orf2#LIN 1244 TAATATTCTCTTATTATCCTTTTAATGTCTGTAGGATCTGTAGTGATGTC 1195 chr2qtel1M 825181 CCCCCTTTCATTTTTGATGTTGGTGATTT---TTTTCTCTTTTTTTTCCC 825227 i ii ii i i --- i i i - C L1M5_orf2#LIN 1194 TCCTTTTTCATTCCTGATATTGGTAATTTGTGTCTTCTCTCTTTTTTTC- 1146 chr2qtel1M 825228 CCTCAACTAAT-TAGCCAGAGATTTATCTGTTTTGTTAGTTTCTTCATAA 825276 -- ii ii i - ? i i vi i ii i i v i C L1M5_orf2#LIN 1145 --TTGATCAGTCTNGCTAGAGGTTTATCAATTTTATTGATCTTTTCAAAG 1098 chr2qtel1M 825277 AACCAACTCTTTGTTTTGTTTA-TTTCTCCAGTTGTGTTTGTGGTCTC 825323 i i v i i v - i - ? ? v v i C L1M5_orf2#LIN 1097 AACCAGCTTTTGGCTTCGTTGATTTTCTCTA-TTGTNTNTTTGTTTTC 1051 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.37 CpG sites = 48, Kimura (unadjusted) = 42.15 Transitions / transversions = 1.92 (48/25) Gap_init rate = 0.03 (7 / 242), avg. gap size = 1.29 (9 / 7) 499 30.80 1.87 1.40 chr2qtel1M 825088 825301 (174699) C L1MC_orf2#LINE/L1 (2007) 1287 1073 m_b104s551i5 3798 chr2qtel1M 825088 CATTTTAGTTAGATTGTCAGACTTGCTGTCATAGAGTTGGGCAAAAGAGC 825137 i vi i i i i iv v vv v iv vi C L1MC_orf2#LIN 1287 CATTTCATCTAGGTTATCAAATTTGTGGGCATAGAGTTGTTCATAGTATT 1238 chr2qtel1M 825138 TCCTAATTATTGATTTAATTTCTTTTTCATTGATAATGAATTCCCCCCTT 825187 i i v ivv v iv vvv i?i i vv i C L1MC_orf2#LIN 1237 CCTTTATTATCCTTTTAATGTCCATGGGATCNGTAGTGATGTCCCCTCTT 1188 chr2qtel1M 825188 TCATTTTTGATGTTGGTGATTT---TTTTCTCTTTTTTTTCCCCCTCAAC 825234 i i i i --- i i ---i i ii C L1MC_orf2#LIN 1187 TCATTTCTGATATTAGTAATTTGTGTCTTCTCTCTTTTTT---TCTTAGT 1141 chr2qtel1M 825235 TAA-TTAGCCAGAGATTTATCTGTTTTGTTAGTTTCTTCATAAAACCAAC 825283 i-i i i ii vi i ii i i v i i C L1MC_orf2#LIN 1140 TAGCCTGGCTAGAGGCTTATCAATTTTATTGATCTTTTCAAAGAACCAGC 1091 chr2qtel1M 825284 TCTTTGTTTTGTTTATTT 825301 i v i v C L1MC_orf2#LIN 1090 TTTTGGTTTCGTTGATTT 1073 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.11 CpG sites = 43, Kimura (unadjusted) = 41.98 Transitions / transversions = 1.95 (43/22) Gap_init rate = 0.02 (5 / 213), avg. gap size = 1.40 (7 / 5) 236 31.00 3.36 5.13 chr2qtel1M 826239 826357 (173643) MIRc#SINE/MIR 83 199 (69) m_b104s601i6 3799 chr2qtel1M 826239 AGCTGCTGGGATTTGGGTCAAATCACTGAATCCCTCTGAA-CTGGGTGGC 826287 - v ii v v i v i i i- vi vv MIRc#SINE/MIR 83 AGCTG-TGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTC 131 chr2qtel1M 826288 CTAAGTTGTACAAGTAGTGAGAATGAAGGCACTTTCTCTGT---TGTCCC 826334 v vi - i i v v i ---i i v i i---iv v MIRc#SINE/MIR 132 CTCATCTGTA-AAATGGGGATAATAA---TACCTGCCCTGCCTACCTCAC 177 chr2qtel1M 826335 AGATTTACTGTGAGAATCCAAAT 826357 iv ii i - MIRc#SINE/MIR 178 AGGGTTGTTGTGAGGAT-CAAAT 199 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 41.06 CpG sites = 20, Kimura (unadjusted) = 41.06 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.07 (8 / 118), avg. gap size = 1.25 (10 / 8) 711 31.33 5.94 3.80 chr2qtel1M 826491 826928 (173072) L1ME5_3end#LINE/L1 56 502 (439) m_b104s551i6 3800 chr2qtel1M 826491 CTCCAATTGATAAATGGTCAAAAGGT-TGTACA----ATTTTCAGATGAA 826535 i v v v i i - v ---- v v i L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chr2qtel1M 826536 AAAA---GAAAAATCATTTTTAGTCCTATGAAAAAATGATCTAAATCGCT 826582 i --- iiii vi--- iv v i i v v v ii L1ME5_3end#LI 106 GAAACCCGAAAGGCTAAC---AAGCATATGAAGAGATGCTCAAACTCATT 152 chr2qtel1M 826583 GTTGATCAGAGAAATGTAAATGAAGACAATTCTGAGCTACCAG-----AT 826627 iv i i v i ivv v i v----- i L1ME5_3end#LI 153 AGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACAC 202 chr2qtel1M 826628 CTTTCATATTGGCTAAGATGACAGGGAAAGATAATGATGAGTGTTGAAG- 826676 v i v i v i v v ii vvi vii iv - L1ME5_3end#LI 203 CTATTAGACTGGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTGGCGA 252 chr2qtel1M 826677 GGATGAGGGAAAACTGGGTTATTAATACATTGTTTTTGGAATTGTGAACT 826726 v i ? iv ivivi v i i i vv i v ii L1ME5_3end#LI 253 GGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACT 302 chr2qtel1M 826727 GATCCAGTCATTCTGGAGAATAATATGGAGCTATGCCTAAAGGGTTA--T 826774 i v i ii v -- vi i i ---- i -- L1ME5_3end#LI 303 GGTGCAGCCATTCTGGAGAGCAATCTGG--CAGTACTTA----GTCAAAT 346 chr2qtel1M 826775 CACGGTGTAC--ATACCCTTTGATCCAGCAGTGTCTCTACTGAGCCTGTA 826822 i -i i -- v i i vi v v i iv i L1ME5_3end#LI 347 TA-AGTATACGCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATA 395 chr2qtel1M 826823 TCCCAAAGAGATT---ATAAAGG-AGAGAAAAGAACCCACATGTGCAAAA 826868 i --- i v -vv v ii i---- i i ii L1ME5_3end#LI 396 TCCCAAAGAAATTCTCACACAGGTCCATAAGGGG----ACATGTACGAGG 441 chr2qtel1M 826869 ATGTTTGTAGTAGCTCTCTCTGTAGTGGAGGGAGGACTATGGGGA----T 826914 ii v i vi v i i v -- v - i i----i L1ME5_3end#LI 442 ATGTTCATTGCAGCGTTGTTTGTGGTGGCGG--GGAGT-TGGAGGCAACC 488 chr2qtel1M 826915 TGAGTATGCATCAC 826928 i i v L1ME5_3end#LI 489 TGGGTGTCCATCAC 502 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.74 CpG sites = 79, Kimura (unadjusted) = 42.17 Transitions / transversions = 1.49 (79/53) Gap_init rate = 0.06 (27 / 437), avg. gap size = 1.59 (43 / 27) 13 18.71 0.00 5.26 chr2qtel1M 826949 826988 (173012) (TTTTTG)n#Simple_repeat 1 38 (0) m_b104s252i4 3801 chr2qtel1M 826949 TTTTAGTTTACTTGTCTTTGTTTTTGTTTCTCATTTTTTT 826988 v -- i i vv v (TTTTTG)n#Sim 1 TTTTTGTTT--TTGTTTTTGTTTTTGTTTTTGTTTTTGTT 38 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 16 22.13 0.00 0.00 chr2qtel1M 828298 828329 (171671) (T)n#Simple_repeat 1 32 (0) m_b104s252i5 3802 chr2qtel1M 828298 TTTTTGTTTTTGTTTTTAATATATTTTTTTTT 828329 v v vv v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 32 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 17 16.14 0.00 0.00 chr2qtel1M 828392 828420 (171580) (T)n#Simple_repeat 1 29 (0) m_b104s252i7 3802 chr2qtel1M 828392 TTTCTTTCTTTCTTTTTTTTTTTTTCTTT 828420 i i i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 185 35.61 3.75 2.89 chr2qtel1M 829143 829382 (170618) L2#LINE/L2 1953 2194 (888) m_b104s601i7 3803 chr2qtel1M 829143 TCAAAGTTTCGTCCCTTTC-CTCAATCTTTCCAGCTTCTTCTCTGACTTA 829191 iiv ivi - v i vvvv v - v viiv i L2#LINE/L2 1953 TCAGGCTTTCGTCCCCACCACTCCACCGAAACTGCT-CTTGTCAAGGTCA 2001 chr2qtel1M 829192 TCAAAAGGTCTTATCTTTCCAAGTCCA-TGGAGCTCATCTCCCCAATCCC 829240 i viiviiii iv v i i - --- -v i i i - L2#LINE/L2 2002 CCAATGACCTCCACGTTGCTAAATCCAATGG---TCA-ATTCTCAGTCC- 2046 chr2qtel1M 829241 TGATTTT-TTTGATTGTTCTTCAGCCTTTGACATTCCTGGTGACTCTCTC 829289 v i -i iiv? vv v ivvi i v i L2#LINE/L2 2047 TCATCTTACTTGACCTNTCAGCAGCATTTGACACAGTTGATCACTCCCTC 2096 chr2qtel1M 829290 TCCTCCAGGGTTCTCTCTTCTCTTAGTTTTTAGGACACGGCTCTTTCCTG 829339 iiiiiiiiiiiv i v i i ii vi v i L2#LINE/L2 2097 CTTCTTGAAACACTTTCTTCACTTGGCTTCCAGGACACCACACTCTCCTG 2146 chr2qtel1M 829340 ACTTTCC-CCT-CCTTATCTGCCCA---CTTCTCTGTCTTC-TTACTGG 829382 ii - - i - v i--- v i - i L2#LINE/L2 2147 GTTTTCCTCCTACCTCA-CTGGCCGCTCCTTCTCAGTCTCCTTTGCTGG 2194 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 49.76 CpG sites = 53, Kimura (unadjusted) = 51.60 Transitions / transversions = 1.77 (53/30) Gap_init rate = 0.06 (14 / 239), avg. gap size = 1.14 (16 / 14) 12 9.24 0.00 4.17 chr2qtel1M 829536 829560 (170440) (TCCC)n#Simple_repeat 1 24 (0) m_b104s252i8 3804 chr2qtel1M 829536 TCCCTCCCACCCTCCACCCCCTCCC 829560 v - i (TCCC)n#Simpl 1 TCCCTCCCTCCCTCC-CTCCCTCCC 24 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 1674 28.68 1.76 1.43 chr2qtel1M 829873 830498 (169502) C L1ME4c_3end#LINE/L1 (191) 639 12 m_b104s551i7 3805 chr2qtel1M 829873 TTCTGCTCATTTCACTTAGCATCAGTTCATGTAATTCTCTCCAAGCTTCT 829922 iv i i vv i- ivi i v i v C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATA-AACATTTTCCATGTTGCT 591 chr2qtel1M 829923 CTGTATTCATCCTGCTGGTCATTTCTTACAGAATA-ATAATATTCCATAA 829971 vii v v v iv vi - vv iv i- vi C L1ME4c_3end#L 590 ACATAGTCTTCATAATTATCATTT-TTAATGGCTGCATAATATTCCATCG 542 chr2qtel1M 829972 CATTCATATACCACAATTTACCCAACCATTCTCCAATTGCTGGGCATCCA 830021 vi ?v i i ii i v i i ii C L1ME4c_3end#L 541 AGTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTA 492 chr2qtel1M 830022 CTCAGTTTCCAGCTTCTAGCCACTACAAACGGGGCTGCCACAAACATTTT 830071 vviv ii i v i i i iiiv v ii i C L1ME4c_3end#L 491 GGTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTT 442 chr2qtel1M 830072 GGCTCACATTAGTCCCTTTCCCTTCTTT---AGTATCTCCTTGGGGTATA 830118 v iv i - -- i i --- v i i i v C L1ME4c_3end#L 441 CGTGCATAT-AG--CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAA 395 chr2qtel1M 830119 AGCCCAGGAGAAACACTGCTGGATCAAAGGGTATGCACAGTTTGATAACT 830168 vv i viiv i i i v v v ii C L1ME4c_3end#L 394 TTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCT 345 chr2qtel1M 830169 TTTTGAGCATAATTCCAGATTCCTCTCCAGAATGGTTGGATTCGTTCACA 830218 i vivi i v v i v i i v v iivi i C L1ME4c_3end#L 344 CTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACA 295 chr2qtel1M 830219 GCTCCACCAACAATGTATCAGTGTCACC-GTTTTCCCACATCCCCTCCAA 830267 ?iv i v ? - - iv i ? i v i C L1ME4c_3end#L 294 NTGCCACCAGCAATGTATGAGNGT-ACCAGTTTCACCGCANCCTCGCCAG 246 chr2qtel1M 830268 CAC------TCATCATTTTTCCCTGTCATCTTAGCCAATCTGACAGGTGT 830311 i------ i v --- vvv i v i i i i i C L1ME4c_3end#L 245 CATTGGGTATTATCAATTTT---TTAAATTTTTGCTAATTTAATAGGCGT 199 chr2qtel1M 830312 GTAGTGGTATCTCAGAGTTGTCTTAATTTGCATTTCTCTGATTAATAATG 830361 iv i vv ii i v ii C L1ME4c_3end#L 198 AAAATGGTATCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACTAGCG 149 chr2qtel1M 830362 ATTTGGAACACTCTTTCATATGAGTGGTAATGATTTCAATTTCATCATCT 830411 vv v i i i i vv v v iv ? vv v v ? C L1ME4c_3end#L 148 AGGTTGAACATTTTTCCATGTGTTTGTTTACTANTTGTATTTCCTCTTNT 99 chr2qtel1M 830412 GAAAATTGTCTGTTCATATCCTTTGACCATTTATCAATTGGAGAATGGCT 830461 vi i v v i vv v v C L1ME4c_3end#L 98 GTGAATTGTCTGTTCATGTCCTTTGCCCATTTATCTATTGGGGTCTTGAT 49 chr2qtel1M 830462 TGGTTTCTTATAAATGAGAGTCAGCTCTCTATATATT 830498 ?vv v vv i v i ? C L1ME4c_3end#L 48 NTTTTTCTTATCAATTTGAATGAGCTCTTTATATANT 12 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.11 CpG sites = 95, Kimura (unadjusted) = 37.43 Transitions / transversions = 1.16 (95/82) Gap_init rate = 0.02 (13 / 625), avg. gap size = 1.54 (20 / 13) 505 31.17 3.51 3.51 chr2qtel1M 830360 830758 (169242) C L1M5_orf2#LINE/L1 (0) 3294 2896 m_b104s551i9 3805 chr2qtel1M 830360 TGATTTGGAACACTCTTTCATATGAGTGGTAATGATTTCAATTTCATCAT 830409 ?v v i iii i vv iv iiiv v? v v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr2qtel1M 830410 CTGAAAATTGTCTGTTCATATCCTTTGACCATTTATCAATTGGAGAATGG 830459 i vi v vi i v v ?v ---i v C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGG---GTTG 3198 chr2qtel1M 830460 CTTGGTTTCTTATAAATGAG----AGTCAGCTCTCTATATATTTTGGAAA 830505 i vi i ? v v ?---- -v i i i v C L1M5_orf2#LIN 3197 TTTGTCTTTTTNTTATTGANTTGTAG-GAGTTCTTTATATATTCTGGATA 3149 chr2qtel1M 830506 TGAGTCCTTTATCAGA-ACCTTTAACTGTGAAGATGTTTTCCCAGTTTGT 830554 i i - iv v -?i ii v v i ? i C L1M5_orf2#LIN 3148 CGAGTCCTTTGTCAGATATATGT-NTTGCAAATATTTTCTCCCANTCTGT 3100 chr2qtel1M 830555 TGCTTCCCTTCTAATCTTGTTTACATTAGTTTTGTTTGTACAGAAGCTTT 830604 v v i v i v v iv ivi vvv? vi i C L1M5_orf2#LIN 3099 GGCTTGCCTTTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTT 3050 chr2qtel1M 830605 TTAATTTGATGTAATCAA-------AATTTTCTATTTTGTGATCAATAAT 830647 v v ? i v ------- i v i i --- ?i C L1M5_orf2#LIN 3049 TAATTTTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGGT---TNGT 3003 chr2qtel1M 830648 GGTCTCTAGTTCGTCTTTAGTCACAAATTTCTTCCTCTTCCACAAGTCTG 830697 v i i ivv v v --- v i i v v?i - i vv C L1M5_orf2#LIN 3002 GCTTTTTGTGTCCTGTTTA---AGAAATCTTTGCCTANCCCA-AGGTCAC 2957 chr2qtel1M 830698 AGAGATAAACTATCCTATG--TTCCTCCAATTTGTTTATAATCTCGTTCT 830745 ii -- i v -- i i ivvvv i i ii?ii C L1M5_orf2#LIN 2956 GAAGAT--ATTCTCCTATGTTTTCTTCTAGAAGTTTTATAGTTTTANCTT 2909 chr2qtel1M 830746 TTATGTCTAAATC 830758 ii i ii C L1M5_orf2#LIN 2908 TTACATTTAGGTC 2896 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.51 CpG sites = 64, Kimura (unadjusted) = 42.92 Transitions / transversions = 1.14 (64/56) Gap_init rate = 0.05 (18 / 398), avg. gap size = 1.56 (28 / 18) 553 29.63 2.17 2.17 chr2qtel1M 830360 830635 (169365) C L1M2_orf2#LINE/L1 (0) 3291 3016 m_b104s551i8 3805 chr2qtel1M 830360 TGATTTGGAACACTCTTTCATATGAGTGGTAATGATTTCAATTTCATCAT 830409 v v i i i ivv v iiiv vv v v v C L1M2_orf2#LIN 3291 TGATGTTGAGCATTTTTTCATATACCTGTTGGCCATTTGTATGTCTTCTT 3242 chr2qtel1M 830410 CTGAAAATTGTCTGTTCATATCCTTTGACCATTTATCAATTGGAGAATGG 830459 i i v i vi v v ? i vv -- C L1M2_orf2#LIN 3241 TTGAGAAATGTCTATTCAGGTCCTTTGCCCATTTTTNAATCGGATTAT-- 3194 chr2qtel1M 830460 CTTGGTTTCTTATAAATGAGA-GTC--AGCTCTCTATATATTTTGGAAAT 830506 - v i iiviv v- i-- i ii i v C L1M2_orf2#LIN 3193 -TTGTTTTTTTGCTGTTGAGTTGTTTGAGTTCCTTATATATTCTGGATAT 3145 chr2qtel1M 830507 GAGTCCTTTATCAGAACCTTTAACTGTGAAGATGTTTTCCCAGTTTGTTG 830556 v i i i vv?v vivi ii v v i v i v C L1M2_orf2#LIN 3144 TAATCCCTTGTCAGATGNATAGTTTGCAAATATTTTCTCCCATTCTGTAG 3095 chr2qtel1M 830557 CTTCCCTTCTAATCTTGTTTACATTAGTTTTGTTTG---TACAGAAGCTT 830603 v vi ii v iii --v - iv --- i C L1M2_orf2#LIN 3094 GTTGTCTCTTCACTCTGTT--GATT-GTTTCCTTTGCTGTGCAGAAGCTT 3048 chr2qtel1M 830604 TTTAATTTGATGTAATCAAAATTTTCTATTTT 830635 i vv v v C L1M2_orf2#LIN 3047 TTTAGTTTGATGTAATCCCATTTGTCTATTTT 3016 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.88 CpG sites = 39, Kimura (unadjusted) = 38.48 Transitions / transversions = 0.95 (39/41) Gap_init rate = 0.03 (9 / 275), avg. gap size = 1.33 (12 / 9) 18 26.92 0.00 5.00 chr2qtel1M 832294 832356 (167644) (TA)n#Simple_repeat 1 60 (0) m_b104s252i9 3806 chr2qtel1M 832294 TATTTATAGTTAGCTATACTATATATATATATACACACCATATATAACTG 832343 v vv vv - i i -i vv i (TA)n#Simple_ 1 TATATATATATATATATA-TATATATATATATATATA-TATATATATATA 48 chr2qtel1M 832344 TATAGTTACTATA 832356 vv - (TA)n#Simple_ 49 TATATATA-TATA 60 Matrix = Unknown Transitions / transversions = 0.44 (4/9) Gap_init rate = 0.05 (3 / 62), avg. gap size = 1.00 (3 / 3) 309 22.62 13.10 0.00 chr2qtel1M 836433 836516 (163484) MIR3#SINE/MIR 111 205 (3) m_b104s601i8 3807 chr2qtel1M 836433 TCACTGAATCTCAGTTTCC-CATTTATAAAATGAGTAGGTTAG------- 836474 v iii - i i vi i ------- MIR3#SINE/MIR 111 TCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGAT 160 chr2qtel1M 836475 GATCTTGTAGGTCCCTTCCAG---TGATCATCTAGGAGCCTATAA 836516 ivv --- ivv v vi i MIR3#SINE/MIR 161 GATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTATGA 205 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.37 CpG sites = 11, Kimura (unadjusted) = 27.37 Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.04 (3 / 83), avg. gap size = 3.67 (11 / 3) 271 29.04 6.78 0.80 chr2qtel1M 836616 836733 (163267) C L2b_3end#LINE/L2 (10) 456 332 m_b104s601i9 3808 chr2qtel1M 836616 TCAGCAAACTTTTA---AGTGCCTGCTATCAGCCAGGCCCTGGGCTGTGC 836662 i iv --- i i i vv ? v iv C L2b_3end#LINE 456 TCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGC 407 chr2qtel1M 836663 CCCAGGAACATATATAGAGA-CAAGG--GACTT--CCCCTGCTCTCCTGG 836707 v ii i i i -iii v - i-- ?i--i i vi C L2b_3end#LINE 406 GCTGGGGATACA-GCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGG 358 chr2qtel1M 836708 AGGTCACAGACAGCTGGGGCAGGCAG 836733 v v viv v i C L2b_3end#LINE 357 AGCTCACAGTCTAGTGGGGGAGACAG 332 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.12 CpG sites = 21, Kimura (unadjusted) = 38.94 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.04 (5 / 117), avg. gap size = 1.80 (9 / 5) 493 28.81 12.45 3.15 chr2qtel1M 836871 837103 (162897) C MIRb#SINE/MIR (0) 268 15 m_b104s601i10 3809 chr2qtel1M 836871 AATACCATACCTAGCATTTATACAGCACCTGCT--GTGACATGCAGTGTG 836918 vi v v v vv i i i -- v v v C MIRb#SINE/MIR 268 AATAATAGAGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTG 219 chr2qtel1M 836919 TCA------------GTATTGTCTCATTTTATCCTCATGAGAATCCTAGG 836956 ii ------------ i i v ii v i iv C MIRb#SINE/MIR 218 CTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCG 169 chr2qtel1M 836957 ACTCAGGTGCCATTATTGTGCCCTTCTTACAGATAAAGTCACTGAGGCCG 837006 vvi --- i v v i i i vv iv C MIRb#SINE/MIR 168 AGGTAGGT---ATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC 122 chr2qtel1M 837007 ACAGAGGTCTTGTAAGTTGC--------------CTAGCAAGTTGCTAAG 837042 v ivv v -------------- i v vi C MIRb#SINE/MIR 121 AGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAG 72 chr2qtel1M 837043 GTGGGATGAACACTCAGGTCTTGCTGA-TTGAAGGCCCTGTTCATACTTT 837091 vi vviv i vv - iv i ----- i i i C MIRb#SINE/MIR 71 CCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCC-----CGTGCTCT 27 chr2qtel1M 837092 TCCCCTTGTACC 837103 i vi i C MIRb#SINE/MIR 26 TTCCACTGCACC 15 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.15 CpG sites = 32, Kimura (unadjusted) = 36.88 Transitions / transversions = 0.97 (32/33) Gap_init rate = 0.05 (12 / 232), avg. gap size = 3.08 (37 / 12) 17 12.53 0.00 0.00 chr2qtel1M 837424 837449 (162551) (T)n#Simple_repeat 1 26 (0) m_b104s252i10 3810 chr2qtel1M 837424 TTTTTGTTTGTTCTTTTTTTTTTTTT 837449 v v i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 16 17.47 2.44 2.44 chr2qtel1M 838021 838061 (161939) (TTA)n#Simple_repeat 1 41 (0) m_b104s252i11 3811 chr2qtel1M 838021 TTTTTTTTTTAATTAATTAAT-TTATTATTATTATTATTTTT 838061 v v v v - v - v (TTA)n#Simple 1 TTATTATTATTATT-ATTATTATTATTATTATTATTATTATT 41 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 454 22.99 0.00 8.77 chr2qtel1M 838231 838354 (161646) C MIRc#SINE/MIR (153) 115 2 m_b104s601i11 3812 chr2qtel1M 838231 GGGGTTAAGTGACTTGCCTAGGGTCACACGGCTAGGAAGTGTGAAGTGTC 838280 i i i i v - v v i C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTG-GCAGAGCC 67 chr2qtel1M 838281 TGAGACCAGATTTGAACTCGGGTCCTCCTGACTTCAAGGTTGGTGCTCTA 838330 - i ----- i i i i i viii v C MIRc#SINE/MIR 66 -GGGAC-----TCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTT 23 chr2qtel1M 838331 TCTTCTGTGCCATCTAGCTGCCCC 838354 iv ii i---i i C MIRc#SINE/MIR 22 TCCACTGCACCAC---ACTGCCTC 2 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.31 CpG sites = 20, Kimura (unadjusted) = 28.62 Transitions / transversions = 3.33 (20/6) Gap_init rate = 0.08 (10 / 123), avg. gap size = 1.00 (10 / 10) 414 22.38 0.73 8.66 chr2qtel1M 838852 838988 (161012) MIR1_Amn#SINE/MIR 5 131 (99) m_b104s601i13 3813 chr2qtel1M 838852 GAGGCAGCTTAGTGGCTCAGTGGATAGAGCACCAGCCCTGAAGTCAGGGG 838901 i--- iii ii v iv i v - i MIR1_Amn#SINE 5 GAGGCAGT---GTGGTCTAGTGGATAGAGCACTGGACTGGGACTC-GGGA 50 chr2qtel1M 838902 GACCCAAGTTCAAATTTGGGCCTAGAATCTTAACACTTCCTGGCTGTGTG 838951 iii ? ? iiv ------ -iv ?v i? ? MIR1_Amn#SINE 51 GACCTGGGTTCNANTCCCGGC------TCT-GCCACTNGCCNGCTGNGTG 93 chr2qtel1M 838952 ACCCTGGGCAAGTCACTTAA-CTCAAAATGGCTCAGTT 838988 i ? - vvvi? v MIR1_Amn#SINE 94 ACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTT 131 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.03 CpG sites = 18, Kimura (unadjusted) = 29.03 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.09 (12 / 136), avg. gap size = 1.00 (12 / 12) 491 21.79 0.00 9.01 chr2qtel1M 838852 838972 (161028) MIRc#SINE/MIR 2 112 (156) m_b104s601i12 3813 chr2qtel1M 838852 GAGGCAGCTTAGTGGCTCAGTGGATAGAGCACCAGCCCTGAAGTCAGGGG 838901 iv i --- v ii v i i ii MIRc#SINE/MIR 2 GAGGCAGTGTGGTG---CAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr2qtel1M 838902 GACCCAAGTTCAAATTTGGGCCTAGAATCTTAACACTTCCTGGCTGTGTG 838951 iii i i iiv ------ -iv v i MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGC------TCT-GCCACTTACTAGCTGTGTG 91 chr2qtel1M 838952 ACCCTGGGCAAGTCACTTAAC 838972 i MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAAC 112 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 25.34 CpG sites = 18, Kimura (unadjusted) = 26.63 Transitions / transversions = 3.00 (18/6) Gap_init rate = 0.08 (10 / 120), avg. gap size = 1.00 (10 / 10) 582 27.00 5.24 4.40 chr2qtel1M 839011 839258 (160742) L1ME5_3end#LINE/L1 124 373 (568) m_b104s551i10 3814 chr2qtel1M 839011 AGGCTTATGAAAAAATTTTCTAAATCATT------CAGAGAA-TGTAAAT 839053 i v i i vi v v ------ - i L1ME5_3end#LI 124 AAGCATATGAAGAGATGCTCAAACTCATTAGTAATCAGAGAAATGCAAAT 173 chr2qtel1M 839054 TAAGACAATTCTGAGTTATCATTGTACATCTCTCAGAGTGGCTAAGATAA 839103 i ivv v i v i v i v v i v L1ME5_3end#LI 174 TAAAACAACAATGAGATATCACTTTACACCTATTAGACTGGCAAAAATTA 223 chr2qtel1M 839104 GAGGAAAAGATCAATGACAAATGTTGGATGGGATGTGGGAAAACTGGGAG 839153 iiivvi - v i vvi i ? iv i v L1ME5_3end#LI 224 GAAAGCTGGAT-AATGCCAAGTGTTGGCGAGGATGTGGGGANATAGGAAC 272 chr2qtel1M 839154 ACTAATACATTGTTGC---AATTGTGAACTGATCCAGTCAATCTGGAGAA 839200 v v i i i v---i v ii i v i v i L1ME5_3end#LI 273 CCTCATGCACTGCTGGTGGGAGTGTAGACTGGTGCAGCCATTCTGGAGAG 322 chr2qtel1M 839201 CAATATGGAACTA---AGCCTAAAAGGCTTGTGTATACCTTGTGTATACC 839247 v v v --- i - ---- iv ----- i L1ME5_3end#LI 323 CAATCTGGCAGTACTTAGTC-AAA----TTAAGTATAC-----GCATACC 362 chr2qtel1M 839248 TTCTAACCCAG 839258 i v i L1ME5_3end#LI 363 CTATGACCCAG 373 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 34.16 CpG sites = 34, Kimura (unadjusted) = 34.16 Transitions / transversions = 1.13 (34/30) Gap_init rate = 0.06 (15 / 247), avg. gap size = 1.60 (24 / 15) 435 33.76 4.85 4.85 chr2qtel1M 839016 839345 (160655) L1ME3A_3end#LINE/L1 129 458 (462) m_b104s551i11 3814 chr2qtel1M 839016 TATGAAAA-------AATTTTCTAAATCATTCAGAGAATGTAAATTAAGA 839058 ------- i iv v i ivi ii i i L1ME3A_3end#L 129 TATGAAAAGGTGCTCAACTTCATTAGTCATCAGGGAAATGCAAATTAAAA 178 chr2qtel1M 839059 CAATTCTGAGTTATCATTGTACATCTCTCAGAGTGGCTAAGATAAGAGGA 839108 v ivv ? v i i ii i ivi i i i i iii L1ME3A_3end#L 179 CCACAATGNGATACCACTACACACCCACCAGAATGGCTAAAATGAAAAAG 228 chr2qtel1M 839109 AAAGATCAATGACAAATGTTGGATGGGATGTGGGAAAACTGGGAGACTAA 839158 v - iv i vvi iiv i i vv v L1ME3A_3end#L 229 ACAGA-CAATACCAAGTGTTGGCGAGGATGTGGAGCAACCGGAACTCTCA 277 chr2qtel1M 839159 TACATTGT---TGCAATTGTGAACTGATCCAGTCAATCTGGAGAACAATA 839205 i i--- vi v i i i v ii v i i vi v L1ME3A_3end#L 278 TACACTGCTGGTGGGAGTGTAAATTGGTACAACCACTTTGGAAAACTGTT 327 chr2qtel1M 839206 TGGAACTAAGCCTA--AAAGGCTTGTGTATACCTTGTGTATACCTTCTAA 839253 v v --i -- --i vii ----- i i v i L1ME3A_3end#L 328 TGGCAGTA--TCTACTAAAG--CTGAACATA-----TGCATACCCTATGA 368 chr2qtel1M 839254 CCCAGGTGTGTCTCTATTAAACCTGTATCATAAAGATAAAGAATAAAGGA 839303 vvi vi v vi iiiv i i vv v - v vi v viv L1ME3A_3end#L 369 CCCAGCAATTCCACTCCTAGGTATATACCCAACAGA-AATGCGTACATAT 417 chr2qtel1M 839304 GTT----AAAAGGACCCACATGTGCAAAAATATTTGTAACAGCCCT 839345 ---- ----- i i i ii i v L1ME3A_3end#L 418 GTTCACCAAAAG-----ACATGTACAAGAATGTTCATAGCAGCACT 458 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 45.86 CpG sites = 65, Kimura (unadjusted) = 47.11 Transitions / transversions = 1.59 (65/41) Gap_init rate = 0.06 (20 / 329), avg. gap size = 1.60 (32 / 20) 13 27.99 0.00 0.00 chr2qtel1M 839765 839807 (160193) (TGTTTAT)n#Simple_repeat 1 43 (0) m_b104s252i12 3815 chr2qtel1M 839765 TGTGTATAGTTTCTATTTTATTGTTTGTTCTTGGTTGTTTTTT 839807 v v v vv i v vi v (TGTTTAT)n#Si 1 TGTTTATTGTTTATTGTTTATTGTTTATTGTTTATTGTTTATT 43 Matrix = Unknown Transitions / transversions = 0.25 (2/8) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 484 22.99 0.00 8.77 chr2qtel1M 841318 841441 (158559) C MIRc#SINE/MIR (153) 115 2 m_b104s601i14 3816 chr2qtel1M 841318 GGAGTTAAGTGACTTGCCCAGAGTCACACAGCTAGAAAGTATAAGGTGTC 841367 ii ii v ---- --- C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGT----GG---C 73 chr2qtel1M 841368 TGAGACCAGATTTGAATTCAGGTCCTCCTGAGTTAAAGGCTGATGCTCTA 841417 v v vi i i ii i v iv v iii v C MIRc#SINE/MIR 72 AGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTT 23 chr2qtel1M 841418 TCCACTGTGCCACCTAGCTGCCCC 841441 ii ---i i C MIRc#SINE/MIR 22 TCCACTGCACCAC---ACTGCCTC 2 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 26.90 CpG sites = 18, Kimura (unadjusted) = 28.17 Transitions / transversions = 2.25 (18/8) Gap_init rate = 0.08 (10 / 123), avg. gap size = 1.00 (10 / 10) 461 30.26 6.52 9.25 chr2qtel1M 843532 844252 (155748) C HERVK3#LTR/ERVK (2022) 5180 4478 m_b104s701i0 3817 chr2qtel1M 843532 CTTGTTGGCACCCATCTGATTCCTTCTCCACCTGTGGAGATACAAGCAAG 843581 vv ivi i iv i vi v ii i i vi C HERVK3#LTR/ER 5180 CTTGAGGGCACCCACACGGTTTGTCCATCTCCTGTAAAAACACAAGCATA 5131 chr2qtel1M 843582 CCCTCTTCCCCAAG-CAGTTAACCTATCTGGTCCCTTCCATTCACCACTT 843630 ? v - v i i i - v i -ii ? C HERVK3#LTR/ER 5130 CCCTCNTCCCCACGTCAGTAAATCCACC-GGACCTTTCCATT-GTCNCTT 5083 chr2qtel1M 843631 --TCTGGATCTCTCTACATCACCTGGTGATTATCTAAAGATAGTGGAGCT 843678 -- i ivv i i i v i -------- ---i ---- i C HERVK3#LTR/ER 5082 CTTCCGGGGATTTCCATAACACTT--------TC---GGATA----AACT 5048 chr2qtel1M 843679 GCTCACACTGAACATTGCTCTTCTGATGGGTTATAAAACCTGTCTGCTGG 843728 -i --- --- v -- i i iivv vvi vii v C HERVK3#LTR/ER 5047 -TTC---CT---CTTT--TCCTCTAACACTTGCCAATGTCTTTCTGCTGG 5007 chr2qtel1M 843729 AGCCAGTGCATCTTTATCAAAAATTAAAAAA--TTAATGCTATAGAAAAC 843776 i vvvv iv i ii i i? -- v - v v ii C HERVK3#LTR/ER 5006 AGTCTTACCATCCGTACCAGGAGTCNAAAAAATTTAAAG-TAAATAAGGC 4958 chr2qtel1M 843777 TAAATTTAGAAGTTCT--CTAGGGT--TACCTGTGGCTCC----CCCTTT 843818 v --- i --i ii -- vi - v ---- ?iii C HERVK3#LTR/ER 4957 TAAATGT---AGTTTTGATTGAGGTGGTAGTTG-GCCTCCTATACCNCCC 4912 chr2qtel1M 843819 CTTTTGTTTTTGGAGGA-GTGTCTTAATGTCTC-TGTTTCTTCTCTCTAC 843866 i vv iv - i iv i v- vi -- v i C HERVK3#LTR/ER 4911 TTTTTGTTTTTTCAACATGCGTTGTAATGTTTGATGTGCC--CGCTCTAT 4864 chr2qtel1M 843867 GATTGCCTGACTTTGAGGATTAAAGGGTATGCCAGTGGTGTGTAAAATCT 843916 i vv i v i iv v i v v v vv i vi----- C HERVK3#LTR/ER 4863 AATGCCTTGTCCTCTAGGATTATAAGGAATTCCTGTTTTATGGG-----T 4819 chr2qtel1M 843917 TATACTGTGCACAAAAGTGTTCAAAATGTTTGGA----------AGTCTA 843956 ---- v iv vvi - i ---------- v C HERVK3#LTR/ER 4818 TATA----GCCCAAAGCTGTAAGAAAT-TTTGAAAAGCATGACTAGTATA 4774 chr2qtel1M 843957 TGTGGGTTCATTATCTGTTTTTATTTCTTGTGGCACACCCATAATTGCAA 844006 v i i i v v v vv i iv vvv C HERVK3#LTR/ER 4773 AGCGGGTCCATTGTCAGTTTTTAATTGTTTAGGTATCCCCATATGAGCAA 4724 chr2qtel1M 844007 ATGCTTATATGAGGAATTCA------GTGACCACTCGGGCTGTCTTTTTT 844050 v v i - vi vv i------i ----- ivii C HERVK3#LTR/ER 4723 ATGATGACA-GACAATGTCGCCGTACATGACCA-----GCTGTCTCACCT 4680 chr2qtel1M 844051 GCTGCTGGCAT------TGCAAAA-GTGAATCCTGAAAAGGTGTCTACCA 844093 i -- ------ iv -i ----- v i i-- C HERVK3#LTR/ER 4679 GTT--TGGCATGTAGCATGCAGCATATGA-----GAATAAGTGTCTAT-- 4639 chr2qtel1M 844094 CAAGGTGGATAAAAGACAG--ACAC---CCAAAAGAT-TTATAATGGATC 844137 -- ? -v i i v i -- vi --- i v -i -i vi v C HERVK3#LTR/ER 4638 --AGNT-CACAGAACATAGCTAAGCTTGCCAAAGGCTGCTAT-GTGTGTA 4593 chr2qtel1M 844138 ACATCCATTTGCCAGATTTCATTGGGTCTCAAACCACCAGGGTT-CTTCC 844186 v vvi v vv - v? C HERVK3#LTR/ER 4592 ACATCCATTTGCCAGATTTCATTTGGAGCCAAACCTCGTGGGTTACANCC 4543 chr2qtel1M 844187 --CTGGAGGCAGTGTAGGAGCGTGGAAAGGAAGGCAAGCCGTACAGGCTT 844234 -- iv --- ii v?v iv v v vv iv v C HERVK3#LTR/ER 4542 TTCTACAG---GTGCGGCNCCAGGGACATGCTGGCAAGTAGGACAGGCTT 4496 chr2qtel1M 844235 TTATTATGCTCCTAGCTT 844252 v i? ivi C HERVK3#LTR/ER 4495 GTACNATAGCCCTAGCTT 4478 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.79 CpG sites = 101, Kimura (unadjusted) = 39.84 Transitions / transversions = 1.04 (101/97) Gap_init rate = 0.11 (82 / 720), avg. gap size = 1.37 (112 / 82) 579 25.08 8.20 4.76 chr2qtel1M 843803 844229 (155771) C HERVK14C#LTR/ERVK (2323) 5111 4671 m_b104s701i1 3817 chr2qtel1M 843803 CTGTGGCTCCCCCTTTCT----TTTGTTTTTGGAG--GAGTGTCTTAATG 843846 v i i ---- v i-- -? i v C HERVK14C#LTR/ 5111 CTCTGGTTCCCCCCTTCTGTCTTTTGTTTTTGTAATTGAG-NTTTTAAGG 5063 chr2qtel1M 843847 TCTCTGTTTCTTCTCTCTACGATTGCCTGACTTTGAGGATTAAAGGGTAT 843896 - vi vvi vi v i v i ? i i v v C HERVK14C#LTR/ 5062 T-TCGATTAGCTCGTTCAACAATGGCTTGNCCTTGAGAATTATAGGGGAT 5014 chr2qtel1M 843897 GCCAGTGGTGTGTAAAATCTTATACTG-TGCACAAAAGTGTTCAAAATGT 843945 ? i? vv v ?vi i - v vi v i? ?i i?v C HERVK14C#LTR/ 5013 NCCAGTANTGTGTTTAATGTNCCATTGTTGAAGGAACGCNTNTAAAGNTT 4964 chr2qtel1M 843946 T----TGGAAGTCTATGTGGGTTCATTATCTGTTTTTATTTCTTGTGGCA 843991 ----?? v i ---- -i i ? v ? i v C HERVK14C#LTR/ 4963 TACTANNGTAGCC----TGGG-CCATTGTCNGTTTTAATNTTTTGTGGAA 4919 chr2qtel1M 843992 CACCCATAATTGCAAATGCTTATATGAG---GAAT-TCAGTGACCACTCG 844037 ii i i? i ----- i v i---i - vv v v vv C HERVK14C#LTR/ 4918 TGCCCATGACNGCGAA-----ACAGGAAAGCAAATGTCTTTTAACACGAG 4874 chr2qtel1M 844038 -GGCTGTCTTTTTTGCTGCTGGCA--TTGC-----AAAAGTGAATCCTGA 844079 -i ? i i?ii i -- -- ? -----v i ----- C HERVK14C#LTR/ 4873 CAGCNGCCTCNCCTGTT--TGGCAAGTNGCCCANACAAAATGA-----GA 4831 chr2qtel1M 844080 AAAGGTGTCTACCACAAGGTGGATAAAAGACAGACACCCAAA-AGATTTA 844128 i vii? vi iiv ? ? viv -i? vv C HERVK14C#LTR/ 4830 AAAGGTATCTACAGTNACATGGACGTANGANAGTTTCCCAAATGNAGGTA 4781 chr2qtel1M 844129 TAATGGATCACATCCATTTGCCAGATTTCATTGGGTCTCAAACCACCAGG 844178 i- i ? i ? viv? i ?vi v v v? C HERVK14C#LTR/ 4780 C-ATGGGTNACGTCCATTTGCCANAGCGNATTAGGNGCCAATCCTCGNGG 4732 chr2qtel1M 844179 GTT--CT----TCCCTGGA---GGCAG-TGTAGGAGCGTGGAAAGGAAGG 844218 -- ?---- v --- - v - v v v?? i C HERVK14C#LTR/ 4731 GTTAACNCCAGTCCCTTGATGTGGCAGTTGTAGCA-CCTGGCACNNAGGG 4683 chr2qtel1M 844219 CAA-GCCGTACA 844229 - ii ? C HERVK14C#LTR/ 4682 CAATGTTGNACA 4671 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 32.40 CpG sites = 54, Kimura (unadjusted) = 34.05 Transitions / transversions = 1.12 (54/48) Gap_init rate = 0.08 (36 / 426), avg. gap size = 1.56 (56 / 36) 526 34.13 3.18 3.18 chr2qtel1M 845166 845731 (154269) C HERVK3#LTR/ERVK (3651) 3551 2986 m_b104s701i2 3817 chr2qtel1M 845166 GCTTCTTTTGTAAGCTGGCGTGGTGAATTTAAAGGAGTGTGTCCCCTTAA 845215 i v ? i v i v ? i vi v iivi i C HERVK3#LTR/ER 3551 GCCTCTTTAGTNAGTTGCCGCGGGGAATTTAANGAAGAATCTCCTTGCAG 3502 chr2qtel1M 845216 AATGTCATATAGGGGTTGCAATTGATTGGTAGCTAAGCCTAGCACTGGAC 845265 ii v vi v iv vvv i v v vi ii i C HERVK3#LTR/ER 3501 GGTTTGGTAAAGATGTGTAAGTTGATAGGTAGCAATACCTAGCATCGGGC 3452 chr2qtel1M 845266 CCATCCATTGGATATCTCCTATCAATTTTTGGAAATCATTCAAAGTATTT 845315 v v v vi i vi v i i v v C HERVK3#LTR/ER 3451 GCAGCCAATTAATATCCCCTAATAATTGTTGAAAATCATTTAAAGTCTGT 3402 chr2qtel1M 845316 AACTTCTCTGTTCTTAAAGACAGTTTTTGTACTGTAAGTGCCTTAGGGTA 845365 ---- ii vi v ii vi v - -- - v viv - C HERVK3#LTR/ER 3401 AAC----CTGTCTTTACGGAGAACTACTTT-CTG--AG-GCCGTACACT- 3361 chr2qtel1M 845366 TCTTTC-------ATA--TCCTCAATATTGAAAAGGAGCATGCCTTTGAA 845406 i ------- -- v i ? iv v i v vviv v C HERVK3#LTR/ER 3360 TCTCTCCGTAACAATAGTTCCTAAGTANTGGTATGGGGAAGTTGTTTGCA 3311 chr2qtel1M 845407 TTTTTTCTGTAGCAATATGAAGTTTGTAGTTTCTTAGTGTTTCTATGGTC 845456 ii i v ? v vi v vi v vv i iv iiiviv v - C HERVK3#LTR/ER 3310 CCTTCTCTGGAGCNATTTTGAGATTCCATTTAGTCAAAGCCCGCTTTGT- 3262 chr2qtel1M 845457 TTTTGTAGATATGCT--TCTAACATTT-ATCCCTCAGGTGCACACCCCAA 845503 i v ii -i -- v v - iv - v i-i vv C HERVK3#LTR/ER 3261 TTCTCTGAATA-ACTGATGTAAGATTTGATCTGT-AGGAGCG-GCCAAAA 3215 chr2qtel1M 845504 -AATGTCATCCATGTAATGCAACAATATTACC-TTTGGAAACACTTTTCT 845551 - i i? - ii i v v -v v - v i C HERVK3#LTR/ER 3214 GAATATCATCCATANAATG-AATGATGTAAGCAGTGGGAAACA-TATTCC 3167 chr2qtel1M 845552 CA--CTGGAGTAAGAGCAG--CAGCAACATACATTTGGCACAAGGTAGGG 845597 v -- vvvv viv v -- vi v i --- i i iv i C HERVK3#LTR/ER 3166 GAGGCTCCTTTAATGCCCGTCCTACAAAATGC---TGACATAGCGTAGGA 3120 chr2qtel1M 845598 CTATTTTTCATTCCCTGTGGCAAAATTGTCCATTCATATCTTTTATAAGG 845647 i vvv v i v i i v v v vvvv vv C HERVK3#LTR/ER 3119 CTGTTAAGCATGCCTTGGGGTAAAACTTTCCATTGATAACGAGAAACAGG 3070 chr2qtel1M 845648 CTCAGCTAAGTTAACACTGGGCATGGAAAAGGCAAATCTTTCCATATCCT 845697 i vvi vii i vvi ii i vvvv v C HERVK3#LTR/ER 3069 TTCTCTTTGATTAATAGAAGGCACAGAGAAGGCAAATCGAGGCTTATCCT 3020 chr2qtel1M 845698 CCTTATCCAGAGGGATAGAATGGAAACAATCCTT 845731 i ii vi i? v v vi C HERVK3#LTR/ER 3019 TCTCGTGTAANGGTATAGTAAAGAAACAATCCTT 2986 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 44.33 CpG sites = 85, Kimura (unadjusted) = 46.65 Transitions / transversions = 0.83 (85/102) Gap_init rate = 0.05 (26 / 565), avg. gap size = 1.38 (36 / 26) 627 29.13 4.51 4.51 chr2qtel1M 845240 845638 (154362) C HERVK14#LTR/ERVK (2671) 3425 3027 m_b104s701i3 3817 chr2qtel1M 845240 ATTGGTAGCTAAGCCTAGCACTGGACCCATCCATTGGATATCTCCTATCA 845289 v vv v ivii vv v vi i vi C HERVK14#LTR/E 3425 ATAGGTAGGAATGCCTAAAGTTGGACGAATCCAATTAATGTCTCCTAATA 3376 chr2qtel1M 845290 ATTTTTGGAAATCATTCAAAGTATTTAACTTCTCTGTTC----TTAAAGA 845335 i i v v v v ---- i v- C HERVK14#LTR/E 3375 ATTTTTGGAAATCATTTAAGGTTTTTAAATTATCTCTTCGAATTTGAAC- 3327 chr2qtel1M 845336 CAGTTTTTGTACTGTAA--GTGCCTTAGGGTATCTTTCATATCCTCAATA 845383 ---i viviv -- ii i ivvv i - - vi C HERVK14#LTR/E 3326 ---CTTTTGAGGCTTAATAGCACTTTGTTCTACCTT-CAT-TCCTAGATA 3282 chr2qtel1M 845384 TTGAAAAGGAGCATGCCTTTGAATTTTTTCTGTAGCAATA-TGAAGTTTG 845432 i i vivv i v v vi v - v vii C HERVK14#LTR/E 3281 TTGAAAGGGAGTAGAAGTTTGGATTTTATCGGGGGCTATAATTAACCCTG 3232 chr2qtel1M 845433 TAGTTTCT-TAGTGTTT-CTA--TGGTCTTTTGTAG-ATATGCTTCTAAC 845477 iv iv i -i iv - -- ---- - i -i v ---v C HERVK14#LTR/E 3231 CCGCATTTACAGCCTTTTCTAACTG----TTTGTAGCACA-ACATC---A 3190 chr2qtel1M 845478 ATTTATCCCT-----CAGGTGCACACCCCAAAATGTCATCCATGTAATGC 845522 iv ----- v --- i i - C HERVK14#LTR/E 3189 ATTCTTCCCTAGTTTCAGCTGCACAC---AGAATATCATCCATGTAATG- 3144 chr2qtel1M 845523 AACAATATTAC-CTTTGGAAACACTTTTCTCACTGGAGTAAGAGCAGCAG 845571 i i v -i vv vv i v vv v vvivv C HERVK14#LTR/E 3143 GATAATATAACATTTTTTAAACTGTTCTCTAACTGGCTTAATAGCTTTCC 3094 chr2qtel1M 845572 CAACATACATTTGGCACAAGGTAGGGCTATTTTTCATTCCCTGTGGCAAA 845621 i vi i v vi v vv v i i iv C HERVK14#LTR/E 3093 CGACATAAGTTTGACAAATAGTCGGGCTATTTAGCATGCCTTGTGGTAGT 3044 chr2qtel1M 845622 ATTGTCCATTCATATCT 845638 i v v vi C HERVK14#LTR/E 3043 ACTTTCCAATGGTATCT 3027 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.67 CpG sites = 49, Kimura (unadjusted) = 37.07 Transitions / transversions = 0.79 (49/62) Gap_init rate = 0.07 (27 / 398), avg. gap size = 1.33 (36 / 27) 597 28.34 6.86 6.86 chr2qtel1M 845252 845732 (154268) C HERVK#LTR/ERVK (3777) 3759 3279 m_b104s701i4 3817 chr2qtel1M 845252 GCCTAGCACTGGACCCATCCATTGGATATCTCCTATCAATTTTTGGAAAT 845301 vii v vv v vi v i i C HERVK#LTR/ERV 3759 GCCTAGAGTTGGCCGAATCCAATTAATATCTCCTAGCAATTTTTGAAAGT 3710 chr2qtel1M 845302 CATTCAAAGTATTTAACTTCTCTGTTCTTAAAGACAGTTTTTGTACTGTA 845351 i v v iv v v --------- v i v v C HERVK#LTR/ERV 3709 CATTTAATGTTTTTAATGTGTCTTTTCTTA---------TTTCTATTTTT 3669 chr2qtel1M 845352 AGTGCCTTAGGGTATCTTTCATATCCTC--------------AATATTGA 845387 v v ---- i - -------------- v C HERVK#LTR/ERV 3668 TGTGGCTTA----ATTTTTC-TATCCTCTACCTGCATCCCTAAATAATGA 3624 chr2qtel1M 845388 AAAGGAGCATGCCTTTGAATTTTTTCTGTAGCAATATGAAGTTTGTAGTT 845437 i vivv i v --- ---- vvi vvi - C HERVK#LTR/ERV 3623 AAAGGAGTAGAGGTTTGAATCTTATC---AG----ATGCTATTGCCAG-T 3582 chr2qtel1M 845438 TCTTAGTGTTTCTATGGTCT-TTTGTAGATATGCTTCTAAC--------- 845477 i -- i vvi vvv -i i v -- v --------- C HERVK#LTR/ERV 3581 CCT--GCGTTGGCAACCTCTGCTTGCAGAAATG--TGTAACAGTCAATTA 3536 chr2qtel1M 845478 ATTTATCCCTCA-----GGTGCACACCCCAAAATGTCATCCATGTAATGC 845522 i i i----- vv --- i v ii - C HERVK#LTR/ERV 3535 ATTTGTCTCTCGTTTCTGCAGCACA---CAAAATATCATCAACATAATG- 3490 chr2qtel1M 845523 AACAATATTACCTTTGGAAACACTTTTCTC--ACTGGAGTAAGAGCAGCA 845570 ii v vv iv - v -- vvv vvv C HERVK#LTR/ERV 3489 AATGATATAACAGTCTGAAA-ACTTGTCTCTAACTGGTTGAAGAGCTCGA 3441 chr2qtel1M 845571 GCAACATACATTTGGCACAAGGTAGGGCTATTTTTCATTCCCTGTGGCAA 845620 v v vi i i v vi v i vvv v C HERVK#LTR/ERV 3440 GCTACAAAAGTCTGACAAATAGTTGGACTATTAAGCATTCCCTGAGGCAA 3391 chr2qtel1M 845621 AATTGTCCATTCATATCTTTTATAAGGCTCAGCTA--AGTTAACACTGGG 845668 v i v i v v i vv ivvv i -vi -- v vvi - C HERVK#LTR/ERV 3390 CACTTTCCACTGAAACCTGGTGGCTGGTTC-TTTATTATTTATGGCT-GG 3343 chr2qtel1M 845669 CATGGAAAAGGCAAATCTTTCCATATCCTCCTTATCCAGAGGGATAGAAT 845718 i i v i v?v v ivv i i v v C HERVK#LTR/ERV 3342 TATAGTAAAGGCAAATTTTTCANAATCCTGCTCTGCCAGAGGAATGGTAA 3293 chr2qtel1M 845719 GGAAACAATCCTTC 845732 ii i C HERVK#LTR/ERV 3292 AAAAGCAATCCTTC 3279 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 35.09 CpG sites = 49, Kimura (unadjusted) = 35.75 Transitions / transversions = 0.63 (49/78) Gap_init rate = 0.08 (39 / 480), avg. gap size = 1.69 (66 / 39) 15 18.25 0.00 8.51 chr2qtel1M 846402 846452 (153548) (CCT)n#Simple_repeat 1 47 (0) m_b104s252i13 3818 chr2qtel1M 846402 CCTCCTCCTCCTCGGCCAGACTCCCTCCTCCTCCTTCGCTGTCCTCCCTC 846451 vv -vv - i v -v - (CCT)n#Simple 1 CCTCCTCCTCCTCCTCC-TCCT-CCTCCTCCTCCTCCTC-CTCCT-CCTC 46 chr2qtel1M 846452 C 846452 (CCT)n#Simple 47 C 47 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.08 (4 / 50), avg. gap size = 1.00 (4 / 4) 21 30.03 0.00 5.32 chr2qtel1M 847145 847243 (152757) (GGGGGC)n#Simple_repeat 1 94 (0) m_b104s252i14 3819 chr2qtel1M 847145 GGGGAAGGGGGCCTGGGCGGAAGTGGGGGGGGCTGGGCAGACGTGGGAGC 847194 iv vv ii i v -- i iv i i (GGGGGC)n#Sim 1 GGGGGCGGGGGCGGGGGCGGGGGCGGGGGCGG--GGGCGGGGGCGGGGGC 48 chr2qtel1M 847195 GGAAGAAGTCACGGGGCCGGGGGCGGGGTCTGCGGGGCCGGGGGCGGGG 847243 ii vi vvi v --- v (GGGGGC)n#Sim 49 GGGGGCGGGGGCGGGGGCGGGGGCGGGG---GCGGGGGCGGGGGCGGGG 94 Matrix = Unknown Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.05 (5 / 98), avg. gap size = 1.00 (5 / 5) 16 23.90 7.50 1.18 chr2qtel1M 847778 847857 (152143) (CTCCCGG)n#Simple_repeat 1 85 (0) m_b104s252i16 3820 chr2qtel1M 847778 CTTCCGGC-GCCGGCT--CAGC-CGCGGCT-CTGGGTCCCAGGTCCGAGC 847822 i -v -- i - v - i v i v vi (CTCCCGG)n#Si 1 CTCCCGGCTCCCGGCTCCCGGCTCCCGGCTCCCGGCTCCCGGCTCCCGGC 50 chr2qtel1M 847823 TCGCGGCTTCGGGGCTCCCAGC-CCAGGCTCCCCGC 847857 v - vv i - v v (CTCCCGG)n#Si 51 TCCCGGC-TCCCGGCTCCCGGCTCCCGGCTCCCGGC 85 Matrix = Unknown Transitions / transversions = 0.60 (6/10) Gap_init rate = 0.08 (6 / 79), avg. gap size = 1.17 (7 / 6) 71 16.54 3.92 0.63 chr2qtel1M 848420 848572 (151428) (TCC)n#Simple_repeat 1 158 (0) m_b104s252i17 3821 chr2qtel1M 848420 TCCTCC-CCTCCTCCT-CTCC-CCTCTTCCTCCCTCCTCTTCCTCC-CC- 848464 - - - i - i - - (TCC)n#Simple 1 TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT-CCTCCTCCTCCTCCTCCT 49 chr2qtel1M 848465 CCTCCTCCTCC-CCTCCTCCCCCTTACCTTCTTTCTCTTCCCCCTCTTCC 848513 - i ivi i i i i i i (TCC)n#Simple 50 CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC 99 chr2qtel1M 848514 TCCTCCTCCTGCTCTTCCCTCTCCCCCTCCAACTCCTGCTCCTCCTCCTC 848563 v i ii i vv v (TCC)n#Simple 100 TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC 149 chr2qtel1M 848564 TTCCTGCTC 848572 i v (TCC)n#Simple 150 CTCCTCCTC 158 Matrix = Unknown Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.05 (7 / 152), avg. gap size = 1.00 (7 / 7) 12 28.77 5.97 0.00 chr2qtel1M 849894 849960 (150040) (AATATA)n#Simple_repeat 1 71 (0) m_b104s252i18 3822 chr2qtel1M 849894 AATATATGT-TAAACAT-AGTAAAAATATATCT-TAAAT-CCAATATAAC 849939 vi - i - i v vv - -iv v (AATATA)n#Sim 1 AATATAAATATAAATATAAATATAAATATAAATATAAATATAAATATAAA 50 chr2qtel1M 849940 CATACGTATTTATATAATTAT 849960 i vi vv v (AATATA)n#Sim 51 TATAAATATAAATATAAATAT 71 Matrix = Unknown Transitions / transversions = 0.60 (6/10) Gap_init rate = 0.06 (4 / 66), avg. gap size = 1.00 (4 / 4) 230 33.38 0.68 4.23 chr2qtel1M 850287 850433 (149567) C L1ME4c_3end#LINE/L1 (275) 555 414 m_b104s551i12 3823 chr2qtel1M 850287 ATGATATTCCATAACACTGACATACCATAACTTAACTTATTCAGTCATTC 850336 i vivii? ii i - vi v --- C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTT-ACTTAACCATTC---C 510 chr2qtel1M 850337 TCAATTCATGGGAATCCCCTCAGTTCCCAGTTTCTTGCTACTACAAA-AG 850385 i v vv iv iivvviv i i i i i i - i C L1ME4c_3end#L 509 CCTATTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAA 460 chr2qtel1M 850386 TACTCCAAGAAATGTTTTTGTACATGTGAGTCGTTTTCCCTCCTTTAA 850433 ii v vi ii i i i i - - v i i i C L1ME4c_3end#L 459 CGCTGCAATGAACATCTTCGTGCATAT-AG-CTTTTTCCTTCTTTTGA 414 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.84 CpG sites = 32, Kimura (unadjusted) = 47.57 Transitions / transversions = 2.13 (32/15) Gap_init rate = 0.05 (7 / 146), avg. gap size = 1.00 (7 / 7) 302 30.87 1.60 4.10 chr2qtel1M 850287 850411 (149589) C L1ME3G_3end#LINE/L1 (376) 548 427 m_b104s551i13 3823 chr2qtel1M 850287 ATGATATTCCATAACACTGACATACCATAACTTAACTTATTCAGTCATTC 850336 ii ii iv i ----- i i ii C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCA-----TAATTTATTTAACCATTC 504 chr2qtel1M 850337 TCA-ATTCATGGGAATCCCCTCAGTTCCCAGTTTCTTGCTACTACAAA-A 850384 i v- v iv iivvviv i i i i i - C L1ME3G_3end#L 503 CCCTATTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACA 454 chr2qtel1M 850385 GTACTCCAAGAAATGTTTTTGTACATG 850411 i i v vi ii ii C L1ME3G_3end#L 453 ATGCTGCAATGAACATCCTTGTACATG 427 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.08 CpG sites = 27, Kimura (unadjusted) = 42.67 Transitions / transversions = 2.70 (27/10) Gap_init rate = 0.06 (7 / 124), avg. gap size = 1.00 (7 / 7) 467 33.22 10.00 3.34 chr2qtel1M 851800 852559 (147441) C L1PREC2_orf2#LINE/L1 (811) 2483 1675 m_b105s551i2 3824 chr2qtel1M 851800 ATAGCATTAAAGGTGTGGATTATTTGGGGCAGTCTTGCCATTTTTAT-AT 851848 i vv ii ii v v v v i- C L1PREC2_orf2# 2483 ATAGCATTGAATCTGTAAATTGCTTTGGGCAGTATGGCCATTTTAACGAT 2434 chr2qtel1M 851849 CCTGATGCAGCCTAGCC-CAAGCACTGGATATTCCTTTAGCT-TTTAAGT 851896 vi v vv v -ii iv i i ii ii vi - iv C L1PREC2_orf2# 2433 ATTGATTCTTCCTATCCATGAGCATGGAATGTTTTTCCATTTGTTTGTGT 2384 chr2qtel1M 851897 TGTCATGCATTACTTTAAGGATGGCATTGCAA--CTGAATTTGTACAACT 851944 ii vivv v i v vv iv i -- v -- v iv C L1PREC2_orf2# 2383 CATCTCTGATTTCTTTGAGCAGTGTTTTGTAATTCTCA--TTGTAGAGAT 2336 chr2qtel1M 851945 CTTTTA-----------------ATTCCTAGATATTGAATCCTCATTTTA 851977 i ----------------- i vv i iv v i C L1PREC2_orf2# 2335 CTTTCACCTCCCTGGTTAGCTGTATTCCTAGGTATTTTATTCTTTTTGTG 2286 chr2qtel1M 851978 CTTATTTGGAGTGGGATTTTTCTCTCAATTATTGCTTCCTGGACTT---T 852024 viv vv i vivi iii - v -- v i --- C L1PREC2_orf2# 2285 GCAATTGTGAATGGGATTGCGTTCCTGATT-TGGCT--CTCGGCTTGGCT 2239 chr2qtel1M 852025 GTTTCTATTTCCTAGAAATA------ATCTTGGGAG---GATTCTGTGTG 852065 vi iv viv i i------ i v v v--- i i - C L1PREC2_orf2# 2238 GTTGTTGGTGTATAGGAATGCTAGTGATTTTTGTACATTGATTTTGTAT- 2190 chr2qtel1M 852066 TAACCTGCAACTTTGCATAAACTGTTAA--ATCTTAACTATCCTACTTAA 852113 --- v vv ii v -- v ? vv v i -- ii C L1PREC2_orf2# 2189 ---CCTGAAACTTTGCTGAAGTTGTTTATCAGCTNAAGGAGCTT--TTGG 2145 chr2qtel1M 852114 TGTCTCTGCTGA--TTACCTGTGTATTTCCAAGTGAAGCATCCTGTCATC 852161 ------- i --i -- v vv i ii iv v v i C L1PREC2_orf2# 2144 -------GCCGAGACTA--TGGGGTTTTCTAGATATAGAATCATGTCGTC 2104 chr2qtel1M 852162 AACAAA-GGGGCTAGTTTGAGCTCCTCTTTACCCATGTTTAT-TCCTTTC 852209 vi -i v vi i v i v vv -i v C L1PREC2_orf2# 2103 TGCAAACAGGGATAGTTTGACTTCCTCTCTTCCTATTTGGATGCCCTTTA 2054 chr2qtel1M 852210 TTTCATTTCTCTTGTTTTGTTGCTATTGCTAGCATTGTCA---------- 852249 - ii vi v v i v i vi ---------- C L1PREC2_orf2# 2053 TTTC-TTTCTCTTGCCTGATTGCTCTGGCCAGGACTTCCAATACTATGTT 2005 chr2qtel1M 852250 GAA---GAGTAGGGAAAGTAAACATTCTTGCTTTACCCCTGCATTTATTG 852296 --- i v i viii i ii iiv v iv i vv C L1PREC2_orf2# 2004 GAATAGGAGTGGTGAGAGAGGGCATCCTTGTCTTGTGCCGGTTTTCAAGG 1955 chr2qtel1M 852297 GAAATGTTTCTAACACAACCCCATTTCATGCAATGCT---TTTAAGTTTT 852343 i i i i vivvv ivi iii i --- v ii v C L1PREC2_orf2# 1954 GGAATGCTTCCAGCTTTTGCCCATTCAGTATGATGTTGGCTGTGGGTTTG 1905 chr2qtel1M 852344 TGATAGATA----TTATGACCTTGAAA-ATGGTCCCACTAGGCCTGTACT 852388 v i---- v ii ii- v iv v vi -- v C L1PREC2_orf2# 1904 TCATAGATGGCTCTTATTATTTTGAGGTATGTTCCTTCAATACCT--AGT 1857 chr2qtel1M 852389 TCTAATTAC-GTTTTTACC-TCA---GAAGTGG-------TCCAAAGCAC 852426 - v v v- v - v --- v v ------- v vi C L1PREC2_orf2# 1856 T-TATTGAGAGTTTTTAACATGAAGGGATGTTGAATTTTATCGAAAGCCT 1808 chr2qtel1M 852427 TCCCTTCATCTGTTGAAATGACTGTATGGTTTTAAATGT-TTTGGTT-TA 852474 ii v i i i iii i --- - i - i C L1PREC2_orf2# 1807 TTTCTGCATCTATTGAGATAATCATGTGGTTTT---TGTCTTTAGTTCTG 1761 chr2qtel1M 852475 TA-ATATAATGGATTATGTTCATTGTTTTCCTAGTGTTGAACTATTCTTA 852523 v- i i i i ii i v v vvi i vi i C L1PREC2_orf2# 1760 TTTATGTGATGAATCACATTTATTGATTTGCGTATGTTGAACCAACCTTG 1711 chr2qtel1M 852524 CATCCTTGGTACAAATTCCACTTGAGCATGATGAAT 852559 iv v i vi i v i i i C L1PREC2_orf2# 1710 CATCCCAGGGATAAAGCCTACTTGATCGTGGTGGAT 1675 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 43.93 CpG sites = 132, Kimura (unadjusted) = 45.17 Transitions / transversions = 1.18 (132/112) Gap_init rate = 0.07 (51 / 759), avg. gap size = 2.02 (103 / 51) 542 32.17 8.54 3.79 chr2qtel1M 851948 852603 (147397) C L1M1_orf2#LINE/L1 (979) 2315 1630 m_b105s551i3 3824 chr2qtel1M 851948 TTAATTCCTAGATATTGAATCCTCATTT-TACTTATTTGGAGTGGGATTT 851996 i v ii - - ivi vvi i v C L1M1_orf2#LIN 2315 TTAATTCCTAGGTATTTAATTTT-ATTTGTGGCTATTGTAAATGGGATTA 2267 chr2qtel1M 851997 TTCTCTCAATTATTGCTTCCTGGACTTTGTTT-CTATTTCC---TAGAAA 852042 i i i ii vi vi --i -- i- i vv --- C L1M1_orf2#LIN 2266 CTTTTTTGATTTCTTTTTC--AGA--TTGTTCACTGTTGGCATATAGAAA 2221 chr2qtel1M 852043 TA------ATCTTGGGA-G--GATTCTGTGTGTAACCTGCAACTTTGCAT 852083 i------ i v v - -- i i ---- i vv C L1M1_orf2#LIN 2220 TGCTACTGATTTTTGTATGTTGATTTTGTAT----CCTGCAACTTTACTG 2175 chr2qtel1M 852084 AAACTGTTAAATCTTAACTATCCTACTTAATGTCTCTGCTGATTACCTGT 852133 vi ------ v vi i v - i v i i? iv v vii iv C L1M1_orf2#LIN 2174 AATTTGTT------TATCAGTTCTAAT-AGTTTTTTNGTGGAGTCTTTAG 2132 chr2qtel1M 852134 GTATTTCCAAGTGAAGCATCCTGTCATCAACAAA-GGGGCTAGTTTGAGC 852182 v i iv iv v i vi -ii v i vi C L1M1_orf2#LIN 2131 GTTTTTCCAAATATAAGATCATATCATCTGCAAACAAGGATAATTTGACT 2082 chr2qtel1M 852183 TCCTCTTTACCCATGTTTAT-TCCTTTCTTTCATTTCTCTTGTTTTGTTG 852231 i i v v v vv -i v - i vi C L1M1_orf2#LIN 2081 TCTTCCTTTCCAATTTGGATGCCCTTTATTTC-TTTCTCTTGTCTGATTG 2033 chr2qtel1M 852232 CTATTGCTAGCATTGTCAG-------------AAGAGTAGGGAAAGTAAA 852268 v v v i vi ------------- v i v iii C L1M1_orf2#LIN 2032 CTCTAGCTAGGACTTCCAGTACTATGTTGAATAACAGTGGTGAAAGTGGG 1983 chr2qtel1M 852269 CATTCTTGCTTTACCCCTGCATTTATTGGAAATGTTTCTAACACAACCCC 852318 i iiv iii v vvi vv v i ii iivivv C L1M1_orf2#LIN 1982 CATCCTTGTCGTGTTCCAGATCTTAGAGGAAAGGCTTTCAGTTTTTCCCC 1933 chr2qtel1M 852319 ATTTCATGCAATGCT---TTTAAGTTTTTGATAGATA----TTATGACCT 852361 ivi iii i --- v ii i v vi v i---- v iv C L1M1_orf2#LIN 1932 ATTCAGTATGATACTAGCTGTGGGTCTGTCGTATATGGCTTTTATTATGT 1883 chr2qtel1M 852362 TGAAA-ATGGTCCCACTAGGCCTGTACTTCTAATTACGTTTTTACCTCA- 852409 ii- v iv vi iivvi i i --iv -- - C L1M1_orf2#LIN 1882 TGAGGTATGTTCCTTCTATACCCAGTTTTTTGA--GGGTTTTTA--TCAT 1837 chr2qtel1M 852410 GAAGTGGT-----------CCAAA-GCACTCCCTTCATCTGTTGAAATGA 852447 v i -----------i - vi ii vv vi C L1M1_orf2#LIN 1836 GAAGGGATGTTGAATTTTATCAAATGCTTTTTCAGCATCAATTGAAATGA 1787 chr2qtel1M 852448 CTGTATGGTTTTAAATGT--TTTGGTTTAT-AATATAATGGATTATGTTC 852494 iii --- -- iiv i i -i i v i ii v C L1M1_orf2#LIN 1786 TCATATGGTTTT---TGTCCTTCATTCTGTTGATATGATGTATCACATTG 1740 chr2qtel1M 852495 ATTGTTTTCCTAGTGTTGAACTATTCTTACATCCTTGGTACAAATTCCAC 852544 v v vvi i i i i? v i i C L1M1_orf2#LIN 1739 ATTGATTTGCGTATGTTGAACCATCCTTGCATCCCNGGGATAAATCCCAC 1690 chr2qtel1M 852545 TTGAGCATGATGAATGATTCCTTGGAATGCAGGGTGG---TTGTTTTGGA 852591 iv - i vv i vv v --- i v v- C L1M1_orf2#LIN 1689 TTGGTCATGATGAATGA-TCTTTTTAATGTATTGTTGAATTCGGTTTGC- 1642 chr2qtel1M 852592 TAGGATTTTGTT 852603 v C L1M1_orf2#LIN 1641 TAGTATTTTGTT 1630 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 42.70 CpG sites = 116, Kimura (unadjusted) = 43.57 Transitions / transversions = 1.33 (116/87) Gap_init rate = 0.07 (44 / 655), avg. gap size = 1.86 (82 / 44) 653 33.59 8.14 1.20 chr2qtel1M 852137 852603 (147397) C L1PB_orf2#LINE/L1 (1166) 2128 1630 m_b105s551i4 3824 chr2qtel1M 852137 TTTCCAAGTGAAGCATCCTGTCATCAACAAAGGG-GCTAGTTTGAGCTCC 852185 i i i? vv v i i vi - vi vi C L1PB_orf2#LIN 2128 TTTCTAGGTANACGATCATATCATCAGCAAACAGCGACAGTTTGACTTCC 2079 chr2qtel1M 852186 TCTTTACCCATGTTTAT-TCCTTTCTTTCATTTCTCTTGTTTTGTTGCTA 852234 v v vv -i v - i vi v C L1PB_orf2#LIN 2078 TCTTTACCGATTTGGATGCCCTTTATTTC-TTTCTCTTGTCTGATTGCTC 2030 chr2qtel1M 852235 TTGCTAGCATTGTCAG-------------AAGAGTAGGGAAAGTAAACAT 852271 v v i vi ------------- ii i v i iii C L1PB_orf2#LIN 2029 TGGCTAGGACTTCCAGTACTATGTTGAANAGAAGTGGTGAGAGTGGGCAT 1980 chr2qtel1M 852272 TCTTGCTTTACCCCTGCATTTATTGGAAATGTTTCTAACACAACCCCATT 852321 i ii iii v ivi i vv i i ii vivv C L1PB_orf2#LIN 1979 CCTTGTCTTGTTCCAGTTCTCAGGGGGAATGCTTTCAACTTTTCCCCATT 1930 chr2qtel1M 852322 TCATGCAATGCT---TTTAAGTTTTTGATAGATA----TTATGACCTTGA 852364 ivi ii? i --- v ii v v i---- v ? i C L1PB_orf2#LIN 1929 CAGTATNATGTTGGCTGTGGGTTTGTCATAGATGGCTTTTATTACNTTAA 1880 chr2qtel1M 852365 AA-ATGGTCCCACTAGGCCTGTACTTCTAATTACGTTTTTACCTCAGAAG 852413 ii- vi iv? v vi vi v i --iv v i vi i i C L1PB_orf2#LIN 1879 GGTATGTCCCTTNTATGCCGATTTTGCTGA--GGGTTTTAATCATAAAGG 1832 chr2qtel1M 852414 -----TGG------TCCAAAGCACTCCCTTCATCTGTTGAAATGACTGTA 852452 ----- ------ v v vi ii v i i iii i C L1PB_orf2#LIN 1831 GATGCTGGATTTTGTCAAATGCTTTTTCTGCATCTATTGAGATGATCATG 1782 chr2qtel1M 852453 TGGTTTTAAATGTTTTGGTTTATA---ATATAATGGATTATGTTCATTGT 852499 i --- viv v i--- i ii v i ii i v C L1PB_orf2#LIN 1781 TGATTTT---TGTTTTTAATTCTGTTTATGTGGTGTATCACATTTATTGA 1735 chr2qtel1M 852500 TTTCCTAGTGTTGAACTATTCTTACATCCTTGGTACAAATTCCACTTGAG 852549 i v vvi i i i i i i ii vi v C L1PB_orf2#LIN 1734 CTTGCGTATGTTAAACCATCCCTGCATCCCTGGTATGAAACCCACTTGAT 1685 chr2qtel1M 852550 CATGATGAATGATTCCTTGGA-ATGCAGGGTGGTTGTTTTGGATAGGATT 852598 i i v iii v - v vvv i vvv i v v C L1PB_orf2#LIN 1684 CATGGTGGATTATCTTTTTGATATGCTGTTGGATTCGGTTAGCTAGTATT 1635 chr2qtel1M 852599 TTGTT 852603 C L1PB_orf2#LIN 1634 TTGTT 1630 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 46.94 CpG sites = 92, Kimura (unadjusted) = 46.94 Transitions / transversions = 1.46 (92/63) Gap_init rate = 0.03 (16 / 466), avg. gap size = 2.75 (44 / 16) 11 18.98 0.00 7.69 chr2qtel1M 853023 853064 (146936) (ATTTATT)n#Simple_repeat 1 39 (0) m_b105s252i0 3825 chr2qtel1M 853023 ATTTATCATTTAAATTTTTTGTTATTTCCTATTCATCTATTT 853064 i -- v i vi i - (ATTTATT)n#Si 1 ATTTATTATTT--ATTATTTATTATTTATTATTTAT-TATTT 39 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.07 (3 / 41), avg. gap size = 1.00 (3 / 3) 18 17.53 2.13 2.13 chr2qtel1M 857253 857299 (142701) (GGAAAGG)n#Simple_repeat 1 47 (0) m_b105s252i1 3826 chr2qtel1M 857253 GGAAAGGGCTTA-GGGAAAGGGGAAAGGGGAGGAGGGAAGGAGGGAAA 857299 vvv - iii i - (GGAAAGG)n#Si 1 GGAAAGGGGAAAGGGGAAAGGGGAAAGGGGAAAGGGGAAAG-GGGAAA 47 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.04 (2 / 46), avg. gap size = 1.00 (2 / 2) 244 29.43 11.95 1.71 chr2qtel1M 858211 858369 (141631) C L1PREC2_orf2#LINE/L1 (1051) 2243 2069 m_b105s551i5 3827 chr2qtel1M 858211 TGGATTTTGTCAGTAATATTTAGAAATGCTGATGGTTTGCCTTTGTTTAT 858260 v v --- ii i v i ii i viv vii v C L1PREC2_orf2# 2243 TGGCTGTTGT---TGGTGTATAGGAATGCTAGTGATTTTTGTACATTGAT 2197 chr2qtel1M 858261 TTTATATCCTGCAGTTTTCCTAAAGCTGTTAATTGTTTCAAGTAGGTTTT 858310 i v ii v i i v iivi ? v v C L1PREC2_orf2# 2196 TTTGTATCCTGAAACTTTGCTGAAGTTGTTTATCAGCTNAAGGAGCTTTT 2147 chr2qtel1M 858311 TG--------CATGA--TTCTCTAGG-ATAG--------CATCTGCAAAG 858341 v --------i i-- i i- -------- i v C L1PREC2_orf2# 2146 GGGCCGAGACTATGGGGTTTTCTAGATATAGAATCATGTCGTCTGCAAAC 2097 chr2qtel1M 858342 AATGATAGTGGTATTTCCTCACTGCCTA 858369 iv vvv i v v C L1PREC2_orf2# 2096 AGGGATAGTTTGACTTCCTCTCTTCCTA 2069 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.47 CpG sites = 25, Kimura (unadjusted) = 38.53 Transitions / transversions = 1.19 (25/21) Gap_init rate = 0.04 (7 / 158), avg. gap size = 3.14 (22 / 7) 262 28.28 0.00 0.00 chr2qtel1M 858228 858326 (141674) C L1M1_orf2#LINE/L1 (1065) 2229 2131 m_b105s551i6 3827 chr2qtel1M 858228 ATTTAGAAATGCTGATGGTTTGCCTTTGTTTATTTTATATCCTGCAGTTT 858277 v iv i viv v v i ii C L1M1_orf2#LIN 2229 ATATAGAAATGCTACTGATTTTTGTATGTTGATTTTGTATCCTGCAACTT 2180 chr2qtel1M 858278 TCCTAAAGCTGTTAATTGTTTCAAGTAGGTTTTTGCATGATTCTCTAGG 858326 v i vi v iiv v i v ?vvv v i C L1M1_orf2#LIN 2179 TACTGAATTTGTTTATCAGTTCTAATAGTTTTTTNGTGGAGTCTTTAGG 2131 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.11 CpG sites = 12, Kimura (unadjusted) = 36.11 Transitions / transversions = 0.75 (12/16) Gap_init rate = 0.00 (0 / 98), avg. gap size = 0.0 (0 / 0) 393 25.09 9.89 5.82 chr2qtel1M 858385 858566 (141434) C MIRb#SINE/MIR (65) 203 15 m_b105s601i0 3828 chr2qtel1M 858385 GTGTTGTCTCATTTCATCCTCATGAGAACCCTA-GATCTCGCGTGCCATT 858433 ii i v ii v i- vv v - --- C MIRb#SINE/MIR 203 GCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAG-GT---ATT 158 chr2qtel1M 858434 ATTGTGCCCTTTTTATAGATAAAGTCACTGAGGCAGACAGAGGTCTTGTA 858483 i v v i i i vv vv v ivv C MIRb#SINE/MIR 157 ATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTA 108 chr2qtel1M 858484 AGTTG--------------ACTAGCAAGTTGCTGAGATGGGAT--GAACA 858517 v --------------i i v v vi -- v C MIRb#SINE/MIR 107 ACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACC 58 chr2qtel1M 858518 CTGAGGTCTTGCTAA-TTCAAGGCCCTGTTCACACTTTTCCCCTTGCACC 858566 -- vv i - i i - ----i i i vi C MIRb#SINE/MIR 57 C--AGGTCTGTCTGACTCCAAAGCCC-GT----GCTCTTTCCACTGCACC 15 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.04 CpG sites = 21, Kimura (unadjusted) = 30.88 Transitions / transversions = 0.95 (21/22) Gap_init rate = 0.08 (15 / 181), avg. gap size = 1.93 (29 / 15) 16 4.50 0.00 0.00 chr2qtel1M 858891 858913 (141087) (TTTA)n#Simple_repeat 1 23 (0) m_b105s252i2 3829 chr2qtel1M 858891 TTTATTTATTTATTTATTTTTTT 858913 v (TTTA)n#Simpl 1 TTTATTTATTTATTTATTTATTT 23 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 434 26.52 0.00 8.77 chr2qtel1M 859593 859716 (140284) C MIRc#SINE/MIR (153) 115 2 m_b105s601i1 3830 chr2qtel1M 859593 GGGGTTAAGTGACTTGCCCAGGGTCACACAGCTAGGAAGTTTGAAGTGTT 859642 i i v ------- vi C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGT-------GGC 73 chr2qtel1M 859643 TGAGATCAGATTTGAACTCGGGTCCTCCTGACTTCAGGGTTGGTGTTCTA 859692 v vivi i i i i i i i viii i v C MIRc#SINE/MIR 72 AGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTT 23 chr2qtel1M 859693 TCTTCTGTGCCATCTAGCTGCCCC 859716 iv ii i---i i C MIRc#SINE/MIR 22 TCCACTGCACCAC---ACTGCCTC 2 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.41 CpG sites = 22, Kimura (unadjusted) = 34.23 Transitions / transversions = 2.75 (22/8) Gap_init rate = 0.08 (10 / 123), avg. gap size = 1.00 (10 / 10) 439 24.84 0.00 5.94 chr2qtel1M 860250 860356 (139644) MIRc#SINE/MIR 12 112 (156) m_b105s601i2 3831 chr2qtel1M 860250 GGCATAGTGGATAGAGCACCAGCCCTGAAGTCAGGGGGACCCAAGTTCAA 860299 iii v ii v i i ii iii i MIRc#SINE/MIR 12 GGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGA 61 chr2qtel1M 860300 ATTTGCCCTAAAACCATAACACTTCCTGGCTGTGTGACCCTGGGCAAGTC 860349 i --- ---ii iv iv v i i MIRc#SINE/MIR 62 GT---CCC---GGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTC 105 chr2qtel1M 860350 ACTTAAC 860356 MIRc#SINE/MIR 106 ACTTAAC 112 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.98 CpG sites = 20, Kimura (unadjusted) = 32.09 Transitions / transversions = 4.00 (20/5) Gap_init rate = 0.06 (6 / 106), avg. gap size = 1.00 (6 / 6) 379 33.76 4.86 6.07 chr2qtel1M 860357 860706 (139294) L1ME3A_3end#LINE/L1 110 455 (465) m_b105s551i7 3832 chr2qtel1M 860357 TCCAAACGGCTCAGTTAAA---ATGAAAAAA-----AAATTTTTTCTAAA 860398 i iv -- --- ii----- v iv --- i L1ME3A_3end#L 110 TCCAAATGGCCAA--TAAACATATGAAAAGGTGCTCAACTTCATT---AG 154 chr2qtel1M 860399 TCATTCAGAGAATGTAAATTAAGACAATTCTGAGTTATCATTGTACATCT 860448 ivi ii i i v ivv ? v i i ii i i L1ME3A_3end#L 155 TCATCAGGGAAATGCAAATTAAAACCACAATGNGATACCACTACACACCC 204 chr2qtel1M 860449 CTCAGAGTGGCTAAGATAAGAGGAAAAGATCAATGACAAATGTTGGATGG 860498 vi i i i i iii v - iv i vvi L1ME3A_3end#L 205 ACCAGAATGGCTAAAATGAAAAAGACAGA-CAATACCAAGTGTTGGCGAG 253 chr2qtel1M 860499 GATGTGGGAAAACTGGGAGACTAATACATTGT---TGCAATTGTGAACTA 860545 iiv i i vv v i i--- vi v i i i L1ME3A_3end#L 254 GATGTGGAGCAACCGGAACTCTCATACACTGCTGGTGGGAGTGTAAATTG 303 chr2qtel1M 860546 ATCCAGTCAATCTGGAGAACAACATGGAACTAAGCCTA--AAAGGCTTGT 860593 i v ii v i i viiv v v --i -- --i v L1ME3A_3end#L 304 GTACAACCACTTTGGAAAACTGTTTGGCAGTA--TCTACTAAAG--CTGA 349 chr2qtel1M 860594 GTATACCTTGTGTATACCTTCTAACCCAGGTGTGTCTCTATTAAACCTGT 860643 ii ----- i i v i vvi vi v vi iiiv i L1ME3A_3end#L 350 ACATA-----TGCATACCCTATGACCCAGCAATTCCACTCCTAGGTATAT 394 chr2qtel1M 860644 ATCATAAAGATAAAGAATAAAGGAGTT----AAAAGGACCCACATGTGCA 860689 i vv v - v vi v viv ---- ----- i L1ME3A_3end#L 395 ACCCAACAGA-AATGCGTACATATGTTCACCAAAAG-----ACATGTACA 438 chr2qtel1M 860690 AAAATATTTGTAACAGC 860706 i i ii i L1ME3A_3end#L 439 AGAATGTTCATAGCAGC 455 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 46.11 CpG sites = 70, Kimura (unadjusted) = 47.32 Transitions / transversions = 1.71 (70/41) Gap_init rate = 0.07 (26 / 349), avg. gap size = 1.46 (38 / 26) 393 28.00 5.61 3.20 chr2qtel1M 860359 860572 (139428) L1ME4b_3end#LINE/L1 112 330 (562) m_b105s551i8 3832 chr2qtel1M 860359 CAAACGGCTCAGTTAAA-ATGAAAAAAAAATTTTT--TCTAAATCAT--T 860403 i -- - - vi i vi i--i v v -- L1ME4b_3end#L 112 CAAATGGCTC--TTAAACAT-ATGAAAAGATGCTCAACCTCACTCATAAT 158 chr2qtel1M 860404 CAGAGAA-TGTAAATTAAGACAATTCTGAGTTATCATTGTACATCTCTCA 860452 v - i i v iv v i v v i v L1ME4b_3end#L 159 AAGAGAAATGCAAATTAAAACTACACTGAGATACCATTTTTCACCTATCA 208 chr2qtel1M 860453 GAGTGGCTAAGATAAGAGGAAAAGATCAATGACAAA---TGTTGGATGGG 860499 v v v ---- v ii i v --- vvi L1ME4b_3end#L 209 GATTGGCAAAGATCA----AAAAGTTTGATAACACACTGTGTTGGCGAGG 254 chr2qtel1M 860500 ATGTGGGAAAACTGGGAGACTAATACATTGT---TGCAATTGTGAACTAA 860546 i i v v vv v i--- vi v i i ii L1ME4b_3end#L 255 GTGTGGGGAAACAGGCACTCTCATACATTGCTGGTGGGAGTGTAAATTGG 304 chr2qtel1M 860547 TCCAGTCAATCTGGAGAACAACATGG 860572 v ii vv v ii iv L1ME4b_3end#L 305 TACAACCTCTATGGAGGGCAATTTGG 330 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 35.40 CpG sites = 28, Kimura (unadjusted) = 35.40 Transitions / transversions = 0.93 (28/30) Gap_init rate = 0.06 (13 / 213), avg. gap size = 1.46 (19 / 13) 383 33.38 3.26 5.32 chr2qtel1M 860403 860709 (139291) L1ME3B_3end#LINE/L1 158 458 (531) m_b105s551i10 3832 chr2qtel1M 860403 TCAGAGAA-TGTAAATTAAGACAATTCTGAGTTATCATTGTACATCTCTC 860451 i - i i v ivv v i i ii i ivi L1ME3B_3end#L 158 TCAGGGAAATGCAAATTAAAACCACAATGAGATACCACTACACACCCACC 207 chr2qtel1M 860452 AGAGTGGCTAAGATAAGAGGAAAAGAT---CAATGACAAATGTTGGATGG 860498 ? v i ----v? vi--- iv i vvi L1ME3B_3end#L 208 AGANTGGCAAAAAT----TNAAAAGTCTGACAATACCAAGTGTTGGCGAG 253 chr2qtel1M 860499 GATGTGGGAAAACTGGGAGACTAATACATTGT---TGCAATTGTGAACTA 860545 iiv v i vv v i i--- vi v i i i L1ME3B_3end#L 254 GATGTGGAGCAACGGGAACTCTCATACACTGCTGGTGGGAGTGTAAATTG 303 chr2qtel1M 860546 ATCCAGTCAATCTGGAGAACAACATGGAACTAAGCCTA--AAAGGCTTGT 860593 i v ii v i i iiv v i --i -- -- v L1ME3B_3end#L 304 GTACAACCACTTTGGAAAACAGTTTGGCATTA--TCTANTAAAG--TTGA 349 chr2qtel1M 860594 GTATACCTTGTGTATACCTTCTAACCCAGGTGTGTCTCTATTAAACCTGT 860643 iv ----- i i v i vvi vi v vi iiiv i L1ME3B_3end#L 350 AGATAC-----GCATACCCTATGACCCAGCAATTCCACTCCTAGGTATAT 394 chr2qtel1M 860644 ATCATAAAGATAAAGAATAAAGGAGT-TAAAAGGACCCACATGTGCAAAA 860692 i v i - v vi iv viv -i vv --? i i L1ME3B_3end#L 395 ACCCTAGAGA-AACGCGTGCACATGTGCACCAGGA--NACATGTACAAGA 441 chr2qtel1M 860693 ATATTTGTAACAGCCTT 860709 i ii i v L1ME3B_3end#L 442 ATGTTCATAGCAGCATT 458 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 45.72 CpG sites = 57, Kimura (unadjusted) = 46.39 Transitions / transversions = 1.43 (57/40) Gap_init rate = 0.07 (21 / 306), avg. gap size = 1.24 (26 / 21) 519 27.77 3.18 5.09 chr2qtel1M 860403 860622 (139378) L1ME5_3end#LINE/L1 158 373 (568) m_b105s551i9 3832 chr2qtel1M 860403 TCAGAGAA-TGTAAATTAAGACAATTCTGAGTTATCATTGTACATCTCTC 860451 - i i ivv v i v i v i L1ME5_3end#LI 158 TCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCTATT 207 chr2qtel1M 860452 AGAGTGGCTAAGATAAGAGGAAAAGATCAATGACAAATGTTGGATGGGAT 860501 v v i v iiivvi - v i vvi L1ME5_3end#LI 208 AGACTGGCAAAAATTAGAAAGCTGGAT-AATGCCAAGTGTTGGCGAGGAT 256 chr2qtel1M 860502 GTGGGAAAACTGGGAGACTAATACATTGT---TGCAATTGTGAACTAATC 860548 i ? iv i vv v i i i--- vi v ii ii v L1ME5_3end#LI 257 GTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACTGGTG 306 chr2qtel1M 860549 CAGTCAATCTGGAGAACAACATGGAACTA---AGCCTAAAAGGCTTGTGT 860595 i v i iv v v --- i - ---- iv L1ME5_3end#LI 307 CAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTC-AAA----TTAAGT 351 chr2qtel1M 860596 ATACCTTGTGTATACCTTCTAACCCAG 860622 ----- i i v i L1ME5_3end#LI 352 ATAC-----GCATACCCTATGACCCAG 373 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 35.53 CpG sites = 32, Kimura (unadjusted) = 35.53 Transitions / transversions = 1.23 (32/26) Gap_init rate = 0.06 (14 / 219), avg. gap size = 1.29 (18 / 14) 15 24.62 0.00 0.00 chr2qtel1M 861125 861167 (138833) (TGTTTAT)n#Simple_repeat 1 43 (0) m_b105s252i3 3833 chr2qtel1M 861125 TGTGTATAGTTTCTATTTTATTGTTTGTTCTTTGTTGTTTTTT 861167 v v v vv i v i v (TGTTTAT)n#Si 1 TGTTTATTGTTTATTGTTTATTGTTTATTGTTTATTGTTTATT 43 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 475 23.86 0.00 8.77 chr2qtel1M 862678 862801 (137199) C MIRc#SINE/MIR (153) 115 2 m_b105s601i3 3834 chr2qtel1M 862678 GGAGTTAAGTGACTTGCCCAGAGTCACACAGCTAGAAAGTATAAGGTGTC 862727 ii ii v ---- --- C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGT----GG---C 73 chr2qtel1M 862728 TGAGACCAGATTTGAATTCAGGTCCTCCTGAGTTAAAGGCTGATGTTCTA 862777 v v vi i i ii i v iv v iii i v C MIRc#SINE/MIR 72 AGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTT 23 chr2qtel1M 862778 TCCACTGTGCCACCTAGCTGCCCC 862801 ii ---i i C MIRc#SINE/MIR 22 TCCACTGCACCAC---ACTGCCTC 2 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.31 CpG sites = 19, Kimura (unadjusted) = 29.62 Transitions / transversions = 2.38 (19/8) Gap_init rate = 0.08 (10 / 123), avg. gap size = 1.00 (10 / 10) 252 31.53 6.05 7.07 chr2qtel1M 865187 865500 (134500) C HERVK13#LTR/ERVK (2377) 5739 5429 m_b105s701i0 3835 chr2qtel1M 865187 GAGTGTCTTAATGTCTCTGTTTCTTCTCTCTGATTGCCTGACTTTGAGGA 865236 i v v - i vi ------ vv v i i ii C HERVK13#LTR/E 5739 GAGTGTTTTATTGGCTC-GTTCCACC------AAGGCCTGTCCTCGAGAG 5697 chr2qtel1M 865237 TTAAAGGGTATGCCAGTGGTGTGTAAAAT--CTTATA-CTGTGCACAAAA 865283 v v v viv -- ii i- v ii--- C HERVK13#LTR/E 5696 TTATAGGGGATGCCAGTTGTGTGAGTAATTGCCCATGTCTGAGTG---AA 5650 chr2qtel1M 865284 GTGTTCAAAA----TGTTTGGAAGTCTATGTGGGTTCATTATCTGTTTT- 865328 v v i ----i i ---- v vvi vi i v - C HERVK13#LTR/E 5649 CTTTTTAAAAGCAGCGCT----AGTGTAGCCGGGGCCGTTATCAGTTTTT 5604 chr2qtel1M 865329 -ATTTCTTGTGCACA--CCATAATTGCAAATGCTTATATGAG-GAAT--- 865371 -i i - v -- ii vi ----- i ? i- v --- C HERVK13#LTR/E 5603 AGTTTCTCG-GGACAGCCCATAACCGAGAA-----ACANGAAAGCATATG 5560 chr2qtel1M 865372 TCAGTGACCACTCGGGCTGT-CTTTTTGCTGCT-GGCA--TTGCAAAAGT 865417 iv v v i-- i i - iiv i i - i -- v vv ii C HERVK13#LTR/E 5559 TCGTTTAACAT--GAGCCGTACTTTCCCCCGTTTGACAAGTGGCCCAGAT 5512 chr2qtel1M 865418 GAATCCTGAAAAGGTGTCTACCACAAGGTGGATAAAAGACAGACACCCAA 865467 i vivv v iviiv vi v v vivv C HERVK13#LTR/E 5511 AAAATGAGAAAAGGTGTCAATAGTTACATGTATAAAAGAAAGCTTGCCAA 5462 chr2qtel1M 865468 AAGATTTATAATGGATCACATCCATTTGCCAGA 865500 vvvv ii i C HERVK13#LTR/E 5461 AAGCAGGATAATGAGTCACGTCCATTTGCCAGA 5429 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.13 CpG sites = 47, Kimura (unadjusted) = 41.72 Transitions / transversions = 1.04 (47/45) Gap_init rate = 0.10 (32 / 313), avg. gap size = 1.28 (41 / 32) 405 32.76 4.89 3.54 chr2qtel1M 865222 865528 (134472) C HERVK11#LTR/ERVK (2683) 5270 4960 m_b105s701i1 3835 chr2qtel1M 865222 GCCTGACTTTGAGGATTAAAGGGTATGCCAGTGGTGTGTAAAATCTTATA 865271 v ii iv i v v i ii i vi iiivi C HERVK11#LTR/E 5270 GCCTGTCCCTGAGGATTGTAAGGGATTCCGGTAATATGGGAAATTCCCCA 5221 chr2qtel1M 865272 CTGT-GCACAAA--AGTGTTCAAAATGTTTGGAAGTCTATGTGGGTTCAT 865318 - i -- i --- vvi ivv iiv vii vv i C HERVK11#LTR/E 5220 CTGTTGCATAAATAAAT---CAAAAGCCTTACTAACATATCCAGGGGCGT 5174 chr2qtel1M 865319 TATCTGT-TTTATTTCTTGTGCA--CACCATAATTGCAAATGCTTATATG 865365 i - vv i v -- v i - ------- C HERVK11#LTR/E 5173 TGTCTGTCTTTATTTGATATGGAAGCCCCATAACTGCAAA-GC------- 5132 chr2qtel1M 865366 AGGAATTCAG-TGACC----ACTCGGGCTGT-CTTTTTGCTGCT-GGCA- 865407 i v - vii---- vi i - i iiv i - - C HERVK11#LTR/E 5131 AAGAATACAGATGTTTTTTAACATGGGCCGTGCCTTCCCCTGTTTGGCAA 5082 chr2qtel1M 865408 -TTGCAAAAGTGAATCCTGAAAAGGTGTCTACCACAAGGTGGATAAAAGA 865456 - v vv ii i v i i viv vi v i v v C HERVK11#LTR/E 5081 GTAGCCCAGATAAAACCTGAGAAGGTATCTACAGAAACATGCACATATGA 5032 chr2qtel1M 865457 CAGACACCCAAAAGATTTATAATGGATCACATCCATTTGCCAGATTTCAT 865506 ? v vv i vi vv ii v vv? C HERVK11#LTR/E 5031 NAGTCTGCCAAAGGAGCTAACATGAGTCACATCCATTTGCCATAAANCAT 4982 chr2qtel1M 865507 TGGGTCTCAAACCACCAGGGTT 865528 i vv i ii v ii i C HERVK11#LTR/E 4981 TAGGAGTTAGGCCTCTGGGATT 4960 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 42.74 CpG sites = 53, Kimura (unadjusted) = 44.58 Transitions / transversions = 1.20 (53/44) Gap_init rate = 0.07 (21 / 306), avg. gap size = 1.24 (26 / 21) 567 27.95 7.11 6.44 chr2qtel1M 866587 867064 (132936) C HERVK#LTR/ERVK (3777) 3759 3279 m_b105s701i2 3835 chr2qtel1M 866587 GCCTAGCACTGGACCCATCCATTGGATATCTCCTATCAATTTTGGAAA-T 866635 vii v vv v vi v v - C HERVK#LTR/ERV 3759 GCCTAGAGTTGGCCGAATCCAATTAATATCTCCTAGCAATTTTTGAAAGT 3710 chr2qtel1M 866636 CATTCAAAGTATTTAACTTCTCTGTTCTTAAAGACAGTTTTGTACTGTAA 866685 i v v iv v v -------- v i v vv C HERVK#LTR/ERV 3709 CATTTAATGTTTTTAATGTGTCTTTTCTTA--------TTTCTATTTTTT 3668 chr2qtel1M 866686 GTGCCTTAGGGTATCTTTCATATCCTC--------------AATATTGAA 866721 v ---- i - -------------- v C HERVK#LTR/ERV 3667 GTGGCTTA----ATTTTTC-TATCCTCTACCTGCATCCCTAAATAATGAA 3623 chr2qtel1M 866722 AAGGAGCATGCCTTTGAATTTTTCTGTAAGCAATATGAAGTTTGTAGTTT 866771 i vivv i ------ v i- vvi vvi - i C HERVK#LTR/ERV 3622 AAGGAGTAGAGGTTTGAATCTT------ATCAG-ATGCTATTGCCAG-TC 3581 chr2qtel1M 866772 CTTAGTGTTTCTATGGTCT-TTTGTAGATATGCTTCTAAC---------A 866811 -- i vvi vvv -i i v -- v --------- C HERVK#LTR/ERV 3580 CT--GCGTTGGCAACCTCTGCTTGCAGAAATG--TGTAACAGTCAATTAA 3535 chr2qtel1M 866812 TTTATCCCTCAGGT-TGCA-CACCCAAAATGTCATCCATGTAATGCAACA 866859 i i ivv - - v i v ii - ii C HERVK#LTR/ERV 3534 TTTGTCTCTCGTTTCTGCAGCACACAAAATATCATCAACATAATG-AATG 3486 chr2qtel1M 866860 ATATTACCTTTGGAAACACTTTTCTC--ACTGGAGTAAGACAGC---AGC 866904 v vv iv - v -- vvv -- --- C HERVK#LTR/ERV 3485 ATATAACAGTCTGAAA-ACTTGTCTCTAACTGGTTGAAG--AGCTCGAGC 3439 chr2qtel1M 866905 AACATACATTTGGCACAAGGTAGGGCTATTTTTCATTCCCTGTGGCAAAA 866954 v v vi i i v vi v i vvv v v C HERVK#LTR/ERV 3438 TACAAAAGTCTGACAAATAGTTGGACTATTAAGCATTCCCTGAGGCAACA 3389 chr2qtel1M 866955 TTGTCCATTCATATCTTTTATAAGGCTCAGCTA--AGTTAACACTGGGCA 867002 i v i v v i vv ivvv i -vi -- v vvi - i C HERVK#LTR/ERV 3388 CTTTCCACTGAAACCTGGTGGCTGGTTC-TTTATTATTTATGGCT-GGTA 3341 chr2qtel1M 867003 TGGAAAAGGCAAATCTTTCCATATCCTCCTTATCCAGAGGGATAGAATGG 867052 i v i v?v v ivv i i v vii C HERVK#LTR/ERV 3340 TAGTAAAGGCAAATTTTTCANAATCCTGCTCTGCCAGAGGAATGGTAAAA 3291 chr2qtel1M 867053 AAACAATCCTTC 867064 i C HERVK#LTR/ERV 3290 AAGCAATCCTTC 3279 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 34.48 CpG sites = 48, Kimura (unadjusted) = 35.13 Transitions / transversions = 0.62 (48/77) Gap_init rate = 0.08 (40 / 477), avg. gap size = 1.62 (65 / 40) 18 15.52 0.00 8.51 chr2qtel1M 867742 867792 (132208) (CCT)n#Simple_repeat 1 47 (0) m_b105s252i4 3836 chr2qtel1M 867742 CCTCCTCCTCCTCGGCCAGACTCCCTCCTCCTCCTCCGCTGTCCTCCCTC 867791 vv -vv - v -v - (CCT)n#Simple 1 CCTCCTCCTCCTCCTCC-TCCT-CCTCCTCCTCCTCCTC-CTCCT-CCTC 46 chr2qtel1M 867792 C 867792 (CCT)n#Simple 47 C 47 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.08 (4 / 50), avg. gap size = 1.00 (4 / 4) 21 30.03 0.00 5.32 chr2qtel1M 868485 868583 (131417) (GGGGGC)n#Simple_repeat 1 94 (0) m_b105s252i5 3837 chr2qtel1M 868485 GGGGAAGGGGGCCTGGGCGGAAGTGGGGGGGGCTGGGCAGACGTGGGAGC 868534 iv vv ii i v -- i iv i i (GGGGGC)n#Sim 1 GGGGGCGGGGGCGGGGGCGGGGGCGGGGGCGG--GGGCGGGGGCGGGGGC 48 chr2qtel1M 868535 GGAAGAAGTCACGGGGCCGGGGGCGGGGTCTGCGGGGCCGGGGGCGGGG 868583 ii vi vvi v --- v (GGGGGC)n#Sim 49 GGGGGCGGGGGCGGGGGCGGGGGCGGGG---GCGGGGGCGGGGGCGGGG 94 Matrix = Unknown Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.05 (5 / 98), avg. gap size = 1.00 (5 / 5) 16 23.90 7.50 1.18 chr2qtel1M 869118 869197 (130803) (CTCCCGG)n#Simple_repeat 1 85 (0) m_b105s252i7 3838 chr2qtel1M 869118 CTTCCGGC-GCCGGCT--CAGC-CGCGGCT-CTGGGTCCCAGGTCCGAGC 869162 i -v -- i - v - i v i v vi (CTCCCGG)n#Si 1 CTCCCGGCTCCCGGCTCCCGGCTCCCGGCTCCCGGCTCCCGGCTCCCGGC 50 chr2qtel1M 869163 TCGCGGCTTCGGGGCTCCCAGC-CCAGGCTCCCCGC 869197 v - vv i - v v (CTCCCGG)n#Si 51 TCCCGGC-TCCCGGCTCCCGGCTCCCGGCTCCCGGC 85 Matrix = Unknown Transitions / transversions = 0.60 (6/10) Gap_init rate = 0.08 (6 / 79), avg. gap size = 1.17 (7 / 6) 31 22.36 1.25 1.25 chr2qtel1M 869762 869841 (130159) (TCC)n#Simple_repeat 1 80 (0) m_b105s252i8 3839 chr2qtel1M 869762 TCCTCCCCCTCCT-CTCCTTTCTCCCCTTCCTCCTCCTCCCCTTTTTCCT 869810 i - - i i i i i ii (TCC)n#Simple 1 TCCTCCTCCTCCTCCTCC-TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT 49 chr2qtel1M 869811 CCTCCTCCTGCTGCTGCTGCTGCTGCTGCTC 869841 v v v v v v v (TCC)n#Simple 50 CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC 80 Matrix = Unknown Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.03 (2 / 79), avg. gap size = 1.00 (2 / 2) 30 10.62 0.00 0.00 chr2qtel1M 870007 870057 (129943) (CACTCA)n#Simple_repeat 1 51 (0) c_b105s251i0 3840 chr2qtel1M 870007 CACTCACACTCACACACACACTCACACACTCCCTCACACTCACACACACA 870056 v v v v v (CACTCA)n#Sim 1 CACTCACACTCACACTCACACTCACACTCACACTCACACTCACACTCACA 50 chr2qtel1M 870057 C 870057 (CACTCA)n#Sim 51 C 51 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 234 28.83 4.67 2.75 chr2qtel1M 871107 871213 (128787) C MIRb#SINE/MIR (17) 251 143 m_b105s601i4 3841 chr2qtel1M 871107 TTATAAAGTATCTACT--GAGCACAGACACTTGAGTTAAGCACCTTAC-- 871152 vi iiii -- v - i - v i i i -- C MIRb#SINE/MIR 251 TTATTGAGCGCTTACTATGTGC-CAGGCACT-GTGCTAAGCGCTTTACAT 204 chr2qtel1M 871153 -CAATATTTCTTGGGAACCTCACCACAAAATTTGCAAGCCAGGTTTCATT 871201 - v i v vvi v v v-ii i vi v i C MIRb#SINE/MIR 203 GCATTATCTCATTTAATCCTCACAACAAC-CCTGCGAGGTAGGTATTATT 155 chr2qtel1M 871202 TTCCCCATTATA 871213 v v C MIRb#SINE/MIR 154 ATCCCCATTTTA 143 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.43 CpG sites = 16, Kimura (unadjusted) = 37.04 Transitions / transversions = 1.14 (16/14) Gap_init rate = 0.06 (6 / 106), avg. gap size = 1.33 (8 / 6) 12 22.67 0.00 0.00 chr2qtel1M 871560 871591 (128409) (TATATG)n#Simple_repeat 1 32 (0) m_b105s252i9 3842 chr2qtel1M 871560 TATGTGTACTTATACATGCATATGTATATGTA 871591 i iv i i i (TATATG)n#Sim 1 TATATGTATATGTATATGTATATGTATATGTA 32 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 16 11.70 0.00 0.00 chr2qtel1M 871722 871749 (128251) (CTAT)n#Simple_repeat 1 28 (0) m_b105s252i10 3843 chr2qtel1M 871722 CTATGTATGTATGTATCTATCTATCTAT 871749 v v v (CTAT)n#Simpl 1 CTATCTATCTATCTATCTATCTATCTAT 28 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 56 21.23 0.00 0.00 chr2qtel1M 871750 871868 (128132) (ACAC)n#Simple_repeat 1 119 (0) m_b105s252i11 3844 chr2qtel1M 871750 ACACACACACTCACTCACACATTCACAGACACACAATCACACACACACAC 871799 v v iv v vv (ACAC)n#Simpl 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50 chr2qtel1M 871800 ATTCCCTCACATTCACACACACACACATTCACATACACACACTCATTCAC 871849 iv v v iv iv i v iv (ACAC)n#Simpl 51 ACACACACACACACACACACACACACACACACACACACACACACACACAC 100 chr2qtel1M 871850 ACACTCACTCACACGCACA 871868 v v i (ACAC)n#Simpl 101 ACACACACACACACACACA 119 Matrix = Unknown Transitions / transversions = 0.47 (7/15) Gap_init rate = 0.00 (0 / 118), avg. gap size = 0.0 (0 / 0) 12 28.77 5.97 0.00 chr2qtel1M 872900 872966 (127034) (AATATA)n#Simple_repeat 1 71 (0) m_b105s252i12 3845 chr2qtel1M 872900 AATATATGT-TAAACAT-AGTAAAAATATATCT-TAAAT-CCAATATAAC 872945 vi - i - i v vv - -iv v (AATATA)n#Sim 1 AATATAAATATAAATATAAATATAAATATAAATATAAATATAAATATAAA 50 chr2qtel1M 872946 CATACGTATTTATATAATTAT 872966 i vi vv v (AATATA)n#Sim 51 TATAAATATAAATATAAATAT 71 Matrix = Unknown Transitions / transversions = 0.60 (6/10) Gap_init rate = 0.06 (4 / 66), avg. gap size = 1.00 (4 / 4) 261 32.50 0.00 5.63 chr2qtel1M 873293 873442 (126558) C L1ME4c_3end#LINE/L1 (275) 555 414 m_b105s551i11 3846 chr2qtel1M 873293 ATGATATTCCATAACACTGACATACCATAACTTAACTTATTCAGTCATTC 873342 i vivii? ii i - ---- ii C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTT-ACTT----AACCATTC 511 chr2qtel1M 873343 TCCAATTCATGGGAATCCCCCTCAGTTCCCAGTTTCTTGCTACTACAAAA 873392 i v vv iv iivvv i- i i i i i i v C L1ME4c_3end#L 510 CCCTATTGTTGGACATTTAGGTT-GTTTCCAATTTTTCGCTATTATAAAT 462 chr2qtel1M 873393 AGGACTCCAAGAAATGTTTTTGTACATGTGAGTCGTTTTCCCTCCTTTAA 873442 ivi v vi ii i i i i - - v i i i C L1ME4c_3end#L 461 AACGCTGCAATGAACATCTTCGTGCATAT-AG-CTTTTTCCTTCTTTTGA 414 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.40 CpG sites = 32, Kimura (unadjusted) = 45.82 Transitions / transversions = 2.29 (32/14) Gap_init rate = 0.05 (8 / 149), avg. gap size = 1.00 (8 / 8) 330 31.23 0.00 4.92 chr2qtel1M 873293 873420 (126580) C L1ME3G_3end#LINE/L1 (376) 548 427 m_b105s551i12 3846 chr2qtel1M 873293 ATGATATTCCATAACACTGACATACCATAACTTAACTTATTCAGTCATTC 873342 ii ii iv i i ----- i ii C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTA-----TTTAACCATTC 504 chr2qtel1M 873343 TCCAATTCATGGGAATCCCCCTCAGTTCCCAGTTTCTTGCTACTACAAAA 873392 i v v iv iivvv i- i i i i i v C L1ME3G_3end#L 503 CCCTATTGATGGACATTTAGGTT-GTTTCCAATTTTTCGCTATTACAAAC 455 chr2qtel1M 873393 AGGACTCCAAGAAATGTTTTTGTACATG 873420 ivi v vi ii ii C L1ME3G_3end#L 454 AATGCTGCAATGAACATCCTTGTACATG 427 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.47 CpG sites = 27, Kimura (unadjusted) = 43.02 Transitions / transversions = 2.45 (27/11) Gap_init rate = 0.05 (6 / 127), avg. gap size = 1.00 (6 / 6) 438 33.85 9.87 3.21 chr2qtel1M 874810 875569 (124431) C L1PREC2_orf2#LINE/L1 (811) 2483 1675 m_b105s551i13 3847 chr2qtel1M 874810 ATAGCATTAAAGGTGTGGATTATTTGGGGCAGTCTTGCCATTTTTAT-AT 874858 i vv ii ii v v v v i- C L1PREC2_orf2# 2483 ATAGCATTGAATCTGTAAATTGCTTTGGGCAGTATGGCCATTTTAACGAT 2434 chr2qtel1M 874859 CCTGATGCAGCCTAGCC-CAAGCACTGGATATTCCTTTAGCT-TTTAAGT 874906 vi v vv v -ii iv i i ii ii vi - iv C L1PREC2_orf2# 2433 ATTGATTCTTCCTATCCATGAGCATGGAATGTTTTTCCATTTGTTTGTGT 2384 chr2qtel1M 874907 TGTCATGCATTACTTTAAGGATGGCATTGCAA--CTGAATTTGTACAACT 874954 ii vivv v i v vv iv i -- v -- v iv C L1PREC2_orf2# 2383 CATCTCTGATTTCTTTGAGCAGTGTTTTGTAATTCTCA--TTGTAGAGAT 2336 chr2qtel1M 874955 CTTTTA-----------------ATTCCTAGATATTGAATCCACATTTTA 874987 i ----------------- i vv i viv v i C L1PREC2_orf2# 2335 CTTTCACCTCCCTGGTTAGCTGTATTCCTAGGTATTTTATTCTTTTTGTG 2286 chr2qtel1M 874988 CTTATTTGGAGTGGGATTTTTCTCTCAATTATTGCTTCCTGGACTT---T 875034 viv vv i vivi iii - v -- v i --- C L1PREC2_orf2# 2285 GCAATTGTGAATGGGATTGCGTTCCTGATT-TGGCT--CTCGGCTTGGCT 2239 chr2qtel1M 875035 GTTTCTATTTCCTAGAAATA------ATCTTGGGAG---GATTCTGTGTG 875075 vi iv viv i i------ i v v v--- i i - C L1PREC2_orf2# 2238 GTTGTTGGTGTATAGGAATGCTAGTGATTTTTGTACATTGATTTTGTAT- 2190 chr2qtel1M 875076 TAACCTGCAACTTTGCATAAACTGTTAA--ATCTTAACTATCCTACTTGA 875123 --- v vv ii v -- v ? vv v i -- i C L1PREC2_orf2# 2189 ---CCTGAAACTTTGCTGAAGTTGTTTATCAGCTNAAGGAGCTT--TTGG 2145 chr2qtel1M 875124 TGTCTCTGCTGA--TTACCTGTGTATTTCCAAGTGAAGCATCCTGTCATC 875171 ------- i --i -- v vv i ii iv v v i C L1PREC2_orf2# 2144 -------GCCGAGACTA--TGGGGTTTTCTAGATATAGAATCATGTCGTC 2104 chr2qtel1M 875172 AACAA-CGGGGCTAGTTTGAGCTCTTCTTTACCCATGTTTATTCCTTTCT 875220 vi - i v vi i i v i v vv v i iv C L1PREC2_orf2# 2103 TGCAAACAGGGATAGTTTGACTTCCTCTCTTCCTATTTGGATGCCCTTTA 2054 chr2qtel1M 875221 TTCCTTTCTCTTGTTTTGTTGCTATTGCTAGCATTGTCA----------G 875260 i ii vi v v i v i vi ---------- C L1PREC2_orf2# 2053 TTTCTTTCTCTTGCCTGATTGCTCTGGCCAGGACTTCCAATACTATGTTG 2004 chr2qtel1M 875261 AA---GAGTAGGGAAAGTAAACATTCTTGCTTTACCCCTGCATTTATTGG 875307 --- i v i viii i ii iiv v iv i vv C L1PREC2_orf2# 2003 AATAGGAGTGGTGAGAGAGGGCATCCTTGTCTTGTGCCGGTTTTCAAGGG 1954 chr2qtel1M 875308 AAATGTTTCTAACACAACCCCATTTCATGCAATGCT---TTTAAGTTTTT 875354 i i i i vivvv ivi iii i --- v ii v C L1PREC2_orf2# 1953 GAATGCTTCCAGCTTTTGCCCATTCAGTATGATGTTGGCTGTGGGTTTGT 1904 chr2qtel1M 875355 GATAGATA----TTATGACCTTGAAA-ATGGTCCCACTAGGCCTGTACTT 875399 v i---- v ii ii- v iv v vi -- v C L1PREC2_orf2# 1903 CATAGATGGCTCTTATTATTTTGAGGTATGTTCCTTCAATACCT--AGTT 1856 chr2qtel1M 875400 CTAATTAC-GTTTTTACC-TCA---GAAGTGG-------TCCAAAGCACT 875437 - v v v- v - v --- v v ------- v vi C L1PREC2_orf2# 1855 -TATTGAGAGTTTTTAACATGAAGGGATGTTGAATTTTATCGAAAGCCTT 1807 chr2qtel1M 875438 CCCTTCATCTGTTGAAATGACTGTATGGTTTTAAATGT-TTTGGTT-TAT 875485 ii v i i i iii i --- - i - i C L1PREC2_orf2# 1806 TTCTGCATCTATTGAGATAATCATGTGGTTTT---TGTCTTTAGTTCTGT 1760 chr2qtel1M 875486 A-ATATAATGGATTATGTTCATTGTTTTCCTAGTGTTGAACTATTCTTAC 875534 v- i i i i ii i v v vvi i vi i C L1PREC2_orf2# 1759 TTATGTGATGAATCACATTTATTGATTTGCGTATGTTGAACCAACCTTGC 1710 chr2qtel1M 875535 ATCCTTGGTACAAATTCCACTTGAGCATAATGAAT 875569 iv v i vi i v i ii i C L1PREC2_orf2# 1709 ATCCCAGGGATAAAGCCTACTTGATCGTGGTGGAT 1675 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 45.15 CpG sites = 135, Kimura (unadjusted) = 46.42 Transitions / transversions = 1.18 (135/114) Gap_init rate = 0.06 (49 / 759), avg. gap size = 2.06 (101 / 49) 517 33.05 8.46 3.57 chr2qtel1M 874958 875572 (124428) C L1M1_orf2#LINE/L1 (979) 2315 1672 m_b105s551i14 3847 chr2qtel1M 874958 TTAATTCCTAGATATTGAATCCACATTT-TACTTATTTGGAGTGGGATTT 875006 i v ii-i - ivi vvi i v C L1M1_orf2#LIN 2315 TTAATTCCTAGGTATTTAATTT-TATTTGTGGCTATTGTAAATGGGATTA 2267 chr2qtel1M 875007 TTCTCTCAATTATTGCTTCCTGGACTTTGTTT-CTATTTCC---TAGAAA 875052 i i i ii vi vi --i -- i- i vv --- C L1M1_orf2#LIN 2266 CTTTTTTGATTTCTTTTTC--AGA--TTGTTCACTGTTGGCATATAGAAA 2221 chr2qtel1M 875053 TA------ATCTTGGGA-G--GATTCTGTGTGTAACCTGCAACTTTGCAT 875093 i------ i v v - -- i i ---- i vv C L1M1_orf2#LIN 2220 TGCTACTGATTTTTGTATGTTGATTTTGTAT----CCTGCAACTTTACTG 2175 chr2qtel1M 875094 AAACTGTTAAATCTTAACTATCCTACTTGATGTCTCTGCTGATTACCTGT 875143 vi ------ v vi i v v - v i i? iv v vii iv C L1M1_orf2#LIN 2174 AATTTGTT------TATCAGTTCTAATAG-TTTTTTNGTGGAGTCTTTAG 2132 chr2qtel1M 875144 GTATTTCCAAGTGAAGCATCCTGTCATCAACAA-CGGGGCTAGTTTGAGC 875192 v i iv iv v i vi - ii v i vi C L1M1_orf2#LIN 2131 GTTTTTCCAAATATAAGATCATATCATCTGCAAACAAGGATAATTTGACT 2082 chr2qtel1M 875193 TCTTCTTTACCCATGTTTATTCCTTTCTTTCCTTTCTCTTGTTTTGTTGC 875242 i v v v vv v i iv i i vi C L1M1_orf2#LIN 2081 TCTTCCTTTCCAATTTGGATGCCCTTTATTTCTTTCTCTTGTCTGATTGC 2032 chr2qtel1M 875243 TATTGCTAGCATTGTCAG-------------AAGAGTAGGGAAAGTAAAC 875279 v v v i vi ------------- v i v iii C L1M1_orf2#LIN 2031 TCTAGCTAGGACTTCCAGTACTATGTTGAATAACAGTGGTGAAAGTGGGC 1982 chr2qtel1M 875280 ATTCTTGCTTTACCCCTGCATTTATTGGAAATGTTTCTAACACAACCCCA 875329 i iiv iii v vvi vv v i ii iivivv C L1M1_orf2#LIN 1981 ATCCTTGTCGTGTTCCAGATCTTAGAGGAAAGGCTTTCAGTTTTTCCCCA 1932 chr2qtel1M 875330 TTTCATGCAATGCT---TTTAAGTTTTTGATAGATA----TTATGACCTT 875372 ivi iii i --- v ii i v vi v i---- v iv C L1M1_orf2#LIN 1931 TTCAGTATGATACTAGCTGTGGGTCTGTCGTATATGGCTTTTATTATGTT 1882 chr2qtel1M 875373 GAAA-ATGGTCCCACTAGGCCTGTACTTCTAATTACGTTTTTACCTCA-G 875420 ii- v iv vi iivvi i i --iv -- - C L1M1_orf2#LIN 1881 GAGGTATGTTCCTTCTATACCCAGTTTTTTGA--GGGTTTTTA--TCATG 1836 chr2qtel1M 875421 AAGTGGT-----------CCAAA-GCACTCCCTTCATCTGTTGAAATGAC 875458 v i -----------i - vi ii vv vi i C L1M1_orf2#LIN 1835 AAGGGATGTTGAATTTTATCAAATGCTTTTTCAGCATCAATTGAAATGAT 1786 chr2qtel1M 875459 TGTATGGTTTTAAATGT--TTTGGTTTAT-AATATAATGGATTATGTTCA 875505 ii --- -- iiv i i -i i v i ii v C L1M1_orf2#LIN 1785 CATATGGTTTT---TGTCCTTCATTCTGTTGATATGATGTATCACATTGA 1739 chr2qtel1M 875506 TTGTTTTCCTAGTGTTGAACTATTCTTACATCCTTGGTACAAATTCCACT 875555 v v vvi i i i i? v i i C L1M1_orf2#LIN 1738 TTGATTTGCGTATGTTGAACCATCCTTGCATCCCNGGGATAAATCCCACT 1689 chr2qtel1M 875556 TGAGCATAATGAATGAT 875572 iv i C L1M1_orf2#LIN 1688 TGGTCATGATGAATGAT 1672 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 44.83 CpG sites = 115, Kimura (unadjusted) = 45.47 Transitions / transversions = 1.42 (115/81) Gap_init rate = 0.06 (39 / 614), avg. gap size = 1.92 (75 / 39) 624 34.10 8.37 1.20 chr2qtel1M 875147 875612 (124388) C L1PB_orf2#LINE/L1 (1166) 2128 1630 m_b105s551i15 3847 chr2qtel1M 875147 TTTCCAAGTGAAGCATCCTGTCATCAACAA-CGGGGCTAGTTTGAGCTCT 875195 i i i? vv v i i - i v vi vi i C L1PB_orf2#LIN 2128 TTTCTAGGTANACGATCATATCATCAGCAAACAGCGACAGTTTGACTTCC 2079 chr2qtel1M 875196 TCTTTACCCATGTTTATTCCTTTCTTTCCTTTCTCTTGTTTTGTTGCTAT 875245 v v vv v i iv i i vi v C L1PB_orf2#LIN 2078 TCTTTACCGATTTGGATGCCCTTTATTTCTTTCTCTTGTCTGATTGCTCT 2029 chr2qtel1M 875246 TGCTAGCATTGTCAG-------------AAGAGTAGGGAAAGTAAACATT 875282 v v i vi ------------- ii i v i iii i C L1PB_orf2#LIN 2028 GGCTAGGACTTCCAGTACTATGTTGAANAGAAGTGGTGAGAGTGGGCATC 1979 chr2qtel1M 875283 CTTGCTTTACCCCTGCATTTATTGGAAATGTTTCTAACACAACCCCATTT 875332 ii iii v ivi i vv i i ii vivv i C L1PB_orf2#LIN 1978 CTTGTCTTGTTCCAGTTCTCAGGGGGAATGCTTTCAACTTTTCCCCATTC 1929 chr2qtel1M 875333 CATGCAATGCT---TTTAAGTTTTTGATAGATA----TTATGACCTTGAA 875375 vi ii? i --- v ii v v i---- v ? i i C L1PB_orf2#LIN 1928 AGTATNATGTTGGCTGTGGGTTTGTCATAGATGGCTTTTATTACNTTAAG 1879 chr2qtel1M 875376 A-ATGGTCCCACTAGGCCTGTACTTCTAATTACGTTTTTACCTCAGAAG- 875423 i- vi iv? v vi vi v i --iv v i vi i i - C L1PB_orf2#LIN 1878 GTATGTCCCTTNTATGCCGATTTTGCTGA--GGGTTTTAATCATAAAGGG 1831 chr2qtel1M 875424 -TG---------GTCCAAAGCACTCCCTTCATCTGTTGAAATGACTGTAT 875463 - --------- v v vi ii v i i iii i C L1PB_orf2#LIN 1830 ATGCTGGATTTTGTCAAATGCTTTTTCTGCATCTATTGAGATGATCATGT 1781 chr2qtel1M 875464 GGTTTTAAATGTTTTGGTTTATA---ATATAATGGATTATGTTCATTGTT 875510 i --- viv v i--- i ii v i ii i vi C L1PB_orf2#LIN 1780 GATTTT---TGTTTTTAATTCTGTTTATGTGGTGTATCACATTTATTGAC 1734 chr2qtel1M 875511 TTCCTAGTGTTGAACTATTCTTACATCCTTGGTACAAATTCCACTTGAGC 875560 v vvi i i i i i i ii vi v C L1PB_orf2#LIN 1733 TTGCGTATGTTAAACCATCCCTGCATCCCTGGTATGAAACCCACTTGATC 1684 chr2qtel1M 875561 ATAATGAATGATTCCTTGGA-ATTCAGGGTGG--TTGTTTGGATAGGATT 875607 ii i v iii v - v -v v -- i v i v v C L1PB_orf2#LIN 1683 ATGGTGGATTATCTTTTTGATATGC-TGTTGGATTCGGTTAGCTAGTATT 1635 chr2qtel1M 875608 TTGTT 875612 C L1PB_orf2#LIN 1634 TTGTT 1630 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 47.81 CpG sites = 96, Kimura (unadjusted) = 48.25 Transitions / transversions = 1.57 (96/61) Gap_init rate = 0.04 (17 / 465), avg. gap size = 2.65 (45 / 17) 637 31.64 9.47 1.81 chr2qtel1M 875161 875572 (124428) C L1M2_orf2#LINE/L1 (1180) 2111 1669 m_b105s551i16 3847 chr2qtel1M 875161 ATCCTGTCATCAACAA-CGGGGCTAGTTTGAGCTCTTCTTTACCCATGTT 875209 v vi - i vi i vi i i v v v v C L1M2_orf2#LIN 2111 ATCATGTCATCTGCAAACAGGGACAATTTGACTTCCTCCTTTCCAATTTG 2062 chr2qtel1M 875210 TATTCCTTTCTTTCCTTTCTCTTGTTTTGTTGCTATTGCTAGCATTGTCA 875259 v v iv i ii vi v v v i vi C L1M2_orf2#LIN 2061 GATGCCTTTTATTTCTTTCTCTTGCCTAATTGCTCTGGCTAGGACTTCCA 2012 chr2qtel1M 875260 G-------------AAGAGTAGGGAAAGTAAACATTCTTGCTTTACCCCT 875296 ------------- ii i v iii i ii iii v C L1M2_orf2#LIN 2011 GTACTATGTTGAATAGAAGTGGTGAAAGTGGGCATCCTTGTCTTGTTCCA 1962 chr2qtel1M 875297 GCATTTATTGGAAATGTTTCTAACACAACCCCATTTCATGCAATGCT--- 875343 ?vi vv v i ii vivv ivi iii i --- C L1M2_orf2#LIN 1961 GNTCTTAGAGGAAAGGCTTTCAACTTTTCCCCATTCAGTATGATGTTAGC 1912 chr2qtel1M 875344 TTTAAGTTTTTGATAGATA----TTATGACCTTGAAA-ATGGTCCCACTA 875388 v ii v v v i---- viiv ii- i v iv C L1M2_orf2#LIN 1911 TGTGGGTTTGTCATATATGGCCTTTATTGTGTTGAGGTACGTTCCTTCTA 1862 chr2qtel1M 875389 GGCCTGTACTT-CTAATTACGTTTTTACCTCA-GAAGTGGT--------- 875427 vi i- i -i i --iv -- - v i --------- C L1M2_orf2#LIN 1861 TACCTA-ATTTGTTGA--GAGTTTTTA--TCATGAAGGGATGTTGAATTT 1817 chr2qtel1M 875428 --CCAAA-GCACTCCCTTCATCTGTTGAAATGACTGTATGGTTTTAAATG 875474 --i - vi ii v i i iii --- C L1M2_orf2#LIN 1816 TATCAAATGCTTTTTCTGCATCTATTGAGATGATCATATGGTTTT---TG 1770 chr2qtel1M 875475 T--TTTGGTTTA-TAATATAATGGATTATGTTCATTGTTTTCCTAGTGTT 875521 -- iiv i i- i i i v i i i v v vvi C L1M2_orf2#LIN 1769 TCCTTCATTCTGTTGATGTGATGTATCACGTTTATTGATTTGCGTATGTT 1720 chr2qtel1M 875522 GAACTATTCTTACATCCTTGGTACAAATTCCACTTGAGCATAATGAATGA 875571 i i i i v i i v ii ? ? C L1M2_orf2#LIN 1719 GAACCATCCTTGCATCCCTGGGATAAATCCCACTTGATCATGGTGNATNA 1670 chr2qtel1M 875572 T 875572 C L1M2_orf2#LIN 1669 T 1669 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 42.57 CpG sites = 81, Kimura (unadjusted) = 43.50 Transitions / transversions = 1.72 (81/47) Gap_init rate = 0.05 (20 / 411), avg. gap size = 2.35 (47 / 20) 11 18.98 0.00 7.69 chr2qtel1M 876031 876072 (123928) (ATTTATT)n#Simple_repeat 1 39 (0) m_b105s252i13 3848 chr2qtel1M 876031 ATTTATCATTTAAATTTTTTGTTATTTCCTATTCATCTATTT 876072 i -- v i vi i - (ATTTATT)n#Si 1 ATTTATTATTT--ATTATTTATTATTTATTATTTAT-TATTT 39 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.07 (3 / 41), avg. gap size = 1.00 (3 / 3) 258 23.33 6.32 5.21 chr2qtel1M 879494 879588 (120412) MIR3#SINE/MIR 106 201 (7) m_b105s601i5 3849 chr2qtel1M 879494 TCCCTTCTCTG--CTTGAGTTTGCTC--CTGTAAATTGGAGAGGGTTGGA 879539 v i -- i v v -- v - i MIR3#SINE/MIR 106 TCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATG-AGGGGGTTGGA 154 chr2qtel1M 879540 -TGGATTCTTGAATTCTGAAGTGACTTTCAACTCT-ACATCTTATAACTT 879587 - i ---- vi i i vv i i - ii i i i MIR3#SINE/MIR 155 CTAGA----TGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTC 200 chr2qtel1M 879588 T 879588 MIR3#SINE/MIR 201 T 201 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.85 CpG sites = 14, Kimura (unadjusted) = 28.85 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.10 (9 / 94), avg. gap size = 1.22 (11 / 9) 380 21.80 0.00 7.23 chr2qtel1M 881593 881681 (118319) C MIRb#SINE/MIR (62) 206 124 m_b105s601i6 3850 chr2qtel1M 881593 CATGCATTATCAGTGTCTCATTTTATCCTCATGAGAATCCTAGGACTTGG 881642 ------ v ii v i iv vv i C MIRb#SINE/MIR 206 CATGCATTATC------TCATTTAATCCTCACAACAACCCTGCGAGGTAG 163 chr2qtel1M 881643 GGATTATTATTTCTGTTTTACAGATAAAGAAACTGAAGC 881681 v ii ii i i i C MIRb#SINE/MIR 162 GTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGC 124 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 26.33 CpG sites = 12, Kimura (unadjusted) = 26.33 Transitions / transversions = 2.00 (12/6) Gap_init rate = 0.07 (6 / 88), avg. gap size = 1.00 (6 / 6) 16 16.52 0.00 0.00 chr2qtel1M 882007 882033 (117967) (T)n#Simple_repeat 1 27 (0) m_b105s252i14 3851 chr2qtel1M 882007 TTATTTTATCTTGTTTTTTTTTTTTTT 882033 v v i v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTT 27 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 15 17.62 0.00 5.00 chr2qtel1M 882007 882048 (117952) (TTATT)n#Simple_repeat 1 40 (0) m_b105s252i15 3852 chr2qtel1M 882007 TTATTTTATCTTGTTTTTTTTTTTTTTAACTAATATTTTATT 882048 i i v v - - vv (TTATT)n#Simp 1 TTATTTTATTTTATTTTATTTTATTTT-A-TTTTATTTTATT 40 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.05 (2 / 41), avg. gap size = 1.00 (2 / 2) 17 5.00 0.00 0.00 chr2qtel1M 882079 882099 (117901) (T)n#Simple_repeat 1 21 (0) m_b105s252i16 3853 chr2qtel1M 882079 TTCTTTTTTTTTTTTTTTTTT 882099 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTT 21 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 15 24.93 0.00 2.08 chr2qtel1M 882533 882581 (117419) (TCTTTGT)n#Simple_repeat 1 48 (0) m_b105s252i17 3854 chr2qtel1M 882533 TCTCTGTCATTTTTTCTTTACTTCCTTGTAAATTGTTCTTTGTTCTGTG 882581 i iv v -v i vvv v (TCTTTGT)n#Si 1 TCTTTGTTCTTTGTTCTTT-GTTCTTTGTTCTTTGTTCTTTGTTCTTTG 48 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.02 (1 / 48), avg. gap size = 1.00 (1 / 1) 322 25.27 4.40 0.00 chr2qtel1M 886866 886956 (113044) MIR3#SINE/MIR 111 205 (3) m_b105s601i7 3855 chr2qtel1M 886866 TCACTGAGTCTCAGTTTCC-CATTTATAAAATGAGGGGGGTGTACTTCTT 886914 v i i - i i v v vvv MIR3#SINE/MIR 111 TCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGAT 160 chr2qtel1M 886915 GGCCTTGTAGTTCCCTTCCAG---TGATCATCTGGGATCCTATAA 886956 ii ivv v --- ivv iv i i MIR3#SINE/MIR 161 GATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTATGA 205 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.04 CpG sites = 11, Kimura (unadjusted) = 31.04 Transitions / transversions = 0.92 (11/12) Gap_init rate = 0.02 (2 / 90), avg. gap size = 2.00 (4 / 2) 261 31.86 5.59 3.42 chr2qtel1M 887052 887194 (112806) C L2d2_3end#LINE/L2 (6) 549 404 m_b105s601i8 3856 chr2qtel1M 887052 CAAGTTGGCAAACTTTTA---AGTGCCTGTGAAAAGCCAGGCTCTGGGCT 887098 i iii iv --- i iiviviv v v v C L2d2_3end#LIN 549 CAAATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCT 500 chr2qtel1M 887099 AAGCACCA-GGAACATA-AAAGATGCAAAGGACAT--CCCCTGCTCTCCT 887144 i i ii- iiv - v i v i --i i vv C L2d2_3end#LIN 499 AGGCGCTGTGGGGGATACAAAGAAGTATAAGACATGGTCCCTGCCCTCAA 450 chr2qtel1M 887145 GGAGGTCACAGACT-GCTGGGGCAGACAGTACACCAGTAAGTATATAAAA 887193 v i iv - i - iv ---- ii ii i C L2d2_3end#LIN 449 GGAGCTTACAATCTAGTTGGGG-AGACAAGACA----TAAACACGTGAAA 405 chr2qtel1M 887194 A 887194 C L2d2_3end#LIN 404 A 404 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.64 CpG sites = 29, Kimura (unadjusted) = 43.77 Transitions / transversions = 1.93 (29/15) Gap_init rate = 0.07 (10 / 142), avg. gap size = 1.30 (13 / 10) 222 29.09 6.02 4.76 chr2qtel1M 887067 887232 (112768) C L2d_3end#LINE/L2 (26) 490 323 m_b105s601i9 3856 chr2qtel1M 887067 TTAAGTGCCTGTGAAAAGCCAGGCTCTGGGCTAAGCACCA---GGAAC-A 887112 i i iiv viv ivi v v i i ii--- - C L2d_3end#LINE 490 TTGAGCGCCTACTATGTGCTCAGCACTGTGCTAGGCGCTGTGGGGAACGA 441 chr2qtel1M 887113 TAAAAGATGCAAAGGACAT--CCCCTGCTCTCCTGGAGGTCACAGACT-G 887159 ? ? - i v i --i i vv v i iv - C L2d_3end#LINE 440 NAAAANA-GTATAAGACATGGTCCCTGCCCTCAAGGAGCTTACAATCTAG 392 chr2qtel1M 887160 CTGGGGCAGACAGTACACCAGTAAGTATATAAAAACCCATTATGGAGCAA 887209 i - -- v i ii --i i i -- v vi i C L2d_3end#LINE 391 TTGGGG-AGACA--AGACTAACA--CACATGAAA--CAATTAGAGAACAA 349 chr2qtel1M 887210 -ATAA-ATTGGATA-AATTTAGGGCT 887232 - i - iv v - v v C L2d_3end#LINE 348 TACAAGACAGTATATAATTAAGTGCT 323 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.57 CpG sites = 28, Kimura (unadjusted) = 38.72 Transitions / transversions = 1.56 (28/18) Gap_init rate = 0.09 (15 / 165), avg. gap size = 1.20 (18 / 15) 294 27.53 6.87 2.94 chr2qtel1M 887068 887198 (112802) C L2b_3end#LINE/L2 (25) 441 306 m_b105s601i10 3856 chr2qtel1M 887068 TAAGTGCCTGTGAAAAGCCAGGCTCTGGGCTAAGCACCAGGAACATAAAA 887117 i i iiviviv ? v i i ii i i i ivi C L2b_3end#LINE 441 TGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGGGATACAGCG 392 chr2qtel1M 887118 GATGCAAAGGACA---TC---CCCTGCTCTCCTGGAGGTCACAGACTGCT 887161 - v v i ---? --- i vi v v iv C L2b_3end#LINE 391 G-TGAACAAGACAGACNCGGTCCCTGCCCTCACGGAGCTCACAGTCTAGT 343 chr2qtel1M 887162 GGGGCAGACAGTACACCAGTAAGTATATAA--A-AACCCA 887198 v - i-- ?i v i -- - C L2b_3end#LINE 342 GGGGGAGACAG-ACAT--GTAANCAGACAATNATAACCCA 306 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.56 CpG sites = 22, Kimura (unadjusted) = 36.66 Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.06 (8 / 130), avg. gap size = 1.62 (13 / 8) 327 30.25 13.81 0.84 chr2qtel1M 887305 887514 (112486) C MIRc#SINE/MIR (0) 268 32 m_b105s601i11 3857 chr2qtel1M 887305 AATAA-AATAATGTAGCTAGCATTTATACAACACCT-ACTGTGTGTCATG 887352 - i?i-- vi i i i i - v v iiv v C MIRc#SINE/MIR 268 AATAATAATAACNC--CTTACATTTGTATAGCACTTTACAGTTTACAAAG 221 chr2qtel1M 887353 CACTGT---AT-CA--ATATTATTTTATCCTCATGAAAACCCTAGGACTT 887396 i v --- - -- v i v ii v iv vv C MIRc#SINE/MIR 220 CGCTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGT 171 chr2qtel1M 887397 GTGT---GC---TATTGTTGTGCCCATTTTAGAGGTAAAGAAACTGTGGC 887440 iv i--- --- i i v v i i i v C MIRc#SINE/MIR 170 AGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGC 121 chr2qtel1M 887441 -AAAAGAGGTCCTGTAACTTG----------AATAGCAAATTACTGACAT 887479 -v i ivv i ----------v i v i v v i v C MIRc#SINE/MIR 120 TCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAG 71 chr2qtel1M 887480 GGAAGGAAT----ACTCAGAGCTTGCTGATTCAAGGTCC 887514 i vv i i---- i iv v i v i C MIRc#SINE/MIR 70 AGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCC 32 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.02 CpG sites = 34, Kimura (unadjusted) = 39.83 Transitions / transversions = 1.17 (34/29) Gap_init rate = 0.06 (12 / 209), avg. gap size = 2.58 (31 / 12) 501 22.79 11.92 1.20 chr2qtel1M 887310 887460 (112540) C MIR#SINE/MIR (0) 262 96 m_b105s601i12 3857 chr2qtel1M 887310 AATAATGTAGCTAGCATTTATACAACACCTACTGTGTGTCATGCACTGTA 887359 -- i vv i i i i i v v C MIR#SINE/MIR 262 AATAAT--AGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTT 215 chr2qtel1M 887360 TCAA------------TATTA-----TTTTATCCTCATGAAAACCCTAGG 887392 ii ------------ ----- v ii v v C MIR#SINE/MIR 214 CTAAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATG 165 chr2qtel1M 887393 ACTTGTGTGCTATTGTTGTGCCCATTTTAGAGGTAAAGAAACTGTGGCA- 887441 vv iv i i i v v i i i v - C MIR#SINE/MIR 164 AGGTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCAC 115 chr2qtel1M 887442 AAAGAGGTCCTGTAACTTG 887460 i ivv C MIR#SINE/MIR 114 AGAGAGGTTAAGTAACTTG 96 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 26.67 CpG sites = 19, Kimura (unadjusted) = 27.60 Transitions / transversions = 1.27 (19/15) Gap_init rate = 0.03 (5 / 150), avg. gap size = 4.00 (20 / 5) 572 29.69 7.01 2.85 chr2qtel1M 889423 889793 (110207) C HERVK#LTR/ERVK (2335) 5201 4816 m_b106s701i0 3858 chr2qtel1M 889423 TCTCCCTCTTTTTGTTTTTTGATAAAT----CTCTTGAGGGTCTGATTAG 889468 i i v v i iv ---- - v iiv C HERVK#LTR/ERV 5201 TCTCCCCCTTCTTTTTGTTTAACCAATTGAGCT-TTGAGTGTTCTATTAG 5153 chr2qtel1M 889469 TCCTTTCTACAGTGGCCTGTCCTGTGGGGTTGTAAGGAATTCCCAAAATA 889518 i v vi vv ii i ------- C HERVK#LTR/ERV 5152 TTCTTTCAACTATGGCCTGTCCTTGGGAATTATAAGGAATTCC------- 5110 chr2qtel1M 889519 TGATGAATGGAGAATTC----CTG---TAAGAACTGTTTTAATATTTT-- 889559 v v viv i---- --- i v vv ?ii -- C HERVK#LTR/ERV 5109 TGTTGTATGTGTAATTTTCCACTGATTTAAGAATTTTTGGAANGCTTTAC 5060 chr2qtel1M 889560 TGAGGTATATGAGGGTCCATTATCGGTCTTGATGGTGTGTGGGATACCCA 889609 ivi viv-- i i i i i vv v v i iv C HERVK#LTR/ERV 5059 TACAGTATCCT--GGCCCATTGTCAGTTTTAATTTTTTCTGGAACTCCCA 5012 chr2qtel1M 889610 TAGAAGCAAAACAGTGAAATAAGTGATTTATCACATGTGAAGCAGCTTCC 889659 iiv iviv i v v v v i vi i C HERVK#LTR/ERV 5011 TGACAGCAAAACAAGATAATAAATGTTTTTTAACATGGGAAGTACTTTCT 4962 chr2qtel1M 889660 CCTCCTTGAGAGGATACAAATACAAAGCCTGAATAAGTATCGACTGTAAC 889709 vii iv v i vv ii iiv i v C HERVK#LTR/ERV 4961 CCTGTCTGGCAGGTTGCCCATATGAAATGTGAATAAGTATCAACTGTTAC 4912 chr2qtel1M 889710 ATGAATGCATG----TTTTACCCTT--------ATGTATAACATCCATTT 889747 i ii? ---- i v vvv -------- ii i C HERVK#LTR/ERV 4911 ATGGACANATGACAATCTTCCAAATGAAGGTACATGCGTGACATCCATTT 4862 chr2qtel1M 889748 GCCATATATCATTTGG-CGTGCCACTTCTGGGGTTAATTGCTGTCCC 889793 vvv v - iii-v i i i v i i C HERVK#LTR/ERV 4861 GCCATAACGCATTAGGACACA-GACCTCTGGGATTAACTCCTGCCTC 4816 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.37 CpG sites = 58, Kimura (unadjusted) = 38.89 Transitions / transversions = 1.18 (58/49) Gap_init rate = 0.05 (18 / 370), avg. gap size = 2.06 (37 / 18) 272 28.00 3.85 3.85 chr2qtel1M 890655 890836 (109164) C L1MC1_3end#LINE/L1 (447) 633 452 m_b106s551i0 3859 chr2qtel1M 890655 GCTCATTTCACTCAGCATCAGTTCGTGTAAGTCTC-TCCAGGCCTTTCTG 890703 iv i i vi - v i v i - v i --- C L1MC1_3end#LI 633 GCTTCTTTCACTTAGTAATA-TGCATTTAAGTTTCCTCCATGTCTTT--- 588 chr2qtel1M 890704 AAATCAT--CCTGTTGG-TCATTTCTTAC-AGAAC--AATAATATTCCAT 890747 --- -- i v i - vi- vi -- C L1MC1_3end#LI 587 ---TCATGGCTTGATAGCTCATTTCTTTTTAGCGCTGAATAATATTCCAT 541 chr2qtel1M 890748 AATATTCATATACCACAATTTATTGAGCCATTCTCCAACTGATGGGCATC 890797 vi v vv i i v v v v v i C L1MC1_3end#LI 540 TGTCTGGATGTACCACAGTTTATTTATCCATTCACCTACTGAAGGACATC 491 chr2qtel1M 890798 CTCTCAGTTTCCAGTTTCTAGCCACTCTAAAGAGGGCTG 890836 i vviv i iv i i v i v i v ii C L1MC1_3end#LI 490 TTGGTTGCTTCCAAGTTTTGGCAATTATGAATAAAGCTG 452 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.62 CpG sites = 25, Kimura (unadjusted) = 35.50 Transitions / transversions = 1.04 (25/24) Gap_init rate = 0.07 (12 / 181), avg. gap size = 1.17 (14 / 12) 340 28.43 0.00 0.00 chr2qtel1M 890735 890836 (109164) C L1ME2z_3end#LINE/L1 (638) 553 452 m_b106s551i1 3859 chr2qtel1M 890735 AATAATATTCCATAATATTCATATACCACAATTTATTGAGCCATTCTCCA 890784 i i vi vv i i v v v C L1ME2z_3end#L 553 AGTAGTATTCCATTGTATGAATATACCACAGTTTGTTTATCCATTCTCCT 504 chr2qtel1M 890785 ACTGATGGGCATCCTCTCAGTTTCCAGTTTCTAGCCACTCTAAAGAGGGC 890834 ii i i ivvv v i i i i v i v ii C L1ME2z_3end#L 503 GTTGATGGACACCTGGGCTGTTTCCAGTTTTTGGCTATTATGAATAAAGC 454 chr2qtel1M 890835 TG 890836 C L1ME2z_3end#L 453 TG 452 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.69 CpG sites = 17, Kimura (unadjusted) = 36.69 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.00 (0 / 101), avg. gap size = 0.0 (0 / 0) 446 32.85 3.41 2.79 chr2qtel1M 891699 892196 (107804) C HERVK#LTR/ERVK (4026) 3510 3010 m_b106s701i2 3858 chr2qtel1M 891699 CAAAATATCATCTATGTCATGGAGGATGACTGCACTGGGGTAATGTTTCC 891748 v ii v i v - ivi v vv iv iv v i C HERVK#LTR/ERV 3510 CAAAATATCATCAACATAATGAATGAT-ATAACAGTCTGAAAACTTGTCT 3462 chr2qtel1M 891749 TTATCTTGCT-AATAGTTCTAGCAACATACCATTGGCATATAGTAGGGCT 891797 i v v i - v i v v v vvvi i v v i C HERVK#LTR/ERV 3461 CTAACTGGTTGAAGAGCTCGAGCTACAAAAGTCTGACAAATAGTTGGACT 3412 chr2qtel1M 891798 ATTTTTCATACTTGGTGGCAATACCTTCCACTGAAATCTCTTCATAGGAA 891847 vvv v iiv v i i i vv viiv vv C HERVK#LTR/ERV 3411 ATTAAGCATTCCCTGAGGCAACACTTTCCACTGAAACCTGGTGGCTGGTT 3362 chr2qtel1M 891848 TTAGAGAATTATATAT---TGGTACTGAGAAAGCAAATTT---ATA--CC 891889 i vv --- v --- iv vi i --- ? -- C HERVK#LTR/ERV 3361 CTTTA---TTATTTATGGCTGGTATAGTAAAGGCAAATTTTTCANAATCC 3315 chr2qtel1M 891890 TGTCCT--CAGGGTGAAGGGATATAGAGTAAAAGCAATGTTTAATATCTA 891937 ii -- i - v --- i --- vi v v v C HERVK#LTR/ERV 3314 TGCTCTGCCAGAG-GAATGG---TAAA---AAAGCAATCCTTCAGATCAA 3272 chr2qtel1M 891938 TTATCCATAAAGGCCATTCCCTGGGGATCATGTTTGGGGGTGACAAACCT 891987 vvv v ii ? vii i iv i v v C HERVK#LTR/ERV 3271 TTATAATTAAAGGCCAATCTTTNGGGATCATGGCCGGAGAGGGCAACCCG 3222 chr2qtel1M 891988 GCCTGTAAAGAACCTATGTTTTCCAGTACTGATTTTGCTTGTCTCAAATA 892037 vi v i iv i vv vv v v vv ?i vvvi i i v C HERVK#LTR/ERV 3221 GGTTGGAGAGGCCCCATGGGTTGAATTACGGCGTTNACGGCCCTTAAGTC 3172 chr2qtel1M 892038 TGTTAACATTCTCCATTTACCAAATTTTTTCTTTATAACAAATACAGGAG 892087 v v v i i vi vv v i C HERVK#LTR/ERV 3171 AGTTAACATGCGCCATCTGCCTGATTTTTTCTGAATTACAAACACAGGAG 3122 chr2qtel1M 892088 AGTTCCATGTGCT-GTTTGTTTCCTTAATGTGT---TTAATTCTAATTAT 892133 i v - v- vvi vvvv i i --- -- i i C HERVK#LTR/ERV 3121 AATTCCAAG-GCGAGAACGAAGGCTCAATATGTCCCTT--TTCTAACTGT 3075 chr2qtel1M 892134 TCTTACACTAATTGATATAGAGTGACT--TTTTTTCTTTGGCTTTGGTCA 892181 ? vii vi i i ivv i--i vi ivvi i C HERVK#LTR/ERV 3074 TCNTTTGCTAATAAATGTAAAGCCTCCAGCTTTTGTTTTGGTAGCGGCCA 3025 chr2qtel1M 892182 TTGCTTCACCTATAC 892196 i v i i C HERVK#LTR/ERV 3024 CTGATTTACCCATAC 3010 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 42.94 CpG sites = 70, Kimura (unadjusted) = 44.00 Transitions / transversions = 0.79 (70/89) Gap_init rate = 0.04 (22 / 497), avg. gap size = 1.41 (31 / 22) 636 31.37 1.77 1.77 chr2qtel1M 891699 892094 (107906) C HERVK14#LTR/ERVK (2932) 3164 2769 m_b106s701i1 3858 chr2qtel1M 891699 CAAAATATCATCTATGTCATGGAGGATGACTGCACTGGGGTAATGTTTCC 891748 i i v vi - ivi i vvvvv ivv i C HERVK14#LTR/E 3164 CAGAATATCATCCATGTAATGGATAAT-ATAACATTTTTTAAACTGTTCT 3116 chr2qtel1M 891749 TTATCTTGCT-AATAGTTCTAGCAACATACCATTGGCATATAGTAGGGCT 891797 i v v - i i vv i vvv i v v C HERVK14#LTR/E 3115 CTAACTGGCTTAATAGCTTTCCCGACATAAGTTTGACAAATAGTCGGGCT 3066 chr2qtel1M 891798 ATTTTTCATACTTGGTGGCAATACCTTCCACTGAAATCTCTTCATAGGAA 891847 vv i i v i i i v iv v i iiv vv C HERVK14#LTR/E 3065 ATTTAGCATGCCTTGTGGTAGTACTTTCCAATGGTATCTGTCCGCTGGTT 3016 chr2qtel1M 891848 TTAGAGAATTATATATTG---GTACTGAGAAAGCAAATTTATACCTGTCC 891894 i vv --- v v --- v v vi v - v ivi C HERVK14#LTR/E 3015 CTTTA---TTATTTATGGCGGGAACAGTAAAAGCAAATTTTT-CATAATC 2970 chr2qtel1M 891895 TCAGG--GTGAAGGGATATAGAGTAAAAGCAATGTTTAATATCTATTATC 891942 ii -- iv i - i viv vi v v i - C HERVK14#LTR/E 2969 TTGGGCAGCTAAAGGA-ATGGTAAAAAAGCAATCCTTTAGATCTATCA-C 2922 chr2qtel1M 891943 CATAA-AGGCCATTCCCTGGGGATCATGTTTGGGGGTGACAAACCTGCCT 891991 i i - v vii v vv iv i iv vi C HERVK14#LTR/E 2921 TATGAGAGGCCAGTATTTTGGGATCATTGTTGGGGAGGGCAGCCCTGGTT 2872 chr2qtel1M 891992 GTAAAGAACCTATGTTTTCCAGTACTGATTTTGCTTGTCTCAAATATGTT 892041 i iv v i vv vv vi v vv vi vvvi i v C HERVK14#LTR/E 2871 GCAGTGCACCCATGGGTTGAATCACAGCATTAACAGCCCTTAAATCTGTT 2822 chr2qtel1M 892042 AACATTCTCCATTTACCAAATTTTTTCTTTATAACAAATACAGGAGAGTT 892091 v vi v i i C HERVK14#LTR/E 2821 AACATTCTCCATTTCCCTGATTTTTTCTTAATGACAAATACAGGAGAATT 2772 chr2qtel1M 892092 CCA 892094 C HERVK14#LTR/E 2771 CCA 2769 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.97 CpG sites = 52, Kimura (unadjusted) = 40.80 Transitions / transversions = 0.74 (52/70) Gap_init rate = 0.03 (11 / 395), avg. gap size = 1.27 (14 / 11) 497 20.26 1.71 7.21 chr2qtel1M 893403 893519 (106481) MIRc#SINE/MIR 3 113 (155) m_b106s601i4 3860 chr2qtel1M 893403 AGCTAGT-TGGTGGAGTGGATAGAGCACCAGCCCTGAAGTCAGGAGGACC 893451 vi - v v ii v i i i MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chr2qtel1M 893452 TGAGTTCAAAT-TTGGCTTCAGACATGTAACACTTCCTGGCTATGTGACC 893500 i i i -ii i------ i-- v i i MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTC------TGC--CACTTACTAGCTGTGTGACC 94 chr2qtel1M 893501 CTGGGCAAGTCACTTAATC 893519 i i MIRc#SINE/MIR 95 TTGGGCAAGTCACTTAACC 113 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 22.04 CpG sites = 17, Kimura (unadjusted) = 24.55 Transitions / transversions = 3.40 (17/5) Gap_init rate = 0.09 (10 / 116), avg. gap size = 1.00 (10 / 10) 223 34.36 11.35 1.95 chr2qtel1M 894962 895243 (104757) L2#LINE/L2 2037 2344 (738) m_b106s601i5 3861 chr2qtel1M 894962 TTCTCCATCTTCATTCTCCTTGACTTCTC-------TTTGGGCT--TTGA 895002 vi i ii v i ? ------- ivvi-- L2#LINE/L2 2037 TTCTCAGTCCTCATCTTACTTGACCTNTCAGCAGCATTTGACACAGTTGA 2086 chr2qtel1M 895003 T-ACTTTTTTTTTCCATGA--TGCTCTCT-------GCTCTCTAGGGT-- 895040 - iii ii i- --ii i ------- - i ii-- L2#LINE/L2 2087 TCACTCCCTCCTTCT-TGAAACACTTTCTTCACTTGGCT-TCCAGGACAC 2134 chr2qtel1M 895041 -----TTTCCTGATTTCCCCCCTTCTTATTCTCTGACTACTTCTTTTC-- 895083 ----- i i i i v i --- v i ii i i -- L2#LINE/L2 2135 CACACTCTCCTGGTTTTCCTCCTACCT---CACTGGCCGCTCCTTCTCAG 2181 chr2qtel1M 895084 TATCTTTT--TAGATATTCCTGAGATCAA-AATTTCCAACCATATGGGTC 895130 v i -- i v vi v vv vv-i ii i? v i vv i v L2#LINE/L2 2182 TCTCCTTTGCTGGTTCCTCCTCATCTCCCCGACCTCTNAACGTTGGAGTG 2231 chr2qtel1M 895131 CCTTGGAATTCTGTCTCTGATCCTCTTTCTCTTTCCT-TCTATATTACTT 895179 iii iii v ii iv - ii - i i vvi L2#LINE/L2 2232 CCCCAGGGCTCAGTCCTTGGACCTCTT-CTCTTCTCTATCTACACTCACT 2280 chr2qtel1M 895180 TTCTTGTTGATTTCATCAGCTACTACGAATTTAATTGCTATCTATATTTT 895229 ii ? v i viv vii i iv v i i vi L2#LINE/L2 2281 CCCTNGGTGATCTCATCCAGTCTCATGGCTTTAAATACCATCTATATGCT 2330 chr2qtel1M 895230 GATGATTTTCAAAT 895243 i ii L2#LINE/L2 2331 GATGACTCCCAAAT 2344 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 48.08 CpG sites = 66, Kimura (unadjusted) = 50.52 Transitions / transversions = 2.28 (66/29) Gap_init rate = 0.06 (16 / 281), avg. gap size = 2.38 (38 / 16) 227 31.15 8.98 5.81 chr2qtel1M 895557 895723 (104277) L2#LINE/L2 2560 2731 (351) m_b106s601i6 3861 chr2qtel1M 895557 GAGTCATCCTGGCCTCCTCAGTATTCCTGACTACATATACATGTATATCC 895606 v v -- v i -- - i iv ---i i L2#LINE/L2 2560 GAGTCATCCTTGACTCCTC--TCTTTCT--CT-CACACCC---CACATCC 2601 chr2qtel1M 895607 AAT--ATGGTGCAAATGTCCATCAGTTTCACCATTGCAGCATCTCCAGAA 895654 -- vi- -i ii i i ii v iiv ii v L2#LINE/L2 2602 AATCCATCA-GCAAAT-CCTGTCGGCTCTACCTTCAAAATATATCCAGAA 2649 chr2qtel1M 895655 TATG-CC--------CCATT----CTACCACTATTCATGTGCATGTCTAG 895691 vi - -------- ii---- i i ii vv v v i vvv L2#LINE/L2 2650 TCCGACCACTTCTCACCACCTCCACTGCCACCACCCTGGTCCAAGCCACC 2699 chr2qtel1M 895692 ATCACCTCATGCTTGGGTTATTAAAATAGCCT 895723 i vi i i i iv L2#LINE/L2 2700 ATCATCTCTCGCCTGGATTACTGCAATAGCCT 2731 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.74 CpG sites = 31, Kimura (unadjusted) = 42.13 Transitions / transversions = 1.72 (31/18) Gap_init rate = 0.08 (14 / 166), avg. gap size = 1.79 (25 / 14) 349 31.13 11.17 1.17 chr2qtel1M 895725 896270 (103730) L1PB_orf2#LINE/L1 1950 2549 (745) m_b106s551i2 3862 chr2qtel1M 895725 ATTCCCAATAAGATCAGGGGTGAAACAATGTTGC--ATTTTCATTAGTAT 895772 vv i v v iiii i v v -- i i ii v vi L1PB_orf2#LIN 1950 ATTCCCCCTGAGAACTGGAACAAGACAAGGATGCCCACTCTCACCACTTC 1999 chr2qtel1M 895773 AATGCAACATTGTACTAGAAATGATAGCTTTAGCAA------AAAAGAAA 895816 v? v v i i vv ivv ------ i L1PB_orf2#LIN 2000 TNTTCAACATAGTACTGGAAGTCCTAGCCAGAGCAATCAGACAAGAGAAA 2049 chr2qtel1M 895817 GAAATTA-GAGTA--------GGTAATGAAGAA-CCAAATCTACCATGCT 895856 v - i i -------- v i -i - ii iivv L1PB_orf2#LIN 2050 GAAATAAAGGGCATCCAAATCGGTAAAGAGGAAGTCAAA-CTGTCGCTGT 2098 chr2qtel1M 895857 TTGCAGATGATATGA-------CATAGACAATCCTAGAGAATCACCTAAA 895899 v ------- v v i i v vi i i L1PB_orf2#LIN 2099 TTGCTGATGATATGATCGTNTACCTAGAAAACCCTAAAGACTCCTCCAGA 2148 chr2qtel1M 895900 AAACTTCAAGAAACAGTTAACAACTTTAGCAAAATTGAAAGGTATAAAAT 895949 i i v viii v ?i v i i vv?i i i L1PB_orf2#LIN 2149 AAGCTCCTAGAACTGATAAANGAATTCAGCAAAGTTTCNGGATACAAAAT 2198 chr2qtel1M 895950 AAACTGATATAAATCATCAGC----------AGAAAGAACTACAAAG--- 895986 v ivv i i vi ---------- vv v i v v --- L1PB_orf2#LIN 2199 TAATGTACACAAATCAGTAGCTCTNCTATACACCAACAGCGACCAAGCTG 2248 chr2qtel1M 895987 ------------AGAA----ATCCCATTTAACATAACTGTAGACAATATA 896020 ------------ ---- i v vv i i i v v L1PB_orf2#LIN 2249 AGAATCAAATCAAGAACTCAACCCCTTTTACAATAGCTGCAAAAAAAATA 2298 chr2qtel1M 896021 AAATATTTGAGTGTCTACCT-GCCAAGAGAAATCCAGGAACTATATCTAC 896069 i ii vi v -i - ii vv i v v ivviv L1PB_orf2#LIN 2299 AAATACTTAGGAATATACCTAACCAAG-GAGGTGAAAGACCTCTACAAGG 2347 chr2qtel1M 896070 ACAATTATAAAACACTTTTCACAGAAAT-ATAGTTTTATATAAGAAATTA 896118 v i i vi v v - -viv i i iv v i L1PB_orf2#LIN 2348 AAAACTACAAAACACTGCTGAAAGAAATCATAG-ACGACACAAACAAATG 2396 chr2qtel1M 896119 GAAGAATGTCAAGTGCTTATGAGTAGCCAAGAT-AATAAAATGAAAATAA 896167 iv ii vvi i ii i vi ii - vvi i L1PB_orf2#LIN 2397 GAAACACATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAATGA 2446 chr2qtel1M 896168 CAATTCTACCAAAAATCAATGTACTTATTCAGTGCCATACCAATCAAACT 896217 v v i i- v vv i v v v v L1PB_orf2#LIN 2447 CCATACTGCCAAAAG-CAATCTACAAATTCAATGCAATTCCCATCAAAAT 2495 chr2qtel1M 896218 GTAAGAA--ATTACTTCATAGAGCTGGAAAAATACTAA--CAAAAATTCA 896263 iiv vv -- - i i i - - -- v L1PB_orf2#LIN 2496 ACCACCATCATT-CTTCACAGAACTAGAAAAA-AC-AATCCTAAAATTCA 2542 chr2qtel1M 896264 TTTGGAA 896270 v L1PB_orf2#LIN 2543 TATGGAA 2549 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.65 CpG sites = 87, Kimura (unadjusted) = 41.29 Transitions / transversions = 1.07 (87/81) Gap_init rate = 0.04 (22 / 545), avg. gap size = 3.09 (68 / 22) 757 24.71 1.22 3.75 chr2qtel1M 896328 896655 (103345) L1M4_orf2#LINE/L1 1552 1871 (1423) m_b106s551i3 3863 chr2qtel1M 896328 CCTAAACCAAA-AAAGGCTTAAACAGAGAAAGAAAATTACAAACCAATCT 896376 v i - i v v - iii i i v L1M4_orf2#LIN 1552 CCAAAACCAGACAAAGACATCA-CAAGAAAAGAAAACTACAGACCAATAT 1600 chr2qtel1M 896377 CCCTGATGAATATAGATGTAAAATTTTTAAATAAAATATTAGCAAAAAGA 896426 v i v ii v i i vv L1M4_orf2#LIN 1601 CCCTTATGAATATAGATGCAAAAATCCTCAACAAAATACTAGCAAACCGA 1650 chr2qtel1M 896427 TTATACCAACATATGTTCAGGATAATACACTTTGACCAAGTGGGATTTAT 896476 v vi v ivvv v iv L1M4_orf2#LIN 1651 ATCCAGCAACATATAAAAAGGATTATACACCATGACCAAGTGGGATTTAT 1700 chr2qtel1M 896477 ATCAAGAATGCAGGGCTGGCTCAGTGTCAGAAAAACATATCA---TAATT 896523 vi i i i i iii ?v v - --- v L1M4_orf2#LIN 1701 CCCAGGAATGCAAGGTTGGTTCAACATNCGAAAATCA-ATCAATGTAATA 1749 chr2qtel1M 896524 GACAATTATGGTATCAATATCAAAACCAATCAAAATCATATAATAATCTC 896573 v v ------ i vv v vvi iv i i i v L1M4_orf2#LIN 1750 CACCA------TATTAATAGAATAAAGGACAAAAACCACATGATCATCTC 1793 chr2qtel1M 896574 ATTAGATACAAAAAAAAGCTTTTGCCAAAATATGGCACCCATTCCTATTA 896623 v ii - i v v viii v -- v L1M4_orf2#LIN 1794 AATAGACGC-AGAAAAAGCATTTGACAAAATCCAACACCCTTTC--ATGA 1840 chr2qtel1M 896624 AAAAAACAAAAAACAAACTAGAGAGCATAAGG 896655 v vvv - ii v L1M4_orf2#LIN 1841 TAAAAACACTCAACAAACTAG-GAATAGAAGG 1871 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 29.75 CpG sites = 37, Kimura (unadjusted) = 30.25 Transitions / transversions = 0.90 (37/41) Gap_init rate = 0.04 (14 / 327), avg. gap size = 1.14 (16 / 14) 506 29.32 6.42 3.80 chr2qtel1M 896758 897193 (102807) C L1P3_orf2#LINE/L1 (2825) 469 23 m_b106s551i4 3864 chr2qtel1M 896758 TTGATTTATCTAGTTCTGAGAATGCAAGGTTGAGATCTCCCACTATTATA 896807 i i i vi v i viiv i ii v C L1P3_orf2#LIN 469 TTGATCTGTCTAATATTGACAGTGGGGTGTTAAAGTCTCCCACTATTATT 420 chr2qtel1M 896808 GTTTTG----CTATTTCTTCTTGCAGCTCTCT--------TCTTTAAGAA 896845 v v ---- vv ii i v --------v v C L1P3_orf2#LIN 419 GTGTGGGAGTCTAAGTCTCTTTGTAGGTCTCTAAGAACTTGCTTTATGAA 370 chr2qtel1M 896846 TTTAGATGTTACACCACTTGGTGCATATATGTTTAATATTGATATTGCTT 896895 i i i i v vvi i v i iv v v viv C L1P3_orf2#LIN 369 TCTGGGTGCTCCTGTATTGGGTGCATATATATTTAGGATAGTTAGCTCTT 320 chr2qtel1M 896896 CATTATCTACGCTA--CCCTTTAGCAAGATATAGTGCTCTTCCTTATGTC 896943 - i - i ii i-- v vv i i i i -- C L1P3_orf2#LIN 319 C-TTGT-TGCATTGATCCCTTTACCATTATGTAATGCCCTTCTTT--GTC 274 chr2qtel1M 896944 TTAATTAGATCAATTT-TTGCTTT------TGCTTGATTTGAAATCAGGA 896986 vv - -- - v ------ i v iv i ii C L1P3_orf2#LIN 273 TTTTTT-GATC--TTTGTTGGTTTAAAGTCTGTTTTATCAGAGACTAGGA 227 chr2qtel1M 896987 TGGCTACCCCTGCTT-TTTTGGCTTTACCTGAAGCATAGCAGATTGTGCT 897035 v v - v v v v-v v i i i ?v v C L1P3_orf2#LIN 226 TTGCAACCCCTGCTTTTTTTTGCTTTCCATT-TGCTTGGTAAATNTTCCT 178 chr2qtel1M 897036 CCAGCCTTTTACCTTTACTCTATATATATTGCCCTGCTTCAAGTG---TG 897082 v i ii v vi i i i -- ii --- v --- C L1P3_orf2#LIN 177 CCATCCCTTTATTTTGAGCCTATGTGTGT--CTTTG---CACGTGAGATG 133 chr2qtel1M 897083 AG--TCCTGTAAACAACATATTGTAGGATTCTGACTTTTAATCCAGTTTG 897130 i -- v v i i ii vv i ii i v i C L1P3_orf2#LIN 132 GGTCTCCTGAATACAGCACACCGATGGGTCTTGACTCTTTATCCAATTTG 83 chr2qtel1M 897131 GATTAAATCCATCTCCACTTTATTGGGGAGTTTA-CCCAATCACATTTAT 897179 ---iv i ii v i-i v vi - v i v C L1P3_orf2#LIN 82 ---CCAGTCTGTGTCT-TTTAATTGGGGCATTTAGCCCATTTACATTTAA 37 chr2qtel1M 897180 GGTTAAAATTACTA 897193 v ii C L1P3_orf2#LIN 36 GGTTAATATTGTTA 23 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.77 CpG sites = 68, Kimura (unadjusted) = 38.16 Transitions / transversions = 1.24 (68/55) Gap_init rate = 0.06 (26 / 435), avg. gap size = 1.73 (45 / 26) 231 24.67 9.79 3.90 chr2qtel1M 897070 897263 (102737) C L1MEi_5end#LINE/L1 (15) 2197 1993 m_b106s551i6 3864 chr2qtel1M 897070 TGCTTCAAGTGTGAGTCCTGTAAACAACATATTGTAGGATTCTGACTTTT 897119 i i i vv i i v iv i vvi C L1MEi_5end#LI 2197 TGTTTTAGGTGTGTCTCTTGTAAACAGCATATAGCTGGATTTTTTTTTTT 2148 chr2qtel1M 897120 AATCCAGTTTGGATTAAATCCATCTCCACTTTATTGGG-GAGTTT-ACCC 897167 i i - -- -- vivi v i - - i C L1MEi_5end#LI 2147 AATCCAATCT-GAT--AATC--TCTGTCTTTTAATAGGTGAGTTTAATCC 2103 chr2qtel1M 897168 AATCACATTTATGGTTAAAATTACTAAT---TCTG----TATTTCCTGCA 897210 v i v ---i i --- i ---- ivv C L1MEi_5end#LI 2102 ATTTACATTTATTGT---GATTACTGATATATTTGGACTTATTTCTACCA 2056 chr2qtel1M 897211 TCT-------TGTTAACCCCTAATTATGCTTTTCTTTTTCCTT---TCCC 897250 ------- vv ivi v i ? ii ? i --- i C L1MEi_5end#LI 2055 TCTTATTTTGTGTTTTCTGTTTATCATNCTTTTTCTTTNCTTTTTCTCTC 2006 chr2qtel1M 897251 CCTTCCCCCCTTC 897263 i iv C L1MEi_5end#LI 2005 CTTTCCTGCCTTC 1993 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 31.17 CpG sites = 28, Kimura (unadjusted) = 31.17 Transitions / transversions = 1.56 (28/18) Gap_init rate = 0.07 (14 / 193), avg. gap size = 1.93 (27 / 14) 357 21.12 5.37 4.67 chr2qtel1M 897070 897218 (102782) C L1MEh_5end#LINE/L1 (7) 2228 2079 m_b106s551i5 3864 chr2qtel1M 897070 TGCTTCAAGTGTGAGTCCTGTAAACAACATATTGTAGGATTCTGACTTTT 897119 i i vv i i i v i vi ? C L1MEh_5end#LI 2228 TGTTTTAAGTGTGTCTCTTGTAGACAGCATATTGTTGGATTTTGTTTTTN 2179 chr2qtel1M 897120 AATCCAGTTTGGATTAAATCCATCTCCACTTTATTGGGGAGTTT-ACCCA 897168 i i i---? iv v i-i v v - C L1MEh_5end#LI 2178 AATCCAATCTGA---NAATCTCTGTCT-TTTAATTGGTGAGTTTAACCCA 2133 chr2qtel1M 897169 ATCACATTTATGGTTAAAATTACTA----ATTCTG---TATTTCCTGCAT 897211 v i v --- i---- ?v --- ivv C L1MEh_5end#LI 2132 TTTACATTTATTGT---AATTACTGNTATATTNGGACTTATTTCTGCCAT 2086 chr2qtel1M 897212 CTTGTTA 897218 i C L1MEh_5end#LI 2085 CTTATTA 2079 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 25.81 CpG sites = 17, Kimura (unadjusted) = 25.81 Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.07 (10 / 148), avg. gap size = 1.50 (15 / 10) 240 30.84 1.96 1.46 chr2qtel1M 897783 897986 (102014) L1M3_orf2#LINE/L1 2498 2702 (586) m_b106s551i7 3863 chr2qtel1M 897783 CATTATTTTAGAGAAGTAGAAAAAA--ATAACAAAATTCATCTGGAAGAA 897830 - v i -- vvi v vv L1M3_orf2#LIN 2498 CATT-TTTTACAGAAATAGAAAAAACAATCCTAAAATTCATATGGAACCA 2546 chr2qtel1M 897831 GAAAAGTTCAAGAATATCACGGGAAATAATGGGAAAAAATGCAAAGGATG 897880 v vi vv v vvii v vv i i vivv i v L1M3_orf2#LIN 2547 CAAAAGACCCCGAATAGCCAAAGCAATCTTGAGAAAGAAGAACAAAGCTG 2596 chr2qtel1M 897881 GTGGCTTAGCAGTACC-AATCCTAAAACTATGTTGTAAAGCAGCAGTAAT 897929 v v vi v v -i iii - i ii vi L1M3_orf2#LIN 2597 GAGGCATCACACTTCCTGATTTCAAAA-TATATTACAAAGCTACAGTAAT 2645 chr2qtel1M 897930 C-AAACGATTTGGTACTGGCTAAGAAATAAGAGTGGTGGATCAGTGAAAT 897978 - ii v vv i i iivi -i i i i i i L1M3_orf2#LIN 2646 CAAAACAGTATGGTACTGGCATAAAAACAGACAT-ATAGACCAATGGAAC 2694 chr2qtel1M 897979 AGATTAGA 897986 v L1M3_orf2#LIN 2695 AGAATAGA 2702 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.28 CpG sites = 31, Kimura (unadjusted) = 40.28 Transitions / transversions = 1.00 (31/31) Gap_init rate = 0.03 (6 / 203), avg. gap size = 1.17 (7 / 6) 259 31.70 6.85 4.80 chr2qtel1M 897895 898507 (101493) L1MD_orf2#LINE/L1 2618 3242 (52) m_b106s551i8 3863 chr2qtel1M 897895 CCAATCCTAAAACTATGTTGTAAAGCAGCAGTAATCAA-ACGATTTGGTA 897943 i iii i - ii i v vi - ?i v L1MD_orf2#LIN 2618 CCGATTTCAAGACT-TACTATATAGCTACAGTAATCAAGACNGTGTGGTA 2666 chr2qtel1M 897944 CTGGCTAAGAAATAAGAGTGGTGGATCAGTGAAATAGATTAGATACATAC 897993 i vi ii - vvvi i i i i v v ----- L1MD_orf2#LIN 2667 TTGGCGGAGGGATA-GACACATAGATCAATGGAACAGAATAGAGA----- 2710 chr2qtel1M 897994 AACACAATAATCAAGGCCTATAGCAATGTA--------GTATTTGATAAA 898035 - v iv -- i i i vv i i--------i v i L1MD_orf2#LIN 2711 -ACCCAGAAAT--AGACCCACACAAATATGCCCAACTGATTTTTGACAAA 2757 chr2qtel1M 898036 CCCTCAAACTCCAGGTTC--TGGAAATAAGAACTCACTATCTGACAGAAA 898083 vviv vv v -- -- ii- i ivvv v iii i vi L1MD_orf2#LIN 2758 GGTGCAAAAGCAA--TTCAATGGAGG-AAGGATAGCCTTTTCAACAAATG 2804 chr2qtel1M 898084 TTGCTGGAAAAAATGGAAAATAATAGGCCAGAAGTTCAGCATTGACTTAT 898133 v iv v v viv v i iv v i v i i v L1MD_orf2#LIN 2805 GTGCTGGAGCAATTGGACATCCATAGGCAAAAAAATGAACCTCGACCTAA 2854 chr2qtel1M 898134 ATCTCACACCCTATACCAAAATAAGATAAAAATGGGTACAT-TATCTGGG 898182 i i v v iv v i - -v ii iii L1MD_orf2#LIN 2855 ACCTCACACCTTATACAAAAATTAACTCAAAATGGAT-CATAGACTTAAA 2903 chr2qtel1M 898183 CATAAGGAATGATACCATAAA-----TAAATTAGAACA--AGAGACAATC 898225 ii iivi i v i ----- i vv i --i v L1MD_orf2#LIN 2904 TGTAAAACGTAAAACTATAAAACTTTTAGAAAAAAACATAGGAGAAAATC 2953 chr2qtel1M 898226 TATCTGATCTTTGGAGAAGGGAGGAATT--TA----TGACATAAGTATAG 898269 vivv vv vv i vi i i -- ---- iv ---- i L1MD_orf2#LIN 2954 TTCGGGATCTAGGGCTAGGCAAAGAGTTCTTAGACTTGACACCA----AA 2999 chr2qtel1M 898270 AACATTATC----AAGGGCAAAATCCACACTTTGG-TTACATTAAA-TTA 898313 i iv ---- i v iv i vv -i v i - L1MD_orf2#LIN 3000 AGCACGATCCATAAAAGGAAAAATTGATAAATTGGACTTCATCAAAATTA 3049 chr2qtel1M 898314 AAAGTTTTTGC---ACAAACAAAACCAACAGA-AACAGGATTAAAAAGGA 898359 ii ---i i -- i -- v v- v v iiv L1MD_orf2#LIN 3050 AAAACTTTTGCTCTGCGAA--AGACC--CTGTTAAGAGGATGAAAAGACA 3095 chr2qtel1M 898360 AGTAAAAAGCTGGGAAAAAAT-TTTA-AAGCCAGTATATCTGATAAAGAT 898407 iv v ii i - i- i -i i i iv L1MD_orf2#LIN 3096 AGCTACAGACTGGGAGAAAATATTTGCAAACCA-CATATCCGACAAAGGA 3144 chr2qtel1M 898408 CTCATTTCTAAAATATATAAAGAACTGTGTCAAATAT-----ATAAGAAT 898452 ?i v i -- v vv -----i i v L1MD_orf2#LIN 3145 CTNGTATCTAGAATATATAAAGAAC--TCTCAAAACTCAACAGTAAAAAA 3192 chr2qtel1M 898453 ACAAGTCATTGCCCAACTGATACATGGTCAAAGGATATGACCAGACAAGT 898502 iiv --- i iiv v v i i v? -- L1MD_orf2#LIN 3193 ACAAACAAT---CCAATTAGAAAATGGGCAAAAGACATGAANAGACA--T 3237 chr2qtel1M 898503 TTTAC 898507 i L1MD_orf2#LIN 3238 TTCAC 3242 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.65 CpG sites = 106, Kimura (unadjusted) = 42.78 Transitions / transversions = 1.34 (106/79) Gap_init rate = 0.08 (46 / 612), avg. gap size = 1.57 (72 / 46) 300 26.93 3.54 2.50 chr2qtel1M 898302 898499 (101501) L1M3_orf2#LINE/L1 3031 3230 (58) m_b106s551i9 3863 chr2qtel1M 898302 TACATTAAATTAAAA-GTTTTTGCACAAACAAAACCAACAG-AAACAGGA 898349 i i - i i i- ivv i-v ii L1M3_orf2#LIN 3031 TACATCAAACTAAAAAGCTTCTGCACAG-CAAAGGAAACAATCAACAGAG 3079 chr2qtel1M 898350 TTAAAAAGGAAGTAAAAAGCTGGGAAAAAAT-TTTA-AAGCCAGTATATC 898397 v i v viv viiiv i - i- i - L1M3_orf2#LIN 3080 TGAAAAGGCAACCTACGGAATGGGAGAAAATATTTGCAAACCA-TATATC 3128 chr2qtel1M 898398 TGATAAAGATCTCATTTCTAAAATATATAAAGAACTGTGTCAAAT--ATA 898445 i ivi v v i i v?vv v -- L1M3_orf2#LIN 3129 TGATAAGGGGTTAATATCCAAAATATATAAGGAACTCNTACAACTCAATA 3178 chr2qtel1M 898446 -TAAGAATACAAGTCATTGCCCAACTGATACATGGTCAAAGGATATGACC 898494 -i i v i v --- i i ? v v v iv vi L1M3_orf2#LIN 3179 GCAAAAAAACAAATAA---CCCGATTNAAAAATGGGCAAAGGACCTGAAT 3225 chr2qtel1M 898495 AGACA 898499 L1M3_orf2#LIN 3226 AGACA 3230 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 32.87 CpG sites = 29, Kimura (unadjusted) = 34.48 Transitions / transversions = 1.26 (29/23) Gap_init rate = 0.06 (11 / 197), avg. gap size = 1.09 (12 / 11) 302 20.79 4.62 3.82 chr2qtel1M 898370 898499 (101501) L1M4_orf2#LINE/L1 3106 3236 (58) m_b106s551i10 3863 chr2qtel1M 898370 TGGGAAAAAAT-TTTA-AAGCCAGTATATCTGATAAAGATCTCATTTCTA 898417 i - i- ii - i iv ?i v i L1M4_orf2#LIN 3106 TGGGAGAAAATATTTGCAAATCA-TATATCTGATAAGGGACTNGTATCCA 3154 chr2qtel1M 898418 AAATATATAAAGAACTGTGTCA----AATATATAAGAATACAAGTCATTG 898463 i v vv ---- i - i v i v --- L1M4_orf2#LIN 3155 GAATATATAAAGAACTCTTACAACTCAACA-ATAAAAAGACAAATAA--- 3200 chr2qtel1M 898464 CCCAACTGATACATGGTCAAAGGATATGACCAGACA 898499 i ? v v v v vi L1M4_orf2#LIN 3201 CCCAATTNAAAAATGGGCAAAGGATTTGAATAGACA 3236 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 25.09 CpG sites = 14, Kimura (unadjusted) = 25.09 Transitions / transversions = 1.17 (14/12) Gap_init rate = 0.06 (8 / 129), avg. gap size = 1.38 (11 / 8) 511 24.64 1.89 2.37 chr2qtel1M 898414 898625 (101375) L1ME3Cz_3end#LINE/L1 7 217 (780) m_b106s551i11 3863 chr2qtel1M 898414 TCTAAAATATATAAAGAACTGTGTCAAATATATAAGAATACAAGTCATTG 898463 i i vivv vv --v v --i L1ME3Cz_3end# 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAA--AAAGACA--A 52 chr2qtel1M 898464 CCCAACTGATACATGGTCAAAGGATATGACCAGACAAGTTTTACACGATG 898513 iv v v v v i v ivi v v v L1ME3Cz_3end# 53 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chr2qtel1M 898514 AAAT--GAA-AGCCATTTATAGTTATGAAAAAATGCTTA-TATCACTATT 898559 i-- -i v v - vv i i -iv v L1ME3Cz_3end# 103 AAACCCGAATGGCCAATAA-ACATATGAAAAGATGCTCAACCTCACTAGT 151 chr2qtel1M 898560 GATAAAAGAAATCCAAATTAAAACAAGTCTGAGGTACCACCTCACACCTC 898609 i v ii v ? vvv i ii iv L1ME3Cz_3end# 152 AATCAGGGAAATGCAAATTAAAACNACAATGAGATACCATTTCACACCCA 201 chr2qtel1M 898610 TCAGATTGGCTAAGAT 898625 v i L1ME3Cz_3end# 202 TCAGATTGGCAAAAAT 217 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 30.11 CpG sites = 21, Kimura (unadjusted) = 30.11 Transitions / transversions = 0.70 (21/30) Gap_init rate = 0.04 (8 / 211), avg. gap size = 1.12 (9 / 8) 15 18.73 0.00 0.00 chr2qtel1M 900399 900430 (99570) (TCC)n#Simple_repeat 1 32 (0) m_b106s252i0 3865 chr2qtel1M 900399 TCCTCTTCTTCCTCCTCTTTCCCCTCCTCCTC 900430 i i i i i (TCC)n#Simple 1 TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC 32 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 191 25.26 2.04 11.11 chr2qtel1M 902603 902700 (97300) C L3b_3end#LINE/CR1 (176) 1030 941 m_b106s601i7 3866 chr2qtel1M 902603 GTACTTGCCAACTTCTCACAGTCTTTACAGAATGTTCTTTAGAATATC-- 902650 ii iv - v ----- i v ivvv -- C L3b_3end#LINE 1030 GTGTTTAACAACT-CTCACTGTC-----AGGAAGTTCTTCCTTATATCTA 987 chr2qtel1M 902651 ACTTAAATCACTTCTGCTGAAGAAGAAAGGTCCTATTATCCTCTTGCTCT 902700 i v iv v vvv i--- i - i C L3b_3end#LINE 986 ACCTAAATCCCTCATGCTGCAGTTTAAG---CCCATT-TCCTCTTGTTCT 941 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.56 CpG sites = 10, Kimura (unadjusted) = 30.56 Transitions / transversions = 0.83 (10/12) Gap_init rate = 0.11 (11 / 97), avg. gap size = 1.09 (12 / 11) 19 0.00 0.00 0.00 chr2qtel1M 902844 902864 (97136) (C)n#Simple_repeat 1 21 (0) m_b106s252i1 3867 chr2qtel1M 902844 CCCCCCCCCCCCCCCCCCCCC 902864 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCC 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 396 21.42 0.81 9.65 chr2qtel1M 902875 902998 (97002) C MIR1_Amn#SINE/MIR (115) 115 2 m_b106s601i9 3868 chr2qtel1M 902875 GGTTAAGAGACTTGCC-AGGGTCACACAGCCAGGAAGTGTTAAGTGTCTG 902923 ? v - i ? ?i v? vi ------- C MIR1_Amn#SINE 115 GGTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNAGTGGCA-------G 73 chr2qtel1M 902924 AGACCAGATTTGAACTCAGGTCCTCCTGACTTCAAGGCTGGTGCTCTATC 902973 v vi ? ? i - i v i v v ii C MIR1_Amn#SINE 72 AGCCGGGANTNGAACCCAGGTC-TCCCGAGTCCCAGTCCAGTGCTCTATC 24 chr2qtel1M 902974 CACTGTGCCACCTAGCTGTCCCCTT 902998 ivi ---i i i i C MIR1_Amn#SINE 23 CACTAGACCAC---ACTGCCTCCCT 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.96 CpG sites = 15, Kimura (unadjusted) = 27.27 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.10 (12 / 123), avg. gap size = 1.00 (12 / 12) 507 18.52 0.91 6.73 chr2qtel1M 902875 902984 (97016) C MIRc#SINE/MIR (155) 113 10 m_b106s601i8 3868 chr2qtel1M 902875 GGTTAAGAGACTTGCC-AGGGTCACACAGCCAGGAAGTGTTAAGTGTCTG 902923 v - i i ------- v v C MIRc#SINE/MIR 113 GGTTAAGTGACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGCAG 71 chr2qtel1M 902924 AGACCAGATTTGAACTCAGGTCCTCCTGACTTCAAGGCTGGTGCTCTATC 902973 v vi i i i i i v ii v C MIRc#SINE/MIR 70 AGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTC 21 chr2qtel1M 902974 CACTGTGCCAC 902984 ii C MIRc#SINE/MIR 20 CACTGCACCAC 10 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 20.32 CpG sites = 12, Kimura (unadjusted) = 21.56 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.07 (8 / 109), avg. gap size = 1.00 (8 / 8) 294 26.53 8.55 5.77 chr2qtel1M 903022 903173 (96827) MIR3#SINE/MIR 46 201 (7) m_b106s601i10 3869 chr2qtel1M 903022 GACCTTGGTTGCAGGAGCCAACTCTGCCACTTAGAAATGA--GCATGAGC 903069 v vi vv- ii --- v ?i-- ii v MIR3#SINE/MIR 46 GACCTGGGTTCTAGTC-CCGGCTCTGCCACT---AACTNGCTGTGTGACC 91 chr2qtel1M 903070 TTTAGCAAATCTCTT---TTCT----GCTTGAGTTTCCTC--CTGTAAAT 903110 vi i v ---i ---- i v -- v MIR3#SINE/MIR 92 TTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAA 141 chr2qtel1M 903111 TGGAGAAGGTTGGTTGCATTTTTTAAT-TCTGAAGTGACTTTCAGCTCT- 903158 - ii ---- i vvv i - i i vv i - MIR3#SINE/MIR 142 T-GAGGGGGTTGG----ACTAGATGATCTCTAAGGTCCCTTCCAGCTCTG 186 chr2qtel1M 903159 ACGTCTCATGACTTT 903173 i iii i i MIR3#SINE/MIR 187 ACATTCTATGATTCT 201 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.90 CpG sites = 23, Kimura (unadjusted) = 34.00 Transitions / transversions = 1.53 (23/15) Gap_init rate = 0.10 (15 / 151), avg. gap size = 1.47 (22 / 15) 273 22.62 13.10 0.00 chr2qtel1M 904599 904682 (95318) MIR3#SINE/MIR 111 205 (3) m_b106s601i11 3870 chr2qtel1M 904599 TCACTGAATCTCAGTTTCC-CATTTATAAAATGAGTGGGTTAG----GAT 904643 v iii - i i v i ---- MIR3#SINE/MIR 111 TCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGAT 160 chr2qtel1M 904644 CATGT---AGGTCCCTTGCAG---TGATCATGTGGGATCCTATAA 904682 v v --- v --- ivv v iv i i MIR3#SINE/MIR 161 GATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTATGA 205 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.20 CpG sites = 10, Kimura (unadjusted) = 27.20 Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.05 (4 / 83), avg. gap size = 2.75 (11 / 4) 268 28.91 6.50 1.55 chr2qtel1M 904781 904903 (95097) C L2b_3end#LINE/L2 (10) 456 328 m_b106s601i12 3871 chr2qtel1M 904781 TCAGCAAACTTTTA---AGTGCCTGCTATCAGCCAGGCCTTGGGCTGTGC 904827 i iv --- i i i vv ?i v iv C L2b_3end#LINE 456 TCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGC 407 chr2qtel1M 904828 CCCAGGAACATATATAGAGA-CAAGG--GACTT--CCCCTGCTCTCCTGG 904872 v ii i i i -iii v - i-- ?i--i i vi C L2b_3end#LINE 406 GCTGGGGATACA-GCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGG 358 chr2qtel1M 904873 AGGTCACAGACAGCTGGGGCAGGCAGTACAT 904903 v v viv v i - C L2b_3end#LINE 357 AGCTCACAGTCTAGTGGGGGAGACAG-ACAT 328 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.12 CpG sites = 22, Kimura (unadjusted) = 38.76 Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.05 (6 / 122), avg. gap size = 1.67 (10 / 6) 289 32.22 12.02 2.76 chr2qtel1M 905036 905268 (94732) C MIRb#SINE/MIR (0) 268 15 m_b106s601i13 3872 chr2qtel1M 905036 AATACCATACCTAGCATTTATACAGCATCTGCT--GTGACATGCAGTGTG 905083 vi v v v vv iii i -- v v v C MIRb#SINE/MIR 268 AATAATAGAGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTG 219 chr2qtel1M 905084 TCA------------GTATTGTCTCGTTTTATCCTCATGAGAATCTTAGG 905121 ii ------------ i i i v ii v i i iv C MIRb#SINE/MIR 218 CTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCG 169 chr2qtel1M 905122 ACTTGGGTGCTATTATTGTGCCTTTTTTTGGGCAA--AAATTG-GATT-- 905166 vv i ii iv-- v vii iii -- i - ii -- C MIRb#SINE/MIR 168 AGGTAGGTATTATTATCC--CCATTTTACAGATGAGGAAACTGAGGCTCA 121 chr2qtel1M 905167 --GTGCCCAATT---TGGCACAA--TCCTACCTC-AGCAAGTTGCTGAGG 905208 -- v vii v --- v v -- vi vv - i v v v C MIRb#SINE/MIR 120 GAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGC 71 chr2qtel1M 905209 TGGGATGAATACTCAGGTCTGGCTGA-TTCAAGGCCCTGTTCACACTTTT 905257 i vviv i v - i i - ----i i C MIRb#SINE/MIR 70 CGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCC-GT----GCTCTT 26 chr2qtel1M 905258 TCCCTTGTACC 905268 vi i C MIRb#SINE/MIR 25 TCCACTGCACC 15 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.96 CpG sites = 40, Kimura (unadjusted) = 43.29 Transitions / transversions = 1.21 (40/33) Gap_init rate = 0.07 (17 / 232), avg. gap size = 2.06 (35 / 17) 17 8.91 0.00 0.00 chr2qtel1M 905582 905605 (94395) (T)n#Simple_repeat 1 24 (0) m_b106s252i2 3873 chr2qtel1M 905582 TTTTTTTGTGTTTTTTTTTTTTTT 905605 v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTT 24 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 12 12.09 0.00 6.90 chr2qtel1M 905893 905923 (94077) (ATTTT)n#Simple_repeat 1 29 (0) m_b106s252i3 3874 chr2qtel1M 905893 ATTGTATTTTTATTTTTAATTTATTGTATTT 905923 v - - v v (ATTTT)n#Simp 1 ATTTTA-TTTTA-TTTTATTTTATTTTATTT 29 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2) 13 10.47 6.45 0.00 chr2qtel1M 905894 905924 (94076) (TTGTAT)n#Simple_repeat 1 33 (0) m_b106s252i4 3874 chr2qtel1M 905894 TTGTATTTTTATTTTTAATT-TA-TTGTATTTG 905924 v v v - - (TTGTAT)n#Sim 1 TTGTATTTGTATTTGTATTTGTATTTGTATTTG 33 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2) 19 30.69 0.00 0.00 chr2qtel1M 905925 905988 (94012) (AAAAA)n#Simple_repeat 1 64 (0) m_b106s252i5 3875 chr2qtel1M 905925 AAAAAAAAAACAGTAAGGAAAAAAAAGAAAACAGAAAAGGAATACAAAAC 905974 v iv ii i v i ii v v v (AAAAA)n#Simp 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr2qtel1M 905975 AAAATAAAGCAAAA 905988 v iv (AAAAA)n#Simp 51 AAAAAAAAAAAAAA 64 Matrix = Unknown Transitions / transversions = 1.00 (8/8) Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0) 17 30.82 0.00 2.90 chr2qtel1M 906161 906231 (93769) (ATAC)n#Simple_repeat 1 69 (0) m_b106s252i6 3876 chr2qtel1M 906161 ATACATTTATGTATACTTACATAGATATATCCATTCATACACAGTCATAA 906210 vi ii v v i v v i -- v (ATAC)n#Simpl 1 ATACATACATACATACATACATACATACATACATACATACATA--CATAC 48 chr2qtel1M 906211 ACACAATCCCACATACAGACA 906231 i vv vi v (ATAC)n#Simpl 49 ATACATACATACATACATACA 69 Matrix = Unknown Transitions / transversions = 0.70 (7/10) Gap_init rate = 0.03 (2 / 70), avg. gap size = 1.00 (2 / 2) 549 16.65 2.26 9.68 chr2qtel1M 908375 908507 (91493) C MIRb#SINE/MIR (141) 127 4 m_b106s601i14 3877 chr2qtel1M 908375 AGGCTTTCAGAGA---TAAGTGATTTGTGCAGGATCACACAGCTAGGAAG 908421 -- --- i i iv i i ---- C MIRb#SINE/MIR 127 AGGCT--CAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAG---- 84 chr2qtel1M 908422 TGTTAAGTGTCTGAGGCCAGATTTGAACCCAGGTCTGCCTGACTTCAGGG 908471 --- v v v vi i i i ii C MIRb#SINE/MIR 83 ---TAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAG 37 chr2qtel1M 908472 CTGGTGCTCTGTCCACTGCTCCACCTAGCTGCCCCT 908507 iv v v --- C MIRb#SINE/MIR 36 CCCGTGCTCTTTCCACTGCACCAC---GCTGCCCCT 4 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 17.90 CpG sites = 12, Kimura (unadjusted) = 18.90 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.10 (13 / 132), avg. gap size = 1.15 (15 / 13) 16 0.00 0.00 0.00 chr2qtel1M 908523 908540 (91460) (A)n#Simple_repeat 1 18 (0) m_b106s252i7 3878 chr2qtel1M 908523 AAAAAAAAAAAAAAAAAA 908540 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAA 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 221 26.47 23.53 0.00 chr2qtel1M 910985 911086 (88914) MIRc#SINE/MIR 3 128 (140) m_b106s601i15 3879 chr2qtel1M 910985 AGCCAGTGTAGTGGGATGGAAAGATCACTAGATTGGGATTCAG--AGGTC 911032 v i vii v i i v v -- ii MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chr2qtel1M 911033 AAGGCTTGAA-------------ATT------CTGGGT--TCTTGGGAAA 911061 vi i i i------------- i ------ v --i v MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 102 chr2qtel1M 911062 GTAATTTAATTTCACTGA-TCTCAGT 911086 v i ii v -i MIRc#SINE/MIR 103 GTCACTTAACCTCTCTGAGCCTCAGT 128 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.15 CpG sites = 17, Kimura (unadjusted) = 33.68 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.05 (5 / 101), avg. gap size = 4.80 (24 / 5) 583 29.47 12.43 2.52 chr2qtel1M 913881 914242 (85758) L2#LINE/L2 2038 2434 (648) m_b106s601i16 3880 chr2qtel1M 913881 TCTGAAGCCTCATTTTCCTGAATTTCTCTCCAGCCTTTGACAATGGTGAC 913930 v iv i v vi ii ? vv v vv v i L2#LINE/L2 2038 TCTCAGTCCTCATCTTACTTGACCTNTCAGCAGCATTTGACACAGTTGAT 2087 chr2qtel1M 913931 CACTCTCTCTTTCTCTAGATATTT----------------AAGACA--GC 913962 i i iv i i i ---------------- i --i L2#LINE/L2 2088 CACTCCCTCCTTCTTGAAACACTTTCTTCACTTGGCTTCCAGGACACCAC 2137 chr2qtel1M 913963 ACTTTCCTGGCTTTCCTTCTACCAATCCAACCACTACTTCATGATCTTCT 914012 i i i vvv iii i v viii i L2#LINE/L2 2138 ACTCTCCTGGTTTTCCTCCTACCTCACTGGCCGCTCCTTCTCAGTCTCCT 2187 chr2qtel1M 914013 TTCTTGGGTCTTCCTCCAGATCACACC--CCTTCAGTCATAG--GTGTCC 914058 vi v i --- v v -- ii?iv i v -- i L2#LINE/L2 2188 TTGCTGGTTCCTCCTC---ATCTCCCCGACCTCTNAACGTTGGAGTGCCC 2234 chr2qtel1M 914059 -----CTC-CTCCTTGGTCCTCTTCTCTTCTCTCTCTACACTAAT----- 914097 ----- -v v v v i----- L2#LINE/L2 2235 CAGGGCTCAGTCCTTGGACCTCTTCTCTTCTCTATCTACACTCACTCCCT 2284 chr2qtel1M 914098 ---TGATCTCATCAGCTACTTTGGATTTAA----TGTCTTTATTCTGATG 914140 --- viv viiv v ----ii v v L2#LINE/L2 2285 NGGTGATCTCATCCAGTCTCATGGCTTTAAATACCATCTATATGCTGATG 2334 chr2qtel1M 914141 ATTCACAGATCTTTTACCTTTCCTGCCATAATTTCTCTTCTGATTTTTAG 914190 i v i --- iv i v vvi ii ii vi ii L2#LINE/L2 2335 ACTCCCAAA---TTTATATCTCCAGCCCGGACCTCTCCCCTGAACTCCAG 2381 chr2qtel1M 914191 TCTTG--CATCTATACTGACCTGCCTGG---CTACACTAAGTCATGTTTA 914235 v i --i i - - i ii i--- v vi -- i L2#LINE/L2 2382 ACTCGTATATCCA-ACTG-CCTACTCGACATCTCCACTTGG--ATGTCTA 2427 chr2qtel1M 914236 AAAAGTA 914242 v i i L2#LINE/L2 2428 ATAGGCA 2434 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.02 CpG sites = 61, Kimura (unadjusted) = 38.93 Transitions / transversions = 1.42 (61/43) Gap_init rate = 0.06 (20 / 361), avg. gap size = 2.75 (55 / 20) 205 29.79 0.00 0.00 chr2qtel1M 915801 915847 (84153) C L2b_3end#LINE/L2 (25) 441 395 m_b106s601i17 3881 chr2qtel1M 915801 TAAGTGCCGGCTATATGCCAGGCTCTGAGCTAACCTCCAGGAATATA 915847 i i vi i i ? v iv v ii i i C L2b_3end#LINE 441 TGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGGGATACA 395 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.72 CpG sites = 10, Kimura (unadjusted) = 41.66 Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 19 10.82 0.00 3.23 chr2qtel1M 918775 918806 (81194) (AC)n#Simple_repeat 1 31 (0) m_b106s252i8 3882 chr2qtel1M 918775 ACACACTACACACCCCCACACACACACTCACA 918806 - v v v (AC)n#Simple_ 1 ACACAC-ACACACACACACACACACACACACA 31 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 252 25.00 1.37 1.37 chr2qtel1M 919452 919524 (80476) MIR1_Amn#SINE/MIR 3 75 (155) m_b106s601i18 3883 chr2qtel1M 919452 GAAAGGCAATATGGTG-GGTGGAAAGATCCCTAGACTGGGACTCGGAGGA 919500 ii i i v-i v v v i ii MIR1_Amn#SINE 3 GGGAGGCAGTGTGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGAGA 52 chr2qtel1M 919501 CAAGGGTTGACATTCTAGGTTCTG 919524 vv -v? ? iv i MIR1_Amn#SINE 53 CCTGGGTT-CNANTCCCGGCTCTG 75 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.03 CpG sites = 10, Kimura (unadjusted) = 32.03 Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.03 (2 / 72), avg. gap size = 1.00 (2 / 2) 254 22.92 11.43 4.46 chr2qtel1M 920331 920435 (79565) MIR3#SINE/MIR 90 201 (7) m_b106s601i19 3884 chr2qtel1M 920331 CTTTGAGCCAATC------CTTTTCTG--CTTGAGTTTGCTC--CTGTAA 920370 i i v i ------ i i -- i v v -- MIR3#SINE/MIR 90 CCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAA 139 chr2qtel1M 920371 ATTGGAGAGGGTTGG-TTGGATTCTTGAATTCTGAGGTGACTTTCAGCTC 920419 v - i -i i ---- vi i vv i MIR3#SINE/MIR 140 AATG-AGGGGGTTGGACTAGAT----GATCTCTAAGGTCCCTTCCAGCTC 184 chr2qtel1M 920420 T-ACATTTCAAGATTTT 920435 - ii v i MIR3#SINE/MIR 185 TGACATTCTATGATTCT 201 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.26 CpG sites = 15, Kimura (unadjusted) = 28.26 Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.10 (10 / 104), avg. gap size = 1.70 (17 / 10) 288 26.19 4.76 0.00 chr2qtel1M 922178 922261 (77739) MIR3#SINE/MIR 111 198 (10) m_b106s601i20 3885 chr2qtel1M 922178 TCACTGAATCTCAGTTTTCCC-TTTATAAAATGACTGGGTTGCATTCCAT 922226 v iii i i - i i vv v i vv MIR3#SINE/MIR 111 TCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGAT 160 chr2qtel1M 922227 GACCTTGTAGGTCCCTTCCAG---TGATCGTCTATTAT 922261 i ivv --- ivv v MIR3#SINE/MIR 161 GATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGAT 198 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.54 CpG sites = 11, Kimura (unadjusted) = 32.54 Transitions / transversions = 1.00 (11/11) Gap_init rate = 0.02 (2 / 83), avg. gap size = 2.00 (4 / 2) 550 28.77 13.68 0.00 chr2qtel1M 923126 923337 (76663) C MIR#SINE/MIR (4) 258 18 m_b106s601i21 3886 chr2qtel1M 923126 ATAGCTAGTATTTATACAGCACCTACTGTGTGATA--TACTGT------- 923166 ii vv i i i vi --i ------- C MIR#SINE/MIR 258 ATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGC 209 chr2qtel1M 923167 -----ATAAATATTGGCTCATTCTTTTCTCATGAGAACCCTAGGACTTGG 923211 ----- i vi ii ivv i ii v v vv i C MIR#SINE/MIR 208 GCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGGTAG 159 chr2qtel1M 923212 GTGCTATTATTGTGCCTATTTTACAGATAAAGAAACTGAGGCAAACAGAG 923261 i i v i i i v v C MIR#SINE/MIR 158 GTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAG 109 chr2qtel1M 923262 GGCCTGTAACTTG--------------ATTAGCAAGTTGCTGAGGTGGGA 923297 vivv --------------ii i v v vi C MIR#SINE/MIR 108 GTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGA 59 chr2qtel1M 923298 TGAATACTCAAGCCTTGTTGATTCA-AGACCTTTCTGTTAA 923337 vviv i i vv v v v i - v v v v C MIR#SINE/MIR 58 TTCGAACCCAGGCAGTCTGGCTCCAGAGCCCGTGCTCTTAA 18 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.51 CpG sites = 30, Kimura (unadjusted) = 36.69 Transitions / transversions = 0.97 (30/31) Gap_init rate = 0.02 (5 / 211), avg. gap size = 5.80 (29 / 5) 12 13.96 6.25 0.00 chr2qtel1M 925154 925185 (74815) (GAGGCA)n#Simple_repeat 1 34 (0) m_b107s252i0 3887 chr2qtel1M 925154 GAGGCTGAAG-A-AAGCAGAGGCAGAGGCAAAGG 925185 v i - - i i (GAGGCA)n#Sim 1 GAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGG 34 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.06 (2 / 31), avg. gap size = 1.00 (2 / 2) 320 28.14 3.59 4.22 chr2qtel1M 928025 928191 (71809) C ERV24B_Prim#LTR/ERV1 (2378) 5235 5070 m_b107s701i0 3888 chr2qtel1M 928025 TGAAATTGGTACTTTTATCATTATGTATTTTTAATGACACCCCCCCATAA 928074 i vi ? i i i ii v v ii iv iv ii - ?i? C ERV24B_Prim#L 5235 TAAAATGAGTNCCTCTGTCGCTATGAAGTTCCAGAGGAATTCCCC-ANGN 5187 chr2qtel1M 928075 TAGAATCACTTTTTTCTTAGAAGATTTTTGCTACC-CAAAAGCAATG--- 928120 ?i v - ? v ? ii vvi i- v i vi ?--- C ERV24B_Prim#L 5186 NGGAATAA-TNTTTTCTAANAGAATTTTACTTACTGCTAAGGCCGTNGCT 5138 chr2qtel1M 928121 --TCAGTATGATAGAGTAAGACTTTGACCCACTGGGAAAACATACAGACC 928168 -- v i --- -- ?i iv v i i i i C ERV24B_Prim#L 5137 CTTCTGCATG---GA--AANGCTTCTACCCAATGAGAAAACATGCAAATC 5093 chr2qtel1M 928169 ATAAACAAAGCATATTTGTAACC 928191 ? v i i ? C ERV24B_Prim#L 5092 ATNACCAGAACATATTTGTANCC 5070 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.89 CpG sites = 30, Kimura (unadjusted) = 40.24 Transitions / transversions = 2.00 (30/15) Gap_init rate = 0.06 (10 / 166), avg. gap size = 1.30 (13 / 10) 363 24.16 5.51 5.51 chr2qtel1M 928065 928191 (71809) C PRIMA4-int#LTR/ERV1 (2625) 5645 5519 m_b107s701i1 3888 chr2qtel1M 928065 CCCCCCATAATAGAATCACTTTTTTCTTAGAAGATTTTTGCTACCCAAAA 928114 i i i i i v - viv i ----- vv C PRIMA4-int#LT 5645 CTCCCCACAGTGGGATAA-TTTTTTCTAGTAGGATTTTT-----CCAACT 5602 chr2qtel1M 928115 GCAATGTCAGTATGAT-------AGAGTAAGACTTTGACCCACTGGGAAA 928157 v v v - v ------- i v ii ii v C PRIMA4-int#LT 5601 GCCATGGCTGT-TGCTTGCCTGCAGGGAAAAGCTTCAACCCAATGGGAAA 5553 chr2qtel1M 928158 ACATACAGACCATAAACAAAGCATATTTGTAACC 928191 i v vi i i C PRIMA4-int#LT 5552 ACATGCAGACCATTACTAAAACATACTTGTAACC 5519 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 29.61 CpG sites = 16, Kimura (unadjusted) = 29.61 Transitions / transversions = 1.23 (16/13) Gap_init rate = 0.06 (8 / 126), avg. gap size = 1.75 (14 / 8) 189 38.54 5.73 0.00 chr2qtel1M 929908 930099 (69901) L2#LINE/L2 2385 2587 (495) m_b107s601i0 3889 chr2qtel1M 929908 CACACATCCAAATATCTACCAGACATTTTGAATTAGATAGCCAAT-GGCA 929956 ii i v ii iv i iv v i iv i - L2#LINE/L2 2385 CGTATATCCAACTGCCTACTCGACATCTCCACTTGGATGTCTAATAGGCA 2434 chr2qtel1M 929957 ACTTAAACTCCTCATATCCACAA---AACTTATTACCTTTCCC--CAAAT 930001 v i ivv i v --- iv v i i -- i L2#LINE/L2 2435 TCTCAAACTTAACATGTCCAAAACTGAACTCCTGATCTTCCCCCTCAAAC 2484 chr2qtel1M 930002 GCACCCATCTTCCAAATTTCCTTACTTGAG--ACTAACA--TCAGTCC-T 930046 vii i v iiv ivi ii ii v -- v ii -- vi - L2#LINE/L2 2485 CTGCTCCTCCCGCAGTCTTCCCCATCTCAGTNAATGGCAACTCCATCCTT 2534 chr2qtel1M 930047 CCAGTCACCCCAATTCATAACCTCACTTTTATTCTTAAGTCTGTACTATC 930096 ii i viiiiv v iivvv i i i v iviv v L2#LINE/L2 2535 CCAGTTGCTCAGGCCAAAAACCTTGGAGTCATCCTTGACTCCTCTCTTTC 2584 chr2qtel1M 930097 TCT 930099 L2#LINE/L2 2585 TCT 2587 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 55.22 CpG sites = 46, Kimura (unadjusted) = 57.66 Transitions / transversions = 1.64 (46/28) Gap_init rate = 0.03 (6 / 191), avg. gap size = 1.83 (11 / 6) 41 7.82 2.82 1.39 chr2qtel1M 931901 931971 (68029) (TCC)n#Simple_repeat 1 72 (0) c_b107s251i0 3890 chr2qtel1M 931901 TCCTCCTCCTCCT-CTCCTCTTCCTCCTCCTCCTCCTCTTCTTCAC-CCT 931948 - i i i - - (TCC)n#Simple 1 TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC-CTCCT 49 chr2qtel1M 931949 CCTCCTCTTCCTCCCCCTCCTCC 931971 i i (TCC)n#Simple 50 CCTCCTCCTCCTCCTCCTCCTCC 72 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.04 (3 / 70), avg. gap size = 1.00 (3 / 3) 36 0.00 0.00 0.00 chr2qtel1M 932150 932180 (67820) (CA)n#Simple_repeat 1 31 (0) c_b107s251i1 3891 chr2qtel1M 932150 CACACACACACACACACACACACACACACAC 932180 (CA)n#Simple_ 1 CACACACACACACACACACACACACACACAC 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 21 13.68 0.00 0.00 chr2qtel1M 932242 932281 (67719) (CCCTTCA)n#Simple_repeat 1 40 (0) m_b107s252i1 3892 chr2qtel1M 932242 CCCTTCACCCATCTCTCTTCTCCCTTCACCTTTCACCCTT 932281 v v i v i (CCCTTCA)n#Si 1 CCCTTCACCCTTCACCCTTCACCCTTCACCCTTCACCCTT 40 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 243 28.14 4.76 1.85 chr2qtel1M 933137 933241 (66759) C MIRb#SINE/MIR (18) 250 143 m_b107s601i1 3893 chr2qtel1M 933137 TATCAAGTACCTACTAAGTGGCAGACACTTGAATTAAGCATCATAC---C 933183 ii ii i v v i - vii iiiv --- C MIRb#SINE/MIR 250 TATTGAGCGCTTACTATGTGCCAGGCACT-GTGCTAAGCGCTTTACATGC 202 chr2qtel1M 933184 AATATCTC-CATGATCG-CACAACAAAACCTACAAACTAAATTTCATTAT 933231 v -iv i v- v- i i iv ii v i C MIRb#SINE/MIR 201 ATTATCTCATTTAATCCTCACAACAAC-CCTGCGAGGTAGGTATTATTAT 153 chr2qtel1M 933232 CCCCATTTTA 933241 C MIRb#SINE/MIR 152 CCCCATTTTA 143 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.92 CpG sites = 19, Kimura (unadjusted) = 36.77 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.05 (5 / 104), avg. gap size = 1.40 (7 / 5) 18 0.00 0.00 0.00 chr2qtel1M 933383 933402 (66598) (A)n#Simple_repeat 1 20 (0) m_b107s252i2 3894 chr2qtel1M 933383 AAAAAAAAAAAAAAAAAAAA 933402 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAA 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 331 30.15 3.61 2.55 chr2qtel1M 934392 934585 (65415) C L1MC5a_3end#LINE/L1 (2150) 627 432 m_b107s551i0 3895 chr2qtel1M 934392 TTCACTCAGCATCAGTTCCTGTAAGTCTCTCCAGATC--TCTCT-GAAAT 934438 i i vi vv v ii v v ? -- v v - i C L1MC5a_3end#L 627 TTCACTTAACAATATATCCTGGAGATCACTCCATANCAGTATATAGAGAT 578 chr2qtel1M 934439 CATCCTGCTGGTCATTTCTTACAGAATAATAATATCCCATAACATTCATA 934488 v vv -- v - vvvv i ii viii vv i C L1MC5a_3end#L 577 CTTCCTCAT--TCCTTT-TTACAGCTGCATAGTACTCCATTGTGTGGATG 531 chr2qtel1M 934489 TCCCATAACTTACTCAACCATTCCC--ATTGATGGGCATCCC--TTCAGT 934534 v ii i v -- i iiv-- -- C L1MC5a_3end#L 530 TACCATAGTTTATTCAACCAGTCCCCTATTGATGGACATTTGGGTT--GT 483 chr2qtel1M 934535 TTCCAGTTTTTTGTCACTACAAAGAGGGCCGCTACAAATGTTTTTGCGCA 934584 i ii i v iv i v ii ivii i C L1MC5a_3end#L 482 TTCCAGTCTTTTGCTATTACAAATAATGCTGCAATGAATAACCTTGTGCA 433 chr2qtel1M 934585 T 934585 C L1MC5a_3end#L 432 T 432 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.66 CpG sites = 31, Kimura (unadjusted) = 39.66 Transitions / transversions = 1.19 (31/26) Gap_init rate = 0.05 (9 / 193), avg. gap size = 1.33 (12 / 9) 342 30.80 2.45 4.38 chr2qtel1M 934466 934628 (65372) C L1MD1_3end#LINE/L1 (436) 553 394 m_b107s551i1 3895 chr2qtel1M 934466 AATAATATCCCATAACATTCATATCCCATAACTTACTCAACCATTC--CC 934513 i i i iii vv i v i ii ii i -- C L1MD1_3end#LI 553 AGTAGTATTCCATGGTATGGATGTACCACAGTTTGTTTAACCATTCACCC 504 chr2qtel1M 934514 ATTGATGGGCATCCC--TTCAGTTTCCAGTTTTTTGTCACTACAAAGAGG 934561 i v i iv-- -- v ii i i v ii C L1MD1_3end#LI 503 GTTGAAGGACATCTGGGTT--GTTTCCAGTTTTTGGCTATTACGAATAAA 456 chr2qtel1M 934562 GCCGCTACAAATGTTTTTGCGCATGTTTCCCTCCTTTAAGATAAGATAAC 934611 i i ii iv ii v iiv v-- v v v --- C L1MD1_3end#LI 455 GCTGCTATAAACATTCGTGTACAGGTTTTTGTG--TGAACATAAGTT--- 411 chr2qtel1M 934612 TGCTTTTATCTGGGATA 934628 v v v C L1MD1_3end#LI 410 TTCATTTCTCTGGGATA 394 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.06 CpG sites = 31, Kimura (unadjusted) = 41.45 Transitions / transversions = 1.82 (31/17) Gap_init rate = 0.06 (9 / 162), avg. gap size = 1.22 (11 / 9) 410 27.19 3.15 1.55 chr2qtel1M 934467 934593 (65407) C L1ME3G_3end#LINE/L1 (376) 548 420 m_b107s551i2 3895 chr2qtel1M 934467 ATAATATCCCATAACATTCATATCCCATAACTTACTCAACCATTCCC--A 934514 i i ii vv v i i i -- C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr2qtel1M 934515 TTGATGGGCATCC--CTTCAGTTTCCAGTTTTTTGTCACTACAAAGAGGG 934562 i ii--v -- i i ii i v iv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTT--GTTTCCAATTTTTCGCTATTACAAACAATG 451 chr2qtel1M 934563 CCGCTACAAATGTTTTTGCGCATGTTTCCCT 934593 i v ii ii ii ii i? i C L1ME3G_3end#L 450 CTGCAATGAACATCCTTGTACATGCNTCCTT 420 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 35.44 CpG sites = 27, Kimura (unadjusted) = 36.85 Transitions / transversions = 3.86 (27/7) Gap_init rate = 0.03 (4 / 126), avg. gap size = 1.50 (6 / 4) 205 28.57 8.57 0.00 chr2qtel1M 937605 937674 (62326) C MIRb#SINE/MIR (111) 157 82 m_b107s601i2 3896 chr2qtel1M 937605 ACTATTTCT-TTTTGCAAATCAGAACACTG-GGC----AGAGATAAAATA 937648 i ii i- i i v i v - ---- i v i C MIRb#SINE/MIR 157 ATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTA 108 chr2qtel1M 937649 ACTTACTATAAATCACACAGTCAGTA 937674 i ivv ii ii C MIRb#SINE/MIR 107 ACTTGCCCAAGGTCACACAGCTAGTA 82 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.51 CpG sites = 15, Kimura (unadjusted) = 38.51 Transitions / transversions = 3.00 (15/5) Gap_init rate = 0.04 (3 / 69), avg. gap size = 2.00 (6 / 3) 17 18.93 1.85 5.77 chr2qtel1M 938549 938602 (61398) (TTA)n#Simple_repeat 1 52 (0) m_b107s252i3 3897 chr2qtel1M 938549 TTATTTGTTATTATTATTAATATTAATTATCATCACTTGTTA-GATAATT 938597 - i v - i i - i -v v (TTA)n#Simple 1 TTA-TTATTATTATTATTATTATT-ATTATTATTA-TTATTATTATTATT 47 chr2qtel1M 938598 GTTAT 938602 i (TTA)n#Simple 48 ATTAT 52 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.08 (4 / 53), avg. gap size = 1.00 (4 / 4) 16 3.96 3.85 0.00 chr2qtel1M 940988 941013 (58987) (TTTCA)n#Simple_repeat 1 27 (0) m_b107s252i4 3898 chr2qtel1M 940988 TTTCATTACATTTCATTTCA-TTCATT 941013 v - (TTTCA)n#Simp 1 TTTCATTTCATTTCATTTCATTTCATT 27 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.04 (1 / 25), avg. gap size = 1.00 (1 / 1) 440 23.46 5.80 7.35 chr2qtel1M 941123 941329 (58671) C HERVK14C#LTR/ERVK (4387) 3047 2844 m_b107s701i2 3899 chr2qtel1M 941123 TTTTTCTCTATTACAAATACAAGGGAGTTCCATG-----ACTGTTTGTTT 941167 i? i vi ? i ? ----- v vv --- C HERVK14C#LTR/ 3047 TTTTTCTTNATTACAAACACTGGNGAATTCCANGGAGAAAATGTGGG--- 3001 chr2qtel1M 941168 CCTCAATGTGTCCTAACTCTAATTGTTCTTGTACTAACTGATGCAGAGCA 941217 - ? vv? vv i vv i ii v C HERVK14C#LTR/ 3000 -CTCNATGTGTCCTTTNTCTAATTGTTCTTTGACTAATTCCTGTAAGGCC 2952 chr2qtel1M 941218 GCTGTTTTTTCTTTAGTCAGGAGACATTGCTCCACCCATATCAGGGTGTC 941267 v iiv i v ?? vi v i ? ? v i?i ?v v v C HERVK14C#LTR/ 2951 CCCAGTTTTTCCTGAGNNAGCGGCCACTGNTCNACCCAAACNGGNTTTTG 2902 chr2qtel1M 941268 AGTAGTCCAAATCATTTTT---GTAGCAG----TGGAGGCCACAGCAGCA 941310 i v? ------ --- v ii ---- i---- i C HERVK14C#LTR/ 2901 GGTCNTCCA------TTTTAAGGGAATAGGNTCTGGAGGCT----CAACA 2862 chr2qtel1M 941311 ATGACCCCCTCCTAAAAAT 941329 i i v - C HERVK14C#LTR/ 2861 GTGGCCGCC-CCTAAAAAT 2844 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 29.87 CpG sites = 22, Kimura (unadjusted) = 30.66 Transitions / transversions = 0.96 (22/23) Gap_init rate = 0.09 (18 / 206), avg. gap size = 1.50 (27 / 18) 195 15.22 10.87 0.00 chr2qtel1M 941447 941492 (58508) C Penelope1_Vert#LINE/Penelope (795) 284 234 m_b107s601i3 3900 chr2qtel1M 941447 GTTTAGCAGACATTTTCTG----CCCCAGTAGGTTACTTAA-CTGTCTCT 941491 ii? ---- v vi v -i C Penelope1_Ver 284 GTTTAGCAGATGNTTTCTGGGTACCACAGTAGCCTTCTTAATTTGTCTCT 235 chr2qtel1M 941492 G 941492 C Penelope1_Ver 234 G 234 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 17.59 CpG sites = 4, Kimura (unadjusted) = 17.59 Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.04 (2 / 45), avg. gap size = 2.50 (5 / 2) 17 4.94 0.00 0.00 chr2qtel1M 942027 942047 (57953) (G)n#Simple_repeat 1 21 (0) m_b107s252i5 3901 chr2qtel1M 942027 GGTGGGGGGGGGGGGGGGGGG 942047 v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGG 21 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 16 4.50 0.00 0.00 chr2qtel1M 942106 942128 (57872) (ATT)n#Simple_repeat 1 23 (0) m_b107s252i6 3902 chr2qtel1M 942106 ATTTTTATTATTATTATTATTAT 942128 v (ATT)n#Simple 1 ATTATTATTATTATTATTATTAT 23 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 14 14.91 5.41 0.00 chr2qtel1M 942255 942291 (57709) (ATAAGT)n#Simple_repeat 1 39 (0) m_b107s252i7 3903 chr2qtel1M 942255 ATATGTTTAAGTATAAGT-TAAATACAA-TATATGTATA 942291 v v - i i - v (ATAAGT)n#Sim 1 ATAAGTATAAGTATAAGTATAAGTATAAGTATAAGTATA 39 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 1522 27.74 3.20 2.54 chr2qtel1M 942577 943201 (56799) C L1ME3G_3end#LINE/L1 (292) 632 4 m_b107s551i3 3904 chr2qtel1M 942577 CTTGCTCATTTCACTCAGCATTAGTTCATATAAGTCTCTCCAGGCCATTC 942626 iv i v vv v iv ii i v i v v C L1ME3G_3end#L 632 CTTGCTTTTTTCACTCAACAATATGTCTTGGAGATCTTTCCATGTCAGTA 583 chr2qtel1M 942627 TG---AAATCATCCTCCTGGTCATTTCTTACCAAACA-ATAATATTCCAT 942672 ii--- i vv v -- -- i v ?ivii- i C L1ME3G_3end#L 582 CATATAGATCTACCTCAT--TC--TTTTTAACNGCTGCATAGTATTCCAT 537 chr2qtel1M 942673 AACATTCATATACCACAATTTATTCAGGCATTCTCTAATTGATGGGCATC 942722 ii vv i i iv i iv i i C L1ME3G_3end#L 536 AGTATGGATATACCATAATTTATTTAACCATTCCCCTATTGATGGACATT 487 chr2qtel1M 942723 CA--TTCAATTTCCAGTTTCTAGCTACTACAAAAAGGGCTGCCACAAACA 942770 i -- --i i i v i v iv v ii C L1ME3G_3end#L 486 TAGGTT--GTTTCCAATTTTTCGCTATTACAAACAATGCTGCAATGAACA 439 chr2qtel1M 942771 TTCTTGCAGATACAGGACCCTT-TCC-CTTCTTTAAG-ATCTCTTTGGAA 942817 i i v i ?---i - v - v v vii - i ? i i C L1ME3G_3end#L 438 TCCTTGTACATGCN---TCCTTGTGCACATGTGCGAGTATTTCTNTAGGA 392 chr2qtel1M 942818 TATAAGCCCAGTAGAAACACTGCTAGATCAAAGGGTATACACAGTTTGAT 942867 v v? ? v viiv i i i i i v --- C L1ME3G_3end#L 391 TAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGCATTTT--- 345 chr2qtel1M 942868 AACTTTTTGACCATAGTTCCAAATCACTCTCCAGAATGGCTGGATATATT 942917 v vivvv v v ii i i ? v ivv C L1ME3G_3end#L 344 AAATTTTAATAGATACTGCCAAATTGCCCTCCAAAANGGCTGTACCAATT 295 chr2qtel1M 942918 CACAATTCCACCAATAATGCATAAATGTCCCAGTTTTCCCACATCCTCCC 942967 i v i ii i i i iv v v i i v C L1ME3G_3end#L 294 TACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCACACCCTCGC 245 chr2qtel1M 942968 CAATATTCCACATTATCTTTCCCTGTCATTCTAGCCAATCTGACAGT--- 943014 i i ?v i vv? ii vvv i v ii v--- C L1ME3G_3end#L 244 CAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATCTGATGGGTGA 195 chr2qtel1M 943015 --AGTGGTAGTTCAGAGTTGTCT-AATTTGCATTTCTCTGATTAATAATG 943061 -- i vi vv i - i v i C L1ME3G_3end#L 194 AAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGATTACTAGTG 145 chr2qtel1M 943062 ACTTGGAGCATCTTTTCATATGGCTAGAAATAGTTTCACTTTCTTCATCT 943111 vv v vi vviiivi vvv i v C L1ME3G_3end#L 144 AGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGTATTTCCTCTTCT 95 chr2qtel1M 943112 GAGAATTGTCTGTTCATATCCTTTGACCATTTATCAATTGGAGGATGACT 943161 v i v v v -- v v C L1ME3G_3end#L 94 GTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTG--GGTTGTCT 47 chr2qtel1M 943162 TGATTTCTTATAGAGTC-----AATTCTCTATATAGTTTGGAAAT 943201 -- v v i----- i i v i v C L1ME3G_3end#L 46 T--TTTCTTATTGATTTGTAGGAGTTCTTTATATATTCTGGATAT 4 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 35.20 CpG sites = 88, Kimura (unadjusted) = 35.75 Transitions / transversions = 1.09 (88/81) Gap_init rate = 0.04 (26 / 624), avg. gap size = 1.38 (36 / 26) 318 29.57 4.60 2.82 chr2qtel1M 943067 943240 (56760) C L1P3_orf2#LINE/L1 (7) 3287 3111 m_b107s551i4 3904 chr2qtel1M 943067 GAGCATCTTTTCATATGGCTAGAAATAGTTTCACTTTCTTCATCTGAGAA 943116 v i vi ivviiiv iv v v v v i C L1P3_orf2#LIN 3287 GAGCTTTTTTTCATATGTTTGTTGGCCGCATAAATGTCTTCTTTTGAGAA 3238 chr2qtel1M 943117 TTGTCTGTTCATATCCTTTGACCATTTATCAATTGGAGGATGACTTG--- 943163 v i v i v ii -- i v -i --- C L1P3_orf2#LIN 3237 GTGTCTGTTCATATCCTTCGCCCACTTTTTGAT--GGGGTTG-TTTGTTT 3191 chr2qtel1M 943164 ATTTCTTATAGA---GTC--AATTCTCTATATAGTTTGGAAATGAGGCCT 943208 v i i --- i-- i ii i v v i v v v C L1P3_orf2#LIN 3190 TTTTCTTGTAAATTTGTTTAAGTTCCTTGTAGATTCTGGATATTAGCCCT 3141 chr2qtel1M 943209 TTATCAGAACCTTTGACTGTAAAAACGTTTTC 943240 i vvvv v i i -- C L1P3_orf2#LIN 3140 TTGTCAGATGGATAGATTGCAAAAA--TTTTC 3111 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.15 CpG sites = 25, Kimura (unadjusted) = 38.10 Transitions / transversions = 1.00 (25/25) Gap_init rate = 0.05 (8 / 173), avg. gap size = 1.62 (13 / 8) 13 8.48 4.00 0.00 chr2qtel1M 943681 943705 (56295) (TCCC)n#Simple_repeat 1 26 (0) m_b107s252i8 3905 chr2qtel1M 943681 TCCCT-CCTTCCTCCCACCCTCCCTC 943705 - i v (TCCC)n#Simpl 1 TCCCTCCCTCCCTCCCTCCCTCCCTC 26 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 200 23.91 12.50 1.25 chr2qtel1M 944674 944745 (55255) MIRc#SINE/MIR 71 150 (118) m_b107s601i4 3906 chr2qtel1M 944674 CTGACACTCAAAAATGGCGTGAGCTTTGAACCAATCCCTT-----CTCTG 944718 v i vv iiv i - i ii v i v ----- MIRc#SINE/MIR 71 CTGCCACTTACTAGCTGTGTGA-CCTTGGGCAAGTCACTTAACCTCTCTG 119 chr2qtel1M 944719 --CTTGAGTTTCCTC--CTGTAAATTGGGGA 944745 -- i v -- v MIRc#SINE/MIR 120 AGCCTCAGTTTCCTCATCTGTAAAATGGGGA 150 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.18 CpG sites = 9, Kimura (unadjusted) = 29.18 Transitions / transversions = 1.12 (9/8) Gap_init rate = 0.06 (4 / 71), avg. gap size = 2.50 (10 / 4) 209 27.03 9.73 5.08 chr2qtel1M 944690 944802 (55198) MIR3#SINE/MIR 84 201 (7) m_b107s601i5 3906 chr2qtel1M 944690 GCGTGAGCTTTGAACCAATCCCTTC-----TCTG--CTTGAGTTTCCTC- 944731 i - i ii v i v ----- -- i v - MIR3#SINE/MIR 84 GTGTGA-CCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCA 132 chr2qtel1M 944732 -CTGTAAATTGGGGAGGCTTGGTTGGATTCTTGAATTTTGAAGTGACTTT 944780 - v i i i v ii i ---- vi i i i vv i MIR3#SINE/MIR 133 TCTGTAAAATGAGGGGGTTGGACTAGA----TGATCTCTAAGGTCCCTTC 178 chr2qtel1M 944781 CAACTTT-AT-TTCTCATGATTTT 944802 i i - i- - i MIR3#SINE/MIR 179 CAGCTCTGACATTCT-ATGATTCT 201 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.54 CpG sites = 21, Kimura (unadjusted) = 35.54 Transitions / transversions = 2.62 (21/8) Gap_init rate = 0.11 (12 / 112), avg. gap size = 1.42 (17 / 12) 186 20.00 2.50 0.00 chr2qtel1M 945437 945476 (54524) C L2c_3end#LINE/L2 (12) 466 426 m_b107s601i6 3907 chr2qtel1M 945437 AATAAGCATTTCTTT-TCACCTACTATTTGCCAGGTGCTGG 945476 i i v v-v i v i C L2c_3end#LINE 466 AACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGG 426 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 17.36 CpG sites = 4, Kimura (unadjusted) = 23.41 Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1) 13 10.76 0.00 9.09 chr2qtel1M 945727 945762 (54238) (TTTTTA)n#Simple_repeat 1 33 (0) m_b107s252i9 3908 chr2qtel1M 945727 TTTTTATTTTTATTCTTATGTTATAGCCTTTTATTT 945762 i - v --i (TTTTTA)n#Sim 1 TTTTTATTTTTATTTTTAT-TTTTA--TTTTTATTT 33 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.09 (3 / 35), avg. gap size = 1.00 (3 / 3) 17 23.99 2.99 2.99 chr2qtel1M 947320 947386 (52614) (GAAAA)n#Simple_repeat 1 67 (0) m_b107s252i10 3909 chr2qtel1M 947320 GAAAA-AACAGCAAGAACAAAAGAAAA-ACAGGAAAGGAATGCAAAACAA 947367 - v - - v - v i i viv v (GAAAA)n#Simp 1 GAAAAGAAAAG-AA-AAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAA 48 chr2qtel1M 947368 AATAAAGTAAAACAAAAGA 947386 v iv v (GAAAA)n#Simp 49 AAGAAAAGAAAAGAAAAGA 67 Matrix = Unknown Transitions / transversions = 0.44 (4/9) Gap_init rate = 0.06 (4 / 66), avg. gap size = 1.00 (4 / 4) 12 18.13 2.44 5.00 chr2qtel1M 947614 947654 (52346) (TACA)n#Simple_repeat 1 40 (0) m_b107s252i11 3910 chr2qtel1M 947614 TACATAGGTAGATATATCCAT-CATACATACACTCACAAACA 947654 vi v i v - - - v (TACA)n#Simpl 1 TACATACATACATACATACATACATACATACA-T-ACATACA 40 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.07 (3 / 40), avg. gap size = 1.00 (3 / 3) 17 21.57 4.88 4.88 chr2qtel1M 948982 949063 (50937) (GAAAAT)n#Simple_repeat 1 82 (0) m_b107s252i12 3911 chr2qtel1M 948982 GATAATGTAATAGAAAAT-AAAATGAAAGTGATCATCAGAAAGTGCAAAT 949030 v v vv - i vv -- i v (GAAAAT)n#Sim 1 GAAAATGAAAATGAAAATGAAAATGAAAATGAAAAT--GAAAATGAAAAT 48 chr2qtel1M 949031 ---AATGAAAGGGAAAGGGAAAAAATGAAAATGGAA 949063 --- iv iv -- i (GAAAAT)n#Sim 49 GAAAATGAAAATGAAAATG--AAAATGAAAATGAAA 82 Matrix = Unknown Transitions / transversions = 0.56 (5/9) Gap_init rate = 0.07 (6 / 81), avg. gap size = 1.33 (8 / 6) 186 34.33 5.00 0.96 chr2qtel1M 949139 949238 (50762) MIRc#SINE/MIR 97 200 (68) m_b107s601i7 3912 chr2qtel1M 949139 GGTCAAGTCCCTCAGTCCCTCTGAGCT--GATGGTCTGAGTTGTCCAAGT 949186 v v i ii i i--ii vvi v vi v- i MIRc#SINE/MIR 97 GGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTA-AAAT 145 chr2qtel1M 949187 AGTGAGAATGA-AAGTGTTCTG--TATTTCACAGGTTTACTGTGGGAATA 949233 i v v i - vv ii -- ii v ii i i v MIRc#SINE/MIR 146 GGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATC 195 chr2qtel1M 949234 CAATG 949238 v MIRc#SINE/MIR 196 AAATG 200 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 47.73 CpG sites = 20, Kimura (unadjusted) = 47.73 Transitions / transversions = 1.43 (20/14) Gap_init rate = 0.04 (4 / 99), avg. gap size = 1.50 (6 / 4) 49 0.00 0.00 0.00 chr2qtel1M 949399 949440 (50560) (GT)n#Simple_repeat 1 42 (0) c_b107s251i2 3913 chr2qtel1M 949399 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 949440 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 42 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 274 29.78 8.57 0.88 chr2qtel1M 950733 950837 (49163) MIRc#SINE/MIR 3 115 (153) m_b107s601i8 3914 chr2qtel1M 950733 AGGCAGTATGATGAAATGGAAAGATCAGTAGATTGGGACTC-TGAGGGCA 950781 i i v i v v i i v v -v i i v MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chr2qtel1M 950782 AAGGTTGAAATTCTGGGTTCTG-----TACT---TCTGTGGCCTCAGGAA 950823 vi vi i i i- i ----- --- v i ii v MIRc#SINE/MIR 53 TGGGTTCGAGTCCC-GGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 101 chr2qtel1M 950824 AGCAATTTAACTTC 950837 iv i i MIRc#SINE/MIR 102 AGTCACTTAACCTC 115 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.10 CpG sites = 19, Kimura (unadjusted) = 39.33 Transitions / transversions = 1.58 (19/12) Gap_init rate = 0.04 (4 / 104), avg. gap size = 2.50 (10 / 4) 282 26.56 7.22 2.97 chr2qtel1M 952686 952782 (47218) C L3#LINE/CR1 (912) 3187 3087 m_b107s601i9 3915 chr2qtel1M 952686 ATTCAAGTCATTGG-AAAAATGTTAAACAGACCAGGAGCGAGCCCCTAGC 952734 i i- i iv iv i vv vv C L3#LINE/CR1 3187 ATCCAAGTCATTGATAAAAATGTTGAACAGGACAGGGCCAAGGACAGAGC 3138 chr2qtel1M 952735 CCACATGTGTC------CCAGAGACCTCTTGGTATGTTGGCATTGGACAA 952778 --- v ------ i iivvi v i i iv v C L3#LINE/CR1 3137 CC---TGTGGCACGCCACTAGAGACCTCCCTCCAGGTTGACATCGATCCA 3091 chr2qtel1M 952779 TTAA 952782 C L3#LINE/CR1 3090 TTAA 3087 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.69 CpG sites = 13, Kimura (unadjusted) = 33.27 Transitions / transversions = 1.08 (13/12) Gap_init rate = 0.05 (5 / 96), avg. gap size = 2.00 (10 / 5) 27 8.35 0.00 0.00 chr2qtel1M 955835 955873 (44127) (CCT)n#Simple_repeat 1 39 (0) c_b107s251i3 3916 chr2qtel1M 955835 CCTCCTCCTCCTCCTCCTCTTCCTCCCCCTCTTCCTCCT 955873 i i i (CCT)n#Simple 1 CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT 39 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 37 4.88 0.00 0.00 chr2qtel1M 955896 955938 (44062) (ACAG)n#Simple_repeat 1 43 (0) c_b107s251i4 3917 chr2qtel1M 955896 ACAGGCAGACAGACAGACAGACAGACAAACAGACAGACAGACA 955938 i i (ACAG)n#Simpl 1 ACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACA 43 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 25 18.89 0.00 0.00 chr2qtel1M 956014 956067 (43933) (CCCTTCA)n#Simple_repeat 1 54 (0) m_b107s252i13 3918 chr2qtel1M 956014 CCCTAAAACCTTCAACCTTCACCCGTCTCCCTTTTCCCTTCACCTTTCAC 956063 vv v v v v iv i (CCCTTCA)n#Si 1 CCCTTCACCCTTCACCCTTCACCCTTCACCCTTCACCCTTCACCCTTCAC 50 chr2qtel1M 956064 CCTT 956067 (CCCTTCA)n#Si 51 CCTT 54 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 235 33.36 2.40 4.07 chr2qtel1M 957032 957156 (42844) C MIRb#SINE/MIR (3) 265 143 m_b107s601i10 3919 chr2qtel1M 957032 AAGAAAACCAGCATTTGTTATAAAGTATCTACTAAGCTGCAGACACTTGA 957081 v i i i v i i--- iiii v ivv i - v C MIRb#SINE/MIR 265 AATAGAGCTACCATTTATTG---AGCGCTTACTATGTGCCAGGCACT-GT 220 chr2qtel1M 957082 GTTAAGCACCTTGC---CAGTATCTTCATGGATCCTCACAGGAAAATCAG 957128 i i i i --- v ivv vi iv v-i v C MIRb#SINE/MIR 219 GCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAAC-CCTG 171 chr2qtel1M 957129 CAAGCTACATTGTATTATCTCCTTTTTA 957156 i v vi vv i v C MIRb#SINE/MIR 170 CGAGGTAGGTATTATTATCCCCATTTTA 143 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 40.66 CpG sites = 22, Kimura (unadjusted) = 45.27 Transitions / transversions = 1.22 (22/18) Gap_init rate = 0.05 (6 / 124), avg. gap size = 1.33 (8 / 6) 472 23.97 0.83 6.14 chr2qtel1M 957739 957858 (42142) MIRc#SINE/MIR 2 115 (153) m_b107s601i11 3920 chr2qtel1M 957739 GAAGCTAGGTGGTGCAGTGGATAGAGCACCAGCCCTAAAGTCAGGAGGAC 957788 i viv v ii v i ii i MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr2qtel1M 957789 CTGAGTTCAAATCTAGCTTCAGACACTTAACACTTCCTATCTGTGTGCCC 957838 i i i iv vi v v ------- v v MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTGACC 94 chr2qtel1M 957839 CAGGGC-AGTCACTTAATCCC 957858 iv - i i MIRc#SINE/MIR 95 TTGGGCAAGTCACTTAACCTC 115 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.09 CpG sites = 16, Kimura (unadjusted) = 29.36 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.07 (8 / 119), avg. gap size = 1.00 (8 / 8) 26 0.00 7.50 2.38 chr2qtel1M 957873 957912 (42088) (AAAC)n#Simple_repeat 1 42 (0) c_b107s251i5 3921 chr2qtel1M 957873 AAACAAACAAACAAACAAACAAA-ACAAC-AACAAA-AAACAA 957912 - - - - (AAAC)n#Simpl 1 AAACAAACAAACAAACAAACAAACA-AACAAACAAACAAACAA 42 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.10 (4 / 39), avg. gap size = 1.00 (4 / 4) 16 15.91 0.00 0.00 chr2qtel1M 957926 957953 (42047) (T)n#Simple_repeat 1 28 (0) m_b107s252i14 3922 chr2qtel1M 957926 TTTGTTTTTCTTTTTCTTTATTTTTTTT 957953 v i i v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 28 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 15 21.59 2.33 0.00 chr2qtel1M 957926 957968 (42032) (TTTCTT)n#Simple_repeat 1 44 (0) m_b107s252i15 3923 chr2qtel1M 957926 TTTGTTTTTCTTTTTCTTTAT-TTTTTTTGAAGCTTTTTATTTT 957968 v v - i vvvv v (TTTCTT)n#Sim 1 TTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTT 44 Matrix = Unknown Transitions / transversions = 0.14 (1/7) Gap_init rate = 0.02 (1 / 42), avg. gap size = 1.00 (1 / 1) 17 20.50 1.85 3.77 chr2qtel1M 958147 958200 (41800) (AAAGAA)n#Simple_repeat 1 53 (0) m_b107s252i16 3924 chr2qtel1M 958147 AAAGGGAAA-AAAATGAAAAAGAAAAAGAAATTCAAGCAAACAACAACAA 958195 ii - v vvv -- v v v (AAAGAA)n#Sim 1 AAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAA--AAAGAAAAAGAA 48 chr2qtel1M 958196 AAAGA 958200 (AAAGAA)n#Sim 49 AAAGA 53 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.06 (3 / 53), avg. gap size = 1.00 (3 / 3) 264 33.95 2.23 2.69 chr2qtel1M 958382 958605 (41395) C L1ME4c_3end#LINE/L1 (191) 639 417 m_b107s551i5 3925 chr2qtel1M 958382 TTCTGCTCATTTCACTCAGCATCAGTTCATGTAAGACTCTTCATGCCTTT 958431 iv i i i vv i- v i i i -- v C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATA-AACATTTTCCATG--TTG 593 chr2qtel1M 958432 CTGAAATTGTCCTGCTGATTGT--TTCTTACAGATTGT-T--TCTTCCAT 958476 - v v i vv i i -- i vv ii i- -- v C L1ME4c_3end#L 592 CT-ACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCAT 544 chr2qtel1M 958477 CACCTTCATGTACCATTACTTGTCCAGCTGTTCTCCAATTGAGGGACATC 958526 ivv ?v v i iiii i ii i v vv i C L1ME4c_3end#L 543 CGAGTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATT 494 chr2qtel1M 958527 CCCTCAGTTCCCAGTTTCTCACCACTGCAAAAAGGGCTGCCACAAACATT 958576 ivvviv i i i i i i ii v iv v ii i C L1ME4c_3end#L 493 TAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATC 444 chr2qtel1M 958577 TTTGTTCATGTGGGACTTTTCTATCCTTT 958605 i v i i -- iiv i C L1ME4c_3end#L 443 TTCGTGCATATAG--CTTTTTCCTTCTTT 417 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 45.01 CpG sites = 46, Kimura (unadjusted) = 47.72 Transitions / transversions = 1.64 (46/28) Gap_init rate = 0.04 (9 / 223), avg. gap size = 1.22 (11 / 9) 267 34.62 0.00 0.00 chr2qtel1M 958484 958587 (41413) C L1MD1_3end#LINE/L1 (456) 533 430 m_b107s551i6 3925 chr2qtel1M 958484 ATGTACCATTACTTGTCCAGCTGTTCTCCAATTGAGGGACATCCCCTCAG 958533 ivii ii i ii v vi i ivvviv C L1MD1_3end#LI 533 ATGTACCACAGTTTGTTTAACCATTCACCCGTTGAAGGACATCTGGGTTG 484 chr2qtel1M 958534 TTCCCAGTTTCTCACCACTGCAAAAAGGGCTGCCACAAACATTTTTGTTC 958583 i i vi i i i i v ii i i iv v C L1MD1_3end#LI 483 TTTCCAGTTTTTGGCTATTACGAATAAAGCTGCTATAAACATTCGTGTAC 434 chr2qtel1M 958584 ATGT 958587 v C L1MD1_3end#LI 433 AGGT 430 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 43.78 CpG sites = 24, Kimura (unadjusted) = 49.57 Transitions / transversions = 2.00 (24/12) Gap_init rate = 0.00 (0 / 103), avg. gap size = 0.0 (0 / 0) 20 0.00 6.67 0.00 chr2qtel1M 960384 960413 (39587) (TTTA)n#Simple_repeat 1 32 (0) m_b107s252i17 3926 chr2qtel1M 960384 TTTATTTATTTATTT-TTTATTTA-TTATTTA 960413 - - (TTTA)n#Simpl 1 TTTATTTATTTATTTATTTATTTATTTATTTA 32 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.07 (2 / 29), avg. gap size = 1.00 (2 / 2) 252 28.99 7.75 3.73 chr2qtel1M 961811 961939 (38061) MIR3#SINE/MIR 68 201 (7) m_b107s601i12 3927 chr2qtel1M 961811 CTGACACTCACAAATGGCATGAGCTTTGAGCAAATCCCTTT-----TCTG 961855 v v v?iiv ii - i i i v i----- MIR3#SINE/MIR 68 CTGCCACTAACTNGCTGTGTGA-CCTTGGGCAAGTCACTTCACCTCTCTG 116 chr2qtel1M 961856 --CTTGACTTTCCTCAT--ATAAATTGGGGAGGGTTGGTTGGCTTCTTGA 961901 -- i v v --i v i - ---i vvv MIR3#SINE/MIR 117 GGCCTCAGTTTCCTCATCTGTAAAATGAGG-GGGTTGG---ACTAGATGA 162 chr2qtel1M 961902 ATTTTGAAGTGACTTTCAGCTCT-ACATCTCATGACTTT 961939 vi i i i vv i - iii i i MIR3#SINE/MIR 163 TCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCT 201 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.35 CpG sites = 22, Kimura (unadjusted) = 38.35 Transitions / transversions = 1.57 (22/14) Gap_init rate = 0.07 (9 / 128), avg. gap size = 1.67 (15 / 9) 11 20.73 1.69 9.09 chr2qtel1M 964356 964414 (35586) (ATGAAA)n#Simple_repeat 1 55 (0) m_b108s252i0 3928 chr2qtel1M 964356 ATAAAAATAAAACTGAAAGTGATCACCAGAAAATGCACACAATG-AAAGG 964404 i i v i -- vvv - - - - v (ATGAAA)n#Sim 1 ATGAAAATGAAAATGAAAATGA--AAATGAAAATG-A-A-AATGAAAATG 45 chr2qtel1M 964405 AAAAGGAAAA 964414 v (ATGAAA)n#Sim 46 AAAATGAAAA 55 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.10 (6 / 58), avg. gap size = 1.00 (6 / 6) 27 3.46 9.84 1.52 chr2qtel1M 965397 965457 (34543) (ACAATTCTAGTT)n#Simple_repeat 1 66 (0) c_b108s251i0 3929 chr2qtel1M 965397 ACAATTCTAGTTAC-A--CTTGTCACAATTCTAGTTAC-ATT-T-GTTAC 965440 - -- v i - - - (ACAATTCTAGTT 1 ACAATTCTAGTTACAATTCTAGTTACAATTCTAGTTACAATTCTAGTTAC 50 chr2qtel1M 965441 AATATCTAGTTACAATT 965457 - (ACAATTCTAGTT 51 AAT-TCTAGTTACAATT 66 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.10 (6 / 60), avg. gap size = 1.17 (7 / 6) 285 29.60 9.60 0.00 chr2qtel1M 966352 966476 (33524) C HERVK9#LTR/ERVK (1642) 4379 4243 m_b108s701i0 3930 chr2qtel1M 966352 TCTCCAGATTGGAATGAAGCCATAAGGAATTGAGAATGTATATCCACAGT 966401 v v v vvi vi v vivi i vv C HERVK9#LTR/ER 4379 TCTCCTGATTGGCATGTAGCCCAGACAAAGTGAGAAAAGGTGTCCACACA 4330 chr2qtel1M 966402 TACATGGACACA--CTA-TCTCTTAAA---------GTGAGTAATGTCCA 966439 v i -- - ii ---------i v i ii C HERVK9#LTR/ER 4329 TACATGTACATAAGCTAGTCTCCCAAACGAGGGAACATGTGTGACATCCA 4280 chr2qtel1M 966440 TTTGCCTTAAAGCATTAAATTTCAAACCATAAGGGTT 966476 vv i v ii i v vii i C HERVK9#LTR/ER 4279 TTTGCCAAAGAGAATTAGGTTCCAATCCTCGAGGATT 4243 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.77 CpG sites = 19, Kimura (unadjusted) = 38.20 Transitions / transversions = 1.06 (19/18) Gap_init rate = 0.02 (3 / 124), avg. gap size = 4.00 (12 / 3) 322 24.52 2.75 2.75 chr2qtel1M 967482 967590 (32410) C HERVK14#LTR/ERVK (3263) 2833 2725 m_b108s701i1 3931 chr2qtel1M 967482 CTTGGATCAATAAACATTCTCCATTCCCCAAATTTCCTTCTT-ATAACAA 967530 ii vi v i vi -i - i C HERVK14#LTR/E 2833 CTTAAATCTGTTAACATTCTCCATTTCCCTGATTT-TTTCTTAATGACAA 2785 chr2qtel1M 967531 ATTCTGGGGAATTCCAAAGACTTAGAAA--AGCTTGTAAATGTCCTTGGT 967578 v v i i iv-- -- vi v v i vv C HERVK14#LTR/E 2784 ATACAGGAGAATTCCAAGGGG--AGAAAGTAGGCTCTATATGTCCCTTTT 2737 chr2qtel1M 967579 TAAGTTGTTCCT 967590 vv i C HERVK14#LTR/E 2736 GCAATTGTTCCT 2725 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 29.97 CpG sites = 13, Kimura (unadjusted) = 29.97 Transitions / transversions = 1.00 (13/13) Gap_init rate = 0.05 (5 / 108), avg. gap size = 1.20 (6 / 5) 12 16.26 0.00 8.11 chr2qtel1M 968074 968113 (31887) (AATATT)n#Simple_repeat 1 37 (0) m_b108s252i1 3932 chr2qtel1M 968074 AATATTAATTCCAAATATTAATATTGATTTTTGAATATTA 968113 - viv - v v - (AATATT)n#Sim 1 AATATTAA-TATTAATATTAATATT-AATATT-AATATTA 37 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.08 (3 / 39), avg. gap size = 1.00 (3 / 3) 48 5.38 1.72 0.00 chr2qtel1M 968539 968596 (31404) (TG)n#Simple_repeat 1 59 (0) c_b108s251i1 3933 chr2qtel1M 968539 TGTGTGTGTGAATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATG 968588 vi i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr2qtel1M 968589 TGTG-GTGT 968596 - (TG)n#Simple_ 51 TGTGTGTGT 59 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.02 (1 / 57), avg. gap size = 1.00 (1 / 1) 16 5.27 0.00 0.00 chr2qtel1M 970628 970647 (29353) (A)n#Simple_repeat 1 20 (0) m_b108s252i2 3934 chr2qtel1M 970628 AAAAAAAAAAAAAAAAAGAA 970647 i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAA 20 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 199 36.56 0.00 0.00 chr2qtel1M 971188 971280 (28720) L2#LINE/L2 2390 2482 (600) m_b108s601i1 3935 chr2qtel1M 971188 ATCCAAATTCCTTCCAGACATTTTGAAGTAGATAGCCAATGGGCATCTCA 971237 v v v iv i iv vv i iv i i L2#LINE/L2 2390 ATCCAACTGCCTACTCGACATCTCCACTTGGATGTCTAATAGGCATCTCA 2439 chr2qtel1M 971238 AACTCACCATATTACCAACAAAACCTATTACCTCTTCTCTGAA 971280 i v i ivvv vi iiv v i iii i v L2#LINE/L2 2440 AACTTAACATGTCCAAAACTGAACTCCTGATCTTCCCCCTCAA 2482 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 51.49 CpG sites = 18, Kimura (unadjusted) = 51.49 Transitions / transversions = 1.12 (18/16) Gap_init rate = 0.00 (0 / 92), avg. gap size = 0.0 (0 / 0) 11 26.13 0.00 6.12 chr2qtel1M 971669 971720 (28280) (GGCGGA)n#Simple_repeat 1 49 (0) m_b108s252i3 3936 chr2qtel1M 971669 GGCGCAGCCTGGCAGGCGGTGGCCCAGGGGGAGTGTGAGCCCGGAGGCGG 971718 v v - - v vv v vvv -v (GGCGGA)n#Sim 1 GGCGGAGGC-GG-AGGCGGAGGCGGAGGCGGAGGCGGAG-GCGGAGGCGG 47 chr2qtel1M 971719 AG 971720 (GGCGGA)n#Sim 48 AG 49 Matrix = Unknown Transitions / transversions = 0.00 (0/10) Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.00 (3 / 3) 305 21.88 0.00 0.00 chr2qtel1M 974151 974214 (25786) C MIR3#SINE/MIR (64) 144 81 m_b108s601i2 3937 chr2qtel1M 974151 TCATTTTCCAGATGAGGACACTGGGGACAAAAGGGCTGGAGTGGCTTTCT 974200 v v i v v i i v i i v i C MIR3#SINE/MIR 144 TCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCC 95 chr2qtel1M 974201 CCGGGTCACACAGC 974214 vi C MIR3#SINE/MIR 94 CAAGGTCACACAGC 81 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 26.06 CpG sites = 7, Kimura (unadjusted) = 26.06 Transitions / transversions = 1.00 (7/7) Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0) 269 22.27 1.32 5.48 chr2qtel1M 974152 974227 (25773) C MIR#SINE/MIR (120) 142 70 m_b108s601i3 3937 chr2qtel1M 974152 CATTTTCCAGATGAGGACACTGGGG-ACAAAAGGGCTGGAGTGGCTTTCT 974200 v v i - i ii i i- ii v i C MIR#SINE/MIR 142 CATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTA-AGTAACTTGCC 94 chr2qtel1M 974201 CCGGGTCACACAGCTTTTAGGAAATGG 974227 vi --- v i C MIR#SINE/MIR 93 CAAGGTCACACAGC---TAGTAAGTGG 70 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.24 CpG sites = 11, Kimura (unadjusted) = 27.24 Transitions / transversions = 2.20 (11/5) Gap_init rate = 0.07 (5 / 75), avg. gap size = 1.00 (5 / 5) 510 24.09 7.47 2.19 chr2qtel1M 974346 974519 (25481) C MIR3#SINE/MIR (19) 189 7 m_b108s601i4 3938 chr2qtel1M 974346 TGGCAGACCCTGAAGGGGAGT--GGAATTTTCTTCTCCAGC----TCATT 974389 v v iv ivv -- ii iv vv i ---- C MIR3#SINE/MIR 189 TGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATT 140 chr2qtel1M 974390 TTACAAATGAGGTAACTGAGGC--AGGCAGGGTGAAGTGACTTGCCCAGG 974437 i v -- iv - i C MIR3#SINE/MIR 139 TTACAGATGAGGAAACTGAGGCCCAGAGAGG-TGAAGTGACTTGCCCAAG 91 chr2qtel1M 974438 ATCACACAGC----TAGTGTCTGAGACAAGATTCAAAGTCAGATCCTCCT 974483 i ---- v v v ii i vi vi i - C MIR3#SINE/MIR 90 GTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGT-CTCCT 42 chr2qtel1M 974484 GAGTCCAAGGCCA-GCCCTCCATCGACAGGGCCACTC 974519 v v v i- i -- vi vvi C MIR3#SINE/MIR 41 GACTCCCAGTCCGTGCTCTC--TCTGCTCAGCCACTC 7 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.69 CpG sites = 20, Kimura (unadjusted) = 29.32 Transitions / transversions = 0.95 (20/21) Gap_init rate = 0.05 (9 / 173), avg. gap size = 1.89 (17 / 9) 558 21.80 4.48 0.72 chr2qtel1M 974384 974517 (25483) C MIRc#SINE/MIR (120) 148 10 m_b108s601i5 3938 chr2qtel1M 974384 CTCATTTTACAAATGAGGTAACTGAGGC--AGGCAGGGTGAAGTGACTTG 974431 i i v -- iv v - C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTT-AAGTGACTTG 100 chr2qtel1M 974432 CCCAGGATCACACAGCT----AGTGTCTGAGACAAGATTCAAAGTCAGAT 974477 i i ---- v v v ii i i vi i C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGT 50 chr2qtel1M 974478 CCTCCTGAGTCCAAGGCCAGCCCTCCATCGACAGGGCCAC 974517 i v v iv iv v v vi C MIRc#SINE/MIR 49 CTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 24.01 CpG sites = 15, Kimura (unadjusted) = 26.00 Transitions / transversions = 1.07 (15/14) Gap_init rate = 0.02 (3 / 133), avg. gap size = 2.33 (7 / 3) 228 29.12 2.88 0.94 chr2qtel1M 975015 975118 (24882) C L1M1_orf2#LINE/L1 (1629) 1665 1560 m_b108s551i0 3939 chr2qtel1M 975015 AATATATTGTCAAATATAG---GACAGGATTTGGTTTAAAATTATTGAGG 975061 i ii vii --- vi v v v ii v viv C L1M1_orf2#LIN 1665 AATGTATTGTTGAATTCGGTTTGCTAGTATTTTGTTGAGGATTTTTGCAT 1616 chr2qtel1M 975062 CAATATTCACTAATGATATTGGCTTGGGGTTTATTTTCTTTGTTTTGACT 975111 ii iv i vi vi i v v v - C L1M1_orf2#LIN 1615 CAATATTCATCAGAGATATTGGCCTGTAGTTTTCTTTTTTTGATGTGTC- 1567 chr2qtel1M 975112 TTTGTCT 975118 C L1M1_orf2#LIN 1566 TTTGTCT 1560 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 35.79 CpG sites = 16, Kimura (unadjusted) = 37.51 Transitions / transversions = 1.14 (16/14) Gap_init rate = 0.02 (2 / 103), avg. gap size = 2.00 (4 / 2) 840 30.49 6.54 5.21 chr2qtel1M 975567 976040 (23960) C L1ME5_3end#LINE/L1 (389) 552 73 m_b108s551i2 3940 chr2qtel1M 975567 ATAATATTCCATCACAAACATATACTGCAGGTTGTGCAGCCATTACCCAA 975616 i i viiivi vi ii vv iivi v i vi v C L1ME5_3end#LI 552 ATAGTACTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCA 503 chr2qtel1M 975617 TTGATGAGCATCCACCTCAGTTTCCACTTCTTTGTCACCACTAAAGA-GT 975665 v ii i vv i- ii vi iii i v vi - i C L1ME5_3end#LI 502 GTGATGGACACCCAGGTT-GCCTCCAACTCCCCGCCACCACAAACAACGC 454 chr2qtel1M 975666 TGCTATAAATATTTTTGTACATATAGATCATTTT---CCTGGTTTT---- 975708 v i i ii i i v--i v v --- -- v ---- C L1ME5_3end#LI 453 TGCAATGAACATCCTCGTACATGTC--CCCTTATGGACCTG--TGTGAGA 408 chr2qtel1M 975709 ATCTCTTTGGAATACAGATTTACTAGTAGAATTGCTGGGTCAAAGGGTGT 975758 i i i v iii vv ii v i C L1ME5_3end#LI 407 ATTTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTAT 358 chr2qtel1M 975759 AGGTA------GTTTTAC-AAGTCCTGTGGGTATAGTTCCAAATTGCTTT 975801 iv ------i v - v ----------- i i C L1ME5_3end#LI 357 GCGTATACTTAATTTGACTAAGTACTG-----------CCAGATTGCTCT 319 chr2qtel1M 975802 ACAGAATTGTTGGATCAGTATACAATTTCACCAACAGT--ATTAGTGTCT 975849 v v i v i v v ii i -- v v ii C L1ME5_3end#LI 318 CCAGAATGGCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTC 269 chr2qtel1M 975850 CAGTTTTCCCACATCCTCTCCAATATTTGTCATTTT--GATTTTCT--TT 975895 vi ? i v i i v v --iii -- C L1ME5_3end#LI 268 CTATNTCCCCACATCCTCGCCAACACTTGGCATTATCCAGCTTTCTAATT 219 chr2qtel1M 975896 TCTGATAGCCAATCTAATAGAAGTAAGGCAGTATCTCAGAATTGTTTTAA 975945 i ---- i iv i iii vvi C L1ME5_3end#LI 218 TTTG----CCAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAA 173 chr2qtel1M 975946 TTAGCATTTGTCCAATCAATAGTGATTT----------TCCATATGGCTA 975985 v v ii i v i v ---------- i vi i C L1ME5_3end#LI 172 TTTGCATTTCTCTGATTACTAATGAGTTTGAGCATCTCTTCATATGCTTG 123 chr2qtel1M 975986 TAGAGAATTTCAGATTAATTCATCTGAAAACTGACTTCCTGTTTTTATCA 976035 -v vv i i vvi v v i ---- iv v C L1ME5_3end#LI 122 T-TAGCCTTTCGGGTTTCCTCTTCTGTAAATTG----CCTGTTCATATCC 78 chr2qtel1M 976036 TTTAC 976040 i C L1ME5_3end#LI 77 TTTGC 73 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.01 CpG sites = 82, Kimura (unadjusted) = 40.60 Transitions / transversions = 1.49 (82/55) Gap_init rate = 0.07 (34 / 473), avg. gap size = 1.65 (56 / 34) 941 29.61 5.78 2.33 chr2qtel1M 975567 975981 (24019) C L1ME4c_3end#LINE/L1 (275) 555 127 m_b108s551i1 3940 chr2qtel1M 975567 ATAATATTCCATCACAAACATATACTGCAGGTTGTGCAGCCATTACCCAA 975616 iviv?v i iii iv iivi i v v C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chr2qtel1M 975617 TTGATGAGCATCCACCTCAGTTTCCACTTCTTTGTCACCACTAAAGA--G 975664 v ii ii vv i- v i i ii ii - v -- C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTT-GTTTCCAATTTTTCGCTATTA-TAAATAACG 458 chr2qtel1M 975665 TTGCTATAAATATTTTTGTACATATAGATCATTTTCCTGGTTTT-----A 975709 i v i i i i i v -- vv ----- C L1ME4c_3end#L 457 CTGCAATGAACATCTTCGTGCATATAGCT--TTTTCCTTCTTTTGAATTA 410 chr2qtel1M 975710 TCTCTTTGGAATACAGATTTACTAGTAGAATTGCTGGGTCAAAGGGTGTA 975759 i i i i v vviii vv i i i i C L1ME4c_3end#L 409 TTTCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATG 360 chr2qtel1M 975760 GGTAGTTTTACAAGTCCTG-TGGGTATAGTTCCAAATTGCTTTACAGAAT 975808 iii v iiiv i - iv -- v v i v C L1ME4c_3end#L 359 AACATTTTTATGGCTCTTGATACGTAT--TGCCAAATTGCTTTCCAAAAG 312 chr2qtel1M 975809 TGTTGGATCAGTATACAATTTCACCAACA--GTATTAGTGTCTCAGTTTT 975856 v v i i v ? vi i -- v ? vi i C L1ME4c_3end#L 311 GGTTGTACCAATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTTTC 262 chr2qtel1M 975857 CCCACATCCTCTCCAATATTTGTCATT-TTGATTTTCT---TTTCTGATA 975902 v i ? v ii v vi - ii i --- i --- C L1ME4c_3end#L 261 ACCGCANCCTCGCCAGCATTGGGTATTATCAATTTTTTAAATTTTTG--- 215 chr2qtel1M 975903 GCCAATCTAATAGAAGTAAGGCAGTATCTCAGAATTGTTTTAATTAGCAT 975952 - i i iv iiii vvi i v C L1ME4c_3end#L 214 -CTAATTTAATAGGCGTAAAATGGTATCTCATTGTTGCTTTAATTTGCAT 166 chr2qtel1M 975953 TTGTCCAATCAATAGTGA----------TTTTCCATATG 975981 v iii i v i ---------- i C L1ME4c_3end#L 165 TTCTTTGATTACTAGCGAGGTTGAACATTTTTCCATGTG 127 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.67 CpG sites = 77, Kimura (unadjusted) = 39.83 Transitions / transversions = 1.79 (77/43) Gap_init rate = 0.04 (17 / 414), avg. gap size = 2.00 (34 / 17) 21 4.00 0.00 0.00 chr2qtel1M 976264 976289 (23711) (TC)n#Simple_repeat 1 26 (0) m_b108s252i4 3941 chr2qtel1M 976264 TCTCTCTCTCTCTCTCTCTCTTTCTC 976289 i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTC 26 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 444 23.80 0.00 6.19 chr2qtel1M 976312 976414 (23586) C MIRc#SINE/MIR (153) 115 19 m_b108s601i6 3942 chr2qtel1M 976312 GGGGTTAAGTGACTTGCCCATCGTCACACTGCTAGGAAATGTTAAATGTT 976361 i vv v v i vi i - ii C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGA-GCC 67 chr2qtel1M 976362 GAGGTCAGATTTGAACTCAGATCCTCCTGATTTCAAGGCTGGTGCTCTAT 976411 i ----- i i i i i i i v ii v C MIRc#SINE/MIR 66 GGG-----ACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTT 22 chr2qtel1M 976412 CCA 976414 C MIRc#SINE/MIR 21 CCA 19 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 26.60 CpG sites = 16, Kimura (unadjusted) = 29.61 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.06 (6 / 102), avg. gap size = 1.00 (6 / 6) 15 30.84 1.19 4.94 chr2qtel1M 976607 976690 (23310) (TCTCTT)n#Simple_repeat 1 81 (0) m_b108s252i5 3943 chr2qtel1M 976607 TCTCTCTCCCTTTCTCTTATTCCTACTACATTC-CTTTTCCTCACCTCTT 976655 i i vi i v - v - ii -vi (TCTCTT)n#Sim 1 TCTCTTTCTCTTTCTCTTTCTCTTTCT-CTTTCTCTTTCTCT-TTCTCTT 48 chr2qtel1M 976656 AATTTTATATTTTTCTCTTTTCTTTTTTCCTTTCT 976690 vv i - v i - i ii (TCTCTT)n#Sim 49 TCTCTT-TCTCTTTCTC-TTTCTCTTTCTCTTTCT 81 Matrix = Unknown Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.06 (5 / 83), avg. gap size = 1.00 (5 / 5) 424 21.85 2.40 8.47 chr2qtel1M 976701 976825 (23175) C MIR#SINE/MIR (139) 123 6 m_b108s601i7 3944 chr2qtel1M 976701 CTGAGACA-ATTGGAATCAAGTGACTTGCCCAAGATCACATAGCTAGAAA 976749 i - vv iii i i i i v C MIR#SINE/MIR 123 CTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAA 74 chr2qtel1M 976750 GTACTGATTGTCTGAGCC-TGATTTGAACTCGGGTCATTTTGACTTCAGA 976798 ------- v v -v i i i - v i i i C MIR#SINE/MIR 73 G-------TGGCAGAGCCGGGATTCGAACCCAGG-CAGTCTGGCTCCAGA 32 chr2qtel1M 976799 GCACAGGTGCTC-TATCCACTGTGCCAT 976825 v -- - v i i C MIR#SINE/MIR 31 GCCC--GTGCTCTTAACCACTATGCTAT 6 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 25.10 CpG sites = 16, Kimura (unadjusted) = 26.30 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.10 (13 / 124), avg. gap size = 1.00 (13 / 13) 439 20.80 0.84 11.11 chr2qtel1M 976716 976834 (23166) C MIRb#SINE/MIR (154) 114 7 m_b108s601i8 3944 chr2qtel1M 976716 TCAAGTGACTTGCCCAAGATCACATAGCTAGAAAGTACTGATTGTCTGAG 976765 i i i i v ------- v v C MIRb#SINE/MIR 114 TTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAG-------TGGCAGAG 72 chr2qtel1M 976766 CC-TGATTTGAACTCGGGTCATTTTGACTTCAGAGCACAGGTGCTCTATC 976814 -v i i i vv i i i v -- v C MIRb#SINE/MIR 71 CCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCC--GTGCTCTTTC 24 chr2qtel1M 976815 CACTGTGCCATCTAGCTACC 976834 ii i--- i C MIRb#SINE/MIR 23 CACTGCACCAC---GCTGCC 7 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 22.08 CpG sites = 14, Kimura (unadjusted) = 24.56 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.11 (13 / 118), avg. gap size = 1.00 (13 / 13) 16 3.41 6.25 3.03 chr2qtel1M 977737 977768 (22232) (TAAAAA)n#Simple_repeat 1 33 (0) m_b108s252i6 3945 chr2qtel1M 977737 TAAAAATAAAAA-AAAAA-AATAATAATAAATAA 977768 - - v - (TAAAAA)n#Sim 1 TAAAAATAAAAATAAAAATAAAAATAA-AAATAA 33 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.10 (3 / 31), avg. gap size = 1.00 (3 / 3) 17 18.53 0.00 0.00 chr2qtel1M 977738 977768 (22232) (A)n#Simple_repeat 1 31 (0) m_b108s252i7 3945 chr2qtel1M 977738 AAAAATAAAAAAAAAAAATAATAATAAATAA 977768 v v v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 31 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 405 27.38 14.50 1.01 chr2qtel1M 978315 978576 (21424) C L1ME3G_3end#LINE/L1 (273) 651 355 m_b108s551i3 3946 chr2qtel1M 978315 TGTACAATATTCTTCTG-GTTCTGCTTGTT-CACTGAGCATCACTTCTTG 978362 i- iv -ivii v - v i vi iv C L1ME3G_3end#L 651 TGTACG-TATCGTTCTGCAACTTGCTTTTTTCACTCAACAATATGTCTTG 603 chr2qtel1M 978363 TAAATCTTTCTAGGCCTTTCTA---AAATCAATCTGTTTCTCATTTTTAT 978409 v i i v i vv vi --- i v i vv -- v i C L1ME3G_3end#L 602 GAGATCTTTCCATGTCAGTACATATAGATCTACCTCATTCT--TTTTAAC 555 chr2qtel1M 978410 AGA---ATAATATTGCATA-TATC-ATACATCATAATTCATTCAGCTATT 978454 ? v--- i v - v- i i i i i i C L1ME3G_3end#L 554 NGCTGCATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATT 505 chr2qtel1M 978455 CCCCCACTGATGGGCATCTCAGTT---TCCCATTCTTTGCTCCCACAGAA 978501 i i i i vi --- v i i vii i v C L1ME3G_3end#L 504 CCCCTATTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAAC 455 chr2qtel1M 978502 AA--CTGCTACAAACTTCCT-GT---------TTTATG------------ 978527 -- v ii v - ---------i i ------------ C L1ME3G_3end#L 454 AATGCTGCAATGAACATCCTTGTACATGCNTCCTTGTGCACATGTGCGAG 405 chr2qtel1M 978528 -ATCTCTTTGGGATACAGACCCAGTAGCAGCATTGCTGGATCAAAGAATA 978576 - i ? i v v? ? v ii v i ii C L1ME3G_3end#L 404 TATTTCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTA 355 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.95 CpG sites = 43, Kimura (unadjusted) = 35.82 Transitions / transversions = 1.54 (43/28) Gap_init rate = 0.06 (15 / 261), avg. gap size = 2.73 (41 / 15) 253 23.70 10.38 4.46 chr2qtel1M 979819 979924 (20076) MIR3#SINE/MIR 90 201 (7) m_b108s601i9 3947 chr2qtel1M 979819 CTTTGAGCAGATCCCTTC-----TCTG--CTTGACTTTCCTC--CTGTAA 979859 i i ii v ----- -- i v v -- MIR3#SINE/MIR 90 CCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAA 139 chr2qtel1M 979860 ATTGGGGAGGGTTGG-TTGGATTCTTGAATTCTGAAGTGACTTTCAGCTC 979908 v i - -i i ---- vi i i vv i MIR3#SINE/MIR 140 AATGAGG-GGGTTGGACTAGAT----GATCTCTAAGGTCCCTTCCAGCTC 184 chr2qtel1M 979909 T-ACATCTCATGACTTT 979924 - iii i i MIR3#SINE/MIR 185 TGACATTCTATGATTCT 201 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.77 CpG sites = 17, Kimura (unadjusted) = 29.77 Transitions / transversions = 2.43 (17/7) Gap_init rate = 0.10 (10 / 105), avg. gap size = 1.60 (16 / 10) 212 30.45 9.32 4.14 chr2qtel1M 982587 982747 (17253) MIR#SINE/MIR 48 216 (46) m_b108s601i10 3948 chr2qtel1M 982587 CTGGGTGTGAATTCC-----TGTCTC-----AACTATAGGACTTTGGCTC 982626 vi i ----- i v ----- i i iv i v- MIR#SINE/MIR 48 CTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGG-C 96 chr2qtel1M 982627 AAGTTCCTCTATCT-TCTGAGCT--GGTGGCCTGAGTTGTGAAAGTAGTG 982673 v iv i - v i--i vv v vi i - i v MIR#SINE/MIR 97 AAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAA-TGGGG 145 chr2qtel1M 982674 ACAGTGAAAGTATTCTGTGTTGTCACAAGTTTATTGTGAGGATTCAATAT 982723 i i i v i- iiv --- i i v i v iv MIR#SINE/MIR 146 ATAATAATAGTAC-CTACCT---CATAGGGTTGTTGTGAGGATTAAATGA 191 chr2qtel1M 982724 ATTTGTGCTTG--AAGCCCATTAGAA 982747 i vi i v -- v - MIR#SINE/MIR 192 GTTAATACATGTAAAGCGC-TTAGAA 216 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.15 CpG sites = 27, Kimura (unadjusted) = 40.27 Transitions / transversions = 1.35 (27/20) Gap_init rate = 0.07 (12 / 160), avg. gap size = 1.83 (22 / 12) 49 2.22 0.00 0.00 chr2qtel1M 982849 982894 (17106) (GT)n#Simple_repeat 1 46 (0) c_b108s251i2 3949 chr2qtel1M 982849 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGTGT 982894 i (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 46 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 413 22.63 8.91 3.77 chr2qtel1M 985241 985442 (14558) C L3#LINE/CR1 (775) 3324 3113 m_b108s601i11 3950 chr2qtel1M 985241 TTCATTTT-CTGATATTAGGCCCAGGTCTCTTC--CCTG--GAGGATTCT 985285 i -i i - v -- vi i -- -- - i? C L3#LINE/CR1 3324 TTCATCTTGTTGGT-TTCGGCCCA--TCGTTCCAGCCTGTCGAG-ATCNT 3279 chr2qtel1M 985286 TTATAATCCTGA--CTGTCATCCAAT-TATTCATT--CTCTCCCAGCTTT 985330 vv i -- ?i- vii -- i C L3#LINE/CR1 3278 TTTGAATCTTGATTCTGTCATCCANCGTATTAGCTATCCCTCCCAGCTTT 3229 chr2qtel1M 985331 GCTTTGTCAG-AAATATAGTTGAGTA--CTCTCTCTGCCTTCATGATCAA 985377 iv ii v - v - v i i -- ii v i --i C L3#LINE/CR1 3228 GTGTCATCTGCAAATTT-GATAAGCATGCCTTCTATGTCTTCAT--CCAA 3182 chr2qtel1M 985378 GTCATTGG-AAAAATCTTAAACAGCCCAGGAGCAAGCACCCAGCCCT--- 985423 i- v i vv iv v vv --- C L3#LINE/CR1 3181 GTCATTGATAAAAATGTTGAACAGGACAGGGCCAAGGACAGAGCCCTGTG 3132 chr2qtel1M 985424 -CATCTCTCCCAGAGACCTC 985442 - - v iv i C L3#LINE/CR1 3131 GCA-CGCCACTAGAGACCTC 3113 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.05 CpG sites = 25, Kimura (unadjusted) = 27.78 Transitions / transversions = 1.32 (25/19) Gap_init rate = 0.09 (19 / 201), avg. gap size = 1.37 (26 / 19) 379 24.37 2.78 8.82 chr2qtel1M 989347 989454 (10546) MIRc#SINE/MIR 26 127 (141) m_b108s601i12 3951 chr2qtel1M 989347 AACACCAGCCCTGAAGTCTGGAGGACCTGAGTTCAAATCTGGCCTCAGAC 989396 i ii v i i v i i i i iv v v v MIRc#SINE/MIR 26 AGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCC 75 chr2qtel1M 989397 ATTTAACATTTCTTATCTATGTAACCCTGGGCAAGTCACTTAA---CTCC 989443 i -------i v i i i --- i MIRc#SINE/MIR 76 ACTTA-------CTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCT 118 chr2qtel1M 989444 AATTGCCTCAG 989454 i -- MIRc#SINE/MIR 119 GA--GCCTCAG 127 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.02 CpG sites = 17, Kimura (unadjusted) = 30.55 Transitions / transversions = 2.43 (17/7) Gap_init rate = 0.09 (10 / 107), avg. gap size = 1.20 (12 / 10) 23 3.71 0.00 0.00 chr2qtel1M 989456 989483 (10517) (A)n#Simple_repeat 1 28 (0) m_b108s252i8 3952 chr2qtel1M 989456 AAAAAAGAAAAAAAAAAAAAAAAAAAAA 989483 i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA 28 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 17 12.68 0.00 0.00 chr2qtel1M 989501 989526 (10474) (T)n#Simple_repeat 1 26 (0) m_b108s252i9 3953 chr2qtel1M 989501 TTTGTTTTTCTTTTTTTTTCTTTTTT 989526 v i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 16 12.17 5.56 0.00 chr2qtel1M 989712 989747 (10253) (AAATGA)n#Simple_repeat 1 38 (0) m_b108s252i10 3954 chr2qtel1M 989712 AAAGGAAAA--AAAATGAAAAAGAAAATGAAATTCAAA 989747 v -- v v v (AAATGA)n#Sim 1 AAATGAAAATGAAAATGAAAATGAAAATGAAAATGAAA 38 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.03 (1 / 35), avg. gap size = 2.00 (2 / 1) 12 32.88 0.00 0.00 chr2qtel1M 989717 989765 (10235) (AAA)n#Simple_repeat 1 49 (0) m_b108s252i11 3954 chr2qtel1M 989717 AAAAAAAATGAAAAAGAAAATGAAATTCAAACCAACAACAACAAAAAAA 989765 vi i vi vvv vv v v v (AAA)n#Simple 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 49 Matrix = Unknown Transitions / transversions = 0.30 (3/10) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 380 33.33 1.30 1.30 chr2qtel1M 989931 990161 (9839) C L1ME4c_3end#LINE/L1 (191) 639 409 m_b108s551i4 3955 chr2qtel1M 989931 TTCTGCTCATTTCACTCAGCATCAGTTCATGTAGATCTCTCCAGGCCTCT 989980 iv i i i vv iv v i - v iiv C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATAAACATTT-TCCATGTTGCT 591 chr2qtel1M 989981 CTGAAATCATCCTGCCGATCGTTTCTTATAGAACAATAATATTACATCAC 990030 viiv i v v iviv i i v i vvvv v iv C L1ME4c_3end#L 590 ACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCGA 541 chr2qtel1M 990031 ATTCATAAACTATAACTTACTCAATCATTCTCCAATTCATGGGGATTCAC 990080 i ?v iv i i i i i v vv iv i v C L1ME4c_3end#L 540 GTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAG 491 chr2qtel1M 990081 TCAGTTCCCAGTTTCTTGCTACTACAAA-AGGGTTCCAATACATATTTTT 990129 viv i i i i i i - iv i v iv i i i C L1ME4c_3end#L 490 GTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTC 441 chr2qtel1M 990130 GTACATGTGAGTCGTTTTCCCTCCTTT--ATTAT 990161 i i - - v i i -- C L1ME4c_3end#L 440 GTGCATAT-AG-CTTTTTCCTTCTTTTGAATTAT 409 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 43.29 CpG sites = 43, Kimura (unadjusted) = 45.73 Transitions / transversions = 1.30 (43/33) Gap_init rate = 0.02 (5 / 230), avg. gap size = 1.20 (6 / 5) 219 20.30 10.74 6.35 chr2qtel1M 990820 990940 (9060) MIR3#SINE/MIR 81 206 (2) m_b108s601i13 3956 chr2qtel1M 990820 GCGGTGTCGAGTTTTGAGCAAATCCCTTC-----TCTG--CTTGAGTTTG 990862 v - -ii i i v ----- -- i v v MIR3#SINE/MIR 81 GCTGTGT-GA-CCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTC 128 chr2qtel1M 990863 CTC--CTGTAAATTGGAGAGGGTTGG-TTGGATTCTTGAATTTTGAAGTG 990909 -- v - i -i i ---- vi i i i v MIR3#SINE/MIR 129 CTCATCTGTAAAATG-AGGGGGTTGGACTAGAT----GATCTCTAAGGTC 173 chr2qtel1M 990910 ACTTTCAGCTCT-AT-TTCTCATGATTTT-TGAT 990940 v i - i- - i - MIR3#SINE/MIR 174 CCTTCCAGCTCTGACATTCT-ATGATTCTATGAT 206 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 24.31 CpG sites = 15, Kimura (unadjusted) = 24.31 Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.12 (15 / 120), avg. gap size = 1.40 (21 / 15) 203 31.56 8.64 4.14 chr2qtel1M 994543 994704 (5296) MIR#SINE/MIR 48 216 (46) m_b108s601i15 3957 chr2qtel1M 994543 CTGGGTGTGAATTCCAGTCTCAGCTGCT-----GCTTTTGGA-----GAC 994582 vi i i - v ii ----- v vv ----- i MIR#SINE/MIR 48 CTGGGTTCGAATCCCGG-CTCTGCCACTTACTAGCTGTGTGACCTTGGGC 96 chr2qtel1M 994583 AAGTTCCTCAACCCCT--GTGGAATAATGTCCTGAATTGGGCTTATACTG 994630 v i i -- vvvi i v v vi ---- v v MIR#SINE/MIR 97 AAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTG----TAAAATG 142 chr2qtel1M 994631 GGAATGAAAGTATTCTGTGTTATCACAGATTTATTGTGAGGATTGAATTT 994680 i i v i v viv iii- i iv i i vv MIR#SINE/MIR 143 GGGATAATAATAGTACCTACC-TCATAGGGTTGTTGTGAGGATTAAATGA 191 chr2qtel1M 994681 ATTTGTGCTTG--AAGCCCATTAGAA 994704 i vi i v -- v - MIR#SINE/MIR 192 GTTAATACATGTAAAGCGC-TTAGAA 216 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.54 CpG sites = 25, Kimura (unadjusted) = 41.71 Transitions / transversions = 1.04 (25/24) Gap_init rate = 0.07 (11 / 161), avg. gap size = 1.91 (21 / 11) 204 30.66 8.82 6.47 chr2qtel1M 994543 994678 (5322) MIRb#SINE/MIR 55 193 (75) m_b108s601i14 3957 chr2qtel1M 994543 CTGGGTGTGAATTCCAGTCTCAGCTGCT-----GCTTTTGGA-----GAC 994582 vi i i - v ii ----- v vv ----- i MIRb#SINE/MIR 55 CTGGGTTCGAATCCCGG-CTCTGCCACTTACTAGCTGTGTGACCTTGGGC 103 chr2qtel1M 994583 AAGTTCCTCAACCCCTGTGGAA--TAATGTCCTGAATTGGGCTTATACTG 994630 v i i v iiv--i i v v vi ---- v v MIRb#SINE/MIR 104 AAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTG----TAAAATG 149 chr2qtel1M 994631 GGAATGAAAGTATTCTGTGTTATCACAGATTTATTGTGAGGATTGAAT 994678 i i v i -i i---iv i iv i i MIRb#SINE/MIR 150 GGGATAATAATA-CCTA---CCTCGCAGGGTTGTTGTGAGGATTAAAT 193 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.76 CpG sites = 23, Kimura (unadjusted) = 40.75 Transitions / transversions = 1.44 (23/16) Gap_init rate = 0.09 (12 / 135), avg. gap size = 1.75 (21 / 12) 22 0.00 3.70 0.00 chr2qtel1M 994831 994857 (5143) (GT)n#Simple_repeat 1 28 (0) m_b108s252i12 3958 chr2qtel1M 994831 GTGTGTGTGTGTGTGTGTGTGTG-GTGT 994857 - (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGT 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.04 (1 / 26), avg. gap size = 1.00 (1 / 1) 242 39.46 4.86 0.00 chr2qtel1M 998308 998492 (1508) L2#LINE/L2 2393 2586 (496) m_b108s601i16 3959 chr2qtel1M 998308 CAAATAGCTACCAGACATTTTGAATTAGATAGCCAATGGGCATCTGAAAC 998357 v iv iv i iv v i iv i i v L2#LINE/L2 2393 CAACTGCCTACTCGACATCTCCACTTGGATGTCTAATAGGCATCTCAAAC 2442 chr2qtel1M 998358 TCATCATATCCAGAACAAAATCTATTATCTTTCC---CAGATC-ATTCCC 998403 i v i i vi iiiv v i --- i i -ii i L2#LINE/L2 2443 TTAACATGTCCAAAACTGAACTCCTGATCTTCCCCCTCAAACCTGCTCCT 2492 chr2qtel1M 998404 TCTTCCATATTCC----CTTACTTGA-GGTACCATCACTCCTCCAGTCAC 998448 i iv vi v ---- i v ?i - i v vi ii i ii L2#LINE/L2 2493 CCCGCAGTCTTCCCCATCTCAGTNAATGGCAACTCCATCCTTCCAGTTGC 2542 chr2qtel1M 998449 CAAAATTCATAACCCCCATTTTATTCTTAATTCTGCATTATCTC 998492 iv iiiiv v iivivv i i i i iv vi v L2#LINE/L2 2543 TCAGGCCAAAAACCTTGGAGTCATCCTTGACTCCTCTCTTTCTC 2586 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 59.72 CpG sites = 47, Kimura (unadjusted) = 61.11 Transitions / transversions = 1.81 (47/26) Gap_init rate = 0.02 (4 / 184), avg. gap size = 2.25 (9 / 4) 331 32.29 5.49 3.31 chr2qtel1M 999314 999550 (450) C L3#LINE/CR1 (771) 3328 3087 m_b108s601i17 3960 chr2qtel1M 999314 AAACTTCATCTTAT-GATATTAAGGCCAGGTCTCTCCA--CTGTGAGGAT 999360 i i - i - vi v -- vi -- vii C L3#LINE/CR1 3328 AAATTTCATCTTGTTGGT-TTCGGCCCA--TCGTTCCAGCCTGTCGAGAT 3282 chr2qtel1M 999361 TTGTTTTCATCCTGACTCTTGTCATCCA----ATTCCTCTTTTCCCCCAA 999406 i?v vv i i - ---- vviiv ii i i C L3#LINE/CR1 3281 CNTTTTGAATCTTGATTCT-GTCATCCANCGTATTAGCTATCCCTCCCAG 3233 chr2qtel1M 999407 TTTTGCTTTGTCAG-AGATGTTGTTGATTGGGCTCTCTTTCTCTTCATGC 999455 i iv ii v - i - v i viiv ii v v v C L3#LINE/CR1 3232 CTTTGTGTCATCTGCAAAT-TTGATAAGCATGCCTTCTATGTCTTCATCC 3184 chr2qtel1M 999456 TGAAGCCACTGGCAAAC-TCTTAAACAGCTCAGGATTGAGCACCCAGCCC 999504 -- i i ii v- v i vv iiii v vv C L3#LINE/CR1 3183 --AAGTCATTGATAAAAATGTTGAACAGGACAGGGCCAAGGACAGAGCCC 3136 chr2qtel1M 999505 ATAT----CTCTCCCAGAGACCTCCTGGTATGTTGGCATTGAACAATTAA 999550 - i ---- v iv i ivvi v i i v v C L3#LINE/CR1 3135 -TGTGGCACGCCACTAGAGACCTCCCTCCAGGTTGACATCGATCCATTAA 3087 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 41.42 CpG sites = 42, Kimura (unadjusted) = 43.78 Transitions / transversions = 1.31 (42/32) Gap_init rate = 0.06 (14 / 236), avg. gap size = 1.50 (21 / 14) 291 33.00 10.92 4.84 chr3ptel1M 40 332 (999668) C L2#LINE/L2 (475) 2607 2298 m_b109s601i0 3961 chr3ptel1M 40 TGAATTGAATGTTTATATTTAATGAGGAGAATGGGAAGTTAAAGAGAACT 89 i i vvi-i v i - i ii - i i i i vi C L2#LINE/L2 2607 TGGATTGGATGTGGG-GTGTGA-GAGAAAGA-GAGGAGTCAAGGATGACT 2561 chr3ptel1M 90 CCTAGGGTGCAAATATGAATGACCATAAGGATGG---------TAACAAA 130 v v viviiiv iii iiv --------- ? vi C L2#LINE/L2 2560 CCAAGGTTTTTGGCCTGAGCAACTGGAAGGATGGAGTTGCCATTNACTGA 2511 chr3ptel1M 131 AATAGGTAAG--TACAGAGGGCAATTAGGTTTTCAGCAAAGTAAAAT--- 175 i i v -- i i ii -- vi --- viii v i --- C L2#LINE/L2 2510 GATGGGGAAGACTGCGGGAGG--AGCAGGTTT---GAGGGGGAAGATCAG 2466 chr3ptel1M 176 GATATCTGTTT--AACATATTGGGTTTGGGTTGTCTACAAGTAGACA--C 221 vv v --i i ii i v i i--- -- C L2#LINE/L2 2465 GAGTTCAGTTTTGGACATGTTAAGTTTGAGATGCCTAT---TAGACATCC 2419 chr3ptel1M 222 AGTTCAAATTACCCAACAGGCAGTTGTTAATCTAGAAG--TGGAGCTCAG 269 iv vi iv ii v ii --i v vi -- i C L2#LINE/L2 2418 AAGTGGAGATGTCGAGTAGGCAGTTG--GATATACGAGTCTGGAGTTCAG 2371 chr3ptel1M 270 GAGAGAGTCTCAGGC--------TAACTTTT---ATCGTCTG-ATGAGAG 307 i vii i -------- v v---i i v - - v C L2#LINE/L2 2370 GGGAGAGGTCCGGGCTGGAGATATAAATTTGGGAGTCATCAGCAT-ATAG 2322 chr3ptel1M 308 ATGATAATTGAATCCATGGAAACTG 332 i v i v - i C L2#LINE/L2 2321 ATGGTATTTAAAGCCAT-GAGACTG 2298 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 44.24 CpG sites = 60, Kimura (unadjusted) = 46.35 Transitions / transversions = 1.88 (60/32) Gap_init rate = 0.08 (24 / 292), avg. gap size = 1.96 (47 / 24) 56 0.00 0.00 0.00 chr3ptel1M 343 390 (999610) (TA)n#Simple_repeat 1 48 (0) c_b109s251i0 3962 chr3ptel1M 343 TATATATATATATATATATATATATATATATATATATATATATATATA 390 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATA 48 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 418 19.66 8.94 0.75 chr3ptel1M 895 1017 (998983) Charlie4#DNA/hAT-Charlie 3231 3363 (15) m_b109s502i0 3963 chr3ptel1M 895 TGATCATTAAATTTCCATATAATTAATTTCCTTTGTAATCCAACATATTT 944 v i v v ii v ii Charlie4#DNA/ 3231 TGATAACTATATTTCAATATAATTGGTTTCCTTTGTAATCCTATGTATTT 3280 chr3ptel1M 945 TATTTTATATATTTTATAAACTTCATTCTGAGAAA-----CAT---TTTC 986 ii - v v i i----- ---i Charlie4#DNA/ 3281 TATTTTATGCA-TTTAAAAACATTATTCTGAGAAGGGGTCCATAGGCTTC 3329 chr3ptel1M 987 -CCTGATTTCC--AGAGGTCCATGATGTAAAAAA 1017 - v i v -- i iiii Charlie4#DNA/ 3330 ACCAGACTGCCAAAGGGGTCCATGGCACAAAAAA 3363 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 23.38 CpG sites = 16, Kimura (unadjusted) = 23.38 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.04 (5 / 122), avg. gap size = 2.40 (12 / 5) 12 20.98 5.33 6.76 chr3ptel1M 1968 2042 (997958) (CAGTCT)n#Simple_repeat 1 74 (0) m_b109s252i0 3964 chr3ptel1M 1968 CAGTCTCAATCT--GACCCAGTCTCCTTCAGCAGTCTGATAGCCTGACAG 2015 i -- v i vv -v --i i -- (CAGTCT)n#Sim 1 CAGTCTCAGTCTCAGTCTCAGTCTCAGTC-TCAGTCT--CAGTCT--CAG 45 chr3ptel1M 2016 TCTTA-AC-CAGTCTCAGTTTGAGTCTCA 2042 i -v - i v (CAGTCT)n#Sim 46 TCTCAGTCTCAGTCTCAGTCTCAGTCTCA 74 Matrix = Unknown Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.11 (8 / 74), avg. gap size = 1.12 (9 / 8) 14 19.17 0.00 2.70 chr3ptel1M 3547 3584 (996416) (CAAAAA)n#Simple_repeat 1 37 (0) m_b109s252i1 3965 chr3ptel1M 3547 CAAAAACAAATACAACCTAAAAAAACTCAAACAAAAAC 3584 v -vv v vv (CAAAAA)n#Sim 1 CAAAAACAAAAACAA-AAACAAAAACAAAAACAAAAAC 37 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 14 33.38 0.00 0.00 chr3ptel1M 5712 5767 (994233) (AAA)n#Simple_repeat 1 56 (0) m_b109s252i2 3966 chr3ptel1M 5712 AAAAGAGAAAATAAAGAAAAATCCCCTTAAAAAAAAAAAAAAACAAACAA 5761 i i v i vvvvvvv v v (AAA)n#Simple 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr3ptel1M 5762 TAACAA 5767 v v (AAA)n#Simple 51 AAAAAA 56 Matrix = Unknown Transitions / transversions = 0.25 (3/12) Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0) 13 25.65 0.00 4.17 chr3ptel1M 6193 6242 (993758) (AAAAGC)n#Simple_repeat 1 48 (0) m_b109s252i3 3967 chr3ptel1M 6193 AATAGAAAAACACACAAGCAAAAAGTAAAAAAAAAAAGAAAGGCAAAAGC 6242 v v -i v - i iv iv i (AAAAGC)n#Sim 1 AAAAGCAAAA-GCAAAAGC-AAAAGCAAAAGCAAAAGCAAAAGCAAAAGC 48 Matrix = Unknown Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.04 (2 / 49), avg. gap size = 1.00 (2 / 2) 15 15.61 2.78 0.00 chr3ptel1M 6198 6233 (993767) (AAAAAGA)n#Simple_repeat 1 37 (0) m_b109s252i4 3967 chr3ptel1M 6198 AAAAACACACAAGCAAAAAGTAAAAA-AAAAAAGAAA 6233 v v v v v - (AAAAAGA)n#Si 1 AAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAA 37 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) 259 28.29 10.28 1.00 chr3ptel1M 6760 7216 (992784) L1M5_orf2#LINE/L1 2791 3289 (5) m_b109s551i0 3968 chr3ptel1M 6760 CTGTTTGATAAAAATTGCTGGGAAAATTGGAAA-CTAAATGGCAGAAACT 6808 v ii i viv i v v - i v v i v L1M5_orf2#LIN 2791 CTTTTCAACAAATGGTGCTGGAACAATTGGATATCCATATGGAAAAAAAT 2840 chr3ptel1M 6809 GG-CATTGATCA--ACTTAAC-CCTTA-ACCAAGATAAGGTCAAAAATGG 6853 i-?v i i v-- i v - v - v i v iv ? i - L1M5_orf2#LIN 2841 GAANCTCGACCCCTACCTCACACCATACACAAAAATTAATTCNAGA-TGG 2889 chr3ptel1M 6854 TTCAT-GACC---AGGTAAAA-ATAAAATTTTAAAAATT-----AGGGAA 6893 v - --- v -? i v v ----- ii L1M5_orf2#LIN 2890 ATCATAGACCTAAATGTAAAAGNTAAAACTATAAAACTTCTAGAAGAAAA 2939 chr3ptel1M 6894 CATAGGATATTTACCTCTCGACCTGTGGA-AGGGAAGGTCTTTATAAAAA 6942 v v vv i vi vv ?- v i vi iv v L1M5_orf2#LIN 2940 CATAGGAGAATATCTTCGTGACCTTGGGNTAGGCAAAGATTTCTTAAACA 2989 chr3ptel1M 6943 AGA-ACAGAA----TCAACGATCAAAAA------TGA-AAATTTTATTAT 6980 i - i ----i? v v i ------ - vv i ?i L1M5_orf2#LIN 2990 GGACACAAAAAGCACNAACCATAAAAGAAAAAATTGATAAATTGGACTNC 3039 chr3ptel1M 6981 ACCAAACTGAAAAATTTTTG----TCAAAACAAAACAATAACAAA-TTAG 7025 i v v i i ---- v v v iv v - v i L1M5_orf2#LIN 3040 ATCAAAATTAAAAACTTCTGCTCNTCAAAAGACACCGTTAAGAAAATGAA 3089 chr3ptel1M 7026 AAGGGAAG--AAAAACTGG---AAAATATTTTTAAT-CAAAGGTTCATAA 7069 v -- v i ? --- vi ?- v vi iiivv L1M5_orf2#LIN 3090 AAGGCAAGCCACAGANTGGGAGAAAATATTTGCAANACATATATCTGACA 3139 chr3ptel1M 7070 AAGGCCTCATTTTCAAAATATA---AGAATTAACTCTAATTTA-TAAAAA 7115 v i v i i --- i v- vi ? i - ? L1M5_orf2#LIN 3140 AAGGACTCGTATCCAGAATATATAAAGAACTC-CTACAANTCAATAANAA 3188 chr3ptel1M 7116 ATCAAAACCATTC-TCCAATTGAAAAATGGTCAAAGGGAGATAAACAGAA 7164 -- i v viv-i v? v i - vv i v L1M5_orf2#LIN 3189 A--AAGACAAACAACCCAATANAAAAATGGGCAAAAG-ACTTGAACAGAC 3235 chr3ptel1M 7165 A-TTCTCAGATGAAAA-ATTGAAACTATTTCTAGTCATATGAAAAGATGT 7212 - v i v i - ?v iviiivv iv i i L1M5_orf2#LIN 3236 ACTTCACAAAAGAAGATATNCAAATGGCCAATAAGCACATGAAAAGATGC 3285 chr3ptel1M 7213 CCAA 7216 i L1M5_orf2#LIN 3286 TCAA 3289 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.05 CpG sites = 60, Kimura (unadjusted) = 37.11 Transitions / transversions = 0.88 (60/68) Gap_init rate = 0.06 (29 / 456), avg. gap size = 1.79 (52 / 29) 280 25.25 13.47 4.01 chr3ptel1M 7081 7377 (992623) L1MC3_3end#LINE/L1 7 330 (2202) m_b109s551i1 3968 chr3ptel1M 7081 TTCAAAATATAAGAATTAACTCT---AATTTA----TAAAAAATCAAAAC 7123 i vi v- --- i i ---- i v -- L1MC3_3end#LI 7 TCCAAAATATACAAAG-AACTCTTAAAACTCAACAATAAGAAAACAAA-- 53 chr3ptel1M 7124 CATTCTCCAATTGAAAAATGGTCAAAGGGAGATAAACAGAAATTCTCA-- 7171 --vi i v i - vv i v i- -- L1MC3_3end#LI 54 CA--ACCCAATTAAAAAATGGGCAAAAG-ATCTGAACAGACAC-CTCACC 99 chr3ptel1M 7172 ------GATG-AAAAATTGAAACTATTTCTAGTCATATGAAAAGATGTCC 7214 ------ i- v i v v v ----- - ii L1MC3_3end#LI 100 AAAGAAGATATACAGATGGCAAATA-----AG-CATATGAAAAGATGCTC 143 chr3ptel1M 7215 AA----GTTTATTAACAGAGAAAT-CAAATTAAGACAACTCTAAG-TACT 7258 ----i i i vi i v - i vv i - i L1MC3_3end#LI 144 AACATCATTTGTCATTAGGGAATTGCAAATTAAAACAACAATGAGATACC 193 chr3ptel1M 7259 A----ACACC--TTCGATTGGCTAAGACAGGAAAAA--AATAAT----GA 7296 ---- -- v v i ivvi --i i ----i? L1MC3_3end#LI 194 ACTACACACCTATTAGAATGGCTAAAATCCAAAAAACTGACAATACCAAN 243 chr3ptel1M 7297 TGTTTTGGGGGATGGGAAAAAACTGG--CT-TGATGCATTGTTGGT-GGA 7342 i vvv i v i iv v -- - v v i - L1MC3_3end#LI 244 TGCTGGCGAGGATGCGGAGCAACAGGAACTCTCATTCATTGCTGGTGGGA 293 chr3ptel1M 7343 GTTT-GAACAATCCAACCATTTTGGAAG-TAGTTTGG 7377 i vi-i iii v i i -i L1MC3_3end#LI 294 ATGCAAAATGGTACAGCCACTTTGGAAGACAGTTTGG 330 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 31.73 CpG sites = 42, Kimura (unadjusted) = 31.73 Transitions / transversions = 1.40 (42/30) Gap_init rate = 0.10 (30 / 296), avg. gap size = 1.77 (53 / 30) 842 27.08 10.15 2.58 chr3ptel1M 7128 7669 (992331) L1ME5_3end#LINE/L1 56 637 (304) m_b109s551i2 3968 chr3ptel1M 7128 CTCCAATTGAAAAATGGTCAAAGGGAGATAAACAGA-AATTCTCAGATGA 7176 i v v - v i i- iv v L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGG-ATATGAACAGGCAATTTACAGAAGA 104 chr3ptel1M 7177 --AAAATTGAAA--CTATTTCTAGTCATATGAAAAGATGTCCAAGTTTAT 7222 -- vii -- v-- v - i ii ii i L1ME5_3end#LI 105 GGAAACCCGAAAGGCTAA--CAAG-CATATGAAGAGATGCTCAAACTCAT 151 chr3ptel1M 7223 TAA----CAGAGAAAT-CAAATTAAGACAACTCTAAG-TACTA----ACA 7262 i---- - i vv i - ii ---- L1ME5_3end#LI 152 TAGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACA 201 chr3ptel1M 7263 CCT--TCGATTGGCTAAGACAGGAAAA--AAATAATG--ATGTTTTGG-- 7304 -- v i v i ivi i--ii -- v v -- L1ME5_3end#LI 202 CCTATTAGACTGGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTGGCG 251 chr3ptel1M 7305 GGGATGGGAAAAAACTGG---CTTGATGCATTGTTGGTGG-AGTTTGAAC 7350 i v iii ? iv --- i v i i - v ii L1ME5_3end#LI 252 AGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGAC 301 chr3ptel1M 7351 -AATCCAACCATTTTGGA-AGTAGTTTGGAACTA-TTA---AAAGTTATC 7394 -ii v i i - i i i v v - --- v v vi L1ME5_3end#LI 302 TGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTAAGT 351 chr3ptel1M 7395 AAACTTGCATACCC---GTCCAAGT-------TTACTGGGATTATATCCC 7434 v -- --- v v i-------i v vv L1ME5_3end#LI 352 ATAC--GCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATATCCC 399 chr3ptel1M 7435 AAAGAA-TTATAAAA-AGG-----AAAGGGACCTGTATGTGCACGAATGT 7477 - v v v - ----- i ---- i iv i L1ME5_3end#LI 400 AAAGAAATTCTCACACAGGTCCATAAGGGGAC----ATGTACGAGGATGT 445 chr3ptel1M 7478 TTGTGGCAGCCCTTTTTGTAGTGGCTAGAAACTGGAAACTGAATGGATGT 7527 ii v vi v i vi i ii ii vivv i L1ME5_3end#LI 446 TCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGGGTGT 495 chr3ptel1M 7528 CCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATATGAAAATTATGGA 7577 v v i v iii v iv v v ii L1ME5_3end#LI 496 CCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACACCATGGA 545 chr3ptel1M 7578 ATATTACTGT-TCTGTAAGAAATGACCAACAGGATGATTTCAGAAAG--G 7624 i i - i-v v v iii vi vi -- v v v --i L1ME5_3end#LI 546 GTACTA-TGCAGCAGTTAGAAGCAACGGACTAGATG--TACACATAGCAA 592 chr3ptel1M 7625 CCTGGAGAGA-CTTACACGAAC-TGATGCTGAGTGAAATGAGCAGGA 7669 v vi - v -- - ii vi i i L1ME5_3end#LI 593 CATGGATGGATCTTAAA--AACATAGTGCTGAGTGAAAAAAGTAAGA 637 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 33.91 CpG sites = 82, Kimura (unadjusted) = 34.51 Transitions / transversions = 1.34 (82/61) Gap_init rate = 0.08 (41 / 541), avg. gap size = 1.71 (70 / 41) 17 6.12 5.56 2.70 chr3ptel1M 8093 8128 (991872) (AAATAA)n#Simple_repeat 1 37 (0) m_b109s252i6 3969 chr3ptel1M 8093 AAATAAAAGGTATAAAT-AAAA-AAAAATAAAAATAAA 8128 -i v - - (AAATAA)n#Sim 1 AAATAAAA-ATAAAAATAAAAATAAAAATAAAAATAAA 37 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.09 (3 / 35), avg. gap size = 1.00 (3 / 3) 27 0.00 2.56 2.56 chr3ptel1M 8501 8539 (991461) (AAAG)n#Simple_repeat 1 39 (0) m_b109s252i7 3970 chr3ptel1M 8501 AAAGAAAGAAAGAAAGAAA-AAAGAAAGAAAGAAAAGAAA 8539 - - (AAAG)n#Simpl 1 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG-AAAGAAA 39 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2) 21 24.86 0.00 0.00 chr3ptel1M 8501 8545 (991455) (A)n#Simple_repeat 1 45 (0) m_b109s252i8 3971 chr3ptel1M 8501 AAAGAAAGAAAGAAAGAAAAAAGAAAGAAAGAAAAGAAAAACAAA 8545 i i i i i i i i v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 45 Matrix = Unknown Transitions / transversions = 8.00 (8/1) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 11 24.79 0.00 0.00 chr3ptel1M 8532 8565 (991435) (AAAACC)n#Simple_repeat 1 34 (0) m_b109s252i9 3971 chr3ptel1M 8532 AAAAGAAAAACAAATCCCAAACCCACAACCAAAA 8565 vv v vv v v (AAAACC)n#Sim 1 AAAACCAAAACCAAAACCAAAACCAAAACCAAAA 34 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 17 17.24 0.00 2.50 chr3ptel1M 10569 10609 (989391) (CAATACA)n#Simple_repeat 1 40 (0) m_b109s252i10 3972 chr3ptel1M 10569 CAATTACACAATTCACAATGCACAATGCACAAAATACATTA 10609 - v i i v i v (CAATACA)n#Si 1 CAA-TACACAATACACAATACACAATACACAATACACAATA 40 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 331 32.37 3.64 1.19 chr3ptel1M 10932 11178 (988822) C L1MC_orf2#LINE/L1 (1464) 1830 1578 m_b109s551i3 3973 chr3ptel1M 10932 GTGTTTTATCTTGTTAAAAGCCTTTTCTGCATCTATTGATATAGTTATAT 10981 vv i i v i ii i i C L1MC_orf2#LIN 1830 GTGTTGGATTTTGTCAAATGCTTTTTCTGCATCTATTGATATGATCATGT 1781 chr3ptel1M 10982 GATTTTGGGTTCTTAGC--ATTATTTTCATTATTTTCA-TAAT---TCTC 11025 vvv ii --i iv v v viv v - --- i i C L1MC_orf2#LIN 1780 GATTTTTCTTCTTTAGCCTGTTGATGTGATGGATTACATTAATTGATTTT 1731 chr3ptel1M 11026 CTAATTTTAAAGCAAC--TACATTTTTTTTTTATAAAATCCAATCTGGCT 11073 v v i v i -- i -- vii vvv - v ii ii C L1MC_orf2#LIN 1730 CGAATGTTGAACCAGCCTTGCA--TACCTGGGAT-AAATCCCACTTGGTC 1684 chr3ptel1M 11074 GTAATGTATAATATTTATGATTTGTTGCTGTACTCTCCTTGCTAATATTT 11123 ii vi v v vii i v i vvi C L1MC_orf2#LIN 1683 GTGGTGTATAATTCTTTTTATACATTGTTGGATTCGATTTGCTAATATTT 1634 chr3ptel1M 11124 TATTTGAAATATTTAT-TCAGTTTTCACTCAAGATGCTAATCTGTAATTT 11172 i viii v ii- vi v ivvi ii ii i C L1MC_orf2#LIN 1633 TGTTGAGGATTTTTGCATCTATGTTCATGAGAGATATTGGTCTGTAGTTT 1584 chr3ptel1M 11173 TCTCTT 11178 i C L1MC_orf2#LIN 1583 TCTTTT 1578 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 43.04 CpG sites = 46, Kimura (unadjusted) = 43.79 Transitions / transversions = 1.39 (46/33) Gap_init rate = 0.03 (8 / 246), avg. gap size = 1.50 (12 / 8) 47 5.89 0.00 0.00 chr3ptel1M 12120 12173 (987827) (AT)n#Simple_repeat 1 54 (0) c_b109s251i1 3974 chr3ptel1M 12120 ATATACATACATATATATATATATATATATATATATATATATACATATAT 12169 i i i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr3ptel1M 12170 ATAT 12173 (AT)n#Simple_ 51 ATAT 54 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 229 14.72 1.43 2.90 chr3ptel1M 12214 12283 (987717) Tigger2#DNA/TcMar-Tigger 205 273 (2445) m_b109s502i1 3975 chr3ptel1M 12214 CCATTTTATCATTTACTATCA-AAAGTACTATCATACATATATTATAAAC 12262 i i - i - - i v v v Tigger2#DNA/T 205 CTATTTTATCATTTACTACCATAAAATA-TA-CACAAATCTATTATAAAA 252 chr3ptel1M 12263 AGTTAAATTTTCTTAAAACTT 12283 v v i Tigger2#DNA/T 253 AGTTAAAATTTATCAAAACTT 273 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 16.44 CpG sites = 5, Kimura (unadjusted) = 16.44 Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.04 (3 / 69), avg. gap size = 1.00 (3 / 3) 334 29.13 3.88 0.00 chr3ptel1M 12409 12511 (987489) Tigger2#DNA/TcMar-Tigger 784 890 (1828) m_b109s502i2 3976 chr3ptel1M 12409 AGAAGGAAATTTATGAAGTAGTTGCTGCAGCTGTACCAGAAAGAGC--AA 12456 i ii iv i iii v i v -- Tigger2#DNA/T 784 AAAAGGAAATTCGTGAAGCCGTCGCTGCAGCTACGCCAGCAGGCGCGAAA 833 chr3ptel1M 12457 ATTTTGCAG--TGTGCAAGATATTACTCTATCTTGCTTAGAAATTGCAAA 12504 ii v-- v i i iivi i i iv v v iv Tigger2#DNA/T 834 ACCTTGCACTTTTTGCGAAATACCTTTTTATCTCGTATTGAAAATGCAGC 883 chr3ptel1M 12505 TTTTATG 12511 Tigger2#DNA/T 884 TTTTATG 890 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 30.46 CpG sites = 20, Kimura (unadjusted) = 38.62 Transitions / transversions = 2.00 (20/10) Gap_init rate = 0.02 (2 / 102), avg. gap size = 2.00 (4 / 2) 34 20.61 0.00 0.00 chr3ptel1M 12881 12953 (987047) (TATATA)n#Simple_repeat 1 73 (0) m_b109s252i11 3977 chr3ptel1M 12881 TATATGTCTATATCTATATCTAGATATATAGATAGATATAGATATCTATA 12930 i v v v v v v v v (TATATA)n#Sim 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr3ptel1M 12931 GATATATAGATTTATATAGATAT 12953 v v v v (TATATA)n#Sim 51 TATATATATATATATATATATAT 73 Matrix = Unknown Transitions / transversions = 0.08 (1/12) Gap_init rate = 0.00 (0 / 72), avg. gap size = 0.0 (0 / 0) 38 25.70 0.00 0.00 chr3ptel1M 14428 14519 (985481) (AT)n#Simple_repeat 1 92 (0) m_b109s252i12 3978 chr3ptel1M 14428 ATATAGATAGATAGATATAGATTTAGTTATATCTCTAGATATATATATAT 14477 v v v v v vv v v v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr3ptel1M 14478 ATATATGTTTATATATACACACACATATGTGTGTATTTATAT 14519 i v i i i i i i i v (AT)n#Simple_ 51 ATATATATATATATATATATATATATATATATATATATATAT 92 Matrix = Unknown Transitions / transversions = 0.67 (8/12) Gap_init rate = 0.00 (0 / 91), avg. gap size = 0.0 (0 / 0) 42 0.00 3.92 1.92 chr3ptel1M 15068 15118 (984882) (TGTTGCTAACT)n#Simple_repeat 1 52 (0) c_b109s251i2 3979 chr3ptel1M 15068 TGTTGCTAACTTTGTTGCTAACTTGTTGCTAAC-TGTTGCTAAC-TGTTG 15115 - - - (TGTTGCTAACT) 1 TGTTGCTAAC-TTGTTGCTAACTTGTTGCTAACTTGTTGCTAACTTGTTG 49 chr3ptel1M 15116 CTA 15118 (TGTTGCTAACT) 50 CTA 52 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.06 (3 / 50), avg. gap size = 1.00 (3 / 3) 36 0.00 0.00 0.00 chr3ptel1M 17077 17107 (982893) (TA)n#Simple_repeat 1 31 (0) c_b109s251i3 3980 chr3ptel1M 17077 TATATATATATATATATATATATATATATAT 17107 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATAT 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 319 29.75 5.34 0.46 chr3ptel1M 18196 18401 (981599) C PRIMA41-int#LTR/ERV1 (3659) 4097 3882 m_b109s701i0 3981 chr3ptel1M 18196 GCTGGGGCAAAGCTCAGTTTAGCTTTCAGGGTCTTAAAAGCCTTGGCCTG 18245 ? i vi?v i vv ? v i? - vii C PRIMA41-int#L 4097 GCNGGAGCTGNTCCCAGTTTCTCTTTNAGGGTATTAAAAGTNT-GTTTTG 4049 chr3ptel1M 18246 --ATCAGGGTCACATTCAAGGGG---AAGTGTG-TCCTTGAAGAGAATCA 18289 --i i?vvi v ? i --- v vi - vv vv C PRIMA41-int#L 4048 CAGTTNCTATCCCATTCNAAGGGNTCACGTCCGCTCCTTTTAGAGCCTCA 3999 chr3ptel1M 18290 TAGAAGGGCTTGGCAATAACTCCAAAGTTAAGCATCCAGATTCTACAAAC 18339 v i ? v ?vi viiii ? i v?vv?vi i v C PRIMA41-int#L 3998 TATAAAGGCTTNGCTATANGCCCAAATCCGGGNACCCATNAANAGCAGAA 3949 chr3ptel1M 18340 TCCAGCCATGTTCAGGAAAATGCACAGCTGTTTCTCAGAGGCAGACTCAG 18389 ? vii ii iiv ? ii vvvvi i? v C PRIMA41-int#L 3948 TCCNGCCATTCCCAAAAAAGCCCNCAGCTGTTTCTTGGTCTGGGGNTCCG 3899 chr3ptel1M 18390 GGAGT-----GATGGCC 18401 ??----- C PRIMA41-int#L 3898 GGANNNCCAAGATGGCC 3882 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 40.88 CpG sites = 30, Kimura (unadjusted) = 42.78 Transitions / transversions = 0.97 (30/31) Gap_init rate = 0.02 (5 / 205), avg. gap size = 2.40 (12 / 5) 17 0.00 0.00 0.00 chr3ptel1M 18573 18591 (981409) (T)n#Simple_repeat 1 19 (0) m_b109s252i13 3982 chr3ptel1M 18573 TTTTTTTTTTTTTTTTTTT 18591 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 531 17.55 0.00 6.80 chr3ptel1M 18606 18715 (981285) C MIRc#SINE/MIR (156) 112 10 m_b109s601i1 3983 chr3ptel1M 18606 GTTAAGTGACTTGCCCAGGGTCACACAGCTAGGAAGTATTAAGTGTCTGA 18655 i ------- v v C MIRc#SINE/MIR 112 GTTAAGTGACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGCAGA 70 chr3ptel1M 18656 GACCAGATTTGAACTCAGGTAGTTCTGACTTCAGGGCTAGTGCTCTACCC 18705 v vi i i i vv i i i v i vi C MIRc#SINE/MIR 69 GCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCC 20 chr3ptel1M 18706 ACTGCACCAC 18715 C MIRc#SINE/MIR 19 ACTGCACCAC 10 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 18.90 CpG sites = 10, Kimura (unadjusted) = 20.08 Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.06 (7 / 109), avg. gap size = 1.00 (7 / 7) 367 24.79 4.98 7.65 chr3ptel1M 18731 18931 (981069) C PABL_B-int#LTR/ERV1 (4164) 2958 2763 m_b109s701i1 3981 chr3ptel1M 18731 TCTCTCAAATCTTGAGTCAGTGCTCATCCAAACATGGGGGAGGAGGGGAC 18780 i i v? i ?ii ivi ? i vv i? ----i C PABL_B-int#LT 2958 TCTCTTAAGTCTTTNGCCAGNATTTCCCCAAANATAGTTGGNGAG----T 2913 chr3ptel1M 18781 TGTGAGAGAAGCCCTGAGGTAGGACTACCTA----TGCT--AATTG-GTG 18823 v v --- v i ? v ?ii i ---- i -- i - i? C PABL_B-int#LT 2912 TTTTA---AACCCTTGAGGNAGCACNGTCCAACAATACTGAAACTGNGCN 2866 chr3ptel1M 18824 GTGATTGCTCCTCTGGATTTGCCCATTCAGAAGCAAAAAGAAATTA-TGA 18872 i i ----- ? i i ?i i i v --- ??- i C PABL_B-int#LT 2865 GCGGT-----CTCNGGGTCTNTCCATTCAAAGGCAAACA---ATNNCTGG 2824 chr3ptel1M 18873 GTCTTTATG--CTGTGGTATGCAAAAGAAAACGTCTTTAAGATCTAAAGA 18920 ? i ii -- v?? ? ii i v viv C PABL_B-int#LT 2823 NTCTCTGCGTCCANNGGNATGCAAAAGAAGGCATCTTTTAGATCTAACAC 2774 chr3ptel1M 18921 AGAAAACCATT 18931 v ? C PABL_B-int#LT 2773 TGNAAACCATT 2763 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 33.28 CpG sites = 32, Kimura (unadjusted) = 35.20 Transitions / transversions = 2.29 (32/14) Gap_init rate = 0.10 (20 / 200), avg. gap size = 1.25 (25 / 20) 373 31.94 3.51 1.14 chr3ptel1M 18775 18945 (981055) C HERV4_I#LTR/ERV1 (3120) 3419 3245 m_b109s701i2 3981 chr3ptel1M 18775 GGGGACTGTGAGAGAAGCCCTGAGGTAGGACTACCTATGCTAATTGGTGG 18824 i i vvvii v v ii i v ivv v v C HERV4_I#LTR/E 3419 GGGGGCTATCCCGAAAGCCCTGAGGGAGCACTGTCCAAGTGTATTGTTGT 3370 chr3ptel1M 18825 TGATTGCTCC----TCTGGATTTGCCCATTCAGAAGCAAAAAGAAATTAT 18870 -- v i---- iv v i i iv iv C HERV4_I#LTR/E 3369 T--TTTCTCTGGTATTAGGATTTTCCCATTCAAAGGCAAAAAGGTATTGG 3322 chr3ptel1M 18871 GAGTCTTTATGCTGTGGTATGCAAAAGAAAACGTCTTTAAGATCTAAAGA 18920 v vvivv v v v v i i i v i iiiv C HERV4_I#LTR/E 3321 GACTCTGGGGCCAGAGGAATGGAGAAGAAAGCATCTTTTAGGTCTAGGAC 3272 chr3ptel1M 18921 AGAAAACCATTGTGTGT--CCTGACAC 18945 v i v ii -- i C HERV4_I#LTR/E 3271 TGAGAACCATTTTGCATCCCCTGGCAC 3245 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 41.12 CpG sites = 26, Kimura (unadjusted) = 42.13 Transitions / transversions = 0.93 (26/28) Gap_init rate = 0.02 (4 / 170), avg. gap size = 2.00 (8 / 4) 11 20.84 0.00 2.94 chr3ptel1M 19112 19146 (980854) (TGGGGA)n#Simple_repeat 1 34 (0) m_b109s252i14 3984 chr3ptel1M 19112 TGGGGGTGGGGGGTGGGGAGGGGAATGGGTCTGGG 19146 i - i v i vv (TGGGGA)n#Sim 1 TGGGGAT-GGGGATGGGGATGGGGATGGGGATGGG 34 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 17 0.00 0.00 0.00 chr3ptel1M 26062 26080 (973920) (A)n#Simple_repeat 1 19 (0) m_b109s252i15 3985 chr3ptel1M 26062 AAAAAAAAAAAAAAAAAAA 26080 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAA 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 19 0.00 0.00 0.00 chr3ptel1M 26999 27019 (972981) (CA)n#Simple_repeat 1 21 (0) m_b109s252i16 3986 chr3ptel1M 26999 CACACACACACACACACACAC 27019 (CA)n#Simple_ 1 CACACACACACACACACACAC 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 chr3ptel1M 27302 27319 (972681) (AC)n#Simple_repeat 1 18 (0) m_b109s252i17 3987 chr3ptel1M 27302 ACACACACACACACACAC 27319 (AC)n#Simple_ 1 ACACACACACACACACAC 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 14 13.96 2.22 6.98 chr3ptel1M 28896 28940 (971060) (TTTTCT)n#Simple_repeat 1 43 (0) m_b109s252i18 3988 chr3ptel1M 28896 TTTGCATTTT-GTTTTCTTTCTCAGATTTTCTTTTTCTTCTTTCTT 28940 v v -v i --v - (TTTTCT)n#Sim 1 TTTTCTTTTTCTTTTTCTTTTTC--TTTTTCTTTTTCTT-TTTCTT 43 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4) 12 12.03 3.70 0.00 chr3ptel1M 29219 29245 (970755) (GTTT)n#Simple_repeat 1 28 (0) m_b109s252i19 3989 chr3ptel1M 29219 GTTTTTTTGTTTATTTCTTTG-TTGTTT 29245 v i v - (GTTT)n#Simpl 1 GTTTGTTTGTTTGTTTGTTTGTTTGTTT 28 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.04 (1 / 26), avg. gap size = 1.00 (1 / 1) 221 32.54 7.86 4.10 chr3ptel1M 30276 30746 (969254) L2#LINE/L2 1919 2406 (676) m_b109s601i2 3990 chr3ptel1M 30276 CCCCTTCCCCCATATGCCCCCTCTC---CCCTCCCAGATCAGG-TCTCCT 30321 i i i ----i i i--- v i vi - i v L2#LINE/L2 1919 CCTCTCCTCCCAT----TCTCTCTTGAACCCACTCCAATCAGGCTTTCGT 1964 chr3ptel1M 30322 TCTTTCC--TCCACC-----TTCTCA-GTCT-TGTCCCCTACATTCTCCT 30362 i iiv -- ----- v v- v-v v v iivi v L2#LINE/L2 1965 CCCCACCACTCCACCGAAACTGCTCTTGTCAAGGTCACCAATGACCTCCA 2014 chr3ptel1M 30363 CTTTTTCTGAGACCAGGGAGCTCTCCTTAATGCTCATTTTTCTCAATCTG 30412 v v- i iv iv iv vv i i i v i v ii i ? L2#LINE/L2 2015 CGTTG-CTAAATCCAATGGTCAATTCTCAGTCCTCATCTTACTTGACCTN 2063 chr3ptel1M 30413 TCCCCAGCGTTTGACATATGTGATCCCTCTCTCCTT---GAGACTCTCCT 30459 vv i i vv v i --- i v i- L2#LINE/L2 2064 TCAGCAGCATTTGACACAGTTGATCACTCCCTCCTTCTTGAAACACTT-T 2112 chr3ptel1M 30460 CTTCTCCAAGGTTTTAGGACAGGACTCTCTCCAGCCTTTCCTCCTCCCTC 30509 v ivi v ii vv v v vi v L2#LINE/L2 2113 CTTCACTTGGCTTCCAGGACACCACACTCTCCTGGTTTTCCTCCTACCTC 2162 chr3ptel1M 30510 -TT--CCACCCCTTCTCCATCTTCTGTACTGGATCTTCCTCTAGATCATA 30556 -i -- i i vi i v i v i vvvvi vii L2#LINE/L2 2163 ACTGGCCGCTCCTTCTCAGTCTCCTTTGCTGGTTCCTCCTCATCTCCCCG 2212 chr3ptel1M 30557 TTCTCTAATCACTGGTGTTCCCC----CTC-----CTAGCCTCCCTCTTT 30597 vi ? v ii v v ---- -----i i v ii i i L2#LINE/L2 2213 ACCTCTNAACGTTGGAGTGCCCCAGGGCTCAGTCCTTGGACCTCTTCTCT 2262 chr3ptel1M 30598 TTTCCCTCTACACGAA------TG--GATCTCATCAGCTGGCATGCATTT 30639 i iv vv ------? -- viv vv vv L2#LINE/L2 2263 TCTCTATCTACACTCACTCCCTNGGTGATCTCATCCAGTCTCATGGCTTT 2312 chr3ptel1M 30640 AAGTGCCATTTCTGTGCTAATGATTTACTGATTTACAAATTCTTCCTGCC 30689 i i i v i i i iv vi i ------------- L2#LINE/L2 2313 AAATACCATCTATATGCTGATGACTCCCAAATTTATA------------- 2349 chr3ptel1M 30690 TCTCCTGCCCCGATTTCTCTGCTAATCTTCAGCCCTACAT-CCCTACTGA 30738 v v ii iv i v i v iiii -i v - L2#LINE/L2 2350 TCTCCAGCCCGGACCTCTCCCCTGAACTCCAGACTCGTATATCCAACTG- 2398 chr3ptel1M 30739 CCTGCCTG 30746 i ii L2#LINE/L2 2399 CCTACTCG 2406 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 42.13 CpG sites = 80, Kimura (unadjusted) = 44.22 Transitions / transversions = 1.19 (80/67) Gap_init rate = 0.07 (34 / 470), avg. gap size = 1.68 (57 / 34) 247 35.96 12.03 2.31 chr3ptel1M 30664 30979 (969021) L2b_3end#LINE/L2 86 431 (35) m_b109s601i3 3990 chr3ptel1M 30664 TTACTGATTTACAAATTCTTCCTGC-CTCTCCTGCCCC--GATTTCT--- 30707 i v iiv i iv vi v? - ? i i -- iii i --- L2b_3end#LINE 86 TTGCTGTTCCTCGAACACGCCANGCTCNCTCCCGCCTCAGGGCCTTTGCA 135 chr3ptel1M 30708 -CTGCTAATCT-TCAGCCCT--ACATCCCTACTGACCT----GCCTGGTT 30749 -? iv i- v iv-- ii i v iv ---- ii L2b_3end#LINE 136 CNTGCTGTTCCCTCTGCCTGGAACGCCCTTCCCCACCTCTTCGCCTGGCC 185 chr3ptel1M 30750 ACCTTTAAGTCATGTTTAAA-----AACTAAAA-GCCATCTA----GGGA 30789 v iiv v vi v i----- i v - i i v---- L2b_3end#LINE 186 AACTCCTACTCATCCTTCAGGTCTCAGCTCAAATGTCACCTCCTCCGGGA 235 chr3ptel1M 30790 ACGGCTTCTTTAACTCCTCTTGCT---TCTTGGGCTTTCC------CTCT 30830 - v i ii i i i vv i--- vv v ii ------ i i L2b_3end#LINE 236 A-GCCCTCCCTGACCCCCCAGGCCGGGTCAGGCGCCCTCCTCTGGGCCCC 284 chr3ptel1M 30831 GCTAATTATTTCCTA----TTTCAACTGTACAGTGTGCTATTTGCATA-C 30875 v i i iv vi i---- i viii i ?- v - i? i i- L2b_3end#LINE 285 CCCAGTCCTACCCTGCCACTCTGGGTTATN-ATTGT-CTGNTTACATGTC 332 chr3ptel1M 30876 TGTCTCCTTCATTAGACTGTAAGCTCCTTGAGGACTGGGACTGAAGTGAG 30925 ii i i v i v i -? vv L2b_3end#LINE 333 TGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCG-NGTCTG 381 chr3ptel1M 30926 TGTGAGTGTGTGTTTGTGTGTGTAGCAGTTTGTAGCAGAATACCTGACAC 30975 v --- viiiivv i vi-v iviv v i?i i L2b_3end#LINE 382 TCT---TGTTCACCGCTGTATCC-CCAGCGCCTAGCACAGNGCCTGGCAC 427 chr3ptel1M 30976 ATAG 30979 i L2b_3end#LINE 428 ACAG 431 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 48.94 CpG sites = 70, Kimura (unadjusted) = 53.93 Transitions / transversions = 1.71 (70/41) Gap_init rate = 0.07 (22 / 315), avg. gap size = 2.09 (46 / 22) 330 16.68 1.47 2.99 chr3ptel1M 30851 30918 (969082) L2c_3end#LINE/L2 337 403 (75) m_b109s601i4 3990 chr3ptel1M 30851 ACTGTACAGTGTGCTATTTGCATA-CTGTCTCCTTCATTAGACTGTAAGC 30899 i - v - i i ? i- i i i L2c_3end#LINE 337 ATTGTA-ATTGT-CTGTTTACNTGTCTGTCTCCTCCACTAGACTGTGAGC 384 chr3ptel1M 30900 TCCTTGAGGACTGGGACTG 30918 i v i L2c_3end#LINE 385 TCCTTGAGGGCAGGGACCG 403 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 18.01 CpG sites = 9, Kimura (unadjusted) = 19.97 Transitions / transversions = 4.50 (9/2) Gap_init rate = 0.04 (3 / 67), avg. gap size = 1.00 (3 / 3) 458 24.86 0.76 5.56 chr3ptel1M 31251 31382 (968618) MIRc#SINE/MIR 2 127 (141) m_b109s601i5 3991 chr3ptel1M 31251 GGGGCAGCTAGATGTTGCAGTGGAGAGAGCATCAGCCCTGAAGTCAGGAG 31300 i i---i v i iii v i i i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr3ptel1M 31301 GACCTGACTCCAAATCCAGCCTCAGACACTTAATTTCTAGCTGTGGAACC 31350 iv i i i v v v v ---- vi MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCCACTTA----CTAGCTGTGTGACC 94 chr3ptel1M 31351 CTGGGCAAATCATTTAATCCCAATT-GCCTCAG 31382 i i i i i vv v- MIRc#SINE/MIR 95 TTGGGCAAGTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 29.85 CpG sites = 20, Kimura (unadjusted) = 31.05 Transitions / transversions = 1.82 (20/11) Gap_init rate = 0.06 (8 / 131), avg. gap size = 1.00 (8 / 8) 18 16.12 7.02 1.67 chr3ptel1M 33650 33706 (966294) (AGAGAA)n#Simple_repeat 1 60 (0) m_b109s252i20 3992 chr3ptel1M 33650 AGAGAAAG-GAAA-AGAAAGAGAGACAGAGAGA-AAAGAGGCAGATCCAA 33696 - - i v i - iv -vv (AGAGAA)n#Sim 1 AGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGA-GAAA 49 chr3ptel1M 33697 GTGAAA-AGAA 33706 v - (AGAGAA)n#Sim 50 GAGAAAGAGAA 60 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.09 (5 / 56), avg. gap size = 1.00 (5 / 5) 273 20.73 13.46 2.61 chr3ptel1M 34776 34879 (965121) MIR3#SINE/MIR 87 201 (7) m_b109s601i6 3993 chr3ptel1M 34776 TGACCTTGGAGCAAACCACTTC-----CCTGAGCTTCAGTTTCACC--CT 34818 - ii -----i i i vi -- MIR3#SINE/MIR 87 TGACCTTGG-GCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCT 135 chr3ptel1M 34819 CTAAACTGAAGAAGGTTGGACT-----CTTACTATAGTGTCTTTCAGCTC 34863 v v - ii -----v iv vi vi i MIR3#SINE/MIR 136 GTAAAATG-AGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTC 184 chr3ptel1M 34864 T-AC-TTCTCATGACTTT 34879 - - - i i MIR3#SINE/MIR 185 TGACATTCT-ATGATTCT 201 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 25.00 CpG sites = 14, Kimura (unadjusted) = 25.00 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.08 (8 / 103), avg. gap size = 2.12 (17 / 8) 22 10.46 0.00 0.00 chr3ptel1M 38597 38627 (961373) (T)n#Simple_repeat 1 31 (0) m_b110s252i0 3994 chr3ptel1M 38597 TTCTTTACTTTTTTTTTTTTTTTTTTTTTTT 38627 i vi (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 31 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 40 8.88 1.67 0.00 chr3ptel1M 39216 39275 (960725) (AC)n#Simple_repeat 1 61 (0) c_b110s251i0 3995 chr3ptel1M 39216 ACACACATACACCCACACCCACAC-CACACACACACACACACACACACAT 39264 i v v - i (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50 chr3ptel1M 39265 ACACATACACA 39275 i (AC)n#Simple_ 51 ACACACACACA 61 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.02 (1 / 59), avg. gap size = 1.00 (1 / 1) 15 4.77 0.00 0.00 chr3ptel1M 41028 41049 (958951) (TCAA)n#Simple_repeat 1 22 (0) m_b110s252i1 3996 chr3ptel1M 41028 TCAGTCAATCAATCAATCAATC 41049 i (TCAA)n#Simpl 1 TCAATCAATCAATCAATCAATC 22 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 203 22.71 14.42 2.59 chr3ptel1M 41100 41203 (958797) MIR3#SINE/MIR 92 207 (1) m_b110s601i0 3997 chr3ptel1M 41100 TTGGGCAAATC-------CTGTCTCTATTTCAGTTTCCTC--CTGTATAT 41140 i ------- v vviii -- - v MIR3#SINE/MIR 92 TTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTA-AA 140 chr3ptel1M 41141 TTAAGAAGGTTGCACTCTTTAAT-TCTAAAAGGT---TTTCAGCTGT-AT 41185 v i ii v vvv i - -- --- i v - i MIR3#SINE/MIR 141 ATGAGGGGGTTGGACTAGATGATCTCT--AAGGTCCCTTCCAGCTCTGAC 188 chr3ptel1M 41186 ATTTTATGACTTT-TGATT 41203 i i i - MIR3#SINE/MIR 189 ATTCTATGATTCTATGATT 207 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 27.55 CpG sites = 13, Kimura (unadjusted) = 27.55 Transitions / transversions = 1.30 (13/10) Gap_init rate = 0.09 (9 / 103), avg. gap size = 2.00 (18 / 9) 531 31.21 6.28 0.85 chr3ptel1M 42252 42474 (957526) C MIRc#SINE/MIR (31) 237 3 m_b110s601i1 3998 chr3ptel1M 42252 CTTTATAGATTA-AAAATAAAACCACATA--TTAGGTCACT--AACTTCA 42296 i v - iiivvvi -- vv i -- v i C MIRc#SINE/MIR 237 CTTTACAGTTTACAAAGCGCTTTCACATACATTATCTCATTTGATCCTCA 188 chr3ptel1M 42297 CCATAACTTTCCAAGTTAGGT------GATATTTTTATCCTTATTTCAGA 42340 v i ii vii v i------ i v ii i v C MIRc#SINE/MIR 187 CAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACA 138 chr3ptel1M 42341 GTTGAGGAAACTGAGGCAAACAGTATTTAACTGACTTGCCAGAGGT-AGA 42389 v vv v viv v vi - v C MIRc#SINE/MIR 137 GATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACA 88 chr3ptel1M 42390 CAGTTATTAATTGTCCAAGGTTTAATTCAAACTCAGGTACACATGATTTT 42439 i v v v vi vivvi i i i viv v i ii C MIRc#SINE/MIR 87 CAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCC 38 chr3ptel1M 42440 CTGCCCAGGACTC--TCCACTGTACTACTGACTCCCT 42474 vv i vi -- i i -- v C MIRc#SINE/MIR 37 AAGTCCAGTGCTCTTTCCACTGCACCAC--ACTGCCT 3 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.58 CpG sites = 34, Kimura (unadjusted) = 40.90 Transitions / transversions = 0.97 (34/35) Gap_init rate = 0.04 (8 / 222), avg. gap size = 2.00 (16 / 8) 192 15.91 4.35 4.35 chr3ptel1M 43484 43529 (956471) MIR1_Amn#SINE/MIR 105 150 (80) m_b110s601i2 3999 chr3ptel1M 43484 GTCA-TTGGCTCCTCAATGAATCTCAGTTTCC-CATCTATAAAATGAG 43529 - ?i ii -- ?ii - i i MIR1_Amn#SINE 105 GTCACTTNACCTCTC--TGNGCCTCAGTTTCCTCATCTGTAAAATGGG 150 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 20.27 CpG sites = 7, Kimura (unadjusted) = 20.27 Transitions / transversions = 1.00 (7/0) Gap_init rate = 0.09 (4 / 45), avg. gap size = 1.00 (4 / 4) 282 23.26 10.47 0.00 chr3ptel1M 43494 43579 (956421) MIR3#SINE/MIR 109 203 (5) m_b110s601i3 3999 chr3ptel1M 43494 CCTCAATGAATCTCAGTTTCC-CATCTATAAAATGAGTGGTTTGCACTCC 43542 vv iii - i v v v vv MIR3#SINE/MIR 109 CCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAG 158 chr3ptel1M 43543 ATGGCCC-----ATCCCTTCCAG---TGATCATCTGTGATCCTAT 43579 ii i-----i --- ivv i i MIR3#SINE/MIR 159 ATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTAT 203 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.22 CpG sites = 11, Kimura (unadjusted) = 28.22 Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.04 (3 / 85), avg. gap size = 3.00 (9 / 3) 229 31.84 7.89 0.82 chr3ptel1M 43650 43763 (956237) C L2b_3end#LINE/L2 (10) 456 335 m_b110s601i4 4000 chr3ptel1M 43650 TCAGTAAACA---ATTAAGGGCCTGGTACATGGCAG-CCCTGGGCTGAGC 43695 ii i --- i i v iv iii v - ? v ii C L2b_3end#LINE 456 TCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGC 407 chr3ptel1M 43696 ACCAGGAACATAA-AGTGAGATAAG---GA-ACATCCTCTGCTCTCGTGG 43740 i ii i i i i-i - i --- -? ivi i i ii C L2b_3end#LINE 406 GCTGGGGATACAGCGGTGA-ACAAGACAGACNCGGTCCCTGCCCTCACGG 358 chr3ptel1M 43741 AGGTCACAGAATGGTGGGGCAGA 43763 v vv i v C L2b_3end#LINE 357 AGCTCACAGTCTAGTGGGGGAGA 335 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.35 CpG sites = 27, Kimura (unadjusted) = 46.34 Transitions / transversions = 3.00 (27/9) Gap_init rate = 0.05 (6 / 113), avg. gap size = 1.67 (10 / 6) 421 26.03 16.96 3.97 chr3ptel1M 43891 44114 (955886) C MIRb#SINE/MIR (0) 268 17 m_b110s601i5 4001 chr3ptel1M 43891 AATAAAGTAGCTAGCACTTATACAGC----ACTATGTGTCATGCAC---- 43932 viv v i vv ---- i v ---- C MIRb#SINE/MIR 268 AATAATAGAGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTG 219 chr3ptel1M 43933 --AGG------------ATTGTCTTATTTAATCCTGATGGCAACC-TGAG 43967 -- i ------------ i i v iii - v C MIRb#SINE/MIR 218 CTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCG 169 chr3ptel1M 43968 GGCTTTGCTGATATTATTAAGCCTATTTTACAGATAAAGAAAACTGAATC 44017 i ---- iv i vv i -i i iv C MIRb#SINE/MIR 168 AG----GTAGGTATTATTATCCCCATTTTACAGAT-GAGGAAACTGAGGC 124 chr3ptel1M 44018 AAACAGAGGTTCTATAACTTG----AG----------TAGCAAGCTTCTA 44053 vv v vvi ---- ---------- i ivv vi C MIRb#SINE/MIR 123 TCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAG 74 chr3ptel1M 44054 AGGTGTGATTAAAAGTCTGGTCTTTCTGACT-TAAGGCCCTACCCATAGT 44102 vi v vi vi v v -i i ----- i iv C MIRb#SINE/MIR 73 AGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAG-----CCCGTGCT 29 chr3ptel1M 44103 CTATCCACTGTA 44114 v i C MIRb#SINE/MIR 28 CTTTCCACTGCA 17 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 30.47 CpG sites = 28, Kimura (unadjusted) = 32.51 Transitions / transversions = 1.00 (28/28) Gap_init rate = 0.08 (18 / 223), avg. gap size = 2.67 (48 / 18) 331 32.29 11.21 3.03 chr3ptel1M 45063 45276 (954724) C MIRc#SINE/MIR (26) 242 12 m_b110s601i6 4002 chr3ptel1M 45063 TAGCACTTATACAGTACTGTGTATCACT----CATGGCATCATCTTACTT 45108 - -i iiiv v i ---- i- i i i C MIRc#SINE/MIR 242 TAGCACTT-TACAGT-TTACAAAGCGCTTTCACATA-CATTATCTCATTT 196 chr3ptel1M 45109 TATTCTCAAGACAGCT---TGA---AGACTTTGCTGAAATTATTAAGCCC 45152 v i vi i i--- --- i vvv v iv vv C MIRc#SINE/MIR 195 GATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCC 146 chr3ptel1M 45153 ATTTGACAGATAAAGAAAAATGAATCAAACAGAGGTCCTACAACTTG--- 45199 v -i i v iv vv v ivviii --- C MIRc#SINE/MIR 145 ATTTTACAGAT-GAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCC 97 chr3ptel1M 45200 -----------ACTAGCAAGCTTCTGAGGTGGGATTAAAAGTCTGGTCTT 45238 -----------i i ivv v vi i vi vi v C MIRc#SINE/MIR 96 AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTT 47 chr3ptel1M 45239 CCTGATTTAAGGCCCTATTTATGTCTATCCACTATACC 45276 i iv i i vi vi--- v ii C MIRc#SINE/MIR 46 CCTGACTCCAAGTCCAGTGC---TCTTTCCACTGCACC 12 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.90 CpG sites = 37, Kimura (unadjusted) = 43.46 Transitions / transversions = 1.23 (37/30) Gap_init rate = 0.06 (12 / 213), avg. gap size = 2.58 (31 / 12) 24 0.00 0.00 0.00 chr3ptel1M 47699 47724 (952276) (AC)n#Simple_repeat 1 26 (0) m_b110s252i2 4003 chr3ptel1M 47699 ACACACACACACACACACACACACAC 47724 (AC)n#Simple_ 1 ACACACACACACACACACACACACAC 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 47 0.00 0.00 0.00 chr3ptel1M 47725 47764 (952236) (AT)n#Simple_repeat 1 40 (0) c_b110s251i1 4004 chr3ptel1M 47725 ATATATATATATATATATATATATATATATATATATATAT 47764 (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATAT 40 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 13 18.38 0.00 0.00 chr3ptel1M 47801 47831 (952169) (TTCTT)n#Simple_repeat 1 31 (0) m_b110s252i3 4005 chr3ptel1M 47801 TTCTTTTCTTATCATTCCTTTTTTTTTTTTT 47831 v v i i i (TTCTT)n#Simp 1 TTCTTTTCTTTTCTTTTCTTTTCTTTTCTTT 31 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 948 30.35 6.26 2.14 chr3ptel1M 49838 50332 (949668) L1ME4c_3end#LINE/L1 126 640 (190) m_b110s551i0 4006 chr3ptel1M 49838 ACATATAGGAACTGATGTTCTAAATCACCATGGATCAGAGAAATGCAAAT 49887 i i i --i v vv i i vvi i L1ME4c_3end#L 126 ACACATGGAAA--AATGTTCAACCTCGCTAGTAATCAAAGAAATGCAAAT 173 chr3ptel1M 49888 TAAGACCATACTGAGATATCTCTACACACCTCTCAGACTGGCTAAGATGA 49937 ii v i v i vi vi i v i i i i v i -- L1ME4c_3end#L 174 TAAAGCAACAATGAGATACCATTTTACGCCTATTAAATTAGCAAAAAT-- 221 chr3ptel1M 49938 CAGGTAAA-----GATAATGACCACTCCTGGAGGGGATGTGGGAAAACTG 49982 ---v ----- iv v v v i ? i vi L1ME4c_3end#L 222 ---TTAAAAAATTGATAATACCCAATGCTGGCGAGGNTGCGGTGAAACTG 268 chr3ptel1M 49983 GGACACTAATACATTGTTGATGGAGTTGTGAAGTGATCCAACCCTTCTAG 50032 v ? v i i vi? i v i v i i L1ME4c_3end#L 269 GTACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGG 318 chr3ptel1M 50033 AGAGAATTTTGGCCGTAT-TCTCAAAAGTTATCAAACTGTGCAGACCCTT 50081 i v v vi i- v i ii v v v v L1ME4c_3end#L 319 AAAGCAATTTGGCAATACGTATCAAGAGCCATAAAAATGTTCATACCCTT 368 chr3ptel1M 50082 TAATCAACTAGTGCTTCTACTGGGCTTATATCCCAAAGAGAT--CTTAAA 50129 i i v v i v iv v vv v i i i --i i L1ME4c_3end#L 369 TGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAA 418 chr3ptel1M 50130 GGAGGGAAAGGGACCCATATGTGCAAAAATGC---TTG------------ 50164 i i ii -- i ii i i i--- ------------ L1ME4c_3end#L 419 AGAAGGAAAAAG--CTATATGCACGAAGATGTTCATTGCAGCGTTATTTA 466 chr3ptel1M 50165 ---TGGCAAGAAACTGGAAACTGAGTGCATGCCCATCAGCTGGAGAATGG 50211 --- i i i i vivv iv i v iiv i L1ME4c_3end#L 467 TAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAATGG 516 chr3ptel1M 50212 CTGAATAAGTTATGGTATATGAATGCTATGGAATATTATTGTTCTATAAG 50261 i i i i i v? iv v vvvv i v i L1ME4c_3end#L 517 TTAAGTAAATTATGGTACATCNACTCGATGGAATATTATGCAGCCATTAA 566 chr3ptel1M 50262 AAATGACCAGCAGGATGAT--TTCAGCAAGGCCTGGAGAG---ACATGAA 50306 iv vi v v i-- vi -- v i i---vi v L1ME4c_3end#L 567 AAATGATAATTATGAAGACTATGTAGCAA--CATGGAAAATGTTTATGAT 614 chr3ptel1M 50307 CTGATGCTGAGTGAAATGAGCAGAAT 50332 v i i i vi L1ME4c_3end#L 615 ATAATGTTAAGTGAAAAAAGCAGAAT 640 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.36 CpG sites = 85, Kimura (unadjusted) = 40.49 Transitions / transversions = 1.37 (85/62) Gap_init rate = 0.04 (19 / 494), avg. gap size = 2.21 (42 / 19) 82 2.50 1.22 0.00 chr3ptel1M 51039 51120 (948880) (CT)n#Simple_repeat 1 83 (0) c_b110s251i2 4007 chr3ptel1M 51039 CTCTCTCTC-CTCTCTCTCTCTTTCTCTCTCTCTCTCTTTCTCTCTCTCT 51087 - i i (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chr3ptel1M 51088 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 51120 (CT)n#Simple_ 51 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 83 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.01 (1 / 81), avg. gap size = 1.00 (1 / 1) 36 0.00 0.00 0.00 chr3ptel1M 51121 51159 (948841) (AC)n#Simple_repeat 1 39 (0) m_b110s252i4 4008 chr3ptel1M 51121 ACACACACACACACACACACACACACACACACACACACA 51159 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACA 39 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 18 25.32 0.00 0.00 chr3ptel1M 51169 51210 (948790) (TC)n#Simple_repeat 1 42 (0) m_b110s252i5 4009 chr3ptel1M 51169 TCTGTCTCTCATTCTCCCTTTCTCTCCCTGTGGCTCTCTCTC 51210 v vi i i i v vv (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 42 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 18 36.20 2.97 0.97 chr3ptel1M 51860 51960 (948040) (TC)n#Simple_repeat 1 103 (0) m_b110s252i6 4010 chr3ptel1M 51860 TCTCTTTTTTACTCTCTTGTTCTTTTTCTCTTTGTCTTTTCCTCTCATTC 51909 i i iv ivi i i i v i ii vi (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr3ptel1M 51910 TCT-TCTCTTTTTCTGCT-TATATCTGTTTCTCTGACTCT-TATTACTGT 51956 - i i - - v v v i vv - v iv v (TC)n#Simple_ 51 TCTCTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 99 chr3ptel1M 51957 CTCT 51960 (TC)n#Simple_ 100 CTCT 103 Matrix = Unknown Transitions / transversions = 1.33 (16/12) Gap_init rate = 0.04 (4 / 100), avg. gap size = 1.00 (4 / 4) 15 17.81 2.63 0.00 chr3ptel1M 52904 52941 (947059) (TAAAA)n#Simple_repeat 1 39 (0) m_b110s252i7 4011 chr3ptel1M 52904 TAATAAAAAATAAAATAAAATAAAA-AATCTATAGTAAA 52941 v v - vv v i (TAAAA)n#Simp 1 TAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAA 39 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 340 33.15 8.74 1.25 chr3ptel1M 54009 54454 (945546) L2#LINE/L2 1919 2397 (685) m_b110s601i7 4012 chr3ptel1M 54009 CCTCCCCCTCATATATCCTCTCT----CCCGCCCCAGGTCAGG-TGTCCT 54053 i ii ---i i ---- i i i- - v v L2#LINE/L2 1919 CCTCTCCTCC---CATTCTCTCTTGAACCCACTCCAA-TCAGGCTTTCGT 1964 chr3ptel1M 54054 TCTTTCC--TCCACCTTTTCAG-TCTTGTC-----CGCTATATGTTCCTC 54095 i iiv -- vvvv v - ----- i i - vi ii L2#LINE/L2 1965 CCCCACCACTCCACCGAAACTGCTCTTGTCAAGGTCACCA-ATGACCTCC 2013 chr3ptel1M 54096 TCTTT-CTGAGACCAGGGAGCTCTCCTCAATGGTCATTTTTCTCAACCTA 54144 v v - i iv iv iv vv i i vv i v ii ? L2#LINE/L2 2014 ACGTTGCTAAATCCAATGGTCAATTCTCAGTCCTCATCTTACTTGACCTN 2063 chr3ptel1M 54145 TACCCAGCCTTTGGCACAGGAGATCCTTCTCTCCTTCCTGAG--ACTGTC 54192 vvv v i vv vi i i i-- v L2#LINE/L2 2064 TCAGCAGCATTTGACACAGTTGATCACTCCCTCCTTCTTGAAACACTTTC 2113 chr3ptel1M 54193 TTCTCTAAGGTTTTAGGACA--AGACTCTGCAATCTTTCCTCTT-CCTCT 54239 v vi v ii -- v v vivi i - v L2#LINE/L2 2114 TTCACTTGGCTTCCAGGACACCACACTCTCCTGGTTTTCCTCCTACCTCA 2163 chr3ptel1M 54240 TT--CAGC-ACTTCTCTGTCTTCTGTACTGGATCTTCCTCCAGATCACAT 54286 i -- v -v v i v i v i vvvvi v iv L2#LINE/L2 2164 CTGGCCGCTCCTTCTCAGTCTCCTTTGCTGGTTCCTCCTCATCTCCCCGA 2213 chr3ptel1M 54287 CCTCTAATCACTGG---GCCCC----CCC--TTGCTGGCTCTCCTCTTTT 54327 ? v ii --- ---- i -- ivi vi i i L2#LINE/L2 2214 CCTCTNAACGTTGGAGTGCCCCAGGGCTCAGTCCTTGGACCTCTTCTCTT 2263 chr3ptel1M 54328 TTCCCTCTACACGAA------AG--GATCTCATCAGCTACTATGTATTTA 54369 i iv vv ------? -- viv vii vv L2#LINE/L2 2264 CTCTATCTACACTCACTCCCTNGGTGATCTCATCCAGTCTCATGGCTTTA 2313 chr3ptel1M 54370 ATCACCATCTTTGTGCTAATGATTTACTGATTTATAAATTTTTCCTGTAT 54419 vi v i i i iv vi vv iivv i v - L2#LINE/L2 2314 AATACCATCTATATGCTGATGACTCCCAAATTTATATCTCCAGCCCGGA- 2362 chr3ptel1M 54420 CCCCTACCCCAATTTCTCTGCTAACATAGCTAGCT 54454 i v ii vi ivvi vii v i i L2#LINE/L2 2363 CCTCTCCCCTGAACTCCAGACTCGTATATCCAACT 2397 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.36 CpG sites = 74, Kimura (unadjusted) = 45.00 Transitions / transversions = 1.03 (74/72) Gap_init rate = 0.05 (22 / 445), avg. gap size = 2.05 (45 / 22) 219 31.30 0.00 15.79 chr3ptel1M 54451 54560 (945440) C MIRb#SINE/MIR (170) 98 4 m_b110s601i9 4013 chr3ptel1M 54451 AGCTCACAGAGGTAGGAAGTGTCAAGTGTTGTGTCTGAGGCCGAATTTAA 54500 v v v v v ------------ v v i ii C MIRb#SINE/MIR 98 AGGTCACACAGCTAGTAAGTGGCA------------GAGCCGGGATTCGA 61 chr3ptel1M 54501 ACTCGGATCCTTCTGACTTCAGGGCTAGCACTCCATCCACTGTGCCATCC 54550 i i i iv i ii iv ii iv ii i-- C MIRb#SINE/MIR 60 ACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCACCAC-- 13 chr3ptel1M 54551 AGGTGCCACT 54560 - v v C MIRb#SINE/MIR 12 -GCTGCCCCT 4 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.65 CpG sites = 17, Kimura (unadjusted) = 40.38 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.14 (15 / 109), avg. gap size = 1.00 (15 / 15) 238 31.21 0.00 14.12 chr3ptel1M 54451 54547 (945453) C MIRc#SINE/MIR (173) 95 11 m_b110s601i8 4013 chr3ptel1M 54451 AGCTCACAGAGGTAGGAAGTGTCAAGTGTTGTGTCTGAGGCCGAATTTAA 54500 v v v v v ------------ v v i i ii C MIRc#SINE/MIR 95 AGGTCACACAGCTAGTAAGTGGCA------------GAGCCGGGACTCGA 58 chr3ptel1M 54501 ACTCGGATCCTTCTGACTTCAGGGCTAGCACTCCATCCACTGTGCCA 54547 i i i i i i i v i ii iv ii C MIRc#SINE/MIR 57 ACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCA 11 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.87 CpG sites = 17, Kimura (unadjusted) = 41.20 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.12 (12 / 96), avg. gap size = 1.00 (12 / 12) 931 30.74 1.20 1.69 chr3ptel1M 54603 55019 (944981) L1ME4c_3end#LINE/L1 225 639 (191) m_b110s551i1 4014 chr3ptel1M 54603 AAAAAATAATGATG---AATGTTGGAGGGGATGCGGAAAAACTGGGACAC 54649 v i i i--- i v i ? vi v ? L1ME4c_3end#L 225 AAAAATTGATAATACCCAATGCTGGCGAGGNTGCGGTGAAACTGGTACNC 274 chr3ptel1M 54650 TGATGTATTGTTGGTGGAGTTGTGAATGAATCCAACCATTCTGGAGAGCA 54699 v ii i vi? i vii v v i i L1ME4c_3end#L 275 TCATACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGCA 324 chr3ptel1M 54700 ATCAGGAATTATGCCCAAAAAGTTCTCAAACTGTGCATACCCTTTGACCC 54749 iv v v i iviv i iiv v v v L1ME4c_3end#L 325 ATTTGGCAATACGTATCAAGAGCCATAAAAATGTTCATACCCTTTGACCC 374 chr3ptel1M 54750 AGCAGTGCTATGACTGGACTTATATCCCAAAGAGATACT--AAAGAAAGG 54797 i i v i ivv ivv v i i i v -- ii L1ME4c_3end#L 375 AGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAAGAAGG 424 chr3ptel1M 54798 AAAGGGACCTGTATGTGCCAAAATGTTTGTGGCAGCCCTGTTTGTAGTGG 54847 ii -- i ii v i ii v vi i i i i L1ME4c_3end#L 425 AAAAAG--CTATATGCACGAAGATGTTCATTGCAGCGTTATTTATAATAG 472 chr3ptel1M 54848 CCAGAAACTGGAAACTGGGTGGATGCCCATCAGTTGGAGAATGGTTGGGT 54897 v i i vivv ii i v i v i ii L1ME4c_3end#L 473 CGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAATGGTTAAGT 522 chr3ptel1M 54898 AAATTGTGATATATGAATGTGATGGAATATTATTGTTCTATAAGAAATGA 54947 i i i v? ivi vvvv i v i L1ME4c_3end#L 523 AAATTATGGTACATCNACTCGATGGAATATTATGCAGCCATTAAAAATGA 572 chr3ptel1M 54948 CCAGCAGGATGAATACAGAGAGGCTTGGAGAGACTTACATGAACTGATGC 54997 iv vi v v v iiv vii v - i iv vi vv i i L1ME4c_3end#L 573 TAATTATGAAGACTATGTAGCAACATGGA-AAATGTTTATGATATAATGT 621 chr3ptel1M 54998 TAAGTGAAATAAATGAGCAGAA 55019 - --- L1ME4c_3end#L 622 TAAGTGAAA-AA---AGCAGAA 639 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.38 CpG sites = 73, Kimura (unadjusted) = 41.25 Transitions / transversions = 1.38 (73/53) Gap_init rate = 0.02 (9 / 416), avg. gap size = 1.33 (12 / 9) 12 29.85 3.17 1.56 chr3ptel1M 55704 55766 (944234) (AAGA)n#Simple_repeat 1 64 (0) m_b110s252i8 4015 chr3ptel1M 55704 AAG-AAGAAAGAAAAAGAAAAACTGAGAAAGAAA-ACAAAATGCAAGCAA 55751 - i i i vvi - v i v v - (AAGA)n#Simpl 1 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG-AA 49 chr3ptel1M 55752 ATAACAACAGAGAGA 55766 v vi v i (AAGA)n#Simpl 50 AGAAAGAAAGAAAGA 64 Matrix = Unknown Transitions / transversions = 0.88 (7/8) Gap_init rate = 0.05 (3 / 62), avg. gap size = 1.00 (3 / 3) 15 17.03 4.00 4.00 chr3ptel1M 58415 58464 (941536) (AAAGGGG)n#Simple_repeat 1 50 (0) m_b110s252i9 4016 chr3ptel1M 58415 AAAAGGG-AAGTAGAAA-TGGAAAGGGGATAGCAGAAAAAGGGGAAAGGG 58462 i - vi -v v -- ii (AAAGGGG)n#Si 1 AAAGGGGAAAGGGGAAAGGGGAAAGGGGAAAG--GGGAAAGGGGAAAGGG 48 chr3ptel1M 58463 GA 58464 (AAAGGGG)n#Si 49 GA 50 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.08 (4 / 49), avg. gap size = 1.00 (4 / 4) 21 16.78 1.67 5.17 chr3ptel1M 58616 58675 (941325) (AAAAGGG)n#Simple_repeat 1 58 (0) m_b110s252i10 4017 chr3ptel1M 58616 AAAAGTGGGAGA-GGAAAAGTGAAAAGGAAAAAGGGTAAAAGGGAACGGA 58664 - i i - v i - vi i (AAAAGGG)n#Si 1 AAAAG-GGAAAAGGGAAAAGGGAAAAGGGAAAAGGG-AAAAGGGAAAAGG 48 chr3ptel1M 58665 AAGAAAGGGAA 58675 i - (AAAAGGG)n#Si 49 GA-AAAGGGAA 58 Matrix = Unknown Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.07 (4 / 59), avg. gap size = 1.00 (4 / 4) 1158 29.83 10.95 1.49 chr3ptel1M 58804 61260 (938740) L1MD_orf2#LINE/L1 24 2709 (585) m_b110s551i2 4018 chr3ptel1M 58804 ATTAGTAATCGAATGAAATGTGAATGGGATGAACCCA--AAAGAGGAGGC 58851 i i iiv v i vv i iv -- vv ii i L1MD_orf2#LIN 24 ATCAATAATTACATTAAATGTAAATGGTCTAAATACACCAATTAAAAGAC 73 chr3ptel1M 58852 AGA---TAGCAGAG--GATCAAAAGTCG-AACCCTACAATATGTT---TA 58892 --- i -- i iv i-i v v i --- L1MD_orf2#LIN 74 AGAGATTGGCAGAGTGGATTAAAAAACATGACCCAACTATATGCTGTCTA 123 chr3ptel1M 58893 -AAGAAAC-CATTTAAAACAGGGAGATACATACAG------AGTAAAGGG 58934 - - i v i viiv i vii ------ i L1MD_orf2#LIN 124 CAAGAAACTCACTTCAAATATAACGATATAGGTAGGTTGAAAGTAAAAGG 173 chr3ptel1M 58935 GCTGGAGCAGCATCTGTTATGC-----TTCAGGTGAAGTAAAAAAG-GTA 58978 i- iv iv v iii ----- v vvvi v iv i - i L1MD_orf2#LIN 174 A-TGGAAAAAGATATACCATGCAAACATTAATCAAAAGAAAGCAGGAGTG 222 chr3ptel1M 58979 GCCATCCTACT--CAGATCAAGTAAA------AGCAAAATTGATCTAATT 59020 i vi v -- v i ------ --- v-- L1MD_orf2#LIN 223 GCTATATTAATATCAGATAAAGTAGACTTCAGAGCAAA---GAA--AATT 267 chr3ptel1M 59021 AAAAGAGATA-AGAAGGAAACTATATCTTACTAAAAGG-TATATAGACAA 59068 vv i - i v i i vv iv - vv vv v L1MD_orf2#LIN 268 ACCAGAGACAGAGAGGGACATTACATAATGATAAAAGGGTCAATCCACCA 317 chr3ptel1M 59069 TGAAGCAATATCAGTATTAAAAAA--ATGCACCAAGTGGTATAGCATCAA 59116 v vv v i vi viv-- iiiii v v? L1MD_orf2#LIN 318 AGAAGACATAGCAATCCTAAATGTGTATGCACCAAACAACAGAGCTNCAA 367 chr3ptel1M 59117 CTTCCA--AAGGAGAAGTTAAGAAA---GACAGAAGAAATAGACAGCAAA 59161 vv v i-- v i ii i v i --- v i --- L1MD_orf2#LIN 368 AATACGTGAAGCAAAAACTGATAGAACTGAAAGGAGAAATAGACA---AA 414 chr3ptel1M 59162 ACTATAAT---AGCGGGAGACCTCAAT--CTTGACCTCAG-ATTTAATA- 59204 v i i --- iv i i-- iivvi - v i - L1MD_orf2#LIN 415 TCCACAATTATAGTTGGAGACTTCAACACCCCTCTCTCAGCAATTGATAG 464 chr3ptel1M 59205 AACAAAT-CACAAAAAAATAAGAAAGAAATTAAAGAGGTAAATAGAAATT 59253 v -v i vi iv i v vi iv ? i - v ii L1MD_orf2#LIN 465 AACAACTAGACAGAAAATCAGCAAGGATATAGAAGAACTNAACA-ACACC 513 chr3ptel1M 59254 AAAAAC--ACTAGGTATGATAGATCTCTG-AGAAAAC----GAAAGGGAT 59296 vv -- vi i v i v iv i i- v ----vvv ivi i L1MD_orf2#LIN 514 ATCAACCAACAGGATCTAATCGACATTTATAGAACACTCCACCCAACAAC 563 chr3ptel1M 59297 AGAAAGGAGATATTTTCTTCTCAGCAGCTCATGGAAC---CACACAAAAT 59343 v - i v i iv i ivv i i ---i - i L1MD_orf2#LIN 564 AGCA-GAATACACATTCTTTTCAAGTGCCCACGGAACATNTAC-CAAGAT 611 chr3ptel1M 59344 TGACCA-ATATTAGGACATAAAG---ACCCCAAAA---TTAAATGCA--G 59384 v - vi i v i--- i v --- v v -- L1MD_orf2#LIN 612 AGACCATATCCTGGGCCATAAAACAAACCTCAACAAATTTAAAAGAATTG 661 chr3ptel1M 59385 GAAGGAAAAAGAAAA-GTTTTC-GATCA-AATGCAATAAAAC-------C 59424 i vv v v ivi- i - i - v v ------- L1MD_orf2#LIN 662 AAATCATACAGAGTGTGTTCTCTGACCACAATGGAATCAAACTAGAAATC 711 chr3ptel1M 59425 ATTAACAAAAAGTTAGGTGTAAATAAATCAAAAGTAATTGGAAACTAAAT 59474 v i v ivv v - vv v -i v i L1MD_orf2#LIN 712 AATAACAGAAAGATAACAGGAAA-ATCTCCAAA-CACTTGGAAACTAAAC 759 chr3ptel1M 59475 AAC-TATCT-TAAAGAATGATTGGGTGAAACAGCAAATT---ATAGACA- 59518 -i ii - v vvv v v v i i--- vi v - L1MD_orf2#LIN 760 AACACACTTCTAAATAATCCATGGGTCAAAGAGGAAGTCTCAAGGGAAAT 809 chr3ptel1M 59519 ---AAAATAACTT--ACCGATAATGACAACGGTGAGACATCATACCAAAA 59563 --- vv -- i -- v i ivi v v i L1MD_orf2#LIN 810 TAAAAAATACATTGAACTGA--ATGAAAATGAAAATACAACATATCAAAA 857 chr3ptel1M 59564 TTTGTGGGATGCAGCCAAAG-GGTAATAAGGGGAAAACTTTATCTCCTTA 59612 i i -i iv i i i - vv vi L1MD_orf2#LIN 858 TTTGTGGGACGCAGCTAAAGCAGTGCTGAGAGGGAAA-TTTATAGCACTA 906 chr3ptel1M 59613 GAGGCTTACTTGAACAAAAAGAGAAAAAAT----AATGAAT--TTTAA-- 59654 i v ? v v i-- i i ---- v -- i -- L1MD_orf2#LIN 907 AATGCNTACATTAG--AAAAGAGGAAAAGTCTCAAATCAATAATCTAAGC 954 chr3ptel1M 59655 ------CTTAAAAAGCTAGAAAAA--AGACCAAATTAAAAAACCCCAA-- 59694 ------ i i ? -- v v ---- -- L1MD_orf2#LIN 955 TCCCACCTCAAGAANCTAGAAAAAGAAGAGCAAAATAAA----CCCAAAG 1000 chr3ptel1M 59695 CAATTATAAACTTGAAATT--TAAAATTAAAAGGAGAAATTAAT--AATT 59740 vi v ivvv i v -- iv i v i -- L1MD_orf2#LIN 1001 CAAGCAGAAGGAAGGAAATAATAAAGATAAGAGCAGAAATCAATGAAATT 1050 chr3ptel1M 59741 TGAAATAAAAAAACTAT-TAACTAATAAATAAAATTTAAGAGTTGGTTTT 59789 vi i i v -v ivv v i iv- i i i L1MD_orf2#LIN 1051 GAAAACAGAAAAACAATAGAGAAAATCAATGAAACA-AAAAGCTGGTTCT 1099 chr3ptel1M 59790 ATGAAAA--CCAA-AAAATTGATAAACCTTTGG--AAATTGATTAGATAA 59834 v --i - i i i -- i i iv iiv L1MD_orf2#LIN 1100 TTGAAAAGATCAATAAAATTGACAAACCTCTAGCAAGACTGACAAAGAAA 1149 chr3ptel1M 59835 AGGAGGGAGGAAA---AAATTAGTG-TCTTAA-AATGAAAAGGGAGAACC 59879 ii i i i --- vii- v i i- vi i --- L1MD_orf2#LIN 1150 AAAAGAGAGAAGACACAAATTACCAATATCAGGAATGAAACAGGGGA--- 1196 chr3ptel1M 59880 TTTCCACCAATGAA---GAGGAAATTAGAGAAATAA--AAGGAGTTTTTT 59924 - vi i vv v--- vi v i i iii -- i i vi vi L1MD_orf2#LIN 1197 -TATCACTACAGACCCTGCAGACATCAAAAGGATAATAAGGGAATACTAC 1245 chr3ptel1M 59925 GT-CAACTTTATCCAA------TTGATAACCTA-ATGAAATGGATGATAT 59966 v- i iv v------ i i - iv vv L1MD_orf2#LIN 1246 GAACAACTCTACGCACATAAATTTGACAACTTAGATGAAATGGACCAATT 1295 chr3ptel1M 59967 CTCC--AAAATAAGGACTTCCCAGACTAACAGAGGAGGAAGTAATTA--T 60012 ii -- i vii v v?i v vv i? v i iv -- L1MD_orf2#LIN 1296 CCTCGAAAAACACAAACTACCANAACTCACCCAANATGAAATAGATAATT 1345 chr3ptel1M 60013 TAA---GTCCCAT--TTAGAAAAGAAAAGAAA--AGGAATTAAACAACTC 60055 i --- i i --i vv i vvi --v v v? v L1MD_orf2#LIN 1346 TGAATAGCCCTATAACTATTAAGGAAATTGAATTCGTAATTTNAAAACTC 1395 chr3ptel1M 60056 CC----AAGAAAAACCCAGGACCAGATGGATTTATTGAA----TTTACCA 60097 ---- vvi v v i i i ---- i L1MD_orf2#LIN 1396 CCCAAAAAGAAATCTCCAGGCCCAGATGGTTTCACTGGAGAATTCTACCA 1445 chr3ptel1M 60098 AACATTTAAAGAACAATT--C-CCAAT-GTATATAAATTATTTGATAAAA 60143 i v -- - -v i i vi v iv v L1MD_orf2#LIN 1446 AACGTTTAAAGAAGAATTAACACCAATTCTACACAATCTCTTCCAGAAAA 1495 chr3ptel1M 60144 TAGG-GAAGAAGGAGT-CCACCAAATTCCTTCTATGACAC-AGAATGGTA 60190 i- i i ii- iv v i v i vi - v viiv L1MD_orf2#LIN 1496 TAGAAGAGGAGGGAACACTTCCCAACTCATTTTATGAGGCCAGTATTACC 1545 chr3ptel1M 60191 CTGATACCTAAACCGGTAGGCTGAAACAG-----AGAAAGAAAACTATAG 60235 v --- i vi i ----- i i L1MD_orf2#LIN 1546 CTGATACCAAAACC---AGACAAAGACAGTACAAAAAAAGAAAACTACAG 1592 chr3ptel1M 60236 ACCAATCTCCCTAATGAATATTGATGCTAAAATCTTAAATAAAATATTAG 60285 v v i v i v i v i L1MD_orf2#LIN 1593 ACCAATATCCCTCATGAACATAGACGCAAAAATCCTCAACAAAATATTAG 1642 chr3ptel1M 60286 CAAA-AGACTACAGAAAATCATCCCCAGGA-TAC-CACCATGATCAA-TA 60331 -? v v v vvi vvvv i - i- i - i L1MD_orf2#LIN 1643 CAAATNGAATTCAGCAATATATAAAAAGAATTATACACCATGACCAAGTG 1692 chr3ptel1M 60332 GGATTTATACC-GGAATG-GGGTTTGGTTCAAT-TTAGGAAAACTATCAG 60378 i v - ? -ii vi - v i v v i L1MD_orf2#LIN 1693 GGGTTTATTCCAGGNATGCAAGGCTGGTTCAATATTCGAAAATCAATCAA 1742 chr3ptel1M 60379 -ATAATTGGCCATATTAATA-ACCAAACTA-AAAAACCAT-TGCTCATCT 60424 -i ivi i -i i vv - i i- v v L1MD_orf2#LIN 1743 TGTAATCCACCATATTAACAGGCTAAAGAAGAAAAATCACATGATCATAT 1792 chr3ptel1M 60425 CAATAGATG----AAAAAAATTTGATAAAATCCAACATCCATTCTTATTA 60470 v ---- iv i i i v iv L1MD_orf2#LIN 1793 CAATTGATGCAGAAAAAGCATTTGACAAAATTCAACACCCATTCATGATA 1842 chr3ptel1M 60471 AAAACACTTGAGAGTATAGGAA-AAATGGACTTTTCCTTAA---AAT-AA 60515 v iii? ivv - i v ivvi i ---i - L1MD_orf2#LIN 1843 AAAACTCTCAGNAAACTAGGAATAGAGGGGAACTTCCTCAACTTGATAAA 1892 chr3ptel1M 60516 TAGTATCTATTTAAAAAC---CATCAAA---CATATGTAATGGGGACAAA 60559 v i -iv --- v v --- iv v v i L1MD_orf2#LIN 1893 GAGCATCTA-CAAAAAACCTACAGCTAACATCATACTTAATGGTGAAAGA 1941 chr3ptel1M 60560 CTG-CCACCATTCCAATAAGA-CGG--AGGAAACAAGGTTGCCCAC-ATC 60604 -vii iv i vv - -- vi ii v i i -v L1MD_orf2#LIN 1942 CTGAATGCTTTCCCCCTAAGATCGGGAACAAGGCAAGGATGTCCGCTCTC 1991 chr3ptel1M 60605 ACTGTTC-TATTT--TAT-TTATTAGAAATGCTAGCTATGGCAATAAGAG 60650 iii - i--i -v i i i v i vv iv L1MD_orf2#LIN 1992 ACCACTCTTATTCAACATAGTACTGGAAGTTCTAGCCAGTGCAATAAGGC 2041 chr3ptel1M 60651 CTGAGAAAGAATTAAAGGA---AAAGAATAGGAA-GAGGAAACCAAATT- 60695 vv i i v i i--- v v i i - i iv i - L1MD_orf2#LIN 2042 AAGAAAAGGAAATAAAAGGCATACAGATTGGAAAGGAAGAAATAAAACTG 2091 chr3ptel1M 60696 TCACTCTTTTGTGATGATATGATGGTATACTTAGAGAACCCCAGAGATTC 60745 v v vvv i v v v i i ii v L1MD_orf2#LIN 2092 TCCCTATTTGCAGATGACATGATTGTCTACGTAGAAAATCCCAAGGAATC 2141 chr3ptel1M 60746 TATAAAAAG--TTAAAGAAATAATCCACAATTTTAGCAAAGTTGT-GGTT 60792 i i-- ivv v vviii v i i i i- v L1MD_orf2#LIN 2142 TACAAAAAAACTCCTAGAACTAATAAGTGAGTTCAGCAAGGTCGCAGGAT 2191 chr3ptel1M 60793 ATAAAA-AAACCCACATAAGTC-ATCAGATTCTTATATATCA-CAAAAAA 60839 i i -? vi v i - iiv ii ii - vi L1MD_orf2#LIN 2192 ACAAGATNAACATACAAAAATCAATTGTATTTCTATATACTAGCAATGAA 2241 chr3ptel1M 60840 TCC-----AACAGTCAGTTACAAAGAGAAACTCATTTAAAGTAATACT-- 60882 iv ----- v -v i v v v vvi v i --ii -- L1MD_orf2#LIN 2242 CACGTGGAAACCG-AAATTAAAAATACAATACCATTTACAAT--CGCTCA 2288 chr3ptel1M 60883 -GATAGTATAAAAAATTTAGA-ATCTATCTGCCAAGGGAAAAT---CAGA 60927 -i v iv i v i i- vv iv --- v --- i L1MD_orf2#LIN 2289 AAAAAAAATGAAATACTTAGGTATAAATCTAACAA---AACATGTACAGG 2335 chr3ptel1M 60928 AACTTTATGAGCAAAACTACAAAACACTT-CCACACAAATTAAGTCTGAT 60976 vi v vvv i v-iv v v i ivvv L1MD_orf2#LIN 2336 ACTTGTATGCTGAAAACTACAAAACGCTGATGAAAGAAATCAAAGAAGAT 2385 chr3ptel1M 60977 GTAACT-AATGAAAATAT-TA-AATGCTC-TTGATTCG-AGA---AATTT 61018 v v - i i v i- -vi i - v v - --- iv L1MD_orf2#LIN 2386 CTAAATAAATGGAGAGACATACCGTGTTCATGGATTGGAAGACTCAACAT 2435 chr3ptel1M 61019 AATAAAGATG--AAATACCCTTAAACTAATCTATTTATTTA--GCAATAC 61064 i -- v vi ii i i ? ivvi -- v L1MD_orf2#LIN 2436 AGTAAAGATGTCAATTCTCCCCAAATTGATNTACAGGTTTAACGCAATTC 2485 chr3ptel1M 61065 CAATCAGATTCC---CAAAACTTTTGAT-GACCTAGAAAAAATAAAAC-A 61109 v i v --- i i vi - iv v i? v vv - L1MD_orf2#LIN 2486 CTATCAAAATCCCAGCAAGATTTTTTGTAGATATAGACAAGNTTATTCTA 2535 chr3ptel1M 61110 AAGTTCAT-TGGAAA-ACAAAAGATCAAGAAT--TTGGAA-----TTAAA 61150 i i - -i i v v --i ii ----- i L1MD_orf2#LIN 2536 AAATTTATATGGAAAGGCAAAGGAACTAGAATAGCTAAAACAATTTTGAA 2585 chr3ptel1M 61151 AAAAATCAAATTAA--TGGGTAG-----CTGTACCAGATCT-AAAATTTA 61192 i -- i v -- vi -----? v v i - i i L1MD_orf2#LIN 2586 AAAGA--AGAATAAAGTGGGAGGAATCANTCTACCCGATTTCAAGACTTA 2633 chr3ptel1M 61193 A-AGACAGCT---GTTACTAAAACA-TCTGG-ATTGGC--AGAAATAGAC 61234 v- v i --- v ii i ?- v - -- ii L1MD_orf2#LIN 2634 CTATATAGCTACAGTAATCAAGACNGTGTGGTATTGGCGGAGGGATAGAC 2683 chr3ptel1M 61235 TAGTTGATCAATGGAATAGGTTAGGG 61260 vvi v i iv i L1MD_orf2#LIN 2684 ACATAGATCAATGGAACAGAATAGAG 2709 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.26 CpG sites = 382, Kimura (unadjusted) = 39.09 Transitions / transversions = 1.12 (382/340) Gap_init rate = 0.07 (175 / 2456), avg. gap size = 1.77 (309 / 175) 1888 27.47 10.72 1.22 chr3ptel1M 59311 61260 (938740) L1M5_orf2#LINE/L1 577 2709 (585) m_b110s551i3 4018 chr3ptel1M 59311 TTCTTCTCAGCAGCTCATGGAAC---CACACAAAATTGACCA-ATATTAG 59356 i ivv v ---i - i v - ?i i L1M5_orf2#LIN 577 TTCTTTTCAAGTGCACATGGAACATTTAC-CAAGATAGACCATATNCTGG 625 chr3ptel1M 59357 GACATAAA----GACCC--CAAAATTAAATGCAGGAAGGAAA-----AAG 59395 v ---- v i --i v ? --- vv -----v L1M5_orf2#LIN 626 GCCATAAAACAAGTCTCAATAAATTTNAA---AGGATTGAAATCATACAG 672 chr3ptel1M 59396 AAAA-GTTTTC-GATCA-AATGCAAT-------AAAACCATTAACAAAAA 59435 iv - i - i - v -------i i v L1M5_orf2#LIN 673 AGTATGTTCTCTGACCACAATGGAATTAAATTAGAAATCAATAACAAAAA 722 chr3ptel1M 59436 GTTAGGTGTAAATAAATCAAAAGTAATTGGAAACTAAATAAC-TATCT-T 59483 v ?v -- i v vi vv i v i i -i ii - L1M5_orf2#LIN 723 GATANCT--AGAAAATCCCCAAATATTTGGAAATTAAACAACACACTTCT 770 chr3ptel1M 59484 AAAGAATGATTGGGTGAAACAGCAAATTATA---GACA----AAAATAAC 59526 v ivvv v v iv i i --- v ---- vi L1M5_orf2#LIN 771 AAATAACCCATGGGTCAAAGAAGAAATCACAANGGAAATTAGAAAATATT 820 chr3ptel1M 59527 TT--ACCGATAATGACAACGGTGAGACATCATACCAAAATTTGTGGGATG 59574 -- i -- ? i ivi v v i L1M5_orf2#LIN 821 TTGAACTGA--ATGANAATGAAAATACAACATATCAAAATTTGTGGGATG 868 chr3ptel1M 59575 CAGCCAAAG-GGTAATAAGGGGAAAACTTTATCTCCTTAGAGGCTTAC-T 59622 i -i iv v i i - vv ? i v ? i- L1M5_orf2#LIN 869 CAGCTAAAGCAGTGCTTAGAGGGAAA-TTTATAGCNTTAAATGCNTATAT 917 chr3ptel1M 59623 TGAACAAAAAGAGAA----AAAAT-AATGA------ATTTTAACTTAAAA 59661 ii v i i i---- - ------v ii v i L1M5_orf2#LIN 918 TAGAAAAGAAGAAAGGCTTAAAATCAATGATCTAAGCTTCCACCTTAAGA 967 chr3ptel1M 59662 AGCTAGAAAAA--AGACCAAATTAAAAAACCCCAA--CAATTATAAACTT 59707 -- v ---- --? v v ivvv L1M5_orf2#LIN 968 AGCTAGAAAAAGAAGAGCAAATTAAA----CCCAAAGNAAGTAGAAGGAA 1013 chr3ptel1M 59708 GAAATT--TAAAATTAAAAGGAGAAATTAATAATTTGAAATAAAAAAACT 59755 i v -- iv i v i ----- i - v L1M5_orf2#LIN 1014 GGAAATAATAAAGATAAGAGCAGAAATCAAT-----GAAATAGAAAA-CA 1057 chr3ptel1M 59756 ATTAACTAATAAATAAAATT--------TAAGAGTTGGTTTTATGAAAA- 59796 v? ?vi i v i--------i i i i v - L1M5_orf2#LIN 1058 AANANACAATAGAGAAAATCAACGAAGCCAAAAGCTGGTTCTTTGAAAAG 1107 chr3ptel1M 59797 -CCAA-AAAATTGATAAACCTTTGG--AAATTGATTAGATAAAGGAGGGA 59842 -i - i i -- i i i iiv ii i L1M5_orf2#LIN 1108 ATCAATAAAATTGATAAACCTCTAGCNAGACTGATCAAGAAAAAAAGAGA 1157 chr3ptel1M 59843 GGAAA---AAATTAGTG-TCTTAA-AATGAAAAGGGAGAACCTTTCCACC 59887 i i --- vii- v i i- i - v iv i v L1M5_orf2#LIN 1158 GAAGACACAAATTACCAATATCAGGAATGAAAAAGGAGA-CATCACTACA 1206 chr3ptel1M 59888 AATGAAGAGGAAATTAGAGAAATAAAAGGAGTTTTTTGT---CAACTTTA 59934 i vvvivi v i iii v i vv v i --- L1M5_orf2#LIN 1207 GATCCTACAGACATTAAAAGGATAATAAGAGAATATTATGAACAACTTTA 1256 chr3ptel1M 59935 T-CCAAT-----TGATAACCTA-ATGAAATGGATGA-TATCTCCAAAATA 59976 - ----- ? i - ii - vi iv vv L1M5_orf2#LIN 1257 TGCCAATAAATTTGANAACTTAGATGAAATGGACAAATTCCTTGAAAAAC 1306 chr3ptel1M 59977 AGGACTTCCCAGA-CTAACAGAGGAGGAAGTA---ATTATTAA--GTCCC 60020 vi ? v i - i ?v i i i --- v v v -- i i L1M5_orf2#LIN 1307 ACAANTTACCAAAACTGACNCAAGAAGAAATAGAAAATCTGAATAGCCCT 1356 chr3ptel1M 60021 AT--TTAGAAAAGAAAAGAAAA--GGAATTAAACAACTCCC----AAGAA 60062 --i vv vvi v-- v v v i ---- L1M5_orf2#LIN 1357 ATATCTATTAAAGAAATTGAATTTGTAATTAAAAACCTTCCCACAAAGAA 1406 chr3ptel1M 60063 AAACCCAGGACCAGATGGATTTATTG---AATT-TACCAAACATTTAAAG 60108 vi v v i i --- - i L1M5_orf2#LIN 1407 AACTCCAGGCCCAGATGGCTTCACTGGTGAATTCTACCAAACATTTAAGG 1456 chr3ptel1M 60109 AACAA-T--TCCCAATGT-ATATAAATTATTTGATAAAATAGGGAA-GAA 60153 v - -- v v - i i i v iv v ii - i L1M5_orf2#LIN 1457 AAGAAATAATACCAATCTTACACAAACTCTTCCAGAAAATAGAAAAAGAG 1506 chr3ptel1M 60154 GGAGT-CCACCAAATTCCTTCTATGACAC-AGAATGGTACTGATACCTAA 60201 ii- iv v i v i vi - v ?iiv v L1M5_orf2#LIN 1507 GGAACACTTCCCAACTCATTTTATGAGGCCAGCATNACCCTGATACCAAA 1556 chr3ptel1M 60202 ACCGGT--AGGCTGAAACAGAGAAAGAAAACTATAGACCAATCTCCCTAA 60249 ? v-- i viivv iii i i v v L1M5_orf2#LIN 1557 ACCNGACAAAGACATTACAAGAAAAGAAAATTACAGACCAATATCCCTCA 1606 chr3ptel1M 60250 TGAATATTGATGCTAAAATCTTAAATAAAATATTAGCAAA-AGACTACAG 60298 i v v i ? i -v v v L1M5_orf2#LIN 1607 TGAACATAGATGCAAAAATCCTNAACAAAATATTAGCAAATCGAATCCAG 1656 chr3ptel1M 60299 AAAATCATCCCCAGGATA--CCACCATGATCAA-TAGGATTTATACC-GG 60344 v vvi vvvv --v i i - i i v - L1M5_orf2#LIN 1657 CAATATATAAAAAGGATAATACATCATGACCAAGTGGGGTTTATCCCAGG 1706 chr3ptel1M 60345 AATG-GGGTTTGGTTCAAT-TTAGGAAAACTATCAG-ATAATTGGCCATA 60391 -ii v i i- v i v v i-i vi L1M5_orf2#LIN 1707 AATGCAAGGTTGGTTTAACATTCGAAAATCAATCAATGTAATTCACCATA 1756 chr3ptel1M 60392 TTAATA-ACCAAACTA-AAAAACCAT-TGCTCATCTCAATAGATG----A 60434 i - vi vv - i - v ---- L1M5_orf2#LIN 1757 TTAACAGAATAAAGGAGAAAAATCATATGATCATCTCAATAGATGCAGAA 1806 chr3ptel1M 60435 AAAAAATTTGATAAAATCCAACATCCATTCTTATTAAAAACACTTGAGAG 60484 iv i i i v iv v iiiv i L1M5_orf2#LIN 1807 AAAGCATTTGACAAAATTCAACACCCATTCATGATAAAAACTCTCAGCAA 1856 chr3ptel1M 60485 TATAGGAA-AAATGGACTTTTCCTTAAAATAATA----GTATCTATTTAA 60529 vv - i v ivvi i vv i ---- i -iv L1M5_orf2#LIN 1857 ACTAGGAATAGAAGGGAACTTCCTCAACCTGATAAAGGGCATCTA-CGAA 1905 chr3ptel1M 60530 AAAC---CATCAAA---CATATGTAATGGGGACAAACTG-CCACCATTCC 60572 --- v ? --- iv v v ? -v?i iv i L1M5_orf2#LIN 1906 AAACCTACAGCNAACATCATACTTAATGGTGAAANACTGAANGCTTTCCC 1955 chr3ptel1M 60573 AATAAGA-CGG--AGGAAACAAGGTTGCCCAC-ATCACTG-TTCTATTT- 60616 vv - -- vi i v i i -? ii- i- L1M5_orf2#LIN 1956 CCTAAGATCGGGAACAAGACAAGGATGTCCGCTNTCACCACTTCTATTCA 2005 chr3ptel1M 60617 -TATT-TATTAGAAATGCTAGCTATGGCAATAAGAGCTGAGAAAGAATTA 60664 -i - i i ii v i vv ivvv i v L1M5_orf2#LIN 2006 ACATTGTACTGGAGGTCCTAGCCAGTGCAATAAGGCAAGAAAAAGAAATA 2055 chr3ptel1M 60665 AAGGA---AAAGAATAGGAA-GAGGAAACCAAATT-TCACTCTTTTGTGA 60709 i i--- v i i - i iv i - ?i v ivvv L1M5_orf2#LIN 2056 AAAGGCATAAAGATTGGAAAGGAAGAAATAAAACTGTCNTTATTCGCAGA 2105 chr3ptel1M 60710 TGATATGATGGTATACTTAGAGAACCCCAGAGATTCTATAAA-AAGTTAA 60758 i v ? v i i ? i v i - ii v L1M5_orf2#LIN 2106 TGACATGATTGTNTACGTAGAAAATCCNAAAGAATCTACAAANAAACTAC 2155 chr3ptel1M 60759 -AGAAATAATCCACAATTTTAGCAAAGTTG-TGGTTATAAAA-AAACCCA 60805 - v vviii v i i -? v i ii-v ivi L1M5_orf2#LIN 2156 TAGAACTAATAAGTGAATTTAGCAAGGTCGCNGGATACAAGGTCAATATA 2205 chr3ptel1M 60806 CATAAGTC-ATCAGATTCTTATATATC----ACAAAAAATCCAACAGTC- 60849 v i - iiv ii ii---- v ivi v i v- L1M5_orf2#LIN 2206 CAAAAATCAATTGTATTTCTATATACTAGCAACAAACAATTGGAAAATGA 2255 chr3ptel1M 60850 AGTTACAAAGAGAAACTCATTTAAAGTAATA-CTGATAGTATAAAAAATT 60898 i v? i v vvi v i ii - vi v ii ? v i L1M5_orf2#LIN 2256 AATTTNAAAAACAATACCATTTACAATAGCATCAAAAAACATNAAATACT 2305 chr3ptel1M 60899 TA-GAATCTATCTGCCAAGGGAAAAT---CAGAAACTTTATGAGCAAAAC 60944 - vv iv --- ? --- ii v ? iivvv L1M5_orf2#LIN 2306 TAGGAATAAATCTAACAA---AANATGTGCAAGACCTNTACACTGAAAAC 2352 chr3ptel1M 60945 TACAAAACACTTCC-ACACAAATTAAGTCTGATGTAACT-AATGAAAATA 60992 i v i- v v ivvv iv v - i i v L1M5_orf2#LIN 2353 TACAAAACATTGCTGAGAGAAATTAAAGAAGACCTAAATAAATGGAGAGA 2402 chr3ptel1M 60993 T-TA-AATGCTCTTGATTCGAGAAATTTAATA-----AAGATG--AAATA 61033 - -v i v iv i ii i i i ----- -- v v L1M5_orf2#LIN 2403 TATACCATGTTCATGGATTGGAAGACTCAATATTGTNAAGATGTCAATTC 2452 chr3ptel1M 61034 CCCTTAAACTAATCTATTTATTTA--GCAATACCAATCAGATTCCCAAAA 61081 i ii i i vv i -- v i v iv L1M5_orf2#LIN 2453 TCCCCAAATTGATCTATAGATTCAATGCAATCCCAATCAAAATCCCAGCA 2502 chr3ptel1M 61082 ----CTTTTGATGACCTAGAAAAAATAAAAC-AAAGTTCAT-TGGAAA-A 61124 ----i vv vv v v iv i vv - i i - -i L1M5_orf2#LIN 2503 GGTTTTTTTGTAGAAATTGACAAGCTGATTCTAAAATTTATATGGAAATG 2552 chr3ptel1M 61125 CAAAAGATCAAGAAT-------------TTGGAATTAAAAAAAATCAAAT 61161 i i ? ------------- i -- i i iv i L1M5_orf2#LIN 2553 CAAAGGACCNAGAATAGCCAAAACAATCTTGAAA--AAGAAGAACAAAGT 2600 chr3ptel1M 61162 TAATGGG-TAGCTGTACCAGATCT-AAAATTTA----AAGACAGCTGTTA 61205 iiv i- vi vv ? ? - i i ---- ii vi v v L1M5_orf2#LIN 2601 TGGAGGACTTACACTACCNGATNTCAAGACTTATTATAAAGCTACAGTAA 2650 chr3ptel1M 61206 CTAAAACA-TCTGG-ATTGGCAGAA--ATAGACTAGTTGATCAATGGAAT 61251 ii i - v - iv -- v i v i L1M5_orf2#LIN 2651 TCAAGACAGTGTGGTATTGGCGTAAGGATAGACAAATAGATCAATGGAAC 2700 chr3ptel1M 61252 AGGTTAGGG 61260 iv i L1M5_orf2#LIN 2701 AGAATAGAG 2709 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.15 CpG sites = 288, Kimura (unadjusted) = 35.57 Transitions / transversions = 1.20 (288/241) Gap_init rate = 0.07 (130 / 1949), avg. gap size = 1.81 (235 / 130) 16 10.08 2.94 2.94 chr3ptel1M 62378 62411 (937589) (ATAA)n#Simple_repeat 1 34 (0) m_b110s252i11 4019 chr3ptel1M 62378 ATAAAAAGATTTAATAAATAAATAAATAAA-AAAT 62411 v - v v - (ATAA)n#Simpl 1 ATAAATA-AATAAATAAATAAATAAATAAATAAAT 34 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2) 24 19.09 2.90 2.90 chr3ptel1M 62475 62543 (937457) (TTAT)n#Simple_repeat 1 69 (0) m_b110s252i12 4020 chr3ptel1M 62475 TTATTTATTTATTTATTTTTCCTTTTTTTTAAGTATTT-TTTTTTTATTT 62523 v iiv v vv - v - (TTAT)n#Simpl 1 TTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTA-TT 49 chr3ptel1M 62524 TATTATAGTAACTT-TTTATT 62543 - v v i - (TTAT)n#Simpl 50 TATT-TATTTATTTATTTATT 69 Matrix = Unknown Transitions / transversions = 0.38 (3/8) Gap_init rate = 0.06 (4 / 68), avg. gap size = 1.00 (4 / 4) 766 24.01 11.69 2.59 chr3ptel1M 62995 63490 (936510) C L1ME3G_3end#LINE/L1 (378) 546 7 m_b110s551i4 4021 chr3ptel1M 62995 AATATTCCAT--CACACATATACCA--ATTTACCCAACCATTCTCCT--T 63038 i --i iiv -- iii i -- C L1ME3G_3end#L 546 AGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTATT 497 chr3ptel1M 63039 GATGGGCATCC-----CTCCCCAGCTT----CTAATACAAACAGGGCTGC 63079 i ii-----v ii ii ---- v iv C L1ME3G_3end#L 496 GATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCTGC 447 chr3ptel1M 63080 A-CAAACATT-TTGGACATACTGGTCCTTTCCCTTCTTT---AGTATTCC 63124 -ii i- v i ?-- viv viv v --- i C L1ME3G_3end#L 446 AATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATTTC 399 chr3ptel1M 63125 TTTAAA------GCCCAGTAGAAACACTGCTGGATCAAAGGGGATGCAAG 63168 ? ii------? ? v viiv i i v ivi C L1ME3G_3end#L 398 TNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGCA 349 chr3ptel1M 63169 TTTTAAACTTTT-TGGGCATAATTCCAGATTGTTTTCCAGAATGGTTG-A 63216 i v- i -- v v i iii i ? i - C L1ME3G_3end#L 348 TTTTAAATTTTAATAG--ATACTGCCAAATTGCCCTCCAAAANGGCTGTA 301 chr3ptel1M 63217 TTG--TTCCGCTCC-ACCAACAATGTATTAGTGT--CCGTTTTCCCAAGC 63261 iii-- v i - i i v v -- i vi C L1ME3G_3end#L 300 CCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCACAC 251 chr3ptel1M 63262 CC-CTCCAACAATCACTTATTTTTTC---CTGTCA--TCTTAGCCAATCT 63305 - v v ?i--- v v --- v i -- i v C L1ME3G_3end#L 250 CCTCGCCAACACTNG---ATATTATCAANCTTTTAAATTTTTGCCAATCT 204 chr3ptel1M 63306 GACAGGGTGTAG--TGGTATCTGAG-GTC--TTTAATTTG-ATTTTT-TG 63348 i- v i-- v v- i-- - ii- C L1ME3G_3end#L 203 GAT-GGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTG 155 chr3ptel1M 63349 ATTAATAATGAT-TTGGAAAT--TTTCATAGGAGGGTAATG---ATTTCA 63392 v i v- iiv -- v --vv v --- vv C L1ME3G_3end#L 154 ATTACTAGTGAGGTTGAGCATCTTTTCATATG--TTTATTGGCCATTTGT 107 chr3ptel1M 63393 ATTTCATCATCTGAAAATT--TTGTTCATATCCTTTGACCATTTATCAAT 63440 v v vi --i v v v C L1ME3G_3end#L 106 ATTTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTAT 57 chr3ptel1M 63441 TGAGAATGGCTTGGTTTCTTATAAATT----AGAGTCATTTCATATATTT 63486 - iv v -- vi ----i iv - i C L1ME3G_3end#L 56 TG-GGTTGTCTT--TTTCTTATTGATTTGTAGGAGTTCTTT-ATATATTC 11 chr3ptel1M 63487 TGAA 63490 i C L1ME3G_3end#L 10 TGGA 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 29.68 CpG sites = 66, Kimura (unadjusted) = 29.99 Transitions / transversions = 1.32 (66/50) Gap_init rate = 0.08 (41 / 495), avg. gap size = 1.76 (72 / 41) 336 26.77 6.02 3.15 chr3ptel1M 63405 63620 (936380) C L1M3_orf2#LINE/L1 (54) 3234 3013 m_b110s551i5 4021 chr3ptel1M 63405 GAAAATTTTGTTCATATCCTTTGACCATTTATCAATTGAGAATGGCTTGG 63454 vv i i vi v v ? i i -- vii v C L1M3_orf2#LIN 3234 GAAATGTCTATTCAGGTCCTTTGCCCATTTTTNAATCGGG--TTATTTGT 3187 chr3ptel1M 63455 TTTCTTA----TAAATT---AGAGTCATTTCATATATTTTGAA-ATGAGG 63496 i i---- i i ---? ivi - i - v iv C L1M3_orf2#LIN 3186 TTTTTTGCTATTGAGTTGTANGAGTTCCTT-ATATATTTTGGATATTAAC 3138 chr3ptel1M 63497 CCTTTATCAGAATCTTTAATTGGAAGATGTTTTC--CCAGTTTGTTGCTT 63544 i - v v ii v v i i -- v ii v v C L1M3_orf2#LIN 3137 CCCTTATCAGA-TATATGGTTTGCAAATATTTTCTCCCATTCCGTAGGTT 3089 chr3ptel1M 63545 CCCTTCTAATCTTGTTTACATTAGTTTTGTTTG---TACAGAAGCTTTTT 63591 v i v iii v -- - iv --- i C L1M3_orf2#LIN 3088 GCCTTTTCACTCTGTTGA--TT-GTTTCCTTTGCTGTGCAGAAGCTTTTT 3042 chr3ptel1M 63592 AATTTGATGTAATCAAAAATATCTATTTT 63620 i i vv vv i C L1M3_orf2#LIN 3041 AGTTTGATGTAGTCCCACTTGTCTATTTT 3013 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.70 CpG sites = 31, Kimura (unadjusted) = 34.17 Transitions / transversions = 1.24 (31/25) Gap_init rate = 0.06 (12 / 215), avg. gap size = 1.67 (20 / 12) 252 22.28 8.55 4.10 chr3ptel1M 63834 63950 (936050) HERVK14#LTR/ERVK 4999 5120 (976) m_b110s701i0 4022 chr3ptel1M 63834 GGTGGAGAGAT---C---CAAAGAGCAATGAATGGAAGGAACAGACTAAC 63877 i --- --- viv --i - - i HERVK14#LTR/E 4999 GGTGGAGGGATGCACATACAAAGAGCTGGGAA--AAAGGAA-AGA-TAAT 5044 chr3ptel1M 63878 AGCTTGGGGCAGAGGTTTTGCTTGTGTCTCTACAAATGGACA---AGGAA 63924 v?iv v v v ii - --- vi HERVK14#LTR/E 5045 TNTATGGGGAAGAGGATTTGCTTGTGTCTCTCCAGGT-GACAATCAGGTG 5093 chr3ptel1M 63925 TCCA-ATGGGTGTCCACTCACCATGTG 63950 i ii-i i iv v v HERVK14#LTR/E 5094 CCTGTGTGGGTGCCCACCAAACATCTG 5120 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 27.17 CpG sites = 14, Kimura (unadjusted) = 27.17 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.08 (9 / 116), avg. gap size = 1.67 (15 / 9) 19 24.44 0.00 0.00 chr3ptel1M 65836 65888 (934112) (TTTTTGT)n#Simple_repeat 1 53 (0) m_b110s252i13 4023 chr3ptel1M 65836 TTTTTCACTTCTGTTATTTGTATTTTGTTTTATTTTTTATTTTTTTTCTT 65885 vvi i v v v v v v v (TTTTTGT)n#Si 1 TTTTTGTTTTTTGTTTTTTGTTTTTTGTTTTTTGTTTTTTGTTTTTTGTT 50 chr3ptel1M 65886 TTT 65888 (TTTTTGT)n#Si 51 TTT 53 Matrix = Unknown Transitions / transversions = 0.22 (2/9) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 223 20.83 13.89 0.00 chr3ptel1M 68384 68455 (931545) C MIR#SINE/MIR (106) 156 75 m_b110s601i10 4024 chr3ptel1M 68384 ACCATTATT-TCTC---TCTACAAATGAGAAAACTGAG---CAGAGA--T 68424 i - i --- i i i --- -- C MIR#SINE/MIR 156 ACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGT 107 chr3ptel1M 68425 AAAATAATTTGCCATATATTACA-GGCTAATA 68455 v i i vv vi i -i i C MIR#SINE/MIR 106 TAAGTAACTTGCCCAAGGTCACACAGCTAGTA 75 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 25.35 CpG sites = 11, Kimura (unadjusted) = 25.35 Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.07 (5 / 71), avg. gap size = 2.00 (10 / 5) 12 13.90 6.82 4.44 chr3ptel1M 69423 69466 (930534) (ACAGAC)n#Simple_repeat 1 45 (0) m_b110s252i14 4025 chr3ptel1M 69423 ACAGA-ACAAACATA-ACACAGATATTCTG-CACAGACACAGATACA 69466 - i i - i -- v - i (ACAGAC)n#Sim 1 ACAGACACAGACACAGACACAGACA--CAGACACAGACACAGACACA 45 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.12 (5 / 43), avg. gap size = 1.00 (5 / 5) 1110 26.90 4.18 4.41 chr3ptel1M 69960 70414 (929586) L1ME5_3end#LINE/L1 58 511 (430) m_b110s551i6 4026 chr3ptel1M 69960 CCAATTGATAAATGGCCAAAAGATA--AATGGCCAATCTTTCAGATGAAG 70007 v v v i -- ii v - v v i L1ME5_3end#LI 58 CCAATAGAAAAATGGGCAAAGGATATGAACAGGCAAT-TTACAGAAGAGG 106 chr3ptel1M 70008 AAATT-GAAA--CTATTTGTAGTCATATAAAAAGGTGCTCCAAATCACTA 70054 ii- -- ---ii iv i i i v v i L1ME5_3end#LI 107 AAACCCGAAAGGCTA---ACAAGCATATGAAGAGATGCTCAAACTCATTA 153 chr3ptel1M 70055 TTGATCAAAGAAATGCAAATTAAGACAATTCTGAGATACTACTACATACC 70104 v i i i ivv ii vi i L1ME5_3end#LI 154 GTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACC 203 chr3ptel1M 70105 TATCAGATTAGCTAAGATGACAAAA--AGACAATGACAAATGTTGGAGTG 70152 i i i v i v v i--i i v i v v L1ME5_3end#LI 204 TATTAGACTGGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTGGCGAG 253 chr3ptel1M 70153 GATGTGGGAAAAGTGGGACAGTGATGCATT-TTGGTGGAACTGTGAACAG 70201 i ? vv i vv v i -i i v ii v L1ME5_3end#LI 254 GATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACTG 303 chr3ptel1M 70202 ATCCAACCATTCTGGACAGTAATCTGGAACTA--TGATCAAA--AAGCTA 70247 i v i v i v v -- ii -- - L1ME5_3end#LI 304 GTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTAAG-TA 352 chr3ptel1M 70248 TCAAACTGTGCATCCTCTTTGACCCAGTAGTGTTATTACTGGGCTTATAT 70297 --- --- v i v i i viiii v iv L1ME5_3end#LI 353 T---AC---GCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATAT 396 chr3ptel1M 70298 CCCAGAGATATCTTAAAGAAAGG---A-AAGGGGCCCCCACATGTGCAAA 70343 i v ii -v v v --- - ----- i i i L1ME5_3end#LI 397 CCCAAAGAAATTCT-CACACAGGTCCATAAGGGG-----ACATGTACGAG 440 chr3ptel1M 70344 AATGTTTGTGACAACCCTTTTTGTAGTGGCAAGAAACTGGA---AACTGA 70390 i ii vi i vi v i ii i ii --- ivi L1ME5_3end#LI 441 GATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTG 490 chr3ptel1M 70391 GGGAATTCCCATCAATTGGAGAAT 70414 --- vi v v i L1ME5_3end#LI 491 GG---TGTCCATCACTGGGAGAGT 511 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.22 CpG sites = 71, Kimura (unadjusted) = 34.34 Transitions / transversions = 1.54 (71/46) Gap_init rate = 0.07 (30 / 454), avg. gap size = 1.30 (39 / 30) 20 17.41 0.00 2.17 chr3ptel1M 71080 71126 (928874) (TATTT)n#Simple_repeat 1 46 (0) m_b110s252i15 4027 chr3ptel1M 71080 TATTATGTTTTATTTGTTTTTTTTTTCGATTTATTTTATTTTATTTT 71126 v i - v v iiv (TATTT)n#Simp 1 TATTTTATTTTATTT-TATTTTATTTTATTTTATTTTATTTTATTTT 46 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.02 (1 / 46), avg. gap size = 1.00 (1 / 1) 20 22.19 0.00 0.00 chr3ptel1M 71087 71128 (928872) (T)n#Simple_repeat 1 42 (0) m_b110s252i16 4027 chr3ptel1M 71087 TTTTATTTGTTTTTTTTTTCGATTTATTTTATTTTATTTTTT 71128 v v ivv v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 42 Matrix = Unknown Transitions / transversions = 0.14 (1/7) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 1708 26.35 0.55 1.66 chr3ptel1M 71640 72187 (927813) C L1ME3G_3end#LINE/L1 (376) 548 7 m_b110s551i7 4028 chr3ptel1M 71640 ATAATATTCCATAACATTCATATACCACAATTTACTCAACCATTCTCCAA 71689 i ii vv i i i i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr3ptel1M 71690 TTGATGGGCATCCATTCATTTTCCAGCTTCTGGCCATTACAAACAGGGCT 71739 i ii vvivv ii i v i iv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr3ptel1M 71740 GCCACAAACATTTTGGCACATACAGGTCCCTTTCC-C-TTTTTTAGTATC 71787 v ii ii v i i ?-- i v v - - v viv i C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATT 401 chr3ptel1M 71788 TCTTTAGGGAATAAGCCCAGTAGAGACACTGCTGGATCAAAGGGTATGCA 71837 ? iv v v? ? v v iv i i i C L1ME3G_3end#L 400 TCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCG 351 chr3ptel1M 71838 CAGTTTGATAACTTTTGGGGCATAGTTCCAAATTGCTCTCCAGAATGGCT 71887 v --- v iiviv v v i i ? C L1ME3G_3end#L 350 CATTTT---AAATTTTAATAGATACTGCCAAATTGCCCTCCAAAANGGCT 304 chr3ptel1M 71888 GGATGTATTCACGATTCCACCAACAATGTATCAGTGTCCCTGTTTTCCCA 71937 v ivv i iv i i i v v v i i C L1ME3G_3end#L 303 GTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCA 254 chr3ptel1M 71938 CATCC-CTCCAACATTCTGCATTATCTTTCCCTGTCATTCTGGCCAATCT 71986 i - v i ?vii vv? ii vvv i v C L1ME3G_3end#L 253 CACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATCT 204 chr3ptel1M 71987 GACAGGTGTATAGTGGTATCTCAGAGTTGTCTTAATTTGCATTTCTCTGA 72036 ii v v i vv i i C L1ME3G_3end#L 203 GATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGA 154 chr3ptel1M 72037 TCAATAGTGATTTGGAACACTCTTTCATATTAGTAGTAATAGTTTTAATT 72086 i v vv v i iii vvv v iiivi vv C L1ME3G_3end#L 153 TTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGTATT 104 chr3ptel1M 72087 TCATCATCTGAAAATTGTCTGTTCATATCCTTTGACCATTTATCAATTGG 72136 v v vi i v v v C L1ME3G_3end#L 103 TCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGG 54 chr3ptel1M 72137 AGAATGGCTTGATTTCTTATAAATTAGAATCAATTCTCTATATATTTTGG 72186 iv-- v -- vi v v vv i i i C L1ME3G_3end#L 53 GT--TGTCTT--TTTCTTATTGATTTGTAGGAGTTCTTTATATATTCTGG 8 chr3ptel1M 72187 A 72187 C L1ME3G_3end#L 7 A 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.50 CpG sites = 71, Kimura (unadjusted) = 33.34 Transitions / transversions = 1.00 (71/71) Gap_init rate = 0.02 (12 / 547), avg. gap size = 1.00 (12 / 12) 409 28.89 2.17 2.17 chr3ptel1M 72044 72319 (927681) C L1M5_orf2#LINE/L1 (0) 3294 3019 m_b110s551i8 4028 chr3ptel1M 72044 TGATTTGGAACACTCTTTCATATTAGTAGTAATAGTTTTAATTTCATCAT 72093 ?v v i iii i vvv v iiivi v? v v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr3ptel1M 72094 CTGAAAATTGTCTGTTCATATCCTTTGACCATTTATCAATTGGA--GAAT 72141 i vi v vi i v v ?v i-- vv C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTT 3195 chr3ptel1M 72142 GGCTTGATTTCTTATAAATTAGAATCAATTCTCTATATATTTTGGAAATG 72191 v -- ? vi ? v v vv i i i v i C L1M5_orf2#LIN 3194 GTCTT--TTTNTTATTGANTTGTAGGAGTTCTTTATATATTCTGGATACG 3147 chr3ptel1M 72192 AGTCCTTTATCAGA-ATCTTTAACTATAAAAATGTTTTCCCAGTTTATTG 72240 i - v v -?i ii v v i ? i i v C L1M5_orf2#LIN 3146 AGTCCTTTGTCAGATATATGT-NTTGCAAATATTTTCTCCCANTCTGTGG 3098 chr3ptel1M 72241 TTTCCCTTCTAATCTTGCCTGTATTGGTTTTGTTT---GTGCAAAAACTT 72287 i v i v i -- - vi v iv --- v i ii C L1M5_orf2#LIN 3097 CTTGCCTTTTCATTTT--CT-TAACGGTGTCTTTTGANGAGCAGAAGTTT 3051 chr3ptel1M 72288 TTCAATTTGATATAATCAAAATTTTCAATTTT 72319 v v i? i v v v C L1M5_orf2#LIN 3050 TTAATTTTGATGNAGTCCAATTTATCAATTTT 3019 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.02 CpG sites = 36, Kimura (unadjusted) = 38.22 Transitions / transversions = 0.86 (36/42) Gap_init rate = 0.03 (9 / 275), avg. gap size = 1.33 (12 / 9) 1144 32.36 3.81 3.62 chr3ptel1M 73932 75034 (924966) L1PREC2_orf2#LINE/L1 2190 3294 (0) m_b111s551i0 4029 chr3ptel1M 73932 ATACAAAATAAATCCCCCAAAATCCTCAGCACTTTTATATATCACCAACA 73981 v viv v vii i ii --- L1PREC2_orf2# 2190 ATACAAAATCAATGTACAAAAATCACTAGCATTCCTATA---CACCAACA 2236 chr3ptel1M 73982 AAATCCAACAGCAAGAGATACA--AAGA--GAAATTCCATTCAAAATAAC 74027 v v -iv i vi v -- i -- v i v vi L1PREC2_orf2# 2237 ACAGCCAA-GCCGAGAGCCAAATCAGGAACGCAATCCCATTCACAATTGC 2285 chr3ptel1M 74028 TGGCGACAGCATAAAATATTTGGGAATCTATCTA-CCAAAGGAAAGTCAG 74076 iivvi v v ii i vi v - -- i i v i L1PREC2_orf2# 2286 CACAAAAAGAATAAAATACCTAGGAATACAGCTAACCA--GGGAGGTGAA 2333 chr3ptel1M 74077 GAAT-TATATAAGCAAAATTACAAAAAACTTTCCACATAAAT-AAAGTCA 74124 ii - v i vv i v vii v v - i vi- L1PREC2_orf2# 2334 AGATCTCTACAATGAGAATTACAAAACACTGCTCAAAGAAATCAGAGAT- 2382 chr3ptel1M 74125 GATTTAAATAATTGGAAAAATATTAAGTGCTCTTGGATAGACCGAGCGAA 74174 ivi i v i vvi v ivv iiv L1PREC2_orf2# 2383 GACACAAACAAATGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAA 2432 chr3ptel1M 74175 TATAATAAAGATGGCAATACTCCCTAAACTAATCTATTTATTTAGTGCTA 74224 vi v i v v i vi i ivv i i L1PREC2_orf2# 2433 TATCGTTAAAATGGCCATACTGCCCAAAGCAATTTACAGATTCAATGCTA 2482 chr3ptel1M 74225 TACCAATCAGACTTCCAAGAAAATATTTTAATGATCTAGAAAAAAATAAC 74274 v v i v vi v vi i vv v v - i L1PREC2_orf2# 2483 TTCCTATCAAACTACCAATGACATTCTTCACAGAACTAGAAAAAACT-AT 2531 chr3ptel1M 74275 AACAAAATTCATATGGAAGAATAAAAGATTGAGAAT-CTCGAGGGAAT-- 74321 vvi vv v vivv -vi i v -- L1PREC2_orf2# 2532 TTTAAAATTCATATGGAACCAAAAAAGAGCCCGAATAGCCAAGGCAATCC 2581 chr3ptel1M 74322 TAATGAAAAAAAAATCAAATGAAGGTGGCCTAGCTCTACCTGATCTAAAA 74371 vv i -- - vv v v vi v i ii v L1PREC2_orf2# 2582 TAAGCAAAAAGAA--CAAA-GCTGGAGGCATCACGCTACCCGACTTCAAA 2628 chr3ptel1M 74372 CTATATTATAAAGCAGCAGTCACCAAAACCATTTGGTATTGGCTAAGAAA 74421 i i ii vi v viiv i ivv i L1PREC2_orf2# 2629 CTATACTACAGGGCTACAGTAACCAAAACAGCATGGTACTGGTACAAAAA 2678 chr3ptel1M 74422 TAGATTAGTTGATCAGTGGAATAGGTTAG---GTTCATAAGACAAAATAG 74468 i ivvi v i i i iv --- ii v - i iiiv L1PREC2_orf2# 2679 CAGACACATAGACCAATGGAACAGAATAGAGAGCCCAGAA-ATAAGGCCG 2727 chr3ptel1M 74469 TCCA-CTATAGCATTCTAGTGTTTGACAAA-CT--CAAAGATCCTAACTT 74514 iv - i i vv ii v i - -- i -- v i vv L1PREC2_orf2# 2728 CACACCTACAACCATCTGATCTTCGACAAAGCTGACAAAAA--CAAGCAA 2775 chr3ptel1M 74515 TTGGGATAAGAACTCATTGTTTGACAAAAACTGCTGGGATAACTTTAAAA 74564 v - i vi i ii i viv ---iiv L1PREC2_orf2# 2776 TGGGGA-AAGGACTCCCTATTCAATAAATGGTGCTGGGATAACT---GGC 2821 chr3ptel1M 74565 TAG---TATGGCAGAA-ATTAGGCATGGACCCACACTTAACACCGTATAC 74610 --- - - iiivv viv i v i L1PREC2_orf2# 2822 TAGCCATAT-GCAGAAGATTGAAACTGGACCCCTTCCTTACACCATATAC 2870 chr3ptel1M 74611 CAAGATAAGATCAAAATGGGTCCATTATTTAGGGATAAAGAACGAGATTA 74660 v i v iv i i iv vv i iivi ivv i i i L1PREC2_orf2# 2871 AAAAATCAACTCAAGATGGATTAAAGACTTAAATGTAAAACCCAAAACTA 2920 chr3ptel1M 74661 TAAATAAATTAGGGAAACA---TAGGATAGTTTACC-TCTTAGACTTGTA 74706 - viiv i i --- vv --- - ii i v ivi L1PREC2_orf2# 2921 TAAA-AACCCTGGAAGACAACCTAGGCAA---TACCATTCTGGACATAGG 2966 chr3ptel1M 74707 GAGGAGAAAGAAAATTGTGACCAAAGATGAACTAGAGATCATTATTG--- 74753 i v i v ii vv ii - i i -- i - i v -- --- L1PREC2_orf2# 2967 AACGGGCAAAGATTTCATGA-CGAAGACG--CCA-AAAGCA--ATTGCAA 3010 chr3ptel1M 74754 ----ATCACAAAATAGAAAATTTTGATTATACCAAATTAAAAACCCTTTG 74799 ---- v - v v v vv ivv ii i i v i i L1PREC2_orf2# 3011 CAAAAGCA-AAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTG 3059 chr3ptel1M 74800 TA---CAAACAAAACTAATGCAAACAAGATTAGA-AGGGAAACAATAAAC 74845 i --- vi vi--- - v i - iv v v i i v L1PREC2_orf2# 3060 CACAGCAAAAGAAACTATC---AAC-AGAGTAAACAGACAACCTACAGAA 3105 chr3ptel1M 74846 TGGGAAAACATCTTCACAGTTAAAGGTTCTGATAAAGGCCTCATTTCCAA 74895 i v ? ii iviv v vv i i v v i L1PREC2_orf2# 3106 TGGGAGAAAATNTTTGCAAACTATGCATCTGACAAAGGTCTAATATCCAG 3155 chr3ptel1M 74896 AATATATAGAGAATTGACTCTAATTTATAAG---AAATCAAGCCATTCTC 74942 v v ii i v vv v i --- v i v -- i L1PREC2_orf2# 3156 CATCTATAAGGAACTTAAACAAATTTACAAGAAAAAAACAAACAA--CCC 3203 chr3ptel1M 74943 CAAATGATAAATGGTCAAAGGATATGAGCAGACAATTTTCAGATGATGAA 74992 - v i v i v i i v i v v v L1PREC2_orf2# 3204 C-ATTAAAAAGTGGGCAAAGGACATGAACAGACACTTTTCAAAAGAAGAC 3252 chr3ptel1M 74993 AT---TGAAACTATTTCCACTCATATGAAAGAGTGTTCCAAATCA 75034 --- vii i ---v vv i iv i v v L1PREC2_orf2# 3253 ATACATGCGGCCA---ACAAGCATATGAAAAAAAGCTCAACATCA 3294 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 42.01 CpG sites = 177, Kimura (unadjusted) = 43.16 Transitions / transversions = 1.06 (177/167) Gap_init rate = 0.06 (61 / 1102), avg. gap size = 1.34 (82 / 61) 1730 27.85 2.23 2.07 chr3ptel1M 74896 75522 (924478) L1ME4c_3end#LINE/L1 12 639 (191) m_b111s551i1 4029 chr3ptel1M 74896 AATATATAGAGAATTGACTCTAATTTATAAGAAA----TCAAGCCATTCT 74941 ? i ii v i v v ---- v ----i L1ME4c_3end#L 12 ANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAAGAC----C 57 chr3ptel1M 74942 CCAAATGATAAATGGTCAAAGGATATGAGCAGACAATTTTCAGATGATGA 74991 vv v i i iv ? v v L1ME4c_3end#L 58 CCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAGGA 107 chr3ptel1M 74992 AATTGAAACTATTTCCACTCATATGAAAGAGTGTTCCAAATCACTATTGA 75041 vv ?ivi vvv vv i i i i v vv i v i L1ME4c_3end#L 108 AATACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTAGTAA 157 chr3ptel1M 75042 TCAGAGAAATACAAATTAAGACAACTCTGAGATACCACTACACACCTGTC 75091 i i ii vv i vi i i i L1ME4c_3end#L 158 TCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCTATT 207 chr3ptel1M 75092 AGATTGGCTAAGATGACAGGAAAAAATAATGATG---AATGCTGGAGGGG 75138 i i v i v---vi v i i i--- v i L1ME4c_3end#L 208 AAATTAGCAAAAATT---TAAAAAATTGATAATACCCAATGCTGGCGAGG 254 chr3ptel1M 75139 ATGTGGGAAAACTGGGACACTGATGCATTGTGGGTGGAGTTGTGAATGAA 75188 ? i vi v ? v i iv vi? i vii L1ME4c_3end#L 255 NTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGG 304 chr3ptel1M 75189 TCTAACCATTCTGGAGAGCAATCTGGAAATATGCCCCAAAAGTTATCAAA 75238 vi v i i i v i ivi i ii v L1ME4c_3end#L 305 TACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAAA 354 chr3ptel1M 75239 CTGTGCATACCCTTTGACCCAGCAGTGCTACTACTGGGCTTATACCCCAA 75288 v v i i v i v vv v i i L1ME4c_3end#L 355 ATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAA 404 chr3ptel1M 75289 AGAGATACT---AAAGAAGGGAAAAGGACCTATGTG--CCAAAATGTTTG 75333 i i v --- i --- i -- v i ii L1ME4c_3end#L 405 GGAAATAATTCAAAAGAAGGAAAAAG---CTATATGCACGAAGATGTTCA 451 chr3ptel1M 75334 TGGCAGCCCTGTTTGTAGTGGCTAGAAACTGGAAAATGAA--TGGATGTC 75381 v vi i i i i v i i --v -- ii L1ME4c_3end#L 452 TTGCAGCGTTATTTATAATAGCGAAAAATTGGAAA--CAACCTAAATGTC 499 chr3ptel1M 75382 CATCAATTGGAGAATGGTTGGGTAAATTGTGGTATAAGAATGTTATGGAA 75431 v v i ii i i vv? iviv L1ME4c_3end#L 500 CAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAA 549 chr3ptel1M 75432 TATTATTGTTCTGTAAGAAATGACCAGCAGGAGGAATACAGAGAGGCTTG 75481 vvvv ii v i iv vi v i v iiv vii v L1ME4c_3end#L 550 TATTATGCAGCCATTAAAAATGATAATTATGAAGACTATGTAGCAACATG 599 chr3ptel1M 75482 GAGAGACTTACATGAACTGATGTTAAGTGAAATGAGCAGAA 75522 i ivv -i vv i vi L1ME4c_3end#L 600 GAAAATGTT-TATGATATAATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 34.70 CpG sites = 94, Kimura (unadjusted) = 36.00 Transitions / transversions = 1.22 (94/77) Gap_init rate = 0.03 (18 / 626), avg. gap size = 1.50 (27 / 18) 13 4.76 0.00 4.35 chr3ptel1M 75946 75969 (924031) (AAAG)n#Simple_repeat 1 23 (0) m_b111s252i0 4030 chr3ptel1M 75946 AAAAAAAGAAAGAAAGAAAAGAAA 75969 i - (AAAG)n#Simpl 1 AAAGAAAGAAAGAAAG-AAAGAAA 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 38 0.00 0.00 0.00 chr3ptel1M 77919 77951 (922049) (TG)n#Simple_repeat 1 33 (0) c_b111s251i0 4031 chr3ptel1M 77919 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 77951 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 33 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 14 29.03 1.67 1.67 chr3ptel1M 77956 78015 (921985) (ATAT)n#Simple_repeat 1 60 (0) m_b111s252i1 4032 chr3ptel1M 77956 ATGTATATCAT-TACATATAGATATGTTGAAATCTATATATCTATCCATC 78004 i - - i v i vv v v v vi v (ATAT)n#Simpl 1 ATATATAT-ATATATATATATATATATATATATATATATATATATATATA 49 chr3ptel1M 78005 TATCTATCTAT 78015 v v (ATAT)n#Simpl 50 TATATATATAT 60 Matrix = Unknown Transitions / transversions = 0.40 (4/10) Gap_init rate = 0.03 (2 / 59), avg. gap size = 1.00 (2 / 2) 21 9.39 0.00 0.00 chr3ptel1M 77986 78019 (921981) (ATCT)n#Simple_repeat 1 34 (0) m_b111s252i2 4033 chr3ptel1M 77986 ATCTATATATCTATCCATCTATCTATCTATCAAT 78019 v i v (ATCT)n#Simpl 1 ATCTATCTATCTATCTATCTATCTATCTATCTAT 34 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 20 19.17 3.17 3.17 chr3ptel1M 78748 78810 (921190) (AAAGA)n#Simple_repeat 1 63 (0) m_b111s252i3 4034 chr3ptel1M 78748 AAAGACACAGATAAG-AAA-AACAGAAAAGGAATGCAAAATAAAATAAAA 78795 - v v - - v i v - v v (AAAGA)n#Simp 1 AAAGA-AAAGAAAAGAAAAGAAAAGAAAAGAAAAG-AAAAGAAAAGAAAA 48 chr3ptel1M 78796 CAAAACAGAAGAAAA 78810 v v i (AAAGA)n#Simp 49 GAAAAGAAAAGAAAA 63 Matrix = Unknown Transitions / transversions = 0.25 (2/8) Gap_init rate = 0.06 (4 / 62), avg. gap size = 1.00 (4 / 4) 14 17.32 7.14 3.45 chr3ptel1M 78750 78805 (921195) (AGAAAC)n#Simple_repeat 1 58 (0) m_b111s252i4 4034 chr3ptel1M 78750 AGACACAGATAAGAAAAACAGAAAAGGAATGCA-AAATA-AAATA-AAAC 78796 v - v i vi -i - i - i - (AGAAAC)n#Sim 1 AGAAACAGA-AACAGAAACAGAAACAGAA-ACAGAAACAGAAACAGAAAC 48 chr3ptel1M 78797 A-AAACAGAA 78805 - (AGAAAC)n#Sim 49 AGAAACAGAA 58 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.11 (6 / 55), avg. gap size = 1.00 (6 / 6) 18 24.78 0.00 0.00 chr3ptel1M 78875 78914 (921086) (AT)n#Simple_repeat 1 40 (0) m_b111s252i5 4035 chr3ptel1M 78875 ATATGTATATATATATACACACACAGACATATATATACAT 78914 i i i i i v i i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATAT 40 Matrix = Unknown Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 33 0.00 0.00 0.00 chr3ptel1M 78920 78947 (921053) (AC)n#Simple_repeat 1 28 (0) c_b111s251i1 4036 chr3ptel1M 78920 ACACACACACACACACACACACACACAC 78947 (AC)n#Simple_ 1 ACACACACACACACACACACACACACAC 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 18 31.68 0.00 0.00 chr3ptel1M 79117 79168 (920832) (AT)n#Simple_repeat 1 52 (0) m_b111s252i7 4037 chr3ptel1M 79117 ATATATTTATATATACATATGTAGATATACACAAACACATACACAGACAT 79166 v i i v i i v i i i i v i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr3ptel1M 79167 AT 79168 (AT)n#Simple_ 51 AT 52 Matrix = Unknown Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 417 23.18 0.00 6.59 chr3ptel1M 82802 82898 (917102) MIRc#SINE/MIR 25 115 (153) m_b111s601i0 4038 chr3ptel1M 82802 GAGCACCAACCCTGAAGTCAGGAGGACCTGAGTTCAAATCTGGTCTCAGA 82851 iiiv i i i i i i iv v v v MIRc#SINE/MIR 25 GAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGC 74 chr3ptel1M 82852 CATTTAACACTTCTAGCTGTGTGATCCTGGGCACCTCACTTAACCCC 82898 i ------ i i vv i MIRc#SINE/MIR 75 CACTTA------CTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 26.87 CpG sites = 14, Kimura (unadjusted) = 28.45 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.06 (6 / 96), avg. gap size = 1.00 (6 / 6) 283 19.75 7.41 0.00 chr3ptel1M 85956 86036 (913964) MIRc#SINE/MIR 121 207 (61) m_b111s601i1 4038 chr3ptel1M 85956 GTCTCCGTCTCCTCATCTGT-GAATGGGGCTAATAAAAGC--CCCTCCCT 86002 i v i -i v v v -- v MIRc#SINE/MIR 121 GCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCT 170 chr3ptel1M 86003 -CCTCCCA--TCCGCTGTGGGGATCTAATGAGGTAAT 86036 - v --vii i i v i MIRc#SINE/MIR 171 ACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAAT 207 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 23.07 CpG sites = 8, Kimura (unadjusted) = 23.07 Transitions / transversions = 1.00 (8/8) Gap_init rate = 0.05 (4 / 80), avg. gap size = 1.50 (6 / 4) 12 19.11 2.63 2.63 chr3ptel1M 87411 87448 (912552) (TCTTCC)n#Simple_repeat 1 38 (0) m_b111s252i8 4039 chr3ptel1M 87411 TCTTCCTCTCCCTCCATTTCTGTCCTCTTCC-CTTCATC 87448 i ivii - - v (TCTTCC)n#Sim 1 TCTTCCTCTTCCTCTTCCTCT-TCCTCTTCCTCTTCCTC 38 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 12 16.38 5.88 0.00 chr3ptel1M 87724 87757 (912243) (TCAG)n#Simple_repeat 1 36 (0) m_b111s252i9 4040 chr3ptel1M 87724 TCGGTCAGTCAGTCAG-CAGACA-TTTGTCAGGCAG 87757 i - v - iv v (TCAG)n#Simpl 1 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG 36 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2) 502 23.56 9.49 0.58 chr3ptel1M 88589 88746 (911254) C MIRb#SINE/MIR (6) 262 91 m_b111s601i2 4041 chr3ptel1M 88589 AGAGCAAACATTTATT-----CTC-CTATGTGCCAGGCATTGTGCTAAGT 88632 v v ----- i- i i C MIRb#SINE/MIR 262 AGAGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGC 213 chr3ptel1M 88633 CCTTTAGAAACATTAGATCCTGTGGTACTCACAGAAATCCTGAGAGGAAG 88682 v v vi vv v v ii v iv i v v C MIRb#SINE/MIR 212 GCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAG 163 chr3ptel1M 88683 G----ATTACACCCTAATTTCCAGATAAAGAAGCTAAAGC----AGAGCT 88724 ---- i- i v v i i i i i ---- v C MIRb#SINE/MIR 162 GTATTATTAT-CCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGT 114 chr3ptel1M 88725 GAGGGAGCTT-CACAGGGTCACA 88746 v i v i - v i C MIRb#SINE/MIR 113 TAAGTAACTTGCCCAAGGTCACA 91 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.62 CpG sites = 18, Kimura (unadjusted) = 28.49 Transitions / transversions = 0.95 (18/19) Gap_init rate = 0.04 (6 / 157), avg. gap size = 2.67 (16 / 6) 182 27.93 5.67 10.13 chr3ptel1M 91061 91307 (908693) C L2#LINE/L2 (2585) 497 261 m_b111s601i3 4042 chr3ptel1M 91061 AAGGGAGGCTGTGACATCAGTGAAGGAGCCGAGCTTCAGTGATAGCTAGA 91110 i i v v v v i - ii i ? v v v C L2#LINE/L2 497 AGGGGAAGCAGTGTCCTCAGGGGAG-AGCCAGGTTTCNGTTAGAGCAAGA 449 chr3ptel1M 91111 AGATGGAAGGAGTGGGGAGAGA--AGGTTG-GGATGAAGAGGCATTCATT 91157 i i i ii vvv -- - - v i v -- C L2#LINE/L2 448 AGGTGAAGGGAACGTTCAGAGAAGAGGTTGAGGAT-ACGGGGGATT--TT 402 chr3ptel1M 91158 ACCTATGAAAAA--G-GCATTTCAGAGGACACAATAAAGGTGGGGGATGG 91204 i iv vii -- - vi i i i --------- v C L2#LINE/L2 401 GCTGATGACGGACCGTGAGTTCCAGAGGGCACAGT---------GGAAGG 361 chr3ptel1M 91205 GAATAAGGAACCAGATGATGGAGACTGGGGAATCGGGTTTGGAT-GATGA 91253 vv v iiii i- - i -- ii v iv i ?- iv C L2#LINE/L2 360 GTTTCAGGAGTTGGG-GA-GGGG--TGGGAGATGGGGTCAGAANAGGAGA 315 chr3ptel1M 91254 TTTACAGGG--GT-TTGGAATT----TCTGGGACGTGGAGGGTATGACCA 91296 v i -- - v i ?---- i ivi - - - C L2#LINE/L2 314 TGTACAGAGCCGTATGGGGATNAGAGTCCGGGGGAT-GAGGG-ATGACC- 268 chr3ptel1M 91297 GATATGAGAGT 91307 ---- i C L2#LINE/L2 267 ----TGGGAGT 261 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.15 CpG sites = 37, Kimura (unadjusted) = 36.34 Transitions / transversions = 1.48 (37/25) Gap_init rate = 0.13 (32 / 246), avg. gap size = 1.19 (38 / 32) 309 32.33 5.04 2.10 chr3ptel1M 91921 92059 (907941) C L3#LINE/CR1 (1) 4098 3956 m_b111s601i4 4043 chr3ptel1M 91921 ATAAAGTTTTAGAATCTTAC--TTGAAATAAAA-TTACAGAGCAGTCCAG 91967 i i ivi i v-- i vii v- v iv - i C L3#LINE/CR1 4098 ATAGAATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCA-TCTAG 4050 chr3ptel1M 91968 TC-AGGTTCCCAGTTAATTCAGGAATGCCTTCTAGGGCCTCTCT---AAG 92013 - ivi vii v v vii v i --- C L3#LINE/CR1 4049 TCCAACCTCCCATCCAATGCAGGAATCCCTTCTACAACATCCCTGACAAG 4000 chr3ptel1M 92014 TGACCACTTCCAGCTTCTGATTAAATGTTTTCAGATGCCGTGAGCT 92059 ii -- i v i iiii i vvi v v C L3#LINE/CR1 3999 TGGTCA--TCCAGCCTCTGCTTGAACACCTCCAGTGACGGGGAGCT 3956 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 44.11 CpG sites = 27, Kimura (unadjusted) = 44.11 Transitions / transversions = 1.59 (27/17) Gap_init rate = 0.05 (7 / 138), avg. gap size = 1.43 (10 / 7) 244 34.07 5.15 2.88 chr3ptel1M 92074 92209 (907791) MIR3#SINE/MIR 6 144 (64) m_b111s601i5 4044 chr3ptel1M 92074 AGAAGAGCAGAGCATGGCAAGTCCATGAGGATGGAAGGGAGCAGACCCGC 92123 ivi v vi vi -- i - iv i vv v i v MIR3#SINE/MIR 6 AGAGTGGCTGAGCAGAGAGAG--CACG-GACTGGGAGTCAGGAGACCTGG 52 chr3ptel1M 92124 ATTCTGGTCGTGAGCTC-----CCAATTAACTCCGTGGTCTTAGAGAAGT 92168 i i vi - ----- i i ?i vi ii i iv MIR3#SINE/MIR 53 GTTCTAGTCCCG-GCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGT 101 chr3ptel1M 92169 CACTACAGTGCTCCAAGTCTC--TGTGCTCCTTTATAAAAAGA 92209 v viv iii i -- v v v i i v MIR3#SINE/MIR 102 CACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGA 144 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 44.69 CpG sites = 26, Kimura (unadjusted) = 47.61 Transitions / transversions = 1.37 (26/19) Gap_init rate = 0.04 (6 / 135), avg. gap size = 1.83 (11 / 6) 191 22.92 2.08 0.00 chr3ptel1M 92380 92427 (907573) C X6A_LINE#LINE/CR1 (474) 604 556 m_b111s601i6 4045 chr3ptel1M 92380 TATTTATTTTTTATCT-CTTTCAGATGAAGAGACTGGGACTGAATGCAG 92427 v vi ? i - v v iiii i C X6A_LINE#LINE 604 TATTTCTGCTNTGTCTTCTTTGAGATGAAGTGACCAAAACTGAACGCAG 556 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 25.80 CpG sites = 7, Kimura (unadjusted) = 28.81 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.02 (1 / 47), avg. gap size = 1.00 (1 / 1) 268 27.27 12.59 0.00 chr3ptel1M 94394 94536 (905464) C MIR1_Amn#SINE/MIR (66) 164 4 m_b111s601i7 4046 chr3ptel1M 94394 TCAG-ATCTGTCTCCTCATTT-ATAATTAAAGAAACAG-GGCCGAGGGAG 94440 - vv v i - i iv i i v - ?v i C MIR1_Amn#SINE 164 TCAGTATCATTATCCCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAG 115 chr3ptel1M 94441 A-GAATTGATTTGTCGGGAGTC--CCAGCAG-TGAG-GGCAG-------- 94477 i-? v i i viii --? ? -i? - -------- C MIR1_Amn#SINE 114 GTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNAGTGGCAGAGCCGGGA 65 chr3ptel1M 94478 TATGAAGTCGGGCCTCATGA-TCCAAGCCCAGCAA-CTTTCTACTAAATC 94525 ?v? vi i i vi - v i iiv- v i i i C MIR1_Amn#SINE 64 NTNGAACCCAGGTCTCCCGAGTCCCAGTCCAGTGCTCTATCCACTAGACC 15 chr3ptel1M 94526 ATGCTGCCTCC 94536 ii C MIR1_Amn#SINE 14 ACACTGCCTCC 4 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.33 CpG sites = 25, Kimura (unadjusted) = 37.56 Transitions / transversions = 1.79 (25/14) Gap_init rate = 0.07 (10 / 142), avg. gap size = 1.80 (18 / 10) 19 14.92 0.00 0.00 chr3ptel1M 95812 95842 (904158) (A)n#Simple_repeat 1 31 (0) m_b111s252i10 4047 chr3ptel1M 95812 AAAAAAAAAAAAAAGAAAAGAAAAAGAAGAA 95842 i i i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 31 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 12 11.13 6.90 0.00 chr3ptel1M 96123 96151 (903849) (TATT)n#Simple_repeat 1 31 (0) m_b111s252i11 4048 chr3ptel1M 96123 TATTTCTTT-TTT-TTAATTTATTTATTCAT 96151 v - - v i (TATT)n#Simpl 1 TATTTATTTATTTATTTATTTATTTATTTAT 31 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.07 (2 / 28), avg. gap size = 1.00 (2 / 2) 544 27.69 9.58 0.55 chr3ptel1M 96981 97147 (902853) C MIRc#SINE/MIR (84) 184 3 m_b111s601i8 4049 chr3ptel1M 96981 CAATACTGAAAAGTAGAT------GACACTAATGTTCCCATTTTACATAT 97024 iv vi i ii------ ii i v i i v C MIRc#SINE/MIR 184 CAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGAT 135 chr3ptel1M 97025 GAGGAAACGGGGAC--AAACAGATTAAGTGACTTGCCTAGGATCACCCAG 97072 v i i -- i v i i i i v C MIRc#SINE/MIR 134 GAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAG 85 chr3ptel1M 97073 T-----AGTGTCTAAGGCTAGAGTTGAACTCGGAACTCCCTGACTCTAGG 97117 i----- v vi v vi v i i i iv i i i C MIRc#SINE/MIR 84 CTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr3ptel1M 97118 TCCAG-G--TTTTCCACTGTTACTTAGCTGCCT 97147 - --i -i ivvi C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTG-CACCACACTGCCT 3 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.15 CpG sites = 31, Kimura (unadjusted) = 36.15 Transitions / transversions = 2.07 (31/15) Gap_init rate = 0.04 (6 / 166), avg. gap size = 2.83 (17 / 6) 259 38.10 2.38 0.00 chr3ptel1M 97150 97275 (902725) C L3#LINE/CR1 (393) 3706 3578 m_b111s601i9 4050 chr3ptel1M 97150 TTCTCCACAGGGCATGACCTCAAGTTCCTATACCATCTAAGCTGC---CT 97196 ii i v i iii v vi vi ivi ii --- i C L3#LINE/CR1 3706 TTCCTCATATGACATGGTTTCCAGACCCTTCACCATCCTGGTCGCTCTCC 3657 chr3ptel1M 97197 TGTGTACCTTCTCCAACTTCTCAATGACCTTTGTAAAACTTGGCAACCAT 97246 v v viv ii v v i iv iv iv v C L3#LINE/CR1 3656 TCTGGACGCGCTCCAGTTTGTCAATGTCCCTCTTAAAATGTGGCGCCCAG 3607 chr3ptel1M 97247 TACTGAGCTCCACATCTCAAATGAAATCT 97275 v i v v i iii i vii C L3#LINE/CR1 3606 AACTGAACGCAATACTCCAGATGTGGTCT 3578 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 50.97 CpG sites = 29, Kimura (unadjusted) = 56.20 Transitions / transversions = 1.53 (29/19) Gap_init rate = 0.01 (1 / 125), avg. gap size = 3.00 (3 / 1) 338 37.80 0.91 8.09 chr3ptel1M 97298 97628 (902372) C L3#LINE/CR1 (580) 3519 3211 m_b111s601i10 4050 chr3ptel1M 97298 TCAGTACAGCCTGAGATCACTTGAACTTTCCTGACCGCCATCTTGTATTC 97347 i i i i ii v v i ii i v iv iii i v C L3#LINE/CR1 3519 TTAATGCAGCCTAAGATTGCATTAGCTTTTTTGGCAGCCACATCACACTG 3470 chr3ptel1M 97348 ATGGAGC-TATGATGCTGGTAGCTC--TTATAATCCACTCAAGGCTTTTT 97394 v vv - viv v ii - --i v i - -- ii C L3#LINE/CR1 3469 TTGGCTCATATTGAGCTTGCGG-TCAACTAAAACCC-CT--AGGTCTTTT 3424 chr3ptel1M 97395 TTCGGTCAAATTGTGGTTTAGCCCTACGTCTTCCATTTTGTACTTGGGAA 97444 ivv -i i iv i v vv iviii ii v v C L3#LINE/CR1 3423 TCACGT-GAACTGCTGCTAAGCCAGATCCTCTCCATCCTGTACTTGTGCA 3375 chr3ptel1M 97445 GAAGGCTCTGTGTGTATGTGTGTGTGAGATGGAAGAATGAGACTTGACAT 97494 vv ii i v v-- iv ivi iii ivvv v v v vv i vi - C L3#LINE/CR1 3374 GTTGATTTTTTGA--ACCTAAATGCAGGACTTTACATTTATCCCTGTTA- 3328 chr3ptel1M 97495 AATGTCATCTTAATGACTTTGGTCCTATGTCCAATCGCCTCAAGGGTTTT 97544 v iv ii i i vvi i v v viv i ivi? C L3#LINE/CR1 3327 AATTTCATCTTGTTGGTTTCGGCCCATCGTTCCAGCCTGTCGAGATCNTT 3278 chr3ptel1M 97545 CTGAGTCCTGACTCTGTCATTCAGTGTGTGAGCTGTTTTCTTCTCAAAAT 97594 i i i i i ?i i v -------------- C L3#LINE/CR1 3277 TTGAATCTTGATTCTGTCATCCANCGTATTAGCT--------------AT 3242 chr3ptel1M 97595 CCTCACCTCAGTTCTGTATCATCTGCAAAATTTG 97628 i--i i i i i - C L3#LINE/CR1 3241 CCC--TCCCAGCTTTGTGTCATCTGC-AAATTTG 3211 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 51.79 CpG sites = 69, Kimura (unadjusted) = 55.49 Transitions / transversions = 1.50 (69/46) Gap_init rate = 0.08 (27 / 330), avg. gap size = 1.04 (28 / 27) 437 28.45 4.58 0.74 chr3ptel1M 97705 97835 (902165) MIR#SINE/MIR 6 141 (121) m_b111s601i11 4051 chr3ptel1M 97705 ATAATAAAGTAGCTA-TAATGCCAGCCCTAGAATCAAAAGGATCTGAGTT 97753 ii v i i -v iii vi i i ii i vv -i i MIR#SINE/MIR 6 ATAGCATAGTGGTTAAGAGCACGGGCTCTGGAGCCAGACTG-CCTGGGTT 54 chr3ptel1M 97754 CAAATCT-GAC-CT--CAGTTACTTGCTGTGTGACCCTGAGCAAATCACT 97799 i i- i - -- v v i i i i MIR#SINE/MIR 55 CGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACT 104 chr3ptel1M 97800 TAACC-CTATTTACTTTAGTTTTCTTATCTATAAAAT 97835 - v v i i i i i i MIR#SINE/MIR 105 TAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAAT 141 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.02 CpG sites = 28, Kimura (unadjusted) = 38.38 Transitions / transversions = 3.11 (28/9) Gap_init rate = 0.05 (6 / 130), avg. gap size = 1.17 (7 / 6) 452 24.53 4.72 0.00 chr3ptel1M 97730 97835 (902165) MIRc#SINE/MIR 35 145 (123) m_b111s601i12 4051 chr3ptel1M 97730 CCTAGAATCAAAAGGATCTGAGTTCAAATCT-GAC-CT--CAGTTACTTG 97775 i i i ii i i i i i i- i - -- v v MIRc#SINE/MIR 35 CTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAG 84 chr3ptel1M 97776 CTGTGTGACCCTGAGCAAATCACTTAACC-CTATTTACTTTAGTTTTCTT 97824 i i i - v vvi i i i i MIRc#SINE/MIR 85 CTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTC 134 chr3ptel1M 97825 ATCTATAAAAT 97835 i MIRc#SINE/MIR 135 ATCTGTAAAAT 145 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.27 CpG sites = 21, Kimura (unadjusted) = 31.77 Transitions / transversions = 4.20 (21/5) Gap_init rate = 0.04 (4 / 105), avg. gap size = 1.25 (5 / 4) 236 19.49 4.88 6.17 chr3ptel1M 98005 98086 (901914) C Charlie1b#DNA/hAT-Charlie (15) 508 428 m_b111s502i0 4052 chr3ptel1M 98005 TTTTAAATCTCAAAAACCCTTAAAA---TTAAAAATTAATGAGAAGCCCT 98051 vii ii v v v --- v i ----- C Charlie1b#DNA 508 TTTTTGGTCTCAGGACCCCTTTACACTCTTAAAAATTATTGAGGA----- 464 chr3ptel1M 98052 CCCTAAACAGCTTTTGTTTATGTTGAATATA-CTAT 98086 i v v iv - C Charlie1b#DNA 463 CCCCAAAGAGCTTTTGTTTATGTGGGTTATATCTAT 428 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 22.65 CpG sites = 7, Kimura (unadjusted) = 22.65 Transitions / transversions = 0.88 (7/8) Gap_init rate = 0.09 (7 / 81), avg. gap size = 1.29 (9 / 7) 15 25.87 4.55 1.47 chr3ptel1M 98482 98547 (901453) (TAAA)n#Simple_repeat 1 68 (0) m_b111s252i12 4053 chr3ptel1M 98482 TAAATAAAAAGCTATAATAAATAAAT-AA-AAAGAAATGTATAACAACAG 98529 v iv - - - v iv vv v v (TAAA)n#Simpl 1 TAAATAAATAAATA-AATAAATAAATAAATAAATAAATAAATAAATAAAT 49 chr3ptel1M 98530 GAA-AAAAAAAGAAATTAA 98547 i - v v v (TAAA)n#Simpl 50 AAATAAATAAATAAATAAA 68 Matrix = Unknown Transitions / transversions = 0.27 (3/11) Gap_init rate = 0.06 (4 / 65), avg. gap size = 1.00 (4 / 4) 273 36.36 0.00 0.00 chr3ptel1M 98704 98780 (901220) C L2c_3end#LINE/L2 (38) 440 364 m_b111s601i13 4054 chr3ptel1M 98704 TGTGCCAAGTACTGAGGATAAAAAGAAAGGTGAAAATCAGTTCTTACCAT 98753 i ii i v viii i i vv i i i i v C L2c_3end#LINE 440 TGTGCCAGGCGCTGGGGATACAAAGATGAATAAGACACGGTCCCTGCCCT 391 chr3ptel1M 98754 TGAGAAGCTCATAATCTAATAAAGAGG 98780 ii i i i i ii ii C L2c_3end#LINE 390 CAAGGAGCTCACAGTCTAGTGGAGGAG 364 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 50.94 CpG sites = 23, Kimura (unadjusted) = 57.76 Transitions / transversions = 4.60 (23/5) Gap_init rate = 0.00 (0 / 76), avg. gap size = 0.0 (0 / 0) 896 26.15 9.35 0.86 chr3ptel1M 99816 100132 (899868) C L1MC_orf2#LINE/L1 (1092) 2202 1863 m_b111s551i2 4055 chr3ptel1M 99816 ATTTACTTTATATCCTGCTACTTAGCTAAAATTATTTATTGTTTCAACTA 99865 v i i v i v v iii iv v vv C L1MC_orf2#LIN 2202 ATTAACCTTGTATCCTGCAACCTTGCTATAATCGCTTATTAGTTCCAGGA 2153 chr3ptel1M 99866 ACTTGTTAGTTGAGTCTTTAGTAATTTCTAAGTATGTCAT-ACGTAGCCT 99914 ii v v i v v v v vi viiv - i vii C L1MC_orf2#LIN 2152 GTTTTTTTGTCGATTCTTTCGGATTTTCTACATAGACAATCATGTCATCT 2103 chr3ptel1M 99915 GCAAA--AACATAGTTTTATTATCTTATTT---ATTCTGAAT-CCT---A 99955 i -- v i - vi --- v v - --- C L1MC_orf2#LIN 2102 GCGAACAAAGACAGTTTTATT-TCTTCCTTCCCAATCTGTATACCTTTTA 2054 chr3ptel1M 99956 TTTATTTTTCTTCTTTTATTGCTATT-GCTAGGATTTGCAATACAGTACT 100004 vi v i - - i v i ii ii C L1MC_orf2#LIN 2053 TTTCCTTTTCTTGTCTTATTGC-ATTAGCTAGGACTTCCAGTACGATGTT 2005 chr3ptel1M 100005 GAACAATATTGGTGACAGTGAACATCCTTGCTTCACACCTGATCTTATTG 100054 v iv v v v i i iiiv vi C L1MC_orf2#LIN 2004 GAAAAGGAGTGGTGAGAGGGGACATCCTTGCCTTGTTCCTGATCTTAGCG 1955 chr3ptel1M 100055 GGAAGGCTTCTAAC------CCATTAGAGAT-ATGCTTGCTGATGGCTT- 100096 i ? ii------ iiv - i v vv i - C L1MC_orf2#LIN 1954 GGAAAGCTTCNAGTTTCTCACCATTAAGTATGATGTTAGCTGTAGGTTTT 1905 chr3ptel1M 100097 ---TAGATGATTTTTTATCAGTTTAATGAAAAATCC-----ATT 100132 --- - i iv i - i iv ----- C L1MC_orf2#LIN 1904 TTGTAGATG-TTCTTTATCAAGTTGA-GGAAGTTCCCCTCTATT 1863 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 31.17 CpG sites = 62, Kimura (unadjusted) = 32.98 Transitions / transversions = 1.21 (46/38) Gap_init rate = 0.05 (15 / 316), avg. gap size = 2.07 (31 / 15) 46 4.35 0.00 0.00 chr3ptel1M 100133 100180 (899820) (TA)n#Simple_repeat 1 48 (0) c_b111s251i2 4056 chr3ptel1M 100133 TATATATATATATATATATATATATATATATATACATATATATGTATA 100180 i i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATA 48 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 896 26.15 9.35 0.86 chr3ptel1M 100181 100290 (899710) C L1MC_orf2#LINE/L1 (1432) 1862 1740 m_b111s551i2 4055 chr3ptel1M 100181 C-AGTTT--CAAGTGTTTTTA--AT--AGGAGTGTTATACTTTCTCAAAA 100223 - --ii v -- -- v i iv i v v C L1MC_orf2#LIN 1862 CTAGTTTGCTGAGAGTTTTTATCATGAATGGGTGTTGGATTTTGTCAAAT 1813 chr3ptel1M 100224 GGTTTTTCTGCATTCATTGATATAATCACATGGTTTTAA------AATTT 100267 v ii i ii i vv------ iii C L1MC_orf2#LIN 1812 GCTTTTTCTGCATCTATTGATATGATCATGTGATTTTTCTTCTTTAGCCT 1763 chr3ptel1M 100268 TTTGATCTGATTAATTATATTAA 100290 v v vi i C L1MC_orf2#LIN 1762 GTTGATGTGATGGATTACATTAA 1740 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 31.17 CpG sites = 62, Kimura (unadjusted) = 32.98 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.05 (5 / 109), avg. gap size = 2.60 (13 / 5) 921 35.56 4.31 4.04 chr3ptel1M 100572 101336 (898664) MamRTE1#LINE/RTE-BovB 558 1324 (2488) m_b111s601i14 4057 chr3ptel1M 100572 ACCATTACCACATAGAATGTGTGCATACTTATAGACAAT-ACAAAATC-- 100618 i vv i ii vv v ii --- vi i - i i v -- MamRTE1#LINE/ 558 ACCATTGCGTCATGGAACATCAGGACGCT---ATGCGATGACGAGAACAG 604 chr3ptel1M 100619 CAGTAGACCTGAAAGAAGAATAGCTCTTGTGGTGAGAGAACTCAACAGGT 100668 v v v ii v i v iiv v vvv i MamRTE1#LINE/ 605 CAGTCGTCCAGAAAGAAGAACGGCACTCGTCGCACGTGAACTGTCCAGAT 654 chr3ptel1M 100669 ATCACAGCCAA-ATAGCAGCCTTGAATGAAACAAAGACTGAGAAATAAAG 100717 - iv i i - v v vi ii v - vvvvi i MamRTE1#LINE/ 655 A-CGGAGTCGACATCGCCGCACTGAGCGAAACCA-GACTTCCTGATGAAG 702 chr3ptel1M 100718 ACCTGCTTACTGAAGTAGGAGTTATATACACATTTTTCTAGAATGG-CTG 100766 iv v i v iii v iiiv? i v i i iv - v MamRTE1#LINE/ 703 GACAGCTCACGGAGACAGGTGCCGGNTACGCCTTCTTCTGGAGAGGTCTT 752 chr3ptel1M 100767 CAGTG---AAAGGGAATGCCATTAAGTTGGTGTAGGTTTTGCAATCAAA- 100812 vv v--- i v vv iv i ---- i vi i i - MamRTE1#LINE/ 753 CCCTCTTCAGAGCGACGGCTCTCA----GGCGTCAGCTTTGCAATCAGAC 798 chr3ptel1M 100813 ----ACTAATCTAGTAAATAAG-CTCATATCCTTTCCAAAAGGAGTTAAT 100857 ---- vi ------i - vi vvi v v i vi ? i MamRTE1#LINE/ 799 AGTCACTTGTCT------CAAGNCTCCCAAATTTGCCCAGAGGCATNAGT 842 chr3ptel1M 100858 GACAGGTTCATGACAATCCAATTGCCATTTGCAGGAAAA-TGCCCCACCA 100906 v vi v vv v ivi i ?- i v iv -i i?ii MamRTE1#LINE/ 843 GACCGTCTGATGACCCTACGCCTACN-TCTGAAACAAAAGCGCTNTGCCA 891 chr3ptel1M 100907 CCATCATCCATACCTATGCCTCAACCATGACGAATCCTGATTGCATCAAA 100956 i viii v i v v i vivivv MamRTE1#LINE/ 892 CCGTCATCAGCGCATATGCCCCCACCATGACGAATACCGATGAGGAGAAA 941 chr3ptel1M 100957 GAAAAATGTTATGAAGA-CTGGG-AGACCTTTGTCATCAAT-GTCCCAAA 101003 i vi ii i - i- -- ii i- ii- v v MamRTE1#LINE/ 942 GAAAGATTCTACAAGGATCTGGACAGAC--TCATCG-CAGCGGTACCAAC 988 chr3ptel1M 101004 AGATGACAAGCTTATAATTCTGCGTGCCTTTAATGCTGGAGTAGGCTCAG 101053 vv v vi ivi v v vi i i vv v v vvv MamRTE1#LINE/ 989 ATCTGACAAGCTGATCGTCACGGGAGATTTCAACGCACGTGTCGGCAGCG 1038 chr3ptel1M 101054 ACTATC-AGACATGGCAAGAAGTCCTTGAGAGGAGTGGAGTTGGAAACAG 101102 - ii - i i vi i v i iivv?vii ii vvv MamRTE1#LINE/ 1039 A-TGCCGAAACGTGGAGAAAAGTCATCGGACCNCACGGGATTGGAAAGCT 1087 chr3ptel1M 101103 AAACAGCAGTGCTCATTTACTATTGAAGACTTAG-GCATCT------CAT 101145 ? i v --- vi ---- i - v v ------ MamRTE1#LINE/ 1088 NAACAGCAATGGTC---TACTCCTG----CTCAGCGAATGTGCCAAGCAT 1130 chr3ptel1M 101146 GATCTTGTCATCACCAGCCCTGAATTCTGTTTACCTAAATGCAATAAA-A 101194 v v i v i v iivv i ii -i ivi v - MamRTE1#LINE/ 1131 CAGCTCGTAATCACCAACACCATCTTCCGCCTACC-GAATAAGAGAAAGA 1179 chr3ptel1M 101195 CTTCATGGATGCACACTCACAG--CAAACATTGGCAT-TTATTAGACCAT 101241 v -- i vi --i i v - i - ii MamRTE1#LINE/ 1180 CATCATGGATG--CACCCAAGGTCTAAGCAGTGGCATCTCATT-GATTAT 1226 chr3ptel1M 101242 GTGATTAT--AAGAA-GAGACAGATAGGATGTGGGCATGACAAAGAGAAT 101288 i v ii --i v i- i vviv vviv v viviivv MamRTE1#LINE/ 1227 ATCATCGTTCGACAGCGGGACCTGAAGGATGTTTAGATTACTGCAGCTAT 1276 chr3ptel1M 101289 GTGTGGTGCAGAGTACTGGACAGATCATAGACTTATCCTCTCCAAGCT 101336 i i v i v i v v v v v i MamRTE1#LINE/ 1277 GCGTGGCGCCGAGTGCTGGACCGACCATCGCCTGATACGCTCCAAACT 1324 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 41.96 CpG sites = 134, Kimura (unadjusted) = 49.84 Transitions / transversions = 1.06 (134/127) Gap_init rate = 0.07 (51 / 764), avg. gap size = 1.25 (64 / 51) 13 17.02 0.00 9.30 chr3ptel1M 101580 101626 (898374) (TGAAAA)n#Simple_repeat 1 43 (0) m_b111s252i13 4058 chr3ptel1M 101580 TGAAAATGATGAGGAAATTCAGAAGCTGATAAATGAAAAATGAAAAT 101626 vi v v -- iv - - (TGAAAA)n#Sim 1 TGAAAATGAAAATGAAAAT--GAAAATGA-AAATG-AAAATGAAAAT 43 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.09 (4 / 46), avg. gap size = 1.00 (4 / 4) 386 31.35 10.79 4.76 chr3ptel1M 101970 102247 (897753) MamRTE1#LINE/RTE-BovB 2001 2294 (1518) m_b111s601i15 4057 chr3ptel1M 101970 GTTTCAA---TTGAAGAAGTTTTGAATGCTATTAG-GCTACTTTTATG-- 102013 i i --- iv?v vi i i - i --- v v -- MamRTE1#LINE/ 2001 GCTCCAACTTTTGAAGAAGTCANCACCGCTGTCAGAGCCA---TGAAGAA 2047 chr3ptel1M 102014 TGGTAAAGCACCAAGTGCTGATCCTATTCCATCTGAGATTTACA---AAG 102060 v ivi vv vvi v vv v --- i MamRTE1#LINE/ 2048 TGGTAAAGCTCTCGGACCTGATGGCATACCTGCTGAGATTTTCAAGCAGG 2097 chr3ptel1M 102061 TTGGGGATATATTGCTCATATGAAAGCTGAATGAAATTTTC--CAGATTA 102108 vv v iii i --- viv v iiiv -- --i MamRTE1#LINE/ 2098 AAGGGGAGACGCTGCTTA---GACGTCTGCATAGGCTTTTCTTCAG--CA 2142 chr3ptel1M 102109 TATGACAAGAG----GAGATTATGCCCCAGGAGTTCAAGGACACCTCCAT 102154 ---- ---- ivv v v i ii v i MamRTE1#LINE/ 2143 TATG----GAGTACCGAGGAAATGCCGCAGGATTTCAAAGATGCCACTAT 2188 chr3ptel1M 102155 TGT--CCATCTTTATAAAGGTAAAGAAAATAGATTGTCCTGTGATAATCA 102202 ii -- i - i i v i vi iv iii -v i ii ii MamRTE1#LINE/ 2189 CATCACCATCTTCA-AGAAGAAAGGCGAGAAAGCTG-ACTGCGGCAACTA 2236 chr3ptel1M 102203 TAGTGGGGTC-------------TTGCTGGCAACATTCTTCCCAAAGTCC 102239 v i vi ------------- v i vv i MamRTE1#LINE/ 2237 TCGCGGCATCTCNCTGCTCTCCATTGCTGGCAAGATCCTGGCCAGAGTCC 2286 chr3ptel1M 102240 TTCTTAAT 102247 vi MamRTE1#LINE/ 2287 TTCTGGAT 2294 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.41 CpG sites = 46, Kimura (unadjusted) = 41.98 Transitions / transversions = 1.24 (46/37) Gap_init rate = 0.08 (22 / 277), avg. gap size = 2.00 (44 / 22) 586 27.36 6.25 3.16 chr3ptel1M 102520 102919 (897081) C L1M3_orf2#LINE/L1 (2850) 438 27 m_b111s551i3 4055 chr3ptel1M 102520 GAAGATTTCCTTCTATTATAGTACTGTTGTCTATCTCCACCTGTAATTCA 102569 - i v v i i i iv vi i v C L1M3_orf2#LIN 438 GAAG-TCTCCTACTATTATTGTATTGCTGTCTATTTCTCCCTTCAGTTCT 390 chr3ptel1M 102570 TTTAAGTTTTCTTTTAAAAACT-AGGTGCTATAGTATTTGGTACAAATAG 102618 v i vv vi v v i - viii i v i v v C L1M3_orf2#LIN 389 GTCAATATTTGCTTTATATATTTAGGTGCTCCGATGTTGGGTGCATATAT 340 chr3ptel1M 102619 GTTCATTATTGTTATTGCTTCATTGTTTGTAGTA--TCTTTTATCAAAAC 102666 i i v vv - ? - v v i--i vv i C L1M3_orf2#LIN 339 ATTTATAATTGTTATATCTTC-TTGNT-GAATTGACCCTTTTATCATTAT 292 chr3ptel1M 102667 GTAATCACCTTGTTTATCTCTTTTAATTAAATCTATG--TTAGCCTTAAC 102714 i v? v i v i i-- i i v -- ivv iv i C L1M3_orf2#LIN 291 ATAATGNCCTTCTTTGTCTCTTGTGAC--AGTTTTTGACTTAAAGTCTAT 244 chr3ptel1M 102715 TCTATCTGAGATCATGATTGCTACCCCTGCCCTTTTTTTG-TATGAGATG 102763 i i v v vv v i i i v - iv vv C L1M3_orf2#LIN 243 TTTGTCTGATATAAGTATAGCCACCCCTGCTCTCTTTTGGTTACCATTTG 194 chr3ptel1M 102764 AACCATAATAAAATTCTACTCCA-ACCTTCAATTTCAGCTCTATGTAT-- 102810 --- ii- v ii vi -v v - i -- C L1M3_orf2#LIN 193 ---CATGG-AATATCTTTTTCCATCCCTTCACTTTCAGC-CTATGTGTGT 149 chr3ptel1M 102811 ------AGCTATCAAGT--ATTTTTTGTAAACAACATATTGTTGAATTCT 102852 ------ ? -- --i i i ii i v i ii C L1M3_orf2#LIN 148 CCTTAAANCTA--AAGTGAGTCTCTTGTAGGCAGCATATAGTTGGATCTT 101 chr3ptel1M 102853 GATTTTTAATCCATTCTGCT-TTCAA----TTTTG--TGG-GTGTTTTAT 102894 v v v i-i v ---- -- - v v C L1M3_orf2#LIN 100 GTTTTTTTATCCATTCAGCCACTCTATGTCTTTTGATTGGAGAGTTTAAT 51 chr3ptel1M 102895 CCCATTCACATCGAAAGTTATAATT 102919 - i iv v v C L1M3_orf2#LIN 50 -CCATTTACATTTAAAGTAATTATT 27 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 34.40 CpG sites = 54, Kimura (unadjusted) = 34.85 Transitions / transversions = 1.04 (54/52) Gap_init rate = 0.06 (24 / 399), avg. gap size = 1.58 (38 / 24) 284 26.96 6.09 0.00 chr3ptel1M 102820 102934 (897066) C L1M4b_5end#LINE/L1 (17) 3220 3099 m_b111s551i4 4055 chr3ptel1M 102820 GTATTTTTTGTAAACAACATATTGTTGAATTCTGATTTTTAATCCATTCT 102869 i i ii i i v i ii v v C L1M4b_5end#LI 3220 GTGTCTCCTGTAGACAGCATATAGTTGGATCTTGTTTTTTAATCCAGTCT 3171 chr3ptel1M 102870 G-----CTTTCAATTTTG--TGGGTGTTTTATCCCATTCACATCGAAAGT 102912 ----- i vvv -- i vv vi iv v C L1M4b_5end#LI 3170 GACAATCTCTGCCTTTTGATTGGATTGTTTAATCCATTCACATTTAATGT 3121 chr3ptel1M 102913 TATAATTACTATTTGTGAATTT 102934 v iv vvv i C L1M4b_5end#LI 3120 TATTATTGATATAGTTGGATTT 3099 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.69 CpG sites = 15, Kimura (unadjusted) = 33.69 Transitions / transversions = 0.94 (15/16) Gap_init rate = 0.02 (2 / 114), avg. gap size = 3.50 (7 / 2) 62 1.66 1.64 0.00 chr3ptel1M 103288 103348 (896652) (AC)n#Simple_repeat 1 62 (0) c_b111s251i3 4059 chr3ptel1M 103288 ACACACACACACACACACACACACACACACACACACACACAC-CCCACAC 103336 - v (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50 chr3ptel1M 103337 ACACACACACAC 103348 (AC)n#Simple_ 51 ACACACACACAC 62 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.02 (1 / 60), avg. gap size = 1.00 (1 / 1) 203 20.68 1.37 7.25 chr3ptel1M 104048 104120 (895880) C L2d2_3end#LINE/L2 (156) 399 331 m_b111s601i16 4060 chr3ptel1M 104048 AATAACAA-ACGAGCATTTAAATGACAGGTCACCAACTAGTAAGGCAGAG 104096 - i - i v -- ivi ii --i i C L2d2_3end#LIN 399 AATAACAATACAAG-ATTTAAATAACAGTTCA--AGACAACAA--TAGAA 355 chr3ptel1M 104097 GAGAGGTCTCAAGGCAGTTCTTGA 104120 v v v v C L2d2_3end#LIN 354 GAGATGTCACAAGGCAGTACATGA 331 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 24.40 CpG sites = 8, Kimura (unadjusted) = 24.40 Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.08 (6 / 72), avg. gap size = 1.00 (6 / 6) 12 27.14 0.00 4.00 chr3ptel1M 106527 106578 (893422) (AATATAA)n#Simple_repeat 1 50 (0) m_b111s252i14 4061 chr3ptel1M 106527 AATATTAGATTTTAGATATGATTAGTATAAAATGTTAAAGATAAAATATT 106576 v i v v i - -v i i v v v (AATATAA)n#Si 1 AATATAAAATATAAAATAT-A-AAATATAAAATATAAAATATAAAATATA 48 chr3ptel1M 106577 AA 106578 (AATATAA)n#Si 49 AA 50 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.00 (2 / 2) 13 18.05 3.03 0.00 chr3ptel1M 106849 106881 (893119) (AAGA)n#Simple_repeat 1 34 (0) m_b111s252i15 4062 chr3ptel1M 106849 AAGAGGGAAAGGAAGAGAGAGAGAAA-AAAGAAA 106881 ii i i i - (AAGA)n#Simpl 1 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 34 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 13 14.21 3.23 0.00 chr3ptel1M 106966 106996 (893004) (TAAAA)n#Simple_repeat 1 32 (0) m_b111s252i16 4063 chr3ptel1M 106966 TAAAATAAAATAAAACAATGTAATA-AAAATA 106996 i vi v - (TAAAA)n#Simp 1 TAAAATAAAATAAAATAAAATAAAATAAAATA 32 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.03 (1 / 30), avg. gap size = 1.00 (1 / 1) 28 0.00 0.00 0.00 chr3ptel1M 108202 108227 (891773) (GGA)n#Simple_repeat 1 26 (0) c_b111s251i4 4064 chr3ptel1M 108202 GGAGGAGGAGGAGGAGGAGGAGGAGG 108227 (GGA)n#Simple 1 GGAGGAGGAGGAGGAGGAGGAGGAGG 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 404 32.11 2.15 2.89 chr3ptel1M 110588 110866 (889134) L1MC_orf2#LINE/L1 2481 2757 (537) m_b111s551i5 4065 chr3ptel1M 110588 AATACCAATCAGACTCCCAAGAAACTATTTTAATGACCTAGAAAAAATAA 110637 v i v iv ii ivv iv v v v i L1MC_orf2#LIN 2481 AATCCCAATCAAAATCCCAGCAAGTTATTTTGTGGATATCGACAAACTGA 2530 chr3ptel1M 110638 CAACAAAATTCATATGGAAGAACAATAGGTCAAGAAT-TTCAAGGGAATT 110686 ivvi i i iiii v ii v -vi viv - L1MC_orf2#LIN 2531 TTCTAAAGTTTATATGGAGAGGCAAAAGACCCAGAATAGCCAACACAAT- 2579 chr3ptel1M 110687 AATGAAAAAGAAAAATCAAATAAAGGTGGCCTAGCTGTACCAGATCT-AA 110735 v ii i iv i v-- v v ii vv v ii - L1MC_orf2#LIN 2580 ATTGAAGGAGAAGAACAAAGTC--GGAGGACTGACACTACCCGACTTCAA 2627 chr3ptel1M 110736 AATTATATTATAAAGCAGCAGTCACCAAAACCATTTGGTATTGGCTAAGA 110785 i i - i vi v i i vi v v ii L1MC_orf2#LIN 2628 GACT-TACTATAAAGCTACAGTAATCAAGACAGTGTGGTATTGGCGAAAG 2676 chr3ptel1M 110786 AATAGAGTAGGCAATCAGTGGAATAGGTTAGATTCACAGGACA-AAATAG 110834 vv ivvi i i iv ---- v vv - L1MC_orf2#LIN 2677 AATAGACAAATAGATCAATGGAACAGAATAG----AGAGCCCAGAAATAG 2722 chr3ptel1M 110835 --TCA-ATAACTATAGCGATCTAGTGTTTGACAAA 110866 --i - v iv v ii v L1MC_orf2#LIN 2723 ACCCACATAAATATAGTCAACTGATCTTTGACAAA 2757 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 42.75 CpG sites = 46, Kimura (unadjusted) = 42.75 Transitions / transversions = 1.12 (46/41) Gap_init rate = 0.05 (13 / 278), avg. gap size = 1.08 (14 / 13) 447 32.96 4.03 3.59 chr3ptel1M 111436 111907 (888093) L1P3_orf2#LINE/L1 2782 3255 (39) m_b111s551i6 4066 chr3ptel1M 111436 AAGAATTCACTATTTGACAAAAACTGCTGG-AAAACTGGAAAAGTATG-G 111483 i v i i viv i - vv ivi i- L1P3_orf2#LIN 2782 AAGGATTCCCTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATATG 2831 chr3ptel1M 111484 CAGAAACTAGGCACTG-ACCCACAGTTAACACCGTACATCAAGATAAGAT 111532 viv iv - vivvi v v i iv i v iv L1P3_orf2#LIN 2832 CAGAAAACTGAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACT 2881 chr3ptel1M 111533 CAAAATGGGTTCATGATCTAGGCATAAAGAATGAGATTATAAATAAATTA 111582 i i v v ii ii i iivv i i ii v vvi L1P3_orf2#LIN 2882 CAAGATGGATTAAAGACTTAAACGTAAGACCTAAAACCATAAAAACCCTA 2931 chr3ptel1M 111583 GAAGAA--CATAGGATCGTTTACCTCTCAG-ACTTGTGGAGGAGGAAGGA 111629 -- v -- iv - vi - v iv v v i v i L1P3_orf2#LIN 2932 GAAGAAAACCTAGG--CAAT-ACCATTCAGGACATAGGCATGGGCAAAGA 2978 chr3ptel1M 111630 ATTTGTGACTAAAGAAGAACTAGAGATAATTATTGATCA-----CAAAAT 111674 v ii iv --- i i iii vii-- v ----- L1P3_orf2#LIN 2979 CTTCATGACTAAAACA---CCAAAAGCAATGGC--AACAAAAGCCAAAAT 3023 chr3ptel1M 111675 AGAAAATTTTGATTATACTAAATTAAAAAGCTTTTGTACAAATAAAACTA 111724 v v v vv ivv i i i i i i-i vv L1P3_orf2#LIN 3024 TGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAG-CAAAAGAA 3072 chr3ptel1M 111725 ATGTGGATAGCATTAGAA--AGGAAGCAA--TAAATAATGGGAAAAGATT 111770 i----- v i i-- iv i -- v v i i L1P3_orf2#LIN 3073 AC-----TATCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATT 3117 chr3ptel1M 111771 TT-ACAGCTAAAGGTTCTGATAAAGGCCTCATCTCCAAAATATATAGAGA 111819 -i iiiv vvvv i v v v i v i ii L1P3_orf2#LIN 3118 TTTGCAATCTATCCATCTGACAAAGGGCTAATATCCAGAATCTACAAGGA 3167 chr3ptel1M 111820 ATTGATTCTAATTTATAAGAAAT---CAAGCCATTCTCCAACTGATAAAT 111866 i v vv v i v--- i v -- i v vi - i L1P3_orf2#LIN 3168 ACTTAAACAAATTTACAAGAAAAAAACAAACAA--CCCCATCAAA-AAGT 3214 chr3ptel1M 111867 GGTCAAAGGCTATGAACAGACAATTTTCAGATGATGAAATT 111907 v i v v i i v v v L1P3_orf2#LIN 3215 GGGCGAAGGATATGAACAGACACTTCTCAAAAGAAGACATT 3255 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 43.49 CpG sites = 78, Kimura (unadjusted) = 44.28 Transitions / transversions = 1.08 (78/72) Gap_init rate = 0.06 (27 / 471), avg. gap size = 1.33 (36 / 27) 267 31.82 4.33 4.71 chr3ptel1M 111670 111946 (888054) L1M1_orf2#LINE/L1 3019 3294 (0) m_b111s551i7 4066 chr3ptel1M 111670 AAAATAGAAAATTTTGATTATACTAAATTAAAAAGCTTTTGTACA---AA 111716 i v v vv i i ii i i i --- L1M1_orf2#LIN 3019 AAAATGGACAAATGGGATCACATCAAGTTAAAAAGCTTCTGCACAGCAAA 3068 chr3ptel1M 111717 TAAAACTAATGTGGATAGCATTAGAAAGGAAGCAAT--AAATAATGGGAA 111764 vi - -----i i v- vi i ii i-- v v i L1M1_orf2#LIN 3069 GGAAAC-AAT-----CAACAA-AGTGAAGAGACAACCCACAGAATGGGAG 3111 chr3ptel1M 111765 AAGAT-TTTACAG-CTA---AAGGTTCTGATAAAGGCCTCATCTCCAAAA 111809 i - i i- --- ---- i i vi v vv i L1M1_orf2#LIN 3112 AAAATATTTGCAAACTACCCA----TCTGACAAGGGATTAATAACCAGAA 3157 chr3ptel1M 111810 TATATAGAGAATTGATTCTAATTTATAAGAAATCAAGCC--ATTCTCCAA 111857 ii ii v vv v v i i -- ii -- vv i L1M1_orf2#LIN 3158 TATATAAGGAGCTCAAACAACTCTATAGGAAA--AAATCTAATAATCCGA 3205 chr3ptel1M 111858 CTGATAAATGGTCAAAGGCTATGAACAGACAATTTTCAGATGATGAAATT 111907 i i v v i v v i v i i v v v v L1M1_orf2#LIN 3206 TTAAAAAATGGGCAAAAGATCTGAATAGACATTTCTCAAAAGAAGACATA 3255 chr3ptel1M 111908 GAAACTATTTCTACTCATATGAAAGAGTGTTCCAAATCA 111946 v iviivvvi vv ii i v v L1M1_orf2#LIN 3256 CAAATGGCAAACAGGCATATGAAAAGGTGCTCAACATCA 3294 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.73 CpG sites = 46, Kimura (unadjusted) = 42.39 Transitions / transversions = 1.21 (46/38) Gap_init rate = 0.07 (19 / 276), avg. gap size = 1.32 (25 / 19) 1461 28.17 5.27 1.75 chr3ptel1M 111808 112414 (887586) L1ME4c_3end#LINE/L1 12 639 (191) m_b111s551i8 4066 chr3ptel1M 111808 AATATATAGAGAATTGATTCTAATTTATAAGAAA----TCAAGCCATTCT 111853 ? i ii v v v ---- v ----i L1ME4c_3end#L 12 ANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAAGAC----C 57 chr3ptel1M 111854 CCAACTGATAAATGGTCAAAGGCTATGAACAGACAATTTTCAGATGATGA 111903 iv v vi iv ? v v L1ME4c_3end#L 58 CCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAGGA 107 chr3ptel1M 111904 AATTGAAACTATTTCTACTCATATGAAAGAGTGTTCCAAATCACTATTGA 111953 vv ?ivi vvvi vv i i i i v vv i v i L1ME4c_3end#L 108 AATACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTAGTAA 157 chr3ptel1M 111954 TCAGAGAAATGCAAATTAAGACAACTCTGAGATACCACTACACACCTGTC 112003 i ii vv i vi i i i L1ME4c_3end#L 158 TCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCTATT 207 chr3ptel1M 112004 AGATTGGCCAAGATGACAGAAAAAGATAATGACAAATGTTGGAGTGGATG 112053 i i v i vvv i vv iv v i v v ? L1ME4c_3end#L 208 AAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGCTGGCGAGGNTG 257 chr3ptel1M 112054 TGGGAAAACTGGGATACC--TGCTTTGTTGGTGGAGTTGTGAACAGATCC 112101 i vi v i? i-- i v i vi? i iv i v L1ME4c_3end#L 258 CGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGTAC 307 chr3ptel1M 112102 AACCATTCTGGAGAGCAATTTGGAACTA-GACTCAAAAAGTTATCAAACT 112150 v i i v v - vv - i ii v v L1ME4c_3end#L 308 AACCCTTTTGGAAAGCAATTTGGCAATACGTATC-AAGAGCCATAAAAAT 356 chr3ptel1M 112151 GTGCATAACCTTTGATCCAGAAGTGTTACTACTGGACTTATACCCCAAAG 112200 v v i v i vii v ivv v i i i L1ME4c_3end#L 357 GTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGG 406 chr3ptel1M 112201 AGAT-ATT--AAGGAAGGGAAAGGGACCTACATGTGCCAAAATGTTTGTG 112247 i - -- i i i --- i ii v i ii v L1ME4c_3end#L 407 AAATAATTCAAAAGAAGGAAAAAG---CTATATGCACGAAGATGTTCATT 453 chr3ptel1M 112248 GCAGCCCTTTTTGTAGTGGCTAAAAACTGGAAATTGAAC--GGATGTCC- 112294 vi v i i i v i i-- --ii - L1ME4c_3end#L 454 GCAGCGTTATTTATAATAGCGAAAAATTGGAAAC--AACCTAAATGTCCA 501 chr3ptel1M 112295 ---ATTGGAGAATGGCTGAATCAATT----------------ATGGAATA 112325 --- v i i i i v ---------------- L1ME4c_3end#L 502 ACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATA 551 chr3ptel1M 112326 TTATTGTTCTGTAAGAAATGACCATCAGGATGACTACATAGAGTCTTGGA 112375 vvvv ii v i iv i v v ii viv v L1ME4c_3end#L 552 TTATGCAGCCATTAAAAATGATAATTATGAAGACTATGTAGCAACATGGA 601 chr3ptel1M 112376 GAGACTTACATGAACTGATGCTAAGTGAAATGAGCAGAA 112414 i ivv -i vv i i vi L1ME4c_3end#L 602 AAATGTT-TATGATATAATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 35.59 CpG sites = 89, Kimura (unadjusted) = 36.39 Transitions / transversions = 1.13 (89/79) Gap_init rate = 0.03 (20 / 606), avg. gap size = 2.15 (43 / 20) 17 23.12 0.00 0.00 chr3ptel1M 113182 113217 (886783) (A)n#Simple_repeat 1 36 (0) m_b112s252i0 4067 chr3ptel1M 113182 AAAAAACAAAACAAAAAACTAACCAAAAAAAACAAA 113217 v v vv vv v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 36 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 13 14.48 7.89 0.00 chr3ptel1M 114863 114900 (885100) (GAAGCA)n#Simple_repeat 1 41 (0) m_b112s252i2 4068 chr3ptel1M 114863 GAGGCTGAAG-A-AAGCAGAGGCAGAAGCA-AAGGACAAGC 114900 i v - - i - v v (GAAGCA)n#Sim 1 GAAGCAGAAGCAGAAGCAGAAGCAGAAGCAGAAGCAGAAGC 41 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.08 (3 / 37), avg. gap size = 1.00 (3 / 3) 606 22.56 0.73 6.15 chr3ptel1M 115363 115499 (884501) C MIRc#SINE/MIR (120) 148 19 m_b112s601i0 4069 chr3ptel1M 115363 CTCATTTTACAACTGAGAAGACTGAGG-TCAAGAAGGTTTAGTGACTTGT 115411 i iv i i - iii v i C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr3ptel1M 115412 CCACAGTCACACAACTAGTAAGTGTCTCAGGCTGGATTTGAAGTCAGCGA 115461 vi i v vv v v i i vi ----- C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCC----- 54 chr3ptel1M 115462 GATAGATTTTCCTGACTCCAAGCCCAGCACTCTATCTA 115499 --- i i i ii v i C MIRc#SINE/MIR 53 ---AGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCA 19 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 26.38 CpG sites = 19, Kimura (unadjusted) = 27.48 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.07 (9 / 136), avg. gap size = 1.00 (9 / 9) 13 17.50 0.00 3.03 chr3ptel1M 115708 115741 (884259) (ACATTT)n#Simple_repeat 1 33 (0) m_b112s252i3 4070 chr3ptel1M 115708 ACATTTACAATGCTTTTTACATTTTACATTTACA 115741 v vviv - (ACATTT)n#Sim 1 ACATTTACATTTACATTTACA-TTTACATTTACA 33 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 232 30.57 6.93 2.86 chr3ptel1M 116030 116130 (883870) C MIR#SINE/MIR (0) 262 158 m_b112s601i1 4071 chr3ptel1M 116030 AATAACAGTCAAGATTTATATGGTGCTTATCATATACC--TTA-TGTCTT 116076 i ii v vvi i ii i i --vi - ii C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCT 213 chr3ptel1M 116077 AAGTCCT---CATA-ATCACTCTATTCTTAAATCCTCACAATAACCCTGG 116122 iv --- i- i viii i--- i iv C MIR#SINE/MIR 212 AAGCGCTTTACATGTATTAACTCATTT---AATCCTCACAACAACCCTAT 166 chr3ptel1M 116123 GAAGTGGG 116130 i i C MIR#SINE/MIR 165 GAGGTAGG 158 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.92 CpG sites = 23, Kimura (unadjusted) = 42.77 Transitions / transversions = 3.29 (23/7) Gap_init rate = 0.07 (7 / 100), avg. gap size = 1.43 (10 / 7) 1762 29.88 4.25 3.31 chr3ptel1M 116190 117508 (882492) C L1M5_orf2#LINE/L1 (1762) 1532 202 m_b112s551i3 4072 chr3ptel1M 116190 TCATAAAAGGAATTTGGCAGGACTCCTTCTTTCCCTATTTTTTCAAATAA 116239 v i v v vii i ii i vi v i C L1M5_orf2#LIN 1532 TCATAAAATGAGTTGGGAAGTGTTCCCTCTTTTTCTATTTTCTGGAAGAG 1483 chr3ptel1M 116240 TTTACATAGTATTGGAATGATTTGTCCTTTGAATGTTTGGTA-AATTCAC 116288 iii iv v v v i i i - C L1M5_orf2#LIN 1482 TTTGTGTAAGATTGGTATTATTTCTTCCTTAAATGTTTGGTAGAATTCAC 1433 chr3ptel1M 116289 ATGTAAATTCATCTGGCCCCGGAGATTTTTAGCTAGGGAACTAATTAATA 116338 vv i vi v i v i vvv i i iv vv v C L1M5_orf2#LIN 1432 CAGTGAAGCCATCTGGGCCTGGAGTTTTCTTTGTGGGAAGGTTTTTAATT 1383 chr3ptel1M 116339 GCTTGTTCTATTTCTTTTTCTAAA-ATGGGACTATTTAAATAATTGATTT 116387 i vvi v v-v i - i i i i vv iv C L1M5_orf2#LIN 1382 ACAAATTCAATTTCTTTA-ATAGATATAGGGCTATTCAGATTTTCTATTT 1334 chr3ptel1M 116388 CCTCTTTTGTTAGCCTGGGCAATCTATATTTTTGTAGATATTC-TCTATT 116436 i v? i ii v i ?i i i vv iv i- i C L1M5_orf2#LIN 1333 CTTCTTGNGTCAGTTTTGGTAANTTGTGTTTTTCAAGGAATTTGTCCATT 1284 chr3ptel1M 116437 TTATTTAGATTGTCAAATTTATTGGCCTATAGTTAGGCAAAATAACTCCT 116486 i i ii ? v v ivv v viii C L1M5_orf2#LIN 1283 TCATCTAAGTTNTCAAATTTATTGGCATAAAGTTGTTCATAATATTCTCT 1234 chr3ptel1M 116487 AATTATTGCTCTAATTTCCTCTTCATTGGTGGAGAATTCTCCCTTTTCAT 116536 v ivi i v ivivvv iv i v vv i C L1M5_orf2#LIN 1233 TATTATCCTTTTAATGTCTGTAGGATCTGTAGTGATGTCTCCTTTTTCAT 1184 chr3ptel1M 116537 TTTTGAGATGAACAATTCG-ATTTTCT-TCTTTACGTTTTCA-AATCAAA 116583 ii v viii i -i i - --- v-i iv C L1M5_orf2#LIN 1183 TCCTGATATTGGTAATTTGTGTCTTCTCTCTTT---TTTTCTTGATCAGT 1137 chr3ptel1M 116584 TTAACTAATGGTTTATCTATTTTGTTGGATTTTTCATAAAACTAATTCTT 116633 i ?i iv v i ivi v i i ii i C L1M5_orf2#LIN 1136 CTNGCTAGAGGTTTATCAATTTTATTGATCTTTTCAAAGAACCAGCTTTT 1087 chr3ptel1M 116634 AGTTTTATTTATTAATTCAATAGTTTTCTTATTTTCAATTTTATTAATCT 116683 i i ii v vvi v v ? ?i i v i i i C L1M5_orf2#LIN 1086 GGCTTCGTTGATTTTCTCTATTGTNTNTTTGTTTTCTATTTCATTGATTT 1037 chr3ptel1M 116684 CTCCTTTTATTTTCAGAATTTCCAATTTGGTATTTAATTGAGGGTTTTTA 116733 v i i i vv vvii vv i ?v vi --- C L1M5_orf2#LIN 1036 CTGCTCTTATCTTTATTATTTCCTTCCTTCTACTTNCTTTGGG---TTTA 990 chr3ptel1M 116734 ATTTG---TTCTTTTTCTAGCTTTTTTAGTTGTAAGCCCAAATTATTGAT 116780 --- i v v v ii i i C L1M5_orf2#LIN 989 ATTTGCTCTTCTTTTTCTAGCTTCTTAAGGTGGAAGCTTAGATCATTGAT 940 chr3ptel1M 116781 TTT--CTCTTTATTTTATGC-AA-GTAAGCATCTGGAGATATAAAATTTC 116826 --vi v i v v - -i ? i ii? v v i C L1M5_orf2#LIN 939 TTTAAGCCTTTCTTCTTTTCTAATATANGCATTTAANGCTATAAATTTCC 890 chr3ptel1M 116827 CGCTTATAACCTCTTTGGCTGCATCCCACAAATTTTGGTATGTTGTCTCA 116876 v v vv iv i i v iv C L1M5_orf2#LIN 889 CTCTAAGCACTGCTTTAGCTGCATCCCACAAATTTTGATATGTTGTATTT 840 chr3ptel1M 116877 TTATTCTCATTCACTTGGATGAAATTATTGATTGTGTCTATGATTTGCTG 116926 i ? v vi viv v vi i viv?i i vi v C L1M5_orf2#LIN 839 TCATTNTCATTCAGTTCAAAATATTTTCTAATTTCCNTTGTGATTTCTTC 790 chr3ptel1M 116927 TTTCACCCATTCATTCTTTAGGATTAGATTATTTAATTTCCAATTAATTT 116976 v vvi v i v ivi i --- v C L1M5_orf2#LIN 789 TTTGACCCATGGGTTATTTAGAAGTGTGTTGTTTAATTTCCA---AATAT 743 chr3ptel1M 116977 TTGGTTTATTTTCTCCTTG-CCTTATATTGCATGTGATTTTT------AT 117019 -vv vv? i- i v i -- - i ------ C L1M5_orf2#LIN 742 TTGG-GGATTTTCTAGNTATCTTTTTGTT--AT-TGATTTCTAATTTAAT 697 chr3ptel1M 117020 TTCATCATGATCTCAAAAAA-ATACATT-TACTATTTCTGCCTTTTTGCA 117067 i ii i-- i i - vi - iv vii i ?iv C L1M5_orf2#LIN 696 TCCATTGTGG--TCAGAGAACATACTCTGTATGATTTCAATCCTTTNAAA 649 chr3ptel1M 117068 TTT-----GATTTGAAGTTTTTATGCCCTAATACATGGTTAATTTTTGCA 117112 ----- i ---- v i i? i iv i v i C L1M5_orf2#LIN 648 TTTATTGAGACTTG----TTTTATGGCCCAGNATATGGTCTATCTTGGTA 603 chr3ptel1M 117113 TAAGTTCCATGAACCACTGAGAAAAAAGTAAACTTTCTGTCTCCATT--- 117159 v v vi vvi i i v iv -- i?viii --- C L1M5_orf2#LIN 602 AATGTTCCATGTGCACTTGAAAAGAATGTGTA--TTCTGCNGTTGTTGGG 555 chr3ptel1M 117160 --CAATTTTCTCCAAAGATCTATCATGCCTAACTTTTCTAACA-TTTTGT 117206 --? i v vi vi v i v i - v vvi i i - v C L1M5_orf2#LIN 554 TGNAGTGTTCTATAAATGTCAATTAGGTC-AAGTTGGTTGATAGTGTTGT 506 chr3ptel1M 117207 TTA---CTTCCTTAACTTCTTTCTTATTTATTTTGTGCT--TTGATCTAT 117251 i --- iv -- i v v -- - -- v C L1M5_orf2#LIN 505 TCAAATCTTCTATA--TCCTTACTGATT--TTTTGT-CTACTTGTTCTAT 461 chr3ptel1M 117252 CTAGATCTGAGAGAACAAGATTGAGAACCTCCACTAGCATAATTTTG--- 117298 v vvv iv?ivi i i v ii ? --- v --- C L1M5_orf2#LIN 460 CAATTACTGAGAGAGGNGTGTTAAAATCTCCNACT---ATAATTGTGGAT 414 chr3ptel1M 117299 CTGTCTATTTCTTCTTATA--TCTCTCAACTCCT-CTTCTAGGAATTTGA 117345 i i v -- v ii ii - vv v v C L1M5_orf2#LIN 413 TTGTCTATTTCTCCTTTTAGTTCTGTCAGTTTTTGCTTCATGTATTTTGA 364 chr3ptel1M 117346 ATGTGCTACCACTTGGTGCATATGTGTTTAGTATTGATATTGCTTCATTA 117395 - iv iii i v iiii v v vv v v C L1M5_orf2#LIN 363 A-GCTCTGTTATTAGGTGCATACACATTTAGGATTGTTATGTCTTCTTGA 315 chr3ptel1M 117396 TCTATGGTACCCTTT----AGTA--AAATATTGTTTCCTCCCTTATCTTT 117439 vv v - ---- v -- i----- ii i i C L1M5_orf2#LIN 314 TGAATTG-ACCCTTTTATCATTATGAAATG-----TCCCTCTTTATCTCT 271 chr3ptel1M 117440 TTCAATTAGATCTATCTTTGCTTT------TACTTAATCTGAGATCAGGA 117483 vvi --- --- ii i ------ vi v i iv C L1M5_orf2#LIN 270 GGTAAT---AT---TTCTTGCCTTGAAGTCTACTTTGTCTGATATTAATA 227 chr3ptel1M 117484 TTGCTACCCCTGCCTTTTTTTTTTT 117508 v i ? v i i v? C L1M5_orf2#LIN 226 TAGCCACNCCAGCTTTCTTTTGNTT 202 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.55 CpG sites = 206, Kimura (unadjusted) = 39.70 Transitions / transversions = 1.18 (206/175) Gap_init rate = 0.05 (70 / 1318), avg. gap size = 1.43 (100 / 70) 2256 28.86 1.87 1.76 chr3ptel1M 117522 118484 (881516) L1M5_orf2#LINE/L1 1552 2515 (779) m_b112s551i4 4072 chr3ptel1M 117522 CCTAAACCAGATAGGGTGAAAACAGAAAAAGAAAATTATAGACC------ 117565 v ? i ii vv vv ii i ------ L1M5_orf2#LIN 1552 CCAAAACCNGACAAAGACATTACAAGAAAAGAAAATTACAGACCAATATC 1601 chr3ptel1M 117566 --TAATGAATATTGATGCAAAAATCTTAAATAAAATATTAGCAACAAGAT 117613 -- v i v i ? i vvv v L1M5_orf2#LIN 1602 CCTCATGAACATAGATGCAAAAATCCTNAACAAAATATTAGCAAATCGAA 1651 chr3ptel1M 117614 TACAAAAAGTCATTCTCAGGATAATACACTATAACCAATTAGT-TTTATA 117662 v iv vvi vvvv ii i v i v- v L1M5_orf2#LIN 1652 TCCAGCAATATATAAAAAGGATAATACATCATGACCAAGTGGGGTTTATC 1701 chr3ptel1M 117663 CCAAGAATGCAAGAATACAGGGCTGGTTCAATATTAGGAAAACTATTAGC 117712 i -------- i i i v i v v i ii L1M5_orf2#LIN 1702 CCAGGAATGCAAG--------GTTGGTTTAACATTCGAAAATCAATCAAT 1743 chr3ptel1M 117713 ATAATCAACTATATCAATA-ACCAAACTAAGAAAAATCATATGATTATTT 117761 i iv i i i - vi v-i i i L1M5_orf2#LIN 1744 GTAATTCACCATATTAACAGAATAAAG-GAGAAAAATCATATGATCATCT 1792 chr3ptel1M 117762 CAATAGATGCATAAAAAGCATTTGATAAAATCCAACACCCATTCCTATTA 117811 v i i v iv L1M5_orf2#LIN 1793 CAATAGATGCAGAAAAAGCATTTGACAAAATTCAACACCCATTCATGATA 1842 chr3ptel1M 117812 AAAACACT-AGAAAGTATAGGAAT--AAGTGGACTTTTCCTTAAAATGAT 117858 v - v ii- -- v i -- i vv L1M5_orf2#LIN 1843 AAAACTCTCAGCAAAC-TAGGAATAGAAGGGAAC--TTCCTCAACCTGAT 1889 chr3ptel1M 117859 AAATAGCATCTATTTAAAACCATCAGCAAGCACCACATGGAATGGAGACA 117908 vi ivv vv ? i i i ivv v v L1M5_orf2#LIN 1890 AAAGGGCATCTACGAAAAACCTACAGCNAACATCATACTTAATGGTGAAA 1939 chr3ptel1M 117909 ACCTAGAACCATTCCCAATAAGATCAGTAGTAAAACAAAGCTGCCCACTA 117958 ?v ii ?v v vv i v ii i i v i i ? L1M5_orf2#LIN 1940 NACTGAANGCTTTCCCCCTAAGATCGGGAACAAGACAAGGATGTCCGCTN 1989 chr3ptel1M 117959 TTACCATTACTATTCAATATTGTATTAGAAATGTTAATTCTGACAATAAG 118008 i i v i i i ii vi iiivvvi L1M5_orf2#LIN 1990 TCACCACTTCTATTCAACATTGTACTGGAGGTCCTAGCCAGTGCAATAAG 2039 chr3ptel1M 118009 AGAAGAAAAAGAGATTAAAGGAATTAGAGTATGTAATGAGGAAACCAAAT 118058 iv i v v v iii vv v v i iv i L1M5_orf2#LIN 2040 GCAAGAAAAAGAAATAAAAGGCATAAAGATTGGAAAGGAAGAAATAAAAC 2089 chr3ptel1M 118059 TATCACTCTTTGCAGATGATATGATGGTATTCTTAAAGAACCCTAGAGAA 118108 i ?i v i i v ? v v i i i ? i L1M5_orf2#LIN 2090 TGTCNTTATTCGCAGATGACATGATTGTNTACGTAGAAAATCCNAAAGAA 2139 chr3ptel1M 118109 TCAATTAAAAAATTACTAGAACCAATTCACAACTTTAGCAAAGTTGCAGG 118158 v iv ? i i vviii v i i ? L1M5_orf2#LIN 2140 TCTACAAANAAACTACTAGAACTAATAAGTGAATTTAGCAAGGTCGCNGG 2189 chr3ptel1M 118159 ATACAAAATAAATCCACATAAATCATCAGCATTTTTATATATTACCAAGA 118208 ii v vi v viv i i i v v L1M5_orf2#LIN 2190 ATACAAGGTCAATATACAAAAATCAATTGTATTTCTATATACTAGCAACA 2239 chr3ptel1M 118209 A--AATTCAGCAGCAAGAGATACAGAAAGAAATTCCATTTGAAATAACTG 118256 -- -- v iv v i vi?i iv v iv i vv L1M5_orf2#LIN 2240 AACAATT--GGAAAATGAAATTTNAAAAACAATACCATTTACAATAGCAT 2287 chr3ptel1M 118257 TTGATAGTATAAAATATTTAAGAATCTTTCTGCCAATGGAAAAT---CAG 118303 ivi v ii ? i i vvv iv --- ? --- i L1M5_orf2#LIN 2288 CAAAAAACATNAAATACTTAGGAATAAATCTAACAA---AANATGTGCAA 2334 chr3ptel1M 118304 GAACTATATGAGCAAAATTACAAAACATTTTCCACACAAATAAAGTCAGA 118353 v ? iivvv i viiv v v v ivv L1M5_orf2#LIN 2335 GACCTNTACACTGAAAACTACAAAACATTGCTGAGAGAAATTAAAGAAGA 2384 chr3ptel1M 118354 TCTAATCAGCTGAAAAAATATCAAGTGCTCATGGATAGGCTGAGCAAATA 118403 i vi iv i i i vvvi i v vv viv L1M5_orf2#LIN 2385 CCTAAATAAATGGAGAGATATACCATGTTCATGGATTGGAAGACTCAATA 2434 chr3ptel1M 118404 TAATAAAAATGGCACTATTACCTAAATCAATCTACTTATTTAGCACCATA 118453 vi ? i v v vi v i ii ivv i iii v v L1M5_orf2#LIN 2435 TTGTNAAGATGTCAATTCTCCCCAAATTGATCTATAGATTCAATGCAATC 2484 chr3ptel1M 118454 CCAATCAAATTCTCAAGAAATTATTTTATAG 118484 v i iv ii v i L1M5_orf2#LIN 2485 CCAATCAAAATCCCAGCAGGTTTTTTTGTAG 2515 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.98 CpG sites = 143, Kimura (unadjusted) = 37.85 Transitions / transversions = 1.10 (143/130) Gap_init rate = 0.03 (25 / 962), avg. gap size = 1.40 (35 / 25) 600 30.05 2.37 4.14 chr3ptel1M 118500 118794 (881206) L1ME4c_3end#LINE/L1 350 639 (191) m_b112s551i5 4072 chr3ptel1M 118500 TAACAAAGTTCAT---CTTTGACCCAGCAGTGTTTCTACTGGGCCTATAA 118546 v v --- i i viiv v vv v - L1ME4c_3end#L 350 TAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTA- 398 chr3ptel1M 118547 AAGAGATCCCAAAGAGAT--CTTAAAGGAAGGAAAAGGATCCACATGTGC 118594 ------ i i i --i i i i -- i i ii L1ME4c_3end#L 399 ------TCCTAAGGAAATAATTCAAAAGAAGGAAAAAG--CTATATGCAC 440 chr3ptel1M 118595 AAAAATGTTTATGGCAGCCCTTTCTGTAGTGGCCAGAAATTGGAAACTGA 118644 i i i v vi v i i i i v i -- L1ME4c_3end#L 441 GAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAAC--A 488 chr3ptel1M 118645 A--TAGATGCACATCAGAAGGAGAATGGCTGAATAAATGATGGTATATTA 118692 -- i iv v iv i i i i v i i? L1ME4c_3end#L 489 ACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCN 538 chr3ptel1M 118693 ATGTTATGGAATATTATTGTTCTATAAGAAACGATCATAAGGATGATTTC 118742 iviv vvvv i v i i v v v v i vi L1ME4c_3end#L 539 ACTCGATGGAATATTATGCAGCCATTAAAAATGATAATTATGAAGACTAT 588 chr3ptel1M 118743 AGAGAGGCCTGGAGAAACATACAGGAACTGATGTTAAGTGAAATGAGAAG 118792 iv vii v - ii vi v vv i vi v L1ME4c_3end#L 589 GTAGCAACATGGA-AAATGTTTATGATATAATGTTAAGTGAAAAAAGCAG 637 chr3ptel1M 118793 AA 118794 L1ME4c_3end#L 638 AA 639 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.31 CpG sites = 48, Kimura (unadjusted) = 39.51 Transitions / transversions = 1.30 (48/37) Gap_init rate = 0.05 (15 / 294), avg. gap size = 1.27 (19 / 15) 19 20.27 0.00 0.00 chr3ptel1M 119932 119967 (880033) (T)n#Simple_repeat 1 36 (0) m_b112s252i4 4073 chr3ptel1M 119932 TTTCTTTTTCTTTTTTCTTCTTCTTTCTTTTTTTTT 119967 i i i i i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 36 Matrix = Unknown Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 561 22.95 2.38 3.20 chr3ptel1M 120304 120429 (879571) C MIRc#SINE/MIR (141) 127 3 m_b112s601i2 4074 chr3ptel1M 120304 CTGAGGC--AGTTGGGTTAAGTGACTTACCCAGGGCCACATAGCTAAGTG 120351 -- vvi i i i i i--- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG--- 81 chr3ptel1M 120352 TTAAATGTCTAAGGCCAGATTAGAACTCAGGTCCTCCTGACTTCAAGGCT 120401 - i v vi v vi i v i i i v i C MIRc#SINE/MIR 80 -TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCC 32 chr3ptel1M 120402 AGTGCTCTATCCACTACATCA-ACTATTT 120429 v i i - iii C MIRc#SINE/MIR 31 AGTGCTCTTTCCACTGCACCACACTGCCT 3 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.32 CpG sites = 19, Kimura (unadjusted) = 28.32 Transitions / transversions = 2.11 (19/9) Gap_init rate = 0.05 (6 / 125), avg. gap size = 1.17 (7 / 6) 26 0.00 0.00 0.00 chr3ptel1M 121601 121625 (878375) (T)n#Simple_repeat 1 25 (0) c_b112s251i0 4075 chr3ptel1M 121601 TTTTTTTTTTTTTTTTTTTTTTTTT 121625 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 236 21.19 0.00 17.95 chr3ptel1M 123297 123388 (876612) C L2c_3end#LINE/L2 (6) 472 395 m_b112s601i3 4076 chr3ptel1M 123297 TCAGTCAACAAGCCTTTATTAAACACCTACTGTGTTCCAGGAAACGCTAA 123346 v i v i i i i v --- ii C L2c_3end#LINE 472 TCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGG---CGCTGG 426 chr3ptel1M 123347 GCAAGTACGGAGGAGATGAAAGCTTCAGACCCGTGATCCCTG 123388 v -- ---ii ---- v v -- i C L2c_3end#LINE 425 GGA--TAC---AAAGATGAA----TAAGACAC--GGTCCCTG 395 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 22.75 CpG sites = 10, Kimura (unadjusted) = 24.45 Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.15 (14 / 91), avg. gap size = 1.00 (14 / 14) 294 33.78 0.69 8.15 chr3ptel1M 125133 125277 (874723) L2c_3end#LINE/L2 330 464 (14) m_b112s601i4 4077 chr3ptel1M 125133 AGCTTGCTTTGAGAATATGCGCTTGCAGGT-TGTTTCCCCCGTGAGCCTG 125181 i iv vi v i vi i i ?v - i i iiv v L2c_3end#LINE 330 AACTTGTATTGTAATTGTCTGTTTACNTGTCTGTCTCCTCCACTAGACTG 379 chr3ptel1M 125182 TGAGCGCCTGGAGGGAGGGGGCCACGTTCTGCCTCTTTTTATCTCCTCAG 125231 v v vi i ii ii iiiiv i i v i L2c_3end#LINE 380 TGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTATCCCCAG 429 chr3ptel1M 125232 CCCTAGCCCACCGCCCGGCACATAACTGACGCTTAATGAATTCTTG 125277 ----------- i iiv i i i vi L2c_3end#LINE 430 -----------CGCCTGGCACATAGTAGGCGCTCAATAAATGTTTG 464 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 46.72 CpG sites = 31, Kimura (unadjusted) = 48.27 Transitions / transversions = 2.21 (31/14) Gap_init rate = 0.08 (12 / 144), avg. gap size = 1.00 (12 / 12) 329 27.41 5.60 0.76 chr3ptel1M 125153 125277 (874723) L2b_3end#LINE/L2 322 452 (14) m_b112s601i5 4077 chr3ptel1M 125153 GCTTGCAGGT-TGTTTCCCCCGTGAGCCTGTGAGCGCCTGGAGGGAGGGG 125201 ? i v - i iiv v v vv vi L2b_3end#LINE 322 GNTTACATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGG 371 chr3ptel1M 125202 GCCACGTTCTGCCTCTTT-----TTATCTCCTCAGC-CCTAGCCCACCGC 125245 i i? - i iv -----i i v i - v v? L2b_3end#LINE 372 ACCGNG-TCTGTCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGC 420 chr3ptel1M 125246 CCGGCACATAACTGACGCTTAATGAATTCTTG 125277 i i iiv i i i i vi L2b_3end#LINE 421 CTGGCACACAGTAGGCGCTCAGTAAATATTTG 452 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.01 CpG sites = 21, Kimura (unadjusted) = 36.35 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.03 (4 / 124), avg. gap size = 2.00 (8 / 4) 207 23.97 9.21 1.22 chr3ptel1M 126799 126874 (873126) C MIRb#SINE/MIR (132) 136 55 m_b112s601i6 4078 chr3ptel1M 126799 AGTAAACCGAGGCTCCCCGGGGTGAAGTAACTTGCTCCTAGTCACACA-- 126846 v i vvv i v i vvi -- C MIRb#SINE/MIR 136 AGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGC 87 chr3ptel1M 126847 -AGCACACTGCAGAGT---GATATCG-ATCCAG 126874 - i viiv i--- - - i C MIRb#SINE/MIR 86 TAGTAAGTGGCAGAGCCGGGAT-TCGAACCCAG 55 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.18 CpG sites = 9, Kimura (unadjusted) = 29.18 Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.07 (5 / 75), avg. gap size = 1.60 (8 / 5) 211 25.00 0.00 0.00 chr3ptel1M 126799 126846 (873154) C MIR3#SINE/MIR (78) 130 83 m_b112s601i7 4078 chr3ptel1M 126799 AGTAAACCGAGGCTCCCCGGGGTGAAGTAACTTGCTCCTAGTCACACA 126846 v i i vvv i i i vvi C MIR3#SINE/MIR 130 AGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACA 83 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.69 CpG sites = 6, Kimura (unadjusted) = 30.69 Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 20 17.24 4.17 0.00 chr3ptel1M 127407 127454 (872546) (ATACAT)n#Simple_repeat 1 50 (0) m_b112s252i5 4079 chr3ptel1M 127407 ATACATATAC--ATACACATACACATACATATGCATATGTATGTATATAT 127454 -- i i i ii i i (ATACAT)n#Sim 1 ATACATATACATATACATATACATATACATATACATATACATATACATAT 50 Matrix = Unknown Transitions / transversions = 1.00 (7/0) Gap_init rate = 0.02 (1 / 47), avg. gap size = 2.00 (2 / 1) 261 19.57 0.00 0.00 chr3ptel1M 128196 128241 (871759) C EutTc1-N1#DNA/TcMar-Tc1 (0) 588 543 m_b112s502i0 4080 chr3ptel1M 128196 CAGGGTATCTCAAGTATCTTGGGGCAGATTTAAGCTTTAATAGCTT 128241 i i ivi v v i i C EutTc1-N1#DNA 588 CAGGGTGTCCCAAAAGTCTTGGTGCAGTTTTAAGCTTTAATAACCT 543 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 23.23 CpG sites = 6, Kimura (unadjusted) = 23.23 Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 361 20.08 27.40 1.09 chr3ptel1M 128285 128430 (871570) C MIRc#SINE/MIR (2) 266 83 m_b112s601i8 4081 chr3ptel1M 128285 TAATAATGATAGCTAACATTCATAGAGC-TTTGATA-TTCAGAAAGTACT 128332 i i?v v ii v -i v i - i v ii C MIRc#SINE/MIR 266 TAATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCGCT 217 chr3ptel1M 128333 TT---ATGACTGATCTCATTTGATCTT--------------GAGA----- 128360 --- ivv v i -------------- i----- C MIRc#SINE/MIR 216 TTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGC 167 chr3ptel1M 128361 --GACAGGT----------CCATTTCATAGATGAGGGAAC--AGGCAGTC 128396 -- i ---------- i i i -- -- C MIRc#SINE/MIR 166 AGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGC--TC 119 chr3ptel1M 128397 AGCA--GTTAAGTGACTTGTCCAGGATCACACAGCT 128430 vi-- i i i C MIRc#SINE/MIR 118 AGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCT 83 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 23.29 CpG sites = 20, Kimura (unadjusted) = 24.34 Transitions / transversions = 2.22 (20/9) Gap_init rate = 0.08 (11 / 145), avg. gap size = 3.82 (42 / 11) 214 27.25 3.64 13.25 chr3ptel1M 128927 129091 (870909) L2#LINE/L2 2229 2379 (703) m_b112s601i9 4082 chr3ptel1M 128927 GTGCCCTCGGGTTCCTGTTCTGGGCTCTTCTCCCTCCCTAGAAGGAATCT 128976 iv i v- i v vi ii i i ---------- L2#LINE/L2 2229 GTGCCCCAGGGCTCA-GTCCTTGGACCTCTTCTCTTC----------TCT 2267 chr3ptel1M 128977 TACAATCTACATATCTATCTCACTTAGTGATCTCATCAAAACCTTTGAAT 129026 ---- --- vv v ?i v iv iiv iv L2#LINE/L2 2268 ----ATCTACA---CTCACTCCCTNGGTGATCTCATCCAGTCTCATGGCT 2310 chr3ptel1M 129027 TTAA-TGACATC---ATTCTGCTGATTCTCAAATTTAAGTTTCCTACCAC 129072 - iv --- v v i i vi i vi - L2#LINE/L2 2311 TTAAATACCATCTATATGCTGATGACTCCCAAATTTATATCTCCAGCC-C 2359 chr3ptel1M 129073 AG--TTTTCCCACTGACCTCC 129091 i --i i - v L2#LINE/L2 2360 GGACCTCTCCC-CTGAACTCC 2379 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.21 CpG sites = 22, Kimura (unadjusted) = 34.28 Transitions / transversions = 1.29 (22/17) Gap_init rate = 0.14 (23 / 164), avg. gap size = 1.13 (26 / 23) 220 32.14 12.50 0.00 chr3ptel1M 129082 129193 (870807) L2#LINE/L2 2457 2582 (500) m_b112s601i10 4082 chr3ptel1M 129082 ACTGACCTCCCAATATTTTCCCCCAAAAC--CTTTTCCTA------TCAT 129123 v ii v ii i v -- ii ii------ vi L2#LINE/L2 2457 ACTGAACTCCTGATCTTCCCCCTCAAACCTGCTCCTCCCGCAGTCTTCCC 2506 chr3ptel1M 129124 TAAACCACCCAATG------CCATCTTCCCAGTCCCCCAGGCTTGAAATC 129167 i vvi vi? ------ i i iv i ivi i L2#LINE/L2 2507 CATCTCAGTNAATGGCAACTCCATCCTTCCAGTTGCTCAGGCCAAAAACC 2556 chr3ptel1M 129168 TGGGAGTTATCCTTGATATCTTTGTT 129193 v i ivi i v L2#LINE/L2 2557 TTGGAGTCATCCTTGACTCCTCTCTT 2582 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 43.05 CpG sites = 24, Kimura (unadjusted) = 44.98 Transitions / transversions = 2.00 (24/12) Gap_init rate = 0.03 (3 / 111), avg. gap size = 4.67 (14 / 3) 201 35.10 13.61 2.14 chr3ptel1M 129237 129530 (870470) L2#LINE/L2 2674 3000 (82) m_b112s601i11 4082 chr3ptel1M 129237 CTGCCTCTATCCTGGT--GAGTACAC--TCACCTCATTATC-CCTGAACT 129281 v i i --i i- -- i ---- - i i L2#LINE/L2 2674 CTGCCACCACCCTGGTCCAAGC-CACCATCATCTC----TCGCCTGGATT 2718 chr3ptel1M 129282 GTTACAGGAGCTGC-------ATCTACCTGCCTCCAG---TGCACCC--- 129318 ii i iv iv -------i v i v--- v --- L2#LINE/L2 2719 ACTGCAATAGCCTCCTAACTGGTCTCCCTGCTTCCACCCTTGCCCCCCTN 2768 chr3ptel1M 129319 ---TCTAT-CT-------GTCACCGGAGTGATTTTCCTAATGTGCAGGTC 129357 --- - ------- ivi i ii ii vii i i L2#LINE/L2 2769 CAGTCTATTCTCAACACAGCAGCCAGAGTGATCCTTTTAAAACGTAAGTC 2818 chr3ptel1M 129358 TCTCTGTATCACTG-TCTGCTCAAAAGACTCCATTGGCTCCGCATTGCCT 129406 vvviii i v- vv v i v iv vi L2#LINE/L2 2819 AGATCATGTCACTCCTCTGCTCAAAACCCTCCAATGGCTTCCCATCTCAC 2868 chr3ptel1M 129407 CCTTGATCAAATCTGAAATGCCCTCTTTGGAGCTCAAAGACCTTCATAAT 129456 i vvii v v ii i v iiv vv vviv i v v i L2#LINE/L2 2869 TCAGAGTAAAAGCCAAAGTCCTTACAATGGCCTACAAGGCCCTACATGAT 2918 chr3ptel1M 129457 CCAGTCTCTT----CTCCTCAG---TTTTCTTATACCTTATTCCCTCACA 129499 ii i ii---- ii v --- iv iv -- i i i v v L2#LINE/L2 2919 CTGGTCCCCCGTTACCTCTCTGACCTCATCTCCTACC--ACTCTCCCCCT 2966 chr3ptel1M 129500 CGTGTACTCTGATTCAATGACACT---CTCCCTG 129530 ivi i v i iiv --- i L2#LINE/L2 2967 CGCTCACTCCGCTCCAGCCACACTGGCCTCCTTG 3000 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 47.76 CpG sites = 62, Kimura (unadjusted) = 49.89 Transitions / transversions = 1.59 (62/39) Gap_init rate = 0.07 (20 / 293), avg. gap size = 2.35 (47 / 20) 224 30.10 23.83 1.04 chr3ptel1M 129522 129756 (870244) L2b_3end#LINE/L2 147 434 (32) m_b112s601i12 4082 chr3ptel1M 129522 CTCTCCCTGGGAATGTCCT---CTACCTTCTC---TGGCT---------- 129555 v - i i --- i ii --- i---------- L2b_3end#LINE 147 CTCTGCCTGG-AACGCCCTTCCCCACCTCTTCGCCTGGCCAACTCCTACT 195 chr3ptel1M 129556 --TCTTTAAGAGCCC-GCT-AAAC-TCCCCTGCTGCAGAGGAGGCCTTTC 129600 -- i v iv i - - i- v v v i -- i i i L2b_3end#LINE 196 CATCCTTCAGGTCTCAGCTCAAATGTCACCTCCTCCGG--GAAGCCCTCC 243 chr3ptel1M 129601 CCAACTCCTC---CTAAGTCCGTTGCCTTCTTCT-------CTTACTTGT 129640 ii i i --- iii v vi i i ------- ii v iv L2b_3end#LINE 244 CTGACCCCCCAGGCCGGGTCAGGCGCCCTCCTCTGGGCCCCCCCAGTCCT 293 chr3ptel1M 129641 AGCTTGT-----TGGCACATA----TCTGCTTGC-----TGTCTTTCCTA 129676 v i i----- vvi ?---- ? i ----- ii i L2b_3end#LINE 294 ACCCTGCCACTCTGGGTTATNATTGTCTGNTTACATGTCTGTCTCCCCCA 343 chr3ptel1M 129677 TTATATTGTAAACT---TGAGGGCAGGGA------CTGTTTTTTGC-CTC 129716 i v i i i --- ------ i v v - iv L2b_3end#LINE 344 CTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCTTGTTCACCG 393 chr3ptel1M 129717 TTGTAACTCCAGTGCCTGGAATATGGTA-GGCACTTAATAG 129756 i v i i i v i v? iv- vi i L2b_3end#LINE 394 CTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAG 434 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.82 CpG sites = 48, Kimura (unadjusted) = 41.54 Transitions / transversions = 2.18 (48/22) Gap_init rate = 0.08 (19 / 234), avg. gap size = 3.11 (59 / 19) 391 24.53 6.60 0.00 chr3ptel1M 129655 129760 (870240) L2c_3end#LINE/L2 349 461 (17) m_b112s601i13 4082 chr3ptel1M 129655 TATCTGCTTG-CTGTCTTTCCTATTATATTGTAAACT---TGAGGGCAGG 129700 i i i ? - iii i i v i i i --- L2c_3end#LINE 349 TGTTTACNTGTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGG 398 chr3ptel1M 129701 GAC--TGTTTTTTGCCTCTT-GTAACTCCAGTGCCTGGAATATGGTAGGC 129747 -- i v v v - v i i v i i L2c_3end#LINE 399 GACCGTGTCTTATTCATCTTTGTATCCCCAGCGCCTGGCACATAGTAGGC 448 chr3ptel1M 129748 ACTTAATAGTTGT 129760 i i iv L2c_3end#LINE 449 GCTCAATAAATGT 461 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.64 CpG sites = 19, Kimura (unadjusted) = 31.56 Transitions / transversions = 2.71 (19/7) Gap_init rate = 0.04 (4 / 105), avg. gap size = 1.75 (7 / 4) 183 20.15 4.48 11.11 chr3ptel1M 130045 130111 (869889) C X17_LINE#LINE/CR1 (36) 260 198 m_b112s601i14 4083 chr3ptel1M 130045 ATCTAGTCCATTGTCCAAGTCAAGGCAGGA---TTTCCTACTGTGATGGG 130091 ? iv - i ?v --- i i ii - i C X17_LINE#LINE 260 ATCTNGTCCATCCTCC-AGCCANTGCAGGATTGTTCCCTGCCATGA-GGA 213 chr3ptel1M 130092 CTGTTCCTCCTTCAGGTGCT 130111 i i ----- i C X17_LINE#LINE 212 TTATT-----TTCAAGTGCT 198 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 25.63 CpG sites = 10, Kimura (unadjusted) = 25.63 Transitions / transversions = 5.00 (10/2) Gap_init rate = 0.12 (8 / 66), avg. gap size = 1.25 (10 / 8) 18 14.73 0.00 0.00 chr3ptel1M 130912 130941 (869059) (C)n#Simple_repeat 1 30 (0) m_b112s252i7 4084 chr3ptel1M 130912 CCCCCCCCACCCCCCACCCCCCCCTCCTCC 130941 v v i i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 30 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 316 29.92 13.29 0.56 chr3ptel1M 131082 131239 (868761) C L3#LINE/CR1 (1491) 2608 2431 m_b112s601i15 4085 chr3ptel1M 131082 TTCTCT-AGGACTTTGGCATAAAGTGCATCTGTGT------ACTTGGCCT 131124 i - v ii v iv i v i v i------ iv C L3#LINE/CR1 2608 TTCTTTCAGTACCCTGGGATGTAATTCGTCTGGGCCTGGAGACTTGAACT 2559 chr3ptel1M 131125 CTTTCAGGGCAGCT-----CTGCTCTTACTAGCTCTT-----ATCTTGGA 131164 v i ii i ----- - v i ----- i C L3#LINE/CR1 2558 CATTTAAAGCGGCTAGGTGCT-CTCTTACTATCTCCTCACCTATCTTGGG 2510 chr3ptel1M 131165 TATCAACTCCTCCTTAGTCACTTTGGTCCTGACCCTTAGAGTCCAAAGGC 131214 iv i ii iiv iv v i iv i vv ii ii C L3#LINE/CR1 2509 CTTCAATTCCCTCTTAACGATGTTTGTTCTACCCTTTCCAGTCTGAAGAT 2460 chr3ptel1M 131215 CATTCTC--TGGCAGAGCAAAC--AAGCA 131239 -- ii v i -- C L3#LINE/CR1 2459 CATTCTCCTTGATAGAGAAGACGGAAGCA 2431 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.73 CpG sites = 31, Kimura (unadjusted) = 40.04 Transitions / transversions = 1.94 (31/16) Gap_init rate = 0.04 (7 / 157), avg. gap size = 3.14 (22 / 7) 467 24.11 12.09 2.00 chr3ptel1M 132122 132303 (867697) MIRc#SINE/MIR 32 231 (37) m_b112s601i16 4086 chr3ptel1M 132122 GGATTAGTGGTTGGGAAGACATGAGTGTGAACCCTTTCTCACACTCTCAG 132171 i v vi ii v i vi ii ivv vvv v i v MIRc#SINE/MIR 32 GGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTAC 81 chr3ptel1M 132172 GAGTTCTGTGACCTTGGGTTAGTTATTTAAC----CTGAGCTTCAATTTT 132217 v i v iv i i ---- i i i MIRc#SINE/MIR 82 TAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTC 131 chr3ptel1M 132218 CTCAGTTGTAAAAT-GGGATAATAGTA---GCCCT---TATGCTGA---G 132257 vi - i --- --- i- v --- MIRc#SINE/MIR 132 CTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTAC-CTCACAGG 180 chr3ptel1M 132258 ATTG--GTGAGGTTCCAAAAACAAGA-AATGTAT---AAA--GCTTCAAA 132299 i -- v --- ii - --- -- iiv MIRc#SINE/MIR 181 GTTGTTGTGAGGATC---AAATGAGATAATGTATGTGAAAGCGCTTTGTA 227 chr3ptel1M 132300 AACT 132303 MIRc#SINE/MIR 228 AACT 231 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.10 CpG sites = 25, Kimura (unadjusted) = 29.71 Transitions / transversions = 1.39 (25/18) Gap_init rate = 0.07 (13 / 181), avg. gap size = 2.00 (26 / 13) 16 26.78 1.35 5.63 chr3ptel1M 132304 132377 (867623) (TAT)n#Simple_repeat 1 71 (0) m_b112s252i8 4087 chr3ptel1M 132304 TATTATTGGTAATATTATCATTGTTTATT-TTAGGAGTAATTATAATGGT 132352 iv v i -v - vv - v v -- (TAT)n#Simple 1 TATTATTATTATTATTATTATT-ATTATTATTATTA-TTATTATTAT--T 46 chr3ptel1M 132353 ACTATTATTTCAAATATTATGATTA 132377 i viv v v (TAT)n#Simple 47 ATTATTATTATTATTATTATTATTA 71 Matrix = Unknown Transitions / transversions = 0.36 (4/11) Gap_init rate = 0.07 (5 / 73), avg. gap size = 1.00 (5 / 5) 197 31.57 12.35 2.25 chr3ptel1M 132445 132606 (867394) C L3#LINE/CR1 (2046) 2053 1876 m_b112s601i17 4085 chr3ptel1M 132445 AAGAGCTTCCTGTCCTTCTCGGGCTTACCCTCCCAGTTAGATAATTAGCT 132494 ii? i i i i- i i i ivv iii vvi?i - C L3#LINE/CR1 2053 AAGAGCTTCCCANCCCTCTTGAGCC-ATCTTTCTTTTTGAGTCTCNGGC- 2006 chr3ptel1M 132495 CATGGCACCCTACCTAAGATTTTTCCAATTTTTCTAAAATTGGGAT---- 132540 v i v vv-- i ii v i i iv vv ---- C L3#LINE/CR1 2005 CATGGAATCATACCTCT--TTTCTCTGAATTTTTTGAAATCTGCTTTTCC 1958 chr3ptel1M 132541 --GTATA-TCTG-ATTATGTGCAGA------GCT----CTTTCCT--CTA 132574 -- v - - vi i ii ------i ---- i -- C L3#LINE/CR1 1957 TCGTAAAGTCTGGAACATATGTGGACTTTTAACTTTTCCTTTCTTGGCTA 1908 chr3ptel1M 132575 TTACAAATTCTGAGATGGAATGGCTGCTTCTC 132606 i i i iv vvi C L3#LINE/CR1 1907 TTACGAACTCTAAGATGACATGGCACTTTCTC 1876 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 42.90 CpG sites = 33, Kimura (unadjusted) = 44.12 Transitions / transversions = 1.94 (33/17) Gap_init rate = 0.07 (11 / 161), avg. gap size = 2.18 (24 / 11) 229 34.62 6.42 5.35 chr3ptel1M 133822 134117 (865883) C L1ME3G_3end#LINE/L1 (395) 529 231 m_b112s551i6 4088 chr3ptel1M 133822 ACATACCATAAGTTATTCAGTCATTCCCC-ATTAATGGGCATCCTTTCCA 133870 i v i ii - i i iivvviii C L1ME3G_3end#L 529 ATATACCATAATTTATTTAACCATTCCCCTATTGATGGACATTTAGGTTG 480 chr3ptel1M 133871 TTTCTAATTTTTTTAGAAACTAGAAATAGAGCACAAAAAGAGCACAAAAT 133920 i i-- vv i v i iv --------v vvi i C L1ME3G_3end#L 479 TTTCCAATTTTTC--GCTATTACAAACAATGC--------TGCAATGAAC 440 chr3ptel1M 133921 ATTTTTGTATATACAGATTCTTTT-----TCTCCGAG---GTCT-TAGAT 133961 ii i i --? i v ----- v v ---v - i- C L1ME3G_3end#L 439 ATCCTTGTACATGC--NTCCTTGTGCACATGTGCGAGTATTTCTNTAGG- 393 chr3ptel1M 133962 GTAAAGATCTAATAGCAATGTTGCTGCGTCAAAGAGAATCCCCACTTTGA 134011 i i v?i ? iv iiivi v i v v v i i C L1ME3G_3end#L 392 ATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGCATTTTAA 343 chr3ptel1M 134012 TAGTCCGTTGGACATAGTTTGGTATTATTCTCTAGAATGTTTGAACTGTT 134061 - v iiiv i i iv ii--iv iii i i ? vi v iiv C L1ME3G_3end#L 342 -ATTTTAATAGATACTGCC--AAATTGCCCTCCAAAANGGCTGTACCAAT 296 chr3ptel1M 134062 TCACAGTTCTACTAACAGTG-----GATTA----TTTTCCCACATCATCT 134102 i v i i i i ----- v ---- i i v v C L1ME3G_3end#L 295 TTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCACACCCTCG 246 chr3ptel1M 134103 TCAGCATTTGTCATT 134117 i i i ? vi C L1ME3G_3end#L 245 CCAACACTNGATATT 231 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 49.92 CpG sites = 63, Kimura (unadjusted) = 50.69 Transitions / transversions = 1.85 (63/34) Gap_init rate = 0.07 (22 / 295), avg. gap size = 1.59 (35 / 22) 255 32.85 4.81 6.34 chr3ptel1M 133910 134117 (865883) C L1MA3_3end#LINE/L1 (613) 439 235 m_b112s551i7 4088 chr3ptel1M 133910 GAGCACAAA-ATATTTTTGTATATACAGATTCTTTTTCTCCGAGGTCTTA 133958 ii i - v i i - v iii i------- i C L1MA3_3end#LI 439 GAGTGCAGATATCTCTTCG-ATATACTGATTTCCTTTCTT-------TTG 398 chr3ptel1M 133959 GATGTAAAGATCTAATAGCAATGTTGCTGCGTCAAAGAGAATCCCCACTT 134008 -- v v i ii iiivi vi v vi v v i i i C L1MA3_3end#LI 397 G--GTATATACCTAGCAGTGGGATTGCTGGATCATATGGTAGCTCTATTT 350 chr3ptel1M 134009 TGATAGTCCGTTGGACATAGTTTGGTATTATTCTCTAGAATGTTTGAACT 134058 -- iiv iiv - vi iviv i i i v i v v C L1MA3_3end#LI 349 T--TAGTTTTTTGAGGA-ACCTCCAAACTGTTCTCCATAGTGGTTGTACT 303 chr3ptel1M 134059 GTTTCACAGTTCTACTAACAGTG------GATTA--TTTTC-CCACATCA 134099 iv i v i i i ------ i v-- - v C L1MA3_3end#LI 302 AATTTACATTCCCACCAACAGTGTACGAGGGTTCCCTTTTCTCCACATCC 253 chr3ptel1M 134100 TCTTCAGCATTTGTCATT 134117 vi i C L1MA3_3end#LI 252 TCGCCAGCATTTGTTATT 235 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 44.40 CpG sites = 41, Kimura (unadjusted) = 45.39 Transitions / transversions = 1.78 (41/23) Gap_init rate = 0.08 (17 / 207), avg. gap size = 1.35 (23 / 17) 351 24.67 4.78 9.58 chr3ptel1M 134433 134683 (865317) C L1M5_orf2#LINE/L1 (882) 2412 2173 m_b112s551i8 4088 chr3ptel1M 134433 ACATGATAATTTATTATTTCCACAGTTATGTAGATCTGTCTTTGTGTGGA 134482 i ------ i iv v v i - ------- C L1M5_orf2#LIN 2412 ACATGGTA------TATCTCTCCATTTATTTAGGTCT-TCTTT------- 2377 chr3ptel1M 134483 AAATTTT-----GTAAT--TGTGTAATTGTGTTCA-TGTA--GTTCTTGG 134522 - i----- i -- v i --- - -- v v C L1M5_orf2#LIN 2376 -AATTTCTCTCAGCAATGTTTTGTAGTT---TTCAGTGTANAGGTCTTGC 2331 chr3ptel1M 134523 TTATATGTTGGCAGGTAGACTCCCAAGTATTTAATATTGTCTGCAGTTAT 134572 vi ? v vi i vv i i ? i v i vv i C L1M5_orf2#LIN 2330 ACATNTTTTGTTAGATTTATTCCTAAGTATTTNATGTTTTTTGATGCTAT 2281 chr3ptel1M 134573 TTTAAATGGAATTTCTCTTTCTGTCTCTTCCTGCTAATT-TTTGCTGTTA 134621 v v vi i ?vvi i v ii - i - i i C L1M5_orf2#LIN 2280 TGTAAATGGTATTGTTTTTNAAATTTCATTTT-CCAATTGTTTGTTGCTA 2232 chr3ptel1M 134622 ATATATAGAAATGCTGATGATATTTGTATGTGGATTTACTTTATATCCTA 134671 i i viv v ---- v i i ?i C L1M5_orf2#LIN 2231 GTATATAGAAATACAATTGATTTTTGTAT----ATTGACCTTGTATCCNG 2186 chr3ptel1M 134672 TAA-CTTGCTAAA 134683 ii - C L1M5_orf2#LIN 2185 CGACCTTGCTAAA 2173 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 30.25 CpG sites = 32, Kimura (unadjusted) = 30.98 Transitions / transversions = 1.33 (32/24) Gap_init rate = 0.12 (29 / 250), avg. gap size = 1.21 (35 / 29) 454 25.92 1.74 3.55 chr3ptel1M 134541 134712 (865288) C L1M1_orf2#LINE/L1 (982) 2312 2144 m_b112s551i9 4088 chr3ptel1M 134541 ACTCCCAAGTATTTAATATTGTCTGCAGTTATTTTAAATGGAATTTCTCT 134590 i i i v i i ii i v i v i C L1M1_orf2#LIN 2312 ATTCCTAGGTATTTAATTTTATTTGTGGCTATTGTAAATGGGATTACTTT 2263 chr3ptel1M 134591 TTCTGTCTCTTCCTGCTAATT-TTTGCTGTTAATATATAGAAATGCTGAT 134639 ivi i ii - vi - ii iii iv C L1M1_orf2#LIN 2262 TTTGATTTCTTTTT-CAGATTGTTCACTGTTGGCATATAGAAATGCTACT 2214 chr3ptel1M 134640 GATATTTGTATGTGGATTTACTTTATATCCTATAAC-TTGCTAAAGTTGT 134688 v v ---- i ii - i i v C L1M1_orf2#LIN 2213 GATTTTTGTATGTTGAT----TTTGTATCCTGCAACTTTACTGAATTTGT 2168 chr3ptel1M 134689 TAATT-GTTTAGACAATTGTTTTAG 134712 v i- ivi i i - ? C L1M1_orf2#LIN 2167 TTATCAGTTCTAATAGTT-TTTTNG 2144 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.88 CpG sites = 32, Kimura (unadjusted) = 33.88 Transitions / transversions = 2.91 (32/11) Gap_init rate = 0.05 (9 / 171), avg. gap size = 1.00 (9 / 9) 240 22.16 10.62 4.17 chr3ptel1M 134746 134858 (865142) C L1MC_orf2#LINE/L1 (1218) 2076 1957 m_b112s551i10 4089 chr3ptel1M 134746 CTTCCCATAATCT--ATAC---TTATTTCCCCAATTTCTTGT----TGGT 134786 -- -- --- i--- ---- v i C L1MC_orf2#LIN 2076 CTTCCCA--ATCTGTATACCTTTTATTTCCT---TTTCTTGTCTTATTGC 2032 chr3ptel1M 134787 AT-AATTAGCATTGCTAATATACTATTGAATTATAGTGGTGATAATGGAC 134835 - ii v i v i i iiv i vviv v iv C L1MC_orf2#LIN 2031 ATTAGCTAGGACTTCCAGTACGATGTTGAAAAGGAGTGGTGAGAGGGGAC 1982 chr3ptel1M 134836 ATCTTTG--TTTTTCCTGATGTTAG 134858 i -- v v C L1MC_orf2#LIN 1981 ATCCTTGCCTTGTTCCTGATCTTAG 1957 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 25.28 CpG sites = 13, Kimura (unadjusted) = 26.67 Transitions / transversions = 1.18 (13/11) Gap_init rate = 0.09 (10 / 112), avg. gap size = 1.70 (17 / 10) 273 28.26 10.53 4.69 chr3ptel1M 134965 135287 (864713) C L1M5_orf2#LINE/L1 (1671) 1623 1283 m_b112s551i11 4088 chr3ptel1M 134965 TTTTGCTTCGATATTCATTAGGAAAGTTGGTTTATAGTTTTTTGTT--TG 135012 v v i v i vi i i i i v -- C L1M5_orf2#LIN 1623 TTTTGCATCTATGTTCATGAGGGATATTGGTCTGTAATTTTCTTTTCTTG 1574 chr3ptel1M 135013 TTTTGGCTCTTCCTGATTTAGATATCAAAATTATATCTGTGTCATAGAAG 135062 vv v i vi ? i v i iii ? iiiv iv i v C L1M5_orf2#LIN 1573 TAATGTCTTTGTCNGGTTTTGGTATCAGGGTNATGCTGGCCTCATAAAAT 1524 chr3ptel1M 135063 ATATTTGGTAGGACTCCTT-TTTTTCCAGT---------AGTTTATGTAA 135102 ivi v v vii i - i v --------- i C L1M5_orf2#LIN 1523 GAGTTGGGAAGTGTTCCCTCTTTTTCTATTTTCTGGAAGAGTTTGTGTAA 1474 chr3ptel1M 135103 TATTGG-ATTAATTGTTCTCTAAGTGTTTGGT----T------ATAAATC 135141 v - v v ii i ---- ------i i v C L1M5_orf2#LIN 1473 GATTGGTATTATTTCTTCCTTAAATGTTTGGTAGAATTCACCAGTGAAGC 1424 chr3ptel1M 135142 TATCTGGACGTAGGTTTGTTTTGTTTTGTTTTTTCCTTCGGTAGCTTGTT 135191 i i v i i--- -i --------- v v v v C L1M5_orf2#LIN 1423 CATCTGGGCCTGGA---GTTTT-CTTTG---------TGGGAAGGTTTTT 1387 chr3ptel1M 135192 TATGACTTTAAATTC--TTTTTCTAA-A---ACAAGATTATTTAAGTATT 135235 v v --- -- i i - --- i i ii i ii v C L1M5_orf2#LIN 1386 AATTAC---AAATTCAATTTCTTTAATAGATATAGGGCTATTCAGATTTT 1340 chr3ptel1M 135236 CTTTTTCTTCTT---TTAATCTGGGCAATTTATATTTTT-ATGAAATTT- 135280 v --- i i i v i ? i i - v i - C L1M5_orf2#LIN 1339 CTATTTCTTCTTGNGTCAGTTTTGGTAANTTGTGTTTTTCAAGGAATTTG 1290 chr3ptel1M 135281 TCTGTTT 135287 ii C L1M5_orf2#LIN 1289 TCCATTT 1283 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.28 CpG sites = 54, Kimura (unadjusted) = 37.28 Transitions / transversions = 1.64 (54/33) Gap_init rate = 0.09 (28 / 322), avg. gap size = 1.79 (50 / 28) 333 26.59 13.37 1.33 chr3ptel1M 134965 135166 (864834) C L1PB_orf2#LINE/L1 (1671) 1623 1398 m_b112s551i12 4088 chr3ptel1M 134965 TTTTGCTTCGATATTCATTAGGAAAGTTGGTTTATAGTTTT--TTGTTTG 135012 ? v v i i i vi i i -- v ? C L1PB_orf2#LIN 1623 TTTNGCATCTATGTTCATCAGGGATATTGGTCTGTAGTTTTCTTTTTTNG 1574 chr3ptel1M 135013 TTTTGGCTCTTCCTGATTTAGATATCAAAATTATATCTGTGTCATAGAA- 135061 v v ii i v i i iii v iiv iv - C L1PB_orf2#LIN 1573 TTATGTCCTTTCCTGGTTTTGGTATTAGGGTGATACTGGCTTCATAGAAT 1524 chr3ptel1M 135062 GATATTTGGTAGGACTCCTTTTTTTCCAGTAGTTTATGTAATATT----- 135106 - v v i i i ii -- vi i v v ----- C L1PB_orf2#LIN 1523 GAT-TTAGGGAGGATTCCCTCTTTCTC--TATCTTGTGGAATAGTGTCAA 1477 chr3ptel1M 135107 --GGATT------AATTGTTCTCTAAGTGTTTGGT----------TATAA 135138 -- ------ v i i i i ---------- i i C L1PB_orf2#LIN 1476 TAGGATTGGTACCAATTCTTCTTTGAATGTCTGGTAGAATTCNGCTGTGA 1427 chr3ptel1M 135139 ATCTATCTGGACGTAGG-TTTGTTTTGTT 135166 ii v v i i- v C L1PB_orf2#LIN 1426 ATCCGTCTGGTCCTGGACTTTTTTTTGTT 1398 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.59 CpG sites = 34, Kimura (unadjusted) = 34.49 Transitions / transversions = 1.79 (34/19) Gap_init rate = 0.05 (10 / 201), avg. gap size = 3.00 (30 / 10) 368 27.81 7.69 0.00 chr3ptel1M 134965 135133 (864867) C L1M1_orf2#LINE/L1 (1671) 1623 1442 m_b112s551i13 4088 chr3ptel1M 134965 TTTTGCTTCGATATTCATTAGGAAAGTTGGTTTATAGTTT--TTTGTTTG 135012 v i i ii vi ii i -- v C L1M1_orf2#LIN 1623 TTTTGCATCAATATTCATCAGAGATATTGGCCTGTAGTTTTCTTTTTTTG 1574 chr3ptel1M 135013 TTTTGGCTCTTCCTGATTTAGATATCAAAATTATATCTGTGTCATAGAAG 135062 v v v i vi i v i iii v iiv iv i v C L1M1_orf2#LIN 1573 ATGTGTCTTTGTCTGGTTTTGGTATCAGGGTAATACTGGCCTCGTAGAAT 1524 chr3ptel1M 135063 ATATTTGGTAGGA-------CTCCTTT-TTTTCCAG--TAGTTTATGTAA 135102 ivi v v ------- i - i i -- iv i C L1M1_orf2#LIN 1523 GAGTTTGGAAGTATTCCCTCCTCCTCTATTTTTCGGAATAGTTTGAGTAG 1474 chr3ptel1M 135103 TATTGG-ATTAATTGTTCTCTAAGTGTTTGGT 135133 v - i v i i C L1M1_orf2#LIN 1473 GATTGGTATTAGTTCTTCTTTAAATGTTTGGT 1442 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.95 CpG sites = 29, Kimura (unadjusted) = 35.85 Transitions / transversions = 1.61 (29/18) Gap_init rate = 0.03 (5 / 168), avg. gap size = 2.60 (13 / 5) 186 26.83 0.00 0.00 chr3ptel1M 135294 135334 (864666) C L3#LINE/CR1 (3117) 982 942 m_b112s601i18 4085 chr3ptel1M 135294 TGATCCAGAAATTCAGATCCTTTTCTTAGATATCATTTGTG 135334 i vi i v v i i i ii C L3#LINE/CR1 982 TGGTCCAGAAAACCAAATCCTGTTCTTCGACACCATCTACG 942 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.15 CpG sites = 8, Kimura (unadjusted) = 35.08 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 210 19.65 11.76 2.70 chr3ptel1M 136463 136530 (863470) L2#LINE/L2 2559 2632 (450) m_b112s601i19 4090 chr3ptel1M 136463 GGAATCATCCTGGACTTCTCACTCTCTCTTACCTACCCCATGTCCTGTCC 136512 i v i v i i -- ii vi L2#LINE/L2 2559 GGAGTCATCCTTGACTCCTCTCTTTCTCTCAC--ACCCCACATCCAATCC 2606 chr3ptel1M 136513 AT-------TTCTGACAGCTCT-CCT 136530 ------- i v i - L2#LINE/L2 2607 ATCAGCAAATCCTGTCGGCTCTACCT 2632 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 21.50 CpG sites = 9, Kimura (unadjusted) = 23.50 Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.06 (4 / 67), avg. gap size = 2.50 (10 / 4) 13 7.16 10.00 0.00 chr3ptel1M 137067 137096 (862904) (ATGGGG)n#Simple_repeat 1 33 (0) m_b112s252i9 4091 chr3ptel1M 137067 ATGGGGGT-GGG-TGGGGATGGGAAT-GGGATG 137096 i - - i - (ATGGGG)n#Sim 1 ATGGGGATGGGGATGGGGATGGGGATGGGGATG 33 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.10 (3 / 29), avg. gap size = 1.00 (3 / 3) 21 4.17 0.00 0.00 chr3ptel1M 137424 137448 (862552) (T)n#Simple_repeat 1 25 (0) m_b112s252i10 4092 chr3ptel1M 137424 TTCTTTTTTTTTTTTTTTTTTTTTT 137448 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 275 29.46 10.08 0.00 chr3ptel1M 137688 137816 (862184) L2-1_AMi#LINE/L2 439 580 (655) m_b112s551i14 4093 chr3ptel1M 137688 TTTTGAGCTGCCTCTCAGATACCTCAAACTGGATGTCTACTAGACATCTT 137737 i i iv i v i i vvvv viv v v i L2-1_AMi#LINE 439 TCTCGGCCTGTCTCTCTGACATCTCCTCGTGGATGTCTAGCCGTCAGCTC 488 chr3ptel1M 137738 AAACTCAACATG--CCAAAAAAGAACTCTTTCTGTGCCCCTCAAAC---- 137781 i -- i v i vv v v i i ---- L2-1_AMi#LINE 489 AAGCTCAACATGGCCTAAAACAGAGCTCTTAATCTTCCCCCCAAGCCTNC 538 chr3ptel1M 137782 -TCTCACTCCC----CTC--TTACTGTCAAGAGCACTGCCAT 137816 -i i i ---- -- i vi v i ii L2-1_AMi#LINE 539 TCCCCATTCCCTTTTCTCGATCACTGTGGACAACACCACCAT 580 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.94 CpG sites = 21, Kimura (unadjusted) = 38.21 Transitions / transversions = 1.24 (21/17) Gap_init rate = 0.04 (5 / 128), avg. gap size = 2.60 (13 / 5) 491 18.89 2.13 9.92 chr3ptel1M 138507 138647 (861353) C Charlie4a#DNA/hAT-Charlie (28) 480 350 m_b112s502i1 4094 chr3ptel1M 138507 GGGCCCCTTTGCCAGTGTGACAAAACCC-CAAACCCCTTTTCAGAATAAA 138555 i v v iii i i-iii i v C Charlie4a#DNA 480 GGACCCCTTTGGCAGTCTGGTGAAGCCTATGGACCCCTTCTCAGAATAAT 431 chr3ptel1M 138556 GGTTTTAAATGCATAAAAATAAGATCCATAGAGTTACAAAGGAAATTATT 138605 v - i v ii ii -- C Charlie4a#DNA 430 GTTTTTAAATGCAT-AAAATAAAATACATAGGATTACAAAGGAAACCA-- 384 chr3ptel1M 138606 ATTATTATTATTTTTATTGAAACAC--TGATCAAAATAGAAAAA 138647 ---------- i -- v vv C Charlie4a#DNA 383 ATTA----------TATTGAAATACAGTTATCAAAATATTAAAA 350 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 22.07 CpG sites = 16, Kimura (unadjusted) = 22.07 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.11 (15 / 140), avg. gap size = 1.07 (16 / 15) 325 29.80 2.80 2.80 chr3ptel1M 139703 139809 (860191) C MIR#SINE/MIR (121) 141 35 m_b112s601i20 4095 chr3ptel1M 139703 ATTTGACAGATGAAGTAACTGAGGCA---AATGATTATATGACTTGTCCA 139749 v i v --- iv i vi i i C MIR#SINE/MIR 141 ATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCCA 92 chr3ptel1M 139750 GGAACACACAATCAGTGTCTGTGGATCCAACTGGGCTTAGGCCTTAGGCA 139799 i iv iii iv-- -ivv i i v v iv ii C MIR#SINE/MIR 91 AGGTCACACAGCTAGTAA--GTGG-CAGAGCCGGGATTCGAACCCAGGCA 45 chr3ptel1M 139800 GTCTGGTGCC 139809 iv C MIR#SINE/MIR 44 GTCTGGCTCC 35 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.69 CpG sites = 19, Kimura (unadjusted) = 39.33 Transitions / transversions = 1.58 (19/12) Gap_init rate = 0.04 (4 / 106), avg. gap size = 1.50 (6 / 4) 21 6.12 0.00 5.56 chr3ptel1M 139887 139924 (860076) (AAAG)n#Simple_repeat 1 36 (0) m_b112s252i11 4096 chr3ptel1M 139887 AAAGAAAGTATAGAAAGAAAGTAAAAAAAGAAAGAAAG 139924 - v - i (AAAG)n#Simpl 1 AAAGAAAG-AAAGAAAGAAAG-AAAGAAAGAAAGAAAG 36 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 202 26.53 11.11 2.27 chr3ptel1M 140342 140422 (859578) C L2a_3end#LINE/L2 (47) 470 383 m_b112s601i21 4097 chr3ptel1M 140342 CACTGGTTTCTAAACAC-GGTGCTG-AGCGGCAAATGAGAAAGAC----- 140384 -- ii i - v v i- i ii ii i v ----- C L2a_3end#LINE 470 CACTG--TTCTAGGCGCTGGGGATACAGCAGTGAACAAAACAGACAAAAG 423 chr3ptel1M 140385 -CCCTGCCCTTG-AGAGCTTACAGGCTAATGGTGGAAGAC 140422 - ii-i vv i v i C L2a_3end#LINE 422 TCCCTGCCCTCATGGAGCTTACATTCTAGTGGGGGGAGAC 383 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.48 CpG sites = 15, Kimura (unadjusted) = 34.53 Transitions / transversions = 2.50 (15/6) Gap_init rate = 0.09 (7 / 80), avg. gap size = 1.57 (11 / 7) 241 27.68 5.26 2.19 chr3ptel1M 140493 140625 (859375) L2b_3end#LINE/L2 330 466 (0) m_b112s601i22 4098 chr3ptel1M 140493 GTGTGTC-CCCCCAGTAGAAGATAA-CCCTGCTGAGAGCAGGGCGCTGGT 140540 v - v vvi i - i i - i vv v? L2b_3end#LINE 330 GTCTGTCTCCCCCACTAGACTGTGAGCTCCG-TGAGGGCAGGGACCGNGT 378 chr3ptel1M 140541 GT-TCTTGTTTTCCCCTTGGTATCCCTAGCACTTTG--CAAGGCTTTGTA 140587 v - iv v -- i i i v -- i? i v i L2b_3end#LINE 379 CTGTCTTGTTCACCGCT--GTATCCCCAGCGCCTAGCACAGNGCCTGGCA 426 chr3ptel1M 140588 TTGTGTAGGT-CGGAGTACCTATTTGATG-ATTAATTAAT 140625 ivvv i- vv vv v - v v L2b_3end#LINE 427 CACAGTAGGCGCTCAGTAAATATTTGTTGAATGAATGAAT 466 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.95 CpG sites = 14, Kimura (unadjusted) = 35.30 Transitions / transversions = 0.64 (14/22) Gap_init rate = 0.07 (9 / 132), avg. gap size = 1.11 (10 / 9) 472 16.89 0.00 4.49 chr3ptel1M 140681 140773 (859227) MIRb#SINE/MIR 110 198 (70) m_b112s601i23 4099 chr3ptel1M 140681 CTGAATCCCTCTCAGCCTCAGTTTCCTCATCTGTAAAAATAAGGGTAATA 140730 v i i v - ii i MIRb#SINE/MIR 110 CTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGT-AAAATGGGGATAATA 158 chr3ptel1M 140731 ATCACACCTACCTTCCAGGGTTGTTACGAGGACCAATTGTGAT 140773 --- iv ii ii v v MIRb#SINE/MIR 159 AT---ACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGAT 198 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 18.08 CpG sites = 10, Kimura (unadjusted) = 19.47 Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.04 (4 / 92), avg. gap size = 1.00 (4 / 4) 248 26.36 3.51 13.46 chr3ptel1M 141027 141140 (858860) L2c_3end#LINE/L2 369 472 (6) m_b112s601i24 4100 chr3ptel1M 141027 CCATGAGGCTG--ATTTCCTGTAAGGATCAGG--CTGTCTTTTGCTTTTC 141072 iv i -- vi - i i- -- i v i ii iv L2c_3end#LINE 369 CCACTAGACTGTGAGCTCCT-TGAGGG-CAGGGACCGTGTCTTATTCATC 416 chr3ptel1M 141073 TTTGTATAGCTAAGGCTTGGTACGATGCCTGGTACATAGCAGGTGCCTAA 141122 vv i -- ---------- i i i ii L2c_3end#LINE 417 TTTGTATCCCCA--GC----------GCCTGGCACATAGTAGGCGCTCAA 454 chr3ptel1M 141123 TAAATGCTTATTGGCTGA 141140 i i iv L2c_3end#LINE 455 TAAATGTTTGTTGAATGA 472 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.49 CpG sites = 19, Kimura (unadjusted) = 33.66 Transitions / transversions = 2.71 (19/7) Gap_init rate = 0.14 (16 / 113), avg. gap size = 1.12 (18 / 16) 294 34.05 1.04 2.11 chr3ptel1M 141045 141140 (858860) L2b_3end#LINE/L2 366 460 (6) m_b112s601i25 4100 chr3ptel1M 141045 GTAAGGATCAGG-CTGTCTTTTGCTTTTCTTTGTATAGCTAAGGCTTGGT 141093 i i i i? - -- i ivi vi vv i iv i i i L2b_3end#LINE 366 GCAGGGACCGNGTCTGTCTT--GTTCACCGCTGTATCCCCAGCGCCTAGC 413 chr3ptel1M 141094 ACGATGCCTGGTACATAGCAGGTGCCTAATAAATGCTTATTGGCTGA 141140 ii? i i i i ii i ii i iv L2b_3end#LINE 414 ACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTTGTTGAATGA 460 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 48.23 CpG sites = 26, Kimura (unadjusted) = 53.27 Transitions / transversions = 4.33 (26/6) Gap_init rate = 0.03 (3 / 95), avg. gap size = 1.00 (3 / 3) 345 26.12 12.31 2.82 chr3ptel1M 141710 141839 (858161) C MIR3#SINE/MIR (53) 155 14 m_b112s601i26 4101 chr3ptel1M 141710 GTTCAACAACCTTGGGGTTTTACAGATGAGGAAACTGAGG--CAACATGG 141757 i vv ii--- -- iviv C MIR3#SINE/MIR 155 GTCCAACCCCCTCA---TTTTACAGATGAGGAAACTGAGGCCCAGAGAGG 109 chr3ptel1M 141758 TGAAGTGCCTTGCTTAGGGTC------CCAGCTCATGTTA-------GAT 141794 v ii i ------ ? i vi vi ------- i C MIR3#SINE/MIR 108 TGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGAC 59 chr3ptel1M 141795 TTGAATTCAGGTCTTCCTGA-GACTAGGCCTTGCCTCCTTTGTCCA 141839 v ii - -vv i v v iii i ii C MIR3#SINE/MIR 58 TAGAACCCAGGTC-TCCTGACTCCCAGTCCGTGCTCTCTCTGCTCA 14 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.61 CpG sites = 21, Kimura (unadjusted) = 33.61 Transitions / transversions = 1.75 (21/12) Gap_init rate = 0.06 (8 / 129), avg. gap size = 2.50 (20 / 8) 393 24.13 12.30 1.48 chr3ptel1M 141727 141848 (858152) C MIRc#SINE/MIR (124) 144 10 m_b112s601i27 4101 chr3ptel1M 141727 TTTTACAGATGAGGAAACTGAGG--CAACATGGTGAAGTGCCTTGCTTAG 141774 -- iviv v v ii i C MIRc#SINE/MIR 144 TTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAA 95 chr3ptel1M 141775 GGTC-C-CAGCTCAT----------GTT-AGATTTGAATTCAGGTCTTCC 141811 - - vi ---------- ii-i i i ii C MIRc#SINE/MIR 94 GGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCC 45 chr3ptel1M 141812 TGAGACTAGGCCTTGCCTCCTTTGTCCATTGCACCAC 141848 vv i i i iv -- v i v i C MIRc#SINE/MIR 44 TGACTCCAAGTCCAG--TGCTCTTTCCACTGCACCAC 10 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.66 CpG sites = 19, Kimura (unadjusted) = 30.10 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.06 (7 / 121), avg. gap size = 2.43 (17 / 7) 702 27.82 8.66 0.40 chr3ptel1M 144312 144542 (855458) MIR#SINE/MIR 10 259 (3) m_b112s601i28 4102 chr3ptel1M 144312 CATAGTG-TTCACAGTGCTAGGTCTGGAGTCAAGAAGAGCTGAGTTCAAA 144360 - v v ii vi v i - vviv i i MIR#SINE/MIR 10 CATAGTGGTTAAGAGCACGGGCTCTGGAGCCA-GACTGCCTGGGTTCGAA 58 chr3ptel1M 144361 TCTCATCTGAGACACTT-C---CTGTGAGACCCTATG----------ATC 144396 i iv vv v - --- v i iv ---------- v MIR#SINE/MIR 59 TCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAAC 108 chr3ptel1M 144397 ATCTGTCTGCCTCGGTTTCCTTGACTGTAAAATAGGGATCATAATAGCTC 144446 v v v i iiv i v iv MIR#SINE/MIR 109 CTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTAC 158 chr3ptel1M 144447 CTGCCTTCCAGGGCTGTTGTAGAGATCAGA-----TAGTACTTATAAAGT 144491 i ivi i iii i i ----- i v i i MIR#SINE/MIR 159 CTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATACATGTAAAGC 208 chr3ptel1M 144492 GCTTAGCCTATTTCCTGGCACATAGTAGGTCCATAATAAATACTAGTTAC 144541 vvi v v i iv vi ii i i MIR#SINE/MIR 209 GCTTAGAACAGTGCCTGGCACATAGTAAGCGCTCAATAAATGTTAGCTAT 258 chr3ptel1M 144542 T 144542 MIR#SINE/MIR 259 T 259 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.81 CpG sites = 36, Kimura (unadjusted) = 35.50 Transitions / transversions = 1.29 (36/28) Gap_init rate = 0.03 (6 / 230), avg. gap size = 3.50 (21 / 6) 223 27.65 3.23 6.67 chr3ptel1M 144890 144982 (855018) L2c_3end#LINE/L2 362 451 (27) m_b112s601i29 4103 chr3ptel1M 144890 GTCTCC-CCATTAAACTGGGAACCCCTTGAAAGCACAGCCTGCTTGGCTT 144938 - i i v i i ii vi v i -- v L2c_3end#LINE 362 GTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCG--TGTCTT 409 chr3ptel1M 144939 TTCTCTCTTGG--TCTTCAGGGTTTACTGGACACACAGTACGTGCT 144982 v iiv v -- ii v i--- - i v i L2c_3end#LINE 410 ATTCATCTTTGTATCCCCAGCGC---CTGG-CACATAGTAGGCGCT 451 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.91 CpG sites = 15, Kimura (unadjusted) = 35.53 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.09 (8 / 92), avg. gap size = 1.12 (9 / 8) 20 13.69 0.00 0.00 chr3ptel1M 146025 146056 (853944) (A)n#Simple_repeat 1 32 (0) m_b112s252i12 4104 chr3ptel1M 146025 AAAATGAAAAAAAAAAAAAAAAAAAACTAAAA 146056 vi vv (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 32 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 12 12.49 0.00 3.70 chr3ptel1M 147066 147093 (852907) (AGAAA)n#Simple_repeat 1 27 (0) m_b112s252i13 4105 chr3ptel1M 147066 AGAGAACAAAAGAAAAAGAACAGAAAAG 147093 i v - v (AGAAA)n#Simp 1 AGAAAAGAAAAG-AAAAGAAAAGAAAAG 27 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 13 10.27 0.00 11.43 chr3ptel1M 147124 147162 (852838) (TTA)n#Simple_repeat 1 35 (0) m_b112s252i15 4106 chr3ptel1M 147124 TTTTTATTTTTACTCATCTATTATTTATTTATTATTATT 147162 v v - i - - - (TTA)n#Simple 1 TTATTATTATTA-TTAT-TATTA-TTA-TTATTATTATT 35 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.11 (4 / 38), avg. gap size = 1.00 (4 / 4) 238 37.62 8.68 1.15 chr3ptel1M 149640 149881 (850119) L1PA6_3end#LINE/L1 94 353 (548) m_b113s551i1 4107 chr3ptel1M 149640 TTTTCTAAGGAAGAAATGTGCCCTCTCCACAGTCAC--GGAAAAATGCTC 149687 i v i v v iiv vvi v v -- i L1PA6_3end#LI 94 TTCTCAAAAGAAGACATTTATGCAGCCAACAGACACATGAAAAAATGCTC 143 chr3ptel1M 149688 CACATCACTAGTTAGTAGAGAAATGC---------------TGACTCACC 149722 vv i i vi --------------- vvi L1PA6_3end#LI 144 ATCATCACTGGTCATCAGAGAAATGCAAATCAAAACCACAATGAGATACC 193 chr3ptel1M 149723 ----CGCTCCTATTAAGTTAGCGAAGATTACAAAAGAGGGAAATGAGCAG 149768 ---- i v vi iiv i vv v ivvi ii vvii L1PA6_3end#LI 194 ATCTCACGCCAGTTAGAATGGCGATCATTAAAAAGTCAGGAAACAACAGA 243 chr3ptel1M 149769 TGTTGGAGGAAGTGTGGGGGAAACAGCCATGGCGGTGCTCCAGTAGTGGA 149818 i iiii - i i vv i vivv i v iiv i i L1PA6_3end#LI 244 TGCTGGAGAGGATGT-GGAGAAATAGGAACGCTTTTACACTGTTGGTGGG 292 chr3ptel1M 149819 GTTGTCAATTGGTCCAGATGTTCTGGAAAGCGCTGGGGAACTCGTCCCCA 149868 iv v i i i ivii v ii iv v viv -- i L1PA6_3end#LI 293 AGTGTAAACTAGTTCAACCATTGTGGAAGACAGTGTGGCGAT--TCCTCA 340 chr3ptel1M 149869 AAGTTCTTAAGCT 149881 i v vi i L1PA6_3end#LI 341 AGGATCTAGAACT 353 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 52.47 CpG sites = 50, Kimura (unadjusted) = 54.26 Transitions / transversions = 1.25 (50/40) Gap_init rate = 0.02 (6 / 241), avg. gap size = 4.00 (24 / 6) 251 25.68 2.70 0.00 chr3ptel1M 149640 149713 (850287) L1PA15_3end#LINE/L1 94 169 (743) m_b113s551i0 4107 chr3ptel1M 149640 TTTTCTAAGGAAGAAATGTGCCCTCTCCACAGTCAC--GGAAAAATGCTC 149687 v i v iii v vvi v iv i-- i L1PA15_3end#L 94 TTTTCAAAAGAAGACATACACGCGGCCAACAAGCATATGAAAAAATGCTC 143 chr3ptel1M 149688 CACATCACTAGTTAGTAGAGAAATGC 149713 v i i v L1PA15_3end#L 144 AACATCACTAATCATTAGAGAAATGC 169 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 31.84 CpG sites = 10, Kimura (unadjusted) = 31.84 Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.01 (1 / 73), avg. gap size = 2.00 (2 / 1) 271 31.00 11.36 1.03 chr3ptel1M 149674 149849 (850151) L1ME4a_3end#LINE/L1 130 323 (548) m_b113s551i2 4107 chr3ptel1M 149674 ACGGAAAAATGCTCCACATCACTAGTTAGTAGAGAAATGC---------- 149713 i i ? i v v v vi i ---------- L1ME4a_3end#L 130 ATGAAAANATGTTCAACCTCACTAGTAATCAAAGAAATGCAAATTAAAAC 179 chr3ptel1M 149714 -----TGACTCACCCGCT----CCTATTAAGTTAGCGAAGATTACAAAAG 149754 ----- vvi vvi ---- i i i i -i L1ME4a_3end#L 180 AACAATGAGATACCATTTTTCACCTATCAAATTGGCAAAGATT-TAAAAG 228 chr3ptel1M 149755 AGGGA-AATGAGCAGTGTTGGAGGAAGTGTGGGGGAAACAGCCATGGCGG 149803 vv - ivv v iii - ? i v ivvivi L1ME4a_3end#L 229 ATTGATAATACCCAGTGTTGGCGAGGGTGT-GGNGAAACGGGCACTCTCA 277 chr3ptel1M 149804 TGCTCCAGTAGTGGAGTTGTCAATTGGTCCAGATGTTCTGGAAAGC 149849 i v iiv i iiv v v iviv ii L1ME4a_3end#L 278 TACACTGCTGGTGGGAGTGTAAATTGGTACAACCTTTCTGGAGGGC 323 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 40.68 CpG sites = 30, Kimura (unadjusted) = 41.69 Transitions / transversions = 1.25 (30/24) Gap_init rate = 0.03 (6 / 175), avg. gap size = 3.67 (22 / 6) 748 25.53 2.09 1.56 chr3ptel1M 149987 150177 (849823) C MIR#SINE/MIR (0) 262 71 m_b113s601i1 4108 chr3ptel1M 149987 AATAA-AACTGGGAACATTGATGTCACGCTTATCGTGGACTGGGTACTGG 150035 - i --- v vvvi iii vi ii i v C MIR#SINE/MIR 262 AATAATAGCT---AACATTTATTGAGCGCTTACTATGTGCCAGGCACTGT 216 chr3ptel1M 150036 ACTGAGAGTTTTACAAGTAATATCTTATTTGATTCTCACAACAACCATTG 150085 v i v i v v v i i i v vv C MIR#SINE/MIR 215 TCTAAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTAT 166 chr3ptel1M 150086 GAGGTAGATGCTGTTATTAT-CCCATTTCATAGCTGAGGAAACTGAGG-- 150132 i i i - i i v -- C MIR#SINE/MIR 165 GAGGTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCA 116 chr3ptel1M 150133 CAGATGGATTCAGTGACTTGCCTAGGGTCCCGTGGCCAGGGAGTG 150177 vi i v i i i v iii i vi C MIR#SINE/MIR 115 CAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTG 71 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.99 CpG sites = 29, Kimura (unadjusted) = 31.99 Transitions / transversions = 1.53 (29/19) Gap_init rate = 0.03 (6 / 190), avg. gap size = 1.17 (7 / 6) 26 21.31 3.30 4.44 chr3ptel1M 156133 156223 (843777) (TCCT)n#Simple_repeat 1 90 (0) m_b113s252i0 4109 chr3ptel1M 156133 TCCTTCC-TCCTTCCTTCC-CCTTTTCTCCCTTGCTCCCTCCCTCTTCTT 156180 - -i i i i v i i - i (TCCT)n#Simpl 1 TCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT-TCCTT 49 chr3ptel1M 156181 CGCTCTCTCCTTCC-CCCTTCTCTCCCCTTCCCGTCCTTCCTTC 156223 vi ii -i - -i - v (TCCT)n#Simpl 50 CCTTCCTTCCTTCCTTCCTTC-CT-TCCTT-CCTTCCTTCCTTC 90 Matrix = Unknown Transitions / transversions = 4.00 (12/3) Gap_init rate = 0.08 (7 / 90), avg. gap size = 1.00 (7 / 7) 208 28.72 4.12 3.06 chr3ptel1M 157905 158001 (841999) C L2c_3end#LINE/L2 (34) 444 347 m_b113s601i2 4110 chr3ptel1M 157905 ACTTTCTGCCAGGCCCTGGAGGCATAAATATTCAAACACGAC-CAGTCTC 157953 v v v i ii i v --i i v - i - C L2c_3end#LINE 444 ACTATGTGCCAGGCGCTGGGGATACAAAGAT--GAATAAGACACGGTC-C 398 chr3ptel1M 157954 CTACTCCCAA--AGGTTACAACCCCATGG-GGAGAGAGTAACCCAAACAG 158000 i i i -- v i ii ivi - v vv ?vi C L2c_3end#LINE 397 CTGCCCTCAAGGAGCTCACAGTCTAGTGGAGGAGACAGACANGTAAACAG 348 chr3ptel1M 158001 A 158001 C L2c_3end#LINE 347 A 347 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.01 CpG sites = 16, Kimura (unadjusted) = 37.78 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.06 (6 / 96), avg. gap size = 1.17 (7 / 6) 14 30.69 0.00 4.55 chr3ptel1M 159620 159688 (840312) (AGG)n#Simple_repeat 1 66 (0) m_b113s252i1 4111 chr3ptel1M 159620 AGGAGGAAGATGAGCAGGAAAGAGTCAGCAAGAGGAAGGAGCCCGAGAAG 159669 i v v - i -v v i - vvv i (AGG)n#Simple 1 AGGAGGAGGAGGAGGAGG-AGGAG-GAGGAGGAGG-AGGAGGAGGAGGAG 47 chr3ptel1M 159670 ACGGAGGCCGACGAGGAGG 159688 iv vv v (AGG)n#Simple 48 GAGGAGGAGGAGGAGGAGG 66 Matrix = Unknown Transitions / transversions = 0.45 (5/11) Gap_init rate = 0.04 (3 / 68), avg. gap size = 1.00 (3 / 3) 14 16.25 2.70 2.70 chr3ptel1M 159848 159884 (840116) (AGGG)n#Simple_repeat 1 37 (0) m_b113s252i2 4112 chr3ptel1M 159848 AGGGAGAGAGAGAAGGGAGGGA-GGAGAGATGGGGGGA 159884 i - i - i v i (AGGG)n#Simpl 1 AGGGAGGGAG-GGAGGGAGGGAGGGAGGGAGGGAGGGA 37 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 193 16.72 0.00 5.56 chr3ptel1M 161604 161641 (838359) C L2d_3end#LINE/L2 (19) 497 462 m_b113s601i3 4113 chr3ptel1M 161604 GTATTTATTAAGCACCTACTGTGCGCTCTAGGCACGGT 161641 i i i i --i v C L2d_3end#LINE 497 GTATTTATTGAGCGCCTACTATGTGCTC--AGCACTGT 462 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 16.18 CpG sites = 5, Kimura (unadjusted) = 19.66 Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 15 6.29 2.56 8.11 chr3ptel1M 162278 162316 (837684) (GTGCCAT)n#Simple_repeat 1 37 (0) m_b113s252i3 4114 chr3ptel1M 162278 GTACCATGTGCCATGTGCCATGCTGGCCACGGTGCC-TGT 162316 i - - -v - (GTGCCAT)n#Si 1 GTGCCATGTGCCATGTGCCATG-T-GCCA-TGTGCCATGT 37 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.11 (4 / 38), avg. gap size = 1.00 (4 / 4) 19 22.06 9.09 2.56 chr3ptel1M 162978 163087 (836913) (AGGGGA)n#Simple_repeat 1 117 (0) m_b113s252i4 4115 chr3ptel1M 162978 AGGAGATCGGTACGGGGATGGGG-CGTGGGAGGGGGCGGCGTAGGGG-AG 163025 i vv v v v -v v i iv v v - (AGGGGA)n#Sim 1 AGGGGAAGGGGAAGGGGAAGGGGAAGGGGAAGGGGAAGGGGAAGGGGAAG 50 chr3ptel1M 163026 AGG--GGGGAAGTGG-A-GGGAGGGAGAAGTGG--GGGAAAGTGG-A-GG 163067 i -- v - - i i v -- i v - - (AGGGGA)n#Sim 51 GGGAAGGGGAAGGGGAAGGGGAAGGGGAAGGGGAAGGGGAAGGGGAAGGG 100 chr3ptel1M 163068 GAAGGGGAATTGGGGGAAGG 163087 --- (AGGGGA)n#Sim 101 GAAGGGGAA---GGGGAAGG 117 Matrix = Unknown Transitions / transversions = 0.54 (7/13) Gap_init rate = 0.10 (11 / 109), avg. gap size = 1.18 (13 / 11) 190 22.51 9.72 1.28 chr3ptel1M 163469 163540 (836460) MIR3#SINE/MIR 68 145 (63) m_b113s601i4 4116 chr3ptel1M 163469 CCGCCACCATCTCCTTGTGCCGGCCTGCAGC------CTTCCTCTCTCTG 163512 i i v ?vi i- i vvi ------ vi MIR3#SINE/MIR 68 CTGCCACTAACTNGCTGTGT-GACCTTGGGCAAGTCACTTCACCTCTCTG 116 chr3ptel1M 163513 G-CCTCAGTTTCCTCATCTCTAGGATGGG 163540 - v ii i MIR3#SINE/MIR 117 GGCCTCAGTTTCCTCATCTGTAAAATGAG 145 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.92 CpG sites = 10, Kimura (unadjusted) = 27.92 Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.04 (3 / 71), avg. gap size = 2.67 (8 / 3) 195 14.63 2.44 0.00 chr3ptel1M 163500 163540 (836460) MIR#SINE/MIR 103 144 (118) m_b113s601i5 4116 chr3ptel1M 163500 CTTCCTCTCTCTG-GCCTCAGTTTCCTCATCTCTAGGATGGG 163540 vvi - v ii MIR#SINE/MIR 103 CTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGG 144 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 16.35 CpG sites = 3, Kimura (unadjusted) = 16.35 Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 13 25.84 0.00 4.17 chr3ptel1M 166248 166297 (833703) (GCCC)n#Simple_repeat 1 48 (0) m_b113s252i5 4117 chr3ptel1M 166248 GCCGGCCCCCAGGCCCCGCCCGCCCCTCGGGCCCTCCCAGCCGCCCGCCC 166297 v v vv - - v vv v iv (GCCC)n#Simpl 1 GCCCGCCCGCCCG-CCCGCCCG-CCCGCCCGCCCGCCCGCCCGCCCGCCC 48 Matrix = Unknown Transitions / transversions = 0.11 (1/9) Gap_init rate = 0.04 (2 / 49), avg. gap size = 1.00 (2 / 2) 20 7.75 7.32 0.00 chr3ptel1M 167379 167419 (832581) (CCTGCCC)n#Simple_repeat 1 44 (0) m_b113s252i6 4118 chr3ptel1M 167379 CCTGCCCCCTGCCCCCTG-CCCC-G-ACCCTGCCCGCGGCCCCC 167419 - - -v v v (CCTGCCC)n#Si 1 CCTGCCCCCTGCCCCCTGCCCCCTGCCCCCTGCCCCCTGCCCCC 44 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.07 (3 / 40), avg. gap size = 1.00 (3 / 3) 12 29.39 4.84 0.00 chr3ptel1M 167820 167881 (832119) (GCCCGG)n#Simple_repeat 1 65 (0) m_b113s252i7 4119 chr3ptel1M 167820 GCCCGGGCCCTTGCCC--GCGGGGACCCCTCCCTGGGTCCTTGCCC-CGC 167866 vv -- vv i vvv i i vv -v (GCCCGG)n#Sim 1 GCCCGGGCCCGGGCCCGGGCCCGGGCCCGGGCCCGGGCCCGGGCCCGGGC 50 chr3ptel1M 167867 CCGGGCCCTTGCCCG 167881 vv (GCCCGG)n#Sim 51 CCGGGCCCGGGCCCG 65 Matrix = Unknown Transitions / transversions = 0.25 (3/12) Gap_init rate = 0.03 (2 / 61), avg. gap size = 1.50 (3 / 2) 12 13.67 0.00 0.00 chr3ptel1M 169191 169214 (830786) (CTC)n#Simple_repeat 1 24 (0) m_b113s252i8 4120 chr3ptel1M 169191 CTGCTCGTCCTCCTCCTCCCCCTC 169214 v v i (CTC)n#Simple 1 CTCCTCCTCCTCCTCCTCCTCCTC 24 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 222 14.71 0.00 0.00 chr3ptel1M 170053 170086 (829914) C MIR1_Amn#SINE/MIR (73) 157 124 m_b113s601i6 4121 chr3ptel1M 170053 CACTGTTCCCACTTTACAGATGAGGAAACGGAGG 170086 i i i i v C MIR1_Amn#SINE 157 CATTATCCCCATTTTACAGATGAGGAAACTGAGG 124 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 16.89 CpG sites = 4, Kimura (unadjusted) = 16.89 Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 198 24.53 5.66 0.00 chr3ptel1M 171723 171775 (828225) MIR3#SINE/MIR 116 171 (37) m_b113s601i8 4122 chr3ptel1M 171723 GAGCCTCAGTCTCCTCACCAGTAAAAT---GGGGCAGGCCTCAAGGGTCT 171769 i i i v --- iv v vi v i MIR3#SINE/MIR 116 GGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCT 165 chr3ptel1M 171770 AAAAGG 171775 vv MIR3#SINE/MIR 166 CTAAGG 171 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.86 CpG sites = 6, Kimura (unadjusted) = 29.86 Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.02 (1 / 52), avg. gap size = 3.00 (3 / 1) 217 9.68 0.00 0.00 chr3ptel1M 171723 171753 (828247) MIRb#SINE/MIR 122 152 (116) m_b113s601i7 4122 chr3ptel1M 171723 GAGCCTCAGTCTCCTCACCAGTAAAATGGGG 171753 i i v MIRb#SINE/MIR 122 GAGCCTCAGTTTCCTCATCTGTAAAATGGGG 152 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 10.46 CpG sites = 2, Kimura (unadjusted) = 10.46 Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 318 32.84 10.37 3.43 chr3ptel1M 174388 174551 (825449) L3#LINE/CR1 3114 3288 (811) m_b113s601i9 4123 chr3ptel1M 174388 AAGGCTCCAGTGGAGAGCTCCAGGGCTCTATGCTCACTGCTGTGTGTGTG 174437 i v i v v iv i v iiviv vi----- L3#LINE/CR1 3114 AGGTCTCTAGTGGCGTGCCACAGGGCTCTGTCCTTGGCCCTGTCC----- 3158 chr3ptel1M 174438 GTTTTTCACATTTTTATTAATGTCTTGGGCAAAGGT-------GTATG-- 174478 - v iv i v iii ii------- i -- L3#LINE/CR1 3159 -TGTTCAACATTTTTATCAATGACTTGGATGAAGACATAGAAGGCATGCT 3207 chr3ptel1M 174479 ------ACCTGCAGACGACTCAAAGCCAGGA-AGAGAGCTCTCACCCTGA 174521 ------ ii i v ii -i v vvi v? i L3#LINE/CR1 3208 TATCAAATTTGCAGATGACACAAAGCTGGGAGGGATAGCTAATACGNTGG 3257 chr3ptel1M 174522 AGAACA-AATTAGGACTTTGGATCAACTCAA 174551 vi - i i i ivii ?v v i L3#LINE/CR1 3258 ATGACAGAATCAAGATTCAAAANGATCTCGA 3288 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.83 CpG sites = 32, Kimura (unadjusted) = 46.07 Transitions / transversions = 1.60 (32/20) Gap_init rate = 0.06 (10 / 163), avg. gap size = 2.30 (23 / 10) 466 20.78 4.14 7.09 chr3ptel1M 176881 177025 (822975) MIRc#SINE/MIR 8 148 (120) m_b113s601i10 4124 chr3ptel1M 176881 GTATGTGTGCGCGTGCAAA-AGC-CTGGGGCAGGGG--AGAAAGCTCTGG 176926 i - i- v - - iviv i -- i vi MIRc#SINE/MIR 8 GTGTG-GTGCA-GTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGG 55 chr3ptel1M 176927 GCTCCGACTTCCGATGGGGCCTCCAGCATTTCCTGGCTGTGTGACCTTGA 176976 i - v i i------ iiv i v i i MIRc#SINE/MIR 56 GTTC-GAGTCCCGG------CTCTGCCACTTACTAGCTGTGTGACCTTGG 98 chr3ptel1M 176977 CCAGGTCACTTAACCTCGTCT--GCCTCAGTTTTCCCATCTGCAAAATGA 177024 v i - -- i i i i MIRc#SINE/MIR 99 GCAAGTCACTTAACCTC-TCTGAGCCTCAGTTTCCTCATCTGTAAAATGG 147 chr3ptel1M 177025 G 177025 MIRc#SINE/MIR 148 G 148 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 25.12 CpG sites = 20, Kimura (unadjusted) = 25.12 Transitions / transversions = 2.50 (20/8) Gap_init rate = 0.10 (14 / 144), avg. gap size = 1.14 (16 / 14) 13 23.08 0.00 4.76 chr3ptel1M 177596 177639 (822361) (GCC)n#Simple_repeat 1 42 (0) m_b113s252i9 4125 chr3ptel1M 177596 GCCGCCACTGCTCGCCGTCTCCGCTGGCCTCCTCGGCCGCCGCC 177639 i i - i v -v v v v (GCC)n#Simple 1 GCCGCCGCCGC-CGCCGCCGCCGC-CGCCGCCGCCGCCGCCGCC 42 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2) 12 15.30 3.45 0.00 chr3ptel1M 178857 178885 (821115) (TCCTG)n#Simple_repeat 1 30 (0) m_b113s252i10 4126 chr3ptel1M 178857 TCCTGTCCTGTCCT-TCCAGTTCTTTTCTG 178885 - v i v i (TCCTG)n#Simp 1 TCCTGTCCTGTCCTGTCCTGTCCTGTCCTG 30 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1) 295 22.18 0.00 7.35 chr3ptel1M 180909 180981 (819019) MIRb#SINE/MIR 114 181 (87) m_b113s601i11 4127 chr3ptel1M 180909 ACTTTTAAGAGCCCCTTCAGTTTCCTCATCTGTAAAGTGGGGGTAACAGT 180958 i i vv --- i i i i MIRb#SINE/MIR 114 ACCTCTCTGAGCC---TCAGTTTCCTCATCTGTAAAATGGGGATAATAAT 160 chr3ptel1M 180959 GGCTCCACCCCGTAGGACTGGTG 180981 iv -- i i ii v MIRb#SINE/MIR 161 ACCT--ACCTCGCAGGGTTGTTG 181 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.22 CpG sites = 11, Kimura (unadjusted) = 27.22 Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.07 (5 / 72), avg. gap size = 1.00 (5 / 5) 300 22.03 1.69 0.00 chr3ptel1M 180923 180981 (819019) MIR#SINE/MIR 118 177 (85) m_b113s601i12 4127 chr3ptel1M 180923 CTTCAGTTTCCTCATCTGTAAAGTGGGGGTAACAGTGGCTCC-ACCCCGT 180971 i i i i i i iv - i i MIR#SINE/MIR 118 CCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTCAT 167 chr3ptel1M 180972 AGGACTGGTG 180981 ii v MIR#SINE/MIR 168 AGGGTTGTTG 177 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.86 CpG sites = 11, Kimura (unadjusted) = 27.86 Transitions / transversions = 5.50 (11/2) Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1) 21 3.71 3.57 0.00 chr3ptel1M 181240 181267 (818733) (CT)n#Simple_repeat 1 29 (0) m_b113s252i11 4128 chr3ptel1M 181240 CTCTCTCTCTCTCTCTCTCTCTTTC-CTC 181267 i - (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTC 29 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 228 31.07 6.61 1.57 chr3ptel1M 182191 182311 (817689) L1HS_3end#LINE/L1 53 179 (723) m_b113s551i3 4129 chr3ptel1M 182191 ACAGTCCCTAATTGATAAGTGGTCAAAGGAGAGGAACAAGCTGTTCTTGA 182240 ii -- ii v v i v v ii vv ii L1HS_3end#LIN 53 ACAACCCC--ATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAA 100 chr3ptel1M 182241 GAGAAGCAATCCACACTTCGAGCAGCCACGTGAAGAAATGCCC------- 182283 i vv ii ii vv v iv iv i i ------- L1HS_3end#LIN 101 AAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATCATCA 150 chr3ptel1M 182284 CCGCTCA-CAGAGAGATGTAAATGAAAAC 182311 i vi - i i v L1HS_3end#LIN 151 CTGGCCATCAGAGAAATGCAAATCAAAAC 179 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 40.02 CpG sites = 22, Kimura (unadjusted) = 41.50 Transitions / transversions = 1.47 (22/15) Gap_init rate = 0.03 (4 / 120), avg. gap size = 2.50 (10 / 4) 18 21.98 0.00 0.00 chr3ptel1M 182377 182413 (817587) (AC)n#Simple_repeat 1 37 (0) m_b113s252i12 4130 chr3ptel1M 182377 ACACACTCACACACACAGACACACTCTCAAAGATACA 182413 v v v v v v i (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACA 37 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 224 33.80 10.36 4.53 chr3ptel1M 190019 190269 (809731) C L2a_3end#LINE/L2 (252) 265 1 m_b114s601i0 4131 chr3ptel1M 190019 TTTGAACAAGATTAAGGACTAAAAAAGGCTCCCTGTAAAAATAAAAAGCG 190068 i i i i --- v viii i v ? vi ii i v ---- C L2a_3end#LINE 265 TTTAAATAGGGT---GGTCAGGGAAGGCCTCNCTGAGAAGGTGACA---- 223 chr3ptel1M 190069 GTTCTAGCTGGGACTTGAAGGCAGGAGACAGAGCA--------------- 190103 - iv vii i - v vi i--------------- C L2a_3end#LINE 222 -TTTGAGCAAAGACCTGAAGG-AGGTGAGGGAGCGAGCCATGCGGATATC 175 chr3ptel1M 190104 --GAGGAAGAGCTTTCCAGGCAG-GGAAGCAGCCAGAGAAAATGCCCAGG 190150 -- i v - i i v v v v v i C L2a_3end#LINE 174 TGGGGGAAGAGCGTTCCAGGCAGAGGGAACAGCAAGTGCAAAGGCCCTGA 125 chr3ptel1M 190151 GCTGAGAG-ATGGAGGATCTTATTTGTGGGACAGCAAGGTGGCCGGACT- 190198 vi i -i vvv i- v i i v i v i vv - C L2a_3end#LINE 124 GGCGGGAGCGTGCCTGG-CGTGTTCGAGGAACAGCAAGGAGGCCAGTGTG 76 chr3ptel1M 190199 CCCGAATCCCAAAGTGCCCGTAGGTGAATGAGGT-----ATAAGACTGGA 190243 v i i --v ii vv vi v iv v ----- i iiii C L2a_3end#LINE 75 GCTGGA--GCGGAGTGAGCGAGGGGGAGAGTGGTAGGAGATGAGGTCAGA 28 chr3ptel1M 190244 AAGGTGG-GAGAGGGCAGGTGATGTAG 190269 i ii- i i v i v C L2a_3end#LINE 27 GAGGTAACGGGGGGCCAGATCATGTAG 1 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.07 CpG sites = 47, Kimura (unadjusted) = 47.00 Transitions / transversions = 1.38 (47/34) Gap_init rate = 0.07 (18 / 250), avg. gap size = 2.11 (38 / 18) 184 37.84 8.39 1.57 chr3ptel1M 190057 190354 (809646) C AmnL2-1#LINE/L2 (145) 2468 2151 m_b114s601i1 4131 chr3ptel1M 190057 AAATAAAAAGCGGTTCTAGCTGGGACTTGAAGGCAG-------------G 190093 i v i vii v ii ? i i i?v ------------- C AmnL2-1#LINE/ 2468 AGAAAAGATATGTTTTCAGNTGAGATTTGAAANGAGATGGAGAGTCGATG 2419 chr3ptel1M 190094 AGACAGAG---CAGAGGAAGAGCT-TTCCAGGCAG-GGAAGCAGCCAGAG 190138 i i ---i v - - iii -i i v viii C AmnL2-1#LINE/ 2418 AGGCGGAGAGATACAGGAAG-GCTGTTCCAGATGGCAGGAGCTGCAGAGG 2370 chr3ptel1M 190139 AAAATGCCCAGG-GCTGAGAGATGGAGGATCTTATTTGT-GGGACAGCAA 190186 i v i vv -i ii v - v - vv i v v- vi C AmnL2-1#LINE/ 2369 AGAAGGCTCTCGCACCAACAG-TGGCG-AGATTGTGTGAAGGGACAGAGA 2322 chr3ptel1M 190187 GGTGGCCGG-ACTCCCGAATCCCAAAGTGCCCGTAGGTGAAT---GAGGT 190232 v -i vvvvi v vv ii v vv v v i --- iv C AmnL2-1#LINE/ 2321 GGAGGCCGGTGCTAGACGAGCGGAGGGAGCGGGGAGGGGAGTAGAGAGAG 2272 chr3ptel1M 190233 ATAAGACTGGAAAGGTGGGAGAGGGCAGGTG-ATGTAGGGCTTTGAGCCC 190281 i iiiv vi i vvi i i v- v i i ivv C AmnL2-1#LINE/ 2271 ACAAGGTCCGTGAGGTAGGCTGGAGCAAGTCCATGGAGGGTTTTAAAAAC 2222 chr3ptel1M 190282 CAAATGGAGGATTTTGTGTTGAATCCTGGAAGTGCTAGGAAGCCCCTGGA 190331 v iivi ivi vii i i vviv i i vv C AmnL2-1#LINE/ 2221 AAGGAAGGCAATTTTGAACTGGATCCTGAAATGAATGGGGAGCCAGTGGA 2172 chr3ptel1M 190332 CTCTTGCATGGGGAGGGGGGAGA 190354 --v iv i v v C AmnL2-1#LINE/ 2171 --GTTGTTTGAGGATGGGGGTGA 2151 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 53.47 CpG sites = 59, Kimura (unadjusted) = 54.93 Transitions / transversions = 1.13 (59/52) Gap_init rate = 0.05 (14 / 297), avg. gap size = 2.14 (30 / 14) 269 34.52 3.55 1.49 chr3ptel1M 190073 190269 (809731) C L2d_3end#LINE/L2 (315) 201 1 m_b114s601i2 4131 chr3ptel1M 190073 TAGCTGGGACTTGAAGGCAGGAGACAGAGCAGAGGAAGAGCTTTCCAGGC 190122 i v i i i viv - v - v i i v C L2d_3end#LINE 201 TGGGTAGGATTTGGATAGAG-AGAGAG-GAAGGGGAAGGGCATTCCAGGC 154 chr3ptel1M 190123 AGGGA-AGCAGCCAGAGAAAATGCCCAG-GGCTGAGAGATGGAGGATCTT 190170 i i- i i vv v v v - v ii vii v i i- v C L2d_3end#LINE 153 GGGGGGAACGGCGTGAGCAAAGGCGCAGAGGCGGGAATGCGCAAGG-CGT 105 chr3ptel1M 190171 ATTTGTGGGACAGCAAGGTGGCCGGACT-CCCGAATCCCAAAGTGCCCGT 190219 i i v ii i v i v -v i i v vv ii v vi i C L2d_3end#LINE 104 GTTCGGGGGACAGTGAAGAGACCGGCCTGACTGGAGCGGAGGGTTCGTGC 55 chr3ptel1M 190220 AGGTG---AATGAGGTATAAGACTGGAAAGGT-GGGAGAGGGCAGGTGAT 190265 v v --- i i iv i ? - v i v i vi C L2d_3end#LINE 54 TGGGGAGTAGTGGGAGATAAGGCTGGANAGGTAGGGTGGGGCCAGATCGT 5 chr3ptel1M 190266 GTAG 190269 v C L2d_3end#LINE 4 GGAG 1 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.07 CpG sites = 36, Kimura (unadjusted) = 47.83 Transitions / transversions = 1.16 (36/31) Gap_init rate = 0.04 (8 / 196), avg. gap size = 1.25 (10 / 8) 354 34.94 3.94 3.57 chr3ptel1M 190104 190382 (809618) C L2#LINE/L2 (1) 3081 2802 m_b114s601i3 4131 chr3ptel1M 190104 GAGGAAGAGCTTTCCAGGCAG-GGAAGCAGCCAGAGAAAATGCCCAGGGC 190152 i v - i i v v v v v i v C L2#LINE/L2 3081 GGGGAAGAGCGTTCCAGGCAGAGGGAACAGCAAGTGCAAAGGCCCTGAGG 3032 chr3ptel1M 190153 TGAGAG-ATGGAGGATCTTATTTGTGGGACAGCAAGGTGGCCGGACTC-C 190200 i i -i vvv i- v i i v i v i vv v- C L2#LINE/L2 3031 CGGGAGCGTGCCTGG-CGTGTTCGAGGAACAGCAAGGAGGCCAGTGTGGC 2983 chr3ptel1M 190201 CGAATCCCAAAGTGCCCGTAGGTGAATGAGGTA-----TAAGACTGGAAA 190245 i i v --ii vv vi v iv v ----- i iiii i C L2#LINE/L2 2982 TGGAGC--GGAGTGAGCGAGGGGGAGAGTGGTAGGAGATGAGGTCAGAGA 2935 chr3ptel1M 190246 GGTGGGAGAGGGC-AGGTGATGTAGGGCTTTG-AGCCCCAAATG-GAGGA 190292 iivi i i - i v i - v -- v -i C L2#LINE/L2 2934 GGTAACGGGGGACCAGATCATGTAGGGCCTTGTAGGCC--ATTGTAAGGA 2887 chr3ptel1M 190293 TTTTGTGTTGAATCCTGGAAGTGCTAGGAAGCCCCTGGACTCTTGCATGG 190342 i vv vv ii iiv v v i vi vvv viiv v C L2#LINE/L2 2886 CTTTGGCTTTTACTCTGAGTGAGATGGGAAGCCATTGGAGGGTTTTGAGC 2837 chr3ptel1M 190343 GGAGGGGGGAGACAGTCAAACCTGCTGAGCTTTAGGAAAG 190382 i i v v iii vi i i --- i -- C L2#LINE/L2 2836 AGAGGAGTGACATGATCTGACTTAC---GTTTTA--AAAG 2802 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.75 CpG sites = 50, Kimura (unadjusted) = 48.23 Transitions / transversions = 1.14 (50/44) Gap_init rate = 0.06 (17 / 278), avg. gap size = 1.24 (21 / 17) 313 23.37 13.16 2.38 chr3ptel1M 192569 192682 (807318) MIRb#SINE/MIR 5 130 (138) m_b114s601i4 4132 chr3ptel1M 192569 GGGGCAGCTAGGGGGGGCAGTGGAGAGAGCCCCAGCCCGCAAGTCAGGAG 192618 --- v v i v vi iivvi ivi MIRb#SINE/MIR 5 GGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACA 51 chr3ptel1M 192619 GACCTGAGTGCAAATC-------------TTCCCAGCCGTGTGACCCTGG 192655 i v i ------------- v i i i MIRb#SINE/MIR 52 GACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 101 chr3ptel1M 192656 GC-AGTCACTTAACCCCAAT-TGCCTCAG 192682 - i i vv -v MIRb#SINE/MIR 102 GCAAGTTACTTAACCTCTCTGAGCCTCAG 130 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.18 CpG sites = 14, Kimura (unadjusted) = 28.43 Transitions / transversions = 1.17 (14/12) Gap_init rate = 0.05 (6 / 113), avg. gap size = 3.00 (18 / 6) 337 22.77 14.85 0.00 chr3ptel1M 192582 192682 (807318) MIRc#SINE/MIR 12 127 (141) m_b114s601i5 4132 chr3ptel1M 192582 GGGGCAGTGGAGAGAGCCCCAGCCCGCAAGTCAGGAGGACCTGAGTGCAA 192631 v i v ii v ivvi i i v i MIRc#SINE/MIR 12 GGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGA 61 chr3ptel1M 192632 ATC-------------TTCCCAGCCGTGTGACCCTGGGC-AGTCACTTAA 192667 i ------------- v i i i - MIRc#SINE/MIR 62 GTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAA 111 chr3ptel1M 192668 CCCCAAT-TGCCTCAG 192682 i vv -v MIRc#SINE/MIR 112 CCTCTCTGAGCCTCAG 127 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.19 CpG sites = 13, Kimura (unadjusted) = 27.55 Transitions / transversions = 1.30 (13/10) Gap_init rate = 0.03 (3 / 100), avg. gap size = 5.00 (15 / 3) 181 27.93 21.71 1.09 chr3ptel1M 192981 193132 (806868) MIRc#SINE/MIR 24 206 (62) m_b114s601i6 4133 chr3ptel1M 192981 AGAGTGCCGGACCGTGAGCCAGGAAGGC----------GACC----TTTG 193016 ii i ivv i i ---------- v ---- i MIRc#SINE/MIR 24 AGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTG 73 chr3ptel1M 193017 CTACCTGC---CTCTG-GGCC--GGGAAAATC--TCAGCCGCTCTGCCAG 193058 i i i --- v - i -- v i -- i i v -- MIRc#SINE/MIR 74 CCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTG--AG 121 chr3ptel1M 193059 CCTCAGTTCCCACAGCACAGAAATGGGCACGACA------GCCCT---TA 193099 i v v vvvi v ii i ------ --- MIRc#SINE/MIR 122 CCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTA 171 chr3ptel1M 193100 GCC--CAGGGATGCCAGAAGGAGCAAAGGAGATGA 193132 v i-- v iiivi v v i MIRc#SINE/MIR 172 CCTCACAGGGTTGTTGTGAGGATCAAATGAGATAA 206 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.02 CpG sites = 25, Kimura (unadjusted) = 36.02 Transitions / transversions = 1.47 (25/17) Gap_init rate = 0.07 (11 / 151), avg. gap size = 3.18 (35 / 11) 228 31.89 8.26 1.55 chr3ptel1M 193012 193132 (806868) MIRb#SINE/MIR 72 200 (68) m_b114s601i7 4133 chr3ptel1M 193012 CTTTGCTACCTGC---CTCTG-GGCC--GGGAAAAT--CTCAGCCGCTCT 193053 i i i i --- v - i -- v i -- i i v MIRb#SINE/MIR 72 CTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCT 121 chr3ptel1M 193054 GCCAGCCTCAGTTCCCACAGCACAGAAATGGGCACGACAGCCCTTAGCC- 193102 -- i v v vvvi v ii i iiv i v i- MIRb#SINE/MIR 122 G--AGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTACCTC 169 chr3ptel1M 193103 -CAGGGATGCCAGAAGGAGCAAAGGAGATGA 193132 - v iiivi vi v i MIRb#SINE/MIR 170 GCAGGGTTGTTGTGAGGATTAAATGAGATAA 200 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.20 CpG sites = 23, Kimura (unadjusted) = 43.20 Transitions / transversions = 1.53 (23/15) Gap_init rate = 0.07 (8 / 120), avg. gap size = 1.50 (12 / 8) 411 24.64 1.69 7.14 chr3ptel1M 198893 199010 (800990) MIRc#SINE/MIR 37 148 (120) m_b114s601i8 4134 chr3ptel1M 198893 TGGAGTCAGGGAGACTAATCTCCCCGAGTTCAAATCTGGCCTCAGACACT 198942 i -------- i i i i iv v v v MIRc#SINE/MIR 37 TGGAGTCAGGAAGAC--------CTGGGTTCGAGTCCCGGCTCTGCCACT 78 chr3ptel1M 198943 TCCTAGCAAGGTGATCCTGCGCAAGTCACATAACTACTCC--GCCACAAT 198990 v viv i i v v iv i-- v i MIRc#SINE/MIR 79 TACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGT 128 chr3ptel1M 198991 TTCTTCATCAGTCAAATGAG 199010 i v v i MIRc#SINE/MIR 129 TTCCTCATCTGTAAAATGGG 148 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.77 CpG sites = 14, Kimura (unadjusted) = 30.06 Transitions / transversions = 1.08 (14/13) Gap_init rate = 0.08 (9 / 117), avg. gap size = 1.11 (10 / 9) 343 24.34 6.37 8.44 chr3ptel1M 198894 199050 (800950) MIR3#SINE/MIR 36 189 (19) m_b114s601i9 4134 chr3ptel1M 198894 GGAGTCAGGGAGACTAATCTCCCCGAGTTCAAATCTGGCCTCAGACACTT 198943 - -------- i i v i iv v v v v MIR3#SINE/MIR 36 GGAGTCAGG-AGAC--------CTGGGTTCTAGTCCCGGCTCTGCCACTA 76 chr3ptel1M 198944 CCTAGCAAGGTGATCCTGCGCAAGTCACATAACTACTCC--GCCACAATT 198991 v ? viv i i v v v iv i-- v i MIR3#SINE/MIR 77 ACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTT 126 chr3ptel1M 198992 TCTTCATCAGTCAAATGA----GCTGGAGAAGGAGA----TAAGGAACCC 199033 i v v ---- i vv iv ---- -v MIR3#SINE/MIR 127 TCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGG-TCCC 175 chr3ptel1M 199034 CTCCAATATCTCTGACA 199050 i i--- MIR3#SINE/MIR 176 TTCCAG---CTCTGACA 189 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.72 CpG sites = 15, Kimura (unadjusted) = 29.72 Transitions / transversions = 0.75 (15/20) Gap_init rate = 0.10 (16 / 156), avg. gap size = 1.44 (23 / 16) 191 18.18 0.00 0.00 chr3ptel1M 200664 200696 (799304) C L2d_3end#LINE/L2 (27) 489 457 m_b114s601i10 4135 chr3ptel1M 200664 TAAGCGCCCACTGTGTGCTCGGCACTTTGCCAG 200696 i i i i v i C L2d_3end#LINE 489 TGAGCGCCTACTATGTGCTCAGCACTGTGCTAG 457 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 21.84 CpG sites = 5, Kimura (unadjusted) = 21.84 Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 180 29.91 2.73 2.73 chr3ptel1M 203225 203334 (796666) L2b_3end#LINE/L2 260 369 (97) m_b114s601i11 4136 chr3ptel1M 203225 GGCCATCTGCCCTGCCAGGAGCCCCAGCCAAAACCCCACTTCCTCTTT-- 203272 i vvi v ivv i v- ivv iv v v v i -- L2b_3end#LINE 260 GGTCAGGCGCCCTCCTCTGGGCCCCC-CCAGTCCTACCCTGCCACTCTGG 308 chr3ptel1M 203273 -TCATTACTTCCTGCTTATCCTGTAGGTTCTCCCCCCTTGGCCTGTGAGC 203321 - i ? i vi ? - v vv - vi i v L2b_3end#LINE 309 GTTATNATTGTCTGNTTA-CATGTCTGT-CTCCCCCACTAGACTGTGAGC 356 chr3ptel1M 203322 TCCTGGAGGGCAG 203334 vv L2b_3end#LINE 357 TCCGTGAGGGCAG 369 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.69 CpG sites = 12, Kimura (unadjusted) = 39.14 Transitions / transversions = 0.60 (12/20) Gap_init rate = 0.05 (5 / 109), avg. gap size = 1.20 (6 / 5) 190 18.03 0.00 4.00 chr3ptel1M 203283 203334 (796666) L2c_3end#LINE/L2 348 397 (81) m_b114s601i12 4136 chr3ptel1M 203283 CTGCTTATCCTGTAGGTTCTCCCCCCTTGGCCTGTGAGCTCCTGGAGGGC 203332 i - ? vv - i vi i v v L2c_3end#LINE 348 CTGTTTA-CNTGTCTGT-CTCCTCCACTAGACTGTGAGCTCCTTGAGGGC 395 chr3ptel1M 203333 AG 203334 L2c_3end#LINE 396 AG 397 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 21.12 CpG sites = 4, Kimura (unadjusted) = 21.12 Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.00 (2 / 2) 331 25.51 2.00 2.00 chr3ptel1M 206285 206384 (793616) C Charlie4a#DNA/hAT-Charlie (13) 495 396 m_b114s502i0 4137 chr3ptel1M 206285 CCTTTTTGGCTTCATGGAGCTGACTCAGGCAGGTAGGGGACATCTTGGGG 206334 v ivi v i-- iv viv v vii vv i C Charlie4a#DNA 495 CCTTTTTTGTGCCATGGACCC--CTTTGGCAGTCTGGTGAAGCCTATGGA 448 chr3ptel1M 206335 CCTCTTCCCAGAATAAT--TTTTAAATGCATGAAATAAAATATGAAGGGT 206382 i i -- i iiv i C Charlie4a#DNA 447 CCCCTTCTCAGAATAATGTTTTTAAATGCATAAAATAAAATACATAGGAT 398 chr3ptel1M 206383 TA 206384 C Charlie4a#DNA 397 TA 396 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 31.73 CpG sites = 14, Kimura (unadjusted) = 31.73 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.03 (3 / 99), avg. gap size = 1.33 (4 / 3) 25 36.14 2.11 2.84 chr3ptel1M 207751 207892 (792108) (TCCC)n#Simple_repeat 1 141 (0) m_b114s252i0 4138 chr3ptel1M 207751 TCCTTCCATCCTTCTCTCCCT-CCTTTTTCTCCTTCTTCCCTCCTTTCTT 207799 i v i i - iii - i i -i ii (TCCC)n#Simpl 1 TCCCTCCCTCCCTCCCTCCCTCCCTCCCTC-CCTCCCTCCCTCC-CTCCC 48 chr3ptel1M 207800 TCCCTTCATCTCTTCTTACTTTCTGTCCTTCCAT-CCTTCCTTCTTCCTC 207848 i v i i i - ii iv i v - i i i - (TCCC)n#Simpl 49 TCCCTCCCTCCCTCCCT-CCCTCCCTCCCTCCCTCCCTCCCTCCCTCC-C 96 chr3ptel1M 207849 TCCCTTTCT-CCTTCCTCCCTTCCTCCATTCTTTCCTTCCTTCCT 207892 ii - i i v i i i i i (TCCC)n#Simpl 97 TCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCT 141 Matrix = Unknown Transitions / transversions = 6.20 (31/5) Gap_init rate = 0.05 (7 / 141), avg. gap size = 1.00 (7 / 7) 13 16.04 0.00 12.77 chr3ptel1M 210319 210371 (789629) (GGA)n#Simple_repeat 1 47 (0) m_b114s252i1 4139 chr3ptel1M 210319 GGAGGAGCGAAGACAGAGGAGGAGTAGTCAGGCAGGACCAGGGAGGAGAG 210368 - i -i v -v - vv - - (GGA)n#Simple 1 GGAGGAG-GAGGA-GGAGGAGGAGGAG-GAGG-AGGAGGA-GGAGGAG-G 44 chr3ptel1M 210369 AGG 210371 (GGA)n#Simple 45 AGG 47 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.12 (6 / 52), avg. gap size = 1.00 (6 / 6) 259 34.98 9.09 0.76 chr3ptel1M 214230 214350 (785650) L2c_3end#LINE/L2 342 472 (6) m_b114s601i13 4140 chr3ptel1M 214230 AATCATTCATCGGCAGGTCGCGTCCCCCCCACGAAGCTG----CTC---- 214271 ii iii ivi ?v -i i i v ii ---- ---- L2c_3end#LINE 342 AATTGTCTGTTTACNTGTC-TGTCTCCTCCACTAGACTGTGAGCTCCTTG 390 chr3ptel1M 214272 --GGCAGCAATGGC-TTTTGTCCCGTTTTTTACCCCCAATGCCCAGCATA 214318 -- vi iv i- i i i vvi v i ii ii i L2c_3end#LINE 391 AGGGCAGGGACCGTGTCTTATTCATCTTTGTATCCCCAGCGCCTGGCACA 440 chr3ptel1M 214319 CAGTAGGCGCTTAATCAGTGCTCCATGACTGA 214350 i i v i i ivv v L2c_3end#LINE 441 TAGTAGGCGCTCAATAAATGTTTGTTGAATGA 472 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 50.20 CpG sites = 30, Kimura (unadjusted) = 52.08 Transitions / transversions = 2.50 (30/12) Gap_init rate = 0.04 (5 / 120), avg. gap size = 2.40 (12 / 5) 28 20.20 2.13 5.49 chr3ptel1M 214904 214997 (785003) (CGGCC)n#Simple_repeat 1 91 (0) m_b114s252i2 4141 chr3ptel1M 214904 CGGCCCGGCCTCCGCCGCCTTCGGAGCCCGGCTCAGCCCGGCCCGGCCCG 214953 - v - vvi v - i i (CGGCC)n#Simp 1 CGGCCCGGCC-CGGCC-CGGCCCG-GCCCGGCCCGGCCCGGCCCGGCCCG 47 chr3ptel1M 214954 GCCCCCGCCCGGCTC--CCCTTCCAGGCCCCGACCCCGCCCCGCCC 214997 - v i -- vv v - i v v (CGGCC)n#Simp 48 G-CCCGGCCCGGCCCGGCCCGGCCCGG-CCCGGCCCGGCCCGGCCC 91 Matrix = Unknown Transitions / transversions = 0.50 (5/10) Gap_init rate = 0.06 (6 / 93), avg. gap size = 1.17 (7 / 6) 41 1.66 6.15 2.99 chr3ptel1M 215121 215185 (784815) (CCG)n#Simple_repeat 1 67 (0) c_b114s251i0 4142 chr3ptel1M 215121 CCGCC-CCGCC-CCGCC-CCGCGCGCC-CGCGGCGCCGCCGCCGCCGCCG 215166 - - - - - - v (CCG)n#Simple 1 CCGCCGCCGCCGCCGCCGCCGC-CGCCGC-CGCCGCCGCCGCCGCCGCCG 48 chr3ptel1M 215167 CCGCCGCCGCCGCCGCCGC 215185 (CCG)n#Simple 49 CCGCCGCCGCCGCCGCCGC 67 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.09 (6 / 64), avg. gap size = 1.00 (6 / 6) 11 18.50 10.20 0.00 chr3ptel1M 216206 216254 (783746) (CCGCCTC)n#Simple_repeat 1 54 (0) m_b114s252i3 4143 chr3ptel1M 216206 CCGCCCCCCG-CT-CCG-CTCTC-CCTCTC-ACGCCCGCCTCCCGCTGCC 216250 i - - - i - i -v v iv (CCGCCTC)n#Si 1 CCGCCTCCCGCCTCCCGCCTCCCGCCTCCCGCCTCCCGCCTCCCGCCTCC 50 chr3ptel1M 216251 CCCC 216254 v (CCGCCTC)n#Si 51 CGCC 54 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.10 (5 / 48), avg. gap size = 1.00 (5 / 5) 335 28.41 11.28 2.07 chr3ptel1M 219577 219709 (780291) C MIRc#SINE/MIR (120) 148 4 m_b114s601i14 4144 chr3ptel1M 219577 CTCATTTTCCAGATGAGGAAACTGAGGCATGGAGGGG-GAAGGATCTTCC 219625 i v vii i -v viv v C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr3ptel1M 219626 CCAGCGTGGCAGAGCTAGTATTTTTCT-------GATTTTAACTCCAATC 219668 iv vi v vv vv v------- i iv i vii C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTC 49 chr3ptel1M 219669 TTCTTGACACTAG-------GCACTCTCCACTGTGCCACTTAACTGTC 219709 i v i i------- v i ii --- i C MIRc#SINE/MIR 48 TTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC---ACTGCC 4 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.08 CpG sites = 19, Kimura (unadjusted) = 36.28 Transitions / transversions = 1.06 (19/18) Gap_init rate = 0.05 (6 / 132), avg. gap size = 3.00 (18 / 6) 15 25.04 0.00 2.08 chr3ptel1M 220256 220304 (779696) (TGTTTTA)n#Simple_repeat 1 48 (0) m_b114s252i4 4145 chr3ptel1M 220256 TGCTTTCTGTTTTGTTATGTATGTTGTATTGTTTTATCTTTGATCTTTT 220304 i v i vv v v - v v v (TGTTTTA)n#Si 1 TGTTTTATGTTTTATGTTTTATGTTTTA-TGTTTTATGTTTTATGTTTT 48 Matrix = Unknown Transitions / transversions = 0.25 (2/8) Gap_init rate = 0.02 (1 / 48), avg. gap size = 1.00 (1 / 1) 12 26.35 5.56 0.00 chr3ptel1M 220260 220313 (779687) (TTATG)n#Simple_repeat 1 57 (0) m_b114s252i5 4145 chr3ptel1M 220260 TTCTGTTTTGTTATG-TATGTTGTATTGTTTTATCTT-TGATCT-TTTTA 220306 v v - i i i v v - v v - v i (TTATG)n#Simp 1 TTATGTTATGTTATGTTATGTTATGTTATGTTATGTTATGTTATGTTATG 50 chr3ptel1M 220307 TTATCTT 220313 v (TTATG)n#Simp 51 TTATGTT 57 Matrix = Unknown Transitions / transversions = 0.50 (4/8) Gap_init rate = 0.06 (3 / 53), avg. gap size = 1.00 (3 / 3) 259 20.35 0.00 4.69 chr3ptel1M 221020 221086 (778914) C tRNA-Lys-AAA#tRNA (0) 76 13 m_b114s502i1 4146 chr3ptel1M 221020 TGGCGCCCAACGTGGGGCTTGAACCCTGGACCCTCAGATCTGAAAAGATC 221069 i vvv i i-- - C tRNA-Lys-AAA# 76 TGGCGCCCGAACAGGGACTTGAACCCTGGACCCTCAGATT--AAAAG-TC 30 chr3ptel1M 221070 TGAACTTTTATCACCTG 221086 vvi i i iv C tRNA-Lys-AAA# 29 TGATGCTCTACCGACTG 13 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 19.99 CpG sites = 7, Kimura (unadjusted) = 23.93 Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.05 (3 / 66), avg. gap size = 1.00 (3 / 3) 13 26.92 0.00 3.92 chr3ptel1M 222037 222089 (777911) (GGCCCT)n#Simple_repeat 1 51 (0) m_b114s252i6 4147 chr3ptel1M 222037 GGCTCCAGGTCCAGCCCCTGTGCCCGCCCCCTGGGCCTGCCGCTTGCCCT 222086 - v i v v - vvv v v v v (GGCCCT)n#Sim 1 GGC-CCTGGCCCTGGCCCTG-GCCCTGGCCCTGGCCCTGGCCCTGGCCCT 48 chr3ptel1M 222087 GGC 222089 (GGCCCT)n#Sim 49 GGC 51 Matrix = Unknown Transitions / transversions = 0.10 (1/10) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.00 (2 / 2) 22 3.96 0.00 0.00 chr3ptel1M 222334 222359 (777641) (C)n#Simple_repeat 1 26 (0) m_b114s252i7 4148 chr3ptel1M 222334 CCCCCCCCCCCCCCCCCCCCCGCCCC 222359 v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCC 26 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 290 28.46 5.80 5.80 chr3ptel1M 222730 222867 (777133) MIR#SINE/MIR 116 253 (9) m_b114s601i15 4149 chr3ptel1M 222730 TGCCT--GTTTCCTCAGCCACGAAATGG---TGATGACAGCACCTGCCTC 222774 -- v iiii --- i i i i i MIR#SINE/MIR 116 TGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTC 165 chr3ptel1M 222775 A-AGGGTTACTGGGGGAATCAAGTGAGAGAAATATTTGGATAAATGGGAT 222823 - ii v i i i i -vv iv -- ----ii MIR#SINE/MIR 166 ATAGGGTTGTTGTGAGGATTAAATGAG-TTAATACATG--TAAA----GC 208 chr3ptel1M 222824 ATTTGCAA-AGCACTTGGTCAAGTA-TAAACACTATCTAAATGTTA 222867 ii iv - ii i - vi - i i vvv MIR#SINE/MIR 209 GCTTAGAACAGTGCCTGG-CACATAGTAAGCGCTCAATAAATGTTA 253 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.27 CpG sites = 27, Kimura (unadjusted) = 38.07 Transitions / transversions = 2.70 (27/10) Gap_init rate = 0.09 (13 / 137), avg. gap size = 1.23 (16 / 13) 194 21.22 0.00 11.63 chr3ptel1M 225483 225530 (774470) C L2a_3end#LINE/L2 (10) 507 465 m_b115s601i1 4150 chr3ptel1M 225483 TCAGCAAGTGTTTGTTTGGTTAAACACCTACTATGTGTCACGCACTGT 225530 i i i i -----i i i i v C L2a_3end#LINE 507 TCAACAAATATTTATT-----GAGCGCCTACTATGTGCCAGGCACTGT 465 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 23.00 CpG sites = 8, Kimura (unadjusted) = 26.35 Transitions / transversions = 8.00 (8/1) Gap_init rate = 0.11 (5 / 47), avg. gap size = 1.00 (5 / 5) 30 9.62 1.69 1.69 chr3ptel1M 225671 225729 (774271) (GGCCATGGA)n#Simple_repeat 1 59 (0) c_b115s251i0 4151 chr3ptel1M 225671 GGCCATGGAGGCTGTGGAGGCCATGGAGGCCATTGG-GGTTGTGGAGGCC 225719 ii - - iii (GGCCATGGA)n# 1 GGCCATGGAGGCCATGGAGGCCATGGAGGCCA-TGGAGGCCATGGAGGCC 49 chr3ptel1M 225720 ATGGAGGCCA 225729 (GGCCATGGA)n# 50 ATGGAGGCCA 59 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.03 (2 / 58), avg. gap size = 1.00 (2 / 2) 12 10.99 9.76 2.27 chr3ptel1M 227415 227455 (772545) (CAGGTGG)n#Simple_repeat 1 44 (0) m_b115s252i2 4152 chr3ptel1M 227415 CAGGTGGCA-GTGCCAGGT-G--TTTGGCATGGTGACAGGTGGCA 227455 - v - --vv - i (CAGGTGG)n#Si 1 CAGGTGGCAGGTGGCAGGTGGCAGGTGGCA-GGTGGCAGGTGGCA 44 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.10 (4 / 40), avg. gap size = 1.25 (5 / 4) 592 26.04 0.00 4.00 chr3ptel1M 227903 228058 (771942) C MIR#SINE/MIR (64) 198 49 m_b115s601i2 4153 chr3ptel1M 227903 TATTAGCACAACTCTGCTCTTTAAAACCACCTCATGAGTTAGATGCAATT 227952 i v -- i iv i i v v ii v i i v C MIR#SINE/MIR 198 TATTAACTCA--TTTAATCCTCACAACAACCCTATGAGGTAGGTACTATT 151 chr3ptel1M 227953 ACTATCCCCATTCTACATGTGAAGAAACTGAGGCAGACCGAGGGGAAGTG 228002 i i vi i v vv vv i C MIR#SINE/MIR 150 ATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTA 101 chr3ptel1M 228003 ACTCGCCTGGGATCACACAGCTAGTTAGTGAGTGTCTGAGGCAGGATTTG 228052 i iii i v i---- v v i i C MIR#SINE/MIR 100 ACTTGCCCAAGGTCACACAGCTAGTAAGTGG----CAGAGCCGGGATTCG 55 chr3ptel1M 228053 AATACA 228058 iv C MIR#SINE/MIR 54 AACCCA 49 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 30.66 CpG sites = 23, Kimura (unadjusted) = 32.66 Transitions / transversions = 1.44 (23/16) Gap_init rate = 0.04 (6 / 155), avg. gap size = 1.00 (6 / 6) 543 25.23 9.78 3.06 chr3ptel1M 227904 228087 (771913) C MIRc#SINE/MIR (61) 207 12 m_b115s601i3 4153 chr3ptel1M 227904 ATTAGCACAACTCTGCTCTTTAAAACCACCTCATGAGTTAGAT---GCA- 227949 v v -- i v i i v v iii v ii--- - C MIRc#SINE/MIR 207 ATTATCTCA--TTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAG 160 chr3ptel1M 227950 --ATTACTATCCCCATTCTACATGTGAAGAAACTGAGGCAGACCGAGGGG 227997 -- i i vi i vv vv vv C MIRc#SINE/MIR 159 GTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTT 110 chr3ptel1M 227998 AAGTGACTCGCCTGGGATCACACAGCTAGTTAGTGAGTGTCTGAGGCAGG 228047 i iii i v i---- v v i C MIRc#SINE/MIR 109 AAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGG----CAGAGCCGGG 64 chr3ptel1M 228048 ATTTGAATACATGGCTTCC--AT----------GTGCTCTGTCCACTGTC 228085 i i iv v v -- i---------- v iv C MIRc#SINE/MIR 63 ACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCA 14 chr3ptel1M 228086 CC 228087 C MIRc#SINE/MIR 13 CC 12 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 29.63 CpG sites = 24, Kimura (unadjusted) = 31.25 Transitions / transversions = 1.14 (24/21) Gap_init rate = 0.06 (11 / 183), avg. gap size = 2.18 (24 / 11) 240 29.16 4.12 1.00 chr3ptel1M 228539 228635 (771365) C L3#LINE/CR1 (289) 3810 3711 m_b115s601i4 4154 chr3ptel1M 228539 AATCCCCCCTCTGGGAAACGGTCCCTCAGAAACTCTGGCTCAGCAGTCAT 228588 i i iivivi i i i i v i iviivv vi C L3#LINE/CR1 3810 AATCCCTCTTCCACATGACAGCCCTTCAAATATTTGAAGACAGCTATCAT 3761 chr3ptel1M 228589 GTCTC--TGGAGTCTTGTCTTCTAACAGGCTAAACA-CCCCACTT-CTTC 228634 --ivi v -v - v - C L3#LINE/CR1 3760 GTCTCCTCTAAGTCTTCTCTTCT-CCAGGCTAAACATCCCCAGTTCCTTC 3712 chr3ptel1M 228635 A 228635 C L3#LINE/CR1 3711 A 3711 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 38.13 CpG sites = 17, Kimura (unadjusted) = 38.13 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.04 (4 / 96), avg. gap size = 1.25 (5 / 4) 222 15.38 0.00 0.00 chr3ptel1M 229312 229350 (770650) C L2b_3end#LINE/L2 (12) 454 416 m_b115s601i5 4155 chr3ptel1M 229312 AACAAGCATGTACATAGCACCTACTGTGTGCCAGGCGCT 229350 ii v vv i ? C L2b_3end#LINE 454 AACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCT 416 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 14.80 CpG sites = 3, Kimura (unadjusted) = 17.81 Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 211 19.61 3.77 3.77 chr3ptel1M 230353 230405 (769595) C L2c_3end#LINE/L2 (1) 477 425 m_b115s601i6 4156 chr3ptel1M 230353 TTCAGTTCACTTCAATAGACAT--GGTAAGTGCCTACTGTGTGCCCGGTG 230400 - - i i --iv i i i v i C L2c_3end#LINE 477 TTCA-TTCA-TTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCG 430 chr3ptel1M 230401 CTGAG 230405 i C L2c_3end#LINE 429 CTGGG 425 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 18.63 CpG sites = 8, Kimura (unadjusted) = 23.81 Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.06 (3 / 52), avg. gap size = 1.33 (4 / 3) 247 29.51 15.57 0.00 chr3ptel1M 230688 230809 (769191) C MIRc#SINE/MIR (98) 170 30 m_b115s601i7 4157 chr3ptel1M 230688 AGGGGGGGC--GCGTCATTCTCCCCTTGTTGCAGAGGAGAAGACTGAGTC 230735 vi -- ii i v v v i v i i v C MIRc#SINE/MIR 170 AGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGC 121 chr3ptel1M 230736 TCAGAGAGA--------------CAA--TCACACAGCTAGGAAGCATCCC 230769 i-------------- -- v iiv vv C MIRc#SINE/MIR 120 TCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAG 71 chr3ptel1M 230770 TGACAGCGTTTGGACCCAGAGC-TCACAACCCAGAGTCCAG 230809 v v i vii i i iv - vii i vi C MIRc#SINE/MIR 70 AGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAG 30 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 35.67 CpG sites = 20, Kimura (unadjusted) = 38.32 Transitions / transversions = 1.25 (20/16) Gap_init rate = 0.03 (4 / 121), avg. gap size = 4.75 (19 / 4) 268 33.33 2.02 0.00 chr3ptel1M 231313 231411 (768589) C L3#LINE/CR1 (1308) 2791 2691 m_b115s601i8 4154 chr3ptel1M 231313 CCCTTCCAGAATGGTCCTGACAGTTAAGGTCAAGCTCATTGGCCTGTGGG 231362 v i vv v i ivii ii v i ii i i v C L3#LINE/CR1 2791 CCGTTCTAGAATTTTGCCGGGGATCGACGTCAAGCTTACCGGTCTGTAGT 2742 chr3ptel1M 231363 TTTCTGACTCTTGCTCTCT--CCTTTTTGAAAATCAGAATGACATCCGTC 231410 ? v v ivv i i -- i ? vi ? i? ii i C L3#LINE/CR1 2741 TTNCAGAATCCATCTTTTTTCCCTTTTTAAAANTAGGNACNACATTTGCC 2692 chr3ptel1M 231411 C 231411 C L3#LINE/CR1 2691 C 2691 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 42.89 CpG sites = 21, Kimura (unadjusted) = 49.30 Transitions / transversions = 1.75 (21/12) Gap_init rate = 0.01 (1 / 98), avg. gap size = 2.00 (2 / 1) 302 28.05 0.00 1.22 chr3ptel1M 231458 231540 (768460) C L2b_3end#LINE/L2 (1) 465 384 m_b115s601i9 4158 chr3ptel1M 231458 TTCAGTCAGTCAACAAGCATTTATTAAGTATCCAATGTGTACCAGGCACT 231507 v v ii i i iii i v i ? C L2b_3end#LINE 465 TTCATTCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCT 416 chr3ptel1M 231508 CTACTAAGTTCTGGAGAACTCACAGGTGAAAAA 231540 v i i iv - i iv vv v C L2b_3end#LINE 415 GTGCTAGGCGCTGG-GGATACAGCGGTGAACAA 384 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 32.65 CpG sites = 14, Kimura (unadjusted) = 36.80 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.01 (1 / 82), avg. gap size = 1.00 (1 / 1) 282 26.47 15.69 0.00 chr3ptel1M 232167 232268 (767732) C MIR#SINE/MIR (80) 182 65 m_b115s601i10 4159 chr3ptel1M 232167 CTTCCCAATGGCCCCA-GAGGGAGGTGCTGCTATTATCCCCA-TTTATGG 232214 i v iii i - v i ii - ii C MIR#SINE/MIR 182 CCTCACAACAACCCTATGAGGTAGGTACTATTATTATCCCCATTTTACAG 133 chr3ptel1M 232215 CTGAGGAACCCCGGGCAGACAGAGG--------------CAAGGTGACGC 232250 v v ivi v v -------------- v i C MIR#SINE/MIR 132 ATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACAC 83 chr3ptel1M 232251 AGCTAATGAGCATCTGAG 232268 i i iiv v C MIR#SINE/MIR 82 AGCTAGTAAGTGGCAGAG 65 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 33.68 CpG sites = 17, Kimura (unadjusted) = 33.68 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.03 (3 / 101), avg. gap size = 5.33 (16 / 3) 23 35.33 4.09 3.49 chr3ptel1M 232471 232641 (767359) (TG)n#Simple_repeat 1 172 (0) m_b115s252i3 4160 chr3ptel1M 232471 TGTATGTG-GTATGTGATGTATGTGTACATGTGTGCATGTAGCAGGT-TG 232518 i - i - i iii ii - iiv - (TG)n#Simple_ 1 TGTGTGTGTGTGTGTG-TGTGTGTGTGTGTGTGTGTGTGT-GTGTGTGTG 48 chr3ptel1M 232519 TGACGTATGTACGTG-GTGACATGTGTATGTG-GTGTGTG-GCACACGTG 232565 -i i ii - -ii i - - iiiii (TG)n#Simple_ 49 TG-TGTGTGTGTGTGTGTG-TGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 96 chr3ptel1M 232566 TAGGATGTGTATATGTGTG-GTGTGTCACACATTGTG-GTGTGTGACACG 232613 - vi i i - vvvvvvv - -iii (TG)n#Simple_ 97 T-GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG-TGTG 144 chr3ptel1M 232614 TGTGTGTGCATGTGCATGCGTGTTTGTG 232641 ii ii i v (TG)n#Simple_ 145 TGTGTGTGTGTGTGTGTGTGTGTGTGTG 172 Matrix = Unknown Transitions / transversions = 3.30 (33/10) Gap_init rate = 0.08 (13 / 170), avg. gap size = 1.00 (13 / 13) 289 34.16 12.56 2.87 chr3ptel1M 234177 234399 (765601) C L3#LINE/CR1 (356) 3743 3500 m_b115s601i11 4161 chr3ptel1M 234177 TCTCCTCCAGACTGGACGTGCAGACTTC-TTCAGCTGAGTCTCATACAAT 234225 i i ii i v vv v - i i vvi ii i C L3#LINE/CR1 3743 TCTTCTCCAGGCTAAACATCCCCAGTTCCTTCAACCGTTCCTCATATGAC 3694 chr3ptel1M 234226 GTGGACTCAATTCAATGCTCTCCACCTCCTTGGCTGCCCTCCTCTGCATA 234275 i v----- v vi i i vi i ii i v ii C L3#LINE/CR1 3693 ATGGT-----TTCCAGACCCTTCACCATCCTGGTCGCTCTCCTCTGGACG 3649 chr3ptel1M 234276 CATGTTAGCATATCTA-GCCCTTCTTCTA--------CCC---------- 234306 iivii iv i v - i i vv -------- ---------- C L3#LINE/CR1 3648 CGCTCCAGTTTGTCAATGTCCCTCTTAAAATGTGGCGCCCAGAACTGAAC 3599 chr3ptel1M 234307 ------TTCCAAATGGGGCCCGACAAGGGCAGAGT--AGGGGGACCCTCT 234348 ------i i v i i v v -- v -- v C L3#LINE/CR1 3598 GCAATACTCCAGATGTGGTCTGACCAGCGCAGAGTACAGCGGGA--CTAT 3551 chr3ptel1M 234349 GATGTCCCTGTTCCTGGAAGTTCTGTGCCTCCTCATGCAGCCCCAGATTG 234398 v iv vv?i vii v iivi vi v iv C L3#LINE/CR1 3550 TACCTCCCTTGNTCTGGACACTATACTTCTATTAATGCAGCCTAAGATTG 3501 chr3ptel1M 234399 C 234399 C L3#LINE/CR1 3500 C 3500 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 44.15 CpG sites = 43, Kimura (unadjusted) = 47.79 Transitions / transversions = 1.39 (43/31) Gap_init rate = 0.06 (13 / 222), avg. gap size = 2.69 (35 / 13) 720 36.48 1.30 0.00 chr3ptel1M 237660 237966 (762034) C L3#LINE/CR1 (2931) 1168 858 m_b115s601i12 4161 chr3ptel1M 237660 CTTGGTACTCTTTGTGGCACTGGGCTGGGCAGATCAATAGCAGCCGCTCT 237709 i ? ii iii i i iiv i vvi v iv vvvi vvi i C L3#LINE/CR1 1168 CCTGNTATCCTCCATAGTATCCGGTTTTACAGTTTTATCTGGGCATTTTT 1119 chr3ptel1M 237710 CTCCATTCCCCTCC--TTTCCATTTAGAGTCCTCATCATCAGATTTACAA 237757 i i v i v-- vi i v v i ivi i C L3#LINE/CR1 1118 TTTCCTTTCCCTCAAATTTCAGTTTAAAGTCCTCTTGATCAGGTCGGCGA 1069 chr3ptel1M 237758 GACTCCAGGCAAATCCATT-TTAGTGGCTCTTGTTAAGTGCACTTCAAAT 237806 v ? ? iv i - vvi iii i v ii i ivvi C L3#LINE/CR1 1068 GTCTCCNGNCAAACACGTTCTTCCCGGTCTTCGTGAGATGCACTCCGTCC 1019 chr3ptel1M 237807 CTGGCTTGGAGCCCATCATCCCTATATTTCAAGTTGTGGTCCAGAAAATT 237856 ? iv i i ivi i?i iii ii C L3#LINE/CR1 1018 CTNGCCAGGAGCCCATCGTTCTGGTATCNTAAGCCATGGTCCAGAAAACC 969 chr3ptel1M 237857 TAATTCTTTTCTCCACCA-GATTTCCCTGGCCAGCCATTCACTCCCAAAA 237905 v i v i iv -v i v v i ii i v v C L3#LINE/CR1 968 AAATCCTGTTCTTCGACACCATCTACGTAGCCAGCTGTTCACTTCCCATA 919 chr3ptel1M 237906 GGCACCTTCGCCTTCCAAAGTCCTTGCCTTTTATTGACCACAGTGAAGAA 237955 vv v ivi vivi iv i ivviv v v C L3#LINE/CR1 918 TCCTCCTTTCTCTTCCAAAGTCACGACCTTCAACTGGAAGAAGAGATGAA 869 chr3ptel1M 237956 AATACCACTTG 237966 i i C L3#LINE/CR1 868 AACACCACCTG 858 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 47.57 CpG sites = 67, Kimura (unadjusted) = 53.76 Transitions / transversions = 1.49 (67/45) Gap_init rate = 0.01 (3 / 306), avg. gap size = 1.33 (4 / 3) 326 30.81 11.68 2.80 chr3ptel1M 238437 238633 (761367) C L3#LINE/CR1 (3679) 420 207 m_b115s601i13 4161 chr3ptel1M 238437 TCTTTCTTCCCTTCCT-TGTCTGCCCCCACGTTCCTCTGTTCTCCAATC- 238484 i ii - v ----- i i iii v i - C L3#LINE/CR1 420 TCTTTCTCCTTTTCCTCTGTGT-----CACATTCTTCCACTCGCCAACCT 376 chr3ptel1M 238485 CTGCTCCCAGGCTGAGCTTCTCCGCTGCCT-CTCACATCCCTCTTTTCTT 238533 vvv v v i vv v i iv i - v -vi i ii C L3#LINE/CR1 375 CTTGACGCTGGTTTTGATTCCCTTCCGCCTCCTCAGA-ATCTTTTTCTTT 327 chr3ptel1M 238534 CTGGTTTC--TCCTCAA-----------ACCCTCTC-ACAAAGTGCTAAG 238569 ? -- vi ----------- i ? - vi vivi v v C L3#LINE/CR1 326 CTGNTTTCCTTCCTGGATTATTTCTTCCATCCTNTCTAGGAACCCTTCAT 277 chr3ptel1M 238570 ACTTCCTGACAAGCTGGAGAGCAGAGA-GCATTCCCCGAG-----TTGCC 238613 v ii i i i v i - i i i ----- ii C L3#LINE/CR1 276 CCTCTCTAATAAGCCGGAGCGTAGAGAGGCGTTCCTCAAGCCCTTTCACC 227 chr3ptel1M 238614 TTCTCTTCCAGAAAGGAGGC 238633 i i v i i C L3#LINE/CR1 226 TTCTCCTCTAGCAGGGAGAC 207 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 39.26 CpG sites = 37, Kimura (unadjusted) = 42.08 Transitions / transversions = 1.68 (37/22) Gap_init rate = 0.07 (14 / 196), avg. gap size = 2.07 (29 / 14) 26 11.81 5.17 1.67 chr3ptel1M 238819 238876 (761124) (TCCT)n#Simple_repeat 1 60 (0) m_b115s252i4 4162 chr3ptel1M 238819 TCC-TCCTTCCTCCCTCCTTTCCTT-CTTCCTTCCTTCCCTTCTTTCCTT 238866 - i i i - - i (TCCT)n#Simpl 1 TCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT-CCTTCCTTCCTT 49 chr3ptel1M 238867 -CATCTTTCCT 238876 - v i (TCCT)n#Simpl 50 CCTTCCTTCCT 60 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.07 (4 / 57), avg. gap size = 1.00 (4 / 4) 17 13.95 5.88 3.85 chr3ptel1M 238925 238975 (761025) (TCTA)n#Simple_repeat 1 52 (0) m_b115s252i6 4163 chr3ptel1M 238925 TCTAACTAT-TATCTATCT-TC-ATCTCTCTATTCCTATCCACCTCTTTA 238971 v - - - v - - i i v i (TCTA)n#Simpl 1 TCTATCTATCTATCTATCTATCTATCTATCTA-T-CTATCTATCTATCTA 48 chr3ptel1M 238972 TCTA 238975 (TCTA)n#Simpl 49 TCTA 52 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.10 (5 / 50), avg. gap size = 1.00 (5 / 5) 577 35.41 15.93 0.55 chr3ptel1M 239189 239665 (760335) L3#LINE/CR1 2537 3086 (1013) m_b115s601i14 4164 chr3ptel1M 239189 GAGTCCTTCCCTGCTTGGGATGAGTTTGAGTCACCTGATCCAGATGAACT 239238 iv i vv i vii ii v v ii i i L3#LINE/CR1 2537 GAGCACCTAGCCGCTTTAAATGAGTTCAAGTCTCCAGGCCCAGACGAATT 2586 chr3ptel1M 239239 ACATTCCTGAAGACTGAAAGAA-----AGATGGAGCTGTG--ACTGCTGA 239281 i v iiv ----- viiii i -- i v L3#LINE/CR1 2587 ACATCCCAGGGTACTGAAAGAACTTGCAGATGTGATCGCGGAACCGCTGT 2636 chr3ptel1M 239282 TAGGAG--TTTGGGAAAT---GTA----GTAAGAGACTCCAGAAGCCTGG 239322 ii v i-- i --- v ---- v iiv v L3#LINE/CR1 2637 CGGTAATCTTTGAGAAATCACGGAGAACGGAAGAGGTGCCAGAAGACTGG 2686 chr3ptel1M 239323 AAAAAGGAAAACCCCATCCTGATGTTCAGAATAAGGAAGA------GAAT 239366 i vi v ivi?i ? iv ?v i i - i i ------ v L3#LINE/CR1 2687 AGACGGGCAAATGTNGTNCCTANTTTTAAAA-AGGGAAAAAAGATGGATT 2735 chr3ptel1M 239367 CTGCCAAT--CAG-CCAAGGGGTCCCACTTAGCTTCCTTGC-AGATTCT- 239411 ?v i-- - iivii iiiv v v v i iv - i - L3#LINE/CR1 2736 CTGNAAACTACAGACCGGTAAGCTTGACGTCGATCCCCGGCAAAATTCTA 2785 chr3ptel1M 239412 ----GTCCCACAAAAGAGATGACCAGAAGATATACAGAA----AAGCATT 239453 ---- vvii iv v iiiv viiii ivi ---- iv L3#LINE/CR1 2786 GAACGGATTATTAAACAGATGGTTTGTGAGCACTTAGAAAAGGAAGCGGT 2835 chr3ptel1M 239454 GATCACCCAGAGCCCATTGGGCTTCATCAAGAGCCGGTTGCACCAAACCG 239503 ivi viivv v ii i vi iiii ii L3#LINE/CR1 2836 GATCACTAGGAGCCAGCATGGGTTCACTAAGAACAAGTCATGCCAAACTA 2885 chr3ptel1M 239504 ATCTTCTTTCCTTTTCATGTGGGCTCCCTAAAT---TAAATCAGATGAAA 239550 i iv ivvi i v iv i i--- i iv v L3#LINE/CR1 2886 ACCTCATTTCCTTTTTTGATAGGGTTACTAGACTGGTAGATCAGGGGAAT 2935 chr3ptel1M 239551 GCTGTGAA------------GAAT------AAAGCATTTGACAAAGTGTC 239582 i ii ------------ i ------ i v L3#LINE/CR1 2936 GCCGTAGACANAGTGTATCTGGATTTCAGCAAGGCATTTGACAAAGTCTC 2985 chr3ptel1M 239583 CC----------------CAAGTTGGAGAGAAGTGAGCTAGACAATAGGA 239616 i ---------------- v i vi i i ii v L3#LINE/CR1 2986 TCATGATATCCTTGTGGACAAGATGGAGAAATATGGGCTGGATGATAGTA 3035 chr3ptel1M 239617 AAATGA----CATTTAGAGTTGACTGAAAGGACAGACCAGAAACATGGTT 239662 v i v ----v iiv i ii v ivi v vi vi -- L3#LINE/CR1 3036 CAGTTAGGTGGATTCGTAGCTGGTTGAACGACTATACCCAAAAGGTG--T 3083 chr3ptel1M 239663 TGA 239665 L3#LINE/CR1 3084 TGA 3086 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 46.07 CpG sites = 106, Kimura (unadjusted) = 51.39 Transitions / transversions = 1.71 (106/62) Gap_init rate = 0.04 (20 / 476), avg. gap size = 3.95 (79 / 20) 187 27.78 0.00 1.85 chr3ptel1M 239804 239858 (760142) L3#LINE/CR1 4043 4096 (3) m_b115s601i15 4165 chr3ptel1M 239804 GGTTGGGACCATGGGGCTTCGGAGGTCCCTTTCAACTATGGAGATCTGTC 239853 - i viv i i vi i v iiiv v L3#LINE/CR1 4043 GGTTGG-ACTAGATGACCTCTAAGGTCCCTTCCAACTCTGAGATTCTGTG 4091 chr3ptel1M 239854 ATTCT 239858 L3#LINE/CR1 4092 ATTCT 4096 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 35.67 CpG sites = 9, Kimura (unadjusted) = 35.67 Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1) 384 24.17 9.83 6.74 chr3ptel1M 239899 240071 (759929) MIRb#SINE/MIR 5 182 (86) m_b115s601i16 4166 chr3ptel1M 239899 GGGGCAGCTAGATGGTGTAGTGTGCATTTAGGGTTAGAAAACTGGAGTCA 239948 ---i i - v --- i ivv iivvi MIRb#SINE/MIR 5 GGGGCAGC---GTGGTGCAGTG-GAA---AGAGCACGGGCTTTGGAGTCA 47 chr3ptel1M 239949 TGAAGATCTGAATTCAAATCCAACCTTAGACACT--CT---TGCATGACC 239993 viv i ii i viv iv v -- --- ii MIRb#SINE/MIR 48 GACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACC 97 chr3ptel1M 239994 TG-----------TTAA-CTCTGTTTGCCTCAGTTTCCTCACCTGTGAAA 240031 v----------- - v vv i i MIRb#SINE/MIR 98 TTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAA 147 chr3ptel1M 240032 TGAGGATCATGATAGTACCTCCCTCTGAGGGAGTTGTTGT 240071 i --- i i v vv -- MIRb#SINE/MIR 148 TGGGG---ATAATAATACCTACCTCGCAGG--GTTGTTGT 182 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 27.04 CpG sites = 21, Kimura (unadjusted) = 29.64 Transitions / transversions = 1.17 (21/18) Gap_init rate = 0.09 (16 / 172), avg. gap size = 1.81 (29 / 16) 370 26.36 13.00 1.35 chr3ptel1M 239915 240114 (759886) MIR1_Amn#SINE/MIR 8 230 (0) m_b115s601i17 4166 chr3ptel1M 239915 GTAGTGTGCATTTAG-GGTTAGAAAACTGGAGTCAT-----GAAGATCTG 239958 i -i i - v iv v viv----- i i MIR1_Amn#SINE 8 GCAGTGTG-GTCTAGTGGATAGAGCACTGGACTGGGACTCGGGAGACCTG 56 chr3ptel1M 239959 AATTCAAATCCAACCTTAGACACTC-----TTGCATGACCTG-------- 239995 ii ? ? viv iv v ?-----i ?i v-------- MIR1_Amn#SINE 57 GGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGT 106 chr3ptel1M 239996 ----TTAACTCTGTTTGCCTCAGTTTCCTCACCTGTGAAATGAGGATCAT 240041 ---- ? v v v? i i i v MIR1_Amn#SINE 107 CACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGGATAAT 156 chr3ptel1M 240042 GATAGT-ACCTCCCTCTGAGGGAGTTGTTGTACAGC-ACTTA-GCACCAT 240088 v - i ivv ii v i - - v v - v - v vvi MIR1_Amn#SINE 157 GATACTGACCTCCTTTGTAAAGTGCT-TTG-AGATCTACTGATGAAAAGT 204 chr3ptel1M 240089 GCTATAGAACTGTTAGTTATTATTAT 240114 i v vv i v MIR1_Amn#SINE 205 GCTACATAAGAGCTAGGTATTATTAT 230 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 33.27 CpG sites = 24, Kimura (unadjusted) = 34.04 Transitions / transversions = 0.86 (24/28) Gap_init rate = 0.06 (11 / 199), avg. gap size = 2.64 (29 / 11) 418 20.88 12.88 2.05 chr3ptel1M 239940 240071 (759929) MIR#SINE/MIR 33 178 (84) m_b115s601i18 4166 chr3ptel1M 239940 CTGGAGTCATGAAGATCTGAATTCAAATCCAACCTTAGACACT--CT--- 239984 i - vvii ii i viv iv v -- --- MIR#SINE/MIR 33 CTGGAGCCA-GACTGCCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGC 81 chr3ptel1M 239985 TGCATGACCTG-----------TTAAC-TCTGTTTGCCTCAGTTTCCTCA 240022 ii v----------- - v v MIR#SINE/MIR 82 TGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCA 131 chr3ptel1M 240023 CCTGTGAAATGAGGATCATGATAGTACCTCCCTCTGAGGGAGTTGTTGT 240071 i i i v i v vv -- MIR#SINE/MIR 132 TCTGTAAAATGGGGATAATAATAGTACCTACCTCATAGG--GTTGTTGT 178 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 22.75 CpG sites = 14, Kimura (unadjusted) = 24.75 Transitions / transversions = 1.08 (14/13) Gap_init rate = 0.05 (7 / 131), avg. gap size = 2.86 (20 / 7) 216 29.63 0.00 0.00 chr3ptel1M 241063 241116 (758884) C L2c_3end#LINE/L2 (222) 256 203 m_b115s601i19 4167 chr3ptel1M 241063 GGAAGATTAGGGAAGGCTTCACAAAGGAAGCGGTGCCTGAGTAAAGCCTT 241112 ii i i v ii i i iiii ivi ? C L2c_3end#LINE 256 GGGGGGTCAGGGAAGGCTTCCCGGAGGAGGTGACATCTGAGCTGAGNCTT 207 chr3ptel1M 241113 GAAG 241116 C L2c_3end#LINE 206 GAAG 203 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 39.93 CpG sites = 14, Kimura (unadjusted) = 43.70 Transitions / transversions = 7.00 (14/2) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 211 27.12 3.39 0.00 chr3ptel1M 241067 241125 (758875) C L2d2_3end#LINE/L2 (302) 253 193 m_b115s601i20 4167 chr3ptel1M 241067 GATTAGGGAAGGCTTCACAAAGGAAGCGGTGCCTGAGTAAAGCCTTGAAG 241116 i i ii i i ?iii ivii C L2d2_3end#LIN 253 GGTCAGGGAAGGCTTCACGGAGGAGGTGGNATTTGAGCTGGGCCTTGAAG 204 chr3ptel1M 241117 A--GGGAAGAA 241125 i-- v i C L2d2_3end#LIN 203 GATGGGTAGGA 193 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 35.08 CpG sites = 14, Kimura (unadjusted) = 38.20 Transitions / transversions = 7.00 (14/2) Gap_init rate = 0.02 (1 / 58), avg. gap size = 2.00 (2 / 1) 382 27.15 0.38 1.06 chr3ptel1M 241779 242826 (757174) (CA)n#Simple_repeat 1 1041 (0) m_b115s252i7 4168 chr3ptel1M 241779 CACACACACACACTGACACGCTCATACACACACACTGACACACATCATAC 241828 vv i v i vv - i (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACA-CACAC 49 chr3ptel1M 241829 ACTGACACGCTCATACACACACATCACACTCAGTGACACGCTCATACACA 241878 vv i v i - v vvv i v i (CA)n#Simple_ 50 ACACACACACACACACACACACA-CACACACACACACACACACACACACA 98 chr3ptel1M 241879 CACATACAGTGACATGCTCATACACATACACACATCACACTCAGTGACAT 241928 i vvv ii v i i - v vvv i (CA)n#Simple_ 99 CACACACACACACACACACACACACACACACACA-CACACACACACACAC 147 chr3ptel1M 241929 GCTCATACACACACTCACACACTCTCACACACACTGACATGCTCATGCAC 241978 i v i v v v vv ii v ii (CA)n#Simple_ 148 ACACACACACACACACACACACACACACACACACACACACACACACACAC 197 chr3ptel1M 241979 ATACACACACTGACATGCTCATACACACACACTGACACACACTCACTCAC 242028 i vv ii v i vv v v (CA)n#Simple_ 198 ACACACACACACACACACACACACACACACACACACACACACACACACAC 247 chr3ptel1M 242029 ACACACTGACACGCTCATACACACACACTGACACTCACACACACACACAC 242078 vv i v i vv v (CA)n#Simple_ 248 ACACACACACACACACACACACACACACACACACACACACACACACACAC 297 chr3ptel1M 242079 ATCACACTCACAGTGACACGCTCATACACACACACAGTGACATGCTCATA 242128 - v vvv i v i vvv ii v i (CA)n#Simple_ 298 A-CACACACACACACACACACACACACACACACACACACACACACACACA 346 chr3ptel1M 242129 CACATACACACATCACACTCAGTGACATGCTCATACACACACTCACACAC 242178 i - v vvv ii v i v (CA)n#Simple_ 347 CACACACACACA-CACACACACACACACACACACACACACACACACACAC 395 chr3ptel1M 242179 TCTCACACACACTGACATGCTCATGCACACACTCACACACTGACATGCTC 242228 v v vv ii v ii v vv ii v (CA)n#Simple_ 396 ACACACACACACACACACACACACACACACACACACACACACACACACAC 445 chr3ptel1M 242229 ATACACACACACTGACACACACTCACTCACACACACTGACACGCTCATAC 242278 i vv v v vv i v i (CA)n#Simple_ 446 ACACACACACACACACACACACACACACACACACACACACACACACACAC 495 chr3ptel1M 242279 ACACACTGACACACACACATA-ACACACACATCACACTCACAGTGACACG 242327 vv i - - v vvv i (CA)n#Simple_ 496 ACACACACACACACACACACACACACACACA-CACACACACACACACACA 544 chr3ptel1M 242328 CTCATACACACACTCAGTGACATGCTCATACACACACTCACATACTCTCA 242377 v i v vvv ii v i v i v v (CA)n#Simple_ 545 CACACACACACACACACACACACACACACACACACACACACACACACACA 594 chr3ptel1M 242378 CACACACTGACATGCTCATACACACACTGACACGCTCATACACACACTGA 242427 vv ii v i vv i v i vv (CA)n#Simple_ 595 CACACACACACACACACACACACACACACACACACACACACACACACACA 644 chr3ptel1M 242428 CACACACACACA-ACACACACTGACACGTTCCTACACACACATCACACTC 242476 - vv iiv vi - v (CA)n#Simple_ 645 CACACACACACACACACACACACACACACACACACACACACA-CACACAC 693 chr3ptel1M 242477 ACACTGACATGCTCATACACACACTCACTCACACACTCTCACACACACTG 242526 vv ii v i v v v v vv (CA)n#Simple_ 694 ACACACACACACACACACACACACACACACACACACACACACACACACAC 743 chr3ptel1M 242527 ACATGCTCATACACACACTGACACGCTCATACACACACTGACACACACAC 242576 ii v i vv i v i vv (CA)n#Simple_ 744 ACACACACACACACACACACACACACACACACACACACACACACACACAC 793 chr3ptel1M 242577 ACA-ACACACACTGATGCATTCCTACACACACATCACACTCACACTGACA 242625 - vv ii iv vi - v vv (CA)n#Simple_ 794 ACACACACACACACACACACACACACACACACA-CACACACACACACACA 842 chr3ptel1M 242626 TGCTCATACACACACTCACTCACACACTCTCACACACACTGACATGCTCA 242675 ii v i v v v v vv ii v (CA)n#Simple_ 843 CACACACACACACACACACACACACACACACACACACACACACACACACA 892 chr3ptel1M 242676 TACACACACTAACACACACTCACACACACTGACATGCTCATACACACACT 242725 i vv v vv ii v i v (CA)n#Simple_ 893 CACACACACACACACACACACACACACACACACACACACACACACACACA 942 chr3ptel1M 242726 GACATACTCACACACATA-ACACACACTGACACGATCATACACACACATC 242774 v i v i - vv - - i - (CA)n#Simple_ 943 CACACACACACACACACACACACACACACACAC-A-CACACACACACA-C 989 chr3ptel1M 242775 ACACTCACACTGACATGCTCATACACGCACACATATTCACACACACACAC 242824 v vv ii v i i i iv (CA)n#Simple_ 990 ACACACACACACACACACACACACACACACACACACACACACACACACAC 1039 chr3ptel1M 242825 AC 242826 (CA)n#Simple_ 1040 AC 1041 Matrix = Unknown Transitions / transversions = 0.60 (88/146) Gap_init rate = 0.01 (15 / 1047), avg. gap size = 1.00 (15 / 15) 20 17.86 8.33 0.00 chr3ptel1M 243930 243944 (756056) (AG)n#Simple_repeat 1 16 (49) m_b115s252i8 4169 chr3ptel1M 243930 AGAGAGGGAAAAAG-G 243944 i i i - (AG)n#Simple_ 1 AGAGAGAGAGAGAGAG 16 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.07 (1 / 14), avg. gap size = 1.00 (1 / 1) 37 5.69 3.64 0.00 chr3ptel1M 243945 243999 (756001) (AGAGAC)n#Simple_repeat 1 57 (0) c_b115s251i1 4170 chr3ptel1M 243945 AGAGAAAGAGACAGAGACAGAGAC--AGACAGAGACAGAGACAGACAAAG 243992 v -- v v (AGAGAC)n#Sim 1 AGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAG 50 chr3ptel1M 243993 AGACAGA 243999 (AGAGAC)n#Sim 51 AGACAGA 57 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.02 (1 / 54), avg. gap size = 2.00 (2 / 1) 20 17.86 8.33 0.00 chr3ptel1M 244000 244043 (755957) (AG)n#Simple_repeat 17 64 (1) m_b115s252i8 4171 chr3ptel1M 244000 CAGAGAGAG-GAG-GGGGGAAAGAGA-AGAG-GAGAGGGAGAGGGAGA 244043 v - - i i i - - i i (AG)n#Simple_ 17 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 64 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.09 (4 / 43), avg. gap size = 1.00 (4 / 4) 330 21.05 3.70 12.00 chr3ptel1M 245094 245201 (754799) L2c_3end#LINE/L2 377 476 (2) m_b115s601i21 4172 chr3ptel1M 245094 CTGTGACCTC--TGAGCTCAAG--CTCTGTCTTGTTTTTCTTTGAATCTC 245139 v -- vv i -- iv i iv v -- L2c_3end#LINE 377 CTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTATC-- 424 chr3ptel1M 245140 TGGTTCTTAGCCCAGTGTCTGGCATATAGTAGGTGCTTAATAAATGTTTA 245189 ---------- i i i i i i L2c_3end#LINE 425 ----------CCCAGCGCCTGGCACATAGTAGGCGCTCAATAAATGTTTG 464 chr3ptel1M 245190 TCAACTGATTGA 245201 ii v v L2c_3end#LINE 465 TTGAATGAATGA 476 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 20.78 CpG sites = 12, Kimura (unadjusted) = 24.83 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.13 (14 / 107), avg. gap size = 1.14 (16 / 14) 332 28.74 0.00 0.00 chr3ptel1M 245115 245201 (754799) L2b_3end#LINE/L2 378 464 (2) m_b115s601i22 4172 chr3ptel1M 245115 TCTGTCTTGTTTTTCTTTGAATCTCTGGTTCTTAGCCCAGTGTCTGGCAT 245164 ivi vi v i ii iv i v ? i i L2b_3end#LINE 378 TCTGTCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCAC 427 chr3ptel1M 245165 ATAGTAGGTGCTTAATAAATGTTTATCAACTGATTGA 245201 i i i i i i ii v v L2b_3end#LINE 428 ACAGTAGGCGCTCAGTAAATATTTGTTGAATGAATGA 464 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 35.08 CpG sites = 18, Kimura (unadjusted) = 39.10 Transitions / transversions = 2.57 (18/7) Gap_init rate = 0.00 (0 / 86), avg. gap size = 0.0 (0 / 0) 296 28.85 11.54 0.00 chr3ptel1M 246328 246431 (753569) C L3#LINE/CR1 (407) 3692 3577 m_b115s601i23 4173 chr3ptel1M 246328 TGGTCTCAAGGCCCTTCCCCACTCTGGTCCTTTTCCTTTGGACACTCCCC 246377 i v i v ii vi i i i v i C L3#LINE/CR1 3692 TGGTTTCCAGACCCTTCACCATCCTGGTCGCTCTCCTCTGGACGCGCTCC 3643 chr3ptel1M 246378 GGCCAGTCAGCGTCTTTGTT-----------CCCAG-ATGGAACAGGATG 246415 i iiv ii ii v ----------- - iv ivi i C L3#LINE/CR1 3642 AGTTTGTCAATGTCCCTCTTAAAATGTGGCGCCCAGAACTGAACGCAATA 3593 chr3ptel1M 246416 CTCCAGGTGTGGCCTG 246431 i i C L3#LINE/CR1 3592 CTCCAGATGTGGTCTG 3577 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 35.49 CpG sites = 22, Kimura (unadjusted) = 38.83 Transitions / transversions = 2.75 (22/8) Gap_init rate = 0.02 (2 / 103), avg. gap size = 6.00 (12 / 2) 258 22.44 0.00 4.48 chr3ptel1M 248962 249031 (750969) C MIR#SINE/MIR (58) 204 138 m_b115s601i24 4174 chr3ptel1M 248962 TACATGTATTCACAAATATTACAAATGTCACAATAATCCTCCGAGGTGGA 249011 v vv v --- viv i i vi i i C MIR#SINE/MIR 204 TACATGTATTAACTCATTT---AATCCTCACAACAACCCTATGAGGTAGG 158 chr3ptel1M 249012 TACTATCATTATCCCCATCT 249031 i i C MIR#SINE/MIR 157 TACTATTATTATCCCCATTT 138 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 26.89 CpG sites = 8, Kimura (unadjusted) = 26.89 Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.04 (3 / 69), avg. gap size = 1.00 (3 / 3) 16 12.03 5.56 0.00 chr3ptel1M 249078 249113 (750887) (GTATCT)n#Simple_repeat 1 38 (0) m_b115s252i9 4175 chr3ptel1M 249078 GTATCTG-AGCGATA-CTGTATCTGTCTCTGTATCTGT 249113 - v vi - v (GTATCT)n#Sim 1 GTATCTGTATCTGTATCTGTATCTGTATCTGTATCTGT 38 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 33 0.00 0.00 0.00 chr3ptel1M 250397 250424 (749576) (TG)n#Simple_repeat 1 28 (0) c_b115s251i2 4176 chr3ptel1M 250397 TGTGTGTGTGTGTGTGTGTGTGTGTGTG 250424 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTG 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 12 16.93 0.00 0.00 chr3ptel1M 250544 250570 (749430) (TCCC)n#Simple_repeat 1 27 (0) m_b115s252i10 4177 chr3ptel1M 250544 TCCCTCCCTCCCTCCACCCCTTCCCCC 250570 vi i i (TCCC)n#Simpl 1 TCCCTCCCTCCCTCCCTCCCTCCCTCC 27 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 555 23.01 10.86 5.60 chr3ptel1M 251633 251853 (748147) MIRc#SINE/MIR 10 241 (27) m_b115s601i25 4178 chr3ptel1M 251633 GCGGCACAGTGGGCAGAGCTCTCACTGGGCATGGAGTCAGGAGGCCCTGA 251682 i ii iv ---- i v i v i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGC----ACTGGACTTGGAGTCAGGAAGACCTGG 55 chr3ptel1M 251683 GTTCAAAC----GCAATGCCAGAGACTTACCAGCTGTGTGATGCCGGGCA 251728 i ii---- vv ---- i ivii MIRc#SINE/MIR 56 GTTCGAGTCCCGGCTCTGCC----ACTTACTAGCTGTGTGACCTTGGGCA 101 chr3ptel1M 251729 AGTCGCATAAACCCCTGTTTGCCTCAGTTTTCTCAAGCTATGAAATTGGA 251778 i - v i v vv i - v i i v i MIRc#SINE/MIR 102 AGTCAC-TTAACCTCTCTGAGCCTCAGTTTCCTC-ATCTGTAAAATGGGG 149 chr3ptel1M 251779 ACATAATCATA---GCACTATCT-CCT-----GGT----------GTCAG 251809 -- v --- v ii - ----- ----------i i MIRc#SINE/MIR 150 --ATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAA 197 chr3ptel1M 251810 ATGGGATAATATTTGC-AAAGCTCTTAGCAAAGTGTCTAAATGCT 251853 i i v i- v v i v v- i MIRc#SINE/MIR 198 ATGAGATAATGTATGTGAAAGCGCTTTGTAAACTGTA-AAGTGCT 241 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 27.48 CpG sites = 29, Kimura (unadjusted) = 28.16 Transitions / transversions = 1.53 (29/19) Gap_init rate = 0.09 (19 / 220), avg. gap size = 1.95 (37 / 19) 27 25.55 0.00 1.32 chr3ptel1M 251932 252001 (747999) (CACTCT)n#Simple_repeat 1 70 (6) m_b115s252i11 4179 chr3ptel1M 251932 CACACTCACACACACACGCACACACACACTCACTCTCTCTCTCTCTTTCT 251981 v v v v v v v v v v i v (CACTCT)n#Sim 1 CACTCTCACTCTCACTCTCACTCTCACTCTCACTCTCACTCTCACTCTCA 50 chr3ptel1M 251982 CTCTCTCTCTCTCTCTCTCT 252001 v v v (CACTCT)n#Sim 51 CTCTCACTCTCACTCTCACT 70 Matrix = Unknown Transitions / transversions = 0.07 (1/14) Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0) 35 6.70 0.00 2.08 chr3ptel1M 251960 252001 (747999) (CT)n#Simple_repeat 1 42 (6) m_b115s252i13 4179 chr3ptel1M 251960 CTCACTCTCTCTCTCTCTTTCTCTCTCTCTCTCTCTCTCTCT 252001 v i (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 42 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 43 0.00 0.00 0.00 chr3ptel1M 252002 252038 (747962) (CA)n#Simple_repeat 1 37 (0) c_b115s251i3 4180 chr3ptel1M 252002 CACACACACACACACACACACACACACACACACACAC 252038 (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACAC 37 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 392 33.95 11.65 2.32 chr3ptel1M 252622 253016 (746984) L2b_3end#LINE/L2 9 439 (27) m_b115s601i26 4181 chr3ptel1M 252622 TCTGCCCTTGCCACCTTTCCAGTCT--TCTTCACCTTCTTCCCCACTGGA 252669 v ii i i i i -- i vv iv ii vi vv L2b_3end#LINE 9 TCTGGCCCCGCTACCTCTCCGGCCTCATCTCCTACCACTCTCCCCTTGCT 58 chr3ptel1M 252670 GTCTCTGGGCCAATGAAACTGGACTCCTGACTGTTCTATAAACAAGACCC 252719 vv vv iiv v v vi ivii v --- L2b_3end#LINE 59 CACTCTGCTCCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACACG---C 105 chr3ptel1M 252720 TCTGCTTCTTGGCATCCCAAGA--TTTGCTCCAGCTGTTCCCCCCACAGC 252767 iv? i?i vv ii i i i-- v ?v i ii -- L2b_3end#LINE 106 CANGCTCNCTCCCGCCTCAGGGCCTTTGCACNTGCTGTTCCCTCTGC--C 153 chr3ptel1M 252768 TGGAAT---CTCTCCCTCCTCCT------------TTCTGCTAAG----- 252797 i--- ii v i ------------ i i v v----- L2b_3end#LINE 154 TGGAACGCCCTTCCCCACCTCTTCGCCTGGCCAACTCCTACTCATCCTTC 203 chr3ptel1M 252798 AGGGTTCCCTGCT------TC-CCTTCTCCAGGAGGCCCTTCCTGATCTC 252840 -- i v ------ - i i i i i i L2b_3end#LINE 204 AGG--TCTCAGCTCAAATGTCACCTCCTCCGGGAAGCCCTCCCTGACCCC 251 chr3ptel1M 252841 CTTAATGCTG---CTGCTTTCCCTCTCCTGATGCATCCAA-CTTATTCTG 252886 i-- v i --- v vivi ii iv iiv vi i- i ii L2b_3end#LINE 252 CC--AGGCCGGGTCAGGCGCCCTCCTCTGGGCCCCCCCAGTCCTACCCTG 299 chr3ptel1M 252887 TCCCTATA--TTCTGTTTGTCTG----CAT-TCTGTCTGCTCCATTTGAT 252929 i v v i-- v ?v ---- - v i i v i L2b_3end#LINE 300 CCACTCTGGGTTATNATTGTCTGNTTACATGTCTGTCTCCCCCACTAGAC 349 chr3ptel1M 252930 TGTGAACTTCTTGAGGACAGAGACTATCTTGCATCTTTTTT----TTGTA 252975 i i v i i ii?v i-ii v i----i L2b_3end#LINE 350 TGTGAGCTCCGTGAGGGCAGGGACCGNGTC-TGTCTTGTTCACCGCTGTA 398 chr3ptel1M 252976 CTTCTAGCCTTTAACCTAGGTCTCGCTATACAGGAAGCGCT 253016 iii i vii i vi ?v ii vi i v i L2b_3end#LINE 399 TCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCT 439 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 44.19 CpG sites = 84, Kimura (unadjusted) = 49.01 Transitions / transversions = 1.79 (84/47) Gap_init rate = 0.06 (23 / 394), avg. gap size = 2.43 (56 / 23) 474 35.01 9.29 4.79 chr3ptel1M 253020 253439 (746561) L3#LINE/CR1 3243 3680 (419) m_b115s601i27 4182 chr3ptel1M 253020 TGACTGACACGCTGGATAACAAAGTC------CCAAAGGATCTTGGTGGG 253063 ii i i ? i i i ------ v ? i iii L3#LINE/CR1 3243 TAGCTAATACGNTGGATGACAGAATCAAGATTCAAAANGATCTCGACAGG 3292 chr3ptel1M 253064 CTCAAGC-AGGGGCTGAATCCAATTGGATCGAATTCTGTACGGGTCAATA 253112 vi i - v i v ivi vi ivii v i v i L3#LINE/CR1 3293 CTGGAACGATGGGCCGAAACCAACAAGATGAAATTTAACAGGGATAAATG 3342 chr3ptel1M 253113 TCAAGTTTCTC-CTCGGATTTGGAAATTTTGCTTCACAAGTTCAAGTCCA 253161 v iiiv -i ii i iii v ivi v v i -vii L3#LINE/CR1 3343 TAAAGTCCTGCATTTAGGTTCAAAAAATCAACTGCACAAGTACAGG-ATG 3391 chr3ptel1M 253162 GAGAGGTTCAGGCTTAGGTCAAGATTATTCAC----AAATGATCTGG--- 253204 v v -- iv --i ---- v i i --- L3#LINE/CR1 3392 GAGAGGATCTGGCTTAG--CAGCA--GTTCACGTGAAAAAGACCTAGGGG 3437 chr3ptel1M 253205 ----AGCAGATCAAGAGTTTAATGCGAGTAGTCAGCATGATGTGACAGCC 253250 ---- iv i ivi i i ii iviv ii i v - L3#LINE/CR1 3438 TTTTAGTTGACCGCAAGCTCAATATGAGCCAACAGTGTGATGTGGCTG-C 3486 chr3ptel1M 253251 CCCAAGAGGTGGTGCTTGCCTTGGC-GCAT--GTAGGAACAAAGGG---- 253293 vv i v ii vvv i v - --i i ii v v ---- L3#LINE/CR1 3487 CAAAAAAGCTAATGCAATCTTAGGCTGCATTAATAGAAGTATAGTGTCCA 3536 chr3ptel1M 253294 ------GGGAGG-----GCCCCAC-ACACTGTGCCCTGGTCAGAGCCCAT 253331 ------ ----- i i -ii v v v v L3#LINE/CR1 3537 GANCAAGGGAGGTAATAGTCCCGCTGTACTCTGCGCTGGTCAGACCACAT 3586 chr3ptel1M 253332 GGAGAAGGCTGGGTCCA-TTCGGGGTCTGTTTGCTTAGCCACAGGATAGG 253380 vvi ivii v i - v i----------- vvv i L3#LINE/CR1 3587 CTGGAGTATTGCGTTCAGTTCTGGGC-----------GCCACATTTTAAG 3625 chr3ptel1M 253381 AAGGGTATTGATGACCTGAAGATTGTCTGTCATATGAGGGCCAGTCAAGG 253430 i ii ii v i vvi --- v v i v -i i i L3#LINE/CR1 3626 AGGGACATTGACAAACTGGAGCGCGTC---CAGAGGAGAGCGA-CCAGGA 3671 chr3ptel1M 253431 GAATGGAGG 253439 vii i L3#LINE/CR1 3672 TGGTGAAGG 3680 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 47.09 CpG sites = 87, Kimura (unadjusted) = 50.17 Transitions / transversions = 1.64 (87/53) Gap_init rate = 0.08 (34 / 419), avg. gap size = 1.76 (60 / 34) 185 34.10 11.03 5.05 chr3ptel1M 253372 253652 (746348) L3#LINE/CR1 3667 3963 (136) m_b115s601i28 4182 chr3ptel1M 253372 CAGGATAG-GAAGGGTATTGATGACCTGAAGATTGTCTGTCATATGAGGG 253420 i - --------- i i iii -- i L3#LINE/CR1 3667 CAGGATGGTGAAGGGT---------CTGGAAACCAT--GTCATATGAGGA 3705 chr3ptel1M 253421 CCAGTCAAGGGAATGGAGGA-GACCAGGCTGAAGGGGAGGAGAC-CAGGG 253468 v i ii i iv i - vii v i ii i -i i L3#LINE/CR1 3706 ACGGTTGAAGGAACTGGGGATGTTTAGCCTGGAGAAGAGAAGACTTAGAG 3755 chr3ptel1M 253469 CTGAGGT----GCAGCATTTACAGTTTTG--GGGCCATGAGGATTTGGCG 253512 vv vi ---- v iv i v vv -- ii ---v v vi L3#LINE/CR1 3756 GAGACATGATAGCTGTCTTCAAATATTTGAAGGGCTGT---CATGTGGAA 3802 chr3ptel1M 253513 GGGGGACT-GCCGTGTTCTGCTTGACCTCAG---------TTTGGAACAA 253552 i i - v v i iv i ii ---------i v v L3#LINE/CR1 3803 GAGGGATTAGACTTATTCTGTGTGGCTCCAGAGGGCAGAACTAGGACCAA 3852 chr3ptel1M 253553 GAGAGAAAAGCCGAAGG--GGCCAA----GGGTTTACATCAGGAACGAGC 253596 vi ivii iiiv -- vi ---- v iv i v - i L3#LINE/CR1 3853 TGGGTGGAAGTTACAGGGAGGCAGATTTCGGCTCAATATAAGGAA-GAAC 3901 chr3ptel1M 253597 TC----ACAATTAGAGTTATGTCAAGATGGAAGGGGAGTCTTTGGGAAG- 253641 i---- i i i viv i v vvv i i ? i - L3#LINE/CR1 3902 TTTCTAACAATCAGAGCTGTCCAAAAATGGAATGGGCTGCCTCGNGAGGT 3951 chr3ptel1M 253642 -GGGAGCTCTTC 253652 - v ii L3#LINE/CR1 3952 AGTGAGCTCCCC 3963 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 46.78 CpG sites = 57, Kimura (unadjusted) = 48.29 Transitions / transversions = 1.68 (57/34) Gap_init rate = 0.10 (27 / 280), avg. gap size = 1.70 (46 / 27) 28 16.47 4.26 6.52 chr3ptel1M 254551 254644 (745356) (GAG)n#Simple_repeat 1 92 (0) m_b115s252i14 4183 chr3ptel1M 254551 GAAGAGGAGGAGGAGGGAGG-GAAGAAGGAGG-GGAAAAGGAAGAGGGAG 254598 i - - i i - ii i - (GAG)n#Simple 1 GAGGAGGAGGAGGA-GGAGGAGGAGGAGGAGGAGGAGGAGGAGGA-GGAG 48 chr3ptel1M 254599 GAGAGAGATAGGAAGAAGGA-AAGGGGGAGGAGGGACTA-GAGGAGGA 254644 - -v - i -i i - vv - (GAG)n#Simple 49 GAG-GAG-GAGG-AGGAGGAGGAGGAGGAGGA-GGAGGAGGAGGAGGA 92 Matrix = Unknown Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.11 (10 / 93), avg. gap size = 1.00 (10 / 10) 609 27.01 9.63 0.99 chr3ptel1M 255052 255238 (744762) C MIRc#SINE/MIR (51) 217 15 m_b115s601i29 4184 chr3ptel1M 255052 TTTTACCTACATTATCTTCTTGGGCACTCACAGCAACCCTG----GCAGT 255097 i v iv v iiv i ---- i v C MIRc#SINE/MIR 217 TTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGG 168 chr3ptel1M 255098 CATGGAA------------CCCGTTTTATAGATGGAGAAACTGAGACTGA 255135 v v ------------ i i ii i v C MIRc#SINE/MIR 167 CAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCA 118 chr3ptel1M 255136 TCACGGCTAAGTGATGTGCCTAGTCTCCCACAGCCAGCAAGTGTCTGAGG 255185 vviv i iv i ivv v i i v v v C MIRc#SINE/MIR 117 GAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGC 68 chr3ptel1M 255186 CAGGATTTGAACCC--GTCTTCTTGGCTTCCAGCCCAACACCGTCCTTTC 255233 i i i -- i i i v i iii -- i i C MIRc#SINE/MIR 67 CGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGC--TCTTTCC 20 chr3ptel1M 255234 ACTAC 255238 i C MIRc#SINE/MIR 19 ACTGC 15 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 32.84 CpG sites = 31, Kimura (unadjusted) = 34.55 Transitions / transversions = 1.63 (31/19) Gap_init rate = 0.03 (5 / 186), avg. gap size = 4.00 (20 / 5) 263 13.33 0.00 0.00 chr3ptel1M 255765 255809 (744191) C MER63D#DNA/hAT-Tip100 (598) 463 419 m_b115s502i0 4185 chr3ptel1M 255765 ACTTTTAAGTTTAATTCGCACCATTAGCATTTCCTCCATCACTTT 255809 ii ii i i C MER63D#DNA/hA 463 ACTTTTAAGTTTAATCTGCATTATTAACATTTTCTCCATCACTTT 419 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 15.51 CpG sites = 6, Kimura (unadjusted) = 15.51 Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 258 20.81 9.59 1.27 chr3ptel1M 256685 256757 (743243) C MIR3#SINE/MIR (110) 98 20 m_b115s601i30 4186 chr3ptel1M 256685 TACCCAGGGTCACACAGCTTGTTA---GCAA----GAAAATAGAACCCAG 256727 i i ?v --- i---- ii v C MIR3#SINE/MIR 98 TGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAG 49 chr3ptel1M 256728 AACTCCGGGCTCCCAGCCCACGATTCTCTC 256757 iv v i i ii -i C MIR3#SINE/MIR 48 GTCTCCTGACTCCCAGTCCGTG-CTCTCTC 20 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 23.83 CpG sites = 11, Kimura (unadjusted) = 25.79 Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.04 (3 / 72), avg. gap size = 2.67 (8 / 3) 198 31.16 6.14 7.08 chr3ptel1M 256914 257027 (742973) C MIRc#SINE/MIR (146) 122 10 m_b115s601i31 4187 chr3ptel1M 256914 GCCCAGGGACAGTGAGTTGCTAAATGCCTACAGTCCCACAGCTGGTACGT 256963 i i viv i vi --- i vi v i v C MIRc#SINE/MIR 122 GCTCAGAGAGGTTAAGTGACT---TGCCCAAGGTCACACAGCTAGTAAGT 76 chr3ptel1M 256964 GTCAGATGGTGAG---CGAGTCTAAGTCTTATTGGCACCCATGGTGTCC- 257009 v - vi i --- ii i i vi i v v ---- - C MIRc#SINE/MIR 75 GGCAGA-GCCGGGACTCGAACCCAGGTCTTCCTGACTCCAA----GTCCA 31 chr3ptel1M 257010 ---CTCTGTCTATTTTGCCAC 257027 --- v i i vii C MIRc#SINE/MIR 30 GTGCTCTTTCCACTGCACCAC 10 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 40.02 CpG sites = 20, Kimura (unadjusted) = 41.69 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.10 (11 / 113), avg. gap size = 1.36 (15 / 11) 22 6.46 0.00 0.00 chr3ptel1M 260244 260276 (739724) (GCAGGG)n#Simple_repeat 1 33 (0) m_b116s252i0 4188 chr3ptel1M 260244 GCAGGAGCAGGGGCAGGGGCAGGGGCAGGAGCA 260276 i i (GCAGGG)n#Sim 1 GCAGGGGCAGGGGCAGGGGCAGGGGCAGGGGCA 33 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 111 15.85 1.02 0.00 chr3ptel1M 262298 262493 (737507) (TG)n#Simple_repeat 1 198 (0) m_b116s252i1 4189 chr3ptel1M 262298 TGTGTGTGTGAGTGTGTCTGTGTATGTGAGTGTGTATATGTGTGTGTTAG 262347 v v i v i i vv (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr3ptel1M 262348 TGCGTGTGTGTGTGAGTTTGTGTGT-TGAGTGTGTGTGTTTGTGTATGAG 262396 i v v - v v i v (TG)n#Simple_ 51 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 100 chr3ptel1M 262397 TGTGTGAGTTTGAGTGTGTGAGTGTGTATGTGTGTGAGTGTCTGTGGATG 262446 v v v v i v v vi (TG)n#Simple_ 101 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 150 chr3ptel1M 262447 ACTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAGGT-TGTG 262493 vv iv - (TG)n#Simple_ 151 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 198 Matrix = Unknown Transitions / transversions = 0.40 (8/20) Gap_init rate = 0.01 (2 / 195), avg. gap size = 1.00 (2 / 2) 298 33.01 15.70 1.48 chr3ptel1M 262527 263061 (736939) C L2#LINE/L2 (228) 2854 2245 m_b116s601i0 4190 chr3ptel1M 262527 CACTGGAGGTAATTGAGCAGGGGGAGGGAGTGACACAATCAGAACTGTGC 262576 i vvv i ----- ii v vi ii i C L2#LINE/L2 2854 CATTGGAGGGTTTTGAGCAGAGG-----AGTGACATGATCTGACTTACGT 2810 chr3ptel1M 262577 CTCAGGAAGATCCC----GCTGCTG-GCTGAG--TGGA----AGGCGGCC 262615 i i ii i v ---- - i -- i ---- v v C L2#LINE/L2 2809 TTTAAAAGGATCACTCTGGCTGCTGTGTTGAGAATAGACTGNAGGGGGGC 2760 chr3ptel1M 262616 CAGAGTCCCCAGCAG-----CCAGC------GCTCCTGCGGAGCTCCTGG 262654 v i vvv- ----- i------ vi i viv v C L2#LINE/L2 2759 AAGGGTGGA-AGCAGGGAGACCAGTTAGGAGGCTATTGCAGTAATCCAGG 2711 chr3ptel1M 262655 TGTGAGAGGATGA-GGTTCAGCCCCAGGTGGGATCAGAGCAGA----GAG 262699 i v v i- i ii v vi viv v v i---- C L2#LINE/L2 2710 CGAGAGATGATGGTGGCTTGGACCAGGGTGGTGGCAGTGGAGGTGGTGAG 2661 chr3ptel1M 262700 AA--------CCCCCAGA-GCATCCTACAAAGTAAAGC-GA-AGGATTGG 262738 --------vii ii -ii ii i- i i - - v C L2#LINE/L2 2660 AAGTGGTCGGATTCTGGATATATTTTG-AAGGTAGAGCCGACAGGATTTG 2612 chr3ptel1M 262739 TCCGGGAGCCATGTGTGAGGAGAGGGTGACAAAGAG-----AAGG-TGA- 262781 iiviv iiiiivi i v v i v v i ----- - - C L2#LINE/L2 2611 CTGATGGATTGGATGTGGGGTGTGAGAGAAAGAGAGGAGTCAAGGATGAC 2562 chr3ptel1M 262782 ----AGAGTGTGAGCCTGGGGGACCGAGAGGATGTTCTCCCCGGTAAC-G 262826 ---- iv v vi i vi i ii vvv iv iv ? - C L2#LINE/L2 2561 TCCAAGGTTTTTGGCCTGAGCAACTGGAAGGATGGAGTTGCCATTNACTG 2512 chr3ptel1M 262827 GGGTGGGCA-------GAGACGAGAAAGTTTAAGGAAACA-ATAACAAGT 262868 i i v ------- i v v i i iiiv - v vi C L2#LINE/L2 2511 AGATGGGGAAGACTGCGGGAGGAGCAGGTTTGAGGGGGAAGATCAGGAGT 2462 chr3ptel1M 262869 TCAATTCTG-ATTTGCTGAGTTTCTGACAAC-ACTAGAACATCC------ 262910 i i - iv i i vv iiv - i - ------ C L2#LINE/L2 2461 TCAGTTTTGGACATGTTAAGTTTGAGATGCCTATTAGA-CATCCAAGTGG 2413 chr3ptel1M 262911 ---TGTTGG--AGGCATTTG-----CTGA---TGGAGGT--GAGCAGAGG 262945 --- i i-- v -----vi --- v -- i v C L2#LINE/L2 2412 AGATGTCGAGTAGGCAGTTGGATATACGAGTCTGGAGTTCAGGGGAGAGG 2363 chr3ptel1M 262946 TCAGGGCTGGATA-ACTAGCAGAGGAG-CATCACCATAGCGACGATGATT 262993 v v - iv iivvi - v vv i i iv C L2#LINE/L2 2362 TCCGGGCTGGAGATATAAATTTGGGAGTCATCAGCATATAGATGGTATTT 2313 chr3ptel1M 262994 GAATCCATGGGAACCGATGAGATTATCAAGTGAAATG-GCAGAGCAAGAG 263042 i v i viv i i ? - i i - iiv vv C L2#LINE/L2 2312 AAAGCCATGAGACTGGATGAGATCACCNAG-GGAGTGAGTGTAGATAGAG 2264 chr3ptel1M 263043 AAAAGAAGGGCCTCTAGGA 263061 i i vii v C L2#LINE/L2 2263 AAGAGAAGAGGTCCAAGGA 2245 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 43.94 CpG sites = 101, Kimura (unadjusted) = 45.37 Transitions / transversions = 1.38 (101/73) Gap_init rate = 0.07 (39 / 534), avg. gap size = 2.38 (93 / 39) 315 27.91 6.10 9.18 chr3ptel1M 264200 264412 (735588) C L1ME4c_3end#LINE/L1 (272) 558 352 m_b116s551i0 4191 chr3ptel1M 264200 TGCATTAATATTCCA---AGT---TTTAC---AATTTGTTTAGTCATTCC 264240 - --- --- v --- ii ii C L1ME4c_3end#L 558 TGCAT-AATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCC 510 chr3ptel1M 264241 CCAACTTATGGACATCTACTCCTCCGGCCTCTACCCTCCCAGTTTTTTGT 264290 v i vv i ------- -i v ---- i i i i C L1ME4c_3end#L 509 CCTATTGTTGGACATTTA-------GG-TTGT----TTCCAATTTTTCGC 472 chr3ptel1M 264291 TACTACAAGAAGGGCTGCTGTGGACATTTTGGCATAGATTGGGAAG--TT 264338 i i iv iv vi i i v iii v ----- -- C L1ME4c_3end#L 471 TATTATAAATAACGCTGCAATGAACATCTTCGTGCATAT-----AGCTTT 427 chr3ptel1M 264339 ACCCTTCTTTCTGGG--ATCTCCTTGAGATACATGTTTAGCAGTGGAATC 264386 vi - ii-- i ii v viii v i C L1ME4c_3end#L 426 TTCCTTCTTT-TGAATTATTTCCTTAGGATAAATTCCCAGAAGTGGAATT 378 chr3ptel1M 264387 GCTGCGTTAAGGAGTGTGGCTATTTT 264412 i v i i i i ivi C L1ME4c_3end#L 377 ACTGGGTCAAAGGGTATGAACATTTT 352 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 35.78 CpG sites = 38, Kimura (unadjusted) = 36.65 Transitions / transversions = 2.38 (38/16) Gap_init rate = 0.11 (24 / 212), avg. gap size = 1.33 (32 / 24) 242 34.98 1.82 10.34 chr3ptel1M 264221 264440 (735560) C L1ME3E_3end#LINE/L1 (464) 525 323 m_b116s551i1 4191 chr3ptel1M 264221 ACAATTTGTTTAGTCATTCCCCAACTTATGGACATCTACTCCTCCGGCCT 264270 i vi i viiiv i -------- vi C L1ME3E_3end#L 525 ACAATTTATTTATCCATTCTCCTGTCGATGGACATTT--------GGGTT 484 chr3ptel1M 264271 CTACCCTCCCAGTTTTTTGTTACTACAAGAAGGGCTGCTGTGGACATTTT 264320 v ---- i i i iv iv i i i C L1ME3E_3end#L 483 GT----TTCCAGTTTTTTGCTATTACAAACAATGCTGCTATGAACATTCT 438 chr3ptel1M 264321 GGCATAGAT----TGGGAAGTTACCCTTCTTTCTGGGATCTCCTTGAGAT 264366 v i i vi ---- ----- i v -v v v vi ii i ii ii i C L1ME3E_3end#L 437 TGTACATGTCTCCTGG-----TGCAC-ACGTGCAAGAGTTTCTCTAGGGT 394 chr3ptel1M 264367 ACATGTTTAGCAGTGGAATCGCTGCGTTAAGGAGTGTGGCTATTTTAGTC 264416 i iii v i v iivi i i vvi i --- C L1ME3E_3end#L 393 ATATACCTAGGAGTGGAATTGCTGGGTCGTAGGGTATGCGCATCT---TC 347 chr3ptel1M 264417 AGTTTCTTTACATAATTGCACATT 264440 ii ivi v vv v C L1ME3E_3end#L 346 AACTTTACTAGATAATGCCAAATT 323 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 47.25 CpG sites = 45, Kimura (unadjusted) = 49.43 Transitions / transversions = 1.88 (45/24) Gap_init rate = 0.10 (22 / 219), avg. gap size = 1.14 (25 / 22) 886 34.11 10.91 1.64 chr3ptel1M 265011 265624 (734376) C L3#LINE/CR1 (2828) 1271 602 m_b116s601i1 4192 chr3ptel1M 265011 GACATCTGAAGCCATGGGTTTTTACCCAGGGTTTCTTTCTGGGGACTGAC 265060 i ii v vvii vi v ii i? vv i vv C L3#LINE/CR1 1271 GACATCTGAGGCCATAAGTATTGTTTCTAGCTTCTTTTCCNGTTATTTTC 1222 chr3ptel1M 265061 TCCCGTGAATCTCTGGATGTCTCA---ACTGCCATTGCTCTGTCTCTATT 265107 i ? iv iiii v--- iii vi v v i i C L3#LINE/CR1 1221 TCCTGNGAATTACTGGGCACCTCCTCCACTGTTGTTCTTCTTTCTATGTC 1172 chr3ptel1M 265108 GGA----GGATCTCTCAAGGGCATTTACCT---CAATT--A-ATAGACAT 265147 iv ----?v - v vi i iiivi --- i -- -v i i C L3#LINE/CR1 1171 ATACCTGNTATC-CTCCATAGTATCCGGTTTTACAGTTTTATCTGGGCAT 1123 chr3ptel1M 265148 AGGTGATTTTCTCCTCTTC-TCATTTTTTCACAGTTTAAA--TCTCTCA- 265193 --- -- i i i - vv --- --i ii- C L3#LINE/CR1 1122 ---T--TTTTTTCCTTTCCCTCAAATTT---CAGTTTAAAGTCCTCTTGA 1081 chr3ptel1M 265194 -CAAG---ACAAG------GAAAAAC-TGCCTTTCCTCAGCTAC-TGAAG 265231 - i ---i i ------ ?v -i iii iviv v - ii C L3#LINE/CR1 1080 TCAGGTCGGCGAGTCTCCNGNCAAACACGTTCTTCCCGGTCTTCGTGAGA 1031 chr3ptel1M 265232 CATACCTTATCCCTGGCCGGGAGCCCATCCTTTGTGCACTTGAAGCTGTG 265281 iii iiii ? i v ivv i ii?v ii C L3#LINE/CR1 1030 TGCACTCCGTCCCTNGCCAGGAGCCCATCGTTCTGGTATCNTAAGCCATG 981 chr3ptel1M 265282 GCCCAGAAATCTGAAGCCTGTTCTCAGACTCCATCTTTTGGACCAGTTGT 265331 i v ii v iv v vivvii i C L3#LINE/CR1 980 GTCCAGAAAACCAAATCCTGTTCTTCGACACCATCTACGTAGCCAGCTGT 931 chr3ptel1M 265332 TCATCTCCCACCCCAGCTTTTCTCTTCTGATGCTTTG-TGTTCAATGAGT 265380 ii ivi vv i ii v iivi -iv ivi v C L3#LINE/CR1 930 TCACTTCCCATATCCTCCTTTCTCTTCCAAAGTCACGACCTTCAACTGGA 881 chr3ptel1M 265381 ACCAAGGATACAAGGGTCATCTGTGCCTCCATAGT-CTCCAGTTTCCTGA 265429 vv ii iv ivii i i - - i v C L3#LINE/CR1 880 AGAAGAGATGAAAACACCACCTGTGCCCCCA-AGTCCTTCAGTTTCCTGC 832 chr3ptel1M 265430 ACAAGATTCCACTTTCTTTCGCAATGC--------TTTCT-----CTGT- 265465 v i i i vvv vi v vi -------- ----- - C L3#LINE/CR1 831 CCAGGACTTCAAAGTCACTAGAGATGCATTCCAGGTTTCTTCTGACTGTG 782 chr3ptel1M 265466 TCCTTCGTGACCAAGGGAATCACCAGAAGTGGGAGACATCCATCTGCTTT 265515 v vv v v v i vii ivi iv v v C L3#LINE/CR1 781 TCATTCGTTCCCACGTGAATCAGCAGGAGTGGGTAGCGGTCGGCGGGTTT 732 chr3ptel1M 265516 GACAAGTATTGGGAGATTTTCTGTGGTGTTTTGTGTGCCTTCCCTGGGAA 265565 ii v v ii i i vii i i vi i viv i ii C L3#LINE/CR1 731 GATGAGTCTTGGCAGGCTCTCCGTCACGTCTCGGATACACGCTCCAGGAA 682 chr3ptel1M 265566 A--AGCA--------GGTT-----------GTCTGACAGAC-TCTTCCTC 265593 i-- -------- i ----------- - v -v iv C L3#LINE/CR1 681 GACAGCACACCTCCCGATTAGCCACGTCAGGTCTG-CATACGGCCGCCTC 633 chr3ptel1M 265594 CAGTCCCCTCAGCAGGGAGTCACCAAACACC 265624 ivvi i v C L3#LINE/CR1 632 CGTATCCCTCAGCGGGGAGTCACCAACCACC 602 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 43.18 CpG sites = 126, Kimura (unadjusted) = 48.41 Transitions / transversions = 1.57 (126/80) Gap_init rate = 0.05 (32 / 613), avg. gap size = 2.44 (78 / 32) 296 26.84 5.41 6.85 chr3ptel1M 267655 267802 (732198) L2c_3end#LINE/L2 333 478 (0) m_b116s601i2 4193 chr3ptel1M 267655 TTATGTT-TAATTACCTGTGTGAA-GT-TGTTTCTCCCAAGAGGAGGTAA 267701 i i - ii v iv?- - i ii vv ivv i L2c_3end#LINE 333 TTGTATTGTAATTGTCTGTTTACNTGTCTGTCTCCTCCACTAGACTGTGA 382 chr3ptel1M 267702 GCTCCTTGAGGACAGGGAC--TAATTTGCTCATGTCTTCATGT-GCCAGA 267748 i -- ivi ii -- ii i -v v L2c_3end#LINE 383 GCTCCTTGAGGGCAGGGACCGTGTCTTATTCA--TCTTTGTATCCCCAGC 430 chr3ptel1M 267749 GCTTAACTTAGTGGCAGGCA--CAATTCCAACATCTTCATGTTGAATGAA 267796 i ii vi - i i i-- ---- v v -- L2c_3end#LINE 431 GCCTGGCACA-TAGTAGGCGCTCAAT----AAATGTT--TGTTGAATGAA 473 chr3ptel1M 267797 TTGAAT 267802 - L2c_3end#LINE 474 -TGAAT 478 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 33.75 CpG sites = 25, Kimura (unadjusted) = 34.94 Transitions / transversions = 2.08 (25/12) Gap_init rate = 0.11 (16 / 147), avg. gap size = 1.12 (18 / 16) 268 31.24 3.06 2.02 chr3ptel1M 268699 268796 (731204) MIRc#SINE/MIR 26 124 (144) m_b116s601i3 4194 chr3ptel1M 268699 AGTATTGCACCTAGATGCAGGAAGAACCTTTGTCTTG---CTTGTCTCTG 268745 i i v i i vv - vv - i --- ii v MIRc#SINE/MIR 26 AGCACTGGACTTGGAGTCAGGAAG-ACCTGGGT-TCGAGTCCCGGCTCTG 73 chr3ptel1M 268746 ACACTCATTGGCTGTATGATCCCAGGAATGTCTTTTAATCTCTCAATGCC 268795 v i i i i i iii v v vi i viv MIRc#SINE/MIR 74 CCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCC 123 chr3ptel1M 268796 T 268796 MIRc#SINE/MIR 124 T 124 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 38.23 CpG sites = 18, Kimura (unadjusted) = 41.85 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.03 (3 / 97), avg. gap size = 1.67 (5 / 3) 333 30.67 1.55 6.50 chr3ptel1M 269289 269417 (730583) C MIRc#SINE/MIR (82) 186 64 m_b116s601i4 4195 chr3ptel1M 269289 AATAGCTCCGTGAAATGAGTTCTGCAA-TACTATCATCGC-ATTGTACAG 269336 i i i i ii ii ivvv i- i i v - v C MIRc#SINE/MIR 186 AACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAG 137 chr3ptel1M 269337 ATGAGGGAAATGAGGCTCTGAGAGACCGTCTGCATGAATTGATTAAGATT 269386 i v v --- - ivi v vii i i C MIRc#SINE/MIR 136 ATGAGGAAACTGAGGCTCAGAGAG---GT-TAAGTGACTTGCCCAAGGTC 91 chr3ptel1M 269387 ACGCAGTTAATGAGGAAGCCCCAGAGCCAGG 269417 i i i i vii---- i C MIRc#SINE/MIR 90 ACACAGCTAGTAAGTGG----CAGAGCCGGG 64 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 40.26 CpG sites = 26, Kimura (unadjusted) = 41.78 Transitions / transversions = 2.36 (26/11) Gap_init rate = 0.08 (10 / 128), avg. gap size = 1.00 (10 / 10) 289 28.37 1.49 7.94 chr3ptel1M 269301 269434 (730566) C MIR1_Amn#SINE/MIR (58) 172 47 m_b116s601i5 4195 chr3ptel1M 269301 AAATGAGTTCTGCAATACTATCATCGCATTGTACAGATGAGGGAAATGAG 269350 v v v i vi i -- v v i v C MIR1_Amn#SINE 172 AAAGGAGGTCAGTATCATTATC--CCCATTTTACAGATGAGGAAACTGAG 125 chr3ptel1M 269351 GCTCTGAGAGACCGTCTGCATGAATTGATTAAGATTACGCAGTTAATGAG 269400 ? v --- -?ivi v vii i i ? i?iii? C MIR1_Amn#SINE 124 GCNCAGAGAG---GT-NAAGTGACTTGCCCAAGGTCACNCAGCNGGCNAG 79 chr3ptel1M 269401 GAAGCCCCAGAGCCAGG--TGCGTCCAAGATCTCTC 269434 vii---- i -- ?viv v i i C MIR1_Amn#SINE 78 TGG----CAGAGCCGGGANTNGAACCCAGGTCTCCC 47 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 37.30 CpG sites = 20, Kimura (unadjusted) = 38.71 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.08 (11 / 133), avg. gap size = 1.09 (12 / 11) 283 30.48 4.44 7.63 chr3ptel1M 269327 269461 (730539) C MIR3#SINE/MIR (65) 143 13 m_b116s601i6 4195 chr3ptel1M 269327 CATTGTACAGATGAGGGAAATGAGGCTCTGAGAGACCGTCTGCA-TGAAT 269375 v i v i v i----- v - v C MIR3#SINE/MIR 143 CATTTTACAGATGAGGAAACTGAGGCCCAGAGAGG-----TGAAGTGACT 99 chr3ptel1M 269376 TGATTAAGATTACGCAGTTAATGAGGAAGCCCCAGAGCCAGG--TGCGTC 269423 vii i i i i? i v vii---- i -- iviv C MIR3#SINE/MIR 98 TGCCCAAGGTCACACAGCNAGTTAGTGG----CAGAGCCGGGACTAGAAC 53 chr3ptel1M 269424 CAAGATCTCT---CCCCTACCCTGGAATCCCTCATGCCCAG 269461 v i i--- i i vi i viv i - i C MIR3#SINE/MIR 52 CCAGGTCTCCTGACTCCCAGTCCGTGCTCTCTC-TGCTCAG 13 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 38.23 CpG sites = 24, Kimura (unadjusted) = 41.06 Transitions / transversions = 1.71 (24/14) Gap_init rate = 0.10 (13 / 134), avg. gap size = 1.23 (16 / 13) 216 26.49 7.14 1.12 chr3ptel1M 269681 269764 (730236) MamRTE1#LINE/RTE-BovB 2731 2819 (993) m_b116s601i7 4196 chr3ptel1M 269681 GGAAATTCTTCCAAATCAAT--GCTCCCAGCATCAGTC---AGTCATTTA 269725 i v i-- v v - --- v v MamRTE1#LINE/ 2731 GGAAACTCTTCCAACTCAACAGGCTACGAGCATCA-TCGAAAGTCCTTGA 2779 chr3ptel1M 269726 -ACACTTGTGAATCAGCTACTGTGTGCCAGGTCCTGTGCT 269764 - v ii vv vv i i i iivvv MamRTE1#LINE/ 2780 GACAGTCATCCAGGAACTGCTGTATGCCGATGACTGTGCT 2819 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 31.07 CpG sites = 9, Kimura (unadjusted) = 32.77 Transitions / transversions = 0.69 (9/13) Gap_init rate = 0.05 (4 / 83), avg. gap size = 1.75 (7 / 4) 360 24.31 10.71 0.81 chr3ptel1M 269715 269826 (730174) C L2a_3end#LINE/L2 (2) 515 393 m_b116s601i8 4197 chr3ptel1M 269715 TCAGTCATTTAACA----CTTGTGAATCAGCTACTGTGTGCCAGGTCCTG 269760 v i ----i i vi v iv i iv C L2a_3end#LINE 515 TCATTCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTG 466 chr3ptel1M 269761 TGCTAA--GCTGA----ACAG--ATGAAGAAAGGTGAGAAACAGTCCCTG 269802 v i-- i---- --i v ivv v - C L2a_3end#LINE 465 TTCTAGGCGCTGGGGATACAGCAGTGAACAAAACAGACAAA-AGTCCCTG 417 chr3ptel1M 269803 CTTTCATGGAGCTTGGATCCTTGT 269826 ii iv i v C L2a_3end#LINE 416 CCCTCATGGAGCTTACATTCTAGT 393 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 28.57 CpG sites = 15, Kimura (unadjusted) = 29.86 Transitions / transversions = 1.25 (15/12) Gap_init rate = 0.05 (5 / 111), avg. gap size = 2.60 (13 / 5) 398 27.89 6.15 0.73 chr3ptel1M 270203 270332 (729668) L2a_3end#LINE/L2 373 509 (8) m_b116s601i9 4198 chr3ptel1M 270203 TTCAGTGTGTTGTTCCCCACCATTTGTTTGTAAGTTCCTGGAAGGCAGGG 270252 i v -i ii v i v vv i vv i L2a_3end#LINE 373 TTTATTGT-CTGTCTCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGG 421 chr3ptel1M 270253 TCTTT-GTTTGTATT------TATTGAACTCGCAGTGCTTTAAACAAGAC 270295 v - i v ------ ii v ii v i i vi ivi L2a_3end#LINE 422 ACTTTTGTCTGTTTTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGC 471 chr3ptel1M 270296 CTGGGACATAGAAGGTGCTTAATAAATACTT-TTGGAT 270332 v v i i i - i L2a_3end#LINE 472 CTGGCACATAGTAGGCGCTCAATAAATATTTGTTGAAT 509 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 33.34 CpG sites = 21, Kimura (unadjusted) = 35.77 Transitions / transversions = 1.40 (21/15) Gap_init rate = 0.03 (4 / 129), avg. gap size = 2.25 (9 / 4) 198 36.06 7.42 2.01 chr3ptel1M 270342 270624 (729376) C L2d2_3end#LINE/L2 (244) 311 14 m_b116s601i10 4199 chr3ptel1M 270342 TACAGGCTATA----TTGGAGAAAATCATCAGAGGGA-AGATC--TA-GC 270383 i v ----i iv i iv vvi - -- ?- v C L2d2_3end#LIN 311 TACAGACAATAANTGCTATAGGAGTTCAGAGGAGGGAGAGATCACTNCGG 262 chr3ptel1M 270384 ATTAAGGGGGGCTGGAAAAAGCTTCTTGTAGAAAGTGGAATTTTGGTTG- 270432 ii i- i v iii ii i vi v i i ? vi i - C L2d2_3end#LIN 261 GCTG-GAGTGGTCAGGGAAGGCTTCACGGAGGAGGTGGNATTTGAGCTGG 213 chr3ptel1M 270433 -CCAACTAAATCCAGATCAATCAG---TGG-T-GGTAGAAAGGGAGGAG- 270475 - --i i ---i vii vi --- - - i i i i - C L2d2_3end#LIN 212 GCC--TTGAA---GGATGGGTAGGATTTGGATAGGTGGAGAGGAAGGGGA 168 chr3ptel1M 270476 -GAGCATTCCAGGCTGGGGTTTTTTTA-GAG-AAACCCCCAGAGTCAGGA 270522 - i v vvvivvii- - vv v v i C L2d2_3end#LIN 167 AGGGCATTCCAGGCGGGGGGAACGGCGTGAGCAAAGGCGCAGAGGCGGGA 118 chr3ptel1M 270523 GATGGAGAGTCTCATATGAAGAAGAGCAAGAGGATCA--TTCACTGGACT 270570 i?vv vi v vii vi ii i v ii vi i -- vi vi C L2d2_3end#LIN 117 ANGCGCAAGGCGTGTTCGGGGGACAGTGAGTAGACCAGTTTGGCTGGAGC 68 chr3ptel1M 270571 GAAGAGTACGTGCAGGGGTGTGAGGTGTGAGAATACTGGAAAAGTGTGTG 270620 i i v ? vi iiv v v v vi i ?iv v C L2d2_3end#LIN 67 GGAGGGTTCGTGNAGGGGAATAGTGGGAGATAAGGCTGGAAAGGNAGGTT 18 chr3ptel1M 270621 AGGG 270624 i C L2d2_3end#LIN 17 GGGG 14 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 48.25 CpG sites = 59, Kimura (unadjusted) = 52.89 Transitions / transversions = 1.44 (59/41) Gap_init rate = 0.07 (19 / 282), avg. gap size = 1.42 (27 / 19) 319 29.80 6.12 9.92 chr3ptel1M 270908 271544 (728456) C L2-1_AMi#LINE/L2 (597) 638 24 m_b116s551i2 4200 chr3ptel1M 270908 TGGAGAGTGG---GAGTGAGAGATAACTCCTAGGTTGTGAACCTGAGGGA 270954 i v --- vii i v i ii ii v C L2-1_AMi#LINE 638 TAGAGAGAGGTCCGAGTCGAAGATGACGCCCAGGTTACGGGCCTGAGTGA 589 chr3ptel1M 270955 CTAGGAGGCTATTGTTGTTCTCTACAATGAC--AGGGGAGGTAAGATGGG 271002 vi v v iv v v i i i-- iii v vi- C L2-1_AMi#LINE 588 CAGGCAGGATGGTGGTGTTGTCCACAGTGATCGAGAAAAGGGAATG-GGG 540 chr3ptel1M 271003 AGAGGG--TGGTTAGGGAAAGAT---GAGTTCAGTTTTGG--CATGCTGA 271045 ?i -- --- i --- i v i -- i C L2-1_AMi#LINE 539 AGNAGGCTTGG---GGGGAAGATTAAGAGCTCTGTTTTAGGCCATGTTGA 493 chr3ptel1M 271046 GCTTGA---GAAATCTATAGGACACCCTCTGTGAGATGTCCAATGGGCA- 271091 --- viv --- i v viv vi vi i - C L2-1_AMi#LINE 492 GCTTGAGCTGACGGCTA---GACATCCACGAGGAGATGTCAGAGAGACAG 446 chr3ptel1M 271092 GCTGGAGTCTAAACCCGGAGGTCAACCAAGAGGTTAGAACTAGATAAGTA 271141 i iii i v iiii vivv ivvi v iv i v v i C L2-1_AMi#LINE 445 GCCGAGATTTTAGTTTGGACAGAAGGAGACAGGTCTGGAGTAGAGAGGTA 396 chr3ptel1M 271142 GAT-TGAGAACCATCATCGTAGAGAAGACAAATGAATCCATGGGAGCCAA 271190 - v ii ------- v v ii iv iii vvv vi C L2-1_AMi#LINE 395 GATCTGTGAGTCA-------ACAGATGGTAGTTGAATTTGTGTTTGCGGA 353 chr3ptel1M 271191 TGAGATCACCAAGGAAGGTAGGATGGTGAAAGAAGAAAAGAGGTCC-ATG 271239 i v -- i i i vv i i i v - v C L2-1_AMi#LINE 352 TGAGATTACCCAG--AGATAAGGTGTAGAGAGAAGAGAAGGGGACCAAGG 305 chr3ptel1M 271240 ATAGAA-CTTGAAGGACACTCAGGGTTAAAGGGCATGATCTGGAGGAGGA 271288 i i- i vi i v i vi -- v -------- ---- C L2-1_AMi#LINE 304 ACAGAGCCCTGTGGAACCCCCACAG--AAAGTG--------GGAGG---- 269 chr3ptel1M 271289 TACAACAAGGGAG-ACAGAGAAGGAGTGATCAGAGGGGGAGAAGGAGAAA 271337 ------ i - iv vv i i i v i -- C L2-1_AMi#LINE 268 ------AAGGAAGAATTGCCAAGGAGCGATTAGAGAGGTAGGAGGAG--A 227 chr3ptel1M 271338 CAGAAGA-AGAGAGTTGTCTTAGAAATCTAGAGAG-----------AAGG 271375 i i - ----- vii ii v i ----------- i C L2-1_AMi#LINE 226 CGGAGGACAGA-----GTCACGGAAGCCAAGGGAGGACAAGATTTCAAGA 182 chr3ptel1M 271376 AG---GTGATCCATAGTGTCAAGGGCTGGC--ACAGGTCTAGGA-AATGA 271419 ---i i v iv i - -- v -i C L2-1_AMi#LINE 181 AGAGCATGGTCGACTGTGTCAAAGGC-GGCTGACAGGTCAAGGAGGATGA 133 chr3ptel1M 271420 GGACTGAGAAAAGGCTGCTG-GGTTTGGCAATGAAGAGATCATAAGGAAC 271468 iv v vv i - - i v v i v ii C L2-1_AMi#LINE 132 GGATGGAGTACTGGTT-CTGAGATTTGGCTAGGAAGAGGTCATTAGAGAC 84 chr3ptel1M 271469 TTGGGAGAGGGCAGTTTTGGTGGAATGGTGAGGTCAGACTGGTTAAGAAA 271518 viv v ---- - ii vv --i vv vv --- i C L2-1_AMi#LINE 83 GCTGCA----GCAG-TTCAGTGGACAG--AAGGAAAGAAAGG---AGAGA 44 chr3ptel1M 271519 GCTGAAGGAAAGAAAGTGGAAGCAGC 271544 i ? ------ i ? C L2-1_AMi#LINE 43 GTTGNAG------AGGNGGAAGCAGC 24 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 37.02 CpG sites = 99, Kimura (unadjusted) = 39.09 Transitions / transversions = 1.38 (99/72) Gap_init rate = 0.12 (78 / 636), avg. gap size = 1.28 (100 / 78) 328 33.56 10.15 2.68 chr3ptel1M 271673 272263 (727737) C L2#LINE/L2 (1348) 1734 1101 m_b116s601i11 4199 chr3ptel1M 271673 TGAGATAGGAGTGAGAGAGCGGATAATCTGTTGGA------------AG- 271709 vii -- v v - i ------------ - C L2#LINE/L2 1734 TGATGCAGGAG--AGAGAGGGGAGAAT-TGCTGGAGCGATGTCCTTGAGT 1688 chr3ptel1M 271710 AGACGGGATGGAGGGGAATCACTTGTGTCGGTAGAGGATTTTGCCTCAAC 271759 i i v iiv i vvv iiivi i iv v i iv C L2#LINE/L2 1687 AGGCGAGAGGGGATGGGATCTAGTGCACAAGTGGAGGGGTTGGCCTTAGA 1638 chr3ptel1M 271760 AAGGAGAAAGGCCACCTC-TTCATGGGAGAAGGAG--AAGACAG------ 271800 v v v v vi - i i i v iv -- i ------ C L2#LINE/L2 1637 TAGGAGCACGGACAGTTCATCCGTAGTAACAGGAGGGAAGGCAGAGTATG 1588 chr3ptel1M 271801 TGG-CA-GGAGACATCTACCTGTG-AGATGAGGGGGAGAGGAGAAAG--- 271844 - -i vi vv vv v - v v v - ??v --- C L2#LINE/L2 1587 TGGGCACAGATGCAGGTAGGTGGGTAGATGTGGTGGTG-GGAGNNTGTGG 1539 chr3ptel1M 271845 -AGCTCTCAGCAAATGGCCTCCATTTTTTTCTGTGAAATATGAGGCCAGG 271893 - i vv vi v i i i - v v i v C L2#LINE/L2 1538 AAGTTCTCTTCTGATTGCTTCTATTTTCT-CAGTGAAATAGGAAGCAAGG 1490 chr3ptel1M 271894 TACAT-AGCTTAGAGAGTGGGGA----GGGGGAGCCATTGGAGGGCTAAG 271938 - - -- i ---- i vii vi i C L2#LINE/L2 1489 T-CATCAGCT--GAGAGTGAGGATAGGGGAGGAGGTGTTGGAGGTTTGAG 1443 chr3ptel1M 271939 AAGAGATGAGGTTTGTTTGGAACAGCTGCTGTGGAGACTGGGATAGTGAG 271988 i v i-vv v i i ii iivv v v i C L2#LINE/L2 1442 GAGAGAGGAGA-AGGTGTGAAATAGTCGTCTAGGAGAGTGGGAGAGTGAA 1394 chr3ptel1M 271989 C-CAGTAAAGGCTTGTAAAAGGATGGTTTTGTCATACTTGGGGTTCAGCG 272037 i-v v ii ivv iv ? v iivv ivii i vi ii viv C L2#LINE/L2 1393 TGGACTAGGGAAATGTAGTANGATTGCCGGGCAGCATTAAGGGCCCACTT 1344 chr3ptel1M 272038 GAGACTG--AGTAAGGTAAACTTGTGCTGGATATGCTCCGGATAGCTTCA 272085 ii ?--i v -- i i iviv iivviiv v v i i vii C L2#LINE/L2 1343 GAGGTTNGTGGTCA--TGAATTTAAAGTGAGACCAGTCAGCATGGTTGTG 1296 chr3ptel1M 272086 TGGTTTTTCCCA-CCTTGCTCAGCAATAAGTGGGTGAGAG---GGA--AG 272129 v ii - vi i -- iv?i vii --- -- C L2#LINE/L2 1295 TGTTTTTCTCCAGCCACGTTCAGC--TGCNCGGGTGCAGGCGCGGAGTAG 1248 chr3ptel1M 272130 GCAGCGAGTGGTGGCAGTGACCCATGGCTGAGACTTAGCTGGGCAAG-A- 272177 i v -- - v v v v i ? ii v ii i - - C L2#LINE/L2 1247 GCGGAGAGT--TGG-ATTTAACCAGGGTTGNGGTTTTGCCAGGCGAGTAC 1201 chr3ptel1M 272178 GTCGTGACAGGATAAGGAGCAAGGGATTCAAGAG-------AAGAGGGCA 272220 v vii ii -i i v ii i ------- i i ii C L2#LINE/L2 1200 GACGAAGCGAGA-GAGGGGCAAGGGAGTTGAGGGTATATGCAAGGGAGTG 1152 chr3ptel1M 272221 --TGTGAAGCTGAAC--TGGAGTC-AAGGTGGG---GAAGGGAAAGGAGG 272262 -- i i v v ?i -- i - v --- i iv C L2#LINE/L2 1151 ATTATAATGATNGACCATGGAATCTAAGCTGGGTAAGGAGGGAAGTGAGG 1102 chr3ptel1M 272263 A 272263 C L2#LINE/L2 1101 A 1101 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 44.17 CpG sites = 109, Kimura (unadjusted) = 46.82 Transitions / transversions = 1.30 (109/84) Gap_init rate = 0.07 (41 / 590), avg. gap size = 1.88 (77 / 41) 181 32.24 0.00 5.36 chr3ptel1M 273421 273479 (726521) L2c_3end#LINE/L2 350 405 (73) m_b116s601i12 4201 chr3ptel1M 273421 GTTTATGTGCAAACTGTCTCTTCTATCCAGTTGTCAGATCCCCGAGGTCA 273470 i? i--- i i iiviii v v ii v L2c_3end#LINE 350 GTTTACNTGT---CTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCA 396 chr3ptel1M 273471 GAGATCATG 273479 i i i L2c_3end#LINE 397 GGGACCGTG 405 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 43.75 CpG sites = 14, Kimura (unadjusted) = 47.52 Transitions / transversions = 3.50 (14/4) Gap_init rate = 0.05 (3 / 58), avg. gap size = 1.00 (3 / 3) 556 32.16 2.99 1.69 chr3ptel1M 273508 273741 (726259) L3b_3end#LINE/CR1 376 612 (594) m_b116s601i13 4202 chr3ptel1M 273508 CTGAAAAAATCTTTCTTGACTTGAATTTTTGATTGAGTTGAATGAGAGGA 273557 ii vi ivviv v iv?iv iii i?iv ii v L3b_3end#LINE 376 CCAAAACGATCTCGACAGACTAGAACGNCGGGCCGAANCCAACAAGATGA 425 chr3ptel1M 273558 AATTGAGTAGGGACATACATGTTAAATATTAACA-TTGGGT--AATATCA 273604 v ii -- v i v i vi i- - -- v vv? L3b_3end#LINE 426 AATTCAACAGGGA--TAAACGTAAAGTCCTG-CACTTGGGTTCAAAAAAN 472 chr3ptel1M 273605 CATTC---CAGGGACAATATGAGGGAGCCACGGCAAGACAGCAGTAAATT 273651 v --- ii v iv i v i vvii i?v v L3b_3end#LINE 473 CAATCGCGCGAGTACAGGATGGGGGAGACGCGGCTTAGCAGCAGCNCATG 522 chr3ptel1M 273652 TGAAAAAGATCTGAGGG-TTTAGGTGAGCCACAAGCTCAACACAAGTCAA 273700 i i - v - i i ii i L3b_3end#LINE 523 TGAAAAAGACCTGGGGGTTTTAGTTGA-CCGCAAGCTCAATATGAGTCAG 571 chr3ptel1M 273701 TACCCTGACGTGGCTGCCCAGAAAGCCAAAGAGCTCATGAG 273741 i vivi i v i i v v v v i L3b_3end#LINE 572 CAGTGCGACGCGGCTGCCAAAAAAGCTAATGCGATCTTGGG 612 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 36.05 CpG sites = 42, Kimura (unadjusted) = 44.33 Transitions / transversions = 1.31 (42/32) Gap_init rate = 0.03 (8 / 233), avg. gap size = 1.38 (11 / 8) 14 13.12 0.00 0.00 chr3ptel1M 273812 273837 (726163) (GAGG)n#Simple_repeat 1 26 (0) m_b116s252i2 4203 chr3ptel1M 273812 GAGGGAGGAAAAGAGGGAGGGAGGGA 273837 i ii (GAGG)n#Simpl 1 GAGGGAGGGAGGGAGGGAGGGAGGGA 26 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 35 14.35 4.05 1.32 chr3ptel1M 274293 274366 (725634) (CTC)n#Simple_repeat 1 76 (0) m_b116s252i3 4204 chr3ptel1M 274293 CTCCTCCTCCTCTTCCTCCTCCTTCTCTTTTTCCTTCT-CTCCTTTTCCT 274341 i i i ii i - ii (CTC)n#Simple 1 CTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT 50 chr3ptel1M 274342 -CTCCTCCTCC-CCTCTTTCCTCCTCC 274366 - - -i (CTC)n#Simple 51 CCTCCTCCTCCTCCTC-CTCCTCCTCC 76 Matrix = Unknown Transitions / transversions = 1.00 (9/0) Gap_init rate = 0.05 (4 / 73), avg. gap size = 1.00 (4 / 4) 425 34.78 2.46 2.83 chr3ptel1M 274811 275094 (724906) C L3#LINE/CR1 (685) 3414 3132 m_b116s601i14 4205 chr3ptel1M 274811 CTGCTGCAGAGCACCAGCTATCC-CTCCGTCCC-TATCGGAGAAGTTGGT 274858 vi -- -- - i i- iiv v v i C L3#LINE/CR1 3414 CTGCTGCTAAGC--CAG--ATCCTCTCCATCCTGTACTTGTGCAGTTGAT 3369 chr3ptel1M 274859 TGGG-GAGCCCATATGTTAAGATTTTCTCTCAGTTTCTGTTTAATTGAGT 274907 vvv- i i v i- i i viv ivi ii v vvi C L3#LINE/CR1 3368 TTTTTGAACCTAAATGC-AGGACTTTACATTTATCCCTGTTAAATTTCAT 3320 chr3ptel1M 274908 CTTAGTAGGATTGGCCCGAAAATGTTCTAGACTCTCAAGAAAATGT-GGC 274956 iv i vv i --- vi i v v i vv? v - iv C L3#LINE/CR1 3319 CTTGTTGGTTTCGGCCC---ATCGTTCCAGCCTGTCGAGATCNTTTTGAA 3273 chr3ptel1M 274957 TGCCGGGTCTGTTATA-ACCACGTGGGGTTTTCTCGGTAGTTTAGCGTCA 275005 vii iv i v- ? iii vi v v i iivvi i v i C L3#LINE/CR1 3272 TCTTGATTCTGTCATCCANCGTATTAGCTATCCCTCCCAGCTTTGTGTCA 3223 chr3ptel1M 275006 TTTGCAAATTAGGGAAGCGTGCCGTCTCTGCCTT-ATCAAAGTCACTGAT 275054 i v iv i v v i - v i C L3#LINE/CR1 3222 TCTGCAAATTTGATAAGCATGCCTTCTATGTCTTCATCCAAGTCATTGAT 3173 chr3ptel1M 275055 CAAGCC-CGGAACGGCTCAGCTCCAAGCACGGATCCCTGCG 275094 v ivi-iv i vv vv v i v i C L3#LINE/CR1 3172 AAAAATGTTGAACAGGACAGGGCCAAGGACAGAGCCCTGTG 3132 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 45.45 CpG sites = 49, Kimura (unadjusted) = 48.17 Transitions / transversions = 1.04 (49/47) Gap_init rate = 0.05 (15 / 283), avg. gap size = 1.00 (15 / 15) 494 23.62 3.91 0.76 chr3ptel1M 276485 276612 (723388) MIR3#SINE/MIR 9 140 (68) m_b116s601i15 4206 chr3ptel1M 276485 GCAGCT-AGCAGCACCAAGTACCAGCTTGGAGTCAGAGGACCCGAGTTCA 276533 ii - - vvi i vii v ii i i v MIR3#SINE/MIR 9 GTGGCTGAGCAG-AGAGAGCACGGACTGGGAGTCAGGAGACCTGGGTTCT 57 chr3ptel1M 276534 AATCCTGCCTCAGACACTTCTTAGCTGTGTGAC--TGTACAAGTCACCTC 276581 i i v v v vvi ? -- vi i MIR3#SINE/MIR 58 AGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTC 107 chr3ptel1M 276582 ACTTGTCT--GCCTCAGTTTCCTCCCCTGTAAA 276612 i v -- vi MIR3#SINE/MIR 108 ACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAA 140 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 27.99 CpG sites = 17, Kimura (unadjusted) = 29.12 Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.03 (4 / 127), avg. gap size = 1.50 (6 / 4) 505 20.14 10.37 0.68 chr3ptel1M 276501 276635 (723365) MIRb#SINE/MIR 29 176 (92) m_b116s601i17 4206 chr3ptel1M 276501 AGTACCAGCTT-GGAGTCAGA-GGACCCGAGTTCAAATCCTGCCTCAGAC 276548 i vi - -i i i i i v v v MIRb#SINE/MIR 29 AGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTCTGCC 78 chr3ptel1M 276549 ACTTCTTAGCTGTGTGAC--TGTACAAGTCACCTCACTTGTCT--GCCTC 276594 vi -- vi i i v i v -- MIRb#SINE/MIR 79 ACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTC 128 chr3ptel1M 276595 AGTTTCCTCCCCTGTAA-------ATAAT-ACACTTCCCTCCTGAGGGT 276635 vi ------- - i i v vi- MIRb#SINE/MIR 129 AGTTTCCTCATCTGTAAAATGGGGATAATAATACCTACCTCGC-AGGGT 176 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 21.89 CpG sites = 16, Kimura (unadjusted) = 23.83 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.05 (7 / 134), avg. gap size = 2.14 (15 / 7) 521 19.64 5.36 0.00 chr3ptel1M 276501 276612 (723388) MIRc#SINE/MIR 26 143 (125) m_b116s601i16 4206 chr3ptel1M 276501 AGTACCAG-CTTGGAGTCAG-AGGACCCGAGTTCAAATCCTGCCTCAGAC 276548 i ii - - i i i i i i v v v MIRc#SINE/MIR 26 AGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCC 75 chr3ptel1M 276549 ACTTCTTAGCTGTGTGAC--TGTACAAGTCACCTCACTTGTCT--GCCTC 276594 vi -- vi i v i v -- MIRc#SINE/MIR 76 ACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTC 125 chr3ptel1M 276595 AGTTTCCTCCCCTGTAAA 276612 vi MIRc#SINE/MIR 126 AGTTTCCTCATCTGTAAA 143 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 20.93 CpG sites = 14, Kimura (unadjusted) = 23.24 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.04 (4 / 111), avg. gap size = 1.50 (6 / 4) 262 37.00 2.33 1.54 chr3ptel1M 278273 278401 (721599) C L3#LINE/CR1 (452) 3647 3518 m_b116s601i18 4207 chr3ptel1M 278273 GTTCCCATTTGTCTGTGGTTCCCTTAAAAGATG-CACTCATTCCTGAAGA 278321 i vi vi vii i vi - i i vvv vi C L3#LINE/CR1 3647 GCTCCAGTTTGTCAATGTCCCTCTTAAAATGTGGCGCCCAGAACTGAACG 3598 chr3ptel1M 278322 TGGCTTTCCAGATGCTTTCTGGCCAGGGGAAAGGGT--CAGAATGCCATG 278369 iiiivi ivv i v v i vii-- i i -- i v C L3#LINE/CR1 3597 CAATACTCCAGATGTGGTCTGACCAGCGCAGAGTACAGCGGGA--CTATT 3550 chr3ptel1M 278370 GCCTCTTTTTGTCTGGATAATGAATTTCTATT 278401 i ii v? i v iv i C L3#LINE/CR1 3549 ACCTCCCTTGNTCTGGACACTATACTTCTATT 3518 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 49.50 CpG sites = 29, Kimura (unadjusted) = 54.62 Transitions / transversions = 1.61 (29/18) Gap_init rate = 0.03 (4 / 128), avg. gap size = 1.25 (5 / 4) 12 17.10 0.00 5.71 chr3ptel1M 280615 280651 (719349) (CAATAA)n#Simple_repeat 1 35 (0) m_b116s252i4 4208 chr3ptel1M 280615 CAAAAAGCAATAACAATTACAAAAAAAGATAAAAATA 280651 v - v v v - v (CAATAA)n#Sim 1 CAATAA-CAATAACAATAACAATAACA-ATAACAATA 35 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 13 15.16 11.76 0.00 chr3ptel1M 282214 282264 (717736) (ATAAGT)n#Simple_repeat 1 57 (0) m_b116s252i5 4209 chr3ptel1M 282214 ATATGT-TAAGT-TAA--ATATGTTAAAGTATAAGT-TAAATACAA-TAT 282257 v - - -- v vv - i i - (ATAAGT)n#Sim 1 ATAAGTATAAGTATAAGTATAAGTATAAGTATAAGTATAAGTATAAGTAT 50 chr3ptel1M 282258 ATGTATA 282264 v (ATAAGT)n#Sim 51 AAGTATA 57 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.10 (5 / 50), avg. gap size = 1.20 (6 / 5) 354 32.87 1.39 2.82 chr3ptel1M 285891 286034 (713966) C X17_LINE#LINE/CR1 (152) 144 3 m_b116s601i19 4210 chr3ptel1M 285891 TGGGAGGA-AACTTTACC-TCAAATAAGTCTCAAAGACAGGAAGTCCTTC 285938 ?v- i ii v- v ii ivv vi i ii C X17_LINE#LINE 144 TGGGAGNTTAATTCCACAGTCTAATAGATCTCGCTGTTAGGAAATTTTTC 95 chr3ptel1M 285939 CTGACATCCAGTCTAAATGTTCTTCTCCTTGCCTTCTCCCCACTGCTCTT 285988 i i i v i i v iivi vi i i i C X17_LINE#LINE 94 CTGATATTCAGCCTAAATTTTCCTTTGCTCAATTTCATCCCATTACTCCT 45 chr3ptel1M 285989 AGTTCCGCCATCTGGGGCCAAGCAAAGCAAGACCAATTCCTTTTCC 286034 vii vi v i ?v v ii v---- i i C X17_LINE#LINE 44 AGTTATACCCCCTTGGACCANCCTAAATAAT----ATCCCTTCTCC 3 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 45.17 CpG sites = 30, Kimura (unadjusted) = 46.60 Transitions / transversions = 1.88 (30/16) Gap_init rate = 0.04 (6 / 143), avg. gap size = 1.00 (6 / 6) 1081 29.35 8.70 4.08 chr3ptel1M 285927 286466 (713534) C L3#LINE/CR1 (193) 3906 3343 m_b116s601i20 4210 chr3ptel1M 285927 AGGAAGTCCTTCCTGACATCCAGTCTAAATGTTCTTCTCCTTGCCTTCTC 285976 i i v i iv i v v v i i iv iv iv C L3#LINE/CR1 3906 AGAAAGTTCTTCCTTATATTGAGCCGAAATCTGCCTCCCTGTAACTTCCA 3857 chr3ptel1M 285977 CCCACTGCTCTTAGTTCCGCCATCTGGGGCCAAGCAAAGCAAGACCAATT 286026 i v i i v i vi i ii v i i C L3#LINE/CR1 3856 CCCATTGGTCCTAGTTCTGCCCTCTGGAGCCACACAGAATAAGTCTAATC 3807 chr3ptel1M 286027 CCTTTTCCACATGGTCGTTCTTC----ATGTG--------TCCCA---CT 286061 i iiv ii ---- v -------- vi --- C L3#LINE/CR1 3806 CCTCTTCCACATGACAGCCCTTCAAATATTTGAAGACAGCTATCATGTCT 3757 chr3ptel1M 286062 GCTCCATGCCTTTTCTTCGCTGGGATAAACATTCCCTAGTTCTTTCAA-- 286109 v i v i i v ii v - i i -- C L3#LINE/CR1 3756 CCTCTAAGTCTTCTCTTCTCCAGGCTAAACA-TCCCCAGTTCCTTCAACC 3708 chr3ptel1M 286110 -----TCATATGGCAAAAACACAATACTCTTCACCCTGCTG---GCTCCC 286151 ----- i viiviv v v i v v --- i C L3#LINE/CR1 3707 GTTCCTCATATGACATGGTTTCCAGACCCTTCACCATCCTGGTCGCTCTC 3658 chr3ptel1M 286152 ACACTCTAGATACTCTCCAGTTGTCCAATGATTTTGGTCAAATCTGGCTC 286201 --- i ii v vvi viii vv v v v C L3#LINE/CR1 3657 ---CTCTGGACGCGCTCCAGTTTGTCAATGTCCCTCTTAAAATGTGGCGC 3611 chr3ptel1M 286202 CCAGAACTTGA--TAACACTCCTGAAACTGAATGGTCATGGATCAGTTTG 286249 vi --i i v --- -- --v i ivii C L3#LINE/CR1 3610 CCAGAACTGAACGCAATACTCCAGA---TG--TGGTC--TGACCAGCGCA 3568 chr3ptel1M 286250 AA-------GGGATGAT--CCTCTCCTTATTCCTGGCCATT---TTTCT- 286286 i ------- iv -- - i? - v i ---i - C L3#LINE/CR1 3567 GAGTACAGCGGGACTATTACCTC-CCTTGNT-CTGGACACTATACTTCTA 3520 chr3ptel1M 286287 CCAATTCAGCCTTGGATCTCATCCAATTTCTTAG-ATGCAAATCACATCA 286335 ii v vi iv iviv i i - vv v iii C L3#LINE/CR1 3519 TTAATGCAGCCTAAGATTGCATTAGCTTTTTTGGCAGCCACATCACACTG 3470 chr3ptel1M 286336 TTGACTCATGTTGATCTTGAAGTCAACCCAAATTCCTTAATATTTTCTGA 286385 i i v vi iv ii vii v iiiv C L3#LINE/CR1 3469 TTGGCTCATATTGAGCTTGCGGTCAACTAAAACCCCTAGGTCTTTTTCAC 3420 chr3ptel1M 286386 AACAATTGCTATCTAAACATAGCAAA-CCCCT-AATCTTATACTTTTGAA 286433 ivv i i- i ---- i - i -v i i v v C L3#LINE/CR1 3419 GTGAACTGCTG-CTAAGC----CAGATCCTCTCCATCCTGTACTTGTGCA 3375 chr3ptel1M 286434 GTTG--TTTTAGAATCTATAGGTAATGTAG--TTTTA 286466 -- v i ----- i --i C L3#LINE/CR1 3374 GTTGATTTTTTGAACCTA-----AATGCAGGACTTTA 3343 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 37.24 CpG sites = 91, Kimura (unadjusted) = 38.58 Transitions / transversions = 1.49 (91/61) Gap_init rate = 0.07 (39 / 539), avg. gap size = 1.79 (70 / 39) 345 37.47 2.93 3.48 chr3ptel1M 286581 286956 (713044) C CR1-3_Croc#LINE/CR1 (1320) 2285 1912 m_b116s551i3 4211 chr3ptel1M 286581 GCTTTTGA--CTATAAAGATCTCTTTGAATTCTGA--CCATCAT--ATTA 286624 iv -- i vi ii i vi v--? i v -- vii C CR1-3_Croc#LI 2285 GCTTTCCAATCTGTCGAGATCCTTCTGAATTGCGCTCNCGTCCTCCAACG 2236 chr3ptel1M 286625 TGTTAGCTGTTCATGTCACCTTTGTGTAACCTGCAAGTCTGATAACCACG 286674 v vi i v vi vi i vii iii v v vv v C CR1-3_Croc#LI 2235 TGTTCGCAATCCTTCCCAGTTTCGTGTCGTCTGCAAACTTGCTCAAGAAG 2186 chr3ptel1M 286675 CCACTTCTGTCATTATCCAAATTATTTGTAAAAGTGTTTTTTTTTAAAAA 286724 ivii v i vi i vi vii ------------ C CR1-3_Croc#LI 2185 CTTTCTATGCCAGCATCCAAATCATTAATAAACACGTT------------ 2148 chr3ptel1M 286725 AAATTACATAGTACCAAGCATATATCTCTGAAGTATTTCACT-GAAGATT 286773 i ivi iv vi v v i v i i vi v i i - ivi C CR1-3_Croc#LI 2147 GAACAGCACCGGGCCCAGGACAGACCCCTGTGGGACTCCACTCGAAACCT 2098 chr3ptel1M 286774 TCTTCAAATTTGACATTGCACCAGTAATGATTATTTTTTCGATCCAGCTA 286823 i v v v i v vv iv i iii vvv v i C CR1-3_Croc#LI 2097 CCTGCCATTCTGACATGGACCCGTTAATAATTACCCTTTGCTTGCGGCTA 2048 chr3ptel1M 286824 CCAA-CCAGGTATGGATAGACAGCTGTATTA---TCATCCAGCCTTCATT 286869 iii - v vv vv v-i v --- ii iv C CR1-3_Croc#LI 2047 TTGAGCCAGTTATCTATCCACC-TTGTAGTAGTTTTGTCCAGCCCACATT 1999 chr3ptel1M 286870 TCTTCCTCTTTTCTTTAAGAACATCAGGACATATTCTGTCAAATGCTTTG 286919 i vvi v i v i vi v vviv iii v i C CR1-3_Croc#LI 1998 TCTCCAATTTGTTTATGAGAAGGTCATGCGGGACCTTGTCAAAAGCCTTG 1949 chr3ptel1M 286920 CTGAAATCTGGACAAACTATATTTATAGCATTCTCTT 286956 i ii i v ii i i C CR1-3_Croc#LI 1948 CTGAAGTCCAGATACACTATATCCACAGCATTCCCTT 1912 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 48.84 CpG sites = 75, Kimura (unadjusted) = 53.99 Transitions / transversions = 1.23 (75/61) Gap_init rate = 0.05 (19 / 375), avg. gap size = 1.26 (24 / 19) 185 30.00 15.00 0.00 chr3ptel1M 286960 287019 (712981) C L3#LINE/CR1 (1208) 2891 2823 m_b116s601i21 4210 chr3ptel1M 286960 TAAGGTTAATCTGGTGTGACCTATTCTCAACGAAGAAAGGCTG------- 287002 i i i ii i i i ii vvv v ------- C L3#LINE/CR1 2891 TGAGGTTAGTTTGGCATGACTTGTTCTTAGTGAACCCATGCTGGCTCCTA 2842 chr3ptel1M 287003 --GATCATTGTGTCCTTTT 287019 -- ii iv C L3#LINE/CR1 2841 GTGATCACCGCTTCCTTTT 2823 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 37.90 CpG sites = 13, Kimura (unadjusted) = 40.91 Transitions / transversions = 2.60 (13/5) Gap_init rate = 0.03 (2 / 59), avg. gap size = 4.50 (9 / 2) 15 24.54 0.00 0.00 chr3ptel1M 287192 287234 (712766) (TTTGT)n#Simple_repeat 1 43 (0) m_b116s252i6 4212 chr3ptel1M 287192 TTGGTTTTCTTTTGTTCTCTATTATATTTTTTTATTTTGTTTT 287234 v v i v v i v v i (TTTGT)n#Simp 1 TTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTT 43 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 34 10.48 0.00 0.00 chr3ptel1M 287294 287345 (712655) (AT)n#Simple_repeat 1 52 (0) c_b116s251i0 4213 chr3ptel1M 287294 ATATATATATATATATATATATATATACATACATACATATATGGATATAT 287343 i i i iv (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr3ptel1M 287344 AT 287345 (AT)n#Simple_ 51 AT 52 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 13 21.41 4.65 0.00 chr3ptel1M 288952 288994 (711006) (AAAGTT)n#Simple_repeat 1 45 (0) m_b116s252i7 4214 chr3ptel1M 288952 AAAGTTAAAGTTAAA-ATAGATTTAATG-AAAAGTGAAAAATAAA 288994 -v i v v -v v iv (AAAGTT)n#Sim 1 AAAGTTAAAGTTAAAGTTAAAGTTAAAGTTAAAGTTAAAGTTAAA 45 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.00 (2 / 2) 236 36.84 5.26 0.00 chr3ptel1M 289615 289728 (710272) C L3#LINE/CR1 (1265) 2834 2715 m_b116s601i22 4210 chr3ptel1M 289615 CTGCTTCCTTTTTGAGACAGTTGCTGACCAT--GATTCATA---TATTCT 289659 i iv iiiiv ii vi -- v v ---ii C L3#LINE/CR1 2834 CCGCTTCCTTTTCTAAGTGCTCACAAACCATCTGTTTAATAATCCGTTCT 2785 chr3ptel1M 289660 AGAGCTTTGCCAGGAATTGAAAACAAGC-CAGTGACCCACAGGCTGCATG 289708 ii i i i viv -i vi ii iii vi ? vi C L3#LINE/CR1 2784 AGAATTTTGCCGGGGATCGACGTCAAGCTTACCGGTCTGTAGTTTNCAGA 2735 chr3ptel1M 289709 CTCCAGGGTCTTTCCCCTTT 289728 v vvv i i C L3#LINE/CR1 2734 ATCCATCTTTTTTCCCTTTT 2715 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 44.04 CpG sites = 28, Kimura (unadjusted) = 55.43 Transitions / transversions = 2.00 (28/14) Gap_init rate = 0.03 (3 / 113), avg. gap size = 2.00 (6 / 3) 207 35.77 11.28 3.69 chr3ptel1M 290299 290626 (709374) C L2b_3end#LINE/L2 (1) 465 114 m_b116s601i24 4215 chr3ptel1M 290299 TTCGTGCAATCAGTCAAACATTTATAAAGTCCCCACCAAGTTCCAGGTGC 290348 i v v i- i ivi iv i iiv v i? C L2b_3end#LINE 465 TTCATTCATTCAA-CAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNC 417 chr3ptel1M 290349 TGTGCTGGTCACTGAG--TAAAAC-----CCAAAGCAGTCCCTGTTCC-A 290390 i v i i -- v i -----v ii v ? v i -i C L2b_3end#LINE 416 TGTGCTAGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTG 367 chr3ptel1M 290391 CATTCTATGAAGT-----------TGGAAGAGACA-ACAGGGGCCTAG-- 290426 vi - i i i----------- ii - v viv?i -- C L2b_3end#LINE 366 CCCTC-ACGGAGCTCACAGTCTAGTGGGGGAGACAGACATGTAANCAGAC 318 chr3ptel1M 290427 AGTGCAGAATACAGCAGCCACAGAG-AAATCTCTGG-----CAGAGGGAA 290470 i -? v iv - ivi i - iiv vv ----- iii C L2b_3end#LINE 317 AAT-NATAACCCAG-AGTGGCAGGGTAGGACTGGGGGGGCCCAGAGGAGG 270 chr3ptel1M 290471 ATA-CTGA--CAG-CTGGGGCAGGAGGGAAGG--TTCAGGAAATGTCTCA 290514 iii- -- i - vivv i -- i v ii------ C L2b_3end#LINE 269 GCGCCTGACCCGGCCTGGGGGGTCAGGGAGGGCTTCCCGGAGG------A 226 chr3ptel1M 290515 GGTAACTCCTGAACTGGGTCTTGAAGAA-AACAAAAAATT--CAAGAAGG 290561 i vii i i v i i -i vv ii i -- v iv i C L2b_3end#LINE 225 GGTGACATTTGAGCTGAGACCTGAAGGATGAGTAGGAGTTGGCCAGGCGA 176 chr3ptel1M 290562 TGAAGTATGGTCAAAAAGTATTTTAGGCAGGACAGCCAGGTGGTGCAAAG 290611 v i iv --- ii ii ii iiviiv vv? C L2b_3end#LINE 175 AGAGGTGGGG---AAGGGCGTTCCAGGCAGAGGGAACAGCANGTGCAAAG 129 chr3ptel1M 290612 GAATGGAGATGGGAG 290626 vviv ii C L2b_3end#LINE 128 GCCCTGAGGCGGGAG 114 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 48.29 CpG sites = 73, Kimura (unadjusted) = 53.28 Transitions / transversions = 1.82 (73/40) Gap_init rate = 0.08 (27 / 327), avg. gap size = 1.85 (50 / 27) 216 30.77 0.00 1.54 chr3ptel1M 290299 290364 (709636) C L2a_3end#LINE/L2 (1) 516 452 m_b116s601i23 4215 chr3ptel1M 290299 TTCGTGCAATCAGTCAAACATTTATAAAGTCCCCACCAAGTTCCAGGTGC 290348 i v v i- i vi iv i i v v ii C L2a_3end#LINE 516 TTCATTCATTCAA-CAAATATTTATTGAGCGCCTACTATGTGCCAGGCAC 468 chr3ptel1M 290349 TGTGCTGGTCACTGAG 290364 v i v i i C L2a_3end#LINE 467 TGTTCTAGGCGCTGGG 452 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 35.78 CpG sites = 12, Kimura (unadjusted) = 40.96 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.02 (1 / 65), avg. gap size = 1.00 (1 / 1) 212 33.79 0.00 1.35 chr3ptel1M 290306 290380 (709620) C L2d2_3end#LINE/L2 (8) 547 474 m_b116s601i25 4215 chr3ptel1M 290306 AATCAGTCAAACATTTATAAAGTCCCCACCAAGTTCCAGGTGCTGTGCTG 290355 i- i vi iv i iiv v v ii i C L2d2_3end#LIN 547 AATCAA-CAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTA 499 chr3ptel1M 290356 GTCACTGAGTAAAACCCAAAGCAGT 290380 v i v viii iv v C L2d2_3end#LIN 498 GGCGCTGTGGGGGATACAAAGAAGT 474 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 41.73 CpG sites = 15, Kimura (unadjusted) = 46.76 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.01 (1 / 74), avg. gap size = 1.00 (1 / 1) 190 20.87 3.45 9.09 chr3ptel1M 290864 290921 (709079) L2a_3end#LINE/L2 388 442 (75) m_b116s601i26 4216 chr3ptel1M 290864 CTCCCATCATAATGCAAACTCTTTGAGGACAGGGAATGTCTTTCCTTCTG 290913 i ii v i i iv i ---- -iv L2a_3end#LINE 388 CCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGA----CTTT-TGTCTG 432 chr3ptel1M 290914 TTT--TTCAC 290921 -- L2a_3end#LINE 433 TTTTGTTCAC 442 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 25.20 CpG sites = 8, Kimura (unadjusted) = 25.20 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.11 (6 / 57), avg. gap size = 1.17 (7 / 6) 181 35.72 1.53 8.13 chr3ptel1M 291021 291151 (708849) C AmnL2-1#LINE/L2 (358) 2255 2133 m_b116s601i27 4217 chr3ptel1M 291021 AAGCTCGAGTAGGGCCATAATGTGAAGAATTTTAAGTGCCAGATGGGGCC 291070 i v i i v ----- i ii ivi v i-ii v C AmnL2-1#LINE/ 2255 AGGCTGGAGCAAGTCCAT-----GGAGGGTTTTAAAAACAAGG-AAGGCA 2212 chr3ptel1M 291071 ATG--GACATTTGATCATGGAAGTAATAAGGAATCGCTGGAATTTGTCAA 291118 v-- - i v v i vv ii ii iv i vv ii C AmnL2-1#LINE/ 2211 ATTTTGA-ACTGGATCCTGAAATGAATGGGGAGCCAGTGGAGTTGTTTGA 2163 chr3ptel1M 291119 GTAGGGAAGTAATGTGGGCAGACTAGTTCTTTG 291151 v v ii i v ivi --- C AmnL2-1#LINE/ 2162 GGATGGGGGTGATGTGGTCGCGC---TTCTTTG 2133 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 47.13 CpG sites = 26, Kimura (unadjusted) = 50.47 Transitions / transversions = 1.53 (26/17) Gap_init rate = 0.08 (11 / 130), avg. gap size = 1.09 (12 / 11) 295 31.07 0.00 3.45 chr3ptel1M 291272 291361 (708639) MIRc#SINE/MIR 3 89 (179) m_b116s601i28 4218 chr3ptel1M 291272 AGGCAATTAGGCAATGCAGTGAATAGAGGGTCAGCCCTTGAGTCAGGAAA 291321 i --- iii i v viiii v i v i MIRc#SINE/MIR 3 AGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAG 49 chr3ptel1M 291322 GAGTGAGTTCAAATTCAGCCTCAGACACTTACTAGCTTTG 291361 ivv i i i i v v v v v MIRc#SINE/MIR 50 ACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTG 89 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 39.37 CpG sites = 16, Kimura (unadjusted) = 41.37 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.03 (3 / 89), avg. gap size = 1.00 (3 / 3) 253 22.94 4.55 10.84 chr3ptel1M 291581 291668 (708332) L2d2_3end#LINE/L2 403 485 (70) m_b116s601i29 4219 chr3ptel1M 291581 CCTTTCAACCACTTTTGTGTGTTGTCCACTCCAACTCCCTTTAAAATATA 291630 i -- iiv i v i- i ------ i v i L2d2_3end#LIN 403 CTTTTCA--CGTGTTTATGTCTTGTCT-CCCCAACT------AGATTGTA 443 chr3ptel1M 291631 AGTTCCTTGAGGGAAAGGACTATAT----TGCTTGTTTGTAT 291668 i v i i i ---- i v L2d2_3end#LIN 444 AGCTCCTTGAGGGCAGGGACCATGTCTTATACTTCTTTGTAT 485 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 26.46 CpG sites = 13, Kimura (unadjusted) = 28.30 Transitions / transversions = 2.60 (13/5) Gap_init rate = 0.11 (10 / 87), avg. gap size = 1.30 (13 / 10) 247 31.04 1.00 9.78 chr3ptel1M 291594 291693 (708307) L2c_3end#LINE/L2 351 442 (36) m_b116s601i30 4219 chr3ptel1M 291594 TTTGTGTGT-TGTCCACTCCAACTCCCTTTAAAATATAAGTTCCTTGAGG 291642 ii? - iv -------i i v i i i L2c_3end#LINE 351 TTTACNTGTCTGTCTCCTCCA-------CTAGACTGTGAGCTCCTTGAGG 393 chr3ptel1M 291643 GAAAGGACTATATTGCTTGTTTGTATTTGGATTTCTAGTGCTTGACATTT 291692 v i ii i -- i ii v v ii i i i i iv L2c_3end#LINE 394 GCAGGGACCGTGT--CTTATTCATCTTTGTATCCCCAGCGCCTGGCACAT 441 chr3ptel1M 291693 A 291693 L2c_3end#LINE 442 A 442 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 39.59 CpG sites = 22, Kimura (unadjusted) = 44.12 Transitions / transversions = 3.67 (22/6) Gap_init rate = 0.10 (10 / 99), avg. gap size = 1.00 (10 / 10) 115 3.44 0.84 0.00 chr3ptel1M 291724 291842 (708158) (TC)n#Simple_repeat 1 120 (0) c_b116s251i1 4220 chr3ptel1M 291724 TCTCTCTCTGTGTGTCTC-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 291772 v v v - (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr3ptel1M 291773 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 291822 (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chr3ptel1M 291823 TCTCTCTCTCTCTCTTTCTC 291842 i (TC)n#Simple_ 101 TCTCTCTCTCTCTCTCTCTC 120 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.01 (1 / 118), avg. gap size = 1.00 (1 / 1) 329 33.01 2.22 2.22 chr3ptel1M 292790 293105 (706895) C L1ME4c_3end#LINE/L1 (174) 656 341 m_b116s551i4 4221 chr3ptel1M 292790 GTATA-ACATTTTCCTAGTTCTGCTCACTTCATTTTAAATTAGTTCATGT 292838 ? - v iv - ivi i v v vv -- C L1ME4c_3end#L 656 GTANATACAATTTTGTA-TTCTGCTTTTTTCACTTAACATTATATCAT-- 610 chr3ptel1M 292839 AAGC-CCTTCCAGGTTTTTCTGATA-TCATCCTGCTTGTCATTCTTA-TA 292885 i -ii v vi vi- - v v iv i i - i C L1ME4c_3end#L 609 AAACATTTTCCATGTTGCTAC-ATAGTCTTCATAATTATCATTTTTAATG 561 chr3ptel1M 292886 GCACAATAAGTATTC-ATCACAACCATATATCACAACTTGTCCATCAATT 292934 vvv - - iviv?v i i i i iiii v v C L1ME4c_3end#L 560 GCTGCATAA-TATTCCATCGAGTNGATGTACCATAATTTACTTAACCATT 512 chr3ptel1M 292935 CCCCAACAGATGGCCATCCCCTCAATTTCCAATTTTTTGTCATCACAAAA 292984 v iv v v iivvvivi i ii i i v C L1ME4c_3end#L 511 CCCCTATTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAAT 462 chr3ptel1M 292985 AGAACTTCCCTGAATATTTTTGTATATAAAGATCTTT--TTCATTTAAAA 293032 ivi v vv i i i ii v v i -- v --i C L1ME4c_3end#L 461 AACGCTGCAATGAACATCTTCGTGCATATAGCTTTTTCCTTCTTTT--GA 414 chr3ptel1M 293033 AAAATCTCTTTGCAATGTAGACCTAGTGGTGGTATTGCTGGGCCAAAGGC 293082 vv i i ivi iv vv i vi v i i v C L1ME4c_3end#L 413 ATTATTTCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGG 364 chr3ptel1M 293083 TATACACAGTTTTATGGAACTTG 293105 iv v vv C L1ME4c_3end#L 363 TATGAACATTTTTATGGCTCTTG 341 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 42.37 CpG sites = 52, Kimura (unadjusted) = 44.67 Transitions / transversions = 1.04 (52/50) Gap_init rate = 0.04 (13 / 315), avg. gap size = 1.08 (14 / 13) 530 28.18 4.41 2.16 chr3ptel1M 293115 293386 (706614) C L1ME5_3end#LINE/L1 (660) 281 4 m_b116s551i5 4222 chr3ptel1M 293115 TGCATTAGTGCCCCAATTTTCCCACATCCCCTTTACTATTTGTCATTTTT 293164 v v ii v ? i i vii vi i v v i C L1ME5_3end#LI 281 TGCATGAGGGTTCCTATNTCCCCACATCCTCGCCAACACTTGGCATTATC 232 chr3ptel1M 293165 C--TTTTCCA--TTATATTAG-CTAATTCGATATGAGGAGATACCTCAGA 293209 --i i -- v iii - -v i i i i v i vv C L1ME5_3end#LI 231 CAGCTTTCTAATTTTTGCCAGTCTAAT-AGGTGTAAAGTGATATCTCATT 183 chr3ptel1M 293210 ATTATTTTAATTTACAGTTCTTTAATCAATAGTAATTTAGAGCATTT--T 293257 i i i v i i i v i i v v i -- C L1ME5_3end#LI 182 GTTGTTTTAATTTGCATTTCTCTGATTACTAATGAGTTTGAGCATCTCTT 133 chr3ptel1M 293258 CATATAACTATAGATAGCATT---GATTTCTTCATTTGAAAACTGCCTTT 293304 ivi i --- v --- i i v i v i v C L1ME5_3end#LI 132 CATATGCTTGT---TAGCCTTTCGGGTTTCCTCTTCTGTAAATTGCCTGT 86 chr3ptel1M 293305 TCATATTCTTTGCCCATTTACCAATTGGGG--AATGACTTATATTCTTTC 293352 i vi v --?vi v - - vi C L1ME5_3end#LI 85 TCATATCCTTTGCCCATTTTTCTATTGGGGTTNCCGTCTT-T-TTCTTGT 38 chr3ptel1M 293353 AAATTTGGATGAATTCTCTGTATATTTCAGAAAT 293386 vi v v i ii ii v C L1ME5_3end#LI 37 TGATTTGCAGGAGTTCCTTGTATATTCTAGATAT 4 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 36.13 CpG sites = 45, Kimura (unadjusted) = 36.75 Transitions / transversions = 1.50 (45/30) Gap_init rate = 0.04 (12 / 271), avg. gap size = 1.50 (18 / 12) 926 29.53 6.40 3.17 chr3ptel1M 293393 294095 (705905) C L1M5_orf2#LINE/L1 (1241) 2053 1329 m_b116s551i6 4222 chr3ptel1M 293393 TTTCTTTTTTTCCTCTTATTGCTATAGCTAGTATTTCTAATACAGTATTG 293442 i ivi vv i v ii i i i i C L1M5_orf2#LIN 2053 TTTCTTTTTCTTGCCTTATTGCACTGGCTAGGACCTCCAGTACAATGTTG 2004 chr3ptel1M 293443 AACAATAGTGATGAAAATGGTCAATCTTGCTCCCCCTCCCCCCCGTCTTA 293492 i iv i ? ii v vi ----i i vii vi C L1M5_orf2#LIN 2003 AATAGAAGTGGTGANAGCGGACATCCTTG----TCTTGTTCCCGATCTTA 1958 chr3ptel1M 293493 TTTGGAATACTTTTAGCTTATCTCCATTACAGATAATACTTGCTGATAG- 293541 vvv vi ? i i? v v viv i ii ? - - C L1M5_orf2#LIN 1957 GGGGGAAAGCNTTCAGTNTTTCACCATTAAGTATGATGTTNGCTG-TAGG 1909 chr3ptel1M 293542 -TTTTAG-ATATGTTCTACATATCATTTAAAGGAAAGCTTCATTTATTCT 293589 - v - v ii --v vv vi iviii v i i C L1M5_orf2#LIN 1908 TTTTTCGTAGATGCCCT--TTATCAGGTTGAGGAAGTTCCCTTCTATTCC 1861 chr3ptel1M 293590 TATACTTTCT-ATTATTTTTAATAGGAATGGATGCCATATCTTTTCAAAA 293638 -ii v - vvi vi v i iiiv i v - C L1M5_orf2#LIN 1860 TA-GTTTGCTGAGAGTTTTTATCATGAATGGGTGTTGAATTTTGTC-AAA 1813 chr3ptel1M 293639 AGATTTTTCTGCATCTACTGAGATAATCATATGATTTTT---GTTAGTTT 293685 v v i i ---v vi i C L1M5_orf2#LIN 1812 TGCTTTTTCTGCATCTATTGAGATGATCATATGATTTTTCTCCTTTATTC 1763 chr3ptel1M 293686 TGTTACTGATATAATCGATTATG-TGGTGGTTTTCCTAATATTAAACCAG 293734 --- ii vi ii- i v v i v i i C L1M5_orf2#LIN 1762 TGTTA---ATATGGTGAATTACATTGATTGATTTTCGAATGTTAAACCAA 1716 chr3ptel1M 293735 TCCTGCATTCTTGGAATAAATCCTATCTGCTCATGGT-CATT-------- 293775 i i i i i i ii v i -i -------- C L1M5_orf2#LIN 1715 CCTTGCATTCCTGGGATAAACCCCACTTGGTCATGATGTATTATCCTTTT 1666 chr3ptel1M 293776 ----TATTTCTGCAATCTATTTCTTGGTATTTTATTTTAAATGTTTTCAC 293821 ---- v v v v vi ii i ?vii v v i C L1M5_orf2#LIN 1665 TATATATTGCTGGATTCGATTTGCTAATATTTTGTTNAGGATTTTTGCAT 1616 chr3ptel1M 293822 CAATATTTATTAGAGAAGTT-GTCT----TTCTCTGTTTTTG------CT 293860 v i i v i vi - ---- i v i ------ C L1M5_orf2#LIN 1615 CTATGTTCATGAGGGATATTGGTCTGTAATTTTCTTTTCTTGTAATGTCT 1566 chr3ptel1M 293861 CTTCCTGGTTTAGGTATCAGCACCATAT--GTGTGATTAAAAGAAACTTG 293908 i vi ? v vii? ii-- iv v - vi ii v C L1M5_orf2#LIN 1565 TTGTCNGGTTTTGGTATCAGGGTNATGCTGGCCTCA-TAAAATGAGTTGG 1517 chr3ptel1M 293909 ATAGTATT---TCTTTTTGCATTTTATTTCATATTATTTTGTTCATATTA 293955 iv i --- vi v vvv v ------- ii i v C L1M5_orf2#LIN 1516 GAAGTGTTCCCTCTTTTTCTATTTTCTGGAAGA-------GTTTGTGTAA 1474 chr3ptel1M 293956 TTTTGGAATCAATTGTTCTTTAAATGTTTAGTAGATTTCACTGGTGAATC 294005 vv v i v v i i v ii v C L1M5_orf2#LIN 1473 GATTGGTATTATTTCTTCCTTAAATGTTTGGTAGAATTCACCAGTGAAGC 1424 chr3ptel1M 294006 CATCTGG--TTAGAGGAATTTTTTCT-TAGGAAGCTCATTGATGTCTTCT 294052 --i --- i i i - i v iv i vv vvv C L1M5_orf2#LIN 1423 CATCTGGGCCT---GGAGTTTTCTTTGTGGGAAGGTTTTTAATTACAAAT 1377 chr3ptel1M 294053 TCAATTTCTTT--TG---ATAGGGTTATTTTAGTATTCCAATTCTTCT 294095 -- i--- i ivii v i v C L1M5_orf2#LIN 1376 TCAATTTCTTTAATAGATATAGGGCTATTCAGATTTTCTATTTCTTCT 1329 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 38.87 CpG sites = 116, Kimura (unadjusted) = 39.12 Transitions / transversions = 1.36 (116/85) Gap_init rate = 0.06 (41 / 702), avg. gap size = 1.66 (68 / 41) 16 0.00 0.00 0.00 chr3ptel1M 294830 294850 (705150) (TGTT)n#Simple_repeat 1 21 (0) m_b116s252i8 4223 chr3ptel1M 294830 TGTTTGTTTGTTTGTTTGTTT 294850 (TGTT)n#Simpl 1 TGTTTGTTTGTTTGTTTGTTT 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 13 26.36 6.35 0.00 chr3ptel1M 296076 296138 (703862) (TTTTTAC)n#Simple_repeat 1 67 (0) m_b116s252i9 4224 chr3ptel1M 296076 TTGTTATTCTTTGCTTGTT--TTTTT-TTTTATTCTTGTTTTTTTTTCCT 296122 v i i i v -- -i v v v vi v (TTTTTAC)n#Si 1 TTTTTACTTTTTACTTTTTACTTTTTACTTTTTACTTTTTACTTTTTACT 50 chr3ptel1M 296123 TTTTA-ATTTGACTTTT 296138 -v v (TTTTTAC)n#Si 51 TTTTACTTTTTACTTTT 67 Matrix = Unknown Transitions / transversions = 0.56 (5/9) Gap_init rate = 0.05 (3 / 62), avg. gap size = 1.33 (4 / 3) 182 26.00 1.96 1.96 chr3ptel1M 296686 296736 (703264) L3#LINE/CR1 3895 3945 (154) m_b116s601i31 4225 chr3ptel1M 296686 GAAAAATCTTCATCACTCTCAGAGCCATCC-AAAATGGCCTGGGCTGTCC 296734 i ii - v vv ii - vv i i L3#LINE/CR1 3895 GAAGAACTTTC-TAACAATCAGAGCTGTCCAAAAATGGAATGGGCTGCCT 3943 chr3ptel1M 296735 TG 296736 i L3#LINE/CR1 3944 CG 3945 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.80 CpG sites = 8, Kimura (unadjusted) = 32.81 Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.04 (2 / 50), avg. gap size = 1.00 (2 / 2) 19 19.74 5.06 6.41 chr3ptel1M 296936 297014 (702986) (GA)n#Simple_repeat 1 78 (0) m_b117s252i1 4226 chr3ptel1M 296936 GAGAGA-AGCAGAGATGCAGATA-AGAGAGAG-GGGATATATGAG-GAGC 296981 - - - - v - - i v v - - - (GA)n#Simple_ 1 GAGAGAGAG-AGAGA-G-AGAGAGAGAGAGAGAGAGAGAGA-GAGAGAG- 45 chr3ptel1M 296982 AGGCAGGGAGGGACAGAGGGAGAGAGAAAGGGA 297014 iv i i v i i i (GA)n#Simple_ 46 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 78 Matrix = Unknown Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.12 (9 / 78), avg. gap size = 1.00 (9 / 9) 242 28.39 17.28 2.15 chr3ptel1M 297801 297962 (702038) C L3#LINE/CR1 (108) 3991 3806 m_b117s601i0 4227 chr3ptel1M 297801 CAGACACTACTGGATGACCTCCAATAATGAGGAGCTCACTCACTGTGAAC 297850 v v i v vv i i i i vv ----v? C L3#LINE/CR1 3991 CAGCCTCTGCTTGAACACCTCCAGTGACGGGGAGCTCACTACCT----CN 3946 chr3ptel1M 297851 CAAGGAAGTTCCTTCCATTTTTGAA------TGA--GATGGAG------- 297885 i v ii v i ------ -- v i i------- C L3#LINE/CR1 3945 CGAGGCAGCCCATTCCATTTTTGGACAGCTCTGATTGTTAGAAAGTTCTT 3896 chr3ptel1M 297886 -CCTAAATGGGATT---CTCTGCCCCTC-----CCTCCA-CCGTTGCTCC 297925 - i v v iiii---v i i ----- i - i v C L3#LINE/CR1 3895 CCTTATATTGAGCCGAAATCTGCCTCCCTGTAACTTCCACCCATTGGTCC 3846 chr3ptel1M 297926 TGG-GCTA--CTCTGGGACCAAACAGAATACAAATAATCC 297962 i -v i-- ii v vivv C L3#LINE/CR1 3845 TAGTTCTGCCCTCTGGAGCCACACAGAATAAGTCTAATCC 3806 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 33.86 CpG sites = 25, Kimura (unadjusted) = 36.87 Transitions / transversions = 1.25 (25/20) Gap_init rate = 0.08 (13 / 161), avg. gap size = 2.46 (32 / 13) 180 32.24 0.00 5.36 chr3ptel1M 297978 298036 (701964) C L3#LINE/CR1 (336) 3763 3708 m_b117s601i1 4227 chr3ptel1M 297978 CATGTTGCCTCCGAGCCTTCTCTTCCCCAGGGTGGGTCTCTTCTTCAGAT 298027 iv ii i i v iii--- v ii v C L3#LINE/CR1 3763 CATGTCTCCTCTAAGTCTTCTCTTCTCCAGGCTAAA---CATCCCCAGTT 3717 chr3ptel1M 298028 CCCTTGATC 298036 i ii i C L3#LINE/CR1 3716 CCTTCAACC 3708 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 46.22 CpG sites = 14, Kimura (unadjusted) = 46.22 Transitions / transversions = 3.50 (14/4) Gap_init rate = 0.05 (3 / 58), avg. gap size = 1.00 (3 / 3) 191 23.46 2.99 4.55 chr3ptel1M 299620 299686 (700314) MIR3#SINE/MIR 110 175 (33) m_b117s601i2 4228 chr3ptel1M 299620 CTCTCCTGGGAAACTCAGTGTCTTCATCTCTACAGTGAGGGGGGAGG--T 299667 - v-- v i v v i vv -- MIR3#SINE/MIR 110 CTCTC-TGGGC--CTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACT 156 chr3ptel1M 299668 GATTGGTCTCTCAGATCTC 299686 iiv i v i i MIR3#SINE/MIR 157 AGATGATCTCTAAGGTCCC 175 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 28.25 CpG sites = 7, Kimura (unadjusted) = 28.25 Transitions / transversions = 0.88 (7/8) Gap_init rate = 0.06 (4 / 66), avg. gap size = 1.25 (5 / 4) 17 2.94 11.43 0.00 chr3ptel1M 300221 300255 (699745) (TTCTT)n#Simple_repeat 1 39 (0) m_b117s252i3 4229 chr3ptel1M 300221 TTC-TTTCTTTTCTTTTC--TTCTTTTC-TTTCTTCTCT 300255 - -- - i (TTCTT)n#Simp 1 TTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCT 39 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.09 (3 / 34), avg. gap size = 1.33 (4 / 3) 103 1.96 0.00 1.89 chr3ptel1M 300270 300377 (699623) (TTTC)n#Simple_repeat 1 106 (0) c_b117s251i0 4230 chr3ptel1M 300270 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 300319 (TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 50 chr3ptel1M 300320 TCTTTCTTTCTTTCCTTCTTTCTTTCTTCTCTTTCCTTCTTTCTTTCTTT 300369 i - i - (TTTC)n#Simpl 51 TCTTTCTTTCTTTCTTTCTTTCTTTCTT-TCTTTCTTTCTTTCTTTC-TT 98 chr3ptel1M 300370 TCTTTCTT 300377 (TTTC)n#Simpl 99 TCTTTCTT 106 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.02 (2 / 107), avg. gap size = 1.00 (2 / 2) 19 16.96 4.26 0.00 chr3ptel1M 300575 300621 (699379) (GGAGGT)n#Simple_repeat 1 49 (0) m_b117s252i4 4231 chr3ptel1M 300575 GGAGGTGGAAGTGG-GATGGAGGTAG-GGTGGGGGTGGGGGTGTAGCTG 300621 i - i i - i i v v (GGAGGT)n#Sim 1 GGAGGTGGAGGTGGAGGTGGAGGTGGAGGTGGAGGTGGAGGTGGAGGTG 49 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.04 (2 / 46), avg. gap size = 1.00 (2 / 2) 21 3.44 0.00 3.23 chr3ptel1M 300804 300835 (699165) (TCC)n#Simple_repeat 1 31 (0) m_b117s252i5 4232 chr3ptel1M 300804 TCCTTCCTCCTCCTCCTCCTCCTCTTCCTCCT 300835 - i (TCC)n#Simple 1 TCC-TCCTCCTCCTCCTCCTCCTCCTCCTCCT 31 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 315 24.45 3.23 3.23 chr3ptel1M 300925 301017 (698983) C MIR3#SINE/MIR (3) 205 113 m_b117s601i3 4233 chr3ptel1M 300925 TCATTAGCTCACAGCATGTCAGAGCTGCAAGAGACCTCCAAGACCA---A 300971 viiv i v v i ivi i --- C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTA 156 chr3ptel1M 300972 GTCCACCCATTCTGCCATTTTACATAGAAGGTACCTGAAGTCCAGA 301017 v -ii -- v vi v v i i C MIR3#SINE/MIR 155 GTCCAACC-CCCT--CATTTTACAGATGAGGAAACTGAGGCCCAGA 113 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 30.01 CpG sites = 12, Kimura (unadjusted) = 30.01 Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.04 (4 / 92), avg. gap size = 1.50 (6 / 4) 436 24.41 9.45 0.00 chr3ptel1M 301236 301362 (698638) MIRc#SINE/MIR 129 267 (1) m_b117s601i4 4234 chr3ptel1M 301236 TTCCTGATCTGTAAAATGGAGATAGTCACAGC------ACCTATCTCCCA 301279 v i i v i v ------i i v MIRc#SINE/MIR 129 TTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACA 178 chr3ptel1M 301280 AGGCTGT--CGAGGACCAAACAAGATCATATTTGTG-AAGCATTTTGTAA 301326 i i --i i ii v i v - ii MIRc#SINE/MIR 179 GGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTTTGTAA 228 chr3ptel1M 301327 ACTTCCTGGTGCGATCTAAATGT---GGGCTAGGATTAT 301362 vivvi v vi --- ? i vv MIRc#SINE/MIR 229 ACTGTAAAGTGCTATACAAATGTAAGGNGTTATTATTAT 267 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 29.25 CpG sites = 18, Kimura (unadjusted) = 30.40 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.03 (4 / 126), avg. gap size = 3.00 (12 / 4) 22 26.72 2.99 0.00 chr3ptel1M 301547 301613 (698387) (CT)n#Simple_repeat 1 69 (0) m_b117s252i6 4235 chr3ptel1M 301547 CTCCCTCT-TCTCTCTCTCTCTGGAT-TCTCCCAGTAGCTCCCTCCCTCT 301594 i - vvv - i vv vv i i (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chr3ptel1M 301595 CTCCCTCCCTCCCTCTATC 301613 i i i v (CT)n#Simple_ 51 CTCTCTCTCTCTCTCTCTC 69 Matrix = Unknown Transitions / transversions = 0.88 (7/8) Gap_init rate = 0.03 (2 / 66), avg. gap size = 1.00 (2 / 2) 200 24.10 8.43 0.00 chr3ptel1M 301681 301763 (698237) L2a_3end#LINE/L2 428 517 (0) m_b117s601i5 4236 chr3ptel1M 301681 GTCTGCTTT-CTCAGT-CTGTATGTC-AGTGTCTGGTCT--TGACTGGCA 301725 i -i v - vi - i i i vvi-- v L2a_3end#LINE 428 GTCTGTTTTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCA 477 chr3ptel1M 301726 CATAGTAG--GCTTCATAAATGTTGGTTGATTGGTTGAGT 301763 -- iv i v v iv i L2a_3end#LINE 478 CATAGTAGGCGCTCAATAAATATTTGTTGAATGAATGAAT 517 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 27.79 CpG sites = 11, Kimura (unadjusted) = 29.49 Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.06 (5 / 82), avg. gap size = 1.40 (7 / 5) 201 15.91 4.55 0.00 chr3ptel1M 301720 301763 (698237) L2c_3end#LINE/L2 433 478 (0) m_b117s601i6 4236 chr3ptel1M 301720 CTGGCACATAGTAGGC--TTCATAAATGTTGGTTGATTGGTTGAGT 301763 -- iv v v iv i L2c_3end#LINE 433 CTGGCACATAGTAGGCGCTCAATAAATGTTTGTTGAATGAATGAAT 478 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 17.91 CpG sites = 3, Kimura (unadjusted) = 17.91 Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.02 (1 / 43), avg. gap size = 2.00 (2 / 1) 388 29.11 4.48 2.56 chr3ptel1M 301861 302128 (697872) C L1M4_orf2#LINE/L1 (1956) 1338 1066 m_b117s551i0 4237 chr3ptel1M 301861 TATCTCT-CTTGTGTTAATTTGGGGTGTTTTCTATTTTTTGCAGGAAAT- 301908 i - v i i v - iv v i i i-i v - C L1M4_orf2#LIN 1338 TATTTCTTCTTGAGTCAGTTTCGG-TAGTTTGTGTCTTTC-TAGGAATTT 1291 chr3ptel1M 301909 ---CATTTCCTTTAAATCCTCCCTTTTGCCAGCACCTAATTGTGTGTGGC 301955 --- v i ii iv ivv iii ivi vii i i C L1M4_orf2#LIN 1290 GTCCATTTCATCTAGGTTATCTAATTTGTTGGCATACAATTGTTCATAGT 1241 chr3ptel1M 301956 AGCCTCTGCTCCTTCTTTTCATTTTTGT----TCTGCTCATTATGAACAG 302001 vi i vv vv i i i ---- v - vi v vv -- C L1M4_orf2#LIN 1240 ATTCCCTTATAATCCTTTTTATTTCTGTAAGGTCGG-TAGTAATGTCC-- 1194 chr3ptel1M 302002 GCCTTGTTCATTTTTTATTGGGAGTAATTTGATTTTCCTCTCTCTTATT- 302050 - iv ii v vv- v i i i v - C L1M4_orf2#LIN 1193 -CCTCTTTCATTCCTGATTTT-AGTAATTTGAGTCTTCTCTCTTTTTTTC 1146 chr3ptel1M 302051 TTAATCAGACCAGCTCAAGGGTTATTGATTTTGTTCATCTTTTCCAAGAA 302100 ii v i v v i ii v v C L1M4_orf2#LIN 1145 TTGGTCAGTCTAGCTAAAGGTTTGTCAATTTTGTTGATCTTTTCAAAGAA 1096 chr3ptel1M 302101 CCGGCTTTTGGTTTGGTT--TTTTCTTTAT 302128 ii v -- i C L1M4_orf2#LIN 1095 CCAACTTTTGGTTTCGTTGATTTTCTCTAT 1066 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 37.72 CpG sites = 43, Kimura (unadjusted) = 37.72 Transitions / transversions = 1.30 (43/33) Gap_init rate = 0.04 (12 / 267), avg. gap size = 1.58 (19 / 12) 239 39.00 1.00 0.00 chr3ptel1M 302144 302243 (697757) C MIR3#SINE/MIR (29) 179 79 m_b117s601i7 4238 chr3ptel1M 302144 GGGAAGGATGTGAAAG-TCATGTCGCCTGACCTTCTGACTTTACATGTGA 302192 i i iv v i - v v i ii ii v i vi C MIR3#SINE/MIR 179 GGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGA 130 chr3ptel1M 302193 AAAAGCTTCAGCCTGTAGAATTTGAATGACTCACTCAAAATCATCCATCA 302242 ii i vvi iiv iv vi i ii i ii iv v ? C MIR3#SINE/MIR 129 GGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGCN 80 chr3ptel1M 302243 A 302243 C MIR3#SINE/MIR 79 A 79 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 61.05 CpG sites = 26, Kimura (unadjusted) = 61.05 Transitions / transversions = 2.00 (26/13) Gap_init rate = 0.01 (1 / 99), avg. gap size = 1.00 (1 / 1) 292 34.59 3.01 0.00 chr3ptel1M 302236 302368 (697632) C L2d_3end#LINE/L2 (0) 516 380 m_b117s601i8 4239 chr3ptel1M 302236 TCCATCAATCAACCAACAAACGTTTATTAAGTCTTTCTTATGGGCCAGGC 302285 v i iii i ivii vi v ivi C L2d_3end#LINE 516 TCAATCAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGC 467 chr3ptel1M 302286 AGC-TGCTAGATTTTA-GGGTTGCAACAACA-AGCACAAAACATGCACCC 302332 vi- iivi i- vvi i ? v - i i i vv C L2d_3end#LINE 466 ACTGTGCTAGGCGCTGTGGGGAACGANAAAANAGTATAAGACATGGTCCC 417 chr3ptel1M 302333 TCTTCTCCAGGAGACT-CACTCTAACAAGACAGACAA 302368 vii v vi - v iivi iv C L2d_3end#LINE 416 TGCCCTCAAGGAGCTTACAATCTAGTTGGGGAGACAA 380 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 44.63 CpG sites = 28, Kimura (unadjusted) = 49.08 Transitions / transversions = 1.56 (28/18) Gap_init rate = 0.03 (4 / 132), avg. gap size = 1.00 (4 / 4) 222 31.85 8.11 6.67 chr3ptel1M 302240 302535 (697465) C L2a_3end#LINE/L2 (2) 515 216 m_b117s601i9 4239 chr3ptel1M 302240 TCAATCAACCAACAAACGTTTATTAAGTCTTTCTTATGGGCCAGGCAGCT 302289 v vi ii i ivii vi v - C L2a_3end#LINE 515 TCATTCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCA-CT 467 chr3ptel1M 302290 G--CTAGATTTTAGGGTTGCAACAACAAGCACAAAACATGCA-----CCC 302332 -- iivi i v i i iii -- vi ----- C L2a_3end#LINE 466 GTTCTAGGCGCTGGGGATACAGCAGTGA--ACAAAACAGACAAAAGTCCC 419 chr3ptel1M 302333 TCTTCTCCAGGAGACT-CACTCTAAC-----AAGACAGACAACATAT--- 302373 vii vv vi - i ii-----i i v i--- C L2a_3end#LINE 418 TGCCCTCATGGAGCTTACATTCTAGTGGGGGGAGACAGACAATAAACAAA 369 chr3ptel1M 302374 TCTATAAGAGTTTGTTAAAAAGAAAAAAAAATTAGGTGATTTGGGAAGAA 302423 vv ------- viv v iv vi i i i-- iv vi C L2a_3end#LINE 368 TAAATAAG-------TAAAATATATAGTATGTCAGATGG--TGATAAGTG 328 chr3ptel1M 302424 TTG-GGAAAAGTGAAATCAAAGAAAACTAGTCAGGGGACATGTAATGGTG 302472 i i- i --- - v iiv i--i i v v i ? C L2a_3end#LINE 327 CTATGGAGAA---AAAT-AAAGCAGGGTAA--GGGGGATAGGGAGTGNTG 284 chr3ptel1M 302473 AGGTAG-GAGTGTATTATGGGAATTGTGGGTAG--AAGCATGGGATCCCT 302519 i v? - i ii? vvv v i- i -- i v v vv ? C L2a_3end#LINE 283 GGGGNGAGGGTGTGCNATTTTAAATA-GGGTGGTCAGGGAAGGCCTCNCT 235 chr3ptel1M 302520 ----AGATGAAATTCTGAGC 302535 ---- i v - C L2a_3end#LINE 234 GAGAAGGTGACATT-TGAGC 216 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 42.49 CpG sites = 52, Kimura (unadjusted) = 43.84 Transitions / transversions = 1.44 (52/36) Gap_init rate = 0.10 (29 / 295), avg. gap size = 1.52 (44 / 29) 13 14.69 3.33 0.00 chr3ptel1M 303103 303132 (696868) (TCCC)n#Simple_repeat 1 31 (0) m_b117s252i7 4240 chr3ptel1M 303103 TCTCTGCCTGCCTCCCTCCCT-CCACCCTCC 303132 i v v - v (TCCC)n#Simpl 1 TCCCTCCCTCCCTCCCTCCCTCCCTCCCTCC 31 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 366 33.42 11.85 3.55 chr3ptel1M 303308 303466 (696534) C L2#LINE/L2 (483) 2599 2430 m_b117s601i10 4239 chr3ptel1M 303308 ATGTGGGGCAAGGAAGAAGGAG--GAATTTGGGATGGCTC-AGAGTTTGT 303354 iiv ii i -- i ivi i - ii v C L2#LINE/L2 2599 ATGTGGGGTGTGAGAGAAAGAGAGGAGTCAAGGATGACTCCAAGGTTTTT 2550 chr3ptel1M 303355 GAACTGGGGTGACTAGAGAAAATGGGGT-GCTTTTCA--AAACTAGAAAA 303401 iv i -ii i - ii i - iv ? --i iv i ii C L2#LINE/L2 2549 GGCCTGAG-CAACTGGA-AGGATGGAGTTGCCATTNACTGAGATGGGGAA 2502 chr3ptel1M 303402 ATTTAGAAGAGGGGTAAATGTG-GGGGAAAGATGA----TTC--TTTTGG 303444 ivi ivii i i ii v - i v ---- -- C L2#LINE/L2 2501 GACTGCGGGAGGAGCAGGTTTGAGGGGGAAGATCAGGAGTTCAGTTTTGG 2452 chr3ptel1M 303445 ACATGTTGACTCTCAGAAAAAG 303466 i v i v vivvv C L2#LINE/L2 2451 ACATGTTAAGTTTGAGATGCCT 2430 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 45.81 CpG sites = 121, Kimura (unadjusted) = 47.65 Transitions / transversions = 2.38 (38/16) Gap_init rate = 0.06 (9 / 158), avg. gap size = 1.67 (15 / 9) 32 0.00 0.00 0.00 chr3ptel1M 303467 303496 (696504) (TTGT)n#Simple_repeat 1 30 (0) c_b117s251i1 4241 chr3ptel1M 303467 TTGTTTGTTTGTTTGTTTGTTTGTTTGTTT 303496 (TTGT)n#Simpl 1 TTGTTTGTTTGTTTGTTTGTTTGTTTGTTT 30 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 366 33.42 11.85 3.55 chr3ptel1M 303497 303910 (696090) C L2#LINE/L2 (653) 2429 1981 m_b117s601i10 4239 chr3ptel1M 303497 TTAAATGGGCAATAAGCTGGTTTTAGGATTAGG--GTTAGTGGTAT-AGG 303543 i iivv vvi v- i v i-- v -- i vvi i- v C L2#LINE/L2 2429 TTAGACATCCAAGTGGA-GATGTC--GAGTAGGCAGTTGGATATACGAGT 2383 chr3ptel1M 303544 GTAGGACCCAGGAGAGAGACTGAGGCTGGATATAGAGATTTGGGAGTCAT 303593 v i iiii i iiivi v v i C L2#LINE/L2 2382 CTGGAGTTCAGGGGAGAGGTCCGGGCTGGAGATATAAATTTGGGAGTCAT 2333 chr3ptel1M 303594 CTGC--AGAGAAGATATTTAGCCCCATGGAAGATT--ATGGGGCTGCCA- 303638 v -- v v i ivv -- i -- i iiii ?- C L2#LINE/L2 2332 CAGCATATAGATGGTATTTAAAGCCATG--AGACTGGATGAGATCACCNA 2285 chr3ptel1M 303639 -GGAGAGAA---AGAGAAGGAAGAGAAAAGGACCCAGGAAAAAATCTTAG 303684 - v i--- v ii i v v vvi ii i i C L2#LINE/L2 2284 GGGAGTGAGTGTAGATAGAGAAGAGAAGAGGTCCAAGGACTGAGCCCTGG 2235 chr3ptel1M 303685 TGTCTATTCCCAAATTAGAATGT-GAAAAATTAACAATGATTTCACAAAA 303733 v --i i v vi ?ii v - iii iv i vi v viivi i C L2#LINE/L2 2234 GG--CACTCCAACGTTNAGAGGTCGGGGAGATGAGGAGGAACCAGCAAAG 2187 chr3ptel1M 303734 GAGA--GGAAA---------ACTGAGAGAAAAGGA--------------- 303757 -- ii --------- v iv ii --------------- C L2#LINE/L2 2186 GAGACTGAGAAGGAGCGGCCAGTGAGGTAGGAGGAAAACCAGGAGAGTGT 2137 chr3ptel1M 303758 --TATCACAAAAACAAAGATGAAAAAAAT-CCACAAGAAG--AGAAGTCA 303802 -- i viii i v - i i -iiv --i i -i C L2#LINE/L2 2136 GGTGTCCTGGAAGCCAAG-TGAAGAAAGTGTTTCAAGAAGGAGGGAGT-G 2089 chr3ptel1M 303803 ATCAATAATGTCTGATTCTGCAGAGAAGCCTGG-AAGA-----ACAAAGA 303846 ivi vi v v ? i i vi - ----- vi C L2#LINE/L2 2088 ATCAACTGTGTCAAATGCTGCTGANAGGTCAAGTAAGATGAGGACTGAGA 2039 chr3ptel1M 303847 ATTTTTTAAAGGCCATTTGATTTTGCAA---ATAAGTCATTACTGGTAAC 303893 ------- i v v ---iv i --- i C L2#LINE/L2 2038 ATT-------GACCATTGGATTTAGCAACGTGGAGGTCAT---TGGTGAC 1999 chr3ptel1M 303894 TTTG--AGGAACAGGTTTC 303910 i -- i i - C L2#LINE/L2 1998 CTTGACAAGAGCA-GTTTC 1981 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 45.81 CpG sites = 121, Kimura (unadjusted) = 47.65 Transitions / transversions = 1.73 (83/48) Gap_init rate = 0.09 (38 / 413), avg. gap size = 1.97 (75 / 38) 352 24.43 9.22 1.32 chr3ptel1M 304584 304724 (695276) L2c_3end#LINE/L2 296 447 (31) m_b117s601i11 4242 chr3ptel1M 304584 CCCTGTTAATTATCTCCAATTTA--CCTTGTCTGTAGCTTA-ATTA-GAC 304629 iv - iii v v --v i vv i i- i-i i L2c_3end#LINE 296 CCCTGTCTAT-ACTCCCATTATAGCACTTATCATTAACTTGTATTGTAAT 344 chr3ptel1M 304630 TGAGTATTTGCTCGT-TGTCTCTTCCCACCGGACTGGGAGCTCCTTGAGA 304678 vv i i ?i - i - ii v i L2c_3end#LINE 345 TGTCTGTTTACNTGTCTGTCTCCTCC-ACTAGACTGTGAGCTCCTTGAGG 393 chr3ptel1M 304679 GCAGGCAC--TGGCTT-TTC-CCTT----TCCCCAGTGCCTAGTACATAA 304720 v -- v - -i ---- i i i i L2c_3end#LINE 394 GCAGGGACCGTGTCTTATTCATCTTTGTATCCCCAGCGCCTGGCACATAG 443 chr3ptel1M 304721 TAAG 304724 i L2c_3end#LINE 444 TAGG 447 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 29.88 CpG sites = 23, Kimura (unadjusted) = 30.98 Transitions / transversions = 2.09 (23/11) Gap_init rate = 0.07 (10 / 140), avg. gap size = 1.50 (15 / 10) 273 24.68 2.60 0.00 chr3ptel1M 304878 304954 (695046) C L2d_3end#LINE/L2 (2) 514 436 m_b117s601i12 4243 chr3ptel1M 304878 AGTCAATCAGTCAACTAGGCTATATTAAGCACCTACTATTTGGCAAGACC 304927 i i v vv v i i v viv vv C L2d_3end#LINE 514 AATCAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCAC 465 chr3ptel1M 304928 TGTGCTAA--ACTGTGGGAATAGAAAAAA 304954 i--i i vv ? C L2d_3end#LINE 464 TGTGCTAGGCGCTGTGGGGAACGANAAAA 436 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 26.94 CpG sites = 8, Kimura (unadjusted) = 30.49 Transitions / transversions = 0.73 (8/11) Gap_init rate = 0.01 (1 / 76), avg. gap size = 2.00 (2 / 1) 208 33.36 7.44 8.33 chr3ptel1M 304880 305121 (694879) C L2b_3end#LINE/L2 (2) 464 225 m_b117s601i13 4243 chr3ptel1M 304880 TCAATCAGTCAACTAGGCTATATTAAGCACCTACTATTTGGCAAGACCTG 304929 v v v ivv v i i i i v v i v? C L2b_3end#LINE 464 TCATTCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTG 415 chr3ptel1M 304930 TGCTAAACTGTGGGAATAGA--AAAAAATCAGTCCCAACAGCCAAGATAT 304977 ii vv i v --iivi iv ----- v ?v i vi C L2b_3end#LINE 414 TGCTAGGCGCTGGGGATACAGCGGTGAACAAG-----ACAGACNCGGTCC 370 chr3ptel1M 304978 TCATTCTATCCATGGGGGGGGGGGATACATTCTAATGGGGGAGA------ 305021 iiiii --- i i vv------i v i ------ C L2b_3end#LINE 369 CTGCCCT---CACGGAGCT------CACAGTCTAGTGGGGGAGACAGACA 329 chr3ptel1M 305022 ---AAGCACGACAATGATGAACAAACAAGAGCCACGCAGTAAGGACTGGT 305068 --- ? - ? ---- v v ivi ivi - v C L2b_3end#LINE 328 TGTAANCA-GACAATNAT----AACCCAGAGTGGCAGGGT-AGGACTGGG 285 chr3ptel1M 305069 GTTCCTCTCAGAGGGAAGAC--ACCC-ATGTGGAGG----AGAAAGGCTT 305111 vvv i vv ii iv v -- -iiv i ----i i i C L2b_3end#LINE 284 GGGGCCCAGAGGAGGGCGCCTGACCCGGCCTGGGGGGTCAGGGAGGGCTT 235 chr3ptel1M 305112 CCTGCAGAAG 305121 i v i C L2b_3end#LINE 234 CCCGGAGGAG 225 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 43.00 CpG sites = 40, Kimura (unadjusted) = 46.35 Transitions / transversions = 1.18 (40/34) Gap_init rate = 0.11 (26 / 241), avg. gap size = 1.46 (38 / 26) 249 29.66 1.19 9.68 chr3ptel1M 304880 305047 (694953) C L2a_3end#LINE/L2 (2) 515 361 m_b117s601i14 4243 chr3ptel1M 304880 TCAATCAGTCAACTAGGCTATATTAAGCACCTACTATTTGGCAAGACCTG 304929 v v v ivv v i i v v i vv C L2a_3end#LINE 515 TCATTCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTG 466 chr3ptel1M 304930 TGCTAAACTGTGGGAATAGAA-AAAAATCAGTCCCAACAGCCAAGATATT 304978 v ii vv i v i- ivi v i---- v i -i i C L2a_3end#LINE 465 TTCTAGGCGCTGGGGATACAGCAGTGAACAA----AACAGACAAAA-GTC 421 chr3ptel1M 304979 CATTCTATCCATGGGGGGGGGGGATACATTCTAATGGGGGAGAAAGCACG 305028 v v iv - i vv------ i - i - - C L2a_3end#LINE 420 CCTGCCCT-CATGGAGCT------TACATTCTAGTGGGGG-GAGA-CA-G 381 chr3ptel1M 305029 ACAAT-GATGAACAAACAAG 305047 -i ii i i C L2a_3end#LINE 380 ACAATAAACAAATAAATAAG 361 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 36.82 CpG sites = 23, Kimura (unadjusted) = 37.87 Transitions / transversions = 1.05 (23/22) Gap_init rate = 0.10 (17 / 167), avg. gap size = 1.00 (17 / 17) 347 35.09 13.17 0.84 chr3ptel1M 306028 306346 (693654) C L2#LINE/L2 (868) 2214 1857 m_b117s601i15 4244 chr3ptel1M 306028 GTGGGGGTGATGCAGATGA----GCAAAGGGAACTGACAGGGAACCG--- 306070 v v vi v ---- ii v i i v --- C L2#LINE/L2 2214 GTCGGGGAGATGAGGAGGAACCAGCAAAGGAGACTGAGAAGGAGCGGCCA 2165 chr3ptel1M 306071 -------AGGAAAAGAACTAGGAGAGGACAGTGTCCCTGAGACC---TGG 306110 ------- ii i i viii iv ii --- i C L2#LINE/L2 2164 GTGAGGTAGGAGGAAAACCAGGAGAGTGTGGTGTCCTGGAAGCCAAGTGA 2115 chr3ptel1M 306111 GGGGAGGCCTTCAAGAAG------CTAAATGGCAGTGGCAAGGGCTTCCG 306154 i ii vvi ------v i viii v v iv v i C L2#LINE/L2 2114 AGAAAGTGTTTCAAGAAGGAGGGAGTGATCAACTGTGTCAAATGCTGCTG 2065 chr3ptel1M 306155 AGGAAAGTTGAGAAGCATGAGAA--AAGACATTGA------GGTTTGGCA 306196 --? i ii v iv i --i - ------ i i C L2#LINE/L2 2064 A--NAGGTCAAGTAAGATGAGGACTGAGA-ATTGACCATTGGATTTAGCA 2018 chr3ptel1M 306197 GTCGGGAGGTCACT-----CCTCGGAGAGAGCAGTGTCCACTGAACGATG 306241 iivv i ----- i ivi v viiv ii i C L2#LINE/L2 2017 ACGTGGAGGTCATTGGTGACCTTGACAAGAGCAGTTTCGGTGGAGTGGTG 1968 chr3ptel1M 306242 AGGCTGAAAGCCAGACCTCAG-AGAATCAAGAG-GAGT---TCCAAAGGA 306286 i vi v iivv -i iv - i ---vvv i C L2#LINE/L2 1967 GGGACGAAAGCCTGATTGGAGTGGGTTCAAGAGAGAATGGGAGGAGAGGA 1918 chr3ptel1M 306287 ACTGGAAACCTTGGATGCAGATGTCCTCCTC-AAGAATTTAGCCCCAAAG 306335 i i vvi ii ii iiv iiii - i i v ivi C L2#LINE/L2 1917 ATTGGAGACAGCGAGTATAGACAACTCTTTCGAGGAGTTTTGCTGTAAAG 1868 chr3ptel1M 306336 GGGGACAGGAA 306346 ii ii C L2#LINE/L2 1867 GGGAGCAGAGA 1857 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 48.91 CpG sites = 74, Kimura (unadjusted) = 50.95 Transitions / transversions = 2.00 (74/37) Gap_init rate = 0.05 (15 / 318), avg. gap size = 3.00 (45 / 15) 389 27.22 11.24 0.00 chr3ptel1M 306346 306514 (693486) C MIR#SINE/MIR (10) 252 65 m_b117s601i16 4245 chr3ptel1M 306346 AGCATTT-TAAAGCACCCACTAGGTGCCTGGCGCTGTGC-AAGCACTTT- 306392 i - vi i ii v v i v - i - C MIR#SINE/MIR 252 AACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGCGCTTTA 203 chr3ptel1M 306393 ----TACAAA----TTTCAGCC---CAACAATGCTGTGAGGCAGGGGCTC 306431 ---- iv ---- v v --- iv i i vi v C MIR#SINE/MIR 202 CATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGGTAGGTACTA 153 chr3ptel1M 306432 TTGGGATCCC-ATTTTATAGCCGAGGACACTGAGGCAAAATGAGGT---G 306477 ivv - i vi v v iv --- C MIR#SINE/MIR 152 TTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAG 103 chr3ptel1M 306478 TCCCATCTGCAAGGTTGCTGAGCT-GCCTGGGGCAGAG 306514 vv v viv ii vv - ivv v C MIR#SINE/MIR 102 TAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAG 65 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 32.23 CpG sites = 20, Kimura (unadjusted) = 33.95 Transitions / transversions = 0.77 (20/26) Gap_init rate = 0.05 (9 / 168), avg. gap size = 2.11 (19 / 9) 284 29.40 5.65 3.97 chr3ptel1M 310160 310283 (689717) C L2b_3end#LINE/L2 (10) 456 331 m_b117s601i17 4246 chr3ptel1M 310160 TCAAAAGACACTTA-TGAACACCTACTGCGTGCACAG--TCTAC-CTGGG 310205 v i i i - i i i - --? ii- i C L2b_3end#LINE 456 TCAACAAATATTTACTGAGCGCCTACTGTGTGC-CAGGCNCTGTGCTAGG 408 chr3ptel1M 310206 CACTGAAGGTCCTGAAGTCCAAAAGGCAA--GCAGCTCCTGCCCTCA-AG 310252 i ii i v v vi vv v i i--? i ii -i C L2b_3end#LINE 407 CGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGG 358 chr3ptel1M 310253 AGCTTGCAGTCCTTTGGGTGGAAGAAATAGA 310283 ii i----i ii i i C L2b_3end#LINE 357 AGCTCACAGTCT----AGTGGGGGAGACAGA 331 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 34.14 CpG sites = 28, Kimura (unadjusted) = 41.85 Transitions / transversions = 4.00 (28/7) Gap_init rate = 0.08 (10 / 123), avg. gap size = 1.20 (12 / 10) 345 28.65 8.70 1.35 chr3ptel1M 312048 312185 (687815) C MIRc#SINE/MIR (120) 148 1 m_b117s601i18 4247 chr3ptel1M 312048 CTCAATTGACAGACTGGGAAACTGAGGC-AAACAAGACTATTTGACTTGT 312096 i v v ivi -v ivi ii vv i C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr3ptel1M 312097 TCAGCTTCATACAACTAGTGTCTG--AGAAT--GGATTTATGCTCA-GTG 312141 i ivv i i ivv -- ii-- i iivi i - v C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTC 49 chr3ptel1M 312142 CTCCTG------AATCCAGGGCTCTGTCCATTCTGCCCCCCACTGCCTCG 312185 i ------ i v v -- v v C MIRc#SINE/MIR 48 TTCCTGACTCCAAGTCCAGTGCTCTTTCCA--CTGCACCACACTGCCTCG 1 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 35.63 CpG sites = 22, Kimura (unadjusted) = 36.95 Transitions / transversions = 1.29 (22/17) Gap_init rate = 0.05 (7 / 137), avg. gap size = 2.00 (14 / 7) 504 32.85 7.91 0.87 chr3ptel1M 312360 312789 (687211) L2#LINE/L2 1475 1934 (1148) m_b117s601i19 4248 chr3ptel1M 312360 ACTTTTGGGTGGATGTTCT-GCCTCCTAGTTTACAGAAAGAGCTGAAGCC 312408 i ii v - vi - i v i v i i iiv v L2#LINE/L2 1475 ACTCTCAGCTG-ATGACCTTGCTTCCTATTTCACTGAGAAAATAGAAGCA 1523 chr3ptel1M 312409 ATTCACTGTCAGCTCTCCCTTGTCCCTTCTTGCCCATCTTCCATCACTCA 312458 ivivv vv i ii v v??ii iv ivv v v -- ii L2#LINE/L2 1524 ATCAGAAGAGAACTTCCACANNCTCCCACCACCACATCTACC--CACCTA 1571 chr3ptel1M 312459 GCCCCCTTCTGC-CCCATCTCCTCTTCCTACCAACTCGC----ACGAGGA 312503 - iv v i- iv v v v vv ii i---- iivi L2#LINE/L2 1572 -CCTGCATCTGTGCCCACATACTCTGCCTTCCCTCCTGTTACTACGGATG 1620 chr3ptel1M 312504 AGCCGTCTCC-CTGCTGACCAAGGCCAAGCCTTCC-CCTGCCCAATGG-T 312550 i i ivi- v iv i v i - i iv v i - L2#LINE/L2 1621 AACTGTCCGTGCTCCTATCTAAGGCCAACCCCTCCACTTGTGCACTAGAT 1670 chr3ptel1M 312551 CCCCTTCCATCCCAGCTCCTCCAGCACACTGCTCCT-CTGTTGTCCCCGC 312599 v i v i iv v v v ii v- vi v v L2#LINE/L2 1671 CCCATCCCCTCTCGCCTACTCAAGGACATCGCTCCAGCAATTCTCCCCTC 1720 chr3ptel1M 312600 TTTCTCTT--ATTTTTAATCAATCCCTGTCCACTGGCTCATTTCCTACTG 312647 i i -- iv i ivv v i v i vv v L2#LINE/L2 1721 TCTCTCCTGCATCATCAATTTTTCCCTCTCTACTGGATCATTCCCATCAG 1770 chr3ptel1M 312648 TCTATAAACATGATTATATCTCTCCCATCCTGAAAAAACA-------TCC 312690 iv i v vv? i i v ------- L2#LINE/L2 1771 CATACAAACATGCTGTNATTTCTCCCATCTTTAAAAAACAAAAATTCTCC 1820 chr3ptel1M 312691 CT------CACTTCAGCCTT------CCATCCTATATCTCTCCTGCCCTT 312728 ------ ? vv i------ ii i v v v L2#LINE/L2 1821 CTTGACCCCACNTCCCCCTCCAGCTACCGCCCCATTTCTCTGCTCCCCTT 1870 chr3ptel1M 312729 TGTGGCTAAATTCAT---AAAATTTGTCTACACCAGGAGCCTCCGCTGCC 312775 iii v i v --- i v i iv vv i iv v L2#LINE/L2 1871 TACAGCAAAACTCCTCGAAAGAGTTGTCTATACTCGCTGTCTCCAATTCC 1920 chr3ptel1M 312776 TCTCCTCCCATCCT 312789 i L2#LINE/L2 1921 TCTCCTCCCATTCT 1934 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 42.88 CpG sites = 71, Kimura (unadjusted) = 44.56 Transitions / transversions = 1.03 (71/69) Gap_init rate = 0.04 (16 / 429), avg. gap size = 2.38 (38 / 16) 26 5.48 2.63 0.00 chr3ptel1M 313723 313760 (686240) (GTGTGAGT)n#Simple_repeat 1 39 (0) c_b117s251i2 4249 chr3ptel1M 313723 GTGTGTGTGTGT-AGTGTGTTAGTGTGTGAGTGTGTGAG 313760 v - v (GTGTGAGT)n#S 1 GTGTGAGTGTGTGAGTGTGTGAGTGTGTGAGTGTGTGAG 39 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 36 4.81 0.00 0.00 chr3ptel1M 313945 313987 (686013) (GTGTGAGTGT)n#Simple_repeat 1 43 (0) c_b117s251i3 4250 chr3ptel1M 313945 GTGTGTGTGTGTGTGAGTGTGTGTGAGCGTGTGTGAGTGTGTG 313987 v i (GTGTGAGTGT)n 1 GTGTGAGTGTGTGTGAGTGTGTGTGAGTGTGTGTGAGTGTGTG 43 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 30 2.56 2.38 2.38 chr3ptel1M 314091 314132 (685868) (TGTGAGTGTG)n#Simple_repeat 1 42 (0) c_b117s251i4 4251 chr3ptel1M 314091 TGTGAGTGTGTGTGAGTGTGTGGTGAGCGTGTGTGAGT-TGTG 314132 - i - (TGTGAGTGTG)n 1 TGTGAGTGTGTGTGAGTGTGT-GTGAGTGTGTGTGAGTGTGTG 42 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.05 (2 / 41), avg. gap size = 1.00 (2 / 2) 30 8.12 0.00 0.00 chr3ptel1M 314734 314772 (685228) (GT)n#Simple_repeat 1 39 (0) c_b117s251i5 4252 chr3ptel1M 314734 GTGTGTGTGTGTGTGTGTGTGAGCGTGTGTGAGTGTGTG 314772 v i v (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 39 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 15 23.72 0.00 0.00 chr3ptel1M 315363 315402 (684598) (GCAGG)n#Simple_repeat 1 40 (0) m_b117s252i8 4253 chr3ptel1M 315363 GCGGGGCTGTGCAGGGCAGGGCAGGACGGAGCGGGGCTGG 315402 i v v i i i i v (GCAGG)n#Simp 1 GCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGG 40 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 18 11.64 0.00 5.13 chr3ptel1M 315434 315474 (684526) (GACTGAC)n#Simple_repeat 1 39 (0) m_b117s252i9 4254 chr3ptel1M 315434 GACTGACGACTGACGACGGACCCACCGATCGACTGACGCCT 315474 v - v i - v (GACTGAC)n#Si 1 GACTGACGACTGACGACTGA-CGACTGA-CGACTGACGACT 39 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 32 0.00 0.00 0.00 chr3ptel1M 315611 315640 (684360) (GCG)n#Simple_repeat 1 30 (0) c_b117s251i6 4255 chr3ptel1M 315611 GCGGCGGCGGCGGCGGCGGCGGCGGCGGCG 315640 (GCG)n#Simple 1 GCGGCGGCGGCGGCGGCGGCGGCGGCGGCG 30 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 13 9.78 0.00 0.00 chr3ptel1M 315763 315784 (684216) (GCC)n#Simple_repeat 1 22 (0) m_b117s252i11 4256 chr3ptel1M 315763 GCCGCGGCCGCCGCCGCCTCCG 315784 v v (GCC)n#Simple 1 GCCGCCGCCGCCGCCGCCGCCG 22 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 20 10.11 3.12 0.00 chr3ptel1M 316017 316048 (683952) (GT)n#Simple_repeat 1 33 (0) m_b117s252i12 4257 chr3ptel1M 316017 GTGTGTGTGTGTGTGTGTGTG-GCGCGAGTGTG 316048 - i i v (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 33 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 13 12.39 5.41 2.63 chr3ptel1M 317160 317196 (682804) (CTGGCC)n#Simple_repeat 1 38 (0) m_b117s252i13 4258 chr3ptel1M 317160 CTGGGCCTGG--CTGGCTCAGGCCCTGGCCCTCAGCCCT 317196 v -- i v -i (CTGGCC)n#Sim 1 CTGGCCCTGGCCCTGGCCCTGGCCCTGGCCCT-GGCCCT 38 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.50 (3 / 2) 18 18.06 0.00 7.41 chr3ptel1M 317597 317654 (682346) (CTCTGT)n#Simple_repeat 1 54 (0) m_b117s252i14 4259 chr3ptel1M 317597 CTCTTTCTCTGTCTCTGTTACTCTGCCTATGCTTCTTTCTCTATACCTCT 317646 v - - i v ii v i -- (CTCTGT)n#Sim 1 CTCTGTCTCTGTCTCTG-T-CTCTGTCTCTGTCTCTGTCTCTGT--CTCT 46 chr3ptel1M 317647 GCCTCTGT 317654 i (CTCTGT)n#Sim 47 GTCTCTGT 54 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.07 (4 / 57), avg. gap size = 1.00 (4 / 4) 108 5.60 5.99 0.00 chr3ptel1M 317658 317824 (682176) (TC)n#Simple_repeat 1 177 (0) c_b117s251i7 4260 chr3ptel1M 317658 TCTCTGTCTCTGTCTCTCTTTGTCTCTGTCTCTCTCT-TCT-TCTCTCTC 317705 v v i v v - - (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr3ptel1M 317706 TCTTTCT-TAT-TCTCTCTCTTTCT-TC-CTCTCTC-CTCTCTCT-TC-C 317748 i - v - i - - - - - (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chr3ptel1M 317749 TCTCTCTCTCTC-CTCTCTCTCTCCCTCTCTCTCTCTCTCTCTCTCTCTC 317797 - i (TC)n#Simple_ 101 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 150 chr3ptel1M 317798 TCTCTCTCTCTCTCTCTCTCTCTCTCT 317824 (TC)n#Simple_ 151 TCTCTCTCTCTCTCTCTCTCTCTCTCT 177 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.06 (10 / 166), avg. gap size = 1.00 (10 / 10) 297 31.37 4.93 3.47 chr3ptel1M 319005 319146 (680854) MIRc#SINE/MIR 96 239 (29) m_b117s601i20 4261 chr3ptel1M 319005 TGAGCAAACTATTTTTTCCCTTTTTGGGTCTCAGTAGGCTCATCTTTAAA 319054 i iii i v--v i i i i vvv v MIRc#SINE/MIR 96 TGGGCAAGTCACTTA--ACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAA 143 chr3ptel1M 319055 ATGGGGGTACTGTTATTTG-CTTGCCCACCTGCAGCGAGTT----TGGGG 319099 i v iv ii - i i - vv i ---- i MIRc#SINE/MIR 144 ATGGGGATAATAATACCTGCCCTGCCTACCT-CACAGGGTTGTTGTGAGG 192 chr3ptel1M 319100 --TAGATGAGGCAATCTCTGTACAGCTGGTGATTAGAAACAGTCAAGTG 319146 --i i ii v v iv ivi v -- iv v v MIRc#SINE/MIR 193 ATCAAATGAGATAATGTATGTGAAAGCGCT--TTGTAAACTGTAAAGTG 239 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 40.63 CpG sites = 25, Kimura (unadjusted) = 41.92 Transitions / transversions = 1.39 (25/18) Gap_init rate = 0.06 (8 / 141), avg. gap size = 1.50 (12 / 8) 299 35.12 5.33 1.28 chr3ptel1M 320314 320463 (679537) MIRc#SINE/MIR 7 162 (106) m_b117s601i21 4262 chr3ptel1M 320314 AATGTCCTGTAATATGAATTGAACCAGACTTTGGGTT-GGA------GAG 320356 i vv i i ivi vv v ii v i i- ------ i MIRc#SINE/MIR 7 AGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGG 56 chr3ptel1M 320357 CTCGTGTCCTGGCTCCTACACAGATTAATGAGGTGAGAGTTTGGGCCCGC 320406 i v i ivv vv i iiv-- v vi vv i MIRc#SINE/MIR 57 TTCGAGTCCCGGCTCTGCCACTTACTAGCT--GTGTGACCTTGGGCAAGT 104 chr3ptel1M 320407 CACTTGACCTCTATGGACCTCAGGGTCTGACTCTA-GAAATGAGAATGAG 320455 i v ii vv ivvv i-i i i i v MIRc#SINE/MIR 105 CACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAAT 154 chr3ptel1M 320456 AATACTTG 320463 i MIRc#SINE/MIR 155 AATACCTG 162 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 47.38 CpG sites = 28, Kimura (unadjusted) = 48.69 Transitions / transversions = 1.17 (28/24) Gap_init rate = 0.03 (5 / 149), avg. gap size = 2.00 (10 / 5) 322 33.83 9.09 3.53 chr3ptel1M 322556 322797 (677203) L3#LINE/CR1 2839 3093 (1006) m_b117s601i22 4263 chr3ptel1M 322556 CACCGAGAGCCAGTGCAGCCTTTCCAGGAACAGGGTGGGTT---CTT-CC 322601 iii iiii vi iv i i i viiv ii--- v- L3#LINE/CR1 2839 CACTAGGAGCCAGCATGGGTTCACTAAGAACAAGTCATGCCAAACTAACC 2888 chr3ptel1M 322602 TGGTCTCCTTTTTTGACACGGTTGCCACCCTGGCAGATTGGGGAAGGGGG 322651 vi i i v i i vv i i---- i ii L3#LINE/CR1 2889 TCATTTCCTTTTTTGATAGGGTTACTAGACTGGTAGATC----AGGGGAA 2934 chr3ptel1M 322652 TGCCACTGAGGTCCATTGCGTA----GATTTTAGCAAAGCATCTGACAAA 322697 iiv ---- ?v i ---- i i i L3#LINE/CR1 2935 TGCCGTAGA----CANAGTGTATCTGGATTTCAGCAAGGCATTTGACAAA 2980 chr3ptel1M 322698 CATATTGATG--CTCTTTGTCTAGAAACTGGACCAA-ATGG------TGA 322738 vvivi v --v i vv v iv vv - ------ L3#LINE/CR1 2981 GTCTCTCATGATATCCTTGTGGACAAGATGGAGAAATATGGGCTGGATGA 3030 chr3ptel1M 322739 TTGGAC----AGGTGCCAACCG-AGCAGGTGCACTGGCTGTACCAGAAGA 322783 v v ---- -v vi - v vv vi i i vi ii L3#LINE/CR1 3031 TAGTACAGTTAGGTG-GATTCGTAGCTGGTTGAACGACTATACCCAAAAG 3079 chr3ptel1M 322784 GTAGTCATCCATGG 322797 iv v iv L3#LINE/CR1 3080 GTGTTGATTAATGG 3093 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 45.26 CpG sites = 45, Kimura (unadjusted) = 46.90 Transitions / transversions = 1.32 (45/34) Gap_init rate = 0.07 (17 / 241), avg. gap size = 1.82 (31 / 17) 264 17.55 22.83 0.89 chr3ptel1M 323585 323676 (676324) L2a_3end#LINE/L2 369 480 (37) m_b117s601i23 4264 chr3ptel1M 323585 TTTATGTATTGTC------CTCCCTTTAGAATATAAG-TCCCTGA--GCA 323625 i v ------ i vi i - v -- L2a_3end#LINE 369 TTTGTTTATTGTCTGTCTCCCCCCACTAGAATGTAAGCTCCATGAGGGCA 418 chr3ptel1M 323626 AGGACTCTT-TCTGCCTCTGT------CTGTATTCCCAGC-----GGATA 323663 i i - -i i ------ i ----- i i L2a_3end#LINE 419 GGGACTTTTGTCTG-TTTTGTTCACTGCTGTATCCCCAGCGCCTAGAACA 467 chr3ptel1M 323664 GTACCTGGCATAT 323676 i i L2a_3end#LINE 468 GTGCCTGGCACAT 480 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 20.89 CpG sites = 13, Kimura (unadjusted) = 20.89 Transitions / transversions = 4.33 (13/3) Gap_init rate = 0.08 (7 / 91), avg. gap size = 3.14 (22 / 7) 267 25.37 19.51 0.68 chr3ptel1M 323732 323854 (676146) C MIRc#SINE/MIR (120) 148 3 m_b117s601i24 4265 chr3ptel1M 323732 CTCATCTTGCAGATGAGAAATCCAAGGC--AAATAGGGTAATGTGACTTG 323779 i i i i v ii -- i v v - C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAA-GTGACTTG 100 chr3ptel1M 323780 CCCAGGGTC------------AGCGTCTGAA--GGCAC----ATC---AT 323808 i ------------ i v v i-- v ---- i ---i C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGT 50 chr3ptel1M 323809 CTTTCTGTTTCAAAGTCTGATGCCCTATTCACTTCTCCAC-CTGGCT 323854 i vi v iii i v i v v - v C MIRc#SINE/MIR 49 CTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTGCCT 3 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 31.84 CpG sites = 19, Kimura (unadjusted) = 31.84 Transitions / transversions = 1.58 (19/12) Gap_init rate = 0.06 (7 / 122), avg. gap size = 3.57 (25 / 7) 273 18.97 1.72 0.00 chr3ptel1M 323732 323789 (676211) C MIR1_Amn#SINE/MIR (80) 150 92 m_b117s601i25 4265 chr3ptel1M 323732 CTCATCTTGCAGATGAGAAATCCAAGGCAAATAG-GGTAATGTGACTTGC 323780 i i i i v ii ?v v - ? v C MIR1_Amn#SINE 150 CCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGC 101 chr3ptel1M 323781 CCAGGGTCA 323789 i C MIR1_Amn#SINE 100 CCAAGGTCA 92 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 23.24 CpG sites = 7, Kimura (unadjusted) = 23.24 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.02 (1 / 57), avg. gap size = 1.00 (1 / 1) 21 24.28 0.00 0.00 chr3ptel1M 325226 325279 (674721) (GAGAGA)n#Simple_repeat 1 54 (0) m_b117s252i15 4266 chr3ptel1M 325226 GAGAGAGAGGGAGGAAGAGACAGAAATAGAGAGGGAGGGAGAGGGAGATA 325275 i ii v i v i i i v (GAGAGA)n#Sim 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr3ptel1M 325276 GTGA 325279 v (GAGAGA)n#Sim 51 GAGA 54 Matrix = Unknown Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 12 19.94 5.00 0.00 chr3ptel1M 325362 325401 (674599) (CCCTGC)n#Simple_repeat 1 42 (0) m_b117s252i17 4267 chr3ptel1M 325362 CCCGGGCACTGGCCCT--CCCTACTCCTGCCCCAGCCCCTGC 325401 v v v v -- i i v (CCCTGC)n#Sim 1 CCCTGCCCCTGCCCCTGCCCCTGCCCCTGCCCCTGCCCCTGC 42 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.03 (1 / 39), avg. gap size = 2.00 (2 / 1) 253 30.85 5.32 0.00 chr3ptel1M 326151 326244 (673756) C MIR#SINE/MIR (120) 142 44 m_b117s601i26 4268 chr3ptel1M 326151 CATTTTACTCATGATGAAATCA--GCTTGGAGGCGCTGAGTAACAGTCCC 326198 vv v iii-- vii iv i i vvv C MIR#SINE/MIR 142 CATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCC 93 chr3ptel1M 326199 CGGGTCACACAGCTGGCAGGTGCTAGA-CTGAGA--CCATCCTAAGCAG 326244 vi i i i vi - i i -- v v i i C MIR#SINE/MIR 92 AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGCAG 44 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 39.13 CpG sites = 17, Kimura (unadjusted) = 40.97 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.03 (3 / 93), avg. gap size = 1.67 (5 / 3) 260 29.63 3.70 0.00 chr3ptel1M 326151 326231 (673769) C MIRb#SINE/MIR (119) 149 66 m_b117s601i27 4268 chr3ptel1M 326151 CATTTTACTCATGATGAAATCA--GCTTGGAGGCGCTGAGTAACAGTCCC 326198 vv v iii-- ii iv i i vvv C MIRb#SINE/MIR 149 CATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCC 100 chr3ptel1M 326199 CGGGTCACACAGCTGGCAGGTGCTAGA-CTGAGA 326231 vi i i i vi - i i C MIRb#SINE/MIR 99 AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGA 66 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 37.02 CpG sites = 15, Kimura (unadjusted) = 39.12 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.03 (2 / 80), avg. gap size = 1.50 (3 / 2) 457 26.15 5.38 0.00 chr3ptel1M 326614 326743 (673257) C MER63D#DNA/hAT-Tip100 (589) 472 336 m_b117s502i0 4269 chr3ptel1M 326614 ACATAACACGATTTTAGGTTTAATTTGAAATATTAATGTTTTCTACGTCA 326663 ii iv i i v v ii v i C MER63D#DNA/hA 472 ACACGACACACTTTTAAGTTTAATCTGCATTATTAACATTTTCTCCATCA 423 chr3ptel1M 326664 TTTGCTT-----TAGATAATCAATGAAATAA--AACCAAGTCCCAATTTG 326706 i v ----- i ii i -- i i ii C MER63D#DNA/hA 422 CTTTCTTAAGTCTAGACAATCAACAAAACAATAAATCAAGCCCTGATTTG 373 chr3ptel1M 326707 TAATACTGGTCAGTTTCTGAGGTGAAAATACTCTCAC 326743 iiii v i ii i v v i C MER63D#DNA/hA 372 TAGCGTTTGCCGATTTCCGTGGTGTAAATACTCCCAC 336 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 29.08 CpG sites = 26, Kimura (unadjusted) = 34.24 Transitions / transversions = 3.25 (26/8) Gap_init rate = 0.02 (2 / 129), avg. gap size = 3.50 (7 / 2) 473 26.76 1.39 1.39 chr3ptel1M 327258 327401 (672599) C MIRb#SINE/MIR (117) 151 8 m_b117s601i28 4270 chr3ptel1M 327258 CTCATCTTACAGATGAGGAAACTCAGGCAAACAG-GGTGAAGTGACTGGG 327306 i i v vv v - v i v v C MIRb#SINE/MIR 151 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGC 102 chr3ptel1M 327307 CCAGAGTCACAGAGCTAGGAAGTAGGTGAGGGCAGATTTGAACTCAGGTC 327356 ii v v i vv vvvi i i C MIRb#SINE/MIR 101 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTC 52 chr3ptel1M 327357 TGCTCAGAAT-TAGGACTGGTGCCCCATCCACTTCATCCTAGCTGC 327401 - v v -i iii iv i iv v i vi- C MIRb#SINE/MIR 51 TG-TCTGACTCCAAAGCCCGTGCTCTTTCCACTGCACCAC-GCTGC 8 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 31.29 CpG sites = 18, Kimura (unadjusted) = 33.35 Transitions / transversions = 0.90 (18/20) Gap_init rate = 0.03 (4 / 143), avg. gap size = 1.00 (4 / 4) 27 0.00 0.00 0.00 chr3ptel1M 328095 328120 (671880) (GAGG)n#Simple_repeat 1 26 (0) c_b117s251i8 4271 chr3ptel1M 328095 GAGGGAGGGAGGGAGGGAGGGAGGGA 328120 (GAGG)n#Simpl 1 GAGGGAGGGAGGGAGGGAGGGAGGGA 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 19 13.28 3.45 7.14 chr3ptel1M 328125 328182 (671818) (GAG)n#Simple_repeat 1 56 (0) m_b117s252i18 4272 chr3ptel1M 328125 GAGG-GG-GGAGGAGAGAGAAGAAAGAGGAGGAGGAGAGGGAGAGAGGAG 328172 - - - i i i ii - (GAG)n#Simple 1 GAGGAGGAGGAGGAG-GAGGAGGAGGAGGAGGAGGAGGAGGAG-GAGGAG 48 chr3ptel1M 328173 ACAGGCAGGA 328182 -v - (GAG)n#Simple 49 -GAGG-AGGA 56 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.11 (6 / 57), avg. gap size = 1.00 (6 / 6) 12 21.14 0.00 0.00 chr3ptel1M 328244 328272 (671728) (TCCCT)n#Simple_repeat 1 29 (0) m_b117s252i19 4273 chr3ptel1M 328244 TCCCTTTCCTTCCTCTCTCCTCCCTTCCC 328272 i ii i i (TCCCT)n#Simp 1 TCCCTTCCCTTCCCTTCCCTTCCCTTCCC 29 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 13 12.03 8.33 0.00 chr3ptel1M 328895 328930 (671070) (GCTCCC)n#Simple_repeat 1 39 (0) m_b117s252i20 4274 chr3ptel1M 328895 GCTCCCGCT-GC-CTCCC-CCCGCCCTCCCGCTCCCGCT 328930 -v - - i v v (GCTCCC)n#Sim 1 GCTCCCGCTCCCGCTCCCGCTCCCGCTCCCGCTCCCGCT 39 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.09 (3 / 35), avg. gap size = 1.00 (3 / 3) 255 18.04 6.85 1.30 chr3ptel1M 329926 329998 (670002) MIR1_Amn#SINE/MIR 80 156 (74) m_b117s601i29 4275 chr3ptel1M 329926 TAGCCCGCT-CGTGGTTCTGGGCA-GTGACTTAACCATT---TACCTCAC 329970 ? ? -? iiii - v ? vi ---?i v MIR1_Amn#SINE 80 TNGCCNGCTGNGTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAG 129 chr3ptel1M 329971 TTTCCTCACCTGCAAAACCGGGGGTAAT 329998 i i -i i MIR1_Amn#SINE 130 TTTCCTCATCTGTAAAA-TGGGGATAAT 156 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 23.37 CpG sites = 10, Kimura (unadjusted) = 23.37 Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.06 (4 / 72), avg. gap size = 1.50 (6 / 4) 553 25.15 8.33 0.60 chr3ptel1M 329936 330091 (669909) MIR#SINE/MIR 85 252 (10) m_b117s601i30 4275 chr3ptel1M 329936 GTGGTTCTGGGCA-GTGACTTAACCATT---TACCTCACTTTCCTCACCT 329981 iiii - v vi --- i v i MIR#SINE/MIR 85 GTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCT 134 chr3ptel1M 329982 GCAAAACCGGGGGTAATAGCGGCCCTTCCCTCCC--------TGGCAGAA 330023 i i- i iii iv i v vi-------- vv i MIR#SINE/MIR 135 GTAAAAT-GGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGGA 183 chr3ptel1M 330024 TTAA-TGAGATAATAGCGGTACAGCATTTAGCACAGTGTCTGGCACATAG 330072 - v vvv v ii v i MIR#SINE/MIR 184 TTAAATGAGTTAATACATGTAAAGCGCTTAGAACAGTGCCTGGCACATAG 233 chr3ptel1M 330073 TAGGTGCTTAATAAGTGCT 330091 i i i i i MIR#SINE/MIR 234 TAAGCGCTCAATAAATGTT 252 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 29.67 CpG sites = 25, Kimura (unadjusted) = 31.61 Transitions / transversions = 1.79 (25/14) Gap_init rate = 0.03 (5 / 155), avg. gap size = 2.80 (14 / 5) 13 13.05 0.00 3.70 chr3ptel1M 330092 330119 (669881) (CCT)n#Simple_repeat 1 27 (0) m_b117s252i21 4276 chr3ptel1M 330092 CCTTCCCTTCCTCCCTCCTCCTCCTCCT 330119 i i i - (CCT)n#Simple 1 CCTCCTCCTCCT-CCTCCTCCTCCTCCT 27 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 367 23.66 5.38 0.00 chr3ptel1M 331493 331585 (668415) C MIR#SINE/MIR (118) 144 47 m_b117s601i31 4277 chr3ptel1M 331493 CTCATGTGACAGATTAGGAAATTGAGGCA-AGCATGGCTAAGTGTCTTGC 331541 i v v v i - viv i iv C MIR#SINE/MIR 144 CCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGC 95 chr3ptel1M 331542 CCAGGGCTACACAGCT----AGTGTCTGAGGTTGAATTTGAACTCAGG 331585 i ii ---- v v viv i i i C MIR#SINE/MIR 94 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGG 47 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 25.85 CpG sites = 12, Kimura (unadjusted) = 28.81 Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.02 (2 / 92), avg. gap size = 2.50 (5 / 2) 18 4.71 0.00 0.00 chr3ptel1M 331698 331719 (668281) (C)n#Simple_repeat 1 22 (0) m_b117s252i22 4278 chr3ptel1M 331698 CCCCCCCGCCCCCCCCCCCCCC 331719 v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCC 22 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 106 14.20 1.03 1.55 chr3ptel1M 331935 332128 (667872) (AAGG)n#Simple_repeat 1 193 (0) m_b117s252i23 4279 chr3ptel1M 331935 AAGG-AGGAAGGAAACGAGGGAGGGAAGGAAGGAAAAGAGAGAGGGAAGG 331983 - - v i i - i ii i (AAGG)n#Simpl 1 AAGGAAGGAAGG-AAGGAAGGAAGGAAGGAAGG-AAGGAAGGAAGGAAGG 48 chr3ptel1M 331984 AAGGAAGGAAGGTTTAGAGGAGGGAGGGAAGGAAGGAAGGAAGGAAGGAA 332033 vvvii i i (AAGG)n#Simpl 49 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 98 chr3ptel1M 332034 GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG 332083 (AAGG)n#Simpl 99 GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG 148 chr3ptel1M 332084 AAGCAGCAAAGGAAGGAGAGAGGGGAGAAATG-AGGAAGGAAAGGA 332128 v ivi ii i i i v - - (AAGG)n#Simpl 149 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG-AAGGA 193 Matrix = Unknown Transitions / transversions = 2.43 (17/7) Gap_init rate = 0.03 (5 / 193), avg. gap size = 1.00 (5 / 5) 356 25.97 5.34 2.99 chr3ptel1M 332517 332647 (667353) MIR3#SINE/MIR 21 154 (54) m_b117s601i32 4280 chr3ptel1M 332517 AGGGAGCCAGGTCTAGAGTTCAG---ATCTGTGATCAAATGTAGCCTCAC 332563 i vv v i iiv --- i v v v i viv v vv MIR3#SINE/MIR 21 AGAGAGCACGGACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTG 70 chr3ptel1M 332564 ACACTGACTAG---TGTGACCCTGGCTGGGCAAGTCACTTCACC-CTGTT 332609 v i ? --- i ---- - v v MIR3#SINE/MIR 71 CCACTAACTNGCTGTGTGACCTTGG----GCAAGTCACTTCACCTCTCTG 116 chr3ptel1M 332610 TGCTTCAGTTTCCTCCTCTGTCAAATAAGGACCCTGGA 332647 v i v v i ivvi MIR3#SINE/MIR 117 GGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGA 154 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 32.26 CpG sites = 13, Kimura (unadjusted) = 32.26 Transitions / transversions = 0.65 (13/20) Gap_init rate = 0.05 (7 / 130), avg. gap size = 1.57 (11 / 7) 217 14.67 0.00 4.88 chr3ptel1M 334000 334042 (665958) C MIR1_Amn#SINE/MIR (75) 155 115 m_b118s601i0 4281 chr3ptel1M 334000 TCAGCTCCATTTCCCAGATGAGGAAACTGAGACCGGCAGAGAG 334042 i v i iv i --? C MIR1_Amn#SINE 155 TTATCCCCATTTTACAGATGAGGAAACTGAGGC--NCAGAGAG 115 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 17.02 CpG sites = 4, Kimura (unadjusted) = 17.02 Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.00 (2 / 2) 13 17.78 0.00 3.03 chr3ptel1M 334505 334538 (665462) (GGGGAG)n#Simple_repeat 1 33 (0) m_b118s252i0 4282 chr3ptel1M 334505 GGGGAGGGGGAGGGCCCGGCGCGAGGGGCAGGGG 334538 vvv - v v (GGGGAG)n#Sim 1 GGGGAGGGGGAGGGGGAGG-GGGAGGGGGAGGGG 33 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 514 24.41 20.00 2.07 chr3ptel1M 335013 335217 (664783) C MIRb#SINE/MIR (0) 268 28 m_b118s601i1 4283 chr3ptel1M 335013 AAGGATATAAGTTAGCATTTATATAGCGCCTGCTGTGTGCCAGACACCGT 335062 vi -i i v vv i i i i i C MIRb#SINE/MIR 268 AATAATA-GAGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGT 220 chr3ptel1M 335063 GGCTCTAAGTGCTTCCCG---ATGGTCTCATTGGATTCT----------- 335098 --- i iv i--- vi vi i ----------- C MIRb#SINE/MIR 219 G---CTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCC 173 chr3ptel1M 335099 -GGGAGGGAGGTG-----------ATTGCACAAATGAGGAAACTGAGG-- 335134 - v v i----------- vi i -- C MIRb#SINE/MIR 172 TGCGAGGTAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCT 123 chr3ptel1M 335135 CAAATAGCGCTAAGTGACTTCTTCAAGCT-------------AGTGTCTG 335171 i v - i i vii v ------------- v v C MIRb#SINE/MIR 122 CAGAGAG-GTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAG 74 chr3ptel1M 335172 AGGCTGGATTTGAACTCAGGTCCTTCTGACTCCAGGCCTAGTACTC 335217 v v i i iv iiv iv i C MIRb#SINE/MIR 73 AGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTC 28 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.84 CpG sites = 29, Kimura (unadjusted) = 30.29 Transitions / transversions = 1.45 (29/20) Gap_init rate = 0.05 (10 / 204), avg. gap size = 4.60 (46 / 10) 101 27.09 5.03 1.77 chr3ptel1M 335441 335877 (664123) (CCCTCAC)n#Simple_repeat 1 451 (0) m_b118s252i1 4284 chr3ptel1M 335441 CCCACCCCCCTCA-CCCACA-GCC-C-CCCCTTTTCCCTCA-TCC-CAGC 335484 v v - v -v - - ivi -i - v (CCCTCAC)n#Si 1 CCCTCACCCCTCACCCCTCACCCCTCACCCCTCACCCCTCACCCCTCACC 50 chr3ptel1M 335485 CCT--CCTCTCCTCCCTCATCCCAGCCCCCTCA-CCCTCCTCCCTCATCC 335531 -- i vi i vvv - vi - (CCCTCAC)n#Si 51 CCTCACCCCTCACCCCTCACCCCTCACCCCTCACCCCTCACCCCTCA-CC 99 chr3ptel1M 335532 CAACCCCCACCCCCCCTCATCCCCAGCCCCCTCA-CCCTCTTCCCTCATC 335580 vv v vi v - vvv - vi i (CCCTCAC)n#Si 100 CCTCACCCCTCACCCCTCA-CCCCTCACCCCTCACCCCTCACCCCTCACC 148 chr3ptel1M 335581 CCAGCCCCCTCA-CCCTCCTCCCTCATCCC-CAGCCCCCATACCCTTTTC 335628 vvv - vi i - v i -v ivi (CCCTCAC)n#Si 149 CCTCACCCCTCACCCCTCACCCCTCACCCCTCACCCCTCA-CCCCTCACC 197 chr3ptel1M 335629 CCTTATCCCAGCCCCCTCA-CCCTCTTCCCTTATCCCAGCCCCCTTA-CC 335676 i i vvv - vi i i vvv i - (CCCTCAC)n#Si 198 CCTCACCCCTCACCCCTCACCCCTCACCCCTCACCCCTCACCCCTCACCC 247 chr3ptel1M 335677 CTCCTCCCTCATCCC-CAGCCCCCACCTCCTCTCCTCCCCAGCCCCCACC 335725 vi i - v i - v - i v i - (CCCTCAC)n#Si 248 CTCACCCCTCACCCCTCACCCCTCACC-CCTCACC-CCTCACCCCTCA-C 294 chr3ptel1M 335726 CCCTCTTCCCTCATCCCAGCCCCCTCA-CCCTCCTCCCTCATCCCAAAGC 335774 vi i vvv - vi i vv - (CCCTCAC)n#Si 295 CCCTCACCCCTCACCCCTCACCCCTCACCCCTCACCCCTCACCCCTCA-C 343 chr3ptel1M 335775 CCCCCTCACC-CTCCCCTCATCCCAACCCCCCTCA-CCCTCCTCCCTCAT 335822 i v v - v - vv v - vi i (CCCTCAC)n#Si 344 CCCTCACCCCTCACCCCTCA-CCCCTCACCCCTCACCCCTCACCCCTCAC 392 chr3ptel1M 335823 CCCCAACCCCTCACCCCTTTCCCTTC-CCCATC-CTCC-CAGCCC-CTCC 335868 iv iv i - v - i - v - v (CCCTCAC)n#Si 393 CCCTCACCCCTCACCCCTCACCCCTCACCCCTCACCCCTCACCCCTCACC 442 chr3ptel1M 335869 CATTACCCC 335877 v i (CCCTCAC)n#Si 443 CCTCACCCC 451 Matrix = Unknown Transitions / transversions = 0.66 (38/58) Gap_init rate = 0.07 (29 / 436), avg. gap size = 1.03 (30 / 29) 202 35.94 0.00 0.00 chr3ptel1M 336785 336848 (663152) C L3#LINE/CR1 (3) 4096 4033 m_b118s601i2 4285 chr3ptel1M 336785 AGGATGGCAGAATCCCAGGGCCTGGAGAGGCCTTCGAGGCTGCCCAGTCC 336834 i vi i i iiv i i i v iiii i C L3#LINE/CR1 4096 AGAATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCC 4047 chr3ptel1M 336835 AAGTGCTCGGCCAA 336848 viv i iv C L3#LINE/CR1 4046 AACCTCCCATCCAA 4033 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 54.23 CpG sites = 17, Kimura (unadjusted) = 54.23 Transitions / transversions = 2.83 (17/6) Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0) 331 23.08 9.62 0.00 chr3ptel1M 337362 337465 (662535) C L2c_3end#LINE/L2 (7) 471 358 m_b118s601i3 4286 chr3ptel1M 337362 CAATCGATCTACATTTATTAAGCACCACATATGTGCCAGGCAC-GGAGCT 337410 v i ivv i i vvv i - i v C L2c_3end#LINE 471 CATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGAT 422 chr3ptel1M 337411 A-AGTGCTG---AGGACA--GTCCCTGTCCTTAAGGGGCATACT-TCTA- 337452 - iv v --- i -- i i i vi v- - C L2c_3end#LINE 421 ACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAG 372 chr3ptel1M 337453 -GGAGGAGACAAAC 337465 - i C L2c_3end#LINE 371 TGGAGGAGACAGAC 358 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 25.31 CpG sites = 13, Kimura (unadjusted) = 27.93 Transitions / transversions = 1.18 (13/11) Gap_init rate = 0.07 (7 / 103), avg. gap size = 1.43 (10 / 7) 16 13.63 8.00 1.89 chr3ptel1M 339368 339417 (660583) (CCTGCC)n#Simple_repeat 1 53 (0) m_b118s252i2 4287 chr3ptel1M 339368 CCTGACCCTGCCCCCAGCACC--CCCCT-CCTCAG-CCCTGCCCCTGCCT 339413 v - v v -- - i v - i (CCTGCC)n#Sim 1 CCTGCCCCTG-CCCCTGCCCCTGCCCCTGCCCCTGCCCCTGCCCCTGCCC 49 chr3ptel1M 339414 CTGC 339417 (CCTGCC)n#Sim 50 CTGC 53 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.08 (4 / 49), avg. gap size = 1.25 (5 / 4) 24 5.55 2.50 2.50 chr3ptel1M 339781 339820 (660180) (GAG)n#Simple_repeat 1 40 (0) m_b118s252i3 4288 chr3ptel1M 339781 GAGG-GGATGGAAGAGGAGGAGGAGGAGGAGGAGAAGGAGG 339820 - - i i (GAG)n#Simple 1 GAGGAGGA-GGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGG 40 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 201 27.40 17.81 0.00 chr3ptel1M 340976 341048 (658952) L2c_3end#LINE/L2 381 466 (12) m_b118s601i4 4289 chr3ptel1M 340976 GAGCTCCCTGAGAAAGGGGACCG--------TCCTCTTGGTGTCCCCA-- 341015 i iivi -------- v v i -- L2c_3end#LINE 381 GAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTATCCCCAGC 430 chr3ptel1M 341016 -CTCAG--CAGAGTTAGCAGCCAGCAAATATTTGTT 341048 - iii -- v vi ivi ii i L2c_3end#LINE 431 GCCTGGCACATAGTAGGCGCTCAATAAATGTTTGTT 466 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.58 CpG sites = 14, Kimura (unadjusted) = 35.83 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.06 (4 / 72), avg. gap size = 3.25 (13 / 4) 45 18.72 1.04 1.04 chr3ptel1M 341049 341144 (658856) (CATT)n#Simple_repeat 1 96 (0) m_b118s252i4 4290 chr3ptel1M 341049 CACTCATTCATTCATTCACTCACTCATTCATTCATCCATTCATTCGCTCA 341098 i i i i ii (CATT)n#Simpl 1 CATTCATTCATTCATTCATTCATTCATTCATTCATTCATTCATTCATTCA 50 chr3ptel1M 341099 CTCATTCATCCATTCACTAACTCACTCACCCATT-TTTCTATTCATT 341144 i i i v i i ii -v - (CATT)n#Simpl 51 TTCATTCATTCATTCATTCATTCATTCATTCATTCATTC-ATTCATT 96 Matrix = Unknown Transitions / transversions = 6.50 (13/2) Gap_init rate = 0.02 (2 / 95), avg. gap size = 1.00 (2 / 2) 305 27.93 13.79 1.23 chr3ptel1M 341190 341334 (658666) MIR3#SINE/MIR 20 182 (26) m_b118s601i5 4291 chr3ptel1M 341190 GAGA-AGCA-GGGCTGGGGG--AGGAGGACCTGGAGTTAAATCCTAGTCC 341235 - - i i -- - iv iv i ii ii MIR3#SINE/MIR 20 GAGAGAGCACGGACTGGGAGTCAGGAG-ACCTGGGTTCTAGTCCCGGCTC 68 chr3ptel1M 341236 TACCACTTATTAGCCATGTG--CCTGAACCCAT-ACTTTACCTCT----- 341277 i v i ? ii -- i ii vvi - i ----- MIR3#SINE/MIR 69 TGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGG 118 chr3ptel1M 341278 -----GTT--CTTATGGGTACAGAGGAGGCAGCTGGACTCAGT-AGCTGG 341319 ----- -- i vv - i v vi i vii - v vv MIR3#SINE/MIR 119 CCTCAGTTTCCTCATCTGTA-AAATGAGGGGGTTGGACTAGATGATCTCT 167 chr3ptel1M 341320 AAGGTCCCTCCTGGC 341334 i ii MIR3#SINE/MIR 168 AAGGTCCCTTCCAGC 182 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.66 CpG sites = 27, Kimura (unadjusted) = 36.97 Transitions / transversions = 2.08 (27/13) Gap_init rate = 0.08 (11 / 144), avg. gap size = 2.00 (22 / 11) 61 26.85 4.81 0.46 chr3ptel1M 341858 342065 (657935) (AG)n#Simple_repeat 1 217 (0) m_b118s252i5 4292 chr3ptel1M 341858 AGAGACACCGACAGAGAAAG-GAGAGAGACAGAGAGAG-GAGACACACAG 341905 v vv v i - v - v v v (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr3ptel1M 341906 GAAAACAGAGAAAGAAGGATAGAAGGAGAAAGAGAGAAAGAG-GGGAGAA 341954 ii i v i ii v ii i i - i i (AG)n#Simple_ 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 100 chr3ptel1M 341955 AGA-AAAGAAAGGGAGGAAGAGAGGGAATGGAAGAGAGCAGAGAGAG-GA 342002 - i i i ii i iv ii - - (AG)n#Simple_ 101 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG-AGAGAGAGAGA 149 chr3ptel1M 342003 GAGAAAGAGGGAAGGAGAG-GAGA-AGAGAAGGAGAGGGAGGGTAAG-GG 342049 i i ii - - ii i i vi - i (AG)n#Simple_ 150 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 199 chr3ptel1M 342050 GAGGGA-AGA-AGAGAGA 342065 i - - (AG)n#Simple_ 200 GAGAGAGAGAGAGAGAGA 217 Matrix = Unknown Transitions / transversions = 2.75 (33/12) Gap_init rate = 0.05 (11 / 207), avg. gap size = 1.00 (11 / 11) 15 12.52 0.00 7.89 chr3ptel1M 342053 342093 (657907) (GGAAAAA)n#Simple_repeat 1 38 (0) m_b118s252i6 4293 chr3ptel1M 342053 GGAAGAAGAGAGAAAATAAAAATGGGAAAAAGGAAAAAGGA 342093 i - - vi -i (GGAAAAA)n#Si 1 GGAAAAAG-GA-AAAAGGAAAA-AGGAAAAAGGAAAAAGGA 38 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.07 (3 / 40), avg. gap size = 1.00 (3 / 3) 104 10.09 0.60 0.60 chr3ptel1M 342741 342906 (657094) (CCT)n#Simple_repeat 1 166 (0) c_b118s251i0 4294 chr3ptel1M 342741 CCTCCTTCTCCTCCTCCTCTTCCTCCTCCTCTTCCTCCTCCTCCTCTTCC 342790 i i i i (CCT)n#Simple 1 CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC 50 chr3ptel1M 342791 TCCTCCTCCTCCTCCTCCTCCTTCTCCTCCTCCTCCTCCTTCTCCTCCTC 342840 i i (CCT)n#Simple 51 TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC 100 chr3ptel1M 342841 CTCTTCCTTCTCTTCCTCCTCCTCTTCTTCCTCTTCTTCCTCCTTCT-CT 342889 i i i i i i i i - (CCT)n#Simple 101 CTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT 150 chr3ptel1M 342890 TCTCCCTCCTCCTCCTC 342906 i - (CCT)n#Simple 151 CCT-CCTCCTCCTCCTC 166 Matrix = Unknown Transitions / transversions = 1.00 (15/0) Gap_init rate = 0.01 (2 / 165), avg. gap size = 1.00 (2 / 2) 13 13.25 0.00 0.00 chr3ptel1M 342917 342941 (657059) (CTG)n#Simple_repeat 1 25 (0) m_b118s252i7 4295 chr3ptel1M 342917 CTTCTGCTTCTCCTGCTGCTGCTGC 342941 v v v (CTG)n#Simple 1 CTGCTGCTGCTGCTGCTGCTGCTGC 25 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 17 14.58 0.00 10.00 chr3ptel1M 343620 343674 (656326) (TTCT)n#Simple_repeat 1 50 (0) m_b118s252i8 4296 chr3ptel1M 343620 TTCTCTCTGTGTGTATCTTTCTTTTCTTTCCTTTTTTATTTCTTTTCTTT 343669 i - - v v - i i v - - (TTCT)n#Simpl 1 TTCTTTCT-T-TCTTTCTTTC-TTTCTTTCTTTCTTTCTTTC-TTTC-TT 45 chr3ptel1M 343670 TCTTT 343674 (TTCT)n#Simpl 46 TCTTT 50 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.09 (5 / 54), avg. gap size = 1.00 (5 / 5) 25 5.71 0.00 2.63 chr3ptel1M 343637 343675 (656325) (TTTCT)n#Simple_repeat 1 38 (0) m_b118s252i9 4296 chr3ptel1M 343637 TTTCTTTTCTTTCCTTTTTTATTTCTTTTCTTTTCTTTT 343675 i i - (TTTCT)n#Simp 1 TTTCTTTTCTTTTCTTTTCT-TTTCTTTTCTTTTCTTTT 38 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.03 (1 / 38), avg. gap size = 1.00 (1 / 1) 649 34.92 5.03 0.72 chr3ptel1M 344111 344508 (655492) C L1ME4c_3end#LINE/L1 (191) 639 225 m_b118s551i0 4297 chr3ptel1M 344111 TTCTACTCACTTCACTCAGCATCAGTTCATGCAAGTCTCTCCAGAATTTT 344160 i ivi i i i vv iv vi i - viv vi C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATAAACATTT-TCCATGTTGCT 591 chr3ptel1M 344161 CTGAAATCCTCCTGCTGGTCATTTCTTATAGAACAATAATATTACATAAC 344210 viiv i i v iv vi i v i vvvv v viv C L1ME4c_3end#L 590 ACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCGA 541 chr3ptel1M 344211 ATACACATATCATAACTTGTTCAGCTATTCCCCAACTGATGGGTACCCAC 344260 i ?v ii i i ii i i i v i v ii iii v C L1ME4c_3end#L 540 GTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAG 491 chr3ptel1M 344261 TTAATTTCCAGTCTCTTGGTACTACAAAAAGAGCTGCCACAAACATTCTT 344310 v vi i i i i v i i v iv v ii ii i C L1ME4c_3end#L 490 GTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTC 441 chr3ptel1M 344311 GCACATCTGGGTCTCTTTCCCTCCTTTAAGATCTTTTTGGAATATAAAT- 344359 ii v i -- i i i i iv v iivv iv - C L1ME4c_3end#L 440 GTGCATATAG--CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAATT 393 chr3ptel1M 344360 -CCAGTAGAAGCATTGCTAGGTCAAAGGGTATGCACAGTTTGATAACTTT 344408 - v vi v i i v v v ii i C L1ME4c_3end#L 392 CCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTCT 343 chr3ptel1M 344409 TTGAGCATAGT----AAT--------------GCTGGATCTGTTCACAAC 344440 vivi i v ---- -------------- i v i vi i ?i C L1ME4c_3end#L 342 TGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACANT 293 chr3ptel1M 344441 TCTACCAACAATGTATTAGTGTCCCAGTTTTCCCACATCCCCTCCAACAT 344490 v i i v ? v iv i ? i v i C L1ME4c_3end#L 292 GCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGCAT 243 chr3ptel1M 344491 TGGTCATTATCGTTTTCT 344508 vi iv i C L1ME4c_3end#L 242 TGGGTATTATCAATTTTT 225 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 47.32 CpG sites = 83, Kimura (unadjusted) = 49.90 Transitions / transversions = 1.51 (83/55) Gap_init rate = 0.02 (7 / 397), avg. gap size = 3.29 (23 / 7) 108 24.69 2.90 0.63 chr3ptel1M 344584 344893 (655107) (TCTG)n#Simple_repeat 1 317 (0) m_b118s252i10 4298 chr3ptel1M 344584 TCTGTCTCTGTCTCTTTCCCTCTTTCTCTCT-T-TGTCCGTCTTTATGTC 344631 v v v v iv v v - - i v v (TCTG)n#Simpl 1 TCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTC 50 chr3ptel1M 344632 TGTCTTTGTCTCTCTCTCTCTGATTTTCTGTCTCTCTGTCTTTCTTGGTC 344681 v v v v v vi v v v vvv v (TCTG)n#Simpl 51 TGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTG 100 chr3ptel1M 344682 TCTCTCTGGCTGTCTCTCTATGTCTGTCTCTTTCT-TGTTTCTCTTTCTG 344730 v v v -- v i v - i v v (TCTG)n#Simpl 101 TCTGTCTGTCTGTCTGTC--TGTCTGTCTGTCTGTCTGTCTGTCTGTCTG 148 chr3ptel1M 344731 TCTCTGTCTCTCTCTGTCTCTGTCTCTGTCTGTCTGTCTGTCTATC--TC 344778 v v v v v v v i -- (TCTG)n#Simpl 149 TCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTC 198 chr3ptel1M 344779 TGTCCATCTCTCTCTCTGTCTGTCTCTCTG--TGTCTGTCTTTGTCTCTT 344826 ii v v v -- v v v v (TCTG)n#Simpl 199 TGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTG 248 chr3ptel1M 344827 TCTGTCTCTATCTCTGTCTGTCTGTCTGTCTGTCTCTCACTCTCTCCGTG 344876 v v v v vv v i v (TCTG)n#Simpl 249 TCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTC 298 chr3ptel1M 344877 T-TCT-TCCTTCTTTCAGT 344893 - - iv v v (TCTG)n#Simpl 299 TGTCTGTCTGTCTGTCTGT 317 Matrix = Unknown Transitions / transversions = 0.19 (10/54) Gap_init rate = 0.03 (9 / 309), avg. gap size = 1.22 (11 / 9) 278 31.82 3.51 3.51 chr3ptel1M 346008 346121 (653879) L2a_3end#LINE/L2 389 502 (15) m_b118s601i6 4299 chr3ptel1M 346008 CCCTAGTGGGCTTCAAGGCCCTTGAGTACAGGAACTCCCTTTTTTCATTT 346057 i v i iv vi vi v vi i --- v iii L2a_3end#LINE 389 CCCCACTAGAATGTAAGCTCCATGAGGGCAGGGACT---TTTGTCTGTTT 435 chr3ptel1M 346058 GAGTTAATAGTTGGAAC----GTGCTTAGTACGGTGCCTGGCGCATAGTA 346103 v- v iv i v v ---- i i v i i L2a_3end#LINE 436 T-GTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACATAGTA 484 chr3ptel1M 346104 AGCCCTCTGTAAATGTCT 346121 i v vi i i L2a_3end#LINE 485 GGCGCTCAATAAATATTT 502 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.01 CpG sites = 20, Kimura (unadjusted) = 42.62 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.04 (5 / 113), avg. gap size = 1.60 (8 / 5) 355 19.18 0.00 1.37 chr3ptel1M 346057 346130 (653870) MIR#SINE/MIR 189 261 (1) m_b118s601i7 4300 chr3ptel1M 346057 TGAGTTAATAGTTGGAACGTGCTTAGTACGGTGCCTGGCGCATAGTAAGC 346106 vv v v i v i i MIR#SINE/MIR 189 TGAGTTAATACATGTAAAGCGCTTAGAACAGTGCCTGGCACATAGTAAGC 238 chr3ptel1M 346107 CCTCTGTAAATGTCTCACTGTTAT 346130 v vi - vi i MIR#SINE/MIR 239 GCTCAATAAATGT-TAGCTATTAT 261 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 20.52 CpG sites = 6, Kimura (unadjusted) = 22.19 Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.01 (1 / 73), avg. gap size = 1.00 (1 / 1) 240 26.27 2.22 6.98 chr3ptel1M 346703 346792 (653208) C MIR1_Amn#SINE/MIR (45) 185 100 m_b118s601i8 4301 chr3ptel1M 346703 CAAAGCACTTGCCATACACTAGTTGTTAGAGTGGCAGCCAACCCACTTTA 346752 ---- vvi vv i -- iv vivvv i C MIR1_Amn#SINE 185 CAAAGCACTT----TACAAAGGAGGTCAG--TATCATTATCCCCATTTTA 142 chr3ptel1M 346753 CAAATGATAAAACTGAAGCCCAAAGAGGCTGGGT--CTTGCC 346792 i vi i ? i i?ii -- C MIR1_Amn#SINE 141 CAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGCC 100 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.77 CpG sites = 12, Kimura (unadjusted) = 33.77 Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.08 (7 / 89), avg. gap size = 1.14 (8 / 7) 250 20.41 4.08 0.00 chr3ptel1M 346744 346792 (653208) C MIRb#SINE/MIR (117) 151 101 m_b118s601i9 4301 chr3ptel1M 346744 CCCACTTTACAAATGATAAAACTGAAGCCCAAAGAGGCTGGGT--CTTGC 346791 i i vi i i i i ii -- C MIRb#SINE/MIR 151 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGC 102 chr3ptel1M 346792 C 346792 C MIRb#SINE/MIR 101 C 101 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 25.57 CpG sites = 9, Kimura (unadjusted) = 25.57 Transitions / transversions = 9.00 (9/1) Gap_init rate = 0.02 (1 / 48), avg. gap size = 2.00 (2 / 1) 473 28.62 5.69 2.29 chr3ptel1M 346839 347049 (652951) MIR1_Amn#SINE/MIR 13 230 (0) m_b118s601i11 4302 chr3ptel1M 346839 GTGGCTGGGCGGATAGAGC-CTAGACTTTGAGTCATGGAAGCCTGAATTC 346887 iivi i - i vv v i- ii ii MIR1_Amn#SINE 13 GTGGTCTAGTGGATAGAGCACTGGACTGGGACTCG-GGAGACCTGGGTTC 61 chr3ptel1M 346888 AAATTCTGCCTCATACTCTT-CCTGGTG-GTGACGCTTAGCAAGTCAATC 346935 ? ? i i v vvv v ?- ? v - vi vi v i MIR1_Amn#SINE 62 NANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGTCACTT 111 chr3ptel1M 346936 AAATGGCCCGTGCCTCAGTTTCCCCGTTTGTAAAACTGGGATAACAATAG 346985 ? vivvi i ? i i i iv ii - MIR1_Amn#SINE 112 NACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATGATA- 160 chr3ptel1M 346986 CACCTG-CCTCTCATGTAAAGGGCTGT----CCTATAAATGGTA---GCT 347027 --- - iiv v v ----i ivi iv --- MIR1_Amn#SINE 161 ---CTGACCTCCTTTGTAAAGTGCTTTGAGATCTACTGATGAAAAGTGCT 207 chr3ptel1M 347028 ATATTATTAATAGG-ATTAATAT 347049 i v vviv - v MIR1_Amn#SINE 208 ACATAAGAGCTAGGTATTATTAT 230 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.59 CpG sites = 32, Kimura (unadjusted) = 38.22 Transitions / transversions = 1.19 (32/27) Gap_init rate = 0.06 (12 / 210), avg. gap size = 1.42 (17 / 12) 503 28.39 4.05 2.27 chr3ptel1M 346839 347011 (652989) MIRc#SINE/MIR 10 185 (83) m_b118s601i10 4302 chr3ptel1M 346839 GTGGCTGGGCGGATAGAGC-CTAGACTTTGAGTCATGGAAGCCTGAATTC 346887 ivvi i v - i v v i ii ii MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr3ptel1M 346888 AAATTCTGCCTCATACTCTTCCTGG-TG-GTGACGCTTAGCAAGTCAATC 346935 i i i i v vvv v v i - - vi vi v i MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTT 109 chr3ptel1M 346936 AAATGGCCCGTGCCTCAGTTTCCCCGTTTGTAAAACTGGGATAACAATAG 346985 vivvi i v i i i iv i v MIRc#SINE/MIR 110 AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAC 159 chr3ptel1M 346986 CA--CCTGCCT--CTCATGTAAAGGGCTGT 347011 v-- -- i---- i MIRc#SINE/MIR 160 CTGCCCTGCCTACCTCAC----AGGGTTGT 185 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.59 CpG sites = 27, Kimura (unadjusted) = 36.47 Transitions / transversions = 1.29 (27/21) Gap_init rate = 0.05 (9 / 172), avg. gap size = 1.22 (11 / 9) 466 23.62 1.56 0.78 chr3ptel1M 347400 347527 (652473) C L5#LINE/RTE-X (629) 1634 1506 m_b118s551i1 4303 chr3ptel1M 347400 ATGGACAGCCTGT-GGATGCAAGGCTTCTGATTGAAGCTCCGCTCACGTA 347448 i v - ii? iv i - i v iv ? C L5#LINE/RTE-X 1634 ATAGCCAGCCTGTCGGACANAGCGTTT-TGATCGAAGATCCAGTCNCGTA 1586 chr3ptel1M 347449 GCGCC-TGCCTGCCTGAGAAATGACCAGCGGCTCTTTGGGGATGGAATCA 347497 vviv- i v i iv i?ii i vi C L5#LINE/RTE-X 1585 GATTGGTGCCTGCTTGAGAAATGACCTGTGAGTCCNCAGAGATGGAATAG 1536 chr3ptel1M 347498 AATTGAAGCAATCTCTTGTATTTATAAACC 347527 i i v v C L5#LINE/RTE-X 1535 AGTTGAAGCAGTCTATGGTATTTATAAACC 1506 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 28.68 CpG sites = 18, Kimura (unadjusted) = 29.86 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.02 (3 / 127), avg. gap size = 1.00 (3 / 3) 286 29.50 12.23 0.00 chr3ptel1M 347751 347889 (652111) C MIRc#SINE/MIR (106) 162 7 m_b118s601i12 4304 chr3ptel1M 347751 CAGGTGGTAG-GTGCCCATTTTACAGATGAGGAAAGTGGGAC----AATG 347795 iv v-i v v i i ---- iv C MIRc#SINE/MIR 162 CAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAG 113 chr3ptel1M 347796 GAAAAG------GCCTCAGG--ACACAGCTAGGAT---GCATCCTGGGGG 347834 vv ------ iv -- v v--- vvviv i C MIRc#SINE/MIR 112 GTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGA 63 chr3ptel1M 347835 CTGGACCTCAGGTCCTTGTGAACCC-GGTCCAGCGCACCATGCACTGTGC 347883 v v i i iv vi -i i v iv v ii C MIRc#SINE/MIR 62 CTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCAC 13 chr3ptel1M 347884 TGCCCT 347889 ii v C MIRc#SINE/MIR 12 CACACT 7 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.77 CpG sites = 19, Kimura (unadjusted) = 37.77 Transitions / transversions = 0.86 (19/22) Gap_init rate = 0.04 (6 / 138), avg. gap size = 2.83 (17 / 6) 265 32.09 4.85 7.45 chr3ptel1M 348172 348336 (651664) C MIRc#SINE/MIR (86) 182 22 m_b118s601i13 4305 chr3ptel1M 348172 ACCCTGTTGGGTGGGCAATGACTCAGGGGGGGACAAGTTATCAGACTCAC 348221 vi i --------- vi ii -- i vv i i C MIRc#SINE/MIR 182 ACCCTGTGAGGTAGGCA---------GGGCAGGTA--TTATTATCCCCAT 144 chr3ptel1M 348222 TTTAGAGATGGGTAACCTGAGGCCCCGAGAAGTGCCGTGGATGGCCCAG- 348270 v i v v i v i vvv iv v i- C MIRc#SINE/MIR 143 TTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAG 94 chr3ptel1M 348271 ---ACACAATTGGTTA-TCGCGGTTCCGGG-TTTGACCTCCACTGTCTCT 348315 --- ii i v - v i vv -i i v i viv v ii C MIRc#SINE/MIR 93 GTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCT 44 chr3ptel1M 348316 GCGTCC--GTCCACATGCCCTCT 348336 vv -- -i i i C MIRc#SINE/MIR 43 GACTCCAAGTCCA-GTGCTCTTT 22 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.49 CpG sites = 26, Kimura (unadjusted) = 42.63 Transitions / transversions = 1.13 (26/23) Gap_init rate = 0.10 (17 / 164), avg. gap size = 1.18 (20 / 17) 311 29.91 5.71 2.07 chr3ptel1M 348217 348356 (651644) C MIR3#SINE/MIR (63) 145 1 m_b118s601i14 4305 chr3ptel1M 348217 CTCACTTTAGAGATGGGTAACCTGAGGCCCCGAGAAGTGCCGTGGATGGC 348266 i v i v v v i vv iv v C MIR3#SINE/MIR 145 CTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGC 96 chr3ptel1M 348267 CCAG----ACACAATTGGTTA-TCGCGGTTCCGGGTTTGACCTCCACTGT 348311 i---- ii?i - v i vv vi iivvi -v C MIR3#SINE/MIR 95 CCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCA-GGT 47 chr3ptel1M 348312 CT-CTGCGTCC--GTCCACATGCCCTCTTTGTCCGTTTGCTCTGACAG 348356 - vv -- -- i i i ii iviii v C MIR3#SINE/MIR 46 CTCCTGACTCCCAGTC--CGTGCTCTCTCTGCTCAGCCACTCTGCCAG 1 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.08 CpG sites = 22, Kimura (unadjusted) = 39.30 Transitions / transversions = 1.16 (22/19) Gap_init rate = 0.05 (7 / 139), avg. gap size = 1.57 (11 / 7) 12 21.86 0.00 5.13 chr3ptel1M 351065 351105 (648895) (CCTGG)n#Simple_repeat 1 39 (0) m_b118s252i11 4306 chr3ptel1M 351065 CCTGCTCTGGCTTAGTCCTGGCCTGTCCCCGGTCTGGCCTG 351105 vi i - v -v i i (CCTGG)n#Simp 1 CCTGGCCTGGCCT-GGCCTGGCCTG-GCCTGGCCTGGCCTG 39 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 248 24.62 2.99 2.99 chr3ptel1M 351250 351316 (648684) C MIR3#SINE/MIR (51) 157 91 m_b118s601i15 4307 chr3ptel1M 351250 TGGTCCAGCTCTTCCAACTTACAAATGAGGAAACTGAGGTCTCAGACAG- 351298 i i i iii vi i - i v - C MIR3#SINE/MIR 157 TAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGG-CCCAGAGAGG 109 chr3ptel1M 351299 -GAAGCAACACTGCCTCAG 351316 - ii -i iv C MIR3#SINE/MIR 108 TGAAGTGAC-TTGCCCAAG 91 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.96 CpG sites = 13, Kimura (unadjusted) = 31.96 Transitions / transversions = 4.33 (13/3) Gap_init rate = 0.06 (4 / 66), avg. gap size = 1.00 (4 / 4) 310 33.10 7.37 6.43 chr3ptel1M 351702 352040 (647960) L2b_3end#LINE/L2 115 456 (10) m_b118s601i16 4308 chr3ptel1M 351702 TCCTGGCTCTGGACATTTCCTCTGGCCAATCCCTGGACCTGGACCCCCCT 351751 i v v i v v v ?v iiv vvi v v L2b_3end#LINE 115 TCCCGCCTCAGGGCCTTTGCACNTGCTGTTCCCTCTGCCTGGAACGCCCT 164 chr3ptel1M 351752 --CCCTCCCCCACTCCTGACC---TCCTGGCTC--CCTTTATGTCCTGAC 351794 -- v i iv v i --- i- -- i v iiii L2b_3end#LINE 165 TCCCCACCTCTTCGCCTGGCCAACTCCTA-CTCATCCTTCAGGTCTCAGC 213 chr3ptel1M 351795 TGAGATCCCAGCT--TACAGGAAGCCTCCCCAGCTCCTCCTAGTTCTGAC 351842 v i vi v -- v i ii v vi i vi i----- L2b_3end#LINE 214 TCAAATGTCACCTCCTCCGGGAAGCCCTCCCTGACCCCCCAGGC-----C 258 chr3ptel1M 351843 TGATCTGGCATGGGCCGTGTTTGTCTGGAGCAGCCGCTTGTTTGCACCTG 351892 v i v ---- ---i iv iv -- v iv iivvv L2b_3end#LINE 259 GGGTCAGGC----GCC---CTCCTCTGGGCC--CCCCCAGTCCTACCCTG 299 chr3ptel1M 351893 ----GTTGAGCTGTGATTTGTACCCAGTCAC---TCAATCAGCACT--TA 351933 ----vi i i i ? - -- ii? i --- vi vv v i-- L2b_3end#LINE 300 CCACTCTGGGTTATNATT-GT--CTGNTTACATGTCTGTCTCCCCCACTA 346 chr3ptel1M 351934 GATTGTAAGCCCCTGGAGGTCAGGGACTTCCTTTCACTT-----CCTTTT 351978 i i i vv v iv?v i vv ----- vi v L2b_3end#LINE 347 GACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTG 396 chr3ptel1M 351979 CATCCCCAGAACTTGGCCCA--GCCCGGTATACAGGAGGTGCTTAATGCA 352026 i vi i i v -- i i i v i i i iv L2b_3end#LINE 397 TATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAA 446 chr3ptel1M 352027 TGTTGATTTGTTGA 352040 ---- L2b_3end#LINE 447 T----ATTTGTTGA 456 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.63 CpG sites = 56, Kimura (unadjusted) = 45.51 Transitions / transversions = 1.14 (56/49) Gap_init rate = 0.09 (31 / 338), avg. gap size = 1.52 (47 / 31) 367 21.90 7.56 4.07 chr3ptel1M 351928 352046 (647954) L2d2_3end#LINE/L2 431 553 (2) m_b118s601i17 4308 chr3ptel1M 351928 CACTTAGATTGTAAGCCCCTGGAGGTCAGGGAC--TTCCTTTCACTTCCT 351975 vi i v v -- vi vi - L2d2_3end#LIN 431 CAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACTT-CT 479 chr3ptel1M 351976 TTTCATCCC---CAGAACTTGGCCCA--GCCCGGTATACAGGAGGTGCTT 352020 vi --- vi i i v -- iv i i v i i L2d2_3end#LIN 480 TTGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAGTAGGCGCTC 529 chr3ptel1M 352021 AATGCATGTTGATTTGTTGATT--ATTT 352046 iv ---- -- L2d2_3end#LIN 530 AATAAAT----ATTTGTTGATTTGATTT 553 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 23.95 CpG sites = 14, Kimura (unadjusted) = 26.30 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.08 (9 / 118), avg. gap size = 1.56 (14 / 9) 232 32.18 5.75 0.00 chr3ptel1M 352042 352128 (647872) L2d_3end#LINE/L2 424 515 (1) m_b118s601i18 4309 chr3ptel1M 352042 TATTTTAGGCTGCCTTTCTATCCC----AGCCCTTGGCACGGGCCTG-GC 352086 i i vi ?ii ?iii i ---- v i i i vv - L2d_3end#LINE 424 TGTCTTATACTNTTTTNTCGTTCCCCACAGCGCCTAGCACAGTGCTGAGC 473 chr3ptel1M 352087 ACAAGATACGTGCTTGATGATGACTTGTTATTTGATTGATTG 352128 vii v i ii i vv iv L2d_3end#LINE 474 ACATAGTAGGCGCTCAATAAATACTTGTTGATTGATTGATTG 515 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.44 CpG sites = 19, Kimura (unadjusted) = 46.20 Transitions / transversions = 2.11 (19/9) Gap_init rate = 0.02 (2 / 86), avg. gap size = 2.50 (5 / 2) 223 28.30 0.00 0.00 chr3ptel1M 352935 352987 (647013) MIR3#SINE/MIR 131 183 (25) m_b118s601i19 4310 chr3ptel1M 352935 CATAAGTTAAGGGAGGGAGCTGGGCCACATGGTCTCTGGGGTCTCCTCCA 352984 vv v iv i i i i v i ii i i MIR3#SINE/MIR 131 CATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCA 180 chr3ptel1M 352985 GCT 352987 MIR3#SINE/MIR 181 GCT 183 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.13 CpG sites = 10, Kimura (unadjusted) = 37.13 Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 57 6.28 0.00 0.00 chr3ptel1M 353706 353772 (646228) (GT)n#Simple_repeat 1 67 (0) c_b118s251i1 4311 chr3ptel1M 353706 GTGTGTGTGTGTGTAAATGTGTGTATGTGTGTGTGTGTGTGTGTGTGTGT 353755 ivi i (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50 chr3ptel1M 353756 GTGTGTGTGTGTGTGTG 353772 (GT)n#Simple_ 51 GTGTGTGTGTGTGTGTG 67 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.0 (0 / 0) 28 21.61 0.00 0.00 chr3ptel1M 353779 353842 (646158) (TGTGTG)n#Simple_repeat 1 64 (0) m_b118s252i12 4312 chr3ptel1M 353779 TGGGTGTGAGTGTCTGTGAGTGGATGTAAGTGTGTGAGTGTGTGAGTGTG 353828 v v v v vi iv v v (TGTGTG)n#Sim 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr3ptel1M 353829 TGTATGTGTGAGTG 353842 i v (TGTGTG)n#Sim 51 TGTGTGTGTGTGTG 64 Matrix = Unknown Transitions / transversions = 0.33 (3/9) Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0) 294 37.39 5.85 2.84 chr3ptel1M 354356 354834 (645166) C L2#LINE/L2 (442) 2640 2148 m_b118s601i20 4313 chr3ptel1M 354356 TATCATGATAGTGGAAACAACAGGTTTTAGCAGCAGACTGAATCTGGAGT 354405 iv vi i iv i v iviiiii i i v i C L2#LINE/L2 2640 TATTTTGAAGGTAGAGCCGACAGGATTTGCTGATGGATTGGATGTGGGGT 2591 chr3ptel1M 354406 GCGAG-----GAGGGCAGT---GGA-GATGCCAAGTTGGGATTTGGGGGG 354446 i ----- i v --- - iv v v--- vvv C L2#LINE/L2 2590 GTGAGAGAAAGAGAGGAGTCAAGGATGACTCCAAGGTT---TTTGGCCTG 2544 chr3ptel1M 354447 GG-GGCTGGAAGG-TGGTGGTGCCCTCTGCGGTAAGGAGGACATCTGGAA 354494 i -ii - v v v i?i v vi v i viv vii C L2#LINE/L2 2543 AGCAACTGGAAGGATGGAGTTGCCATTNACTGAGATGGGGAAGACTGCGG 2494 chr3ptel1M 354495 GAGGGAGGAGTTTGGAGAAAGGAGAGT--GAGTTCAGTTCTGGGCCTGCT 354542 - v v v iii i vi-- i i v i C L2#LINE/L2 2493 GAGG-AGCAGGTTTGAGGGGGAAGATCAGGAGTTCAGTTTTGGACATGTT 2445 chr3ptel1M 354543 AATTTTGAGAGATCTACAGGACAT-GAGATCAATATGTC-AGGGGACTGT 354590 v vii ivi -v ii vi v - vi i v C L2#LINE/L2 2444 AAGTTTGAGATGCCTATTAGACATCCAAGTGGAGATGTCGAGTAGGCAGT 2395 chr3ptel1M 354591 GGAGT----GAGACTAGAGGCTAGGAGAGGGATTCGATATGTGTGGAGAG 354636 v ii ---- v i vii i i i i ivv viviv v i C L2#LINE/L2 2394 TGGATATACGAGTCTGGAGTTCAGGGGAGAGGTCCGGGCTGGAGATATAA 2345 chr3ptel1M 354637 GTCTGGGGATCATCTGCAGGGAGGTGCAAATGGACAGCTGGATCGGTGGA 354686 i i ii v viv i -iv vv v i-- -- v iv C L2#LINE/L2 2344 ATTTGGGAGTCATCAGCATATAGATG-GTATTTAAAGCC--AT--GAGAC 2300 chr3ptel1M 354687 TGGATG-GATGGATGGATGCTAGAGCACAGAAAG-GGAGAGAAGA-GTAT 354733 - vivi?iiv vvv iii v - i - vi C L2#LINE/L2 2299 TGGATGAGATCACCNAGGGAGTGAGTGTAGATAGAGAAGAGAAGAGGTCC 2250 chr3ptel1M 354734 ATGGTGT-ATTCCTTGGAAACACCCACAATT---GGTGGGAACCACACAG 354779 v vv - vi v iv v v iv ?--- v iivv iivi C L2#LINE/L2 2249 AAGGACTGAGCCCTGGGGCACTCCAACGTTNAGAGGTCGGGGAGATGAGG 2200 chr3ptel1M 354780 GGAAATGTTCCCCAGAGGAGACTGTTCAGGACCA--TGGAGAAGTCCAGA 354827 i i ---i vv i vvv v i--ii v i -- i C L2#LINE/L2 2199 AGGAA---CCAGCAAAGGAGACTGAGAAGGAGCGGCCAGTGAGGT--AGG 2155 chr3ptel1M 354828 AGGAAGA 354834 i C L2#LINE/L2 2154 AGGAAAA 2148 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 52.11 CpG sites = 93, Kimura (unadjusted) = 53.92 Transitions / transversions = 1.15 (93/81) Gap_init rate = 0.06 (29 / 478), avg. gap size = 1.45 (42 / 29) 200 40.09 9.43 0.00 chr3ptel1M 354766 354977 (645023) C L2#LINE/L2 (954) 2128 1897 m_b118s601i21 4313 chr3ptel1M 354766 TGGGAACCACACAGGGAAA-TGTTCCCCAGAGGAG----------ACTGT 354804 i i viiiii - i vvii ---------- C L2#LINE/L2 2128 TGGAAGCCAAGTGAAGAAAGTGTTTCAAGAAGGAGGGAGTGATCAACTGT 2079 chr3ptel1M 354805 -TCAGG-ACCATGGAGAAGTCCAGAAGGAAGAGGATTTAAAAA-GACCTT 354851 - ii-i iiiv ? i v v i v i v i v- v C L2#LINE/L2 2078 GTCAAATGCTGCTGANAGGTCAAGTAAGATGAGGACTGAGAATTGACCAT 2029 chr3ptel1M 354852 TGGATTTGGC--TTTAGAAG--GTTGGAGACTGGGGAGAGAGCTACCGCA 354897 i --iv i i --i v ivv ivi viiiv i C L2#LINE/L2 2028 TGGATTTAGCAACGTGGAGGTCATTGGTGACCTTGACAAGAGCAGTTTCG 1979 chr3ptel1M 354898 GTTGGATGATGAGCCTGAGAACTGCGTTCCACAGCATTTAGAAAGGAA-- 354945 v ii i i vvi i i ivvi vv vv vi i ii ii -- C L2#LINE/L2 1978 GTGGAGTGGTGGGGACGAAAGCCTGATTGGAGTGGGTTCAAGAGAGAATG 1929 chr3ptel1M 354946 GGAGAAGGGGGAATGGAAGCATTGAATGCAGA 354977 i i i v ii vi i ii C L2#LINE/L2 1928 GGAGGAGAGGAATTGGAGACAGCGAGTATAGA 1897 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 58.31 CpG sites = 56, Kimura (unadjusted) = 63.20 Transitions / transversions = 1.93 (56/29) Gap_init rate = 0.04 (8 / 211), avg. gap size = 2.50 (20 / 8) 268 30.63 6.29 4.11 chr3ptel1M 356313 356455 (643545) C L2a_3end#LINE/L2 (12) 505 360 m_b118s601i23 4314 chr3ptel1M 356313 AACAAATGAGTCATTTATTGGGCATTACCTATGTGCAAAATGTTG--CTA 356360 ----- i iiivv v iiiii -- C L2a_3end#LINE 505 AACAAAT-----ATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTA 461 chr3ptel1M 356361 AGTGCTGGGGACACAG-AGAGAA-AAGTCAGGT---GGTTGCTG-CATTA 356404 i i i - v - iv ii---i iv - v i C L2a_3end#LINE 460 GGCGCTGGGGATACAGCAGTGAACAAAACAGACAAAAGTCCCTGCCCTCA 411 chr3ptel1M 356405 GAGAACTTCCGTTCTCAT-GGGGAAGATGAGACACGGGAGAAATTCATCA 356453 vi i v i vi - i i- vvii v vv v C L2a_3end#LINE 410 TGGAGCTTACATTCTAGTGGGGGGAGAC-AGACAATAAACAAATAAATAA 362 chr3ptel1M 356454 GT 356455 C L2a_3end#LINE 361 GT 360 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.40 CpG sites = 26, Kimura (unadjusted) = 40.94 Transitions / transversions = 1.62 (26/16) Gap_init rate = 0.08 (12 / 142), avg. gap size = 1.25 (15 / 12) 278 29.65 6.40 5.56 chr3ptel1M 356313 356437 (643563) C L2d2_3end#LINE/L2 (12) 543 418 m_b118s601i22 4314 chr3ptel1M 356313 AACAAATGAGTCATTTATTGGGCATTACCTATGTGCAAAATGT--TGCTA 356360 ----- i iiivv i iiiii-- C L2d2_3end#LIN 543 AACAAAT-----ATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTA 499 chr3ptel1M 356361 AGTGCT---GGGGACACAGAGAG--AAAAGTCAGGTGGTTGCTG-CATTA 356404 i i --- i i i-- v v -- iv - v i C L2d2_3end#LIN 498 GGCGCTGTGGGGGATACAAAGAAGTATAAGACA--TGGTCCCTGCCCTCA 451 chr3ptel1M 356405 GAGAACTTCCGTTCTCATGGGGAAGATGAGACA 356437 ii i v iv vi v i ii C L2d2_3end#LIN 450 AGGAGCTTACAATCTAGTTGGGGAGACAAGACA 418 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.14 CpG sites = 25, Kimura (unadjusted) = 40.16 Transitions / transversions = 2.50 (25/10) Gap_init rate = 0.09 (11 / 124), avg. gap size = 1.36 (15 / 11) 237 18.62 23.68 1.08 chr3ptel1M 356785 356860 (643140) MIR3#SINE/MIR 99 191 (17) m_b118s601i24 4315 chr3ptel1M 356785 AGTCACTTTCTCTC-CTGGGCCTCAATTTTCTCATTAATAAAATGAGG-- 356831 ivi - i i ivi -- MIR3#SINE/MIR 99 AGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGG 148 chr3ptel1M 356832 ---------------TTCTAAGGTTCCTTCTTGCTCTAGATGTT 356860 ---------------i i iv - ii MIR3#SINE/MIR 149 GTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCT-GACATT 191 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 22.36 CpG sites = 11, Kimura (unadjusted) = 22.36 Transitions / transversions = 3.67 (11/3) Gap_init rate = 0.05 (4 / 75), avg. gap size = 4.75 (19 / 4) 331 37.80 1.57 0.00 chr3ptel1M 357435 357561 (642439) C L3#LINE/CR1 (75) 4024 3896 m_b118s601i25 4316 chr3ptel1M 357435 TCTCCTCAGCAGCATCCTTGACAAGTGGCTAGGTGAGCTTAGTTCAAGGG 357484 i i vi i i ii vviiiv iv i ii ivi C L3#LINE/CR1 4024 TCCCTTCTACAACATCCCTGACAAGTGGTCATCCAGCCTCTGCTTGAACA 3975 chr3ptel1M 357485 CCTTTGGGGAGGGGGAGCCCACTGCCAGGTGAGA-AGCCCTCCCCACTGT 357533 iii v v i i vv?i i- vii i v C L3#LINE/CR1 3974 CCTCCAGTGACGGGGAGCTCACTACCTCNCGAGGCAGCCCATTCCATTTT 3925 chr3ptel1M 357534 GGGACAGTTCTACACATCAG-GAGTCCTT 357561 v i ivvii i -i i C L3#LINE/CR1 3924 TGGACAGCTCTGATTGTTAGAAAGTTCTT 3896 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 56.32 CpG sites = 33, Kimura (unadjusted) = 58.28 Transitions / transversions = 2.20 (33/15) Gap_init rate = 0.02 (2 / 126), avg. gap size = 1.00 (2 / 2) 100 36.40 0.00 0.25 chr3ptel1M 358946 359001 (640999) (CA)n#Simple_repeat 1 56 (345) m_b118s252i13 4317 chr3ptel1M 358946 CACACACTCACAGGCTCGCACCCTCACAGGCTCACACCTTCACACACTTG 358995 v vi v i v v vi v viv vii (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 chr3ptel1M 358996 CACCCT 359001 v v (CA)n#Simple_ 51 CACACA 56 Matrix = Unknown Transitions / transversions = 0.50 (6/12) Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0) 29 10.03 0.00 0.00 chr3ptel1M 359002 359044 (640956) (CA)n#Simple_repeat 1 43 (0) c_b118s251i2 4317 chr3ptel1M 359002 CACACACACACACACACACTCAGACACACTCACACACTCACAC 359044 v v v v (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACAC 43 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 100 36.40 0.00 0.25 chr3ptel1M 359045 359389 (640611) (CA)n#Simple_repeat 57 400 (1) m_b118s252i13 4317 chr3ptel1M 359045 TCTCCTGTAGCCACACACTCATTCACTCACACACACCCTCCCTCACACAT 359094 v v viii vv v iv v v v v v i (CA)n#Simple_ 57 ACACACACACACACACACACACACACACACACACACACACACACACACAC 106 chr3ptel1M 359095 ATTCACTTATACACACTTACACACATCCCTCACAGGTGCACGCTTTCACA 359144 iv vi i vi - v v viii i viv (CA)n#Simple_ 107 ACACACACACACACACACACACACA-CACACACACACACACACACACACA 155 chr3ptel1M 359145 TACACACATATTCACCCATGTGCACACTCACAAGCATATGTACCTACTCT 359194 i i iv v iiii v vi i iii vi v v (CA)n#Simple_ 156 CACACACACACACACACACACACACACACACACACACACACACACACACA 205 chr3ptel1M 359195 CCCACACATGCAGTCACACACACACAGGCACACACACACTCACACTCTCA 359244 v ii vv vi v v v (CA)n#Simple_ 206 CACACACACACACACACACACACACACACACACACACACACACACACACA 255 chr3ptel1M 359245 CACACACACTCCCACTCCCACACACTCACACTCACTCTCACACACACACA 359294 v v v v v v v v (CA)n#Simple_ 256 CACACACACACACACACACACACACACACACACACACACACACACACACA 305 chr3ptel1M 359295 CACTCACAAGCATATGTACCTACTCTCCCACACATGCAGTCACACACACA 359344 v vi i iii vi v v v ii vv (CA)n#Simple_ 306 CACACACACACACACACACACACACACACACACACACACACACACACACA 355 chr3ptel1M 359345 CAGGCACACACACACTCTCTCTCTCACACACACACACTCCCACAC 359389 vi v v v v v v v (CA)n#Simple_ 356 CACACACACACACACACACACACACACACACACACACACACACAC 400 Matrix = Unknown Transitions / transversions = 0.67 (39/58) Gap_init rate = 0.00 (1 / 344), avg. gap size = 1.00 (1 / 1) 13 0.00 8.70 0.00 chr3ptel1M 360240 360262 (639738) (AGGC)n#Simple_repeat 1 25 (0) m_b118s252i14 4318 chr3ptel1M 360240 AGGCAGGC-GGCAGGCA-GCAGGCA 360262 - - (AGGC)n#Simpl 1 AGGCAGGCAGGCAGGCAGGCAGGCA 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.09 (2 / 22), avg. gap size = 1.00 (2 / 2) 206 31.71 2.41 1.19 chr3ptel1M 360711 360793 (639207) C MIR#SINE/MIR (68) 194 111 m_b118s601i26 4319 chr3ptel1M 360711 AGCTCATCCC-TCCT-ATCACAACCCAAAAGGTTATGCCGATACTTTCTC 360758 i iiv- - iv v vii v v i-iv i v ivi C MIR#SINE/MIR 194 AACTCATTTAATCCTCACAACAACCCTATGAGGTAGGT-ACTATTATTAT 146 chr3ptel1M 360759 CCCTGTTTTACAGATGAGGAACCTGAGGATCAGGG 360793 ii v vv i C MIR#SINE/MIR 145 CCCCATTTTACAGATGAGGAAACTGAGGCACAGAG 111 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.11 CpG sites = 14, Kimura (unadjusted) = 42.11 Transitions / transversions = 1.17 (14/12) Gap_init rate = 0.04 (3 / 82), avg. gap size = 1.00 (3 / 3) 223 27.61 1.37 5.71 chr3ptel1M 360721 360793 (639207) C MIRb#SINE/MIR (81) 187 118 m_b118s601i27 4319 chr3ptel1M 360721 TCCT-ATCACAACCCAAAAGGTTATGCCGATACTTTCTCCCCTGTTTTAC 360769 - iv vivii v ---- i i v ivi ii C MIRb#SINE/MIR 187 TCCTCACAACAACCCTGCGAGGTA----GGTATTATTATCCCCATTTTAC 142 chr3ptel1M 360770 AGATGAGGAACCTGAGGATCAGGG 360793 v v i C MIRb#SINE/MIR 141 AGATGAGGAAACTGAGGCTCAGAG 118 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.87 CpG sites = 11, Kimura (unadjusted) = 35.12 Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.07 (5 / 72), avg. gap size = 1.00 (5 / 5) 252 33.93 7.27 0.85 chr3ptel1M 360745 360854 (639146) C MIRc#SINE/MIR (105) 163 47 m_b118s601i28 4319 chr3ptel1M 360745 GCCGATACTTTCTCCCCTGTTTTACAGATGAGGAACCTGAGGATCAGGGT 360794 v i i v ivi ii v v i v C MIRc#SINE/MIR 163 GCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGA 114 chr3ptel1M 360795 GTTCCCGTGGTTTAATCCATG----ATATTTAGCAT----CAGAGCTAAG 360836 v ivv ii ivi v v ---- i vi i v---- iii C MIRc#SINE/MIR 113 GGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGG 64 chr3ptel1M 360837 CCCTGACCCCATGATCTT 360854 v ii v - i C MIRc#SINE/MIR 63 ACTCGAACCCA-GGTCTT 47 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.07 CpG sites = 21, Kimura (unadjusted) = 46.66 Transitions / transversions = 1.31 (21/16) Gap_init rate = 0.03 (3 / 109), avg. gap size = 3.00 (9 / 3) 302 33.76 15.92 0.00 chr3ptel1M 362190 362346 (637654) C L3#LINE/CR1 (154) 3945 3764 m_b118s601i29 4320 chr3ptel1M 362190 CAAGGCATCCCACTTCCTCTTGGAACAGCTCAAATTGTAAGGA------- 362232 i v i i v i v i vi v i ------- C L3#LINE/CR1 3945 CGAGGCAGCCCATTCCATTTTTGGACAGCTCTGATTGTTAGAAAGTTCTT 3896 chr3ptel1M 362233 ------------CCG---TCAGCCTCTTTGAATTGTCCAGCTCCAGTTCC 362267 ------------ --- v ii v viv v iviv v C L3#LINE/CR1 3895 CCTTATATTGAGCCGAAATCTGCCTCCCTGTAACTTCCACCCATTGGTCC 3846 chr3ptel1M 362268 TGGCTCTGCCCTGTGGGGT--CAGAGGGCAACATACATCACTCTTCTGTA 362315 i i v i i-- v iii vvivv v iii C L3#LINE/CR1 3845 TAGTTCTGCCCTCTGGAGCCACACAGAATAAGTCTAATCCCTCTTCCACA 3796 chr3ptel1M 362316 TGAAGGTCCTTTAGA-GCTTGAAAATAGATAT 362346 vi i i i -ii i i v C L3#LINE/CR1 3795 TGACAGCCCTTCAAATATTTGAAGACAGCTAT 3764 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.29 CpG sites = 31, Kimura (unadjusted) = 46.51 Transitions / transversions = 1.41 (31/22) Gap_init rate = 0.03 (5 / 156), avg. gap size = 5.00 (25 / 5) 209 34.30 0.00 4.11 chr3ptel1M 362427 362502 (637498) MIR3#SINE/MIR 134 206 (2) m_b118s601i30 4321 chr3ptel1M 362427 CTCTGAGATAAAGTATGGATTGGATTTGGTGGCCTGCAAGGTCCCTCTGA 362476 v i i i i --- i i v i ii vi iiv MIR3#SINE/MIR 134 CTGTAAAATGAGG---GGGTTGGACTAGATGATCTCTAAGGTCCCTTCCA 180 chr3ptel1M 362477 GCTCCTAAATTCAGGGATTCTGGAAT 362502 iv v viv ivi MIR3#SINE/MIR 181 GCTCTGACATTCTATGATTCTATGAT 206 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 48.31 CpG sites = 16, Kimura (unadjusted) = 48.31 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.04 (3 / 75), avg. gap size = 1.00 (3 / 3) 209 40.18 2.38 3.20 chr3ptel1M 362491 362616 (637384) C L3#LINE/CR1 (4) 4095 3971 m_b118s601i31 4322 chr3ptel1M 362491 GGATTCTGGAATCTCCCAGACATAAAGAGCCTCAGTGAACATGTAGTTCA 362540 i ivii vv viiv i ii i v iv v i C L3#LINE/CR1 4095 GAATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCA 4046 chr3ptel1M 362541 ATCCATTATACCTCACGTCAAA---CTTTCCACAATCTGTCCAGCAAGTG 362587 i ivii -- iv i ivii --- i i iv vi iii C L3#LINE/CR1 4045 ACCTCCCAT--CCAATGCAGGAATCCCTTCTACAACATCCCTGACAAGTG 3998 chr3ptel1M 362588 TCCATCCAGATTCTAAGCCTGCCCATCTC 362616 vi vi -- i vv i C L3#LINE/CR1 3997 GTCATCCAGCCTCT--GCTTGAACACCTC 3971 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 62.69 CpG sites = 32, Kimura (unadjusted) = 62.69 Transitions / transversions = 1.88 (32/17) Gap_init rate = 0.04 (5 / 125), avg. gap size = 1.40 (7 / 5) 256 26.58 10.02 0.62 chr3ptel1M 362617 363055 (636945) C L3#LINE/CR1 (166) 3933 3454 m_b118s601i32 4322 chr3ptel1M 362617 TTCGAGCCTTGGAGCAGATCTAAT----AGAAGGTT--TCTACAAATCAA 362660 v vii - v i ---- i -- ivi v ii C L3#LINE/CR1 3933 TTCCATTTTTGGA-CAGCTCTGATTGTTAGAAAGTTCTTCCTTATATTGA 3885 chr3ptel1M 362661 GACTAAATGGACATCTTTGCAACTTCT-CCCACTGTTC-----TCTGCTC 362704 v v vvi v ii i i- i v ----- i C L3#LINE/CR1 3884 GCCGAAATCTGCCTCCCTGTAACTTCCACCCATTGGTCCTAGTTCTGCCC 3835 chr3ptel1M 362705 TCCGAGACCAACCCATATAAATACAA---CTCT-CAACCNNNNNNNNNNN 362750 i iii vv viv i vi --- - v v??????????? C L3#LINE/CR1 3834 TCTGGAGCCACACAGAATAAGTCTAATCCCTCTTCCACATGACAGCCCTT 3785 chr3ptel1M 362751 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 362800 ?????????????????????????????????????????????????? C L3#LINE/CR1 3784 CAAATATTTGAAGACAGCTATCATGTCTCCTCTAAGTCTTCTCTTCTCCA 3735 chr3ptel1M 362801 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNATCTG 362850 ?????????????????????????????????????????????v iiv C L3#LINE/CR1 3734 GGCTAAACATCCCCAGTTCCTTCAACCGTTCCTCATATGACATGGTTTCC 3685 chr3ptel1M 362851 AGAG--TTCTCCCTCCTGGCATCCTTTCTGTGAATGTATTTCAATTCATC 362898 v-- v v ivv ii i v i i iii i i ii C L3#LINE/CR1 3684 AGACCCTTCACCATCCTGGTCGCTCTCCTCTGGACGCGCTCCAGTTTGTC 3635 chr3ptel1M 362899 AATGTCTTTCCTAAAAT---GCATCC--CACTCTATG--GTAC-CCAAAT 362940 ii i --- ii --v vv i --i - i C L3#LINE/CR1 3634 AATGTCCCTCTTAAAATGTGGCGCCCAGAACTGAACGCAATACTCCAGAT 3585 chr3ptel1M 362941 GTGTCCT---CAGGGCTGGGTACCCTGG---------CTCCAGTGA---- 362974 vi --- v v i vvi --------- vv ?---- C L3#LINE/CR1 3584 GTGGTCTGACCAGCGCAGAGTACAGCGGGACTATTACCTCCCTTGNTCTG 3535 chr3ptel1M 362975 GGCTCAGTGGCTCC-TTAATGCAGCCCAGGAAAGCTCTC-CTTTTCCCTG 363022 i v vi ivi i- i i vv vi v- --i C L3#LINE/CR1 3534 GACACTATACTTCTATTAATGCAGCCTAAGATTGCATTAGCTTTT--TTG 3487 chr3ptel1M 363023 ATTTCCATATGGCACCACTGACCTATGTCGGGC 363055 iivv i vi iii i ii i i i C L3#LINE/CR1 3486 GCAGCCACATCACACTGTTGGCTCATATTGAGC 3454 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.74 CpG sites = 70, Kimura (unadjusted) = 49.86 Transitions / transversions = 1.52 (70/46) Gap_init rate = 0.04 (19 / 438), avg. gap size = 2.47 (47 / 19) 319 27.19 2.83 2.83 chr3ptel1M 362740 362845 (637155) C CR1-3_Croc#LINE/CR1 (825) 2780 2675 m_b118s551i2 4322 chr3ptel1M 362740 ATGGCAACTCTTCAAGTACTTGAAAACAGCTATCAGGTTCCCCCCAA--- 362786 i i i i v v i i iv --- C CR1-3_Croc#LI 2780 ATGGCAGCCCTTCAAGTATTTGAAGACTGCTATCATGTCCCCTCTTAAGC 2731 chr3ptel1M 362787 GCCTTTTCCTCTTCAGGCTACACGTGCCCAGTCCATTCACTCAGTCCTTG 362836 ---v i iv i i ii v vi vv i C CR1-3_Croc#LI 2730 GCCTTTTCC---GCAAGCTGAACATGCCTAGCTCCTTCAGCCTCTCCTCG 2684 chr3ptel1M 362837 AGTGGCCTG 362845 vi i i C CR1-3_Croc#LI 2683 TATGACTTG 2675 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 33.43 CpG sites = 18, Kimura (unadjusted) = 34.98 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.04 (4 / 105), avg. gap size = 1.50 (6 / 4) 558 27.27 18.58 0.00 chr3ptel1M 363103 363355 (636645) C L3#LINE/CR1 (659) 3440 3141 m_b118s601i33 4323 chr3ptel1M 363103 AAATCCCCAGGTTGCTTTCAGATGAGCTTCTGCCCAGCCACA-CCTCACT 363151 i i ivi vi i v iv v - v i C L3#LINE/CR1 3440 AAACCCCTAGGTCTTTTTCACGTGAACTGCTGCTAAGCCAGATCCTCTCC 3391 chr3ptel1M 363152 GAGCTG--CTTTTG--GTGGATTTTGAAATTCTAATT-TAGAACTTTCCA 363196 ivv -- v -- v vvi vi v -i i v C L3#LINE/CR1 3390 ATCCTGTACTTGTGCAGTTGATTTTTTGAACCTAAATGCAGGACTTTACA 3341 chr3ptel1M 363197 TT----------ACATTTCATCCTATTAGATTCAGCCCA-CATTCTAGC- 363234 ---------- v i i i v i - i i - C L3#LINE/CR1 3340 TTTATCCCTGTTAAATTTCATCTTGTTGGTTTCGGCCCATCGTTCCAGCC 3291 chr3ptel1M 363235 TGTCAC----------AGTCCTGACTCCGCCATTTGGGGTGTTAGCTATA 363274 iv---------- i i i i i iii?v i v C L3#LINE/CR1 3290 TGTCGAGATCNTTTTGAATCTTGATTCTGTCATCCANCGTATTAGCTATC 3241 chr3ptel1M 363275 CCTCTCA--------------GCAAATTAAATCA--ATGCCATCTGTGCC 363308 i -------------- vi v -- v i i C L3#LINE/CR1 3240 CCTCCCAGCTTTGTGTCATCTGCAAATTTGATAAGCATGCCTTCTATGTC 3191 chr3ptel1M 363309 TTCATT---ATCAGTCAGGAACATTTTGAATGGCTCAGGACCAAGGACAG 363355 i---i v v vi v v ii vv i C L3#LINE/CR1 3190 TTCATCCAAGTCATTGATAAAAATGTTGAACAGGACAGGGCCAAGGACAG 3141 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.34 CpG sites = 39, Kimura (unadjusted) = 34.78 Transitions / transversions = 1.30 (39/30) Gap_init rate = 0.04 (11 / 252), avg. gap size = 4.27 (47 / 11) 28 14.38 0.00 0.00 chr3ptel1M 363416 363461 (636539) (G)n#Simple_repeat 1 46 (0) m_b118s252i15 4324 chr3ptel1M 363416 GGGGGGGGGGGGGGGCTGGAGAGAGGTGGGGGGGGGGGGGGGGGGG 363461 vv i i i v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 46 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 825 36.86 5.38 2.72 chr3ptel1M 363483 363984 (636016) C L3#LINE/CR1 (1036) 3063 2549 m_b118s601i34 4323 chr3ptel1M 363483 TTCAATCC-TTCTGAATTCACCTAACTGCATTGTGGTCTAGCTTCCCCAC 363531 i v-i vi i i i i vi i -- vi - C L3#LINE/CR1 3063 TTCAACCAGCTACGAATCCACCTAACTGTACTATCATCCAGC--CCATA- 3017 chr3ptel1M 363532 TTTCTGTATAGGAGCCACAGGGAGAGGA-AAGAGCTTTTGTCTCATATTT 363580 vi vvviv i v vv -i vi vv iii C L3#LINE/CR1 3016 TTTCTCCATCTTGTCCACAAGGATATCATGAGAGACTTTGTCAAATGCCT 2967 chr3ptel1M 363581 AATGGAAGGATAAGTAAATAATATCTAAAGTACTTCCTCCACTGAGCAGT 363630 viiv ivvi ii v iv? i vi i i i iiv iiv v C L3#LINE/CR1 2966 TGCTGAAATCCAGATACACTNTGTCTACGGCATTCCCCTGATCTACCAGT 2917 chr3ptel1M 363631 TATCCTGGGGGTAAGGGCAGGGAGGAAGGCAGAATAAAGCTAGTCTGCCC 363680 ---- i --- vvvi vvi ii --i i i i i v v C L3#LINE/CR1 2916 ----CTAG---TAACCCTATCAAAAAAGG--AAATGAGGTTAGTTTGGCA 2876 chr3ptel1M 363681 AGATCTTCTCTTGGTA-----------GCTCTTTGGGACCTTTGCTTCCT 363719 v ii vi i i----------- i v v i vii C L3#LINE/CR1 2875 TGACTTGTTCTTAGTGAACCCATGCTGGCTCCTAGTGATCACCGCTTCCT 2826 chr3ptel1M 363720 TTTTTGGATAGATTCACTAACCTTCTCTTTTGTGATGCATTCAAAAATTT 363769 i iii i--i v v v vi i v i v i C L3#LINE/CR1 2825 TTTCTAAGTG--CTCACAAACCATCTGTTTAATAATCCGTTCTAGAATTT 2778 chr3ptel1M 363770 TGCCCAGAATTAAAGACAGACTCTCTGGCCTATGGTGTGAAGACT---TT 363816 vi i ii v v ii iv i i i i v ?v v --- i C L3#LINE/CR1 2777 TGCCGGGGATCGACGTCAAGCTTACCGGTCTGTAGTTTNCAGAATCCATC 2728 chr3ptel1M 363817 TTTTTTCCC-CCTGAAGACTAGG----ACATTTGTCCTCCTGCA-CCGTG 363860 -ii v i ? ---- i vi v -i v v C L3#LINE/CR1 2727 TTTTTTCCCTTTTTAAAANTAGGNACNACATTTGCCCGTCTCCAGTCTTC 2678 chr3ptel1M 363861 TAGTACCTCATCCA-TCCCTGAGATCT---GAATATCATTGACAAGGCCT 363906 i i v i- i i v i ---i v i ii iv vi C L3#LINE/CR1 2677 TGGCACCTCTTCCGTTCTCCGTGATTTCTCAAAGATTACCGACAGCGGTT 2628 chr3ptel1M 363907 CAGAAGTCACCTTTGCTAGTTCTTTTAGTACCAAAGGACACAGTTC-TCA 363955 v vii v i v i vvi iii i - v C L3#LINE/CR1 2627 CCGCGATCACATCTGCAAGTTCTTTCAGTACCCTGGGATGTAATTCGTCT 2578 chr3ptel1M 363956 CAGGCAGGTGACTTGACCTCCCTAAGGGC 363984 vi v v v v vi v ii C L3#LINE/CR1 2577 GGGCCTGGAGACTTGAACTCATTTAAAGC 2549 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 49.27 CpG sites = 106, Kimura (unadjusted) = 53.64 Transitions / transversions = 1.43 (106/74) Gap_init rate = 0.05 (24 / 501), avg. gap size = 1.71 (41 / 24) 470 30.59 13.45 1.12 chr3ptel1M 364010 364247 (635753) C MIRc#SINE/MIR (0) 268 2 m_b118s601i35 4325 chr3ptel1M 364010 AATAGCAAAAACAGCAGGTCATCTTTATAAAAAGCTCCAGTGTTTTCTGA 364059 ii v ?v --- i iv i v ivi ii vv v vi C MIRc#SINE/MIR 268 AATAATAATAACNCC---TTACATTTGTATAGCACTTTACAGTTTACAAA 222 chr3ptel1M 364060 ATGCTCT-ATGTGAACT--CTCCTTAGATCCTCATGGTCATTTGGTGAAG 364106 ii i - ii iv i -- v v iiiiv iiiv i C MIRc#SINE/MIR 221 GCGCTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGG 172 chr3ptel1M 364107 ------GGGAAGTTTTTAATATCCCCATTTTGCAGATGAGGAAGTGGCCG 364150 ------ v v v v i iiv vv C MIRc#SINE/MIR 171 TAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGG 122 chr3ptel1M 364151 CTCAGAGA--TT--GTCACTTGCACAGGGTTACAGAAATAGGAAGT---- 364192 -- -- v v i i v iv v ---- C MIRc#SINE/MIR 121 CTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCA 72 chr3ptel1M 364193 -------------ATCCCAGGGCTTCCTCTCTTCAAGTACAACCCATTAT 364229 ------------- v v vv i v iiv vi v C MIRc#SINE/MIR 71 GAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTT 22 chr3ptel1M 364230 TCCCTG--TCACACTGCCTC 364247 i v --i C MIRc#SINE/MIR 21 CCACTGCACCACACTGCCTC 2 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.52 CpG sites = 37, Kimura (unadjusted) = 40.24 Transitions / transversions = 1.06 (37/35) Gap_init rate = 0.05 (11 / 237), avg. gap size = 3.18 (35 / 11) 382 35.13 10.37 1.59 chr3ptel1M 364316 364720 (635280) C L3#LINE/CR1 (1640) 2459 2020 m_b118s601i36 4323 chr3ptel1M 364316 CATTGTCCAGAGCAGAGAAGACAGACACAAAATAGGAATTGAATCATTCC 364365 v vviii i vi i i vi i C L3#LINE/CR1 2459 CATTCTCCTTGATAGAGAAGACGGAAGCAAAATAGGAGTTGAGTAGTTCT 2410 chr3ptel1M 364366 CCTTTCT-TTTGTCACTTCCTGTCATC---CCATCGACCCAAAGCTAGC- 364410 v - i ii vi iv i--- vi v - - C L3#LINE/CR1 2409 GCTTTCTCTCTGTCATCTGTTAACATTACGCCATCTGCCCCAAGC-AGCG 2361 chr3ptel1M 364411 ATCCAGTCTCTTTGATGATGCTTTCTCCCC-AAGATAGCTTT-AAAAACC 364458 iv v ? vv vv v iiv i - v - i C L3#LINE/CR1 2360 GGCCTGTCNCTTTCTTTTTCCTTCTGCTCCGAACATAGCTTTGAAAAGCC 2311 chr3ptel1M 364459 ACAACAAAATCATAATAAAAACATC--------AGCCTCAGCTTA-TCCG 364499 vi?vivvvi ii vv v iv iv i-------- i - i C L3#LINE/CR1 2310 TTNTTTTTGTTGTCCTTAGCATTTTTTTTTGCAAGCCTCAGCTCATTCTG 2261 chr3ptel1M 364500 GCCTTTAGTGTCTGGGACATGGTTCTT----GTGTGTG-TATCC------ 364538 v iv iivv ivi ---- iv - ii ------ C L3#LINE/CR1 2260 GGCTTTAGCCTTCCTGACACTATTCTTACAGGCTTGTGNTACTCTCTCTT 2211 chr3ptel1M 364539 -ATCCTTTGTTAC-TGCTGTTTTGCAAGGTTTT--TCCAAATCCATCTGG 364584 -i v i- iiv i v v vv i -- v vi v i ii C L3#LINE/CR1 2210 TGTCCTTGGTTATATGTCCTCTTTCCATCTTCTGATACATGTCCTTTTAA 2161 chr3ptel1M 364585 A---TGAT------GAGCTCCTTGTGTCTCCCCATGTATCCCTTCCAATG 364625 --- i------ ii? ii i ?vv v i vvi ii -v C L3#LINE/CR1 2160 AATCTGACATCAGAGAATNCTCTATGNAGCCACGTTGGTTTCTT-AAATG 2112 chr3ptel1M 364626 -ACTATGTTGTTCCCTTCTCACTGGAAGGGTTCTTTTTGA-TGCCTTCAG 364673 -v viv iv i i i i ---- iv v i - ivv C L3#LINE/CR1 2111 CCCTCCCTCTTTTCTTCCTCATTGGA----TCATTTGTAATTGTAGTCAG 2066 chr3ptel1M 364674 AATTGTATTCTCAAGAGTTTACCATTCATCCTGTGCTTATTTCTCCT 364720 vi i i i v ?i v i v -i i i i C L3#LINE/CR1 2065 AATTTCATTTTTAAGAGCTTCCCANCCCTCTTGAGC-CATCTTTCTT 2020 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 48.91 CpG sites = 78, Kimura (unadjusted) = 49.93 Transitions / transversions = 1.26 (78/62) Gap_init rate = 0.06 (24 / 404), avg. gap size = 2.04 (49 / 24) 259 35.71 2.63 1.74 chr3ptel1M 364930 365043 (634957) C MIRc#SINE/MIR (152) 116 2 m_b118s601i37 4326 chr3ptel1M 364930 AGAAGTTAGGGAGCTTGCC---AGTCACATGGCCCACCTGCATCAGAGGA 364976 i i vii ---i ii iviivv iiv vv C MIRc#SINE/MIR 116 AGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCC 67 chr3ptel1M 364977 GGGATTTGCACGCAGGGTCTCCCCACCCCCGAGTTCGGCTCTCTAGCTAC 365026 i i v v - i iiv i i i i iv vv i C MIRc#SINE/MIR 66 GGGACTCGAACCCA-GGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCAC 18 chr3ptel1M 365027 TTCACCAGGGTTGCCTC 365043 v -vii C MIRc#SINE/MIR 17 TGCACCA-CACTGCCTC 2 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 49.33 CpG sites = 25, Kimura (unadjusted) = 51.21 Transitions / transversions = 1.67 (25/15) Gap_init rate = 0.03 (3 / 113), avg. gap size = 1.67 (5 / 3) 393 26.27 5.92 7.33 chr3ptel1M 366343 366494 (633506) MIRb#SINE/MIR 4 153 (115) m_b118s601i38 4327 chr3ptel1M 366343 AGGGGCAGCAAGATGGCACCTTGGATAGAGCATTATCTCCAAAGTCAGG- 366391 i--- ii vv v iviv iiii i- MIRb#SINE/MIR 4 AGGGGCAGCG---TGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGAC 50 chr3ptel1M 366392 AGACCTGAATTCAAATCCAGACTCAGACACTTAATACTTTTTAGTTGTGT 366441 ii i v i v v -------i i MIRb#SINE/MIR 51 AGACCTGGGTTCGAATCCCGGCTCTGCCACTTA-------CTAGCTGTGT 93 chr3ptel1M 366442 GACCCTAGGCAAGTCATGTAACCCCAACT--GCCTCAA------CAACAA 366483 i i i iv i -v -- i------ v vi MIRb#SINE/MIR 94 GACCTTGGGCAAGTTACTTAACCTC-TCTGAGCCTCAGTTTCCTCATCTG 142 chr3ptel1M 366484 AAAAATGGAGA 366494 v i MIRb#SINE/MIR 143 TAAAATGGGGA 153 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.17 CpG sites = 24, Kimura (unadjusted) = 33.43 Transitions / transversions = 1.85 (24/13) Gap_init rate = 0.09 (14 / 151), avg. gap size = 1.43 (20 / 14) 19 17.04 4.62 4.62 chr3ptel1M 367615 367679 (632321) (AGAGAC)n#Simple_repeat 1 65 (0) m_b118s252i17 4328 chr3ptel1M 367615 AGAGATAGAGACAGAG--AGAGACAGAGA-AGAGGGAGGGAGAGAGGAGA 367661 i -- - iv i v - v (AGAGAC)n#Sim 1 AGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGA-GACA 49 chr3ptel1M 367662 GGGAGCGGGAGCCAGAGA 367679 i - -i v (AGAGAC)n#Sim 50 GAGA-C-AGAGACAGAGA 65 Matrix = Unknown Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.08 (5 / 64), avg. gap size = 1.20 (6 / 5) 12 9.52 0.00 4.17 chr3ptel1M 367888 367912 (632088) (GAAG)n#Simple_repeat 1 24 (0) m_b118s252i18 4329 chr3ptel1M 367888 GAAGAAAGGAAAGAAGGAAGGGAAG 367912 i i - (GAAG)n#Simpl 1 GAAGGAAGGAAGGAAGGAA-GGAAG 24 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 142 14.55 2.62 0.74 chr3ptel1M 371525 371791 (628209) (GAAG)n#Simple_repeat 1 272 (0) m_b119s252i0 4330 chr3ptel1M 371525 GAAGGAAGGAAAGAATGGAGTGGGGAAGGAATGAA-GAGGGAAGAGGGGA 371573 i v i vii v - i iii (GAAG)n#Simpl 1 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 50 chr3ptel1M 371574 AGGGAGGAAGGGAGAGAGGAAGGAAGGAAGG-AGGAAAG-AGG-AGGAA- 371619 i i ii - i - - - (GAAG)n#Simpl 51 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG 100 chr3ptel1M 371620 GAAGGAAGGAAGGAAGGGATTGAGGGGGGAAGGAAGGAAGGAGGGAAAGA 371669 i vvi ii i i (GAAG)n#Simpl 101 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 150 chr3ptel1M 371670 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG 371719 (GAAG)n#Simpl 151 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG 200 chr3ptel1M 371720 GAAGGAAGGAAGGAAGGAAGGAAGG-AGAAAGATAGAAAGGGAGGGGAGG 371768 - i iv i - i i (GAAG)n#Simpl 201 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA-GGAAGGAAGG 249 chr3ptel1M 371769 GAGGAA-GAGTGAGAAGAAGGAAG 371791 i - iv - i (GAAG)n#Simpl 250 AAGGAAGGAAGGA-AGGAAGGAAG 272 Matrix = Unknown Transitions / transversions = 3.86 (27/7) Gap_init rate = 0.03 (9 / 266), avg. gap size = 1.00 (9 / 9) 238 25.01 0.00 1.92 chr3ptel1M 372295 372347 (627653) L2d2_3end#LINE/L2 414 465 (90) m_b119s601i0 4331 chr3ptel1M 372295 TTTATATATTGCATTTCCCAATTTAAATGTAAGTTCTTTGAGGGCAGAGG 372344 i v i-i i i vi v i i i i L2d2_3end#LIN 414 TTTATGTCTTGT-CTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGA 462 chr3ptel1M 372345 CCA 372347 L2d2_3end#LIN 463 CCA 465 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 32.26 CpG sites = 10, Kimura (unadjusted) = 32.26 Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.02 (1 / 52), avg. gap size = 1.00 (1 / 1) 365 31.57 1.74 0.86 chr3ptel1M 372385 372499 (627501) C MIR#SINE/MIR (140) 122 7 m_b119s601i1 4332 chr3ptel1M 372385 TGAGGCA-ATTGGGGTTAAGTGACTTGCCTAGAATCCCACAGCTAGTAAG 372433 - vv i i i iii v C MIR#SINE/MIR 122 TGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAG 73 chr3ptel1M 372434 TATTTGAGGTCAAATTTGAATTCAGGTCTTCATGATCCCAGACCCAGCA- 372482 iviv vivii i ii ivv - iii v v ii- C MIR#SINE/MIR 72 TGGCAGAGCCGGGATTCGAACCCAGGCAGTC-TGGCTCCAGAGCCCGTGC 24 chr3ptel1M 372483 TTTTACCCTCTGAGCTA 372499 i v v iv C MIR#SINE/MIR 23 TCTTAACCACTATGCTA 7 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 39.47 CpG sites = 22, Kimura (unadjusted) = 42.59 Transitions / transversions = 1.57 (22/14) Gap_init rate = 0.03 (3 / 114), avg. gap size = 1.00 (3 / 3) 426 32.00 0.00 0.00 chr3ptel1M 372395 372494 (627506) C MIRc#SINE/MIR (153) 115 16 m_b119s601i2 4332 chr3ptel1M 372395 GGGGTTAAGTGACTTGCCTAGAATCCCACAGCTAGTAAGTATTTGAGGTC 372444 i i iii v iviv viv C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 66 chr3ptel1M 372445 AAATTTGAATTCAGGTCTTCATGATCCCAGACCCAGCATTTTACCCTCTG 372494 ii i i ii v ii iii iii i vi v C MIRc#SINE/MIR 65 GGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTG 16 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 41.48 CpG sites = 24, Kimura (unadjusted) = 45.41 Transitions / transversions = 3.00 (24/8) Gap_init rate = 0.00 (0 / 99), avg. gap size = 0.0 (0 / 0) 215 31.35 1.45 2.94 chr3ptel1M 372478 372546 (627454) L2b_3end#LINE/L2 389 456 (10) m_b119s601i3 4333 chr3ptel1M 372478 CAGCATTTTACCCTCTGAGC-TAATACATAGTCTAATGCACATAGTAAGC 372526 v ii v i i v v - ii v? i i-- i i L2b_3end#LINE 389 CACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTG--GCACACAGTAGGC 436 chr3ptel1M 372527 ACTTAATAAAGGCTTGTTGA 372546 i i i vii L2b_3end#LINE 437 GCTCAGTAAATATTTGTTGA 456 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 38.77 CpG sites = 15, Kimura (unadjusted) = 44.44 Transitions / transversions = 2.50 (15/6) Gap_init rate = 0.04 (3 / 68), avg. gap size = 1.00 (3 / 3) 225 25.53 0.00 3.92 chr3ptel1M 372497 372549 (627451) L2d2_3end#LINE/L2 498 548 (7) m_b119s601i4 4333 chr3ptel1M 372497 CTAATACATAGTCTAATGCACATAGTAAGCACTTAATAAAGGCTTGTTGA 372546 ii vv i -- i i i i vii L2d2_3end#LIN 498 CTAGCACAGTGCCT--TGCACACAGTAGGCGCTCAATAAATATTTGTTGA 545 chr3ptel1M 372547 CTT 372549 i L2d2_3end#LIN 546 TTT 548 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.99 CpG sites = 10, Kimura (unadjusted) = 33.11 Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.00 (2 / 2) 237 17.78 2.17 2.17 chr3ptel1M 372503 372548 (627452) L2d_3end#LINE/L2 461 506 (10) m_b119s601i5 4333 chr3ptel1M 372503 CATAGT-CTAATGCACATAGTAAGCACTTAATAAAGGCTTGTTGACT 372548 i - i - i i i vi i L2d_3end#LINE 461 CACAGTGCTGA-GCACATAGTAGGCGCTCAATAAATACTTGTTGATT 506 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 18.50 CpG sites = 7, Kimura (unadjusted) = 21.41 Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.04 (2 / 45), avg. gap size = 1.00 (2 / 2) 30 8.35 0.00 0.00 chr3ptel1M 372578 372616 (627384) (AC)n#Simple_repeat 1 39 (0) c_b119s251i0 4334 chr3ptel1M 372578 ACACATACACACACACATACACACACGCACACACACACA 372616 i i i (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACA 39 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 275 32.81 3.88 0.75 chr3ptel1M 372817 372945 (627055) C L2d2_3end#LINE/L2 (305) 250 118 m_b119s601i6 4335 chr3ptel1M 372817 CAAGGGAGACTCGGGTGGAGAAGAGAGCACTTGAGCTGGATCTTGGAGGA 372866 i i i ivi-i i ivi ? i ii i C L2d2_3end#LIN 250 CAGGGAAGGCTTCA-CGGAGGAGGTGGNATTTGAGCTGGGCCTTGAAGGA 202 chr3ptel1M 372867 AGAGAAGGATTT--ATGACTTGA---GGAGGGACTGAATATTCCAGGAAG 372911 v i v -- iiv v --- i ivv iii vi C L2d2_3end#LIN 201 TGGGTAGGATTTGGATAGGTGGAGAGGAAGGGGAAGGGCATTCCAGGCGG 152 chr3ptel1M 372912 ATGGCACAACCTGGGCAAAGGCAGGGAGGAGGGA 372945 iv v ii v i ivi v C L2d2_3end#LIN 151 GGGGAACGGCGTGAGCAAAGGCGCAGAGGCGGGA 118 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 40.34 CpG sites = 28, Kimura (unadjusted) = 46.28 Transitions / transversions = 2.00 (28/14) Gap_init rate = 0.02 (3 / 128), avg. gap size = 2.00 (6 / 3) 340 35.27 4.04 5.71 chr3ptel1M 372905 373349 (626651) C L2#LINE/L2 (79) 3003 2566 m_b119s601i7 4335 chr3ptel1M 372905 CAGGAAGATGGCACAACCTGGGCAAAG-GCAGGGAG-GAGGGAGATGAAG 372952 v iv - iiv viii - v v - i - iv C L2#LINE/L2 3003 CAGCAAGGAGGC-CAGTGTGGCTGGAGCGGAGTGAGCGAGGGGGA-GAGT 2956 chr3ptel1M 372953 GGAAGACAAATAATATCCAAAGAAATGGTAAGAATGAGTGGGAACTGCAT 373002 v i- i i vi --- i - ---i --- i iiv C L2#LINE/L2 2955 GGTAGG-AGATGAGGTC---AGAGA-GGTAA---CG---GGGGACCAGAT 2917 chr3ptel1M 373003 C-TGAAGAGCTTTAACAGCCACATG---GGGCTTGTACTTTTG-TAAAGG 373047 - v i i ivvi i- --- i vvi i- vvii C L2#LINE/L2 2916 CATGTAGGGCCTTGTAGGCCAT-TGTAAGGACTTTGGCTTTTACTCTGAG 2868 chr3ptel1M 373048 TGAAA-GGGAA-TCACCAGAATTGGTTGTATG--GGAGAGTCACATGACC 373093 i - -i iii i-- v iv -- ii v i C L2#LINE/L2 2867 TGAGATGGGAAGCCATTGGAG--GGTTTTGAGCAGAGGAGTGACATGATC 2820 chr3ptel1M 373094 AAATCTTGGTTTAAAGAAAAATCATTTCAATAGCTGTG---AGTTCAATG 373140 vi ii vv v - ii i iiiiiv --- --- i C L2#LINE/L2 2819 TGACTTACGTTTTAA-AAGGATCACTCTGGCTGCTGTGTTGAG---AATA 2774 chr3ptel1M 373141 GATTGGAAAGAG--AAGAAATGAATCATGGAGACCCATCAGGAATCTACT 373188 i ? ii i -- iivv v v vi i iv i C L2#LINE/L2 2773 GACTGNAGGGGGGCAAGGGTGGAAGCAGGGAGACCAGTTAGGAGGCTATT 2724 chr3ptel1M 373189 GCAATGATATAGGCAAGGACTG-TGAAGGCCTGAACTATGGTAAGGGCTG 373237 i i vi i iiv - iv i i i v iiv v C L2#LINE/L2 2723 GCAGTAATCCAGGCGAGAGATGATGGTGGCTTGGACCAGGGTGGTGGCAG 2674 chr3ptel1M 373238 GGTAAGGGAGGAGGAG-GGTCTGGATCCATGAGATGTGATGGGGGTATTA 373286 v v i v iv i - - i vv v i vv ii vvi C L2#LINE/L2 2673 TGGAGGTGGTGAGAAGTGGTC-GGATTCTGGATATATTTTGAAGGTAGAG 2625 chr3ptel1M 373287 ATGACAAAGTTTGTCAACTGATTGGATCTATGAGGAGAAAGGGGGAGAGA 373336 vi iii iii iv -- i i v vi -- i i C L2#LINE/L2 2624 CCGACAGGATTTGCTGATGGATTGGA--TGTGGGGTGTGA--GAGAAAGA 2579 chr3ptel1M 373337 GAGAAGGGAAGAA 373349 i vv i C L2#LINE/L2 2578 GAGGAGTCAAGGA 2566 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 49.04 CpG sites = 94, Kimura (unadjusted) = 50.54 Transitions / transversions = 1.74 (94/54) Gap_init rate = 0.08 (37 / 444), avg. gap size = 1.16 (43 / 37) 21 24.14 3.57 2.35 chr3ptel1M 373350 373425 (626575) (GAGAGA)n#Simple_repeat 1 76 (9) m_b119s252i1 4336 chr3ptel1M 373350 GAGGGAAACGAGAGGGAGGAAGAGGGAG-GAGGGAGACAGAGACAGAGAA 373398 i i - i ii i - i v v i (GAGAGA)n#Sim 1 GAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 49 chr3ptel1M 373399 ACAGAGAGACAGTTGGGAGAAAGA-AAA 373425 v v -v i i - i (GAGAGA)n#Sim 50 AGAGAGAGAGAG-AGAGAGAGAGAGAGA 76 Matrix = Unknown Transitions / transversions = 2.20 (11/5) Gap_init rate = 0.05 (4 / 75), avg. gap size = 1.00 (4 / 4) 36 2.94 0.00 0.00 chr3ptel1M 373426 373460 (626540) (AG)n#Simple_repeat 1 35 (0) c_b119s251i1 4337 chr3ptel1M 373426 AGAGAGAGAAAGAGAGAGAGAGAGAGAGAGAGAGA 373460 i (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 35 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 269 34.31 7.41 0.69 chr3ptel1M 373808 373942 (626058) L3#LINE/CR1 2790 2933 (1166) m_b119s601i8 4338 chr3ptel1M 373808 GAATCATAAAAAGGATG---CATCAGGACATCAGAAAGGGAAGTAATGCT 373854 i i v vi ---ii v v - i i iii v L3#LINE/CR1 2790 GGATTATTAAACAGATGGTTTGTGAGCAC-TTAGAAAAGGAAGCGGTGAT 2838 chr3ptel1M 373855 CACAGAGGGTGGGCATGGATTCAGCAAGAAGAAGCCG-ACTACGCCCACT 373903 vii i ivi i vi v i i-i i vi iv i L3#LINE/CR1 2839 CACTAGGAGCCAGCATGGGTTCACTAAGAACAAGTCATGCCAAACTAACC 2888 chr3ptel1M 373904 TCATCTC--TTTCTAATA--ATTATTTGACAAGC--ATCAAGGAA 373942 i -- i i --i i v vi i-- i i L3#LINE/CR1 2889 TCATTTCCTTTTTTGATAGGGTTACTAGACTGGTAGATCAGGGGA 2933 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 48.13 CpG sites = 33, Kimura (unadjusted) = 49.92 Transitions / transversions = 2.54 (33/13) Gap_init rate = 0.04 (6 / 134), avg. gap size = 1.83 (11 / 6) 212 10.00 0.00 0.00 chr3ptel1M 373940 373969 (626031) C L3#LINE/CR1 (4) 4095 4066 m_b119s601i10 4339 chr3ptel1M 373940 GAATCACAAAATCTCAGAGCTAGAAGGGAC 373969 i i i C L3#LINE/CR1 4095 GAATCACAGAATCTCAGAGTTGGAAGGGAC 4066 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 11.16 CpG sites = 3, Kimura (unadjusted) = 11.16 Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 505 23.72 2.84 4.32 chr3ptel1M 374067 374207 (625793) C MIR3#SINE/MIR (63) 145 7 m_b119s601i12 4340 chr3ptel1M 374067 CTTATTTTACAGATGAGAAAACTGAAGCAAATAGAGTT-AAGTGACTTGC 374115 i i i vv v v - C MIR3#SINE/MIR 145 CTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGC 96 chr3ptel1M 374116 CCAGGATCACACAGCTGGTAAGTGTCTGAGACCAGATCTGAACTCAGGAA 374165 i i ?i v v v v vi iiv i --- C MIR3#SINE/MIR 95 CCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAG--- 49 chr3ptel1M 374166 AAGTCTTTCTGACTCT--ATCCCTTC-CTCACTACTTAATTTCTC 374207 -- - i i--i v v - v i i iiiv C MIR3#SINE/MIR 48 --GTC-TCCTGACTCCCAGTCCGTGCTCTCTCTGCTCAGCCACTC 7 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.21 CpG sites = 18, Kimura (unadjusted) = 29.21 Transitions / transversions = 1.29 (18/14) Gap_init rate = 0.06 (9 / 140), avg. gap size = 1.11 (10 / 9) 593 18.94 0.86 4.46 chr3ptel1M 374067 374182 (625818) C MIRc#SINE/MIR (120) 148 37 m_b119s601i11 4340 chr3ptel1M 374067 CTTATTTTACAGATGAGAAAACTGAAGCAAATAGAG-TTAAGTGACTTGC 374115 ii i i vv v - C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr3ptel1M 374116 CCAGGATCACACAGCTGGTAAGTGTCTGAGACCAGATCTGAACTCAGGAA 374165 i i i v v v vi iii i --- C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAG--- 52 chr3ptel1M 374166 AAGTCTTTCTGACTCTA 374182 -- i i C MIRc#SINE/MIR 51 --GTCTTCCTGACTCCA 37 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 21.14 CpG sites = 14, Kimura (unadjusted) = 22.31 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.05 (6 / 115), avg. gap size = 1.00 (6 / 6) 411 30.73 9.19 1.51 chr3ptel1M 374212 374396 (625604) C L3#LINE/CR1 (29) 4070 3872 m_b119s601i13 4341 chr3ptel1M 374212 GAGACTTGAGAAGCC-TAAAATCCAATCCCTCCTTGACAAGGCA------ 374254 i i v i i - vv i i i i v i-- v ------ C L3#LINE/CR1 4070 GGGACCTTAGAGGTCATCTAGTCCAACCTCCCATC--CAATGCAGGAATC 4023 chr3ptel1M 374255 ---TCTATGCTATACATGACAAGCTATCACCCAACTCCCACTTGAAGACC 374301 --- iivi v v ivi i i ii ii v C L3#LINE/CR1 4022 CCTTCTACAACATCCCTGACAAGTGGTCATCCAGCCTCTGCTTGAACACC 3973 chr3ptel1M 374302 TTCAAGGAGGGGGCATCTCCCT-CCTCCCAAGGTAACCTGCTCCACTTTG 374350 i iv v - v v - ? i i i iii i v C L3#LINE/CR1 3972 TCCAGTGACGGGG-AGCTCACTACCTCNCGAGGCAGCCCATTCCATTTTT 3924 chr3ptel1M 374351 GAAAAGGTCACATTGTT-----GTT-TTCCTGATATGTTTCCTAAATTTG 374394 i v v vv ----- - v vvvv v i C L3#LINE/CR1 3923 GGACAGCTCTGATTGTTAGAAAGTTCTTCCTTATATTGAGCCGAAATCTG 3874 chr3ptel1M 374395 CC 374396 C L3#LINE/CR1 3873 CC 3872 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 39.89 CpG sites = 31, Kimura (unadjusted) = 40.84 Transitions / transversions = 1.24 (31/25) Gap_init rate = 0.05 (9 / 184), avg. gap size = 2.22 (20 / 9) 458 25.74 21.11 0.42 chr3ptel1M 374420 374618 (625382) C L3#LINE/CR1 (301) 3798 3559 m_b119s601i14 4341 chr3ptel1M 374420 ACATAACAGTCCTTCGGATATTTGAAGGCCAATTTCATG--TCCTCCAGA 374467 i i ii i viv v -- i - C L3#LINE/CR1 3798 ACATGACAGCCCTTCAAATATTTGAAGACAGCTATCATGTCTCCTCTA-A 3750 chr3ptel1M 374468 GCTTTCTGCTCTCCAAGTCAAATTTTCCTC-TTCCTTCAGCCACTCCCC- 374515 ii vi i ii iv i iv- i ii i - C L3#LINE/CR1 3749 GTCTTCTCTTCTCCAGGCTAAACATCCCCAGTTCCTTCAACCGTTCCTCA 3700 chr3ptel1M 374516 -----CACTTTTCACAGA--------CAT-------GCTCTCC------- 374538 ----- ivv iv -------- ------- ------- C L3#LINE/CR1 3699 TATGACATGGTTTCCAGACCCTTCACCATCCTGGTCGCTCTCCTCTGGAC 3650 chr3ptel1M 374539 -CGTTTC------TCTATGCCCTCCCTAAAATGCAATGTCCAGAATTGAA 374581 - i i ------ v i ii i iiii i i C L3#LINE/CR1 3649 GCGCTCCAGTTTGTCAATGTCCCTCTTAAAATGTGGCGCCCAGAACTGAA 3600 chr3ptel1M 374582 TGC-ATATTCCA-ATGTAG-CTGACAAGAGTAGAG-GCAGC 374618 i - i - i - v v i -i C L3#LINE/CR1 3599 CGCAATACTCCAGATGTGGTCTGACCAGCGCAGAGTACAGC 3559 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 31.10 CpG sites = 39, Kimura (unadjusted) = 33.54 Transitions / transversions = 3.25 (39/12) Gap_init rate = 0.07 (13 / 198), avg. gap size = 3.31 (43 / 13) 214 28.11 12.20 4.55 chr3ptel1M 375851 375932 (624068) L2c_3end#LINE/L2 373 460 (18) m_b119s601i15 4342 chr3ptel1M 375851 TAGAACATAAGCTCCCTCTGCAAGACCAGGGATGGTGT--TATT--TTTT 375896 vii i i ----i iv iv -- -- i L2c_3end#LINE 373 TAGACTGTGAGCTCCTT----GAGGGCAGGGACCGTGTCTTATTCATCTT 418 chr3ptel1M 375897 T------CTAGCGCTTGGCACAGAATAAGTGACTGACAAATG 375932 ------ i i v i i i viii i L2c_3end#LINE 419 TGTATCCCCAGCGCCTGGCACATAGTAGGCGCTCAATAAATG 460 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 35.83 CpG sites = 17, Kimura (unadjusted) = 38.09 Transitions / transversions = 3.40 (17/5) Gap_init rate = 0.09 (7 / 81), avg. gap size = 2.00 (14 / 7) 231 28.20 7.87 4.35 chr3ptel1M 376534 376622 (623378) MIR3#SINE/MIR 98 189 (19) m_b119s601i16 4343 chr3ptel1M 376534 AAGCCACTTCAGTTCTCTGA-----AGTT--CTCAGAGCTCTGTTAAATC 376576 i vi i----- -- ---- v v MIR3#SINE/MIR 98 AAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCA----TCTGTAAAATG 143 chr3ptel1M 376577 GGGTGGTTGGCTTCCATGGCCTCTGGAGTCCTTTCTCACTGTAATA 376622 i v vi vv ii iii i ivi v i i MIR3#SINE/MIR 144 AGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACA 189 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 36.65 CpG sites = 15, Kimura (unadjusted) = 36.65 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.07 (6 / 88), avg. gap size = 1.83 (11 / 6) 291 20.48 7.41 3.57 chr3ptel1M 376758 376838 (623162) C MIR3#SINE/MIR (9) 199 116 m_b119s601i17 4344 chr3ptel1M 376758 AATCATATTAT-TTACAGCTGGAAGGGACTTCAGAGCTGCTCTAGTCTTT 376806 vv - i v i i v vv --- C MIR3#SINE/MIR 199 AATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTC--- 153 chr3ptel1M 376807 TGCCCTCCTC-TTATACAAATGAGGA----GAGGCTC 376838 iiv i - v i ---- i C MIR3#SINE/MIR 152 CAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCC 116 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 24.13 CpG sites = 8, Kimura (unadjusted) = 24.13 Transitions / transversions = 1.00 (8/8) Gap_init rate = 0.07 (6 / 80), avg. gap size = 1.50 (9 / 6) 13 24.67 3.70 6.33 chr3ptel1M 378407 378487 (621513) (GGAAG)n#Simple_repeat 1 79 (0) m_b119s252i2 4345 chr3ptel1M 378407 GGAAGGGCA-GGTAGGGCAGAGATGGGAAGCTGCAAGGGAAGGAAATGAT 378455 v - v v i v -- v i v iv (GGAAG)n#Simp 1 GGAAGGGAAGGGAAGGGAAGGGAAGGGAAG--GGAAGGGAAGGGAAGGGA 48 chr3ptel1M 378456 GGGGCAAAGGAA--AAAGAGGACAGAGGAGGGAA 378487 i - i --i - - i i (GGAAG)n#Simp 49 AGGG-AAGGGAAGGGAAG-GGA-AGGGAAGGGAA 79 Matrix = Unknown Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.09 (7 / 80), avg. gap size = 1.14 (8 / 7) 523 20.77 7.81 2.22 chr3ptel1M 379133 379260 (620740) C L2a_3end#LINE/L2 (6) 511 377 m_b119s601i18 4346 chr3ptel1M 379133 TCATCCAATGAGCATTTATTG----TCTACTAGGTGCCAGGAATTGTTCT 379178 i ii ii ----i v v i C L2a_3end#LINE 511 TCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCT 462 chr3ptel1M 379179 AAATGCTGGGGATACA--AATAA--GAAATAGA-ATCAGTCCCTG-CCTC 379222 iii -- i i --i i - vv - C L2a_3end#LINE 461 AGGCGCTGGGGATACAGCAGTGAACAAAACAGACAAAAGTCCCTGCCCTC 412 chr3ptel1M 379223 AAGAAGCTTACAATCTAATAAGGGAAGGCAAGGGACAA 379260 v i v i ii i i --- C L2a_3end#LINE 411 ATGGAGCTTACATTCTAGTGGGGGGAGACA---GACAA 377 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 24.34 CpG sites = 20, Kimura (unadjusted) = 25.47 Transitions / transversions = 3.33 (20/6) Gap_init rate = 0.06 (8 / 127), avg. gap size = 1.62 (13 / 8) 419 24.46 6.54 3.82 chr3ptel1M 379138 379290 (620710) C L2d2_3end#LINE/L2 (11) 544 388 m_b119s601i19 4346 chr3ptel1M 379138 CAATGAGCATTTATTG----TCTACTAGGTGCCAGGAATTGTTCTAAATG 379183 ii ii ----i iv v v i v iii C L2d2_3end#LIN 544 CAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCG 495 chr3ptel1M 379184 CTG---GGGATACAAATAAGAAATAGAATCAGTCCCTGCC-TCAAGAAGC 379229 --- v v vv vvii - i C L2d2_3end#LIN 494 CTGTGGGGGATACAAAGAAGTATAAGACATGGTCCCTGCCCTCAAGGAGC 445 chr3ptel1M 379230 TTACAATCTAATAAGGGAAGGCAAGGGACAAAGGAAGGCTTTAAAAAG-- 379277 i -v i i iv i -v v ---- i -- C L2d2_3end#LIN 444 TTACAATCTAGT-TGGGGAGACAAGACATAAA-CACG----TGAAAAGTT 401 chr3ptel1M 379278 GAATAGGAATACA 379290 i iv C L2d2_3end#LIN 400 AAATAACAATACA 388 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.25 CpG sites = 21, Kimura (unadjusted) = 30.24 Transitions / transversions = 1.40 (21/15) Gap_init rate = 0.07 (10 / 152), avg. gap size = 1.60 (16 / 10) 17 31.36 2.11 4.30 chr3ptel1M 379788 379882 (620118) (TTC)n#Simple_repeat 1 93 (0) m_b119s252i3 4347 chr3ptel1M 379788 TTCTTC-TCTTTCTCTTCATGTTCTTCATCCTCCTTCTCTCACTTTCTTT 379836 - ii v v - i i - vii i (TTC)n#Simple 1 TTCTTCTTCTTCTTCTTCTTCTTCTTC-TTCTTCTTCT-TCTTCTTCTTC 48 chr3ptel1M 379837 GTTTTTTGCTTGAATCTTCCTCTAGCTTCTCCTTCCT-TTCCTCCTC 379882 v i i v -vv i -v i i - i i (TTC)n#Simple 49 TTCTTCTTCTT-CTTCTTCTTCT-TCTTCTTCTTCTTCTTCTTCTTC 93 Matrix = Unknown Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.06 (6 / 94), avg. gap size = 1.00 (6 / 6) 35 0.00 0.00 0.00 chr3ptel1M 380849 380880 (619120) (TCC)n#Simple_repeat 1 32 (0) c_b119s251i2 4348 chr3ptel1M 380849 TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC 380880 (TCC)n#Simple 1 TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC 32 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 27 7.96 0.00 0.00 chr3ptel1M 380881 380920 (619080) (ATC)n#Simple_repeat 1 40 (0) m_b119s252i4 4349 chr3ptel1M 380881 ATCATCATCATCATCATCATCCTCATCCTCATCATCCTCA 380920 v v v (ATC)n#Simple 1 ATCATCATCATCATCATCATCATCATCATCATCATCATCA 40 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 343 22.84 15.48 1.13 chr3ptel1M 382415 382569 (617431) C Eulor6C#DNA/Crypton (29) 179 3 m_b119s502i0 4350 chr3ptel1M 382415 AATAAGAGATCTAGATCCTAATAGCATTACCACACCCCAGGGGGTGCTTC 382464 v i v iiv i? i? i vv i i v i C Eulor6C#DNA/C 179 AATTAAAGAGCCGTATTNTGNTAGTATTAAGACACTCCGGGGCGTGCTTT 130 chr3ptel1M 382465 --CGTTCCATTATACATCATGCCT-----GG--------CTGGGTCTCCA 382499 --i v? - i - ----- -------- v i ?? C Eulor6C#DNA/C 129 ATTGGNCCATTA-ATAT-ATGCCTCGAGTGGTCGAAGTACTTGGCCTNNA 82 chr3ptel1M 382500 --TTTGT----CACTGAGTACC--AGGCATGTGGTAATAGTCCTGTAAAA 382541 --i ---- i viv i -- iv i v v? C Eulor6C#DNA/C 81 GCCTTGTGCCTCGCAACGCACCCGAGGCATGTATTAATGGACCANTAAAA 32 chr3ptel1M 382542 CATGCCCTGTTGGGTCTTAATGCT-TATT 382569 i i v i- C Eulor6C#DNA/C 31 CACGCCCTGTCGTGTCTTAATGCCATATT 3 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 24.45 CpG sites = 21, Kimura (unadjusted) = 29.26 Transitions / transversions = 1.50 (21/14) Gap_init rate = 0.06 (9 / 154), avg. gap size = 2.89 (26 / 9) 308 24.27 4.81 0.93 chr3ptel1M 383006 383109 (616891) L3#LINE/CR1 900 1007 (3092) m_b119s601i20 4351 chr3ptel1M 383006 TTCAGAAGAGAGAG-AGGACTGGGGAAGTGAGCAGGAGGCTA---AAATG 383051 ii i - ivv i vv --- i L3#LINE/CR1 900 TTTGGAAGAGAAAGGAGGATATGGGAAGTGAACAGCTGGCTACGTAGATG 949 chr3ptel1M 383052 ATGTTTGAGAATGGCATTTGGATTTCTAGGACTATGACTTAAAATG-CAG 383100 i ivi ii v v - i i ?i i- L3#LINE/CR1 950 GTGTCGAAGAACAGGATTTGGTTTTCT-GGACCATGGCTTANGATACCAG 998 chr3ptel1M 383101 AAGGAGGAG 383109 v v i L3#LINE/CR1 999 AACGATGGG 1007 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.10 CpG sites = 16, Kimura (unadjusted) = 30.56 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.04 (4 / 103), avg. gap size = 1.50 (6 / 4) 43 21.41 0.00 0.00 chr3ptel1M 383110 383199 (616801) (GAG)n#Simple_repeat 1 90 (0) m_b119s252i5 4352 chr3ptel1M 383110 GAGGCAGAGGAGGAAGAGGAGGAGGAAGAAGAAGAGGAGGAAGAGAACAA 383159 vi i i i i i i vi (GAG)n#Simple 1 GAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA 50 chr3ptel1M 383160 GAAGGAGGAAGAGGAGGAAGAGGAGGAGAAGGAGAAGAAG 383199 i i i i i i (GAG)n#Simple 51 GGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG 90 Matrix = Unknown Transitions / transversions = 7.00 (14/2) Gap_init rate = 0.00 (0 / 89), avg. gap size = 0.0 (0 / 0) 265 38.75 1.88 0.00 chr3ptel1M 383243 383402 (616598) L3#LINE/CR1 1244 1406 (2693) m_b119s601i21 4351 chr3ptel1M 383243 AGGAACAGTGCCCATGGCCTTTGATGTCCACACACAAATTTATAAAACAC 383292 i i i ii iv i i i v vi i i ii i L3#LINE/CR1 1244 AGAAACAATACTTATGGCCTCAGATGTCTATATACCAATGCACAGAGTAT 1293 chr3ptel1M 383293 GGTGGACAAGCAGGATGAA-TTCAAATCCCAATGCAATAACCCAAA-AGG 383340 vvi i i? iii ? - v iii ii vi vvi - v L3#LINE/CR1 1294 GGGTAATAAANAAAGTNAACTTGAAATTTTAACACAAGGAGGTAAATACG 1343 chr3ptel1M 383341 ACCAGACAAATCTCA-TGTGACTGGGGAAACTGCGACCCCAGACTAGAAC 383389 i vv i ii v -i v v viiiv v i vv i i L3#LINE/CR1 1344 ATCTCATAGGTATCACCGAGACTTGGTGGGATGGGACTCATGACTGGAAT 1393 chr3ptel1M 383390 ACAGCTCTGGAAG 383402 i vv L3#LINE/CR1 1394 ACGGCGATGGAAG 1406 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 56.91 CpG sites = 40, Kimura (unadjusted) = 60.02 Transitions / transversions = 1.82 (40/22) Gap_init rate = 0.02 (3 / 159), avg. gap size = 1.00 (3 / 3) 276 35.40 1.77 0.00 chr3ptel1M 383621 383733 (616267) C L3#LINE/CR1 (619) 3480 3366 m_b119s601i22 4353 chr3ptel1M 383621 ATATCACATTATTGATGCAGCTGGAGCTTGTGGTCTATCCAGCCTCC--G 383668 i i i iiv vv v i v iiv iv i -- C L3#LINE/CR1 3480 ACATCACACTGTTGGCTCATATTGAGCTTGCGGTCAACTAAAACCCCTAG 3431 chr3ptel1M 383669 ATCTTCCCCAGATAACCTGCTCCTTCTTCAGACCTCCGCCATCTTGTATT 383718 i iii vi i v v vvvi i ii v i i C L3#LINE/CR1 3430 GTCTTTTTCACGTGAACTGCTGCTAAGCCAGATCCTCTCCATCCTGTACT 3381 chr3ptel1M 383719 CTTGCTGTTGCTTTT 383733 iv v v C L3#LINE/CR1 3380 TGTGCAGTTGATTTT 3366 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 46.24 CpG sites = 23, Kimura (unadjusted) = 49.72 Transitions / transversions = 1.35 (23/17) Gap_init rate = 0.01 (1 / 112), avg. gap size = 2.00 (2 / 1) 253 34.11 3.01 3.01 chr3ptel1M 383624 383756 (616244) C L3b_3end#LINE/CR1 (627) 579 447 m_b119s601i23 4353 chr3ptel1M 383624 TCACATTATTGATGCAGCTGGAGCTTGTGGTCTA-TCCAGCCTCC-GATC 383671 i i ii iv vv v i v - vv i i - i C L3b_3end#LINE 579 TCGCACTGCTGACTCATATTGAGCTTGCGGTCAACTAAAACCCCCAGGTC 530 chr3ptel1M 383672 TTCCCCAGATAACCTGCTCCTTCTTCAGACCTCCGCCATCTTGTATTCTT 383721 iii v i?v v vvvi ivii v i i vi C L3b_3end#LINE 529 TTTTTCACATGNGCTGCTGCTAAGCCGCGTCTCCCCCATCCTGTACTCGC 480 chr3ptel1M 383722 GCTGTTGCTTTTCCCCCAGGA--CAAGTGTGGGATTT 383756 vi ? ii---- i -- ii i C L3b_3end#LINE 479 GCGATTGNTTTTTT----GAACCCAAGTGCAGGACTT 447 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 41.28 CpG sites = 27, Kimura (unadjusted) = 48.73 Transitions / transversions = 1.59 (27/17) Gap_init rate = 0.05 (7 / 132), avg. gap size = 1.14 (8 / 7) 302 31.66 6.99 1.53 chr3ptel1M 383903 384088 (615912) MIR3#SINE/MIR 1 196 (12) m_b119s601i24 4354 chr3ptel1M 383903 CTGGACAGAAATAGCTCAGGA-AGAGA-CATAGGGCTGTGAA-CAGGAGA 383949 - i- i v v - - i- i v i- MIR3#SINE/MIR 1 CTGG-CAGAG-TGGCTGAGCAGAGAGAGCAC-GGACTGGGAGTCAGGAGA 47 chr3ptel1M 383950 GCAAGATTCTAGTCCTCTCCCTGCCGC-AGC-CACAGGG-AATTTTCTCC 383996 v vi i ivv i i - i -?i v v -i ii vvv MIR3#SINE/MIR 48 CCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGC 97 chr3ptel1M 383997 AA-TTATTTCATGCTTCTGAGTCTCAGTTTCTGGGTTCATGACAGGAGCA 384045 - i i ivii i i ivvi iii i v v vi MIR3#SINE/MIR 98 AAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGG 147 chr3ptel1M 384046 GCTTAGACT-GCTGG-CTCT--GGCCTCCTC--GCTCTTATGTTCTCTG 384088 v i - v i- -- i i i -- v ii v MIR3#SINE/MIR 148 GGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATG 196 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 41.25 CpG sites = 36, Kimura (unadjusted) = 43.25 Transitions / transversions = 1.64 (36/22) Gap_init rate = 0.08 (14 / 185), avg. gap size = 1.14 (16 / 14) 12 11.25 6.90 0.00 chr3ptel1M 384134 384162 (615838) (TTTC)n#Simple_repeat 1 31 (0) m_b119s252i6 4355 chr3ptel1M 384134 TTTCTTTCTTTCCTTC-TCATTTC-TTCTTT 384162 i - iv - (TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT 31 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.07 (2 / 28), avg. gap size = 1.00 (2 / 2) 577 24.73 1.29 6.08 chr3ptel1M 384210 384364 (615636) MIRb#SINE/MIR 4 151 (117) m_b119s601i25 4356 chr3ptel1M 384210 AGTGGCAGCTAGGTGATGGGGTAGATAGAGTCCCAGCTCTGGAGTCAGGA 384259 v --- i vi i v iv vi i iv MIRb#SINE/MIR 4 AGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGAC 50 chr3ptel1M 384260 AGACAACTTCTTAAATTCAAATCTGGACTCAAATGCTTACTAGCT-TGTG 384308 ------i iii i iv i vivii - MIRb#SINE/MIR 51 AGAC------CTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTG 94 chr3ptel1M 384309 ACCCTAGGTAAGTTACTTTGC-TCTGTTTGCCTCAGTTTACTCATCTGTA 384357 i i i vi - v vv v MIRb#SINE/MIR 95 ACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTA 144 chr3ptel1M 384358 AAATGAG 384364 i MIRb#SINE/MIR 145 AAATGGG 151 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.62 CpG sites = 22, Kimura (unadjusted) = 30.64 Transitions / transversions = 1.57 (22/14) Gap_init rate = 0.07 (11 / 154), avg. gap size = 1.00 (11 / 11) 220 35.29 4.80 4.80 chr3ptel1M 384774 384898 (615102) L2a_3end#LINE/L2 377 501 (16) m_b119s601i26 4357 chr3ptel1M 384774 TTTTCTGTTTTCTTGCCTCATTAAAATGTAAGTGCCC-----GCTAAGGG 384818 v i i --- i i i iv v----- -- L2a_3end#LINE 377 TTGTCTGTCTCC---CCCCACTAGAATGTAAGCTCCATGAGGGC--AGGG 421 chr3ptel1M 384819 ATTACCTCTCT-TTTTGCTTGTATTTGTAGGTCTAGTGCTCATCACAGTA 384867 i -ii v - i iiivvi vvi i i ii vv i L2a_3end#LINE 422 ACT-TTTGTCTGTTTTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTG 470 chr3ptel1M 384868 TCTGGCATTTAATCAGTGTCTAATAGATGTT 384898 i iv i vi i iii i i L2a_3end#LINE 471 CCTGGCACATAGTAGGCGCTCAATAAATATT 501 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 48.39 CpG sites = 30, Kimura (unadjusted) = 52.08 Transitions / transversions = 2.50 (30/12) Gap_init rate = 0.06 (8 / 124), avg. gap size = 1.50 (12 / 8) 13 15.91 0.00 0.00 chr3ptel1M 384927 384954 (615046) (ATCC)n#Simple_repeat 1 28 (0) m_b119s252i7 4358 chr3ptel1M 384927 ATCCATCCATCTATCCATCTCTACATCC 384954 i iv v (ATCC)n#Simpl 1 ATCCATCCATCCATCCATCCATCCATCC 28 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 368 26.10 7.96 1.67 chr3ptel1M 385076 385188 (614812) C L2d_3end#LINE/L2 (3) 513 394 m_b119s601i27 4359 chr3ptel1M 385076 ATCAATGAGTCAATAAGCATTTATTAAGCTCCAATTATGTTCTAAGCAGT 385125 v i i i i v v i v v v C L2d_3end#LINE 513 ATCAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACT 464 chr3ptel1M 385126 ATGCTAA--ATTCTAGGGATGCATAGA-------AAGGCAGAATCTCAAT 385166 i i--ii v i vvv ? i ------- i vii i -- C L2d_3end#LINE 463 GTGCTAGGCGCTGTGGGGAACGANAAAANAGTATAAGACATGGTCCC--T 416 chr3ptel1M 385167 CCCCTCAAGGAACTCACAATCT 385188 v i i C L2d_3end#LINE 415 GCCCTCAAGGAGCTTACAATCT 394 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 31.85 CpG sites = 17, Kimura (unadjusted) = 33.23 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.04 (4 / 112), avg. gap size = 2.75 (11 / 4) 25 10.76 0.00 0.00 chr3ptel1M 385357 385396 (614604) (TGA)n#Simple_repeat 1 40 (0) m_b119s252i8 4360 chr3ptel1M 385357 TGATGATGATTATGGTGATGATGGTGATGATGATGATTAT 385396 v i i v (TGA)n#Simple 1 TGATGATGATGATGATGATGATGATGATGATGATGATGAT 40 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 180 40.90 1.28 1.28 chr3ptel1M 386100 386255 (613745) AmnL2-1#LINE/L2 2153 2308 (305) m_b119s601i28 4361 chr3ptel1M 386100 ACTCTCCTACTCAT-CAACTCCAAAGGCTCCCCATTCTGTCTGAAATCAA 386148 i i v v v- vv vv iiiii v AmnL2-1#LINE/ 2153 ACCCCCATCCTCAAACAACTCCACTGGCTCCCCATTCATTTCAGGATCCA 2202 chr3ptel1M 386149 AAAGAAAATTATCTGTTTTACTTTT-AAGCCATATATAGTCTGGCTTTGA 386197 ivvv ii vii ii - i v vi i v v iiii AmnL2-1#LINE/ 2203 GTTCAAAATTGCCTTCCTTGTTTTTAAAACCCTCCATGGACTTGCTCCAG 2252 chr3ptel1M 386198 TCTATTTTTCCAGTCTCATTGGACATTACCCCCACCCCATCTCCTTTTTG 386247 i ii iv viii ii ivvv vi i vi vv -i ii AmnL2-1#LINE/ 2253 CCTACCTCACGGACCTTGTCTCTCTCTACTCCCCTCCCCGCTCC-CTCCG 2301 chr3ptel1M 386248 TTGCGTCT 386255 i - AmnL2-1#LINE/ 2302 CT-CGTCT 2308 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 61.48 CpG sites = 38, Kimura (unadjusted) = 63.15 Transitions / transversions = 1.52 (38/25) Gap_init rate = 0.03 (4 / 155), avg. gap size = 1.00 (4 / 4) 595 30.05 7.02 5.96 chr3ptel1M 387748 387871 (612129) C L1ME4a_3end#LINE/L1 (215) 656 535 m_b119s551i0 4362 chr3ptel1M 387748 TATATGCAATATTTTCCTGATTCTGTTCATTTCACTTTGCATCACTTCAT 387797 i i v v ---- ?i i iv vi i iv C L1ME4a_3end#L 656 TATATACAGTTTTGT----ANCCTGCTTTTTTCACTTAACATTATATCAT 611 chr3ptel1M 387798 GTAAGTTGTTCCCATGTTTTCCAAAATCATCCT-----GATGTCATTTCT 387842 vivi - iv i-- - i -----i ii ? i C L1ME4a_3end#L 610 GAGCATT-TTCCCATGTCATT--AAAT-ATTCTTCGAAAACATNATTTTT 565 chr3ptel1M 387843 TATAACACAATAATATTCCATT-TA-GAATC 387871 v ii vvv - - i - C L1ME4a_3end#L 564 AATGGCTGCATAATATTCCATTNTATGGAT- 535 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 40.27 CpG sites = 105, Kimura (unadjusted) = 40.59 Transitions / transversions = 1.67 (20/12) Gap_init rate = 0.10 (12 / 123), avg. gap size = 1.33 (16 / 12) 30 0.00 0.00 0.00 chr3ptel1M 387872 387897 (612103) (AT)n#Simple_repeat 1 26 (0) c_b119s251i3 4363 chr3ptel1M 387872 ATATATATATATATATATATATATAT 387897 (AT)n#Simple_ 1 ATATATATATATATATATATATATAT 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 595 30.05 7.02 5.96 chr3ptel1M 387898 388370 (611630) C L1ME4a_3end#LINE/L1 (337) 534 53 m_b119s551i0 4362 chr3ptel1M 387898 GTACATTTAATCATATATCCAACTTATTCAGCCATTTCTCTAATTAATGA 387947 ------- ------ i i i ? i i - iv i C L1ME4a_3end#L 534 GTAC-------CATA------ATTTATTTAACCANTCCCCTA-TTGTTGG 499 chr3ptel1M 387948 GCATCCCCTCAATTTCTAATTCTTTGCCACCACAAA----------A-GA 387986 i iivvvivi i i i i ii i ---------- - C L1ME4a_3end#L 498 ACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAATGCTGCGATGA 449 chr3ptel1M 387987 ACA--------AATAAGTC---ACCCAC-CCTTT--TTATCTCTTGGTGA 388022 --------v i ---ii? -i i -- i i viv C L1ME4a_3end#L 448 ACATCCTTGTACATAAATCTTTGTNCACATCTCTGATTATTTCCTTAGGA 399 chr3ptel1M 388023 TATAGACCTAGTAGTAGTATTTCTGGATCAAAGGATATGCATAATTTTAT 388072 v vv v i v v i i ? i v - C L1ME4a_3end#L 398 TAAATTCCTAGAAGTGGAATTACTGGGTCAAAGGGTATGNACATTTTTA- 350 chr3ptel1M 388073 AATCCTTTGAGTACAT--TTCCATATGGTTCTCCAGAATGGTTGGATCAG 388120 iv i - -- v v v ii v v i i C L1ME4a_3end#L 349 AGGCTTTTGA-TACATATTGCCAAATTGCCCTCCAGAAAGGTTGTACCAA 301 chr3ptel1M 388121 TTCACAACTCCATCAACAATGCATTCATGTCCCAGTTCATGTCCTACATG 388170 i vii i i i i vviv v v i---i? i i- C L1ME4a_3end#L 300 TTTACACTCCCACCAGCAGTGTATGAGAGTGCCCGTTT---CNCCACAC- 255 chr3ptel1M 388171 CCT--CCAACATTTGTCCCTGTC---CTTTT---CCTATCAGCCAATCTG 388212 -- i v vivi i --- ---i v -- i C L1ME4a_3end#L 254 CCTCGCCAACACTGGGTATTATCAATCTTTTAAATCTTT--GCCAATTTG 207 chr3ptel1M 388213 ACAGGCACCTATGAGGTAGTACCTCAGAGTTGTTTTAATTTGCATTTTTC 388262 i ---- ivi ii i i vv i i C L1ME4a_3end#L 206 ATAGG----TGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCTT 161 chr3ptel1M 388263 TAACCAATGATCATCTAGAGCACTGTTTTATATGACTATAGATAGTTTTG 388312 i ii v ii v vv v i i?v i vi v iivi vv C L1ME4a_3end#L 160 TGATTACTAGTGAGGTTGAACATNTTTTCATATGTTTATTGGCCATTTGT 111 chr3ptel1M 388313 ATTTCTTTATTTGAAAATTGCTTGTTCATATCATTTGATTACTTATCAAT 388362 iv vi ii i v vii i v v C L1ME4a_3end#L 110 ATTTCTTCTTTTGTGAATTGTCTGTTCATGTCCTTTGCCCATTTTTCTAT 61 chr3ptel1M 388363 TAGGGAGT 388370 i v C L1ME4a_3end#L 60 TGGGGTGT 53 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 40.27 CpG sites = 105, Kimura (unadjusted) = 40.59 Transitions / transversions = 1.63 (85/52) Gap_init rate = 0.08 (36 / 472), avg. gap size = 1.69 (61 / 36) 614 31.56 7.44 2.94 chr3ptel1M 387910 388366 (611634) C L1ME3G_3end#LINE/L1 (395) 529 53 m_b119s551i1 4362 chr3ptel1M 387910 ATATATC-CAACTTATTCAGCCATTTCTCTAATTAATGAGCATCCCCTCA 387958 i -i i i i i i - i ii iivvviv C L1ME3G_3end#L 529 ATATACCATAATTTATTTAACCATTCCCCTA-TTGATGGACATTTAGGTT 481 chr3ptel1M 387959 ATTTCTAATTCTTTGCCACCACAAAAGA----ACAAATAA-------GT- 387996 i i i i i ii vi ----i vv ------- - C L1ME3G_3end#L 480 GTTTCCAATTTTTCGCTATTACAAACAATGCTGCAATGAACATCCTTGTA 431 chr3ptel1M 387997 CACCCACCCTTTT-------------TATCTCTTGGTGATATAGACCTAG 388033 iv ?i v ------------- i ?viv v v? ? C L1ME3G_3end#L 430 CATGCNTCCTTGTGCACATGTGCGAGTATTTCTNTAGGATAGATNCCNAG 381 chr3ptel1M 388034 TAGTAGTATTTCTGGATCAAAGGATATGCATAATTTTATAATCCTTTGAG 388083 v i v v i i ii - - --- v i C L1ME3G_3end#L 380 AAGTGGAATTGCTGGGTCAAAGGGTATGCGCA-TTTTA-AAT---TTTAA 336 chr3ptel1M 388084 TACAT--TTCCATATGGTTCTCCAGAATGGTTGGATCAGTTCACAACTCC 388131 v -- v v v ii i ? i v i i i vii C L1ME3G_3end#L 335 TAGATACTGCCAAATTGCCCTCCAAAANGGCTGTACCAATTTACACTCCC 286 chr3ptel1M 388132 ATCAACAATGCATTCATGTCCCAGTTCATGTCCTACATGCCTC--CAACA 388179 i i i i vviv v v i---i i i- -- C L1ME3G_3end#L 285 ACCAGCAGTGTATGAGAGTACCCGTTT---CCCCACAC-CCTCGCCAACA 240 chr3ptel1M 388180 TTTGTCCCTGTC---CTTTTCC-TATCAGCCAATCTGACAGGCACCTATG 388225 i ? vivi i --- vv- v iv ii ---- ivi C L1ME3G_3end#L 239 CTNGATATTATCAANCTTTTAAATTTTTGCCAATCTGATGGG----TGAA 194 chr3ptel1M 388226 AGGTAGTACCTCAGAGTTGTTTTAATTTGCATTTTTCTAACCAATGATCA 388275 ii i i vv ii i ii v ii v C L1ME3G_3end#L 193 AAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGATTACTAGTGA 144 chr3ptel1M 388276 TCTAGAGCACTGTTTTATATGACTATAGATAGTTTTGATTTCTTTATTTG 388325 vv v iiv i vi v iivi vv i iv i C L1ME3G_3end#L 143 GGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGTATTTCCTCTTCTG 94 chr3ptel1M 388326 AAAATTGCTTGTTCATATCATTTGATTACTTATCAATTAGG 388366 vi i v vii i v v i C L1ME3G_3end#L 93 TGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGGG 53 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 42.65 CpG sites = 86, Kimura (unadjusted) = 43.50 Transitions / transversions = 1.59 (86/54) Gap_init rate = 0.05 (23 / 456), avg. gap size = 2.09 (48 / 23) 807 28.34 3.64 5.11 chr3ptel1M 388011 388367 (611633) C L1ME5_3end#LINE/L1 (534) 407 56 m_b119s551i2 4362 chr3ptel1M 388011 ATCTCTTGGTGATATAGACCTAGTAGTAGTATTTCTGGATCAAAGGATAT 388060 i v v v i v ii v v i v i C L1ME5_3end#LI 407 ATTTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTAT 358 chr3ptel1M 388061 GCATA-ATTTTATAATCCTTTGAGTA--CATTTCCATATGGTTCTCCAGA 388107 i - i --- --- v --i i v v v i C L1ME5_3end#LI 357 GCGTATACTT---AAT---TTGACTAAGTACTGCCAGATTGCTCTCCAGA 314 chr3ptel1M 388108 ATGGTTGGATCAGTTCACAACTCCATCAACAATGCATTCATGTCCCAGTT 388157 i v i ii vii i i i vviv i ---- C L1ME5_3end#LI 313 ATGGCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCC---- 268 chr3ptel1M 388158 CATGTCCT-ACATGCCTC--CAACATTTGTCCCTGTCC-TTTTCCTA--- 388200 i ? i- - -- i v vi i -vi i --- C L1ME5_3end#LI 267 TATNTCCCCACAT-CCTCGCCAACACTTGGCATTATCCAGCTTTCTAATT 219 chr3ptel1M 388201 TCAGCCAATCTGACAGGCACCTATGAGGTAGTACCTCAGAGTTGTTTTAA 388250 iv i i i ---- i i i ii i vv C L1ME5_3end#LI 218 TTTGCCAGTCTAATAGG----TGTAAAGTGATATCTCATTGTTGTTTTAA 173 chr3ptel1M 388251 TTTGCATTTTTCTAACCAATGATCATCTAGAGCACTGTTTTATATGACTA 388300 i i ii v i v vi v iivi i vi i C L1ME5_3end#LI 172 TTTGCATTTCTCTGATTACTAATGAGTTTGAGCATCTCTTCATATGCTTG 123 chr3ptel1M 388301 TAGATAGTTTT---GATTTCTTTATTTGAAAATTGCTTGTTCATATCATT 388347 --- ii --- i i iv i v i v C L1ME5_3end#LI 122 T---TAGCCTTTCGGGTTTCCTCTTCTGTAAATTGCCTGTTCATATCCTT 76 chr3ptel1M 388348 TGATTACTTATCAATTAGGG 388367 vii i v v i C L1ME5_3end#LI 75 TGCCCATTTTTCTATTGGGG 56 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 36.08 CpG sites = 62, Kimura (unadjusted) = 37.12 Transitions / transversions = 1.82 (62/34) Gap_init rate = 0.07 (25 / 356), avg. gap size = 1.24 (31 / 25) 424 26.35 3.27 8.22 chr3ptel1M 388689 388841 (611159) MIRc#SINE/MIR 3 148 (120) m_b119s601i29 4364 chr3ptel1M 388689 AGGCAGCTAGGTGCCACAGTAGATAGCATGCTGCTCCTGGAGTCAGGAAG 388738 ivv --- i v viii vv i MIRc#SINE/MIR 3 AGGCAGTGTGGTGC---AGTGGAAAGAGCACTGGACTTGGAGTCAGGAAG 49 chr3ptel1M 388739 ACTCATTTTCCTGAGTTTAAATTTGGCCTCAGACAGTTACTTGCTGTGTG 388788 -------- i ii i iiv v v v v v MIRc#SINE/MIR 50 AC--------CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTG 91 chr3ptel1M 388789 GTCCTGACCAAGTCACTTCACACTGTTTGCAC--CAA-TCCCTCA--TGT 388833 ii i iv v - v i vi -- i- i -- MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAAC-CTCTCTGAGCCTCAGTTTCCTCATCTGT 140 chr3ptel1M 388834 AAAATGAG 388841 i MIRc#SINE/MIR 141 AAAATGGG 148 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 31.74 CpG sites = 21, Kimura (unadjusted) = 32.93 Transitions / transversions = 1.31 (21/16) Gap_init rate = 0.10 (15 / 152), avg. gap size = 1.13 (17 / 15) 216 30.73 9.43 1.75 chr3ptel1M 390244 390402 (609598) C L2#LINE/L2 (501) 2581 2411 m_b119s601i30 4365 chr3ptel1M 390244 AGTGAGAAGTCCAGGATGACATCTAGGTTGTGAGCCTGAGTGACAGCGAG 390293 v i v vi v v vi ii v vi C L2#LINE/L2 2581 AGAGAGGAGTCAAGGATGACTCCAAGGTTTTTGGCCTGAGCAACTGGAAG 2532 chr3ptel1M 390294 GATG----TACCAGTA------ATAGGGAAG--TTTGAAAGGGG-GGGGT 390330 ---- i v ?------ i -- vi ii i -i v C L2#LINE/L2 2531 GATGGAGTTGCCATTNACTGAGATGGGGAAGACTGCGGGAGGAGCAGGTT 2482 chr3ptel1M 390331 TGGGGGGAGCGGTGAAAGTGAGTTC--TGTTGGACACACTGAGTTTGAAA 390378 i iiv i v i--- -- v iii i i C L2#LINE/L2 2481 TGAGGGGGAAGATCAG---GAGTTCAGTTTTGGACATGTTAAGTTTGAGA 2435 chr3ptel1M 390379 GGGCGACGGAACAGCCAGGGGGGG 390402 v v v ivii v i v i C L2#LINE/L2 2434 TGCCTATTAGACATCCAAGTGGAG 2411 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 40.03 CpG sites = 28, Kimura (unadjusted) = 41.16 Transitions / transversions = 1.40 (28/20) Gap_init rate = 0.05 (8 / 158), avg. gap size = 2.25 (18 / 8) 17 11.59 0.00 0.00 chr3ptel1M 391448 391476 (608524) (TGAT)n#Simple_repeat 1 29 (0) m_b119s252i9 4366 chr3ptel1M 391448 TGGTTGATTGACTGACTGATTGATTGATT 391476 i i i (TGAT)n#Simpl 1 TGATTGATTGATTGATTGATTGATTGATT 29 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 234 27.31 1.45 4.48 chr3ptel1M 392874 392942 (607058) L2b_3end#LINE/L2 394 460 (6) m_b119s601i31 4367 chr3ptel1M 392874 CTGTATCTGCAGGGCTCAGCCCAGTGTCGGCCACACA-TAAATGCTGGAT 392922 iv v ii v ? i v v - iii vii L2b_3end#LINE 394 CTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGT 443 chr3ptel1M 392923 AAATAAGCTTTGCTAACTGA 392942 --- i i v L2b_3end#LINE 444 AAATA---TTTGTTGAATGA 460 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 33.17 CpG sites = 11, Kimura (unadjusted) = 35.61 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.06 (4 / 68), avg. gap size = 1.00 (4 / 4) 231 26.36 15.09 3.39 chr3ptel1M 393465 393570 (606430) MIR3#SINE/MIR 35 152 (56) m_b119s601i32 4368 chr3ptel1M 393465 GGGAAGCAGGAGAGTTGAGTGCTAATCCTGACT------CTAACTTTGTG 393508 iv vi i v i i i ------ ?vv MIR3#SINE/MIR 35 GGGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTG 84 chr3ptel1M 393509 TGTGTTCTTGGAATATTTATTTAAATTCT----------ATTTCTACACG 393548 vi ivv v i i v vi ----------i iv --- MIR3#SINE/MIR 85 TGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTC--- 131 chr3ptel1M 393549 ATCTGTATAAATGAAGAGGTTG 393570 - i i MIR3#SINE/MIR 132 ATCTGTA-AAATGAGGGGGTTG 152 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 32.16 CpG sites = 15, Kimura (unadjusted) = 33.66 Transitions / transversions = 1.25 (15/12) Gap_init rate = 0.06 (6 / 105), avg. gap size = 3.33 (20 / 6) 17 16.89 0.00 0.00 chr3ptel1M 394255 394288 (605712) (TCAT)n#Simple_repeat 1 34 (0) m_b119s252i10 4369 chr3ptel1M 394255 TCACTCATTCCCTCATTTGTTCATTCATTCATTC 394288 i vi ii (TCAT)n#Simpl 1 TCATTCATTCATTCATTCATTCATTCATTCATTC 34 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 80 26.56 2.17 0.86 chr3ptel1M 395124 395353 (604647) (TGGA)n#Simple_repeat 1 233 (0) m_b119s252i11 4370 chr3ptel1M 395124 TGGAGGGA--GATAGAAGGGATAGGTGGAAGGAAGAGTGGAGGGAAAGAA 395171 v -- i v - i i v v ii v - v i (TGGA)n#Simpl 1 TGGATGGATGGATGGATG-GATGGATGGATGGATGGATGGATGG-ATGGA 48 chr3ptel1M 395172 TGGATGGATGGATGGATGAATGAATGGGTGGGTGGATAAATGGAGAGACA 395221 i i i i ii vi ii (TGGA)n#Simpl 49 TGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATG 98 chr3ptel1M 395222 GATGGATGAGTGGATGGACAGAT-GATGGACAGAT-GATGGACAGATGGA 395269 ii ii - ii - ii (TGGA)n#Simpl 99 GATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGA 148 chr3ptel1M 395270 TGGACGGATGGATGAATGGGTGGGTGGATAAATGGACAGACAGATGGGTG 395319 i i i i ii ii ii i (TGGA)n#Simpl 149 TGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATG 198 chr3ptel1M 395320 AGTGGATGGATGGACAGAT-GATAGACAGATGGAT 395353 ii ii - i ii (TGGA)n#Simpl 199 GATGGATGGATGGATGGATGGATGGATGGATGGAT 233 Matrix = Unknown Transitions / transversions = 5.86 (41/7) Gap_init rate = 0.03 (6 / 229), avg. gap size = 1.17 (7 / 6) 12 19.97 2.27 4.65 chr3ptel1M 396814 396857 (603143) (GAGAAA)n#Simple_repeat 1 43 (0) m_b119s252i12 4371 chr3ptel1M 396814 GAAAAGGGGAAAGGAGAGAAGAGAAAG-GAAAAAGTTAGAGACAG 396857 i i i - - - i vv v (GAGAAA)n#Sim 1 GAGAAAGAGAAA-GAGA-AAGAGAAAGAGAAAGAGAAAGAGAAAG 43 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.07 (3 / 43), avg. gap size = 1.00 (3 / 3) 298 24.72 1.30 5.41 chr3ptel1M 397567 397643 (602357) MIRc#SINE/MIR 120 193 (75) m_b119s601i33 4372 chr3ptel1M 397567 AACCTCAGTTTCCTCATCTGTAAAATAGAAGCACTGAAAAAGGCTTGAAC 397616 i i iiii v ---- vi i vv MIRc#SINE/MIR 120 AGCCTCAGTTTCCTCATCTGTAAAATGGGGATAAT----AATACCTGCCC 165 chr3ptel1M 397617 TCCTAATCTCATA-GGTGGTTGTGAGGA 397643 v iv i i - v MIRc#SINE/MIR 166 TGCCTACCTCACAGGGTTGTTGTGAGGA 193 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.64 CpG sites = 11, Kimura (unadjusted) = 30.64 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.07 (5 / 76), avg. gap size = 1.00 (5 / 5) 327 27.80 6.19 7.29 chr3ptel1M 398345 398441 (601559) L2c_3end#LINE/L2 364 459 (19) m_b119s601i34 4373 chr3ptel1M 398345 CTCCTCCATT------TGAGTTCCTCAAGGGCAGAGATTGCCTGTTGCCT 398388 i ------ i ii i ii iv v iiii L2c_3end#LINE 364 CTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTC 413 chr3ptel1M 398389 TTCTTTGTATGCTCAGCACTTAGTTTGTGACACATAGAAAGTACTTAATA 398438 v v i i i------- i v i ii i L2c_3end#LINE 414 ATCTTTGTATCCCCAGCGCC-------TGGCACATAGTAGGCGCTCAATA 456 chr3ptel1M 398439 AAT 398441 L2c_3end#LINE 457 AAT 459 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 31.74 CpG sites = 20, Kimura (unadjusted) = 37.60 Transitions / transversions = 4.00 (20/5) Gap_init rate = 0.08 (8 / 96), avg. gap size = 1.62 (13 / 8) 194 34.10 1.11 2.25 chr3ptel1M 398419 398508 (601492) C MIRb#SINE/MIR (174) 94 6 m_b119s601i35 4374 chr3ptel1M 398419 CACATAGAAAGTACTTAATAAATCTGAACTCTGGAGG-AGATCTTACTGA 398467 i vv vv iii i v i iiv ii i vv- i vv C MIRb#SINE/MIR 94 CACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGA 45 chr3ptel1M 398468 CTCCAGATCTGGCACTCTATCCACATGTCACCAAGCTGCCC 398508 i v iv ii v - - v C MIRb#SINE/MIR 44 CTCCAAAGCCCGTGCTCTTTCCAC-TG-CACCACGCTGCCC 6 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 42.45 CpG sites = 16, Kimura (unadjusted) = 46.56 Transitions / transversions = 1.14 (16/14) Gap_init rate = 0.03 (3 / 89), avg. gap size = 1.00 (3 / 3) 204 22.03 0.00 4.00 chr3ptel1M 398456 398507 (601493) C MIRc#SINE/MIR (215) 53 4 m_b119s601i36 4374 chr3ptel1M 398456 AGATCTTACTGACTCCAGATCTGGCACTCTATCCACATGTCACCAAGCTG 398505 i v ii ii ii v - - vi C MIRc#SINE/MIR 53 AGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCAC-TG-CACCACACTG 6 chr3ptel1M 398506 CC 398507 C MIRc#SINE/MIR 5 CC 4 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 27.10 CpG sites = 8, Kimura (unadjusted) = 27.10 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.00 (2 / 2) 547 29.33 11.61 2.81 chr3ptel1M 398963 399453 (600547) C L1ME4b_3end#LINE/L1 (359) 533 1 m_b119s551i3 4375 chr3ptel1M 398963 ATATACCACAGCTTATTCAGCCATTTCCTAATTGAAGGGCATCCCTCAA- 399011 i i ii i i v i iv v i --- i i- C L1ME4b_3end#L 533 ATGTACCATAATTTATTTAACCAGTCCCCTATTGATGGACAT---TTAGG 487 chr3ptel1M 399012 ---TTTCCAGTTCTTTGCCACCACAAAAAGAGCTACCATAAACATTTCCC 399058 --- i ii i ii v iv i v i i ---v C L1ME4b_3end#L 486 TTGTTTCCAATCTTTTGCTATTACAAACAATGCTGCAATGAATA---ACC 440 chr3ptel1M 399059 TT----ATAGGTCGTTTTTCTTTTTCTTTGA-TATAT----GGAATACAG 399099 ---- v i iv viv v- vi - ----i i v v C L1ME4b_3end#L 439 TTGTACATACGTCATTTCGCACATG-TGCGAGTATATCTGTAGGATAAAT 391 chr3ptel1M 399100 ACCTAGTAGAGGTGTTGCTGGACTCAAGGGTA----CAGTTGTATAATCC 399145 v v v vi iiiv ---- v -- -- C L1ME4b_3end#L 390 TCCTAGAAGTGGAATTGCTGGGTCAAAGGGTATGTGCATTTGTA--AT-- 345 chr3ptel1M 399146 TTTGG-GGATAGTTTCAAATTGATCTCTAGAAATGTTGGATCAATTCATA 399194 i-i v vi vi i v i v v i i i C L1ME4b_3end#L 344 TTTGATAGATATTGCCAAATTGCCCTCCATAGAGGTTGTACCAATTTACA 295 chr3ptel1M 399195 GATCCAG-AACAATGTATTAGTATCCCTATTTTCCTTATCCCCCTCCA-- 399241 vvi v- i v vi v i i ivvv i v -- C L1ME4b_3end#L 294 CTCCCACCAGCAATGTATGAGAGTGCCTGTTTCCCCACACCCTCGCCAAC 245 chr3ptel1M 399242 -----------------TCTTTGGTCATT-----TTTGGTAGGTGTGAAG 399269 ----------------- i i v ----- i i vi i C L1ME4b_3end#L 244 ACAGTGTGTTATCAAACTTTTTGATCTTTGCCAATCTGATAGGTGAAAAA 195 chr3ptel1M 399270 TGGTACCTCAGAGTTGTTTTAATTTGCATTT-TC-AACCAATAGTGATAT 399317 i v v - -v ii vv vi C L1ME4b_3end#L 194 TGGTATCTCAGTGTAGTTTTAATTTGCATTTCTCTTATTATGAGTGAGGT 145 chr3ptel1M 399318 ATAGAA---TTTTATATTATTATAGGAATATTT-CATTTC---TTCTGGA 399360 vv v --- i vv - iivi -i --- vi C L1ME4b_3end#L 144 TGAGCATCTTTTCATATGTTTA-AGAGCCATTTGTATTTCCTTTTCTGTG 96 chr3ptel1M 399361 AACTATATGTTCGTATCCTTTTATCATTTGTCAATAAAGGAATGGCTTTT 399410 i v i vvi v v vii vvi v v i C L1ME4b_3end#L 95 AACTGTCTGTTCATATCCTTTGCCCATTTTTCTATTGGGTTGTTGGTCTT 46 chr3ptel1M 399411 ATTTTTAGAAATTTG-----GCTCTTCCCTATATATTTGAGAAATGAG 399453 v i vvi ----- --- v i v C L1ME4b_3end#L 45 TTTCTTATTGATTTGTAGGAGCTCTT---TATATATTAGGGAAATTAG 1 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 37.25 CpG sites = 73, Kimura (unadjusted) = 37.93 Transitions / transversions = 1.09 (73/67) Gap_init rate = 0.07 (32 / 490), avg. gap size = 2.25 (72 / 32) 12 12.03 3.70 0.00 chr3ptel1M 400126 400152 (599848) (GTTT)n#Simple_repeat 1 28 (0) m_b119s252i13 4376 chr3ptel1M 400126 GTTTTTTTGTTTG-TTATTTGTTTTTTT 400152 v - i v (GTTT)n#Simpl 1 GTTTGTTTGTTTGTTTGTTTGTTTGTTT 28 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.04 (1 / 26), avg. gap size = 1.00 (1 / 1) 1525 29.37 2.82 2.50 chr3ptel1M 400557 401195 (598805) C L1ME5_3end#LINE/L1 (297) 644 4 m_b119s551i4 4377 chr3ptel1M 400557 TCCTGGTTCT-GCTCATTTCACTCAGCATCA-GTTCATGTAAG-TCTCTC 400603 i v -i iv ii - -- v - iv C L1ME5_3end#LI 644 TTCTGTTTCTTACTTTTTTCACTCAGCACTATGTT--TTTAAGATCCATC 597 chr3ptel1M 400604 CAGGCCTCTCTGTATTCATCCTGCTGGTCATTTCTTACAGAACAATAATA 400653 v iiv v i v iv iiv iii v v vvvv i C L1ME5_3end#LI 596 CATGTTGCTATGTGTACATCTAGTCCGTTGCTTCTAACTGCTGCATAGTA 547 chr3ptel1M 400654 TTCTATAACATTCATATATCACAATTTACCCAACCATTCTCCAATTGATG 400703 i i iiii v vi i v i v i v v C L1ME5_3end#LI 546 CTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCAGTGATG 497 chr3ptel1M 400704 GGCATCCATTCATT--TTCCAGCTTCTGGCCACTACAAAAAGGGCTGCCA 400751 i i v--i --i i i iv i v iv v C L1ME5_3end#LI 496 GACACCCAG--GTTGCCTCCAACTCCCCGCCACCACAAACAACGCTGCAA 449 chr3ptel1M 400752 CAAACATTTTGGCACAGACTGGCCCCTTTC---CCTTCTTTAGTATCTCC 400798 ii ii v i --- v vi--- viv v v i i C L1ME5_3end#LI 448 TGAACATCCTCGTACA---TGTCCCCTTATGGACCTGTGTGAGAATTTCT 402 chr3ptel1M 400799 TTGGGGTATAAATCCAGTAGAAGCACTGCTGGGTCAAAGGGTATGCACAG 400848 i v i v vi v i v ii v C L1ME5_3end#LI 401 TTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATGCGTAT 352 chr3ptel1M 400849 TTTGATAACTTT-TTGGGCATCGTTCCAAATTCCTCTCCAGAATGGTTGG 400897 vi -- i v-i ii i ii -- i v i v C L1ME5_3end#LI 351 ACT--TAATTTGACTAAGTACTG--CCAGATTGCTCTCCAGAATGGCTGC 306 chr3ptel1M 400898 ATGTATTCACGATTCCACCAACAATGCATCAGTGTCCCTGTTTTCCTGCA 400947 ivvi ii iv i i i v v i i ? i ii C L1ME5_3end#LI 305 ACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATNTCCCCACA 256 chr3ptel1M 400948 TCCCCTCCAACATTCTGCATTATCTTTCCCTGTCATCCTAGACGATCTGA 400997 i v i iv ivv ii v v ii v v ii i C L1ME5_3end#LI 255 TCCTCGCCAACACTTGGCATTATCCAGCTTTCTAATTTTTGCCAGTCTAA 206 chr3ptel1M 400998 CAGGTGTGTAGTGGTATCTCAGAGTTGTCTTAATTTGCATTTCTCTGATT 401047 i iv i vv i C L1ME5_3end#LI 205 TAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATTTCTCTGATT 156 chr3ptel1M 401048 AATAATGATTTGGAGCATATTTTCATATGACTAGAAATAG--TTTC-AAT 401094 v v v v i - v --v -- -ii C L1ME5_3end#LI 155 ACTAATGAGTTTGAGCATCTCTTCATATG-CTTG--TTAGCCTTTCGGGT 109 chr3ptel1M 401095 TTC----TTTGAGAATTGTCTGTTCATATCCTTTGACCATTTATCAATTG 401140 ---- i vi i v v v C L1ME5_3end#LI 108 TTCCTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTG 59 chr3ptel1M 401141 GAG--AATGGCTTGATTTCTTATAAATTAGAGTCAATTCTCTATATATTT 401188 i --?vi v -- i vi v vivv i ii i i C L1ME5_3end#LI 58 GGGTTNCCGTCTT--TTTCTTGTTGATTTGCAGGAGTTCCTTGTATATTC 11 chr3ptel1M 401189 TGGAAAT 401195 i v C L1ME5_3end#LI 10 TAGATAT 4 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 37.59 CpG sites = 105, Kimura (unadjusted) = 38.39 Transitions / transversions = 1.35 (105/78) Gap_init rate = 0.04 (26 / 638), avg. gap size = 1.31 (34 / 26) 573 27.76 4.97 4.03 chr3ptel1M 401053 401495 (598505) C L1M5_orf2#LINE/L1 (0) 3294 2848 m_b119s551i5 4377 chr3ptel1M 401053 TGATTTGGAGCATATTTTCATATGACTAGAAATAGTTTCAAT---TTCTT 401099 ?v v v i vi vviiivi v? --- C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr3ptel1M 401100 T-GAGAATTGTCTGTTCATATCCTTTGACCATTTATCAATTGGA--GAAT 401146 - v v vi i v v ?v i-- vv C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTT 3195 chr3ptel1M 401147 GGCTTGATTTCTTA-TAAATTAGAGTCAATTCTCTATATATTTTGGAAAT 401195 v -- ? - i ? iv -v i i i v i C L1M5_orf2#LIN 3194 GTCTT--TTTNTTATTGANTTGTAG-GAGTTCTTTATATATTCTGGATAC 3148 chr3ptel1M 401196 GAGGCCTTTATCAGA-ACCTTTGATTGTAAAAATGTTTTCCCAGTTTATT 401244 v i - iv v -? i v v i ? i i v C L1M5_orf2#LIN 3147 GAGTCCTTTGTCAGATATATGT-NTTGCAAATATTTTCTCCCANTCTGTG 3099 chr3ptel1M 401245 GCTTCCCTTCTAATCTTGTCTGCATTAGTTTTGTTG--GTACAAAAACTT 401292 v i v i v ivi iv - i - -- vi i ii C L1M5_orf2#LIN 3098 GCTTGCCTTTTCATTTTCTTAACGGT-GTCTT-TTGANGAGCAGAAGTTT 3051 chr3ptel1M 401293 TTCAATTTGATATAATCAA-------AATTTTCTATTTTGTAGTCAATAG 401335 v v i? i v ------- i v i i --- ? C L1M5_orf2#LIN 3050 TTAATTTTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGGT---TNG 3004 chr3ptel1M 401336 TGGTCTCTAGTTCTTCTTTGGTCATAAATCCCTTCCTCTTCCACAGGTCT 401385 v i i ivv i v i--- v ii v v?i - v C L1M5_orf2#LIN 3003 TGCTTTTTGTGTCCTGTTTA---AGAAATCTTTGCCTANCCCA-AGGTCA 2958 chr3ptel1M 401386 GAGAGGTAAACTATCCTATG--CTCTTCC--AATTTATTTATAATCTCAT 401431 vii i -- i v --i i-- v -- i i i ? C L1M5_orf2#LIN 2957 CGAAGAT--ATTCTCCTATGTTTTCTTCTAGAAGT--TTTATAGTTTTAN 2912 chr3ptel1M 401432 TCTTTATGCCTAGGTC-ATGAACCCATTTTGACCTTATCTTGGTATATGG 401480 ii iiii - - i i ? vi v i v i C L1M5_orf2#LIN 2911 CTTTTACATTTAGGTCTATG-ATCCATCTNGAATTAATTTTTGTGTATGG 2863 chr3ptel1M 401481 TGTTAAGTGTGGGTC 401495 v i iv C L1M5_orf2#LIN 2862 TGTGAGGTAGGGGTC 2848 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 35.57 CpG sites = 66, Kimura (unadjusted) = 36.74 Transitions / transversions = 1.27 (66/52) Gap_init rate = 0.06 (28 / 442), avg. gap size = 1.43 (40 / 28) 35 23.27 0.00 0.00 chr3ptel1M 402140 402224 (597776) (TGTGTG)n#Simple_repeat 1 85 (0) m_b119s252i14 4378 chr3ptel1M 402140 TGTGTGTGTATGTGTGTGTGGTTGTATTTGTGTGCGTGTGAGCTTGTGTG 402189 i vv i v i v iv (TGTGTG)n#Sim 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr3ptel1M 402190 TGAGTGAGATTGTGAGTGTGTGTGGTTGTGTATGT 402224 v v vv v vv i (TGTGTG)n#Sim 51 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 85 Matrix = Unknown Transitions / transversions = 0.42 (5/12) Gap_init rate = 0.00 (0 / 84), avg. gap size = 0.0 (0 / 0) 269 22.39 5.63 5.63 chr3ptel1M 402707 402777 (597223) C L2c_3end#LINE/L2 (12) 466 396 m_b119s601i37 4379 chr3ptel1M 402707 AACCAGCCTTTATTAAGCACCTACTATATGCCAGGCCCTGCCTTGAGAT- 402755 v i v i i i v ---- i - C L2c_3end#LINE 466 AACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTG----GGGATA 421 chr3ptel1M 402756 TGAGGATA---CAGATACAGTCCCT 402777 ii i i---v i i C L2c_3end#LINE 420 CAAAGATGAATAAGACACGGTCCCT 396 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 23.53 CpG sites = 11, Kimura (unadjusted) = 27.73 Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.09 (6 / 70), avg. gap size = 1.33 (8 / 6) 287 23.08 1.92 0.00 chr3ptel1M 402715 402766 (597234) C L2a_3end#LINE/L2 (20) 497 445 m_b119s601i38 4379 chr3ptel1M 402715 TTTATTAAGCACCTACTATATGCCAGGCCCTGCCTTGAG-ATTGAGGATA 402763 i i i v iii ii -ii i C L2a_3end#LINE 497 TTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGCGCTGGGGATA 448 chr3ptel1M 402764 CAG 402766 C L2a_3end#LINE 447 CAG 445 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 24.33 CpG sites = 11, Kimura (unadjusted) = 30.18 Transitions / transversions = 11.00 (11/1) Gap_init rate = 0.02 (1 / 51), avg. gap size = 1.00 (1 / 1) 198 32.00 0.00 0.00 chr3ptel1M 402777 402826 (597174) C L2d2_3end#LINE/L2 (10) 545 496 m_b119s601i39 4380 chr3ptel1M 402777 TCAACAAACAACCATTATGCACCCACTGCATGGGGGGCACTATGTTGGGC 402826 i vii iv i i ii vii i i i C L2d2_3end#LIN 545 TCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGC 496 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 42.46 CpG sites = 13, Kimura (unadjusted) = 46.57 Transitions / transversions = 4.33 (13/3) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 318 19.61 0.00 0.00 chr3ptel1M 404088 404138 (595862) C L2d2_3end#LINE/L2 (9) 546 496 m_b119s601i40 4381 chr3ptel1M 404088 ATCAGTAAACATTCATTAGGTGCCTACTGTGTGCCAGGCACTGTGCCAAG 404137 ii i i ii i v i i C L2d2_3end#LIN 546 ATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGG 497 chr3ptel1M 404138 C 404138 C L2d2_3end#LIN 496 C 496 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 21.57 CpG sites = 9, Kimura (unadjusted) = 24.30 Transitions / transversions = 9.00 (9/1) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 317 21.43 0.00 0.00 chr3ptel1M 404089 404144 (595856) C L2b_3end#LINE/L2 (10) 456 401 m_b119s601i41 4381 chr3ptel1M 404089 TCAGTAAACATTCATTAGGTGCCTACTGTGTGCCAGGCACTGTGCCAAGC 404138 ii i i i ii i ? i i C L2b_3end#LINE 456 TCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGC 407 chr3ptel1M 404139 CCCGGG 404144 v i C L2b_3end#LINE 406 GCTGGG 401 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 25.27 CpG sites = 11, Kimura (unadjusted) = 28.01 Transitions / transversions = 11.00 (11/1) Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0) 277 19.68 4.59 1.49 chr3ptel1M 405968 406163 (593837) C HERVIP10FH#LTR/ERV1 (4122) 980 779 m_b119s701i0 4382 chr3ptel1M 405968 TCTCTCTCTGTCTCTCTGCCTCTGTCTTTCTGTCTGTCTCTGTCTCTGTC 406017 i v i i v i v v iv i C HERVIP10FH#LT 980 TCTCTCTTTGACTTTCTGTCTCTCTCTCTCTCTCTGACTCCCTCTTTGTC 931 chr3ptel1M 406018 TCTCTGTCTCT--CTCTCTTTGTCTCTGTCTGTCTCTCTGTCTCTGTCTC 406065 -- i i v -- i v iv i C HERVIP10FH#LT 930 TCTCTGTCTCTTCCTCTCTCTGCCTCTCTCT--CTCTTTGACTCCCTCTT 883 chr3ptel1M 406066 TGTCTCTCTCTGTCTCTCTCTCTCTCTCTCTTTTTCTGTCTCTGTCTCTC 406115 v i i i i v vi C HERVIP10FH#LT 882 TGTCTCTCTCTCTCCCTCTCTCTCTCTTTCTCTCTCTCTCTCTTCCTCTC 833 chr3ptel1M 406116 TGTCTCTGTCTCT-GTCGCTGTTGCTGTCTC------TCTCTCTCTGATT 406158 v v -v v v v i- ------ i i vi C HERVIP10FH#LT 832 TCTCTCTCTCTCTCTTCTCTCTTTCC-TCTCTGCTGGTCTTTCCCTGCCT 784 chr3ptel1M 406159 CTGCC 406163 C HERVIP10FH#LT 783 CTGCC 779 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 23.03 CpG sites = 20, Kimura (unadjusted) = 23.03 Transitions / transversions = 1.11 (20/18) Gap_init rate = 0.03 (6 / 195), avg. gap size = 2.00 (12 / 6) 242 28.05 2.44 0.00 chr3ptel1M 407295 407376 (592624) L1P3_orf2#LINE/L1 1768 1851 (1443) m_b119s551i6 4383 chr3ptel1M 407295 AATAATAAAAGCTACAGGATTAG-TCAATAGATACTAATAAGGTTTTTGA 407343 i i i i v v- i vi v ii i L1P3_orf2#LIN 1768 AATGACAAAAACCACATGATTATCTCAATAGATGCAGAAAAGGCCTTCGA 1817 chr3ptel1M 407344 C-AACTCCAACACTCATTTCTGTTTAAAAGTCTC 407376 i- v i i v iv i v v L1P3_orf2#LIN 1818 TAAAATTCAACACCCCTTCATGCTAAAAACTCTC 1851 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 34.24 CpG sites = 14, Kimura (unadjusted) = 36.20 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.02 (2 / 81), avg. gap size = 1.00 (2 / 2) 259 32.37 2.82 3.18 chr3ptel1M 407626 407909 (592091) L1M5_orf2#LINE/L1 2186 2468 (826) m_b120s551i1 4384 chr3ptel1M 407626 CAAAATATAAGATAGATATACATAA-TTGATTAGTATTTTTATATATAAA 407674 ?ii i i vi v - ii - i iv i L1M5_orf2#LIN 2186 CNGGATACAAGGTCAATATACAAAAATCAATT-GTATTTCTATATACTAG 2234 chr3ptel1M 407675 CAGCAAAGTCCAACAAGAAGAGCTACAA----AAAAAGAACTGCATTCAA 407720 i --- ivi i -- iv ---- v ivv i v L1M5_orf2#LIN 2235 CAACAAA---CAATTGGAAAA--TGAAATTTNAAAAACAATACCATTTAC 2279 chr3ptel1M 407721 AATAGCCACAGCAGCTTTAAAATATATAGAAGTGCATCTACCGAGATGTA 407770 vv iv iviv ? iv i i iv v i i ?i i L1M5_orf2#LIN 2280 AATAGCATCAAAAAACATNAAATACTTAGGAATAAATCTAACAAAANATG 2329 chr3ptel1M 407771 TCCAGGGACTATA---TGAATCTAATTATAAAATACTCTTTGCAGAAATA 407817 v i iv ? --- --- i i i i vi viv v L1M5_orf2#LIN 2330 TGCAAGACCTNTACACTGAA---AACTACAAAACATTGCTGAGAGAAATT 2376 chr3ptel1M 407818 AAAATAGATCTAAATAATTGGAAAAAAATGAATTGTTCGTGGTTAGGTCA 407867 iv i v i i v ivvv i v v vvi L1M5_orf2#LIN 2377 AAAGAAGACCTAAATAAATGGAGAGATATACCATGTTCATGGATTGGAAG 2426 chr3ptel1M 407868 AGTCAATATAACAAAAATGTTAATACTACTTAAATGAATTTA 407909 v vii? i i v v ii vi i L1M5_orf2#LIN 2427 ACTCAATATTGTNAAGATGTCAATTCTCCCCAAATTGATCTA 2468 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 44.81 CpG sites = 51, Kimura (unadjusted) = 44.81 Transitions / transversions = 1.34 (51/38) Gap_init rate = 0.04 (12 / 283), avg. gap size = 1.42 (17 / 12) 211 14.96 1.67 10.91 chr3ptel1M 407928 407987 (592013) MIRc#SINE/MIR 2 56 (212) m_b120s601i0 4385 chr3ptel1M 407928 GAGGCAGCTAGCTGGTG-ACTATATAGAGCACTAGATCTCCTGGAGTCAG 407976 - i-- - v iv v i --- i MIRc#SINE/MIR 2 GAGGCAG-TG--TGGTGCAGTGGAAAGAGCACTGGA---CTTGGAGTCAG 45 chr3ptel1M 407977 GAAGACCTGAG 407987 i MIRc#SINE/MIR 46 GAAGACCTGGG 56 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 16.72 CpG sites = 5, Kimura (unadjusted) = 16.72 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.12 (7 / 59), avg. gap size = 1.00 (7 / 7) 484 26.50 2.99 0.58 chr3ptel1M 408001 408167 (591833) L1ME5_3end#LINE/L1 120 290 (651) m_b120s551i2 4384 chr3ptel1M 408001 TAGCAATCATATGAAAA--TGCTCTAAGTCGCCAACAATTAAAGAAAGAC 408048 i v i -- v v iii ii i i vi L1ME5_3end#LI 120 TAACAAGCATATGAAGAGATGCTCAAACTCATTAGTAATCAGAGAAATGC 169 chr3ptel1M 408049 AAATTAAAACAACTAT-ACATTTCCCTCTCCTACCTAGCAGATTAACAAA 408097 v - v v v i v - vi i ii L1ME5_3end#LI 170 AAATTAAAACAACAATGAGATATCACTTTAC-ACCTATTAGACTGGCAAA 218 chr3ptel1M 408098 AATGACAAAAGAGAAAAATGGCTAGTGTTGGAGAGGCTATGGGTAAAT-- 408145 v v ivv i v v v v v i v ? -- L1ME5_3end#LI 219 AATTAGAAAGCTGGATAATGCCAAGTGTTGGCGAGGATGTGGGGANATAG 268 chr3ptel1M 408146 GGACACTGGTGCCCTGTTGGTG 408167 i v vi v i L1ME5_3end#LI 269 GAACCCTCATGCACTGCTGGTG 290 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 33.21 CpG sites = 21, Kimura (unadjusted) = 33.21 Transitions / transversions = 0.91 (21/23) Gap_init rate = 0.02 (4 / 166), avg. gap size = 1.50 (6 / 4) 415 28.58 16.24 0.83 chr3ptel1M 408005 408318 (591682) L1ME4a_3end#LINE/L1 124 485 (386) m_b120s551i3 4384 chr3ptel1M 408005 AATCATATGAAAA--TGCTCTAAGTCGCCAACAATTAAAGAAAGACAAAT 408052 v -- i v vv i i ii i vi L1ME4a_3end#L 124 AAACATATGAAAANATGTTCAACCTCACTAGTAATCAAAGAAATGCAAAT 173 chr3ptel1M 408053 TAAAACAACTATACATTTCCCTCTCCTACCTAGCAGATTAACAAAAATGA 408102 v iviv v v i iii v i ii i v- L1ME4a_3end#L 174 TAAAACAACAATGAGATACCATTTTTCACCTATCAAATTGGCAAAGATT- 222 chr3ptel1M 408103 CAAAAGA-GAAAAATGGCTAGTGTTGGAGAGGCTATGGGTAAATGGACA- 408150 i -vi v iv i v v i ?v i i - L1ME4a_3end#L 223 TAAAAGATTGATAATACCCAGTGTTGGCGAGGGTGTGGNGAAACGGGCAC 272 chr3ptel1M 408151 -CTGGTGCCCTGTTGGTG-----------------AAGC--TCTG----- 408175 - vi i v i ----------------- v -- ----- L1ME4a_3end#L 273 TCTCATACACTGCTGGTGGGAGTGTAAATTGGTACAACCTTTCTGGAGGG 322 chr3ptel1M 408176 --ATCTGA-AATATGTCCAGAAAGTTGCCAAAGTATGCATGCCCTCCAAC 408222 -- i i- vivi iiviv i i ? i iii L1ME4a_3end#L 323 CAATTTGGCAATATGTATCAAAAGCCTTAAAAATGTNCATACCCTTTGAC 372 chr3ptel1M 408223 CCCG---TTACA-TTTTAGGCCTTTATCCCCAAAGAAATTGTTTTGAAAA 408268 v --- v - i vv - i i - iv iv i v L1ME4a_3end#L 373 CCAGTAATTCCACTTCTAGGAATTTAT-CCTAAGGAAA-TAATCAGAGAT 420 chr3ptel1M 408269 G-GAAAAGAGA-CAATGTATAAGAATATT-------------TCTATGAT 408303 - ? v i -iv i i i ------------- i i L1ME4a_3end#L 421 GTGNACAAAGATTTATGTACAAGGATGTTCATCGCAGCATTATTTATAAT 470 chr3ptel1M 408304 AGCCAAAAATTTGAA 408318 v v L1ME4a_3end#L 471 AGCGAAAAATTGGAA 485 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 37.02 CpG sites = 53, Kimura (unadjusted) = 37.56 Transitions / transversions = 1.47 (53/36) Gap_init rate = 0.05 (16 / 313), avg. gap size = 3.38 (54 / 16) 410 26.32 14.91 0.00 chr3ptel1M 408433 408546 (591454) C L2d2_3end#LINE/L2 (0) 555 425 m_b120s601i1 4386 chr3ptel1M 408433 TCAAA-CAAAT-AATAAGCATTT-TTAAGTGCTTACCATGTGCCACGCAC 408479 - - i ii - i i i ii v v C L2d2_3end#LIN 555 TCAAATCAAATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCAC 506 chr3ptel1M 408480 TATACTAAATGCTG------------AGAGGTATAAGCTA--ATCCTTGT 408515 i i iii ------------ i vi --i i i C L2d2_3end#LIN 505 TGTGCTAGGCGCTGTGGGGGATACAAAGAAGTATAAGACATGGTCCCTGC 456 chr3ptel1M 408516 TCTCAAGGAGTTCCCAGTTCAGTTGGAGGGA 408546 i i iv i ii i i C L2d2_3end#LIN 455 CCTCAAGGAGCTTACAATCTAGTTGGGGAGA 425 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 32.60 CpG sites = 26, Kimura (unadjusted) = 35.61 Transitions / transversions = 6.50 (26/4) Gap_init rate = 0.04 (5 / 113), avg. gap size = 3.40 (17 / 5) 347 29.87 2.86 4.35 chr3ptel1M 408443 408582 (591418) C L2c_3end#LINE/L2 (12) 466 329 m_b120s601i2 4386 chr3ptel1M 408443 AATAAGCATTT-TTAAGTGCTTACCATGTGCCACGCACTATACTAAATGC 408491 i i - i i i i v i ivi---i i C L2c_3end#LINE 466 AACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGG---GATAC 420 chr3ptel1M 408492 TGAGAGGTATAAGCTA--ATCCTTGTTCTCAAGGAGTTCCCAGTTCAGTT 408539 vi v v vi --i i ii i v ii - C L2c_3end#LINE 419 AAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAG-T 371 chr3ptel1M 408540 GGAGGGAAATGGGTACGGACAACATGTATATAAAA-ACAAGATA 408582 - i ii ii ? v - vii vv v - v C L2c_3end#LINE 370 GGA-GGAGACAGACANGTA-AACAGACAATTACAATACAAGTTA 329 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 37.82 CpG sites = 27, Kimura (unadjusted) = 40.47 Transitions / transversions = 2.08 (27/13) Gap_init rate = 0.06 (9 / 139), avg. gap size = 1.11 (10 / 9) 12 8.44 0.00 7.41 chr3ptel1M 409872 409900 (590100) (GGGGA)n#Simple_repeat 1 27 (0) m_b120s252i0 4387 chr3ptel1M 409872 GGGTAGGGGAACAGGGAGGGGAGGGGAGG 409900 v - -i (GGGGA)n#Simp 1 GGGGAGGGG-A-GGGGAGGGGAGGGGAGG 27 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.07 (2 / 28), avg. gap size = 1.00 (2 / 2) 258 26.61 9.77 4.95 chr3ptel1M 410206 410379 (589621) L1MC3_3end#LINE/L1 452 633 (1899) m_b120s551i5 4384 chr3ptel1M 410206 CAGCCCTCTTTGTAGTGGCTAGAAACTGGAAACTGAAT--GGATGCCCAT 410253 ii v ii i v i i i -- i--i i v L1MC3_3end#LI 452 CAGCTTTATTCATAATCGCCAAAAACTGGAAGC--AACCAAGATGTCCTT 499 chr3ptel1M 410254 CAGTTGGAGAAT--------AAATTGTGGTATATGAATATTATGGAATAT 410295 i v v -------- i i vv iv L1MC3_3end#LI 500 CAATAGGTGAATGGATAAACAAACTGTGGTACATCCATACAATGGAATAT 549 chr3ptel1M 410296 TATTGTTCTGT---AAGAAATGA-CCAACAGG--ATGATTTCAGAAAGGC 410339 vvv vi --- - i v i -- i ------ i L1MC3_3end#LI 550 TATTCAGCGATAAAAAGAAATGAGCTATCAAGCCACGA------AAAGAC 593 chr3ptel1M 410340 CTGGA-GAGGCTTACACGAACTGATGCTGAGTGAAATGAGC 410379 v - iv v i v - iv i vi L1MC3_3end#LI 594 ATGGATGAATCTTAAATGCA-TATTGCTAAGTGAAAGAAGC 633 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 32.70 CpG sites = 25, Kimura (unadjusted) = 33.62 Transitions / transversions = 1.32 (25/19) Gap_init rate = 0.09 (15 / 173), avg. gap size = 1.73 (26 / 15) 323 21.51 8.60 0.00 chr3ptel1M 410206 410298 (589702) L1ME3A_3end#LINE/L1 452 552 (368) m_b120s551i4 4384 chr3ptel1M 410206 CAGCCCTCTTTGTAGTGGCTAGAAACTGGAAACTGAATGGATGCCCAT-- 410253 v v i i i i?? ?ivviii i -- L1ME3A_3end#L 452 CAGCACTATTCGTAATAGCCNNAAACTGGAAACNACCCAAATGTCCATCA 501 chr3ptel1M 410254 -CAGT----TGGA-GAATAAATTGTGGTATATGAATATTATGGAATATTA 410297 - ---- -i vv i iv i L1ME3A_3end#L 502 ACAGTAGAATGGATAAATAAATTGTGGTATATTCACACAATGGAATACTA 551 chr3ptel1M 410298 T 410298 L1ME3A_3end#L 552 T 552 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 25.51 CpG sites = 13, Kimura (unadjusted) = 27.06 Transitions / transversions = 1.86 (13/7) Gap_init rate = 0.04 (4 / 92), avg. gap size = 2.00 (8 / 4) 16 16.93 0.00 0.00 chr3ptel1M 410829 410855 (589145) (A)n#Simple_repeat 1 27 (0) m_b120s252i1 4388 chr3ptel1M 410829 AAATAAAAGAAAAAAAAAAGAAAGAAA 410855 v i i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAA 27 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 14 4.35 4.17 0.00 chr3ptel1M 410834 410857 (589143) (AAAG)n#Simple_repeat 1 25 (0) m_b120s252i2 4388 chr3ptel1M 410834 AAAGAAA-AAAAAAAGAAAGAAAGA 410857 - i (AAAG)n#Simpl 1 AAAGAAAGAAAGAAAGAAAGAAAGA 25 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 264 30.39 1.23 2.50 chr3ptel1M 410921 411001 (588999) C L2d2_3end#LINE/L2 (73) 482 403 m_b120s601i3 4389 chr3ptel1M 410921 CAGAGAAATGGGAGATG-GGTCCCTGTCCTCAGGGAGCTCCCACTTTGGT 410969 i i ivi ii- i i iv v i i C L2d2_3end#LIN 482 CAAAGAAGTATAAGACATGGTCCCTGCCCTCAAGGAGCTTACAATCTAGT 433 chr3ptel1M 410970 TGGAGAAATGGTTCATGAAACATATATAAAAG 411001 i i iiivv - ii i- C L2d2_3end#LIN 432 TGGGGAGACAAGACAT-AAACACGTG-AAAAG 403 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 39.98 CpG sites = 19, Kimura (unadjusted) = 42.68 Transitions / transversions = 3.80 (19/5) Gap_init rate = 0.04 (3 / 80), avg. gap size = 1.00 (3 / 3) 22 17.64 7.23 3.49 chr3ptel1M 411011 411083 (588917) (GGAGAA)n#Simple_repeat 1 77 (9) m_b120s252i3 4390 chr3ptel1M 411011 GGAG-AGG-GAAGGACAAGGAAGGAGGAGTAGGA-AAGG-GAA-GACAAG 411055 - - v - i v - - - v (GGAGAA)n#Sim 1 GGAGAAGGAGAAGGAGAAGG-AGAAGGAGAAGGAGAAGGAGAAGGAGAAG 49 chr3ptel1M 411056 GAAGGGGATGAGGGAGGA-GAGAAGGGGA 411083 iii - i i - i (GGAGAA)n#Sim 50 GAGAAGGA-GAAGGAGAAGGAGAAGGAGA 77 Matrix = Unknown Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.11 (8 / 72), avg. gap size = 1.00 (8 / 8) 26 0.00 0.00 0.00 chr3ptel1M 411084 411108 (588892) (AGG)n#Simple_repeat 1 25 (0) c_b120s251i0 4391 chr3ptel1M 411084 AGGAGGAGGAGGAGGAGGAGGAGGA 411108 (AGG)n#Simple 1 AGGAGGAGGAGGAGGAGGAGGAGGA 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 201 35.62 0.93 3.81 chr3ptel1M 412018 412125 (587875) L2c_3end#LINE/L2 364 468 (10) m_b120s601i4 4392 chr3ptel1M 412018 CCTCTCTGCATAGACTAAGAGGTCCTGGGTGACAGCTCCTG-ATTTTGCC 412066 ii ii - iv v v iv i vvv i -i i iii L2c_3end#LINE 364 CTCCTCCAC-TAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATT 412 chr3ptel1M 412067 TTTCTCTGCACCCCTATTGTTGCCAGGCTTGTAGTAGGAGCTTAAGAGAA 412116 iv i i i i -- i- v vii v i v i v L2c_3end#LINE 413 CATCTTTGTATCCCCA--GC-GCCTGGCACATAGTAGGCGCTCAATAAAT 459 chr3ptel1M 412117 GCTTGTTGA 412125 i L2c_3end#LINE 460 GTTTGTTGA 468 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 47.33 CpG sites = 24, Kimura (unadjusted) = 51.35 Transitions / transversions = 1.85 (24/13) Gap_init rate = 0.05 (5 / 107), avg. gap size = 1.00 (5 / 5) 183 33.33 3.85 0.00 chr3ptel1M 412060 412137 (587863) L2d_3end#LINE/L2 436 516 (0) m_b120s601i5 4392 chr3ptel1M 412060 TTTTGCCTTTCTCTGCACC-CCTATTGT--TGCCAGGCTTGTAGTAGGAG 412106 ?i v i ii v - viii-- iii vii v L2d_3end#LINE 436 TTTTNTCGTTCCCCACAGCGCCTAGCACAGTGCTGAGCACATAGTAGGCG 485 chr3ptel1M 412107 CTTAAGAGAAGCTTGTTGATGGACTGGTGGA 412137 i v i vi v i i v L2d_3end#LINE 486 CTCAATAAATACTTGTTGATTGATTGATTGA 516 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 47.53 CpG sites = 17, Kimura (unadjusted) = 47.53 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.03 (2 / 77), avg. gap size = 1.50 (3 / 2) 191 28.87 1.23 10.74 chr3ptel1M 413726 413888 (586112) L2a_3end#LINE/L2 275 423 (94) m_b120s601i6 4393 chr3ptel1M 413726 CCTCCCCCCCATCAGGTTCTGTGGTTCTCATCTTCCCTAAGCCTTTTCTG 413775 ? ? vvii i vvii i i i v i v --- --- L2a_3end#LINE 275 CCTCNCCCCCANCACTCCCTATCCCCCTTACCCTGCTTTA---TTTT--- 318 chr3ptel1M 413776 AGTCCCCAGATGCTACTCCCCACCACAAATTACCTTCTATTGAT-TTTTA 413824 -- i v - - ivi iv-- v v v -- - L2a_3end#LINE 319 --TCTCCATA-GC-ACTTATCACCATC--TGACATACTAT--ATATTTTA 360 chr3ptel1M 413825 TTTGCTAATATATGTATGTGTAT-TATCACCCCAGGGAGAATGTCAGTTC 413873 i ii v v i v - v - v v vv- v i L2a_3end#LINE 361 CTTATTTATTTGTTTAT-TGTCTGTCTCCCCCCACT-AGAATGTAAGCTC 408 chr3ptel1M 413874 CCTGAGAGCAAGGAC 413888 v i i L2a_3end#LINE 409 CATGAGGGCAGGGAC 423 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 36.93 CpG sites = 20, Kimura (unadjusted) = 36.93 Transitions / transversions = 0.91 (20/22) Gap_init rate = 0.11 (18 / 162), avg. gap size = 1.00 (18 / 18) 280 31.39 0.00 1.16 chr3ptel1M 413804 413890 (586110) L2d_3end#LINE/L2 338 423 (93) m_b120s601i7 4393 chr3ptel1M 413804 ATTACCTTCTATTGATTTTTATTTGCTAATATATGTATGTGTATTATCAC 413853 i ii v v i i v i v-i i i vv v i v L2d_3end#LINE 338 ACTGTCTTGTATTGTTCTCTAATTGTTT-CATGTGTGTTAGTCTTGTCTC 386 chr3ptel1M 413854 CCCAGGGAGAATGTCAGTTCCCTGAGAGCAAGGACCA 413890 ivv v v i i i i L2d_3end#LINE 387 CCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCA 423 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 41.69 CpG sites = 15, Kimura (unadjusted) = 41.69 Transitions / transversions = 1.25 (15/12) Gap_init rate = 0.01 (1 / 86), avg. gap size = 1.00 (1 / 1) 282 21.79 0.00 0.00 chr3ptel1M 414423 414500 (585500) C L1ME4c_3end#LINE/L1 (745) 85 8 m_b120s551i6 4394 chr3ptel1M 414423 TCATATCCTTTGACCATTTATCAATTGGGGACTGCCTTGTATTCTTATAA 414472 i v v v vvv ?v v v C L1ME4c_3end#L 85 TCATGTCCTTTGCCCATTTATCTATTGGGGTCTTGATNTTTTTCTTATCA 36 chr3ptel1M 414473 ATTTGAGTCAGTTTCCTATATATTTTAG 414500 i v i iii ? v? C L1ME4c_3end#L 35 ATTTGAATGAGCTCTTTATATANTANAG 8 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 26.99 CpG sites = 6, Kimura (unadjusted) = 26.99 Transitions / transversions = 0.55 (6/11) Gap_init rate = 0.00 (0 / 77), avg. gap size = 0.0 (0 / 0) 297 35.82 4.48 0.00 chr3ptel1M 416923 417056 (582944) C L3#LINE/CR1 (62) 4037 3898 m_b120s601i8 4395 chr3ptel1M 416923 TCTGAT-CATGAGTCTATTCCACGAT---TCTGA-AAATGCTTAGCTTGC 416967 ii - v i iv i i i---i - i v i v iv C L3#LINE/CR1 4037 TCCAATGCAGGAATCCCTTCTACAACATCCCTGACAAGTGGTCATCCAGC 3988 chr3ptel1M 416968 TGCCAATTGGATCCCACTTCTGATGGAGATCTCACTATTTCCTGAGTCAG 417017 iv iiv i iv v ivv i i v ii ?i v C L3#LINE/CR1 3987 CTCTGCTTGAACACCTCCAGTGACGGGGAGCTCACTACCTCNCGAGGCAG 3938 chr3ptel1M 417018 CTCAGCCC-TTTTGGGGTAAGATTAATTGTTTAAAAGTTC 417056 i vi - v ii ivvi i vi C L3#LINE/CR1 3937 CCCATTCCATTTTTGGACAGCTCTGATTGTTAGAAAGTTC 3898 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 48.87 CpG sites = 30, Kimura (unadjusted) = 52.04 Transitions / transversions = 1.67 (30/18) Gap_init rate = 0.03 (4 / 133), avg. gap size = 1.50 (6 / 4) 191 28.07 1.72 1.72 chr3ptel1M 417599 417656 (582344) C MIR1_Amn#SINE/MIR (158) 72 15 m_b120s601i9 4396 chr3ptel1M 417599 AGCCAGAACTTGAACTCAGTGCTTCTTAG-CCCAGTTTCTATACTCTCTC 417647 i i ? ? i vv i iv - i- vi i v C MIR1_Amn#SINE 72 AGCCGGGANTNGAACCCAGGTCTCCCGAGTCCCAGTC-CAGTGCTCTATC 24 chr3ptel1M 417648 CATTGGATC 417656 i i i C MIR1_Amn#SINE 23 CACTAGACC 15 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 32.73 CpG sites = 11, Kimura (unadjusted) = 38.77 Transitions / transversions = 2.20 (11/5) Gap_init rate = 0.04 (2 / 57), avg. gap size = 1.00 (2 / 2) 286 20.37 0.00 0.00 chr3ptel1M 419198 419251 (580749) MER63B#DNA/hAT-Tip100 383 436 (0) m_b120s502i0 4397 chr3ptel1M 419198 CTTTTATTTTTCTTTTGGAGAGCCGGGTGTTAAACATTTGCCTGCCCACC 419247 v iiiii v i v v MER63B#DNA/hA 383 CTTTTTTTTTTCCCCCAGAGAGCCGGTTGTTAAACATTTACCAGCACACC 432 chr3ptel1M 419248 ACCG 419251 i MER63B#DNA/hA 433 ACTG 436 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 24.28 CpG sites = 7, Kimura (unadjusted) = 24.28 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 43 20.50 0.00 0.00 chr3ptel1M 421179 421268 (578732) (ATCC)n#Simple_repeat 1 90 (0) m_b120s252i4 4398 chr3ptel1M 421179 ATCTATCCATTCAAGCATCCATGAATATATGCATCCATCCCTCCATTCAT 421228 i i vv vv vi v v i (ATCC)n#Simpl 1 ATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCAT 50 chr3ptel1M 421229 CCACTCATCCATCCATCTGTCCATCCATCCATTCATCCAT 421268 ii ii i (ATCC)n#Simpl 51 CCATCCATCCATCCATCCATCCATCCATCCATCCATCCAT 90 Matrix = Unknown Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.00 (0 / 89), avg. gap size = 0.0 (0 / 0) 232 13.66 0.00 4.55 chr3ptel1M 421279 421324 (578676) HAL1b#LINE/L1 2206 2249 (172) m_b120s551i7 4399 chr3ptel1M 421279 ATCCATCCATCCATCCATCTGTCCATCCATTCATGAATGTATGCAT 421324 i v i i-- v i HAL1b#LINE/L1 2206 ATCCATCCATCCATCCATCTATCCTTCTATC--TGTATATATGCAT 2249 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 15.27 CpG sites = 4, Kimura (unadjusted) = 15.27 Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.04 (2 / 45), avg. gap size = 1.00 (2 / 2) 34 22.64 2.20 1.09 chr3ptel1M 421326 421416 (578584) (CATC)n#Simple_repeat 1 92 (0) m_b120s252i5 4400 chr3ptel1M 421326 CATCCATCTATCCATCCATCCATCCATCTAT-GGTCCACCTCTCCATCTG 421374 i i -vi i iv ii (CATC)n#Simpl 1 CATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCA 50 chr3ptel1M 421375 TCTGCCCATTCATCTATCCATCCAACTGCTCCA-CCATCCATC 421416 iii i i v -vv - (CATC)n#Simpl 51 TCCATCCATCCATCCATCCATCCATC-CATCCATCCATCCATC 92 Matrix = Unknown Transitions / transversions = 2.40 (12/5) Gap_init rate = 0.03 (3 / 90), avg. gap size = 1.00 (3 / 3) 238 19.15 0.00 0.00 chr3ptel1M 421940 421986 (578014) C LTR81C#LTR/Gypsy (223) 930 884 m_b120s502i1 4401 chr3ptel1M 421940 GTGTTTCAGATTTTCTCCTCCTTCCCCCACTCCCTCCCTAGATGGCA 421986 v i i ii iii v C LTR81C#LTR/Gy 930 GTCTTTCAGATTTCCTCCTCCTCCCCCTGCTCCTCTCCAAGATGGCA 884 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 23.03 CpG sites = 7, Kimura (unadjusted) = 23.03 Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 16 18.74 0.00 4.55 chr3ptel1M 422050 422095 (577905) (AAAAG)n#Simple_repeat 1 44 (0) m_b120s252i6 4402 chr3ptel1M 422050 AAGAGAAATCAAATCAAAAGGAAAGAAAATGAGAAAGAAAACAAAA 422095 i vv vv i - - v (AAAAG)n#Simp 1 AAAAGAAAAGAAAAGAAAAGAAAAGAAAA-GA-AAAGAAAAGAAAA 44 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.04 (2 / 45), avg. gap size = 1.00 (2 / 2) 723 30.61 3.81 4.04 chr3ptel1M 422297 422742 (577258) C L1ME3_3end#LINE/L1 (271) 638 194 m_b120s551i8 4403 chr3ptel1M 422297 GTCCTGCTCATTTCACTCAGCATCAGTTCATGTGAGTCTC-TCCAGGCCT 422345 iv iv i i ? vv - vi - v iiv C L1ME3_3end#LI 638 GTCTGGCTTCTTTCGCTCAACATNATGTC-TGTGAGATTCATCCATGTTG 590 chr3ptel1M 422346 TTCTGAA-ATCATCCTGTTGGTCATTTCTTATAGAACAATAATATTCCAT 422394 vi vi- ? viv- v iv i v vvvvi i C L1ME3_3end#LI 589 TTGCGTGTANCAGTA-GTTCGTTCTTTTTTATTGCTGTGTAGTATTCCAT 541 chr3ptel1M 422395 AACATTCGTATACCAGAACTTATT--------CTCCAGCTGATGGGCATC 422436 vii vvi v i -------- ? v i i i C L1ME3_3end#LI 540 TGTATGAATATACCACAATTTATTTATCCATTCTNCTGTTGATGGACATT 491 chr3ptel1M 422437 CACTCAGTTTCCAGTTTCTG-CCACTACAAA-AGGGCTGCCACAAACATT 422484 iivviv i? - i i ii - ii i ii C L1ME3_3end#LI 490 TGGGTTGTTTCCAGTTTTNGGCTATTATGAATAAAGCTGCTATGAACATT 441 chr3ptel1M 422485 TTTGCACATGTGGGTCCCTTTCTTTAAGATCTGC-TTCTTTAAGATCTCT 422533 i i ----- i vv vi v v -i v ---- C L1ME3_3end#LI 440 CTTGTACATGT-----CTTTTGGTGGACATATGCACTCATT----TCTCT 400 chr3ptel1M 422534 TTGGGATATAAGCCCAACAGAGGCACTGCTGGATCAAAGGGTATGCACA- 422582 v v -- i iv v v i i v v ii - C L1ME3_3end#LI 399 TGGGTATATA--CCTAGGAGTGGAATTGCTGGGTCATAGGGTAGGCGTAT 352 chr3ptel1M 422583 GTTTGATAACTCTTTGGGA-ATAGTTACAAATTGCTCTCCATA-TGGTTG 422630 ii----- i v - v vv iv i i v - C L1ME3_3end#LI 351 GTTTAG-----CTTTAGTAGATACTGCCAAACAGTTTTCCAAAGTGGTTG 307 chr3ptel1M 422631 GATCCGTTCACAGTTCCACCAACAATGCATTAGTGTCCCAGTTTTCCCAT 422680 v i vi i v i i i v v i vii i C L1ME3_3end#LI 306 TACCAATTTACACTCCCACCAGCAATGTATGAGAGTTCCAGTTGCTCCAC 257 chr3ptel1M 422681 ATCC-CTCTAACATTTATCATTGTCTTTTCCTGTCATCTTAGCCAGTCTG 422729 - v i i ivi vv iii v v i v C L1ME3_3end#LI 256 ATCCTCGCCAACACTTGGTATTGTCAGTCTTTTTAATTTTAGCCATTCTG 207 chr3ptel1M 422730 AGAAGTGTGTAGT 422742 ivii C L1ME3_3end#LI 206 GTGGGTGTGTAGT 194 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.53 CpG sites = 72, Kimura (unadjusted) = 40.73 Transitions / transversions = 1.22 (72/59) Gap_init rate = 0.06 (28 / 445), avg. gap size = 1.25 (35 / 28) 824 28.49 4.17 4.46 chr3ptel1M 422383 422742 (577258) C L1ME3A_3end#LINE/L1 (368) 552 194 m_b120s551i9 4403 chr3ptel1M 422383 ATAATATTCCATAACATTCGTATACCAGAACTTATTC-TCCA-------G 422424 i viii vvi v i i- ------- C L1ME3A_3end#L 552 ATAGTATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTACTG 503 chr3ptel1M 422425 CTGATGGGCATCCACTCAGTTTCCAGTTTCTG-CCACTACAAA-AGGGCT 422472 i i iiivvi? ?? - i i i - v C L1ME3A_3end#L 502 TTGATGGACATTTGGGTNGTTTCCAGTTTNNGGCTATTACGAATAGTGCT 453 chr3ptel1M 422473 GCCACAAACATTTTTGCACATGTGGGTCCCTTTCTTTAAGATCTGCTTCT 422522 i ii i i ----- i vv v v v ----- C L1ME3A_3end#L 452 GCTATGAACATTCTTGTACATGT-----CTTTTGGTGAACATATG----- 413 chr3ptel1M 422523 TTAAG-ATCTCTTTGGGATATAAGCCCAACAGAGGCACTGCTGGATCAAA 422571 - v - i v v i vi i iv v v i i v C L1ME3A_3end#L 412 -TACGCATTTCTGTTGGGTATATACCTAGGAGTGGAATTGCTGGGTCATA 364 chr3ptel1M 422572 GGGTATGCACA-GTTTGATAACTCTTTGGGA-ATAGTTACAAATTGCTCT 422619 i - iii----- i v - v vv iv i i C L1ME3A_3end#L 363 GGGTATGCATATGTTCAG-----CTTTAGTAGATACTGCCAAACAGTTTT 319 chr3ptel1M 422620 CCATA-TGGTTGGATCCGTTCACAGTTCCACCAACAATGCATTAGTGTCC 422668 v - v i vi i v i i i i v v i C L1ME3A_3end#L 318 CCAAAGTGGTTGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTTC 269 chr3ptel1M 422669 CAGTTTTCCCATATCC-CTCTAACATTTATCATTGTCTTTTCCTGTCATC 422717 i vii i - v i i ivi v iii v i C L1ME3A_3end#L 268 CGGTTGCTCCACATCCTCGCCAACACTTGGTATTGTCTGTCTTTTTCATT 219 chr3ptel1M 422718 TTAGCCAGTCTGAGAAGTGTGTAGT 422742 v ivii C L1ME3A_3end#L 218 TTAGCCATTCTGGTGGGTGTGTAGT 194 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 36.45 CpG sites = 60, Kimura (unadjusted) = 37.42 Transitions / transversions = 1.58 (60/38) Gap_init rate = 0.07 (25 / 359), avg. gap size = 1.24 (31 / 25) 187 33.33 0.00 0.00 chr3ptel1M 423011 423070 (576930) L2#LINE/L2 2362 2421 (661) m_b120s601i10 4404 chr3ptel1M 423011 ATCTCTCCCCTAAACTCGAATACAACATCGCCAGCTGGCTGCTGGGCATC 423060 i i v ivvivii vv i v i v i L2#LINE/L2 2362 ACCTCTCCCCTGAACTCCAGACTCGTATATCCAACTGCCTACTCGACATC 2411 chr3ptel1M 423061 TCTACCTGAA 423070 i i i L2#LINE/L2 2412 TCCACTTGGA 2421 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 42.75 CpG sites = 12, Kimura (unadjusted) = 45.86 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0) 569 24.27 11.90 3.13 chr3ptel1M 423409 423761 (576239) L1ME4a_3end#LINE/L1 279 661 (210) m_b120s551i11 4405 chr3ptel1M 423409 ATACTGTTGGTGGAGTTGTGGACTGATTCAACCATTGGGGAGAGCAGTTT 423458 i i iiv ii i i v v vv i i L1ME4a_3end#L 279 ACACTGCTGGTGGGAGTGTAAATTGGTACAACCTTTCTGGAGGGCAATTT 328 chr3ptel1M 423459 GGAACTATG-ATCAAAGGACTATAAGACTGTGTATACCTT-----CCAGC 423502 v v - i v - i v ?i i ----- i L1ME4a_3end#L 329 GGCAATATGTATCAAAAGCCT-TAAAAATGTNCATACCCTTTGACCCAGT 377 chr3ptel1M 423503 AATACCACTACTAGG--TTTACACCTTAA--AAACATCCCAAAAGGGGGA 423548 v v -- i-- i -- i vi vi i v v ? L1ME4a_3end#L 378 AATTCCACTTCTAGGAATTTAT--CCTAAGGAAATAATCAGAGATGTGNA 425 chr3ptel1M 423549 -AAGGACCTATTAGTACAACGATATTTATAGCAGCTCTTTTTGTGGTGGC 423597 - i ii -- v i i v vi v i ii i L1ME4a_3end#L 426 CAAAGATTTAT--GTACAAGGATGTTCATCGCAGCATTATTTATAATAGC 473 chr3ptel1M 423598 TAAAAATGTATAAATAA----AAT--CCATGAATTGGGGGAATGGC-AAA 423640 v - iv i ---- -- vv -i ? i- L1ME4a_3end#L 474 GAAAAAT-TGGAAACAACCTAAATGTCCAACAAT-AGGGGANTGGTTAAA 521 chr3ptel1M 423641 CAAGTTATGGTATATGATTGTAATGGAATATTATTATGTTATAAGAAATG 423690 i i i vvv i? vvv ii v i ? L1ME4a_3end#L 522 TAAATTATGGTACATCCATANAATGGAATATTATGCAGCCATTAAAAATN 571 chr3ptel1M 423691 ATG----AGCAGACAGATTTCAGAAAT-ACATGG----ATAC---TGATA 423728 ----v v - v ---- - ---- i --- L1ME4a_3end#L 572 ATGTTTTCGAAGA-ATATTT----AATGACATGGGAAAATGCTCATGATA 616 chr3ptel1M 423729 CA-----AAGTGAAATGAACAGAATAC-------TGTATGCAGTA 423761 i ----- vi i i? ------- i i L1ME4a_3end#L 617 TAATGTTAAGTGAAAAAAGCAGGNTACAAAACTGTATATACAGTA 661 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 30.72 CpG sites = 49, Kimura (unadjusted) = 30.72 Transitions / transversions = 1.44 (49/34) Gap_init rate = 0.07 (26 / 352), avg. gap size = 2.08 (54 / 26) 607 26.33 6.02 2.92 chr3ptel1M 423409 423674 (576326) L1ME3Cz_3end#LINE/L1 275 548 (449) m_b120s551i10 4405 chr3ptel1M 423409 ATACTGTTGGTGGAGTTGTGGACTGATTCAACCATTGGGGAGAGCAGTTT 423458 i i iiv ii i i v i vv i L1ME3Cz_3end# 275 ACACTGCTGGTGGGAGTGTAAATTGGTACAACCACTTTGGAGAGCAATTT 324 chr3ptel1M 423459 GGAACTAT-GATCAAAGGACTATAAGACTGTGTATACCTT-----CCAGC 423502 v v -v vi --- vv - i i i ----- L1ME3Cz_3end# 325 GGCAATATCTAGTAAAG---TTGAAGA-TGCGCATACCCTACGACCCAGC 370 chr3ptel1M 423503 AATACCACTACTAGGTTTACACCTTAAAAACA---TCCCAAAAGGGGGAA 423549 v v v i i i i v --- v v v v viv L1ME3Cz_3end# 371 AATTCCACTTCTAGGTATATACCCTAGAGAAACTCTCGCACATGTGCACA 420 chr3ptel1M 423550 AGGACCTATTAGTACAACGATATTTATAGCAGCTCTTTTTGTGGTGGCTA 423599 vvi -- v i i v vi v ii i v L1ME3Cz_3end# 421 AGGAGACAT--GTACAAGGATGTTCATTGCAGCATTGTTTGTAATAGCGA 468 chr3ptel1M 423600 AAAATGTATAAA-----TAAA-ATCCATGAATTGGGGGAATGG-CAAACA 423642 - iv ----- -i v - i -i i L1ME3Cz_3end# 469 AAAAT-TGGAAACAACCTAAATGTCCATCAA-TAGGGGAATGGATAAATA 516 chr3ptel1M 423643 AGTTATGGTATATGATTGTAATGGAATATTAT 423674 i i vvv ii i L1ME3Cz_3end# 517 AATTGTGGTATATTCATACAATGGAATACTAT 548 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 32.35 CpG sites = 36, Kimura (unadjusted) = 32.93 Transitions / transversions = 1.12 (36/32) Gap_init rate = 0.05 (14 / 265), avg. gap size = 1.71 (24 / 14) 35 24.88 0.91 2.78 chr3ptel1M 423929 424038 (575962) (TCCT)n#Simple_repeat 1 108 (0) m_b120s252i7 4406 chr3ptel1M 423929 TCTTTCTTTTCTTCCTTCCTCTCTCTCCCCTCCTCTCACTCAGT-GTTCT 423977 i i i - - i i - vi vv -v i (TCCT)n#Simpl 1 TCCTTCCTTCCTTCCTTCCT-TC-CTTCCTTCCT-TCCTTCCTTCCTTCC 47 chr3ptel1M 423978 TTCCTTCCTTTCTTCATTTGTTCGTTCATTCGTTCATTCATTCCTTTCTT 424027 i v iv v v v v v i (TCCT)n#Simpl 48 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 97 chr3ptel1M 424028 CCTTCCTTTCT 424038 i (TCCT)n#Simpl 98 CCTTCCTTCCT 108 Matrix = Unknown Transitions / transversions = 1.00 (11/11) Gap_init rate = 0.04 (4 / 109), avg. gap size = 1.00 (4 / 4) 13 5.27 0.00 0.00 chr3ptel1M 424944 424963 (575037) (AAC)n#Simple_repeat 1 20 (0) m_b120s252i8 4407 chr3ptel1M 424944 AACAATAACAACAACAACAA 424963 i (AAC)n#Simple 1 AACAACAACAACAACAACAA 20 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 44 0.00 2.44 0.00 chr3ptel1M 424971 425011 (574989) (AC)n#Simple_repeat 1 42 (0) c_b120s251i1 4408 chr3ptel1M 424971 ACACACA-ACACACACACACACACACACACACACACACACAC 425011 - (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACAC 42 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 204 27.41 3.45 11.94 chr3ptel1M 426167 426311 (573689) MamTip2b#DNA/hAT-Tip100 148 281 (168) m_b120s601i11 4409 chr3ptel1M 426167 GTAAAGGTATGG-CTCAAAACTACCTCTATTGATATGCCAGAA-GTAACA 426214 v i v - v i vvi i i v v iv - v v MamTip2b#DNA/ 148 GTTAAGGCATTGTCTCTAGAAGGCCTCTGTTAAAATGCAAATATGTTACC 197 chr3ptel1M 426215 TGGGCATGGGGTAACCTGGAACATGATCATTTAAGCCACTGTAAATGAT- 426263 v-- ----- ------- i i v iiv - MamTip2b#DNA/ 198 TGGGA--GGGGTAAC-----ACAT-------TAAGCCATTATCAGCCATT 233 chr3ptel1M 426264 AAAATCTGGATGTG--TTAGTGAATATCAGATTTTCCTTCCTCTCACCCA 426311 v i viii -- v-- vv i?? ?v i MamTip2b#DNA/ 234 AACACCTTAGCGTGAATTAGTT--TATCAGATTAGCTNNCCNGTCACCTA 281 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 33.73 CpG sites = 16, Kimura (unadjusted) = 34.91 Transitions / transversions = 0.84 (16/19) Gap_init rate = 0.14 (20 / 144), avg. gap size = 1.05 (21 / 20) 239 27.55 4.08 0.00 chr3ptel1M 427184 427281 (572719) L2-1_AMi#LINE/L2 445 546 (689) m_b120s551i12 4410 chr3ptel1M 427184 CCAGTCTTTTAGACATCTCAAACTGGATGTCCAGCGGACATCATAAACTC 427233 v i iv vvvv i v v v vi i L2-1_AMi#LINE 445 CCTGTCTCTCTGACATCTCCTCGTGGATGTCTAGCCGTCAGCTCAAGCTC 494 chr3ptel1M 427234 AGCATGTCC-AAAACAGAACTC-AAGCCTTCCACTCCTACCT--TCCCTA 427279 i v - i -v ii v i vvi -- i L2-1_AMi#LINE 495 AACATGGCCTAAAACAGAGCTCTTAATCTTCCCCCCAAGCCTNCTCCCCA 544 chr3ptel1M 427280 TT 427281 L2-1_AMi#LINE 545 TT 546 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 34.51 CpG sites = 12, Kimura (unadjusted) = 34.51 Transitions / transversions = 0.80 (12/15) Gap_init rate = 0.03 (3 / 97), avg. gap size = 1.33 (4 / 3) 222 35.29 1.18 0.00 chr3ptel1M 427319 427403 (572597) L2#LINE/L2 2559 2644 (438) m_b120s601i12 4411 chr3ptel1M 427319 GAAATTATCCTGAACTCCTCACTCTCACTC-CACCCCATATCCAATAGAG 427367 i i i vi v i v - i vv v L2#LINE/L2 2559 GGAGTCATCCTTGACTCCTCTCTTTCTCTCACACCCCACATCCAATCCAT 2608 chr3ptel1M 427368 TGCCCAGGTCTGTTGATTTCAGTTTTACAACATTTC 427403 iiv v ivi i ii ii vi i v i v L2#LINE/L2 2609 CAGCAAATCCTGTCGGCTCTACCTTCAAAATATATC 2644 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 47.51 CpG sites = 18, Kimura (unadjusted) = 49.88 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.01 (1 / 84), avg. gap size = 1.00 (1 / 1) 359 33.47 4.74 2.31 chr3ptel1M 427595 427805 (572195) L2#LINE/L2 2618 2833 (249) m_b120s601i13 4411 chr3ptel1M 427595 CTGTTGATTTTTACTCTGCACCATCTCTCCA-AATCTGTCC-CTTCTCTC 427642 i ii i - - v vv v v - i v - v L2#LINE/L2 2618 CTGTCGGCTCT-AC-CTTCAAAATATATCCAGAATCCGACCACTTCTCAC 2665 chr3ptel1M 427643 TTCCAACATTGTCCCCACTCTGG-ACAGACCCTCTTTACCTCACATTTGG 427691 iv vv i i v i -v ii vi v i i v iii L2#LINE/L2 2666 CACCTCCACTGCCACCACCCTGGTCCAAGCCACCATCATCTCTCGCCTGG 2715 chr3ptel1M 427692 ATCATTGTAGTAGCTGCTGGA--GATTTGCCTGCCTCAGTCTCT--TCCC 427737 i i i i iv ivi -- i i v i vii ii --i L2#LINE/L2 2716 ATTACTGCAATAGCCTCCTAACTGGTCTCCCTGCTTCCACCCTTGCCCCC 2765 chr3ptel1M 427738 CTTTAATCCATCCTCCATTTAGAAACTTCAGA---ATTTTCCTAAAACCT 427784 ?i i i i v ivi v i -- --- ii ii v L2#LINE/L2 2766 CTNCAGTCTATTCTCAACACAGCAGC--CAGAGTGATCCTTTTAAAACGT 2813 chr3ptel1M 427785 CAGGTCTGATCATGTTACTCC 427805 - i v i L2#LINE/L2 2814 -AAGTCAGATCATGTCACTCC 2833 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 44.39 CpG sites = 45, Kimura (unadjusted) = 47.28 Transitions / transversions = 1.88 (45/24) Gap_init rate = 0.05 (11 / 210), avg. gap size = 1.36 (15 / 11) 322 35.37 7.02 3.56 chr3ptel1M 427990 428288 (571712) L2b_3end#LINE/L2 147 455 (11) m_b120s601i14 4411 chr3ptel1M 427990 CTCTGGCT--ATCCCCCTTCCTT-CTTCCAATTCAACTAGTGACCTCTCT 428036 v -- v v ii- i --- iv i iv v iiv L2b_3end#LINE 147 CTCTGCCTGGAACGCCCTTCCCCACCTC---TTCGCCTGGCCAACTCCTA 193 chr3ptel1M 428037 GGCTTCCTTTAA-TCCCAACCAAAATCGCACTTT-TACAGGAATATTTCT 428084 vv v i i- i i iv vv i i- v i vvii i L2b_3end#LINE 194 CTCATCCTTCAGGTCTCAGCTCAAATGTCACCTCCTCCGGGAAGCCCTCC 243 chr3ptel1M 428085 CCAACCCCTC---TTATTTCTAGAGTCTTCCTCTCTTAATTATTTCCTAT 428131 ii i ---iiivv vi v i i ---iiviviii vi L2b_3end#LINE 244 CTGACCCCCCAGGCCGGGTCAGGCGCCCTCCTCT---GGGCCCCCCCAGT 290 chr3ptel1M 428132 T-TAACCTGT-A-TCTGGAATGATAACTATTTACTTGTTTGCATG-CTCT 428177 i- v i- - i- v ? i i i ---- ? i - v L2b_3end#LINE 291 CCTACCCTGCCACTCTGGG-TTATNATTGTCT----GNTTACATGTCTGT 335 chr3ptel1M 428178 CTTCCTGAATACGTTGTGAGCTCCTTGAAG--AATTAC--TTTTTGTCTC 428223 i iv v vii v i -- ivv --?v i i L2b_3end#LINE 336 CTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCTT 385 chr3ptel1M 428224 TTTT-----TGTATCACCAGTGTTTAGCTTAGTGCCTGACACATAGTAGG 428268 v i----- v i ii vi ? i i L2b_3end#LINE 386 GTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGG 435 chr3ptel1M 428269 TACCTAATGAATGTTGATTG 428288 ii ii i i i vi L2b_3end#LINE 436 CGCTCAGTAAATATTTGTTG 455 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 48.02 CpG sites = 65, Kimura (unadjusted) = 51.89 Transitions / transversions = 1.76 (65/37) Gap_init rate = 0.08 (23 / 298), avg. gap size = 1.39 (32 / 23) 426 30.99 6.25 1.19 chr3ptel1M 428129 428288 (571712) L2d2_3end#LINE/L2 377 544 (11) m_b120s601i15 4411 chr3ptel1M 428129 TATTTAA--CCTGTATCTGGAATGATAACTATTTACTTGTTTGCATGCTC 428176 -- i - vv v- v i v iii vi v L2d2_3end#LIN 377 TATTTAAATCTTGTAT-TGTTATT-TAACTTTTCACGTGTTTATGTCTTG 424 chr3ptel1M 428177 TCTTCCTGAATACGTTGTGAGCTCCTTGAAGA-----ATTACTTTTTGTC 428221 i ii v vi i i i----- ii iv i i v L2d2_3end#LIN 425 TCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATA 474 chr3ptel1M 428222 TCTTTTTGTATCACC---AGTGTTTAGCTTAGTGCCTGACACATAGTAGG 428268 ii i v --- i ii vi vi i L2d2_3end#LIN 475 CTTCTTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAGTAGG 524 chr3ptel1M 428269 TACCTAATGAATGTTGATTG 428288 ii ii i i vi L2d2_3end#LIN 525 CGCTCAATAAATATTTGTTG 544 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 40.05 CpG sites = 34, Kimura (unadjusted) = 42.52 Transitions / transversions = 2.27 (34/15) Gap_init rate = 0.03 (5 / 159), avg. gap size = 2.40 (12 / 5) 257 34.25 6.35 2.68 chr3ptel1M 428423 428674 (571326) C L2#LINE/L2 (2138) 944 684 m_b120s601i16 4412 chr3ptel1M 428423 GGAGAGATGGTAGCT--TG----TGACCAGA---AAAGCAGAACCATCTC 428463 i i v i i -- ---- v i--- ii i vi vvv C L2#LINE/L2 944 GGAGGGGTTGCAGTTATTGGTAATGACAAGGTCTAGGGTATGACCATGGG 895 chr3ptel1M 428464 CATGGGTGGCTGAGGTAAGCTGGAGTAGTCAGA-CATGGGAAGTGCATAG 428512 vi i i v v -iv - v i v viv C L2#LINE/L2 894 AGTGAGTGGCTGAGGTAGGGTGGAGGA-CAAGATCATTGGAGGAGAGGAG 846 chr3ptel1M 428513 ATTAAGGACCTGGGAATGTAGAGTATCTG-AGGAACACCAATGTGTA-GC 428560 i i v i ivvi i iv - v i v i v -ii C L2#LINE/L2 845 GTCAAGGAACTGAGAGGCCAGGGTATTGGAAGGATCATCTACGTGGATAT 796 chr3ptel1M 428561 TGATTTCCTCTAGA---ATGATAGGAGGAG-ATGGGAGGAGAGGAAACTG 428606 vv vi v --- i v -i v - v-i v C L2#LINE/L2 795 TGAAATCACCAAGAATTATGACAGGAGTAGTGTTGGA-GAGAGT-GACAG 748 chr3ptel1M 428607 TGAGACAGGCATCACACTCACTCAGAAAGGAATGCAAATGTATCAGGAGA 428656 v viii v v viiv i v iv vi i - i v i C L2#LINE/L2 747 TGAGCCAGGAGCTAAAATCTTCAAGGAATGAGGGGGAGTG-ACCCGGAGG 699 chr3ptel1M 428657 CCTGGTCTGGATGGGTGC 428674 i - -- i iv C L2#LINE/L2 698 TC-GG--TAGATGACTGC 684 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 46.07 CpG sites = 44, Kimura (unadjusted) = 46.84 Transitions / transversions = 1.10 (44/40) Gap_init rate = 0.06 (15 / 251), avg. gap size = 1.53 (23 / 15) 243 27.03 2.67 1.32 chr3ptel1M 430834 430908 (569092) C L3#LINE/CR1 (251) 3848 3773 m_b120s601i17 4413 chr3ptel1M 430834 TCCCAGCTCTGCCTTCTGGGGCCAAGC--ACTAAGACCCAATCCTTCTTG 430881 i i i i vi -- v -i i i v C L3#LINE/CR1 3848 TCCTAGTTCTGCCCTCTGGAGCCACACAGAATAAG-TCTAATCCCTCTTC 3800 chr3ptel1M 430882 GACATCCAAGCTTATCAAATATTAAAA 430908 v vvv iiv vi C L3#LINE/CR1 3799 CACATGACAGCCCTTCAAATATTTGAA 3773 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 34.11 CpG sites = 11, Kimura (unadjusted) = 34.11 Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.03 (2 / 74), avg. gap size = 1.50 (3 / 2) 332 22.81 13.11 2.99 chr3ptel1M 430927 431048 (568952) L2#LINE/L2 1965 2098 (984) m_b120s601i18 4414 chr3ptel1M 430927 CCTCAGCACTCAACTGAAACTGCTCCTGCCATAAGTCACCAAGGAGCTT- 430975 i v v i i i - i v v i- L2#LINE/L2 1965 CCCCACCACTCCACCGAAACTGCTCTTGTCA-AGGTCACCAATGACCTCC 2013 chr3ptel1M 430976 ---TTACT----------GTT--TTCTCAGCTGTCATCCTTCTTGAGCCT 431010 --- i ---------- i-- iiv i v - - L2#LINE/L2 2014 ACGTTGCTAAATCCAATGGTCAATTCTCAGTCCTCATCTTACTTGA-CC- 2061 chr3ptel1M 431011 TTATCTGAAACCTTTGACATCGTGGATTACTCTTTCCT 431048 - ? v v i v iv v i ii L2#LINE/L2 2062 -TNTCAGCAGCATTTGACACAGTTGATCACTCCCTCCT 2098 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 26.91 CpG sites = 16, Kimura (unadjusted) = 28.11 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.07 (8 / 121), avg. gap size = 2.50 (20 / 8) 12 20.36 0.00 0.00 chr3ptel1M 431758 431786 (568214) (TTTC)n#Simple_repeat 1 29 (0) m_b120s252i9 4415 chr3ptel1M 431758 TTTCTTTTTTTCTTTCTTGTTCTCTTCCT 431786 i vi i i (TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTTTCTTTCT 29 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 55 17.22 4.76 0.76 chr3ptel1M 431904 432029 (567971) (AG)n#Simple_repeat 1 131 (0) m_b120s252i10 4416 chr3ptel1M 431904 AGATGAGAGAGAGAGAACGAGACAGAGAGAGAGA-AGAAAAAAAAAAAGA 431952 - iv v - i i i i i (AG)n#Simple_ 1 AGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 49 chr3ptel1M 431953 GAGA-ACACACAGAGAGA-AGAGACAGAGAGATAG-GACAGAGAGA-AGA 431998 - v v v - v v - v - (AG)n#Simple_ 50 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 99 chr3ptel1M 431999 AAGAGACAGAGAGAGAGAGAAAG-GGGAGGGA 432029 i v i - i i (AG)n#Simple_ 100 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 131 Matrix = Unknown Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.06 (7 / 125), avg. gap size = 1.00 (7 / 7) 31 23.18 4.84 3.17 chr3ptel1M 435184 435307 (564693) (TTTATA)n#Simple_repeat 1 126 (0) m_b120s252i11 4417 chr3ptel1M 435184 TTTCTTTTAAAATTAATTAATTAT-TTTATATCTATATATTTAATCATAA 435232 v v v v v - v - i v v v i v (TTTATA)n#Sim 1 TTTATATTTATATTTA-TATTTATATTTATATTTATATTTATATTTATAT 49 chr3ptel1M 435233 TAATATTTATAATTTTATATTATTTTTAT-TTTAAATTTA-AAATA-ATT 435279 v v v - v - v - vv - (TTTATA)n#Sim 50 TTATATTTATATTTATAT-TTATATTTATATTTATATTTATATTTATATT 98 chr3ptel1M 435280 TA-ATTGATA-TAATTTTAAATGATTTATA 435307 - v - v v -v - (TTTATA)n#Sim 99 TATATTTATATTTATATT-TAT-ATTTATA 126 Matrix = Unknown Transitions / transversions = 0.10 (2/21) Gap_init rate = 0.08 (10 / 123), avg. gap size = 1.00 (10 / 10) 17 22.22 1.59 4.92 chr3ptel1M 435264 435326 (564674) (TAAATAA)n#Simple_repeat 1 61 (0) m_b120s252i12 4418 chr3ptel1M 435264 TAAATTTAAAATAATTTAATTGATATAATTTTAAATGATTTATAAT-ACT 435312 vvv -- v i - vv i vv - v (TAAATAA)n#Si 1 TAAATAATAAATAA--TAAATAATA-AATAATAAATAATAAATAATAAAT 47 chr3ptel1M 435313 AATAAATAATAAAT 435326 (TAAATAA)n#Si 48 AATAAATAATAAAT 61 Matrix = Unknown Transitions / transversions = 0.22 (2/9) Gap_init rate = 0.06 (4 / 62), avg. gap size = 1.00 (4 / 4) 16 13.95 5.88 3.85 chr3ptel1M 435347 435397 (564603) (AAGAAA)n#Simple_repeat 1 52 (0) m_b120s252i13 4418 chr3ptel1M 435347 AAGAGAAAATCAAAACAAAAGGAAAGAG-AAAAG--AAAGAAAAAGAGGA 435393 - vv v i i - -- -i (AAGAAA)n#Sim 1 AAGA-AAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGA-AA 48 chr3ptel1M 435394 AAGA 435397 (AAGAAA)n#Sim 49 AAGA 52 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.08 (4 / 50), avg. gap size = 1.25 (5 / 4) 274 23.10 25.58 0.80 chr3ptel1M 435537 435837 (564163) C L1ME4a_3end#LINE/L1 (238) 633 259 m_b120s551i13 4419 chr3ptel1M 435537 TTTTTCACTC--CATCGT-TCATGAAATCTTTCCCCTTT---TAAA-ATT 435579 i-- ii - ivvi v v --- - C L1ME4a_3end#L 633 TTTTTCACTTAACATTATATCATGAGCATTTTCCCATGTCATTAAATATT 584 chr3ptel1M 435580 ATTCG------TCATTTTTAATAG--AAATAATATTCTATTAC-TTCATA 435620 v ------ ? i --iv i ?i- vv i C L1ME4a_3end#L 583 CTTCGAAAACATNATTTTTAATGGCTGCATAATATTCCATTNTATGGATG 534 chr3ptel1M 435621 TACCATAACTTATTCAGCCATTCC------------CACTCA----GTTT 435654 i i i ? ------------ i i ---- C L1ME4a_3end#L 533 TACCATAATTTATTTAACCANTCCCCTATTGTTGGACATTTAGGTTGTTT 484 chr3ptel1M 435655 CCAACTCT--GCCACCACAAA-AGAGCTGCAA-------CCGTG------ 435688 i i -- i ii i - iv i ------- v ------ C L1ME4a_3end#L 483 CCAATTTTTCGCTATTATAAATAATGCTGCGATGAACATCCTTGTACATA 434 chr3ptel1M 435689 -ATCCTTTTCC---TCCTTTATGATTTCCTTGGGATACAAACCCTA---- 435730 - i v ? --- ii v v i - vi ---- C L1ME4a_3end#L 433 AATCTTTGTNCACATCTCTGATTATTTCCTTAGGATA-AATTCCTAGAAG 385 chr3ptel1M 435731 TGGCACTTTGCTGGGT---------TGCACAGTCTGATAGCCCTTGGAAT 435771 v -- i --------- ? v i v vi ii iv i C L1ME4a_3end#L 384 TGGAA--TTACTGGGTCAAAGGGTATGNACATTTTTAAGGCTTTTGATAC 337 chr3ptel1M 435772 A----GCCAGATTG--TTTCAGAATG--TGGATCATTTTAC-CTC---CC 435809 ---- i --i i v -- v i v - --- C L1ME4a_3end#L 336 ATATTGCCAAATTGCCCTCCAGAAAGGTTGTACCAATTTACACTCCCACC 287 chr3ptel1M 435810 AACAATGTATCAGTGTCTCAGTTTCCTC 435837 i i v v vi v ?i C L1ME4a_3end#L 286 AGCAGTGTATGAGAGTGCCCGTTTCNCC 259 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 28.60 CpG sites = 43, Kimura (unadjusted) = 29.09 Transitions / transversions = 1.65 (43/26) Gap_init rate = 0.08 (24 / 300), avg. gap size = 3.33 (80 / 24) 404 21.68 24.24 2.18 chr3ptel1M 435571 435834 (564166) C L1ME4c_3end#LINE/L1 (248) 582 262 m_b120s551i14 4419 chr3ptel1M 435571 TTTAAAATTATTCGTCATTTTTAATAG--AAATAATATTCTATT-ACTTC 435617 i v ---- i --iv i i- v ?v C L1ME4c_3end#L 582 TTCATAATTAT----CATTTTTAATGGCTGCATAATATTCCATCGAGTNG 537 chr3ptel1M 435618 ATATACCATAACTTATTCAGCCATTCCC------------ACTCAG---- 435651 i i i i i ------------ i i ---- C L1ME4c_3end#L 536 ATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAGGTTG 487 chr3ptel1M 435652 TTTCCAACTCT--GCCACCACAAA-AGAGCTGCAAC---------CGTG- 435688 i i -- i ii i - iv i--------- - C L1ME4c_3end#L 486 TTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTCGTGC 437 chr3ptel1M 435689 ----ATCCTTTTCCTCCTTT---ATGATTTCCTTGGGATACAAACCCTA- 435730 ---- v i i --- v i - vi i - C L1ME4c_3end#L 436 ATATAGCTTTTTCCTTCTTTTGAATTATTTCCTTAGGATA-AATTCCCAG 388 chr3ptel1M 435731 ---TGGCACTTTGCTGGGT---------TGCACAGTCTGATAGCCCTTG- 435767 --- v -- i --------- v v i v i i - C L1ME4c_3end#L 387 AAGTGGAA--TTACTGGGTCAAAGGGTATGAACATTTTTATGGCTCTTGA 340 chr3ptel1M 435768 ---GAATAGCCAGATTGTTT--CAGAATG--TGGATCATTTTAC----CT 435806 --- v v i i -- i v -- v i v ---- i C L1ME4c_3end#L 339 TACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACANTGCC 290 chr3ptel1M 435807 CCCAACAATGTATCAGTGTCTCAGTTTC 435834 v i v ? vi C L1ME4c_3end#L 289 ACCAGCAATGTATGAGNGTACCAGTTTC 262 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 26.09 CpG sites = 36, Kimura (unadjusted) = 26.64 Transitions / transversions = 1.80 (36/20) Gap_init rate = 0.09 (23 / 263), avg. gap size = 3.09 (71 / 23) 13 19.26 2.22 4.55 chr3ptel1M 436915 436959 (563041) (GGTTCTT)n#Simple_repeat 1 44 (0) m_b120s252i14 4420 chr3ptel1M 436915 GGTTCTTGGTTCTTCCATTGGAAGTTCTTGGGTTC-TGGTCCTTGG 436959 -vi vvvi - - i (GGTTCTT)n#Si 1 GGTTCTTGGTTCTT-GGTTCTTGGTTCTT-GGTTCTTGGTTCTTGG 44 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.07 (3 / 44), avg. gap size = 1.00 (3 / 3) 531 25.31 8.31 5.50 chr3ptel1M 438816 439116 (560884) L1ME5_3end#LINE/L1 206 514 (427) m_b120s551i15 4421 chr3ptel1M 438816 TCAGATTGGCTAAGATGACAGGAAAATTCAATGAAG---AATGTTGGAGA 438862 i i v i v --- ii vi i v --- i v L1ME5_3end#LI 206 TTAGACTGGCAAAAATTA---GAAAGCTGGATAATGCCAAGTGTTGGCGA 252 chr3ptel1M 438863 GGATTTGGGAAAACTGGGACAC--ATACATAGTTGGTGAAACTGTGAACA 438910 v i ? iv i v -- i iv i ii v ii v L1ME5_3end#LI 253 GGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACT 302 chr3ptel1M 438911 GAACCAGCCATTCTGGAGAGCAATCTGGAACTA--TGCTCAAA--AAGTT 438956 ivv v v -- iv -- - L1ME5_3end#LI 303 GGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTAAG-T 351 chr3ptel1M 438957 ATCAAACTGTGCAGACCCTTTGA-CCAGCAAT---GTTTCTGG--CTATA 439000 --- --- v v - --- i i --v L1ME5_3end#LI 352 AT---AC---GCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATA 395 chr3ptel1M 439001 TCCCAAAGAGATCTTAAAGGAGG---GAAAGGACCGGCTTG-GCCAAAAT 439046 i ii v viv ---iv i-- i v -i v ii L1ME5_3end#LI 396 TCCCAAAGAAATTCTCACACAGGTCCATAAGGG--GACATGTACGAGGAT 443 chr3ptel1M 439047 GTTTGTGGTAGCCCCTGTTTGTAGTGGCCAGAATCTGG----AACTTGGT 439092 ii v i - vi i vi i vi ---- i - L1ME5_3end#LI 444 GTTCATTGCAG-CGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGG- 491 chr3ptel1M 439093 GGCTGCCCATCAGCT--GAGAATGGA 439116 -- i - -- i L1ME5_3end#LI 492 G--TGTCCATCA-CTGGGAGAGTGGA 514 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 31.81 CpG sites = 43, Kimura (unadjusted) = 31.81 Transitions / transversions = 1.48 (43/29) Gap_init rate = 0.09 (28 / 300), avg. gap size = 1.50 (42 / 28) 354 23.16 9.30 2.92 chr3ptel1M 439225 439353 (560647) C MIRb#SINE/MIR (119) 149 13 m_b120s601i19 4422 chr3ptel1M 439225 CATTTTACAGATGAG--AACTGAGGC--AAATGGG---ATTGACTTGCC- 439266 -- -- i vi --- v i - C MIRb#SINE/MIR 149 CATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCC 100 chr3ptel1M 439267 AGGATCACACAGCTAATAAAGTGCCTCAAGCCAGAGTT-GAAGTCAGATC 439315 i i i - v -vi i ii - vi i C MIRb#SINE/MIR 99 AAGGTCACACAGCTAGT-AAGTGGC-AGAGCCGGGATTCGAACCCAGGTC 52 chr3ptel1M 439316 ---CTGACCCTAGAGAGGGCACCTGTTTGCTATGGCACCAC 439353 --- i i i vvv ii- v - i iv C MIRb#SINE/MIR 51 TGTCTGACTCCAAAGCCCGTG-CTCTTT-CCACTGCACCAC 13 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 27.43 CpG sites = 19, Kimura (unadjusted) = 28.58 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.08 (10 / 128), avg. gap size = 1.60 (16 / 10) 53 0.00 0.00 0.00 chr3ptel1M 446165 446209 (553791) (AT)n#Simple_repeat 1 45 (0) c_b121s251i0 4423 chr3ptel1M 446165 ATATATATATATATATATATATATATATATATATATATATATATA 446209 (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATA 45 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 404 27.46 1.71 3.48 chr3ptel1M 446235 446351 (553649) MIRc#SINE/MIR 13 127 (141) m_b121s601i0 4424 chr3ptel1M 446235 GTGCAGTGGAT-GAGCACCAGCCCTAAAGTCAGGAGGGCCAGAGTTCAAA 446283 v- ii v i ii i i v i i - MIRc#SINE/MIR 13 GTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGA- 61 chr3ptel1M 446284 TCTGTCTAGAACTTAACACTTCCTAGCTGCATGACCCTGGACAAGTCATA 446333 --- iv ivii iv v ii i i iv MIRc#SINE/MIR 62 ---GTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACT 108 chr3ptel1M 446334 TAACCCCAATT-GCCTCAG 446351 i vv v- MIRc#SINE/MIR 109 TAACCTCTCTGAGCCTCAG 127 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 33.99 CpG sites = 20, Kimura (unadjusted) = 35.43 Transitions / transversions = 1.82 (20/11) Gap_init rate = 0.05 (6 / 116), avg. gap size = 1.00 (6 / 6) 270 31.65 1.25 1.25 chr3ptel1M 446839 446918 (553082) C L2d2_3end#LINE/L2 (73) 482 403 m_b121s601i1 4425 chr3ptel1M 446839 CAGAGAAATGGGAGATG-GGTCCCTGTCCTCAGGGAGCTCCCACTTTGGT 446887 i i ivi ii- i i iv v i i C L2d2_3end#LIN 482 CAAAGAAGTATAAGACATGGTCCCTGCCCTCAAGGAGCTTACAATCTAGT 433 chr3ptel1M 446888 TGGAGAAATGGTTCATGAAACATATATAAAG 446918 i i iiivv - ii iv C L2d2_3end#LIN 432 TGGGGAGACAAGACAT-AAACACGTGAAAAG 403 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 42.05 CpG sites = 19, Kimura (unadjusted) = 44.82 Transitions / transversions = 3.17 (19/6) Gap_init rate = 0.03 (2 / 79), avg. gap size = 1.00 (2 / 2) 215 29.35 2.13 2.13 chr3ptel1M 446856 446949 (553051) C L2b_3end#LINE/L2 (92) 374 281 m_b121s601i2 4425 chr3ptel1M 446856 GGTCCCTGTCCTCAGGGAGCTCCCACTTTGGTTGGAGAAATGGTTCATGA 446905 i v v v i i v i i ii -v v C L2b_3end#LINE 374 GGTCCCTGCCCTCACGGAGCTCACAGTCTAGTGGGGGAGACAG-ACATGT 326 chr3ptel1M 446906 AACATATATAAAGATCAGCCTGGGAG--AGGGAAGGACAAGGAAGG 446949 -?i v i v? v v v i v -- v vi ii C L2b_3end#LINE 325 AA-NCAGACAATNATAACCCAGAGTGGCAGGGTAGGACTGGGGGGG 281 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 38.71 CpG sites = 13, Kimura (unadjusted) = 38.71 Transitions / transversions = 0.93 (13/14) Gap_init rate = 0.03 (3 / 93), avg. gap size = 1.33 (4 / 3) 36 18.71 2.50 0.00 chr3ptel1M 446950 447029 (552971) (AGG)n#Simple_repeat 1 82 (0) m_b121s252i0 4426 chr3ptel1M 446950 AGGAGTAGGA-AAGGAAGACAAGGAAGGGGATGAGG-GGAGGAGAAGGGG 446997 v -i i vi i i v - i i (AGG)n#Simple 1 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG 50 chr3ptel1M 446998 AAGGAGGAGGAGGAGGAGGAGGAGGAAGATGA 447029 i i v (AGG)n#Simple 51 GAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA 82 Matrix = Unknown Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.03 (2 / 79), avg. gap size = 1.00 (2 / 2) 216 34.65 0.93 3.81 chr3ptel1M 447942 448049 (551951) L2c_3end#LINE/L2 364 468 (10) m_b121s601i3 4427 chr3ptel1M 447942 CCTCTCTGCATAGACTAAGAGGTCCTGGGTGACAGCTCCTG-ATTTTGCC 447990 ii ii - iv v v iv i vvv i -i i iii L2c_3end#LINE 364 CTCCTCCAC-TAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATT 412 chr3ptel1M 447991 TTTCTCTGTACCCCTATTGTTGCCAGGCTTGTAGTAGGAGCTTAAGAGAA 448040 iv i i i -- i- v vii v i v i v L2c_3end#LINE 413 CATCTTTGTATCCCCA--GC-GCCTGGCACATAGTAGGCGCTCAATAAAT 459 chr3ptel1M 448041 GCTTGTTGA 448049 i L2c_3end#LINE 460 GTTTGTTGA 468 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 45.23 CpG sites = 23, Kimura (unadjusted) = 49.08 Transitions / transversions = 1.77 (23/13) Gap_init rate = 0.05 (5 / 107), avg. gap size = 1.00 (5 / 5) 253 32.56 0.00 1.16 chr3ptel1M 449735 449821 (550179) L2d_3end#LINE/L2 338 423 (93) m_b121s601i4 4428 chr3ptel1M 449735 ATTACCTTCTATTGATTTTTATTTGCTAATATATGTATGTGTATTATCAC 449784 i ii v v i i v i v-i i i vv v i v L2d_3end#LINE 338 ACTGTCTTGTATTGTTCTCTAATTGTTT-CATGTGTGTTAGTCTTGTCTC 386 chr3ptel1M 449785 CCCAGGGAGAATGTCAGTTCCCTGAGATCAAGGACCA 449821 ivv v v i i iv i L2d_3end#LINE 387 CCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCA 423 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 43.66 CpG sites = 15, Kimura (unadjusted) = 43.66 Transitions / transversions = 1.15 (15/13) Gap_init rate = 0.01 (1 / 86), avg. gap size = 1.00 (1 / 1) 282 21.79 0.00 0.00 chr3ptel1M 450356 450433 (549567) C L1ME4c_3end#LINE/L1 (745) 85 8 m_b121s551i0 4429 chr3ptel1M 450356 TCATATCCTTTGACCATTTATCAATTGGGGACTGCCTTGTATTCTTATAA 450405 i v v v vvv ?v v v C L1ME4c_3end#L 85 TCATGTCCTTTGCCCATTTATCTATTGGGGTCTTGATNTTTTTCTTATCA 36 chr3ptel1M 450406 ATTTGAGTCAGTTTCCTATATATTTTAG 450433 i v i iii ? v? C L1ME4c_3end#L 35 ATTTGAATGAGCTCTTTATATANTANAG 8 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 26.99 CpG sites = 6, Kimura (unadjusted) = 26.99 Transitions / transversions = 0.55 (6/11) Gap_init rate = 0.00 (0 / 77), avg. gap size = 0.0 (0 / 0) 297 35.82 4.48 0.00 chr3ptel1M 452872 453005 (546995) C L3#LINE/CR1 (62) 4037 3898 m_b121s601i5 4430 chr3ptel1M 452872 TCTGAT-CATGAGTCTATTCCACGAT---TCTGA-AAATGCTTAGCTTGC 452916 ii - v i iv i i i---i - i v i v iv C L3#LINE/CR1 4037 TCCAATGCAGGAATCCCTTCTACAACATCCCTGACAAGTGGTCATCCAGC 3988 chr3ptel1M 452917 TGCCAATTGGATCCCACTTCTGATGGAGATCTCACTATTTCCTGAGTCAG 452966 iv iiv i iv v ivv i i v ii ?i v C L3#LINE/CR1 3987 CTCTGCTTGAACACCTCCAGTGACGGGGAGCTCACTACCTCNCGAGGCAG 3938 chr3ptel1M 452967 CTCAGCCC-TTTTGGGGTAAGATTAATTGTTTAAAAGTTC 453005 i vi - v ii ivvi i vi C L3#LINE/CR1 3937 CCCATTCCATTTTTGGACAGCTCTGATTGTTAGAAAGTTC 3898 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 48.87 CpG sites = 30, Kimura (unadjusted) = 52.04 Transitions / transversions = 1.67 (30/18) Gap_init rate = 0.03 (4 / 133), avg. gap size = 1.50 (6 / 4) 191 28.07 1.72 1.72 chr3ptel1M 453554 453611 (546389) C MIR1_Amn#SINE/MIR (158) 72 15 m_b121s601i6 4431 chr3ptel1M 453554 AGCCAGAACTTGAACTCAGTGCTTCTTAG-CCCAGTTTCTATACTCTCTC 453602 i i ? ? i vv i iv - i- vi i v C MIR1_Amn#SINE 72 AGCCGGGANTNGAACCCAGGTCTCCCGAGTCCCAGTC-CAGTGCTCTATC 24 chr3ptel1M 453603 CATTGGATC 453611 i i i C MIR1_Amn#SINE 23 CACTAGACC 15 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 32.73 CpG sites = 11, Kimura (unadjusted) = 38.77 Transitions / transversions = 2.20 (11/5) Gap_init rate = 0.04 (2 / 57), avg. gap size = 1.00 (2 / 2) 245 18.55 0.00 3.70 chr3ptel1M 455187 455242 (544758) MER63B#DNA/hAT-Tip100 383 436 (0) m_b121s502i0 4432 chr3ptel1M 455187 CTTTTTATTTTTCTTTTTGGAGAGCCGGGTGTTAAACATTTGCCTGCCCA 455236 - iiii-i v i v v MER63B#DNA/hA 383 CTTTTT-TTTTTCCCCC-AGAGAGCCGGTTGTTAAACATTTACCAGCACA 430 chr3ptel1M 455237 CCACCG 455242 i MER63B#DNA/hA 431 CCACTG 436 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 21.85 CpG sites = 7, Kimura (unadjusted) = 21.85 Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.04 (2 / 55), avg. gap size = 1.00 (2 / 2) 265 22.00 0.00 0.00 chr3ptel1M 455193 455242 (544758) MER63C#DNA/hAT-Tip100 881 930 (0) m_b121s502i1 4432 chr3ptel1M 455193 ATTTTTCTTTTTGGAGAGCCGGGTGTTAAACATTTGCCTGCCCACCACCG 455242 i iiiii v i v v i MER63C#DNA/hA 881 ATTTTTTTCCCCAGAGAGCCGGTTGTTAAACATTTACCAGCACACCACTG 930 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 27.10 CpG sites = 8, Kimura (unadjusted) = 27.10 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 43 20.50 0.00 0.00 chr3ptel1M 457203 457292 (542708) (ATCC)n#Simple_repeat 1 90 (0) m_b121s252i1 4433 chr3ptel1M 457203 ATCTATCCATTCAAGCATCCATGAATATATGCATCCATCCCTCCATTCAT 457252 i i vv vv vi v v i (ATCC)n#Simpl 1 ATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCAT 50 chr3ptel1M 457253 CCACTCATCCATCCATCTGTCCATCCATCCATTCATCCAT 457292 ii ii i (ATCC)n#Simpl 51 CCATCCATCCATCCATCCATCCATCCATCCATCCATCCAT 90 Matrix = Unknown Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.00 (0 / 89), avg. gap size = 0.0 (0 / 0) 232 13.66 0.00 4.55 chr3ptel1M 457303 457348 (542652) HAL1b#LINE/L1 2206 2249 (172) m_b121s551i1 4434 chr3ptel1M 457303 ATCCATCCATCCATCCATCTGTCCATCCATTCATGAATGTATGCAT 457348 i v i i-- v i HAL1b#LINE/L1 2206 ATCCATCCATCCATCCATCTATCCTTCTATC--TGTATATATGCAT 2249 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 15.27 CpG sites = 4, Kimura (unadjusted) = 15.27 Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.04 (2 / 45), avg. gap size = 1.00 (2 / 2) 34 22.64 2.20 1.09 chr3ptel1M 457350 457440 (542560) (CATC)n#Simple_repeat 1 92 (0) m_b121s252i2 4435 chr3ptel1M 457350 CATCCATCTATCCATCCATCCATCCATCTAT-GGTCCACCTCTCCATCTG 457398 i i -vi i iv ii (CATC)n#Simpl 1 CATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCA 50 chr3ptel1M 457399 TCTGCCCATTCATCTATCCATCCAACTGCTCCA-CCATCCATC 457440 iii i i v -vv - (CATC)n#Simpl 51 TCCATCCATCCATCCATCCATCCATC-CATCCATCCATCCATC 92 Matrix = Unknown Transitions / transversions = 2.40 (12/5) Gap_init rate = 0.03 (3 / 90), avg. gap size = 1.00 (3 / 3) 239 14.90 0.00 2.13 chr3ptel1M 457977 458024 (541976) C LTR81C#LTR/Gypsy (223) 930 884 m_b121s502i2 4436 chr3ptel1M 457977 GTGTTTCAGATTTTCTCCTCCTTCCCCCACTCCCTCCCCTAGATGGCA 458024 v i i ii - i v C LTR81C#LTR/Gy 930 GTCTTTCAGATTTCCTCCTCCTCCCCCTGCT-CCTCTCCAAGATGGCA 884 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 16.96 CpG sites = 5, Kimura (unadjusted) = 16.96 Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.02 (1 / 47), avg. gap size = 1.00 (1 / 1) 14 7.79 0.00 6.90 chr3ptel1M 458104 458134 (541866) (AAAAG)n#Simple_repeat 1 29 (0) m_b121s252i3 4437 chr3ptel1M 458104 AAAAGGAAAGAAAATGAGAAAGAAAACAAAA 458134 i - - v (AAAAG)n#Simp 1 AAAAGAAAAGAAAA-GA-AAAGAAAAGAAAA 29 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2) 771 31.10 3.12 4.04 chr3ptel1M 458336 458784 (541216) C L1ME3_3end#LINE/L1 (271) 638 194 m_b121s551i2 4438 chr3ptel1M 458336 GTCCTGCTCATTTCACTCAGCATCAGTTCATGTGAGTCTC-TCCAGGCCT 458384 iv iv i i ? vv - vi - v iiv C L1ME3_3end#LI 638 GTCTGGCTTCTTTCGCTCAACATNATGTC-TGTGAGATTCATCCATGTTG 590 chr3ptel1M 458385 TTCTGAA-ATCATCCTGTTGGTCATTTCTTATAGAACAATAATATTCCAT 458433 vi vi- ? viv- v iv i v vvvvi i C L1ME3_3end#LI 589 TTGCGTGTANCAGTA-GTTCGTTCTTTTTTATTGCTGTGTAGTATTCCAT 541 chr3ptel1M 458434 AACATTCGTATACCAGAACTTATT--------CTCCAGCTGATGGGCATC 458475 vii vvi v i -------- ? v i i i C L1ME3_3end#LI 540 TGTATGAATATACCACAATTTATTTATCCATTCTNCTGTTGATGGACATT 491 chr3ptel1M 458476 CACTCAGTTTCCAGTTTCTTGCCACTACAAAAAGGGCTGCCACAAACATT 458525 iivviv i?v i i ii v ii i ii C L1ME3_3end#LI 490 TGGGTTGTTTCCAGTTTTNGGCTATTATGAATAAAGCTGCTATGAACATT 441 chr3ptel1M 458526 TTTGCACATGTGGGTCCCTTTCTTTAAGATCTGC-TTCTTTAAGATCTCT 458574 i i ----- i vv vi v v -i v ---- C L1ME3_3end#LI 440 CTTGTACATGT-----CTTTTGGTGGACATATGCACTCATT----TCTCT 400 chr3ptel1M 458575 TTGGGATATAAGCCCAACAGAGGCACTGCTGGATCAAAGGGTATGCACA- 458623 v v -- i iv v v i i v v ii - C L1ME3_3end#LI 399 TGGGTATATA--CCTAGGAGTGGAATTGCTGGGTCATAGGGTAGGCGTAT 352 chr3ptel1M 458624 GTTTGATAACTCTTTGGGA-ATAGTTACAAATTGCTCTCCATA-TGGTTG 458671 ii----- i v - v vv iv i i v - C L1ME3_3end#LI 351 GTTTAG-----CTTTAGTAGATACTGCCAAACAGTTTTCCAAAGTGGTTG 307 chr3ptel1M 458672 GATCCGTTCACAGTTCCACCAACAATGCATTAGTGTCCCAGTTTTCCCAT 458721 v i vi i v i i i v v i vii i C L1ME3_3end#LI 306 TACCAATTTACACTCCCACCAGCAATGTATGAGAGTTCCAGTTGCTCCAC 257 chr3ptel1M 458722 ATCCCCTCTAACATTTATCATTGTCTTTTCCTGTCATCTTAGCCAGTCTG 458771 i v i i ivi vv iii v v i v C L1ME3_3end#LI 256 ATCCTCGCCAACACTTGGTATTGTCAGTCTTTTTAATTTTAGCCATTCTG 207 chr3ptel1M 458772 AGAAGTGTGTAGT 458784 ivii C L1ME3_3end#LI 206 GTGGGTGTGTAGT 194 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 40.36 CpG sites = 73, Kimura (unadjusted) = 41.57 Transitions / transversions = 1.20 (73/61) Gap_init rate = 0.06 (25 / 448), avg. gap size = 1.28 (32 / 25) 872 29.12 3.31 4.46 chr3ptel1M 458422 458784 (541216) C L1ME3A_3end#LINE/L1 (368) 552 194 m_b121s551i3 4438 chr3ptel1M 458422 ATAATATTCCATAACATTCGTATACCAGAACTTATTC-TCCA-------G 458463 i viii vvi v i i- ------- C L1ME3A_3end#L 552 ATAGTATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTACTG 503 chr3ptel1M 458464 CTGATGGGCATCCACTCAGTTTCCAGTTTCTTGCCACTACAAAAAGGGCT 458513 i i iiivvi? ??v i i i v v C L1ME3A_3end#L 502 TTGATGGACATTTGGGTNGTTTCCAGTTTNNGGCTATTACGAATAGTGCT 453 chr3ptel1M 458514 GCCACAAACATTTTTGCACATGTGGGTCCCTTTCTTTAAGATCTGCTTCT 458563 i ii i i ----- i vv v v v ----- C L1ME3A_3end#L 452 GCTATGAACATTCTTGTACATGT-----CTTTTGGTGAACATATG----- 413 chr3ptel1M 458564 TTAAG-ATCTCTTTGGGATATAAGCCCAACAGAGGCACTGCTGGATCAAA 458612 - v - i v v i vi i iv v v i i v C L1ME3A_3end#L 412 -TACGCATTTCTGTTGGGTATATACCTAGGAGTGGAATTGCTGGGTCATA 364 chr3ptel1M 458613 GGGTATGCACA-GTTTGATAACTCTTTGGGA-ATAGTTACAAATTGCTCT 458660 i - iii----- i v - v vv iv i i C L1ME3A_3end#L 363 GGGTATGCATATGTTCAG-----CTTTAGTAGATACTGCCAAACAGTTTT 319 chr3ptel1M 458661 CCATA-TGGTTGGATCCGTTCACAGTTCCACCAACAATGCATTAGTGTCC 458709 v - v i vi i v i i i i v v i C L1ME3A_3end#L 318 CCAAAGTGGTTGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTTC 269 chr3ptel1M 458710 CAGTTTTCCCATATCCCCTCTAACATTTATCATTGTCTTTTCCTGTCATC 458759 i vii i i v i i ivi v iii v i C L1ME3A_3end#L 268 CGGTTGCTCCACATCCTCGCCAACACTTGGTATTGTCTGTCTTTTTCATT 219 chr3ptel1M 458760 TTAGCCAGTCTGAGAAGTGTGTAGT 458784 v ivii C L1ME3A_3end#L 218 TTAGCCATTCTGGTGGGTGTGTAGT 194 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 37.47 CpG sites = 61, Kimura (unadjusted) = 38.45 Transitions / transversions = 1.52 (61/40) Gap_init rate = 0.06 (22 / 362), avg. gap size = 1.27 (28 / 22) 187 33.33 0.00 0.00 chr3ptel1M 459053 459112 (540888) L2#LINE/L2 2362 2421 (661) m_b121s601i7 4439 chr3ptel1M 459053 ATCTCTCCCCTAAACTCGAATACAACATCGCCAGCTGGCTGCTGGGCATC 459102 i i v ivvivii vv i v i v i L2#LINE/L2 2362 ACCTCTCCCCTGAACTCCAGACTCGTATATCCAACTGCCTACTCGACATC 2411 chr3ptel1M 459103 TCTACCTGAA 459112 i i i L2#LINE/L2 2412 TCCACTTGGA 2421 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 42.75 CpG sites = 12, Kimura (unadjusted) = 45.86 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0) 569 24.27 11.90 3.13 chr3ptel1M 459454 459806 (540194) L1ME4a_3end#LINE/L1 279 661 (210) m_b121s551i5 4440 chr3ptel1M 459454 ATACTGTTGGTGGAGTTGTGGACTGATTCAACCATTGGGGAGAGCAGTTT 459503 i i iiv ii i i v v vv i i L1ME4a_3end#L 279 ACACTGCTGGTGGGAGTGTAAATTGGTACAACCTTTCTGGAGGGCAATTT 328 chr3ptel1M 459504 GGAACTATG-ATCAAAGGACTATAAGACTGTGTATACCTT-----CCAGC 459547 v v - i v - i v ?i i ----- i L1ME4a_3end#L 329 GGCAATATGTATCAAAAGCCT-TAAAAATGTNCATACCCTTTGACCCAGT 377 chr3ptel1M 459548 AATACCACTACTAGG--TTTACACCTTAA--AAACATCCCAAAAGGGGGA 459593 v v -- i-- i -- i vi vi i v v ? L1ME4a_3end#L 378 AATTCCACTTCTAGGAATTTAT--CCTAAGGAAATAATCAGAGATGTGNA 425 chr3ptel1M 459594 -AAGGACCTATTAGTACAACGATATTTATAGCAGCTCTTTTTGTGGTGGC 459642 - i ii -- v i i v vi v i ii i L1ME4a_3end#L 426 CAAAGATTTAT--GTACAAGGATGTTCATCGCAGCATTATTTATAATAGC 473 chr3ptel1M 459643 TAAAAATGTATAAATAA----AAT--CCATGAATTGGGGGAATGGC-AAA 459685 v - iv i ---- -- vv -i ? i- L1ME4a_3end#L 474 GAAAAAT-TGGAAACAACCTAAATGTCCAACAAT-AGGGGANTGGTTAAA 521 chr3ptel1M 459686 CAAGTTATGGTATATGATTGTAATGGAATATTATTATGTTATAAGAAATG 459735 i i i vvv i? vvv ii v i ? L1ME4a_3end#L 522 TAAATTATGGTACATCCATANAATGGAATATTATGCAGCCATTAAAAATN 571 chr3ptel1M 459736 ATG----AGCAGACAGATTTCAGAAAT-ACATGG----ATAC---TGATA 459773 ----v v - v ---- - ---- i --- L1ME4a_3end#L 572 ATGTTTTCGAAGA-ATATTT----AATGACATGGGAAAATGCTCATGATA 616 chr3ptel1M 459774 CA-----AAGTGAAATGAACAGAATAC-------TGTATGCAGTA 459806 i ----- vi i i? ------- i i L1ME4a_3end#L 617 TAATGTTAAGTGAAAAAAGCAGGNTACAAAACTGTATATACAGTA 661 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 30.72 CpG sites = 49, Kimura (unadjusted) = 30.72 Transitions / transversions = 1.44 (49/34) Gap_init rate = 0.07 (26 / 352), avg. gap size = 2.08 (54 / 26) 607 26.33 6.02 2.92 chr3ptel1M 459454 459719 (540281) L1ME3Cz_3end#LINE/L1 275 548 (449) m_b121s551i4 4440 chr3ptel1M 459454 ATACTGTTGGTGGAGTTGTGGACTGATTCAACCATTGGGGAGAGCAGTTT 459503 i i iiv ii i i v i vv i L1ME3Cz_3end# 275 ACACTGCTGGTGGGAGTGTAAATTGGTACAACCACTTTGGAGAGCAATTT 324 chr3ptel1M 459504 GGAACTAT-GATCAAAGGACTATAAGACTGTGTATACCTT-----CCAGC 459547 v v -v vi --- vv - i i i ----- L1ME3Cz_3end# 325 GGCAATATCTAGTAAAG---TTGAAGA-TGCGCATACCCTACGACCCAGC 370 chr3ptel1M 459548 AATACCACTACTAGGTTTACACCTTAAAAACA---TCCCAAAAGGGGGAA 459594 v v v i i i i v --- v v v v viv L1ME3Cz_3end# 371 AATTCCACTTCTAGGTATATACCCTAGAGAAACTCTCGCACATGTGCACA 420 chr3ptel1M 459595 AGGACCTATTAGTACAACGATATTTATAGCAGCTCTTTTTGTGGTGGCTA 459644 vvi -- v i i v vi v ii i v L1ME3Cz_3end# 421 AGGAGACAT--GTACAAGGATGTTCATTGCAGCATTGTTTGTAATAGCGA 468 chr3ptel1M 459645 AAAATGTATAAA-----TAAA-ATCCATGAATTGGGGGAATGG-CAAACA 459687 - iv ----- -i v - i -i i L1ME3Cz_3end# 469 AAAAT-TGGAAACAACCTAAATGTCCATCAA-TAGGGGAATGGATAAATA 516 chr3ptel1M 459688 AGTTATGGTATATGATTGTAATGGAATATTAT 459719 i i vvv ii i L1ME3Cz_3end# 517 AATTGTGGTATATTCATACAATGGAATACTAT 548 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 32.35 CpG sites = 36, Kimura (unadjusted) = 32.93 Transitions / transversions = 1.12 (36/32) Gap_init rate = 0.05 (14 / 265), avg. gap size = 1.71 (24 / 14) 31 29.26 0.83 3.39 chr3ptel1M 459963 460083 (539917) (CTTT)n#Simple_repeat 1 118 (0) m_b121s252i4 4441 chr3ptel1M 459963 CTTTCCATTTGTCTTTCTTTCTTCCTTCCTCTCTCTCCCCCTCCTCTCAC 460012 iv i v i i i i iii -i iv (CTTT)n#Simpl 1 CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT-TTCTTTC 49 chr3ptel1M 460013 TCGCGTTTCTTTCCTTCCTTTC-TTCATTTGTTCGTTCATTCGTTCATTC 460061 iv - - i - v iv v v v v (CTTT)n#Simpl 50 TTTC-TTTCTTT-CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC 97 chr3ptel1M 460062 ATTCCTTTCTTCCTTCCTTTCT 460083 - i i i (CTTT)n#Simpl 98 -TTTCTTTCTTTCTTTCTTTCT 118 Matrix = Unknown Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.04 (5 / 120), avg. gap size = 1.00 (5 / 5) 13 5.27 0.00 0.00 chr3ptel1M 461000 461019 (538981) (AAC)n#Simple_repeat 1 20 (0) m_b121s252i5 4442 chr3ptel1M 461000 AACAATAACAACAACAACAA 461019 i (AAC)n#Simple 1 AACAACAACAACAACAACAA 20 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 49 0.00 0.00 0.00 chr3ptel1M 461027 461068 (538932) (AC)n#Simple_repeat 1 42 (0) c_b121s251i1 4443 chr3ptel1M 461027 ACACACACACACACACACACACACACACACACACACACACAC 461068 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACAC 42 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 194 26.31 3.47 12.88 chr3ptel1M 462226 462369 (537631) MamTip2b#DNA/hAT-Tip100 148 279 (170) m_b121s601i8 4444 chr3ptel1M 462226 GTAAAGGTATGG-CTCAAAAACTACCTCTATTGATATGCCAGAA-GTAAC 462273 v i v - v i v-i i i v v iv - v MamTip2b#DNA/ 148 GTTAAGGCATTGTCTCTAGAAG-GCCTCTGTTAAAATGCAAATATGTTAC 196 chr3ptel1M 462274 ATGGGCATGGGGTAACCTGGAACATGATCATTTAAGCCACTGTAAATGAT 462323 v v-- ----- ------- i i v iiv MamTip2b#DNA/ 197 CTGGGA--GGGGTAAC-----ACAT-------TAAGCCATTATCAGCCAT 232 chr3ptel1M 462324 -AAAATCTGGATGTG--TTAGTGAATATCAGATTTTCCTTCCTCTCACC 462369 - v i viii -- v-- vv i?? ?v MamTip2b#DNA/ 233 TAACACCTTAGCGTGAATTAGTT--TATCAGATTAGCTNNCCNGTCACC 279 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 31.88 CpG sites = 15, Kimura (unadjusted) = 33.05 Transitions / transversions = 0.83 (15/18) Gap_init rate = 0.15 (21 / 143), avg. gap size = 1.05 (22 / 21) 239 27.55 4.08 0.00 chr3ptel1M 463250 463347 (536653) L2-1_AMi#LINE/L2 445 546 (689) m_b121s551i6 4445 chr3ptel1M 463250 CCAGTCTTTTAGACATCTCAAACTGGATGTCCAGCGGACATCATAAACTC 463299 v i iv vvvv i v v v vi i L2-1_AMi#LINE 445 CCTGTCTCTCTGACATCTCCTCGTGGATGTCTAGCCGTCAGCTCAAGCTC 494 chr3ptel1M 463300 AGCATGTCC-AAAACAGAACTC-AAGCCTTCCACTCCTACCT--TCCCTA 463345 i v - i -v ii v i vvi -- i L2-1_AMi#LINE 495 AACATGGCCTAAAACAGAGCTCTTAATCTTCCCCCCAAGCCTNCTCCCCA 544 chr3ptel1M 463346 TT 463347 L2-1_AMi#LINE 545 TT 546 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 34.51 CpG sites = 12, Kimura (unadjusted) = 34.51 Transitions / transversions = 0.80 (12/15) Gap_init rate = 0.03 (3 / 97), avg. gap size = 1.33 (4 / 3) 221 40.35 0.88 0.00 chr3ptel1M 463357 463470 (536530) L2#LINE/L2 2530 2644 (438) m_b121s601i9 4446 chr3ptel1M 463357 TTCTCTTAGTTCTATGAGCTCATAGCCCAGAAATTATCCTGAACTCCTCA 463406 i iii viviii iv v i iv i i i vi v L2#LINE/L2 2530 TCCTTCCAGTTGCTCAGGCCAAAAACCTTGGAGTCATCCTTGACTCCTCT 2579 chr3ptel1M 463407 CTCTCACTC-CACCCCATATCCAATAGAGTGCCCAGGTCTGTTGATTTCA 463455 i v - i vv viiv v ivi i ii ii L2#LINE/L2 2580 CTTTCTCTCACACCCCACATCCAATCCATCAGCAAATCCTGTCGGCTCTA 2629 chr3ptel1M 463456 GTTTTACAACATTTC 463470 vi i v i v L2#LINE/L2 2630 CCTTCAAAATATATC 2644 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 60.23 CpG sites = 29, Kimura (unadjusted) = 62.49 Transitions / transversions = 1.71 (29/17) Gap_init rate = 0.01 (1 / 113), avg. gap size = 1.00 (1 / 1) 340 32.84 4.21 3.24 chr3ptel1M 463663 463876 (536124) L2#LINE/L2 2618 2833 (249) m_b121s601i10 4446 chr3ptel1M 463663 CTGTTGATTTTTATCTCTGCACCATCTCTCCA-AATCTGTCC-CTTCTCT 463710 i ii i - i i-- vv v v - i v - v L2#LINE/L2 2618 CTGTCGGCTCT-ACCTT--CAAAATATATCCAGAATCCGACCACTTCTCA 2664 chr3ptel1M 463711 CTTCCAACATTGTCCCCCACTCTGG-ACAGACCCTCTTTACCTCACATTT 463759 iv vv i - v i -v ii vi v i i v iii L2#LINE/L2 2665 CCACCTCCACTG-CCACCACCCTGGTCCAAGCCACCATCATCTCTCGCCT 2713 chr3ptel1M 463760 GGATCATTGTAGTAGCTGCTGGA--GATTTGCCTGCCTC-AGTCTCTTCC 463806 i i i i iv ivi -- i i v i - vi ivi L2#LINE/L2 2714 GGATTACTGCAATAGCCTCCTAACTGGTCTCCCTGCTTCCACCCTTGCCC 2763 chr3ptel1M 463807 CCCTTTAATCCATCCTCCATTTAGAAACTTCAGA---ATTTTCCTAAAAC 463853 ?i i i i v ivi v i -- --- ii ii L2#LINE/L2 2764 CCCTNCAGTCTATTCTCAACACAGCAGC--CAGAGTGATCCTTTTAAAAC 2811 chr3ptel1M 463854 CTCAGGTCTGATCATGTTACTCC 463876 v - i v i L2#LINE/L2 2812 GT-AAGTCAGATCATGTCACTCC 2833 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 43.07 CpG sites = 44, Kimura (unadjusted) = 45.86 Transitions / transversions = 1.83 (44/24) Gap_init rate = 0.06 (13 / 213), avg. gap size = 1.23 (16 / 13) 317 34.90 6.64 3.88 chr3ptel1M 464062 464362 (535638) L2b_3end#LINE/L2 147 455 (11) m_b121s601i11 4446 chr3ptel1M 464062 CTCTGGCT--ATCCCCCTTCCTT-CTTCCAATTCAACTAGTGACCTCTCT 464108 v -- v v ii- i --- iv i iv v iiv L2b_3end#LINE 147 CTCTGCCTGGAACGCCCTTCCCCACCTC---TTCGCCTGGCCAACTCCTA 193 chr3ptel1M 464109 GGCTTCCTTTAA-TCCCAACCAAAATCGCACTTT-TACAGGAATATTTCT 464156 vv v i i- i i iv vv i i- v i vvii i L2b_3end#LINE 194 CTCATCCTTCAGGTCTCAGCTCAAATGTCACCTCCTCCGGGAAGCCCTCC 243 chr3ptel1M 464157 CCAACCCCTCTTATTTCTAG--AGTCTTCCCTCTCTTAATTATTTCCTAT 464204 ii i -- vvi vi -- v vi ii viiii--ii i v L2b_3end#LINE 244 CTGACCCCCC--AGGCCGGGTCAGGCGCCCTCCTCTGGGCC--CCCCCAG 289 chr3ptel1M 464205 T--TAACCTGT-A-TCTGGAATGATAACTATTTACTTGTTTGCATG-CTC 464249 -- v i- - i- v ? i i i ---- ? i - v L2b_3end#LINE 290 TCCTACCCTGCCACTCTGGG-TTATNATTGTCT----GNTTACATGTCTG 334 chr3ptel1M 464250 TCTTCCTGAATACGTTGTGAGCTCCTTGAAG--AATTACTTT-TTTGTCT 464296 i iv v vii v i -- ivv iv?- i L2b_3end#LINE 335 TCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCT 384 chr3ptel1M 464297 CTTTT-----TGTATCACCAGTGTTTAGCTTAGTGCCTGACACATAGTAG 464341 iv i----- v i ii vi ? i i L2b_3end#LINE 385 TGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAG 434 chr3ptel1M 464342 GTACCTAATGAATGTTGATTG 464362 ii ii i i i vi L2b_3end#LINE 435 GCGCTCAGTAAATATTTGTTG 455 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 47.07 CpG sites = 64, Kimura (unadjusted) = 50.77 Transitions / transversions = 1.73 (64/37) Gap_init rate = 0.08 (24 / 300), avg. gap size = 1.33 (32 / 24) 408 30.35 6.21 1.79 chr3ptel1M 464202 464362 (535638) L2d2_3end#LINE/L2 377 544 (11) m_b121s601i12 4446 chr3ptel1M 464202 TATTTAA--CCTGTATCTGGAATGATAACTATTTACTTGTTTGCATGCTC 464249 -- i - vv v- v i v iii vi v L2d2_3end#LIN 377 TATTTAAATCTTGTAT-TGTTATT-TAACTTTTCACGTGTTTATGTCTTG 424 chr3ptel1M 464250 TCTTCCTGAATACGTTGTGAGCTCCTTGAAGA-----ATTACTTTTTTGT 464294 i ii v vi i i i----- ii - v i i L2d2_3end#LIN 425 TCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCA-TGTCTTAT 473 chr3ptel1M 464295 CTCTTTTTGTATCACC---AGTGTTTAGCTTAGTGCCTGACACATAGTAG 464341 vii i v --- i ii vi vi i L2d2_3end#LIN 474 ACTTCTTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAGTAG 523 chr3ptel1M 464342 GTACCTAATGAATGTTGATTG 464362 ii ii i i vi L2d2_3end#LIN 524 GCGCTCAATAAATATTTGTTG 544 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 38.80 CpG sites = 33, Kimura (unadjusted) = 41.20 Transitions / transversions = 2.20 (33/15) Gap_init rate = 0.04 (6 / 160), avg. gap size = 2.17 (13 / 6) 285 34.65 1.89 3.35 chr3ptel1M 464541 464752 (535248) C L2#LINE/L2 (2190) 892 684 m_b121s601i13 4447 chr3ptel1M 464541 TGGGTGGCTGAGGTAAGCTGGAGTAGTCAGA-CATGGGAAGTGCATAGAT 464589 i i v v -iv - v i v viv i C L2#LINE/L2 892 TGAGTGGCTGAGGTAGGGTGGAGGA-CAAGATCATTGGAGGAGAGGAGGT 844 chr3ptel1M 464590 TAAGGACCTGGGAATGTAGAGTATCTGAGGGAACACCAATGTGTAGGCTG 464639 i v i ivvi i iv i v i v i v vii C L2#LINE/L2 843 CAAGGAACTGAGAGGCCAGGGTATTGGAAGGATCATCTACGTGGATATTG 794 chr3ptel1M 464640 ATTTCCTCTAGA---ATGATAGGAGGAGATGGGGAGGAGAGGAAACTGTG 464686 vv vi v --- i v - vv ii v-i v C L2#LINE/L2 793 AAATCACCAAGAATTATGACAGGAGTAG-TGTTGGAGAGAGT-GACAGTG 746 chr3ptel1M 464687 AGACAGGCATCACACTCACTCAGAAAGGAATGCAAATGTATCAGGAGACC 464736 v viii v v viiv i v iv vi i - i v ii C L2#LINE/L2 745 AGCCAGGAGCTAAAATCTTCAAGGAATGAGGGGGAGTG-ACCCGGAGGTC 697 chr3ptel1M 464737 TGGTCTGGATGGGTGC 464752 - -- i iv C L2#LINE/L2 696 -GG--TAGATGACTGC 684 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 46.44 CpG sites = 36, Kimura (unadjusted) = 47.35 Transitions / transversions = 1.03 (36/35) Gap_init rate = 0.04 (9 / 211), avg. gap size = 1.22 (11 / 9) 243 27.03 2.67 1.32 chr3ptel1M 466933 467007 (532993) C L3#LINE/CR1 (251) 3848 3773 m_b121s601i14 4448 chr3ptel1M 466933 TCCCAGCTCTGCCTTCTGGGGCCAAGC--ACTAAGACCCAATCCTTCTTG 466980 i i i i vi -- v -i i i v C L3#LINE/CR1 3848 TCCTAGTTCTGCCCTCTGGAGCCACACAGAATAAG-TCTAATCCCTCTTC 3800 chr3ptel1M 466981 GACATCCAAGCTTATCAAATATTAAAA 467007 v vvv iiv vi C L3#LINE/CR1 3799 CACATGACAGCCCTTCAAATATTTGAA 3773 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 34.11 CpG sites = 11, Kimura (unadjusted) = 34.11 Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.03 (2 / 74), avg. gap size = 1.50 (3 / 2) 332 22.81 13.11 2.99 chr3ptel1M 467027 467148 (532852) L2#LINE/L2 1965 2098 (984) m_b121s601i15 4449 chr3ptel1M 467027 CCTCAGCACTCAACTGAAACTGCTCCTGCCATAAGTCACCAAGGAGCTT- 467075 i v v i i i - i v v i- L2#LINE/L2 1965 CCCCACCACTCCACCGAAACTGCTCTTGTCA-AGGTCACCAATGACCTCC 2013 chr3ptel1M 467076 ---TTACT----------GTT--TTCTCAGCTGTCATCCTTCTTGAGCCT 467110 --- i ---------- i-- iiv i v - - L2#LINE/L2 2014 ACGTTGCTAAATCCAATGGTCAATTCTCAGTCCTCATCTTACTTGA-CC- 2061 chr3ptel1M 467111 TTATCTGAAACCTTTGACATCGTGGATTACTCTTTCCT 467148 - ? v v i v iv v i ii L2#LINE/L2 2062 -TNTCAGCAGCATTTGACACAGTTGATCACTCCCTCCT 2098 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 26.91 CpG sites = 16, Kimura (unadjusted) = 28.11 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.07 (8 / 121), avg. gap size = 2.50 (20 / 8) 273 21.25 1.16 4.79 chr3ptel1M 468027 468199 (531801) HERVIP10FH#LTR/ERV1 808 974 (4128) m_b121s701i0 4450 chr3ptel1M 468027 GAAACAAAGATGAGAGAGAGAGAGAGACAGAGACAGAGAGAGAGAGACAG 468076 v i v v ii v v HERVIP10FH#LT 808 GAAAGAGAGAAGAGAGAGAGAGAGAGAGAGGAAGAGAGAGAGAGAGAAAG 857 chr3ptel1M 468077 AGACACACACACACACAGAGACAGAGACACACAGAGAGAGACAGAGACAG 468126 ------ v v v vi v v v i v i -- HERVIP10FH#LT 858 AG------AGAGAGAGGGAGAGAGAGAGACAAAGAGGGAGTCAAAG--AG 899 chr3ptel1M 468127 AGAGATAGAGACAGAGAGACAGAGACAGAGAGACAGAGAGAGAG--AGAG 468174 v iv v iv i i -- HERVIP10FH#LT 900 AGAGAGAGGCAGAGAGAGGAAGAGACAGAGAGACAAAGAGGGAGTCAGAG 949 chr3ptel1M 468175 AAGGAGGGATCAAAAGAAATTCAAA 468199 ii i vvi v v HERVIP10FH#LT 950 AGAGAGAGAGAGACAGAAAGTCAAA 974 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 24.96 CpG sites = 14, Kimura (unadjusted) = 24.96 Transitions / transversions = 0.67 (14/21) Gap_init rate = 0.05 (9 / 172), avg. gap size = 1.11 (10 / 9) 227 28.20 0.00 7.48 chr3ptel1M 470097 470211 (529789) C L1PREC2_orf2#LINE/L1 (739) 2555 2449 m_b121s551i7 4451 chr3ptel1M 470097 TTTTGCTCCTCCAAAGGAATTCTGGGATTATTTTGCATAGCGCTATGCAA 470146 v -- v v i iii vi viv iv i v i C L1PREC2_orf2# 2555 TTTTGGT--TCCATATGAATTTTAAAATAGTTTTTTCTAGTTCTGTGAAG 2508 chr3ptel1M 470147 TGCAAATGCTCGTGTGGCAGTTTGATTGTTACAAGAATGAATCTGTAAAT 470196 ---- - i - i v vv i iv v C L1PREC2_orf2# 2507 ----AATG-TCAT-TGGTAGTTTGATAGGAATAGCATTGAATCTGTAAAT 2464 chr3ptel1M 470197 TACTTTGAGTAGCAT 470211 i i i i C L1PREC2_orf2# 2463 TGCTTTGGGCAGTAT 2449 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 35.88 CpG sites = 17, Kimura (unadjusted) = 35.88 Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.07 (8 / 114), avg. gap size = 1.00 (8 / 8) 278 31.78 12.09 1.09 chr3ptel1M 470321 470899 (529101) C L1M1_orf2#LINE/L1 (981) 2313 1672 m_b121s551i8 4452 chr3ptel1M 470321 AACTTCCAGATATTTTTATTCATTTTGTAGTTATTTTTAATAGAATTTCT 470370 i i i i vvv i - i i v v i i v C L1M1_orf2#LIN 2313 AATTCCTAGGTATTTAATTTTATTT-GTGGCTATTGTAAATGGGATTACT 2265 chr3ptel1M 470371 CTTT--ATTTCCTCCTGAAATT---TATTATT--CATA----AAT----- 470404 i -- i ii v i ---i i i -- ---- ----- C L1M1_orf2#LIN 2264 TTTTTGATTTCTTTTTCAGATTGTTCACTGTTGGCATATAGAAATGCTAC 2215 chr3ptel1M 470405 ---TTTCTTTA-GTGGATTTTATTGTGTTTGTCTGCTTTTCTGAAGCTTT 470450 --- i v - v --- i iivv vi v vi v C L1M1_orf2#LIN 2214 TGATTTTTGTATGTTGATTTT---GTATCCTGCAACTTTACTGAATTTGT 2168 chr3ptel1M 470451 TAATTATCTCAATTAATTTCTTTGAGGACTTTCTGGATTTTTCTAAATAA 470500 v i vi v v i i ? v v i i i i i v C L1M1_orf2#LIN 2167 TTATCAGTTCTAATAGTTTTTTNGTGGAGTCTTTAGGTTTTTCCAAATAT 2118 chr3ptel1M 470501 ATCATCACATCTTCAACAAATCAAGACAATTTG-TTTCCCCTTTACTAAT 470549 vv i v vi iv i i -i ii i v i C L1M1_orf2#LIN 2117 AAGATCATATCATCTGCAAACAAGGATAATTTGACTTCTTCCTTTCCAAT 2068 chr3ptel1M 470550 TTGTACACCTATAATTTAATTCTATTTTCT------TCTTGCTATG---- 470589 v ii iv v vv v v ------ v v ---- C L1M1_orf2#LIN 2067 TTGGATGCCCTTTATTTCTTTCTCTTGTCTGATTGCTCTAGCTAGGACTT 2018 chr3ptel1M 470590 -TAATTCTGTGTTAATTAACAATGGAGAAAGGGGGTAACCTTG-CTTGGT 470637 -i i v i i v i v v i v - v v C L1M1_orf2#LIN 2017 CCAGTACTATGTTGAATAACAGTGGTGAAAGTGGGCATCCTTGTCGTGTT 1968 chr3ptel1M 470638 CCCTATGTTTATTCGAAAAGCATGTGGTATTAACCTTTTT-------TAT 470680 vv -i vvv i v vii v vv iv i------- i C L1M1_orf2#LIN 1967 CCAGAT-CTTAGAGGAAAGGCTTTCAGTTTTTCCCCATTCAGTATGATAC 1919 chr3ptel1M 470681 T-----TTAGTC------ATATGTTTTTTCTTATATTAAAAT-TGGCTGT 470718 ----- vi ------ vi v i i ii - viiv C L1M1_orf2#LIN 1918 TAGCTGTGGGTCTGTCGTATATGGCTTTTATTATGTTGAGGTATGTTCCT 1869 chr3ptel1M 470719 TCCATGCC-----------AGGCATAAATTATG------TGTTGCCTTTT 470751 i i -----------i iv vv i ------ vv C L1M1_orf2#LIN 1868 TCTATACCCAGTTTTTTGAGGGTTTTTATCATGAAGGGATGTTGAATTTT 1819 chr3ptel1M 470752 TTCCGGGGTTTTTCCTGAATCCATTGATATGATCATGTAGTTTAAGGTTT 470801 v viiv i i v v v v i i vv vii C L1M1_orf2#LIN 1818 ATCAAATGCTTTTTCAGCATCAATTGAAATGATCATATGGTTTTTGTCCT 1769 chr3ptel1M 470802 TCTATTATTTTAATTTGTTTAATTATATCAATTATTTTTGCA-ATGTTGA 470850 - v v i v v vv i i ii iv - i- C L1M1_orf2#LIN 1768 TC-ATTCTGTTGATATGATGTATCACATTGATTGATTT-GCGTATGTTGA 1721 chr3ptel1M 470851 AACATCCTTGCATCCCTATTATCAATACAACTTAGTTGTGACAAGTAAT 470899 v ?ivv v v v i ii ii i i C L1M1_orf2#LIN 1720 ACCATCCTTGCATCCCNGGGATAAATCCCACTTGGTCATGATGAATGAT 1672 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 42.03 CpG sites = 94, Kimura (unadjusted) = 42.33 Transitions / transversions = 1.07 (94/88) Gap_init rate = 0.04 (26 / 578), avg. gap size = 2.96 (77 / 26) 294 31.46 12.75 2.19 chr3ptel1M 470436 470890 (529110) C L1PB_orf2#LINE/L1 (1112) 2182 1681 m_b121s551i9 4452 chr3ptel1M 470436 CTTTTCTGAAGCTTTTAATTATCTCAATTAATTTCTTTGAGGACTTTCTG 470485 v vii? v i vi v vv ii ii v v i i i C L1PB_orf2#LIN 2182 CTTTGCTGAATTCNTTTATCAGTTCTAGGAGCTTTCTGGAGGAGTCTTTA 2133 chr3ptel1M 470486 GATTTTTCTAAATAAATCATCACATCTTCAACAAATCAAGACAATTTG-T 470534 iv ii ? iv i v i iviv i -i C L1PB_orf2#LIN 2132 GGGTTTTCTAGGTANACGATCATATCATCAGCAAACAGCGACAGTTTGAC 2083 chr3ptel1M 470535 TTCCCCTTTACTAATTTGTACACCTATAATTTAATTCTATTTTCTTCTTG 470584 i ii v ii iv v vv v v vv C L1PB_orf2#LIN 2082 TTCCTCTTTACCGATTTGGATGCCCTTTATTTCTTTCTCTTGTCTGATTG 2033 chr3ptel1M 470585 CTATG-----------TAATTCTGTGTTAATTAACAATGGAGAAAGGGGG 470623 v -----------i i v i i v? iv i v i v C L1PB_orf2#LIN 2032 CTCTGGCTAGGACTTCCAGTACTATGTTGAANAGAAGTGGTGAGAGTGGG 1983 chr3ptel1M 470624 TAACCTTG-CTTGGTCCCTATGTTTATTCGAAAAGCATGTGGTATTAACC 470672 i v - v v--- i-- iiiii v i-- v i i C L1PB_orf2#LIN 1982 CATCCTTGTCTTGTTCCA---GTTC--TCAGGGGGAATGC--TTTCAACT 1940 chr3ptel1M 470673 TTTT-----------TTATTTTAG-----------TCATA--TGTTTTTT 470698 i----------- ? v i ----------- -- vi C L1PB_orf2#LIN 1939 TTTCCCCATTCAGTATNATGTTGGCTGTGGGTTTGTCATAGATGGCTTTT 1890 chr3ptel1M 470699 CTTATATTAAAAT-TGGCTGTTCCATGCCA-----------GGCATAAAT 470736 v i? ii - v iv ?i i----------- iv v C L1PB_orf2#LIN 1889 ATTACNTTAAGGTATGTCCCTTNTATGCCGATTTTGCTGAGGGTTTTAAT 1840 chr3ptel1M 470737 TATG------TGTTGCCTTTTTTCCGGGGTTTTTCCTGAATCCATTGATA 470780 i i------ i vv v viiv i i v i v C L1PB_orf2#LIN 1839 CATAAAGGGATGCTGGATTTTGTCAAATGCTTTTTCTGCATCTATTGAGA 1790 chr3ptel1M 470781 TGATCATGTAGTTTAAGGTTTTCTATTATTTTAATTTGTTTAATTATATC 470830 ii -vv iv v v v v v vv i i - C L1PB_orf2#LIN 1789 TGATCATGTGATTT-TTGTTTTTAATTCTGTTTATGTGGTGTATCACAT- 1742 chr3ptel1M 470831 AATTATT--TTTGCA-ATGTTGAAACATCCTTGCATCCCTATTATCAATA 470877 -- --i i- i v i iv v vv C L1PB_orf2#LIN 1741 --TTATTGACTTGCGTATGTTAAACCATCCCTGCATCCCTGGTATGAAAC 1694 chr3ptel1M 470878 CAACTTAGTTGTG 470890 v ii ii C L1PB_orf2#LIN 1693 CCACTTGATCATG 1681 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 40.98 CpG sites = 76, Kimura (unadjusted) = 42.62 Transitions / transversions = 1.19 (76/64) Gap_init rate = 0.05 (22 / 454), avg. gap size = 3.14 (69 / 22) 362 26.08 2.34 3.55 chr3ptel1M 470730 470900 (529100) C L1MC_orf2#LINE/L1 (1455) 1839 1671 m_b121s551i10 4452 chr3ptel1M 470730 CATAAATTATGTGTTGCCTTTTTTCCGGGGTTTTTCCTGAATCCATTGAT 470779 i vi- vv v viiv i i v i C L1MC_orf2#LIN 1839 CATGAATGG-GTGTTGGATTTTGTCAAATGCTTTTTCTGCATCTATTGAT 1791 chr3ptel1M 470780 ATGATCATGTAGTTTAAGGTTTTCTATTA---TTTTAATTTGTTTAATTA 470826 ii ---v i - --- v i v v vi C L1MC_orf2#LIN 1790 ATGATCATGTGATTT---TTCTTCT-TTAGCCTGTTGATGTGATGGATTA 1745 chr3ptel1M 470827 TATCAATT-ATTTTTGCAATGTTGAAACATCCTTGCATCCCTATTATCAA 470875 i i - i - v v v ivv v C L1MC_orf2#LIN 1744 CATTAATTGATTTTCG-AATGTTGAACCAGCCTTGCATACCTGGGATAAA 1696 chr3ptel1M 470876 TACAACTTAGTTGTGACAAGTAATT 470900 v v i i iiivi C L1MC_orf2#LIN 1695 TCCCACTTGGTCGTGGTGTATAATT 1671 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 30.61 CpG sites = 22, Kimura (unadjusted) = 32.38 Transitions / transversions = 1.05 (22/21) Gap_init rate = 0.05 (8 / 170), avg. gap size = 1.25 (10 / 8) 226 21.15 1.92 0.00 chr3ptel1M 471097 471148 (528852) C L2b_3end#LINE/L2 (5) 461 409 m_b121s601i16 4453 chr3ptel1M 471097 TTCAATCAATAAACATTTACTAAATGCCTACTATGTACCACCACCTGT-C 471145 v i i i ii i i vvv? - C L2b_3end#LINE 461 TTCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGC 412 chr3ptel1M 471146 TAG 471148 C L2b_3end#LINE 411 TAG 409 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 23.38 CpG sites = 7, Kimura (unadjusted) = 26.03 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.02 (1 / 51), avg. gap size = 1.00 (1 / 1) 200 35.27 13.02 4.37 chr3ptel1M 471137 471474 (528526) L2#LINE/L2 2527 2892 (190) m_b121s601i17 4454 chr3ptel1M 471137 CCACCTGTCTAGT----CAGATTACAAATTTTTGCACTAGCCTCAAGCCT 471182 i iv i ---- iii v ii v viii v ii vi i L2#LINE/L2 2527 CCATCCTTCCAGTTGCTCAGGCCAAAAACCTTGGAGTCATCCTTGACTCC 2576 chr3ptel1M 471183 TCACTTCC-CTCACCCTCCAC--CC--TCTATCAGTTTCTGACTCTTAAC 471227 v i - v i -- -- i i----i v i iv L2#LINE/L2 2577 TCTCTTTCTCTCACACCCCACATCCAATCCATCAGC----AAATCCTGTC 2622 chr3ptel1M 471228 ACTTTTGTTTCCACATCACGTTATATGTCCA---TCC--CTGTTTGTT-- 471270 ivi i iii i v ------- i --- -- iii v i-- L2#LINE/L2 2623 GGCTCTACCTTCAAA-------ATATATCCAGAATCCGACCACTTCTCAC 2665 chr3ptel1M 471271 TGCTTGTACAAGCACCACCTGAATCGGGACC-TCAGAACTTCT-ACCTG- 471317 ii i vi viv ivii viii -i vv ii -i - L2#LINE/L2 2666 CACCTCCACTGCCACCACCCTGGTCCAAGCCACCATCATCTCTCGCCTGG 2715 chr3ptel1M 471318 ATTATTACAATAGTTTTCTAACTGGCCTCTGTGCCTGCAATTCCTT---C 471364 i i ii i i iv i v --i --- L2#LINE/L2 2716 ATTACTGCAATAGCCTCCTAACTGGTCTCCCTGCTTCCA--CCCTTGCCC 2763 chr3ptel1M 471365 TCCTT---TTTATTCCTTCATAAAGC-----------------TACACCA 471394 i ?--- i - iv i v ----------------- v v i L2#LINE/L2 2764 CCCTNCAGTCTATT-CTCAACACAGCAGCCAGAGTGATCCTTTTAAAACG 2812 chr3ptel1M 471395 CAGGTCTCATCATGTTATTTCCTTGATCAATAAGCTTCGGTGG-TTCCCA 471443 i i vv i i i ii v v vv i ii - L2#LINE/L2 2813 TAAGTCAGATCATGTCACTCCTCTGCTCAAAACCCTCCAATGGCTTCCCA 2862 chr3ptel1M 471444 -ATTACTAATGAGCTCAAATACAAACTTCTCA 471474 -v i v - - v vv v i i L2#LINE/L2 2863 TCTCACTCA-GAG-TAAAAGCCAAAGTCCTTA 2892 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 49.55 CpG sites = 76, Kimura (unadjusted) = 51.57 Transitions / transversions = 2.00 (76/38) Gap_init rate = 0.09 (31 / 337), avg. gap size = 1.94 (60 / 31) 733 26.61 8.96 2.10 chr3ptel1M 472092 472448 (527552) C L1ME4c_3end#LINE/L1 (191) 639 259 m_b121s551i11 4455 chr3ptel1M 472092 TTCTGTTTGTTTCACTCAGCATCAGTTCATGTAAATCTTTCCCAGCCTTT 472141 i v i i i vv -- iv i -iv v C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCAT--AAACATTTTCCA-TGTTG 593 chr3ptel1M 472142 TTAAAATTAGCTTGTTCGTCATT----TTTTTAATAGAACAATAATATTC 472187 i v -- -- v i v ---- i vvvv C L1ME4c_3end#L 592 CTACA--TAG--TCTTCATAATTATCATTTTTAATGGCTGCATAATATTC 547 chr3ptel1M 472188 TATTACCTTCATATACCATAACTTATTCAGCCATTCCCC----------- 472226 i iivv ?v i i i i i ----------- C L1ME4c_3end#L 546 CATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGAC 497 chr3ptel1M 472227 ACTCAG----TTTCCAACTCTTTGCCACCACAAAAAGAGCTGC--T--AC 472268 i i ---- i i i i ii i v iv -- -- C L1ME4c_3end#L 496 ATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAAC 447 chr3ptel1M 472269 ACCT--GTGGAT----CCTTTTCCCTCCTTT--ATGATTTCCTTGGGATA 472310 i -- v ---- i i i -- v i C L1ME4c_3end#L 446 ATCTTCGTGCATATAGCTTTTTCCTTCTTTTGAATTATTTCCTTAGGATA 397 chr3ptel1M 472311 CAAACCCACTAATGGCACTGCTGGATCCAAGGGTGTGCACAGTCTGATAG 472360 v vv vv i v i i i v i v v i v i C L1ME4c_3end#L 396 AATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGG 347 chr3ptel1M 472361 CCCTTTGAGA-ATAGCTCCAGATTGCTCTCCAGAATGGTGGGATCATTTC 472409 i - v -i viv i i i v v v i v i C L1ME4c_3end#L 346 CTCTT-GATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTT 298 chr3ptel1M 472410 ACAACTCCCCCAACAATGTATCAGTGTCTCAGTTTCCCC 472448 ?iv v i v ? vi v C L1ME4c_3end#L 297 ACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCACC 259 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 32.49 CpG sites = 51, Kimura (unadjusted) = 33.86 Transitions / transversions = 1.21 (51/42) Gap_init rate = 0.05 (17 / 356), avg. gap size = 2.35 (40 / 17) 447 31.92 10.73 2.95 chr3ptel1M 472096 472505 (527495) C L1MD2_3end#LINE/L1 (473) 633 193 m_b121s551i12 4455 chr3ptel1M 472096 GTTTGTTTCACTCAGCATCAGTTCATGTAAATCTTTCCCAGCCTTTTTAA 472145 i v v v i v vv i iv v -- v iv C L1MD2_3end#LI 633 GCTTTTTTCACTCAGCATAATTCCCTTGAGATCCATCCAAG--TTGTTGC 586 chr3ptel1M 472146 AATTAGC--TTGTTCGTCATTTTTTTAATAGAACAATAATATTCTATTAC 472193 ivv v -- v -- ii v v vvv i i i vii C L1MD2_3end#LI 585 GTGTATCAATAGTTCGT--TCCTTTTTATTGCTGAGTAGTATTCCATGGT 538 chr3ptel1M 472194 CTTCATATACCATAACTTATTCAGCCATTC-CCCACT------CA----- 472231 v vv i i ii i i i - ii ------ ----- C L1MD2_3end#LI 537 ATGGATGTACCACAGTTTGTTTAACCATTCACCCGTTGAAGGACATTTGG 488 chr3ptel1M 472232 ---GTTTCCAACTCTTTGCCACCACAAAAAGAGCTGCTA----CACCTGT 472274 --- ii i v i ii i v i ---- iii C L1MD2_3end#LI 487 GTTGTTTCCAGTTTTTGGCTATTACGAATAAAGCTGCTATGAACATTCGT 438 chr3ptel1M 472275 G----GATCCTTTT----CCCTCCTTTATGATTTCCTTGGGATACAAACC 472316 ---- i ii v ----v v vvv v v ii v vi C L1MD2_3end#LI 437 GTACAGGTTTTTGTGTGAACATAAGTTTTCATTTCTCTGGGATAAATGCC 388 chr3ptel1M 472317 CACTAATGGCACTGCTGGATCCAAGGGT--GTGCACAGTCTGATAGCCCT 472364 vv i vv i i vv v --? iiv ---- iii C L1MD2_3end#LI 387 CAAGAGTGCAATTGCTGGGTCGTATGGTAANTGCATGTT----TAGTTTT 342 chr3ptel1M 472365 TTGAGAATAGCT-CCAGATTGCTCTCCAGAATGGTGGGATCATTTCACAA 472413 v i --i - i i i i i iv v i i v C L1MD2_3end#LI 341 ATAAGAA--ACTGCCAAACTGTTTTCCAGAGTGGCTGTACCATTTTACAT 294 chr3ptel1M 472414 CTCCCCCAACAATGTATCAGTGTCTCAGTT--------TCCCCTCCAACT 472455 ii v i v vii -------- i v i v C L1MD2_3end#LI 293 TCCCACCAGCAATGTATGAGTGATCCAGTTTCTCCGCATCCTCGCCAGCA 244 chr3ptel1M 472456 TTTATCATTGCC----TTTCCTGCCATCTTAACCATTCTGAGAGGTGTGA 472501 ivii i ---- ii --- i i v v C L1MD2_3end#LI 243 TTTGGTGTTGTCACTATTTTTT---ATTTTAGCCATTCTGATAGGTGTGT 197 chr3ptel1M 472502 AGTG 472505 C L1MD2_3end#LI 196 AGTG 193 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 41.25 CpG sites = 72, Kimura (unadjusted) = 43.05 Transitions / transversions = 1.31 (72/55) Gap_init rate = 0.06 (25 / 409), avg. gap size = 2.28 (57 / 25) 525 29.17 12.84 2.50 chr3ptel1M 472179 472505 (527495) C L1ME5_3end#LINE/L1 (389) 552 193 m_b121s551i13 4455 chr3ptel1M 472179 ATAATATTCTATTACCTTCATATACCATAACTTATTCAGCCATTCCCC-- 472226 i i i viiv v vi i vi iii v i i -- C L1ME5_3end#LI 552 ATAGTACTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCA 503 chr3ptel1M 472227 ---------ACTCAGTTT----CCAACTCTTTGCCACCACAAAAAGAGCT 472263 --------- i v ---- iii v iv C L1ME5_3end#LI 502 GTGATGGACACCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCT 453 chr3ptel1M 472264 GC--T--ACACCTGTGGATCCTTTTCCCT------CCTTTATGA---TTT 472300 -- -- i ivi v - v v i ------ v i --- C L1ME5_3end#LI 452 GCAATGAACATCCTCGTA-CATGTCCCCTTATGGACCTGTGTGAGAATTT 404 chr3ptel1M 472301 CCTTGGGATACAAACCCACTAATGGCACTGCTGGATCCAAGGGTGTGCAC 472350 i i v vv ii v i i vv i ii C L1ME5_3end#LI 403 CTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATGCGT 354 chr3ptel1M 472351 AGTCTGATAGCCCTTTGA--GAATAGCTCCAGATTGCTCTCCAGAATGGT 472398 vv -- i--- --i i viv i C L1ME5_3end#LI 353 ATACT--TAA---TTTGACTAAGTACTGCCAGATTGCTCTCCAGAATGGC 309 chr3ptel1M 472399 GGGATCATTTCACAACTCCC-CCAACAATGTATCAGTGTCTCAGTTTCCC 472447 v v i v ii - - i i i v v ii vi ? C L1ME5_3end#LI 308 TGCACCAGTCTAC-ACTCCCACCAGCAGTGCATGAGGGTTCCTATNTCCC 260 chr3ptel1M 472448 --------CTCCAACTTTTATCATTGCC---TTTCCTGCCATCTTAACCA 472486 -------- v vi iv ii ---i i i-- i vi C L1ME5_3end#LI 259 CACATCCTCGCCAACACTTGGCATTATCCAGCTTTCTA--ATTTTTGCCA 212 chr3ptel1M 472487 TTCTGAGAGGTGTGAAGTG 472505 v i v i C L1ME5_3end#LI 211 GTCTAATAGGTGTAAAGTG 193 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 36.38 CpG sites = 57, Kimura (unadjusted) = 38.49 Transitions / transversions = 1.58 (57/36) Gap_init rate = 0.06 (20 / 326), avg. gap size = 2.55 (51 / 20) 220 30.48 11.11 1.27 chr3ptel1M 472507 472722 (527278) L3#LINE/CR1 3839 4075 (24) m_b121s601i18 4456 chr3ptel1M 472507 AGAAGGAGGAGAAA-GAGTGGAAGTTAGAAGGAGGCTGACTGAGG---AA 472552 vv vv - i v i v i vv --- L3#LINE/CR1 3839 AGAACTAGGACCAATGGGTGGAAGTTACAGGGAGGCAGATTTCGGCTCAA 3888 chr3ptel1M 472553 ACTTATGAGGCAATGCCTGA-GGTGAGCAGTTGTGCAGAA--GGAGCAGC 472599 vv v v i v v vi i -ii v - i v i -- iii v L3#LINE/CR1 3889 TATAAGGAAGAACTTTCTAACAATCAG-AGCTGTCCAAAAATGGAATGGG 3937 chr3ptel1M 472600 CTGCCTCCTGAGG-AGAG-GCTCCAC--CCCGGGTGG---------AGAG 472636 v? - v - v -- v v v --------- L3#LINE/CR1 3938 CTGCCTCGNGAGGTAGTGAGCTCCCCGTCACTGGAGGTGTTCAAGCAGAG 3987 chr3ptel1M 472637 TCTGGAGAACCATTTGTCTGGGGCATCCCTGAGGGAATTCCTGTCTGTTG 472686 v vi i v iii iviv i i --ii L3#LINE/CR1 3988 GCTGGATGACCACTTGTCAGGGATGTTGTAGAAGGGATTCCTG--CATTG 4035 chr3ptel1M 472687 GG-GGGAG--TGAGCTACAAG-TCACCGAGATCCCTCTCA 472722 i- -- ii v v -i v ii i ii L3#LINE/CR1 4036 GATGGGAGGTTGGACTAGATGACCTCTAAGGTCCCTTCCA 4075 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 40.00 CpG sites = 33, Kimura (unadjusted) = 40.00 Transitions / transversions = 1.03 (33/32) Gap_init rate = 0.07 (14 / 215), avg. gap size = 1.93 (27 / 14) 410 29.38 20.70 0.88 chr3ptel1M 473337 473621 (526379) C L3#LINE/CR1 (615) 3484 3144 m_b121s601i19 4457 chr3ptel1M 473337 AGTCACATCAAGCTGCTGATTCCCATTGAGTTTCCAGTCTACCCAGACCA 473386 i vi i ii vi i v i v iv i v C L3#LINE/CR1 3484 AGCCACATCACACTGTTGGCTCATATTGAGCTTGCGGTCAACTAAAACCC 3435 chr3ptel1M 473387 ATCGATCTTTT---------CT-CTCC--AGACAAATCCATTCAATGGCG 473424 v v i --------- - v -- v i vi v vvi C L3#LINE/CR1 3434 CTAGGTCTTTTTCACGTGAACTGCTGCTAAGCCAGATCCTCTCCATCCTG 3385 chr3ptel1M 473425 T-CTCTT----TTGA--TTTTACATCCAGATGTGAGATTTTACA------ 473461 - iv ---- -- iv i i i iii i ------ C L3#LINE/CR1 3384 TACTTGTGCAGTTGATTTTTTGAACCTAAATGCAGGACTTTACATTTATC 3335 chr3ptel1M 473462 --------------------TGGGTTTGGTCC--CGTTTCGTAGCCTTTG 473489 -------------------- v i i -- i -- v v C L3#LINE/CR1 3334 CCTGTTAAATTTCATCTTGTTGGTTTCGGCCCATCGTTCC--AGCCTGTC 3287 chr3ptel1M 473490 AAAATCTCTTTGGATTAGGATTCAATCATCCAGCTTGTTAAC--GTGCTC 473537 i i ?i i ivv vi ? v i i --viv C L3#LINE/CR1 3286 GAGATCNTTTTGAATCTTGATTCTGTCATCCANCGTATTAGCTATCCCTC 3237 chr3ptel1M 473538 TCA--TTTGTATCTTCTGCAGATGGGACAACCATAACTTCTCTG-CTG-- 473582 i -- i v i vv i v iv v - v-- C L3#LINE/CR1 3236 CCAGCTTTGTGTCATCTGCAAATTTGATAAGCATGCCTTCTATGTCTTCA 3187 chr3ptel1M 473583 ---GAGTCGTC-AGAGGATTG-TGACCAGGACCAGGACCAGGAA 473621 ---i i i- v ii v - v - i i i C L3#LINE/CR1 3186 TCCAAGTCATTGATAAAAATGTTGAACAGGA-CAGGGCCAAGGA 3144 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 36.95 CpG sites = 48, Kimura (unadjusted) = 38.73 Transitions / transversions = 1.37 (48/35) Gap_init rate = 0.07 (19 / 284), avg. gap size = 3.26 (62 / 19) 55 4.92 0.00 1.56 chr3ptel1M 473780 473844 (526156) (TG)n#Simple_repeat 1 64 (0) c_b121s251i2 4458 chr3ptel1M 473780 TGTGTGAGTGTGTATGAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 473829 v i v (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr3ptel1M 473830 TGTGTGTGTGATGTG 473844 - (TG)n#Simple_ 51 TGTGTGTGTG-TGTG 64 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.02 (1 / 64), avg. gap size = 1.00 (1 / 1) 221 28.84 1.63 4.17 chr3ptel1M 475769 475891 (524109) L3#LINE/CR1 1343 1462 (2637) m_b121s601i20 4459 chr3ptel1M 475769 GATATCAGCAGAGTCACTAAG-CCTGGGGGGTTGGGCTTTCTTGTCTAGA 475817 v vvi vi ii - i v v vi - v v i L3#LINE/CR1 1343 GATCTCATAGGTATCACCGAGACTTGGTGGGATGGGACT-CATGACTGGA 1391 chr3ptel1M 475818 AGGGGGCAGTGAAAGTTTAAAGCCTGGTCAGGAGGAGAAACAGAT-TATT 475866 viv ii i vv ? v i v ii --- - ? L3#LINE/CR1 1392 ATACGGCGATGGAAGGGTANACCTTGTTCAAAAG---AAACAGATCTANT 1438 chr3ptel1M 475867 CTGAGGGGAGAGGAGAAGAGCACTG 475891 vvi - ? iv L3#LINE/CR1 1439 AGAAGGGGAG-GNAGAGTAGCACTG 1462 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 35.07 CpG sites = 16, Kimura (unadjusted) = 37.91 Transitions / transversions = 0.89 (16/18) Gap_init rate = 0.06 (7 / 122), avg. gap size = 1.00 (7 / 7) 657 26.29 6.51 5.83 chr3ptel1M 476142 476448 (523552) L1ME5_3end#LINE/L1 206 514 (427) m_b121s551i14 4460 chr3ptel1M 476142 TCAGATTGGCTAAGATGACAGGAAAATTCAATGAAG---AATGTTGGAGA 476188 i i v i v --- ii vi i v --- i v L1ME5_3end#LI 206 TTAGACTGGCAAAAATTA---GAAAGCTGGATAATGCCAAGTGTTGGCGA 252 chr3ptel1M 476189 GGATTTGGGAAAACTGGGACAC--ATACATAGTTGGTGAAACTGTGAACA 476236 v i ? iv i v -- i iv i ii v ii v L1ME5_3end#LI 253 GGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACT 302 chr3ptel1M 476237 GAACCAGCCATTCTGGAGAGCAATCTGGAACTA--TGCTCAAA--AAGTT 476282 ivv v v -- iv -- - L1ME5_3end#LI 303 GGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTAAG-T 351 chr3ptel1M 476283 ATCAAACTGTGCAGACCCTTTGA-CCAGCAAT---GTTTCTGGGCTAATA 476328 --- --- v v - --- i i ivv L1ME5_3end#LI 352 AT---AC---GCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATA 395 chr3ptel1M 476329 TCCCAAAGAGATCTTAAAGGAGG----GAAAGGGACCGGCTTGTGCCAAA 476374 i ii v viv ----v i v---- i v ii L1ME5_3end#LI 396 TCCCAAAGAAATTCTCACACAGGTCCATAAGGGGACA----TGTACGAGG 441 chr3ptel1M 476375 ATGTTTGTGGTAGCCCTGTTTGTAGTGGCCAGAATCTGGA---AACTTGA 476421 ii v i vi i vi i vi --- i i L1ME5_3end#LI 442 ATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGG 491 chr3ptel1M 476422 GTGGCTGCCCATCAGCTGGAGAATGGA 476448 ---- i viv i L1ME5_3end#LI 492 G----TGTCCATCACTGGGAGAGTGGA 514 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 33.23 CpG sites = 44, Kimura (unadjusted) = 33.23 Transitions / transversions = 1.38 (44/32) Gap_init rate = 0.08 (26 / 306), avg. gap size = 1.46 (38 / 26) 425 23.60 6.82 3.68 chr3ptel1M 476561 476692 (523308) C MIRb#SINE/MIR (119) 149 14 m_b121s601i21 4461 chr3ptel1M 476561 CATTTTACAGATGAGTAAACTGAGG--CAAATGGG---ATTGACTTGCCC 476605 v -- i vi --- v i C MIRb#SINE/MIR 149 CATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCC 100 chr3ptel1M 476606 AGGATCACACAGCTAATAAAGTGCCTCAAGCCAGAGTT-GAAGTCAGATC 476654 i i i - v -vi i ii - vi i C MIRb#SINE/MIR 99 AAGGTCACACAGCTAGT-AAGTGGC-AGAGCCGGGATTCGAACCCAGGTC 52 chr3ptel1M 476655 ---CTGACCCTAGAGAGGGCACTCTGTGTGCTATGGCACCA 476692 --- i i i vvv ii --- v i iv C MIRb#SINE/MIR 51 TGTCTGACTCCAAAGCCCGTGCTCT---TTCCACTGCACCA 14 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 27.99 CpG sites = 19, Kimura (unadjusted) = 29.13 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.07 (9 / 131), avg. gap size = 1.56 (14 / 9) 205 24.24 13.64 0.00 chr3ptel1M 480273 480338 (519662) C MIR3#SINE/MIR (16) 192 118 m_b121s601i22 4462 chr3ptel1M 480273 GAATGTCAGA--TGGTGTGTTTCCTAG----CATCC---CCAACCCCTTC 480313 -- viv vvi i ---- i--- i C MIR3#SINE/MIR 192 GAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTC 143 chr3ptel1M 480314 AGGTTATGGAGAAGGAAACTAAGGC 480338 vv ii vi i C MIR3#SINE/MIR 142 ATTTTACAGATGAGGAAACTGAGGC 118 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.76 CpG sites = 9, Kimura (unadjusted) = 29.76 Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.05 (3 / 65), avg. gap size = 3.00 (9 / 3) 246 23.33 26.73 2.40 chr3ptel1M 481544 481644 (518356) Charlie4a#DNA/hAT-Charlie 1 125 (383) m_b122s502i0 4463 chr3ptel1M 481544 CAAGAGTTCTTAATCTGGGATCCATCATGGACAGATTTCACAAGGATTGC 481593 i i i i i --- i v vii vii i Charlie4a#DNA 1 CAGGGGTTCTTAACCTGGGGTCCGT---GGATAGAATTCAGGGGGTCCGT 47 chr3ptel1M 481594 AAAC---------------------ATCTTTATTTTCA-TGGCC-----C 481616 i --------------------- - ii ----- Charlie4a#DNA 48 GAACTTGGATGGGGAAAAAAATTACATCTTTATTTTCACTAACCTCTAAC 97 chr3ptel1M 481617 TGAAACTGAACATTTCTTTTAATGATGA 481644 i v i i i v Charlie4a#DNA 98 TGAAATTTAGCATTTCCTTCAATTATGA 125 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 26.72 CpG sites = 18, Kimura (unadjusted) = 29.79 Transitions / transversions = 3.60 (18/5) Gap_init rate = 0.06 (6 / 100), avg. gap size = 5.00 (30 / 6) 327 23.68 1.32 0.00 chr3ptel1M 481658 481733 (518267) Charlie4a#DNA/hAT-Charlie 432 508 (0) m_b122s502i1 4464 chr3ptel1M 481658 TTTTTCTGAGAAGGGGTTCATAAGCTCCTGCACATTGCCTAAGGGGACTG 481707 v i i i vv v i v v ii Charlie4a#DNA 432 TTATTCTGAGAAGGGGTCCATAGGCTTCACCAGACTGCCAAAGGGGTCCA 481 chr3ptel1M 481708 TGACACATAAAAGACTCAT-ACCCCTG 481733 i v ii v v- Charlie4a#DNA 482 TGGCACAAAAAAGGTTAAGAACCCCTG 508 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 28.70 CpG sites = 9, Kimura (unadjusted) = 28.70 Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.01 (1 / 75), avg. gap size = 1.00 (1 / 1) 245 20.88 0.00 7.55 chr3ptel1M 482670 482726 (517274) C MIR#SINE/MIR (0) 262 210 m_b122s601i0 4465 chr3ptel1M 482670 AACGATAGTTAATGGACCTTTATTAAGCATCTACTATGTGCCAAGTACTG 482719 ii i ---- v i iii i i C MIR#SINE/MIR 262 AATAATAGCTAA----CATTTATTGAGCGCTTACTATGTGCCAGGCACTG 217 chr3ptel1M 482720 TGCTAAG 482726 v C MIR#SINE/MIR 216 TTCTAAG 210 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 23.00 CpG sites = 9, Kimura (unadjusted) = 25.65 Transitions / transversions = 4.50 (9/2) Gap_init rate = 0.07 (4 / 56), avg. gap size = 1.00 (4 / 4) 257 15.38 0.00 0.00 chr3ptel1M 482688 482726 (517274) C MIRb#SINE/MIR (16) 252 214 m_b122s601i1 4465 chr3ptel1M 482688 TTTATTAAGCATCTACTATGTGCCAAGTACTGTGCTAAG 482726 i iii i i C MIRb#SINE/MIR 252 TTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAG 214 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 15.16 CpG sites = 6, Kimura (unadjusted) = 18.39 Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 15 32.88 0.00 0.00 chr3ptel1M 482744 482800 (517200) (ACAC)n#Simple_repeat 1 57 (0) m_b122s252i1 4466 chr3ptel1M 482744 ACAGACACAGGGACATACACAAACACATGTTTGCGCACCCACACAAACAC 482793 v viv i v iiivii i v v (ACAC)n#Simpl 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50 chr3ptel1M 482794 ACACACA 482800 (ACAC)n#Simpl 51 ACACACA 57 Matrix = Unknown Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0) 56 0.00 0.00 0.00 chr3ptel1M 484157 484204 (515796) (TA)n#Simple_repeat 1 48 (0) c_b122s251i0 4467 chr3ptel1M 484157 TATATATATATATATATATATATATATATATATATATATATATATATA 484204 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATA 48 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 439 24.84 0.81 5.08 chr3ptel1M 484230 484352 (515648) MIRc#SINE/MIR 10 127 (141) m_b122s601i2 4468 chr3ptel1M 484230 GTGGTGCAGTGGATAGAGCACCAGCCCTAAAGTCAGGAGGGCCAGAGTTC 484279 v ii v i ii i i v i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr3ptel1M 484280 AAATCTGGTCTCAGAACTTAACACTTCCTAGCTGCATGACCCTGGACAAG 484329 i i iv v ------ iv v ii i i MIRc#SINE/MIR 60 GAGTCCCGGCTC------TGCCACTTACTAGCTGTGTGACCTTGGGCAAG 103 chr3ptel1M 484330 TCATATAACCCCAATT-GCCTCAG 484352 iv i vv v- MIRc#SINE/MIR 104 TCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 29.62 CpG sites = 18, Kimura (unadjusted) = 30.89 Transitions / transversions = 1.64 (18/11) Gap_init rate = 0.06 (7 / 122), avg. gap size = 1.00 (7 / 7) 219 28.92 2.11 8.99 chr3ptel1M 484558 484652 (515348) L3#LINE/CR1 2750 2838 (1261) m_b122s601i3 4469 chr3ptel1M 484558 CTGATTAGCTTTGCATCAATTTCTAGTAAAATTCTAGAACAGATTGCTAA 484607 i i v vi i i ii ii i i ii L3#LINE/CR1 2750 CCGGTAAGCTTGACGTCGATCCCCGGCAAAATTCTAGAACGGATTATTAA 2799 chr3ptel1M 484608 AGAAGCCAG--TGTGAACTGACATGGTTTAGAAGAAGAAACTGTCAT 484652 -v vii -- i -- ----- i i i v v L3#LINE/CR1 2800 A-CAGATGGTTTGTGAGC--AC-----TTAGAAAAGGAAGCGGTGAT 2838 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 29.25 CpG sites = 19, Kimura (unadjusted) = 38.95 Transitions / transversions = 3.17 (19/6) Gap_init rate = 0.10 (9 / 94), avg. gap size = 1.11 (10 / 9) 328 30.99 1.51 9.19 chr3ptel1M 484599 484797 (515203) L3#LINE/CR1 2836 3020 (1079) m_b122s601i4 4469 chr3ptel1M 484599 GATTGCTAAAGAAGCCAGTGTGAACTGACATGGTTTAGAAGAAGAAACTG 484648 ii -- i ii iii v ----- v v vv - L3#LINE/CR1 2836 GATCACTA--GGAGCCAGCATGGGTTCAC-----TAAGAACAAGTCA-TG 2877 chr3ptel1M 484649 TCATTCTAACCCTATTTCTTCTCTTTGAACAACAACCAAGTTATTCATCT 484698 i vv ii i i - -------ivii i viv L3#LINE/CR1 2878 CCAAACTAACCTCATTTCCTTT-TTTGA-------TAGGGTTACTAGACT 2919 chr3ptel1M 484699 GGTAGAAATGTGGGATGCTGTGGATCCTAAT-TACCTGGATTGGGGGAAG 484747 vvv v i i i - v? i - i vvi v L3#LINE/CR1 2920 GGTAGATCAGGGGAATGCCGTAGA-CANAGTGTATCTGGATTTCAGCAAG 2968 chr3ptel1M 484748 ACATCTGACAGCATTCTTCACGCTGTTCTTGTGGACA--ATGGAGAGAGA 484795 i i ivi iii i v i i -- i v L3#LINE/CR1 2969 GCATTTGACAAAGTCTCTCATGATATCCTTGTGGACAAGATGGAGAAATA 3018 chr3ptel1M 484796 TG 484797 L3#LINE/CR1 3019 TG 3020 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 40.54 CpG sites = 35, Kimura (unadjusted) = 41.53 Transitions / transversions = 1.67 (35/21) Gap_init rate = 0.10 (19 / 198), avg. gap size = 1.05 (20 / 19) 343 29.79 1.48 3.01 chr3ptel1M 484807 484941 (515059) L3#LINE/CR1 3072 3204 (895) m_b122s601i5 4469 chr3ptel1M 484807 CCCAAAAGGGAAGTGGGCACTGGATCAGTGCCATGATGGAAGGAAGTTTC 484856 vi-v ivi v ii i vvv i i i L3#LINE/CR1 3072 CCCAAAAGGTG-TTGATTAATGGATCGATGTCAACCTGGAGGGAGGTCTC 3120 chr3ptel1M 484857 TCGTGTAGCGCCCCAGGGATCTGTGTTCTGCTCAGTGCTGCTCAACATTT 484906 v vv i v v vi iv i v v i L3#LINE/CR1 3121 TAGTGGCGTGCCACAGGGCTCTGTCCTTGGCCCTGTCCTGTTCAACATTT 3170 chr3ptel1M 484907 TCCTTAATGGCAGACCAAATGA--ACTTAGAAGGCAT 484941 iv i i ---iiii -- v L3#LINE/CR1 3171 TTATCAATGAC---TTGGATGAAGACATAGAAGGCAT 3204 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 37.41 CpG sites = 21, Kimura (unadjusted) = 38.66 Transitions / transversions = 1.17 (21/18) Gap_init rate = 0.04 (5 / 134), avg. gap size = 1.20 (6 / 5) 297 34.09 12.60 1.69 chr3ptel1M 484962 485334 (514666) L3#LINE/CR1 2512 2924 (1175) m_b122s601i6 4470 chr3ptel1M 484962 CAAGACAAGTGAGGAGATTATAAAAGCAGCATCCCACTGCTCACAGTAAG 485011 i i vi i - i ivi i ivv i i L3#LINE/CR1 2512 CAAGATAGGTGAGGAGATAGTAAGAG-AGCACCTAGCCGCTTTAAATGAG 2560 chr3ptel1M 485012 TGCA-GTCACCAGAGTCAGACAAAGCTCATTGTATGGAAAATGGTAAAAA 485060 v - v ivi i viv ivi - iv v iv i v L3#LINE/CR1 2561 TTCAAGTCTCCAGGCCCAGACGAATTACATCCCA-GGGTACTGAAAGAAC 2609 chr3ptel1M 485061 TCAGTGATAAGTGGG-GCTGAAAAACTGGC----ATCTGTGAAGAAGTCA 485105 iivv -- iv- v vvi v ---- v - i L3#LINE/CR1 2610 TTGCAGAT--GTGATCGCGGAACCGCTGTCGGTAATCTTTGA-GAAATCA 2656 chr3ptel1M 485106 TGGAGCTTGAGAGAGATATCGTAGGACTTGAAAGAGGTGA-TG------- 485147 i vvi ii i ii iv i v i vi ii - ------- L3#LINE/CR1 2657 CGGAGAACGGAAGAGGTGCCAGAAGACTGGAGACGGGCAAATGTNGTNCC 2706 chr3ptel1M 485148 -ATTTTTTTAAAGGGAAGAA-----------------TACAGGC-----A 485174 - ? vv i ----------------- i ----- L3#LINE/CR1 2707 TANTTTTAAAAAGGGAAAAAAGATGGATTCTGNAAACTACAGACCGGTAA 2756 chr3ptel1M 485175 GTTGAACAT--------GGTCACATTTACAAGCAGATTATAAATGAAAAG 485216 i vi i -------- iv v ivvi i i v vv i v L3#LINE/CR1 2757 GCTTGACGTCGATCCCCGGCAAAATTCTAGAACGGATTATTAAACAGATG 2806 chr3ptel1M 485217 GACTGTGAGACCTTAGAAAGGAGAGC--TGATCACCAGGAATGAAGTCTG 485264 vi vv i ii -- i ii-v iv L3#LINE/CR1 2807 GTTTGTGAGCACTTAGAAAAGGAAGCGGTGATCACTAGGAGC-CAGCATG 2855 chr3ptel1M 485265 AGTTCCAGTCAGGTGGGGCCAGGCCAGATCAACTCCATTGCCTTATTTGG 485314 i - v v ivvii i v i ii ii v v i L3#LINE/CR1 2856 GGTT-CACTAAGAACAAGTCATGCCAAACTAACCTCATTTCCTTTTTTGA 2904 chr3ptel1M 485315 CAGCGTAACAAAATAGGTAG 485334 i v v v i iv L3#LINE/CR1 2905 TAGGGTTACTAGACTGGTAG 2924 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 43.18 CpG sites = 71, Kimura (unadjusted) = 47.27 Transitions / transversions = 1.31 (71/54) Gap_init rate = 0.05 (17 / 372), avg. gap size = 3.18 (54 / 17) 193 30.44 0.00 1.45 chr3ptel1M 485344 485413 (514587) L3#LINE/CR1 2982 3050 (1049) m_b122s601i7 4470 chr3ptel1M 485344 TTTCTTATGCTGTCTTTGTGGAGAAGATAAACAAGTAAGAACATTAATTA 485393 i i v i i v ii v i v ii - vi v L3#LINE/CR1 2982 TCTCTCATGATATCCTTGTGGACAAGATGGAGAAATATGGGC-TGGATGA 3030 chr3ptel1M 485394 AAGGACAGTTAGGGAGGTTC 485413 v v vi i L3#LINE/CR1 3031 TAGTACAGTTAGGTGGATTC 3050 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 40.09 CpG sites = 12, Kimura (unadjusted) = 40.09 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.01 (1 / 69), avg. gap size = 1.00 (1 / 1) 32 0.00 0.00 0.00 chr3ptel1M 485756 485785 (514215) (AAC)n#Simple_repeat 1 30 (0) c_b122s251i1 4471 chr3ptel1M 485756 AACAACAACAACAACAACAACAACAACAAC 485785 (AAC)n#Simple 1 AACAACAACAACAACAACAACAACAACAAC 30 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 41 0.00 0.00 0.00 chr3ptel1M 485930 485964 (514036) (AC)n#Simple_repeat 1 35 (0) c_b122s251i2 4472 chr3ptel1M 485930 ACACACACACACACACACACACACACACACACACA 485964 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACA 35 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 20 26.96 2.60 1.28 chr3ptel1M 485994 486070 (513930) (AAATAA)n#Simple_repeat 1 78 (0) m_b122s252i2 4473 chr3ptel1M 485994 AAAGAATAATCAAAA-CAAAAGGGGAA-AACAATAAGAAATAAAAACCAA 486041 v v v -v viii - v - iv (AAATAA)n#Sim 1 AAATAAAAATAAAAATAAAAATAAAAATAAAAATAA-AAATAAAAATAAA 49 chr3ptel1M 486042 ACCAAAAATAAAAATTTAAGTGAAAATAA 486070 vi vv i i (AAATAA)n#Sim 50 AATAAAAATAAAAATAAAAATAAAAATAA 78 Matrix = Unknown Transitions / transversions = 0.70 (7/10) Gap_init rate = 0.04 (3 / 76), avg. gap size = 1.00 (3 / 3) 580 33.22 4.42 1.22 chr3ptel1M 486240 486556 (513444) C L1ME4c_3end#LINE/L1 (191) 639 313 m_b122s551i0 4474 chr3ptel1M 486240 TTCTGTTTCATTTGCTCAGCCTCAGCTCATGTAAGTTTTACCATGTT-TT 486288 i iv ii i i v i vv iv vi - -i C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATAAACATTTT-CCATGTTGCT 591 chr3ptel1M 486289 CCAAAATCTACCTGCTCATCATTTCTTATAGCACAATAGTACTCCATTAC 486338 v v i v v iv i i v i vvv i i iiv C L1ME4c_3end#L 590 ACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCGA 541 chr3ptel1M 486339 ATTAATACACCACGATTTGTTCAGCCATTCCCCAACTGATGGACATCCCC 486388 i ?i ii ii ii i i v i v iivv C L1ME4c_3end#L 540 GTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAG 491 chr3ptel1M 486389 TCAATTTCCAATTCTTTATCACCACAAAAAGAGTTGCTATAAATATTTTT 486438 vivi i iiii ii i v iv i v i i i i C L1ME4c_3end#L 490 GTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTC 441 chr3ptel1M 486439 GTACACATAGGTCCTTTTCTCTTTTTT--ATGATCTCTTTGAGATATAGA 486486 i i -- i ii i -- v i i ii v vv C L1ME4c_3end#L 440 GTGCATATAG--CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAATT 393 chr3ptel1M 486487 CCTAGTAATGGTATTGCTGG----------ATGCGCAGTTTTATAGCCCT 486526 i v i v i ---------- vi v i i - C L1ME4c_3end#L 392 CCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTC- 344 chr3ptel1M 486527 TTGGT-CATAGTTTCGAATTGCTTTCCAGAA 486556 i - i v vi i i C L1ME4c_3end#L 343 TTGATACGTATTGCCAAATTGCTTTCCAAAA 313 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 44.12 CpG sites = 69, Kimura (unadjusted) = 46.78 Transitions / transversions = 1.97 (69/35) Gap_init rate = 0.03 (8 / 316), avg. gap size = 2.25 (18 / 8) 276 31.08 8.62 5.70 chr3ptel1M 486304 486593 (513407) C L1PA16_3end#LINE/L1 (341) 572 275 m_b122s551i1 4474 chr3ptel1M 486304 TCATCATTTCTTATAGCACAATAGTACTCCATTACATTAATACACCACGA 486353 i iv i i vvvi i viii vv ii iv C L1PA16_3end#L 572 TCGTTCTTTTTTATGGCTGCGTAGTATTCCATGGTGTATATGTACCACAT 523 chr3ptel1M 486354 TTTGTTCAGCCATTCCCCAACTGATGGACATCCCCTCAATT---TCCAAT 486400 v i v v v vii i --- vii --- vv C L1PA16_3end#L 522 TTTCTTTATCCAATCCACCGTTGATGGGCA---CCTAGGTTGATTCCATG 476 chr3ptel1M 486401 TCTTTATCACCACAAAAAGAGTTGCTATAAATATTTTTGTACACATAGGT 486450 iii iiiii v v i v i i vivv i ii -- C L1PA16_3end#L 475 TCTTTGCTATTGTGAATAGTGCTGCGATGAACATACGAGTGCATGT--GT 428 chr3ptel1M 486451 CCTTTT-------CTCTTTTTTATGATCTCTTTGAGATATAGACCTAGTA 486493 i ------- vv v ---- ii i - v i C L1PA16_3end#L 427 CTTTTTGGTAGAACGATTTATT----TTCCTTTGGG-TATATACCCAGTA 383 chr3ptel1M 486494 ATGGTATTGCTGG-----ATGCGCAGTTTTAT----AGCCCTTTGGTCAT 486534 v ----- - i i i ---- ii ivv - C L1PA16_3end#L 382 ATGGGATTGCTGGGTCGAATG-GTAGTTCTGTTTTAAGTTCTTTGAGAA- 335 chr3ptel1M 486535 AGTTTCGAATTGCTTTCCAGAATGTC--AAC-AA---ACATTTCTTAGAC 486578 vi i i i v i v -- - --- i ----- C L1PA16_3end#L 334 ATCTCCAAACTGCTTTCCACAGTGGCTGAACTAATTTACATTCC-----C 290 chr3ptel1M 486579 ACCAACTGTGCTTAA 486593 v iv C L1PA16_3end#L 289 ACCAACAGTGTATAA 275 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 39.08 CpG sites = 51, Kimura (unadjusted) = 41.64 Transitions / transversions = 1.50 (51/34) Gap_init rate = 0.08 (24 / 289), avg. gap size = 1.75 (42 / 24) 308 20.97 0.00 0.00 chr3ptel1M 486845 486906 (513094) MIR3#SINE/MIR 147 208 (0) m_b122s601i8 4475 chr3ptel1M 486845 GGGTTAGACTAGGTGGTTGCTGAGATGCCTTTCAACTCTTAAATTCTGTG 486894 i i i iv i i v i i v v i MIR3#SINE/MIR 147 GGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATG 196 chr3ptel1M 486895 ATTCTATGATTC 486906 MIR3#SINE/MIR 197 ATTCTATGATTC 208 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 25.37 CpG sites = 9, Kimura (unadjusted) = 25.37 Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0) 183 31.03 3.37 2.22 chr3ptel1M 486960 487048 (512952) C MIRc#SINE/MIR (6) 262 173 m_b122s601i9 4476 chr3ptel1M 486960 AATAATAGTTCACATTTATGTAAGAATCTAAAGCTTACAAAGGA--TCCG 487007 i?vi i i i iv v i v i vi-- i i C MIRc#SINE/MIR 262 AATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCGCTTTCA 213 chr3ptel1M 487008 TAGGCATTTTCTCCTTGCATTTTCTCATAGCAA-CCTATGAG 487048 i vi v v vv -- i i i - i C MIRc#SINE/MIR 212 CATACATTATCTCATTTGA--TCCTCACAACAACCCTGTGAG 173 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 40.35 CpG sites = 17, Kimura (unadjusted) = 42.45 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.05 (4 / 88), avg. gap size = 1.25 (5 / 4) 270 32.64 0.81 7.83 chr3ptel1M 487373 487495 (512505) MIRc#SINE/MIR 3 117 (151) m_b122s601i10 4477 chr3ptel1M 487373 AGACAGCATGATGTAATGGATGTCAAACAAGTCTTGGGGCTAGGAAGAAA 487422 i ii i i i vivviv vi v i ii --- MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAG--- 49 chr3ptel1M 487423 AGAAAACCTGGGTTC-AGTTCTGCTTCTGGCATAGTTTGGTTGTGTGGAC 487471 ----- - i i vi v ivvvi i i - MIRc#SINE/MIR 50 -----ACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGT-GAC 93 chr3ptel1M 487472 TATGGATAGGTCATTTAACTTCTC 487495 iv ii i i i MIRc#SINE/MIR 94 CTTGGGCAAGTCACTTAACCTCTC 117 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 43.46 CpG sites = 25, Kimura (unadjusted) = 45.16 Transitions / transversions = 2.08 (25/12) Gap_init rate = 0.08 (10 / 122), avg. gap size = 1.00 (10 / 10) 292 29.06 6.51 2.27 chr3ptel1M 488108 488276 (511724) L1ME3C_3end#LINE/L1 374 549 (321) m_b122s551i2 4478 chr3ptel1M 488108 TTCCACTGCTATGCCTGTACCCCAAAGAAA---TCAAA-----GAAAGAG 488149 v v iv i i i --- iv ----- v vi L1ME3C_3end#L 374 TTCCACTCCTAGGTATATACCCTAGAGAAACTCTCGCACGTGTGCACAAG 423 chr3ptel1M 488150 GAAACATATAGGCACAAAATAT--AGTGCAGTTTTGTTCGTAGTACCAAA 488197 i i -- - i i -- v iv i i v i L1ME3C_3end#L 424 GAGACATGTA--CA-AGAATGTTCATTGCAGCATTGTTTGTAATAGCGAA 470 chr3ptel1M 488198 GAACTGAAAACTAAGGGAATGCCCATCAGCAGGAGGAAGATCAAATGAGT 488247 i i i v vvvi i i i v ivi i i L1ME3C_3end#L 471 AAATTGGAAACAACCTAAATGTCCATCAACAGGAGAATGGATAAATAAAT 520 chr3ptel1M 488248 AAAGCTCTATGCATGATAA-GAAATACTAT 488276 viv v v v - i - i L1ME3C_3end#L 521 TGTGGTATATTCAT-ACAATGGAATACTAT 549 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.82 CpG sites = 28, Kimura (unadjusted) = 37.81 Transitions / transversions = 1.40 (28/20) Gap_init rate = 0.05 (8 / 168), avg. gap size = 1.88 (15 / 8) 17 0.00 0.00 0.00 chr3ptel1M 488509 488529 (511471) (CAT)n#Simple_repeat 1 21 (0) m_b122s252i3 4479 chr3ptel1M 488509 CATCATCATCATCATCATCAT 488529 (CAT)n#Simple 1 CATCATCATCATCATCATCAT 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 201 25.00 0.00 0.00 chr3ptel1M 488532 488579 (511421) C MIRb#SINE/MIR (11) 257 210 m_b122s601i11 4480 chr3ptel1M 488532 TAGCATTTATATAATGTCTATTATATTCCAGACACTGTGCTAAGCTCT 488579 v vv ii ii i i v i v C MIRb#SINE/MIR 257 TACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCT 210 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 28.02 CpG sites = 7, Kimura (unadjusted) = 31.04 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 406 27.87 1.61 1.61 chr3ptel1M 489298 489421 (510579) C MIR3#SINE/MIR (11) 197 74 m_b122s601i12 4481 chr3ptel1M 489298 TCATAAACTTTCAAAACTTGAATGGACTCCAGAAATCATCTAGCCCAACT 489347 i v v i i v v iii i i i C MIR3#SINE/MIR 197 TCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACC 148 chr3ptel1M 489348 TAATTCTTTTTACAGACTAGGAAACTGAAGCCTGGAGATGATG--GCAGA 489395 i-vi v iv i ii - i -- iiiv C MIR3#SINE/MIR 147 C-CCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGA-GGTGAAGTGAC 100 chr3ptel1M 489396 TTGTCCAAGACGGCAAAGAAAGTTAG 489421 i iivi v v? C MIR3#SINE/MIR 99 TTGCCCAAGGTCACACAGCNAGTTAG 74 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 36.86 CpG sites = 23, Kimura (unadjusted) = 36.86 Transitions / transversions = 2.09 (23/11) Gap_init rate = 0.02 (3 / 123), avg. gap size = 1.33 (4 / 3) 48 4.17 0.00 0.00 chr3ptel1M 489529 489578 (510422) (CA)n#Simple_repeat 1 50 (0) c_b122s251i3 4482 chr3ptel1M 489529 CACACACACACATACATACACACACACACACACACACACACACACACACA 489578 i i (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 595 27.58 4.58 3.29 chr3ptel1M 490174 490413 (509587) C L1ME2z_3end#LINE/L1 (610) 581 339 m_b122s551i3 4483 chr3ptel1M 490174 ATCAGTTTGTTCGTCATTTTTTAAGTAGAACAATAATGTTCTGTTGCTTT 490223 v- ivi -- v vvv i i i ii iv v C L1ME2z_3end#L 581 ATCAGTA-GTTCGTTCCTTTTTA--TTGCTGAGTAGTATTCCATTGTATG 535 chr3ptel1M 490224 CATATACCACAACCTGTTCAGCCAATCTCCAACTGATGGGCATCTGTATG 490273 v iii i v v vii i i viiv C L1ME2z_3end#L 534 AATATACCACAGTTTGTTTATCCATTCTCCTGTTGATGGACACCTGGGCT 485 chr3ptel1M 490274 TTTTCCAATTTTTTGCTACCATGTAAAAAGCTGCTACAAACATTTTTGCA 490323 v i v ii v v ii i i C L1ME2z_3end#L 484 GTTTCCAGTTTTTGGCTATTATGAATAAAGCTGCTATGAACATTCTTGTA 435 chr3ptel1M 490324 CACATGGGTCCTTTTCCCTCCTTAATG-----ATTTCCTTGGGATACAGA 490368 ----i i vivvv v - ----- ii v i v v C L1ME2z_3end#L 434 CA----AGTCTTTTTGTGGACATA-TGTTTTCATTTCTCTTGGGTAAATA 390 chr3ptel1M 490369 CCCAGGAATGGCACTGCTGGGTCAAAGGGTA--TGCA----CAGTTTTAT 490412 i i v i v -- i ----i C L1ME2z_3end#L 389 CCTAGGAGTGGAATTGCTGGGTCATAGGGTAGGTGTATGTTTAGTTTTAT 340 chr3ptel1M 490413 A 490413 C L1ME2z_3end#L 339 A 339 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.10 CpG sites = 36, Kimura (unadjusted) = 35.10 Transitions / transversions = 1.29 (36/28) Gap_init rate = 0.05 (11 / 239), avg. gap size = 1.73 (19 / 11) 736 28.30 0.93 0.93 chr3ptel1M 490206 490419 (509581) C L1ME4c_3end#LINE/L1 (275) 555 342 m_b122s551i4 4483 chr3ptel1M 490206 ATAATGTTCTGTTGCTTTCATATACCACAACCTGTTCAGCCAATCTCCAA 490255 i ii i vv ?v i i ii ii i i v i v C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chr3ptel1M 490256 CTGATGGGCATCTGTATGTTTTCCAATTTTTTGCTACCATGTAAAAAGCT 490305 i v i i ivi vv i ii iv v v C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCT 456 chr3ptel1M 490306 GCTACAAACATTTTTGCACACATGGGTCCTTTTCCCTCCTT--AATGATT 490353 v ii i i ii i i -- i i i -- v C L1ME4c_3end#L 455 GCAATGAACATCTTCGTGCATATAG--CTTTTTCCTTCTTTTGAATTATT 408 chr3ptel1M 490354 TCCTTGGGATACAGACCCAGGAATGGCACTGCTGGGTCAAAGGGTATGCA 490403 i v vv i i v i i v C L1ME4c_3end#L 407 TCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAA 358 chr3ptel1M 490404 CAGTTTTATAGCCCTT 490419 v i i C L1ME4c_3end#L 357 CATTTTTATGGCTCTT 342 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.00 CpG sites = 40, Kimura (unadjusted) = 37.37 Transitions / transversions = 2.00 (40/20) Gap_init rate = 0.01 (3 / 213), avg. gap size = 1.33 (4 / 3) 280 28.77 0.00 0.00 chr3ptel1M 496246 496318 (503682) C L3#LINE/CR1 (73) 4026 3954 m_b122s601i13 4484 chr3ptel1M 496246 AATCCCTGCTATACTTTTTCTGACTAGTTGTCTTCCAGTCTTTACTTGAA 496295 v i viv ii v v v i i i C L3#LINE/CR1 4026 AATCCCTTCTACAACATCCCTGACAAGTGGTCATCCAGCCTCTGCTTGAA 3977 chr3ptel1M 496296 GACCTCCAGTAACAAAGGTCCCA 496318 v i iii iv i C L3#LINE/CR1 3976 CACCTCCAGTGACGGGGAGCTCA 3954 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 35.27 CpG sites = 13, Kimura (unadjusted) = 37.53 Transitions / transversions = 1.62 (13/8) Gap_init rate = 0.00 (0 / 72), avg. gap size = 0.0 (0 / 0) 295 29.26 5.64 3.69 chr3ptel1M 497458 497936 (502064) L1M5_orf2#LINE/L1 2798 3285 (9) m_b122s551i5 4485 chr3ptel1M 497458 ACAAAAACTGTTGGAAAAACTGGAAGAGAGTATAGCAGAAACTAGACATA 497507 viv i v i vivvvi i v i v ii ?v v L1M5_orf2#LIN 2798 ACAAATGGTGCTGGAACAATTGGATATCCATATGGAAAAAAATGAANCTC 2847 chr3ptel1M 497508 GACCAATATCTTATACCGTGTACCAAGAT-AA----GGAGGGTTTGT-GA 497551 vv i i i i ii v i - ----i v v ii - L1M5_orf2#LIN 2848 GACCCCTACCTCACACCATACACAAAAATTAATTCNAGATGGATCATAGA 2897 chr3ptel1M 497552 TTTATACATAAAGGATGATACCATAAGCAAATT--AGAAGAA--CATAGA 497597 ii v ii i ? i v i -- v -- -- i L1M5_orf2#LIN 2898 CCTAAATGTAAAAGNTAAAACTATAA--AACTTCTAGAAGAAAACATAGG 2945 chr3ptel1M 497598 ATTTTTTATTTGTAAGATCTATGGATAAGGGAAGAATTTAGGACCAGAGA 497647 vvv v v i -- i vv ? i vi v ivvi v i-- L1M5_orf2#LIN 2946 AGAATATCTTCGT--GACCTTGGGNTAGGCAAAGATTTCTTAAACAGG-- 2991 chr3ptel1M 497648 AAATATAAGAGCACT---TATAAAAGGTAAAACAGATCATTTTGGTTATA 497694 v i - i ?---i iv iv v v v ii ?i L1M5_orf2#LIN 2992 ACACA-AAAAGCACNAACCATAAAAGAAAAAATTGATAAATTGGACTNCA 3040 chr3ptel1M 497695 T-AAAATTGAAGAGATTTTGCAC----AAACACAACCAATGCAGGCAAAA 497739 - i i v- i v ---- v - iv i- -- L1M5_orf2#LIN 3041 TCAAAATTAAAAAC-TTCTGCTCNTCAAAAGACA-CCGTTA-AG--AAAA 3085 chr3ptel1M 497740 TTAAAAGGGATGA-AGAGATTGAGAAAAAAAATTAG-AACAAGTATCTCT 497787 v v v v- v ? i i v v - ? vi v L1M5_orf2#LIN 3086 TGAAAAGGCAAGCCACAGANTGGGAGAAAATATTTGCAANACATATATCT 3135 chr3ptel1M 497788 GACAAAGGCATTGTTTCTTAAATATATAAAAAACT-----AAATCAAATT 497832 vv i v ivi i ----- ? -- L1M5_orf2#LIN 3136 GACAAAGGACTCGTATCCAGAATATATAAAGAACTCCTACAANTCAA--T 3183 chr3ptel1M 497833 TACAAAAATACAAGCATTCACCAATTGATAAATGGTCAAAAGATATGAAT 497882 v ? v i vi-- v? v v iv i L1M5_orf2#LIN 3184 AANAAAAAGACAAACAAC--CCAATANAAAAATGGGCAAAAGACTTGAAC 3231 chr3ptel1M 497883 AGGCCGTTTTCAGATGAAGAAAT-CAAAGTTAATCTATAGTGATATGAAA 497931 i vv iv i v v - -- iii v ivv i L1M5_orf2#LIN 3232 AGACACTTCACAAAAGAAGATATNCAAA--TGGCCAATAAGCACATGAAA 3279 chr3ptel1M 497932 A-ATGC 497936 - L1M5_orf2#LIN 3280 AGATGC 3285 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 37.56 CpG sites = 66, Kimura (unadjusted) = 38.63 Transitions / transversions = 0.96 (66/69) Gap_init rate = 0.06 (31 / 478), avg. gap size = 1.45 (45 / 31) 1009 28.93 5.01 2.85 chr3ptel1M 497803 498421 (501579) L1ME4a_3end#LINE/L1 7 638 (233) m_b122s551i6 4485 chr3ptel1M 497803 TCTTAAATATATAAAAAACT-----AAATCAAATTTACAAAAATACAAGC 497847 i v i i ----- -- v v v i i L1ME4a_3end#L 7 TCCTTAATATATAAAGAGCTCTTACAAATCAA--TAAGAAAAAGACGAAC 54 chr3ptel1M 497848 ATTCACCAATTGATAAATGGTCAAAAGATATGAATAGGCCGTTTTCAGAT 497897 -- v v v v i i i i vi iv i v L1ME4a_3end#L 55 A--CCCCAATAGAAAAATGGGCAAAGGACATGAACAGACAATTCACAAAA 102 chr3ptel1M 497898 GAAGAAAT-CAAAGTTAATCTATAGTGATATGAAAA-ATGCACTAAATCA 497945 - -- iii v ivv - iv v vv L1ME4a_3end#L 103 GAAGAAATACAAA--TGGCCAATAAACATATGAAAANATGTTCAACCTCA 150 chr3ptel1M 497946 TTA----TTAGAGAA-TACCAATTAAAACAACTCTGAGGTATCACCTCAC 497990 i ---- i i - i v vv i i ii iv L1ME4a_3end#L 151 CTAGTAATCAAAGAAATGCAAATTAAAACAACAATGAGATACCATTTTTC 200 chr3ptel1M 497991 ACTTAACATATTAATAA-GACAAAAAAGGAAACATGATA---AATGTTAG 498036 i v v iii - ivv - vvv i --- i i L1ME4a_3end#L 201 ACCTATCAAATTGGCAAAGATTTAAAAG-ATTGATAATACCCAGTGTTGG 249 chr3ptel1M 498037 AGGGGATTGGGAAAAATGGG-ATACTAATGCACTGTTGGTGGAGTTATGA 498085 v i i vv ?i i - iv v i i iiv i i L1ME4a_3end#L 250 CGAGGGTGTGGNGAAACGGGCACTCTCATACACTGCTGGTGGGAGTGTAA 299 chr3ptel1M 498086 ATGGAGTCAACCATTCTGGAGAACAATATGGAACTTTGC-CCAAAGGCTA 498134 v ivv v ii v v v v i-i i iv L1ME4a_3end#L 300 ATTGGTACAACCTTTCTGGAGGGCAATTTGGCAATATGTATCAAAAGCCT 349 chr3ptel1M 498135 TAAAATTG--CATATCCTTTGATCCAGCAATACTACTGATAGT-CTTTAT 498181 v -- i i i v i vv v-v L1ME4a_3end#L 350 TAAAAATGTNCATACCCTTTGACCCAGTAATTCCACTTCTAGGAATTTAT 399 chr3ptel1M 498182 TCCAAAG--AT-ATCAAAAAGGCGA--AAAGAATTAACTATTTGCACAAA 498226 i i i -- - i i v i ?-- v ------ i i L1ME4a_3end#L 400 CCTAAGGAAATAATCAGAGATGTGNACAAAGATTTA------TGTACAAG 443 chr3ptel1M 498227 AATATTTATAGCAGCTTTTTTTGTGGTAGCTAAGAATTGGAAATCAAAAA 498276 i i i v v v i ii v i - vvv L1ME4a_3end#L 444 GATGTTCATCGCAGCATTATTTATAATAGCGAAAAATTGGAAA-CAACCT 492 chr3ptel1M 498277 GGATGCTCAGCAACTAGGGAATGGTTAAAGAAGCAGTAGTATATTATTAT 498326 ii ii i ivi ? v iivi i i ivv ? L1ME4a_3end#L 493 AAATGTCCAACAATAGGGGANTGGTTAAATAAATTATGGTACATCCATAN 542 chr3ptel1M 498327 GATGGAATATTATGT-GCTATAAGAAATGATAT----GCAGAGTGATTTC 498371 i i- i v i ? i ---- v i - - L1ME4a_3end#L 543 AATGGAATATTATGCAGCCATTAAAAATNATGTTTTCGAAGAAT-ATTT- 590 chr3ptel1M 498372 AGAAAAACCTGGAAAGACTTACATGAATTTATGCAAAGTAAAGTGAGCAG 498421 -- vi v i i iviv vv v iv i ivi L1ME4a_3end#L 591 --AATGACATGGGAAAATGCTCATGATATAATGTTAAGTGAAAAAAGCAG 638 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 37.32 CpG sites = 99, Kimura (unadjusted) = 37.88 Transitions / transversions = 1.32 (99/75) Gap_init rate = 0.06 (34 / 618), avg. gap size = 1.44 (49 / 34) 73 1.51 0.00 0.00 chr3ptel1M 499682 499748 (500252) (GA)n#Simple_repeat 1 67 (0) c_b122s251i4 4486 chr3ptel1M 499682 GAGAGAGAGAGACAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 499731 v (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr3ptel1M 499732 GAGAGAGAGAGAGAGAG 499748 (GA)n#Simple_ 51 GAGAGAGAGAGAGAGAG 67 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.0 (0 / 0) 283 22.37 3.80 3.80 chr3ptel1M 500001 500079 (499921) C L2b_3end#LINE/L2 (18) 448 370 m_b122s601i14 4487 chr3ptel1M 500001 TATTTA---AGTGCCTACTATGTGTCAGGCACTGTTCTAAGAGCTGGGGA 500047 --- i i i ? v i v C L2b_3end#LINE 448 TATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGGGA 399 chr3ptel1M 500048 TTCAAAGAAAGACACGAGAAAGCTCCCAGTCC 500079 v iv ivii v v i --- ? i C L2b_3end#LINE 398 TACAGCGGTGAACAAGACAGA---CNCGGTCC 370 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 24.25 CpG sites = 10, Kimura (unadjusted) = 27.94 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.05 (4 / 78), avg. gap size = 1.50 (6 / 4) 202 16.29 20.00 13.33 chr3ptel1M 500004 500088 (499912) C L2c_3end#LINE/L2 (24) 454 365 m_b122s601i16 4487 chr3ptel1M 500004 TTAAGTGCCTACTATGTGTCAGGCACTGTTCTAAGAGCTGGGGATTCAAA 500053 i i i ------------ v C L2c_3end#LINE 454 TTGAGCGCCTACTATGTGCCAGGC------------GCTGGGGATACAAA 417 chr3ptel1M 500054 GA-----AAGACACG------------AGAAAGCTCCCAGTCCAATGCAG 500086 ----- ------------ iii v i i v C L2c_3end#LINE 416 GATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAGTGGAG 367 chr3ptel1M 500087 AA 500088 i C L2c_3end#LINE 366 GA 365 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 17.40 CpG sites = 9, Kimura (unadjusted) = 19.10 Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.17 (14 / 84), avg. gap size = 2.07 (29 / 14) 317 12.50 0.00 0.00 chr3ptel1M 500004 500051 (499949) C L2a_3end#LINE/L2 (24) 493 446 m_b122s601i15 4487 chr3ptel1M 500004 TTAAGTGCCTACTATGTGTCAGGCACTGTTCTAAGAGCTGGGGATTCA 500051 i i i i v v C L2a_3end#LINE 493 TTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGCGCTGGGGATACA 446 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 11.54 CpG sites = 4, Kimura (unadjusted) = 13.86 Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 234 28.16 5.83 0.00 chr3ptel1M 501657 501759 (498241) C MIRb#SINE/MIR (119) 149 41 m_b122s601i17 4488 chr3ptel1M 501657 CGTTTCACAGATGTAGACACTGAG-CT--GAGAGGTTAAGCTTCTTGTCC 501703 i i vi v - -- ivv i C MIRb#SINE/MIR 149 CATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCC 100 chr3ptel1M 501704 ACAGCCACTGGGCTAGAAACCGTCTCGGGTGGGGTTTG-ACCAAAGTC-- 501750 vi i vvi v vi v vvi vi i i - v i -- C MIRb#SINE/MIR 99 AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTG 50 chr3ptel1M 501751 TCTGGCTCC 501759 i C MIRb#SINE/MIR 49 TCTGACTCC 41 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 32.83 CpG sites = 15, Kimura (unadjusted) = 35.79 Transitions / transversions = 1.07 (15/14) Gap_init rate = 0.04 (4 / 102), avg. gap size = 1.50 (6 / 4) 707 25.40 1.05 1.05 chr3ptel1M 504254 504444 (495556) MIRb#SINE/MIR 64 254 (14) m_b122s601i18 4489 chr3ptel1M 504254 AATCTCCTCTCAGAAACTGCCTGGCTATGTGACCCTAGCCA-GTCACTTG 504302 i vv v vv vv i i i i v - i i MIRb#SINE/MIR 64 AATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTA 113 chr3ptel1M 504303 ACTTTTGCCTGCCTCAGTTTCCTCATCTGTAAAATAGAAAGAATAGTGCC 504352 i i vivv i ii v i i MIRb#SINE/MIR 114 ACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACC 163 chr3ptel1M 504353 CACCTTCCAGACTTGTTGTGTGAGGATGAAGTGAGAT-ATGTGAGATATG 504401 i iv iv -- v i - iiv vv v MIRb#SINE/MIR 164 TACCTCGCAGGGTTGT--TGTGAGGATTAAATGAGATAATGCATGTAAAG 211 chr3ptel1M 504402 TGCTTAGCATAGTGCTTGCCACATAGTAAACACTATATAAATG 504444 i i i v i i vv MIRb#SINE/MIR 212 CGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAAATG 254 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 29.17 CpG sites = 26, Kimura (unadjusted) = 31.47 Transitions / transversions = 1.18 (26/22) Gap_init rate = 0.02 (4 / 190), avg. gap size = 1.00 (4 / 4) 51 37.83 0.51 0.00 chr3ptel1M 504485 504682 (495318) (CAG)n#Simple_repeat 1 199 (0) m_b122s252i4 4490 chr3ptel1M 504485 CAG-AGAAGGAGGAGAAGGAAGAGGAGCAGCAGCAGCAGCAGCAGCAATA 504533 - v v v v v iv v ii (CAG)n#Simple 1 CAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA 50 chr3ptel1M 504534 GTAATAGCAGCAGGAACAGTAATAGTAACAGTAGCAGCAGTAATAGTAAT 504583 i ii v i i ii i i i i ii i ii (CAG)n#Simple 51 GCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGC 100 chr3ptel1M 504584 AGTAGCAGCAGCTATAGTAGTAATAATAACAACAGTAATAGTAACAGCAG 504633 i vii i i ii ii i i i ii i i (CAG)n#Simple 101 AGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG 150 chr3ptel1M 504634 CAGCAACAGCAATAGTGACAGTAACAGTAGCAGCAGCAGCAGTTGCAGC 504682 i ii iii i i i iv (CAG)n#Simple 151 CAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGC 199 Matrix = Unknown Transitions / transversions = 4.50 (45/10) Gap_init rate = 0.01 (1 / 197), avg. gap size = 1.00 (1 / 1) 49 0.00 0.00 0.00 chr3ptel1M 505374 505415 (494585) (AC)n#Simple_repeat 1 42 (0) c_b122s251i5 4491 chr3ptel1M 505374 ACACACACACACACACACACACACACACACACACACACACAC 505415 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACAC 42 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 278 20.00 3.33 0.00 chr3ptel1M 505712 505771 (494229) C MIR#SINE/MIR (0) 262 201 m_b122s601i19 4492 chr3ptel1M 505712 AATAATAGCTAGCATTTATAGGGAACCTACTATGTACGAGACAC--TCCC 505759 i v i vi i i v i -- i i C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCT 213 chr3ptel1M 505760 AAGCACTTTACA 505771 i C MIR#SINE/MIR 212 AAGCGCTTTACA 201 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 19.76 CpG sites = 9, Kimura (unadjusted) = 24.17 Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.02 (1 / 59), avg. gap size = 2.00 (2 / 1) 18 0.00 0.00 3.85 chr3ptel1M 505774 505800 (494200) (AAAT)n#Simple_repeat 1 26 (0) m_b122s252i5 4493 chr3ptel1M 505774 AAATAAAATAAATAAATAAATAAATAA 505800 - (AAAT)n#Simpl 1 AAAT-AAATAAATAAATAAATAAATAA 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.04 (1 / 26), avg. gap size = 1.00 (1 / 1) 576 28.06 8.66 3.46 chr3ptel1M 506334 506691 (493309) L1ME5_3end#LINE/L1 132 507 (434) m_b122s551i7 4494 chr3ptel1M 506334 GAAGAAGTGCTCTAAATCACT--TGATTACAGAAATGCAAATGAAGACAT 506381 ii v v i -- i i v v i v L1ME5_3end#LI 132 GAAGAGATGCTCAAACTCATTAGTAATCAGAGAAATGCAAATTAAAACAA 181 chr3ptel1M 506382 C--TAAGATCTCACCTC---CC----AGATTGGTCAACATGACTAAGAAG 506422 -- i v i i--- ---- i iv v v vv vv L1ME5_3end#LI 182 CAATGAGATATCACTTTACACCTATTAGACTGGCAAAAATTAGAAAGCTG 231 chr3ptel1M 506423 AGCCAT---AAATGTTGGAGGGGATGTGGGGAAATTGGGATACTAGTACA 506469 iiiv --- i v i ? v i iv vi i L1ME5_3end#LI 232 GATAATGCCAAGTGTTGGCGAGGATGTGGGGANATAGGAACCCTCATGCA 281 chr3ptel1M 506470 TTGTTGGTGGAGTTGTGAACTGATCCAACCCTCCTGGAGAACAACTTGAA 506519 i i iiv ii i v i v i i ii i- L1ME5_3end#LI 282 CTGCTGGTGGGAGTGTAGACTGGTGCAGCCATTCTGGAGAGCAATCTGG- 330 chr3ptel1M 506520 ACAGT-----GTCCAAATTGCTATCAAACTGCATCCCCTTTGGCCTGTCA 506564 - ----- - i-- vi v - v v i iiv L1ME5_3end#LI 331 -CAGTACTTAGTC-AAATTA--AGTATAC-GCATACCCTATGACCCAGCA 375 chr3ptel1M 506565 GTGTCTCTACTGGATTTGTTTCCCAAAGAGAT---CAAAAAGGGC----- 506606 i vi v v i v i v i --- v v v ----- L1ME5_3end#LI 376 ATTCCGCTCCTGGGTATATATCCCAAAGAAATTCTCACACAGGTCCATAA 425 chr3ptel1M 506607 GGGGA-AGGGAGGAG-ACCTTCATGTGC--CCTTCCCTTTTGTGGTGGCA 506652 - v v v - iv - -- v v--- i L1ME5_3end#LI 426 GGGGACATGTACGAGGATGTTCAT-TGCAGCGTTG---TTTGTGGTGGCG 471 chr3ptel1M 506653 AAGCATTGGAAGCCGAGGTGGGATGCTCGTCAATTGGGA 506691 ii vi i - i vv - ii i - i L1ME5_3end#LI 472 GGGAGTTGGAGG-CAACCTGGG-TGTCCATC-ACTGGGA 507 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.63 CpG sites = 54, Kimura (unadjusted) = 36.09 Transitions / transversions = 1.26 (54/43) Gap_init rate = 0.07 (24 / 357), avg. gap size = 1.83 (44 / 24) 485 30.85 3.58 3.58 chr3ptel1M 508413 508859 (491141) L1M5_orf2#LINE/L1 2848 3294 (0) m_b122s551i8 4495 chr3ptel1M 508413 GACCCACACCTAACACCGTATACCAAGATAAGATCAAAATGGGTCCAT-G 508461 vi v i i v i v iv ? i i - - L1M5_orf2#LIN 2848 GACCCCTACCTCACACCATACACAAAAATTAATTCNAGATGGATC-ATAG 2896 chr3ptel1M 508462 ATTAAGGCATAAAGAATGAGATTATAAATAAATT--AGAGGAA--CGTAG 508507 iiv iiii ii? i i i -- v -- i -- i L1M5_orf2#LIN 2897 ACCTAAATGTAAAAGNTAAAACTATAAA--ACTTCTAGAAGAAAACATAG 2944 chr3ptel1M 508508 GATAGTTTACCTCTCAGACCTGTGGAGGAGGAAGAAATTTGTGACCAAAG 508557 v i -- i iivv - i?v v i i v ---i v L1M5_orf2#LIN 2945 GAGAAT--ATCTTCGTGACCT-TGGGNTAGGCAAAGATTTCT---TAAAC 2988 chr3ptel1M 508558 ATGAACTAGAGATCATTATTGATCACAAAATAGAAAATT-------TTGA 508600 v vvi i i v i? --- i i v i ------- v L1M5_orf2#LIN 2989 AGGACACAAAAAGCACNA---ACCATAAAAGAAAAAATTGATAAATTGGA 3035 chr3ptel1M 508601 TTACATCAAATTTAAAAACCTTTGTACAAACAAAACTAATGCAAACAAGA 508650 i ? v i i iv ?vvv ivi vi iv v i L1M5_orf2#LIN 3036 CTNCATCAAAATTAAAAACTTCTGCTCNTCAAAAGACACCGTTAAGAAAA 3085 chr3ptel1M 508651 TTAGAAGGGAAGAAACAAACTGGGAAAACATTTTCACAGTTAAAGAT-TC 508699 v i v vv i ? i v v ii i-? v v - L1M5_orf2#LIN 3086 TGAAAAGGCAAGCCACAGANTGGGAGAAAATATTTGCAA-NACATATATC 3134 chr3ptel1M 508700 TGATAAAGGCCTCATTTCCAAAATATATAGAGAATTGACTCTAATTT-AT 508748 i v i v i i i -v vi ? i- L1M5_orf2#LIN 3135 TGACAAAGGACTCGTATCCAGAATATATAAAGAACT-CCTACAANTCAAT 3183 chr3ptel1M 508749 AAGAAATCAAGCCATTC--TCCAACAGATAAATGGTCAAAGGATATGAAC 508796 ? -- v vv --i i ? v v i iv L1M5_orf2#LIN 3184 AANAAA--AAGACAAACAACCCAATANAAAAATGGGCAAAAGACTTGAAC 3231 chr3ptel1M 508797 GGACAATTTTCAGATGATGAAATTGAAACTATTTCTACTCATATGAAAGA 508846 i v iv i v v v ?v iviiivv vv i ii L1M5_orf2#LIN 3232 AGACACTTCACAAAAGAAGATATNCAAATGGCCAATAAGCACATGAAAAG 3281 chr3ptel1M 508847 GTGTTCCAAATCA 508859 i i v v? L1M5_orf2#LIN 3282 ATGCTCAACNTCA 3294 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 41.15 CpG sites = 73, Kimura (unadjusted) = 42.40 Transitions / transversions = 1.22 (73/60) Gap_init rate = 0.05 (23 / 446), avg. gap size = 1.39 (32 / 23) 1530 28.14 2.21 2.02 chr3ptel1M 508713 509256 (490744) L1ME3G_3end#LINE/L1 4 548 (376) m_b122s551i9 4495 chr3ptel1M 508713 ATTTCCAAAATATATAGAGAATTGACTCTAATTTATAAGAAATCAAGCCA 508762 v i i i vviv v iv -- v L1ME3G_3end#L 4 ATATCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAA--AAGACA 51 chr3ptel1M 508763 TTCTCCAACAGATAAATGGTCAAAGGATATGAACGGACAATTTTCAGATG 508812 --vi i v v i i iv v L1ME3G_3end#L 52 --ACCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAG 99 chr3ptel1M 508813 ATGAAATTGAAACTATTTCTACTCATATGAAAGAGTGTTCCAAATCACTA 508862 v vv iviiivv vv iii i v vv L1ME3G_3end#L 100 AGGAAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTA 149 chr3ptel1M 508863 TTGATCAGAGAAATGCAAATTAAGACAACTCTGAGATACCACTACACACC 508912 v i i i vv i viv L1ME3G_3end#L 150 GTAATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACC 199 chr3ptel1M 508913 TGTCAGATTGATGACAG--GAAAAAG----TAACGGTGAATGTTGCAGGG 508956 ii iii v i--v i?---- iivi? i vv i L1ME3G_3end#L 200 CATCAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAG 249 chr3ptel1M 508957 GATGCAGGAAAACTGGAACATTGATGCATTGTGGATGGAGTTGTGAACGA 509006 i ii i v v vi v i i iv i iiv i ivi L1ME3G_3end#L 250 GGTGTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTG 299 chr3ptel1M 509007 ATCCAACCATTCTGGAGAGCAATCTGGAATTATGCCCA--AAAAGTTATC 509054 i v i ? i i i v v -- i -- v --- L1ME3G_3end#L 300 GTACAGCCNTTTTGGAGGGCAATTTGGCAGTAT--CTATTAAAATTT--- 344 chr3ptel1M 509055 AAACTGTGCATACCCTTTGATCCAGCAGTGCTACTACTGGGCTTATACCT 509104 v i i i v i v ? ?v v i i L1ME3G_3end#L 345 AAAATGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCC 394 chr3ptel1M 509105 CAAAGAGATATTCA-AGAAG-GGAAAGGGACCTATGTGCCAAAATGTTTG 509152 i ? i i i- v v - v v i ?vi i v ii ii L1ME3G_3end#L 395 TANAGAAATACTCGCACATGTGCACAAGGANGCATGTACAAGGATGTTCA 444 chr3ptel1M 509153 TGGCAGCCCTGTTTGTAGTGGCCAGAAACTGGAAACTGAA--TGGATGCC 509200 v vi i i v i i -- -- ii i L1ME3G_3end#L 445 TTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAAC--AACCTAAATGTC 492 chr3ptel1M 509201 CATCAGTTGGAGAATGGTTGGGTAAATTGTGGTATATGAATGTTATGGAA 509250 i v i iii i vv ii L1ME3G_3end#L 493 CATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAA 542 chr3ptel1M 509251 TATTAT 509256 i L1ME3G_3end#L 543 TACTAT 548 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 36.26 CpG sites = 89, Kimura (unadjusted) = 36.89 Transitions / transversions = 1.46 (89/61) Gap_init rate = 0.03 (17 / 543), avg. gap size = 1.35 (23 / 17) 1491 29.95 2.74 1.59 chr3ptel1M 508721 509341 (490659) L1ME4c_3end#LINE/L1 12 639 (191) m_b122s551i10 4495 chr3ptel1M 508721 AATATATAGAGAATTGACTCTAATTTATAAGAAA----TCAAGCCATTCT 508766 ? i ii v i v v ---- v ----i L1ME4c_3end#L 12 ANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAAGAC----C 57 chr3ptel1M 508767 CCAACAGATAAATGGTCAAAGGATATGAACGGACAATTTTCAGATGATGA 508816 i v i i iv ? v v L1ME4c_3end#L 58 CCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAGGA 107 chr3ptel1M 508817 AATTGAAACTATTTCTACTCATATGAAAGAGTGTTCCAAATCACTATTGA 508866 vv ?ivi vvvi vv i i i i v vv i v i L1ME4c_3end#L 108 AATACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTAGTAA 157 chr3ptel1M 508867 TCAGAGAAATGCAAATTAAGACAACTCTGAGATACCACTACACACCTGTC 508916 i ii vv i vi i i i L1ME4c_3end#L 158 TCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCTATT 207 chr3ptel1M 508917 AGATTGATGACAG---GAAAAAGTAACGGTG---AATGTTGCAGGGGATG 508960 i iiii v i---i v i iii i--- i vv i ? L1ME4c_3end#L 208 AAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGCTGGCGAGGNTG 257 chr3ptel1M 508961 CAGGAAAACTGGAACATTGATGCATTGTGGATGGAGTTGTGAACGAATCC 509010 i vi v ?i v i iv i vi? i ivii v L1ME4c_3end#L 258 CGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGTAC 307 chr3ptel1M 509011 AACCATTCTGGAGAGCAATCTGGAATTATGCCCAAAAAGTTATCAAACTG 509060 v i i i v v i iviv i ii v v L1ME4c_3end#L 308 AACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAAAATG 357 chr3ptel1M 509061 TGCATACCCTTTGATCCAGCAGTGCTACTACTGGGCTTATACCTCAAAGA 509110 v i i i v i v vv v i ii i L1ME4c_3end#L 358 TTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGA 407 chr3ptel1M 509111 GAT-ATTC--AAGAAGGGAAAGGGACCTATGTGC-C-AAAATGTTTGTGG 509155 i - -- i i --- i - - i ii v L1ME4c_3end#L 408 AATAATTCAAAAGAAGGAAAAAG---CTATATGCACGAAGATGTTCATTG 454 chr3ptel1M 509156 CAGCCCTGTTTGTAGTGGCCAGAAACTGGAAACTGAA--TGGATGCCCAT 509203 vi i i i i v i i -- -- ii i v L1ME4c_3end#L 455 CAGCGTTATTTATAATAGCGAAAAATTGGAAAC--AACCTAAATGTCCAA 502 chr3ptel1M 509204 CAGTTGGAGAATGGTTGGGTAAATTGTGGTATATGAATGTTATGGAATAT 509253 i v i ii i i v? iviv L1ME4c_3end#L 503 CAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATAT 552 chr3ptel1M 509254 TATTGTTCTGTAACAAATGACCAGCAGGATGAATACAGAGATGCTTGGAG 509303 vvvv ii v v iv vi v v v iiv vvi v - L1ME4c_3end#L 553 TATGCAGCCATTAAAAATGATAATTATGAAGACTATGTAGCAACATGGA- 601 chr3ptel1M 509304 AGACTTACATGAACTGATGCTGAATGAAATGAGCAGAA 509341 i iv vi vv i i i i vi L1ME4c_3end#L 602 AAATGTTTATGATATAATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 38.59 CpG sites = 108, Kimura (unadjusted) = 40.01 Transitions / transversions = 1.44 (108/75) Gap_init rate = 0.03 (18 / 620), avg. gap size = 1.50 (27 / 18) 33 16.78 2.27 4.65 chr3ptel1M 509742 509829 (490171) (AAT)n#Simple_repeat 1 86 (0) m_b122s252i6 4496 chr3ptel1M 509742 AATAAAAAGTTATAATTATTAAAAATAATAATAATAA-AATTA-AATAAA 509789 v - v - v v - v - - (AAT)n#Simple 1 AATAATAA-TAATAA-TAATAATAATAATAATAATAATAATAATAAT-AA 47 chr3ptel1M 509790 TAAAAAGCTATAATAATAATAATAATAAATTTAAAAATAA 509829 v -iv vvv v (AAT)n#Simple 48 TAATAA-TAATAATAATAATAATAATAATAATAATAATAA 86 Matrix = Unknown Transitions / transversions = 0.09 (1/11) Gap_init rate = 0.07 (6 / 87), avg. gap size = 1.00 (6 / 6) 206 34.73 0.00 1.39 chr3ptel1M 509901 509973 (490027) OldhAT1#DNA/hAT-Ac 2553 2624 (218) m_b122s601i20 4497 chr3ptel1M 509901 TCCCCCCTTTACTGAAGAGGTCTGGGCTGCTGTGTTGGGTAGCTAGCACA 509950 i i iv i i ii iv i - i v i v OldhAT1#DNA/h 2553 TCCTCCCCTCCCTAAAAAAATCCTGGCTGCCG-GCTGGCTAGCTGGCAAA 2601 chr3ptel1M 509951 CATTACTTAATACATCCATGTGC 509973 i iv vi i v i ii OldhAT1#DNA/h 2602 TACAAGCTGAAACACCTGTGTGC 2624 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 47.86 CpG sites = 18, Kimura (unadjusted) = 50.87 Transitions / transversions = 2.57 (18/7) Gap_init rate = 0.01 (1 / 72), avg. gap size = 1.00 (1 / 1) 195 22.86 0.00 0.00 chr3ptel1M 511408 511442 (488558) L2c_3end#LINE/L2 430 464 (14) m_b122s601i21 4498 chr3ptel1M 511408 CACTTAGCACACAGTAAGCACTCAATAAGTGCTTG 511442 i i i i i i i i L2c_3end#LINE 430 CGCCTGGCACATAGTAGGCGCTCAATAAATGTTTG 464 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 21.87 CpG sites = 8, Kimura (unadjusted) = 30.55 Transitions / transversions = 1.00 (8/0) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 443 20.61 5.11 4.35 chr3ptel1M 511636 511772 (488228) C Charlie1a#DNA/hAT-Charlie (0) 1455 1318 m_b122s502i2 4499 chr3ptel1M 511636 CAGTGGTTCTCAAACCTTT-GTTCTCAGTATC--TTCATGTTGATTAAAA 511682 i i - v v i -- i iii v- C Charlie1a#DNA 1455 CAGCGGTTCTCAAACTTTTTGGTCTCAGGACCCCTTTACACTC-TTAAAA 1407 chr3ptel1M 511683 AAACTATCGAGGATCTCTTCAAAGAGTTTTTGTTCACATGGGTTATATTT 511732 --i i i i --- i i ii i C Charlie1a#DNA 1406 A--TTATTGAGGACCCC---AAAGAGCTTTTGTTTATGTGGGTTATATCT 1362 chr3ptel1M 511733 ATACTTGTTTACTATATTAGAAATAAAAAAT----AACTTTTAA 511772 vvv i i v v ---- i C Charlie1a#DNA 1361 ATCGATATTTACCATATTAGAAATTAAAACTGAGAAATTTTTAA 1318 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 23.84 CpG sites = 19, Kimura (unadjusted) = 24.88 Transitions / transversions = 2.38 (19/8) Gap_init rate = 0.07 (9 / 136), avg. gap size = 1.44 (13 / 9) 19 28.14 5.11 5.11 chr3ptel1M 517110 517246 (482754) (CTCCTTT)n#Simple_repeat 1 137 (0) m_b122s252i7 4500 chr3ptel1M 517110 CTCCCTT-TCCTTTC-CCTTT-TCTCTTCCCCCTTC-CTTTTCTCCCTAG 517155 i - - - ii i i - i i vv (CTCCTTT)n#Si 1 CTCCTTTCTCCTTTCTCCTTTCTCCTTTCTCCTTTCTCCTTTCTCCTTTC 50 chr3ptel1M 517156 T--TTCCCCCTTCCTTCCTTTTCCACCATCCCTCCTTTTTCCCTCCTTTC 517203 -- i i i - - - v - ii i i i - i (CTCCTTT)n#Si 51 TCCTTTCTCCTTTC-TCC-TTT-CTCC-TTTCTCCTTTCTCCTTTC-TCC 95 chr3ptel1M 517204 TGACACTCTTCCTCCTCTTTCCTTTC-CCTTCCCTTCTTCCTCC 517246 vv v - i i i - -i i i (CTCCTTT)n#Si 96 TTTCTC-CTTTCTCCTTTCTCCTTTCTCCTT-TCTCCTTTCTCC 137 Matrix = Unknown Transitions / transversions = 3.67 (22/6) Gap_init rate = 0.10 (13 / 136), avg. gap size = 1.08 (14 / 13) 283 25.99 0.00 11.54 chr3ptel1M 518299 518385 (481615) MIR3#SINE/MIR 109 186 (22) m_b122s601i22 4501 chr3ptel1M 518299 CCTTCTTGGGTTTCAGATACTTAATTTTTCTGGTCTGTAAAATGAGAATG 518348 iii ii --------- i vi iiv MIR3#SINE/MIR 109 CCTCTCTGGGCCTCAG---------TTTCCTCATCTGTAAAATGAGGGGG 149 chr3ptel1M 518349 TTAGACCAGATGACCTCAAAGCTCCATCACAGTTCTG 518385 i i i v v v iv i MIR3#SINE/MIR 150 TTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTG 186 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 32.80 CpG sites = 14, Kimura (unadjusted) = 32.80 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.10 (9 / 86), avg. gap size = 1.00 (9 / 9) 15 20.36 0.00 0.00 chr3ptel1M 518396 518424 (481576) (T)n#Simple_repeat 1 29 (0) m_b122s252i8 4502 chr3ptel1M 518396 TTCTTATTTCTTTTCTTTTCTTTTTTTTT 518424 i v i i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 13 23.55 4.44 0.00 chr3ptel1M 518399 518443 (481557) (TTATT)n#Simple_repeat 1 47 (0) m_b122s252i9 4502 chr3ptel1M 518399 TTA-TTTCTTTTCTTTTCTTTTTTTTTAATTAAAGCT-TTTTATTTT 518443 - v v v v v v vvi - (TTATT)n#Simp 1 TTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTT 47 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.05 (2 / 44), avg. gap size = 1.00 (2 / 2) 12 21.84 2.70 0.00 chr3ptel1M 519162 519198 (480802) (CCCCAG)n#Simple_repeat 1 38 (0) m_b123s252i2 4503 chr3ptel1M 519162 CCCCTGGCCC-TCCCCGGCCCCAGCTTCAGCCACAGCC 519198 v v -v i ii v (CCCCAG)n#Sim 1 CCCCAGCCCCAGCCCCAGCCCCAGCCCCAGCCCCAGCC 38 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 208 33.63 5.31 0.00 chr3ptel1M 519733 519845 (480155) C MIRc#SINE/MIR (120) 148 30 m_b123s601i1 4504 chr3ptel1M 519733 CCTTTTATACAGCAGGGGAAACTGAGGCTTGGGAGCCAAAAAAGACATGC 519782 iv v vv i ii iiivvvv iv v C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr3ptel1M 519783 CCAAGGACACA-AGGGAGT-TGTCTCAGACCAGAGGCTAGAGTTC---TA 519827 v - vv -v vv v v i i v iii --- v C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTC 49 chr3ptel1M 519828 TTTCTGG-TCCAGGCCAAG 519845 i i- i i v C MIRc#SINE/MIR 48 TTCCTGACTCCAAGTCCAG 30 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.96 CpG sites = 17, Kimura (unadjusted) = 44.96 Transitions / transversions = 0.81 (17/21) Gap_init rate = 0.04 (4 / 112), avg. gap size = 1.50 (6 / 4) 212 29.41 2.35 0.00 chr3ptel1M 519737 519821 (480179) C MIR3#SINE/MIR (67) 141 55 m_b123s601i2 4504 chr3ptel1M 519737 TTATACAGCAGGGGAAACTGAGGCTTGGGAGCCAAAAAAGACATGCCCAA 519786 v vv i iii iiivvvi iv v C MIR3#SINE/MIR 141 TTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAA 92 chr3ptel1M 519787 GGACACA-AGGGAGTT-GTCTCAGACCAGAGGCTAGA 519821 v - v? - vv v v i i C MIR3#SINE/MIR 91 GGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGA 55 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.12 CpG sites = 11, Kimura (unadjusted) = 38.12 Transitions / transversions = 0.79 (11/14) Gap_init rate = 0.02 (2 / 84), avg. gap size = 1.00 (2 / 2) 184 34.67 7.47 0.54 chr3ptel1M 519957 520130 (479870) C L2#LINE/L2 (544) 2538 2353 m_b123s601i3 4505 chr3ptel1M 519957 CTGGGAGGATGAAGGAG---AGGACAAAGA-GGAGAGGAAGGAGAGATGG 520002 i i vv ---vv? vi - i i vv v i - C L2#LINE/L2 2538 CTGGAAGGATGGAGTTGCCATTNACTGAGATGGGGAAGACTGCGGGA-GG 2490 chr3ptel1M 520003 AAAAGG----AAAGGGGTGAT--GGGATTC--TCTGGGGCCTGTTGAGTT 520044 iv ---- ii iv -- ii -- i v i v i C L2#LINE/L2 2489 AGCAGGTTTGAGGGGGAAGATCAGGAGTTCAGTTTTGGACATGTTAAGTT 2440 chr3ptel1M 520045 TGAAGTATCAATGAAAAATCCAAGAGGAAA-GTCCTATAAATAGCTGGAG 520093 ii ii v v i v v i - vvi iii i v C L2#LINE/L2 2439 TGAGATGCCTATTAGACATCCAAGTGGAGATGTCGAGTAGGCAGTTGGAT 2390 chr3ptel1M 520094 ATGCAAAGCTTTAATTCAGAAGAAATCTTGGGTCTGG 520130 i i iv vv i ii i vv iv v C L2#LINE/L2 2389 ATACGAGTCTGGAGTTCAGGGGAGAGGTCCGGGCTGG 2353 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 47.40 CpG sites = 34, Kimura (unadjusted) = 48.54 Transitions / transversions = 1.31 (34/26) Gap_init rate = 0.04 (7 / 173), avg. gap size = 2.00 (14 / 7) 220 34.52 3.57 0.00 chr3ptel1M 521076 521159 (478841) C MIRb#SINE/MIR (82) 186 100 m_b123s601i4 4506 chr3ptel1M 521076 CTTTGCAATAAGCCCGGGGACTAGTAATTGTCAGTTCCCTTTGACACG-G 521124 i ii i v i v iiv vv i i vii v v vi- C MIRb#SINE/MIR 186 CCTCACAACAACCCTGCGAGGTAGGTATTATTATCCCCATTTTACAGATG 137 chr3ptel1M 521125 GGGAGGCTGAGGTTCAGGGAGGTT--GTGATTTTCCC 521159 i ii i i -- i i v C MIRb#SINE/MIR 136 AGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCC 100 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 49.16 CpG sites = 19, Kimura (unadjusted) = 49.16 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.02 (2 / 83), avg. gap size = 1.50 (3 / 2) 310 22.50 7.50 0.00 chr3ptel1M 521954 522033 (477967) C MIRc#SINE/MIR (33) 235 150 m_b123s601i5 4507 chr3ptel1M 521954 TTATGGTTTGCAAAGGGCTTT-ACATATGTTAACTC--TCAGCCCTCACA 522000 ii i v - ii v -- iiii C MIRc#SINE/MIR 235 TTACAGTTTACAAAGCGCTTTCACATACATTATCTCATTTGATCCTCACA 186 chr3ptel1M 522001 GCCACCCTGGGAGGGAGGCA---CTGTTATTATTGT 522033 i v v v --- v v i C MIRc#SINE/MIR 185 ACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTAT 150 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.32 CpG sites = 11, Kimura (unadjusted) = 27.32 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.04 (3 / 79), avg. gap size = 2.00 (6 / 3) 337 20.00 3.08 0.00 chr3ptel1M 521966 522030 (477970) C MIR#SINE/MIR (50) 212 146 m_b123s601i6 4507 chr3ptel1M 521966 AAGGGCTTTACATATGTTAACTC--TCAGCCCTCACAGCCACCCTGGGAG 522013 v i i -- i ii i v iv C MIR#SINE/MIR 212 AAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAG 163 chr3ptel1M 522014 GGAGGCACTGTTATTAT 522030 v i i C MIR#SINE/MIR 162 GTAGGTACTATTATTAT 146 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 23.94 CpG sites = 9, Kimura (unadjusted) = 23.94 Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.02 (1 / 64), avg. gap size = 2.00 (2 / 1) 576 22.90 6.11 0.00 chr3ptel1M 522108 522238 (477762) C MIRc#SINE/MIR (120) 148 10 m_b123s601i7 4507 chr3ptel1M 522108 CCCATTTTACAGATGAGGTAACTGAAG-TAAATGGGATTAAGTGACTTAT 522156 v i - v iv i i ii C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr3ptel1M 522157 CCATGGTGACACAGCCGATAAGTGTCTGAGGCCAGATTTGAACTCAGGTC 522206 v v iii v v v vi i i i C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTC 49 chr3ptel1M 522207 TTGCCGA-------TCCAGCACTCTAGCCACTGTGCCAC 522238 v i ------- ii vv ii C MIRc#SINE/MIR 48 TTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.80 CpG sites = 18, Kimura (unadjusted) = 27.88 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.02 (2 / 130), avg. gap size = 4.00 (8 / 2) 309 31.25 3.03 5.43 chr3ptel1M 522250 522381 (477619) C MIRc#SINE/MIR (115) 153 25 m_b123s601i8 4508 chr3ptel1M 522250 TTATTTCCCTTTGGTGGATGAGATGATGGAAGC--AGAGACTCCTCAGCA 522297 ii v viii ivi iv i -- vvi- v ii C MIRc#SINE/MIR 153 TTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGT-TAAGTG 105 chr3ptel1M 522298 ACTTGCC-AAGATCAC-CAATTCTTACATATGTGAGGCAGCACTCAAACC 522345 - i - ii vv vi ivvv v i v i C MIRc#SINE/MIR 104 ACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACC 55 chr3ptel1M 522346 CAGGCTTCCCTGACTCCAATTTGGTTCCCAGTGCCC 522381 ii i v ------ i C MIRc#SINE/MIR 54 CAGGTCTTCCTGACTCCAAGT------CCAGTGCTC 25 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.87 CpG sites = 23, Kimura (unadjusted) = 41.65 Transitions / transversions = 1.44 (23/16) Gap_init rate = 0.08 (10 / 131), avg. gap size = 1.10 (11 / 10) 217 26.98 3.17 0.00 chr3ptel1M 522393 522455 (477545) L2c_3end#LINE/L2 338 402 (76) m_b123s601i9 4509 chr3ptel1M 522393 TTCTAGCCGGCCCTCTACCTGT-TGTCTCCCCCACTGGAATG-GGGCTCC 522440 v iii v iv i ? - i i v - i L2c_3end#LINE 338 TTGTAATTGTCTGTTTACNTGTCTGTCTCCTCCACTAGACTGTGAGCTCC 387 chr3ptel1M 522441 CTGAAAGCAGGAGCC 522455 i ii ii L2c_3end#LINE 388 TTGAGGGCAGGGACC 402 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.52 CpG sites = 13, Kimura (unadjusted) = 36.52 Transitions / transversions = 3.25 (13/4) Gap_init rate = 0.03 (2 / 62), avg. gap size = 1.00 (2 / 2) 193 25.00 4.17 0.00 chr3ptel1M 522415 522462 (477538) L2a_3end#LINE/L2 382 431 (86) m_b123s601i10 4509 chr3ptel1M 522415 TGTCTCCCCC-ACTGGAATG-GGGCTCCCTGAAAGCAGGAGCCTCAGTTT 522462 - i -ii v ii ii i iv i L2a_3end#LINE 382 TGTCTCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTCT 431 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.83 CpG sites = 10, Kimura (unadjusted) = 32.83 Transitions / transversions = 5.00 (10/2) Gap_init rate = 0.04 (2 / 47), avg. gap size = 1.00 (2 / 2) 26 13.64 5.26 0.00 chr3ptel1M 523392 523448 (476552) (GGGA)n#Simple_repeat 1 60 (0) m_b123s252i3 4510 chr3ptel1M 523392 GGGGGGGAGGGA-GGCGGGAGGG-GGAAGGGAGGGA-GGAATGAGGGAGG 523438 i - v - i - iv (GGGA)n#Simpl 1 GGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGG 50 chr3ptel1M 523439 AAGGAAGGGA 523448 i i (GGGA)n#Simpl 51 GAGGGAGGGA 60 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.05 (3 / 56), avg. gap size = 1.00 (3 / 3) 18 14.81 0.00 2.56 chr3ptel1M 523624 523663 (476337) (AAAGGGG)n#Simple_repeat 1 39 (0) m_b123s252i4 4511 chr3ptel1M 523624 AAAGGGGGAGGGGGGGTGGGGAAAGGGGGAAAGGGGAAAG 523663 i i iiv - (AAAGGGG)n#Si 1 AAAGGGGAAAGGGGAAAGGGGAAA-GGGGAAAGGGGAAAG 39 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1) 17 15.49 0.00 0.00 chr3ptel1M 526091 526119 (473881) (A)n#Simple_repeat 1 29 (0) m_b123s252i5 4512 chr3ptel1M 526091 AACAAAAAAACAAAAAAAATAAAACAAAA 526119 v v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA 29 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 12 23.53 3.33 5.08 chr3ptel1M 526450 526509 (473491) (TACAAA)n#Simple_repeat 1 59 (0) m_b123s252i6 4513 chr3ptel1M 526450 TACAAATA-AAATAAAAAATTTTCCTGACAAATTC-AATACAAAATGAAA 526497 - - v vivvv - v - - iv (TACAAA)n#Sim 1 TACAAATACAAAT-ACAAATACAAAT-ACAAATACAAATAC-AAATACAA 47 chr3ptel1M 526498 GTACAACTACAA 526509 i v (TACAAA)n#Sim 48 ATACAAATACAA 59 Matrix = Unknown Transitions / transversions = 0.38 (3/8) Gap_init rate = 0.08 (5 / 59), avg. gap size = 1.00 (5 / 5) 17 4.94 0.00 0.00 chr3ptel1M 526664 526684 (473316) (T)n#Simple_repeat 1 21 (0) m_b123s252i7 4514 chr3ptel1M 526664 TTTTTTTTTTTTTTGTTTTTT 526684 v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTT 21 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 13 15.91 0.00 0.00 chr3ptel1M 527040 527067 (472933) (GGGAG)n#Simple_repeat 1 28 (0) m_b123s252i8 4515 chr3ptel1M 527040 GGGAGGGGTGGGGGAGGGAGGGGCGGGG 527067 v ii v (GGGAG)n#Simp 1 GGGAGGGGAGGGGAGGGGAGGGGAGGGG 28 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 345 29.20 6.19 0.00 chr3ptel1M 528360 528472 (471528) C MIR3#SINE/MIR (2) 206 87 m_b123s601i11 4516 chr3ptel1M 528360 ATCAAAGCAGCTTAGA---TTTGTGCTGGAGGGGCATTTAGATGTCAACT 528406 v v v v --- iv v i vvi vi v C MIR3#SINE/MIR 206 ATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCT 157 chr3ptel1M 528407 GGTCCAACCTTTTC-TTTCA---ATAAGGAAATTGAAGCTTGGAGATGTG 528452 i iii - i --- i i i iii v C MIR3#SINE/MIR 156 AGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTG 107 chr3ptel1M 528453 AAGCTTCCTGCACAAAGCCA 528472 ivv i v i i C MIR3#SINE/MIR 106 AAGTGACTTGCCCAAGGTCA 87 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.94 CpG sites = 19, Kimura (unadjusted) = 37.94 Transitions / transversions = 1.36 (19/14) Gap_init rate = 0.03 (3 / 112), avg. gap size = 2.33 (7 / 3) 559 19.72 0.81 5.93 chr3ptel1M 529052 529175 (470825) MIRc#SINE/MIR 10 127 (141) m_b123s601i12 4517 chr3ptel1M 529052 GTGATGCAGTAGATAGAGCACCAGTCCTGAAGTCAGGAGGACCTGAGTTC 529101 i i v ii v i i i i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr3ptel1M 529102 AAATCTGGTCTCAGACACTTAACACTGCCTAGCTGTATGACCCTGAGCAA 529151 i i iv v v v ------- i i i MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTGACCTTGGGCAA 102 chr3ptel1M 529152 GTCACTTAACCTCAAT-TGCCTCAG 529175 vv -v MIRc#SINE/MIR 103 GTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 22.07 CpG sites = 14, Kimura (unadjusted) = 23.18 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.07 (8 / 123), avg. gap size = 1.00 (8 / 8) 308 33.25 5.11 6.87 chr3ptel1M 529311 529917 (470083) L1ME3Cz_3end#LINE/L1 13 609 (388) m_b123s551i1 4518 chr3ptel1M 529311 ATACATAGGGAACTCATTCAAAAGTATAAAGACAAAAGTTTTTCCCCAAT 529360 i ii v v vvv ii v i ----ivv L1ME3Cz_3end# 13 ATATATAAAGAACTCCTACAAATCAATAAGAAAAAGA----CAACCCAAT 58 chr3ptel1M 529361 AGA----TAGTCAAAGGATATGGACTAATATTTCTCAAAAGAACAAAAGC 529406 ---- i v i viii v v i iv vv L1ME3Cz_3end# 59 AGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGGAAACCC 108 chr3ptel1M 529407 AAACTATCATATTTAAAATGTAATCATATTAAAAAATTTAGAATGCTCAT 529456 i ivii ----------i v v i ------- - L1ME3Cz_3end# 109 GAATGGCCA----------ATAAACATATGAAAAGAT-------GCTCA- 140 chr3ptel1M 529457 AAATCACTAATAATTAGAGAAATGCACATTAAATTAACTTTGAGATACCA 529506 vv i i i v vi? vv L1ME3Cz_3end# 141 ACCTCACTAGTAATCAGGGAAATGCAAATTAAAACNACAATGAGATACCA 190 chr3ptel1M 529507 CCTTATACCTATCAGATTGACAAAGATGACAAAAATGGAAAAGGA--AAA 529554 ii i i i i i v-i i vvi v iv -- i L1ME3Cz_3end# 191 TTTCACACCCATCAGATTGGCAAAAATT-TAAAAGTCTGACAATACCAAG 239 chr3ptel1M 529555 TGTCGGAGGGACTGTGGATAAATGTGCATCCTAGTACACTGC--ATGGG- 529601 i v i iv v i v v ii vi --i - L1ME3Cz_3end# 240 TGTTGGCGAGGATGTGGAGAAACGGGAACTCTCATACACTGCTGGTGGGA 289 chr3ptel1M 529602 GT-----------CAGCCATTCCAGAAAGCACATTAGGATTATGCCCCAT 529640 ----------- i i iii i vv i v v -- ivi L1ME3Cz_3end# 290 GTGTAAATTGGTACAACCACTTTGGAGAGCAATTTGGCAATAT--CTAGT 337 chr3ptel1M 529641 -AAGTTACTAAACTGTGTATTAGCCTTTGATCCGGCAAAGCCAATACCAG 529689 - i-- iv i i - v vi i i vv v v i L1ME3Cz_3end# 338 AAAGTTG--AAGATGCGCA-TACCCTACGACCCAGCAATTCCACTTCTAG 384 chr3ptel1M 529690 ACCAGTAATCTCAAAGACA---TCCCAGAAAGGAGAAAGGACCCAGATGT 529736 iivvi vi - i v --- v v viv viv vv -- L1ME3Cz_3end# 385 GTATATACCCT-AGAGAAACTCTCGCACATGTGCACAAGGAGAC--ATGT 431 chr3ptel1M 529737 ACCAGAGTGTCCAGAGAAGCAT--TTTG---TAGCAAAGAACTAGACACT 529781 v ii i vv v -- --- i i i i v v L1ME3Cz_3end# 432 ACAAGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACA 481 chr3ptel1M 529782 CAGTAGGTGGCTATCAATTGAGAAGTGGCTGGACATACTAGGGTGCTATT 529831 vvv ii v i v i i i v ii i v i iv i- L1ME3Cz_3end# 482 ACCTAAATGTCCATCAATAGGGGAATGGATAAATAAATTGTGGTA-TATT 530 chr3ptel1M 529832 GAGTCATTAGAAAAAAAATTTTAAATAG-AGTGAATGAAAAGAATGAACT 529880 v vv v i ------ vi v i - --- i v L1ME3Cz_3end# 531 CATACAATGG------AATACTATACAGCAGT---TAAAATGAATGAACT 571 chr3ptel1M 529881 T-ATCAATAAAGAAAAACATAGGAGAATTGTGAAAATA 529917 v- v i viv vv i ivi ivii i L1ME3Cz_3end# 572 AGATCTACATGTATCAACATGGATAAATCTCAAAAACA 609 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 43.37 CpG sites = 100, Kimura (unadjusted) = 44.97 Transitions / transversions = 1.14 (100/88) Gap_init rate = 0.09 (52 / 606), avg. gap size = 1.38 (72 / 52) 566 32.51 5.22 4.21 chr3ptel1M 529311 529827 (470173) L1ME4a_3end#LINE/L1 13 534 (337) m_b123s551i0 4518 chr3ptel1M 529311 ATACATAGGGAACTCATTCAAAAGTATAAAGACAAAAGTTTTTCCCCAAT 529360 i ii i v v vvv ii v i vvvviv L1ME4a_3end#L 13 ATATATAAAGAGCTCTTACAAATCAATAAGAAAAAGACGAACACCCCAAT 62 chr3ptel1M 529361 AGA----TAGTCAAAGGATATGGACTAATATTTCTCAAAAGAACAAAAGC 529406 ---- i v i i vi i v v v vi L1ME4a_3end#L 63 AGAAAAATGGGCAAAGGACATGAACAGACAATTCACAAAAGAAGAAATAC 112 chr3ptel1M 529407 AAACTATCATATTTAAAATGTAATCATATTAAAAAATTTAGAATGCTCAT 529456 ivii ----------i v v ? ------- i - L1ME4a_3end#L 113 AAATGGCCA----------ATAAACATATGAAAANAT-------GTTCA- 144 chr3ptel1M 529457 AAATCACTAATAATTAGAGAAATGCACATTAAATTAACTTTGAGATACCA 529506 vv i i i v vi vv L1ME4a_3end#L 145 ACCTCACTAGTAATCAAAGAAATGCAAATTAAAACAACAATGAGATACCA 194 chr3ptel1M 529507 CCTTATACCTATCAGATTGACAAAGATGACAAAAATGGAAAAGG-AAAAT 529555 ii vi i i vvv i v v vi-vv i L1ME4a_3end#L 195 TTTTTCACCTATCAAATTGGCAAAGATTTAAAAGATTGATAATACCCAGT 244 chr3ptel1M 529556 GTCGGAGGGACTGTGGATAAATGTGCATCCTAGTACACTGC--ATGGG-G 529602 i v i iv ?v i v ii vi --i - L1ME4a_3end#L 245 GTTGGCGAGGGTGTGGNGAAACGGGCACTCTCATACACTGCTGGTGGGAG 294 chr3ptel1M 529603 T-----------CAGCCATTCCAGAAAGCACATTAGGATTATGCCCCATA 529641 ----------- i v ii ii vv i v v ivi v L1ME4a_3end#L 295 TGTAAATTGGTACAACCTTTCTGGAGGGCAATTTGGCAATATGTATCAAA 344 chr3ptel1M 529642 AGTTACTAAACTGTGTATTAGCCTTTGATCCGGCAAAGCCAATACCAGAC 529691 iiviv v ?i - v i i i vv v v i i- L1ME4a_3end#L 345 AGCCTTAAAAATGTNCA-TACCCTTTGACCCAGTAATTCCACTTCTAGG- 392 chr3ptel1M 529692 CAGTAATCTCAAAGACAT-CCCAGAAAGGAGA--AAGGACCCAGATGTAC 529738 v v v ii i v -vi i v v ?-- i iii-- L1ME4a_3end#L 393 AATTTATCCTAAGGAAATAATCAGAGATGTGNACAAAGATTT--ATGTAC 440 chr3ptel1M 529739 CAGAGTGTCCAGAGAAGCATT-----TTGTAGCAAAGAACTAGACACTCA 529783 v ii i vv v ----- vi i i i i v vvv L1ME4a_3end#L 441 AAGGATGTTCATCGCAGCATTATTTATAATAGCGAAAAATTGGAAACAAC 490 chr3ptel1M 529784 GTAGGTGGCTATCAATTGAGAAGTGGCTGGACATACTAGGGTGC 529827 v ii v i v v i i ? i ii i v i v i L1ME4a_3end#L 491 CTAAATGTCCAACAATAGGGGANTGGTTAAATAAATTATGGTAC 534 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 43.36 CpG sites = 84, Kimura (unadjusted) = 44.09 Transitions / transversions = 1.09 (84/77) Gap_init rate = 0.06 (30 / 516), avg. gap size = 1.63 (49 / 30) 228 42.72 0.00 0.97 chr3ptel1M 529945 530048 (469952) C MIR#SINE/MIR (98) 164 62 m_b123s601i13 4519 chr3ptel1M 529945 AAGCAAATACACATTCATGTTCCCATTCTGTGGATGAAGAAACTAAGATT 529994 i i ii -i vv i i i iii i i iiv C MIR#SINE/MIR 164 AGGTAGGTAC-TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCA 116 chr3ptel1M 529995 CCAAGAGTTGAATTGCTCCATGTAAGGCCATAGAACTAGTCAGAAATGGG 530044 vi v v v iviiiiivi i i v i v viiii i C MIR#SINE/MIR 115 CAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGA 66 chr3ptel1M 530045 ACCG 530048 i C MIR#SINE/MIR 65 GCCG 62 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 73.58 CpG sites = 32, Kimura (unadjusted) = 73.58 Transitions / transversions = 2.67 (32/12) Gap_init rate = 0.01 (1 / 103), avg. gap size = 1.00 (1 / 1) 258 40.22 0.00 0.00 chr3ptel1M 529957 530048 (469952) C MIRc#SINE/MIR (111) 157 66 m_b123s601i14 4519 chr3ptel1M 529957 ATTCATGTTCCCATTCTGTGGATGAAGAAACTAAGATTCCAAGAGTTGAA 530006 vv i i i iii i i ii vi v v C MIRc#SINE/MIR 157 ATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAA 108 chr3ptel1M 530007 TTGCTCCATGTAAGGCCATAGAACTAGTCAGAAATGGGACCG 530048 v viiiiivi i i v i v viiii ii C MIRc#SINE/MIR 107 GTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 66 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 64.56 CpG sites = 26, Kimura (unadjusted) = 64.56 Transitions / transversions = 2.36 (26/11) Gap_init rate = 0.00 (0 / 91), avg. gap size = 0.0 (0 / 0) 277 28.54 4.49 12.41 chr3ptel1M 532882 533037 (466963) L2c_3end#LINE/L2 324 468 (10) m_b123s601i15 4520 chr3ptel1M 532882 ATCATCAATTTGTCCCATGAGTGTTGGATTGTGTGTAATGGTTTGCACAT 532931 i i viii i v i------ v v?v i i---- L2c_3end#LINE 324 ATCATTAACTTGTATTGTAATTGTC------TGTTTACNTGTCTGT---- 363 chr3ptel1M 532932 TACTTCTCACATTAGACTTGGAGCTCCTTGAAGGCTG-----CTCTTTTG 532976 -- i - i vv i v -----v v i i L2c_3end#LINE 364 --CTCCTC-CACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTA 410 chr3ptel1M 532977 CCCTTCTTTGTAACCTCAGTGCTCA--ACAGAGCATCTGGCACTTTTAAT 533024 ii v v i i iii-- v i --- i -- i L2c_3end#LINE 411 TTCATCTTTGTATCCCCAGCGCCTGGCACATAGTA---GGCGC--TCAAT 455 chr3ptel1M 533025 AAATGCTTGATGA 533037 i v L2c_3end#LINE 456 AAATGTTTGTTGA 468 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.79 CpG sites = 25, Kimura (unadjusted) = 37.19 Transitions / transversions = 1.79 (25/14) Gap_init rate = 0.13 (20 / 155), avg. gap size = 1.25 (25 / 20) 373 28.26 8.38 4.62 chr3ptel1M 533272 533438 (466562) C MIRc#SINE/MIR (68) 200 28 m_b123s601i16 4521 chr3ptel1M 533272 CATTTAAGCATCCCAGCAACCCCG----------AGGGCAGATGTGATTA 533311 i v v v i i ---------- i --- C MIRc#SINE/MIR 200 CATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGT---ATTA 154 chr3ptel1M 533312 TTATCCCAATTTTTACCGATAAGGACGCAGAA---CAGACCGAAACAAAG 533358 v - v i vi v i--- -- iiiv C MIRc#SINE/MIR 153 TTATCCCCATTTT-ACAGATGAGGAAACTGAGGCTCAGA--GAGGTTAAG 107 chr3ptel1M 533359 TGATATCCACAAG-TCAGACAGCTGATAACTGCATGAGAAGCAGATTTTG 533407 iv v v - v ii v vv-- iv i ivi i C MIRc#SINE/MIR 106 TGACTTGCCCAAGGTCACACAGCTAGTAAGTGGC--AGAGCCGGGACTCG 59 chr3ptel1M 533408 AGCCCGCATTTTCCCAGCTCCAAGTCTAATG 533438 i ivi i iii i i C MIRc#SINE/MIR 58 AACCCAGGTCTTCCTGACTCCAAGTCCAGTG 28 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.54 CpG sites = 27, Kimura (unadjusted) = 36.57 Transitions / transversions = 1.50 (27/18) Gap_init rate = 0.07 (11 / 166), avg. gap size = 2.00 (22 / 11) 285 25.33 0.95 6.00 chr3ptel1M 533513 533617 (466383) C L2d2_3end#LINE/L2 (305) 250 151 m_b123s601i17 4522 chr3ptel1M 533513 CAGAGAAGATCTCAGGGAGGAGGTGGCCCTTGAGCTGAGCCTTAAAGGAC 533562 i iii v ?vi i i i C L2d2_3end#LIN 250 CAGGGAAGGCTTCACGGAGGAGGTGGNATTTGAGCTGGGCCTTGAAGGAT 201 chr3ptel1M 533563 ATA-AGGATTCTCTAAAAGTCAGAGGTGAGAAGGGAAGGAAGGCATTCCT 533611 ivi- - vv v i -i --ii i -- i v C L2d2_3end#LIN 200 GGGTAGGATT-TGGATAGGT-GGAG--AGGAAGGGGA--AGGGCATTCCA 157 chr3ptel1M 533612 GTCAGG 533617 v i C L2d2_3end#LIN 156 GGCGGG 151 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.86 CpG sites = 17, Kimura (unadjusted) = 32.44 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.07 (7 / 104), avg. gap size = 1.00 (7 / 7) 252 25.64 7.69 0.00 chr3ptel1M 533794 533871 (466129) C Charlie4a#DNA/hAT-Charlie (38) 470 387 m_b123s502i0 4523 chr3ptel1M 533794 GGCAGCCAGGTCAGGTCTACAGATCCCTGCTCAGAATCATGCTTGT-AAT 533842 i v v i i ii i v v i v - C Charlie4a#DNA 470 GGCAGTCTGGTGAAGCCTATGGACCCCTTCTCAGAATAATGTTTTTAAAT 421 chr3ptel1M 533843 AC-----ATAAAGCCCACAAAATTACAAAGGGAA 533871 i ----- iiv i ii i C Charlie4a#DNA 420 GCATAAAATAAAATACATAGGATTACAAAGGAAA 387 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 32.80 CpG sites = 14, Kimura (unadjusted) = 32.80 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.03 (2 / 77), avg. gap size = 3.00 (6 / 2) 254 21.43 3.57 0.00 chr3ptel1M 534012 534067 (465933) C L3#LINE/CR1 (320) 3779 3722 m_b123s601i18 4524 chr3ptel1M 534012 ATCTGAATACAGCTATCACGTCCCTCCTGGG--TTCTCTTCTGCAAGTTA 534059 i v i i ii ii -- v i i C L3#LINE/CR1 3779 ATTTGAAGACAGCTATCATGTCTCCTCTAAGTCTTCTCTTCTCCAGGCTA 3730 chr3ptel1M 534060 ATCATCCC 534067 v C L3#LINE/CR1 3729 AACATCCC 3722 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.33 CpG sites = 9, Kimura (unadjusted) = 26.33 Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.02 (1 / 55), avg. gap size = 2.00 (2 / 1) 514 30.76 10.05 0.44 chr3ptel1M 534143 534351 (465649) MIRc#SINE/MIR 23 251 (17) m_b123s601i19 4525 chr3ptel1M 534143 AAAAGTGCTGTTCCTCAGAATTGGGAAGAGTCCAGCTGGAAACCTG-CTC 534191 i ii v-v ii i ii viivi i v iv i - MIRc#SINE/MIR 23 AAGAGCACTGG-ACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTC 71 chr3ptel1M 534192 AGATACTGTCT---TGGGTGACCCTCGGCAAGTCACTTAACCTCTC--AC 534236 v vi vv --- v i v -- v MIRc#SINE/MIR 72 TGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAG 121 chr3ptel1M 534237 CTTCGGTCTGCTAATCTGTACATTGGGGATAATAGAAGC------ATTTG 534280 i i i v v v v iv v ------iii i MIRc#SINE/MIR 122 CCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTA 171 chr3ptel1M 534281 CCTCCCAGACTGGCTGGGAG-------TGAGATGACATATGT-AAAGTGT 534322 v iv v i v ------- i ii - i i MIRc#SINE/MIR 172 CCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGC 221 chr3ptel1M 534323 TTTGCAAACCTCATAGCCCT-TATGGATGT 534351 i ivi v iv - iii MIRc#SINE/MIR 222 TTTGTAAACTGTAAAGTGCTATACAAATGT 251 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.23 CpG sites = 38, Kimura (unadjusted) = 40.90 Transitions / transversions = 1.46 (38/26) Gap_init rate = 0.04 (8 / 208), avg. gap size = 2.75 (22 / 8) 221 34.15 4.03 3.20 chr3ptel1M 534339 534462 (465538) C L3#LINE/CR1 (439) 3660 3536 m_b123s601i20 4524 chr3ptel1M 534339 CCCTTATGGATGTTCACTGGGTCAGCAAATGTCCTCCCAAAACTGTGGCA 534388 i i v i iv v ii v iiv - ii iv v i C L3#LINE/CR1 3660 CTCCTCTGGACGCGCTCCAGTTTGTCAA-TGTCCCTCTTAAAATGTGGCG 3612 chr3ptel1M 534389 -CTACAACTGAACTGAAGCCCTCTGA-GGGGTCTGAT--GTATGGAGGAC 534434 - i v vv vv ii v - v i-- iiii v C L3#LINE/CR1 3611 CCCAGAACTGAACGCAATACTCCAGATGTGGTCTGACCAGCGCAGAGTAC 3562 chr3ptel1M 534435 A-TGGGACAATGGTGAGCCCCCTTACTCT 534462 -i v --- v v i i? C L3#LINE/CR1 3561 AGCGGGACTA---TTACCTCCCTTGNTCT 3536 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.86 CpG sites = 23, Kimura (unadjusted) = 47.60 Transitions / transversions = 1.28 (23/18) Gap_init rate = 0.07 (8 / 123), avg. gap size = 1.12 (9 / 8) 26 3.13 3.03 0.00 chr3ptel1M 535351 535383 (464617) (CCTC)n#Simple_repeat 1 34 (0) c_b123s251i0 4526 chr3ptel1M 535351 CCTCCCTCCCTCCCTCCCTCCTTCCCT-CCTCCC 535383 i - (CCTC)n#Simpl 1 CCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCC 34 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 43 30.88 3.59 1.51 chr3ptel1M 535384 535570 (464430) (TC)n#Simple_repeat 8 199 (0) m_b123s252i9 4527 chr3ptel1M 535384 CCCATCTCTC-CTTTGTATCTCAATCTCTTTCCCTCTGTCTCTATGTCTT 535432 i - - i v v vv i i v v v i (TC)n#Simple_ 8 CTC-TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 56 chr3ptel1M 535433 TTCCCCTGGGTGTATAAATCTGTGTGTCTCTGTGTGTCTCTGTCTGCT-T 535481 ii i vvv v v vvv v v v v v v v - - (TC)n#Simple_ 57 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT-CTCT 105 chr3ptel1M 535482 GTCTCTGTCTCAGTGTCTCTTTGTATCTCTGTTTCTGTCTCCCCCTC-CT 535530 v v vv v i v v v i v i i - (TC)n#Simple_ 106 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 155 chr3ptel1M 535531 CCCTCTTTCTCTCTCTC-CTGTCTC-CTC-CACT-TCTCTTTCT 535570 i i - v - - v - i (TC)n#Simple_ 156 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 199 Matrix = Unknown Transitions / transversions = 0.45 (15/33) Gap_init rate = 0.05 (9 / 186), avg. gap size = 1.00 (9 / 9) 12 13.69 6.25 0.00 chr3ptel1M 536392 536423 (463577) (CCAT)n#Simple_repeat 1 34 (0) m_b123s252i10 4528 chr3ptel1M 536392 CCATCCTCCCATCCATCCTTCCCTCC--CCATCC 536423 vi v v -- (CCAT)n#Simpl 1 CCATCCATCCATCCATCCATCCATCCATCCATCC 34 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.03 (1 / 31), avg. gap size = 2.00 (2 / 1) 308 36.76 9.06 1.40 chr3ptel1M 536581 536911 (463089) L2#LINE/L2 398 753 (2329) m_b123s601i21 4529 chr3ptel1M 536581 CAATAAATTCCCTTTCATCTTAAGTCTTTTCCTTCTCCAGTCCTTCCATA 536630 ii v iivi i v ii i ii vvv iv i i iv L2#LINE/L2 398 CAGCAAAATCCCCCGTATCCTCAACCTCTTCTCTGAACGTTCCCTTCACC 447 chr3ptel1M 536631 TTCTGGTTCTCATTCAAATTGGGCTTCCTCCTAATGGAG-----TTTCCC 536675 v i v i?v iiv ii i i - v----- i L2#LINE/L2 448 TTCTTGCTCTAACNGAAACCTGGCTCTCCCCTGA-GGACACTGCTTCCCC 496 chr3ptel1M 536676 AGCCTCCCTTGCCAGCACTGGCTGCCCTTTCATTCCCTACCCC------- 536718 v vv iv v iiv iii i - i vi ? ------- L2#LINE/L2 497 TGCAGCCCTCTCAAGTGGTGGCTGTTTTCTC-TCCCACANCCCTCGTACC 545 chr3ptel1M 536719 -CTGGGCATGG--GAGGAGCCG-TATATTCCTCACTCTCTGTCCCCACTT 536764 - v -- v i iv - i vi ii iiii iv i L2#LINE/L2 546 ACTGGGCCTGGAGGTGGGGTAGGTGTCCTCCTTGCTCCTCATTGCCGCTT 595 chr3ptel1M 536765 CCAGGC---TCTCTGTCACT-CTAACTCAGTTATCTCTTCTCTGAGGTTC 536810 i --- iv v - vv v ivi i i vv i ivi L2#LINE/L2 596 CCAGACCATTCTCCCTCCCTCCTCCCTAAAACACCCCAGCTTTGAATCTC 645 chr3ptel1M 536811 AT----TCGACCCATATGTCT--CTACCAAT-GTGGTTCTGGTCATTACC 536853 ---- iiv i ivv i-- vv -v v vii --- L2#LINE/L2 646 ATGTCATCAGACTATACCACCCGCTACCCCTCCTTGTTGCAGTCAT---C 692 chr3ptel1M 536854 TACTGACCACCACGACCCCCTCCCTCCTTCCTCAGAGAATTCAGTCCCTG 536903 i v iv v v i i v iii v i ii L2#LINE/L2 693 TACCGACCTCCGGGTCACTCCCCCTCATTCCTTGAAGATTTTAGCTCCTG 742 chr3ptel1M 536904 ---CCCTGTCA 536911 --- v L2#LINE/L2 743 GCTCACTGTCA 753 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 50.25 CpG sites = 71, Kimura (unadjusted) = 53.52 Transitions / transversions = 1.45 (71/49) Gap_init rate = 0.05 (16 / 330), avg. gap size = 2.19 (35 / 16) 21 17.73 0.00 0.00 chr3ptel1M 537637 537674 (462326) (A)n#Simple_repeat 1 38 (0) m_b123s252i11 4530 chr3ptel1M 537637 AAAAAGACACTAAAGCAAAAAAAAAAAAAAAAAAAAAA 537674 i v vv iv (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 38 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 18 0.00 0.00 0.00 chr3ptel1M 538923 538942 (461058) (A)n#Simple_repeat 1 20 (0) m_b123s252i12 4531 chr3ptel1M 538923 AAAAAAAAAAAAAAAAAAAA 538942 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAA 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 224 21.59 3.53 6.83 chr3ptel1M 539819 540725 (459275) (AGACAG)n#Simple_repeat 1 879 (0) m_b123s252i13 4532 chr3ptel1M 539819 AGACAGAG-GAGAGAAAAAGACAAAGGAAAGAGACAGGGACAGGGACAAT 539867 -v v i i - v i i iv (AGACAG)n#Sim 1 AGACAGAGACAGAGACAGAGACAGA-GACAGAGACAGAGACAGAGACAGA 49 chr3ptel1M 539868 GACAAGAGACAGACTGAGAAGCAG-GAGAGAGA-AGAGACAACAGAAGGA 539915 - vvv ii - v - - v vi - (AGACAG)n#Sim 50 GAC-AGAGACAGAGACAGAGACAGAGACAGAGACAGAGAC-AGAGACAG- 96 chr3ptel1M 539916 ATCACAGAGACAGGGACAAAGGAAAGGGACACGGAGACGGGGACAAGGGA 539965 -v i i - v i -- i i - i (AGACAG)n#Sim 97 A-GACAGAGACAGAGACAGA-GACAGAGACA--GAGACAGAGAC-AGAGA 141 chr3ptel1M 539966 AAGGGACACGGAGACAGGGACAAGGGAAAGGGACACGGAGACAGGGACAG 540015 v i -- i - i v i -- i (AGACAG)n#Sim 142 CAGAGACA--GAGACAGAGAC-AGAGACAGAGACA--GAGACAGAGACAG 186 chr3ptel1M 540016 AG-GAAAGACACAGACAGGGACAGAGGAAAGAGACAAGGAGACAGGGACA 540064 -v i v i - v - - i (AGACAG)n#Sim 187 AGACAGAGACAGAGACAGAGACAGA-GACAGAGAC-A-GAGACAGAGACA 233 chr3ptel1M 540065 GAGGAAAGAGACAAGGAGACAGGGACAGAGGAAAGAGACAAGGAGACAGG 540114 - v - - i - v - - i (AGACAG)n#Sim 234 GA-GACAGAGAC-A-GAGACAGAGACAGA-GACAGAGAC-A-GAGACAGA 277 chr3ptel1M 540115 GACAGAG-GAAAGGGAGAG-CGGGGAGA-AGGGA-AGACAGGGACA-AG- 540158 -v i iv - i i v - iv - i - - (AGACAG)n#Sim 278 GACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGA 327 chr3ptel1M 540159 GAG-GAAAG-GACAG-GAGAGGGACAAGGGAAAAGAGAC-GGGATGGGGA 540204 v - v - - v i - i - v - i ii i (AGACAG)n#Sim 328 CAGAGACAGAGACAGAGACAGAGAC-AGAG-ACAGAGACAGAGACAGAGA 375 chr3ptel1M 540205 -AGGGAAAGGGACACGGAGACAGAGACAAAGGAAAGGGACACGGAGACAG 540253 - i v i -- i - v i -- (AGACAG)n#Sim 376 CAGAGACAGAGACA--GAGACAGAGACAGA-GACAGAGACA--GAGACAG 420 chr3ptel1M 540254 GGACAGAGGAAAGACACAGAGACAGGGACAGAGGAAAGAGACAAGGAGAC 540303 i - v v i - v - - (AGACAG)n#Sim 421 AGACAGA-GACAGAGACAGAGACAGAGACAGA-GACAGAGAC-A-GAGAC 466 chr3ptel1M 540304 AGGGACAGAGGAAAGACACAGAGACAGGGACAGAGGAAAGAGACAAGGAG 540353 i - v v i - v - - (AGACAG)n#Sim 467 AGAGACAGA-GACAGAGACAGAGACAGAGACAGA-GACAGAGAC-A-GAG 512 chr3ptel1M 540354 ACAGGGACAGAGGAAAAGGGACACGGAGACGGGGACAAGGGAAAGAGACA 540403 i - - v i -- i i - i v (AGACAG)n#Sim 513 ACAGAGACAGA-G-ACAGAGACA--GAGACAGAGAC-AGAGACAGAGACA 557 chr3ptel1M 540404 CGGAGACGGGGACAAGGGAAAGGGACACGGAGACAGAGACAAAGGAAAGG 540453 -- i i - i v i -- i - v i (AGACAG)n#Sim 558 --GAGACAGAGAC-AGAGACAGAGACA--GAGACAGAGACAGA-GACAGA 601 chr3ptel1M 540454 GACACGGAGACAGGGACAGAGGAAAGACACAGAGACAGGGACAGAGGAAA 540503 -- i - v v i - v (AGACAG)n#Sim 602 GACA--GAGACAGAGACAGA-GACAGAGACAGAGACAGAGACAGA-GACA 647 chr3ptel1M 540504 GAGACAAGGAGACAGGGACAGAGGAAAAAACAG-G-CAGGGACAAGGAAA 540551 - - i iv i i - - i ii v (AGACAG)n#Sim 648 GAGAC-A-GAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACA 695 chr3ptel1M 540552 GAGACGGAGACAG-GGCAAGGAAAGACAC-GAGACAGGGAGGGA-AAAGA 540598 i - i ii v v - i vi - v (AGACAG)n#Sim 696 GAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGA 745 chr3ptel1M 540599 -ACGGGGGGAAAGGGAAAGGGA-AG-GAAAG-GACAAAGAAAAAGGAGAC 540644 - --i i v i v i - - v - i v i - v - (AGACAG)n#Sim 746 GAC--AGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGA-GACA- 791 chr3ptel1M 540645 GGGCCA-AGGAAAACA-AGAGAC-GGGACAGAGGAAAGAG-CA-AGACAG 540689 i v - iv i v - - i - v - - (AGACAG)n#Sim 792 GAGACAGAGACAGAGACAGAGACAGAGACAGA-GACAGAGACAGAGACAG 840 chr3ptel1M 540690 -GGC-GGGAGGGACACGGAGACGGGGAAAGCCAC-GAGA 540725 - i - i vi v i i i v vv - (AGACAG)n#Sim 841 AGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGA 879 Matrix = Unknown Transitions / transversions = 1.39 (86/62) Gap_init rate = 0.10 (92 / 906), avg. gap size = 1.00 (92 / 92) 17 11.25 0.00 0.00 chr3ptel1M 542338 542366 (457634) (AGG)n#Simple_repeat 1 29 (0) m_b123s252i14 4533 chr3ptel1M 542338 AGGAGGAGGAAGAGGAGGAGGAGATGGAG 542366 i iv (AGG)n#Simple 1 AGGAGGAGGAGGAGGAGGAGGAGGAGGAG 29 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 251 28.20 11.20 0.72 chr3ptel1M 545978 546102 (453898) C MIR3#SINE/MIR (15) 193 56 m_b123s601i22 4534 chr3ptel1M 545978 AGAGGGGTAGAGCTGGGCTGGGATCCCGGAGATTCCTGGGTCCGATGCCC 546027 iv vi iv- i iii iviivi i iv C MIR3#SINE/MIR 193 AGAATGTCAGAGCTGGAA-GGGACCTTAGAGATCATCTAGTCCAACCCCC 145 chr3ptel1M 546028 GC--TTTACAAGTGAGGGAACAGAGGCCCCTCGAGG-GAAGGGCCTCG-A 546073 v -- ii i v vvv - v v i -v C MIR3#SINE/MIR 144 TCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCC 95 chr3ptel1M 546074 CGTGGTCAC---------TAG-GACAGAGCCGGGGCTAG 546102 iv --------- - i i C MIR3#SINE/MIR 94 CAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAG 56 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.23 CpG sites = 20, Kimura (unadjusted) = 36.23 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.05 (6 / 124), avg. gap size = 2.50 (15 / 6) 12 19.78 2.27 4.65 chr3ptel1M 546384 546427 (453573) (CCCAGGC)n#Simple_repeat 1 43 (0) m_b123s252i15 4535 chr3ptel1M 546384 CCCTGGCACCTCAGCACCCAGG-CCGGGGCCCCCAGCCCCAGGCC 546427 v - - vv - vi vi (CCCAGGC)n#Si 1 CCCAGGC-CC-CAGGCCCCAGGCCCCAGGCCCCAGGCCCCAGGCC 43 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.07 (3 / 43), avg. gap size = 1.00 (3 / 3) 204 29.73 10.73 3.18 chr3ptel1M 547534 547738 (452262) L2b_3end#LINE/L2 88 307 (159) m_b123s601i23 4536 chr3ptel1M 547534 GCTGCCCCCC--ACAGGACATGGGCTCTCCC--CTCAGGGTCTTTGCTGA 547579 ii i -- v v ? vv ? -- i vv? L2b_3end#LINE 88 GCTGTTCCTCGAACACGCCANGCTCNCTCCCGCCTCAGGGCCTTTGCACN 137 chr3ptel1M 547580 GGCCACTGTCTGTGC-TGG--CATCCTGCCCCTCCTCAGGGACCCCCTG- 547625 v iii vi v - -- ii v v v----i v - L2b_3end#LINE 138 TGCTGTTCCCTCTGCCTGGAACGCCCTTCCCCACCTCT----TCGCCTGG 183 chr3ptel1M 547626 -CAATCCCTAGCTTTTC--TCAGA-CTCGGCTCTACTGCTGCCACCTTCA 547671 - ii - iv -- i- i v v iii v i i L2b_3end#LINE 184 CCAACTCCTA-CTCATCCTTCAGGTCTCAGCTCAAATGTCACCTCCTCCG 232 chr3ptel1M 547672 GGAAGCCAG---TGA----CAGGGCCGAGT---GTGGTCTAGTGTGGCCC 547711 vv--- ---- vi i --- i vi vv v v L2b_3end#LINE 233 GGAAGCCCTCCCTGACCCCCCAGGCCGGGTCAGGCGCCCTCCTCTGGGCC 282 chr3ptel1M 547712 AGTCCAGCCTCATTCTGCCCAGCTCTG 547738 vvi i ii ii --i L2b_3end#LINE 283 CCCCCAGTCCTACCCTGCC--ACTCTG 307 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.01 CpG sites = 32, Kimura (unadjusted) = 39.54 Transitions / transversions = 1.19 (32/27) Gap_init rate = 0.09 (18 / 204), avg. gap size = 1.61 (29 / 18) 26 18.78 0.00 3.23 chr3ptel1M 547740 547803 (452197) (CCTGC)n#Simple_repeat 1 62 (0) m_b123s252i16 4537 chr3ptel1M 547740 CCTGCCCTGCTCTGCCCATTCCTGCCCTGCCCATCCCAGCTCTGCCCTGT 547789 i vvi vv v i - (CCTGC)n#Simp 1 CCTGCCCTGCCCTGCCCTGCCCTGCCCTGCCCTGCCCTGCCCTGCCCTG- 49 chr3ptel1M 547790 CCCACCCCCTGCCC 547803 -iv (CCTGC)n#Simp 50 CCC-TGCCCTGCCC 62 Matrix = Unknown Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.03 (2 / 63), avg. gap size = 1.00 (2 / 2) 282 31.79 10.00 2.94 chr3ptel1M 548863 549212 (450788) L1MA5_3end#LINE/L1 12 385 (662) m_b123s551i3 4538 chr3ptel1M 548863 AATATATAGAGAACTGAGTCAAGTTTATAG--AAAAAACAAGAGAGCCAT 548910 i ii v iv v iv i -- ------- L1MA5_3end#LI 12 AATATACAAGGAACTCAAACAACTCAACAGCAAAAAAACAA-------AT 54 chr3ptel1M 548911 TTCCTGATTGATAA-TGGTCAAAGGATATGAATAGTTATT-------AGA 548952 vvi i ? v - v ? v vi ------- L1MA5_3end#LI 55 AATCCGATTNAAAAATGGGCAAANGATCTGAATAGACATTTCTCAAAAGA 104 chr3ptel1M 548953 AGA-ACTTAAATTTTCTA-----AAAAGAAAAAAACTTCTAAAACACTAA 548996 - ivi vvi v ----- v v vvi v v v L1MA5_3end#LI 105 AGACATACAAATGGCCAACAGGTATATGAAAAAATGCTCAACATCACTAA 154 chr3ptel1M 548997 TAATTAGAGAAATGTACGTTGTAACTCTAGTTTTCCACATCCTATCATCC 549046 v i i i vi iiv ivi i v--vv i v v i L1MA5_3end#LI 155 TCATCAGGGAAATGCAAATCAAAACCACAATG--AGATATCATCTCACCC 202 chr3ptel1M 549047 ------GAATGGCTAAAATGACAGAAAAGGAAAATGATAAATGCTGGGGG 549090 ------ vv v v i i vii i i v i L1MA5_3end#LI 203 CAGTTAGAATGGCTATTATCAAAAAGACAAAAAATAACAAATGCTGGCGA 252 chr3ptel1M 549091 AGATGTGGAAAAGTGGGGACACTAATGCACTGCCAGTGCAATCATGAGCT 549140 i i i iv i v v i iii vi vii i ii L1MA5_3end#LI 253 GGATGCGGAGAAAAGGGAACTCTTATACACTGTTGGTGGGAATGTAAATT 302 chr3ptel1M 549141 GGTCTGG---TTTTGGACAACAATTTGGAACTACGCCCAAAGGGCTGTAA 549187 i vii --- v v i v iv v - i iii i- L1MA5_3end#LI 303 AGTACAGCCATTATGGAAAACAGTATGGAGGTTC-CTCAAAAAACTA-AA 350 chr3ptel1M 549188 AACAG----------TGACCCTGCAAAACCACTAC 549212 i ---------- i v vv L1MA5_3end#LI 351 AATAGAACTACCATATGATCCAGCAATCCCACTAC 385 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 41.68 CpG sites = 58, Kimura (unadjusted) = 42.72 Transitions / transversions = 1.16 (58/50) Gap_init rate = 0.05 (19 / 349), avg. gap size = 2.42 (46 / 19) 306 32.29 7.26 1.88 chr3ptel1M 548863 549165 (450835) L1MB4_3end#LINE/L1 12 330 (597) m_b123s551i2 4538 chr3ptel1M 548863 AATATATAGAGAACTGAGTCAAGTTTATAG--AAAAAACAAGAGAGCCAT 548910 i vvvv v iv i i-- ivi v v L1MB4_3end#LI 12 AATATATAAAGAACTCCTACAACTCAACAACAAAAAAACAAACAACCCAA 61 chr3ptel1M 548911 TTCCTGATTGATAATGGTCAAAGGATATGAATAGTTATT-------AGAA 548953 ?------i v v iv vi ------- L1MB4_3end#LI 62 TTN------AAAAATGGGCAAAGGACTTGAATAGACATTTCTCCAAAGAA 105 chr3ptel1M 548954 GA-ACTTAAATTTTCTAAAAA-----GAAAAAAACTTCTAAAACACTAAT 548997 - ivi vvi v v i----- i vvi v v v i L1MB4_3end#LI 106 GATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCACTAGT 155 chr3ptel1M 548998 AATTAGAGAAATGTACGTTGTAACTCTAGT---TTTCCACATCCTATC-A 549043 v i i vi iiv ivi i ---v v v vi i - L1MB4_3end#LI 156 CATTAGGGAAATGCAAATCAAAACCACAATGAGATACCACTTCACACCCA 205 chr3ptel1M 549044 TCCGAATGGCTAAAATGACAGAAAAGGAAAATGATAAATGCTGGGGGAGA 549093 iiv i v? v v i v i i i i v ii L1MB4_3end#LI 206 CTAGGATGGCTATNATCAAAAAAACGGAAAATAACAAGTGTTGGCGAGGA 255 chr3ptel1M 549094 TGTGGAAAAGTGGGGACACTAATGCACTGCCAGTGCAATCATGAGCTGGT 549143 i i v i v vi i ii vi vii i iv L1MB4_3end#LI 256 TGTGGAGAAATTGGAACCCTCGTGCATTGCTGGTGGGAATGTAAAATGGT 305 chr3ptel1M 549144 -CTG--GTTTTGGACAACAATTTGG 549165 - v -- i v v i L1MB4_3end#LI 306 GCAGCCGCTGTGGAAAACAGTTTGG 330 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 42.90 CpG sites = 50, Kimura (unadjusted) = 43.50 Transitions / transversions = 1.09 (50/46) Gap_init rate = 0.05 (14 / 302), avg. gap size = 2.00 (28 / 14) 17 18.22 0.00 0.00 chr3ptel1M 549635 549665 (450335) (T)n#Simple_repeat 1 31 (0) m_b123s252i18 4539 chr3ptel1M 549635 TTTTTTTTCTTTTAATTTTTGTTTTTGTTTT 549665 i vv v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 31 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 610 32.37 9.48 3.36 chr3ptel1M 549843 550264 (449736) L2c_3end#LINE/L2 26 472 (6) m_b123s601i24 4540 chr3ptel1M 549843 TCTCCGGACACATTACATCTCCTTCC-TCCTCACCCCATATGCACAAGTC 549891 i v v iv v iv i - i vv v v i L2c_3end#LINE 26 TCTCCAGCCTCATCTCCTCCACTCCCCTCCTCGCCCACTATGCTCCAGCC 75 chr3ptel1M 549892 TTCTTCTACCCAGTGGCCCTGGCCTCCAAACACGAACCTCCATCTCTTAG 549941 vivi v- v i?v v vi --- i --- iv vi -- L2c_3end#LINE 76 ACACTG-AACTNCTTGCATT---CCCCAAACACG---CCGCAGTTCTT-- 116 chr3ptel1M 549942 CTCCAGGCT--GGGCAGTCATTCTCCCTGGCCCCCCGGACCCGAAATGTT 549989 - v v -- ? vv iiiv viv vi i v - i i -- L2c_3end#LINE 117 -TCCTGCCTCCGNGCCTTTGCACATGCTGTTCCCTCTG-CCTGGAATG-- 162 chr3ptel1M 549990 CTCTCTTCTCAGCTCTGTTCAC-TGAC---CTCCTGATCTTCATTTAAGT 550035 -- i vv iv i - i --- iv v v i ? L2c_3end#LINE 163 --CTCTTCCCCCCTCCTTCCACCTGGCTAACTCCTACTCATCCTTCAAGN 210 chr3ptel1M 550036 CCCAACTAAAATCTCGCCTGTCGCAGGAAGCTTTTCCCAGTCCACC---- 550081 i i v i v i viiv i i i iiii v ---- L2c_3end#LINE 211 CTCAGCTCAGATGTCACCTCCTCCGGGAAGCCTTCCCTGACCCCCCAAGN 260 chr3ptel1M 550082 TTAATGCCAATGCTGTCC--------CCCA-------CTAATTATGT--C 550114 i i vivii iv -------- ------- ivi ii-- L2c_3end#LINE 261 CTAGTCTAGGTGCCCTCCTCTGTGCTCCCATAGCACCCTGTCTATACTCC 310 chr3ptel1M 550115 CTTTCTAGC--------TTGACTTCATTTGTA--TATTTAGTTGCATGT- 550153 v v -------- i vvv -- i i iv i ? - L2c_3end#LINE 311 CATTATAGCACTTATCATTAACTTGTATTGTAATTGTCTGTTTACNTGTC 360 chr3ptel1M 550154 TGTCTTCCCCATTAGATGATAAGCTCCTCAAGGG-AGGAACTGTTTTTTG 550202 i i i ivi i ii - i i v i i L2c_3end#LINE 361 TGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTA 410 chr3ptel1M 550203 CCTTTCTTTATATCCCCATTGCTTAGCACATAGTAGGTGCTTCATAAATG 550252 iiiv i vi i i i iv L2c_3end#LINE 411 TTCATCTTTGTATCCCCAGCGCCTGGCACATAGTAGGCGCTCAATAAATG 460 chr3ptel1M 550253 CTTGCTGACTGA 550264 i i v L2c_3end#LINE 461 TTTGTTGAATGA 472 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.89 CpG sites = 78, Kimura (unadjusted) = 44.61 Transitions / transversions = 1.44 (78/54) Gap_init rate = 0.06 (27 / 421), avg. gap size = 2.04 (55 / 27) 214 25.51 20.41 0.00 chr3ptel1M 550282 550379 (449621) C MIRc#SINE/MIR (38) 230 113 m_b123s601i25 4541 chr3ptel1M 550282 GTGTAAAAAGCTCTTT-------ATCATTT-ATT--GTCCTCACTGTATC 550321 v v v ------- i i - --i vii v C MIRc#SINE/MIR 230 GTTTACAAAGCGCTTTCACATACATTATCTCATTTGATCCTCACAACAAC 181 chr3ptel1M 550322 CC----AGGGAGTCAAGGC-----TTGTT-CCTTCACTGGACAAATAAGC 550361 ---- v v i ----- i -i ii i vv i i v C MIRc#SINE/MIR 180 CCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGG 131 chr3ptel1M 550362 AAACTGAGGCCCAGAGGG 550379 i i C MIRc#SINE/MIR 130 AAACTGAGGCTCAGAGAG 113 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.93 CpG sites = 15, Kimura (unadjusted) = 31.93 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.06 (6 / 97), avg. gap size = 3.33 (20 / 6) 255 30.39 1.23 2.50 chr3ptel1M 550299 550379 (449621) C MIRb#SINE/MIR (73) 195 116 m_b123s601i26 4541 chr3ptel1M 550299 TCATTTATTGTCCTCACTGTATCCCAGGGAGTCAAGGCTTGTT-CCTTCA 550347 --i vii v v v vi i vv i -i ii C MIRb#SINE/MIR 195 TCATTTA--ATCCTCACAACAACCCTGCGAGGTAGGTATTATTATCCCCA 148 chr3ptel1M 550348 CTGGACAAATAAGCAAACTGAGGCCCAGAGGG 550379 i vv i i v i i C MIRb#SINE/MIR 147 TTTTACAGATGAGGAAACTGAGGCTCAGAGAG 116 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.09 CpG sites = 14, Kimura (unadjusted) = 40.09 Transitions / transversions = 1.40 (14/10) Gap_init rate = 0.04 (3 / 80), avg. gap size = 1.00 (3 / 3) 203 18.60 2.33 0.00 chr3ptel1M 550342 550384 (449616) C MIR3#SINE/MIR (61) 147 104 m_b123s601i27 4541 chr3ptel1M 550342 CCTTCACTGGACAAATAAGCAAACTGAGGCCCAGAG-GGCGAAG 550384 i i vv i i v - i C MIR3#SINE/MIR 147 CCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAG 104 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 21.76 CpG sites = 5, Kimura (unadjusted) = 21.76 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.02 (1 / 42), avg. gap size = 1.00 (1 / 1) 188 35.09 0.00 0.00 chr3ptel1M 551409 551465 (448535) MIR3#SINE/MIR 119 175 (33) m_b123s601i28 4542 chr3ptel1M 551409 CCCCGGTTTCCTCCTTTGGGAGATGGGGAAGTTGGATTCCATGGGCCATG 551458 i i v i vi i i ii i vv iv iv i MIR3#SINE/MIR 119 CCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTA 168 chr3ptel1M 551459 GGATCCC 551465 i i MIR3#SINE/MIR 169 AGGTCCC 175 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 51.29 CpG sites = 14, Kimura (unadjusted) = 51.29 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0) 360 26.50 5.98 0.00 chr3ptel1M 552257 552373 (447627) L2b_3end#LINE/L2 335 458 (8) m_b123s601i29 4543 chr3ptel1M 552257 TCTTCCCCCTCAGACTGTATGTTCC-TGAGGACAGGTACCACCTTTG-CT 552304 i vii iv i - i v i?v i - L2b_3end#LINE 335 TCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCT 384 chr3ptel1M 552305 T-TTGCCCGCT-TAGTGACAGCACTTAGCCCAGTGCTTGGCAGACAA--- 552349 - vv - vivv i i v ? i v i--- L2b_3end#LINE 385 TGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAG 434 chr3ptel1M 552350 GTGTTTAGTAAATGTTGGTTCAGT 552373 i i i i v v i L2b_3end#LINE 435 GCGCTCAGTAAATATTTGTTGAAT 458 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.24 CpG sites = 18, Kimura (unadjusted) = 34.17 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.04 (5 / 116), avg. gap size = 1.40 (7 / 5) 26 15.44 0.00 0.00 chr3ptel1M 553551 553593 (446407) (G)n#Simple_repeat 1 43 (0) m_b123s252i19 4544 chr3ptel1M 553551 GGGGCAGGGGGGGTCGAGGGGGGGGGGGGGGGGGGTGGGGGGG 553593 vi vv i v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 43 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 208 23.26 4.65 0.00 chr3ptel1M 553641 553683 (446317) C L2c_3end#LINE/L2 (12) 466 422 m_b123s601i30 4545 chr3ptel1M 553641 AACAGGCACTTACTAAGCACCTGCTGTGTGCCGGGCA--GGGGAT 553683 ii i i i i i i i i-- C L2c_3end#LINE 466 AACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGAT 422 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 24.01 CpG sites = 10, Kimura (unadjusted) = 31.29 Transitions / transversions = 1.00 (10/0) Gap_init rate = 0.02 (1 / 42), avg. gap size = 2.00 (2 / 1) 12 11.25 6.90 0.00 chr3ptel1M 553873 553901 (446099) (GAGG)n#Simple_repeat 1 31 (0) m_b123s252i20 4546 chr3ptel1M 553873 GAGGGA-GG-GGGAGGGAGGGGCAGAGGGAG 553901 - - ivi (GAGG)n#Simpl 1 GAGGGAGGGAGGGAGGGAGGGAGGGAGGGAG 31 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.07 (2 / 28), avg. gap size = 1.00 (2 / 2) 351 32.78 4.76 4.76 chr3ptel1M 556217 556405 (443595) MIR1_Amn#SINE/MIR 42 230 (0) m_b124s601i1 4547 chr3ptel1M 556217 GGCTCTGGAAGGTCTGAGTCTAGATGCCCCCATAGATATTTCCTAACTG- 556265 i - i ii i ii?i? v vv viv vi i ?v i?i - MIR1_Amn#SINE 42 GACTC-GGGAGACCTGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGN 90 chr3ptel1M 556266 -TGGTCCTGGCCAAGTGAT----CCTGTTTG--CCTCAGTTTCCTCATCT 556308 - ii i v v i---- v i -- MIR1_Amn#SINE 91 GTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCT 140 chr3ptel1M 556309 GCAAAATGGGGGTGATGGCAGC-ACCTCCCTCCCAGGAGGAGGTGTTGTG 556357 i i i ii vi- i ivi ----- i i v MIR1_Amn#SINE 141 GTAAAATGGGGATAATGATACTGACCTCCTTTGTA-----AAGTGCTTTG 185 chr3ptel1M 556358 AGGATCCAATGAGACAGCAAGGACTGTATAAAATGGAGCAATCATCAT 556405 - i v viv -- vi ii i vvv vv i i MIR1_Amn#SINE 186 A-GATCTACTGATGAA--AAGTGCTACATAAGAGCTAGGTATTATTAT 230 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.61 CpG sites = 37, Kimura (unadjusted) = 46.61 Transitions / transversions = 1.68 (37/22) Gap_init rate = 0.07 (14 / 188), avg. gap size = 1.29 (18 / 14) 481 25.30 9.09 2.44 chr3ptel1M 556217 556370 (443630) MIR#SINE/MIR 29 192 (70) m_b124s601i0 4547 chr3ptel1M 556217 GGCTCTGGA---AG---GTCTGAGTCTAGATGCCCCCATAGATATTTCCT 556260 --- --- i i iiii v vv viv vi i v MIR#SINE/MIR 29 GGCTCTGGAGCCAGACTGCCTGGGTTCGAATCCCGGCTCTGCCACTTACT 78 chr3ptel1M 556261 AACTGTG--GTCCTGGCCAAGTGAT----CCTGTTTG--CCTCAGTTTCC 556302 i --ii i v v i---- v i -- MIR#SINE/MIR 79 AGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCC 128 chr3ptel1M 556303 TCATCTGCAAAATGGGGGTGATGGCAGCACCTCCCTCCCAGGAGGAGGTG 556352 i i i iii i v vi ---- v MIR#SINE/MIR 129 TCATCTGTAAAATGGGGATAATAATAGTACCTACCTCATAGG----GTTG 174 chr3ptel1M 556353 TTGTGAGGATCCAATGAG 556370 iv MIR#SINE/MIR 175 TTGTGAGGATTAAATGAG 192 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.71 CpG sites = 24, Kimura (unadjusted) = 31.83 Transitions / transversions = 1.71 (24/14) Gap_init rate = 0.06 (9 / 153), avg. gap size = 2.00 (18 / 9) 12 4.71 4.55 0.00 chr3ptel1M 557005 557026 (442974) (AGAC)n#Simple_repeat 1 23 (0) m_b124s252i0 4548 chr3ptel1M 557005 AGA-AGACAGACAGACACACAGA 557026 - v (AGAC)n#Simpl 1 AGACAGACAGACAGACAGACAGA 23 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.05 (1 / 21), avg. gap size = 1.00 (1 / 1) 240 29.03 6.45 0.00 chr3ptel1M 559366 559427 (440573) L3#LINE/CR1 3945 4010 (89) m_b124s601i2 4549 chr3ptel1M 559366 GGAAGCTAATGAGCCTCCCATCCCTGGAAGCATTCAAGCAAAGGC----C 559411 ?i v i ii i v i ii i ----i L3#LINE/CR1 3945 GNGAGGTAGTGAGCTCCCCGTCACTGGAGGTGTTCAAGCAGAGGCTGGAT 3994 chr3ptel1M 559412 GACTGTCTGCCAAGGA 559427 iiii i i L3#LINE/CR1 3995 GACCACTTGTCAGGGA 4010 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.22 CpG sites = 16, Kimura (unadjusted) = 42.45 Transitions / transversions = 8.00 (16/2) Gap_init rate = 0.02 (1 / 61), avg. gap size = 4.00 (4 / 1) 184 6.36 0.77 1.56 chr3ptel1M 560085 560343 (439657) (GGAA)n#Simple_repeat 1 257 (0) m_b124s252i1 4550 chr3ptel1M 560085 GGAAGTAAAGGGAGGGAAGGAGGGACAGAGAGGAAGGAAGGAAGGAAGGA 560134 -i - i i - ii (GGAA)n#Simpl 1 GGAAG-GAA-GGAAGGAAGGAAGGA-AGGAAGGAAGGAAGGAAGGAAGGA 47 chr3ptel1M 560135 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG 560184 (GGAA)n#Simpl 48 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG 97 chr3ptel1M 560185 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 560234 (GGAA)n#Simpl 98 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 147 chr3ptel1M 560235 AGGAAGGAAGGAAGGAAGGAAGAAAGGAAGGAGAGAGAGGGAGAGAGGAA 560284 i - ii i ii (GGAA)n#Simpl 148 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA-AGGAAGGAAGGAAGGAA 196 chr3ptel1M 560285 GGAAGGAGGGAAGGAAGGAAGAAAGGAAGGAAGG-AGGGAGGGAGGAAGG 560333 i i - i i (GGAA)n#Simpl 197 GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG 246 chr3ptel1M 560334 AAGGAA-GAAG 560343 - (GGAA)n#Simpl 247 AAGGAAGGAAG 257 Matrix = Unknown Transitions / transversions = 1.00 (15/0) Gap_init rate = 0.02 (6 / 258), avg. gap size = 1.00 (6 / 6) 194 30.87 8.23 3.64 chr3ptel1M 560775 560932 (439068) L3#LINE/CR1 3935 4099 (0) m_b124s601i3 4551 chr3ptel1M 560775 GGGCTGTCTCAAAGGGGCCAGAGTGGCTCTCCTCCTCACTGAAGGGCTTT 560824 i i?ii v---- iv- i v i vv i L3#LINE/CR1 3935 GGGCTGCCTCGNGAGGT----AGTGAG-CTCCCCGTCACTGGAGGTGTTC 3979 chr3ptel1M 560825 GCCCTCA-GCTGCCTGA-TGCTGGCC-----TGGTGCTGGGGGGAGTCCT 560867 ivv vv - vv -ii v i ----- v iv ii v L3#LINE/CR1 3980 AAGCAGAGGCTGGATGACCACTTGTCAGGGATGTTGTAGAAGGGATTCCT 4029 chr3ptel1M 560868 -CGTCAGTTAGGA-GTTGGACCAGA-GGCCTCCAGGGCTCCCGT--AGCC 560912 - i ii v i - i - i i i - v -- i i L3#LINE/CR1 4030 GCATTGGATGGGAGGTTGGACTAGATGACCTCTAAGG-TCCCTTCCAACT 4078 chr3ptel1M 560913 CTGGGA-CCTGTGACTCCACC 560932 i -i i i i L3#LINE/CR1 4079 CTGAGATTCTGTGATTCTATC 4099 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.84 CpG sites = 30, Kimura (unadjusted) = 42.04 Transitions / transversions = 1.76 (30/17) Gap_init rate = 0.09 (14 / 157), avg. gap size = 1.36 (19 / 14) 127 21.38 0.73 0.73 chr3ptel1M 561815 562088 (437912) (AGGAGG)n#Simple_repeat 1 274 (0) m_b124s252i2 4552 chr3ptel1M 561815 AGGAGGGGGAAGAAGAGAACAGGGAGGAGGAGGAGGGAGGAGGAAGAGGA 561864 i i i i vii - i (AGGAGG)n#Sim 1 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA-GGAGGAGGAGGAGGA 49 chr3ptel1M 561865 AGAGGAAGAGGAGGGGGAGGAGGAGGAAGAAGAAGAAGAAGAGAACAGGG 561914 i i i i i i i i i vii (AGGAGG)n#Sim 50 GGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGG 99 chr3ptel1M 561915 AGGAGGAAGAGGAGGAGGAAGAAGAGAACTGGGAGGAGGAAGAGGAGGGA 561964 i i i i vvi i ii (AGGAGG)n#Sim 100 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG 149 chr3ptel1M 561965 AAGGAGGAGGAGGAGGAGGAAGAAGAAGATAACAGGGAGGAGGAGGAGGG 562014 i i i i vi vii - (AGGAGG)n#Sim 150 GAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA-GG 198 chr3ptel1M 562015 AGGAGGAAGAGGAGGAGGAAGAGGAGG-GGA-GAAGAGGAGAAGGAGAAG 562062 i i - - i i i (AGGAGG)n#Sim 199 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG 248 chr3ptel1M 562063 AAGGAAGAGGGGGAGGAGAAGGAGGA 562088 i i i i (AGGAGG)n#Sim 249 GAGGAGGAGGAGGAGGAGGAGGAGGA 274 Matrix = Unknown Transitions / transversions = 7.00 (42/6) Gap_init rate = 0.01 (4 / 273), avg. gap size = 1.00 (4 / 4) 65 32.39 2.99 1.85 chr3ptel1M 561823 562090 (437910) (GAA)n#Simple_repeat 1 271 (0) m_b124s252i3 4552 chr3ptel1M 561823 GAAGAAG-AGAACAGGGAGGAGGAGGAG-GGAGGAGGAAGAGGAAGAGGA 561870 - v i i i i i -i i i i i (GAA)n#Simple 1 GAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA 50 chr3ptel1M 561871 AGAGGAGGGGGAGGAGGAGGAAGAAGAAGAAGAAG-AGAACAGGGAGGAG 561919 i i ii i i i - v -i i i (GAA)n#Simple 51 AGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA-AGAAGAA 99 chr3ptel1M 561920 GAAGAGGAGGAGGAAGAAG-AGAACTGGGAGGAGGAAGAGGAGGGAAAGG 561968 i i i - -vii i i i i i i i (GAA)n#Simple 100 GAAGAAGAAGAAGAAGAAGAAGAA-GAAGAAGAAGAAGAAGAAGAAGAAG 148 chr3ptel1M 561969 AGGAGGAGGAGGAGGAAGAAGAAG-ATAACAGGGAGGAGGAGGAG-GGAG 562016 i i i i i - v v i i i i i -i i (GAA)n#Simple 149 AAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAA 198 chr3ptel1M 562017 GAGGAAGAGGAGGAGGAAGAGGAGGGGAGAAG-AGGAGAAGGAGAAGAAG 562065 i i i i i -i i - i i - (GAA)n#Simple 199 GAAGAAGAAGAAGAAGAAGAAGA-AGAAGAAGAAGAAGAAGAAGAAGAA- 246 chr3ptel1M 562066 GAAG-AGGGGGAGGAGAAGGAGGAAG 562090 - ii i i - i (GAA)n#Simple 247 GAAGAAGAAGAAGAAGAA-GAAGAAG 271 Matrix = Unknown Transitions / transversions = 11.60 (58/5) Gap_init rate = 0.05 (13 / 267), avg. gap size = 1.00 (13 / 13) 24 12.06 0.00 0.00 chr3ptel1M 563350 563385 (436615) (CA)n#Simple_repeat 1 36 (0) m_b124s252i4 4553 chr3ptel1M 563350 CACACACTCACACATTCACACACACACACGCACACA 563385 v iv i (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACA 36 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 195 36.25 11.25 2.30 chr3ptel1M 564704 564943 (435057) L3#LINE/CR1 3214 3474 (625) m_b124s601i4 4554 chr3ptel1M 564704 ATTGGCCCAGAGCTCAAAG-TGGG-GGGAGAGCTCACACACTGGGGGGCA 564751 v vv vii v - - v v i i? iv i L3#LINE/CR1 3214 ATTTGCAGATGACACAAAGCTGGGAGGGATAGCTAATACGNTGGATGACA 3263 chr3ptel1M 564752 GTATC----CCCAAGATGCCC---ACAGGCCAGAA-GGGGGACCCA---C 564790 v ----ii i ? vi --- ii - iv i v --- L3#LINE/CR1 3264 GAATCAAGATTCAAAANGATCTCGACAGGCTGGAACGATGGGCCGAAACC 3313 chr3ptel1M 564791 AGAAGGGGAGAACACAGCATGGGGATG---GTGGA------CACTGGGGC 564831 iv i ivii ivi i -- i--- ii ------ i vi i L3#LINE/CR1 3314 AACAAGATGAAATTTAACA--GGGATAAATGTAAAGTCCTGCATTTAGGT 3361 chr3ptel1M 564832 TCAAGAAATCCCCTTCCCACATTGAAGATG-AGGGAATTT---TTCACTG 564877 i vv v v vi vv i - i i i --- vi v L3#LINE/CR1 3362 TCAAAAAATCAACTGCACAAGTACAGGATGGAGAGGATCTGGCTTAGCAG 3411 chr3ptel1M 564878 TGCCTTGGGGGAGAAAGGATCTAGAG-TGCTGGTCAACTGATGTAAGCTC 564926 iivi iiv v i - i i - vi i ii i ---i L3#LINE/CR1 3412 CAGTTCACGTGAAAAAG-ACCTAGGGGTTTTAGTTGACCG---CAAGCTC 3457 chr3ptel1M 564927 CCCACAAAGCAACAGTG 564943 vvi ii iv L3#LINE/CR1 3458 AATATGAGCCAACAGTG 3474 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 51.36 CpG sites = 53, Kimura (unadjusted) = 53.24 Transitions / transversions = 1.66 (53/32) Gap_init rate = 0.07 (17 / 239), avg. gap size = 1.94 (33 / 17) 459 26.48 10.71 3.33 chr3ptel1M 564996 565163 (434837) C MIR#SINE/MIR (10) 252 73 m_b124s601i5 4555 chr3ptel1M 564996 AGCCTTGATTAAGCACCTACTGTGGGCCACGCACTGTGCTAAGGGCTTTA 565045 i v v i i i i v v v v C MIR#SINE/MIR 252 AACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGCGCTTTA 203 chr3ptel1M 565046 CCAAAAATGCCTTATTT-ATCCTGAAAATAACAACCACCCTGAAAGGGAA 565094 vviv v iv i - ------ v v ivi v i C MIR#SINE/MIR 202 CATGTATTAACTCATTTAATCC------TCACAACAACCCTATGAGGTAG 159 chr3ptel1M 565095 ATGCTGTTATTGTTCCAATGT------TGAGGAAACTGAAGCAAACAGA- 565137 i i i i i v v ------ i v v - C MIR#SINE/MIR 158 GTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAG 109 chr3ptel1M 565138 -TCAAG---------CAGGACCACACAGCCAGGGAG 565163 - i --------- i ii i vi C MIR#SINE/MIR 108 GTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAG 73 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.32 CpG sites = 23, Kimura (unadjusted) = 33.25 Transitions / transversions = 1.15 (23/20) Gap_init rate = 0.07 (11 / 167), avg. gap size = 2.18 (24 / 11) 448 27.23 8.96 6.45 chr3ptel1M 565000 565211 (434789) C MIRb#SINE/MIR (16) 252 36 m_b124s601i6 4555 chr3ptel1M 565000 TTGATTAAGCACCTACTGTGGGCCACGCACTGTGCTAAGGGCTTTACCAA 565049 v i i i i v v v vvi C MIRb#SINE/MIR 252 TTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACATG 203 chr3ptel1M 565050 AAATGCCTTATTT-ATCCTGAAAATAACAACCACCCTGAAAGGGAAATGC 565098 v v ii i - ------ v v vi v ii ii C MIRb#SINE/MIR 202 CATTATCTCATTTAATCC------TCACAACAACCCTGCGAGGTAGGTAT 159 chr3ptel1M 565099 TGTTAT---TGTTCCAATGTTGAGGAAACTGAAG--CAAACAGATCAAG- 565142 i ---ii ii vv v i -- i v i i - C MIRb#SINE/MIR 158 TATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGT 109 chr3ptel1M 565143 --------CAGGACCACACAGCCAGGGAGGACCCAGGCAGATCAAGCAGG 565184 -------- i ii i vi v----- v --- i C MIRb#SINE/MIR 108 AACTTGCCCAAGGTCACACAGCTAGTAAGT-----GGCAGAGC---CGGG 67 chr3ptel1M 565185 ACC---ACACAGCTATGGCAGA-TCCAAAGC 565211 ii--- v v v v v - C MIRb#SINE/MIR 66 ATTCGAACCCAGGTCTGTCTGACTCCAAAGC 36 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.23 CpG sites = 30, Kimura (unadjusted) = 34.54 Transitions / transversions = 1.25 (30/24) Gap_init rate = 0.10 (21 / 211), avg. gap size = 1.57 (33 / 21) 218 29.15 8.04 15.79 chr3ptel1M 565027 565250 (434750) C MIRc#SINE/MIR (36) 232 24 m_b124s601i7 4555 chr3ptel1M 565027 CACTGTGCTAAGGGCTTTACCAAA-AATGCCTTATTT-ATCCTGAAAATA 565074 v v i v v vv v - v ii i - v ----- C MIRc#SINE/MIR 232 CAGTTTACAAAGCGCTTTCACATACATTATCTCATTTGATCCTCA----- 188 chr3ptel1M 565075 ACAACCACCCTGAAAGGGAAAT------GCTGTTATTGTTCCAATGTTGA 565118 - v vi v iii------ v i i i v v iv C MIRc#SINE/MIR 187 -CAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTAC 139 chr3ptel1M 565119 GGAAACTGAAGCAAACAGATCAAGCAGGACCACACAGCCAGGGAGGACCC 565168 i --- i - v -------- i i------- i --ii C MIRc#SINE/MIR 138 AGA---TGAGG-AAACTGA--------GGCT-------CAGAGAGG--TT 110 chr3ptel1M 565169 AGGCAGATCAAGCAGGACCACACAGCTA-----TGGCAGATCCAAAGCTG 565213 i iiiv iivv i ii ----- v i----- C MIRc#SINE/MIR 109 AAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG-----G 65 chr3ptel1M 565214 GACTTGAACTCAGGTTTT-----CTCCGAGTCTCAGGGCTCT 565250 i i i ----- i - v C MIRc#SINE/MIR 64 GACTCGAACCCAGGTCTTCCTGACTCCAAGTC-CAGTGCTCT 24 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.71 CpG sites = 33, Kimura (unadjusted) = 37.42 Transitions / transversions = 1.50 (33/22) Gap_init rate = 0.17 (38 / 223), avg. gap size = 1.34 (51 / 38) 12 24.12 0.00 0.00 chr3ptel1M 565811 565844 (434156) (TGC)n#Simple_repeat 1 34 (0) m_b124s252i5 4556 chr3ptel1M 565811 TGCTGCTGACGCTGCCCTTCCGGCTGCTGCTGCT 565844 vi ivi v v (TGC)n#Simple 1 TGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT 34 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 13 20.20 4.84 4.84 chr3ptel1M 568553 568614 (431386) (ATGGAGC)n#Simple_repeat 1 62 (0) m_b124s252i6 4557 chr3ptel1M 568553 ATGGAGCATGGAG-A-GTCGGATGGAGCATGGCGAGC-TGGGGACGGTGA 568599 - - vv v - - - i - ivv (ATGGAGC)n#Si 1 ATGGAGCATGGAGCATGGAGCATGGAGCAT-G-GAGCATGGAG-CATGGA 47 chr3ptel1M 568600 GCGGCGAGCATGGAG 568614 ivv (ATGGAGC)n#Si 48 GCATGGAGCATGGAG 62 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.10 (6 / 61), avg. gap size = 1.00 (6 / 6) 17 20.99 1.75 5.45 chr3ptel1M 569780 569836 (430164) (GGGA)n#Simple_repeat 1 55 (0) m_b124s252i7 4558 chr3ptel1M 569780 GGGA-GGAGGAGAGAGATGAAGAAGAAGAAGGAGGGGGAGGGAGGGAAGG 569828 - - i v i -i i i - i i (GGGA)n#Simpl 1 GGGAGGGAGG-GAGGGAGGGAG-GGAGGGAGG-GAGGGAGGGAGGGAGGG 47 chr3ptel1M 569829 AAGGAGGG 569836 i (GGGA)n#Simpl 48 AGGGAGGG 55 Matrix = Unknown Transitions / transversions = 8.00 (8/1) Gap_init rate = 0.07 (4 / 56), avg. gap size = 1.00 (4 / 4) 66 23.27 4.39 0.94 chr3ptel1M 569782 569986 (430014) (GAGAGA)n#Simple_repeat 1 212 (0) m_b124s252i8 4558 chr3ptel1M 569782 GAG-GAG-GAGAGAGATGA-AGA-AGA-AGAAGGAGGGGGAGGGAGGGAA 569826 - - - - - - ii i i i i i (GAGAGA)n#Sim 1 GAGAGAGAGAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 49 chr3ptel1M 569827 GGAAGGAGGGGAAGACAGAGACAGAGACAGAAAGA-AGAGAAACAGGGAG 569875 i ii i ii v v v i - i v i (GAGAGA)n#Sim 50 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 99 chr3ptel1M 569876 AGACAGAGATATACACAGAGAAAGAGCAGAGAGA-AGA-AGAG-GAGGGA 569922 v v v v v i - - - - i (GAGAGA)n#Sim 100 AGAGAGAGAGAGAGAGAGAGAGAGAG-AGAGAGAGAGAGAGAGAGAGAGA 148 chr3ptel1M 569923 GAGACAGAGAGACACAGAGTCAGAGAGATAGAGAGAGAGAGAAACAGACA 569972 v v v vv v i v v (GAGAGA)n#Sim 149 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 198 chr3ptel1M 569973 AAAACAGAGACAGA 569986 i i v v (GAGAGA)n#Sim 199 GAGAGAGAGAGAGA 212 Matrix = Unknown Transitions / transversions = 1.11 (21/19) Gap_init rate = 0.05 (11 / 204), avg. gap size = 1.00 (11 / 11) 43 0.00 0.00 0.00 chr3ptel1M 570238 570274 (429726) (GT)n#Simple_repeat 1 37 (0) c_b124s251i0 4559 chr3ptel1M 570238 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 570274 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 37 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 97 0.00 1.16 0.00 chr3ptel1M 570275 570360 (429640) (GA)n#Simple_repeat 1 87 (0) c_b124s251i1 4560 chr3ptel1M 570275 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 570324 (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr3ptel1M 570325 GAGAGAG-GAGAGAGAGAGAGAGAGAGAGAGAGAGAG 570360 - (GA)n#Simple_ 51 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 87 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.01 (1 / 85), avg. gap size = 1.00 (1 / 1) 64 25.48 5.05 0.00 chr3ptel1M 570364 570581 (429419) (GACAGA)n#Simple_repeat 1 229 (0) m_b124s252i10 4561 chr3ptel1M 570364 GACAGACACAGAGACACAG--AGAGACAGAGACAGGGGGATGGAGGGAGG 570411 v v -- i iv vi vi i (GACAGA)n#Sim 1 GACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGA 50 chr3ptel1M 570412 AAGACAGAGACACAGACACAGAGATGGGGAAAGAGACAGAGA-AG-GAAA 570459 v v v v v ii i v - - v (GACAGA)n#Sim 51 CAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACA 100 chr3ptel1M 570460 GGAACAGACACACAGAGATAGAGGAAAAGAGAGACAGAGGAGGAAAAAGA 570509 ii v v v v vii i v ivi i v (GACAGA)n#Sim 101 GAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGA 150 chr3ptel1M 570510 GACAGACACACACATAGAGACAG-G-CAGAGTCAGAG--AGAAACAGA-A 570554 v v v i - - v -- i - (GACAGA)n#Sim 151 GACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGA 200 chr3ptel1M 570555 AAG-GA-GGAGAGAGACACAGGGACAGAG 570581 v - -i v v i (GACAGA)n#Sim 201 CAGAGACAGAGACAGAGACAGAGACAGAG 229 Matrix = Unknown Transitions / transversions = 0.74 (20/27) Gap_init rate = 0.04 (9 / 217), avg. gap size = 1.22 (11 / 9) 209 19.70 0.25 0.00 chr3ptel1M 571948 572351 (427649) (TG)n#Simple_repeat 1 405 (0) m_b124s252i11 4562 chr3ptel1M 571948 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGTGTGTGAGTGTGAGAGTA 571997 i v v v i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr3ptel1M 571998 TGTGTGTCTGTGAGTGTATGTGTGTGTGAGAATGTGAGTGTGTGTGGGTG 572047 v v i v vi v v (TG)n#Simple_ 51 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 100 chr3ptel1M 572048 TACATGTGTGTGAGAGAGTGTGTGAGTGAGTGTAAATGTGTGTGTGAGTA 572097 iii v v v v v ivi v i (TG)n#Simple_ 101 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 150 chr3ptel1M 572098 TGTGTGTGGGTGGGTGTGCATGTGTGTGTGTGGGTGTGCATGTGTGTGTG 572147 v v ii v ii (TG)n#Simple_ 151 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 200 chr3ptel1M 572148 AGTGTGTGTGAGGGAGAGTGTGTGAGTGTGAGTGTGAGTGTATGTGAGTG 572197 v v v v v v v v i v (TG)n#Simple_ 201 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 250 chr3ptel1M 572198 TGTGTGTCTCTGT-TGTGAGTGTGTGTATGTGAGTGTGTGTGTTTGTGAG 572246 v v - v i v v v (TG)n#Simple_ 251 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 300 chr3ptel1M 572247 AGAGTATGTGTGTCTGTGAGTGTGTGTGTGTGTGAGTGTGTCTGTGAGTG 572296 v v i v v v v v (TG)n#Simple_ 301 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 350 chr3ptel1M 572297 TGTGTGTGTATGAGAGAACATGCATGTGTGTGTGTGTGAGTGTGAGTGTG 572346 i v v viii ii v v (TG)n#Simple_ 351 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 400 chr3ptel1M 572347 TGAGT 572351 v (TG)n#Simple_ 401 TGTGT 405 Matrix = Unknown Transitions / transversions = 0.49 (23/47) Gap_init rate = 0.00 (1 / 403), avg. gap size = 1.00 (1 / 1) 15 38.66 0.00 0.00 chr3ptel1M 574226 574277 (425723) (GG)n#Simple_repeat 1 52 (0) m_b124s252i12 4563 chr3ptel1M 574226 GGGGGGGGGGAAAGGGGAAAGGGGGAAAAAGGGGGGAAAGGGGGGGGGGG 574275 iii iii iiiii iii (GG)n#Simple_ 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 50 chr3ptel1M 574276 GG 574277 (GG)n#Simple_ 51 GG 52 Matrix = Unknown Transitions / transversions = 1.00 (14/0) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 33 18.51 0.00 0.00 chr3ptel1M 577792 577852 (422148) (CA)n#Simple_repeat 1 61 (0) m_b124s252i13 4564 chr3ptel1M 577792 CACACACACTCATTCACACTTATTCACACACACACTCACACACACACGCA 577841 v iv vi iv v i (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 chr3ptel1M 577842 CACACTCACAC 577852 v (CA)n#Simple_ 51 CACACACACAC 61 Matrix = Unknown Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 227 29.30 8.89 7.10 chr3ptel1M 577910 578089 (421911) MIR1_Amn#SINE/MIR 3 185 (45) m_b124s601i8 4565 chr3ptel1M 577910 GGGAGCCACAGGCGGGGTC-AGTGGTTAGACCACTGCGGCCCAAGTCAGG 577958 v --- i v - v v - i iviiiiiv MIR1_Amn#SINE 3 GGGAGGCA---GTGTGGTCTAGTGGATAGAGCACTG-GACTGGGACTCGG 48 chr3ptel1M 577959 AAGATCCAGATTCCAGCGCGGCCTGAGACCCTTCCTAGCATAGCGACCTT 578008 i i ii i ? ?iv v v vv v v ?v i? vv? i MIR1_Amn#SINE 49 GAGACCTGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTT 98 chr3ptel1M 578009 CAGTAAGTCACCTGACATC---GTG-----------TCATCCGTAACCTG 578044 vi i i ? v --- ? ----------- i vv MIR1_Amn#SINE 99 GGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATG 148 chr3ptel1M 578045 GGGAAACAGCAGCACCG-CCTCCGCGGTTTGTTACAAGGGGCTTTG 578089 -- i iiiii i - ---- --- i v MIR1_Amn#SINE 149 GGG--ATAATGATACTGACCTCC----TTTGT---AAAGTGCTTTG 185 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.43 CpG sites = 28, Kimura (unadjusted) = 40.43 Transitions / transversions = 1.33 (28/21) Gap_init rate = 0.09 (17 / 179), avg. gap size = 1.71 (29 / 17) 276 30.97 14.19 0.00 chr3ptel1M 577928 578082 (421918) MIRc#SINE/MIR 16 192 (76) m_b124s601i9 4565 chr3ptel1M 577928 CAGTGGTTAGACCACTGCGGCCCAAGTCAGGAAGATCCAGATTCCAGCGC 577977 vv v viviivi i ii i v iv MIRc#SINE/MIR 16 CAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCC 65 chr3ptel1M 577978 GGCCTGAGACCCTTCCTAGCATAGCGACCTTCAGTAAGTCACCTGACATC 578027 v v vv v v v vvv i vi i i i v MIRc#SINE/MIR 66 CGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 chr3ptel1M 578028 G-TG-------------TCATCCGTAACCTGGGGA----AACAGCAGCAC 578059 v- ------------- i vv ---- i v v v MIRc#SINE/MIR 116 TCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCC 165 chr3ptel1M 578060 CGCCT-CCGC---GGTTTGTTACAAGG 578082 i - v --- v iii MIRc#SINE/MIR 166 TGCCTACCTCACAGGGTTGTTGTGAGG 192 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.08 CpG sites = 20, Kimura (unadjusted) = 40.08 Transitions / transversions = 0.71 (20/28) Gap_init rate = 0.03 (5 / 154), avg. gap size = 4.40 (22 / 5) 13 12.53 0.00 0.00 chr3ptel1M 578130 578155 (421845) (TCCCC)n#Simple_repeat 1 26 (0) m_b124s252i14 4566 chr3ptel1M 578130 TCCCCTCCGCGCCCCTCCCCTCTCCT 578155 v v i (TCCCC)n#Simp 1 TCCCCTCCCCTCCCCTCCCCTCCCCT 26 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 15 21.14 0.00 0.00 chr3ptel1M 580172 580200 (419800) (A)n#Simple_repeat 1 29 (0) m_b124s252i15 4567 chr3ptel1M 580172 AAAAAAGAGAAAAAAAAGAGAAAGAAAAA 580200 i i i i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA 29 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 28 22.28 1.45 0.00 chr3ptel1M 581692 581760 (418240) (GAGAGA)n#Simple_repeat 1 70 (0) m_b124s252i16 4568 chr3ptel1M 581692 GAGAAGGAGAGGGAAGGAGAAAGCGAGGGAGAG-GAGAGAAAGGGAGAGA 581740 ii i ii i v i - i i (GAGAGA)n#Sim 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr3ptel1M 581741 GAGACAGAGACATAGAGAGA 581760 v v v (GAGAGA)n#Sim 51 GAGAGAGAGAGAGAGAGAGA 70 Matrix = Unknown Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.01 (1 / 68), avg. gap size = 1.00 (1 / 1) 17 18.36 0.00 0.00 chr3ptel1M 581919 581955 (418045) (TCTGTG)n#Simple_repeat 1 37 (0) m_b124s252i17 4569 chr3ptel1M 581919 TCTGTATCTGTGTCTGGCTTTGTGTCTATGTGTGTGT 581955 i vv i i v (TCTGTG)n#Sim 1 TCTGTGTCTGTGTCTGTGTCTGTGTCTGTGTCTGTGT 37 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 17 29.69 0.00 1.85 chr3ptel1M 581921 581975 (418025) (TG)n#Simple_repeat 1 54 (0) m_b124s252i18 4569 chr3ptel1M 581921 TGTATCTGTGTCTGGCTTTGTGTCTATGTGTGTGTGCGTACAGAGTGTGT 581970 i v v vv v v i i -vv v (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT-GTGTGTGTGT 49 chr3ptel1M 581971 GTTTG 581975 v (TG)n#Simple_ 50 GTGTG 54 Matrix = Unknown Transitions / transversions = 0.30 (3/10) Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1) 30 5.18 0.00 2.44 chr3ptel1M 581981 582022 (417978) (GTGTGAGT)n#Simple_repeat 1 41 (0) c_b124s251i2 4570 chr3ptel1M 581981 GTGTGTGTGTGTGAGTGTGTGAGTGTGTGGGTGTTGTGAGTG 582022 v i - (GTGTGAGT)n#S 1 GTGTGAGTGTGTGAGTGTGTGAGTGTGTGAGTG-TGTGAGTG 41 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.02 (1 / 41), avg. gap size = 1.00 (1 / 1) 180 26.98 3.17 0.00 chr3ptel1M 583650 583712 (416288) C L2b_3end#LINE/L2 (19) 447 383 m_b124s601i10 4571 chr3ptel1M 583650 ATTTA-AGGGTGCCCACAGTG-GCCAGGCTTCGTGCGAGCCCGTGGGGAT 583697 -v i i i v - ?ii v v vv C L2b_3end#LINE 447 ATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGGGAT 398 chr3ptel1M 583698 GCAGAGGCAAAAAGG 583712 i v ii v i C L2b_3end#LINE 397 ACAGCGGTGAACAAG 383 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.20 CpG sites = 9, Kimura (unadjusted) = 34.64 Transitions / transversions = 1.12 (9/8) Gap_init rate = 0.03 (2 / 62), avg. gap size = 1.00 (2 / 2) 678 33.94 2.42 2.87 chr3ptel1M 583948 584402 (415598) L1ME5_3end#LINE/L1 211 663 (278) m_b124s551i0 4572 chr3ptel1M 583948 CTGGTAAAATAACAGGAAA--AAATAACCATGAATGCTCGAGAGGATACG 583995 i - vi i i--ii ivvii i i v v ii L1ME5_3end#LI 211 CTGGCAAAA-ATTAGAAAGCTGGATAATGCCAAGTGTTGGCGAGGATGTG 259 chr3ptel1M 583996 GGAAAACTGGGACAACGATGCCTTGTTGGTGGAATTGTGAACGAATCCAC 584045 i ? iv i vviv vi i i v ii vii v v L1ME5_3end#LI 260 GGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACTGGTGCAG 309 chr3ptel1M 584046 CCATTCTGAAGAGCAATCTGGAATTATGCCGAAAAAGTTATTGAACTGTG 584095 i v v iviv vv v v v iv --- L1ME5_3end#LI 310 CCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTAAGTATAC---G 356 chr3ptel1M 584096 CATCCCCTTTGACCCAGCAGTGTTTCTACTGGGCTTATACCCCAAGGAGA 584145 v v i viiv v iv i i i L1ME5_3end#LI 357 CATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATATCCCAAAGAAA 406 chr3ptel1M 584146 TACTAAAGAAGGG----AAAGGGACCTGTATGTGCCAAAATGTTTGTGGC 584191 v v viv v---- i v i ---- ii ii v L1ME5_3end#LI 407 TTCTCACACAGGTCCATAAGGGGACATGTACG----AGGATGTTCATTGC 452 chr3ptel1M 584192 AGCCCTGTTTGAAGTGGCCAGAAACTGGAAAAGGAATGGATGCCCATCAA 584241 vi vi vi i ii iiviivv i i v L1ME5_3end#LI 453 AGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGGGTGTCCATCAC 502 chr3ptel1M 584242 CTGGAGAATGGTTGGGTAAATTGTGGTATATGAATGTTATGGAATATTAT 584291 iv i v i v iv v iiii i i L1ME5_3end#LI 503 TGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACACCATGGAGTACTAT 552 chr3ptel1M 584292 TGTTCTGTAAGAAACGACCAACAGGATGATTTCAGAAAGGCCTGGAGAGA 584341 vvvv v v i i vi vi vviv v ivii v vi L1ME5_3end#LI 553 GCAGCAGTTAGAAGCAACGGACTAGATGTACACATAGCAACATGGATGGA 602 chr3ptel1M 584342 ATTACACGAAC-TGATGCTGAGTGAAATGAGC-AGAACCAG---GAGATC 584386 vi -i vi - ii vi i- v --- -- L1ME5_3end#LI 603 TCT-TAAAAACATAGTGCTGAGTGAAAAAAGTAAGAAACAGAATGAGA-- 649 chr3ptel1M 584387 ATTATATACCTCAATA 584402 -- ? v v L1ME5_3end#LI 650 --TNTATAACACAATA 663 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 45.71 CpG sites = 80, Kimura (unadjusted) = 46.56 Transitions / transversions = 1.14 (80/70) Gap_init rate = 0.04 (18 / 454), avg. gap size = 1.33 (24 / 18) 874 33.67 0.75 1.01 chr3ptel1M 583978 584376 (415624) L1ME4c_3end#LINE/L1 242 639 (191) m_b124s551i1 4572 chr3ptel1M 583978 AATGCTCGAGAGGATACGGGAAAACTGGGACAACGATGCCTTGTTGGTGG 584027 v v ? i vi v ?viv i v i L1ME4c_3end#L 242 AATGCTGGCGAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGG 291 chr3ptel1M 584028 AATTGTGAACGAATCCACCCATTCTGAAGAGCAATCTGGAATTATGCCGA 584077 v ? i ivii v v v i i i i v v i ivvv L1ME4c_3end#L 292 CANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATC 341 chr3ptel1M 584078 AAAAGTTATTGAACTGTGCATCCCCTTTGACCCAGCAGTGTTTCTACTGG 584127 i ii vi v v v i i viiv v L1ME4c_3end#L 342 AAGAGCCATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGG 391 chr3ptel1M 584128 GCTTATACCCCAAGGAGATACT---AAAGAAGGGAAAGGGACCTGTATGT 584174 vv v i i i v --- i i --- i i L1ME4c_3end#L 392 GAATTTATCCTAAGGAAATAATTCAAAAGAAGGAAAAAG---CTATATGC 438 chr3ptel1M 584175 GCCAAAATGTTTGTGGCAGCCCTGTTTGAAGTGGCCAGAAACTGGAAAAG 584224 i v i ii v vi i iv i i v i i vi L1ME4c_3end#L 439 ACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACA 488 chr3ptel1M 584225 GAATGGATGCCCATCAACTGGAGAATGGTTGGGTAAATTGTGGTATATGA 584274 ivv ii i v iv i ii i i v? L1ME4c_3end#L 489 ACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCN 538 chr3ptel1M 584275 ATGTTATGGAATATTATTGTTCTGTAAGAAACGACCAACAGGATGATTTC 584324 iviv vvvv ii v i i iv vi v v i vi L1ME4c_3end#L 539 ACTCGATGGAATATTATGCAGCCATTAAAAATGATAATTATGAAGACTAT 588 chr3ptel1M 584325 AGAAAGGCCTGGAGAGAATTACACGAACTGATGCTGAGTGAAATGAGCAG 584374 iv ivii v i ivi -i i vv i i i vi L1ME4c_3end#L 589 GTAGCAACATGGAAAATGTT-TATGATATAATGTTAAGTGAAAAAAGCAG 637 chr3ptel1M 584375 AA 584376 L1ME4c_3end#L 638 AA 639 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 45.79 CpG sites = 75, Kimura (unadjusted) = 46.76 Transitions / transversions = 1.29 (75/58) Gap_init rate = 0.01 (5 / 398), avg. gap size = 1.40 (7 / 5) 16 0.00 0.00 0.00 chr3ptel1M 584796 584812 (415188) (A)n#Simple_repeat 1 17 (0) m_b124s252i19 4573 chr3ptel1M 584796 AAAAAAAAAAAAAAAAA 584812 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 13 12.69 0.00 0.00 chr3ptel1M 584990 585015 (414985) (GCAGA)n#Simple_repeat 1 26 (0) m_b124s252i20 4574 chr3ptel1M 584990 GCAGAGCAGAGCAGAGGTGAGCACAG 585015 vv v (GCAGA)n#Simp 1 GCAGAGCAGAGCAGAGCAGAGCAGAG 26 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 232 34.94 4.82 0.00 chr3ptel1M 586526 586608 (413392) C L3#LINE/CR1 (212) 3887 3801 m_b124s601i11 4575 chr3ptel1M 586526 TGGGCCAAGAGCGGTCTTGCTG--AC--CCACTGAAAAAGCCTGGTTCTG 586571 i i i v v i iv -- -- iv vviiv i C L3#LINE/CR1 3887 TGAGCCGAAATCTGCCTCCCTGTAACTTCCACCCATTGGTCCTAGTTCTG 3838 chr3ptel1M 586572 ACTCCTGGGATCCCACAGAACAAGTCCAGTTCCTTCT 586608 v ii iii v i i i i ii C L3#LINE/CR1 3837 CCCTCTGGAGCCACACAGAATAAGTCTAATCCCTCTT 3801 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 48.16 CpG sites = 20, Kimura (unadjusted) = 50.74 Transitions / transversions = 2.22 (20/9) Gap_init rate = 0.02 (2 / 82), avg. gap size = 2.00 (4 / 2) 248 33.75 4.81 6.52 chr3ptel1M 586611 586797 (413203) L3#LINE/CR1 3522 3705 (394) m_b124s601i12 4576 chr3ptel1M 586611 GAGGTGTCATGTCCAGGGACAAGAAGGGGGTAGTTGGGTCTCTGATGGGA 586660 i i vi i?- -- i i --i i - v vi- L3#LINE/CR1 3522 GAAGTATAGTGTCCAGAN-CAAG--GGAGGTAAT--AGTCCC-GCTGTA- 3564 chr3ptel1M 586661 CCTCAGATCTCTAGTAAGACCCTACATCCGGA-CGTCCTGGTCACCTCCG 586709 - v -- v i v -- i -ii ivi v vi i L3#LINE/CR1 3565 -CTCTG--CGCTGGTCAGACC--ACATCTGGAGTATTGCGTTCAGTTCTG 3609 chr3ptel1M 586710 GGCTCTGTGTCCCAGGCACAACGTGGCCAAGCTAACGAAAGTCCAGAG-- 586757 v iiii iii i vivi i v v i iiv viv -- L3#LINE/CR1 3610 GGCGCCACATTTTAAGAGGGACATTGACAAACTGGAGCGCGTCCAGAGGA 3659 chr3ptel1M 586758 -----ATCAGG-TGGTGAAGGGCCTTGGGACCCTGGCAGACGAGAA 586797 ----- i - i v ii v v v i i L3#LINE/CR1 3660 GAGCGACCAGGATGGTGAAGGGTCTGGAAACCATGTCATATGAGGA 3705 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.38 CpG sites = 38, Kimura (unadjusted) = 47.67 Transitions / transversions = 1.81 (38/21) Gap_init rate = 0.09 (16 / 186), avg. gap size = 1.31 (21 / 16) 300 30.28 13.57 0.44 chr3ptel1M 587354 587552 (412448) C Tigger23a#DNA/TcMar-Tigger (13) 760 536 m_b124s502i0 4577 chr3ptel1M 587354 CCTTACAGAACAGAAGCGATCCTGACAAGCTGCTTGGTGAGCGAGTGTCT 587403 i i i v v v i ?i vvi i v C Tigger23a#DNA 760 CTTTACGGAATAGATGCGTTCCTGAAAAGTTGNCTGTAAAGCGAATTTCT 711 chr3ptel1M 587404 GCACA-CGGGCCCAACATTTCCACCGACTTTCACAAAATCATTGGAGA-- 587450 i ? - iii v iv i ii iv v vv -- C Tigger23a#DNA 710 GTANATCGAATCCTATTTTCCCATTGACTTTCATTATAAAATTGGAGATG 661 chr3ptel1M 587451 ---TTGTTTGGG---------GGGCAGGGGATGCAATAAAATCCCATCTA 587488 --- v i --------- v vvii i i v ii C Tigger23a#DNA 660 CGTTTCTCTGGGAAAAAATTTGGCCCTAAGACGTAATAAAATCACACTTA 611 chr3ptel1M 587489 ATAAGG--------CTTTGGAAAGCATCACACT---AGG-AAGATGAGAA 587526 v v -------- vi v - i i --- - i v C Tigger23a#DNA 610 AGAATGCAGCAAACCTTTTAAAATCA-CATATTTAAAGGAAAAATGATAA 562 chr3ptel1M 587527 CTGCGTGACAAAGCCCTGATCATACT 587552 i viv i iivi i v C Tigger23a#DNA 561 TTTTCTGATAAAATATTAATAATACT 536 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 38.63 CpG sites = 34, Kimura (unadjusted) = 40.36 Transitions / transversions = 1.31 (34/26) Gap_init rate = 0.04 (8 / 198), avg. gap size = 3.50 (28 / 8) 46 26.87 4.64 2.53 chr3ptel1M 587668 587861 (412139) (GAGAAG)n#Simple_repeat 1 198 (0) m_b124s252i21 4578 chr3ptel1M 587668 GAGATGTGAAAATGGGGAGCAGAGGGAGGGGGTAGAAAGGAGAGGGAGAG 587717 v - i v i i v i ii - - i i (GAGAAG)n#Sim 1 GAGAAG-GAGAAGGAGAAGGAGAAGGAGAAGG-AG-AAGGAGAAGGAGAA 47 chr3ptel1M 587718 AAAGAAGGGGAAGG-GAAGGAGAGGGGGAGGAAGAA-GAAAAGGAAGAGG 587765 ii i - i i i i - i - i (GAGAAG)n#Sim 48 GGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGG-AGAAG 96 chr3ptel1M 587766 GAGAGGGA-AAGGGGGAGG-GGAGG-GCAGGGAAAAGA-AAGGA-CAGG- 587809 i - i i - i - v ii i - -v - (GAGAAG)n#Sim 97 GAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGA 146 chr3ptel1M 587810 GTCGGGGAGGGAGAAGGGCAGGGAGAAGAGGGAAAGAGAGAGA-AAGGAG 587858 vv i i iv i - i i ii - (GAGAAG)n#Sim 147 GAAGGAGAAGGAGAAGGAGAAGGAGAAG-GAGAAGGAGAAGGAGAAGGAG 195 chr3ptel1M 587859 AAG 587861 (GAGAAG)n#Sim 196 AAG 198 Matrix = Unknown Transitions / transversions = 4.00 (32/8) Gap_init rate = 0.07 (14 / 193), avg. gap size = 1.00 (14 / 14) 53 20.74 6.10 1.16 chr3ptel1M 587688 587851 (412149) (AGAGGG)n#Simple_repeat 1 172 (0) m_b124s252i22 4579 chr3ptel1M 587688 AGAGGGAGGGGGTAGAAAGGAGAGGGAGAGAAAGAAGGGGAAGG-GAAGG 587736 i - - i ii i i i - i (AGAGGG)n#Sim 1 AGAGGGAGAGGG-AG-AGGGAGAGGGAGAGGGAGAGGGAGAGGGAGAGGG 48 chr3ptel1M 587737 AGAGGGGGAGGAAGAAGAAAAGGAAGAGGGAGAGGGAAAGGGGGAGGG-G 587785 i i i i i i i i - (AGAGGG)n#Sim 49 AGAGGGAGAGGGAGAGGGAGAGGGAGAGGGAGAGGGAGAGGGAGAGGGAG 98 chr3ptel1M 587786 AGGG-CAGGGA-AAAGA-AAGGACAGGG-TCGGG-GAGGGAGAAGGGCAG 587830 -v - ii - i v -vv - i iv (AGAGGG)n#Sim 99 AGGGAGAGGGAGAGGGAGAGGGAGAGGGAGAGGGAGAGGGAGAGGGAGAG 148 chr3ptel1M 587831 GGAGA---AGAGGGAAAGAGAGAG 587851 --- i i (AGAGGG)n#Sim 149 GGAGAGGGAGAGGGAGAGGGAGAG 172 Matrix = Unknown Transitions / transversions = 4.60 (23/5) Gap_init rate = 0.06 (10 / 163), avg. gap size = 1.20 (12 / 10) 635 28.66 0.60 1.82 chr3ptel1M 588229 588395 (411605) L3#LINE/CR1 2864 3028 (1071) m_b124s601i13 4580 chr3ptel1M 588229 AAGAACAGGTCGCACCGAG-TAACCCCGTTTCCTTTTTGGATGGGGTTAC 588277 i iii i i- i i v i L3#LINE/CR1 2864 AAGAACAAGTCATGCCAAACTAACCTCATTTCCTTTTTTGATAGGGTTAC 2913 chr3ptel1M 588278 TAGACTAGGAGATCCAGGGCGAGGCTTTAAAAATAGTTCGCCTAGATTTT 588327 i v - vi v iv i v ? viii i i L3#LINE/CR1 2914 TAGACTGGTAGAT-CAGGGGAATGCCGTAGACANAGTGTATCTGGATTTC 2962 chr3ptel1M 588328 GGCAAAGCATCTGACAGAGAGCCTCATGCTAGCCTCTCGCAGGCAGGATG 588377 i i i i vvi v v -- i ii i i L3#LINE/CR1 2963 AGCAAGGCATTTGACAAAGTCTCTCATGATATC--CTTGTGGACAAGATG 3010 chr3ptel1M 588378 AAGAGAGACGACTTGAAT 588395 i i v i ivi i L3#LINE/CR1 3011 GAGAAATATGGGCTGGAT 3028 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.61 CpG sites = 34, Kimura (unadjusted) = 38.70 Transitions / transversions = 2.62 (34/13) Gap_init rate = 0.02 (4 / 166), avg. gap size = 1.00 (4 / 4) 426 36.97 10.58 2.57 chr3ptel1M 588256 588652 (411348) L3b_3end#LINE/CR1 2 429 (777) m_b124s601i14 4580 chr3ptel1M 588256 TTTCCTTTTTGGATGGGGTTACTAGACTAGGAGATCCAGGGCGAGGCTTT 588305 i? vi iii iii ? v - vi v? iv L3b_3end#LINE 2 TTTCCTCNTAAGATAAAGCCGCTANACTAGCAGAT-CAGGGGAATNCCAT 50 chr3ptel1M 588306 AAAAATAGTTCGCCTAGATTTTGGCAAAGCATCTGACAGAGAGCCTCATG 588355 i v viii v ii i i i vvi i L3b_3end#LINE 51 AGACATAGTGTATCTTGATTTCAGCAAGGCATTTGACAAAGTCTCTCGTG 100 chr3ptel1M 588356 CTAGCCTCTCGCAGGCAGGATGAAGAGAGACGACTTGAATCGTGAC--GC 588403 v v -- ii i i i i i vii ivi i ?vi ii-- i L3b_3end#LINE 101 ATATC--CTCGTGGACAAGACGGAGAAATGTGGGCTGGANAATGGTCAGT 148 chr3ptel1M 588404 TGG---CTCCCA---AGTTCCAAAGCCAGA---GAGGGCCGTGGAGTGCG 588444 i ---i ?i ---i vv v i i? ---i i v v v?ivv L3b_3end#LINE 149 TAGACATTCNTAGCTGGTTGAACAACCGNACCCAAAGGACGTTGATNAAT 198 chr3ptel1M 588445 GGG--GGTG---GGCTGCTGAG-GTCTCCGG-GGAGCGCCGTGGGGACCT 588487 ?-- i ---iv vv i - ii - v i ii vi L3b_3end#LINE 199 GGNTCGATGTCAACCTGGAGGGAGTCTCTAGTGGCGTGCCGCAGGGCTCT 248 chr3ptel1M 588488 GTTCCCCAATACGTGGGGCTGT--TGCTTTACGTTTTGTCAATGACCTGG 588535 i i-------- vvi -- ii v vv v i i L3b_3end#LINE 249 GTCCT--------TGGCCTTGTCCTGTCTGAATTTGTATCAATGACTTGG 290 chr3ptel1M 588536 TTAAAGACATAAGAGG--------CAAACTCCTT-------GAAACTGCA 588570 v i i iiii i -------- i ivi?------- i vi L3b_3end#LINE 291 ATGAAGATACGGAAAGCAGCTTATCAAATTTGCNAGTGGCAGAAGCTGGG 340 chr3ptel1M 588571 AACAACAGTCAG---GTCAG----AATGTCAGGAACCCAAAAGACTGTGA 588613 i i i ii i--- ii ---- vi v v v iivi L3b_3end#LINE 341 AGCGACGGCTAATACGTTGGATGCAAAATCAGGATCCAAAACGATCTCGA 390 chr3ptel1M 588614 CAGGAAAGCTTATGAGGCAAAAATTAACAAGAGCAAATT 588652 ivv vvii?vi vi ?ii vv L3b_3end#LINE 391 CAGACTAGAACGNCGGGCCGAANCCAACAAGATGAAATT 429 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 50.53 CpG sites = 93, Kimura (unadjusted) = 57.38 Transitions / transversions = 1.86 (93/50) Gap_init rate = 0.06 (24 / 396), avg. gap size = 2.21 (53 / 24) 239 20.45 0.00 0.00 chr3ptel1M 588690 588733 (411267) C L2d_3end#LINE/L2 (10) 506 463 m_b124s601i15 4581 chr3ptel1M 588690 AATCAAGAAGCACTGATTAAGCACTTACTATGTGCTGAGCACCG 588733 v i i v i i i v i C L2d_3end#LINE 506 AATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTG 463 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 21.50 CpG sites = 6, Kimura (unadjusted) = 24.51 Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 202 30.95 0.00 7.69 chr3ptel1M 588692 588761 (411239) C L2a_3end#LINE/L2 (10) 507 443 m_b124s601i16 4581 chr3ptel1M 588692 TCAAGAAGCACTGATTAAGCACTTACTATGTGCTGAGCACCGACAGCAGA 588741 v ii i v i i i iii i ---vivv C L2a_3end#LINE 507 TCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTG---TTCTA 461 chr3ptel1M 588742 GGGTCACTGAAGATACGGCA 588761 -- i ii i C L2a_3end#LINE 460 GG--CGCTGGGGATACAGCA 443 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.17 CpG sites = 15, Kimura (unadjusted) = 42.84 Transitions / transversions = 3.00 (15/5) Gap_init rate = 0.07 (5 / 69), avg. gap size = 1.00 (5 / 5) 205 33.33 2.53 1.25 chr3ptel1M 590929 591007 (408993) L2c_3end#LINE/L2 396 475 (3) m_b124s601i17 4582 chr3ptel1M 590929 AGGGACCCTGCTTCCGCCTTTCTTTATGTCCCTGGTGCCCG-CACACAGG 590977 v ii i-iiiiv i i ii i i - i v L2c_3end#LINE 396 AGGGACCGTGTCTT-ATTCATCTTTGTATCCCCAGCGCCTGGCACATAGT 444 chr3ptel1M 590978 TGGTGCTTA-CAAATGTTGGCTGACTGGCTG 591007 v i i -i v i v iv L2c_3end#LINE 445 AGGCGCTCAATAAATGTTTGTTGAATGAATG 475 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.78 CpG sites = 19, Kimura (unadjusted) = 47.96 Transitions / transversions = 2.71 (19/7) Gap_init rate = 0.04 (3 / 78), avg. gap size = 1.00 (3 / 3) 34 8.42 5.88 4.65 chr3ptel1M 591526 591540 (408460) (GAGAAAG)n#Simple_repeat 1 13 (73) m_b124s252i23 4583 chr3ptel1M 591526 GAGAAAGGAGAGAGA 591540 - - (GAGAAAG)n#Si 1 GAGAAAGGAGA-A-A 13 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.14 (2 / 14), avg. gap size = 1.00 (2 / 2) 27 3.12 0.00 2.94 chr3ptel1M 591541 591575 (408425) (AGAGAATG)n#Simple_repeat 1 34 (0) c_b124s251i3 4584 chr3ptel1M 591541 AGAGAACTGAGAGGATGAGAGAATGAGAGAATGAG 591575 - i (AGAGAATG)n#S 1 AGAGAA-TGAGAGAATGAGAGAATGAGAGAATGAG 34 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 34 8.42 5.88 4.65 chr3ptel1M 591576 591644 (408356) (GAGAAAG)n#Simple_repeat 14 85 (1) m_b124s252i23 4585 chr3ptel1M 591576 GAGGAGAGGAG-AAGGAGAAAGGGAGAAAGGAGAAAGGGGAAAGGA-AGA 591623 - i - - i - i (GAGAAAG)n#Si 14 GA-GAAAGGAGAAAGGAGAAA-GGAGAAAGGAGAAAGGAGAAAGGAGAAA 61 chr3ptel1M 591624 AGA-AAAGGTG-AA-GAGAAGGGA 591644 i - v - - i (GAGAAAG)n#Si 62 GGAGAAAGGAGAAAGGAGAAAGGA 85 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.10 (7 / 68), avg. gap size = 1.00 (7 / 7) 365 30.00 2.73 0.00 chr3ptel1M 591659 591768 (408232) L3#LINE/CR1 3922 4034 (65) m_b124s601i18 4586 chr3ptel1M 591659 CCCAGAGTGAGATGAGCCAGCTGCTGAGAGAGGGAG-GCCCTGACACTGG 591707 v i i ii i iiv vv? iv v -v i v L3#LINE/CR1 3922 CCAAAAATGGAATGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGTCACTGG 3971 chr3ptel1M 591708 AGGGCTTCAAGCAAAGGCTAGAGAGCCACTGATCA--GATAGTGTAAGAG 591755 vv i i vii vi -- iv ii L3#LINE/CR1 3972 AGGTGTTCAAGCAGAGGCTGGATGACCACTTGTCAGGGATGTTGTAGAAG 4021 chr3ptel1M 591756 GGACTTTTGCATT 591768 i ii L3#LINE/CR1 4022 GGATTCCTGCATT 4034 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.53 CpG sites = 20, Kimura (unadjusted) = 40.11 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.02 (2 / 109), avg. gap size = 1.50 (3 / 2) 11 12.46 2.33 10.00 chr3ptel1M 591825 591867 (408133) (AAGGAA)n#Simple_repeat 1 40 (0) m_b124s252i25 4587 chr3ptel1M 591825 AAGCGAAAAGG-AAGGGAACAGGCACAAAGGGGAAAGGAGAAGG 591867 - - i v - - - i i (AAGGAA)n#Sim 1 AAG-GAAAAGGAAAAGGAAAAGG-A-AAA-GGAAAAGGAAAAGG 40 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.12 (5 / 42), avg. gap size = 1.00 (5 / 5) 24 3.57 0.00 0.00 chr3ptel1M 593759 593787 (406213) (CA)n#Simple_repeat 1 29 (0) m_b125s252i3 4588 chr3ptel1M 593759 CACACACACACACACGCACACACACACAC 593787 i (CA)n#Simple_ 1 CACACACACACACACACACACACACACAC 29 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 292 36.58 7.98 2.39 chr3ptel1M 593990 594227 (405773) C L3#LINE/CR1 (123) 3976 3726 m_b125s601i1 4589 chr3ptel1M 593990 CACCTCTAAGGCCCGGGACCTCTCCAGCCTCTCCCCGGGCAGCTTCTTCC 594039 i iv v v v v i ---i ? vi iiv C L3#LINE/CR1 3976 CACCTCCAGTGACGGGGAGCTCACTA---CCTCNCGAGGCAGCCCATTCC 3930 chr3ptel1M 594040 ACTTTCA---AGGTCTCCCAGTTGGCAAGTCCTTTCCC---CTGAGGATT 594083 i ii--- v vviv i v i i ii---i vvvv C L3#LINE/CR1 3929 ATTTTTGGACAGCTCTGATTGTTAGAAAGTTCTTCCTTATATTGAGCCGA 3880 chr3ptel1M 594084 AATCTGTCTG--------TTCTCCGCATTGTCCTTAGTCCTGCTCCCCAG 594125 i v-------- iv v vi i i i i ii C L3#LINE/CR1 3879 AATCTGCCTCCCTGTAACTTCCACCCATTGGTCCTAGTTCTGCCCTCTGG 3830 chr3ptel1M 594126 TACCAATCAGAAGACGAGCCCTCCTCCTCCTTCTGGAGTTCAGCTCTCCA 594175 vi vv v v ---i vv ii iiv vvv i i C L3#LINE/CR1 3829 AGCCACACAGAATAAG---TCTAATCCCTCTTCCACATGACAGCCCTTCA 3783 chr3ptel1M 594176 GACACCCAAAGTCAGCCCCGGGGTCTC-----AGAGTCCTCTTCTCCACC 594220 i i iiii v iviviv ----- vv i vv C L3#LINE/CR1 3782 AATATTTGAAGACAGCTATCATGTCTCCTCTAAGTCTTCTCTTCTCCAGG 3733 chr3ptel1M 594221 TTGAACA 594227 i i C L3#LINE/CR1 3732 CTAAACA 3726 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 52.16 CpG sites = 46, Kimura (unadjusted) = 52.16 Transitions / transversions = 1.18 (46/39) Gap_init rate = 0.04 (10 / 237), avg. gap size = 2.50 (25 / 10) 233 27.84 3.38 15.04 chr3ptel1M 594721 594859 (405141) C L2c_3end#LINE/L2 (8) 470 348 m_b125s601i2 4590 chr3ptel1M 594721 ATTCAACT--CATTTGTTAGGAGCCCCCTGTGTGTCAGGCCCAGGTCCCC 594768 v-- i ii v iv i i ---------- C L2c_3end#LINE 470 ATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGC---------- 431 chr3ptel1M 594769 ACTGGGGAAACTATGATGGAAACAAAATGTTACCCT--CCTCAAGAAGCC 594816 i v v v i v vi v i v - -- i i C L2c_3end#LINE 430 GCTGGGGATACAAAGATGAATAAGACACGGT-CCCTGCCCTCAAGGAGCT 382 chr3ptel1M 594817 CCTAATGTTTTACTGGTGCAAGAGGAAAAGAACGAGGAATCCA 594859 vi i ------ i --- i vii i? v v vi C L2c_3end#LINE 381 CACAGT------CTAGTG---GAGGAGACAGACANGTAAACAG 348 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.01 CpG sites = 20, Kimura (unadjusted) = 35.48 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.16 (22 / 138), avg. gap size = 1.09 (24 / 22) 51 2.13 0.00 0.00 chr3ptel1M 594860 594907 (405093) (AC)n#Simple_repeat 1 48 (0) c_b125s251i1 4591 chr3ptel1M 594860 ACACATACACACACACACACACACACACACACACACACACACACACAC 594907 i (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACAC 48 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 246 21.52 9.43 3.57 chr3ptel1M 596888 596993 (403007) L2c_3end#LINE/L2 343 454 (24) m_b125s601i3 4592 chr3ptel1M 596888 ATTGTCT---TATCTGTGCTGTCTCCTCCAAAGAGAAGGTGCGCTC--TG 596932 --- i? - v-v vv v -- L2c_3end#LINE 343 ATTGTCTGTTTACNTGT-CTGTCTCCTCCAC-TAGACTGTGAGCTCCTTG 390 chr3ptel1M 596933 AAACCAGG-ACC-TGACTTACTTTTTCATGTGTCACCTCAGTGCATGTCA 596980 iiv - - v i iv iiv i -- i i v v L2c_3end#LINE 391 AGGGCAGGGACCGTGTCTTATTCATCTTTGTATC--CCCAGCGCCTGGCA 438 chr3ptel1M 596981 CATAGT---CACTCAA 596993 --- i L2c_3end#LINE 439 CATAGTAGGCGCTCAA 454 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 23.34 CpG sites = 11, Kimura (unadjusted) = 25.92 Transitions / transversions = 1.00 (11/11) Gap_init rate = 0.09 (9 / 105), avg. gap size = 1.56 (14 / 9) 307 28.66 11.68 0.66 chr3ptel1M 597014 597150 (402850) C L2c_3end#LINE/L2 (0) 478 327 m_b125s601i4 4593 chr3ptel1M 597014 ATTAATCCTTTCACCCAACATT-----AGCCCCCTACTGTGTACCAGGCA 597058 v i v v v ----- v - i i i C L2c_3end#LINE 478 ATTCATTCATTCAACAAACATTTATTGAGCGCC-TACTATGTGCCAGGCG 430 chr3ptel1M 597059 CTGGAGAT--AGAGACAAAAAA------GCTCCTGTCCCCGAAGAACTTA 597100 i -- i ii v ------ ii i i i i i i C L2c_3end#LINE 429 CTGGGGATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCA 380 chr3ptel1M 597101 TGTTCTACTGGGAGAAACA-ACATATACATGGAAAA--ACAAACCAAAGT 597147 iiv v ii i - ?i v ii v -- vv iv C L2c_3end#LINE 379 CAGTCTAGTGGAGGAGACAGACANGTAAACAGACAATTACAATACAAGTT 330 chr3ptel1M 597148 CAT 597150 v C L2c_3end#LINE 329 AAT 327 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.69 CpG sites = 25, Kimura (unadjusted) = 37.94 Transitions / transversions = 1.79 (25/14) Gap_init rate = 0.04 (6 / 136), avg. gap size = 2.83 (17 / 6) 424 34.55 2.56 4.64 chr3ptel1M 597480 597831 (402169) L1ME2_3end#LINE/L1 231 575 (336) m_b125s551i0 4594 chr3ptel1M 597480 TGGCAGGAATAAATGTTAGAGGGGACGTGGGAAAACTGCGACACTAGTGC 597529 i iv vi i v i i iiv vi v vi i L1ME2_3end#LI 231 TGACAATACCAAATGTTGGCGAGGATGTGGAGCAACTGGAACTCTCATAC 280 chr3ptel1M 597530 ATTGTTGGTAGAGTTATGAGCTGATCCAACCATTT--GAGGACAATTTGG 597577 i i iiv i i iv i v i -- ii ?i L1ME2_3end#LI 281 ATTGCTGGTGGGAGTGTAAAATGGTACAACCACTTTGGAAAACNGTTTGG 330 chr3ptel1M 597578 -AATTATGTCCAAAGGGCTAGCAAACTGTGCAC--ACCCCTTGCTCCAGC 597624 - i viv vi v-----i -i i -- iv vi L1ME2_3end#LI 331 CAGTTTCTTATAAAGT-----TAAAC-ATACACCTACCCTATGACCCAGC 374 chr3ptel1M 597625 AGGGTCTCTACTGGGTCTGTATCCCAAAGAGATCATAAAGGAGGG----A 597670 ivvi v v i v v i v i i v v viv v v---- L1ME2_3end#LI 375 AATTCCACTCCTAGGTATTTACCCAAGAGAAATGAAAACATATGTCCACA 424 chr3ptel1M 597671 AAAGGACCCACATGGACACAAAATTTCTGTACCGGCCCTTTTTGTAGTGG 597720 i i---- v ?i vv -i v i ii v ii i i L1ME2_3end#LI 425 AAAAGACT----TGTACANGAATGTTC-ATAGCAGCTTTATTCATAATAG 469 chr3ptel1M 597721 TAAGGAACTGGAAGCTGATGGAAGATGCCCATCAACTGGGGGATGTCTAA 597770 ivvii i -i ivv - i v ? i vv L1ME2_3end#LI 470 CCCAAAACTGGAAAC-AACCCAA-ATGTCCATCAACAGGNGAATGGATAA 517 chr3ptel1M 597771 AGAAGTTATGGTATATGAATTCAATAGAATGTTATTATTCTATAAGAAGT 597820 v i i vv v i --- i i vii v iv L1ME2_3end#LI 518 ACAAATTGTGGTATATTCATACAATGGAA---TACTACTCAGCAATAAAA 564 chr3ptel1M 597821 AGAAGCGGACT 597831 i i i L1ME2_3end#LI 565 AGGAACGAACT 575 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 48.71 CpG sites = 68, Kimura (unadjusted) = 48.71 Transitions / transversions = 1.42 (68/48) Gap_init rate = 0.06 (20 / 351), avg. gap size = 1.25 (25 / 20) 314 34.59 3.14 3.64 chr3ptel1M 597487 597900 (402100) L1MA10_3end#LINE/L1 238 649 (432) m_b125s551i1 4594 chr3ptel1M 597487 AATAAATGTTAGAGGGGACGTGGGAAAACTGCGACACTAGTGCATTGTTG 597536 i i i v i i ii ?? vi v v i i L1MA10_3end#L 238 AACAAGTGTTGGCGAGGATGTGGAGAAANNGGAACCCTTGTACACTGTTG 287 chr3ptel1M 597537 GTAGAGTTATGAGCTGATCCAACCATTT--GAGGACAATTTGGAATTATG 597584 i iiv i i i? i v i i v-- ii i v iv - v L1MA10_3end#L 288 GTGGGAATGTAAANTGGTGCAGCCACTATGGAAAACAGTATGGAGGT-TC 336 chr3ptel1M 597585 TCCAAAGGGCTAGCAAACTGTGCAC-ACCCCTTGCTCCAGCAGGGTCTCT 597633 ii iiii -- v i- v - viv v ivvi v L1MA10_3end#L 337 CTCAAAAAATTA--AAAATA-GAACTACCATATGATCCAGCAATCCCACT 383 chr3ptel1M 597634 ACTGGGTCTGTATCCCAAAGAGATCATAAAGGAGG-----GAAAAGGACC 597678 v v i v - ii- vv ----- i i--- L1MA10_3end#L 384 TCTGGGTATATATCCAAAAGA-ATTG-AAATCAGGATCTCGAAGAGA--- 428 chr3ptel1M 597679 CACATGGACACAAAATTTCTGTACCGGCCCTTTTTGTAGTGGTAAGGAAC 597728 i iv v v vv vv vv i -i vi v iii i i iv i vv L1MA10_3end#L 429 TATCTGCACTCCCATGTTCATTGC-AGCATTATTCACAATAGCCAAGATA 477 chr3ptel1M 597729 TGGAAGCTGATGGAAGATGCCCATCAACTGGGGGATGTCTAAAGAAGTTA 597778 i -i ivv - i i v iv i vv iv i L1MA10_3end#L 478 TGGAAAC-AACCTAA-ATGTCCATCGACGGATGAATGGATAAAGAAAATG 525 chr3ptel1M 597779 TGGTATATGAATTCAATAGAATGTTATTATTCTATAAGAAGTAGAAGCGG 597828 iv v i i vvv iv i -- vii L1MA10_3end#L 526 TGGTATATACATACAATGGAATATTATTCAGCCTTAAAAA--AGAAGGAA 573 chr3ptel1M 597829 A--CTG--ATTTCAGAAAAGCCTGCAAAGACTTGCATGAACTGATGCTAA 597874 -- -- vv v - v v vii i v v vv v L1MA10_3end#L 574 ATCCTGCCATTTGCGACAA-CATGGATGAACCTGGAGGACATTATGCTAA 622 chr3ptel1M 597875 GGGAAGTGAG-CAGAACCAGGAGAACA 597900 v i i - ?vv i i L1MA10_3end#L 623 GTGAAATAAGCCAGNCACAGAAGGACA 649 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 47.69 CpG sites = 73, Kimura (unadjusted) = 48.18 Transitions / transversions = 1.12 (73/65) Gap_init rate = 0.05 (21 / 413), avg. gap size = 1.33 (28 / 21) 664 33.55 1.27 1.59 chr3ptel1M 597491 597805 (402195) L1ME4c_3end#LINE/L1 242 555 (275) m_b125s551i2 4594 chr3ptel1M 597491 AATGTTAGAGGGGACGTGGGAAAACTGCGACACTAGTGCATTGTTGGTAG 597540 i i v i ?i i vi vv ? vi i i i L1ME4c_3end#L 242 AATGCTGGCGAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGG 291 chr3ptel1M 597541 AGTTATGAGCTGATCCAACCATTT--GAGGACAATTTGGAATTATGTCCA 597588 vi? i i ii i v v -- iii v v i viv L1ME4c_3end#L 292 CANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATC 341 chr3ptel1M 597589 AAGGGCTAGCAAACTGTGCACACCCCTTGCTCCAGCAGGGTCTCTACTGG 597638 i i vv v v i i vi i ivvi v v L1ME4c_3end#L 342 AAGAGCCATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGG 391 chr3ptel1M 597639 GTCTGTATCCCAAAGAGATCAT--AAAGGAGGGAAAAGGACCCACATGGA 597686 vv v i i i v -- i i i -- i i v L1ME4c_3end#L 392 GAATTTATCCTAAGGAAATAATTCAAAAGAAGGAAAAAG--CTATATGCA 439 chr3ptel1M 597687 CACAAAATTTCTGTACCGGCCCTTTTTGTAGTGGTAAGGAACTGGAAGCT 597736 i- i v iii vv i vi v i i i ii ii i i - L1ME4c_3end#L 440 CG-AAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAAC- 487 chr3ptel1M 597737 GATGGAAGATGCCCATCAACTGGGGGATGTCTAAAGAAGTTATGGTATAT 597786 i ivv - i v iv i vi iv i i L1ME4c_3end#L 488 AACCTAA-ATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACAT 536 chr3ptel1M 597787 GAATTCAATAGAATGTTAT 597805 v? i i i i L1ME4c_3end#L 537 CNACTCGATGGAATATTAT 555 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 44.41 CpG sites = 66, Kimura (unadjusted) = 47.68 Transitions / transversions = 1.74 (66/38) Gap_init rate = 0.02 (7 / 314), avg. gap size = 1.29 (9 / 7) 17 0.00 3.57 3.57 chr3ptel1M 598179 598206 (401794) (GGAG)n#Simple_repeat 1 28 (0) m_b125s252i4 4595 chr3ptel1M 598179 GGAGGGA-GGAGGGATGGGAGGGAGGGAG 598206 - - (GGAG)n#Simpl 1 GGAGGGAGGGAGGGA-GGGAGGGAGGGAG 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.07 (2 / 27), avg. gap size = 1.00 (2 / 2) 21 10.85 0.00 0.00 chr3ptel1M 598805 598834 (401166) (A)n#Simple_repeat 1 30 (0) m_b125s252i5 4596 chr3ptel1M 598805 AAAAAAAAAAAAAAAAAAAAACCCAAAAAA 598834 vvv (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 30 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 18 10.49 4.35 4.35 chr3ptel1M 599075 599120 (400880) (CCTTTT)n#Simple_repeat 1 46 (0) m_b125s252i6 4597 chr3ptel1M 599075 CCCTTTCCTTTCCCCTTTTCCTTTTTTCCTTT--TTTTCCTTTTCCTT 599120 i -i - i i -- (CCTTTT)n#Sim 1 CCTTTTCCTTT-TCCTTTTCC-TTTTCCTTTTCCTTTTCCTTTTCCTT 46 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.07 (3 / 45), avg. gap size = 1.33 (4 / 3) 26 15.96 0.00 0.00 chr3ptel1M 599139 599181 (400819) (C)n#Simple_repeat 1 43 (0) m_b125s252i7 4598 chr3ptel1M 599139 CCCCCCCCCCTTCCCCCCTTCCCTCCCCCACCCCCCCCCCCCC 599181 ii ii i v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 43 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 15 5.56 0.00 0.00 chr3ptel1M 599197 599215 (400785) (C)n#Simple_repeat 1 19 (0) m_b125s252i8 4598 chr3ptel1M 599197 CCCCCCCCCCCCCCCCTCC 599215 i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCC 19 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 25 27.30 3.76 5.34 chr3ptel1M 599259 599391 (400609) (TTCCCCC)n#Simple_repeat 1 131 (0) m_b125s252i9 4599 chr3ptel1M 599259 TTGCCCGTCCCCCCTTCCCCCTTTCCCCTTCCCCCCTTTTCCC-CCCTTT 599307 v v i i - ii -i iii (TTCCCCC)n#Si 1 TTCCCCCTTCCCCCTTCCCCCTTCCCCCTT-CCCCCTTCCCCCTTCCCCC 49 chr3ptel1M 599308 TTCCCCTTTTCCCCTT--TCCTTCCCTTCTTTGCCCTT--TTCTTCCCTT 599353 i i --i -i iv --ii -i (TTCCCCC)n#Si 50 TTCCCCCTTCCCCCTTCCCCCTTCCC-CCTTCCCCCTTCCCCCTTCCC-C 97 chr3ptel1M 599354 TTTCTTTTCTTCCCTTTTTTCCCCCTTCTCCCCTTTCC 599391 i -iii --ii - i (TTCCCCC)n#Si 98 CTTC-CCCCTTCCC--CCTTCCCCCTTC-CCCCTTCCC 131 Matrix = Unknown Transitions / transversions = 7.67 (23/3) Gap_init rate = 0.08 (10 / 132), avg. gap size = 1.20 (12 / 10) 17 13.61 7.58 5.97 chr3ptel1M 599269 599334 (400666) (CCCCTT)n#Simple_repeat 1 67 (0) m_b125s252i10 4600 chr3ptel1M 599269 CCCCTTCCCCCTTTCCCCTTCCCC--CCTTTTCCCC-CCTTTTTCCCCTT 599315 - - -- ii -i iii -- (CCCCTT)n#Sim 1 CCCCTT-CCCC-TTCCCCTTCCCCTTCCCCTTCCCCTTCCCCTTCCCC-- 46 chr3ptel1M 599316 TTCCCCTT-TCCTT-CCCTTC 599334 -i - (CCCCTT)n#Sim 47 TTCCCCTTCCCCTTCCCCTTC 67 Matrix = Unknown Transitions / transversions = 1.00 (7/0) Gap_init rate = 0.12 (8 / 65), avg. gap size = 1.12 (9 / 8) 25 27.30 3.76 5.34 chr3ptel1M 599259 599391 (400609) (TTCCCCC)n#Simple_repeat 1 131 (0) m_b125s252i9 4599 chr3ptel1M 599259 TTGCCCGTCCCCCCTTCCCCCTTTCCCCTTCCCCCCTTTTCCC-CCCTTT 599307 v v i i - ii -i iii (TTCCCCC)n#Si 1 TTCCCCCTTCCCCCTTCCCCCTTCCCCCTT-CCCCCTTCCCCCTTCCCCC 49 chr3ptel1M 599308 TTCCCCTTTTCCCCTT--TCCTTCCCTTCTTTGCCCTT--TTCTTCCCTT 599353 i i --i -i iv --ii -i (TTCCCCC)n#Si 50 TTCCCCCTTCCCCCTTCCCCCTTCCC-CCTTCCCCCTTCCCCCTTCCC-C 97 chr3ptel1M 599354 TTTCTTTTCTTCCCTTTTTTCCCCCTTCTCCCCTTTCC 599391 i -iii --ii - i (TTCCCCC)n#Si 98 CTTC-CCCCTTCCC--CCTTCCCCCTTC-CCCCTTCCC 131 Matrix = Unknown Transitions / transversions = 7.67 (23/3) Gap_init rate = 0.08 (10 / 132), avg. gap size = 1.20 (12 / 10) 17 16.23 2.33 2.33 chr3ptel1M 600408 600450 (399550) (CCCTC)n#Simple_repeat 1 43 (0) m_b125s252i11 4601 chr3ptel1M 600408 CCCACCCGACCCCT-CCCTACCCCCCCCCCCCCTGCCCCTCCCC 600450 v vv - v i i - (CCCTC)n#Simp 1 CCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCT-CCCCTCCCC 43 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.00 (2 / 2) 188 25.96 4.59 4.59 chr3ptel1M 600809 600917 (399083) L2#LINE/L2 2222 2330 (752) m_b125s601i5 4602 chr3ptel1M 600809 CATGGGCGT-CCCCAGGGCTCTCTCCCAGTCACTCTTC-CTTCTCCAG-- 600854 i v v - vv iv vvv - i v-- L2#LINE/L2 2222 CGTTGGAGTGCCCCAGGGCTCAGTCCTTGGACCTCTTCTCTTCTCTATCT 2271 chr3ptel1M 600855 ACACTGTCCCCCTGGATGATCTCATCATCCCCCAGAGAGTCCTCAAAGTC 600904 vv i ? i vvvi i vi --- i i --i L2#LINE/L2 2272 ACACTCACTCCCTNGGTGATCTCATCCAGTCTCATGG---CTTTAAA--T 2316 chr3ptel1M 600905 ACAATCTA-ATGCT 600917 v - L2#LINE/L2 2317 ACCATCTATATGCT 2330 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.95 CpG sites = 11, Kimura (unadjusted) = 32.32 Transitions / transversions = 0.69 (11/16) Gap_init rate = 0.08 (9 / 108), avg. gap size = 1.11 (10 / 9) 192 35.00 1.25 0.00 chr3ptel1M 600925 601004 (398996) L2#LINE/L2 2400 2480 (602) m_b125s601i6 4602 chr3ptel1M 600925 CTGCCTGACGTCACCATTTGG-TGTCCCGGAGGCCCCTTGGGCTTCAGGT 600973 i ii i v i - iviv vi iiii v vi L2#LINE/L2 2400 CTACTCGACATCTCCACTTGGATGTCTAATAGGCATCTCAAACTTAACAT 2449 chr3ptel1M 600974 CTCTAAAGCAGATCTCATTCTCTTCCCCCCC 601004 v i i v v v vv i L2#LINE/L2 2450 GTCCAAAACTGAACTCCTGATCTTCCCCCTC 2480 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.40 CpG sites = 16, Kimura (unadjusted) = 48.84 Transitions / transversions = 1.33 (16/12) Gap_init rate = 0.01 (1 / 79), avg. gap size = 1.00 (1 / 1) 248 34.51 2.63 0.86 chr3ptel1M 601111 601224 (398776) C MIRc#SINE/MIR (92) 176 61 m_b125s601i7 4603 chr3ptel1M 601111 TGAGGTGGAGAATAGCAG-CCTCCTTAGCTCCGCTCCATGGAAG-GGAAA 601158 i iv i-i -iv iv v i ii ii ii v - C MIRc#SINE/MIR 176 TGAGGTAGGCAG-GGCAGGTATTATTATCCCCATTTTACAGATGAGGAAA 128 chr3ptel1M 601159 CTGAGGCACCAAGAAATAAAGGGGGTTGTCCAGGATCAAAGAGCCAGTGA 601208 v vi ii v v iv i i i v v i i C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAA 78 chr3ptel1M 601209 GGGG-GGCACCGAGACT 601224 v -i vi i C MIRc#SINE/MIR 77 GTGGCAGAGCCGGGACT 61 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 48.90 CpG sites = 25, Kimura (unadjusted) = 48.90 Transitions / transversions = 1.79 (25/14) Gap_init rate = 0.04 (4 / 113), avg. gap size = 1.00 (4 / 4) 281 31.30 6.09 0.00 chr3ptel1M 601126 601240 (398760) C MIR1_Amn#SINE/MIR (67) 163 42 m_b125s601i8 4603 chr3ptel1M 601126 CAGCCTCCTTAGCTCCGCTCCATGGAAG-GGAAACTGAGGCACCAAGAAA 601174 iv v v i ii ii ii v - ? vi ii C MIR1_Amn#SINE 163 CAGTATCATTATCCCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGG 114 chr3ptel1M 601175 TAAAGGGGGTTGTCCAGGATCAAAGAGCCAGTGAGGGG-GGCACCGAGAC 601223 ? v iv i i i v?v ?i i? v -i vi i ? C MIR1_Amn#SINE 113 TNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNAGTGGCAGAGCCGGGAN 64 chr3ptel1M 601224 TT-----TGGGGCTTCTGAGTC 601240 ?-----ii v i i C MIR1_Amn#SINE 63 TNGAACCCAGGTCTCCCGAGTC 42 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.99 CpG sites = 24, Kimura (unadjusted) = 46.83 Transitions / transversions = 2.00 (24/12) Gap_init rate = 0.03 (3 / 114), avg. gap size = 2.33 (7 / 3) 20 11.53 2.63 0.00 chr3ptel1M 601813 601850 (398150) (ATGG)n#Simple_repeat 1 39 (0) m_b125s252i12 4604 chr3ptel1M 601813 ATGAATGGATGGATGGACAG-TGGATGGATGGATGTATG 601850 i ii - v (ATGG)n#Simpl 1 ATGGATGGATGGATGGATGGATGGATGGATGGATGGATG 39 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 193 26.65 4.84 3.17 chr3ptel1M 602110 602171 (397829) L2d2_3end#LINE/L2 474 536 (19) m_b125s601i9 4605 chr3ptel1M 602110 ATCTCTGTGTGTCCCTGGCACAG-GC--AGCAGGGCACCTGGCACAGAGC 602156 ii v i i-- - -- vi ii v v i L2d2_3end#LIN 474 ACTTCTTTGTATCCCC--CACAGCGCCTAGCACAGTGCCTTGCACACAGT 521 chr3ptel1M 602157 AGATGGTTAATAAAT 602171 ii v i L2d2_3end#LIN 522 AGGCGCTCAATAAAT 536 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.79 CpG sites = 11, Kimura (unadjusted) = 34.45 Transitions / transversions = 2.20 (11/5) Gap_init rate = 0.07 (4 / 61), avg. gap size = 1.25 (5 / 4) 286 34.18 18.12 0.86 chr3ptel1M 602174 602471 (397529) C L3#LINE/CR1 (147) 3952 3604 m_b125s601i10 4606 chr3ptel1M 602174 TGCCTCCTG-GACAGTCCCTTCAGCTCTGGGTGAGCTCTCAGGATGGGGA 602222 i ?i - i i v vii i v vv v vvi vi i C L3#LINE/CR1 3952 TACCTCNCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGATTGTTAGAA 3903 chr3ptel1M 602223 AATT-TTCCTGACATCCAGTCCCGAGCTGCCACTTCCATAACGTGCAGGC 602271 i - v i iv i vvi v v i- ii v v vv C L3#LINE/CR1 3902 AGTTCTTCCTTATATTGAGCCGAAATCTGCCTCC-CTGTAACTTCCACCC 3854 chr3ptel1M 602272 GTTGAGTCTGGCTCTGCC--CTGGGCCCAGCAAGAACAAG-------CCG 602312 i ivi i i -- iv vvv i ------- v C L3#LINE/CR1 3853 ATTGGTCCTAGTTCTGCCCTCTGGAGCCACACAGAATAAGTCTAATCCCT 3804 chr3ptel1M 602313 CTTCCCCGCAAAGGCCCAGCAAATGC---------GGTGTCCT---TCCC 602350 v iii vi vv ii--------- v i v --- i C L3#LINE/CR1 3803 CTTCCACATGACAGCCCTTCAAATATTTGAAGACAGCTATCATGTCTCCT 3754 chr3ptel1M 602351 CTG--------CCTCCCCTGGCT----CTCCTGCCAGCTCCTTTAATGGA 602388 i-------- i i v ----v -- i i iv v C L3#LINE/CR1 3753 CTAAGTCTTCTCTTCTCCAGGCTAAACATCC--CCAGTTCCTTCAACCGT 3706 chr3ptel1M 602389 CCCTC--------------CCACGTCCCTGCCCATCCTGGTTGC-CTTTT 602423 i -------------- vii i vv i - ii C L3#LINE/CR1 3705 TCCTCATATGACATGGTTTCCAGACCCTTCACCATCCTGGTCGCTCTCCT 3656 chr3ptel1M 602424 CCAGTCA----CTAATTTGTCAGCCTCCTTTCTAAACCGGGGCACCCAGG 602469 ii v i---- i i iiv i ii vi v i i C L3#LINE/CR1 3655 CTGGACGCGCTCCAGTTTGTCAATGTCCCTCTTAAAATGTGGCGCCCAGA 3606 chr3ptel1M 602470 AC 602471 C L3#LINE/CR1 3605 AC 3604 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.08 CpG sites = 59, Kimura (unadjusted) = 47.70 Transitions / transversions = 1.40 (59/42) Gap_init rate = 0.05 (14 / 297), avg. gap size = 4.07 (57 / 14) 262 19.08 4.98 0.43 chr3ptel1M 602864 603084 (396916) HERVIP10FH#LTR/ERV1 787 1017 (4085) m_b125s701i0 4607 chr3ptel1M 602864 CAGAGAGAGAC----AGAAAC-AAAGAGAGACAGACAGACAGAGACAGAG 602908 i i ---- i v- - v v v HERVIP10FH#LT 787 CAGGGAAAGACCAGCAGAGAGGAAAGAGAGA-AGAGAGAGAGAGAGAGAG 835 chr3ptel1M 602909 AG--AGACAGAGAGAGACAGAGAGAGAGACAAAGAGAGAGAGAGACAGAG 602956 -- v v i v ii i HERVIP10FH#LT 836 AGGAAGAGAGAGAGAGAGAAAGAGAGAGAGAGGGAGAGAGAGAGACAAAG 885 chr3ptel1M 602957 AGAGAGACAAAGAGAGAGAGAAACAGAGA----CAGAGACAGAGAGACAG 603002 i v ii ----v i HERVIP10FH#LT 886 AGGGAGTCAAAGAGAGAGAGAGGCAGAGAGAGGAAGAGACAGAGAGACAA 935 chr3ptel1M 603003 ACAGAGAGAAAGATAAAGAGAGAGAGACAGAGAGACAGAGACAGAGACAA 603052 v i vv v i i v i v i v HERVIP10FH#LT 936 AGAGGGAGTCAGAGAGAGAGAGAGAGACAGAAAGTCAAAGAGAGAAAGAA 985 chr3ptel1M 603053 AGAGACAGACAGAGGGAGAAAGACAGAGACAG 603084 v i i v v iiv i i HERVIP10FH#LT 986 AGAGAGAGATAGAAGTAGTAAAGAAAAAACAG 1017 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 22.21 CpG sites = 22, Kimura (unadjusted) = 22.21 Transitions / transversions = 1.10 (22/20) Gap_init rate = 0.02 (5 / 220), avg. gap size = 2.40 (12 / 5) 368 32.26 7.74 0.00 chr3ptel1M 603314 603468 (396532) C L3#LINE/CR1 (1245) 2854 2688 m_b125s601i11 4606 chr3ptel1M 603314 ACACTGGCTCCTC---AACATCCTCCCCTGTTCCATGTGCTCACCAGCTA 603360 ii v--- v i viii v i v v i i C L3#LINE/CR1 2854 ATGCTGGCTCCTAGTGATCACCGCTTCCTTTTCTAAGTGCTCACAAACCA 2805 chr3ptel1M 603361 TCCCTTTAAT-ACGCGCCCTAGAACTTGCCCAGAAAGCAAAGTCGGGCTC 603409 iv - iv ii i vv i ii v i v ii i C L3#LINE/CR1 2804 TCTGTTTAATAATCCGTTCTAGAATTTTGCCGGGGATCGACGTCAAGCTT 2755 chr3ptel1M 603410 AC-------TA-TTTACAGATTTCCTTCTCTTCCCTTTCCTGAAAATGGC 603451 ------- - ? v i v ii i i i ii i ? i v C L3#LINE/CR1 2754 ACCGGTCTGTAGTTTNCAGAATCCATCTTTTTTCCCTTTTTAAAANTAGG 2705 chr3ptel1M 603452 AACGACGTTTATCCGCC 603468 ? ? i ii i C L3#LINE/CR1 2704 NACNACATTTGCCCGTC 2688 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.26 CpG sites = 35, Kimura (unadjusted) = 46.92 Transitions / transversions = 2.33 (35/15) Gap_init rate = 0.03 (4 / 154), avg. gap size = 3.00 (12 / 4) 16 9.71 0.00 0.00 chr3ptel1M 603882 603903 (396097) (G)n#Simple_repeat 1 22 (0) m_b125s252i13 4608 chr3ptel1M 603882 GGGGCGGGGGGGGGGGGAGGGG 603903 v i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGG 22 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 33 30.38 3.03 3.03 chr3ptel1M 604223 604387 (395613) (TGCCC)n#Simple_repeat 1 165 (0) m_b125s252i14 4609 chr3ptel1M 604223 TGCCCTGTGCTGCCCTCCCCCACTCTGCTCTGCCCCTGGCTCTGTACTGC 604272 iv v ii i i - - i iv (TGCCC)n#Simp 1 TGCCCTGCCCTGCCCTGCCCTGCCCTGCCCTG-CCCT-GCCCTGCCCTGC 48 chr3ptel1M 604273 CCCTCCC-ACTCTGTGCTGCCC--CCTGGCCCTGCTCTACCCCCACACAC 604319 iv -i i iv -- iv i i ivv vii (TGCCC)n#Simp 49 CCTGCCCTGCCCTGCCCTGCCCTGCCCTGCCCTGCCCTGCCCTGCCCTGC 98 chr3ptel1M 604320 TCTGCCCTACCCCTCCCGGCCCTGCTCTGCCC--CCTGGCTCTGTGCTGT 604367 i i iv v i -- iv i iv - (TGCCC)n#Simp 99 CCTGCCCTGCCCTGCCCTGCCCTGCCCTGCCCTGCCCTGCCCTGCCCTG- 147 chr3ptel1M 604368 CCCCTGACCCTGCTCTGCCC 604387 - - i (TGCCC)n#Simp 148 -CCCTG-CCCTGCCCTGCCC 165 Matrix = Unknown Transitions / transversions = 1.92 (25/13) Gap_init rate = 0.05 (8 / 164), avg. gap size = 1.25 (10 / 8) 202 29.51 3.28 0.00 chr3ptel1M 604789 604849 (395151) L3#LINE/CR1 4037 4099 (0) m_b125s601i12 4610 chr3ptel1M 604789 ACAGGAGAACCGACCGG-TGGCCCCCAAGGCCCCTTCCAGCCCTAAG-TT 604836 ii iviv ii - i i i i i i i - L3#LINE/CR1 4037 ATGGGAGGTTGGACTAGATGACCTCTAAGGTCCCTTCCAACTCTGAGATT 4086 chr3ptel1M 604837 CTGTGACTGTTTC 604849 i v v L3#LINE/CR1 4087 CTGTGATTCTATC 4099 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.69 CpG sites = 14, Kimura (unadjusted) = 40.69 Transitions / transversions = 3.50 (14/4) Gap_init rate = 0.03 (2 / 60), avg. gap size = 1.00 (2 / 2) 16 4.55 0.00 0.00 chr3ptel1M 605251 605273 (394727) (TCC)n#Simple_repeat 1 23 (0) m_b125s252i15 4611 chr3ptel1M 605251 TCCTCCTCCTCCTTCTCCTCCTC 605273 i (TCC)n#Simple 1 TCCTCCTCCTCCTCCTCCTCCTC 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 497 36.05 3.75 0.30 chr3ptel1M 605626 605945 (394055) L1ME4c_3end#LINE/L1 242 572 (258) m_b125s551i3 4612 chr3ptel1M 605626 AACGTTGGAGGGGACATGGGAAGCCTGGGACACTAAGGCATGGTTGG--- 605672 i i v i ?iii vi iv v ? v vi v i --- L1ME4c_3end#L 242 AATGCTGGCGAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGG 291 chr3ptel1M 605673 --GAGTGAAATGATCCAACC--TTCGGAAAGCAATCTGG-AATATGCCCA 605717 --?v i v i v -- i i - i iviv L1ME4c_3end#L 292 CANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATC 341 chr3ptel1M 605718 AAGGGCTGTAAAACGG--CATCCTCTCTGGTCCAGCAGTGTCTCCACTGG 605765 i ii vv -- v i i ii i i vi v iv L1ME4c_3end#L 342 AAGAGCCATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGG 391 chr3ptel1M 605766 GTCCGCATCCCA--GAAAGACCCTAAGAGAGGGAGCAGACCCACATGTGC 605813 vvivi i -- v viii i i i- i v i i ii L1ME4c_3end#L 392 GAATTTATCCTAAGGAAATAATTCAAAAGAAGGAA-AAAGCTATATGCAC 440 chr3ptel1M 605814 AGAAATGTTTGTGGCAGCCATTTCTATAGTAGCAAAGAAAGGGAAGCCGG 605863 ii i ii v vv v i i i i vv i viv L1ME4c_3end#L 441 GAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAAC 490 chr3ptel1M 605864 GGGGCTGCCCATCAGCTGGGGAGCAGCTGCACAAATTGTGGTATATGAAC 605913 vviiv i v iiv iii i ivii i i v? L1ME4c_3end#L 491 CTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNAC 540 chr3ptel1M 605914 GGTATGGAATGTTATTGTTCCATAAAAAATGA 605945 vvv i vvvv v L1ME4c_3end#L 541 TCGATGGAATATTATGCAGCCATTAAAAATGA 572 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 49.69 CpG sites = 68, Kimura (unadjusted) = 52.35 Transitions / transversions = 1.45 (68/47) Gap_init rate = 0.02 (7 / 319), avg. gap size = 1.86 (13 / 7) 17 13.20 0.00 2.94 chr3ptel1M 606184 606218 (393782) (TTGT)n#Simple_repeat 1 34 (0) m_b125s252i16 4613 chr3ptel1M 606184 TTTTTTGTTGGTTTTGTTTGTTTGCTTGTTTTTTT 606218 v v - i v (TTGT)n#Simpl 1 TTGTTTGTTTG-TTTGTTTGTTTGTTTGTTTGTTT 34 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 340 36.04 0.00 0.00 chr3ptel1M 606484 606680 (393320) L1ME3G_3end#LINE/L1 434 630 (294) m_b125s551i4 4614 chr3ptel1M 606484 AAAAATGTTTGTGGCAGCCCTGTTTGTAGCAGCTAGAAGCTGGAAAATGA 606533 ii ii v vi ii v i ii vviv L1ME3G_3end#L 434 AAGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAAC 483 chr3ptel1M 606534 ATGGATGCCCATCAATTGGAGAATGGTTGGATAAATGGTGATATATGAAT 606583 v ii i v i ii vi i vv L1ME3G_3end#L 484 CTAAATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCAT 533 chr3ptel1M 606584 GTTGTAGAATATTATTGTTCTGTAACAAATGACCAGCAGGATGAATACAG 606633 ii i i i vvvv ? v v vi iv vvi vv iiv L1ME3G_3end#L 534 ACTATGGAATACTATGCAGCNGTTAAAAAGAATGAGGTAGATCTATATGT 583 chr3ptel1M 606634 AATGGCTTGGAGAGACTTACATAAACTGATGCTGAATGAATTGAGCA 606680 v i v i ii v vi vv iv i i vvi L1ME3G_3end#L 584 ACTGACATGGAAAGATCTCCAAGACATATTGTTGAGTGAAAAAAGCA 630 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 50.87 CpG sites = 38, Kimura (unadjusted) = 50.87 Transitions / transversions = 1.15 (38/33) Gap_init rate = 0.00 (0 / 196), avg. gap size = 0.0 (0 / 0) 13 4.76 0.00 4.35 chr3ptel1M 606999 607022 (392978) (GGGA)n#Simple_repeat 1 23 (0) m_b125s252i17 4615 chr3ptel1M 606999 GGGAGGGGGTGGAGGGAGGGAGGG 607022 i - (GGGA)n#Simpl 1 GGGAGGGAG-GGAGGGAGGGAGGG 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 226 24.19 4.84 0.00 chr3ptel1M 607151 607212 (392788) MIRc#SINE/MIR 110 174 (94) m_b125s601i13 4616 chr3ptel1M 607151 AACCCCTCTGGCCCTCACCTACTCCACCTGTCAAATGGGGAGAACATT-- 607198 i iv vi v ii i v v i v -- MIRc#SINE/MIR 110 AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAC 159 chr3ptel1M 607199 -TGCCCTGTCTCCCT 607212 - i v MIRc#SINE/MIR 160 CTGCCCTGCCTACCT 174 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.58 CpG sites = 8, Kimura (unadjusted) = 29.58 Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.03 (2 / 61), avg. gap size = 1.50 (3 / 2) 355 27.31 2.96 7.75 chr3ptel1M 607723 607857 (392143) MIRc#SINE/MIR 16 144 (124) m_b125s601i14 4617 chr3ptel1M 607723 CGGTGCTGAGAGCGCTGGGCCTGGAGTCGGGTAGAGCCCAGCTCTGAGTT 607772 i vvi i i i i v -------i i MIRc#SINE/MIR 16 CAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA-------CCTGGGTT 58 chr3ptel1M 607773 CAAATCTTTCTTCAAACGCTTCACTAGTGGGGTGACCCAGGGCAAGTCTC 607822 i i iivvi viv i - iv v iv v MIRc#SINE/MIR 59 CGAGTCCCGGCTCTGCCACTT-ACTAGCTGTGTGACCTTGGGCAAGTCAC 107 chr3ptel1M 607823 CT---CTCCCTGTTTGCCTCC-TACCCTCATCTGTAAAA 607857 i --- i --v v- vi MIRc#SINE/MIR 108 TTAACCTCTCTG--AGCCTCAGTTTCCTCATCTGTAAAA 144 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.15 CpG sites = 20, Kimura (unadjusted) = 34.62 Transitions / transversions = 1.43 (20/14) Gap_init rate = 0.09 (12 / 134), avg. gap size = 1.17 (14 / 12) 43 33.99 1.38 2.31 chr3ptel1M 609141 609358 (390642) (CCTC)n#Simple_repeat 1 216 (0) m_b125s252i18 4618 chr3ptel1M 609141 CCTCTCTCCAGCCC-CCCTCCCCCCTCTGTCTTCCTCCCAGCGTTCCATC 609189 i vv - i - vi i -v vi v (CCTC)n#Simpl 1 CCTCCCTCCCTCCCTCCCTCCCTCC-CTCCCTCCCTCCC-TCCCTCCCTC 48 chr3ptel1M 609190 CATCCATCCCTCCTTCGGACCTTCCAT-TCTCCATCCTTCCCTCCTATCC 609238 v v i vvv i v -i v i -v (CCTC)n#Simpl 49 CCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCC-CTCC 97 chr3ptel1M 609239 TTCCAAAAATCCATCCCCCTATCCCTCCTGTCCTTCCCTCTGTCCTTCCA 609288 i vvvvv v i iv -v i iv i v (CCTC)n#Simpl 98 CTCCCTCCCTCCCTCCCTCCCTCCCTCC-CTCCCTCCCTCCCTCCCTCCC 146 chr3ptel1M 609289 TCCATCCATCCACT-TCTCCTTCCACCCCCCCCACATTCCCTCCTTCTGT 609337 v v - -i i vi i v vi i iv (CCTC)n#Simpl 147 TCCCTCCCTCC-CTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCT 195 chr3ptel1M 609338 CCTTCCATCCATTCCTCCATC 609358 i v v i v (CCTC)n#Simpl 196 CCCTCCCTCCCTCCCTCCCTC 216 Matrix = Unknown Transitions / transversions = 0.73 (24/33) Gap_init rate = 0.04 (8 / 217), avg. gap size = 1.00 (8 / 8) 51 30.71 2.53 2.53 chr3ptel1M 609170 609406 (390594) (CTTC)n#Simple_repeat 1 237 (0) m_b125s252i19 4618 chr3ptel1M 609170 CTTCCTCCCAGCGTTCCATCCATCCATCCCTCCTTCGGACCTTCCATTC- 609218 i vv v v v v i vvv v i - (CTTC)n#Simpl 1 CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT 50 chr3ptel1M 609219 TCCATCCTTCCCTCCTATCCTTCCAAAAATCCATCC-CCCTATCCCTCCT 609267 v i - vvvvv v -i - i (CTTC)n#Simpl 51 TCCTTCCTTCCTTCCT-TCCTTCCTTCCTTCCTTCCTTCCT-TCCTTCCT 98 chr3ptel1M 609268 GTCCTTCCCTCTGTCCTTCCATCCATCCATCC-ACTTCTCCTTCCACCCC 609316 - i iv v v v -v i - vi i (CTTC)n#Simpl 99 -TCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT-TCCTTCCTTCCT 146 chr3ptel1M 609317 CCCCACATTCCCTCCTTCTGTCCTTCCATCCATTCC-TCCATCAGTCTTT 609365 i iv v i iv v - - v vv i (CTTC)n#Simpl 147 TCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC-TTCCTTCCTTCCTTCCTT 195 chr3ptel1M 609366 CTGAGCCTTCTTTTGTT-CTT-CGTCCATCCACCCCTCCTTCC 609406 -vvv i iv - - v v vi i (CTTC)n#Simpl 196 C-CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 237 Matrix = Unknown Transitions / transversions = 0.54 (20/37) Gap_init rate = 0.05 (12 / 236), avg. gap size = 1.00 (12 / 12) 465 24.00 0.81 5.93 chr3ptel1M 609573 609696 (390304) MIRc#SINE/MIR 10 127 (141) m_b125s601i15 4619 chr3ptel1M 609573 GTGGCTCAGTGGATAGGGCACTAGCCCTGAAGTCAGCAGGACCTGACTTC 609622 iv v i i v i i v i iv MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr3ptel1M 609623 AAATCTGACCTCAGACACTTAACACTGCCTGACTGTGTGACCCTGGGCAA 609672 i i iviv v v ------- ii i MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTGACCTTGGGCAA 102 chr3ptel1M 609673 GTCACTTCA-CTCCCACTGCCTCAG 609696 v - i vvv MIRc#SINE/MIR 103 GTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.81 CpG sites = 15, Kimura (unadjusted) = 29.19 Transitions / transversions = 1.15 (15/13) Gap_init rate = 0.07 (8 / 123), avg. gap size = 1.00 (8 / 8) 284 28.72 16.31 1.23 chr3ptel1M 609751 609891 (390109) C MIRc#SINE/MIR (62) 206 45 m_b125s601i16 4620 chr3ptel1M 609751 TTATCTCATGGGATCCTCATGA--------TGATGTCGGCAGAGAGAGAA 609792 vv ii -------- v v i vii -- C MIRc#SINE/MIR 206 TTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGG-- 159 chr3ptel1M 609793 TACTATTGTCCTC-TCTTCCAGA-GAAGAAACTGAAACTGAGAG-GGACA 609839 i i i - i v - i ii v - vi C MIRc#SINE/MIR 158 TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTA 109 chr3ptel1M 609840 GGCGGTT--CCC-----CACA-----AGCGAACGTCTGAGGCAGGATCCC 609877 i i ii -- ----- ----- ii ii v v v i ii v C MIRc#SINE/MIR 108 AGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCG 59 chr3ptel1M 609878 GACTCAGGGGTTCC 609891 i i vv C MIRc#SINE/MIR 58 AACCCAGGTCTTCC 45 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.61 CpG sites = 26, Kimura (unadjusted) = 37.82 Transitions / transversions = 1.86 (26/14) Gap_init rate = 0.06 (9 / 140), avg. gap size = 2.78 (25 / 9) 244 13.77 15.25 1.49 chr3ptel1M 610700 610758 (389242) MIRb#SINE/MIR 118 184 (84) m_b125s601i17 4621 chr3ptel1M 610700 CTCTAGCACCTCAGTTTCCTCATCTGTGAAAT-GGGATTAT--------C 610740 - vi i - v -------- MIRb#SINE/MIR 118 CTCT-GAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTAC 166 chr3ptel1M 610741 CTCACAGGGCTGTGGAGA 610758 i i v v MIRb#SINE/MIR 167 CTCGCAGGGTTGTTGTGA 184 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 13.38 CpG sites = 4, Kimura (unadjusted) = 15.30 Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.05 (3 / 58), avg. gap size = 3.33 (10 / 3) 207 29.49 7.69 0.00 chr3ptel1M 611765 611842 (388158) L2b_3end#LINE/L2 359 442 (24) m_b125s601i18 4622 chr3ptel1M 611765 CGTAAGCTCAAGGACCGTGTC---CTGGCTG---GCTGTATGCCCACTGC 611808 i vv i ? --- v i v--- v vi L2b_3end#LINE 359 CGTGAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTGTATCCCCAGCGC 408 chr3ptel1M 611809 TCCGCCTGGGGCATGACGCATAGTAGGTGCTTGG 611842 iiv vii ? v i i i i ii L2b_3end#LINE 409 CTAGCACAGNGCCTGGCACACAGTAGGCGCTCAG 442 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.70 CpG sites = 14, Kimura (unadjusted) = 40.12 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.03 (2 / 77), avg. gap size = 3.00 (6 / 2) 650 26.29 1.26 1.90 chr3ptel1M 613471 613629 (386371) MIRc#SINE/MIR 24 181 (87) m_b125s601i19 4623 chr3ptel1M 613471 AAAGCACCAGGCCTGGAGTCAGGAAGGTCTGAGTTCAAATCCAGCCCCAG 613520 i ii i i ii i i i v v i v MIRc#SINE/MIR 24 AGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTG 73 chr3ptel1M 613521 ACACTCACTGGCTGTGTGACCCTGGACAAGCCACTTCACCCCATTG-GCC 613569 v i i i i i v i vi - MIRc#SINE/MIR 74 CCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCC 123 chr3ptel1M 613570 TCAGCTTCCCCATCTGTAAAATGAGCTTGAGAAGGGAATCAGTCCAGTCT 613619 i i i --- v viiv i v i v i MIRc#SINE/MIR 124 TCAGTTTCCTCATCTGTAAAATGGG---GATAATAATACCTGCCCTGCCT 170 chr3ptel1M 613620 -CTTTACCAGG 613629 - i i vi MIRc#SINE/MIR 171 ACCTCACAGGG 181 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.92 CpG sites = 29, Kimura (unadjusted) = 33.95 Transitions / transversions = 2.42 (29/12) Gap_init rate = 0.03 (5 / 158), avg. gap size = 1.00 (5 / 5) 188 36.91 1.18 1.18 chr3ptel1M 613927 614011 (385989) C AmnL2-1#LINE/L2 (2491) 122 38 m_b125s601i20 4624 chr3ptel1M 613927 TAGAGCTTCTGGTGAGG-CAATATCGGAGAAGAAGAAATGTGGCTGGGAG 613975 ii i i ii -ii v i i i-ii iv ii C AmnL2-1#LINE/ 122 TGAAGTTCCCAGTGAGGATGAAATCAGAGAAGGAGAAAC-CAGTAGGGGA 74 chr3ptel1M 613976 GGGGAGGATATCGGGATCAAATTTCTCCGATAAGGG 614011 i i vi v v i v i vvii C AmnL2-1#LINE/ 73 GAGGAAGTCATAGGGATAAGATGTTTGAAGTAAGGG 38 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 56.76 CpG sites = 23, Kimura (unadjusted) = 56.76 Transitions / transversions = 2.88 (23/8) Gap_init rate = 0.02 (2 / 84), avg. gap size = 1.00 (2 / 2) 12 9.12 4.17 0.00 chr3ptel1M 615048 615071 (384929) (CTCC)n#Simple_repeat 1 25 (0) m_b125s252i20 4625 chr3ptel1M 615048 CTCCCTCCCTCTC-CCCTCCCCCCC 615071 i - i (CTCC)n#Simpl 1 CTCCCTCCCTCCCTCCCTCCCTCCC 25 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 197 35.46 3.61 4.88 chr3ptel1M 616020 616185 (383815) C L2#LINE/L2 (1560) 1522 1359 m_b125s601i21 4626 chr3ptel1M 616020 GCCTCCACAGTCTCAATAGAACAGAAGGCCGGGCCTTCAGCC-AGGG-GA 616067 i i ivv i ii i i i vi i v i- i - C L2#LINE/L2 1522 GCTTCTATTTTCTCAGTGAAATAGGAAGCAAGGTCATCAGCTGAGAGTGA 1473 chr3ptel1M 616068 G--CAGGAGAGGAGGCAATAGGGAGCTCAGAAGAGGGGGG--GTTTTGGG 616113 --i i iiv i i ivi v i i i -- v v ii C L2#LINE/L2 1472 GGATAGGGGAGGAGGTGTTGGAGGTTTGAGGAGAGAGGAGAAGGTGTGAA 1423 chr3ptel1M 616114 GCAGCCGTGGAAAAGAGCAGGGGACGTCACAAAGGCCCCAGGGAGGCGCA 616163 ii i vv ii ii i - ---i v vv i iii i C L2#LINE/L2 1422 ATAGTCGTCTAGGAGAGTGGGAGA-GT---GAATGGACTAGGGAAATGTA 1377 chr3ptel1M 616164 GTAAGCGGGATTGTGGGGCAGC 616185 ----? iv C L2#LINE/L2 1376 GTA----NGATTGCCGGGCAGC 1359 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 53.40 CpG sites = 41, Kimura (unadjusted) = 53.40 Transitions / transversions = 2.73 (41/15) Gap_init rate = 0.07 (12 / 165), avg. gap size = 1.17 (14 / 12) 40 12.94 2.56 1.27 chr3ptel1M 616441 616518 (383482) (TCTGTC)n#Simple_repeat 1 79 (0) m_b125s252i21 4627 chr3ptel1M 616441 TCTGATCTCTGACT-T-TCATTTTCTGTGTGTCTGTCTCTCTCTGTGTGT 616488 - v - - vi v v v v v v (TCTGTC)n#Sim 1 TCTG-TCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCT 49 chr3ptel1M 616489 CTGTCTCTGTCTCTGTCTCTGTCTCTGTCT 616518 (TCTGTC)n#Sim 50 CTGTCTCTGTCTCTGTCTCTGTCTCTGTCT 79 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.04 (3 / 77), avg. gap size = 1.00 (3 / 3) 71 1.56 0.00 0.00 chr3ptel1M 616519 616583 (383417) (CA)n#Simple_repeat 1 65 (0) c_b125s251i2 4628 chr3ptel1M 616519 CACACACACACACACACATACACACACACACACACACACACACACACACA 616568 i (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 chr3ptel1M 616569 CACACACACACACAC 616583 (CA)n#Simple_ 51 CACACACACACACAC 65 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0) 24 24.44 1.20 3.70 chr3ptel1M 616719 616801 (383199) (CCCCCTC)n#Simple_repeat 1 81 (0) m_b125s252i23 4629 chr3ptel1M 616719 CCTCCTGTCCCCTCCCCCTGCCCCTTCTCACCCCCCGCCCCTGTCCCCCT 616768 i vi iv -i v i v -i (CCCCCTC)n#Si 1 CCCCCTCCCCCCTCCCCCCTCCCC-CCTCCCCCCTCCCCCCT-CCCCCCT 48 chr3ptel1M 616769 GCCCCCT-GTCCCTCACCCTCCACCCCCTCCCCC 616801 v -vi - i iv (CCCCCTC)n#Si 49 CCCCCCTCCCCCCTC-CCCCCTCCCCCCTCCCCC 81 Matrix = Unknown Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.05 (4 / 82), avg. gap size = 1.00 (4 / 4) 12 18.48 7.84 1.85 chr3ptel1M 617579 617629 (382371) (GCCTCCT)n#Simple_repeat 1 54 (0) m_b125s252i24 4630 chr3ptel1M 617579 GCC-CCT-CCCCCTGCCAGC-CCCTCCTTCCTGCTGGCTCCTGGCTGCCT 617625 - - i vv -v v v v v - (GCCTCCT)n#Si 1 GCCTCCTGCCTCCTGCCTCCTGCCTCCTGCCTCCTGCCTCCTGCCT-CCT 49 chr3ptel1M 617626 -CCTC 617629 - (GCCTCCT)n#Si 50 GCCTC 54 Matrix = Unknown Transitions / transversions = 0.14 (1/7) Gap_init rate = 0.10 (5 / 50), avg. gap size = 1.00 (5 / 5) 188 23.08 0.00 0.00 chr3ptel1M 618267 618305 (381695) C MIR#SINE/MIR (117) 145 107 m_b125s601i22 4631 chr3ptel1M 618267 CCCCATTCTACAGAGAAGGACCCTGTTGTACAGAGAAGT 618305 i vi vv vv i i C MIR#SINE/MIR 145 CCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGT 107 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.68 CpG sites = 4, Kimura (unadjusted) = 27.68 Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 12 16.85 0.00 5.71 chr3ptel1M 619655 619691 (380309) (GCCCCT)n#Simple_repeat 1 35 (0) m_b125s252i25 4632 chr3ptel1M 619655 GCCCAAGCCCACTGCCCCCCCCCCTTGGCCCTGCCCC 619691 vv - iv - v (GCCCCT)n#Sim 1 GCCCCTGCCC-CTGCCCCTGCCCC-TGCCCCTGCCCC 35 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 257 30.02 0.96 7.14 chr3ptel1M 619714 619817 (380183) L2a_3end#LINE/L2 419 516 (1) m_b125s601i23 4633 chr3ptel1M 619714 GGGA-TCTTGTGTGCTTTTCTTTGTTCCCACATTGGCCCCCAGCCCCAGG 619762 - i v - v iii v iii ---- v --v L2a_3end#LINE 419 GGGACTTTTGTCTG-TTTTGTTCACTGCTGTAT----CCCCAGCGCC--T 461 chr3ptel1M 619763 AGAACATAGCCTGGTGTGCAGCAAGCAATTAATAAATGTTTGTGGAATTA 619812 vv iiiii i i iv i i v v L2a_3end#LINE 462 AGAACAGTGCCTGGCACATAGTAGGCGCTCAATAAATATTTGTTGAATGA 511 chr3ptel1M 619813 GAGAA 619817 iv L2a_3end#LINE 512 ATGAA 516 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.80 CpG sites = 18, Kimura (unadjusted) = 39.56 Transitions / transversions = 1.64 (18/11) Gap_init rate = 0.08 (8 / 103), avg. gap size = 1.00 (8 / 8) 16 17.19 0.00 4.88 chr3ptel1M 619871 619913 (380087) (AGCCC)n#Simple_repeat 1 41 (0) m_b125s252i26 4634 chr3ptel1M 619871 AGGCCAGACAAGCCCCAGCCCATGCCCAGCCCTGCCCCACCCA 619913 v v v - - v vi (AGCCC)n#Simp 1 AGCCCAGCCCAG-CCCAGCCCA-GCCCAGCCCAGCCCAGCCCA 41 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.00 (2 / 2) 31 0.00 0.00 0.00 chr3ptel1M 620870 620903 (379097) (A)n#Simple_repeat 1 34 (0) m_b125s252i27 4635 chr3ptel1M 620870 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 620903 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 34 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 285 40.44 3.68 0.00 chr3ptel1M 620928 621063 (378937) C L3#LINE/CR1 (3290) 809 669 m_b125s601i24 4636 chr3ptel1M 620928 GATGC---CCAGGGTCCTTCTGGGAGTATCACTTATCCTAACCT-AATCA 620973 --- v i ivv i i ii i iv v - C L3#LINE/CR1 809 GATGCATTCCAGGTTTCTTCTGACTGTGTCATTCGTTCCCACGTGAATCA 760 chr3ptel1M 620974 CCAGCAACGGGGAGTAGCCATCAGACTGGACAAGTCTTTAGAGATTCCCC 621023 v v ii v ii i iv i ii v ii viv ii i C L3#LINE/CR1 759 GCAGGAGTGGGTAGCGGTCGGCGGGTTTGATGAGTCTTGGCAGGCTCTCC 710 chr3ptel1M 621024 ATCCCAGCTT-CATATGGGCCTTGGCAAGATGGTGCCTCTC 621063 i v iv i-v iiv iiii v ii ii vi C L3#LINE/CR1 709 GTCACGTCTCGGATACACGCTCCAGGAAGACAGCACACCTC 669 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 51.17 CpG sites = 37, Kimura (unadjusted) = 64.11 Transitions / transversions = 2.06 (37/18) Gap_init rate = 0.02 (3 / 135), avg. gap size = 1.67 (5 / 3) 283 30.30 4.04 0.00 chr3ptel1M 621362 621460 (378540) MIR1_Amn#SINE/MIR 44 146 (84) m_b125s601i25 4637 chr3ptel1M 621362 CTCAGGGGACTCAGCCCTCAATCT----ACTGTCACTGCCCAGTTCTGAA 621407 i i iii viii? ? i----v i ?v ? i v? vi MIR1_Amn#SINE 44 CTCGGGAGACCTGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTG 93 chr3ptel1M 621408 GTCCTGGGCATGGCACATAACTCCACTGGGCCTCAGTTTCATTGTCTGTC 621457 ii i v v v ? ii v ? v ii v MIR1_Amn#SINE 94 ACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTA 143 chr3ptel1M 621458 AAA 621460 MIR1_Amn#SINE 144 AAA 146 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.81 CpG sites = 19, Kimura (unadjusted) = 44.86 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.01 (1 / 98), avg. gap size = 4.00 (4 / 1) 269 37.30 4.44 0.71 chr3ptel1M 621363 621497 (378503) MIR3#SINE/MIR 40 179 (29) m_b125s601i26 4637 chr3ptel1M 621363 TCAGGGGACTCAGCCCTCAATCT----ACTGTCACTGCCCAGTTCTGAAG 621408 i iii viiii i i----v i iv i? i v vii MIR3#SINE/MIR 40 TCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGA 89 chr3ptel1M 621409 TCCTGGGCATGGCACATAACTCCACTGGGCCTCAGTTTCATTGTCTGTCA 621458 i i v v v v ii v v ii - MIR3#SINE/MIR 90 CCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGT-A 138 chr3ptel1M 621459 AACCAAACGACCTCTGTGAGAT--TCTCTTAATTCTCTTCC 621497 vii iv ivi vviiv -- v iv i MIR3#SINE/MIR 139 AAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCC 179 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 55.37 CpG sites = 31, Kimura (unadjusted) = 55.37 Transitions / transversions = 1.63 (31/19) Gap_init rate = 0.02 (3 / 134), avg. gap size = 2.33 (7 / 3) 289 29.73 0.00 0.00 chr3ptel1M 621387 621460 (378540) MIRc#SINE/MIR 71 144 (124) m_b125s601i27 4637 chr3ptel1M 621387 CTGTCACTGCCCAGTTCTGAAGTCCTGGGCATGGCACATAACTCCACTGG 621436 i vv i i v viii i v v v ii v i MIRc#SINE/MIR 71 CTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGA 120 chr3ptel1M 621437 GCCTCAGTTTCATTGTCTGTCAAA 621460 v ii v MIRc#SINE/MIR 121 GCCTCAGTTTCCTCATCTGTAAAA 144 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.64 CpG sites = 12, Kimura (unadjusted) = 38.64 Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.00 (0 / 73), avg. gap size = 0.0 (0 / 0) 243 30.12 4.82 0.00 chr3ptel1M 621710 621792 (378208) C L2c_3end#LINE/L2 (18) 460 374 m_b125s601i28 4638 chr3ptel1M 621710 CATTCATTTATCGC----TACCTGAAAATCACTGAGGCCACAAAGAAAAC 621755 i v v ---- iv vv iv i i vi vi v C L2c_3end#LINE 460 CATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGATACAAAGATGAA 411 chr3ptel1M 621756 CAAAGAATGGCCCCTGCCCTCAAGAAGCTTACATTCT 621792 i iiv i i i i v C L2c_3end#LINE 410 TAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCT 374 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.50 CpG sites = 14, Kimura (unadjusted) = 39.43 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.01 (1 / 82), avg. gap size = 4.00 (4 / 1) 219 39.60 4.25 5.30 chr3ptel1M 622030 622429 (377571) C L2#LINE/L2 (78) 3004 2609 m_b125s601i29 4638 chr3ptel1M 622030 ACAGGGAGCAGGA-AGTTTGGCTGGAACATAGAG-GCAAGGAGGAA--TG 622075 vi v v- v i iv v - i i i-- C L2#LINE/L2 3004 ACAGCAAGGAGGCCAGTGTGGCTGGAGCGGAGTGAGCGAGGGGGAGAGTG 2955 chr3ptel1M 622076 GAAAAAACAGAGGGCCTAAAAAAATA--GGGTTAGAAATAGGCTTCAGGC 622123 v ii ivv v -- i i ii -- --- i vi i-- v - C L2#LINE/L2 2954 GTAGGAGATGAGGTC--AGAGAGGTAACGGG---GGACCAGA--TCATG- 2913 chr3ptel1M 622124 TGCTAACAGACCTAGAACACAACTGGGGGCATTTCGGTTTGATCCTTGAG 622173 --- i-- i v v vi v i vii v i i i vvv ii C L2#LINE/L2 2912 ---TAG--GGCCTTGTAGGCCATTGTAAGGACTTTGGCTTTTACTCTGAG 2868 chr3ptel1M 622174 -ACGATACAGAGCCTCTTGAGTTTACTGAGTAGGAGAGATGACATG-TCA 622221 -iv ivii vi v vv vi i ii - - v C L2#LINE/L2 2867 TGAGATGGGAAGCCATTGGAGGGTTTTGAGCAGAGGAG-TGACATGATCT 2819 chr3ptel1M 622222 GACCTGGACTTTTGGAAAATCACT-TGTTGGCTAAATGGAGGGTGGACTC 622270 i ivii vii ii - viv ivi v ii i v C L2#LINE/L2 2818 GACTTACGTTTTAAAAGGATCACTCTGGCTGCTGTGTTGAGAATAGACTG 2769 chr3ptel1M 622271 GCAAAGGGAGAGATCTGAGGCAG-----CCAATGCCCCAGCAGCCATTGC 622315 ?viii vi iviv i ----- i ---ivi vi i C L2#LINE/L2 2768 NAGGGGGGCAAGGGTGGAAGCAGGGAGACCAGT---TAGGAGGCTATTGC 2722 chr3ptel1M 622316 AACAATCCAGGTACGAGAAGATAGGTGTCTGCACTTTGAGGGGGTAGCAC 622365 ii iiv v i vv ii v --iii v i v C L2#LINE/L2 2721 AGTAATCCAGGCGAGAGATGATGGTGGCTTGGAC--CAGGGTGGTGGCAG 2674 chr3ptel1M 622366 AGTCAGAAGAGGGAAA-GGGCATATTTGAGAGATA--CTGAAGATGCAAG 622412 v vvi vi v i i- v iv ivi v --i i -- ii C L2#LINE/L2 2673 TGGAGGTGGTGAGAAGTGGTCGGATTCTGGATATATTTTGAAGGT--AGA 2626 chr3ptel1M 622413 ATTGACCAGAGGTGTTG 622429 iii vi vv i C L2#LINE/L2 2625 GCCGACAGGATTTGCTG 2609 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 55.96 CpG sites = 89, Kimura (unadjusted) = 59.76 Transitions / transversions = 1.46 (89/61) Gap_init rate = 0.08 (31 / 399), avg. gap size = 1.23 (38 / 31) 34 28.99 1.00 0.00 chr3ptel1M 624781 624880 (375120) (GT)n#Simple_repeat 1 101 (0) m_b125s252i28 4639 chr3ptel1M 624781 GTGTATGTGGGGGGAAGGGTGTGAGTGTGTGAGTGTGTGGGGGGGTGAAT 624830 i v v viv v v v v v v vi (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50 chr3ptel1M 624831 GTGTGTATGTGAG-GGGTGTGTGTATGGGGGTGTATGTTTGTGTTTCTGT 624879 i v - v i v v i v v v (GT)n#Simple_ 51 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 100 chr3ptel1M 624880 G 624880 (GT)n#Simple_ 101 G 101 Matrix = Unknown Transitions / transversions = 0.33 (6/18) Gap_init rate = 0.01 (1 / 99), avg. gap size = 1.00 (1 / 1) 15 10.85 3.33 0.00 chr3ptel1M 625150 625179 (374821) (CCAGG)n#Simple_repeat 1 31 (0) m_b125s252i29 4640 chr3ptel1M 625150 CCAGCCCAGGCCAGG-CTGCCCAGGCCAGGC 625179 v - v v (CCAGG)n#Simp 1 CCAGGCCAGGCCAGGCCAGGCCAGGCCAGGC 31 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 14 23.26 2.22 0.00 chr3ptel1M 625829 625873 (374127) (GCGGGGG)n#Simple_repeat 1 46 (0) m_b125s252i30 4641 chr3ptel1M 625829 GCTGGGGGGGAGGGGCGGCGGGCCGGGAGC-GGGGCTGGGGGGAGG 625873 v v i v v i - vi v (GCGGGGG)n#Si 1 GCGGGGGGCGGGGGGCGGGGGGCGGGGGGCGGGGGGCGGGGGGCGG 46 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 53 3.29 0.00 3.12 chr3ptel1M 626113 626178 (373822) (GCTCCG)n#Simple_repeat 1 64 (0) c_b125s251i3 4642 chr3ptel1M 626113 GCTCGGGCTCCGGCCCCGGCTCCGGCTCCGGCTCCGGCTCCGGCTCCGGC 626162 v i (GCTCCG)n#Sim 1 GCTCCGGCTCCGGCTCCGGCTCCGGCTCCGGCTCCGGCTCCGGCTCCGGC 50 chr3ptel1M 626163 TCCCGGCTCCCGGCTC 626178 - - (GCTCCG)n#Sim 51 T-CCGGCT-CCGGCTC 64 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.03 (2 / 65), avg. gap size = 1.00 (2 / 2) 16 0.00 0.00 4.35 chr3ptel1M 626280 626303 (373697) (GGA)n#Simple_repeat 1 23 (0) m_b125s252i31 4643 chr3ptel1M 626280 GGAGGAGGAGGAGGAGGGAGGAGG 626303 - (GGA)n#Simple 1 GGAGGAGGAGGAGGA-GGAGGAGG 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 291 33.34 4.55 4.55 chr3ptel1M 626938 627091 (372909) MIR1_Amn#SINE/MIR 9 162 (68) m_b125s601i30 4644 chr3ptel1M 626938 CAGGGTGGCTTAGTAAGTCCAGAGCTTTGAGCTGGAGGCCCAAAGAT--- 626984 v ii iii -- vi ii iivi vii i--- MIR1_Amn#SINE 9 CAGTGTGGTCTAGTGGAT--AGAGCACTGGACTGGGACTCGGGAGACCTG 56 chr3ptel1M 626985 GGT--AATTCCTACGTACT-TCAGACACTTCCTGTAGGGCCCTGGGGGAA 627031 --? ? ii- iv -i vv?i i?v ?iv i i v--- MIR1_Amn#SINE 57 GGTTCNANTCCCG-GCTCTGCCACTNGCCNGCTGNGTGACCTTGGGC--- 102 chr3ptel1M 627032 AAAATCGCTTGCTTTCTCTGAGCCTCAGCTCCCCCATCTGTAGACTGAGA 627081 - i i ?vii ? i i i i v i i MIR1_Amn#SINE 103 -AAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGG 151 chr3ptel1M 627082 ACGGT-ACACT 627091 iii - i MIR1_Amn#SINE 152 ATAATGATACT 162 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 50.52 CpG sites = 37, Kimura (unadjusted) = 52.33 Transitions / transversions = 3.08 (37/12) Gap_init rate = 0.07 (11 / 153), avg. gap size = 1.27 (14 / 11) 315 33.34 2.75 3.70 chr3ptel1M 627008 627116 (372884) MIRc#SINE/MIR 80 187 (81) m_b125s601i31 4644 chr3ptel1M 627008 ACTTCCTGTAGGGCCCTGGGGGAAAAAATCGCTTGCTTTCTCTGAGCCTC 627057 vv iv i i v---- i i ivii MIRc#SINE/MIR 80 ACTAGCTGTGTGACCTTGGGC----AAGTCACTTAACCTCTCTGAGCCTC 125 chr3ptel1M 627058 AGCTCCCCCATCTGTAGACTGAGAACGGTACACTCCACATTAC---CCTT 627104 i i i i v i i iii vvvi ii vi i --- i MIRc#SINE/MIR 126 AGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTC 175 chr3ptel1M 627105 GCAGGATTGTTG 627116 i i MIRc#SINE/MIR 176 ACAGGGTTGTTG 187 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 47.65 CpG sites = 25, Kimura (unadjusted) = 47.65 Transitions / transversions = 2.50 (25/10) Gap_init rate = 0.05 (5 / 108), avg. gap size = 1.40 (7 / 5) 357 38.12 6.44 0.00 chr3ptel1M 628618 628819 (371181) C L3#LINE/CR1 (41) 4058 3844 m_b125s601i32 4645 chr3ptel1M 628618 GTCACTCTGTCCACTCTGTCA-CCGAC-CAGGAGTGCTCCCTGTGCTACA 628665 iiiv vi vi - i i- i v iii iiivi iv C L3#LINE/CR1 4058 GTCATCTAGTCCAACCTCCCATCCAATGCAGGAATCCCTTCTACAACATC 4009 chr3ptel1M 628666 CCTGCGCAG-GGTC------TCTTGGTTGGGAAAACTCCAGGGAAAGGGA 628708 vvv - ------i iv i v i v v v vi C L3#LINE/CR1 4008 CCTGACAAGTGGTCATCCAGCCTCTGCTTGAACACCTCCAGTGACGGGGA 3959 chr3ptel1M 628709 GCCTGCCACTTCTCTAAGTAGCTCAGGTCACTGTGGGAT-GCTCT---TG 628754 iii i i ? v i i i vvi i v v i- --- C L3#LINE/CR1 3958 GCTCACTACCTCNCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGATTG 3909 chr3ptel1M 628755 GGAATAGATTTTTCCTGACATCCAGGTAAAAATTGCCCTGTGGTCACTCC 628804 vv iv ii i v i iv vii vi iiviv v i C L3#LINE/CR1 3908 TTAGAAAGTTCTTCCTTATATTGAGCCGAAATCTGCCTCCCTGTAACTTC 3859 chr3ptel1M 628805 CCCCCATTGCTCCTA 628819 v v C L3#LINE/CR1 3858 CACCCATTGGTCCTA 3844 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 53.93 CpG sites = 45, Kimura (unadjusted) = 56.28 Transitions / transversions = 1.41 (45/32) Gap_init rate = 0.03 (6 / 201), avg. gap size = 2.17 (13 / 6) 763 31.43 14.53 0.91 chr3ptel1M 628810 629387 (370613) C L2#LINE/L2 (516) 2566 1911 m_b125s601i33 4646 chr3ptel1M 628810 ATTGCTCCTAAGCTGTGAACCTGAGGGACTGGGATGATGG--TT---CTT 628854 vi v i i v vii vi i v -- ---v C L2#LINE/L2 2566 ATGACTCCAAGGTTTTTGGCCTGAGCAACTGGAAGGATGGAGTTGCCATT 2517 chr3ptel1M 628855 GACAGAGATATCGGGGAGGGTGCAGAATGCTTAGG-----AGGGGAGCAT 628899 ? v i-- i iv i i v vvi -----i iv C L2#LINE/L2 2516 NACTGAGATG--GGGAAGACTGCGGGAGGAGCAGGTTTGAGGGGGAAGAT 2469 chr3ptel1M 628900 GGATGAGTTCCGTTCTAGAAGTATT-----TAAGGCATCTATGGGATATC 628944 v- v v i i vi i ----- i iiii vi i C L2#LINE/L2 2468 C-AGGAGTTCAGTTTTGGACATGTTAAGTTTGAGATGCCTATTAGACATC 2420 chr3ptel1M 628945 CAGTTCAAGATGTCTACTAAGTAGT-AGATTGAGGAG---GGAGGCCAGC 628990 iv vi v v i i -i vv v --- vi v C L2#LINE/L2 2419 CAAGTGGAGATGTCGAGTAGGCAGTTGGATATACGAGTCTGGAGTTCAGG 2370 chr3ptel1M 628991 AGAGGGACTGGGCCAGGAAAGGTCAATTTGAGAATCATCAATTT-CAAAT 629039 i i iiiv v v i vi v i i iiv -i i C L2#LINE/L2 2369 GGAGAGGTCCGGGCTGGAGATATAAATTTGGGAGTCATCAGCATATAGAT 2320 chr3ptel1M 629040 --CATGAAAATCCTTGGGAGCGGAAGAGATCATGCAAGGGAGAGA-TCTA 629086 --i vv v v i vi v i- ? v - v C L2#LINE/L2 2319 GGTATTTAAAGCCATGAGACTGGATGAGATCAC-CNAGGGAGTGAGTGTA 2271 chr3ptel1M 629087 GAGGGAGAAAAGGAGCGGCTCCGGCACGGAGTCTATGGGACA-GCCACAG 629135 vi i i v ii vi v v i i- i -v vv C L2#LINE/L2 2270 GATAGAGAAGAGAAGAGGTCCAAGGACTGAGCCC-TGGGGCACTCCAACG 2222 chr3ptel1M 629136 CTGA----TCCG------GAGGAGGATCCAGCAAAGCAGA--GAGAAGGG 629173 i ? ---- v ------ v v -- i C L2#LINE/L2 2221 TTNAGAGGTCGGGGAGATGAGGAGGAACCAGCAAAGGAGACTGAGAAGGA 2172 chr3ptel1M 629174 ATGGTCAAAGGGGGAGGAGGAGAAGCGGAAGGAGTAT------CTAGAA- 629216 ii i iv i v i v i i - i ------ i - C L2#LINE/L2 2171 GCGGCCAGTGAGGTAGGAGGAAAACCAGGA-GAGTGTGGTGTCCTGGAAG 2123 chr3ptel1M 629217 --TGGAGAGAAAAGACTTTCAAGGAGCAGAG-GCGAT--GCGATGTCTGA 629261 --vi v ii vv i v i - i --i vi vi C L2#LINE/L2 2122 CCAAGTGAAGAAAGTGTTTCAAGAAGGAGGGAGTGATCAACTGTGTCAAA 2073 chr3ptel1M 629262 GGCTGCCCAAAGGT----GACAATGAGGGTGCAGAAAAGGCC-------- 629299 v iv ? ----v vi iivv vv i -------- C L2#LINE/L2 2072 TGCTGCTGANAGGTCAAGTAAGATGAGGACTGAGAATTGACCATTGGATT 2023 chr3ptel1M 629300 -----ACGGAGAGATCCCCGGTGACTTTGCTGAGGCCAGTTTGAGTGGAA 629344 ----- vi i vii i vii iv vi i C L2#LINE/L2 2022 TAGCAACGTGGAGGTCATTGGTGACCTTGACAAGAGCAGTTTCGGTGGAG 1973 chr3ptel1M 629345 TGA-------------------GGAATGTTCTCAGGAGAGAAAAGGAGGA 629375 i------------------- i vvi i vi C L2#LINE/L2 1972 TGGTGGGGACGAAAGCCTGATTGGAGTGGGTTCAAGAGAGAATGGGAGGA 1923 chr3ptel1M 629376 GAGACAGTGGAG 629387 iv v C L2#LINE/L2 1922 GAGGAATTGGAG 1911 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.30 CpG sites = 100, Kimura (unadjusted) = 42.23 Transitions / transversions = 1.25 (100/80) Gap_init rate = 0.05 (28 / 577), avg. gap size = 3.21 (90 / 28) 16 23.26 0.00 3.85 chr3ptel1M 629598 629651 (370349) (GGAAGGG)n#Simple_repeat 1 52 (0) m_b126s252i0 4647 chr3ptel1M 629598 GGATGAGGGATGGGGAGGAGGCGGAAGGGGGGGTGACAGAAGGGGGAAGG 629647 v i v - i v - iv ivi (GGAAGGG)n#Si 1 GGAAGGGGGAAGGGG-GAAGGGGGAA-GGGGGAAGGGGGAAGGGGGAAGG 48 chr3ptel1M 629648 GGGA 629651 (GGAAGGG)n#Si 49 GGGA 52 Matrix = Unknown Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.04 (2 / 53), avg. gap size = 1.00 (2 / 2) 19 0.00 0.00 0.00 chr3ptel1M 629728 629748 (370252) (G)n#Simple_repeat 1 21 (0) m_b126s252i1 4648 chr3ptel1M 629728 GGGGGGGGGGGGGGGGGGGGG 629748 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGG 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 19 8.65 5.41 0.00 chr3ptel1M 630764 630800 (369200) (GTGTGA)n#Simple_repeat 1 39 (0) m_b126s252i3 4649 chr3ptel1M 630764 GTGTGTGTATGAATGTGAGTGTGAGTGT--GTGTGAGTG 630800 v i i -- (GTGTGA)n#Sim 1 GTGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTG 39 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.03 (1 / 36), avg. gap size = 2.00 (2 / 1) 14 28.44 4.69 0.00 chr3ptel1M 632006 632069 (367931) (CCCCAG)n#Simple_repeat 1 67 (0) m_b126s252i4 4650 chr3ptel1M 632006 CCCCAGCCCCGGCCCC-GTGGCCGCCTCAGACCCTG-CCCAGCTCCGGCC 632053 i - ivv v i v v - i i (CCCCAG)n#Sim 1 CCCCAGCCCCAGCCCCAGCCCCAGCCCCAGCCCCAGCCCCAGCCCCAGCC 50 chr3ptel1M 632054 TC-TCCTGAGCCCCGGC 632069 i -v iv i (CCCCAG)n#Sim 51 CCAGCCCCAGCCCCAGC 67 Matrix = Unknown Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.05 (3 / 63), avg. gap size = 1.00 (3 / 3) 12 28.98 0.00 5.26 chr3ptel1M 632408 632467 (367533) (CCCGGG)n#Simple_repeat 1 57 (0) m_b126s252i5 4651 chr3ptel1M 632408 CCAGGGCCCTCCCCCGGGACCCCGGGGACCCCCCCCGGGCCCTCCCCCAG 632457 v vvv -- - v vvv vvv i (CCCGGG)n#Sim 1 CCCGGGCCCGGGCCCGGG--CCC-GGGCCCGGGCCCGGGCCCGGGCCCGG 47 chr3ptel1M 632458 GCCCGGACCC 632467 i (CCCGGG)n#Sim 48 GCCCGGGCCC 57 Matrix = Unknown Transitions / transversions = 0.18 (2/11) Gap_init rate = 0.05 (3 / 59), avg. gap size = 1.00 (3 / 3) 120 30.74 0.74 1.50 chr3ptel1M 633350 633753 (366247) (AGAC)n#Simple_repeat 1 401 (0) m_b126s252i6 4652 chr3ptel1M 633350 AGACGGACAGACGGGCAGGCAAGGAGCTGGTCACACAGACAGACAGACAG 633399 i i i i iiv vii v v (AGAC)n#Simpl 1 AGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAG 50 chr3ptel1M 633400 ACGGACAAGTGGCCAGATGGTGATACAGACAGACAGACAGACAGACACAC 633449 i iiii v ii vv v v (AGAC)n#Simpl 51 ACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGAC 100 chr3ptel1M 633450 GGGCAGGCAGCCAGTCACACACAGACAGACAGATGGGCAGGCAGTCAGCC 633499 i i i v -- v ii i i v v (AGAC)n#Simpl 101 AGACAGACAGACAG--ACAGACAGACAGACAGACAGACAGACAGACAGAC 148 chr3ptel1M 633500 GGATGGACAGACAGGCAGGCAGGCAGACAGACGGATGGGCAGGCAGCCGG 633549 i ii i i i i ii i i v i (AGAC)n#Simpl 149 AGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAG 198 chr3ptel1M 633550 TCACACAGAAAGACAGACAGAGGGACAAATGGCCAG-CTG-GTGACATGG 633597 v v v vi i ii v - v -vv -- (AGAC)n#Simpl 199 ACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACA--G 246 chr3ptel1M 633598 ACAGACAGGCAGGCAGACAGACGGACAGGCAGGCAGATGGATGGGCAGGA 633647 i i i i i ii ii i iv (AGAC)n#Simpl 247 ACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGAC 296 chr3ptel1M 633648 AGCCAGTCACACAGACAGGCAGACAAGTGGCCATCTGGTAAAAATAGATA 633697 v v v i iiii v vvii - v i i i (AGAC)n#Simpl 297 AGACAGACAGACAGACAGACAGACAGACAGACAGACAG-ACAGACAGACA 345 chr3ptel1M 633698 GACTGACAGATAGACAGTCCCACAGACAGACAGACA-ACTGGCCACACAG 633746 v i v vv - -i v v (AGAC)n#Simpl 346 GACAGACAGACAGACAGACAGACAGACAGACAGACAGAC-AGACAGACAG 394 chr3ptel1M 633747 ACAGACA 633753 (AGAC)n#Simpl 395 ACAGACA 401 Matrix = Unknown Transitions / transversions = 1.69 (61/36) Gap_init rate = 0.02 (9 / 403), avg. gap size = 1.00 (9 / 9) 186 31.58 1.75 0.00 chr3ptel1M 633849 633905 (366095) C MIR#SINE/MIR (51) 211 154 m_b126s601i2 4653 chr3ptel1M 633849 AGGGTTTCCCAGGCATGACCTCACT-GACCCTCACAATGACCCTGTGATG 633897 v i iv v i v v i -i i ii i v C MIR#SINE/MIR 211 AGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGG 162 chr3ptel1M 633898 TGGCCACT 633905 i vi C MIR#SINE/MIR 161 TAGGTACT 154 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.59 CpG sites = 11, Kimura (unadjusted) = 42.59 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.02 (1 / 56), avg. gap size = 1.00 (1 / 1) 216 23.53 1.96 0.00 chr3ptel1M 633853 633903 (366097) C MIRc#SINE/MIR (51) 217 166 m_b126s601i3 4653 chr3ptel1M 633853 TTTCCCAGGCATGACCTCACT-GACCCTCACAATGACCCTGTGATGTGGC 633901 v vi v i i - i ii v i v C MIRc#SINE/MIR 217 TTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGG 168 chr3ptel1M 633902 CA 633903 C MIRc#SINE/MIR 167 CA 166 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.76 CpG sites = 7, Kimura (unadjusted) = 28.76 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.02 (1 / 50), avg. gap size = 1.00 (1 / 1) 181 20.84 2.04 2.04 chr3ptel1M 635679 635727 (364273) C L2d_3end#LINE/L2 (16) 500 452 m_b126s601i4 4654 chr3ptel1M 635679 CAAGCATTTATATGGCGCCTACTACCTGCCCAGGCACT-TGGGAGGCTCT 635727 i vvi iv i - - vv v C L2d_3end#LINE 500 CAAGTATTTATTGAGCGCCTACTATGTGCTCA-GCACTGTGCTAGGCGCT 452 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 24.43 CpG sites = 4, Kimura (unadjusted) = 24.43 Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.04 (2 / 48), avg. gap size = 1.00 (2 / 2) 200 19.05 0.00 2.38 chr3ptel1M 635679 635721 (364279) C L2c_3end#LINE/L2 (14) 464 423 m_b126s601i5 4654 chr3ptel1M 635679 CAAGCATTTATATGGCGCCTACTACCTGCCCAGGCACTTGGGA 635721 i vvi iv - i v C L2c_3end#LINE 464 CAAACATTTATTGAGCGCCTACTATGTG-CCAGGCGCTGGGGA 423 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 19.19 CpG sites = 4, Kimura (unadjusted) = 22.11 Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.02 (1 / 42), avg. gap size = 1.00 (1 / 1) 20 23.89 3.12 1.54 chr3ptel1M 637354 637417 (362583) (AGGA)n#Simple_repeat 1 65 (0) m_b126s252i7 4655 chr3ptel1M 637354 AGGAAGGGGGGAAGGAGGGGGGGAAGGAAGG--GGAAAGAGGGAAAGGGA 637401 ii i ii -- i i - i (AGGA)n#Simpl 1 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG-AAGGAA 49 chr3ptel1M 637402 GGAAAGAAAAAAGCAA 637417 i ii v (AGGA)n#Simpl 50 GGAAGGAAGGAAGGAA 65 Matrix = Unknown Transitions / transversions = 11.00 (11/1) Gap_init rate = 0.03 (2 / 63), avg. gap size = 1.50 (3 / 2) 13 24.72 0.00 0.00 chr3ptel1M 640060 640097 (359903) (CAGCACC)n#Simple_repeat 1 38 (0) m_b126s252i8 4656 chr3ptel1M 640060 CAGCCCCCGGGACCGGGCACCCAGCACTCACCTCCCAG 640097 v i v vi i v v (CAGCACC)n#Si 1 CAGCACCCAGCACCCAGCACCCAGCACCCAGCACCCAG 38 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 13 9.84 8.16 6.00 chr3ptel1M 645244 645292 (354708) (GTGCCCC)n#Simple_repeat 1 50 (0) m_b126s252i9 4657 chr3ptel1M 645244 GTGCCCAGTGCCCATGTG-CCCGGGCCCCGCTGCCACCTTG---CGTGCC 645289 v -i - v - - v --- (GTGCCCC)n#Si 1 GTGCCCCGTGCCC-CGTGCCCCGTGCCCCG-TGCC-CCGTGCCCCGTGCC 47 chr3ptel1M 645290 CCG 645292 (GTGCCCC)n#Si 48 CCG 50 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.10 (5 / 48), avg. gap size = 1.40 (7 / 5) 23 17.72 3.39 1.67 chr3ptel1M 648236 648294 (351706) (TGC)n#Simple_repeat 1 60 (0) m_b126s252i10 4658 chr3ptel1M 648236 TGCTGCTG-TTCTGCTGTGGCTGCTGCTGCTGCTGCT-CTGCCAGGGCCT 648283 - v iv - - v vvv (TGC)n#Simple 1 TGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG-CTGCTGCT 49 chr3ptel1M 648284 GCTGCAGCCGC 648294 v i (TGC)n#Simple 50 GCTGCTGCTGC 60 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.05 (3 / 58), avg. gap size = 1.00 (3 / 3) 295 29.63 8.64 4.14 chr3ptel1M 648890 649051 (350949) C MIRc#SINE/MIR (63) 205 37 m_b126s601i6 4659 chr3ptel1M 648890 TATCACAATTGGTGTTTCATGGCAGAAATGGGAGCTGGGGGAGAGGGGCT 648939 v v i -ii iii ivvv v v i v- i vi v C MIRc#SINE/MIR 205 TATCTCATTTGAT-CCTCACAACAACCCTGTGAGGTAGGC-AGGGCAGGT 158 chr3ptel1M 648940 ATTCTTATCCCCCTTGGACAGACAGCTGAAGAAACAGGACACT-----AG 648984 v v vv ---- i -v vi ----- C MIRc#SINE/MIR 157 ATTATTATCCCCATTTTACAGA----TGAGGAAAC-TGAGGCTCAGAGAG 113 chr3ptel1M 648985 GTGAAGCATCTGGCTC--GGGCCCCCAGCTAGGAAATGGCCAT------A 649026 v iiv v i -- v v v v i viv------ C MIRc#SINE/MIR 112 GTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGA 63 chr3ptel1M 649027 TTTGAACCC-GGCCTTCCTGCCTCCA 649051 i i - i v C MIRc#SINE/MIR 62 CTCGAACCCAGGTCTTCCTGACTCCA 37 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.96 CpG sites = 20, Kimura (unadjusted) = 37.96 Transitions / transversions = 0.77 (20/26) Gap_init rate = 0.07 (11 / 161), avg. gap size = 1.91 (21 / 11) 193 30.56 4.17 0.00 chr3ptel1M 651047 651118 (348882) L2#LINE/L2 2391 2465 (617) m_b126s601i7 4660 chr3ptel1M 651047 TCCGACTGTTTATTGGCCGTCTCCAACAGATTGTCTTGTAG--ATTTC-A 651093 i ii i v v i viv iv vi -- i - L2#LINE/L2 2391 TCCAACTGCCTACTCGACATCTCCACTTGGATGTCTAATAGGCATCTCAA 2440 chr3ptel1M 651094 ACTCTTCCTGTCCCAAGCTGGACTC 651118 ivv v v i i L2#LINE/L2 2441 ACTTAACATGTCCAAAACTGAACTC 2465 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.09 CpG sites = 12, Kimura (unadjusted) = 40.09 Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.03 (2 / 71), avg. gap size = 1.50 (3 / 2) 15 5.48 0.00 0.00 chr3ptel1M 651531 651549 (348451) (T)n#Simple_repeat 1 19 (0) m_b126s252i11 4661 chr3ptel1M 651531 TTTTTTTGTTTTTTTTTTT 651549 v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 253 33.46 6.60 2.73 chr3ptel1M 651624 651835 (348165) C MamRTE1#LINE/RTE-BovB (505) 3307 3088 m_b126s601i8 4662 chr3ptel1M 651624 AGGACTTCCTTTTCCCTGGT-ATCTTACCCTGTCTGCTGATCTTCAGAAT 651672 i v v --- - i ii i i vvi i v v v C MamRTE1#LINE/ 3307 AGGACCTCGTTGT---TGGTGATCCTGTCTTGCCATTTAATGTTAAGTAT 3261 chr3ptel1M 651673 CTCCCCAAGACAATTCAAATGGAAGCCATTCA-GCTTCCTGCCGT--CGT 651719 vv i vv iii iv vi i - iii - vvv v vi -- C MamRTE1#LINE/ 3260 GGCTCGTAGGTGACGCTGATGAAA-CTGCTCAAGAAGCCGGATGTGACGT 3212 chr3ptel1M 651720 GCTGCCGCTG-TCCAGATTTCATGGGCACACAGAAACTT---CAGCAC-A 651764 - iv v - i i ii v ii ? iv --- ? i - C MamRTE1#LINE/ 3211 -CTGTGGCAGGTCCAGGTCTCACAGCCGTANAGAAGGTTGGACANCGCTA 3163 chr3ptel1M 651765 GGGCTCTGTAGACCTTCGTTTTGGTAGTCGGGC-TAATACCTCATC--TC 651811 vv iiv -v v i - i i v i i--iv C MamRTE1#LINE/ 3162 TCGCTCTGTAGACCTTTAGTTTGGT-CTGGAGCTTGATGCCACGTTGGCG 3114 chr3ptel1M 651812 TCCCACTCTGTCAG--AGCCTCTCAA 651835 i v v -- i C MamRTE1#LINE/ 3113 CCACACTCTGTCTGCCAGCCTCCCAA 3088 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.79 CpG sites = 38, Kimura (unadjusted) = 46.23 Transitions / transversions = 1.23 (38/31) Gap_init rate = 0.07 (15 / 211), avg. gap size = 1.33 (20 / 15) 473 24.99 4.49 2.52 chr3ptel1M 652416 652571 (347429) MIR3#SINE/MIR 31 189 (19) m_b126s601i9 4663 chr3ptel1M 652416 GATTGTGAAACAG-AGAAATGGGACTGTTCAAATCTGGCCTCAGATACTG 652464 i v iv - vv ---- v i iv v v vi i MIR3#SINE/MIR 31 GACTGGGAGTCAGGAGACCTGGG----TTCTAGTCCCGGCTCTGCCACTA 76 chr3ptel1M 652465 CCTAGCTGTGTGACCT-GGGCAAGTCGCTTCACC-CTGTTGGCCTCGGTT 652512 v ? - i - v v i MIR3#SINE/MIR 77 ACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTT 126 chr3ptel1M 652513 TTCTCATCTGTAAAATGA----ACTGGAGAAGAAAATGGCAAAGGACTCC 652558 i ----ii vv vi vv v v i i MIR3#SINE/MIR 127 TCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCT 176 chr3ptel1M 652559 CACATATCTGCCA 652571 iv vv v MIR3#SINE/MIR 177 TCCAGCTCTGACA 189 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.70 CpG sites = 15, Kimura (unadjusted) = 30.70 Transitions / transversions = 0.65 (15/23) Gap_init rate = 0.05 (8 / 155), avg. gap size = 1.38 (11 / 8) 197 36.50 9.18 5.22 chr3ptel1M 652729 653153 (346847) C L2#LINE/L2 (76) 3006 2566 m_b126s601i10 4664 chr3ptel1M 652729 GGATGGGAAAGAGGCCAGGCTCACTGGA-TGGAA--AGCCA-------AG 652768 i ii v i vv vi -i i-- v ------- C L2#LINE/L2 3006 GAACAGCAAGGAGGCCAGTGTGGCTGGAGCGGAGTGAGCGAGGGGGAGAG 2957 chr3ptel1M 652769 TGGAAGAAGCC-----TGGAAAGGTGG-GAGGGAACAGGTTCTGAAAGGG 652812 v i vi-----ii i ii- i v i iv v - C L2#LINE/L2 2956 TGGTAGGAGATGAGGTCAGAGAGGTAACGGGGGACCAGATCATGTA-GGG 2908 chr3ptel1M 652813 GGTTGAATGC--TTGCAGAGCATTTTGTATTTATCCTGAAGGTAATGAGG 652860 vv v v -- i ii vv v iv ii iv vi i i C L2#LINE/L2 2907 CCTTGTAGGCCATTGTAAGGACTTTGGCTTTTACTCTGAGTGAGATGGGA 2858 chr3ptel1M 652861 AGCCATGGGAGTTTGTTGAGCAG-GGGGAGACAT----TG--TCATATT- 652902 v vv v - i v ---- -- i ii - C L2#LINE/L2 2857 AGCCATTGGAGGGTTTTGAGCAGAGGAGTGACATGATCTGACTTACGTTT 2808 chr3ptel1M 652903 ---GAGTGTC-CTCAAGGTGAGGAATGAAGAATGGATTGAAATAGGGAGA 652948 ---i vi - vi v vv vi vi i i ? ivi vi C L2#LINE/L2 2807 TAAAAGGATCACTCTGGCTGCTGTGTTGAGAATAGACTGNAGGGGGGCAA 2758 chr3ptel1M 652949 GACTTGAGGCAAGCCGACTTCCCCCCTCCCTTGCCTCGAGCATCTATTGT 652998 iv v i i vv --------- vv -----ii viv i C L2#LINE/L2 2757 GGGTGGAAGCAGGGAGAC---------CAGTT-----AGGAGGCTATTGC 2722 chr3ptel1M 652999 AATAGTCCAAGTGTGAGATGATGAGGTGATTAAATCCATGATGAGATCAC 653048 i i i i v -- ii viiv v i iviv v C L2#LINE/L2 2721 AGTAATCCAGGCGAGAGATGAT--GGTGGCTTGGACCAGGGTGGTGGCAG 2674 chr3ptel1M 653049 TAAGTGAAGCAGAATAAAGCAAGAAAAGGATCCTGGACAAAACTGGGAGG 653098 i--- i ii vivi iiiv---v i i v vi v i C L2#LINE/L2 2673 TG---GAGGTGGTGAGAAGTGGT---CGGATTCTGGATATATTTTGAAGG 2630 chr3ptel1M 653099 -ATACTCA-------TGGTTAAAAGGTGGGATGTGGAGTATGAGC-CGAG 653139 - v vi i------- v i i vi i v i i v-vi C L2#LINE/L2 2629 TAGAGCCGACAGGATTTGCTGATGGATTGGATGTGGGGTGTGAGAGAAAG 2580 chr3ptel1M 653140 AAAGGAGACAAAGA 653153 i v i C L2#LINE/L2 2579 AGAGGAGTCAAGGA 2566 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 50.11 CpG sites = 83, Kimura (unadjusted) = 52.23 Transitions / transversions = 1.30 (83/64) Gap_init rate = 0.09 (38 / 424), avg. gap size = 1.63 (62 / 38) 208 38.26 2.01 0.00 chr3ptel1M 652754 652902 (347098) C AmnL2-1#LINE/L2 (323) 2290 2139 m_b126s601i11 4664 chr3ptel1M 652754 GGATGGAAAGCCAAGTGGAAGAAGCCTGGAAAGGTGGGAGGGAACAGGTT 652803 iv ii ivi v ii v viiv vi i vv i i i C AmnL2-1#LINE/ 2290 GGGAGGGGAGTAGAGAGAGACAAGGTCCGTGAGGTAGGCTGGAGCAAGTC 2241 chr3ptel1M 652804 CTGAAAGGGGGTTGAATGCTTGCAGAGCA-TTTTGTATTT-ATCCTGAAG 652851 vvii vv i vi vv v ii - v i v- i C AmnL2-1#LINE/ 2240 CATGGAGGGTTTTAAAAACAAGGAAGGCAATTTTGAACTGGATCCTGAAA 2191 chr3ptel1M 652852 GTAATGAGGAGCCATGGGAGTTTGTTGAGCA-GGGGGAGACATTGTCATA 652900 vv i vv vv v - v ii v iii C AmnL2-1#LINE/ 2190 TGAATGGGGAGCCAGTGGAGTTGTTTGAGGATGGGGGTGATGTGGTCGCG 2141 chr3ptel1M 652901 TT 652902 i C AmnL2-1#LINE/ 2140 CT 2139 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 51.90 CpG sites = 29, Kimura (unadjusted) = 54.82 Transitions / transversions = 1.04 (29/28) Gap_init rate = 0.02 (3 / 148), avg. gap size = 1.00 (3 / 3) 465 21.55 0.85 0.85 chr3ptel1M 653589 653705 (346295) MER63D#DNA/hAT-Tip100 340 456 (605) m_b126s502i0 4665 chr3ptel1M 653589 GAGCATTTACACCCTGGAAGACAATAAACTTTCCAAATCAGAGTTGGAAG 653638 i vi iv iii vi v i i v vv MER63D#DNA/hA 340 GAGTATTTACACCACGGAAATCGGCAAACGCTACAAATCAGGGCTTGATT 389 chr3ptel1M 653639 TATTGTTT-GCTGATTGTCTAGACATAGGAAAGTGATGGGAAAAAATGCT 653687 - i v i - i i MER63D#DNA/hA 390 TATTGTTTTGTTGATTGTCTAGACTTAAGAAAGTGAT-GGAGAAAATGTT 438 chr3ptel1M 653688 AATTATACAAATTAAATT 653705 v i i i MER63D#DNA/hA 439 AATAATGCAGATTAAACT 456 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 23.68 CpG sites = 16, Kimura (unadjusted) = 26.02 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.02 (2 / 116), avg. gap size = 1.00 (2 / 2) 82 21.05 2.62 0.51 chr3ptel1M 653877 654067 (345933) (TTCC)n#Simple_repeat 1 195 (0) m_b126s252i12 4666 chr3ptel1M 653877 TTCCTTCCCTCCTTCCTTCC-TCCCCCCTTTCTTCCTTCCCTCCTTTCTT 653925 i - ii i i i (TTCC)n#Simpl 1 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 50 chr3ptel1M 653926 CCCTCCCTCCTTTCCCGCC-T-CTTTCTTCTCTCCCTCCCTCCCTCCTTC 653973 i i - iv - - i ii i i i (TTCC)n#Simpl 51 CCTTCCTTCC-TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC 99 chr3ptel1M 653974 CTGCCTTCCTTCCTTCTTTTCTTCCCTCCCTCCCTCTTTCCTCCCTCCCT 654023 v i i i i i i i i (TTCC)n#Simpl 100 CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT 149 chr3ptel1M 654024 CCCTCCCTTCC-TCTTCCCTCCCTTCCTT-CTTCCTTTCTCCATTC 654067 i i - i i i - i i v (TTCC)n#Simpl 150 TCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC 195 Matrix = Unknown Transitions / transversions = 10.00 (30/3) Gap_init rate = 0.03 (6 / 190), avg. gap size = 1.00 (6 / 6) 305 30.75 4.55 1.47 chr3ptel1M 654085 654216 (345784) C L2b_3end#LINE/L2 (0) 466 331 m_b126s601i12 4667 chr3ptel1M 654085 ATCCATGTACTTCACAAATACTT-CTGGGGGCCTGCTGTGTAGCCACAGC 654133 i vi i iv i - i v i - viv? C L2b_3end#LINE 466 ATTCATTCATTCAACAAATATTTACTGAGCGCCTACTGTGT-GCCAGGCN 418 chr3ptel1M 654134 TTGTGTGAGGCTCTGGGGGTGATAGAAAAAAAAAGGA-AGAT--GG--CA 654178 i iv v i - i viivi v i - i-- -- v C L2b_3end#LINE 417 CTGTGCTAGGCGCTGGGGAT-ACAGCGGTGAACAAGACAGACNCGGTCCC 369 chr3ptel1M 654179 AGCCCTCATGGAGATTATCCTCCAGGGGAGGAGAGAAA 654216 v i v i ivv i v i v i C L2b_3end#LINE 368 TGCCCTCACGGAGCTCACAGTCTAGTGGGGGAGACAGA 331 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.50 CpG sites = 23, Kimura (unadjusted) = 41.16 Transitions / transversions = 1.35 (23/17) Gap_init rate = 0.05 (6 / 131), avg. gap size = 1.33 (8 / 6) 185 40.91 5.17 1.67 chr3ptel1M 655056 655229 (344771) L3#LINE/CR1 165 344 (3755) m_b126s601i13 4668 chr3ptel1M 655056 CTTGGAGCAAAGAGCAGTTTTGTATGCAGAGGGTTCAAGGTCATCTCCAT 655105 i ii i?vv v i v i viviii v v vi v L3#LINE/CR1 165 CCTGAGGCGNTCACCAATTATGTGTGCTATAAATGCAAGCTGGTCTCCCT 214 chr3ptel1M 655106 CCCAGAGGTCACAGCAAAAGGGCTG-------GCTTTCCTATGCTCCAGG 655148 v i vv vi ii v------- i ii i i v L3#LINE/CR1 215 GCTAGAGGAGAAGGTGAAAGGGCTTGAGGAACGCCTCTCTACGCTCCGGC 264 chr3ptel1M 655149 TGCCCAGAGGTCCAGCAAATCCTTATCTAGTCAGGAGGCTGGACGTAA-- 655196 vvii i--viiii vvv -i v? v vvi vi -- L3#LINE/CR1 265 TTATTAGAGA--GGATGAAGGGTT-CCTAGANAGGATGGAAGAAATAATC 311 chr3ptel1M 655197 CAGGGGGGAAGGGAAGGAGAAGAGGTCTCCTAG 655229 ii i?v iii i i vi iv L3#LINE/CR1 312 CAGGAAGGAAANCAGAAAGAAAAAGATTCTGAG 344 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 59.77 CpG sites = 40, Kimura (unadjusted) = 64.22 Transitions / transversions = 1.33 (40/30) Gap_init rate = 0.03 (5 / 173), avg. gap size = 2.40 (12 / 5) 353 33.81 6.37 4.33 chr3ptel1M 656030 656233 (343767) C MIRc#SINE/MIR (42) 226 19 m_b126s601i14 4669 chr3ptel1M 656030 ATGAAATGCTCCCTT-TAGATGGTCTCACTTGATCTTCACAGCGATCATG 656078 ii ii ii vi- v vi i i i i i v C MIRc#SINE/MIR 226 ACAAAGCGCTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTG 177 chr3ptel1M 656079 GGAGG--GACA----TGCTGTCACTGTCTC---TTTACTGATGAGGAAAC 656119 v -- i ----v v i i i i i --- v C MIRc#SINE/MIR 176 TGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAAC 127 chr3ptel1M 656120 TGAGGTTGGGGGGGGGGGTAAGGGG-TTGGCAAGGGTCGGTGAGCTAGGA 656168 i --vi i i v v i- v v i ivvv v C MIRc#SINE/MIR 126 TGAGGCT--CAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTA 79 chr3ptel1M 656169 AAAGCAGCCTGCCAGTGTCGGAAGTGAGACGTGAG--CTCCGAACCCCAA 656216 i------- v v i i v vii viii --i vi i C MIRc#SINE/MIR 78 AG-------TGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAA 36 chr3ptel1M 656217 TTCGAGGGTTTTCTCCA 656233 v v v i i i C MIRc#SINE/MIR 35 GTCCAGTGCTCTTTCCA 19 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.99 CpG sites = 40, Kimura (unadjusted) = 46.97 Transitions / transversions = 1.54 (40/26) Gap_init rate = 0.07 (15 / 203), avg. gap size = 1.47 (22 / 15) 151 21.00 0.90 0.60 chr3ptel1M 656754 657085 (342915) (TCTC)n#Simple_repeat 1 333 (0) m_b126s252i13 4670 chr3ptel1M 656754 TCTCTCTCTCTCTCTCTCTCTCTTTCTCTTTCTCTCTCTCTTTCTCTGTC 656803 i i i v (TCTC)n#Simpl 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr3ptel1M 656804 TGTCTCTGTCTCTGTTTCTGTCTCTGTCTGTCTCTGTCTCTCTCTCTGTC 656853 v v v i v v v v v (TCTC)n#Simpl 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chr3ptel1M 656854 TCTGTGTGTGTGTGTGTGTGTCT-TGTCTCTGTCTCTCTGATTCTCTTTC 656902 v v v v v v v v v - v v vvi i (TCTC)n#Simpl 101 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 150 chr3ptel1M 656903 TTTGTCTCTCTGTTTCTCT-TTTATCTCTGTCTCTCTCTAATTCTGTCTC 656951 i v v i - i v v vvi v (TCTC)n#Simpl 151 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 200 chr3ptel1M 656952 TGCCTCTGTCTCTCTGATTCTCTCTTTCTGTGTGTCTCTCTGTCTATCTC 657001 vi v vvi i v v v v v (TCTC)n#Simpl 201 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 250 chr3ptel1M 657002 TGTCTATCTCTGCATCTGTCTGTCTCTGTGTCTGTCTGTCTCTCTCTCT- 657050 v v - - v v v v v v - (TCTC)n#Simpl 251 TCTCTCTCTCT-C-TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 298 chr3ptel1M 657051 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCCT 657085 i (TCTC)n#Simpl 299 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 333 Matrix = Unknown Transitions / transversions = 0.30 (14/46) Gap_init rate = 0.02 (5 / 331), avg. gap size = 1.00 (5 / 5) 51 0.00 0.00 0.00 chr3ptel1M 657086 657129 (342871) (AC)n#Simple_repeat 1 44 (0) c_b126s251i0 4671 chr3ptel1M 657086 ACACACACACACACACACACACACACACACACACACACACACAC 657129 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACAC 44 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 16 20.95 0.00 0.00 chr3ptel1M 658373 658405 (341595) (C)n#Simple_repeat 1 33 (0) m_b126s252i16 4672 chr3ptel1M 658373 CCCCCCCCCCCCCCCCCAACCACCACCACTCCC 658405 vv v v v i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 33 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 13 26.25 0.00 2.17 chr3ptel1M 658369 658415 (341585) (CCCACC)n#Simple_repeat 1 46 (0) m_b126s252i15 4673 chr3ptel1M 658369 CCAACCCCCCCCCCCCCCCCCAACCACCACCACTCCCATCACCCTCA 658415 v v v - v v iv vi i (CCCACC)n#Sim 1 CCCACCCCCACCCCCACCCCC-ACCCCCACCCCCACCCCCACCCCCA 46 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.02 (1 / 46), avg. gap size = 1.00 (1 / 1) 14 10.84 3.23 0.00 chr3ptel1M 659906 659932 (340068) (GAAA)n#Simple_repeat 1 28 (4) m_b126s252i17 4674 chr3ptel1M 659906 GAAAAAAAGACAGAAAGAAA-AAAGAGA 659932 i v - i (GAAA)n#Simpl 1 GAAAGAAAGAAAGAAAGAAAGAAAGAAA 28 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.04 (1 / 26), avg. gap size = 1.00 (1 / 1) 20 21.93 3.17 0.00 chr3ptel1M 659913 659932 (340068) (AGAG)n#Simple_repeat 1 21 (44) m_b126s252i18 4674 chr3ptel1M 659913 AGACAGAAAGA-AAAAAGAGA 659932 v i - i i (AGAG)n#Simpl 1 AGAGAGAGAGAGAGAGAGAGA 21 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.05 (1 / 19), avg. gap size = 1.00 (1 / 1) 51 0.00 0.00 0.00 chr3ptel1M 659933 659978 (340022) (AAGG)n#Simple_repeat 1 46 (0) c_b126s251i1 4675 chr3ptel1M 659933 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 659978 (AAGG)n#Simpl 1 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 46 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 20 21.93 3.17 0.00 chr3ptel1M 659979 660005 (339995) (AGAG)n#Simple_repeat 22 49 (16) m_b126s252i18 4676 chr3ptel1M 659979 A-AAAGGGAGGGAGGGAAAGAGGGAGGG 660005 - i i i i i i i (AGAG)n#Simpl 22 AGAGAGAGAGAGAGAGAGAGAGAGAGAG 49 Matrix = Unknown Transitions / transversions = 1.00 (7/0) Gap_init rate = 0.04 (1 / 26), avg. gap size = 1.00 (1 / 1) 212 0.94 2.29 0.90 chr3ptel1M 660006 660223 (339777) (GAAA)n#Simple_repeat 1 221 (0) c_b126s251i2 4677 chr3ptel1M 660006 GAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA 660055 (GAAA)n#Simpl 1 GAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA 50 chr3ptel1M 660056 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 660105 (GAAA)n#Simpl 51 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 100 chr3ptel1M 660106 G-AAGTAAAGAAAGAAAGAGAGAGAG-AA-AAAGAAAGAAAGAAAGAAAG 660152 - - i i - - (GAAA)n#Simpl 101 GAAAG-AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG 149 chr3ptel1M 660153 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG-AA-AAAGAA 660200 - - (GAAA)n#Simpl 150 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAA 199 chr3ptel1M 660201 AGAAAGAAAGAAAAGAAAGAAAG 660223 - (GAAA)n#Simpl 200 AGAAAGAAAG-AAAGAAAGAAAG 221 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.03 (7 / 217), avg. gap size = 1.00 (7 / 7) 20 21.93 3.17 0.00 chr3ptel1M 660224 660237 (339763) (AGAG)n#Simple_repeat 50 63 (2) m_b126s252i18 4678 chr3ptel1M 660224 GAGAGAGAGAGAGA 660237 (AGAG)n#Simpl 50 GAGAGAGAGAGAGA 63 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 13), avg. gap size = 0.0 (0 / 0) 91 9.47 0.74 0.00 chr3ptel1M 660712 660846 (339154) (CA)n#Simple_repeat 1 136 (0) c_b126s251i3 4679 chr3ptel1M 660712 CACACACATACACACACACACACACACACTCTCTCTCTCTCACACACACA 660761 i v v v v v v (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 chr3ptel1M 660762 TACACACACACACACACACACTCTCACACACACACACACACACATACACA 660811 i v v i (CA)n#Simple_ 51 CACACACACACACACACACACACACACACACACACACACACACACACACA 100 chr3ptel1M 660812 CACACACACACACACACACACACACAAAC-CACACA 660846 v - (CA)n#Simple_ 101 CACACACACACACACACACACACACACACACACACA 136 Matrix = Unknown Transitions / transversions = 0.33 (3/9) Gap_init rate = 0.01 (1 / 134), avg. gap size = 1.00 (1 / 1) 11 15.78 6.52 4.26 chr3ptel1M 661796 661841 (338159) (GAAATG)n#Simple_repeat 1 47 (0) m_b126s252i19 4680 chr3ptel1M 661796 GAAAAAGAAATGG-AA-GGAATATGCATAGGCAAATAGGAAAT-GAAAT 661841 vi - - - v v v v - - (GAAATG)n#Sim 1 GAAATGGAAATGGAAATGGAA-ATGGAAATGGAAAT-GGAAATGGAAAT 47 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.11 (5 / 45), avg. gap size = 1.00 (5 / 5) 15 11.44 4.76 4.76 chr3ptel1M 662883 662924 (337076) (ATGT)n#Simple_repeat 1 42 (0) m_b126s252i20 4681 chr3ptel1M 662883 ATGTATGTGGATGTATGTATATATG--TGTCTGTATATATGCAT 662924 -- i -- v i i (ATGT)n#Simpl 1 ATGTATGT--ATGTATGTATGTATGTATGTATGTATGTATGTAT 42 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.07 (3 / 41), avg. gap size = 1.33 (4 / 3) 17 9.36 2.78 2.78 chr3ptel1M 663009 663044 (336956) (TTCCCTC)n#Simple_repeat 1 36 (0) m_b126s252i21 4682 chr3ptel1M 663009 TTCCATATTCTCTCCTTCCCTCTTCCCTC-TCCCTCT 663044 v v i - - (TTCCCTC)n#Si 1 TTCCCTCTTCCCT-CTTCCCTCTTCCCTCTTCCCTCT 36 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 315 35.44 4.69 3.16 chr3ptel1M 663238 663642 (336358) L1PA8A_3end#LINE/L1 1 411 (467) m_b126s551i0 4683 chr3ptel1M 663238 CTCATTTGCAAGCTCTATAAGGAACTAGTCCAAATTTGT--GAAAAATAA 663285 v v v iiv i i vivv ii-- v v L1PA8A_3end#L 1 CTAATATCCAGAATTTACAAGGAACTTAAACAAATTTACAAGAAAAAAAC 50 chr3ptel1M 663286 GAGCCATTTC-TCAAGTGATAAGTGTTCAAAGCATGTGATTACACATCTT 663334 i i v iii - i---- vv v i vi v i--- L1PA8A_3end#L 51 AAACAACCCCATCAAA----AAGTGGGCAAAGGATATGAACAGACAC--- 93 chr3ptel1M 663335 TTTTTAGAGGGAGAAATTCAAACTATCAATAGCCATAAGGGAAAAACACT 663384 i i i i i v i vi vii i iv v ii -i L1PA8A_3end#L 94 TTCTCAAAAGAAGACATTTACGCGGCCAACAAACATATGAAAAAAA-GCT 142 chr3ptel1M 663385 CTAAATCACCAATAATTAAAGAAATGCAAATTCAAACTCCTTTGAGATAC 663434 v v ii v i i iv iv vv L1PA8A_3end#L 143 CAACATCACTGATCATCAGAGAAATGCAAATCAAAACCACAATGAGATAC 192 chr3ptel1M 663435 TTCCTTACATCCATCAGATTGACAAAGTTGACAAAAAG--GGGAAATGAC 663482 ivi i ii vi v i i -- ivi --i ii i L1PA8A_3end#L 193 CATCTCACGCCAGTCAGAATGGCGA--TTATTAAAAAGTCAGGAAACAAT 240 chr3ptel1M 663483 AAATGCTGGAGCAAGTGTGGGAAAACAGGTAAATTAGTGCA---TTGGT- 663528 i v viiv ii i v vii vv i --- - L1PA8A_3end#L 241 AGATGCTGGCGAGGCTGTGGAGAAATAGGAACGCTTTTACACTGTTGGTG 290 chr3ptel1M 663529 -GAATG--ACTTAATCTGGCCAT------AAACAATTTATAACTGTGCTC 663569 - -- v i iiii ------ i i-- ii vi v ii L1PA8A_3end#L 291 GGAATGTAAATTAGTTCAACCATTGTGGAAGACAG--TATGGCGATTCCT 338 chr3ptel1M 663570 CAA-AATATTAAACTATGTACATTCTTTAAAACAGCAATATCTTTAATAA 663618 -i v vi i viv i iiv i vv vi v v ii L1PA8A_3end#L 339 CAAGGATCTAGAACCAGAAATACCATTTGACCCAGCAATCCCATTACTGG 388 chr3ptel1M 663619 ATCTGTGCCCCAAAGAAATAAAAA 663642 i v i i- i v L1PA8A_3end#L 389 GTATATA-CCCAAAGGAATATAAA 411 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 48.43 CpG sites = 86, Kimura (unadjusted) = 50.55 Transitions / transversions = 1.62 (86/53) Gap_init rate = 0.05 (22 / 404), avg. gap size = 1.45 (32 / 22) 332 33.93 4.46 2.63 chr3ptel1M 663246 663581 (336419) L1MA7_3end#LINE/L1 9 350 (688) m_b126s551i1 4683 chr3ptel1M 663246 CAAGCTCTATAAGGAACTAGTCCAAATTTGTGAAAAATAAGAGCCATTTC 663295 iv v vivv v ivi - iv v i vvv vv L1MA7_3end#LI 9 CAAAATATATAAGGAACTCAAACAACTCAAT-AGCAAGAAAACAAATAAC 57 chr3ptel1M 663296 TCAAGTGATAAGTGTTCAAAGCATGTGATTACACATCTTTTTTTAGAGGG 663345 i i v i v i vv v iv v v --- i i i i i L1MA7_3end#LI 58 CCGATTAAAAAATGGGCAAAGGACCTGAATAGACAT---TTCTCAAAAGA 104 chr3ptel1M 663346 AGAAATTCAAACTATCAATAGCCATAAGGGAAAAACACTCTAAATCACCA 663395 v v ivii i vi -v i ii v v i L1MA7_3end#LI 105 AGACATACAAATGGCCAACAGATATA-TGAAAAAATGCTCAACATCACTA 153 chr3ptel1M 663396 ATAATTAAAGAAATGCAAATTCAAACTCCTTTGAGATACTTCCTTACATC 663445 v i ii v iv vv iiv i i L1MA7_3end#LI 154 ATCATCAGGGAAATGCAAATTAAAACCACAATGAGATATCACCTCACACC 203 chr3ptel1M 663446 CATCAGATTGACAAAGTTGACAAAAAGGGGAA--ATGACAAATGCTGGAG 663493 ii i v i v -- iv iv -- i i i v L1MA7_3end#LI 204 TGTTAGAATGGCTA--TTATCAAAAAGACGAAAGATAACAAGTGTTGGCG 251 chr3ptel1M 663494 CAAGTGTGGGAAAACAGGTAAATTAGTGCA---TTGGT--GAATG--ACT 663536 viii ii vi v vvi v i --- -- -- v L1MA7_3end#LI 252 AGGATGTGGAGAAAAGGGAACCCTTGTACACTGTTGGTGGGAATGTAAAT 301 chr3ptel1M 663537 TAATCTGGCCAT------AAACAATTTATAACTGTGCTCCAAAATATTAA 663580 i vii ------ i-- iivv v ii v i L1MA7_3end#LI 302 TAGTACAGCCATTATGGAAAACAG--TATGGAGGTTCCTCAAAAAACTAA 349 chr3ptel1M 663581 A 663581 L1MA7_3end#LI 350 A 350 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 45.69 CpG sites = 59, Kimura (unadjusted) = 46.26 Transitions / transversions = 1.13 (59/52) Gap_init rate = 0.04 (14 / 335), avg. gap size = 1.71 (24 / 14) 413 34.57 0.72 2.55 chr3ptel1M 663251 663529 (336471) L1PA12_3end#LINE/L1 14 287 (628) m_b126s551i2 4683 chr3ptel1M 663251 TCTATAAGGAACTAGTCCAAATTTGTGAAAAATAAGAGCCATTTCTCAAG 663300 vivv iii i - i vvv ivv i v v L1PA12_3end#L 14 TCTATAAGGAACTTAAACAAATTTACAAGAAA-AAAACAAACAACCCCAT 62 chr3ptel1M 663301 TGATAAGTGTTCAAAGCATGTGATTACACATCTTTTTTTAGAGGGAGAAA 663350 i v vv v ii vi v i--- i i i i i v L1PA12_3end#L 63 TAAAAAGTGGGCAAAGGACATGAACAGACAC---TTCTCAAAAGAAGACA 109 chr3ptel1M 663351 TTCAAACTATCAATAGCCATAAGGGAAAAACACTCTAAATCACCAATAAT 663400 v vi vii i ii v ii -i v v ii v L1PA12_3end#L 110 TACATGCGGCCAACAATCATATGAAAAAAA-GCTCAACATCACTGATCAT 158 chr3ptel1M 663401 TAAAGAAATGCAAATTCAAACTCCTTTGAGATACTTCCTTACATCCATCA 663450 i iv iv vv ivi i i vi L1PA12_3end#L 159 TAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTCACACCAGTCA 208 chr3ptel1M 663451 GATTGACAAAGTTGACAAAAAG--GGGAAATGACAAATGCTGGAGCAAGT 663498 v i v -- ivi --iii i i v viiv L1PA12_3end#L 209 GAATGGCTA--TTATTAAAAAGTCAAAAAATAACAGATGCTGGCGAGGTT 256 chr3ptel1M 663499 GTGGGAAAACAGGTAAATTAGTGCATTGGTG 663529 ii v v vii v? i i v L1PA12_3end#L 257 GTGGAGAAAAAGGAACGCTTNTACACTGTTG 287 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 47.38 CpG sites = 53, Kimura (unadjusted) = 48.10 Transitions / transversions = 1.29 (53/41) Gap_init rate = 0.03 (8 / 278), avg. gap size = 1.12 (9 / 8) 295 33.36 6.92 4.32 chr3ptel1M 663253 663772 (336228) L1ME3G_3end#LINE/L1 16 548 (376) m_b126s551i3 4683 chr3ptel1M 663253 TATAAGGAACTAGTCCAAATTTGTGAAAAATAAGAGCCATTTCTCAAGTG 663302 i vv v ivi i i - - v --- i vv L1ME3G_3end#L 16 TATAAAGAACTCCTACAAATCAATAAGAAA-AAGA-CAA---CCCAATAG 60 chr3ptel1M 663303 ATAAGTGTTCAAAGCATGTGATTACACATCTTTTTTTAGAGGGAGAAATT 663352 v i vv v i vi vi v--- ivi i ii v L1ME3G_3end#L 61 AAAAATGGGCAAAGGATATGAACAGGCAA---TTCACAGAAGAGGAAATA 107 chr3ptel1M 663353 CAAACTATCAATAGCCATAAGGGAAAAACACTCTAAATCACCAATAATTA 663402 ivii iv -v i i ii v vv i i i L1ME3G_3end#L 108 CAAATGGCCAATAAACATA-TGAAAAGATGCTCAACCTCACTAGTAATCA 156 chr3ptel1M 663403 AAGAAATGCAAATTCAAACTCCTTTGAGATACTTCCTTACATCCATCAGA 663452 ii v vv vv ivii v i L1ME3G_3end#L 157 GGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCATCAGA 206 chr3ptel1M 663453 TTGACAAAGTTGACAAAAAGGGGAAATGACAAATGCTGGAGCAAGTGTGG 663502 i iv vvv i?vv iv iv ? i i v vii L1ME3G_3end#L 207 TTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGTGTGG 256 chr3ptel1M 663503 GAAAACAGGTAAATTAGTGCATTGGT-----GAATG--ACTTAATCTGGC 663545 i i vvi vi i i v ----- i -- v ii vii L1ME3G_3end#L 257 GGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTACAGC 306 chr3ptel1M 663546 CAT------AAACAATTTATAACTGTGCTCCAAAATATTAAACTATGTAC 663589 ? ------iii ivv v i vivii - v ii i i L1ME3G_3end#L 307 CNTTTTGGAGGGCAATTTGGCAGTATCTATTAAAAT-TTAAAATGCGCAT 355 chr3ptel1M 663590 ATTCTTTAAAACAGCAATAT--CTTTAATAAATCTGTGCCCCAAAGAAAT 663637 ii i vv vi-- iv?vi? i -- i ? L1ME3G_3end#L 356 ACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTAT--CCTANAGAAAT 403 chr3ptel1M 663638 A-------------AAAAAAAGGCTCATATATACAAACAT-----TTGTA 663669 ------------- v ii ? ---- i iv ----- i L1ME3G_3end#L 404 ACTCGCACATGTGCACAAGGANGC----ATGTACAAGGATGTTCATTGCA 449 chr3ptel1M 663670 TTACTGGTTTTGTGGGGGCAAAGAA--GGAGA-AACTGATATCCCACCTA 663716 vi i -- iivi i i -- i - iv v ---ii i L1ME3G_3end#L 450 GCATTG--TTTGTAATAGCGAAAAATTGGAAACAACCTAAAT---GTCCA 494 chr3ptel1M 663717 TCAATTGGGGATTGGCTAACTATATTATATTTTTTTTCAATGTGGTAGAA 663766 v v i v v i--v v v v iivi i L1ME3G_3end#L 495 TCAATAGGGGAATGGTTAAATAAATTATG--GTATATCCATACTATGGAA 542 chr3ptel1M 663767 TACTAT 663772 L1ME3G_3end#L 543 TACTAT 548 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 45.42 CpG sites = 95, Kimura (unadjusted) = 46.59 Transitions / transversions = 1.34 (95/71) Gap_init rate = 0.06 (31 / 519), avg. gap size = 1.90 (59 / 31) 340 24.10 2.22 7.81 chr3ptel1M 664173 664307 (335693) MIR1_Amn#SINE/MIR 1 128 (102) m_b126s601i15 4684 chr3ptel1M 664173 TAGGGAG-CAGCTAGTGTTGCAGTGGATGGAGCACCAGCCCTGAAGTCAG 664221 - i-- v vi i ii v iv i v i MIR1_Amn#SINE 1 TAGGGAGGCAGT--GTGGTCTAGTGGATAGAGCACTGGACTGGGACTCGG 48 chr3ptel1M 664222 AATGACCTGAGTTCCAGTCTGGTCTCAGATACTTAATACTTCCTGGCTGT 664271 i - i ? ? iv v v vi ?i------- i? ? MIR1_Amn#SINE 49 GA-GACCTGGGTTCNANTCCCGGCTCTGCCACTNG-------CCNGCTGN 90 chr3ptel1M 664272 GGGACTCTGGGCAAGTCA-TTAATCCCAAT-TGCCTCA 664307 v ii - ? i i vv -? MIR1_Amn#SINE 91 GTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCA 128 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.52 CpG sites = 18, Kimura (unadjusted) = 31.79 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.10 (13 / 134), avg. gap size = 1.00 (13 / 13) 438 22.94 0.89 6.60 chr3ptel1M 664186 664297 (335703) MIRc#SINE/MIR 10 115 (153) m_b126s601i16 4684 chr3ptel1M 664186 GTGTTGCAGTGGATGGAGCACCAGCCCTGAAGTCAGAATGACCTGAGTTC 664235 v vi ii v i i i v i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr3ptel1M 664236 CAGTCTGGTCTCAGATACTTAATACTTCCTGGCTGTGGGACTCTGGGCAA 664285 v iv v v vi ------- i v ii MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTGACCTTGGGCAA 102 chr3ptel1M 664286 GTCA-TTAATCCC 664297 - i i MIRc#SINE/MIR 103 GTCACTTAACCTC 115 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.75 CpG sites = 14, Kimura (unadjusted) = 27.75 Transitions / transversions = 1.40 (14/10) Gap_init rate = 0.07 (8 / 111), avg. gap size = 1.00 (8 / 8) 16 9.26 0.00 0.00 chr3ptel1M 664310 664332 (335668) (A)n#Simple_repeat 1 23 (0) m_b126s252i22 4685 chr3ptel1M 664310 AAAAAGAAAAATAAAAAAAAAAA 664332 i v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAA 23 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 190 36.37 0.65 4.76 chr3ptel1M 664499 664651 (335349) L3#LINE/CR1 2882 3028 (1071) m_b126s601i17 4686 chr3ptel1M 664499 ATTAACATAATTCTATTTTTTAACAAGATTGATAAACCAGCAGATGAAAG 664548 i v v iiv i i i i iv i ii i v ii L3#LINE/CR1 2882 ACTAACCTCATTTCCTTTTTTGATAGGGTTACTAGACTGGTAGATCAGGG 2931 chr3ptel1M 664549 GAATTCAGTGTTCATCATTTGCTTAGATTTTAGTAAAGCTTTTTAATAGA 664598 v v ivv ?vi v iii i i i i -v i i i L3#LINE/CR1 2932 GAATGCCGTAGACANAGTGTATCTGGATTTCAGCAAGGC-ATTTGACAAA 2980 chr3ptel1M 664599 GTATTTACAAGCCATTCTCCAGTTGATAA-ATGGTCAAAGAATATGAACA 664647 v i - v vi i i-- v i - --- ii ii v L3#LINE/CR1 2981 GTCTCT-CATGATATCCTT--GTGGACAAGATGG---AGAAATATGGGCT 3024 chr3ptel1M 664648 GAAT 664651 i L3#LINE/CR1 3025 GGAT 3028 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 54.25 CpG sites = 36, Kimura (unadjusted) = 54.25 Transitions / transversions = 2.12 (36/17) Gap_init rate = 0.05 (8 / 152), avg. gap size = 1.00 (8 / 8) 28 0.00 0.00 0.00 chr3ptel1M 664656 664682 (335318) (T)n#Simple_repeat 1 27 (0) c_b126s251i4 4687 chr3ptel1M 664656 TTTTTTTTTTTTTTTTTTTTTTTTTTT 664682 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTT 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 1030 32.65 1.02 0.41 chr3ptel1M 665022 665510 (334490) L1ME4a_3end#LINE/L1 82 573 (298) m_b126s551i4 4688 chr3ptel1M 665022 ATGAACAGAATATTC-TAATGAAAACAATG-AAACCATTTTTAGTTATAT 665069 vv -i vii iv i- iviiivv ivi L1ME4a_3end#L 82 ATGAACAGACAATTCACAAAAGAAGAAATACAAATGGCCAATAAACATAT 131 chr3ptel1M 665070 GAAAAAGTGCTCTGAATCACTATTGATCAGAGAAATGCAGATTAAGACAA 665119 ?i i vivv v i i i i L1ME4a_3end#L 132 GAAAANATGTTCAACCTCACTAGTAATCAAAGAAATGCAAATTAAAACAA 181 chr3ptel1M 665120 CTCTGAGGTACCACTACATACCTGTCAGATTGACTAGGATGACAGGAAAA 665169 vv i i vivi i i i v i vvv iii vv L1ME4a_3end#L 182 CAATGAGATACCATTTTTCACCTATCAAATTGGCAAAGATTTAAAAGATT 231 chr3ptel1M 665170 GATAATGATAAATGTTTGAAGGGATGTGGGAAAACTGGGACATTGATGCA 665219 iviv i v vii i ?i v v vi v i L1ME4a_3end#L 232 GATAATACCCAGTGTTGGCGAGGGTGTGGNGAAACGGGCACTCTCATACA 281 chr3ptel1M 665220 TTGTGGGTGGAGTTGTGAATGCATCCTACCATTCTGGAGAGCAGTCTGGA 665269 i iv iiv i vvi v v v i i i v L1ME4a_3end#L 282 CTGCTGGTGGGAGTGTAAATTGGTACAACCTTTCTGGAGGGCAATTTGGC 331 chr3ptel1M 665270 ACTATGCTCAAAAAGGTATTAAACTGTGCAGACCCTTTGGCCCAGCAGTG 665319 v iviv viv v v ? v i i i v L1ME4a_3end#L 332 AATATGTATCAAAAGCCTTAAAAATGTNCATACCCTTTGACCCAGTAATT 381 chr3ptel1M 665320 CTACTACTGGGCTTATACCCCAAGGAGATACT-AAAGAAGGGAA-AGGGA 665367 i v i vv v i i i v - i v v ? - ii L1ME4a_3end#L 382 CCACTTCTAGGAATTTATCCTAAGGAAATAATCAGAGATGTGNACAAAGA 431 chr3ptel1M 665368 CCTGTATGTGCCAAAATGTTTGTGGTAGCCCTGTTTGTGGTGGCCAGAAA 665417 -- v i v ii ii v i vi i i ii i v i L1ME4a_3end#L 432 --TTTATGTACAAGGATGTTCATCGCAGCATTATTTATAATAGCGAAAAA 479 chr3ptel1M 665418 CTGGAAACTGAGTGGATGCCCATCAGT-GGGGAATGGCTGAATAAGTTAT 665466 i vivv ii i v i - ? i i i L1ME4a_3end#L 480 TTGGAAACAACCTAAATGTCCAACAATAGGGGANTGGTTAAATAAATTAT 529 chr3ptel1M 665467 GGGATATGTATGTTATGGAATATTATTGTTCTATAAGAAATGAT 665510 v i vi i?v vvvv i v i ? L1ME4a_3end#L 530 GGTACATCCATANAATGGAATATTATGCAGCCATTAAAAATNAT 573 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 44.52 CpG sites = 88, Kimura (unadjusted) = 44.91 Transitions / transversions = 1.24 (88/71) Gap_init rate = 0.01 (7 / 488), avg. gap size = 1.00 (7 / 7) 977 33.65 2.23 2.80 chr3ptel1M 665066 665603 (334397) L1ME5_3end#LINE/L1 128 662 (279) m_b126s551i6 4688 chr3ptel1M 665066 ATATGAAAAAGTGCTCTGAATCACTATTGATCAGAGAAATGCAGATTAAG 665115 i ii vi v i v i i i L1ME5_3end#LI 128 ATATGAAGAGATGCTCAAACTCATTAGTAATCAGAGAAATGCAAATTAAA 177 chr3ptel1M 665116 ACAACTCTGAGGTACCACTACATACCTGTCAGATTGACTAGGATGACAGG 665165 vv i i vi i i i i i v ii v v ii L1ME5_3end#LI 178 ACAACAATGAGATATCACTTTACACCTATTAGACTGGCAAAAATTAGAAA 227 chr3ptel1M 665166 AAAAGATAATGATAAATGTTTGAAGGGATGTGGGAAAACTGGGACATTGA 665215 ivvi vi i v vii i ? iv i vi v L1ME5_3end#LI 228 GCTGGATAATGCCAAGTGTTGGCGAGGATGTGGGGANATAGGAACCCTCA 277 chr3ptel1M 665216 TGCATTGTGGGTGGAGTTGTGAATGCATCCTACCATTCTGGAGAGCAGTC 665265 i iv iiv ii ivvi v vi i L1ME5_3end#LI 278 TGCACTGCTGGTGGGAGTGTAGACTGGTGCAGCCATTCTGGAGAGCAATC 327 chr3ptel1M 665266 TGGAACTA--TGCTCAAAAAGGTATTAAAC-TGTGCAGACCCTTTGGCCC 665312 v v -- iv ------ ii- ii v v i L1ME5_3end#LI 328 TGGCAGTACTTAGTCAA------ATTAAGTATACGCATACCCTATGACCC 371 chr3ptel1M 665313 AGCAGTGCTACTACTGGGCTTATACCCCAAGGAGATACTAAAGAAGG--- 665359 i v ii v iv i i i v v viv --- L1ME5_3end#LI 372 AGCAATTCCGCTCCTGGGTATATATCCCAAAGAAATTCTCACACAGGTCC 421 chr3ptel1M 665360 -GAAAGGGACCTGTATGTGCCAAAATGTTTGTGGTAGCCCTGTTTGTGGT 665408 -v i v i ---- ii ii v i vi L1ME5_3end#LI 422 ATAAGGGGACATGTACG----AGGATGTTCATTGCAGCGTTGTTTGTGGT 467 chr3ptel1M 665409 GGCCAGAAACTGGAAACTGAGTGGATGCCCATCAGTGGG-GAATGGCTGA 665457 vi i ii ii vivv i i v - i v ii L1ME5_3end#LI 468 GGCGGGGAGTTGGAGGCAACCTGGGTGTCCATCACTGGGAGAGTGGATAG 517 chr3ptel1M 665458 ATAAGTTATGGGATATGTATGTTATGGAATATTATTGTTCTATAAGAAAT 665507 i iv i viv i iiii i i vvvv vi v ii L1ME5_3end#LI 518 GTAAAATGTGGTGGATGCACACCATGGAGTACTATGCAGCAGTTAGAAGC 567 chr3ptel1M 665508 GATCAGCAGGATGATTTCAGAGAGACTTATATGAACTTGCAAAGCAAAGT 665557 i ivii vi vviv v vi v iv i ii vv i v L1ME5_3end#LI 568 AACGGACTAGATGTACACATAGCAACATGGATGGATCTTAAAAACATAGT 617 chr3ptel1M 665558 AGAACCTGAGAGAACAATGT---GCACAGCAACAAGAT-TATACAACAAT 665603 i---- v v v ---iv - ii - vv L1ME5_3end#LI 618 G----CTGAGTGAAAAAAGTAAGAAACAG-AATGAGATNTATAACACAAT 662 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 44.64 CpG sites = 104, Kimura (unadjusted) = 46.51 Transitions / transversions = 1.44 (104/72) Gap_init rate = 0.04 (22 / 537), avg. gap size = 1.23 (27 / 22) 1097 30.57 0.70 1.18 chr3ptel1M 665066 665492 (334508) L1ME3G_3end#LINE/L1 124 548 (376) m_b126s551i5 4688 chr3ptel1M 665066 ATATGAAAAAGTGCTCTGAATCACTATTGATCAGAGAAATGCAGATTAAG 665115 ii vivv v i i i i L1ME3G_3end#L 124 ATATGAAAAGATGCTCAACCTCACTAGTAATCAGGGAAATGCAAATTAAA 173 chr3ptel1M 665116 ACAACTCTGAGGTACCACTACATACCTGTCAGATTGACTAGGATGACAGG 665165 vv i i vivi ii i v ii vvv ii L1ME3G_3end#L 174 ACAACAATGAGATACCATTTTTCACCCATCAGATTGGCAAAAATTTAAAA 223 chr3ptel1M 665166 AAAAGATAATGATAAATGTTTGAAGGGATGTGGGAAAACTGGGACATTGA 665215 i?vv ivi? i v vii i i v v vi v L1ME3G_3end#L 224 GNTTGATAATATCNAGTGTTGGCGAGGGTGTGGGGAAACGGGTACTCTCA 273 chr3ptel1M 665216 TGCATTGTGGGTGGAGTTGTGAATGCATCCTACCATTCTGGAGAGCAGTC 665265 i i iv iiv i vvi v vi ? i i i i L1ME3G_3end#L 274 TACACTGCTGGTGGGAGTGTAAATTGGTACAGCCNTTTTGGAGGGCAATT 323 chr3ptel1M 665266 TGGAACTATGCTCAAAAAGGTATTAAACTGTGCAGACCCTTTGGCCCAGC 665315 v v viviv v--- v i v i L1ME3G_3end#L 324 TGGCAGTATCTATTAAAAT---TTAAAATGCGCATACCCTTTGACCCAGC 370 chr3ptel1M 665316 AGTGCTACTACTGGGCTTATACCCCAAGGAGATACT-AAAGAAGGG-AAA 665363 i v i v ? ?v v i i ?i i -iv v v v - v L1ME3G_3end#L 371 AATTCCACTTCTNGGNATCTATCCTANAGAAATACTCGCACATGTGCACA 420 chr3ptel1M 665364 GGGACCTGTATGTGCCAAAATGTTTGTGGTAGCCCTGTTTGTGGTGGCCA 665413 i --? i i v ii ii v i vi ii i v L1ME3G_3end#L 421 AGGA--NGCATGTACAAGGATGTTCATTGCAGCATTGTTTGTAATAGCGA 468 chr3ptel1M 665414 GAAACTGGAAACTGAGTGGATGCCCATCAGT-GGGGAATGGCTGAATAAG 665462 i i vivv ii i i - i i i L1ME3G_3end#L 469 AAAATTGGAAACAACCTAAATGTCCATCAATAGGGGAATGGTTAAATAAA 518 chr3ptel1M 665463 TTATGGGATATGTATGTTATGGAATATTAT 665492 v vi ii i L1ME3G_3end#L 519 TTATGGTATATCCATACTATGGAATACTAT 548 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 40.16 CpG sites = 76, Kimura (unadjusted) = 41.43 Transitions / transversions = 1.43 (76/53) Gap_init rate = 0.02 (8 / 426), avg. gap size = 1.00 (8 / 8) 288 34.12 0.00 0.00 chr3ptel1M 665982 666066 (333934) L3#LINE/CR1 2976 3060 (1039) m_b126s601i18 4686 chr3ptel1M 665982 ATAAAGTATCTGACGCTGTTCTCATGGAGAAGATGAAGAGATATGGATTA 666031 i v v i v i i ii v i i ii i L3#LINE/CR1 2976 ACAAAGTCTCTCATGATATCCTTGTGGACAAGATGGAGAAATATGGGCTG 3025 chr3ptel1M 666032 GATGGGCACCTAGTTAAATGCTTTCATCACTGGTT 666066 ivviivi ii vv i vi L3#LINE/CR1 3026 GATGATAGTACAGTTAGGTGGATTCGTAGCTGGTT 3060 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.92 CpG sites = 19, Kimura (unadjusted) = 48.29 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.00 (0 / 84), avg. gap size = 0.0 (0 / 0) 322 38.04 9.05 0.93 chr3ptel1M 666235 666433 (333567) L3#LINE/CR1 2976 3190 (909) m_b126s601i19 4689 chr3ptel1M 666235 ACATAATCTGTCTCATGCTATTCTTGTGAA-AAGCTGTAGAGAAGCCGGC 666283 v i -- v i i - v v i viiv L3#LINE/CR1 2976 ACAAAGTCT--CTCATGATATCCTTGTGGACAAGATGGAGAAATATGGGC 3023 chr3ptel1M 666284 CGGTTCATGTCACAACGAGACAGGTTTGGCTCTAGGTGC-CATCTGCACT 666332 i v v ivi iiv iii i i vvv i v v- iv ii i L3#LINE/CR1 3024 TGGATGATAGTACAGTTAGGTGGATTCGTAGCTGGTTGAACGACTATACC 3073 chr3ptel1M 666333 CA-----TGCT----------TTGATGCCAGCTGGGAAGGAGGCCTTTCA 666367 ----- i ---------- i i i iv i i i vi L3#LINE/CR1 3074 CAAAAGGTGTTGATTAATGGATCGATGTCAACCTGGAGGGAGGTCTCTAG 3123 chr3ptel1M 666368 GGGAGGATCCCGGGCATCCGTGCTGGACTCTGCGACCTTAGACATTTTTG 666417 v v vii v i vv i v v i i ivviv vi i L3#LINE/CR1 3124 TGGCGTGCCACAGGGCTCTGTCCTTGGCCCTGTCCTGTTCAACATTTTTA 3173 chr3ptel1M 666418 CCAATAGCTT-AATGGA 666433 i ii -i i L3#LINE/CR1 3174 TCAATGACTTGGATGAA 3190 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 52.66 CpG sites = 45, Kimura (unadjusted) = 56.05 Transitions / transversions = 1.50 (45/30) Gap_init rate = 0.04 (7 / 198), avg. gap size = 2.86 (20 / 7) 500 30.33 3.46 4.37 chr3ptel1M 666907 667137 (332863) L1MD1_3end#LINE/L1 325 553 (436) m_b127s551i2 4690 chr3ptel1M 666907 GTTTGGGACTGTGCTCAAAAAGTTATCAAACTGTGCAG--ACCCTTTGGC 666954 v v v - i ii --- -i i-- v vi i L1MD1_3end#LI 325 GTTTGGCAGTTT-CTTAAAAAACTA---AAC-ATGCAACTACCATACGAC 369 chr3ptel1M 666955 CCAGCAGTGTTACTACTGACCTTATATCCCAAAGAGAT-----CTTAAAG 666999 i vvi v iv v v i i ----- v- L1MD1_3end#LI 370 CCAGCAATTGCACTCCTGGGCATTTATCCCAGAGAAATGAAAACTTAT-G 418 chr3ptel1M 667000 GAGGGAAAGGGACCTGTATATGCCAAAATGTTTGTGGCAGCCCTGTTTGT 667049 vvviv v iii i i ---- i i ii i i L1MD1_3end#LI 419 TTCACACAAAAACCTGTACACG----AATGTTTATAGCAGCTTTATTCGT 464 chr3ptel1M 667050 AGTGGCCAGAAACTGGAAACTGGGTGGATGCCCATCAGTGGG-GAATGGC 667098 i i i vivvii i v ii - i L1MD1_3end#LI 465 AATAGCCAAAAACTGGAAACAACCCAGATGTCCTTCAACGGGTGAATGGT 514 chr3ptel1M 667099 TGAATAAACTGTGATTTCTGAATATTATGGAATATTATT 667137 i i i viv vv ii i i L1MD1_3end#LI 515 TAAACAAACTGTGGTACATCCATACCATGGAATACTACT 553 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 37.28 CpG sites = 42, Kimura (unadjusted) = 40.40 Transitions / transversions = 1.68 (42/25) Gap_init rate = 0.06 (13 / 230), avg. gap size = 1.38 (18 / 13) 593 29.56 1.46 0.97 chr3ptel1M 666932 667136 (332864) L1ME3G_3end#LINE/L1 343 548 (376) m_b127s551i3 4690 chr3ptel1M 666932 TCAAACTGTGCAGACCCTTTGGCCCAGCAGTGTTACTACTGACCTTATAT 666981 i v i v i i vii v ?iv?v v L1ME3G_3end#L 343 TTAAAATGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTAT 392 chr3ptel1M 666982 CCCAAAGAGAT-CTTAAAGGAGGG-AAAGGGACCTGTATATGCCAAAATG 667029 i ? i - iiv viv v - v i --? i i i v ii L1ME3G_3end#L 393 CCTANAGAAATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATG 440 chr3ptel1M 667030 TTTGTGGCAGCCCTGTTTGTAGTGGCCAGAAACTGGAAACTGGGTGGATG 667079 ii v vi i i v i i vivv ii L1ME3G_3end#L 441 TTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATG 490 chr3ptel1M 667080 CCCATCAGT-GGGGAATGGCTGAATAAACTGTGATTTCTGAATATTATGG 667128 i i - i i i i i v v vv i L1ME3G_3end#L 491 TCCATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGG 540 chr3ptel1M 667129 AATATTAT 667136 i L1ME3G_3end#L 541 AATACTAT 548 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 38.16 CpG sites = 37, Kimura (unadjusted) = 39.99 Transitions / transversions = 1.61 (37/23) Gap_init rate = 0.02 (5 / 204), avg. gap size = 1.00 (5 / 5) 438 35.05 2.17 1.81 chr3ptel1M 666945 667220 (332780) L1MC5a_3end#LINE/L1 360 636 (2141) m_b127s551i4 4690 chr3ptel1M 666945 ACCCTTTGGCCCAGCAGTGTTACTACTGACCTTATATCCCAAAGAGATCT 666994 i i vii v iivvv v i v ivi L1MC5a_3end#L 360 ACCCTTTGACCCAGCAATCCCACTTCTAGGAATCTATCCCGAAGATACAC 409 chr3ptel1M 666995 TA--AAGGAGGGAAAGGGACCTGTATATGCCAAAATGTTTGTGGCAGCCC 667042 ?-- ii vivi i? -- iii v iiv i ii v vi L1MC5a_3end#L 410 TNGCAAAAATACGAAANGAC--GTATGCACAAGGTTATTCATTGCAGCAT 457 chr3ptel1M 667043 TGTTTGTAGTGGCCAGAAACTGGAAACTGGGTGGATGCCCATCAGT-GGG 667091 i i i v i i vivviii i i - L1MC5a_3end#L 458 TATTTGTAATAGCAAAAGACTGGAAACAACCCAAATGTCCATCAATAGGG 507 chr3ptel1M 667092 GAATGGCTGAATAAACTGTGATTTCTGAATATTATGGAATATTATTGTTC 667141 v i i i viv vv i iv i i vvvv L1MC5a_3end#L 508 GACTGGTTGAATAAACTATGGTACATCCACACAATGGAGTACTATGCAGC 557 chr3ptel1M 667142 TGTAAGAAATGACCAGCAGGAGGATTTC---AGAAAGGACTGGACTGATT 667188 - v -- vv i i --- v vv ?vv v i L1MC5a_3end#L 558 TGTAA-AAAGGA--ATGAGGAAGATCTCTATATACTGNTATGGAGTGATC 604 chr3ptel1M 667189 GACAAGAAGTGATGCTGAGGGAAATGAGCAGG 667220 vv i vi iv i i v vi i L1MC5a_3end#L 605 TCCAGGATATATTGTTAAGTGAAAAAAGCAAG 636 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 47.97 CpG sites = 52, Kimura (unadjusted) = 49.43 Transitions / transversions = 1.21 (52/43) Gap_init rate = 0.03 (8 / 275), avg. gap size = 1.38 (11 / 8) 16 0.00 0.00 0.00 chr3ptel1M 668651 668670 (331330) (AAT)n#Simple_repeat 1 20 (0) m_b127s252i0 4691 chr3ptel1M 668651 AATAATAATAATAATAATAA 668670 (AAT)n#Simple 1 AATAATAATAATAATAATAA 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 249 28.24 10.69 0.00 chr3ptel1M 669516 669646 (330354) C L2d_3end#LINE/L2 (4) 512 368 m_b127s601i2 4692 chr3ptel1M 669516 TCAATCGA-CAACGAGTATGGATTGAGCTCCTATGATGCCCCGAG-ACTG 669563 i - i vv v iv iv iv - C L2d_3end#LINE 512 TCAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTG 463 chr3ptel1M 669564 CG--AGATG----AGGGAAAGGGACAAAAG--TGAGGCA--GCCCCTGGC 669603 i -- ii ----i v i? v ? -- i i -- i v C L2d_3end#LINE 462 TGCTAGGCGCTGTGGGGAACGANAAAANAGTATAAGACATGGTCCCTGCC 413 chr3ptel1M 669604 CCAAAGGGGCTCCCA--TGAGTGGGGGAGATGGCACTGACAAATA 669646 iv i iv --iv v iiiv i v i C L2d_3end#LINE 412 CTCAAGGAGCTTACAATCTAGTTGGGGAGACAAGACTAACACACA 368 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 35.91 CpG sites = 22, Kimura (unadjusted) = 37.18 Transitions / transversions = 1.47 (22/15) Gap_init rate = 0.05 (7 / 130), avg. gap size = 2.00 (14 / 7) 260 27.42 0.00 3.57 chr3ptel1M 670744 670830 (329170) C L3b_3end#LINE/CR1 (457) 749 666 m_b127s601i3 4693 chr3ptel1M 670744 TCACCAGATTATCCATGTCATGCTTCAACTCCGGCACCCAAAAGCCCGGA 670793 v i? v i vivi v ? vi ?i i --- v C L3b_3end#LINE 749 TCTCCAANTTCTCCACGTCCCTTTTAAANTGTGGNGCCCAGAA---CTGA 703 chr3ptel1M 670794 ATGCAGAACTCAGGTTGAGTTTTGGCCAGGGCAGAGT 670830 i v vi ? ? vii i v C L3b_3end#LINE 702 ACGCAGTACTCCAGNTGNGGCCTGACCAGCGCAGAGT 666 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 33.49 CpG sites = 12, Kimura (unadjusted) = 37.42 Transitions / transversions = 1.09 (12/11) Gap_init rate = 0.03 (3 / 86), avg. gap size = 1.00 (3 / 3) 298 30.89 16.02 1.90 chr3ptel1M 670823 671053 (328947) L3#LINE/CR1 3260 3522 (577) m_b127s601i4 4694 chr3ptel1M 670823 GGCAGAGTCCGGGAGACAGAACGCCCTCAACAGACCAGA----TATTCTG 670868 i i -ii vv i ? vi i i ii ---- ivv i L3#LINE/CR1 3260 GACAGAATC-AAGATTCAAAANGATCTCGACAGGCTGGAACGATGGGCCG 3308 chr3ptel1M 670869 AATCCAGCAGAAGGAAATTTTAATGGGATTAATGTGAAATTAAAAATCGA 670918 v i ii v v vv v i i ivviv iv L3#LINE/CR1 3309 AAACCAACAAGATGAAATTTAACAGGGATAAATGTAAAGTCCTGCATTTA 3358 chr3ptel1M 670919 GGTTCAAAAGAAATCAACTTCCTAAGCAT----------GAATC------ 670952 -- v vi i i---------- i ------ L3#LINE/CR1 3359 GGTTCAAA--AAATCAACTGCACAAGTACAGGATGGAGAGGATCTGGCTT 3406 chr3ptel1M 670953 -------ATTCC--TAAA--AGATCTGAGGGGTCTTAGTGGACCTCGGGT 670991 -------i v-- i -- i - i v v ii - L3#LINE/CR1 3407 AGCAGCAGTTCACGTGAAAAAGACCT-AGGGGTTTTAGTTGACCGCAAG- 3454 chr3ptel1M 670992 TTCAATGTGAGTGAAGA----AATATGGTAGCCCAAAGATGGCGTGCATT 671037 i i iv v ----i i iv v i vvvvi v L3#LINE/CR1 3455 CTCAATATGAGCCAACAGTGTGATGTGGCTGCCAAAAAAGCTAATGCAAT 3504 chr3ptel1M 671038 CTTAGAC--CCTGAATAG 671053 i -- v v L3#LINE/CR1 3505 CTTAGGCTGCATTAATAG 3522 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 39.66 CpG sites = 39, Kimura (unadjusted) = 41.18 Transitions / transversions = 1.26 (39/31) Gap_init rate = 0.06 (13 / 230), avg. gap size = 3.23 (42 / 13) 13 15.44 9.30 0.00 chr3ptel1M 673428 673470 (326530) (GTCTCGGT)n#Simple_repeat 1 47 (0) m_b127s252i1 4695 chr3ptel1M 673428 GTCTCGGTG-CTCGGTG-CTC-CTGTCT-GGTGTTCCCTTGGCTCGG 673470 - - -v - ii vv v (GTCTCGGT)n#S 1 GTCTCGGTGTCTCGGTGTCTCGGTGTCTCGGTGTCTCGGTGTCTCGG 47 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.10 (4 / 42), avg. gap size = 1.00 (4 / 4) 19 21.76 0.00 0.00 chr3ptel1M 673852 673889 (326111) (C)n#Simple_repeat 1 38 (0) m_b127s252i2 4696 chr3ptel1M 673852 CCCCCTCCCCTCCCTCTCCCCTGCCCCCCCCCCCCACC 673889 i i i i iv v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 38 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 208 17.08 3.92 8.16 chr3ptel1M 674851 674901 (325099) MIR#SINE/MIR 193 241 (21) m_b127s601i5 4697 chr3ptel1M 674851 TTTATACACGTACGGCTGGCACTTAG--CAGTGTTTGGCACATAGTAAGT 674898 v i vi ----i -- ii i MIR#SINE/MIR 193 TTAATACATGTAAAGC----GCTTAGAACAGTGCCTGGCACATAGTAAGC 238 chr3ptel1M 674899 GCT 674901 MIR#SINE/MIR 239 GCT 241 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 14.73 CpG sites = 6, Kimura (unadjusted) = 19.91 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.10 (5 / 50), avg. gap size = 1.20 (6 / 5) 343 19.44 2.78 0.00 chr3ptel1M 676249 676320 (323680) C MIR#SINE/MIR (118) 144 71 m_b127s601i6 4698 chr3ptel1M 676249 CTCATTTTACA-ATGAGGAAACTGAGGCAAACAG-GGTGTAGTGACCTGC 676296 i - v v - vv i i C MIR#SINE/MIR 144 CCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGC 95 chr3ptel1M 676297 CCAGGATCACGTGGCTAATAACTG 676320 i i iii i v C MIR#SINE/MIR 94 CCAAGGTCACACAGCTAGTAAGTG 71 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 22.98 CpG sites = 9, Kimura (unadjusted) = 22.98 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.03 (2 / 71), avg. gap size = 1.00 (2 / 2) 13 20.15 0.00 2.86 chr3ptel1M 676682 676717 (323283) (TTG)n#Simple_repeat 1 35 (0) m_b127s252i4 4699 chr3ptel1M 676682 TTCTTTTTGTTGTTGCTCTTTTTGTTGATTGTTTTT 676717 v v i v v - v (TTG)n#Simple 1 TTGTTGTTGTTGTTGTTGTTGTTGTTG-TTGTTGTT 35 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) 190 35.78 3.09 2.04 chr3ptel1M 677922 678018 (321982) C L3#LINE/CR1 (1414) 2685 2588 m_b127s601i7 4700 chr3ptel1M 677922 CAGACTTTCGTTGCCCCTCTGCCGTTCTTCACGAACTC---AAGACCAAG 677968 v ii -- v v i ii vi --- ii vv C L3#LINE/CR1 2685 CAGTCTTCTG--GCACCTCTTCCGTTCTCCGTGATTTCTCAAAGATTACC 2638 chr3ptel1M 677969 GGCAGTGGTTCTGAGACTGCGCCTGAGAGTGGTGGCTGTGCTCGAGGATG 678018 i i i v iii ii vi vv vv v i i vi C L3#LINE/CR1 2637 GACAGCGGTTCCGCGATCACATCTGCAAGTTCTTTCAGTACCCTGGGATG 2588 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 44.56 CpG sites = 20, Kimura (unadjusted) = 50.74 Transitions / transversions = 1.43 (20/14) Gap_init rate = 0.03 (3 / 96), avg. gap size = 1.67 (5 / 3) 14 12.24 3.70 9.80 chr3ptel1M 678752 678805 (321195) (CCTT)n#Simple_repeat 1 51 (0) m_b127s252i5 4701 chr3ptel1M 678752 CCTCTCCTGTCTCTT-ATTCCTTCCTTCCCTCTCCCTCCCTCC-TCCTTT 678799 - - - -v - - i i - i (CCTT)n#Simpl 1 CCT-TCCT-TC-CTTCCTTCCTTCCTT-CCT-TCCTTCCTTCCTTCCTTC 45 chr3ptel1M 678800 CTTGCT 678805 v (CCTT)n#Simpl 46 CTTCCT 51 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.13 (7 / 53), avg. gap size = 1.00 (7 / 7) 15 12.63 5.71 0.00 chr3ptel1M 679508 679542 (320458) (GGGGCG)n#Simple_repeat 1 37 (0) m_b127s252i6 4702 chr3ptel1M 679508 GGGGCGGGAGCGGGGGC-GAGGC-AGGGAGGGGGCGG 679542 i - i -i v (GGGGCG)n#Sim 1 GGGGCGGGGGCGGGGGCGGGGGCGGGGGCGGGGGCGG 37 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 20 30.70 1.49 0.00 chr3ptel1M 683687 683753 (316247) (GGA)n#Simple_repeat 1 68 (0) m_b127s252i7 4703 chr3ptel1M 683687 GGAGAAGGAGGAAGA-GAAGAAGAGGAGGAGGGAAAAGAGGAGGGCAAGG 683735 i i - i i iii i ivi (GGA)n#Simple 1 GGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGG 50 chr3ptel1M 683736 AACAAGAGGGTGAGGAGG 683753 iv i iv (GGA)n#Simple 51 AGGAGGAGGAGGAGGAGG 68 Matrix = Unknown Transitions / transversions = 4.33 (13/3) Gap_init rate = 0.02 (1 / 66), avg. gap size = 1.00 (1 / 1) 49 3.85 1.85 0.00 chr3ptel1M 684139 684192 (315808) (TA)n#Simple_repeat 1 55 (0) c_b127s251i0 4704 chr3ptel1M 684139 TATA-ATATATATGTATGTATATATATATATATATATATATATATATATA 684187 - i i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr3ptel1M 684188 TATAT 684192 (TA)n#Simple_ 51 TATAT 55 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.02 (1 / 53), avg. gap size = 1.00 (1 / 1) 419 28.44 3.67 0.00 chr3ptel1M 684453 684561 (315439) C MIR#SINE/MIR (77) 185 73 m_b127s601i8 4705 chr3ptel1M 684453 AGTCTTTACAACTCCCCTG-GAGGTGGACGCAATCGTCACCTCCATTTTA 684501 i i i vv i- i iii v ii i i i C MIR#SINE/MIR 185 AATCCTCACAACAACCCTATGAGGTAGGTACTATTATTATCCCCATTTTA 136 chr3ptel1M 684502 CAGA---GGGAACTGAAGCAGGACAAGGTTAAGTGGCTTGACCAGGATCA 684548 --- i i viivi ii v i i C MIR#SINE/MIR 135 CAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCA 86 chr3ptel1M 684549 CAGAGTTAGCAAG 684561 v i i C MIR#SINE/MIR 85 CACAGCTAGTAAG 73 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 38.55 CpG sites = 24, Kimura (unadjusted) = 38.55 Transitions / transversions = 3.43 (24/7) Gap_init rate = 0.02 (2 / 108), avg. gap size = 2.00 (4 / 2) 189 15.15 0.00 0.00 chr3ptel1M 685138 685170 (314830) C MIRc#SINE/MIR (218) 50 18 m_b127s601i9 4706 chr3ptel1M 685138 TCTTCCTAATTCCAGGGCCAGTGCTCTATCCAC 685170 i i i v v C MIRc#SINE/MIR 50 TCTTCCTGACTCCAAGTCCAGTGCTCTTTCCAC 18 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 17.11 CpG sites = 3, Kimura (unadjusted) = 17.11 Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 240 21.59 0.00 4.62 chr3ptel1M 685703 685770 (314230) C L3#LINE/CR1 (825) 3274 3210 m_b127s601i10 4707 chr3ptel1M 685703 AATCTTGACTCTGCTCAGACCCACCCCATTAGCTGTCTCTTCTAGCTTTT 685752 i - --i ? vi i i i i v C L3#LINE/CR1 3274 AATCTTGATTCTG-TCA--TCCANCGTATTAGCTATCCCTCCCAGCTTTG 3228 chr3ptel1M 685753 AGTCATCTAAAAACTTAA 685770 v iv i i C L3#LINE/CR1 3227 TGTCATCTGCAAATTTGA 3210 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 26.84 CpG sites = 10, Kimura (unadjusted) = 26.84 Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.04 (3 / 67), avg. gap size = 1.00 (3 / 3) 432 34.18 13.77 2.32 chr3ptel1M 685871 686451 (313549) C L3#LINE/CR1 (1070) 3029 2384 m_b127s601i11 4707 chr3ptel1M 685871 CATCCACCTCAT-----TTCATCTTGCCCCCCAAAA-ACAATCTAAGATT 685914 v i ----- i i v v ii - iv vvi i C L3#LINE/CR1 3029 CATCCAGCCCATATTTCTCCATCTTGTCCACAAGGATATCATGAGAGACT 2980 chr3ptel1M 685915 TGCTCAAAT-CCTCA-TGAA-TCAAGAGTAAGCGATAATTACAGCCTTCC 685961 vv - ii- - v - vi v? ivi i v C L3#LINE/CR1 2979 TTGTCAAATGCCTTGCTGAAATCCAGA-TACACTNTGTCTACGGCATTCC 2931 chr3ptel1M 685962 TCCCAGCTATCAA------AA----ACCAAAACTCAAAAAAATGACGTCA 686001 i iv v i i------ ---- i --- ii v i C L3#LINE/CR1 2930 CCTGATCTACCAGTCTAGTAACCCTATCAAAA---AAGGAAATGAGGTTA 2884 chr3ptel1M 686002 GCCCTGTATATGACCTGT-----ATGGACAAATG---GCT--TAATGAGA 686041 ii- -ii i -----i i vv --- -- i vv C L3#LINE/CR1 2883 GTT-TG-GCATGACTTGTTCTTAGTGAACCCATGCTGGCTCCTAGTGATC 2836 chr3ptel1M 686042 ACC---TAGTCTCCTAGGGGACATATTCATCAGCTGT---------CGCT 686079 --- vv i i i v - vi ivv i v --------- i C L3#LINE/CR1 2835 ACCGCTTCCTTTTCTAAGTG-CTCACAAACCATCTGTTTAATAATCCGTT 2787 chr3ptel1M 686080 CT-GA--TGTGAC----ATTCAAGTAAAGCTCAGTGGTTCACTGTTAGGA 686122 - -- v v ---- iv v v i vi iiiiv v?v C L3#LINE/CR1 2786 CTAGAATTTTGCCGGGGATCGACGTCAAGCTTACCGGTCTGTAGTTTNCA 2737 chr3ptel1M 686123 GATAGTATTCATTTCCCCTTTGTGATAATTGGGGA----ATCAGTTC-TC 686167 vvvi iiv i v i - ? i ? ---- iv ii - C L3#LINE/CR1 2736 GAATCCATCTTTTTTCCCTTTTTAA-AANTAGGNACNACATTTGCCCGTC 2688 chr3ptel1M 686168 TTC------CTGGCCCCTCTTCTG-CCT-----ATCTTACAAAGATCACC 686205 i ------ v i -i ----- i iv i C L3#LINE/CR1 2687 TCCAGTCTTCTGGCACCTCTTCCGTTCTCCGTGATTTCTCAAAGATTACC 2638 chr3ptel1M 686206 AGCAATGGTCCAGCCAAGTCCATCAGTGAGGTCATTCAGGAACTTGATTG 686255 ii ii i v - i viv v ii v v v v i --- C L3#LINE/CR1 2637 GACAGCGGTTCCG-CGATCACATCTGCAAGTTCTTTCAGTACCCTG---G 2592 chr3ptel1M 686256 GAGCATAGATCATGTAGGCATGGACATGTGGATTCATCAAGAACAACCAA 686305 -ii iv i v i v v iv i i iv i i ii i i C L3#LINE/CR1 2591 GA-TGTAATTCGTCTGGGCCTGGAGACTTGAACTCATTTAAAGCGGCTAG 2543 chr3ptel1M 686306 AT-CTATCTTACT-TCT-----------TTGGGGTTCCTTTGCCTTTGTC 686342 i - v - ----------- v vv v i - v C L3#LINE/CR1 2542 GTGCTCTCTTACTATCTCCTCACCTATCTTGGGCTTCAATTCCCTCT-TA 2494 chr3ptel1M 686343 ATTATTTTTGTCCTGTACTGTCTAGCTCAGCACTTCCTCTCCTCAGTAGT 686392 iv v i iiv v i iiiiiviv ivi iii v C L3#LINE/CR1 2493 ACGATGTTTGTTCTACCCTTTCCAGTCTGAAGATCATTCTCCTTGATAGA 2444 chr3ptel1M 686393 GAAGTCAGAAGTCAAGTAAGGCTTGGAGTCCTT-TGCATCTCCTCT-TTA 686440 v i iv i i iv - vv - v iii - i C L3#LINE/CR1 2443 GAAGACGGAAGCAAAATAGGAGTT-GAGTAGTTCTGCTTTCTCTCTGTCA 2395 chr3ptel1M 686441 CCCATGATCAT 686451 i ii v v C L3#LINE/CR1 2394 TCTGTTAACAT 2384 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 44.33 CpG sites = 114, Kimura (unadjusted) = 48.08 Transitions / transversions = 1.43 (114/80) Gap_init rate = 0.07 (40 / 580), avg. gap size = 2.38 (95 / 40) 646 30.55 1.50 9.76 chr3ptel1M 686700 687098 (312902) L1ME4c_3end#LINE/L1 12 380 (450) m_b127s551i5 4708 chr3ptel1M 686700 AATATATAGAGATTTGAGTCAAATTTGTAAGAATACAAGTCATTCCCCAG 686749 ? i vi v v vi v v? viv vv i L1ME4c_3end#L 12 ANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAAGACCCCAA 61 chr3ptel1M 686750 TTGATAAATGGTCAAAAGATGGTTTTCTGATGGTCAAAACAAGTGGTTTT 686799 v v i i--------- ----- iiiii iv L1ME4c_3end#L 62 TAGATAAATGGGCAAAGGAC---------ATG-----AACAGACAATTCA 97 chr3ptel1M 686800 CAGATAAAGAAATTAAAGCTAGATTCTCTAACCATATGAAAAAATACATT 686849 ? vi i - v i? -- vvvi v i i i---- L1ME4c_3end#L 98 CANAAGAGGAAAT-ACAANTAG--TAAACAAACACATGGAAAAATG---- 140 chr3ptel1M 686850 TTTTTCAATTACTAATCTCTAATCACTATTAATTAGAGAAATGCAAATTA 686899 --- ii------------ i v i i L1ME4c_3end#L 141 ---TTCAACC------------TCGCTAGTAATCAAAGAAATGCAAATTA 175 chr3ptel1M 686900 AAACAACTCTGAAATAGCACCCTACACCTATCAGATTGGCTAATATGACA 686949 i vv i v iii i i i i v v vvv L1ME4c_3end#L 176 AAGCAACAATGAGATACCATTTTACGCCTATTAAATTAGCAAAAATTTAA 225 chr3ptel1M 686950 GAAAAGGAAA------AATGTTGGAAGGGATGTGGGAAAACTGGGACACT 686993 i vv v ------ i vii ? i vi v ? L1ME4c_3end#L 226 AAAATTGATAATACCCAATGCTGGCGAGGNTGCGGTGAAACTGGTACNCT 275 chr3ptel1M 686994 AATGCATTATTGATGGAGTTATGAACTGATCCAACCATTCTGGAGAGTAA 687043 v i ii i vi? i i i i v v i i i L1ME4c_3end#L 276 CATACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGCAA 325 chr3ptel1M 687044 TTTGGAACTTTGCTCAAAGGGCTATCAAACTATGCATCCCCTTGCATTCA 687093 v v vi iviv i i v v i v v vv ii L1ME4c_3end#L 326 TTTGGCAATACGTATCAAGAGCCATAAAAATGTTCATACCCTTTGACCCA 375 chr3ptel1M 687094 GCAAT 687098 i L1ME4c_3end#L 376 GTAAT 380 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 38.40 CpG sites = 61, Kimura (unadjusted) = 40.78 Transitions / transversions = 1.24 (61/49) Gap_init rate = 0.09 (37 / 398), avg. gap size = 1.14 (42 / 37) 659 26.88 3.31 13.68 chr3ptel1M 686744 687105 (312895) L1ME5_3end#LINE/L1 56 384 (557) m_b127s551i6 4708 chr3ptel1M 686744 CCCCAGTTGATAAATGGTCAAAAGATGGTTTTCTGATGGTCAAAACAAGT 686793 i v v v i --------- ----- i i L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGAT---------ATG-----AACAGGC 91 chr3ptel1M 686794 GGTTTTCAGATAAAGAAATT---AAAGCTAGATTCTCTAACCATATGAAA 686840 ii v vi i ii--- i i------i v i L1ME5_3end#LI 92 AATTTACAGAAGAGGAAACCCGAAAGGCTAA------CAAGCATATGAAG 135 chr3ptel1M 686841 AAATACATTTTTTTCAATTACTAATCTCTAATCACTATTAATTAGAGAAA 686890 i i ------- ------------ v i v i L1ME5_3end#LI 136 AGATGC-------TCAA------------ACTCATTAGTAATCAGAGAAA 166 chr3ptel1M 686891 TGCAAATTAAAACAACTCTGAAATAGCACCCTACACCTATCAGATTGGCT 686940 vv i v ii i i v L1ME5_3end#LI 167 TGCAAATTAAAACAACAATGAGATATCACTTTACACCTATTAGACTGGCA 216 chr3ptel1M 686941 AATATGACA------GAAAAGGAAAAATGTTGGAAGGGATGTGGGAAAAC 686984 v v v ------ v v vv i vii i ? i L1ME5_3end#LI 217 AAAATTAGAAAGCTGGATAATGCCAAGTGTTGGCGAGGATGTGGGGANAT 266 chr3ptel1M 686985 TGGGACACTAATGCATTATTGATGGAGTTATGAACTGATCCAACCATTCT 687034 v i v v i ii i iiv i ii i v i L1ME5_3end#LI 267 AGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACTGGTGCAGCCATTCT 316 chr3ptel1M 687035 GGAGAGTAATTTGGAACT--TTGCTCAAAGGGCTATCAAAC-TATGCATC 687081 i i v v -- iv ------ i ii- i v L1ME5_3end#LI 317 GGAGAGCAATCTGGCAGTACTTAGTCAA------ATTAAGTATACGCATA 360 chr3ptel1M 687082 CCCTTGCATTCAGCAATATAGCTC 687105 vvv ii viv L1ME5_3end#LI 361 CCCTATGACCCAGCAATTCCGCTC 384 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 32.67 CpG sites = 50, Kimura (unadjusted) = 33.64 Transitions / transversions = 1.47 (50/34) Gap_init rate = 0.14 (49 / 361), avg. gap size = 1.16 (57 / 49) 49 25.74 1.15 4.14 chr3ptel1M 688694 688867 (311133) (GTCT)n#Simple_repeat 1 169 (0) m_b127s252i8 4709 chr3ptel1M 688694 GTCT-TCTGTGTGTTAGTCTGTCTGCCTGTGATTGCTTGTCTGCCAGTCT 688742 - v iv i --i ii i v (GTCT)n#Simpl 1 GTCTGTCTGTCTGTCTGTCTGTCTGTCTGT--CTGTCTGTCTGTCTGTCT 48 chr3ptel1M 688743 GTCTGTCTCTGAATCTGTCTGCCTGACTGTATGTTTGCCTGTGTCTGAGT 688792 v vvi i v v i i v v vv (GTCT)n#Simpl 49 GTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGT 98 chr3ptel1M 688793 CTTTCTGCCTGTGACTGTCTGCCTGTGTTGGAGTCTGTCTGCCTGTGACT 688842 v i -- i v vvvv i -- (GTCT)n#Simpl 99 CTGTCTGTCTGT--CTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGT--CT 144 chr3ptel1M 688843 G-CTCATCTGCCTGTGTGTCTGCCTG 688867 - -i i v i (GTCT)n#Simpl 145 GTCT-GTCTGTCTGTCTGTCTGTCTG 169 Matrix = Unknown Transitions / transversions = 0.84 (16/19) Gap_init rate = 0.05 (9 / 173), avg. gap size = 1.00 (9 / 9) 314 23.15 6.00 4.95 chr3ptel1M 688868 688967 (311033) MIRb#SINE/MIR 56 156 (112) m_b127s601i12 4710 chr3ptel1M 688868 TGGTTTAGAATCAGAGTTCTAAAAGGGACTCTGCCATCTGAGTGACCTTG 688917 v v vvi i ---- vv - i i v v MIRb#SINE/MIR 56 TGGGTTCGAATCCCGGCTCT----GCCACT-TACTAGCTGTGTGACCTTG 100 chr3ptel1M 688918 GACAAGT------ACCTCTCAGAGCCTCAGTTTGCTCATCTAGAGGGTGG 688961 i ------ v v iv iii MIRb#SINE/MIR 101 GGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGG 150 chr3ptel1M 688962 GAATGA 688967 i i MIRb#SINE/MIR 151 GGATAA 156 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 26.49 CpG sites = 11, Kimura (unadjusted) = 27.92 Transitions / transversions = 1.00 (11/11) Gap_init rate = 0.06 (6 / 99), avg. gap size = 1.83 (11 / 6) 335 16.90 8.45 0.00 chr3ptel1M 688900 688970 (311030) MIR1_Amn#SINE/MIR 82 158 (72) m_b127s601i13 4710 chr3ptel1M 688900 GCCATCTGAGTGACCTTGGACAAGT------ACCTCTCAGAGCCTCAGTT 688943 ?v ? i ------ v ? MIR1_Amn#SINE 82 GCCNGCTGNGTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTT 131 chr3ptel1M 688944 TGCTCATCTAGAGGGTGGGAATGACGA 688970 v iv iii i i i MIR1_Amn#SINE 132 TCCTCATCTGTAAAATGGGGATAATGA 158 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 20.54 CpG sites = 8, Kimura (unadjusted) = 20.54 Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.01 (1 / 70), avg. gap size = 6.00 (6 / 1) 437 27.13 5.43 0.00 chr3ptel1M 689639 689767 (310233) C MIRb#SINE/MIR (53) 215 80 m_b127s601i14 4711 chr3ptel1M 689639 AGCGCTTTATAA--ATT-TCTCATTTGATCCCCACGATGGCCCTGGGA-- 689683 i v-- - i i i iii v -- C MIRb#SINE/MIR 215 AGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGG 166 chr3ptel1M 689684 -ATCCAGTGTCATCTCCATTTCATGAAGGAGGAAACCAAAGCAAAGAG-G 689731 - vvi v i i i i iii v ii i vv - C MIRb#SINE/MIR 165 TAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAG 116 chr3ptel1M 689732 GTGAGGTAACTGTCCCAGCATCACACAGGTAGTGAG 689767 v i vv ivi v i C MIRb#SINE/MIR 115 GTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAG 80 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 34.78 CpG sites = 22, Kimura (unadjusted) = 34.78 Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.04 (5 / 128), avg. gap size = 1.40 (7 / 5) 205 9.09 3.03 0.00 chr3ptel1M 689858 689890 (310110) MIR3#SINE/MIR 113 146 (62) m_b127s601i15 4712 chr3ptel1M 689858 TCTGGGC-TCAATTTCCTCCTCTGTAAAGTGAGG 689890 - i v i MIR3#SINE/MIR 113 TCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGG 146 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 9.78 CpG sites = 2, Kimura (unadjusted) = 9.78 Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 195 34.15 2.55 9.05 chr3ptel1M 690014 690248 (309752) L3#LINE/CR1 1371 1591 (2508) m_b127s601i16 4713 chr3ptel1M 690014 GGGATGAGACCAGTGGCCAGAA-ATGACTCTTGGGAGGAATATCTTATCT 690062 i ivi i ii - i i vv v iii v ? i i ii L3#LINE/CR1 1371 GGGATGGGACTCATGACTGGAATACGGCGATGGAAGGGTANACCTTGTTC 1420 chr3ptel1M 690063 AAAAAGAGGATCAAAATGTAGGTGGGGGAGGGGAGGGAAAGAGGATGAGG 690112 ii -- i-- i v ?v---i i ? i --------- L3#LINE/CR1 1421 AAAAGAA--AC--AGATCTANT---AGAAGGGGAGGNAGAG--------- 1454 chr3ptel1M 690113 GTAGCATTGCTATGTTTAAAAAAAAT-CACCATTTGGGGAAATCGAGGAG 690161 - i - iv i i v - - vi v v v i L3#LINE/CR1 1455 -TAGCACTG-TATGTCAAGAAGATATACACC-TGCGTGGAAATCCACGAA 1501 chr3ptel1M 690162 TCAGAACGGGGGACACGTGGTGGA---CATCTGGGCAAGGAGGAAGGGGA 690208 i v i- vi vi i ? --- i ii vi i ii L3#LINE/CR1 1502 CCTGAG-GGTAGAAGCGCGNTGGAGAGCATTTGGGTGAGGATAAAAGGAG 1550 chr3ptel1M 690209 ACAGAG-TGGAAATCCTATTTTCGTGGGAAGAAATGGCAGA 690248 v i-ii i vv iv i iv v ivi L3#LINE/CR1 1551 AGAGAAACAGAAGTGATATCGTTGTGGGAGTATACTACAGA 1591 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 45.72 CpG sites = 49, Kimura (unadjusted) = 49.61 Transitions / transversions = 2.04 (49/24) Gap_init rate = 0.10 (24 / 234), avg. gap size = 1.08 (26 / 24) 223 27.39 4.05 1.32 chr3ptel1M 690496 690569 (309431) C L2a_3end#LINE/L2 (0) 517 442 m_b127s601i17 4714 chr3ptel1M 690496 ATACCTGCATTCGACAAGCATTTATTATGCACCAACTAGGTGCAGAGCAT 690545 v v v i ii iv i v v vii i C L2a_3end#LINE 517 ATTCATTCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCAC 468 chr3ptel1M 690546 TCTTGCTGGGACATGGGG---CAGCAG 690569 v - i vvv --- C L2a_3end#LINE 467 TGTT-CTAGGCGCTGGGGATACAGCAG 442 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 32.27 CpG sites = 9, Kimura (unadjusted) = 34.28 Transitions / transversions = 0.82 (9/11) Gap_init rate = 0.03 (2 / 73), avg. gap size = 2.00 (4 / 2) 96 28.98 4.86 1.80 chr3ptel1M 692603 693034 (306966) (AG)n#Simple_repeat 1 445 (0) m_b127s252i9 4715 chr3ptel1M 692603 AGGGAGAGCAAGCAAAAGAGGGATGGGA-AGAG-GGGACGGGGAGAGAGA 692650 i vi vi i i - i - - i vi i (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGA 49 chr3ptel1M 692651 CA-AGAGATATAAACAGAGACAAACCGAGAGAGGCAGAGAAGGAGAGAG- 692698 v - v v i v v i vv iv ii - (AG)n#Simple_ 50 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 99 chr3ptel1M 692699 GAGAGAGAAACGGA-ACAGAGACAGAGAGGGACGGAGAGAAAGTG-GAGA 692746 i vi - v v i vi i v - (AG)n#Simple_ 100 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 149 chr3ptel1M 692747 GGGTGAGACAGAGAG-GAG-GAG-GAGAGAGAGAGACTGGTACAGAGGGA 692793 i v v - - - vv iv v i (AG)n#Simple_ 150 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 199 chr3ptel1M 692794 GGGAGTAAAGAGAAAGACAAACCAAAGAGATAGAGAGAAACGGGACACGG 692843 i - i i v i -v i v i - i v - i (AG)n#Simple_ 200 GAGAG-AGAGAGAGAGAGAGA-GAGAGAGAGAGAGAGAGA-GAGAGA-GA 245 chr3ptel1M 692844 GAG-GGGAG-GAAAGAAAGTG-GAGAGGGTGAGACAG-GAGAAAGAAAAA 692889 - i - i i v - i v v - i i i (AG)n#Simple_ 246 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 295 chr3ptel1M 692890 GGCAGACGGAG-GAGAGAGAAAGACA-AGTACAAAAAGGGACAGAGGGA- 692936 iv vi - i v - - v i i i v i - (AG)n#Simple_ 296 GAGAGAGAGAGAGAGAGAGAGAGAGAGAG-AGAGAGAGAGAGAGAGAGAG 344 chr3ptel1M 692937 AGAGACAGACAGAG-GAAAGACAGACATAGAGAGATGGGGA-AAAGCAG- 692983 v v - i v v v vi i - i - - (AG)n#Simple_ 345 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG-AGA 393 chr3ptel1M 692984 GAGAGATGGGAGGGGGACAGA-AGAGGGAGAAGGAAAG-GGGAGAAACAG 693031 - i i i v - i ii i - i i v (AG)n#Simple_ 394 GAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 442 chr3ptel1M 693032 AGA 693034 (AG)n#Simple_ 443 AGA 445 Matrix = Unknown Transitions / transversions = 1.36 (57/42) Gap_init rate = 0.07 (29 / 431), avg. gap size = 1.00 (29 / 29) 185 24.39 0.00 0.00 chr3ptel1M 693488 693528 (306472) C L2d_3end#LINE/L2 (9) 507 467 m_b127s601i18 4716 chr3ptel1M 693488 CACTCAGCCAGCACTTATTCAGCACCTGCTGTGTGCTGAGC 693528 v i v i i v i i i v C L2d_3end#LINE 507 CAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGC 467 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 26.69 CpG sites = 6, Kimura (unadjusted) = 30.16 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 18 20.23 0.00 2.17 chr3ptel1M 693572 693618 (306382) (CCCAGC)n#Simple_repeat 1 46 (0) m_b127s252i10 4717 chr3ptel1M 693572 CCCAGCCCCGGGCGCAGCCACCAAGCCCAGCCCCTGCCCCGGGCCCA 693618 i v v - iv v i v (CCCAGC)n#Sim 1 CCCAGCCCCAGCCCCAGCC-CCAGCCCCAGCCCCAGCCCCAGCCCCA 46 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.02 (1 / 46), avg. gap size = 1.00 (1 / 1) 17 15.30 0.00 0.00 chr3ptel1M 693979 694007 (305993) (C)n#Simple_repeat 1 29 (0) m_b127s252i11 4718 chr3ptel1M 693979 CCCTCCCCGCCCCCCCCCCGCCCCTCCCC 694007 i v v i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC 29 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 331 24.42 3.49 0.00 chr3ptel1M 695253 695338 (304662) MIRc#SINE/MIR 60 148 (120) m_b127s601i19 4719 chr3ptel1M 695253 GAGTTCAGA-TCTGG-ACGTATTAGCTGTGTGGCACTGGACAAATCACGT 695300 i v i- v- v i i vi i i v MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTT 109 chr3ptel1M 695301 CACCCTGCTT-GCCTCCATTTCTTCATCTGTAAAATGAG 695338 v iiv v- vi i i MIRc#SINE/MIR 110 AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 30.07 CpG sites = 12, Kimura (unadjusted) = 30.07 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.04 (3 / 85), avg. gap size = 1.00 (3 / 3) 335 23.61 1.39 0.00 chr3ptel1M 695267 695338 (304662) MIR#SINE/MIR 72 144 (118) m_b127s601i20 4719 chr3ptel1M 695267 ACGTATTAGCTGTGTGGCACTGGACAAATCACGTCACCCTGCT-TGCCTC 695315 v i i vi i i i v v iiv - MIR#SINE/MIR 72 ACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTC 121 chr3ptel1M 695316 CATTTCTTCATCTGTAAAATGAG 695338 vi i i MIR#SINE/MIR 122 AGTTTCCTCATCTGTAAAATGGG 144 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 29.18 CpG sites = 11, Kimura (unadjusted) = 29.18 Transitions / transversions = 1.83 (11/6) Gap_init rate = 0.01 (1 / 71), avg. gap size = 1.00 (1 / 1) 222 26.59 6.32 1.00 chr3ptel1M 695695 695789 (304211) L2#LINE/L2 2062 2161 (921) m_b127s601i21 4720 chr3ptel1M 695695 TCTCTGCAGCCTTTGACACAGTGGGTCACCCTCTTC-TCTTAAATGGCTT 695743 ? v v v i i i i - i vvi L2#LINE/L2 2062 TNTCAGCAGCATTTGACACAGTTGATCACTCCCTCCTTCTTGAAACACTT 2111 chr3ptel1M 695744 CTCTCCA---GGTTCTCAGAGGACTTCTCTCTCCTA--TTTCCTGCTCCT 695788 - i --- i ii iiv iv v i-- v v i L2#LINE/L2 2112 -TCTTCACTTGGCTTCCAGGACACCACACTCTCCTGGTTTTCCTCCTACC 2160 chr3ptel1M 695789 T 695789 L2#LINE/L2 2161 T 2161 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 34.17 CpG sites = 15, Kimura (unadjusted) = 34.17 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.04 (4 / 94), avg. gap size = 1.75 (7 / 4) 17 0.00 4.17 0.00 chr3ptel1M 696877 696900 (303100) (GTT)n#Simple_repeat 1 25 (0) m_b127s252i12 4721 chr3ptel1M 696877 GTT-TTGTTGTTGTTGTTGTTGTTG 696900 - (GTT)n#Simple 1 GTTGTTGTTGTTGTTGTTGTTGTTG 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 414 29.84 2.38 1.57 chr3ptel1M 697801 697926 (302074) C MIRc#SINE/MIR (126) 142 16 m_b127s601i22 4722 chr3ptel1M 697801 TTATAAATGAGGAAACTAAGGC--AGAAAGGATTAAATGATTAGCCTAGA 697848 i i i -- i - i i v i ii C MIRc#SINE/MIR 142 TTACAGATGAGGAAACTGAGGCTCAGAGAGG-TTAAGTGACTTGCCCAAG 94 chr3ptel1M 697849 CAGGCACAGCTAATAACTGCTTAAAGCCAG-ATTTGAAATCGGGTTTTCT 697897 vvvi i v vi- i i - i i vi i i i C MIRc#SINE/MIR 93 GTCACACAGCTAGTAAGTGGC-AGAGCCGGGACTCGAACCCAGGTCTTCC 45 chr3ptel1M 697898 TGACTCCAGGCCTGGCATTCTATATACTG 697926 i i ii iii v vi C MIRc#SINE/MIR 44 TGACTCCAAGTCCAGTGCTCTTTCCACTG 16 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 38.10 CpG sites = 28, Kimura (unadjusted) = 41.06 Transitions / transversions = 3.11 (28/9) Gap_init rate = 0.03 (4 / 125), avg. gap size = 1.25 (5 / 4) 752 27.08 7.13 5.08 chr3ptel1M 698027 698489 (301511) L1M4_orf2#LINE/L1 1412 1883 (1411) m_b127s551i7 4723 chr3ptel1M 698027 CAAAACCAGATAAATTCACAAGTTAATTCTACCAAACATTTAAAGAACAA 698076 ii? iiv vi v v L1M4_orf2#LIN 1412 CAGGNCCAGATGGCTTCACTGGTGAATTCTACCAAACATTTAAAGAAGAA 1461 chr3ptel1M 698077 TTCATTCTGATGTCATATAAGCTATTTGGAAAAATAGGCAAAGA------ 698120 v iv ii viivi i i v ivi ivi i ------ L1M4_orf2#LIN 1462 TTAACACCAATCCTTCACAAACTCTTCCAAAAAATAGAAGAGGAGGGAAC 1511 chr3ptel1M 698121 -------AATTTCTTTTATAATACAAATATGGCACTGATAACTAAACCAA 698163 ------- i iv i i vi v i vi v v v i L1M4_orf2#LIN 1512 ACTTCCCAACTCATTCTATGAGGCCAGTATTACCCTGATACCAAAACCAG 1561 chr3ptel1M 698164 GAAGAG------CAAATAAAGAAAACTGGACCAATTTGGACCAATTTTTC 698207 iv i ------ iv iv -------- - v i L1M4_orf2#LIN 1562 ACAAAGACATCACAAGAAAAGAAAACTACA--------GACCAA-TATCC 1602 chr3ptel1M 698208 CTAATGAATATTGATGCAAAAATTTTGAATAAAATACT--TAA---GATT 698252 v v ii v i --i --- v L1M4_orf2#LIN 1603 CTTATGAATATAGATGCAAAAATCCTCAACAAAATACTAGCAAACCGAAT 1652 chr3ptel1M 698253 ACAAAAATATATCACAAAGATCATACACTATAACCAGATAAG-TTTATAC 698301 v iv i v v i i i i ii ii - v L1M4_orf2#LIN 1653 CCAGCAACATATAAAAAGGATTATACACCATGACCAAGTGGGATTTATCC 1702 chr3ptel1M 698302 CAGGAATACAAGGCTGGTTCCACAATCAATATTGTGGAAATT-ATCAGCA 698350 i i v -------- ?i i i- iii L1M4_orf2#LIN 1703 CAGGAATGCAAGGTTGGTTCAACA--------TNCGAAAATCAATCAATG 1744 chr3ptel1M 698351 TAATTTAACATATCAAAAAAGCAA---ACAAA---CATATAATTATTTCA 698394 vi v i v i ii --- --- i i i i L1M4_orf2#LIN 1745 TAATACACCATATTAATAGAATAAAGGACAAAAACCACATGATCATCTCA 1794 chr3ptel1M 698395 ATAGATGCAGAAAAGGTTTTTGACAAAATACAATACTCGTTCCTATTTAA 698444 i i iv v i i v v ------ L1M4_orf2#LIN 1795 ATAGACGCAGAAAAAGCATTTGACAAAATCCAACACCCTTTCAT------ 1838 chr3ptel1M 698445 AAAAAAAACACTAGAGAGCATAGAAATA-AATGAAGCTTACCTTAA 698489 i v vi v ivv i - v i i - i L1M4_orf2#LIN 1839 GATAAAAACACTCAACAAACTAGGAATAGAAGGGAACTT-CCTCAA 1883 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 34.17 CpG sites = 74, Kimura (unadjusted) = 34.90 Transitions / transversions = 1.64 (74/45) Gap_init rate = 0.07 (34 / 462), avg. gap size = 1.68 (57 / 34) 38 0.00 9.43 0.00 chr3ptel1M 698510 698562 (301438) (ATTAGAGAA)n#Simple_repeat 1 58 (0) c_b127s251i1 4724 chr3ptel1M 698510 ATTAGAGAAA-T-GAGAAATTAGAG-AATTAGAGAAATTAGAGAAA-T-G 698554 - - - - - (ATTAGAGAA)n# 1 ATTAGAGAAATTAGAGAAATTAGAGAAATTAGAGAAATTAGAGAAATTAG 50 chr3ptel1M 698555 AGAAATTA 698562 (ATTAGAGAA)n# 51 AGAAATTA 58 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.10 (5 / 52), avg. gap size = 1.00 (5 / 5) 372 29.85 12.13 2.89 chr3ptel1M 699670 700114 (299886) C L1MC4_3end#LINE/L1 (2158) 631 147 m_b127s551i8 4725 chr3ptel1M 699670 TTCTCTTCACTTTGTAACAGTTCATTTAAG-----TCCAGGTTTTTCTG- 699713 - v i ? - v ----- v ? vi - C L1MC4_3end#LI 631 TTCT-TTCACTTAGCAANA-TGCATTTAAGATTCATCCATGTTNTTGCGT 584 chr3ptel1M 699714 AAACCTGT----TATTTCTTTT----ACACAATAGTATTTCATCACAATC 699755 i? i v ----i i ----i vv i i iii vvv C L1MC4_3end#LI 583 GNATCAGTAGTTCATTCCTTTTTATCGCTGAGTAGTATTCCATTGTATGG 534 chr3ptel1M 699756 ACATACCACAACTTATCTAGCTATTAGCATCCCATGAA------------ 699793 ii ii i i v i -- i ivv ------------ C L1MC4_3end#LI 533 ATGTACCACAGTTTGTTTATCCATT--CACCTGTTGAAGGACATCTNGGT 486 chr3ptel1M 699794 --TTTTGAATTCTTTGCCACCACAAAAGGAACTGCTGTAATTATTTTTGT 699841 -- iv i? i v ? ii ii vii i i vi iv C L1MC4_3end#LI 485 TGTTTCCAGNTTTTGGCNATTATGAATAAAGCTGCTATAAACATTCGTGT 436 chr3ptel1M 699842 ACATAAAATTCCTTTTTAAAAAT-------CATTTTG---GGATACAGAC 699881 ---ii ii v v ii v ------- ? i?--- i v v C L1MC4_3end#LI 435 ACA---GGTTTTTGTGTGGACATANGTTTTCANTTCNCTTGGGTAAATAC 389 chr3ptel1M 699882 CCA----TGCTATTGCTTGATCAAAGGGTA--TACATGGTTTTATAGCCC 699925 i ---- ?v v i v v -- ii v ---- ii C L1MC4_3end#LI 388 CTAGGAGTGNGATTGCTGGGTCATATGGTAANTGTATGTTT----AGCTT 343 chr3ptel1M 699926 TTTGGACATAGTTCCAAATTGTTTTCCAAAATGGCTGTACTAACAACTAT 699975 ? i- v v v v i i i vivvvi C L1MC4_3end#LI 342 TNTA-AGAAACTGCCAAACTGTTTTCCAAAGTGGCTGTACCATTTTGCAT 294 chr3ptel1M 699976 ACCAAC-AGCAAT-----AGTGTCCCTATTTTTTCACATCTG----AACA 700015 v v - ----- v i ?i vi i iv---- i C L1MC4_3end#LI 293 TCCCACCAGCAATGTATGAGAGTTCCNGTTGCTCCACATCCTCGCCAGCA 244 chr3ptel1M 700016 TTTGTCCTTTTCCTTTTCTGTCATTCTAGCCAGCATCTGACAAGTGTGAG 700065 viv v vv ? i v v i v-- i i i vi C L1MC4_3end#LI 243 TTTGGTATTGTCAGTNTTTTTGATTTTAGCCAT--TCTAATAGGTGTGTA 196 chr3ptel1M 700066 GTGATACCCGAGAGTTGTTTTAATTTGCATTTCTCTTATCAATAGTGAT 700114 i i iv vv v i v v v? i C L1MC4_3end#LI 195 GTGGTATCTCATTGTGGTTTTAATTTGCATTTCCCTAATGACNAATGAT 147 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 39.38 CpG sites = 72, Kimura (unadjusted) = 40.61 Transitions / transversions = 1.26 (72/57) Gap_init rate = 0.06 (27 / 444), avg. gap size = 2.52 (68 / 27) 544 33.58 8.75 0.49 chr3ptel1M 699737 700113 (299887) C L1ME4c_3end#LINE/L1 (275) 555 148 m_b127s551i9 4725 chr3ptel1M 699737 ATAGTATTTCATCACAATCACATACCACAACTTATCTAGCTATTAGCATC 699786 i i iviv?v ii i i ii i i vv v v C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chr3ptel1M 699787 CCAT--GA----------ATTTTGAATTCTTTGCCACCACAAAAGGAACT 699824 iii -- ----------i iv i i i ii i viivi C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCT 456 chr3ptel1M 699825 GCTGTAATTATTTTTGTACATAAAA----TTCCTTTTTAAAAATCATTT- 699869 vi i vi i i i v i---- i vvi i - C L1ME4c_3end#L 455 GCAATGAACATCTTCGTGCATATAGCTTTTTCCTTCTTTTGAATTATTTC 406 chr3ptel1M 699870 --TGGGATACAGACCCA----TGCTATTGCTTGATCAAAGGGTATACATG 699913 -- i v vv ---- vv i v i iv ii C L1ME4c_3end#L 405 CTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACA 356 chr3ptel1M 699914 GTTTTATAGCCCTTTGGACATAGTTCCAAATTGTTTTCCAAAATGGCTGT 699963 v i i viv i v v i v i C L1ME4c_3end#L 355 TTTTTATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGT 306 chr3ptel1M 699964 ACTAA-CAACTATACCAACAGCAAT-----AGTGTCCCTATTTTTTCACA 700007 i -iv v? i v ----- ? v vi ivi i C L1ME4c_3end#L 305 ACCAATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCA 256 chr3ptel1M 700008 TCTG----AACATTTGTCCTTTTCCTTTTCTGTCATTCTAGCCAGCATCT 700053 ? iv---- i v viv v vv i vvv i v i -- i C L1ME4c_3end#L 255 NCCTCGCCAGCATTGGGTATTATCAATTTTTTAAATTTTTGCTA--ATTT 208 chr3ptel1M 700054 GACAAGTGTGAGGTGATACCCGAGAGTTGTTTTAATTTGCATTTCTCTTA 700103 i i i i i ii i i iv vv i i v C L1ME4c_3end#L 207 AATAGGCGTAAAATGGTATCTCATTGTTGCTTTAATTTGCATTTCTTTGA 158 chr3ptel1M 700104 TCAATAGTGA 700113 i v i C L1ME4c_3end#L 157 TTACTAGCGA 148 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 43.08 CpG sites = 76, Kimura (unadjusted) = 47.17 Transitions / transversions = 1.52 (76/50) Gap_init rate = 0.03 (11 / 376), avg. gap size = 3.18 (35 / 11) 589 29.73 7.86 2.69 chr3ptel1M 699799 700116 (299884) C L1ME5_3end#LINE/L1 (463) 478 145 m_b127s551i10 4725 chr3ptel1M 699799 AATTCTTTGCCACCACAAAAGGAACTGCTGTAATTATTTTTGTACATA-- 699846 i iii viivi vi i vi ii i i-- C L1ME5_3end#LI 478 AACTCCCCGCCACCACAAACAACGCTGCAATGAACATCCTCGTACATGTC 429 chr3ptel1M 699847 -----AAATTCCTTTTTAAAAATCATTTTGGGATACAGACCCA----TGC 699887 ----- vivv v v i i ivi i v ----i v C L1ME5_3end#LI 428 CCCTTATGGACCTGTGTGAGAATTTCTTTGGGATATATACCCAGGAGCGG 379 chr3ptel1M 699888 TATTGCTTGATCAAAGGGTATACATGGTTTTATAGCCCTTTGG--ACATA 699935 v v i v i i ivvi -----v i-- vi C L1ME5_3end#LI 378 AATTGCTGGGTCATAGGGTATGCGTATACTTA-----ATTTGACTAAGTA 334 chr3ptel1M 699936 GTTCCAAATTGTTTTCCAAAATGGCTGTACTAA-CAACTATACCAACAGC 699984 v v i i i i i i i- v vv v v C L1ME5_3end#LI 333 CTGCCAGATTGCTCTCCAGAATGGCTGCACCAGTCTACACTCCCACCAGC 284 chr3ptel1M 699985 AAT-----AGTGTCCCTATTTTTTCACATCTG----AACATTTGTCCTTT 700025 i ----- v i ? iii iv---- i v v v C L1ME5_3end#LI 283 AGTGCATGAGGGTTCCTATNTCCCCACATCCTCGCCAACACTTGGCATTA 234 chr3ptel1M 700026 TCC--TTTTCTGTCATTCTAGCCAGCATCTGACAAGTGTGAGGTGATACC 700073 --i i-- i v -- i i i i i i C L1ME5_3end#LI 233 TCCAGCTTTCTA--ATTTTTGCCAG--TCTAATAGGTGTAAAGTGATATC 188 chr3ptel1M 700074 CGAGAGTTGTTTTAATTTGCATTTCTCTTATCAATAGTGATTT 700116 iv vv v i v i v C L1ME5_3end#LI 187 TCATTGTTGTTTTAATTTGCATTTCTCTGATTACTAATGAGTT 145 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 36.51 CpG sites = 54, Kimura (unadjusted) = 39.21 Transitions / transversions = 1.42 (54/38) Gap_init rate = 0.05 (17 / 317), avg. gap size = 2.00 (34 / 17) 509 32.38 3.00 3.00 chr3ptel1M 700118 700550 (299450) L1M5_orf2#LINE/L1 2862 3294 (0) m_b127s551i11 4723 chr3ptel1M 700118 ACTGTACACCAAGATAAGGTCAAAATGGGTTCAT-GACCTAGGCATAAAG 700166 ii v i v iv ? i i - - iiii i L1M5_orf2#LIN 2862 ACCATACACAAAAATTAATTCNAGATGGAT-CATAGACCTAAATGTAAAA 2910 chr3ptel1M 700167 AATGAAATTATTAATAAATTAGAGGAACACAGGATAGTTTACCTCTCAGA 700216 i? i i v vvvvi i v viiv vv i iivv L1M5_orf2#LIN 2911 GNTAAAACTATAAAACTTCTAGAAGAAAACATAGGAGAATATCTTCGTGA 2960 chr3ptel1M 700217 CCTGTGGAAGGGGAAGGAATTTATGATCAAAGAAGAACTAGAGATCATTA 700266 vv ?vi v i v i---- i v i vvi i i v i? L1M5_orf2#LIN 2961 CCTTGGGNTAGGCAAAGATTTC----TTAAACAGGACACAAAAAGCACNA 3006 chr3ptel1M 700267 CTGATCACAAAATAGAAAATT-------TCGACTATACCAAACTGAAAAG 700309 --- i i v i ------- v ?i i v v i L1M5_orf2#LIN 3007 ---ACCATAAAAGAAAAAATTGATAAATTGGACTNCATCAAAATTAAAAA 3053 chr3ptel1M 700310 TTTTTGTACAAATAAAACTAATGCAGACAAGATTAGAAGGGAAGCAATAA 700359 i i iv ?vvv ivi vi ivi v i v i v v i i L1M5_orf2#LIN 3054 CTTCTGCTCNTCAAAAGACACCGTTAAGAAAATGAAAAGGCAAGCCACAG 3103 chr3ptel1M 700360 ACTGGGAAAATATTTTTACAGTCAAAGGTTCTGATAAAGGCCTCATTTCC 700409 ? i v v i i?vv vivv i v i v L1M5_orf2#LIN 3104 ANTGGGAGAAAATATTTGCAANACATATATCTGACAAAGGACTCGTATCC 3153 chr3ptel1M 700410 AAAATATAGAGAGAATT-----AACTCTAATTTATAAAAAATCAAGCCAT 700454 i v i i ----- ? v -- v ? iv i v i L1M5_orf2#LIN 3154 AGAATATATAAAGAACTCCTACAANTCAA--TAANAAAAAGACAAACAAC 3201 chr3ptel1M 700455 TCTCCAATTGAAAAATGGTCAAAGGATATGAACAGACGATTCTCAGAAGA 700504 --- v? v i iv iv v i L1M5_orf2#LIN 3202 ---CCAATANAAAAATGGGCAAAAGACTTGAACAGACACTTCACAAAAGA 3248 chr3ptel1M 700505 AGAAATTGAAACTATTTCTAGTCATATGAAAAGATGCTCCAAGTCA 700550 v ?v iviiivv iv i v v? L1M5_orf2#LIN 3249 AGATATNCAAATGGCCAATAAGCACATGAAAAGATGCTCAACNTCA 3294 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 43.75 CpG sites = 70, Kimura (unadjusted) = 45.08 Transitions / transversions = 1.06 (70/66) Gap_init rate = 0.04 (16 / 432), avg. gap size = 1.62 (26 / 16) 1516 30.35 2.72 1.26 chr3ptel1M 700404 701027 (298973) L1ME5_3end#LINE/L1 4 636 (305) m_b127s551i12 4723 chr3ptel1M 700404 ATTTCCAAAATATAGAGAGAATTAACTCTAATTTATAAAAAATCAAGCCA 700453 v i i v ii i vviv v iv i i -- v i L1ME5_3end#LI 4 ATATCTAGAATATACAAGGAACTCCTGCAAATCAACAAGAAA--AAGACG 51 chr3ptel1M 700454 TT--CTCCAATTGAAAAATGGTCAAAGGATATGAACAGACGATTCTCAGA 700501 v?-- i v v i i iv L1ME5_3end#LI 52 GNAACCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGA 101 chr3ptel1M 700502 AGAAGAAATTGAAACTATTTCTAGTCATATGAAAAGATGCTCCAAGTCAT 700551 i iivi vvii vvi iv i v v L1ME5_3end#LI 102 AGAGGAAACCCGAAAGGCTAACAAGCATATGAAGAGATGCTCAAACTCAT 151 chr3ptel1M 700552 TATAAATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACA 700601 vv i vv i i vi L1ME5_3end#LI 152 TAGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACA 201 chr3ptel1M 700602 CCTGTCAGATTGGCAGATGACAGGAAA--AAATAATGATGATTGTTGGAG 700649 i i i i vivi i i--ii vii v v L1ME5_3end#LI 202 CCTATTAGACTGGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTGGCG 251 chr3ptel1M 700650 GGGATGCGGGAAAACTGGGACATTGATGCATTGTTGGTGGAGTTGTGAAC 700699 i i i ? iv i vi v i i iiv ii L1ME5_3end#LI 252 AGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGAC 301 chr3ptel1M 700700 GAATCCAACCATTCTGGAGAGCAATCTGGAACTA--TGCTCAAA--AAGT 700745 vii v i v v -- iv -- L1ME5_3end#LI 302 TGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTAAGT 351 chr3ptel1M 700746 -TAT-CAAACTGTGCATACCCAGCAGTGTTACTACTGGGCTTATATCCCA 700793 - i- v iv iii- i viii v iv L1ME5_3end#LI 352 ATACGCATACCCTATG-ACCCAGCAATTCCGCTCCTGGGTATATATCCCA 400 chr3ptel1M 700794 AAGAGATCATAAAGAAGG----GAAAGGGACCTGTATGTGCACGAGTTTG 700839 i iv v viv ----v i v i v v i-- ii L1ME5_3end#LI 401 AAGAAATTCTCACACAGGTCCATAAGGGGACATGTACGAGGAT--GTTCA 448 chr3ptel1M 700840 TGGCAGCCCTGTTTGTAGTGGCTAGAAACTGGAAACTGAATGGATGTCCA 700889 v vi i vi i ii ii vivv i L1ME5_3end#LI 449 TTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGGGTGTCCA 498 chr3ptel1M 700890 TCAGTTGGAGAATGGCTGAATAAATTGTGGTATATGAAAATTATGGAATA 700939 v v i v iii v iv v v ii i L1ME5_3end#LI 499 TCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACACCATGGAGTA 548 chr3ptel1M 700940 TTACTGT-TCTGTAAGAAATGACCAACAGGATGATTTCAGAAAGGCCTGG 700988 i - i-v v v iii vi vi vviv v ivii v L1ME5_3end#LI 549 CTA-TGCAGCAGTTAGAAGCAACGGACTAGATGTACACATAGCAACATGG 597 chr3ptel1M 700989 AGAGA-CTTACACGAAC-TGATGCTGAGTGAAATGAGCAGG 701027 vi - v -- - ii vi i i L1ME5_3end#LI 598 ATGGATCTTAAA--AACATAGTGCTGAGTGAAAAAAGTAAG 636 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 38.76 CpG sites = 108, Kimura (unadjusted) = 40.18 Transitions / transversions = 1.37 (108/79) Gap_init rate = 0.03 (18 / 623), avg. gap size = 1.39 (25 / 18) 15 13.67 0.00 0.00 chr3ptel1M 701381 701404 (298596) (G)n#Simple_repeat 1 24 (0) m_b127s252i13 4726 chr3ptel1M 701381 GGGGGGGGGGGAGGGGGTGCGGGG 701404 i v v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGG 24 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 21 23.14 1.45 2.94 chr3ptel1M 701463 701531 (298469) (ATAAAA)n#Simple_repeat 1 68 (0) m_b127s252i14 4727 chr3ptel1M 701463 ATAAATATAACCTGTAAAAAAAAGGCTATTAAATAAAAATAAAAA-AAAA 701511 v -vvi v iiv -v - (ATAAAA)n#Sim 1 ATAAAAATAA-AAATAAAAATAAAAATA-AAAATAAAAATAAAAATAAAA 48 chr3ptel1M 701512 AAAAAAAAAAAAAAAGAAAT 701531 v v v i (ATAAAA)n#Sim 49 ATAAAAATAAAAATAAAAAT 68 Matrix = Unknown Transitions / transversions = 0.44 (4/9) Gap_init rate = 0.04 (3 / 68), avg. gap size = 1.00 (3 / 3) 28 8.34 0.00 0.00 chr3ptel1M 701493 701530 (298470) (A)n#Simple_repeat 1 38 (0) m_b127s252i15 4728 chr3ptel1M 701493 AAATAAAAATAAAAAAAAAAAAAAAAAAAAAAAAGAAA 701530 v v i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 38 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 704 33.84 4.32 2.33 chr3ptel1M 703207 703669 (296331) L1ME3Cz_3end#LINE/L1 76 547 (450) m_b127s551i13 4729 chr3ptel1M 703207 ATACAAACAGGCAGCTTTTAGA-GAAGAAACTAAAGCTATCTATAACCAT 703255 ii ii ivi - i ivi iivii v v L1ME3Cz_3end# 76 ATATGAACAGGCAATTCACAGAAGAGGAAACCCGAATGGCCAATAAACAT 125 chr3ptel1M 703256 CTGAGAGAATGTTCTATATCACTATTTATTAGAGAAATGAACATTAAAAC 703305 v i ii i v iv v v i i v v L1ME3Cz_3end# 126 ATGAAAAGATGCTCAACCTCACTAGTAATCAGGGAAATGCAAATTAAAAC 175 chr3ptel1M 703306 AACTCTGAAATACTA--TCACACCTATCAGATTGTCTCATAAAACAGAAA 703353 ? vv i i -- i --v v vivi L1ME3Cz_3end# 176 NACAATGAGATACCATTTCACACCCATCAGATTG--GCAAAAATTTAAAA 223 chr3ptel1M 703354 G---GAAAATAACAAATATTTGAAGGGATGGGAAAGAATTGGGATACTGA 703400 --- v v i i v vii v i ii iv i iv v L1ME3Cz_3end# 224 GTCTGACAATACCAAGTGTTGGCGAGGATGTGGAGAAACGGGAACTCTCA 273 chr3ptel1M 703401 TGCACTTTTGGTGGAGTTCTGAAATGTTTTGACCATTCTAAAGAGCAAGT 703450 i vi iiv v i v v vii i i ii v L1ME3Cz_3end# 274 TACACTGCTGGTGGGAGTGTAAATTGGTACAACCACTTTGGAGAGCAATT 323 chr3ptel1M 703451 TAAAATTATGTCCAATGGTCTATAAAACTATCCATATCCTTTGATCCACC 703500 iiv -- i i i iivv - i iv iiv i vi i v L1ME3Cz_3end# 324 TGGCA--ATATCTAGTAAAGT-TGAAGATGCGCATACCCTACGACCCAGC 370 chr3ptel1M 703501 AATATCTCTGCTAAGTCTGTATCTCAGA-------TCAAAAA---GAAGA 703540 vi v v i v i i ii ------- iv v --- v v L1ME3Cz_3end# 371 AATTCCACTTCTAGGTATATACCCTAGAGAAACTCTCGCACATGTGCACA 420 chr3ptel1M 703541 AAGAGTCCATTTGTACAAAGATATCTATATTTGCCCTTTTTGTAGTGGCA 703590 i --- iv i i ii vviv vi v i i i L1ME3Cz_3end# 421 AGGAG---ACATGTACAAGGATGTTCATTGCAGCATTGTTTGTAATAGCG 467 chr3ptel1M 703591 AACAATTGGACA----TTGAGGGGTATCCATCAAGTGGGAAATGGTTAAA 703636 v v ----i i ---i i vv i v L1ME3Cz_3end# 468 AAAAATTGGAAACAACCTAA---ATGTCCATCAATAGGGGAATGGATAAA 514 chr3ptel1M 703637 CAAGTTGTGATATGTGATTGTAATGTAATATTA 703669 i i i i vvv ii v i L1ME3Cz_3end# 515 TAAATTGTGGTATATTCATACAATGGAATACTA 547 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 43.95 CpG sites = 90, Kimura (unadjusted) = 46.89 Transitions / transversions = 1.43 (90/63) Gap_init rate = 0.04 (17 / 462), avg. gap size = 1.82 (31 / 17) 438 34.86 5.57 3.57 chr3ptel1M 703254 703720 (296280) L1MA5_3end#LINE/L1 128 603 (444) m_b127s551i14 4729 chr3ptel1M 703254 ATCTGAGAGAATGTTCTATATCACTATTTATTAGAGAAATGAACATTAAA 703303 v i i i v i v i i i v v i L1MA5_3end#LI 128 ATATGAAAAAATGCTCAACATCACTAATCATCAGGGAAATGCAAATCAAA 177 chr3ptel1M 703304 ACAACTCTGAAATACTATCACACCT--ATCAGATTG--TCTCATAAAACA 703349 v vv i ii v i--i i v -- v i v v L1MA5_3end#LI 178 ACCACAATGAGATATCATCTCACCCCAGTTAGAATGGCTATTATCAAAAA 227 chr3ptel1M 703350 GAAAGGAAAATAACAAATATTTGAAGGGATGGGAAAGAATTGGGATACTG 703399 v i- ii v vii v i ii vv i iv v L1MA5_3end#LI 228 GACAA-AAAATAACAAATGCTGGCGAGGATGCGGAGAAAAGGGAACTCTT 276 chr3ptel1M 703400 ATGCACTTTTGGTGGAGTTCTGAAATGTTTTGACCATTCTAAAGAGCAAG 703449 i v iiv v i v iv viii v ii i i iv L1MA5_3end#LI 277 ATACACTGTTGGTGGGAATGTAAATTAGTACAGCCATTATGGAAAACAGT 326 chr3ptel1M 703450 TTAAAATTATGTCCAATGGTCT----ATAAAACTATCCATATCCTTTGAT 703495 v ii iv - vii viiv ---- i - ----- L1MA5_3end#LI 327 ATGGAGGT-TCCTCAAAAAACTAAAAATAGAACTA-CCATA-----TGAT 369 chr3ptel1M 703496 CCACCAATATCTCTGCTAAGTCTGTATCTCAGATCAAAAAGAAGAAAGAG 703545 v vi v i ii v ? ------ iii i -- i L1MA5_3end#LI 370 CCAGCAATCCCACTACTGGGTATNTATC------CAAAGGAAAGGA--AA 411 chr3ptel1M 703546 TCCATTTGT-ACAAAGATATCTATATTTGCCCTTTTTGTAGTGGCA---- 703590 vi v -iv i ii i i- v v i v ii ---- L1MA5_3end#LI 412 TCAGTATGTCGAAGAGATATCTGCACTC-CCATGTTTATTGCAGCACTAT 460 chr3ptel1M 703591 -AACAATTG----GACATTGAG-------GGGTATCCATCAAGTGGGAAA 703628 -v v ---- i v i-------ii i vv ivi L1MA5_3end#LI 461 TCACAATAGCCAAGATATGGAATCAACCTAAGTGTCCATCAACAGATGAA 510 chr3ptel1M 703629 TGGTTAAACAAGTTGTGATATGTGATTGTAATGTAATATTACTGTGCTTT 703678 v v iv i i ivviii v i i vv iv L1MA5_3end#LI 511 TGGATAAAGAAAATGTGGTATATATACACAATGGAATACTATTCAGCCAT 560 chr3ptel1M 703679 AAAAAATACGGGAAGGCTATT-TTCAGAAAAACCTGGAAGGGC 703720 v vv i vv i i- iviiv v v i L1MA5_3end#LI 561 AAAAAAGAATGAAATCCTGTCATTCGCGGCAACATGGATGAGC 603 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 46.97 CpG sites = 89, Kimura (unadjusted) = 48.71 Transitions / transversions = 1.31 (89/68) Gap_init rate = 0.06 (26 / 466), avg. gap size = 1.65 (43 / 26) 42 0.00 0.00 0.00 chr3ptel1M 704373 704408 (295592) (TG)n#Simple_repeat 1 36 (0) c_b128s251i0 4730 chr3ptel1M 704373 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 704408 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 36 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 18 35.24 0.00 0.00 chr3ptel1M 704411 704475 (295525) (TG)n#Simple_repeat 1 65 (0) m_b128s252i1 4730 chr3ptel1M 704411 TGTGCATGTGCGCATGTGCATGTGCATGTGTGTGTGTGTGAGAGAGAGGG 704460 ii i ii ii ii v v v v v (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr3ptel1M 704461 AGAGAGTGTGTATGT 704475 v v v i (TG)n#Simple_ 51 TGTGTGTGTGTGTGT 65 Matrix = Unknown Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0) 20 6.24 0.00 5.56 chr3ptel1M 704409 704446 (295554) (CATGTG)n#Simple_repeat 1 36 (0) m_b128s252i0 4731 chr3ptel1M 704409 CATGTGCATGTGCGCATGTGCATGTGCATGTGTGTGTG 704446 -- ii (CATGTG)n#Sim 1 CATGTGCATGT--GCATGTGCATGTGCATGTGCATGTG 36 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 42 0.00 0.00 0.00 chr3ptel1M 704373 704408 (295592) (TG)n#Simple_repeat 1 36 (0) c_b128s251i0 4730 chr3ptel1M 704373 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 704408 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 36 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 18 35.24 0.00 0.00 chr3ptel1M 704411 704475 (295525) (TG)n#Simple_repeat 1 65 (0) m_b128s252i1 4730 chr3ptel1M 704411 TGTGCATGTGCGCATGTGCATGTGCATGTGTGTGTGTGTGAGAGAGAGGG 704460 ii i ii ii ii v v v v v (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr3ptel1M 704461 AGAGAGTGTGTATGT 704475 v v v i (TG)n#Simple_ 51 TGTGTGTGTGTGTGT 65 Matrix = Unknown Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0) 432 29.21 5.08 6.15 chr3ptel1M 704556 704752 (295248) MIRb#SINE/MIR 4 198 (70) m_b128s601i0 4732 chr3ptel1M 704556 AAGGGCAGCCAGATGGTGCAGTAGATAGGATCCCTGCCT-GGAATTAGAA 704604 i ---i i v iiiv vv i - i i v MIRb#SINE/MIR 4 AGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGAC 50 chr3ptel1M 704605 AGACTCATTTTCCTGAGTTCAAGCCCAGCCTCAGACACTT-CTAGCTGTA 704653 -------- i i ii v v v v - i MIRb#SINE/MIR 51 AGAC--------CTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTG 92 chr3ptel1M 704654 TGTCGCTGGGCAAGTCACTTAGCACTGTTT--TCCTCAGTTCCCTCCTCT 704701 v vi i i - v i --v i v MIRb#SINE/MIR 93 TGACCTTGGGCAAGTTACTTAAC-CTCTCTGAGCCTCAGTTTCCTCATCT 141 chr3ptel1M 704702 ATATTAATGGATTAAGAAGAGTTA------AACAATGTTGAAATGATTGA 704745 i vv vv iv v v vi ------ iviv vi v i MIRb#SINE/MIR 142 GTAAAATGGGGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAA 191 chr3ptel1M 704746 ATAACAT 704752 i v MIRb#SINE/MIR 192 ATGAGAT 198 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.73 CpG sites = 27, Kimura (unadjusted) = 37.43 Transitions / transversions = 1.00 (27/27) Gap_init rate = 0.08 (16 / 196), avg. gap size = 1.38 (22 / 16) 465 20.92 4.00 7.59 chr3ptel1M 704562 704711 (295289) MIRc#SINE/MIR 3 147 (121) m_b128s601i1 4732 chr3ptel1M 704562 AGCCAG-ATGGTGCAGTAGATAGGATCCCTG--CCTGGAATTAGAAAGAC 704608 v -i i - i v v -- i i i i MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGA-AAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr3ptel1M 704609 TCATTTTCCTGAGTTCAAGCCCAGCCTCAGACACTT-CTAGCTGTATGTC 704657 -------- i i i v v v v - i v MIRc#SINE/MIR 52 --------CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGAC 93 chr3ptel1M 704658 GCTGGGCAAGTCACTTAGCACTGTTT--TCCTCAGTTCCCTCCTCTATAT 704705 vi i - v i --v i v i - MIRc#SINE/MIR 94 CTTGGGCAAGTCACTTAAC-CTCTCTGAGCCTCAGTTTCCTCATCTGTA- 141 chr3ptel1M 704706 TAATGG 704711 v MIRc#SINE/MIR 142 AAATGG 147 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 23.79 CpG sites = 16, Kimura (unadjusted) = 24.74 Transitions / transversions = 1.23 (16/13) Gap_init rate = 0.10 (15 / 149), avg. gap size = 1.13 (17 / 15) 259 27.79 4.68 5.29 chr3ptel1M 704758 704928 (295072) L2#LINE/L2 2445 2614 (468) m_b128s601i2 4733 chr3ptel1M 704758 AACATCTCCAAATTTGAATTCATTGTCTTTATTCTTGAGCCTTCCCAGCT 704807 v vi i v vi ivii ii i v i -- L2#LINE/L2 2445 AACATGTCCAAAACTGAACTCCTGATCTTCCCCCTCAAACCTGCTC--CT 2492 chr3ptel1M 704808 TCCTTA-TCTTCCTTAT-TATTTAAAAGGCA-----ATCCTCCCACTTCC 704850 i vi - ii - vvv ? v ----- i v v L2#LINE/L2 2493 CCCGCAGTCTTCCCCATCTCAGTNAATGGCAACTCCATCCTTCCAGTTGC 2542 chr3ptel1M 704851 CCAGGCTCCCAAACTAAGAGTCA-CCTGGACTTCTCACTATCTCTCAACC 704899 i ivvv v vi - v i v v -- L2#LINE/L2 2543 TCAGGCCAAAAACCTTGGAGTCATCCTTGACTCCTCTCTTTCTCTCA--C 2590 chr3ptel1M 704900 ACCTCCCTCCCCATCTAATCTATTACCAA 704928 ----- v i i i v L2#LINE/L2 2591 ACC-----CCACATCCAATCCATCAGCAA 2614 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.32 CpG sites = 22, Kimura (unadjusted) = 35.32 Transitions / transversions = 0.96 (22/23) Gap_init rate = 0.08 (13 / 170), avg. gap size = 1.31 (17 / 13) 342 28.05 0.00 1.22 chr3ptel1M 706233 706315 (293685) L2c_3end#LINE/L2 391 472 (6) m_b128s601i3 4733 chr3ptel1M 706233 AGAGCAAGGGCTAGCTTTTGCTGTTCTTTGTGATCTCCAGCTCCTGGGAC 706282 i i i iivv i ii vv - i v v L2c_3end#LINE 391 AGGGCAGGGACCGTGTCTTATTCATCTTTGT-ATCCCCAGCGCCTGGCAC 439 chr3ptel1M 706283 ACAGTAGGTGCTTAATAAATACTCATTGACTGA 706315 i i i ii ii v L2c_3end#LINE 440 ATAGTAGGCGCTCAATAAATGTTTGTTGAATGA 472 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.72 CpG sites = 16, Kimura (unadjusted) = 36.96 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.01 (1 / 82), avg. gap size = 1.00 (1 / 1) 478 25.88 1.31 4.03 chr3ptel1M 707691 707843 (292157) C MIR1_Amn#SINE/MIR (62) 168 20 m_b128s601i4 4734 chr3ptel1M 707691 GAGGTGCCATTTCCTTCTCCAGCTCATTTGACAGATGCAGAAACTGGGGC 707740 - vi v v v ---i v vi i C MIR1_Amn#SINE 168 GAGGT-CAGTATCATTATCC---CCATTTTACAGATGAGGAAACTGAGGC 123 chr3ptel1M 707741 A-AACAAAGTGAAGTGACTTGCCCAGGATGACACAGCTAG-GAATGATCC 707788 ?- ivi i ? i i v ? ?i -? i i- v C MIR1_Amn#SINE 122 NCAGAGAGGTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNAGTGG-CA 74 chr3ptel1M 707789 AAGGCTGGATTTGAACTCGGACCTTCCCAACTCCAGATCTGGCACCCTAT 707838 i v v ? ? i i ii i v iii - ii ii i C MIR1_Amn#SINE 73 GAGCCGGGANTNGAACCCAGGTCTCCCGAGTCCCAG-TCCAGTGCTCTAT 25 chr3ptel1M 707839 CCACT 707843 C MIR1_Amn#SINE 24 CCACT 20 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.25 CpG sites = 26, Kimura (unadjusted) = 35.25 Transitions / transversions = 2.17 (26/12) Gap_init rate = 0.05 (8 / 152), avg. gap size = 1.00 (8 / 8) 427 26.14 1.97 6.90 chr3ptel1M 707713 707864 (292136) C MIR3#SINE/MIR (63) 145 1 m_b128s601i6 4734 chr3ptel1M 707713 CTCATTTGACAGATGCAGAAACTGGGGCA-AACAAAGTGAAGTGACTTGC 707761 v vi i v- ivi i C MIR3#SINE/MIR 145 CTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGC 96 chr3ptel1M 707762 CCAGGATGACACAGCTAG-GAATGATCCAAGGCTGGATTTGAACTCGGAC 707810 i i v ? -v i i- vi v v i v i i ii C MIR3#SINE/MIR 95 CCAAGGTCACACAGCNAGTTAGTGG-CAGAGCCGGGACTAGAACCCAGGT 47 chr3ptel1M 707811 CTTCCCAACTCCAGATCTG-GCACCCTATCCACTGCTTCCTAGCAAGTCT 707859 - ii vii i - v i ----- ---i v v C MIR3#SINE/MIR 46 C-TCCTGACTCCCAGTCCGTGCTCTCT-----CTGCT---CAGCCACTCT 6 chr3ptel1M 707860 GTCAG 707864 i C MIR3#SINE/MIR 5 GCCAG 1 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.15 CpG sites = 23, Kimura (unadjusted) = 33.25 Transitions / transversions = 1.64 (23/14) Gap_init rate = 0.09 (13 / 151), avg. gap size = 1.00 (13 / 13) 538 29.32 0.75 0.00 chr3ptel1M 707713 707845 (292155) C MIRc#SINE/MIR (120) 148 15 m_b128s601i5 4734 chr3ptel1M 707713 CTCATTTGACAGATGCAGAAACTGGGGCA-AACAAAGTGAAGTGACTTGC 707761 i v vi i v- ivi i v C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr3ptel1M 707762 CCAGGATGACACAGCTAGGAATGATCCAAGGCTGGATTTGAACTCGGACC 707811 i i v v vviv vi v v i i i i ii C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTC 49 chr3ptel1M 707812 TTCCCAACTCCAGATCTGGCACCCTATCCACTGC 707845 ii ii ii ii i v C MIRc#SINE/MIR 48 TTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGC 15 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.43 CpG sites = 25, Kimura (unadjusted) = 38.72 Transitions / transversions = 1.79 (25/14) Gap_init rate = 0.01 (1 / 132), avg. gap size = 1.00 (1 / 1) 194 36.20 2.52 2.52 chr3ptel1M 707922 708040 (291960) L3#LINE/CR1 3239 3357 (742) m_b128s601i7 4735 chr3ptel1M 707922 GGAAAAGCTGACAAACTTACTGACAGAATCGGGGTCCTAAA-GTTGCCTA 707970 i v i i vi? viv ii i i v - v vi v L3#LINE/CR1 3239 GGGATAGCTAATACGNTGGATGACAGAATCAAGATTCAAAANGATCTCGA 3288 chr3ptel1M 707971 GTGGCAATCAAACATTAGACTGATGCTAAGAAGGAGATGTTTAACGGGGG 708020 vv -- vi iv i i i vi i v iv vi i i L3#LINE/CR1 3289 CAGGC--TGGAACGATGGGCCGAAACCAACAAGATGAAATTTAACAGGGA 3336 chr3ptel1M 708021 TCAGTCTGA--TCCTTCTATTT 708040 v i v i -- v - L3#LINE/CR1 3337 TAAATGTAAAGTCCTGC-ATTT 3357 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.55 CpG sites = 23, Kimura (unadjusted) = 51.67 Transitions / transversions = 1.21 (23/19) Gap_init rate = 0.04 (5 / 118), avg. gap size = 1.20 (6 / 5) 225 31.02 0.00 7.45 chr3ptel1M 708279 708379 (291621) L2c_3end#LINE/L2 382 475 (3) m_b128s601i8 4736 chr3ptel1M 708279 AGTCTCTTGAGGGCAGGAAATGCTTTCCTTTTTTCATGTATTAGGATTCC 708328 iii i vi - v -- v v v -- v i L2c_3end#LINE 382 AGCTCCTTGAGGGCAGGGACCG-TGTC--TTATTCATCTTT--GTATCCC 426 chr3ptel1M 708329 CACCACTTAAGGCACGCGATAAGTGCTTAATAAGGGCCTGTTGATTTTAT 708378 v i i -- iiii i i i iv ii v vv L2c_3end#LINE 427 CAGCGCCT--GGCACATAGTAGGCGCTCAATAAATGTTTGTTGAATGAAT 474 chr3ptel1M 708379 G 708379 L2c_3end#LINE 475 G 475 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.89 CpG sites = 18, Kimura (unadjusted) = 41.32 Transitions / transversions = 1.64 (18/11) Gap_init rate = 0.07 (7 / 100), avg. gap size = 1.00 (7 / 7) 241 25.69 2.60 3.95 chr3ptel1M 708880 708956 (291044) MIRc#SINE/MIR 2 77 (191) m_b128s601i9 4737 chr3ptel1M 708880 GAGGCAGGGAGGTGAGGTAGCATCTGGAATACTGGGCCTGGAGTCAGGAA 708929 v v vi i v ---i ii i i MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAA---AGAGCACTGGACTTGGAGTCAGGAA 48 chr3ptel1M 708930 CACCTGAG--CAAATCCAGCCTCAGCTAC 708956 v i -- i i v v v i MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCCAC 77 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.08 CpG sites = 11, Kimura (unadjusted) = 32.08 Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.05 (4 / 76), avg. gap size = 1.25 (5 / 4) 370 27.41 0.90 4.67 chr3ptel1M 708947 709057 (290943) MIRb#SINE/MIR 134 240 (28) m_b128s601i10 4738 chr3ptel1M 708947 CCTCAGCTACAGTTGGGGCGATAATAGCTCTCATCTCTCTGGGTTGCTGT 708996 v ii ivvv - iiv ii i v v i MIRb#SINE/MIR 134 CCTCATCTGTAAAATGGG-GATAATAATACCTACCTCGCAGGGTTGTTGT 182 chr3ptel1M 708997 GAAGACCCAGTGAGACAATATTTGTACAAAGTGCTTAATGCACAGTGCC- 709045 i iiv i i iiv -- i -- - MIRb#SINE/MIR 183 GAGGATTAAATGAGATAATGCATGT--AAAGCGCTTA--GCACAGTGCCT 228 chr3ptel1M 709046 AGCACATGGTGA 709057 i i i MIRb#SINE/MIR 229 GGCACATAGTAA 240 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.12 CpG sites = 20, Kimura (unadjusted) = 35.67 Transitions / transversions = 2.22 (20/9) Gap_init rate = 0.05 (6 / 110), avg. gap size = 1.00 (6 / 6) 21 5.94 0.00 5.41 chr3ptel1M 709357 709395 (290605) (TCTGTT)n#Simple_repeat 1 37 (0) m_b128s252i2 4739 chr3ptel1M 709357 TCTGTTTCTGTTTTTCTGTTTCTTTCTCTGTTTCTGTTT 709395 -- v i (TCTGTT)n#Sim 1 TCTGTTTCTG--TTTCTGTTTCTGTTTCTGTTTCTGTTT 37 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2) 31 9.11 0.00 0.00 chr3ptel1M 709397 709443 (290557) (TCTG)n#Simple_repeat 1 47 (0) c_b128s251i1 4740 chr3ptel1M 709397 TCTGTCTGTCTGTCTCTCTCTCTCTCTCTCTGTCTGTCTGTCTGTCT 709443 v v v v (TCTG)n#Simpl 1 TCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCT 47 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 190 32.57 15.65 3.91 chr3ptel1M 709738 709852 (290148) C L2a_3end#LINE/L2 (1) 516 389 m_b128s601i11 4741 chr3ptel1M 709738 TTCATTCGGTCCAAGCAGCATTTATTAAGCACCCACTTATTGTGTGCCA- 709786 i- i vv ii i i ---- i i - C L2a_3end#LINE 516 TTCATTCA-TTCAACAAATATTTATTGAGCGCC----TACTATGTGCCAG 472 chr3ptel1M 709787 ----------AAACACTGGAGACACGG-GGT------AACCACCAGCAGC 709819 ---------- ii i i i i -i ------ viv iv i C L2a_3end#LINE 471 GCACTGTTCTAGGCGCTGGGGATACAGCAGTGAACAAAACAGACAAAAGT 422 chr3ptel1M 709820 CCCTGCTTGGAAGGAACGGATATCTTCCTGGGG 709852 iivv v i vv i ii vv C L2a_3end#LINE 421 CCCTGCCCTCATGGAGCTTACATTCTAGTGGGG 389 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.10 CpG sites = 24, Kimura (unadjusted) = 45.58 Transitions / transversions = 2.00 (24/12) Gap_init rate = 0.08 (9 / 114), avg. gap size = 2.56 (23 / 9) 235 32.34 2.02 6.32 chr3ptel1M 709738 709836 (290164) C L2c_3end#LINE/L2 (1) 477 383 m_b128s601i12 4741 chr3ptel1M 709738 TTCATTCGGTCCAAGCAGCATTTATTAAGCACCCACTTATTGTGTGCCAA 709787 i- i vv i i i ---- i i - C L2c_3end#LINE 477 TTCATTCA-TTCAACAAACATTTATTGAGCGCC----TACTATGTGCC-A 434 chr3ptel1M 709788 AACACTGGAGACAC-GGGGTAACCACCA-GCAGCCCCTGCTTGGAAGGAA 709835 ii i i i -ii i i vi vv -i i i iivv i C L2c_3end#LINE 433 GGCGCTGGGGATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAG 384 chr3ptel1M 709836 C 709836 C L2c_3end#LINE 383 C 383 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.93 CpG sites = 23, Kimura (unadjusted) = 46.26 Transitions / transversions = 3.29 (23/7) Gap_init rate = 0.08 (8 / 98), avg. gap size = 1.00 (8 / 8) 201 28.77 5.48 0.00 chr3ptel1M 710115 710187 (289813) C MIR3#SINE/MIR (31) 177 101 m_b128s601i13 4742 chr3ptel1M 710115 AGGGGGCCTCCGAGGGCCTCAGGAC--GCCCCCTCATTTTACTGAGGAG- 710161 i i iv iv v vi v --i v v - C MIR3#SINE/MIR 177 AAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGG 128 chr3ptel1M 710162 -AGCTGGGACTCAGAAAGGGGCAGGGA 710187 - i i i i i v v v C MIR3#SINE/MIR 127 AAACTGAGGCCCAGAGAGGTGAAGTGA 101 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.85 CpG sites = 11, Kimura (unadjusted) = 36.85 Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.04 (3 / 72), avg. gap size = 1.33 (4 / 3) 12 5.56 0.00 0.00 chr3ptel1M 710400 710418 (289582) (GGA)n#Simple_repeat 1 19 (0) m_b128s252i3 4743 chr3ptel1M 710400 GGAGGAGGAGGAGGGGGAG 710418 i (GGA)n#Simple 1 GGAGGAGGAGGAGGAGGAG 19 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 81 24.18 2.26 0.89 chr3ptel1M 713412 713632 (286368) (GTGA)n#Simple_repeat 1 224 (0) m_b128s252i4 4744 chr3ptel1M 713412 GTGAAAGAGGGAGGGCATGAG-G-GAGAGTGAGTGAATGAGTGAGGAAAT 713459 iv v v vi - - v i vi i (GTGA)n#Simpl 1 GTGAGTGAGTGAGTGAGTGAGTGAGTGAGTGAGTGAGTGAGTGAGTGAGT 50 chr3ptel1M 713460 GAATGAATAAATGAGTGAGTGAGTGAATGAATCAGTGAATTAATGAGTGA 713509 i i i i i i v i v i (GTGA)n#Simpl 51 GAGTGAGTGAGTGAGTGAGTGAGTGAGTGAGTGAGTGAGTGAGTGAGTGA 100 chr3ptel1M 713510 GTGAATGAGT-AGATGAATGAATTTGTGAGTGAATGAAGGAGTAAATTAA 713558 i - - i i vv i iv i i v i (GTGA)n#Simpl 101 GTGAGTGAGTGAG-TGAGTGAGTGAGTGAGTGAGTGAGTGAGTGAGTGAG 149 chr3ptel1M 713559 TGAGTGAGTG-GTGAGTAAGTGAATGAGTAAATGAGGGAGTAAATGATTA 713607 - i i i i v i i v i (GTGA)n#Simpl 150 TGAGTGAGTGAGTGAGTGAGTGAGTGAGTGAGTGAGTGAGTGAGTGAGTG 199 chr3ptel1M 713608 AGCGAGTGAGTGAGT-AGATGAGAGA 713632 i - - v (GTGA)n#Simpl 200 AGTGAGTGAGTGAGTGAG-TGAGTGA 224 Matrix = Unknown Transitions / transversions = 1.93 (29/15) Gap_init rate = 0.03 (7 / 220), avg. gap size = 1.00 (7 / 7) 259 27.52 2.41 3.66 chr3ptel1M 714700 714782 (285218) MIR3#SINE/MIR 101 182 (26) m_b128s601i14 4745 chr3ptel1M 714700 TTACTTAACCCCAGCTCTGGGTCTCAGTTTCCTAGTTTGTGAAA-GGGGA 714748 i v i --- i vi i i - i i MIR3#SINE/MIR 101 TCACTTCACCTC---TCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGG 147 chr3ptel1M 714749 GGTCCCA-TGGATGCCCTCTGTGACCTCATCCAGC 714782 ivv - i vi iv ii i v MIR3#SINE/MIR 148 GGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGC 182 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.85 CpG sites = 15, Kimura (unadjusted) = 35.85 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.06 (5 / 82), avg. gap size = 1.00 (5 / 5) 94 20.77 0.00 0.00 chr3ptel1M 714885 715072 (284928) (ATGA)n#Simple_repeat 1 188 (0) m_b128s252i5 4746 chr3ptel1M 714885 ATGAATGAGTAAATTAAAGAGTGAGTGAGTGAATGAATGAATGAATGAAT 714934 i i v v i i i (ATGA)n#Simpl 1 ATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAAT 50 chr3ptel1M 714935 GAGTAAATGAGTGAATAAATGAGTGAATGAATAAGTGAATGAGTGAGTGA 714984 i i i i i i i i i (ATGA)n#Simpl 51 GAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGA 100 chr3ptel1M 714985 ATGAATGAGGAAATGAATGAATGAATGAGGGAATGAATGAATAAGTGGGT 715034 ivi iv i i ii (ATGA)n#Simpl 101 ATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAAT 150 chr3ptel1M 715035 GAATGAGTGAGTGAGTGAATGAAAGAGTATATTAATGA 715072 i i i v i iv v (ATGA)n#Simpl 151 GAATGAATGAATGAATGAATGAATGAATGAATGAATGA 188 Matrix = Unknown Transitions / transversions = 3.71 (26/7) Gap_init rate = 0.00 (0 / 187), avg. gap size = 0.0 (0 / 0) 318 23.68 17.54 0.00 chr3ptel1M 715753 715866 (284134) MIR1_Amn#SINE/MIR 26 159 (71) m_b128s601i15 4747 chr3ptel1M 715753 TAGAATATGGGGGGGGGGC---GGAGATCTGAATTCAAATGTTG-CTTTA 715798 ii iv ivv i --- i ii ? ? vii - i i MIR1_Amn#SINE 26 TAGAGCACTGGACTGGGACTCGGGAGACCTGGGTTCNANTCCCGGCTCTG 75 chr3ptel1M 715799 GTACTTAC--------------TGGGCAAGTCAC--AACCTCTGTCTACT 715832 vi ?i -------------- --? v v?i i MIR1_Amn#SINE 76 CCACTNGCCNGCTGNGTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCC 125 chr3ptel1M 715833 TCTGTTTCCTTATCTGTAAAATGGGAATAATAAT 715866 v i i i MIR1_Amn#SINE 126 TCAGTTTCCTCATCTGTAAAATGGGGATAATGAT 159 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.97 CpG sites = 19, Kimura (unadjusted) = 31.38 Transitions / transversions = 2.38 (19/8) Gap_init rate = 0.04 (4 / 113), avg. gap size = 5.00 (20 / 4) 425 21.87 21.18 0.49 chr3ptel1M 715772 715941 (284059) MIRc#SINE/MIR 46 250 (18) m_b128s601i16 4747 chr3ptel1M 715772 GGAGATCTGAATTCAAATGTTG-CTTTAGTACTTACT------------- 715807 i i ii i i vii - i ivi ------------- MIRc#SINE/MIR 46 GAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCT 95 chr3ptel1M 715808 -GGGCAAGTCAC--AACCTCTGTCTACTTCTGTTTCCTTATCTGTAAAAT 715854 - -- v vvi i v i MIRc#SINE/MIR 96 TGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAAT 145 chr3ptel1M 715855 GGGAATAATAATTACCTG---TGC---------AATATTGATGCGAGGAA 715892 i - --- --------- ivi v i v MIRc#SINE/MIR 146 GGGGATAATAAT-ACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGAT 194 chr3ptel1M 715893 CAGATGAGATATT-CAT---AAAGCATTTTGTAAATT---TAGTGTTCTA 715935 i v -i --- ii i ---v i v MIRc#SINE/MIR 195 CAAATGAGATAATGTATGTGAAAGCGCTTTGTAAACTGTAAAGTGCTATA 244 chr3ptel1M 715936 TAAATG 715941 i MIRc#SINE/MIR 245 CAAATG 250 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 24.22 CpG sites = 25, Kimura (unadjusted) = 26.68 Transitions / transversions = 2.08 (25/12) Gap_init rate = 0.06 (10 / 169), avg. gap size = 3.70 (37 / 10) 13 10.03 0.00 0.00 chr3ptel1M 716179 716200 (283800) (TCC)n#Simple_repeat 1 22 (0) m_b128s252i6 4748 chr3ptel1M 716179 TCCTCTCCCTCCTCCTCCTCCT 716200 ii (TCC)n#Simple 1 TCCTCCTCCTCCTCCTCCTCCT 22 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 63 31.72 1.20 2.43 chr3ptel1M 716595 716844 (283156) (CCCT)n#Simple_repeat 1 247 (0) m_b128s252i7 4749 chr3ptel1M 716595 CCCTCCCTTTCCACCTGCCTGCCTTCTCCCCTCCCTCTCTCCCTCCCTCT 716644 ii iv v v i ii i - (CCCT)n#Simpl 1 CCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTC- 49 chr3ptel1M 716645 CATCTTCCCCCTTCTTCTGTCCCTTCTTCCCCTTCAT-CCTCTCTGATTT 716693 v -i i i i iv i i - i v - i vvi i (CCCT)n#Simpl 50 CCTC-CCTCCCTCCCTCCCTCCCTCCCT-CCCTCCCTCCCTCCCTCCCTC 97 chr3ptel1M 716694 CTTCCTTCCCTCTCATCCTCCCT-CTTCTCTCCTTCCCTCCCTCTCATCC 716742 i i i vi - i i i i vi (CCCT)n#Simpl 98 CCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCC 147 chr3ptel1M 716743 TTTATCTCTCCCCTGCCTTCTTCCCTCCCTCCCTCCTTCGGTCCTTTCCC 716792 iiv i - v i i i vv i i i (CCCT)n#Simpl 148 TCCCTCCCT-CCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCT 196 chr3ptel1M 716793 ACCTTCTTTCCTCCCTCTGTCCTTCCATCCCTCCCTTTCCCTGACT-CCT 716841 v i i i iv i v -- vv - (CCCT)n#Simpl 197 CCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCC--TCCCTCCCTCCCT 244 chr3ptel1M 716842 CCC 716844 (CCCT)n#Simpl 245 CCC 247 Matrix = Unknown Transitions / transversions = 2.16 (41/19) Gap_init rate = 0.04 (9 / 249), avg. gap size = 1.00 (9 / 9) 638 32.86 4.93 0.79 chr3ptel1M 718554 718918 (281082) L1PA17_3end#LINE/L1 1 380 (533) m_b128s551i1 4750 chr3ptel1M 718554 CTCATTTCTCAAATATATAGAAAACTGAGTCAAATTCATTAAAATATGAA 718603 v v ivi v iii v iv - vi i v vi L1PA17_3end#L 1 CTAATATCCAGAATCTATAAGGAACTTAAACAAAT-CAACAAGAAAAAAA 49 chr3ptel1M 718604 GTCATTTCTCAATTGACAAATGATCAAAGGCTACAAACAGGCAGTTTTCA 718653 vvv vv i v i v i iv vi ii i v i L1PA17_3end#L 50 CAAATAACCCCATTAAAAAGTGGGCAAAGGACATGAACAGACACTTCTCA 99 chr3ptel1M 718654 GG----------CAAACTATCTATAGTCATATGAAAAAAT----AAC--T 718687 ii---------- i vii v i iv ---- --i L1PA17_3end#L 100 AAAGAAGACATACAAGCGGCCAACAAACATATGAAAAAATGCTCAACATC 149 chr3ptel1M 718688 ACTGATCCTC-GAGAAATGCACATTAAAACAGCTCTGAGGTGCCACCTCA 718736 i v - v i vi vv i i i L1PA17_3end#L 150 ACTAATCATCAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTCA 199 chr3ptel1M 718737 CATCAATCAGATTAGCTCATATGACAAAAAAGAAAAATGTGAGATGTTGG 718786 i i v i vv v v ivvi ivv L1PA17_3end#L 200 CACCAGTCAGAATGGCTATTATTAAAAAGTCAAAAAATAACAGATGTTGG 249 chr3ptel1M 718787 AAGGGATGGGGAAAACTGGG-ACACTTATGCACTGTTAGTGGAGTTGTGG 718835 vii ? v i vv - i i i iiv ii L1PA17_3end#L 250 CGAGGNTGCGGAGAAAAGGGAACGCTTATACACTGTTGGTGGGAATGTAA 299 chr3ptel1M 718836 ATTTGTCCAACCATTCTGGAGAACAACTTGGAACTAAGCCCAAAGGGCCA 718885 v i i vi v i i ii iv -vv i ii i L1PA17_3end#L 300 ATTAGTTCAGCCCCTGTGGAAAGCAGTTTGGAGAT-TTCTCAAAGAACTA 348 chr3ptel1M 718886 TAAAACCAAGCATTCACTCTGCCCAACAATACC 718918 - ivi i vvi i vi i v L1PA17_3end#L 349 -AAAATAGAACTACCATTCGACCCAGCAATCCC 380 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 43.68 CpG sites = 67, Kimura (unadjusted) = 44.70 Transitions / transversions = 1.29 (67/52) Gap_init rate = 0.02 (8 / 364), avg. gap size = 2.62 (21 / 8) 11 18.70 4.35 4.35 chr3ptel1M 720878 720923 (279077) (CGGGGA)n#Simple_repeat 1 46 (0) m_b128s252i8 4751 chr3ptel1M 720878 CGGGGAC-GGAACGGGG-CTGGACCGGGGTCACGGCCCCGGGGACGGG 720923 - i - v iv -- vvv (CGGGGA)n#Sim 1 CGGGGACGGGGACGGGGACGGGGACGGGG--ACGGGGACGGGGACGGG 46 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.09 (4 / 45), avg. gap size = 1.00 (4 / 4) 27 21.11 3.41 3.41 chr3ptel1M 721196 721283 (278717) (CTC)n#Simple_repeat 1 88 (0) m_b128s252i9 4752 chr3ptel1M 721196 CTCCTCCGCAGCTCC-CC-CCGCGTCTTCC-GCTTCTCCTCCTCCTCCTC 721242 v -- - - v v i -v i (CTC)n#Simple 1 CTCCTCCTC--CTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC 48 chr3ptel1M 721243 CTCCCTCTTCCCGGTCCTCCTTCCCTTTCTCCCCCTCCTCC 721283 - i ivv i i i i i (CTC)n#Simple 49 CT-CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC 88 Matrix = Unknown Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.07 (6 / 87), avg. gap size = 1.00 (6 / 6) 215 29.60 2.25 0.14 chr3ptel1M 721471 722182 (277818) (CTCT)n#Simple_repeat 1 727 (0) m_b128s252i10 4753 chr3ptel1M 721471 CTCTCCTTGTCTCTCTCTCTCTGTCTCTGGGTGTCTCTCTCTGTCTCTGG 721520 ii v v vvv v v vv (CTCT)n#Simpl 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chr3ptel1M 721521 ATGTCTCTCTCTGTATCTCTCT-TCTCTC-CTGTCTGTCTCTTTCTGTCT 721568 v v v v - - v v i v (CTCT)n#Simpl 51 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 100 chr3ptel1M 721569 CTGTATCTGTCCAATTCTGTCTGTCTC-CTC-CTC-CCCTCTCTTTCTGT 721615 v v v ivvi v v - - - i i v (CTCT)n#Simpl 101 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 150 chr3ptel1M 721616 GTGTCTTGGTGTCTCTGTCTCTGTCT-TCTCTC-CTCTCTATCTCTGCCT 721663 v v ivv v v v - - v vi (CTCT)n#Simpl 151 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 200 chr3ptel1M 721664 CTGTGTATCTCTGATTCTGTCTCTCTCT-TCTC-CCCTTTC-CTGTCTCT 721710 v v v vvi v - - i i - v (CTCT)n#Simpl 201 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 250 chr3ptel1M 721711 GTGTCTCTCTGTATGTCTCTGTCTCTGTGTCTTTGTCTCCGTCTCTGTGT 721760 v v v v v v v v i v iv v v (CTCT)n#Simpl 251 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 300 chr3ptel1M 721761 GTCACTCAGTCTTTCTTTCCATCTCTATGTCTGTCTGTGTATGTCTCTGT 721810 v v vv i i iv v v v v v v v v (CTCT)n#Simpl 301 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 350 chr3ptel1M 721811 CTCTATGTGTCTCTCTCTTTCTGTCTCTCTGTCCATCTTTCTGTCTCTCT 721860 v v v i v v iv i v (CTCT)n#Simpl 351 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 400 chr3ptel1M 721861 GTCTTTGTCTGTCTCTGTCTCTCT-TCTCTCATGTCTGTCTCTATGGGTG 721909 v i v v v - - v v v vvv v (CTCT)n#Simpl 401 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TCTCTCTCTCTCTCTCTC 449 chr3ptel1M 721910 TGTCCCTCTCTGTCTGTCTCTGTCTCTGT-TCT-TCCCAATCTGTCTCTA 721957 v i v v v v - - i vv v v (CTCT)n#Simpl 450 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 499 chr3ptel1M 721958 TATGTCTCTCAGTCTTTCTGTGTCTCTATCCATCTCTGTGTCTTTCTGTC 722007 v v vv i v v v iv v v i v (CTCT)n#Simpl 500 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 549 chr3ptel1M 722008 TCT-TCTCTC-CTCTGTCTCTTTGTGTCTGTCTGTCTCTC-CTCTCTGTG 722054 - - v i v v v v - v v (CTCT)n#Simpl 550 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 599 chr3ptel1M 722055 TGTCTCTCTGTCTCTGTCACAATCTTTCAGTCTTTCTGTCTCTCTGTCCA 722104 v v v v vv i vv i v v iv (CTCT)n#Simpl 600 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 649 chr3ptel1M 722105 TCTCCATGTCTCTGCCTGCCCCACCCCCTGTCTGTCTGTATCTGTCTATC 722154 iv v vi vi i v i i v v v v v v (CTCT)n#Simpl 650 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 699 chr3ptel1M 722155 TATCTGTCTGTCTGTCTCTCTCTCTTTC 722182 v v v v i (CTCT)n#Simpl 700 TCTCTCTCTCTCTCTCTCTCTCTCTCTC 727 Matrix = Unknown Transitions / transversions = 0.27 (37/136) Gap_init rate = 0.02 (17 / 711), avg. gap size = 1.00 (17 / 17) 13 17.09 2.33 4.76 chr3ptel1M 722410 722452 (277548) (ACTTGG)n#Simple_repeat 1 42 (0) m_b128s252i11 4754 chr3ptel1M 722410 ACTTGGAACTTGGCCCTGGAGGGTGGGCTTGGACTT-GAATTGG 722452 - v i -vv i - v (ACTTGG)n#Sim 1 ACTTGG-ACTTGGACTTGGA-CTTGGACTTGGACTTGGACTTGG 42 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.07 (3 / 42), avg. gap size = 1.00 (3 / 3) 568 31.70 7.59 4.17 chr3ptel1M 722521 722915 (277085) L2b_3end#LINE/L2 57 464 (2) m_b128s601i17 4755 chr3ptel1M 722521 CTCAGCTCCGCGTGTGCAGTGCCACTGGCCATCCGGCTGTTCCTTGAACA 722570 - i --- v ivv vi iv i L2b_3end#LINE 57 CTCA-CTCTGC---TCCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACA 102 chr3ptel1M 722571 AGATCCGCCATCTCCAGACTTGGGGATTTTTC-TGTGCCGTTCCCCCTGC 722619 v viv? iv? v v ii vi v -i? i i L2b_3end#LINE 103 CGCCANGCTCNCTCCCGCCTCAGGGCCTTTGCACNTGCTGTTCCCTCTGC 152 chr3ptel1M 722620 ----AAT--CCTCCCTCATACC--CACTT--CCTA-TCTTCCTTGAC-TT 722657 ---- i-- i i ivi -- i i -- v - i v iiv - L2b_3end#LINE 153 CTGGAACGCCCTTCCCCACCTCTTCGCCTGGCCAACTCCTACTCATCCTT 202 chr3ptel1M 722658 CAAATCCCAGAAAAAAAAAAATCATCTCTGCGGAAGGAAGCCTTTCTTTC 722707 ii i vvv vi--- i iv v -- i i --- L2b_3end#LINE 203 CAGGTCTCAGCTCAAATG---TCACCTCCTCCG--GGAAGCCCTCC---C 244 chr3ptel1M 722708 TGCCCTTCCAGTGC---TCA--CATCTTCCTC----CTCCTCTTGCTCCT 722748 v ii vv --- -- ii i ---- i i iv ii iv L2b_3end#LINE 245 TGACCCCCCAGGCCGGGTCAGGCGCCCTCCTCTGGGCCCCCCCAGTCCTA 294 chr3ptel1M 722749 TTTTCTCATCTATAGTTTGTC--TATCTATAGTCCATATTTGTTTGCT-- 722794 iii vi - v i v i ?-- i i?-v v i i i v i-- L2b_3end#LINE 295 CCCTGCCA-CTCTGGGTTATNATTGTCTGN-TTACATGTCTGTCTCCCCC 342 chr3ptel1M 722795 AGTAGTCTCTCATGAACTCCTTGAAGGCAGGGGCTGTCTTTTGCTTCTTT 722844 v v ---i i v i i i ?v i vv v i L2b_3end#LINE 343 ACTAGACT---GTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCTTGTTC 389 chr3ptel1M 722845 ----TTGTATCTCCAGCACTTAGTACAGTACCCAGAACATAGTAGGTACT 722890 ----i i i i i ?i ii v i ii L2b_3end#LINE 390 ACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCT 439 chr3ptel1M 722891 TAATAAATGCTTGTTGACTGACTGA 722915 i i ii v v L2b_3end#LINE 440 CAGTAAATATTTGTTGAATGAATGA 464 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.81 CpG sites = 76, Kimura (unadjusted) = 44.34 Transitions / transversions = 1.73 (76/44) Gap_init rate = 0.08 (30 / 394), avg. gap size = 1.57 (47 / 30) 16 17.12 0.00 4.88 chr3ptel1M 722969 723011 (276989) (ACAG)n#Simple_repeat 1 41 (0) m_b128s252i12 4756 chr3ptel1M 722969 ACAGAAAGAGAGGCAGACAGACAGACTGACTGGAAGAGACAGA 723011 v v i v -i - v (ACAG)n#Simpl 1 ACAGACAGACAGACAGACAGACAGACAGAC-AG-ACAGACAGA 41 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.00 (2 / 2) 86 39.58 1.91 2.40 chr3ptel1M 723224 723852 (276148) (CAGA)n#Simple_repeat 1 626 (0) m_b128s252i13 4757 chr3ptel1M 723224 CAGACAGACGGAAGGGTGGACAGACAGACAGACTGACGAGA-AGGCAAGC 723272 i vi iii v - - i ii (CAGA)n#Simpl 1 CAGACAGACAGACAGACAGACAGACAGACAGACAGAC-AGACAGACAGAC 49 chr3ptel1M 723273 AGATGCTCAGACAGACAAGCAGAGAGACTGACAGGGACAGACAGATAATA 723322 iivv ii v v -- i ivv (CAGA)n#Simpl 50 AGACAGACAGACAGACAGACAGACAGACAGACA--GACAGACAGACAGAC 97 chr3ptel1M 723323 AGGCAAGCTGATGGAAGGACGGACAGATGGATGGACAGACGGACGAGA-A 723371 i ii v ii vi i ii ii i - - (CAGA)n#Simpl 98 AGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGAC-AGACA 146 chr3ptel1M 723372 GCCAAACAGATGCTCAAACAGACAAGCAGAGAGACTGGCAGCCACAGGGA 723421 v i iivv i ii v v i v v vi (CAGA)n#Simpl 147 GACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGA 196 chr3ptel1M 723422 CAGACAGA-TGATAAGGCAAGCTGACAGACCCAAAGA-AG-CAGAGGAAT 723468 -v -v i ii v vv v - - vii i (CAGA)n#Simpl 197 CAGACAGACAGA-CAGACAGACAGACAGACAGACAGACAGACAGACAGAC 245 chr3ptel1M 723469 GGACCACCAAGCAGCTGGACTGGCAGATGGGCGGACAGACGGAGGCATGA 723518 i viv ii vii v i ii i i -- i - (CAGA)n#Simpl 246 AGACAGACAGACAGACAGACAGACAGACAGACAGACAGAC--AGACA-GA 292 chr3ptel1M 723519 GAAACCAAGCAGATGCTCAGACAGACAAGCAGAGAGATTGGCAGCCAGCC 723568 v i - ii iivv ii v iv i v v (CAGA)n#Simpl 293 CAGA-CAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGAC 341 chr3ptel1M 723569 AAGA-AG-CAGAGGAATGGACCAG-CAAGCAGCTGGACTGGCAAACAGAC 723615 - - - vii ii - - ii vii v i i (CAGA)n#Simpl 342 -AGACAGACAGACAGACAGA-CAGACAGACAGACAGACAGACAGACAGAC 389 chr3ptel1M 723616 AGAAAGACAGATAGCGAGACATTCAAGA-AAACATACAGACGGACAAGCA 723664 v i vv vv - - i v i ii (CAGA)n#Simpl 390 AGACAGACAGACAGACAGACAGAC-AGACAGACAGACAGACAGACAGACA 438 chr3ptel1M 723665 AACAGATAGGCAGGAGGTACAAATGGACAGACAGGCAAGCAGACAGGGAC 723714 i i i - viv i ii i ii iv v (CAGA)n#Simpl 439 GACAGACAGACA-GACAGACAGACAGACAGACAGACAGACAGACAGACAG 487 chr3ptel1M 723715 GGGGA-AGACTGATACATAGACAAGCAGCCAAATAGAAAAACAAGCAGAT 723763 ivi - v i v i ii v i i v i ii i (CAGA)n#Simpl 488 ACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGAC 537 chr3ptel1M 723764 GGA-TGAGTGGCCAGACAAGTAGACAGACTTGTGGATAGATGGACAGAAA 723812 i -v -ii v iii vviii i ii v (CAGA)n#Simpl 538 AGACAGA-CAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACA 586 chr3ptel1M 723813 GACAGTCAGGACATAGTAACAG-CAGGGAGACGCAGAGACA 723852 v - v vvi - iv iv v (CAGA)n#Simpl 587 GACAGACA-GACAGACAGACAGACAGACAGACAGACAGACA 626 Matrix = Unknown Transitions / transversions = 1.73 (114/66) Gap_init rate = 0.04 (27 / 628), avg. gap size = 1.00 (27 / 27) 71 32.08 2.22 3.95 chr3ptel1M 723891 724250 (275750) (AGGG)n#Simple_repeat 1 354 (0) m_b128s252i14 4758 chr3ptel1M 723891 AGGAAGGAAGGGACAGAGACAGACAGAGAGACAGAG-GGGTTGGGGGGGG 723939 i i vi iv iv i iv i - vv i i (AGGG)n#Simpl 1 AGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAG 50 chr3ptel1M 723940 AGAGGGAGAAAAGGAGGGAGGGAGGAAGAGTAGGAGACAGAGTG-GGGAC 723988 i ii i i - v - vi v - v (AGGG)n#Simpl 51 GGAGGGAGGGAGGGAGGGAGGGAGGGAG-GGAGG-GAGGGAGGGAGGGAG 98 chr3ptel1M 723989 AAACAGAGGG-GGAAGGAGAGGAAGAGGAAGAGAGGGAGGAAGGGAGAAT 724037 ii vi - i - -- i i i iiv (AGGG)n#Simpl 99 GGAGGGAGGGAGGGAGG-GAGG--GAGGGAGGGAGGGAGGGAGGGAGGGA 145 chr3ptel1M 724038 GGGATGGAGAGACAGACAGAATGGGAGAGA-AGAGGAAGAGA-GAAGGGG 724085 v i vi -i i - i -i i i - i i (AGGG)n#Simpl 146 GGGAGGGAGGGAGGGA-GGGA-GGGAGGGAGGGAGGGAGGGAGGGAGGGA 193 chr3ptel1M 724086 GAGACAGAGAGAGGCAGAGAGACAGAGA-GGA-GGAGGGGGAAAGGGAGA 724133 i vi i v i iv i - - i ii - (AGGG)n#Simpl 194 GGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAG- 242 chr3ptel1M 724134 GAGAGGGAAGAAGGGAGAGTGGGTTGGGGGGAAAGACAGAGAGACAGAGG 724183 - i i i v vv i ii vi i vi (AGGG)n#Simpl 243 G-GAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGG 291 chr3ptel1M 724184 GGGGAGAGGGGGGAAGGGAGAGGAAGAGGGGGAGGGAGAGGGAGAGGGAA 724233 i - i i - - i i i i i - (AGGG)n#Simpl 292 GAGG-GAGGGAGGGAGGGAG-GG-AGGGAGGGAGGGAGGGAGGGAGGG-A 337 chr3ptel1M 724234 GGGA-GGAGGAGAGAGAG 724250 - - i (AGGG)n#Simpl 338 GGGAGGGAGG-GAGGGAG 354 Matrix = Unknown Transitions / transversions = 2.82 (62/22) Gap_init rate = 0.06 (22 / 359), avg. gap size = 1.00 (22 / 22) 88 31.61 3.68 0.27 chr3ptel1M 723899 724251 (275749) (AGAGAG)n#Simple_repeat 1 365 (0) m_b128s252i15 4758 chr3ptel1M 723899 AGGGACAGAGACAGACAGAGAGACAGAG-GGGTTGGGGGGGGAGAGGGAG 723947 i v v v v - i vvi i i i i (AGAGAG)n#Sim 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr3ptel1M 723948 AAAAGGAGGGAGGGAGGAAGAGTAG-GAGACAGAGTG-GGGACAAACAGA 723995 i ii i i ii - - v v - i v i v (AGAGAG)n#Sim 51 AGAGAGAGAGAGAGAGAGAGAG-AGAGAGAGAGAGAGAGAGAGAGAGAGA 99 chr3ptel1M 723996 GGGGGAAGGAGAGGAAGAGGAAGAGAGGGAGGAAGGGAGAATGGGATGGA 724045 i i ii ii ii i ii i iv i vi (AGAGAG)n#Sim 100 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 149 chr3ptel1M 724046 GAGACAGACAGAATGGGAGAGA-AGAGGAAGAGAGA-AGGGGGAGACAGA 724093 v v iv i - ii - i i v (AGAGAG)n#Sim 150 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 199 chr3ptel1M 724094 GAGAGGCAGAGAGACAGAGAG-GAG-GAGGGGGAAAGGGAGAGAGAGGGA 724141 iv v - - i i i i i (AGAGAG)n#Sim 200 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 249 chr3ptel1M 724142 -AGA-AGGGAGAGTGGGTTGGGGGGAAAGACAGAGAGACAGAG-GGGGGA 724188 - - i v i vvi i i i v v - i i (AGAGAG)n#Sim 250 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 299 chr3ptel1M 724189 GAGGGGGGAAGGGAGAGGAAGAGGGGGAGGGAGAGGGAGAGGGA-AGGGA 724237 i i ii i ii i i i i i - i (AGAGAG)n#Sim 300 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 349 chr3ptel1M 724238 G-GAG-GAGAGAGAGA 724251 - - (AGAGAG)n#Sim 350 GAGAGAGAGAGAGAGA 365 Matrix = Unknown Transitions / transversions = 2.78 (64/23) Gap_init rate = 0.04 (14 / 352), avg. gap size = 1.00 (14 / 14) 12 8.10 3.57 3.57 chr3ptel1M 726004 726031 (273969) (GAGGG)n#Simple_repeat 1 28 (0) m_b128s252i16 4759 chr3ptel1M 726004 GAGGGGAGGGCA-GGAAGGGGAGGGAGAG 726031 v - i - (GAGGG)n#Simp 1 GAGGGGAGGGGAGGGGAGGGGAGGG-GAG 28 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.07 (2 / 27), avg. gap size = 1.00 (2 / 2) 94 20.51 4.74 2.14 chr3ptel1M 726023 726296 (273704) (GAGA)n#Simple_repeat 1 281 (0) m_b128s252i17 4760 chr3ptel1M 726023 GAGGGAGAGAGAGA-AAAAAAACAGAGACAGACTGAGAGAGAAAGAAATG 726071 i - i i i v v vv i i - (GAGA)n#Simpl 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA-G 49 chr3ptel1M 726072 AAAGA-AGGGAGGGAGGGA-AGGGAGACA-AGAGAGAGACAGTGAAAGAT 726118 i - i i i - i v - v v i - (GAGA)n#Simpl 50 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA- 98 chr3ptel1M 726119 GAAAGAGAG-GAGAGAGACAGAGATGAAAGAG-GAGAGAG-GAGAGAGA- 726164 i - v - i - - - (GAGA)n#Simpl 99 GAGAGAGAGAGAGAGAGAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAG 147 chr3ptel1M 726165 AAAGAAATGAAAGA-AGAGAGGGAGAGA-AGGAAGACAGAGGGAGATGAA 726212 i i - i - i - ii v i - i (GAGA)n#Simpl 148 AGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA-GAG 195 chr3ptel1M 726213 AGA-AGGGAGAAAGAGACAGAGAAAGAAAAAGATGAGAGA-AGGGAAGGA 726260 - i i v i i i - - i ii (GAGA)n#Simpl 196 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA-GAGAGAGAGAGAGAGA 244 chr3ptel1M 726261 GACAGAGACAGAG-GAGAGAGAGGGAGGGGAAGAGAG 726296 v v - i i ii (GAGA)n#Simpl 245 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 281 Matrix = Unknown Transitions / transversions = 2.83 (34/12) Gap_init rate = 0.07 (19 / 273), avg. gap size = 1.00 (19 / 19) 11 27.58 0.00 0.00 chr3ptel1M 726721 726759 (273241) (AGAGAAC)n#Simple_repeat 1 39 (0) m_b128s252i18 4761 chr3ptel1M 726721 AGGGACCAGAGATTCTAGAACAGAGAACAGCGGACTGAG 726759 i v vivv v i v (AGAGAAC)n#Si 1 AGAGAACAGAGAACAGAGAACAGAGAACAGAGAACAGAG 39 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 35 12.66 9.01 3.42 chr3ptel1M 726891 727001 (272999) (TATTAATA)n#Simple_repeat 1 117 (0) m_b128s252i20 4762 chr3ptel1M 726891 TATTATTATACTTAATATA-TATTATTTTATTATTTTTAATA-ATT-ATA 726937 v - - v v v - v - - (TATTAATA)n#S 1 TATTAATATA-TTAATATATTAATATATTAATA-TATTAATATATTAATA 48 chr3ptel1M 726938 TTATTATATATATTAATATA-TATTATA-T-ATA-ATAAATA-ATTAACA 726982 - - - v - - - v - i (TATTAATA)n#S 49 -TATTA-ATATATTAATATATTAATATATTAATATATTAATATATTAATA 96 chr3ptel1M 726983 T-GTAAAATAAT-ATAAATTA 727001 -v v v - v (TATTAATA)n#S 97 TATTAATATATTAATATATTA 117 Matrix = Unknown Transitions / transversions = 0.09 (1/11) Gap_init rate = 0.13 (14 / 110), avg. gap size = 1.00 (14 / 14) 210 36.66 6.34 2.03 chr3ptel1M 727123 727264 (272736) C L2#LINE/L2 (2207) 875 728 m_b128s601i18 4763 chr3ptel1M 727123 GTAGAGGTCTGAGAGGTCATTGGAACCACATAAACTGAGGCACTGGGAAG 727172 i v ---i i ivviviv iiiii v i i C L2#LINE/L2 875 GTGGAGGAC---AAGATCATTGGAGGAGAGGAGGTCAAGGAACTGAGAGG 829 chr3ptel1M 727173 CCAGAGGACTT-AGGGAGTATCAATGT--CCATTCCAGTCTCCTGGCAG- 727218 i v i v- i vi v i --vi vv i v vi v v- C L2#LINE/L2 828 CCAGGGTATTGGAAGGATCATCTACGTGGATATTGAAATCACCAAGAATT 779 chr3ptel1M 727219 AGGGCAGAAAT-----TAAAGAGAGAAAGGCTGAGCCAGGTGCTAAACTC 727263 v i i i ----- ii vi viv v v C L2#LINE/L2 778 ATGACAGGAGTAGTGTTGGAGAGAGTGACAGTGAGCCAGGAGCTAAAATC 729 chr3ptel1M 727264 T 727264 C L2#LINE/L2 728 T 728 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 50.58 CpG sites = 28, Kimura (unadjusted) = 52.05 Transitions / transversions = 1.22 (28/23) Gap_init rate = 0.05 (7 / 141), avg. gap size = 1.71 (12 / 7) 16 15.40 2.78 0.00 chr3ptel1M 728355 728390 (271610) (ATGG)n#Simple_repeat 1 37 (0) m_b128s252i21 4764 chr3ptel1M 728355 ATGGCT-GCTGGGAGGATGGATGGATGGATGGTTGGA 728390 v - v iv v (ATGG)n#Simpl 1 ATGGATGGATGGATGGATGGATGGATGGATGGATGGA 37 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) 228 39.10 0.00 1.82 chr3ptel1M 729209 729320 (270680) L3#LINE/CR1 3845 3954 (145) m_b128s601i19 4765 chr3ptel1M 729209 AGGACCAAGAGGTGCAAGTAACAGGCAGAAAGCTCTGACCTCGATGCCAA 729258 vi v v v iv v i viv i iiv i L3#LINE/CR1 3845 AGGACCAATGGGTGGAAGTTACAGGGAGGCAGATTTCGGCTCAATATAAG 3894 chr3ptel1M 729259 AAAGTCCTTCCTTGTGATTACAGCAATCATTTGCAGTAGAACAGGCTTCC 729308 i vv i viii i v vi --iviv i i ii v L3#LINE/CR1 3895 GAAGAACTTTCTAACAATCAGAGCTGTC--CAAAAATGGAATGGGCTGCC 3942 chr3ptel1M 729309 CGGTGTGGGAAT 729320 iv ? v v i L3#LINE/CR1 3943 TCGNGAGGTAGT 3954 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 55.89 CpG sites = 23, Kimura (unadjusted) = 57.94 Transitions / transversions = 1.15 (23/20) Gap_init rate = 0.02 (2 / 111), avg. gap size = 1.00 (2 / 2) 26 0.00 0.00 0.00 chr3ptel1M 729540 729564 (270436) (TCC)n#Simple_repeat 1 25 (0) c_b128s251i2 4766 chr3ptel1M 729540 TCCTCCTCCTCCTCCTCCTCCTCCT 729564 (TCC)n#Simple 1 TCCTCCTCCTCCTCCTCCTCCTCCT 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 215 25.86 0.00 1.72 chr3ptel1M 729841 729899 (270101) C L3#LINE/CR1 (76) 4023 3966 m_b128s601i20 4767 chr3ptel1M 729841 CCCCACCACAATTACCCCTCACTAATGATCATAGAGCTTCTGCTTAGAGA 729890 iv i i- i v v i i vv i ii v C L3#LINE/CR1 4023 CCCTTCTACAAC-ATCCCTGACAAGTGGTCATCCAGCCTCTGCTTGAACA 3975 chr3ptel1M 729891 CCTCCAGTG 729899 C L3#LINE/CR1 3974 CCTCCAGTG 3966 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.50 CpG sites = 9, Kimura (unadjusted) = 32.50 Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1) 41 0.00 0.00 0.00 chr3ptel1M 729915 729949 (270051) (TG)n#Simple_repeat 1 35 (0) c_b128s251i3 4768 chr3ptel1M 729915 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 729949 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 35 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 17 9.65 0.00 5.71 chr3ptel1M 730461 730497 (269503) (ATTTT)n#Simple_repeat 1 35 (0) m_b128s252i22 4769 chr3ptel1M 730461 ATTTAATCCTTATTTTATTTTATTTTTTATTTATTTT 730497 v -i v - (ATTTT)n#Simp 1 ATTTTAT-TTTATTTTATTTTATTTTAT-TTTATTTT 35 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 466 21.98 1.46 10.32 chr3ptel1M 730499 730635 (269365) C MIRc#SINE/MIR (141) 127 2 m_b128s601i21 4770 chr3ptel1M 730499 CTGAGGC--AATTGGGTTAAGTCCCTTGCCCAAGGTCACACAACTAGGAT 730546 -- ivvi vv i --- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG--- 81 chr3ptel1M 730547 GTATTAAGTATCTGACCAGGTCAAATTTGCACTCGGGTCCTCCTGACTTC 730596 ---- iv v v v ---i i i v i i i i C MIRc#SINE/MIR 80 ----TAAGTGGCAGAGCCGG---GACTCGAACCCAGGTCTTCCTGACTCC 38 chr3ptel1M 730597 AGAACTAGTGCTCTATCCACTGCGCCACCTAACTGCCCC 730635 iiv i v i --- i C MIRc#SINE/MIR 37 AAGTCCAGTGCTCTTTCCACTGCACCAC---ACTGCCTC 2 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 25.08 CpG sites = 16, Kimura (unadjusted) = 26.17 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.10 (14 / 136), avg. gap size = 1.07 (15 / 14) 18 0.00 0.00 0.00 chr3ptel1M 733270 733289 (266711) (G)n#Simple_repeat 1 20 (0) m_b128s252i23 4771 chr3ptel1M 733270 GGGGGGGGGGGGGGGGGGGG 733289 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGG 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 16 23.47 0.00 0.00 chr3ptel1M 733405 733439 (266561) (C)n#Simple_repeat 1 35 (0) m_b128s252i24 4772 chr3ptel1M 733405 CCCCCCCCCCCCCTCCCCCACAGGGGCCCCCCCCC 733439 i v vvvvv (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 35 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 27 11.06 0.00 0.00 chr3ptel1M 733471 733509 (266491) (G)n#Simple_repeat 1 39 (0) m_b128s252i25 4773 chr3ptel1M 733471 GGGGGGGGGGGGCCGGGGGGGGGGGGGGAGGGGGGAGGG 733509 vv i i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 39 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 13 25.16 0.00 2.27 chr3ptel1M 735913 735957 (264043) (GGGCTCG)n#Simple_repeat 1 44 (0) m_b128s252i26 4774 chr3ptel1M 735913 GGGCTCGGGGCTCTGGGGCGGGGGGCAGGGGCCGCTTGGCTCTGG 735957 - vv vv v v vv v (GGGCTCG)n#Si 1 GGGCTCGGGGCTC-GGGGCTCGGGGCTCGGGGCTCGGGGCTCGGG 44 Matrix = Unknown Transitions / transversions = 0.00 (0/9) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 16 19.93 3.57 3.57 chr3ptel1M 738298 738353 (261647) (CCCCT)n#Simple_repeat 1 56 (0) m_b128s252i28 4775 chr3ptel1M 738298 CCCCTCTCCT-GCC-CCCCACCCTTCCCCTCCCTTACTCTTCTCTCCTCC 738345 i -v - v i i v i i i - (CCCCT)n#Simp 1 CCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCC-CC 49 chr3ptel1M 738346 TCTCCCTC 738353 - (CCCCT)n#Simp 50 TC-CCCTC 56 Matrix = Unknown Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.07 (4 / 55), avg. gap size = 1.00 (4 / 4) 43 28.08 4.52 3.59 chr3ptel1M 738293 738513 (261487) (CTCTCC)n#Simple_repeat 1 223 (0) m_b128s252i27 4776 chr3ptel1M 738293 CTCTGCCCCTCTCCTGCCCCCCACCCT-TCCC-CTCCCTTACTCT-TCTC 738339 v i - vi i v - - iv i - i (CTCTCC)n#Sim 1 CTCTCCCTCTC-CCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCC 49 chr3ptel1M 738340 TCCTCCTCTCCCTCTCTCTGTGTCTGT-CTTCATCTCTCTCTTTGTGTCT 738388 ii i v vi v - i - i ii v vi (CTCTCC)n#Sim 50 TCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTC-TCCCTCTCCCTCTCCCT 98 chr3ptel1M 738389 GTCTCTGTCTCTCTACCTCCTTCCT-T-CCTTTCCCTCTCTCCCT-TTTT 738435 v i v i v - i - - i i i -ii i (CTCTCC)n#Sim 99 CTCCCTCTCCCTCTCCCT-CTCCCTCTCCCTCTCCCTCTCCCTCTCCCTC 147 chr3ptel1M 738436 TCTCT-TCCCTTCCCCTCTTCCATCTCCCTTCCCCTCTCCCCCTTCTCCT 738484 i - ii - v ii i - - (CTCTCC)n#Sim 148 TCCCTCTCCCTCTCCCTC-TCCCTCTCCCTCTCCCTCTCCCTC-TC-CCT 194 chr3ptel1M 738485 -TCCC-CTCCCTGCCTCCCCCCCCCCCGCCC 738513 - - -- i i i v (CTCTCC)n#Sim 195 CTCCCTCTCCCT--CTCCCTCTCCCTCTCCC 223 Matrix = Unknown Transitions / transversions = 2.36 (33/14) Gap_init rate = 0.08 (18 / 220), avg. gap size = 1.00 (18 / 18) 33 34.71 0.47 6.40 chr3ptel1M 738299 738513 (261487) (CCCT)n#Simple_repeat 1 203 (0) m_b128s252i29 4776 chr3ptel1M 738299 CCCTCTCCTGCCCCCCACCCTTCCCCTCCCTTACTCTTCTCTCCTCCTCT 738348 - v i v - - iv -i - - (CCCT)n#Simpl 1 CCCTC-CCTCCCTCCCTCCC-T-CCCTCCCTCCCTC-CCTC-CCTCC-CT 44 chr3ptel1M 738349 CCCTCTCTCTGTGTCTGTCTTCATCTCTCTCTTTGTGTCTGTCTCTGTCT 738398 i iv vi -i i -i i ii viv iv i vi (CCCT)n#Simpl 45 CCCTCCCTCCCTCCCT-CCCTC-CCTCCCTCCCTCCCTCCCTCCCTCCCT 92 chr3ptel1M 738399 CTCTACCTCCTTCCTTCCTTTCCCTCTCTCCCTTTTTTCTCTTCCCTTCC 738448 i v i i -i i - iii - i i (CCCT)n#Simpl 93 CCCTCCCTCCCTCCCTCC-CTCCCTCCCTCCC-TCCCTC-CCTCCCTCCC 139 chr3ptel1M 738449 CCTCTTCC-ATCTCCCTTCCCCTCTCCCCCTTCTCCTTCCCCTCCCTGCC 738497 i i i -vi i i i i -i i - v (CCCT)n#Simpl 140 TCCCTCCCTCCCTCCCTCCCTCCCTCCCTC-CCTCCCT-CCCTCCCTCCC 187 chr3ptel1M 738498 TCCCCCCCCCCCGCCC 738513 i i v (CCCT)n#Simpl 188 TCCCTCCCTCCCTCCC 203 Matrix = Unknown Transitions / transversions = 2.92 (38/13) Gap_init rate = 0.07 (14 / 214), avg. gap size = 1.00 (14 / 14) 13 19.49 0.00 2.78 chr3ptel1M 741560 741596 (258404) (CGCGGGG)n#Simple_repeat 1 36 (0) m_b129s252i0 4777 chr3ptel1M 741560 CGCGCTGCGGGAGGCGTCCGGGCGCGGGGGGCGGGGC 741596 vv v i - v v (CGCGGGG)n#Si 1 CGCGGGGCGCGGGGCG-CGGGGCGCGGGGCGCGGGGC 36 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 18 9.05 0.00 7.89 chr3ptel1M 741878 741918 (258082) (GGGCG)n#Simple_repeat 1 38 (0) m_b129s252i1 4778 chr3ptel1M 741878 GGGCGGGGCAAGGGGCGGGGCGGGACCGGGAAGGGGCGGGG 741918 -- -v iv (GGGCG)n#Simp 1 GGGCGGGGC--GGGGCGGGGCGGG-GCGGGGCGGGGCGGGG 38 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.07 (3 / 40), avg. gap size = 1.00 (3 / 3) 232 18.03 1.61 1.61 chr3ptel1M 745740 745801 (254199) Charlie4#DNA/hAT-Charlie 26 87 (3291) m_b129s502i0 4779 chr3ptel1M 745740 GGGCCCCAAAGGGGTTTGGGGA-GGATTTCAGGGGGTCTGAGAACTTGGA 745788 i v ii v -i v i v Charlie4#DNA/ 26 GGACCCCCAAGGGGTCCGTGGATAGAATTCAGGGGGTCCGTGAACTTGGA 75 chr3ptel1M 745789 CTGGGAGAACATT 745801 - i v Charlie4#DNA/ 76 -TGGGAAAAAATT 87 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 16.88 CpG sites = 6, Kimura (unadjusted) = 20.81 Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.03 (2 / 61), avg. gap size = 1.00 (2 / 2) 200 33.47 1.44 2.34 chr3ptel1M 746686 747589 (252411) (AGAT)n#Simple_repeat 1 896 (0) m_b129s252i2 4780 chr3ptel1M 746686 AGAGAGATGGAGGGATAGGTCGTTACATAGATGGGGAGATA-ATGGATGC 746734 v i vi i v v v i iv - i iv (AGAT)n#Simpl 1 AGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAG 50 chr3ptel1M 746735 ATGGATACGTAGGTGGAT-GGTAGATAGATAGATAGAGATGATAGCTAGA 746783 i vi i i - i v - v (AGAT)n#Simpl 51 ATAGATAGATAGATAGATAGATAGATAGATAGATAGATA-GATAGATAGA 99 chr3ptel1M 746784 CAGACAGACAGATAGAGGGATGGATGTATATGATAGATAGATAGACAGAC 746833 i i i vi i iv - i i (AGAT)n#Simpl 100 TAGATAGATAGATAGATAGATAGATAGATA-GATAGATAGATAGATAGAT 148 chr3ptel1M 746834 AGATAGACAGATAGATATATGGATCGAGATAGACAGACACAGACAGACAG 746883 i v i -- i -- i i i (AGAT)n#Simpl 149 AGATAGATAGATAGATAGATAGAT--AGATAGATAG--ATAGATAGATAG 194 chr3ptel1M 746884 CTAGCTAGCTAGAT-GATAGATAAATAGATGGATGGATAGAGATGATAGC 746932 v v v - i i i v - v (AGAT)n#Simpl 195 ATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATA-GATAGA 243 chr3ptel1M 746933 TAGACAGACAGACAGATAGAGGGATGGATGTATATGATAGATAGATAGAC 746982 i i i vi i iv - i (AGAT)n#Simpl 244 TAGATAGATAGATAGATAGATAGATAGATAGATA-GATAGATAGATAGAT 292 chr3ptel1M 746983 AGATAGACTTACACATACAGCTAGAGGTAAATATATAGTTAGACATGGAT 747032 -- v i v i v -- i v v -- i (AGAT)n#Simpl 293 AGATAGA--TAGATAGATAGATAGA--TAGATAGATAGATAG--ATAGAT 336 chr3ptel1M 747033 GGACGGTTACATAGATGGGGAGATAGATGAATGGATGGATACATAGATAT 747082 i ii v v i iv ii i i v v (AGAT)n#Simpl 337 AGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAG 386 chr3ptel1M 747083 GTAGGTGGATGGGTTGATATATATACACTCACACATATAGCTAG--AGAT 747130 i i i i i v v v i vvi v i v v -- (AGAT)n#Simpl 387 ATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGAT 436 chr3ptel1M 747131 AGGTA-ATGGATGGATGGATAGATACATAGCTACATGGATGGAT-TTTAT 747178 i - i i i v v v i i -vv v (AGAT)n#Simpl 437 AGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAG 486 chr3ptel1M 747179 ATACATACA-A-ATAGCTAAATATGTAGTTTAATAGTTACACAGGAGGAT 747226 v v - - v i vi v vi v v i ivi (AGAT)n#Simpl 487 ATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGAT 536 chr3ptel1M 747227 TGATGGATCCATAGGTGCAT-GAGTAGGCAGGACAGACAGCTATATACAT 747275 v i vv i iv - - ii - i i v v v (AGAT)n#Simpl 537 AGATAGATAGATAGATAGATAGA-TAGATA-GATAGATAGATAGATAGAT 584 chr3ptel1M 747276 ACATACATATATATTTAGATACGTAGTTTGATAGTTACATGGATGGAAAG 747325 v v v vv vi v v v v i i v (AGAT)n#Simpl 585 AGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAG 634 chr3ptel1M 747326 ACAGA-AGAATGGATAGGTGGACGGACGGATGGATGGCTAGATACAGAGG 747374 i - - i i i ii ii i i v v v i (AGAT)n#Simpl 635 ATAGATAG-ATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGA 683 chr3ptel1M 747375 CGCATGGTTGGATAGAAAGATACATGCACACATACATATGTAG-CAGACA 747423 iiv i v i v v iv i v v vi -i i (AGAT)n#Simpl 684 TAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATA 733 chr3ptel1M 747424 CACAGTTTGATAGACACATGGACGGATGGTTGGACAGACGGATGAATAGA 747473 v i v v i v i ii i v i i ii ii (AGAT)n#Simpl 734 GATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGA 783 chr3ptel1M 747474 GATGCATAGATACGTAAGTGCAAAGGCACATA-ATGGATAAGTAGACATA 747522 v - - vi ii iv v ii v - i - - v v (AGAT)n#Simpl 784 TA-G-ATAGATAGATAGATAGATAGATAGATAGATAGAT-AG-ATAGATA 829 chr3ptel1M 747523 CATACATACATAGGGAGCTAGACACATAGTTTGAGAGTCACATAGATGGA 747572 v v v iv v i v v v v vi v i (AGAT)n#Simpl 830 GATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGA 879 chr3ptel1M 747573 TGGACAGATGGATGGAT 747589 i i i i (AGAT)n#Simpl 880 TAGATAGATAGATAGAT 896 Matrix = Unknown Transitions / transversions = 1.20 (126/105) Gap_init rate = 0.04 (33 / 903), avg. gap size = 1.03 (34 / 33) 260 33.34 1.10 1.10 chr3ptel1M 747669 747759 (252241) L2c_3end#LINE/L2 361 451 (27) m_b129s601i0 4781 chr3ptel1M 747669 TGTCTTC-CCTTTAGACCTCCAGCATCCTGGGAGCAGGGATCCCTTCCTA 747717 i - vi iviv vi i i i i viv i L2c_3end#LINE 361 TGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTA 410 chr3ptel1M 747718 TTTATGAGCACATGGCCCAGTGTCTGGCGCACAGTAGGAGCT 747759 i vvviii v- i i i i v L2c_3end#LINE 411 TTCATCTTTGTATC-CCCAGCGCCTGGCACATAGTAGGCGCT 451 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.17 CpG sites = 19, Kimura (unadjusted) = 46.32 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.02 (2 / 90), avg. gap size = 1.00 (2 / 2) 17 38.65 5.20 1.68 chr3ptel1M 748154 748326 (251674) (GAGA)n#Simple_repeat 1 179 (0) m_b129s252i3 4782 chr3ptel1M 748154 GAGGGAAAAAAAG-GAAAGAGAGA-AAAGA-AGAAAAAAAGAGAGAG-GG 748199 i i i i - i - i - i i i - i (GAGA)n#Simpl 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr3ptel1M 748200 GAG-GAAATCACAGAAGGAGAGGGAGGAAGGAAGAATCAGA-ATATGGGA 748247 - i -v v ii i ii ii ivv - v - i (GAGA)n#Simpl 51 GAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA-GAGA 98 chr3ptel1M 748248 GGGATGA-AAAGAGGGAGAG-GAAAGGGAGGAAGGAAGTCAAAAGGAGAG 748295 i - - i i - i i ii ii vv i ii (GAGA)n#Simpl 99 GAGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 147 chr3ptel1M 748296 AGGGAAGGAGGAAGA-AGAGGGAGAAAAAGAG 748326 i ii ii - i i i (GAGA)n#Simpl 148 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 179 Matrix = Unknown Transitions / transversions = 5.71 (40/7) Gap_init rate = 0.07 (12 / 172), avg. gap size = 1.00 (12 / 12) 15 16.12 0.00 5.26 chr3ptel1M 748346 748385 (251615) (GAAAAG)n#Simple_repeat 1 38 (0) m_b129s252i4 4783 chr3ptel1M 748346 GAAAAGGAAAAAGAATAAGGGAGGAGAAAAGGAAAGAGGA 748385 i - i iii - (GAAAAG)n#Sim 1 GAAAAGGAAAAGGAA-AAGGAAAAGGAAAAGGAAA-AGGA 38 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 337 29.21 17.33 1.72 chr3ptel1M 748398 748599 (251401) C MIRc#SINE/MIR (20) 248 16 m_b129s601i1 4784 chr3ptel1M 748398 TTTGTTTAGCACTG---AGCTAATAA-GCACATAGCCATTT-TTACTCCA 748442 v v--- i v i - i v vvv vi- iii C MIRc#SINE/MIR 248 TTTGTATAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATCTCA 199 chr3ptel1M 748443 TGGAATCCTCACAACAGTCCTGAGAGGAAGA------AGTTCTTCCCTTA 748486 vvi ii v v i------ v v --v C MIRc#SINE/MIR 198 TTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATT--ATTA 151 chr3ptel1M 748487 TCTCC-----CCAAATAAGGAAACTGAGAC------AGGCTGA--GGTTT 748523 i -----v i i i ------ i i -- ii C MIRc#SINE/MIR 150 TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTT 101 chr3ptel1M 748524 A---AAGG-------GCCAGGAAGTGCTTAATTCTGGATTTGAACTCAGA 748563 i--- ------- i v vivi vi v i i i i C MIRc#SINE/MIR 100 GCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGG 51 chr3ptel1M 748564 TCCCCTCAACTCC-AGTCCAGTGGTGTCCTTTGACTG 748599 ii iii - --v i iv C MIRc#SINE/MIR 50 TCTTCCTGACTCCAAGTCCAGTG--CTCTTTCCACTG 16 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.64 CpG sites = 35, Kimura (unadjusted) = 38.32 Transitions / transversions = 1.52 (35/23) Gap_init rate = 0.07 (14 / 201), avg. gap size = 2.79 (39 / 14) 447 33.79 6.52 2.44 chr3ptel1M 749055 749606 (250394) C L1ME4c_3end#LINE/L1 (255) 575 2 m_b129s551i0 4785 chr3ptel1M 749055 TCATCATTTCTTACAGCACAAGAGTAATTCATCATTATCAGATACCACAG 749104 i i v ii vvv v i v i ivvv?v vi i i C L1ME4c_3end#L 575 TTATCATTTTTAATGGCTGCATAATATTCCATCGAGTNGATGTACCATAA 526 chr3ptel1M 749105 TTTGTTCATCTACTCCCCGACTGAGAGGCATCCCCTCAATTTCCAATTCT 749154 ii i v i i v i vvi i iivvvivi i C L1ME4c_3end#L 525 TTTACTTAACCATTCCCCTATTGTTGGACATTTAGGTTGTTTCCAATTTT 476 chr3ptel1M 749155 TTGTCCCCAGAACAGAGTGGCTGTAATG--TTTTTTTATGTAAGGTCCTT 749202 i iivii v - v ii- i --iv i ii i ------- C L1ME4c_3end#L 475 TCGCTATTATAA-ATAAC-GCTGCAATGAACATCTTCGTGCA-------T 435 chr3ptel1M 749203 TTA--TTTTTACTTCTTTT-TTTTATCCCTTTGGGGATA------CAGAC 749243 v -- v -vv ii i -i ------ v C L1ME4c_3end#L 434 ATAGCTTTTTCCTTCTTTTGAATTATTTCCTT-AGGATAAATTCCCAGAA 386 chr3ptel1M 749244 CTAGTATTACTAAGTTAAA-GGTATGCATGGTTTTATAGCCCTTTGGGCA 749292 v i v ii i - v iiv i i vivi i C L1ME4c_3end#L 385 GTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTCTTGATACG 336 chr3ptel1M 749293 TAGTTCCAAATTGCGCTGCAGAATGGTTGAATCAGTTCACAATTCCACCA 749342 v v vi v i v v i i i ? v C L1ME4c_3end#L 335 TATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACANTGCCACCA 286 chr3ptel1M 749343 ACAGTGCACTGATATTTCATTTTTCCCATATTCCCTTCACCATTTCACAT 749392 i i i ivii?i vi v iv ii ?i i vi v vvii C L1ME4c_3end#L 285 GCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGCATTGGGTAT 236 chr3ptel1M 749393 TTTC--CTTTTTAAAATTCTGCTAGCCAATCTAATAGTTATGAGGTGGTA 749440 v --i v i ---- i vii i ii C L1ME4c_3end#L 235 TATCAATTTTTTAAATTTTTGCT----AATTTAATAGGCGTAAAATGGTA 190 chr3ptel1M 749441 CTTCAGAATTGTTTTAATTTCCATTTCTCCAATCAATAGAGAGG----AC 749486 ii vvi i v iii i v v ---- C L1ME4c_3end#L 189 TCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACTAGCGAGGTTGAAC 140 chr3ptel1M 749487 ATTATA-GATAGCTTTGATTACT------------TCATCAGAAAA---- 749519 v v-v ivv v ------------ v ?v vi ---- C L1ME4c_3end#L 139 ATTTTTCCATGTGTTTGTTTACTANTTGTATTTCCTCTTNTGTGAATTGT 90 chr3ptel1M 749520 CTGTTCATGTGTTTTGATCATTTATCAGTTGAGGAATAGCTCTTATTTTT 749569 vi vi vi i vv v v ? v i C L1ME4c_3end#L 89 CTGTTCATGTCCTTTGCCCATTTATCTATTGGGGTCTTGATNTTTTTCTT 40 chr3ptel1M 749570 -TAAATTTGACTCCATTCTCTTCATGTTTGAGAAAATA 749606 - v v vvii i vi i? v? v v C L1ME4c_3end#L 39 ATCAATTTGAATGAGCTCTTTATATANTANAGATATTA 2 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 44.67 CpG sites = 100, Kimura (unadjusted) = 47.23 Transitions / transversions = 1.22 (100/82) Gap_init rate = 0.05 (25 / 551), avg. gap size = 2.00 (50 / 25) 481 29.09 4.31 4.31 chr3ptel1M 749219 749473 (250527) C L1PREC2_3end#LINE/L1 (496) 411 157 m_b129s551i1 4785 chr3ptel1M 749219 TTTTTATCCCTTTGGGGATACAGACCTAGTA------TTACTAAGTTAAA 749262 v i v i -- i ------ i ii ii C L1PREC2_3end# 411 TTTATATTCCTTTGGGTATATA--CCCAGTAATGGGATTGCTGGGTCGAA 364 chr3ptel1M 749263 -GGTATGCATGGTTTTATAGCCCTTTG-GGCATAGTTCCAAATTGCGCTG 749310 - - iviv - i - v v -- v i vi v C L1PREC2_3end# 363 TGGTA-GTTCTGTTTT-TAGCTCTTTGAGGAATCG--CCACACTGCTTTC 318 chr3ptel1M 749311 CAGAATGGTTGAATCAGTTCACAATTCCACCAACAGTGCACTGATATTTC 749360 v ii i i v i i iviiii i C L1PREC2_3end# 317 CACAATGGTTGAACTAATTTACACTCCCACCAACAGTGTATAAGCGTTCC 268 chr3ptel1M 749361 ATTTTTCCCATATTCCCTTCACCATTTCACATTTTC---CTTTTTAAAAT 749407 v ii ii vi i vi v i vvi i--- --- C L1PREC2_3end# 267 CTTTTCTCCGCAACCTCGCCAGCATCTGTTATTTTTTGACTTTTTAA--- 221 chr3ptel1M 749408 TCTGCTAGCCAATCTAATAGTTATGAGGTGGTACTTCAGAATTGTTTTAA 749457 -- iv v i iv v i i ii vvi v i C L1PREC2_3end# 220 --TAATAGCCATTCTGACTGGTGTGAGATGGTATCTCATTGTGGTTTTGA 173 chr3ptel1M 749458 TTTCCATTTCTCCAAT 749473 v i C L1PREC2_3end# 172 TTTGCATTTCTCTAAT 157 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 36.03 CpG sites = 45, Kimura (unadjusted) = 38.25 Transitions / transversions = 1.73 (45/26) Gap_init rate = 0.06 (15 / 254), avg. gap size = 1.47 (22 / 15) 13 11.07 0.00 6.45 chr3ptel1M 755793 755825 (244175) (ACTAA)n#Simple_repeat 1 31 (0) m_b129s252i5 4786 chr3ptel1M 755793 ACTAAACTAAACTAAACCGGTGACTAAACTAAA 755825 - -vvi (ACTAA)n#Simp 1 ACTAAACTAAACTAAA-C-TAAACTAAACTAAA 31 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.06 (2 / 32), avg. gap size = 1.00 (2 / 2) 17 0.00 0.00 0.00 chr3ptel1M 756218 756236 (243764) (A)n#Simple_repeat 1 19 (0) m_b129s252i6 4787 chr3ptel1M 756218 AAAAAAAAAAAAAAAAAAA 756236 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAA 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 535 20.18 2.70 1.79 chr3ptel1M 756291 756401 (243599) C MIRb#SINE/MIR (41) 227 116 m_b129s601i2 4788 chr3ptel1M 756291 GGCATTTTGTTAAGTGCTTTATAAACATCATCTCATTTGATCCTCA---C 756337 i v i i i vi i i --- C MIRb#SINE/MIR 227 GGCACTGTGCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAAC 178 chr3ptel1M 756338 AACCCTGGGGGATGGGTGTTGTTCTATCCCCATTTTATGGATGAGGACAC 756387 v i i i i i -- ii v C MIRb#SINE/MIR 177 AACCCTGCGAGGTAGGTATTAT--TATCCCCATTTTACAGATGAGGAAAC 130 chr3ptel1M 756388 TGAGGCAGGGAAAG 756401 vvi i C MIRb#SINE/MIR 129 TGAGGCTCAGAGAG 116 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 23.10 CpG sites = 16, Kimura (unadjusted) = 24.35 Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.03 (3 / 110), avg. gap size = 1.67 (5 / 3) 434 20.89 25.32 0.00 chr3ptel1M 756293 756450 (243550) C MIRc#SINE/MIR (36) 232 35 m_b129s601i3 4788 chr3ptel1M 756293 CATTTTGTTAAGTGCTTT-ATAAACATCATCTCATTTGATCCTCACAAC- 756340 v iiv i - i v i - C MIRc#SINE/MIR 232 CAGTTTACAAAGCGCTTTCACATACATTATCTCATTTGATCCTCACAACA 183 chr3ptel1M 756341 --CCTGGGGGATGGGT------GTTGTT-CTATCCCCATTTTATGGATGA 756381 -- v i i i i------ v i -i ii C MIRc#SINE/MIR 182 ACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGA 133 chr3ptel1M 756382 GGACACTGAGG--CAGGGA----AAGAAACCAGC-----------CAGCT 756414 v -- i ---- vi iv ----------- C MIRc#SINE/MIR 132 GGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCT 83 chr3ptel1M 756415 -----GCG-------TGGGATTTGAACTTTGTTCTTCCTGACTTCAAG 756450 ----- i -------i i i iiv v i C MIRc#SINE/MIR 82 AGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 22.69 CpG sites = 23, Kimura (unadjusted) = 25.26 Transitions / transversions = 2.30 (23/10) Gap_init rate = 0.06 (10 / 157), avg. gap size = 4.00 (40 / 10) 12 25.56 0.00 0.00 chr3ptel1M 756503 756539 (243461) (ATATTTT)n#Simple_repeat 1 37 (0) m_b129s252i7 4789 chr3ptel1M 756503 ATATGTTATTTTTTACTTTGAAGATCTTATATTTTAT 756539 v v iv vv v i (ATATTTT)n#Si 1 ATATTTTATATTTTATATTTTATATTTTATATTTTAT 37 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 21 13.48 0.00 0.00 chr3ptel1M 757766 757798 (242202) (C)n#Simple_repeat 1 33 (0) m_b129s252i8 4790 chr3ptel1M 757766 CCCCCCCTCCCCCCCTTCCCCCCCCCCGCCCCC 757798 i ii v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 33 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 19 20.06 5.26 0.00 chr3ptel1M 757956 758012 (241988) (GGGGC)n#Simple_repeat 1 60 (0) m_b129s252i9 4791 chr3ptel1M 757956 GGGGCGGGGCGGGGCCGTAGGGGGCGGGGC--GGAGAGGCGGGGC-CTGA 758002 v viv -- v i -vv v (GGGGC)n#Simp 1 GGGGCGGGGCGGGGCGGGGCGGGGCGGGGCGGGGCGGGGCGGGGCGGGGC 50 chr3ptel1M 758003 TGGGCGGGGC 758012 v (GGGGC)n#Simp 51 GGGGCGGGGC 60 Matrix = Unknown Transitions / transversions = 0.25 (2/8) Gap_init rate = 0.04 (2 / 56), avg. gap size = 1.50 (3 / 2) 12 17.44 0.00 5.88 chr3ptel1M 758037 758072 (241928) (CTGGG)n#Simple_repeat 1 34 (0) m_b129s252i10 4791 chr3ptel1M 758037 CTGGGACTGGAATCGGCTGGGATGGGCCGGGGCTGG 758072 - iv v v - v (CTGGG)n#Simp 1 CTGGG-CTGGGCTGGGCTGGGCTGGG-CTGGGCTGG 34 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 259 19.23 0.00 0.00 chr3ptel1M 758359 758410 (241590) C L2b_3end#LINE/L2 (16) 450 399 m_b129s601i4 4792 chr3ptel1M 758359 AGCACTGACTGAGCGCCACCTGTTTGCCAGGCTCCGTGCAAGGTGCTGGG 758408 ii i v vv v ? i v i C L2b_3end#LINE 450 AATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGG 401 chr3ptel1M 758409 GA 758410 C L2b_3end#LINE 400 GA 399 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 20.43 CpG sites = 5, Kimura (unadjusted) = 22.87 Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 221 17.50 0.00 0.00 chr3ptel1M 758410 758449 (241551) C L2c_3end#LINE/L2 (16) 462 423 m_b129s601i5 4793 chr3ptel1M 758410 AGCACTGATTGAGCGCCGCCTGTATGCCAGGCGCTGGGGA 758449 i i v vv i i C L2c_3end#LINE 462 AACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGA 423 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 20.14 CpG sites = 4, Kimura (unadjusted) = 20.14 Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 230 15.00 0.00 0.00 chr3ptel1M 758449 758488 (241512) C L2c_3end#LINE/L2 (16) 462 423 m_b129s601i6 4793 chr3ptel1M 758449 AGCACTGATTGAGCGCCACCTGTGTGCCAGGCGCTGGGGA 758488 i i v vv i C L2c_3end#LINE 462 AACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGA 423 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 16.81 CpG sites = 3, Kimura (unadjusted) = 16.81 Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 217 17.50 0.00 0.00 chr3ptel1M 758488 758527 (241473) C L2c_3end#LINE/L2 (16) 462 423 m_b129s601i7 4794 chr3ptel1M 758488 AGCACTGATTGAGCGCCGCCTGTGTGCCAGGTGCTGGGGA 758527 i i v vv i i C L2c_3end#LINE 462 AACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGA 423 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 17.13 CpG sites = 4, Kimura (unadjusted) = 20.14 Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 262 21.15 0.00 0.00 chr3ptel1M 758568 758619 (241381) C L2b_3end#LINE/L2 (16) 450 399 m_b129s601i8 4794 chr3ptel1M 758568 AGCACTGATTGAGCGCCACCTGTATGCCAGGCTCCGTGCAAGGCACTGGG 758617 ii i v i vv i ? i v i C L2b_3end#LINE 450 AATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGG 401 chr3ptel1M 758618 GA 758619 C L2b_3end#LINE 400 GA 399 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 23.38 CpG sites = 7, Kimura (unadjusted) = 26.03 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 239 23.08 0.00 0.00 chr3ptel1M 758619 758670 (241330) C L2b_3end#LINE/L2 (16) 450 399 m_b129s601i9 4794 chr3ptel1M 758619 AGCACTGATTGGGCACCGCCTGTGTGCCAGGCTCCGTGCAAGGTGCTGGG 758668 ii i v i i i vv ? i v i C L2b_3end#LINE 450 AATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGG 401 chr3ptel1M 758669 GA 758670 C L2b_3end#LINE 400 GA 399 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 23.66 CpG sites = 8, Kimura (unadjusted) = 29.16 Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 743 29.82 5.49 2.67 chr3ptel1M 760144 760398 (239602) MIRb#SINE/MIR 7 268 (0) m_b129s601i10 4795 chr3ptel1M 760144 GGCTCCATGATACACTGGACCGGACGGCAGAACTAGCATCAGAAGGAGCC 760193 vv i i i v vv ii ivvi vvi i vi vi v i MIRb#SINE/MIR 7 GGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCT 56 chr3ptel1M 760194 GAGTTCAAAGCTTGCCTCGGACACT----AGCTGTGTGACCCTGAACAAG 760239 i i v ii v v v ---- i ii MIRb#SINE/MIR 57 GGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAG 106 chr3ptel1M 760240 GCCCTTCACCTCT----GCCTCGGTTTCCCTACCTGTAAAACGGGGATGC 760285 viv v ---- i ii i i --- MIRb#SINE/MIR 107 TTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGA--- 153 chr3ptel1M 760286 TAAGAGCACTTCCCTCCCAGGACTGTTGTGAGG-TTCAGTGA---AATGT 760331 v ii i v v ii - v i --- i MIRb#SINE/MIR 154 TAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGC 203 chr3ptel1M 760332 CTCTAAAGTGCCT--CGCAGCGACTGGCACCCAGTGGGTGCTACATAAAT 760379 v v i i -- i i v vi ii i vv MIRb#SINE/MIR 204 ATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAAAT 253 chr3ptel1M 760380 GCCGAGCATTTTCATTATT 760398 ---- i vi ii MIRb#SINE/MIR 254 G----GTAGCTCTATTATT 268 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.87 CpG sites = 44, Kimura (unadjusted) = 39.22 Transitions / transversions = 1.47 (44/30) Gap_init rate = 0.05 (12 / 254), avg. gap size = 1.75 (21 / 12) 12 29.02 3.03 3.03 chr3ptel1M 760643 760708 (239292) (GGGAG)n#Simple_repeat 1 66 (0) m_b129s252i11 4796 chr3ptel1M 760643 GGCAGGGAAAGGGA-AGAAGGCCTGGGG-GGTAAGGGGTGGGGAGGGGAG 760690 v i i -i i vvv - vi v (GGGAG)n#Simp 1 GGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAG 50 chr3ptel1M 760691 CGTTGCGAGGTGGGGAGG 760708 - -v v i v (GGGAG)n#Simp 51 -G-GGAGGGGAGGGGAGG 66 Matrix = Unknown Transitions / transversions = 0.67 (6/9) Gap_init rate = 0.06 (4 / 65), avg. gap size = 1.00 (4 / 4) 217 23.33 3.33 0.00 chr3ptel1M 761508 761567 (238433) C L2b_3end#LINE/L2 (20) 446 385 m_b129s601i11 4797 chr3ptel1M 761508 TTCCCTGTGGGCCCACTGTGTGCT-GGCCCTGAGCTAAGCCCCAGGG-TA 761555 iv v v i i- ? v i v ii - C L2b_3end#LINE 446 TTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGGGATA 397 chr3ptel1M 761556 CAGGGATGGACA 761567 v i i C L2b_3end#LINE 396 CAGCGGTGAACA 385 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.02 CpG sites = 8, Kimura (unadjusted) = 29.02 Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.03 (2 / 59), avg. gap size = 1.00 (2 / 2) 197 30.08 8.65 0.89 chr3ptel1M 762179 762282 (237718) L2b_3end#LINE/L2 331 442 (24) m_b129s601i12 4798 chr3ptel1M 762179 TTTGTCTCCCCC--CAGACTGGGAGCTTC-CGGGGGCA-----CCCGGCA 762220 i --i v i -i i ----- v? v v L2b_3end#LINE 331 TCTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCT 380 chr3ptel1M 762221 CCTTTGGCCTCTGTGGTATCCCCCTCACCTAGCACACAG-TAGGTAGAGT 762269 vii vi v i iv vv i v? -iv i v -i L2b_3end#LINE 381 GTCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACA-C 429 chr3ptel1M 762270 AGCGGGCACCCAG 762282 ii i i L2b_3end#LINE 430 AGTAGGCGCTCAG 442 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.69 CpG sites = 18, Kimura (unadjusted) = 40.63 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.05 (5 / 103), avg. gap size = 2.00 (10 / 5) 207 27.37 5.88 1.12 chr3ptel1M 762179 762263 (237737) L2c_3end#LINE/L2 359 447 (31) m_b129s601i13 4798 chr3ptel1M 762179 TTTGTCTCCCCC--CAGACTGGGAGCTTCC-GGGGGCAC--CCGGCACCT 762223 i i --i v i i- i v--v v iii L2c_3end#LINE 359 TCTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCT 408 chr3ptel1M 762224 TTGGCCTCTGTGGTATCCCCCTCACCTAGCACACAGTAGG 762263 vvv v v - vv i i i L2c_3end#LINE 409 TATTCATCTTTG-TATCCCCAGCGCCTGGCACATAGTAGG 447 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.74 CpG sites = 12, Kimura (unadjusted) = 34.54 Transitions / transversions = 1.09 (12/11) Gap_init rate = 0.05 (4 / 84), avg. gap size = 1.50 (6 / 4) 210 21.97 12.50 5.19 chr3ptel1M 766929 767000 (233000) MIR3#SINE/MIR 100 176 (32) m_b129s601i16 4799 chr3ptel1M 766929 GTCACCTGCCCTTTCTGCCCAGCCTCGGTATCTCCATCTGCAAAATGAAG 766978 i vv i ---i i v ii i i MIR3#SINE/MIR 100 GTCACTTCACCTCTCTG---GGCCTCAGTTTCCTCATCTGTAAAATGAGG 146 chr3ptel1M 766979 A---TGGATCTGG------CCTAAGGCCCCT 767000 i--- - i ------i i MIR3#SINE/MIR 147 GGGTTGGA-CTAGATGATCTCTAAGGTCCCT 176 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.61 CpG sites = 12, Kimura (unadjusted) = 27.61 Transitions / transversions = 4.00 (12/3) Gap_init rate = 0.08 (6 / 71), avg. gap size = 2.17 (13 / 6) 227 20.00 4.76 4.76 chr3ptel1M 766929 766991 (233009) MIR1_Amn#SINE/MIR 105 167 (63) m_b129s601i15 4799 chr3ptel1M 766929 GTCACCTGCCCTTTCTGCCCAGCCTCGGTATCTCCATCTGCAAAATGAAG 766978 i ?v i ?--- i v ii i ii MIR1_Amn#SINE 105 GTCACTTNACCTCTCTGN---GCCTCAGTTTCCTCATCTGTAAAATGGGG 151 chr3ptel1M 766979 ATG--GAT-CTGGCCT 766991 i-- - i MIR1_Amn#SINE 152 ATAATGATACTGACCT 167 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 25.63 CpG sites = 10, Kimura (unadjusted) = 25.63 Transitions / transversions = 5.00 (10/2) Gap_init rate = 0.08 (5 / 62), avg. gap size = 1.20 (6 / 5) 262 19.05 20.24 0.00 chr3ptel1M 767045 767128 (232872) C MIRc#SINE/MIR (65) 203 103 m_b129s601i18 4800 chr3ptel1M 767045 TCTCCCTTGGTCCTTGCCACAGCCCAG------AGGCAG-------ATCC 767081 vi i ii v i v ------ ------- iv C MIRc#SINE/MIR 203 TCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTA 154 chr3ptel1M 767082 TGATCCCCCTTTTACAAAGGAGGAAACTGAGG--CAG-GAGGCC-AGTGA 767127 v v i v -- - ii- C MIRc#SINE/MIR 153 TTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGA 104 chr3ptel1M 767128 C 767128 C MIRc#SINE/MIR 103 C 103 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 22.22 CpG sites = 9, Kimura (unadjusted) = 22.22 Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.06 (5 / 83), avg. gap size = 3.40 (17 / 5) 285 22.86 5.71 0.00 chr3ptel1M 767045 767114 (232886) C MIRb#SINE/MIR (71) 197 124 m_b129s601i17 4800 chr3ptel1M 767045 TCTCCCTTGGTCCTTGCCACAGCCCAG--AGGCAG--ATCCTGATCCCCC 767090 vi ii ii v i v -- i -- iv v v C MIRb#SINE/MIR 197 TCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATTATCCCCA 148 chr3ptel1M 767091 TTTTACAAAGGAGGAAACTGAGGC 767114 i v C MIRb#SINE/MIR 147 TTTTACAGATGAGGAAACTGAGGC 124 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.67 CpG sites = 9, Kimura (unadjusted) = 27.67 Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.03 (2 / 69), avg. gap size = 2.00 (4 / 2) 52 24.72 3.27 5.24 chr3ptel1M 768463 768676 (231324) (GGAGGA)n#Simple_repeat 1 210 (0) m_b129s252i12 4801 chr3ptel1M 768463 GGAGAGAGAAGG-GGAAGGGGAGGAAGAAGGA-GAGAGACGGGGAGGGAG 768510 - i - i i - i - - v i ii (GGAGGA)n#Sim 1 GGAG-GAGGAGGAGGAGGAGGAGG-AGGAGGAGGAG-GAGGAGGAGGAGG 47 chr3ptel1M 768511 AGGGGAAGGAGGAGGAAGAGGCAGGAGAAAGGA-AAGGGAAAGAAGAAAG 768559 i i i - -i -i iii i i i (GGAGGA)n#Sim 48 AGGAGGAGGAGGAGGAGGAGG-AGGAG-GAGGAGGAGGAGGAGGAGGAGG 95 chr3ptel1M 768560 A-GAGG-GAAGGGGGAGGGAGGAGAAGACAAAGGACAAAAGAGGAGGAAG 768607 - - i i - i ivii -ii i - (GGAGGA)n#Sim 96 AGGAGGAGGAGGAGGA-GGAGGAGGAGGAGGAGGA-GGAGGAGGAGG-AG 142 chr3ptel1M 768608 GGGAAGGA-AAGGAGAAGGAAGAAGGA-GAGGAGGAGTTAGGACCCAGGA 768655 i i -i i - i - -v -vv (GGAGGA)n#Sim 143 GAGGAGGAGGAGGAGGAGG-AGGAGGAGGAGGAGGAG-GAGGA-GGAGGA 189 chr3ptel1M 768656 TAAGGAGGAGGAGGAGGAGGA 768676 vi (GGAGGA)n#Sim 190 GGAGGAGGAGGAGGAGGAGGA 210 Matrix = Unknown Transitions / transversions = 5.50 (33/6) Gap_init rate = 0.08 (18 / 213), avg. gap size = 1.00 (18 / 18) 36 2.70 0.00 0.00 chr3ptel1M 768693 768730 (231270) (GGGAAG)n#Simple_repeat 1 38 (0) c_b129s251i0 4802 chr3ptel1M 768693 GGGAAGGGAAAGGGGAAGGGGAAGGGGAAGGGGAAGGG 768730 i (GGGAAG)n#Sim 1 GGGAAGGGGAAGGGGAAGGGGAAGGGGAAGGGGAAGGG 38 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 221 20.45 0.00 0.00 chr3ptel1M 769758 769801 (230199) MIRc#SINE/MIR 72 115 (153) m_b129s601i19 4803 chr3ptel1M 769758 TGACGCTTCCCAGCTGTGGGGCCCTGGGCAAGTCACATAACCCC 769801 v i v i v i i v i MIRc#SINE/MIR 72 TGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 24.17 CpG sites = 5, Kimura (unadjusted) = 24.17 Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 86 7.35 0.84 0.84 chr3ptel1M 770553 770671 (229329) (CCT)n#Simple_repeat 1 119 (0) c_b129s251i1 4804 chr3ptel1M 770553 CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTTT 770602 ii (CCT)n#Simple 1 CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC 50 chr3ptel1M 770603 TCTTCCTCTTCCTCCTCTTCTTCC-CCCCCTCCTCCTCCTCCTCCTCCTC 770651 i i i i - i (CCT)n#Simple 51 TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC 100 chr3ptel1M 770652 TTCCTCCTCCTTCCTCCTCC 770671 i - (CCT)n#Simple 101 CTCCTCCTCC-TCCTCCTCC 119 Matrix = Unknown Transitions / transversions = 1.00 (8/0) Gap_init rate = 0.02 (2 / 118), avg. gap size = 1.00 (2 / 2) 60 20.70 0.81 0.00 chr3ptel1M 771074 771196 (228804) (GA)n#Simple_repeat 1 124 (0) m_b129s252i13 4805 chr3ptel1M 771074 GAGAGAGAGGGAG-GGGGGAGAGAAAGAGACAGAGACACAAAGAGAGACA 771122 i - i i i v v v i v (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr3ptel1M 771123 GAAAGGGGGAGAGACAGAGACAGGGAGAGAGAGAAAGGGAGGCAGAGAGA 771172 i i i v v i i i iv (GA)n#Simple_ 51 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 100 chr3ptel1M 771173 GACAGAGACAGAGAGAGAGGGAGA 771196 v v i (GA)n#Simple_ 101 GAGAGAGAGAGAGAGAGAGAGAGA 124 Matrix = Unknown Transitions / transversions = 1.44 (13/9) Gap_init rate = 0.01 (1 / 122), avg. gap size = 1.00 (1 / 1) 18 4.77 0.00 0.00 chr3ptel1M 771214 771235 (228765) (C)n#Simple_repeat 1 22 (0) m_b129s252i14 4806 chr3ptel1M 771214 CCCTCCCCCCCCCCCCCCCCCC 771235 i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCC 22 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 173 15.47 0.34 0.34 chr3ptel1M 771891 772187 (227813) (GGAG)n#Simple_repeat 1 297 (0) m_b129s252i15 4807 chr3ptel1M 771891 GGACGGAAGGAGGGAAGGAAGAAGGGAGGGAGGGAAGGAAGGAGGGAGGG 771940 v i i i i i i (GGAG)n#Simpl 1 GGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGG 50 chr3ptel1M 771941 AGGGAAGGAAGGAAGGAGGGAAGGA-AGAAGGAGGGAGGGAAGGAAGGAG 771989 i i i i -i i i i (GGAG)n#Simpl 51 AGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAG 100 chr3ptel1M 771990 GGGGAGGAAGGAAGAAGGGAGGGAGGGAAGGAAGGAGGGAGGGAGGGAGG 772039 i - i i i i i (GGAG)n#Simpl 101 GGAG-GGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGG 149 chr3ptel1M 772040 GAGGGAAGGAAGGAGGGAGGGAGGGAAGGAAGGAGGGAAGGAAGAAGGGA 772089 i i i i i i i (GGAG)n#Simpl 150 GAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGA 199 chr3ptel1M 772090 GGGAGGGAAGGAAGGAGGGAGGGAGGGAAGGAAGGAGGGAGGGAGGGAGA 772139 i i i i i (GGAG)n#Simpl 200 GGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGG 249 chr3ptel1M 772140 GATGGAGGGAGGGAAGGATGGATAGAGGGATGGAGGGAGGGATGGAGG 772187 v i v vi v v (GGAG)n#Simpl 250 GAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGG 297 Matrix = Unknown Transitions / transversions = 5.67 (34/6) Gap_init rate = 0.01 (2 / 296), avg. gap size = 1.00 (2 / 2) 12 4.77 4.55 0.00 chr3ptel1M 772419 772440 (227560) (AAAG)n#Simple_repeat 1 23 (0) m_b129s252i16 4808 chr3ptel1M 772419 AAAGAAAGAAA-AAGGAAAGAAA 772440 - i (AAAG)n#Simpl 1 AAAGAAAGAAAGAAAGAAAGAAA 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.05 (1 / 21), avg. gap size = 1.00 (1 / 1) 15 21.86 5.66 0.00 chr3ptel1M 773816 773868 (226132) (AAGGG)n#Simple_repeat 1 56 (0) m_b129s252i17 4809 chr3ptel1M 773816 AAGGGTAAGGAAGGGAATGG-GGGGTAAGGAAGGG-AGTG-GGGGTAAGG 773862 v i v -i v i - v -i v i (AAGGG)n#Simp 1 AAGGGAAGGGAAGGGAAGGGAAGGGAAGGGAAGGGAAGGGAAGGGAAGGG 50 chr3ptel1M 773863 AAGGGA 773868 (AAGGG)n#Simp 51 AAGGGA 56 Matrix = Unknown Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.06 (3 / 52), avg. gap size = 1.00 (3 / 3) 82 21.43 0.58 0.00 chr3ptel1M 774417 774588 (225412) (CA)n#Simple_repeat 1 173 (0) m_b129s252i18 4810 chr3ptel1M 774417 CACACACACACACACACACACACACACTCACACATGCACACTCACACTTG 774466 v ii v vii (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 chr3ptel1M 774467 CACATGCACACACACTCACTCTCTCTCACACACTCACACACATACATGCA 774516 ii v v v v v v i ii (CA)n#Simple_ 51 CACACACACACACACACACACACACACACACACACACACACACACACACA 100 chr3ptel1M 774517 CACACACAC-CCCACACATACACTCACACTCACACATTCACACGCTCACA 774565 - v i v v iv i v (CA)n#Simple_ 101 CACACACACACACACACACACACACACACACACACACACACACACACACA 150 chr3ptel1M 774566 TATACTCACACACACTCTCTCAC 774588 i i v v v v (CA)n#Simple_ 151 CACACACACACACACACACACAC 173 Matrix = Unknown Transitions / transversions = 0.78 (14/18) Gap_init rate = 0.01 (1 / 171), avg. gap size = 1.00 (1 / 1) 313 35.44 10.98 0.52 chr3ptel1M 775036 775208 (224792) C MIR3#SINE/MIR (1) 207 17 m_b129s601i20 4811 chr3ptel1M 775036 AGTTCTAACAGCACAGAGGAGCCGGCGTTGGTGGGGGCCA-AATGACCGG 775084 i iv iv v i iv- i i v i vi i v- iv i iv C MIR3#SINE/MIR 207 AATCATAGAATCATAGAAT-GTCAGAGCTGGAAGGGACCTTAGAGATCAT 159 chr3ptel1M 775085 CAAGGCTAAGCTCCTTGTTTTACAGATGAGTAAACCGAGGCTTGGGAA-- 775132 v v i v i ii v i iii ii -- C MIR3#SINE/MIR 158 CTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGG 109 chr3ptel1M 775133 --AAGTGACAGGCCTG------------CAGTAAGTGACAGAAGTGGAAT 775168 -- vv ii------------? v i ivi i i C MIR3#SINE/MIR 108 TGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGAC 59 chr3ptel1M 775169 TTGATCTCAGG--TTCTGCTTGAGAGCCAGGGCTCTCTCCAC 775208 v v i -- i vi vvv i v v ii C MIR3#SINE/MIR 58 TAGAACCCAGGTCTCCTGACTCCCAGTCCGTGCTCTCTCTGC 17 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 49.33 CpG sites = 36, Kimura (unadjusted) = 50.53 Transitions / transversions = 1.44 (36/25) Gap_init rate = 0.03 (6 / 172), avg. gap size = 3.33 (20 / 6) 354 23.89 17.70 0.00 chr3ptel1M 775096 775208 (224792) C MIRb#SINE/MIR (115) 153 21 m_b129s601i21 4811 chr3ptel1M 775096 TCCTTGTTTTACAGATGAGTAAACCGAGGCTTGGGAA----AAGTGACAG 775141 iii v i ii ii ---- i vv C MIRb#SINE/MIR 153 TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTT 104 chr3ptel1M 775142 GCCT-----------GC-AGTAAGTGACAGAAGTGGAATTTGATCTCAGG 775179 i----------- - i ivi i i v i C MIRb#SINE/MIR 103 GCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGG 54 chr3ptel1M 775180 T---TCTG-CTTGAGAGCCAGGGCTCTCTCCAC 775208 --- - iv i v v i C MIRb#SINE/MIR 53 TCTGTCTGACTCCAAAGCCCGTGCTCTTTCCAC 21 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.33 CpG sites = 19, Kimura (unadjusted) = 29.95 Transitions / transversions = 2.38 (19/8) Gap_init rate = 0.04 (5 / 112), avg. gap size = 4.00 (20 / 5) 14 15.34 2.63 2.63 chr3ptel1M 775331 775368 (224632) (CCCTCTT)n#Simple_repeat 1 38 (0) m_b129s252i19 4812 chr3ptel1M 775331 CCCT-TTCCCTCTGCTCTCAGCCCTCTTCCCAGCTTCCC 775368 - v i vv -v (CCCTCTT)n#Si 1 CCCTCTTCCCTCTTCCCTCTTCCCTCTTCCC-TCTTCCC 38 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 15 10.70 3.03 3.03 chr3ptel1M 777760 777792 (222208) (GGGA)n#Simple_repeat 1 33 (0) m_b130s252i0 4813 chr3ptel1M 777760 GGGAGGG-GGGAGAAAGGGGGCGGAGGGAGGGAG 777792 - ii i - (GGGA)n#Simpl 1 GGGAGGGAGGGAGGGAGGGAG-GGAGGGAGGGAG 33 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.06 (2 / 32), avg. gap size = 1.00 (2 / 2) 17 24.64 0.00 5.00 chr3ptel1M 778135 778197 (221803) (CTCCGG)n#Simple_repeat 1 60 (0) m_b130s252i1 4814 chr3ptel1M 778135 CTCCTGGACCCGGCTCCGGCTCCGGCGCTCGGGTCCCTCCCCGGGCTCTG 778184 - vi v - v vv i - i (CTCCGG)n#Sim 1 CTCC-GGCTCCGGCTCCGGCTCCGGCTC-CGGCTCCGGCTCC-GGCTCCG 47 chr3ptel1M 778185 CCTCCAACTTCGG 778197 v ii i (CTCCGG)n#Sim 48 GCTCCGGCTCCGG 60 Matrix = Unknown Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.05 (3 / 62), avg. gap size = 1.00 (3 / 3) 19 17.24 3.03 6.25 chr3ptel1M 779964 780029 (219971) (AGGG)n#Simple_repeat 1 64 (0) m_b130s252i2 4815 chr3ptel1M 779964 AGGGAAGGAGGGAGGGAGGGAGAGAGCG-GGCCGGCTAGGGGAGGGACTG 780012 i i v - vv -v - -v (AGGG)n#Simpl 1 AGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGG-GA-GGGAGGGA-GG 47 chr3ptel1M 780013 GAGAAGAGGG-GGAAGGG 780029 -i - i (AGGG)n#Simpl 48 GAG-GGAGGGAGGGAGGG 64 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.09 (6 / 65), avg. gap size = 1.00 (6 / 6) 17 29.84 0.00 6.10 chr3ptel1M 780372 780458 (219542) (CACACG)n#Simple_repeat 1 82 (0) m_b130s252i3 4816 chr3ptel1M 780372 CACACTCGTACACACCCGTACACACAGACCTGCACACGCAAGTGCACACC 780421 v ii i v i i v - - vii - (CACACG)n#Sim 1 CACACGCACACGCACACGCACACGCACA-C-GCACACGCACACGCACA-C 47 chr3ptel1M 780422 ACGCACTGCAGACCCTCATCTTACAAGCACACGCACA 780458 i i - v v v - vi v (CACACG)n#Sim 48 GCACAC-GCACACGCACA-CGCACACGCACACGCACA 82 Matrix = Unknown Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.06 (5 / 86), avg. gap size = 1.00 (5 / 5) 259 35.12 12.69 2.18 chr3ptel1M 780594 781050 (218950) C L2#LINE/L2 (769) 2313 1810 m_b130s601i0 4817 chr3ptel1M 780594 TAAACCTGTGGACATTGAGAAGATCACCAAATGAGAATAGGGAGAGAAGG 780643 v ii iivv v vi ? -- i i ii viv vi C L2#LINE/L2 2313 TAAAGCCATGAGACTGGATGAGATCACCNA--GGGAGTGAGTGTAGATAG 2266 chr3ptel1M 780644 AGGAGAGAAGGAGGACCA--GACAGAGCCTCAGGG-GCTCAGACACCCAG 780690 i - v -- v iii -i vi iii? C L2#LINE/L2 2265 AGAAGAGAA-GAGGTCCAAGGACTGAGCCCTGGGGCACTCCAACGTTNAG 2217 chr3ptel1M 780691 AGGT--GGGGGGTGAAG----CCCAGAGGATGAAGACCGAG--GGAGAGA 780732 -- i i i ----v vii - i i -- v i C L2#LINE/L2 2216 AGGTCGGGGAGATGAGGAGGAACCAGCAAA-GGAGACTGAGAAGGAGCGG 2168 chr3ptel1M 780733 CC--TGAG------------CCAGGAGAGACCGGGGTCTTGTAAAGCTCG 780768 -- ------------ vvi v i v iv vv C L2#LINE/L2 2167 CCAGTGAGGTAGGAGGAAAACCAGGAGAGTGTGGTGTCCTGGAAGCCAAG 2118 chr3ptel1M 780769 GGATGAAAACGAGCTCCCGAGGAGGGCTTG-TCAGCACCGTC-AGTGCCA 780816 v v ii vviivvvi vv - i vvi - i ii C L2#LINE/L2 2117 TGAAGAAAGTGTTTCAAGAAGGAGGGAGTGATCAACTGTGTCAAATGCTG 2068 chr3ptel1M 780817 TGGAGGCGACAAGAAGGGATAAAGATTGAGAA---AATGTGGGGGCGTTT 780863 iv ?iv v v -i i i i --- vii v ---i C L2#LINE/L2 2067 CTGANAGGTCAAGTA-AGATGAGGACTGAGAATTGACCATTGG---ATTT 2022 chr3ptel1M 780864 GGCAATTCAGAGATCACTTGCAACCCCAGAGACAGAGGAGGGTTCCACTG 780913 i ivii i i v ii ii--- iii vi v viiv C L2#LINE/L2 2021 AGCAACGTGGAGGTCATTGGTGACCTT---GACAAGAGCAGTTTCGGTGG 1975 chr3ptel1M 780914 AGT--------CAGAAGC--GACACGGAAGAGTTC---AGTGAATGAGAG 780950 -------- ii -- ivv iiv i --- v i C L2#LINE/L2 1974 AGTGGTGGGGACGAAAGCCTGATTGGAGTGGGTTCAAGAGAGAATGGGAG 1925 chr3ptel1M 780951 AAAACAAAGTAGAGGC--CAAAAAAAGAC-CCATTATCAAG--------- 780988 i i vi v i i -- i iv v -v vi v i --------- C L2#LINE/L2 1924 GAGAGGAATTGGAGACAGCGAGTATAGACAACTCTTTCGAGGAGTTTTGC 1875 chr3ptel1M 780989 ---AAAGGGGGGAAGAGAAATCGGAGAGAGGCTTGGAGGGCAAGTGGGAT 781035 --- i v v ivi vi v ii v ? i C L2#LINE/L2 1874 TGTAAAGGGGAGCAGAGAAATGGGGCGGTAGCTGGAGGGGGANGTGGGGT 1825 chr3ptel1M 781036 CTGGTGAGAGCTCCT 781050 vi v ii ii C L2#LINE/L2 1824 CAAGGGAGAATTTTT 1810 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 47.59 CpG sites = 94, Kimura (unadjusted) = 50.34 Transitions / transversions = 1.49 (94/63) Gap_init rate = 0.06 (28 / 456), avg. gap size = 2.46 (69 / 28) 537 30.04 6.34 0.93 chr3ptel1M 781238 781442 (218558) C MIRc#SINE/MIR (39) 229 14 m_b130s601i1 4818 chr3ptel1M 781238 TTTATATAGCCGCCTGCAAATACG--ATCTCGTTTGAGCCTCACC-CAAG 781284 i v - i v v i-- i v v- v C MIRc#SINE/MIR 229 TTTACAAAGC-GCTTTCACATACATTATCTCATTTGATCCTCACAACAAC 181 chr3ptel1M 781285 CTTGGGAGGGAG-------TGCTGTCATTATCCTCACTTTGCAGATGAAG 781327 i v v -------v v i i i i i i C MIRc#SINE/MIR 180 CCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGG 131 chr3ptel1M 781328 AAACTACAGCAAATAGAGACT--GTCGTTT-CCCAGGGTCCTACAGCCAG 781374 ivi vv v ii -- vii - i vi i C MIRc#SINE/MIR 130 AAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG 81 chr3ptel1M 781375 CCAGTGTCAGAGGCTGGATTTGAGATCAGGGCTGCCCTTTCTGGAGGCCA 781424 iv v v v i i ivi v -i vv vv i i v C MIRc#SINE/MIR 80 TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCT-TCCTGACTCCAAGTCC 32 chr3ptel1M 781425 GGTGCTCCGGCCACCCCA 781442 i ivv iv C MIRc#SINE/MIR 31 AGTGCTCTTTCCACTGCA 14 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.14 CpG sites = 31, Kimura (unadjusted) = 38.94 Transitions / transversions = 1.03 (31/30) Gap_init rate = 0.03 (7 / 204), avg. gap size = 2.14 (15 / 7) 593 32.19 7.20 4.20 chr3ptel1M 782067 782413 (217587) C L3#LINE/CR1 (137) 3962 3606 m_b130s601i2 4819 chr3ptel1M 782067 GGGAACTCACTTAGCTTCCAAGGCAGCTGAG---GTTTCTGAACAGCTCT 782113 i - v i? i iv v---i i i C L3#LINE/CR1 3962 GGGAGCTCACT-ACCTCNCGAGGCAGCCCATTCCATTTTTGGACAGCTCT 3914 chr3ptel1M 782114 TGACTGATGGAAAGTTTGTCCTGAGGTGCAACTGGAATCTGCTTCCCTCC 782163 - i v i iv v vi vv i i i i vi C L3#LINE/CR1 3913 -GATTGTTAGAAAGTTCTTCCTTATATTGAGCCGAAATCTGCCTCCCTGT 3865 chr3ptel1M 782164 AGCTTTGTTCCATTGCTGCCAGTTCTGCCTTCCAAGGCCAAGCTGAGCAA 782213 i ivvi v v i i iiii vi v ii C L3#LINE/CR1 3864 AACTTCCACCCATTGGTCCTAGTTCTGCCCTCTGGAGCCACACAGAATAA 3815 chr3ptel1M 782214 GGCTCCTGATGTCTCTCACCTCTTCCATGTGACAGCCTGGGGGCCACCCG 782263 ---i i -------v ii ivvviivi iii C L3#LINE/CR1 3814 G---TCTAAT-------CCCTCTTCCACATGACAGCCCTTCAAATATTTG 3775 chr3ptel1M 782264 AAGCCCCGGATC--GCCCTCCCTA---CTGC-CCCCTCCCGTTT-----T 782302 v vvvv -- i ii i --- v - ii v vi ----- C L3#LINE/CR1 3774 AAGACAGCTATCATGTCTCCTCTAAGTCTTCTCTTCTCCAGGCTAAACAT 3725 chr3ptel1M 782303 CTCTGG--CCTCAGAACGTTCCCTCCAAGGA---GGCTT-CAGCCCGGTT 782346 i ii -- ivi v - vv v --- i - v -v C L3#LINE/CR1 3724 CCCCAGTTCCTTCAACCGTT-CCTCATATGACATGGTTTCCAGACC-CTT 3677 chr3ptel1M 782347 CAGCACCC----CTTTTTTGTCTGGGACGTGCCCTACTTT-TCAGGGTCC 782391 v i ---- vi i iv - i i i v - iv C L3#LINE/CR1 3676 CACCATCCTGGTCGCTCTCCTCT-GGACGCGCTCCAGTTTGTCAATGTCC 3628 chr3ptel1M 782392 CTTCCAAAATGTAGCACTCAGA 782413 iii i i i C L3#LINE/CR1 3627 CTCTTAAAATGTGGCGCCCAGA 3606 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.86 CpG sites = 66, Kimura (unadjusted) = 44.09 Transitions / transversions = 1.61 (66/41) Gap_init rate = 0.07 (25 / 346), avg. gap size = 1.60 (40 / 25) 200 18.21 8.20 10.00 chr3ptel1M 782968 783028 (216972) C MIR3#SINE/MIR (125) 83 24 m_b130s601i3 4820 chr3ptel1M 782968 AGGTAGTGAGTGGCAAAGCCAGGAATAAAATC-----CTCCTGACTCTTC 783012 v? v i i v i i ----- --- C MIR3#SINE/MIR 83 AGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGTCTCCTGACTC--- 37 chr3ptel1M 783013 TGACCAGCTGGTGCTC 783028 --- iiv C MIR3#SINE/MIR 36 ---CCAGTCCGTGCTC 24 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 19.26 CpG sites = 6, Kimura (unadjusted) = 21.58 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.12 (7 / 60), avg. gap size = 1.57 (11 / 7) 239 34.96 0.00 2.41 chr3ptel1M 783207 783291 (216709) C L2c_3end#LINE/L2 (7) 471 389 m_b130s601i4 4821 chr3ptel1M 783207 CAGTCAGCCAATCAGCACTAAGTGCCTCCTGTGTGCCAGGGGGCCTGGGG 783256 v i v ivvvi i i i v i v -- C L2c_3end#LINE 471 CATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCG--CTGGGG 424 chr3ptel1M 783257 GCACTAAGAAAGTCAAAAGACAGCCCTCGCTCTCA 783291 ii v viivi i v i i ii i C L2c_3end#LINE 423 ATACAAAGATGAATAAGACACGGTCCCTGCCCTCA 389 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.70 CpG sites = 18, Kimura (unadjusted) = 49.47 Transitions / transversions = 1.64 (18/11) Gap_init rate = 0.02 (2 / 84), avg. gap size = 1.00 (2 / 2) 216 33.13 10.86 6.01 chr3ptel1M 783776 784125 (215875) C L2#LINE/L2 (367) 2715 2350 m_b130s601i5 4821 chr3ptel1M 783776 CCCGGTGTGAGGAGATGAGGGCCCGCACCAAAACTACCGTAGTGTCGGAG 783825 v i v iv iv ii v iiiiviiv i vv v C L2#LINE/L2 2715 CCAGGCGAGAGATGATGGTGGCTTGGACCAGGGTGGTGGCAGTGGAGGTG 2666 chr3ptel1M 783826 GAGAGAAGGGGCGTCCCAGAGTGGGGAGAGAAGGGGCATCCCAGAGGGAG 783875 v v i---- i v vv v -------i iiiii v C L2#LINE/L2 2665 GTGAGAAGTGGT----CGGATTCTGGATA-------TATTTTGAAGGTAG 2627 chr3ptel1M 783876 AAGCAGCAGAGCTCAGCCCCAGAGTGGATTTGGGG-GTGAGAGTGTGGGA 783924 iv ii iii iivivvii v v - viv i C L2#LINE/L2 2626 AGCCGACAGGATTTGCTGATGGATTGGATGTGGGGTGTGAGAGAAAGAGA 2577 chr3ptel1M 783925 GGAGTCAAGGAGGACTCCCGGGCTATGGGTCTGGCC--CTGGGAGGACAT 783972 v vi i v v i iv -- i -- C L2#LINE/L2 2576 GGAGTCAAGGATGACTCCAAGGTTTTTGGCCTGAGCAACTGGAAGG--AT 2529 chr3ptel1M 783973 GGAACAGACTGTT-CCATGTCACAGAAGTGGCAGGAGAC------ATGA- 784014 ------- - - ? v ii -i i ------ v - C L2#LINE/L2 2528 GGA-------GTTGCCAT-TNACTGAGATGG-GGAAGACTGCGGGAGGAG 2488 chr3ptel1M 784015 -AGGCTTGGCAGGGAA-ATAAAGAGCTCAG----GGGCCC------CCTG 784052 - i ivi - v i i ---- i vi------ii C L2#LINE/L2 2487 CAGGTTTGAGGGGGAAGATCAGGAGTTCAGTTTTGGACATGTTAAGTTTG 2438 chr3ptel1M 784053 AGCAGCC------ACTTCCCACTG-------CCAGTGGGTAG--GAAGAT 784087 vv ------ v v v ------- v i i -- i v C L2#LINE/L2 2437 AGATGCCTATTAGACATCCAAGTGGAGATGTCGAGTAGGCAGTTGGATAT 2388 chr3ptel1M 784088 GGGGGACTAGAGAGCAGGAGGGAGGCTGGGGCTGGAAA 784125 iv i v i vv i i iiv i C L2#LINE/L2 2387 ACGAGTCTGGAGTTCAGGGGAGAGGTCCGGGCTGGAGA 2350 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.78 CpG sites = 62, Kimura (unadjusted) = 45.48 Transitions / transversions = 1.32 (62/47) Gap_init rate = 0.10 (34 / 349), avg. gap size = 1.76 (60 / 34) 405 28.66 3.42 2.03 chr3ptel1M 784336 784481 (215519) MIRb#SINE/MIR 4 151 (117) m_b130s601i6 4822 chr3ptel1M 784336 AGGGGCACTGTGGTGCT-CGAGCAGAGGCCGGGCTCAGGA---AGGCTCC 784381 vi v-i iiv vv iv --- i vvv MIRb#SINE/MIR 4 AGGGGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGA 53 chr3ptel1M 784382 TCTTCGGAGTTCAAATCTGGCCTCAGCCACTGCCCAGCTCTGGGACTCGG 784431 i --- i i iv v v vv i v v iiv MIRb#SINE/MIR 54 CCT---GGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTG 100 chr3ptel1M 784432 GGCACGCCGCTTCAC-TCTGTTTGCCTCCGTTTCCTTATCTGTAAAATGA 784480 v iii v - v vv v i i MIRb#SINE/MIR 101 GGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGG 150 chr3ptel1M 784481 G 784481 MIRb#SINE/MIR 151 G 151 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.21 CpG sites = 18, Kimura (unadjusted) = 36.30 Transitions / transversions = 0.78 (18/23) Gap_init rate = 0.04 (6 / 145), avg. gap size = 1.33 (8 / 6) 12 16.47 6.98 2.22 chr3ptel1M 786199 786241 (213759) (AGGTGA)n#Simple_repeat 1 45 (0) m_b130s252i4 4823 chr3ptel1M 786199 AGGTGAAGAAGAA-TTGGAGGTGAAGG-G-GGGTCGGAGGTGAAGG 786241 iv -v i - -i - i (AGGTGA)n#Sim 1 AGGTGAAGGTGAAGGTGAAGGTGAAGGTGAAGGT-GAAGGTGAAGG 45 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.10 (4 / 42), avg. gap size = 1.00 (4 / 4) 32 8.65 2.04 0.00 chr3ptel1M 786837 786885 (213115) (TG)n#Simple_repeat 1 50 (0) c_b130s251i0 4824 chr3ptel1M 786837 TGTGTGTGTGTGTGTCTGCGTGTGTCTGTGTG-GTGTGTGTGTGAGTGTG 786885 v i v - v (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.02 (1 / 48), avg. gap size = 1.00 (1 / 1) 309 34.95 0.97 0.00 chr3ptel1M 788994 789096 (210904) MIRc#SINE/MIR 37 140 (128) m_b130s601i7 4825 chr3ptel1M 788994 TGGAGCCAGGGAGAT-GGGGTTCAAATCCAGACCCAAACACCTGGCGGCC 789042 i i i-v i i v i i viv i ivii i MIRc#SINE/MIR 37 TGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCT 86 chr3ptel1M 789043 GTGTGATCCTGGACAGGTCCCTTAACTTAGGCACCCCTCGCTTTTCTCCA 789092 i i i i v i vvviivv iv i vv MIRc#SINE/MIR 87 GTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCAT 136 chr3ptel1M 789093 CTGT 789096 MIRc#SINE/MIR 137 CTGT 140 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 47.37 CpG sites = 22, Kimura (unadjusted) = 49.33 Transitions / transversions = 1.57 (22/14) Gap_init rate = 0.01 (1 / 102), avg. gap size = 1.00 (1 / 1) 236 32.14 5.95 0.00 chr3ptel1M 789727 789810 (210190) MIR3#SINE/MIR 88 176 (32) m_b130s601i8 4826 chr3ptel1M 789727 GGCCTGGAGGGAGGAACTTCA--AGTCTAGTCCTCGGTTTCCTCA--TGT 789772 i v i vi vv --vv i v i -- MIR3#SINE/MIR 88 GACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGT 137 chr3ptel1M 789773 AGGACGAGAAAACCGAGCTCGATGATCTCCAC-ATCCCT 789810 ii i iiiiii ii v i v-i MIR3#SINE/MIR 138 AAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCT 176 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.39 CpG sites = 18, Kimura (unadjusted) = 44.39 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.04 (3 / 83), avg. gap size = 1.67 (5 / 3) 27 25.44 1.33 0.00 chr3ptel1M 790350 790424 (209576) (GGAA)n#Simple_repeat 1 76 (0) m_b130s252i5 4827 chr3ptel1M 790350 GGAAGGAAGGAATGGGCAAAGGAAGGAAGGAAGG-CTGAAGGACGGGATG 790398 v iivi -vv v i v (GGAA)n#Simpl 1 GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG 50 chr3ptel1M 790399 AGGGAAGGAAGGAGCAAAAGAAGAAA 790424 i ivi i i (GGAA)n#Simpl 51 AAGGAAGGAAGGAAGGAAGGAAGGAA 76 Matrix = Unknown Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.01 (1 / 74), avg. gap size = 1.00 (1 / 1) 15 4.77 0.00 0.00 chr3ptel1M 790557 790578 (209422) (TGAG)n#Simple_repeat 1 22 (0) m_b130s252i6 4828 chr3ptel1M 790557 TGAGTGAGCGAGTGAGTGAGTG 790578 i (TGAG)n#Simpl 1 TGAGTGAGTGAGTGAGTGAGTG 22 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 35 29.44 2.67 1.99 chr3ptel1M 793567 793716 (206284) (TGTTT)n#Simple_repeat 1 151 (0) m_b130s252i7 4829 chr3ptel1M 793567 TGTTTTGTTTTTGTTTT-TATT-TTGTGTTTTCTGTT-TTTAATTTTCCT 793613 - - v - v v v - vi vi (TGTTT)n#Simp 1 TGTTTTG-TTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTT 49 chr3ptel1M 793614 TTACTTTG-TTTGTTTTCCTTGTTTTTGTTTGCCCCTTGTTTTGTTTTGT 793662 ii - vi vv -ivii (TGTTT)n#Simp 50 TTGTTTTGTTTTGTTTTGTTTTGTTTTGTTT-TGTTTTGTTTTGTTTTGT 98 chr3ptel1M 793663 TTTATTTTTTCCCCCTTTCCTTGGGTTGTTTTTATTTTGTTTCCTTGTTA 793712 i v iiivi vi v v vv i iv - i (TGTTT)n#Simp 99 TTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTT-TTG 147 chr3ptel1M 793713 TTTT 793716 (TGTTT)n#Simp 148 TTTT 151 Matrix = Unknown Transitions / transversions = 0.94 (17/18) Gap_init rate = 0.05 (7 / 149), avg. gap size = 1.00 (7 / 7) 16 17.95 5.77 1.85 chr3ptel1M 793771 793822 (206178) (TGGTTT)n#Simple_repeat 1 54 (0) m_b130s252i8 4830 chr3ptel1M 793771 TGATTTTGGTTTTGG-TTTGG-CTT-GTTTTTTTGTGGGTTTTGGGATTT 793817 i - -i - vv v v - v (TGGTTT)n#Sim 1 TGGTTTTGGTTTTGGTTTTGGTTTTGGTTTTGGTTTTGGTTTT-GGTTTT 49 chr3ptel1M 793818 GGATT 793822 v (TGGTTT)n#Sim 50 GGTTT 54 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.08 (4 / 51), avg. gap size = 1.00 (4 / 4) 14 18.44 9.52 1.47 chr3ptel1M 793798 793860 (206140) (TTTTGGGA)n#Simple_repeat 1 68 (0) m_b130s252i9 4831 chr3ptel1M 793798 TTTTGTGGGTTTTGGGA-TTT-GGA--TTGAGATTTTTCCCCTTTTTG-T 793842 - i - - -- i vvvvi vv - (TTTTGGGA)n#S 1 TTTTG-GGATTTTGGGATTTTGGGATTTTGGGATTTTGGGATTTTGGGAT 49 chr3ptel1M 793843 TTTGGGA-TTTAGGATTTT 793860 - i (TTTTGGGA)n#S 50 TTTGGGATTTTGGGATTTT 68 Matrix = Unknown Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.10 (6 / 62), avg. gap size = 1.17 (7 / 6) 284 33.30 6.81 4.08 chr3ptel1M 794970 795160 (204840) MIRc#SINE/MIR 19 214 (54) m_b130s601i9 4832 chr3ptel1M 794970 TGGAGAAGAGAGCTGGGTGGCAGAATGAAAAAAAAGGGCCTGAGTTTTAA 795019 - vi iiv-ii i v ii i ---- i iv i MIRc#SINE/MIR 19 TGGA-AAGAGCACTGGACT-TGGAGTCAGGAAGA----CCTGGGTTCGAG 62 chr3ptel1M 795020 TCCTGCCTCAGAAACT--CTTGC-ATTTTCCCT--GTCGGGTCATTGAAC 795064 i v v vv -- v -i v vv -- v ii i v MIRc#SINE/MIR 63 TCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAAC 112 chr3ptel1M 795065 TTGGCC-TGCCTCAGTTTCCCCATTTCTCAAATGAGAGGCTGACAAGAGT 795113 i vv i-v i i v v -- i v i i v vi MIRc#SINE/MIR 113 CTCTCTGAGCCTCAGTTTCCTCATCTGTAAAAT--GGGGATAATAATACC 160 chr3ptel1M 795114 CGCCC------CCTCCCAGGGCTG-TGAGAGGGTCCCGCGGAATCCTGTT 795156 i ------ v i - v i vvii ii vv v MIRc#SINE/MIR 161 TGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTA 210 chr3ptel1M 795157 TGTG 795160 MIRc#SINE/MIR 211 TGTG 214 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.05 CpG sites = 32, Kimura (unadjusted) = 45.01 Transitions / transversions = 1.10 (32/29) Gap_init rate = 0.07 (14 / 190), avg. gap size = 1.50 (21 / 14) 198 26.25 16.25 0.00 chr3ptel1M 795531 795610 (204390) L2c_3end#LINE/L2 363 455 (23) m_b130s601i10 4833 chr3ptel1M 795531 TCTCTCCCGGTAGAATAAGAG-TCCTTTAGAGGAGGGAT-GTGTTTTGCT 795578 ii iv v iv - v i v i- i ii L2c_3end#LINE 363 TCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATT 412 chr3ptel1M 795579 ----TTTGTATTCC-------TGGCACATGGGAGGTACTTAGT 795610 ---- i ------- i v ii i i L2c_3end#LINE 413 CATCTTTGTATCCCCAGCGCCTGGCACATAGTAGGCGCTCAAT 455 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.73 CpG sites = 15, Kimura (unadjusted) = 33.95 Transitions / transversions = 2.50 (15/6) Gap_init rate = 0.05 (4 / 79), avg. gap size = 3.25 (13 / 4) 13 20.96 3.77 3.77 chr3ptel1M 797196 797248 (202752) (GGGCC)n#Simple_repeat 1 53 (0) m_b130s252i10 4834 chr3ptel1M 797196 GGGCCGGACC-GGCCGGGCAGGGGCACGGGGCCGGAC-AGACTGGCCGGG 797243 i - -v - v v v -i v v (GGGCC)n#Simp 1 GGGCCGGGCCGGGCCGGGC-CGGGC-CGGGCCGGGCCGGGCCGGGCCGGG 48 chr3ptel1M 797244 GCGGG 797248 v (GGGCC)n#Simp 49 CCGGG 53 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.08 (4 / 52), avg. gap size = 1.00 (4 / 4) 12 16.81 7.50 0.00 chr3ptel1M 797494 797533 (202467) (GGCCGG)n#Simple_repeat 1 43 (0) m_b130s252i11 4835 chr3ptel1M 797494 GGCGGGGGCCGGGGCC--GGAAGGGGGGGGGGTC-GGGCCGGG 797533 v -- vv vv i - (GGCCGG)n#Sim 1 GGCCGGGGCCGGGGCCGGGGCCGGGGCCGGGGCCGGGGCCGGG 43 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.50 (3 / 2) 19 21.15 0.00 0.00 chr3ptel1M 798517 798554 (201446) (C)n#Simple_repeat 1 38 (0) m_b130s252i12 4836 chr3ptel1M 798517 CCCCCCCCCCCCCCCCCGTGCTCCCCAGCCCCGCCCCC 798554 viv i vv v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 38 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 28 9.71 0.00 0.00 chr3ptel1M 806057 806100 (193900) (GAGGAG)n#Simple_repeat 1 44 (0) m_b130s252i13 4837 chr3ptel1M 806057 GAGGAGGAAGAGGAGGAGGAGGAGGAAGAGGAGGAGGACCAGGA 806100 i i vv (GAGGAG)n#Sim 1 GAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA 44 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 23 12.56 0.00 0.00 chr3ptel1M 807488 807522 (192478) (C)n#Simple_repeat 1 35 (0) m_b130s252i14 4838 chr3ptel1M 807488 CCCCAGCCACCCCCACCCCCCCCCCCCCCCCCCCC 807522 vv v v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 35 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 13 16.57 0.00 0.00 chr3ptel1M 807810 807836 (192164) (GGC)n#Simple_repeat 1 27 (0) m_b130s252i15 4839 chr3ptel1M 807810 GGCAGAGCCGGCGGTGGCGGCGGCGGC 807836 i v v i (GGC)n#Simple 1 GGCGGCGGCGGCGGCGGCGGCGGCGGC 27 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 13 21.72 0.00 2.63 chr3ptel1M 808105 808143 (191857) (GCCTCG)n#Simple_repeat 1 38 (0) m_b130s252i16 4840 chr3ptel1M 808105 GCCGCGGACTTACCCTCCCCCTCTGGCCTCGGCCTCGGC 808143 v v iiv vv - (GCCTCG)n#Sim 1 GCCTCGGCCTCGGCCTCGGCCTC-GGCCTCGGCCTCGGC 38 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.03 (1 / 38), avg. gap size = 1.00 (1 / 1) 190 30.90 3.15 8.26 chr3ptel1M 811673 811799 (188201) L2#LINE/L2 2026 2146 (936) m_b130s601i11 4841 chr3ptel1M 811673 CCAGCGGTCTGTTCCCATGAAGCCCGTTTCCTCTTAATCCTTGGCTTGTC 811722 ii vi i ---- i --- v --- i i ? L2#LINE/L2 2026 CCAATGGTCAATTCTCA----GTCC---TCATCTTA---CTTGACCTNTC 2065 chr3ptel1M 811723 TGCCGCCTCAGGCGC--TTGGTCACTCTCACCCCCTTGAA--AGTCTCTT 811768 v v v iv i i -- i i v ii -- v i L2#LINE/L2 2066 AGCAGCATTTGACACAGTTGATCACTCCCTCCTTCTTGAAACACTTTCTT 2115 chr3ptel1M 811769 CTCCAGGTTTCCAAGACGTTCCCCTTCTCTG 811799 v iv i i iiiv v iii L2#LINE/L2 2116 CACTTGGCTTCCAGGACACCACACTCTCCTG 2146 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.21 CpG sites = 24, Kimura (unadjusted) = 42.21 Transitions / transversions = 2.00 (24/12) Gap_init rate = 0.10 (12 / 126), avg. gap size = 1.17 (14 / 12) 294 38.86 4.93 0.34 chr3ptel1M 813026 813309 (186691) L1PREC2_3end#LINE/L1 31 327 (580) m_b130s551i0 4842 chr3ptel1M 813026 CAGATTTCTAAGAATATAAGCCATGCTCCGGTTGACAAATGGGCAAAGGA 813075 i vi v v vvv iivi vi i v i L1PREC2_3end# 31 CAAATTTACAAGAAAAAAACAAACAACCCCATTAAAAAGTGGGCAAAGGA 80 chr3ptel1M 813076 CGTGAATGGACAGTCTGGGGATGAACAAGTCGAAGGTATTTAGAGGTCCT 813125 i ii v i vvii v v vi vv v vviiiv v i iviv L1PREC2_3end# 81 CATGAACAGACACTTTTCAAAAGAAGACATACATGCGGCCAACAAGCATA 130 chr3ptel1M 813126 GGAAGAAGGGCTCTAAGTCACT--TGATTGCAGAAATGCAGATGGAAAC- 813172 v i ii v vi -- v iv i vi - L1PREC2_3end# 131 TGAAAAAAAGCTCAATATCACTGATCATTAGAGAAATGCAAATCAAAACC 180 chr3ptel1M 813173 --------ATCTAATTCCTCACCTCCCAGATTGGTCAACATGACCAAG-- 813212 -------- viv ii v vvi v ii vi v vv -- L1PREC2_3end# 181 ACAATGAGATACCATCTCACACCAGTCAGAATGGCTATTATTAAAAAGTC 230 chr3ptel1M 813213 -AAGAGTCATGAATGTCGCAGGGGATGTGGGGAAATTGGGACACTAGTGC 813261 - i i v iii ii vv i v i i vv i i vi i L1PREC2_3end# 231 AAAAAATAACAGATGCTGGCGAGGTTGCGGAGAAAAGGGAACGCTTATAC 280 chr3ptel1M 813262 ATTGTTGGTGGAGTTGTGAACTGATCCAACCCTCTTGGAGAAACACTG 813309 i iiv i i ii i v iv - i v L1PREC2_3end# 281 ACTGTTGGTGGGAGTGTAAATTAGTTCAACCATTGTGGA-AAGCAGTG 327 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 55.08 CpG sites = 59, Kimura (unadjusted) = 56.64 Transitions / transversions = 1.16 (59/51) Gap_init rate = 0.02 (5 / 283), avg. gap size = 3.00 (15 / 5) 424 34.26 5.95 0.38 chr3ptel1M 813051 813302 (186698) L1ME5_3end#LINE/L1 56 321 (620) m_b130s551i1 4842 chr3ptel1M 813051 CTCCGGTTGACAAATGGGCAAAGGACGTGAATGGACAGTCTGGGGATGAA 813100 i ii v v ii ii i i i ivi v i L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chr3ptel1M 813101 CAAGTC-GAAGGTATTTAGAGGTCCTGGAAGAAGGGCTCTAAGTCACT-- 813147 v ii - i -ii v v i ivivv iiv v v i -- L1ME5_3end#LI 106 GAAACCCGAAAG-GCTAACAAGCATATGAAGAGATGCTCAAACTCATTAG 154 chr3ptel1M 813148 TGATTGCAGAAATGCAGATGGAAACATCTA------ATTCCT---CACCT 813188 i iiv i vi v v ------ iv --- L1ME5_3end#LI 155 TAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCT 204 chr3ptel1M 813189 CCCAGATTGGTCAACATGACCAAGAAGAGTCATG---AATGTCGCAGGGG 813235 vii i iv v v vv vv ii v --- i i vv i L1ME5_3end#LI 205 ATTAGACTGGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTGGCGAGG 254 chr3ptel1M 813236 ATGTGGGGAAATTGGGACACTAGTGCATTGTTGGTGGAGTTGTGAACTGA 813285 ? v i v vi i i iiv ii i L1ME5_3end#LI 255 ATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACTGG 304 chr3ptel1M 813286 TCCAACCCTCTTGGAGA 813302 v i v ii L1ME5_3end#LI 305 TGCAGCCATTCTGGAGA 321 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 47.92 CpG sites = 51, Kimura (unadjusted) = 47.92 Transitions / transversions = 1.46 (51/35) Gap_init rate = 0.02 (6 / 251), avg. gap size = 2.67 (16 / 6) 185 30.60 0.00 8.93 chr3ptel1M 815060 815120 (184880) L2a_3end#LINE/L2 454 509 (8) m_b131s601i0 4841 chr3ptel1M 815060 CAGCATCCAAAGAGATGCCCCACTTAGCACACAGTAAGCACTCAATAAGT 815109 ii i i ivii ----- i i i i i L2a_3end#LINE 454 CAGCGCCTAGAACAGTGCC-----TGGCACATAGTAGGCGCTCAATAAAT 498 chr3ptel1M 815110 ACTTGAGGAGT 815120 i vv i L2a_3end#LINE 499 ATTTGTTGAAT 509 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.43 CpG sites = 14, Kimura (unadjusted) = 43.16 Transitions / transversions = 4.67 (14/3) Gap_init rate = 0.08 (5 / 60), avg. gap size = 1.00 (5 / 5) 197 22.50 0.00 0.00 chr3ptel1M 815082 815121 (184879) L2d2_3end#LINE/L2 509 548 (7) m_b131s601i1 4841 chr3ptel1M 815082 CTTAGCACACAGTAAGCACTCAATAAGTACTTGAGGAGTT 815121 i v i i i i vv v L2d2_3end#LIN 509 CCTTGCACACAGTAGGCGCTCAATAAATATTTGTTGATTT 548 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 23.77 CpG sites = 5, Kimura (unadjusted) = 27.12 Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 201 15.15 0.00 0.00 chr3ptel1M 815082 815114 (184886) L2d_3end#LINE/L2 468 500 (16) m_b131s601i2 4841 chr3ptel1M 815082 CTTAGCACACAGTAAGCACTCAATAAGTACTTG 815114 v i i i i L2d_3end#LINE 468 CTGAGCACATAGTAGGCGCTCAATAAATACTTG 500 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 13.87 CpG sites = 4, Kimura (unadjusted) = 17.49 Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 18 17.53 0.00 0.00 chr3ptel1M 818531 818562 (181438) (C)n#Simple_repeat 1 32 (0) m_b131s252i0 4843 chr3ptel1M 818531 CCCCCCCCCCCCCCCCGTTCCCCCCGGCCCCC 818562 vii vv (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 32 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 15 5.56 0.00 0.00 chr3ptel1M 818868 818886 (181114) (G)n#Simple_repeat 1 19 (0) m_b131s252i1 4844 chr3ptel1M 818868 GGGGGGGGGAGGGGGGGGG 818886 i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGG 19 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 21 23.33 0.00 0.00 chr3ptel1M 819348 819392 (180608) (T)n#Simple_repeat 1 45 (0) m_b131s252i2 4845 chr3ptel1M 819348 TTTTCTTTTGTTTTTTTTTTTTTTTAAAATTCCCTTTTTTTTTTT 819392 i v vvvv iii (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 45 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 17 4.94 0.00 0.00 chr3ptel1M 819457 819477 (180523) (T)n#Simple_repeat 1 21 (0) m_b131s252i3 4846 chr3ptel1M 819457 TTTTTTTTTTTTTATTTTTTT 819477 v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTT 21 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 18 43.70 0.00 0.00 chr3ptel1M 819869 819956 (180044) (CC)n#Simple_repeat 1 88 (0) m_b131s252i4 4847 chr3ptel1M 819869 CCCCCCCCCCCCCCCCTTCCCTCCGGGGGCCCCCCTTTTTTCCCCCCCCT 819918 ii i vvvvv iiiiii i (CC)n#Simple_ 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 50 chr3ptel1M 819919 TTTTTCCCCCCCCCTTTTTCCCCCCTTCCCCCCCCCCC 819956 iiiii iiiii ii (CC)n#Simple_ 51 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 88 Matrix = Unknown Transitions / transversions = 4.40 (22/5) Gap_init rate = 0.00 (0 / 87), avg. gap size = 0.0 (0 / 0) 27 15.05 0.00 0.00 chr3ptel1M 820247 820290 (179710) (C)n#Simple_repeat 1 44 (0) m_b131s252i5 4848 chr3ptel1M 820247 CCCCCCCCCCCCCTTCCCCCCCCAAAACCCCCCCCCCCCCCCCC 820290 ii vvvv (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 44 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 537 29.98 13.01 3.53 chr3ptel1M 821949 822363 (177637) C L2#LINE/L2 (491) 2591 2139 m_b131s601i3 4849 chr3ptel1M 821949 TGTGAGGCTGAGAGAG-ACCCAAGGGCGCTTCCC-GGATTTAAGCCTGGG 821996 ivvi - vi ii vi v- v vi i C L2#LINE/L2 2591 TGTGAGAGAAAGAGAGGAGTCAAGGATGACTCCAAGGTTTTTGGCCTGAG 2542 chr3ptel1M 821997 TGACAGGGAAGCTGGTGAGCTGGGAAGCCATTGCCCTCTACAGCAATGGC 822046 ii v i i v v ------------- v i? v vi v C L2#LINE/L2 2541 CAACTGGAAGGATGGAG-------------TTGCCATTNACTGAGATGGG 2505 chr3ptel1M 822047 GAAG-----GGGGGGAGTCGGG--GAGAAACAAAA--AGGAGCTCAATTT 822087 ----- i iv v-- iiiv i -- i i C L2#LINE/L2 2504 GAAGACTGCGGGAGGAGCAGGTTTGAGGGGGAAGATCAGGAGTTCAGTTT 2455 chr3ptel1M 822088 TAGACGCGT--------------CCACTGCACGTCCA-GTGTCAGTTACC 822122 i ii -------------- i i iv i - v- v ii C L2#LINE/L2 2454 TGGACATGTTAAGTTTGAGATGCCTATTAGACATCCAAGTGG-AGATGTC 2406 chr3ptel1M 822123 TAAAAGGTGGTCGGACCCTCGATTCCTGGAGCTCGGGGAGAGAGGTCAGG 822172 v iv ii i iviv v - i i - v C L2#LINE/L2 2405 GAGTAGGCAGTTGGATATACGAGTC-TGGAGTTCAGGG-GAGAGGTCCGG 2358 chr3ptel1M 822173 GCCGGACAGACAGATCTGAGAATCCTT-GCAGAGAGATAGC---TAGAGC 822218 i v v i i i i i v i- v v i i--- i C L2#LINE/L2 2357 GCTGGAGATATAAATTTGGGAGTCATCAGCATATAGATGGTATTTAAAGC 2308 chr3ptel1M 822219 --TGGG---GGGGGAGCTCGCCAACTGAATGAATCCAGAGGGAGAAGAGA 822263 -- i --- iv v i ? vv i i vi vi C L2#LINE/L2 2307 CATGAGACTGGATGAGATCACCNAGGGAGTGAGTGTAGATAGAGAAGAGA 2258 chr3ptel1M 822264 AGAGGACCCTGGTCAGAA-CCTGGGGGTCACCTATGGTTACAGGTTGTGG 822312 v vv v v i- vv v v i v ? v i v C L2#LINE/L2 2257 AGAGGTCCAAGGACTGAGCCCTGGGGCACTCCAACGTTNAGAGGTCGGGG 2208 chr3ptel1M 822313 ---TCTGG------------AGGAGGCAGAGGAGGAGTGGTCAGGGAG-- 822345 --- vv ------------ i v i i i v -- C L2#LINE/L2 2207 AGATGAGGAGGAACCAGCAAAGGAGACTGAGAAGGAGCGGCCAGTGAGGT 2158 chr3ptel1M 822346 -GGAGGAGAACAGAGAGAG 822363 - i vii C L2#LINE/L2 2157 AGGAGGAAAACCAGGAGAG 2139 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.41 CpG sites = 66, Kimura (unadjusted) = 39.68 Transitions / transversions = 1.22 (66/54) Gap_init rate = 0.07 (31 / 414), avg. gap size = 2.26 (70 / 31) 280 20.51 1.52 1.52 chr3ptel1M 822365 822562 (177438) HERVIP10FH#LTR/ERV1 801 998 (4104) m_b131s701i0 4850 chr3ptel1M 822365 CAGAGACAGAGACAGAGA-GAGAAAGAGGCAGAGAGACAAAGGGAGAGAG 822413 -i i v - i iv vi i HERVIP10FH#LT 801 CAGAGA-GGAAAGAGAGAAGAGAGAGAGAGAGAGAGAGGAAGAGAGAGAG 849 chr3ptel1M 822414 ACAGAGAGACAGAGACAAAGAGACAGAGAGACAGAGACAGAGACAAAAAG 822463 v i v v ii v i vi v i HERVIP10FH#LT 850 AGAGAAAGAGAGAGAGAGGGAGAGAGAGAGACAAAGAGGGAGTCAAAGAG 899 chr3ptel1M 822464 ACAGAGAG--AGACAGAGCCAGAAACAGAGAGACAGAGACAGAGCCAGAG 822511 v -- v vv i i vi i HERVIP10FH#LT 900 AGAGAGAGGCAGAGAGAGGAAGAGACAGAGAGACAAAGAGGGAGTCAGAG 949 chr3ptel1M 822512 CCAGAGACAGAGACAGAGAGACACAGAGAGAGACAGACAGACAGACATAG 822561 vv v i --v i v v v v HERVIP10FH#LT 950 AGAGAGAGAGAGACAGAAAG--TCAAAGAGAGAAAGAAAGAGAGAGATAG 997 chr3ptel1M 822562 A 822562 HERVIP10FH#LT 998 A 998 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 24.04 CpG sites = 18, Kimura (unadjusted) = 24.04 Transitions / transversions = 0.82 (18/22) Gap_init rate = 0.03 (5 / 197), avg. gap size = 1.20 (6 / 5) 83 20.81 1.05 1.05 chr3ptel1M 822566 822756 (177244) (AGAGAG)n#Simple_repeat 1 191 (0) m_b131s252i6 4851 chr3ptel1M 822566 AGAGACAGAGAGAGACAGAGACAGACCGAGAGGCAGAGAGAGACAGAGAC 822615 v v v vv iv v v (AGAGAG)n#Sim 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr3ptel1M 822616 AGAGAGAGACAGAGAGAGAAAGAGACAAAGACAG-GAGAGAGACAGAG-G 822663 v i v i v - v - (AGAGAG)n#Sim 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 100 chr3ptel1M 822664 AGAGAGATGGAGAGATGAGACAGACTGAGACAGAGAGAGATGGAGGAAGA 822713 vi - v vv v vi ii (AGAGAG)n#Sim 101 AGAGAGAGAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 149 chr3ptel1M 822714 GAGAGAGACAGACAGATAGCAGACAGGCACAGAGACAGGGAGA 822756 v v v - v iv v v i (AGAGAG)n#Sim 150 GAGAGAGAGAGAGAGAGAG-AGAGAGAGAGAGAGAGAGAGAGA 191 Matrix = Unknown Transitions / transversions = 0.36 (9/25) Gap_init rate = 0.02 (4 / 190), avg. gap size = 1.00 (4 / 4) 313 22.90 8.25 0.96 chr3ptel1M 822889 822985 (177015) C MIRc#SINE/MIR (66) 202 99 m_b131s601i5 4852 chr3ptel1M 822889 CTCCTGTGATCTGCACAACGACCCTGGGA---AGGAAGTGC---TATGCT 822932 v v iv i v --- v v --- vv C MIRc#SINE/MIR 202 CTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTAT 153 chr3ptel1M 822933 TATCCCCATTGGACAAAAGGAGAAACTGAGGCTGCAGGGTGTCT--GTGG 822980 vv i v ii - i v vi -- i C MIRc#SINE/MIR 152 TATCCCCATTTTACAGATGAGGAAACTGAGGCT-CAGAGAGGTTAAGTGA 104 chr3ptel1M 822981 CTGGC 822985 v C MIRc#SINE/MIR 103 CTTGC 99 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.36 CpG sites = 8, Kimura (unadjusted) = 27.36 Transitions / transversions = 0.57 (8/14) Gap_init rate = 0.04 (4 / 96), avg. gap size = 2.25 (9 / 4) 343 26.32 0.00 0.00 chr3ptel1M 822889 822964 (177036) C MIR#SINE/MIR (70) 192 117 m_b131s601i4 4852 chr3ptel1M 822889 CTCCTGTGATCTGCACAACGACCCTGGGAAGGAAGTGCTATGCTTATCCC 822938 v v i iv i iv i v i i vv C MIR#SINE/MIR 192 CTCATTTAATCCTCACAACAACCCTATGAGGTAGGTACTATTATTATCCC 143 chr3ptel1M 822939 CATTGGACAAAAGGAGAAACTGAGGC 822964 vv i v ii C MIR#SINE/MIR 142 CATTTTACAGATGAGGAAACTGAGGC 117 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.74 CpG sites = 10, Kimura (unadjusted) = 32.74 Transitions / transversions = 1.00 (10/10) Gap_init rate = 0.00 (0 / 75), avg. gap size = 0.0 (0 / 0) 19 10.19 7.14 0.00 chr3ptel1M 823321 823362 (176638) (CCCAGC)n#Simple_repeat 1 45 (0) m_b131s252i9 4853 chr3ptel1M 823321 CCCTGCCCCAGCCCCA-CCCC-GCCCCA-CCCCCGCCTCTGCCCC 823362 v - - - v i v (CCCAGC)n#Sim 1 CCCAGCCCCAGCCCCAGCCCCAGCCCCAGCCCCAGCCCCAGCCCC 45 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.07 (3 / 41), avg. gap size = 1.00 (3 / 3) 17 18.35 3.92 1.92 chr3ptel1M 823326 823376 (176624) (CCCCAC)n#Simple_repeat 1 52 (0) m_b131s252i10 4853 chr3ptel1M 823326 CCCCAGCCCCA-CCCC-GCCCCACCCCCGCCTCTGCCCCCCACCCCCGCC 823373 v - -v i - ivv i (CCCCAC)n#Sim 1 CCCCACCCCCACCCCCACCCCCACCCCCACC-CCCACCCCCACCCCCACC 49 chr3ptel1M 823374 GCC 823376 v (CCCCAC)n#Sim 50 CCC 52 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.06 (3 / 50), avg. gap size = 1.00 (3 / 3) 320 28.42 1.48 11.38 chr3ptel1M 824055 824189 (175811) C MIR#SINE/MIR (131) 131 9 m_b131s601i6 4852 chr3ptel1M 824055 TGAGAAAATGTCCCCCGAGGCA-GTTGGGGTTGAGTGACTTGCCCAGGGT 824103 i ------ i -ivv i i i i C MIR#SINE/MIR 131 TGAGGAAA------CTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGT 88 chr3ptel1M 824104 CCCACAGCCGGGAAGTGTTAAGTGTCTGAGACCAGATTTGAACTCGGGTC 824153 v ii ------- v v v vi i i i iv C MIR#SINE/MIR 87 CACACAGCTAG-------TAAGTGGCAGAGCCGGGATTCGAACCCAGGCA 45 chr3ptel1M 824154 CTCCAGACTTCAGGGCTGCTGCTC-CAGCCACTGCGC 824189 v i- i i i ivv -i i ii C MIR#SINE/MIR 44 GTCT-GGCTCCAGAGCCCGTGCTCTTAACCACTATGC 9 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.48 CpG sites = 23, Kimura (unadjusted) = 36.86 Transitions / transversions = 2.09 (23/11) Gap_init rate = 0.12 (16 / 134), avg. gap size = 1.00 (16 / 16) 401 26.24 0.00 7.83 chr3ptel1M 824080 824203 (175797) C MIRc#SINE/MIR (153) 115 1 m_b131s601i7 4852 chr3ptel1M 824080 GGGGTTGAGTGACTTGCCCAGGGTCCCACAGCCGGGAAGTGTTAAGTGTC 824129 i i i v ii ------- v C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGC 73 chr3ptel1M 824130 TGAGACCAGATTTGAACTCGGGTCCTCCAGACTTCAGGGCTGCTGCTCCA 824179 v v vi i i i i i v i i v iiv iv C MIRc#SINE/MIR 72 AGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTT 23 chr3ptel1M 824180 GCCACTGCGCCCCCAGCTGCCCCG 824203 v i v --i i C MIRc#SINE/MIR 22 TCCACTGCACCAC--ACTGCCTCG 1 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.73 CpG sites = 19, Kimura (unadjusted) = 33.07 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.07 (9 / 123), avg. gap size = 1.00 (9 / 9) 239 29.79 12.81 9.05 chr3ptel1M 825499 825701 (174299) L3#LINE/CR1 3689 3898 (201) m_b131s601i8 4854 chr3ptel1M 825499 ACTAGGGTATAAGAGGAGGAGCTTCGGTTGAAGGAGCTGGCTGTATTTAG 825548 i v vi v i------ i vvi i L3#LINE/CR1 3689 ACCATGTCATATGAGGAA------CGGTTGAAGGAACTGGGGATGTTTAG 3732 chr3ptel1M 825549 CCTGGGGCAGAATCCCTGACAGAAGGCTCTG-GGGGATACAATCACTGCC 825597 i v ---------- i iv - i i ii vi i L3#LINE/CR1 3733 CCTGGAGAAG----------AGAAGACTTAGAGGAGACATGATAGCTGTC 3772 chr3ptel1M 825598 TT--------------------ATATGGAGAAAGGATTACCCTCATTCTG 825627 -------------------- i ii i vv i L3#LINE/CR1 3773 TTCAAATATTTGAAGGGCTGTCATGTGGAAGAGGGATTAGACTTATTCTG 3822 chr3ptel1M 825628 CTCGGGGC---AGGG-AGAACCAGAACAGCCATGGG-AAAAGGTACATGT 825672 ivi vv --- - i i -- v -ii v - v L3#LINE/CR1 3823 TGTGGCTCCAGAGGGCAGAACTAGGAC--CAATGGGTGGAAGTTACA-GG 3869 chr3ptel1M 825673 CAGGAAAACCTTTTCTGAATAAGGGGAGG 825701 v v i ii ivv v vii i L3#LINE/CR1 3870 GAGGCAGATTTCGGCTCAATATAAGGAAG 3898 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.43 CpG sites = 33, Kimura (unadjusted) = 39.36 Transitions / transversions = 1.50 (33/22) Gap_init rate = 0.12 (24 / 202), avg. gap size = 1.88 (45 / 24) 299 27.50 2.92 3.52 chr3ptel1M 825832 826174 (173826) L1MC4_5end#LINE/L1 2215 2555 (0) m_b131s551i1 4855 chr3ptel1M 825832 TGAATGTGAATGGGATGAACTCACCCATAAAATGGAAACAGCTAACAGAA 825881 i i v ? ? v v i? viii vv i?v L1MC4_5end#LI 2215 TAAATGTAAATGGGCTNAACTCACCNATTAAAAGANAAAGATTTTCAANT 2264 chr3ptel1M 825882 TGGATCAAAAACCAGAATCTGACAA-----TGTTTACAAGAAACACAATT 825926 ? ? ? v ii i ii v ----- ? i - ii L1MC4_5end#LI 2265 TGGNTNANAAAGCAAGACCCAACTATATGCTGTNTACAAGAGACAC-ACC 2313 chr3ptel1M 825927 TAAAAGGAGAAATACACACAGAGGAAAAATAAAGGACTGGACAGAATTTT 825976 ii vi v v v ivvi iv ? i i---v L1MC4_5end#LI 2314 TAAAAAAAGTGATTCAGAAAGGCTGAAAATAAAGGGATGGANAAAG---A 2360 chr3ptel1M 825977 TATGCTTCAGCCAATGAAAAGAAAAAAAAGGTATCAGGGGTACCAAGCAT 826026 i -ivi v i v i ------ v i- v?v L1MC4_5end#LI 2361 TATAC-CAGGCAAATGGAAACAAAAAAGA------AGGGTTG-CAATNTT 2402 chr3ptel1M 826027 GATCTCA---AAGTTAAAGCTAAAATAAAACTGAACTAAAAGAGAAAAAC 826073 ? v --- iv i ?i v i?v vv v i ? v v L1MC4_5end#LI 2403 NATATCAGACAAAGTAGANTTCAAGNCAAAAAGCATTAAANGAGACAAAG 2452 chr3ptel1M 826074 AAGGAAATTACATTATGATAACGGGTACTATAGATAATAAAATAATATCA 826123 ?v vi v ? v ??? v vv i i ivv v L1MC4_5end#LI 2453 AAGGNCATTTTATAATGNTAAAGGNNNCAATTCACAATGAAGATATAACA 2502 chr3ptel1M 826124 ATACTAAACTCATATGTACCAAATTATATAGCA--CAAATTTTTAAAGGA 826171 vv ivi? i v i ? -- v? v v L1MC4_5end#LI 2503 ATTATAAATATNTATGCACCAAATAACANAGCANCCACNTTTATAAAGCA 2552 chr3ptel1M 826172 AAA 826174 L1MC4_5end#LI 2553 AAA 2555 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 37.68 CpG sites = 42, Kimura (unadjusted) = 37.68 Transitions / transversions = 0.86 (42/49) Gap_init rate = 0.04 (15 / 342), avg. gap size = 1.47 (22 / 15) 16 18.05 5.26 0.00 chr3ptel1M 826693 826730 (173270) (TA)n#Simple_repeat 1 40 (0) m_b131s252i11 4856 chr3ptel1M 826693 TATATGT-TAAATACA-ATATATGTATACATATTTATATA 826730 i - v i - i i v (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATA 40 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 1088 31.11 6.41 3.41 chr3ptel1M 827301 828611 (171389) L1M5_orf2#LINE/L1 1240 2588 (706) m_b131s551i2 4855 chr3ptel1M 827301 TATTTTGCCCAATTATATGTCAATAAATCTAACAATTTAAGTGTAATAGA 827350 v vv i v i i i ? i ii v i L1M5_orf2#LIN 1240 TATTATGAACAACTTTATGCCAATAAATTTGANAACTTAGATGAAATGGA 1289 chr3ptel1M 827351 ATAATTAC---AAAAATATGAATTGTCTAGATTAAC--AAGAAGAAACAT 827395 vv v --- i ii ? ii v i i i -- i v L1M5_orf2#LIN 1290 CAAATTCCTTGAAAAACACAANTTACCAAAACTGACNCAAGAAGAAATAG 1339 chr3ptel1M 827396 AATGTCTAAATAAATCTATTTTAGAAAAAGAAATTAAACC----ATAAAT 827441 vi i ivi v ivivv i ii---- v v L1M5_orf2#LIN 1340 AAAATCTGAATAGCCCTATATCTATTAAAGAAATTGAATTTGTAATTAAA 1389 chr3ptel1M 827442 GCGCTTCCTAAGAAAAAAGCTT--------GAGGAATTTACTAGTGAATT 827483 ivv i vi i i i-------- v iv i i L1M5_orf2#LIN 1390 AACCTTCCCACAAAGAAAACTCCAGGCCCAGATGGCTTCACTGGTGAATT 1439 chr3ptel1M 827484 CGACCAAACATTTAAA-ATCAACTAATTCCAATGTTAGATAAATAATTTG 827532 v i- vv v v v v i ivv iv L1M5_orf2#LIN 1440 CTACCAAACATTTAAGGAAGAAATAATACCAATCTTACACAAACTCTTCC 1489 chr3ptel1M 827533 GAATAATAGCAAA-GAAGGAGTCCTGCTAAACTACTTTTATGAAACAAAT 827581 ii v v - i iiv v iv vv ii v ii L1M5_orf2#LIN 1490 AGAAAATAGAAAAAGAGGGAACACTTCCCAACTCATTTTATGAGGCCAGC 1539 chr3ptel1M 827582 AT------GGTGCTAAAGTAGGA-AGAG----CAAAAATAGAGAAAATTA 827620 ------ i i i iiv? - i ----i v iv i L1M5_orf2#LIN 1540 ATNACCCTGATACCAAAACCNGACAAAGACATTACAAGAAAAGAAAATTA 1589 chr3ptel1M 827621 TAGTCCAATTTCACTAATGAATATAAATATAAAAG-CCTAAATAAAACAC 827669 i v v v v i i ii i- ? i i i L1M5_orf2#LIN 1590 CAGACCAATATCCCTCATGAACATAGATGCAAAAATCCTNAACAAAATAT 1639 chr3ptel1M 827670 TAGCTA---GAAAACAATAATCATTTATCCCAGATTATACATTGTATAAC 827716 v --- vv ii - v vvvvi v ii i---- L1M5_orf2#LIN 1640 TAGCAAATCGAATCCAGCAAT-ATATAAAAAGGATAATACATCATG---- 1684 chr3ptel1M 827717 ATTGTACCAAGTGGGATTTATGTCAGAAATCCACAGATA--TTAACATAA 827764 ----- i vi i v vi v i-- vv L1M5_orf2#LIN 1685 -----ACCAAGTGGGGTTTATCCCAGGAATGCAAGGTTGGTTTAACATTC 1729 chr3ptel1M 827765 GAGAAATCACT-AATATAATTTATTACATCAATAACAACAGTAACAAAAA 827813 - v - i i ii i i i iv vv ivi v L1M5_orf2#LIN 1730 GA-AAATCAATCAATGTAATTCACCATATTAACAGAATAAAGGAGAAAAA 1778 chr3ptel1M 827814 TCACATAATTATATAACTAGATGCAGACAAGGCTTTTCACAAAATACAAC 827863 i i i v v v v i v v v L1M5_orf2#LIN 1779 TCATATGATCATCTCAATAGATGCAGAAAAAGCATTTGACAAAATTCAAC 1828 chr3ptel1M 827864 ACTCATTCCTATTAAAAAAAAACAAAACAATACTC-CAACAAAGTGAAAG 827912 i v iv -------------- - i v -- i L1M5_orf2#LIN 1829 ACCCATTCATGATAAAA--------------ACTCTCAGCAAACT--AGG 1862 chr3ptel1M 827913 TATAGGTATAAATGTACTTTTCCTTAAAATGATAAGAAGTATCTACCTAA 827962 v ---- iv v -- i vv iii i vv L1M5_orf2#LIN 1863 AATAG----AAGGGAAC--TTCCTCAACCTGATAAAGGGCATCTACGAAA 1906 chr3ptel1M 827963 AACCATCAGCAAGCATTACTTGTAATGGGGATATACTAGAAGTCTTCCCA 828012 vv ? i i iviv v v ? ii ? ii v L1M5_orf2#LIN 1907 AACCTACAGCNAACATCATACTTAATGGTGAAANACTGAANGCTTTCCCC 1956 chr3ptel1M 828013 ATAAGATCAATTATGAAACAAGTATGCCCATTATCAATA---GCATTCAA 828059 v iivv ii i v i ii ? vi ---vi L1M5_orf2#LIN 1957 CTAAGATCGGGAACAAGACAAGGATGTCCGCTNTCACCACTTCTATTCAA 2006 chr3ptel1M 828060 TATTGCATTAGAAATGCTAGTAATAACAATAAGAAAAGAAAGAGAAATTG 828109 i i i i ii v iv vvi iv i vi L1M5_orf2#LIN 2007 CATTGTACTGGAGGTCCTAGCCAGTGCAATAAGGCAAGAAAAAGAAATAA 2056 chr3ptel1M 828110 AAGGAATCAGAATGAGGCAATGAGATAATAACACTATCTCTTTTTGCAGA 828159 v v ii v- v v iiv v i ?i v i L1M5_orf2#LIN 2057 AAGGCATAAAGATT-GGAAAGGAAGAAATAAAACTGTCNTTATTCGCAGA 2105 chr3ptel1M 828160 TGATATGATGATATATTTGGAAAATCCTAGAGACTCAACTAAAAAGTTAG 828209 i vi ? iv i ? i v v v ? ii v L1M5_orf2#LIN 2106 TGACATGATTGTNTACGTAGAAAATCCNAAAGAATCTACAAANAAACTAC 2155 chr3ptel1M 828210 T----------------TTTAACTA-GTAGCCGAATATAAAATAAACCCA 828242 ---------------- i v - v ? i i ii v ivi L1M5_orf2#LIN 2156 TAGAACTAATAAGTGAATTTAGCAAGGTCGCNGGATACAAGGTCAATATA 2205 chr3ptel1M 828243 CATAAATCATCAGCATTTCTATATATCACCAACAAAACCTTGCAA----- 828287 v viv i ii v vvv v ----- L1M5_orf2#LIN 2206 CAAAAATCAATTGTATTTCTATATACTAGCAACAAACAATTGGAAAATGA 2255 chr3ptel1M 828288 -----GAAGAGCTACATCTTTTA-AATAATTGTAGACCACATAAAATACC 828331 -----? i i v i i v - iivvi i vv ? i L1M5_orf2#LIN 2256 AATTTNAAAAACAATACCATTTACAATAGCATCAAAAAACATNAAATACT 2305 chr3ptel1M 828332 TGAGAGTGTACCTGCCATGACA-ATCCAGGAACTACACAACCATAATTAT 828380 ii i iv i iv vi ? -i v i v ?i viv v i i L1M5_orf2#LIN 2306 TAGGAATAAATCTAACAAAANATGTGCAAGACCTNTACACTGAAAACTAC 2355 chr3ptel1M 828381 GAAACACTTTGTCT---ACCAATAAAGTCAAACTTAAATAATTGAAGAAA 828427 i -- - --- vv v ivv i i v i i L1M5_orf2#LIN 2356 AAAACA--TTG-CTGAGAGAAATTAAAGAAGACCTAAATAAATGGAGAGA 2402 chr3ptel1M 828428 TAT----TGTCCGTAGATGGACAGAGCTAATAACAACAACAATAATAATG 828473 ---- i i i v iv vii ------- ivi ? vi L1M5_orf2#LIN 2403 TATACCATGTTCATGGATTGGAAGACTCAAT-------ATTGTNAAGATG 2445 chr3ptel1M 828474 ACAATTCTACT----TTAATCTACTTATTCAATGTCATTTCAATTAAATT 828519 v v i---- i ivv iv ii i v L1M5_orf2#LIN 2446 TCAATTCTCCCCAAATTGATCTATAGATTCAATGCAATCCCAATCAAAAT 2495 chr3ptel1M 828520 ACCAA-AAACTATTTTGCTGATCAGGAACAAA-TGATAACACAATTCATT 828567 v i- iii v iv -v vvi i- vvi v i v L1M5_orf2#LIN 2496 CCCAGCAGGTTTTTTTGTAGA-AATTGACAAGCTGATTCTAAAATTTATA 2544 chr3ptel1M 828568 TGGAAGAACAAAAAATCAAGCACA-TCAAAGAGATCTATGTAAAA 828611 ivi ii i ? v i -i ivi - v L1M5_orf2#LIN 2545 TGGAAATGCAAAGGACCNAGAATAGCCAAAACAATCT-TGAAAAA 2588 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 41.52 CpG sites = 218, Kimura (unadjusted) = 42.08 Transitions / transversions = 1.24 (218/176) Gap_init rate = 0.06 (73 / 1310), avg. gap size = 1.78 (130 / 73) 17 32.15 5.41 0.00 chr3ptel1M 828670 828743 (171257) (TA)n#Simple_repeat 1 78 (0) m_b131s252i12 4857 chr3ptel1M 828670 TACATACACATAGATGCATACATA-ATACCTGT-TATATA-ATGTGTAT- 828715 i i i v ii i - iv i - - i i - (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr3ptel1M 828716 TATATATGCACATATATACACACATATA 828743 ii i i i i (TA)n#Simple_ 51 TATATATATATATATATATATATATATA 78 Matrix = Unknown Transitions / transversions = 8.00 (16/2) Gap_init rate = 0.05 (4 / 73), avg. gap size = 1.00 (4 / 4) 231 31.35 7.25 2.48 chr3ptel1M 829273 829465 (170535) L1ME5_3end#LINE/L1 57 258 (683) m_b131s551i3 4855 chr3ptel1M 829273 CCCCATTGATAAATGGCCCAAGGATATG-GCGG--AGCTTTTGGATGGAG 829319 v v v v v -i i -- ii vii v ii L1ME5_3end#LI 57 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAGG 106 chr3ptel1M 829320 AAATC---AAAGCTCTCCAGAACCACCTGAA-AAATGCTCTAAATC---- 829361 i --- i vv v --- iv - i v v ---- L1ME5_3end#LI 107 AAACCCGAAAGGCTAACAAG---CATATGAAGAGATGCTCAAACTCATTA 153 chr3ptel1M 829362 GTCATTAGAGAAACGCCAACTAAAAGAGCTCCGAGGAGTCATCGCCCACC 829411 v i i v i v i vvi ivi iiviv L1ME5_3end#LI 154 GTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACC 203 chr3ptel1M 829412 TACCAGATTGGCCAATGCGATAGAAGG--GGAGAGTGATAACAGTGGAC- 829458 ii i v vii-- i -- v i vi vv v i - L1ME5_3end#LI 204 TATTAGACTGGCAAAAAT--TAGAAAGCTGGATAATGCCAAGTGTTGGCG 251 chr3ptel1M 829459 AGGATGT 829465 L1ME5_3end#LI 252 AGGATGT 258 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 41.41 CpG sites = 31, Kimura (unadjusted) = 41.41 Transitions / transversions = 1.11 (31/28) Gap_init rate = 0.06 (12 / 192), avg. gap size = 1.58 (19 / 12) 278 27.78 7.14 1.85 chr3ptel1M 829273 829426 (170574) L1MC5_3end#LINE/L1 57 218 (2476) m_b131s551i4 4855 chr3ptel1M 829273 CCCCATTGATAAATGGCCCAAGGATATGG-CGGA--GCTTTTGGATGGAG 829319 i v v v i ii i- i -- i ivii vii L1MC5_3end#LI 57 CCCTATAGAAAAATGGGCTAGAGATATGAACAGACAGTTCACAGAAAAAG 106 chr3ptel1M 829320 AAAT-CAAA--GCTCTCCAGAACCACCTGAAAA-ATGCTCTAAATCG--- 829362 - -- i--- ? iv - v vv --- L1MC5_3end#LI 107 AAATGCAAATGGCTCTT---AANCATATGAAAAGATGCTCAACCTCGCTC 153 chr3ptel1M 829363 -TCATTAGAGAAACGCCAACTAAAAGAGCTCCGAGGAGTCATCGCCCACC 829411 - v v i v i vvi v i ivii iv i L1MC5_3end#LI 154 ATAATAAGAGAAATGCAAATTAAAACTACACTGAGATACCATTTCTCACC 203 chr3ptel1M 829412 TACCAGATTGGCCAA 829426 i v L1MC5_3end#LI 204 TATCAGATTGGCAAA 218 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 35.85 CpG sites = 24, Kimura (unadjusted) = 35.85 Transitions / transversions = 1.33 (24/18) Gap_init rate = 0.07 (10 / 153), avg. gap size = 1.40 (14 / 10) 402 30.21 5.62 3.30 chr3ptel1M 829836 830013 (169987) C MIRc#SINE/MIR (49) 219 38 m_b131s601i9 4858 chr3ptel1M 829836 GCTTCAGGATGCTTTAT-TC--TGGGTCCTCA-GGCAACCCTGAGAGCTG 829881 iviv i v - -- v i -ii v v i C MIRc#SINE/MIR 219 GCTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTA 170 chr3ptel1M 829882 GAGACTGCTGGGGGTTTTACTCCCATTTCGCAGATGAGAAAGGAAGACTG 829931 iv vv v viv v ii ii i ----- C MIRc#SINE/MIR 169 GGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAA-----ACTG 125 chr3ptel1M 829932 AGG----GAGAGATGTGATTGGCCTGCCTGGGGTCACACAGCTCCTAGGG 829977 ---- i - i v i i iii vv i v C MIRc#SINE/MIR 124 AGGCTCAGAGAGGT-TAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGT 76 chr3ptel1M 829978 GTCAGCTCTGAGTCT--GCCCCAGGACTCTCTGCCTTC 830013 v vv i i v --iv v ii v i C MIRc#SINE/MIR 75 GGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCC 38 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.50 CpG sites = 28, Kimura (unadjusted) = 39.47 Transitions / transversions = 1.17 (28/24) Gap_init rate = 0.06 (11 / 177), avg. gap size = 1.45 (16 / 11) 34 0.00 0.00 0.00 chr3ptel1M 830399 830427 (169573) (GT)n#Simple_repeat 1 29 (0) c_b131s251i0 4859 chr3ptel1M 830399 GTGTGTGTGTGTGTGTGTGTGTGTGTGTG 830427 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTG 29 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 292 31.68 13.97 3.68 chr3ptel1M 830801 831072 (168928) C L3#LINE/CR1 (91) 4008 3710 m_b131s601i10 4860 chr3ptel1M 830801 CCTGACCAAGAATC-TCCATACCTCCATTTGCAGACCA--GGTGATGGGG 830847 v ivii - -i iii v v v--i i C L3#LINE/CR1 4008 CCTGACAAGTGGTCATCCA-GCCTCTGCTTGAACACCTCCAGTGACGGGG 3960 chr3ptel1M 830848 ACCTCACTACTGCCTGAGGCAGCCCCTGCCCACCTTTAGGGCAGCATT-T 830896 v iv ?i v -i ii - i vi -v C L3#LINE/CR1 3959 AGCTCACTACCTCNCGAGGCAGCCCAT-TCCATTTTT-GGACAGCTCTGA 3912 chr3ptel1M 830897 CTGGTAGAAAAGCCT------GATTGACT-----TCGGTCTACACTGCAG 830935 i v ivi ------v vi----- v i - v i i C L3#LINE/CR1 3911 TTGTTAGAAAGTTCTTCCTTATATTGAGCCGAAATCTGCCT-CCCTGTAA 3863 chr3ptel1M 830936 CT----CCTCTTGGCC---ATTTTGTCCACGCCCGTGGCT-CACGGCACT 830977 ---- iv i ---i i i ---i i vi i- i - v C L3#LINE/CR1 3862 CTTCCACCCATTGGTCCTAGTTCTGCCC---TCTGGAGCCACACAG-AAT 3817 chr3ptel1M 830978 AAGTCTGA---------------GCAGCTCTGTAAAGGAGCCCAGGCTGC 831012 i ---------------i i vi vivvivv i v C L3#LINE/CR1 3816 AAGTCTAATCCCTCTTCCACATGACAGCCCTTCAAATATTTGAAGACAGC 3767 chr3ptel1M 831013 TCTTGGGTCCCTTCCCTCAGCCTTGACTTCTCCGGCCCAAACACCCCCCG 831062 v iiv -- i i v i vv i v i -i i C L3#LINE/CR1 3766 TATCATGT--CTCCTCTAAGTCTTCTCTTCTCCAGGCTAAACA-TCCCCA 3720 chr3ptel1M 831063 GGTGCTTCAA 831072 v v C L3#LINE/CR1 3719 GTTCCTTCAA 3710 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.63 CpG sites = 49, Kimura (unadjusted) = 43.01 Transitions / transversions = 1.44 (49/34) Gap_init rate = 0.07 (20 / 271), avg. gap size = 2.45 (49 / 20) 22 21.30 2.04 0.00 chr3ptel1M 831194 831242 (168758) (TC)n#Simple_repeat 1 50 (0) m_b131s252i13 4861 chr3ptel1M 831194 TCTCT-TGTCTCTCTGTTTCTCTGTGTGTGTCTCTGTCTCTCTGTCTCTC 831242 - v v i v v v v v v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.02 (1 / 48), avg. gap size = 1.00 (1 / 1) 633 29.98 4.79 0.22 chr3ptel1M 831868 832305 (167695) C L1M5_orf2#LINE/L1 (834) 2460 2003 m_b131s551i5 4862 chr3ptel1M 831868 TCTGGACAGAATTGTCATTCTTATTATATTGGCTCAGTCTATCTATGAGC 831917 i iv v ii ? iv iv vvi v i i C L1M5_orf2#LIN 2460 TTTGGGGAGAATTGACATCTTNACAATATTGAGTCTTCCAATCCATGAAC 2411 chr3ptel1M 831918 AATTAT-TATTCCTCCACTTATTTATATCTGCTTG------TGTAAAAAG 831960 - vi - ii i vi v v------ v v iv i C L1M5_orf2#LIN 2410 A-TGGTATATCTCTCCATTTATTTAGGTCTTCTTTAATTTCTCTCAGCAA 2362 chr3ptel1M 831961 TGGTTTGTAATTGTGTTCTTATAGGTCCTGGAT-TTGTCTGGCAGGTAGA 832009 v i v vvviv ? i v i- ?v i vi i vv C L1M5_orf2#LIN 2361 TGTTTTGTAGTTTTCAGTGTANAGGTCTTGCACATNTTTTGTTAGATTTA 2312 chr3ptel1M 832010 CTCCAAAGTTTTTTATATTATCTGCAGTTATTTTAAATGTAATTATTTTT 832059 i v v ? i v i vv i v vv i C L1M5_orf2#LIN 2311 TTCCTAAGTATTTNATGTTTTTTGATGCTATTGTAAATGGTATTGTTTTT 2262 chr3ptel1M 832060 TA----TC-TCTTCCTTTTGGGTTTTGTTAGTA-ATAGAAATGCTGATGA 832103 ? ---- - i vv vv v i - i viv C L1M5_orf2#LIN 2261 NAAATTTCATTTTCCAATTGTTTGTTGCTAGTATATAGAAATACAATTGA 2212 chr3ptel1M 832104 TTTGTTTGCATTTACTCTATATTCTGTAACTTTGCTAAAGTTGTTCATTA 832153 v v ii v ii i i ? ii i v iii i C L1M5_orf2#LIN 2211 TTTTTGTATATTGACCTTGTATCCNGCGACCTTGCTAAATTCACTTATTA 2162 chr3ptel1M 832154 TTTCAAGTAGTTTTTTTTTGGTT-------GATTCTCTAAGAATACCATC 832196 v v ? v i v ------- i v v ? v C L1M5_orf2#LIN 2161 GTTCTAGTAGTTTNTTTGTAGATTCTTTNGGATTTTCTACGTANACAATC 2112 chr3ptel1M 832197 ATTTTATCTGCAAAGAGTGATAATTTTGTTTCCTCATTGCCTATTCCTCT 832246 v i i v i? i i i i v v v iii v C L1M5_orf2#LIN 2111 ATGTCATCTGCGAATAANGACAGTTTTATTTCTTCCTTTCCAATCTTTAT 2062 chr3ptel1M 832247 TCCTTCAATTTCTTTTTCTTGTCTTATTGTTGTAGTTAGCGTTTTTAGTA 832296 v iv i ivv i i viii ii C L1M5_orf2#LIN 2061 GCCTTTTATTTCTTTTTCTTGCCTTATTGCACTGGCTAGGACCTCCAGTA 2012 chr3ptel1M 832297 CAATAGTGA 832305 iv C L1M5_orf2#LIN 2011 CAATGTTGA 2003 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 39.16 CpG sites = 68, Kimura (unadjusted) = 39.99 Transitions / transversions = 1.08 (68/63) Gap_init rate = 0.02 (8 / 437), avg. gap size = 2.75 (22 / 8) 54 1.99 0.00 0.00 chr3ptel1M 832706 832756 (167244) (TG)n#Simple_repeat 1 51 (0) c_b131s251i1 4863 chr3ptel1M 832706 TGTGTGTGTGTGTTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 832755 v (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr3ptel1M 832756 T 832756 (TG)n#Simple_ 51 T 51 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 399 29.94 4.57 6.74 chr3ptel1M 833328 833524 (166476) C MIRb#SINE/MIR (48) 220 28 m_b131s601i11 4864 chr3ptel1M 833328 TGTTCAGTGTCTGACTTTTCACGATCCCATTTGGTTTTTTTGGCAAAGAT 833377 i v i ii v v v- iv i ii ii i---i vi i C MIRb#SINE/MIR 220 TGCTAAGCGCTTTACATG-CATTATCTCATTTAATCCTC---ACAACAAC 175 chr3ptel1M 833378 ACTG-GAGGGGGTGACTATTTCCTTCTTTAGCTCATTTCACAGATGAGGA 833426 v - vi vv i vi -------- i i C MIRb#SINE/MIR 174 CCTGCGAGGTAGGTATTATTATC--------CCCATTTTACAGATGAGGA 133 chr3ptel1M 833427 ACCTGAGG--CAGATAGGATGAAGGGACTTGTCTGGGGTCCCACAG-TAG 833473 v -- v - v vi i iii v - C MIRb#SINE/MIR 132 AACTGAGGCTCAGAGAGG-TTAAGTAACTTGCCCAAGGTCACACAGCTAG 84 chr3ptel1M 833474 GAACTGTCTGAGGCTGGATTTGAA--CAACTC---CCGACTCCAGGGCCA 833518 v v v v v v i -- iv --- i ii v C MIRb#SINE/MIR 83 TAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCC 34 chr3ptel1M 833519 GCCCTC 833524 iv C MIRb#SINE/MIR 33 GTGCTC 28 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.13 CpG sites = 30, Kimura (unadjusted) = 38.92 Transitions / transversions = 1.20 (30/25) Gap_init rate = 0.09 (18 / 196), avg. gap size = 1.22 (22 / 18) 417 22.40 6.84 0.81 chr3ptel1M 833408 833524 (166476) C MIRc#SINE/MIR (120) 148 25 m_b131s601i12 4864 chr3ptel1M 833408 CTCATTTCACAGATGAGGAACCTGAGG--CAGATAGGATGAAGGGACTTG 833455 i i v -- v - v v C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGG-TTAAGTGACTTG 100 chr3ptel1M 833456 TCTGGGGTCCCACAG-TAGGAACTGTCTGAGGCTGGATTTGAA--CAA-- 833500 i iii v - v v v v v v i i -- i-- C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGT 50 chr3ptel1M 833501 -CTCCCGACTCCAGGGCCAGCCCTC 833524 -i i i v iv C MIRc#SINE/MIR 49 CTTCCTGACTCCAAGTCCAGTGCTC 25 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 25.68 CpG sites = 13, Kimura (unadjusted) = 26.83 Transitions / transversions = 1.00 (13/13) Gap_init rate = 0.05 (6 / 116), avg. gap size = 1.50 (9 / 6) 16 13.24 0.00 0.00 chr3ptel1M 835238 835262 (164738) (C)n#Simple_repeat 1 25 (0) m_b131s252i14 4865 chr3ptel1M 835238 CCCCCTCTCCCCCCCCCCCCCACCC 835262 i i v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCC 25 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 480 22.49 4.96 0.79 chr3ptel1M 838774 838894 (161106) C MIRc#SINE/MIR (120) 148 23 m_b131s601i13 4866 chr3ptel1M 838774 CTCGTTTAGCAGATGGAGAAACTGAGGC--AGA-AGGTCAAATGCCTGGC 838820 i i vi ii -- - i i v v C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr3ptel1M 838821 CTAGGGTCACCCAGCTAGGAAGGGTCTACAGCTGGATCT-GAACTCGGGT 838869 i i v v v v - v i iv - i i C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGC-AGAGCCGGGACTCGAACCCAGGT 50 chr3ptel1M 838870 CCTCCTAACTTCAGGACCA--GCTCTT 838894 i i i i v -- C MIRc#SINE/MIR 49 CTTCCTGACTCCAAGTCCAGTGCTCTT 23 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.23 CpG sites = 17, Kimura (unadjusted) = 27.40 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.04 (5 / 120), avg. gap size = 1.40 (7 / 5) 265 32.71 0.93 0.00 chr3ptel1M 841139 841245 (158755) C L1ME3A_3end#LINE/L1 (591) 329 222 m_b131s551i7 4867 chr3ptel1M 841139 CAGATGGCTCTCCAGAATGGTGGGATCAGTTCACAACTCCACCAACCATG 841188 i ii i i i i v v i i i vii i vi C L1ME3A_3end#L 329 CAAACAGTTTTCCAAAGTGGTTGTACCAATTTACACTCCCACCAGCAGTG 280 chr3ptel1M 841189 TATCAGTGTCCCAGCTTTCCCACATCCCCTCCAACA-TTCATCTTCTCTC 841237 v v i i i vii i v - vi v v v C L1ME3A_3end#L 279 TATGAGAGTTCCGGTTGCTCCACATCCTCGCCAACACTTGGTATTGTCTG 230 chr3ptel1M 841238 TCTGTCTC 841245 v i C L1ME3A_3end#L 229 TCTTTTTC 222 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 43.23 CpG sites = 22, Kimura (unadjusted) = 45.00 Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.01 (1 / 106), avg. gap size = 1.00 (1 / 1) 325 27.27 0.00 0.00 chr3ptel1M 841139 841226 (158774) C L1ME5_3end#LINE/L1 (612) 329 242 m_b131s551i6 4867 chr3ptel1M 841139 CAGATGGCTCTCCAGAATGGTGGGATCAGTTCACAACTCCACCAACCATG 841188 v iv v i ii vii i vi C L1ME5_3end#LI 329 CAGATTGCTCTCCAGAATGGCTGCACCAGTCTACACTCCCACCAGCAGTG 280 chr3ptel1M 841189 TATCAGTGTCCCAGCTTTCCCACATCCCCTCCAACATT 841226 i v v i vii? i i v i C L1ME5_3end#LI 279 CATGAGGGTTCCTATNTCCCCACATCCTCGCCAACACT 242 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 35.53 CpG sites = 15, Kimura (unadjusted) = 35.53 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.00 (0 / 87), avg. gap size = 0.0 (0 / 0) 65 8.82 1.72 3.51 chr3ptel1M 841246 841361 (158639) (TCTCTG)n#Simple_repeat 1 114 (0) m_b131s252i15 4868 chr3ptel1M 841246 TCTCTCTCTCTGTGTGTGTCTCTGTCTCTCTGTCTCTGTCTCTGTCTC-- 841293 v v v -- -- (TCTCTG)n#Sim 1 TCTCTGTCTCTGTCTCTGTCTCTG--TCTCTGTCTCTGTCTCTGTCTCTG 48 chr3ptel1M 841294 TCTCTGTCTCTGTCTCTCTCTCTCTCTCTCTCTCTGTCTCTCTGTCTCTC 841343 v v v -- v (TCTCTG)n#Sim 49 TCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTG--TCTCTGTCTCTG 96 chr3ptel1M 841344 TCTCCATCTCTGTCTCTG 841361 ii (TCTCTG)n#Sim 97 TCTCTGTCTCTGTCTCTG 114 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.04 (5 / 115), avg. gap size = 1.20 (6 / 5) 271 21.57 0.00 0.00 chr3ptel1M 841387 841437 (158563) L2d2_3end#LINE/L2 493 543 (12) m_b131s601i15 4869 chr3ptel1M 841387 AGCACATGGCACAGTGCCTGGCAGACTGTAGGCATTTAATAAATGCTTGT 841436 i v i v v v ii i ii L2d2_3end#LIN 493 AGCGCCTAGCACAGTGCCTTGCACACAGTAGGCGCTCAATAAATATTTGT 542 chr3ptel1M 841437 T 841437 L2d2_3end#LIN 543 T 543 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 20.85 CpG sites = 7, Kimura (unadjusted) = 26.03 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 37 4.19 1.96 1.96 chr3ptel1M 841668 841718 (158282) (TCC)n#Simple_repeat 1 51 (0) c_b131s251i2 4870 chr3ptel1M 841668 TCCTCCTCCTCCTCCTCCTCCTCCTCCCCCTCCTGCTCCT-CTCCCTCCT 841716 i v - - (TCC)n#Simple 1 TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT-CCTCCT 49 chr3ptel1M 841717 CC 841718 (TCC)n#Simple 50 CC 51 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (2 / 50), avg. gap size = 1.00 (2 / 2) 34 0.00 0.00 0.00 chr3ptel1M 842088 842119 (157881) (C)n#Simple_repeat 1 32 (0) c_b131s251i3 4871 chr3ptel1M 842088 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 842119 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 32 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 531 22.60 4.61 3.92 chr3ptel1M 845045 845196 (154804) C MIR#SINE/MIR (21) 241 89 m_b131s601i16 4872 chr3ptel1M 845045 AGCACCGACTATGTGCCAGCCAGGCACTGGGCTAAGTGCTTTACAGACAC 845094 i iv ---- vv i vii i C MIR#SINE/MIR 241 AGCGCTTACTATGTGCCAG----GCACTGTTCTAAGCGCTTTACATGTAT 196 chr3ptel1M 845095 GGCTTCTTGTAGGG---ACAAGAGCCTTGGGAGGGAGGTGCTATTATCAC 845141 vivi v v ivv--- v i i iv v i i i C MIR#SINE/MIR 195 TAACTCATTTAATCCTCACAACAACCCTATGAGGTAGGTACTATTATTAT 146 chr3ptel1M 845142 CCCCATGTCACAGATGAGGAAACTGAGGC-CAGCAGAGG---AGCAGGCT 845187 v i - - --- i -i C MIR#SINE/MIR 145 CCCCATTTTACAGATGAGGAAACTGAGGCACAG-AGAGGTTAAGTA-ACT 98 chr3ptel1M 845188 TGCCCAGGG 845196 i C MIR#SINE/MIR 97 TGCCCAAGG 89 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 25.46 CpG sites = 19, Kimura (unadjusted) = 27.34 Transitions / transversions = 1.36 (19/14) Gap_init rate = 0.06 (9 / 151), avg. gap size = 1.44 (13 / 9) 205 24.39 0.00 0.00 chr3ptel1M 846243 846283 (153717) MamTip2b#DNA/hAT-Tip100 223 263 (186) m_b131s601i17 4873 chr3ptel1M 846243 TATCAGTCATTTATACCCTAGTGTGAATGAGCTCACTAGAT 846283 i v i i i v i i ii MamTip2b#DNA/ 223 TATCAGCCATTAACACCTTAGCGTGAATTAGTTTATCAGAT 263 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.70 CpG sites = 8, Kimura (unadjusted) = 31.47 Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 321 15.28 2.65 1.86 chr3ptel1M 846414 847054 (152946) (GGAA)n#Simple_repeat 1 646 (0) m_b131s252i16 4874 chr3ptel1M 846414 GGGAGGAAGAGAGGGAGGGAAGG-AGAGAGAAACGAAGGAGGGGA-GAAG 846461 i - i i - ii i v i i - (GGAA)n#Simpl 1 GGAAGGAAG-GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG 49 chr3ptel1M 846462 GAAAGGAGCAAAGGAGGGAGGGAAGGAAGAAAGGAAGGAGAGAAAG-AGG 846510 - ivi i i i ii i - (GGAA)n#Simpl 50 G-AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG 98 chr3ptel1M 846511 GAGAGAGGAAGGAAGG-AGAGCGGGAGAAAGGAAGGAAGGAAGGAAGGAA 846559 i ii - iiv i i (GGAA)n#Simpl 99 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 148 chr3ptel1M 846560 GGAAGGAAGGAAGGAAGGAAGGAAGGAAGG--GGGAGGGAGGAGGGAAGG 846607 -- i i i (GGAA)n#Simpl 149 GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG 198 chr3ptel1M 846608 AAGGAAGGAAAGAAGGGAGGGAGGGGAGGAAGGAGGGAAGGAAGGAAGGA 846657 i - i i i i (GGAA)n#Simpl 199 AAGGAAGGAAGGAA-GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 247 chr3ptel1M 846658 AGGAAGAGAGGGAGGGAGGAGGGAAGG--GGAAGGAAGGAAAGAAGG-GG 846704 ii i i i -- i -i (GGAA)n#Simpl 248 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG 297 chr3ptel1M 846705 GGAGG-GGGAAGGAGGGGCAAGGAAGG--GGAAAGAGGGAGGGGAGGGAG 846751 i -i -i - -- i i i i i (GGAA)n#Simpl 298 GAAGGAAGGAAGGA-AGG-AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG 345 chr3ptel1M 846752 GAAGGAAGG--GGGAGGGAGGAAGGGA-AAGGGAAGGGGAGGGAGGGA-G 846797 -- i i i -i i - i i i - (GGAA)n#Simpl 346 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA-GGAAGGAAGGAAGG 394 chr3ptel1M 846798 AAGGGGGGAAGGAAGGAAGGGAAGGGAGGGAGGAAGGAGGGAAAGGAGGA 846847 ii - i i i i i (GGAA)n#Simpl 395 AAGGAAGGAAGGAAGGAA-GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 443 chr3ptel1M 846848 AGGAAGGGAGGGAAGGGAGGGAGGGAGGGAGGAAGGAAGGAAGGAAGGGA 846897 - i i i i i - (GGAA)n#Simpl 444 AGGAA-GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA-GGA 491 chr3ptel1M 846898 GGGAGGGGAGGAAGGAGGGAAGCAAGGAAGGAAAGGGA-GAGGGAGGGAA 846946 i i i i v - i - i i (GGAA)n#Simpl 492 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG-AAGGAAGGAAGGAAGGAA 540 chr3ptel1M 846947 GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG 846996 (GGAA)n#Simpl 541 GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG 590 chr3ptel1M 846997 AAGGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGGAGAGAGGGAGGGAGGG 847046 - i - i i i (GGAA)n#Simpl 591 AA-GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG-GAAGGAAGGAAGG 638 chr3ptel1M 847047 AGGGAAGG 847054 i (GGAA)n#Simpl 639 AAGGAAGG 646 Matrix = Unknown Transitions / transversions = 19.50 (78/4) Gap_init rate = 0.04 (25 / 640), avg. gap size = 1.16 (29 / 25) 522 24.28 6.76 2.60 chr3ptel1M 847056 847203 (152797) C MIRb#SINE/MIR (16) 252 99 m_b131s601i18 4875 chr3ptel1M 847056 TCTATTAAGCTGCTGCTTGTGTGTCAGGTGCTGGGCTAAGCATTTTTTA- 847104 i i - vvi i i ii v ii vi - C MIRb#SINE/MIR 252 TTTATTGAGC-GCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACAT 204 chr3ptel1M 847105 --ATGATCTCATCAGATTCTCACAACTACTCTGGGGAGGAGATGCCATTA 847152 -- v ivi i v i v ii v i --- C MIRb#SINE/MIR 203 GCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGT---ATTA 157 chr3ptel1M 847153 TGATTCCCATTTGACAGATGGGAACACTGAGGC------AGGTGAAG-GA 847195 v i v i i v ------ v -i C MIRb#SINE/MIR 156 TTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAA 107 chr3ptel1M 847196 CTGGCCCA 847203 v C MIRb#SINE/MIR 106 CTTGCCCA 99 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.02 CpG sites = 21, Kimura (unadjusted) = 30.03 Transitions / transversions = 1.50 (21/14) Gap_init rate = 0.05 (8 / 147), avg. gap size = 1.75 (14 / 8) 17 13.72 0.00 0.00 chr3ptel1M 847987 848018 (151982) (GGAGGG)n#Simple_repeat 1 32 (0) m_b131s252i17 4876 chr3ptel1M 847987 GGCGGAGGCGGGGAAGGGGGAGGGGGAGGGGG 848018 v i v i (GGAGGG)n#Sim 1 GGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGG 32 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 249 24.05 0.00 17.81 chr3ptel1M 848844 848929 (151071) C MIR3#SINE/MIR (11) 197 125 m_b131s601i19 4877 chr3ptel1M 848844 TCTTAAGACAGCAAAGCCAGGAGGGACCCTCGAGGTCACCTAGACCAATG 848893 v ii iiv i ii i i v i i v --- C MIR3#SINE/MIR 197 TCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCA--- 151 chr3ptel1M 848894 ATCCCCTTCCACGCACCCATTTTACAGATGAGTAAA 848929 i ---------- v C MIR3#SINE/MIR 150 ACCCCCT----------CATTTTACAGATGAGGAAA 125 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.00 CpG sites = 12, Kimura (unadjusted) = 29.00 Transitions / transversions = 2.40 (12/5) Gap_init rate = 0.15 (13 / 85), avg. gap size = 1.00 (13 / 13) 38 0.00 0.00 0.00 chr3ptel1M 849030 849064 (150936) (C)n#Simple_repeat 1 35 (0) c_b131s251i4 4878 chr3ptel1M 849030 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 849064 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 35 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 250 29.41 2.35 0.00 chr3ptel1M 849232 849316 (150684) C L3#LINE/CR1 (77) 4022 3936 m_b131s601i20 4879 chr3ptel1M 849232 CTTTCTA-AACG-CCCAGAGGGGTGCTCACGGGCCCTTTGCTCGAGCCCC 849279 i - i- v vii v ivviv i i i v C L3#LINE/CR1 4022 CCTTCTACAACATCCCTGACAAGTGGTCATCCAGCCTCTGCTTGAACACC 3973 chr3ptel1M 849280 TCCAGGGACAGAGAGCTCCCCACCTCTTCAGGCGACC 849316 v i i v i ?iv ii C L3#LINE/CR1 3972 TCCAGTGACGGGGAGCTCACTACCTCNCGAGGCAGCC 3936 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.20 CpG sites = 15, Kimura (unadjusted) = 39.13 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.02 (2 / 84), avg. gap size = 1.00 (2 / 2) 196 34.17 8.47 0.79 chr3ptel1M 850252 850369 (149631) L2a_3end#LINE/L2 383 509 (8) m_b131s601i21 4880 chr3ptel1M 850252 GTCTATGTCCAC-AGAAGATGGACTCGTTGGGGGGCGGGGATATTTGT-- 850298 vivi - vi iii vv i - i iv -- L2a_3end#LINE 383 GTCTCCCCCCACTAGAATGTAAGCTCCATGAGGG-CAGGGACTTTTGTCT 431 chr3ptel1M 850299 GGGGGGTTCCCTTC-----CCTCCGTGCCTAG--CGATTCCTCACATGCA 850341 vvvv v v ----- i v i -- ii v vi iii L2a_3end#LINE 432 GTTTTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACATA 481 chr3ptel1M 850342 GTACGAGCTTCATAAATGCTTCTTGGAT 850369 v v iv ii v i L2a_3end#LINE 482 GTAGGCGCTCAATAAATATTTGTTGAAT 509 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.08 CpG sites = 21, Kimura (unadjusted) = 46.66 Transitions / transversions = 1.11 (21/19) Gap_init rate = 0.04 (5 / 117), avg. gap size = 2.20 (11 / 5) 22 3.85 0.00 0.00 chr3ptel1M 850956 850982 (149018) (G)n#Simple_repeat 1 27 (0) m_b131s252i18 4881 chr3ptel1M 850956 GGGGGGGGGGGGGGGGGGGGGGGGAGG 850982 i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGG 27 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 491 25.34 5.52 2.00 chr3ptel1M 852187 852331 (147669) MIRb#SINE/MIR 2 151 (117) m_b132s601i1 4882 chr3ptel1M 852187 AAATGGGCAGCTAGGTGGCGCAGTGGTTAGAACCTGGGGTCAGGAGT--- 852233 i v --- i vv i vi v iv --- MIRb#SINE/MIR 2 AGAGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAG 48 chr3ptel1M 852234 ---AACC-GTGTTCATACCCAACCTCAGACTGTTACTAGTTGGGTGACCC 852279 ---i - v iv i viv v v vv i v i MIRb#SINE/MIR 49 ACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCT 98 chr3ptel1M 852280 TGACCAAGTTATTTAACC-CTGTGCGCCTCAGTTTCCTTACCTGCAGAAT 852328 iv i - v v i i i i MIRb#SINE/MIR 99 TGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAAT 148 chr3ptel1M 852329 GAG 852331 i MIRb#SINE/MIR 149 GGG 151 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.26 CpG sites = 18, Kimura (unadjusted) = 31.23 Transitions / transversions = 1.00 (18/18) Gap_init rate = 0.05 (7 / 144), avg. gap size = 1.57 (11 / 7) 16 0.00 0.00 0.00 chr3ptel1M 853555 853571 (146429) (A)n#Simple_repeat 1 17 (0) m_b132s252i1 4883 chr3ptel1M 853555 AAAAAAAAAAAAAAAAA 853571 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 17 9.91 8.89 2.08 chr3ptel1M 853633 853677 (146323) (TCC)n#Simple_repeat 1 48 (0) m_b132s252i2 4884 chr3ptel1M 853633 TCC-CCTCCT-CTCCTCC-CCATCTCCTCCTCCCTCCTCC-CAGCCTCC 853677 - - - vi - - vv (TCC)n#Simple 1 TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT-CCTCCTCCTCCTCCTCC 48 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.11 (5 / 44), avg. gap size = 1.00 (5 / 5) 28 0.00 0.00 0.00 chr3ptel1M 855969 855994 (144006) (CCT)n#Simple_repeat 1 26 (0) c_b132s251i0 4885 chr3ptel1M 855969 CCTCCTCCTCCTCCTCCTCCTCCTCC 855994 (CCT)n#Simple 1 CCTCCTCCTCCTCCTCCTCCTCCTCC 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 16 11.70 0.00 0.00 chr3ptel1M 856060 856087 (143913) (CCG)n#Simple_repeat 1 28 (0) m_b132s252i3 4886 chr3ptel1M 856060 CCGCAGCCGCCGCCGCCGCCGCGCCCGC 856087 v vv (CCG)n#Simple 1 CCGCCGCCGCCGCCGCCGCCGCCGCCGC 28 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 19 30.41 0.00 0.00 chr3ptel1M 856159 856222 (143778) (GCT)n#Simple_repeat 1 64 (0) m_b132s252i4 4887 chr3ptel1M 856159 GCTGCTGCTGCCGCTGCGGAGCCCGATGCTGGGGCTGCCGGCGCTCAGGC 856208 i v vvv i v vv i vi vvv (GCT)n#Simple 1 GCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC 50 chr3ptel1M 856209 CGCTGCTGCTGCTG 856222 i (GCT)n#Simple 51 TGCTGCTGCTGCTG 64 Matrix = Unknown Transitions / transversions = 0.45 (5/11) Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0) 18 9.22 3.57 9.43 chr3ptel1M 856275 856330 (143670) (CCCGCGC)n#Simple_repeat 1 53 (0) m_b132s252i5 4888 chr3ptel1M 856275 CCCG-GGCCCGCGCCCCGCGCCCAGAGCCCCGCCGCCGTCCGCCGCCCAG 856323 - v v v - -- - v (CCCGCGC)n#Si 1 CCCGCGCCCCGCGCCCCGCGCCCCGCGCCCCG-CGCC--CCG-CGCCCCG 46 chr3ptel1M 856324 -GCCGCCG 856330 - - (CCCGCGC)n#Si 47 CGCC-CCG 53 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.13 (7 / 55), avg. gap size = 1.00 (7 / 7) 15 22.67 0.00 0.00 chr3ptel1M 856433 856464 (143536) (GC)n#Simple_repeat 1 32 (0) m_b132s252i6 4889 chr3ptel1M 856433 GCGCATGCGCGCGCACGCGCACAAGCGCGCGC 856464 ii i i iv (GC)n#Simple_ 1 GCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGC 32 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 40 0.00 0.00 0.00 chr3ptel1M 856945 856981 (143019) (C)n#Simple_repeat 1 37 (0) c_b132s251i1 4890 chr3ptel1M 856945 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 856981 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 37 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 485 28.28 11.76 0.82 chr3ptel1M 858200 858420 (141580) C MIRc#SINE/MIR (9) 259 15 m_b132s601i2 4891 chr3ptel1M 858200 AATAGCCTGCGATGATATAACA---TAAAGGTTGCAAA-TG-TTTCCTTT 858244 i?v i i iv vi i --- v v i -i - viv C MIRc#SINE/MIR 259 AACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCGCTTTCACAT 210 chr3ptel1M 858245 ACAA-ATTTCATCGGAT--TCACACCGATCATGGGAGGGAGA---GGC-- 858286 v- i iv -- v i i v v v i--- -- C MIRc#SINE/MIR 209 ACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAG 160 chr3ptel1M 858287 -TGTCCTTATCCCCATTTTACAGATTAGGAGACTGAGG--TAAACAGGGT 858333 - i iv v i --i i v v C MIRc#SINE/MIR 159 GTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTT 110 chr3ptel1M 858334 CAGTGATTTGGCCCGAGTGCCACGGGGCT---------CTGAGGCTGTAT 858374 v i - i - i ivi --------- v v v v i C MIRc#SINE/MIR 109 AAGTGACTT-GCCCAAG-GTCACACAGCTAGTAAGTGGCAGAGCCGGGAC 62 chr3ptel1M 858375 TTGAACTCGGG-CTTGCTGATGCCAGGGCTTGTGCTTTATCCCCCGC 858420 i i i - v iv i v iv i v v i C MIRc#SINE/MIR 61 TCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGC 15 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.91 CpG sites = 33, Kimura (unadjusted) = 36.35 Transitions / transversions = 1.14 (33/29) Gap_init rate = 0.06 (13 / 220), avg. gap size = 2.15 (28 / 13) 217 31.14 8.97 1.19 chr3ptel1M 858706 858783 (141217) C L2c_3end#LINE/L2 (11) 467 384 m_b132s601i3 4892 chr3ptel1M 858706 CATTAAACCTTTATTTGGCCCCTACTGCGTGCCA-------AGGATCCAA 858748 vi v vi v ii -------i v C L2c_3end#LINE 467 CAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGATACAA 418 chr3ptel1M 858749 AGAGAGGTAAAGGACAGCCCTCTGGCCTCGGAGGG 858783 viii iiv i i - v iii i C L2c_3end#LINE 417 AGATGAATAAGACACGGTCC-CTGCCCTCAAGGAG 384 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.09 CpG sites = 16, Kimura (unadjusted) = 42.47 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.03 (2 / 77), avg. gap size = 4.00 (8 / 2) 700 24.73 5.49 0.00 chr3ptel1M 859047 859228 (140772) C MIRc#SINE/MIR (62) 206 15 m_b132s601i4 4893 chr3ptel1M 859047 TCATCTCATAAGATCTTCACAAAAATCCAGGGAGGGAGA---GGC---TA 859090 i vv i v i v v v i--- --- C MIRc#SINE/MIR 206 TTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTA 157 chr3ptel1M 859091 TTATTATCCCCATTTTACAGATAAGGAGACTGAGG--CAAACAAGTTCAG 859138 i i -- i v i v C MIRc#SINE/MIR 156 TTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAG 107 chr3ptel1M 859139 TGATTTACCCCAAGTCCCACAGGTGGCAGATGTCTGAGGCTAGATTTAAA 859188 i i v i v v i i ii v v v vi i ii C MIRc#SINE/MIR 106 TGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAA 57 chr3ptel1M 859189 CTCAGG-CTTTCTGATGCCAGGACTT-TGCTTTATCCCCTGC 859228 i - i iv i v iv- i v v C MIRc#SINE/MIR 56 CCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGC 15 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.59 CpG sites = 25, Kimura (unadjusted) = 30.48 Transitions / transversions = 1.25 (25/20) Gap_init rate = 0.03 (5 / 181), avg. gap size = 2.00 (10 / 5) 244 35.26 0.70 2.14 chr3ptel1M 859682 859823 (140177) L1ME4c_3end#LINE/L1 347 486 (344) m_b132s551i0 4894 chr3ptel1M 859682 CCGTAAAACCATGCTTCTCCTTTGACCTAGAAATACTACTGCTAGCTCTG 859731 i vii v v vi i v v i v i vvv v L1ME4c_3end#L 347 CCATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATT 396 chr3ptel1M 859732 CGTCCCCAAAGAAGGTTTTTTTAAAGGGAAAAAAAATCTGTACCTACAAA 859781 ii - i i i-- vv i i i ii v i ivi i L1ME4c_3end#L 397 TAT-CCTAAGGAAA--TAATTCAAAAGAAGGAAAAAGCTATATGCACGAA 443 chr3ptel1M 859782 AATATTCATAGCATC-TCTTTTCTGGTGGTAAAGAATTGGAAA 859823 i i v v - iv v ii i ii i L1ME4c_3end#L 444 GATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAA 486 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 46.92 CpG sites = 30, Kimura (unadjusted) = 49.99 Transitions / transversions = 1.58 (30/19) Gap_init rate = 0.03 (4 / 141), avg. gap size = 1.00 (4 / 4) 512 21.72 0.74 7.94 chr3ptel1M 859829 859963 (140037) MIRc#SINE/MIR 2 127 (141) m_b132s601i5 4895 chr3ptel1M 859829 GGGGCAGTTGGGTGGTGCAGTGGCTAGAGCCCCAGCCCTGAAGTCAGGAG 859878 i --- vv v ii v i i i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr3ptel1M 859879 GACCCGAGTTCAAATCTGATCTCAGACACTTCACACGTCCTGGCTGTGTG 859928 i i i i iviv v v ------- v i MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCCACT-------TACTAGCTGTGTG 91 chr3ptel1M 859929 ACCCTGGGCAAGTCACTTAACCCCAAT-TGCCTCAG 859963 i i vv -v MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 23.68 CpG sites = 15, Kimura (unadjusted) = 25.80 Transitions / transversions = 1.25 (15/12) Gap_init rate = 0.08 (11 / 134), avg. gap size = 1.00 (11 / 11) 19 0.00 0.00 0.00 chr3ptel1M 861277 861297 (138703) (A)n#Simple_repeat 1 21 (0) m_b132s252i7 4896 chr3ptel1M 861277 AAAAAAAAAAAAAAAAAAAAA 861297 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAA 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 273 31.36 11.49 1.04 chr3ptel1M 861367 861627 (138373) L1PA13_3end#LINE/L1 4 291 (619) m_b132s551i1 4897 chr3ptel1M 861367 ATCTCAAATATCTA---GGAACTGAATCAGATTTATAA----AATACAAG 861409 v v ii --- v v i i ---- v i L1PA13_3end#L 4 ATATCCAGCATCTATAAGGAACTTAAACAAATTTACAAGAAAAAAACAAA 53 chr3ptel1M 861410 TTATTCCTCAACTGATAAATGGCCAAGGGATT----CAGACAGTTTTTCA 861455 iv ii --- i i v i v i iv---- v iv L1PA13_3end#L 54 CAACCCC---ATTAAAAAGTGGGCAAAGGACATGAACAGACACTTTTCAA 100 chr3ptel1M 861456 GAGAA---ATCTAAGCTGTCTGTACTCATA---AAAAATGCTCTAAATCA 861499 i --- vi v v i vii v --- v v v L1PA13_3end#L 101 AAGAAGACATACATGCGGCCAACAATCATATGAAAAAAAGCTCAACATCA 150 chr3ptel1M 861500 CT--TGATTAGAGAAATGCACGTGAA----------AGAAAACACCTCAT 861537 -- v vi v ---------- v v i i L1PA13_3end#L 151 CTGATCATTAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTCAC 200 chr3ptel1M 861538 TCCTTTCAAATGGACTAATATGACAGAAAAGGAAAGTGACAAATGCTAGA 861587 v vv i vv i v v v i ivvii i i i i v L1PA13_3end#L 201 ACCAGTCAGAATGGCTATTATTAAAAAGTCAAAAAATAACAGATGCTGGC 250 chr3ptel1M 861588 GGGGATGTGGA-AAGCTGGGACACGAAGGCACTGCTGCTGG 861627 i v i - ivv i i vv vi i v L1PA13_3end#L 251 GAGGTTGCGGAGAAAAAGGAACGCTTATACACTGTTGGTGG 291 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 39.85 CpG sites = 39, Kimura (unadjusted) = 41.13 Transitions / transversions = 0.93 (39/42) Gap_init rate = 0.04 (11 / 260), avg. gap size = 3.00 (33 / 11) 345 28.08 10.53 1.61 chr3ptel1M 861400 861627 (138373) L1MB3_3end#LINE/L1 44 291 (639) m_b132s551i2 4897 chr3ptel1M 861400 AAAATACAAGTTATTCCTCAACTGATAAATGGCCAAGGGATTC----AGA 861445 v iiv --- i i i ? v v i i i---- L1MB3_3end#LI 44 AAAAAACAAACAA---CCCGATTNAAAAATGGGCAAAGGACTTGAATAGA 90 chr3ptel1M 861446 CAGTTTTTCAGAGAA---ATCTAAGCTGTCTGTA--CTCATAAAAA-ATG 861489 v i i i --- vi iiv i vi -- v i - L1MB3_3end#LI 91 CATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATG 140 chr3ptel1M 861490 CTCTAAATCACT--TGATTAGAGAAATGCACGTGAAA----------GAA 861527 v v -- v i vi v ---------- v L1MB3_3end#LI 141 CTCAACATCACTAATCATTAGGGAAATGCAAATCAAAACCACAATGAGAT 190 chr3ptel1M 861528 AACACCTCATTCCT-TTCAAATGGACTAATATGACAGAAAAGGAAAGTGA 861576 v iv i- vii - v v v i vi i i L1MB3_3end#LI 191 ACCACCTCACACCCATTAGGATGG-CTACTATCAAAAAAACAGAAAATAA 239 chr3ptel1M 861577 CAAATGCTAGAGGGGATGTGGA-AAGCTGGGACACGAAGGCACTGCTGCT 861625 i i i v i - ii i v vviv v L1MB3_3end#LI 240 CAAGTGTTGGCGAGGATGTGGAGAAATTGGAACCCTTGTGCACTGCTGGT 289 chr3ptel1M 861626 GG 861627 L1MB3_3end#LI 290 GG 291 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 35.46 CpG sites = 35, Kimura (unadjusted) = 36.17 Transitions / transversions = 1.25 (35/28) Gap_init rate = 0.05 (12 / 227), avg. gap size = 2.33 (28 / 12) 102 29.80 3.83 4.18 chr3ptel1M 863325 863924 (136076) (TGTGAG)n#Simple_repeat 1 598 (0) m_b132s252i8 4898 chr3ptel1M 863325 TGTGAGTGGGAACGTGAGGGAGGGTCTGAGTG-G-GTGCAAGTGGGACTG 863372 v ii v v i v - - ii v v (TGTGAG)n#Sim 1 TGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTG 50 chr3ptel1M 863373 GGTGAGGGGGTGTGGGTGTAAATGAGCATGTGAGCATATGAATGTGAATG 863422 v v v v i i i i v vi -- i i - - (TGTGAG)n#Sim 51 TGAGTGTGAGTGTGAGTGTGAGTGTGAGTGTGAG--TGTGAGTGTG-A-G 96 chr3ptel1M 863423 TGTGAGTGTAAGTGAACAAGTGGGAGCACGTGTGAATCT--GTGACAGTG 863470 i viviv i v iiv i v -- vv (TGTGAG)n#Sim 97 TGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTG 146 chr3ptel1M 863471 T-AATGTCTGTGTGGGTGTGAATCTATGTGTATGACTGTCAGTGTAACAG 863519 - i vv i - -v i v i v v i vv (TGTGAG)n#Sim 147 TGAGTGTGAGTGTGAGTGTG-A-GTGTGAGTGTGAGTGTGAGTGTGAGTG 194 chr3ptel1M 863520 TGTGTGTGAGTGTATGAATGT-A-TGAGGGTATAAATGTGAATGTGCCTG 863567 v -- i - - v i i i i i vv (TGTGAG)n#Sim 195 TGAGTGTGAGTG--TGAGTGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTG 242 chr3ptel1M 863568 TGTGTGTGAGAAGCGAGCATGTGTTTGTAAGTGTGTGTGTGATTGTGTGT 863617 v -v i -- vv i v v v (TGTGAG)n#Sim 243 TGAGTGTGAG-TGTGAG--TGTGAGTGTGAGTGTGAGTGTGAGTGTGAGT 289 chr3ptel1M 863618 GTGAAGTGAGCACGTGAGTGT--TTAAGAGTGTGTGTGTGAG-AAAAATG 863664 - v vii --v iv v -ivi i (TGTGAG)n#Sim 290 GTG-AGTGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTG 338 chr3ptel1M 863665 AGCATGTGAGTATGAGTGAGAAGCAAGCATGTGAGTGT--GTGTGAGTGT 863712 v vi i v - iiv vi -- (TGTGAG)n#Sim 339 TGAGTGTGAGTGTGAGTGTG-AGTGTGAGTGTGAGTGTGAGTGTGAGTGT 387 chr3ptel1M 863713 GTATGTGTGTGT-A-TGTGAG-AAAAGTGAGCATGTGAGTGTGAAAAGCG 863759 vi v - - -ivi v vi - iv i (TGTGAG)n#Sim 388 GAGTGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTGTG-AGTGTG 436 chr3ptel1M 863760 AGCATGTGTGTGTGTATGTGAG-AAAAGTGAGCATGTGAGTGTGTGTGT- 863807 -- v vi -ivi v vi v - (TGTGAG)n#Sim 437 AG--TGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTGTG 484 chr3ptel1M 863808 A-TGTGAGTGTGTGAG-AAAAGTGATTGTGTGTGT-A-TGAGAAGCATGT 863853 - v v -i iv v v - - v - -- (TGTGAG)n#Sim 485 AGTGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTGTG-AG--TGT 531 chr3ptel1M 863854 GAGTAT--GTGTAAATATGTGTGTTGTATGTGAGAAAAGTGAACGTGTGT 863901 i -- i i i v - - - v - iv ii v (TGTGAG)n#Sim 532 GAGTGTGAGTGTGAGTGTGAGTG-TG-A-GTGTG-AGTGTGAGTGTGAGT 577 chr3ptel1M 863902 GTGAGTGTGCATGAGTGAGGGTG 863924 - - v v (TGTGAG)n#Sim 578 GTGAGTGTG-A-GTGTGAGTGTG 598 Matrix = Unknown Transitions / transversions = 0.84 (62/74) Gap_init rate = 0.07 (44 / 599), avg. gap size = 1.09 (48 / 44) 329 30.73 13.41 0.00 chr3ptel1M 864203 864381 (135619) L3#LINE/CR1 2671 2873 (1226) m_b132s601i6 4899 chr3ptel1M 864203 GGGACCAGGAGGAGGAAGACGGCC---CGTCGTCCCCA--------AAGG 864241 vi i ivv i v ---i ? ? i -------- L3#LINE/CR1 2671 GGTGCCAGAAGACTGGAGACGGGCAAATGTNGTNCCTANTTTTAAAAAGG 2720 chr3ptel1M 864242 GAAGCAA-ACCGAGTTTGCAAACTACTCGTCAGGGAGCGTGGC-TTGGGC 864289 iv - iv v i ? vvii i vi v i - i iv L3#LINE/CR1 2721 GAAAAAAGATGGATTCTGNAAACTACAGACCGGTAAGCTTGACGTCGATC 2770 chr3ptel1M 864290 TCCGGCCACATTCTAGAGCACATCGTTAA----ATGGCTAATGACCACCT 864335 i v v i iv ii ---- i vi v i L3#LINE/CR1 2771 CCCGGCAAAATTCTAGAACGGATTATTAAACAGATGGTTTGTGAGCACTT 2820 chr3ptel1M 864336 GGAAAAGAAGGCTGCGGCGAC---GAGCCCGCCAGGCTCC----AGAACA 864378 i i i v i iiv --- v vv v i ---- L3#LINE/CR1 2821 AGAAAAGGAAGCGGTGATCACTAGGAGCCAGCATGGGTTCACTAAGAACA 2870 chr3ptel1M 864379 GGT 864381 i L3#LINE/CR1 2871 AGT 2873 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.72 CpG sites = 32, Kimura (unadjusted) = 41.67 Transitions / transversions = 1.39 (32/23) Gap_init rate = 0.04 (7 / 178), avg. gap size = 3.43 (24 / 7) 19 28.62 0.00 0.00 chr3ptel1M 864665 864721 (135279) (ATGCC)n#Simple_repeat 1 57 (0) m_b132s252i9 4900 chr3ptel1M 864665 ATGCCGTGCCATGCTGTGCCAAACCGTGTCAGGCTGTGCCATACCGTGCC 864714 i ii vi i i v ii i i (ATGCC)n#Simp 1 ATGCCATGCCATGCCATGCCATGCCATGCCATGCCATGCCATGCCATGCC 50 chr3ptel1M 864715 ATGCGAT 864721 v (ATGCC)n#Simp 51 ATGCCAT 57 Matrix = Unknown Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0) 30 31.63 2.67 2.67 chr3ptel1M 866106 866255 (133745) (CCT)n#Simple_repeat 1 150 (0) m_b132s252i10 4901 chr3ptel1M 866106 CCTCCTCCTTCCTCCTCTCCCTCC-CCTCCCCATTCTCCTCCCCGCTCTT 866154 - ii - i v i i - i (CCT)n#Simple 1 CCTCCTCC-TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC-CTCCT 48 chr3ptel1M 866155 CTTCCTCCTTGACCTCCAGATGTCCCTATGCCCTGTCC-CCCACTCTTCC 866203 i ivv vvv vii viv iiv - iv i (CCT)n#Simple 49 CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC 98 chr3ptel1M 866204 TCTCCCTGACTCCT-CTCCTCCT-CGCCTCTTCTCCCCCCTCCCTCCCCC 866251 ii -v - - v i ii i - i (CCT)n#Simple 99 TCCTCCT-CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT-CCTCCTCC 146 chr3ptel1M 866252 CCCT 866255 i (CCT)n#Simple 147 TCCT 150 Matrix = Unknown Transitions / transversions = 1.77 (23/13) Gap_init rate = 0.05 (8 / 149), avg. gap size = 1.00 (8 / 8) 14 16.91 0.00 2.94 chr3ptel1M 866631 866665 (133335) (GGCCCC)n#Simple_repeat 1 34 (0) m_b132s252i11 4902 chr3ptel1M 866631 GGCTCCGGCCCAGGCCCCCGCCCCGCCGCCCGTCC 866665 i v v v - v (GGCCCC)n#Sim 1 GGCCCCGGCCCCGGCCCCGGCCCCGGC-CCCGGCC 34 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 15 13.67 0.00 0.00 chr3ptel1M 867270 867293 (132707) (C)n#Simple_repeat 1 24 (0) m_b132s252i12 4903 chr3ptel1M 867270 CCCCTCCCCAGCCCCCCCCCCCCC 867293 i vv (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCC 24 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 311 20.34 0.00 1.69 chr3ptel1M 867742 867801 (132199) C L2d2_3end#LINE/L2 (3) 552 494 m_b132s601i7 4904 chr3ptel1M 867742 AGTCACAGTCAACAAGCATTTGTTCAGCACCTCCTGTGTGCCAGGCACTG 867791 i - i ii i v i v v C L2d2_3end#LIN 552 AATCA-AATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTG 504 chr3ptel1M 867792 TGCCAAGTGC 867801 i i i C L2d2_3end#LIN 503 TGCTAGGCGC 494 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 20.15 CpG sites = 9, Kimura (unadjusted) = 24.68 Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.02 (1 / 59), avg. gap size = 1.00 (1 / 1) 83 23.60 5.39 4.55 chr3ptel1M 867914 868284 (131716) (AAGAG)n#Simple_repeat 1 374 (0) m_b132s252i13 4905 chr3ptel1M 867914 AAGAGTAGAG--GGGAAGGGAGGA-AAG-GGAGAGGAAAGAAGAGGGCAG 867959 v -- i i i - - i i i iiv (AAGAG)n#Simp 1 AAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAG 50 chr3ptel1M 867960 AAGAGGAGGAGAGGAAGAGAGAAGATGAAGA-AACAAAGGAAGAAGA-AA 868007 - i i ii - - v i i - - (AAGAG)n#Simp 51 AAGA-GAAGAGAAGAGAAGAGAAGA-GAAGAGAAGAGAAG-AGAAGAGAA 97 chr3ptel1M 868008 AAGGGGGGAAAAGAA-AGAGGAGGA-AGAAGAGGA-AGAAAAGAAGAGAA 868054 i ii i i - i i - i - i (AAGAG)n#Simp 98 GAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAA 147 chr3ptel1M 868055 GATGA-AGAAGAGAAGGAGGAAGAG-GCAGAACAGGAAGAGGAGA-AAGT 868101 vi - - - -iv v - i - - (AAGAG)n#Simp 148 GAGAAGAGAAGAGAA-GA-GAAGAGAAGAGAAGA-GAAGAGAAGAGAAG- 193 chr3ptel1M 868102 AGAAGA-AAAAAAAGTTAGACAGAGGATCAAAAAGAAGAGGAG-GAATA- 868148 - i i -- - i vvi i i - v - (AAGAG)n#Simp 194 AGAAGAGAAGAGAAG--AGA-AGAGAAGAGAAGAGAAGAGAAGAGAAGAG 240 chr3ptel1M 868149 AGGAGGAGAAGAAGAGAAGGGGGAAGAGAAGAGAGAAGAAAAG-AGTGTA 868197 i i - -- i ii i - v v (AAGAG)n#Simp 241 AAGAGAAG-AGAAGAGAA--GAGAAGAGAAGAGAAGAGAAGAGAAGAGAA 287 chr3ptel1M 868198 ATGAAG-GGAGAGAAGAGGA-AG-AGAGAAGAGGAGAGGGGAGGA-AGAA 868243 iv - i i - - i ii i - (AAGAG)n#Simp 288 GAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAA 337 chr3ptel1M 868244 GTGCTCCCAGCAAGAGAAGCAGATTGGAAAAGAGGAGAGGA 868284 v --vvv - - vvi i i i (AAGAG)n#Simp 338 GAG--AAGAG-AAGAGAAG-AGAAGAGAAGAGAAGAGAAGA 374 Matrix = Unknown Transitions / transversions = 2.72 (49/18) Gap_init rate = 0.10 (36 / 370), avg. gap size = 1.03 (37 / 36) 93 20.73 3.36 4.76 chr3ptel1M 867947 868244 (131756) (AAG)n#Simple_repeat 1 294 (0) m_b132s252i14 4905 chr3ptel1M 867947 AAGAAGAGGGCAGAAG-AGGAGGAGAGGAAGAGAGAAGATGAAGAAACAA 867995 -i v - i i i - v iv i (AAG)n#Simple 1 AAGAAGA-AGAAGAAGAAGAAGAAGAAGAAGA-AGAAGAAGAAGAAGAAG 48 chr3ptel1M 867996 AGGAAGAAGAAAAAG-GGGGGAA-AAGAAAGAGGAGGAAGAAGAGGAAGA 868043 i i -i ii - - i i i (AAG)n#Simple 49 AAGAAGAAGAAGAAGAAGAAGAAGAAG-AAGAAGAAGAAGAAGAAGAAGA 97 chr3ptel1M 868044 A-AAGAAG-AGAAGATGAAGAAG-AGAAGGAGGAAGAGGCAGAACAGGAA 868090 - - v - - i i v v i (AAG)n#Simple 98 AGAAGAAGAAGAAGAAGAAGAAGAAGAA-GAAGAAGAAGAAGAAGAAGAA 146 chr3ptel1M 868091 GAGGAGAAAGTAGAAGAAAAAAAAGTTAGACAGAGGATCAAAAAGAAGAG 868140 i ii v i i -v - i vv i i (AAG)n#Simple 147 GAAGAAGAAGAAGAAGAAGAAGAAG-AAGA-AGAAGAAGAAGAAGAAGAA 194 chr3ptel1M 868141 GAGGAATAAGGAGGAGAAGAAG-AGAAGGGGGAAG-AGAAGAGAGAAGAA 868188 i v i i - - ii - - (AAG)n#Simple 195 GAAGAAGAAGAAGAAGAAGAAGAAGAA-GAAGAAGAAGAAGA-AGAAGAA 242 chr3ptel1M 868189 -AAGAGTGTAATGAAG-GGAGAGAAGAGGAAGAGAGAAGAGGAGAGGGGA 868236 - -v - - -i - i - i - ii (AAG)n#Simple 243 GAAGA-AG-AA-GAAGAAGA-AGAAGAAGAAGA-AGAAGAAGA-AGAAGA 286 chr3ptel1M 868237 GGAAGAAG 868244 i (AAG)n#Simple 287 AGAAGAAG 294 Matrix = Unknown Transitions / transversions = 3.00 (36/12) Gap_init rate = 0.08 (24 / 297), avg. gap size = 1.00 (24 / 24) 312 30.00 2.00 0.00 chr3ptel1M 868547 868646 (131354) C MIRb#SINE/MIR (95) 173 72 m_b132s601i8 4906 chr3ptel1M 868547 CTTCAAGGGGATCATTAACGACCCCATTTGACAGATCAGGAAGCTGAGGC 868596 v i viivi viiv v v i C MIRb#SINE/MIR 173 CTGCGAGGTAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGC 124 chr3ptel1M 868597 CGACAGAGCTGATGTGACTGGCCCA--GACAAGCAGCCAATAGGTGTCCG 868644 iv v v v v i v -- v vi i i i v v C MIRb#SINE/MIR 123 TCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAG 74 chr3ptel1M 868645 AG 868646 C MIRb#SINE/MIR 73 AG 72 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.94 CpG sites = 13, Kimura (unadjusted) = 38.49 Transitions / transversions = 0.76 (13/17) Gap_init rate = 0.01 (1 / 99), avg. gap size = 2.00 (2 / 1) 414 25.69 3.40 2.01 chr3ptel1M 868563 868709 (131291) C MIR3#SINE/MIR (57) 151 3 m_b132s601i9 4906 chr3ptel1M 868563 AACGACCCCATTTGACAGATCAGGAAGCTGAGGCCGACAGAGCTGATGTG 868612 vv i v v i v v v v C MIR3#SINE/MIR 151 AACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTG 102 chr3ptel1M 868613 ACTGGCCCA--GACAAGCAGCCAATAGGTGTCCGAGGCTCCTGACTC-AG 868659 v -- v vi ? i vi v v --i vv v- i C MIR3#SINE/MIR 101 ACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAG--CCGGGACTAGAA 54 chr3ptel1M 868660 CCCAGTGTTCTGTGTTTGGCGGTGCGGG--CTCTCTGCCCAGACACTCTG 868707 - iiiv vi vv i v v -- i v C MIR3#SINE/MIR 53 CCCAG-GTCTCCTGACTCCCAGTCCGTGCTCTCTCTGCTCAGCCACTCTG 5 chr3ptel1M 868708 CC 868709 C MIR3#SINE/MIR 4 CC 3 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.74 CpG sites = 13, Kimura (unadjusted) = 31.74 Transitions / transversions = 0.54 (13/24) Gap_init rate = 0.04 (6 / 146), avg. gap size = 1.33 (8 / 6) 18 4.50 0.00 0.00 chr3ptel1M 869307 869329 (130671) (CA)n#Simple_repeat 1 23 (0) m_b132s252i15 4907 chr3ptel1M 869307 CACCCACACACACACACACACAC 869329 v (CA)n#Simple_ 1 CACACACACACACACACACACAC 23 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 18 13.24 2.22 4.55 chr3ptel1M 871500 871544 (128456) (TCCCT)n#Simple_repeat 1 44 (0) m_b132s252i16 4908 chr3ptel1M 871500 TCCCTTCCCTTCCCATCAC-CCCCTCCCAACATCCCTTCCCTTCCC 871544 v v -i i -- v (TCCCT)n#Simp 1 TCCCTTCCCTTCCCTTCCCTTCCCTTCC--CTTCCCTTCCCTTCCC 44 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.07 (3 / 44), avg. gap size = 1.00 (3 / 3) 439 23.29 9.03 3.05 chr3ptel1M 872568 872722 (127278) C MIR3#SINE/MIR (28) 180 17 m_b132s601i10 4909 chr3ptel1M 872568 TGGCAGAGATACTGAAGGGGTCCCCATGTCCTTCTCCTGCTCATTTTACA 872617 v i ivi -- i i vi vv vv i -- C MIR3#SINE/MIR 180 TGGAAGGGACCTT--AGAGATCATCTAGTCCAACCCC--CTCATTTTACA 135 chr3ptel1M 872618 GATGAGGAAACTGAGGTAAACTG-GGTGAAGTGCCTTACCCAGGGTCACA 872666 ivv vv - v i i C MIR3#SINE/MIR 134 GATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACA 85 chr3ptel1M 872667 TGGC----------CAGGACCAGATCT-GAA-CCAGGTCTTCCTGA-TGC 872703 ii ---------- ii i iv - - - - v C MIR3#SINE/MIR 84 CAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGTC-TCCTGACTCC 36 chr3ptel1M 872704 CAGGCCGGGCGTGCTCTGC 872722 v v viv C MIR3#SINE/MIR 35 CAGTCCGTGCTCTCTCTGC 17 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.23 CpG sites = 17, Kimura (unadjusted) = 28.14 Transitions / transversions = 0.94 (17/18) Gap_init rate = 0.06 (10 / 154), avg. gap size = 1.90 (19 / 10) 368 30.53 0.00 0.00 chr3ptel1M 873040 873134 (126866) C MIR#SINE/MIR (81) 181 87 m_b132s601i11 4910 chr3ptel1M 873040 CTCATGGCCACTCTGGGAGGGAGGTGCCGCCCCCACCCCCATTTCACAGT 873089 iii v i iv v i iiiivii i i v C MIR#SINE/MIR 181 CTCACAACAACCCTATGAGGTAGGTACTATTATTATCCCCATTTTACAGA 132 chr3ptel1M 873090 TGAGGAAACTGAGGCAGACAGAGATTGGCTGCCTTGGCCAGGGTC 873134 v v i iiv iv v i C MIR#SINE/MIR 131 TGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTC 87 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.10 CpG sites = 19, Kimura (unadjusted) = 41.10 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.00 (0 / 94), avg. gap size = 0.0 (0 / 0) 303 27.84 1.01 2.04 chr3ptel1M 873048 873146 (126854) C MIR1_Amn#SINE/MIR (50) 180 83 m_b132s601i12 4910 chr3ptel1M 873048 CACTCTGGGAGGGAGGT-GCCGCCCCCACCCCCATTTCACAGTTGAGGAA 873096 i ivi i -iviii vii i i v C MIR1_Amn#SINE 180 CACTTTACAAAGGAGGTCAGTATCATTATCCCCATTTTACAGATGAGGAA 131 chr3ptel1M 873097 ACTGAGGCAGACAGAGATTGGCTGCCTTGGCCAGGGTCTTCCTGAGCTGG 873146 ?v v i ?iiv v v i vi? -- ? C MIR1_Amn#SINE 130 ACTGAGGCNCAGAGAGGTNAAGTGACTTGCCCAAGGTCACNC--AGCNGG 83 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.09 CpG sites = 17, Kimura (unadjusted) = 38.09 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.03 (3 / 98), avg. gap size = 1.00 (3 / 3) 11 24.50 2.22 2.22 chr3ptel1M 873640 873684 (126316) (CCCCCAG)n#Simple_repeat 1 45 (0) m_b132s252i17 4911 chr3ptel1M 873640 CCTCCAGCCCGCAGCCCAGGAGGCCCCCCTCCCCA-CCCCCACCCC 873684 i v -vv v vvi - v (CCCCCAG)n#Si 1 CCCCCAGCCCCCAGCCC-CCAGCCCCCAGCCCCCAGCCCCCAGCCC 45 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.05 (2 / 44), avg. gap size = 1.00 (2 / 2) 205 23.68 0.00 0.00 chr3ptel1M 874244 874281 (125719) C MIR3#SINE/MIR (53) 155 118 m_b132s601i13 4912 chr3ptel1M 874244 GTCTACTTCCTTCACTTGACAGATGGGGAGACTGAGGC 874281 i vii i i v i i C MIR3#SINE/MIR 155 GTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGC 118 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.11 CpG sites = 7, Kimura (unadjusted) = 30.11 Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 264 26.18 0.00 3.08 chr3ptel1M 874626 874692 (125308) C L3#LINE/CR1 (14) 4085 4021 m_b132s601i14 4913 chr3ptel1M 874626 ACCTCAGAACTGGAAGGGGCTTCAGAGGGGCTCTAGTCCATCCCCCCACA 874675 i ii i i i vvv v i i- C L3#LINE/CR1 4085 ATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCAACCTCCCAT- 4037 chr3ptel1M 874676 GTTAAAGCAAGAACCCC 874692 -ii v i i C L3#LINE/CR1 4036 -CCAATGCAGGAATCCC 4021 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.72 CpG sites = 12, Kimura (unadjusted) = 33.72 Transitions / transversions = 2.40 (12/5) Gap_init rate = 0.03 (2 / 66), avg. gap size = 1.00 (2 / 2) 370 32.57 5.91 4.15 chr3ptel1M 875052 875288 (124712) C L2b_3end#LINE/L2 (19) 447 207 m_b132s601i15 4914 chr3ptel1M 875052 ATCTCCTGTTAGCCCCTCCCGTGTGCCAGGCGCTGTGCCAAGTGCTGGGG 875101 i v -- v v i ? i i i C L2b_3end#LINE 447 ATTTACTG--AGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGGG 400 chr3ptel1M 875102 GCCCAA-----AAAGGGCCAAAGCCAGTCCCTGCCCTTGGGGAGCTCACA 875146 iiv i----- vii v i v? i iiv C L2b_3end#LINE 399 ATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGGAGCTCACA 350 chr3ptel1M 875147 ATCTGATGGAAGCGACCA--AAGGAGCCACGTGCAGGATGAC---GGGAA 875191 i ii ii v vi-- v v i? viii- v? i --- i vi C L2b_3end#LINE 349 GTCTAGTGGGGGAGACAGACATGTAANCAGACA-ATNATAACCCAGAGTG 301 chr3ptel1M 875192 TCAGGACCAGATTCAGTGGGCTTAGGGAAGGCTTCCTG--TAGGAGGGGG 875239 v iivi i vi v ii i i viv --iv vvv C L2b_3end#LINE 300 GCAGGGTAGGACTGGGGGGGCCCAGAGGAGGGCGCCTGACCCGGCCTGGG 251 chr3ptel1M 875240 GAGTCTTAGGG-GGGCTCCAAGTCTTAGGGGGGGGGAGA-ATGGTCTGAG 875287 i -- - ----- iii i i v v -v iv C L2b_3end#LINE 250 GGGTC--AGGGAGGGCT-----TCCCGGAGGAGGTGACATTTGAGCTGAG 208 chr3ptel1M 875288 A 875288 C L2b_3end#LINE 207 A 207 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.23 CpG sites = 45, Kimura (unadjusted) = 45.67 Transitions / transversions = 1.55 (45/29) Gap_init rate = 0.07 (16 / 236), avg. gap size = 1.50 (24 / 16) 40 9.34 0.00 0.00 chr3ptel1M 875989 876045 (123955) (CA)n#Simple_repeat 1 57 (0) c_b132s251i2 4915 chr3ptel1M 875989 CACACACACACACACACACACACACACACACACATTCTCACACACTCTCA 876038 iv v v v (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 chr3ptel1M 876039 CACACAC 876045 (CA)n#Simple_ 51 CACACAC 57 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0) 40 0.00 0.00 0.00 chr3ptel1M 876393 876429 (123571) (G)n#Simple_repeat 1 37 (0) c_b132s251i3 4916 chr3ptel1M 876393 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 876429 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 37 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 13 14.26 0.00 6.06 chr3ptel1M 880336 880370 (119630) (TCCC)n#Simple_repeat 1 33 (0) m_b132s252i18 4917 chr3ptel1M 880336 TCCATCCCTCCCTCCCTCCCAGGACTCGCCTCCCT 880370 v -vvv - (TCCC)n#Simpl 1 TCCCTCCCTCCCTCCCTCCC-TCCCTC-CCTCCCT 33 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 13 22.55 2.00 4.08 chr3ptel1M 881066 881115 (118885) (GAGGCG)n#Simple_repeat 1 49 (0) m_b132s252i19 4918 chr3ptel1M 881066 GAAGCGG-GGCGCGGGGTGAGAGGCGGAGACGGAGGGCGAGGCCCTGGCG 881114 i - - i i - i vv vvv (GAGGCG)n#Sim 1 GAGGCGGAGGCG-GAGGCG-GAGGCGGAGGCGGAGGCGGAGGCGGAGGCG 48 chr3ptel1M 881115 G 881115 (GAGGCG)n#Sim 49 G 49 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.06 (3 / 49), avg. gap size = 1.00 (3 / 3) 18 12.16 0.00 0.00 chr3ptel1M 881525 881551 (118449) (C)n#Simple_repeat 1 27 (0) m_b132s252i20 4919 chr3ptel1M 881525 CCCCCTTCCCCCCCCCCCCCCCCCGCC 881551 ii v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCC 27 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 25 24.16 2.11 4.30 chr3ptel1M 882010 882104 (117896) (GGGGGGA)n#Simple_repeat 1 93 (0) m_b132s252i21 4920 chr3ptel1M 882010 GGTGGGAGGCGGAGCCTGGGGAGGGGGGGATGGGGGA-GGCGGAGCCTGG 882058 v - i vvv - v - v -vv (GGGGGGA)n#Si 1 GGGGGGAGG-GGGGAGGGGGGA-GGGGGGAGGGGGGAGGGGGGAG-GGGG 47 chr3ptel1M 882059 GGCGGGGGAGGGGGGA-GGCGGAGCCTGGGGCGGGGGTGGTGGGAGG 882104 iv - v -vv iv v v (GGGGGGA)n#Si 48 GAGGGGGGAGGGGGGAGGGGGGAG-GGGGGAGGGGGGAGGGGGGAGG 93 Matrix = Unknown Transitions / transversions = 0.20 (3/15) Gap_init rate = 0.06 (6 / 94), avg. gap size = 1.00 (6 / 6) 16 7.71 3.57 0.00 chr3ptel1M 882615 882642 (117358) (CCTC)n#Simple_repeat 1 29 (0) m_b132s252i22 4921 chr3ptel1M 882615 CCTTCCT-TCTCCCTCCCTCCCTCCCTCC 882642 i -i (CCTC)n#Simpl 1 CCTCCCTCCCTCCCTCCCTCCCTCCCTCC 29 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 15 19.61 0.00 0.00 chr3ptel1M 889000 889028 (110972) (G)n#Simple_repeat 1 29 (0) m_b133s252i0 4922 chr3ptel1M 889000 GGGAGGGGTGGGTGAGGGGGGCGGGGGGG 889028 i v v i v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG 29 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 26 49.32 0.00 0.00 chr3ptel1M 889331 889522 (110478) (GGGG)n#Simple_repeat 1 192 (0) m_b133s252i1 4923 chr3ptel1M 889331 GGGGCAGGGGTTGGTTGGGGAGGAGGGGGGGAGGAAGGGAGGGGGGGAAG 889380 vi vv vv i i i ii i ii (GGGG)n#Simpl 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 50 chr3ptel1M 889381 GGGGTGGGAAGGGGAGGGCGGGGAAGGAGGGCAGAGAAGGGAAGGAAAGG 889430 v ii i v ii i vi i ii ii iii (GGGG)n#Simpl 51 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 100 chr3ptel1M 889431 AAATAGAAGGGGTGGGGGGGGGGGTGGGAACAAGGGGGGGAGGAAAGGAG 889480 iiivi ii v v iivii i iii i (GGGG)n#Simpl 101 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 150 chr3ptel1M 889481 GGAAGTAAGGGGAGGAGGGGGGAAAGGGGAGGGAGGGAGGGG 889522 ii vii i i iii i i i (GGGG)n#Simpl 151 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 192 Matrix = Unknown Transitions / transversions = 3.92 (51/13) Gap_init rate = 0.00 (0 / 191), avg. gap size = 0.0 (0 / 0) 45 20.22 8.67 1.62 chr3ptel1M 889363 889535 (110465) (GGAAG)n#Simple_repeat 1 185 (0) m_b133s252i2 4923 chr3ptel1M 889363 GGAAGGG-AGGG-GGGGAAGGGGGTGGGAAGGGGAGGGCGGGGAA-GG-A 889408 - -i - iv i vi - - (GGAAG)n#Simp 1 GGAAGGGAAGGGAAGGGAA-GGGAAGGGAAGGGAAGGGAAGGGAAGGGAA 49 chr3ptel1M 889409 GGGCAGAGAAGGGAAGGAAAGGAAATAGAAGGGGTGGG--GGG-GGGGGT 889455 v i i i vi iv -- -i iv (GGAAG)n#Simp 50 GGGAAGGGAAGGGAAGGGAAGGGAAGGGAAGGGAAGGGAAGGGAAGGGAA 99 chr3ptel1M 889456 GGGAA--CAAGGG--GGGGA-GGAAAGG-AGGGAA-GTAAGGGGAGGAGG 889498 --v -- i - i - - v i - i (GGAAG)n#Simp 100 GGGAAGGGAAGGGAAGGGAAGGGAAGGGAAGGGAAGGGAAGGGAAGG-GA 148 chr3ptel1M 889499 GGGGAAAGGGGAGGG-AGGGAGGGGAAAAGGAGGGAAG 889535 i - i - i ii i (GGAAG)n#Simp 149 AGGG-AAGGGAAGGGAAGGGAAGGGAAGGGAAGGGAAG 185 Matrix = Unknown Transitions / transversions = 2.62 (21/8) Gap_init rate = 0.09 (15 / 172), avg. gap size = 1.20 (18 / 15) 18 17.46 1.75 5.45 chr3ptel1M 891264 891320 (108680) (CTGCGC)n#Simple_repeat 1 55 (0) m_b133s252i3 4924 chr3ptel1M 891264 CTGCGCCTGCGTCCCTGC-CCTCCCGTCTGCGCCTGCGCTTGCGCGGGCT 891312 -- - -v i i vv v (CTGCGC)n#Sim 1 CTGCGCCTGCG--CCTGCGCCT-GCGCCTGCGCCTGCGCCTGCGCCTGCG 47 chr3ptel1M 891313 TCTCCGCC 891320 i v (CTGCGC)n#Sim 48 CCTGCGCC 55 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.07 (4 / 56), avg. gap size = 1.00 (4 / 4) 12 25.69 0.00 0.00 chr3ptel1M 894485 894521 (105479) (CCGGACC)n#Simple_repeat 1 37 (0) m_b133s252i4 4925 chr3ptel1M 894485 CCGGGCCCAAGAGCCTGGACCCCACAGCCCGGACCCC 894521 i vi v i iv v (CCGGACC)n#Si 1 CCGGACCCCGGACCCCGGACCCCGGACCCCGGACCCC 37 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 20 4.30 0.00 0.00 chr3ptel1M 894940 894963 (105037) (G)n#Simple_repeat 1 24 (0) m_b133s252i5 4926 chr3ptel1M 894940 GGGGGTGGGGGGGGGGGGGGGGGG 894963 v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGG 24 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 15 22.45 4.17 0.00 chr3ptel1M 896178 896225 (103775) (CCCTCC)n#Simple_repeat 1 50 (0) m_b133s252i6 4927 chr3ptel1M 896178 CCCTCCTCTTTCTCCT-TCCC-CCCCCTCCGCCTCCCCTGCCCCCCCCCC 896225 i i i i -i - v iv i (CCCTCC)n#Sim 1 CCCTCCCCCTCCCCCTCCCCCTCCCCCTCCCCCTCCCCCTCCCCCTCCCC 50 Matrix = Unknown Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.04 (2 / 47), avg. gap size = 1.00 (2 / 2) 17 18.38 0.00 0.00 chr3ptel1M 896195 896225 (103775) (C)n#Simple_repeat 1 31 (0) m_b133s252i7 4927 chr3ptel1M 896195 CCCCCCCCTCCGCCTCCCCTGCCCCCCCCCC 896225 i v i iv (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 31 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 183 29.63 2.44 1.20 chr3ptel1M 896526 896607 (103393) MIRc#SINE/MIR 66 148 (120) m_b133s601i0 4928 chr3ptel1M 896526 CGGCCCCGGACGCTCATCGGCCCTGTGACCCTGGGCCAGTCCCTCGCCCT 896575 i i v- i i iii iv i v v iiv MIRc#SINE/MIR 66 CGGCTCTGC-CACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCT 114 chr3ptel1M 896576 GCCT--GCCTCAGTTTCCCCTTCTGCCCAATGAG 896607 vi -- i v ivv i MIRc#SINE/MIR 115 CTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.12 CpG sites = 15, Kimura (unadjusted) = 39.12 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.02 (2 / 81), avg. gap size = 1.50 (3 / 2) 266 21.12 3.19 4.30 chr3ptel1M 898160 898253 (101747) C MER50-int#LTR/ERV1 (6) 7199 7107 m_b133s701i0 4929 chr3ptel1M 898160 CATCTCCCCCCTCCTCAAGCACTAGACACAAATTCTTTTGG-AAAAGGGC 898208 i v-vi iv v v v v - v v C MER50-int#LTR 7199 CATTTCCCCCCTCA-AGAGTCCAAGACCCCAATTCTTTGGGGAAAATGGA 7151 chr3ptel1M 898209 CGGTGATCTCTAGTCTTCTGTATCTACTTCCTGCTG--GGATGGGCG 898253 iv i --- v i --i v C MER50-int#LTR 7150 CGAAGGTC---AGTCTTCTGTAACTGCTTCCTGCTGACAGAGGGGCG 7107 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 24.80 CpG sites = 7, Kimura (unadjusted) = 24.80 Transitions / transversions = 0.58 (7/12) Gap_init rate = 0.06 (6 / 93), avg. gap size = 1.17 (7 / 6) 459 35.27 4.13 2.54 chr3ptel1M 898409 898795 (101205) C MER66-int#LTR/ERV1 (241) 6435 6043 m_b133s701i1 4929 chr3ptel1M 898409 TTGTAGCCTAGAAGAGACAAATCTCACGAGCAATTTGAAAACGCAAGGAC 898458 ii v ii i v v iv i v v i C MER66-int#LTR 6435 TTGTAATCTAGAAGACACAAACTTTACTAGGAGGTTAAACAAGCAAGGGC 6386 chr3ptel1M 898459 CAAATATGAGC--TGA-AGGATAATAATCAGAAG-------AGAGGTTAG 898498 v v i-- i - i iiv i i ------- v i C MER66-int#LTR 6385 CAAAAATTAGTAATAACAAGATAGCTATCAAAGGTCCTAGGAGAGGTAAA 6336 chr3ptel1M 898499 TAT-AGGTGCCAGTAGGGAC--CATATCCAGGAATCCCACCCAGTGGACT 898545 v i- vv v v v-- iv iiiiv i v- vii iv v C MER66-int#LTR 6335 AACCAGGTGAGACTTGGGAAGGCACTTTTGATAGTCG-ACCAGATATAGT 6287 chr3ptel1M 898546 TGGGGGGTGTAAGAAACTGCTCATGG--AGGTCT-TGCATCCAGGCAGCC 898592 ---- v ---- i - -- vi - i v i i C MER66-int#LTR 6286 TGGGG----TCAG----TGCCC-TGGTTATATCTATGTAACCAGGTAGCT 6246 chr3ptel1M 898593 TTCTGTAAGATTCTCTCTGTGCGCAGCTCAACTTTCCTTGAGTTGTTAAT 898642 v vvv ii i vvi ivv v i vi iv C MER66-int#LTR 6245 TGCTCATAGATCTTTTGAATGTTAACCTCAACCTGTCCAGAGTTGTTAAT 6196 chr3ptel1M 898643 ATACATACAGCAAGAGCTGTTGGCTAGAGCACAGACATCTCCGCTGGGGG 898692 ii i i vvi i iiiv vv vi v vivvvvi C MER66-int#LTR 6195 ATATGTGCAGCAGGTTTTATTAATAACTGCACAGACTCCACCTTGTTCAG 6146 chr3ptel1M 898693 CAAGAAGATAATCTAAAGCCATGCGATTATCCAAAACCATATTAGCCAAG 898742 v v i i v i vv vi v i i i v i C MER66-int#LTR 6145 CTAGTAAATAATCCAACGCTAGTCTGTTATCGAGAACTACATTTGCCAAA 6096 chr3ptel1M 898743 GAGTCGAGAGATTCCTGAATCTCTCTCAAGGAATGAGCCGTTTCGTTGGC 898792 v i i i ii ii i v vv v i v i v C MER66-int#LTR 6095 GAGTCTAGGGACTCTTGAATTCCCTTTAATGCCTGACCTGTGTTGGTGGC 6046 chr3ptel1M 898793 AAA 898795 v C MER66-int#LTR 6045 TAA 6043 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 48.74 CpG sites = 69, Kimura (unadjusted) = 48.74 Transitions / transversions = 1.08 (69/64) Gap_init rate = 0.04 (17 / 386), avg. gap size = 1.53 (26 / 17) 682 29.72 5.68 3.63 chr3ptel1M 900452 900856 (99144) C HERV4_I#LTR/ERV1 (1046) 5493 5081 m_b133s701i2 4929 chr3ptel1M 900452 TGATTCAATTTTTTCACCTTTCCCAGAGG--CGAGG--ACCAGGC-AAGT 900496 - iiii vv i --i --v v -i i C HERV4_I#LTR/E 5493 TGATT-AGCCCTTTCTACTTTCCCGGAGGATTGAGGCCTCCATGCTGAAT 5445 chr3ptel1M 900497 GGAGATGATAAGAGATGTTTAGTCCCTTT---ATCCCTTGGGTTATCTGG 900543 v i ii vvv viiv vv v--- i i i C HERV4_I#LTR/E 5444 GTAAATAGTATTTGATTCCGAGAGCCTTAGCAACCCCTTGAGTTATTTGG 5395 chr3ptel1M 900544 ---AGAAATGAAGGTCCATTATCGTTTCTGTAGAGCT---GGGCAACCAA 900587 --- v v v v i ii - v - --- i v C HERV4_I#LTR/E 5394 GAGATAAAGGACGGGCCGTTATCACTT-TGGAG-GCTCTGGGGTAACCCA 5347 chr3ptel1M 900588 AAC-GGGGTATGATCTCCTTCAGCAGACATTTGATA-CCTTATGGGCCTT 900635 - v v i i iv vvi v - i vi C HERV4_I#LTR/E 5346 AACCGGGGGATTATTTCCTTTAAGAGAACCTTTATAACCTCATTAGCCTT 5297 chr3ptel1M 900636 TTCAACCTCA--AGGAAAAGCTTCCCACCCAGTTAGTGAAAA-ATTAACA 900682 i viiiiii-- iv v- ii i ii-i iv iv C HERV4_I#LTR/E 5296 CTCTGTTCTGGTAGGGTAAGCTTCG-ACCCAGCCAGTAAAGGTGTCTATT 5248 chr3ptel1M 900683 AATACCAAAAGCAACTTAAAACCTCTACCAAGGAGGCATAT---TGAAAT 900729 i i iv iv iv v i - vv --- i C HERV4_I#LTR/E 5247 AGTACTAGCAAAAACTTGTATCCTCTGC-AAGCTGGCATATGGGTGAAGT 5199 chr3ptel1M 900730 CTAACTGCCAATCCTCCCC-GGGTACGTCCTCTCCCTCTGGACTGGCTTC 900778 i i i - v i iiii i ii C HERV4_I#LTR/E 5198 CTAATTGCCAGTCTTCCCCTGGGTAAGTTCCTCTCCTCTGGACTGGTTCT 5149 chr3ptel1M 900779 AGGAGAGGTGGGGTTTAAATTGGGTTCCCTTGGGATTTTTACCTGGGCAC 900828 vv v vi ------v i -- i v vv vi C HERV4_I#LTR/E 5148 ATTAGAGGAGGCATTT------TGTTTCCT--GGGTTGTTAAGTGCACAC 5107 chr3ptel1M 900829 AGATTGGGCAGGCCTGGCACACCTGTTT 900856 -- i i i v i C HERV4_I#LTR/E 5106 AG--TGAGCAGGCTTGACAGACCTGCTT 5081 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 37.68 CpG sites = 68, Kimura (unadjusted) = 38.98 Transitions / transversions = 1.42 (68/48) Gap_init rate = 0.07 (27 / 404), avg. gap size = 1.41 (38 / 27) 407 30.83 5.56 3.37 chr3ptel1M 901241 901851 (98149) C PRIMA41-int#LTR/ERV1 (2858) 4898 4275 m_b133s701i3 4929 chr3ptel1M 901241 AAACAACTTCAATAAGGTGCAGAATTTCTCCCC-AT-TTTAATTGGAAAG 901288 i v v v? i v vvvi- - v v ii ? C PRIMA41-int#L 4898 AAACAGCATCTAANAGATTCAGAATTTCTGAGTGATGTTTTATGGGGGAN 4849 chr3ptel1M 901289 GTTTT-GCTGTCAACAAACCCCTTTCTTTTTCCAAATAGCTCCATGAGCA 901337 vii - ? i i? iv ? i -- ? i ?v C PRIMA41-int#L 4848 CCCTTAGCNGTTAGNAGTCCCCNTTCCTT--CCANATGGCNGCATGAGCA 4801 chr3ptel1M 901338 TGGAAAAATATAAACTT-TATTT-AAATCC-TGTAGATGTTGAC-CTCAT 901383 iv vi v ??i- i -i v- ? ? - i v C PRIMA41-int#L 4800 TGGAGCACCAGAAANNCATACTTGGAATCAGTGNANATGTTGACTCTTAA 4751 chr3ptel1M 901384 CCCCTTCCCAAATTCTAAAGCCTGTTAATCTAAGGAGTTTAATTTC---- 901429 vi i v v? ii --i -? ii v?v i ---- C PRIMA41-int#L 4750 GTCCTTTCCCAATTGNAGGGCC--CTAAT-NAGAGCNATTAATTCCGCCT 4704 chr3ptel1M 901430 -TTGTGCAGAGGCCCAGG-AGGCAATGGTTTGGCCTCCACAGTCT-TTGA 901476 - v v i?v i -v i v vi ?? v i?ii -? v C PRIMA41-int#L 4703 TTTGAGCTGAGGTNGAAGCCGGTAAGGCCTNNGCCTCGATNACCTCNTGT 4654 chr3ptel1M 901477 AGAAT-ACCACAACA-GCC---CCTTTCTCTCCCCATTCTCCAAGAAAGC 901521 v iv - ? i -i --- v ii v ?v v - v C PRIMA41-int#L 4653 TGGCTAACNACAGCATACCCNGCCTTTCTGTTTCCCTNGTGC-ACAAAGC 4605 chr3ptel1M 901522 TGAACCCATCCTTGTGAACCA--CTGTCT--GGGTTCTCCAAAGGGGGTT 901567 ivvi -- i -- ii -- i v i ii vvvv C PRIMA41-int#L 4604 TACTTCCATC--TGTAAACCATTCTACCTCGGGATTATCTAGGGGCTCAT 4557 chr3ptel1M 901568 CCTTTAAGTCAGGTCTACT-AAGTAGACAGAATCTATAACTTCCTCAAAA 901616 v i ?i -i i ivviv i vivi v C PRIMA41-int#L 4556 CCTTTAAGTCCGGCCNGCTGGAGTAAATTTGCTCCATAACTTGTATACAA 4507 chr3ptel1M 901617 TTTGAACAATTCTCT----TGATTGAAGAATAAG--AGAAAAGTGGCAGG 901660 --- ii --- ---- vi vi iv v? -- i ? i i v C PRIMA41-int#L 4506 ---GAATGA---TCTAGGGTGCCTGTGGGTTCNGGCAAANAGGTAGCTGG 4463 chr3ptel1M 901661 AATTTAAAAGTACGACAGACTTGAAGGGACAGGTCCAAAGAACAACAAG- 901709 i-- v vi i v v i vi vi ---i iiiiv v - C PRIMA41-int#L 4462 G--TTCAAAGTTTGGCATACTTTAAGAGTTACATC---GGGGTGTCTAGC 4418 chr3ptel1M 901710 GAGAAACCTTGGTACTT-AGTAAACCTCCCACTGAGAGCCACTGAT-CCC 901757 i ? v i i i - ?iv v vv ? i -i C PRIMA41-int#L 4417 AANAAAGCCTGATATTTNAGTAANTGTCCCCCTGTCANCCACTGGTGTCC 4368 chr3ptel1M 901758 TTTGGCTTTAAAAATCTTTTGAATTCTGT-TGGGATTAAAAACTCTAATT 901806 ? iv ii i iii v i iv -? i i v i? C PRIMA41-int#L 4367 TTTNGCTTCTAGGACCCCCTGTACTTGGTGNGGGGTCAAAACCTCTAGNT 4318 chr3ptel1M 901807 CCCAACCCAAGGGTCAATTTGGAAACTTCCCTCAATTAAAAGGGC 901851 viiiv -? ? i ivvii - ? v ii ? i C PRIMA41-int#L 4317 GTTGTCCCAA-NGTNAGTTTACTGGCTT-CNTCTACCAANAGAGC 4275 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 44.02 CpG sites = 104, Kimura (unadjusted) = 44.35 Transitions / transversions = 1.33 (104/78) Gap_init rate = 0.07 (44 / 610), avg. gap size = 1.25 (55 / 44) 345 28.80 6.15 5.61 chr3ptel1M 903078 903272 (96728) C HERVH48#LTR/ERV1 (4208) 2446 2251 m_b133s701i4 4930 chr3ptel1M 903078 ATTTTCCCTTCAATTCCCATCAC-----CTTATGGGGGGAGGGACGAGTA 903122 i vi v iv ----- ----- ivi i i C HERVH48#LTR/E 2446 ACTTGTCCGTCAATTCCCACAACAGAGACTT-----GGGAGGACTGGGTG 2402 chr3ptel1M 903123 GGACCCGAATGCTCGAGCAGAACGGAGAAAGAAGCCCCGGTGTCAAAGAG 903172 v i viv iii i i i v i vv i i vvv? C HERVH48#LTR/E 2401 GGTCCTGAAAAATTAGGTAAAGCGGAGTAGGTTGCCCCGGTATTAATTTN 2352 chr3ptel1M 903173 AAAAGAG---ACTGGCGTACCTCCTACGTCCAAGGTTACCCTAGGCTCGG 903219 i --- v iv i vvi i v C HERVH48#LTR/E 2351 AAAAAAGCGTACTGGCCTACCCGCCACCGTCAGGGTTACCCTTGGCTCGG 2302 chr3ptel1M 903220 CT---TCGATGATGGAGGTAGGGG-GTCCATGGCCAAGCCAGGGCCCCGT 903265 v ---v i i vv iv - i ------v v C HERVH48#LTR/E 2301 ATGAAGCGATGGTAGTTGCCGGGGCGTCCGT------TCCAGGGCACCGT 2258 chr3ptel1M 903266 CAGTCCT 903272 i C HERVH48#LTR/E 2257 CAGTCTT 2251 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 35.47 CpG sites = 28, Kimura (unadjusted) = 37.20 Transitions / transversions = 1.12 (28/25) Gap_init rate = 0.08 (15 / 194), avg. gap size = 1.53 (23 / 15) 15 0.00 0.00 0.00 chr3ptel1M 903880 903896 (96104) (AC)n#Simple_repeat 1 17 (0) m_b133s252i8 4931 chr3ptel1M 903880 ACACACACACACACACA 903896 (AC)n#Simple_ 1 ACACACACACACACACA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 999 30.73 0.00 0.56 chr3ptel1M 904269 904628 (95372) C HERV1_I#LTR/ERV1 (316) 8485 8128 m_b133s701i5 4932 chr3ptel1M 904269 TGGGCAGGCACATGAACTATTCTGCGAATGCCTTTTGTAATTTCCTTTAC 904318 i v v ii vii v v v ivviv i v v C HERV1_I#LTR/E 8485 TGGACCGGGACATGGGCTAACTTCCGCATCCTGGCAGTGATTTCCATGAC 8436 chr3ptel1M 904319 TACTCGCCCATTATCATCAATTTGCATGCAACAATTAGACAAATTTAACT 904368 vi vi i i i v i i ? v v ii C HERV1_I#LTR/E 8435 AGCTCTTCCATTGTCATCGATTTGTAAGCAGCAGTTNGTCAAATTAAGTT 8386 chr3ptel1M 904369 TTCCACAGACCCCTCCTTCCTCTGCTAGCAAATAATCTAAGACGAGTCGG 904418 ? i i ivvv v i i vi v i vi C HERV1_I#LTR/E 8385 TNCCACAAACTCCTCCTTCTGAGGCTAGGAGATAGTCTAATGCTAGCCTA 8336 chr3ptel1M 904419 TGCTGTAAAACAGCTTCTCGAGTTTGAGTGGCTTGATCAGCTAGCAAATC 904468 vi vv v ii v vvi i i ? i vvii C HERV1_I#LTR/E 8335 TTTTGATATATGGCATCTCTCATCTGGGTNGCCTGTATGGCTAGCAAATC 8286 chr3ptel1M 904469 AAGAGCTTGAGCAGTTTGATTAGTTGTTATCTCCAGAACTGCTTGTAATC 904518 v ii i i v v iii i v i i v i C HERV1_I#LTR/E 8285 CAAGGCTCGGGCTGTTTCATTGACTATGATTTCTAGTACTGCTTGCAATC 8236 chr3ptel1M 904519 TAATTAGCCTATTTAATACATATATATTGGTGTCCTATAACCCCAGCTTC 904568 v v vi vi -- i v v v v vi ? vvvi C HERV1_I#LTR/E 8235 TTATGATTCGGTTTA--ACATGTAAATAGGAGTACGGTANCCCCATGACC 8188 chr3ptel1M 904569 CATCCCGAGCCCATGTGGCTGGCCCATACTCTTTGACAATTCTTTCTGGG 904618 ii ? ? i v v i v i C HERV1_I#LTR/E 8187 CATCTTGNGCCCANGTAGCTGGCCCATAGTATTTGATAATTCTTTCAGGA 8138 chr3ptel1M 904619 GACCATGTAT 904628 i vi C HERV1_I#LTR/E 8137 GGCCATTCAT 8128 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 40.16 CpG sites = 57, Kimura (unadjusted) = 41.12 Transitions / transversions = 1.08 (57/53) Gap_init rate = 0.01 (2 / 359), avg. gap size = 1.00 (2 / 2) 17 0.00 0.00 7.69 chr3ptel1M 905425 905452 (94548) (AAT)n#Simple_repeat 1 26 (0) m_b133s252i9 4933 chr3ptel1M 905425 AATAATAATAATGCAATAATAATAATAA 905452 -- (AAT)n#Simple 1 AATAATAATAAT--AATAATAATAATAA 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.07 (2 / 27), avg. gap size = 1.00 (2 / 2) 1178 36.22 3.92 4.00 chr3ptel1M 905918 907217 (92783) C HERVIP10B3#LTR/ERV1 (2005) 5598 4300 m_b133s701i6 4934 chr3ptel1M 905918 TTTGACTCGAGTGCGATGTGTCCAGCCTCTCTCTTTGGTATGTATCGCCG 905967 i i v v i i vvi? vi v ii ? C HERVIP10B3#LT 5598 TTTGACTCGGGTGTGATGGGTCCATCCTTTTTCGGCNGTTCGGACTGCNG 5549 chr3ptel1M 905968 TATCTGAAGTCATCAGGATCTGGAACAGTCCTTCCCAGCTCAGGGTC-AG 906016 v v v? i vv v iiv v vi -v i v - C HERVIP10B3#LT 5548 TCTCAGTNGTTAGGAGCACTAGGTAAGGTCCTTCCCAG-GCGGGTTCGAG 5500 chr3ptel1M 906017 CTGATGTCTTCCTTCCACGCCCAAACCAGGCCCCAGTCTCCAGGCTAGAA 906066 -- vi i i vviiivi iv v viii i i vi C HERVIP10B3#LT 5499 CT--TTCCCTCTTTCCAACTTTTGATGAGGACGTGATCTCCGGGCTGGTG 5452 chr3ptel1M 906067 CTTATGCACTGTGAATCCTAAGGGAGGAGTCTGAGCAATAAGTCCTTTCA 906116 i vi ? v i v i v ? v v vi v - ? C HERVIP10B3#LT 5451 TTGGTGNACTGGGAATTCGAGGGGTGGNGTCTGTGCTAGGAGGCC-TTNA 5403 chr3ptel1M 906117 GTTGTAAAGTTTTCAGATGTTACAGT-AAAGACAGAAC----ACATTCCT 906161 iv i i ------ v vv vi -i v ---- i vvi C HERVIP10B3#LT 5402 GTCCTGAGG------GAGGAGAAGGTGGAAGACAGACCAAGTATATAGTT 5359 chr3ptel1M 906162 TTAAAAAAACAAATCCTTGGTCTCAAATATTGGA---TCCAAGGAAGAAT 906208 vi i vi i v i ii v --- vivi vi i C HERVIP10B3#LT 5358 TTTGAGAAACTGATCTTTTGTTTCAAACGTAGGAANGTCAGTAGTGGAGT 5309 chr3ptel1M 906209 TTTGA------ATCCCTTTTGGATAAGGGTGACCATAAAGTGATAATCCT 906252 ? v ------ v ------ ?i vvvvi i v iv v C HERVIP10B3#LT 5308 NTAGATAAGGCAACCC------ATANAGCATTTCATAAGGGGATAGGCCG 5265 chr3ptel1M 906253 ACATCCCTTTGGGGTTTTGCTCTAATTCTTAAGAAGGCAAGGGGAGGGCA 906302 ii ii i vviv i vi iv v i C HERVIP10B3#LT 5264 ACATCTTTCCGAGGGGCAGTTCGGATTCTTAGCAAGGCAATGGGAAGGCA 5215 chr3ptel1M 906303 CTTGGTCCAGGGCAATTGTGTCTCTCATGCCAA-TTAGTCAGTTGCTGTT 906351 i ? v i ii v i v viii - i i v v v C HERVIP10B3#LT 5214 TTTNGTCCATGGTAACCGGGTTTCTAAGATTAATTTGGTTAGGTGGTTTT 5165 chr3ptel1M 906352 TAATTTCCTTATCCATCCTTGCCACTTTACCTGAGAAGGGCAGATGCCAC 906401 v vvvi v i i v i i v vi ii i v C HERVIP10B3#LT 5164 TTAGAGTCTGATTCATTCTTTCTACTCTCCCTGATGAGGGTGGGTGCCAG 5115 chr3ptel1M 906402 AGGGTATGTAAGTCCCAGGATATTTCTAGAGCTTGGGCCACAGATAGGAG 906451 i vv v vvv ? v i--------- C HERVIP10B3#LT 5114 GGGGTATGGTATTCCCATTTTATNTCTAGTGCTTGGGCT---------AG 5074 chr3ptel1M 906452 GCTCTTA---------GCTGTAAAACAGGTGTCTTGGTCCGAATCTACCT 906492 v i --------- v i iii vi v v i v iv C HERVIP10B3#LT 5073 CCCCTTAATGACGTGTGCAGTGAAGTGGGTCCCATTGTCTGAATCAATGT 5024 chr3ptel1M 906493 GCTCCACCATCCCACACCTCAGAATGATATGCTCAAGGAGGACTTTTATG 906542 vi i ii vi v vi v ?i v iv vi v iv C HERVIP10B3#LT 5023 TTTCTATTAGTCCAAACCTGGGTATGATATNTTCCAACAGTGCTTTGACT 4974 chr3ptel1M 906543 AC--TGCTGAGGCAGTTGCCCAGGCAAGGGGGGAGGCCTCCATCCATGAA 906590 -- i -- ? v vv vi i iv i i i vvii C HERVIP10B3#LT 4973 ACATTACT--GGCNGTTGCGCTTGGGAAGGGGATGGCTTCTACCCAGTGG 4926 chr3ptel1M 906591 GTCAGATGGTCCACTACGACCAACAGGTATTTGAGACGCCCCACTAATGG 906640 v i i iv i ii ii i ? i v i i iiv C HERVIP10B3#LT 4925 GTGAGGTGGTCTACTATTACTAGTAAATACTTNAGGCGGCCTATTGGGGG 4876 chr3ptel1M 906641 CAGCTCGGTAAAGTCCACCTGAATGCTTTGGAAAGGCCTGATACCAGGGA 906690 vi iv v i i ii v v vv v - C HERVIP10B3#LT 4875 CATTTCGGTGTAGTCAACTTGGACACTTTGGAACGGCCTTAACCCTGGG- 4827 chr3ptel1M 906691 GCCTTCCTCCTTTCTGGACTTG---TCATT-GGGCCGCCCTATTTGTCCT 906736 --- i i iii v vv ?--- v - iivv i v ii C HERVIP10B3#LT 4826 ---TTTCTTCCCCCGGGAGGTNGCTTCTTTAGGGTTTGCTTATTAGTTTT 4780 chr3ptel1M 906737 CTGACAAACGGGACACCCGCTGACCTATTGCCT-GCTATTGTGTACAAGC 906785 iivi v vi?i v iiiivi vvv - ? vv i ? vv C HERVIP10B3#LT 4779 TCTGCACACTANGCAACTATCCGCAACTTGCCTNGCNAGGGTATANATTC 4730 chr3ptel1M 906786 TGGTGCCACCA---ACTT--AGCACCACATCACACAGGTCTTGGACACTT 906830 ivi i vv --- i-- v ii viv iiv? ii C HERVIP10B3#LT 4729 CTATACACCCATAGACTCTGAGGACTGCATCACACATAGCTTGAGGNCCC 4680 chr3ptel1M 906831 CAATGACTACCCTGATGTAAACGTGGGAATACGTGTCTCATACCTGCTGT 906880 i v v i ? ivi ? iv i iv vi ivvv v v C HERVIP10B3#LT 4679 CAGTGAGTTCCTTGATGNAGCTGNGACAGTATTTCCCTCATGAGGGGTTT 4630 chr3ptel1M 906881 GGTCAGTACCTCTCTGCCGTCAGGGAGGAGCCAGTGCCCCTCTTTATCCT 906930 v ii ii i v v v v iv v v vi vvi ii C HERVIP10B3#LT 4629 GGACAACATTTCCCTTCGGTCTGGTAATACCCACTTTCCCTCTGGGTTTT 4580 chr3ptel1M 906931 CCTGAGTGTCAAGGCTTTAGATTTCCTGCTTCTCT---TCTGGGTAAGGG 906977 v ivi v --- --- iiv i i --- v ?ii i C HERVIP10B3#LT 4579 CCTTAGCTCCTA---TTT---TTTTTAGTTTTTCTTGGTCTGCGNGGGAG 4536 chr3ptel1M 906978 AAGGTGGAG---GCATTAGAAGCAGGAATGCCAG-----AATTGG--CAC 907017 i i --- viv i vi vi v ----- iv --v C HERVIP10B3#LT 4535 AAGATGGGGATTGCAGCTGGAGGGGGAAGACAAGGGGTTAGGTGGAAAAC 4486 chr3ptel1M 907018 CATCATCTCCTTCGGACTTACAGATTCCTCTTCTCCAGCCCGTTT-CCCC 907066 viv ii - v --- v i----------- ii i -v iv C HERVIP10B3#LT 4485 GGGCGCCT-CTTGGGA---AGAGG-----------CAGCTTGCTTGGCTA 4451 chr3ptel1M 907067 TCCTATCCGCAAAGCAGTTTCCCCTTGTCTCAAATGAATCTCCTCTTTGG 907116 iiv ? ? i ivi vvv i v ?vvviiii C HERVIP10B3#LT 4450 TTTGATCNGCNAGGTTATTTCCCCGGCTTTCAAAAGANGGGTTCTTTTGG 4401 chr3ptel1M 907117 TGCCCCTGCACATGAATCACTGCAATGTTCTTAGGTAACATAAGATTAGT 907166 i iv v i iv ? v v ii iv i i vv? i ?vi C HERVIP10B3#LT 4400 TGTCCTGGGACATGGACAACNGCTATTTCTTCTGGCAGCTGNAGGTTNTC 4351 chr3ptel1M 907167 CAAAATTTTAATGACCAATGCCCTGTGTGCCAATCCCTTACCTTTACTGT 907216 i v i v? ? ii v ii vi ivi i vi i C HERVIP10B3#LT 4350 TAATACTTGNATNATTAATTCTTTGTGGACCAGGTCTTGGCCTTTACTAT 4301 chr3ptel1M 907217 T 907217 C HERVIP10B3#LT 4300 T 4300 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 51.25 CpG sites = 240, Kimura (unadjusted) = 52.62 Transitions / transversions = 1.13 (240/212) Gap_init rate = 0.05 (70 / 1299), avg. gap size = 1.47 (103 / 70) 335 36.79 1.55 0.00 chr3ptel1M 907254 907446 (92554) C HERVP71A#LTR/ERV1 (4423) 3167 2972 m_b133s701i7 4934 chr3ptel1M 907254 TTCTTTCT---TTCTTTTTTTTTTTTTCTTCACTTATGCAATGAACTAAA 907300 i --- iv i iivi ii v vvii vv C HERVP71A#LTR/ 3167 TTCTCTCTGGGTTTATTCTCCGCTTCCCTTCACTAATCAGGTGTCCTAAA 3118 chr3ptel1M 907301 TGTTTTACCTCACGTTTCACAAATCGCAATTGGTCCTGAAAAATTCTCAG 907350 i v i viv ii ii v i v i i i v i C HERVP71A#LTR/ 3117 TATTTAACTTCTTTTTCTACAAACTGCAATTTGTTCTTAGAGACTCGCAA 3068 chr3ptel1M 907351 TCCCTGTGCTCCTAAATAATTTAACAAACTGATAGTGACTTGGACAAGGT 907400 iv v iiv v i i v i ii vvivv vv C HERVP71A#LTR/ 3067 TCCCCTTTCTCCTAGGAAATTAAGCAAGCTTATGGTGGTTTCTGATACCT 3018 chr3ptel1M 907401 CACTCTTTTCCCTCCCTGCTACAAGAGGATCATCTACATATTGTAA 907446 ivi i iii ii v vv iv i i C HERVP71A#LTR/ 3017 CGGCCCTCCTCTCCCCAGAAATTAAAAGATCATCTACATATTGTAA 2972 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 50.77 CpG sites = 42, Kimura (unadjusted) = 52.97 Transitions / transversions = 1.45 (42/29) Gap_init rate = 0.01 (1 / 192), avg. gap size = 3.00 (3 / 1) 49 0.00 0.00 0.00 chr3ptel1M 909889 909930 (90070) (AC)n#Simple_repeat 1 42 (0) c_b133s251i0 4935 chr3ptel1M 909889 ACACACACACACACACACACACACACACACACACACACACAC 909930 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACAC 42 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 452 28.88 6.63 0.52 chr3ptel1M 909940 910120 (89880) C LTR43-int#LTR/ERV1 (2239) 2559 2368 m_b133s701i8 4934 chr3ptel1M 909940 GCGACAGCCAGAGACTGGGCGTGT--------TCTCTGTTCCTTGCTCTG 909981 ??i ivi vi -------- v i iv i C LTR43-int#LTR 2559 GCGNNGGCCAACAACTGGGCCCGTCTTTTGTCTCTCTCTTCTTCCCTTTG 2510 chr3ptel1M 909982 ACTTTTCAGT-CCTCCTCCA---GGTCCCTGTTATTAAATACCCCAAAGG 910027 i i ?v - i i ---v i v i v i C LTR43-int#LTR 2509 ATTTCTNTGTGCCTCTTTCACTCTGTCTCGGTTATTGAAGACCCCAAAAG 2460 chr3ptel1M 910028 CGAATTCCACTAATTGATTCATTGGAGTCTGGGGTCCTAGTTCCAATTTC 910077 v vv ii v i v i i i v i vvv i i - C LTR43-int#LTR 2459 CTACATTTAGTAGTTCATTTATTGGGGTTTGGGGACCCATGGCTAGTTT- 2411 chr3ptel1M 910078 TGCAGCTTCGGTCTGATATCTGGGGAAGACTGGCTAATAAAAT 910120 iii ivvi i v i i i C LTR43-int#LTR 2410 TGTGACTTTCTCCTAATATCTGGGGCAGACTGACTAATGAAGT 2368 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 37.62 CpG sites = 32, Kimura (unadjusted) = 38.58 Transitions / transversions = 1.60 (32/20) Gap_init rate = 0.02 (4 / 180), avg. gap size = 3.25 (13 / 4) 1214 32.44 4.91 1.11 chr3ptel1M 909971 910662 (89338) C PRIMA41-int#LTR/ERV1 (5353) 2403 1686 m_b133s701i9 4934 chr3ptel1M 909971 TCCTTGCTCTGACTTTTCAGTCCTCCTCCAGGTCCCTGTTATTAAATACC 910020 i vv vi --- iv vv i v i C PRIMA41-int#L 2403 TTCTTGCTCTTTCTGCT---TCCTCTGCCCTGTCCCTGTTATTGAAAACT 2357 chr3ptel1M 910021 CCAAAGGCGAATTCCACTAATTGATTCATTGGAGTCTGGGGTCC--TAGT 910068 ?? ? v vv vv ii ? i v i ? -- i C PRIMA41-int#L 2356 NNAAANGCCACGTCCAAAAGCTGNTCCATAGGAGTTTGGGGNCCCATAGC 2307 chr3ptel1M 910069 TCCAATTTCTGCAGCTTCGGTCTGATATCTGGGGAAGACTGGCTAATAAA 910118 v -- i i vv? v v v v v C PRIMA41-int#L 2306 TGC--TTTTTGTAGCTTCCTNCGGATATCAGGGGCAGACTGGGTTATAAA 2259 chr3ptel1M 910119 ATGGATGCTGAGGACAGCAGTCCCCTCTAAAGAAGTGGGATCTAGGTTAG 910168 v iv iv i vi ivvvi i ivvv i?ii i viv C PRIMA41-int#L 2258 ATGTACTCCCAGAAGGGTTTGTCCTTCCCTTGAGNCAGGGTCAGTGTTAG 2209 chr3ptel1M 910169 TATATTTCCTAATGGCTTCTACGAGGCGCCCCTGAAATAAAGCCAGATTC 910218 i ?v i v v ii i i ii i C PRIMA41-int#L 2208 TATATTTCCTGANTGCCTCAACTAAACGCCCTTGAAACAAAGCTGGATTT 2159 chr3ptel1M 910219 TCATCAGCTGCTTGGGTGATTTCTCTAAGCTTATCGTAATTCACCTGCTT 910268 vvi?v i i ?i i i v ? i i v vv C PRIMA41-int#L 2158 TCATCTTTNCCCTGAGNAACTTCCCTAACCTTNTCATAGTTAACAGGCTT 2109 chr3ptel1M 910269 TTTAATCCCCTTTTTCATACCCTCAATGAGGCAGGTTAGGAAATGATCCC 910318 ? v v vi i v i v ?? ii i v vv v i C PRIMA41-int#L 2108 TNTCATACATTTCTTCATCCCTTCCANNAAACAAGTGACCATATGATCTC 2059 chr3ptel1M 910319 TTTTCTCTCTCTCCCTGCTCCCCTGCTGATAGTTCCAC------------ 910356 ii i ivvv iii v ivi ------------ C PRIMA41-int#L 2058 TCCTCCCCAAGTCCTCACTGCCCCTTTGATAGTTCCACTNTGGGTCTTGA 2009 chr3ptel1M 910357 -------------CAGCCCCTGCTTGATATCTACCGGGG---GAGGTG-- 910388 -------------i v i i ?v ii iv --- i v -- C PRIMA41-int#L 2008 TCTGGAACTGCTATACCTCCTGCCTGATANATGTCATGGCTCGGGTTGCG 1959 chr3ptel1M 910389 -ACGGCCAACTCGTCTCCAAACTTCTGGGCCAGGTCCCAGATCCTCTTTT 910437 -i v ?i v i i v vivv ivi ivvi v i v vi v C PRIMA41-int#L 1958 AGCCGNTACCCCATCTGCATGGGTCCTAGCCGTCCCCAAAATGCGTTGTT 1909 chr3ptel1M 910438 TCTCCTCTATGGTACAACAAGTAGAGAGAAGGATGTTAACATCTCCCCAG 910487 i i iv v v v iv ii i vv v iiv i C PRIMA41-int#L 1908 TCTCTTCCACCGTACAACACGGAGACAACAAAATATGCAGATCCTGCCAA 1859 chr3ptel1M 910488 GACAGATCGTACTGGAGAG-TAACAGCTCTAAACCCCTCAGTAAACTTAG 910536 vi i i? vvvv - vv - i v vi i i vv C PRIMA41-int#L 1858 GTTAAATCANAGGTCAGAGTTAACTTCTC-AAACTCGTCTATGAATTTTC 1810 chr3ptel1M 910537 TGGGATCTTCAGAATATCTGCCCAGTTTCTCCTTAATCTGGGAAAGATCC 910586 iv i ? iv ? vi v ii ivviv i vv i v C PRIMA41-int#L 1809 CTGGATCCTCNGAGAANCGACCAAACTTCTCCTTGCATAGAGCCAAATCA 1760 chr3ptel1M 910587 AACATAGAAAAGGGCACCTGTACTCTAAGCGTTCCCCCCCCCCAGGACTG 910636 i ? v ? vv v ii ?i --v i v C PRIMA41-int#L 1759 GACATAGAAAAGGGNACATGTACTCTNACAGTGCCTTCNTCCC--CATTT 1712 chr3ptel1M 910637 GCCACTTCCCTTAGGGGACAAAGATT 910662 i i v v C PRIMA41-int#L 1711 GCCACCTCTCTAAGTGGACAAAGATT 1686 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 44.86 CpG sites = 110, Kimura (unadjusted) = 45.13 Transitions / transversions = 0.98 (110/112) Gap_init rate = 0.02 (14 / 691), avg. gap size = 3.00 (42 / 14) 24 31.99 0.88 2.70 chr3ptel1M 910718 910830 (89170) (GGGGGA)n#Simple_repeat 1 111 (0) m_b133s252i10 4936 chr3ptel1M 910718 GGGGGAGGGGTAGGAGGGTGAAGGTTTGGG-GCCAGAGTGGCCGGAGGAG 910766 v - v ii vvv - vvi v vv i (GGGGGA)n#Sim 1 GGGGGAGGGGGAGG-GGGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGGAG 49 chr3ptel1M 910767 GTGGTAGAGGAGGAGAAGGTGGAGGAGGAGGAGGTTGGGGGAGGAGGACG 910816 v vi i i i v i - vv i - (GGGGGA)n#Sim 50 GGGGAGGGGGAGGGGGAGGGGGAGGGGGAGG-GGGAGGGGGAGGGGGA-G 97 chr3ptel1M 910817 TGGGAGGGAGCGGG 910830 v i v (GGGGGA)n#Sim 98 GGGGAGGGGGAGGG 111 Matrix = Unknown Transitions / transversions = 0.65 (11/17) Gap_init rate = 0.04 (4 / 112), avg. gap size = 1.00 (4 / 4) 32 19.75 0.00 3.85 chr3ptel1M 910760 910840 (89160) (GGA)n#Simple_repeat 1 78 (0) m_b133s252i11 4936 chr3ptel1M 910760 GGAGGAGGTGGTAGAGGAGGAGAAGGTGGAGGAGGAGGAGGTTGGGGGAG 910809 v vi i v -v i (GGA)n#Simple 1 GGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGG-AGGAGGAG 49 chr3ptel1M 910810 GAGGACGTGGGAGGGAGCGGGAAGAGAAGGA 910840 - vi - vi i i (GGA)n#Simple 50 GAGGA-GGAGGA-GGAGGAGGAGGAGGAGGA 78 Matrix = Unknown Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.04 (3 / 80), avg. gap size = 1.00 (3 / 3) 566 36.05 0.00 1.16 chr3ptel1M 911118 911378 (88622) C MER66-int#LTR/ERV1 (5047) 1629 1372 m_b133s701i10 4934 chr3ptel1M 911118 TTAGGATTCTGGGAAAGGGCCATGAAGGCCTGAACATAGAGAATTTCCAT 911167 i i v i i v ii i ii ivi C MER66-int#LTR 1629 TCAGGATCCTGGTAAAGGGCCATAAAAGCCTGTACATAAGGGACCTCTTC 1580 chr3ptel1M 911168 CCATCTTTCTTGTTTCTTGCAAAACAAGTCCAATTCTCTAATAGGGGTGA 911217 i i vi i i i i i v vv viv iv C MER66-int#LTR 1579 CCATTTTCCTTCCTTTTTACAGAATAAGTCTAATTGTAAAATAGCATTAT 1530 chr3ptel1M 911218 AATTGATAGAGCCATTAATTGGCCATGCCTCATGTTTGTCTAACTTATAG 911267 ivv v i vvv v vii vv v v i i i v C MER66-int#LTR 1529 AACGTAAAGAACCATGTTTAGGCCAAATCTGTTGGTTTTCCAATTTGTAT 1480 chr3ptel1M 911268 TGAGGCCAAACAGAATTACAGAAATAGATAAGCCTTTTCGATTTTAAGTC 911317 iiv i vi i iv iv i i ii i ivvi -- C MER66-int#LTR 1479 TGGACCCAAACGGTGTTGCAATAGAAAATGAGTTTCTTTTTCTTTAAG-- 1432 chr3ptel1M 911318 TCTTAAACCAAATTTGTTCTTATTTCTCAAGAGATAGCCCAATGGAGAAT 911367 - iv viii i iv v ii i i v i i v i C MER66-int#LTR 1431 -CCGAATTTGAATTTGCTCCAATTGCCTAAAAGACACCCTAGTGGCGAGT 1383 chr3ptel1M 911368 CTTTAGGGATG 911378 i iv C MER66-int#LTR 1382 CCTCTGGGATG 1372 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 49.28 CpG sites = 57, Kimura (unadjusted) = 51.72 Transitions / transversions = 1.58 (57/36) Gap_init rate = 0.01 (3 / 260), avg. gap size = 1.00 (3 / 3) 16 13.25 0.00 0.00 chr3ptel1M 911501 911525 (88475) (A)n#Simple_repeat 1 25 (0) m_b133s252i12 4937 chr3ptel1M 911501 AAAAAAAAAAACACAAAAAAAACAA 911525 v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAA 25 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 574 34.26 1.71 1.36 chr3ptel1M 912437 912729 (87271) C L1ME4c_3end#LINE/L1 (275) 555 262 m_b133s551i0 4938 chr3ptel1M 912437 ATAATGTTTCATAACATTCACCTACCACAATTTACCCAACCATTCTCCAA 912486 i i vivi ?v iv i ii i v C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chr3ptel1M 912487 TGCATGGGCGTCCATTCATTTTCCAGTTTCTGGCCACTACAAACAGGGCC 912536 vvv i i ii vvivv i i v i i i i iv i C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCT 456 chr3ptel1M 912537 GCCACGAACACTTCTGCACGCATGGGACCCTTTCCCTTCTTT---AGTAT 912583 v i ii ii ii ii i --- i i --- v C L1ME4c_3end#L 455 GCAATGAACATCTTCGTGCATATAG---CTTTTTCCTTCTTTTGAATTAT 409 chr3ptel1M 912584 CTCTTTGGGGTGTAAGCCCAGTAGAAGCCCTGCAGGGTCAAAGGGTCTGC 912633 i i i i iv vv v vi vvi i v v v C L1ME4c_3end#L 408 TTCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGA 359 chr3ptel1M 912634 ACAGTTCGATACCTTTT--TGAGAAGTTCCAAACCGCTCCCCAGAATGGC 912681 v iv iv i -- iv v v v ii ii i v i C L1ME4c_3end#L 358 ACATTTTTATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGT 309 chr3ptel1M 912682 TGGATGTGTTCACAATTCCACCAACAATGCATTAGTCCCACCAGGTTC 912729 v ivvi i ? v i i v -?vi v C L1ME4c_3end#L 308 TGTACCAATTTACANTGCCACCAGCAATGTATGAG-NGTACCAGTTTC 262 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 46.88 CpG sites = 58, Kimura (unadjusted) = 48.26 Transitions / transversions = 1.41 (58/41) Gap_init rate = 0.02 (6 / 292), avg. gap size = 1.50 (9 / 6) 12 25.69 0.00 0.00 chr3ptel1M 913500 913536 (86464) (GGCGGGG)n#Simple_repeat 1 37 (0) m_b133s252i13 4939 chr3ptel1M 913500 GGCCGGGGCAGAGGGGCGGGAGACAGGGGGCTGGGGG 913536 v vv i i i i v (GGCGGGG)n#Si 1 GGCGGGGGGCGGGGGGCGGGGGGCGGGGGGCGGGGGG 37 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 225 17.95 0.00 0.00 chr3ptel1M 914046 914084 (85916) MIRc#SINE/MIR 110 148 (120) m_b133s601i1 4940 chr3ptel1M 914046 AACCTCTGAGAGCCTCGGTTTCCTCATCTGCAGAAGGAG 914084 vv i i i v i MIRc#SINE/MIR 110 AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 20.74 CpG sites = 4, Kimura (unadjusted) = 20.74 Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 41 36.30 2.31 4.03 chr3ptel1M 914253 914555 (85445) (CCTC)n#Simple_repeat 1 298 (0) m_b133s252i14 4941 chr3ptel1M 914253 CCTCCCTCCCTCTCCTCCC-CCTTCTCCAGCCTCTCCTCCTTTTCTTCCT 914301 - - i - vv - i ii i (CCTC)n#Simpl 1 CCTCCCTCCCTC-CCTCCCTCCCTC-CCTCCCTC-CCTCCCTCCCTCCCT 47 chr3ptel1M 914302 -TGTTTCTTTCTGTGTCTTTCTGTCTCTCCCTCCCTCCCTCTCCTCCC-C 914349 -iv ii ii viv ii iv i - - (CCTC)n#Simpl 48 CCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTC-CCTCCCTC 96 chr3ptel1M 914350 CTTCTCCAGCCTCTCCTCCTTTTCTTCCTTGTTTTCTTTCTGTCTCTCCC 914399 i - vv - -i i i i -iii ii iv i (CCTC)n#Simpl 97 CCTC-CCTCCCTC-CCTCC-CTCCCTCCCT-CCCTCCCTCCCTCCCTCCC 142 chr3ptel1M 914400 TCCCT-CCTCTCATCTCCTCTTTCTCTCTCTCTCTTAGTCTCTTTCAGTT 914448 - - v - ii i i i ivv i ii vvii (CCTC)n#Simpl 143 TCCCTCCCTC-CCTC-CCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCC 190 chr3ptel1M 914449 TCTGTCTCTCTGTGTCTCCCTCCTTCCCTCTCCCTGTTTCTGGGTCTCT- 914497 iv i iv vi i i i iv ii vvv i - (CCTC)n#Simpl 191 TCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTC 240 chr3ptel1M 914498 CTTCCTCTGCTTCCCTCCCTCCCTCTCTTTCTCCCT-CCTCCCTTCC-CC 914545 i - v i i ii - i - (CCTC)n#Simpl 241 CCTCC-CTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCC 289 chr3ptel1M 914546 ATCCCCTCCC 914555 v - (CCTC)n#Simpl 290 CT-CCCTCCC 298 Matrix = Unknown Transitions / transversions = 2.39 (55/23) Gap_init rate = 0.06 (19 / 302), avg. gap size = 1.00 (19 / 19) 487 28.47 4.83 0.66 chr3ptel1M 914719 914863 (85137) MIRc#SINE/MIR 11 161 (107) m_b133s601i2 4942 chr3ptel1M 914719 TGGTCCGGTGGAAGGAGCCCCCAGCTCGGGAGACAG-AAGACCTGGAACT 914767 v i i v ivii i - v - ivii MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGG-AGTCAGGAAGACCTGGGTTC 59 chr3ptel1M 914768 G-GT----ATTTTGCCACCC-TGGGCAATGTGGCTTTGGGCAAATCCTTT 914811 - ----ii i ii-ivi vi i i i vi MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTT 109 chr3ptel1M 914812 TTCCTCTCTGGGTCTCAGTTTCATCATTTGTAAATTGGGAATAAAAGCAT 914861 vv i i v i v i v ii i MIRc#SINE/MIR 110 AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAC 159 chr3ptel1M 914862 CT 914863 MIRc#SINE/MIR 160 CT 161 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.41 CpG sites = 28, Kimura (unadjusted) = 37.59 Transitions / transversions = 2.15 (28/13) Gap_init rate = 0.03 (5 / 144), avg. gap size = 1.60 (8 / 5) 253 32.73 5.29 6.55 chr3ptel1M 914928 915097 (84903) MIR1_Amn#SINE/MIR 2 169 (61) m_b133s601i3 4943 chr3ptel1M 914928 AAAGTGACTGGATGGCTCAGTGGATAGAGCCACTGGGTCTGGAGTCAGGA 914977 ii v i v vi iii - iiiv v i MIR1_Amn#SINE 2 AGGGAGGCAGTGTGGTCTAGTGGATAGAGC-ACTGGACTGGGACTCGGGA 50 chr3ptel1M 914978 AGACCTGAGTTCAAATTTAGCCTCAATCGCTGGTGTAAACTTTAGGTGCC 915027 - i ? ? iiv v vii i ? iv?i----i i? v MIR1_Amn#SINE 51 -GACCTGGGTTCNANTCCCGGCTCTGCCACTNGCCNG----CTGNGTGAC 95 chr3ptel1M 915028 ATTTAGGATTAAGGCTAATTTAACTCCTATTTACCTTA--------ATCT 915069 -i i --i v -- i ? ii v v?i i -------- MIR1_Amn#SINE 96 -CTTGGG--CAAGTC--ACTTNACCTCTCTGNGCCTCAGTTTCCTCATCT 140 chr3ptel1M 915070 GCTAGAGAAGGA-AATGACCCTCCCCTCC 915097 iv i vii - iv vv MIR1_Amn#SINE 141 GTAAAATGGGGATAATGATACTGACCTCC 169 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 47.12 CpG sites = 34, Kimura (unadjusted) = 48.47 Transitions / transversions = 1.89 (34/18) Gap_init rate = 0.08 (13 / 169), avg. gap size = 1.54 (20 / 13) 299 31.10 0.00 8.13 chr3ptel1M 914940 915072 (84928) MIRc#SINE/MIR 11 133 (135) m_b133s601i4 4943 chr3ptel1M 914940 TGGCTCAGTGGATAGAGCCACTGGGTCTGGAGTCAGGAAGACCTGAGTTC 914989 iv v - iii i MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGC-ACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr3ptel1M 914990 AAATTTAGCCTCAATCGCTGGTGTAAACTTTAGGTGCCATTTAGGATTAA 915039 i i iiv v vii i -- iiv i v -- v -i i --i MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACT--TACTAGCTGT--GTGAC-CTTGGG--CAA 102 chr3ptel1M 915040 GGCTAATTTAACTCCTATTTACCTTAATCTGCT 915072 v -- i ii v vvi i i i v MIRc#SINE/MIR 103 GTC--ACTTAACCTCTCTGAGCCTCAGTTTCCT 133 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.35 CpG sites = 25, Kimura (unadjusted) = 41.83 Transitions / transversions = 1.92 (25/13) Gap_init rate = 0.08 (10 / 132), avg. gap size = 1.00 (10 / 10) 598 32.30 7.41 3.57 chr3ptel1M 915558 916016 (83984) C L2c_3end#LINE/L2 (2) 476 1 m_b133s601i5 4944 chr3ptel1M 915558 TCATTCTGTAAATAAACATTCATCAAGTGCCCACTTTGTGTCAGGTCCTG 915607 vv v i i ii i i v i iv C L2c_3end#LINE 476 TCATTCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTG 427 chr3ptel1M 915608 TACCAAATGCTGAAAACTAAATAGAAGCAAATGATTGTTCCTGCCCCCAA 915657 vi---i i -- iv i ----- i i- iv i i C L2c_3end#LINE 426 GG---GATAC--AAAGATGAATA-----AGAC-ACGGTCCCTGCCCTCAA 388 chr3ptel1M 915658 GGGACTGACAATCTAATGAGGGAGACAG-CAGGAAAACA-ACTGT----A 915701 ii v i i ii - ? v - vi ---- C L2c_3end#LINE 387 GGAGCTCACAGTCTAGTGGAGGAGACAGACANGTAAACAGACAATTACAA 338 chr3ptel1M 915702 TACAA-------ACAAGTCCTAT-ATAGGAG---AAGTTGGA-ACAACTG 915739 ------- i v - i --- iiiv i-i v iv C L2c_3end#LINE 337 TACAAGTTAATGATAAGTGCTATAATGGGAGTATAGACAGGGTGCTATGG 288 chr3ptel1M 915740 AACCCTCATGAGGGAAGGCACTAACATTAA----GAGAGGTT-GGGCAGG 915784 i ---v iiii i iv v i i---- i i i- v C L2c_3end#LINE 287 GA---GCACAGAGGAGGGCACCTAGACTAGNCTTGGGGGGTCAGGGAAGG 241 chr3ptel1M 915785 CAT-CCGCAGAAAGTGAGATGT-AGTTGGGACTGAAAGGA--AATCAGAG 915830 v - v i i v v - i i ? vi -- i vi C L2c_3end#LINE 240 CTTCCCGGAGGAGGTGACATCTGAGCTGAGNCTTGAAGGATGAGTAGGAG 191 chr3ptel1M 915831 -AAGCCAG--TAATGAATGGGAGCAGAGTGTTCCGGGCCTTGGGTGAGCC 915877 -v --vi v i v i v ii i vvv viviv C L2c_3end#LINE 190 TTAGCCAGGTGGAAGGAGGGGGGAAGAGCATTCCAGGCAGAGGGAACAGC 141 chr3ptel1M 915878 AGAGGACAATGTCCAGAG--TGGAGAG-GCGGAGGGTCTTGTTTGCAGAA 915924 viv vv v i? i --v i -i v v -- v vi C L2c_3end#LINE 140 ATGTGCAAAGGCNCGGAGGCAGGAAAGAACTGCGG--CGTGTTTGGGGAA 93 chr3ptel1M 915925 CAGCCAGGAATCCAGGTTCACTGAAGGGAAGAGCACACGGTGGGAAGTGA 915974 i- v ? i i vv vi i viv v vi iv v i i C L2c_3end#LINE 92 T-GCAAGNAGTTCAGTGTGGCTGGAGCATAGTGGGCGAGGAGGGGAGTGG 44 chr3ptel1M 915975 AGTGTAAGAAGCTGGAAAGGGAGG-AGGGGGCAGGTTATGAAG 916016 viv v i i v - v i ii ? C L2c_3end#LINE 43 AGGAGATGAGGCTGGAGAGGTAGGCAGGGGCCAGATCGTGNAG 1 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.82 CpG sites = 82, Kimura (unadjusted) = 44.35 Transitions / transversions = 1.34 (82/61) Gap_init rate = 0.07 (34 / 458), avg. gap size = 1.50 (51 / 34) 449 38.09 4.70 2.88 chr3ptel1M 915846 916356 (83644) C L2#LINE/L2 (0) 3082 2563 m_b133s601i6 4944 chr3ptel1M 915846 GGGAGCAGAGTGTTCCGGGCCTTGGGTG-AGCCAGAGGACAATGTCCAGA 915894 i v i i vvv vi- v v v - v i v C L2#LINE/L2 3082 GGGGGAAGAGCGTTCCAGGCAGAGGGAACAGCAAGTGCA-AAGGCCCTGA 3034 chr3ptel1M 915895 GTGGAGAG-GCGGAGGGTCTTGTTTGCAGAACAGCCAGGAATCCAGGTTC 915943 vv i - i vvv - v i vi v iv vv v C L2#LINE/L2 3033 GGCGGGAGCGTGCCTGG-CGTGTTCGAGGAACAGCAAGGAGGCCAGTGTG 2985 chr3ptel1M 915944 ACTGAAGGGAAGAGCACACGGTGGGAAGTGA-AGTGTAAGAAGCTGGAAA 915992 i i v i v vi iv v ii i- viv v i iii i C L2#LINE/L2 2984 GCTGGAGCGGAGTGAGCGAGGGGGAGAGTGGTAGGAGATGAGGTCAGAGA 2935 chr3ptel1M 915993 GGGAGGAGGGGGC-AGGTTATGAAGGGTTTTGCATGTCAATGAAAGA--T 916039 v ivi i - i i v ii i v i v v i-- C L2#LINE/L2 2934 GGTAACGGGGGACCAGATCATGTAGGGCCTTGTAGGCCATTGTAAGGACT 2885 chr3ptel1M 916040 TTGTCTTTGCTTCTGGAGGCCACAGAGAGCCCCAGGAG---TTTGAGCAA 916086 v vvi iiv vv ii ii viv --- i C L2#LINE/L2 2884 TTGGCTTTTACTCTGAGTGAGATGGGAAGCCATTGGAGGGTTTTGAGCAG 2835 chr3ptel1M 916087 AGGAGTTGTGCGGTCAGGCCTGCACTACAGGGAAACTACTTCAGGGACTG 916136 viiii i v i i i ii vi iiiii ii iii vvi C L2#LINE/L2 2834 AGGAGTGACATGATCTGACTTACGTTTTAAAAGGATCACTCTGGCTGCTG 2785 chr3ptel1M 916137 GATGGAGGATGGACTGAAGTGAGGGGAGACTTGGGGCAGGTAG---AGTC 916183 vi v i i ? v i vi iv v ii v --- - C L2#LINE/L2 2784 TGTTGAGAATAGACTGNAGGGGGGCAAGGGTGGAAGCAGGGAGACCAGT- 2736 chr3ptel1M 916184 TCAACAGCTAGTGCAGTGGTCTCGGTGTGAGGTGAAAAAGATGGAAGCAG 916233 viivi v ii iv i v i ------ vi vv C L2#LINE/L2 2735 TAGGAGGCTATTGCAGTAATCCAGGCGAGAGAT------GATGGTGGCTT 2692 chr3ptel1M 916234 CGACAGAGAGTAATGGGAGTAGGACCAGTGAGATATTGCAGTTGGCCAAA 916283 v -v i ii v i iivii vi ---i i vivvv C L2#LINE/L2 2691 GGAC-CAGGGTGGTGGCAGTGGAGGTGGTGAGAAGT---GGTCGGATTCT 2646 chr3ptel1M 916284 GGAGGTGATGCTG-AGGTGAAATCAACCAGA---GATGATGCA------- 916322 vi - vi - ii ii i vi --- v v ------- C L2#LINE/L2 2645 GGATAT-ATTTTGAAGGTAGAGCCGACAGGATTTGCTGATGGATTGGATG 2597 chr3ptel1M 916323 -GGGGTGAGATTGACCAGAGATGATGCAGGGGTGA 916356 - v vv -v v vv i i C L2#LINE/L2 2596 TGGGGTGTGAGAGA-AAGAGAGGAGTCAAGGATGA 2563 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 51.89 CpG sites = 104, Kimura (unadjusted) = 55.33 Transitions / transversions = 1.22 (104/85) Gap_init rate = 0.05 (26 / 510), avg. gap size = 1.50 (39 / 26) 1272 32.06 7.68 4.58 chr3ptel1M 916835 917746 (82254) C L2#LINE/L2 (370) 2712 1774 m_b133s601i7 4945 chr3ptel1M 916835 GACCAGAGGTGATGCAGGGGTGAGATTGACCAGCGGTGATG-CAGGGGTA 916883 i v i ----- ivv v - i - v vi C L2#LINE/L2 2712 GGCGAGAGATGATG-----GTGGCTTGGACCAG-GGTGGTGGCAGTGGAG 2669 chr3ptel1M 916884 GAATGGACCAACTGAGAGTTGGAATTGG--TC-GGAGATGCTACAGAGGT 916930 -- ------ iv -- i -- - v ii viii C L2#LINE/L2 2668 G--TGG------TGAGAAGTGG--TCGGATTCTGGATATATTTTGAAGGT 2629 chr3ptel1M 916931 GAAAGCAACAGGTCTTGGCACCACATTGAATTGAGGGTGAGAGACAGTAA 916980 ii iv i vi viiviiv i vvi v ------ C L2#LINE/L2 2628 AGAGCCGACAGGATTTGCTGATGGATTGGATGTGGGGTGTGAGA------ 2585 chr3ptel1M 916981 AAAAAAAAAAAAAAAATTCCAGGGTGACTCCTGGGTTTTGAGCCTGGGAG 917030 -----i i i ii v v i vi vi i vi C L2#LINE/L2 2584 -----GAAAGAGAGGAGTCAAGGATGACTCCAAGGTTTTTGGCCTGAGCA 2540 chr3ptel1M 917031 ACTGTGAAGGTGGAGGTGCCCTGGACTGTAATAGGGAAGGTAAGAGGAGG 917080 vi i i v v v? vi i iivivi C L2#LINE/L2 2539 ACTGGAAGGATGGAGTTGCCATTNACTGAGATGGGGAAGACTGCGGGAGG 2490 chr3ptel1M 917081 GGAAGGTTTAGGGAGAAAAAACATGATTTCAGTTTTATACATATTTGGCA 917130 i v ii i i i v v v iv i vi iv C L2#LINE/L2 2489 AGCAGGTTTGAGGGGGAAGATCAGGAGTTCAGTTTTGGACATGTTAAGTT 2440 chr3ptel1M 917131 TAAAACGTTTACTGAGTATCCATAGTTCAAGATGTCTAAGAGGCAGTTGG 917180 i i i ii i iiii - v-i v iv C L2#LINE/L2 2439 TGAGATGCCTATTAGACATCCA-AGTG-GAGATGTCGAGTAGGCAGTTGG 2392 chr3ptel1M 917181 AGTTGTGAGACTGGAGGTCAGCAGAGAGGCCAGGACAGGAAAAATAGATT 917230 vv ii v v vi i v i v i v i C L2#LINE/L2 2391 ATATACGAGTCTGGAGTTCAGGGGAGAGGTCCGGGCTGGAGATATAAATT 2342 chr3ptel1M 917231 TGAGAATCACCAGCATAGAGAAGGTCACTGCATTCATAGAAGCTG-ATGA 917279 i i i v v vvi iv vi - ii - C L2#LINE/L2 2341 TGGGAGTCATCAGCATATAGATGGTATTTAAAGCCAT-GAGACTGGATGA 2293 chr3ptel1M 917280 GATGTCTAAATGA---AATG-ATCTAGAGG-GAGAAAAG-----AAGA-- 917317 vv i? iv --- i - vv i- i ----- i -- C L2#LINE/L2 2292 GATCACCNAGGGAGTGAGTGTAGATAGAGAAGAGAAGAGGTCCAAGGACT 2243 chr3ptel1M 917318 -------GGGACA----GAAGCTGTGA--TCTGG------AGGAGAATCC 917348 ------- i ----i v i ?v -- v ------ i v C L2#LINE/L2 2242 GAGCCCTGGGGCACTCCAACGTTNAGAGGTCGGGGAGATGAGGAGGAACC 2193 chr3ptel1M 917349 AGCAAAAGTGACAGAGCA--------CAG--AGATGGGAAAAGAGCTTGG 917388 i v v v -------- -- i i ii i i iv C L2#LINE/L2 2192 AGCAAAGGAGACTGAGAAGGAGCGGCCAGTGAGGTAGGAGGAAAACCAGG 2143 chr3ptel1M 917389 AGGGAG-AACGTCCTGAAAACCCAGAGAG--AAGT-----AAATAACCAG 917430 i v -iii i i v v i-- ----- iv ivvi C L2#LINE/L2 2142 AGAGTGTGGTGTCCTGGAAGCCAAGTGAAGAAAGTGTTTCAAGAAGGAGG 2093 chr3ptel1M 917431 GAGAGATTAATGGTGTCCAAGGCTGCCCGAAGTTCAAAGAGAATGAGAAT 917480 v i iv v v ivi? v iv ii i i C L2#LINE/L2 2092 GAGTGATCAACTGTGTCAAATGCTGCTGANAGGTCAAGTAAGATGAGGAC 2043 chr3ptel1M 917481 TGGGGGGGGAAAAAAGGCCATTGGATTTGGTGATGAAGACGTCACTGGTG 917530 ------- i vv i i ii i vi v i C L2#LINE/L2 2042 TG-------AGAATTGACCATTGGATTTAGCAACGTGGAGGTCATTGGTG 2000 chr3ptel1M 917531 ATTTTGGAAAGGGCAGTTGTGGTG--ATGATGCGGTCAGGAGCCAGATT- 917577 ii iv i vi --i i v v iii v - C L2#LINE/L2 1999 ACCTTGACAAGAGCAGTTTCGGTGGAGTGGTGGGGACGAAAGCCTGATTG 1950 chr3ptel1M 917578 GTGAGGAATGAAGA-AGAAGAAGAGCAGAGGCATCAGGAGGCA-CAAGTG 917625 v v iv v - vii v v i- i - i i C L2#LINE/L2 1949 GAGTGGGTTCAAGAGAGAATGGGAGGAGAGGAATT-GGAGACAGCGAGTA 1901 chr3ptel1M 917626 CAGAC-ACTTTCTTGAG----TTTACTCACAAAGGACAGAAGACACATAT 917670 i - i i i ---- i -ii iv v v v -- C L2#LINE/L2 1900 TAGACAACTCTTTCGAGGAGTTTTGCT-GTAAAGGGGAGCAGAGAAAT-- 1854 chr3ptel1M 917671 GAAGAGAAGAGTTAGTGGGGAAAGAAAGATCCCAGAGAGGA------TTT 917714 -ii iviiv i i v i ? vii i - v i i ------ C L2#LINE/L2 1853 -GGGGCGGTAGCTGGAGGGGGANGTGGGGT-CAAGGGAGAATTTTTGTTT 1806 chr3ptel1M 917715 TATCAGGATGGGGGAGACTTGGGTATATCTAT 917746 v v i i i i?vvi i i i i C L2#LINE/L2 1805 TTTAAAGATGGGAGAAATNACAGCATGTTTGT 1774 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.92 CpG sites = 171, Kimura (unadjusted) = 44.05 Transitions / transversions = 1.58 (171/108) Gap_init rate = 0.07 (68 / 911), avg. gap size = 1.66 (113 / 68) 15 4.77 0.00 0.00 chr3ptel1M 917747 917768 (82232) (CTAT)n#Simple_repeat 1 22 (0) m_b133s252i15 4946 chr3ptel1M 917747 CTATCTATCTATCTGTCTATCT 917768 i (CTAT)n#Simpl 1 CTATCTATCTATCTATCTATCT 22 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 1258 31.60 1.69 2.04 chr3ptel1M 918217 918807 (81193) C L1ME5_3end#LINE/L1 (297) 644 56 m_b133s551i1 4947 chr3ptel1M 918217 TCCTGTTTCT-GCTCATTTCACTCAGCATCA-GTTCCTGTCAG-TCTCTC 918263 i -i iv ii - -- v v - iv C L1ME5_3end#LI 644 TTCTGTTTCTTACTTTTTTCACTCAGCACTATGTT--TTTAAGATCCATC 597 chr3ptel1M 918264 CAGTCTTTTCTGTATTCAGCCTGCTGATCGTTTCTTACAAATA-ATAATA 918312 vvi vi v i v v iv iivi i i v viv i- i C L1ME5_3end#LI 596 CATGTTGCTATGTGTACATCTAGTCCGTTGCTTCTAACTGCTGCATAGTA 547 chr3ptel1M 918313 TTCCATAACATTCATATACCGCAATTTACCCAACCATTCTCCAATTGATG 918362 i iiii v vi i v i v i v v C L1ME5_3end#LI 546 CTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCAGTGATG 497 chr3ptel1M 918363 AGCATCCATTCATTTTCCAGTTTCTAGCCACCACAAAAAGGGCCACCACA 918412 ii i vvivvii ii i iv v iv ii v ii C L1ME5_3end#LI 496 GACACCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCTGCAATG 447 chr3ptel1M 918413 AACATTCTGGCACATACAGGTCCCTTTT----CCTTCTTTAGTATCTCTT 918458 i ---- i v i v---- viv v v i C L1ME5_3end#LI 446 AACATCCT----CGTACATGTCCCCTTATGGACCTGTGTGAGAATTTCTT 401 chr3ptel1M 918459 TGGGGTATAAGCCCAGTAGAAACACTGCTGGATTAAAGGGTAAGCACAGT 918508 i vi v viiv i i i v v ii vv C L1ME5_3end#LI 400 TGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATGCGTATA 351 chr3ptel1M 918509 TTGATAATTCTTTGGGCA--TAATTCCAGATTGCTCTCCAGAATGGTTGG 918556 i -- --- ivi -- v v i v C L1ME5_3end#LI 350 CT--TAATT---TGACTAAGTACTGCCAGATTGCTCTCCAGAATGGCTGC 306 chr3ptel1M 918557 ATGCATTCACAATTCCACCAACAATGCACCAGTGTCCCAGTTTTCCCACA 918606 ivvi ii v i i i iv v i vi ? i C L1ME5_3end#LI 305 ACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATNTCCCCACA 256 chr3ptel1M 918607 TCCCCTCCAACATTCATTCATTATCTTTTCCTGTCATCTTAGCCAATCTG 918656 i v i iiv- ivviii v v i v i i C L1ME5_3end#LI 255 TCCTCGCCAACACTTGG-CATTATCCAGCTTTCTAATTTTTGCCAGTCTA 207 chr3ptel1M 918657 ACAGGTGGGTGGTGGTACCTCAGAGTTGTCTTCATTTGCATTTCTCTGAT 918706 i vivi i i vv i v C L1ME5_3end#LI 206 ATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATTTCTCTGAT 157 chr3ptel1M 918707 CATTAATGACTTGGAGCATCTTTTCATGTGACTACAAATAGTTTCAATTT 918756 i i v v i i vi iiv iivv ivii C L1ME5_3end#LI 156 TACTAATGAGTTTGAGCATCTCTTCATATGCTTGTTAGCCTTTCGGGTTT 107 chr3ptel1M 918757 CTTCATCTGAAAATTATCTCTTCATATCCTTTGACCATTTATCAATTAGA 918806 i v v ii v v v v i i C L1ME5_3end#LI 106 CCTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGGG 57 chr3ptel1M 918807 G 918807 C L1ME5_3end#LI 56 G 56 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 40.82 CpG sites = 105, Kimura (unadjusted) = 42.35 Transitions / transversions = 1.35 (105/78) Gap_init rate = 0.03 (18 / 590), avg. gap size = 1.22 (22 / 18) 1001 33.47 1.60 3.07 chr3ptel1M 918306 918866 (81134) C L1MB8_3end#LINE/L1 (372) 553 1 m_b133s551i2 4947 chr3ptel1M 918306 AATAATATTCCATAACATTCATATACCGCAATTTACCCAACCATTCTCCA 918355 vii vv i v iii v vi C L1MB8_3end#LI 553 AATAATATTCCATTGTATGGATATACCACATTTTATTTATCCATTCATCA 504 chr3ptel1M 918356 ATTGATGAGCATCCATTCATTTTCCAGTTTCTAGCCACCACAAAAAGGGC 918405 i ii iiivvivv v i i i ii ii v iv C L1MB8_3end#LI 503 GTTGATGGACATTTGGGTTGTTTCCACTTTTTGGCTATTATGAATAATGC 454 chr3ptel1M 918406 CACCACAAACATTCTGGCACATACAGGTCCCTTTT-------CCTTCTTT 918448 ii i ii ----iii i --- ------- v viv C L1MB8_3end#LI 453 TGCTATGAACATTC----GTGTACAAGT---TTTTGTGTGGACATATGTT 411 chr3ptel1M 918449 AGTATCTCTTTGGGGTATAAGCCCAGTAGAAACACTGCTGGATTAAAGGG 918498 vvi i i v vi i v viiv i i i v v C L1MB8_3end#LI 410 TTCATTTCTCTTGGGTATATACCTAGGAGTGGAATTGCTGGGTCATATGG 361 chr3ptel1M 918499 TAAGCACAGTTTGATAATTCTTTGGGCATAATTCCAGATTGCTCTCCAGA 918548 vivi vv -- iii i v - v v i i i i C L1MB8_3end#LI 360 TAACTCTATGTT--TAACCTTTTGAGGA-ACTGCCAGACTGTTTTCCAAA 314 chr3ptel1M 918549 ATGGTTGGATGCATTCACAATTCCACCAACAATGCACCAGTGTCCCAGTT 918598 ii i v ivvv i v i i i i iv v i i C L1MB8_3end#LI 313 GCGGCTGCACCATTTTACATTCCCACCAGCAGTGTATGAGGGTTCCAATT 264 chr3ptel1M 918599 TTCCCACATCCCCTCCAACATTCATTCATTATCTTTTCCTGTCATCTTAG 918648 ii i v i ii - v iii v v iv C L1MB8_3end#LI 263 TCTCCACATCCTCGCCAACACTTGTT-ATTATCTGTCTTTTTGATTATAG 215 chr3ptel1M 918649 CCAATCTGACAGGTGGGTGGTGGTACCTCAGAGTTGTCTTCATTTGCATT 918698 vi iiii v vi i vv v i v C L1MB8_3end#LI 214 CCATCCTAGTGGGTGTGAAGTGGTATCTCATTGTGGTTTTGATTTGCATT 165 chr3ptel1M 918699 TCTCTGATCATTAATGACTTGGAGCATCTTTTCATGTGACTACAAATAGT 918748 i v i iv v vi iviiivi C L1MB8_3end#LI 164 TCCCTGATGACTAATGATGTTGAGCATCTTTTCATGTGCTTATTGGCCAT 115 chr3ptel1M 918749 TTCAATTTCTTCATCTGAAAATTATCTCTTCATATCCTTTGACCATTTAT 918798 vv v v iv i v i v v v v C L1MB8_3end#LI 114 TTGTATATCTTCTTTGGAGAAATGTCTATTCAGATCCTTTGCCCATTTTT 65 chr3ptel1M 918799 CAATTAGAGAA--TGGCTTGAACTACTATAAATTTGAGTCAATTCTCTCT 918846 ? i ivv -- v v--i i vi v vivv i i--- C L1MB8_3end#LI 64 NAATTGGGTTATTTGTCTTT--TTATTATTGAGTTGTAAGAGTTCTT--- 20 chr3ptel1M 918847 ATATATATTTTGGAAATGAG 918866 - i v ii C L1MB8_3end#LI 19 -TATATATTCTGGATACAAG 1 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 45.24 CpG sites = 105, Kimura (unadjusted) = 45.93 Transitions / transversions = 1.36 (105/77) Gap_init rate = 0.03 (19 / 560), avg. gap size = 1.37 (26 / 19) 318 34.31 0.71 2.17 chr3ptel1M 918713 918992 (81008) C L1M3_orf2#LINE/L1 (0) 3288 3013 m_b133s551i3 4947 chr3ptel1M 918713 TGACTTGGAGCATCTTTTCATGTGACTACAAATAGTTTCAATTTCTTCAT 918762 iv v i iv iiviiivi vv v v C L1M3_orf2#LIN 3288 TGATGTTGAGCATCTTTTCATATACCTGTTGGCCATTTGTATGTCTTCTT 3239 chr3ptel1M 918763 CTGAAAATTATCTCTTCATATCCTTTGACCATTTATCAATTAGAGAATGG 918812 iv i v i v vi v v ? ii ivv vv C L1M3_orf2#LIN 3238 TGGAGAAATGTCTATTCAGGTCCTTTGCCCATTTTTNAATCGGGTTATTT 3189 chr3ptel1M 918813 CTTGAACTACTATAAATTTGAGTCAATTCTCTCTATATATATTTTGGAAA 918862 v vvvi i vi v vi?v i --- - v C L1M3_orf2#LIN 3188 GTTTTTTTGCTATTGAGTTGTANGAGTTC---CT-TATATATTTTGGATA 3143 chr3ptel1M 918863 TGAGGCCTTTATCAGATCCTTTGGATGTAAAAATGTTTTCCCAGTTCATT 918912 v iv i viv v vv i v v i v i i v C L1M3_orf2#LIN 3142 TTAACCCCTTATCAGATATATGGTTTGCAAATATTTTCTCCCATTCCGTA 3093 chr3ptel1M 918913 GCTTCCCCTCTAATTTTGTCTCCATTAGTTTTGTT--TGTACAAACGCTG 918960 v v i i v i i -- iv iv iiv -- i i v v C L1M3_orf2#LIN 3092 GGTTGCCTTTTCACTCTG--TTGATTGTTTCCTTTGCTGTGCAGAAGCTT 3045 chr3ptel1M 918961 TTTAACTTAATATAATCAAAATTATCTATTTT 918992 ii i i i vv v i C L1M3_orf2#LIN 3044 TTTAGTTTGATGTAGTCCCACTTGTCTATTTT 3013 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 45.46 CpG sites = 44, Kimura (unadjusted) = 46.86 Transitions / transversions = 0.88 (44/50) Gap_init rate = 0.03 (7 / 279), avg. gap size = 1.14 (8 / 7) 15 30.86 0.00 0.00 chr3ptel1M 919150 919193 (80807) (AG)n#Simple_repeat 1 44 (0) m_b133s252i16 4948 chr3ptel1M 919150 AGAGAGGGAGAGATAGAAGGTAAGTGAGAGAGGGGGTGACAGAG 919193 i v ii vi v i i v v (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 44 Matrix = Unknown Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 235 31.60 4.00 5.05 chr3ptel1M 919978 920077 (79923) C MIRc#SINE/MIR (167) 101 3 m_b133s601i8 4949 chr3ptel1M 919978 TGTCCAGGGTCCTATAGCGGGGATGTGCCACAGGTATCAGGA----ACCC 920023 i i vi i vi v v v v ---i i ---- v C MIRc#SINE/MIR 101 TGCCCAAGGTCACACAGCTAGTAAGTGGCAGAG---CCGGGACTCGAACC 55 chr3ptel1M 920024 CGAATCCTCCTGGCTCCAAGGCTAGCCTTCTGTCCACACCATTGCACGGT 920073 iii i i v i ivi v vv iii -- C MIRc#SINE/MIR 54 CAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACAC--T 7 chr3ptel1M 920074 GCCT 920077 C MIRc#SINE/MIR 6 GCCT 3 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.59 CpG sites = 18, Kimura (unadjusted) = 42.47 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.06 (6 / 99), avg. gap size = 1.50 (9 / 6) 205 12.57 5.01 0.96 chr3ptel1M 920760 921158 (78842) (AG)n#Simple_repeat 1 415 (0) m_b133s252i17 4950 chr3ptel1M 920760 AGAGAAGGAGGGAAAGA-AGAGGGAGAG-GTAAGAGAGA-AAAGA-AGGG 920805 ii i i - i - vi - i - i (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr3ptel1M 920806 AGGGAGAAAGA-AAAGAAATAGAGA-AGA-AAAGA-AGAGATAGAG-GAA 920850 i i - i i v - - i - v - i (AG)n#Simple_ 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 100 chr3ptel1M 920851 GGAGATA-ATAGAGAAGGAGAGAGAGAGAGAGA-AGATAG-GATAGGGAC 920897 i v - v ii - v - v i v (AG)n#Simple_ 101 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 150 chr3ptel1M 920898 AGAGACAGAGCAGAGAGA-AAAGAGAGAGAGACAGAGAGAGAGA-AGAAA 920945 v - - i v - i (AG)n#Simple_ 151 AGAGAGAGAG-AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 199 chr3ptel1M 920946 GAAAGAATGAGAGAAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 920995 i iv i (AG)n#Simple_ 200 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 249 chr3ptel1M 920996 GAGAG-GACAGAGAGACGAGAGAGACAGAGAAGGACGAGA-AGAGAGAGA 921043 - v - v ii - - (AG)n#Simple_ 250 GAGAGAGAGAGAGAGA-GAGAGAGAGAGAGAGAGA-GAGAGAGAGAGAGA 297 chr3ptel1M 921044 GAGAGAGA-AGAGAGAGACAG-GAGACAGAGAGAGAGAGAGAGACAGAGA 921091 - v - v v (AG)n#Simple_ 298 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 347 chr3ptel1M 921092 GAGAG-GAGAGAGACGAGACAGAAGGAGAGAGACAGAGA-AGAGAGAGAG 921139 - - v ii v - (AG)n#Simple_ 348 GAGAGAGAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 396 chr3ptel1M 921140 AGAGAGAGAGAGAGAGAGA 921158 (AG)n#Simple_ 397 AGAGAGAGAGAGAGAGAGA 415 Matrix = Unknown Transitions / transversions = 1.50 (27/18) Gap_init rate = 0.06 (24 / 398), avg. gap size = 1.00 (24 / 24) 16 24.88 0.00 0.00 chr3ptel1M 921881 921918 (78082) (CC)n#Simple_repeat 1 38 (0) m_b133s252i18 4951 chr3ptel1M 921881 CCCCCCCCTTCCCAAGGCCCCCCCTTCCCCCCCCCCCC 921918 ii vvvv ii (CC)n#Simple_ 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 38 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 13 14.17 3.23 0.00 chr3ptel1M 922189 922219 (77781) (GCTGGG)n#Simple_repeat 1 32 (0) m_b133s252i19 4952 chr3ptel1M 922189 GCTGCAGGTGGGGGTGGGGC-GGGGCTGGGGC 922219 vi v v - (GCTGGG)n#Sim 1 GCTGGGGCTGGGGCTGGGGCTGGGGCTGGGGC 32 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.03 (1 / 30), avg. gap size = 1.00 (1 / 1) 16 16.05 4.55 2.22 chr3ptel1M 922922 922965 (77035) (AGC)n#Simple_repeat 1 45 (0) m_b133s252i20 4953 chr3ptel1M 922922 AGCCGCCGCAGCCGCAGCA-CAGCAGCCGCCAG-AGCCGCAGCTGC 922965 v v v - v - - v v (AGC)n#Simple 1 AGCAGCAGCAGCAGCAGCAGCAGCAGCAG-CAGCAGCAGCAGCAGC 45 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.07 (3 / 43), avg. gap size = 1.00 (3 / 3) 17 18.38 2.33 0.00 chr3ptel1M 922923 922965 (77035) (GCAGCC)n#Simple_repeat 1 44 (0) m_b133s252i21 4953 chr3ptel1M 922923 GCCGCCGCAGCCGCAG-CACAGCAGCCGCCAGAGCCGCAGCTGC 922965 v - i v v iv i (GCAGCC)n#Sim 1 GCAGCCGCAGCCGCAGCCGCAGCCGCAGCCGCAGCCGCAGCCGC 44 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.02 (1 / 42), avg. gap size = 1.00 (1 / 1) 208 32.65 1.02 3.12 chr3ptel1M 924852 924949 (75051) C L3#LINE/CR1 (107) 3992 3897 m_b133s601i9 4954 chr3ptel1M 924852 CCAGGCTCTGTTTGCACACCTGCAGAGACGGGGCCCTCATT-CCTAAGAC 924900 v i v v v vv i - v?viv C L3#LINE/CR1 3992 CCAGCCTCTGCTTGAACACCTCCAGTGACGGGGAGCTCACTACCTCNCGA 3943 chr3ptel1M 924901 CATATCCACCATTCCCCCTTCAAAAAATTTTAATTTTGAGTAAAGATTT 924949 vii v -- vii iii v ii i i v v - v i C L3#LINE/CR1 3942 GGCAGC--CCATTCCATTTTTGGACAGCTCTGATTGTTAG-AAAGTTCT 3897 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.17 CpG sites = 15, Kimura (unadjusted) = 44.01 Transitions / transversions = 0.94 (15/16) Gap_init rate = 0.04 (4 / 97), avg. gap size = 1.00 (4 / 4) 198 29.10 15.38 3.05 chr3ptel1M 926542 926658 (73342) L2d_3end#LINE/L2 382 512 (4) m_b134s601i1 4955 chr3ptel1M 926542 GTTTCCTCTGCCAGAGGAATAGGCCCTTGAGAGCGCTGAGGGGC------ 926585 i i vi i vvivv vi i ---- i ------ L2d_3end#LINE 382 GTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGC----AGGGACCATGTC 427 chr3ptel1M 926586 ---TCCTTTCTCCTCATCTCCCAC-GTGCCTCGC-CAGGCCTGGGCT--- 926627 --- v ? i i? i ii - i v - vv i v--- L2d_3end#LINE 428 TTATACTNTTTTNTCGTTCCCCACAGCGCCTAGCACAGTGCTGAGCACAT 477 chr3ptel1M 926628 ----GGCCCTTAGTAAATGCTTGTTGGCAGATTGA 926658 ---- v i i i iiv L2d_3end#LINE 478 AGTAGGCGCTCAATAAATACTTGTTGATTGATTGA 512 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.12 CpG sites = 20, Kimura (unadjusted) = 39.13 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.08 (9 / 116), avg. gap size = 2.44 (22 / 9) 34 2.16 6.38 0.00 chr3ptel1M 926711 926757 (73243) (GTTTT)n#Simple_repeat 1 50 (0) c_b134s251i0 4956 chr3ptel1M 926711 GTTTT-TTTT-TTTTGTTTTGTTTTTTTTTGTTTTGTTTTGTTTT-TTTT 926757 - - v - (GTTTT)n#Simp 1 GTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTT 50 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.07 (3 / 46), avg. gap size = 1.00 (3 / 3) 16 16.81 7.50 0.00 chr3ptel1M 930946 930985 (69015) (CT)n#Simple_repeat 1 43 (0) m_b134s252i0 4957 chr3ptel1M 930946 CTCTAACTCTTTGT-TCTCTCTCCCTCTC-CCCTCTCTC-CTC 930985 vv i v - i - i - (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 43 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.08 (3 / 39), avg. gap size = 1.00 (3 / 3) 519 23.85 6.92 0.00 chr3ptel1M 931325 931454 (68546) MIRb#SINE/MIR 124 262 (6) m_b134s601i2 4958 chr3ptel1M 931325 GCCTCAGTGCCCTCCTCTGTCAGACGGGAATAATG-----TCCTTCG-AG 931368 vi v v i i i i----- v i - MIRb#SINE/MIR 124 GCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTACCTCGCAG 173 chr3ptel1M 931369 GGCTGTCGTGAGGAAGCAGTGAGATAATCATTGTAAAGTTCTTC---CAG 931415 i i vvv i vvv iv v--- MIRb#SINE/MIR 174 GGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAG 223 chr3ptel1M 931416 CGCCTGGCACGTAGTAGACACTTAATAAATGCTTGTTCT 931454 i i ii i i v v i MIRb#SINE/MIR 224 TGCCTGGCACATAGTAAGCGCTCAATAAATGGTAGCTCT 262 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.96 CpG sites = 17, Kimura (unadjusted) = 29.10 Transitions / transversions = 1.21 (17/14) Gap_init rate = 0.02 (3 / 129), avg. gap size = 3.00 (9 / 3) 212 32.93 4.65 1.12 chr3ptel1M 932152 932237 (67763) L2a_3end#LINE/L2 413 501 (16) m_b134s601i3 4959 chr3ptel1M 932152 AGGGCAGGGACTGGCTGGCTGGTTTGT--GTTAGTGTGCCTC--GTGCTT 932197 -vi v v --ii iv ii i -- i i L2a_3end#LINE 413 AGGGCAGGGACT-TTTGTCTGTTTTGTTCACTGCTGTATCCCCAGCGCCT 461 chr3ptel1M 932198 ATTACAACGTCTGGAAAATATCAAGTGCTTAATGAACGTT 932237 vv ii i v v vi i i i i ii L2a_3end#LINE 462 AGAACAGTGCCTGGCACATAGTAGGCGCTCAATAAATATT 501 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.68 CpG sites = 19, Kimura (unadjusted) = 46.20 Transitions / transversions = 2.11 (19/9) Gap_init rate = 0.04 (3 / 85), avg. gap size = 1.67 (5 / 3) 37 34.77 2.60 0.00 chr3ptel1M 932327 932480 (67520) (TCCA)n#Simple_repeat 1 158 (0) m_b134s252i1 4960 chr3ptel1M 932327 TCCATCCATTCATCTATTTACCTACCTATGAAT-CATCTATTTATCCATC 932375 i i ii i i i i vv - i ii (TCCA)n#Simpl 1 TCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATC 50 chr3ptel1M 932376 TATTTACCTATCTACAAATCTCTCCATCCATTCA-CTGTCTACCCATCCA 932424 i ii i i i ivv iv i - ii i i (TCCA)n#Simpl 51 CATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCA 100 chr3ptel1M 932425 TTCATTCATCCATCCATTCATCTAT-CATCTGTTTATCTCT-TATCCATC 932472 i i i i - ii ii iv -i (TCCA)n#Simpl 101 TCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATC 150 chr3ptel1M 932473 CATCCATC 932480 (TCCA)n#Simpl 151 CATCCATC 158 Matrix = Unknown Transitions / transversions = 5.67 (34/6) Gap_init rate = 0.03 (4 / 153), avg. gap size = 1.00 (4 / 4) 193 24.49 2.04 0.00 chr3ptel1M 932753 932801 (67199) MIRb#SINE/MIR 205 254 (14) m_b134s601i4 4961 chr3ptel1M 932753 TGTGAAGTGATTC-CACAGTGCCGGGTACACAGTAGGAGATTAATAAGTG 932801 i i v v- v i i i v v i i MIRb#SINE/MIR 205 TGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAAATG 254 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.32 CpG sites = 7, Kimura (unadjusted) = 30.24 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.02 (1 / 48), avg. gap size = 1.00 (1 / 1) 189 27.27 0.00 0.00 chr3ptel1M 932764 932807 (67193) L2c_3end#LINE/L2 423 466 (12) m_b134s601i5 4962 chr3ptel1M 932764 TCCACAGTGCCGGGTACACAGTAGGAGATTAATAAGTGTGCATT 932807 v i v i i v v i i vii L2c_3end#LINE 423 TCCCCAGCGCCTGGCACATAGTAGGCGCTCAATAAATGTTTGTT 466 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.24 CpG sites = 7, Kimura (unadjusted) = 34.71 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 220 22.09 17.44 0.00 chr3ptel1M 932836 932921 (67079) L2d2_3end#LINE/L2 412 512 (43) m_b134s601i6 4963 chr3ptel1M 932836 TATTTGTGTCTT-CCTCCC--AC-AGATGGTAAGCTCACTG-GGGTGGGG 932880 i i -i -- - v vi - ii L2d2_3end#LIN 412 TGTTTATGTCTTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGG 461 chr3ptel1M 932881 GTTGTGCCTCAG------TTG-ATCTCC---AGGGCCCAGCACAGTGCTT 932920 iiii i i v------ - i --- v i i L2d2_3end#LIN 462 ACCATGTCTTATACTTCTTTGTATCCCCCACAGCGCCTAGCACAGTGCCT 511 chr3ptel1M 932921 T 932921 L2d2_3end#LIN 512 T 512 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.60 CpG sites = 15, Kimura (unadjusted) = 27.60 Transitions / transversions = 3.75 (15/4) Gap_init rate = 0.08 (7 / 85), avg. gap size = 2.14 (15 / 7) 24 7.89 0.00 4.76 chr3ptel1M 933959 934002 (65998) (GCGGG)n#Simple_repeat 1 42 (0) m_b134s252i2 4964 chr3ptel1M 933959 GCGAGGCCGGGAGGGGCGGGGCGGGGGCGGGGCCGGGGCGGGGC 934002 i v v - - (GCGGG)n#Simp 1 GCGGGGCGGGGCGGGGCGGGGC-GGGGCGGGG-CGGGGCGGGGC 42 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2) 22 11.52 4.08 2.00 chr3ptel1M 933967 934015 (65985) (GGCAGG)n#Simple_repeat 1 50 (0) m_b134s252i3 4964 chr3ptel1M 933967 GGGAGGGGC-GGGGCGGGGGC-GGGGCCGGGGCGGGGCACAGGGGCAGGG 934014 v - i - v i -i (GGCAGG)n#Sim 1 GGCAGGGGCAGGGGCAGGGGCAGGGGCAGGGGCAGGG-GCAGGGGCAGGG 49 chr3ptel1M 934015 G 934015 (GGCAGG)n#Sim 50 G 50 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.06 (3 / 48), avg. gap size = 1.00 (3 / 3) 240 25.75 12.63 1.90 chr3ptel1M 934033 934127 (65873) C L2a_3end#LINE/L2 (32) 485 381 m_b134s601i7 4965 chr3ptel1M 934033 CTACTGTGTGCCAGGCGCTGAGCTAAGTCCTGGGGATACA---------A 934073 i i vv i iv --------- C L2a_3end#LINE 485 CTACTATGTGCCAGGCACTGTTCTAGGCGCTGGGGATACAGCAGTGAACA 436 chr3ptel1M 934074 AAAGAGGCAAAGG--CCGGCCGGCTCAGGGGGTTTCCTCCCCAA-AGCGG 934120 v i i -- v -- v i i v vii i i-i v C L2a_3end#LINE 435 AAACAGACAAAAGTCCCTGCC--CTCATGGAGCTTACATTCTAGTGGGGG 388 chr3ptel1M 934121 GAGGCGG 934127 i i C L2a_3end#LINE 387 GAGACAG 381 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.92 CpG sites = 15, Kimura (unadjusted) = 32.56 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.05 (5 / 94), avg. gap size = 2.80 (14 / 5) 214 29.52 1.30 5.41 chr3ptel1M 934136 934289 (65711) C L2b_3end#LINE/L2 (196) 270 123 m_b134s601i8 4965 chr3ptel1M 934136 GGCTCTGGACCCGGCATTAAGGGGCAGTGGGAGGGGCTTCCTGTAGGAGG 934185 v iv v vii v -- - i v C L2b_3end#LINE 270 GGCGCCTGACCCGGCCTGGGGGGTCAG--GGAGGG-CTTCCCGGAGGAGG 224 chr3ptel1M 934186 GGGGATTTGGGGTGGGACTTAAGGAAAGCCCGGGAG-AGATCAGGAGCCG 934234 v iv i v i i i i i v vvii -v ii --- C L2b_3end#LINE 223 TGACATTTGAGCTGAGACCTGAAGGATGAGTAGGAGTTGGCCAGG---CG 177 chr3ptel1M 934235 GAGGGGAGGAGGGAGAGTGCTCCAGGCCTGGGGGATGAGCAGAGAC-AAG 934283 i i v - i i i i v- i vv ?ivi - C L2b_3end#LINE 176 AAGAGGTGG-GGAAGGGCGTTCCAGGCA-GAGGGAACAGCANGTGCAAAG 129 chr3ptel1M 934284 GCCATG 934289 v C L2b_3end#LINE 128 GCCCTG 123 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.34 CpG sites = 24, Kimura (unadjusted) = 38.60 Transitions / transversions = 1.26 (24/19) Gap_init rate = 0.07 (10 / 153), avg. gap size = 1.00 (10 / 10) 12 32.33 0.00 0.00 chr3ptel1M 934993 935042 (64958) (CATCTT)n#Simple_repeat 1 50 (0) m_b134s252i4 4966 chr3ptel1M 934993 CATCTTCTACTTCAACTTCTTCGTCTACTCCGTGTACATGGTCATCTTCA 935042 vv v v v vv i i v v vv (CATCTT)n#Sim 1 CATCTTCATCTTCATCTTCATCTTCATCTTCATCTTCATCTTCATCTTCA 50 Matrix = Unknown Transitions / transversions = 0.18 (2/11) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 16 16.80 0.00 0.00 chr3ptel1M 935085 935111 (64889) (G)n#Simple_repeat 1 27 (0) m_b134s252i5 4967 chr3ptel1M 935085 GGGGGCGGGGCGGGGCGGGGCGGGGGG 935111 v v v v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGG 27 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 23 17.11 9.84 4.69 chr3ptel1M 936435 936556 (63444) (CCCAGG)n#Simple_repeat 1 128 (0) m_b134s252i6 4968 chr3ptel1M 936435 CCCAGGCCCTGGCCCCACCCCCATGCCC---CCCAGACCC--CACCAGGC 936479 v - vv v --- i --vv (CCCAGG)n#Sim 1 CCCAGGCCCAGG-CCCAGGCCCAGGCCCAGGCCCAGGCCCAGGCCCAGGC 49 chr3ptel1M 936480 CCGGGCCCTCAGGCCC--CCCCAGACCCACGCCC---CTCAGG-ACAAG- 936522 i - - --v i v --- i -v i - (CCCAGG)n#Sim 50 CCAGG-CC-CAGGCCCAGGCCCAGGCCCAGGCCCAGGCCCAGGCCCAGGC 97 chr3ptel1M 936523 CCAGGCCCTGGCCCACGCCCCCAGGACCCCGGCC 936556 v - -v - v (CCCAGG)n#Sim 98 CCAGGCCCAGGCCCA-G-GCCCAGG-CCCAGGCC 128 Matrix = Unknown Transitions / transversions = 0.42 (5/12) Gap_init rate = 0.10 (12 / 121), avg. gap size = 1.50 (18 / 12) 16 27.06 1.19 6.25 chr3ptel1M 936771 936854 (63146) (GCAGGG)n#Simple_repeat 1 80 (0) m_b134s252i7 4969 chr3ptel1M 936771 GCAGGAGGCAGGGGCTACTGGCTGCGGGGCTGGCCCTGGGGCAAGGGGCC 936820 - - vv --v v vv v - v (GCAGGG)n#Sim 1 GCAGG-GGCAGGGGC-AGGGGC--AGGGGCAGGGGCAGGGGC-AGGGGCA 45 chr3ptel1M 936821 AGAG-TGGGGCGGGGGCTGGGGAAGGACCAGAGGC 936854 i i -v i v v iv i (GCAGGG)n#Sim 46 GGGGCAGGGGCAGGGGCAGGGGCAGGGGCAGGGGC 80 Matrix = Unknown Transitions / transversions = 0.42 (5/12) Gap_init rate = 0.07 (6 / 83), avg. gap size = 1.00 (6 / 6) 226 33.65 5.34 6.98 chr3ptel1M 937590 937720 (62280) C L2c_3end#LINE/L2 (2) 476 348 m_b134s601i9 4970 chr3ptel1M 937590 TCGGTCAGCCAAGAAGCATTTATTAGGCGCCCACGCTGTGCT-GGCCCCA 937638 iv vi v i ii i vv i- v ii C L2c_3end#LINE 476 TCATTCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTG 427 chr3ptel1M 937639 GGG--CCCGAGACAGACACAACAGAG---CTGCCTTTGAGG-GCTCTTAA 937682 --v vi iii i vi vi --- i ii - vi i C L2c_3end#LINE 426 GGGATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAG 377 chr3ptel1M 937683 TTAATTTTAATCAGTGGAGGGGGCAGTGAGGTGAGCGG 937720 ---------ii i i vv ? i i i C L2c_3end#LINE 376 T---------CTAGTGGAGGAGACAGACANGTAAACAG 348 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.57 CpG sites = 28, Kimura (unadjusted) = 48.28 Transitions / transversions = 2.15 (28/13) Gap_init rate = 0.10 (13 / 130), avg. gap size = 1.23 (16 / 13) 323 34.86 1.83 0.00 chr3ptel1M 937749 937857 (62143) MIR#SINE/MIR 77 187 (75) m_b134s601i10 4971 chr3ptel1M 937749 CCAGTTGTGTGGCCCTGGGTGACTCATGTCAGCTCCACTTGCCTCTGTTT 937798 i i i i ii v i iv v v iviv v MIR#SINE/MIR 77 CTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTT 126 chr3ptel1M 937799 TCCCCTCCGTGCAATGGGGACAACAGCAGCGCCTCCCCC--TGAGTTATT 937846 i i v i iv i i ii ii v i --v i i MIR#SINE/MIR 127 CCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTCATAGGGTTGTT 176 chr3ptel1M 937847 GTTGGGATCGA 937857 vi ii MIR#SINE/MIR 177 GTGAGGATTAA 187 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 50.45 CpG sites = 26, Kimura (unadjusted) = 50.45 Transitions / transversions = 2.17 (26/12) Gap_init rate = 0.01 (1 / 108), avg. gap size = 2.00 (2 / 1) 16 24.03 0.00 0.00 chr3ptel1M 940479 940513 (59487) (G)n#Simple_repeat 1 35 (0) m_b134s252i8 4972 chr3ptel1M 940479 GGGGTGGAGGGGGTGGAGGGGAGAAGGGGGGGGGG 940513 v i v i i ii (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 35 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 101 16.75 2.50 0.00 chr3ptel1M 940545 940744 (59256) (AGAG)n#Simple_repeat 1 205 (0) m_b134s252i10 4973 chr3ptel1M 940545 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGACAAAGAG-GAGAGACAG 940593 v i - v (AGAG)n#Simpl 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr3ptel1M 940594 AGACAAAGAG-GAGAAAGAGAGACAGAGACAGACACAGAGAGAGACAGAG 940642 v i - i v v v v v (AGAG)n#Simpl 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 100 chr3ptel1M 940643 AAAGAGAAAGACACAGAGAGAG-GAGAGAGACAGACAGACAGAG-GAAAG 940690 i i v v - v v v - i (AGAG)n#Simpl 101 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 150 chr3ptel1M 940691 AGACAGAAAGACA-AGAAACAGATAGAGAGCGACAGAGAGACAGAGACAG 940739 v i v - i v v v v v v (AGAG)n#Simpl 151 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 200 chr3ptel1M 940740 ACAGA 940744 v (AGAG)n#Simpl 201 AGAGA 205 Matrix = Unknown Transitions / transversions = 0.36 (8/22) Gap_init rate = 0.03 (5 / 199), avg. gap size = 1.00 (5 / 5) 15 22.37 0.00 0.00 chr3ptel1M 940722 940758 (59242) (ACAC)n#Simple_repeat 1 37 (0) m_b134s252i12 4974 chr3ptel1M 940722 ACAGAGAGACAGAGACAGACAGACACACACACACACA 940758 v v v v v v v (ACAC)n#Simpl 1 ACACACACACACACACACACACACACACACACACACA 37 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 642 34.18 2.33 4.50 chr3ptel1M 941257 941642 (58358) C L1ME2z_3end#LINE/L1 (681) 510 133 m_b134s551i0 4975 chr3ptel1M 941257 TTCTCTGGTGGACGGGCACCTGCTGCGTTTCCAGGTCCTGGCCACTACAA 941306 iv v i i vvvi v ii i i ii C L1ME2z_3end#L 510 TTCTCCTGTTGATGGACACCTGGGCTGTTTCCAGTTTTTGGCTATTATGA 461 chr3ptel1M 941307 A-AGGGCTGCCGCAAACGCTCCTGCACATGTGGGCCCCTTTCCG------ 941349 - ii iiii ii i i v ---- ii vi ------ C L1ME2z_3end#L 460 ATAAAGCTGCTATGAACATTCTTGTACAAGT----CTTTTTGTGGACATA 415 chr3ptel1M 941350 TTTTTTAATCTCTTTTAATCAATCTACTTGATCTCAAGTATTGACCCTGC 941399 v v i i iivi -------- vi v v v ivvi C L1ME2z_3end#L 414 TGTTTTCATTTCTCTTGGGTAA--------ATACCTAGGAGTGGAATTGC 373 chr3ptel1M 941400 TGGATCAAAGATT--GTGCCCAACGTTATAACCCTTTGGGCATAATTCCA 941447 i v iv -- i--- i - iiii v ii v - v v C L1ME2z_3end#L 372 TGGGTCATAGGGTAGGTGT---ATGTT-TAGTTTTATAAGAA-ACTGCCA 328 chr3ptel1M 941448 GATCACTCTCCAGAATGGTTGGATTCGTTCACAACTCCACCCACAATGCA 941497 i vi i i i v iivv i vii v i C L1ME2z_3end#L 327 GACCTTTTTCCAAAGTGGTTGTACCATTTTACACTCCCACCAACAATGTA 278 chr3ptel1M 941498 TCAGTGTCCCGGTTTTCCCACATCCCCTCCAACATTCCACATTATCCTTT 941547 v v i vii i v iviii i vv i C L1ME2z_3end#L 277 TGAGAGTTCCGGTTGCTCCACATCCTCGCCAACATTTGGTGTTGTCAGTC 228 chr3ptel1M 941548 CCTGCCATCTTAGCCAAGGGGAGAGGTGTGAGGTGGAGCCTCAGAGTGGT 941597 ii viv i vvvv ivi vi vii vv C L1ME2z_3end#L 227 TTTTTAATTTTAGCCATTCTGGTGGGTGTGTAGTGGTATCTCATTGTGGT 178 chr3ptel1M 941598 CTTAATTTGCATTTCTCTGATCAATAGTGATTTAGAGCATTTTTT 941642 i i v v i v v i C L1ME2z_3end#L 177 TTTAATTTGCATTTCCCTGATGACTAATGATGTTGAGCACTTTTT 133 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 47.43 CpG sites = 75, Kimura (unadjusted) = 47.43 Transitions / transversions = 1.47 (75/51) Gap_init rate = 0.05 (20 / 385), avg. gap size = 1.30 (26 / 20) 481 36.20 2.93 4.59 chr3ptel1M 941267 941709 (58291) C L1PA8_3end#LINE/L1 (419) 500 65 m_b134s551i1 4975 chr3ptel1M 941267 GACGGGCACCTGCTGCGTTTCCAGGTCCTGGCCACTACAAA-AGGGCTGC 941315 i ii vvvi v i i v i i ii - v C L1PA8_3end#LI 500 GATGGGCATTTGGGTTGGTTCCAAGTCTTTGCTATTGTAAATAGTGCTGC 451 chr3ptel1M 941316 CGCAAACGCTCCTGCACATGTGGGCCCCTTTCCGTTTTTTAATCTCTTTT 941365 vii iiv v ii ----i --i vv vv vvi v C L1PA8_3end#LI 450 AATAAACATACGTGTGCATGTG----TCTTT--ATAGTAGAATGATTTAT 407 chr3ptel1M 941366 AATCAATCTACTTGATCTCAAGTATTGACCCTGCTGGATCAAAGATTGTG 941415 vv iviv vv vi v v ivvi i viv i v C L1PA8_3end#LI 406 AATCCTTTGGGTATATACCCAGTAATGGGATTGCTGGGTCAAATGGTATT 357 chr3ptel1M 941416 CCCAACGTTATAACCCTTTGGGCATAATT-CCAGATCACTCTCCAGAATG 941464 i ii-- v ivi i i v -- i- v iiiiii v C L1PA8_3end#LI 356 TCTG--GTTCTAGATCCTTGAGGA--ATCGCCACACTGTCTTCCACAATG 311 chr3ptel1M 941465 GTTGGATTCGTTCACAACTCCACCCACAATGCATCAGTGTCCCGGTTTTC 941514 i i vi i vii v i i vv i i vi ii C L1PA8_3end#LI 310 GTTGAACTAATTTACACTCCCACCAACAGTGTAAAAGCGTTCCTATTTCT 261 chr3ptel1M 941515 CCACATCCCCTCCAACATTCCACATTATCCTTTCCTGCCATCTTA----- 941559 i v i i------ i iv v v i ----- C L1PA8_3end#LI 260 CCACATCCTCGCCAGCATC------TGTTGTTTCCTGACTTTTTAATGAT 217 chr3ptel1M 941560 -GCCAAGGGGAGAGGTGTGAGGTGGAGCCTCAGAGTGGTCTTAATTTGCA 941608 - vvvvi vv i i vii vv i i C L1PA8_3end#LI 216 CGCCATTCTAACTGGCGTGAGATGGTATCTCATTGTGGTTTTGATTTGCA 167 chr3ptel1M 941609 TTTCTCTGATCAATAGTGATTTAGAGCATTTTTTTTTTCATAAAACTAGA 941658 i v vi vvv ---- vivi ivv C L1PA8_3end#LI 166 TTTCTCTAATGACCAGTGATGATGAGC----TTTTTTTCATATGTTTGTT 121 chr3ptel1M 941659 AATGGTTTAATT-TTTTCATCTGGAAAG----TGTTCATACCCTCCGACC 941703 iiiv iv v - i v i ii ---- i i v C L1PA8_3end#LI 120 GGCCGCATAAATGTCTTCTTTTGAGAAGTGTCTGTTCATATCCTTCGCCC 71 chr3ptel1M 941704 GCCTCT 941709 i i i C L1PA8_3end#LI 70 ACTTTT 65 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 49.61 CpG sites = 85, Kimura (unadjusted) = 51.05 Transitions / transversions = 1.25 (85/68) Gap_init rate = 0.06 (26 / 442), avg. gap size = 1.27 (33 / 26) 608 35.72 1.29 2.35 chr3ptel1M 941379 941765 (58235) C L1ME3G_3end#LINE/L1 (535) 389 7 m_b134s551i2 4975 chr3ptel1M 941379 GATCTCAAGTATTGACCCTGCTGGATCAAAGATTGTGCCCAACGTTATAA 941428 ?i ? v v ivvi i iv i v --- v C L1ME3G_3end#L 389 GATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGCA---TTTTAA 343 chr3ptel1M 941429 CCCTTTGGGCATAATTCCAGATCACTCTCCAGAATGGTTGGATTCGTTCA 941478 vii viviv v v i ii i i ? i v iivi i C L1ME3G_3end#L 342 ATTTTAATAGATACTGCCAAATTGCCCTCCAAAANGGCTGTACCAATTTA 293 chr3ptel1M 941479 CAACTCCACCCACAATGCATCAGTGTCCCGGTTTTCCCACATCCCCTCCA 941528 vii vi i i v v v v i i i v C L1ME3G_3end#L 292 CACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCACACCCTCGCCA 243 chr3ptel1M 941529 ACATTCCACATTATCCTTTCCTGCCATCTTAGCCAAGGGGAGAGGTGTGA 941578 i ?v i vv?iii vvv i v vvv vi vi C L1ME3G_3end#L 242 ACACTNGATATTATCAANCTTTTAAATTTTTGCCAATCTGATGGGTGAAA 193 chr3ptel1M 941579 GGTGGAGCCTCAGAGTGGTCTTAATTTGCATTTCTCTGATCAATAGTGAT 941628 ii vii vv v i i i v v C L1ME3G_3end#L 192 AATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGATTACTAGTGAG 143 chr3ptel1M 941629 TTAGAGCATTTTTTTTTTCATAAAACTAGAAATGGTTTA-ATTTTTTCAT 941677 v v ---- i vivi vviiivi i- ii v C L1ME3G_3end#L 142 GTTGAGCA----TCTTTTCATATGTTTATTGGCCATTTGTATTTCCTCTT 97 chr3ptel1M 941678 CTGGAAAG----TGTTCATACCCTCCGACCGCCTCTCAGTTGAGGAATGG 941723 vi v---- i ii v iii i vi i v-- v C L1ME3G_3end#L 96 CTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGGGT--TGT 49 chr3ptel1M 941724 CTCATACTCATAGATATGAGTCTGTTTTCTGTCTGTTTTAGA 941765 iv v i v v vivvv i i i v i i i C L1ME3G_3end#L 48 CTTTTTCTTATTGATTTGTAGGAGTTCTTTATATATTCTGGA 7 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 50.78 CpG sites = 72, Kimura (unadjusted) = 50.78 Transitions / transversions = 1.14 (72/63) Gap_init rate = 0.03 (11 / 386), avg. gap size = 1.27 (14 / 11) 624 35.22 1.55 1.24 chr3ptel1M 941397 941718 (58282) C L1ME4a_3end#LINE/L1 (493) 378 56 m_b134s551i3 4975 chr3ptel1M 941397 TGCTGGATCAAAGATTGTGCCCAACGTTATAACCCTTTGGGCATAATTCC 941446 i i iv i ?v viv vii ii vivi v v C L1ME4a_3end#L 378 TACTGGGTCAAAGGGTATGNACATTTTTAAGGCTTTTGATACATATTGCC 329 chr3ptel1M 941447 AGATCACTCTCCAGAATGGTTGGATTCGTTCACAACTCCACCCACAATGC 941496 i ii i v v iivi i vii vi i i C L1ME4a_3end#L 328 AAATTGCCCTCCAGAAAGGTTGTACCAATTTACACTCCCACCAGCAGTGT 279 chr3ptel1M 941497 ATCAGTGTCCCGGTTTTCCCACATCCCCTCCAACATTCCACATTATCCTT 941546 v v v v i? i i v i vvii vv C L1ME4a_3end#L 278 ATGAGAGTGCCCGTTTCNCCACACCCTCGCCAACACTGGGTATTATCAAT 229 chr3ptel1M 941547 TCCTGCCATCTTAGCCAAGGGGAGAGGTGTGAGGTGGAGCCTCAGAGTGG 941596 iii vvv v vvv v vi ii vii vv v C L1ME4a_3end#L 228 CTTTTAAATCTTTGCCAATTTGATAGGTGAAAAATGGTATCTCATTGTTG 179 chr3ptel1M 941597 TCTTAATTTGCATTTCTCTGATCAATAGTGATTTAGAGCATTTTTTTTTT 941646 i i i v vv v i ---- ? C L1ME4a_3end#L 178 TTTTAATTTGCATTTCTTTGATTACTAGTGAGGTTGAACA----TNTTTT 133 chr3ptel1M 941647 CATAAAACTAGAAATGGTTTA-ATTTTTTCATCTGGAAAG----TGTTCA 941691 vivi vviiivi i- i v i vi v---- C L1ME4a_3end#L 132 CATATGTTTATTGGCCATTTGTATTTCTTCTTTTGTGAATTGTCTGTTCA 83 chr3ptel1M 941692 TACCCTCCGACCGCCTCTCAGTTGAGG 941718 ii ii v iii i vi i C L1ME4a_3end#L 82 TGTCCTTTGCCCATTTTTCTATTGGGG 56 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 49.74 CpG sites = 62, Kimura (unadjusted) = 49.74 Transitions / transversions = 1.24 (62/50) Gap_init rate = 0.02 (6 / 321), avg. gap size = 1.50 (9 / 6) 658 31.71 2.55 2.18 chr3ptel1M 941445 941718 (58282) C L1ME5_3end#LINE/L1 (611) 330 56 m_b134s551i4 4975 chr3ptel1M 941445 CCAGATCACTCTCCAGAATGGTTGGATTCGTTCACAACTCCACCCACAAT 941494 ii i v iiv ii vii vi i C L1ME5_3end#LI 330 CCAGATTGCTCTCCAGAATGGCTGCACCAGTCTACACTCCCACCAGCAGT 281 chr3ptel1M 941495 GCATCAGTGTCCCGGTTTTCCCACATCCCCTCCAACATTCCACATTATCC 941544 v v i vi ? i i v i ivi C L1ME5_3end#LI 280 GCATGAGGGTTCCTATNTCCCCACATCCTCGCCAACACTTGGCATTATCC 231 chr3ptel1M 941545 --TTTCCTGCCATCTTAGCCAAGGGGAGAGGTGTGAGGTGGAGCCTCAGA 941592 --i i i-- i v ivvvi v i i ivii vv C L1ME5_3end#LI 230 AGCTTTCTA--ATTTTTGCCAGTCTAATAGGTGTAAAGTGATATCTCATT 183 chr3ptel1M 941593 GTGGTCTTAATTTGCATTTCTCTGATCAATAGTGATTTAGAGCATTTTTT 941642 v i i v i v v ---- i C L1ME5_3end#LI 182 GTTGTTTTAATTTGCATTTCTCTGATTACTAATGAGTTTGAGCA----TC 137 chr3ptel1M 941643 TTTTCATAAAACTAGAAATGGTTT-AATTTTTTCATCTGGAAAG----TG 941687 i vivi ivv iivv i-ii ii v v v---- C L1ME5_3end#LI 136 TCTTCATATGCTTGTTAGCCTTTCGGGTTTCCTCTTCTGTAAATTGCCTG 87 chr3ptel1M 941688 TTCATACCCTCCGACCGCCTCTCAGTTGAGG 941718 i ii v iii i vi i C L1ME5_3end#LI 86 TTCATATCCTTTGCCCATTTTTCTATTGGGG 56 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 42.53 CpG sites = 53, Kimura (unadjusted) = 43.22 Transitions / transversions = 1.66 (53/32) Gap_init rate = 0.03 (9 / 273), avg. gap size = 1.44 (13 / 9) 219 16.67 0.00 14.29 chr3ptel1M 942728 942783 (57217) C L2b_3end#LINE/L2 (6) 460 412 m_b134s601i11 4976 chr3ptel1M 942728 TCAATCAATACCCATCTACCGCTTTATAAGCACCTACTGTGTGCCAGGCA 942777 v i vvi i ------- i i ? C L2b_3end#LINE 460 TCATTCAACAAATATTTAC-------TGAGCGCCTACTGTGTGCCAGGCN 418 chr3ptel1M 942778 CTGTGC 942783 C L2b_3end#LINE 417 CTGTGC 412 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 16.62 CpG sites = 5, Kimura (unadjusted) = 19.13 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.13 (7 / 55), avg. gap size = 1.00 (7 / 7) 35 0.00 0.00 0.00 chr3ptel1M 943747 943779 (56221) (G)n#Simple_repeat 1 33 (0) c_b134s251i1 4977 chr3ptel1M 943747 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 943779 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 33 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 399 29.21 5.31 7.39 chr3ptel1M 945695 945901 (54099) C MIR1_Amn#SINE/MIR (1) 229 27 m_b134s601i12 4978 chr3ptel1M 945695 TAACAATGGTTGATTTTTATTTCACACTTGTCCTGTGTCAGGCACTGAGC 945744 i ivi iii i v vi v v vv viiv v vi C MIR1_Amn#SINE 229 TAATAATACCTAGCTCTTATGTAGCACTTTTCATCAGTAGATCTCAAAGC 180 chr3ptel1M 945745 CCTTTACAA------TTACTATCTGATTTGATCCTCACAGCAATCCATTT 945788 v ------ i v -- -- ---------- C MIR1_Amn#SINE 179 ACTTTACAAAGGAGGTCAGTATC--ATT--ATCC----------CCATTT 144 chr3ptel1M 945789 CACAGATGGGGAAACTGAGGCAGACAGAAGGCACATGATTTTCCCAGGAT 945838 i i ?v v i v? vi i v i i C MIR1_Amn#SINE 143 TACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGCCCAAGGT 94 chr3ptel1M 945839 CCCACAGCTAG---GT-TTGAAGCC-ACATTTGAACTCAGGCCCTTCTGA 945883 v ? ?i --- -viii -iv ? ? i -i i i C MIR1_Amn#SINE 93 CACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAACCCAGG-TCTCCCGA 45 chr3ptel1M 945884 CTCCTGGACCAGGACACT 945901 v ii v vi v C MIR1_Amn#SINE 44 GTCCCAGTCCAGTGCTCT 27 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.46 CpG sites = 31, Kimura (unadjusted) = 39.36 Transitions / transversions = 1.24 (31/25) Gap_init rate = 0.09 (19 / 206), avg. gap size = 1.37 (26 / 19) 531 25.28 19.10 0.00 chr3ptel1M 945710 945887 (54113) C MIRb#SINE/MIR (16) 252 41 m_b134s601i13 4978 chr3ptel1M 945710 TTTATTTCACACTTGTCCTGTGTCAGGCACTG-----AGCCCTTTACAAT 945754 vvi i iiiv i ----- v vv C MIRb#SINE/MIR 252 TTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACATG 203 chr3ptel1M 945755 TACTATCTGATTTGATCCTCACAGCAATCC-------------------- 945784 i i v i i i -------------------- C MIRb#SINE/MIR 202 CATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATTAT 153 chr3ptel1M 945785 ----ATTTCACAGATGGGGAAACTGAGGCAGACAGAAGGCACATGATTTT 945830 ---- i i vv v i vi vi i i v C MIRb#SINE/MIR 152 CCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTG 103 chr3ptel1M 945831 CCCAGGATCCCACAGCTAG---GT-TTGAAGCC-ACATTTGAACTCAGGC 945875 i i v --- -viii -iv i i i C MIRb#SINE/MIR 102 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGT 53 chr3ptel1M 945876 CCTTCTGACTCC 945887 iv C MIRb#SINE/MIR 52 CTGTCTGACTCC 41 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.00 CpG sites = 28, Kimura (unadjusted) = 31.69 Transitions / transversions = 1.65 (28/17) Gap_init rate = 0.03 (6 / 177), avg. gap size = 5.67 (34 / 6) 429 27.73 4.20 0.00 chr3ptel1M 945783 945901 (54099) C MIRc#SINE/MIR (121) 147 24 m_b134s601i14 4978 chr3ptel1M 945783 CCATTTCACAGATGGGGAAACTGAGGCAGACAGAAGGCACATGATTTTCC 945832 i i vv v i vi vi i v C MIRc#SINE/MIR 147 CCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCC 98 chr3ptel1M 945833 CAGGATCCCACAGCTAG---GT-TTGAAGCC-ACATTTGAACTCAGGCCC 945877 i i v --- -viii -iv i i i i i C MIRc#SINE/MIR 97 CAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCT 48 chr3ptel1M 945878 TTCTGACTCCTGGACCAGGACACT 945901 i vi v vi v C MIRc#SINE/MIR 47 TCCTGACTCCAAGTCCAGTGCTCT 24 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.29 CpG sites = 20, Kimura (unadjusted) = 35.64 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.03 (3 / 118), avg. gap size = 1.67 (5 / 3) 13 19.48 0.00 2.78 chr3ptel1M 946101 946137 (53863) (CCCCCCT)n#Simple_repeat 1 36 (0) m_b134s252i13 4979 chr3ptel1M 946101 CCCCCTTCCCTCTGTGCCCCCTCCCCTCTCCACCCTC 946137 i - iv v i v (CCCCCCT)n#Si 1 CCCCCCTCCC-CCCTCCCCCCTCCCCCCTCCCCCCTC 36 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 244 25.71 7.14 0.00 chr3ptel1M 946870 946939 (53061) C MIRc#SINE/MIR (98) 170 96 m_b134s601i15 4980 chr3ptel1M 946870 AGACTGAGCAGGGACCACA---CCCATTTTACAGATGAGAACACCAAGGC 946916 i v i v ii iv--- i v ii C MIRc#SINE/MIR 170 AGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGC 121 chr3ptel1M 946917 TCCCAAATGC--AGTGATTTGCCCA 946939 vv i v i-- i C MIRc#SINE/MIR 120 TCAGAGAGGTTAAGTGACTTGCCCA 96 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.32 CpG sites = 11, Kimura (unadjusted) = 32.32 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.03 (2 / 69), avg. gap size = 2.50 (5 / 2) 32 2.56 0.00 4.76 chr3ptel1M 947194 947237 (52763) (CAGAGCC)n#Simple_repeat 1 42 (0) c_b134s251i2 4981 chr3ptel1M 947194 CAGAGCCCAGAGCCCAGGAGCCCGGAGCCCAGAGCCCAGGAGCC 947237 - i - (CAGAGCC)n#Si 1 CAGAGCCCAGAGCCCA-GAGCCCAGAGCCCAGAGCCCA-GAGCC 42 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2) 32 3.23 0.00 0.00 chr3ptel1M 948508 948539 (51461) (CA)n#Simple_repeat 1 32 (0) c_b134s251i3 4982 chr3ptel1M 948508 CACACACACACACGCACACACACACACACACA 948539 i (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACA 32 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 193 34.18 5.56 4.27 chr3ptel1M 948541 948702 (51298) L2#LINE/L2 2847 3010 (72) m_b134s601i16 4983 chr3ptel1M 948541 CTTCAATGACCTCCTTTCTCCTCCAGGAGCAAATACAAAACCTGTG---T 948587 i i i iv vii iivv vv ii iv i--- L2#LINE/L2 2847 CTCCAATGGCTTCCCATCTCACTCAGAGTAAAAGCCAAAGTCCTTACAAT 2896 chr3ptel1M 948588 GGCATTCAAAGCCCGTCATCATCTG--CCCCTGCTACACTTC---CTTCC 948632 v v i vv v -- i i vii --- i v L2#LINE/L2 2897 GGCCTACAAGGCCCTACATGATCTGGTCCCCCGTTACCTCTCTGACCTCA 2946 chr3ptel1M 948633 T-TCTGACCCCTGACCCCCCAACACAGAATCTTTGATCTAGTAAACACTG 948681 - iv v vv ivi v ---- ii v i iv - L2#LINE/L2 2947 TCTCCTACCACTCTCCCCCTCGCTCA----CTCCGCTCCAGCCA-CACTG 2991 chr3ptel1M 948682 GCTCCCCTGAGCTGATCATTG 948702 ii i -- v v i L2#LINE/L2 2992 GCCTCCTT--GCTGTTCCTCG 3010 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.21 CpG sites = 29, Kimura (unadjusted) = 46.91 Transitions / transversions = 1.21 (29/24) Gap_init rate = 0.07 (11 / 161), avg. gap size = 1.45 (16 / 11) 183 26.09 5.48 5.48 chr3ptel1M 948689 948761 (51239) MIR#SINE/MIR 189 261 (1) m_b134s601i17 4984 chr3ptel1M 948689 TGAGCTGATCATTGCAGGGCTGTTAGCAAGAGTGCCGGGCACATGGTGCT 948738 i i vvv i ii vv - v v i --- MIR#SINE/MIR 189 TGAGTTAATACATGTAAAGCGCTTAG-AACAGTGCCTGGCACATAG---T 234 chr3ptel1M 948739 AAGTGC----TGGATGTTAACTGTTAT 948761 i ---- ii i i MIR#SINE/MIR 235 AAGCGCTCAATAAATGTTAGCTATTAT 261 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.73 CpG sites = 11, Kimura (unadjusted) = 32.93 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.07 (5 / 72), avg. gap size = 1.60 (8 / 5) 215 32.77 15.87 0.69 chr3ptel1M 948865 948990 (51010) L2b_3end#LINE/L2 319 463 (3) m_b134s601i18 4983 chr3ptel1M 948865 TTTATTTGTATGTGGCTCCTCCCTATTGGACTTTGGGCTCCTCC--GGCA 948912 i i? ii vvv ii i i i v i viv-- L2b_3end#LINE 319 TCTGNTTACATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCA 368 chr3ptel1M 948913 GGGAC------TGCCTT--------TTGAACCCCCAGCCTTTAGCATAGT 948948 ------ i --------i v i vii i ? L2b_3end#LINE 369 GGGACCGNGTCTGTCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGN 418 chr3ptel1M 948949 CCCTGAGATCATGAGAGGCACCT----GATGTTTACTGACTGACTG 948990 v iv - iiiv i ii----i i ii v v L2b_3end#LINE 419 GCCTGGCA-CACAGTAGGCGCTCAGTAAATATTTGTTGAATGAATG 463 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.46 CpG sites = 28, Kimura (unadjusted) = 47.10 Transitions / transversions = 2.15 (28/13) Gap_init rate = 0.04 (5 / 125), avg. gap size = 4.20 (21 / 5) 321 21.30 0.45 0.00 chr3ptel1M 949138 949806 (50194) (TGTGTG)n#Simple_repeat 1 672 (0) m_b134s252i14 4985 chr3ptel1M 949138 TGTATGTGTGTGTGAATGTGAGTGTGTATATGTGTGTGTGTCTGTGTGAT 949187 i vi v i i v vv (TGTGTG)n#Sim 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr3ptel1M 949188 TGTGAGACTGTGTGTGTGAGTCTGTGTGTGTGTCTGAATGTGAGCATATG 949237 v vv v v v vi v ii i (TGTGTG)n#Sim 51 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 100 chr3ptel1M 949238 AGTGTGTGTGCGTGTGTGAGTGGGAGTGTGTGTGTGTGTGTATGTGTGTC 949287 v i v v v i v (TGTGTG)n#Sim 101 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 150 chr3ptel1M 949288 TGTGTGATTGTGAGTCTGAGTGTGTGTCTGTGTGAGTGTGTAAGTGTGAG 949337 vv v v v v v iv v (TGTGTG)n#Sim 151 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 200 chr3ptel1M 949338 TGTGTGTGAGAGAATGTATATGTGAGTGTGTGTGAGTAAACATGTGTGTA 949387 v v vi i i v v iviii i (TGTGTG)n#Sim 201 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 250 chr3ptel1M 949388 TGAGTCTGTGAGTGTGTGTGTGTCTGTGAGTGTCT-TGTGTGAGTGTCTG 949436 v v v v v v - v v (TGTGTG)n#Sim 251 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 300 chr3ptel1M 949437 TGAGTGAGCGTGTGAGTGTGTGTGTGTCTATGAGTGTATGTGAGTGTGTG 949486 v v i v v i v i v (TGTGTG)n#Sim 301 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 350 chr3ptel1M 949487 TGTATGTCTATGAGTGTGTCTGTGAGTGTGTGTGTCTGAGTGTGTCTATG 949536 i v i v v v v v v i (TGTGTG)n#Sim 351 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 400 chr3ptel1M 949537 AGTGTGTGAGTGTGAGTGTGTCTGTGAGT-TGTGAGCATGTGAGTGTGTG 949585 v v v v v - v ii v (TGTGTG)n#Sim 401 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 450 chr3ptel1M 949586 TATGAGTGTGAGTATGTGAGTGTGTGTGAGTGTGAGCATGTGTGTGAGTG 949635 i v v i v v v ii v (TGTGTG)n#Sim 451 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 500 chr3ptel1M 949636 TTTGTGAGTGTGTGTGTCTGTGAGTGTCT-TGTGTGTGTCTGTGAGTGTG 949684 v v v v v - v v (TGTGTG)n#Sim 501 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 550 chr3ptel1M 949685 AGTGTGTGTGTGTCTGAGTGTGTCTGTGAGTGTGAGCATGTGAGTGTGTG 949734 v v v v v v ii v (TGTGTG)n#Sim 551 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 600 chr3ptel1M 949735 AGTGTGTGTGTGTGTGTAAGTGTGAGTGTGTCTGTGAGTGTGAGTATGTG 949784 v iv v v v v i (TGTGTG)n#Sim 601 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 650 chr3ptel1M 949785 AGTGTGTGTGTGAGTGTGTGTG 949806 v v (TGTGTG)n#Sim 651 TGTGTGTGTGTGTGTGTGTGTG 672 Matrix = Unknown Transitions / transversions = 0.39 (35/89) Gap_init rate = 0.00 (3 / 668), avg. gap size = 1.00 (3 / 3) 14 22.11 2.38 0.00 chr3ptel1M 952497 952538 (47462) (GGGGGCA)n#Simple_repeat 1 43 (0) m_b134s252i15 4986 chr3ptel1M 952497 GGGGGAAGGAGG-ACGGGGCAGGGGGCGGGAGGGTGGGAGCAG 952538 v i - v i i vv i (GGGGGCA)n#Si 1 GGGGGCAGGGGGCAGGGGGCAGGGGGCAGGGGGCAGGGGGCAG 43 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.02 (1 / 41), avg. gap size = 1.00 (1 / 1) 497 22.03 4.13 2.44 chr3ptel1M 952672 952792 (47208) MIRb#SINE/MIR 124 246 (22) m_b134s601i19 4987 chr3ptel1M 952672 GCCTCAGTTTCCCTATCTGTAAAACAAGGATGGCTATAGCCCCTCCCTCT 952721 ii iii i--- iiv v v MIRb#SINE/MIR 124 GCCTCAGTTTCCTCATCTGTAAAATGGGGATA---ATAATACCTACCTCG 170 chr3ptel1M 952722 CAGGGCTATGGTGAGGATCAAAGGAGAAAAAG--TGT--AGCCCTCGGCA 952767 i i v i v v v -- -- v ii MIRb#SINE/MIR 171 CAGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGCA 220 chr3ptel1M 952768 CAGTGTCGGGCACATGGCAA-TGCTC 952792 i v i i -i MIRb#SINE/MIR 221 CAGTGCCTGGCACATAGTAAGCGCTC 246 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 25.61 CpG sites = 17, Kimura (unadjusted) = 26.80 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.05 (6 / 120), avg. gap size = 1.33 (8 / 6) 19 0.00 0.00 0.00 chr3ptel1M 954426 954446 (45554) (C)n#Simple_repeat 1 21 (0) m_b134s252i16 4988 chr3ptel1M 954426 CCCCCCCCCCCCCCCCCCCCC 954446 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCC 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 chr3ptel1M 954712 954728 (45272) (G)n#Simple_repeat 1 17 (0) m_b134s252i17 4989 chr3ptel1M 954712 GGGGGGGGGGGGGGGGG 954728 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGG 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 17 4.94 0.00 0.00 chr3ptel1M 955925 955945 (44055) (A)n#Simple_repeat 1 21 (0) m_b134s252i18 4990 chr3ptel1M 955925 AAAAAAAAAAAACAAAAAAAA 955945 v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAA 21 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 22 34.38 0.00 0.00 chr3ptel1M 956124 956200 (43800) (AA)n#Simple_repeat 1 77 (0) m_b134s252i19 4991 chr3ptel1M 956124 AAAAATAACAAAACCAAAAAAAACCAAAAAAAAAAAAAAGCCCCAAAGGG 956173 v v vv vv ivvvv iii (AA)n#Simple_ 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr3ptel1M 956174 GGGGAAAAAAAAAAAAAGGGAAAAAAA 956200 iiii iii (AA)n#Simple_ 51 AAAAAAAAAAAAAAAAAAAAAAAAAAA 77 Matrix = Unknown Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.00 (0 / 76), avg. gap size = 0.0 (0 / 0) 16 22.03 2.00 2.00 chr3ptel1M 956325 956374 (43626) (CAAAAAA)n#Simple_repeat 1 50 (0) m_b134s252i21 4992 chr3ptel1M 956325 CAAAAACCCAAAAAACCAAAAACCCAAAACCCCCAA-AAAAAAAAAAAAA 956373 -v v vv vvvv - v (CAAAAAA)n#Si 1 CAAAAA-ACAAAAAACAAAAAACAAAAAACAAAAAACAAAAAACAAAAAA 49 chr3ptel1M 956374 C 956374 (CAAAAAA)n#Si 50 C 50 Matrix = Unknown Transitions / transversions = 0.00 (0/9) Gap_init rate = 0.04 (2 / 49), avg. gap size = 1.00 (2 / 2) 16 20.95 0.00 0.00 chr3ptel1M 956523 956555 (43445) (A)n#Simple_repeat 1 33 (0) m_b134s252i22 4993 chr3ptel1M 956523 AAAAAAAAAAAACCCCAAAGCAAAAAAAAAAAA 956555 vvvv iv (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 33 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 13 21.50 2.22 2.22 chr3ptel1M 956718 956762 (43238) (AAACCCC)n#Simple_repeat 1 45 (0) m_b134s252i23 4994 chr3ptel1M 956718 AAACCCCAAACCCCAAA-AAAAAAAAATAACCCCTCAAACCCCAAA 956762 -vvv vvvi v - (AAACCCC)n#Si 1 AAACCCCAAACCCCAAACCCCAAACCCCAAACCC-CAAACCCCAAA 45 Matrix = Unknown Transitions / transversions = 0.14 (1/7) Gap_init rate = 0.05 (2 / 44), avg. gap size = 1.00 (2 / 2) 18 29.11 0.00 0.00 chr3ptel1M 956732 956778 (43222) (AA)n#Simple_repeat 1 47 (0) m_b134s252i25 4994 chr3ptel1M 956732 AAAAAAAAAAAATAACCCCTCAAACCCCAAAAAAAAAAAAAAAAAAA 956778 v vvvvvv vvvv (AA)n#Simple_ 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 47 Matrix = Unknown Transitions / transversions = 0.00 (0/11) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 41 19.55 0.00 0.00 chr3ptel1M 956897 956973 (43027) (A)n#Simple_repeat 1 77 (0) m_b134s252i26 4995 chr3ptel1M 956897 AAAAAAAAAAAAAACCATAAAAAAATTTAAAAAAAAAAAAAAAAAAAAAA 956946 vv v vvv (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr3ptel1M 956947 TTTTTAAAAAAAAAAAAACCAAAAAAA 956973 vvvvv vv (A)n#Simple_r 51 AAAAAAAAAAAAAAAAAAAAAAAAAAA 77 Matrix = Unknown Transitions / transversions = 0.00 (0/13) Gap_init rate = 0.00 (0 / 76), avg. gap size = 0.0 (0 / 0) 28 18.36 0.00 0.00 chr3ptel1M 957077 957126 (42874) (A)n#Simple_repeat 1 50 (0) m_b134s252i27 4996 chr3ptel1M 957077 AAAAAAAAACCAAAAAAAAAAATTTTTTAAAAAAAAAAAAAAAAAAAAAA 957126 vv vvvvvv (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 Matrix = Unknown Transitions / transversions = 0.00 (0/8) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 18 22.67 0.00 0.00 chr3ptel1M 957211 957256 (42744) (AAAATTT)n#Simple_repeat 1 46 (0) m_b134s252i28 4997 chr3ptel1M 957211 AAAATTTAAAATTAAAAACCAAAAAAACCAAATTTAAAATTTTAAA 957256 v iiv vviv v (AAAATTT)n#Si 1 AAAATTTAAAATTTAAAATTTAAAATTTAAAATTTAAAATTTAAAA 46 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 16 10.03 0.00 0.00 chr3ptel1M 958469 958490 (41510) (A)n#Simple_repeat 1 22 (0) m_b134s252i30 4998 chr3ptel1M 958469 AAAAAAAAAAAAAAAGGAAAAA 958490 ii (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAA 22 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 22 27.94 4.21 2.06 chr3ptel1M 958459 958553 (41447) (AAAAAGG)n#Simple_repeat 1 97 (0) m_b134s252i29 4999 chr3ptel1M 958459 AAAAAGGGGGAA-AAAAAAAAAAAAAGGAAAAAGGGAAAAGG-GAAGGAA 958506 iii -i ii i -i i i (AAAAAGG)n#Si 1 AAAAAGGAAAAAGGAAAAAGGAAAAAGGAAAAAGGAAAAAGGAAAAAGGA 50 chr3ptel1M 958507 AAAAGGGGAAAAGGTAAGA-G-AAGGGGAAAGGGTGATAGAAGAAAAAG 958553 - i v i - - ii ii - v i i (AAAAAGG)n#Si 51 AAAA-GGAAAAAGGAAAAAGGAAAAAGGAAAAAG-GAAAAAGGAAAAAG 97 Matrix = Unknown Transitions / transversions = 9.00 (18/2) Gap_init rate = 0.06 (6 / 94), avg. gap size = 1.00 (6 / 6) 232 28.73 4.67 5.66 chr3ptel1M 958623 958729 (41271) MIRc#SINE/MIR 10 115 (153) m_b134s601i20 5000 chr3ptel1M 958623 GTGGCACAGTGGAT-GAACCCTCAA--TAAAGTCAGGAGAACCCTGAGGG 958669 ii v- i v vi -- ii ii i--- MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCT---GGG 56 chr3ptel1M 958670 TCCTCTGGTCTCAGACATTAACACTTTCCAACT-TGTGACC-CAGGCAAA 958717 -- vi i - i vi iv v i i - -ii i MIRc#SINE/MIR 57 T--TCGAGTCCC-GGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAG 103 chr3ptel1M 958718 TCATTTTAACTC 958729 i v v MIRc#SINE/MIR 104 TCACTTAACCTC 115 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.10 CpG sites = 20, Kimura (unadjusted) = 38.10 Transitions / transversions = 2.22 (20/9) Gap_init rate = 0.09 (10 / 106), avg. gap size = 1.10 (11 / 10) 184 31.86 13.81 5.43 chr3ptel1M 959186 959424 (40576) C L3#LINE/CR1 (5) 4094 3837 m_b134s601i21 5001 chr3ptel1M 959186 AATCCCA-AGTCTCAGAGCTG-------TCTTGGGGGCTGCCT------- 959220 v - i i -------i i i iiii ------- C L3#LINE/CR1 4094 AATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCAA 4045 chr3ptel1M 959221 TCTCCCACCCCATGGCTGAAGGGTTTCCTCCATCATA--TGCTCAGTGGT 959268 i i v - v i ivvii i v v v-- viv C L3#LINE/CR1 4044 CCTCCCATCCAATG-CAGGAATCCCTTCTACAACATCCCTGACAAGTGGT 3996 chr3ptel1M 959269 CAGTCTCCCAGCTGAGCCCCTGCT-AACCACCA--AGGGA--GGGCGCCC 959313 --- ------ i -i v v-- v -- v i C L3#LINE/CR1 3995 CA---TCC------AGCCTCTGCTTGAACACCTCCAGTGACGGGGAGCTC 3955 chr3ptel1M 959314 CCTGT-TCCTGAGGCAACCCAACTCTCTATTGGGAAAGCTC-AAC----- 959356 v ii- ?i i - i iv v v v -i i----- C L3#LINE/CR1 3954 ACTACCTCNCGAGGCAGCCC-ATTCCATTTTTGGACAGCTCTGATTGTTA 3906 chr3ptel1M 959357 ACAAGATTTTCTTAACATCTCTGA---CAAATCT-TCTTTGAGAAAACTG 959402 iv v i i v i --- ---v -i iivv v vi v C L3#LINE/CR1 3905 GAAAGTTCTTCCTTATAT---TGAGCCGAAATCTGCCTCCCTGTAACTTC 3859 chr3ptel1M 959403 TATCTGGGGGTGCTAATTCTGC 959424 i i iivv v i C L3#LINE/CR1 3858 CACCCATTGGTCCTAGTTCTGC 3837 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.40 CpG sites = 41, Kimura (unadjusted) = 43.21 Transitions / transversions = 1.32 (41/31) Gap_init rate = 0.11 (26 / 238), avg. gap size = 1.81 (47 / 26) 12 13.57 0.00 8.57 chr3ptel1M 962313 962350 (37650) (AAAAAC)n#Simple_repeat 1 35 (0) m_b135s252i0 5002 chr3ptel1M 962313 AAAAACCAAAACTTGAAAACTAAAAACAAATTCAAAAA 962350 v --i - vv (AAAAAC)n#Sim 1 AAAAACAAAAAC--AAAAAC-AAAAACAAAAACAAAAA 35 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.08 (3 / 37), avg. gap size = 1.00 (3 / 3) 185 25.14 0.00 7.69 chr3ptel1M 962397 962452 (37548) C X7B_LINE#LINE/CR1 (0) 250 199 m_b135s601i0 5003 chr3ptel1M 962397 TCCAAGGTGGGGGAGGCCCCCAAAATTTCCTCCTTTCCTCTATCAGAAAA 962446 v vi v i ii iv vv i ---- v C X7B_LINE#LINE 250 TCAAAGGTTAGGGATGTCTTCAAAACATCCTAATTTCCTTTA----ATAA 205 chr3ptel1M 962447 CCCATT 962452 C X7B_LINE#LINE 204 CCCATT 199 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.58 CpG sites = 6, Kimura (unadjusted) = 30.58 Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.07 (4 / 55), avg. gap size = 1.00 (4 / 4) 236 13.89 0.00 0.00 chr3ptel1M 963991 964026 (35974) C L2c_3end#LINE/L2 (12) 466 431 m_b135s601i2 5004 chr3ptel1M 963991 AACCAGCATTTATTAAGTGCCTACTATGTGCCAGAC 964026 v i i i i C L2c_3end#LINE 466 AACAAACATTTATTGAGCGCCTACTATGTGCCAGGC 431 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 12.59 CpG sites = 4, Kimura (unadjusted) = 15.81 Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 205 29.62 4.88 1.18 chr3ptel1M 963985 964066 (35934) C MIR#SINE/MIR (0) 262 178 m_b135s601i1 5005 chr3ptel1M 963985 AGTAAGAACCAGCATTTATTAAGTGCCTACTATGTGCCAGACA-TACATT 964033 i v i i i i i i i - iivi C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCT 213 chr3ptel1M 964034 AT---CTATTCAACTATTCAACTTACTGAGTGCTTA 964066 v--- v v vv - i i v i v i C MIR#SINE/MIR 212 AAGCGCTTTACATGTATT-AACTCATTTAATCCTCA 178 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.02 CpG sites = 15, Kimura (unadjusted) = 39.12 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.04 (3 / 81), avg. gap size = 1.67 (5 / 3) 193 30.85 0.00 8.06 chr3ptel1M 964077 964143 (35857) C L2d_3end#LINE/L2 (6) 510 449 m_b135s601i3 5006 chr3ptel1M 964077 AACTCATCATCAAGCACTGATTGAGTGCTTACTGTGTGCTAAGTGGGGCA 964126 iiv v i i v i i i v ----- C L2d_3end#LINE 510 AATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCA-----GCA 466 chr3ptel1M 964127 TCTTTTTGGATGCTGTG 964143 iiv vi i ii C L2d_3end#LINE 465 CTGTGCTAGGCGCTGTG 449 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.01 CpG sites = 13, Kimura (unadjusted) = 41.67 Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.08 (5 / 66), avg. gap size = 1.00 (5 / 5) 201 25.00 2.27 0.00 chr3ptel1M 964078 964121 (35879) C L2c_3end#LINE/L2 (4) 474 430 m_b135s601i4 5006 chr3ptel1M 964078 ACTCAT-CATCAAGCACTGATTGAGTGCTTACTGTGTGCTAAGTG 964121 i - v i i v i i i i i i C L2c_3end#LINE 474 ATTCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCG 430 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 25.70 CpG sites = 9, Kimura (unadjusted) = 32.69 Transitions / transversions = 4.50 (9/2) Gap_init rate = 0.02 (1 / 43), avg. gap size = 1.00 (1 / 1) 301 33.98 6.80 0.00 chr3ptel1M 966186 966288 (33712) L2c_3end#LINE/L2 362 471 (7) m_b135s601i5 5007 chr3ptel1M 966186 GTCTTCTCCGTTAGCACGTGACCTCCCCGAGGCCAGAGACCAC--CCTGC 966233 i ii vvi v ii v i ii-- i ii L2c_3end#LINE 362 GTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTAT 411 chr3ptel1M 966234 TTGTGTGTGGAACCCAAGCACTTGGCACACAGTAAG-----AACCAGCAT 966278 ii v v v v v i i i i ----- iv iii L2c_3end#LINE 412 TCATCTTTGTATCCCCAGCGCCTGGCACATAGTAGGCGCTCAATAAATGT 461 chr3ptel1M 966279 TTATTAAGTG 966288 i i i L2c_3end#LINE 462 TTGTTGAATG 471 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.05 CpG sites = 25, Kimura (unadjusted) = 49.07 Transitions / transversions = 2.50 (25/10) Gap_init rate = 0.02 (2 / 102), avg. gap size = 3.50 (7 / 2) 231 23.81 0.00 0.00 chr3ptel1M 966264 966305 (33695) C MIR#SINE/MIR (0) 262 221 m_b135s601i6 5008 chr3ptel1M 966264 AGTAAGAACCAGCATTTATTAAGTGCCTGCTATGTGCCAGAC 966305 i v i i i i i i i i C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGC 221 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.56 CpG sites = 9, Kimura (unadjusted) = 31.33 Transitions / transversions = 9.00 (9/1) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 238 16.22 0.00 0.00 chr3ptel1M 966270 966306 (33694) C L2c_3end#LINE/L2 (12) 466 430 m_b135s601i7 5009 chr3ptel1M 966270 AACCAGCATTTATTAAGTGCCTGCTATGTGCCAGACG 966306 v i i i i i C L2c_3end#LINE 466 AACAAACATTTATTGAGCGCCTACTATGTGCCAGGCG 430 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 15.68 CpG sites = 5, Kimura (unadjusted) = 19.03 Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 51 33.68 3.33 0.81 chr3ptel1M 966328 966567 (33433) (CT)n#Simple_repeat 1 246 (0) m_b135s252i1 5010 chr3ptel1M 966328 CTCTTTCT-TTTCT-TCTCTCCCTC-CTTTCCTTTTCAATGACTCTCTGC 966374 i - i - i - i ii i vv vv vi (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chr3ptel1M 966375 CTC-CTCTTTGTGTTTTCCACTCTC-CCCTC-CCCTTTCTCTGTCTCTGT 966421 - i v v i ii v - i - i i v v (CT)n#Simple_ 51 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 100 chr3ptel1M 966422 CTCTCTCCATCTCTGTCTCTCCCCCATCTCTC-CTTTCTTCCTCTTTGGT 966470 iv v i i - - i ii i -v (CT)n#Simple_ 101 CTCTCTCTCTCTCTCTCTCTCTCTC-TCTCTCTCTCTCTCTCTCTCT-CT 148 chr3ptel1M 966471 CTCTGTCTCT-TTTCCCCTTTTCTCTCATTTTGTATGTGTCTCTCTTTCT 966519 v - i i ii i vi i v v v v i (CT)n#Simple_ 149 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 198 chr3ptel1M 966520 TTCTCACTATGTCCCTCTTTCTGCCTTTCTGCCTCTGCCTCTGTCTCT 966567 i v v v i i vi i vi vi v (CT)n#Simple_ 199 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 246 Matrix = Unknown Transitions / transversions = 1.42 (37/26) Gap_init rate = 0.04 (10 / 239), avg. gap size = 1.00 (10 / 10) 276 19.75 0.43 10.90 chr3ptel1M 966583 966815 (33185) C HERVIP10FH#LTR/ERV1 (4110) 992 782 m_b135s701i0 5011 chr3ptel1M 966583 TCTCTCTGTCTTTTCCTTTTCTGACCGTCTGTCTCTTTCTCTCTCTCTGA 966632 v ii i - iv i C HERVIP10FH#LT 992 TCTCTCTTTCTTTCTCTCTT-TGACTTTCTGTCTCTCTCTCTCTCTCTGA 944 chr3ptel1M 966633 CTCTCCCTCCCTCTCTGTCTCTCTCCTGTTTCTCTCTGTCTCTGCTTCTT 966682 ------ i --- i ii v i i C HERVIP10FH#LT 943 CTC------CCTCTTTGTCTCTCT---GTCTCTTCCTCTCTCTGCCTCTC 903 chr3ptel1M 966683 TCTCTGTCTCTGCCTCTTTGACCCACTATCTCTCTCTCTCCCTCTGTCTC 966732 ---------- i v v i v i iv C HERVIP10FH#LT 902 TCTCT----------CTTTGACTCCCTCTTTGTCTCTCTCTCTCCCTCTC 863 chr3ptel1M 966733 TCTCTCTCCTTCTGTCTCTTCCTCACTGTCTCTCTCTTTCTATCTCTGTC 966782 -- v ii viiv i v - C HERVIP10FH#LT 862 TCTCTCT--TTCTCTCTCTCTCTCTTCCTCTCTCTCTCTCTCTCTCT-TC 816 chr3ptel1M 966783 TCTCTCT-CTCTCTATTTATCTCTCTGTGTGTCT 966815 i - ii vi i iv iv C HERVIP10FH#LT 815 TCTCTTTCCTCTCTGCTGGTCTTTCCCTGCCTCT 782 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 23.14 CpG sites = 27, Kimura (unadjusted) = 23.14 Transitions / transversions = 1.93 (27/14) Gap_init rate = 0.10 (24 / 232), avg. gap size = 1.00 (24 / 24) 39 34.60 1.84 0.00 chr3ptel1M 966829 966991 (33009) (CT)n#Simple_repeat 1 166 (0) m_b135s252i2 5012 chr3ptel1M 966829 CTCTGTGCCTCTGTCTCTATCTTTTTGTGTATGTGTCTCTGTTTCTGTCT 966878 v vi v v i i v v v v v v i v (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chr3ptel1M 966879 TTCTCTTTCCCCTTCTCTTTCTCTCTCTTTCTACCTTTCGGTCTCT-TCT 966927 i i i ii i i vi i vv - (CT)n#Simple_ 51 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 100 chr3ptel1M 966928 CTCTCTGTCTCCGTCTGTCTTTGTATTTGTGTCTCTGTCTGTTTCT-TGC 966976 v iv v i v v i v v v v i - vi (CT)n#Simple_ 101 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 150 chr3ptel1M 966977 CCCACT-TTTCTCTCT 966991 i v - i (CT)n#Simple_ 151 CTCTCTCTCTCTCTCT 166 Matrix = Unknown Transitions / transversions = 0.80 (20/25) Gap_init rate = 0.02 (3 / 162), avg. gap size = 1.00 (3 / 3) 42 27.14 5.62 0.53 chr3ptel1M 966830 967007 (32993) (TCTCTG)n#Simple_repeat 1 187 (0) m_b135s252i3 5012 chr3ptel1M 966830 TCTGTGCCTCTGTCTCTATCT-T-TTTGTGTATGTGTCTCTGTTTCTGTC 966877 v i i - - i v v v i (TCTCTG)n#Sim 1 TCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTC 50 chr3ptel1M 966878 T-T-TCTCTTTCCCCTTCTCT-T-TCTCTCTCTTTCTACCTTTCGGTCTC 966923 - - v i iv - - v v viv i v (TCTCTG)n#Sim 51 TCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTC 100 chr3ptel1M 966924 T-TCTC--TCTCTGTCTCCGTCTGTCTTTGTATTTGTGTCTCTGTCTGTT 966970 - -- i v v i v i i v v v (TCTCTG)n#Sim 101 TGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTG 150 chr3ptel1M 966971 TCT-TGCCCCACTTTTCTCTCTATGACTTTGCCTATGT 967007 - i i -iv i v v v i i v (TCTCTG)n#Sim 151 TCTCTGTCTC-TGTCTCTGTCTCTGTCTCTGTCTCTGT 187 Matrix = Unknown Transitions / transversions = 0.82 (18/22) Gap_init rate = 0.06 (10 / 177), avg. gap size = 1.10 (11 / 10) 413 24.76 4.46 2.63 chr3ptel1M 967080 967191 (32809) MIRc#SINE/MIR 3 116 (152) m_b135s601i8 5013 chr3ptel1M 967080 AGGCAGTGTGGAGCAGTGGGTAGAG----AGGCTTGTCTGAGCTGGGAGG 967125 v iv ----i i --- iii i MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTG---GAGTCAGGAAG 49 chr3ptel1M 967126 ACCTGG-TTCAAGCTCTGCCTCCAACACATCGTGGCTGTGTGATCCTGGG 967174 - i ii i v iiv v vv i i i MIRc#SINE/MIR 50 ACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGG 99 chr3ptel1M 967175 CAAGACACTTGACTTTT 967191 v i i i MIRc#SINE/MIR 100 CAAGTCACTTAACCTCT 116 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.60 CpG sites = 19, Kimura (unadjusted) = 31.38 Transitions / transversions = 2.38 (19/8) Gap_init rate = 0.05 (5 / 111), avg. gap size = 1.60 (8 / 5) 19 34.26 2.14 4.38 chr3ptel1M 967212 967351 (32649) (TGCCC)n#Simple_repeat 1 137 (0) m_b135s252i4 5014 chr3ptel1M 967212 TGCCC-ACCCTGCCATGCTCCTGCCCTGGCCTGCCCTACTCTGTCAACAC 967260 -i v - v i i - vvii (TGCCC)n#Simp 1 TGCCCTGCCCTGCCCTGC-CCTGCCCTGCCCTGCCCTGCCCTG-CCCTGC 48 chr3ptel1M 967261 CTTGTCCTGGGCCTG-TCTTACATGCCC-ACTCTGTCATGTGCCCCTCCT 967308 i i - v -i vv v -i i i v -v ivi (TGCCC)n#Simp 49 CCTGCCCT-GCCCTGCCCTGCCCTGCCCTGCCCTGCCCTG-CCCTGCCCT 96 chr3ptel1M 967309 GCTTTGCTATGTGCCCATCCTGTCCCGGGCCTGCCCTGCCTTG 967351 ii iv -v iii - v v i (TGCCC)n#Simp 97 GCCCTGCCCTG-CCCTGCCCTG-CCCTGCCCTGCCCTGCCCTG 137 Matrix = Unknown Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.06 (9 / 139), avg. gap size = 1.00 (9 / 9) 248 28.09 1.11 1.11 chr3ptel1M 968190 968279 (31721) L1P1_orf2#LINE/L1 33 122 (3172) m_b135s551i0 5015 chr3ptel1M 968190 AACTTTACCTATAAATGGACTTAATGATCCAATAAAATAACAGAGAGTGA 968239 vv i v v v vi v v i L1P1_orf2#LIN 33 AACTTTAAATGTAAATGGACTAAATGCTCCAATTAAAAGACACAGACTGG 82 chr3ptel1M 968240 CATGCTAAGTAAGGGAATCAAAGCCC-CCAGTCTGTTGCAT 968279 vii iii -i i ii -i v i i L1P1_orf2#LIN 83 CAAATTGGATAA-AGAGTCAAGACCCATCAGTGTGCTGTAT 122 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 36.20 CpG sites = 15, Kimura (unadjusted) = 36.20 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.02 (2 / 89), avg. gap size = 1.00 (2 / 2) 206 12.50 2.50 0.00 chr3ptel1M 968372 968411 (31589) MIR3#SINE/MIR 104 144 (64) m_b135s601i9 5016 chr3ptel1M 968372 CTGCACC-CTGTGTCTCTCAGTTTCCTCATCTGTAAAATGA 968411 v - v vvi MIR3#SINE/MIR 104 CTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGA 144 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 13.70 CpG sites = 1, Kimura (unadjusted) = 13.70 Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1) 206 11.76 0.00 0.00 chr3ptel1M 968377 968410 (31590) MIR#SINE/MIR 109 142 (120) m_b135s601i10 5016 chr3ptel1M 968377 CCCTGTGTCTCTCAGTTTCCTCATCTGTAAAATG 968410 i v vi MIR#SINE/MIR 109 CTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATG 142 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 12.84 CpG sites = 2, Kimura (unadjusted) = 12.84 Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 79 0.00 0.00 0.00 chr3ptel1M 969000 969066 (30934) (CA)n#Simple_repeat 1 67 (0) c_b135s251i0 5017 chr3ptel1M 969000 CACACACACACACACACACACACACACACACACACACACACACACACACA 969049 (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 chr3ptel1M 969050 CACACACACACACACAC 969066 (CA)n#Simple_ 51 CACACACACACACACAC 67 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.0 (0 / 0) 206 34.24 1.75 2.65 chr3ptel1M 969990 970103 (29897) L3#LINE/CR1 3663 3775 (324) m_b135s601i11 5018 chr3ptel1M 969990 CAGCTAGGAGGCTGAAGGGCCTGGCCCCCGTGTCCCAGAAGGGCCAGTTG 970039 ii i v v i vvv i vi vi iv i L3#LINE/CR1 3663 CGACCAGGATGGTGAAGGGTCTGGAAACCATGTCATATGAGGAACGGTTG 3712 chr3ptel1M 970040 GAGGGAATGTACCTGCTTA-CCT-GAGAAGACTGGGGACAGGTGGGATGA 970087 i i v vivv i - - -- ii vvivi - L3#LINE/CR1 3713 AAGGAACTGGGGATGTTTAGCCTGGAGAAGA--GAAGACTTAGAGGA-GA 3759 chr3ptel1M 970088 TGGGAAAGTTGACTTC 970103 iiv v i v L3#LINE/CR1 3760 CATGATAGCTGTCTTC 3775 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.48 CpG sites = 20, Kimura (unadjusted) = 46.76 Transitions / transversions = 1.11 (20/18) Gap_init rate = 0.04 (5 / 113), avg. gap size = 1.00 (5 / 5) 16 23.72 2.50 0.00 chr3ptel1M 970134 970173 (29827) (TC)n#Simple_repeat 1 41 (0) m_b135s252i5 5019 chr3ptel1M 970134 TCT-TCTTGCTTTCTCTCAGTTCCTCTCCCTCTCTCTCTCT 970173 - iv i vv ii i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 41 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1) 36 20.89 0.00 5.21 chr3ptel1M 970503 970603 (29397) (CTTCCT)n#Simple_repeat 1 96 (0) m_b135s252i6 5020 chr3ptel1M 970503 CTTCCTCCTCCTCCTCCTCTTCCTCCTCTTCCTCATGCCCCTCTTCCTCT 970552 i i i i i v vii (CTTCCT)n#Sim 1 CTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCT 50 chr3ptel1M 970553 CCCTCTTTGCCTTTTCCCTGTTTTCTCCTTTTTCTCCCTCTTCCTCTTCC 970602 i - - i - -i i - ii i (CTTCCT)n#Sim 51 TCCTC-TT-CCTCTT-CCT-CTTCCT-CTTCCTCTTCCTCTTCCTCTTCC 95 chr3ptel1M 970603 T 970603 (CTTCCT)n#Sim 96 T 96 Matrix = Unknown Transitions / transversions = 7.00 (14/2) Gap_init rate = 0.05 (5 / 100), avg. gap size = 1.00 (5 / 5) 409 32.84 2.43 3.94 chr3ptel1M 971918 972123 (27877) C MIR1_Amn#SINE/MIR (15) 215 13 m_b135s601i12 5021 chr3ptel1M 971918 TTTTATTTAGTGCTTGTCCTGTGTCAGGCACTGAGCACATTACAATTACT 971967 i v ii v v vv viiv v vi v vvivv C MIR1_Amn#SINE 215 TCTTATGTAGCACTTTTCATCAGTAGATCTCAAAGCACTTTACAAAGGAG 166 chr3ptel1M 971968 ATCCGATTTGATTCTCAAACAATCCATTTCACAGATGGGGAAACTGAGGC 972017 i v - v v v ------i i i C MIR1_Amn#SINE 165 GTCAG-TATCATTATC------CCCATTTTACAGATGAGGAAACTGAGGC 123 chr3ptel1M 972018 AGACAGAAGGGACACGAGTTTCTCAGAGTCCCACAGCTAG--ATTTG--A 972063 ?v v i v? vii v v i ii v ? ?i -- v v --i C MIR1_Amn#SINE 122 NCAGAGAGGTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNAGTGGCAG 73 chr3ptel1M 972064 AGCC-AGATTTGAACTCAGGCCCTTCTGACTCCTGGACCAGGACCCTGGG 972112 -i ? ? i -i i i v ii v vi i ivv C MIR1_Amn#SINE 72 AGCCGGGANTNGAACCCAGG-TCTCCCGAGTCCCAGTCCAGTGCTCTATC 24 chr3ptel1M 972113 CACAAAGTCAC 972123 v iii C MIR1_Amn#SINE 23 CACTAGACCAC 13 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.77 CpG sites = 32, Kimura (unadjusted) = 45.71 Transitions / transversions = 0.97 (32/33) Gap_init rate = 0.05 (11 / 205), avg. gap size = 1.18 (13 / 11) 493 25.42 19.77 0.00 chr3ptel1M 971919 972095 (27905) C MIRb#SINE/MIR (16) 252 41 m_b135s601i13 5021 chr3ptel1M 971919 TTTATTTAGTGCTTGTCCTGTGTCAGGCACTG-----AGCACATTACAAT 971963 v i iiiv i ----- i v vv C MIRb#SINE/MIR 252 TTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACATG 203 chr3ptel1M 971964 TACTATCCGATTTGATTCTCA-AACAATCC-------------------- 971992 i i iv i i - i -------------------- C MIRb#SINE/MIR 202 CATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATTAT 153 chr3ptel1M 971993 ----ATTTCACAGATGGGGAAACTGAGGCAGACAGAAGGGACACGAGTTT 972038 ---- i i vv v i vv viii v v C MIRb#SINE/MIR 152 CCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTG 103 chr3ptel1M 972039 CTCAGAGTCCCACAGCTAG-ATTTG---AAGCC-AGATTTGAACTCAGGC 972083 i ii v - vv ---i -i i i i C MIRb#SINE/MIR 102 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGT 53 chr3ptel1M 972084 CCTTCTGACTCC 972095 iv C MIRb#SINE/MIR 52 CTGTCTGACTCC 41 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.29 CpG sites = 27, Kimura (unadjusted) = 31.79 Transitions / transversions = 1.50 (27/18) Gap_init rate = 0.04 (7 / 176), avg. gap size = 5.00 (35 / 7) 421 27.73 4.20 0.00 chr3ptel1M 971991 972109 (27891) C MIRc#SINE/MIR (121) 147 24 m_b135s601i14 5021 chr3ptel1M 971991 CCATTTCACAGATGGGGAAACTGAGGCAGACAGAAGGGACACGAGTTTCT 972040 i i vv v i vv vii v v i C MIRc#SINE/MIR 147 CCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCC 98 chr3ptel1M 972041 CAGAGTCCCACAGCTAG-ATTTG---AAGCC-AGATTTGAACTCAGGCCC 972085 ii v - vv ---i -i i i i i i C MIRc#SINE/MIR 97 CAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCT 48 chr3ptel1M 972086 TTCTGACTCCTGGACCAGGACCCT 972109 i vi v vi i C MIRc#SINE/MIR 47 TCCTGACTCCAAGTCCAGTGCTCT 24 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.10 CpG sites = 19, Kimura (unadjusted) = 35.43 Transitions / transversions = 1.36 (19/14) Gap_init rate = 0.03 (3 / 118), avg. gap size = 1.67 (5 / 3) 279 22.86 7.14 0.00 chr3ptel1M 972749 972818 (27182) C MIRc#SINE/MIR (98) 170 96 m_b135s601i15 5022 chr3ptel1M 972749 AGACTGAGCAGGGACCATG---CCCATTTTACAGATGAGAACACTAAGGC 972795 i v i v ii v--- i v i C MIRc#SINE/MIR 170 AGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGC 121 chr3ptel1M 972796 TCCCAAATGC--AGTGATTTGCCCA 972818 vv i v i-- i C MIRc#SINE/MIR 120 TCAGAGAGGTTAAGTGACTTGCCCA 96 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.67 CpG sites = 9, Kimura (unadjusted) = 27.67 Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.03 (2 / 69), avg. gap size = 2.50 (5 / 2) 190 9.09 6.06 0.00 chr3ptel1M 973711 973743 (26257) L2d_3end#LINE/L2 393 427 (89) m_b135s601i16 5023 chr3ptel1M 973711 TAGAATG--AGCTCCCTGAGGGCAGGGCCCATGTC 973743 v -- i v L2d_3end#LINE 393 TAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTC 427 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 9.69 CpG sites = 1, Kimura (unadjusted) = 9.69 Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.03 (1 / 32), avg. gap size = 2.00 (2 / 1) 31 32.49 0.79 2.40 chr3ptel1M 974971 975097 (24903) (TC)n#Simple_repeat 1 125 (0) m_b135s252i7 5024 chr3ptel1M 974971 TCTGTCTCTCTGGGTTTGTTTCTGTCTCTCTGGATTTGTCTCATCTCTAT 975020 v vvv i v i v vvv i v - v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TCTCTCT 49 chr3ptel1M 975021 CTCTCTCTCTAGAGTTTTGTCTCTATCTCAGTTTGTTTC-CTCATCTCTC 975069 vvvvi i v v vv i v i - - (TC)n#Simple_ 50 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TCTCTC 98 chr3ptel1M 975070 TGGTTTGTCTCTATCTCTATCTCTCTCT 975097 -v i v v v (TC)n#Simple_ 99 T-CTCTCTCTCTCTCTCTCTCTCTCTCT 125 Matrix = Unknown Transitions / transversions = 0.33 (8/24) Gap_init rate = 0.03 (4 / 126), avg. gap size = 1.00 (4 / 4) 42 0.00 0.00 0.00 chr3ptel1M 975121 975156 (24844) (CA)n#Simple_repeat 1 36 (0) c_b135s251i1 5025 chr3ptel1M 975121 CACACACACACACACACACACACACACACACACACA 975156 (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACA 36 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 122 17.15 4.21 1.71 chr3ptel1M 975749 976033 (23967) (TG)n#Simple_repeat 1 292 (0) m_b135s252i8 5026 chr3ptel1M 975749 TGTGTGTGTGTGTGTGTGAGGGAGAGAGTGTGTGTGTGTAAGTGTGTGTG 975798 v v v v v iv (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr3ptel1M 975799 TTTGTGTGTCTCTGTGAGTGTGTGTATGAGTGTGTGTGTGAAAGGGACAG 975848 v v v v i v viv v vvv (TG)n#Simple_ 51 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 100 chr3ptel1M 975849 AGAGTGTGTGTGTG-GTGTGTGTGTGAGGATGATGAG-GTGTGTGTGAGT 975896 v v - v vi - v - v (TG)n#Simple_ 101 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG-TGTGTGTGTGTGTGTGT 149 chr3ptel1M 975897 GTG-GTGTTTGTGTG-GTGTGTGTGACTGAG-GTGTGTAGGGTGTAGGGT 975943 - v - vv v - - v - v (TG)n#Simple_ 150 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT-GTGTGT-GTGT 197 chr3ptel1M 975944 GTG-GGGTGTGTGTG-GTGTGTGTGAGAGAG-GTGTGTGTGTAAGTGTAG 975990 - v - v v v - iv - (TG)n#Simple_ 198 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT-G 246 chr3ptel1M 975991 TGTGTG-GAGTGTAGTGTGTGTGTGTGTG-GTGAG-GTG-GAGTGTG 976033 - v - - v - - v (TG)n#Simple_ 247 TGTGTGTGTGTGT-GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 292 Matrix = Unknown Transitions / transversions = 0.14 (5/37) Gap_init rate = 0.06 (17 / 284), avg. gap size = 1.00 (17 / 17) 13 11.18 0.00 6.45 chr3ptel1M 976406 976438 (23562) (GGGGA)n#Simple_repeat 1 31 (0) m_b135s252i9 5027 chr3ptel1M 976406 GGGGAGGGCAGGGCGGGGAGGAGGGGAGGAGAG 976438 v - i - i (GGGGA)n#Simp 1 GGGGAGGGGAGGG-GAGG-GGAGGGGAGGGGAG 31 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.06 (2 / 32), avg. gap size = 1.00 (2 / 2) 14 21.82 0.00 4.55 chr3ptel1M 978283 978328 (21672) (CCCAC)n#Simple_repeat 1 44 (0) m_b135s252i10 5028 chr3ptel1M 978283 CCCACCGCGGCCCCGCCCCACCCCACCCCTGGCCCCCTCACCTCCA 978328 - vi i vvv v i - (CCCAC)n#Simp 1 CCCACC-CCACCCCACCCCACCCCACCCCACCCCACCCCACC-CCA 44 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.04 (2 / 45), avg. gap size = 1.00 (2 / 2) 498 25.61 2.44 1.61 chr3ptel1M 978717 978839 (21161) MIRb#SINE/MIR 124 247 (21) m_b135s601i17 5029 chr3ptel1M 978717 GCCTCGGTTTCCCCATCTGTAAAACAAGGATGGCTATAAGCCTCCCT--C 978764 i i iii iiiv -- v -- MIRb#SINE/MIR 124 GCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATA--CCTACCTCGC 171 chr3ptel1M 978765 AGGGACATGATGAGGATCAAAGGAGACAAAGTGTGTGTAGCCCTTGGCAC 978814 vii vi i v i v ii iv v i MIRb#SINE/MIR 172 AGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGCAC 221 chr3ptel1M 978815 AGTGTCAGGCACACGGCAA-TGCTCA 978839 i v ii i -i MIRb#SINE/MIR 222 AGTGCCTGGCACATAGTAAGCGCTCA 247 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.53 CpG sites = 22, Kimura (unadjusted) = 32.84 Transitions / transversions = 2.44 (22/9) Gap_init rate = 0.03 (4 / 122), avg. gap size = 1.25 (5 / 4) 12 16.74 7.50 0.00 chr3ptel1M 981041 981080 (18920) (GCCTCCT)n#Simple_repeat 1 43 (0) m_b135s252i11 5030 chr3ptel1M 981041 GCCCCCAGCCCCGTGGCT-CT-CCTGCTGCCTCCTGCC-CCTG 981080 i v i v v - - v - (GCCTCCT)n#Si 1 GCCTCCTGCCTCCTGCCTCCTGCCTCCTGCCTCCTGCCTCCTG 43 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.08 (3 / 39), avg. gap size = 1.00 (3 / 3) 13 18.22 0.00 0.00 chr3ptel1M 982793 982823 (17177) (AACAAA)n#Simple_repeat 1 31 (0) m_b135s252i12 5031 chr3ptel1M 982793 AACAAAAACAAGAAAACAAACAACTACAAAA 982823 i v v vv (AACAAA)n#Sim 1 AACAAAAACAAAAACAAAAACAAAAACAAAA 31 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 12 22.64 2.33 2.33 chr3ptel1M 983584 983626 (16374) (ACTCT)n#Simple_repeat 1 43 (0) m_b135s252i13 5032 chr3ptel1M 983584 ACGCTACCCCATTCTATTCCTACTCTACTCATCTCT-CTGTACT 983626 v i i i i - vv - v (ACTCT)n#Simp 1 ACTCTACTCTACTCTACT-CTACTCTACTCTACTCTACTCTACT 43 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.00 (2 / 2) 13 18.65 5.41 0.00 chr3ptel1M 983785 983821 (16179) (AAC)n#Simple_repeat 1 39 (0) m_b135s252i14 5033 chr3ptel1M 983785 AACAA-ATAAAAAACAAAAACAACAACACCATC-ACAAC 983821 - vv v v v v - (AAC)n#Simple 1 AACAACAACAACAACAACAACAACAACAACAACAACAAC 39 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 16 21.98 0.00 0.00 chr3ptel1M 988090 988131 (11869) (AAAGTAA)n#Simple_repeat 1 42 (0) m_b135s252i15 5034 chr3ptel1M 988090 AAGGTGAAAAGAATAAAGTAAATAGTAAAAAGAACAGAGTAA 988131 i i v v v v v i (AAAGTAA)n#Si 1 AAAGTAAAAAGTAAAAAGTAAAAAGTAAAAAGTAAAAAGTAA 42 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 17 18.27 1.82 5.66 chr3ptel1M 988292 988346 (11654) (TTCTTT)n#Simple_repeat 1 53 (0) m_b135s252i17 5035 chr3ptel1M 988292 TTCTCTTTTCTTTTGC-ATTACTTTTCTGTTTTTCTTTTTGCTTACTCTG 988340 - v -v v - v - vi v (TTCTTT)n#Sim 1 TTCT-TTTTCTTTTTCTTTTTCTTTT-TCTTTTTCTTTTT-CTTTTTCTT 47 chr3ptel1M 988341 TTCCTT 988346 i (TTCTTT)n#Sim 48 TTTCTT 53 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.07 (4 / 54), avg. gap size = 1.00 (4 / 4) 442 32.37 0.81 0.81 chr3ptel1M 988499 988744 (11256) L1M2_orf2#LINE/L1 2128 2373 (918) m_b135s551i1 5036 chr3ptel1M 988499 CCCAGAAATTTTACTAAAAAGCTATTAGAAATTATCCACAAGTTTAGCAA 988548 i i i i ii i i ? v v vv i i i i L1M2_orf2#LIN 2128 CCTAAAGACTCCACCAAAAAACTNTTAGAACTGATAAACGAATTCAGTAA 2177 chr3ptel1M 988549 AGTTGCAGGATTCAAAATAAATCTACATAAATCATCAGCATTCTTATATA 988598 v v iv v vi ii ii L1M2_orf2#LIN 2178 AGTTGCAGGATACAAAATCAACATACAAAAATCAGTAGCATTTCTATACG 2227 chr3ptel1M 988599 ACCCTAACAAA--ATCCAACAGTTAGAGATACAAAGAGAAATTCCATTTA 988646 v vvi i -- ii v i-- i vv i i v i L1M2_orf2#LIN 2228 CCAACAACGAACTATCTGAAAA--AGAAATCAAGAAAGCAATCCCATTTA 2275 chr3ptel1M 988647 AAGTAACTACTGATAGCATAAAATATTTAGGAATCTATCTGCGAAGGGAA 988696 v i i vi v iv ii vv i ivvv i i L1M2_orf2#LIN 2276 CAATAGCTACAAAAAAAATAAAATACCTAGGAATAAATTTAACCAAGGAG 2325 chr3ptel1M 988697 AGTCAGGAACTATATAAGCAAAACGACAAAACACTTTTCACAAAGATT 988744 ivvv i v v i ?v v i vv v v i i L1M2_orf2#LIN 2326 GTGAAAGATCTCTACAANGAAAACTATAAAACACTGATGAAAGAAATT 2373 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 41.62 CpG sites = 43, Kimura (unadjusted) = 43.90 Transitions / transversions = 1.19 (43/36) Gap_init rate = 0.01 (3 / 245), avg. gap size = 1.33 (4 / 3) 202 32.93 0.00 1.22 chr3ptel1M 989299 989381 (10619) MamRTE1#LINE/RTE-BovB 3514 3595 (217) m_b135s601i18 5037 chr3ptel1M 989299 TGTACGGCATGGGAGACCCTGGCAGAGGACTCCTCAGCATGGCATGCCCT 989348 v v - i vvii vi vvvi v vvi MamRTE1#LINE/ 3514 TGGACTGC-TGGGAAACAACAGCAGCAGACAGACCAGCCTGGCATGCAGC 3562 chr3ptel1M 989349 CATCAGAGAAGGGGCTGGGCTCTATGAGCAAAG 989381 v ii v iv vv i v MamRTE1#LINE/ 3563 AATCAGGAACGGGGTGGCTCTTTTTGAGCAAAG 3595 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.39 CpG sites = 10, Kimura (unadjusted) = 43.39 Transitions / transversions = 0.59 (10/17) Gap_init rate = 0.01 (1 / 82), avg. gap size = 1.00 (1 / 1) 301 33.98 6.80 0.00 chr3ptel1M 991579 991681 (8319) L2c_3end#LINE/L2 362 471 (7) m_b135s601i19 5038 chr3ptel1M 991579 GTCTTCTCCGTTAGCACGTGACCTCCCCGAGGCCAGAGACCAC--CCTGC 991626 i ii vvi v ii v i ii-- i ii L2c_3end#LINE 362 GTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTAT 411 chr3ptel1M 991627 TTGTGTGTGGAACCCAAGCACTTGGCACACAGTAAG-----AACCAGCAT 991671 ii v v v v v i i i i ----- iv iii L2c_3end#LINE 412 TCATCTTTGTATCCCCAGCGCCTGGCACATAGTAGGCGCTCAATAAATGT 461 chr3ptel1M 991672 TTATTAAGTG 991681 i i i L2c_3end#LINE 462 TTGTTGAATG 471 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.05 CpG sites = 25, Kimura (unadjusted) = 49.07 Transitions / transversions = 2.50 (25/10) Gap_init rate = 0.02 (2 / 102), avg. gap size = 3.50 (7 / 2) 231 23.81 0.00 0.00 chr3ptel1M 991657 991698 (8302) C MIR#SINE/MIR (0) 262 221 m_b135s601i20 5039 chr3ptel1M 991657 AGTAAGAACCAGCATTTATTAAGTGCCTGCTATGTGCCAGAC 991698 i v i i i i i i i i C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGC 221 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.56 CpG sites = 9, Kimura (unadjusted) = 31.33 Transitions / transversions = 9.00 (9/1) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 238 16.22 0.00 0.00 chr3ptel1M 991663 991699 (8301) C L2c_3end#LINE/L2 (12) 466 430 m_b135s601i21 5040 chr3ptel1M 991663 AACCAGCATTTATTAAGTGCCTGCTATGTGCCAGACG 991699 v i i i i i C L2c_3end#LINE 466 AACAAACATTTATTGAGCGCCTACTATGTGCCAGGCG 430 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 15.68 CpG sites = 5, Kimura (unadjusted) = 19.03 Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 59 29.47 4.56 0.80 chr3ptel1M 991721 991961 (8039) (CT)n#Simple_repeat 1 250 (0) m_b135s252i18 5041 chr3ptel1M 991721 CTCTTTCT-TTTCT-TCTCTCCCTC-CTTTC-CTTTCTCAATGACTCTCT 991766 i - i - i - i - i vv vv (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chr3ptel1M 991767 GCCTC-CTCTTTTTCTTTTTCACTCTC-CCCTC-CCCTTTCTCTGTCTCT 991813 vi - i i i i v - i - i i v (CT)n#Simple_ 51 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 100 chr3ptel1M 991814 GTCTCTCTCCATCTCTGTCTCTCCCCCATCTCTC-CTTTCT-TCT-TCTT 991860 v iv v i i - - i - - i (CT)n#Simple_ 101 CTCTCTCTCTCTCTCTCTCTCTCTCTC-TCTCTCTCTCTCTCTCTCTCTC 149 chr3ptel1M 991861 TGGTCTCTGTCTCT-TTTCCCCTTTTCTCTCATTTTGTATGTGTCTCTCT 991909 -v v - i i ii i vi i v v v v (CT)n#Simple_ 150 T-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 198 chr3ptel1M 991910 TTCTTTCTCACTATGTCCCTCTTTCTGCCTTTCTGCCTCTGCCTCTGTCT 991959 i i v v v i i vi i vi vi v (CT)n#Simple_ 199 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 248 chr3ptel1M 991960 CT 991961 (CT)n#Simple_ 249 CT 250 Matrix = Unknown Transitions / transversions = 1.38 (33/24) Gap_init rate = 0.05 (13 / 240), avg. gap size = 1.00 (13 / 13) 293 17.62 1.83 6.70 chr3ptel1M 991977 992195 (7805) C HERVIP10FH#LTR/ERV1 (4110) 992 784 m_b135s701i1 5042 chr3ptel1M 991977 TCTCTCTGTCTTTTCCTTTTCTGACCGTCTGTCTCTTTCTCTCTCTCTGA 992026 v ii i - iv i C HERVIP10FH#LT 992 TCTCTCTTTCTTTCTCTCTT-TGACTTTCTGTCTCTCTCTCTCTCTCTGA 944 chr3ptel1M 992027 CTCTCCCTCCCTCTCTGTCTCTCTCCTGTTTCTCTCTGTCTCTGCTTCTT 992076 ------ i --- i ii v i i C HERVIP10FH#LT 943 CTC------CCTCTTTGTCTCTCT---GTCTCTTCCTCTCTCTGCCTCTC 903 chr3ptel1M 992077 TCTCTGTCT--CTGCCTCTTTGACCCACTATCTCTCTCTCTCTCCCTCTG 992124 v i -- v v i v v i i i v C HERVIP10FH#LT 902 TCTCTCTTTGACTCCCTCTTTGTCTCTCTCTCTCCCTCTCTCTCTCTTTC 853 chr3ptel1M 992125 TCTCTCTCTCTCCTTCTGTCTCTTCCTCACTGTCTCTCTCTCTCTTTCTA 992174 i i v -- v v - i- C HERVIP10FH#LT 852 TCTCTCTCTCTCTTCCTCTCTCT--CTCTCTCTCTCT-TCTCTCTTTCC- 807 chr3ptel1M 992175 TCTCTGTC--TCTCTCTCTCCCT 992195 ii-- i i v C HERVIP10FH#LT 806 TCTCTGCTGGTCTTTCCCTGCCT 784 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 20.36 CpG sites = 23, Kimura (unadjusted) = 20.36 Transitions / transversions = 1.77 (23/13) Gap_init rate = 0.07 (16 / 218), avg. gap size = 1.12 (18 / 16) 67 33.60 1.84 0.36 chr3ptel1M 992201 992472 (7528) (TC)n#Simple_repeat 1 276 (0) m_b135s252i19 5043 chr3ptel1M 992201 TCTCTCTGTGTGTCTCTGTTTCATCTAGCTCTGTGTCTCTCTCTTAGTCT 992250 v v v v i - vv v v ivv (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTC-TCTCTCTCTCTCTCTCTCTCTCTCTCT 49 chr3ptel1M 992251 GCCTCTGTCTCTATCTTTTTGTGTATGTGTCTCTGTTTCTGTCTTTCTCT 992300 vi v v i i v v v v v v i v i (TC)n#Simple_ 50 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 99 chr3ptel1M 992301 TTCCCCTTCTCTTTCTCTCTCTTTCTACCTTTCGGTCTCT-TCTCTCTCT 992349 i i ii i i vi i vv - (TC)n#Simple_ 100 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 149 chr3ptel1M 992350 GTCTCCGTCTGTCTCTGTATTTGTGTCTCTGTCTCTCTCTCTGTCTCTTG 992399 v iv v v v i v v v v iv (TC)n#Simple_ 150 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 199 chr3ptel1M 992400 CCCCCACT-TTTCTCTCTATGACTTTGCCTATGTTTGTCCCCCTC-CCCT 992447 i i v - i v vv i vi v v i v i i - i (TC)n#Simple_ 200 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 249 chr3ptel1M 992448 C-CCCTCCCTCT-TCCCTTTCTGTCTC 992472 - i i - i i v (TC)n#Simple_ 250 CTCTCTCTCTCTCTCTCTCTCTCTCTC 276 Matrix = Unknown Transitions / transversions = 0.74 (31/42) Gap_init rate = 0.02 (6 / 271), avg. gap size = 1.00 (6 / 6) 403 24.76 4.46 2.63 chr3ptel1M 993306 993417 (6583) MIRc#SINE/MIR 3 116 (152) m_b135s601i22 5044 chr3ptel1M 993306 AGGCAGTGTGGAGCAGTGGGTAGAG----AGGCTTGTCTGAGCTGGGAGG 993351 v iv ----i i --- iii i MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTG---GAGTCAGGAAG 49 chr3ptel1M 993352 ACCTGG-TTCAAGCTCTGCCTCCAACACATCGTGGCTGTGTGATCGTGGG 993400 - i ii i v iiv v vv i i v MIRc#SINE/MIR 50 ACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGG 99 chr3ptel1M 993401 CAAGACACTTGACTTTT 993417 v i i i MIRc#SINE/MIR 100 CAAGTCACTTAACCTCT 116 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.40 CpG sites = 18, Kimura (unadjusted) = 31.14 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.05 (5 / 111), avg. gap size = 1.60 (8 / 5) 19 34.26 2.14 4.38 chr3ptel1M 993438 993577 (6423) (TGCCC)n#Simple_repeat 1 137 (0) m_b135s252i20 5045 chr3ptel1M 993438 TGCCC-ACCCTGCCATGCTCCTGCCCTGGCCTGCCCTACTCTGTCAACAC 993486 -i v - v i i - vvii (TGCCC)n#Simp 1 TGCCCTGCCCTGCCCTGC-CCTGCCCTGCCCTGCCCTGCCCTG-CCCTGC 48 chr3ptel1M 993487 CTTGTCCTGGGCCTG-TCTTACATGCCC-ACTCTGTCATGTGCCCCTCCT 993534 i i - v -i vv v -i i i v -v ivi (TGCCC)n#Simp 49 CCTGCCCT-GCCCTGCCCTGCCCTGCCCTGCCCTGCCCTG-CCCTGCCCT 96 chr3ptel1M 993535 GCTTTGCTATGTGCCCATCCTGTCCCGGGCCTGCCCTGCCTTG 993577 ii iv -v iii - v v i (TGCCC)n#Simp 97 GCCCTGCCCTG-CCCTGCCCTG-CCCTGCCCTGCCCTGCCCTG 137 Matrix = Unknown Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.06 (9 / 139), avg. gap size = 1.00 (9 / 9) 218 21.59 10.67 1.22 chr3ptel1M 994608 994682 (5318) MIR3#SINE/MIR 104 185 (23) m_b135s601i23 5044 chr3ptel1M 994608 CTGCACC-CTGTGTCTCTCAGTTTCCTCATCTGTAAAAT----GGGCTGG 994652 v - v vvi ---- i MIR3#SINE/MIR 104 CTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGG 153 chr3ptel1M 994653 AGCAGGAGGTGGCCAA---CCGCTCCAGACTCT 994682 vi iv i vv i --- vi - MIR3#SINE/MIR 154 ACTAGATGATCTCTAAGGTCCCTTCCAG-CTCT 185 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 25.58 CpG sites = 7, Kimura (unadjusted) = 25.58 Transitions / transversions = 0.78 (7/9) Gap_init rate = 0.05 (4 / 74), avg. gap size = 2.25 (9 / 4) 229 11.11 0.00 0.00 chr3ptel1M 994613 994648 (5352) MIR#SINE/MIR 109 144 (118) m_b135s601i24 5044 chr3ptel1M 994613 CCCTGTGTCTCTCAGTTTCCTCATCTGTAAAATGGG 994648 i v vi MIR#SINE/MIR 109 CTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGG 144 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 12.06 CpG sites = 2, Kimura (unadjusted) = 12.06 Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 23 0.00 0.00 0.00 chr3ptel1M 994851 994875 (5125) (A)n#Simple_repeat 1 25 (0) m_b135s252i21 5046 chr3ptel1M 994851 AAAAAAAAAAAAAAAAAAAAAAAAA 994875 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAA 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 47 0.00 0.00 0.00 chr3ptel1M 995250 995289 (4711) (AC)n#Simple_repeat 1 40 (0) c_b135s251i2 5047 chr3ptel1M 995250 ACACACACACACACACACACACACACACACACACACACAC 995289 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACAC 40 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 206 34.24 1.75 2.65 chr3ptel1M 996168 996281 (3719) L3#LINE/CR1 3663 3775 (324) m_b135s601i25 5048 chr3ptel1M 996168 CAGCTAGGAGGCTGAAGGGCCTGGCCCCCGTGTCCCAGAAGGGCCAGTTG 996217 ii i v v i vvv i vi vi iv i L3#LINE/CR1 3663 CGACCAGGATGGTGAAGGGTCTGGAAACCATGTCATATGAGGAACGGTTG 3712 chr3ptel1M 996218 GAGGGAATGTACCTGCTTA-CCT-GAGAAGACGGGGGACAGGTGGGATGA 996265 i i v vivv i - - -- ii vvivi - L3#LINE/CR1 3713 AAGGAACTGGGGATGTTTAGCCTGGAGAAGA--GAAGACTTAGAGGA-GA 3759 chr3ptel1M 996266 TGGGAAAGTTGACTTC 996281 iiv v i v L3#LINE/CR1 3760 CATGATAGCTGTCTTC 3775 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.48 CpG sites = 20, Kimura (unadjusted) = 46.76 Transitions / transversions = 1.11 (20/18) Gap_init rate = 0.04 (5 / 113), avg. gap size = 1.00 (5 / 5) 18 20.47 2.50 0.00 chr3ptel1M 996312 996351 (3649) (TC)n#Simple_repeat 1 41 (0) m_b135s252i22 5049 chr3ptel1M 996312 TCT-TCTTGCTTTCTCTCTGTTCCTCTCCCTCTCTCTCTCT 996351 - iv i v ii i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 41 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1) 54 16.94 0.99 0.00 chr3ptel1M 996686 996786 (3214) (TCC)n#Simple_repeat 1 102 (0) m_b135s252i23 5050 chr3ptel1M 996686 TCCTCCTCCTCC-CCCCTTTCTCTTCTTTCTCCTCCTTCTCCTCCTGTTC 996734 - i i i i i i i vi (TCC)n#Simple 1 TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC 50 chr3ptel1M 996735 TTCCTCCTCCTCCTGCTCCTCCTCCTCCTTGTGCTCCTCCTCCTCCTCTT 996784 i v iv v i (TCC)n#Simple 51 CTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT 100 chr3ptel1M 996785 CC 996786 (TCC)n#Simple 101 CC 102 Matrix = Unknown Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.01 (1 / 100), avg. gap size = 1.00 (1 / 1) 198 22.73 0.00 0.00 chr3ptel1M 996978 997021 (2979) L2b_3end#LINE/L2 402 445 (21) m_b135s601i26 5051 chr3ptel1M 996978 CCAGTGCGTGGCCCAGTGCCTGGCACACAGCCGGTGCCTACTAA 997021 i v i v ? iv i ii v L2b_3end#LINE 402 CCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAA 445 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 22.16 CpG sites = 6, Kimura (unadjusted) = 28.41 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 205 25.37 5.97 0.00 chr3ptel1M 998233 998299 (1701) MIRc#SINE/MIR 93 163 (105) m_b135s601i27 5052 chr3ptel1M 998233 CCTCGGGCACCTCCCCTTCCGACTC--AGCCTTAGTTTCCTCATCTGTGT 998280 i vv v i vv vv -- i iv MIRc#SINE/MIR 93 CCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAA 142 chr3ptel1M 998281 CATGGAG--AATGATGGCTGC 998299 v i -- i iv MIRc#SINE/MIR 143 AATGGGGATAATAATACCTGC 163 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.04 CpG sites = 7, Kimura (unadjusted) = 31.04 Transitions / transversions = 0.70 (7/10) Gap_init rate = 0.03 (2 / 66), avg. gap size = 2.00 (4 / 2) 12 13.67 0.00 0.00 chr3ptel1M 999409 999432 (568) (TGCC)n#Simple_repeat 1 24 (0) m_b135s252i24 5053 chr3ptel1M 999409 TGCCCGCCTGCCTGCCGGCCTTCC 999432 i v v (TGCC)n#Simpl 1 TGCCTGCCTGCCTGCCTGCCTGCC 24 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 34 0.00 0.00 0.00 chr3qtel1M 1994 2024 (997976) (ATC)n#Simple_repeat 1 31 (0) c_b136s251i0 5054 chr3qtel1M 1994 ATCATCATCATCATCATCATCATCATCATCA 2024 (ATC)n#Simple 1 ATCATCATCATCATCATCATCATCATCATCA 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 236 27.59 9.20 0.00 chr3qtel1M 2066 2122 (997878) C L2d2_3end#LINE/L2 (2) 553 491 m_b136s601i0 5055 chr3qtel1M 2066 AAATCA--CTAAGAAACATTTACTAAACGCCTACTGCATACCACGCACTC 2113 --ii v i i i i ii i v v v C L2d2_3end#LIN 553 AAATCAAATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTG 504 chr3qtel1M 2114 TGCTAAAC----T 2122 ii ---- C L2d2_3end#LIN 503 TGCTAGGCGCTGT 491 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 36.83 CpG sites = 17, Kimura (unadjusted) = 36.83 Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.04 (2 / 56), avg. gap size = 3.00 (6 / 2) 31 0.00 0.00 0.00 chr3qtel1M 2123 2151 (997849) (G)n#Simple_repeat 1 29 (0) c_b136s251i1 5056 chr3qtel1M 2123 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG 2151 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG 29 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 236 27.59 9.20 0.00 chr3qtel1M 2152 2180 (997820) C L2d2_3end#LINE/L2 (65) 490 460 m_b136s601i0 5055 chr3qtel1M 2152 AGGTGTAAAAAGAGGCGAAAGAC--GGCCCC 2180 i vi v i iiv -- i C L2d2_3end#LIN 490 GGGGATACAAAGAAGTATAAGACATGGTCCC 460 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 36.83 CpG sites = 17, Kimura (unadjusted) = 36.83 Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.04 (1 / 28), avg. gap size = 2.00 (2 / 1) 41 0.00 0.00 0.00 chr3qtel1M 2572 2609 (997391) (C)n#Simple_repeat 1 38 (0) c_b136s251i2 5057 chr3qtel1M 2572 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 2609 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 38 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 203 28.38 6.67 2.13 chr3qtel1M 2912 3001 (996999) C MIRc#SINE/MIR (39) 229 136 m_b136s601i1 5058 chr3qtel1M 2912 TTTAATAAACGTTTTCTTTCAGTCCTCCCCTCCTCTGATCCCCCTAACAG 2961 vv i i v-- vv v ivi v i i vi i C MIRc#SINE/MIR 229 TTTACAAAGCGCTTTCA--CATACATTATCTCATTTGATCCTCACAACAA 182 chr3qtel1M 2962 CTCGGTGAGG--GGGAGGG-AG---TGGCCATCCCCATTTTAGAGA 3001 i v -- v - --- viii v C MIRc#SINE/MIR 181 CCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGA 136 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 36.03 CpG sites = 12, Kimura (unadjusted) = 36.03 Transitions / transversions = 0.92 (12/13) Gap_init rate = 0.06 (5 / 89), avg. gap size = 1.60 (8 / 5) 230 32.93 0.00 1.22 chr3qtel1M 2994 3076 (996924) C MIRc#SINE/MIR (157) 111 30 m_b136s601i2 5058 chr3qtel1M 2994 TTTAGAGACACTGCCCAGGGCCACAGGGCTGGTGAGTGCTGGAGGAGGAA 3043 v v -i i i vi i i vii vv i C MIRc#SINE/MIR 111 TTAAGTGAC-TTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGA 63 chr3qtel1M 3044 CCTGGATTCAAGTCTTGCTGCCCCCCAGACAAG 3076 ii i ii i v v i v v v C MIRc#SINE/MIR 62 CTCGAACCCAGGTCTTCCTGACTCCAAGTCCAG 30 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 42.71 CpG sites = 16, Kimura (unadjusted) = 44.97 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.01 (1 / 82), avg. gap size = 1.00 (1 / 1) 13 7.52 7.14 0.00 chr3qtel1M 3228 3255 (996745) (GGGGA)n#Simple_repeat 1 30 (0) m_b136s252i0 5059 chr3qtel1M 3228 GGGGAGGGGATGGG-GGGGA-AGGAGGGGA 3255 v - -i (GGGGA)n#Simp 1 GGGGAGGGGAGGGGAGGGGAGGGGAGGGGA 30 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.07 (2 / 27), avg. gap size = 1.00 (2 / 2) 40 14.53 1.10 4.55 chr3qtel1M 3319 3409 (996591) (AAAAAG)n#Simple_repeat 1 88 (0) m_b136s252i1 5060 chr3qtel1M 3319 AACAACAAAAGGAAAAAAGAAAAACAAAACACAGTAAAAAAAAAAAAAAG 3368 v v i - v - v iv i i (AAAAAG)n#Sim 1 AAAAAGAAAAAG-AAAAAGAAAAAGAAAA-AGAAAAAGAAAAAGAAAAAG 48 chr3qtel1M 3369 -AAAAGAAAAAGAAAAAGAAAGAAAGAGAAAGAAAAATAAAA 3409 - - - i v (AAAAAG)n#Sim 49 AAAAAGAAAAAGAAAAAG-AA-AAAGAAAAAGAAAAAGAAAA 88 Matrix = Unknown Transitions / transversions = 0.83 (5/6) Gap_init rate = 0.06 (5 / 90), avg. gap size = 1.00 (5 / 5) 261 23.08 4.62 0.00 chr3qtel1M 3460 3524 (996476) C L2d2_3end#LINE/L2 (23) 532 465 m_b136s601i3 5061 chr3qtel1M 3460 ACTAAGTGGCCACTGTGCGCCAGGCACCGCGCTAAGCCCT---GGGGATA 3506 i i i v i i v i i i v --- C L2d2_3end#LIN 532 ATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGTGGGGGATA 483 chr3qtel1M 3507 CAAAGAGGCAAACGACAT 3524 i i v v C L2d2_3end#LIN 482 CAAAGAAGTATAAGACAT 465 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 26.25 CpG sites = 10, Kimura (unadjusted) = 28.45 Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.02 (1 / 64), avg. gap size = 3.00 (3 / 1) 12 8.02 7.41 0.00 chr3qtel1M 4852 4878 (995122) (GGGA)n#Simple_repeat 1 29 (0) m_b136s252i2 5062 chr3qtel1M 4852 GGGAGGGA-GG-GGGAAGAAGGGAGGGAG 4878 - - i i (GGGA)n#Simpl 1 GGGAGGGAGGGAGGGAGGGAGGGAGGGAG 29 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.08 (2 / 26), avg. gap size = 1.00 (2 / 2) 209 29.39 3.03 4.62 chr3qtel1M 5143 5274 (994726) C L2#LINE/L2 (2945) 137 8 m_b136s601i4 5063 chr3qtel1M 5143 AGTCTAGGTGTTAGAAGGAGGGAGGGGTTCTGTGATCATGTCTCTCACTG 5192 --- ii i v v v i - v ii v v - ? v C L2#LINE/L2 137 AGTCT---TGCCAGGAGCACGCAGAG-TTCTGGGGCCCTCTCT-TNACTC 93 chr3qtel1M 5193 CTCCCAGTT-TGATTCTGAAGCCACGGGAGGGCAGTTTTG-TCCGAGCAG 5240 v ii v-? iiviv i ?v i i i- ? - C L2#LINE/L2 92 CTGCCGATGGNGGCGTGGAGGCCNGGGGAGGGCGGTCTTACTCNGAGC-G 44 chr3qtel1M 5241 CATGGGAATGCCTTGTGTCTCT--CAGAGGGAGGCT 5274 iv v iv v i i-- v v C L2#LINE/L2 43 CATGGGGCTCCCTCTTGACCCCTGCCGATGGAGGCT 8 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 35.53 CpG sites = 19, Kimura (unadjusted) = 39.46 Transitions / transversions = 1.06 (19/18) Gap_init rate = 0.07 (9 / 131), avg. gap size = 1.11 (10 / 9) 67 16.59 0.83 0.00 chr3qtel1M 5684 5804 (994196) (AC)n#Simple_repeat 1 122 (0) m_b136s252i3 5064 chr3qtel1M 5684 ACAGACAGACAGACACACACACACACACACACACACACACGGGGGCACAA 5733 v v v ivivi v (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50 chr3qtel1M 5734 AGAGACAGAGACACACA-ACACAAACATACATACATACATACACACACAC 5782 v v v v - v i i i i (AC)n#Simple_ 51 ACACACACACACACACACACACACACACACACACACACACACACACACAC 100 chr3qtel1M 5783 ACACACACACACACACACACAC 5804 (AC)n#Simple_ 101 ACACACACACACACACACACAC 122 Matrix = Unknown Transitions / transversions = 0.64 (7/11) Gap_init rate = 0.01 (1 / 120), avg. gap size = 1.00 (1 / 1) 409 26.28 8.82 2.07 chr3qtel1M 5816 5951 (994049) MIRc#SINE/MIR 4 148 (120) m_b136s601i5 5065 chr3qtel1M 5816 GACAGTGGGATGGTGCAATGGATAGAACGTAGGGCCCAGAGTCAGGAGGA 5865 i --- i v i iiv i iii i MIRc#SINE/MIR 4 GGCAGTG---TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA 50 chr3qtel1M 5866 CCCGAGTTCAAGTTCACTCGTAAACACTTCC------TGTGAC--TGGGT 5907 i i i i vvv viviv v ------ -- i MIRc#SINE/MIR 51 CCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGC 100 chr3qtel1M 5908 AAG--ACTGTGCCCGTCC--GTCTCAGTTTCCTCCTCTGTAAAATGAG 5951 -- vvi iv i-- i v i MIRc#SINE/MIR 101 AAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 32.25 CpG sites = 22, Kimura (unadjusted) = 33.42 Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.05 (7 / 135), avg. gap size = 2.14 (15 / 7) 363 31.08 4.13 1.61 chr3qtel1M 6471 6591 (993409) L2b_3end#LINE/L2 335 458 (8) m_b136s601i6 5066 chr3qtel1M 6471 TCTCCCCCCTTTCAGACCAAAAACTCTTAGAGGGCAGGAAGCAGGTCTCT 6520 vi -- iivi i ivv i v i? v L2b_3end#LINE 335 TCTCCCCCACT--AGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGT 382 chr3qtel1M 6521 TTTTATTA--ATTGGATCCCCAGAGCTGAGCACAGTGTTCAACACA---T 6565 i vv i --ii v v iv ? iiiii --- L2b_3end#LINE 383 CTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGT 432 chr3qtel1M 6566 AGACGTTTAATAAGTGTTTATTGGAT 6591 i i i i i i i i L2b_3end#LINE 433 AGGCGCTCAGTAAATATTTGTTGAAT 458 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 39.10 CpG sites = 26, Kimura (unadjusted) = 43.87 Transitions / transversions = 2.36 (26/11) Gap_init rate = 0.03 (4 / 120), avg. gap size = 1.75 (7 / 4) 379 25.44 9.91 0.83 chr3qtel1M 7993 8103 (991897) C MIRc#SINE/MIR (138) 130 10 m_b136s601i7 5067 chr3qtel1M 7993 AGACTAAGGCAAACACAGGTTAAAGTGACTTGCCTAGGATCACACAGCTA 8042 i i vv v v - i i i C MIRc#SINE/MIR 130 AAACTGAGGCTCAGAGAGGTTAA-GTGACTTGCCCAAGGTCACACAGCTA 82 chr3qtel1M 8043 AGCTATG-------TAAGATTTGAACTCAGTTCTTCCTG----CAGGCCC 8081 ivvvi -------iii i i i v ---- i i C MIRc#SINE/MIR 81 GTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCC 32 chr3qtel1M 8082 AGCACTCTATCCCCTGCGCCAC 8103 ii v v i C MIRc#SINE/MIR 31 AGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 29.21 CpG sites = 18, Kimura (unadjusted) = 32.10 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.03 (3 / 110), avg. gap size = 4.00 (12 / 3) 524 25.78 0.68 5.67 chr3qtel1M 9243 9390 (990610) C MIRc#SINE/MIR (122) 146 6 m_b136s601i8 5068 chr3qtel1M 9243 CATTTTACAGATGGGGAAATGGAGGCAAACAG-GATTAAGAGACTTGCCC 9291 i iv vv v - i v C MIRc#SINE/MIR 146 CATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCC 97 chr3qtel1M 9292 AGAGTCACACAACTTTTAAGTATCTGAGGCCAGATTTGAATTCAGGAAGA 9341 ii i vv iv v v vi i i ii ----- C MIRc#SINE/MIR 96 AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAG----- 52 chr3qtel1M 9342 GAAGCCTCCCTCACACCAGGCCAGGTACTCTATCCACTACACCACCTTG 9390 --- i i v v i i vi i v i vi C MIRc#SINE/MIR 51 ---GTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTG 6 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 30.97 CpG sites = 20, Kimura (unadjusted) = 32.03 Transitions / transversions = 1.25 (20/16) Gap_init rate = 0.06 (9 / 147), avg. gap size = 1.00 (9 / 9) 15 5.56 0.00 0.00 chr3qtel1M 9589 9607 (990393) (A)n#Simple_repeat 1 19 (0) m_b136s252i4 5069 chr3qtel1M 9589 AAAAAGAAAAAAAAAAAAA 9607 i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAA 19 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 22 4.00 0.00 0.00 chr3qtel1M 9742 9767 (990233) (A)n#Simple_repeat 1 26 (0) m_b136s252i5 5070 chr3qtel1M 9742 AAAAGAAAAAAAAAAAAAAAAAAAAA 9767 i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAA 26 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 446 31.71 6.05 3.17 chr3qtel1M 10357 10571 (989429) L1MD1_3end#LINE/L1 361 581 (408) m_b136s551i0 5071 chr3qtel1M 10357 CCATCCAACTGGGCAGTGCTACTACTGGGCTTCTATCCCAGAGAT----- 10401 v i ivi i vvi v v i v----- L1MD1_3end#LI 361 CCATACGACCCAGCAATTGCACTCCTGGGCATTTATCCCAGAGAAATGAA 410 chr3qtel1M 10402 --CTTACAGGAGGGACAGGGACCTGTATGTGCACGAGTGTTTGTGGCAGC 10449 -- i- vvviv iii ---- i i i L1MD1_3end#LI 411 AACTTAT-GTTCACACAAAAACCTGTA----CACGAATGTTTATAGCAGC 455 chr3qtel1M 10450 CCTCTTTGGAGTGGCCAGAAACTGGAAACAG--TGGATGCCCATCAGCTG 10497 ii v i v i i i i--ii i v i v L1MD1_3end#LI 456 TTTATTCGTAATAGCCAAAAACTGGAAACAACCCAGATGTCCTTCAACGG 505 chr3qtel1M 10498 GGGAATGGCTGAACAAGTGATTGTA----TATGTTAGGGAATATTATTGT 10543 v i i iivi v ----i iii v i i vv L1MD1_3end#LI 506 GTGAATGGTTAAACAAACTGTGGTACATCCATACCATGGAATACTACTCA 555 chr3qtel1M 10544 TCTATAAGAAACAAGGGGCTTAGTTGAT 10571 v v i iv v ii --i L1MD1_3end#LI 556 GCAATAAAAAGGAACGAACT--ATTGAT 581 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 41.24 CpG sites = 41, Kimura (unadjusted) = 42.99 Transitions / transversions = 1.64 (41/25) Gap_init rate = 0.05 (11 / 214), avg. gap size = 1.82 (20 / 11) 457 27.19 6.40 1.67 chr3qtel1M 10369 10540 (989460) L1ME3G_3end#LINE/L1 369 548 (376) m_b136s551i1 5071 chr3qtel1M 10369 GCAGTGCTACTACTGGGCTTCTATCCCAGAGA-----TCTTACAGGAGGG 10413 i v i v ? ?v i ? ----- vi v -v v L1ME3G_3end#L 369 GCAATTCCACTTCTNGGNATCTATCCTANAGAAATACTCGCACATG-TGC 417 chr3qtel1M 10414 ACAGGGACCTGTATGTGCACGAGTGTTTGTGGCAGCCCTCTTTGGAGTGG 10463 i ?-- i i v ii ii v vi v v i i L1ME3G_3end#L 418 ACAAGGAN--GCATGTACAAGGATGTTCATTGCAGCATTGTTTGTAATAG 465 chr3qtel1M 10464 CCAGAAACTGGAAACAG--TGGATGCCCATCAGCTGGGGAATGGCTGAAC 10511 v i i i-- ii i iiv i i i L1ME3G_3end#L 466 CGAAAAATTGGAAACAACCTAAATGTCCATCAATAGGGGAATGGTTAAAT 515 chr3qtel1M 10512 AAGTGATTGTAT----ATGTTAGGGAATATTAT 10540 i v v ---- ii v i L1ME3G_3end#L 516 AAATTATGGTATATCCATACTATGGAATACTAT 548 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 36.08 CpG sites = 29, Kimura (unadjusted) = 36.08 Transitions / transversions = 1.71 (29/17) Gap_init rate = 0.04 (6 / 171), avg. gap size = 2.33 (14 / 6) 433 22.48 0.71 11.02 chr3qtel1M 10631 10770 (989230) C MIRb#SINE/MIR (138) 130 4 m_b136s601i9 5072 chr3qtel1M 10631 CTGAGGCA-ATTGGGGTTAAGTGACTTGCCCGGGGTCACACAGCTGGGAA 10679 v- vv i i ii i --- C MIRb#SINE/MIR 130 CTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAG--- 84 chr3qtel1M 10680 GTATTAAGTGTCTGAGACCAGATTTGAACTCGGGTGCTCCCGACTTCAGG 10729 ---- v v v vi i i i vivi i i ii C MIRb#SINE/MIR 83 ----TAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAA 38 chr3qtel1M 10730 GCTGGTGCTCTCTCCACTGCGCCTGCCACCCAGCTGCCCCT 10770 iv i ----i --- C MIRb#SINE/MIR 37 GCCCGTGCTCTTTCCACTGC----ACCAC---GCTGCCCCT 4 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 25.92 CpG sites = 18, Kimura (unadjusted) = 27.03 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.11 (15 / 139), avg. gap size = 1.00 (15 / 15) 468 22.68 0.82 6.03 chr3qtel1M 10631 10752 (989248) C MIRc#SINE/MIR (141) 127 12 m_b136s601i10 5072 chr3qtel1M 10631 CTGAGGCA-ATTGGGGTTAAGTGACTTGCCCGGGGTCACACAGCTGGGAA 10679 v- vv i ii i --- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG--- 81 chr3qtel1M 10680 GTATTAAGTGTCTGAGACCAGATTTGAACTCGGGTGCTCCCGACTTCAGG 10729 ---- v v v vi i i i i vi i i i C MIRc#SINE/MIR 80 ----TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr3qtel1M 10730 GCTGGTGCTCTCTCCACTGCGCC 10752 v ii i i C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTGCACC 12 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 26.43 CpG sites = 17, Kimura (unadjusted) = 27.67 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.07 (8 / 121), avg. gap size = 1.00 (8 / 8) 16 0.00 0.00 0.00 chr3qtel1M 11319 11336 (988664) (C)n#Simple_repeat 1 18 (0) m_b136s252i6 5073 chr3qtel1M 11319 CCCCCCCCCCCCCCCCCC 11336 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCC 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 19 8.91 5.56 0.00 chr3qtel1M 11686 11721 (988279) (CCT)n#Simple_repeat 1 38 (0) m_b136s252i7 5074 chr3qtel1M 11686 CCTCC-CCACCTCCTCCTCTTCC-CCTCCTCCTCCCCC 11721 - v i - i (CCT)n#Simple 1 CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC 38 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 19 19.22 0.00 0.00 chr3qtel1M 11761 11796 (988204) (G)n#Simple_repeat 1 36 (0) m_b136s252i9 5075 chr3qtel1M 11761 GGGAGGGGCGGGGGAGGGGCGGGGAGGGGGAGGGGG 11796 i v i v i i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 36 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 12 15.85 9.52 0.00 chr3qtel1M 12070 12111 (987889) (GACAG)n#Simple_repeat 1 46 (0) m_b136s252i10 5076 chr3qtel1M 12070 GACCGGA-GGGACAGCACAGGACTGGA-AGG--AGAACAGGTCAGG 12111 v -i v v - -- i v (GACAG)n#Simp 1 GACAGGACAGGACAGGACAGGACAGGACAGGACAGGACAGGACAGG 46 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.07 (3 / 41), avg. gap size = 1.33 (4 / 3) 28 23.17 0.81 8.70 chr3qtel1M 12733 12856 (987144) (CCCCCG)n#Simple_repeat 1 115 (0) m_b136s252i11 5077 chr3qtel1M 12733 CCGCCGCCCCC-TCCCCGCCCGGCAGGGCCCCGCCCCCGTGACCTCCCGC 12781 v -i -- -v v -- - - (CCCCCG)n#Sim 1 CCCCCGCCCCCGCCCCCGCCC--C-CGCCCCCGCCCCC--G-CC-CCCGC 43 chr3qtel1M 12782 CCCGGCCCCCGGCCCAGGTCCGTGGAATCCTGCCCCTCCCCCGCTGCCCG 12831 v - vv - viv vvi vv v -v (CCCCCG)n#Sim 44 CCCCGCCCCC-GCCCCCG-CCCCCGCCCCCGCCCCCGCCCCCGC-CCCCG 90 chr3qtel1M 12832 CCCCCGCCCTCCCCCCCACTCCCGC 12856 i v i i (CCCCCG)n#Sim 91 CCCCCGCCCCCGCCCCCGCCCCCGC 115 Matrix = Unknown Transitions / transversions = 0.40 (6/15) Gap_init rate = 0.09 (11 / 123), avg. gap size = 1.00 (11 / 11) 22 22.67 0.00 0.00 chr3qtel1M 17130 17175 (982825) (A)n#Simple_repeat 1 46 (0) m_b136s252i12 5078 chr3qtel1M 17130 AAAAAAAAAAAATTAAACCAAAAAGGGAAAAAAACTAAAAAAAAAA 17175 vv vv iii vv (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 46 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 22 19.25 0.00 0.00 chr3qtel1M 17847 17888 (982112) (C)n#Simple_repeat 1 42 (0) m_b136s252i13 5079 chr3qtel1M 17847 CCCCCCCCCCCCGCCCCCAAAAACCCCCCCCCCCCCGCCCCC 17888 v vvvvv v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 42 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 18 8.86 2.50 5.13 chr3qtel1M 17890 17929 (982071) (AAAAC)n#Simple_repeat 1 39 (0) m_b136s252i14 5080 chr3qtel1M 17890 AAAACAAAACCAAACCAAA-AAAACAAAAAGCCAAACAAAA 17929 v v - - - v (AAAAC)n#Simp 1 AAAACAAAACAAAACAAAACAAAAC-AAAA-CAAAACAAAA 39 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.08 (3 / 39), avg. gap size = 1.00 (3 / 3) 93 8.91 0.00 0.00 chr3qtel1M 18195 18325 (981675) (C)n#Simple_repeat 1 131 (0) c_b136s251i3 5081 chr3qtel1M 18195 CCCCCCCCTCCCCCACCCCCCAAACCCCCCCCCCCCCCTCCCCCCCCCCC 18244 i v vvv i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 50 chr3qtel1M 18245 ACTCCCCCCCCCCCCCCAACCCCCCCCCCCCCCCCCCCCCCCCACCCCCC 18294 v i vv v (C)n#Simple_r 51 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 100 chr3qtel1M 18295 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 18325 (C)n#Simple_r 101 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 131 Matrix = Unknown Transitions / transversions = 0.38 (3/8) Gap_init rate = 0.00 (0 / 130), avg. gap size = 0.0 (0 / 0) 19 0.00 0.00 0.00 chr3qtel1M 18950 18970 (981030) (C)n#Simple_repeat 1 21 (0) m_b136s252i15 5082 chr3qtel1M 18950 CCCCCCCCCCCCCCCCCCCCC 18970 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCC 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 20 11.25 0.00 0.00 chr3qtel1M 19071 19099 (980901) (C)n#Simple_repeat 1 29 (0) m_b136s252i16 5083 chr3qtel1M 19071 CCCCCCCCGTCCCCCCCCCTCCCCCCCCC 19099 vi i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC 29 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 269 28.93 1.18 2.38 chr3qtel1M 19825 19909 (980091) MIRc#SINE/MIR 96 179 (89) m_b136s601i11 5084 chr3qtel1M 19825 TGAATGAGTCACGCTCGCCTTCTCCAA-CCTCAGTTTCTTCATCTGAGAA 19873 iiii -- iiv i ii - i vi MIRc#SINE/MIR 96 TGGGCAAGTCAC--TTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAA 143 chr3qtel1M 19874 ATGGGCGGAAGAAGTCCCTCAGTGCCTGCCTCACAG 19909 viv v vv iv vv i MIRc#SINE/MIR 144 ATGGGGATAATAATACCTGCCCTGCCTACCTCACAG 179 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 37.50 CpG sites = 14, Kimura (unadjusted) = 37.50 Transitions / transversions = 1.40 (14/10) Gap_init rate = 0.04 (3 / 84), avg. gap size = 1.00 (3 / 3) 18 25.04 0.00 1.89 chr3qtel1M 20270 20323 (979677) (GAG)n#Simple_repeat 1 53 (0) m_b136s252i17 5085 chr3qtel1M 20270 GAGGAGAAGGAGGAGGAGGGGGAGGGGTAGTGAAGATGGTGATGAGGGGG 20319 i i i v - i v iv v i (GAG)n#Simple 1 GAGGAGGAGGAGGAGGAGGAGGAGGAGGAG-GAGGAGGAGGAGGAGGAGG 49 chr3qtel1M 20320 TGGA 20323 v (GAG)n#Simple 50 AGGA 53 Matrix = Unknown Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.02 (1 / 53), avg. gap size = 1.00 (1 / 1) 24 25.08 0.00 0.00 chr3qtel1M 21035 21096 (978904) (AGGA)n#Simple_repeat 1 62 (0) m_b136s252i18 5086 chr3qtel1M 21035 AGGCAGGCAGGTAGATGGGAAGGAGGGAAGGAAGGGAGGAACGGAGGGAG 21084 v v v ivi i i v i i (AGGA)n#Simpl 1 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG 50 chr3qtel1M 21085 GGAGGAAGGGAG 21096 i i (AGGA)n#Simpl 51 GAAGGAAGGAAG 62 Matrix = Unknown Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0) 290 30.52 8.70 2.34 chr3qtel1M 21348 21508 (978492) C L3#LINE/CR1 (1223) 2876 2706 m_b136s601i12 5087 chr3qtel1M 21348 ATGATTTAGTCCCAATGAG-------TGAATCTTAGTAATTA--GAT--C 21386 i iv ii i i------- iv i i i -- v -- C L3#LINE/CR1 2876 ATGACTTGTTCTTAGTGAACCCATGCTGGCTCCTAGTGATCACCGCTTCC 2827 chr3qtel1M 21387 TTTTCTGAATGCTCACAAACTTTATGTTTATTGATGATTAATTC---AGT 21433 i i iv v --- i ivi --- i C L3#LINE/CR1 2826 TTTTCTAAGTGCTCACAAACCATCTGTTTA---ATAATCCGTTCTAGAAT 2780 chr3qtel1M 21434 TTGGCCCCAAATCAGCACCAGTTTTATCAGTTTGTAGTTTTCACAGATAG 21483 v vvii ii ii ivi i i i ? v - vv C L3#LINE/CR1 2779 TTTGCCGGGGATCGACGTCAAGCTTACCGGTCTGTAGTTTNCAGA-ATCC 2731 chr3qtel1M 21484 CAGATTTCTCCTTTTTTGAAAATAG 21508 vvvv i i i ? C L3#LINE/CR1 2730 ATCTTTTTTCCCTTTTTAAAANTAG 2706 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 37.30 CpG sites = 31, Kimura (unadjusted) = 41.83 Transitions / transversions = 1.82 (31/17) Gap_init rate = 0.05 (8 / 160), avg. gap size = 2.25 (18 / 8) 387 20.59 0.00 7.23 chr3qtel1M 21537 21625 (978375) MIRc#SINE/MIR 37 119 (149) m_b136s601i13 5088 chr3qtel1M 21537 TGAAGTCAGGAAGACCCGAGTTCAGATATGATTCCAGACATTAACACTTA 21586 i i i ------ v v i vi iv MIRc#SINE/MIR 37 TGGAGTCAGGAAGACCTGGGTTC------GAGTCCCGGCTCTGCCACTTA 80 chr3qtel1M 21587 CTACCTGTGTGATTCTGGGCAAGTCACGTAACCCCACTG 21625 v iii v i v MIRc#SINE/MIR 81 CTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTG 119 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 24.29 CpG sites = 10, Kimura (unadjusted) = 24.29 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.07 (6 / 88), avg. gap size = 1.00 (6 / 6) 50 4.00 0.00 0.00 chr3qtel1M 26230 26281 (973719) (AT)n#Simple_repeat 1 52 (0) c_b136s251i4 5089 chr3qtel1M 26230 ATATATATATACATACATATATATATATATATATATATATATATATATAT 26279 i i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr3qtel1M 26280 AT 26281 (AT)n#Simple_ 51 AT 52 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 285 34.19 4.78 3.04 chr3qtel1M 26358 26713 (973287) C L1ME4a_3end#LINE/L1 (382) 489 128 m_b136s551i2 5090 chr3qtel1M 26358 TCGTTTCAAATATCTTGCTACCATGAAGAGTGCTGCTCTTAGATATT-TT 26406 i v v i i ii i v i vv v - i i- C L1ME4a_3end#L 489 TTGTTTCCAATTTTTCGCTATTATAAATAATGCTGCGATGA-ACATCCTT 441 chr3qtel1M 26407 GTACAGATTGGACTTTTGTTTCTCTCTTTGACT---TCCTTGGGCTACGT 26453 --- ii ii ?iviv i i --- i v vi C L1ME4a_3end#L 440 GTACA---TAAATCTTTGTNCACATCTCTGATTATTTCCTTAGGATAAAT 394 chr3qtel1M 26454 ACCGGGTAGTGAGCTATCTGGGTTAAAAGG-ATAGACATTCT--AGCCAA 26500 v vi v iiv vv i i - i? i -- v vv C L1ME4a_3end#L 393 TCCTAGAAGTGGAATTACTGGGTCAAAGGGTATGNACATTTTTAAGGCTT 344 chr3qtel1M 26501 TT--TACTTGGGTGATT-TCAAACCAAAAGCCACCATGTTCAGACTGCTT 26547 -- v ----- -i iiivvvv vv v v iiv iiv C L1ME4a_3end#L 343 TTGATACAT-----ATTGCCAAATTGCCCTCCAGAAAGGTTGTACCAATT 299 chr3qtel1M 26548 CACAGTTC-ACCAAAAAAGCATTGGGGTGCCTGTTTTTCCATGGTTTCTT 26596 i v i - iv iv i vi i i i? iivii vi C L1ME4a_3end#L 298 TACACTCCCACCAGCAGTGTATGAGAGTGCCCGTTTCNCCACACCCTCGC 249 chr3qtel1M 26597 CA---CTG--TGGTTCCCATTTTTTATTATCTAAGCCAATTTGCATAGG- 26640 --- -- iv vi v i v- vv - - C L1ME4a_3end#L 248 CAACACTGGGTATTATCAATCTTTTAA-ATCTTTGCCAATTTG-ATAGGT 201 chr3qtel1M 26641 GTAAGGTAAAACTGAGAAGTTATTTTCATTTGGATTTCTTGTACTGTTAG 26690 v ii iiv iivvivv i v v vv i ii C L1ME4a_3end#L 200 GAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCTTTGATTACTAG 151 chr3qtel1M 26691 TGACTTAGAATATATTTTCATAT 26713 vv v i ? C L1ME4a_3end#L 150 TGAGGTTGAACATNTTTTCATAT 128 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 46.46 CpG sites = 63, Kimura (unadjusted) = 47.57 Transitions / transversions = 1.15 (63/55) Gap_init rate = 0.06 (21 / 355), avg. gap size = 1.33 (28 / 21) 443 27.89 10.53 0.00 chr3qtel1M 27635 27824 (972176) C L3#LINE/CR1 (149) 3950 3741 m_b136s601i14 5091 chr3qtel1M 27635 CCTCACG--GTAGCACTTTCCACTTGGGGTC-GCTCTAAGAGT----AAA 27677 ? -- i v v i vv v - i vv ---- i C L3#LINE/CR1 3950 CCTCNCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGATTGTTAGAAAG 3901 chr3qtel1M 27678 TTTTTGCTTCTATCGAAACTACATTTACCTCTTTGCAGCGTACCCCC-TT 27726 i v v i iv v v i i ii i i v v v - C L3#LINE/CR1 3900 TTCTTCCTTATATTGAGCCGAAATCTGCCTCCCTGTAACTTCCACCCATT 3851 chr3qtel1M 27727 GCTCCCGTTTCTGCCCTTGAGA-------AGACTG-GCC--ATCCCCCTT 27766 v iiv ivi ------- v i- i -- i C L3#LINE/CR1 3850 GGTCCTAGTTCTGCCCTCTGGAGCCACACAGAATAAGTCTAATCCCTCTT 3801 chr3qtel1M 27767 CCACGGGATGGCCTCTCAGATACTTGAAGACAGTTACCACGG-TCC-CCA 27814 iv ii ii i i i i i v- - i C L3#LINE/CR1 3800 CCACATGACAGCCCTTCAAATATTTGAAGACAGCTATCATGTCTCCTCTA 3751 chr3qtel1M 27815 GGTCTTCTCT 27824 i C L3#LINE/CR1 3750 AGTCTTCTCT 3741 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 36.15 CpG sites = 32, Kimura (unadjusted) = 36.15 Transitions / transversions = 1.52 (32/21) Gap_init rate = 0.05 (9 / 189), avg. gap size = 2.22 (20 / 9) 427 31.48 1.36 5.16 chr3qtel1M 27949 28169 (971831) C Plat_L3#LINE/CR1 (559) 3014 2802 m_b136s551i3 5092 chr3qtel1M 27949 ACTCTTGGAAGCCATACCTCTCTTAGAGCAGGCAGCCTGAAATCACCTTC 27998 v v i ii v ---- vi v iiiv i v v C Plat_L3#LINE/ 3014 ACTCTTGCATGTCATACTCCTGTTA----ATACATCCCAGTACCACGTTG 2969 chr3qtel1M 27999 GATTTCCTGGCTGTTGACTCC-CATT--TGACTCATATTGAGCTTTTAGT 28045 v ii ii- ivi i v i- -- v ? i C Plat_L3#LINE/ 2968 GCTTTTTTAA-TAACGGCACTACATTGCTGACTCATATTCAGCTTNTGGT 2920 chr3qtel1M 28046 CCACTAGAACTGCCAGGTCTTTTTCAGACAAAAATCCTGTCTGTCTAATC 28095 v vi iv v viiv --- i -- i ii C Plat_L3#LINE/ 2919 CGACTATGACCCCCAGGTCTTTTTCTGCTGTA---CTTG--TGCCTAGCC 2875 chr3qtel1M 28096 ACGCTTTCCCCCATTGTGTATTTGTGAAGTTGTTTTCTTGAACCTGAGCG 28145 - ii i iv vi vv i i vv i i C Plat_L3#LINE/ 2874 A-GTCTTTCCCCATCCTGTATTTGTGCGGTTTGTTTTTCGTCCCTAAGTG 2826 chr3qtel1M 28146 TAAGATTTTACATTTGTTCCTATT 28169 i vv ii i i i C Plat_L3#LINE/ 2825 CACTACCTTGCACTTGTCCCTATT 2802 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 39.98 CpG sites = 40, Kimura (unadjusted) = 42.53 Transitions / transversions = 1.54 (40/26) Gap_init rate = 0.06 (13 / 220), avg. gap size = 1.08 (14 / 13) 15 26.95 2.08 0.00 chr3qtel1M 28291 28338 (971662) (TGTATA)n#Simple_repeat 1 49 (0) m_b136s252i20 5093 chr3qtel1M 28291 TGTACGTGTATATGTAT-TGTGTATGTGCGTGTGTATATACATATATAT 28338 ii - i iii i i i i (TGTATA)n#Sim 1 TGTATATGTATATGTATATGTATATGTATATGTATATGTATATGTATAT 49 Matrix = Unknown Transitions / transversions = 1.00 (10/0) Gap_init rate = 0.02 (1 / 47), avg. gap size = 1.00 (1 / 1) 12 9.78 0.00 0.00 chr3qtel1M 28515 28536 (971464) (AATA)n#Simple_repeat 1 22 (0) m_b136s252i21 5094 chr3qtel1M 28515 AATTAAAAAATAAATAAATAAA 28536 v v (AATA)n#Simpl 1 AATAAATAAATAAATAAATAAA 22 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 13 18.08 5.26 0.00 chr3qtel1M 30197 30234 (969766) (GGCCCT)n#Simple_repeat 1 40 (0) m_b136s252i22 5095 chr3qtel1M 30197 GGCCCGGGCCCTGGCCCTTTCCCT-CCCCGGGGCC-GGCC 30234 v vv -v v v - (GGCCCT)n#Sim 1 GGCCCTGGCCCTGGCCCTGGCCCTGGCCCTGGCCCTGGCC 40 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 154 28.03 2.77 1.46 chr3qtel1M 31431 31971 (968029) (ATCT)n#Simple_repeat 1 548 (0) m_b136s252i23 5096 chr3qtel1M 31431 ATCAATC-ATCTATC-ATCCATCCATATATCTGTCTTTC-ATCTGTCCAT 31477 v - - i i v i v - i i (ATCT)n#Simpl 1 ATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTAT 50 chr3qtel1M 31478 CCATC-ATCCATCCATCCATCTATCAATC-ATCCAACTATCCACCCATTT 31525 i - i i i v - i v i i i i (ATCT)n#Simpl 51 CTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCT 100 chr3qtel1M 31526 ATCCATCTATTCATCTATCAATC-ATCCATCCATTCATTTATCCATCTAT 31574 i ii v - i i ii i i (ATCT)n#Simpl 101 ATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTAT 150 chr3qtel1M 31575 C-ATCTGTCCATCCATCTATCCATCCAGTTATCCATCCAGCTATCTATAC 31623 - i i i i i vi i i v vi (ATCT)n#Simpl 151 CTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCT 200 chr3qtel1M 31624 ATCTATCTATC-ATCCATCCATTTATCCATCTATC-ATCTCTCCATCTAT 31671 - i i i i - v i (ATCT)n#Simpl 201 ATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTAT 250 chr3qtel1M 31672 CTGTCTATC-ATCTGTCCATCCATTTATCTATCCAGCTATCTAGCTATAC 31720 i - i i i i i v v vi (ATCT)n#Simpl 251 CTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCT 300 chr3qtel1M 31721 ATCTGTCCATCCATCCATCCATTTCTCTCTCTGTCTCTGTCTCTCTGTCT 31770 i i i i i i v v i v v v v v v (ATCT)n#Simpl 301 ATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTAT 350 chr3qtel1M 31771 CTGTCTCTCTCCTCTCCTCTCTCTCTCTCTCTTTCTCTCTCTCTGTCTCC 31820 i v -v -v v v v v v v i -v (ATCT)n#Simpl 351 CTATCTATCT-ATCT-ATCTATCTATCTATCTATCTATCTATCTATCT-A 397 chr3qtel1M 31821 TCTGTCTCCTCCCCTCTCTCTTTTCT-TCTGTCTCCTTCTCTCTCT-TCT 31868 i -v - iv v - v - i vii v v - (ATCT)n#Simpl 398 TCTATCT-AT-CTATCTATC-TATCTATCTATCTATCTATCTATCTATCT 444 chr3qtel1M 31869 CTCTTCCTCTCTCTCTCTCTCTCTCTCTGTCT-TCTCTCTCT-TGTCTGT 31916 v vi v v v v v i - v v - i i (ATCT)n#Simpl 445 ATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTAT 494 chr3qtel1M 31917 CTCTCTCTCTCTTCTCTCCCTCTCTCTGTCTTTCTGTCT-TCTTTCTCTT 31965 v v -v v iv v i v i - v -v (ATCT)n#Simpl 495 CTATCTATCT-ATCTATCTATCTATCTATCTATCTATCTATCTATCT-AT 542 chr3qtel1M 31966 CTCTCT 31971 v (ATCT)n#Simpl 543 CTATCT 548 Matrix = Unknown Transitions / transversions = 1.14 (65/57) Gap_init rate = 0.04 (23 / 540), avg. gap size = 1.00 (23 / 23) 193 20.23 4.64 0.78 chr3qtel1M 31652 32147 (967853) (TC)n#Simple_repeat 1 515 (0) m_b136s252i24 5096 chr3qtel1M 31652 TCTATCATCTCTCCATCTATCTGTCTATCATCTGTCCATCCATTTATCTA 31701 v - iv v v v - v iv iv i v v (TC)n#Simple_ 1 TCTCTC-TCTCTCTCTCTCTCTCTCTCTC-TCTCTCTCTCTCTCTCTCTC 48 chr3qtel1M 31702 TCCAGCTATCTAGCTATACATCTGTCCATCCATCCATCCATTTCTCTCTC 31751 ivv v vv v - - v iv iv iv iv i (TC)n#Simple_ 49 TCTCTCTCTCTCTCTCT-C-TCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 96 chr3qtel1M 31752 TGTCTCTGTCTCTCTGTCTCTGTCTCTCTC-CTCTC-CTCTCTCTCTCTC 31799 v v v v - - (TC)n#Simple_ 97 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 146 chr3qtel1M 31800 TCTTTCTCTCTCTCTGTCTC-CTCTGTCTC-CTC-CCCTCTCTCT-TTTC 31845 i v - v - - i - i (TC)n#Simple_ 147 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 196 chr3qtel1M 31846 T-TCTGTCTCCTTCTCTCTCT-TCTCTCTTCCTCTCTCTCTCTCTCTCTC 31893 - v ii - ii (TC)n#Simple_ 197 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 246 chr3qtel1M 31894 TCTGTCT-TCTCTCTCT-TGTCTGTCTCTCTCTCTCT-TCTCTCCCTCTC 31940 v - - v v - i (TC)n#Simple_ 247 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 296 chr3qtel1M 31941 TCTGTCTTTCTGTCT-TCTTTCTCT-TCTCTCTTTTCCTTCCTCTGTCTG 31988 v i v - i - i ii ii v v (TC)n#Simple_ 297 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 346 chr3qtel1M 31989 TC-CCCTC-CTCTCTCTCCCCTTCTCTC-CCCTCTGTCT-TCTCTCTCTC 32034 - i - i ii - i v - (TC)n#Simple_ 347 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 396 chr3qtel1M 32035 TTCCTCTC-CTC-CTCTCTCTGTCTCTCTTCCTCTCTC-CTCTCTCTCT- 32080 ii - - v ii - - (TC)n#Simple_ 397 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 446 chr3qtel1M 32081 TCTC-CTTCCTCTCTCTGTCCTTCTGTC-CTCTCTTCCTCTCTCTCCTTC 32128 - ii v ii v - ii ii (TC)n#Simple_ 447 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 496 chr3qtel1M 32129 CCTTTCCCTTCCTCTCTCT 32147 i i i ii (TC)n#Simple_ 497 TCTCTCTCTCTCTCTCTCT 515 Matrix = Unknown Transitions / transversions = 1.21 (47/39) Gap_init rate = 0.05 (27 / 495), avg. gap size = 1.00 (27 / 27) 235 35.74 3.06 1.51 chr3qtel1M 32771 32966 (967034) L2#LINE/L2 1273 1471 (1611) m_b136s601i15 5097 chr3qtel1M 32771 CTAAATGAAAGTGGAGAAAGGCTCAAAGGGAT-CGCACTGGGCCCACTGC 32819 i i viiv ii v v ivv - vv v i vi L2#LINE/L2 1273 CTGAACGTGGCTGGAGAAAAACACACAACCATGCTGACTGGTCTCACTTT 1322 chr3qtel1M 32820 AAGTTCCCGTTCCACAATCTCGGCCGGGCC-TCGGTGCTGCCGGGCAGTC 32868 i vi vi vv? i iivi - iii v i L2#LINE/L2 1323 AAATTCATGACCACNAACCTCAAGTGGGCCCTTAATGCTGCCCGGCAATC 1372 chr3qtel1M 32869 CTCCTGCACCTTGCCTTATCGGCTCATTCTCCCACCTCCCCTGGG-GCCC 32917 ? v i -i v vi vii i - i i i- v i L2#LINE/L2 1373 NTACTACA-TTTCCCTAGTCCATTCACTCTCCCA-CTCTCCTAGACGACT 1420 chr3qtel1M 32918 GCCTT---TCTTCTCCAAGACCCTAAACCCTCCGCCCCCGCCACGCCTTA 32964 iii i---i vvvvi v v iv v v v - i L2#LINE/L2 1421 ATTTCACACCTTCTCCTCTCTCCTCAAACCTCCAACACCTCCTC-CCCTA 1469 chr3qtel1M 32965 TC 32966 L2#LINE/L2 1470 TC 1471 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 49.82 CpG sites = 38, Kimura (unadjusted) = 50.88 Transitions / transversions = 1.23 (38/31) Gap_init rate = 0.04 (7 / 195), avg. gap size = 1.29 (9 / 7) 17 3.80 0.00 6.90 chr3qtel1M 33215 33245 (966755) (CTCC)n#Simple_repeat 1 29 (0) m_b136s252i26 5098 chr3qtel1M 33215 CTCCCTCCCTCCTCTCCCTGCCTCCCCTCCC 33245 - v - (CTCC)n#Simpl 1 CTCCCTCCCTCC-CTCCCTCCCT-CCCTCCC 29 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2) 398 29.66 1.52 5.51 chr3qtel1M 33434 33565 (966435) MIRc#SINE/MIR 1 127 (141) m_b136s601i16 5099 chr3qtel1M 33434 CGTGGCTGGGTGGCACAGTGGTTAGAGCAGCAGCCCTGAAGTCAGGAGGA 33483 v v v ii vv vii v i i i MIRc#SINE/MIR 1 CGAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA 50 chr3qtel1M 33484 TCTGAGTTTAAATCTGGTCTCAGACACTTAACACATCCCAGCTGTGGGAC 33533 i i ii i iv v v v ------- i v MIRc#SINE/MIR 51 CCTGGGTTCGAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTGAC 93 chr3qtel1M 33534 CCTGAGCAA--TATTTAACCCCACTTGCCTTTAG 33565 i i --i i i v viv i i MIRc#SINE/MIR 94 CTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 37.30 CpG sites = 22, Kimura (unadjusted) = 38.79 Transitions / transversions = 1.47 (22/15) Gap_init rate = 0.06 (8 / 131), avg. gap size = 1.12 (9 / 8) 12 13.05 0.00 3.70 chr3qtel1M 33793 33820 (966180) (CCTT)n#Simple_repeat 1 27 (0) m_b136s252i27 5100 chr3qtel1M 33793 CCTTCCTTCCTTTCTTCTCTCCCTTTCT 33820 i - i i (CCTT)n#Simpl 1 CCTTCCTTCCTTCCTTC-CTTCCTTCCT 27 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 358 27.34 13.28 0.00 chr3qtel1M 34184 34311 (965689) L2d2_3end#LINE/L2 403 547 (8) m_b136s601i17 5101 chr3qtel1M 34184 CTTTTCACATGTTTTTACATGGACTTC---ATCCGATTGGGAACTCCTCG 34230 i v iiv v v i --- iiv vi i i L2d2_3end#LIN 403 CTTTTCACGTGTTTATGTCTTGTCTCCCCAACTAGATTGTAAGCTCCTTG 452 chr3qtel1M 34231 AGCACAGGAAC--TGTCTT---------TGTATCCCC---AGCACTTAAC 34266 vi i -- --------- --- i i i L2d2_3end#LIN 453 AGGGCAGGGACCATGTCTTATACTTCTTTGTATCCCCCACAGCGCCTAGC 502 chr3qtel1M 34267 ACAGTTCCTGACAAATTGTAAGTGCCTAATTCATGTTTATTGATT 34311 v vi v iv i i ii vv i i L2d2_3end#LIN 503 ACAGTGCCTTGCACACAGTAGGCGCTCAATAAATATTTGTTGATT 547 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 31.48 CpG sites = 22, Kimura (unadjusted) = 35.14 Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.03 (4 / 127), avg. gap size = 4.25 (17 / 4) 16 16.52 0.00 0.00 chr3qtel1M 34636 34662 (965338) (A)n#Simple_repeat 1 27 (0) m_b136s252i28 5102 chr3qtel1M 34636 AAAAAAGAAAAAAAATAAAATAAATAA 34662 i v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAA 27 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 315 29.05 11.97 0.63 chr3qtel1M 35116 35257 (964743) C L3b_3end#LINE/CR1 (512) 694 537 m_b136s601i18 5103 chr3qtel1M 35116 CTTCAGGTG--GTCTGACAAG-GCAAAATGGCAGTGAAATTGTC-TCTCC 35161 i ? -- i v - i i i - i ii ??i -i C L3b_3end#LINE 694 CTCCAGNTGNGGCCTGACCAGCGCAGAGTAG-AGCGGGANNATCACCTCC 646 chr3qtel1M 35162 CTT------------ATGCTTCCTGTAACATGACCTTAGATCTCCTTAGC 35199 ------------ ? ivv iiiii iv v v C L3b_3end#LINE 645 CTTGNTCTGTCGGCGATNCTTCTGTTAATGCAGCCCAAGATCGCATTAGC 596 chr3qtel1M 35200 ATTTT-GGCCACCTCAAGGTACTGCTGACTCCCATGGGGTTTACGATCCA 35248 v - vi v ivv i vi v i i i i v C L3b_3end#LINE 595 TTTTTTGGCAGCCGCGTCGCACTGCTGACTCATATTGAGCTTGCGGTCAA 546 chr3qtel1M 35249 CTCAGACCC 35257 v i C L3b_3end#LINE 545 CTAAAACCC 537 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 37.25 CpG sites = 26, Kimura (unadjusted) = 39.75 Transitions / transversions = 1.73 (26/15) Gap_init rate = 0.04 (6 / 141), avg. gap size = 3.00 (18 / 6) 30 5.72 0.00 0.00 chr3qtel1M 35621 35657 (964343) (ATGG)n#Simple_repeat 1 37 (0) c_b136s251i5 5104 chr3qtel1M 35621 ATGGATGAATGGGTGGATGGATGGATGGATGGATGGA 35657 i i (ATGG)n#Simpl 1 ATGGATGGATGGATGGATGGATGGATGGATGGATGGA 37 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 13 4.76 0.00 4.35 chr3qtel1M 36134 36157 (963843) (CCCT)n#Simple_repeat 1 23 (0) m_b136s252i29 5105 chr3qtel1M 36134 CCCTCCCTCCCTCCACCCCCTCCC 36157 - i (CCCT)n#Simpl 1 CCCTCCCTCCCTCC-CTCCCTCCC 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 269 34.02 1.34 1.34 chr3qtel1M 36470 36618 (963382) C L1ME5_3end#LINE/L1 (304) 637 489 m_b136s551i4 5106 chr3qtel1M 36470 TCCTGCTCATTTCACTCAGCATCA-GTTCATGTAAGTCCCGCCAATCCT- 36517 i i iv ii - -- v vi ii v vi - C L1ME5_3end#LI 637 TCTTACTTTTTTCACTCAGCACTATGTT--TTTAAGATCCATCCATGTTG 590 chr3qtel1M 36518 CTCTGTATTCGTCCTGCTGGTCATTTCTTACAGAACAATAATATTCCATA 36567 v i v i iv iiv iii v v vvvv i i i C L1ME5_3end#LI 589 CTATGTGTACATCTAGTCCGTTGCTTCTAACTGCTGCATAGTACTCCATG 540 chr3qtel1M 36568 ACATTCATATACCACAATTTACCCAACCATTCTCCAATTGATGGGCATTC 36617 iii v vi v i v i v v i ii C L1ME5_3end#LI 539 GTGTGCATCCACCACATTTTACCTATCCACTCTCCCAGTGATGGACACCC 490 chr3qtel1M 36618 A 36618 C L1ME5_3end#LI 489 A 489 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 46.96 CpG sites = 29, Kimura (unadjusted) = 46.96 Transitions / transversions = 1.38 (29/21) Gap_init rate = 0.03 (4 / 148), avg. gap size = 1.00 (4 / 4) 296 20.31 0.00 0.00 chr3qtel1M 36555 36618 (963382) C L1ME3G_3end#LINE/L1 (376) 548 485 m_b136s551i5 5106 chr3qtel1M 36555 ATAATATTCCATAACATTCATATACCACAATTTACCCAACCATTCTCCAA 36604 i ii vv i iii i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr3qtel1M 36605 TTGATGGGCATTCA 36618 i i C L1ME3G_3end#L 498 TTGATGGACATTTA 485 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 24.73 CpG sites = 10, Kimura (unadjusted) = 24.73 Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0) 197 30.55 4.11 1.33 chr3qtel1M 36670 36742 (963258) MIR#SINE/MIR 118 192 (70) m_b136s601i19 5107 chr3qtel1M 36670 CCTCAGTTTCTTCATCGATAAAACAGATTAAAAAAAAGGCACCCATTTCC 36719 i vi ii i-v v v vi i i ii v MIR#SINE/MIR 118 CCTCAGTTTCCTCATCTGTAAAATGGG-GATAATAATAGTACCTACCTCA 166 chr3qtel1M 36720 CAGA---ATTATGAGGATAAAATGGG 36742 i i---i i v i MIR#SINE/MIR 167 TAGGGTTGTTGTGAGGATTAAATGAG 192 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 41.47 CpG sites = 15, Kimura (unadjusted) = 41.47 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.03 (2 / 72), avg. gap size = 2.00 (4 / 2) 602 28.35 7.83 0.86 chr3qtel1M 36746 36962 (963038) MIR#SINE/MIR 30 261 (1) m_b136s601i20 5108 chr3qtel1M 36746 GCTCTGTAGTCTAATAGAGTTGAATTCAAATCCAGCTTCCACTATTGACT 36795 v i vi iv v-i ii i v vi ii i i v MIR#SINE/MIR 30 GCTCTGGAGCCAGACTGC-CTGGGTTCGAATCCCGGCTCTGCCACTTACT 78 chr3qtel1M 36796 GGTTGCATGACC--------ATTCTGTCAGCT-----TGTCTCAGTTTCC 36832 i i ii --------i viv v v ----- i MIR#SINE/MIR 79 AGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCC 128 chr3qtel1M 36833 CCATCTGTAAAATGAGGATAATTATAGCTCCTAATTCCCAGGATTGTTGG 36882 i i v iv vi vi i v MIR#SINE/MIR 129 TCATCTGTAAAATGGGGATAATAATAGTACCTACCTCATAGGGTTGTTGT 178 chr3qtel1M 36883 GAGGATTCAATGAGTTAAAAATTGTAAAAATGCTTAGTACAGTAC--GCT 36930 v v vv - ii v i -- vi MIR#SINE/MIR 179 GAGGATTAAATGAGTTAATACATGT-AAAGCGCTTAGAACAGTGCCTGGC 227 chr3qtel1M 36931 ACATACT--GTGTTACATAAGGTCTAGCTATAAT 36962 v -- i i vv ivvi v MIR#SINE/MIR 228 ACATAGTAAGCGCTCAATAAATGTTAGCTATTAT 261 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 34.10 CpG sites = 33, Kimura (unadjusted) = 36.29 Transitions / transversions = 1.18 (33/28) Gap_init rate = 0.03 (6 / 216), avg. gap size = 3.17 (19 / 6) 13 22.60 0.00 0.00 chr3qtel1M 37014 37046 (962954) (TTATCA)n#Simple_repeat 1 33 (0) m_b136s252i30 5109 chr3qtel1M 37014 TTATTGTTATCATCATCATCATTGTTATCATTA 37046 ii i i ii (TTATCA)n#Sim 1 TTATCATTATCATTATCATTATCATTATCATTA 33 Matrix = Unknown Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 229 25.67 5.95 7.23 chr3qtel1M 38423 38506 (961494) C MIR#SINE/MIR (133) 129 47 m_b137s601i0 5110 chr3qtel1M 38423 AAAAAACTGAGACA-----AGCTGAGACAAGGTGCCTAGGGTCACACAGC 38467 ii i ----- v v iii vv i i C MIR#SINE/MIR 129 AGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGC 80 chr3qtel1M 38468 TAGTAAGTGTTAAATGTCTGAGGTGAATTTGAACTCAGG 38506 vi i - i -----v i i i C MIR#SINE/MIR 79 TAGTAAGTGGCAGA-GCC-----GGGATTCGAACCCAGG 47 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.80 CpG sites = 14, Kimura (unadjusted) = 32.80 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.08 (7 / 83), avg. gap size = 1.57 (11 / 7) 328 31.17 9.60 2.11 chr3qtel1M 38510 38686 (961314) C L2d2_3end#LINE/L2 (10) 545 356 m_b137s601i2 5111 chr3qtel1M 38510 TTAAGCAGTACTTATTAAGCACCTAATATGTATTAGGCACTGTGCTAAGA 38559 i vv i i i i v i iiv i v C L2d2_3end#LIN 545 TCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGC 496 chr3qtel1M 38560 TCC-----GGAAATAAAAAGGCAAAAG--ATGGTCCCTGTTCTTAAGGAG 38602 v i----- v i i i i v -- ii i C L2d2_3end#LIN 495 GCTGTGGGGGATACAAAGAAGTATAAGACATGGTCCCTGCCCTCAAGGAG 446 chr3qtel1M 38603 CTCATAGCGTAATGAGTCAGATGATACGAAAACCT--------CTATATA 38644 i i iiv i vi vv ii v iv vi--------i v C L2d2_3end#LIN 445 CTTACAATCTAGTTGGGGAGACAAGACATAAACACGTGAAAAGTTAAATA 396 chr3qtel1M 38645 TCA--ACAAAATATAGACAGGGAAAATTGGAGCCAATCAATAGA 38686 v -- i v i i --- v i vi v - C L2d2_3end#LIN 395 ACAATACAAGATTTAAATA---ACAGTTCAAGACAA-CAATAGA 356 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.85 CpG sites = 33, Kimura (unadjusted) = 41.90 Transitions / transversions = 1.57 (33/21) Gap_init rate = 0.05 (8 / 176), avg. gap size = 2.62 (21 / 8) 366 28.57 6.35 0.00 chr3qtel1M 38510 38635 (961365) C L2d_3end#LINE/L2 (12) 504 371 m_b137s601i1 5111 chr3qtel1M 38510 TTAAGCAGTACTTATTAAGCACCTAATATGTATTAGGCACTGTGCTAAG- 38558 i vv i i i v ii vi i - C L2d_3end#LINE 504 TCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTGTGCTAGGC 455 chr3qtel1M 38559 ---ATCCGGAA--ATAAAAAGGCAAAAG--ATGGTCCCTGTTCTTAAGGA 38601 ---i vv -- ? ?i i v -- ii i C L2d_3end#LINE 454 GCTGTGGGGAACGANAAAANAGTATAAGACATGGTCCCTGCCCTCAAGGA 405 chr3qtel1M 38602 GCTCATAGCGTAATGAGTCAGATGATACGAAAAC 38635 i i iiv i vi vv ii v v v C L2d_3end#LINE 404 GCTTACAATCTAGTTGGGGAGACAAGACTAACAC 371 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.58 CpG sites = 22, Kimura (unadjusted) = 37.93 Transitions / transversions = 1.57 (22/14) Gap_init rate = 0.03 (4 / 125), avg. gap size = 2.00 (8 / 4) 194 20.00 8.89 0.00 chr3qtel1M 38813 38857 (961143) C L2d2_3end#LINE/L2 (0) 555 507 m_b137s601i3 5112 chr3qtel1M 38813 TCCAATCAAACCAGCA----TTTATTAAGCACCTACTATGTGCATGATA 38857 v i i ---- i i i v ii C L2d2_3end#LIN 555 TCAAATCAAATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCA 507 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 21.28 CpG sites = 7, Kimura (unadjusted) = 24.30 Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.02 (1 / 44), avg. gap size = 4.00 (4 / 1) 208 11.12 0.00 2.78 chr3qtel1M 38815 38851 (961149) C L2d_3end#LINE/L2 (9) 507 472 m_b137s601i4 5112 chr3qtel1M 38815 CAATCAAACCAGCATTTATTAAGCACCTACTATGTGC 38851 - v i i i C L2d_3end#LINE 507 CAATCAA-CAAGTATTTATTGAGCGCCTACTATGTGC 472 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 9.23 CpG sites = 3, Kimura (unadjusted) = 12.24 Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 20 24.50 3.61 10.26 chr3qtel1M 39948 40113 (959887) (TTCC)n#Simple_repeat 1 156 (0) m_b137s252i1 5113 chr3qtel1M 39948 TTTCTTCTCCTCCTCCTCTCTCCTCCCAATTC-TCCTCCATTTCTCCATT 39996 i - i i - - i -v i - i v i i v (TTCC)n#Simpl 1 TTCCTTC-CTTCCTTC-CT-TCCTTCC-TTCCTTCCTTCCTTCCTTCCTT 46 chr3qtel1M 39997 CTTTCTCTTCC-TCCTGGTCTTTCC--CCTTTGTCTCTT-CTTCCTCCCT 40042 i - - -- i -- iv ii - i - (TTCC)n#Simpl 47 CCTTC-CTTCCTTCCT--TCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC- 92 chr3qtel1M 40043 TTCCTGCCTTTCTCTTCCTGTTCCCT-TTTCCATTTCCTCCCTCCCCTTC 40091 v - - -- i -i -- i -i (TTCC)n#Simpl 93 TTCCTTCC-TTC-CTTCC--TTCCTTCCTTCC--TTCCTTCCT-TCCTTC 135 chr3qtel1M 40092 CTTTGCTCCCTTCAAGCCTTCC 40113 - v i vvv (TTCC)n#Simpl 136 C-TTCCTTCCTTCCTTCCTTCC 156 Matrix = Unknown Transitions / transversions = 2.11 (19/9) Gap_init rate = 0.13 (21 / 165), avg. gap size = 1.05 (22 / 21) 18 0.00 0.00 0.00 chr3qtel1M 40982 41001 (958999) (T)n#Simple_repeat 1 20 (0) m_b137s252i2 5114 chr3qtel1M 40982 TTTTTTTTTTTTTTTTTTTT 41001 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTT 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 285 25.99 16.53 1.44 chr3qtel1M 41008 41128 (958872) C MIRc#SINE/MIR (120) 148 10 m_b137s601i5 5115 chr3qtel1M 41008 CTCATTTTACAGATGAGGCAAAT-------AGAGAG---AAGTCATTTGC 41047 i v v ------- --- v i C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr3qtel1M 41048 CCAGAGTT-----GCT----AGTGTCTGA-TTTGAACTCAGGAAGATGAA 41087 ii i----- ---- v v -iiv i -- vviiii C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTC--GAACCCAGG 51 chr3qtel1M 41088 TCTTCCTTCCTTCAGAGCCAGCGCTCTATCCACTGTGGCAC 41128 vv i iiv i v iiv C MIRc#SINE/MIR 50 TCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.43 CpG sites = 18, Kimura (unadjusted) = 32.69 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.06 (7 / 120), avg. gap size = 3.14 (22 / 7) 15 22.15 3.70 1.82 chr3qtel1M 43250 43303 (956697) (AAAAG)n#Simple_repeat 1 55 (0) m_b137s252i3 5116 chr3qtel1M 43250 AAAAGGAAAAAAAACCATGGGAAAGAAAAAGCAAAG-AAA-TAAACAAAA 43297 i i vv vi i - v - -v v (AAAAG)n#Simp 1 AAAAGAAAAGAAAAGAAAAGAAAAG-AAAAGAAAAGAAAAGAAAAGAAAA 49 chr3qtel1M 43298 GAAAAG 43303 (AAAAG)n#Simp 50 GAAAAG 55 Matrix = Unknown Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.06 (3 / 53), avg. gap size = 1.00 (3 / 3) 209 19.64 14.29 0.00 chr3qtel1M 43646 43701 (956299) C MIR3#SINE/MIR (60) 148 85 m_b137s601i6 5117 chr3qtel1M 43646 CCTCTCAACTCA-AGATGA---AACTGGGG----GCAAAGTGAAGTCATT 43687 i vi i - --- i ---- vi i v i C MIR3#SINE/MIR 148 CCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACT 99 chr3qtel1M 43688 TGCCCAGGGTCACA 43701 i C MIR3#SINE/MIR 98 TGCCCAAGGTCACA 85 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 23.55 CpG sites = 8, Kimura (unadjusted) = 23.55 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.05 (3 / 55), avg. gap size = 2.67 (8 / 3) 186 38.55 5.84 0.62 chr3qtel1M 43749 43902 (956098) C MIR#SINE/MIR (78) 184 23 m_b137s601i7 5118 chr3qtel1M 43749 ATACCCACAAAGGACCCTCTGATTTAGAAGGAACCATAAGCTCCTTTTT- 43797 v i vi- v vv ivivv ii v v i v - C MIR#SINE/MIR 184 ATCCTCACAACA-ACCCTATGAGGTAGGTACTATTATTATCCCCATTTTA 136 chr3qtel1M 43798 CGGGTGAGGAAA---ACGGACAGGGGGGCTAGGCAAGG----CAGGGCCA 43840 i i --- v v i i i i i vv---- i i C MIR#SINE/MIR 135 CAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCA 86 chr3qtel1M 43841 CACATCCCTCAGGCCTTAGAAGGGAAGTGTGACCCCAGGCC-TCTCAGTC 43889 v ivvi i ivvi ivv iii vi v v- viv C MIR#SINE/MIR 85 CACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGCAGTCTGGCTC 36 chr3qtel1M 43890 TAGACCTGCTGCT 43902 i v ivv C MIR#SINE/MIR 35 CAGAGCCCGTGCT 23 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 53.88 CpG sites = 29, Kimura (unadjusted) = 55.25 Transitions / transversions = 0.97 (29/30) Gap_init rate = 0.03 (5 / 153), avg. gap size = 2.00 (10 / 5) 13 20.51 0.00 4.88 chr3qtel1M 45157 45199 (954801) (GCCGG)n#Simple_repeat 1 41 (0) m_b137s252i4 5119 chr3qtel1M 45157 GCAGGGCCGGGGCCCCGCAGGGCGGGGGCCGGGCAGGACCGGG 45199 v - vv v -v v i (GCCGG)n#Simp 1 GCCGGGCC-GGGCCGGGCCGGGC-CGGGCCGGGCCGGGCCGGG 41 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.00 (2 / 2) 23 12.42 0.00 4.35 chr3qtel1M 46286 46333 (953667) (CCCCGC)n#Simple_repeat 1 46 (0) m_b137s252i6 5120 chr3qtel1M 46286 CCCCTCAGCCGCCCCCGCCCCCTCCCGCCGCCCCCATCCCCCGCCCCC 46333 v vv v - -v (CCCCGC)n#Sim 1 CCCCGCCCCCGCCCCCGCCCCCGCCC-CCGCCCCC-GCCCCCGCCCCC 46 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.04 (2 / 47), avg. gap size = 1.00 (2 / 2) 19 18.74 1.67 5.17 chr3qtel1M 46282 46341 (953659) (CCAGCCC)n#Simple_repeat 1 58 (0) m_b137s252i5 5121 chr3qtel1M 46282 CCTGCCCCTCAGCCGCCCCCGCCCCC-TCCCGCCGCCCCCATCCCCCGCC 46330 v - - - v -v v v v iv (CCAGCCC)n#Si 1 CCAGCCCC-CAG-C-CCCCAGCCCCCAGCCCCCAGCCCCCAGCCCCCAGC 47 chr3qtel1M 46331 CCCCAGCTCCC 46341 i (CCAGCCC)n#Si 48 CCCCAGCCCCC 58 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.07 (4 / 59), avg. gap size = 1.00 (4 / 4) 17 13.72 8.33 0.00 chr3qtel1M 49127 49174 (950826) (GGCTGGG)n#Simple_repeat 1 52 (0) m_b137s252i7 5122 chr3qtel1M 49127 GGCTGGGGCCCGGCGGC--GGGG--GGGGGCGGGGGGCTGGGCGCTGGTG 49172 v i v -- -- v v v (GGCTGGG)n#Si 1 GGCTGGGGGCTGGGGGCTGGGGGCTGGGGGCTGGGGGCTGGGGGCTGGGG 50 chr3qtel1M 49173 GC 49174 (GGCTGGG)n#Si 51 GC 52 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.04 (2 / 47), avg. gap size = 2.00 (4 / 2) 15 22.54 0.00 8.20 chr3qtel1M 50664 50729 (949271) (GGGCCGG)n#Simple_repeat 1 61 (0) m_b137s252i8 5123 chr3qtel1M 50664 GGGCCGGGGGCGGGGGGCCCGGGAGGTGAGGGACCAGGGCCATGGCCCTG 50713 v - i vi i v vi iv v - (GGGCCGG)n#Si 1 GGGCCGGGGGCCGGGGG-CCGGGGGCCGGGGGCCGGGGGCCGGGGGCC-G 48 chr3qtel1M 50714 GGGCGTCCGGAGGGCC 50729 - - - (GGGCCGG)n#Si 49 GGG-G-CCGG-GGGCC 61 Matrix = Unknown Transitions / transversions = 0.83 (5/6) Gap_init rate = 0.08 (5 / 65), avg. gap size = 1.00 (5 / 5) 13 7.81 7.41 0.00 chr3qtel1M 51509 51535 (948465) (GGA)n#Simple_repeat 1 29 (0) m_b137s252i9 5124 chr3qtel1M 51509 GGAGGGGGA-GCGGAGGAGG-GGAGGAGG 51535 i - v - (GGA)n#Simple 1 GGAGGAGGAGGAGGAGGAGGAGGAGGAGG 29 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.08 (2 / 26), avg. gap size = 1.00 (2 / 2) 13 16.80 0.00 0.00 chr3qtel1M 53062 53088 (946912) (CCG)n#Simple_repeat 1 27 (0) m_b137s252i10 5125 chr3qtel1M 53062 CCTCCTCCTCCTCCGCCGCCGCCGCCG 53088 v v v v (CCG)n#Simple 1 CCGCCGCCGCCGCCGCCGCCGCCGCCG 27 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 17 3.19 2.63 8.33 chr3qtel1M 53119 53156 (946844) (CCCCTC)n#Simple_repeat 1 36 (0) m_b137s252i11 5126 chr3qtel1M 53119 CCCCTCCCCCTCCGGCCTCGGCCCCTCCCCC-CCCCCTC 53156 -v -- - (CCCCTC)n#Sim 1 CCCCTCCCCCTCC-CCCTC--CCCCTCCCCCTCCCCCTC 36 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.11 (4 / 37), avg. gap size = 1.00 (4 / 4) 18 20.28 4.00 5.41 chr3qtel1M 53591 53665 (946335) (CCCG)n#Simple_repeat 1 74 (0) m_b137s252i12 5127 chr3qtel1M 53591 CCCGCCCGTCC-CGTGTCCGGCCG-TGTCCTGCCCCGCCC-CCCGCCCGC 53637 i - vi i v -ivv i - - (CCCG)n#Simpl 1 CCCGCCCGCCCGCCCGCCCGCCCGCCCGCCCGC-CCGCCCGCCCGCCCGC 49 chr3qtel1M 53638 GCGCCCCAGCCCCCTCAGCCCGCCCGCC 53665 v - - v - v (CCCG)n#Simpl 50 CCG-CCC-GCCCGC-CCGCCCGCCCGCC 74 Matrix = Unknown Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.09 (7 / 74), avg. gap size = 1.00 (7 / 7) 19 20.80 2.00 0.00 chr3qtel1M 53621 53670 (946330) (CCCCGCC)n#Simple_repeat 1 51 (0) m_b137s252i13 5127 chr3qtel1M 53621 CCCCGCCCCCCG-CCCGCGCGCCCCAGCCCCCTCAGCCCGCCCGCCGCAC 53669 - v v iv v vv v v (CCCCGCC)n#Si 1 CCCCGCCCCCCGCCCCCCGCCCCCCGCCCCCCGCCCCCCGCCCCCCGCCC 50 chr3qtel1M 53670 C 53670 (CCCCGCC)n#Si 51 C 51 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.02 (1 / 49), avg. gap size = 1.00 (1 / 1) 12 10.03 0.00 0.00 chr3qtel1M 54091 54112 (945888) (GGAG)n#Simple_repeat 1 22 (0) m_b137s252i14 5128 chr3qtel1M 54091 GGGGGGAGGGGGGGAGGGAGGG 54112 i i (GGAG)n#Simpl 1 GGAGGGAGGGAGGGAGGGAGGG 22 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 361 28.50 3.82 6.25 chr3qtel1M 54354 54484 (945516) C L2a_3end#LINE/L2 (5) 512 385 m_b137s601i8 5129 chr3qtel1M 54354 TTCAGTCAACAAGCATTTATTTAGCGTCTGCTGTGTGC--AGTCTTGCCC 54401 v ii v i i i --i ivi ii C L2a_3end#LINE 512 TTCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTC 463 chr3qtel1M 54402 T-GGTGCTGGGGATACAG-AGAAAGCCGAGGGGGGGGGAAGGCCAGGGGC 54449 - i - vi i vi --------iv i v ii v C L2a_3end#LINE 462 TAGGCGCTGGGGATACAGCAGTGAACAAA--------ACAGACAAAAGTC 421 chr3qtel1M 54450 CCTGACCCCATGGAGCTT-CCTCCCGATGGGGAGGG 54484 v i - v i iii i i C L2a_3end#LINE 420 CCTGCCCTCATGGAGCTTACATTCTAGTGGGGGGAG 385 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.48 CpG sites = 25, Kimura (unadjusted) = 37.89 Transitions / transversions = 2.50 (25/10) Gap_init rate = 0.09 (12 / 130), avg. gap size = 1.08 (13 / 12) 19 25.69 4.11 1.33 chr3qtel1M 54987 55059 (944941) (GGAGGA)n#Simple_repeat 1 75 (0) m_b137s252i15 5130 chr3qtel1M 54987 GGTGGA-GAGGAAGGGGAGGAGGAGATGGAGGAGGATGGA-CAAAAGGAG 55034 v - i i iv - -v ii (GGAGGA)n#Sim 1 GGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA-GGAGGAGGAGGAG 49 chr3qtel1M 55035 GGAGAGAGGGAGG-GGGGCAGGGGGA 55059 ii ii - i v i (GGAGGA)n#Sim 50 GAGGAGGAGGAGGAGGAGGAGGAGGA 75 Matrix = Unknown Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.06 (4 / 72), avg. gap size = 1.00 (4 / 4) 311 25.61 4.88 0.00 chr3qtel1M 55225 55306 (944694) C MIRc#SINE/MIR (15) 253 168 m_b137s601i9 5131 chr3qtel1M 55225 TCACAATTGC-TAGC---TTAAGGTTTGCAAAGCACTTTCTCCTGTGTTA 55270 i v i- --- vi i i v v iii C MIRc#SINE/MIR 253 TTACATTTGTATAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTA 204 chr3qtel1M 55271 TCTCATTTGATCTTTACAGCAGTCTTGGTAAGTAGG 55306 i i i ii i vv i C MIRc#SINE/MIR 203 TCTCATTTGATCCTCACAACAACCCTGTGAGGTAGG 168 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.94 CpG sites = 15, Kimura (unadjusted) = 32.86 Transitions / transversions = 2.50 (15/6) Gap_init rate = 0.02 (2 / 81), avg. gap size = 2.00 (4 / 2) 268 31.07 10.95 1.33 chr3qtel1M 55247 55383 (944617) C MIRb#SINE/MIR (48) 220 71 m_b137s601i10 5131 chr3qtel1M 55247 TGCAAAGCACTTTCTCCTGTGTTATCTCATTTGATCTTTACAGCAGTCTT 55296 v i v- v ii i i i i ii i C MIRb#SINE/MIR 220 TGCTAAGCGCTTTA-CATGCATTATCTCATTTAATCCTCACAACAACCCT 172 chr3qtel1M 55297 GGTAAGTAGGTGCTATGA----CTTTATGGGGAAGCAGAAGCCTGAGG-- 55340 vv i ii v ---- v v ivi v - i iv -- C MIRb#SINE/MIR 171 GCGAGGTAGGTATTATTATCCCCATTTTACAGATG-AGGAAACTGAGGCT 123 chr3qtel1M 55341 CAAAGACTTTCATCAAAGTG---AGAGTTTCACAG------AGTGGTAGA 55381 i vv v vi vv --- ii iv ------ i C MIRb#SINE/MIR 122 CAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGA 73 chr3qtel1M 55382 AC 55383 i C MIRb#SINE/MIR 72 GC 71 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.02 CpG sites = 24, Kimura (unadjusted) = 41.31 Transitions / transversions = 1.33 (24/18) Gap_init rate = 0.04 (6 / 136), avg. gap size = 2.83 (17 / 6) 23 33.58 4.31 0.83 chr3qtel1M 55945 56060 (943940) (GA)n#Simple_repeat 1 120 (0) m_b137s252i16 5132 chr3qtel1M 55945 GAGAAATAGAGATGAGAGACAAAGA-AGGGGGGGA-AGAGA-AAAGGAAG 55991 i v - v i - i i i - - i ii (GA)n#Simple_ 1 GAGAGAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 49 chr3qtel1M 55992 AG-GAAGGAAACACAGAGCCAGGGAAAGAGAGACACAAAGAAAAAAATGG 56040 - ii i v v vv i i v v i i i i vi (GA)n#Simple_ 50 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 99 chr3qtel1M 56041 GGAG-GAGAGGGAGAGATAGA 56060 i - i v (GA)n#Simple_ 100 AGAGAGAGAGAGAGAGAGAGA 120 Matrix = Unknown Transitions / transversions = 2.00 (20/10) Gap_init rate = 0.05 (6 / 115), avg. gap size = 1.00 (6 / 6) 223 35.17 2.34 3.55 chr3qtel1M 56112 56282 (943718) C L2#LINE/L2 (283) 2799 2631 m_b137s601i11 5129 chr3qtel1M 56112 TCACTTGGGCAACTGAGAGTTGAATAGATTGGGGAGGGGAATGGCTTTGA 56161 iv vi v vvvv i ?i i v v v v- C L2#LINE/L2 2799 TCACTCTGGCTGCTGTGTTGAGAATAGACTGNAGGGGGGCAAGGGTG-GA 2751 chr3qtel1M 56162 GGCAGG----CCGGTTCTCTGGCAACCATCCCAATAGACCAGGCCTAAGA 56207 i ---- i v--- vii i iv i iv vvi C L2#LINE/L2 2750 AGCAGGGAGACCAGTTA---GGAGGCTATTGCAGTAATCCAGGCGAGAGA 2704 chr3qtel1M 56208 TGATTGAGGGTCTGCACTGTGATGGGGGCAAAGTCAGAGGAGAGAAGGGG 56257 - iv ii v iiv i v iv vvi v v v C L2#LINE/L2 2703 TGA-TGGTGGCTTGGACCAGGGTGGTGGCAGTGGAGGTGGTGAGAAGTGG 2655 chr3qtel1M 56258 GAACATTGAAGAGATATTGCTGAAG 56282 vviv vvi v -i C L2#LINE/L2 2654 TCGGATTCTGGATATATT-TTGAAG 2631 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 47.04 CpG sites = 25, Kimura (unadjusted) = 48.14 Transitions / transversions = 0.76 (25/33) Gap_init rate = 0.04 (7 / 170), avg. gap size = 1.43 (10 / 7) 20 20.74 0.00 0.00 chr3qtel1M 56671 56709 (943291) (T)n#Simple_repeat 1 39 (0) m_b137s252i17 5133 chr3qtel1M 56671 TTTTTTTTTTTTTTTTTAATTCTTTTCATTCTCTTTTTT 56709 vv i iv i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 39 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 181 31.18 9.48 3.25 chr3qtel1M 56934 57049 (942951) C L2c_3end#LINE/L2 (3) 475 353 m_b137s601i12 5134 chr3qtel1M 56934 CAATCAATTGATTAAC-TTTAATGAGAAAGCACCTACCGCTTACCAAGC- 56981 v v ii iv - v ---- i iiiv i i - C L2c_3end#LINE 475 CATTCATTCAACAAACATTTATTGAG----CGCCTACTATGTGCCAGGCG 430 chr3qtel1M 56982 -TGTATAGATAAAAATGAA--------AGTCTCTACCATGAAGGAGCTTA 57022 - viv v i i --------i i i v v i C L2c_3end#LINE 429 CTGGGGATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCA 380 chr3qtel1M 57023 TATTCTTTTGGTAGAGACATATACATA 57049 i v vv vi v i ?i C L2c_3end#LINE 379 CAGTCTAGTGGAGGAGACAGACANGTA 353 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.97 CpG sites = 20, Kimura (unadjusted) = 42.09 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.07 (8 / 115), avg. gap size = 1.88 (15 / 8) 220 25.92 5.88 4.65 chr3qtel1M 57763 57847 (942153) C MIRc#SINE/MIR (75) 193 108 m_b137s601i13 5135 chr3qtel1M 57763 TCCTGACACCATTTGTGTTTTCTGGGCAG---AGGTACTGGCAGGGTTTG 57809 v v viiv vvvv i --- i ivi ---- iv C MIRc#SINE/MIR 193 TCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTA----TCC 148 chr3qtel1M 57810 CTATTTTACAGATGAGGAAACTGAGA--CAGACAGGGTAA 57847 i i-- v v C MIRc#SINE/MIR 147 CCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAA 108 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.92 CpG sites = 9, Kimura (unadjusted) = 31.92 Transitions / transversions = 0.75 (9/12) Gap_init rate = 0.07 (6 / 84), avg. gap size = 1.50 (9 / 6) 232 22.95 1.61 1.61 chr3qtel1M 57792 57853 (942147) C MIR#SINE/MIR (102) 160 99 m_b137s601i14 5135 chr3qtel1M 57792 AGGTACTGGCAGGGTTTGCTATTTTACAGATGAGGAAACTGAGACAGACA 57841 ivi vvi ii- i i v v C MIR#SINE/MIR 160 AGGTACTATTATTATCC-CCATTTTACAGATGAGGAAACTGAGGCACAGA 112 chr3qtel1M 57842 G-GGTAAAGTCAC 57853 - v v C MIR#SINE/MIR 111 GAGGTTAAGTAAC 99 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.62 CpG sites = 7, Kimura (unadjusted) = 27.62 Transitions / transversions = 1.00 (7/7) Gap_init rate = 0.03 (2 / 61), avg. gap size = 1.00 (2 / 2) 230 28.41 8.66 2.99 chr3qtel1M 57812 57938 (942062) C MIR3#SINE/MIR (66) 142 9 m_b137s601i15 5135 chr3qtel1M 57812 ATTTTACAGATGAGGAAACTGAGA--CAGACAGGGTAAAGTCAC--ACAC 57857 i-- v - i v --i v C MIR3#SINE/MIR 142 ATTTTACAGATGAGGAAACTGAGGCCCAGAGA-GGTGAAGTGACTTGCCC 94 chr3qtel1M 57858 AGTGTCTCTGCACAG--ATTTGATGATTCATCC-CGACTAGATCC--AGT 57902 iv ---i -- v ii iivv v -v v --i C MIR3#SINE/MIR 93 AAGGTC---ACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGT 47 chr3qtel1M 57903 GCACTGACT--GAATCCCTGTGCTGCCTACCTGCCCAC 57938 viv --v i v iv vi i iiiv C MIR3#SINE/MIR 46 CTCCTGACTCCCAGTCCGTGCTCTCTCTGCTCAGCCAC 9 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.27 CpG sites = 18, Kimura (unadjusted) = 36.27 Transitions / transversions = 1.06 (18/17) Gap_init rate = 0.08 (10 / 126), avg. gap size = 1.50 (15 / 10) 12 22.42 0.00 2.70 chr3qtel1M 58395 58432 (941568) (GGGCCA)n#Simple_repeat 1 37 (0) m_b137s252i18 5136 chr3qtel1M 58395 GGACCAGAGGCAGTGCCAGGCCCTGTGCCGAGGGCCAG 58432 i i v v v v v - (GGGCCA)n#Sim 1 GGGCCAGGGCCAGGGCCAGGGCCAGGGCC-AGGGCCAG 37 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 246 31.40 4.65 0.00 chr3qtel1M 60560 60645 (939355) C MIRb#SINE/MIR (54) 214 125 m_b137s601i16 5137 chr3qtel1M 60560 GCACTTTATAAGCAGCTTCTCAGTCGACCCTGACAGCCACTCTG---GGT 60606 i i v viv v ii i v i v i --- C MIRb#SINE/MIR 214 GCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGT 165 chr3qtel1M 60607 -GCTACTCTCCTTCCCATACTGCAGACCAGGGACCTGAGG 60645 - v i v iv i vi i iv i v C MIRb#SINE/MIR 164 AGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGG 125 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.68 CpG sites = 15, Kimura (unadjusted) = 41.69 Transitions / transversions = 1.25 (15/12) Gap_init rate = 0.02 (2 / 85), avg. gap size = 2.00 (4 / 2) 11 13.33 5.71 2.78 chr3qtel1M 61701 61735 (938265) (GGGGACG)n#Simple_repeat 1 36 (0) m_b137s252i19 5138 chr3qtel1M 61701 GGGGTCGGGGGAGGCGGGGCCTGGGGA--GGGGACGG 61735 v v - v v -- (GGGGACG)n#Si 1 GGGGACGGGGGACG-GGGGACGGGGGACGGGGGACGG 36 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.50 (3 / 2) 26 20.01 1.35 4.17 chr3qtel1M 61815 61888 (938112) (AGG)n#Simple_repeat 1 72 (0) m_b137s252i20 5139 chr3qtel1M 61815 AGGAGGAGGAGGAAGAGGAGGAAGAAGCCCGAGGACCAAGGAGGAGGAAG 61864 i - i vvv -vi i (AGG)n#Simple 1 AGGAGGAGGAGGAGGAGGAGG-AGGAGGAGGAGGA-GGAGGAGGAGGAGG 48 chr3qtel1M 61865 -GGAGGAAGGAGGAAGCGGCGGCGG 61888 - - i v v v (AGG)n#Simple 49 AGGAGG-AGGAGGAGGAGGAGGAGG 72 Matrix = Unknown Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.05 (4 / 73), avg. gap size = 1.00 (4 / 4) 13 29.14 3.12 1.54 chr3qtel1M 61915 61978 (938022) (GGACGG)n#Simple_repeat 1 65 (0) m_b137s252i21 5140 chr3qtel1M 61915 GGACAGGAACAGGAACCGCGCCGGTGAGCGGGGGGGGGTACGGGGA-GGG 61963 i i i i v v v v - iv v - (GGACGG)n#Sim 1 GGACGGGGACGGGGACGGGGACGGGGA-CGGGGACGGGGACGGGGACGGG 49 chr3qtel1M 61964 GA-GCGCCTGGGGACG 61978 - v vvi (GGACGG)n#Sim 50 GACGGGGACGGGGACG 65 Matrix = Unknown Transitions / transversions = 0.67 (6/9) Gap_init rate = 0.05 (3 / 63), avg. gap size = 1.00 (3 / 3) 17 29.35 0.00 0.00 chr3qtel1M 63448 63501 (936499) (CCCC)n#Simple_repeat 1 54 (0) m_b137s252i22 5141 chr3qtel1M 63448 CCCCCCTCCCGCCCTCCCGCCGCCCCCCCCGGGGGGGCCCCCCCCCACCC 63497 i v i v v vvvvvvv v (CCCC)n#Simpl 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 50 chr3qtel1M 63498 CCCC 63501 (CCCC)n#Simpl 51 CCCC 54 Matrix = Unknown Transitions / transversions = 0.18 (2/11) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 13 3.65 2.94 9.38 chr3qtel1M 63992 64025 (935975) (GGGAG)n#Simple_repeat 1 32 (0) m_b137s252i24 5142 chr3qtel1M 63992 GGGAGCGGGAGGGGTAAGGGGAGGGGCGGGG-GGG 64025 - -- v - (GGGAG)n#Simp 1 GGGAG-GGGAGGGG--AGGGGAGGGGAGGGGAGGG 32 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.12 (4 / 33), avg. gap size = 1.00 (4 / 4) 21 0.00 0.00 0.00 chr3qtel1M 64208 64230 (935770) (GA)n#Simple_repeat 1 23 (0) m_b137s252i25 5143 chr3qtel1M 64208 GAGAGAGAGAGAGAGAGAGAGAG 64230 (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAG 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 15 5.48 0.00 0.00 chr3qtel1M 68222 68240 (931760) (CA)n#Simple_repeat 1 19 (0) m_b137s252i26 5144 chr3qtel1M 68222 CACACACACACTCACACAC 68240 v (CA)n#Simple_ 1 CACACACACACACACACAC 19 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 256 25.84 19.10 0.00 chr3qtel1M 69048 69136 (930864) L2a_3end#LINE/L2 376 481 (36) m_b137s601i17 5145 chr3qtel1M 69048 ATGGCCTACCTCCCC--------ATGTAAGCTCCAAGGAGACGGACACTG 69089 v i ii -------- v ii i i iv v L2a_3end#LINE 376 ATTGTCTGTCTCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGACTT 425 chr3qtel1M 69090 TTGTTCATTTTGTCC----TTGAAACCCCAGGGCCCTGAACG-----TGG 69130 iii i ----i v v v iv i----- L2a_3end#LINE 426 TTGTCTGTTTTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGG 475 chr3qtel1M 69131 CACATA 69136 L2a_3end#LINE 476 CACATA 481 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.79 CpG sites = 15, Kimura (unadjusted) = 32.79 Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.03 (3 / 88), avg. gap size = 5.67 (17 / 3) 259 26.40 19.66 0.00 chr3qtel1M 69534 69711 (930289) C L2a_3end#LINE/L2 (15) 502 290 m_b137s601i18 5146 chr3qtel1M 69534 AAACAATTATTGAGCACCTGCTATGTGACAGACATAGTCCTGGGGGTGGG 69583 i v i i v i iv i i v iv C L2a_3end#LINE 502 AAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGCGCTGG 453 chr3qtel1M 69584 GAATA---TAAAGAACAAAAGGG-----AGT--CTGGCCTCGAGGAGCTC 69623 i ---i iv vi ----- -- v iv i C L2a_3end#LINE 452 GGATACAGCAGTGAACAAAACAGACAAAAGTCCCTGCCCTCATGGAGCTT 403 chr3qtel1M 69624 TGAA--CAGTGGGG-----CAAAC--TGTGCAAACAACTACGGACAA--- 69661 vv v--i ----- i -- ivi i v v v v --- C L2a_3end#LINE 402 ACATTCTAGTGGGGGGAGACAGACAATAAACAAATAAATAAGTAAAATAT 353 chr3qtel1M 69662 --ACTATG---GACAG-GATA-----CATGGGGAAAAATCCA-CAGGG-G 69698 -- v --- ii - -----i i vv - -i C L2a_3end#LINE 352 ATAGTATGTCAGATGGTGATAAGTGCTATGGAGAAAAATAAAGCAGGGTA 303 chr3qtel1M 69699 GGGGGCATGGGGA 69711 i v i C L2a_3end#LINE 302 AGGGGGATAGGGA 290 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.27 CpG sites = 26, Kimura (unadjusted) = 33.12 Transitions / transversions = 1.24 (26/21) Gap_init rate = 0.07 (13 / 177), avg. gap size = 2.69 (35 / 13) 284 27.10 9.35 0.00 chr3qtel1M 69534 69640 (930360) C L2d2_3end#LINE/L2 (15) 540 424 m_b137s601i19 5146 chr3qtel1M 69534 AAACAATTATTGAGCACCTGCTATGTGACAGACATAGTCCTGGG---GGT 69580 i v i i i vv i iv v i ---v C L2d2_3end#LIN 540 AAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGT 491 chr3qtel1M 69581 GGGGAATATAAAGAA-CAAAAG----GGAGTCTGGCCTCGAGGAGCTCTG 69625 i i -i v ---- vvi v i ivv C L2d2_3end#LIN 490 GGGGGATACAAAGAAGTATAAGACATGGTCCCTGCCCTCAAGGAGCTTAC 441 chr3qtel1M 69626 AA--CAGTGGGGCAAAC 69640 --i v v i C L2d2_3end#LIN 440 AATCTAGTTGGGGAGAC 424 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.66 CpG sites = 15, Kimura (unadjusted) = 34.07 Transitions / transversions = 1.07 (15/14) Gap_init rate = 0.04 (4 / 106), avg. gap size = 2.50 (10 / 4) 1135 30.60 15.56 1.32 chr3qtel1M 69907 70767 (929233) C L2#LINE/L2 (186) 2896 1915 m_b137s601i20 5146 chr3qtel1M 69907 ATTGGGAAGATTTAATGTTCGACCCTGA-TGTGACAAGCGGTCCCCTGCA 69955 vi i i vivv iv i - v iii vi - vi v C L2#LINE/L2 2896 ATTGTAAGGACTTTGGCTTTTACTCTGAGTGAGATGGGAAG-CCATTGGA 2848 chr3qtel1M 69956 CCTTGTTGAG-AGGGGAATGACATGGGCTG----------------GACC 69988 vvv v - i i iv ---------------- i C L2#LINE/L2 2847 GGGTTTTGAGCAGAGGAGTGACATGATCTGACTTACGTTTTAAAAGGATC 2798 chr3qtel1M 69989 TGTCTGACGGCTGAGTGGATGATGAACTGGAGTGGACAAAGACTGGCGGC 70038 vv i v v v vi ii ? v ivv iv vi C L2#LINE/L2 2797 ACTCTGGCTGCTGTGTTGAGAATAGACTGNAGGGGGGCAAGGGTGGAAGC 2748 chr3qtel1M 70039 AGTG---CCAGCAA-----CTAATACAGTGGTCCAGACATCAGAAGATGA 70080 v --- iv ----- v i ii i ivv v i C L2#LINE/L2 2747 AGGGAGACCAGTTAGGAGGCTATTGCAGTAATCCAGGCGAGAGATGATGG 2698 chr3qtel1M 70081 --GCTCTGGAGCAGCATGAAGGCGG-------GGTCAGAAGGGGGCGGAT 70121 -- - v vi iv i ------- v v v C L2#LINE/L2 2697 TGGCT-TGGACCAGGGTGGTGGCAGTGGAGGTGGTGAGAAGTGGTCGGAT 2649 chr3qtel1M 70122 TCGAGA---GTTGTGAAAG--------ACAAG---TCCT--TGGCCTGGA 70155 vi ---i v i -------- i --- v -- vi C L2#LINE/L2 2648 TCTGGATATATTTTGAAGGTAGAGCCGACAGGATTTGCTGATGGATTGGA 2599 chr3qtel1M 70156 CATGGGGGATAAAAGGAAGTGAGGAGTCCAGGATGAC--CTAGG-----G 70198 ii vi i i i v v -- v ----- C L2#LINE/L2 2598 TGTGGGGTGTGAGAGAAAGAGAGGAGTCAAGGATGACTCCAAGGTTTTTG 2549 chr3qtel1M 70199 GCCTG--------GAAGCATGGA------------CGGAATCGG----AC 70224 -------- v ------------i ii v ---- C L2#LINE/L2 2548 GCCTGAGCAACTGGAAGGATGGAGTTGCCATTNACTGAGATGGGGAAGAC 2499 chr3qtel1M 70225 AGCAAGAGAGGAGGGTGTGCACGAGGGGGATGACGCGTTCAGATTCTGAA 70274 v ii ii vi v - v i ii v v v - i i C L2#LINE/L2 2498 TGCGGGAGGAGCAGGTTTG-AGGGGGAAGATCAGGAGTTCAG-TTTTGGA 2451 chr3qtel1M 70275 CGTTTTGAATTTAAGACGTCTGTGAGACATCTAATCCAAGATTTCCAGTG 70324 i v i i i i i i v i vivi v v i C L2#LINE/L2 2450 CATGTTAAGTTTGAGATGCCTATTAGACATCCAAGTGGAGATGTCGAGTA 2401 chr3qtel1M 70325 GGCAGTTGGAGCTGTGTGATTGACTGAGTGTCGGCCGAGAGGTTAGAGGT 70374 vv ii v vi --- - i vv iv i v C L2#LINE/L2 2400 GGCAGTTGGATATACGAGTCTG---GAGT-TCAGGGGAGAGGTCCGGGCT 2355 chr3qtel1M 70375 GGACAAATGTGTCTGAGAATCGGCAGCATGGAATCGAAAAGGAAATCCAG 70424 v v ivi i i i iv iv ivi iv vvv v v C L2#LINE/L2 2354 GGAGATATAAATTTGGGAGTCATCAGCATATAGATGGTATTTAAAGCCAT 2305 chr3qtel1M 70425 GAGAGCGGATGAGATCA--AATGAAGT-AGT----ATAAAG----GCAAA 70463 vi --? v i - ---- i ---- v i C L2#LINE/L2 2304 GAGACTGGATGAGATCACCNAGGGAGTGAGTGTAGATAGAGAAGAGAAGA 2255 chr3qtel1M 70464 GGGCCCAGGACAGAACCTGGGGGACACTT---------GTGGTGGAGGGG 70504 v v v i iv - i--------- v v i i C L2#LINE/L2 2254 GGTCCAAGGACTGAGCCCTGGGG-CACTCCAACGTTNAGAGGTCGGGGAG 2206 chr3qtel1M 70505 ATCTAGAAGAGGAGCCAGCAAAGGAGAT---GGAGGACTGGTCAGAGAAG 70551 --- i i i--- i vi i v i C L2#LINE/L2 2205 AT---GAGGAGGAACCAGCAAAGGAGACTGAGAAGGAGCGGCCAGTGAGG 2159 chr3qtel1M 70552 TAGGAG---AACCAGGAGAGAATAGGAGACCTGAAAACCCAGAGAGAACA 70598 --- vi - v v i i v v ii v C L2#LINE/L2 2158 TAGGAGGAAAACCAGGAGAGTGT-GGTGTCCTGGAAGCCAAGTGAAGAAA 2110 chr3qtel1M 70599 ATGTGCTGGAGAATATCCAATGATCAAACTTGCCTAAGGCTGTAGGGAGG 70648 i viiiiii iv vvv i viv i v v iv i? C L2#LINE/L2 2109 GTGTTTCAAGAAGGAGGGAGTGATCAACTGTGTCAAATGCTGCTGANAGG 2060 chr3qtel1M 70649 TCAAGGAGAGCAAGGATCGAAAAAAGG-CACT-GATTTGGCAGC-TAGGG 70695 v iiiii ii i vv i- i - i i - i i C L2#LINE/L2 2059 TCAAGTAAGATGAGGACTGAGAATTGACCATTGGATTTAGCAACGTGGAG 2010 chr3qtel1M 70696 ------------------AAGAGCA--TTCAGTGAAATGGGGAGGTTGAA 70725 ------------------ -- i i i v i vi C L2#LINE/L2 2009 GTCATTGGTGACCTTGACAAGAGCAGTTTCGGTGGAGTGGTGGGGACGAA 1960 chr3qtel1M 70726 AGTCAGGCTACAGAGGGTT-AAGAGAGG--GAGAAGAAAGGAACT 70767 i v ii iv v - i-- i i i i C L2#LINE/L2 1959 AGCCTGATTGGAGTGGGTTCAAGAGAGAATGGGAGGAGAGGAATT 1915 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.36 CpG sites = 145, Kimura (unadjusted) = 40.57 Transitions / transversions = 1.26 (145/115) Gap_init rate = 0.05 (43 / 860), avg. gap size = 3.42 (147 / 43) 411 34.87 7.03 1.13 chr3qtel1M 71107 71689 (928311) C L1ME4a_3end#LINE/L1 (227) 644 28 m_b137s551i0 5147 chr3qtel1M 71107 TGTAGATTGTTTTCTTGATTCTGCCACTTTATGTTGGCTTTTTTTTCATG 71156 ?vi i i v i - iv i v vv iviv ii C L1ME4a_3end#L 644 TGTANCCTGCTTTTTTCACT-TAACATTATATCATGAGCATTTTCCCATG 596 chr3qtel1M 71157 CTTCTCTGCATTCATCACATGCAAAATTTCTCATAGCTCAGTAATATTCC 71206 iivi vvii v iv vi v? i v i vvi C L1ME4a_3end#L 595 TCATTAAATATTCTTCGAAAACATNATTTTTAATGGCTGCATAATATTCC 546 chr3qtel1M 71207 GTTACGTTCACATACCACAATTTGCACAGCCATTACCC-----------A 71245 i ?ii vv ii i iivi i ? v ----------- C L1ME4a_3end#L 545 ATTNTATGGATGTACCATAATTTATTTAACCANTCCCCTATTGTTGGACA 496 chr3qtel1M 71246 CT---GTTTCTTCTAACTC--CACTATCA-----AGTGCTGCTA-GAA-A 71283 i --- vi i i i-- i i ----- i v - - C L1ME4a_3end#L 495 TTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAATGCTGCGATGAACA 446 chr3qtel1M 71284 TCAGAGTATTTGGTGACTT-TCTACTTCT-TGGTTACTTCTTTGGGGTGT 71331 vvv iv iivvvi - ?i v - i i i i i iv C L1ME4a_3end#L 445 TCCTTGTACATAAATCTTTGTNCACATCTCTGATTATTTCCTTAGGATAA 396 chr3qtel1M 71332 AAACTTAGCAATGGAGCTTCTAATTCA--GAGTGTGGCTATTTTAGTCAC 71379 vv i v i ii v iiv -- i i ?vi vivvi C L1ME4a_3end#L 395 ATTCCTAGAAGTGGAATTACTGGGTCAAAGGGTATGNACATTTTTAAGGC 346 chr3qtel1M 71380 TGTATTTACATAATTCCAAATTGTT-TCCAAAATGGCCGTCC---TTTGC 71425 v vvv v v ii- i v ii v --- i C L1ME4a_3end#L 345 TTTTGATACATATTGCCAAATTGCCCTCCAGAAAGGTTGTACCAATTTAC 296 chr3qtel1M 71426 ACAGCTCCACCAATAATGTATTAGTGTGCCTATCTTCCTATCACCCCTTC 71475 --ii ii i v v ii i i? i ivv i vi C L1ME4a_3end#L 295 AC--TCCCACCAGCAGTGTATGAGAGTGCCCGTTTCNCCACACCCTCGCC 248 chr3qtel1M 71476 AACATTGACTATTGCTGATTTTTTTTTTTAATCTGTGCCAATTTGCAGGG 71525 i iv ---- ivv i v v vvi C L1ME4a_3end#L 247 AACACTGGGTATT----ATCAATCTTTTAAATCTTTGCCAATTTGATAGG 202 chr3qtel1M 71526 TGTGAGGGGAAACCTCAGTATTACTTTGATGAGCATTTCT----CTATTA 71571 vi iiv iv i v i ii i vv ----i i C L1ME4a_3end#L 201 TGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCTTTGATTACTA 152 chr3qtel1M 71572 GTGATCTGGAGCA-GTTTTCTTGGGGTTGTAAATATTTTGCAG---TTCT 71617 vv v i -? v iv v i viiivv i v--- C L1ME4a_3end#L 151 GTGAGGTTGAACATNTTTTCATATGTTTATTGGCCATTTGTATTTCTTCT 102 chr3qtel1M 71618 TTTGATACCTCTTTGTTCATATCCTTTTACCATTTATCCATTAGGAAAT- 71666 vv vi v i i vv v i i ivi - C L1ME4a_3end#L 101 TTTGTGAATTGTCTGTTCATGTCCTTTGCCCATTTTTCTATTGGGGTGTT 52 chr3qtel1M 71667 -GACTTAATCATATTGATTTACAA 71689 - v vv v ii C L1ME4a_3end#L 51 CGTCTTTTTCTTATTGATTTGTAA 28 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 48.29 CpG sites = 111, Kimura (unadjusted) = 49.38 Transitions / transversions = 1.23 (111/90) Gap_init rate = 0.04 (23 / 582), avg. gap size = 2.09 (48 / 23) 508 35.21 7.18 0.73 chr3qtel1M 71148 71662 (928338) C L1ME4c_3end#LINE/L1 (226) 604 57 m_b137s551i1 5147 chr3qtel1M 71148 TTTTTCATGCTTCTCTGCATTCATCACATGCAAAATTTCTCATAGCTCAG 71197 i i v viii v v i vvi vv i v i vvi C L1ME4c_3end#L 604 TTTTCCATGTTGCTACATAGTCTTCATAATTATCATTTTTAATGGCTGCA 555 chr3qtel1M 71198 TAATATTCCGTTACGTTCACATACCACAATTTGCACAGCCATTACCC--- 71244 i iiv ?v ii i i vi i v --- C L1ME4c_3end#L 554 TAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTAT 505 chr3qtel1M 71245 --------ACT---GTTTCTTCTAACTC--CACTATCA-----AGTGCTG 71276 -------- i --- vi i i i-- i i ----- ii C L1ME4c_3end#L 504 TGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCTG 455 chr3qtel1M 71277 CTAGAAA----TCAGAGTATTTGGTGACTTTCTACTTCTTGGTTACTTCT 71322 v vi ---- iv v i v i ivvi i v i vii i i C L1ME4c_3end#L 454 CAATGAACATCTTCGTGCATATAGCTTTTTCCTTCTTTTGAATTATTTCC 405 chr3qtel1M 71323 TTGGGGTGTAAACTTAGCAATGGAGCTTCTAATTCA--GAGTGTGGCTAT 71370 i i iv vv ii v i ii v iiv -- i i ivi C L1ME4c_3end#L 404 TTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACAT 355 chr3qtel1M 71371 TTTAGTCACTGTATTTACATAATTCCAAATTG-TTTCCAAAATGGCCGT- 71418 vi vi v vvv i v v - v ii - C L1ME4c_3end#L 354 TTTTATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTA 305 chr3qtel1M 71419 CCTTTGCACAGCTCCACCAATAATGTATTAGTGTGCCTATCTTCCTATCA 71468 vv vi ?iv ii v ? i vi i iv iiiv? C L1ME4c_3end#L 304 CCAATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCAN 255 chr3qtel1M 71469 CCCCTTCAACATTGACTATTGCTGATTTTTTTTTTTAATCTGTGCCAATT 71518 i vi i iv ---- ivv v i v i C L1ME4c_3end#L 254 CCTCGCCAGCATTGGGTATT----ATCAATTTTTTAAATTTTTGCTAATT 209 chr3qtel1M 71519 TGCAGGGTGTGAGGGGAAACCTCAGTATTACTTTGATGAGCATTTCT--- 71565 ivvi i i iiv iv i v i i i vv --- C L1ME4c_3end#L 208 TAATAGGCGTAAAATGGTATCTCATTGTTGCTTTAATTTGCATTTCTTTG 159 chr3qtel1M 71566 -CTATTAGTGATCTGGAGCAGTTTTCT-TGGGGTTGTAAATATTTTGCAG 71613 -i i i vv v i v i- v v vv ivv? i v C L1ME4c_3end#L 158 ATTACTAGCGAGGTTGAACATTTTTCCATGTGTTTGTTTACTANTTGTAT 109 chr3qtel1M 71614 TTCTTTTGAT---ACCTCTTTGTTCATATCCTTTTACCATTTATCCATTA 71660 i i v? --- vi v i i vv i i C L1ME4c_3end#L 108 TTCCTCTTNTGTGAATTGTCTGTTCATGTCCTTTGCCCATTTATCTATTG 59 chr3qtel1M 71661 GG 71662 C L1ME4c_3end#L 58 GG 57 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 47.27 CpG sites = 102, Kimura (unadjusted) = 50.11 Transitions / transversions = 1.31 (102/78) Gap_init rate = 0.03 (17 / 514), avg. gap size = 2.41 (41 / 17) 1021 24.81 3.46 0.75 chr3qtel1M 71804 72063 (927937) MIRb#SINE/MIR 2 268 (0) m_b137s601i21 5148 chr3qtel1M 71804 AGAGAGGTTAGGGGGCACAGTACCCAAAGCAGCAAGCCT-GGAGTCAGGA 71852 i iviv v ii ivvv i - ii i - iv MIRb#SINE/MIR 2 AGAGGGGCAGCGTGGTGCAGTGGAAAGAGCA-CGGGCTTTGGAGTCAGAC 50 chr3qtel1M 71853 AGACCTGAGTTTAAATCCAGCCTCGGGCACTTACTAGCTGTGTGACCCTG 71902 i ii v v v v i MIRb#SINE/MIR 51 AGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTG 100 chr3qtel1M 71903 AGCAAGTTACTTTGCTGCTGCTTGCCTCAGTTTCCTCAACTGTAAAATGA 71952 i vi iv vivv v i MIRb#SINE/MIR 101 GGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGG 150 chr3qtel1M 71953 GGATAATAGCAACTGCCTTCTAA---TATGGTGAGGATCAAATGAGATAA 71999 ii v i ivi i--- i v i MIRb#SINE/MIR 151 GGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAA 200 chr3qtel1M 72000 TAGTTCT-CAGTGTTTAGCACAG----TGATACATAGTAGGCACTAAATA 72044 ivv v -v i i ---- ii i i v MIRb#SINE/MIR 201 TGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATA 250 chr3qtel1M 72045 AGTGTTTGCTATTATTATT 72063 i v v -i MIRb#SINE/MIR 251 AATGGTAGCT-CTATTATT 268 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.86 CpG sites = 37, Kimura (unadjusted) = 30.71 Transitions / transversions = 1.37 (37/27) Gap_init rate = 0.02 (6 / 259), avg. gap size = 1.83 (11 / 6) 15 19.61 0.00 0.00 chr3qtel1M 73485 73513 (926487) (T)n#Simple_repeat 1 29 (0) m_b137s252i27 5149 chr3qtel1M 73485 TTTTTTTTCATTTTTTTTATTTCTTTATT 73513 iv v i v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 chr3qtel1M 73645 73661 (926339) (T)n#Simple_repeat 1 17 (0) m_b137s252i28 5150 chr3qtel1M 73645 TTTTTTTTTTTTTTTTT 73661 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTT 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 493 22.37 4.08 2.68 chr3qtel1M 75468 75614 (924386) C MIR1_Amn#SINE/MIR (80) 150 2 m_b138s601i0 5151 chr3qtel1M 75468 CTCATTTTACAGATGAGGAAACTGAGGCAAACAG-GGTGTGGTGATTTGC 75516 i ?v v - ?vi i C MIR1_Amn#SINE 150 CCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGC 101 chr3qtel1M 75517 TCAGAGTCACCCAGCTGGTAAGTGTCTGAG--GGCAGAAGAG---GAGTC 75561 i ii ? ? i? v v -- v ?v? i---ii C MIR1_Amn#SINE 100 CCAAGGTCACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAACCCAGGTC 51 chr3qtel1M 75562 TCCCTGAGCATAAGTTGAATATTCTATCCTCCCTGGCACCACTTAGCTTC 75611 - iviv iv i ii -- v i - viv i C MIR1_Amn#SINE 50 TCCC-GAGTCCCAGTCCAGTGCTCTATC--CACTAG-ACCACACTGCCTC 5 chr3qtel1M 75612 CCT 75614 C MIR1_Amn#SINE 4 CCT 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.80 CpG sites = 19, Kimura (unadjusted) = 28.80 Transitions / transversions = 1.46 (19/13) Gap_init rate = 0.05 (7 / 146), avg. gap size = 1.43 (10 / 7) 17 15.49 0.00 0.00 chr3qtel1M 75882 75910 (924090) (T)n#Simple_repeat 1 29 (0) m_b138s252i0 5152 chr3qtel1M 75882 TTTTTTTTTGTTTTTGATTTTGTTTTTTT 75910 v vv v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 413 20.30 0.71 22.61 chr3qtel1M 76047 76186 (923814) C MIRb#SINE/MIR (150) 118 4 m_b138s601i1 5153 chr3qtel1M 76047 GGGGTTAAGTGACTTGCCCAGATTCACACAGCTAGGAAGTGTTA-AACAC 76095 i i iiv v vi - i vv C MIRb#SINE/MIR 118 GAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 69 chr3qtel1M 76096 AGATTTGAACTCAGGTCTTCCTGACTTCAGGCATAATATCCTGAGAATAA 76145 i i i vi i ----- -ii --------- C MIRb#SINE/MIR 68 GGATTCGAACCCAGGTCTGTCTGACTCCA-----AA-GCCC--------- 34 chr3qtel1M 76146 TAATTCAGGTGCTCTATCCATTGTACCACCTAGCTGCCCCT 76186 -------- v i i --- C MIRb#SINE/MIR 33 --------GTGCTCTTTCCACTGCACCAC---GCTGCCCCT 4 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 21.74 CpG sites = 15, Kimura (unadjusted) = 22.90 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.19 (27 / 139), avg. gap size = 1.00 (27 / 27) 453 25.27 1.10 0.00 chr3qtel1M 76047 76137 (923863) C MIRc#SINE/MIR (153) 115 24 m_b138s601i2 5153 chr3qtel1M 76047 GGGGTTAAGTGACTTGCCCAGATTCACACAGCTAGGAAGTGTTA-AACAC 76095 i iiv v vi - i vv C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 66 chr3qtel1M 76096 AGATTTGAACTCAGGTCTTCCTGACTTCAGGCATAATATCCT 76137 i i i i i i ivi i iii C MIRc#SINE/MIR 65 GGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCT 24 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.75 CpG sites = 17, Kimura (unadjusted) = 32.49 Transitions / transversions = 2.83 (17/6) Gap_init rate = 0.01 (1 / 90), avg. gap size = 1.00 (1 / 1) 462 24.99 0.67 8.70 chr3qtel1M 77538 77686 (922314) MIR#SINE/MIR 7 144 (118) m_b138s601i3 5154 chr3qtel1M 77538 TAGCATAGTAGGCCGATAGAGCGCCGGCCCTGGAGACATGGATACTCATC 77587 - iii -- i v i v -- ------- MIR#SINE/MIR 7 TAGCATAGT-GGTTAA--GAGCACGGGCTCTGGAGCCA--GA-------C 44 chr3qtel1M 77588 TTTGTGAATTCAAATCTGGCCTCAGACACTTTCTAACTGTGTGATCCTGG 77637 viv ii i iv v v v v i i i MIR#SINE/MIR 45 TGCCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 94 chr3qtel1M 77638 CCAAGTCACCAAACCTAATT-TGCTTCTGTTTCTTCATCTTTAAAATGAG 77686 v i iv vvi - i v i v i MIR#SINE/MIR 95 GCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGG 144 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.58 CpG sites = 19, Kimura (unadjusted) = 30.64 Transitions / transversions = 1.27 (19/15) Gap_init rate = 0.09 (13 / 148), avg. gap size = 1.00 (13 / 13) 18 12.16 0.00 0.00 chr3qtel1M 79390 79416 (920584) (AC)n#Simple_repeat 1 27 (0) m_b138s252i1 5155 chr3qtel1M 79390 ACACACACACACACACAAACATGCACA 79416 v ii (AC)n#Simple_ 1 ACACACACACACACACACACACACACA 27 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 674 31.11 7.66 1.48 chr3qtel1M 79935 80443 (919557) L1M5_orf2#LINE/L1 1547 2086 (1208) m_b138s551i0 5156 chr3qtel1M 79935 TGATACCTAAACCAGGGAGAG-CAGCTCAGAAAAAGAAAGCTTTAGGCTA 79983 v ? iv i - viv ii ii vi i i L1M5_orf2#LIN 1547 TGATACCAAAACCNGACAAAGACATTACAAGAAAAGAAAATTACAGACCA 1596 chr3qtel1M 79984 GTTTCCCCAATGAATATTGCTGCAGACATTTAAAATGAAA---------- 80023 i v iv i v v i v iiv? ii ---------- L1M5_orf2#LIN 1597 ATATCCCTCATGAACATAGATGCAAAAATCCTNAACAAAATATTAGCAAA 1646 chr3qtel1M 80024 -CAACTACAGCGATATGTCACAAAGATCATATAGTATGACCCACTAGGAT 80072 - i v v i i v v i v i vi v v i i L1M5_orf2#LIN 1647 TCGAATCCAGCAATATATAAAAAGGATAATACATCATGACCAAGTGGGGT 1696 chr3qtel1M 80073 TTATACCAGGAATGTAGGGCTGATTCAGCACTATAAAAACTACGGATCTA 80122 v i i i i i i i vv v v ivi v L1M5_orf2#LIN 1697 TTATCCCAGGAATGCAAGGTTGGTTTAACATTCGAAAATCAATCAATGTA 1746 chr3qtel1M 80123 GTTGGCCATACCAATAATAAAAAGCAACACAAATCATAT---TATCTCAA 80169 i vi ii i iv v v iv - ---i L1M5_orf2#LIN 1747 ATTCACCATATTAACAGAATAAAGGAGAA-AAATCATATGATCATCTCAA 1795 chr3qtel1M 80170 GAGATGCAGAAAATGCTTTTGACAAAATACGACATCCATTC--------- 80210 v v v v i i --------- L1M5_orf2#LIN 1796 TAGATGCAGAAAAAGCATTTGACAAAATTCAACACCCATTCATGATAAAA 1845 chr3qtel1M 80211 -CTCTT--TAAA-TGGGAAT--AAATGAAGT--CTTAAAATGACAAATAG 80252 - i--i - i -- iv v -- i vv i vi L1M5_orf2#LIN 1846 ACTCTCAGCAAACTAGGAATAGAAGGGAACTTCCTCAACCTGATAAAGGG 1895 chr3qtel1M 80253 TCTTTATCTGAAACCAAAAACAACTATTATCTGTAATTA-GATAAGCTAG 80301 iv i ivvi v v i ? vi i viv vi- v ?i ii L1M5_orf2#LIN 1896 CATCTACGAAAAACCTACAGCNAACATCATACTTAATGGTGAAANACTGA 1945 chr3qtel1M 80302 AAACCATCCTAATAAGATTAGAGGTGAAACCAGGAATTCCATTAGCACCA 80351 ?i iv ivv ii iiiii i v vv ii ?v L1M5_orf2#LIN 1946 ANGCTTTCCCCCTAAGATCGGGAACAAGACAAGGATGTCCGCTNTCACCA 1995 chr3qtel1M 80352 CTATTATCCAATATTCCATTAGAAATTCTAGTTATATTGTAGCAATAAGA 80401 vi i i vi i i ii i ii ---- - i L1M5_orf2#LIN 1996 CTTCTATTCAACATTGTACTGGAGGTCCTAGCCA----GT-GCAATAAGG 2040 chr3qtel1M 80402 CAAGAGAAA-AAATAGGA-----ACAGACTGGAAAAAGGAGCAAACAA 80443 i - ii ----- v i -- iv i L1M5_orf2#LIN 2041 CAAGAAAAAGAAATAAAAGGCATAAAGATTGG--AAAGGAAGAAATAA 2086 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.95 CpG sites = 95, Kimura (unadjusted) = 42.44 Transitions / transversions = 1.56 (95/61) Gap_init rate = 0.04 (21 / 508), avg. gap size = 2.24 (47 / 21) 16 0.00 0.00 0.00 chr3qtel1M 82217 82234 (917766) (A)n#Simple_repeat 1 18 (0) m_b138s252i2 5157 chr3qtel1M 82217 AAAAAAAAAAAAAAAAAA 82234 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAA 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 339 26.87 3.05 2.42 chr3qtel1M 82682 82845 (917155) L1MC_orf2#LINE/L1 83 247 (3047) m_b138s551i1 5158 chr3qtel1M 82682 CAGAATGGGTTAGAAAGCAAAATCCAAAAAC-TATTGTTTACAAGAGACA 82730 i i i i i i i vv i- i i i v L1MC_orf2#LIN 83 CAGAGTGGATCAAAAAACAAGACCCAACTATATGTTGTCTACAAGAAACC 132 chr3qtel1M 82731 CAACTGAAACATAAAGACACATTATTTATT---GTTAAATAGCCGGAGCA 82777 vi v i - vv ---iv ?i vi v L1MC_orf2#LIN 133 CACTTTAAATATAAAGACACA-TATAGATTAAAAGTAAANGGATGGAGAA 181 chr3qtel1M 82778 GAATATATTATGCTTCGGCTGAAGTGAGAAAAAGACTTGGGTAGC-AAAT 82826 ii ii vvvi -- i v i i ii ?v i - v L1MC_orf2#LIN 182 AGATATACCATGCTAACACT--AATCAAAAGAAAGCNGGAGTAGCTATAT 229 chr3qtel1M 82827 ATAATTTCAGACAGAGCAG 82845 - L1MC_orf2#LIN 230 -TAATTTCAGACAGAGCAG 247 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.92 CpG sites = 27, Kimura (unadjusted) = 34.92 Transitions / transversions = 1.69 (27/16) Gap_init rate = 0.04 (7 / 163), avg. gap size = 1.29 (9 / 7) 414 21.96 8.39 7.64 chr3qtel1M 83150 83292 (916708) C MIRc#SINE/MIR (122) 146 3 m_b138s601i4 5159 chr3qtel1M 83150 CATTTTACCGGTAAGGAA-CCGAG----AGAGGGGGGATGAAGTGATTTT 83194 v i i - i ---- i --- v i v C MIRc#SINE/MIR 146 CATTTTACAGATGAGGAAACTGAGGCTCAGAGAGG---TTAAGTGACTTG 100 chr3qtel1M 83195 CCCAGGGGCATACAGCTAGTAAATGTCTGAGCCAGATCT-GAATTCAAAT 83243 i v i i v v i iv - ii ---- C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCC---- 54 chr3qtel1M 83244 AGATAAGTCTTTCTGAC-ACAGGCCCAGCTCTCTT----CTACGCCAC-C 83287 ---- i i -v i i iv ---- i i - C MIRc#SINE/MIR 53 ----AGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACAC 8 chr3qtel1M 83288 TACCT 83292 i C MIRc#SINE/MIR 7 TGCCT 3 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.79 CpG sites = 20, Kimura (unadjusted) = 26.86 Transitions / transversions = 2.22 (20/9) Gap_init rate = 0.12 (17 / 142), avg. gap size = 1.35 (23 / 17) 571 18.24 0.00 8.62 chr3qtel1M 83773 83898 (916102) MIRb#SINE/MIR 3 118 (150) m_b138s601i5 5160 chr3qtel1M 83773 GAGGGGCAGCTAGGTGGCACAGTGGATAGAGCACCAGCCTTGAAGTCAGG 83822 --- ii v vi i i i MIRb#SINE/MIR 3 GAGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGA 49 chr3qtel1M 83823 AGGACCTGAGTTCAAATCTGGTCTCAGACACTTAACACTTCCTAGTTGTG 83872 vi i i iv v v v ------- i MIRb#SINE/MIR 50 CAGACCTGGGTTCGAATCCCGGCTCTGCCACTTA-------CTAGCTGTG 92 chr3qtel1M 83873 TGACCCTGGGCAAGTCACTTAACCCC 83898 i i i MIRb#SINE/MIR 93 TGACCTTGGGCAAGTTACTTAACCTC 118 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 20.07 CpG sites = 14, Kimura (unadjusted) = 21.17 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.08 (10 / 125), avg. gap size = 1.00 (10 / 10) 14 5.00 0.00 0.00 chr3qtel1M 83913 83933 (916067) (GAA)n#Simple_repeat 1 21 (0) m_b138s252i3 5161 chr3qtel1M 83913 GAAAAAGAAGAAGAAGAAGAA 83933 i (GAA)n#Simple 1 GAAGAAGAAGAAGAAGAAGAA 21 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 13 18.80 0.00 5.26 chr3qtel1M 84537 84576 (915424) (AGGGAA)n#Simple_repeat 1 38 (0) m_b138s252i4 5162 chr3qtel1M 84537 AGGGAGGAAGGAAAGTGGAAGGTAAAGGAGAAAGTGAAAG 84576 -i i v i v - v (AGGGAA)n#Sim 1 AGGGA-AAGGGAAAGGGAAAGGGAAAGG-GAAAGGGAAAG 38 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 16 0.00 0.00 0.00 chr3qtel1M 85007 85023 (914977) (A)n#Simple_repeat 1 17 (0) m_b138s252i5 5163 chr3qtel1M 85007 AAAAAAAAAAAAAAAAA 85023 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 1412 24.63 2.58 3.53 chr3qtel1M 86535 87077 (912923) C L1ME3G_3end#LINE/L1 (380) 544 7 m_b138s551i2 5164 chr3qtel1M 86535 TATTCCATAATATTCATATTCCACAATTTATTCAGTCATTCTCCAATTGA 86584 i vv v i i ii i v C L1ME3G_3end#L 544 TATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTATTGA 495 chr3qtel1M 86585 TGGGCATCCATTCAATTTCCAGTTTCTGGCCACTACAAAGAGGGCTGCCA 86634 i ii vvivi i i v i i v iv v C L1ME3G_3end#L 494 TGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCTGCAA 445 chr3qtel1M 86635 CAAACATTCGTGCACATACAGGTCCCTTTCC-CTTCTTT-AGTATCTCTT 86682 ii i v i i ?-- i v v - v v vi- i ? C L1ME3G_3end#L 444 TGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATTTCTN 397 chr3qtel1M 86683 TGGGATATAAGCCCAGTAGAAACACTGCTGGGTCAAAGGGCATGTACAGT 86732 i v v? ? v viiv i i ii v C L1ME3G_3end#L 396 TAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGCATT 347 chr3qtel1M 86733 TTGATAACTTTTTGAGCATAGTTCCAAATTGCTCTCCAGAATGGCTGGAT 86782 i -- i vvv - v v i i ? v i C L1ME3G_3end#L 346 TTAA--ATTTTAATAG-ATACTGCCAAATTGCCCTCCAAAANGGCTGTAC 300 chr3qtel1M 86783 GTATTCACAATTCCACCAACAATGTATCAGTGTCCCAGTTTTCCCACATC 86832 vv i v i i i v v v v i i C L1ME3G_3end#L 299 CAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCACACC 250 chr3qtel1M 86833 CCCTCCAACATTCAGCATTA----CCTTTTCCTGTCATCCTAGCCAATCT 86878 i v i ?iii ----? vv---- ii v C L1ME3G_3end#L 249 CTCGCCAACACTNGATATTATCAANCTTTTAA----ATTTTTGCCAATCT 204 chr3qtel1M 86879 GAGAGGTGTGTAGTGGTATCTCAGAGTTGTCTTAATTTGCATTTCTCTGA 86928 vi viv i vv i i C L1ME3G_3end#L 203 GATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGA 154 chr3qtel1M 86929 TTAATAGTGATTTGGAACA--CTTTCATAAG---AGTGGAAATAGTTTCA 86973 v vv v i --i v --- v vv --- vv C L1ME3G_3end#L 153 TTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCA---TTTGT 107 chr3qtel1M 86974 ATTTCATCATCTGAAAATTGTCTGTTCATATCCTTTGACAATTTATCAAT 87023 v v vi i v v v v C L1ME3G_3end#L 106 ATTTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTAT 57 chr3qtel1M 87024 TGGAGAATGGCTTGATTTCTTATAAA---GTAGAGTCAATTCTCTATATA 87070 iv-- v -- vi --- i--- i i C L1ME3G_3end#L 56 TGGGT--TGTCTT--TTTCTTATTGATTTGTAGG---AGTTCTTTATATA 14 chr3qtel1M 87071 TTTTGGA 87077 i C L1ME3G_3end#L 13 TTCTGGA 7 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 30.02 CpG sites = 64, Kimura (unadjusted) = 30.61 Transitions / transversions = 0.98 (64/65) Gap_init rate = 0.05 (25 / 542), avg. gap size = 1.32 (33 / 25) 283 30.86 1.82 1.82 chr3qtel1M 86973 87137 (912863) C L1P3_orf2#LINE/L1 (39) 3255 3091 m_b138s551i3 5164 chr3qtel1M 86973 AATTTCATCATCTGAAAATTGTCTGTTCATATCCTTTGACAATTTATCAA 87022 v v v i i v i v v i v ii C L1P3_orf2#LIN 3255 AATGTCTTCTTTTGAGAAGTGTCTGTTCATATCCTTCGCCCACTTTTTGA 3206 chr3qtel1M 87023 TTGGAGAATGGCTTG---ATTTCTTATAAAGTAGAGTCAATTCTCTATAT 87069 v ---i v i ---v i v v vv v i ii i v C L1P3_orf2#LIN 3205 TGGG---GTTGTTTGTTTTTTTCTTGTAAATTTGTTTAAGTTCCTTGTAG 3159 chr3qtel1M 87070 ATTTTGGAAATGAGGCCTTTAGCAGAACCTTTGACTGTAAAAATGTTTTC 87119 i v v v iv vvvv v i i v i C L1P3_orf2#LIN 3158 ATTCTGGATATTAGCCCTTTGTCAGATGGATAGATTGCAAAAATTTTCTC 3109 chr3qtel1M 87120 CCAGTTTATTGTTTCCCT 87137 v i i v v v C L1P3_orf2#LIN 3108 CCATTCTGTAGGTTGCCT 3091 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.89 CpG sites = 20, Kimura (unadjusted) = 39.86 Transitions / transversions = 0.67 (20/30) Gap_init rate = 0.02 (4 / 164), avg. gap size = 1.50 (6 / 4) 23 13.32 3.08 6.35 chr3qtel1M 87582 87646 (912354) (AAGA)n#Simple_repeat 1 63 (0) m_b138s252i6 5165 chr3qtel1M 87582 AATAAAG-ATGACAATAAAG-AAGAAAAATAATAAGAAAAAGAAGAGAAA 87629 v - v - v - i - v - i - (AAGA)n#Simpl 1 AAGAAAGAAAGA-AAGAAAGAAAGAAAGA-AAGAA-AGAAAGAA-AGAAA 46 chr3qtel1M 87630 GAAAGAAAGAAAGGAAG 87646 i (AAGA)n#Simpl 47 GAAAGAAAGAAAGAAAG 63 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.09 (6 / 64), avg. gap size = 1.00 (6 / 6) 15 26.74 0.00 2.00 chr3qtel1M 88381 88431 (911569) (ATAT)n#Simple_repeat 1 50 (0) m_b138s252i7 5166 chr3qtel1M 88381 ATAGATAGATAGATAGAGATATATATGGGTATTGATATATATTTATCATA 88430 v v v v v ivi vv v - (ATAT)n#Simpl 1 ATATATATATATATATATATATATATATATATATATATATATATAT-ATA 49 chr3qtel1M 88431 T 88431 (ATAT)n#Simpl 50 T 50 Matrix = Unknown Transitions / transversions = 0.22 (2/9) Gap_init rate = 0.02 (1 / 50), avg. gap size = 1.00 (1 / 1) 238 36.93 1.23 0.82 chr3qtel1M 88524 88766 (911234) C Plat_L3#LINE/CR1 (110) 3463 3220 m_b138s551i4 5167 chr3qtel1M 88524 ATTTTTACCTTAA-GTTCTCCAGGGATGGGGATTCTACCACCTCCCAGGG 88572 i vi - v i i i v vv C Plat_L3#LINE/ 3463 ATTCTTTTCTTAAAGATCTCCAGGGATGGAGACTCCACAACCTCCCTCGG 3414 chr3qtel1M 88573 AAGCCTCTTCTCTTCTGTGATATCTCTAATTATTAGAAAGTTATTCTTGA 88622 v iv ivv v v v vv i i ivi i ii v i v C Plat_L3#LINE/ 3413 TAGCCCGTTCCAGTGTTTTATCACCCTGACAGTCAAGAAGTTCTTCCTTA 3364 chr3qtel1M 88623 TATCTAGCCTTAATTAGCCCCATTTTAACTTCCTCTTATTGCTCCTGGCT 88672 i i i vv ivvi iii i vvv ii v ii v i C Plat_L3#LINE/ 3363 TGTCCAACCGAAATCTCTCCTGCTTTAATTTAAGCCCATTTCCTCTTGTT 3314 chr3qtel1M 88673 CTCTCCTTTGGGGCCAGGCATAAAAACCTAACC--TCTCTTTCACATGTT 88720 vv i? v v v v v v - iii --iv i i v ivv C Plat_L3#LINE/ 3313 CGGTCCTCNGTGGACATGGAGAACAA-CTGGTCAGCGTCCTCCCCATAAA 3265 chr3qtel1M 88721 GGCCCTTTAGATACTGGAAGAAGAGCTATTCTGTTTCTCCTAAGTC 88766 ii i v v - v i vv iv i v i C Plat_L3#LINE/ 3264 AACCCTTCATATACTTGAAG-ACAGTTATTAAGTCACCCCTTAGCC 3220 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 50.49 CpG sites = 44, Kimura (unadjusted) = 52.14 Transitions / transversions = 0.98 (44/45) Gap_init rate = 0.02 (4 / 242), avg. gap size = 1.25 (5 / 4) 219 34.99 3.28 1.61 chr3qtel1M 89966 90087 (909913) C L2d_3end#LINE/L2 (13) 503 380 m_b138s601i6 5168 chr3qtel1M 89966 CAAAGAGCAGCTTTTGAACATTTGCTGGCTGCCAGGCACTGTGCTGAA-- 90013 vi i vi v i iii i ivv ivi iii-- C L2d_3end#LINE 503 CAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTGTGCTAGGCG 454 chr3qtel1M 90014 -TGTGAGGGATTAGAAGGAAGATA-AAAACTCAGTCATTTCCCACAAGGA 90061 - i i iv ? ii? - - i vii vi v v C L2d_3end#LINE 453 CTGTGGGGAACGANAAAANAG-TATAAGACATGGTCCCTGCCCTCAAGGA 405 chr3qtel1M 90062 GCTCCCAAACTAAGATGAGAGGAGAA 90087 iv v - v i ii v C L2d_3end#LINE 404 GCTTACAATCT-AGTTGGGGAGACAA 380 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 47.73 CpG sites = 27, Kimura (unadjusted) = 51.28 Transitions / transversions = 1.80 (27/15) Gap_init rate = 0.04 (5 / 121), avg. gap size = 1.20 (6 / 5) 367 32.96 7.37 3.72 chr3qtel1M 89980 90291 (909709) C L2b_3end#LINE/L2 (25) 441 119 m_b138s601i7 5168 chr3qtel1M 89980 TGAACATTTGCTGGCTGCCAGGCACTGTGCTGAATGTGAGGGAT-TAGAA 90028 i iii i vv ? iiii ivi -i vi C L2b_3end#LINE 441 TGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGGGATACAGCG 392 chr3qtel1M 90029 G-GAAGATAA-AAACTCAGTCATTTCCCACAAGGAGCTCCCAAACTAAGA 90076 - v vi - i ? i vi v v v v iv ivi C L2b_3end#LINE 391 GTGAACAAGACAGACNCGGTCCCTGCCCTCACGGAGCTCACAGTCTAGTG 342 chr3qtel1M 90077 TGAGAGG-AGAAATGGGAACAATTCAGTTCATA--TCAGAGGCATAAAGC 90123 v i i- v vi ? iviv -- ? --i vvii ii i C L2b_3end#LINE 341 GGGGAGACAGACATGTAANCAGACAA--TNATAACCCAGAGTGGCAGGGT 294 chr3qtel1M 90124 ATGGAT--GGAGATCTCAGAGAGGAAGGCA------CAGGC--GGGATAT 90163 - i-- i iv i -- i i------ v -- ivi C L2b_3end#LINE 293 A-GGACTGGGGGGGCCC--AGAGGAGGGCGCCTGACCCGGCCTGGGGGGT 247 chr3qtel1M 90164 CATGGAAGGCTTTCTGTACAAGTTGGGATTTATGGTCAGTCTTGTGGGAA 90213 v i i i v vi v iv iv v v v i vi v C L2b_3end#LINE 246 CAGGGAGGGCTTCCCGGAGGAGGTGACATTTGAGCTGAGACCTGAAGGAT 197 chr3qtel1M 90214 GCCACGGAAGGT-ATGAGGC--AGAGGTGAAGAGGAAGAGCCTTCCAGGC 90260 -viii i v -iiv -- --- i i v C L2b_3end#LINE 196 G-AGTAGGAGTTGGCCAGGCGAAGAGGT---GGGGAAGGGCGTTCCAGGC 151 chr3qtel1M 90261 ACAGGGGAAAAGGGCAGGAG--AAAGCCT--AGGC 90291 v --- vi ? v -- i i-- C L2b_3end#LINE 150 AGAGGG---AACAGCANGTGCAAAGGCCCTGAGGC 119 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.36 CpG sites = 58, Kimura (unadjusted) = 46.13 Transitions / transversions = 1.41 (58/41) Gap_init rate = 0.08 (24 / 311), avg. gap size = 1.46 (35 / 24) 249 30.88 12.99 1.16 chr3qtel1M 90497 90650 (909350) C L2d2_3end#LINE/L2 (320) 235 64 m_b138s601i8 5169 chr3qtel1M 90497 GGATAAGGTAGAGATTC---CTGGGCCATAAAGGGTGGATAGGACCTA-A 90542 vi i ?- i--- v i i i ii i- C L2d2_3end#LIN 235 GGAGGAGGTGGN-ATTTGAGCTGGGCCTTGAAGGATGGGTAGGATTTGGA 187 chr3qtel1M 90543 CAAATGAGAGGGGAATGGGAAATACATTCTGGGCTCTGAGGACAGTTTAA 90592 i ii - i v ivi ii vvv i i i iv i C L2d2_3end#LIN 186 TAGGTG-GAGAGGAAGGGGAAGGGCATTCCAGGCGGGGGGAACGGCGTGA 138 chr3qtel1M 90593 GCAAAGGCATGGAAGGAGG-----GCA--GCA-GTTTAGGG--------G 90626 iii i vi ----- -- i- ii -------- C L2d2_3end#LIN 137 GCAAAGGCGCAGAGGCGGGAANGCGCAAGGCGTGTTCGGGGGACAGTGAG 88 chr3qtel1M 90627 TGGGCCAGCAGGGCTGTAGCACAG 90650 i i ivv v iv C L2d2_3end#LIN 87 TAGACCAGTTTGGCTGGAGCGGAG 64 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.77 CpG sites = 34, Kimura (unadjusted) = 43.16 Transitions / transversions = 2.62 (34/13) Gap_init rate = 0.05 (8 / 153), avg. gap size = 2.75 (22 / 8) 285 31.84 3.48 1.71 chr3qtel1M 90497 90611 (909389) C L2d_3end#LINE/L2 (281) 235 119 m_b138s601i9 5169 chr3qtel1M 90497 GGATAAGGTAGAGATTC---CTGGGCCATAAAGGGTGGATAGGACCTA-A 90542 vi i - i i--- v i i i ii i- C L2d_3end#LINE 235 GGAGGAGGTGG-GACTTGAGCTGGGCCTTGAAGGATGGGTAGGATTTGGA 187 chr3qtel1M 90543 CAAATGAGAGGGGAATGGGAAATACATTCTGGGCTCTGAGGACAGTTTAA 90592 i i - i v ivi ii vvv i i i iv i C L2d_3end#LINE 186 TAGA-GAGAGAGGAAGGGGAAGGGCATTCCAGGCGGGGGGAACGGCGTGA 138 chr3qtel1M 90593 GCAAAGGCATGGAAGGAGG 90611 iii i vi C L2d_3end#LINE 137 GCAAAGGCGCAGAGGCGGG 119 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.38 CpG sites = 27, Kimura (unadjusted) = 45.11 Transitions / transversions = 3.00 (27/9) Gap_init rate = 0.04 (4 / 114), avg. gap size = 1.50 (6 / 4) 205 27.91 0.00 0.00 chr3qtel1M 90675 90717 (909283) MIR3#SINE/MIR 33 75 (133) m_b138s601i10 5170 chr3qtel1M 90675 CTGTGGGTCTGAGGACTTGAGTTCTAATCCCAGCTGTACCATT 90717 v i v ii i i i i v i i MIR3#SINE/MIR 33 CTGGGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACT 75 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.33 CpG sites = 9, Kimura (unadjusted) = 37.26 Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 413 23.82 2.75 3.70 chr3qtel1M 91208 91316 (908684) C MIR#SINE/MIR (105) 157 50 m_b138s601i11 5171 chr3qtel1M 91208 TGCTATTCATTCTCCAGTTTATTTTACAGATGAGGAAACTGAGGCAAACA 91257 i - v ---ii v v C MIR#SINE/MIR 157 TACTATT-ATTATCC---CCATTTTACAGATGAGGAAACTGAGGCACAGA 112 chr3qtel1M 91258 G-GGTTAAATTACTTATCCAGGGATAAATAGTTAAT--GTGTCTGAATCC 91304 - i v ii i vi v i i i -- v v ii v C MIR#SINE/MIR 111 GAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 62 chr3qtel1M 91305 AGATTTGAACTC 91316 i i i C MIR#SINE/MIR 61 GGATTCGAACCC 50 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.07 CpG sites = 16, Kimura (unadjusted) = 29.46 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.06 (6 / 108), avg. gap size = 1.17 (7 / 6) 410 23.70 2.29 9.84 chr3qtel1M 91211 91341 (908659) C MIRc#SINE/MIR (110) 158 37 m_b138s601i12 5171 chr3qtel1M 91211 TATTCATTCTCCAGTTTATTTTACAGATGAGGAAACTGAGGCAAACAG-G 91259 - v ---ii vv v - C MIRc#SINE/MIR 158 TATT-ATTATCC---CCATTTTACAGATGAGGAAACTGAGGCTCAGAGAG 113 chr3qtel1M 91260 GTTAAATTACTTATCCAGGGATAAATAGTTAAT--GTGTCTGAATCCAGA 91307 i v ii i vi v i i i -- v v ii vi C MIRc#SINE/MIR 112 GTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGA 63 chr3qtel1M 91308 TTTGAACTCTCAAAGATGAGTTTTCCTGACTCTA 91341 i i i ---- ---- i i C MIRc#SINE/MIR 62 CTCGAACCC----AG----GTCTTCCTGACTCCA 37 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.82 CpG sites = 18, Kimura (unadjusted) = 29.03 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.11 (14 / 130), avg. gap size = 1.07 (15 / 14) 338 24.21 2.06 2.06 chr3qtel1M 91383 91479 (908521) Charlie4#DNA/hAT-Charlie 4 100 (3278) m_b138s502i0 5172 chr3qtel1M 91383 GGGTTCTTTATCTGAGGTTCATGGACCTCCAGGGGGAATCTGTGGAGAGA 91432 v i i i i i i -- i v Charlie4#DNA/ 4 GGGTTCTTAACCTGGGGTCCACGGACCCCCAAGGGG--TCCGTGGATAGA 51 chr3qtel1M 91433 TTTCAGAGGATCCACGAAGTTGA--GGGAACAACTTTTTTTTTTAATTT 91479 v i i ii v i-- v v viv i v Charlie4#DNA/ 52 ATTCAGGGGGTCCGTGAACTTGGATGGGAAAAAATTACATCTTTATTTT 100 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 25.47 CpG sites = 14, Kimura (unadjusted) = 29.92 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.03 (3 / 96), avg. gap size = 1.33 (4 / 3) 252 15.68 0.00 8.89 chr3qtel1M 91727 91775 (908225) Charlie4#DNA/hAT-Charlie 3302 3346 (32) m_b138s502i1 5173 chr3qtel1M 91727 TTATTCTGAAAAGGGGTCTATGAGCTTCACCAAACTCTCTGCCAGAGAG 91775 i i ii i ---- i i Charlie4#DNA/ 3302 TTATTCTGAGAAGGGGTCCATAGGCTTCACCAGA----CTGCCAAAGGG 3346 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 18.63 CpG sites = 7, Kimura (unadjusted) = 18.63 Transitions / transversions = 1.00 (7/0) Gap_init rate = 0.08 (4 / 48), avg. gap size = 1.00 (4 / 4) 417 25.79 4.20 8.77 chr3qtel1M 92520 92638 (907362) C MIRc#SINE/MIR (153) 115 2 m_b138s601i13 5174 chr3qtel1M 92520 GGGGTTAAATGAC-----CAGGATCACACAGCTAGGAAATGTTAAATATC 92564 i i ----- i i v i vi ------ C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCA------ 72 chr3qtel1M 92565 TGAGGTCAGATTTGAATTCGAGTCCTCCTGACTTCAGGGCTAGTGCTCTC 92614 - vivi i i ii ii i i i v i i C MIRc#SINE/MIR 71 -GAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTT 23 chr3qtel1M 92615 TCCACTGCATTACCTAGCTGCCCC 92638 ii ---i i C MIRc#SINE/MIR 22 TCCACTGCACCAC---ACTGCCTC 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.94 CpG sites = 23, Kimura (unadjusted) = 33.95 Transitions / transversions = 4.60 (23/5) Gap_init rate = 0.09 (11 / 118), avg. gap size = 1.36 (15 / 11) 324 27.96 0.00 0.00 chr3qtel1M 92734 92826 (907174) L1ME4b_3end#LINE/L1 460 552 (340) m_b138s551i5 5175 chr3qtel1M 92734 TTTGTGATGGCAAGAAACTGGAAACCGAGTGGACACCCATCAGTTGGAGA 92783 i i i i i vivv ii iii i v i L1ME4b_3end#L 460 TTTGTAATAGCAAAAGATTGGAAACAACCTAAATGTCCATCAATAGGGGA 509 chr3qtel1M 92784 CTGGCTAATTAAGTTACGGTACATGAATGTAATGGAATATTAT 92826 i v i i vv ii i L1ME4b_3end#L 510 CTGGTTAAATAAATTATGGTACATCCATACAATGGAATACTAT 552 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.15 CpG sites = 19, Kimura (unadjusted) = 37.15 Transitions / transversions = 2.71 (19/7) Gap_init rate = 0.00 (0 / 92), avg. gap size = 0.0 (0 / 0) 207 31.25 11.61 0.00 chr3qtel1M 94861 94972 (905028) L3#LINE/CR1 3784 3908 (191) m_b138s601i14 5176 chr3qtel1M 94861 GGAAGACTGTCATGGAGAAGAGAGATCAGAGCTGTTTGTTTTGGCTCC-G 94909 i i i vi i i vi i ivv v - L3#LINE/CR1 3784 GAAGGGCTGTCATGTGGAAGAGGGATTAGACTTATTCTGTGTGGCTCCAG 3833 chr3qtel1M 94910 GGAGCAGAG-TAGGA---------GGGAACTAC--GAAGGCCGAACTGGG 94947 i i i- --------- i ii -- i v vi v L3#LINE/CR1 3834 AGGGCAGAACTAGGACCAATGGGTGGAAGTTACAGGGAGGCAGATTTCGG 3883 chr3qtel1M 94948 CTACGTGTCCAGAATCACTTCCTAA 94972 vvi i vvi vv i L3#LINE/CR1 3884 CTCAATATAAGGAAGAACTTTCTAA 3908 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.85 CpG sites = 21, Kimura (unadjusted) = 41.85 Transitions / transversions = 1.50 (21/14) Gap_init rate = 0.04 (4 / 111), avg. gap size = 3.25 (13 / 4) 64 14.39 3.82 3.82 chr3qtel1M 95386 95542 (904458) (GTCTCT)n#Simple_repeat 1 157 (0) m_b138s252i8 5177 chr3qtel1M 95386 GTCTCTCCCTATGGTTCTCTGTCTCTGTCTCTGTTTCTCCCTCTCTGTCT 95435 vi v - - -- iv (GTCTCT)n#Sim 1 GTCTCTGTCTCT-G-TCTCTGTCTCTGTCTCTG--TCTCTGTCTCTGTCT 46 chr3qtel1M 95436 CT-T-TCTCACCATGTCTTCGTCTCTCTTTTTGT-T-TGTCTCTGTCTC- 95480 - - vv iv ii v i i - - - (GTCTCT)n#Sim 47 CTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCT 96 chr3qtel1M 95481 -TCTCTGTCTTTCTCTCTGTCTCTGTCTCTGTCTGTCTGTCTCTGTCTCT 95529 - i v -- (GTCTCT)n#Sim 97 GTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTC--TCTGTCTCTGTCTCT 144 chr3qtel1M 95530 GTTTCTCTCCCTG 95542 i v i (GTCTCT)n#Sim 145 GTCTCTGTCTCTG 157 Matrix = Unknown Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.08 (12 / 156), avg. gap size = 1.00 (12 / 12) 278 20.67 4.31 0.46 chr3qtel1M 95543 95751 (904249) C HERVIP10FH#LTR/ERV1 (4104) 998 782 m_b138s701i0 5178 chr3qtel1M 95543 TCTCTCTCTCTGTCTCTGTCTCTTTCTATCTCTCTGTCTTTCTCTCTCTG 95592 v v i v i i iv i i v C HERVIP10FH#LT 998 TCTATCTCTCTCTTTCTTTCTCTCTTTGACTTTCTGTCTCTCTCTCTCTC 949 chr3qtel1M 95593 TCTA--TCTCTCTTTGTTTCTCTGTCTCT------CTCTGTCTGTCTCTT 95634 i-- i i ------ i v i C HERVIP10FH#LT 948 TCTGACTCCCTCTTTGTCTCTCTGTCTCTTCCTCTCTCTGCCTCTCTCTC 899 chr3qtel1M 95635 TCTCTGTCTCTCTCTCTGTCTCTCTCTCTGTGTCTCTGTCTTTTTCTGTC 95684 i v i i viv v i v C HERVIP10FH#LT 898 TCTTTGACTCCCTCTTTGTCTCTCTCTCTCCCTCTCTCTCTCTTTCTCTC 849 chr3qtel1M 95685 TCTCTGTCTCTCTCTCTGTCTCTGTCTCT-TTCTGTCTCTGTCTCTCTGT 95733 v ii v v - v i -i i C HERVIP10FH#LT 848 TCTCTCTCTTCCTCTCTCTCTCTCTCTCTCTTCTCTCTTT-CCTCTCTGC 800 chr3qtel1M 95734 CTGTCGCTCTCTGTTTCT 95751 iv vi i ii C HERVIP10FH#LT 799 TGGTCTTTCCCTGCCTCT 782 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 24.62 CpG sites = 26, Kimura (unadjusted) = 24.62 Transitions / transversions = 1.53 (26/17) Gap_init rate = 0.02 (4 / 208), avg. gap size = 2.50 (10 / 4) 278 17.31 3.85 0.00 chr3qtel1M 95637 95783 (904217) C HERVIP10FH#LTR/ERV1 (4104) 998 846 m_b138s701i1 5178 chr3qtel1M 95637 TCTGTCTCTCTCTCTGTCTCTCTCTCTGTGTCTCTGTCTTTTTCTGTCTC 95686 i i v i i vv i i i v C HERVIP10FH#LT 998 TCTATCTCTCTCTTTCTTTCTCTCTTTGACTTTCTGTCTCTCTCTCTCTC 949 chr3qtel1M 95687 TCTGTCTCTCTCTCTGTCTCT--GTCTCTTTCTGTCTCTGTCTCTCTGTC 95734 v i i -- i v i v C HERVIP10FH#LT 948 TCTGACTCCCTCTTTGTCTCTCTGTCTCTTCCTCTCTCTGCCTCTCTCTC 899 chr3qtel1M 95735 TGT----CGCTCTCTGTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 95780 v ---- v i v v i i C HERVIP10FH#LT 898 TCTTTGACTCCCTCTTTGTCTCTCTCTCTCCCTCTCTCTCTCTTTCTCTC 849 chr3qtel1M 95781 TCT 95783 C HERVIP10FH#LT 848 TCT 846 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 20.01 CpG sites = 15, Kimura (unadjusted) = 20.01 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.01 (2 / 146), avg. gap size = 3.00 (6 / 2) 38 0.00 0.00 0.00 chr3qtel1M 95784 95816 (904184) (CA)n#Simple_repeat 1 33 (0) c_b138s251i0 5179 chr3qtel1M 95784 CACACACACACACACACACACACACACACACAC 95816 (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACAC 33 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 303 24.15 7.75 6.92 chr3qtel1M 96642 96770 (903230) C MIR3#SINE/MIR (59) 149 20 m_b138s601i15 5180 chr3qtel1M 96642 CCCCCTTGTTTTTTTTCTGAGGCAATTG--GC--------ATTAAGTGAC 96681 ii vivvv v i -- --------i v C MIR3#SINE/MIR 149 CCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGAC 100 chr3qtel1M 96682 TTGGCCGGGGTCACACAGCTAGGAAGTGTTAAGTGTCTGAGACCAGATTT 96731 v ii ? ------ - v v v vi i v C MIR3#SINE/MIR 99 TTGCCCAAGGTCACACAGCNA------GTT-AGTGGCAGAGCCGGGACTA 57 chr3qtel1M 96732 GAACTCAAGTTCTCCTGACTTCAGAGCTGGTGCTCTATC 96770 i i - i -v iiv v C MIR3#SINE/MIR 56 GAACCCAGG-TCTCCTGACTCC-CAGTCCGTGCTCTCTC 20 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.68 CpG sites = 14, Kimura (unadjusted) = 29.68 Transitions / transversions = 0.93 (14/15) Gap_init rate = 0.09 (11 / 128), avg. gap size = 1.73 (19 / 11) 385 23.66 0.91 7.77 chr3qtel1M 96658 96767 (903233) C MIR#SINE/MIR (139) 123 21 m_b138s601i16 5180 chr3qtel1M 96658 CTGAGGCA-ATTGGCATTAAGTGACTTGGCCGGGGTCACACAGCTAGGAA 96706 - vv ivi i v ii --- C MIR#SINE/MIR 123 CTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAG--- 77 chr3qtel1M 96707 GTGTTAAGTGTCTGAGACCAGATTTGAACTCAAGTTCTCCTGACTTCAGA 96756 ---- v v v vi i i i ivv - i i C MIR#SINE/MIR 76 ----TAAGTGGCAGAGCCGGGATTCGAACCCAGGCAGT-CTGGCTCCAGA 32 chr3qtel1M 96757 GCTGGTGCTCT 96767 iv C MIR#SINE/MIR 31 GCCCGTGCTCT 21 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.24 CpG sites = 13, Kimura (unadjusted) = 28.60 Transitions / transversions = 1.18 (13/11) Gap_init rate = 0.08 (9 / 109), avg. gap size = 1.00 (9 / 9) 430 23.33 0.94 7.00 chr3qtel1M 96673 96778 (903222) C MIRc#SINE/MIR (157) 111 12 m_b138s601i17 5180 chr3qtel1M 96673 TTAAGTGACTTGGCCGGGGTCACACAGCTAGGAAGTGTTAAGTGTCTGAG 96722 v ii ------- v v C MIRc#SINE/MIR 111 TTAAGTGACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGCAGAG 69 chr3qtel1M 96723 ACCAGATTTGAACTCAAGTTCTCCTGACTTCAGAGCTGGTGCTCTATCAA 96772 v vi i i i i ii i iiv ii v v C MIRc#SINE/MIR 68 CCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCA 19 chr3qtel1M 96773 TTG-ACC 96778 i - C MIRc#SINE/MIR 18 CTGCACC 12 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.17 CpG sites = 15, Kimura (unadjusted) = 28.62 Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.08 (8 / 105), avg. gap size = 1.00 (8 / 8) 73 8.36 0.00 0.00 chr3qtel1M 97391 97493 (902507) (ACACAC)n#Simple_repeat 1 103 (0) m_b138s252i10 5181 chr3qtel1M 97391 ACACATACATACACATACACACACACACATACACACACAAACACACACAT 97440 i i i i v i (ACACAC)n#Sim 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50 chr3qtel1M 97441 ACACACACATACACATACACACACACACACACACACACACACACACACAC 97490 i i (ACACAC)n#Sim 51 ACACACACACACACACACACACACACACACACACACACACACACACACAC 100 chr3qtel1M 97491 ACA 97493 (ACACAC)n#Sim 101 ACA 103 Matrix = Unknown Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.00 (0 / 102), avg. gap size = 0.0 (0 / 0) 37 8.56 0.00 0.00 chr3qtel1M 98306 98355 (901645) (GT)n#Simple_repeat 1 50 (0) c_b138s251i1 5182 chr3qtel1M 98306 GTGTGTGTGCGTGTGTGCATGTGTTTGTGTGTGTGTGTGTGTGTGTGTGT 98355 i ii v (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 229 26.93 4.84 10.17 chr3qtel1M 99192 99315 (900685) C MIRb#SINE/MIR (46) 222 105 m_b138s601i18 5183 chr3qtel1M 99192 TGTGCTTGTAAAGTGTTTTA-AT-TATCTTCTCATTAGATTCTCACAACC 99239 ---- i i - -i iv vi i v C MIRb#SINE/MIR 222 TGTGCT----AAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACA 177 chr3qtel1M 99240 A-CTTGTGA-GTAAGTAGTACTGTGACCCTCACTTTAAAAGAAAGACAAA 99287 - i i - i v i --- i i i ----- v ii i C MIRb#SINE/MIR 176 ACCCTGCGAGGTAGGTATTATT---ATCCCCATTTT-----ACAGATGAG 135 chr3qtel1M 99288 GGGATTCAGGGTCAAACACCT--AGTAACT 99315 ii i v v i v vv -- C MIRb#SINE/MIR 134 GAAACTGAGGCTCAGAGAGGTTAAGTAACT 105 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.66 CpG sites = 20, Kimura (unadjusted) = 34.49 Transitions / transversions = 2.00 (20/10) Gap_init rate = 0.14 (17 / 123), avg. gap size = 1.06 (18 / 17) 235 31.73 11.54 0.00 chr3qtel1M 99195 99298 (900702) C MIRc#SINE/MIR (38) 230 115 m_b138s601i19 5183 chr3qtel1M 99195 GCTTGTAAAGTGTTTTAAT---TATCTTCTCATTAGATTCTCACAACCA- 99240 i ii i i v i---i iv v i v - C MIRc#SINE/MIR 230 GTTTACAAAGCGCTTTCACATACATTATCTCATTTGATCCTCACAACAAC 181 chr3qtel1M 99241 CTTGTGA-GTAAGTA------GTACTGTGACCCTCACTTTA-AAAGAAAG 99282 i - i i ------ i i v i i i - i vi i C MIRc#SINE/MIR 180 CCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGG 131 chr3qtel1M 99283 ACAAAGGGATTCAGGG 99298 v vv i ii i C MIRc#SINE/MIR 130 AAACTGAGGCTCAGAG 115 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.58 CpG sites = 24, Kimura (unadjusted) = 44.46 Transitions / transversions = 2.67 (24/9) Gap_init rate = 0.05 (5 / 103), avg. gap size = 2.40 (12 / 5) 292 23.56 6.36 3.54 chr3qtel1M 99320 99429 (900571) MIR#SINE/MIR 32 144 (118) m_b138s601i20 5184 chr3qtel1M 99320 TCTGGAGC-AG-CTGGATAGAGGGTTGGA---TAGGTCTCAGGCATTTAC 99364 - - vv --- v ---iv - v v i MIR#SINE/MIR 32 TCTGGAGCCAGACTGCCT---GGGTTCGAATCCCGG-CTCTGCCACTTAC 77 chr3qtel1M 99365 CAGCTATGTGTTCCTGAGTAAGTCCCTTTACC-CTATTTGCCTCAGTTT- 99412 i i vi i i i iv v - v v - MIR#SINE/MIR 78 TAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTC 127 chr3qtel1M 99413 TTCATCTGTCAGATAAG 99429 i v i ii MIR#SINE/MIR 128 CTCATCTGTAAAATGGG 144 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.61 CpG sites = 13, Kimura (unadjusted) = 28.61 Transitions / transversions = 1.08 (13/12) Gap_init rate = 0.08 (9 / 109), avg. gap size = 1.22 (11 / 9) 284 35.32 0.00 0.00 chr3qtel1M 99805 100005 (899995) L1PB_orf2#LINE/L1 3094 3294 (0) m_b138s551i7 5185 chr3qtel1M 99805 CAAGCAATAAACTGGGAAAACATTTTTACATTCAAGGGTTCTGATAAAGG 99854 v v i i v i v i i v v vivv i L1PB_orf2#LIN 3094 CAACCCACAGAGTGGGAGAAAATCTTCACAATCTATACATCTGACAAAGG 3143 chr3qtel1M 99855 CTTCATTTCCAAAATATATAGAGAATTGATTCTAATTTATAAGAAATAAA 99904 vi v v i v i i? i v vv v ivii v L1PB_orf2#LIN 3144 ACTAATATCCAGAATCTACAANGAACTCAAACAAATCAGCAAGAAAAAAA 3193 chr3qtel1M 99905 GCCATTCTCCTAATGATAAATGGTCAAAGGATATGAACAGACAATTTTCA 99954 vvv ivv i vii v i v v i i i L1PB_orf2#LIN 3194 CAAACAATCCCATCAAAAAGTGGGCTAAGGACATGAATAGACAATTCTCA 3243 chr3qtel1M 99955 GATGAAGAAACTGAAACCATTTCCACTCATATGAAAGAGTGTTCCAAATC 100004 i v v ivv iviiivv vv i i i v v L1PB_orf2#LIN 3244 AAAGAAGATATACAAATGGCCAACAAACATATGAAAAAATGCTCAACATC 3293 chr3qtel1M 100005 A 100005 L1PB_orf2#LIN 3294 A 3294 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 48.54 CpG sites = 32, Kimura (unadjusted) = 48.54 Transitions / transversions = 0.82 (32/39) Gap_init rate = 0.00 (0 / 200), avg. gap size = 0.0 (0 / 0) 345 30.38 0.00 0.00 chr3qtel1M 99805 99962 (900038) L1PREC2_orf2#LINE/L1 3094 3251 (43) m_b138s551i6 5185 chr3qtel1M 99805 CAAGCAATAAACTGGGAAAACATTTTTACATTCAAGGGTTCTGATAAAGG 99854 v v i i v i v ? i vv v v vv i L1PREC2_orf2# 3094 CAACCTACAGAATGGGAGAAAATNTTTGCAAACTATGCATCTGACAAAGG 3143 chr3qtel1M 99855 CTTCATTTCCAAAATATATAGAGAATTGATTCTAATTTATAAGAAATAAA 99904 ii v v iv v ii i v vv v i v L1PREC2_orf2# 3144 TCTAATATCCAGCATCTATAAGGAACTTAAACAAATTTACAAGAAAAAAA 3193 chr3qtel1M 99905 GCCATTCTCCTAATGATAAATGGTCAAAGGATATGAACAGACAATTTTCA 99954 vvv ivvi i v i v i v i v L1PREC2_orf2# 3194 CAAACAACCCCATTAAAAAGTGGGCAAAGGACATGAACAGACACTTTTCA 3243 chr3qtel1M 99955 GATGAAGA 99962 i v L1PREC2_orf2# 3244 AAAGAAGA 3251 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.35 CpG sites = 19, Kimura (unadjusted) = 39.35 Transitions / transversions = 0.66 (19/29) Gap_init rate = 0.00 (0 / 157), avg. gap size = 0.0 (0 / 0) 1254 27.12 4.55 2.22 chr3qtel1M 99862 100389 (899611) L1ME3G_3end#LINE/L1 7 546 (378) m_b138s551i8 5185 chr3qtel1M 99862 TCCAAAATATATAGAGAATTGATTCTAATTTATAAGAAATAAAGCCATTC 99911 i i i vv v v iv -- v v-- L1ME3G_3end#L 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAA--AAGACAA-- 52 chr3qtel1M 99912 TCCTAAT-GATAAATGGTCAAAGGATATGAACAGACAATTTTCAGATGAA 99960 - i - v v i iv v i L1ME3G_3end#L 53 -CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAG 101 chr3qtel1M 99961 GAAACTGAAACCATTTCCACT---CATATGAAAGAGTGTTCCAAATCACT 100007 - iv -- vv v --- iii i v vv L1ME3G_3end#L 102 GAAA-TACAA--ATGGCCAATAAACATATGAAAAGATGCTCAACCTCACT 148 chr3qtel1M 100008 ATTGATCAGAGAAATGCAAATTAAGACAACTCTGAGCTGTCAACTACACA 100057 v i i i vv v ii - i viv L1ME3G_3end#L 149 AGTAATCAGGGAAATGCAAATTAAAACAACAATGAGATACC-ATTTTTCA 197 chr3qtel1M 100058 GCTGTCATATTGGCTAGAATGACAGGGAAAGATAATGCGGAATGTCAGAG 100107 v ii v v i vvv ii ?vv iiv? i ii v L1ME3G_3end#L 198 CCCATCAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCG 247 chr3qtel1M 100108 AGGATGCGGGAAAACTGGGACACTGATACATTGCTGGTGAAGTTGTGCAC 100157 i i i v v v v i iiiv iv i L1ME3G_3end#L 248 AGGGTGTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAAT 297 chr3qtel1M 100158 GAATCCAGCCATTCTGGAGAGCAATCTGGAATTATGCCCAAAAAGTTATC 100207 vii v ? i i i v v viviv v --- L1ME3G_3end#L 298 TGGTACAGCCNTTTTGGAGGGCAATTTGGCAGTATCTATTAAAATTT--- 344 chr3qtel1M 100208 AAACTGTGCATACCCTTTGATCCAGCAGTGTTACTCCTGGGCTTGTATCC 100257 v i i i vii i ? ?v v L1ME3G_3end#L 345 AAAATGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCC 394 chr3qtel1M 100258 CAGAGAGA----CCCACATGTGCAAAA----------------ATGTTTG 100287 i ? i ---- v v ---------------- ii L1ME3G_3end#L 395 TANAGAAATACTCGCACATGTGCACAAGGANGCATGTACAAGGATGTTCA 444 chr3qtel1M 100288 TGGCAGCCCTTTTTGTAGTGGCCAGAAACTGGAAACTGAGTGGATGCCCA 100337 v vi v i i v i i vivv ii i L1ME3G_3end#L 445 TTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCA 494 chr3qtel1M 100338 TCAGCTCAAGAATGGCTGAATAAATTGTGGTATATGAATGTTATGGAATA 100387 iivvii i i i vv ii L1ME3G_3end#L 495 TCAATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATA 544 chr3qtel1M 100388 TT 100389 i L1ME3G_3end#L 545 CT 546 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.42 CpG sites = 75, Kimura (unadjusted) = 34.73 Transitions / transversions = 1.15 (75/65) Gap_init rate = 0.03 (16 / 527), avg. gap size = 2.25 (36 / 16) 779 30.84 4.61 2.25 chr3qtel1M 99867 100473 (899527) L1MC4a_3end#LINE/L1 12 632 (1997) m_b138s551i9 5185 chr3qtel1M 99867 AATATATAGAGAATTGATTCTAATTTATAAGAAATAAAGCCATTCTCCTA 99916 i i v- vv ? ?iv ? - ii vvvv ii L1MC4a_3end#L 12 AATATATAAAGAACTC-TTAAAANTNGAAAGNAA-AAGACCAAAAACCCG 59 chr3qtel1M 99917 AT-GATAAATGGTCAAAGGATATGAACAGACAATTTTCAGATGAAGAAAC 99965 - v v i i iv i -- ? i L1MC4a_3end#L 60 ATAGAAAAATGGGCAAAAGACATGAACAGACAATTCACAAA--AAGANAT 107 chr3qtel1M 99966 TGAAACCATTTCCACTCATATGAAAGAGTGTTCCAAATCACTATTGATCA 100015 v? iviiiiii vv iii v vv vv i v L1MC4a_3end#L 108 ANAAATGGCCCTTAAACATATGAAAAGATGTTCAACCTCACTCATAATAA 157 chr3qtel1M 100016 GAGAAATGCAAATTAAGACAACTCTGAGCTGTCAACTACACAGCTGTCAT 100065 i v v v ii - i v v v i v L1MC4a_3end#L 158 GAGAAATGCAAATTAAAACTACACTGAGATACC-ATTTCTCACCTATCAG 206 chr3qtel1M 100066 ATTGGCTAGAATGACAGGGAAAGATAATGCGGAATGTCAGAGAGGATGCG 100115 v i vvv ii vvv i ii ivvv ii v v i L1MC4a_3end#L 207 ATTGGCAAAAATTCAAAAGTTTGACAACACACTCTGTTGGCGAGGCTGTG 256 chr3qtel1M 100116 GGAAAACTGGGACACTGATACATTGCTGGTGAAGTTGTGCACGAATCCAG 100165 i v v v v iiiv iiv ?vii v i L1MC4a_3end#L 257 GGGAAACAGGCACTCTCATACATTGCTGGTGGGAATGCAAANTGGTACAA 306 chr3qtel1M 100166 CCATTCTGGAGAGCAATCTGGAATTATGCCCAA-AAAGTTATCAAACTGT 100214 v ? i v i v v -- i - ii - --- i L1MC4a_3end#L 307 CCCTTNTGGAGGGGAATTTGGCAATAT--CTAACAAAACTA-CA---TAT 350 chr3qtel1M 100215 GCA--TACCCTTTGATCCAGCAGTGTTACTCCTGGGCTTGTATCCCAGAG 100262 -- i i vii i i vv v i iii L1MC4a_3end#L 351 GCATTTACCCTTTGACCCAGCAATCCCACTTCTAGGAATTTACCCTGAAG 400 chr3qtel1M 100263 AGAC-CC----ACATGTGCAAAA------ATG----------TTTGTGGC 100291 v - ---- i ------ ---------- ii v L1MC4a_3end#L 401 ATACACCTCCAACATGTACAAAATNACATATGCACAAGGTTATTCATTGC 450 chr3qtel1M 100292 AGCCCTTTTTGTAGTGGCCAGAAACTGGAAACTGAGTGGATGCCCATCAG 100341 vi v i v v i v i vivv ii ??i L1MC4a_3end#L 451 AGCATTGTTTGTAATTGCAAAATATTGGAAACAACCTAAATGCCCATNNA 500 chr3qtel1M 100342 CTCAAGAATGGCTGAATAAATTGTGGTATATGAATGTTATGGAATATTGT 100391 ivvi ? i i i i vv iiiv i i i L1MC4a_3end#L 501 TAGGAGANTGGTTGAATAAACTATGGTACATCCACACAATGGAGTACTAT 550 chr3qtel1M 100392 TATTCTGTAAGAAATGACCAACAGGATGATTTC-AGAAA--GGCCTGGAG 100438 vvvv i - -- vv v i - vi -- iiv L1MC4a_3end#L 551 GCAGCTGTAAAAAA-GA--ATGAGGAAGATCTCTATGAACTGATATGGAG 597 chr3qtel1M 100439 AGACTTACACGAACTGATGCTGAGTGAAATGAGCA 100473 v i v v vv iv i i vi L1MC4a_3end#L 598 TGATTTCCAGGATATATTGTTAAGTGAAAAAAGCA 632 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.09 CpG sites = 96, Kimura (unadjusted) = 41.42 Transitions / transversions = 1.10 (96/87) Gap_init rate = 0.04 (23 / 606), avg. gap size = 1.83 (42 / 23) 14 22.14 3.57 3.57 chr3qtel1M 100926 100981 (899019) (TAAA)n#Simple_repeat 1 56 (0) m_b138s252i11 5186 chr3qtel1M 100926 TAAATAAATAAATTAAAAAAAAAACAATCTGACAGAAA-AAA-AAAAAAA 100973 v v v i -v - v v - - v (TAAA)n#Simpl 1 TAAATAAATAAATAAATAAATAAATAA-AT-AAATAAATAAATAAATAAA 48 chr3qtel1M 100974 GAAATGAA 100981 v i (TAAA)n#Simpl 49 TAAATAAA 56 Matrix = Unknown Transitions / transversions = 0.25 (2/8) Gap_init rate = 0.07 (4 / 55), avg. gap size = 1.00 (4 / 4) 16 28.30 0.00 0.00 chr3qtel1M 100927 100977 (899023) (AAAAA)n#Simple_repeat 1 51 (0) m_b138s252i12 5186 chr3qtel1M 100927 AAATAAATAAATTAAAAAAAAAACAATCTGACAGAAAAAAAAAAAAAGAA 100976 v v vv v vvvi v i i (AAAAA)n#Simp 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr3qtel1M 100977 A 100977 (AAAAA)n#Simp 51 A 51 Matrix = Unknown Transitions / transversions = 0.33 (3/9) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 265 36.55 11.86 2.65 chr3qtel1M 102229 102540 (897460) L2#LINE/L2 2740 3079 (3) m_b138s601i22 5187 chr3qtel1M 102229 GTCAGCCTGCCTCAAGTTACTTCTCACTCCAATCCATGCTGCACTTCACT 102278 vv i v viivivi i v ? i i v vv vivi v L2#LINE/L2 2740 GTCTCCCTGCTTCCACCCTTGCCCCCCTNCAGTCTATTCTCAACACAGCA 2789 chr3qtel1M 102279 ACCAAAGTGGTTTTCCTAAA-TGCAGGTCCAATCATGTC--TCCCCTCCC 102325 i i i ii ii -i i i vi -- i v i L2#LINE/L2 2790 GCCAGAGTGATCCTTTTAAAACGTAAGTCAGATCATGTCACTCCTCTGCT 2839 chr3qtel1M 102326 CAATACACCACAATGGCTTCCTCTTGCCTCCAGGATCAAGTGCAAAA--- 102372 v v iv iv iv vii ii v ivv i--- L2#LINE/L2 2840 CAAAACCCTCCAATGGCTTCCCATCTCACTCAGAGTAAAAGCCAAAGTCC 2889 chr3qtel1M 102373 -TGCAATT-----CAAGCCTCT-CAGAACCCAGCCTCACTTCACCTTTCT 102415 - i v----- v i - vi i ii i i v v i i L2#LINE/L2 2890 TTACAATGGCCTACAAGGCCCTACATGATCTGGTCCCCCGTTACCTCTCT 2939 chr3qtel1M 102416 AAGTTATTCTCTTGTTATTCT----TTAATTTAGTCT------------C 102449 i vi vv i iii i ----i vii i v i------------ L2#LINE/L2 2940 GACCTCATCTCCTACCACTCTCCCCCTCGCTCACTCCGCTCCAGCCACAC 2989 chr3qtel1M 102450 TGGCCTCCTGGTTGTGCCGTGAACA----AGACACTGCCTTCTTTGACTC 102495 v i v vi ---- i - iii --- v L2#LINE/L2 2990 TGGCCTCCTTGCTGTTCCTCGAACACGCCAGGCAC-GCTCCC---GCCTC 3035 chr3qtel1M 102496 TAAGCTTTT---TTTCCTG-ACCATCTATCAAACCTGAAATGCTCTCTC 102540 vii i ---i v -v v -----i i i ii L2#LINE/L2 3036 AGGGCCTTTGCACTTGCTGTTCCCTCT-----GCCTGGAACGCTCTTCC 3079 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 49.91 CpG sites = 69, Kimura (unadjusted) = 53.47 Transitions / transversions = 1.64 (69/42) Gap_init rate = 0.06 (20 / 311), avg. gap size = 2.30 (46 / 20) 599 36.37 4.74 6.91 chr3qtel1M 102395 102837 (897163) L2b_3end#LINE/L2 27 460 (6) m_b138s601i23 5187 chr3qtel1M 102395 CCAGCCTCACTTCACCTTTCTAAGTTATTCTCTTGTTATTC--TTTAATT 102442 i ii ------ --ii i iiv ii -- i iv i L2b_3end#LINE 27 CCGGCCTCATCTC------CTA--CCACTCTCCCCTTGCTCACTCTGCTC 68 chr3qtel1M 102443 TAGTCTC--TGGCCTCCTGGTTGTGCCGTGAACAAGACACTGCCTTCTTT 102490 i i v -- v i v vi v v ?- ii? ii L2b_3end#LINE 69 CAGCCACACTGGCCTCCTTGCTGTTCCTCGAACACGCCAN-GCTCNCTCC 117 chr3qtel1M 102491 -GACTCTAAGCTTTTTTTCCTGACCATCTATCAAACCTGAAATGCTCT-- 102537 - v vii i viv ? vivv iv vi- i i i -- L2b_3end#LINE 118 CGCCTCAGGGCCTTTGCACNTGCTGTTCCCTCTG-CCTGGAACGCCCTTC 166 chr3qtel1M 102538 -----CTCTGGAAAAGAGGAAACATTTGACAGATCTCCCTGTCTTCCTTT 102582 ----- v------------ iii i vi - ivv v i L2b_3end#LINE 167 CCCACCTCTT------------CGCCTGGCCAA-CTCCTACTCATCCTTC 203 chr3qtel1M 102583 AAATTCTAACTGAACTCTCATCTTCTCCAAGAAGCTTTCCCCAAACATTC 102632 ii iii i v v v i i ii ii ii v --- L2b_3end#LINE 204 AGGTCTCAGCTCAAATGTCACCTCCTCCGGGAAGCCCTCCCTGACC---C 250 chr3qtel1M 102633 TTTAATCCTAGTTTGTT--CCTTTTGTGGCCTATTTCCAAT--TACCCTG 102678 iii iv vi iv vi-- ii v v i-iii i -- L2b_3end#LINE 251 CCCAGGCCGGGTCAGGCGCCCTCCTCTGGGCC-CCCCCAGTCCTACCCTG 299 chr3qtel1M 102679 TACATACTTTACTTTGTACACATTTGTTTGTATG-GTGTCTCTCCCGTCA 102727 i---i i ivv i ?vvii i ? ii -v i iii L2b_3end#LINE 300 C---CACTCTGGGTTATNATTGTCTGNTTACATGTCTGTCTCCCCCACTA 346 chr3qtel1M 102728 GATTTTAAGCTCCTTGAGGACAGGGAC--TGTCT--TTTGCTTCCTTTTG 102773 i v i v i --? --i i iv ivi L2b_3end#LINE 347 GACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTG 396 chr3qtel1M 102774 TATCCCTGGTGCTTACCACAATGTCTGACATGTAGAAGGTGCTTAACAAG 102823 ii i i v i? i i iii v i i ii i L2b_3end#LINE 397 TATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAA 446 chr3qtel1M 102824 AGTTTATTGATTGA 102837 vi i v L2b_3end#LINE 447 TATTTGTTGAATGA 460 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 50.62 CpG sites = 105, Kimura (unadjusted) = 55.72 Transitions / transversions = 2.33 (105/45) Gap_init rate = 0.09 (39 / 442), avg. gap size = 1.31 (51 / 39) 35 22.57 3.00 0.98 chr3qtel1M 103765 103864 (896136) (ATAG)n#Simple_repeat 1 102 (0) m_b138s252i13 5188 chr3qtel1M 103765 ATAGCTAGTTAAGTAGACAGGTAGATGGCTAGATAGAT-GATAGATAGAT 103813 v v ii i i i v - (ATAG)n#Simpl 1 ATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGAT 50 chr3qtel1M 103814 AGGTAGACAGACAGAT-GTTGGGATAGATTGCTAGAT-GAGAACTAGTTA 103861 i i i - v -i v v - v iv v (ATAG)n#Simpl 51 AGATAGATAGATAGATAGAT-AGATAGATAGATAGATAGATAGATAGATA 99 chr3qtel1M 103862 GAT 103864 (ATAG)n#Simpl 100 GAT 102 Matrix = Unknown Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.04 (4 / 99), avg. gap size = 1.00 (4 / 4) 11 16.54 5.88 0.00 chr3qtel1M 104306 104339 (895661) (TCTTTC)n#Simple_repeat 1 36 (0) m_b138s252i14 5189 chr3qtel1M 104306 TCTTTCTCTTTCTCCTTC-C-ATCTACTTCTCTCTC 104339 i - -v vi i (TCTTTC)n#Sim 1 TCTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCTTTC 36 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2) 525 29.38 2.42 1.20 chr3qtel1M 104558 104805 (895195) L1M4_orf2#LINE/L1 1632 1882 (1412) m_b138s551i10 5190 chr3qtel1M 104558 CAAAATGCAAGGAAAC----TACAGCAATATATCACAAAGGTTATGCATT 104603 i v v ---- v i v v i i i ii L1M4_orf2#LIN 1632 CAAAATACTAGCAAACCGAATCCAGCAACATATAAAAAGGATTATACACC 1681 chr3qtel1M 104604 ATGACCAGGTGGAGTTCATAGCAGGCATGGAGGACTAGTTCAGTAACAGA 104653 i ii i vv v v i ii i ii v?v L1M4_orf2#LIN 1682 ATGACCAAGTGGGATTTATCCCAGGAATGCAAGGTTGGTTCAACATNCGA 1731 chr3qtel1M 104654 CAAACTATCAGTGTAACGAATTATATCAATAACAAAAACAACACAAATCA 104703 v v v i iiv ii i iv v vi v i L1M4_orf2#LIN 1732 AAATCAATCAATGTAATACACCATATTAATAGAATAAAGGACAAAAACCA 1781 chr3qtel1M 104704 TATGGTAATCTCGA--GATGCAGAAAATTTTTTTTTGACAAAACACAACA 104751 i i v i -- i vviv -- iv L1M4_orf2#LIN 1782 CATGATCATCTCAATAGACGCAGAAAAAGCATTT--GACAAAATCCAACA 1829 chr3qtel1M 104752 TCCATTCCTGTTTAAAACACAGAAAAAAAATAGGAATAAATGGAGCCTTT 104801 i v v v v -vv v v i v iiv i L1M4_orf2#LIN 1830 CCCTTTCATGATAAAAACAC-TCAACAAACTAGGAATAGAAGGGAACTTC 1878 chr3qtel1M 104802 CTTA 104805 i L1M4_orf2#LIN 1879 CTCA 1882 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.47 CpG sites = 38, Kimura (unadjusted) = 38.13 Transitions / transversions = 1.12 (38/34) Gap_init rate = 0.02 (5 / 247), avg. gap size = 1.80 (9 / 5) 425 33.97 1.92 0.95 chr3qtel1M 104576 104887 (895113) L1MC_orf2#LINE/L1 1654 1968 (1326) m_b138s551i12 5190 chr3qtel1M 104576 CAGCAATATATCACAAAGGTTATGCATTATGACCAGGTGGAGTTCATAGC 104625 i i v v iii i ii i i ii i vv L1MC_orf2#LIN 1654 CAACAATGTATAAAAAGAATTATACACCACGACCAAGTGGGATTTATCCC 1703 chr3qtel1M 104626 AGGCATGGAGGACTAGTTCAGTAACAGACAAACTATCAGTGTAACGAATT 104675 i v i i i ii viv v v v i i ivv i L1MC_orf2#LIN 1704 AGGTATGCAAGGCTGGTTCAACATTCGAAAATCAATTAATGTAATCCATC 1753 chr3qtel1M 104676 ATATCAATAACAAAAACAACACAAATCATATGGTAATCTCGA--GATGCA 104723 i i ivvv v v v i i v v i -- L1MC_orf2#LIN 1754 ACATCAACAGGCTAAAGAAGAAAAATCACATGATCATATCAATAGATGCA 1803 chr3qtel1M 104724 GAAAATTTTTTTTTGACAAAACACAACATCCATTCCTGTTTAAAACACAG 104773 vviv -- iv i v v v v -v L1MC_orf2#LIN 1804 GAAAAAGCATTT--GACAAAATCCAACACCCATTCATGATAAAAACTC-T 1850 chr3qtel1M 104774 AAAAAAAATAGGAATAAATGGAGCCTTTCTTACAATGACAAGTAGTCTTT 104823 v iv v i v iiv i i vvv i iv iiv i L1MC_orf2#LIN 1851 CAGCAAACTAGGAATAGAGGGGAACTTCCTCAACTTGATAAAGAACATCT 1900 chr3qtel1M 104824 ATCTGAAACCAAGAGCAATCATTAT-CTGGATTGAAATAAACTAGAAAC- 104871 ivvi v v v v i - vi v vi v ? i - L1MC_orf2#LIN 1901 ACAAAAAACCTACAGCTAACATCATACTTAATGGTGAGAAACTNGAAGCT 1950 chr3qtel1M 104872 --CTCAGTAAGGCCAGAA 104887 -- i iv ii i L1MC_orf2#LIN 1951 TTCCCGCTAAGATCAGGA 1968 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 45.26 CpG sites = 55, Kimura (unadjusted) = 46.46 Transitions / transversions = 1.10 (55/50) Gap_init rate = 0.02 (7 / 311), avg. gap size = 1.29 (9 / 7) 512 31.11 0.73 1.10 chr3qtel1M 104576 104848 (895152) L1MD_orf2#LINE/L1 1654 1925 (1369) m_b138s551i11 5190 chr3qtel1M 104576 CAGCAATATATCACAAAGGTTATGCATTATGACCAGGTGGAGTTCATAGC 104625 v v iii i ii i i i vv L1MD_orf2#LIN 1654 CAGCAATATATAAAAAGAATTATACACCATGACCAAGTGGGGTTTATTCC 1703 chr3qtel1M 104626 AGGCATGGAGGACTAGTTCAGTAACAGACAAACTATCAGTGTAACGAATT 104675 ? v i i i i viv v v v i ivv ii L1MD_orf2#LIN 1704 AGGNATGCAAGGCTGGTTCAATATTCGAAAATCAATCAATGTAATCCACC 1753 chr3qtel1M 104676 ATATCAATAACAAAAACAACACAAATCATATGGTAATCTCGA--GATGCA 104723 i i ivvv v v v i i v v i -- L1MD_orf2#LIN 1754 ATATTAACAGGCTAAAGAAGAAAAATCACATGATCATATCAATTGATGCA 1803 chr3qtel1M 104724 GAAAATTTTTTTTTGACAAAACACAACATCCATTCCTGTTTAAAACACAG 104773 --vviv iv i v v v v -v L1MD_orf2#LIN 1804 GAAAA--AGCATTTGACAAAATTCAACACCCATTCATGATAAAAACTC-T 1850 chr3qtel1M 104774 AAAAAAAATAGGAATAAATGGAGCCTTTCTTACAATGACAAGTAGTCTTT 104823 v i? v i v iiv i i vvv i iv iv i L1MD_orf2#LIN 1851 CAGNAAACTAGGAATAGAGGGGAACTTCCTCAACTTGATAAAGAGCATCT 1900 chr3qtel1M 104824 ATCTGAAACCAAGAGCAATCATTAT 104848 ivvi v v v v i L1MD_orf2#LIN 1901 ACAAAAAACCTACAGCTAACATCAT 1925 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.01 CpG sites = 40, Kimura (unadjusted) = 41.01 Transitions / transversions = 0.91 (40/44) Gap_init rate = 0.01 (4 / 272), avg. gap size = 1.25 (5 / 4) 15 34.23 1.75 0.00 chr3qtel1M 106596 106652 (893348) (AT)n#Simple_repeat 1 58 (0) m_b138s252i15 5191 chr3qtel1M 106596 ATA-ATATATGTATGTATATACACAGATACACACCTATGTAGACACATCC 106644 - i i i i v i i iv i v i i vi (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr3qtel1M 106645 ATATATAT 106652 (AT)n#Simple_ 51 ATATATAT 58 Matrix = Unknown Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.02 (1 / 56), avg. gap size = 1.00 (1 / 1) 23 25.03 0.00 1.49 chr3qtel1M 107872 107939 (892061) (TTTTTGT)n#Simple_repeat 1 67 (0) m_b138s252i16 5192 chr3qtel1M 107872 TTTCTGTTTTTTGTTCATTTTCTTTCCTTTTTTGGTATTTCCTTTTTTTT 107921 i iv v i iv - v iv v (TTTTTGT)n#Si 1 TTTTTGTTTTTTGTTTTTTGTTTTTTGTTTTTT-GTTTTTTGTTTTTTGT 49 chr3qtel1M 107922 TTTTTTTTTTTTACTTTT 107939 v ii (TTTTTGT)n#Si 50 TTTTTGTTTTTTGTTTTT 67 Matrix = Unknown Transitions / transversions = 1.00 (7/7) Gap_init rate = 0.01 (1 / 67), avg. gap size = 1.00 (1 / 1) 37 0.00 0.00 0.00 chr3qtel1M 109892 109923 (890077) (TG)n#Simple_repeat 1 32 (0) c_b138s251i2 5193 chr3qtel1M 109892 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 109923 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 32 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 23 0.00 0.00 0.00 chr3qtel1M 109924 109948 (890052) (AG)n#Simple_repeat 1 25 (0) m_b138s252i17 5194 chr3qtel1M 109924 AGAGAGAGAGAGAGAGAGAGAGAGA 109948 (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGA 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 16 9.55 0.00 0.00 chr3qtel1M 112170 112192 (887808) (A)n#Simple_repeat 1 23 (0) m_b139s252i0 5195 chr3qtel1M 112170 AAAGAGAAAAAAAAAAAAAAAAA 112192 i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAA 23 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 17 8.85 0.00 0.00 chr3qtel1M 113266 113289 (886711) (T)n#Simple_repeat 1 24 (0) m_b139s252i1 5196 chr3qtel1M 113266 TTTTTTTTTTTTTTTTTTCATTTT 113289 iv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTT 24 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 495 22.48 0.81 5.98 chr3qtel1M 113508 113630 (886370) C MIRc#SINE/MIR (141) 127 11 m_b139s601i0 5197 chr3qtel1M 113508 CTGAGGC-AACTGGGGTTAAGTGATTTGCCCAGGGTCACACAGCTACTTA 113556 -v vv i i i ---- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTA---- 82 chr3qtel1M 113557 GTATTAAGTGTCTGAGATCAGATTTGAACTCAGGTGCTCTTGACTTCAGG 113606 --- v v vivi i i i vi i i i C MIRc#SINE/MIR 81 GTA---AGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr3qtel1M 113607 GTTGGTGCTCTCTCCACTGCGCCA 113630 viii i i C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTGCACCA 11 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 24.97 CpG sites = 17, Kimura (unadjusted) = 27.37 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.07 (8 / 122), avg. gap size = 1.00 (8 / 8) 14 20.23 4.00 4.00 chr3qtel1M 114168 114217 (885783) (TTC)n#Simple_repeat 1 50 (0) m_b139s252i2 5198 chr3qtel1M 114168 TTC-TCTTCCTTCTTCCTTCTTC-CCTTTTTCTTTTTCCTCCCCATCATC 114215 - - - -i i i i ii v v (TTC)n#Simple 1 TTCTTCTT-CTTCTT-CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTC 48 chr3qtel1M 114216 TT 114217 (TTC)n#Simple 49 TT 50 Matrix = Unknown Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.08 (4 / 49), avg. gap size = 1.00 (4 / 4) 363 30.07 2.94 4.17 chr3qtel1M 114279 114448 (885552) C MIRc#SINE/MIR (79) 189 22 m_b139s601i1 5199 chr3qtel1M 114279 CACAATAGCCCAGGCACAAAGACAAGGCAAGGGCTGCTACTCCCATGTTA 114328 i i v vv viv i i i vii ii ii v C MIRc#SINE/MIR 189 CACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTA 140 chr3qtel1M 114329 GAGAAGAG-AGACAGCGGCCCAGGCCAAAG---AAGAGACTTTCCCAACC 114374 v v - i v v i --- i --- v v vv C MIRc#SINE/MIR 139 CAGATGAGGAAACTGAGGCTCAG---AGAGGTTAAGTGACTTGCCCAAGG 93 chr3qtel1M 114375 ACACAAAGCAAGAAATTTGCAGAACTGATTCACATTTGAGCCCAGATCTT 114424 v v v v v v i i iv---- i i i i C MIRc#SINE/MIR 92 TCACACAGCTAGTAAGTGGCAGAGCCGGG----ACTCGAACCCAGGTCTT 47 chr3qtel1M 114425 C-TGAATCTAAGACGAGTGCTCCTT 114448 - v i v v i C MIRc#SINE/MIR 46 CCTGACTCCAAGTCCAGTGCTCTTT 22 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.90 CpG sites = 24, Kimura (unadjusted) = 38.86 Transitions / transversions = 0.96 (24/25) Gap_init rate = 0.06 (10 / 169), avg. gap size = 1.20 (12 / 10) 12 15.77 2.56 5.26 chr3qtel1M 115060 115098 (884902) (GTTTT)n#Simple_repeat 1 38 (0) m_b139s252i3 5200 chr3qtel1M 115060 GTTATGTTTTAAGACTTGTTTTG-TTTGTTTGGTTTGGTT 115098 v -- vi - v v (GTTTT)n#Simp 1 GTTTTGTTTT--GTTTTGTTTTGTTTTGTTTTGTTTTGTT 38 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.08 (3 / 38), avg. gap size = 1.00 (3 / 3) 14 8.75 16.33 0.00 chr3qtel1M 116949 116997 (883003) (TGTATA)n#Simple_repeat 1 57 (0) m_b139s252i4 5201 chr3qtel1M 116949 TGT-TATGT-T-TG-ATCTGT-TATGTATATGCATACGTGTATG-AT-T- 116990 - - - - v - i i i - - - (TGTATA)n#Sim 1 TGTATATGTATATGTATATGTATATGTATATGTATATGTATATGTATATG 50 chr3qtel1M 116991 TATATGT 116997 (TGTATA)n#Sim 51 TATATGT 57 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.17 (8 / 48), avg. gap size = 1.00 (8 / 8) 24 34.46 1.72 1.72 chr3qtel1M 118815 118930 (881070) (CT)n#Simple_repeat 1 116 (0) m_b139s252i5 5202 chr3qtel1M 118815 CTCTTACTTTATTTCTCTGTCTGTCTGTC-CTGCTTTCTCTCTGGCTCTC 118863 iv i v i v v v - - i vv (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT-CTCTCTCTCTCTCTCTC 49 chr3qtel1M 118864 TCTAT-TTTTTCTATCACTATCCCTTTGTCTCAACCCTCTCTTTTTGACT 118912 v - i i v v v i i v -v i i i vv (CT)n#Simple_ 50 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TCTCTCTCTCTCTCTCT 98 chr3qtel1M 118913 CTTTATTTGTGTCTCTCT 118930 i v i v v (CT)n#Simple_ 99 CTCTCTCTCTCTCTCTCT 116 Matrix = Unknown Transitions / transversions = 0.72 (13/18) Gap_init rate = 0.03 (4 / 115), avg. gap size = 1.00 (4 / 4) 19 15.81 6.90 1.64 chr3qtel1M 119394 119451 (880549) (ATAA)n#Simple_repeat 1 61 (0) m_b139s252i6 5203 chr3qtel1M 119394 ATAAGTAAA-CAATAAATTAATACTTTTAAT-AACAAATAACT-AATAAA 119440 i -v v -vv v - i v - (ATAA)n#Simpl 1 ATAAATAAATAAATAAATAAATA-AATAAATAAATAAATAAATAAATAAA 49 chr3qtel1M 119441 -AAATAAATAAA 119451 - (ATAA)n#Simpl 50 TAAATAAATAAA 61 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.09 (5 / 57), avg. gap size = 1.00 (5 / 5) 17 12.56 2.86 0.00 chr3qtel1M 119420 119454 (880546) (TAATAAC)n#Simple_repeat 1 36 (0) m_b139s252i7 5203 chr3qtel1M 119420 TAATAACAAATAACTAATAAAAAATAAATAA-AACT 119454 v vv v - (TAATAAC)n#Si 1 TAATAACTAATAACTAATAACTAATAACTAATAACT 36 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 16 7.01 3.12 3.12 chr3qtel1M 119832 119863 (880137) (TTAT)n#Simple_repeat 1 32 (0) m_b139s252i8 5204 chr3qtel1M 119832 TTATTTCTATTATTTATTTATTT-TTAATTTAT 119863 v - - v (TTAT)n#Simpl 1 TTATTTAT-TTATTTATTTATTTATTTATTTAT 32 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.06 (2 / 31), avg. gap size = 1.00 (2 / 2) 476 29.99 4.64 4.00 chr3qtel1M 120053 120375 (879625) L1ME4c_3end#LINE/L1 315 639 (191) m_b139s551i0 5205 chr3qtel1M 120053 TTAGAGAAGAATTTGG-AACAAGCACAGAGAGCTATAAAATTCTGCACAT 120101 i i iv - i v i ivi i v v v i i L1ME4c_3end#L 315 TTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAAAATGTTCATAC 364 chr3qtel1M 120102 CCTTTGACCCAATAATGACATTTCTGGGTTTGTATCCCCAAAAGA----T 120147 i vv i vv v iv ii i ---- L1ME4c_3end#L 365 CCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATT 414 chr3qtel1M 120148 CAAAGAATAGGAAAAAGGACT-TATGTAGGCAAAAATATTTATAGCAGCT 120196 ii - -- - i -- i i i i v v L1ME4c_3end#L 415 CAAAAGA-AGGAAAAAG--CTATATGCA--CGAAGATGTTCATTGCAGCG 459 chr3qtel1M 120197 TT-TTTGTTGTAGCAACAATTTGGAAGTTGGA---GGATGTGAAACATCT 120242 - i vi i v v ii--i ---ii vv viv L1ME4c_3end#L 460 TTATTTATAATAGCGAAAAATTGGAAAC--AACCTAAATGTCCAACAATA 507 chr3qtel1M 120243 GGGGAGTGACTTCACAAGAGATGGTAGAT-GATTATGCTGCAATATTATT 120291 i ii vvii ivv v -? i -i v v v L1ME4c_3end#L 508 GGGGAATGGTTAAGTAAATTATGGTACATCNACT-CGATGGAATATTATG 556 chr3qtel1M 120292 TTGCTATAAGAAATGATGAACT----GGATTATTTCAAAACAGCCTGAGA 120337 iv i v i - i ----i i v --- i i v - L1ME4c_3end#L 557 CAGCCATTAAAAATGAT-AATTATGAAGACTATGT---AGCAACATG-GA 601 chr3qtel1M 120338 AGATTTATATGATATGATACAAAGCTAAGTGAGCAGAA 120375 i v v i iiv iv ivi L1ME4c_3end#L 602 AAATGTTTATGATATAATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.00 CpG sites = 55, Kimura (unadjusted) = 39.65 Transitions / transversions = 1.45 (55/38) Gap_init rate = 0.06 (20 / 322), avg. gap size = 1.40 (28 / 20) 270 13.33 2.22 0.00 chr3qtel1M 122170 122214 (877786) C HERV35I#LTR/ERV1 (36) 6882 6837 m_b139s701i0 5206 chr3qtel1M 122170 GGGGCAAGGGC-AATGATCTCATCTTCTGAAACTTCTTCCTGCTGA 122214 i v -i v i v C HERV35I#LTR/E 6882 GGAGAAAGGGCCGAAGATCTCATCTTCTGAAGCTACTTCCTGCTGA 6837 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 12.30 CpG sites = 3, Kimura (unadjusted) = 14.73 Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 485 23.14 0.82 7.89 chr3qtel1M 124320 124441 (875559) MIRc#SINE/MIR 2 115 (153) m_b139s601i2 5207 chr3qtel1M 124320 GGGGCAGCTAGATGGCTCAGTGGATATAGCACCAGCCCTGAAGTCAGGAG 124369 i i---i iv v v ii v i i i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr3qtel1M 124370 GATCTGAGTTCAAATCCAGACTCAGACACTAACACTTCTTAGCTGTGTGA 124419 i i i i v i ------ iv vi MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCT------CTGCCACTTACTAGCTGTGTGA 92 chr3qtel1M 124420 CCCTGAGCAAGTCACTT-GCCTC 124441 i i -i MIRc#SINE/MIR 93 CCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.39 CpG sites = 19, Kimura (unadjusted) = 28.70 Transitions / transversions = 2.71 (19/7) Gap_init rate = 0.08 (10 / 121), avg. gap size = 1.00 (10 / 10) 261 31.16 0.81 1.63 chr3qtel1M 125299 125422 (874578) L1ME3F_3end#LINE/L1 430 552 (438) m_b139s551i1 5208 chr3qtel1M 125299 ATATGTACAAAAAATATATATAGCAGCTCTCTTC-TCAGGACAAAACATT 125347 i i - i vi v v - v vii v i L1ME3F_3end#L 430 ACATGTACAAGAA-TGTTCATAGCAGCACTGTTCGTAATAGCAAAAAACT 478 chr3qtel1M 125348 TAGAAATTGAGGGAATGAATATCAATTGGAGAATGGCTCAATAAACTGTT 125397 -i ivivvvi vvi i iv v v i v L1ME3F_3end#L 479 -GGAAACAACCCAAATGTCCATCGACAGGAGAATGGATAAATAAATTGTG 527 chr3qtel1M 125398 GTATATGTTTGTAGTGGAATATTAT 125422 viviii i L1ME3F_3end#L 528 GTATATTCACACAATGGAATATTAT 552 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.61 CpG sites = 20, Kimura (unadjusted) = 41.00 Transitions / transversions = 1.11 (20/18) Gap_init rate = 0.02 (3 / 123), avg. gap size = 1.00 (3 / 3) 12 26.10 1.67 5.17 chr3qtel1M 125659 125718 (874282) (CATTTT)n#Simple_repeat 1 58 (0) m_b139s252i9 5209 chr3qtel1M 125659 CATTTTCTATTTCTCTCTTTC-TTTTTAACTTAATTTTTCTTGAAAGTTT 125707 - - vi - i vi v iv vvv - (CATTTT)n#Sim 1 CATTTTC-ATTT-TCATTTTCATTTTCATTTTCATTTTCATTTTCA-TTT 47 chr3qtel1M 125708 TTATTTTCATT 125718 i (CATTTT)n#Sim 48 TCATTTTCATT 58 Matrix = Unknown Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.07 (4 / 59), avg. gap size = 1.00 (4 / 4) 18 25.06 0.00 4.69 chr3qtel1M 126353 126419 (873581) (AAAATA)n#Simple_repeat 1 64 (0) m_b139s252i10 5210 chr3qtel1M 126353 AAAATATCAAATAAACAAATCAAATAAAAATAATAATACCAATTTAAAAG 126402 -v - vvv v -v v v v (AAAATA)n#Sim 1 AAAATA-AAAATAAA-AATAAAAATAAAAATAAAAATA-AAAATAAAAAT 47 chr3qtel1M 126403 AAAAAAAAGGAGAAAAA 126419 v ii v (AAAATA)n#Sim 48 AAAAATAAAAATAAAAA 64 Matrix = Unknown Transitions / transversions = 0.18 (2/11) Gap_init rate = 0.05 (3 / 66), avg. gap size = 1.00 (3 / 3) 13 24.02 5.36 1.72 chr3qtel1M 126355 126410 (873590) (AAAAT)n#Simple_repeat 1 58 (0) m_b139s252i11 5210 chr3qtel1M 126355 AATATCAAAT-AAA-CAAATCAAATAAAA-ATAATAATACCAATTTAAAA 126401 v v - -v v - v - vi vv (AAAAT)n#Simp 1 AAAATAAAATAAAATAAAATAAAATAAAATAAAATAA-AATAAAATAAAA 49 chr3qtel1M 126402 GAAAAAAAA 126410 v v (AAAAT)n#Simp 50 TAAAATAAA 58 Matrix = Unknown Transitions / transversions = 0.10 (1/10) Gap_init rate = 0.07 (4 / 55), avg. gap size = 1.00 (4 / 4) 13 14.69 3.33 0.00 chr3qtel1M 126877 126906 (873094) (TTTG)n#Simple_repeat 1 31 (0) m_b139s252i12 5211 chr3qtel1M 126877 TTTGGTTG-TTGTTGGTTTTTTTGTTTGCTT 126906 v - v v i (TTTG)n#Simpl 1 TTTGTTTGTTTGTTTGTTTGTTTGTTTGTTT 31 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 249 34.92 3.55 4.08 chr3qtel1M 127557 127753 (872247) C L3#LINE/CR1 (2932) 1167 972 m_b139s601i3 5212 chr3qtel1M 127557 CTGTAATTCTTTATAGTCTATACTTTCACCAATATGTGTAAACAATTATC 127606 ?v i ii v viiv i viv v i v iii v v i C L3#LINE/CR1 1167 CTGNTATCCTCCATAGTATCCGGTTTTACAGTTTTATCTGGGCATTTTTT 1118 chr3qtel1M 127607 TCATTTTTTTCCTT---TCTTA-TTTAAAGCTCTTCAGATTATATTTATA 127652 -- ii i i--- i i - ii iiv i vi iviii C L3#LINE/CR1 1117 T--TCCTTTCCCTCAAATTTCAGTTTAAAGTCCTCTTGATCAGGTCGGCG 1070 chr3qtel1M 127653 ACAGTCCAGAAAAATGCATTCTTCTTAGTCTTCTT--CATGCATTATCCC 127700 vvv ? ?v ii i iii v --v i-- v C L3#LINE/CR1 1069 AGTCTCCNGNCAAACACGTTCTTCCCGGTCTTCGTGAGATGCAC--TCCG 1022 chr3qtel1M 127701 TCCCTTTCTGGGAGCTTGTT-TTTTGTTATATTAAGCCAGAGATGGACCA 127749 ?v ii iii i- i v v? ---- v C L3#LINE/CR1 1021 TCCCTNGCCAGGAGCCCATCGTTCTGGTATCNTAAGCC----ATGGTCCA 976 chr3qtel1M 127750 GAAA 127753 C L3#LINE/CR1 975 GAAA 972 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 44.78 CpG sites = 42, Kimura (unadjusted) = 51.77 Transitions / transversions = 1.75 (42/24) Gap_init rate = 0.06 (12 / 196), avg. gap size = 1.25 (15 / 12) 49 20.79 3.65 2.16 chr3qtel1M 128124 128260 (871740) (AGGAG)n#Simple_repeat 1 139 (0) m_b139s252i13 5213 chr3qtel1M 128124 AGAAGAGAAGAAAAAAGGAGAGAAAAGGAGAGGAGAAGAAAGGAAAGGAG 128173 i i ii i i i i i i (AGGAG)n#Simp 1 AGGAGAGGAGAGGAGAGGAGAGGAGAGGAGAGGAGAGGAGAGGAGAGGAG 50 chr3qtel1M 128174 AGGAGGAGAGA-GA-AGAAGGGGAGAGGAGAGGAGAGGAAAAGA-AAGAG 128220 ii - - i i i i - i (AGGAG)n#Simp 51 AGGAGAGGAGAGGAGAGGAGAGGAGAGGAGAGGAGAGGAGAGGAGAGGAG 100 chr3qtel1M 128221 AGGAGA-GAAAGTAGGGGAACAGGGCTAGG-GAGGAAGAGGA 128260 - i v i - v - vv - - (AGGAG)n#Simp 101 AGGAGAGGAGAGGAGAGG-AGA-GGAGAGGAGAGG-AGAGGA 139 Matrix = Unknown Transitions / transversions = 4.75 (19/4) Gap_init rate = 0.06 (8 / 136), avg. gap size = 1.00 (8 / 8) 13 15.04 1.85 10.00 chr3qtel1M 129133 129186 (870814) (GAAAAGA)n#Simple_repeat 1 50 (0) m_b139s252i14 5214 chr3qtel1M 129133 GAAGAAAGAAAAGAAGGACAAAG-GGGAAGCCAAAATGAGAAAAGAGAAG 129181 i i - - - - ii vv - - (GAAAAGA)n#Si 1 GAAAAGAGAAAAG-A-GA-AAAGAGAAAAGAGAAAA-GAGAAAAGAGAA- 45 chr3qtel1M 129182 AAGAG 129186 (GAAAAGA)n#Si 46 AAGAG 50 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.11 (6 / 53), avg. gap size = 1.00 (6 / 6) 16 5.13 6.25 8.51 chr3qtel1M 130366 130413 (869587) (AGAAA)n#Simple_repeat 1 47 (0) m_b139s252i15 5215 chr3qtel1M 130366 AGATAAAGAGAA-AAAAGAAGAAGAAAAG-AAA-AACAGATAAAGAAGAA 130412 - i - - - - v - - (AGAAA)n#Simp 1 AGA-AAAGAAAAGAAAAGAA-AAGAAAAGAAAAGAAAAGA-AAAGAA-AA 46 chr3qtel1M 130413 G 130413 (AGAAA)n#Simp 47 G 47 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.15 (7 / 47), avg. gap size = 1.00 (7 / 7) 550 19.63 0.00 8.85 chr3qtel1M 130441 130563 (869437) C MIRc#SINE/MIR (153) 115 3 m_b139s601i4 5216 chr3qtel1M 130441 GAGATTAAGTGACTTGCCCAGAGTCACATAGCCAGTAAGTGTTAAGTGTC 130490 i ii i i vi ------ C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCA------ 72 chr3qtel1M 130491 TGAGGCTGGATTTGAACTCAGCTCCTCCTGACTCCAGGACTCGTGCTCTA 130540 - v v i i i v i i v iv v C MIRc#SINE/MIR 71 -GAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTT 23 chr3qtel1M 130541 TCCACTGAGCCATCAAGCTGCCT 130563 --- i vi C MIRc#SINE/MIR 22 TCCACTG---CACCACACTGCCT 3 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 21.84 CpG sites = 14, Kimura (unadjusted) = 23.00 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.08 (10 / 122), avg. gap size = 1.00 (10 / 10) 25 30.84 1.80 1.80 chr3qtel1M 130991 131101 (868899) (AAAGAA)n#Simple_repeat 1 111 (0) m_b139s252i17 5217 chr3qtel1M 130991 AAGGAAATTGAAAAAGAATGAAGAATTTAAGAGGGAGAAAGAATTAGACA 131040 i vv -i vvvi i ii i vv v (AAAGAA)n#Sim 1 AAAGAAAAAGAAAAAGAA-AAAGAAAAAGAAAAAGAAAAAGAAAAAGAAA 49 chr3qtel1M 131041 AAG-AAGAGAAAGAGAACAATCAAAAGAAGAAAGAGAAA-AGGAAGGAAC 131088 - i i v vv - i - ii i v (AAAGAA)n#Sim 50 AAGAAAAAGAAAAAGAAAAAGAAAAAGAA-AAAGAAAAAGAAAAAGAAAA 98 chr3qtel1M 131089 AGAATCAGAAAAA 131101 vv (AAAGAA)n#Sim 99 AGAAAAAGAAAAA 111 Matrix = Unknown Transitions / transversions = 0.93 (13/14) Gap_init rate = 0.04 (4 / 110), avg. gap size = 1.00 (4 / 4) 793 34.07 8.77 3.55 chr3qtel1M 132112 133103 (866897) L2#LINE/L2 2033 3074 (8) m_b139s601i5 5218 chr3qtel1M 132112 TCAACCTCCTCA-CCCTCATTATCCTTGACCTTTCTGCAG---------- 132150 -- i -i iv v ? v ---------- L2#LINE/L2 2033 TCAA--TTCTCAGTCCTCATCTTACTTGACCTNTCAGCAGCATTTGACAC 2080 chr3qtel1M 132151 -GCTGGTCACTCTCTCCT-----GGACACTCTCCTGTCTCAATTATATGG 132194 - i i i -----ii i i vv iiii - vii L2#LINE/L2 2081 AGTTGATCACTCCCTCCTTCTTGAAACACTTTCTTCACTTGGCT-TCCAG 2129 chr3qtel1M 132195 AACACCACGGTCTCCTGGCTATCTTCCTATTCCTCCACCCACTCCCTCTC 132244 i iv i v i iii v iiv i i L2#LINE/L2 2130 GACACCACACTCTCCTGGTTTTCCTCCTACCTCACTGGCCGCTCCTTCTC 2179 chr3qtel1M 132245 TATCTCCTGGCCTG---CCTTTTCA---CGCAGGTCATTGATTCT----- 132283 vi vvv --- ii --- v v ii vi ? viv ----- L2#LINE/L2 2180 AGTCTCCTTTGCTGGTTCCTCCTCATCTCCCCGACCTCTNAACGTTGGAG 2229 chr3qtel1M 132284 --CTCCAA--CTCTGTC-TCGG-CTCCTTCT-TCCTCCCTCTATACATAC 132326 -- i i-- v - i - ii - i iv i vi L2#LINE/L2 2230 TGCCCCAGGGCTCAGTCCTTGGACCTCTTCTCTTCTCTATCTACACTCAC 2279 chr3qtel1M 132327 TTCTTTGGCGATTTCACTGGCTCTCATGGATTCCCTTCCCATCTCTCTGT 132376 i i ? i i iiviv v ivvv v v v i L2#LINE/L2 2280 TCCCTNGGTGATCTCATCCAGTCTCATGGCTTTAAATACCATCTATATGC 2329 chr3qtel1M 132377 GGATGATTCTCAAATCCA----CCCTGCTGCAAGCTCTCCAC---ACT-- 132417 v i i ii ----i v ivvi v v --- -- L2#LINE/L2 2330 TGATGACTCCCAAATTTATATCTCCAGCCCGGACCTCTCCCCTGAACTCC 2379 chr3qtel1M 132418 ---CTCACATCTCT-ACTTCCT-CTCAGACATCTTGAATTGCATGTCCAG 132462 --- ii v i- v - - iv v v i i L2#LINE/L2 2380 AGACTCGTATATCCAACTGCCTACTC-GACATCTCCACTTGGATGTCTAA 2428 chr3qtel1M 132463 CAGATGTCTTAAACTAAACA-GACCCTAACAGAACTCATTATCATTCCCC 132511 i iii i v - v vv v v v - L2#LINE/L2 2429 TAGGCATCTCAAACTTAACATGTCCAAAACTGAACTCCTGATC-TTCCCC 2477 chr3qtel1M 132512 CTAAAATCTCCCCAATTCCTGC---CTTCCCTGTTTTTATAAAGGGAAAC 132558 v i v i --i i --- ii i ivi ? v v - L2#LINE/L2 2478 CTCAAACCTGCTC--CTCCCGCAGTCTTCCCCATCTCAGTNAATGGCAA- 2524 chr3qtel1M 132559 ATGGCTCCATTCTCCCAA----TCAAGTC-CCAATCTAGCTGTTGCCTTT 132603 ---- i i i---- i i -vv i v vv iii i L2#LINE/L2 2525 ----CTCCATCCTTCCAGTTGCTCAGGCCAAAAACCTTGGAGTCATCCTT 2570 chr3qtel1M 132604 GA-TCACCCCCATCTCTC-CCCCTTGTCTCCGAGCTCTTGTCAAGGCCTG 132651 - vi i iv - v iiiiv i v iv iiv iv L2#LINE/L2 2571 GACTCCTCTCTTTCTCTCACACCCCACATCCAATCCATCAGCAAATCCTG 2620 chr3qtel1M 132652 TTAGCCTTACCTCTGTACCGTCTCTCACATACTCCCCCTTTTCTCCTCTG 132701 ii ii iiiv vii v iviv v vv v i v v iv L2#LINE/L2 2621 TCGGCTCTACCTTCAAAATATATCCAGAATCCGACCACTTCTCACCACCT 2670 chr3qtel1M 132702 ACATTATAATCATTCTGGTTTTGGCCCTCATCGCTCCAATTCTGAACCAG 132751 v i iiv i ii iivi vi iiii vvvi i ii v L2#LINE/L2 2671 CCACTGCCACCACCCTGGTCCAAGCCACCATCATCTCTCGCCTGGATTAC 2720 chr3qtel1M 132752 GGCAGCAAGTGCCAGGATGGGGTCTGCCCGCCTCAAGCCTCTCCCCACTT 132801 v ii iviv viiv -- v i i v v iv v ? L2#LINE/L2 2721 TGCAATAGCCTCCTAACT--GGTCTCCCTGCTTCCACCCTTGCCCCCCTN 2768 chr3qtel1M 132802 CGGGCCACCCTCTATTCAGCTACCAGGG-GATTTTTCCTAAAGCTCGTA- 132849 i v i ii v iv vi i - ii -i i-- - L2#LINE/L2 2769 CAGTCTATTCTCAACACAGCAGCCAGAGTGATCCTT-TTAAAA--CGTAA 2815 chr3qtel1M 132850 -TCTCATCGTGTCGC-CTTCTGCTCAA-------TAATGGCTTCCCGTTA 132890 - vv i i - i -------i --- L2#LINE/L2 2816 GTCAGATCATGTCACTCCTCTGCTCAAAACCCTCCAATGGCTTCCC---A 2862 chr3qtel1M 132891 TCTC---CAGGATCAAATCCAAAATGCTC----TGTCATTCAAAGCCCTT 132933 --- ii v v i v i---- v v v i - L2#LINE/L2 2863 TCTCACTCAGAGTAAAAGCCAAAGTCCTTACAATGGCCTACAAGGCCC-T 2911 chr3qtel1M 132934 GCACAATC---TCCCTCCCTCCCTCTTT---CCAATCTTTTTACACTTTA 132977 i ii --- i vi v i --- iv ii vv --- L2#LINE/L2 2912 ACATGATCTGGTCCCCCGTTACCTCTCTGACCTCATCTCCTACCACT--- 2958 chr3qtel1M 132978 TTCCACAACACCCACTATGTGATCCAATGGCACTGGCTTCCTGGTTGTT- 133026 i v vv i i vi i-- iivi i v i - L2#LINE/L2 2959 CTCCCCCTCGCTCACTCCGC--TCCAGCCACACTGGCCTCCTTGCTGTTC 3006 chr3qtel1M 133027 -TCAAACAGAAGAGATGGTTGTCCTCCAT-CTCTTGGCTCCAAGCATCCT 133074 - i -----------i i vvv i- ii v vii v iiv L2#LINE/L2 3007 CTCGAACA-----------CGCCAGGCACGCTCCCGCCTCAGGGCCTTTG 3045 chr3qtel1M 133075 CTCTGGCTGTCCCCCGTATCTGCAACACT 133103 v v i iv ii v i L2#LINE/L2 3046 CACTTGCTGTTCCCTCTGCCTGGAACGCT 3074 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 45.34 CpG sites = 195, Kimura (unadjusted) = 47.82 Transitions / transversions = 1.49 (195/131) Gap_init rate = 0.07 (73 / 991), avg. gap size = 1.70 (124 / 73) 271 23.53 2.94 0.00 chr3qtel1M 133241 133308 (866692) DNM1r#Unknown 2476 2545 (2117) m_b139s502i0 5219 chr3qtel1M 133241 ACACATATATGTATATACATGTACATATATGTGTGTGTGTGTGTGTGTGT 133290 iii i i i iii i i i i DNM1r#Unknown 2476 ACGTGTATGTGTGTATATATGTGTGTATATGTGTGTATGTGTGTATATAT 2525 chr3qtel1M 133291 ATGTATGTAT--GTATGTGT 133308 i i -- ? i DNM1r#Unknown 2526 GTGTATATATACGTATNTAT 2545 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 29.96 CpG sites = 16, Kimura (unadjusted) = 32.47 Transitions / transversions = 1.00 (16/0) Gap_init rate = 0.01 (1 / 67), avg. gap size = 2.00 (2 / 1) 237 24.38 1.28 5.33 chr3qtel1M 133242 133319 (866681) DNM1r#Unknown 2475 2549 (2113) m_b139s502i1 5219 chr3qtel1M 133242 CACATATATGTATATACATGTACATATATGTGTGTGTGTGTGTGTGTGTA 133291 i i i i i ---- i i i i i DNM1r#Unknown 2475 CACGTGTATGTGTGTATAT----ATGTGTGTATATGTGTGTATGTGTGTA 2520 chr3qtel1M 133292 TGTATGTATGTATGTGTG-AGGTATACAA 133319 i i i i ii - v? v DNM1r#Unknown 2521 TATATGTGTATATATACGTATNTATAGAA 2549 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 28.34 CpG sites = 16, Kimura (unadjusted) = 32.75 Transitions / transversions = 8.00 (16/2) Gap_init rate = 0.06 (5 / 77), avg. gap size = 1.00 (5 / 5) 270 27.12 1.69 0.00 chr3qtel1M 133320 133378 (866622) C L2c_3end#LINE/L2 (70) 408 349 m_b139s601i6 5220 chr3qtel1M 133320 AAATACAGTTCCTGTCCTCAAGGAATTCCCAGTCCAATGGGAGAGGCA-A 133368 i i i i i ii v i i ii i - C L2c_3end#LINE 408 AGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAGTGGAGGAGACAGA 359 chr3qtel1M 133369 TATAGAAACA 133378 i ?iv C L2c_3end#LINE 358 CANGTAAACA 349 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.08 CpG sites = 14, Kimura (unadjusted) = 38.20 Transitions / transversions = 7.00 (14/2) Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1) 290 27.71 0.00 1.20 chr3qtel1M 133398 133481 (866519) C DNM1r#Unknown (2122) 2540 2458 m_b139s502i2 5221 chr3qtel1M 133398 TACAGATAAATATATATATATATATATATATACACATATACATGTACATA 133447 iv v i i i i i i iii i C DNM1r#Unknown 2540 TACGTATATATACACATATATACACACATACACACATATACACACATATA 2491 chr3qtel1M 133448 AACATACATACATGTACCCATATCTCTTTGCCTC 133481 v i i iv i- i v i i C DNM1r#Unknown 2490 TACACACATACACGTGGCCG-ACCGCCTCGCCTC 2458 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 29.36 CpG sites = 18, Kimura (unadjusted) = 37.27 Transitions / transversions = 3.60 (18/5) Gap_init rate = 0.01 (1 / 83), avg. gap size = 1.00 (1 / 1) 232 32.67 4.72 4.72 chr3qtel1M 134171 134276 (865724) MIR3#SINE/MIR 18 123 (85) m_b139s601i7 5222 chr3qtel1M 134171 CAGAAAGAAC-----TTAAGATTCAGAAATCCTGGCCTCAAATGTGGCCA 134215 i i -----i ii v i iv vi v i v--- i MIR3#SINE/MIR 18 CAGAGAGAGCACGGACTGGGAGTCAGGAGACCTGGGTTCTAGTC---CCG 64 chr3qtel1M 134216 GTTCTGCCAATTTCTTGGTTATAGAAGCTTGAGAAAATCACTTCCCCAGT 134265 i -i vvi ? i i ivi v i v i v vv MIR3#SINE/MIR 65 GCTCTGCCA-CTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCT 113 chr3qtel1M 134266 CTGGATCCTCA 134276 i- MIR3#SINE/MIR 114 CTGGG-CCTCA 123 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 43.40 CpG sites = 20, Kimura (unadjusted) = 45.28 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.06 (6 / 105), avg. gap size = 1.67 (10 / 6) 231 36.97 3.05 4.32 chr3qtel1M 134177 134340 (865660) MIRc#SINE/MIR 32 193 (75) m_b139s601i8 5222 chr3qtel1M 134177 GAACTTAAGATTCAGAAATCCTGGCCTCAAATGTGGCCAGTTCTGCCAAT 134226 i iiii ivi iv vi i i v--- i i -i MIRc#SINE/MIR 32 GGACTTGGAGTCAGGAAGACCTGGGTTCGAGTC---CCGGCTCTGCCA-C 77 chr3qtel1M 134227 TTCTTGGTTATAGAAGCTTGAGAAAATCACTTCCCCAGTCTGGATCCTCA 134276 vi i i i ivi v i v i vv vv - v MIRc#SINE/MIR 78 TTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCT-GAGCCTCA 126 chr3qtel1M 134277 TCTCTCTGCTCT---AACCGGGGAGAGACAATCCTTG--TTGTCTCTCAT 134321 vi ii vv --- vi v - i v i --i i vi - MIRc#SINE/MIR 127 GTTTCCTCATCTGTAAAATGGGGATA-ATAATACCTGCCCTGCCTACC-T 174 chr3qtel1M 134322 CCCTAAGCTGTTGGTAGGA 134340 v vii i vv MIRc#SINE/MIR 175 CACAGGGTTGTTGTGAGGA 193 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 50.52 CpG sites = 34, Kimura (unadjusted) = 53.22 Transitions / transversions = 1.42 (34/24) Gap_init rate = 0.06 (9 / 163), avg. gap size = 1.33 (12 / 9) 13 5.27 0.00 0.00 chr3qtel1M 135368 135387 (864613) (TTG)n#Simple_repeat 1 20 (0) m_b139s252i18 5223 chr3qtel1M 135368 TTGTTGTTGTTGTTATTGTT 135387 i (TTG)n#Simple 1 TTGTTGTTGTTGTTGTTGTT 20 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 482 25.48 1.31 7.64 chr3qtel1M 135470 135622 (864378) C MIRc#SINE/MIR (123) 145 2 m_b139s601i9 5224 chr3qtel1M 135470 ATTTTACAAATGAGGAAACTGAGGC--AAGCAGGTTGAAGTGATTTGCTC 135517 i -- iiv - i i C MIRc#SINE/MIR 145 ATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTT-AAGTGACTTGCCC 97 chr3qtel1M 135518 AAGGCGACCTAGCTGGTAAGTGTCTGAGGATGGTTTTTAACTCATGAAGA 135567 iv vi i v v vvv vi iv i v ---- C MIRc#SINE/MIR 96 AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGG---- 51 chr3qtel1M 135568 TGAATTTTTGTGACTTCGGGCCCAGCACTCTAGCCACTTGCCACCTCATT 135617 ---- i iv i ii i ii vv - - v i C MIRc#SINE/MIR 50 ----TCTTCCTGACTCCAAGTCCAGTGCTCTTTCCAC-TG-CACCACACT 7 chr3qtel1M 135618 GCCCC 135622 i C MIRc#SINE/MIR 6 GCCTC 2 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.54 CpG sites = 21, Kimura (unadjusted) = 31.59 Transitions / transversions = 1.40 (21/15) Gap_init rate = 0.08 (12 / 152), avg. gap size = 1.08 (13 / 12) 245 37.24 7.94 0.87 chr3qtel1M 135596 135809 (864191) C L3#LINE/CR1 (45) 4054 3826 m_b139s601i10 5225 chr3qtel1M 135596 TCTAGCC--ACTTGCCACCTCATTGCCCCAATGCTCACTATTACATTTTT 135643 i -- i v i - v vvv v iiv iv iii C L3#LINE/CR1 4054 TCTAGTCCAACCTCCCATC-CAATGCAGGAATCCCTTCTACAACATCCCT 4006 chr3qtel1M 135644 TATA--TGTCCTTCTAGTTTCTGCCTTAACATTTCCAGGAGGAGAGACCC 135691 v i -- vi v i ii i v ii viivi i v i C L3#LINE/CR1 4005 GACAAGTGGTCATCCAGCCTCTGCTTGAACACCTCCAGTGACGGGGAGCT 3956 chr3qtel1M 135692 CACTACCTCTC-----------TTTC--TTTTGTGCTAGTTCTGGTTGTC 135728 ? ----------- i -- - vi i i i C L3#LINE/CR1 3955 CACTACCTCNCGAGGCAGCCCATTCCATTTTTG-GACAGCTCTGATTGTT 3907 chr3qtel1M 135729 AGTCAGTAGTTTCTGACATCTAACTTCAACTAGATAATTTATAACCTGTT 135778 vv vv i v i iv i ivv iiv vivvii i i viv C L3#LINE/CR1 3906 AGAAAGTTCTTCCTTATATTGAGCCGAAATCTGCCTCCCTGTAACTTCCA 3857 chr3qtel1M 135779 CCCGCTGCTTCTGGCTGTCTCCTCTGGAGCC 135809 ii v i i i v vi C L3#LINE/CR1 3856 CCCATTGGTCCTAGTTCTGCCCTCTGGAGCC 3826 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 52.20 CpG sites = 46, Kimura (unadjusted) = 54.25 Transitions / transversions = 1.39 (46/33) Gap_init rate = 0.03 (6 / 213), avg. gap size = 3.17 (19 / 6) 491 26.05 9.37 8.38 chr3qtel1M 136689 137019 (862981) C L2b_3end#LINE/L2 (6) 460 127 m_b139s601i11 5226 chr3qtel1M 136689 TCATTCAGCAAATTTTT-TTGATCACTTGCTG-ATCTCAAATGCTGTGGT 136736 i v -i v i i i -i vi iii? v C L2b_3end#LINE 460 TCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCT 411 chr3qtel1M 136737 GAGCGAATGCCTG---ATAC--CAAAAAAGAAAGTGAAAACACGGTCTCT 136781 ii ----- --- -- iivi v iii-- i ? i C L2b_3end#LINE 410 AGGCG-----CTGGGGATACAGCGGTGAACAAGAC--AGACNCGGTCCCT 368 chr3qtel1M 136782 --TCTCGACGGGAATTCGCAGTCTAAGGTGTGGG-GTCA--CATGTAACT 136826 --i - - ii i -- v - v -- ?i C L2b_3end#LINE 367 GCCCTC-ACGG-AGCTCACAGTCTA--GTGGGGGAGACAGACATGTAANC 322 chr3qtel1M 136827 A-AC--TCAGTGCGCAGAAAAAACATACAGAAT-GGA-TGGAAGGAAATC 136871 - -- ? vvi v ivii----- ii - - ii i--- C L2b_3end#LINE 321 AGACAATNATAACCCAGAGTGG-----CAGGGTAGGACTGGGGGGG---C 280 chr3qtel1M 136872 TCAGAGAGGAGGGCACTGG---CAGTCT-------CAGAGAAGGGTTCCT 136911 i -- i iv --- i i ------- i i v i C L2b_3end#LINE 279 CCAGAG--GAGGGCGCCTGACCCGGCCTGGGGGGTCAGGGAGGGCTTCCC 232 chr3qtel1M 136912 GCAGAAGATGGTATGTGGGCTCAGTCTTGCAGGAAGCCAG-AGGAGCTGA 136960 v i i ii v i v v i v v -- - i i C L2b_3end#LINE 231 GGAGGAGGTGACATTTGAGCTGAGACCTGAAGGATG--AGTAGGAGTTGG 184 chr3qtel1M 136961 G-AGGC--AGAGGTGAGGGAGGAGAGCCTTCTAGGCATAAGAGACACAGC 137007 v- -- i i --- v i -i i - C L2b_3end#LINE 183 CCAGGCGAAGAGGTGGGGAAGG---GCGTTCCAGGCA-GAGGGA-ACAGC 139 chr3qtel1M 137008 CGGTGCAAAAGC 137019 v? i C L2b_3end#LINE 138 ANGTGCAAAGGC 127 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.67 CpG sites = 56, Kimura (unadjusted) = 34.36 Transitions / transversions = 2.43 (56/23) Gap_init rate = 0.13 (44 / 330), avg. gap size = 1.34 (59 / 44) 182 23.39 9.88 15.58 chr3qtel1M 137096 137176 (862824) L2c_3end#LINE/L2 369 445 (33) m_b139s601i12 5227 chr3qtel1M 137096 CCAATAGACTGTGAACTCCTC-----CAAGGATT---TCTTACTTTTCAC 137137 v i i----- i ii--- i iv vi L2c_3end#LINE 369 CCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTT 418 chr3qtel1M 137138 TGCATCCCCACAATCTCACTGGGTGCCCGGCACATGATA 137176 i ------------ i i ii L2c_3end#LINE 419 TGTATCCCCA------------GCGCCTGGCACATAGTA 445 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 25.23 CpG sites = 13, Kimura (unadjusted) = 29.54 Transitions / transversions = 4.33 (13/3) Gap_init rate = 0.17 (14 / 80), avg. gap size = 1.43 (20 / 14) 29 3.23 0.00 0.00 chr3qtel1M 139256 139287 (860713) (AAC)n#Simple_repeat 1 32 (0) c_b139s251i0 5228 chr3qtel1M 139256 AACAACAACAGCAACAACAACAACAACAACAA 139287 i (AAC)n#Simple 1 AACAACAACAACAACAACAACAACAACAACAA 32 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 11 21.82 2.17 4.44 chr3qtel1M 140094 140139 (859861) (AAAGAC)n#Simple_repeat 1 45 (0) m_b139s252i19 5229 chr3qtel1M 140094 AAAGTCAATATCAAAGAGAAAGTTCAAGGAACTAA-ACAAAGACAAA 140139 v viv v -v i - v - (AAAGAC)n#Sim 1 AAAGACAAAGACAAAGACAAAG-ACAAAG-ACAAAGACAAAGACAAA 45 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.07 (3 / 45), avg. gap size = 1.00 (3 / 3) 1032 32.11 2.46 1.69 chr3qtel1M 140442 140970 (859030) C L1ME4c_3end#LINE/L1 (297) 533 1 m_b139s551i2 5230 chr3qtel1M 140442 TATTATAATTTATCCAGCCATTCCTCAGATGATGAGCGTTCACTTGGTTT 140491 ii iii i i viv v ii i i vv v C L1ME4c_3end#L 533 TACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAGGTTGTTT 484 chr3qtel1M 140492 CCAGTTCCTTGACAATAGGATAAAAGCTGCA-------TTTTTGCACATA 140534 i ii i vi v vi vv v ------- i i ii C L1ME4c_3end#L 483 CCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTCGTGCATA 434 chr3qtel1M 140535 TGGATCCTTTCCTCTTTTTTATAATCTCTTTGGGATACAGATCCAGTAGT 140584 i v ii i i vv v i i i v vvi v C L1ME4c_3end#L 433 TAGCTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAATTCCCAGAAGT 384 chr3qtel1M 140585 GAGATTGCTGGATCAAAAGATATGTGCAGTTTTATAGTGCAGTTCTTTGA 140634 ii i i i i vi v i i----- viv C L1ME4c_3end#L 383 GGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGC-----TCTTGAT 339 chr3qtel1M 140635 GCTTAGTTCCAATTTGCTCTCCAAAATGACTGAATCAGAACATCACT-CC 140683 i v v v v i v ii v i ivvi - ? - C L1ME4c_3end#L 338 ACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTA-CANTGCC 290 chr3qtel1M 140684 ACCAACAATGCATTAGTGTCCCAGTTTTCCCACATCTCCTTTTACATT-- 140731 i i v ? v iv i ? ii viivi -- C L1ME4c_3end#L 289 ACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGCATTGG 240 chr3qtel1M 140732 -TATCATCTTTTCCTGTCATCTTAGCCAATCTGAGATATGTGAAGTGATA 140780 - i vv ii vvv i v i i i v vii i i i C L1ME4c_3end#L 239 GTATTATCAATTTTTTAAATTTTTGCTAATTTAATAGGCGTAAAATGGTA 190 chr3qtel1M 140781 CCTCAGTGTTGTCTCAATTTGCATTTCTCTACTCAGTAGTAATTTGGAGC 140830 i v ii i i iv i v ii vv v i C L1ME4c_3end#L 189 TCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACTAGCGAGGTTGAAC 140 chr3qtel1M 140831 AATTTTTTTCATATGACTAGAAATGACTCTAATTTCTTCATCTGAAAATT 140880 -- i i vi ivvv iv ? ivv i v ? vi C L1ME4c_3end#L 139 A--TTTTTCCATGTGTTTGTTTACTANTTGTATTTCCTCTTNTGTGAATT 92 chr3qtel1M 140881 ATTTGTTCATATCTTTGGACCATTTATCACTTGGAG-AATGATTTGTATT 140929 i i i i v v vv i -vv ? v - C L1ME4c_3end#L 91 GTCTGTTCATGTCCTTTGCCCATTTATCTATTGGGGTCTTGATNTTT-TT 43 chr3qtel1M 140930 CTTA-CAAATTGAGTCATTTCTTTGTATATTTTAGATATGAA 140970 - v i v vi i ? v? v C L1ME4c_3end#L 42 CTTATCAATTTGAATGAGCTCTTTATATANTANAGATATTAA 1 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 42.29 CpG sites = 95, Kimura (unadjusted) = 44.10 Transitions / transversions = 1.32 (95/72) Gap_init rate = 0.03 (15 / 528), avg. gap size = 1.47 (22 / 15) 318 31.71 5.00 3.16 chr3qtel1M 140820 141099 (858901) C L1M3_orf2#LINE/L1 (0) 3288 3004 m_b139s551i3 5230 chr3qtel1M 140820 TAATTTGGAGCAATTTTTTTCATATGACTAGAAATGACTCTAATTTCTTC 140869 i v v -- i iv ivviiiv i ivv v C L1M3_orf2#LIN 3288 TGATGTTGAGCA--TCTTTTCATATACCTGTTGGCCATTTGTATGTCTTC 3241 chr3qtel1M 140870 ATCTGAAAATTATTTGTTCATATCTTTGGACCATTTATCACTTGGAGAAT 140919 v iv i v i i i vi i v v v ? v i i--- C L1M3_orf2#LIN 3240 TTTGGAGAAATGTCTATTCAGGTCCTTTGCCCATTTTTNAATCGGG---T 3194 chr3qtel1M 140920 GATTTGTATTCTTACAAATTGAGTCAT-----TTCTTTGTATATTTTAGA 140964 v v i i v - ii ----- i i i C L1M3_orf2#LIN 3193 TATTTGTTTTTTTGCTA-TTGAGTTGTANGAGTTCCTTATATATTTTGGA 3145 chr3qtel1M 140965 TATGAAGTCTTTATCAGAAATATTAGCTGCAAATTTTTTC-CCTGTTTTC 141013 v vi i v vivi v - ii iiv C L1M3_orf2#LIN 3144 TATTAACCCCTTATCAGATATATGGTTTGCAAATATTTTCTCCCATTCCG 3095 chr3qtel1M 141014 T-GCTTCCCTTCTAATTT------TTGCTGCTTTGACTTTGTGTAAATTC 141056 - v v i v i i------ i v i vi -- i i vv C L1M3_orf2#LIN 3094 TAGGTTGCCTTTTCACTCTGTTGATTGTTTCCTTTGC--TGTGCAGAAGC 3047 chr3qtel1M 141057 TTTTTAATTGAACGTAATCAAAATTATCCA-TTTTGCATTTTAT 141099 i vi i i vv v i i - - i C L1M3_orf2#LIN 3046 TTTTTAGTTTGATGTAGTCCCACTTGTCTATTTTTGC-TTTTGT 3004 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.25 CpG sites = 48, Kimura (unadjusted) = 42.55 Transitions / transversions = 1.26 (48/38) Gap_init rate = 0.05 (14 / 279), avg. gap size = 1.64 (23 / 14) 504 23.39 11.29 0.00 chr3qtel1M 142305 142428 (857572) MIRc#SINE/MIR 10 147 (121) m_b139s601i13 5231 chr3qtel1M 142305 GTAATACAGTGAATAAAGC-------CTGGGGTCAGGAAGATCCGAGTTC 142347 ii i i v i -------i i i i i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr3qtel1M 142348 AAA------CTCATATAATTACTACCTGTGTGATCCTGGACAAGCCATTT 142391 i i------ vvvi v v i i i i i MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTT 109 chr3qtel1M 142392 AACCTCTATTTGTCTCA-TTTCCTCCTCTGTAAAATGG 142428 v vv i - v MIRc#SINE/MIR 110 AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGG 147 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.70 CpG sites = 19, Kimura (unadjusted) = 28.87 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.02 (3 / 123), avg. gap size = 4.67 (14 / 3) 11 28.73 0.00 2.27 chr3qtel1M 142955 142999 (857001) (CTCCCC)n#Simple_repeat 1 44 (0) m_b139s252i20 5232 chr3qtel1M 142955 CTCCATCTCCTCCTTCCTCTGCCTCCCCCTCCTCCCCCTGCCACT 142999 vi i i i - i i i v v (CTCCCC)n#Sim 1 CTCCCCCTCCCCCTCCCCCT-CCCCCTCCCCCTCCCCCTCCCCCT 44 Matrix = Unknown Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 579 25.42 8.47 0.00 chr3qtel1M 143080 143256 (856744) C MIRc#SINE/MIR (50) 218 27 m_b139s601i14 5233 chr3qtel1M 143080 CCTTCACAAATAGGATTTCATTTC-TCCTCACCAAAACGTTGTGGGGCAG 143128 i v i vv i v- v v vi i i C MIRc#SINE/MIR 218 CTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAG 169 chr3qtel1M 143129 GT---GC---TTTTAGAATCTGCATTTTACAGGAGAGGAAACCGAGGA-- 143170 i--- --- v vv iv iv i v-- C MIRc#SINE/MIR 168 GCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC 119 chr3qtel1M 143171 AAACAGATTAAGTGACTTGCTCAGGCTCACACGGCTAGAATGT----GAG 143216 i v i i i v i v v ---- C MIRc#SINE/MIR 118 AGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAG 69 chr3qtel1M 143217 GCAGGGTCTGAACTCGGGTCTTCCTAGATC--AGCACAGTGC 143256 v i iiii i i iiv -- iv C MIRc#SINE/MIR 68 CCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGC 27 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.92 CpG sites = 25, Kimura (unadjusted) = 31.57 Transitions / transversions = 1.25 (25/20) Gap_init rate = 0.03 (6 / 176), avg. gap size = 2.50 (15 / 6) 249 18.01 0.00 2.00 chr3qtel1M 143247 143297 (856703) L2b_3end#LINE/L2 411 460 (6) m_b139s601i15 5234 chr3qtel1M 143247 AGCACAGTGCCAGGCTCACAGTAGGCATTTGGTAACTATTTGGTTGGTTG 143296 ? v v ii ii v - iv L2b_3end#LINE 411 AGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTT-GTTGAATG 459 chr3qtel1M 143297 A 143297 L2b_3end#LINE 460 A 460 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 18.77 CpG sites = 5, Kimura (unadjusted) = 21.28 Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.02 (1 / 50), avg. gap size = 1.00 (1 / 1) 14 24.69 4.44 5.62 chr3qtel1M 144289 144378 (855622) (GAGCAGG)n#Simple_repeat 1 89 (0) m_b139s252i21 5235 chr3qtel1M 144289 GAGCAGGG-GAATGGCAGCACTGAGAGGCGGGAG-GGCGGGCAGGGAGCA 144336 - v - v -- i vv -i v i (GAGCAGG)n#Si 1 GAGCAGGGAGCA-GGGAGCA--GGGAGCAGGGAGCAGGGAGCAGGGAGCA 47 chr3qtel1M 144337 -GGAGCCACGGGAG-GGGGTCTCGGGAGCACAGAGCACAGAGCA 144378 - - - -i vviv vi vi (GAGCAGG)n#Si 48 GGGAG-CA-GGGAGCAGGGAGCAGGGAGCAGGGAGCAGGGAGCA 89 Matrix = Unknown Transitions / transversions = 0.70 (7/10) Gap_init rate = 0.10 (9 / 89), avg. gap size = 1.00 (9 / 9) 14 22.23 2.56 0.00 chr3qtel1M 146352 146390 (853610) (AGGAGC)n#Simple_repeat 1 40 (0) m_b139s252i22 5236 chr3qtel1M 146352 AGGAGCAGGGACAAGGGCAAGAACAAG-GCAGGAGCAGGA 146390 ii i i i i i - (AGGAGC)n#Sim 1 AGGAGCAGGAGCAGGAGCAGGAGCAGGAGCAGGAGCAGGA 40 Matrix = Unknown Transitions / transversions = 1.00 (7/0) Gap_init rate = 0.03 (1 / 38), avg. gap size = 1.00 (1 / 1) 15 34.91 2.11 2.11 chr3qtel1M 146450 146544 (853456) (CAGGGA)n#Simple_repeat 1 95 (0) m_b139s252i23 5237 chr3qtel1M 146450 CAGGAATAGGGAAAGGACCAGGACCATGGGCAGTAACAGGGGCAGAGGA- 146498 i i v iv iv v i vi i - - (CAGGGA)n#Sim 1 CAGGGACAGGGACAGGGACAGGGACAGGGACAGGGACAGGGACAG-GGAC 49 chr3qtel1M 146499 AGGGCTTGGGA-AAGGACTAGCACCAGGGCTAAAGGCAAGGACAGGG 146544 viv - i - viv vi ii i i (CAGGGA)n#Sim 50 AGGGACAGGGACAGGGAC-AGGGACAGGGACAGGGACAGGGACAGGG 95 Matrix = Unknown Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.04 (4 / 94), avg. gap size = 1.00 (4 / 4) 84 32.48 2.86 4.74 chr3qtel1M 146693 147251 (852749) (AGAAAG)n#Simple_repeat 1 549 (0) m_b139s252i24 5238 chr3qtel1M 146693 AGGAAGAAGCAAAG-GGAGGAGGAGGAGGAGGAGGAAGAAGGAAACAGAA 146741 i - - - i i i i i i i - - v (AGAAAG)n#Sim 1 AGAAAG-AG-AAAGAGAAAGAGAAAGAGAAAGAGAAAG-A-GAAAGAGAA 46 chr3qtel1M 146742 AAACAGAGAGGCAGAGATAATGAGAGAAAGACAGAGATAGGGTAGAAGGA 146791 i v i iv - - i i v - -i - i (AGAAAG)n#Sim 47 AGAGAAAGAGAAAGAGA-AA-GAGAAAGAGAAAGAGA-A-AG-AGAAAGA 91 chr3qtel1M 146792 GACA-AGAAATA-AAAGA-AAAGAGACAGAAAGACTTGGAAGAG-CAGAA 146837 v - v - - v i - vvv i -v i (AGAAAG)n#Sim 92 GAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGA-AAGAGAAAGAGAAAGAG 140 chr3qtel1M 146838 AGAGACAAAGACAGAGAGACAGAGAAAGCATCATAGAGAGAGAGAG-CTC 146886 i v v i v vivv v i i -vvv (AGAAAG)n#Sim 141 AAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAA 190 chr3qtel1M 146887 GGAGAAAGAG-AA-AGACAGAGATAGAGATAGAGATAGAAAGATGGGAAG 146934 i - - v v v v i - v i i (AGAAAG)n#Sim 191 AGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGA-AAGAGAAA 239 chr3qtel1M 146935 GGGGGAGAGAGAAAGAGAGACATAGACAGGCAGGGAGAGAGGTAGCCAGA 146984 i ii i i i v v v iiv ii iiv vv (AGAAAG)n#Sim 240 GAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGA 289 chr3qtel1M 146985 GAATGA-AAGGCAGAAAGAGAGAGGGAGGGAGGGAGTAGAGGAAGATTGG 147033 v - i - i i ii ii - iii vv i (AGAAAG)n#Sim 290 GAAAGAGAAAG-AGAAAGAGAAAGAGAAAGAGAAAG-AGAAAGAGAAAGA 337 chr3qtel1M 147034 GTAAAGA-AAGGTGAAATAGGGATAAGCAGAGAAAGACACATACAGGCAG 147082 - - i v v ii v iiv v - - v iv (AGAAAG)n#Sim 338 G-AAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGA-A-AGAGAAAG 384 chr3qtel1M 147083 GGATGGACAAAAAGAGAGAGAACAGGGGAAAACAGGTGGAG-AGGGGAAA 147131 i vi v i i - - i - v ivi - i i (AGAAAG)n#Sim 385 AGAAAGAGAAAGAGAAAGAGAA-A-GAG-AAAGAGAAAGAGAAAGAGAAA 431 chr3qtel1M 147132 GGAGAAACAGAGAG-GAAGACAGCAAGAAAAAGACAGAGAGAGAAAGAGA 147180 - v i - - v v i -- i (AGAAAG)n#Sim 432 -GAGAAAGAGAAAGAGAA-AGAGAAAGAGAAAG--AGAAAGAGAAAGAGA 477 chr3qtel1M 147181 AAGCG-AAGAGAGAGA-ACAGGGGAAGGGAGATGAGGAGGGGGAA-AGAA 147227 v - i - v i i i - v i i i i - (AGAAAG)n#Sim 478 AAGAGAAAGAGAAAGAGAAAGAGAAAGAGA-AAGAGAAAGAGAAAGAGAA 526 chr3qtel1M 147228 AGAAGGTAAGGGATACAG-AAGAGA 147251 - - v i v v - (AGAAAG)n#Sim 527 AG-A-GAAAGAGAAAGAGAAAGAGA 549 Matrix = Unknown Transitions / transversions = 1.38 (77/56) Gap_init rate = 0.08 (42 / 558), avg. gap size = 1.00 (42 / 42) 18 4.00 0.00 3.70 chr3qtel1M 146707 146734 (853266) (GGA)n#Simple_repeat 1 27 (0) m_b139s252i25 5239 chr3qtel1M 146707 GGAGGAGGAGGAGGAGGAGGAAGAAGGA 146734 - i (GGA)n#Simple 1 GGAGGAGGAGGAGGAGGAGG-AGGAGGA 27 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 84 32.48 2.86 4.74 chr3qtel1M 146693 147251 (852749) (AGAAAG)n#Simple_repeat 1 549 (0) m_b139s252i24 5238 chr3qtel1M 146693 AGGAAGAAGCAAAG-GGAGGAGGAGGAGGAGGAGGAAGAAGGAAACAGAA 146741 i - - - i i i i i i i - - v (AGAAAG)n#Sim 1 AGAAAG-AG-AAAGAGAAAGAGAAAGAGAAAGAGAAAG-A-GAAAGAGAA 46 chr3qtel1M 146742 AAACAGAGAGGCAGAGATAATGAGAGAAAGACAGAGATAGGGTAGAAGGA 146791 i v i iv - - i i v - -i - i (AGAAAG)n#Sim 47 AGAGAAAGAGAAAGAGA-AA-GAGAAAGAGAAAGAGA-A-AG-AGAAAGA 91 chr3qtel1M 146792 GACA-AGAAATA-AAAGA-AAAGAGACAGAAAGACTTGGAAGAG-CAGAA 146837 v - v - - v i - vvv i -v i (AGAAAG)n#Sim 92 GAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGA-AAGAGAAAGAGAAAGAG 140 chr3qtel1M 146838 AGAGACAAAGACAGAGAGACAGAGAAAGCATCATAGAGAGAGAGAG-CTC 146886 i v v i v vivv v i i -vvv (AGAAAG)n#Sim 141 AAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAA 190 chr3qtel1M 146887 GGAGAAAGAG-AA-AGACAGAGATAGAGATAGAGATAGAAAGATGGGAAG 146934 i - - v v v v i - v i i (AGAAAG)n#Sim 191 AGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGA-AAGAGAAA 239 chr3qtel1M 146935 GGGGGAGAGAGAAAGAGAGACATAGACAGGCAGGGAGAGAGGTAGCCAGA 146984 i ii i i i v v v iiv ii iiv vv (AGAAAG)n#Sim 240 GAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGA 289 chr3qtel1M 146985 GAATGA-AAGGCAGAAAGAGAGAGGGAGGGAGGGAGTAGAGGAAGATTGG 147033 v - i - i i ii ii - iii vv i (AGAAAG)n#Sim 290 GAAAGAGAAAG-AGAAAGAGAAAGAGAAAGAGAAAG-AGAAAGAGAAAGA 337 chr3qtel1M 147034 GTAAAGA-AAGGTGAAATAGGGATAAGCAGAGAAAGACACATACAGGCAG 147082 - - i v v ii v iiv v - - v iv (AGAAAG)n#Sim 338 G-AAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGA-A-AGAGAAAG 384 chr3qtel1M 147083 GGATGGACAAAAAGAGAGAGAACAGGGGAAAACAGGTGGAG-AGGGGAAA 147131 i vi v i i - - i - v ivi - i i (AGAAAG)n#Sim 385 AGAAAGAGAAAGAGAAAGAGAA-A-GAG-AAAGAGAAAGAGAAAGAGAAA 431 chr3qtel1M 147132 GGAGAAACAGAGAG-GAAGACAGCAAGAAAAAGACAGAGAGAGAAAGAGA 147180 - v i - - v v i -- i (AGAAAG)n#Sim 432 -GAGAAAGAGAAAGAGAA-AGAGAAAGAGAAAG--AGAAAGAGAAAGAGA 477 chr3qtel1M 147181 AAGCG-AAGAGAGAGA-ACAGGGGAAGGGAGATGAGGAGGGGGAA-AGAA 147227 v - i - v i i i - v i i i i - (AGAAAG)n#Sim 478 AAGAGAAAGAGAAAGAGAAAGAGAAAGAGA-AAGAGAAAGAGAAAGAGAA 526 chr3qtel1M 147228 AGAAGGTAAGGGATACAG-AAGAGA 147251 - - v i v v - (AGAAAG)n#Sim 527 AG-A-GAAAGAGAAAGAGAAAGAGA 549 Matrix = Unknown Transitions / transversions = 1.38 (77/56) Gap_init rate = 0.08 (42 / 558), avg. gap size = 1.00 (42 / 42) 12 13.87 0.00 0.00 chr3qtel1M 147915 147938 (852062) (CCCA)n#Simple_repeat 1 24 (0) m_b139s252i26 5240 chr3qtel1M 147915 CCCTCCCACCCACCCACCGCCCCA 147938 v vv (CCCA)n#Simpl 1 CCCACCCACCCACCCACCCACCCA 24 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 15 24.01 0.00 0.00 chr3qtel1M 150148 150186 (849814) (ATA)n#Simple_repeat 1 39 (0) m_b140s252i1 5241 chr3qtel1M 150148 ATGATAATAATACTAATCATTTTTATGAGAATAATAATA 150186 i v v vv v i v (ATA)n#Simple 1 ATAATAATAATAATAATAATAATAATAATAATAATAATA 39 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 chr3qtel1M 150649 150665 (849335) (A)n#Simple_repeat 1 17 (0) m_b140s252i2 5242 chr3qtel1M 150649 AAAAAAAAAAAAAAAAA 150665 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 321 34.52 1.18 0.59 chr3qtel1M 151317 151485 (848515) L1MC5a_3end#LINE/L1 410 579 (2198) m_b140s551i0 5243 chr3qtel1M 151317 TAGTAAAACTAATGGGATCACATGTGCAAAAA--TGTTTGTGGCAGCCCT 151364 ? i v -i ii ?v i i v i-- i ii v vi L1MC5a_3end#L 410 TNGCAAAAATA-CGAAANGACGTATGCACAAGGTTATTCATTGCAGCATT 458 chr3qtel1M 151365 TTTTGTAGCGACAAGAAACTGGAAACTAAGTGGATGCCCATCACTTGGAG 151414 v iiii i i v vviii i v v i L1MC5a_3end#L 459 ATTTGTAATAGCAAAAGACTGGAAACAACCCAAATGTCCATCAATAGGGG 508 chr3qtel1M 151415 AATGGCTGAATAAATTATGGTATATGAATGTTACGGAATATTATCGTTCA 151464 v i i i vv iiiv i i i vvvv v L1MC5a_3end#L 509 ACTGGTTGAATAAACTATGGTACATCCACACAATGGAGTACTATGCAGCT 558 chr3qtel1M 151465 GTAAGAAACGATCAACAAGAT 151485 i ivi v iv L1MC5a_3end#L 559 GTAAAAAGGAATGAGGAAGAT 579 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 46.78 CpG sites = 35, Kimura (unadjusted) = 49.19 Transitions / transversions = 1.52 (35/23) Gap_init rate = 0.01 (2 / 168), avg. gap size = 1.50 (3 / 2) 376 34.20 2.53 2.53 chr3qtel1M 151336 151572 (848428) L1ME5_3end#LINE/L1 430 666 (275) m_b140s551i2 5243 chr3qtel1M 151336 ACATGTGCAAAAATGTTTGTGGCAGCCCTTTTTGTAGCGACAAGAAACTG 151385 i i ii ii v vi v i i i ii i ii L1ME5_3end#LI 430 ACATGTACGAGGATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTG 479 chr3qtel1M 151386 GAAACTAAGTGGATGCCCATCACTTGGAGAATGGCTGAATAAATTATGGT 151435 ii v vv i i v i v iii v i L1ME5_3end#LI 480 GAGGCAACCTGGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGT 529 chr3qtel1M 151436 ATATGAATGTTACGGAATATTATCGTTCAGTAAGAAACGATCAACAAGAT 151485 iv v iiii i i i vvvv v i i ivi v L1ME5_3end#LI 530 GGATGCACACCATGGAGTACTATGCAGCAGTTAGAAGCAACGGACTAGAT 579 chr3qtel1M 151486 GATTTCAGAGAGGCCTGGAGAGA-CTGACGTGAAC-TGATGCTGAGTGAA 151533 vviv v vii v vi - v vi-- - ii L1ME5_3end#LI 580 GTACACATAGCAACATGGATGGATCTTAAA--AACATAGTGCTGAGTGAA 627 chr3qtel1M 151534 ATGAAC-AGAACCAG---GAGATTATTGTATAAGGCAACAGCA 151572 vi ii- v --- ---- ? vi i v L1ME5_3end#LI 628 AAAAGTAAGAAACAGAATGAGA----TNTATAACACAATACCA 666 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 45.47 CpG sites = 48, Kimura (unadjusted) = 48.02 Transitions / transversions = 1.55 (48/31) Gap_init rate = 0.04 (10 / 236), avg. gap size = 1.20 (12 / 10) 377 34.63 0.96 1.45 chr3qtel1M 151336 151543 (848457) L1ME4c_3end#LINE/L1 433 639 (191) m_b140s551i1 5243 chr3qtel1M 151336 ACATGTGCAAAAATGTTTGTGGCAGCCCTTTTTGTAGCGACAAGAAACTG 151385 i ii i i ii v vi v i iiii i i i L1ME4c_3end#L 433 ATATGCACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTG 482 chr3qtel1M 151386 GAAACTAAGTGGATGCCCATCACTTGGAGAATGGCTGAATAAATTATGGT 151435 v vv ii i v v v i i i i L1ME4c_3end#L 483 GAAACAACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGT 532 chr3qtel1M 151436 ATATGAATGTTACGGAATATTAT-CGTTCAGTAAGAAACGATCAACAAGA 151484 i v? iviv i - ivi v - i v vi v L1ME4c_3end#L 533 ACATCNACTCGATGGAATATTATGCAGCCATTAA-AAATGATAATTATGA 581 chr3qtel1M 151485 TGATTTCAGAGAGGCCTGGAGAG-ACTGACGTGAACTGATGCTGAGTGAA 151533 v i viiv vii v i i-ii v -- vv i i i L1ME4c_3end#L 582 AGACTATGTAGCAACATGGAAAATGTTTA--TGATATAATGTTAAGTGAA 629 chr3qtel1M 151534 ATGAACAGAA 151543 vi i L1ME4c_3end#L 630 AAAAGCAGAA 639 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 46.42 CpG sites = 45, Kimura (unadjusted) = 49.40 Transitions / transversions = 1.73 (45/26) Gap_init rate = 0.02 (5 / 207), avg. gap size = 1.00 (5 / 5) 437 30.67 0.00 0.00 chr3qtel1M 151336 151485 (848515) L1ME3Cz_3end#LINE/L1 426 575 (422) m_b140s551i3 5243 chr3qtel1M 151336 ACATGTGCAAAAATGTTTGTGGCAGCCCTTTTTGTAGCGACAAGAAACTG 151385 i ii ii v vi v iiii i i i L1ME3Cz_3end# 426 ACATGTACAAGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTG 475 chr3qtel1M 151386 GAAACTAAGTGGATGCCCATCACTTGGAGAATGGCTGAATAAATTATGGT 151435 v vv ii i v v i v i i L1ME3Cz_3end# 476 GAAACAACCTAAATGTCCATCAATAGGGGAATGGATAAATAAATTGTGGT 525 chr3qtel1M 151436 ATATGAATGTTACGGAATATTATCGTTCAGTAAGAAACGATCAACAAGAT 151485 vv iiv i i vvvv v i vvi v v L1ME3Cz_3end# 526 ATATTCATACAATGGAATACTATACAGCAGTTAAAATGAATGAACTAGAT 575 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 39.15 CpG sites = 25, Kimura (unadjusted) = 40.27 Transitions / transversions = 1.19 (25/21) Gap_init rate = 0.00 (0 / 149), avg. gap size = 0.0 (0 / 0) 474 27.05 0.00 0.00 chr3qtel1M 151337 151458 (848542) L1ME3G_3end#LINE/L1 427 548 (376) m_b140s551i4 5243 chr3qtel1M 151337 CATGTGCAAAAATGTTTGTGGCAGCCCTTTTTGTAGCGACAAGAAACTGG 151386 i ii ii v vi v iiii i i i L1ME3G_3end#L 427 CATGTACAAGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGG 476 chr3qtel1M 151387 AAACTAAGTGGATGCCCATCACTTGGAGAATGGCTGAATAAATTATGGTA 151436 v vv ii i v v i i i L1ME3G_3end#L 477 AAACAACCTAAATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGTA 526 chr3qtel1M 151437 TATGAATGTTACGGAATATTAT 151458 vv ii i i L1ME3G_3end#L 527 TATCCATACTATGGAATACTAT 548 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 33.85 CpG sites = 23, Kimura (unadjusted) = 35.19 Transitions / transversions = 2.30 (23/10) Gap_init rate = 0.00 (0 / 121), avg. gap size = 0.0 (0 / 0) 330 31.71 1.95 3.74 chr3qtel1M 151990 152451 (847549) L1M1_orf2#LINE/L1 854 1307 (1987) m_b140s551i5 5244 chr3qtel1M 151990 AAAACTAATGGGATGCTGCCAAAGCAGTTCTTATGGGAAAGCAT----CT 152035 iv i v v v v vi i iv ---- L1M1_orf2#LIN 854 AAAACCTATGGGATACAGCAAAAGCAGTACTAAGAGGGAAGTTTATAGCT 903 chr3qtel1M 152036 CTAGATGCTTACATGAATAAAACAGAGAAAGAGGAGATCAACAATTGGGC 152085 v ii i v v iv i vvvv i v iivii L1M1_orf2#LIN 904 ATAAGTGCCTACATCAAAAAAGAAGAAAAACTTCAAATAAACAACCTAAC 953 chr3qtel1M 152086 -ATTTAACTAAAATAAAAGCTAGAAAA---AGAATAAATCAA-CATAAAA 152130 - vi v v v --- --- ii i - vi L1M1_orf2#LIN 954 GATGCATCTTAAAGAA---CTAGAAAAGCAAGAGCAAACCAAACCCAAAA 1000 chr3qtel1M 152131 AAAGAACAATTAAATATCAAATTAGAATATCTGAAAATCAAAGGGGAGAT 152180 vv v v vv v --- --- ---- i i vi i L1M1_orf2#LIN 1001 TTAGTAGAAGAAAAGA---AAT---AATA----AAGATCAGAGCAGAAAT 1040 chr3qtel1M 152181 TCACAAATTTGAAATCAAGAAAACTATTGAACTAATAAATATATCTAAGA 152230 vv ii v v v vv vvi v iv v v i L1M1_orf2#LIN 1041 AAATGAAATTGAAATGAAGAAAACAATACAAAAGATCAATGAAACAAAAA 1090 chr3qtel1M 152231 ATTGGTTTTATGAAAAAAAAAACAACAAAATAGACAAACCTTTGATTAGT 152280 i v i?v --- v iiii v L1M1_orf2#LIN 1091 GTTGGTTTTTTGAAAAGNTAAACAA---AATTGACAAACCTTTAGCCAGA 1137 chr3qtel1M 152281 TTGATTAGAAAAATAAAAGAACAAAAGAAAAGTACTAGTATCAAAAATGA 152330 i i ?? ii v i iv i vvv vv v iv i i L1M1_orf2#LIN 1138 CTAANNAAGAAAAAAAGAGAGAAGACCCAAATAAATAAAATCAGAGATGA 1187 chr3qtel1M 152331 AAAGGGTGAATTTACCATCAATGAAAAGGAAATTGAAGCAATAATTGGGG 152380 i v vv v iii ivvivi v ivi v i v L1M1_orf2#LIN 1188 AAAAGGAGACATTACAACTGATACCGCAGAAATTCAAAGGATCATTAGTG 1237 chr3qtel1M 152381 GCTATTTTGTGCAACTGTATGCCAATAAATCTGACAATCTAAAGGAAATA 152430 i v v i iv v i i i L1M1_orf2#LIN 1238 GCTACTATGAGCAACTATATGCCAATAAATTGGAAAATCTAGAAGAAATG 1287 chr3qtel1M 152431 ATGAATATTTTTAAAAATACA 152451 ivv - ii i v i i L1M1_orf2#LIN 1288 GACAA-ATTCCTAGACACATA 1307 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 41.61 CpG sites = 67, Kimura (unadjusted) = 41.99 Transitions / transversions = 0.91 (67/74) Gap_init rate = 0.05 (21 / 461), avg. gap size = 1.24 (26 / 21) 1104 29.58 2.27 1.12 chr3qtel1M 152757 153197 (846803) L1ME4c_3end#LINE/L1 4 449 (381) m_b140s551i6 5245 chr3qtel1M 152757 ATTTCTAAAATATATAGAGAATTGACTCTA-----TAAGAAATCAAGCCA 152801 v ?v ? i ii v i v ----- vv? v v L1ME4c_3end#L 4 ATATCTNTANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAA 53 chr3qtel1M 152802 TTCTCCAATTGATAAATGATCAAAGGATATGAACAGATAATTTTCGGATG 152851 vv i v iv i i iv i? v L1ME4c_3end#L 54 GACCCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAG 103 chr3qtel1M 152852 ATGAAATTGAAACTATTTCCACTCATATGAAAGAGTGTTCCAAATCACTA 152901 v vv ?ivi vvv vv i i i i v vv i L1ME4c_3end#L 104 AGGAAATACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTA 153 chr3qtel1M 152902 TTGATCAGAGAGATGCAAATTAAGACAACTCTGAGATACCGCTACACACC 152951 v i i i ii vv ii vi i L1ME4c_3end#L 154 GTAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCC 203 chr3qtel1M 152952 TGTCAGATTGCCTAAGATGACAGGAAACGATAATGATGAATGTTGGCGGG 153001 i i i iv v i vvv ii vi iviv i i L1ME4c_3end#L 204 TATTAAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGCTGGCGAG 253 chr3qtel1M 153002 GATGTGGGAAAATTGGGACACTGATGCATTGTTGGTGGAGTTATAAACGG 153051 ? i vi i v ? v i i vi? i iv L1ME4c_3end#L 254 GNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTG 303 chr3qtel1M 153052 ATCCAATCATTCTGGAGAGCAGTTTGGAACTGTGCTCAAAAAGCTATCAA 153101 i v i v i i i v v ii iviv i i v L1ME4c_3end#L 304 GTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAA 353 chr3qtel1M 153102 ACTGTGCATACCCTTTGATCCAGCAGTGCTACTAAT--GAACTTATCTCC 153149 v v i i i v i vv -- i -- L1ME4c_3end#L 354 AATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTA--TCC 401 chr3qtel1M 153150 CAAAGAAATACT---AAAGAAGGGAAAGGGACCTGCATGTGCAAAAATAT 153196 i i v --- i i --- ii ii i i i L1ME4c_3end#L 402 TAAGGAAATAATTCAAAAGAAGGAAAAAG---CTATATGCACGAAGATGT 448 chr3qtel1M 153197 T 153197 L1ME4c_3end#L 449 T 449 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 37.56 CpG sites = 73, Kimura (unadjusted) = 39.51 Transitions / transversions = 1.30 (73/56) Gap_init rate = 0.02 (8 / 440), avg. gap size = 1.88 (15 / 8) 14 14.07 4.65 4.65 chr3qtel1M 153925 153967 (846033) (CTCC)n#Simple_repeat 1 43 (0) m_b140s252i3 5246 chr3qtel1M 153925 CTCCCTCCCCATCCCT-CC-CCCTTCCTTCAACCCTCCCTCCTTC 153967 - - - - i i vv i (CTCC)n#Simpl 1 CTCCCT-CCC-TCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTC 43 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.10 (4 / 42), avg. gap size = 1.00 (4 / 4) 234 18.12 4.58 1.65 chr3qtel1M 154130 154719 (845281) (GACAGA)n#Simple_repeat 1 607 (0) m_b140s252i4 5247 chr3qtel1M 154130 GAGAGACACAGTGATAGAGAGACAGACAGAGACAGGGATGGAGCTAGAGA 154179 v v v i v v i ii -- v (GACAGA)n#Sim 1 GACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAG--ACAGA 48 chr3qtel1M 154180 CACAGTGGCAGAGCCAGAGAGAGAGATAGAG--AGACAAAGAGACAGAGA 154227 v v i v v i -- v v (GACAGA)n#Sim 49 GACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGA 98 chr3qtel1M 154228 CAGAGACAGAGCCAGAGAC--AGACAGAGACAGGGACGGAG-C-TAGAGA 154273 v -- i i - -v v (GACAGA)n#Sim 99 CAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACA 148 chr3qtel1M 154274 GAGACAGTGGCAGAGCCAGAGAGAGAGCCAAAGAGCCAGAGAGAGACAGA 154323 v i v v v i vvv v (GACAGA)n#Sim 149 GAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGA 198 chr3qtel1M 154324 GACAGAGACAGAGCCAGAG-C-CAGACAGAGACAGGGACGGAGCTAGAGA 154371 v - -v i i -- v (GACAGA)n#Sim 199 GACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAG--ACAGA 246 chr3qtel1M 154372 GACAGTGGCAGAGCCAGAGAGAGAGCCAAAGAGCCAGAGAGAGACAGAGA 154421 v i v v v i vvv v (GACAGA)n#Sim 247 GACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGA 296 chr3qtel1M 154422 CAGAGACAGAGCCAGAGCCAGAGAC--AGACAGAGACAGGGACAGAGCTA 154469 v v -- i -- (GACAGA)n#Sim 297 CAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAG--A 344 chr3qtel1M 154470 GAGAGACAATGGCAGAGCCAGAGAGAGAGACAGAGACAGAGACA-AGA-A 154517 v iv i v v - - (GACAGA)n#Sim 345 CAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACA 394 chr3qtel1M 154518 GA-AGA-AGA-AGAGAGAGACACACA-AAAGAGACAGAGACAG-GA-AG- 154560 - v - - v v v - v - - - (GACAGA)n#Sim 395 GAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGA 444 chr3qtel1M 154561 GAGTGGGGAAG-GGCAGGCCCAGAGAGAGA-AGAGA-AGAGAGACAGAGA 154607 vv i iv - i ivv v - v - v (GACAGA)n#Sim 445 GACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGA 494 chr3qtel1M 154608 -A-AGA-AGGGGAACAGACAGAGAAAGAGACAGAGACAGAGATA-AGCAG 154653 - - - i iv v v i - - v (GACAGA)n#Sim 495 CAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAG-AC 543 chr3qtel1M 154654 AGGGAAGAGAGACAG-GGGAGAGAACAGAGACAAAAACAGGAAAGACAGA 154702 i - v - iv - i i - i v v (GACAGA)n#Sim 544 AGAG-ACAGAGACAGAGACAGAG-ACAGAGACAGAGACA-GAGACAGAGA 590 chr3qtel1M 154703 CAGGGACAGAGCCAGAG 154719 i v (GACAGA)n#Sim 591 CAGAGACAGAGACAGAG 607 Matrix = Unknown Transitions / transversions = 0.48 (30/62) Gap_init rate = 0.06 (34 / 589), avg. gap size = 1.09 (37 / 34) 151 13.90 2.96 0.00 chr3qtel1M 155927 156196 (843804) (TTCC)n#Simple_repeat 1 278 (0) m_b140s252i5 5248 chr3qtel1M 155927 TTTCTTCCTTTC-TCC-TCCCTCCCTCCCCCCTCCCTTCCTTCCTTCCTT 155974 i i - - i i ii i (TTCC)n#Simpl 1 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 50 chr3qtel1M 155975 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 156024 (TTCC)n#Simpl 51 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 100 chr3qtel1M 156025 TTCCTTCCTTCC-T-CTTCCTTTTTTCCTTCCCTCCTTCCTTCC-TCCTT 156071 - - ii i - (TTCC)n#Simpl 101 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 150 chr3qtel1M 156072 TCTTTCTTCCCTCCTTCCTTTCTTCCTTCCCTCCCTTCATCCTTCCTTTC 156121 i i i i i i i v i (TTCC)n#Simpl 151 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 200 chr3qtel1M 156122 TCCCTTTC-TCCTTCCTTTCTCCCTTCC-TCCTTCCTTTCTTCCCTACCT 156169 i i - i i - i i v i (TTCC)n#Simpl 201 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 250 chr3qtel1M 156170 CCCTCCCTCCTTTCTTTTTTTC-TCCTT 156196 i i i ii i - (TTCC)n#Simpl 251 CCTTCCTTCCTTCCTTCCTTCCTTCCTT 278 Matrix = Unknown Transitions / transversions = 15.50 (31/2) Gap_init rate = 0.03 (8 / 269), avg. gap size = 1.00 (8 / 8) 184 37.59 7.63 0.79 chr3qtel1M 156267 156384 (843616) C L3#LINE/CR1 (14) 4085 3960 m_b140s601i0 5249 chr3qtel1M 156267 ATTTCTGAGTTGTCGTGGGCTCCAGTGGTCCCTCAGTCTA--CCCCCGAC 156314 i v vviv i iii v viii i -- i iv C L3#LINE/CR1 4085 ATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCAACCTCCCATC 4036 chr3qtel1M 156315 CCCCACAAGGACGCACTGTGCGACATCCCCGGGGAGGGATCCCTCAGCCT 156364 vvii i i iv vi v i i i ivi v i vii C L3#LINE/CR1 4035 CAATGCAGGAATCCCTTCTACAACATCCCTGACAAGTGGTCATCCAGCCT 3986 chr3qtel1M 156365 -------GACACCTCGGGTGGACGGGG 156384 -------i vi - C L3#LINE/CR1 3985 CTGCTTGAACACCTCCAGT-GACGGGG 3960 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 55.76 CpG sites = 28, Kimura (unadjusted) = 55.76 Transitions / transversions = 1.75 (28/16) Gap_init rate = 0.03 (3 / 117), avg. gap size = 3.33 (10 / 3) 13 9.98 5.88 2.86 chr3qtel1M 157125 157158 (842842) (CCCT)n#Simple_repeat 1 35 (0) m_b140s252i6 5250 chr3qtel1M 157125 CCCTTCCTCCCT-CCTGCC-CCCTCCCTTCCGTCCC 157158 i - v - - v (CCCT)n#Simpl 1 CCCTCCCTCCCTCCCTCCCTCCCTCCC-TCCCTCCC 35 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.09 (3 / 33), avg. gap size = 1.00 (3 / 3) 443 31.08 2.67 1.32 chr3qtel1M 158223 158372 (841628) L2d_3end#LINE/L2 357 508 (8) m_b140s601i1 5251 chr3qtel1M 158223 TAATCGTTTGGCTTGTTCCCTGCCCCTG-CTCCCGAATTAGATTGTGAGC 158271 i -- v vivi ivi i - v i i L2d_3end#LINE 357 TAATTGTTT--CATGTGTGTTAGTCTTGTCTCCCCAACTAGATTGTAAGC 404 chr3qtel1M 158272 TCCTTAAGAGGAAGGATTAT-TCCTTTAGCCTTTCTTGG--CCGTCTAGT 158318 i i v i ii - i v vi? i? v -- vivi i L2d_3end#LINE 405 TCCTTGAGGGCAGGGACCATGTCTTATACTNTTTTNTCGTTCCCCACAGC 454 chr3qtel1M 158319 ATTTAGCACAATCCCTGGCACACAGTAGGTGTTTAATAAATGTTTATTGA 158368 iii i v ivi i i i i ii i L2d_3end#LINE 455 GCCTAGCACAGTGCTGAGCACATAGTAGGCGCTCAATAAATACTTGTTGA 504 chr3qtel1M 158369 CTGA 158372 i L2d_3end#LINE 505 TTGA 508 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.09 CpG sites = 33, Kimura (unadjusted) = 43.85 Transitions / transversions = 2.54 (33/13) Gap_init rate = 0.03 (5 / 149), avg. gap size = 1.20 (6 / 5) 479 28.22 2.40 0.79 chr3qtel1M 158251 158375 (841625) L2d2_3end#LINE/L2 426 552 (3) m_b140s601i2 5251 chr3qtel1M 158251 CTCCCGAATTAGATTGTGAGCTCCTTAAGAGGAAGGATTATTCCTTTAGC 158300 v i i i i v i ii vi - vv L2d2_3end#LIN 426 CTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTT-ATA 474 chr3qtel1M 158301 CTTTCTTGG---CCGTCTAGTATTTAGCACAATCCCTGGCACACAGTAGG 158347 ii v--- vivi iiii i v v L2d2_3end#LIN 475 CTTCTTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAGTAGG 524 chr3qtel1M 158348 TGTTTAATAAATGTTTATTGACTGAATT 158375 i i i i i i vi L2d2_3end#LIN 525 CGCTCAATAAATATTTGTTGATTTGATT 552 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.34 CpG sites = 24, Kimura (unadjusted) = 37.18 Transitions / transversions = 2.18 (24/11) Gap_init rate = 0.02 (2 / 124), avg. gap size = 2.00 (4 / 2) 60 30.51 2.90 2.53 chr3qtel1M 159145 159420 (840580) (CTTTCT)n#Simple_repeat 1 277 (0) m_b140s252i7 5252 chr3qtel1M 159145 CTTTGCCTGTCTCTCCCTTCTTTCTCCTTTC-CTTTGTCTTTCTCTGCCT 159193 vi v ii - - - v vi (CTTTCT)n#Sim 1 CTTTCTCTTTCTCTTTC-TCTTTCT-CTTTCTCTTTCTCTTTCTCTTTCT 48 chr3qtel1M 159194 TTTTCTCCAT-AC-CTCTATTTCCCCTTC-CCTTCT-TTTC-CTTT-TCC 159237 i iv -v -i v i i - i - - - i (CTTTCT)n#Sim 49 CTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCT 98 chr3qtel1M 159238 ACCTTTGTCTCTGCTTTCTGTCTCTGTCGGTCTCCCTGTCTCTCCTTTCT 159287 vi i v -i i v v vv i i v -i i (CTTTCT)n#Sim 99 TTCTCTTTCTCT-TTCTCTTTCTCTTTCTCTTTCTCTTTCTCT-TTCTCT 146 chr3qtel1M 159288 TTCCTCTTTCTC-TGCTTTTTCTCCATACCTCTTTATTTCCCCTTCCCTT 159336 - - v i iv vi i i v i i i (CTTTCT)n#Sim 147 TT-CTCTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCTT 195 chr3qtel1M 159337 TCCCTTTTCTTTGTCTGCTTTCTGTCTCTCTTTCCCTCTGTTTGTCCCTC 159386 i - i v - v i i i v i v i i (CTTTCT)n#Sim 196 TCTC-TTTCTCTTTCT-CTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCTT 243 chr3qtel1M 159387 TTGCTGCCTCTCTCTGTGTCTCTGTCTCTTTCTC 159420 iv vi i v v v (CTTTCT)n#Sim 244 TCTCTTTCTCTTTCTCTTTCTCTTTCTCTTTCTC 277 Matrix = Unknown Transitions / transversions = 1.41 (38/27) Gap_init rate = 0.05 (15 / 275), avg. gap size = 1.00 (15 / 15) 49 19.22 4.00 4.00 chr3qtel1M 160053 160202 (839798) (AGGA)n#Simple_repeat 1 150 (0) m_b140s252i8 5253 chr3qtel1M 160053 AGAAAGGAAAG-ATGAACAAAAGAATGGAGGGAGGAAGG-AGGAACAAAA 160100 i i - v vi i v i i - vi i (AGGA)n#Simpl 1 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG 50 chr3qtel1M 160101 GAATGGGA-AAAGGAAGGAAAGGAAGG-AGAAAGAAAAGATGG-AGGAAT 160147 - i -i - - i i i v - - (AGGA)n#Simpl 51 GAA-GGAAGGAAGGAAGG-AAGGAAGGAAGGAAGGAAGGAAGGAAGGAA- 97 chr3qtel1M 160148 GGAA-GAAGGAAGGAAAGATGGAAAAGAATGGAAGAAAGGAAAGGAAGAA 160196 - i v - i - i - i (AGGA)n#Simpl 98 GGAAGGAAGGAAGGAAGGAAGG-AAGGAA-GGAAGGAAGG-AAGGAAGGA 144 chr3qtel1M 160197 AGGAAG 160202 (AGGA)n#Simpl 145 AGGAAG 150 Matrix = Unknown Transitions / transversions = 2.83 (17/6) Gap_init rate = 0.08 (12 / 149), avg. gap size = 1.00 (12 / 12) 409 32.52 6.74 3.26 chr3qtel1M 160574 160751 (839249) MIR3#SINE/MIR 3 186 (22) m_b140s601i3 5254 chr3qtel1M 160574 GACAAATTGCTTGGCAGTGGAAAGAGTACTAGATCTGAAGCTGGATGTCC 160623 i i v vi -- ii i i -i iiv i iii iv v MIR3#SINE/MIR 3 GGCAGAGTGGCTG--AGCAGAGAGAGCAC-GGACTGGGAGTCAGGAGACC 49 chr3qtel1M 160624 CGGGTTCAAATCCTC-CTCAGCCATTTAATGCCTGGATGACCCCAGACAA 160672 i v i iv- v i v v ?v vi iii i MIR3#SINE/MIR 50 TGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAA 99 chr3qtel1M 160673 A--GTTTTACCTTTCTGGGCCT----TCCCCCATCTGTAAAGTGGGCTGG 160716 i--ii i i ---- i i i i--- MIR3#SINE/MIR 100 GTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGA---GG 146 chr3qtel1M 160717 GAATT---CTAGAC--TTTCCACGGCCGTTTCCAGTGCTG 160751 ii --- i-- i i v i vi iv MIR3#SINE/MIR 147 GGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTG 186 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.33 CpG sites = 41, Kimura (unadjusted) = 46.70 Transitions / transversions = 2.73 (41/15) Gap_init rate = 0.06 (11 / 177), avg. gap size = 1.64 (18 / 11) 483 26.19 6.35 0.00 chr3qtel1M 160587 160712 (839288) MIRc#SINE/MIR 15 148 (120) m_b140s601i4 5254 chr3qtel1M 160587 GCAGTGGAAAGAGTACTAGATCTGAAG-CTGGATGTCCCGGGTTCAAATC 160635 i i ii i - v v v i i i MIRc#SINE/MIR 15 GCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTC 64 chr3qtel1M 160636 CT-CCTCAGCCATTTAATGCCTGGATGACCCCAGACAAA--GTTTTACCT 160682 i-v v i v iv vi iii i i--ii v MIRc#SINE/MIR 65 CCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCT 114 chr3qtel1M 160683 TTCTGGGCC----TTCCCCCATCTGTAAAGTGGG 160712 i i ---- i i i MIRc#SINE/MIR 115 CTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.42 CpG sites = 24, Kimura (unadjusted) = 33.96 Transitions / transversions = 2.67 (24/9) Gap_init rate = 0.03 (4 / 125), avg. gap size = 2.00 (8 / 4) 262 23.12 9.41 3.33 chr3qtel1M 161726 161810 (838190) C L2c_3end#LINE/L2 (11) 467 378 m_b140s601i5 5255 chr3qtel1M 161726 CAACAAGCATTTATTAAGTGCCTCAAACGGTTTATCAGG-GTT----ACA 161770 i i i --- vi v ii - i ---- i C L2c_3end#LINE 467 CAACAAACATTTATTGAGCGCCT---ACTATGTGCCAGGCGCTGGGGATA 421 chr3qtel1M 161771 CAGAAAGGCAGAAGAC--GGTCTCTGCTCCCAAAGAGC-CACA 161810 i i v v v -- i i i i - C L2c_3end#LINE 420 CAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACA 378 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.19 CpG sites = 14, Kimura (unadjusted) = 29.00 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.08 (7 / 84), avg. gap size = 1.57 (11 / 7) 405 30.45 8.97 2.60 chr3qtel1M 161819 161963 (838037) C MIRb#SINE/MIR (21) 247 94 m_b140s601i6 5256 chr3qtel1M 161819 TAAGCATCGATTAATCACCA--CGTTGTGCAAGGCACTTCACAAATATTG 161866 i iiiv i vvii -- ii v i i i vii i C MIRb#SINE/MIR 247 TGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACATGCATTA 198 chr3qtel1M 161867 CTTC---CAATCCTCACACCAATCCTG--AGGTAAAGTGACATTATCATC 161911 ii ---i v i -- ---- ii i C MIRb#SINE/MIR 197 TCTCATTTAATCCTCACAACAACCCTGCGAGGTA----GGTATTATTATC 152 chr3qtel1M 161912 TCTGCTTTCCAGTTGCGGAAACTGAGGC------AGGCAGAACGACTTGC 161955 i iii v v v ------ ivi iii C MIRb#SINE/MIR 151 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGC 102 chr3qtel1M 161956 CCAGGGCC 161963 i i C MIRb#SINE/MIR 101 CCAAGGTC 94 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.85 CpG sites = 33, Kimura (unadjusted) = 42.54 Transitions / transversions = 3.30 (33/10) Gap_init rate = 0.06 (8 / 144), avg. gap size = 2.12 (17 / 8) 255 27.14 8.57 0.00 chr3qtel1M 161903 161972 (838028) C MIR1_Amn#SINE/MIR (71) 159 84 m_b140s601i7 5256 chr3qtel1M 161903 ATTATCATCTCTGCTTTCCAGTTGCGGAAACTGAGGC------AGGCAGA 161946 i i i iii v v v ------ i?i C MIR1_Amn#SINE 159 ATCATTATCCCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAA 110 chr3qtel1M 161947 ACGACTTGCCCAGGGCCTCTTGACCG 161972 ii i i v ?iii ? C MIR1_Amn#SINE 109 GTGACTTGCCCAAGGTCACNCAGCNG 84 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.59 CpG sites = 15, Kimura (unadjusted) = 38.59 Transitions / transversions = 3.75 (15/4) Gap_init rate = 0.01 (1 / 69), avg. gap size = 6.00 (6 / 1) 22 29.96 3.00 3.00 chr3qtel1M 167673 167772 (832228) (GGAG)n#Simple_repeat 1 100 (0) m_b140s252i10 5257 chr3qtel1M 167673 GGAGGAAGGAAGAGAGGGAGAGAAGAAAGAAAAGGA-GGA-GGAAAAAGG 167720 i i i - i ii ii i - - iii (GGAG)n#Simpl 1 GGAGGGAGGGAGGGAGGGAG-GGAGGGAGGGAGGGAGGGAGGGAGGGAGG 49 chr3qtel1M 167721 GAGATGGGGGGAGGAAAGGAAGGAGGGCGGAAAGGAACG-GGGAGGCAGG 167769 -- i i i i v i i iv - v (GGAG)n#Simpl 50 GAG--GGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGG 97 chr3qtel1M 167770 GAG 167772 (GGAG)n#Simpl 98 GAG 100 Matrix = Unknown Transitions / transversions = 6.33 (19/3) Gap_init rate = 0.06 (6 / 99), avg. gap size = 1.00 (6 / 6) 356 25.38 10.24 0.72 chr3qtel1M 168891 169017 (830983) C MIR3#SINE/MIR (63) 145 7 m_b140s601i9 5258 chr3qtel1M 168891 CTCATTTTACAGATGAGGAAACAGAGG--CAGACGGGGTGAAGTGAC-TG 168937 v -- - i - C MIR3#SINE/MIR 145 CTCATTTTACAGATGAGGAAACTGAGGCCCAGA-GAGGTGAAGTGACTTG 97 chr3qtel1M 168938 TCCAGCATCACACAGCTGG---GAAGCGAGGTCGGATTTAAACTGCAG-- 168982 i ivi ?i --- vi iii i ivi i viv -- C MIR3#SINE/MIR 96 CCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGT 47 chr3qtel1M 168983 --CCTGGCATTCTCTCC--GCT-GCCCAGCCCAGCCGCCC 169017 -- i vii vv -- -v i v i i i C MIR3#SINE/MIR 46 CTCCTGACTCCCAGTCCGTGCTCTCTCTGCTCAGCCACTC 7 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.42 CpG sites = 21, Kimura (unadjusted) = 32.42 Transitions / transversions = 1.91 (21/11) Gap_init rate = 0.06 (8 / 126), avg. gap size = 1.75 (14 / 8) 372 21.43 9.18 0.00 chr3qtel1M 168891 168988 (831012) C MIR#SINE/MIR (118) 144 38 m_b140s601i8 5258 chr3qtel1M 168891 CTCATTTTACAGATGAGGAAACAGAGGCAGA-CGGGGTGAAGTGAC-TGT 168938 i v v -v i v i - i C MIR#SINE/MIR 144 CCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGC 95 chr3qtel1M 168939 CCAGCATCACACAGCTGGGAAGC----GAGGTCGGATTTAAACT---GCA 168981 ivi i v i---- viv ii i--- C MIR#SINE/MIR 94 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGCA 45 chr3qtel1M 168982 GCCTGGC 168988 i C MIR#SINE/MIR 44 GTCTGGC 38 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 22.88 CpG sites = 13, Kimura (unadjusted) = 25.76 Transitions / transversions = 1.62 (13/8) Gap_init rate = 0.04 (4 / 97), avg. gap size = 2.25 (9 / 4) 183 27.65 14.74 4.81 chr3qtel1M 169019 169113 (830887) C L2a_3end#LINE/L2 (24) 493 390 m_b140s601i10 5259 chr3qtel1M 169019 TTAAGTGCTTCCGGTAACCCAGGCACCCTCCACCCTTGGC-CTGGGGACA 169067 i i i v vi ivv iv i ---- v - i C L2a_3end#LINE 493 TTGAGCGCCTACTATGTGCCAGGCACTGTTC----TAGGCGCTGGGGATA 448 chr3qtel1M 169068 CAA-------------AGGCAAATGGTCCCCGGCCTCCAAGAGCTTACAT 169104 i------------- i -i i v vvi C L2a_3end#LINE 447 CAGCAGTGAACAAAACAGACAAA-AGTCCCTGCCCTCATGGAGCTTACAT 399 chr3qtel1M 169105 CCAAATGGG 169113 i v i C L2a_3end#LINE 398 TCTAGTGGG 390 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.90 CpG sites = 15, Kimura (unadjusted) = 35.67 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.07 (7 / 94), avg. gap size = 2.71 (19 / 7) 198 24.07 12.96 0.00 chr3qtel1M 169059 169112 (830888) C L2c_3end#LINE/L2 (49) 429 369 m_b140s601i11 5259 chr3qtel1M 169059 CTGGGGACACAAAGGCAAAT-------GGTCCCCGGCCTCCAAGAGCTTA 169101 i iii ------- i v v i i C L2c_3end#LINE 429 CTGGGGATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCA 380 chr3qtel1M 169102 CATCCAAATGG 169112 vi v i C L2c_3end#LINE 379 CAGTCTAGTGG 369 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.17 CpG sites = 9, Kimura (unadjusted) = 30.17 Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.02 (1 / 53), avg. gap size = 7.00 (7 / 1) 22 9.10 0.00 0.00 chr3qtel1M 169220 169254 (830746) (GGGAGT)n#Simple_repeat 1 35 (0) m_b140s252i11 5260 chr3qtel1M 169220 GGGAGTGGGAGTGGGAGTGGGGGGGGGACTGGGAG 169254 i v v (GGGAGT)n#Sim 1 GGGAGTGGGAGTGGGAGTGGGAGTGGGAGTGGGAG 35 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 192 29.21 15.73 0.00 chr3qtel1M 170333 170421 (829579) MIRc#SINE/MIR 91 193 (75) m_b140s601i12 5261 chr3qtel1M 170333 GGTCTGAGGCAAGTCCCAGGATGTCTTGGAGC-----TTT--TAATCTAT 170375 ii vi v vvi iv iv ----- -- v i MIRc#SINE/MIR 91 GACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGT 140 chr3qtel1M 170376 AGAATGGGGACAAGAATGGCAA--CTAGCCACCTCCCA-----GCTGTGA 170418 i i v iv vi-- iv i v ----- i MIRc#SINE/MIR 141 AAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGA 190 chr3qtel1M 170419 GGA 170421 MIRc#SINE/MIR 191 GGA 193 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.70 CpG sites = 14, Kimura (unadjusted) = 37.70 Transitions / transversions = 1.17 (14/12) Gap_init rate = 0.05 (4 / 88), avg. gap size = 3.50 (14 / 4) 418 30.32 4.49 0.62 chr3qtel1M 175470 175625 (824375) MIRb#SINE/MIR 54 215 (53) m_b140s601i13 5262 chr3qtel1M 175470 CCAGAGTCCAAACTGAGCCTCAGCC--TTCCTCTCTGTGTGACCCTGGCC 175517 v i i i iivv v v -- v vv i v MIRb#SINE/MIR 54 CCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGC 103 chr3qtel1M 175518 AAGACACATCCCCGCTGCCTGCCTCAGTTTCCTCATCTGTAAAATAGGGA 175567 vi v vv v vivv i MIRb#SINE/MIR 104 AAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGA 153 chr3qtel1M 175568 TCGCACCTCCCTGCCTCTC-GGGCCGTGGGGCAG----AGTGAAACGATG 175612 vii -v v i v - ii v v vi ---- i i ii MIRb#SINE/MIR 154 TAATA-ATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATG 202 chr3qtel1M 175613 TTTGCAGAGCGCT 175625 iv i i MIRb#SINE/MIR 203 CATGTAAAGCGCT 215 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.15 CpG sites = 22, Kimura (unadjusted) = 39.19 Transitions / transversions = 0.88 (22/25) Gap_init rate = 0.03 (4 / 155), avg. gap size = 2.00 (8 / 4) 205 31.37 0.00 0.00 chr3qtel1M 177595 177645 (822355) C L2d_3end#LINE/L2 (2) 514 464 m_b140s601i14 5263 chr3qtel1M 177595 AGTCAGTCAGCCATCGAGTACTGAGTGAGCGCCTGCTGTGTGCCTGGGAT 177644 i i ii v i i v v i i iii v i C L2d_3end#LINE 514 AATCAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCAC 465 chr3qtel1M 177645 T 177645 C L2d_3end#LINE 464 T 464 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.08 CpG sites = 12, Kimura (unadjusted) = 44.08 Transitions / transversions = 3.00 (12/4) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 264 5.71 0.00 0.00 chr3qtel1M 180753 180787 (819213) MIRc#SINE/MIR 159 193 (75) m_b140s601i15 5264 chr3qtel1M 180753 CTTGCCCTGCCTACCTCACAGGGCTGTTGTGAGGA 180787 i i MIRc#SINE/MIR 159 CCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGA 193 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 6.07 CpG sites = 2, Kimura (unadjusted) = 6.07 Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 199 25.00 5.77 0.00 chr3qtel1M 180760 180811 (819189) MIR#SINE/MIR 156 210 (52) m_b140s601i16 5264 chr3qtel1M 180760 TGCCTACCTCACAGGGCTGTTGTGAGG---AAATATCCCACAAAAGGTAA 180806 i i i --- ivvii vv v v MIR#SINE/MIR 156 TACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATACATGTAA 205 chr3qtel1M 180807 AGTGC 180811 i MIR#SINE/MIR 206 AGCGC 210 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.10 CpG sites = 7, Kimura (unadjusted) = 30.83 Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.02 (1 / 51), avg. gap size = 3.00 (3 / 1) 410 26.35 3.54 2.63 chr3qtel1M 183524 183636 (816364) MIRc#SINE/MIR 2 115 (153) m_b140s601i17 5265 chr3qtel1M 183524 GGGGCAGCTAGGTGGCGCAGTGGATAGAGCCCCAGCCCTGAAGTCAGGAG 183573 i i--- i v v ii v i i i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr3qtel1M 183574 GACCCAAATTTAACCTCAGATACT--TACTTCCTAGCTGTGTGACCAGGG 183621 iiii ii vii v iiv --i v vv MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 98 chr3qtel1M 183622 GCAAGTCAC--AACCCC 183636 -- i MIRc#SINE/MIR 99 GCAAGTCACTTAACCTC 115 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.33 CpG sites = 20, Kimura (unadjusted) = 33.95 Transitions / transversions = 2.22 (20/9) Gap_init rate = 0.04 (5 / 112), avg. gap size = 1.40 (7 / 5) 16 5.27 0.00 0.00 chr3qtel1M 184672 184691 (815309) (T)n#Simple_repeat 1 20 (0) m_b140s252i12 5266 chr3qtel1M 184672 TTTCTTTTTTTTTTTTTTTT 184691 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTT 20 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 411 29.10 14.29 3.45 chr3qtel1M 185798 186007 (813993) MIRb#SINE/MIR 17 248 (20) m_b141s601i0 5267 chr3qtel1M 185798 TGCAATGAATAGGACACTGCACCTGAAGTTAGGAAGACCCAAGTTCAAAT 185847 i i v ii v vvii i i iv iii i MIRb#SINE/MIR 17 TGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCGAAT 66 chr3qtel1M 185848 AACACCTGGGCTTTGT-AGTTCC---CTATGTAGCTTTGGGCAAGT--CC 185891 ---- i - i i- v v --- i ii i -- i MIRb#SINE/MIR 67 ----CCCGG-CTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACT 111 chr3qtel1M 185892 CA---TTTCTA----TCTGT---CTCAACTGTAAAAT-GGCATAATTCTA 185930 i --- i i---- v --- v - v --- MIRb#SINE/MIR 112 TAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAA---TA 158 chr3qtel1M 185931 GCATCTGCCTCAGAGG---GCAGTGGGGA---------ATGGTATGGGTA 185968 ii i i iv --- iv i --------- ii iiiv MIRb#SINE/MIR 159 ATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTA 208 chr3qtel1M 185969 AAACATTTA-CACAGTGATGGGCACGTAGTAGGCCCTTAA 186007 i ii - viv i i v i MIRb#SINE/MIR 209 AAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAA 248 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 35.99 CpG sites = 43, Kimura (unadjusted) = 39.47 Transitions / transversions = 2.69 (43/16) Gap_init rate = 0.09 (18 / 209), avg. gap size = 2.11 (38 / 18) 241 5.00 12.50 0.00 chr3qtel1M 186743 186782 (813218) C MIR3#SINE/MIR (63) 145 101 m_b141s601i1 5268 chr3qtel1M 186743 CTCATTTTATAGATGAGGAAACTGAGGC----AGAGCT-AAGTGA 186782 i ---- v - C MIR3#SINE/MIR 145 CTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGA 101 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 5.18 CpG sites = 1, Kimura (unadjusted) = 5.18 Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.05 (2 / 39), avg. gap size = 2.50 (5 / 2) 51 20.97 0.00 0.00 chr3qtel1M 187400 187505 (812495) (GCA)n#Simple_repeat 1 106 (0) m_b141s252i0 5269 chr3qtel1M 187400 GCGGCAGCAGCAGTAGCAGGAGCGGCTGCAGCAGCAGGAGCAGCAGCAGT 187449 i i v i v v i (GCA)n#Simple 1 GCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGC 50 chr3qtel1M 187450 AACGGCTGCAGTAGCTGTAGCAATAACAGTAGTAGCTGCAGCAGCAGCAG 187499 i i v i v i ii i i i v (GCA)n#Simple 51 AGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAG 100 chr3qtel1M 187500 CAGCAG 187505 (GCA)n#Simple 101 CAGCAG 106 Matrix = Unknown Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.00 (0 / 105), avg. gap size = 0.0 (0 / 0) 264 24.38 4.82 1.16 chr3qtel1M 187868 187950 (812050) L2-1_AMi#LINE/L2 272 357 (878) m_b141s551i0 5270 chr3qtel1M 187868 CCCACCAACTGTGGGTATCCCACAGGATTCTAGTCTTGGGCCCCCTTCTC 187917 ivv vi i ii - i v i L2-1_AMi#LINE 272 CCCACTTTCTGTGGGGGTTCCACAGGGCTCT-GTCCTTGGTCCCCTTCTC 320 chr3qtel1M 187918 TTCTATC-GTACTTCACCT---GGCGATCTCATCAGC 187950 v -ii i i i --- ii v L2-1_AMi#LINE 321 TTCTCTCTACACCTTATCTCTGGGTAATCTCATCCGC 357 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 30.73 CpG sites = 14, Kimura (unadjusted) = 30.73 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.04 (3 / 82), avg. gap size = 1.67 (5 / 3) 164 23.02 0.27 0.27 chr3qtel1M 188322 188685 (811315) (TGC)n#Simple_repeat 1 364 (0) m_b141s252i1 5271 chr3qtel1M 188322 TGCTG-TGACTGGGGCTGTTACTGTTACTGCTGTAGCTACTACTCTTACT 188370 - - vv i i i i iv i i vi i (TGC)n#Simple 1 TGCTGCTG-CTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT 49 chr3qtel1M 188371 GATGCTGCTGCTGCTGCTGCCGCTCCTGCTCCTGCTGCTGCTGCCGCTCC 188420 v i v v i v (TGC)n#Simple 50 GCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC 99 chr3qtel1M 188421 TGCTCCTGCTGCTCCTGCCGCTCCTGCTCCTGCTACTACTGCTGCTGCCG 188470 v v i v v i i i (TGC)n#Simple 100 TGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG 149 chr3qtel1M 188471 CTCCTACTACTACTGCTGCAGCCGCTAGTGCTGCAGCTACTACTTTTACT 188520 v i i i v i iv v i i vi i (TGC)n#Simple 150 CTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT 199 chr3qtel1M 188521 GCTGTTGCAGCAGCTACTACTGCTAGTGCTGCTGCTGCCGCTCCTGCTGC 188570 i v v i i iv i v (TGC)n#Simple 200 GCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC 249 chr3qtel1M 188571 TGCTGCCGCTCCTGCTCCTGCTGCTGCTGCCGCTCCTGCCGCTGCTGCAG 188620 i v v i v i v (TGC)n#Simple 250 TGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG 299 chr3qtel1M 188621 CCGCTCCTGCTACTACTGCTGCAGCCGCTAGTGCTGCAGCTACTACTCTT 188670 i v i i v i iv v i i vi (TGC)n#Simple 300 CTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT 349 chr3qtel1M 188671 ACTGCTGCTGCTGCT 188685 i (TGC)n#Simple 350 GCTGCTGCTGCTGCT 364 Matrix = Unknown Transitions / transversions = 1.37 (41/30) Gap_init rate = 0.01 (2 / 363), avg. gap size = 1.00 (2 / 2) 150 23.45 0.22 5.49 chr3qtel1M 190690 191149 (808851) (CCTC)n#Simple_repeat 1 437 (0) m_b141s252i2 5272 chr3qtel1M 190690 CCTCCCTCCCTCAGGGCCCTCCCTCTGGCCCCGCCCTCCCTCCGGCCCCG 190739 -vvv -vvi v -vi v (CCTC)n#Simpl 1 CCTCCCTCCCTC-CCTCCCTCCCTC-CCTCCCTCCCTCCCTCC-CTCCCT 47 chr3qtel1M 190740 CCCTCCCTCTGGCCCTCCCTCCGGGCCCGCCCTCCCTCCGGGCCCTCCCT 190789 ivv -vv v -vv (CCTC)n#Simpl 48 CCCTCCCTCCCTCCCTCCCTCC-CTCCCTCCCTCCCTCC-CTCCCTCCCT 95 chr3qtel1M 190790 CCCTCAGGCCCTCCCCTGGGCCCTCCCTCCTGGCCCGCCCTCCCTCCGGC 190839 vvv iivvv -vv v -vi (CCTC)n#Simpl 96 CCCTCCCTCCCTCCCTCCCTCCCTCCCTCC-CTCCCTCCCTCCCTCC-CT 143 chr3qtel1M 190840 CCCTCCCTCCCTCAGGCCCTCCCTCCGGGCCCGCCCTCCCTCCGGCTCCT 190889 vvv -vv v vv - (CCTC)n#Simpl 144 CCCTCCCTCCCTCCCTCCCTCCCTCC-CTCCCTCCCTCCCTCCCTC-CCT 191 chr3qtel1M 190890 CCCTCCCTCCGGCTCCTCCCTCCCTCAGGGCCCCTCCCTCTGGCCCCGCC 190939 vv - --vvi -vvi v (CCTC)n#Simpl 192 CCCTCCCTCCCTC-CCTCCCTCCCTC--CCTCCCTCCCTC-CCTCCCTCC 237 chr3qtel1M 190940 CTCCCTCCAGGCCCTCCCTCCCTCCGGCCCCTCGCTGCCTCCTGCCCCTC 190989 -vv -vi v v -vi (CCTC)n#Simpl 238 CTCCCTCC-CTCCCTCCCTCCCTCC-CTCCCTCCCTCCCTCC-CTCCCTC 284 chr3qtel1M 190990 CCTCCCTCTGGCCCTCCCTCCGGCTCCTCCCTCCCTCAGGGCCCTCCCTC 191039 ivv vv - -vvv (CCTC)n#Simpl 285 CCTCCCTCCCTCCCTCCCTCCCTC-CCTCCCTCCCTC-CCTCCCTCCCTC 332 chr3qtel1M 191040 CTGGCCCGCCCTCCCTCCGGGCCCGCCCT-CCTGGCGCCCTCCCTCCGGG 191088 -vv v -vv v - vv v -vv (CCTC)n#Simpl 333 C-CTCCCTCCCTCCCTCC-CTCCCTCCCTCCCTCCCTCCCTCCCTCC-CT 379 chr3qtel1M 191089 CCCGCCCTCCCTCCGGCTCCTCCCTCCCTCCGGCTCCTCCCTCCCTCAGG 191138 v vv - vv - -vv (CCTC)n#Simpl 380 CCCTCCCTCCCTCCCTC-CCTCCCTCCCTCCCTC-CCTCCCTCCCTC-CC 426 chr3qtel1M 191139 GCCCTCCCTCC 191149 v (CCTC)n#Simpl 427 TCCCTCCCTCC 437 Matrix = Unknown Transitions / transversions = 0.15 (11/72) Gap_init rate = 0.05 (25 / 459), avg. gap size = 1.00 (25 / 25) 16 0.00 0.00 0.00 chr3qtel1M 199365 199381 (800619) (T)n#Simple_repeat 1 17 (0) m_b141s252i3 5273 chr3qtel1M 199365 TTTTTTTTTTTTTTTTT 199381 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTT 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 236 35.25 11.11 0.40 chr3qtel1M 199994 200218 (799782) C MamRTE1#LINE/RTE-BovB (2488) 1324 1076 m_b141s601i2 5274 chr3qtel1M 199994 AGCTTGCAGAGAATGAGTCTATGATACTTCCAGCGCTCTGTGCCACACAT 200043 i v v v v v v i vvv i v i i C MamRTE1#LINE/ 1324 AGTTTGGAGCGTATCAGGCGATGGTCGGTCCAGCACTCGGCGCCACGCAT 1275 chr3qtel1M 200044 TGTCTTCATTACTTTCA-CATCCT----ATCTGTCTCTT--ACAATCACA 200086 v - v v v i v - ----i ivv v i-- i v i C MamRTE1#LINE/ 1274 AG-CTGCAGTAATCTAAACATCCTTCAGGTCCCGCTGTCGAACGATGATA 1226 chr3qtel1M 200087 TGGTCCATTAAATGCTAATGTTT--GCTTCGAGGACA--CA-------TT 200125 ii v v i i v i --i i i i vi -- ------- C MamRTE1#LINE/ 1225 TAATCAATGAGATGCCACTGCTTAGACCTTGGGTGCATCCATGATGTCTT 1176 chr3qtel1M 200126 GCATTTA---AGTAAATAGAAAAC-ATGGTGGTGAGGAGAAGGTCAGGAG 200171 v vi ---i iiii i i-i v vv vi v v v vv C MamRTE1#LINE/ 1175 TCTCTTATTCGGTAGGCGGAAGATGGTGTTGGTGATTACGAGCTGATGCT 1126 chr3qtel1M 200172 ATACACAAGTCTTCAGTA--AGTA-ACCATTGCTGTTGCTGTTTCCAACC 200218 vvi vvivi v i -- - ?vvv i C MamRTE1#LINE/ 1125 TGGCACATTCGCTGAGCAGGAGTAGACCATTGCTGTTNAGCTTTCCAATC 1076 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 42.09 CpG sites = 36, Kimura (unadjusted) = 48.43 Transitions / transversions = 0.84 (36/43) Gap_init rate = 0.05 (11 / 224), avg. gap size = 2.36 (26 / 11) 479 34.60 8.41 5.45 chr3qtel1M 201379 201913 (798087) C MamRTE1#LINE/RTE-BovB (2893) 919 370 m_b141s601i3 5274 chr3qtel1M 201379 ATGGTGGGAACATGGGCACTGATGATGGTAGGATGGCACTTTC--CTGAA 201426 ii iv i i i v ?i i i--i v i C MamRTE1#LINE/ 919 ATGGTGGGGGCATATGCGCTGATGACGGTGGCANAGCGCTTTTGTTTCAG 870 chr3qtel1M 201427 AGGCAATCACATTGTCATAAGCCTGTCATTCA---CTCGGAG---ATAGA 201470 ? i iv ii vv v v v i ? --- v i --- vvi C MamRTE1#LINE/ 869 ANGTAGGCGTAGGGTCATCAGACGGTCACTNATGCCTCTGGGCAAATTTG 820 chr3qtel1M 201471 AAAGCTTTTTGTCTAGATGA-GATCTGATTAGGAAACTCATGCT-----G 201514 ii ?i vv v v - -vi ivi i v i i----- C MamRTE1#LINE/ 819 GGAGNCTTGAGACAAG-TGACTGTCTGATTGCAAAGCTGACGCCTGAGAG 771 chr3qtel1M 201515 TTTTCACTCCCCATCACTGGGGCTACTCTAGACAAACGTGGATCCAGC-T 201563 iiv i ivv vvivvii i iv i vi v i v ? i -i C MamRTE1#LINE/ 770 CCGTCGCTCTGAAGAGGGAAGACCTCTCCAGAAGAAGGCGTANCCGGCAC 721 chr3qtel1M 201564 CTAGCTCAGACAAGTGGCCTTCATTTTCCAGGCATGTTTCACCCAGGGAT 201613 iv v vv iv v ivvvv v vv i i v vv C MamRTE1#LINE/ 720 CTGTCTCCGTGAGCTGTCCTTCATCAGGAAGTCTGGTTTCGCTCAGTGCG 671 chr3qtel1M 201614 GCTATACCTGCCCTGGATGTGATGTGATACCTGCTGAGTTC---TCTCAC 201660 v ii vi i i v v i------ ------ --- viv C MamRTE1#LINE/ 670 GCGATGTCGACTCCGTATCTGG------AC------AGTTCACGTGCGAC 633 chr3qtel1M 201661 AAGAGCTATTCATCTTCCAGGTCTACTG--GATCTCATGTTGTCCGTA-A 201707 i v ii v i v v v -- v -- ii - i - C MamRTE1#LINE/ 632 GAGTGCCGTTCTTCTTTCTGGACGACTGCTGTTCTC--GTCATC-GCATA 586 chr3qtel1M 201708 GTGTCCATATAGTCTATGTAC-CAATGGTCAGTAGAATCAT-ATTTTCAA 201755 i vv iv i - - i v v--- v -i ?? ?ii C MamRTE1#LINE/ 585 GCGTCCTGATGTTCCATG-ACGCAATGGTTATTT---TCTTTGTNNTNGG 540 chr3qtel1M 201756 AAGATTTTGGACATGTTTTTGTGTTTTGACCACAAGACGGGATGTCTGTC 201805 v - vv iv ? i------ i ?vii -ii iii C MamRTE1#LINE/ 539 TAG-TTTTCTATTTGNTTTTGC------ACCGCAAGANTAAA-ACCCACC 498 chr3qtel1M 201806 TGCCACAATAAACAGG----CCAGGATTGAATTT---------------- 201835 v v i i v v ---- ?v ? ---------------- C MamRTE1#LINE/ 497 AGACGCGATAATCTGGTGAGCCAGNTTTGANTTTGGCGAGGCAGGCAACG 448 chr3qtel1M 201836 -TCAGGCCACCTTTTCTAGCTCCTTTCTCACATCACA-TGAGCAATATAT 201883 - i v ?i i i i- iv - iiiii? C MamRTE1#LINE/ 447 TTTAGGGCACCTTTTCTAGNCCCTTCCCCAT-TCGGAGTGAGCAGCGCGN 399 chr3qtel1M 201884 TACTTTGAAAAGACTACTGAGATACCCAGG 201913 - i vi v i i i v i C MamRTE1#LINE/ 398 T-CCTAAACAGGGCTGCTCAGACACCCAGG 370 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 41.80 CpG sites = 96, Kimura (unadjusted) = 49.85 Transitions / transversions = 1.22 (96/79) Gap_init rate = 0.08 (45 / 534), avg. gap size = 1.67 (75 / 45) 586 33.75 2.20 1.25 chr3qtel1M 202967 203284 (796716) L1ME4c_3end#LINE/L1 319 639 (191) m_b141s551i1 5275 chr3qtel1M 202967 AAAACAATTTGGAACTATGCTCAAAAAGTTATCAAATTGTGCATACCCTT 203016 i v v i iviv i ii v v v L1ME4c_3end#L 319 AAAGCAATTTGGCAATACGTATCAAGAGCCATAAAAATGTTCATACCCTT 368 chr3qtel1M 203017 TGATCCAGCAGTGTTTCTACTGGACTTATATCTCAAGGAGAT--CTTAAA 203064 i i i viiv v ivv v ii i --i i L1ME4c_3end#L 369 TGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAA 418 chr3qtel1M 203065 GGAAGGAAAGGGACTCACGTGTGCAAAAATGTTTGTGGCAGACCTCTTTG 203114 i ii - - ii ii i i ii v vvi v i L1ME4c_3end#L 419 AGAAGGAAAAAG-CT-ATATGCACGAAGATGTTCATTGCAGCGTTATTTA 466 chr3qtel1M 203115 TAGTGACAAGAAACTGGAAA----CTGGATGCCCATCTGCTGGAGAATGG 203160 i ii i i i ---- ii i v viiv i L1ME4c_3end#L 467 TAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAATGG 516 chr3qtel1M 203161 CTGAATAAGTTATGGAATATGAATGTTATGGAACCTTATTGTTCTATAAG 203210 i i i i v i v? iviv iv vvvv i v i L1ME4c_3end#L 517 TTAAGTAAATTATGGTACATCNACTCGATGGAATATTATGCAGCCATTAA 566 chr3qtel1M 203211 AAATGATCAGCAGGACGATTTCAGAGAGGCCTGGAGAGACTTATATG-TA 203259 v vi v v i viiv vii v - i iv v - L1ME4c_3end#L 567 AAATGATAATTATGAAGACTATGTAGCAACATGGA-AAATGTTTATGATA 615 chr3qtel1M 203260 CTGATGCTAAGTGAAATGAACAGAA 203284 - i i vi i L1ME4c_3end#L 616 -TAATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 44.64 CpG sites = 65, Kimura (unadjusted) = 47.11 Transitions / transversions = 1.59 (65/41) Gap_init rate = 0.02 (7 / 317), avg. gap size = 1.57 (11 / 7) 381 26.52 0.75 1.50 chr3qtel1M 204526 204659 (795341) L1MEi_5end#LINE/L1 2075 2207 (5) m_b141s551i2 5276 chr3qtel1M 204526 TATAGTTGGTTATAACTATAAATGTGAATGGGACGAACTCATCTATAAAA 204575 - ii v v v i ivii i v L1MEi_5end#LI 2075 TATA-TCAGTAATCACAATAAATGTAAATGGATTAAACTCACCTATTAAA 2123 chr3qtel1M 204576 TGGAAGCAGATGG-CAGAATGGATTAAAAACCAGAATCCTACAATATGTT 204624 v iv - vi- v vv i vi v i L1MEi_5end#LI 2124 AGACAG-AGATTATCAGATTGGATTAAAAAAAAAAATCCAGCTATATGCT 2172 chr3qtel1M 204625 GTTTACAACAAACACATTTGAAGCAGATTGATACA 204659 v i ii i i i vi i L1MEi_5end#LI 2173 GTTTACAAGAGACACACCTAAAACAAAACGACACA 2207 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 32.24 CpG sites = 20, Kimura (unadjusted) = 33.40 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.02 (3 / 133), avg. gap size = 1.00 (3 / 3) 419 21.37 0.85 0.85 chr3qtel1M 204534 204651 (795349) L1MEh_5end#LINE/L1 2113 2230 (5) m_b141s551i3 5276 chr3qtel1M 204534 GTTATAACTATAAATGTGAATGGGACGAACTCATCTATAAAATGGAAGCA 204583 v v v i vii i v v v iv - L1MEh_5end#LI 2113 GTAATTACAATAAATGTAAATGGGTTAAACTCACCAATTAAAAGACAG-A 2161 chr3qtel1M 204584 GA-TGGCAGAATGGATTAAAAACCAGAATCCTACAATATGTTGTTTACAA 204632 - ?v v ? v i v i i L1MEh_5end#LI 2162 GATTNTCAGATTGGATTNAAAAACAAAATCCAACAATATGCTGTCTACAA 2211 chr3qtel1M 204633 CAAACACATTTGAAGCAGA 204651 v i i i i ? L1MEh_5end#LI 2212 GAGACACACTTAAAACANA 2230 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 26.09 CpG sites = 12, Kimura (unadjusted) = 26.09 Transitions / transversions = 0.92 (12/13) Gap_init rate = 0.02 (2 / 117), avg. gap size = 1.00 (2 / 2) 61 0.00 0.00 0.00 chr3qtel1M 205554 205605 (794395) (TC)n#Simple_repeat 1 52 (0) c_b141s251i0 5277 chr3qtel1M 205554 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 205603 (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr3qtel1M 205604 TC 205605 (TC)n#Simple_ 51 TC 52 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 180 16.38 2.13 9.09 chr3qtel1M 205606 205652 (794348) C MIR#SINE/MIR (139) 123 80 m_b141s601i4 5278 chr3qtel1M 205606 CTGAGGCA-ATTGGGTTTAAGTGACATAAGTGCCCAAGATCACACAGC 205652 - vv i v i ----v i C MIR#SINE/MIR 123 CTGAGGCACAGAGAGGTTAAGTAAC----TTGCCCAAGGTCACACAGC 80 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 18.38 CpG sites = 3, Kimura (unadjusted) = 18.38 Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.11 (5 / 46), avg. gap size = 1.00 (5 / 5) 18 12.01 3.92 6.00 chr3qtel1M 206735 206785 (793215) (AAAGA)n#Simple_repeat 1 50 (0) m_b141s252i4 5279 chr3qtel1M 206735 AAAGAGAAAAAAAAGAAAA-TAAAG-AAAGATGAGAAAACAATAAAGAAA 206782 - i -v - vi -i - (AAAGA)n#Simp 1 AAAGA-AAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAA-GA-AAAGAAA 47 chr3qtel1M 206783 AGA 206785 (AAAGA)n#Simp 48 AGA 50 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.10 (5 / 50), avg. gap size = 1.00 (5 / 5) 16 0.00 0.00 0.00 chr3qtel1M 210973 210989 (789011) (T)n#Simple_repeat 1 17 (0) m_b141s252i6 5280 chr3qtel1M 210973 TTTTTTTTTTTTTTTTT 210989 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTT 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 187 37.14 2.84 0.69 chr3qtel1M 211212 211352 (788648) C L2#LINE/L2 (494) 2588 2445 m_b141s601i5 5281 chr3qtel1M 211212 GAGATATAGTGATGAATCCAGGATAACTAGTAGATTGTGGGCTCTTGGGA 211261 v v v v i v i vvv i v v iivv vi C L2#LINE/L2 2588 GAGAGAAAGAGAGGAGTCAAGGATGACTCCAAGGTTTTTGGCCTGAGCAA 2539 chr3qtel1M 211262 GTGGGAATATGGGGTTACTCTGTTCAGTAATAGGGAAGGTCGGTGGAAAG 211311 v i iv i i iv v?v v vi i i- v i i i C L2#LINE/L2 2538 CTGGAAGGATGGAGTTGCCATTNACTGAGATGGGGAAGA-CTGCGGGAGG 2490 chr3qtel1M 211312 A----GTTTAGAAGAGAAGATAATGAATTCTGCTTGGGGTATATT 211352 ---- iiii i v v i v i v ii i C L2#LINE/L2 2489 AGCAGGTTTGAGGGGGAAGATCAGGAGTTCAGTTTTGGACATGTT 2445 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 51.67 CpG sites = 27, Kimura (unadjusted) = 53.15 Transitions / transversions = 1.08 (27/25) Gap_init rate = 0.01 (2 / 140), avg. gap size = 2.50 (5 / 2) 247 26.60 15.96 0.00 chr3qtel1M 211630 211723 (788277) C L2a_3end#LINE/L2 (25) 492 384 m_b141s601i6 5282 chr3qtel1M 211630 TGATCACTCCCTCTGTGCCAGCCACTGCACTAAGTGCTGGGGA-----CA 211674 v i iiv v v iv i i ----- C L2a_3end#LINE 492 TGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGCGCTGGGGATACAGCA 443 chr3qtel1M 211675 G------AAATGGAC----TTCCCTGGAATCAAGAGGCTTCCAGTCTACT 211714 ------ ii ----v vvv v ii v v v C L2a_3end#LINE 442 GTGAACAAAACAGACAAAAGTCCCTGCCCTCATGGAGCTTACATTCTAGT 393 chr3qtel1M 211715 AGAGGGAGA 211723 i i C L2a_3end#LINE 392 GGGGGGAGA 384 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.04 CpG sites = 12, Kimura (unadjusted) = 33.11 Transitions / transversions = 0.92 (12/13) Gap_init rate = 0.03 (3 / 93), avg. gap size = 5.00 (15 / 3) 16 20.82 0.00 0.00 chr3qtel1M 212640 212672 (787328) (T)n#Simple_repeat 1 33 (0) m_b141s252i7 5283 chr3qtel1M 212640 TTTTTTTTATTTTTATTTATTCTTCATTTTTTT 212672 v v v i iv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 33 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 466 35.27 3.09 0.38 chr3qtel1M 213125 213383 (786617) HERV4_I#LTR/ERV1 5266 5531 (1008) m_b141s701i0 5284 chr3qtel1M 213125 CTGGATAGAAGCTTCCCTTGTAGGAAAAGAG--GGA----GAGATCATGA 213168 i v v i iivi v -- v---- i i i HERV4_I#LTR/E 5266 CTGGGTCGAAGCTTACCCTACCAGAACAGAGAAGGCTAATGAGGTTATAA 5315 chr3qtel1M 213169 AAATCTTCCTTCAG-ATATTATACATTGTTTTGGTCTATCC-AGATCACT 213216 ii ii i vv - v v v vii v vi i - v - HERV4_I#LTR/E 5316 AGGTTCTCTTAAAGGAAATAATCCCCCGGTTTGGGTTACCCCAGAGC-CT 5364 chr3qtel1M 213217 TCAGAGTGATAATGGCCCTTCCTTCACCTCACAAATTATTCAAAGTATAG 213266 i i i v i i v v i i vi v HERV4_I#LTR/E 5365 CCAAAGTGATAACGGCCCGTCCTTTATCTCCCAAATAACTCAAGGGGTTG 5414 chr3qtel1M 213267 CAGAGGCACTAAACATCTCCTACCACCTGCACTCTGCCAAGCATCCTTAA 213316 vi v viiv vvv i ii i i v vvi viv i HERV4_I#LTR/E 5415 CTAAGGCTCTCGGAATCAAATACTATTTACATTCAGCATGGAGGCCTCAA 5464 chr3qtel1M 213317 TTATCGGGTGAAGTAGAAAAAATGAATCAAACTCTTTAAAAAGCCCTAAT 213366 iv v vi iiiiv vv vii vi ii HERV4_I#LTR/E 5465 TCCTCCGGGAAAGTAGAAAGGGCTAATCAAACTCTAAAACGGGCGTTAGC 5514 chr3qtel1M 213367 TAAACTTTGCCAAGAGA 213383 i v i i i HERV4_I#LTR/E 5515 TAAGCTATGTCAGGAAA 5531 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 46.24 CpG sites = 51, Kimura (unadjusted) = 49.25 Transitions / transversions = 1.27 (51/40) Gap_init rate = 0.02 (5 / 258), avg. gap size = 1.80 (9 / 5) 337 33.33 2.04 0.00 chr3qtel1M 214463 214609 (785391) C HERVKC4#LTR/ERVK (4161) 1101 952 m_b141s701i1 5285 chr3qtel1M 214463 ATTAACGCTGGGCACTGAAAAGGCAAATCTTCTCATATC--CTTAT-CTA 214509 vii v iv v i iiv v -- i v - C HERVKC4#LTR/E 1101 ATTAACGGCAGGGATGGTAAAGGCAAATTTTTCGAAATCTGCCTCTGCTA 1052 chr3qtel1M 214510 GAGGGATAGAATAGAAACAATCTTTAATGTCTACAACCCAAAGAGGCCAT 214559 i i v v v i i i v vi i ivvv v v C HERVKC4#LTR/E 1051 AAGGAATTGTAAAAAAGCAGTCTTTTAAATCTATAATAACAAGCGGCCAG 1002 chr3qtel1M 214560 TCTCTAGGCAATTGAGTAGGAGATAGAAGTCCAGGCTGAAGAGTTCCCAT 214609 i v iivvi i i i i i ? i v ii i C HERVKC4#LTR/E 1001 TCTTTAGGGAGCATGGTGGGGGATGGGAGCCCNGGTTGTAAGGCTCCCAT 952 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 44.67 CpG sites = 28, Kimura (unadjusted) = 45.96 Transitions / transversions = 1.33 (28/21) Gap_init rate = 0.01 (2 / 146), avg. gap size = 1.50 (3 / 2) 547 28.31 7.23 3.19 chr3qtel1M 214481 214666 (785334) C HERVK#LTR/ERVK (4200) 3336 3148 m_b141s701i2 5285 chr3qtel1M 214481 AAAGGCAAATCTTCTCATA-TCCTTATCT---AGAGGGATAGAATAGAAA 214526 i - ? - vv --- i i v v i i C HERVK#LTR/ERV 3336 AAAGGCAAATTTT-TCANAATCCTGCTCTGCCAGAGGAATGGTAAAAAAG 3288 chr3qtel1M 214527 CAATCTTTAATGTC---TACAACCCAAAGAGGCCATTCTCTAGGCAATTG 214573 i v vi --- i ii--- i v i ? v vivv C HERVK#LTR/ERV 3287 CAATCCTTCAGATCAATTATAATT---AAAGGCCAATCTTTNGGGATCAT 3241 chr3qtel1M 214574 AGTAGGAGATAGAAGTCCAGGCTGAAGAGTTCCCATAGTTTCCAT--CTG 214621 i iv vi v ii i i i vi i v vv -- v C HERVK#LTR/ERV 3240 GGCCGGAGAGGGCAACCCGGGTTGGAGAGGCCCCATGGGTTGAATTACGG 3191 chr3qtel1M 214622 TTCCTTTACTCTTCTTAAATCAGTCAACATCCTCCATTTTCCAGA 214666 -- v ? vvii i i v v i v v C HERVK#LTR/ERV 3190 --CGTTNACGGCCCTTAAGTCAGTTAACATGCGCCATCTGCCTGA 3148 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 35.66 CpG sites = 43, Kimura (unadjusted) = 36.64 Transitions / transversions = 1.08 (28/26) Gap_init rate = 0.05 (10 / 185), avg. gap size = 1.50 (15 / 10) 30 5.72 0.00 0.00 chr3qtel1M 214667 214703 (785297) (T)n#Simple_repeat 1 37 (0) c_b141s251i1 5286 chr3qtel1M 214667 TTTTTTTTTTCTTTTTTTTCTTTTTTTTTTTTTTTTT 214703 i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 37 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 472 30.71 5.91 4.57 chr3qtel1M 214704 214906 (785094) C HERVK11D#LTR/ERVK (4529) 3223 3028 m_b141s701i3 5285 chr3qtel1M 214704 ACAACAAATACAGG-GAATTTCAAGGACTTAGAGAAGGTTGTA-AGTGTC 214751 i - i i v vvi ii i i vv - - C HERVK11D#LTR/ 3223 ACAACAAACACAGGCGAGTTCCATGGAGACAAGGAGGGCTCAATAGTGT- 3175 chr3qtel1M 214752 CTTGGTCA-AGTTGCTCTTGCAGTATATTTACTAAGGCCTGAATTTTATC 214800 - v ii- viv v vv vv v iv i i vv vi i v C HERVK11D#LTR/ 3174 -TTGCTTGTAGTAAATCATTAACAATTTCAATTAAAGCCTCCAACTTGTG 3126 chr3qtel1M 214801 TTTTGTTAAGGGCCACTCTTTTACCCATACTGATGTATCAGTTTTCCACT 214850 v vv iv vi i v v i vv vviv i C HERVK11D#LTR/ 3125 TTTGGAAAGTGGCCACTGCTCTACCCAAACAGGTGACTCACACATCCATT 3076 chr3qtel1M 214851 GAATAGGAACAGGTGAGAGTGCA-GGCAGGCCTTCAACAGCAACACTATC 214899 v?? i------ v? - - v --? i ii ivi i C HERVK11D#LTR/ 3075 GTNNAGGG------GATNG-GCAGGGGAGGC--NCAGCAGTGACGGCACC 3035 chr3qtel1M 214900 TAAAAAG 214906 i C HERVK11D#LTR/ 3034 TAAAAGG 3028 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.95 CpG sites = 58, Kimura (unadjusted) = 40.87 Transitions / transversions = 0.86 (30/35) Gap_init rate = 0.07 (15 / 202), avg. gap size = 1.00 (15 / 15) 547 28.31 7.23 3.19 chr3qtel1M 214704 214848 (785152) C HERVK#LTR/ERVK (4389) 3147 2993 m_b141s701i2 5285 chr3qtel1M 214704 ---------ACAACAAATACAGG-GAATTTCAAGGACTTAGA--GAAGGT 214741 --------- iv i - i --iv -- i C HERVK#LTR/ERV 3147 TTTTTCTGAATTACAAACACAGGAGAATTCCAAGG--CGAGAACGAAGGC 3100 chr3qtel1M 214742 TGTAAGTGTCCTTGGTCAAGTTGCTC--TTGC-AGTATATTTACTAAGGC 214788 vv vi i vv v ii i -- - i v v --- i C HERVK#LTR/ERV 3099 TCAATATGTCCCTTTTCTAACTGTTCNTTTGCTAATAAATGTA---AAGC 3053 chr3qtel1M 214789 CTGAATTTTATCTTTTGTTAAGGGCCACTCTTTTACCCATACTGATGTAT 214838 vv vi v v v iv vv ? i v v C HERVK#LTR/ERV 3052 CTCCAGCTTTTGTTTTGGTAGCGGCCACTGATTTACCCATACNGGTTTTT 3003 chr3qtel1M 214839 CAGTTTTCCA 214848 v C HERVK#LTR/ERV 3002 CTGTTTTCCA 2993 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 35.66 CpG sites = 43, Kimura (unadjusted) = 36.64 Transitions / transversions = 0.68 (15/22) Gap_init rate = 0.07 (10 / 144), avg. gap size = 2.00 (20 / 10) 43 0.00 0.00 0.00 chr3qtel1M 216923 216961 (783039) (ATC)n#Simple_repeat 1 39 (0) c_b141s251i2 5287 chr3qtel1M 216923 ATCATCATCATCATCATCATCATCATCATCATCATCATC 216961 (ATC)n#Simple 1 ATCATCATCATCATCATCATCATCATCATCATCATCATC 39 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 14 25.14 1.61 5.00 chr3qtel1M 217042 217103 (782897) (GTGT)n#Simple_repeat 1 60 (0) m_b141s252i8 5288 chr3qtel1M 217042 GTGTATGTATGTGTGTATGTAGAGATTTGTAAGTGAGTGGGTATGTGTCC 217091 i i i - v - v iv v v i -v (GTGT)n#Simpl 1 GTGTGTGTGTGTGTGTGTGT-GTG-TGTGTGTGTGTGTGTGTGTGTGT-G 47 chr3qtel1M 217092 TGT-TGTGTATGT 217103 - i (GTGT)n#Simpl 48 TGTGTGTGTGTGT 60 Matrix = Unknown Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.07 (4 / 61), avg. gap size = 1.00 (4 / 4) 595 16.67 4.90 0.00 chr3qtel1M 220398 220499 (779501) C U6#snRNA (0) 107 1 c_b141s401i0 5289 chr3qtel1M 220398 AAAAATATGGAGCACTTCATGAATTTGTGTGTCATCCTTGTGCAGGGACT 220447 i i i i i i i C U6#snRNA 107 AAAAATATGGAACGCTTCACGAATTTGCGTGTCATCCTTGCGCAGGGGCC 58 chr3qtel1M 220448 ATGCTAA-----TCTGGACCATTCCAATTGTAGTATATGAGCTACCCATG 220492 ----- v i i v v i v v C U6#snRNA 57 ATGCTAATCTTCTCTGTATCGTTCCAATTTTAGTATATGTGCTGCCGAAG 8 chr3qtel1M 220493 TGAGTAC 220499 i i C U6#snRNA 7 CGAGCAC 1 Matrix = 18p45g.matrix Kimura (with divCpGMod) = 12.41 CpG sites = 12, Kimura (unadjusted) = 19.31 Transitions / transversions = 2.40 (12/5) Gap_init rate = 0.01 (1 / 101), avg. gap size = 5.00 (5 / 1) 14 9.32 0.00 0.00 chr3qtel1M 221509 221531 (778469) (TTG)n#Simple_repeat 1 23 (0) m_b141s252i9 5290 chr3qtel1M 221509 TTGTTGTTGTTGTTGTTTTTTTT 221531 v v (TTG)n#Simple 1 TTGTTGTTGTTGTTGTTGTTGTT 23 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 205 37.23 4.05 1.99 chr3qtel1M 221948 222095 (777905) C MIRb#SINE/MIR (39) 229 79 m_b141s601i7 5291 chr3qtel1M 221948 CATACATTATGTATAATGTTTTATGGCTATCTTCCCTTTTTATTTTCACA 221997 vi i i ivv ii i iivvi iv i v v ii C MIRb#SINE/MIR 229 CAGGCACTGTGCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACA 180 chr3qtel1M 221998 AT----TTGGGAATT-GGTATAAATATAATCCTCACTTTACAAATATGGA 222042 i----i v iv - --- v i i i iv C MIRb#SINE/MIR 179 ACAACCCTGCGAGGTAGGTAT---TATTATCCCCATTTTACAGATGAGGA 133 chr3qtel1M 222043 AACTCAGG-GAAGAGCAGTTTTATGAATTTTCAGGGATCAGAGACTTAGT 222091 v -vv vi vvi i v vi vii i v v vi C MIRb#SINE/MIR 132 AACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGT 83 chr3qtel1M 222092 AAAT 222095 i C MIRb#SINE/MIR 82 AAGT 79 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 51.89 CpG sites = 30, Kimura (unadjusted) = 53.34 Transitions / transversions = 1.25 (30/24) Gap_init rate = 0.04 (6 / 147), avg. gap size = 1.50 (9 / 6) 206 30.98 1.15 3.53 chr3qtel1M 222009 222095 (777905) C MIRc#SINE/MIR (108) 160 76 m_b141s601i8 5291 chr3qtel1M 222009 GGTATAAATATAATCCTCACTTTACAAATATGGAAACTCAGG-GAAGAGC 222057 --- v i i i iv v -vv v C MIRc#SINE/MIR 160 GGTAT---TATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGA 114 chr3qtel1M 222058 AGTTTTATGAATTTTCAGGGATCAGAGACTTAGTAAAT 222095 i vvi v vi vii i v v vi i C MIRc#SINE/MIR 113 GGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGT 76 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 40.25 CpG sites = 12, Kimura (unadjusted) = 40.25 Transitions / transversions = 0.86 (12/14) Gap_init rate = 0.05 (4 / 86), avg. gap size = 1.00 (4 / 4) 374 29.60 7.59 3.31 chr3qtel1M 222616 222905 (777095) C L1M4_orf2#LINE/L1 (1317) 1977 1676 m_b141s551i4 5292 chr3qtel1M 222616 TTGTCTTTTTCACTTCTGATCTTGTTGGGAAGAGCTCTAGTTTAACTTTT 222665 v ---- ivv - ?---- i iii C L1M4_orf2#LIN 1977 TTGTCTTGTTC----CTGATCTTAGGGGGAA-AGCN----TTCAGTCTTT 1937 chr3qtel1M 222666 TAC-----AG-ATAATGTTTTCTTTTCCTTTTTGATAGAGACGCCTTGTT 222709 i ----- - i vv v vvv vi vi v i i i C L1M4_orf2#LIN 1936 CACCATTAAGTATGATGTTAGCTGTGGGTTTTTCGTAGATGCCCTTTATC 1887 chr3qtel1M 222710 ATTTTAAGAAAGGCTTCATTTATTTTTA----------TGTTTTTAATAG 222749 vv i i viii v i ii ---------- vi v C L1M4_orf2#LIN 1886 AGGTTGAGGAAGTTCCCTTCTATTCCTAGTTTGTTGAGTGTTTTTATCAT 1837 chr3qtel1M 222750 GAAGAAGTTTTATATTTTGTCAAAAGCTTTTTCTGCATC--TTAAGATAA 222797 iii v iv v i -- i i C L1M4_orf2#LIN 1836 GAAAGGGTGTTGGATTTTGTCAAATGCTTTTTCTGCGTCTATTGAGATGA 1787 chr3qtel1M 222798 TCTTATGCTTTATGTTGTTTTTGCAATTGGTAAAGTGAATTA---TGTTT 222844 v i v v iv v v v ii vi v --- v C L1M4_orf2#LIN 1786 TCATGTGGTTTTTGTCCTTTATTCTATTAATATGGTGTATTACATTGATT 1737 chr3qtel1M 222845 AAGTTTCCTAATACTG-ACTAACTCTACATTCCTGGCATAGATTCTATTA 222893 i - i v? ii - i ii i v i i i i v C L1M4_orf2#LIN 1736 GA-TTTTCGNATGTTGAACCAACCTTGCATTCCTGGGATAAATCCCACTT 1688 chr3qtel1M 222894 TGCCATAGTGCA 222905 v i i i C L1M4_orf2#LIN 1687 GGTCATGGTGTA 1676 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 37.90 CpG sites = 48, Kimura (unadjusted) = 39.11 Transitions / transversions = 1.37 (48/35) Gap_init rate = 0.06 (16 / 289), avg. gap size = 2.00 (32 / 16) 405 30.42 7.29 3.00 chr3qtel1M 222616 222903 (777097) C L1M4_orf2#LINE/L1 (1317) 1977 1678 m_b142s551i0 5292 chr3qtel1M 222616 TTGTCTTTTTCACTTCTGATCTTGTTGGGAAGAGCTCTAGTTTAACTTTT 222665 v ---- ivv - ?---- i iii C L1M4_orf2#LIN 1977 TTGTCTTGTTC----CTGATCTTAGGGGGAA-AGCN----TTCAGTCTTT 1937 chr3qtel1M 222666 TAC-----AG-ATAATGTTTTCTTTTCCTTTTTGATAGAGACGCCTTGTT 222709 i ----- - i vv v vvv vi vi v i i i C L1M4_orf2#LIN 1936 CACCATTAAGTATGATGTTAGCTGTGGGTTTTTCGTAGATGCCCTTTATC 1887 chr3qtel1M 222710 ATTTTAAGAAAGGCTTCATTTATTTTTA----------TGTTTTTAATAG 222749 vv i i viii v i ii ---------- vi v C L1M4_orf2#LIN 1886 AGGTTGAGGAAGTTCCCTTCTATTCCTAGTTTGTTGAGTGTTTTTATCAT 1837 chr3qtel1M 222750 GAAGAAGTTTTATATTTTGTCAAAAGCTTTTTCTGCATC--TTAAGATAA 222797 iii v iv v i -- i i C L1M4_orf2#LIN 1836 GAAAGGGTGTTGGATTTTGTCAAATGCTTTTTCTGCGTCTATTGAGATGA 1787 chr3qtel1M 222798 TCTTATGCTTTATGTTGTTTTTGCAATTGGTAAAGTGAATTATGTTTA-- 222845 v i v v iv v v v ii vi v ii v -- C L1M4_orf2#LIN 1786 TCATGTGGTTTTTGTCCTTTATTCTATTAATATGGTGTATTACATTGATT 1737 chr3qtel1M 222846 AGTTTCCTAATACTG-ACTAACTCTACATTCCTGGCATAGATTCTATTAT 222894 ii i v? ii - i ii i v i i i i vv C L1M4_orf2#LIN 1736 GATTTTCGNATGTTGAACCAACCTTGCATTCCTGGGATAAATCCCACTTG 1687 chr3qtel1M 222895 GCCATAGTG 222903 i i C L1M4_orf2#LIN 1686 GTCATGGTG 1678 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.44 CpG sites = 50, Kimura (unadjusted) = 40.69 Transitions / transversions = 1.43 (50/35) Gap_init rate = 0.05 (15 / 287), avg. gap size = 2.00 (30 / 15) 316 37.05 6.95 2.56 chr3qtel1M 223138 223511 (776489) C L2#LINE/L2 (1) 3081 2692 m_b142s601i1 5293 chr3qtel1M 223138 GAGGGAGAGCATTCCAGGCAT-GGAAATAGCAAAGGT----GCCTAGATA 223182 i i i v- i i iv i---- iv vi C L2#LINE/L2 3081 GGGGAAGAGCGTTCCAGGCAGAGGGAACAGCAAGTGCAAAGGCCCTGAGG 3032 chr3qtel1M 223183 TGGA---GTATCT----TGTTTCTAGAATAGCCAGAAGGGTAGTATCATT 223225 i i--- ii ---- ivvi i v i vi i vii C L2#LINE/L2 3031 CGGGAGCGTGCCTGGCGTGTTCGAGGAACAGCAAGGAGGCCAGTGTGGCT 2982 chr3qtel1M 223226 GGA-CGGAA-GAGTATATACTGTTGAGTG--AGGTAA-AAGCCTGGAAAG 223270 - i- iivivi-- vv -- vi -i viii i C L2#LINE/L2 2981 GGAGCGGAGTGAGCGAGGG--GGAGAGTGGTAGGAGATGAGGTCAGAGAG 2934 chr3qtel1M 223271 GTAG-GAGGTAGCAGGTTATGGAGGGCTTTCAATGCCAAACTGAGCGTTT 223319 i- i v v i i v i vv v vvv i vii C L2#LINE/L2 2933 GTAACGGGGGACCAGATCATGTAGGGCCTTGTAGGCCATTGTAAGGACTT 2884 chr3qtel1M 223320 CACATTTTATCCTAATGGTAATAACAAGTAAGTG-AGGTTTATTGAGTAA 223368 iivv ii i vv vi iiv iv v - v - i i C L2#LINE/L2 2883 TGGCTTTTACTCTGAGTGAGATGGGAAGCCATTGGAGGGTT-TTGAGCAG 2835 chr3qtel1M 223369 AGAACTGGCAGAGTCAGATCTAC-CTTTAGGAAAATAA----GGTTTTTA 223413 i v i vii v ii -i ii ii v ---- i vi i C L2#LINE/L2 2834 AGGAGTGACATGATCTGACTTACGTTTTAAAAGGATCACTCTGGCTGCTG 2785 chr3qtel1M 223414 -GTTGGAAGAAGAATGGAGGGGAGGGGAGAGACCTGAGGAAGGCAGACAC 223462 - ii iv v ? - vi i --iv i v v - C L2#LINE/L2 2784 TGTTGAGAATAGACTGNAGGGG-GGCAAGGG--TGGAAGCAGGGAGAC-C 2739 chr3qtel1M 223463 CCCTAATCCCCAGCAACTGCAATAG-CCAGACTGGGGGTGATGATGGCCT 223511 vvi i---vvi v i i i- i vi i i i i C L2#LINE/L2 2738 AGTTAG---GAGGCTATTGCAGTAATCCAGGCGAGAGATGATGGTGGCTT 2692 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 51.97 CpG sites = 84, Kimura (unadjusted) = 54.48 Transitions / transversions = 1.65 (84/51) Gap_init rate = 0.06 (24 / 373), avg. gap size = 1.50 (36 / 24) 17 20.54 0.00 0.00 chr3qtel1M 225198 225231 (774769) (AT)n#Simple_repeat 1 34 (0) m_b142s252i1 5294 chr3qtel1M 225198 ATATATAAATAAATACACACATATATGTATATAT 225231 v v i i i i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATAT 34 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 276 26.76 0.00 0.00 chr3qtel1M 225730 225800 (774200) DNM1r#Unknown 2475 2545 (2117) m_b142s502i0 5295 chr3qtel1M 225730 CACATTCATATATATATATATGTATATATACACATATGTGTGTGTGTATG 225779 i vi i i i i i iiii i i i i DNM1r#Unknown 2475 CACGTGTATGTGTGTATATATGTGTGTATATGTGTGTATGTGTGTATATA 2524 chr3qtel1M 225780 TGTGTGTATATATATATATAT 225800 i ii ? DNM1r#Unknown 2525 TGTGTATATATACGTATNTAT 2545 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.87 CpG sites = 18, Kimura (unadjusted) = 38.32 Transitions / transversions = 18.00 (18/1) Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0) 282 25.35 0.00 0.00 chr3qtel1M 225749 225819 (774181) DNM1r#Unknown 2476 2546 (2116) m_b142s502i1 5295 chr3qtel1M 225749 ATGTATATATACACATATGTGTGTGTGTATGTGTGTGTATATATATATAT 225798 i i i iiii i i i i i i DNM1r#Unknown 2476 ACGTGTATGTGTGTATATATGTGTGTATATGTGTGTATGTGTGTATATAT 2525 chr3qtel1M 225799 ATTTACATATATGCATATATA 225819 i v i i i ? DNM1r#Unknown 2526 GTGTATATATACGTATNTATA 2546 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 30.49 CpG sites = 17, Kimura (unadjusted) = 35.38 Transitions / transversions = 17.00 (17/1) Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0) 285 25.32 1.27 0.00 chr3qtel1M 225821 225899 (774101) L1ME3F_3end#LINE/L1 452 531 (459) m_b142s551i1 5296 chr3qtel1M 225821 CAGCTCTTTTC-TCAGAACAAAGAACTAAAAATTGAGGGAATGTCCATCA 225869 v v - v v i i ii ivivvvi i L1ME3F_3end#L 452 CAGCACTGTTCGTAATAGCAAAAAACTGGAAACAACCCAAATGTCCATCG 501 chr3qtel1M 225870 ATTGGGGAATGGATGAATAAATTGTGGTAT 225899 iv i i L1ME3F_3end#L 502 ACAGGAGAATGGATAAATAAATTGTGGTAT 531 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 29.54 CpG sites = 11, Kimura (unadjusted) = 31.38 Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.01 (1 / 78), avg. gap size = 1.00 (1 / 1) 246 20.63 0.00 0.00 chr3qtel1M 225859 225921 (774079) L1MB8_3end#LINE/L1 491 553 (372) m_b142s551i3 5296 chr3qtel1M 225859 AATGTCCATCAATTGGGGAATGGATGAATAAATTGTGGTATTTGGTTATG 225908 i iv i v v vvv ii L1MB8_3end#LI 491 AATGTCCATCAACTGATGAATGGATAAATAAAATGTGGTATATCCATACA 540 chr3qtel1M 225909 AAGAAATATTATT 225921 v i L1MB8_3end#LI 541 ATGGAATATTATT 553 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 24.23 CpG sites = 6, Kimura (unadjusted) = 24.23 Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0) 306 4.88 0.00 0.00 chr3qtel1M 225859 225899 (774101) L1ME3Cz_3end#LINE/L1 487 527 (470) m_b142s551i2 5296 chr3qtel1M 225859 AATGTCCATCAATTGGGGAATGGATGAATAAATTGTGGTAT 225899 v i L1ME3Cz_3end# 487 AATGTCCATCAATAGGGGAATGGATAAATAAATTGTGGTAT 527 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 5.05 CpG sites = 1, Kimura (unadjusted) = 5.05 Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 16 17.55 0.00 8.16 chr3qtel1M 226185 226237 (773763) (GGCTGCT)n#Simple_repeat 1 49 (0) m_b142s252i2 5297 chr3qtel1M 226185 GGCTGGCTGGGTTCTGTTCTGGTGGCTGCTGGTCTCATGGCTTCTGGCTA 226234 - v v -v v - vv v - (GGCTGCT)n#Si 1 GGCT-GCTGGCTGCTG-GCTGCTGGCTGCTGG-CTGCTGGCTGCTGGCT- 46 chr3qtel1M 226235 GCT 226237 (GGCTGCT)n#Si 47 GCT 49 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.08 (4 / 52), avg. gap size = 1.00 (4 / 4) 17 21.06 0.00 0.00 chr3qtel1M 226873 226906 (773094) (AT)n#Simple_repeat 1 34 (0) m_b142s252i3 5298 chr3qtel1M 226873 ATATATAAATACATATACACATATATGTATGTAT 226906 v i i i i i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATAT 34 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 57 9.77 2.65 1.75 chr3qtel1M 227335 227447 (772553) (AT)n#Simple_repeat 1 114 (0) c_b142s251i0 5299 chr3qtel1M 227335 ATATATATATATATATATATATATATATATATAGAAATATATAT-TCCCA 227383 v v - -vi (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATAT-ATA 49 chr3qtel1M 227384 AATATA-ATATATATATGGAAATGTATA-ATATATATATCAAATATATAT 227431 v - iv v i - - v (AT)n#Simple_ 50 TATATATATATATATATATATATATATATATATATATAT-ATATATATAT 98 chr3qtel1M 227432 ATATATATATATATAT 227447 (AT)n#Simple_ 99 ATATATATATATATAT 114 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.04 (5 / 112), avg. gap size = 1.00 (5 / 5) 293 25.30 1.20 0.00 chr3qtel1M 227480 227562 (772438) L1ME3F_3end#LINE/L1 448 531 (459) m_b142s551i4 5300 chr3qtel1M 227480 ATATCAGCTCTTTTC-TCAGAGCAAAGAATTGAAAATTGAGGGAATGCCC 227528 v v v - v v i i i ivivvvi i L1ME3F_3end#L 448 ATAGCAGCACTGTTCGTAATAGCAAAAAACTGGAAACAACCCAAATGTCC 497 chr3qtel1M 227529 ATCAATTGGGGAATGGATGAATAAATTGTGGTAT 227562 i iv i i L1ME3F_3end#L 498 ATCGACAGGAGAATGGATAAATAAATTGTGGTAT 531 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 29.51 CpG sites = 11, Kimura (unadjusted) = 31.24 Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.01 (1 / 82), avg. gap size = 1.00 (1 / 1) 242 22.22 0.00 0.00 chr3qtel1M 227522 227584 (772416) L1MB8_3end#LINE/L1 491 553 (372) m_b142s551i5 5300 chr3qtel1M 227522 AATGCCCATCAATTGGGGAATGGATGAATAAATTGTGGTATTTGGTTATG 227571 i i iv i v v vvv ii L1MB8_3end#LI 491 AATGTCCATCAACTGATGAATGGATAAATAAAATGTGGTATATCCATACA 540 chr3qtel1M 227572 AAGAAATATTATT 227584 v i L1MB8_3end#LI 541 ATGGAATATTATT 553 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 26.56 CpG sites = 7, Kimura (unadjusted) = 26.56 Transitions / transversions = 1.00 (7/7) Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0) 348 30.43 0.00 0.00 chr3qtel1M 230185 230299 (769701) C L1MC5_3end#LINE/L1 (2129) 565 451 m_b142s551i6 5301 chr3qtel1M 230185 TTCTTACAGAACAATAATATTCCATAATATTCATATACTACAATTTATTC 230234 i vvvv i i vi i vv i i i i C L1MC5_3end#LI 565 TTTTTACAGCTGCATAGTACTCCATTGTGTGGATGTACCATAGTTTATTC 516 chr3qtel1M 230235 AGCCACTCTCCAATTGATGGGCATCCACTTAGTTTCCAGTTTCTGGCCAC 230284 i v i v i iiivv v i i v i i C L1MC5_3end#LI 515 AACCAGTCCCCTATTGATGGACATTTGGGTTGTTTCCAGTCTTTTGCTAT 466 chr3qtel1M 230285 TACAAAGAGGCCTGC 230299 v vv C L1MC5_3end#LI 465 TACAAATAGTGCTGC 451 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.86 CpG sites = 19, Kimura (unadjusted) = 39.86 Transitions / transversions = 1.19 (19/16) Gap_init rate = 0.00 (0 / 114), avg. gap size = 0.0 (0 / 0) 411 25.45 0.00 0.00 chr3qtel1M 230198 230307 (769693) C L1ME3A_3end#LINE/L1 (368) 552 443 m_b142s551i7 5301 chr3qtel1M 230198 ATAATATTCCATAATATTCATATACTACAATTTATTCAGCCACTCTCCAA 230247 i vi i vv i i v i v vi C L1ME3A_3end#L 552 ATAGTATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTACTG 503 chr3qtel1M 230248 TTGATGGGCATCCACTTAGTTTCCAGTTTCTGGCCACTACAAAGAGGCCT 230297 i iiivv ? ?? i i i v vv C L1ME3A_3end#L 502 TTGATGGACATTTGGGTNGTTTCCAGTTTNNGGCTATTACGAATAGTGCT 453 chr3qtel1M 230298 GCCACAAACA 230307 i ii C L1ME3A_3end#L 452 GCTATGAACA 443 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 31.61 CpG sites = 17, Kimura (unadjusted) = 33.04 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.00 (0 / 109), avg. gap size = 0.0 (0 / 0) 37 4.82 0.00 2.27 chr3qtel1M 231606 231650 (768350) (TC)n#Simple_repeat 1 44 (0) c_b142s251i1 5302 chr3qtel1M 231606 TCTCTCTCTCTCTCTGTCTCTCTCGTCTCTCTGTCTCTCTCTCTC 231650 v - v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTC-TCTCTCTCTCTCTCTCTCTC 44 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 651 30.36 4.81 2.95 chr3qtel1M 232226 232724 (767276) C L1P4_orf2#LINE/L1 (742) 2552 2045 m_b142s551i8 5303 chr3qtel1M 232226 TGGTCCTACAAATGAATTTTG---TTATTTTTTCTAATTCAGT--AAAAT 232270 i -- v i--- vi v -- C L1P4_orf2#LIN 2552 TGGTTC--CATATGAATTTTAGAATAGTTTTTTCTAATTCTGTGAAAAAT 2505 chr3qtel1M 232271 GATTTTTTGGTAATTTGATTAGGATGGCATTGAATTTATAAATTAGTTTG 232320 iv -- i vi i i i i i i iv C L1P4_orf2#LIN 2504 GACGTT--GGTAGTTTGATAGGAATAGCGTTGAATCTGTAGATTGCTTTG 2457 chr3qtel1M 232321 GGTAAAATTATCATTTTTATTATATTGCTTCTGTCTA--CCATGAACATT 232368 i iv vii v iv v - i -- i v C L1P4_orf2#LIN 2456 GGCAGTATGGCCATTTTAACGATATTGATTCT-TCCAATCCATGAGCATG 2408 chr3qtel1M 232369 TAATACTTCTCCAATTTATATTTG--ATTTT--ATTTTTATAAAAAGATT 232414 v ii i - i v v -- i ?-- i v v iv vv C L1P4_orf2#LIN 2407 GAATGTTTTTCCA-TTTGTTTGTGTCATCTNTGATTTCTTTCAGCAGTGT 2359 chr3qtel1M 232415 TTAATGTAATTTTG-TTATATACTTCTTGGGTTTGTGTTGACAGACATGC 232463 -- i i v- i v vv vviii viv v vi ii ii C L1P4_orf2#LIN 2358 TT--TGTAGTTCTCCTTGTAGAGATCTTTCACCTCCTTGGTTAGATGTAT 2311 chr3qtel1M 232464 TTCCAGGTACTTTATACTATTTAGAGCTATTTTAAATGGGGT--ATTTCT 232511 i i i vi v ivi v i --vv C L1P4_orf2#LIN 2310 TCCTAGGTATTTTATTTTTTTTGTGGCTATTGTAAATGGGATTGCGTTCT 2261 chr3qtel1M 232512 TACCATTT--CTTCTTGC-AGAATTTTGTTTGTGATACATAGGAATGCTG 232558 i-- -- iiiv -v iv i v ---i i i C L1P4_orf2#LIN 2260 TG--ATTTGGCTCTCAGCTTGAACGTTATTGGTG---TATAGAAATGCTA 2216 chr3qtel1M 232559 ATGAATAATATGGATTTACTTCACATCCTGCTACTTTCCTAAAG----TT 232604 v v vv i iv v i iii vv v i ---- C L1P4_orf2#LIN 2215 CTGATTTTTGTACATTGATTTTGTATCCTGAAACTTTACTGAAGTCGTTT 2166 chr3qtel1M 232605 ATTGTTTCTACTAACTTTTTAATTGAGTTTTGGGGATTTTCCAAGTGT-- 232652 iiv vv i i iiiv i vi i i i i -- C L1P4_orf2#LIN 2165 ATCAGTTCTAGGAGCCTTTTGGCGGAGTCTTTAGGGTTTTCTAGGTATAG 2116 chr3qtel1M 232653 -ACCATATTGTCTGTAAAGACAGAGAGAGTTTTATCACTTTGTTTTCTAT 232701 - i i v ii -- v v iiv iv i C L1P4_orf2#LIN 2115 AATCATATCGTCAGCGAAG--AGAGATAGTTTGACTTCTTCTTTTCCTAT 2068 chr3qtel1M 232702 TCAGATCCCTTTTATGTCTTTTT 232724 ii v v i C L1P4_orf2#LIN 2067 TTGGATGCCTTTTATTTCTTTCT 2045 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.71 CpG sites = 86, Kimura (unadjusted) = 40.21 Transitions / transversions = 1.41 (86/61) Gap_init rate = 0.05 (27 / 498), avg. gap size = 1.44 (39 / 27) 16 7.40 3.23 3.23 chr3qtel1M 235182 235212 (764788) (CTT)n#Simple_repeat 1 31 (0) m_b142s252i4 5304 chr3qtel1M 235182 CTTCTTTCTTCTTCTTCTT-TTTTTTTTCTTC 235212 - - i i (CTT)n#Simple 1 CTTC-TTCTTCTTCTTCTTCTTCTTCTTCTTC 31 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2) 16 9.26 0.00 0.00 chr3qtel1M 236799 236821 (763179) (CT)n#Simple_repeat 1 23 (0) m_b142s252i5 5305 chr3qtel1M 236799 CTCTCTCTGTCTCTCTCTCTTTC 236821 v i (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTC 23 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 24 9.39 0.00 0.00 chr3qtel1M 236821 236854 (763146) (CA)n#Simple_repeat 1 34 (0) m_b142s252i6 5306 chr3qtel1M 236821 CACACACACACACACAAACACACACATAAACACA 236854 v i v (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACA 34 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 423 22.58 3.23 0.00 chr3qtel1M 239046 239138 (760862) MIR#SINE/MIR 49 144 (118) m_b142s601i2 5307 chr3qtel1M 239046 TGAGTTCAAATCTGGACTTAGACAGTTCCTAGCTGTGT--TTGTGGGTAA 239093 i i iv i iv v v v --iiv i MIR#SINE/MIR 49 TGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 98 chr3qtel1M 239094 GTCATTTAACC-CTGTTTCCCTCAGTTTCCTCATCTGTAAAATAAG 239138 i i - v v v ii MIR#SINE/MIR 99 GTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGG 144 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 25.81 CpG sites = 12, Kimura (unadjusted) = 27.29 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.02 (2 / 92), avg. gap size = 1.50 (3 / 2) 334 23.86 1.60 9.48 chr3qtel1M 239873 239997 (760003) MIRb#SINE/MIR 3 118 (150) m_b142s601i3 5308 chr3qtel1M 239873 GAGTGGGCAGCTAGGTGGTGTAGTGGATAGCTCACCAGCCCTGAA-TTAG 239921 - --- i v vv vi ii i - i MIRb#SINE/MIR 3 GAG-GGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAG 48 chr3qtel1M 239922 AAGTGCCTGAGTTTCAAATCTGGCTCACAGACACACATTTCCTAGCTGTG 239971 vivi i iv vi i -----ii - i v MIRb#SINE/MIR 49 ACAGACCTGGGTTCGAATCCCGGCTC-----TGC-CACTTACTAGCTGTG 92 chr3qtel1M 239972 TGACCTGTGGG-AAGTCAATTAACCCC 239997 - - i v i MIRb#SINE/MIR 93 TGACCT-TGGGCAAGTTACTTAACCTC 118 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.70 CpG sites = 17, Kimura (unadjusted) = 29.21 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.10 (13 / 124), avg. gap size = 1.00 (13 / 13) 312 33.54 3.14 2.50 chr3qtel1M 240248 240406 (759594) L2a_3end#LINE/L2 75 234 (283) m_b142s601i4 5309 chr3qtel1M 240248 CCACATGCTGTGTCTCCTAACT-CTGATCAAATACACT--GTATGCACTA 240294 -- - i vi -i vv i i i i-- i i v iv L2a_3end#LINE 75 CCACA--CTG-GCCTCCTTGCTGTTCCTCGAACACGCCAGGCACGCTCCC 121 chr3qtel1M 240295 AGCTTAGA--CTTTGTACTGGCTCGTCTCCCTTGCCTGAAAGGTTCTTCT 240342 iv i i-- i v - ii ii i v i i L2a_3end#LINE 122 GCCTCAGGGCCTTTGCACTTGCT-GTTCCCTCTGCCTGGAACGCTCTTCC 170 chr3qtel1M 240343 TCCTCATCTTGGTCTCATACCTTCCCTGGCTTCCTGCAGGACTGAGCTCA 240392 i vv v iv iv viiv vi vi i v v vv L2a_3end#LINE 171 CCCAGATATCCGCATGGCTCGCTCCCTCACCTCCTTCAGGTCTTTGCTCA 220 chr3qtel1M 240393 AATATCACCTTCCC 240406 i i L2a_3end#LINE 221 AATGTCACCTTCTC 234 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.47 CpG sites = 31, Kimura (unadjusted) = 46.24 Transitions / transversions = 1.48 (31/21) Gap_init rate = 0.04 (7 / 158), avg. gap size = 1.29 (9 / 7) 289 33.79 6.45 4.52 chr3qtel1M 240362 240578 (759422) L2b_3end#LINE/L2 238 458 (8) m_b142s601i5 5309 chr3qtel1M 240362 CCTTCCCTGGCTTCCTGCAGGACTGAGCTCAAATATCACCTTCCCCT--- 240408 i i ii -- - i i - ii--- i i i --- L2b_3end#LINE 238 CCCTCCCTGACCCCC--CAGG-CCGGG-TCAGG---CGCCCTCCTCTGGG 280 chr3qtel1M 240409 -TCATCCATTCTT--TATGTCACT-TA---TATGAACTGAGTTATTCACA 240451 -i vi v i --iv i - i--- ? -- vivi i? i L2b_3end#LINE 281 CCCCCCCAGTCCTACCCTGCCACTCTGGGTTATNA--TTGTCTGNTTACA 328 chr3qtel1M 240452 TTTCT-CCTCTTACCTTTAGATTATGAACCCCTTGTGATAAGAGAATGAG 240500 v -i ii- vi i i i i v v ivv i vi ? L2b_3end#LINE 329 TGTCTGTCTCCC-CCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNG 377 chr3qtel1M 240501 TTT-TTGCGTTT-CCTTT-CATCCCTAACATTCTGCACAGTGCCTGGCAC 240547 i - ivi i- vi -i i i iiiiv ? L2b_3end#LINE 378 TCTGTCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCAC 427 chr3qtel1M 240548 TCTGCAAGTGCCCCAAAGATATTTGTGGAAT 240578 v v i i i i viv i v L2b_3end#LINE 428 ACAGTAGGCGCTCAGTAAATATTTGTTGAAT 458 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 45.06 CpG sites = 50, Kimura (unadjusted) = 50.20 Transitions / transversions = 2.50 (50/20) Gap_init rate = 0.09 (19 / 216), avg. gap size = 1.26 (24 / 19) 16 23.32 1.92 1.92 chr3qtel1M 241237 241288 (758712) (TCTGAC)n#Simple_repeat 1 52 (0) m_b142s252i7 5310 chr3qtel1M 241237 TCTGAATATGTCACTGCCTCCCGACTCTAACTCTAACCCTAAC-CTGACT 241285 v v v v v - i i i i i - (TCTGAC)n#Sim 1 TCTGACTCTGACTCTGACT-CTGACTCTGACTCTGACTCTGACTCTGACT 49 chr3qtel1M 241286 CTG 241288 (TCTGAC)n#Sim 50 CTG 52 Matrix = Unknown Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.00 (2 / 2) 21 24.38 6.19 3.45 chr3qtel1M 241759 241871 (758129) (TATTC)n#Simple_repeat 1 116 (0) m_b142s252i8 5311 chr3qtel1M 241759 TACTCTAAT-TATTCTTATATTTTCT-TTCTAATCTGTTCTCCAGATCTG 241806 i v - vv v v - v i -- -v i (TATTC)n#Simp 1 TATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCT--A-TTCTA 47 chr3qtel1M 241807 TT-T-TTCTAATGTTTCCCATTCTGTTCTATT-T-TTC-ATCCTTTTTCT 241851 - - v v v i i i - - - i - v (TATTC)n#Simp 48 TTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTC-TATTCT 96 chr3qtel1M 241852 ATTTTATTTTATTATTTTCT 241871 i i v v (TATTC)n#Simp 97 ATTCTATTCTATTCTATTCT 116 Matrix = Unknown Transitions / transversions = 0.69 (9/13) Gap_init rate = 0.10 (11 / 112), avg. gap size = 1.00 (11 / 11) 14 12.74 0.00 8.11 chr3qtel1M 241830 241869 (758131) (TTTTATT)n#Simple_repeat 1 37 (0) m_b142s252i9 5312 chr3qtel1M 241830 TTCTATTTTTCATCCTTTTTCTATTTTATTTTATTATTTT 241869 i i -- v v - (TTTTATT)n#Si 1 TTTTATTTTTTAT--TTTTTATTTTTTATTTT-TTATTTT 37 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.08 (3 / 39), avg. gap size = 1.00 (3 / 3) 13 16.57 0.00 11.11 chr3qtel1M 242643 242692 (757308) (TTTCT)n#Simple_repeat 1 45 (0) m_b142s252i10 5313 chr3qtel1M 242643 TTTCTTATCTGCTTCTTTTGTATATTCTCATCTTTTCTTAATTCTCTTCT 242692 v -i v - - iv -- i (TTTCT)n#Simp 1 TTTCTTTTCT-TTTCTTTTCT-T-TTCTTTTCTTTTCTT--TTCTTTTCT 45 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.10 (5 / 49), avg. gap size = 1.00 (5 / 5) 25 31.44 3.65 2.90 chr3qtel1M 244559 244695 (755305) (AAGG)n#Simple_repeat 1 138 (0) m_b142s252i11 5314 chr3qtel1M 244559 AATGAAAGAAGGAAGGAA-AAATAAAGAAACAAAAAGAAGCAA-GAA-GA 244605 v i -i vi i -ii i v - - (AAGG)n#Simpl 1 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAA-GGAAGGAAGGAAGGAAGGA 49 chr3qtel1M 244606 CAAAAGGAAGGAAAGAAAGAAGAGAGAAGAAAAAAGGAAATAAAGATGAA 244655 vii i i - - i ii iv i v i (AAGG)n#Simpl 50 AGGAAGGAAGGAAGGAAGGAAG-GA-AGGAAGGAAGGAAGGAAGGAAGGA 97 chr3qtel1M 244656 ATGAATGAAAAAAAAAAAGAAATGAAGGAAGG--GGGAGGAA 244695 v - i ii ii i v -- i (AAGG)n#Simpl 98 AGGAA-GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 138 Matrix = Unknown Transitions / transversions = 3.00 (24/8) Gap_init rate = 0.06 (8 / 136), avg. gap size = 1.12 (9 / 8) 413 25.94 0.81 5.98 chr3qtel1M 244744 244866 (755134) MIR#SINE/MIR 7 123 (139) m_b142s601i6 5315 chr3qtel1M 244744 TGGTACAGTGGCTTAGAGCACCAGTCCTGAAGTCAGAGGACTTGAGTTCA 244793 i i i i v vi ii i i vvi i i i MIR#SINE/MIR 7 TAGCATAGTGGTTAAGAGCACGGGCTCTGGAGCCAGACTGCCTGGGTTCG 56 chr3qtel1M 244794 GATCTGGTCTCAGACACTTAAAACTTCTGAGCTGTGTGACAGTGGGCAAG 244843 i iv v v v --- ---- vv MIR#SINE/MIR 57 AATCCCGGCTCTGCCACTT---ACT----AGCTGTGTGACCTTGGGCAAG 99 chr3qtel1M 244844 TAATTTAACCCCAAT-TGCCTCAG 244866 v i i vv - MIR#SINE/MIR 100 TTACTTAACCTCTCTGTGCCTCAG 123 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.03 CpG sites = 17, Kimura (unadjusted) = 32.32 Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.07 (8 / 122), avg. gap size = 1.00 (8 / 8) 15 7.86 3.70 0.00 chr3qtel1M 244888 244914 (755086) (AAAC)n#Simple_repeat 1 28 (0) m_b142s252i12 5316 chr3qtel1M 244888 AAACAAACTAACAAACAAA-AACCAAAC 244914 v - v (AAAC)n#Simpl 1 AAACAAACAAACAAACAAACAAACAAAC 28 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.04 (1 / 26), avg. gap size = 1.00 (1 / 1) 636 31.62 8.12 2.02 chr3qtel1M 245115 245582 (754418) C L1MB2_3end#LINE/L1 (366) 552 57 m_b142s551i9 5317 chr3qtel1M 245115 ATAATGTGCCATTACAATTAGATATCACATCCTGTTCAGCCATTC--CC- 245161 i v ii vv v i ii i v -- - C L1MB2_3end#LI 552 ATAATATTCCATTGTATGTATATACCACATTTTGTTTATCCATTCATCCG 503 chr3qtel1M 245162 ----------CTT----TACT---AAATCTTAGCCACTACAAAAGA-GCT 245193 ---------- ---- i --- vv i i i iii vi - C L1MB2_3end#LI 502 TCGATGGACACTTGGGTTGCTTCCACCTCTTGGCTATTGTGAATAATGCT 453 chr3qtel1M 245194 ATTATAAATA-GTTTGTGCAAATAATTCCTTC----CCCT-TTTTTACCT 245237 ii i i - vv - ii ---- -i i vi C L1MB2_3end#LI 452 GCTATGAACATGGGTGTGCAAATA-TCTCTTCGAGACCCTGCTTTCAATT 404 chr3qtel1M 245238 CTTTTGGATGTAGGCCTAATAGTGTCACTGTCAGATCAAAGGGTGCAAAG 245287 i vi i iv vv i iii v v ---- i C L1MB2_3end#LI 403 CTTTTGGATATATACCCAGAAGTGGGATTGCTGGATCATATGGT----AA 358 chr3qtel1M 245288 TTTTATATTCTA-----TTGGGCAGAGTTCCAAATTGCTCTCCAGAATAG 245332 i - i ----- i v - viv v i i i v iii C L1MB2_3end#LI 357 TTCTAT-TTTTAATTTTTTGAGGA-ACCGCCATACTGTTTTCCATAGCGG 310 chr3qtel1M 245333 TTGGATCAGTTCACAACTCTACCAACA-TGTATTAGTATCCTACTTTTTC 245381 i v i v i vii i - i iv vi i i v i C L1MB2_3end#LI 309 CTGCACCATTTTACATTCCCACCAACAGTGCACAAGGGTTCCAATTTCTC 260 chr3qtel1M 245382 CACATTGCCTCCTACATTTATTATTTTCCTATTATTTTGTCATATTAGAC 245431 ivi v v i i - i v -- v v C L1MB2_3end#LI 259 CACATCCTCGCCAACACTTGTTATTTTC-TGTTTTTTTG--ATAGTAGCC 213 chr3qtel1M 245432 AATCTGATCAGTGTCAGGTGATACCTCAGAGATGTTTTAATTTGCATTTA 245481 vi i vi v i vv vv i v C L1MB2_3end#LI 212 ATCCTAATGGGTGTGAGGTGATATCTCATTGTGGTTTTGATTTGCATTTC 163 chr3qtel1M 245482 TCTCCTCAGTAGTGATTTAGAAG-----TTTATATGAGTACAGATAGTTT 245526 i vv v v v v iv----- i vv iiv iivi C L1MB2_3end#LI 162 CCTAATGATTAGTGATGTTGAGCATCTTTTCATATGCTTGTTGGCCATTT 113 chr3qtel1M 245527 TGAGTTCTTTATCTGAAAACTGCCTGTTCATATCCTTTGACCATTTATCA 245576 vv vv iv iv i v i i vi v v ? C L1MB2_3end#LI 112 GTATATCTTCTTTGGAGAAATGTCTATTCAAGTCCTTTGCCCATTTTTNA 63 chr3qtel1M 245577 ACTGAG 245582 ii i C L1MB2_3end#LI 62 ATCGGG 57 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.19 CpG sites = 82, Kimura (unadjusted) = 42.39 Transitions / transversions = 1.30 (82/63) Gap_init rate = 0.05 (22 / 467), avg. gap size = 2.18 (48 / 22) 727 28.74 4.32 3.72 chr3qtel1M 245237 245583 (754417) C L1ME5_3end#LINE/L1 (537) 404 56 m_b142s551i10 5317 chr3qtel1M 245237 TCTTTTGGATGTAGGCCTAATAGTGTCACTGTCAGATCAAAGGGT--GCA 245284 v i vi i iv i vv i iii i v -- i C L1ME5_3end#LI 404 TCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATGCG 355 chr3qtel1M 245285 AAGTTTTATATTCTATTGGGCAGAGT---TCCAAATTGCTCTCCAGAATA 245331 ------ i iv v i vi ---v i i C L1ME5_3end#LI 354 ------TATACTTAATTTGACTAAGTACTGCCAGATTGCTCTCCAGAATG 311 chr3qtel1M 245332 GTTGGATCAGTTCACAACTCTACCAACA-TGTATTAGTAT-CCTACTTTT 245379 i v i ii vii i i - i v vi - - ? i C L1ME5_3end#LI 310 GCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTA-TNTC 262 chr3qtel1M 245380 TCCACATTGCCTCCTACATTTATTATTTTCCTATTATTTTGTCATATTAG 245429 i ivi v v i ivi v - --ii v v v v C L1ME5_3end#LI 261 CCCACATCCTCGCCAACACTTGGCATTATCC-A--GCTTTCTAATTTTTG 215 chr3qtel1M 245430 ACAATCTGATCAGTGTCAGGTGATACCTCAGAGATGTTTTAATTTGCATT 245479 v i i vi v i i vv v C L1ME5_3end#LI 214 CCAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATT 165 chr3qtel1M 245480 TATCTCCTCAGTAGTGATTTAGAAG-----TTTATATGAGTACAGATAG- 245523 v vv i v i v v iv----- i vv --- v - C L1ME5_3end#LI 164 TCTCTGATTACTAATGAGTTTGAGCATCTCTTCATATGCTT---GTTAGC 118 chr3qtel1M 245524 -TTTTGAGTT-CTTTATCTGAAAACTGCCTGTTCATATCCTTTGACCATT 245571 - i i - i iv v i v C L1ME5_3end#LI 117 CTTTCGGGTTTCCTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCCATT 68 chr3qtel1M 245572 TATCAACTGAGG 245583 v v i i C L1ME5_3end#LI 67 TTTCTATTGGGG 56 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.62 CpG sites = 52, Kimura (unadjusted) = 37.06 Transitions / transversions = 1.18 (52/44) Gap_init rate = 0.06 (21 / 346), avg. gap size = 1.33 (28 / 21) 12 17.67 2.38 4.88 chr3qtel1M 245749 245790 (754210) (CATGTTT)n#Simple_repeat 1 41 (0) m_b142s252i13 5318 chr3qtel1M 245749 CATTTTACATGTTGTGATGCTCTC-TGTATCTTGTTTCATGTT 245790 v v - v - i - v v (CATGTTT)n#Si 1 CATGTTTCATGTT-TCATG-TTTCATGTTTCATGTTTCATGTT 41 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.07 (3 / 41), avg. gap size = 1.00 (3 / 3) 16 20.99 0.00 2.50 chr3qtel1M 246619 246659 (753341) (GAG)n#Simple_repeat 1 40 (0) m_b142s252i14 5319 chr3qtel1M 246619 GAGGAAGAAGGAAGAGGAGTAACAGGAGGAAGAGAAGGAGG 246659 - i i v iv i i (GAG)n#Simple 1 GAGG-AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGG 40 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 185 27.50 0.00 0.00 chr3qtel1M 247891 247930 (752070) C L2d_3end#LINE/L2 (0) 516 477 m_b142s601i7 5320 chr3qtel1M 247891 TTAGTCAGTCAGCCAAAAAGGATTTATTAAGCACCTGTTA 247930 i i i ii v v i i ii C L2d_3end#LINE 516 TCAATCAATCAATCAACAAGTATTTATTGAGCGCCTACTA 477 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.98 CpG sites = 9, Kimura (unadjusted) = 37.29 Transitions / transversions = 4.50 (9/2) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 13 17.38 6.38 2.04 chr3qtel1M 250969 251015 (748985) (TTCCTC)n#Simple_repeat 1 49 (0) m_b142s252i15 5321 chr3qtel1M 250969 TTCCTCTTCC-C-TCCTCTACCTACAAACT-TTCTTCTTTCTCTTCTTCT 251015 - - v - vvv - i i i (TTCCTC)n#Sim 1 TTCCTCTTCCTCTTCCTCTTCCT-CTTCCTCTTCCTCTTCCTCTTCCTCT 49 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.09 (4 / 46), avg. gap size = 1.00 (4 / 4) 525 21.82 1.53 5.56 chr3qtel1M 253453 253583 (746417) MIRc#SINE/MIR 2 127 (141) m_b142s601i8 5322 chr3qtel1M 253453 GAGCTAG-GTTGCACAGTGAATAGAGCACCAGCCCTGAAGTCGGGAAGAC 253501 vi - v ii i v ii v i i i MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr3qtel1M 253502 CTGAATTCAAATCTGGTCCCAGACACTTAACACTTCCTAGCTGTGTGACC 253551 ii i i iv v i v v ------- MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTGACC 94 chr3qtel1M 253552 CTGGGCAAGTCACTTAACCTCAATT-GCCTCAG 253583 i vv v- MIRc#SINE/MIR 95 TTGGGCAAGTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 25.08 CpG sites = 16, Kimura (unadjusted) = 26.17 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.07 (9 / 130), avg. gap size = 1.00 (9 / 9) 20 0.00 0.00 0.00 chr3qtel1M 253585 253606 (746394) (A)n#Simple_repeat 1 22 (0) m_b142s252i16 5323 chr3qtel1M 253585 AAAAAAAAAAAAAAAAAAAAAA 253606 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAA 22 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 284 32.20 3.30 1.86 chr3qtel1M 254431 254642 (745358) C HERVK11#LTR/ERVK (2761) 5192 4978 m_b142s701i0 5324 chr3qtel1M 254431 CCAACATG--CAGGTCCATTTTCTGTTTTTATTGCCTGTGGTACACCCAT 254478 i i-- vv i v i vvv i v vv C HERVK11#LTR/E 5192 CTAACATATCCAGGGGCGTTGTCTGTCTTTATTTGATATGGAAGCCCCAT 5143 chr3qtel1M 254479 GATTGCAAATGCCTGTGTA-ACAAGTTCAGTGACCACTCGGGCCGTCTCT 254527 i i - vv vi - v v ivv i v---i vi C HERVK11#LTR/E 5142 AACTGCAAA-GCAAGAATACAGATGTTTTTTAACA---TGGGCCGTGCCT 5097 chr3qtel1M 254528 TTTGCTGCT-GATA--TTGCAAAAGTGATTCCTGAAAAGCTGTCTACCAT 254574 iiv i - ii -- v vv ii i vv i v i viv C HERVK11#LTR/E 5096 TCCCCTGTTTGGCAAGTAGCCCAGATAAAACCTGAGAAGGTATCTACAGA 5047 chr3qtel1M 254575 AACATGGATAAAAGACAGACGACCAAAG-ATTTATAATGGGTCACATCCA 254623 v i v v ? v vi - vi vv i C HERVK11#LTR/E 5046 AACATGCACATATGANAGTCTGCCAAAGGAGCTAACATGAGTCACATCCA 4997 chr3qtel1M 254624 CTTGCCAAATTTCATTGGG 254642 i v vv? i C HERVK11#LTR/E 4996 TTTGCCATAAANCATTAGG 4978 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 42.07 CpG sites = 29, Kimura (unadjusted) = 42.88 Transitions / transversions = 0.76 (29/38) Gap_init rate = 0.04 (9 / 211), avg. gap size = 1.22 (11 / 9) 291 33.05 2.47 1.63 chr3qtel1M 256424 256666 (743334) L1PREC2_orf2#LINE/L1 3050 3294 (0) m_b142s551i11 5325 chr3qtel1M 256424 AAAGCCTTTGTACAAACAAAACTAA-TGCAAACAAGATTAGAAGGGAAGC 256472 i i i i i- vv - iiv iii v iv iv v L1PREC2_orf2# 3050 AGAGCTTCTGCACAG-CAAAAGAAACTATCAACAGAGTAAACAGACAACC 3098 chr3qtel1M 256473 AACAAACTGGGAAAACATCTT--CAATTAAAGGTTCTGAAAAAGGCCTCC 256520 v i v i v ? -- viv v vv v i vv L1PREC2_orf2# 3099 TACAGAATGGGAGAAAATNTTTGCAAACTATGCATCTGACAAAGGTCTAA 3148 chr3qtel1M 256521 CTTCCAAAATATATAGAGAATTGACTCAAATTTATAAGAAAT---CAAGC 256567 iv iv v ii i v vv i v--- i L1PREC2_orf2# 3149 TATCCAGCATCTATAAGGAACTTAAACAAATTTACAAGAAAAAAACAAAC 3198 chr3qtel1M 256568 CATTCTCCAATCGATAAACGGTCAAAGGATATGAACAGACAATTTTCAGA 256617 v -- i - ii v ii v i v i L1PREC2_orf2# 3199 AA--CCCCA-TTAAAAAGTGGGCAAAGGACATGAACAGACACTTTTCAAA 3245 chr3qtel1M 256618 TGATGAAATTGAAACTATTACCACTCATATGAAAGAGTGTTCCAAATCA 256666 v v v vv vi viii v vv i iv i v v L1PREC2_orf2# 3246 AGAAGACATACATGCGGCCAACAAGCATATGAAAAAAAGCTCAACATCA 3294 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 44.30 CpG sites = 37, Kimura (unadjusted) = 44.30 Transitions / transversions = 0.88 (37/42) Gap_init rate = 0.03 (7 / 242), avg. gap size = 1.43 (10 / 7) 342 29.38 2.34 1.39 chr3qtel1M 256453 256666 (743334) L1M5_orf2#LINE/L1 3079 3294 (0) m_b142s551i12 5325 chr3qtel1M 256453 AACAAGATTAGAAGGGAAGCAACAAACTGGGA--AAACATCTTCAATTAA 256500 v i v i v v i ? -- i i v ?- v L1M5_orf2#LIN 3079 AAGAAAATGAAAAGGCAAGCCACAGANTGGGAGAAAATATTTGCAAN-AC 3127 chr3qtel1M 256501 AGGT-TCTGAAAAAGGCCTCCCTTCCAAAATATATAGAGAATTGACTCAA 256549 vi - v v viv i i i vviv L1M5_orf2#LIN 3128 ATATATCTGACAAAGGACTCGTATCCAGAATATATAAAGAACTCCTACAA 3177 chr3qtel1M 256550 ATTTATAAGAAATCAAGCCATTC--TCCAATCGATAAACGGTCAAAGGAT 256597 ? iv ? -- v vv --i v? v i v i i L1M5_orf2#LIN 3178 NTCAATAANAAA--AAGACAAACAACCCAATANAAAAATGGGCAAAAGAC 3225 chr3qtel1M 256598 ATGAACAGACAATTTTCAGATGATGAAATTGAAACTATTACCACTCATAT 256647 v v iv i v v v ?v iviii vi vv i L1M5_orf2#LIN 3226 TTGAACAGACACTTCACAAAAGAAGATATNCAAATGGCCAATAAGCACAT 3275 chr3qtel1M 256648 GAAAGAGTGTTCCAAATCA 256666 iii i v v? L1M5_orf2#LIN 3276 GAAAAGATGCTCAACNTCA 3294 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.23 CpG sites = 28, Kimura (unadjusted) = 39.23 Transitions / transversions = 0.82 (28/34) Gap_init rate = 0.03 (6 / 213), avg. gap size = 1.33 (8 / 6) 1515 29.84 1.27 1.27 chr3qtel1M 256528 257155 (742845) L1ME4c_3end#LINE/L1 12 639 (191) m_b142s551i13 5325 chr3qtel1M 256528 AATATATAGAGAATTGACTCAAATTTATAAGAAA----TCAAGCCATTCT 256573 ? i ii v i v ---- v ----i L1ME4c_3end#L 12 ANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAAGAC----C 57 chr3qtel1M 256574 CCAATCGATAAACGGTCAAAGGATATGAACAGACAATTTTCAGATGATGA 256623 v i v i iv ? v v L1ME4c_3end#L 58 CCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAGGA 107 chr3qtel1M 256624 AATTGAAACTATTACCACTCATATGAAAGAGTGTTCCAAATCACTATTAA 256673 vv ?ivi v v vv i i i i v vv i v L1ME4c_3end#L 108 AATACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTAGTAA 157 chr3qtel1M 256674 TCAGAGAA-TGCAAATTAAGACAACTCTGAGATACCACTACACACCTGTC 256722 i - ii vv i vi i i i L1ME4c_3end#L 158 TCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCTATT 207 chr3qtel1M 256723 AGATTGGCTAAGATGACAGGAAAAAATAATGATGAATGTTGGAGGGGATG 256772 i i v i vvv ii vvi iviv i v i ? L1ME4c_3end#L 208 AAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGCTGGCGAGGNTG 257 chr3qtel1M 256773 CGGGAAAACTTGGACACTGATGCATTGTTGGTGGAGTTGTGAACGAATCT 256822 vi v v ? v i i vi? i ivii vi L1ME4c_3end#L 258 CGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGTAC 307 chr3qtel1M 256823 AACCATTCTGGAGAGAAATATGGAATTATGCCCAAAAAGTAATCAAACTG 256872 v i i v v v v i iviv i iv v v L1ME4c_3end#L 308 AACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAAAATG 357 chr3qtel1M 256873 TGCATACCCTTTGACGCAGCAGTGCTACTACTGGGCTTATACCACAAGGA 256922 v v i i v i v vv v i vi L1ME4c_3end#L 358 TTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGA 407 chr3qtel1M 256923 CATA---CTAAAGAAGGGAAAAGGACCTATATGTGCCAAAATGTTTGTGG 256969 v --- v i --- ii v i ii v L1ME4c_3end#L 408 AATAATTCAAAAGAAGGAAAAAG---CTATATGCACGAAGATGTTCATTG 454 chr3qtel1M 256970 CAGCCCTGTTTGTAGTGGCTAGAAACTGGAAAATGAATGGATGCCCATCA 257019 vi i i i i v i i vvivv ii i v L1ME4c_3end#L 455 CAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACA 504 chr3qtel1M 257020 ATTGGAGAATGATTGAGTAAATTGTGGTATACAAATGTTATGGAATAATA 257069 v i i i i i iv? iviv v L1ME4c_3end#L 505 ATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATATTA 554 chr3qtel1M 257070 TTTTTCTGTAAGAAATGACCAGCAGCATGAATACAGAGAGGCTTGGAGAG 257119 vivv ii v i iv vi vv v v iiv vii v - i L1ME4c_3end#L 555 TGCAGCCATTAAAAATGATAATTATGAAGACTATGTAGCAACATGGA-AA 603 chr3qtel1M 257120 ACTTACATGAACTGATGCTAAGTGAAATGAGCAGAA 257155 iv vi vv i i vi L1ME4c_3end#L 604 ATGTTTATGATATAATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.13 CpG sites = 95, Kimura (unadjusted) = 39.20 Transitions / transversions = 1.06 (95/90) Gap_init rate = 0.02 (11 / 627), avg. gap size = 1.45 (16 / 11) 453 33.74 3.47 5.15 chr3qtel1M 257846 258220 (741780) C HERVK11#LTR/ERVK (4510) 3443 3075 m_b142s701i1 5324 chr3qtel1M 257846 TTATCCAGAGGGATAGAATAGAAACAATCCTTAATATGTATAACCCACAG 257895 vi i vi vi v i i v vv ivvv C HERVK11#LTR/E 3443 TTATGTAAAGCAATATGAAAAAAACAATCTTTAAGATCAATAACTATGAG 3394 chr3qtel1M 257896 AGGTCATTCCCTAGGCAACTGAGTAAGGGATGGAAGCCCAGGCTAAAGAG 257945 i v iii i vivi i i vv v vv i i ii vi C HERVK11#LTR/E 3393 AGGCCAATTTTTAGGTATTAAAGCAGGGGCAGGCATGCCGGGTTGGACGG 3344 chr3qtel1M 257946 TTCCCATAGTTTCCAT--CTGTTCATTCACTTTTCTCAAATCAGTCAATA 257993 ii v iv -- v -- v ivvii i i i vi C HERVK11#LTR/E 3343 CCCCCATAGGTTTAATTACAG--CATTAATGGCCCTTAAATCGGTTACCA 3296 chr3qtel1M 257994 TCCTCCATTTTCCAGATTTCTTTTATAG-AGCAAAATACAAGGGAATTGC 258042 v i v v v v- -- i i i v C HERVK11#LTR/E 3295 TCCGCCACTTGCCTGATTTCTTTTTTACTAG--AAACACAGGAGAATTCC 3248 chr3qtel1M 258043 AAGGACTTAGAGAAGGTTGAAAGTGTCCTTGGTCAAGTTGCTCCTGTACT 258092 i ivvv vv vi v ------ ivv v v C HERVK11#LTR/E 3247 AGGGGGAAAGAGAAGGTTCCACATTTC------CAAGTTGTAACTGTTCA 3204 chr3qtel1M 258093 ATATCTAAT-------AAGACCTGAATTTTTCCTGGGTAAG-GGCCACTG 258134 iv v i ------- v iiv i i vi v - C HERVK11#LTR/E 3203 GAAACCAATTGAGTTAAAGCCTCCAGTTTTTCTTTAGAAAGCGGCCACTG 3154 chr3qtel1M 258135 TTCCACCC--ACTGTTGTATCAATTTTCAGTTAGAAGGGAATAGAGGTAA 258182 i vv i -- v v i iv vi iv i i - i v C HERVK11#LTR/E 3153 CTGAATCCAAACGGGTGTGTCAGATTTCCATTGTAAAGGGATAG-GATCA 3105 chr3qtel1M 258183 GGGTTGGCAGACATTCATCAGCAGCCCTGACTAAAAAG 258220 ------ i i --iv i viv C HERVK11#LTR/E 3104 GG------AGGCGT--GGCAGCGGCCGCCACTAAAAAG 3075 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.01 CpG sites = 60, Kimura (unadjusted) = 45.50 Transitions / transversions = 1.00 (60/60) Gap_init rate = 0.06 (24 / 374), avg. gap size = 1.33 (32 / 24) 733 28.12 3.06 2.12 chr3qtel1M 257850 258176 (741824) C HERVK14C#LTR/ERVK (4226) 3208 2879 m_b142s701i2 5324 chr3qtel1M 257850 CCAGAGGGATAGAATAGAAACAATCCTTAATATGTATAACCCACAGAGGT 257899 i i v v i i v v v ivvi i? i C HERVK14C#LTR/ 3208 CTAGAGGAATAGTAAAGAAGCAGTCCTTCAAATCTATAACTATTAANGGC 3159 chr3qtel1M 257900 CATTCCCTAGGCAACTGAGTAAGGGATGGAAGCCCAGGCTAAAGAGTTCC 257949 v i v v vvi iii ? v v iv ? ii C HERVK14C#LTR/ 3158 CAGTCTCTAGGAATCATGGCGGGGGANGGCAGCCCTGGCTGCAGNGCCCC 3109 chr3qtel1M 257950 CATAGTTTCCAT--CTGTTCATTCACTTTTCTCAAATCAGTCAATATCCT 257997 ? v v? -- -- v vvi vi i i i ii ? v C HERVK14C#LTR/ 3108 CATNGGTTGNATGACTG--CATTGACGGCTCGTAAGTCGGTTAGCATNCG 3061 chr3qtel1M 257998 CCATTTTCCAGATTTCTTTTATAGAGCAAAATACAAGGGAATTGCAAGGA 258047 i v i i i v? vvi -i vi ? v ? C HERVK14C#LTR/ 3060 CCATCTGCCGGATTTTTTCTTNATTACAAA-CACTGGNGAATTCCANGGA 3012 chr3qtel1M 258048 CTTAGAGAA----GGTTGAAAGTGTCCTTGGTCAAGTTGCTCCTGTACTA 258093 ---- i ---- i v? v v? v i i i vv C HERVK14C#LTR/ 3011 ----GAAAATGTGGGCTCNATGTGTCCTTTNTCTAATTGTTCTTTGACTA 2966 chr3qtel1M 258094 TATCTAATAAGACCTG-AATTTTTCCTGGGTAAG-GGCCACTGTTCCACC 258141 vv ivi i iv- i i ?? - ? ? C HERVK14C#LTR/ 2965 ATTCCTGTAAGGCCCCCAGTTTTTCCTGAGNNAGCGGCCACTGNTCNACC 2916 chr3qtel1M 258142 C--ACTGTTGTATCAATTTTCAGTTAGAAGGGAATAG 258176 -- ? v?v v vii i? vi vv C HERVK14C#LTR/ 2915 CAAACNGGNTTTTGGGTCNTCCATTTTAAGGGAATAG 2879 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.82 CpG sites = 45, Kimura (unadjusted) = 38.47 Transitions / transversions = 1.00 (45/45) Gap_init rate = 0.04 (12 / 326), avg. gap size = 1.42 (17 / 12) 488 17.17 8.08 0.00 chr3qtel1M 259535 259633 (740367) C U6#snRNA (0) 107 1 c_b142s401i0 5326 chr3qtel1M 259535 AAAAATATGGAGCACTTCATGAATTT---TGTCATCCTTCTGCAGGGACC 259581 i i i --- vi i C U6#snRNA 107 AAAAATATGGAACGCTTCACGAATTTGCGTGTCATCCTTGCGCAGGGGCC 58 chr3qtel1M 259582 ATGCTAATCTT-----TATCATTCCAATTTTAATAAATGAGGGACCCATG 259626 ----- i i v v vvi v v C U6#snRNA 57 ATGCTAATCTTCTCTGTATCGTTCCAATTTTAGTATATGTGCTGCCGAAG 8 chr3qtel1M 259627 TGAGTAC 259633 i i C U6#snRNA 7 CGAGCAC 1 Matrix = 18p37g.matrix Kimura (with divCpGMod) = 13.85 CpG sites = 10, Kimura (unadjusted) = 19.73 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.02 (2 / 98), avg. gap size = 4.00 (8 / 2) 22 0.00 3.70 0.00 chr3qtel1M 261316 261342 (738658) (GT)n#Simple_repeat 1 28 (0) m_b143s252i0 5327 chr3qtel1M 261316 GTGTGTGTGTGTGTGTGTGTGTGT-TGT 261342 - (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGT 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.04 (1 / 26), avg. gap size = 1.00 (1 / 1) 34 27.26 0.79 4.07 chr3qtel1M 261523 261564 (738436) (CCT)n#Simple_repeat 1 41 (82) m_b143s252i1 5328 chr3qtel1M 261523 CCTCCTCTTATTCCTCCTCCTCCTCCTCCTCCTCCTCCCTCC 261564 i vi - (CCT)n#Simple 1 CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT-CCTCC 41 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.02 (1 / 41), avg. gap size = 1.00 (1 / 1) 132 2.43 2.83 8.09 chr3qtel1M 261565 261811 (738189) (TCT)n#Simple_repeat 1 235 (0) c_b143s251i0 5329 chr3qtel1M 261565 TCTT-TTCTTCTT-TCTCTTCTTTCTCTCCTCTTTCTTCTCTCTTCTTCT 261612 - - - - - i - - (TCT)n#Simple 1 TCTTCTTCTTCTTCT-TCTTC-TTCT-TCTTC-TTCTTCT-TCTTCTTCT 45 chr3qtel1M 261613 TCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTTTTCTTCTTCTTC 261662 i (TCT)n#Simple 46 TCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTC 95 chr3qtel1M 261663 TTCTTCTTTCTTCTTTCTTC-TCTTTCTTCCATTCTCTCTTCCTCTCTCT 261711 - - - - - - - i - (TCT)n#Simple 96 TTCTTC-TTCTTC-TTCTTCTTC-TTCTT-C-TTCT-TCTTCTTCT-TCT 138 chr3qtel1M 261712 TC-TCTTCCTTCTTCTTCTTTCTTCTTCTTCTTCTTCTTC-TCTCTCTTG 261759 - - - - - - (TCT)n#Simple 139 TCTTCTT-CTTCTTCTTC-TTCTTCTTCTTCTTCTTCTTCTTCT-TCTT- 184 chr3qtel1M 261760 CTTCTTCTTCTTCTTCTGC-TCTTCTTCTCTCTTCATCTT-TCTCTCTCT 261807 v - - v - - - (TCT)n#Simple 185 CTTCTTCTTCTTCTTCTTCTTCTTCTTCT-TCTTCTTCTTCT-TCT-TCT 231 chr3qtel1M 261808 TCTT 261811 (TCT)n#Simple 232 TCTT 235 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.11 (26 / 246), avg. gap size = 1.00 (26 / 26) 28 31.30 1.96 4.70 chr3qtel1M 261812 261923 (738077) (TCT)n#Simple_repeat 42 148 (1) m_b143s252i2 5329 chr3qtel1M 261812 TTTCCTTCGTATCATCTTTCTTCCTCTT-TCCTTCCTTTTCTGCTTTCTC 261860 i i - - v - i - i i i v ii (TCT)n#Simple 42 TCTTCTTC-T-TCTTC-TTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTC 88 chr3qtel1M 261861 CTCCTCCTCATGATCTTTCTT-TCCTTCTCCTTCCTTTTTATTCCTTCTT 261909 i i i v vv - - i i - i v - - (TCT)n#Simple 89 TTCTTCTTCTTCTTC-TTCTTCTTCTTCTTCTT-CTTCTTCTT-CTTC-T 134 chr3qtel1M 261910 TCTTCCTCTTTTTC 261923 i i (TCT)n#Simple 135 TCTTCTTCTTCTTC 148 Matrix = Unknown Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.08 (9 / 111), avg. gap size = 1.00 (9 / 9) 34 27.26 0.79 4.07 chr3qtel1M 261812 261895 (738105) (CCT)n#Simple_repeat 42 122 (1) m_b143s252i1 5330 chr3qtel1M 261812 TTTCCTTCGTATCATCTTTCTTCCTCTTTCCTTCCTTTTCTGCTTTCTCC 261861 ii i viv v -i i -i - ii iv i i (CCT)n#Simple 42 CCTCCTCCTCCTCCTC-CTCCTCCTC-CTCC-TCCTCCTCCTCCTCCTCC 88 chr3qtel1M 261862 TCCTCCTCATGATCTTTCT-TTCCTTCTCCTTCCT 261895 v vv i i -i i - (CCT)n#Simple 89 TCCTCCTCCTCCTCCTCCTCCTCCTCCTCC-TCCT 122 Matrix = Unknown Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.06 (5 / 83), avg. gap size = 1.00 (5 / 5) 132 2.43 2.83 8.09 chr3qtel1M 261565 261811 (738189) (TCT)n#Simple_repeat 1 235 (0) c_b143s251i0 5329 chr3qtel1M 261565 TCTT-TTCTTCTT-TCTCTTCTTTCTCTCCTCTTTCTTCTCTCTTCTTCT 261612 - - - - - i - - (TCT)n#Simple 1 TCTTCTTCTTCTTCT-TCTTC-TTCT-TCTTC-TTCTTCT-TCTTCTTCT 45 chr3qtel1M 261613 TCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTTTTCTTCTTCTTC 261662 i (TCT)n#Simple 46 TCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTC 95 chr3qtel1M 261663 TTCTTCTTTCTTCTTTCTTC-TCTTTCTTCCATTCTCTCTTCCTCTCTCT 261711 - - - - - - - i - (TCT)n#Simple 96 TTCTTC-TTCTTC-TTCTTCTTC-TTCTT-C-TTCT-TCTTCTTCT-TCT 138 chr3qtel1M 261712 TC-TCTTCCTTCTTCTTCTTTCTTCTTCTTCTTCTTCTTC-TCTCTCTTG 261759 - - - - - - (TCT)n#Simple 139 TCTTCTT-CTTCTTCTTC-TTCTTCTTCTTCTTCTTCTTCTTCT-TCTT- 184 chr3qtel1M 261760 CTTCTTCTTCTTCTTCTGC-TCTTCTTCTCTCTTCATCTT-TCTCTCTCT 261807 v - - v - - - (TCT)n#Simple 185 CTTCTTCTTCTTCTTCTTCTTCTTCTTCT-TCTTCTTCTTCT-TCT-TCT 231 chr3qtel1M 261808 TCTT 261811 (TCT)n#Simple 232 TCTT 235 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.11 (26 / 246), avg. gap size = 1.00 (26 / 26) 28 31.30 1.96 4.70 chr3qtel1M 261812 261923 (738077) (TCT)n#Simple_repeat 42 148 (1) m_b143s252i2 5329 chr3qtel1M 261812 TTTCCTTCGTATCATCTTTCTTCCTCTT-TCCTTCCTTTTCTGCTTTCTC 261860 i i - - v - i - i i i v ii (TCT)n#Simple 42 TCTTCTTC-T-TCTTC-TTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTC 88 chr3qtel1M 261861 CTCCTCCTCATGATCTTTCTT-TCCTTCTCCTTCCTTTTTATTCCTTCTT 261909 i i i v vv - - i i - i v - - (TCT)n#Simple 89 TTCTTCTTCTTCTTC-TTCTTCTTCTTCTTCTT-CTTCTTCTT-CTTC-T 134 chr3qtel1M 261910 TCTTCCTCTTTTTC 261923 i i (TCT)n#Simple 135 TCTTCTTCTTCTTC 148 Matrix = Unknown Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.08 (9 / 111), avg. gap size = 1.00 (9 / 9) 26 6.67 1.82 7.69 chr3qtel1M 261995 262049 (737951) (AAT)n#Simple_repeat 1 52 (0) m_b143s252i4 5331 chr3qtel1M 261995 AATAATAATAATATATCAATAAT-CTAATAATAATAAGATCTAATAATAA 262043 - - -v v -v (AAT)n#Simple 1 AATAATAATAATA-AT-AATAATAATAATAATAATAATA-ATAATAATAA 47 chr3qtel1M 262044 GTAATA 262049 - (AAT)n#Simple 48 -TAATA 52 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.09 (5 / 54), avg. gap size = 1.00 (5 / 5) 13 5.27 0.00 0.00 chr3qtel1M 262108 262127 (737873) (AAC)n#Simple_repeat 1 20 (0) m_b143s252i5 5332 chr3qtel1M 262108 AACAACAACAACAACAATAA 262127 i (AAC)n#Simple 1 AACAACAACAACAACAACAA 20 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 263 29.31 6.41 3.75 chr3qtel1M 262170 262325 (737675) C MIR#SINE/MIR (30) 232 73 m_b143s601i0 5333 chr3qtel1M 262170 TATGTATACATACATTTTTGCATAATATTTTATACTTATCTTCCCATTAT 262219 ii- vi i v vi - iiii i iv ivv i vv C MIR#SINE/MIR 232 TATGTGC-CAGGCACTGTTCTA-AGCGCTTTACATGTATTAACTCATTTA 185 chr3qtel1M 262220 ATTTTCACAGC----TTAGGAA-TCAGTATGATTATAATCCTTACTTTGA 262264 ii i ----i v i- vi iv v ii i - C MIR#SINE/MIR 184 ATCCTCACAACAACCCTATGAGGTAGGTACTATTATTATCCCCATTTT-A 136 chr3qtel1M 262265 CAAGATGAG-AAATTCAGGAAACAAAG---TTAAGTGGATT-CCCAACGG 262309 - - i v v - i --- iiv - - C MIR#SINE/MIR 135 CA-GATGAGGAAACTGAGGCA-CAGAGAGGTTAAGTAACTTGCCCAA-GG 89 chr3qtel1M 262310 TCCCACACCTAGTAAG 262325 v v C MIR#SINE/MIR 88 TCACACAGCTAGTAAG 73 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.24 CpG sites = 27, Kimura (unadjusted) = 38.49 Transitions / transversions = 1.59 (27/17) Gap_init rate = 0.07 (11 / 155), avg. gap size = 1.45 (16 / 11) 286 26.00 1.25 3.85 chr3qtel1M 262365 262444 (737556) MIRc#SINE/MIR 43 120 (148) m_b143s601i1 5334 chr3qtel1M 262365 CAGGAGGACCTCAGTTCAAATCCAGGCTGAGACACTTGCTAG-TGTGTAT 262413 i vi i i v vv v i - iv MIRc#SINE/MIR 43 CAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGA 92 chr3qtel1M 262414 ATTTAGACAAAATGACTTAATTTTGCTCTGA 262444 vi i i i- v ii -- MIRc#SINE/MIR 93 CCTTGGGCAAG-TCACTTAACCT--CTCTGA 120 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 30.72 CpG sites = 12, Kimura (unadjusted) = 32.68 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.05 (4 / 79), avg. gap size = 1.00 (4 / 4) 16 24.13 2.90 4.41 chr3qtel1M 262687 262755 (737245) (CAAAG)n#Simple_repeat 1 68 (0) m_b143s252i6 5335 chr3qtel1M 262687 CAGAGGAAAGGAAAGGGAAG-GAA-CAAAGGCAAGGCAAAGCAAAGCACA 262734 i v v vi -i - - i v (CAAAG)n#Simp 1 CAAAGCAAAGCAAAGCAAAGCAAAGCAAA-GCAAAGCAAAGCAAAGCAAA 49 chr3qtel1M 262735 TCATGTACAGAGCAATAGCAA 262755 v -ivi i - (CAAAG)n#Simp 50 GCA-AAGCAAAGCAA-AGCAA 68 Matrix = Unknown Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.07 (5 / 68), avg. gap size = 1.00 (5 / 5) 17 11.00 4.88 2.38 chr3qtel1M 262690 262730 (737270) (AGGAA)n#Simple_repeat 1 42 (0) m_b143s252i7 5336 chr3qtel1M 262690 AGGAAAGGAAAGGGAAGG-AA-CAAAGGCAAGGCAAAGCAAAG 262730 i - -v v - v (AGGAA)n#Simp 1 AGGAAAGGAAAGGAAAGGAAAGGAAAGGAAAGG-AAAGGAAAG 42 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.07 (3 / 40), avg. gap size = 1.00 (3 / 3) 270 25.87 6.82 4.83 chr3qtel1M 264592 264855 (735145) L1M4_orf2#LINE/L1 3019 3287 (7) m_b143s551i0 5337 chr3qtel1M 264592 AAAATAGA-AAATTTGATTATATCAAA-TTGAAAAGTTTTG--CTACAAA 264637 - v i vi - i v -- v L1M4_orf2#LIN 3019 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 3068 chr3qtel1M 264638 CAAAACTAATGCAGACAAGAAGGAAGCAATA---AGAGTGGGAAAACATT 264684 vi v - vv v ivi ii ii iv--- i i v v L1M4_orf2#LIN 3069 GGACACTA-TCAAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAATA 3117 chr3qtel1M 264685 TTTACAG-TCAAAGGTTCTGA-AGAGGCCTCATTTCCAAAA-ATATAGAG 264731 i i- v vi - - ii v ?i v i - i L1M4_orf2#LIN 3118 TTTGCAAATCATATAT-CTGATAAGGGACTNGTATCCAGAATATATAAAG 3166 chr3qtel1M 264732 AAATTGACTCT---AATTTA----TAAAAAT-CAAACCATTCTCCAGTTG 264773 ----- --- i i ---- v- iv i--- i ? L1M4_orf2#LIN 3167 AA-----CTCTTACAACTCAACAATAAAAAGACAAATAAC---CCAATTN 3208 chr3qtel1M 264774 ATAAAATGGTCAAAGGATATGCACAGACAATTTCTCAGATGAAGAAAGTT 264823 - v v v i - vi v v - v L1M4_orf2#LIN 3209 A-AAAATGGGCAAAGGATTTGAATAGAC-ATTTCTCCAAAGAAGATA-TA 3255 chr3qtel1M 264824 GAAACTATTTCTAGCCACTTGAAAAGATGCTC 264855 v iviiivv iv v L1M4_orf2#LIN 3256 CAAATGGCCAATAAGCACATGAAAAGATGCTC 3287 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.44 CpG sites = 33, Kimura (unadjusted) = 32.44 Transitions / transversions = 1.03 (33/32) Gap_init rate = 0.09 (23 / 263), avg. gap size = 1.35 (31 / 23) 669 28.51 4.36 4.87 chr3qtel1M 264711 265123 (734877) L1PA6_3end#LINE/L1 1 411 (490) m_b143s551i1 5337 chr3qtel1M 264711 CTCATTTCCAAAA-ATATAGAGAAATTGACTCTAATTTATAA----AAAT 264755 v v i -v i i v i v- v i ---- v L1PA6_3end#LI 1 CTAATATCCAGAATCTACAAAGAACTTAAA-CAAATTTACAAGAAAAAAA 49 chr3qtel1M 264756 CAAACCATTCTCCAGTTGATAAAATGGTCAAAGGATATGCACAGACAATT 264805 v -- i -- v v i v v -i L1PA6_3end#LI 50 CAAACAA--CCCCA--TCAAAAAGTGGGCAAAGGATATGAACAGACA-CT 94 chr3qtel1M 264806 TCTCAGATGAAGAAAGTT--GAAACTATTTCTAGCCACTTGAAAAGATGC 264853 i v v v -- v i i ---vi v v i L1PA6_3end#LI 95 TCTCAAAAGAAGACATTTATGCAGCCA---ACAGACACATGAAAAAATGC 141 chr3qtel1M 264854 TCTAAGTCATTATTAATCAAAGAAATGCAAATTAAGACAACTCTGAGATA 264903 vvvi i iv v i i i v vv L1PA6_3end#LI 142 TCATCATCACTGGTCATCAGAGAAATGCAAATCAAAACCACAATGAGATA 191 chr3qtel1M 264904 TGACCATACACTTGTCAGGATTGGC------TAGGAATGACAGGAAAAAT 264947 iv i vi i iv i i - ------ ii - v -- i L1PA6_3end#LI 192 CCATCTCACGCCAGTTAGAA-TGGCGATCATTAAAAA-GTCAGG--AAAC 237 chr3qtel1M 264948 AATGGCAATGTTGGAGGGGCATGTGGGAAAACTGCGACAATGATACATTG 264997 ii -- i i - ii iv vi iv vv i L1PA6_3end#LI 238 AACAG--ATGCTGGAGAGG-ATGTGGAGAAATAGGAACGCTTTTACACTG 284 chr3qtel1M 264998 TTGGTGGAA---TAA--TACATCTAGCATTCTAGAGAGCAATTTGGAACT 265042 i --- -- vv v v v i iii i v viv L1PA6_3end#LI 285 TTGGTGGGAGTGTAAACTAGTTCAACCATTGTGGAAGACAGTGTGGCGAT 334 chr3qtel1M 265043 ATGCTCAAAAAGCTATCAAACTTTGCATACCCTTTCATCCAGCAGTGTTA 265092 - v ii v --i vviv v v i ii vii L1PA6_3end#LI 335 -TCCTCAAGGATCTA--GAACTAGAAATACCATTTGACCCAGCGATCCCA 381 chr3qtel1M 265093 CTACTGGGCTTATATCCCAAAAGATTTTAAA 265123 i iv - i v L1PA6_3end#LI 382 TTACTGGGTATATA-CCCAAAGGATTATAAA 411 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.78 CpG sites = 58, Kimura (unadjusted) = 36.36 Transitions / transversions = 1.07 (58/54) Gap_init rate = 0.06 (26 / 412), avg. gap size = 1.46 (38 / 26) 1051 25.75 5.49 5.27 chr3qtel1M 264765 265256 (734744) L1ME5_3end#LINE/L1 56 548 (393) m_b143s551i2 5337 chr3qtel1M 264765 CTCCAGTTGATAAAATGGTCAAAGGATATGCACAGACAATTTCTCAGATG 264814 i i v - v v i v- v L1ME5_3end#LI 56 CCCCAATAGA-AAAATGGGCAAAGGATATGAACAGGCAATTTA-CAGAAG 103 chr3qtel1M 264815 AAGAAAGTTGAAA--CTATTTCTAGCCACTTGAAAAGATGCTCTAAGTCA 264862 i vii -- v-- v - iv i v v L1ME5_3end#LI 104 AGGAAACCCGAAAGGCTAA--CAAGC-ATATGAAGAGATGCTCAAACTCA 150 chr3qtel1M 264863 TTATTAATCAAAGAAATGCAAATTAAGACAACTCTGAGATATGACCATAC 264912 v i i vv v iv L1ME5_3end#LI 151 TTAGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTAC 200 chr3qtel1M 264913 ACTTGTCAGGATTGGCTAGGAATGACAGGAA---AAATAATGGCAA-TGT 264958 i i i - i - ii --i i ---ii v - L1ME5_3end#LI 201 ACCTATTA-GACTGGC-AAAAAT--TAGAAAGCTGGATAATGCCAAGTGT 246 chr3qtel1M 264959 TGGAGGGGCATGTGGGAAAACTGCGACAATGATACATTGTTGGTGGAATA 265008 v i - i ? iv vi vv v i i i i vv L1ME5_3end#LI 247 TGGCGAGG-ATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGT 295 chr3qtel1M 265009 ATACATCTAG------CATTCTAGAGAGCAATTTGGAACTA--TGCTCAA 265050 i v - i ------ i i v v -- iv L1ME5_3end#LI 296 GTAGA-CTGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAA 344 chr3qtel1M 265051 A--AAGCTATCAAACTTTGCATACCCTTTCATCCAGCAGTGTTACTACTG 265098 -- - --- --- v v i i viii v L1ME5_3end#LI 345 ATTAAG-TAT---AC---GCATACCCTATGACCCAGCAATTCCGCTCCTG 387 chr3qtel1M 265099 GGCTTATATCCCAAA-AGATTTTAAAGAAGG------GAGGGACCTGATA 265141 iv - i i v viv ------ii --- i L1ME5_3end#LI 388 GGTATATATCCCAAAGAAATTCTCACACAGGTCCATAAGGGGAC---ATG 434 chr3qtel1M 265142 TGCAAGAATGTTTGTGGCAGTCCTCATTGT---TAGTGTCCAGAAAGTGG 265188 i i i ii v ---- i --- i v vi i iv L1ME5_3end#LI 435 TACGAGGATGTTCATTGCAG----CGTTGTTTGTGGTGGCGGGGAGTTGG 480 chr3qtel1M 265189 AAACTGAGTGGATGCCCATCAATTGGAGAATAGCTA-ATGAATTGTGAGT 265237 ii vivv i i v v i i v -i i v - L1ME5_3end#LI 481 AGGCAACCTGGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTG-GT 529 chr3qtel1M 265238 ATATGAATATTATGGAATA 265256 iv v i ii i L1ME5_3end#LI 530 GGATGCACACCATGGAGTA 548 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 30.99 CpG sites = 70, Kimura (unadjusted) = 32.32 Transitions / transversions = 1.40 (70/50) Gap_init rate = 0.07 (36 / 491), avg. gap size = 1.47 (53 / 36) 488 30.20 7.30 5.14 chr3qtel1M 264843 265376 (734624) L1MC1_3end#LINE/L1 131 675 (405) m_b143s551i3 5337 chr3qtel1M 264843 TGAAAAGATGCTCTAAGTCATTAT-TAATCAAAGAAATGCAAATTAAGAC 264891 i vi - - v ii i L1MC1_3end#LI 131 TGAAAAGATGCTCCACATCA-TATGTCATCAGGGAAATGCAAATTAAAAC 179 chr3qtel1M 264892 AACTCTGAGATATGACCATACACTTGTCAGGATTGGCTAGGAATGACAGG 264941 vv iv i i i i i i - i -i -- vi L1MC1_3end#LI 180 AACAATGAGATACCACTACACACCTATTAGAA-TGGCCA-AAAT--CCAG 225 chr3qtel1M 264942 AAAAATAATGGC----AATGTTGGAGGGGCATGTGGGAAAACTGCGACAA 264987 v v i iii ---- i v i - iiv v vi vv L1MC1_3end#LI 226 AACACTGACAACACCAAATGCTGGCGAGG-ATGTGGAGCAACAGGAACTC 274 chr3qtel1M 264988 TGATACATTGTTGGTGG--------AATAATACATCTAGCATTCTAGAGA 265029 v v i -------- ii v --- i i i ii L1MC1_3end#LI 275 TCATTCATTGCTGGTGGGAATGCAAAATGGTACAGC---CACTTTGGAAG 321 chr3qtel1M 265030 GCAATTTGGAACTATGCTCAAAAAGCT-ATCAAACTTTGCATACCCTTTC 265078 i i v v - v i v i - v v i --- v viv L1MC1_3end#LI 322 ACAGTTTGGCAGT-TTCTTACAAAACTAAACATACTCT---TACCATACG 367 chr3qtel1M 265079 ATCCAGCAGTGTTACTACTGGGCTTATATCCCAAAAGATTTTAAAG---- 265124 i vvii v v iv v - i v v i---- L1MC1_3end#LI 368 ATCCAGCAATCGCGCTCCTTGGTATTTA-CCCAAAGGAGTTGAAAACTTA 416 chr3qtel1M 265125 ----AAGGGAGGGACCTGATATGCAAGAATGTTTGTGGCAGTCCTCATTG 265170 ----v viv iii ---ii v i i i - i i v L1MC1_3end#LI 417 TGTCCACACAAAAACCTG---CACACGGATGTTTATAGCAG-CTTTATTC 462 chr3qtel1M 265171 TTAGTGTCCAGAAAGTGGA---AACTGAGTGGATGCCCATCAATTGGAGA 265217 v i vv i vv --- ii --- i v i v v L1MC1_3end#LI 463 ATAATTGCCAAAACTTGGAAGCAACCAA---GATGTCCTTCAGTAGGTGA 509 chr3qtel1M 265218 ATAGCT-AATGAATTGTGAGTATATGAATATTATGGAATATATTGTTCTT 265266 i v - i i - i vv v iv -- i -- L1MC1_3end#LI 510 ATGGATAAATAAACTGTG-GTACATCCAGACAATGGA--ATATTATTC-- 554 chr3qtel1M 265267 AAGGC-AAAACCAACAGGGTGATT--GTCA--GAAAGGCCTGGA-GAGAC 265310 iv - vv vv i iv i-- i --i i v - i L1MC1_3end#LI 555 AGCGCTAAAAAGAAATGAGCTATCAAGCCATGAAAAGACATGGAGGAAAC 604 chr3qtel1M 265311 TTA----CATGTTGAGGAGTGAAATGAGCAGCACTAGGAAATCATTATAT 265356 ---- i ivvi vi -- v vv vvii i L1MC1_3end#LI 605 TTAAATGCATATTACTAAGTGAAAGAAGC--CAATCTGAAAAGGCTACAT 652 chr3qtel1M 265357 ACT---TAACAACAACTATATGA 265376 --- i ivv L1MC1_3end#LI 653 ACTGTATGATTCCAACTATATGA 675 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.85 CpG sites = 84, Kimura (unadjusted) = 39.55 Transitions / transversions = 1.22 (84/69) Gap_init rate = 0.08 (42 / 533), avg. gap size = 1.60 (67 / 42) 12 18.27 5.41 0.00 chr3qtel1M 265619 265655 (734345) (TATACT)n#Simple_repeat 1 39 (0) m_b143s252i8 5338 chr3qtel1M 265619 TATACATATA-TTGTATTTA-ACTTATACTTTAACATAT 265655 v - i i - vv v (TATACT)n#Sim 1 TATACTTATACTTATACTTATACTTATACTTATACTTAT 39 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 12 29.42 1.25 6.58 chr3qtel1M 269324 269403 (730597) (GTATAT)n#Simple_repeat 1 76 (0) m_b143s252i9 5339 chr3qtel1M 269324 GTGTATGTATGTGTGCATGTAGTATTTGTATGTGAGTGGGTATGTGTCCT 269373 i i ii - v i - - iv i -v (GTATAT)n#Sim 1 GTATATGTATATGTATATGTA-TATGTATATGT-A-TATGTATATGT-AT 46 chr3qtel1M 269374 GTTGT-TATGTATATAGGTTTATAAATGTAT 269403 -v - ivi v i v (GTATAT)n#Sim 47 -ATGTATATGTATATGTATATGTATATGTAT 76 Matrix = Unknown Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.08 (6 / 79), avg. gap size = 1.00 (6 / 6) 12 26.29 3.57 1.75 chr3qtel1M 269587 269642 (730358) (ATTTTAA)n#Simple_repeat 1 57 (0) m_b143s252i10 5340 chr3qtel1M 269587 ATTTTGATTTTCTTATTTTACA-TTTAAGTTTTAAATAAATAAA-TATAA 269634 i v ivv v - i -vv - v (ATTTTAA)n#Si 1 ATTTTAAATTTTAAATTTTAAATTTTAAATTTTAAAT-TTTAAATTTTAA 49 chr3qtel1M 269635 TTTTGAAA 269642 v v (ATTTTAA)n#Si 50 ATTTTAAA 57 Matrix = Unknown Transitions / transversions = 0.33 (3/9) Gap_init rate = 0.05 (3 / 55), avg. gap size = 1.00 (3 / 3) 487 14.61 7.87 0.00 chr3qtel1M 272628 272716 (727284) C U6#snRNA (0) 107 12 m_b143s502i0 5341 chr3qtel1M 272628 AAAAATATGGAGCACTTTCTGAATTTGTGTGTCATCCTTGT-CA-GGGCT 272675 i i ivi i i- - i C U6#snRNA 107 AAAAATATGGAACGCTTCACGAATTTGCGTGTCATCCTTGCGCAGGGGCC 58 chr3qtel1M 272676 ATGCTAA-----TCTGGACCATTCCAATTTTAGTATATGAGCTACC 272716 ----- v i i v i C U6#snRNA 57 ATGCTAATCTTCTCTGTATCGTTCCAATTTTAGTATATGTGCTGCC 12 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 10.30 CpG sites = 10, Kimura (unadjusted) = 16.69 Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.03 (3 / 88), avg. gap size = 2.33 (7 / 3) 16 13.24 0.00 0.00 chr3qtel1M 273955 273979 (726021) (AC)n#Simple_repeat 1 25 (0) m_b143s252i11 5342 chr3qtel1M 273955 ACACACACACACATACCCACATACA 273979 i v i (AC)n#Simple_ 1 ACACACACACACACACACACACACA 25 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 219 36.57 4.48 0.00 chr3qtel1M 273988 274121 (725879) C MIR#SINE/MIR (51) 211 72 m_b143s601i2 5343 chr3qtel1M 273988 AATGTTTTATAGCTATCTTCCCTTTTTATTTTCACAAT----TTGGGAAT 274033 ii i i vv ivv i v v ii i----i iv iv C MIR#SINE/MIR 211 AGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGG 162 chr3qtel1M 274034 T-GGTATAATTATAATACTCACGTTACAAATATGGAAACTCAGGGA-AGA 274081 - iv v v i iv i iv v v - C MIR#SINE/MIR 161 TAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGA 112 chr3qtel1M 274082 GCAGTTTTATGAATTTTCAGGGATCAGAGACCTAGTAAAT 274121 vi vvi i v vi vii i v v v i C MIR#SINE/MIR 111 GAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGT 72 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 49.78 CpG sites = 25, Kimura (unadjusted) = 51.26 Transitions / transversions = 1.04 (25/24) Gap_init rate = 0.02 (3 / 133), avg. gap size = 2.00 (6 / 3) 400 28.27 8.25 3.96 chr3qtel1M 274617 274907 (725093) C L1M4_orf2#LINE/L1 (1314) 1980 1678 m_b143s551i4 5344 chr3qtel1M 274617 TCCTTGTCCTTTTCACTTCTGATCTTGTTGGGAAGAGCTCTAGTTTAACT 274666 i v ---- ivv - ?---- i iii C L1M4_orf2#LIN 1980 TCCTTGTCTTGTTC----CTGATCTTAGGGGGAA-AGCN----TTCAGTC 1940 chr3qtel1M 274667 TTTTAC-----AG-ATAATATTTTCTTTTGCTTTTAGATAGAGATGGC-- 274708 i ----- - i i vv v v v vvi -- v -- C L1M4_orf2#LIN 1939 TTTCACCATTAAGTATGATGTTAGCTGTGGGTTTTTCGTAGA--TGCCCT 1892 chr3qtel1M 274709 TTGTCATTTTAAGAAAGCCTTCATTTATTTTTA----------TGTTTTT 274748 i vv i i iiii v i ii ---------- C L1M4_orf2#LIN 1891 TTATCAGGTTGAGGAAGTTCCCTTCTATTCCTAGTTTGTTGAGTGTTTTT 1842 chr3qtel1M 274749 AATAGGAAGAAGTTCTATGTTTTGTCAAAAGCTTTTTCTGCATCT--TGA 274796 vi v iii vi ivi v i -- C L1M4_orf2#LIN 1841 ATCATGAAAGGGTGTTGGATTTTGTCAAATGCTTTTTCTGCGTCTATTGA 1792 chr3qtel1M 274797 GATAATCTAATGGTTTATGTTGTTTTTACAATTGGTAAAGTCAATTA--- 274843 i vvi v iv v v v ii vi vv --- C L1M4_orf2#LIN 1791 GATGATCATGTGGTTTTTGTCCTTTATTCTATTAATATGGTGTATTACAT 1742 chr3qtel1M 274844 TGTTTAAGTTTCTTAATACTGA-CCAACTTTACATTCCTGGCATAGATTC 274892 v i v v? - ii - i i v i i C L1M4_orf2#LIN 1741 TGATTGATTTTCGNA-TGTTGAACCAACCTTGCATTCCTGGGATAAATCC 1693 chr3qtel1M 274893 TACTATGCCATAGTG 274907 i vv i i C L1M4_orf2#LIN 1692 CACTTGGTCATGGTG 1678 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.48 CpG sites = 44, Kimura (unadjusted) = 36.64 Transitions / transversions = 1.26 (44/35) Gap_init rate = 0.07 (19 / 290), avg. gap size = 1.89 (36 / 19) 237 29.43 0.00 2.35 chr3qtel1M 275076 275162 (724838) C L1M1_orf2#LINE/L1 (1673) 1621 1537 m_b143s551i5 5345 chr3qtel1M 275076 TTGCATCAATATTCATTAGGGAAATTGGTCTATAAGGGGTTTTTTCTCTG 275125 i i v i i -- vv i i i C L1M1_orf2#LIN 1621 TTGCATCAATATTCATCAGAGATATTGGCCTGTA--GTTTTCTTTTTTTG 1574 chr3qtel1M 275126 ATTTTGCTTTTCTTCATTTAGATATCAAAACAATATT 275162 v vv vii vi v i iiii i C L1M1_orf2#LIN 1573 ATGTGTCTTTGTCTGGTTTTGGTATCAGGGTAATACT 1537 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.87 CpG sites = 16, Kimura (unadjusted) = 38.87 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.02 (2 / 86), avg. gap size = 1.00 (2 / 2) 12 17.53 3.12 0.00 chr3qtel1M 275348 275379 (724621) (ACAC)n#Simple_repeat 1 33 (0) m_b143s252i12 5346 chr3qtel1M 275348 ACA-ACAACCACACACACATACACGCACAAACA 275379 - vv i i v (ACAC)n#Simpl 1 ACACACACACACACACACACACACACACACACA 33 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 246 30.45 4.62 1.49 chr3qtel1M 275630 275759 (724241) C L1M2_orf2#LINE/L1 (1759) 1532 1399 m_b143s551i6 5345 chr3qtel1M 275630 GTTTCAAAGGAGGAATTTAGTAGA---CTCTTTCTTTCCTTTTTTTCAAA 275676 ii iv i v i i v ?--- i iiii vv vi C L1M2_orf2#LIN 1532 GCCTCGTAGAATGAGTTTGGAAGNATTCCCTCCTCTTCAATTTTTTGGAA 1483 chr3qtel1M 275677 TAGTTTACACAGTATTGG-ATTAATTGTTCCTTAAACATTTCAGAGAATT 275725 iviv v - i v i ii viv C L1M2_orf2#LIN 1482 TAGTTTGAGAAGAATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAATT 1433 chr3qtel1M 275726 TACTTGT--ATCCATCTGGTCCTAGCAATTTTTCTT 275759 i viv -- v ? i --ii C L1M2_orf2#LIN 1432 CAGCAGTGAAGCCATCNGGTCCTGG--GCTTTTCTT 1399 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.05 CpG sites = 24, Kimura (unadjusted) = 41.46 Transitions / transversions = 1.60 (24/15) Gap_init rate = 0.04 (5 / 129), avg. gap size = 1.60 (8 / 5) 14 16.50 11.11 1.45 chr3qtel1M 276465 276527 (723473) (ATTCAT)n#Simple_repeat 1 69 (0) m_b143s252i13 5347 chr3qtel1M 276465 ATTCCTATTCAGTTTTC-TA--CATATGCATA-TCATATTCA-CTTTTTA 276509 v - v - -- v - -v iv (ATTCAT)n#Sim 1 ATTCATATTCA-TATTCATATTCATATTCATATTCATATTCATATTCATA 49 chr3qtel1M 276510 -TAAAATTC-TATTCATCTT 276527 - v v - v (ATTCAT)n#Sim 50 TTCATATTCATATTCATATT 69 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.11 (7 / 62), avg. gap size = 1.14 (8 / 7) 309 32.46 1.29 10.56 chr3qtel1M 276529 276683 (723317) MIRc#SINE/MIR 2 143 (125) m_b143s601i3 5348 chr3qtel1M 276529 GGGGCAGT-TGGTAGTGGTACAGATCGAATACGGTGTCTAGAGCCAAGAT 276577 i - - ii iv i -- ii v viii i i i v MIRc#SINE/MIR 2 GAGGCAGTGTGGT-GCAGTGGAAA--GAGCACTGGACTTGGAGTCAGGAA 48 chr3qtel1M 276578 GATTTCTATTAATGAGTTCAACTCTGTCCTCAGACACTTCCTAGCTGTAT 276627 ii -------- i i v ivvv v v v i MIRc#SINE/MIR 49 GACCT--------GGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGT 90 chr3qtel1M 276628 AATCTTGGGTAAATCA-TTAATTCTATTAATCCTATTCACTTTAATTCAT 276676 i i i i - iiiivi i v --- v -vi MIRc#SINE/MIR 91 GACCTTGGGCAAGTCACTTAACCTCTCTGAGCC---TCAGTTT-CCTCAT 136 chr3qtel1M 276677 CTGTAAA 276683 MIRc#SINE/MIR 137 CTGTAAA 143 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.03 CpG sites = 30, Kimura (unadjusted) = 44.39 Transitions / transversions = 2.00 (30/15) Gap_init rate = 0.11 (17 / 154), avg. gap size = 1.00 (17 / 17) 14 16.97 6.25 2.00 chr3qtel1M 277118 277165 (722835) (TATTT)n#Simple_repeat 1 50 (0) m_b143s252i14 5349 chr3qtel1M 277118 TATTTT-TCTCATTTTCTGTTA-TGT-TTTCATTTTATTTTATCATTATT 277164 - i i v v - v - i -v (TATTT)n#Simp 1 TATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTAT-TTTATT 49 chr3qtel1M 277165 T 277165 (TATTT)n#Simp 50 T 50 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.09 (4 / 47), avg. gap size = 1.00 (4 / 4) 16 27.79 2.35 4.82 chr3qtel1M 277365 277449 (722551) (CTTTTT)n#Simple_repeat 1 83 (0) m_b143s252i15 5350 chr3qtel1M 277365 CTTTTTCTATTTTCAGTATTTTCAGCTGTTTTC-TTTTGATTGTCTTCCT 277413 - vv v i ivv - - vv v ii (CTTTTT)n#Sim 1 CTTTTTCT-TTTTCTTTTTCTTTTTCT-TTTTCTTTTTCTTTTTCTTTTT 48 chr3qtel1M 277414 TTCTATATTTTTCTTCTTC-TTCTCTTATTTGCTTTT 277449 i i v v i - i - - (CTTTTT)n#Sim 49 CTTTTTCTTTTTCTTTTTCTTTTTCTT-TTT-CTTTT 83 Matrix = Unknown Transitions / transversions = 0.80 (8/10) Gap_init rate = 0.07 (6 / 84), avg. gap size = 1.00 (6 / 6) 16 10.03 0.00 0.00 chr3qtel1M 277615 277636 (722364) (T)n#Simple_repeat 1 22 (0) m_b143s252i16 5351 chr3qtel1M 277615 TTCTTCTTTTTTTTTTTTTTTT 277636 i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTT 22 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 385 29.48 5.48 0.87 chr3qtel1M 278237 278455 (721545) C L1MC_orf2#LINE/L1 (1273) 2021 1793 m_b143s551i7 5352 chr3qtel1M 278237 ATTTCTAATTCAATATTGAATA--AGTGGCAATAACTTGCAGGCTTGCTT 278284 i i i v i i v -- ii v ivvvi vv i C L1MC_orf2#LIN 2021 ACTTCCAGTACGATGTTGAAAAGGAGTGGTGAGAGGGGACATCCTTGCCT 1972 chr3qtel1M 278285 CACTTCTAATCTTAGTAGGA---CTTCTAGTTTATT-CCATTAAAGATCA 278330 iii i i ii --- ? v i- iv v C L1MC_orf2#LIN 1971 TGTTCCTGATCTTAGCGGGAAAGCTTCNAGTTTCTCACCATTAAGTATGA 1922 chr3qtel1M 278331 TGGTTGTTCTTGGTTTCAGATAGAAATTACATATCA-TTTGAAGAGAG-- 278377 v v i v v ivvi vi viv -v i - -- C L1MC_orf2#LIN 1921 TGTTAGCTGTAGGTTTTTTGTAGATGTTCTTTATCAAGTTGAGGA-AGTT 1873 chr3qtel1M 278378 --GCTCCATTCCTATGATTTCT-AGTGTTTTAAATAGAAATGGATGTTTT 278424 --v i - v v - v v vi vi i vv C L1MC_orf2#LIN 1872 CCCCTCTATTCCTA-GTTTGCTGAGAGTTTTTATCATGAATGGGTGTTGG 1824 chr3qtel1M 278425 ATGTTCCCAAAAGCTTTTTCTGCATCTCTTG 278455 v vi v v C L1MC_orf2#LIN 1823 ATTTTGTCAAATGCTTTTTCTGCATCTATTG 1793 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.48 CpG sites = 30, Kimura (unadjusted) = 38.01 Transitions / transversions = 0.88 (30/34) Gap_init rate = 0.04 (9 / 218), avg. gap size = 1.56 (14 / 9) 273 35.59 8.29 3.85 chr3qtel1M 278730 279103 (720897) C L2#LINE/L2 (1) 3081 2692 m_b143s601i4 5353 chr3qtel1M 278730 GAGGGAGAGCATTCCAGGCAT-GGAAATAGCAA----AGATGCCCAGATA 278774 i i i v- i i ---- i v v vi C L2#LINE/L2 3081 GGGGAAGAGCGTTCCAGGCAGAGGGAACAGCAAGTGCAAAGGCCCTGAGG 3032 chr3qtel1M 278775 T---AGAGTGTCT----TGTTTCTAGAATAGCCAAAAGGGTAGTATCATT 278817 i--- v i ---- ivvi i v ii vi i vii C L2#LINE/L2 3031 CGGGAGCGTGCCTGGCGTGTTCGAGGAACAGCAAGGAGGCCAGTGTGGCT 2982 chr3qtel1M 278818 GGA-CGTAAGAGTATATACTGTTGAGTGAGGTA------AAGGCCTGGAA 278860 - --- iviiivv vv v v ------i i -i i C L2#LINE/L2 2981 GGAGCG---GAGTGAGCGAGGGGGAGAGTGGTAGGAGATGAGGTC-AGAG 2936 chr3qtel1M 278861 AGGTAG-GAGGTGGCAGGTTATGGAGGGCTTTCAATGCCAAACTGAGTGG 278909 i- i viv i i v i vv v vvv i viv C L2#LINE/L2 2935 AGGTAACGGGGGACCAGATCATGTAGGGCCTTGTAGGCCATTGTAAGGAC 2886 chr3qtel1M 278910 TTCACATTTTATCCTAATGGTAATAACGAGTAAGT-GAGGTTTATTTAGA 278958 iivv ii i vv vi iivi iv v - v - v v C L2#LINE/L2 2885 TTTGGCTTTTACTCTGAGTGAGATGGGAAGCCATTGGAGGGTT-TTGAGC 2837 chr3qtel1M 278959 AAAGAAGTGTCAGAGTCAGATCTAC-CTTTAGGAAAATAA----GGTTTT 279003 i i v vii v ii -i ii ii v ---- i vi C L2#LINE/L2 2836 AGAGGAGTGACATGATCTGACTTACGTTTTAAAAGGATCACTCTGGCTGC 2787 chr3qtel1M 279004 TA-GTTGGAAGAAGAATGGAGTGGAAGGGAG--AGATCTGAGGAAGGCAG 279050 i- ----- i v ? i i -- iviv i v v C L2#LINE/L2 2786 TGTGTTG-----AGAATAGACTGNAGGGGGGCAAGGGTGGAAGCAGGGAG 2742 chr3qtel1M 279051 ACACCCCTACCCCCCAGG-TACTGCAATAG-CCAGACTGGGGGTGATGAT 279098 - vvi ----vv - i i i- i vi i i i C L2#LINE/L2 2741 AC-CAGTTA----GGAGGCTATTGCAGTAATCCAGGCGAGAGATGATGGT 2697 chr3qtel1M 279099 GGCCT 279103 i C L2#LINE/L2 2696 GGCTT 2692 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 48.19 CpG sites = 74, Kimura (unadjusted) = 50.51 Transitions / transversions = 1.37 (74/54) Gap_init rate = 0.08 (29 / 373), avg. gap size = 1.59 (46 / 29) 262 29.14 1.97 0.65 chr3qtel1M 279978 280006 (719994) L1ME4a_3end#LINE/L1 402 429 (442) m_b143s551i8 5354 chr3qtel1M 279978 TAAGGAACTTAATCACATTTATATATATA 280006 v - v vv i i? i v L1ME4a_3end#L 402 TAAGGAAAT-AATCAGAGATGTGNACAAA 429 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.39 CpG sites = 20, Kimura (unadjusted) = 38.46 Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1) 31 0.00 0.00 0.00 chr3qtel1M 280007 280033 (719967) (TG)n#Simple_repeat 1 27 (0) c_b143s251i1 5355 chr3qtel1M 280007 TGTGTGTGTGTGTGTGTGTGTGTGTGT 280033 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGT 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 262 29.14 1.97 0.65 chr3qtel1M 280034 280155 (719845) L1ME4a_3end#LINE/L1 430 554 (317) m_b143s551i8 5354 chr3qtel1M 280034 ATTTACAGATATGCATATATATC--AGCTCT-TTTCTCAGAGCAAAGAAT 280080 iiv i v v i vi -- vi - v v v i i L1ME4a_3end#L 430 ATTTATGTACAAGGATGTTCATCGCAGCATTATTTATAATAGCGAAAAAT 479 chr3qtel1M 280081 TGAAAATTGAGAGAATGTCCATCAATTGGGGAATGGATGAATAAATTGTG 280130 i ivivvvi v v ? v i i L1ME4a_3end#L 480 TGGAAACAACCTAAATGTCCAACAATAGGGGANTGGTTAAATAAATTATG 529 chr3qtel1M 280131 GTATATGGTTATGAAGAAATATTAT 280155 i vvv ?i v i L1ME4a_3end#L 530 GTACATCCATANAATGGAATATTAT 554 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.39 CpG sites = 20, Kimura (unadjusted) = 38.46 Transitions / transversions = 0.89 (17/19) Gap_init rate = 0.02 (2 / 121), avg. gap size = 1.50 (3 / 2) 313 26.92 0.96 0.00 chr3qtel1M 280052 280155 (719845) L1ME3F_3end#LINE/L1 448 552 (438) m_b143s551i9 5354 chr3qtel1M 280052 ATATCAGCTCTTTTC-TCAGAGCAAAGAATTGAAAATTGAGAGAATGTCC 280100 v v v - v v i i i ivivvvi L1ME3F_3end#L 448 ATAGCAGCACTGTTCGTAATAGCAAAAAACTGGAAACAACCCAAATGTCC 497 chr3qtel1M 280101 ATCAATTGGGGAATGGATGAATAAATTGTGGTATATGGTTATGAAGAAAT 280150 i iv i i vvvi ii v i L1ME3F_3end#L 498 ATCGACAGGAGAATGGATAAATAAATTGTGGTATATTCACACAATGGAAT 547 chr3qtel1M 280151 ATTAT 280155 L1ME3F_3end#L 548 ATTAT 552 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.27 CpG sites = 14, Kimura (unadjusted) = 33.70 Transitions / transversions = 1.00 (14/14) Gap_init rate = 0.01 (1 / 103), avg. gap size = 1.00 (1 / 1) 16 21.28 0.00 0.00 chr3qtel1M 280384 280416 (719584) (AG)n#Simple_repeat 1 33 (0) m_b143s252i17 5356 chr3qtel1M 280384 AGAGAGGCAGGAAGAGAGGCAGAGAGAGAGAGA 280416 iv ii iv (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 33 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 322 29.22 4.30 4.30 chr3qtel1M 282936 283121 (716879) C L1MC3_3end#LINE/L1 (1904) 628 443 m_b143s551i10 5357 chr3qtel1M 282936 TTTCACTTAGCATCACTTCATATAAATCTC-TCCAGGCTTTTCTGAAATT 282984 vi - v v ivi - v ii ii ---- C L1MC3_3end#LI 628 TTTCACTTAGCAATA-TGCATTTAAGATTCATCCATGTCTTTTCG----T 584 chr3qtel1M 282985 ATCCTACTGG-TCATTTC---TTACAGAACAATAATATTTCATAATATTC 283030 iv i iv i - --- iv vvv i vi vv C L1MC3_3end#LI 583 GGCTTGATAGCTCATTTCTTTTTATCGCTGAATAATATTCCATTGTATGG 534 chr3qtel1M 283031 ATATACTACAATTTATTCAGCCACTCTTCAATTGATAGGCATCCACTTAG 283080 i i i i i v i vi v vi i --- i C L1MC3_3end#LI 533 ATGTACCACAGTTTGTTTATCCATTCACCTATTGAAGGACAT---CTTGG 487 chr3qtel1M 283081 T---TTCCAGTTTCTGGCCACTACAAAGAGGGCTGCCACAAACA 283121 --- i v i ii v ii i i C L1MC3_3end#LI 486 TTGCTTCCAGTTTTTGGCGATTATGAATAAAGCTGCTATAAACA 443 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.34 CpG sites = 32, Kimura (unadjusted) = 38.29 Transitions / transversions = 1.60 (32/20) Gap_init rate = 0.06 (12 / 185), avg. gap size = 1.33 (16 / 12) 333 32.17 0.00 0.00 chr3qtel1M 282999 283113 (716887) C L1MC5_3end#LINE/L1 (2129) 565 451 m_b143s551i11 5357 chr3qtel1M 282999 TTCTTACAGAACAATAATATTTCATAATATTCATATACTACAATTTATTC 283048 i vvvv i i i vi i vv i i i i C L1MC5_3end#LI 565 TTTTTACAGCTGCATAGTACTCCATTGTGTGGATGTACCATAGTTTATTC 516 chr3qtel1M 283049 AGCCACTCTTCAATTGATAGGCATCCACTTAGTTTCCAGTTTCTGGCCAC 283098 i v ii v i i iiivv v i i v i i C L1MC5_3end#LI 515 AACCAGTCCCCTATTGATGGACATTTGGGTTGTTTCCAGTCTTTTGCTAT 466 chr3qtel1M 283099 TACAAAGAGGGCTGC 283113 v v C L1MC5_3end#LI 465 TACAAATAGTGCTGC 451 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.54 CpG sites = 22, Kimura (unadjusted) = 43.54 Transitions / transversions = 1.47 (22/15) Gap_init rate = 0.00 (0 / 114), avg. gap size = 0.0 (0 / 0) 411 26.36 0.00 0.00 chr3qtel1M 283012 283121 (716879) C L1ME3A_3end#LINE/L1 (368) 552 443 m_b143s551i12 5357 chr3qtel1M 283012 ATAATATTTCATAATATTCATATACTACAATTTATTCAGCCACTCTTCAA 283061 i i vi i vv i i v i v vi C L1ME3A_3end#L 552 ATAGTATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTACTG 503 chr3qtel1M 283062 TTGATAGGCATCCACTTAGTTTCCAGTTTCTGGCCACTACAAAGAGGGCT 283111 i i iiivv ? ?? i i i v v C L1ME3A_3end#L 502 TTGATGGACATTTGGGTNGTTTCCAGTTTNNGGCTATTACGAATAGTGCT 453 chr3qtel1M 283112 GCCACAAACA 283121 i ii C L1ME3A_3end#L 452 GCTATGAACA 443 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.43 CpG sites = 19, Kimura (unadjusted) = 34.94 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.00 (0 / 109), avg. gap size = 0.0 (0 / 0) 230 14.55 3.51 3.51 chr3qtel1M 284214 284270 (715730) C L1PA4_3end#LINE/L1 (305) 597 541 m_b143s551i13 5358 chr3qtel1M 284214 CCATGTTTTT-CTAAGGTCACTGAACTCATCATTTCTTATAGC-ACAGTA 284261 iii - v v - i i -i - C L1PA4_3end#LI 597 CCATGTCCCTACAAAGGACA-TGAACTCATCATTTTTTATGGCTGCA-TA 550 chr3qtel1M 284262 GTATTCCAT 284270 C L1PA4_3end#LI 549 GTATTCCAT 541 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 16.58 CpG sites = 6, Kimura (unadjusted) = 16.58 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.07 (4 / 56), avg. gap size = 1.00 (4 / 4) 280 25.62 8.53 7.51 chr3qtel1M 284238 284448 (715552) C L1MC5_3end#LINE/L1 (2121) 573 361 m_b143s551i14 5359 chr3qtel1M 284238 CTCATCATTTCTTATAGC-ACAGTAGTATTCCATTAGAATAACATATGAC 284286 ivi i i -i - i ivivvi ii iv i C L1MC5_3end#LI 573 CTCATTCCTTTTTACAGCTGCA-TAGTACTCCATTGTGTGGATGTACCAT 525 chr3qtel1M 284287 AATTTGTTCAATCATTTCCCAATT--------TTTAGGTGTCTATAAATT 284328 i i i v i v -------- i --- i --- C L1MC5_3end#LI 524 AGTTTATTCAACCAGTCCCCTATTGATGGACATTTGGGT---TGT---TT 481 chr3qtel1M 284329 CCAGTTCTTTGCACCAC-ACAAAGAGTACT-C--TAAATACTTTGGTAGA 284374 ii --i i- v i - -- i vii v iv C L1MC5_3end#LI 480 CCAGTCTTTTGC--TATTACAAATAGTGCTGCAATGAATAGCCTTGTGCA 433 chr3qtel1M 284375 TAGGGGGTCTTTTCCTTTTTTTTCC--TG-ATCATTTGAAAAAATAGA-- 284419 v --- v v v -- - - ii --- -- C L1MC5_3end#LI 432 TACG---TCTTTTCGTATTTTTGCCAGTGTATC-TTTGGGA---TAGATT 390 chr3qtel1M 284420 CAAAGCAGTGGTATTGTTGGGTCAAAGGG 284448 vv v v i C L1MC5_3end#LI 389 CCTAGAAGTGGGATTGCTGGGTCAAAGGG 361 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.26 CpG sites = 31, Kimura (unadjusted) = 32.26 Transitions / transversions = 1.63 (31/19) Gap_init rate = 0.11 (24 / 210), avg. gap size = 1.42 (34 / 24) 39 6.71 0.00 0.00 chr3qtel1M 284452 284498 (715502) (TC)n#Simple_repeat 1 47 (0) c_b143s251i2 5360 chr3qtel1M 284452 TCTCTCTCTCTCTTTCTATTTCTCTCTCTCTCTCTCTCTCTCTCTCT 284498 i v i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 47 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 583 31.10 7.92 3.18 chr3qtel1M 284949 285579 (714421) C L1PB_orf2#LINE/L1 (590) 2704 2045 m_b143s551i15 5361 chr3qtel1M 284949 TTCTGT--CACTGATCTGCATTTCTATTTCT-TAGTCATACCAGATAGTT 284995 -- i i iii vi i - vivi viiv C L1PB_orf2#LIN 2704 TTCTGTTCCATTGGTCTATGTGCCTATTTTTATACCAGTACCATGCTGTT 2655 chr3qtel1M 284996 TTTACAATTACTGTCTTATAAGATACT----AGTACTATTAACCTG--CC 285039 viii i iv i iv v ---- - viv iv --v C L1PB_orf2#LIN 2654 TTGGTGACTATGGCCTTATAGTATAGTTTGAAGT-CGGGTAATGTGATGC 2606 chr3qtel1M 285040 CTCC----TTACTTTTTTTTATTAGT--TCCTTTGA-------GATTCTT 285076 ---- ii i vv -- v i------- ii C L1PB_orf2#LIN 2605 CTCCAGATTTGTTCTTTTTGCTTAGTCTTGCTTTGGCTATGCGGGCTCTT 2556 chr3qtel1M 285077 GACTGGTCCTACAAATGAATTTTG---TTATTTTTTCTAATTCAGTAAA- 285122 vvi i -- v i--- i i v i - C L1PB_orf2#LIN 2555 TTTTGGTTC--CATATGAATTTTAGGATTGTTTTTTCTAGTTCTGTGAAG 2508 chr3qtel1M 285123 -ATGATTTTTTGGTAATTTGATTAGGATGGCATTGAATTTGTCAATTAGT 285171 - vv -- v vi i v vi iv C L1PB_orf2#LIN 2507 AATGATGGT--GGTATTTTGATGGGAATTGCATTGAATTTGTAGATTGCT 2460 chr3qtel1M 285172 TTGGGTAAAATTATCATTTTTATTATATTGCTTCTGTCTACCCATGAACA 285221 v i iv vi i iv v ii i i i C L1PB_orf2#LIN 2459 TTTGGCAGTATGGTCATTTTCACAATATTGATTCTACCCATCCATGAGCA 2410 chr3qtel1M 285222 TTTAATACTTCTCCA---ATTTAGATT-----TGATTTTATTTTTATAAA 285263 vvi iiv i ---i ivi i----- i-- i -iv C L1PB_orf2#LIN 2409 TGGGATGTGTTTCCATTTGTTTGTGTCGTCTATGATTTC--TTTCA-GCA 2363 chr3qtel1M 285264 ATGTTTTTAATGTAATTTTG-TTATATACTTCTTGGGTTTGTGTTGACAG 285312 i ---- i v- i v vv vviii viv v vi C L1PB_orf2#LIN 2362 GTGTTTT----GTAGTTTTCCTTGTAGAGGTCTTTCACCTCCTTGGTTAG 2317 chr3qtel1M 285313 ACATACTTCCAGGTATTTTATACTATTTAGAGCTATTTTAAATGGGGT-- 285360 ii i i i i vi v iv v v -- C L1PB_orf2#LIN 2316 GTATATTCCTAAGTATTTTATTTTTTTTGCAGCTATTGTAAAAGGGGTTG 2267 chr3qtel1M 285361 ATTTCTTACCATTTC-TTCTTCCAGAATTTTGTTTG----TGATATATAG 285405 v i-- v- -- ---i v i ---- i i C L1PB_orf2#LIN 2266 AGTTCTTG--ATTTGATTCT--CAG---CTTGGTCGCTGTTGGTGTATAG 2224 chr3qtel1M 285406 GAATGCTGATGAATAATATGGATTTACTTCACATCCTGCTACTTTCCTAA 285455 ? iv iv v vi i iv v i iii ? vv v i C L1PB_orf2#LIN 2223 NAGAGCTACTGATTTGTGTACATTAATTTTGTATCCNGAAACTTTGCTGA 2174 chr3qtel1M 285456 A----GTTATTGTTTCTAATAACTTTTTAGTTGAGCTTTTGGGATTTTCC 285501 ----v iiv iv i i i vv ii i i i C L1PB_orf2#LIN 2173 ATTCNTTTATCAGTTCTAGGAGCTTTCTGGAGGAGTCTTTAGGGTTTTCT 2124 chr3qtel1M 285502 AGGTGTAC---CATATTATCTGTAAAGACAGAGAGAATTTTACCACTTTG 285548 i? --- i v i -- v v i v iv i iv C L1PB_orf2#LIN 2123 AGGTANACGATCATATCATCAGCAA--ACAGCGACAGTTTGACTTCCTCT 2076 chr3qtel1M 285549 TTTTCTATTCAGATCCCTTTTATGTCTTTTT 285579 vi v ii v i v i C L1PB_orf2#LIN 2075 TTACCGATTTGGATGCCCTTTATTTCTTTCT 2045 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.20 CpG sites = 111, Kimura (unadjusted) = 41.78 Transitions / transversions = 1.41 (111/79) Gap_init rate = 0.06 (39 / 630), avg. gap size = 1.82 (71 / 39) 775 29.15 4.20 2.56 chr3qtel1M 285080 285579 (714421) C L1M2_orf2#LINE/L1 (742) 2549 2042 m_b143s551i16 5361 chr3qtel1M 285080 TGGTCCTACAAATGAATTTTG---TTATTTTTTCTAATTCAGTAAA--AT 285124 i -- v i i--- ? v v i -- C L1M2_orf2#LIN 2549 TGGTTC--CATACGAATTTTAGGATTNTTTTTTCTATTTCTGTGAAGAAT 2502 chr3qtel1M 285125 GATTTTTTGGTAATTTGATTAGGATGGCATTGAATTTGTCAATTAGTTTG 285174 -- iv v vi v i vi iiv C L1M2_orf2#LIN 2501 G--TCATTGGTATTTTGATAGGGATTGCATTGAATCTGTAGATCGCTTTG 2454 chr3qtel1M 285175 GGTAAAATTATCATTTTTATTATATTGCTTCTGTCTACCCATGAACATTT 285224 iv vi? v iv iv vi v i i vv C L1M2_orf2#LIN 2453 GGTAGTATGGNCATTTTAACAATATTAATTCTTCCAATCCATGAGCATGG 2404 chr3qtel1M 285225 AATACTTCTCCA---ATTTAGATTTGATTTTATTTTTATAA--AATGTTT 285269 i ii i ---? ivi iivv iv i v v -- i C L1M2_orf2#LIN 2403 GATATCTTTCCATTTNTTTGTGTCCTCTTCAATTTCTTTCATCAGTGTTT 2354 chr3qtel1M 285270 T-TAATGTAATTTTGTTATATACTTCTTGGGTTTGTGTTGACAGACATAC 285318 - i ---- i? i v vv vviii viv v vi i iv i C L1M2_orf2#LIN 2353 TATAGT----TTTCNTTGTAGAGATCTTTCACCTCCTTGGTTAAATTTAT 2308 chr3qtel1M 285319 TTCCAGGTATTTTATACTATTTAGAGCTATTTTAAATGGGGT--ATTTCT 285366 i i vi v iv v i --v C L1M2_orf2#LIN 2307 TCCTAGGTATTTTATTTTTTTTGTAGCTATTGTAAATGGGATTGCTTTCT 2258 chr3qtel1M 285367 TACCATTTCTTCTTCCAGA-ATTTTGTTTGTGATATATAGGAATGCTGAT 285415 i-- - i - v i vv iii i iv C L1M2_orf2#LIN 2257 TG--ATTTCTT-TTTCAGATAGTTCGTTGTTGGCGTATAGAAATGCTACT 2211 chr3qtel1M 285416 GAATAATATGGATTTACTTCACATCCTGCTACTTTCCTAAA---G-TTAT 285461 v vv i ivi v i iii v v i --- - C L1M2_orf2#LIN 2210 GATTTTTGTATGTTGATTTTGTATCCTGCAACTTTACTGAATTCGTTTAT 2161 chr3qtel1M 285462 TGTTTCTAATAACTTTTTAGTTGAGCTTTTGGGATTTTCCAGGTGT---A 285508 iiv ? ii i v ii i ? i ?i i --- C L1M2_orf2#LIN 2160 CAGTTCTAANAGTTTTTTGGTGGAGTCTTTAGGNTTTTCTANATATAAGA 2111 chr3qtel1M 285509 CCATATTATCTGTAAAGACAGAGAGAATTTTACCACTTTGTTTTCTATTC 285558 i i i i -- i v v iv i iv i v i C L1M2_orf2#LIN 2110 TCATGTCATCTGCAA--ACAGGGACAATTTGACTTCCTCCTTTCCAATTT 2063 chr3qtel1M 285559 AGATCCCTTTTATGTCTTTTT 285579 i v v i C L1M2_orf2#LIN 2062 GGATGCCTTTTATTTCTTTCT 2042 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.21 CpG sites = 83, Kimura (unadjusted) = 38.68 Transitions / transversions = 1.41 (83/59) Gap_init rate = 0.05 (23 / 499), avg. gap size = 1.48 (34 / 23) 18 7.16 3.33 0.00 chr3qtel1M 288048 288077 (711923) (CTT)n#Simple_repeat 1 31 (0) m_b143s252i18 5362 chr3qtel1M 288048 CTTCTTCTTCTTCTTCTT-TTTTTTTTCTTC 288077 - i i (CTT)n#Simple 1 CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTC 31 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 16 8.83 0.00 4.00 chr3qtel1M 289672 289697 (710303) (CT)n#Simple_repeat 1 25 (0) m_b143s252i19 5363 chr3qtel1M 289672 CTCTCTCTGTCTCGTCTCTCTCTTTC 289697 v - i (CT)n#Simple_ 1 CTCTCTCTCTCTC-TCTCTCTCTCTC 25 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 25), avg. gap size = 1.00 (1 / 1) 26 8.83 0.00 0.00 chr3qtel1M 289697 289732 (710268) (CA)n#Simple_repeat 1 36 (0) m_b143s252i20 5364 chr3qtel1M 289697 CACACACACACACACAAACACACACATAAACACACA 289732 v i v (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACA 36 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 257 28.91 1.69 6.19 chr3qtel1M 291038 291155 (708845) C L3#LINE/CR1 (258) 3841 3729 m_b143s601i5 5365 chr3qtel1M 291038 TCTGTCCT-TGAAGCTAAAACAAACAGATCTGATCTCTCTTCTACATGAC 291086 i - i i v vvi i ii i i i C L3#LINE/CR1 3841 TCTGCCCTCTGGAGCCACACAGAATAAGTCTAATCCCTCTTCCACATGAC 3792 chr3qtel1M 291087 ACGCCTTCAGAAGTCTTAAAGGTATATGTACCATGAAAACTGACTCAGAA 291136 vv i vi - i -- i vv i ---v -v vi i C L3#LINE/CR1 3791 AGCCCTTCAAATAT-TTGAAG--ACAGCTATCATG---TCT-CCTCTAAG 3749 chr3qtel1M 291137 TATGCTCTTGTTCA-GCTAA 291155 v v v i - C L3#LINE/CR1 3748 TCTTCTCTTCTCCAGGCTAA 3729 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.20 CpG sites = 18, Kimura (unadjusted) = 37.20 Transitions / transversions = 1.29 (18/14) Gap_init rate = 0.08 (9 / 117), avg. gap size = 1.00 (9 / 9) 423 23.66 3.23 0.00 chr3qtel1M 291915 292007 (707993) MIR#SINE/MIR 49 144 (118) m_b143s601i6 5366 chr3qtel1M 291915 TGAGTTCAAATCTGGACTTAAACACTTCCTAGCTGTGT--TTGTGGGTAA 291962 i i iv i iviv v --iiv i MIR#SINE/MIR 49 TGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 98 chr3qtel1M 291963 ATCATTTAACC-CTGTTTCCCTCAGTTTCCTCATCTGTAAAATAAG 292007 i i i - v v v ii MIR#SINE/MIR 99 GTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGG 144 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 27.64 CpG sites = 14, Kimura (unadjusted) = 29.20 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.02 (2 / 92), avg. gap size = 1.50 (3 / 2) 384 24.28 0.00 7.76 chr3qtel1M 292742 292866 (707134) MIRb#SINE/MIR 3 118 (150) m_b143s601i7 5367 chr3qtel1M 292742 GAGTGGGCAGCTAGGTGGTGTAGTGGATAGCTCACCAGCCCTGAATTAAG 292791 - --- i v vv vi ii i v v MIRb#SINE/MIR 3 GAG-GGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAG 48 chr3qtel1M 292792 AAGTGCCTGAGTTCAAATCTGGCCACAGACACAATACTTCCTAGCTGTGT 292841 vivi i i iv v v v v ----- v MIRb#SINE/MIR 49 ACAGACCTGGGTTCGAATCCCGGCTCTGCCAC-----TTACTAGCTGTGT 93 chr3qtel1M 292842 GACCTTGGGGAAGTCAATTAACCCC 292866 v i v i MIRb#SINE/MIR 94 GACCTTGGGCAAGTTACTTAACCTC 118 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.04 CpG sites = 12, Kimura (unadjusted) = 29.21 Transitions / transversions = 0.75 (12/16) Gap_init rate = 0.07 (9 / 124), avg. gap size = 1.00 (9 / 9) 221 33.02 0.00 1.94 chr3qtel1M 293174 293278 (706722) L2a_3end#LINE/L2 132 234 (283) m_b143s601i8 5368 chr3qtel1M 293174 CTTTGTACTGGCCGTCTCTCCCATGGCTGAAAGGTTCTTCTTCCTCATCT 293223 i v i - i i - v i v i ii vv v L2a_3end#LINE 132 CTTTGCACTTGCTGT-TCCCTC-TGCCTGGAACGCTCTTCCCCCAGATAT 179 chr3qtel1M 293224 TGGTCTCATACCTTCCCTGGCTTCCTGCAAGACTGAGCTCAAATATCACC 293273 iv iv viiv vi vi i v i v vv i L2a_3end#LINE 180 CCGCATGGCTCGCTCCCTCACCTCCTTCAGGTCTTTGCTCAAATGTCACC 229 chr3qtel1M 293274 TTCCC 293278 i L2a_3end#LINE 230 TTCTC 234 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 44.45 CpG sites = 18, Kimura (unadjusted) = 44.45 Transitions / transversions = 1.12 (18/16) Gap_init rate = 0.02 (2 / 104), avg. gap size = 1.00 (2 / 2) 206 27.74 5.56 6.54 chr3qtel1M 293326 293433 (706567) L2d2_3end#LINE/L2 425 531 (24) m_b143s601i9 5369 chr3qtel1M 293326 TCTCCTCTTACCTTGAGATTATGAGC--CTTGTGGTAAGAGAATGAGTTT 293373 i -- v -- i i -- v vv i viiv i L2d2_3end#LIN 425 TCTCCCC--AACT--AGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCT 470 chr3qtel1M 293374 TAGCCTTCTCTTTGATCCT----AACATTCAGCACAGTGCCTGGCACCCT 293419 vv i v - i---- i iiii v v - L2d2_3end#LIN 471 TATACTTCTTTGT-ATCCCCCACAGCGCCTAGCACAGTGCCTTGCACAC- 518 chr3qtel1M 293420 TGTAAGTGCCTCAA 293433 v i i - L2d2_3end#LIN 519 AGTAGGCG-CTCAA 531 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.32 CpG sites = 16, Kimura (unadjusted) = 35.39 Transitions / transversions = 1.33 (16/12) Gap_init rate = 0.08 (9 / 107), avg. gap size = 1.44 (13 / 9) 459 33.98 4.07 11.88 chr3qtel1M 294240 294583 (705417) L3#LINE/CR1 3683 4002 (97) m_b143s601i10 5370 chr3qtel1M 294240 CTGAAAACTGTATTGGAGATGGGAAAT--TTGAAAGGAATTAAAAGGCTT 294287 i ii i i-- v i i i-- i i v viii v i L3#LINE/CR1 3683 CTGGAAACCATGTC--ATATGAGGAACGGTTGAAGGAACTGGGGATGTTT 3730 chr3qtel1M 294288 --CTTGGAGAATGATTCATAGTAGGAAGGGACTCAAGAGAGAGA--ATAG 294333 -- i ------------- iii i iii v -- L3#LINE/CR1 3731 AGCCTGGAGAA-------------GAGAAGACTTAGAGGAGACATGATAG 3767 chr3qtel1M 294334 --GTCTAATTCTAATATTTAAAGGGCCTACATATATATAAGTGCTTAGTG 294381 -- --- v i ivv i iv vi v v -- L3#LINE/CR1 3768 CTGTCT---TCAAATATTTGAAGGGCTGTCATGTGGAAGAGGGATTAG-- 3812 chr3qtel1M 294382 GGTTTTTTTTGGTTAGTTTGTTTTATGCCTGACTCCAAAGG-CAAAACCA 294430 ---------------ii i i i -- i i - i i L3#LINE/CR1 3813 ---------------ACTTATTCTGTG--TGGCTCCAGAGGGCAGAACTA 3845 chr3qtel1M 294431 GAAACAATGAG---ATGTGACAAGTAGGGCTATGTGAGACTAAATGTCAG 294477 i v i --- v v i v vvv v vi - v i v L3#LINE/CR1 3846 GGACCAATGGGTGGAAGTTACAGGGAGGCAGATTTCGG-CTCAATATAAG 3894 chr3qtel1M 294478 GAACAACTTCCTAATAACAGGATCTGTCACAGAATG--ACAGGCTTCCCC 294525 v i i ivi v vv i -- ii v i L3#LINE/CR1 3895 GAAGAACTTTCTAACAATCAGAGCTGTCCAAAAATGGAATGGGCTGCCTC 3944 chr3qtel1M 294526 AAGAGGCGACAGAATCTTTACCCCTGGAGGTTTTCAGTCAAAAGTTGGGA 294575 i? iiiiiiiv iiiii v v iv i i i iv L3#LINE/CR1 3945 GNGAGGTAGTGAGCTCCCCGTCACTGGAGGTGTTCAAGCAGAGGCTGGAT 3994 chr3qtel1M 294576 GGCCAATT 294583 i v L3#LINE/CR1 3995 GACCACTT 4002 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 44.95 CpG sites = 68, Kimura (unadjusted) = 47.64 Transitions / transversions = 1.94 (68/35) Gap_init rate = 0.13 (45 / 343), avg. gap size = 1.16 (52 / 45) 187 21.15 3.85 0.00 chr3qtel1M 295533 295584 (704416) C L3#LINE/CR1 (802) 3297 3244 m_b143s601i11 5371 chr3qtel1M 295533 TTCAGCCT--CCAGCTCTCTCTGAATCTTGGTTCTGCCATACTGCAGATT 295580 i -- v v ?i i i i v v? iv C L3#LINE/CR1 3297 TCCAGCCTGTCGAGATCNTTTTGAATCTTGATTCTGTCATCCANCGTATT 3248 chr3qtel1M 295581 AGCT 295584 C L3#LINE/CR1 3247 AGCT 3244 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 23.70 CpG sites = 6, Kimura (unadjusted) = 26.35 Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.02 (1 / 51), avg. gap size = 2.00 (2 / 1) 30 26.46 0.00 1.25 chr3qtel1M 295899 295979 (704021) (CTC)n#Simple_repeat 1 80 (0) m_b143s252i21 5372 chr3qtel1M 295899 CTCCTCCTGCTCCTCTTCTTCCTCCTCATTTTCCTCTTCCTCAACCTCCT 295948 v i i v ii i vv (CTC)n#Simple 1 CTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT 50 chr3qtel1M 295949 TTTCTTTCTTCTTCTCTTTTCTCCTCCTCCT 295979 ii i i i i -i i (CTC)n#Simple 51 CCTCCTCCTCCTCCTC-CTCCTCCTCCTCCT 80 Matrix = Unknown Transitions / transversions = 3.25 (13/4) Gap_init rate = 0.01 (1 / 80), avg. gap size = 1.00 (1 / 1) 29 25.46 2.42 4.96 chr3qtel1M 295900 296023 (703977) (TCCTCT)n#Simple_repeat 1 121 (0) m_b143s252i22 5372 chr3qtel1M 295900 TCCTCCTGCTCCTCTTCTTCCTCCTCATTTTCCTCTTCCTCAACCTCCTT 295949 i v i i i v i vv i i (TCCTCT)n#Sim 1 TCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTC 50 chr3qtel1M 295950 TTCTTTCTTCTT-CTCTT-TTC-TCCTCCTCCTTTTTCACTGTCATCATT 295996 i - i - -i - i i i v - v -- (TCCTCT)n#Sim 51 CTC-TTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCT-TCCTC--T 96 chr3qtel1M 295997 ATCATTTTCATCATCCTCCTTTCTCTT 296023 - v i v v - i (TCCTCT)n#Sim 97 -TCCTCTTCCTCTTCCT-CTTCCTCTT 121 Matrix = Unknown Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.07 (9 / 123), avg. gap size = 1.00 (9 / 9) 201 14.72 0.00 2.94 chr3qtel1M 296758 296792 (703208) C L3#LINE/CR1 (1673) 2426 2393 m_b144s601i0 5371 chr3qtel1M 296758 AGAGGTTGAATAATTCTGCTTTACTTTCTGTCATC 296792 ii i i - i C L3#LINE/CR1 2426 AGGAGTTGAGTAGTTCTGCTTT-CTCTCTGTCATC 2393 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 17.42 CpG sites = 5, Kimura (unadjusted) = 17.42 Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 17 29.84 0.00 0.00 chr3qtel1M 297388 297444 (702556) (AAAAGA)n#Simple_repeat 1 57 (0) m_b144s252i2 5373 chr3qtel1M 297388 AAAATAAAAAATGACAGAATAGGAAAAAAAATCAGAAAAGGAAAATAAAA 297437 v ivi v v i i vv i vi (AAAAGA)n#Sim 1 AAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAA 50 chr3qtel1M 297438 AAGCAAA 297444 v (AAAAGA)n#Sim 51 AAGAAAA 57 Matrix = Unknown Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0) 46 2.33 0.00 0.00 chr3qtel1M 299333 299376 (700624) (GT)n#Simple_repeat 1 44 (0) c_b144s251i0 5374 chr3qtel1M 299333 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGTGTGT 299376 i (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 44 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 55 11.86 5.76 4.26 chr3qtel1M 300149 300287 (699713) (AGAA)n#Simple_repeat 1 141 (0) m_b144s252i3 5375 chr3qtel1M 300149 AGAAATGAAAGAAAGAAAAAAAAGAAATAAAAAGAAGCAAGATA-AAAG- 300196 - - i v i - v v - - (AGAA)n#Simpl 1 AGAAA-GAAAGAAAG-AAAGAAAGAAAGAAAGA-AAGAAAGAAAGAAAGA 47 chr3qtel1M 300197 AAGGAAGGAAGGCAGAAA-AAAGAGAGAAAGAAA-AAAG-AA-AAAGAAA 300242 i i iv - i - - - (AGAA)n#Simpl 48 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 97 chr3qtel1M 300243 GAAAGAAAGGAAAGGAAATAAA-CATGAAATGAATGAAAG-AAGAAA 300287 - - v -v v - v - (AGAA)n#Simpl 98 GAAAGAAA-GAAA-GAAAGAAAGAAAGAAA-GAAAGAAAGAAAGAAA 141 Matrix = Unknown Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.10 (14 / 138), avg. gap size = 1.00 (14 / 14) 926 31.62 2.89 1.91 chr3qtel1M 300552 301070 (698930) C L1ME4c_3end#LINE/L1 (274) 556 33 m_b144s551i0 5376 chr3qtel1M 300552 CATAATGTGCCATTACAATCAGATGTAACAT--TCTGTTCAGCCTTTCTC 300599 i v -- i vi? v -- i ii i i v i C L1ME4c_3end#L 556 CATAATATTCCAT--CGAGTNGATGTACCATAATTTACTTAACCATTCCC 509 chr3qtel1M 300600 CAATTCAGGGGCA----AACCCTTACCACTTCTTAGCCATCACAAA-AGA 300644 v vvv i ----iiiiv v v i v i i i - iv C L1ME4c_3end#L 508 CTATTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAAC 459 chr3qtel1M 300645 GCTATTATAAATAATTTTATGGAAATAGGTTCTTCCCCCTGCCCTTT--- 300691 iiv i i vi ii v v v i ii ---- --- C L1ME4c_3end#L 458 GCTGCAATGAACATCTTCGTGCATATAGCTTTTTCCTTCT----TTTGAA 413 chr3qtel1M 300692 TTATCTCTATTGGATACAAGCCTAATAGTGTTACTATCAGATCAAATGAT 300741 i iv v v vv i iv vv i iii i v i C L1ME4c_3end#L 412 TTATTTCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGT 363 chr3qtel1M 300742 GCAAAGTTTTTTATT-CTATTGG-GCATAGTTCCAAATTGCTCTTCAGAA 300789 iii vv v- v i-i i v v i i i C L1ME4c_3end#L 362 ATGAACATTTTTATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAA 313 chr3qtel1M 300790 TAGTTGGATCAGTTCACAACTCTACCAACAATGTGTTAGTGTCCTAGTTT 300839 vi v i i i ?iv i i i v ? v i C L1ME4c_3end#L 312 GGGTTGTACCAATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTTT 263 chr3qtel1M 300840 TCCCACATCCCCTCCAACATTTATTATTTTCCTAATTTTTTTGTCATATC 300889 iv i ? i v i viv v -- vi-- v i C L1ME4c_3end#L 262 CACCGCANCCTCGCCAGCATTGGGTATTATC--AATTTTTTAA--ATTTT 217 chr3qtel1M 300890 AGACAATCTAATAGGTGTCAAGTGGTACCTCAGAGATGTTTTAATTTGCA 300939 v vi i i v i i vv v i C L1ME4c_3end#L 216 TGCTAATTTAATAGGCGTAAAATGGTATCTCATTGTTGCTTTAATTTGCA 167 chr3qtel1M 300940 TTTTTCTGATCAGTAGTGATTTAGAACAGTTT---ATATGAGTACAGATA 300986 i i i v i vv v v --- i vv iivv iv C L1ME4c_3end#L 166 TTTCTTTGATTACTAGCGAGGTTGAACATTTTTCCATGTGTTTGTTTACT 117 chr3qtel1M 300987 GCTTTGATTTCTTTGTTTGAAAACTGCCTGTTCATATCCTTTGACCATTT 301036 i? vv i iv ? vi i i i v C L1ME4c_3end#L 116 ANTTGTATTTCCTCTTNTGTGAATTGTCTGTTCATGTCCTTTGCCCATTT 67 chr3qtel1M 301037 ATCAACTGAGGAATTACTAGTATTCTTATAAATT 301070 v i i vv iv ?v v v C L1ME4c_3end#L 66 ATCTATTGGGGTCTTGATNTTTTTCTTATCAATT 33 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.72 CpG sites = 88, Kimura (unadjusted) = 42.85 Transitions / transversions = 1.21 (88/73) Gap_init rate = 0.03 (17 / 518), avg. gap size = 1.47 (25 / 17) 927 21.84 5.07 5.45 chr3qtel1M 300772 301047 (698953) C L1ME5_3end#LINE/L1 (611) 330 56 m_b144s551i1 5376 chr3qtel1M 300772 CCAAATTGCTCTTCAGAATAGTTGGATCAGTTCACAACTCTACCAACAAT 300821 i i i i v i ii vii i i i C L1ME5_3end#LI 330 CCAGATTGCTCTCCAGAATGGCTGCACCAGTCTACACTCCCACCAGCAGT 281 chr3qtel1M 300822 GTGTTAGTGT-CCTAGTTTTCCCACATCCCCTCCAACATTT---ATTAT- 300866 ii v v - - ? i i v i --- - C L1ME5_3end#LI 280 GCATGAGGGTTCCTA-TNTCCCCACATCCTCGCCAACACTTGGCATTATC 232 chr3qtel1M 300867 ---TTTCCTAATTTTTTTGTCATATCAGACAATCTAATAGGTGTCAAGTG 300913 ---i i ----------- v i v C L1ME5_3end#LI 231 CAGCTTTCTAATTTTT-----------GCCAGTCTAATAGGTGTAAAGTG 193 chr3qtel1M 300914 GTACCTCAGAGATGTTTTAATTTGCATTTTTCTGATCAGTAGTGATTTAG 300963 i i vv v i i v i v v C L1ME5_3end#LI 192 ATATCTCATTGTTGTTTTAATTTGCATTTCTCTGATTACTAATGAGTTTG 143 chr3qtel1M 300964 AACA---GTTTATATGAGTACAGATAGCTTT---GATTTCTTTGTTTGAA 301007 i ---v i vv --- v i --- i i iv i v C L1ME5_3end#LI 142 AGCATCTCTTCATATGCTT---GTTAGCCTTTCGGGTTTCCTCTTCTGTA 96 chr3qtel1M 301008 AACTGCCTGTTCATATCCTTTGACCATTTATCAACTGAGG 301047 i v v v i i C L1ME5_3end#LI 95 AATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGGGG 56 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 26.47 CpG sites = 35, Kimura (unadjusted) = 26.47 Transitions / transversions = 1.59 (35/22) Gap_init rate = 0.08 (21 / 275), avg. gap size = 1.38 (29 / 21) 19 18.30 1.89 3.85 chr3qtel1M 302102 302154 (697846) (AGG)n#Simple_repeat 1 52 (0) m_b144s252i4 5377 chr3qtel1M 302102 AGCAGGA-GAGGAAGAGGGAAGAGGAGCAGCAGGAGGACGAGAAGGATGC 302150 v - i - i v v v i - v (AGG)n#Simple 1 AGGAGGAGGAGGAGGA-GGAGGAGGAGGAGGAGGAGGAGGAGGAGGA-GG 48 chr3qtel1M 302151 AGGA 302154 (AGG)n#Simple 49 AGGA 52 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.06 (3 / 52), avg. gap size = 1.00 (3 / 3) 17 20.54 0.00 0.00 chr3qtel1M 303556 303589 (696411) (AT)n#Simple_repeat 1 34 (0) m_b144s252i6 5378 chr3qtel1M 303556 ATATATAAATAAATACACACATATATGTATATAT 303589 v v i i i i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATAT 34 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 266 27.14 0.00 0.00 chr3qtel1M 304095 304164 (695836) DNM1r#Unknown 2477 2546 (2116) m_b144s502i0 5379 chr3qtel1M 304095 CATATATATATATATATATGTATATATACACATATGTGTGTGTATGTGTG 304144 i i i i i i i iiii i i i i DNM1r#Unknown 2477 CGTGTATGTGTGTATATATGTGTGTATATGTGTGTATGTGTGTATATATG 2526 chr3qtel1M 304145 TGTGTATATATATATTTACA 304164 i ii ? i DNM1r#Unknown 2527 TGTATATATACGTATNTATA 2546 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.22 CpG sites = 19, Kimura (unadjusted) = 40.01 Transitions / transversions = 1.00 (19/0) Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0) 308 20.90 0.00 0.00 chr3qtel1M 304113 304179 (695821) DNM1r#Unknown 2479 2545 (2117) m_b144s502i1 5379 chr3qtel1M 304113 TGTATATATACACATATGTGTGTGTATGTGTGTGTGTATATATATATTTA 304162 i i ii i i i i i v i DNM1r#Unknown 2479 TGTATGTGTGTATATATGTGTGTATATGTGTGTATGTGTGTATATATGTG 2528 chr3qtel1M 304163 CATATATGCATATATAT 304179 i i i ? DNM1r#Unknown 2529 TATATATACGTATNTAT 2545 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 24.82 CpG sites = 13, Kimura (unadjusted) = 27.07 Transitions / transversions = 13.00 (13/1) Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.0 (0 / 0) 285 25.32 1.27 0.00 chr3qtel1M 304180 304258 (695742) L1ME3F_3end#LINE/L1 452 531 (459) m_b144s551i2 5380 chr3qtel1M 304180 CAGCTCTTTTC-TCAGAACAAAGAACTAAAAATTGAGGGAATGTCCATCA 304228 v v - v v i i ii ivivvvi i L1ME3F_3end#L 452 CAGCACTGTTCGTAATAGCAAAAAACTGGAAACAACCCAAATGTCCATCG 501 chr3qtel1M 304229 ATTGGGGAATGGATGAATAAATTGTGGTAT 304258 iv i i L1ME3F_3end#L 502 ACAGGAGAATGGATAAATAAATTGTGGTAT 531 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 29.54 CpG sites = 11, Kimura (unadjusted) = 31.38 Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.01 (1 / 78), avg. gap size = 1.00 (1 / 1) 246 20.63 0.00 0.00 chr3qtel1M 304218 304280 (695720) L1MB8_3end#LINE/L1 491 553 (372) m_b144s551i4 5380 chr3qtel1M 304218 AATGTCCATCAATTGGGGAATGGATGAATAAATTGTGGTATTTGGTTATG 304267 i iv i v v vvv ii L1MB8_3end#LI 491 AATGTCCATCAACTGATGAATGGATAAATAAAATGTGGTATATCCATACA 540 chr3qtel1M 304268 AAGAAATATTATT 304280 v i L1MB8_3end#LI 541 ATGGAATATTATT 553 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 24.23 CpG sites = 6, Kimura (unadjusted) = 24.23 Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0) 306 4.88 0.00 0.00 chr3qtel1M 304218 304258 (695742) L1ME3Cz_3end#LINE/L1 487 527 (470) m_b144s551i3 5380 chr3qtel1M 304218 AATGTCCATCAATTGGGGAATGGATGAATAAATTGTGGTAT 304258 v i L1ME3Cz_3end# 487 AATGTCCATCAATAGGGGAATGGATAAATAAATTGTGGTAT 527 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 5.05 CpG sites = 1, Kimura (unadjusted) = 5.05 Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 16 17.55 0.00 8.16 chr3qtel1M 304544 304596 (695404) (GGCTGCT)n#Simple_repeat 1 49 (0) m_b144s252i7 5381 chr3qtel1M 304544 GGCTGGCTGGGTTCTGTTCTGGTGGCTGCTGGTCTCATGGCTTCTGGCTA 304593 - v v -v v - vv v - (GGCTGCT)n#Si 1 GGCT-GCTGGCTGCTG-GCTGCTGGCTGCTGG-CTGCTGGCTGCTGGCT- 46 chr3qtel1M 304594 GCT 304596 (GGCTGCT)n#Si 47 GCT 49 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.08 (4 / 52), avg. gap size = 1.00 (4 / 4) 17 21.06 0.00 0.00 chr3qtel1M 305230 305263 (694737) (AT)n#Simple_repeat 1 34 (0) m_b144s252i8 5382 chr3qtel1M 305230 ATATATAAATACATATACACATATATGTATGTAT 305263 v i i i i i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATAT 34 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 38 0.00 0.00 0.00 chr3qtel1M 305695 305727 (694273) (AT)n#Simple_repeat 1 33 (0) c_b144s251i1 5383 chr3qtel1M 305695 ATATATATATATATATATATATATATATATATA 305727 (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATA 33 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 32 26.48 2.00 2.00 chr3qtel1M 305731 305830 (694170) (AT)n#Simple_repeat 1 100 (0) m_b144s252i9 5383 chr3qtel1M 305731 ATATATATTCCCAAATATA-ATATATATATGGGAAATGTATA-ATATATA 305778 vivi v - -iv v i - (AT)n#Simple_ 1 ATATATATATATATATATATATATATATAT-ATATATATATATATATATA 49 chr3qtel1M 305779 TATCAAATATATATATATGTGTGTGTGTGTGTGTATTTACATATATGTAT 305828 - v i i i i i i i i v i i (AT)n#Simple_ 50 TAT-ATATATATATATATATATATATATATATATATATATATATATATAT 98 chr3qtel1M 305829 AT 305830 (AT)n#Simple_ 99 AT 100 Matrix = Unknown Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.04 (4 / 99), avg. gap size = 1.00 (4 / 4) 293 25.30 1.20 0.00 chr3qtel1M 305831 305913 (694087) L1ME3F_3end#LINE/L1 448 531 (459) m_b144s551i5 5384 chr3qtel1M 305831 ATATCAGCTCTTTTC-TCAGAGCAAAGAATTGAAAATTGAGGGAATGCCC 305879 v v v - v v i i i ivivvvi i L1ME3F_3end#L 448 ATAGCAGCACTGTTCGTAATAGCAAAAAACTGGAAACAACCCAAATGTCC 497 chr3qtel1M 305880 ATCAATTGGGGAATGGATGAATAAATTGTGGTAT 305913 i iv i i L1ME3F_3end#L 498 ATCGACAGGAGAATGGATAAATAAATTGTGGTAT 531 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 29.51 CpG sites = 11, Kimura (unadjusted) = 31.24 Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.01 (1 / 82), avg. gap size = 1.00 (1 / 1) 242 22.22 0.00 0.00 chr3qtel1M 305873 305935 (694065) L1MB8_3end#LINE/L1 491 553 (372) m_b144s551i6 5384 chr3qtel1M 305873 AATGCCCATCAATTGGGGAATGGATGAATAAATTGTGGTATTTGGTTATG 305922 i i iv i v v vvv ii L1MB8_3end#LI 491 AATGTCCATCAACTGATGAATGGATAAATAAAATGTGGTATATCCATACA 540 chr3qtel1M 305923 AAGAAATATTATT 305935 v i L1MB8_3end#LI 541 ATGGAATATTATT 553 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 26.56 CpG sites = 7, Kimura (unadjusted) = 26.56 Transitions / transversions = 1.00 (7/7) Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0) 260 26.79 2.63 1.74 chr3qtel1M 306636 306749 (693251) HERVK3#LTR/ERVK 5060 5174 (2028) m_b144s701i0 5385 chr3qtel1M 306636 AGTGATGTGGAGAGACCCAGAA--AGTGGTGAATGGAAAGGGCCAGATAG 306683 v i i vv i -- ? ii- v - i i HERVK3#LTR/ER 5060 AGTGTTATGGAAATCCCCGGAAGAAGNGAC-AATGGAAAGGTCC-GGTGG 5107 chr3qtel1M 306684 GCTAACTG-CTTGGGGGAGAGGGTTTGCTTGTATCTCTACAGGTGGAGAA 306732 ii v - v i? v i i i v iv i HERVK3#LTR/ER 5108 ATTTACTGACGTGGGGANGAGGGTATGCTTGTGTTTTTACAGGAGATGGA 5157 chr3qtel1M 306733 GGAATCAGATGGGTGCC 306749 vi i ivi HERVK3#LTR/ER 5158 CAAACCGTGTGGGTGCC 5174 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.19 CpG sites = 19, Kimura (unadjusted) = 35.06 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.04 (4 / 113), avg. gap size = 1.25 (5 / 4) 15 15.61 2.78 0.00 chr3qtel1M 308284 308319 (691681) (TTTTTAA)n#Simple_repeat 1 37 (0) m_b144s252i10 5386 chr3qtel1M 308284 TTTTTAATTTTT-ATTTTTTATTATAACTTTTTATTT 308319 - v v v v v (TTTTTAA)n#Si 1 TTTTTAATTTTTAATTTTTAATTTTTAATTTTTAATT 37 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) 348 30.43 0.00 0.00 chr3qtel1M 308542 308656 (691344) C L1MC5_3end#LINE/L1 (2129) 565 451 m_b144s551i7 5387 chr3qtel1M 308542 TTCTTACAGAACAATAATATTCCATAATATTCATATACTACAATTTATTC 308591 i vvvv i i vi i vv i i i i C L1MC5_3end#LI 565 TTTTTACAGCTGCATAGTACTCCATTGTGTGGATGTACCATAGTTTATTC 516 chr3qtel1M 308592 AGCCACTCTCCAATTGATGGGCATCCACTTAGTTTCCAGTTTCTGGCCAC 308641 i v i v i iiivv v i i v i i C L1MC5_3end#LI 515 AACCAGTCCCCTATTGATGGACATTTGGGTTGTTTCCAGTCTTTTGCTAT 466 chr3qtel1M 308642 TACAAAGAGGCCTGC 308656 v vv C L1MC5_3end#LI 465 TACAAATAGTGCTGC 451 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.86 CpG sites = 19, Kimura (unadjusted) = 39.86 Transitions / transversions = 1.19 (19/16) Gap_init rate = 0.00 (0 / 114), avg. gap size = 0.0 (0 / 0) 411 25.45 0.00 0.00 chr3qtel1M 308555 308664 (691336) C L1ME3A_3end#LINE/L1 (368) 552 443 m_b144s551i8 5387 chr3qtel1M 308555 ATAATATTCCATAATATTCATATACTACAATTTATTCAGCCACTCTCCAA 308604 i vi i vv i i v i v vi C L1ME3A_3end#L 552 ATAGTATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTACTG 503 chr3qtel1M 308605 TTGATGGGCATCCACTTAGTTTCCAGTTTCTGGCCACTACAAAGAGGCCT 308654 i iiivv ? ?? i i i v vv C L1ME3A_3end#L 502 TTGATGGACATTTGGGTNGTTTCCAGTTTNNGGCTATTACGAATAGTGCT 453 chr3qtel1M 308655 GCCACAAACA 308664 i ii C L1ME3A_3end#L 452 GCTATGAACA 443 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 31.61 CpG sites = 17, Kimura (unadjusted) = 33.04 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.00 (0 / 109), avg. gap size = 0.0 (0 / 0) 46 3.96 0.00 0.00 chr3qtel1M 309975 310026 (689974) (TCTCTCTGTC)n#Simple_repeat 1 52 (0) c_b144s251i2 5388 chr3qtel1M 309975 TCTCTCTCTCTCTCTCTGTCTCTCTCTGTCTCTCTCTGTCTCTCTCTCTC 310024 v v (TCTCTCTGTC)n 1 TCTCTCTGTCTCTCTCTGTCTCTCTCTGTCTCTCTCTGTCTCTCTCTGTC 50 chr3qtel1M 310025 TC 310026 (TCTCTCTGTC)n 51 TC 52 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 632 30.21 5.02 2.95 chr3qtel1M 310602 311099 (688901) C L1P4_orf2#LINE/L1 (742) 2552 2045 m_b144s551i9 5389 chr3qtel1M 310602 TGGTCCTACAAATGAATTTTG---TTATTTTTTCTAATTCAGT--AAAAT 310646 i -- v i--- vi v -- C L1P4_orf2#LIN 2552 TGGTTC--CATATGAATTTTAGAATAGTTTTTTCTAATTCTGTGAAAAAT 2505 chr3qtel1M 310647 GATTTTTTGGTAATTTGATTAGGATGGCATTGAATTTATAAATTAGTTTG 310696 iv -- i vi i i i i i i iv C L1P4_orf2#LIN 2504 GACGTT--GGTAGTTTGATAGGAATAGCGTTGAATCTGTAGATTGCTTTG 2457 chr3qtel1M 310697 GGTAAAATTATCATTTTTATTATATTGCTTCTGTCTA--CCATGAACATT 310744 i iv vii v iv v - i -- i v C L1P4_orf2#LIN 2456 GGCAGTATGGCCATTTTAACGATATTGATTCT-TCCAATCCATGAGCATG 2408 chr3qtel1M 310745 TAATACTTCTCCAATTTATATTTG--ATTTT--ATTTTTATAAAAAGATT 310790 v ii i - i v v -- i ?-- i v v iv vv C L1P4_orf2#LIN 2407 GAATGTTTTTCCA-TTTGTTTGTGTCATCTNTGATTTCTTTCAGCAGTGT 2359 chr3qtel1M 310791 TTAATGTAATTTTG-TTATATACTTCTTGGGTTTGTGTTGACAGACATGC 310839 -- i i v- i v vv vviii viv v vi ii ii C L1P4_orf2#LIN 2358 TT--TGTAGTTCTCCTTGTAGAGATCTTTCACCTCCTTGGTTAGATGTAT 2311 chr3qtel1M 310840 TTCCAGGTACTTTATACTATTTAGAGCTATTTTAAATGGGGT--ATTTCT 310887 i i i vi v ivi v i --vv C L1P4_orf2#LIN 2310 TCCTAGGTATTTTATTTTTTTTGTGGCTATTGTAAATGGGATTGCGTTCT 2261 chr3qtel1M 310888 TACCATTT--CTTCTTGC-AGAATTTTGTTTGTGATACATAGGAATGCTG 310934 i-- -- iiiv -v iv i v ---i i i C L1P4_orf2#LIN 2260 TG--ATTTGGCTCTCAGCTTGAACGTTATTGGTG---TATAGAAATGCTA 2216 chr3qtel1M 310935 ATGAATAATATGGATTTACTTCACATCCTGCTACTTTCCTAAAG----TT 310980 v v vv i iv v i iii vv v i ---- C L1P4_orf2#LIN 2215 CTGATTTTTGTACATTGATTTTGTATCCTGAAACTTTACTGAAGTCGTTT 2166 chr3qtel1M 310981 ATTGTTTCTACTAACTTTTTAATTGAGTTTTGGGGATTTTCCAAGTGT-- 311028 iiv vv i i iiiv i vi i i i i -- C L1P4_orf2#LIN 2165 ATCAGTTCTAGGAGCCTTTTGGCGGAGTCTTTAGGGTTTTCTAGGTATAG 2116 chr3qtel1M 311029 -ACCATATTGTCTGTAAAGACAGAGAGAGTTTTATCACTTTGTTTTCTAT 311077 - i i v ii -- v v iiv iv i C L1P4_orf2#LIN 2115 AATCATATCGTCAGCGAAG--AGAGATAGTTTGACTTCTTCTTTTCCTAT 2068 chr3qtel1M 311078 TCAGAT-CCTTTTATGTCTTTTT 311099 ii - v i C L1P4_orf2#LIN 2067 TTGGATGCCTTTTATTTCTTTCT 2045 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.49 CpG sites = 86, Kimura (unadjusted) = 39.98 Transitions / transversions = 1.43 (86/60) Gap_init rate = 0.06 (28 / 497), avg. gap size = 1.43 (40 / 28) 18 7.16 3.33 0.00 chr3qtel1M 313570 313599 (686401) (CTT)n#Simple_repeat 1 31 (0) m_b144s252i11 5390 chr3qtel1M 313570 CTTCTTCTTCTTCTTCTT-TTTTTTTTCTTC 313599 - i i (CTT)n#Simple 1 CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTC 31 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 16 9.26 0.00 0.00 chr3qtel1M 315207 315229 (684771) (CT)n#Simple_repeat 1 23 (0) m_b144s252i12 5391 chr3qtel1M 315207 CTCTCTCTGTCTCTCTCTCTTTC 315229 v i (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTC 23 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 26 8.83 0.00 0.00 chr3qtel1M 315229 315264 (684736) (CA)n#Simple_repeat 1 36 (0) m_b144s252i13 5392 chr3qtel1M 315229 CACACACACACACACAAACACACACATAAACACACA 315264 v i v (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACA 36 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 257 28.91 1.69 6.19 chr3qtel1M 316581 316698 (683302) C L3#LINE/CR1 (258) 3841 3729 m_b144s601i1 5393 chr3qtel1M 316581 TCTGTCCT-TGAAGCTAAAACAAACAGATCTGATCTCTCTTCTACATGAC 316629 i - i i v vvi i ii i i i C L3#LINE/CR1 3841 TCTGCCCTCTGGAGCCACACAGAATAAGTCTAATCCCTCTTCCACATGAC 3792 chr3qtel1M 316630 ACGCCTTCAGAAGTCTTAAAGGTATATGTACCATGAAAACTGACTCAGAA 316679 vv i vi - i -- i vv i ---v -v vi i C L3#LINE/CR1 3791 AGCCCTTCAAATAT-TTGAAG--ACAGCTATCATG---TCT-CCTCTAAG 3749 chr3qtel1M 316680 TATGCTCTTGTTCA-GCTAA 316698 v v v i - C L3#LINE/CR1 3748 TCTTCTCTTCTCCAGGCTAA 3729 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.20 CpG sites = 18, Kimura (unadjusted) = 37.20 Transitions / transversions = 1.29 (18/14) Gap_init rate = 0.08 (9 / 117), avg. gap size = 1.00 (9 / 9) 423 22.58 3.23 0.00 chr3qtel1M 317463 317555 (682445) MIR#SINE/MIR 49 144 (118) m_b144s601i2 5394 chr3qtel1M 317463 TGAGTTCAAATCTGGACTTAGACAGTTCCTAGCTGTGT--TTGTGGGTAA 317510 i i iv i iv v v v --iiv i MIR#SINE/MIR 49 TGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 98 chr3qtel1M 317511 GTCATTTAACC-CTGTTTCCCTCAGTTTCCTCATCTGTAAAATAAG 317555 i i - v v v ii MIR#SINE/MIR 99 GTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGG 144 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 25.81 CpG sites = 12, Kimura (unadjusted) = 27.29 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.02 (2 / 92), avg. gap size = 1.50 (3 / 2) 384 24.28 0.00 7.76 chr3qtel1M 318290 318414 (681586) MIRb#SINE/MIR 3 118 (150) m_b144s601i3 5395 chr3qtel1M 318290 GAGTGGGCAGCTAGGTGGTGTAGTGGATAGCTCACCAGCCCTGAATTAAG 318339 - --- i v vv vi ii i v v MIRb#SINE/MIR 3 GAG-GGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAG 48 chr3qtel1M 318340 AAGTGCCTGAGTTCAAATCTGGCCACAGACACAATACTTCCTAGCTGTGT 318389 vivi i i iv v v v v ----- v MIRb#SINE/MIR 49 ACAGACCTGGGTTCGAATCCCGGCTCTGCCAC-----TTACTAGCTGTGT 93 chr3qtel1M 318390 GACCTTGGGGAAGTCAATTAACCCC 318414 v i v i MIRb#SINE/MIR 94 GACCTTGGGCAAGTTACTTAACCTC 118 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.04 CpG sites = 12, Kimura (unadjusted) = 29.21 Transitions / transversions = 0.75 (12/16) Gap_init rate = 0.07 (9 / 124), avg. gap size = 1.00 (9 / 9) 251 30.10 0.00 1.94 chr3qtel1M 318727 318831 (681169) L2a_3end#LINE/L2 132 234 (283) m_b144s601i4 5396 chr3qtel1M 318727 CTTTGTACTGGCCGTCTCCCCCTTGCCTGAAAGGTTCTTCTTCCTCATCT 318776 i v i - i - i v i ii vv v L2a_3end#LINE 132 CTTTGCACTTGCTGT-TCCCTCT-GCCTGGAACGCTCTTCCCCCAGATAT 179 chr3qtel1M 318777 TGGTCTCATACCTTCCCTGGCTTCCTGCAGGACTGAGCTCAAATATCACC 318826 iv iv viiv vi vi i v v vv i L2a_3end#LINE 180 CCGCATGGCTCGCTCCCTCACCTCCTTCAGGTCTTTGCTCAAATGTCACC 229 chr3qtel1M 318827 TTCCC 318831 i L2a_3end#LINE 230 TTCTC 234 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.08 CpG sites = 16, Kimura (unadjusted) = 39.08 Transitions / transversions = 1.07 (16/15) Gap_init rate = 0.02 (2 / 104), avg. gap size = 1.00 (2 / 2) 300 34.26 6.48 4.07 chr3qtel1M 318787 319002 (680998) L2b_3end#LINE/L2 238 458 (8) m_b144s601i5 5396 chr3qtel1M 318787 CCTTCCCTGGCTTCCTGCAGGACTGAGCTCAAATATCACCTTCCCCT--- 318833 i i ii -- - i i - ii--- i i i --- L2b_3end#LINE 238 CCCTCCCTGACCCCC--CAGG-CCGGG-TCAGG---CGCCCTCCTCTGGG 280 chr3qtel1M 318834 -TCATCCATTCTT--TATGTCACT-TA---TATGAACTGAGTTATTCACA 318876 -i vi v i --iv i - i--- ? -- vivi i? i L2b_3end#LINE 281 CCCCCCCAGTCCTACCCTGCCACTCTGGGTTATNA--TTGTCTGNTTACA 328 chr3qtel1M 318877 TTTCT-CCTCTTACCTTAGATTATGAACCCCTTGTGATAAGAGAATGAGT 318925 v -i iiv vi i i i i v v ivv i vi ? L2b_3end#LINE 329 TGTCTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGT 378 chr3qtel1M 318926 TT-TTGCGTTT-CCTTT-CATCCCTAACATTCTGCACAGTGCCTGGCACT 318972 i - ivi i- vi -i i i iiiiv ? v L2b_3end#LINE 379 CTGTCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACA 428 chr3qtel1M 318973 CTGCAAGTGCCCCAAAGATATTTGTGGAAT 319002 v i i i i viv i v L2b_3end#LINE 429 CAGTAGGCGCTCAGTAAATATTTGTTGAAT 458 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 45.91 CpG sites = 50, Kimura (unadjusted) = 51.12 Transitions / transversions = 2.38 (50/21) Gap_init rate = 0.08 (18 / 215), avg. gap size = 1.28 (23 / 18) 16 23.32 1.92 1.92 chr3qtel1M 319662 319713 (680287) (TCTGAC)n#Simple_repeat 1 52 (0) m_b144s252i14 5397 chr3qtel1M 319662 TCTGAATATGTCACTGCCTCCCGACTCTAACTCTAACCCTAAC-CTGACT 319710 v v v v v - i i i i i - (TCTGAC)n#Sim 1 TCTGACTCTGACTCTGACT-CTGACTCTGACTCTGACTCTGACTCTGACT 49 chr3qtel1M 319711 CTG 319713 (TCTGAC)n#Sim 50 CTG 52 Matrix = Unknown Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.00 (2 / 2) 23 26.43 4.35 3.45 chr3qtel1M 320187 320301 (679699) (TATTC)n#Simple_repeat 1 116 (0) m_b144s252i15 5398 chr3qtel1M 320187 TACTCTAAT-TATTCTTATATTTTCTCTTTCTAATCTGTTCTCCAGATCT 320235 i v - vv v v -v v i -- -v (TATTC)n#Simp 1 TATTCTATTCTATTCTATTCTATTCT-ATTCTATTCTATTCT--A-TTCT 46 chr3qtel1M 320236 GTT-T-TTCTAATGTTTCCCATTCTGTTCTATT-TTTTC-ATCCTTTTCT 320281 i - - v v v i i i - v - i v (TATTC)n#Simp 47 ATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCT 96 chr3qtel1M 320282 ATTTTATTTTATTATTTTCT 320301 i i v v (TATTC)n#Simp 97 ATTCTATTCTATTCTATTCT 116 Matrix = Unknown Transitions / transversions = 0.60 (9/15) Gap_init rate = 0.08 (9 / 114), avg. gap size = 1.00 (9 / 9) 228 26.09 5.80 0.00 chr3qtel1M 320899 320967 (679033) C L1M8_5end#LINE/L1 (2282) 73 1 m_b144s551i10 5399 chr3qtel1M 320899 TCTGTTT--ATGGAGAAATCTGGAGAGCTTGAAATGTTCTGAC-CTGCT- 320944 -- i ii ii i v v vii v v - i i- C L1M8_5end#LIN 73 TCTGTTTTTATGGGGGGATTCGGGGAGATTCAAAAACTATGCCGCCGCCG 24 chr3qtel1M 320945 CTGCCACCTTCCCAGAGTCCTCC 320967 i i i C L1M8_5end#LIN 23 CCGCCATCTTCCCAGAATCCTCC 1 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 25.06 CpG sites = 13, Kimura (unadjusted) = 33.74 Transitions / transversions = 2.60 (13/5) Gap_init rate = 0.04 (3 / 68), avg. gap size = 1.33 (4 / 3) 29 38.31 1.40 0.69 chr3qtel1M 323000 323142 (676858) (AAGG)n#Simple_repeat 1 144 (0) m_b144s252i16 5400 chr3qtel1M 323000 AATGAAAGAAGGAAGGAAAAAATAAAGAAACAAAAAGAAGCAA-GAA-GA 323047 v i ii vi i -ii i v - - (AAGG)n#Simpl 1 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAA-GGAAGGAAGGAAGGAAGGA 49 chr3qtel1M 323048 CAAAAGGAAGGAAAGAAAGAAGAGAGAGAGAAAGAAAAAAAGGAAATAAA 323097 vii i i ii ii i i ii iv i (AAGG)n#Simpl 50 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG 99 chr3qtel1M 323098 GATGAAATGAATGAAAAAAAAAAGAAATGAAGGAAGGGGGGAGGG 323142 v i v v ii ii i v ii i (AAGG)n#Simpl 100 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG 144 Matrix = Unknown Transitions / transversions = 3.44 (31/9) Gap_init rate = 0.02 (3 / 142), avg. gap size = 1.00 (3 / 3) 451 25.67 0.76 5.56 chr3qtel1M 323187 323318 (676682) MIRc#SINE/MIR 2 127 (141) m_b144s601i6 5401 chr3qtel1M 323187 GAAGCTAGGTGGTACAGTGGCTAGAGCACCAGTCCTGAAGTCAAGAGGAC 323236 i viv i vv ii v i i i i MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr3qtel1M 323237 TTGAGTTCAGATCTGGTCTCAGACACTTAAAACTTCTGAGCTGTGTGACA 323286 i i iii iv v v v --- ---- v MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTT---ACT----AGCTGTGTGACC 94 chr3qtel1M 323287 GTGGGCAAGTAATTTAACCCCAATT-GCCTCAG 323318 v v i i vv v- MIRc#SINE/MIR 95 TTGGGCAAGTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 30.57 CpG sites = 17, Kimura (unadjusted) = 31.74 Transitions / transversions = 1.13 (17/15) Gap_init rate = 0.06 (8 / 131), avg. gap size = 1.00 (8 / 8) 17 10.11 3.12 0.00 chr3qtel1M 323338 323369 (676631) (CAAA)n#Simple_repeat 1 33 (0) m_b144s252i18 5402 chr3qtel1M 323338 CAAA-AAACAAACTAACAAACAAAAAACCAAAC 323369 - v v v (CAAA)n#Simpl 1 CAAACAAACAAACAAACAAACAAACAAACAAAC 33 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 651 31.40 8.12 2.02 chr3qtel1M 323570 324037 (675963) C L1MB2_3end#LINE/L1 (366) 552 57 m_b144s551i11 5403 chr3qtel1M 323570 ATAATGTGCCATTACAATTAGATATCACATCCTGTTCAGCCATTC--CC- 323616 i v ii vv v i ii i v -- - C L1MB2_3end#LI 552 ATAATATTCCATTGTATGTATATACCACATTTTGTTTATCCATTCATCCG 503 chr3qtel1M 323617 ----------CTT----TACT---AAATCTTAGCCACTACAAAAGA-GCT 323648 ---------- ---- i --- vv i i i iii vi - C L1MB2_3end#LI 502 TCGATGGACACTTGGGTTGCTTCCACCTCTTGGCTATTGTGAATAATGCT 453 chr3qtel1M 323649 ATTATAAATA-GTTTGTGCAAATAATTCCTTC----CCCT-TTTTTACCT 323692 ii i i - vv - ii ---- -i i vi C L1MB2_3end#LI 452 GCTATGAACATGGGTGTGCAAATA-TCTCTTCGAGACCCTGCTTTCAATT 404 chr3qtel1M 323693 CTTTTGGATGTAGGCCTAATAGTGTCACTGTCAGATCAAAGGGTGCAAAG 323742 i vi i iv vv i iii v v ---- i C L1MB2_3end#LI 403 CTTTTGGATATATACCCAGAAGTGGGATTGCTGGATCATATGGT----AA 358 chr3qtel1M 323743 TTTTATATTCTA-----TTGGGCAGAGTTCCAAATTGCTCTCCAGAATAG 323787 i - i ----- i v - viv v i i i v iii C L1MB2_3end#LI 357 TTCTAT-TTTTAATTTTTTGAGGA-ACCGCCATACTGTTTTCCATAGCGG 310 chr3qtel1M 323788 TTGGATCAGTTCACAACTCTACCAACA-TGTATTAGTATCCTACTTTTTC 323836 i v i v i vii i - i iv vi i i v i C L1MB2_3end#LI 309 CTGCACCATTTTACATTCCCACCAACAGTGCACAAGGGTTCCAATTTCTC 260 chr3qtel1M 323837 CACATTGCCTCCTACATTTATTATTTTCCTATTATTTTGTCATATTAGAC 323886 ivi v v i i - i v -- v v C L1MB2_3end#LI 259 CACATCCTCGCCAACACTTGTTATTTTC-TGTTTTTTTG--ATAGTAGCC 213 chr3qtel1M 323887 AATCTGATCGGTGTCAGGTGATACCTCAGAGATGTTTTAATTTGCATTTA 323936 vi i v v i vv vv i v C L1MB2_3end#LI 212 ATCCTAATGGGTGTGAGGTGATATCTCATTGTGGTTTTGATTTGCATTTC 163 chr3qtel1M 323937 TCTCCTCAGTAGTGATTTAGAAG-----TTTATATGAGTACAGATAGTTT 323981 i vv v v v v iv----- i vv iiv iivi C L1MB2_3end#LI 162 CCTAATGATTAGTGATGTTGAGCATCTTTTCATATGCTTGTTGGCCATTT 113 chr3qtel1M 323982 TGAGTTCTTTATCTGAAAACTGCCTGTTCATATCCTTTGACCATTTATCA 324031 vv vv iv iv i v i i vi v v ? C L1MB2_3end#LI 112 GTATATCTTCTTTGGAGAAATGTCTATTCAAGTCCTTTGCCCATTTTTNA 63 chr3qtel1M 324032 ACTGAG 324037 ii i C L1MB2_3end#LI 62 ATCGGG 57 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.77 CpG sites = 81, Kimura (unadjusted) = 41.96 Transitions / transversions = 1.29 (81/63) Gap_init rate = 0.05 (22 / 467), avg. gap size = 2.18 (48 / 22) 741 28.44 4.32 3.72 chr3qtel1M 323692 324038 (675962) C L1ME5_3end#LINE/L1 (537) 404 56 m_b144s551i12 5403 chr3qtel1M 323692 TCTTTTGGATGTAGGCCTAATAGTGTCACTGTCAGATCAAAGGGT--GCA 323739 v i vi i iv i vv i iii i v -- i C L1ME5_3end#LI 404 TCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATGCG 355 chr3qtel1M 323740 AAGTTTTATATTCTATTGGGCAGAGT---TCCAAATTGCTCTCCAGAATA 323786 ------ i iv v i vi ---v i i C L1ME5_3end#LI 354 ------TATACTTAATTTGACTAAGTACTGCCAGATTGCTCTCCAGAATG 311 chr3qtel1M 323787 GTTGGATCAGTTCACAACTCTACCAACA-TGTATTAGTAT-CCTACTTTT 323834 i v i ii vii i i - i v vi - - ? i C L1ME5_3end#LI 310 GCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTA-TNTC 262 chr3qtel1M 323835 TCCACATTGCCTCCTACATTTATTATTTTCCTATTATTTTGTCATATTAG 323884 i ivi v v i ivi v - --ii v v v v C L1ME5_3end#LI 261 CCCACATCCTCGCCAACACTTGGCATTATCC-A--GCTTTCTAATTTTTG 215 chr3qtel1M 323885 ACAATCTGATCGGTGTCAGGTGATACCTCAGAGATGTTTTAATTTGCATT 323934 v i i v v i i vv v C L1ME5_3end#LI 214 CCAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATT 165 chr3qtel1M 323935 TATCTCCTCAGTAGTGATTTAGAAG-----TTTATATGAGTACAGATAG- 323978 v vv i v i v v iv----- i vv --- v - C L1ME5_3end#LI 164 TCTCTGATTACTAATGAGTTTGAGCATCTCTTCATATGCTT---GTTAGC 118 chr3qtel1M 323979 -TTTTGAGTT-CTTTATCTGAAAACTGCCTGTTCATATCCTTTGACCATT 324026 - i i - i iv v i v C L1ME5_3end#LI 117 CTTTCGGGTTTCCTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCCATT 68 chr3qtel1M 324027 TATCAACTGAGG 324038 v v i i C L1ME5_3end#LI 67 TTTCTATTGGGG 56 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.10 CpG sites = 51, Kimura (unadjusted) = 36.52 Transitions / transversions = 1.16 (51/44) Gap_init rate = 0.06 (21 / 346), avg. gap size = 1.33 (28 / 21) 12 17.67 2.38 4.88 chr3qtel1M 324204 324245 (675755) (CATGTTT)n#Simple_repeat 1 41 (0) m_b144s252i19 5404 chr3qtel1M 324204 CATTTTACATGTTGTGATGCTCTC-TGTATCTTGTTTCATGTT 324245 v v - v - i - v v (CATGTTT)n#Si 1 CATGTTTCATGTT-TCATG-TTTCATGTTTCATGTTTCATGTT 41 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.07 (3 / 41), avg. gap size = 1.00 (3 / 3) 16 13.23 0.00 2.94 chr3qtel1M 325068 325102 (674898) (AAGAGG)n#Simple_repeat 1 34 (0) m_b144s252i20 5405 chr3qtel1M 325068 AAGAGGAAGAAGGAAGAGGAGTAACAAGAGGAAGA 325102 - iv iv (AAGAGG)n#Sim 1 AAGAGGAAG-AGGAAGAGGAAGAGGAAGAGGAAGA 34 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 12 9.71 0.00 0.00 chr3qtel1M 325909 325930 (674070) (TTCT)n#Simple_repeat 1 22 (0) m_b144s252i21 5406 chr3qtel1M 325909 TTATTTCTTTCTTTCCTTCTTT 325930 v i (TTCT)n#Simpl 1 TTCTTTCTTTCTTTCTTTCTTT 22 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 301 25.27 9.89 0.00 chr3qtel1M 327628 327718 (672282) C L2d2_3end#LINE/L2 (34) 521 422 m_b144s601i7 5407 chr3qtel1M 327628 ATTATGTGCTAGGCATTCTACTAAGTGCTA---GGAATACAAAG--GCAA 327672 i i v i v i i i i--- i -- i v C L2d2_3end#LIN 521 ACTGTGTGCAAGGCACTGTGCTAGGCGCTGTGGGGGATACAAAGAAGTAT 472 chr3qtel1M 327673 AAGATA--GCGCTTACCCTCAA--AGCATAAAATCTACTTGGGAAAAAAA 327718 i -- iv i i -- v v v i i v C L2d2_3end#LIN 471 AAGACATGGTCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGGAGACAA 422 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 30.19 CpG sites = 15, Kimura (unadjusted) = 31.86 Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.04 (4 / 90), avg. gap size = 2.25 (9 / 4) 203 33.33 7.14 0.00 chr3qtel1M 327646 327729 (672271) C L2c_3end#LINE/L2 (40) 438 349 m_b144s601i8 5407 chr3qtel1M 327646 TACTAAGTGCTAGGAATACAAAGGCAA--AAGATA--GCGCTTACCCTCA 327691 i i i i i i iii -- i -- iv i i C L2c_3end#LINE 438 TGCCAGGCGCTGGGGATACAAAGATGAATAAGACACGGTCCCTGCCCTCA 389 chr3qtel1M 327692 A--AGCATAAAATCTACTTGGGAAAAAAAATGTGCAAACA 327729 -- vi v i v v i i i v i ii? i C L2c_3end#LINE 388 AGGAGCTCACAGTCTAGTGGAGGAGACAGACANGTAAACA 349 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 47.37 CpG sites = 22, Kimura (unadjusted) = 50.02 Transitions / transversions = 3.67 (22/6) Gap_init rate = 0.04 (3 / 83), avg. gap size = 2.00 (6 / 3) 182 28.57 3.19 3.19 chr3qtel1M 327981 328074 (671926) L3#LINE/CR1 2176 2269 (1830) m_b144s601i9 5408 chr3qtel1M 327981 TCAGAAATAGGACCAAGGACACACACCTAAGGAGAAAGCTGGAATATCAA 328030 ivv vvi i i v i v vvi i ? - L3#LINE/CR1 2176 TCAGAAGATGGAAAGAGGACATATAACCAAGGACAAAGAGAGAGTANCA- 2224 chr3qtel1M 328031 TCCAGCCTGTCAGAAATGGTATCAACAGAGC---AGCTGAGAAAGAG 328074 - v v - i i iv ii --- iv v L3#LINE/CR1 2225 -CAAGCCTGTAAG-AATAGTGTCAGGAAGGCTAAAGCCCAGAATGAG 2269 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.92 CpG sites = 13, Kimura (unadjusted) = 36.92 Transitions / transversions = 1.00 (13/13) Gap_init rate = 0.04 (4 / 93), avg. gap size = 1.50 (6 / 4) 17 17.88 3.70 3.70 chr3qtel1M 329387 329440 (670560) (TCCTCT)n#Simple_repeat 1 54 (0) m_b144s252i22 5409 chr3qtel1M 329387 TCCTGTTCCTCTTCCTCTT-CTC-TACTCTTAAAACTTTCTTCTTTCTCT 329434 v - - v -vvv - i i (TCCTCT)n#Sim 1 TCCTCTTCCTCTTCCTCTTCCTCTTCCTCTT-CCTC-TTCCTCTTCCTCT 48 chr3qtel1M 329435 TCTTCT 329440 i (TCCTCT)n#Sim 49 TCCTCT 54 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.08 (4 / 53), avg. gap size = 1.00 (4 / 4) 545 21.02 1.53 5.56 chr3qtel1M 331912 332042 (667958) MIRc#SINE/MIR 2 127 (141) m_b144s601i10 5410 chr3qtel1M 331912 GAGCTAG-GTTGTACAGTGAATAGAGCACCAGCCCTGAAGTCGGGAAGAC 331960 vi - v i i v ii v i i i MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr3qtel1M 331961 CTGAATTCAAATCTGGTCCCAGACACTTAACACTTCCTAGCTGTGTGACC 332010 ii i i iv v i v v ------- MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTGACC 94 chr3qtel1M 332011 CTGGGCAAGTCACTTAACCTCAATT-GCCTCAG 332042 i vv v- MIRc#SINE/MIR 95 TTGGGCAAGTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 23.88 CpG sites = 15, Kimura (unadjusted) = 24.95 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.07 (9 / 130), avg. gap size = 1.00 (9 / 9) 21 0.00 0.00 0.00 chr3qtel1M 332044 332066 (667934) (A)n#Simple_repeat 1 23 (0) m_b144s252i23 5411 chr3qtel1M 332044 AAAAAAAAAAAAAAAAAAAAAAA 332066 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAA 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 284 32.20 3.30 1.86 chr3qtel1M 332885 333096 (666904) C HERVK11#LTR/ERVK (2761) 5192 4978 m_b144s701i1 5412 chr3qtel1M 332885 CCAACATG--CAGGTCCATTTTCTGTTTTTATTGCCTGTGGTACACCCAT 332932 i i-- vv i v i vvv i v vv C HERVK11#LTR/E 5192 CTAACATATCCAGGGGCGTTGTCTGTCTTTATTTGATATGGAAGCCCCAT 5143 chr3qtel1M 332933 GATTGCAAATGCCTGTGTA-ACAAGTTCAGTGACCACTCGGGCCGTCTCT 332981 i i - vv vi - v v ivv i v---i vi C HERVK11#LTR/E 5142 AACTGCAAA-GCAAGAATACAGATGTTTTTTAACA---TGGGCCGTGCCT 5097 chr3qtel1M 332982 TTTGCTGCT-GATA--TTGCAAAAGTGATTCCTGAAAAGCTGTCTACCAT 333028 iiv i - ii -- v vv ii i vv i v i viv C HERVK11#LTR/E 5096 TCCCCTGTTTGGCAAGTAGCCCAGATAAAACCTGAGAAGGTATCTACAGA 5047 chr3qtel1M 333029 AACATGGATAAAAGACAGACGACCAAAG-ATTTATAATGGGTCACATCCA 333077 v i v v ? v vi - vi vv i C HERVK11#LTR/E 5046 AACATGCACATATGANAGTCTGCCAAAGGAGCTAACATGAGTCACATCCA 4997 chr3qtel1M 333078 CTTGCCAAATTTCATTGGG 333096 i v vv? i C HERVK11#LTR/E 4996 TTTGCCATAAANCATTAGG 4978 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 42.07 CpG sites = 29, Kimura (unadjusted) = 42.88 Transitions / transversions = 0.76 (29/38) Gap_init rate = 0.04 (9 / 211), avg. gap size = 1.22 (11 / 9) 291 33.05 2.47 1.63 chr3qtel1M 334894 335136 (664864) L1PREC2_orf2#LINE/L1 3050 3294 (0) m_b145s551i0 5413 chr3qtel1M 334894 AAAGCCTTTGTACAAACAAAACTAA-TGCAAACAAGATTAGAAGGGAAGC 334942 i i i i i- vv - iiv iii v iv iv v L1PREC2_orf2# 3050 AGAGCTTCTGCACAG-CAAAAGAAACTATCAACAGAGTAAACAGACAACC 3098 chr3qtel1M 334943 AACAAACTGGGAAAACATCTT--CAATTAAAGGTTCTGAAAAAGGCCTCC 334990 v i v i v ? -- viv v vv v i vv L1PREC2_orf2# 3099 TACAGAATGGGAGAAAATNTTTGCAAACTATGCATCTGACAAAGGTCTAA 3148 chr3qtel1M 334991 CTTCCAAAATATATAGAGAATTGACTCAAATTTATAAGAAAT---CAAGC 335037 iv iv v ii i v vv i v--- i L1PREC2_orf2# 3149 TATCCAGCATCTATAAGGAACTTAAACAAATTTACAAGAAAAAAACAAAC 3198 chr3qtel1M 335038 CATTCTCCAATCGATAAACGGTCAAAGGATATGAACAGACAATTTTCAGA 335087 v -- i - ii v ii v i v i L1PREC2_orf2# 3199 AA--CCCCA-TTAAAAAGTGGGCAAAGGACATGAACAGACACTTTTCAAA 3245 chr3qtel1M 335088 TGATGAAATTGAAACTATTACCACTCATATGAAAGAGTGTTCCAAATCA 335136 v v v vv vi viii v vv i iv i v v L1PREC2_orf2# 3246 AGAAGACATACATGCGGCCAACAAGCATATGAAAAAAAGCTCAACATCA 3294 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 44.30 CpG sites = 37, Kimura (unadjusted) = 44.30 Transitions / transversions = 0.88 (37/42) Gap_init rate = 0.03 (7 / 242), avg. gap size = 1.43 (10 / 7) 342 29.38 2.34 1.39 chr3qtel1M 334923 335136 (664864) L1M5_orf2#LINE/L1 3079 3294 (0) m_b145s551i1 5413 chr3qtel1M 334923 AACAAGATTAGAAGGGAAGCAACAAACTGGGA--AAACATCTTCAATTAA 334970 v i v i v v i ? -- i i v ?- v L1M5_orf2#LIN 3079 AAGAAAATGAAAAGGCAAGCCACAGANTGGGAGAAAATATTTGCAAN-AC 3127 chr3qtel1M 334971 AGGT-TCTGAAAAAGGCCTCCCTTCCAAAATATATAGAGAATTGACTCAA 335019 vi - v v viv i i i vviv L1M5_orf2#LIN 3128 ATATATCTGACAAAGGACTCGTATCCAGAATATATAAAGAACTCCTACAA 3177 chr3qtel1M 335020 ATTTATAAGAAATCAAGCCATTC--TCCAATCGATAAACGGTCAAAGGAT 335067 ? iv ? -- v vv --i v? v i v i i L1M5_orf2#LIN 3178 NTCAATAANAAA--AAGACAAACAACCCAATANAAAAATGGGCAAAAGAC 3225 chr3qtel1M 335068 ATGAACAGACAATTTTCAGATGATGAAATTGAAACTATTACCACTCATAT 335117 v v iv i v v v ?v iviii vi vv i L1M5_orf2#LIN 3226 TTGAACAGACACTTCACAAAAGAAGATATNCAAATGGCCAATAAGCACAT 3275 chr3qtel1M 335118 GAAAGAGTGTTCCAAATCA 335136 iii i v v? L1M5_orf2#LIN 3276 GAAAAGATGCTCAACNTCA 3294 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.23 CpG sites = 28, Kimura (unadjusted) = 39.23 Transitions / transversions = 0.82 (28/34) Gap_init rate = 0.03 (6 / 213), avg. gap size = 1.33 (8 / 6) 1541 29.01 1.75 1.91 chr3qtel1M 334998 335626 (664374) L1ME4c_3end#LINE/L1 12 639 (191) m_b145s551i2 5413 chr3qtel1M 334998 AATATATAGAGAATTGACTCAAATTTATAAGAAA----TCAAGCCATTCT 335043 ? i ii v i v ---- v ----i L1ME4c_3end#L 12 ANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAAGAC----C 57 chr3qtel1M 335044 CCAATCGATAAACGGTCAAAGGATATGAACAGACAATTTTCAGATGATGA 335093 v i v i iv ? v v L1ME4c_3end#L 58 CCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAGGA 107 chr3qtel1M 335094 AATTGAAACTATTACCACTCATATGAAAGAGTGTTCCAAATCACTATTAA 335143 vv ?ivi v v vv i i i i v vv i v L1ME4c_3end#L 108 AATACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTAGTAA 157 chr3qtel1M 335144 TCAGAG-AATGCAAATTAAGACAACTCTGAGATACCACTACACACCTGTC 335192 i - ii vv i vi i i i L1ME4c_3end#L 158 TCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCTATT 207 chr3qtel1M 335193 AGATTGGCTAAGATGACAGGGAAAAAATAATGATG---AATGTTGGAGGG 335239 i i v i ----vvi v i i i--- i v i L1ME4c_3end#L 208 AAATTAGCAAAAAT----TTAAAAAATTGATAATACCCAATGCTGGCGAG 253 chr3qtel1M 335240 GATGCGGGAAAACTTGGACACTGATGCATTGTTGGTGGAGTTGTGAACGA 335289 ? vi v v ? v i i vi? i ivi L1ME4c_3end#L 254 GNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTG 303 chr3qtel1M 335290 ATCCAACCATTCTGGAGAGAAATATGGAATTATGCCCAAAAAGTAATCAA 335339 i v v i i v v v v i iviv i iv v L1ME4c_3end#L 304 GTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAA 353 chr3qtel1M 335340 ACTGTGCATACCCTTTGACGCAGCAGTGCTACTACTGGGCTTATACCACA 335389 v v v i i v i v vv v i vi L1ME4c_3end#L 354 AATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTA 403 chr3qtel1M 335390 AGGACATA---CTAAAGAAGGGAAAAGGACCTATATGTGCCAAAATGTTT 335436 v --- v i --- ii v i i L1ME4c_3end#L 404 AGGAAATAATTCAAAAGAAGGAAAAAG---CTATATGCACGAAGATGTTC 450 chr3qtel1M 335437 GTGGCAGCCCTGTTTGTAGTGGCTAGAAACTGGAAAATGAATGGATGCCC 335486 i v vi i i i i v i i vvivv ii i L1ME4c_3end#L 451 ATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCC 500 chr3qtel1M 335487 ATCAATTGGAGAATGATTGAGTAAATTGTGGTATACAAATGTTATGGAAT 335536 v v i i i i i iv? iviv L1ME4c_3end#L 501 AACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAAT 550 chr3qtel1M 335537 AATATTTTTCTGTAAGAAATGACCAGCACATAGAATACAGAGAGGCTTGG 335586 v vivv ii v i iv vi iiv v iiv vii v L1ME4c_3end#L 551 ATTATGCAGCCATTAAAAATGATAATTATGAAGACTATGTAGCAACATGG 600 chr3qtel1M 335587 AGAGACTTACATGAACTGATGCTAAGTGAAATGAGCAGAA 335626 - i iv vi vv i i vi L1ME4c_3end#L 601 A-AAATGTTTATGATATAATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.81 CpG sites = 95, Kimura (unadjusted) = 37.87 Transitions / transversions = 1.13 (95/84) Gap_init rate = 0.03 (16 / 628), avg. gap size = 1.44 (23 / 16) 729 28.27 2.70 4.40 chr3qtel1M 336314 336683 (663317) C HERVK14C#LTR/ERVK (4226) 3208 2845 m_b145s701i1 5414 chr3qtel1M 336314 CCAGAGGGATAGAATAGAAACAATCCTTAATATGTATAACCCACAGAGGT 336363 i i v v i i v v v ivvi i? i C HERVK14C#LTR/ 3208 CTAGAGGAATAGTAAAGAAGCAGTCCTTCAAATCTATAACTATTAANGGC 3159 chr3qtel1M 336364 CATTCCCTAGGCAACTGAGTAAGGGATGGAAGCCCAGGCTAAAGAGTTCC 336413 v i v v vvi iii ? v v iv ? ii C HERVK14C#LTR/ 3158 CAGTCTCTAGGAATCATGGCGGGGGANGGCAGCCCTGGCTGCAGNGCCCC 3109 chr3qtel1M 336414 CATAGTTTCCAT--CTGTTCATTCACTTTTCTCAAATCAGTCAATATCCT 336461 ? v v? -- -- v vvi vi i i i ii ? v C HERVK14C#LTR/ 3108 CATNGGTTGNATGACTG--CATTGACGGCTCGTAAGTCGGTTAGCATNCG 3061 chr3qtel1M 336462 CCATTTTCCAGATTTCTTTTATAGAGCAAAATACAAGGGAATTGCAAGGA 336511 i v i i i v? vvi -i vi ? v ? C HERVK14C#LTR/ 3060 CCATCTGCCGGATTTTTTCTTNATTACAAA-CACTGGNGAATTCCANGGA 3012 chr3qtel1M 336512 CTTAGAGAA----GGTTGAAAGTGTCCTTGGTCAAGTTGCTCCTGTACTA 336557 ---- i ---- i v? v v? v i i i vv C HERVK14C#LTR/ 3011 ----GAAAATGTGGGCTCNATGTGTCCTTTNTCTAATTGTTCTTTGACTA 2966 chr3qtel1M 336558 TATCTAATAAGACCTG-AATTTTTCCTGGGTAAG-GGCCACTGTTCCACC 336605 vv ivi i iv- i i ?? - ? ? C HERVK14C#LTR/ 2965 ATTCCTGTAAGGCCCCCAGTTTTTCCTGAGNNAGCGGCCACTGNTCNACC 2916 chr3qtel1M 336606 C--ACTGTTGTATCAATTTTCAGTTAGAAGGGAATAGAGGTAAGGGTTGG 336653 -- ? v?v v vii i? vi vv ------ ?vi C HERVK14C#LTR/ 2915 CAAACNGGNTTTTGGGTCNTCCATTTTAAGGGAATAG------GNTCTGG 2872 chr3qtel1M 336654 CAGACATTCAGCAGCAGCCCTGACTAAAAA 336683 - i -- i ii vivv C HERVK14C#LTR/ 2871 -AGGC--TCAACAGTGGCCGCCCCTAAAAA 2845 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.11 CpG sites = 51, Kimura (unadjusted) = 38.61 Transitions / transversions = 1.04 (51/49) Gap_init rate = 0.06 (21 / 369), avg. gap size = 1.24 (26 / 21) 416 11.24 11.11 1.12 chr3qtel1M 337988 338068 (661932) C U6#snRNA (0) 107 19 m_b145s502i0 5415 chr3qtel1M 337988 AAAAATATGGAGTCACTTCATGAATTT---TGTCATCCTTCTGC-GGGAC 338033 i- i i --- vi - i C U6#snRNA 107 AAAAATATGGAA-CGCTTCACGAATTTGCGTGTCATCCTTGCGCAGGGGC 59 chr3qtel1M 338034 CATGCTAATCTT-----TATCATTCCAATTTTAATAAATG 338068 ----- i i v C U6#snRNA 58 CATGCTAATCTTCTCTGTATCGTTCCAATTTTAGTATATG 19 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 7.11 CpG sites = 7, Kimura (unadjusted) = 12.44 Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.05 (4 / 80), avg. gap size = 2.50 (10 / 4) 37 2.86 0.00 0.00 chr3qtel1M 339740 339775 (660225) (GT)n#Simple_repeat 1 36 (0) c_b145s251i0 5416 chr3qtel1M 339740 GTGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 339775 i (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 36 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 27 0.00 0.00 3.45 chr3qtel1M 339967 339996 (660004) (TCC)n#Simple_repeat 1 29 (0) c_b145s251i1 5417 chr3qtel1M 339967 TCCTCCTCCTCCTCCTCCTTCCTCCTCCTC 339996 - (TCC)n#Simple 1 TCCTCCTCCTCCTCCTCC-TCCTCCTCCTC 29 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 157 13.17 4.76 3.31 chr3qtel1M 340000 340356 (659644) (CTT)n#Simple_repeat 1 362 (0) m_b145s252i0 5418 chr3qtel1M 340000 CTCCTT-TTCTTCTTGTTCTTCTTCTTTTTCTTCTTCTTCTTCTTCTTCT 340048 i - v i (CTT)n#Simple 1 CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCT 50 chr3qtel1M 340049 TCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTGCCTCTGCTTCTTC 340098 v i v (CTT)n#Simple 51 TCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTC 100 chr3qtel1M 340099 TGCTTCTT-TTC-TCTT-TTCTTCCTCTT-TTCTTACCTTCCCTCTCTCT 340144 v - - - i - -- - i - (CTT)n#Simple 101 TTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTT--CTT-CTTCT-TCT 146 chr3qtel1M 340145 CCTCTCTTCTTCCTC-TCCTCCTCTCTCTTCTTCTTCTTCTTCTTCTTCT 340193 i - i - i i - (CTT)n#Simple 147 TCT-TCTTCTTCTTCTTCTTCTTCT-TCTTCTTCTTCTTCTTCTTCTTCT 194 chr3qtel1M 340194 T-TTC-TCTTC-TCTT-TTCTTCCTCTTCTT-TTTTCCTTC-ACCTCTTC 340237 - - - - i - i i -v i (CTT)n#Simple 195 TCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTC 244 chr3qtel1M 340238 TTCCTCTCTCTTCTT-TGCTT-TTCCTCCT-TTCTCTCATTTCCTTCTCT 340284 i - - v - i i - - v i i - (CTT)n#Simple 245 TTCTTCT-TCTTCTTCTTCTTCTTCTTCTTCTTCT-TCTTCTTCTTCT-T 291 chr3qtel1M 340285 CTTCTCCCTCTCCTT-TTCTCTCCTCCTCATCTTTCTTCCTTC-TCTTCA 340332 i i i - - i i v - - - v (CTT)n#Simple 292 CTTCTTCTTCTTCTTCTTCT-TCTTCTTCTTC-TTCTT-CTTCTTCTTCT 338 chr3qtel1M 340333 ACTTGTATTCCTTCATTTACTTCT 340356 v v vi i v i v (CTT)n#Simple 339 TCTTCTTCTTCTTCTTCTTCTTCT 362 Matrix = Unknown Transitions / transversions = 1.86 (26/14) Gap_init rate = 0.08 (29 / 356), avg. gap size = 1.00 (29 / 29) 32 9.02 1.49 6.25 chr3qtel1M 340401 340467 (659533) (AAT)n#Simple_repeat 1 64 (0) m_b145s252i1 5419 chr3qtel1M 340401 AATAATAATCAAAATAATAATAATATATCAATAAT-CTAATAATAATAAG 340449 v v - - -v v (AAT)n#Simple 1 AATAATAATAATAATAATAATAATA-AT-AATAATAATAATAATAATAAT 48 chr3qtel1M 340450 ATCTAATAATAAGTAATA 340467 -v - (AAT)n#Simple 49 A-ATAATAATAA-TAATA 64 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.08 (5 / 66), avg. gap size = 1.00 (5 / 5) 13 5.27 0.00 0.00 chr3qtel1M 340526 340545 (659455) (AAC)n#Simple_repeat 1 20 (0) m_b145s252i2 5420 chr3qtel1M 340526 AACAACAACAACAACAATAA 340545 i (AAC)n#Simple 1 AACAACAACAACAACAACAA 20 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 410 29.86 3.82 1.88 chr3qtel1M 340588 340744 (659256) C MIR#SINE/MIR (30) 232 73 m_b145s601i0 5421 chr3qtel1M 340588 TATGTATACATACATTTTTGCATAATATTTTATACTTATCTTCCCATTAT 340637 ii- vi i v vi - iiii i iv ivv i vv C MIR#SINE/MIR 232 TATGTGC-CAGGCACTGTTCTA-AGCGCTTTACATGTATTAACTCATTTA 185 chr3qtel1M 340638 ATTTTCACAGC----TTAGGAA-TCAGTATGATTATAATCCTTACTTTAC 340682 ii i ----i v i- vi iv v ii i C MIR#SINE/MIR 184 ATCCTCACAACAACCCTATGAGGTAGGTACTATTATTATCCCCATTTTAC 135 chr3qtel1M 340683 AGATGAGGAAATTCAGGGAAACAGAAGTTAAGTGGATT-CCCAACGGTCC 340731 i v v v v i iiv - - v C MIR#SINE/MIR 134 AGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCCAA-GGTCA 86 chr3qtel1M 340732 CACACCTAGTAAG 340744 v C MIR#SINE/MIR 85 CACAGCTAGTAAG 73 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.99 CpG sites = 27, Kimura (unadjusted) = 39.21 Transitions / transversions = 1.42 (27/19) Gap_init rate = 0.04 (6 / 156), avg. gap size = 1.50 (9 / 6) 331 27.42 0.00 3.57 chr3qtel1M 340779 340865 (659135) MIRc#SINE/MIR 37 120 (148) m_b145s601i1 5422 chr3qtel1M 340779 TGAAAGCAGGAGGACCTCAGTTCAAATCCAGGCTGAGACACTTGCTAGCT 340828 i iv i vi i i v vv v i MIRc#SINE/MIR 37 TGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCT 86 chr3qtel1M 340829 GTGTATATTTAGACAAAATGACTTAATTTTGCTCTGA 340865 ivvi i i - i v ii -- MIRc#SINE/MIR 87 GTGTGACCTTGGGC-AAGTCACTTAACCT--CTCTGA 120 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.18 CpG sites = 14, Kimura (unadjusted) = 35.06 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.03 (3 / 86), avg. gap size = 1.00 (3 / 3) 16 24.13 2.90 4.41 chr3qtel1M 341112 341180 (658820) (CAAAG)n#Simple_repeat 1 68 (0) m_b145s252i3 5423 chr3qtel1M 341112 CAGAGGAAAGGAAAGGGAAG-GAA-CAAAGGCAAGGCAAAGCAAAGCACA 341159 i v v vi -i - - i v (CAAAG)n#Simp 1 CAAAGCAAAGCAAAGCAAAGCAAAGCAAA-GCAAAGCAAAGCAAAGCAAA 49 chr3qtel1M 341160 TCATGTACAGAGCAATAGCAA 341180 v -ivi i - (CAAAG)n#Simp 50 GCA-AAGCAAAGCAA-AGCAA 68 Matrix = Unknown Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.07 (5 / 68), avg. gap size = 1.00 (5 / 5) 17 11.00 4.88 2.38 chr3qtel1M 341115 341155 (658845) (AGGAA)n#Simple_repeat 1 42 (0) m_b145s252i4 5424 chr3qtel1M 341115 AGGAAAGGAAAGGGAAGG-AA-CAAAGGCAAGGCAAAGCAAAG 341155 i - -v v - v (AGGAA)n#Simp 1 AGGAAAGGAAAGGAAAGGAAAGGAAAGGAAAGG-AAAGGAAAG 42 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.07 (3 / 40), avg. gap size = 1.00 (3 / 3) 11 24.50 2.22 2.22 chr3qtel1M 341648 341692 (658308) (GGAGTT)n#Simple_repeat 1 45 (0) m_b145s252i5 5425 chr3qtel1M 341648 GGAG-TGGATTTGGAGTTTGAGGTGGCACTGGTGTTAGAATTAGGA 341692 - v v v vii v i i - (GGAGTT)n#Sim 1 GGAGTTGGAGTTGGAGTTGGAGTTGGAGTTGGAGTTGGAGTT-GGA 45 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.05 (2 / 44), avg. gap size = 1.00 (2 / 2) 631 28.82 6.27 4.71 chr3qtel1M 342643 343312 (656688) L1M5_orf2#LINE/L1 2615 3294 (0) m_b145s551i3 5426 chr3qtel1M 342643 TACCAGATCTAAA-----ATTATAAAGCAGCAGTTACCAAAACCATTTTG 342687 ? ? v ----- vi v i i vi v v L1M5_orf2#LIN 2615 TACCNGATNTCAAGACTTATTATAAAGCTACAGTAATCAAGACAGTGTGG 2664 chr3qtel1M 342688 TATTGGC-TAAGAAATAAAC---TAGATGAACAATGAAATAGATTAG--- 342730 - i - i --- --- i i v --- L1M5_orf2#LIN 2665 TATTGGCGTAAGGA-TAGACAAATAGAT---CAATGGAACAGAATAGAGA 2710 chr3qtel1M 342731 GTTCAAAGGACAAAGCAGCTAATAATCTTAATAATGTAGTGTTTGGCAAA 342780 i i i- i i v vi vv - v vi?i ? - ii v i L1M5_orf2#LIN 2711 GTCCAGAA-ATAGACCCACACATA-TATGGNCANT-TGATTTTTGACAAA 2757 chr3qtel1M 342781 C---CCAAAGACCCCAGTTT--TTGGGATAAGAC---CTCACGATTTGAC 342822 v--- ? ---- i i-- v v i i--- i---- ii L1M5_orf2#LIN 2758 GGTGCCAANG----CAATTCAGTGGGGAAAGGATAGTCTT----TTCAAC 2799 chr3qtel1M 342823 AAAAATTGCTGGGAAAATTGGAAATTAGTGTGGCAGAAA-CGAGGCATTG 342871 viv i v v ivi i v i -i i? - i L1M5_orf2#LIN 2800 AAATGGTGCTGGAACAATTGGATATCCATATGGAAAAAAATGAANC-TCG 2848 chr3qtel1M 342872 ACCCACACTTAACACCATACACCAAGATAAGGTCAAAATGGGTTCAT-GA 342920 vi i v v i v iv ? i i - - L1M5_orf2#LIN 2849 ACCCCTACCTCACACCATACACAAAAATTAATTCNAGATGGAT-CATAGA 2897 chr3qtel1M 342921 CCTAGGCATTAAGAATGAGATTATAAATAAATTGGAAGAG--CATAGGAT 342968 iiii v ii? i i i vvvvi i i-- v L1M5_orf2#LIN 2898 CCTAAATGTAAAAGNTAAAACTATAAAACTTCTAGAAGAAAACATAGGAG 2947 chr3qtel1M 342969 AGTTTACCTTTCAGACCTGTGGAAGAGGAACGAATTTATGACCAAAGAAA 343018 i -- i ivv - i?v v vii v ---i v ii L1M5_orf2#LIN 2948 AAT--ATCTTCGTGACCT-TGGGNTAGGCAAAGATTTCT---TAAACAGG 2991 chr3qtel1M 343019 AACTAGAGATCATTATTGATCACAAAATAGAAAATT-------TTGATTA 343061 vvi i i v i? --- i i v i ------- v i ? L1M5_orf2#LIN 2992 ACACAAAAAGCACNA---ACCATAAAAGAAAAAATTGATAAATTGGACTN 3038 chr3qtel1M 343062 TATCAAATTGAAAAGTTTTTG---TACAAACAAAAC---TAATGCAGACA 343105 i v v ii i ---?v vi v --- - v i ii L1M5_orf2#LIN 3039 CATCAAAATTAAAAACTTCTGCTCNTCAAAAGACACCGTTAA-GAAAATG 3087 chr3qtel1M 343106 AGAAGGGAAGCAATAAAGTGGGAAAACATTTTTACAGTCAAAGGT-TCTG 343154 i v v i i ? i v v i i?- v vi - L1M5_orf2#LIN 3088 AAAAGGCAAGCCACAGANTGGGAGAAAATATTTGCAAN-ACATATATCTG 3136 chr3qtel1M 343155 AAGAAGGCCTCATTTCCAAAATATATAGAGAATTGACTCTAATTTA-TAA 343203 vi v i v i i i v- vi ? i - L1M5_orf2#LIN 3137 ACAAAGGACTCGTATCCAGAATATATAAAGAACTC-CTACAANTCAATAA 3185 chr3qtel1M 343204 GAAAT---CAAACCATTCTCCAGTTGATAAATGGTCAAAGGATATGCACA 343250 ? v--- v i--- i v? v v i iv v L1M5_orf2#LIN 3186 NAAAAAGACAAACAAC---CCAATANAAAAATGGGCAAAAGACTTGAACA 3232 chr3qtel1M 343251 GACAATTCTCAGATGAAGAAATTGAAACTATTTCTAGCCACTTGAAAAGA 343300 v v i v v ?v iviiivv iv v L1M5_orf2#LIN 3233 GACACTTCACAAAAGAAGATATNCAAATGGCCAATAAGCACATGAAAAGA 3282 chr3qtel1M 343301 TGCTCTAAGTCA 343312 v v? L1M5_orf2#LIN 3283 TGCTCAACNTCA 3294 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.89 CpG sites = 102, Kimura (unadjusted) = 38.69 Transitions / transversions = 1.24 (102/82) Gap_init rate = 0.07 (48 / 669), avg. gap size = 1.54 (74 / 48) 784 31.12 4.95 4.14 chr3qtel1M 343169 343815 (656185) L1MC2_3end#LINE/L1 7 658 (433) m_b145s551i5 5426 chr3qtel1M 343169 TCCAAAATATATAGAGAA---TTGACTCTAATTTATAAGAAATCAAACCA 343215 i i --- i vv v viv v v L1MC2_3end#LI 7 TCCAAAATATACAAAGAACTCTTAAAACTCAACAATAAGAAAACAAACAA 56 chr3qtel1M 343216 TTCTCCAGTTGATAAATGGTCAAAGGATATGCACAGACAATTCTCAGATG 343265 i--- i ? v v i v v vi v vi v L1MC2_3end#LI 57 C---CCAATTNAAAAATGGGCAAAAGATCTGAACAGACACCTCACCAAAG 103 chr3qtel1M 343266 AAGAAATTGAAACTATTTCTAGCCACTTGAAAAGATGCTCTAAGTCATTA 343315 v vv i iviivvv iv iv v vi - L1MC2_3end#LI 104 AAGATATACAGATGGCAAATAAGCATATGAAAAGATGCTCAACATCA-TA 152 chr3qtel1M 343316 T-TAATCAAAGAAATGCAAATTAAGACAACTCTGAGATATGACTATACAC 343364 - v i ii v i vv iv i L1MC2_3end#LI 153 TGTCATTAGGGAATTGCAAATTAAAACAACAATGAGATACCACTACACAC 202 chr3qtel1M 343365 TTGTCAGATTGGCTAGAATGACAGGGAAAAATAATGCGCAATGTTGGAGG 343414 i i i v i vvv iiv vvi i ii vv i v i L1MC2_3end#LI 203 CTATTAGAATGGCTAAAATCCAAAACACTGACAACACCAAATGCTGGCGA 252 chr3qtel1M 343415 GGCTGTGGAA-AACTGCGACAATGATACATTGTTGGTGGAATAATACA-- 343461 v i- v vi vv v v i i-- i -- L1MC2_3end#LI 253 GGATGTGGAGCAACAGGAACTCTCATTCATTGCTGGTGGG--AATGCAAA 300 chr3qtel1M 343462 ----TCTAGGCATTCTAGAGAGCAATTTGGAACTATGCTCAAAAAGCT-A 343506 ---- vi v i i i iii i v v - v i v - L1MC2_3end#LI 301 ATGGTACAGCCACTTTGGAAGACAGTTTGGCAGT-TTCTTACAAAGCTAA 349 chr3qtel1M 343507 TCAAACTCTGCATACCCTTTCATCCAGCAGTGTTACTACTGGGCTTATAT 343556 v v ? --- v viv i vvii v v iv v i L1MC2_3end#LI 350 ACATANTCT---TACCATACGATCCAGCAATCGCGCTCCTTGGTATTTAC 396 chr3qtel1M 343557 CCCAAAGAGATTTTAAAGA---AGG----GAGAGGGACCTGTATATGCAA 343599 v v --- i i --- v ----v v iii i ---- v L1MC2_3end#LI 397 CCAAATGAG---TTGAAAACTTATGTCCACACAAAAACCTGCA----CAC 439 chr3qtel1M 343600 GAATGTTTGTGGCAGTCCTCATT-GTAGTGTCCAGAAAGTGGA---AACT 343645 i i - i i -i i vv i vv --- i L1MC2_3end#LI 440 GAATGTTTATAGCAG-CTTTATTCATAATTGCCAAAACTTGGAAGCAACC 488 chr3qtel1M 343646 GAGTGGATGCCCATCAATTGGAGAATAGCTGAATGAATTGTGGTATATGA 343695 i --- i v v v i v i ii i i vv L1MC2_3end#LI 489 AA---GATGTCCTTCAATAGGTGAATGGATAAACAAACTGTGGTACATCC 535 chr3qtel1M 343696 ATATTATGGAATATTATTGTTCTGT---AAGAAATGA-CCAACAGGGTGA 343741 iv vvv vi --- - i v i vii- L1MC2_3end#LI 536 ATACAATGGAATATTATTCAGCGATAAAAAGAAATGAGCTATCAAGCCA- 584 chr3qtel1M 343742 TGTCAGAAAGGCCTGGAGAGACT-----TACATGTTGAGGAGTGAAATGA 343786 --- ii i v ii i----- i i vvi vi L1MC2_3end#LI 585 ---CGAAAAGACATGGAGGAACCTTAAATGCATATTGCTAAGTGAAAGAA 631 chr3qtel1M 343787 GCAGCACTAGGAAATCATTATATACTTTA 343815 -- v vv vvii i v L1MC2_3end#LI 632 GC--CAGTCTGAAAAGGCTACATACTGTA 658 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.07 CpG sites = 95, Kimura (unadjusted) = 40.91 Transitions / transversions = 0.97 (95/98) Gap_init rate = 0.06 (40 / 646), avg. gap size = 1.48 (59 / 40) 1296 29.22 1.47 1.85 chr3qtel1M 343169 343712 (656288) L1ME3G_3end#LINE/L1 7 548 (376) m_b145s551i4 5426 chr3qtel1M 343169 TCCAAAATATATAGAGAATTGACTCTAATTTATAAGAAATCAAACCATTC 343218 i i i vviv v iv -- iv --v L1ME3G_3end#L 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAA--AAGACA--A 52 chr3qtel1M 343219 TCCAGTTGATAAATGGTCAAAGGATATGCACAGACAATTCTCAGATGAAG 343268 i i v v v v i v v i L1ME3G_3end#L 53 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chr3qtel1M 343269 AAATTGAAACTATTTCTAGCCACTTGAAAAGATGCTCTAAGTCATTATTA 343318 vv iviiivv iv iv v vv i v L1ME3G_3end#L 103 AAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTA 152 chr3qtel1M 343319 ATCAAAGAAATGCAAATTAAGACAACTCTGAGATATGACTATACACTTGT 343368 ii i vv iv i v v iii L1ME3G_3end#L 153 ATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCAT 202 chr3qtel1M 343369 CAGATTGGCTAGAATGACAGGGAAAAATAATGCGCAATGTTGGAGGGGCT 343418 v i vvv ii ?vvi iiv? i v i v L1ME3G_3end#L 203 CAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGT 252 chr3qtel1M 343419 GT-GGAAAACTGCGACAATGATACATTGTTGGTGGAATAATACATC---- 343463 - i v vv vv v i i i vvi v i---- L1ME3G_3end#L 253 GTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTA 302 chr3qtel1M 343464 TAGGCATTCTAGAGAGCAATTTGGAACTATGC-TCAAAAAGCTATCAAAC 343512 i v ? i i i v v vi- i --- - i v L1ME3G_3end#L 303 CAGCCNTTTTGGAGGGCAATTTGGCAGTATCTATTAAAA---T-TTAAAA 348 chr3qtel1M 343513 TCTGCATACCCTTTCATCCAGCAGTGTTACTACTGGGCTTATATCCCAAA 343562 vi v i i vii v ? ?v v i ? L1ME3G_3end#L 349 TGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANA 398 chr3qtel1M 343563 GAGAT-TTTAAAGAAG-GGAGAGGGACCTGTATATGCAAGAATGTTTGTG 343610 i -i iiv v v - v v i --? i i i i ii v L1ME3G_3end#L 399 GAAATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTCATT 446 chr3qtel1M 343611 GCAGTCCTCATTGTAGTGTCCAGAAAGTGGAAACTGAGTGGATGCCCATC 343660 ivi vv i iv v i v vivv ii i L1ME3G_3end#L 447 GCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATC 496 chr3qtel1M 343661 AATTGGAGAATAGCTGAATGAATTGTGGTATATGAATATTATGGAATATT 343710 v i i i i i i vv i i L1ME3G_3end#L 497 AATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACT 546 chr3qtel1M 343711 AT 343712 L1ME3G_3end#L 547 AT 548 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.55 CpG sites = 80, Kimura (unadjusted) = 38.20 Transitions / transversions = 1.05 (80/76) Gap_init rate = 0.03 (15 / 543), avg. gap size = 1.20 (18 / 15) 12 18.27 5.41 0.00 chr3qtel1M 344080 344116 (655884) (TATACT)n#Simple_repeat 1 39 (0) m_b145s252i6 5427 chr3qtel1M 344080 TATACATATA-TTGTATTTA-ACTTATACTTTAACATAT 344116 v - i i - vv v (TATACT)n#Sim 1 TATACTTATACTTATACTTATACTTATACTTATACTTAT 39 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 185 30.61 0.00 0.00 chr3qtel1M 344370 344418 (655582) C L2c_3end#LINE/L2 (45) 433 385 m_b145s601i2 5428 chr3qtel1M 344370 GGCACTGGGCATACAAAGACAAACAAAAAACACTCTGTGCTGTTGAGGA 344418 i v ii i i v iv iv iv ii C L2c_3end#LINE 433 GGCGCTGGGGATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGA 385 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.41 CpG sites = 10, Kimura (unadjusted) = 41.39 Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 21 22.24 5.62 3.30 chr3qtel1M 345104 345192 (654808) (ATGT)n#Simple_repeat 1 91 (0) m_b145s252i7 5429 chr3qtel1M 345104 ATGTATGTGACATATTTGTGTCTCTATGTTTGTAACATAGGTA--TATGT 345151 - ii v i v v v - ii v -- (ATGT)n#Simpl 1 ATGTATGT-ATGTATGTATGTATGTATGTATGT-ATGTATGTATGTATGT 48 chr3qtel1M 345152 ATGTATCTA--TATGTGTGTATGTAAGTGTAT-TGTAATGTCTG 345192 v -- i v i i - - v (ATGT)n#Simpl 49 ATGTATGTATGTATGTATGTATGTATGTATGTATGT-ATGTATG 91 Matrix = Unknown Transitions / transversions = 1.00 (8/8) Gap_init rate = 0.07 (6 / 88), avg. gap size = 1.33 (8 / 6) 383 29.71 3.79 4.29 chr3qtel1M 345614 345824 (654176) C HERVK11#LTR/ERVK (2766) 5187 4978 m_b145s701i2 5430 chr3qtel1M 345614 ATATACAGGTCCATTGTCTGTTTTTATTGGTTGTGGCACACCCATAATTG 345663 v vv i i v v i v vv i C HERVK11#LTR/E 5187 ATATCCAGGGGCGTTGTCTGTCTTTATTTGATATGGAAGCCCCATAACTG 5138 chr3qtel1M 345664 CAAATGCTTGTATAAGGAATTCA-ATGACC----ACTCGGGCTGTCTCTT 345708 - ------- i v - vii---- vi i vi C HERVK11#LTR/E 5137 CAAA-GC-------AAGAATACAGATGTTTTTTAACATGGGCCGTGCCTT 5096 chr3qtel1M 345709 TTGCTGCT-GGTA--TTGCAAAAGTGAATCCTGAAAAGGTGTCTACTACA 345755 iiv i - i -- v vv ii i v i i viv C HERVK11#LTR/E 5095 CCCCTGTTTGGCAAGTAGCCCAGATAAAACCTGAGAAGGTATCTACAGAA 5046 chr3qtel1M 345756 ACATGGATAAAAGATAAATGACCAAAAATATTTATAATGGCTCACATCCA 345805 v i v v ? ivivi ii- vi vv iv C HERVK11#LTR/E 5045 ACATGCACATATGANAGTCTGCCAAAGG-AGCTAACATGAGTCACATCCA 4997 chr3qtel1M 345806 TTTGCCAAATTTCATTGGG 345824 v vv? i C HERVK11#LTR/E 4996 TTTGCCATAAANCATTAGG 4978 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.12 CpG sites = 29, Kimura (unadjusted) = 38.72 Transitions / transversions = 0.94 (29/31) Gap_init rate = 0.06 (13 / 210), avg. gap size = 1.31 (17 / 13) 12 24.24 3.51 3.51 chr3qtel1M 348096 348152 (651848) (ATTTTAA)n#Simple_repeat 1 57 (0) m_b145s252i8 5431 chr3qtel1M 348096 ATTTTGATTTTTCTTATTTTACA-TTTAAGTTTTAAATAAATAAA-TATA 348143 i v -vv v - i -vv - v (ATTTTAA)n#Si 1 ATTTTAAATTTT-AAATTTTAAATTTTAAATTTTAAAT-TTTAAATTTTA 48 chr3qtel1M 348144 ATTTTGAAA 348152 v v (ATTTTAA)n#Si 49 AATTTTAAA 57 Matrix = Unknown Transitions / transversions = 0.22 (2/9) Gap_init rate = 0.07 (4 / 56), avg. gap size = 1.00 (4 / 4) 552 13.18 5.43 1.04 chr3qtel1M 351191 351282 (648718) C U6#snRNA (0) 107 12 m_b145s502i1 5432 chr3qtel1M 351191 AAAAATATGGAGCACTTTCATGAATTTGTGTGTCATCCTTGTGCAGGGTC 351240 i i - i i i v C U6#snRNA 107 AAAAATATGGAACGCTT-CACGAATTTGCGTGTCATCCTTGCGCAGGGGC 59 chr3qtel1M 351241 TATGCTAA-----TCTGGACCATTCCAATTTTAGTATATGAGCTACC 351282 i ----- v i i v i C U6#snRNA 58 CATGCTAATCTTCTCTGTATCGTTCCAATTTTAGTATATGTGCTGCC 12 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 8.78 CpG sites = 9, Kimura (unadjusted) = 14.82 Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.02 (2 / 91), avg. gap size = 3.00 (6 / 2) 16 13.24 0.00 0.00 chr3qtel1M 352560 352584 (647416) (AC)n#Simple_repeat 1 25 (0) m_b145s252i9 5433 chr3qtel1M 352560 ACACACACACACATACCCACATACA 352584 i v i (AC)n#Simple_ 1 ACACACACACACACACACACACACA 25 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 219 36.57 4.48 0.00 chr3qtel1M 352593 352726 (647274) C MIR#SINE/MIR (51) 211 72 m_b145s601i3 5434 chr3qtel1M 352593 AATGTTTTATAGCTATCTTCCCTTTTTATTTTCACAAT----TTGGGAAT 352638 ii i i vv ivv i v v ii i----i iv iv C MIR#SINE/MIR 211 AGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGG 162 chr3qtel1M 352639 T-GGTATAATTATAATACTCACGTTACAAATATGGAAACTCAGGGA-AGA 352686 - iv v v i iv i iv v v - C MIR#SINE/MIR 161 TAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGA 112 chr3qtel1M 352687 GCAGTTTTATGAATTTTCAGGGATCAGAGACCTAGTAAAT 352726 vi vvi i v vi vii i v v v i C MIR#SINE/MIR 111 GAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGT 72 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 49.78 CpG sites = 25, Kimura (unadjusted) = 51.26 Transitions / transversions = 1.04 (25/24) Gap_init rate = 0.02 (3 / 133), avg. gap size = 2.00 (6 / 3) 400 28.27 8.25 3.96 chr3qtel1M 353222 353512 (646488) C L1M4_orf2#LINE/L1 (1314) 1980 1678 m_b145s551i6 5435 chr3qtel1M 353222 TCCTTGTCCTTTTCACTTCTGATCTTGTTGGGAAGAGCTCTAGTTTAACT 353271 i v ---- ivv - ?---- i iii C L1M4_orf2#LIN 1980 TCCTTGTCTTGTTC----CTGATCTTAGGGGGAA-AGCN----TTCAGTC 1940 chr3qtel1M 353272 TTTTAC-----AG-ATAATATTTTCTTTTGCTTTTAGATAGAGATGGC-- 353313 i ----- - i i vv v v v vvi -- v -- C L1M4_orf2#LIN 1939 TTTCACCATTAAGTATGATGTTAGCTGTGGGTTTTTCGTAGA--TGCCCT 1892 chr3qtel1M 353314 TTGTCATTTTAAGAAAGCCTTCATTTATTTTTA----------TGTTTTT 353353 i vv i i iiii v i ii ---------- C L1M4_orf2#LIN 1891 TTATCAGGTTGAGGAAGTTCCCTTCTATTCCTAGTTTGTTGAGTGTTTTT 1842 chr3qtel1M 353354 AATAGGAAGAAGTTCTATGTTTTGTCAAAAGCTTTTTCTGCATCT--TGA 353401 vi v iii vi ivi v i -- C L1M4_orf2#LIN 1841 ATCATGAAAGGGTGTTGGATTTTGTCAAATGCTTTTTCTGCGTCTATTGA 1792 chr3qtel1M 353402 GATAATCTAATGGTTTATGTTGTTTTTACAATTGGTAAAGTCAATTA--- 353448 i vvi v iv v v v ii vi vv --- C L1M4_orf2#LIN 1791 GATGATCATGTGGTTTTTGTCCTTTATTCTATTAATATGGTGTATTACAT 1742 chr3qtel1M 353449 TGTTTAAGTTTCTTAATACTGA-CCAACTTTACATTCCTGGCATAGATTC 353497 v i v v? - ii - i i v i i C L1M4_orf2#LIN 1741 TGATTGATTTTCGNA-TGTTGAACCAACCTTGCATTCCTGGGATAAATCC 1693 chr3qtel1M 353498 TACTATGCCATAGTG 353512 i vv i i C L1M4_orf2#LIN 1692 CACTTGGTCATGGTG 1678 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.48 CpG sites = 44, Kimura (unadjusted) = 36.64 Transitions / transversions = 1.26 (44/35) Gap_init rate = 0.07 (19 / 290), avg. gap size = 1.89 (36 / 19) 237 29.43 0.00 2.35 chr3qtel1M 353681 353767 (646233) C L1M1_orf2#LINE/L1 (1673) 1621 1537 m_b145s551i7 5436 chr3qtel1M 353681 TTGCATCAATATTCATTAGGGAAATTGGTCTATAAGGGGTTTTTTCTCTG 353730 i i v i i -- vv i i i C L1M1_orf2#LIN 1621 TTGCATCAATATTCATCAGAGATATTGGCCTGTA--GTTTTCTTTTTTTG 1574 chr3qtel1M 353731 ATTTTGCTTTTCTTCATTTAGATATCAAAACAATATT 353767 v vv vii vi v i iiii i C L1M1_orf2#LIN 1573 ATGTGTCTTTGTCTGGTTTTGGTATCAGGGTAATACT 1537 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.87 CpG sites = 16, Kimura (unadjusted) = 38.87 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.02 (2 / 86), avg. gap size = 1.00 (2 / 2) 12 17.53 3.12 0.00 chr3qtel1M 353953 353984 (646016) (ACAC)n#Simple_repeat 1 33 (0) m_b145s252i10 5437 chr3qtel1M 353953 ACA-ACAACCACACACACATACACGCACAAACA 353984 - vv i i v (ACAC)n#Simpl 1 ACACACACACACACACACACACACACACACACA 33 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 246 30.45 4.62 1.49 chr3qtel1M 354235 354364 (645636) C L1M2_orf2#LINE/L1 (1759) 1532 1399 m_b145s551i8 5436 chr3qtel1M 354235 GTTTCAAAGGAGGAATTTAGTAGA---CTCTTTCTTTCCTTTTTTTCAAA 354281 ii iv i v i i v ?--- i iiii vv vi C L1M2_orf2#LIN 1532 GCCTCGTAGAATGAGTTTGGAAGNATTCCCTCCTCTTCAATTTTTTGGAA 1483 chr3qtel1M 354282 TAGTTTACACAGTATTGG-ATTAATTGTTCCTTAAACATTTCAGAGAATT 354330 iviv v - i v i ii viv C L1M2_orf2#LIN 1482 TAGTTTGAGAAGAATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAATT 1433 chr3qtel1M 354331 TACTTGT--ATCCATCTGGTCCTAGCAATTTTTCTT 354364 i viv -- v ? i --ii C L1M2_orf2#LIN 1432 CAGCAGTGAAGCCATCNGGTCCTGG--GCTTTTCTT 1399 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.05 CpG sites = 24, Kimura (unadjusted) = 41.46 Transitions / transversions = 1.60 (24/15) Gap_init rate = 0.04 (5 / 129), avg. gap size = 1.60 (8 / 5) 14 16.50 11.11 1.45 chr3qtel1M 355070 355132 (644868) (ATTCAT)n#Simple_repeat 1 69 (0) m_b145s252i11 5438 chr3qtel1M 355070 ATTCCTATTCAGTTTTC-TA--CATATGCATA-TCATATTCA-CTTTTTA 355114 v - v - -- v - -v iv (ATTCAT)n#Sim 1 ATTCATATTCA-TATTCATATTCATATTCATATTCATATTCATATTCATA 49 chr3qtel1M 355115 -TAAAATTC-TATTCATCTT 355132 - v v - v (ATTCAT)n#Sim 50 TTCATATTCATATTCATATT 69 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.11 (7 / 62), avg. gap size = 1.14 (8 / 7) 309 32.46 1.29 10.56 chr3qtel1M 355134 355288 (644712) MIRc#SINE/MIR 2 143 (125) m_b145s601i4 5439 chr3qtel1M 355134 GGGGCAGT-TGGTAGTGGTACAGATCGAATACGGTGTCTAGAGCCAAGAT 355182 i - - ii iv i -- ii v viii i i i v MIRc#SINE/MIR 2 GAGGCAGTGTGGT-GCAGTGGAAA--GAGCACTGGACTTGGAGTCAGGAA 48 chr3qtel1M 355183 GATTTCTATTAATGAGTTCAACTCTGTCCTCAGACACTTCCTAGCTGTAT 355232 ii -------- i i v ivvv v v v i MIRc#SINE/MIR 49 GACCT--------GGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGT 90 chr3qtel1M 355233 AATCTTGGGTAAATCA-TTAATTCTATTAATCCTATTCACTTTAATTCAT 355281 i i i i - iiiivi i v --- v -vi MIRc#SINE/MIR 91 GACCTTGGGCAAGTCACTTAACCTCTCTGAGCC---TCAGTTT-CCTCAT 136 chr3qtel1M 355282 CTGTAAA 355288 MIRc#SINE/MIR 137 CTGTAAA 143 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.03 CpG sites = 30, Kimura (unadjusted) = 44.39 Transitions / transversions = 2.00 (30/15) Gap_init rate = 0.11 (17 / 154), avg. gap size = 1.00 (17 / 17) 14 16.97 6.25 2.00 chr3qtel1M 355725 355772 (644228) (TATTT)n#Simple_repeat 1 50 (0) m_b145s252i12 5440 chr3qtel1M 355725 TATTTT-TCTCATTTTCTGTTA-TGT-TTTCATTTTATTTTATCATTATT 355771 - i i v v - v - i -v (TATTT)n#Simp 1 TATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTAT-TTTATT 49 chr3qtel1M 355772 T 355772 (TATTT)n#Simp 50 T 50 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.09 (4 / 47), avg. gap size = 1.00 (4 / 4) 18 22.95 2.30 7.23 chr3qtel1M 355972 356058 (643942) (CTTTTT)n#Simple_repeat 1 83 (0) m_b145s252i13 5441 chr3qtel1M 355972 CTTTTTCTATTTTCAGTATTTTCAGCTGTTTTCTTTTTGATTGTCTTCCT 356021 - vv v i ivv - vv v -- (CTTTTT)n#Sim 1 CTTTTTCT-TTTTCTTTTTCTTTTTCT-TTTTCTTTTTCTTTTTCTT--T 46 chr3qtel1M 356022 TTC-TATAATTTTTCTTCTTC-TTCTCTTATTTGCTTTT 356058 - v vv i - i - - (CTTTTT)n#Sim 47 TTCTTTTTCTTTTTCTTTTTCTTTTTCTT-TTT-CTTTT 83 Matrix = Unknown Transitions / transversions = 0.36 (4/11) Gap_init rate = 0.09 (8 / 86), avg. gap size = 1.00 (8 / 8) 19 8.35 0.00 0.00 chr3qtel1M 356224 356249 (643751) (T)n#Simple_repeat 1 26 (0) m_b145s252i14 5442 chr3qtel1M 356224 TTCTTCTTTTTTTTTTTTTTTTTTTT 356249 i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 385 29.48 5.48 0.87 chr3qtel1M 356851 357069 (642931) C L1MC_orf2#LINE/L1 (1273) 2021 1793 m_b145s551i9 5443 chr3qtel1M 356851 ATTTCTAATTCAATATTGAATA--AGTGGCAATAACTTGCAGGCTTGCTT 356898 i i i v i i v -- ii v ivvvi vv i C L1MC_orf2#LIN 2021 ACTTCCAGTACGATGTTGAAAAGGAGTGGTGAGAGGGGACATCCTTGCCT 1972 chr3qtel1M 356899 CACTTCTAATCTTAGTAGGA---CTTCTAGTTTATT-CCATTAAAGATCA 356944 iii i i ii --- ? v i- iv v C L1MC_orf2#LIN 1971 TGTTCCTGATCTTAGCGGGAAAGCTTCNAGTTTCTCACCATTAAGTATGA 1922 chr3qtel1M 356945 TGGTTGTTCTTGGTTTCAGATAGAAATTACATATCA-TTTGAAGAGAG-- 356991 v v i v v ivvi vi viv -v i - -- C L1MC_orf2#LIN 1921 TGTTAGCTGTAGGTTTTTTGTAGATGTTCTTTATCAAGTTGAGGA-AGTT 1873 chr3qtel1M 356992 --GCTCCATTCCTATGATTTCT-AGTGTTTTAAATAGAAATGGATGTTTT 357038 --v i - v v - v v vi vi i vv C L1MC_orf2#LIN 1872 CCCCTCTATTCCTA-GTTTGCTGAGAGTTTTTATCATGAATGGGTGTTGG 1824 chr3qtel1M 357039 ATGTTCCCAAAAGCTTTTTCTGCATCTCTTG 357069 v vi v v C L1MC_orf2#LIN 1823 ATTTTGTCAAATGCTTTTTCTGCATCTATTG 1793 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.48 CpG sites = 30, Kimura (unadjusted) = 38.01 Transitions / transversions = 0.88 (30/34) Gap_init rate = 0.04 (9 / 218), avg. gap size = 1.56 (14 / 9) 16 0.00 4.17 4.17 chr3qtel1M 358602 358625 (641375) (GT)n#Simple_repeat 1 24 (0) m_b145s252i15 5444 chr3qtel1M 358602 GTGTGTGTGTGT-TGTGTAGTGTGT 358625 - - (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGT-GTGTGT 24 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.09 (2 / 23), avg. gap size = 1.00 (2 / 2) 265 23.46 1.22 1.22 chr3qtel1M 358647 358728 (641272) L1ME3F_3end#LINE/L1 452 533 (457) m_b145s551i10 5445 chr3qtel1M 358647 CAGCTCTTTTC-TCAGAGCAAAGAATTGAAAATTGAGAGGAATGTCCATC 358695 v v - v v i i i i-i vvvi L1ME3F_3end#L 452 CAGCACTGTTCGTAATAGCAAAAAACTGGAAAC-AACCCAAATGTCCATC 500 chr3qtel1M 358696 CAATTGGGAATGGATGAATAAATTGTGGTATAT 358728 v vvv i i L1ME3F_3end#L 501 GACAGGAGAATGGATAAATAAATTGTGGTATAT 533 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 28.20 CpG sites = 8, Kimura (unadjusted) = 28.20 Transitions / transversions = 0.73 (8/11) Gap_init rate = 0.02 (2 / 81), avg. gap size = 1.00 (2 / 2) 312 29.77 4.30 4.30 chr3qtel1M 361487 361672 (638328) C L1MC2_3end#LINE/L1 (463) 628 443 m_b145s551i11 5446 chr3qtel1M 361487 TTTCACTTAGCATCAGTTTATATAAA-TCTCTCCAGGCTTTTCTGAAATT 361535 vi - vi v i- ii v ii ii ---- C L1MC2_3end#LI 628 TTTCACTTAGCAATA-TGCATTTAAGGTTCCTCCATGTCTTTTCG----T 584 chr3qtel1M 361536 ATCCTGCTGG-TCATTTCTT---ACAGAACAATAATATTCCATAATATTC 361581 iv i v i - --- iv vvv vi vv C L1MC2_3end#LI 583 GGCTTGATAGCTCATTTCTTTTTATCGCTGAATAATATTCCATTGTATGG 534 chr3qtel1M 361582 ATATACTACAATTTATTCAGCCACTCTTCAATTGATAGGCATCCACTTAG 361631 i i i i i v i vi v vi i --- i C L1MC2_3end#LI 533 ATGTACCACAGTTTGTTTATCCATTCACCTATTGAAGGACAT---CTTGG 487 chr3qtel1M 361632 T---TTCCAGTTTCTGGCCACTACAAAGAGGGCTGCCACAAACA 361672 --- iv i v i ii v ii i i C L1MC2_3end#LI 486 TTGCTTCCAAGTTTTGGCAATTATGAATAAAGCTGCTATAAACA 443 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.39 CpG sites = 33, Kimura (unadjusted) = 39.36 Transitions / transversions = 1.65 (33/20) Gap_init rate = 0.06 (12 / 185), avg. gap size = 1.33 (16 / 12) 347 31.30 0.00 0.00 chr3qtel1M 361550 361664 (638336) C L1MC5_3end#LINE/L1 (2129) 565 451 m_b145s551i12 5446 chr3qtel1M 361550 TTCTTACAGAACAATAATATTCCATAATATTCATATACTACAATTTATTC 361599 i vvvv i i vi i vv i i i i C L1MC5_3end#LI 565 TTTTTACAGCTGCATAGTACTCCATTGTGTGGATGTACCATAGTTTATTC 516 chr3qtel1M 361600 AGCCACTCTTCAATTGATAGGCATCCACTTAGTTTCCAGTTTCTGGCCAC 361649 i v ii v i i iiivv v i i v i i C L1MC5_3end#LI 515 AACCAGTCCCCTATTGATGGACATTTGGGTTGTTTCCAGTCTTTTGCTAT 466 chr3qtel1M 361650 TACAAAGAGGGCTGC 361664 v v C L1MC5_3end#LI 465 TACAAATAGTGCTGC 451 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.78 CpG sites = 21, Kimura (unadjusted) = 41.78 Transitions / transversions = 1.40 (21/15) Gap_init rate = 0.00 (0 / 114), avg. gap size = 0.0 (0 / 0) 424 25.45 0.00 0.00 chr3qtel1M 361563 361672 (638328) C L1ME3A_3end#LINE/L1 (368) 552 443 m_b145s551i13 5446 chr3qtel1M 361563 ATAATATTCCATAATATTCATATACTACAATTTATTCAGCCACTCTTCAA 361612 i vi i vv i i v i v vi C L1ME3A_3end#L 552 ATAGTATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTACTG 503 chr3qtel1M 361613 TTGATAGGCATCCACTTAGTTTCCAGTTTCTGGCCACTACAAAGAGGGCT 361662 i i iiivv ? ?? i i i v v C L1ME3A_3end#L 502 TTGATGGACATTTGGGTNGTTTCCAGTTTNNGGCTATTACGAATAGTGCT 453 chr3qtel1M 361663 GCCACAAACA 361672 i ii C L1ME3A_3end#L 452 GCTATGAACA 443 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 31.82 CpG sites = 18, Kimura (unadjusted) = 33.27 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.00 (0 / 109), avg. gap size = 0.0 (0 / 0) 230 14.55 3.51 3.51 chr3qtel1M 362765 362821 (637179) C L1PA3_3end#LINE/L1 (305) 597 541 m_b145s551i14 5447 chr3qtel1M 362765 CCATGTTTTT-CTAAGGTCACTGAACTCATCATTTCTTATAGC-ACAGTA 362812 iii - v v - i i -i - C L1PA3_3end#LI 597 CCATGTCCCTACAAAGGACA-TGAACTCATCATTTTTTATGGCTGCA-TA 550 chr3qtel1M 362813 GTATTCCAT 362821 C L1PA3_3end#LI 549 GTATTCCAT 541 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 16.58 CpG sites = 6, Kimura (unadjusted) = 16.58 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.07 (4 / 56), avg. gap size = 1.00 (4 / 4) 280 25.62 8.53 7.51 chr3qtel1M 362789 362999 (637001) C L1MC5_3end#LINE/L1 (2121) 573 361 m_b145s551i15 5448 chr3qtel1M 362789 CTCATCATTTCTTATAGC-ACAGTAGTATTCCATTAGAATAACATATGAC 362837 ivi i i -i - i ivivvi ii iv i C L1MC5_3end#LI 573 CTCATTCCTTTTTACAGCTGCA-TAGTACTCCATTGTGTGGATGTACCAT 525 chr3qtel1M 362838 AATTTGTTCAATCATTTCCCAATT--------TTTAGGTGTCTATAAATT 362879 i i i v i v -------- i --- i --- C L1MC5_3end#LI 524 AGTTTATTCAACCAGTCCCCTATTGATGGACATTTGGGT---TGT---TT 481 chr3qtel1M 362880 CCAGTTCTTTGCACCAC-ACAAAGAGTACT-C--TAAATACTTTGGTAGA 362925 ii --i i- v i - -- i vii v iv C L1MC5_3end#LI 480 CCAGTCTTTTGC--TATTACAAATAGTGCTGCAATGAATAGCCTTGTGCA 433 chr3qtel1M 362926 TAGGGGGTCTTTTCCTTTTTTTTCC--TG-ATCATTTGAAAAAATAGA-- 362970 v --- v v v -- - - ii --- -- C L1MC5_3end#LI 432 TACG---TCTTTTCGTATTTTTGCCAGTGTATC-TTTGGGA---TAGATT 390 chr3qtel1M 362971 CAAAGCAGTGGTATTGTTGGGTCAAAGGG 362999 vv v v i C L1MC5_3end#LI 389 CCTAGAAGTGGGATTGCTGGGTCAAAGGG 361 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.26 CpG sites = 31, Kimura (unadjusted) = 32.26 Transitions / transversions = 1.63 (31/19) Gap_init rate = 0.11 (24 / 210), avg. gap size = 1.42 (34 / 24) 44 6.16 0.00 0.00 chr3qtel1M 363003 363053 (636947) (TC)n#Simple_repeat 1 51 (0) c_b145s251i2 5449 chr3qtel1M 363003 TCTCTCTCTCTCTTTCTATTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 363052 i v i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr3qtel1M 363053 T 363053 (TC)n#Simple_ 51 T 51 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 408 30.30 8.60 4.97 chr3qtel1M 363295 364131 (635869) C L1MC_orf2#LINE/L1 (384) 2910 2045 m_b145s551i16 5448 chr3qtel1M 363295 TTTTATAGCTAGGTCATAT-ATACATTTT----TAATCTTTTCTGGGTAA 363339 i vi - - v ---- i ----- i C L1MC_orf2#LIN 2910 TTTTACATTTAGGTC-TATGATCCATTTTGAGTTAATTTTT-----GTGA 2867 chr3qtel1M 363340 ATGGAATAAGACAATAGTCTGTGCC------CATTATTATGCCATATTGC 363383 v vi ------ i ------ v v - i v v C L1MC_orf2#LIN 2866 AGGGTGTAAG------GTCTGTGTCTAGATTCATTTTTTTGC-ATGTGGA 2824 chr3qtel1M 363384 TTTTCAGTTTTTCCCAAAATTTTTATCGGAAAA--TAACTTCTTATCC-- 363429 v i v viv viv i i i i-- v - v -- C L1MC_orf2#LIN 2823 TGTCCAGTTGTTCCAGCACCATTTGTTGAAAAGACTATCTT-TTCTCCAT 2775 chr3qtel1M 363430 TGAAATCTTAAGTTTTCACATTTGTCAATTACCAAGTAAC-ATAATTATT 363478 ? --- ivv v v v vv i iv i - v v C L1MC_orf2#LIN 2774 TGNA---TTGCCTTTGCTCCTTTGTCAAAGATCAGTTGACTATATTTATG 2728 chr3qtel1M 363479 TGCTGCTATAAATTGTG---TCTACTTTCTGT--CACTGATCTGCATTTC 363523 vvv --- v --- viv -- i iiv v C L1MC_orf2#LIN 2727 TGGGTCTAT---TTCTGGGCTCTCTATTCTGTTCCATTGATCTATTTGTC 2681 chr3qtel1M 363524 TATTTCTTAGTCA-TACCAGATAGTTTTTACAATTACTGT--CTT----A 363566 ii v i - v iv i ---i -- ----i C L1MC_orf2#LIN 2680 TATTCTTTCGCCAATACCACACTGTCTT---GATTACTGTAGCTTTATAG 2634 chr3qtel1M 363567 TAAG------ATACTAGTACTATTAACCTGCCCTCCTTACTTTT------ 363604 ------ vv vi v i i ii iv vv i ii i ------ C L1MC_orf2#LIN 2633 TAAGTCTTGAAGTCGGGTAGTGTCAGTCCTCCGACTTTGTTCTTCTCCTT 2584 chr3qtel1M 363605 -----TTTTATTAGTTCCTTTGAGATTCTTGACTGGTCCTACAAATGAAT 363649 ----- v i i i vi i i vi i v ---- v v i i C L1MC_orf2#LIN 2583 CAATATTGTGTTGGCTATTCTGGGTCTTTTGCCT----CTCCATATAAAC 2538 chr3qtel1M 363650 TTTG---TTATTTTTTCTA-ATTCAGTAAAATGATTTTTTGGTAATTTGA 363695 i--- i v v v - i -i i i vi v v C L1MC_orf2#LIN 2537 TTTAGAATCAGTTTGTCGATATCCA-CAAAATAACTTGCTGGGATTTTGA 2489 chr3qtel1M 363696 TTAGGATGGCATTGAATTTGTCAATTAGTTTGGGTAAAATTATCATTTTT 363745 i v i i vi i iv v i i iv i v C L1MC_orf2#LIN 2488 TTGGGATTGCATTGAATCTATAGATCAAGTTGGGAAGAACTGACATCTTG 2439 chr3qtel1M 363746 ATTATATTGCTTCTGTCTACCCATGAACATTTAATACTTCTCCA---ATT 363792 iv vv vi i vv ii --- C L1MC_orf2#LIN 2438 ACAATATTGAGTCTTCCTATCCATGAACATGGAATATCTCTCCATTTATT 2389 chr3qtel1M 363793 TAGA-----TTTGATTTTATTTTTATAAAATGTTTTTAATGTAATTTT-G 363836 ?----- --i i v i - ---- i -v C L1MC_orf2#LIN 2388 TAGNTCTTCTTTGATTT--CTTTCATCAGA-GTTT----TGTAGTTTTCC 2346 chr3qtel1M 363837 TTATATACTTCTTGGGTTTGTGTTGACAGACATACTTCCAGGTATTTTAT 363886 i vv viiv i v vi iv ivi i i i C L1MC_orf2#LIN 2345 TCATATAGATCTTGTACATATTTTGTTAGATTTATACCTAAGTATTTCAT 2296 chr3qtel1M 363887 ACTATTTAGA---GCTATTTTAAATGG---GGTATTTCTTACCATTTCTT 363930 -- - i i--- v v ---v i - -- vv C L1MC_orf2#LIN 2295 --T-TTTGGGGGTGCTAATGTAAATGGTATTGTGTTT-TTA--ATTTCAA 2252 chr3qtel1M 363931 CTTCCAGAATTTTGTTTGTGATATATAGGAATGCTGATGAATAATATGGA 363980 v ?vvv ii vv i v viv v vv i iv C L1MC_orf2#LIN 2251 ATTCCANTTGTTCATTGCTGGTATATAGGAAAGCGATTGACTTTTGTATA 2202 chr3qtel1M 363981 TTTACTTCACATCCTGCTACTTTCCTAAAG----TTATTGTTTCTAATAA 364026 v i iii v i v v i---- iv i iv i C L1MC_orf2#LIN 2201 TTAACCTTGTATCCTGCAACCTTGCTATAATCGCTTATTAGTTCCAGGAG 2152 chr3qtel1M 364027 CTTTTTAGTTGAGCTTTTGGGATTTTCCAGGTGTAC---CATATT-TCTG 364072 i v i vii v i vi iv --- i i- C L1MC_orf2#LIN 2151 TTTTTTTGTCGATTCTTTCGGATTTTCTACATAGACAATCATGTCATCTG 2102 chr3qtel1M 364073 TAAAGACAGAGAGAATTTTACCACTTTGTTTTCTATTCAGATCCCTTTTA 364122 ii -- i v i iiv iv ii v iiiv v C L1MC_orf2#LIN 2101 CGA--ACAAAGACAGTTTTATTTCTTCCTTCCCAATCTGTATACCTTTTA 2054 chr3qtel1M 364123 TGTCTTTTT 364131 v i C L1MC_orf2#LIN 2053 TTTCCTTTT 2045 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.35 CpG sites = 127, Kimura (unadjusted) = 39.80 Transitions / transversions = 1.11 (127/114) Gap_init rate = 0.08 (67 / 836), avg. gap size = 1.72 (115 / 67) 543 31.15 8.10 3.18 chr3qtel1M 363502 364131 (635869) C L1PB_orf2#LINE/L1 (590) 2704 2045 m_b145s551i17 5448 chr3qtel1M 363502 TTCTGT--CACTGATCTGCATTTCTATTTCT-TAGTCATACCAGATAGTT 363548 -- i i iii vi i - vivi viiv C L1PB_orf2#LIN 2704 TTCTGTTCCATTGGTCTATGTGCCTATTTTTATACCAGTACCATGCTGTT 2655 chr3qtel1M 363549 TTTACAATTACTGTCTTATAAGATACT----AGTACTATTAACCTG--CC 363592 viii i iv i iv v ---- - viv iv --v C L1PB_orf2#LIN 2654 TTGGTGACTATGGCCTTATAGTATAGTTTGAAGT-CGGGTAATGTGATGC 2606 chr3qtel1M 363593 CTCC----TTACTTTTTTTTATTAGT--TCCTTTGA-------GATTCTT 363629 ---- ii i vv -- v i------- ii C L1PB_orf2#LIN 2605 CTCCAGATTTGTTCTTTTTGCTTAGTCTTGCTTTGGCTATGCGGGCTCTT 2556 chr3qtel1M 363630 GACTGGTCCTACAAATGAATTTTG---TTATTTTTTCTAATTCAGTAAA- 363675 vvi i -- v i--- i i v i - C L1PB_orf2#LIN 2555 TTTTGGTTC--CATATGAATTTTAGGATTGTTTTTTCTAGTTCTGTGAAG 2508 chr3qtel1M 363676 -ATGATTTTTTGGTAATTTGATTAGGATGGCATTGAATTTGTCAATTAGT 363724 - vv -- v vi i v vi iv C L1PB_orf2#LIN 2507 AATGATGGT--GGTATTTTGATGGGAATTGCATTGAATTTGTAGATTGCT 2460 chr3qtel1M 363725 TTGGGTAAAATTATCATTTTTATTATATTGCTTCTGTCTACCCATGAACA 363774 v i iv vi i iv v ii i i i C L1PB_orf2#LIN 2459 TTTGGCAGTATGGTCATTTTCACAATATTGATTCTACCCATCCATGAGCA 2410 chr3qtel1M 363775 TTTAATACTTCTCCA---ATTTAGATT-----TGATTTTATTTTTATAAA 363816 vvi iiv i ---i ivi i----- --i i -iv C L1PB_orf2#LIN 2409 TGGGATGTGTTTCCATTTGTTTGTGTCGTCTATGATTT--CTTTCA-GCA 2363 chr3qtel1M 363817 ATGTTTTTAATGTAATTTT-GTTATATACTTCTTGGGTTTGTGTTGACAG 363865 i ---- i -v i v vv vviii viv v vi C L1PB_orf2#LIN 2362 GTGTTT----TGTAGTTTTCCTTGTAGAGGTCTTTCACCTCCTTGGTTAG 2317 chr3qtel1M 363866 ACATACTTCCAGGTATTTTATACTATTTAGAGCTATTTTAAATGGGGT-- 363913 ii i i i i vi v iv v v -- C L1PB_orf2#LIN 2316 GTATATTCCTAAGTATTTTATTTTTTTTGCAGCTATTGTAAAAGGGGTTG 2267 chr3qtel1M 363914 ATTTCTTACCATTTC-TTCTTCCAGAATTTTGTTTG----TGATATATAG 363958 v i-- v- -- ---i v i ---- i i C L1PB_orf2#LIN 2266 AGTTCTTG--ATTTGATTCT--CAG---CTTGGTCGCTGTTGGTGTATAG 2224 chr3qtel1M 363959 GAATGCTGATGAATAATATGGATTTACTTCACATCCTGCTACTTTCCTAA 364008 ? iv iv v vi i iv v i iii ? vv v i C L1PB_orf2#LIN 2223 NAGAGCTACTGATTTGTGTACATTAATTTTGTATCCNGAAACTTTGCTGA 2174 chr3qtel1M 364009 A----GTTATTGTTTCTAATAACTTTTTAGTTGAGCTTTTGGGATTTTCC 364054 ----v iiv iv i i i vv ii i i i C L1PB_orf2#LIN 2173 ATTCNTTTATCAGTTCTAGGAGCTTTCTGGAGGAGTCTTTAGGGTTTTCT 2124 chr3qtel1M 364055 AGGTGTAC---CATATT-TCTGTAAAGACAGAGAGAATTTTACCACTTTG 364100 i? --- i- v i -- v v i v iv i iv C L1PB_orf2#LIN 2123 AGGTANACGATCATATCATCAGCAA--ACAGCGACAGTTTGACTTCCTCT 2076 chr3qtel1M 364101 TTTTCTATTCAGATCCCTTTTATGTCTTTTT 364131 vi v ii v i v i C L1PB_orf2#LIN 2075 TTACCGATTTGGATGCCCTTTATTTCTTTCT 2045 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.29 CpG sites = 111, Kimura (unadjusted) = 41.88 Transitions / transversions = 1.41 (111/79) Gap_init rate = 0.06 (40 / 629), avg. gap size = 1.80 (72 / 40) 735 29.21 4.41 2.56 chr3qtel1M 363633 364131 (635869) C L1M2_orf2#LINE/L1 (742) 2549 2042 m_b145s551i18 5448 chr3qtel1M 363633 TGGTCCTACAAATGAATTTTG---TTATTTTTTCTAATTCAGTAAA--AT 363677 i -- v i i--- ? v v i -- C L1M2_orf2#LIN 2549 TGGTTC--CATACGAATTTTAGGATTNTTTTTTCTATTTCTGTGAAGAAT 2502 chr3qtel1M 363678 GATTTTTTGGTAATTTGATTAGGATGGCATTGAATTTGTCAATTAGTTTG 363727 -- iv v vi v i vi iiv C L1M2_orf2#LIN 2501 G--TCATTGGTATTTTGATAGGGATTGCATTGAATCTGTAGATCGCTTTG 2454 chr3qtel1M 363728 GGTAAAATTATCATTTTTATTATATTGCTTCTGTCTACCCATGAACATTT 363777 iv vi? v iv iv vi v i i vv C L1M2_orf2#LIN 2453 GGTAGTATGGNCATTTTAACAATATTAATTCTTCCAATCCATGAGCATGG 2404 chr3qtel1M 363778 AATACTTCTCCA---ATTTAGATTTGATTTTATTTTTATAA--AATGTTT 363822 i ii i ---? ivi iivv iv i v v -- i C L1M2_orf2#LIN 2403 GATATCTTTCCATTTNTTTGTGTCCTCTTCAATTTCTTTCATCAGTGTTT 2354 chr3qtel1M 363823 T-TAATGTAATTTTGTTATATACTTCTTGGGTTTGTGTTGACAGACATAC 363871 - i ---- i? i v vv vviii viv v vi i iv i C L1M2_orf2#LIN 2353 TATAGT----TTTCNTTGTAGAGATCTTTCACCTCCTTGGTTAAATTTAT 2308 chr3qtel1M 363872 TTCCAGGTATTTTATACTATTTAGAGCTATTTTAAATGGGGT--ATTTCT 363919 i i vi v iv v i --v C L1M2_orf2#LIN 2307 TCCTAGGTATTTTATTTTTTTTGTAGCTATTGTAAATGGGATTGCTTTCT 2258 chr3qtel1M 363920 TACCATTTCTTCTTCCAGA-ATTTTGTTTGTGATATATAGGAATGCTGAT 363968 i-- - i - v i vv iii i iv C L1M2_orf2#LIN 2257 TG--ATTTCTT-TTTCAGATAGTTCGTTGTTGGCGTATAGAAATGCTACT 2211 chr3qtel1M 363969 GAATAATATGGATTTACTTCACATCCTGCTACTTTCCTAAA---G-TTAT 364014 v vv i ivi v i iii v v i --- - C L1M2_orf2#LIN 2210 GATTTTTGTATGTTGATTTTGTATCCTGCAACTTTACTGAATTCGTTTAT 2161 chr3qtel1M 364015 TGTTTCTAATAACTTTTTAGTTGAGCTTTTGGGATTTTCCAGGTGT---A 364061 iiv ? ii i v ii i ? i ?i i --- C L1M2_orf2#LIN 2160 CAGTTCTAANAGTTTTTTGGTGGAGTCTTTAGGNTTTTCTANATATAAGA 2111 chr3qtel1M 364062 CCATATT-TCTGTAAAGACAGAGAGAATTTTACCACTTTGTTTTCTATTC 364110 i i i- i -- i v v iv i iv i v i C L1M2_orf2#LIN 2110 TCATGTCATCTGCAA--ACAGGGACAATTTGACTTCCTCCTTTCCAATTT 2063 chr3qtel1M 364111 AGATCCCTTTTATGTCTTTTT 364131 i v v i C L1M2_orf2#LIN 2062 GGATGCCTTTTATTTCTTTCT 2042 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.31 CpG sites = 83, Kimura (unadjusted) = 38.79 Transitions / transversions = 1.41 (83/59) Gap_init rate = 0.05 (24 / 498), avg. gap size = 1.46 (35 / 24) 18 7.16 3.33 0.00 chr3qtel1M 366606 366635 (633365) (CTT)n#Simple_repeat 1 31 (0) m_b145s252i16 5450 chr3qtel1M 366606 CTTCTTCTTCTTCTTCTT-TTTTTTTTCTTC 366635 - i i (CTT)n#Simple 1 CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTC 31 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 16 0.00 0.00 0.00 chr3qtel1M 366737 366753 (633247) (T)n#Simple_repeat 1 17 (0) m_b145s252i17 5451 chr3qtel1M 366737 TTTTTTTTTTTTTTTTT 366753 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTT 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 16 9.26 0.00 0.00 chr3qtel1M 368247 368269 (631731) (CT)n#Simple_repeat 1 23 (0) m_b145s252i18 5452 chr3qtel1M 368247 CTCTCTCTGTCTCTCTCTCTTTC 368269 v i (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTC 23 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 26 8.83 0.00 0.00 chr3qtel1M 368269 368304 (631696) (CA)n#Simple_repeat 1 36 (0) m_b145s252i19 5453 chr3qtel1M 368269 CACACACACACACACAAACACACACATAAACACACA 368304 v i v (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACA 36 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 183 21.15 3.85 0.00 chr3qtel1M 374025 374076 (625924) C L3#LINE/CR1 (802) 3297 3244 m_b146s601i0 5454 chr3qtel1M 374025 TTCAGCCT--CCAGCTCTCTCTGAATCTTGGTTCTGCCATACTGCAGATT 374072 i -- v v ?i i i i v v? iv C L3#LINE/CR1 3297 TCCAGCCTGTCGAGATCNTTTTGAATCTTGATTCTGTCATCCANCGTATT 3248 chr3qtel1M 374073 AGCT 374076 C L3#LINE/CR1 3247 AGCT 3244 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 23.70 CpG sites = 6, Kimura (unadjusted) = 26.35 Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.02 (1 / 51), avg. gap size = 2.00 (2 / 1) 30 26.46 0.00 1.25 chr3qtel1M 374391 374471 (625529) (CTC)n#Simple_repeat 1 80 (0) m_b146s252i0 5455 chr3qtel1M 374391 CTCCTCCTGCTCCTCTTCTTCCTCCTCATTTTCCTCTTCCTCAACCTCCT 374440 v i i v ii i vv (CTC)n#Simple 1 CTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT 50 chr3qtel1M 374441 TTTCTTTCTTCTTCTCTTTTCTCCTCCTCCT 374471 ii i i i i -i i (CTC)n#Simple 51 CCTCCTCCTCCTCCTC-CTCCTCCTCCTCCT 80 Matrix = Unknown Transitions / transversions = 3.25 (13/4) Gap_init rate = 0.01 (1 / 80), avg. gap size = 1.00 (1 / 1) 29 25.46 2.42 4.96 chr3qtel1M 374392 374515 (625485) (TCCTCT)n#Simple_repeat 1 121 (0) m_b146s252i1 5455 chr3qtel1M 374392 TCCTCCTGCTCCTCTTCTTCCTCCTCATTTTCCTCTTCCTCAACCTCCTT 374441 i v i i i v i vv i i (TCCTCT)n#Sim 1 TCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTC 50 chr3qtel1M 374442 TTCTTTCTTCTT-CTCTT-TTC-TCCTCCTCCTTTTTCACTGTCATCATT 374488 i - i - -i - i i i v - v -- (TCCTCT)n#Sim 51 CTC-TTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCT-TCCTC--T 96 chr3qtel1M 374489 ATCATTTTCATCATCCTCCTTTCTCTT 374515 - v i v v - i (TCCTCT)n#Sim 97 -TCCTCTTCCTCTTCCT-CTTCCTCTT 121 Matrix = Unknown Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.07 (9 / 123), avg. gap size = 1.00 (9 / 9) 201 14.72 0.00 2.94 chr3qtel1M 375250 375284 (624716) C L3#LINE/CR1 (1673) 2426 2393 m_b146s601i1 5454 chr3qtel1M 375250 AGAGGTTGAATAATTCTGCTTTACTTTCTGTCATC 375284 ii i i - i C L3#LINE/CR1 2426 AGGAGTTGAGTAGTTCTGCTTT-CTCTCTGTCATC 2393 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 17.42 CpG sites = 5, Kimura (unadjusted) = 17.42 Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 17 29.84 0.00 0.00 chr3qtel1M 375880 375936 (624064) (AAAAGA)n#Simple_repeat 1 57 (0) m_b146s252i2 5456 chr3qtel1M 375880 AAAATAAAAAATGACAGAATAGGAAAAAAAATCAGAAAAGGAAAATAAAA 375929 v ivi v v i i vv i vi (AAAAGA)n#Sim 1 AAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAA 50 chr3qtel1M 375930 AAGCAAA 375936 v (AAAAGA)n#Sim 51 AAGAAAA 57 Matrix = Unknown Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0) 44 2.44 0.00 0.00 chr3qtel1M 377824 377865 (622135) (GT)n#Simple_repeat 1 42 (0) c_b146s251i0 5457 chr3qtel1M 377824 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGTGTGT 377865 i (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 42 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 55 11.86 5.76 4.26 chr3qtel1M 378638 378776 (621224) (AGAA)n#Simple_repeat 1 141 (0) m_b146s252i3 5458 chr3qtel1M 378638 AGAAATGAAAGAAAGAAAAAAAAGAAATAAAAAGAAGCAAGATA-AAAG- 378685 - - i v i - v v - - (AGAA)n#Simpl 1 AGAAA-GAAAGAAAG-AAAGAAAGAAAGAAAGA-AAGAAAGAAAGAAAGA 47 chr3qtel1M 378686 AAGGAAGGAAGGCAGAAA-AAAGAGAGAAAGAAA-AAAG-AA-AAAGAAA 378731 i i iv - i - - - (AGAA)n#Simpl 48 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 97 chr3qtel1M 378732 GAAAGAAAGGAAAGGAAATAAA-CATGAAATGAATGAAAG-AAGAAA 378776 - - v -v v - v - (AGAA)n#Simpl 98 GAAAGAAA-GAAA-GAAAGAAAGAAAGAAA-GAAAGAAAGAAAGAAA 141 Matrix = Unknown Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.10 (14 / 138), avg. gap size = 1.00 (14 / 14) 971 31.62 2.89 1.91 chr3qtel1M 379039 379557 (620443) C L1ME4c_3end#LINE/L1 (274) 556 33 m_b146s551i0 5459 chr3qtel1M 379039 CATAATGTGCCATTACAATCAGATGTAACAT--TCTGTTCAGCCTTTCTC 379086 i v -- i vi? v -- i ii i i v i C L1ME4c_3end#L 556 CATAATATTCCAT--CGAGTNGATGTACCATAATTTACTTAACCATTCCC 509 chr3qtel1M 379087 CAATTCAGGGGCA----AACCCTTACCACTTCTTAGCCATCACAAA-AGA 379131 v vvv i ----iiiiv v v i v i i i - iv C L1ME4c_3end#L 508 CTATTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAAC 459 chr3qtel1M 379132 GCTATTATAAATAATTTTATGGAAATAGGTTCTTCCCCCTGCCCTTT--- 379178 iiv i i vi ii v v v i ii ---- --- C L1ME4c_3end#L 458 GCTGCAATGAACATCTTCGTGCATATAGCTTTTTCCTTCT----TTTGAA 413 chr3qtel1M 379179 TTATCTCTATTGGATACAAGCCTAATAGTGTTACTATCAGATCAAATGAT 379228 i iv v v vv i iv vv i iii i v i C L1ME4c_3end#L 412 TTATTTCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGT 363 chr3qtel1M 379229 GCAAAGTTTTTTATT-CTATTGG-GCATAGTTCCAAATTGCTCTTCAGAA 379276 iii vv v- v i-i i v v i i i C L1ME4c_3end#L 362 ATGAACATTTTTATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAA 313 chr3qtel1M 379277 TAGTTGGATCAGTTCACAACTCTACCAACAATGTGTTAGTGTCCTAGTTT 379326 vi v i i i ?iv i i i v ? v i C L1ME4c_3end#L 312 GGGTTGTACCAATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTTT 263 chr3qtel1M 379327 TCCCACATCCCCTCCAACATTTATTATTTTCCTAATTTTTTTGTCATATC 379376 iv i ? i v i viv v -- vi-- v i C L1ME4c_3end#L 262 CACCGCANCCTCGCCAGCATTGGGTATTATC--AATTTTTTAA--ATTTT 217 chr3qtel1M 379377 AGACAATCTAATAGGTGTCAAGTGGTACCTCAGAGATGTTTTAATTTGCA 379426 v vi i i v i i vv v i C L1ME4c_3end#L 216 TGCTAATTTAATAGGCGTAAAATGGTATCTCATTGTTGCTTTAATTTGCA 167 chr3qtel1M 379427 TTTTTCTGATCAGTAGTGATTTAGAACAGTTT---ATATGAGTACAGATA 379473 i i i v i vv v v --- i vv iivv iv C L1ME4c_3end#L 166 TTTCTTTGATTACTAGCGAGGTTGAACATTTTTCCATGTGTTTGTTTACT 117 chr3qtel1M 379474 GCTTTGATTTCTTTGTTTGAAAACTGCCTGTTCATATCCTTTGACCATTT 379523 i? vv i iv ? vi i i i v C L1ME4c_3end#L 116 ANTTGTATTTCCTCTTNTGTGAATTGTCTGTTCATGTCCTTTGCCCATTT 67 chr3qtel1M 379524 ATCAACTGAGGAATTACTAGTATTCTTATAAATT 379557 v i i vv iv ?v v v C L1ME4c_3end#L 66 ATCTATTGGGGTCTTGATNTTTTTCTTATCAATT 33 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 40.72 CpG sites = 88, Kimura (unadjusted) = 42.85 Transitions / transversions = 1.21 (88/73) Gap_init rate = 0.03 (17 / 518), avg. gap size = 1.47 (25 / 17) 19 18.30 1.89 3.85 chr3qtel1M 380589 380641 (619359) (AGG)n#Simple_repeat 1 52 (0) m_b146s252i4 5460 chr3qtel1M 380589 AGCAGGA-GAGGAAGAGGGAAGAGGAGCAGCAGGAGGACGAGAAGGATGC 380637 v - i - i v v v i - v (AGG)n#Simple 1 AGGAGGAGGAGGAGGA-GGAGGAGGAGGAGGAGGAGGAGGAGGAGGA-GG 48 chr3qtel1M 380638 AGGA 380641 (AGG)n#Simple 49 AGGA 52 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.06 (3 / 52), avg. gap size = 1.00 (3 / 3) 14 23.16 0.00 4.26 chr3qtel1M 381381 381429 (618571) (TTAAG)n#Simple_repeat 1 47 (0) m_b146s252i5 5461 chr3qtel1M 381381 TTAATTTAAGTTACAACAATTTAAGATAATTTAAGTTACAAGTTAATTT 381429 v vivi v v v -- v (TTAAG)n#Simp 1 TTAAGTTAAGTTAAGTTAAGTTAAGTTAAGTTAAGTT--AAGTTAAGTT 47 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.04 (2 / 48), avg. gap size = 1.00 (2 / 2) 392 39.36 3.68 3.36 chr3qtel1M 383249 383574 (616426) C L2b_3end#LINE/L2 (15) 451 125 m_b146s601i2 5462 chr3qtel1M 383249 AAACATTTTCTAAGGAAGCATTATGTGCCAGGTATTTTGCTAAGTGCTAG 383298 i v i vivvi i i i?i v i i i C L2b_3end#LINE 451 AAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGG 402 chr3qtel1M 383299 GAATACAAAGAAAGGCAAA--AGATA--GTTCCTGCCCTCAAACAGGATA 383344 i iv iviii i-- i?-- i viv vvi C L2b_3end#LINE 401 GGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGGAGCTCA 352 chr3qtel1M 383345 AAATCTAATTGGGAAAA-AAATGTGCAAACA-ACTTTGTATGAATAAGAA 383392 v i i v i i - i ii i ? - vv -? i viv i C L2b_3end#LINE 351 CAGTCTAGTGGGGGAGACAGACATGTAANCAGACAAT-NATAACCCAGAG 303 chr3qtel1M 383393 TAGGACTGTGTAATAAGTTGGACACATTCAGGAGATGAGCAGGTG-CTAG 383441 i v -- v iv --i iviviii ii - i ivv - iv C L2b_3end#LINE 302 TGGCA--GGGTAGGA--CTGGGGGGGCCCAGAGGA-GGGCGCCTGACCCG 258 chr3qtel1M 383442 GAGGAGGAGGGCTTGGGAAAGGCTTCCTGTAGAAGGTAGAATTTCCATTA 383491 vvvi i -- ii i i i v i iiv vvii i C L2b_3end#LINE 257 GCCTGGGGGG--TCAGGGAGGGCTTCCCGGAGGAGGTGACATTTGAGCTG 210 chr3qtel1M 383492 GGATTTTTAAAAAGCCAG--GGA---AATCAGACAGAATGGACAGTGAAG 383536 i --ii i iiiiv -- ---iii i - vi iii v C L2b_3end#LINE 209 AGA--CCTGAAGGATGAGTAGGAGTTGGCCAGGC-GAAGAGGTGGGGAAG 163 chr3qtel1M 383537 AATTTTCCAAGCATGGGGAAAAGTCAGAACAAATGCTC 383574 iiiv i vi v iv? vi v i C L2b_3end#LINE 162 GGCGTTCCAGGCAGAGGGAACAGCANGTGCAAAGGCCC 125 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 57.79 CpG sites = 83, Kimura (unadjusted) = 62.77 Transitions / transversions = 2.02 (83/41) Gap_init rate = 0.06 (18 / 325), avg. gap size = 1.28 (23 / 18) 414 32.54 2.38 0.00 chr3qtel1M 383249 383374 (616626) C L2d2_3end#LINE/L2 (15) 540 412 m_b146s601i3 5462 chr3qtel1M 383249 AAACATTTTCTAAGGAAGCATTATGTGCCAGGTATTTTGCTAAGTGCTA- 383297 i vi i vivvi i i v i i v i i i- C L2d2_3end#LIN 540 AAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGT 491 chr3qtel1M 383298 --GGAATACAAAGAAAGGCAAAAGATAGTTCCTGCCCTCAAACAGGATAA 383345 -- i ivii i v i i iv vv v C L2d2_3end#LIN 490 GGGGGATACAAAGAAGTATAAGACATGGTCCCTGCCCTCAAGGAGCTTAC 441 chr3qtel1M 383346 AATCTAATTGGGAAAAAAATGTGCAAACA 383374 i i i v viiii C L2d2_3end#LIN 440 AATCTAGTTGGGGAGACAAGACATAAACA 412 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 42.06 CpG sites = 27, Kimura (unadjusted) = 45.07 Transitions / transversions = 1.93 (27/14) Gap_init rate = 0.02 (2 / 125), avg. gap size = 1.50 (3 / 2) 60 33.31 4.02 2.99 chr3qtel1M 384440 384837 (615163) (CTTTT)n#Simple_repeat 1 402 (0) m_b146s252i6 5463 chr3qtel1M 384440 CTCTTCTTCTTCCTCACATTTCCTCCTCTTTTTCCTTCATATCTTCTTCC 384489 i - i iv - i ii iii v v - i (CTTTT)n#Simp 1 CTTTTCTT-TTCTTTTC-TTTTCTTTTCTTTTCTTTTCTTTTCTT-TTCT 47 chr3qtel1M 384490 TGT-TTTTCTCTT-TTTCCTGTT-TTCTCCTTTC-TGTCTTTCCTTTTAC 384535 v - i - i v - i i - v i - (CTTTT)n#Simp 48 TTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTT-C 96 chr3qtel1M 384536 CTCCCTTTCTCTATT-TTTTTTTTCCTTTCTGTTTTCTTTTTTTTTTCCT 384584 i ii - v - i i - v - i i (CTTTT)n#Simp 97 TTTTCTTT-TCTTTTCTTTTCTTTTCTTT-TCTTTTC-TTTTCTTTTCTT 143 chr3qtel1M 384585 TT-TACTCCAATATTTTCCCTTTTTCTATTTTCTTTCCCTATCTCTTC-C 384632 - vi ivv v ii i i v i i v i -i (CTTTT)n#Simp 144 TTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTT 193 chr3qtel1M 384633 ATC-TTTCTTCAACCTTCTTTCTATTTTC-ACAAATTTC-TTTC-TTTC- 384677 v - ivvii - v -vivvv - - - (CTTTT)n#Simp 194 TTCTTTTCTTTTCTTTTCTTT-TCTTTTCTTTTCTTTTCTTTTCTTTTCT 242 chr3qtel1M 384678 TCCCAATTCTCTTATTTGTTGTTTC-TTCCTTGTCTTTCCCTCTATTTCC 384726 ii vv i v - iv - i v i i i v i (CTTTT)n#Simp 243 TTTCTTTTCTTTTCTTT-TCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTC 291 chr3qtel1M 384727 CTTTGTGTTTTCTTCTTTTCTCCAGCTCTTCTTTT-TTCTTTTCCCTTTT 384775 i v v i i -ivv i - i i ii (CTTTT)n#Simp 292 TTTTCTTTTCTTTTCTTTTCT-TTTCTTTTCTTTTCTTTTCTTTTCTTTT 340 chr3qtel1M 384776 CTCCTCATCTCTTGTTTTCTTC-TTTCATTT-GCTTCAGTTCTTCTCTTT 384823 ii v i - i i - v -vi vv i (CTTTT)n#Simp 341 CTTTTCTTTTCTT-TTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTT 389 chr3qtel1M 384824 TTTTTTCTTTATCT 384837 i - (CTTTT)n#Simp 390 TCTTTTCTTT-TCT 402 Matrix = Unknown Transitions / transversions = 1.68 (62/37) Gap_init rate = 0.07 (28 / 397), avg. gap size = 1.00 (28 / 28) 646 29.91 9.50 1.68 chr3qtel1M 385420 385861 (614139) C L1ME3Cz_3end#LINE/L1 (468) 529 54 m_b146s551i1 5464 chr3qtel1M 385420 ATATACCAAACTTT-----TCAATTCTCCAATTGATGAGCCTCCATCCAA 385464 v v ----- v i v ii v ii vvivi C L1ME3Cz_3end# 529 ATATACCACAATTTATTTATCCATTCCCCTATTGATGGACATTTAGGTTG 480 chr3qtel1M 385465 TTTCCAGTTTCTAGCCAC-ACAAA-AAGGGTCCA-CAAATATTTCTGTAC 385511 i i v i i- - v v v -ii i iii C L1ME3Cz_3end# 479 TTTCCAATTTTTCGCTATTACAAACAATGCTGCAATGAACATCCTTGTAC 430 chr3qtel1M 385512 ATTGGCATC-CCTTTTCCCTTTTTACGA---TTGCTTTGGGAT-TA-AGC 385555 ----i - v v viv v i --- v i i i - - v C L1ME3Cz_3end# 429 AT----GTCTCCTTGTGCACATGTGCGAGAGTTTCTCTAGGGTATATACC 384 chr3qtel1M 385556 TCAAAATAAACTTG---GATCAAAGGGTAAGCACAGTTTGAAATTT--TG 385600 vi i ii v --- i iv v i vi v v -- i C L1ME3Cz_3end# 383 TAGAAGTGGAATTGCTGGGTCGTAGGGTATGCGCATCTTCAACTTTACTA 334 chr3qtel1M 385601 AGCATAGTTAAATTG-TCTCTGGAATGGTTGGATGCATTCACAATTCCAC 385649 iii v ii - iii i v ivv i v i C L1ME3Cz_3end# 333 GATATTGCCAAATTGCTCTCCAAAGTGGTTGTACCAATTTACACTCCCAC 284 chr3qtel1M 385650 CAACAATGTATCAGTGTCCCAGTTTTTCCCCATCCCCTCCAACATTT--C 385697 i i v v i v i v i v i --i C L1ME3Cz_3end# 283 CAGCAGTGTATGAGAGTTCCCGTTTCTCCACATCCTCGCCAACACTTGGT 234 chr3qtel1M 385698 ATTATC---TTTTTCCTGTCATCCCAGCCAATCTGG-AAGTGTGTAGTGG 385743 i ---i vv---- iiiv i-ii v i C L1ME3Cz_3end# 233 ATTGTCAGACTTTTAA----ATTTTTGCCAATCTGATGGGTGTGAAATGG 188 chr3qtel1M 385744 TATCTCAGAGTGGTCTTAATT--CATTTATCTGATCATTAATGA-TTTGG 385790 vv ? i -- vi i i i -v i C L1ME3Cz_3end# 187 TATCTCATTGTNGTTTTAATTTGCATTTCCCTGATTACTAGTGAGGTTGA 138 chr3qtel1M 385791 ACATCTTTTT-CATGGCTA-GAAATATTTCAATTTCTTCATCTG------ 385832 i i-i vi -viivi ivii i v ------ C L1ME3Cz_3end# 137 GCATCTTTTCATATGTTTATTGGCCATTCGGGTTTCCTCTTCTGTGAATT 88 chr3qtel1M 385833 GT---TTCATATCCTTT--CCATTTATCAAGTGG 385861 i--- -- v v v C L1ME3Cz_3end# 87 GCCTGTTCATATCCTTTGCCCATTTTTCTATTGG 54 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 38.41 CpG sites = 78, Kimura (unadjusted) = 39.60 Transitions / transversions = 1.50 (78/52) Gap_init rate = 0.07 (29 / 441), avg. gap size = 1.72 (50 / 29) 670 29.47 7.37 1.75 chr3qtel1M 385420 385799 (614201) C L1ME3A_3end#LINE/L1 (387) 533 133 m_b146s551i2 5464 chr3qtel1M 385420 ATATACCAAACTTT-----TCAATTCTCCAATTGATGAGCCTCCATCCAA 385464 v v ----- v v vi ii v iiivvi?i C L1ME3A_3end#L 533 ATATACCACAATTTATTTATCCATTCTACTGTTGATGGACATTTGGGTNG 484 chr3qtel1M 385465 TTTCCAGTTTCTAGCCAC-ACAAAAAGGGT--CCACAAATATTTCTGTAC 385511 ??i i i- i v v i-- i ii i ii C L1ME3A_3end#L 483 TTTCCAGTTTNNGGCTATTACGAATAGTGCTGCTATGAACATTCTTGTAC 434 chr3qtel1M 385512 ATTGGCATCCCTTTTC-----CCTTTTTACG-ATTGCT-TTGGGATTA-A 385553 ------vi v----- v v v - v - vv - C L1ME3A_3end#L 433 AT------GTCTTTTGGTGAACATATGTACGCATTTCTGTTGGGTATATA 390 chr3qtel1M 385554 GCTCAAAATAAACTTG---GATCAAAGGGTAAGCACAGTTTGAAATTTTG 385600 v vii i ii v --- i v v i vv v iv v C L1ME3A_3end#L 389 CCTAGGAGTGGAATTGCTGGGTCATAGGGTATGCATATGTTCAGCTTTAG 340 chr3qtel1M 385601 AGCATA--GTTAAATTGTCT-CTGGAATGGTTGGATGCATTCACAATTCC 385647 viv -- ii iv i - iii i v ivv i v i C L1ME3A_3end#L 339 TAGATACTGCCAAACAGTTTTCCAAAGTGGTTGTACCAATTTACACTCCC 290 chr3qtel1M 385648 ACCAACAATGTATCAGTGTCCCAGTTTTTCCCCATCCCCTCCAACATTT- 385696 i i v v i i vi v i v i - C L1ME3A_3end#L 289 ACCAGCAGTGTATGAGAGTTCCGGTTGCTCCACATCCTCGCCAACACTTG 240 chr3qtel1M 385697 -CATTATCTTTTTCCTGTCATCCCAGCCAATCTGG-AAGTGTGTAGTGGT 385744 -i i v i ii - iii v -ii C L1ME3A_3end#L 239 GTATTGTCTGTCTTTT-TCATTTTAGCCATTCTGGTGGGTGTGTAGTGGT 191 chr3qtel1M 385745 ATCTCAGAGTGGTCTTAATT--CATTTATCTGATCATTAATG-ATTTGGA 385791 ? vv i -- vi v i - v ii C L1ME3A_3end#L 190 ATCNCATTGTGGTTTTAATTTGCATTTCCCTGATGACTAATGAAGTTGAG 141 chr3qtel1M 385792 CATCTTTT 385799 i C L1ME3A_3end#L 140 CACCTTTT 133 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 38.07 CpG sites = 63, Kimura (unadjusted) = 38.98 Transitions / transversions = 1.34 (63/47) Gap_init rate = 0.06 (22 / 379), avg. gap size = 1.59 (35 / 22) 647 25.92 8.84 1.59 chr3qtel1M 385568 385861 (614139) C L1ME4b_3end#LINE/L1 (520) 372 58 m_b146s551i3 5464 chr3qtel1M 385568 TGGATCAAAGGGTAAGCACAGTTTGAAATTTTGA---GCATAGTTAAATT 385614 i v ii - v ---ii v ii C L1ME4b_3end#L 372 TGGGTCAAAGGGTATGTGCA-TTTGTAATTTTGATAGATATTGCCAAATT 324 chr3qtel1M 385615 GTC-TCTGGAATGGTTGGATGCATTCACAATTCCACCAACAATGTATCAG 385663 i - iiv iv v ivv i v i i v C L1ME4b_3end#L 323 GCCCTCCATAGAGGTTGTACCAATTTACACTCCCACCAGCAATGTATGAG 274 chr3qtel1M 385664 TGTCCCAGTTTTTCCCCATCCCCTCCAACAT--TTCATTATC---TTTTT 385708 v v v ii v i i v i-- vii ---i C L1ME4b_3end#L 273 AGTGCCTGTTTCCCCACACCCTCGCCAACACAGTGTGTTATCAAACTTTT 224 chr3qtel1M 385709 CCTGTCATCCCAGCCAATCTGG-AAGTGTGTAGTGGTATCTCAGAGTGGT 385757 ---- v iiv i- i viv i v i C L1ME4b_3end#L 223 ----TGATCTTTGCCAATCTGATAGGTGAAAAATGGTATCTCAGTGTAGT 178 chr3qtel1M 385758 CTTAATT--CATTTATCTGATCATTAATGA-TTTGGACATCTTTTT-CAT 385803 i -- v v i v i -v ii i-i C L1ME4b_3end#L 177 TTTAATTTGCATTTCTCTTATTATGAGTGAGGTTGAGCATCTTTTCATAT 128 chr3qtel1M 385804 GGCT-AGAAATATTTCAATTTCTTCATCTG------GT---TTCATATCC 385843 vi - ivi vv i iv ------ --- C L1ME4b_3end#L 127 GTTTAAGAGCCATTTGTATTTCCTTTTCTGTGAACTGTCTGTTCATATCC 78 chr3qtel1M 385844 TTT--CCATTTATCAAGTGG 385861 -- v v v C L1ME4b_3end#L 77 TTTGCCCATTTTTCTATTGG 58 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 32.43 CpG sites = 42, Kimura (unadjusted) = 32.43 Transitions / transversions = 1.27 (42/33) Gap_init rate = 0.06 (17 / 293), avg. gap size = 1.82 (31 / 17) 679 26.51 4.31 0.83 chr3qtel1M 385568 385799 (614201) C L1ME3_3end#LINE/L1 (537) 372 133 m_b146s551i4 5464 chr3qtel1M 385568 TGGATCAAAGGGTAAGCACA-GTTTGAAATTTTGAGCATA--GTTAAATT 385614 i v i ii - - iv v viv -- ii iv C L1ME3_3end#LI 372 TGGGTCATAGGGTAGGCGTATGTTT-AGCTTTAGTAGATACTGCCAAACA 324 chr3qtel1M 385615 GTCT-CTGGAATGGTTGGATGCATTCACAATTCCACCAACAATGTATCAG 385663 i - iii i v ivv i v i i v C L1ME3_3end#LI 323 GTTTTCCAAAGTGGTTGTACCAATTTACACTCCCACCAGCAATGTATGAG 274 chr3qtel1M 385664 TGTCCCAGTTTTTCCCCATCCCCTCCAACATTT--CATTATCTTTTTCCT 385711 v i vi v i v i --i i vv i ii C L1ME3_3end#LI 273 AGTTCCAGTTGCTCCACATCCTCGCCAACACTTGGTATTGTCAGTCTTTT 224 chr3qtel1M 385712 GTCATCCCAGCCAATCTGG-AAGTGTGTAGTGGTATCTCAGAGTGGTCTT 385760 - v iii v -ii vv i C L1ME3_3end#LI 223 -TAATTTTAGCCATTCTGGTGGGTGTGTAGTGGTATCTCATTGTGGTTTT 175 chr3qtel1M 385761 AATT--CATTTATCTGATCATTAATGAT-TTGGACATCTTTT 385799 -- vi v i - ii i C L1ME3_3end#LI 174 AATTTGCATTTCCCTGATGACTAATGATGTTGAGCACCTTTT 133 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 33.04 CpG sites = 38, Kimura (unadjusted) = 33.72 Transitions / transversions = 1.65 (38/23) Gap_init rate = 0.04 (9 / 231), avg. gap size = 1.33 (12 / 9) 2255 26.29 10.79 2.94 chr3qtel1M 385934 388147 (611853) C L1M5_orf2#LINE/L1 (171) 3123 741 m_b146s551i5 5464 chr3qtel1M 385934 TGTAAA-ATGTTTTCCCAGTTTATTGTTTCCTTTCTAGTCTGCATTA--- 385979 i - v i ? i i v i v i i vi i v - --- C L1M5_orf2#LIN 3123 TGCAAATATTTTCTCCCANTCTGTGGCTTGCCTTTTCATTTTC-TTAACG 3075 chr3qtel1M 385980 GTTTTGTTTGTACA--AAAACTTTTTAACTTC-ATATAATCAAATTTTTC 386026 v iv v?v -- i v i i- i? i v v C L1M5_orf2#LIN 3074 GTGTCTTTTGANGAGCAGAAGTTTTTAATTTTGATGNAGTCCAATTTATC 3025 chr3qtel1M 386027 TATTTTGTGATCAATAATGATCTCGGTCTTTTTG-GTCC--------AAA 386067 v v vv --- v i - ? vv - -------- C L1M5_orf2#LIN 3024 AATTTTTTCTT---TTATGGT-TNGTGCTTTTTGTGTCCTGTTTAAGAAA 2979 chr3qtel1M 386068 TTCCTTCCTCCTCCACAGTTAAGAAACTAT---CCTATGTTTTCT----- 386109 iii v v?i vi i v iv --- ----- C L1M5_orf2#LIN 2978 TCTTTGCCTANCCCAAGGTCACGAAGATATTCTCCTATGTTTTCTTCTAG 2929 chr3qtel1M 386110 -AATTTACTTATGTCATTCTTT---TCTAGATCTTGAACCCATTTTGACT 386155 - i vv vi v i ?ii --- i i vvi i i ? v C L1M5_orf2#LIN 2928 AAGTTTTATAGTTTTANCTTTTACATTTAGGTCTATGATCCATCTNGAAT 2879 chr3qtel1M 386156 TTATCTTT-TGTACTGTGTTAAAT--GGGTCAAGG--CCTGTTTCTCCAT 386200 v i - iv v ii -- i ?-- v v i C L1M5_orf2#LIN 2878 TAATTTTTGTGTATGGTGTGAGGTAGGGGTCGAGNTTCATTTTTTTCCAT 2829 chr3qtel1M 386201 ACA-AT-TTCAATT-TTCCAGCAGT-TTTGTCAAACAGTAAATTCTTATC 386246 ii- - i - vi- ii v vvv i - C L1M5_orf2#LIN 2828 ATGGATATCCAATTGTTCCAGCACCATTTGTTGAAAAGACTATCCTT-TC 2780 chr3qtel1M 386247 CCCAAAGCTGGGGT-CTTTGGG---TTTGTCAAACACTA---GTTC---T 386286 --- iiv - ? v--- v ii --- ?i --- C L1M5_orf2#LIN 2779 CCCA---CTGAATTGCNTTGGCACCTTTGTCAAAAATCAANTGNCCATAT 2733 chr3qtel1M 386287 ATGTTTTGA-CTATTT-TGTCCTTTGAACCTGACCTATTCCACTGATCAA 386334 v v i- - vv i ---- ivi i i v C L1M5_orf2#LIN 2732 ATGTGTGGGTCTATTTCTGGACTCT----CTATTCTGTTCCATTGATCTA 2687 chr3qtel1M 386335 CGAGTCTATTTCTTGGCCAG-ACCAAATGGTTTTGGTGACTGCTGCTTTA 386383 ivv iii vv i- v iv i i v iv C L1M5_orf2#LIN 2686 TTTGTCTATCCTTACGCCAATACCACACTGTCTTGATTACTGTAGCTTTA 2637 chr3qtel1M 386384 -AATATGTTTT-AGATTACGAAG----AGGCCACCTTCCTTGATTTTTTT 386427 - v i - ? i?v v ---- v v vv i - i i C L1M5_orf2#LIN 2636 TAATAAGTCTTGANATCNGGTAGTGTAAGTCCTCCAACTTTG-TTCTTCT 2588 chr3qtel1M 386428 TTTTCATTAG-TTCCCTTGAAAAT-CTTGACCTTTTCTTCTTCCAGATAA 386475 -- - vii ivv - ? ii i vivi v C L1M5_orf2#LIN 2587 TTTTCA--AGATTGTTTTGGCTATTCTNGGTCCTTTGCATTTCCATATAA 2540 chr3qtel1M 386476 ATTTTAT------TTTATTTTTTTCTAGGTCATTAAAATAATTTTGGGGG 386519 v------i i ivv ------i v ii vvv C L1M5_orf2#LIN 2539 ATTTTAGAATCAGCTTGTCAATTTCTA------CAAAAAAACCTGCTGGG 2496 chr3qtel1M 386520 GATCTGATTGGTAT-GCATTAAATAAATAGATTAGTTAAAGTAATATTGT 386568 iv i v - i vv i i vii v iv v C L1M5_orf2#LIN 2495 ATTTTGATTGGGATTGCATTGAATCTATAGATCAATTTGGGGAGAATTGA 2446 chr3qtel1M 386569 TA-CTTTATTATATTCCAAACCCTATCCAAGGCATTAATAT--------T 386609 i - ? iv ---i vi - vv v i -------- C L1M5_orf2#LIN 2445 CATCTTNACAATATT---GAGTCT-TCCAATCCATGAACATGGTATATCT 2400 chr3qtel1M 386610 TTCCAGTTGTG-AGATCTGTCTTTA---TTTTTAA--AGTGTTTTGTAGT 386653 i v i v- i - --- i i v -- i C L1M5_orf2#LIN 2399 CTCCATTTATTTAGGTCT-TCTTTAATTTCTCTCAGCAATGTTTTGTAGT 2351 chr3qtel1M 386654 TTTT-GT-TATAGTTTCTG-AC-TTTTTTGACAGAAG-ATTCCGAAATAT 386698 i- - ? v ii - - ? vi vv- v i C L1M5_orf2#LIN 2350 TTTCAGTGTANAGGTCTTGCACATNTTTTGTTAGATTTATTCCTAAGTAT 2301 chr3qtel1M 386699 TTTATACTATTGGAT--TATTTTAATTGGAATT--TCTTTGTATCTCTTG 386744 ? ii v v -- v v v -- i ?iv i v v C L1M5_orf2#LIN 2300 TTNATGTTTTTTGATGCTATTGTAAATGGTATTGTTTTTNAAATTTCATT 2251 chr3qtel1M 386745 TGTTGGATTTTTTGT-----ATGTATAAAAAT----TTGA-----GGAT- 386779 - ivi v -----i i i ---- ----- v - C L1M5_orf2#LIN 2250 T-TCCAATTGTTTGTTGCTAGTATATAGAAATACAATTGATTTTTGTATA 2202 chr3qtel1M 386780 TTATTTTTGTATCCCA-AACTTTGCTAAAGTTATCAATTATTTCTAATAG 386828 ivii ?i-i i v i iiv v i C L1M5_orf2#LIN 2201 TTGACCTTGTATCCNGCGACCTTGCTAAATTCACTTATTAGTTCTAGTAG 2152 chr3qtel1M 386829 CTTTTTTAGTAGAAT-TCTGGGATTT-CTAAGTAAAACATCATATCATCT 386876 i ? - v - i ? - v ? vv i C L1M5_orf2#LIN 2151 TTTNTTT-GTAGATTCTTTNGGATTTTCTACGTANACAATCATGTCATCT 2103 chr3qtel1M 386877 GTAAA-GGTGATTAATTTGGTTTCC-CATTACCTACTCTAATTCTTTTCA 386924 ii -ii? i- i vi i- v v v iii v v i i C L1M5_orf2#LIN 2102 GCGAATAANGAC-AGTTTTATTTCTTCCTTTCCAATCTTTATGCCTTTTA 2054 chr3qtel1M 386925 TTC---TTTCTCAATTTATTGC-----CTAGGGAAATTTCTAATACAATA 386966 i--- iivi ----- --- ii i i i C L1M5_orf2#LIN 2053 TTTCTTTTTCTTGCCTTATTGCACTGGCTAGG---ACCTCCAGTACAATG 2007 chr3qtel1M 386967 TTGAATAATAATGGTGATAGTGGACAATCTTGTTTCCT--CTGATCTTAC 387014 iv i ? i vi i iv -- i v C L1M5_orf2#LIN 2006 TTGAATAGAAGTGGTGANAGCGGACATCCTTGTCTTGTTCCCGATCTTAG 1957 chr3qtel1M 387015 TGGGAATGGTT---ATTTATCCCCATTAA-TATGAATACTTCCAACAGA- 387059 v v v? ---i ? v v - - ii ?v vii i- C L1M5_orf2#LIN 1956 GGGGAAAGCNTTCAGTNTTTCACCATTAAGTATGA-TGTTNGCTGTAGGT 1908 chr3qtel1M 387060 ----AATGGTATGACAATTTT----TCGGAAAAGT--CCTT-TATTCCTA 387098 ----vi i - v vv v ---- i iii -- - C L1M5_orf2#LIN 1907 TTTTCGTAG-ATGCCCTTTATCAGGTTGAGGAAGTTCCCTTCTATTCCTA 1859 chr3qtel1M 387099 ---TA-TAAGTGTTTTTAATAGGAATGGATGTTGA--TTTATCAAATG-T 387141 --- i- i v vi v i -- i - C L1M5_orf2#LIN 1858 GTTTGCTGAGAGTTTTTATCATGAATGGGTGTTGAATTTTGTCAAATGCT 1809 chr3qtel1M 387142 TTTTCTGCATCTATTAA-ATGATCATATGATTTTTGT---TAATTTGGTT 387187 i - v --- v iv C L1M5_orf2#LIN 1808 TTTTCTGCATCTATTGAGATGATCATATGATTTTTCTCCTTTATTCTGTT 1759 chr3qtel1M 387188 ATTATATAGTCAATTATGGTAAT--ATTTTCCTAT-TGAAAAGGGTCCTG 387234 -- i v iiv i -- vv - v vviii i C L1M5_orf2#LIN 1758 A--ATATGGTGAATTACATTGATTGATTTTCGAATGTTAAACCAACCTTG 1711 chr3qtel1M 387235 CATTCCTGT-ATAAACCT-ACCTGGTCATAGTGTATTATCCTG---GGAT 387279 v- i- i ii v---iv C L1M5_orf2#LIN 1710 CATTCCTGGGATAAACCCCACTTGGTCATGATGTATTATCCTTTTTATAT 1661 chr3qtel1M 387280 GATTTTTGAATC----TTTTTAATATTTTATTTGAGATTTTTGCATCAAT 387325 - vi i i---- vi i ?ii v C L1M5_orf2#LIN 1660 -ATTGCTGGATTCGATTTGCTAATATTTTGTTNAGGATTTTTGCATCTAT 1612 chr3qtel1M 387326 ATTCATTAGGGA-GTTTATCTTT--TTTCCTTCTGTTTTCAT---CCTAT 387369 i v -i vi v -- i i v v v ---ii i C L1M5_orf2#LIN 1611 GTTCATGAGGGATATTGGTCTGTAATTTTCTTTTCTTGTAATGTCTTTGT 1562 chr3qtel1M 387370 CTGGTTT-GGTA-CAGACT-ATTCTTGTC----AAAAGGAATTTAGTAGT 387412 ? - - iv - v v i ---- v i vi v C L1M5_orf2#LIN 1561 CNGGTTTTGGTATCAGGGTNATGCTGGCCTCATAAAATGAGTTGGGAAGT 1512 chr3qtel1M 387413 -TTCCTTCATTC-CTTTTTTC--AAATAGTTTATATAAATTTGGT--TAC 387456 - i v i- v --i v i i iv -- i C L1M5_orf2#LIN 1511 GTTCCCTCTTTTTCTATTTTCTGGAAGAGTTTGTGTAAGATTGGTATTAT 1462 chr3qtel1M 387457 TTGTTCTTTAAAT-TTTGGTAGAATTCA---ATTAAACCATCTGGTCCTG 387502 v i - ---i v i v C L1M5_orf2#LIN 1461 TTCTTCCTTAAATGTTTGGTAGAATTCACCAGTGAAGCCATCTGGGCCTG 1412 chr3qtel1M 387503 GGGCTT------------GGTT---GATTAAAACCTGTTCTATTTCTTTT 387537 i i ------------ ---i v ---i v v C L1M5_orf2#LIN 1411 GAGTTTTCTTTGTGGGAAGGTTTTTAATTACAA---ATTCAATTTCTTTA 1365 chr3qtel1M 387538 TCTAAAATGGGACTATTTAAACAATTTCT---TCCTCCTCTGTTAATTCA 387584 vivi v i i i i i-- --- i i v? i i iv C L1M5_orf2#LIN 1364 ATAGATATAGGGCTATTCAGAT--TTTCTATTTCTTCTTGNGTCAGTTTT 1317 chr3qtel1M 387585 GG------GTTATTTTTAAGGTATTCATCCATTTCATTTAGGTTATCAAA 387628 ------ vv i v ii i i ? C L1M5_orf2#LIN 1316 GGTAANTTGTGTTTTTCAAGGAATTTGTCCATTTCATCTAAGTTNTCAAA 1267 chr3qtel1M 387629 TTTA---GGATAAATTT---CGGAAAGCAACTC-CTAATTATTGCTTTTT 387671 --- v v --- iv v--- i - v -- i C L1M5_orf2#LIN 1266 TTTATTGGCATAAAGTTGTTCATAAT---ATTCTCTTATTAT--CCTTTT 1222 chr3qtel1M 387672 AATTTCCTCT----TCAATAGTGACGAGGTCTCCCTTCTCATT--TGAAG 387715 v - v ---- vi i --- i i -- -v C L1M5_orf2#LIN 1221 AATGTC-TGTAGGATCTGTAGTGATG---TCTCCTTTTTCATTCCTGA-T 1177 chr3qtel1M 387716 ACTAATAATTTAT-TTTTCTTCCTTTTTAT---AATCAAATTTACCAAAA 387761 i ii i - i ii v ---i ivi ?i i i i C L1M5_orf2#LIN 1176 ATTGGTAATTTGTGTCTTCTCTCTTTTTTTCTTGATCAGTCTNGCTAGAG 1127 chr3qtel1M 387762 GTTTATTA-TTTTGTTG-TTTTTTCATAAAAC-AACTCTTAGTTTTATTT 387808 i - i - i v i - i i i i ii v C L1M5_orf2#LIN 1126 GTTTATCAATTTTATTGATCTTTTCAAAGAACCAGCTTTTGGCTTCGTTG 1077 chr3qtel1M 387809 ATTAATTCAAAAGGTT-TTTTTTTACTTTCCATTTTATTAATTTCACGTT 387857 vvi v ---- - ? ? ii i i i -i i C L1M5_orf2#LIN 1076 ATTTTCTCTA----TTGTNTNTTTGTTTTCTATTTCATTGATTTC-TGCT 1032 chr3qtel1M 387858 TTTAT-TTTAGAATTTCAAGTTTAGTATTTGATTGGGGTTTTTTAATTTG 387906 i - vv vvvii vv i ?v v --- C L1M5_orf2#LIN 1031 CTTATCTTTATTATTTCCTTCCTTCTACTTNCTTTGGGTTT---AATTTG 985 chr3qtel1M 387907 CTCTT---TTTCTAGCTTTTTAAGTTGCAAGCCCAATTCATTGATCTT-- 387951 --- i v v ii iv i -- C L1M5_orf2#LIN 984 CTCTTCTTTTTCTAGCTTCTTAAGGTGGAAGCTTAGATCATTGATTTTAA 935 chr3qtel1M 387952 --CTCTTTCCCTATTTCATGCAAGTAAGGCTCTAGAGATACAAAATTTCC 387999 -- i i i i v i v ii ? i ---- i i? v i v i C L1M5_orf2#LIN 934 GCCTTTCTTCTTTTCTAATATANGCA----TTTAANGCTATAAATTTCCC 889 chr3qtel1M 388000 CATTATTACCGCTTGGGCTGCCTCCCCCAAATGTTGGTATGTTGTCTCAT 388049 iv v vi i vi v v v i v iv C L1M5_orf2#LIN 888 TCTAAGCACTGCTTTAGCTGCATCCCACAAATTTTGATATGTTGTATTTT 839 chr3qtel1M 388050 TGTTGTCATTCTCTTGGGTGAAATTAT----TAATTGTGTCTATGATTTG 388095 ii ? ----i v v v ---- viv?i i v C L1M5_orf2#LIN 838 CATTNTCATTC----AGTTCAAAATATTTTCTAATTTCCNTTGTGATTTC 793 chr3qtel1M 388096 CTGTTTCACCTATTCATTCTTTAGAA-TGAGATTATTTAGTTTACAAATA 388144 i v v i vvi v - v - i i v C L1M5_orf2#LIN 792 TTCTTTGACCCATGGGTTATTTAGAAGTGTG-TTGTTTAATTTCCAAATA 744 chr3qtel1M 388145 CTT 388147 i C L1M5_orf2#LIN 743 TTT 741 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 33.38 CpG sites = 321, Kimura (unadjusted) = 33.91 Transitions / transversions = 1.32 (321/244) Gap_init rate = 0.08 (178 / 2213), avg. gap size = 1.74 (309 / 178) 327 27.95 6.40 5.56 chr3qtel1M 390319 390443 (609557) C L2d2_3end#LINE/L2 (7) 548 423 m_b146s601i4 5465 chr3qtel1M 390319 AAATTAATGAATGAGAATTT--TG-GCACTCAATCTATGTCAGGCACTTT 390365 i ii ---- -- - i ii v v i iv v C L2d2_3end#LIN 548 AAATCAACAAAT----ATTTATTGAGCGCCTACTGTGTGCAAGGCACTGT 503 chr3qtel1M 390366 GCTAAGTGCTAGAGTTACAGATATAAA-AAGCA----AGATAGTTCCTGT 390410 i i --- vivi i - i ---- v i i i C L2d2_3end#LIN 502 GCTAGGCGCT---GTGGGGGATACAAAGAAGTATAAGACATGGTCCCTGC 456 chr3qtel1M 390411 GCTGAAAGAGTTTACATTTTAATAGGGGAAACA 390443 v v i i v i i v i C L2d2_3end#LIN 455 CCTCAAGGAGCTTACAATCTAGTTGGGGAGACA 423 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 33.76 CpG sites = 22, Kimura (unadjusted) = 36.54 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.09 (11 / 124), avg. gap size = 1.36 (15 / 11) 338 35.50 11.75 4.39 chr3qtel1M 390538 390920 (609080) MamRTE1#LINE/RTE-BovB 895 1304 (2508) m_b146s601i5 5466 chr3qtel1M 390538 TCATCAGTATATATTATTTTACCATGACAAACCCTAATAGGATCAAAGAA 390587 iii vviiii i iv ii ii ivv MamRTE1#LINE/ 895 TCATCAGCGCATATGCCCCCACCATGACGAATACCGATGAGGAGAAAGAA 944 chr3qtel1M 390588 AACTTAAATAAAGACCTGGAGATCTTCACC--------ATCAATGT---- 390625 iv vv i i i v vvi i -------- i ii ---- MamRTE1#LINE/ 945 AGATTCTACAAGGATCTGGACAGACTCATCGCAGCGGTACCAACATCTGA 994 chr3qtel1M 390626 ---GCTTATAATTCTGGGTGACTTCAATACACGAGTAGGCACAGACTATC 390672 --- v vi ivi v i ii v v vv - ii MamRTE1#LINE/ 995 CAAGCTGATCGTCACGGGAGATTTCAACGCACGTGTCGGCAGCGA-TGCC 1043 chr3qtel1M 390673 -AGTCAT-------ATTCCTTAAGAGCA-ATAGAATAAGAAACAGCAATA 390713 - iv i ------- v v ii- v ?- ii i vi -- v?- MamRTE1#LINE/ 1044 GAAACGTGGAGAAAAGTCATCG-GACCNCACGGGATTGGAAA--GCTN-A 1089 chr3qtel1M 390714 GCAGCAATCATTTATTACTGAAGACTT-GCACATCT------CATCTGCT 390756 i vi i i v ---- i- iv v ------ v MamRTE1#LINE/ 1090 ACAGCAATGGTCTACTCCTG----CTCAGCGAATGTGCCAAGCATCAGCT 1135 chr3qtel1M 390757 C---ATGACCTACATTGTCTTCTGTTTACC---TAAACTTAAGACTTCGC 390800 --- v v iii i ii --- ivvv v ii MamRTE1#LINE/ 1136 CGTAATCACCAACACCATCTTCCGCCTACCGAATAAGAGAAAGACATCAT 1185 chr3qtel1M 390801 AGATGCACAC----TCACAGCAGTCATTGATACTTAGTAGACTATATC-- 390844 i v ---- vv ---- ii ii vi v i -- MamRTE1#LINE/ 1186 GGATGCACCCAAGGTCTAAGCAG----TGGCATCTCATTGATTATATCAT 1231 chr3qtel1M 390845 --CTTGAAAGAAGAGACAGAAAGGATGGGAAAGTGACAAAGGCAATGTGT 390892 --i i v -v i vvi vvv ii v vivi v i MamRTE1#LINE/ 1232 CGTTCGACAG-CGGGACCTGAAGGATGTTTAGATTACTGCAGCTATGCGT 1280 chr3qtel1M 390893 GACTCACACAGAGTACTTGACTGATCGT 390920 ----i i v i v i i i MamRTE1#LINE/ 1281 G----GCGCCGAGTGCTGGACCGACCAT 1304 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 42.53 CpG sites = 76, Kimura (unadjusted) = 50.74 Transitions / transversions = 1.41 (76/54) Gap_init rate = 0.08 (31 / 382), avg. gap size = 2.03 (63 / 31) 336 27.84 5.93 8.70 chr3qtel1M 391450 391567 (608433) MIRb#SINE/MIR 4 118 (150) m_b146s601i6 5467 chr3qtel1M 391450 AGGGGTAGCTAGATGGCACAGTAGATAAAACATGGACCCTGGAG------ 391493 i ---i ii i v i i i i ii ------ MIRb#SINE/MIR 4 AGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGAC 50 chr3qtel1M 391494 -GAGCTCAGTTTAAATTCAGCTTCAGACACTTATCACTTCCCAGATATGT 391542 - v vi ii i v vi v v ------- i v i MIRb#SINE/MIR 51 AGACCTGGGTTCGAATCCCGGCTCTGCCACTTA-------CTAGCTGTGT 93 chr3qtel1M 391543 GACCCTGGGCAAGTCACTTAATCCC 391567 i i i i MIRb#SINE/MIR 94 GACCTTGGGCAAGTTACTTAACCTC 118 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 32.08 CpG sites = 22, Kimura (unadjusted) = 36.85 Transitions / transversions = 2.75 (22/8) Gap_init rate = 0.10 (12 / 117), avg. gap size = 1.42 (17 / 12) 320 39.59 1.68 3.42 chr3qtel1M 392135 392372 (607628) MamRTE2#LINE/RTE-BovB 7 240 (1312) m_b146s551i6 5468 chr3qtel1M 392135 CACTGCTGACAAAATTCTTGCCAAAGTTCTCCTTAGTAGGCTGACCTTTC 392184 i i iv i iv v i i i v iiv i -- ii MamRTE2#LINE/ 7 CACCGCCGGAAAGATCATTGCAAGAATCCTCCTGAACCGACT--CCTCCC 54 chr3qtel1M 392185 ACCTG--GAAGATGGTCACCATCTACCTGAAAGCCTGTGTGGCTTCAGAG 392232 i -- - v ----- v v vvi v i v i MamRTE2#LINE/ 55 ACTTGCTGAAGA-GCT-----TCTCCCGGAATCTCAGCGTGGGTTTAGAG 98 chr3qtel1M 392233 GGCTGAGAAATAC--TTAATATGATGTTTGTTGCCCAATAACTCCAGGAA 392280 viii? iiii --i i i i v iii i ivi i ? MamRTE2#LINE/ 99 CATCNAGAGGCGCAACTGATACGGTCTTCACTGCTCGCCAGCTNCAGGAA 148 chr3qtel1M 392281 AAGTGCCAGGAGAAGCACAGAGGTCACCACACAATGTTTGTTGTTTTGAT 392330 i i iv i i i vv vii i iiiiv iv i vi? v v MamRTE2#LINE/ 149 AAATGCCAAGAACAACATAAACCTCTTTATATGGCCTTCCTCGACNTCAG 198 chr3qtel1M 392331 TAAGGCCTTTGATACCACCATTCATGAGGTCTTACAGAAAAT 392372 v iv iii v i i iv iii ii MamRTE2#LINE/ 199 GAAGGCCTTTGACTCTGTCAGTCGTGAAGCATTGTGGAGGAT 240 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 54.69 CpG sites = 63, Kimura (unadjusted) = 63.81 Transitions / transversions = 2.25 (63/28) Gap_init rate = 0.04 (10 / 237), avg. gap size = 1.20 (12 / 10) 19 0.00 3.23 3.23 chr3qtel1M 393185 393215 (606785) (TCTTT)n#Simple_repeat 1 31 (0) m_b146s252i7 5469 chr3qtel1M 393185 TCTTTTCTTTTCTTTT-TTTTCTTTTTCTTTT 393215 - - (TCTTT)n#Simp 1 TCTTTTCTTTTCTTTTCTTTTC-TTTTCTTTT 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2) 18 15.51 0.00 0.00 chr3qtel1M 393187 393216 (606784) (T)n#Simple_repeat 1 30 (0) m_b146s252i8 5469 chr3qtel1M 393187 TTTTCTTTTCTTTTTTTTCTTTTTCTTTTT 393216 i i i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 30 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 416 26.92 0.00 8.62 chr3qtel1M 393234 393359 (606641) C MIRb#SINE/MIR (152) 116 1 m_b146s601i8 5470 chr3qtel1M 393234 GGGTAAGTGATATGCTCAGGATCACACAGCTAGGAAGTGTTAAGTATCTG 393283 v i iv i i i v ---- i --- C MIRb#SINE/MIR 116 GGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTG----GCA---G 74 chr3qtel1M 393284 AAATCAGATTTGAAGTCAGGTCCTCCTGTTTTCAGGGCTGGTGCTCTCTC 393333 ivivi i vi ivi vi i ii iv i C MIRb#SINE/MIR 73 AGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTC 24 chr3qtel1M 393334 CACTGCACCACCTCGCTACTCTTCTG 393359 --- i i i C MIRb#SINE/MIR 23 CACTGCACCA---CGCTGCCCCTCTG 1 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 31.96 CpG sites = 22, Kimura (unadjusted) = 34.74 Transitions / transversions = 2.44 (22/9) Gap_init rate = 0.08 (10 / 125), avg. gap size = 1.00 (10 / 10) 423 25.11 0.00 6.73 chr3qtel1M 393234 393344 (606656) C MIRc#SINE/MIR (155) 113 10 m_b146s601i7 5470 chr3qtel1M 393234 GGGTAAGTGATATGCTCAGGATCACACAGCTAGGAAGTGTTAAGTATCTG 393283 v iv i i i v ---- i --- C MIRc#SINE/MIR 113 GGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTG----GCA---G 71 chr3qtel1M 393284 AAATCAGATTTGAAGTCAGGTCCTCCTGTTTTCAGGGCTGGTGCTCTCTC 393333 ivivi i i vi i vi i i v ii i C MIRc#SINE/MIR 70 AGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTC 21 chr3qtel1M 393334 CACTGCACCAC 393344 C MIRc#SINE/MIR 20 CACTGCACCAC 10 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 28.77 CpG sites = 18, Kimura (unadjusted) = 31.68 Transitions / transversions = 2.25 (18/8) Gap_init rate = 0.06 (7 / 110), avg. gap size = 1.00 (7 / 7) 482 32.56 4.93 6.36 chr3qtel1M 393876 394321 (605679) L3#LINE/CR1 1770 2209 (1890) m_b146s601i9 5471 chr3qtel1M 393876 TCTCCATCAAAAGATGGGGAAATCAACAAGGGAAAATTTCATTCTAGATG 393925 -- i i i i i v i i v vii i i iv L3#LINE/CR1 1770 TCTC--TCAGAAGGTAGAGGAAGCAACGAGGGGAACTGCTACTCTGGACT 1817 chr3qtel1M 393926 CAACCTTTATCAAGAGGGAAGAGTTGGTTCCTGGAGTGACAAT--ATGGG 393973 i iii v i v i ii vv i iv i -- i L3#LINE/CR1 1818 TAATTCTGACCAACAAGGAAGAACTGGTTGGTGAAGTGGAAGTCGATAGG 1867 chr3qtel1M 393974 AACATTATATGGTGAGGGAA-GCCAACTGATTCATTTCTGAGTTAGAAAG 394022 v ---- - ii i- -- -- i iv v v - L3#LINE/CR1 1868 AACCTT----GG-GAGAAAGTGCCA--TG--TCATCTTAGAGTTCGTAA- 1907 chr3qtel1M 394023 TTAGGTATATATAGTATATAAAT--AAGGTTTATATATAT---AAACCTT 394067 - vi - v v v - - i -- i ii i i --- i i L3#LINE/CR1 1908 -TAGCCA-AGAAAGGA-A-AAGTTAAAAGTCCACATATGTTCCAGACTTT 1953 chr3qtel1M 394068 AGAATTTGAAAGAGCAGACTTCACAGAATACAGAGGAAAAGTAATCAGGA 394117 vi --- i i i v i v - vii - v L3#LINE/CR1 1954 ACGA---GGAAAAGCAGATTTCAAAAAATTCAGA-GAAAAGAGGT-ATGA 1998 chr3qtel1M 394118 TCTCAGGAACTAAAATTCTGAGAGAGAATACAGCCTGGAAAGAATGAGAA 394167 ii v iv ?i i i vi i - v ii iiiii i i? i L3#LINE/CR1 1999 TTCCATGGCCNGAGACTCAAAAAGA-AAGATGGCTCAAGAGGGNTGGGAA 2047 chr3qtel1M 394168 ACTCTCAA----GAAACTC-----ACAAACACAAGTAATGCTGCTGAGGA 394208 i i ---- i ----- vi i i - iiv L3#LINE/CR1 2048 GCTCTTAAAAATGAAATTCTGACTACAATTACAAATGAT-CCAATGAGGA 2096 chr3qtel1M 394209 GGAGAACATCTACTGTA---AAAAGAACAATATAGAAACAGAGAAAAATC 394255 i i v vvv vv i --- i i v ii i vv? v i? v L3#LINE/CR1 2097 AGAAAAGAGGGAGGGCATTTAAGAAACCAACGTGGCTNCATAGAGNATTC 2146 chr3qtel1M 394256 ATTTACTTCATTGAACTCTTAAAATG-CATGT-TTAGAAGGTGGAAACAA 394303 vi v iv -- -- i v - - i i -i L3#LINE/CR1 2147 TCTGATGTCA--GA--TTTTAAAAGGACATGTATCAGAAGATGGAAA-GA 2191 chr3qtel1M 394304 AGGCAGAGAATACAGGAC 394321 i i v v ivv L3#LINE/CR1 2192 GGACATATAACCAAGGAC 2209 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 44.18 CpG sites = 89, Kimura (unadjusted) = 45.64 Transitions / transversions = 1.89 (89/47) Gap_init rate = 0.08 (37 / 445), avg. gap size = 1.35 (50 / 37) 33 29.54 2.56 0.84 chr3qtel1M 395680 395796 (604204) (TC)n#Simple_repeat 1 119 (0) m_b146s252i10 5472 chr3qtel1M 395680 TCTCTCTCCCTCTTCCTC-CGCCTTCTTTTTATCTCTCTCATCTCAATTT 395728 i ii - v ii i i v - vv i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TCTCTCTCT 49 chr3qtel1M 395729 CTCAGTCTCT-TATGTTTCTTTCTTGCT-TCTCTGTCTCTCTTTCTGACT 395776 vv - v v i i iv - v i vv (TC)n#Simple_ 50 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 99 chr3qtel1M 395777 CTATTTCTATCTCTCTGTCT 395796 v i v v (TC)n#Simple_ 100 CTCTCTCTCTCTCTCTCTCT 119 Matrix = Unknown Transitions / transversions = 0.87 (13/15) Gap_init rate = 0.03 (4 / 116), avg. gap size = 1.00 (4 / 4) 29 32.66 1.50 1.50 chr3qtel1M 395678 395810 (604190) (TTTCTC)n#Simple_repeat 1 133 (0) m_b146s252i9 5473 chr3qtel1M 395678 TTTCTCTCTCCCTCT-TCCTCCGCCTTCTTTTTATCTCTCTCATCTCAAT 395726 i i i - i i v i i v i - i vv (TTTCTC)n#Sim 1 TTTCTCTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCTTTCTC-TTTCTCT 49 chr3qtel1M 395727 TTCTCAGTCTCTTATGTTTCTTTCTTGCT-TCTCTGTCTCTCTTTCTGAC 395775 vv - v i i i v - i v i vvi (TTTCTC)n#Sim 50 TTCTCTTTCTCTT-TCTCTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCTT 98 chr3qtel1M 395776 TCTATTTCTATCTCTCTGTCTGTTACTCATTTTCT 395810 v v i v v v v i (TTTCTC)n#Sim 99 TCTCTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCT 133 Matrix = Unknown Transitions / transversions = 1.00 (17/17) Gap_init rate = 0.03 (4 / 132), avg. gap size = 1.00 (4 / 4) 205 33.83 0.00 5.00 chr3qtel1M 395916 395999 (604001) C MamRTE1#LINE/RTE-BovB (349) 3463 3384 m_b146s601i10 5474 chr3qtel1M 395916 TTCTTCTGTCCTCCTTGTGAGTGCTTGTCTCATGGGAGTTCTCCATAAAA 395965 i i ivv i v i i ivvv i v i v i C MamRTE1#LINE/ 3463 TTCTTCTGCCCTCCCTGCTTGCGGTTGCCCCACTTCAGCTCACCGTACAG 3414 chr3qtel1M 395966 TAGTCTTTTGGGCAAAAGTACTTCTGTCATTCAT 395999 i iivi i ---- v v i C MamRTE1#LINE/ 3413 CAGCTGCTTGGGTA----TCCTGCTGTCATCCAT 3384 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 41.95 CpG sites = 16, Kimura (unadjusted) = 46.60 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.05 (4 / 83), avg. gap size = 1.00 (4 / 4) 18 15.27 2.63 0.00 chr3qtel1M 396899 396936 (603064) (AAGAA)n#Simple_repeat 1 39 (0) m_b146s252i11 5475 chr3qtel1M 396899 AAGGAAGAAAAAGGAAAGAAAAGAAGA-AAAAGAAAAGA 396936 i ii i i - (AAGAA)n#Simp 1 AAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGA 39 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 180 32.06 1.27 1.27 chr3qtel1M 398353 398431 (601569) L2c_3end#LINE/L2 355 433 (45) m_b146s601i11 5476 chr3qtel1M 398353 CATGT-TGTGCCTTCCTAGGAGAATCAGATGTCCTCAACGGCACAGAGTG 398401 ? - vi i - vv v vv vv ii v vi vi L2c_3end#LINE 355 CNTGTCTGTCTCCTCC-ACTAGACTGTGAGCTCCTTGAGGGCAGGGACCG 403 chr3qtel1M 398402 TGTTGTGTTTGTCTTTGTATGCCCAGTACC 398431 iv i ii v ii L2c_3end#LINE 404 TGTCTTATTCATCTTTGTATCCCCAGCGCC 433 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 38.51 CpG sites = 12, Kimura (unadjusted) = 43.05 Transitions / transversions = 0.92 (12/13) Gap_init rate = 0.03 (2 / 78), avg. gap size = 1.00 (2 / 2) 451 24.98 5.84 3.57 chr3qtel1M 398532 398668 (601332) C L2a_3end#LINE/L2 (0) 517 378 m_b146s601i12 5477 chr3qtel1M 398532 ACTCCTCCATT-AATAAACATT-ATTAAGTGTCTTCTATGTACCAGGCAC 398579 i v i - i i - i i i v i C L2a_3end#LINE 517 ATTCATTCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCAC 468 chr3qtel1M 398580 TGTGTTATAAACGCTGGGAGTCC--TAATGGAGGTAAAA-AGAC---AGG 398623 -- v ii ii v --i i i --i - --- v C L2a_3end#LINE 467 --TGTTCTAGGCGCTGGGGATACAGCAGTGAA--CAAAACAGACAAAAGT 422 chr3qtel1M 398624 CCCTGTCCTTAAGGAGTTTACAATTTAATGGGGAAATGATGAACA 398668 i i v i v i i ii - iii C L2a_3end#LINE 421 CCCTGCCCTCATGGAGCTTACATTCTAGTGGGGGGA-GACAGACA 378 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 31.20 CpG sites = 26, Kimura (unadjusted) = 32.42 Transitions / transversions = 3.71 (26/7) Gap_init rate = 0.07 (10 / 136), avg. gap size = 1.30 (13 / 10) 384 26.01 8.72 3.89 chr3qtel1M 398537 398708 (601292) C L2d_3end#LINE/L2 (8) 508 329 m_b146s601i13 5477 chr3qtel1M 398537 TCCATTAATAAACATT-ATTAAGTGTCTTCTATGTACCAGGCACTGTGTT 398585 v i i ii - i i i v i ivi i C L2d_3end#LINE 508 TCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTGTGCT 459 chr3qtel1M 398586 ATAAACGCTG---GGAGTCCTAATGGAGGTA-AAAAGACAGGCCCTGTCC 398631 --ii --- iivv? vi? - - i v ii v i C L2d_3end#LINE 458 A--GGCGCTGTGGGGAACGANAAAANAG-TATAAGACATGGTCCCTGCCC 412 chr3qtel1M 398632 TTAAGGAGTTTACAATTTAA-TGGGGAAAT--GATGAACAGCCAAATGTA 398678 i i i i- i i-- iv -- v v C L2d_3end#LINE 411 TCAAGGAGCTTACAATCTAGTTGGGGAGACAAGACTAACA--CACATGAA 364 chr3qtel1M 398679 -----CAGAAAACAAACTAC-AGCCGGGATA-AATTA 398708 -----i i -- - v i v - C L2d_3end#LINE 363 ACAATTAGAGAACAA--TACAAGACAGTATATAATTA 329 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 32.08 CpG sites = 30, Kimura (unadjusted) = 34.04 Transitions / transversions = 2.31 (30/13) Gap_init rate = 0.09 (15 / 171), avg. gap size = 1.47 (22 / 15) 317 32.85 0.00 0.00 chr3qtel1M 399147 399283 (600717) C L1MC_orf2#LINE/L1 (3070) 224 88 m_b146s551i7 5478 chr3qtel1M 399147 GCTACTCCTATTTTTTTTACTTTACCTGAACCATAATATATTCTGCTCCA 399196 ?ii i vvv vivvv v ii ii v C L1MC_orf2#LIN 224 GCTACTCCNGCTTTCTTTTGATTAGTGTTAGCATGGTATATCTTTCTCCA 175 chr3qtel1M 399197 GCCTTTTAGCTTCACTCTGTATGTATCACTATGCTTTAAATACATTTCTT 399246 v ? vi i v i i vi ii v i ivi C L1MC_orf2#LIN 174 TCCNTTTACTTTTAATCTATATGTGTCTTTATATTTAAAGTGGGTTTCTT 125 chr3qtel1M 399247 GTAAGCAACATATTGCAGGATTCTGGCTTTTAATACA 399283 ii v iv i ii vi i v C L1MC_orf2#LIN 124 GTAGACAACATATAGTTGGGTCTTGTTTTTTGATCCA 88 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 45.58 CpG sites = 26, Kimura (unadjusted) = 45.58 Transitions / transversions = 1.37 (26/19) Gap_init rate = 0.00 (0 / 136), avg. gap size = 0.0 (0 / 0) 302 32.56 2.33 0.00 chr3qtel1M 399178 399306 (600694) C L1MEc_5end#LINE/L1 (50) 2477 2346 m_b146s551i8 5478 chr3qtel1M 399178 CATAATATATTCTGCTCCAGCCTTTTAGCTTCACTCTGTATGTATCACTA 399227 ii ii vi v vi i vi i v i vi C L1MEc_5end#LI 2477 CATGGTATATCTTTTTCCATCCTTTTACTTTTAACCTATTTGTGTCTTTA 2428 chr3qtel1M 399228 TGCTTTAAATACATTTCTTGTAAGCAACATATTGCAGGATTCTGGCTTTT 399277 ii v i i?i i i v iv i ii vi C L1MEc_5end#LI 2427 TATTTAAAGTGNGTTTCTTGTAGGCAGCATATAGTTGGGTCTTGCTTTTT 2378 chr3qtel1M 399278 AATACAATATGCTA---TCTGCTTCTGCATTG 399306 v v v vi --- i i vv C L1MEc_5end#LI 2377 TATCCAATCTGACAATCTCTGCCTTTTAATTG 2346 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 45.08 CpG sites = 26, Kimura (unadjusted) = 45.08 Transitions / transversions = 1.62 (26/16) Gap_init rate = 0.01 (1 / 128), avg. gap size = 3.00 (3 / 1) 426 28.24 0.00 0.00 chr3qtel1M 400590 400674 (599326) Charlie1b#DNA/hAT-Charlie 1 85 (438) m_b146s502i0 5479 chr3qtel1M 400590 CAGTGGTTCTCAAAGTATGGTCTAGAGAATCCTGGGGATTTCTGAAACTT 400639 i i ii i vi i ii i i ii Charlie1b#DNA 1 CAGCGGTTCTCAAAGTGTGGTCCGGGGACCCCTGGGGGTCCCCGAGACCC 50 chr3qtel1M 400640 TTTTAGAGGGTCTACAAATTCAAAAGTAGTTTTAT 400674 i i ii i iv v v i Charlie1b#DNA 51 TTTCAGGGGGTCCGCGAGGTCAAAACTATTTTCAT 85 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 28.60 CpG sites = 20, Kimura (unadjusted) = 38.93 Transitions / transversions = 5.00 (20/4) Gap_init rate = 0.00 (0 / 84), avg. gap size = 0.0 (0 / 0) 571 14.88 3.23 2.40 chr3qtel1M 400667 400790 (599210) Charlie1a#DNA/hAT-Charlie 1331 1455 (0) m_b146s502i1 5480 chr3qtel1M 400667 AGTTTTA-TTTCCAATATGGTAAATATCTATAAATATAATCCAGATAAAC 400715 - i v i i v Charlie1a#DNA 1331 AGTTTTAATTTCTAATATGGTAAATATCGATAGATATAACCCACATAAAC 1380 chr3qtel1M 400716 AAAAAGGCTTTGGAGAGATCCTCAATAATTTTTAATATGATAAA--GATA 400763 ivv --- i v vvi -- i v Charlie1a#DNA 1381 AAAAGCTCTTTGG---GGTCCTCAATAATTTTTAAGAGTGTAAAGGGGTC 1427 chr3qtel1M 400764 CTGAAAAC-AAAAGTTTGAGAACCACTG 400790 i v - i Charlie1a#DNA 1428 CTGAGACCAAAAAGTTTGAGAACCGCTG 1455 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 15.70 CpG sites = 9, Kimura (unadjusted) = 16.65 Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.05 (6 / 123), avg. gap size = 1.17 (7 / 6) 28 5.32 0.00 0.00 chr3qtel1M 400940 400978 (599022) (TCTATA)n#Simple_repeat 1 39 (0) m_b146s252i12 5481 chr3qtel1M 400940 TCTATATCTATATCTATATCTATACCTATATCTTTATCT 400978 i v (TCTATA)n#Sim 1 TCTATATCTATATCTATATCTATATCTATATCTATATCT 39 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 53 0.00 0.00 0.00 chr3qtel1M 400980 401024 (598976) (TA)n#Simple_repeat 1 45 (0) c_b146s251i1 5482 chr3qtel1M 400980 TATATATATATATATATATATATATATATATATATATATATATAT 401024 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATAT 45 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 591 32.66 6.76 3.73 chr3qtel1M 403180 403726 (596274) C L1ME1_3end#LINE/L1 (351) 575 13 m_b146s551i9 5483 chr3qtel1M 403180 AGCTCATCATTTCTTATAGCACAGCAGTATTTAATTACAATAATGTACCA 403229 i i ivi i v vv i iv ii vvi i C L1ME1_3end#LI 575 AGTTCGTTCCTTTTTATTGCTGAGTAGTATTCCATTGTATGGATATACCA 526 chr3qtel1M 403230 CAATTTGTTCAATCATTTCCCAATTGATATGTGTCTGCA--AATTCTAGT 403277 i vi iv ?i iviii i vi--iv i C L1ME1_3end#LI 525 CAATTTGTTTATCCATTCACCNGTTGATGGACATTTGGGTTGTTTCCAGT 476 chr3qtel1M 403278 TCTTTGC-ACCACACAAAGAGCTACTCTAAATA---GTTTAGAAG----- 403318 i v - ii iv v i i v i i --- v v ----- C L1ME1_3end#LI 475 TTTTGGCTATTACGAATAAAGCTGCTATGAACATTCGTGTACAAGTCTTT 426 chr3qtel1M 403319 ATATGGG---ATCTTTTCCTTTTTTCTGATCATTTGAAAAAACAGACCAA 403365 i i i--- v v i i-------- iiv i -- v C L1ME1_3end#LI 425 GTGTGGACATATGTTTTCATTTCTC--------TTGGGTAAATA--CCTA 386 chr3qtel1M 403366 GTAGTGGTTTTTCTGGGTCAAAAG--AAATTTAA---TAATTCTG-AATA 403409 v vv v v v -- i v v--- i i ?- v C L1ME1_3end#LI 385 GGAGTGGAATTGCTGGGTCATATGGTAAGTGTATGTTTAACTTTNTAAGA 336 chr3qtel1M 403410 TAATTTTAGATTGCTCTCCAAAATGGTTAAATCAGTTCACAATTTCATCA 403459 v v vii i i i i i i iv i v ii v ii i C L1ME1_3end#LI 335 AACTGCCAAACTGTTTTCCAAAGTGGCTGTACCATTTTGCATTCCCACCA 286 chr3qtel1M 403460 AAAATGAATTAGCATCCCAATTTTTCCACATTCCCTCCAACATTTG---T 403506 iv v v vi i i vi i i v i --- C L1ME1_3end#LI 285 GCAATGTATGAGAGTTCCAGTTGCTCCACATCCTCGCCAACACTTGGTAT 236 chr3qtel1M 403507 TGCTTTTCCCTTCAATCGTTTTAGCCAATCTTGTTGTTCTATAATGACAC 403556 iivv ii i --- v vi v v v i i ii i C L1ME1_3end#LI 235 TGTCAGTCTTTTTAAT---TTTAGCCATTCTAATAGGTGTGTAGTGGTAT 189 chr3qtel1M 403557 CTCAAAGTTGTTTTCATTTGGATTTTTCTAAT---CAATGA--TTGAGAT 403601 vv v v v ii ---i -- -- C L1ME1_3end#LI 188 CTCATTGTGGTTTTAATTTGCATTTCCCTAATGACTAATGATGTTGAG-- 141 chr3qtel1M 403602 AATTTTATCATATGATCAT---------AAATGTGTTCCTAGAATAGAAA 403642 v i v i v i ---------iv i v i ---- i vi C L1ME1_3end#LI 140 CATCTTTTCATGTGCTTATTTGCCATCCGTATATCTTCTT----TGGTGA 95 chr3qtel1M 403643 AGTGCCTGTTCATATGCTCTAACCATTTATCAGTTGGATGGATAGTGACT 403692 i v vi i iv v i i i v v v v-i C L1ME1_3end#LI 94 AGTGTCTGTTCAAATCTTTTGCCCATTTTTTAATTGGGTTGTTTGTT-TT 46 chr3qtel1M 403693 CATATTCATATAGATTTGACAATGTTTTATATAT 403726 v - vv v v i vi C L1ME1_3end#LI 45 CTTATT-ATTGAGTTTTGAGAGTTCTTTATATAT 13 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 43.39 CpG sites = 97, Kimura (unadjusted) = 44.44 Transitions / transversions = 1.29 (97/75) Gap_init rate = 0.06 (33 / 546), avg. gap size = 1.76 (58 / 33) 608 29.63 7.74 3.09 chr3qtel1M 403361 403670 (596330) C L1PA7_3end#LINE/L1 (511) 390 67 m_b146s551i10 5483 chr3qtel1M 403361 ACCAAGTAGTGGTTTTTCTGGGTCAAAAGAAATTTAATAATTCTGAATAT 403410 v i vv v v iv v- ii ii vi C L1PA7_3end#LI 390 ACCCAGTAATGGGATTGCTGGGTCAAATGGTATTTC-TGGTTCTAGATCC 342 chr3qtel1M 403411 ------AATT-TTAGATTGCTCTCCAAAATGGTTAAATCAGTTCACAATT 403453 ------ i-ii v i iii v i ii i i v i C L1PA7_3end#LI 341 TTGAGGAATCGCCACACTGTCTTCCACAATGGTTGAACTAATTTACACTC 292 chr3qtel1M 403454 TCATCAAAAATGAATTAGCATCCCAATTTTTCCACATTCCCTCCAACATT 403503 i i v i v vv i i v i i i i i C L1PA7_3end#LI 291 CCACCAACAGTGTAAAAGCGTTCCTATTTCTCCACATCCTCTCCAGCATC 242 chr3qtel1M 403504 TGTTGCTTTT---CCCTTCAATCGTTTTAGCCAATCTTGTTGTTCTATAA 403550 i ii--- ii i vi i--- v vii viv ivi C L1PA7_3end#LI 241 TGTTGTTTCCTGACTTTTTAATGATC---GCCATTCTAACTGGCGTGAGA 195 chr3qtel1M 403551 TGACACCTCAAAGTTGTTTTCATTTGGATTTTTCTAAT---CAATGAT-- 403595 ii i vv v v v i --- i -- C L1PA7_3end#LI 194 TGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTAATGACCAGTGATGA 145 chr3qtel1M 403596 TGAGATAATTTTATCATATGAT---------CATAAATGTGTTCCTAGAA 403636 v -- v v --------- v i ---- C L1PA7_3end#LI 144 TGAGCT--TTTTTTCATATGTTTGTTGGCCGCATAAATGTCTTCTT---- 101 chr3qtel1M 403637 TAGAAAAGTGCCTGTTCATATGCTCTAACCATTT 403670 v i i v iiiv i C L1PA7_3end#LI 100 TTGAGAAGTGTCTGTTCATATCCTTCGCCCACTT 67 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.26 CpG sites = 55, Kimura (unadjusted) = 39.12 Transitions / transversions = 1.62 (55/34) Gap_init rate = 0.05 (16 / 309), avg. gap size = 2.12 (34 / 16) 1374 31.78 6.67 1.50 chr3qtel1M 404377 405456 (594544) C L1M5_orf2#LINE/L1 (795) 2499 1365 m_b146s551i11 5483 chr3qtel1M 404377 TGGTAATTTGATTAGGATGGCATTGAATTTATAAATTAGTTTGGGTAAAA 404426 v v i v i i i i v i C L1M5_orf2#LIN 2499 TGGGATTTTGATTGGGATTGCATTGAATCTATAGATCAATTTGGGGAGAA 2450 chr3qtel1M 404427 TTATCATTTTTATTATACTGCTTCTGTCTACCCATGAACATTTAATATGT 404476 iv i ? iv i vv vi v i vvv v C L1M5_orf2#LIN 2449 TTGACATCTTNACAATATTGAGTCTTCCAATCCATGAACATGGTATATCT 2400 chr3qtel1M 404477 CTTCA---ATTTATATTTGATTTTATTTATATAAAAAGTTTTTTATGTAA 404523 i --- vi i vv v v v v iv i v -- i C L1M5_orf2#LIN 2399 CTCCATTTATTTAGGTCTTCTTTAATTTCTCTCAGCAATGTTT--TGTAG 2352 chr3qtel1M 404524 TTT--AGTTATATACTTCTTGGGTTTGTTTTGGCAGACATGCTCCCAGGT 404571 -- - i ? vv viiv ? vi iv ii i i C L1M5_orf2#LIN 2351 TTTTCAG-TGTANAGGTCTTGCACATNTTTTGTTAGATTTATTCCTAAGT 2303 chr3qtel1M 404572 ATTTTACACTATCTTGA-ACTATTTTAAATGAGA-TATTTCTCACTATTT 404619 ? iii - i -i v iv - i i ? v- C L1M5_orf2#LIN 2302 ATTTNATGTT-TTTTGATGCTATTGTAAATGGTATTGTTTTTNAA-ATTT 2255 chr3qtel1M 404620 CTTCTTGCAGAATT-TTGGTTG-TAATACATGGGAATGCTGATGAATTGT 404667 v i v -- - v - i i i i i viv v v C L1M5_orf2#LIN 2254 CATTTTCC--AATTGTTTGTTGCTAGTATATAGAAATACAATTGATTTTT 2207 chr3qtel1M 404668 GTGCATTTACTTCACATCCTGCTACTTTCCTAA----AGTTATTGTTTCC 404713 ii v i iii ? v i v ---- v iv i C L1M5_orf2#LIN 2206 GTATATTGACCTTGTATCCNGCGACCTTGCTAAATTCACTTATTAGTTCT 2157 chr3qtel1M 404714 ACTAACTTCTTAGTTGAATCTTTGGGATTTTCCAAATAG---ATCATATT 404760 v ii ? v v v ? i vi ?--- i i C L1M5_orf2#LIN 2156 AGTAGTTTNTTTGTAGATTCTTTNGGATTTTCTACGTANACAATCATGTC 2107 chr3qtel1M 404761 GTTTATAAAGAGAGAAAGTTTTATCACTTTGTTTTCTATTCAGGTCTCTC 404810 i i iii v i? v iv iv i v iivvi vi i C L1M5_orf2#LIN 2106 ATCTGCGAATAANGACAGTTTTATTTCTTCCTTTCCAATCTTTATGCCTT 2057 chr3qtel1M 404811 TTATGTCTTTTTTTTTTCTTATTGCTATTGCTAGGATTTTCAATACAATA 404860 v i vi vv v ii i i i C L1M5_orf2#LIN 2056 TTATTTCTTTTTCTTGCCTTATTGCACTGGCTAGGACCTCCAGTACAATG 2007 chr3qtel1M 404861 T----------TGGTGGCAATGAGTATTTTTGTTTCATATCTGATCATAC 404900 ---------- i? ii iii ii i ii vi i v v C L1M5_orf2#LIN 2006 TTGAATAGAAGTGGTGANAGCGGACATCCTTGTCTTGTTCCCGATCTTAG 1957 chr3qtel1M 404901 TGGG-AAGATTTCTTTGCTTAATCCCTTTACAAATAATACTAGATAATAG 404949 v - v? vv ?i v -- v viv i ii ? v ivvi C L1M5_orf2#LIN 1956 GGGGAAAGCNTTCAGTNTTTCA--CCATTAAGTATGATGTTNGCTGTAGG 1909 chr3qtel1M 404950 TTTTAGATAGATGGATTTTTTTTATAAATTTAAGAAAAAATCCATTTA-T 404998 vvi ----iii v iv i i ivvi v i - C L1M5_orf2#LIN 1908 TTTTTCGTAGATG----CCCTTTATCAGGTTGAGGAAGTTCCCTTCTATT 1863 chr3qtel1M 404999 GCTAATATTTTCAAGGATTTTTAAAAATAATCTGTATGTTGTACTTTATT 405048 v i - viii ii vv vv -- vi v i i i C L1M5_orf2#LIN 1862 CCTAGT-TTGCTGAGAGTTTTTATCATGAA--TGGGTGTTGAATTTTGTC 1816 chr3qtel1M 405049 AAA-ACATTTTCTGCATCTGTTGAGATAATCATAC--CTTTTCACTTTTA 405095 -i v i i i--i v i C L1M5_orf2#LIN 1815 AAATGCTTTTTCTGCATCTATTGAGATGATCATATGATTTTTCTCCTTTA 1766 chr3qtel1M 405096 T--TATTGATATAATTAATTATGTTAGTAGTTTTCCTTATAGTAAACCAT 405143 -- i i ii v ii ii v v i vv iv v C L1M5_orf2#LIN 1765 TTCTGTTAATATGGTGAATTACATTGATTGATTTTCGAATGTTAAACCAA 1716 chr3qtel1M 405144 ACCTGCATTGCTGGTATAAATCTCATTTTG-------------------T 405174 v i v v i i i v ------------------- C L1M5_orf2#LIN 1715 CCTTGCATTCCTGGGATAAACCCCACTTGGTCATGATGTATTATCCTTTT 1666 chr3qtel1M 405175 TATATTTTGTTGTGATCTTTTAGGTATTATTTTGTTA------------- 405211 v i viv vv v v v ?------------- C L1M5_orf2#LIN 1665 TATATATTGCTGGATTCGATTTGCTAATATTTTGTTNAGGATTTTTGCAT 1616 chr3qtel1M 405212 ----GTTTATTAATGAACTTAGCCCACAGTTTGCTTTCTCTGTGTTTACT 405257 ---- i v iv vv i i iii i v iii iv vv C L1M5_orf2#LIN 1615 CTATGTTCATGAGGGATATTGGTCTGTAATTTTCTTTTCTTGTAATGTCT 1566 chr3qtel1M 405258 CTTCCTGGTTTGAATATCAGTATGATATTTGTTTCACAAAACAAGTTTGG 405307 i vi ? vii vi ? ii v ii i ii v C L1M5_orf2#LIN 1565 TTGTCNGGTTTTGGTATCAGGGTNATGCTGGCCTCATAAAATGAGTTGGG 1516 chr3qtel1M 405308 TAG-ATTCCTTCTTTGCCTTTTATTCCAAATATTTTATTTAATATTGGAA 405356 v -i i vi v v iivi v v i v v v C L1M5_orf2#LIN 1515 AAGTGTTCCCTCTTTTTCTATTTTCTGGAAGAGTTTGTGTAAGATTGGTA 1466 chr3qtel1M 405357 ATAGTTGACCTTTAAACATTTGATAGAATCCATTTGTAAATCTATCTAGT 405406 v v vvi i ii i i iiv i v i i v C L1M5_orf2#LIN 1465 TTATTTCTTCCTTAAATGTTTGGTAGAATTCACCAGTGAAGCCATCTGGG 1416 chr3qtel1M 405407 CCTGGTAATTTTTTT--TAGGAAGCTCATATGTAATGTATTCAATGTCTT 405454 - i i -- i v iv vvi v iiv v C L1M5_orf2#LIN 1415 CCTGG-AGTTTTCTTTGTGGGAAGGTTTTTAATTACAAATTCAATTTCTT 1367 chr3qtel1M 405455 TA 405456 C L1M5_orf2#LIN 1366 TA 1365 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 42.55 CpG sites = 189, Kimura (unadjusted) = 43.42 Transitions / transversions = 1.27 (189/149) Gap_init rate = 0.03 (36 / 1079), avg. gap size = 2.47 (89 / 36) 26 0.00 0.00 0.00 chr3qtel1M 406350 406374 (593626) (TTAAA)n#Simple_repeat 1 25 (0) c_b146s251i2 5484 chr3qtel1M 406350 TTAAATTAAATTAAATTAAATTAAA 406374 (TTAAA)n#Simp 1 TTAAATTAAATTAAATTAAATTAAA 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 218 36.41 9.22 0.65 chr3qtel1M 407526 407666 (592334) C L3#LINE/CR1 (178) 3921 3769 m_b146s601i14 5485 chr3qtel1M 407526 ATAACTATAGTTGTTAGAAAACATTTCTGGACATTTAGCCCCAAT-TACC 407574 i i v ii iivi ivv i v vv - i C L3#LINE/CR1 3921 ACAGCTCTGATTGTTAGAAAGTTCTTCCTTATATTGAGCCGAAATCTGCC 3872 chr3qtel1M 407575 TTT-TGTATCTCTCTTCCACT----------CTATCCT-TGAAGCTAAAA 407612 ii- v ii vi i ---------- ii - i i v v C L3#LINE/CR1 3871 TCCCTGTAACTTCCACCCATTGGTCCTAGTTCTGCCCTCTGGAGCCACAC 3822 chr3qtel1M 407613 CAAACAGATCTGACCTCTCTTTTCCATGACATGCTGTCAGAAGCCTTAAA 407662 vi i ii i i i iiv vv iv - vvi i C L3#LINE/CR1 3821 AGAATAAGTCTAATCCCTCTTCCACATGACAGCCCTTCA-AATATTTGAA 3773 chr3qtel1M 407663 GATA 407666 i C L3#LINE/CR1 3772 GACA 3769 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 53.25 CpG sites = 33, Kimura (unadjusted) = 53.25 Transitions / transversions = 1.83 (33/18) Gap_init rate = 0.04 (5 / 140), avg. gap size = 2.80 (14 / 5) 261 26.71 2.53 5.19 chr3qtel1M 408258 408336 (591664) C Charlie4#DNA/hAT-Charlie (0) 3378 3302 m_b147s502i0 5486 chr3qtel1M 408258 CAAAGATTCT-AAGCTTTAATACATCTTGG-CTTCTCTGGCAGGGAGTTT 408305 ii i - v vv iiii v - ii i ---- i C Charlie4#DNA/ 3378 CAGGGGTTCTTAACCTTTTTTGTGCCATGGACCCCTTTGGCAG----TCT 3333 chr3qtel1M 408306 GGTGAAGCTCATAGACCTCTTTTCAGAATAA 408336 ii i i i C Charlie4#DNA/ 3332 GGTGAAGCCTATGGACCCCTTCTCAGAATAA 3302 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.52 CpG sites = 16, Kimura (unadjusted) = 35.52 Transitions / transversions = 4.00 (16/4) Gap_init rate = 0.08 (6 / 78), avg. gap size = 1.00 (6 / 6) 391 26.74 7.69 2.19 chr3qtel1M 408346 408475 (591525) C Charlie4#DNA/hAT-Charlie (3238) 140 4 m_b147s502i1 5486 chr3qtel1M 408346 ATAATTAAACTAATTTTTAAACTTTAATAAGAGATTGTTTAAAACAAAGT 408395 i vv v vi i i i v i iv v i v C Charlie4#DNA/ 140 ATAATTGAAGGAAATGCTAAATTTCAGTTAGAGGTTAGTGAAAATAAAGA 91 chr3qtel1M 408396 TGT--------CCCCCTCAACTTCATGGATCCTCTGAAATCTCTCTACAC 408437 -------- vii v i i i v v i i- C Charlie4#DNA/ 90 TGTAATTTTTTCCCATCCAAGTTCACGGACCCCCTGAATTCTATCCACG- 42 chr3qtel1M 408438 ATAACCCA--GGAGATTCATGGACCTCAGGTTAAGAACCC 408475 --i v-- i i i i i C Charlie4#DNA/ 41 --GACCCCTTGGGGGTCCGTGGACCCCAGGTTAAGAACCC 4 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 30.49 CpG sites = 21, Kimura (unadjusted) = 34.10 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.04 (5 / 129), avg. gap size = 2.60 (13 / 5) 383 21.30 2.04 4.17 chr3qtel1M 408537 408634 (591366) MIR#SINE/MIR 49 144 (118) m_b147s601i1 5487 chr3qtel1M 408537 TGAGTTCAAATATAGACTCAGACACTTCCTAGATGTAGTGTTTACCT-GA 408585 i i viv i v v v v - --- - i MIR#SINE/MIR 49 TGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGT-GTG---ACCTTGG 94 chr3qtel1M 408586 AAAAGTCCTTTAACC-CTGTTTGCCTCAGTTTCCTCATCTGTAAAATAAG 408634 iv ivi - v v ii MIR#SINE/MIR 95 GCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGG 144 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 23.81 CpG sites = 10, Kimura (unadjusted) = 25.20 Transitions / transversions = 1.00 (10/10) Gap_init rate = 0.06 (6 / 97), avg. gap size = 1.00 (6 / 6) 221 31.82 0.00 0.00 chr3qtel1M 409102 409167 (590833) C MIRc#SINE/MIR (192) 76 11 m_b147s601i2 5488 chr3qtel1M 409102 TGGGAGAAGCAACATTCCAACCCAGGACTTCCTGACTCTACATCCAATAC 409151 v iv iiv i v v i vi i i C MIRc#SINE/MIR 76 TGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGC 27 chr3qtel1M 409152 TTCGTTAACTCCAACA 409167 iiv iv v v C MIRc#SINE/MIR 26 TCTTTCCACTGCACCA 11 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.61 CpG sites = 11, Kimura (unadjusted) = 42.19 Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0) 394 25.74 0.74 7.94 chr3qtel1M 409401 409535 (590465) MIRc#SINE/MIR 2 127 (141) m_b147s601i3 5489 chr3qtel1M 409401 GAGACAGCTAGATGGTGCAATGGATAGATCCCTAGCCCTCAAGACAGGAG 409450 i i---i i v v v i v i vi v i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr3qtel1M 409451 GAACTGAGTACAAATTTGGCCTCAGACACTTAAGACTTTCTAGGTGTGTG 409500 v i v i i iiv v v v ------- v MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTG 91 chr3qtel1M 409501 ACCCAGGGCAAGTCACTTAACCCCAGTT-GCCTCAG 409535 iv i vv v- MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 30.38 CpG sites = 15, Kimura (unadjusted) = 31.52 Transitions / transversions = 0.88 (15/17) Gap_init rate = 0.08 (11 / 134), avg. gap size = 1.00 (11 / 11) 15 14.13 0.00 3.12 chr3qtel1M 409536 409568 (590432) (CAAA)n#Simple_repeat 1 32 (0) m_b147s252i0 5490 chr3qtel1M 409536 CAAAAATACCAAACAAACAAAGGAACAAACAAA 409568 v - v vi (CAAA)n#Simpl 1 CAAACA-AACAAACAAACAAACAAACAAACAAA 32 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 12 24.01 0.00 2.50 chr3qtel1M 409810 409850 (590150) (ACACTGT)n#Simple_repeat 1 40 (0) m_b147s252i1 5491 chr3qtel1M 409810 ACTCTGATCACAATACACTGATATACCATACACTGTACACT 409850 v vv vi - i ii (ACACTGT)n#Si 1 ACACTGTACACTGTACACTG-TACACTGTACACTGTACACT 40 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 568 27.75 5.76 6.08 chr3qtel1M 409861 410190 (589810) L2b_3end#LINE/L2 130 458 (8) m_b147s601i4 5492 chr3qtel1M 409861 TTTGTACTGGCCGTCTCCCCCATGCCTGAAAGGTTCCCCTTCCTCA--TC 409908 i ?v i - i - i v --- i -- L2b_3end#LINE 130 TTTGCACNTGCTGT-TCCCTC-TGCCTGGAACG---CCCTTCCCCACCTC 174 chr3qtel1M 409909 TTGGTCT---CATACCTTCCCCAGCTTCCTGCAGGACTGAGCTCAAATAT 409955 v i --- vvi i v i --- v v v i L2b_3end#LINE 175 TTCGCCTGGCCAACTCCTACTCA---TCCTTCAGGTCTCAGCTCAAATGT 221 chr3qtel1M 409956 CACCTTCTACTGGAAGCTTTCCATGAAACTCCCAACTC----CCTGCTCT 410001 i v v ii v v- i ivi ---- vv v i L2b_3end#LINE 222 CACCTCCTCCGGGAAGCCCTCCCTGAC-CCCCCAGGCCGGGTCAGGCGCC 270 chr3qtel1M 410002 TTCCTCTCTGACATCCCCCTGCATCCATTCTTTATGTCACT-TA---TAT 410047 i vv v -- v i-i i ii ---- i - i--- L2b_3end#LINE 271 CTCCTCTGGGCC--CCCCCAGT-CCTACCCT----GCCACTCTGGGTTAT 313 chr3qtel1M 410048 GAACTGAGTTGTTCACATTTCT-CCTCTTACCTTAGATTATGAGCCCCTT 410096 ? -- vivi ? i v -i iiv vi i i i v L2b_3end#LINE 314 NA--TTGTCTGNTTACATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGT 361 chr3qtel1M 410097 GTGGTAAGAGACTGAGTTT---TTGCCTTC-CCTCTG-ATCCCTAACATT 410141 v vv i i ? i --- -- - v - i i iii L2b_3end#LINE 362 GAGGGCAGGGACCGNGTCTGTCTTG--TTCACCGCTGTATCCCCAGCGCC 409 chr3qtel1M 410142 CAGCACAGTGCCTGGCACCCTGTAAGTGCTCCAAAGATGCTTGTGGAAT 410190 i ? v v i i viv i ii v L2b_3end#LINE 410 TAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTTGTTGAAT 458 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.68 CpG sites = 50, Kimura (unadjusted) = 36.25 Transitions / transversions = 1.39 (50/36) Gap_init rate = 0.09 (29 / 329), avg. gap size = 1.34 (39 / 29) 14 20.09 5.66 1.82 chr3qtel1M 411247 411299 (588701) (TCTGAC)n#Simple_repeat 1 55 (0) m_b147s252i2 5493 chr3qtel1M 411247 TCTGAATCTCTCTCTGAGCCCT---TCTGAGTCTGTCTCTGGCTCTAACT 411293 v vv - i --- v v i i (TCTGAC)n#Sim 1 TCTGACTCTGACTCTGA-CTCTGACTCTGACTCTGACTCTGACTCTGACT 49 chr3qtel1M 411294 CTGGCT 411299 i (TCTGAC)n#Sim 50 CTGACT 55 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.04 (2 / 52), avg. gap size = 2.00 (4 / 2) 42 27.39 0.00 3.73 chr3qtel1M 414307 414445 (585555) (AAGG)n#Simple_repeat 1 134 (0) m_b147s252i3 5494 chr3qtel1M 414307 AATGAAAGAAGGAAGAAAAAAACAAAGAAACAAAAAGTAGCAAGACGAAA 414356 v i i ii vi i -ii i v v -- i (AAGG)n#Simpl 1 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAA-GGAAGGAAGGAAG--GAAG 47 chr3qtel1M 414357 AAAGGAAGGAAGGAGGGAAGGAAGGAAGGAAGGAACGGAAAGGAAATAAA 414406 i i - - iv i (AAGG)n#Simpl 48 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA-GG-AAGGAAGGAAG 95 chr3qtel1M 414407 GGTGAAATGAATGAAAAAAGAAATGAAGGAAGGGAGGAA 414445 iv i v v ii i v i (AAGG)n#Simpl 96 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 134 Matrix = Unknown Transitions / transversions = 2.22 (20/9) Gap_init rate = 0.04 (5 / 138), avg. gap size = 1.00 (5 / 5) 498 23.14 0.81 5.93 chr3qtel1M 414495 414618 (585382) MIRc#SINE/MIR 10 127 (141) m_b147s601i5 5495 chr3qtel1M 414495 GTGGCACAGTGGGTAGGCCAACAACCTTGAAGTCAGGAGGACCTGAGTTC 414544 ii iv iv viiiv i i i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr3qtel1M 414545 AAATCTGGTCTCAGACACTTAAGACTTCCTAGCTGTGTGACTTTGGGCAA 414594 i i iv v v v ------- i MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTGACCTTGGGCAA 102 chr3qtel1M 414595 GTCATTTAACCCCAATT-GCCTCAG 414618 i i vv v- MIRc#SINE/MIR 103 GTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.91 CpG sites = 16, Kimura (unadjusted) = 28.11 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.07 (8 / 123), avg. gap size = 1.00 (8 / 8) 612 31.21 4.43 3.34 chr3qtel1M 414856 415329 (584671) C L1ME3G_3end#LINE/L1 (416) 508 30 m_b147s551i0 5496 chr3qtel1M 414856 CATTCCCCAATTCATGGGCGT----ACCCTTACCAGTTCTTAGCCACCAC 414901 v v i i ----iiiv v i i v i ii C L1ME3G_3end#L 508 CATTCCCCTATTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTAC 459 chr3qtel1M 414902 AAAAAGAGCTGTTATAAATAATTTTGTGCAAATAGATTCTT-TCCCCTTT 414950 v iv iv i i vii i -- iv? i - v v v v C L1ME3G_3end#L 458 AAACAATGCTGCAATGAACATCCTTGTACA--TGCNTCCTTGTGCACATG 411 chr3qtel1M 414951 TTTTA--ACCTCTGTTGGATACAGACTAAATAATGTTACTGTCAGATCAA 414998 viv -- ii ? v v v? i? iv i vv i iii i C L1ME3G_3end#L 410 TGCGAGTATTTCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAA 361 chr3qtel1M 414999 AGGGT--GCAAAGTTTTATATTCTATTGATA-ATAGTTCCACATTGCTCT 415045 -- iv - v --- i - v v v i C L1ME3G_3end#L 360 AGGGTATGCGCA-TTTTAAATT---TTAATAGATACTGCCAAATTGCCCT 315 chr3qtel1M 415046 CCAGAATAGTTGGATGAGTTCACAACTCTACCACCAGTGTATTAATGTCC 415095 i ?i i v iv i i vii i v v iv v C L1ME3G_3end#L 314 CCAAAANGGCTGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTAC 265 chr3qtel1M 415096 TAGTTTTTCCATACTCCCCCCTACATTTATGATTTTCCTATTATTTTGTC 415145 iv ii i i i v v i --? v --- i v?i v i C L1ME3G_3end#L 264 CCGTTTCCCCACACCCTCGCCAACACT--NGATAT---TATCAANCTTTT 220 chr3qtel1M 415146 ACA--TTAGACAATCTGATCAGTATCGGGTGGTAATTCAGAGATGTTTTA 415193 v -- v v vi ivviii vi vv v C L1ME3G_3end#L 219 AAATTTTTGCCAATCTGATGGGTGAAAAATGGTATCTCATTGTTGTTTTA 170 chr3qtel1M 415194 ATTTGCATTTATCTAATCAGTAGTGA--TTTAGAA----GTTATATGAGT 415237 vi i i v -- v v ----v i vv C L1ME3G_3end#L 169 ATTTGCATTTCCCTGATTACTAGTGAGGTTGAGCATCTTTTCATATGTTT 120 chr3qtel1M 415238 ACAGATAGTTTTGATTTGTTTATC--TGAACTGCCAGTTCATATCCTTTG 415285 iv iivi vv vi iv -- i v C L1ME3G_3end#L 119 ATTGGCCATTTGTATTTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTG 70 chr3qtel1M 415286 ACCATTTGTCAACTGAGGAATTA-CTAGTATTCTTATAAATTTGT 415329 v v v i i --- i- -- v vi C L1ME3G_3end#L 69 CCCATTTTTCTATTGGG---TTGTCT--TTTTCTTATTGATTTGT 30 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.18 CpG sites = 74, Kimura (unadjusted) = 41.94 Transitions / transversions = 1.07 (74/69) Gap_init rate = 0.05 (26 / 473), avg. gap size = 1.42 (37 / 26) 14 21.41 4.65 0.00 chr3qtel1M 416918 416960 (583040) (TCT)n#Simple_repeat 1 45 (0) m_b147s252i4 5497 chr3qtel1M 416918 TCTTCTTCTACTTCTTCTGATCCTTAATC-CCTT-TACTTCTTCT 416960 v vv i vv -i - v (TCT)n#Simple 1 TCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCT 45 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.00 (2 / 2) 235 38.67 5.75 6.36 chr3qtel1M 418087 418260 (581740) C MIRc#SINE/MIR (75) 193 21 m_b147s601i6 5498 chr3qtel1M 418087 TCCTTCCAACAGCTCAACAATATAGATAAGACAAAGACTCTC--CCCCAA 418134 iv i i viii vi ii i i iiv i v i-- v C MIRc#SINE/MIR 193 TCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCAT 144 chr3qtel1M 418135 CTTAGAAAAGAGTGTTAGAAGTGAAGACTGCAAA-------AGTGATTTT 418177 i v i v ----- iivi i - i ------- i v C MIRc#SINE/MIR 143 TTTACAGATGAG-----GAAACTGAGGCT-CAGAGAGGTTAAGTGACTTG 100 chr3qtel1M 418178 TTCAAGACTATATGACCAAGAAATTTTCAGAGATGACAATAATTGGGGCC 418227 ii iii i iii i iv i vv- vi i----i i v ii C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGG-CAGAGCCGG----GACTCGAACC 55 chr3qtel1M 418228 CAGGGCTTTTCAA-TCTAAGACCAGTGCTCTTTC 418260 v iiii - i v C MIRc#SINE/MIR 54 CAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTC 21 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 59.45 CpG sites = 46, Kimura (unadjusted) = 61.09 Transitions / transversions = 2.71 (46/17) Gap_init rate = 0.08 (14 / 173), avg. gap size = 1.50 (21 / 14) 387 39.36 3.68 3.36 chr3qtel1M 418947 419272 (580728) C L2b_3end#LINE/L2 (15) 451 125 m_b147s601i7 5499 chr3qtel1M 418947 AAACATTTTCTAAGGAAGCATTATGTGCCAGGTATTTTGCTAAGTGCTAG 418996 i v i vivvi i i i?i v i i i C L2b_3end#LINE 451 AAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGG 402 chr3qtel1M 418997 GAATACAAAGAAAGGCAAA--AGATA--GTTCCTGCCCTCAAACAGGATA 419042 i iv iviii i-- i?-- i viv vvi C L2b_3end#LINE 401 GGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGGAGCTCA 352 chr3qtel1M 419043 AAATCTAATTGGGAAAA-AAATGTGCAAACA-ACTTTGTATGAATAAGAA 419090 v i i v i i - i ii i ? - vv -? i viv i C L2b_3end#LINE 351 CAGTCTAGTGGGGGAGACAGACATGTAANCAGACAAT-NATAACCCAGAG 303 chr3qtel1M 419091 TAGGACTGTGTAATAAGTTGGACACATTCAGGAGATGAGCAGGTG-CTAG 419139 i v -- v iv --i iviviii ii - i ivv - iv C L2b_3end#LINE 302 TGGCA--GGGTAGGA--CTGGGGGGGCCCAGAGGA-GGGCGCCTGACCCG 258 chr3qtel1M 419140 GAGGAGGAGGGCTTGGGAAAGGCTTCCTGTAGAAGGTAGAATTTCCATTA 419189 vvvi i -- ii i i i v i iiv vvii i C L2b_3end#LINE 257 GCCTGGGGGG--TCAGGGAGGGCTTCCCGGAGGAGGTGACATTTGAGCTG 210 chr3qtel1M 419190 GGATTTTTAAAAAGCCAG--GGA---AATCAGACAGAATGGACAGTGAAG 419234 i --ii i iiiiv -- ---iii i - vi iii v C L2b_3end#LINE 209 AGA--CCTGAAGGATGAGTAGGAGTTGGCCAGGC-GAAGAGGTGGGGAAG 163 chr3qtel1M 419235 AATTTTCCAAGCATGGGGAAAAGTCAGAACAAATGCTC 419272 iiiv i vi v iv? vi v i C L2b_3end#LINE 162 GGCGTTCCAGGCAGAGGGAACAGCANGTGCAAAGGCCC 125 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 57.79 CpG sites = 83, Kimura (unadjusted) = 62.77 Transitions / transversions = 2.02 (83/41) Gap_init rate = 0.06 (18 / 325), avg. gap size = 1.28 (23 / 18) 408 32.54 2.38 0.00 chr3qtel1M 418947 419072 (580928) C L2d2_3end#LINE/L2 (15) 540 412 m_b147s601i8 5499 chr3qtel1M 418947 AAACATTTTCTAAGGAAGCATTATGTGCCAGGTATTTTGCTAAGTGCTA- 418995 i vi i vivvi i i v i i v i i i- C L2d2_3end#LIN 540 AAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGT 491 chr3qtel1M 418996 --GGAATACAAAGAAAGGCAAAAGATAGTTCCTGCCCTCAAACAGGATAA 419043 -- i ivii i v i i iv vv v C L2d2_3end#LIN 490 GGGGGATACAAAGAAGTATAAGACATGGTCCCTGCCCTCAAGGAGCTTAC 441 chr3qtel1M 419044 AATCTAATTGGGAAAAAAATGTGCAAACA 419072 i i i v viiii C L2d2_3end#LIN 440 AATCTAGTTGGGGAGACAAGACATAAACA 412 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.06 CpG sites = 27, Kimura (unadjusted) = 45.07 Transitions / transversions = 1.93 (27/14) Gap_init rate = 0.02 (2 / 125), avg. gap size = 1.50 (3 / 2) 16 16.12 0.00 0.00 chr3qtel1M 420576 420603 (579397) (T)n#Simple_repeat 1 28 (0) m_b147s252i5 5500 chr3qtel1M 420576 TTTTTTTTATATTTTTTTTTAATTTTTT 420603 v v vv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 28 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 574 26.89 8.85 0.00 chr3qtel1M 421267 421571 (578429) C L1ME4a_3end#LINE/L1 (496) 375 44 m_b147s551i1 5501 chr3qtel1M 421267 TGGATCAAAGGGTAAGCACAGTTTGATAATTTTT--TGGATGTT-CCAAA 421313 i v ? v v viii -- iv i - C L1ME4a_3end#L 375 TGGGTCAAAGGGTATGNACATTTTTAAGGCTTTTGATACATATTGCCAAA 326 chr3qtel1M 421314 TTG-TCTCTGGAATGGTTGGATGCATTCACAATTCCACCAACAATGT-TC 421361 -i ii v v ivv i v i i i - v C L1ME4a_3end#L 325 TTGCCCTCCAGAAAGGTTGTACCAATTTACACTCCCACCAGCAGTGTATG 276 chr3qtel1M 421362 AGTGT-CCCATTTTCCCACATCCCCTCCAACATTCATCATTATCTTTCCT 421410 v - i i? i i v i vivi vv i C L1ME4a_3end#L 275 AGAGTGCCCGTTTCNCCACACCCTCGCCAACACTGGGTATTATCAATCTT 226 chr3qtel1M 421411 GT-CATCCCAGCCAATCTGAGAAGTG--TTATGGTATCTCAATG--GTCT 421455 v -v iiv i v i --vv v -- i C L1ME4a_3end#L 225 TTAAATCTTTGCCAATTTGATAGGTGAAAAATGGTATCTCATTGTTGTTT 176 chr3qtel1M 421456 TAATTTGT-TTTATCTGATCATTAATGA-TTTGGACATC-TTTCATGGCT 421502 i- v i i i i -v i ?- ivv C L1ME4a_3end#L 175 TAATTTGCATTTCTTTGATTACTAGTGAGGTTGAACATNTTTTCATATGT 126 chr3qtel1M 421503 GAAATG----TTTCAATTTCTTCAT---CAAATTTTC------TATCCTT 421539 vv v ---- vv v ---ii v ------ i C L1ME4a_3end#L 125 TTATTGGCCATTTGTATTTCTTCTTTTGTGAATTGTCTGTTCATGTCCTT 76 chr3qtel1M 421540 TGGCCATTTATCAAGTGGAGAATTTGATTTTT 421571 v v v v i vi i vi C L1ME4a_3end#L 75 TGCCCATTTTTCTATTGGGGTGTTCGTCTTTT 44 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.08 CpG sites = 41, Kimura (unadjusted) = 34.07 Transitions / transversions = 1.00 (41/41) Gap_init rate = 0.05 (14 / 304), avg. gap size = 1.93 (27 / 14) 1369 26.12 12.05 3.02 chr3qtel1M 421636 423826 (576174) C L1M5_orf2#LINE/L1 (174) 3120 738 m_b147s551i2 5501 chr3qtel1M 421636 AAATGTTTTTTCCCAGTTTTT---TTTCCTTTCTAGTCTCATTA---GTT 421679 i i ? i v --- v ii v i - --- v C L1M5_orf2#LIN 3120 AAATATTTTCTCCCANTCTGTGGCTTGCCTTTTCATTTTC-TTAACGGTG 3072 chr3qtel1M 421680 TTGTTTGTA---CAAAAACTTTT--TCTTCATATAATCAAA------AAT 421718 iv v?--- i ii -- i v i? i v ------ C L1M5_orf2#LIN 3071 TCTTTTGANGAGCAGAAGTTTTTAATTTTGATGNAGTCCAATTTATCAAT 3022 chr3qtel1M 421719 TTTCTATTTTGTGATCAATAATGATCTCAGGTCTTCTTTGGTCCAAATTC 421768 i v i i i?i iv -- i iiv i v iiv-- ii C L1M5_orf2#LIN 3021 TTTTTCTTTTATGGTTNGTGCT--TTTTGTGTCCTGTTTAAG--AAATCT 2976 chr3qtel1M 421769 CTTCCTCCTCCACAGGTC-TGAAGTAAACTATCCTATGTTTT--TCTA-- 421813 i v v?i - -i - v i v -- -- C L1M5_orf2#LIN 2975 TTGCCTANCCCA-AGGTCACGAAG-ATATTCTCCTATGTTTTCTTCTAGA 2928 chr3qtel1M 421814 ATTTACTTAT-GTCAT-TCTTTTGC---TAGATCTG-AACCCATTTTGAC 421857 v -- - iv -? i --- i i-i i i ? v C L1M5_orf2#LIN 2927 AGTT--TTATAGTTTTANCTTTTACATTTAGGTCTATGATCCATCTNGAA 2880 chr3qtel1M 421858 TTTATCTTT-TGTAC--TTTTAAATGTGGGTCAAGGCCTGGTTTCT-CCA 421903 v i - i-- v v ii iv i ?iiiiv i - C L1M5_orf2#LIN 2879 TTAATTTTTGTGTATGGTGTGAGGTAGGGGTCGAGNTTCATTTTTTTCCA 2830 chr3qtel1M 421904 TACCAAATTTCCAATTTTCCCAGCGT--TTTGTCAAACAGTAAATTCTTA 421951 i-ii v v i ii-- ii v vvv i - C L1M5_orf2#LIN 2829 TAT-GGATATCCAATTGTTCCAGCACCATTTGTTGAAAAGACTATCCTT- 2782 chr3qtel1M 421952 TCCCCAAAGCTGGGGT-CTTTGGG---TTTGTCAAACCACTAGATTGCTA 421997 --- iiv - ? v--- -- v vi ? ?iv C L1M5_orf2#LIN 2781 TCCCCA---CTGAATTGCNTTGGCACCTTTGTCAAA--AATCAANTGNCC 2737 chr3qtel1M 421998 AT-TAT---TGACTTTTTTCCTTTAAC---CTGACCTATTCCACT-ATCA 422039 - --- iv i v i v-i --- ivi i i - v C L1M5_orf2#LIN 2736 ATATATGTGTGGGTCTATTTCTG-GACTCTCTATTCTGTTCCATTGATCT 2688 chr3qtel1M 422040 ACG-GTCTAT--TTCGGCCGA---CAAATGGTTTTGGTGACTGCTGCTTT 422083 iv- -- vv i --- v iv i i v iv C L1M5_orf2#LIN 2687 ATTTGTCTATCCTTACGCCAATACCACACTGTCTTGATTACTGTAGCTTT 2638 chr3qtel1M 422084 A-AATATAGTTTTAGATTACGACAGC--AGGCCACCTTCA--CTTGTTTT 422128 - - i ii?v v? ii i-- i i -- i --i i C L1M5_orf2#LIN 2637 ATAATA-AGTCTTGANATCNGGTAGTGTAAGTC--CTCCAACTTTGTTCT 2591 chr3qtel1M 422129 T--TTTTCA---TTGGTTCCCTTAAAATCTTGA-CCTTTTCTTCTTCAGA 422172 -- --- v ivvi v-- ? i- v v i i v C L1M5_orf2#LIN 2590 TCTTTTTCAAGATTGTTTTGGCTAT--TCTNGGTCCTTTGCATTTCCATA 2543 chr3qtel1M 422173 TAAATTTTAT------TTTATTTTTTTCTAGGTCATTAAAATAATTTTGG 422216 v------i i ivv ------i v ii - v C L1M5_orf2#LIN 2542 TAAATTTTAGAATCAGCTTGTCAATTTCTA------CAAAAAAACCT-GC 2500 chr3qtel1M 422217 GGGGATC---GTTGG--TTGCATTAAATAAATAGATTAGTT-----AAAA 422256 v i---i -- i vv i i ----- i C L1M5_orf2#LIN 2499 TGGGATTTTGATTGGGATTGCATTGAATCTATAGATCAATTTGGGGAGAA 2450 chr3qtel1M 422257 ATAATATTGTACTTTATTATATTCCAAACCT----ATCCAAGG-CATAAT 422301 v i i ---- ? iv --i ii ---- v i- ii C L1M5_orf2#LIN 2449 TTGACAT----CTTNACAATATT--GAGTCTTCCAATCCATGAACATGGT 2406 chr3qtel1M 422302 AT---TTTCCAGTT--TGAGATCTGTCTTTA-TTTGTGTAAAAAGTGTTT 422345 --- i v -- v i - - v v v iv i C L1M5_orf2#LIN 2405 ATATCTCTCCATTTATTTAGGTCT-TCTTTAATTTCTCTCAGCAATGTTT 2357 chr3qtel1M 422346 TGT-GTTTGC--TCTATAG-TTTTGACTTTGCCTTGACAGACAGATTCCG 422391 - v -- v ? - i vviv ?ii vi ivv v C L1M5_orf2#LIN 2356 TGTAGTTTTCAGTGTANAGGTCTTGCACATNTTTTGTTAGATTTATTCCT 2307 chr3qtel1M 422392 AAATATTTTATACTATTGGAT--TATTTTAATTGGAATTTCTTTTGT--T 422437 i ? ii v v -- v v v vi ?v-- C L1M5_orf2#LIN 2306 AAGTATTTNATGTTTTTTGATGCTATTGTAAATGGTATTGTTTTTNAAAT 2257 chr3qtel1M 422438 CTCTTTTTTTGGAT-TTTGTTAGTGATGTATAAAAA--------ATTCCC 422478 i v iiiiv - iv ii i i -------- iii C L1M5_orf2#LIN 2256 TTCATTTTCCAATTGTTTGTTGCTAGTATATAGAAATACAATTGATTTTT 2207 chr3qtel1M 422479 GGG-ATTTATTTTGTATCCTAAACTTTTGC-AAAGTTATCAATTATTTCT 422526 vi- v ii ?ivivii - v i iiv v C L1M5_orf2#LIN 2206 GTATATTGACCTTGTATCCNGCGACCTTGCTAAATTCACTTATTAGTTCT 2157 chr3qtel1M 422527 AAT-GCTTTTTAGTAGAATCTCTGGG--TTTCTA-ATAAAACATCATATC 422572 i - i ? v v i ? -- -i ? vv i C L1M5_orf2#LIN 2156 AGTAGTTTNTTTGTAGATTCTTTNGGATTTTCTACGTANACAATCATGTC 2107 chr3qtel1M 422573 ATCTG----TAAAG---GTGTTAATTTGTTTTCATTCCTACTCTAATTCC 422615 ---- ? --- v -- vi i v v iii v v C L1M5_orf2#LIN 2106 ATCTGCGAATAANGACAGTTTTA--TTTCTTCCTTTCCAATCTTTATGCC 2059 chr3qtel1M 422616 TTTCATTTCTTTCTC--AATTTTTTGCCTTGA----AATTTCTAATACAA 422659 i i --ivi v vi i----i ii i i C L1M5_orf2#LIN 2058 TTTTATTTCTTTTTCTTGCCTTATTGCACTGGCTAGGACCTCCAGTACAA 2009 chr3qtel1M 422660 T-TTGAATAATAATGGTGATAGTGGAAATC-TTGT-TTCCTCCCTATCTT 422706 - iv i ? i v - - vi v C L1M5_orf2#LIN 2008 TGTTGAATAGAAGTGGTGANAGCGGACATCCTTGTCTTGTTCCCGATCTT 1959 chr3qtel1M 422707 ACTGGGAATGGTTCCA--ATTTC-CCATTAA-TATGATATTA-------- 422744 vv v v? i --? - - i ?-------- C L1M5_orf2#LIN 1958 AGGGGGAAAGCNTTCAGTNTTTCACCATTAAGTATGATGTTNGCTGTAGG 1909 chr3qtel1M 422745 -TTTAAATAGGTGCAGCAATTTTCAGA-----AAAGTCCTTTTCCTATAC 422788 - vvi i -- vv v i-----i i ii - v C L1M5_orf2#LIN 1908 TTTTTCGTAGATGC--CCTTTATCAGGTTGAGGAAGTTCCCTTC-TATTC 1862 chr3qtel1M 422789 CT-------CAAGTGTTTTTA-AAGGAATGGATGTTGGATTTTATCAAAT 422830 -------ii v -v v i i i C L1M5_orf2#LIN 1861 CTAGTTTGCTGAGAGTTTTTATCATGAATGGGTGTTGAATTTTGTCAAAT 1812 chr3qtel1M 422831 -CTTTTTCTGCATCTATTAA-ATGATCATATGATTTTT-----TAATTTG 422873 - i - ----- v iv C L1M5_orf2#LIN 1811 GCTTTTTCTGCATCTATTGAGATGATCATATGATTTTTCTCCTTTATTCT 1762 chr3qtel1M 422874 GTTATTGTATAGTCAATTA--TTAATACTTTTCCTAAT--TGAAGCAGTC 422919 --i i v -- i vvv i v -- i v ii C L1M5_orf2#LIN 1761 GTTA--ATATGGTGAATTACATTGATTGATTTTCGAATGTTAAACCAACC 1714 chr3qtel1M 422920 CTGCATTCCTGT-ATAAACCT-ACCTGGTCAT-ATTTATTATCCCTGGGG 422966 i v- i- i - v i vvvi C L1M5_orf2#LIN 1713 TTGCATTCCTGGGATAAACCCCACTTGGTCATGATGTATTATCCTTTTTA 1664 chr3qtel1M 422967 -ATGATTTTTCGAATC--TTTTTTAATATTTTATTT-GGATTTTT--ATC 423010 - - vi v v -- vi i ?- -- C L1M5_orf2#LIN 1663 TAT-ATTGCTGGATTCGATTTGCTAATATTTTGTTNAGGATTTTTGCATC 1615 chr3qtel1M 423011 AATATTCATTGGGGAGATTTATCTGTAATTTTCCTTC-------TGTTTT 423053 v i vi v vi i i------- i C L1M5_orf2#LIN 1614 TATGTTCATGAGGGATATTGGTCTGTAATTTTCTTTTCTTGTAATGTCTT 1565 chr3qtel1M 423054 CATCCTATCGGTTTTGGGTA-CAA---TATGTCTGTTC----AAAAGGAA 423095 ii ----? - - i---? - vi ---- v i C L1M5_orf2#LIN 1564 TGTC----NGGTTTT-GGTATCAGGGTNATG-CTGGCCTCATAAAATGAG 1521 chr3qtel1M 423096 TTTAGTAGT-TTCCTTCATTCCCTATTTTTC--AAATGTTTATATAACAT 423142 vi v - i v ii ii-- iv i i v C L1M5_orf2#LIN 1520 TTGGGAAGTGTTCCCTCTTTTTCTATTTTCTGGAAGAGTTTGTGTAAGAT 1471 chr3qtel1M 423143 TTGAGTTACTTGTTCTTTAAAT-TTTGG--GAATTCA----TTAAACCAT 423185 v vi i v i - -- ---- v i C L1M5_orf2#LIN 1470 TGGTATTATTTCTTCCTTAAATGTTTGGTAGAATTCACCAGTGAAGCCAT 1421 chr3qtel1M 423186 CTGGTCCTGGGGTTTTTTCT-TGGG-------TTGATTA-AAACCTTTTC 423226 v i i i - ------- i - ---- C L1M5_orf2#LIN 1420 CTGGGCCTGGAGTTTTCTTTGTGGGAAGGTTTTTAATTACAAA----TTC 1375 chr3qtel1M 423227 TATTTCTTTTTCTAAAAATGGGACTATTTAAACAATTTC---TTCCTCCT 423273 v - vv i v i i i i i-- --- i i C L1M5_orf2#LIN 1374 AATTTC-TTTAATAGATATAGGGCTATTCAGAT--TTTCTATTTCTTCTT 1328 chr3qtel1M 423274 CTGTTAATTCAGG---GTTATATTTTT-AAGGTATTCATCCATTTCA-CT 423318 v? i i iv ---? i i - v ii - C L1M5_orf2#LIN 1327 GNGTCAGTTTTGGTAANTTGTGTTTTTCAAGGAATTTGTCCATTTCATCT 1278 chr3qtel1M 423319 TAGTTATCAAATTTTTT------AAATT-TCCGAAACAACTCCTAATTA- 423360 v ? v ------ i - i iv i viii v - C L1M5_orf2#LIN 1277 AAGTTNTCAAATTTATTGGCATAAAGTTGTTCATAATATTCTCTTATTAT 1228 chr3qtel1M 423361 CTTTTTAATTTCCTCT----TCAATAGTGACGAGGGTCTCCCTTCTCATT 423406 i v - v ---- vi i---- i i C L1M5_orf2#LIN 1227 CCTTTTAATGT-CTGTAGGATCTGTAGTGAT----GTCTCCTTTTTCATT 1183 chr3qtel1M 423407 --TGAAGACTAATAATTTG-ATTTTTTCTTCCTTTTTA-TAATCAAATTT 423452 -- - v i ii -i i i iii v- i ivi ? C L1M5_orf2#LIN 1182 CCTG-ATATTGGTAATTTGTGTCTTCTCTCTTTTTTTCTTGATCAGTCTN 1134 chr3qtel1M 423453 A--AAAAGTTTTT--ATTTT-TTG-TTTTTTCATAAAAAACCAACTCTTA 423496 i-- i i v -- - - i -- i i i i C L1M5_orf2#LIN 1133 GCTAGAGGTTTATCAATTTTATTGATCTTTTC--AAAGAACCAGCTTTTG 1086 chr3qtel1M 423497 GTTTT-TTTATTAATTCAAAGGTTTTTTTACTTTCAATTTTATTAATTTC 423545 i i- v vvi v vv ? ? ii v i i C L1M5_orf2#LIN 1085 GCTTCGTTGATTTTCTCTATTGTNTNTTTGTTTTCTATTTCATTGATTTC 1036 chr3qtel1M 423546 TCCTTTTTATTTTTTAAATTTCA--AGTTTAATTTGATTGGGGTTTTTAA 423593 v - i i vvv v--vv iv i ?v v -- C L1M5_orf2#LIN 1035 TGC-TCTTATCTTTATTATTTCCTTCCTTCTACTTNCTTTGGG--TTTAA 989 chr3qtel1M 423594 TTTGCTCTT-TTTTCCT---TTTTTAAGTTC---GCCCAATTCATTGATC 423636 - i --- i v v--- ii iv i C L1M5_orf2#LIN 988 TTTGCTCTTCTTTTTCTAGCTTCTTAAGGTGGAAGCTTAGATCATTGATT 939 chr3qtel1M 423637 TT---TCTTTCCCTATTTCTTAAGTAAGGTTCTAGAGATACAAAATTTCC 423683 ---i iiiv v vi ? vv i i? v i v i C L1M5_orf2#LIN 938 TTAAGCCTTTCTTCTTTTCTAATATANGCATTTAANGCTATAAATTTCCC 889 chr3qtel1M 423684 ATT-ATTACC-CTTGGGCTGCCTCCC-CAAATGTTGGTAATTTG---TCT 423727 vi - vi i- vi v - v i vv --- i C L1M5_orf2#LIN 888 TCTAAGCACTGCTTTAGCTGCATCCCACAAATTTTGATATGTTGTATTTT 839 chr3qtel1M 423728 CATTGTTGTTTCCTTGGGTGAAATTAT----TAATTGTGTCTATGATTTG 423773 ? ii ---- ii v v v ---- viv?i i v C L1M5_orf2#LIN 838 CATTNTCAT----TCAGTTCAAAATATTTTCTAATTTCCNTTGTGATTTC 793 chr3qtel1M 423774 -TGTTTCACCTATTCATTCTTTAGAA-TGAGTTATTTAGTTTACAAATCT 423821 - v v i vvi v - v i i v v C L1M5_orf2#LIN 792 TTCTTTGACCCATGGGTTATTTAGAAGTGTGTTGTTTAATTTCCAAATAT 743 chr3qtel1M 423822 TTTGG 423826 v C L1M5_orf2#LIN 742 TTGGG 738 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.28 CpG sites = 324, Kimura (unadjusted) = 33.80 Transitions / transversions = 1.40 (324/231) Gap_init rate = 0.09 (191 / 2190), avg. gap size = 1.76 (336 / 191) 321 27.11 6.40 5.56 chr3qtel1M 425958 426082 (573918) C L2d2_3end#LINE/L2 (7) 548 423 m_b147s601i9 5502 chr3qtel1M 425958 AAATTAATGAATGAGAATTT--TG-GCACTCAATCTATGTCAGGCACTTT 426004 i ii ---- -- - i ii v v i iv v C L2d2_3end#LIN 548 AAATCAACAAAT----ATTTATTGAGCGCCTACTGTGTGCAAGGCACTGT 503 chr3qtel1M 426005 GCTAAGTGCTAGAGTTACAGATATAAA-AAG--CAAG--ATAGTTCCTGT 426049 i i --- vivi i - --i -- i i i C L2d2_3end#LIN 502 GCTAGGCGCT---GTGGGGGATACAAAGAAGTATAAGACATGGTCCCTGC 456 chr3qtel1M 426050 GCTGAAAGAGTTTACATTTTAATAGGGGAAACA 426082 v v i i v i i v i C L2d2_3end#LIN 455 CCTCAAGGAGCTTACAATCTAGTTGGGGAGACA 423 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.50 CpG sites = 22, Kimura (unadjusted) = 35.23 Transitions / transversions = 2.20 (22/10) Gap_init rate = 0.10 (12 / 124), avg. gap size = 1.25 (15 / 12) 321 33.00 4.00 0.00 chr3qtel1M 425980 426079 (573921) C L2a_3end#LINE/L2 (28) 489 386 m_b147s601i10 5502 chr3qtel1M 425980 GCACTCAATCTATGTCAGGCACTTTGCTAAGTGCTAGAGTTACAG--ATA 426027 i ii v v i i v v i i i i v --i i C L2a_3end#LINE 489 GCGCCTACTATGTGCCAGGCACTGTTCTAGGCGCTGGGGATACAGCAGTG 440 chr3qtel1M 426028 TAAAAAGCAA--GATAGTTCCTGTGCTGAAAGAGTTTACATTTTAATAGG 426075 v v i i--i v i iv v vi i i i i C L2a_3end#LINE 439 AACAAAACAGACAAAAGTCCCTGCCCTCATGGAGCTTACATTCTAGTGGG 390 chr3qtel1M 426076 GGAA 426079 i C L2a_3end#LINE 389 GGGA 386 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.29 CpG sites = 22, Kimura (unadjusted) = 46.14 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.02 (2 / 99), avg. gap size = 2.00 (4 / 2) 322 35.77 11.75 4.39 chr3qtel1M 426177 426559 (573441) MamRTE1#LINE/RTE-BovB 895 1304 (2508) m_b147s601i11 5503 chr3qtel1M 426177 TCATCAGTATATATTATTTTACCATGACAAACCCTAATAGGATCAAAGAA 426226 iii vviiii i iv ii ii ivv MamRTE1#LINE/ 895 TCATCAGCGCATATGCCCCCACCATGACGAATACCGATGAGGAGAAAGAA 944 chr3qtel1M 426227 AACTTAAATAAAGACCTGGAGATCTTCACC--------ATCAATGT---- 426264 iv vv i i i v vvi i -------- i ii ---- MamRTE1#LINE/ 945 AGATTCTACAAGGATCTGGACAGACTCATCGCAGCGGTACCAACATCTGA 994 chr3qtel1M 426265 ---GCTTATAATTCTGGGTGACTTCAATACAAGAGTAGGCACAGACTATC 426311 --- v vi ivi v i ii v v v vv - ii MamRTE1#LINE/ 995 CAAGCTGATCGTCACGGGAGATTTCAACGCACGTGTCGGCAGCGA-TGCC 1043 chr3qtel1M 426312 -AGTCAT-------ATTCCTTAAGAGCA-ATAGAATCAGAAACAGCAATA 426352 - iv i ------- v v ii- v ?- ii i ii -- v?- MamRTE1#LINE/ 1044 GAAACGTGGAGAAAAGTCATCG-GACCNCACGGGATTGGAAA--GCTN-A 1089 chr3qtel1M 426353 GCAGCAATCATTTATTACTGAAGACTT-GCACATCT------CATCTGCT 426395 i vi i i v ---- i- iv v ------ v MamRTE1#LINE/ 1090 ACAGCAATGGTCTACTCCTG----CTCAGCGAATGTGCCAAGCATCAGCT 1135 chr3qtel1M 426396 C---ATGACCTACATTGTCTTCTGTTTACC---TAAACTTAAGACTTCGC 426439 --- v v iii i ii --- ivvv v ii MamRTE1#LINE/ 1136 CGTAATCACCAACACCATCTTCCGCCTACCGAATAAGAGAAAGACATCAT 1185 chr3qtel1M 426440 AGATGCACAC----TCACAGCAGTCATTGATACTTAGTAGACTATATC-- 426483 i v ---- vv ---- ii ii vi v i -- MamRTE1#LINE/ 1186 GGATGCACCCAAGGTCTAAGCAG----TGGCATCTCATTGATTATATCAT 1231 chr3qtel1M 426484 --CTTGAAAGAAGAGACAGAAAGGATGGGAAAGTGACAAAGGCAATGTGT 426531 --i i v -v i vvi vvv ii v vivi v i MamRTE1#LINE/ 1232 CGTTCGACAG-CGGGACCTGAAGGATGTTTAGATTACTGCAGCTATGCGT 1280 chr3qtel1M 426532 GACTCACACAGAGTACTTGACTGATCGT 426559 ----i i v i v i i i MamRTE1#LINE/ 1281 G----GCGCCGAGTGCTGGACCGACCAT 1304 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.07 CpG sites = 77, Kimura (unadjusted) = 51.38 Transitions / transversions = 1.43 (77/54) Gap_init rate = 0.08 (31 / 382), avg. gap size = 2.03 (63 / 31) 342 27.84 5.93 8.70 chr3qtel1M 427089 427206 (572794) MIRb#SINE/MIR 4 118 (150) m_b147s601i12 5504 chr3qtel1M 427089 AGGGGTAGCTAGATGGCACAGTAGATAAAACATGGACCCTGGAG------ 427132 i ---i ii i v i i i i ii ------ MIRb#SINE/MIR 4 AGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGAC 50 chr3qtel1M 427133 -GAGCTCAGTTTAAATTCAGCTTCAGACACTTATCACTTCCCAGATATGT 427181 - v vi ii i v vi v v ------- i v i MIRb#SINE/MIR 51 AGACCTGGGTTCGAATCCCGGCTCTGCCACTTA-------CTAGCTGTGT 93 chr3qtel1M 427182 GACCCTGGGCAAGTCACTTAATCCC 427206 i i i i MIRb#SINE/MIR 94 GACCTTGGGCAAGTTACTTAACCTC 118 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.08 CpG sites = 22, Kimura (unadjusted) = 36.85 Transitions / transversions = 2.75 (22/8) Gap_init rate = 0.10 (12 / 117), avg. gap size = 1.42 (17 / 12) 310 39.59 1.68 3.42 chr3qtel1M 427773 428010 (571990) MamRTE2#LINE/RTE-BovB 7 240 (1312) m_b147s551i3 5505 chr3qtel1M 427773 CACTGCTGACAAAATTCTTGCCAAAGTTCTCCTTAGTAGGCTGACCTTTC 427822 i i iv i iv v i i i v iiv i -- ii MamRTE2#LINE/ 7 CACCGCCGGAAAGATCATTGCAAGAATCCTCCTGAACCGACT--CCTCCC 54 chr3qtel1M 427823 ACCTG--GAAGATGGTCACCATCTACCTGAAAGCCTGTGTGGCTTCAGAG 427870 i -- -- ---- v v v vvi v i v i MamRTE2#LINE/ 55 ACTTGCTGAAGA--G----CTTCTCCCGGAATCTCAGCGTGGGTTTAGAG 98 chr3qtel1M 427871 GGCTGAGAAATAC--TTAATATGATGTTTGTTGCCCAATAACTCCAGGAA 427918 viii? iiii --i i i i v iii i ivi i ? MamRTE2#LINE/ 99 CATCNAGAGGCGCAACTGATACGGTCTTCACTGCTCGCCAGCTNCAGGAA 148 chr3qtel1M 427919 AAGTGCCAGGAGAAGCACAGAGGTCACCACACAATGTTTGTTGTTTTGAT 427968 i i iv i i i vv vii i iiiiv iv i vi? v v MamRTE2#LINE/ 149 AAATGCCAAGAACAACATAAACCTCTTTATATGGCCTTCCTCGACNTCAG 198 chr3qtel1M 427969 TAAGGCCTTTGATACCACCATTCATGAGGTCTTACAGAAAAT 428010 v iv iii v i i iv iii ii MamRTE2#LINE/ 199 GAAGGCCTTTGACTCTGTCAGTCGTGAAGCATTGTGGAGGAT 240 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 54.69 CpG sites = 63, Kimura (unadjusted) = 63.81 Transitions / transversions = 2.25 (63/28) Gap_init rate = 0.04 (10 / 237), avg. gap size = 1.20 (12 / 10) 19 0.00 3.23 3.23 chr3qtel1M 428823 428853 (571147) (TCTTT)n#Simple_repeat 1 31 (0) m_b147s252i6 5506 chr3qtel1M 428823 TCTTTTCTTTTCTTTT-TTTTCTTTTTCTTTT 428853 - - (TCTTT)n#Simp 1 TCTTTTCTTTTCTTTTCTTTTC-TTTTCTTTT 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2) 18 15.51 0.00 0.00 chr3qtel1M 428825 428854 (571146) (T)n#Simple_repeat 1 30 (0) m_b147s252i7 5506 chr3qtel1M 428825 TTTTCTTTTCTTTTTTTTCTTTTTCTTTTT 428854 i i i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 30 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 426 26.92 0.00 8.62 chr3qtel1M 428872 428997 (571003) C MIRb#SINE/MIR (152) 116 1 m_b147s601i14 5507 chr3qtel1M 428872 GGGTAAGTGATATGCTCAGGATCACACAGCTAGGAAGTGTTAAGTATCTG 428921 v i iv i i i v vi i-- v i C MIRb#SINE/MIR 116 GGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAG--AGCCG 69 chr3qtel1M 428922 AAATCAGATTTGAAGTCAGGTCCTCCTGTTTTCAGGGCTGGTGCTCTCTC 428971 i----- i vi ivi vi i ii iv i C MIRb#SINE/MIR 68 G-----GATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTC 24 chr3qtel1M 428972 CACTGCACCACCTCGCTACTCTTCTG 428997 --- i i i C MIRb#SINE/MIR 23 CACTGCACCA---CGCTGCCCCTCTG 1 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.96 CpG sites = 22, Kimura (unadjusted) = 34.74 Transitions / transversions = 2.44 (22/9) Gap_init rate = 0.08 (10 / 125), avg. gap size = 1.00 (10 / 10) 435 25.11 0.00 6.73 chr3qtel1M 428872 428982 (571018) C MIRc#SINE/MIR (155) 113 10 m_b147s601i13 5507 chr3qtel1M 428872 GGGTAAGTGATATGCTCAGGATCACACAGCTAGGAAGTGTTAAGTATCTG 428921 v iv i i i v vi i-- v i C MIRc#SINE/MIR 113 GGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAG--AGCCG 66 chr3qtel1M 428922 AAATCAGATTTGAAGTCAGGTCCTCCTGTTTTCAGGGCTGGTGCTCTCTC 428971 i----- i i vi i vi i i v ii i C MIRc#SINE/MIR 65 G-----GACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTC 21 chr3qtel1M 428972 CACTGCACCAC 428982 C MIRc#SINE/MIR 20 CACTGCACCAC 10 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.77 CpG sites = 18, Kimura (unadjusted) = 31.68 Transitions / transversions = 2.25 (18/8) Gap_init rate = 0.06 (7 / 110), avg. gap size = 1.00 (7 / 7) 474 32.91 4.74 6.35 chr3qtel1M 429514 429977 (570023) L3#LINE/CR1 1770 2226 (1873) m_b147s601i15 5508 chr3qtel1M 429514 TCTCCATCAAAAGATGGGGAAATCAACAAGGGAAAATTTCATTCTAGATG 429563 -- i i i i i v i i v vii i i iv L3#LINE/CR1 1770 TCTC--TCAGAAGGTAGAGGAAGCAACGAGGGGAACTGCTACTCTGGACT 1817 chr3qtel1M 429564 CAACCTTTATCAAGAGGGAAGAGTTGGTTCCTGGAGTGACAAT--ATGGG 429611 i iii v i v i ii vv i iv i -- i L3#LINE/CR1 1818 TAATTCTGACCAACAAGGAAGAACTGGTTGGTGAAGTGGAAGTCGATAGG 1867 chr3qtel1M 429612 AACATTATATGGTGAGGGAA-GCCAACTGATTCATTTCTGAGTTAGAAAG 429660 v ---- - ii i- -- -- i iv v v - L3#LINE/CR1 1868 AACCTT----GG-GAGAAAGTGCCA--TG--TCATCTTAGAGTTCGTAA- 1907 chr3qtel1M 429661 TTAGGTATATATAGTATATAAAT--AAGGTTTATATATAT---AAACCTT 429705 - vi - v v v - - i -- i ii i i --- i i L3#LINE/CR1 1908 -TAGCCA-AGAAAGGA-A-AAGTTAAAAGTCCACATATGTTCCAGACTTT 1953 chr3qtel1M 429706 AGAATTTGAAAGAGCAGACTTCACAGAATACAGAGGAAAAGTAATCAGGA 429755 vi --- i i i v i v - vii - v L3#LINE/CR1 1954 ACGA---GGAAAAGCAGATTTCAAAAAATTCAGA-GAAAAGAGGT-ATGA 1998 chr3qtel1M 429756 TCTCAGGAACTAAAATTCTGAGAGAGAATACAGCCTGGAAAGAATGAGAA 429805 ii v iv ?i i i vi i - v ii iiiii i i? i L3#LINE/CR1 1999 TTCCATGGCCNGAGACTCAAAAAGA-AAGATGGCTCAAGAGGGNTGGGAA 2047 chr3qtel1M 429806 ACTCTCAA----GAAACTC-----ACAAACACAAGTAATGCTGCTGAGGA 429846 i i ---- i ----- vi i i - iiv L3#LINE/CR1 2048 GCTCTTAAAAATGAAATTCTGACTACAATTACAAATGAT-CCAATGAGGA 2096 chr3qtel1M 429847 GGAGAACATCTACTGTA---AAAAGAACAATATAGAAACAGAGAAAAATC 429893 i i v vvv vv i --- i i v ii i vv? v i? v L3#LINE/CR1 2097 AGAAAAGAGGGAGGGCATTTAAGAAACCAACGTGGCTNCATAGAGNATTC 2146 chr3qtel1M 429894 ATTTACTTCATTGAACTCTTAAAATG-CATGT-TTAGAAGGTGGAAACAA 429941 vi v iv -- -- i v - - i i -i L3#LINE/CR1 2147 TCTGATGTCA--GA--TTTTAAAAGGACATGTATCAGAAGATGGAAA-GA 2191 chr3qtel1M 429942 AGGCAGAGAATACAGGACGGGTAGCAAAGTGCTACA 429977 i i v v ivv iiiv - i i?i L3#LINE/CR1 2192 GGACATATAACCAAGGACAAAGAG-AGAGTANCACA 2226 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 45.19 CpG sites = 95, Kimura (unadjusted) = 46.63 Transitions / transversions = 1.98 (95/48) Gap_init rate = 0.08 (38 / 463), avg. gap size = 1.34 (51 / 38) 33 29.54 2.56 0.84 chr3qtel1M 431318 431434 (568566) (TC)n#Simple_repeat 1 119 (0) m_b147s252i9 5509 chr3qtel1M 431318 TCTCTCTCCCTCTTCCTC-CGCCTTCTTTTTATCTCTCTCATCTCAATTT 431366 i ii - v ii i i v - vv i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TCTCTCTCT 49 chr3qtel1M 431367 CTCAGTCTCT-TATGTTTCTTTCTTGCT-TCTCTGTCTCTCTTTCTGACT 431414 vv - v v i i iv - v i vv (TC)n#Simple_ 50 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 99 chr3qtel1M 431415 CTATTTCTATCTCTCTGTCT 431434 v i v v (TC)n#Simple_ 100 CTCTCTCTCTCTCTCTCTCT 119 Matrix = Unknown Transitions / transversions = 0.87 (13/15) Gap_init rate = 0.03 (4 / 116), avg. gap size = 1.00 (4 / 4) 29 32.66 1.50 1.50 chr3qtel1M 431316 431448 (568552) (TTTCTC)n#Simple_repeat 1 133 (0) m_b147s252i8 5510 chr3qtel1M 431316 TTTCTCTCTCCCTCT-TCCTCCGCCTTCTTTTTATCTCTCTCATCTCAAT 431364 i i i - i i v i i v i - i vv (TTTCTC)n#Sim 1 TTTCTCTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCTTTCTC-TTTCTCT 49 chr3qtel1M 431365 TTCTCAGTCTCTTATGTTTCTTTCTTGCT-TCTCTGTCTCTCTTTCTGAC 431413 vv - v i i i v - i v i vvi (TTTCTC)n#Sim 50 TTCTCTTTCTCTT-TCTCTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCTT 98 chr3qtel1M 431414 TCTATTTCTATCTCTCTGTCTGTTACTCATTTTCT 431448 v v i v v v v i (TTTCTC)n#Sim 99 TCTCTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCT 133 Matrix = Unknown Transitions / transversions = 1.00 (17/17) Gap_init rate = 0.03 (4 / 132), avg. gap size = 1.00 (4 / 4) 207 33.83 0.00 5.00 chr3qtel1M 431554 431637 (568363) C MamRTE1#LINE/RTE-BovB (349) 3463 3384 m_b147s601i16 5511 chr3qtel1M 431554 TTCTTCTGTCCTCCTTGTGAGTGCTTGTCTCATGGGAGTTCTCCATAAAA 431603 i i ivv i v i i ivvv i v i v i C MamRTE1#LINE/ 3463 TTCTTCTGCCCTCCCTGCTTGCGGTTGCCCCACTTCAGCTCACCGTACAG 3414 chr3qtel1M 431604 TAGTCTTTTGGGCAAAAGTACTTCTGTCATTCAT 431637 i iivi i ---- v v i C MamRTE1#LINE/ 3413 CAGCTGCTTGGGTA----TCCTGCTGTCATCCAT 3384 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.95 CpG sites = 16, Kimura (unadjusted) = 46.60 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.05 (4 / 83), avg. gap size = 1.00 (4 / 4) 18 15.27 2.63 0.00 chr3qtel1M 432537 432574 (567426) (AAGAA)n#Simple_repeat 1 39 (0) m_b147s252i10 5512 chr3qtel1M 432537 AAGGAAGAAAAAGGAAAGAAAAGAAGA-AAAAGAAAAGA 432574 i ii i i - (AAGAA)n#Simp 1 AAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGA 39 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 186 30.61 0.00 0.00 chr3qtel1M 434021 434069 (565931) L2c_3end#LINE/L2 385 433 (45) m_b147s601i17 5513 chr3qtel1M 434021 TCCTCAACGGCACAGAGTGTGTTGTGTTTGTCTTTGTATGCCCAGTACC 434069 ii v vi vi iv i ii v ii L2c_3end#LINE 385 TCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTATCCCCAGCGCC 433 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.05 CpG sites = 10, Kimura (unadjusted) = 41.39 Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 453 24.98 5.84 3.57 chr3qtel1M 434170 434306 (565694) C L2a_3end#LINE/L2 (0) 517 378 m_b147s601i18 5514 chr3qtel1M 434170 ACTCCTCCATT-AATAAACATT-ATTAAGTGTCTTCTATGTACCAGGCAC 434217 i v i - i i - i i i v i C L2a_3end#LINE 517 ATTCATTCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCAC 468 chr3qtel1M 434218 TGTGTTATAAACGCTGGGAGTCC--TAATGGAGGTAAAA-AGAC---AGG 434261 -- v ii ii v --i i i --i - --- v C L2a_3end#LINE 467 --TGTTCTAGGCGCTGGGGATACAGCAGTGAA--CAAAACAGACAAAAGT 422 chr3qtel1M 434262 CCCTGTCCTTAAGGAGTTTACAATTTAATGGGGAAATGATGAACA 434306 i i v i v i i ii - iii C L2a_3end#LINE 421 CCCTGCCCTCATGGAGCTTACATTCTAGTGGGGGGA-GACAGACA 378 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.20 CpG sites = 26, Kimura (unadjusted) = 32.42 Transitions / transversions = 3.71 (26/7) Gap_init rate = 0.07 (10 / 136), avg. gap size = 1.30 (13 / 10) 383 26.46 8.14 3.33 chr3qtel1M 434175 434346 (565654) C L2d_3end#LINE/L2 (8) 508 329 m_b147s601i19 5514 chr3qtel1M 434175 TCCATTAATAAACATT-ATTAAGTGTCTTCTATGTACCAGGCACTGTGTT 434223 v i i ii - i i i v i ivi i C L2d_3end#LINE 508 TCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTGTGCT 459 chr3qtel1M 434224 ATAAACGCTG-GGAGTCCTAATGGAG-GTA-AAAAGACAGGCCCTGTCCT 434270 --ii - i vv v ?vii ?- - i v ii v i C L2d_3end#LINE 458 A--GGCGCTGTGGGGAACGANAAAANAGTATAAGACATGGTCCCTGCCCT 411 chr3qtel1M 434271 TAAGGAGTTTACAATTTAA-TGGGGAAAT--GATGAACAGCCAAATGTA- 434316 i i i i- i i-- iv -- v v - C L2d_3end#LINE 410 CAAGGAGCTTACAATCTAGTTGGGGAGACAAGACTAACA--CACATGAAA 363 chr3qtel1M 434317 ----CAGAAAACAAACTAC-AGCCGGGATA-AATTA 434346 ----i i -- - v i v - C L2d_3end#LINE 362 CAATTAGAGAACAA--TACAAGACAGTATATAATTA 329 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.69 CpG sites = 30, Kimura (unadjusted) = 34.68 Transitions / transversions = 2.14 (30/14) Gap_init rate = 0.09 (16 / 171), avg. gap size = 1.25 (20 / 16) 303 31.62 0.73 0.73 chr3qtel1M 434785 434921 (565079) C L1MC_orf2#LINE/L1 (3070) 224 88 m_b147s551i4 5515 chr3qtel1M 434785 GCTACTCCTATTTT-TTTTACTTTACCTGAACCATAATATATTCTGCTCC 434833 ?ii - iv viiv v i - ii ii v C L1MC_orf2#LIN 224 GCTACTCCNGCTTTCTTTTGATTAGTGTTAGC-ATGGTATATCTTTCTCC 176 chr3qtel1M 434834 AGCCTTTTAGCTTCACTCTGTATGTATCACTATGCTTTAAATACATTTCT 434883 v ? vi i v i i vi ii v i ivi C L1MC_orf2#LIN 175 ATCCNTTTACTTTTAATCTATATGTGTCTTTATATTTAAAGTGGGTTTCT 126 chr3qtel1M 434884 TGTAAGCAACATATTGCAGGATTCTGGCTTTTAATACA 434921 ii v iv i ii vi i v C L1MC_orf2#LIN 125 TGTAGACAACATATAGTTGGGTCTTGTTTTTTGATCCA 88 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 44.07 CpG sites = 28, Kimura (unadjusted) = 44.07 Transitions / transversions = 1.87 (28/15) Gap_init rate = 0.01 (2 / 136), avg. gap size = 1.00 (2 / 2) 288 32.56 2.33 0.00 chr3qtel1M 434816 434944 (565056) C L1MEc_5end#LINE/L1 (50) 2477 2346 m_b147s551i5 5515 chr3qtel1M 434816 CATAATATATTCTGCTCCAGCCTTTTAGCTTCACTCTGTATGTATCACTA 434865 ii ii vi v vi i vi i v i vi C L1MEc_5end#LI 2477 CATGGTATATCTTTTTCCATCCTTTTACTTTTAACCTATTTGTGTCTTTA 2428 chr3qtel1M 434866 TGCTTTAAATACATTTCTTGTAAGCAACATATTGCAGGATTCTGGCTTTT 434915 ii v i i?i i i v iv i ii vi C L1MEc_5end#LI 2427 TATTTAAAGTGNGTTTCTTGTAGGCAGCATATAGTTGGGTCTTGCTTTTT 2378 chr3qtel1M 434916 AATACAATATGCTA---TCTGCTTCTGCATTG 434944 v v v vi --- i i vv C L1MEc_5end#LI 2377 TATCCAATCTGACAATCTCTGCCTTTTAATTG 2346 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 45.08 CpG sites = 26, Kimura (unadjusted) = 45.08 Transitions / transversions = 1.62 (26/16) Gap_init rate = 0.01 (1 / 128), avg. gap size = 3.00 (3 / 1) 16 5.27 0.00 0.00 chr3qtel1M 435598 435617 (564383) (AC)n#Simple_repeat 1 20 (0) m_b147s252i11 5516 chr3qtel1M 435598 ACATACACACACACACACAC 435617 i (AC)n#Simple_ 1 ACACACACACACACACACAC 20 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 425 28.24 0.00 0.00 chr3qtel1M 436229 436313 (563687) Charlie1b#DNA/hAT-Charlie 1 85 (438) m_b147s502i2 5517 chr3qtel1M 436229 CAGTGGTTCTCAAAGTATGGTCTAGAGAATCCTGGGGATTTCTGAAACTT 436278 i i ii i vi i ii i i ii Charlie1b#DNA 1 CAGCGGTTCTCAAAGTGTGGTCCGGGGACCCCTGGGGGTCCCCGAGACCC 50 chr3qtel1M 436279 TTTTAGAGGGTCTACAAATTCAAAAGTAGTTTTAT 436313 i i ii i iv v v i Charlie1b#DNA 51 TTTCAGGGGGTCCGCGAGGTCAAAACTATTTTCAT 85 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 28.60 CpG sites = 20, Kimura (unadjusted) = 38.93 Transitions / transversions = 5.00 (20/4) Gap_init rate = 0.00 (0 / 84), avg. gap size = 0.0 (0 / 0) 560 14.88 3.23 2.40 chr3qtel1M 436306 436429 (563571) Charlie1a#DNA/hAT-Charlie 1331 1455 (0) m_b147s502i3 5518 chr3qtel1M 436306 AGTTTTA-TTTCCAATATGGTAAATATCTATAAATATAATCCAGATAAAC 436354 - i v i i v Charlie1a#DNA 1331 AGTTTTAATTTCTAATATGGTAAATATCGATAGATATAACCCACATAAAC 1380 chr3qtel1M 436355 AAAAAGGCTTTGGAGAGATCCTCAATAATTTTTAATATGATAAA--GATA 436402 ivv --- i v vvi -- i v Charlie1a#DNA 1381 AAAAGCTCTTTGG---GGTCCTCAATAATTTTTAAGAGTGTAAAGGGGTC 1427 chr3qtel1M 436403 CTGAAAAC-AAAAGTTTGAGAACCACTG 436429 i v - i Charlie1a#DNA 1428 CTGAGACCAAAAAGTTTGAGAACCGCTG 1455 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 15.70 CpG sites = 9, Kimura (unadjusted) = 16.65 Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.05 (6 / 123), avg. gap size = 1.17 (7 / 6) 22 6.33 0.00 0.00 chr3qtel1M 436579 436611 (563389) (TCTATA)n#Simple_repeat 1 33 (0) m_b147s252i12 5519 chr3qtel1M 436579 TCTATATCTATATCTATACCTATATCTTTATCT 436611 i v (TCTATA)n#Sim 1 TCTATATCTATATCTATATCTATATCTATATCT 33 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 53 0.00 0.00 0.00 chr3qtel1M 436613 436657 (563343) (TA)n#Simple_repeat 1 45 (0) c_b147s251i0 5520 chr3qtel1M 436613 TATATATATATATATATATATATATATATATATATATATATATAT 436657 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATAT 45 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 530 32.66 6.76 3.73 chr3qtel1M 439013 439559 (560441) C L1ME1_3end#LINE/L1 (351) 575 13 m_b147s551i6 5521 chr3qtel1M 439013 AGCTCATCATTTCTTATAGCACAGCAGTATTTAATTACAATAATGTACCA 439062 i i ivi i v vv i iv ii vvi i C L1ME1_3end#LI 575 AGTTCGTTCCTTTTTATTGCTGAGTAGTATTCCATTGTATGGATATACCA 526 chr3qtel1M 439063 CAATTTGTTCAATCATTTCCCAATTGATATGTGTCTGCA--AATTCTAGT 439110 i vi iv ?i iviii i vi--iv i C L1ME1_3end#LI 525 CAATTTGTTTATCCATTCACCNGTTGATGGACATTTGGGTTGTTTCCAGT 476 chr3qtel1M 439111 TCTTTGC-ACCACACAAAGAGCTACTCTAAATA---GTTTAGAAG----- 439151 i v - ii iv v i i v i i --- v v ----- C L1ME1_3end#LI 475 TTTTGGCTATTACGAATAAAGCTGCTATGAACATTCGTGTACAAGTCTTT 426 chr3qtel1M 439152 ATATGGG---ATCTTTTCCTTTTTTCTGATCATTTGAAAAAACAGACCAA 439198 i i i--- v v i i-------- iiv i -- v C L1ME1_3end#LI 425 GTGTGGACATATGTTTTCATTTCTC--------TTGGGTAAATA--CCTA 386 chr3qtel1M 439199 GTAGTGGTTTTTCTGGGTCAAAAG--AAATTTAA---TAATTCTG-AATA 439242 v vv v v v -- i v v--- i i ?- v C L1ME1_3end#LI 385 GGAGTGGAATTGCTGGGTCATATGGTAAGTGTATGTTTAACTTTNTAAGA 336 chr3qtel1M 439243 TAATTTTAGATTGCTCTCCAAAATGGTTAAATCAGTTCACAATTTCATCA 439292 v v vii i i i i i i iv i v ii v ii i C L1ME1_3end#LI 335 AACTGCCAAACTGTTTTCCAAAGTGGCTGTACCATTTTGCATTCCCACCA 286 chr3qtel1M 439293 AAAATGAATTAGCATCCCAATTTTTCCACATTCCCTCCAACATTTG---T 439339 iv v v vi i i vi i i v i --- C L1ME1_3end#LI 285 GCAATGTATGAGAGTTCCAGTTGCTCCACATCCTCGCCAACACTTGGTAT 236 chr3qtel1M 439340 TGCTTTTCCCTTCAATCGTTTTAGCCAATCTTGTTGTTCTATAATGACAC 439389 iivv ii i --- v vi v v v i i ii i C L1ME1_3end#LI 235 TGTCAGTCTTTTTAAT---TTTAGCCATTCTAATAGGTGTGTAGTGGTAT 189 chr3qtel1M 439390 CTCAAAGTTGTTTTCATTTGGATTTTTCTAAT---CAATGA--TTGAGAT 439434 vv v v v ii ---i -- -- C L1ME1_3end#LI 188 CTCATTGTGGTTTTAATTTGCATTTCCCTAATGACTAATGATGTTGAG-- 141 chr3qtel1M 439435 AATTTTATCATATGATCAT---------AAATGTGTTCCTAGAATAGAAA 439475 v i v i v i ---------iv i v i ---- i vi C L1ME1_3end#LI 140 CATCTTTTCATGTGCTTATTTGCCATCCGTATATCTTCTT----TGGTGA 95 chr3qtel1M 439476 AGTGCCTGTTCATATGCTCTAACCATTTATCAGTTGGATGGATAGTGACT 439525 i v vi i iv v i i i v v v v-i C L1ME1_3end#LI 94 AGTGTCTGTTCAAATCTTTTGCCCATTTTTTAATTGGGTTGTTTGTT-TT 46 chr3qtel1M 439526 CATATTCATATAGATTTGACAATGTTTTATATAT 439559 v - vv v v i vi C L1ME1_3end#LI 45 CTTATT-ATTGAGTTTTGAGAGTTCTTTATATAT 13 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.39 CpG sites = 97, Kimura (unadjusted) = 44.44 Transitions / transversions = 1.29 (97/75) Gap_init rate = 0.06 (33 / 546), avg. gap size = 1.76 (58 / 33) 576 29.63 7.74 3.09 chr3qtel1M 439194 439503 (560497) C L1PA7_3end#LINE/L1 (511) 390 67 m_b147s551i7 5521 chr3qtel1M 439194 ACCAAGTAGTGGTTTTTCTGGGTCAAAAGAAATTTAATAATTCTGAATAT 439243 v i vv v v iv v- ii ii vi C L1PA7_3end#LI 390 ACCCAGTAATGGGATTGCTGGGTCAAATGGTATTTC-TGGTTCTAGATCC 342 chr3qtel1M 439244 ------AATT-TTAGATTGCTCTCCAAAATGGTTAAATCAGTTCACAATT 439286 ------ i-ii v i iii v i ii i i v i C L1PA7_3end#LI 341 TTGAGGAATCGCCACACTGTCTTCCACAATGGTTGAACTAATTTACACTC 292 chr3qtel1M 439287 TCATCAAAAATGAATTAGCATCCCAATTTTTCCACATTCCCTCCAACATT 439336 i i v i v vv i i v i i i i i C L1PA7_3end#LI 291 CCACCAACAGTGTAAAAGCGTTCCTATTTCTCCACATCCTCTCCAGCATC 242 chr3qtel1M 439337 TGTTGCTTTT---CCCTTCAATCGTTTTAGCCAATCTTGTTGTTCTATAA 439383 i ii--- ii i vi i--- v vii viv ivi C L1PA7_3end#LI 241 TGTTGTTTCCTGACTTTTTAATGATC---GCCATTCTAACTGGCGTGAGA 195 chr3qtel1M 439384 TGACACCTCAAAGTTGTTTTCATTTGGATTTTTCTAAT---CAATGAT-- 439428 ii i vv v v v i --- i -- C L1PA7_3end#LI 194 TGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTAATGACCAGTGATGA 145 chr3qtel1M 439429 TGAGATAATTTTATCATATGAT---------CATAAATGTGTTCCTAGAA 439469 v -- v v --------- v i ---- C L1PA7_3end#LI 144 TGAGCT--TTTTTTCATATGTTTGTTGGCCGCATAAATGTCTTCTT---- 101 chr3qtel1M 439470 TAGAAAAGTGCCTGTTCATATGCTCTAACCATTT 439503 v i i v iiiv i C L1PA7_3end#LI 100 TTGAGAAGTGTCTGTTCATATCCTTCGCCCACTT 67 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.26 CpG sites = 55, Kimura (unadjusted) = 39.12 Transitions / transversions = 1.62 (55/34) Gap_init rate = 0.05 (16 / 309), avg. gap size = 2.12 (34 / 16) 1263 31.68 6.67 1.50 chr3qtel1M 440210 441289 (558711) C L1M5_orf2#LINE/L1 (795) 2499 1365 m_b147s551i8 5521 chr3qtel1M 440210 TGGTAATTTGATTAGGATGGCATTGAATTTATAAATTAGTTTGGGTAAAA 440259 v v i v i i i i v i C L1M5_orf2#LIN 2499 TGGGATTTTGATTGGGATTGCATTGAATCTATAGATCAATTTGGGGAGAA 2450 chr3qtel1M 440260 TTATCATTTTTATTATACTGCTTCTGTCTACCCATGAACATTTAATATGT 440309 iv i ? iv i vv vi v i vvv v C L1M5_orf2#LIN 2449 TTGACATCTTNACAATATTGAGTCTTCCAATCCATGAACATGGTATATCT 2400 chr3qtel1M 440310 CTTCA---ATTTATATTTGATTTTATTTATATAAAAAGTTTTTTATGTAA 440356 i --- vi i vv v v v v iv i v -- i C L1M5_orf2#LIN 2399 CTCCATTTATTTAGGTCTTCTTTAATTTCTCTCAGCAATGTTT--TGTAG 2352 chr3qtel1M 440357 TTT--AGTTATATACTTCTTGGGTTTGTTTTGGCAGACATGCTCCCAGGT 440404 -- - i ? vv viiv ? vi iv ii i i C L1M5_orf2#LIN 2351 TTTTCAG-TGTANAGGTCTTGCACATNTTTTGTTAGATTTATTCCTAAGT 2303 chr3qtel1M 440405 ATTTTACACTATCTTGA-ACTATTTTAAATGAGA-TATTTCTCACTATTT 440452 ? iii - i -i v iv - i i ? v- C L1M5_orf2#LIN 2302 ATTTNATGTT-TTTTGATGCTATTGTAAATGGTATTGTTTTTNAA-ATTT 2255 chr3qtel1M 440453 CTTCTTGCAGAATT-TTGGTTG-TAATACATGGGAATGCTGATGAATTGT 440500 v i v -- - v - i i i i i viv v v C L1M5_orf2#LIN 2254 CATTTTCC--AATTGTTTGTTGCTAGTATATAGAAATACAATTGATTTTT 2207 chr3qtel1M 440501 GTGCATTTACTTCACATCCTGCTACTTTCCTAA----AGTTATTGTTTCC 440546 ii v i iii ? v i v ---- v iv i C L1M5_orf2#LIN 2206 GTATATTGACCTTGTATCCNGCGACCTTGCTAAATTCACTTATTAGTTCT 2157 chr3qtel1M 440547 ACTAACTTCTTAGTTGAATCTTTGGGATTTTCCAAATAG---ATCATATT 440593 v ii ? v v v ? i vi ?--- i i C L1M5_orf2#LIN 2156 AGTAGTTTNTTTGTAGATTCTTTNGGATTTTCTACGTANACAATCATGTC 2107 chr3qtel1M 440594 GTTTATAAAGAGAGAAAGTTTTATCACTTTGTTTTCTATTCAGGTCTCTC 440643 i i iii v i? v iv iv i v iivvi vi i C L1M5_orf2#LIN 2106 ATCTGCGAATAANGACAGTTTTATTTCTTCCTTTCCAATCTTTATGCCTT 2057 chr3qtel1M 440644 TTATGTCTTTTTTTTTTCTTATTGCTATTGCTAGGATTTTCAATACAATA 440693 v i vi vv v ii i i i C L1M5_orf2#LIN 2056 TTATTTCTTTTTCTTGCCTTATTGCACTGGCTAGGACCTCCAGTACAATG 2007 chr3qtel1M 440694 T----------TGGTGGCAATGAGTATTTTTGTTTCATATCTGATCATAC 440733 ---------- i? ii iii ii i ii vi i v v C L1M5_orf2#LIN 2006 TTGAATAGAAGTGGTGANAGCGGACATCCTTGTCTTGTTCCCGATCTTAG 1957 chr3qtel1M 440734 TGGG-AAGATTTCTTTGCTTAATCCCTTTACAAATAATACTAGATAATGG 440782 v - v? vv ?i v -- v viv i ii ? v ivv C L1M5_orf2#LIN 1956 GGGGAAAGCNTTCAGTNTTTCA--CCATTAAGTATGATGTTNGCTGTAGG 1909 chr3qtel1M 440783 TTTTAGATAGATGGATTTTTTTTATAAATTTAAGAAAAAATCCATTTA-T 440831 vvi ----iii v iv i i ivvi v i - C L1M5_orf2#LIN 1908 TTTTTCGTAGATG----CCCTTTATCAGGTTGAGGAAGTTCCCTTCTATT 1863 chr3qtel1M 440832 GCTAATATTTTCAAGGATTTTTAAAAATAATCTGTATGTTGTACTTTATT 440881 v i - viii ii vv vv -- vi v i i i C L1M5_orf2#LIN 1862 CCTAGT-TTGCTGAGAGTTTTTATCATGAA--TGGGTGTTGAATTTTGTC 1816 chr3qtel1M 440882 AAA-ACATTTTCTGCATCTGTTGAGATAATCATAC--CTTTTCACTTTTA 440928 -i v i i i--i v i C L1M5_orf2#LIN 1815 AAATGCTTTTTCTGCATCTATTGAGATGATCATATGATTTTTCTCCTTTA 1766 chr3qtel1M 440929 T--TATTGATATAATTAATTATGTTAGTAGTTTTCCTTATAGTAAACCAT 440976 -- i i ii v ii ii v v i vv iv v C L1M5_orf2#LIN 1765 TTCTGTTAATATGGTGAATTACATTGATTGATTTTCGAATGTTAAACCAA 1716 chr3qtel1M 440977 ACCTGCATTGCTGGTATAAATCTCATTTTG-------------------T 441007 v i v v i i i v ------------------- C L1M5_orf2#LIN 1715 CCTTGCATTCCTGGGATAAACCCCACTTGGTCATGATGTATTATCCTTTT 1666 chr3qtel1M 441008 TATATTTTGTTGTGATCTTTTAGGTATTATTTTGTTA------------- 441044 v i viv vv v v v ?------------- C L1M5_orf2#LIN 1665 TATATATTGCTGGATTCGATTTGCTAATATTTTGTTNAGGATTTTTGCAT 1616 chr3qtel1M 441045 ----GTTTATTAATGAACTTAGCCCACAGTTTGCTTTCTCTGTGTTTACT 441090 ---- i v iv vv i i iii i v iii iv vv C L1M5_orf2#LIN 1615 CTATGTTCATGAGGGATATTGGTCTGTAATTTTCTTTTCTTGTAATGTCT 1566 chr3qtel1M 441091 CTTCCTGGTTTGAATATCAGTATGATATTTGTTTCACAAAACAAGTTTGG 441140 i vi ? vii vi ? ii v ii i ii v C L1M5_orf2#LIN 1565 TTGTCNGGTTTTGGTATCAGGGTNATGCTGGCCTCATAAAATGAGTTGGG 1516 chr3qtel1M 441141 TAG-ATTCCTTCTTTGCCTTTTATTCCAAATATTTTATTTAATATTGGAA 441189 v -i i vi v v iivi v v i v v v C L1M5_orf2#LIN 1515 AAGTGTTCCCTCTTTTTCTATTTTCTGGAAGAGTTTGTGTAAGATTGGTA 1466 chr3qtel1M 441190 ATAGTTGACCTTTAAACATTTGATAGAATCCATTTGTAAATCTATCTAGT 441239 v v vvi i ii i i iiv i v i i v C L1M5_orf2#LIN 1465 TTATTTCTTCCTTAAATGTTTGGTAGAATTCACCAGTGAAGCCATCTGGG 1416 chr3qtel1M 441240 CCTGGTAATTTTTTT--TAGGAAGCTCATATGTAATGTATTCAATGTCTT 441287 - i i -- i v iv vvi v iiv v C L1M5_orf2#LIN 1415 CCTGG-AGTTTTCTTTGTGGGAAGGTTTTTAATTACAAATTCAATTTCTT 1367 chr3qtel1M 441288 TA 441289 C L1M5_orf2#LIN 1366 TA 1365 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 42.36 CpG sites = 188, Kimura (unadjusted) = 43.23 Transitions / transversions = 1.26 (188/149) Gap_init rate = 0.03 (36 / 1079), avg. gap size = 2.47 (89 / 36) 26 0.00 0.00 0.00 chr3qtel1M 442183 442207 (557793) (TTAAA)n#Simple_repeat 1 25 (0) c_b147s251i1 5522 chr3qtel1M 442183 TTAAATTAAATTAAATTAAATTAAA 442207 (TTAAA)n#Simp 1 TTAAATTAAATTAAATTAAATTAAA 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 216 36.41 9.22 0.65 chr3qtel1M 443359 443499 (556501) C L3#LINE/CR1 (178) 3921 3769 m_b147s601i20 5523 chr3qtel1M 443359 ATAACTATAGTTGTTAGAAAACATTTCTGGACATTTAGCCCCAAT-TACC 443407 i i v ii iivi ivv i v vv - i C L3#LINE/CR1 3921 ACAGCTCTGATTGTTAGAAAGTTCTTCCTTATATTGAGCCGAAATCTGCC 3872 chr3qtel1M 443408 TTT-TGTATCTCTCTTCCACT----------CTATCCT-TGAAGCTAAAA 443445 ii- v ii vi i ---------- ii - i i v v C L3#LINE/CR1 3871 TCCCTGTAACTTCCACCCATTGGTCCTAGTTCTGCCCTCTGGAGCCACAC 3822 chr3qtel1M 443446 CAAACAGATCTGACCTCTCTTTTCCATGACATGCTGTCAGAAGCCTTAAA 443495 vi i ii i i i iiv vv iv - vvi i C L3#LINE/CR1 3821 AGAATAAGTCTAATCCCTCTTCCACATGACAGCCCTTCA-AATATTTGAA 3773 chr3qtel1M 443496 GATA 443499 i C L3#LINE/CR1 3772 GACA 3769 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 53.25 CpG sites = 33, Kimura (unadjusted) = 53.25 Transitions / transversions = 1.83 (33/18) Gap_init rate = 0.04 (5 / 140), avg. gap size = 2.80 (14 / 5) 261 26.71 2.53 5.19 chr3qtel1M 444091 444169 (555831) C Charlie4#DNA/hAT-Charlie (0) 3378 3302 m_b147s502i4 5524 chr3qtel1M 444091 CAAAGATTCT-AAGCTTTAATACATCTTGG-CTTCTCTGGCAGGGAGTTT 444138 ii i - v vv iiii v - ii i ---- i C Charlie4#DNA/ 3378 CAGGGGTTCTTAACCTTTTTTGTGCCATGGACCCCTTTGGCAG----TCT 3333 chr3qtel1M 444139 GGTGAAGCTCATAGACCTCTTTTCAGAATAA 444169 ii i i i C Charlie4#DNA/ 3332 GGTGAAGCCTATGGACCCCTTCTCAGAATAA 3302 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.52 CpG sites = 16, Kimura (unadjusted) = 35.52 Transitions / transversions = 4.00 (16/4) Gap_init rate = 0.08 (6 / 78), avg. gap size = 1.00 (6 / 6) 391 26.74 7.69 2.19 chr3qtel1M 444179 444308 (555692) C Charlie4#DNA/hAT-Charlie (3238) 140 4 m_b147s502i5 5524 chr3qtel1M 444179 ATAATTAAACTAATTTTTAAACTTTAATAAGAGATTGTTTAAAACAAAGT 444228 i vv v vi i i i v i iv v i v C Charlie4#DNA/ 140 ATAATTGAAGGAAATGCTAAATTTCAGTTAGAGGTTAGTGAAAATAAAGA 91 chr3qtel1M 444229 TGT--------CCCCCTCAACTTCATGGATCCTCTGAAATCTCTCTACAC 444270 -------- vii v i i i v v i i- C Charlie4#DNA/ 90 TGTAATTTTTTCCCATCCAAGTTCACGGACCCCCTGAATTCTATCCACG- 42 chr3qtel1M 444271 ATAACCCA--GGAGATTCATGGACCTCAGGTTAAGAACCC 444308 --i v-- i i i i i C Charlie4#DNA/ 41 --GACCCCTTGGGGGTCCGTGGACCCCAGGTTAAGAACCC 4 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 30.49 CpG sites = 21, Kimura (unadjusted) = 34.10 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.04 (5 / 129), avg. gap size = 2.60 (13 / 5) 383 21.30 2.04 4.17 chr3qtel1M 444370 444467 (555533) MIR#SINE/MIR 49 144 (118) m_b147s601i21 5525 chr3qtel1M 444370 TGAGTTCAAATATAGACTCAGACACTTCCTAGATGTAGTGTTTACCT-GA 444418 i i viv i v v v v - --- - i MIR#SINE/MIR 49 TGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGT-GTG---ACCTTGG 94 chr3qtel1M 444419 AAAAGTCCTTTAACC-CTGTTTGCCTCAGTTTCCTCATCTGTAAAATAAG 444467 iv ivi - v v ii MIR#SINE/MIR 95 GCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGG 144 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 23.81 CpG sites = 10, Kimura (unadjusted) = 25.20 Transitions / transversions = 1.00 (10/10) Gap_init rate = 0.06 (6 / 97), avg. gap size = 1.00 (6 / 6) 406 25.74 0.74 7.94 chr3qtel1M 445225 445359 (554641) MIRc#SINE/MIR 2 127 (141) m_b148s601i1 5526 chr3qtel1M 445225 GAGACAGCTAGATGGTGCAATGGATAGATCCCTAGCCCTCAAGACAGGAG 445274 i i---i i v v v i v i vi v i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr3qtel1M 445275 GAACTGAGTACAAATTTGGCCTCAGACACTTAAGACTTTCTAGGTGTGTG 445324 v i v i i iiv v v v ------- v MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTG 91 chr3qtel1M 445325 ACCCAGGGCAAGTCACTTAACCCCAGTT-GCCTCAG 445359 iv i vv v- MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.38 CpG sites = 15, Kimura (unadjusted) = 31.52 Transitions / transversions = 0.88 (15/17) Gap_init rate = 0.08 (11 / 134), avg. gap size = 1.00 (11 / 11) 15 14.13 0.00 3.12 chr3qtel1M 445360 445392 (554608) (CAAA)n#Simple_repeat 1 32 (0) m_b148s252i0 5527 chr3qtel1M 445360 CAAAAATACCAAACAAACAAAGGAACAAACAAA 445392 v - v vi (CAAA)n#Simpl 1 CAAACA-AACAAACAAACAAACAAACAAACAAA 32 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 12 24.01 0.00 2.50 chr3qtel1M 445634 445674 (554326) (ACACTGT)n#Simple_repeat 1 40 (0) m_b148s252i1 5528 chr3qtel1M 445634 ACTCTGATCACAATACACTGATATACCATACACTGTACACT 445674 v vv vi - i ii (ACACTGT)n#Si 1 ACACTGTACACTGTACACTG-TACACTGTACACTGTACACT 40 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 625 29.66 5.85 4.56 chr3qtel1M 445685 446009 (553991) L2b_3end#LINE/L2 130 458 (8) m_b148s601i2 5529 chr3qtel1M 445685 TTTGTACTGGCCGTCTCCCCCATGCCTGAAAGGTTCCCCTTCCTCA--TC 445732 i ?v i - i - i v --- i -- L2b_3end#LINE 130 TTTGCACNTGCTGT-TCCCTC-TGCCTGGAACG---CCCTTCCCCACCTC 174 chr3qtel1M 445733 TTGGTCT---CATACCTTCCCCAGCTTCCTGCAGGACTGAGCTCAAATAT 445779 v i --- vvi i v i --- v v v i L2b_3end#LINE 175 TTCGCCTGGCCAACTCCTACTCA---TCCTTCAGGTCTCAGCTCAAATGT 221 chr3qtel1M 445780 CACCTTCTACTGGAAGCTTTCCAAAGACTCCCAACTC----CTGACTCTT 445825 i v v ii vviiv i ivi ---- v i v ii L2b_3end#LINE 222 CACCTCCTCCGGGAAGCCCTCCCTGACCCCCCAGGCCGGGTCAGGCGCCC 271 chr3qtel1M 445826 CTCTCTGACATCCCCTCATCCATTCTTTATGTCACT-TA---TATGAACT 445871 ii i-ii i vi v v ii -- i - i--- ? -- L2b_3end#LINE 272 TCCTCTGG-GCCCCCCCAGTCCTACCCT--GCCACTCTGGGTTATNA--T 316 chr3qtel1M 445872 GAGTTGTTCACATTTCT-CCTCTTACCTTAGATTATGAGCCCCTTGTGGT 445920 vivi ? i v -i iiv vi i i i v v v L2b_3end#LINE 317 TGTCTGNTTACATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGG 366 chr3qtel1M 445921 AAGAGACTGAGTTT---TTGCCTTC-CCTCTG-ATCCCTAACATTCAGCA 445965 v i i ? i --- -- - v - i i iiii L2b_3end#LINE 367 CAGGGACCGNGTCTGTCTTG--TTCACCGCTGTATCCCCAGCGCCTAGCA 414 chr3qtel1M 445966 CAGTGCCTGGCACCCTGTAAGTGCTCCAAAGATGCTTGTGGAAT 446009 ? v v i i viv i ii v L2b_3end#LINE 415 CAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTTGTTGAAT 458 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.34 CpG sites = 57, Kimura (unadjusted) = 40.04 Transitions / transversions = 1.63 (57/35) Gap_init rate = 0.07 (24 / 324), avg. gap size = 1.42 (34 / 24) 14 20.09 5.66 1.82 chr3qtel1M 447068 447120 (552880) (TCTGAC)n#Simple_repeat 1 55 (0) m_b148s252i2 5530 chr3qtel1M 447068 TCTGAATCTCTCTCTGAGCCCT---TCTGAGTCTGTCTCTGGCTCTAACT 447114 v vv - i --- v v i i (TCTGAC)n#Sim 1 TCTGACTCTGACTCTGA-CTCTGACTCTGACTCTGACTCTGACTCTGACT 49 chr3qtel1M 447115 CTGGCT 447120 i (TCTGAC)n#Sim 50 CTGACT 55 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.04 (2 / 52), avg. gap size = 2.00 (4 / 2) 199 27.68 5.00 6.06 chr3qtel1M 449415 449514 (550486) C MamRTE1#LINE/RTE-BovB (2335) 1477 1379 m_b148s601i3 5531 chr3qtel1M 449415 GCACTCACAGCTGGGCTTCCCT--TCTAAGTTAGGCCAACCATTCCATTA 449462 i ii v i -- i --? v vi ii?vvii - C MamRTE1#LINE/ 1477 GTACTTGCAGCTGGGGTTCCTTGNTCCAA--NAGGGCTGCTGNGATGTT- 1431 chr3qtel1M 449463 GTACTAGAGATTCTTGTAGTTGTCCTCCATTCTTCCCAGGAGC---ATAT 449509 vv ? v i i vi - i -- --- ii C MamRTE1#LINE/ 1430 GTCATANAGCTCCTTGCAGGCGT-CTTCATTCT--CCAGGAGCTTGACGT 1384 chr3qtel1M 449510 TGAAC 449514 i C MamRTE1#LINE/ 1383 TGAGC 1379 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.68 CpG sites = 17, Kimura (unadjusted) = 37.49 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.08 (8 / 99), avg. gap size = 1.38 (11 / 8) 41 24.23 3.01 2.24 chr3qtel1M 450119 450251 (549749) (AAGG)n#Simple_repeat 1 134 (0) m_b148s252i3 5532 chr3qtel1M 450119 AATGAAAGAAGGAA-GAAAAAACAAAGAAACAAAAGTAGCAAGACGAA-A 450166 v i - ii vi i vi i v v -- -i (AAGG)n#Simpl 1 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG--GAAGG 48 chr3qtel1M 450167 AAGGAAGGAAGAGAGGAAGGAAGGAAGGAAGGAACGAAAGGAAATAAGG- 450215 ii - i iv - (AAGG)n#Simpl 49 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA-GGAAGGAAGGAAGGA 97 chr3qtel1M 450216 TGAAATGAATGAAAAAAGAAATGAAGGAAGG-AGGAA 450251 v i v v ii i v - (AAGG)n#Simpl 98 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 134 Matrix = Unknown Transitions / transversions = 1.60 (16/10) Gap_init rate = 0.05 (7 / 132), avg. gap size = 1.00 (7 / 7) 14 13.28 9.52 0.00 chr3qtel1M 450199 450240 (549760) (AATGA)n#Simple_repeat 1 46 (0) m_b148s252i4 5533 chr3qtel1M 450199 AACGAAAGGAAATAAGGTGAAATG-AATGAAA--AAA-GAAATGAA 450240 i v i ii - -- - (AATGA)n#Simp 1 AATGAAATGAAATGAAATGAAATGAAATGAAATGAAATGAAATGAA 46 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.07 (3 / 41), avg. gap size = 1.33 (4 / 3) 41 24.23 3.01 2.24 chr3qtel1M 450119 450251 (549749) (AAGG)n#Simple_repeat 1 134 (0) m_b148s252i3 5532 chr3qtel1M 450119 AATGAAAGAAGGAA-GAAAAAACAAAGAAACAAAAGTAGCAAGACGAA-A 450166 v i - ii vi i vi i v v -- -i (AAGG)n#Simpl 1 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG--GAAGG 48 chr3qtel1M 450167 AAGGAAGGAAGAGAGGAAGGAAGGAAGGAAGGAACGAAAGGAAATAAGG- 450215 ii - i iv - (AAGG)n#Simpl 49 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA-GGAAGGAAGGAAGGA 97 chr3qtel1M 450216 TGAAATGAATGAAAAAAGAAATGAAGGAAGG-AGGAA 450251 v i v v ii i v - (AAGG)n#Simpl 98 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 134 Matrix = Unknown Transitions / transversions = 1.60 (16/10) Gap_init rate = 0.05 (7 / 132), avg. gap size = 1.00 (7 / 7) 488 20.24 3.25 7.63 chr3qtel1M 450301 450423 (549577) MIRc#SINE/MIR 10 127 (141) m_b148s601i4 5534 chr3qtel1M 450301 GTGGCACAGTGGGTAGACCTAACAACCTTGAAGTCAGGAGGACCTGAGTT 450350 ii iv v - viiiv i i i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGC-ACTGGACTTGGAGTCAGGAAGACCTGGGTT 58 chr3qtel1M 450351 CAAATCT-GTCTCAGACACTTAAGACTTCTAGCTGTGTGACTTTGGGCAA 450399 i i i- v v v ------ i MIRc#SINE/MIR 59 CGAGTCCCGGCTCTGCCACTTA------CTAGCTGTGTGACCTTGGGCAA 102 chr3qtel1M 450400 GTCATTTAACC---CTAATTACCTCAG 450423 i --- i --i MIRc#SINE/MIR 103 GTCACTTAACCTCTCTGA--GCCTCAG 127 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 23.03 CpG sites = 16, Kimura (unadjusted) = 24.21 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.09 (11 / 122), avg. gap size = 1.18 (13 / 11) 281 32.31 5.41 1.90 chr3qtel1M 450689 451095 (548905) C L1MC5a_3end#LINE/L1 (2300) 477 57 m_b148s551i0 5535 chr3qtel1M 450689 GTTCTTAGCCACCACAAAAGA-GCTGTTATAAATAATTTTGTGCAAATAG 450737 ii v i ii vi - iv i ii -- v C L1MC5a_3end#L 477 GTCTTTTGCTATTACAAATAATGCTGCAATGAATAACCTTGTGCA--TAC 430 chr3qtel1M 450738 ATTCTTTCCT-TTTTAACC----TCTATTGGATACAGA---CTAAATAAT 450779 i i? v - vi ?---- v v v iv i --- i - i C L1MC5a_3end#L 429 GTCNTTTCGTATTTTTGCNAGTGTATCTTCGGGATAGATTCCTAGA-AGT 381 chr3qtel1M 450780 GTTACTGTCAGATCAAAGGTGCAAGTTT-TATATTCTATTGATA-ATAGT 450827 vv i iii i - i i vi- i vv v v - v C L1MC5a_3end#L 380 GGGATTGCTGGGTCAAAGG-GTAAATGCATATGTAATTTTGCTAGATATT 332 chr3qtel1M 450828 TCCACATTGCTCTC-AGAATAGTTGGATGAGTTCACATCTCTACCACCAG 450876 v v v i - v ivi v iv v ii ii i v i C L1MC5a_3end#L 331 GCCAAATTCCCCTCCATAGGGGTTGTACCATTTTGCATTCCCACCAGCAA 282 chr3qtel1M 450877 TGTATTAATGT-CCTAGTTTTCCATACTCCCCCCTACAT-TTATGATTTT 450924 v iv - iv ii i vi i v v v-v - v C L1MC5a_3end#L 281 TGTATGAGAGTGCCTGTTTCCCCACAGCCTCGCCAACAGAGTATG-TTGT 233 chr3qtel1M 450925 CCTATTATTTTGTCACATTAGACAATCTGATCAGTATCGGGTGGTAATTC 450974 vv i -- v- iv v v vi ivviii vi C L1MC5a_3end#L 232 CAAACT--TTTGG-ATTTTTGCCAATCTGATAGGTGAGAAATGGTATCTC 186 chr3qtel1M 450975 AGAGATGTTTTAATTTGCATTTATCTAATCAGTAGTGA--TTTAGAA--- 451019 v vv v v i vv -- v v --- C L1MC5a_3end#L 185 AGTGTAGTTTTAATTTGCATTTCTCTTATTATGAGTGAGGTTGAGCATCT 136 chr3qtel1M 451020 -GTTATATGAGTACAGATAGTTTTGATTTGTTTATC--TGAACTGCCAGT 451066 -v i vv vi iivi vv v v -- i v C L1MC5a_3end#L 135 TTTCATATGTTTAAGGGCCATTTGCATTTCTTTTTCTGTGAACTGTCTGT 86 chr3qtel1M 451067 TCATATCCTTTGACCATTTGTCAACTGAG 451095 i v v v i i C L1MC5a_3end#L 85 TCATATCTTTTGCCCATTTTTCTATTGGG 57 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 42.61 CpG sites = 61, Kimura (unadjusted) = 43.05 Transitions / transversions = 0.90 (61/68) Gap_init rate = 0.05 (21 / 406), avg. gap size = 1.43 (30 / 21) 316 31.14 5.59 3.88 chr3qtel1M 450710 451013 (548987) C L1PB1_3end#LINE/L1 (443) 455 147 m_b148s551i1 5535 chr3qtel1M 450710 GCTGTTATAAATAATTTTGTGCAAATAGATTCTTTC---------CTTTT 450750 i i vviv i vv - --------- i C L1PB1_3end#LI 455 GCTGCTATAAACATGCGTGTGCAAGTATCTT-TTTCGTATAATGACTTCT 407 chr3qtel1M 450751 TAACCTCTATTGGATACAGACTAAATAATGTTACTGTCAGATCAAA-GGT 450799 vv --- i v v iv i i vv i iii - C L1PB1_3end#LI 406 TTTCCTCT---GGGTAGATACCCAGTAGTGGGATTGCTGGATCAAATGGT 360 chr3qtel1M 450800 G---CAAGTTTTATATTCTATTGATAATAGTTCCACATTGCTCTC-AGAA 450845 i--- v v -i - i vi - vi i i i - v i C L1PB1_3end#LI 359 AGTTCTACTTTTA-GTTCT-TTAAGGA-ATCTCCACACTGTTTTCCATAG 313 chr3qtel1M 450846 TAGTTGGATGAGTTCACATCTCTACCACCAGTGTATTAATGTCCTAGTTT 450895 i v iv i ii i v vv i i ivv C L1PB1_3end#LI 312 TGGTTGTACTAGTTTACATTCCCACCAGCAGTGTAGAAGTGTTCCCTTTT 263 chr3qtel1M 450896 T-CCATACTCCCCCCTACATTTATGATTTTCCTATTATTTTGTCACATTA 450944 i- ii ii v v v i v iiv - ---- C L1PB1_3end#LI 262 CACCGCATCCACGCCAACATCTATTATTTTTTGATT-TTTTG----ATTA 218 chr3qtel1M 450945 --GACAATCTGATCAGTATCGGGTGGTAATTCAGAGATGTTTTAATTTGC 450992 -- v v viivi vi vi viv vv vv i C L1PB1_3end#LI 217 TGGCCATTCTTGCAGGAGTAAGGTGGTATCGCATTGTGGTTTTGATTTGC 168 chr3qtel1M 450993 ATTTATCTAATCAGTAGTGAT 451013 vi i v C L1PB1_3end#LI 167 ATTTCCCTGATCATTAGTGAT 147 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.30 CpG sites = 48, Kimura (unadjusted) = 41.04 Transitions / transversions = 1.12 (48/43) Gap_init rate = 0.06 (18 / 303), avg. gap size = 1.61 (29 / 18) 450 30.41 4.71 2.30 chr3qtel1M 450756 451095 (548905) C L1ME3G_3end#LINE/L1 (524) 400 53 m_b148s551i2 5535 chr3qtel1M 450756 TCTATTGGATACAGACTAAATAATGTTACTGTCAGATCAAAGG---TGCA 450802 ? v v v? i? iv i vv i iii i --- i C L1ME3G_3end#L 400 TCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCG 351 chr3qtel1M 450803 AGTTTTATATTCTATTGATA-ATAGTTCCACATTGCTCTC-AGAATAGTT 450850 vi v i --- - v v v i - i ?i i C L1ME3G_3end#L 350 CATTTTAAATTTTA---ATAGATACTGCCAAATTGCCCTCCAAAANGGCT 304 chr3qtel1M 450851 GGATGAGTTCACATCTCTACCACCAGTGTATTAATGTCCTAGTTT-TCCA 450899 v iv i i iii i v v iv v iv -i C L1ME3G_3end#L 303 GTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCA 254 chr3qtel1M 450900 TACTCCCCCCTACATTTATGATTTTCCTATTATTTTGTCACA--TTAGAC 450947 i i i v v i --? v --- i v?i v i v -- v v C L1ME3G_3end#L 253 CACCCTCGCCAACACT--NGATAT---TATCAANCTTTTAAATTTTTGCC 209 chr3qtel1M 450948 AATCTGATCAGTATCGGGTGGTAATTCAGAGATGTTTTAATTTGCATTTA 450997 vi ivviii vi vv v v C L1ME3G_3end#L 208 AATCTGATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTC 159 chr3qtel1M 450998 TCTAATCAGTAGTGA--TTTAGAA----GTTATATGAGTACAGATAGTTT 451041 i i i v -- v v ----v i vv iv iivi C L1ME3G_3end#L 158 CCTGATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTT 109 chr3qtel1M 451042 TGATTTGTTTATC--TGAACTGCCAGTTCATATCCTTTGACCATTTGTCA 451089 vv vi iv -- i v v v v C L1ME3G_3end#L 108 GTATTTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCT 59 chr3qtel1M 451090 ACTGAG 451095 i i C L1ME3G_3end#L 58 ATTGGG 53 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.04 CpG sites = 51, Kimura (unadjusted) = 40.55 Transitions / transversions = 1.02 (51/50) Gap_init rate = 0.05 (16 / 339), avg. gap size = 1.50 (24 / 16) 452 30.52 4.85 2.18 chr3qtel1M 450829 451096 (548904) C L1ME5_3end#LINE/L1 (611) 330 56 m_b148s551i3 5535 chr3qtel1M 450829 CCACATTGCTCTC-AGAATAGTTGGATGAGTTCACATCTCTACCACCAGT 450877 v - i i v iv ii iii i v C L1ME5_3end#LI 330 CCAGATTGCTCTCCAGAATGGCTGCACCAGTCTACACTCCCACCAGCAGT 281 chr3qtel1M 450878 GTATTAATGT-CCTAGTTTTCCATACTCCCCCCTACATTTATGATTTTCC 450926 i v iv - v? ii i ii i v v i ivv v C L1ME5_3end#LI 280 GCATGAGGGTTCCTATNTCCCCACATCCTCGCCAACACTTGGCATTATCC 231 chr3qtel1M 450927 TATTATTTTGTCACATTAGACAATCTGATCAGTATCGGGTGGTAATTCAG 450976 - --ii v v iv v v i i vi i vii i vi v C L1ME5_3end#LI 230 -A--GCTTTCTAATTTTTGCCAGTCTAATAGGTGTAAAGTGATATCTCAT 184 chr3qtel1M 450977 AGATGTTTTAATTTGCATTTATCTAATCAGTAGTGATTTAGAAG------ 451020 v v v i i v i v v iv------ C L1ME5_3end#LI 183 TGTTGTTTTAATTTGCATTTCTCTGATTACTAATGAGTTTGAGCATCTCT 134 chr3qtel1M 451021 TTATATGAGTACAGATAGTTTT---GATTTGTTTATCTG--AACTGCCAG 451065 i vv --- v ii --- i vi iv -- i v C L1ME5_3end#LI 133 TCATATGCTT---GTTAGCCTTTCGGGTTTCCTCTTCTGTAAATTGCCTG 87 chr3qtel1M 451066 TTCATATCCTTTGACCATTTGTCAACTGAGG 451096 v v v i i C L1ME5_3end#LI 86 TTCATATCCTTTGCCCATTTTTCTATTGGGG 56 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.20 CpG sites = 43, Kimura (unadjusted) = 40.20 Transitions / transversions = 1.16 (43/37) Gap_init rate = 0.04 (11 / 267), avg. gap size = 1.73 (19 / 11) 184 27.50 0.00 0.00 chr3qtel1M 453440 453479 (546521) C L2d_3end#LINE/L2 (0) 516 477 m_b148s601i5 5536 chr3qtel1M 453440 TTAGTCAGTCAGCCAAAAAGGATTTATTAAGCACCTGTTA 453479 i i i ii v v i i ii C L2d_3end#LINE 516 TCAATCAATCAATCAACAAGTATTTATTGAGCGCCTACTA 477 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.98 CpG sites = 9, Kimura (unadjusted) = 37.29 Transitions / transversions = 4.50 (9/2) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 358 33.18 3.95 6.36 chr3qtel1M 453892 454068 (545932) C MIRc#SINE/MIR (75) 193 21 m_b148s601i6 5537 chr3qtel1M 453892 TCCTTCTAACAGCTCAGCAATATAGACAGGGCAATGACTGCCTCCCCCAC 453941 ivi i i v ii vi i ivv i iiivi i C MIRc#SINE/MIR 193 TCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCAT 144 chr3qtel1M 453942 CTTAGAGAAGAGTGTTAGAAGTGAAGACT--GCGA----AAGTGATTTTT 453985 i v v ----- iivi i -- v ---- -i v C MIRc#SINE/MIR 143 TTTACAGATGAG-----GAAACTGAGGCTCAGAGAGGTTAAGTGA-CTTG 100 chr3qtel1M 453986 TCCAAGACTATATAACCAAGAAATTTTCAGAGCTGACACTTATTGGAGCC 454035 i iii i i i i- v v vv i iv i---- i C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCT-AGTAAGTGGCAGAGCCGGGACTC----GAACC 55 chr3qtel1M 454036 CAGGCCTT-TTGAATCCAAGACCAGTATTCTTTC 454068 i -i v v ii C MIRc#SINE/MIR 54 CAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTC 21 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.13 CpG sites = 37, Kimura (unadjusted) = 46.51 Transitions / transversions = 2.06 (37/18) Gap_init rate = 0.08 (14 / 176), avg. gap size = 1.29 (18 / 14) 359 37.12 9.83 4.68 chr3qtel1M 454721 455127 (544873) C L2b_3end#LINE/L2 (16) 450 24 m_b148s601i7 5536 chr3qtel1M 454721 AATATTTATTAAGGAAGCTATTATGTGCCAGGCATTTTGCCAAGTGCTAG 454770 i i viv- i i ?i v i i i i C L2b_3end#LINE 450 AATATTTACTGAGCGC-CTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGG 402 chr3qtel1M 454771 GAATACAAAGA-----AAGGCAAAGATAGCTCCTGCCCTCAAACAGCATA 454815 i iv i----- i i v?ii ii viv vi C L2b_3end#LINE 401 GGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGGAGCTCA 352 chr3qtel1M 454816 AAATCTAATTGGGAAAAATGTGCAAACAACTTTGTA--TGAATAAGAATA 454863 v i i v i i ----- i ---- --iii i v? C L2b_3end#LINE 351 CAGTCTAGTGGGGGAGA-----CAGACA----TGTAANCAGACAATNATA 311 chr3qtel1M 454864 AGACTGTGTAATAAATTGGACACATTCAGAAGAC---GAGGAAGGCACTA 454910 vv v v iii iiv i i--- i vi ii i --- i i iv C L2b_3end#LINE 310 ACCCAGAGTGGCAGGGTAGG---ACTGGGGGGGCCCAGAGGAGGGCGCCT 264 chr3qtel1M 454911 GGATGAG---GAGGGCTTGGGAAAGGCTTCCTGTAAAAGGT-AGATTCT- 454955 ivivi --- i v ii i i i v ii - v iv- C L2b_3end#LINE 263 GACCCGGCCTGGGGGGTCAGGGAGGGCTTCCCGGAGGAGGTGACATTTGA 214 chr3qtel1M 454956 GTTAGGATTTTTTAAAG-----CCAGGA---AGTCAGACAGAATGGGCAG 454997 i ii ---ii i -----vi ---i i i - vi ii C L2b_3end#LINE 213 GCTGAGA---CCTGAAGGATGAGTAGGAGTTGGCCAGGC-GAAGAGGTGG 168 chr3qtel1M 454998 TGGAGAATTTTCCAACCATGGGGAA-AGTCAGAACAGATGCTCCAAGCCA 455046 v i iiiv iv vi - iv? vi i v i ii v i C L2b_3end#LINE 167 GGAAGGGCGTTCCAGGCAGAGGGAACAGCANGTGCAAAGGCCCTGAGGCG 118 chr3qtel1M 455047 AGACATGGAG---GCTGTGTT-------CATCA--GAGGCTGAT---ACT 455081 i -- v? --- vi ------- v -- iii ---i C L2b_3end#LINE 117 GG--AGNGAGCNTGGCGTGTTCGAGGAACAGCAAGGAGGCCAGTGTGGCT 70 chr3qtel1M 455082 GGGTCAAGAATGAGGGAAAGCAAAATGA-GGGAAAGCAGGCAAAAGA 455127 iv - i vi ii v i i i-i i vv vii C L2b_3end#LINE 69 GGAGC-AGAGTGAGCAAGGGGAGAGTGGTAGGAGATGAGGCCGGAGA 24 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 50.84 CpG sites = 101, Kimura (unadjusted) = 57.65 Transitions / transversions = 2.35 (101/43) Gap_init rate = 0.08 (34 / 406), avg. gap size = 1.76 (60 / 34) 378 34.10 10.03 4.62 chr3qtel1M 454721 455049 (544951) C L2c_3end#LINE/L2 (16) 462 117 m_b148s601i8 5536 chr3qtel1M 454721 AATATTTATTAAGGAAGCTATTATGTGCCAGGCATTTTGCCAAGTGCTAG 454770 i i viv- i ------------ i C L2c_3end#LINE 462 AACATTTATTGAGCGC-CTACTATGTGCCAGGC------------GCTGG 426 chr3qtel1M 454771 GAATACAAAGAAAGGCAA-AGATAGCTCCTGCCCTCAAACAGCATAAAAT 454819 i viiii - v ii ii iv vi v i C L2c_3end#LINE 425 GGATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGT 376 chr3qtel1M 454820 CTAATTGGGAAAA-----ATGT--GCAAACAACT-TTGTATGAA-TAAGA 454860 i v i i i ----- ? --i i i -ivi ii i- vi C L2c_3end#LINE 375 CTAGTGGAGGAGACAGACANGTAAACAGACAATTACAATACAAGTTAATG 326 chr3qtel1M 454861 ATAAG-ACTGT-------GTAATAAATTGGACACATTCAGAAGAC-GAGG 454901 -i i ------- - i iv iii vv vi iv - C L2c_3end#LINE 325 ATAAGTGCTATAATGGGAGT-ATAGACAGGGTGCTATGGGAGCACAGAGG 277 chr3qtel1M 454902 AAGGCACTAGGATGAG----GAGGGCTTGGGAAAGGCTTCCTGTAAAAGG 454947 i ivi iv ---- i v ii i i v ii C L2c_3end#LINE 276 AGGGCACCTAGACTAGNCTTGGGGGGTCAGGGAAGGCTTCCCGGAGGAGG 227 chr3qtel1M 454948 TAGATTCTGTTAG--GATTTTTTAAAG----CCAGGA---AGTCAGACAG 454988 iivv -- -- v?i v i ----vi --- i iii C L2c_3end#LINE 226 TGACATCTG--AGCTGAGNCTTGAAGGATGAGTAGGAGTTAGCCAGGTGG 179 chr3qtel1M 454989 AATGGGCAGTGGAGAATTTTCCAACCATGGGGAA-AGTCAGAACAGATGC 455037 v i vi v i iiv iv vi - ivv vi i v C L2c_3end#LINE 178 AAGGAGGGGGGAAGAGCATTCCAGGCAGAGGGAACAGCATGTGCAAAGGC 129 chr3qtel1M 455038 TCCAAGCCAAGA 455049 ? vi v i C L2c_3end#LINE 128 NCGGAGGCAGGA 117 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 47.22 CpG sites = 71, Kimura (unadjusted) = 49.30 Transitions / transversions = 1.97 (71/36) Gap_init rate = 0.09 (29 / 328), avg. gap size = 1.69 (49 / 29) 438 26.12 3.57 0.87 chr3qtel1M 454721 454832 (545168) C L2d2_3end#LINE/L2 (16) 539 425 m_b148s601i9 5536 chr3qtel1M 454721 AATATTTATTAAGGAAGCTATTATGTGCCAGGCATTTTGCCAAGTGCTA- 454769 i viv- i i v i v i i i i- C L2d2_3end#LIN 539 AATATTTATTGAGCGC-CTACTGTGTGCAAGGCACTGTGCTAGGCGCTGT 491 chr3qtel1M 454770 --GGAATACAAAGAAAGGCAA-AGATAGCTCCTGCCCTCAAACAGCATAA 454816 -- i ivii - v i ii iv v v C L2d2_3end#LIN 490 GGGGGATACAAAGAAGTATAAGACATGGTCCCTGCCCTCAAGGAGCTTAC 441 chr3qtel1M 454817 AATCTAATTGGGAAAA 454832 i i i C L2d2_3end#LIN 440 AATCTAGTTGGGGAGA 425 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.72 CpG sites = 20, Kimura (unadjusted) = 33.54 Transitions / transversions = 2.22 (20/9) Gap_init rate = 0.04 (4 / 111), avg. gap size = 1.25 (5 / 4) 25 25.08 1.01 5.26 chr3qtel1M 455644 455742 (544258) (TCTTCTT)n#Simple_repeat 1 95 (0) m_b148s252i5 5538 chr3qtel1M 455644 TCTCTCTTTCCTTTTTTATGGTTTTGTTCATCCCT-TATCTTTCTTCTTC 455692 - - i v -vi v v i i - v ii (TCTTCTT)n#Si 1 TCT-TCTTT-CTTCTTTCT-TCTTTCTTCTTTCTTCTTTCTTCTTTCTTC 47 chr3qtel1M 455693 TATCTTCCTTCTTCTCTTCATCTAATTTTTTTCTTCCTTCTTCATTTCTT 455742 v i - v vvi i i - (TCTTCTT)n#Si 48 TTTCTTCTTTCTTCT-TTCTTCTTTCTTCTTTCTTCTTTCTTC-TTTCTT 95 Matrix = Unknown Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.06 (6 / 98), avg. gap size = 1.00 (6 / 6) 14 20.39 4.35 5.88 chr3qtel1M 455681 455749 (544251) (TCTTATT)n#Simple_repeat 1 68 (0) m_b148s252i6 5538 chr3qtel1M 455681 TCTTTCTTCTTCTATCTTCCTTCTTCTCTTCATCTAATT-TT-TTTCTTC 455728 vi v v vi v - - - v - - v (TCTTATT)n#Si 1 TCTTATTTCTTATTTCTTATTTCTTAT-TTC-T-TATTTCTTATTTCTTA 47 chr3qtel1M 455729 CTTCTTCATTTCTTAGTT-TTA 455749 i - v - (TCTTATT)n#Si 48 TTTCTT-ATTTCTTATTTCTTA 68 Matrix = Unknown Transitions / transversions = 0.38 (3/8) Gap_init rate = 0.10 (7 / 68), avg. gap size = 1.00 (7 / 7) 24 10.03 5.08 5.08 chr3qtel1M 455684 455742 (544258) (TTC)n#Simple_repeat 1 59 (0) m_b148s252i7 5539 chr3qtel1M 455684 TTCTTCTTCTATCTTCCTTCTTC-TCTTCATCTAATT-TTTTTCTTCCTT 455731 - - - v vv - i - (TTC)n#Simple 1 TTCTTCTTCT-TCTT-CTTCTTCTTCTTCTTCTTCTTCTTCTTCTT-CTT 47 chr3qtel1M 455732 CTTCAT-TTCTT 455742 v - (TTC)n#Simple 48 CTTCTTCTTCTT 59 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.10 (6 / 58), avg. gap size = 1.00 (6 / 6) 25 25.08 1.01 5.26 chr3qtel1M 455644 455742 (544258) (TCTTCTT)n#Simple_repeat 1 95 (0) m_b148s252i5 5538 chr3qtel1M 455644 TCTCTCTTTCCTTTTTTATGGTTTTGTTCATCCCT-TATCTTTCTTCTTC 455692 - - i v -vi v v i i - v ii (TCTTCTT)n#Si 1 TCT-TCTTT-CTTCTTTCT-TCTTTCTTCTTTCTTCTTTCTTCTTTCTTC 47 chr3qtel1M 455693 TATCTTCCTTCTTCTCTTCATCTAATTTTTTTCTTCCTTCTTCATTTCTT 455742 v i - v vvi i i - (TCTTCTT)n#Si 48 TTTCTTCTTTCTTCT-TTCTTCTTTCTTCTTTCTTCTTTCTTC-TTTCTT 95 Matrix = Unknown Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.06 (6 / 98), avg. gap size = 1.00 (6 / 6) 14 20.39 4.35 5.88 chr3qtel1M 455681 455749 (544251) (TCTTATT)n#Simple_repeat 1 68 (0) m_b148s252i6 5538 chr3qtel1M 455681 TCTTTCTTCTTCTATCTTCCTTCTTCTCTTCATCTAATT-TT-TTTCTTC 455728 vi v v vi v - - - v - - v (TCTTATT)n#Si 1 TCTTATTTCTTATTTCTTATTTCTTAT-TTC-T-TATTTCTTATTTCTTA 47 chr3qtel1M 455729 CTTCTTCATTTCTTAGTT-TTA 455749 i - v - (TCTTATT)n#Si 48 TTTCTT-ATTTCTTATTTCTTA 68 Matrix = Unknown Transitions / transversions = 0.38 (3/8) Gap_init rate = 0.10 (7 / 68), avg. gap size = 1.00 (7 / 7) 12 15.22 0.00 10.00 chr3qtel1M 456505 456548 (543452) (CCTTCTA)n#Simple_repeat 1 40 (0) m_b148s252i8 5540 chr3qtel1M 456505 CCTTCTTCCTACTCTACCTTCAAATTGTCTACCTTCTCTCCTTC 456548 v -- v vi - -v (CCTTCTA)n#Si 1 CCTTCTACCT--TCTACCTTCTACCT-TCTACCTTCT-ACCTTC 40 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.09 (4 / 43), avg. gap size = 1.00 (4 / 4) 308 29.67 14.29 1.27 chr3qtel1M 459936 460075 (539925) C MamRTE1#LINE/RTE-BovB (2777) 1035 878 m_b148s601i10 5541 chr3qtel1M 459936 TGCCTACTCTTGTATTAAAGTCATCCAGAATAATAAGC-------ACATT 459978 v v v ii i i vi ivi ii v ------- ii C MamRTE1#LINE/ 1035 TGCCGACACGTGCGTTGAAATCTCCCGTGACGATCAGCTTGTCAGATGTT 986 chr3qtel1M 459979 GAT--------GATGATATCT---CAGGTCTTTATATAAGTTTTTCTTTG 460017 i -------- -i --- i i i v - i v C MamRTE1#LINE/ 985 GGTACCGCTGCGATGA-GTCTGTCCAGATCCTTGTAGAA-TCTTTCTTTC 938 chr3qtel1M 460018 ACCTC-TCAAGGTTTGTCATGGTGAGATAATATACACTGATGAGGGTGGT 460066 v - iivi i i ivv i i v i C MamRTE1#LINE/ 937 TCCTCATCGGTATTCGTCATGGTGGGGGCATATGCGCTGATGACGGTGGC 888 chr3qtel1M 460067 -TGGTGCTTT 460075 -?i i C MamRTE1#LINE/ 887 ANAGCGCTTT 878 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.54 CpG sites = 28, Kimura (unadjusted) = 40.28 Transitions / transversions = 2.15 (28/13) Gap_init rate = 0.05 (7 / 139), avg. gap size = 3.14 (22 / 7) 499 21.23 0.72 8.53 chr3qtel1M 461658 461796 (538204) MIRb#SINE/MIR 2 130 (138) m_b148s601i11 5542 chr3qtel1M 461658 AGAGGGGCAGCTAGGTGGCACAGTGGATAGAGCACCAGTCCTGGAGTCAG 461707 --- ii v vi iii MIRb#SINE/MIR 2 AGAGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAG 48 chr3qtel1M 461708 GAGGCACCTCAGTTCAAATCTGGTCTCAGACAGTTAACACTTCCCAGCTC 461757 ivi - vi i iv v ------- iv v i v MIRb#SINE/MIR 49 ACAG-ACCTGGGTTCGAATCCCGGCTC-------TGCCACTTACTAGCTG 90 chr3qtel1M 461758 TGTGACCCTGGGCAAGTCACTTAACCTCAATT-GCCTCAG 461796 i i vv v- MIRb#SINE/MIR 91 TGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAG 130 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.04 CpG sites = 15, Kimura (unadjusted) = 25.08 Transitions / transversions = 1.25 (15/12) Gap_init rate = 0.09 (12 / 138), avg. gap size = 1.00 (12 / 12) 14 8.46 0.00 3.85 chr3qtel1M 463061 463087 (536913) (GGAA)n#Simple_repeat 1 26 (0) m_b148s252i9 5543 chr3qtel1M 463061 GGAAGGGGTGGAAGGAAGGAAGGAAGG 463087 - iv (GGAA)n#Simpl 1 GGAA-GGAAGGAAGGAAGGAAGGAAGG 26 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 26), avg. gap size = 1.00 (1 / 1) 15 21.18 0.00 0.00 chr3qtel1M 464595 464632 (535368) (CCCCCA)n#Simple_repeat 1 38 (0) m_b148s252i10 5544 chr3qtel1M 464595 CCCCCAACCACAGTCTCACCCCCACCTCCAACCCCACC 464632 v v vi i i v (CCCCCA)n#Sim 1 CCCCCACCCCCACCCCCACCCCCACCCCCACCCCCACC 38 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 544 27.39 2.52 5.84 chr3qtel1M 467405 467722 (532278) HERVK14C#LTR/ERVK 2847 3154 (4280) m_b148s701i0 5545 chr3qtel1M 467405 TTTAGGCAGGGCTGCTGTTGAAGGCCTGCCAACACTTTCACCTGTTCCTA 467454 viv ii -- v vi ?------- i iv HERVK14C#LTR/ 2847 TTTAGGGGCGGCCACTGTTGA--GCCTCCAGAN-------CCTATTCCCT 2887 chr3qtel1M 467455 TCTAATGGAAAACTGATACACCAGTGTGAATAGAACAGTGGCCCTTAGGT 467504 vv ?i iv v v? ? v ii ? ? vi ??v HERVK14C#LTR/ 2888 TAAAATGGANGACCCAAAANCCNGTTTGGGTNGANCAGTGGCCGCTNNCT 2937 chr3qtel1M 467505 GAGAGATAAAATTCAGGCCTCGTTAGATATAATTCAGGAGCAACTTGATC 467554 v - v v vvi iiivi vv i iv i i i v ?v HERVK14C#LTR/ 2938 CAG-GAAAAACTGGGGGCCTTACAGGAATTAGTCAAAGAACAATTAGANA 2986 chr3qtel1M 467555 AAGGACACTTACAACC----TTCTCTAAGCCCTTGGAATTACCCAATATT 467600 v ?v i ---- i ---- ? v? i i HERVK14C#LTR/ 2987 AAGGACACATNGAGCCCACATTTTCT----CCNTGGAATTCNCCAGTGTT 3032 chr3qtel1M 467601 TGTTGTAAGAAAGAAATCTGGGAAATGGAGGATGTTGACTGATTTAAGAA 467650 vi ? ii i i v i v ? i i i i v i HERVK14C#LTR/ 3033 TGTAATNAAGAAAAAATCCGGCAGATGGCGNATGCTAACCGACTTACGAG 3082 chr3qtel1M 467651 AGGTAAATGAACAG--ATGGAAACTATGAGAACTCTTCAGCCTGGACTTA 467698 vv v -- -- ?v v ? i ii ? v v i vv HERVK14C#LTR/ 3083 CCGTCAATG--CAGTCATNCAACCNATGGGGGCNCTGCAGCCAGGGCTGC 3130 chr3qtel1M 467699 CATCCCCTAGTCA--ATTGCCTAGAG 467722 ? i- i -- - HERVK14C#LTR/ 3131 CNTCCCCC-GCCATGATT-CCTAGAG 3154 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.63 CpG sites = 42, Kimura (unadjusted) = 37.31 Transitions / transversions = 1.05 (42/40) Gap_init rate = 0.07 (21 / 317), avg. gap size = 1.24 (26 / 21) 299 30.90 2.20 2.20 chr3qtel1M 467918 468099 (531901) HERVKC4#LTR/ERVK 996 1177 (4085) m_b148s701i1 5546 chr3qtel1M 467918 TAGAGAATGGCCTTTTTGGTT--TATAGACATTAAGGATTGTTTCTATTC 467965 i v vi -- -- iv v i i i i v v HERVKC4#LTR/E 996 TAAAGACTGGCCGCTT--GTTATTATAGATTTAAAAGACTGCTTTTTTAC 1043 chr3qtel1M 467966 TATCCCTCTAGATAAGGAAGAATTGAAAAGATTTGCCTTTTCACTGCCCA 468015 v i i vvi v v vi i v vv v ii HERVKC4#LTR/E 1044 AATTCCTTTAGCAGAGGCAGATTTCGAAAAATTTGCCTTTACCATCCCTG 1093 chr3qtel1M 468016 GCGTTAACTTAGCTGAG-CCTTATAA-AAGATATGAATGGACAGTTTTGC 468063 v -- i vi -v i ii i-v v v vi i HERVKC4#LTR/E 1094 CCGTTAA--TAACAAAGAACCTGCAGCCAGATATCATTGGAAGGTTTTAC 1141 chr3qtel1M 468064 CACAGGGAATGAAAAACAGCCCTACTATGTGTCAAA 468099 v i v vv i i vi v HERVKC4#LTR/E 1142 CCCGGGGTATGTTAAACAGTCCCACAGTTTGTCAAA 1177 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.39 CpG sites = 26, Kimura (unadjusted) = 40.21 Transitions / transversions = 0.90 (26/29) Gap_init rate = 0.04 (7 / 181), avg. gap size = 1.14 (8 / 7) 485 30.52 5.19 5.19 chr3qtel1M 467940 468440 (531560) HERVK14#LTR/ERVK 2925 3425 (2671) m_b148s701i2 5546 chr3qtel1M 467940 ATAGACATTAAGGATTGTTTCTATTCTATCCCTCTAGATAAGGAAGAAT- 467988 iv v i i v v i i i v ivvv v - HERVK14#LTR/E 2925 ATAGATCTAAAGGATTGCTTTTTTACCATTCCTTTAGCTGCCCAAGATTA 2974 chr3qtel1M 467989 TGAAAAGATTTGCCTTTTCACTGC-CCAGCGTTAACT--TAGCTGAGCCT 468035 - i -- i- v vv v -- iv- i v HERVK14#LTR/E 2975 TGAAAA-ATTTGCTTTT--ACTGTTCCCGCCATAAATAATAAA-GAACCA 3020 chr3qtel1M 468036 TATAAAAGATATGAATGGACAGTTTTGCCACAGGGAATGAAAAACAGCCC 468085 vvvi v iv v v vi i i v vv i HERVK14#LTR/E 3021 GCGGACAGATACCATTGGAAAGTACTACCACAAGGCATGCTAAATAGCCC 3070 chr3qtel1M 468086 TACTATGTGTCAAATGTATATTGCTGCTGCTCTTGCTCCGATAAGAAAAG 468135 v v iv i i vvivv v ivv ii v i v HERVK14#LTR/E 3071 GACTATTTGTCAAACTTATGTCGGGAAAGCTATTAAGCCAGTTAGAGAAC 3120 chr3qtel1M 468136 CATTTCCCAAA-GTAATGTTATTACATTACATGGATGATATATTGGGATG 468184 vi vvv - v i i- vi --- HERVK14#LTR/E 3121 AGTTTAAAAAATGTTATATTATC-CATTACATGGATGATATTCTG---TG 3166 chr3qtel1M 468185 TGCACCTG----------AGGATCAA----ATGTTAGAAGCATGTCTACA 468220 v ---------- i ii ----i i v i - - v HERVK14#LTR/E 3167 TGCAGCTGAAACTAGGGAAGAATTGATGTTGTGCTACAAACA-GT-TAGA 3214 chr3qtel1M 468221 AAAAACCATAGAAACACTAAGGAACTACAAATTACACATAGCTCCAGAAA 468270 ii ii i vi ivi i --------- vvi i v v HERVK14#LTR/E 3215 AAAGGCTGTAAATGCGGCAGGG---------TTAATTATAGCCCCCGATA 3255 chr3qtel1M 468271 AAATTCAAAGACATGCTCCTTTTTAATATTTAGGATATGAA-GTATACCC 468319 i vviv i i i i - - v v - HERVK14#LTR/E 3256 AAATCCAAACTTCTACTCCCTTTCAATATCTAGGA-ATGAAGGTAGAAC- 3303 chr3qtel1M 468320 TAAGATGC--TTACAATTCAAAAACTGTCCTTAA----GAACAGAGAAGC 468363 - ii -- vivi iv ---- i ---- v v vi HERVK14#LTR/E 3304 -AAAGTGCTATTAAGCCTCAAAAGGT----TCAAATTCGAAGAGATAATT 3348 chr3qtel1M 468364 TAAACACATTGAATGATTTTCAGAAATTGATAGGAAATATCCAATAGATG 468413 v v i i i iv i i iv v i v HERVK14#LTR/E 3349 TAAAAACCTTAAATGATTTCCAAAAATTATTAGGAGACATTAATTGGATT 3398 chr3qtel1M 468414 CATCCAGTGTTAGGCTTGACTATCTAT 468440 i iiv v vv i HERVK14#LTR/E 3399 CGTCCAACTTTAGGCATTCCTACCTAT 3425 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.63 CpG sites = 71, Kimura (unadjusted) = 39.66 Transitions / transversions = 0.96 (71/74) Gap_init rate = 0.07 (35 / 500), avg. gap size = 1.49 (52 / 35) 254 31.38 6.06 6.06 chr3qtel1M 469501 469863 (530137) HERVK#LTR/ERVK 4837 5199 (2337) m_b148s701i3 5546 chr3qtel1M 469501 GGTTTGAGATCCAATGAAATTTGACAAATGGATGTGACCCATTATAAAT- 469549 i v vi i viv v i v v -i vv - HERVK#LTR/ERV 4837 GGTCTGTGTCCTAATGCGTTATGGCAAATGGATGTCACGCAT-GTACCTT 4885 chr3qtel1M 469550 CTTTTGGTCGCCTGTCTTTTATCCATGTTGTGGTAGACACCCTTTCAGGA 469599 v vv vi v ? i viii v i iiv viv HERVK#LTR/ERV 4886 CATTTGGAAGATTGTCATNTGTCCATGTAACAGTTGATACTTATTCACAT 4935 chr3qtel1M 469600 TTCACTTATGG--AA--TACCAG-CAGCAAAAGAAACAGCCCAAGT---- 469640 -- -- -- i - v i iiv vv v ---- HERVK#LTR/ERV 4936 TTCA--TATGGGCAACCTGCCAGACAGGAGAAAGTACTTCCCATGTTAAA 4983 chr3qtel1M 469641 GGTCACTTAATTCCTTATACAAGCATTTGCAATTATGGGTGTGCCACAAG 469690 iiv i v vi i ------- vi i v v v i HERVK#LTR/ERV 4984 AAACATTTATTATCTTGT-------TTTGCTGTCATGGGAGTTCCAGAAA 5026 chr3qtel1M 469691 CAATAAAAATAGATAATGGACCTGCATA---TACTTCAAAACATTTTGCA 469737 v v iv i i v v --- v -- i ? iiiv HERVK#LTR/ERV 5027 AAATTAAAACTGACAATGGGCCAGGATACTGTAGT--AAAGCNTTCCAAA 5074 chr3qtel1M 469738 CACTTTTGTGCACAGTATAGGCTTTTACACACCACTGGCATACCTTTCAA 469787 v i i ivii- iv iiv vi i v v v v vi HERVK#LTR/ERV 5075 AATTCTTAAAT-CAGTGGAAAATTACACATACAACAGGAATTCCTTATAA 5123 chr3qtel1M 469788 TCCTCAAGGACAGGCAATAGTAGAGAGGAGAAACTGAGGCATTAAGATGC 469837 i i v v i ---- i ----- ii ii HERVK#LTR/ERV 5124 TTCCCAAGGACAGGCCATAGTTGAAAG----AACTAA-----TAGAACAC 5164 chr3qtel1M 469838 TC---GTCCAA------AAACAAAAGAAAGGGGGA 469863 --- ii ------ ii HERVK#LTR/ERV 5165 TCAAAGCTCAATTGGTTAAACAAAAAGAAGGGGGA 5199 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.29 CpG sites = 57, Kimura (unadjusted) = 41.80 Transitions / transversions = 1.14 (57/50) Gap_init rate = 0.08 (30 / 362), avg. gap size = 1.47 (44 / 30) 475 31.56 2.76 2.76 chr3qtel1M 469522 469811 (530189) HERVK11#LTR/ERVK 4990 5279 (2674) m_b148s701i4 5546 chr3qtel1M 469522 TGACAAATGGATGTGACCCATTATAAATCTTTTGGTCGCCTGTCTTTTAT 469571 i i vv iv i iv v ? v v i HERVK11#LTR/E 4990 TGGCAAATGGATGTGACTCATGTTAGCTCCTTTGGCAGACTNTCATATGT 5039 chr3qtel1M 469572 CCATGTTGTGGTAGACACCCTTTCAGGATTCACTTATGGAATACC----- 469616 v viv i i i v i -- v iv i----- HERVK11#LTR/E 5040 GCATGTTTCTGTAGATACCTTCTCAGGTTTTA--TCTGGGCTACTTGCCA 5087 chr3qtel1M 469617 AGCAGCAAAAGAAACAGCCCAAGTGGTCACTTAATTCCTTATACAAGCAT 469666 i vii iv i -- v v vvv vv iv v vv - HERVK11#LTR/E 5088 AACAGGGGAAGGCACGGCCCA--TGTTAAAAAACATCTGTATTCTTGC-T 5134 chr3qtel1M 469667 TTGCAATTATGGGTGTGCCACAAGCAATAAAAATAGATAATGGACCTGCA 469716 i vv v i vvv i i i i vv v HERVK11#LTR/E 5135 TTGCAGTTATGGGGCTTCCATATCAAATAAAGACAGACAACGCCCCTGGA 5184 chr3qtel1M 469717 TATACTTCAAAACATTTTGCACACT--TTTGTGC-ACAGTATAGGCTTTT 469763 ii vvv ivv --- i -- i - ivi iv i HERVK11#LTR/E 5185 TATGTTAGTAAGGCTTTTG---ATTTATTTATGCAACAGTGGGGAATTTC 5231 chr3qtel1M 469764 ACACACCACTGGCATACCTTTCAATCCTCAAGGACAGGCAATAGTAGA 469811 v i ii i v v v i vi i i HERVK11#LTR/E 5232 CCATATTACCGGAATCCCTTACAATCCTCAGGGACAGGCTGTGGTGGA 5279 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.80 CpG sites = 42, Kimura (unadjusted) = 41.57 Transitions / transversions = 0.89 (42/47) Gap_init rate = 0.04 (11 / 289), avg. gap size = 1.45 (16 / 11) 584 28.43 3.06 2.12 chr3qtel1M 472165 472491 (527509) C HERVK14C#LTR/ERVK (4226) 3208 2879 m_b148s701i5 5547 chr3qtel1M 472165 CCAGAGGGATAGAATAGAAACAATCCTTAATATGTATAACCCACAGAGGT 472214 i i v v i i v v v ivvi i? i C HERVK14C#LTR/ 3208 CTAGAGGAATAGTAAAGAAGCAGTCCTTCAAATCTATAACTATTAANGGC 3159 chr3qtel1M 472215 CATTCCCTGGGCAACTGAGTAGGGGATGGAAGCCCAGGCTAAAGAGTTCC 472264 v i i v v vvi ii ? v v iv ? ii C HERVK14C#LTR/ 3158 CAGTCTCTAGGAATCATGGCGGGGGANGGCAGCCCTGGCTGCAGNGCCCC 3109 chr3qtel1M 472265 CATAGTTTCCAT--CTGTTCATTCACTTTTCTAAAATCAGTCAACATCCC 472312 ? v v? -- -- v vvi vv i i i i ? v C HERVK14C#LTR/ 3108 CATNGGTTGNATGACTG--CATTGACGGCTCGTAAGTCGGTTAGCATNCG 3061 chr3qtel1M 472313 TCTATTTTCCAGATTTCTTTTATAGAGCAAAATACAGAGGGATTCAAGGA 472362 i - i v i i i v? vvi -i v i? i v ? i C HERVK14C#LTR/ 3060 CC-ATCTGCCGGATTTTTTCTTNATTACAAA-CACTGGNGAATTCCANGG 3013 chr3qtel1M 472363 CTTAGAGAA----GGTTGAAAGCGTCCTTGGTCAAGTTGCTCCTGTACTA 472408 --- i ---- i v? v i v? v i i i vv C HERVK14C#LTR/ 3012 ---AGAAAATGTGGGCTCNATGTGTCCTTTNTCTAATTGTTCTTTGACTA 2966 chr3qtel1M 472409 TATCTAATAAGGCCTG-AATTTTTCCTGGGTAAG-GGCCACTGTTCCACC 472456 vv ivi iv- i i ?? - ? ? C HERVK14C#LTR/ 2965 ATTCCTGTAAGGCCCCCAGTTTTTCCTGAGNNAGCGGCCACTGNTCNACC 2916 chr3qtel1M 472457 C--ACTGGTGTATCAATTTTCAATTGGATGGGAATAG 472491 -- ? ?v v vii i? v vv v C HERVK14C#LTR/ 2915 CAAACNGGNTTTTGGGTCNTCCATTTTAAGGGAATAG 2879 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.35 CpG sites = 45, Kimura (unadjusted) = 39.00 Transitions / transversions = 0.98 (45/46) Gap_init rate = 0.04 (12 / 326), avg. gap size = 1.42 (17 / 12) 483 18.18 8.08 0.00 chr3qtel1M 473869 473967 (526033) C U6#snRNA (0) 107 1 c_b148s401i0 5548 chr3qtel1M 473869 AAAAATATGAAGCACTTCATGAATTT---TGTCATCCTTCTGCAGGGACC 473915 i i i i --- vi i C U6#snRNA 107 AAAAATATGGAACGCTTCACGAATTTGCGTGTCATCCTTGCGCAGGGGCC 58 chr3qtel1M 473916 ATGCTGATCTT-----TATCATTCCAATTTTAATAGATGAGCTATCCATG 473960 i ----- i i v v ii v v C U6#snRNA 57 ATGCTAATCTTCTCTGTATCGTTCCAATTTTAGTATATGTGCTGCCGAAG 8 chr3qtel1M 473961 TGAGTAC 473967 i i C U6#snRNA 7 CGAGCAC 1 Matrix = 18p39g.matrix Kimura (with divCpGMod) = 15.23 CpG sites = 13, Kimura (unadjusted) = 21.44 Transitions / transversions = 2.60 (13/5) Gap_init rate = 0.02 (2 / 98), avg. gap size = 4.00 (8 / 2) 23 0.00 0.00 0.00 chr3qtel1M 474110 474134 (525866) (A)n#Simple_repeat 1 25 (0) m_b148s252i11 5549 chr3qtel1M 474110 AAAAAAAAAAAAAAAAAAAAAAAAA 474134 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAA 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 53 3.85 0.00 0.00 chr3qtel1M 475687 475740 (524260) (GT)n#Simple_repeat 1 54 (0) c_b148s251i0 5550 chr3qtel1M 475687 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGTATGTGTGTGTGTGT 475736 i i (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50 chr3qtel1M 475737 GTGT 475740 (GT)n#Simple_ 51 GTGT 54 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 15 18.25 3.64 5.56 chr3qtel1M 476224 476278 (523722) (AAT)n#Simple_repeat 1 54 (0) m_b148s252i12 5551 chr3qtel1M 476224 AATAATAATGAAGATCAATAAT-CTAATAATAAGTAATAGATCAAAGTTA 476272 - v vi -v - - v v i v (AAT)n#Simple 1 AATAATAAT-AATAATAATAATAATAATAATAA-TAATA-ATAATAATAA 47 chr3qtel1M 476273 TAA-AAT 476278 - (AAT)n#Simple 48 TAATAAT 54 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.09 (5 / 54), avg. gap size = 1.00 (5 / 5) 14 12.53 0.00 0.00 chr3qtel1M 476320 476345 (523655) (AAC)n#Simple_repeat 1 26 (0) m_b148s252i13 5552 chr3qtel1M 476320 AACAACAACAACAACAATAAGAAGAA 476345 i v v (AAC)n#Simple 1 AACAACAACAACAACAACAACAACAA 26 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 21 20.31 3.92 0.00 chr3qtel1M 476350 476400 (523600) (AT)n#Simple_repeat 1 53 (0) m_b148s252i14 5553 chr3qtel1M 476350 ATATGTGTTTGTCTATCCATATATA-ATGTATATATCTATATAT-TATAT 476397 i i v i v vi - i v - (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr3qtel1M 476398 ATA 476400 (AT)n#Simple_ 51 ATA 53 Matrix = Unknown Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.04 (2 / 50), avg. gap size = 1.00 (2 / 2) 328 31.45 4.14 1.34 chr3qtel1M 476401 476545 (523455) C MIR#SINE/MIR (41) 221 73 m_b148s601i12 5554 chr3qtel1M 476401 CATTTTTGTATAATATTTTATACTTATCTTCCCATTATATTTTCACAGC- 476449 i v v - iiii i iv ivv i vv ii i - C MIR#SINE/MIR 221 CACTGTTCTA-AGCGCTTTACATGTATTAACTCATTTAATCCTCACAACA 173 chr3qtel1M 476450 ---TTGGGAA-TCGGTATGATTATAAGCCTTACTTTACAGATGATGAAAT 476495 ---i iv i- v iv v v ii i v i C MIR#SINE/MIR 172 ACCCTATGAGGTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAAC 123 chr3qtel1M 476496 TCAGGGAAACAGAAGTTATGTGGATT-CCCAATGATCCCACACCTAGTAA 476544 v v v v i v iiv - - i v v C MIR#SINE/MIR 122 TGAGGCACAGAGAGGTTAAGTAACTTGCCCAA-GGTCACACAGCTAGTAA 74 chr3qtel1M 476545 G 476545 C MIR#SINE/MIR 73 G 73 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.30 CpG sites = 24, Kimura (unadjusted) = 41.63 Transitions / transversions = 1.14 (24/21) Gap_init rate = 0.04 (6 / 144), avg. gap size = 1.33 (8 / 6) 259 29.83 0.00 4.76 chr3qtel1M 476580 476667 (523333) MIRc#SINE/MIR 37 120 (148) m_b148s601i13 5555 chr3qtel1M 476580 TGAAAGCAAGAAGGACCTCAGTTCCGATCCAGGCTCAGACACTTACAAGC 476629 i iv i - vi vii v v v v MIRc#SINE/MIR 37 TGGAGTCAGGAAG-ACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGC 85 chr3qtel1M 476630 TATGTATACTTAGACAAAATGACTTCATTTTGTTCTGA 476667 i ivv i i - i v v ii --i MIRc#SINE/MIR 86 TGTGTGACCTTGGGC-AAGTCACTTAACCT--CTCTGA 120 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.80 CpG sites = 14, Kimura (unadjusted) = 38.80 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.05 (4 / 87), avg. gap size = 1.00 (4 / 4) 13 26.46 2.90 4.41 chr3qtel1M 476914 476982 (523018) (CAAAG)n#Simple_repeat 1 68 (0) m_b148s252i15 5556 chr3qtel1M 476914 CAGAGGAAAGGGAAGGGAAG-GAA-CAAAGGCAAGGCAAAGCAAAGCACA 476961 i v vi vi -i - - i v (CAAAG)n#Simp 1 CAAAGCAAAGCAAAGCAAAGCAAAGCAAA-GCAAAGCAAAGCAAAGCAAA 49 chr3qtel1M 476962 TCATGTACAGAGCAATAGCAA 476982 v -ivi i - (CAAAG)n#Simp 50 GCA-AAGCAAAGCAA-AGCAA 68 Matrix = Unknown Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.07 (5 / 68), avg. gap size = 1.00 (5 / 5) 17 20.54 0.00 0.00 chr3qtel1M 477137 477170 (522830) (T)n#Simple_repeat 1 34 (0) m_b148s252i16 5557 chr3qtel1M 477137 TTTTTTTTTTTTCTTTTTGTTCTGTTTCTTCTTT 477170 i v i v i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 34 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 521 28.03 5.63 4.85 chr3qtel1M 478449 479123 (520877) L1M5_orf2#LINE/L1 2615 3294 (0) m_b148s551i4 5558 chr3qtel1M 478449 TACTAGATCT-AAAATTATATTATAAAGCAGCAGTTACCAAAACCATTTG 478497 i? ? - i i - vi v i i vi v L1M5_orf2#LIN 2615 TACCNGATNTCAAGACT-TATTATAAAGCTACAGTAATCAAGACAGTGTG 2663 chr3qtel1M 478498 GTATTGGC-TAAGAAATAGACTAGAT-GATCAATGGAATAGATTAGA--- 478542 - -i - i - i v --- L1M5_orf2#LIN 2664 GTATTGGCGTAAG-GATAGAC-AAATAGATCAATGGAACAGAATAGAGAG 2711 chr3qtel1M 478543 TTCAAAGGACAAAACAGCCA-ATAACTTTAATAATCTAGTGTTTGACAAA 478591 i i ---- v v v - i vv v ii?v ?i ii v L1M5_orf2#LIN 2712 TCCAGA----AATAGACCCACACATATATGGNCANTTGATTTTTGACAAA 2757 chr3qtel1M 478592 ---CCCAAAGACCCCAGTTT--TGGGGATAAGACCGCACGATTTGACAAA 478636 ---v ? ---- i i-- v i iv i- vv ii L1M5_orf2#LIN 2758 GGTGCCAANG----CAATTCAGTGGGGAAAGGATAGT-CTTTTCAACAAA 2802 chr3qtel1M 478637 AATTGCTGGGAAAATTGGAAATTAGTAT-GATAAAACTAGGCATTGACCC 478685 viv i v v ivi - v v iii?v i L1M5_orf2#LIN 2803 TGGTGCTGGAACAATTGGATATCCATATGGAAAAAAATGAANCTCGACCC 2852 chr3qtel1M 478686 ACACTTAACACCAAACACCAAGATAAGGTCTAAATGGGCTCAT-GACCTA 478734 vi i v v v i v iv ? i i- - L1M5_orf2#LIN 2853 CTACCTCACACCATACACAAAAATTAATTCNAGATGGA-TCATAGACCTA 2901 chr3qtel1M 478735 GGCATAAAGAATGAGATAATCAATAAA----TTGGAAG--ACCATAGGAT 478778 iiii ii? i i ---- v ----i i -- v v L1M5_orf2#LIN 2902 AATGTAAAAGNTAAAA----CTATAAAACTTCTAGAAGAAAACATAGGAG 2947 chr3qtel1M 478779 AGTTTACCTCTCAGACCTGTGGAAGAGGAACAAATTTATGACCAAACAAG 478828 i-- i iivv - i?v v v i v ---i i L1M5_orf2#LIN 2948 AA--TATCTTCGTGACCT-TGGGNTAGGCAAAGATTTCT---TAAACAGG 2991 chr3qtel1M 478829 AACTAGAGATCATTATTGATCACAAAATAGAAAAT-------TTTGATTA 478871 vvi i i v i? --- i i v i ------- v i ? L1M5_orf2#LIN 2992 ACACAAAAAGCACNA---ACCATAAAAGAAAAAATTGATAAATTGGACTN 3038 chr3qtel1M 478872 TATCAAATTGAAAAAATTTTGTACAAACAAAACTAATGCAGATAAG---A 478918 i v v v i iv -?v --i ii v v --- L1M5_orf2#LIN 3039 CATCAAAATTAAAAACTTCTGCTC-NTCAAAA--GACACCGTTAAGAAAA 3085 chr3qtel1M 478919 TTAGAAGGGAAGCAGTAAAGTGGGAAAACATTTTTACAGTCAAAGGT-TC 478967 v i v vii i ? i v v i i-? v vi - L1M5_orf2#LIN 3086 TGAAAAGGCAAGCCACAGANTGGGAGAAAATATTTGCAA-NACATATATC 3134 chr3qtel1M 478968 TGATAAAGGCCTCATTTCCAATATATAGAGAGAATTGACTGTAATTT-AT 479016 i v i v iv v i i -v ii ? i- L1M5_orf2#LIN 3135 TGACAAAGGACTCGTATCCAGAATATATAAAGAACT-CCTACAANTCAAT 3183 chr3qtel1M 479017 AAGAAATCAAGCCATTC--TCCAATTCATAAATTGTCAAAGGATATGAAC 479064 ? -- v vv --i v? v v v i iv L1M5_orf2#LIN 3184 AANAAA--AAGACAAACAACCCAATANAAAAATGGGCAAAAGACTTGAAC 3231 chr3qtel1M 479065 AAACAATTCTC-AAAGAA---ATTGAAACTATTTCTTGCCATATGAAAAG 479110 i v v - --- ?v iviiivv viv i L1M5_orf2#LIN 3232 AGACACTTCACAAAAGAAGATATNCAAATGGCCAATAAGCACATGAAAAG 3281 chr3qtel1M 479111 ATGCTCCAAGTCA 479123 v v? L1M5_orf2#LIN 3282 ATGCTCAACNTCA 3294 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.38 CpG sites = 97, Kimura (unadjusted) = 37.15 Transitions / transversions = 1.17 (97/83) Gap_init rate = 0.08 (51 / 674), avg. gap size = 1.39 (71 / 51) 1279 27.56 3.00 1.48 chr3qtel1M 478984 479517 (520483) L1ME3G_3end#LINE/L1 7 548 (376) m_b148s551i5 5558 chr3qtel1M 478984 TCCAATATATAGAGAGAATTGACTGTAATTTA-TAAGAAATCAAGCCATT 479032 iv v i i v- ii v i - -- v -- L1ME3G_3end#L 7 TCCAGAATATATAAAGAACTC-CTACAAATCAATAAGAAA--AAGACA-- 51 chr3qtel1M 479033 CTCCAATTCATAAATTGTCAAAGGATATGAACAAACAATTCTCAAA---- 479078 vi vv v v v ii v i ---- L1ME3G_3end#L 52 ACCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAG 101 chr3qtel1M 479079 GAAATTGAAACTATTTCTTGCCATATGAAAAGATGCTCCAAGTCATTATT 479128 vv iviiivv viv v vv i v L1ME3G_3end#L 102 GAAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGT 151 chr3qtel1M 479129 AATCACAGAAATGCACATTAACACAACGCTGAGATACCACTACACACCTG 479178 vi v v iv i viv ii L1ME3G_3end#L 152 AATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCA 201 chr3qtel1M 479179 TCAGATTGGCTAGAATGACAGGGAAAGATAATGCGCAATGTTGGAGGGGA 479228 v i vvv ii ?vv iiv? i v i i L1ME3G_3end#L 202 TCAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGG 251 chr3qtel1M 479229 TGTGGGAAAACTGGGACACTGATACATTGTTGGTGGAATAATACATC--- 479275 i v v v v i i i vvi v i--- L1ME3G_3end#L 252 TGTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGT 301 chr3qtel1M 479276 -CAGCCATTCTGGAGAGCAATTTGGAACTATGCTCAAAAAGTTATCAAAC 479324 - ? i i v v - vvv i -- i v L1ME3G_3end#L 302 ACAGCCNTTTTGGAGGGCAATTTGGCAGTAT-CTATTAAAAT--TTAAAA 348 chr3qtel1M 479325 TGTGCATACCCTTTGATCCAGCAGTGTTACTACAGGACTTATATCCCAAA 479374 i i i vii v v? i?v v i ? L1ME3G_3end#L 349 TGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANA 398 chr3qtel1M 479375 G--ATATTT-TAAAGGGAAAGGGGCATGTATGTGCAAGAATGTTTGTGGC 479421 -- i i-i v v viv vii v ? i i i ii v L1ME3G_3end#L 399 GAAATACTCGCACATGTGCACAAGGANGCATGTACAAGGATGTTCATTGC 448 chr3qtel1M 479422 AGTCCTCTTTGTAGTGGCCAGAAACTGGAAA----CTGAGTTTCCATCAA 479467 ivi v i i v i i ---- i i v L1ME3G_3end#L 449 AGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCAA 498 chr3qtel1M 479468 TTGGAGAATAGCTGAATGAATTGTGGTATATGACTATTATGGGATATTAT 479517 v i i i i i i vvv i i i L1ME3G_3end#L 499 TAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACTAT 548 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.83 CpG sites = 75, Kimura (unadjusted) = 35.43 Transitions / transversions = 1.07 (75/70) Gap_init rate = 0.03 (15 / 533), avg. gap size = 1.60 (24 / 15) 718 27.62 8.12 5.56 chr3qtel1M 479015 479593 (520407) L1MC1_3end#LINE/L1 41 633 (447) m_b148s551i6 5558 chr3qtel1M 479015 ATAAGAAATCAAGCCATTCTCCAATTCATAAATTGTCAAAGGATATGAAC 479064 v i i v i--- i ? v v v v i iv ? L1MC1_3end#LI 41 ATAAGAAAACGAACAAC---CCGATTNAAAAATGGGCCAAAGACCTNAAC 87 chr3qtel1M 479065 AAACAATTC-TCAAAGAA---------ATTGAAACTATTTCTTGCCATAT 479104 i vi -i --------- v v v ------iv L1MC1_3end#LI 88 AGACACCTCACCAAAGAAGATATACAGATGGCAAATA------AGCATAT 131 chr3qtel1M 479105 GAAAAGATGCTCCAAGTCATTAT-TAATCACAGAAATGCACATTAACACA 479153 vi - - v vi v v L1MC1_3end#LI 132 GAAAAGATGCTCCACATCA-TATGTCATCAGGGAAATGCAAATTAAAACA 180 chr3qtel1M 479154 ACGCTGAGATACCACTACACACCTGTCAGATTGGCTAGAATGACAGGGAA 479203 iv i i v i i -- vi i v L1MC1_3end#LI 181 ACAATGAGATACCACTACACACCTATTAGAATGGCCAAAAT--CCAGAAC 228 chr3qtel1M 479204 A--GATAATGCGCAATGTTGGAGGGGATGTGGGAAAACTGGGACACTGAT 479251 -- i ii vv i v i iiv v i v v L1MC1_3end#LI 229 ACTGACAACACCAAATGCTGGCGAGGATGTGGAGCAACAGGAACTCTCAT 278 chr3qtel1M 479252 ACATTGTTGGTGGAATAATACA------TCCAGCCATTCTGGAGAGCAAT 479295 v i i-- i ------ v i i iii i L1MC1_3end#LI 279 TCATTGCTGGTGGG--AATGCAAAATGGTACAGCCACTTTGGAAGACAGT 326 chr3qtel1M 479296 TTGGAACTATGCTCA-AAAAGTTATCAAACTGTGCATACCCTTTGATCCA 479344 v v - v i - v v v v v --- v vi L1MC1_3end#LI 327 TTGGCAGT-TTCTTACAAAACTAAACATACTCT---TACCATACGATCCA 372 chr3qtel1M 479345 GCA---GTGTTACTACAGGACTTATATCCCAAAGATATTTTAAAGGGAA- 479390 --- i i v -ii v i --- ivi ----- ii - L1MC1_3end#LI 373 GCAATCGCGCTCCT-TGGTATTTA---CCCAAAGGAGTT-----GAAAAC 413 chr3qtel1M 479391 --AGGGGCATGTA------TGTGCAAGAATGTTTGTGGCAGTCCTCTTTG 479432 -- v vv iii ------ ii v i i i iii v ii L1MC1_3end#LI 414 TTATGTCCACACAAAAACCTGCACACGGATGTTTATAGCAGCTTTATTCA 463 chr3qtel1M 479433 TAGTGGCCAGAAACTGGA---AACTGAG-TTTCCATCAATTGGAGAATAG 479478 i v i vi --- ii - v v i v v i L1MC1_3end#LI 464 TAATTGCCAAAACTTGGAAGCAACCAAGATGTCCTTCAGTAGGTGAATGG 513 chr3qtel1M 479479 CTGAATGAATTGTGGTATATGACTATTATGGGATATTATTGTTCTCT--- 479525 v i i i i vvvv iv i vvv v --- L1MC1_3end#LI 514 ATAAATAAACTGTGGTACATCCAGACAATGGAATATTATTCAGCGCTAAA 563 chr3qtel1M 479526 AAGAAATGA-CCAGCAGG--ATGATTTCAGAAAGGCCTGGA-AAGACTTA 479571 - i v i -- ------ i v -i i L1MC1_3end#LI 564 AAGAAATGAGCTATCAAGCCATGA------AAAGACATGGAGGAAACTTA 607 chr3qtel1M 479572 ----CATGTTGTGGAGTGAAATGAGC 479593 ---- i iivi vi L1MC1_3end#LI 608 AATGCATATTACTAAGTGAAAGAAGC 633 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.16 CpG sites = 83, Kimura (unadjusted) = 35.31 Transitions / transversions = 1.22 (83/68) Gap_init rate = 0.09 (50 / 578), avg. gap size = 1.60 (80 / 50) 12 18.27 5.41 0.00 chr3qtel1M 479885 479921 (520079) (TATACT)n#Simple_repeat 1 39 (0) m_b148s252i17 5559 chr3qtel1M 479885 TATACATATA-TTGTATTTA-ACTTATACTTTAACATAT 479921 v - i i - vv v (TATACT)n#Sim 1 TATACTTATACTTATACTTATACTTATACTTATACTTAT 39 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 192 33.33 1.27 1.27 chr3qtel1M 480189 480267 (519733) C L2c_3end#LINE/L2 (45) 433 355 m_b148s601i14 5560 chr3qtel1M 480189 GACACTGGGCATACAAAGACAAACAGAAAACACTCTTTGCCGTTGAGGAC 480238 i i v ii i ii v iv ii v ii v C L2c_3end#LINE 433 GGCGCTGGGGATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAG 384 chr3qtel1M 480239 ATCTGATTCTCCTAGGAAGGAACA-ACATG 480267 v vv v vv - i ii - ? C L2c_3end#LINE 383 CTCACAGTCTAGT-GGAGGAGACAGACANG 355 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.66 CpG sites = 15, Kimura (unadjusted) = 46.43 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.03 (2 / 78), avg. gap size = 1.00 (2 / 2) 256 22.42 0.00 1.72 chr3qtel1M 483847 483905 (516095) C L2c_3end#LINE/L2 (220) 258 201 m_b149s601i0 5560 chr3qtel1M 483847 TTGGGGGTTTCAGGGAAGGCCTCCTGCAGAAGGTGATATTTAAAGTCACT 483896 v - i i v i i i i iv v v? C L2c_3end#LINE 258 TTGGGGGGT-CAGGGAAGGCTTCCCGGAGGAGGTGACATCTGAGCTGAGN 210 chr3qtel1M 483897 CTTGCAGGA 483905 v C L2c_3end#LINE 209 CTTGAAGGA 201 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.14 CpG sites = 7, Kimura (unadjusted) = 27.52 Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1) 229 27.59 5.43 5.43 chr3qtel1M 483848 483939 (516061) C L2b_3end#LINE/L2 (212) 254 163 m_b149s601i1 5560 chr3qtel1M 483848 TGGGGGTTTCAGGGAAGGCCTCCTGCAGAAGGTGATATTTAAAGTCACTC 483897 v - i i i v i i i iv v vv C L2b_3end#LINE 254 TGGGGGGT-CAGGGAGGGCTTCCCGGAGGAGGTGACATTTGAGCTGAGAC 206 chr3qtel1M 483898 TTGCAGGAATTCCAGTAA-----AGCTAAGAGACAGAGATGAGGAAG 483939 i v ---iv i-----i i i v - i i C L2b_3end#LINE 205 CTGAAGGA---TGAGTAGGAGTTGGCCAGGCGA-AGAGGTGGGGAAG 163 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.69 CpG sites = 15, Kimura (unadjusted) = 35.53 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.07 (6 / 91), avg. gap size = 1.67 (10 / 6) 205 33.39 0.00 4.44 chr3qtel1M 483856 483949 (516051) C L2d_3end#LINE/L2 (265) 251 162 m_b149s601i2 5560 chr3qtel1M 483856 TCAGGGAAGGCCTCCTGCAGAAGGTGATATTTAAAGTCACTCTTGCAGGA 483905 i v v i iv i i iv vivi v C L2d_3end#LINE 251 TCAGGGAAGGCTTCGTGGAGGAGGTGGGACTTGAGCTGGGCCTTGAAGGA 202 chr3qtel1M 483906 ATTCCAGTAAAGCTAAGAGACAGAGATGAGGAAGCATATGGGCA 483949 ---ivi iiii vi v v - viv v C L2d_3end#LINE 201 ---TGGGTAGGATTTGGATAGAGAGA-GAGGAAGGGGAAGGGCA 162 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.10 CpG sites = 16, Kimura (unadjusted) = 45.10 Transitions / transversions = 1.14 (16/14) Gap_init rate = 0.04 (4 / 93), avg. gap size = 1.00 (4 / 4) 290 24.68 4.94 4.94 chr3qtel1M 484195 484356 (515644) L1M4_orf2#LINE/L1 3133 3294 (0) m_b149s551i0 5561 chr3qtel1M 484195 TCTGATAAAGGCCCCGTTTCTAAAATATATGGAGAATT-----GACCCAA 484239 i v i? v i i ii i -----i i L1M4_orf2#LIN 3133 TCTGATAAGGGACTNGTATCCAGAATATATAAAGAACTCTTACAACTCAA 3182 chr3qtel1M 484240 AGTTATAAGAATTCCATTCATTCTCCAATTGATAAATGGTCAAAGGATAT 484289 --iv i vv v v v i--- ? v v v L1M4_orf2#LIN 3183 --CAATAAAAAGACAAATAAC---CCAATTNAAAAATGGGCAAAGGATTT 3227 chr3qtel1M 484290 GAAGAGACAATTTTCAGATGAAGAAATTACAACCATTTCTAGT---CATA 484336 v v i vi v v - -- vv i i --- i L1M4_orf2#LIN 3228 GAATAGACATTTCTCCAAAGAAGATA-TACAA--ATGGCCAATAAGCACA 3274 chr3qtel1M 484337 TGAAAAGGTGCTCCAAATCA 484356 i v v L1M4_orf2#LIN 3275 TGAAAAGATGCTCAACATCA 3294 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 30.61 CpG sites = 18, Kimura (unadjusted) = 30.61 Transitions / transversions = 0.90 (18/20) Gap_init rate = 0.06 (10 / 161), avg. gap size = 1.60 (16 / 10) 1270 27.55 1.00 1.82 chr3qtel1M 484264 484762 (515238) L1ME3G_3end#LINE/L1 54 548 (376) m_b149s551i1 5561 chr3qtel1M 484264 CCAATTGATAAATGGTCAAAGGATATGAAGAGACAATTTTCAGATGAAGA 484313 v v v v i iv v i L1ME3G_3end#L 54 CCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGGA 103 chr3qtel1M 484314 AATTACAACCATTTCTAGT---CATATGAAAAGGTGCTCCAAATCACTAT 484360 - -- vv i i --- i v vv v L1ME3G_3end#L 104 AA-TACAA--ATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAG 150 chr3qtel1M 484361 TGATCAGAGAAATGCAAATTAAGACAACTCTGAGATACTGCTCCACACCT 484410 i i i vv iii iiv i L1ME3G_3end#L 151 TAATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCC 200 chr3qtel1M 484411 GTCAGATTGACTAAGATGACAGGGAAAGATAATAATGAATGTTGGAGGGG 484460 i i v i vvv ii ?vv vi? i v i L1ME3G_3end#L 201 ATCAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGG 250 chr3qtel1M 484461 ATGTGGGGAAACTGGGACACTAATACATTGTTGGTGGAACTGTGAACGGA 484510 i v v v v i i i v i iv i L1ME3G_3end#L 251 GTGTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGG 300 chr3qtel1M 484511 TCCAACCTTTCTGGAGAGCAGTTGGGAACTATGCTCAAAAAATTATCAAA 484560 v i ? i i i v v v - vvv -- i L1ME3G_3end#L 301 TACAGCCNTTTTGGAGGGCAATTTGGCAGTAT-CTATTAAAAT--TTAAA 347 chr3qtel1M 484561 CTGAGCATACTCTTTGATCCAGCAGTGTCTCTACTGGGCTTATATCCCAA 484610 v v i i i vi v v ? ?v v i ? L1ME3G_3end#L 348 ATGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTAN 397 chr3qtel1M 484611 AAAGAT-CTTAAAGAAG-GGAAAGGGACCCACGTCTGCCAAAATGTTTGT 484658 i i - iiv v v - v v i ?v i -- i v ii ii L1ME3G_3end#L 398 AGAAATACTCGCACATGTGCACAAGGANGCATG--TACAAGGATGTTCAT 445 chr3qtel1M 484659 GGCAGCTCTTTTTGTAGTGGTAAGAAACTGAAAAGTGAATGGATACCCAA 484708 v vi v i i ii i i i vvivv ii ii - L1ME3G_3end#L 446 TGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCC-A 494 chr3qtel1M 484709 TCAGCTGGGGAATGGCTGAGTAAATTATGGGATATGAACCTTATGGGATA 484758 iiv i i i v vv ivi i L1ME3G_3end#L 495 TCAATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATA 544 chr3qtel1M 484759 TTAT 484762 i L1ME3G_3end#L 545 CTAT 548 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.86 CpG sites = 73, Kimura (unadjusted) = 35.58 Transitions / transversions = 1.18 (73/62) Gap_init rate = 0.02 (12 / 498), avg. gap size = 1.17 (14 / 12) 12 19.90 2.86 0.00 chr3qtel1M 485254 485288 (514712) (AAATAT)n#Simple_repeat 1 36 (0) m_b149s252i0 5562 chr3qtel1M 485254 AAATATAAAGCTTTA-ATAAAAATAAATATATATAT 485288 vv vv - v v (AAATAT)n#Sim 1 AAATATAAATATAAATATAAATATAAATATAAATAT 36 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 228 32.26 5.43 1.49 chr3qtel1M 486905 487033 (512967) L3#LINE/CR1 3961 4094 (5) m_b149s601i3 5563 chr3qtel1M 486905 CCTGTCCTTGGAAGTTTTCAGGCCACCTCAGG--GGTCACTTGTT-GGGT 486951 i vi i v i vivvv v -- ii i- v L3#LINE/CR1 3961 CCCGTCACTGGAGGTGTTCAAGCAGAGGCTGGATGACCACTTGTCAGGGA 4010 chr3qtel1M 486952 TGG-GCAGAGTGGGGATCCCTTTCCTGTA---GAGGTTACATTCAAGGGC 486997 v- i i-- i vivi v --- iv i vi v i L3#LINE/CR1 4011 TGTTGTAGAA--GGGATTCCTGCATTGGATGGGAGGTTGGACTAGATGAC 4058 chr3qtel1M 486998 AACTAAGGCCTCTTCCAACTCTCATATTTGGTGCTT 487033 vv i i v v iv v L3#LINE/CR1 4059 CTCTAAGGTCCCTTCCAACTCTGAGATTCTGTGATT 4094 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.42 CpG sites = 20, Kimura (unadjusted) = 42.77 Transitions / transversions = 0.95 (20/21) Gap_init rate = 0.05 (6 / 128), avg. gap size = 1.50 (9 / 6) 229 22.22 0.00 0.00 chr3qtel1M 489245 489298 (510702) C MIRc#SINE/MIR (205) 63 10 m_b149s601i4 5564 chr3qtel1M 489245 ATTCCAACCCAGGTCTTCCTGACTCCACGTCCAATACTTCATTAACTCCA 489294 i v v i i iiv iv v C MIRc#SINE/MIR 63 ACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCA 14 chr3qtel1M 489295 ACAC 489298 v C MIRc#SINE/MIR 13 CCAC 10 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.56 CpG sites = 6, Kimura (unadjusted) = 26.56 Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 199 37.66 7.49 2.03 chr3qtel1M 489397 489583 (510417) L2d2_3end#LINE/L2 48 244 (311) m_b149s601i5 5565 chr3qtel1M 489397 TTTCCTTGTACATATAGTGTGCTACAGCCCTGCTGGCCCAC-------CC 489439 i i ?i iv ivv vi v vvi i i ------- L2d2_3end#LIN 48 TTCCCCTNCACGAACCCTCCGCTCCAGCCAAACTGGTCTACTCACTGTCC 97 chr3qtel1M 489440 CTAGAAATGGTCCTTCCTGTTTTTATCCC-ATCCCTTTGTTTAAGTAGTC 489488 iv vvv i i v vi? iiiii i -iiv i i v iv i L2d2_3end#LIN 98 CCCGAACACGCCTTGCGCNTTCCCGCCTCTGCGCCTTTGCTCACGCCGTT 147 chr3qtel1M 489489 CTCAAAGCCCAGAGTGCTCTTCCCATTCCCATTTCTCACATG---AAGTC 489535 i vvv ii i i v -- i - v i--- i L2d2_3end#LIN 148 CCCCCCGCCTGGAATGCCCTTCCCCTTCC--TCTC-CACCTATCCAAATC 194 chr3qtel1M 489536 CTATCTATTCTTTATGGTCCAG---GAATCTCTGCCTTTTCCTTCCAGTC 489582 i i i i v i ---i -? ii ii v vv i L2d2_3end#LIN 195 CTACCCATCCTTCAAGGCCCAGCTCAAAT-NCCACCTCCTCCGTGAAGCC 243 chr3qtel1M 489583 T 489583 L2d2_3end#LIN 244 T 244 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 52.31 CpG sites = 44, Kimura (unadjusted) = 57.55 Transitions / transversions = 1.76 (44/25) Gap_init rate = 0.04 (8 / 186), avg. gap size = 2.25 (18 / 8) 249 32.66 3.88 1.90 chr3qtel1M 489472 489574 (510426) L2d_3end#LINE/L2 131 235 (281) m_b149s601i6 5565 chr3qtel1M 489472 CCTTTGTTTAAGTAGTCCTCAAAGCCCAGAGTGCTCTTCCCATTCCCATT 489521 i i v iv i i vvv ii i i v iv i L2d_3end#LINE 131 CCTTTGCTCACGCCGTTCCCCCCGCCTGGAATGCCCTTCCCCTTCCTCTC 180 chr3qtel1M 489522 TCTCACAT-GAAGTCCTATCTATTCTTTATGGTCCAG---GAATCTCTGC 489567 -i -v i i i i i v i ---i i - ii L2d_3end#LINE 181 TCTC-TATCCAAATCCTACCCATCCTTCAAGGCCCAGCTCAAGTC-CCAC 228 chr3qtel1M 489568 CTTTTCC 489574 ii L2d_3end#LINE 229 CTCCTCC 235 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 46.45 CpG sites = 24, Kimura (unadjusted) = 46.45 Transitions / transversions = 2.67 (24/9) Gap_init rate = 0.04 (4 / 102), avg. gap size = 1.50 (6 / 4) 197 16.22 0.00 0.00 chr3qtel1M 489953 489989 (510011) OldhAT1#DNA/hAT-Ac 2222 2258 (584) m_b149s601i7 5566 chr3qtel1M 489953 AGTTTATTTAGAACTGAGAAGTCAGCTTTTGCAAGCT 489989 ? v vi v v v OldhAT1#DNA/h 2222 ANTGTATTGGGAACTGAGAAGTCAGCTGTGGCCAGCT 2258 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 18.95 CpG sites = 1, Kimura (unadjusted) = 18.95 Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 500 32.37 7.89 3.47 chr3qtel1M 490500 490803 (509197) L2b_3end#LINE/L2 144 460 (6) m_b149s601i8 5567 chr3qtel1M 490500 TTCCTC-ACATGGAAGGCTCTCCTCCTCACCTCT--GCCTGGTACCTTTC 490546 i -i v v i -- i -- i- vvi L2b_3end#LINE 144 TCCCTCTGCCTGGAACGCCCT--TCCCCACCTCTTCGCCTGGC-CAACTC 190 chr3qtel1M 490547 CTAGCT--TCATAAAAGATTGAGCTC------TATCTTCTCCAGGAAGCC 490588 - -- v vv i vi v ------i i i i L2b_3end#LINE 191 CTA-CTCATCCTTCAGGTCTCAGCTCAAATGTCACCTCCTCCGGGAAGCC 239 chr3qtel1M 490589 TTCTCTAAAACCCCCAAAT--GCTT--GTGCCTTCCTCTCAAGGTTCCCT 490634 i i -i v iii-- v i-- i i --- vi i L2b_3end#LINE 240 CTCCCT-GACCCCCCAGGCCGGGTCAGGCGCCCTCCTCT---GGGCCCCC 285 chr3qtel1M 490635 TTCATCCATGCCATATGCCTCT--ACTATGAACAGTTATT--CATGTTTC 490680 iivi - i v iivv --ii ? viivi i? -- i v L2b_3end#LINE 286 CCAGTCC-TACCCTGCCACTCTGGGTTATNATTGTCTGNTTACATGTCTG 334 chr3qtel1M 490681 TC-CTCTCACCTTAGACTGTGAATTCCTTGTGGGAAGAGACTGAGT---T 490726 - i i -- ii v v v i i ? --- L2b_3end#LINE 335 TCTCCCCCAC--TAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGT 382 chr3qtel1M 490727 TTTGTCTTCCTTTTAATTCCTTGCATGCAATAGA-TACCTGGCATCCAGT 490775 i iiv vi vv i iv iivi ii v -?i iv L2b_3end#LINE 383 CTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGT 432 chr3qtel1M 490776 AAGTGCTCAAAAGATGCTTGTGTGATGA 490803 i i iv i ii vvi L2b_3end#LINE 433 AGGCGCTCAGTAAATATTTGTTGAATGA 460 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.36 CpG sites = 62, Kimura (unadjusted) = 45.66 Transitions / transversions = 1.88 (62/33) Gap_init rate = 0.07 (22 / 303), avg. gap size = 1.59 (35 / 22) 213 26.09 1.30 5.41 chr3qtel1M 490936 491012 (508988) L3#LINE/CR1 4025 4098 (1) m_b149s601i9 5568 chr3qtel1M 490936 TTCCAACAGTTTGATGGAATAT-GGACAAGACTGAATCCTGAGAGGTTTC 490984 vi - v i vi - v - -- vvi ii L3#LINE/CR1 4025 TTCCTGCA-TTGGATGGGAGGTTGGACTAGA-TGA--CCTCTAAGGTCCC 4070 chr3qtel1M 490985 TTTCTCTTCTGAAATTCTGCGATTCTGT 491012 i vvi i i i L3#LINE/CR1 4071 TTCCAACTCTGAGATTCTGTGATTCTAT 4098 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.65 CpG sites = 11, Kimura (unadjusted) = 32.65 Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.07 (5 / 76), avg. gap size = 1.00 (5 / 5) 247 33.69 8.76 4.96 chr3qtel1M 491573 491903 (508097) L3b_3end#LINE/CR1 733 1075 (131) m_b149s601i10 5568 chr3qtel1M 491573 CATGAAGCTAATTTGGATAG-GCTTGAAGGTATGC--CAGA---GATT-- 491614 i i -- ? v - i iii viv -- i --- -- L3b_3end#LINE 733 CGTGGAG--AANTTGGAGAGAGTTCAGAGGAGAGCAACAAAAATGATTAA 780 chr3qtel1M 491615 -GGACTGGAAAAGGGCAAATTTGGG----------AGGAATTGAGAGGCT 491653 - i v v vv v i ---------- i i vvv L3b_3end#LINE 781 AGGGCTGGAAAATGGGACCTATGAGGAAAGGTTAAAGGAACTGGGATTAT 830 chr3qtel1M 491654 TCCTGGAGACTGAGGAGTAGTAGGGAAGGACTCGGGAGACACAGAACAAG 491703 ---- v ii ----- i - vi i ?v vv i - L3b_3end#LINE 831 TC----AGCCTGGAGA-----AGAGAAGG-CTGAGGGGNGACTTAATAA- 869 chr3qtel1M 491704 TCTTCTTCCAGTATCTGAAGGACCAACATGTGAAAGA--GAGATTCAGGT 491751 i?v v v iii vi i ii i -- v i- v L3b_3end#LINE 870 CNGTCTTCAAGTATATGAAGGGTTATTACGTAGAGGACGGTGAC-CAGCT 918 chr3qtel1M 491752 TTTCTTCCTGGTCCCCAAAGAGAGAATCAGGAGCAATGAG---AGATTGT 491798 v i v vvi v ii i v iv ii v i --- i i i L3b_3end#LINE 919 GTTCTCCATCTCCACTGAGGACAGAACAAGAGGAAATGGGCTTAAACTGC 968 chr3qtel1M 491799 TACAGTGAAAACAATAAAGACTAGATATCAAGAACAACTTATT-AC--TT 491845 vi - iii-- vv ii v i v vi - -- v L3b_3end#LINE 969 AGCA-TGAGGG--ATTTAGGTTAGATATAAGGAAGAACTTCCTGACAGTG 1015 chr3qtel1M 491846 GGAGCTGTCACAGA--AGATCAGGCTTCCCTTGGAGGTGGAAGAATCACC 491893 i i i v v --i vii i v vvv v vi v L3b_3end#LINE 1016 AGAGTTGTTAAACACTGGAATGGGTTACCGAGGGAGGTTGCGGAATCTCC 1065 chr3qtel1M 491894 ATCTTTGAAG 491903 v i i L3b_3end#LINE 1066 TTCTCTGGAG 1075 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.89 CpG sites = 58, Kimura (unadjusted) = 46.70 Transitions / transversions = 1.21 (58/48) Gap_init rate = 0.08 (28 / 330), avg. gap size = 1.64 (46 / 28) 441 30.35 5.28 7.17 chr3qtel1M 491637 491920 (508080) L3#LINE/CR1 3712 3990 (109) m_b149s601i11 5568 chr3qtel1M 491637 GGAGGAATTGAG-AGGCTT--CCTGGAGACTGAGGAGTAGTAGGGAAGGA 491683 i i i - v i -- ------------ i - L3#LINE/CR1 3712 GAAGGAACTGGGGATGTTTAGCCTGGAGA------------AGAGAAG-A 3748 chr3qtel1M 491684 CTCGGGAGACACAGAACAAGTCTTCTTCCAGTATCTGAAGGACCAACATG 491733 ii ii v vi i - iiv v i i i iiv L3#LINE/CR1 3749 CTTAGAGGAGACATGATA-GCTGTCTTCAAATATTTGAAGGGCTGTCATG 3797 chr3qtel1M 491734 TGAAAGAGAGATTCAGGTT--TTCTTCCTGGTCCCCAAAGAG-AGAATCA 491780 i i - ii -- viv - i i i - ii L3#LINE/CR1 3798 TGGAAGAGGGATT-AGACTTATTCTGTGTGG-CTCCAGAGGGCAGAACTA 3845 chr3qtel1M 491781 GGAGCAATGAGAGATTGTTACAGTGAAAACA-ATAAAGACTAGATATCAA 491829 v i v ivv - i ii - vvv i vi v i L3#LINE/CR1 3846 GGACCAATGGGTGGAAGTTACAG-GGAGGCAGATTTCGGCTCAATATAAG 3894 chr3qtel1M 491830 GAACAACTTATT-AC--TTGGAGCTGTCACAGAA---GATCAGGCTTCCC 491873 v vi - -- ii - i --- vii v i L3#LINE/CR1 3895 GAAGAACTTTCTAACAATCAGAGCTGTC-CAAAAATGGAATGGGCTGCCT 3943 chr3qtel1M 491874 TTGGAGGTGGAAGAATCACCATCTTTGAAGGCA--AAAGTTCAGAGGCT 491920 iv? i viiiv v i vi i ii--v -- L3#LINE/CR1 3944 CGNGAGGTAGTGAGCTCCCCGTCACTGGAGGTGTTCAAG--CAGAGGCT 3990 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.61 CpG sites = 53, Kimura (unadjusted) = 40.98 Transitions / transversions = 1.96 (53/27) Gap_init rate = 0.10 (29 / 283), avg. gap size = 1.21 (35 / 29) 17 30.34 3.49 1.14 chr3qtel1M 492677 492762 (507238) (TTCCTC)n#Simple_repeat 1 88 (0) m_b149s252i1 5569 chr3qtel1M 492677 TTCCTCATCAGATTCCTCATTCTCTT-C-CTTATTATTAATGTATTCACA 492724 v vvv v i - - vi v vv v - i v v (TTCCTC)n#Sim 1 TTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCT-TCCTCT 49 chr3qtel1M 492725 ACCTCTT-CTTTTTCTCTTCCTCTTCCTTCTCCTCCTCC 492762 v - i i ii i (TTCCTC)n#Sim 50 TCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCC 88 Matrix = Unknown Transitions / transversions = 0.62 (8/13) Gap_init rate = 0.05 (4 / 85), avg. gap size = 1.00 (4 / 4) 13 18.44 0.00 3.12 chr3qtel1M 492765 492797 (507203) (ATT)n#Simple_repeat 1 32 (0) m_b149s252i2 5570 chr3qtel1M 492765 ATTATTATTATAATACTTCTTTTTATTGATTAT 492797 v vv v v - (ATT)n#Simple 1 ATTATTATTATTATTATTATTATTATT-ATTAT 32 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 18 21.91 2.90 4.41 chr3qtel1M 495994 496062 (503938) (AAAGGG)n#Simple_repeat 1 68 (0) m_b149s252i3 5571 chr3qtel1M 495994 AAAGGAGAAGGGGAAAGGAAAAGGGAAAATGTAACAG-AAGGGAATACAG 496042 - i i iv v vi - - vi (AAAGGG)n#Sim 1 AAAGG-GAAAGGGAAAGGGAAAGGGAAAGGGAAAGGGAAAGGGAA-AGGG 48 chr3qtel1M 496043 AAA-TGTGAGGGAAAGGAGAA 496062 -v vi - (AAAGGG)n#Sim 49 AAAGGGAAAGGGAAAGG-GAA 68 Matrix = Unknown Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.07 (5 / 68), avg. gap size = 1.00 (5 / 5) 258 22.14 2.20 5.68 chr3qtel1M 496212 496302 (503698) L1M4c_5end#LINE/L1 2380 2467 (33) m_b149s551i2 5572 chr3qtel1M 496212 CTTTAACCATAAATGGAACGGGGTAAACTCCCTAA--AAAGAAGAAGGAT 496259 vii -----v i i -- ii v ?i L1M4c_5end#LI 2380 CTTTAAATGTAAATGGA-----TTAAACTCTCCAATCAAAAGACANAGAT 2424 chr3qtel1M 496260 TAGAGGAATGGATTAAAAAGCCGAATCCTACAATATGTTGTTT 496302 i v? i v?i v v i i L1M4c_5end#LI 2425 TGGCNGAATGGATTAAAAAACANGATCCAACTATATGCTGTCT 2467 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 28.00 CpG sites = 12, Kimura (unadjusted) = 28.00 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.07 (6 / 90), avg. gap size = 1.17 (7 / 6) 695 23.51 16.97 2.65 chr3qtel1M 496700 498390 (501610) L1M5_orf2#LINE/L1 573 2499 (795) m_b149s551i3 5572 chr3qtel1M 496700 CACTTTCTTTTCACAGTTCA--TGGAACCTATAC-AAAATAGACCATATT 496746 v - v -- v v - i ? L1M5_orf2#LIN 573 CACATTCTTTTCA-AGTGCACATGGAACATTTACCAAGATAGACCATATN 621 chr3qtel1M 496747 -TAGGACATAAAACCCAAACC--AATA-----GTAAGGA---AAAT-ATA 496784 - i v -- ii -- -----?v --- - L1M5_orf2#LIN 622 CTGGGCCATAAAAC--AAGTCTCAATAAATTTNAAAGGATTGAAATCATA 669 chr3qtel1M 496785 AATGATTCT-TTTTCAGACCACGATGCAATAAAAATTA-----CACCAAC 496828 v - v v - i v i v v - ----- vi L1M5_orf2#LIN 670 CA-GAGTATGTTCTCTGACCACAATGGAATTAAA-TTAGAAATCAATAAC 717 chr3qtel1M 496829 AAAATCAGG------GAAAGTGACCAAAAAATAATTG-AAACTAAATAAT 496871 -- i------ i vv --- v - i i - L1M5_orf2#LIN 718 AAAA--AGATANCTAGAAAATCCCCAAA---TATTTGGAAATTAAACAA- 761 chr3qtel1M 496872 CCCATT---AAAGAATGATTGGG-----AAAAAAATCATA--GAATAATT 496911 v i --- v ivvv -----i i i -- i - L1M5_orf2#LIN 762 CACACTTCTAAATAACCCATGGGTCAAAGAAGAAATCACAANGGA-AATT 810 chr3qtel1M 496912 A----ATAATTCACCCCAAGAAATGACAATAATGAGACATCATATCAAAA 496957 ---- v iivv ii --- ? i vi v v L1M5_orf2#LIN 811 AGAAAATATTTTGAACTGA---ATGANAATGAAAATACAACATATCAAAA 857 chr3qtel1M 496958 TGTGTGG-ATGCAGCCAAAG-GGTAAT--AAGGGAAATTTA---ATTTAG 497000 v - i -i iv --i ---v? i L1M5_orf2#LIN 858 TTTGTGGGATGCAGCTAAAGCAGTGCTTAGAGGGAAATTTATAGCNTTAA 907 chr3qtel1M 497001 A-GGTTAC-TTGCAAAAGTAGAGAAAGG--TAA---CAAT----TGGACT 497039 - v? i- iv --i -- --- ---- iii L1M5_orf2#LIN 908 ATGCNTATATTAGAAAAG--AAGAAAGGCTTAAAATCAATGATCTAAGCT 955 chr3qtel1M 497040 TGCAACTTAAAATGCTAGAAAAGGAA---CAAATTAAAAAACCCCCATCA 497086 v v i v i --- ----- vvi L1M5_orf2#LIN 956 TCCACCTTAAGAAGCTAGAAAAAGAAGAGCAAATTAAA-----CCCAAAG 1000 chr3qtel1M 497087 AAAACACTAAACTTGAAATT-TAAAAATAAAAA-AGAGATCAATAAAATT 497134 ? ii vv iivvv v- i i i- i i v L1M5_orf2#LIN 1001 NAAGTAGAAGGAAGGAAATAATAAAGATAAGAGCAGAAATCAATGAAATA 1050 chr3qtel1M 497135 GAAAA-----AAACTATTAATTAATTTAA---AACTAAGA-TTGGTTCTT 497175 ----- ? v vi vv v i --- i i i -i L1M5_orf2#LIN 1051 GAAAACAAANANACAATAGAGAAAATCAACGAAGCCAAAAGCTGGTTCTT 1100 chr3qtel1M 497176 -GAAAAAACCAA-AAAATAGACAAACCCTTAGTAAATCTGATTTAAAAAA 497223 - i i - v i ii i? iv i- i L1M5_orf2#LIN 1101 TGAAAAGATCAATAAAATTGATAAACCTCTAGCNAGACTGATC-AAGAAA 1149 chr3qtel1M 497224 AGGAAAGTGAAAAT-CAAATTGT---TATTTAAAA--AAAAAGGAGA--- 497264 ii i v i i- ii--- ivii -- --- L1M5_orf2#LIN 1150 AAAAGAGAGAAGACACAAATTACCAATATCAGGAATGAAAAAGGAGACAT 1199 chr3qtel1M 497265 ----AC---TCCCATAA----TGAAAGGA-AATTAGAGAATAATTAGGAA 497302 ---- --- i i i---- i - v - v L1M5_orf2#LIN 1200 CACTACAGATCCTACAGACATTAAAAGGATAATAAGAGAATA-TTATGAA 1248 chr3qtel1M 497303 TTACTTTAACTTTATGGCAATAAATC-GACAACTTAAAAAGAA-GGA-AA 497349 i------ v i- ? i vii - - L1M5_orf2#LIN 1249 C------AACTTTATGCCAATAAATTTGANAACTTAGATGAAATGGACAA 1292 chr3qtel1M 497350 ATACCC-AAAAAATAGGGC---CCGA--TTAATA-GGGAAGAAATA-AAT 497391 v i-i i vii?--- i --i i i?-ii - v L1M5_orf2#LIN 1293 ATTCCTTGAAAAACACAANTTACCAAAACTGACNCAAGAAGAAATAGAAA 1342 chr3qtel1M 497392 ATCCAAA-------ATATCTAGAAAAAGAAATAGAA-----AAGCAAACC 497429 ii ------- vv - v ----- vi -- L1M5_orf2#LIN 1343 ATCTGAATAGCCCTATATCTATTAAA-GAAATTGAATTTGTAATTAAA-- 1389 chr3qtel1M 497430 AAC--TCCTG----AAAAATCCCAGGACC-GATGGTTTT----TTGAATT 497468 -- ii----i ii v - i i----v L1M5_orf2#LIN 1390 AACCTTCCCACAAAGAAAACTCCAGGCCCAGATGGCTTCACTGGTGAATT 1439 chr3qtel1M 497469 CTACCAAACATTTAAAGAACAATTAACCCC---TGTATATAAACA--TCT 497513 i v v iv ---iv i i v-- i L1M5_orf2#LIN 1440 CTACCAAACATTTAAGGAAGAAATAATACCAATCTTACACAAACTCTTCC 1489 chr3qtel1M 497514 GAAAAATAGGGACTGAAGGG-----TCCAAAACCCTTTT-TAAACACAGA 497557 ii ii vv i i----- v vi v - i ivv v L1M5_orf2#LIN 1490 AGAAAATAGAAAAAGAGGGAACACTTCCCAACTCATTTTATGAGGCCAGC 1539 chr3qtel1M 497558 CCGGGTTTGATACCTAAATCAGGGTGAAA----ACAAGAAAAAAAG---- 497599 vi?ivii v i ? ivvi i ---- i i---- L1M5_orf2#LIN 1540 ATNACCCTGATACCAAAACCNGACAAAGACATTACAAGAAAAGAAAATTA 1589 chr3qtel1M 497600 --GACCAA---CCCTCTAATGAATAT---CGTCAAAATCTTTAA---AAT 497638 -- --- -- i ---i iv i ? --- L1M5_orf2#LIN 1590 CAGACCAATATCCCTC--ATGAACATAGATGCAAAAATCCTNAACAAAAT 1637 chr3qtel1M 497639 ATTAGCAAAAAAGATTACAGAAAAATCATTCCA-GGATAATATACTA-GA 497686 vvii i- v v - vvv - i ii - L1M5_orf2#LIN 1638 ATTAGCAAATCGAATC-CAGCAATAT-ATAAAAAGGATAATACATCATGA 1685 chr3qtel1M 497687 CCAAGTGGA-TTTATACCAGAAAT-TA----TGGC--AATA--GGAAAAC 497726 i- v i -i ---- i-- i --v i L1M5_orf2#LIN 1686 CCAAGTGGGGTTTATCCCAGGAATGCAAGGTTGGTTTAACATTCGAAAAT 1735 chr3qtel1M 497727 T--TCAATATAATTC--CATATTAA--AACCAAATTAAAAAAACCATATG 497770 i-- i -- --i vi vv i i L1M5_orf2#LIN 1736 CAATCAATGTAATTCACCATATTAACAGAATAAAGGAGAAAAATCATATG 1785 chr3qtel1M 497771 ATCATTCCAATAG-TG---AAAAAGCATTTGATAAAATCCA--AACCATT 497814 ii - --- i i -- v L1M5_orf2#LIN 1786 ATCATCTCAATAGATGCAGAAAAAGCATTTGACAAAATTCAACACCCATT 1835 chr3qtel1M 497815 CCTAATAAAAA--ATTAG--AAT--GGAATAAATGG--AC--CCTTAA-- 497852 v i --v i -- i-- i v -- -- i -- L1M5_orf2#LIN 1836 CATGATAAAAACTCTCAGCAAACTAGGAATAGAAGGGAACTTCCTCAACC 1885 chr3qtel1M 497853 -AATAGCAGGGGC--------AATATTTAAACC--ACATCATCATGAATG 497891 -i -- i -------- v ii v v -- vv v L1M5_orf2#LIN 1886 TGATA--AAGGGCATCTACGAAAAACCTACAGCNAACATCATACTTAATG 1933 chr3qtel1M 497892 GGGAAAAACTGGAATCTTTCCCAGTAAGATCGGG--TGAAGCAAGGTTGT 497939 v ? i ?v vv --ii ii v L1M5_orf2#LIN 1934 GTGAAANACTGAANGCTTTCCCCCTAAGATCGGGAACAAGACAAGGATGT 1983 chr3qtel1M 497940 CCACTGTCACCATTATTATTCAA-ATTA-ATTAGAAACACTAGCC--CGG 497985 i ? i vi - i- i i iiiv --i v L1M5_orf2#LIN 1984 CCGCTNTCACCACTTCTATTCAACATTGTACTGGAGGTCCTAGCCAGTGC 2033 chr3qtel1M 497986 AAAGAGTC----GAAAGAGATTAAAGGAATCAGAATAGG--CGGAGGCCA 498029 vi v ----i i v v v ii v --v i -- L1M5_orf2#LIN 2034 AATAAGGCAAGAAAAAGAAATAAAAGGCATAAAGATTGGAAAGGAAG--A 2081 chr3qtel1M 498030 AATATA-----CCTT----GCAA--GATATGATGGT-TACTTAGAGAACC 498067 v ----- ? ---- i-- i v - v i i L1M5_orf2#LIN 2082 AATAAAACTGTCNTTATTCGCAGATGACATGATTGTNTACGTAGAAAATC 2131 chr3qtel1M 498068 CTAAAGATTCT---GAAAAACTATTAGAAATAATCCATAACTTTTAGCAA 498114 ? v ---i ? i v vvi i v- L1M5_orf2#LIN 2132 CNAAAGAATCTACAAANAAACTACTAGAACTAATAAGTGAA-TTTAGCAA 2180 chr3qtel1M 498115 AGTTG---------------ATTTA-AAAAATCCCTAAATCCTGTTT--- 498145 i i --------------- v - ---- iv i --- L1M5_orf2#LIN 2181 GGTCGCNGGATACAAGGTCAATATACAAAAATC----AATTGTATTTCTA 2226 chr3qtel1M 498146 TATACTCACCAACAAAACCAACAGCAA---GAA--TCGAGAAAT----TC 498186 - v -- iv v --- -- i? i i----i L1M5_orf2#LIN 2227 TATACT-AGCAACAAA--CAATTGGAAAATGAAATTTNAAAAACAATACC 2273 chr3qtel1M 498187 ATTTCAAAATAACGTCGAAAAA----AAATATTTGGGAATCTATCTACCA 498232 - v i i i ---- i i vv v L1M5_orf2#LIN 2274 ATTT-ACAATAGCATCAAAAAACATNAAATACTTAGGAATAAATCTAACA 2322 chr3qtel1M 498233 AAGGAAAATCAGGAATTATA---TGATAAATTAAAAAACTTTCC----AA 498275 i? vivv i vi ? --- - i v v v ---- i L1M5_orf2#LIN 2323 AAANATGTGCAAGACCTNTACACTGA-AAACTACAAAACATTGCTGAGAG 2371 chr3qtel1M 498276 AAATAAAGTCAGACTTAA--AAATTGA-AAATAT-CAATGCCC-TGGATA 498320 v ivv i -- v - i - v ii - v L1M5_orf2#LIN 2372 AAATTAAAGAAGACCTAAATAAATGGAGAGATATACCATGTTCATGGATT 2421 chr3qtel1M 498321 GGTCGAGCTAATATT---AAAATG-CAAAACCCCCTAAACTAATCTATTT 498366 vv vii --- i - vv i i i i vv L1M5_orf2#LIN 2422 GGAAGACTCAATATTGTNAAGATGTCAATTCTCCCCAAATTGATCTATAG 2471 chr3qtel1M 498367 ATTTATT----TGCCAATCAGACTTCCA 498390 i v ---- v i v i L1M5_orf2#LIN 2472 ATTCAATGCAATCCCAATCAAAATCCCA 2499 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 29.10 CpG sites = 225, Kimura (unadjusted) = 29.37 Transitions / transversions = 1.39 (225/162) Gap_init rate = 0.10 (164 / 1690), avg. gap size = 2.06 (338 / 164) 721 23.14 16.13 1.15 chr3qtel1M 497438 498119 (501881) L1MD_orf2#LINE/L1 1403 2185 (1109) m_b149s551i4 5572 chr3qtel1M 497438 AAAAATC-CCAGGACC-GATGGTTTT-TTG---AATTCTACCAAACATTT 497481 i - v - i-i --- i L1MD_orf2#LIN 1403 AGAAATCTCCAGGCCCAGATGGTTTCACTGGAGAATTCTACCAAACGTTT 1452 chr3qtel1M 497482 AAAGAACAATTAACCCC---TGTATATAAACA--TCTGAAAAATAG---- 497522 v v --- v i i v v-- iii ---- L1MD_orf2#LIN 1453 AAAGAAGAATTAACACCAATTCTACACAATCTCTTCCAGAAAATAGAAGA 1502 chr3qtel1M 497523 GGACTGAAGGGTCCAAAACCCTTTTTAAACACAGACCGG-GTT----TGA 497567 vv viv i vv i v vi--- i i -i ---- L1MD_orf2#LIN 1503 GGAGGGAACACTTCCCAACTCATTTTATG---AGGCCAGTATTACCCTGA 1549 chr3qtel1M 497568 TACCTAAATCAGGGTGAAAACA--AGAAAAAAAG---------GACCAA- 497605 v i i-ii i -- v --------- - L1MD_orf2#LIN 1550 TACCAAAACCAGA-CAAAGACAGTACAAAAAAAGAAAACTACAGACCAAT 1598 chr3qtel1M 497606 --CCCTCTAATGAATAT---CGTCAAAATCTTTAA---AATATTAGCAAA 497647 -- -- i --- iv i i --- L1MD_orf2#LIN 1599 ATCCCTC--ATGAACATAGACGCAAAAATCCTCAACAAAATATTAGCAAA 1646 chr3qtel1M 497648 AAAGATTACAGAAAAATCATTCCAGGA-TAATATACTA-GACCAAGTGGA 497695 v?ii - v v - vvv i - v i i - i L1MD_orf2#LIN 1647 TNGAATT-CAGCAATAT-ATAAAAAGAATTATACACCATGACCAAGTGGG 1694 chr3qtel1M 497696 -TTTATACCAGAAAT-TA----TGG--CAATA--GGAAAACT--TCAATA 497733 - v i? -i ---- -- --v ii-- i L1MD_orf2#LIN 1695 GTTTATTCCAGGNATGCAAGGCTGGTTCAATATTCGAAAATCAATCAATG 1744 chr3qtel1M 497734 TAATTC--CATATTAAAA--CCAAATTAAAAAAACCATATGATCATTCCA 497779 i -- v -- i vv i i i vi L1MD_orf2#LIN 1745 TAATCCACCATATTAACAGGCTAAAGAAGAAAAATCACATGATCATATCA 1794 chr3qtel1M 497780 ATAG-TG---AAAAAGCATTTGATAAAATCCAAA--CCATTCCTAATAAA 497823 v - --- i i v-- v i L1MD_orf2#LIN 1795 ATTGATGCAGAAAAAGCATTTGACAAAATTCAACACCCATTCATGATAAA 1844 chr3qtel1M 497824 AAATT--AGAA---T-GGAATAAATGG--AC--CCTTAA-------AATA 497856 v i-- ? --- - i v -- -- i ------- v L1MD_orf2#LIN 1845 AACTCTCAGNAAACTAGGAATAGAGGGGAACTTCCTCAACTTGATAAAGA 1894 chr3qtel1M 497857 GCAGGGGCAATA--TTTAAACC--ACATCATCATGAATGGGGAAAAACTG 497902 vvvi v --ii v v -- vv v v i L1MD_orf2#LIN 1895 GCATCTACAAAAAACCTACAGCTAACATCATACTTAATGGTGAAAGACTG 1944 chr3qtel1M 497903 GAATCTTTCCCAGTAAGATCGGG--TGAAGCAAGGTTGTCCACTGTCACC 497950 i vv vv --ii i v i v L1MD_orf2#LIN 1945 AATGCTTTCCCCCTAAGATCGGGAACAAGGCAAGGATGTCCGCTCTCACC 1994 chr3qtel1M 497951 ATTATTATTCAAATTA--ATTAGAAACACTAGCC--CGGAAAGAGTC--G 497994 i v vv -- i i iiv --i v vi v -- L1MD_orf2#LIN 1995 ACTCTTATTCAACATAGTACTGGAAGTTCTAGCCAGTGCAATAAGGCAAG 2044 chr3qtel1M 497995 AAA--GAGATTAAAGGAAT-CAGA----ATAGGCGGAGGCCAAA-TATAC 498036 -- i v v - ---- v vi iiiv - i v L1MD_orf2#LIN 2045 AAAAGGAAATAAAAGGCATACAGATTGGAAAGGAAGAAATAAAACTGTCC 2094 chr3qtel1M 498037 C---TTGCAA--GATATGATGGT-TACTTAGAGAACCCTAAAGATTCT-- 498078 --- i-- i v - v i i i i v -- L1MD_orf2#LIN 2095 CTATTTGCAGATGACATGATTGTCTACGTAGAAAATCCCAAGGAATCTAC 2144 chr3qtel1M 498079 -GAAAAACTATTAGAAATAATCCATAACTTTTAGCAAAGTTG 498119 -i vi v vvi i -v i i i L1MD_orf2#LIN 2145 AAAAAAACTCCTAGAACTAATAAGTGA-GTTCAGCAAGGTCG 2185 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 27.58 CpG sites = 83, Kimura (unadjusted) = 28.20 Transitions / transversions = 1.14 (83/73) Gap_init rate = 0.09 (58 / 681), avg. gap size = 2.05 (119 / 58) 28 25.86 3.16 1.03 chr3qtel1M 499873 499967 (500033) (AATA)n#Simple_repeat 1 97 (0) m_b149s252i4 5573 chr3qtel1M 499873 AATAAA-AAGTTACTATAATAATGAAATAAATAAATAAATAAATAAATTT 499921 - i v v - vv vv (AATA)n#Simpl 1 AATAAATAAATAAATA-AATAAATAAATAAATAAATAAATAAATAAATAA 49 chr3qtel1M 499922 TTAAAAAAATTTTTAAA-AAAGAACT-ACTATTTAAAAAAAAAAAGAA 499967 v v vvv - v v - v vv v v v (AATA)n#Simpl 50 ATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAA 97 Matrix = Unknown Transitions / transversions = 0.05 (1/19) Gap_init rate = 0.04 (4 / 94), avg. gap size = 1.00 (4 / 4) 996 31.53 2.87 1.79 chr3qtel1M 500205 500866 (499134) L1ME4c_3end#LINE/L1 7 675 (155) m_b149s551i5 5572 chr3qtel1M 500205 TCTCAAATATATGAAGAATTGCCTCAAATATATAAGAAT----TCAAGCC 500250 ?v ? i ii vvi vv v---- v L1ME4c_3end#L 7 TCTNTANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAAGAC 56 chr3qtel1M 500251 ATTCTCCAATTGATAAATGGTCAAAGAATAGCAACAGACAATTTTCAGAT 500300 ----i v v i i vv iv ? v L1ME4c_3end#L 57 ----CCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAA 102 chr3qtel1M 500301 GA--AATTAAAACCATTTC-TAGTCATATGAAAAAGTGCTCTAAATCACT 500347 -- v v ?i v vv-i iv i i i i v vv i L1ME4c_3end#L 103 GAGGAAATACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCT 152 chr3qtel1M 500348 ACTGATCAGAGAAATGCCAATTAAGACAATTCTGATATACTAATACATAC 500397 v i i v ii ivv v i v vi ii L1ME4c_3end#L 153 AGTAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGC 202 chr3qtel1M 500398 TTCCCAGATTGACTAAGATGGTAAGAAAA--AATAATGACAAATGTTGGA 500445 i vii i ii v i -- v i --i iv v i v L1ME4c_3end#L 203 CTATTAAATTAGCAAAAAT--TTAAAAAATTGATAATACCCAATGCTGGC 250 chr3qtel1M 500446 GGGGATGTGGGGAAAACTGGGGCAC--ATACATTGTTGATGGAATTGTGA 500493 i ? i v - vi ? -- i i v ? i L1ME4c_3end#L 251 GAGGNTGCGGTGAAA-CTGGTACNCTCATACATTGCTGGTGGCANTGTAA 299 chr3qtel1M 500494 ACTGATCCAGCCATTTTGGAAAACAATTTGGAACTCTGC-TCAAAATGTT 500542 i i v i v i v v vi i- i - ii L1ME4c_3end#L 300 ATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGA-GCC 348 chr3qtel1M 500543 ATCAAACTGTACATACC-TTTGATCCAGCAGTGTTTCTATTGGGACTATA 500591 v v v - i i i viiv vi v v L1ME4c_3end#L 349 ATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTA 398 chr3qtel1M 500592 TTCCAAAGAGATA--TTAAAGGAGGGAAAGAGACCCACATATGCAGAAAT 500639 i i i i -- i i i i -- i i iii ii i L1ME4c_3end#L 399 TCCTAAGGAAATAATTCAAAAGAAGGAAAAAG--CTATATGCACGAAGAT 446 chr3qtel1M 500640 GTTTGTGGCAGCCATTTTTGTAGTGTCAAGGAACTGGAAATTGAGTGGAT 500689 ii v vv v i i iv i ii i ivivv ii L1ME4c_3end#L 447 GTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAAT 496 chr3qtel1M 500690 GCCCATCAATTGGAGAACAGCTGAATAAGTAATGGTATATTAATGTTATG 500739 i v v i ii i i i i v i i? iviv L1ME4c_3end#L 497 GTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATG 546 chr3qtel1M 500740 GAATATTATTGTTCTATAAGAAACAATCAGCAGGATAATTTTAGAAAGGC 500789 vvvv i v i ii v vi v vi i v iv ivii L1ME4c_3end#L 547 GAATATTATGCAGCCATTAAAAATGATAATTATGAAGACTATGTAGCAAC 596 chr3qtel1M 500790 CTGGAGAGACTTACATGAACTGATGCTAAGTGAAATGAGCAGAATCAAGA 500839 v - i iv vi vv i i vi - vi L1ME4c_3end#L 597 ATGGA-AAATGTTTATGATATAATGTTAAGTGAAAAAAGCAGAAT-ACAA 644 chr3qtel1M 500840 AATCAT-TGTAC---ATGACAACAACAATAT 500866 ii - ? --- iv v i L1ME4c_3end#L 645 AATTGTATNTACGCTATGATTACAACTATGT 675 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.08 CpG sites = 120, Kimura (unadjusted) = 43.07 Transitions / transversions = 1.41 (120/85) Gap_init rate = 0.03 (22 / 661), avg. gap size = 1.41 (31 / 22) 1051 27.70 3.15 3.54 chr3qtel1M 500210 500748 (499252) L1ME3G_3end#LINE/L1 12 548 (376) m_b149s551i6 5572 chr3qtel1M 500210 AATATATGAAGAATTGCCTCAAATATATAAGAATTCAAGCCATTCTCCAA 500259 i i v iv vv --v v --vi L1ME3G_3end#L 12 AATATATAAAGAACTCCTACAAATCAATAAGAA--AAAGACA--ACCCAA 57 chr3qtel1M 500260 TTGATAAATGGTCAAAGAATAGCAACAGACAATTTTCAGATGA--AATTA 500307 v v v i vv i iv v -- v L1ME3G_3end#L 58 TAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGGAAATA 107 chr3qtel1M 500308 AAACCATTTCTAGT---CATATGAAAAAGTGCTCTAAATCACTACTGATC 500354 v -- vv i i --- ii v vv v i L1ME3G_3end#L 108 CAA--ATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTAATC 155 chr3qtel1M 500355 AGAGAAATGCCAATTAAGACAATTCTGATATACTAATACATACTTCCCAG 500404 i v i ivv v i v vivi iivi L1ME3G_3end#L 156 AGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCATCAG 205 chr3qtel1M 500405 ATTGACTAAGATGGTAAGAAAA--AATAATGACAAATGTTGGAGGGGATG 500452 i v i -- v i i?--i iv ? i v i i L1ME3G_3end#L 206 ATTGGCAAAAAT--TTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGTG 253 chr3qtel1M 500453 TGGGGAAAACTGGG---GCACATACATTGTTGATGGAATTGTGAACTGAT 500499 --i ---v v i i i i v i i i L1ME3G_3end#L 254 TGGGGAAA--CGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGT 301 chr3qtel1M 500500 CCAGCCATTTTGGAAAACAATTTGGAAC--TCTGCTCAAAATGTTATCAA 500547 v ? iii v v-- i- i ---- i L1ME3G_3end#L 302 ACAGCCNTTTTGGAGGGCAATTTGGCAGTATCTA-TTAAAAT----TTAA 346 chr3qtel1M 500548 ACTGTACATA-CCTTTGATCCAGCAGTGTTTCTATTGGGACTATATTCCA 500596 v ii - i i viiv vi ? ?v v i i L1ME3G_3end#L 347 AATGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTA 396 chr3qtel1M 500597 AAGAGATATT---AAAGGAGGGAAAGAGACCCACATATGCAGAAATGTTT 500643 ? i i --- v v v viv - --?i i i iii i L1ME3G_3end#L 397 NAGAAATACTCGCACATGTGCACAAG-GA--NGCATGTACAAGGATGTTC 443 chr3qtel1M 500644 GTGGCAGCCATT-TTTGTAGTGTCAAGGAACTGGAAATTGAGTGGATGCC 500692 i v - - i iv i ii i ivivv ii i L1ME3G_3end#L 444 ATTGCAG-CATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTC 492 chr3qtel1M 500693 CATCAATTGGAGAACAGCTGAATAAGTAATGGTATATTAATGTTATGGAA 500742 v i ii i i i v iv ii L1ME3G_3end#L 493 CATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAA 542 chr3qtel1M 500743 TATTAT 500748 i L1ME3G_3end#L 543 TACTAT 548 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.12 CpG sites = 85, Kimura (unadjusted) = 36.10 Transitions / transversions = 1.44 (85/59) Gap_init rate = 0.05 (27 / 538), avg. gap size = 1.33 (36 / 27) 295 35.01 1.55 4.80 chr3qtel1M 500998 501126 (498874) L2b_3end#LINE/L2 332 456 (10) m_b149s601i12 5574 chr3qtel1M 500998 CTG-CTTCTTCATTGGACTGTGAGTTTTGTAGCAGCAGAAACTTTTTATT 501046 - i ii i i i ii iivi ii i----i?v L2b_3end#LINE 332 CTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACC----GNG 377 chr3qtel1M 501047 TTTGTCTTTGTTTTTCTTTGTATCTTTATTACTTAGCACAATATCTTTCA 501096 i - ivi vi iii vii i i?ii vv L2b_3end#LINE 378 TCTGTCTT-GTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCA 426 chr3qtel1M 501097 TGTAGTAGATGATTAATAAA-ATATTGTTGA 501126 iii ii v i i - - L2b_3end#LINE 427 CACAGTAGGCGCTCAGTAAATAT-TTGTTGA 456 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 47.14 CpG sites = 35, Kimura (unadjusted) = 55.28 Transitions / transversions = 4.38 (35/8) Gap_init rate = 0.06 (8 / 128), avg. gap size = 1.00 (8 / 8) 17 9.12 0.00 0.00 chr3qtel1M 503069 503092 (496908) (A)n#Simple_repeat 1 24 (0) m_b149s252i5 5575 chr3qtel1M 503069 AAAAAAAAAAAAGAAAAAGAAAAA 503092 i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAA 24 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 18 16.55 2.44 0.00 chr3qtel1M 503070 503110 (496890) (AAAAAG)n#Simple_repeat 1 42 (0) m_b149s252i6 5575 chr3qtel1M 503070 AAAAAAAAAAAGAAAAAGAAAAATAGGAAG-TAAAGAAGAAG 503110 i v ii -v i (AAAAAG)n#Sim 1 AAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAG 42 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 12 22.01 4.76 0.00 chr3qtel1M 503368 503409 (496591) (AATAAAG)n#Simple_repeat 1 44 (0) m_b149s252i7 5576 chr3qtel1M 503368 AAGAAATAA-AAAAAATAGATTATAAAGAAT-AAGAAAACAGAA 503409 v v - i i vv - v v (AATAAAG)n#Si 1 AATAAAGAATAAAGAATAAAGAATAAAGAATAAAGAATAAAGAA 44 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.05 (2 / 41), avg. gap size = 1.00 (2 / 2) 31 0.00 0.00 0.00 chr3qtel1M 504017 504043 (495957) (TG)n#Simple_repeat 1 27 (0) c_b149s251i0 5577 chr3qtel1M 504017 TGTGTGTGTGTGTGTGTGTGTGTGTGT 504043 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGT 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 14 7.28 6.90 0.00 chr3qtel1M 505028 505056 (494944) (ATTAA)n#Simple_repeat 1 31 (0) m_b149s252i8 5578 chr3qtel1M 505028 ATTAAA-GAAATTTAATTAAATT-AATTAAA 505056 -v v - (ATTAA)n#Simp 1 ATTAAATTAAATTAAATTAAATTAAATTAAA 31 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.07 (2 / 28), avg. gap size = 1.00 (2 / 2) 15 20.40 6.78 1.61 chr3qtel1M 505078 505136 (494864) (ATGTGT)n#Simple_repeat 1 62 (0) m_b149s252i9 5579 chr3qtel1M 505078 ATGTGT-T-TGTATGTG-GGGTGCATGTGAATG-ATAGTGTGTGTATGTA 505123 - - -iv i v -i - i i (ATGTGT)n#Sim 1 ATGTGTATGTGTATGTGTATGTGTATGTGTATGTGTA-TGTGTATGTGTA 49 chr3qtel1M 505124 TCTATATATGTAT 505136 v i i (ATGTGT)n#Sim 50 TGTGTATGTGTAT 62 Matrix = Unknown Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.09 (5 / 58), avg. gap size = 1.00 (5 / 5) 43 2.50 0.00 0.00 chr3qtel1M 505312 505352 (494648) (AT)n#Simple_repeat 1 41 (0) c_b149s251i1 5580 chr3qtel1M 505312 ATATGTATATATATATATATATATATATATATATATATATA 505352 i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATA 41 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 207 22.92 0.00 0.00 chr3qtel1M 507379 507426 (492574) C MIRc#SINE/MIR (211) 57 10 m_b149s601i13 5581 chr3qtel1M 507379 ACCCAGGTCTTCCTGACTCCACGTCCAATACTTCATTAGCTCCAACAC 507426 v i i iiv ivi v v C MIRc#SINE/MIR 57 ACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.70 CpG sites = 6, Kimura (unadjusted) = 27.70 Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 199 37.66 7.49 2.03 chr3qtel1M 507525 507711 (492289) L2d2_3end#LINE/L2 48 244 (311) m_b149s601i14 5582 chr3qtel1M 507525 TTTCCTTGTACATATAGTGTGCTACAGCCCTGCTGGCCCAC-------CC 507567 i i ?i iv ivv vi v vvi i i ------- L2d2_3end#LIN 48 TTCCCCTNCACGAACCCTCCGCTCCAGCCAAACTGGTCTACTCACTGTCC 97 chr3qtel1M 507568 CTAGAAATGGTCCTTCCTGTTTTTATCCC-ATCCCTTTGTTTAAGTAGTC 507616 iv vvv i i v vi? iiiii i -iiv i i v iv i L2d2_3end#LIN 98 CCCGAACACGCCTTGCGCNTTCCCGCCTCTGCGCCTTTGCTCACGCCGTT 147 chr3qtel1M 507617 CTCAAAGCCCAGAGTGCTCTTCCCATTCCCATTTCTCACATG---AAGTC 507663 i vvv ii i i v -- i - v i--- i L2d2_3end#LIN 148 CCCCCCGCCTGGAATGCCCTTCCCCTTCC--TCTC-CACCTATCCAAATC 194 chr3qtel1M 507664 CTATCTATTCTTTATGGTCCAG---GAATCTCTGCCTTTTCCTTCCAGTC 507710 i i i i v i ---i -? ii ii v vv i L2d2_3end#LIN 195 CTACCCATCCTTCAAGGCCCAGCTCAAAT-NCCACCTCCTCCGTGAAGCC 243 chr3qtel1M 507711 T 507711 L2d2_3end#LIN 244 T 244 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 52.31 CpG sites = 44, Kimura (unadjusted) = 57.55 Transitions / transversions = 1.76 (44/25) Gap_init rate = 0.04 (8 / 186), avg. gap size = 2.25 (18 / 8) 249 32.66 3.88 1.90 chr3qtel1M 507600 507702 (492298) L2d_3end#LINE/L2 131 235 (281) m_b149s601i15 5582 chr3qtel1M 507600 CCTTTGTTTAAGTAGTCCTCAAAGCCCAGAGTGCTCTTCCCATTCCCATT 507649 i i v iv i i vvv ii i i v iv i L2d_3end#LINE 131 CCTTTGCTCACGCCGTTCCCCCCGCCTGGAATGCCCTTCCCCTTCCTCTC 180 chr3qtel1M 507650 TCTCACAT-GAAGTCCTATCTATTCTTTATGGTCCAG---GAATCTCTGC 507695 -i -v i i i i i v i ---i i - ii L2d_3end#LINE 181 TCTC-TATCCAAATCCTACCCATCCTTCAAGGCCCAGCTCAAGTC-CCAC 228 chr3qtel1M 507696 CTTTTCC 507702 ii L2d_3end#LINE 229 CTCCTCC 235 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 46.45 CpG sites = 24, Kimura (unadjusted) = 46.45 Transitions / transversions = 2.67 (24/9) Gap_init rate = 0.04 (4 / 102), avg. gap size = 1.50 (6 / 4) 359 34.80 7.41 3.24 chr3qtel1M 507899 508195 (491805) L2b_3end#LINE/L2 127 435 (31) m_b149s601i16 5583 chr3qtel1M 507899 GCTTTTGTACTGATCATGTCTCCTGTGCCTGAAAGGCTCTCCTCCTCACC 507948 i i ?-- vv ii v i v i -- i L2b_3end#LINE 127 GCCTTTGCACN--TGCTGTTCCCTCTGCCTGGAACGCCCT--TCCCCACC 172 chr3qtel1M 507949 TCTAC-TTTGTACCTTTCCTGACT--TCATGAAAGACTGAGCTCAAACCC 507995 v -ii vv vvi - -- v vv i v v ivi L2b_3end#LINE 173 TCTTCGCCTGGCCAACTCCT-ACTCATCCTTCAGGTCTCAGCTCAAATGT 221 chr3qtel1M 507996 AGTCTTCTACAGGAAGCTTTCCCTGAAACCCTCAACTACCT-ATGCCTTC 508044 vii i v i ii vv ivii iivv - v vii L2b_3end#LINE 222 CACCTCCTCCGGGAAGCCCTCCCTGACCCCCCAGGCCGGGTCAGGCGCCC 271 chr3qtel1M 508045 CTCTCTGAGGTTCCCTTCCATCCATGCTCTATGCCTCT--TCTATGAATT 508092 ii i --- ii vi v i i iivv --vi -? L2b_3end#LINE 272 TCCTCTGGG---CCCCCCCAGTCCTACCCTGCCACTCTGGGTTAT-NATT 317 chr3qtel1M 508093 GAGTTATTCACATTTCT-TCTCTCACACT-----------TTCTTGTGGG 508130 -vi i? i v - i v ----------- i v v L2b_3end#LINE 318 G-TCTGNTTACATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGG 366 chr3qtel1M 508131 AAGAGACTGAGT---TTTTGCCTTCCTTTTAATCCCTAACATTCAGCA-G 508176 v i i ? --- i iiiv vi vv i i iiii -i L2b_3end#LINE 367 CAGGGACCGNGTCTGTCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACA 416 chr3qtel1M 508177 GCACCTGGTATCCAGTAAG 508195 ?i i iv i L2b_3end#LINE 417 GNGCCTGGCACACAGTAGG 435 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 47.29 CpG sites = 60, Kimura (unadjusted) = 50.24 Transitions / transversions = 1.50 (60/40) Gap_init rate = 0.06 (18 / 296), avg. gap size = 1.78 (32 / 18) 182 23.65 2.63 5.41 chr3qtel1M 508340 508415 (491585) L3#LINE/CR1 4025 4098 (1) m_b149s601i17 5584 chr3qtel1M 508340 TTCCAACAGTTTGTTGGAATGT-GGACAAGACTGAAACCTGAGAGGTCTC 508388 vi - v v i v - v - -- vvi i L3#LINE/CR1 4025 TTCCTGCA-TTGGATGGGAGGTTGGACTAGA-TGA--CCTCTAAGGTCCC 4070 chr3qtel1M 508389 TTC-ATTTCTGAAGGTCTGTGATTCTGT 508415 - vi iiv i L3#LINE/CR1 4071 TTCCAACTCTGAGATTCTGTGATTCTAT 4098 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.52 CpG sites = 8, Kimura (unadjusted) = 28.52 Transitions / transversions = 0.89 (8/9) Gap_init rate = 0.08 (6 / 75), avg. gap size = 1.00 (6 / 6) 355 32.65 2.64 6.88 chr3qtel1M 509188 509414 (490586) L3#LINE/CR1 3712 3929 (170) m_b149s601i18 5585 chr3qtel1M 509188 GGAGGAATTGAG-AGGCTT--CCTGGAGACTGAGGAGTAGTAGGGAAGGA 509234 i i i - v i -- ------------ i - L3#LINE/CR1 3712 GAAGGAACTGGGGATGTTTAGCCTGGAGA------------AGAGAAG-A 3748 chr3qtel1M 509235 CTCAGGAGATACAGAACAAGTCTTCTTCTGGTATCAGAAGGACCAACAGG 509284 i ii v vi i - iiv vii iv i iiv v L3#LINE/CR1 3749 CTTAGAGGAGACATGATA-GCTGTCTTCAAATATTTGAAGGGCTGTCATG 3797 chr3qtel1M 509285 TGAAAGAGAGATTCGGGTT-TTTTGCCTGGTCCCCAAAGAG-AGAAGCAG 509332 i i v iv - i iv - i i i - vi L3#LINE/CR1 3798 TGGAAGAGGGATTAGACTTATTCTGTGTGG-CTCCAGAGGGCAGAACTAG 3846 chr3qtel1M 509333 GAGCAATGAGAGATTGTTACAGTGAGGACAATTAAGGCTAGATATCAAAA 509382 v i v ivv v vvi vv vi v ii L3#LINE/CR1 3847 GACCAATGGGTGGAAGTTACAGGGAGGCAGATTTCGGCTCAATATAAGGA 3896 chr3qtel1M 509383 ACAGCTTATTACTTATT-GAACAGTCTGGAAAT 509414 v i vi viv i- i v iii L3#LINE/CR1 3897 AGAACTTTCTAACAATCAGAGCTGTCCAAAAAT 3929 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.25 CpG sites = 41, Kimura (unadjusted) = 44.25 Transitions / transversions = 1.46 (41/28) Gap_init rate = 0.09 (20 / 226), avg. gap size = 1.05 (21 / 20) 13 9.26 0.00 0.00 chr3qtel1M 509608 509630 (490370) (GTTT)n#Simple_repeat 1 23 (0) m_b149s252i11 5586 chr3qtel1M 509608 GTTTTTTTGTTTGTTTATTTGTT 509630 v i (GTTT)n#Simpl 1 GTTTGTTTGTTTGTTTGTTTGTT 23 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 255 31.88 4.35 0.00 chr3qtel1M 511070 511138 (488862) C L2d2_3end#LINE/L2 (8) 547 476 m_b149s601i19 5587 chr3qtel1M 511070 AATCAAAAAGCATTTATCAAGTATTTACTATATGCAAGGCACAGTATTAA 511119 v ii ii iiii i i v ii i C L2d2_3end#LIN 547 AATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAG 498 chr3qtel1M 511120 GTCCC---GGGGGTGCAAGAAA 511138 iv i--- i i ii C L2d2_3end#LIN 497 GCGCTGTGGGGGATACAAAGAA 476 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.01 CpG sites = 19, Kimura (unadjusted) = 47.37 Transitions / transversions = 6.33 (19/3) Gap_init rate = 0.01 (1 / 68), avg. gap size = 3.00 (3 / 1) 256 28.95 10.84 6.36 chr3qtel1M 511510 511675 (488325) C MIRc#SINE/MIR (75) 193 21 m_b149s601i20 5588 chr3qtel1M 511510 TTCTCCCAATAA----GTGAGGAATAGAGAAAGGCCAGGACTGTCTCCCT 511555 i v i ---- -- - v i vi v i i ivi i C MIRc#SINE/MIR 193 TCCTCACAACAACCCTGTGAGG--TAG-GCAGGGCAGGTATTATTATCCC 147 chr3qtel1M 511556 CATT--AGAGATGAGGG---TG-GGAGCAAAGATTGTGG--AAGTGACTT 511597 -- v i--- - vv i ---- -- C MIRc#SINE/MIR 146 CATTTTACAGATGAGGAAACTGAGGCTCAGAGA----GGTTAAGTGACTT 101 chr3qtel1M 511598 TTCCAAACCTATA-----AGAAATTTGCAAAGCTGACCCATATTGGAGCC 511642 vi ivii i ----- v v v i i iv---- i v i C MIRc#SINE/MIR 100 GCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGG----ACTCGAACC 55 chr3qtel1M 511643 TAAGCCTTT-TGACTCTAAGACCAATCCTCCTTC 511675 i i i i- i v i v i C MIRc#SINE/MIR 54 CAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTC 21 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.94 CpG sites = 28, Kimura (unadjusted) = 38.03 Transitions / transversions = 1.65 (28/17) Gap_init rate = 0.11 (18 / 165), avg. gap size = 1.61 (29 / 18) 15 29.49 1.89 1.89 chr3qtel1M 512233 512285 (487715) (AT)n#Simple_repeat 1 53 (0) m_b149s252i12 5589 chr3qtel1M 512233 ATTTATCATATATACATGTATACATGTGTGTGTGTATATCT-TATTTGTA 512281 v - i i i i i i i i v - v i (AT)n#Simple_ 1 ATATAT-ATATATATATATATATATATATATATATATATATATATATATA 49 chr3qtel1M 512282 TATA 512285 (AT)n#Simple_ 50 TATA 53 Matrix = Unknown Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.00 (2 / 2) 324 28.92 6.90 1.64 chr3qtel1M 512303 512418 (487582) C L2b_3end#LINE/L2 (6) 460 339 m_b149s601i21 5587 chr3qtel1M 512303 TCATTCAA---ACATTTCCTAAAGAACTATTATGTGCCAGGTACTATGCT 512349 --- i v i iviv i i i? i C L2b_3end#LINE 460 TCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCT 411 chr3qtel1M 512350 AA----TAAAAAGAAAG-AATACAACAAGGGCAAAAATAGTCCTTTCCCT 512394 i---- iiii v v -ii i- i- i v?ii i v C L2b_3end#LINE 410 AGGCGCTGGGGATACAGCGGTG-AACAAGA-CAGACNCGGTCCCTGCCCT 363 chr3qtel1M 512395 CAAGGAGCACAAAATCTAATGGGG 512418 v v v i i C L2b_3end#LINE 362 CACGGAGCTCACAGTCTAGTGGGG 339 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.81 CpG sites = 23, Kimura (unadjusted) = 39.58 Transitions / transversions = 2.30 (23/10) Gap_init rate = 0.04 (5 / 115), avg. gap size = 2.00 (10 / 5) 40 2.61 0.00 0.00 chr3qtel1M 512463 512501 (487499) (TG)n#Simple_repeat 1 39 (0) c_b149s251i2 5590 chr3qtel1M 512463 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTTGTGT 512501 v (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 39 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 17 18.09 4.76 4.76 chr3qtel1M 512510 512572 (487428) (GAGG)n#Simple_repeat 1 63 (0) m_b149s252i13 5591 chr3qtel1M 512510 GATGGGGGGAGGGA-GG-GGGAGGGA-AAAATAAGGGAGGGAGGAAGAAG 512556 v i - - -ii ivi -- i (GAGG)n#Simpl 1 GAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGG--GAGG 48 chr3qtel1M 512557 GAGAGAGGGAGGAGAG 512572 i - (GAGG)n#Simpl 49 GAGGGAGGGAGG-GAG 63 Matrix = Unknown Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.10 (6 / 62), avg. gap size = 1.00 (6 / 6) 230 39.02 3.57 2.35 chr3qtel1M 512604 512771 (487229) C L2b_3end#LINE/L2 (213) 253 84 m_b149s601i22 5587 chr3qtel1M 512604 GAGGGCTTGGGAAGGGCTTCCTGTAAAAATTGGGATTT-AATTAGGACTT 512652 i v ii i i v ii iv iv - ii ii i C L2b_3end#LINE 253 GGGGGGTCAGGGAGGGCTTCCCGGAGGAGGTGACATTTGAGCTGAGACCT 204 chr3qtel1M 512653 TAAGAAAGCCTGAGAAGTCAGTAA---GAATGGACAGTGGAGAACTTTCC 512699 v i v vv - i ii iv --- vi iii v i ii v C L2b_3end#LINE 203 GAAGGATGAGT-AGGAGTTGGCCAGGCGAAGAGGTGGGGAAGGGCGTTCC 155 chr3qtel1M 512700 AAGCATGAAGAAAAGTCAGCACAAATACCCAAAGCCAAAACATGGAGGAT 512749 i viii v iv? ii vi vi v iii-- v? v? C L2b_3end#LINE 154 AGGCAGAGGGAACAGCANGTGCAAAGGCCCTGAGGCGGG--AGNGAGCNT 107 chr3qtel1M 512750 --CTTGTTTATCAAACAGCCAAGG 512771 -- v iivvi - C L2b_3end#LINE 106 GGCGTGTTCGAGGAACAG-CAAGG 84 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 56.45 CpG sites = 41, Kimura (unadjusted) = 61.21 Transitions / transversions = 1.78 (41/23) Gap_init rate = 0.04 (7 / 167), avg. gap size = 1.43 (10 / 7) 15 11.76 5.13 2.50 chr3qtel1M 513367 513405 (486595) (TTCTTAG)n#Simple_repeat 1 40 (0) m_b149s252i14 5592 chr3qtel1M 513367 TTCTTAGTT-TT-TTTCTTCCTTCTTCATTTCTTAGTTCTT 513405 - -v vv - v (TTCTTAG)n#Si 1 TTCTTAGTTCTTAGTTCTTAGTTCTT-AGTTCTTAGTTCTT 40 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.08 (3 / 38), avg. gap size = 1.00 (3 / 3) 12 29.46 4.76 4.76 chr3qtel1M 513424 513528 (486472) (TCTCCT)n#Simple_repeat 1 105 (0) m_b149s252i15 5593 chr3qtel1M 513424 TCTCCTTGCTTCTTCT-CTACATCC-TCTTACTGTTCTTC-CTTTC-CCT 513469 - i - v - - ivi v i - i - (TCTCCT)n#Sim 1 TCTCCTT-CTCCTTCTCCTTC-TCCTTCTCCTTCTCCTTCTCCTTCTCCT 48 chr3qtel1M 513470 ATTTTC-TCTAATTCCCTTTAACTTTCTCCTTCCTCTTCTCAAGCACTCC 513518 - i i - vv i i vv i ii --viv (TCTCCT)n#Sim 49 -TCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTC--CTTCTCC 95 chr3qtel1M 513519 TTCTCCTCCT 513528 i (TCTCCT)n#Sim 96 TTCTCCTTCT 105 Matrix = Unknown Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.10 (10 / 104), avg. gap size = 1.00 (10 / 10) 209 28.18 10.13 1.16 chr3qtel1M 515542 515620 (484380) L2d2_3end#LINE/L2 450 535 (20) m_b149s601i23 5594 chr3qtel1M 515542 TTAAAGG--GGGACTAT--CTTTTGCTCCTTTTGTATCCCT---AGTGCT 515584 i i -- i -- v i i - i--- i i L2d2_3end#LIN 450 TTGAGGGCAGGGACCATGTCTTATACTTCTTT-GTATCCCCCACAGCGCC 498 chr3qtel1M 515585 TAGCACAGTTTTTGGC-TATACTAGATGATTGATAGA 515620 vii v -i i v ii v ii i L2d2_3end#LIN 499 TAGCACAGTGCCTTGCACACAGTAGGCGCTCAATAAA 535 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.67 CpG sites = 17, Kimura (unadjusted) = 38.09 Transitions / transversions = 3.40 (17/5) Gap_init rate = 0.06 (5 / 78), avg. gap size = 1.80 (9 / 5) 222 28.57 3.17 0.00 chr3qtel1M 515558 515620 (484380) L2a_3end#LINE/L2 433 497 (20) m_b149s601i24 5594 chr3qtel1M 515558 TTTTGCTC-CTTTTGTATCCCTAGTGCTTAGCACAGTTTTTGGC-TATAC 515605 i - vi i i i v vii -i v L2a_3end#LINE 433 TTTTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACATAG 482 chr3qtel1M 515606 TAGATGATTGATAGA 515620 ii v ii i L2a_3end#LINE 483 TAGGCGCTCAATAAA 497 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.86 CpG sites = 13, Kimura (unadjusted) = 38.19 Transitions / transversions = 2.60 (13/5) Gap_init rate = 0.03 (2 / 62), avg. gap size = 1.00 (2 / 2) 302 25.97 1.30 0.00 chr3qtel1M 516005 516081 (483919) MIR1_Amn#SINE/MIR 82 159 (71) m_b149s601i25 5595 chr3qtel1M 516005 GTTCGCTTGGGGGTCT-GAACAAGTGATTTAATGTCCCTGAGCCTTATTT 516053 ii? v? v ii - ii v i ? iv i ? i v MIR1_Amn#SINE 82 GCCNGCTGNGTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTT 131 chr3qtel1M 516054 TAATCATCTGTAAAGTGGGAATAATAAT 516081 vv i i i MIR1_Amn#SINE 132 TCCTCATCTGTAAAATGGGGATAATGAT 159 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.40 CpG sites = 13, Kimura (unadjusted) = 35.40 Transitions / transversions = 1.86 (13/7) Gap_init rate = 0.01 (1 / 76), avg. gap size = 1.00 (1 / 1) 477 21.85 3.33 0.81 chr3qtel1M 516020 516139 (483861) MIRc#SINE/MIR 96 218 (50) m_b149s601i26 5595 chr3qtel1M 516020 TGAACAAGTGATTTAATGTCCCTGAGCCTTATTTTAATCATCTGTAAAGT 516069 ii v i iv i i v vv i MIRc#SINE/MIR 96 TGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAAT 145 chr3qtel1M 516070 GGGAATAATAATCCCCTG--CTATCTACTTCACTGGGTTGGTTTGAGGAA 516117 i -v -- ii i v v v v MIRc#SINE/MIR 146 GGGGATAATAAT-ACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGAT 194 chr3qtel1M 516118 TATAGGATATAA-GTCTG-GAAAG 516139 i v v v - v - MIRc#SINE/MIR 195 CAAATGAGATAATGTATGTGAAAG 218 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.94 CpG sites = 12, Kimura (unadjusted) = 25.94 Transitions / transversions = 0.86 (12/14) Gap_init rate = 0.03 (4 / 119), avg. gap size = 1.25 (5 / 4) 521 24.47 21.28 0.00 chr3qtel1M 516165 516352 (483648) C MIRb#SINE/MIR (14) 254 27 m_b149s601i27 5596 chr3qtel1M 516165 CAATTATTAAGCACCTACAATATGCCAGACACT------------TTACA 516202 v i i i v i i ------------ C MIRb#SINE/MIR 254 CATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACA 205 chr3qtel1M 516203 AAAATCATCTCATTGGACTCTCACAACAGCTCTGGGAGGT---------- 516242 viv i vi ii i i v ---------- C MIRb#SINE/MIR 204 TGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATT 155 chr3qtel1M 516243 ----CCATTTAATAG-TTAGGAAATTGAA--TCAGACAGAAACAGTGACT 516285 ---- v i - v i i-- v ivvv i C MIRb#SINE/MIR 154 ATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACT 105 chr3qtel1M 516286 TGCCCAGTATCACAGAGCTAGGAAGTGGT----------TTGGAATTCAG 516325 ivi v v i---------- v ii C MIRb#SINE/MIR 104 TGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAG 55 chr3qtel1M 516326 GACTTCCTGAATCT-AAGCCCAGCCTCT 516352 v vi v i- ivv C MIRb#SINE/MIR 54 GTCTGTCTGACTCCAAAGCCCGTGCTCT 27 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.52 CpG sites = 25, Kimura (unadjusted) = 30.03 Transitions / transversions = 1.19 (25/21) Gap_init rate = 0.04 (7 / 187), avg. gap size = 5.71 (40 / 7) 734 17.17 15.51 2.54 chr3qtel1M 516544 516788 (483212) C Charlie1a#DNA/hAT-Charlie (154) 1301 1026 m_b149s502i0 5597 chr3qtel1M 516544 TTTGAAAAGAATATTTAATCCATTACATAATATCACAAATAACA---TTT 516590 i v v v i iv v i --- C Charlie1a#DNA 1301 TTTAAAAATAATAATAAACCCATTACATGTTAACATAAATAACATATTTT 1252 chr3qtel1M 516591 TATAATTATAAAATGATTCTATTTTC--AAAAAAAAAAGT-------GAA 516631 i ---- i i v -- v i ------- C Charlie1a#DNA 1251 TATGA----AAAATAACTATATTTTCCAAAACAAAAAAATTTAGTGAGAA 1206 chr3qtel1M 516632 ATGTGGCATTATTTTGCATATTTTTTTCAAACCAC-TAAAGGCCTGGC-- 516678 iv i i --- v i v - v v i -- C Charlie1a#DNA 1205 GAGTGGCATTGTTTTACA---TTTTTGCAAATCTCTTTAATGTCTGGCTT 1159 chr3qtel1M 516679 --TGCAAAATAACTAGACTTTCATATCTG--TCTGCATCCAATCT----- 516719 -- iv i i i i i i -- i ----- C Charlie1a#DNA 1158 AATAGAAGACAGCTGGATTCTCATATCTGCTTCTGCATTCAATCTGTTGC 1109 chr3qtel1M 516720 --------------GTTGAAGTATATGAAGAAAATCTGGCCTCAGACAGA 516755 -------------- i v C Charlie1a#DNA 1108 GATATGTTGTTTTGGTTGAAGTATATGAAGAAAATCCGGCCTCACACAGA 1059 chr3qtel1M 516756 TATGTAGTTCAAAAAGGGAAGAATAATTTAATA 516788 vi i i v C Charlie1a#DNA 1058 TATGTAGTTGGAAAAGGGAGGAGTATTTTAATA 1026 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 19.33 CpG sites = 25, Kimura (unadjusted) = 19.85 Transitions / transversions = 1.56 (25/16) Gap_init rate = 0.06 (15 / 244), avg. gap size = 3.00 (45 / 15) 516 25.20 2.48 1.64 chr3qtel1M 516837 516957 (483043) L2d_3end#LINE/L2 393 514 (2) m_b149s601i28 5598 chr3qtel1M 516837 TAGATTGTAAACTCTCTGAGGGTAGAGACAATCTTTCACCTCCTTTTTCT 516886 i ii i i v v i i ivii? ?ii L2d_3end#LINE 393 TAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACTNTTTTNTC 442 chr3qtel1M 516887 GTGCCT---AGTGTTTAGCATAGTGCTTAGTCCACATACGAGGCACTTAA 516933 v i--- i ii i v -- vv i i L2d_3end#LINE 443 GTTCCCCACAGCGCCTAGCACAGTGCTGAG--CACATAGTAGGCGCTCAA 490 chr3qtel1M 516934 TAAATATTTATTGATTGACTGACT 516957 i i i i L2d_3end#LINE 491 TAAATACTTGTTGATTGATTGATT 514 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.30 CpG sites = 23, Kimura (unadjusted) = 33.35 Transitions / transversions = 3.29 (23/7) Gap_init rate = 0.03 (3 / 120), avg. gap size = 1.67 (5 / 3) 12 25.32 2.38 0.00 chr3qtel1M 517037 517078 (482922) (TTAA)n#Simple_repeat 1 43 (0) m_b149s252i16 5599 chr3qtel1M 517037 TTGATT-ATTAATTTATTGGAGAGTAAATTAATTAATTAAGTA 517078 i - v iivv i v v (TTAA)n#Simpl 1 TTAATTAATTAATTAATTAATTAATTAATTAATTAATTAATTA 43 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.02 (1 / 41), avg. gap size = 1.00 (1 / 1) 24 28.25 2.60 0.00 chr3qtel1M 517317 517393 (482607) (CT)n#Simple_repeat 1 79 (0) m_b149s252i17 5600 chr3qtel1M 517317 CTCTCTCTGTGTCTGTCTCCCTCCCTCTCCATCT-TCCCTCCCTCTGTCC 517365 v v v i i iv - i i v i (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chr3qtel1M 517366 ATATCACAC-CCCCCCCTCTCTCTCTCTC 517393 v v v v - i i i (CT)n#Simple_ 51 CTCTCTCTCTCTCTCTCTCTCTCTCTCTC 79 Matrix = Unknown Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.03 (2 / 76), avg. gap size = 1.00 (2 / 2) 18 0.00 0.00 0.00 chr3qtel1M 517393 517412 (482588) (CA)n#Simple_repeat 1 20 (0) m_b149s252i18 5601 chr3qtel1M 517393 CACACACACACACACACACA 517412 (CA)n#Simple_ 1 CACACACACACACACACACA 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 12 20.44 2.44 2.44 chr3qtel1M 519194 519234 (480766) (TTATTTG)n#Simple_repeat 1 41 (0) m_b150s252i0 5602 chr3qtel1M 519194 TTATTGGCTATTTGATATCT-TTATGTGTTTTTTTTTTATTT 519234 v i v i - v - v v (TTATTTG)n#Si 1 TTATTTGTTATTTGTTATTTGTTATTTG-TTATTTGTTATTT 41 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 17 17.30 5.13 0.00 chr3qtel1M 519359 519397 (480603) (TA)n#Simple_repeat 1 41 (0) m_b150s252i1 5603 chr3qtel1M 519359 TAGATAT-TAAATATATTCAAATATAAAT-TATATATATAT 519397 v - v vi v v - (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATAT 41 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2) 339 29.99 2.68 1.77 chr3qtel1M 520700 520811 (479189) HERV4_I#LTR/ERV1 3242 3354 (3185) m_b150s701i0 5604 chr3qtel1M 520700 CAAGTGTCCCAGGGGACACAA---GGCTTTCTATCTTAGATCTTAAAGAT 520746 i -- ii --- i i vi i i v HERV4_I#LTR/E 3242 CAGGTG--CCAGGGGATGCAAAATGGTTCTCAGTCCTAGACCTAAAAGAT 3289 chr3qtel1M 520747 GCTTTCCTTTGCATACTACTGAATTAAGATTCATAATTTTGTTTTGCCCT 520796 i i v v iv iviiv v vi viiv i HERV4_I#LTR/E 3290 GCTTTCTTCTCCATTCCTCTGGCCCCAGAGTCCCAATACCTTTTTGCCTT 3339 chr3qtel1M 520797 CGAAGGGACAAATCC 520811 i v iv HERV4_I#LTR/E 3340 TGAATGGGAAAATCC 3354 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 39.61 CpG sites = 20, Kimura (unadjusted) = 39.61 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.03 (3 / 111), avg. gap size = 1.67 (5 / 3) 25 7.32 4.65 0.00 chr3qtel1M 520929 520971 (479029) (TTTGT)n#Simple_repeat 1 45 (0) m_b150s252i2 5605 chr3qtel1M 520929 TTTGTTTT-TTGGGTTTTG-TTTGTTTTGTTTTGTTTTGTCTTGT 520971 - vv - i (TTTGT)n#Simp 1 TTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGT 45 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.00 (2 / 2) 392 25.95 0.76 0.00 chr3qtel1M 521268 521398 (478602) PABL_B-int#LTR/ERV1 4029 4160 (2962) m_b150s701i1 5604 chr3qtel1M 521268 TTGCCCTCAC-AGAGTTTTAAAATTGGGGAAAGGAATGACAGTGAACATC 521316 i ? - ii ?v i vvvv ? v v? i? i PABL_B-int#LT 4029 TCGCCCTNACCAGAGCCTTNCAACTGTCCCAAGGNAAGAGNGCNAACATT 4078 chr3qtel1M 521317 TACACTGACTCGAAATATGTTTTTCATATTTTTCACACTTATGGGGCCCT 521366 v i i? i?vvi vv ? ii ?i i ?v PABL_B-int#LT 4079 TACACTGACTCCAAGTATGCNTTCNTGGTAGTNCATGCNCACGGGGCNAT 4128 chr3qtel1M 521367 ATGAAAAGAAAGGAGACTTTTGACAACAAAAA 521398 v i i i ?i i ??? ?i ? PABL_B-int#LT 4129 CTGGAAAGAAAGGGGGCTNCTAANNNCNGANA 4160 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.81 CpG sites = 20, Kimura (unadjusted) = 38.68 Transitions / transversions = 1.43 (20/14) Gap_init rate = 0.01 (1 / 130), avg. gap size = 1.00 (1 / 1) 342 27.97 3.42 2.03 chr3qtel1M 521270 521415 (478585) HUERS-P3#LTR/ERV1 5009 5156 (3763) m_b150s701i2 5604 chr3qtel1M 521270 GCCCTCACA-GAGTTTTAAAATTGGGGAAAGGAATGACAGTGAACATCTA 521318 i i - ivi vi ii v i v ii iv i HUERS-P3#LTR/ 5009 GCTCTTACAAGAGCACTTGAATTAAGCAAGGGAAAGGTAGCTAACATTTA 5058 chr3qtel1M 521319 CACTGACTCGAAATATGTTTTTCATA-TTTTTCACACTTATGGGGCCCTA 521367 v i -i v - i i ii i vv v v HUERS-P3#LTR/ 5059 CACTGACTCCAAGTATG-CTTTCTTAGTTCTCCATGCTCATGCTGCCATT 5107 chr3qtel1M 521368 TGAAAAGAAAGGAGACTTT-TGACAACAAA--AATCATCCTATTAAATGT 521414 i i - v i - v v v --i - v i HUERS-P3#LTR/ 5108 TGGAAGGAAA-GACATTTTCTTACCACTAATGGATC-TCCTATAAAATAT 5155 chr3qtel1M 521415 C 521415 HUERS-P3#LTR/ 5156 C 5156 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 36.00 CpG sites = 24, Kimura (unadjusted) = 36.00 Transitions / transversions = 1.50 (24/16) Gap_init rate = 0.05 (7 / 145), avg. gap size = 1.14 (8 / 7) 409 25.96 0.95 0.95 chr3qtel1M 521289 521393 (478607) HERV15#LTR/ERV1 4788 4892 (3859) m_b150s701i3 5604 chr3qtel1M 521289 ATTGGGGAAAGGAATGACAGTGAACATCTACACTGACTCGAAATATGTTT 521338 vv i i v v i v i i i i HERV15#LTR/ER 4788 ATTGGCCAAGGGGAAGAAAGTAAACATATATACTGACTCAAGATATGCTT 4837 chr3qtel1M 521339 TT-CATATTTTTCACACTTATGGGGCCCTATGAAAAGAAAGGAGACTTTT 521387 - - iii v i ii vv iv i ii HERV15#LTR/ER 4838 TTGCA-ACCCTGCACGCCCATGGGGCAATATACAAAGAGAGAGGACTTTT 4886 chr3qtel1M 521388 GACAAC 521393 v HERV15#LTR/ER 4887 GACTAC 4892 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 31.36 CpG sites = 17, Kimura (unadjusted) = 32.84 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.02 (2 / 104), avg. gap size = 1.00 (2 / 2) 544 32.81 3.36 4.00 chr3qtel1M 522805 523131 (476869) L1ME5_3end#LINE/L1 313 637 (304) m_b150s551i0 5606 chr3qtel1M 522805 TCCTGGAGAGAAATTTGGAACTA--TGCTCAAA--AAGTTATCAAACTGT 522850 i v i v v -- iv -- - --- --- L1ME5_3end#LI 313 TTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTAAGT-AT---AC--- 355 chr3qtel1M 522851 GCATACCCTTTGACCCAGCAGTGCTACTACTGGGCTTATATCCTAAAGAG 522900 v i v ii v iv i i L1ME5_3end#LI 356 GCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATATCCCAAAGAA 405 chr3qtel1M 522901 ATCTTAAAGAAGG-----GAAAGGACCTGTATGTGCCAAAATGCTTGTGG 522945 ii v viv -----i ii v i ---- ii i ii v L1ME5_3end#LI 406 ATTCTCACACAGGTCCATAAGGGGACATGTACG----AGGATGTTCATTG 451 chr3qtel1M 522946 CAGGCCTCTTTGTAGTATCCAGAAACTGGAAACTGAGTGGATTCCCATCA 522995 vvi v i iv vi i ii ii vivv i vi L1ME5_3end#LI 452 CAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGGGTGTCCATCA 501 chr3qtel1M 522996 ATTGGAGAATGGCTGAATAAATTGTGGTATATGAATATTATGGAATATTA 523045 v v i v iii v iv v i ii i i L1ME5_3end#LI 502 CTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACACCATGGAGTACTA 551 chr3qtel1M 523046 TTCTTCTCTAAGAAACGACCAGCAGAATGAATAGAGAGAGGCTTGAAGAG 523095 v vv vv v i i vii vii v i v v vii v i vi L1ME5_3end#LI 552 TGCAGCAGTTAGAAGCAACGGACTAGATGTACACATAGCAACATGGATGG 601 chr3qtel1M 523096 A-CTTACATGAAC-TGATGCTGAGTGAAATGAGCAGGA 523131 - v -- - ii vi i i L1ME5_3end#LI 602 ATCTTAAA--AACATAGTGCTGAGTGAAAAAAGTAAGA 637 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 43.26 CpG sites = 59, Kimura (unadjusted) = 44.50 Transitions / transversions = 1.34 (59/44) Gap_init rate = 0.06 (18 / 326), avg. gap size = 1.33 (24 / 18) 735 25.64 1.26 2.11 chr3qtel1M 522808 523046 (476954) L1ME3G_3end#LINE/L1 312 548 (376) m_b150s551i1 5606 chr3qtel1M 522808 TGGAGAGAAATTTGGAACTATGCTCAAAAAGTTATCAAACTGTGCATACC 522857 i v v v - vvv i --i v i L1ME3G_3end#L 312 TGGAGGGCAATTTGGCAGTAT-CTATTAAAATT--TAAAATGCGCATACC 358 chr3qtel1M 522858 CTTTGACCCAGCAGTGCTACTACTGGGCTTATATCCTAAAGAGAT-CTTA 522906 i v i v ? ?v v ? i - ii L1ME3G_3end#L 359 CTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAGAAATACTCG 408 chr3qtel1M 522907 AAGAAGGGAA--AGGACCTGTATGTGCCAAAATGCTTGTGGCAGGCCTCT 522954 v v v v v -- ?-- i i v ii i ii v vvi v L1ME3G_3end#L 409 CACATGTGCACAAGGAN--GCATGTACAAGGATGTTCATTGCAGCATTGT 456 chr3qtel1M 522955 TTGTAGTATCCAGAAACTGGAAACTGAGTGGATTCCCATCAATTGGAGAA 523004 i v v i i vivv ii vi v i L1ME3G_3end#L 457 TTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCAATAGGGGAA 506 chr3qtel1M 523005 TGGCTGAATAAATTGTGGTATATGAATATTATGGAATATTAT 523046 i i i vv i i L1ME3G_3end#L 507 TGGTTAAATAAATTATGGTATATCCATACTATGGAATACTAT 548 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 31.04 CpG sites = 30, Kimura (unadjusted) = 32.38 Transitions / transversions = 1.00 (30/30) Gap_init rate = 0.03 (7 / 238), avg. gap size = 1.14 (8 / 7) 265 22.53 1.39 1.39 chr3qtel1M 523605 523676 (476324) HERV30#LTR/ERV1 7963 8034 (223) m_b150s701i4 5607 chr3qtel1M 523605 TTTGCTC-CTATTGGGCCCCTGCATTTTTAACCTACTTTTGAGATTTGTT 523653 i - iv i- v v v i HERV30#LTR/ER 7963 TTTACTCGCCTTTGGGCCT-TGCATTTTTAACCTCCTTGTCAAATTTGTT 8011 chr3qtel1M 523654 TCCTTCAGGCTTCAAGTTATGAA 523676 i v iv i ii v HERV30#LTR/ER 8012 TCCTCCAGGATCGAGGCCATCAA 8034 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 25.27 CpG sites = 9, Kimura (unadjusted) = 27.19 Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.03 (2 / 71), avg. gap size = 1.00 (2 / 2) 303 25.10 1.11 7.06 chr3qtel1M 523773 523862 (476138) HERV4_I#LTR/ERV1 6422 6506 (33) m_b150s701i5 5608 chr3qtel1M 523773 GACCCCTAGTAAGTAGGGATAGCTCTATGCCCTTTATCAGCATGAAGCAG 523822 i i i i ----- i ivvi HERV4_I#LTR/E 6422 GATCCCCAATAGGTAGGGA-----CTACGCCCCAAGTCAGCATGAAGCAG 6466 chr3qtel1M 523823 CTTCAGAAGATGAGATC-TCCATCCCTTTGTTCCAAATAAA 523862 i v -i i - vi i iii vv HERV4_I#LTR/E 6467 TTACAGAAGA-AAGACCATCGGTCCCTCTGCCTCCCATAAA 6506 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 29.99 CpG sites = 15, Kimura (unadjusted) = 31.83 Transitions / transversions = 2.50 (15/6) Gap_init rate = 0.08 (7 / 89), avg. gap size = 1.00 (7 / 7) 328 22.25 0.00 3.17 chr3qtel1M 523782 523846 (476154) MER83A-int#LTR/ERV1 4163 4225 (41) m_b150s701i6 5608 chr3qtel1M 523782 TAAGTAGGGATAGCTCTATGCCCTTTATCAGCATGAAGCAGCTTCAGAAG 523831 i vi i i i vi v i --i MER83A-int#LT 4163 TAGGTAGGGCCAACTCTACGCCCCTGGTCAGCAGGAAGCAGTT--GGAAG 4210 chr3qtel1M 523832 ATGAGATCTCCATCC 523846 i i i MER83A-int#LT 4211 ATGAGACCTTCACCC 4225 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 25.47 CpG sites = 11, Kimura (unadjusted) = 27.78 Transitions / transversions = 3.67 (11/3) Gap_init rate = 0.03 (2 / 64), avg. gap size = 1.00 (2 / 2) 304 21.89 1.09 5.68 chr3qtel1M 523802 523893 (476107) HERV35I#LTR/ERV1 6831 6918 (0) m_b150s701i7 5608 chr3qtel1M 523802 CCCTTTATCAGCATGAAGCAGCTTCAGAAGATGAGATCTCCATCCCTTTG 523851 v - v i i iv v HERV35I#LTR/E 6831 CCCTGT-TCAGCAGGAAGTAGCTTCAGAAGATGAGATCTTCGGCCCTTTC 6879 chr3qtel1M 523852 TTCCAAATAA-AATTGGGGTACAAACTGCTTGAGAGGGGGAAA 523893 i iv v - vvi iv v - i--- i HERV35I#LTR/E 6880 TCCTTAAGAATAAGGAGGGTGAAATCT-CTC---AGGGGGGAA 6918 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 24.45 CpG sites = 9, Kimura (unadjusted) = 25.95 Transitions / transversions = 0.90 (9/10) Gap_init rate = 0.07 (6 / 91), avg. gap size = 1.00 (6 / 6) 13 21.93 4.65 0.00 chr3qtel1M 524539 524581 (475419) (AACATA)n#Simple_repeat 1 45 (0) m_b150s252i3 5609 chr3qtel1M 524539 AACATTAACAGAAAC-TAAAAAAAAACA-AAAAATTAAAAGAAAC 524581 v v - v v - v v v v (AACATA)n#Sim 1 AACATAAACATAAACATAAACATAAACATAAACATAAACATAAAC 45 Matrix = Unknown Transitions / transversions = 0.00 (0/8) Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.00 (2 / 2) 440 25.94 0.81 5.98 chr3qtel1M 525068 525190 (474810) C MIRc#SINE/MIR (141) 127 11 m_b150s601i0 5610 chr3qtel1M 525068 CTGAGGC-AATTGGGATTAAGTGACTTGCCCAGGGTCATATAGCTAGGAA 525116 -v vv i i i i i v C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAA 78 chr3qtel1M 525117 GTATTAAGGGTCTGAGGTCAAATCTGAACTCAGGTCTTCCCGACTTCAGG 525166 ivi ii -- i i ----- iii i i i i C MIRc#SINE/MIR 77 GTGGCAGAG--CCGGG-----ACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr3qtel1M 525167 GTTGGTGCTCTATCCACTGTGCCA 525190 viii v ii C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTGCACCA 11 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 30.96 CpG sites = 23, Kimura (unadjusted) = 33.74 Transitions / transversions = 3.29 (23/7) Gap_init rate = 0.07 (8 / 122), avg. gap size = 1.00 (8 / 8) 281 27.60 4.97 7.95 chr3qtel1M 525636 525816 (474184) L1MC5_3end#LINE/L1 357 532 (2162) m_b150s551i2 5611 chr3qtel1M 525636 TTTACTCTGCCATCTTGACTCTGCC-TCCC-CTACTTGG--TCTATTTCT 525681 i ------ i v v- - v v -- ii - L1MC5_3end#LI 357 TTTACCCT------TTGACCCAGCAATCCCACTTCTAGGAATCTATCCC- 399 chr3qtel1M 525682 AAAAGATG-ATTAGAAGAAATG-GAAAAGAGCCCATG---GGGGCTAAAA 525726 - i- i i v i i- - vi ---ii --- L1MC5_3end#LI 400 -AAAGATACACTGGCAAAAATACGAAAAGA-CGTATGCACAAGGCTA--- 444 chr3qtel1M 525727 TTTTATAGCAGCCTTCCTTGTGGGGGGCAAAGAACTGGAAATTATAGAGA 525776 - i v vi vi iivi - ii iv ivv i L1MC5_3end#LI 445 -TTCATTGCAGCACTATTTGTAATAG-CAAAAGACTGGAAACAACCCAAA 492 chr3qtel1M 525777 TGCCCATCAATTTGGGAATGGATGAACAAGTTATGATATA 525816 i vv v v i ii i i L1MC5_3end#LI 493 TGTCCATCAATAGGGGACTGGTTGAATAAACTATGGTACA 532 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.50 CpG sites = 29, Kimura (unadjusted) = 35.50 Transitions / transversions = 1.71 (29/17) Gap_init rate = 0.11 (20 / 180), avg. gap size = 1.15 (23 / 20) 317 30.94 0.93 4.85 chr3qtel1M 525728 525941 (474059) L1ME1_3end#LINE/L1 445 650 (276) m_b150s551i3 5611 chr3qtel1M 525728 TTTATAGCAGCCTTCCTTGTGGGGGGCAAAGAACTGGAAATTATAGAGAT 525777 i i vi i iivi v - iv ivv i L1ME1_3end#LI 445 TTCATAGCAGCTTTATTCGTAATAGCCAAA-AACTGGAAACAACCCAAAT 493 chr3qtel1M 525778 GCCCATCAATTTGGGAATGGATGAACAAGTTATGATATAGGATTATGACA 525827 i i?v v i i i i vvvv ii ii L1ME1_3end#LI 494 GTCCATCAACNGGTGAATGGATAAACAAATTGTGGTATATCCATACAATG 543 chr3qtel1M 525828 GGATGCTACTGTGCTATAAGAAATGATGAGCTCAGTGATTTAAAAAAAAA 525877 i i vv v i ivi i i - v ------- v v L1ME1_3end#LI 544 GAATACTACTCAGCAATAAAAAGGAACGAACT-ACTGAT-------ACAC 585 chr3qtel1M 525878 AAAAAAACATGCATAGACTTACACAAA-ATAATGAAGAGTGAAATAA-CC 525925 iv v v ii ii - v ?- v vv v - L1ME1_3end#LI 586 GCAACAACATGGATGAATCT-CAAAANCATTATGCTGAGTGAAAGAAGCC 634 chr3qtel1M 525926 AGAACCTAGAGAATAC 525941 vv v i ? L1ME1_3end#LI 635 AGACACAAAAGANTAC 650 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 38.82 CpG sites = 33, Kimura (unadjusted) = 41.33 Transitions / transversions = 1.10 (33/30) Gap_init rate = 0.06 (12 / 213), avg. gap size = 1.00 (12 / 12) 19 27.87 5.00 1.20 chr3qtel1M 526051 526130 (473870) (AT)n#Simple_repeat 1 83 (0) m_b150s252i4 5612 chr3qtel1M 526051 ATATCTGATAAATA-ACAT-TATAGA-ATAATTTTACACACATACACATA 526097 v - v - i - v - vv v i i i i i (AT)n#Simple_ 1 ATATAT-ATATATATATATATATATATATATATATATATATATATATATA 49 chr3qtel1M 526098 CATATATATACAT-TATATACATATTTGTATCTA 526130 i i - i v i v (AT)n#Simple_ 50 TATATATATATATATATATATATATATATATATA 83 Matrix = Unknown Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.06 (5 / 79), avg. gap size = 1.00 (5 / 5) 15 12.16 0.00 0.00 chr3qtel1M 526846 526872 (473128) (TTCA)n#Simple_repeat 1 27 (0) m_b150s252i5 5613 chr3qtel1M 526846 TTTATTCATTCATTCATTGATCCATTC 526872 i v i (TTCA)n#Simpl 1 TTCATTCATTCATTCATTCATTCATTC 27 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 33 0.00 0.00 0.00 chr3qtel1M 526873 526900 (473100) (GT)n#Simple_repeat 1 28 (0) c_b150s251i0 5614 chr3qtel1M 526873 GTGTGTGTGTGTGTGTGTGTGTGTGTGT 526900 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGT 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 315 28.65 7.63 1.44 chr3qtel1M 526992 527122 (472878) C L2a_3end#LINE/L2 (10) 507 369 m_b150s601i1 5615 chr3qtel1M 526992 TCGATAAACATATATTAAGTGCTGACTATGTATCATGCACTTTGCTAAGT 527041 i i i v i i iv ii v v v i i C L2a_3end#LINE 507 TCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGC 458 chr3qtel1M 527042 GCTAGAGATAC--CAA-GAGGA----AGATAATCGTACCTACTCTCA--- 527081 i i -- i- iv ---- i vv v i i --- C L2a_3end#LINE 457 GCTGGGGATACAGCAGTGAACAAAACAGACAAAAGTCCCTGCCCTCATGG 408 chr3qtel1M 527082 AGTTCCCAATCTAATAGGGAGAGCACATGGAAACAAACAGA 527122 i iv v i i i - - iv i i C L2a_3end#LINE 407 AGCTTACATTCTAGTGGGGGGAG-ACA-GACAATAAACAAA 369 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 35.29 CpG sites = 25, Kimura (unadjusted) = 37.90 Transitions / transversions = 2.08 (25/12) Gap_init rate = 0.05 (6 / 130), avg. gap size = 2.00 (12 / 6) 230 25.40 1.59 0.00 chr3qtel1M 528184 528246 (471754) L1ME3G_3end#LINE/L1 485 548 (376) m_b150s551i4 5616 chr3qtel1M 528184 TGAATGCCCATCAGTTGAAGGATGGCTGAATAAATTAT-GTATACAAATG 528232 i i i v ii i i i - ivv i L1ME3G_3end#L 485 TAAATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCATA 534 chr3qtel1M 528233 TTATTGAATATTAT 528246 i v i L1ME3G_3end#L 535 CTATGGAATACTAT 548 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 32.78 CpG sites = 12, Kimura (unadjusted) = 32.78 Transitions / transversions = 3.00 (12/4) Gap_init rate = 0.02 (1 / 62), avg. gap size = 1.00 (1 / 1) 2833 29.74 4.07 1.24 chr3qtel1M 528817 530389 (469611) L1M5_orf2#LINE/L1 828 2444 (850) m_b150s551i5 5617 chr3qtel1M 528817 GAATAACAATGAGA---CAACATACCAAAATTTATAGGATGCAGCCAAAG 528863 i ? i --- i i i i L1M5_orf2#LIN 828 GAATGANAATGAAAATACAACATATCAAAATTTGTGGGATGCAGCTAAAG 877 chr3qtel1M 528864 CAGTTCTTAG-GGGAAATGTTATCTCTCTAGATGTTTACAT--GAATAAA 528910 v - - vv ?i i i? i -- v i L1M5_orf2#LIN 878 CAGTGCTTAGAGGGAAAT-TTATAGCNTTAAATGCNTATATTAGAAAAGA 926 chr3qtel1M 528911 ATAAAGAG--AAGATCAATGAATTGGACATGCAACTAAAAAATCTAAAAA 528958 v iv-- i vi iii v v v v i v i L1M5_orf2#LIN 927 AGAAAGGCTTAAAATCAATGATCTAAGCTTCCACCTTAAGAAGCTAGAAA 976 chr3qtel1M 528959 AAAAATA-CAAATTAAAAACACCCAA-TTAAATACAAAATTTGAAATTCT 529006 i v - ---- -v? i v iivvv vv L1M5_orf2#LIN 977 AAGAAGAGCAAATTAAA----CCCAAAGNAAGTAGAAGGAAGGAAATAAT 1022 chr3qtel1M 529007 GAAAATAAAAGAAGAGATTAACAAAACTGAAA----------------GA 529040 i i i v i i ii iv ---------------- L1M5_orf2#LIN 1023 AAAGATAAGAGCAGAAATCAATGAAATAGAAAACAAANANACAATAGAGA 1072 chr3qtel1M 529041 AAGC--ATGGAATTAAAAGTTGATTTTAATGAAAAAACTCTAGTTTATTT 529088 ii-- i i iii i i i v- i - - i vv v L1M5_orf2#LIN 1073 AAATCAACGAAGCCAAAAGCTGGTTCTT-TGAAAAGA-TC-AATAAAATT 1119 chr3qtel1M 529089 GGTTA---TTTAACT----TGATTAGAAAAGGAAAGAAGAAAAT-CAAGT 529130 i v --- i i ?---- i ii ii iii i i- i L1M5_orf2#LIN 1120 GATAAACCTCTAGCNAGACTGATCAAGAAAAAAAGAGAGAAGACACAAAT 1169 chr3qtel1M 529131 TATCAATATCAAAAATGAAAAGGGTAAAC-TTACCACCAATGA-AGAGAA 529178 i ii i - i - i i vi vv- v v L1M5_orf2#LIN 1170 TACCAATATCAGGAATGAAAAAGG-AGACATCACTACAGATCCTACAGAC 1218 chr3qtel1M 529179 AATTAAAGTAATACTTAGGAGCTCTTTTGCCCAACTCTATGCTAATAAAT 529228 - ivi v v iiiv v v vv i i L1M5_orf2#LIN 1219 A-TTAAAAGGATAATAAGAGAATATTATGAACAACTTTATGCCAATAAAT 1267 chr3qtel1M 529229 CAGATAATCTAAGTAAAATGAATGAACACTTACAAAAACATAAATTAGCC 529278 iv ? ii ii i i ii iv i vv i ? v v L1M5_orf2#LIN 1268 TTGANAACTTAGATGAAATGGACAAATTCCTTGAAAAACACAANTTACCA 1317 chr3qtel1M 529279 AGGTTAGCAGAGGAGGAAATACATTACTTAAATAGTCCCAT-TTTAGAAA 529327 iii ii ?v i i v vv ii i i i - i vv L1M5_orf2#LIN 1318 AAACTGACNCAAGAAGAAATAGAAAATCTGAATAGCCCTATATCTATTAA 1367 chr3qtel1M 529328 AAGAAATTGAACAGGTCATTAATGAACTCCCTAAGAAAAAATCTCCAGGG 529377 - ivv v vi v i i vi i v v L1M5_orf2#LIN 1368 A-GAAATTGAATTTGTAATTAAAAACCTTCCCACAAAGAAAACTCCAGGC 1416 chr3qtel1M 529378 CCAGATGAATTTACAAGTGAATTGTACCAAACATTTTAA----AAACAAT 529423 iv i vi v v i---- i L1M5_orf2#LIN 1417 CCAGATGGCTTCACTGGTGAATTCTACCAAACATTTAAGGAAGAAATAAT 1466 chr3qtel1M 529424 TCCAATATTATATAAGCTATTTGGGAACACAGGGGAAGAAGGAGTTCTAT 529473 v v i i i v ivi v i iii i iiv vi L1M5_orf2#LIN 1467 ACCAATCTTACACAAACTCTTCCAGAAAATAGAAAAAGAGGGAACACTTC 1516 chr3qtel1M 529474 GAAATTCCTTTTGTGACACAAATATGGTGCAAATATCTGAAACAGGAAAG 529523 vv i v i vi v ii ?iiv vi i vi v ? iv i L1M5_orf2#LIN 1517 CCAACTCATTTTATGAGGCCAGCATNACCCTGATACCAAAACCNGACAAA 1566 chr3qtel1M 529524 GCTAACTCAGAGAAAGAAAATTAGAGACCAATTTCCCTAATGAATATTAA 529573 vi viv iii v v v i vi L1M5_orf2#LIN 1567 GACATTACAAGAAAAGAAAATTACAGACCAATATCCCTCATGAACATAGA 1616 chr3qtel1M 529574 TGCGAACATTTTAAATAAAATATAAGCAAAGAAATTACAGCAATTTATGA 529623 i v ii ? i v vvi v v v i L1M5_orf2#LIN 1617 TGCAAAAATCCTNAACAAAATATTAGCAAATCGAATCCAGCAATATATAA 1666 chr3qtel1M 529624 CCAGTATAATACACAATGACCAAATGAGATTTGTACCAGGAAT-CAATGC 529672 vv v iv i i i i v - v i L1M5_orf2#LIN 1667 AAAGGATAATACATCATGACCAAGTGGGGTTTATCCCAGGAATGCAAGGT 1716 chr3qtel1M 529673 TGGTTCACTATCAGGAAAAAAAGTCAGCATAATTGACT-TATGCA-ATAA 529720 i vi i-v vv i iii v i- vv - v L1M5_orf2#LIN 1717 TGGTTTAACATT-CGAAAATCAATCAATGTAATTCACCATATTAACAGAA 1765 chr3qtel1M 529721 TAAAACTAGCAGAAATCATACAATTACATCAATAGATGCAGAAAAAGCAT 529770 i-v - i ii i iv L1M5_orf2#LIN 1766 TAAAG-GAG-AAAAATCATATGATCATCTCAATAGATGCAGAAAAAGCAT 1813 chr3qtel1M 529771 TTGACAAAATACAACACCCATTGATGTTAAAAAATACTAGAAAGTATAAG 529820 v v v v vii v ii- i L1M5_orf2#LIN 1814 TTGACAAAATTCAACACCCATTCATGATAAAAACTCTCAGCAAAC-TAGG 1862 chr3qtel1M 529821 AATAAATTGAGTTTTCCTTAAAATGGTAAATAGCATCTATCTAAAACCAT 529870 i vv iivi i vv i vi ivv vv L1M5_orf2#LIN 1863 AATAGAAGGGAACTTCCTCAACCTGATAAAGGGCATCTACGAAAAACCTA 1912 chr3qtel1M 529871 CAGCAAGAATTATATGTAATGGGAATAAGCTAGAAGA-TTCCCAGTAAGA 529919 ? iv i iv vi v ?i ii ? v- vv L1M5_orf2#LIN 1913 CAGCNAACATCATACTTAATGGTGAAANACTGAANGCTTTCCCCCTAAGA 1962 chr3qtel1M 529920 TCAAGGAAGAAACAA----------TATCACCACTATTATTCAATATTGA 529959 ii i vi i ---------- ? vi i v L1M5_orf2#LIN 1963 TCGGGAACAAGACAAGGATGTCCGCTNTCACCACTTCTATTCAACATTGT 2012 chr3qtel1M 529960 ACAAGAAATGTTAGCTTTAGCAATAAGAGAAGAAAAAGAAATTGAAGGGA 530009 vi ii vi ivvv iv vi v L1M5_orf2#LIN 2013 ACTGGAGGTCCTAGCCAGTGCAATAAGGCAAGAAAAAGAAATAAAAGGCA 2062 chr3qtel1M 530010 TAAAAGTCGACAATTAGGAAACAAAATTATCATTCTTTGTATGTGATTTG 530059 ii i iv vv i i i i ? v i i vi iv L1M5_orf2#LIN 2063 TAAAGATTGGAAAGGAAGAAATAAAACTGTCNTTATTCGCAGATGACATG 2112 chr3qtel1M 530060 ATGGTATACATAGAAAATCCTAGAGAATCAACTAA-AAACTACTAGAAAC 530108 v ? i ? i v v - vi L1M5_orf2#LIN 2113 ATTGTNTACGTAGAAAATCCNAAAGAATCTACAAANAAACTACTAGAACT 2162 chr3qtel1M 530109 AATTCATAACTTCAGTAAAGTTGAAGG-TATAAAGGAAATCCACATAAAT 530157 vvi i v i i i i v? - i i vv vi v L1M5_orf2#LIN 2163 AATAAGTGAATTTAGCAAGGTCGCNGGATACAAGGTCAATATACAAAAAT 2212 chr3qtel1M 530158 CATTGACATTTCTATATGTTACCAACAAAGCTCAGCAGCAAA---AGATA 530204 v vii ii v --- iiv v --- i v L1M5_orf2#LIN 2213 CAATTGTATTTCTATATACTAGCAACAAA---CAATTGGAAAATGAAATT 2259 chr3qtel1M 530205 GAAAGAGAAATCCCATTTAAAATAACTATAGATAATATAAAACATTTGGA 530254 v? i iv v v i vvi i v i ? i i i i L1M5_orf2#LIN 2260 TNAAAAACAATACCATTTACAATAGCATCAAAAAACATNAAATACTTAGG 2309 chr3qtel1M 530255 AGTCTACCTGCCAAGACAAAGCCAGGAACTATATGAATAAAATTACAAAA 530304 i vv i iv i ? vivv i v ? iivvv i L1M5_orf2#LIN 2310 AATAAATCTAACAAAANATGTGCAAGACCTNTACACTGAAAACTACAAAA 2359 chr3qtel1M 530305 TACTTTTCACACAAATTAAGCTAGATCTAAATAATTGGA-AGA-GTATCA 530352 i i vi v v v ivv i v - -i i L1M5_orf2#LIN 2360 CATTGCTGAGAGAAATTAAAGAAGACCTAAATAAATGGAGAGATATACCA 2409 chr3qtel1M 530353 GGTGCTCATAGGTAGGCTGAGCTAATATAATAAAAAT 530389 -- i i i v vv vii vi ? i L1M5_orf2#LIN 2410 --TGTTCATGGATTGGAAGACTCAATATTGTNAAGAT 2444 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 38.92 CpG sites = 264, Kimura (unadjusted) = 39.69 Transitions / transversions = 1.33 (264/198) Gap_init rate = 0.03 (45 / 1572), avg. gap size = 1.87 (84 / 45) 331 34.10 3.23 3.23 chr3qtel1M 530405 530807 (469193) L1PREC2_orf2#LINE/L1 2508 2910 (384) m_b150s551i6 5618 chr3qtel1M 530405 CTTTGTAGAGCTAAAAATAATAATAATAATAAAATTCATCTAGAAGAACA 530454 iii i i v iv v- -- v i vv v L1PREC2_orf2# 2508 CTTCACAGAACTAGAAAAAACTATT-T--TAAAATTCATATGGAACCAAA 2554 chr3qtel1M 530455 AAAGGTCATGAAT-TTCAAGGGAATTAATGAGAAAAAAAATGCAAAGAAA 530503 iv vi -vi v iv- i v i -i vv- L1PREC2_orf2# 2555 AAAGAGCCCGAATAGCCAAGGCAATCC-TAAGCAAAAAGA-ACAAAGCT- 2601 chr3qtel1M 530504 GGGGGCCTAGCTGTACCAGACCTAAAACTATATAATAAAGCTGCAATCAT 530553 i v vi vv v i v iv i ii i i v i L1PREC2_orf2# 2602 GGAGGCATCACGCTACCCGACTTCAAACTATACTACAGGGCTACAGTAAC 2651 chr3qtel1M 530554 CAAAGTCTTTTGCTACTGGTTAAGAAATAGAGTGGTGAATCA-TGAAATA 530602 iivviv v vv i i vvvi ii i - i i L1PREC2_orf2# 2652 CAAAACAGCATGGTACTGGTACAAAAACAGACACATAGACCAATGGAACA 2701 chr3qtel1M 530603 GGTTAG---GTTCACAAGATATAGTAGTCAATGACTATAATAATCTAATG 530649 iv --- ii v - vi iv i-- iiv i iv i v L1PREC2_orf2# 2702 GAATAGAGAGCCCAGAA-ATAAGGCCGC--ACACCTACAACCATCTGATC 2748 chr3qtel1M 530650 TTCGATAAA-CT--CAAAGACTCCAGCTTTTAAGATAAGAACTCACTATT 530696 i - -- i --v vv vii - i v L1PREC2_orf2# 2749 TTCGACAAAGCTGACAAAAAC--AAGCAATGGGGA-AAGGACTCCCTATT 2795 chr3qtel1M 530697 TGACAAAAATTGCTGGGAAAACTGGATA-TAGTATGGCAGAAACTAGGTA 530745 ii i viv v v -ivi - iv v iv L1PREC2_orf2# 2796 CAATAAATGGTGCTGGGATAACTGGCTAGCCATAT-GCAGAAGATTGAAA 2844 chr3qtel1M 530746 TTGAACA----TCTAACACCCTATACCAAAACAAGGTTGAAATGGGCTTA 530791 i i v----i v v v iv iv ii i ii v L1PREC2_orf2# 2845 CTGGACCCCTTCCTTACACCATATACAAAAATCAACTCAAGATGGATTAA 2894 chr3qtel1M 530792 TGATTTAGACATAAAA 530807 v i i ii L1PREC2_orf2# 2895 AGACTTAAATGTAAAA 2910 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 46.27 CpG sites = 73, Kimura (unadjusted) = 46.75 Transitions / transversions = 1.22 (73/60) Gap_init rate = 0.05 (20 / 402), avg. gap size = 1.30 (26 / 20) 81 4.76 0.00 0.00 chr3qtel1M 531251 531337 (468663) (AG)n#Simple_repeat 1 87 (0) c_b150s251i1 5619 chr3qtel1M 531251 AGAGAGAGAGAGAGACAGAGAGACAGAGAGACAGAGAGACAGAGAGAGAG 531300 v v v v (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr3qtel1M 531301 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 531337 (AG)n#Simple_ 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 87 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 86), avg. gap size = 0.0 (0 / 0) 251 31.74 6.77 3.44 chr3qtel1M 531370 531679 (468321) L1PB_orf2#LINE/L1 2975 3294 (0) m_b150s551i7 5620 chr3qtel1M 531370 AGGACTTTGTGGCCAAAGAACTAGAAATATGATG----AAATACAAA-AT 531414 ii i ii v i i ii -i ---- v - L1PB_orf2#LIN 2975 AGGACTTCATGACCAAGAACCCAAAAGCA-AATGCAACAAAAACAAAGAT 3023 chr3qtel1M 531415 GGATAATTTTGATTGCATTAAATTAAAAGGGTTTTGCACAAACTAAACTA 531464 ii i? vv i vv i ii v i ii- v vv L1PB_orf2#LIN 3024 AAATAGNTGGGACTTAATTAAACTAAAGAGCTTCTGCACGG-CAAAAGGA 3072 chr3qtel1M 531465 ATTCAGTCA--AGATTAGAAAGGAAAC--AGAAAGCTCAGGGGAAATTTT 531510 -- -- v i v iv -- v i - vi i i i L1PB_orf2#LIN 3073 A--CAGTCAGCAGAGTAAACAGACAACCCACAGAG-TGGGAGAAAATCTT 3119 chr3qtel1M 531511 TACAGCCACTGTTTCTGATAAAGGCCTCATTTCTAAACTATGTAGAGAAT 531560 i ii vv iiv i v v v i i v v ii i? i L1PB_orf2#LIN 3120 CACAATCTATACATCTGACAAAGGACTAATATCCAGAATCTACAANGAAC 3169 chr3qtel1M 531561 TGACTCAAATTTATAAGAATA---CAAGCCATTTTCCAATTGACAAATGA 531607 v vv ivii v --- i v --- v ii v i i L1PB_orf2#LIN 3170 TCAAACAAATCAGCAAGAAAAAAACAAACAAT---CCCATCAAAAAGTGG 3216 chr3qtel1M 531608 TTGAAGAAAATAAA--GACAATTTTCAAA-GAA---AT-TAAA--GCCAT 531648 viv i v i -- i - --- -i -- - L1PB_orf2#LIN 3217 GCTAAGGACATGAATAGACAATTCTCAAAAGAAGATATACAAATGGCCA- 3265 chr3qtel1M 531649 TTCTAGTCATATGAAAAATCACTCTATATCA 531679 --vi iv vii v i L1PB_orf2#LIN 3266 --ACAAACATATGAAAAAATGCTCAACATCA 3294 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 42.62 CpG sites = 57, Kimura (unadjusted) = 43.24 Transitions / transversions = 1.50 (57/38) Gap_init rate = 0.07 (21 / 309), avg. gap size = 1.52 (32 / 21) 279 33.05 5.58 3.27 chr3qtel1M 531370 531638 (468362) L1P3_orf2#LINE/L1 2975 3249 (45) m_b150s551i8 5620 chr3qtel1M 531370 AGGACTTTGTGGCCAAAGAACTAGAAATA-TG---ATGAAATACAAAATG 531415 i ii i i iv i i ii - --- ii vv v L1P3_orf2#LIN 2975 AAGACTTCATGACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATT 3024 chr3qtel1M 531416 GATAATTTTGATTGCATTAAATTAAAAGGGTTTTGCACA---AACTAAAC 531462 i v vv ivv i ii v i --- vv L1P3_orf2#LIN 3025 GACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAAC 3074 chr3qtel1M 531463 TAATTCAGTCAAGATTAGAAAGGAA---ACAGAAAGCTCAGGGGAAATTT 531509 -- - iii v iv i v --- --- vi i i L1P3_orf2#LIN 3075 TA--TCA-TCAGAGTGAACAGGCAACCTACAGAA---TGGGAGAAAATTT 3118 chr3qtel1M 531510 TTACAGCCACTGTTTCTGATAAAGGCCTCATTTCTAAACTATGTAGAGAA 531559 i ii vv viv i v v v i i v v ii ii L1P3_orf2#LIN 3119 TTGCAATCTATCCATCTGACAAAGGGCTAATATCCAGAATCTACAAGGAA 3168 chr3qtel1M 531560 TTGACTCAAATTTATAAG---AATACAAGCCATTTTCCAATTGACAAATG 531606 i v vv i --- v i v ---i v ii v i L1P3_orf2#LIN 3169 CTTAAACAAATTTACAAGAAAAAAACAAACAA---CCCCATCAAAAAGTG 3215 chr3qtel1M 531607 ATTGAAGAAAATAA--AGACAATTTTCAAAGAAA 531638 ivi i v i -- v i ii L1P3_orf2#LIN 3216 GGCGAAGGATATGAACAGACACTTCTCAAAAGAA 3249 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 44.54 CpG sites = 51, Kimura (unadjusted) = 45.27 Transitions / transversions = 1.46 (51/35) Gap_init rate = 0.06 (15 / 268), avg. gap size = 1.60 (24 / 15) 515 24.87 7.11 3.04 chr3qtel1M 531539 531791 (468209) L1MA8_3end#LINE/L1 4 266 (772) m_b150s551i9 5620 chr3qtel1M 531539 ATTTCTAAACTATGTAGAGAATT-----GACTCAAATTTATAAGAATACA 531583 v i v i ii i -----i -- vii v L1MA8_3end#LI 4 ATATCCAAAATATATAAGGAACTCAAACAACTCAA--TAGCAAGAAAACA 51 chr3qtel1M 531584 AGCCATTTTCCAATTGACAAATGATTGAAGAAAATAAA--GACAATTTTC 531631 --- vvi i ? v ivii i vv i -- v i L1MA8_3end#LI 52 A---ATAACCCGATTNAAAAATGGGCAAAGGACCTGAATAGACATTTCTC 98 chr3qtel1M 531632 AAA----GAAAT-TAAA--GCCATTTCTAGTCATATGAAAAATCACTCTA 531674 ---- v -i -- ---vi vi vii v L1MA8_3end#LI 99 AAAAGAAGACATACAAATGGCCA---ACAGGTATATGAAAAAATGCTCAA 145 chr3qtel1M 531675 TATCACTATTAATTAGAGAAATGCAAATTAAGACAACTCTGAGATACCAC 531724 i v v i i i v vv i L1MA8_3end#LI 146 CATCACTAATCATCAGGGAAATGCAAATTAAAACCACAATGAGATATCAC 195 chr3qtel1M 531725 CTCACCCCTCTCAGATTGGCTAAGAT-GACAAGA-AAAAGATGATAAATG 531772 v v i v vv -i v -i i i i L1MA8_3end#LI 196 CTCACACCTGTTAGAATGGCTATTATCAAAAAGACGAAAGATAACAAGTG 245 chr3qtel1M 531773 TTGGAG-GGATATGG-GAAAA 531791 v - i - L1MA8_3end#LI 246 TTGGCGAGGATGTGGAGAAAA 266 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 29.66 CpG sites = 33, Kimura (unadjusted) = 30.84 Transitions / transversions = 1.18 (33/28) Gap_init rate = 0.07 (17 / 252), avg. gap size = 1.53 (26 / 17) 209 14.63 7.32 0.00 chr3qtel1M 532590 532630 (467370) C L2c_3end#LINE/L2 (7) 471 428 m_b150s601i2 5621 chr3qtel1M 532590 CAATCAATAAACATTTC---AGTACCTACTATGTGCCAGGCACT 532630 v i v--- ii i C L2c_3end#LINE 471 CATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCT 428 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 10.76 CpG sites = 4, Kimura (unadjusted) = 16.55 Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.03 (1 / 40), avg. gap size = 3.00 (3 / 1) 325 33.95 1.88 7.95 chr3qtel1M 533186 533345 (466655) C L3#LINE/CR1 (3366) 733 583 m_b150s601i3 5622 chr3qtel1M 533186 TTGATAAGTCTTGGGAGGTTCTCGGTTATATCTCGAATACATGGCCCAAA 533235 i v i v i ii i i vi ii C L3#LINE/CR1 733 TTGATGAGTCTTGGCAGGCTCTCCGTCACGTCTCGGATACACGCTCCAGG 684 chr3qtel1M 533236 AAGATAAAGGCCTTCTCAACTA-CTATTATCAGA--TGGATCAATAGGAA 533282 i ivivv i i i i - i -ii i-- v -------- C L3#LINE/CR1 683 AAGACAGCACACCTCCCGATTAGCCA-CGTCAGGTCTGCAT--------A 643 chr3qtel1M 533283 CAACTACCTTGGGATCCCTAAAAAGGAAACCCTCAACTACCAACCACCTG 533332 ii ii iv v v ivi i ii vi i - v vi C L3#LINE/CR1 642 CGGCCGCCTCCGTATCCCTCAGCGGGGAGTCACCAACCACC-ACGACGCG 594 chr3qtel1M 533333 ATTCTCTTCTCCC 533345 -- ii C L3#LINE/CR1 593 --TCTCTTCCTCC 583 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 37.91 CpG sites = 36, Kimura (unadjusted) = 48.75 Transitions / transversions = 2.57 (36/14) Gap_init rate = 0.09 (14 / 159), avg. gap size = 1.07 (15 / 14) 196 31.48 13.61 0.60 chr3qtel1M 533566 533712 (466288) C L3#LINE/CR1 (3745) 354 189 m_b150s601i4 5622 chr3qtel1M 533566 CTCCCACCTACTC----TCTTCCTCTTTTT--TGACCCCACTGGAGC-TT 533608 i i v ---- ii i -- vv iiv vi- C L3#LINE/CR1 354 CTTCCGCCTCCTCAGAATCTTTTTCTTTCTGNTTTCCTTCCTGGATTATT 305 chr3qtel1M 533609 CCTTTCTGCTTCCTTGGGAATACTTCATTGGCCCTAACAATCTGGA---- 533654 i i vv i ?ii i iv ivv i i v i ---- C L3#LINE/CR1 304 TCTTCCATCCTNTCTAGGAACCCTTCATCCTCTCTAATAAGCCGGAGCGT 255 chr3qtel1M 533655 ----AGACAT--CTTGGGTCCCCTTCA---TCTCCTCTAGAGGAAGGATC 533695 ---- i i -- iii - i --- vi iii i C L3#LINE/CR1 254 AGAGAGGCGTTCCTCAAG-CCCTTTCACCTTCTCCTCTAGCAGGGAGACC 206 chr3qtel1M 533696 AGCCTGCACTTGGAGCA 533712 i i iv C L3#LINE/CR1 205 AGCTTGCATTTATAGCA 189 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 40.36 CpG sites = 33, Kimura (unadjusted) = 44.29 Transitions / transversions = 2.54 (33/13) Gap_init rate = 0.05 (8 / 146), avg. gap size = 2.62 (21 / 8) 266 24.55 2.36 10.17 chr3qtel1M 534349 534475 (465525) L2c_3end#LINE/L2 349 466 (12) m_b150s601i5 5623 chr3qtel1M 534349 TATTTGCATGT-TGTCTTC-CAATTAGATTGT-AGCTCTTTGATGGCAGG 534395 i i ? - i - v i i - i v L2c_3end#LINE 349 TGTTTACNTGTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGG 398 chr3qtel1M 534396 AACTGATTTTTTTTTTTTTTTTGTACTTTATATCCTTTGTATTTGCCTGG 534445 i i ------- v i v ii - i iiv i---- L2c_3end#LINE 399 GACCG-------TGTCTTATTCAT-CTTTGTATCCCCAGC----GCCTGG 436 chr3qtel1M 534446 CATACAGCAGGTGCTTCATAAATTTTTTTT 534475 i i i i iv v v L2c_3end#LINE 437 CACATAGTAGGCGCTCAATAAATGTTTGTT 466 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 27.18 CpG sites = 20, Kimura (unadjusted) = 31.11 Transitions / transversions = 2.50 (20/8) Gap_init rate = 0.12 (15 / 126), avg. gap size = 1.00 (15 / 15) 367 30.16 12.31 4.78 chr3qtel1M 534632 534826 (465174) C L3#LINE/CR1 (57) 4042 3834 m_b150s601i6 5624 chr3qtel1M 534632 TTCCATCTAATCCAG----CCCATCT-TAACATACTTAACAGCCAGTCAT 534676 i i v ---- v -i v i i ivii C L3#LINE/CR1 4042 TCCCATCCAATGCAGGAATCCCTTCTACAACATCCCTGACAAGTGGTCAT 3993 chr3qtel1M 534677 CCAGTCTTTGCATAGGTACCTTTGGTATCAGGGGGCCCACTACCCACCCA 534726 i i v iiii iii iv i i i iv? v C L3#LINE/CR1 3992 CCAGCCTCTGCTTGAACACCTCCAGTGACGGGGAGCTCACTACCTCNCGA 3943 chr3qtel1M 534727 GACAACACTCATTTTATTTCTGGATGGCTAGCTTTTAGTGTT-GGAAGTT 534775 i --i i ii i ----i i v v - i C L3#LINE/CR1 3942 GGCA--GCCCATTCCATTTTTGGA----CAGCTCTGATTGTTAGAAAGTT 3899 chr3qtel1M 534776 ------------------AAAGCTTGCTCTTTGCAGCTTCCATGCATTCA 534807 ------------------ v vv ii i i ---- ii C L3#LINE/CR1 3898 CTTCCTTATATTGAGCCGAAATCTGCCTCCCTGTAACTTC----CACCCA 3853 chr3qtel1M 534808 TTGCTTCCAGTTTTACTCT 534826 v i i i i i C L3#LINE/CR1 3852 TTGGTCCTAGTTCTGCCCT 3834 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 41.12 CpG sites = 42, Kimura (unadjusted) = 42.16 Transitions / transversions = 3.00 (42/14) Gap_init rate = 0.07 (14 / 194), avg. gap size = 2.43 (34 / 14) 272 27.80 2.34 10.08 chr3qtel1M 535222 535349 (464651) MamRTE1#LINE/RTE-BovB 313 431 (3381) m_b150s601i7 5625 chr3qtel1M 535222 GGCCCGGGCCATTG-TCTTCTCATTG--GACTGAAGCAACAGTGGCATTC 535268 i vi - vii vi i -- ?- i i iiv i MamRTE1#LINE/ 313 GGCCCAGGATATTGGTCGCTTAGTCGCTGAN-GAGGCAGCAGCACCGTTC 361 chr3qtel1M 535269 AGCAGCCCTCTGGGTGTCTGAGCAGTCTTTTTTTTTTTTTAAGGACTTTC 535318 i v?i i i v -------- ?iviv MamRTE1#LINE/ 362 GGCAGCGNCCTGGGTGTCTGAGCAGCCCTGTTT--------AGGANCGCG 403 chr3qtel1M 535319 CTGCTCATTTTCTGGTATGATAAAGGGGCTA 535349 i ii--- v ivi ? MamRTE1#LINE/ 404 CTGCTCACTCC---GAATGGGGAAGGGNCTA 431 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 29.28 CpG sites = 22, Kimura (unadjusted) = 37.82 Transitions / transversions = 2.20 (22/10) Gap_init rate = 0.11 (14 / 127), avg. gap size = 1.07 (15 / 14) 259 36.12 2.69 3.24 chr3qtel1M 535620 535805 (464195) MamRTE1#LINE/RTE-BovB 1140 1324 (2488) m_b150s601i8 5625 chr3qtel1M 535620 ATCATCAATACTGTCTTCCATTTGCCTAAATGGAATAAAACTTCACGGAT 535669 i i ii iii i v vvi iv i v i MamRTE1#LINE/ 1140 ATCACCAACACCATCTTCCGCCTACCGAATAAGAGAAAGACATCATGGAT 1189 chr3qtel1M 535670 ACAGCCTCATAGC--AAATACTGGCATTTAATAGTCTCTGTGATTGTTAG 535717 i -- i vi i-- ii v i v v vi v i v i v MamRTE1#LINE/ 1190 GCA--CCCAAGGTCTAAGCAGTGGCATCTCATTGATTATATCATCGTTCG 1237 chr3qtel1M 535718 G-AGAAGAGGCAGACAGGATGCGAGAGTGACAAAGGCAATGTGAGGCGCA 535766 i- vi iiv v - ivviii v vivi v i v v MamRTE1#LINE/ 1238 ACAGCGGGACCTGA-AGGATGTTTAGATTACTGCAGCTATGCGTGGCGCC 1286 chr3qtel1M 535767 GAGTGCTGGACTTTTGATCACAGAC--ATGCTCTCCAAGCT 535805 ---i i iv v -- i v i MamRTE1#LINE/ 1287 GAGTGCTGGAC---CGACCATCGCCTGATACGCTCCAAACT 1324 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 45.85 CpG sites = 38, Kimura (unadjusted) = 51.37 Transitions / transversions = 1.41 (38/27) Gap_init rate = 0.05 (9 / 185), avg. gap size = 1.22 (11 / 9) 282 30.43 0.86 0.86 chr3qtel1M 537328 537443 (462557) MamRTE1#LINE/RTE-BovB 3087 3202 (610) m_b150s601i9 5625 chr3qtel1M 537328 TTTGGGAAGCCCCGAAGGAAAGTGTGA-GCAAGAAGAGGTATTGGGCTGC 537376 i ivvv iiv i i- v - v v i iii v MamRTE1#LINE/ 3087 TTTGGGAGGCTGGCAGACAGAGTGTGGCGCCA-ACGTGGCATCAAGCTCC 3135 chr3qtel1M 537377 CTACCAAACTTAAGGTCTACAGAGCCCTTGTGCTGACCTCATTGTTGTAC 537426 vv v vv v i ? v vvvi vi ? MamRTE1#LINE/ 3136 AGACCAAACTAAAGGTCTACAGAGCGATAGCGNTGTCCAACCTTCTNTAC 3185 chr3qtel1M 537427 ACCTGTGAAACCTGGAC 537443 iv i MamRTE1#LINE/ 3186 GGCTGTGAGACCTGGAC 3202 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 37.36 CpG sites = 15, Kimura (unadjusted) = 40.14 Transitions / transversions = 0.75 (15/20) Gap_init rate = 0.02 (2 / 115), avg. gap size = 1.00 (2 / 2) 234 30.42 2.86 10.77 chr3qtel1M 539718 539857 (460143) C L2#LINE/L2 (273) 2809 2680 m_b150s601i10 5626 chr3qtel1M 539718 TTTAGGAAAATCGGTTTGGTGACTGACTGGAAGATGGACTGGAGTA---- 539763 ii ii iv i ivi vv v ii i ? vi---- C L2#LINE/L2 2809 TTTAAAAGGATCACTCTGGCTGCTGTGTTGAGAATAGACTGNAGGGGGGC 2760 chr3qtel1M 539764 AAAAGTGCCCGAGGCAGGCAGACCAATGACCCTGGCAGGCTATCACAATA 539813 ii --- i v i ----- i v ii i C L2#LINE/L2 2759 AAGGGTG---GAAGCAGGGAGACCAGT-----TAGGAGGCTATTGCAGTA 2718 chr3qtel1M 539814 ATCCAGGTGGTAGATGTTAGATGTAAGGGTCTACACCAGGGTAG 539857 i iv ---- --iv ii iv i C L2#LINE/L2 2717 ATCCAGGCGAGAGAT----GATG--GTGGCTTGGACCAGGGTGG 2680 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 40.06 CpG sites = 27, Kimura (unadjusted) = 41.54 Transitions / transversions = 2.45 (27/11) Gap_init rate = 0.11 (15 / 139), avg. gap size = 1.20 (18 / 15) 545 24.99 4.37 2.87 chr3qtel1M 540749 540954 (459046) L1ME5_3end#LINE/L1 114 322 (619) m_b150s551i10 5627 chr3qtel1M 540749 AAAAGCTATCTATAGTCATATGAAAAAAATTTTCTAAATCATTACTGACC 540798 i --- i iv i i - vi v v v i i L1ME5_3end#LI 114 AAAGGCTA---ACAAGCATATGAAGAGA-TGCTCAAACTCATTAGTAATC 159 chr3qtel1M 540799 AGAGAAAGGCAAATTAAAACAACTCTGAGCTA-CATTTCAT-CCT-TCAG 540845 v vv v - i i i- - i L1ME5_3end#LI 160 AGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCTATTAG 209 chr3qtel1M 540846 ATTTGCTAAAATGGCAGAAAA--GGAAAATGATAAATGCTGAAG-GGATG 540892 i v v --i i-- v vi i i iv - L1ME5_3end#LI 210 ACTGGCAAAAAT--TAGAAAGCTGGATAATGCCAAGTGTTGGCGAGGATG 257 chr3qtel1M 540893 TGAGAAAACATTAAAACTC---CACTGTTGGTGGAATTGTAAACTGAGCC 540939 i i ? i vv vv --- i i v i ivv L1ME5_3end#LI 258 TGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACTGGTGC 307 chr3qtel1M 540940 GACCATTCTGGAAAG 540954 ii i L1ME5_3end#LI 308 AGCCATTCTGGAGAG 322 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 31.22 CpG sites = 29, Kimura (unadjusted) = 31.22 Transitions / transversions = 1.38 (29/21) Gap_init rate = 0.06 (12 / 205), avg. gap size = 1.25 (15 / 12) 473 31.66 5.87 3.76 chr3qtel1M 540760 541202 (458798) L1ME3Cz_3end#LINE/L1 118 569 (428) m_b150s551i11 5627 chr3qtel1M 540760 ATAGTCATATGAAAAAAATTTTCTAAATCATTACTGACCAGAGAAAGGCA 540809 iv i - vi v vv i v i i i v L1ME3Cz_3end# 118 ATAAACATATGAAAAGA-TGCTCAACCTCACTAGTAATCAGGGAAATGCA 166 chr3qtel1M 540810 AATTAAAACAACTCTGAGCTA-CATTT--CATCCTTCAGATTTGCTAAAA 540856 ? vv v - -- i v v v L1ME3Cz_3end# 167 AATTAAAACNACAATGAGATACCATTTCACACCCATCAGATTGGCAAAAA 216 chr3qtel1M 540857 TGGCAGAAAAG---GAAAATGATAAATGCTGAAG-GGATGTGAGAAAACA 540902 v---v --- v ivi i i iv - iii i L1ME3Cz_3end# 217 TT---TAAAAGTCTGACAATACCAAGTGTTGGCGAGGATGTGGAGAAACG 263 chr3qtel1M 540903 TTAAAACTC-----CACTGTTGGTGGAATTGTAAACTGAGCCGACCATTC 540947 --ii ----- i i v i ivv i i i L1ME3Cz_3end# 264 --GGAACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTACAACCACTT 311 chr3qtel1M 540948 TGGAAAGTCA-TTGGAACTATGCCCAAAGGACTATAAAACCTTGTGTTCC 540996 i iv - v v -- i ivii v - i ivivi ii v L1ME3Cz_3end# 312 TGGAGAGCAATTTGGCAATAT--CTAGTAAAGT-TGAAGATGCGCATACC 358 chr3qtel1M 540997 CTTTGA-CCATGAATACTATGACCAGGTCTGTGACCCAGAGAGA-TAAAA 541044 vi - vv v i ivv i v i iv i i - vvvi L1ME3Cz_3end# 359 CTACGACCCAGCAATTCCACTTCTAGGTATATACCCTAGAGAAACTCTCG 408 chr3qtel1M 541045 AACAAAAAGAAAAAGGATCTATAAGCACAAAAATAT---TTACAGTCATT 541091 v - viv v v vvi -- i ii i --- i - L1ME3Cz_3end# 409 CAC-ATGTGCACAAGGAGACAT--GTACAAGGATGTTCATTGCAG-CATT 454 chr3qtel1M 541092 CTTTTAGTGGTGGCAAAGAATTGGAAA----TTGAGGAT-TCCACCAGTT 541136 v -- ii i i i ----i i -- - i i v L1ME3Cz_3end# 455 GTTT--GTAATAGCGAAAAATTGGAAACAACCTAA--ATGTCCATCAATA 500 chr3qtel1M 541137 GGGGAATAGCCGGACAAGTTGCTGTGTCTTATTGTGATGGAATGCTGT-T 541185 i viii i i iv i v vv iii i i -i L1ME3Cz_3end# 501 GGGGAATGGATAAATAAATTGTGGTATATTCATACAATGGAATACTATAC 550 chr3qtel1M 541186 GG--GTTATAAGAAATGAA 541202 i -- v vi L1ME3Cz_3end# 551 AGCAGTTAAAATGAATGAA 569 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 40.57 CpG sites = 79, Kimura (unadjusted) = 42.66 Transitions / transversions = 1.41 (79/56) Gap_init rate = 0.07 (30 / 442), avg. gap size = 1.43 (43 / 30) 525 30.13 5.77 3.33 chr3qtel1M 540765 541145 (458855) L1ME4c_3end#LINE/L1 127 516 (314) m_b150s551i12 5627 chr3qtel1M 540765 CATATGAAAAAAATTTTCTAAATCATTACTGACCAGAGAAAGGCAAATTA 540814 i i - v v vv ii v i i i v L1ME4c_3end#L 127 CACATGGAAAAA-TGTTCAACCTCGCTAGTAATCAAAGAAATGCAAATTA 175 chr3qtel1M 540815 AAACAACTCTGAGCTA-CATTTCAT-CCT-TCAGATTTGCTAAAATGGCA 540861 i vv v - i i- - i i v v vvv L1ME4c_3end#L 176 AAGCAACAATGAGATACCATTTTACGCCTATTAAATTAGCAAAAATTTAA 225 chr3qtel1M 540862 GAAAAGGAAAATGATAAATGCTGAAG-GGATGTGAGAAAACATTAAAACT 540910 i vv v iviv iv - ? i ivi -- iiv ? L1ME4c_3end#L 226 AAAATTGATAATACCCAATGCTGGCGAGGNTGCGGTGAAAC--TGGTACN 273 chr3qtel1M 540911 C-----CACTGTTGGTGGAATTGTAAACTGAGCCGACCATTCTGGAAAGT 540955 ----- i i v ? i ivv i v i i L1ME4c_3end#L 274 CTCATACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGC 323 chr3qtel1M 540956 CA-TTGGAACTATGCCCAAAGGACTATAAAACCTTGTGTTCCCTTTGA-C 541003 v - v v i iviv ii i viv vii v - L1ME4c_3end#L 324 AATTTGGCAATACGTATCAAGAGCCATAAAAATGTTCATACCCTTTGACC 373 chr3qtel1M 541004 CATGAATACTATGACCAGGTCTGTGACCCAGAGAGATAA---AAAACAAA 541050 vv v i ivv ii vv v iv i ii i --- -- i L1ME4c_3end#L 374 CAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAA--AGA 421 chr3qtel1M 541051 AAGAAAAAGGATCTATAAGCACAAAAATAT---TTACAGTCATTCTTTTA 541097 i --- v i i i --- i - i v -- L1ME4c_3end#L 422 AGGAAAAAG---CTATATGCACGAAGATGTTCATTGCAG-CGTTATTT-- 465 chr3qtel1M 541098 GTGGTGGCAAAGAATTGGAAA----TTGAGGAT-TCCACCAGTTGGGGAA 541142 i ii i i i ----i i -- - v i v L1ME4c_3end#L 466 ATAATAGCGAAAAATTGGAAACAACCTAA--ATGTCCAACAATAGGGGAA 513 chr3qtel1M 541143 TAG 541145 i L1ME4c_3end#L 514 TGG 516 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 36.82 CpG sites = 63, Kimura (unadjusted) = 40.01 Transitions / transversions = 1.31 (63/48) Gap_init rate = 0.06 (24 / 380), avg. gap size = 1.46 (35 / 24) 529 24.73 7.21 5.31 chr3qtel1M 540765 540986 (459014) L1PA2_3end#LINE/L1 127 352 (550) m_b150s551i13 5627 chr3qtel1M 540765 CATATGAAAAAAATTTTCTAAATCATTACTGACCA---GAGAAAGGCAAA 540811 i - vi --- i i --- v L1PA2_3end#LI 127 CACATGAAAAAA-TGCTC---ATCATCACTGGCCATCAGAGAAATGCAAA 172 chr3qtel1M 540812 TTAAAACAACTCTGAGCTACATTTCATCCTTCAGATTTGCTAAAATGGCA 540861 i v vv v ---- -- v iiv i i L1PA2_3end#LI 173 TCAAAACCACAATGAGATAC----CATC--TCACACCAGTTAGAATGGCA 216 chr3qtel1M 540862 G------AAAAG---GAAAATGATAAATGCTGAAG-GGATGTGAGAAAAC 540901 i------ --- i ii i ii i - iii i L1PA2_3end#LI 217 ATCATTAAAAAGTCAGGAAACAACAGGTGCTGGAGAGGATGTGGAGAAAT 266 chr3qtel1M 540902 ATTAAAACTC---CACTGTTGGTGGAATTGTAAACTGAGCCGACCATTCT 540948 vv v i--- i i iivi i v L1PA2_3end#LI 267 AGGAACACTTTTACACTGTTGGTGGGACTGTAAACTAGTTCAACCATTGT 316 chr3qtel1M 540949 GGAAAGTCATTGGAACTATGCCCAAAGGACTATAAAAC 540986 - v vii v v iv i - v i L1PA2_3end#LI 317 GG-AAGTCAGTGTGGCGATTCCTCAGGGA-TCTAGAAC 352 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 30.93 CpG sites = 33, Kimura (unadjusted) = 30.93 Transitions / transversions = 1.74 (33/19) Gap_init rate = 0.08 (17 / 221), avg. gap size = 1.65 (28 / 17) 12 15.85 0.00 3.45 chr3qtel1M 541800 541829 (458171) (TTTTA)n#Simple_repeat 1 29 (0) m_b150s252i6 5628 chr3qtel1M 541800 TTTTATTTTATCTTCTGTGTATTTTGTTTT 541829 i v - v i (TTTTA)n#Simp 1 TTTTATTTTATTTTAT-TTTATTTTATTTT 29 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 285 15.67 5.13 1.86 chr3qtel1M 542001 542156 (457844) C HERVIP10FH#LTR/ERV1 (4107) 995 835 m_b150s701i8 5629 chr3qtel1M 542001 ATCTCTGTCATTTCTCTTTCTCT----CTTTCTCTTTCTCTCTCTCTCTC 542046 v - i i ---- v i C HERVIP10FH#LT 995 ATCTCTCTC-TTTCTTTCTCTCTTTGACTTTCTGTCTCTCTCTCTCTCTC 947 chr3qtel1M 542047 AGAGTCTCTCTCT--CTCTCTGTCTCTCTCTCTGTCTCTGTCTCTTTCTC 542094 v v i i -- ii -- i i C HERVIP10FH#LT 946 TGACTCCCTCTTTGTCTCTCTGTCTCTTCCTC--TCTCTGCCTCTCTCTC 899 chr3qtel1M 542095 TTTCT--CTCTCTCTCTGTCTCTGTCTCTCTCTCTTTCTTTCTTTCTCTG 542142 i i -- i i v i i i v C HERVIP10FH#LT 898 TCTTTGACTCCCTCTTTGTCTCTCTCTCTCCCTCTCTCTCTCTTTCTCTC 849 chr3qtel1M 542143 TCTCTCTCTCTCTC 542156 ii C HERVIP10FH#LT 848 TCTCTCTCTTCCTC 835 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 18.09 CpG sites = 18, Kimura (unadjusted) = 18.09 Transitions / transversions = 3.00 (18/6) Gap_init rate = 0.04 (6 / 155), avg. gap size = 1.83 (11 / 6) 16 9.71 0.00 0.00 chr3qtel1M 542399 542420 (457580) (A)n#Simple_repeat 1 22 (0) m_b150s252i7 5630 chr3qtel1M 542399 AAAAAAAAAAAAAAAAGTAAAA 542420 iv (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAA 22 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 30 0.00 0.00 0.00 chr3qtel1M 543301 543326 (456674) (CA)n#Simple_repeat 1 26 (0) c_b150s251i2 5631 chr3qtel1M 543301 CACACACACACACACACACACACACA 543326 (CA)n#Simple_ 1 CACACACACACACACACACACACACA 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 18 24.83 1.28 8.22 chr3qtel1M 543482 543559 (456441) (AC)n#Simple_repeat 1 73 (0) m_b150s252i8 5632 chr3qtel1M 543482 ACACAGCAGCACAAACACAATCACACATATATGCAAATATATGCGAGCAC 543531 - - v vv i i ii v i i ii - - (AC)n#Simple_ 1 ACACA-CA-CACACACACACACACACACACACACACACACACAC-A-CAC 46 chr3qtel1M 543532 TCACACACACACACATGAC-CAGCACACA 543559 v -v - - (AC)n#Simple_ 47 ACACACACACACACA-CACACA-CACACA 73 Matrix = Unknown Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.09 (7 / 77), avg. gap size = 1.00 (7 / 7) 17 16.12 0.00 0.00 chr3qtel1M 543736 543770 (456230) (AGAGAC)n#Simple_repeat 1 35 (0) m_b150s252i9 5633 chr3qtel1M 543736 AGAGACAGACAAACAGACAGAGACAGAGAAACAGA 543770 v v v v v (AGAGAC)n#Sim 1 AGAGACAGAGACAGAGACAGAGACAGAGACAGAGA 35 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 401 33.61 2.85 2.02 chr3qtel1M 544249 544494 (455506) C L2c_3end#LINE/L2 (222) 256 9 m_b150s601i11 5634 chr3qtel1M 544249 GAGGGGTCTGGGAAAGGTCTCTTGAAGAAGATGAGATCTGAAGCAAGCCT 544298 i v - ii ii i i i v ivii ? C L2c_3end#LINE 256 GGGGGGTCAGGGAA-GGCTTCCCGGAGGAGGTGACATCTGAGCTGAGNCT 208 chr3qtel1M 544299 TGAAGG--GAAAAAGAA--ATCCAAGAGTTGGAAGAAAAGAGACAAAGCA 544344 -- iv i i-- v i --- i ii i iv i C L2c_3end#LINE 207 TGAAGGATGAGTAGGAGTTAGCCAGG---TGGAAGGAGGGGGGAAGAGCA 161 chr3qtel1M 544345 TTCCAGACATAGAGGATAGCCAGGGCAAAGGTATGAAGGT-GAAAGGTGG 544393 i v i i i vv v i?i i i- i i viv C L2c_3end#LINE 160 TTCCAGGCAGAGGGAACAGCATGTGCAAAGGCNCGGAGGCAGGAAAGAAC 111 chr3qtel1M 544394 AGAGTCATGTT--AGGACAGCAAGAAGGTGAGTGTTGCTGGATCTTGGCA 544441 v v v i --i vv ? v v v v v i ii C L2c_3end#LINE 110 TGCGGCGTGTTTGGGGAATGCAAGNAGTTCAGTGTGGCTGGAGCATAGTG 61 chr3qtel1M 544442 CCTACAGAGAGAAAGAACGTATGTGAAAACTGGAAAGGTGGGAAGGAGCC 544491 vviivi i i iviiv v vi - ii i i v i C L2c_3end#LINE 60 GGCGAGGAGGGGAGTGGAGGAGATG-AGGCTGGAGAGGTAGGCAGGGGCC 12 chr3qtel1M 544492 AGA 544494 C L2c_3end#LINE 11 AGA 9 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 44.33 CpG sites = 51, Kimura (unadjusted) = 47.70 Transitions / transversions = 1.70 (51/30) Gap_init rate = 0.04 (9 / 245), avg. gap size = 1.33 (12 / 9) 299 28.04 3.60 3.60 chr3qtel1M 544792 544902 (455098) L1ME3G_3end#LINE/L1 438 548 (376) m_b150s551i14 5635 chr3qtel1M 544792 ATGTTTGTGGTAGACCTTTTTGTAGTGGCGAGGAACTGGAGAC----TGA 544837 ii v i vvi v i i ii i i ---- i L1ME3G_3end#L 438 ATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAA 487 chr3qtel1M 544838 GTGGCTTCCCATCAGTTAGAGAATGGCTGAATAAGTTATGGTATGTGAAT 544887 i ----i i vi i i i i i vv L1ME3G_3end#L 488 ATG----TCCATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCAT 533 chr3qtel1M 544888 GCTATGGGATATTAT 544902 i i i L1ME3G_3end#L 534 ACTATGGAATACTAT 548 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 37.70 CpG sites = 23, Kimura (unadjusted) = 37.70 Transitions / transversions = 3.29 (23/7) Gap_init rate = 0.05 (5 / 110), avg. gap size = 1.60 (8 / 5) 20 0.00 0.00 0.00 chr3qtel1M 545488 545509 (454491) (A)n#Simple_repeat 1 22 (0) m_b150s252i10 5636 chr3qtel1M 545488 AAAAAAAAAAAAAAAAAAAAAA 545509 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAA 22 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 267 20.69 0.00 0.00 chr3qtel1M 545585 545642 (454358) L1ME3Cz_3end#LINE/L1 488 545 (452) m_b150s551i15 5637 chr3qtel1M 545585 ATGCCCATCAATTGGGCAATGGCTGAATAAATAGTGGTATGTGATTATGA 545634 i v v v i v i vvv ii L1ME3Cz_3end# 488 ATGTCCATCAATAGGGGAATGGATAAATAAATTGTGGTATATTCATACAA 537 chr3qtel1M 545635 TGGAATAC 545642 L1ME3Cz_3end# 538 TGGAATAC 545 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 24.25 CpG sites = 5, Kimura (unadjusted) = 24.25 Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0) 16 21.70 0.00 0.00 chr3qtel1M 546268 546299 (453701) (A)n#Simple_repeat 1 32 (0) m_b150s252i11 5638 chr3qtel1M 546268 AAAAGCAAAATAAGAAATAAAAAGAAAAAAAA 546299 iv v i v i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 32 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 184 28.26 0.00 0.00 chr3qtel1M 546516 546561 (453439) C L2#LINE/L2 (1153) 1929 1884 m_b150s601i12 5634 chr3qtel1M 546516 GAGAAGGGAGGGCCTGAAGGCAGCCAGTATAGATGACTCTTCCAAG 546561 i i i ivi i i v ii i i C L2#LINE/L2 1929 GGGAGGAGAGGAATTGGAGACAGCGAGTATAGACAACTCTTTCGAG 1884 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 35.22 CpG sites = 11, Kimura (unadjusted) = 39.15 Transitions / transversions = 5.50 (11/2) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 29 7.36 0.00 2.27 chr3qtel1M 547795 547839 (452161) (CTC)n#Simple_repeat 1 44 (0) c_b150s251i3 5639 chr3qtel1M 547795 CTCCATCCTGCTCTTCCTCCTCTTCCTCCTCCTCCTCCTCCTCCT 547839 - v i i (CTC)n#Simple 1 CTCC-TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT 44 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 30 20.80 4.17 3.09 chr3qtel1M 547924 548019 (451981) (CTC)n#Simple_repeat 1 97 (0) m_b150s252i12 5640 chr3qtel1M 547924 CTCCTCCCTCCTCACTCTTTGTACCCCT-CTTCACCTTCTCC-CCT-TTC 547970 - - i iv v i - i v i - -i (CTC)n#Simple 1 CTCCT-CCTCCTC-CTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC 48 chr3qtel1M 547971 TTCCTCCTCCTCCTATTCCTCCTTCT-CTCCCCCTACCTCCTCTCCCTCC 548019 i vi i - i - ii (CTC)n#Simple 49 CTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT-CCTCCTCCTCCTCC 97 Matrix = Unknown Transitions / transversions = 3.00 (12/4) Gap_init rate = 0.07 (7 / 95), avg. gap size = 1.00 (7 / 7) 54 22.42 4.35 3.23 chr3qtel1M 548097 548280 (451720) (CCTCTC)n#Simple_repeat 1 186 (0) m_b150s252i13 5641 chr3qtel1M 548097 CCTCCCCCTCCGTCTTCTCCCTCTCCCTC-CCCGCCCCCTTTTCCT-TTT 548144 i - vi i - v i i i - ii (CCTCTC)n#Sim 1 CCTCTCCCT-CTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCC 49 chr3qtel1M 548145 C-CTGCCTCTCCC-CTTCCT-TCCCCTTCCCTCCCCCT-TCCTTCCCTCT 548190 - v - i - ii i - i i i (CCTCTC)n#Sim 50 CTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCT 99 chr3qtel1M 548191 CTTCCTTTTCCTGCT-CCTC-CCTTCCCTCTTCTCCCTCCCCCTCCCCCT 548238 i i i - - - i i - i i i (CCTCTC)n#Sim 100 CTCCCTCTCCCT-CTCCCTCTCCCTCTC-CCTCTCCCTCTCCCTCTCCCT 147 chr3qtel1M 548239 CTTCCCCTCCCCTTTCCCTTCTCCTTCTCCTTCTTCCATCTC 548280 i i - i - i i - v (CCTCTC)n#Sim 148 CTCCCTCT-CCCTCTCCC-TCTCCCTCTCCCTC-TCCCTCTC 186 Matrix = Unknown Transitions / transversions = 7.00 (28/4) Gap_init rate = 0.08 (14 / 183), avg. gap size = 1.00 (14 / 14) 223 21.67 0.00 7.69 chr3qtel1M 549848 549917 (450083) C L2d_3end#LINE/L2 (0) 516 452 m_b150s601i13 5642 chr3qtel1M 549848 TCAGTGAATCAATACACCAAGATATATTTATTAAGTTCCTACTGTGTGCC 549897 i v - v --- i iv i - C L2d_3end#LINE 516 TCAATCAATCAAT-CAACAAG---TATTTATTGAGCGCCTACTATGTG-C 472 chr3qtel1M 549898 TTGCCCCTATGCTAAGGGCT 549917 iiv v i i v C L2d_3end#LINE 471 TCAGCACTGTGCTAGGCGCT 452 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 23.71 CpG sites = 8, Kimura (unadjusted) = 25.76 Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.07 (5 / 69), avg. gap size = 1.00 (5 / 5) 221 24.26 5.66 6.67 chr3qtel1M 549854 549959 (450041) C L2d2_3end#LINE/L2 (3) 552 448 m_b150s601i14 5642 chr3qtel1M 549854 AATCAATACACCAAGATATATTTATTAAGTTCCTACTGTGTGCCTTGCCC 549903 --- i v v i iv v-v v v C L2d2_3end#LIN 552 AATCAA---ATCAACAAATATTTATTGAGCGCCTACTGTGTGCA-AGGCA 507 chr3qtel1M 549904 CTATGCTAAGGGCT-TGGAT--TACAGAGA--TA-AAAACAAACTGATCC 549947 i i v - iv-- i -- - i --- i C L2d2_3end#LIN 506 CTGTGCTAGGCGCTGTGGGGGATACAAAGAAGTATAAGACA---TGGTCC 460 chr3qtel1M 549948 TGGCCTGTGAGG 549959 iv ivii C L2d2_3end#LIN 459 CTGCCCTCAAGG 448 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 28.25 CpG sites = 13, Kimura (unadjusted) = 29.68 Transitions / transversions = 1.18 (13/11) Gap_init rate = 0.10 (11 / 105), avg. gap size = 1.18 (13 / 11) 280 25.28 4.55 1.10 chr3qtel1M 549865 549952 (450048) C L2b_3end#LINE/L2 (11) 455 365 m_b150s601i15 5642 chr3qtel1M 549865 CAAGATATATTTATTAAGTTCCTACTGTGTGCCTTGCCCCTATGCTAAGG 549914 v v i i iv -v v ? i i v C L2b_3end#LINE 455 CAACAAATATTTACTGAGCGCCTACTGTGTGCC-AGGCNCTGTGCTAGGC 407 chr3qtel1M 549915 GCTTGGATTACAGAGATA---AAAACAAACT-GATCCTGGCC 549952 v iv v i i--- i i ?- i iv C L2b_3end#LINE 406 GCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCC 365 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 30.51 CpG sites = 12, Kimura (unadjusted) = 32.25 Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.03 (3 / 87), avg. gap size = 1.67 (5 / 3) 14 12.53 0.00 0.00 chr3qtel1M 550824 550849 (449151) (GGAG)n#Simple_repeat 1 26 (0) m_b150s252i14 5643 chr3qtel1M 550824 GGAGGGAGTGCGGAAGGGAGGGAGGG 550849 v v i (GGAG)n#Simpl 1 GGAGGGAGGGAGGGAGGGAGGGAGGG 26 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 13 11.69 3.57 0.00 chr3qtel1M 552516 552543 (447457) (CTCC)n#Simple_repeat 1 29 (0) m_b150s252i15 5644 chr3qtel1M 552516 CTCCCTCCCTGCCTCTC-CTCTCCCTCCC 552543 v i - i (CTCC)n#Simpl 1 CTCCCTCCCTCCCTCCCTCCCTCCCTCCC 29 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 974 27.21 2.65 3.74 chr3qtel1M 552681 553058 (446942) L1ME3A_3end#LINE/L1 178 551 (369) m_b150s551i16 5645 chr3qtel1M 552681 ACCACAACTCTAAGATACCACTACACACCTGTCAGATTGGCTAAGATGAC 552730 --- i? iii v i v L1ME3A_3end#L 178 ACCACAA---TGNGATACCACTACACACCCACCAGAATGGCTAAAATGAA 224 chr3qtel1M 552731 AGGAAAAAATAATGATGATTGTTGGAGGGGATGTGGGAAAACTGGGACAT 552780 iii v i i ivii v v i iiv i i vi L1ME3A_3end#L 225 AAAGACAGACAATACCAAGTGTTGGCGAGGATGTGGAGCAACCGGAACTC 274 chr3qtel1M 552781 TGATTCATTGTTGGTGGAGTTGTGAACTGAATCCAACCATTTTGAGAGAT 552830 v v i i iiv i i -i v i ii i i L1ME3A_3end#L 275 TCATACACTGCTGGTGGGAGTGTAAATTG-GTACAACCACTTTGGAAAAC 323 chr3qtel1M 552831 AGTTTGGAACTATGCTCAAAAAGTTATCAAAC-TGTGCATACCCTTTGAT 552879 v v v - vvv i ---i - i v i L1ME3A_3end#L 324 TGTTTGGCAGTAT-CTACTAAAGCT---GAACATATGCATACCCTATGAC 369 chr3qtel1M 552880 CCAGCAGTGTTACTTACTGGAT-TATATCCCAAAGAGAT-TATAAAGAAG 552927 i vii i- i i - i v v i -ii v v v L1ME3A_3end#L 370 CCAGCAATTCCACTC-CTAGGTATATACCCAACAGAAATGCGTACATATG 418 chr3qtel1M 552928 ----GGAAAGGACCTGTATGTGCACGAATGTTTGTGGCAGCCCT-TTTGT 552972 ----vv i ---- i v ii i v - i L1ME3A_3end#L 419 TTCACCAAAAGAC----ATGTACAAGAATGTTCATAGCAGCACTATTCGT 464 chr3qtel1M 552973 AGTGGCTAGAAACTGGAAACTG-ATGGATGTCCATCAGTTG-AGAATGGC 553020 i i i?? ?i-viii iiv - v L1ME3A_3end#L 465 AATAGCCNNAAACTGGAAACNACCCAAATGTCCATCAACAGTAGAATGGA 514 chr3qtel1M 553021 TGAATAAATTGTAGGTATATGAAAATTATGGAATATTA 553058 i - vv v iv i L1ME3A_3end#L 515 TAAATAAATTGT-GGTATATTCACACAATGGAATACTA 551 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 34.08 CpG sites = 63, Kimura (unadjusted) = 35.47 Transitions / transversions = 1.75 (63/36) Gap_init rate = 0.06 (21 / 377), avg. gap size = 1.14 (24 / 21) 790 27.81 5.43 5.43 chr3qtel1M 552684 553143 (446857) L1ME5_3end#LINE/L1 178 637 (304) m_b150s551i17 5645 chr3qtel1M 552684 ACAACTCTAAGATACCACTACACACCTGTCAGATTGGCTAAGATGACAGG 552733 vv i i vi i i i v i v --- L1ME5_3end#LI 178 ACAACAATGAGATATCACTTTACACCTATTAGACTGGCAAAAATTA---G 224 chr3qtel1M 552734 AAAA---AATAATGATGATTGTTGGAGGGGATGTGGGAAAACTGGGACAT 552780 i---i vii v v i i ? iv i vi L1ME5_3end#LI 225 AAAGCTGGATAATGCCAAGTGTTGGCGAGGATGTGGGGANATAGGAACCC 274 chr3qtel1M 552781 TGATTCATTGTTGGTGGAGTTGTGAACTGAATCCAACCATTTT-GAGAGA 552829 v v i i iiv ii -i v i i - - L1ME5_3end#LI 275 TCATGCACTGCTGGTGGGAGTGTAGACTG-GTGCAGCCATTCTGGAGAG- 322 chr3qtel1M 552830 TAGTTTGGAACTA--TGCTCAAA--AAGTTATCAAACTGTGCATACCCTT 552875 i i i v v -- iv -- - --- --- v L1ME5_3end#LI 323 CAATCTGGCAGTACTTAGTCAAATTAAG-TAT---AC---GCATACCCTA 365 chr3qtel1M 552876 TGATCCAGCAGTGTTACTTACTGGAT-TATATCCCAAAGAGATTATAAAG 552924 i i viii i- i - i v v vi L1ME5_3end#LI 366 TGACCCAGCAATTCCGCTC-CTGGGTATATATCCCAAAGAAATTCTCACA 414 chr3qtel1M 552925 AAGG-----GAAAGGACCTGTATGTGCACGAATGTTTGTGGCAGCCCT-T 552968 v -----i ii ---- i iv i ii v vi - L1ME5_3end#LI 415 CAGGTCCATAAGGGGAC----ATGTACGAGGATGTTCATTGCAGCGTTGT 460 chr3qtel1M 552969 TTGTAGTGGCTAGAAACTGGA---AACTGATGGATGTCCATCAGT-TGAG 553014 i vi i ii --- i-- i v -v L1ME5_3end#LI 461 TTGTGGTGGCGGGGAGTTGGAGGCAACC--TGGGTGTCCATCACTGGGAG 508 chr3qtel1M 553015 AATGGCTGAATAAATTGTAGGTATATGAAAATTATGGAATATTACTGT-T 553063 i v iii v - iv v v ii i i - i-v L1ME5_3end#LI 509 AGTGGATAGGTAAAATGT-GGTGGATGCACACCATGGAGTACTA-TGCAG 556 chr3qtel1M 553064 CTGTAAGAAATGACCAACAGGATGATTTCAGAAAG--GCCTGGAGAGA-C 553110 v v iii vi vi -- v v v --i v vi - L1ME5_3end#LI 557 CAGTTAGAAGCAACGGACTAGATG--TACACATAGCAACATGGATGGATC 604 chr3qtel1M 553111 TTACACGAAC-TGATGCTGAG-GAAATGAGTAGGA 553143 v -- - ii - vi i L1ME5_3end#LI 605 TTAAA--AACATAGTGCTGAGTGAAAAAAGTAAGA 637 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.20 CpG sites = 75, Kimura (unadjusted) = 35.99 Transitions / transversions = 1.63 (75/46) Gap_init rate = 0.08 (39 / 459), avg. gap size = 1.28 (50 / 39) 394 33.51 2.93 2.93 chr3qtel1M 554182 554556 (445444) L1P3_orf2#LINE/L1 2881 3255 (39) m_b150s551i18 5646 chr3qtel1M 554182 TCAAAATGGGTTCATGATCTAGGCATAAAGAATGAGATCATAAATAAATT 554231 i i v v ii ii i iivv i i i v vvi L1P3_orf2#LIN 2881 TCAAGATGGATTAAAGACTTAAACGTAAGACCTAAAACCATAAAAACCCT 2930 chr3qtel1M 554232 GGAAGAG--CATAGGATAGTTTACCTCTCAG-ACCTGTGGAAGAGGAAGG 554278 i i-- v vv --- vi - v iv v v i v i L1P3_orf2#LIN 2931 AGAAGAAAACCTAGGCAA---TACCATTCAGGACATAGGCATGGGCAAAG 2977 chr3qtel1M 554279 AATTTATGACCAAAGAAGAAGTAGAGATCACTATTGACTACAAAATTGAA 554328 v i i iv vv iv vi vi v ivi vvv v L1P3_orf2#LIN 2978 ACTTCATGACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGAC 3027 chr3qtel1M 554329 AATTTTGATTATATCAAATTGAAAAGTTTTTGTACA---AATAAAACTA- 554374 v vv ivv i i i i i i i --- vi - L1P3_orf2#LIN 3028 AAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTAT 3077 chr3qtel1M 554375 -ATGCAGGCAAGATTAGAAGGGAAACAATAAACTGGGAAAACATTTTTAC 554423 - ----- iii v iv v v v i i v i v i L1P3_orf2#LIN 3078 CAT-----CAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGC 3122 chr3qtel1M 554424 AGTCAAAGGTTCTGATAAAGGCCTCATTTCCAAAATATATAAAGAATTGA 554473 i v vvvv i v v v i v i i i v L1P3_orf2#LIN 3123 AATCTATCCATCTGACAAAGGGCTAATATCCAGAATCTACAAGGAACTTA 3172 chr3qtel1M 554474 CTCTAATTTATAAGAAAT---CAAGCCATTCTCCAATTGATAAATGGTCA 554520 vv v i v--- i v -- i - ii v i v i L1P3_orf2#LIN 3173 AACAAATTTACAAGAAAAAAACAAACAA--CCCCA-TCAAAAAGTGGGCG 3219 chr3qtel1M 554521 AAGGATATGAACAGACAATTTTCAGATGATGAAATT 554556 v i i v v v L1P3_orf2#LIN 3220 AAGGATATGAACAGACACTTCTCAAAAGAAGACATT 3255 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 44.03 CpG sites = 59, Kimura (unadjusted) = 45.01 Transitions / transversions = 0.94 (59/63) Gap_init rate = 0.05 (17 / 374), avg. gap size = 1.29 (22 / 17) 380 28.30 3.99 3.99 chr3qtel1M 554320 554595 (445405) L1M4_orf2#LINE/L1 3019 3294 (0) m_b150s551i19 5646 chr3qtel1M 554320 AAAATTGAAAATTTTGATTATATCAAATTGAAAAGTTTTTGTAC---AAA 554366 v v v v i vi v v ii i --- L1M4_orf2#LIN 3019 AAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAA 3068 chr3qtel1M 554367 TAAAACTAATGCAGGCAAGATTAGAAGGGAAACAATAAACTGGGAAAACA 554416 vi v --v i v - v i iv v v i i v i v L1M4_orf2#LIN 3069 GGACACTA--TCAAGAAAG-TGAAAAGACAACCCACAGAATGGGAGAAAA 3115 chr3qtel1M 554417 TTTTTACAG-TCAAAGGTTCTGATAAAGGCCTCATTTCCAAAATATATAA 554465 v i i- v vi - i v ?i v i L1M4_orf2#LIN 3116 TATTTGCAAATCATATAT-CTGATAAGGGACTNGTATCCAGAATATATAA 3164 chr3qtel1M 554466 AGAATTGACTCT---AATTT----ATAAGAAATCAAGCCATTCTCCAATT 554508 ---- --- i i---- i iv --- vvi L1M4_orf2#LIN 3165 AGA----ACTCTTACAACTCAACAATAAAAAGACAA---ATAACCCAATT 3207 chr3qtel1M 554509 GATAAATGGTCAAAGGATATGAACAGACAATTTTCAGATGATGAAATTAA 554558 ? v v v i v i vi v v v vv L1M4_orf2#LIN 3208 NAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACA 3257 chr3qtel1M 554559 AATTATTACTACTCATTTGAAAGAATGTTCCAAATCA 554595 viii v vv iv ii i v v L1M4_orf2#LIN 3258 AATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 3294 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 36.06 CpG sites = 33, Kimura (unadjusted) = 36.06 Transitions / transversions = 0.79 (33/42) Gap_init rate = 0.05 (15 / 275), avg. gap size = 1.47 (22 / 15) 399 27.95 2.97 2.97 chr3qtel1M 554320 554555 (445445) L1PREC2_orf2#LINE/L1 3019 3254 (40) m_b150s551i20 5646 chr3qtel1M 554320 AAAATTGAAAATTTTGATTATATCAAATTGAAAAGTTTTTGTACA---AA 554366 v v vv ivv i i i i i i i --- L1PREC2_orf2# 3019 AAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAA 3068 chr3qtel1M 554367 TAAAACTAATGCAGGCAAGATTAGA-AGGGAAACAATAAACTGGGAAAAC 554415 vi --v i- - v i - iv v v i i v i v L1PREC2_orf2# 3069 AGAAACTA--TCAA-CA-GAGTAAACAGACAACCTACAGAATGGGAGAAA 3114 chr3qtel1M 554416 ATTTTTACAGTCAAAGGTTCTGATAAAGGCCTCATTTCCAAAATATATAA 554465 ? i iv v v vv i i v v iv v L1PREC2_orf2# 3115 ATNTTTGCAAACTATGCATCTGACAAAGGTCTAATATCCAGCATCTATAA 3164 chr3qtel1M 554466 AGAATTGACTCTAATTTATAAGAAAT---CAAGCCATTCTCCAATTGATA 554512 i i v vv v i v--- i v -- i - i v L1PREC2_orf2# 3165 GGAACTTAAACAAATTTACAAGAAAAAAACAAACAA--CCCCA-TTAAAA 3211 chr3qtel1M 554513 AATGGTCAAAGGATATGAACAGACAATTTTCAGATGATGAAAT 554555 i v i v i v v v L1PREC2_orf2# 3212 AGTGGGCAAAGGACATGAACAGACACTTTTCAAAAGAAGACAT 3254 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.37 CpG sites = 29, Kimura (unadjusted) = 35.37 Transitions / transversions = 0.83 (29/35) Gap_init rate = 0.04 (10 / 235), avg. gap size = 1.40 (14 / 10) 1132 28.63 7.59 2.03 chr3qtel1M 554449 555054 (444946) L1ME5_3end#LINE/L1 4 642 (299) m_b150s551i22 5646 chr3qtel1M 554449 ATTTCCAAAATATATAAAGAATTGACTCTAATTTATAAGAAATCAAGCCA 554498 v i i i i i vviv v iv i -- v i L1ME5_3end#LI 4 ATATCTAGAATATACAAGGAACTCCTGCAAATCAACAAGAAA--AAGACG 51 chr3qtel1M 554499 TT--CTCCAATTGATAAATGGTCAAAGGATATGAACAGACAATTTTCAGA 554546 v?-- i v v v i v L1ME5_3end#LI 52 GNAACCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGA 101 chr3qtel1M 554547 TGATGAAATTAAAATTATTACTACTCATTTGAAAGAATGTTCCAAATCAC 554596 v v iivi vvii vi vv v iii i v v i L1ME5_3end#LI 102 AGAGGAAACCCGAAAGGCTAACAAGCATATGAAGAGATGCTCAAACTCAT 151 chr3qtel1M 554597 TATTGATCAGAGAAATGGAAATTAAGACAACTCTGAGATACCACTACACA 554646 v i v i vv i vi L1ME5_3end#LI 152 TAGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACA 201 chr3qtel1M 554647 CCTGTCAGATTGGCTAGAATGAAGGAAC---ATAACACGGAATGTTG--A 554691 i i i v i v iii i --- ii vi i --i L1ME5_3end#LI 202 CCTATTAGACTGGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTGGCG 251 chr3qtel1M 554692 GGGAT---GGGAAAAAGGGACACTGATACATTGATGGCGGAATTTGGGAA 554738 i --- ? v i v v i i v i i v vvi v L1ME5_3end#LI 252 AGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGAC 301 chr3qtel1M 554739 TAATCCAGCCATTCT-GAGGGCAATTTGGAACTA--TGCCCAAAAGTTAT 554785 ii v - i i v v -- ivi -- - L1ME5_3end#LI 302 TGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAA--TTA- 348 chr3qtel1M 554786 CAAACTGTGCATACCTT-TGATCCAGCAGTGTCTCTACTGGGCTTATACC 554834 - ivv ii i - i i vi v v iv i L1ME5_3end#LI 349 -AGTATACGCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATATC 397 chr3qtel1M 554835 CCAAAGAGATACT-AAAAAGG-----AAAGGGACCTGTATGTGCCAAATG 554878 i v - v v ----- i v i v ---i L1ME5_3end#LI 398 CCAAAGAAATTCTCACACAGGTCCATAAGGGGACATGTACGAG---GATG 444 chr3qtel1M 554879 TTT-TGGGAGCCCTGTTTGTAGT---TAGAAGTTGAAA--AATGAATGGA 554922 i- v v vi i ---vi i i i-- i--v i L1ME5_3end#LI 445 TTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAAC--CTGGG 492 chr3qtel1M 554923 TGCCCAGCATT--GAGAATGGTTGAGTAAATTGTGGT--ATG-AAACGA- 554966 i v i -- i v ii v -- - v v - L1ME5_3end#LI 493 TGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACACCAT 542 chr3qtel1M 554967 -AATTATTATTCTGTA---AGAAATGACCAGCAGGATGAATACAGAGA-- 555010 -i v i v v i --- iii vii vi v i v v-- L1ME5_3end#LI 543 GGAGTACTATGCAGCAGTTAGAAGCAACGGACTAGATGTACACATAGCAA 592 chr3qtel1M 555011 ---GGATTTGGA-CTTAGATGAATGATGCTAAGCGAAA----TAAGAACC 555052 --- -- - i viv ii i i ---- v L1ME5_3end#LI 593 CATGGA--TGGATCTTAAAAACATAGTGCTGAGTGAAAAAAGTAAGAAAC 640 chr3qtel1M 555053 AG 555054 L1ME5_3end#LI 641 AG 642 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.70 CpG sites = 95, Kimura (unadjusted) = 37.07 Transitions / transversions = 1.27 (95/75) Gap_init rate = 0.06 (34 / 605), avg. gap size = 1.74 (59 / 34) 1216 25.64 4.89 2.29 chr3qtel1M 554449 554959 (445041) L1ME3G_3end#LINE/L1 4 527 (397) m_b150s551i21 5646 chr3qtel1M 554449 ATTTCCAAAATATATAAAGAATTGACTCTAATTTATAAGAAATCAAGCCA 554498 v i i vviv v iv -- v L1ME3G_3end#L 4 ATATCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAA--AAGACA 51 chr3qtel1M 554499 TTCTCCAATTGATAAATGGTCAAAGGATATGAACAGACAATTTTCAGATG 554548 --vi v v v i iv v L1ME3G_3end#L 52 --ACCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAG 99 chr3qtel1M 554549 ATGAAATTAAAATTATTACTACTCATTTGAAAGAATGTTCCAAATCACTA 554598 v vv viii v vv v ii i v vv L1ME3G_3end#L 100 AGGAAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTA 149 chr3qtel1M 554599 TTGATCAGAGAAATGGAAATTAAGACAACTCTGAGATACCACTACACACC 554648 v i i v i vv i viv L1ME3G_3end#L 150 GTAATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACC 199 chr3qtel1M 554649 TGTCAGATTGGCTAGAAT---GAAGGAACATAACACGGAATGTT---GAG 554692 ii v i ---i ?vvv i iv? i --- L1ME3G_3end#L 200 CATCAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAG 249 chr3qtel1M 554693 GG-ATGGGAAAAAGGG-ACACTGATACATTGATGGCGGAATTTGGGAATA 554740 -i i v - v v i v i i v vvii v i L1ME3G_3end#L 250 GGTGTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTG 299 chr3qtel1M 554741 ATCCAGCCATTCT-GAGGGCAATTTGGAACTATGCCCA--AAAGTTATCA 554787 i v ? i - v v -- i -- i -- i L1ME3G_3end#L 300 GTACAGCCNTTTTGGAGGGCAATTTGGCAGTAT--CTATTAAAAT--TTA 345 chr3qtel1M 554788 AACTGTGCATA-CCTTTGATCCAGCAGTGTCTCTACTGGGCTTATACCCC 554836 v i - i i vi v v ? ?v v i i L1ME3G_3end#L 346 AAATGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCT 395 chr3qtel1M 554837 AAAGAGATACTAAAAA----GGAAAGGGACCTGTATGTGCCA-AATGTTT 554881 ? i viv v---- v v i --? i i v -i i L1ME3G_3end#L 396 ANAGAAATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTC 443 chr3qtel1M 554882 -TGGGAGCCCTGTTTG---TAGTTAGAAGTTGAAAAATGAA--TGGATGC 554925 - v v vi --- iv i i i --v -- ii i L1ME3G_3end#L 444 ATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAA--CAACCTAAATGT 491 chr3qtel1M 554926 CCAGCATT--GAGAATGGTTGAGTAAATTGTGGTAT 554959 v v -- i i i i L1ME3G_3end#L 492 CCATCAATAGGGGAATGGTTAAATAAATTATGGTAT 527 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 31.35 CpG sites = 63, Kimura (unadjusted) = 32.24 Transitions / transversions = 0.97 (63/65) Gap_init rate = 0.05 (25 / 510), avg. gap size = 1.48 (37 / 25) 41 0.00 0.00 0.00 chr3qtel1M 555438 555472 (444528) (AT)n#Simple_repeat 1 35 (0) c_b151s251i0 5647 chr3qtel1M 555438 ATATATATATATATATATATATATATATATATATA 555472 (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATA 35 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 227 30.09 0.00 12.35 chr3qtel1M 556103 556193 (443807) L2c_3end#LINE/L2 380 460 (18) m_b151s601i0 5648 chr3qtel1M 556103 TAAGCTCTTCCAAAGCAGGGGCTGTCTTTTGTTTTAAATCCTTCATTTGG 556152 i i iv ii i i v i i i--- ----- v L2c_3end#LINE 380 TGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTC---ATC-----TTTGT 421 chr3qtel1M 556153 ATTCCTATAGTGCCTGGTACACAGTAGGTATTTAAATAATG 556193 i i -- i i i iii i vv L2c_3end#LINE 422 ATCCCCA--GCGCCTGGCACATAGTAGGCGCTCAATAAATG 460 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.26 CpG sites = 19, Kimura (unadjusted) = 41.14 Transitions / transversions = 3.80 (19/5) Gap_init rate = 0.11 (10 / 90), avg. gap size = 1.00 (10 / 10) 322 35.68 5.04 1.08 chr3qtel1M 557288 557644 (442356) L1ME5_3end#LINE/L1 32 402 (539) m_b151s551i2 5649 chr3qtel1M 557288 AAATGTATAAAAATAAAA-GCCATTTCCCATATGATAAATGATCAAAAGA 557336 vv i i v i - v? vii v - v iv i L1ME5_3end#LI 32 AAATCAACAAGAAAAAGACGGNAACCCCAATA-GAAAAATGGGCAAAGGA 80 chr3qtel1M 557337 TATTAACAG----TTTTTAGATGGAGTAATCAGAA---CTAT--AGTATG 557377 v ---- vi v ii v i v --- v-- i i L1ME5_3end#LI 81 TATGAACAGGCAATTTACAGAAGAGGAAACCCGAAAGGCTAACAAGCATA 130 chr3qtel1M 557378 TCAAAAAAAAAAAAAGTGCCCTATTGATTGGGAAAATGCAAATTAAAACA 557427 v i i vivvv iiv vi v i ii ii L1ME5_3end#LI 131 TGAAGAGATGCTCAAACTCATTAGTAATCAGAGAAATGCAAATTAAAACA 180 chr3qtel1M 557428 ATTCTGTGGTACTGCCTCATAACTATTAGACTGGC------CAGGAGGAC 557471 ivv v i iii i i i v ------i i i vi L1ME5_3end#LI 181 ACAATGAGATATCACTTTACACCTATTAGACTGGCAAAAATTAGAAAGCT 230 chr3qtel1M 557472 AGAAAATGACAAATGGTGGAGGAGATATGGGGAAAATGATTTACTAAT-- 557519 i v v i v v ii i ? vv ivviv v -- L1ME5_3end#LI 231 GGATAATGCCAAGTGTTGGCGAGGATGTGGGGANATAGGAACCCTCATGC 280 chr3qtel1M 557520 ATTGTTGATCAAGTTGTGAACTGATTCAAAAATTCTACAGAGCAATTTGT 557569 i i i viiiv ii i v ivv iv i - L1ME5_3end#LI 281 ACTGCTGGTGGGAGTGTAGACTGGTGCAGCCATTCTGGAGAGCAATCTG- 329 chr3qtel1M 557570 AACTGTACCCAAAAGACTGCAAAACTATGCATGCCCTTTGACCCAGCAAT 557619 -i v ii ivvi v -i ivv i i v L1ME5_3end#LI 330 -GCAGTACTTAGTCAAAT-TAAGTATACGCATACCCTATGACCCAGCAAT 377 chr3qtel1M 557620 ATAACTATCAGATCTGTATTCCAAA 557644 vivi viii i v i i L1ME5_3end#LI 378 TCCGCTCCTGGGTATATATCCCAAA 402 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 49.55 CpG sites = 72, Kimura (unadjusted) = 50.71 Transitions / transversions = 1.33 (72/54) Gap_init rate = 0.03 (10 / 356), avg. gap size = 2.20 (22 / 10) 360 35.05 3.89 2.30 chr3qtel1M 557398 557654 (442346) L1MA8_3end#LINE/L1 151 411 (627) m_b151s551i3 5649 chr3qtel1M 557398 CTATTGATTGGGAAAATGCAAATTAAAACAATTCTGTGGTACTGCCTCAT 557447 v v ii i v ivv v i iii i L1MA8_3end#LI 151 CTAATCATCAGGGAAATGCAAATTAAAACCACAATGAGATATCACCTCAC 200 chr3qtel1M 557448 AACTATTAGACTGGC------CAGGAGGACAGAAAATGACAAATGGTGGA 557491 v i v ------ ii i ii i i i v v L1MA8_3end#LI 201 ACCTGTTAGAATGGCTATTATCAAAAAGACGAAAGATAACAAGTGTTGGC 250 chr3qtel1M 557492 GGAGATATGGGGAAAATGA----TTTACTAATATTGTTGATCAAGTTGTG 557537 ii i i v i----i i -- i i i viiiv i L1MA8_3end#LI 251 GAGGATGTGGAGAAAAGGGAACCCTTGC--ACACTGTTGGTGGGAATGTA 298 chr3qtel1M 557538 AACTGATTCAAAAATTCTACAGAGCAATTTGTAACTGTACCCAAAAGACT 557587 i ii v ivv v iv i i i v v iv - v i i i L1MA8_3end#LI 299 AATTAGTACAGCCATTATGGAAAACAGTATGGAGGT-TCCTCAAAAAATT 347 chr3qtel1M 557588 GCAAAACTATGCATGCCCTTTGACCCAGCAATATAACTATCAGATCTGTA 557637 -- v vivv i v v i viv iii i v i L1MA8_3end#LI 348 --AAAAATAGAACTACCATATGATCCAGCAATCCCACTACTGGGTATATA 395 chr3qtel1M 557638 TTCCAAAAGCGATTAAA 557654 - i vi v L1MA8_3end#LI 396 -TCCAAAGGAAATGAAA 411 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 48.97 CpG sites = 55, Kimura (unadjusted) = 49.79 Transitions / transversions = 1.67 (55/33) Gap_init rate = 0.03 (8 / 256), avg. gap size = 2.00 (16 / 8) 256 21.33 11.11 1.01 chr3qtel1M 558079 558168 (441832) L2d2_3end#LINE/L2 412 510 (45) m_b151s601i1 5650 chr3qtel1M 558079 TGTTTTAATGTTCTCTTCCCACATTAGATTGTAAGCTTCTTGA-GGCAGA 558127 vvi v v i - i i - i L2d2_3end#LIN 412 TGTTTATGTCTTGTCTCCCCA-ACTAGATTGTAAGCTCCTTGAGGGCAGG 460 chr3qtel1M 558128 CACTTTTTCTTA------TTTGTATCTC---CATTACTTAGCACAGTGTC 558168 v iv v ------ i --- vii i i L2d2_3end#LIN 461 GACCATGTCTTATACTTCTTTGTATCCCCCACAGCGCCTAGCACAGTGCC 510 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 23.84 CpG sites = 11, Kimura (unadjusted) = 25.51 Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.04 (4 / 89), avg. gap size = 2.75 (11 / 4) 363 24.88 2.46 7.76 chr3qtel1M 558254 558375 (441625) C MIRc#SINE/MIR (119) 149 34 m_b151s601i2 5651 chr3qtel1M 558254 CCTCATTTTATGTATGAGGAA-TTGAA--TCAAACAGGGTTAAGTGACTT 558300 i iiv -i i-- i v - C MIRc#SINE/MIR 149 CCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGG-TTAAGTGACTT 101 chr3qtel1M 558301 GTTCAGGGTCACCCAGCTTGGAAGTGTCTGAAGTCATGTTTGAACTCAAG 558350 ii i v v v v v ------ iiv i i i C MIRc#SINE/MIR 100 GCCCAAGGTCACACAGCTAGTAAGTGGCAGA------GCCGGGACTCGAA 57 chr3qtel1M 558351 CCAAGGATACTTTCTGCCTCCAGAT 558375 v --v i v ii C MIRc#SINE/MIR 56 CCCAGG--TCTTCCTGACTCCAAGT 34 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.23 CpG sites = 17, Kimura (unadjusted) = 30.81 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.09 (11 / 121), avg. gap size = 1.09 (12 / 11) 289 31.75 12.87 0.52 chr3qtel1M 559645 559815 (440185) C MIR1_Amn#SINE/MIR (27) 203 12 m_b151s601i3 5652 chr3qtel1M 559645 CTTCTCATTATCTGATT------CATCCTTCAAGGTAGAT-GCCATTATT 559687 i i viv i------ iii v i v i -ivi i C MIR1_Amn#SINE 203 CTTTTCATCAGTAGATCTCAAAGCACTTTACAAAGGAGGTCAGTATCATT 154 chr3qtel1M 559688 ATCCTTGTATTACAAATCAGGAAACTGAGGT----AGAGGATCAATGA-T 559732 iii v i v i---- v?v i - C MIR1_Amn#SINE 153 ATCCCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACT 104 chr3qtel1M 559733 TGCCCTGGGATGCCCAGCTCTCTG--GACAGA------ATTCGAGTACAG 559774 vi vii ? ?vv ?i-- i ------ ? ? iiv C MIR1_Amn#SINE 103 TGCCCAAGGTCACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAACCCAG 54 chr3qtel1M 559775 ATCTTACCAATTCTTGGCCTAGAA--TTATCTACTGCACCACA 559815 i i- i v iii i i vi--i i iv C MIR1_Amn#SINE 53 GTCTC-CCGAGTCCCAGTCCAGTGCTCTATCCACTAGACCACA 12 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.06 CpG sites = 37, Kimura (unadjusted) = 46.28 Transitions / transversions = 2.18 (37/17) Gap_init rate = 0.05 (8 / 170), avg. gap size = 2.88 (23 / 8) 352 29.12 10.20 1.89 chr3qtel1M 559669 559815 (440185) C MIRc#SINE/MIR (101) 167 9 m_b151s601i4 5652 chr3qtel1M 559669 CAAGGTAGATGCCATTATTATCCTTGTATTACAAATCAGGAAACTGAGGT 559718 i i i --- iii v i v i C MIRc#SINE/MIR 167 CAGGGCAGGT---ATTATTATCCCCATTTTACAGATGAGGAAACTGAGGC 121 chr3qtel1M 559719 ----AGAGGATCAATGA-TTGCCCTGGGATGCCCAGCTC-TCTG-GACAG 559761 ---- v v i - vi vii v v- vv - i C MIRc#SINE/MIR 120 TCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAG 71 chr3qtel1M 559762 A------ATTCGAGTACAGATCTTACCAATTCTTGGCCTAGAA--TTATC 559803 ------ i iiv i v ii i ivi i i vi--i v C MIRc#SINE/MIR 70 AGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTC 21 chr3qtel1M 559804 TACTGCACCACA 559815 i C MIRc#SINE/MIR 20 CACTGCACCACA 9 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.46 CpG sites = 27, Kimura (unadjusted) = 38.46 Transitions / transversions = 1.80 (27/15) Gap_init rate = 0.06 (9 / 146), avg. gap size = 2.00 (18 / 9) 189 28.99 2.50 5.13 chr3qtel1M 559915 559994 (440006) L2c_3end#LINE/L2 399 476 (2) m_b151s601i5 5653 chr3qtel1M 559915 GACTAT-TTTTGCCTCTTTTTGTATCCCCAATATGTGCCTGGAA-ATAAT 559962 ii - i iiiiv i ---- i v - i L2c_3end#LINE 399 GACCGTGTCTTATTCATCTTTGTATCCCCA----GCGCCTGGCACATAGT 444 chr3qtel1M 559963 AAGCACTTAATAAATAAATGTGTAATGATTAA 559994 i i i ivv vv v i L2c_3end#LINE 445 AGGCGCTCAATAAATGTTTGTTGAATGAATGA 476 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.74 CpG sites = 15, Kimura (unadjusted) = 38.45 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.08 (6 / 79), avg. gap size = 1.00 (6 / 6) 380 38.89 0.86 3.98 chr3qtel1M 560221 560453 (439547) C L2#LINE/L2 (258) 2824 2599 m_b151s601i6 5654 chr3qtel1M 560221 TGGTCACACTTTTACTTTAAGAAAATCCCTTTGGTCACTTAATGGAGGAT 560270 i vv viii i ii v i iii vvi v i C L2#LINE/L2 2824 TGATCTGACTTACGTTTTAAAAGGATCACTCTGGCTGCTGTGTTGAGAAT 2775 chr3qtel1M 560271 GGACTAAAGTGAGGAGAGACAAGAGGCAAGAAGAACCCCCAGC-AGCCAG 560319 i i? v i vi ivvi i i i ---- i- vvi C L2#LINE/L2 2774 AGACTGNAGGGGGGCAAGGGTGGAAGCAGGGAGA----CCAGTTAGGAGG 2729 chr3qtel1M 560320 CTACTATAGCAACTCATGTGATAGTGAAGTGATGAGGGTCTGCACCAGGA 560369 i ii i ii v i ---- ii iv ii v i C L2#LINE/L2 2728 CTATTGCAGTAATCCAGGCGA----GAGATGATGGTGGCTTGGACCAGGG 2683 chr3qtel1M 560370 TGG-GGCAGTGTCAGAGGGGAAGAGGGGGATGTATCGGAGAGATGGTATG 560418 - -v iv vi i v vi v ivvi v iv v C L2#LINE/L2 2682 TGGTGGCAGTG-GAGGTGGTGAGAAGTGGTCGGATTCTGGATATATTTTG 2634 chr3qtel1M 560419 GAGACAAAATTGACTAGAGATGCTGCAGAGTTGAA 560453 i ii i iii vi vv vv ii i C L2#LINE/L2 2633 AAGGTAGAGCCGACAGGATTTGCTGATGGATTGGA 2599 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 54.72 CpG sites = 55, Kimura (unadjusted) = 59.09 Transitions / transversions = 1.72 (55/32) Gap_init rate = 0.05 (11 / 232), avg. gap size = 1.00 (11 / 11) 904 35.74 8.85 3.43 chr3qtel1M 560390 561496 (438504) C L2#LINE/L2 (217) 2865 1701 m_b151s601i7 5654 chr3qtel1M 560390 AGAGGGGGATGTATCGGAGAGATGGTATGGAG-ACAAAATTGACTAGAGA 560438 v i vvi i ---- v v - v ii v vv vv C L2#LINE/L2 2865 AGATGGGAAGCCATTGGAG----GGTTTTGAGCAGAGGAGTGACATGATC 2820 chr3qtel1M 560439 TGCTGCAGAGTTGAAAAAGACCAGAGAAGCTGCAGAGGTGA-AATGGATC 560487 vivi viv v i i vvvvi v v v - i ii C L2#LINE/L2 2819 TGACTTACGTTTTAAAAGGATCACTCTGGCTGCTGTGTTGAGAATAGACT 2770 chr3qtel1M 560488 AGAGATGGTGCAGAACTGAAAT-----GGATCAGAGATGGTGCAGAACTG 560532 i? iv - iiiv i v-----i i vv v iv v-- i C L2#LINE/L2 2769 GNAGGGGG-GCAAGGGTGGAAGCAGGGAGACCAGTTAGGAGGCT--ATTG 2723 chr3qtel1M 560533 AAATGGATCAGAGAAGCTGCAGAGGTGAAATGGACCAGAGAAGCTGCAGA 560582 v i iivi ivi vviiiiv ivv i vi iv v C L2#LINE/L2 2722 CAGTAATCCAGGCGAGAGATGATGGTGGCTTGGACCAGGGTGGTGGCAGT 2673 chr3qtel1M 560583 GGTGAAATGGCCCAGAGATGGTGCAGAAGTGAAATGGA--CCAGAGATGG 560630 ------------- i - iv-i -- ii v iv C L2#LINE/L2 2672 GG-------------AGGTGGTG-AGAAGTGGT-CGGATTCTGGATATAT 2638 chr3qtel1M 560631 TGCAGAAGTGAAATGGACAGGCCTTGGCACCATGTTAGATATGGACAGTG 560680 viii i ii iiv vi viiviivi i i ivv C L2#LINE/L2 2637 TTTGAAGGTAGAGCCGACAGGATTTGCTGATGGATTGGATGTGGGGTGTG 2588 chr3qtel1M 560681 AGAGA-------GAGTAAAGAGTG----CAACGTGAT---CCTGAAAGAC 560716 ------- v ii ---- v vv --- ivi C L2#LINE/L2 2587 AGAGAAAGAGAGGAGTCAAGGATGACTCCAAGGTTTTTGGCCTGAGCAAC 2538 chr3qtel1M 560717 TGGAAGAACGAGGGTGCCCGCTACAATAATTTAGCAGACAGATGGCAG-- 560764 i i ii v vvi? vivi vvi v v vv vi -- C L2#LINE/L2 2537 TGGAAGGATGGAGTTGCCATTNACTGAGATGGGGAAGACTGCGGGAGGAG 2488 chr3qtel1M 560765 --GGATTGGGGAAGAA-ACAATGGGTTCTAATTTGGACATGTTGAGTTTA 560811 -- v i ii - iv v i viv i i C L2#LINE/L2 2487 CAGGTTTGAGGGGGAAGATCAGGAGTTCAGTTTTGGACATGTTAAGTTTG 2438 chr3qtel1M 560812 AGATGAATGTCTATTGGACATCCAGTTCAAAATGTCTTTAAGATAGTAAG 560861 ----i i iv vi i vvvv ii vi C L2#LINE/L2 2437 AGATG----CCTATTAGACATCCAAGTGGAGATGTCGAGTAGGCAGTTGG 2392 chr3qtel1M 560862 AGATTCAAGA-------TCAACAGGGAGGTTGAGGCAGGAGAGTTTGTTT 560904 v v i v------- ivi i ivi v -------- C L2#LINE/L2 2391 ATATACGAGTCTGGAGTTCAGGGGAGAGGTCCGGGCTGGAGA-------- 2350 chr3qtel1M 560905 TATGTATGTATGTATCATAAGCATAGCAGA-GGTAATTTAATTCATGAGA 560953 iv v iv vi v -i - v v vi C L2#LINE/L2 2349 TATAAATTTGGGAGTCATCAGCATA-TAGATGGTATTTAAAGCCATGAGA 2301 chr3qtel1M 560954 GCCAACAAGGTCACCAAGTGAAATAGTATGGAAAAAGAAGAGAAGAGAGC 561003 vivi ii i ? v ivv i i v i iv C L2#LINE/L2 2300 CTGGATGAGATCACCNAGGGAGTGAGTGTAGATAGAGAAGAGAAGAGGTC 2251 chr3qtel1M 561004 CCAGGACAGAACCCTGAGGGA-----ATGGACAG-GGTCTGG------AG 561041 v v i i v ----- i vv? - v ------ C L2#LINE/L2 2250 CAAGGACTGAGCCCTGGGGCACTCCAACGTTNAGAGGTCGGGGAGATGAG 2201 chr3qtel1M 561042 GAGGACCCGGCAAAGGAGACATGGAAGGAATAAGTAGTCAG--AGAAAGA 561089 v i vvi iiiivi v -- i i C L2#LINE/L2 2200 GAGGAACCAGCAAAGGAGACTGAGAAGGAGCGGCCAGTGAGGTAGGAGGA 2151 chr3qtel1M 561090 GAACCAGAAAAGAGTGGATGTCCCTGAAAATCTAGAGAAAAGAGAGGACT 561139 i i i v - - i ii v v i i v vvii C L2#LINE/L2 2150 AAACCAGGAGAGTGTGG-TGT-CCTGGAAGCCAAGTGAAGAAAGTGTTTC 2103 chr3qtel1M 561140 CAGGACGAAAGAGTGACTAACAGTGTTTAATGCCACAGAACTGTCCAG-- 561187 v i v ii ii v iv ii v ?vv v -- C L2#LINE/L2 2102 AAGAAGGAGGGAGTGATCAACTGTGTCAAATGCTGCTGANAGGTCAAGTA 2053 chr3qtel1M 561188 -----------GAGAATGAGTCACTGGATCTGATCACTAAGAGCCTGACA 561226 ----------- viii i i iiiv vvi viiivii C L2#LINE/L2 2052 AGATGAGGACTGAGAATTGACCATTGGATTTAGCAACGTGGAGGTCATTG 2003 chr3qtel1M 561227 GTCACTTTGGAGGGGGCAGTTTGGGTGGAATGATAATGTCAAAGGTCAAA 561276 v i ivii i v i i iiv v i i i vi C L2#LINE/L2 2002 GTGACCTTGACAAGAGCAGTTTCGGTGGAGTGGTGGGGACGAAAGCCTGA 1953 chr3qtel1M 561277 CCATCGCAGGTTTGGAAGACA----GAGGAGAG--AT--------GCCAT 561312 iiivv ii iiii v ---- -- -------- v v C L2#LINE/L2 1952 TTGGAGTGGGTTCAAGAGAGAATGGGAGGAGAGGAATTGGAGACAGCGAG 1903 chr3qtel1M 561313 CATAGATGATGAATTT---GAGTTTAGCCACAAAGGGCAGAGGAGATCTA 561359 i ii ivvv i--- v iii v vi vv i C L2#LINE/L2 1902 TATAGACAACTCTTTCGAGGAGTTTTGCTGTAAAGGGGAGCAGAGAAATG 1853 chr3qtel1M 561360 GAATGACAGTTAGCCGGGTAGAT-GGGTCAAGTGAGGATTGGGG------ 561402 iii ii i i vv v ?i - v i vvv ------ C L2#LINE/L2 1852 GGGCGGTAGCTGGAGGGGGANGTGGGGTCAAGGGAGAATTTTTGTTTTTT 1803 chr3qtel1M 561403 -GAGATTGGTTAGATTTATAG---GTTTGAAGG-----AGCAAGGAGCCA 561443 -i v vv i - ? i --- v v -----i v v v C L2#LINE/L2 1802 AAAGATGGGAGAAA-TNACAGCATGTTTGTATGCTGATGGGAATGATCCA 1754 chr3qtel1M 561444 G-AGAGAGACTAATGATCTGGTGGAGTAGGCAAGA-TGGGGAGAATCCCT 561491 - ivv -- vi i iv i vi -v iv C L2#LINE/L2 1753 GTAGAGAGGGAAA--AATTGATGATGCAGGAGAGAGAGGGGAGAATTGCT 1706 chr3qtel1M 561492 GGAGC 561496 C L2#LINE/L2 1705 GGAGC 1701 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 48.68 CpG sites = 207, Kimura (unadjusted) = 50.58 Transitions / transversions = 1.18 (207/175) Gap_init rate = 0.06 (69 / 1106), avg. gap size = 2.00 (138 / 69) 248 36.08 12.44 2.95 chr3qtel1M 561426 562076 (437924) C L2#LINE/L2 (1351) 1731 1021 m_b151s601i8 5654 chr3qtel1M 561426 TGAAGGAGCAAGGAGCCAGAGAGAGACT--AATGATCTGGTGGAGTAGGC 561473 v vi ii --i ivvi -- ii v vv v C L2#LINE/L2 1731 TGCAGGAGAGAGAGG--GGAGAATTGCTGGAGCGATGTCCTTGAGTAGGC 1684 chr3qtel1M 561474 AAGATGGGGA--GAATCCCTGGAGCAGATAGAGGG-TCAACCTTGGCCAG 561520 i - -- i ivvv vi ii i - iii i vi C L2#LINE/L2 1683 GAGA-GGGGATGGGATCTAGTGCACAAGTGGAGGGGTTGGCCTTAGATAG 1635 chr3qtel1M 561521 GAGTCAGACCATTTCAGC-ATGG-AAGATGGGGGAAGGAAGGAGGGAAGG 561568 ivv iv v v -i i - v v i v iiviviv C L2#LINE/L2 1634 GAGCACGGACAGTTCATCCGTAGTAACAGGAGGGAAGGCAGAGTATGTGG 1585 chr3qtel1M 561569 ATAGGGGTTTCTGAGGGAGGGAAGGGGAGAAGA-GGAAGTTCATGGCAAA 561617 ii vi i vivv vi v v iv v iv i- i ??ii v iv C L2#LINE/L2 1584 GCACAGATGCAGGTAGGTGGGTAGATGTGGTGGTGGGAGNNTGTGGAAGT 1535 chr3qtel1M 561618 TGGTCTCAGGTTTTTTTTTTTTTTTTA-CAAAACA------AAGAGTTTC 561660 vvii v i vi i v i i -ii i ------ iviv C L2#LINE/L2 1534 TCTCTTCTGATTGCTTCTATTTTCTCAGTGAAATAGGAAGCAAGGTCATC 1485 chr3qtel1M 561661 AGCTGAGAGAGGGG----GAGAGGAAG-------GCTTTG------GAGG 561693 v i ---- i i ------- v ------ C L2#LINE/L2 1484 AGCTGAGAGTGAGGATAGGGGAGGAGGTGTTGGAGGTTTGAGGAGAGAGG 1435 chr3qtel1M 561694 AG-----------CCATTGTCAGGGAGGG-----GAGTAAGCTGATGAGG 561727 -----------ivi i vi i ----- i iiv iv C L2#LINE/L2 1434 AGAAGGTGTGAAATAGTCGTCTAGGAGAGTGGGAGAGTGAATGGACTAGG 1385 chr3qtel1M 561728 GAGCTATAGTAAGATTGCCTGGTAGCATCAAGGGCCCAGTGGA-GTGTGT 561776 iv i ? v i i v v - v? C L2#LINE/L2 1384 GAAATGTAGTANGATTGCCGGGCAGCATTAAGGGCCCACTTGAGGTTNGT 1335 chr3qtel1M 561777 -CCCGTAAACCTGGAGTGGGCCCTGTCAGGA------TGTGATTTTCTCT 561819 -vi i i ii ii i v v v ------ v i C L2#LINE/L2 1334 GGTCATGAATTTAAAGTGAGACCAGTCAGCATGGTTGTGTGTTTTTCTCC 1285 chr3qtel1M 561820 ACCTTCATTTACCAACATGTATGTGGGCATGGAGGAGGTCAGATGGTGAG 561869 v iv i i v vi ?i vi ii ii v - i vi vi C L2#LINE/L2 1284 AGCCACGTTCAGCTGCNCGGGTGCAGGCGCGGAGTAGG-CGGAGAGTTGG 1236 chr3qtel1M 561870 AGTGATCCAAGACTGGAGCTTT--------------------TGGGGGTG 561899 v v v i ii ?i i --------------------i i i v C L2#LINE/L2 1235 ATTTAACCAGGGTTGNGGTTTTGCCAGGCGAGTACGACGAAGCGAGAGAG 1186 chr3qtel1M 561900 GGGCACGTTTGGGCTCATGGTAGAGATCAAGGGATTCAGGAGA-----GG 561944 v --v i i v v v vi- v v vv v -----? C L2#LINE/L2 1185 GGGCAAG--GGAGTTGAGGGTATATG-CAAGGGAGTGATTATAATGATNG 1139 chr3qtel1M 561945 AGCACAAGGGCTGAGCTGGGTCGCCAATGGGGAGAAGTAGAGGGAATAGC 561994 v iiiiiv i ----- v i i - iv i-- C L2#LINE/L2 1138 ACCATGGAATCTAAGCTGGGT-----AAGGAGGGAAGT-GAGGACATG-- 1097 chr3qtel1M 561995 TAGAGCGGGGGAGAGAGCCTGAGAGGGCTGAGGGGTCAAGGGAGAGTAGG 562044 - i - v i vvv i i iv vi i v vv v C L2#LINE/L2 1096 -AGGG-GGGTGAGGGACAGTGAAAAGGTGGTAGGATCAATGGATTGGAGG 1049 chr3qtel1M 562045 GTCATGTAAGGGGAGTCAGAGGGTTTTCAGAG 562076 vi vv ---- i ii ii v ii C L2#LINE/L2 1048 TCCCGGT----GGGGTCGAAGAATTGTTGGAG 1021 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 48.47 CpG sites = 128, Kimura (unadjusted) = 52.04 Transitions / transversions = 1.28 (128/100) Gap_init rate = 0.06 (39 / 650), avg. gap size = 2.62 (102 / 39) 23 14.60 0.00 0.00 chr3qtel1M 566671 566708 (433292) (G)n#Simple_repeat 1 38 (0) m_b151s252i0 5655 chr3qtel1M 566671 GGGCGGGGGGGGGGGGGGGGGGGGGGAAGTGGAGGGGG 566708 v ii v i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 38 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 191 14.00 16.00 0.00 chr3qtel1M 566763 566812 (433188) C MIR1_Amn#SINE/MIR (62) 168 111 m_b151s601i9 5656 chr3qtel1M 566763 GAGAGCAGTGTCA-------CATTTTACAGATAAGGAAAGTGAGACCCAG 566805 iv i ------- i v i ? C MIR1_Amn#SINE 168 GAGGTCAGTATCATTATCCCCATTTTACAGATGAGGAAACTGAGGCNCAG 119 chr3qtel1M 566806 -GAGGCAA 566812 - i? C MIR1_Amn#SINE 118 AGAGGTNA 111 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 16.56 CpG sites = 5, Kimura (unadjusted) = 16.56 Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.04 (2 / 49), avg. gap size = 4.00 (8 / 2) 199 13.51 2.70 0.00 chr3qtel1M 566776 566812 (433188) C MIR3#SINE/MIR (65) 143 106 m_b151s601i10 5656 chr3qtel1M 566776 CATTTTACAGATAAGGAAAGTGAGACCCAG-GAGGCAA 566812 i v i - ii C MIR3#SINE/MIR 143 CATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGA 106 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 15.32 CpG sites = 4, Kimura (unadjusted) = 15.32 Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 325 32.11 0.00 8.85 chr3qtel1M 567285 567407 (432593) C MIRb#SINE/MIR (154) 114 2 m_b151s601i11 5657 chr3qtel1M 567285 TTTGGTGACTTGTCAAGGGTCACGCAGCTAGAAAGTGTTAAGTATCTCAG 567334 vi i i v i i v vi i------- C MIRb#SINE/MIR 114 TTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAG-------AG 72 chr3qtel1M 567335 GCCATGTTTGAACTTGAGTCCTCCTAAATCCAGAGCTGGTGCCCTATCCA 567384 v vivi i iiii ivi i v i iv i v C MIRb#SINE/MIR 71 CCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCA 22 chr3qtel1M 567385 CTGTGCCCTCCAGCTGCCCCACT 567407 ii vi--- v C MIRb#SINE/MIR 21 CTGCACCAC---GCTGCCCCTCT 2 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.23 CpG sites = 23, Kimura (unadjusted) = 43.46 Transitions / transversions = 1.77 (23/13) Gap_init rate = 0.08 (10 / 122), avg. gap size = 1.00 (10 / 10) 192 36.76 6.48 1.77 chr3qtel1M 567976 568083 (431917) C L2d_3end#LINE/L2 (1) 515 403 m_b151s601i12 5658 chr3qtel1M 567976 CAAGCGGTTGATCA-CAGACATTTATCAGGCACCCACAGGGTGCTAGCCA 568024 v ii ii - iii iii i i viv viv C L2d_3end#LINE 515 CAATCAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCA 466 chr3qtel1M 568025 CTGTCTGATACACAAGGGATGCACTGACCAAA------AGGCCAAAGTCT 568068 viv vi i viv -- v vi ?v ------ i v vi i C L2d_3end#LINE 465 CTGTGCTAGGCGCTGTGG--GGAACGANAAAANAGTATAAGACATGGTCC 418 chr3qtel1M 568069 CTGCCCTCGGGGAGC 568083 ii C L2d_3end#LINE 417 CTGCCCTCAAGGAGC 403 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 48.18 CpG sites = 24, Kimura (unadjusted) = 54.23 Transitions / transversions = 1.60 (24/15) Gap_init rate = 0.04 (4 / 107), avg. gap size = 2.25 (9 / 4) 331 28.42 5.26 0.00 chr3qtel1M 567989 568083 (431917) C L2a_3end#LINE/L2 (13) 504 405 m_b151s601i13 5658 chr3qtel1M 567989 ACAGACATTTATCAGGCACCCACAGGGTGCTAGCCACTGTCTGATACACA 568038 i i iii i i viv i v iiv vi i v C L2a_3end#LINE 504 ACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGCGCT 455 chr3qtel1M 568039 AGGGAT---GCACTGACCAAA--AGGCCAAAGTCTCTGCCCTCGGGGAGC 568083 i --- v v -- i v i iv C L2a_3end#LINE 454 GGGGATACAGCAGTGAACAAAACAGACAAAAGTCCCTGCCCTCATGGAGC 405 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.60 CpG sites = 17, Kimura (unadjusted) = 37.01 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.02 (2 / 94), avg. gap size = 2.50 (5 / 2) 14 31.23 4.23 0.00 chr3qtel1M 569093 569163 (430837) (CCAT)n#Simple_repeat 1 74 (0) m_b151s252i1 5659 chr3qtel1M 569093 CCACCCATGGATCCCTCTATTCTTTC-TCCATCCATGGATCCCTCTATTC 569141 i vv v i i v i - vv v i i (CCAT)n#Simpl 1 CCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCC 50 chr3qtel1M 569142 TTTC-TCCAT-CTTCTGTCCATCC 569163 v i - - v ii (CCAT)n#Simpl 51 ATCCATCCATCCATCCATCCATCC 74 Matrix = Unknown Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.04 (3 / 70), avg. gap size = 1.00 (3 / 3) 510 19.44 0.00 5.10 chr3qtel1M 570493 570595 (429405) MIRc#SINE/MIR 18 115 (153) m_b151s601i14 5660 chr3qtel1M 570493 GTGGATAGAGCATTAGCTCTGAAGTCAGGAAGACCTGAGTTCAAATCTGG 570542 v i i vii i i i i iv MIRc#SINE/MIR 18 GTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCG 67 chr3qtel1M 570543 CCTCAGGCACAACACTTCCTAGCTGTGTGACTCTGGGCAAGTCACTTAAC 570592 v v v ----- v ii MIRc#SINE/MIR 68 GCTCTGCCAC-----TTACTAGCTGTGTGACCTTGGGCAAGTCACTTAAC 112 chr3qtel1M 570593 CCC 570595 i MIRc#SINE/MIR 113 CTC 115 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 21.54 CpG sites = 12, Kimura (unadjusted) = 22.87 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.05 (5 / 102), avg. gap size = 1.00 (5 / 5) 298 29.23 9.27 8.21 chr3qtel1M 571468 571672 (428328) C L2d2_3end#LINE/L2 (2) 553 347 m_b151s601i15 5661 chr3qtel1M 571468 AAATCAAATATTGACAACAATGATTAGTCAAAACATTAAACATCTATTAC 571517 ----- vv --------i i i ii i ii C L2d2_3end#LIN 553 AAATCAAAT-----CAACAAATATT--------TATTGAGCGCCTACTGT 517 chr3qtel1M 571518 GTGCCAATCACTGTGCTAAATGCT---GGGGATACAAAAAAGAGGCAAAA 571564 v iv iii --- i -vii i C L2d2_3end#LIN 516 GTGCAAGGCACTGTGCTAGGCGCTGTGGGGGATACAAAGAAG-TATAAGA 468 chr3qtel1M 571565 GTTGGTCCCTGCCATGTAGGAG--TCCAGTCTGAAGGGGGAG-------- 571604 vv v vv -- v i iivv -------- C L2d2_3end#LIN 467 CATGGTCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGGAGACAAGACA 418 chr3qtel1M 571605 --AGCCTGCAAATAGTTAAAAACCAAAGTA--ATTTACAGAGTAATAGG- 571649 -- i vi ii v v v vii -- --- i i v- C L2d2_3end#LIN 417 TAAACACGTGAAAAGTTAAATAACAATACAAGATTTA---AATAACAGTT 371 chr3qtel1M 571650 -AAGTCATTAACACAGGAAAAGCC 571672 - v vi i v i i v i C L2d2_3end#LIN 370 CAAGACAACAATAGAAGAGATGTC 347 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.48 CpG sites = 32, Kimura (unadjusted) = 38.08 Transitions / transversions = 1.39 (32/23) Gap_init rate = 0.11 (23 / 204), avg. gap size = 1.57 (36 / 23) 318 32.00 14.55 2.27 chr3qtel1M 571502 571776 (428224) C L2b_3end#LINE/L2 (23) 443 136 m_b151s601i17 5661 chr3qtel1M 571502 ATTAAACATCTATTACGTGCCAATCACTGTGCTAAATGCTGGGGATACAA 571551 i i i ii i ii iv ? iii i C L2b_3end#LINE 443 ACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGGGATACAG 394 chr3qtel1M 571552 ----AAAAGAGGCAAAAGTTGGTCCCTGCCATGTAGGAG-TC-CAGTCTG 571595 ----i vi i - i v?i v vvv - - i C L2b_3end#LINE 393 CGGTGAACAAGAC-AGACNCGGTCCCTGCCCTCACGGAGCTCACAGTCTA 345 chr3qtel1M 571596 AAGGGGGAGA---GCCTGCAAATAG----TTAAAAACCAAAGTAATTTAC 571638 iv ---i v i ?i ---- ? v v i i----i C L2b_3end#LINE 344 GTGGGGGAGACAGACATGTAANCAGACAATNATAACCCAGAGTG----GC 299 chr3qtel1M 571639 AGAGTA---------------ATAGGAAGTCA-TTAACACAG---GAAAA 571669 i --------------- v i v i-i i v i --- iiii C L2b_3end#LINE 298 AGGGTAGGACTGGGGGGGCCCAGAGGAGGGCGCCTGACCCGGCCTGGGGG 249 chr3qtel1M 571670 GCCCTGGAAGGCTTTCTGTAGAAACTGGGAGTTTAACTGGGACTTGGAAG 571719 i vv i i i v i iv iv v v i i i i i C L2b_3end#LINE 248 GTCAGGGAGGGCTTCCCGGAGGAGGTGACATTTGAGCTGAGACCTGAAGG 199 chr3qtel1M 571720 CCAGGGACATCAATAG---AGTCGAGGA----GGGAA-AGCATGCCAGGC 571761 -- v iii vv i v --- v i ---- -i i v C L2b_3end#LINE 198 --ATGAGTAGGAGTTGGCCAGGCGAAGAGGTGGGGAAGGGCGTTCCAGGC 151 chr3qtel1M 571762 ACAGGGCACTGAATG 571776 v v v v ? C L2b_3end#LINE 150 AGAGGGAACAGCANG 136 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.21 CpG sites = 55, Kimura (unadjusted) = 45.13 Transitions / transversions = 1.77 (55/31) Gap_init rate = 0.07 (18 / 274), avg. gap size = 2.61 (47 / 18) 334 28.22 6.99 3.38 chr3qtel1M 571502 571644 (428356) C L2a_3end#LINE/L2 (23) 494 347 m_b151s601i16 5661 chr3qtel1M 571502 ATTAAACATCTATTACGTGCCAATCACTGTGCTAAATGCTGGGGATACAA 571551 i i ii i i iv v iii i C L2a_3end#LINE 494 ATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGCGCTGGGGATACAG 445 chr3qtel1M 571552 --------AAAAGAGGCAAAAGTTGGTCCCTGCCATGTAGGAG--TCCAG 571591 -------- v i ---- v vvv -- v v C L2a_3end#LINE 444 CAGTGAACAAAACAGACAAAA----GTCCCTGCCCTCATGGAGCTTACAT 399 chr3qtel1M 571592 TCTGAAGGGGGAGAGCCTGCAAATAGTTAAAAACCAAAGTAATTTACAGA 571641 - iv i v v vv ivi v vvv vv i v C L2a_3end#LINE 398 TCT-AGTGGGGGGAGACAGACAATAAACAAATAAATAAGTAAAATATATA 350 chr3qtel1M 571642 GTA 571644 C L2a_3end#LINE 349 GTA 347 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.48 CpG sites = 17, Kimura (unadjusted) = 35.63 Transitions / transversions = 0.77 (17/22) Gap_init rate = 0.05 (7 / 142), avg. gap size = 2.14 (15 / 7) 214 39.63 1.23 2.48 chr3qtel1M 571841 572003 (427997) C L2#LINE/L2 (160) 2922 2762 m_b151s601i18 5661 chr3qtel1M 571841 CTGGATTATTAAGAGCTTTTAATGCCA--AACAGAGCATTACCTATTTAC 571888 ii i vv i i vv v --ivv ii v iv - C L2#LINE/L2 2922 CCAGATCATGTAGGGCCTTGTAGGCCATTGTAAGGACTTTGGCT-TTTAC 2874 chr3qtel1M 571889 TCCTAGAAATTATGGGGATCCACTTGAGTTTGTTGAGTGAGGGTGGATAA 571938 iv vi v- i v i v vv v iiii v vivv C L2#LINE/L2 2873 TCTGAGTGAG-ATGGGAAGCCATTGGAGGGTTTTGAGCAGAGGAGTGACA 2825 chr3qtel1M 571939 TGACGTCAGATCTGTGCTTTAGGAAAATCACTTTAGTGGCAGAATGAGGA 571988 -- v ii ii i ii ii i i iv v vi vii C L2#LINE/L2 2824 TGA--TCTGACTTACGTTTTAAAAGGATCACTCTGGCTGCTGTGTTGAGA 2777 chr3qtel1M 571989 ATGGTCTGGAGAGAG 572003 i v ? i i C L2#LINE/L2 2776 ATAGACTGNAGGGGG 2762 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 58.21 CpG sites = 36, Kimura (unadjusted) = 59.71 Transitions / transversions = 1.33 (36/27) Gap_init rate = 0.03 (5 / 162), avg. gap size = 1.20 (6 / 5) 12 9.24 0.00 4.17 chr3qtel1M 573540 573564 (426436) (GGGA)n#Simple_repeat 1 24 (0) m_b151s252i2 5662 chr3qtel1M 573540 GGGAGGGGGTGGAGGGTGGGAGGGA 573564 i - v (GGGA)n#Simpl 1 GGGAGGGAG-GGAGGGAGGGAGGGA 24 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 12 20.98 2.44 2.44 chr3qtel1M 575895 575935 (424065) (CCCCGC)n#Simple_repeat 1 41 (0) m_b151s252i3 5663 chr3qtel1M 575895 CCTCGCCCTCACCACCCGCCTCGGGCCCC-TCCCCGCCCCCG 575935 i i i - i v v -i (CCCCGC)n#Sim 1 CCCCGCCCCCGCC-CCCGCCCCCGCCCCCGCCCCCGCCCCCG 41 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 14 11.95 8.16 3.92 chr3qtel1M 576826 576874 (423126) (CCTCGCC)n#Simple_repeat 1 51 (0) m_b151s252i4 5664 chr3qtel1M 576826 CCTCGGCCCCTCGGCCC-CTCCCC-CACCCCTCAGTCCCTC-CCCC-GGC 576871 - v - v - i - i - -v (CCTCGCC)n#Si 1 CCTC-GCCCCTCGCCCCTCGCCCCTCGCCCCTC-GCCCCTCGCCCCTCGC 48 chr3qtel1M 576872 CCC 576874 (CCTCGCC)n#Si 49 CCC 51 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.12 (6 / 48), avg. gap size = 1.00 (6 / 6) 593 23.84 5.96 0.00 chr3qtel1M 576905 577055 (422945) MIR#SINE/MIR 55 214 (48) m_b151s601i19 5665 chr3qtel1M 576905 CAAATCCAGCCTCAG--ACATCCTGGCCGAGTGACCCCGGATAGGTCACT 576952 i v v v -- v v i i v ii ii i i MIR#SINE/MIR 55 CGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACT 104 chr3qtel1M 576953 TCACTGCCC---GCCTCAGTTTCCTTATCTGTAAAATGGGGATCATAATA 576999 v iv i --- i v MIR#SINE/MIR 105 TAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATA 154 chr3qtel1M 577000 GCCCCTCCCTCCCAAGGTCAC--TGAGGATCAAATGAGATCATAGCTGCA 577047 iv v vi i iii-- i v v vv i MIR#SINE/MIR 155 GTACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATACATGTA 204 chr3qtel1M 577048 AA--GCTTAG 577055 -- MIR#SINE/MIR 205 AAGCGCTTAG 214 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.19 CpG sites = 20, Kimura (unadjusted) = 29.12 Transitions / transversions = 1.25 (20/16) Gap_init rate = 0.03 (4 / 150), avg. gap size = 2.25 (9 / 4) 256 27.69 3.08 0.00 chr3qtel1M 577483 577547 (422453) C L2b_3end#LINE/L2 (15) 451 385 m_b151s601i20 5666 chr3qtel1M 577483 AAGCATTTATTAAGCACCAACTGTATGCCAGGCACTGTGCTTAATGCAGG 577532 ii i i i v i ? viii v C L2b_3end#LINE 451 AAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGG 402 chr3qtel1M 577533 AAGTCAAGC--TGAGCA 577547 iii vv -- i C L2b_3end#LINE 401 GGATACAGCGGTGAACA 385 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.19 CpG sites = 13, Kimura (unadjusted) = 37.37 Transitions / transversions = 2.60 (13/5) Gap_init rate = 0.02 (1 / 64), avg. gap size = 2.00 (2 / 1) 242 27.71 4.90 0.94 chr3qtel1M 577728 577829 (422171) L3#LINE/CR1 3655 3760 (339) m_b151s601i21 5667 chr3qtel1M 577728 GAGGAG-GCAGCCAGGACGG-ACAGGGCCCGGCTCCCATTGCGCATGAAG 577775 - ii i -iv i i vvv vv ii i L3#LINE/CR1 3655 GAGGAGAGCGACCAGGATGGTGAAGGGTCTGGAAACCATGTCATATGAGG 3704 chr3qtel1M 577776 ACACAG---AAGGAGCTGGCCATGTTTGGGCTGAAGGAGACAAGACCGGG 577822 - i --- i vv i v i i v ivi L3#LINE/CR1 3705 A-ACGGTTGAAGGAACTGGGGATGTTTAGCCTGGAGAAGAGAAGACTTAG 3753 chr3qtel1M 577823 AGGACAC 577829 v L3#LINE/CR1 3754 AGGAGAC 3760 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.32 CpG sites = 16, Kimura (unadjusted) = 35.39 Transitions / transversions = 1.33 (16/12) Gap_init rate = 0.04 (4 / 101), avg. gap size = 1.50 (6 / 4) 41 30.42 3.69 4.17 chr3qtel1M 579216 579432 (420568) (GGAG)n#Simple_repeat 1 216 (0) m_b151s252i6 5668 chr3qtel1M 579216 GGAAGG-GGGAGGGACAGCAGGAAGAGAGGGAAGACAGAAAAGG-GGGAA 579263 i - -i v i i - iv ii i - i (GGAG)n#Simpl 1 GGAGGGAGGGAGGGA-GGGAGGGAGGGAGGG-AGGGAGGGAGGGAGGGAG 48 chr3qtel1M 579264 GGAGGGAGAGAAGGAAGAAAGG-GGAGGGGAGGGATGGGGTGGAAGGAGG 579312 i i i i i - ii - iv i (GGAG)n#Simpl 49 GGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGA-GGGAGGGAGGGAGG 97 chr3qtel1M 579313 GA-GAAAGGAAAGAGGAAAGAGACAGAAAGGA-GGAGGGA-GGAAGAAAG 579359 - i i ii -i i -i i i - - i i i (GGAG)n#Simpl 98 GAGGGAGGGAGGGAGG-GAGGGA-GGGAGGGAGGGAGGGAGGGAGGGAGG 145 chr3qtel1M 579360 AAGAGAAAAGAGGGGGCAAAGGGGGGTGAG-GGGAGAGA-GGAGTAGAGG 579407 i - i ii i vi i i v i - i - -i (GGAG)n#Simpl 146 GAG-GGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAG-GGAGG 193 chr3qtel1M 579408 GAGGGAGAGGAGGGAGGAAAGGGAG 579432 - -i (GGAG)n#Simpl 194 GAGGGAG-GGAGGGAGG-GAGGGAG 216 Matrix = Unknown Transitions / transversions = 8.40 (42/5) Gap_init rate = 0.08 (17 / 216), avg. gap size = 1.00 (17 / 17) 1092 30.77 3.73 0.57 chr3qtel1M 579578 580087 (419913) L1ME4c_3end#LINE/L1 4 529 (301) m_b151s551i4 5669 chr3qtel1M 579578 ATTTCTGAAATATATAAAGAACTGTGTCACATTTATAAGAATACAAGTCA 579627 v ?v ? i vvv v v v v? viv L1ME4c_3end#L 4 ATATCTNTANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAA 53 chr3qtel1M 579628 TTCCCCAGTTGATAAATGGTCAGAGGATATGAACAGATAATTTTCAGATG 579677 vv i v v i i i iv ? v L1ME4c_3end#L 54 GACCCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAG 103 chr3qtel1M 579678 ATGAAATTAAATCCATCTATGGTCATATGAAGAAATGCTCTCAGTCACAA 579727 v vv ?ivi vv iiiv i i i i vvvv i v L1ME4c_3end#L 104 AGGAAATACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTA 153 chr3qtel1M 579728 TTGATCAGAGAAATGCAAATTAAGACAAC--TGAGGTACTATGGCACACT 579775 v i i ii -- i i vvi i i L1ME4c_3end#L 154 GTAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCC 203 chr3qtel1M 579776 TCTCAGATTGGCTAGGATGACAGGAAAAGCTGAT------CAGTGTTGGA 579819 v i i i v ii v---vi ii ------ i i v L1ME4c_3end#L 204 TATTAAATTAGCAAAAATT---TAAAAAATTGATAATACCCAATGCTGGC 250 chr3qtel1M 579820 GGGGATGTGGGAAAACTGGGACACTGATACATTGTTGGTGGAACTGTGAA 579869 i ? i vi v ? v i v ? i L1ME4c_3end#L 251 GAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAA 300 chr3qtel1M 579870 CGGAGCCAACCAGTATGGAAAGCAATTTGAAACTGGGCCCAAAGGGCTAT 579919 iv ivv vv v iv v iv iviv i i L1ME4c_3end#L 301 TTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCAT 350 chr3qtel1M 579920 TAAACTCTGCATACCTTTTGATCCATCAGTGTTTCTACTGGGCTCGTATG 579969 v v v v i i vi i viiv v vviv v L1ME4c_3end#L 351 AAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATC 400 chr3qtel1M 579970 TCAAAGAAATTAG--AAAAGAAGGAAAAGG--------ACCAA-ATGTTT 580008 ii i v v-- i -------- v - i L1ME4c_3end#L 401 CTAAGGAAATAATTCAAAAGAAGGAAAAAGCTATATGCACGAAGATGTTC 450 chr3qtel1M 580009 GTAGCAGCTCTTTTTTTGGTGGCAACGAATTGGAAAATGAGTAGATGCCC 580058 i v vi v v ii i i vi vvivv i i L1ME4c_3end#L 451 ATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCC 500 chr3qtel1M 580059 CTCAGTTGGGGAATGGCTGAATAATTTGT 580087 vv i v i i i v i L1ME4c_3end#L 501 AACAATAGGGGAATGGTTAAGTAAATTAT 529 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 39.60 CpG sites = 76, Kimura (unadjusted) = 40.93 Transitions / transversions = 0.95 (76/80) Gap_init rate = 0.02 (8 / 509), avg. gap size = 2.75 (22 / 8) 483 22.38 0.85 5.31 chr3qtel1M 580431 580548 (419452) MIRb#SINE/MIR 4 116 (152) m_b151s601i22 5670 chr3qtel1M 580431 AAGGGCAGCTAGATGGCACAGTGGATAGAGCACCAGCCCTGAAGTCAGGA 580480 i ---i ii v vi ii i iv MIRb#SINE/MIR 4 AGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGAC 50 chr3qtel1M 580481 GGACCCGAGTTCAAATCTGACCTCAGACACTTAACCCTAA-TGTGTGACC 580529 i i i i iviv v v --- i- MIRb#SINE/MIR 51 AGACCTGGGTTCGAATCCCGGCTCTGCCACTTA---CTAGCTGTGTGACC 97 chr3qtel1M 580530 CTGGGCAAGTCACTTAACC 580548 i i MIRb#SINE/MIR 98 TTGGGCAAGTTACTTAACC 116 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 23.79 CpG sites = 18, Kimura (unadjusted) = 27.56 Transitions / transversions = 2.57 (18/7) Gap_init rate = 0.06 (7 / 117), avg. gap size = 1.00 (7 / 7) 502 20.60 0.95 2.91 chr3qtel1M 580444 580548 (419452) MIRc#SINE/MIR 11 113 (155) m_b151s601i23 5670 chr3qtel1M 580444 TGGCACAGTGGATAGAGCACCAGCCCTGAAGTCAGGAGGACCCGAGTTCA 580493 ii v ii v i i i i i i MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr3qtel1M 580494 AATCTGACCTCAGACACTTAACCCTAA-TGTGTGACCCTGGGCAAGTCAC 580542 i iviv v v --- i- i MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTA---CTAGCTGTGTGACCTTGGGCAAGTCAC 107 chr3qtel1M 580543 TTAACC 580548 MIRc#SINE/MIR 108 TTAACC 113 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 22.24 CpG sites = 15, Kimura (unadjusted) = 24.89 Transitions / transversions = 2.50 (15/6) Gap_init rate = 0.04 (4 / 104), avg. gap size = 1.00 (4 / 4) 30 0.00 0.00 0.00 chr3qtel1M 580563 580595 (419405) (A)n#Simple_repeat 1 33 (0) m_b151s252i7 5671 chr3qtel1M 580563 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 580595 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 33 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 29 0.00 0.00 0.00 chr3qtel1M 580618 580642 (419358) (AG)n#Simple_repeat 1 25 (0) c_b151s251i1 5672 chr3qtel1M 580618 AGAGAGAGAGAGAGAGAGAGAGAGA 580642 (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGA 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 220 29.59 18.37 0.00 chr3qtel1M 582040 582137 (417863) C MIRb#SINE/MIR (106) 162 47 m_b151s601i24 5673 chr3qtel1M 582040 GTTCTGCTGTGCCCATTTCCTAGATGAGGCAATTGACTCCCAGGAA---- 582085 vi ii i v ivi v i vv i ii ---- C MIRb#SINE/MIR 162 GTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTT 113 chr3qtel1M 582086 ---------GCTCAAGGGCACAAGGCTGGCGGGCGGCCAAGTCGGG-TTT 582125 --------- i v vi i iii i vi i - i C MIRb#SINE/MIR 112 AAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTC 63 chr3qtel1M 582126 GA---CA-GTCTGTCT 582137 --- - C MIRb#SINE/MIR 62 GAACCCAGGTCTGTCT 47 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.93 CpG sites = 20, Kimura (unadjusted) = 39.73 Transitions / transversions = 2.22 (20/9) Gap_init rate = 0.05 (5 / 97), avg. gap size = 3.60 (18 / 5) 16 0.00 0.00 0.00 chr3qtel1M 583254 583271 (416729) (A)n#Simple_repeat 1 18 (0) m_b151s252i8 5674 chr3qtel1M 583254 AAAAAAAAAAAAAAAAAA 583271 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAA 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 46 0.00 0.00 0.00 chr3qtel1M 584536 584574 (415426) (AC)n#Simple_repeat 1 39 (0) c_b151s251i2 5675 chr3qtel1M 584536 ACACACACACACACACACACACACACACACACACACACA 584574 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACA 39 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 183 34.03 4.21 1.02 chr3qtel1M 584595 584689 (415311) C L3#LINE/CR1 (251) 3848 3751 m_b151s601i25 5676 chr3qtel1M 584595 TCCTGATTCTAGCTCCAGGGGTCAAGCAGAATGA--CTGAT-ACTTTCCC 584641 ii iv ii v i i vi i -- i -v i i C L3#LINE/CR1 3848 TCCTAGTTCTGCCCTCTGGAGCCACACAGAATAAGTCTAATCCCTCTTCC 3799 chr3qtel1M 584642 A-GGGCCTGTCCTTCATAGCCTTGAATTCAGCTCTTCTATCTGCCTCCA 584689 -iv v v i v vvi vv v iv i - i C L3#LINE/CR1 3798 ACATGACAGCCCTTCAAATATTTGAAGACAGCTATCATGTCT-CCTCTA 3751 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.80 CpG sites = 18, Kimura (unadjusted) = 46.80 Transitions / transversions = 1.29 (18/14) Gap_init rate = 0.04 (4 / 94), avg. gap size = 1.25 (5 / 4) 182 22.45 2.04 0.00 chr3qtel1M 584863 584911 (415089) L2b_3end#LINE/L2 340 389 (77) m_b151s601i26 5677 chr3qtel1M 584863 CCTAACGGACTGTGAGCTGC-TGAGGGCAGGGTCCAGCTCTGAGTTCTTC 584911 i vii v - v i?v vv v L2b_3end#LINE 340 CCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCTTGTTC 389 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 24.70 CpG sites = 4, Kimura (unadjusted) = 27.36 Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.02 (1 / 48), avg. gap size = 1.00 (1 / 1) 185 32.05 0.00 4.00 chr3qtel1M 584878 584955 (415045) C OldhAT1#DNA/hAT-Ac (808) 2034 1960 m_b151s601i27 5678 chr3qtel1M 584878 GCTGCTGAGGGCAGGGTCCAGCTCTGAGTTCTTCCTCCAGACTTTCCTGC 584927 iv v ?v --i v v -i v i v i v i ii C OldhAT1#DNA/h 2034 GCTGCTGGTGTCANTGT--GGCTGTTA-CTGTTTCACTAGTCTCTTTTGC 1988 chr3qtel1M 584928 ATTCTCTGACCTTACAGGACGAAGTCTT 584955 i iv v v v ii C OldhAT1#DNA/h 1987 ACTCTCTGATGTTCCAGGAAGACGTTCT 1960 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.12 CpG sites = 12, Kimura (unadjusted) = 43.12 Transitions / transversions = 1.00 (12/12) Gap_init rate = 0.04 (3 / 77), avg. gap size = 1.00 (3 / 3) 191 26.92 0.00 0.00 chr3qtel1M 585070 585121 (414879) C MIRb#SINE/MIR (38) 230 179 m_b151s601i28 5679 chr3qtel1M 585070 CCAGCCACCGCACTAAGCCCTTCACAAATATCATCTCACTTGATCTACAC 585119 v i ii v i vii i i i iv C MIRb#SINE/MIR 230 CCAGGCACTGTGCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCAC 181 chr3qtel1M 585120 AA 585121 C MIRb#SINE/MIR 180 AA 179 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.13 CpG sites = 10, Kimura (unadjusted) = 35.13 Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 217 31.06 15.20 2.13 chr3qtel1M 588165 588289 (411711) MIR#SINE/MIR 116 256 (6) m_b151s601i29 5680 chr3qtel1M 588165 TGCCTCTGTTTCCCCAAGTGTAACACGGAGGTCCTAACAGC-CCTTCCCC 588213 v i vv v i i i vv i i- v i MIR#SINE/MIR 116 TGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTC 165 chr3qtel1M 588214 --------------AGGATCAGAGGAG---ACAGCTGTAGAGC-CTTACT 588245 -------------- i i v --- i vv i - -- MIR#SINE/MIR 166 ATAGGGTTGTTGTGAGGATTAAATGAGTTAATACATGTAAAGCGCTTA-- 213 chr3qtel1M 588246 TGGCCAGGTCCTAGTCCACAGGAGGCGCTACTTAGATGCTAATT 588289 - iv vv i iv i v i vvv i i ii MIR#SINE/MIR 214 -GAACAGTGCCTGGCACATAGTAAGCGCTCAATAAATGTTAGCT 256 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.00 CpG sites = 20, Kimura (unadjusted) = 41.00 Transitions / transversions = 1.11 (20/18) Gap_init rate = 0.06 (7 / 124), avg. gap size = 3.14 (22 / 7) 277 5.26 0.00 0.00 chr3qtel1M 590149 590186 (409814) MIR#SINE/MIR 116 153 (109) m_b151s601i30 5681 chr3qtel1M 590149 TGCCTCAGTTTCCTCATCTGTAAAATGGGGATCAAAAT 590186 v v MIR#SINE/MIR 116 TGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAAT 153 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 5.48 CpG sites = 0, Kimura (unadjusted) = 5.48 Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 264 15.51 1.69 1.69 chr3qtel1M 590150 590208 (409792) MIRc#SINE/MIR 121 179 (89) m_b151s601i32 5681 chr3qtel1M 590150 GCCTCAGTTTCCTCATCTGTAAAATGGGGATCAAAATCACCCTCCCC-CC 590198 v v - iv i- MIRc#SINE/MIR 121 GCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAAT-ACCTGCCCTGCC 169 chr3qtel1M 590199 CCCCCCAGAG 590208 iv i v MIRc#SINE/MIR 170 TACCTCACAG 179 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 17.42 CpG sites = 4, Kimura (unadjusted) = 17.42 Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.03 (2 / 58), avg. gap size = 1.00 (2 / 2) 269 10.88 0.00 2.17 chr3qtel1M 590150 590196 (409804) MIRb#SINE/MIR 124 169 (99) m_b151s601i31 5681 chr3qtel1M 590150 GCCTCAGTTTCCTCATCTGTAAAATGGGGATCAAAATCACCCTCCCC 590196 v v - iv i MIRb#SINE/MIR 124 GCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAAT-ACCTACCTC 169 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 11.75 CpG sites = 2, Kimura (unadjusted) = 11.75 Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.02 (1 / 46), avg. gap size = 1.00 (1 / 1) 203 32.83 0.00 3.28 chr3qtel1M 592975 593037 (406963) MIR#SINE/MIR 132 192 (70) m_b152s601i0 5682 chr3qtel1M 592975 TTTGTAAGATGGGGACCCCAACAGCACCTTCCTTCTCAGGTGGCCGCGAG 593024 i i ivvi i i v iv vi v ii i MIR#SINE/MIR 132 TCTGTAAAATGGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAG 181 chr3qtel1M 593025 GGTCAGAGATGAG 593037 i i-- i MIR#SINE/MIR 182 GATT--AAATGAG 192 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.23 CpG sites = 14, Kimura (unadjusted) = 46.23 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.03 (2 / 62), avg. gap size = 1.00 (2 / 2) 12 20.99 0.00 5.00 chr3qtel1M 594150 594191 (405809) (GGGAGAA)n#Simple_repeat 1 40 (0) m_b152s252i0 5683 chr3qtel1M 594150 GGGAGTGGGGAGCCACGGGATACAGGTGAAGGGAGAAGGGAG 594191 vi -- v v vi v (GGGAGAA)n#Si 1 GGGAGAAGGGAG--AAGGGAGAAGGGAGAAGGGAGAAGGGAG 40 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.05 (2 / 41), avg. gap size = 1.00 (2 / 2) 42 30.88 1.89 3.85 chr3qtel1M 594285 594496 (405504) (AAGG)n#Simple_repeat 1 208 (0) m_b152s252i1 5684 chr3qtel1M 594285 AAGGATGGAAGGAAGGGCAATTGCACGGACGGATGGAAGGGTGGATGGAT 594334 v - - -- v v v v iv v v (AAGG)n#Simpl 1 AAGGAAGGAAGGAA-GG-AA--GGAAGGAAGGAAGGAAGGAAGGAAGGAA 46 chr3qtel1M 594335 CGAAGGATGGACAGATGG-TTGAATGAATGGATCAATGGAAAGATGGAGG 594383 v v vi v -vv v - vvi v i v i (AAGG)n#Simpl 47 GGAAGGAAGGAAGGAAGGAAGGAAGGAA-GGAAGGAAGGAAGGAAGGAAG 95 chr3qtel1M 594384 AAAGGATGG-ATGAGGAAAAGATGGAAGGATGGAGGGAAGGATGGGGGGT 594432 i v - v i i i v v i v ii v (AAGG)n#Simpl 96 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 145 chr3qtel1M 594433 A-GATGGAAGGATGG-ATCAATGAACTGAAATGGATGGATGGATGAAAAG 594480 - v v - vv v -- i - v v v i i (AAGG)n#Simpl 146 AGGAAGGAAGGAAGGAAGGAAGGAA--GGAA-GGAAGGAAGGAAGGAAGG 192 chr3qtel1M 594481 AAGGATGGACGGAAGG 594496 v v (AAGG)n#Simpl 193 AAGGAAGGAAGGAAGG 208 Matrix = Unknown Transitions / transversions = 0.43 (15/35) Gap_init rate = 0.06 (12 / 211), avg. gap size = 1.00 (12 / 12) 207 36.14 6.80 3.29 chr3qtel1M 594507 594712 (405288) L2#LINE/L2 2372 2584 (498) m_b152s601i1 5685 chr3qtel1M 594507 TGACCTCCAATCCC--ACCTCCAACAGCCTTTCAGACCTCT------GGA 594548 v iv i -- iv v viiv v ------ L2#LINE/L2 2372 TGAACTCCAGACTCGTATATCCAACTGCCTACTCGACATCTCCACTTGGA 2421 chr3qtel1M 594549 TGTCTGGTAGACATGGTACCCTCAG--TGTCCAGGA--GAACTTCT--CT 594592 ii i vvi vv i i-- ii -- i --ii L2#LINE/L2 2422 TGTCTAATAGGCATCTCAAACTTAACATGTCCAAAACTGAACTCCTGATC 2471 chr3qtel1M 594593 TTCCCCCGGAGCCCTCCCCACTCCTCTACCTTCCCTATTTCTCTAGAAGG 594642 vv iv v i vii v vii i i vv ?i v L2#LINE/L2 2472 TTCCCCCTCAAACCTGCTCCTCCCGCAGTCTTCCCCATCTCAGTNAATGG 2521 chr3qtel1M 594643 TCCCACCATGCTACATGCTCCCAGTTTTTCAGCCTCCCAACCTCTGAACT 594692 --- ----i v v i vi v ivvv iv iii L2#LINE/L2 2522 ---CA----ACTCCATCCTTCCAGTTGCTCAGGCCAAAAACCTTGGAGTC 2564 chr3qtel1M 594693 TCCAGTGATTCTATTGTCTC 594712 vi vv i ivi v i L2#LINE/L2 2565 ATCCTTGACTCCTCTCTTTC 2584 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 51.06 CpG sites = 38, Kimura (unadjusted) = 51.06 Transitions / transversions = 1.12 (38/34) Gap_init rate = 0.06 (12 / 205), avg. gap size = 1.75 (21 / 12) 261 34.67 3.15 2.34 chr3qtel1M 594966 595092 (404908) L2b_3end#LINE/L2 333 460 (6) m_b152s601i2 5685 chr3qtel1M 594966 TATCTCTCCTGTTAGACTGCAAACAGCTGGCGGCCAGGGCCCTGCATTTG 595015 i i iii ii i vv vv v v v - ?i i L2b_3end#LINE 333 TGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACC-GNGTCTG 381 chr3qtel1M 595016 C--AATTCCCAGTTGTA--CCAGGGGCTCAGCTCAACTTCATGGCACACA 595061 i--vi v v i -- vi v ii v i?vi - L2b_3end#LINE 382 TCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCC-TGGCACACA 430 chr3qtel1M 595062 GTAAGTGCCTACTAAGTGCTGGCCGACATGA 595092 i i ii v i ii v ii - L2b_3end#LINE 431 GTAGGCGCTCAGTAAATATTTGTTGA-ATGA 460 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 48.54 CpG sites = 27, Kimura (unadjusted) = 50.24 Transitions / transversions = 1.69 (27/16) Gap_init rate = 0.04 (5 / 126), avg. gap size = 1.40 (7 / 5) 24 11.80 2.08 2.08 chr3qtel1M 602158 602205 (397795) (CTCC)n#Simple_repeat 1 48 (0) m_b152s252i2 5686 chr3qtel1M 602158 CTCTCTCCCCTCCCTCCCTACCTCCCT-CCTGCCCCCCTCCCTCCCCCC 602205 i - v - v i i (CTCC)n#Simpl 1 CTCCCT-CCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCC 48 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.04 (2 / 47), avg. gap size = 1.00 (2 / 2) 285 27.12 1.68 1.11 chr3qtel1M 603020 603198 (396802) L1MC4_5end#LINE/L1 2376 2555 (0) m_b152s551i0 5687 chr3qtel1M 603020 GAAATGAAAAAGAAGGGTAGCAAATCTGATCTTATACAAGGCAAAA--CA 603067 ii v v?i ? v i v i i i ?-- L1MC4_5end#LI 2376 GAAACAAAAAAGAAGGGTTGCAATNTTNATATCAGACAAAGTAGANTTCA 2425 chr3qtel1M 603068 AAAAATAGATCTAATTAAAAGAGATAAGGAAGGAAGCTACAGCTTTCTAA 603117 i?v v i v -- ? i i ?vii vi vvv v? L1MC4_5end#LI 2426 AGNCAAAAAGC--ATTAAANGAGACAAAGAAGGNCATTTTATAATGNTAA 2473 chr3qtel1M 603118 AAGTTCC-ATAGACAATGCAGCGATATCACTACTAAACATATATGCACCA 603166 i ??? - vv v vv v v vv i ? L1MC4_5end#LI 2474 AGGNNNCAATTCACAATGAAGATATAACAATTATAAATATNTATGCACCA 2523 chr3qtel1M 603167 AGTGGTATAGCATCCAAATTCTTAGGGGAAAA 603198 i iii ? ? v? iv ii v L1MC4_5end#LI 2524 AATAACANAGCANCCACNTTTATAAAGCAAAA 2555 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 37.76 CpG sites = 23, Kimura (unadjusted) = 37.76 Transitions / transversions = 0.92 (23/25) Gap_init rate = 0.02 (4 / 178), avg. gap size = 1.25 (5 / 4) 1372 30.42 1.23 1.23 chr3qtel1M 603425 603993 (396007) L1ME4a_3end#LINE/L1 71 639 (232) m_b152s551i1 5688 chr3qtel1M 603425 GAACAAAGGATATGAACAGACAATTCTCAGATGAAGAAATTGAAACTATT 603474 ii i v i v vv iviii L1ME4a_3end#L 71 GGGCAAAGGACATGAACAGACAATTCACAAAAGAAGAAATACAAATGGCC 120 chr3qtel1M 603475 TCTAGTCATATGAAAAGATGTTCCAAGTCATTATTAATCAGAGAAATGCA 603524 vv iv ? v vv i v i L1ME4a_3end#L 121 AATAAACATATGAAAANATGTTCAACCTCACTAGTAATCAAAGAAATGCA 170 chr3qtel1M 603525 AATTAAGACAACTCTAAGATACCACTACACACCTGTCAGATAGGCTAAGA 603574 i vv i i viv i i v v L1ME4a_3end#L 171 AATTAAAACAACAATGAGATACCATTTTTCACCTATCAAATTGGCAAAGA 220 chr3qtel1M 603575 TGACAGGAAAAAATAATGATGATTGTTGGAGGGGATGCAGGAAAACTGGG 603624 vvv iii vvi iviv v v i i ii ?i v v L1ME4a_3end#L 221 TTTAAAAGATTGATAATACCCAGTGTTGGCGAGGGTGTGGNGAAACGGGC 270 chr3qtel1M 603625 ACATTGATGCATGGTTGGTGGAATTGCGAGCGAATCCAACCATTCTGGAG 603674 vi v i iv i i v ii iivii v v L1ME4a_3end#L 271 ACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTACAACCTTTCTGGAG 320 chr3qtel1M 603675 AGTAGTTTGGAACTATGCTCAAAAAGTTATCAAACTGTCCATACCCTTTG 603724 i i i v v iviv iiv v v ? L1ME4a_3end#L 321 GGCAATTTGGCAATATGTATCAAAAGCCTTAAAAATGTNCATACCCTTTG 370 chr3qtel1M 603725 ATCCAGCAGTGTTACTACTGGGATTATATCCCAAAGAGATCAT-AAAGAA 603773 i i i vii v i v v i i i v - i v L1ME4a_3end#L 371 ACCCAGTAATTCCACTTCTAGGAATTTATCCTAAGGAAATAATCAGAGAT 420 chr3qtel1M 603774 GGGAA-AGGGACCTGTATGTGCACGAATGTTTGTGGCAGCCCTCTTTGTA 603822 v ? - ii -- v i v i ii v vi v i L1ME4a_3end#L 421 GTGNACAAAGA--TTTATGTACAAGGATGTTCATCGCAGCATTATTTATA 468 chr3qtel1M 603823 GTGGCTAAAAACCGGAAACTGAATGGATGTCCATCAGTTGGAGAATGGCT 603872 i i v ii vivv ii v i v i ? i L1ME4a_3end#L 469 ATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGANTGGTT 518 chr3qtel1M 603873 GAATAAATTGTGGTATATGAATATTATGGAATATTATTGTTCTGTAAGAA 603922 i i i vv ?v vvvv ii v i L1ME4a_3end#L 519 AAATAAATTATGGTACATCCATANAATGGAATATTATGCAGCCATTAAAA 568 chr3qtel1M 603923 ATGA-----CCAACAGGATAATTTCAGAAAGGCCTGGAGAGACTTACACG 603967 ? -----i i - i v ---- v i v ii i iviv i L1ME4a_3end#L 569 ATNATGTTTTCGA-AGAATATTT----AATGACATGGGAAAATGCTCATG 613 chr3qtel1M 603968 AACTGATGCTGAGTGAAATGAGCAGG 603993 vv i i i vi L1ME4a_3end#L 614 ATATAATGTTAAGTGAAAAAAGCAGG 639 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 40.27 CpG sites = 94, Kimura (unadjusted) = 40.58 Transitions / transversions = 1.22 (94/77) Gap_init rate = 0.02 (10 / 568), avg. gap size = 1.40 (14 / 10) 16 0.00 0.00 0.00 chr3qtel1M 604458 604474 (395526) (A)n#Simple_repeat 1 17 (0) m_b152s252i3 5689 chr3qtel1M 604458 AAAAAAAAAAAAAAAAA 604474 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 382 31.35 7.13 4.12 chr3qtel1M 604478 605445 (394555) L1M1_orf2#LINE/L1 629 1624 (1670) m_b152s551i2 5687 chr3qtel1M 604478 ACAGAA-AAATCTCACAACCAAATGCAGAAAGGCAGAAATG---TCAAAT 604523 i - i i v --- v i iiiv i--- i- L1M1_orf2#LIN 629 ACAAAACAAGTCTTAAAAC---ATTCAAAAAAATTGAAATAATATCAAG- 674 chr3qtel1M 604524 ACATCCTTTTCAGAACATGATGCAAAAAAACCAAAATTACATGCAGTAAA 604573 - - i v v ii v v i i v ----- i - L1M1_orf2#LIN 675 -CATC-TTCTCTGACCACAATGGAATAAAACTAGAAAT-----CAATAA- 716 chr3qtel1M 604574 GGGCCATGAAAAGAT----AAACT-TAAAAACTAATTGAACATTAAACAA 604618 ---- v ii iv ---- - v vv v - L1M1_orf2#LIN 717 ----CAAGAGGAATTTTGGAAACTATACAAACACATGGAA-ATTAAACAA 761 chr3qtel1M 604619 TCTAATCCTAAAGCATTCCAAACAAGAATCAATAAAACAATCAAAAC--- 604665 v iv i vv -- iv--- ii i iv i i v--- L1M1_orf2#LIN 762 TATGCTCCTGAATGA--CCAGT---GGGTCAATGAAGAAATTAAGAAGGA 806 chr3qtel1M 604666 AAATAAACAATTTCATACAAGAGAAGGCCAATACTGAGACA-AACGTACC 604714 v i v v iv v - v vi i-- i - i L1M1_orf2#LIN 807 AATTGAAAAATTTCTTGAAACA-AATGATAATG--GAAACACAACATACC 853 chr3qtel1M 604715 AAAATTTATGGGATGCAGCCAAAGCAATTGTTAGGAGAAATTTTATATCT 604764 ii i v i vv v ii i v v L1M1_orf2#LIN 854 AAAACCTATGGGATACAGCAAAAGCAGTACTAAGAGGGAAGTTTATAGCT 903 chr3qtel1M 604765 CTAAATGTTTACATGAGTAAAAAAGAGAAAGAGGAGCTCAATGAATTGGG 604814 v i ii v iv i i vvvv iv v ii vi iiv L1M1_orf2#LIN 904 ATAAGTGCCTACATCAAAAAAGAAGAAAAACTTCAAATAAACAACCTAAC 953 chr3qtel1M 604815 CCTGCAATTTAAAAAGCTAGAA----AAGAACAAATTAAGAATTCCCAAT 604860 vv vi i i ---- i ii -- ii vv L1M1_orf2#LIN 954 GATGCATCTTAAAGAACTAGAAAAGCAAGAGCAAACCA--AACCCAAAAT 1001 chr3qtel1M 604861 TAAATACCAAATTAGAAAATCTAAAACTAAAAGGAGAAATCAGTAAAATT 604910 - i vv i vv vvv iv v i v v i i L1M1_orf2#LIN 1002 T-AGTAGAAGAAAAGAAATAATAAAGATCAGAGCAGAAATAAATGAAATT 1050 chr3qtel1M 604911 AA----AAGTAAACTGCTGAACTAATGAATAAAACTAAGAACTGGTTTAA 604956 i ---- v viivv vvi v i v i ii vv L1M1_orf2#LIN 1051 GAAATGAAGAAAACAATACAAAAGATCAATGAAACAAAAAGTTGGTTTTT 1100 chr3qtel1M 604957 TGAGGGAAAAAAACAATAAAATAGATAAAACTTT-----GACTCATTGAC 605001 ---- i?vv i v i v ----- v ??i - L1M1_orf2#LIN 1101 T----GAAAAGNTAAACAAAATTGACAAACCTTTAGCCAGACTAANNAA- 1145 chr3qtel1M 605002 TTTAAAAAATGAAATA----TCAAATTACCAGTATCAAAAATGAAAAAGG 605047 --v v i v ----i v vi iv i i L1M1_orf2#LIN 1146 --GAAAAAAAGAGAGAAGACCCAAATAAATAAAATCAGAGATGAAAAAGG 1193 chr3qtel1M 605048 TGAATTGATCACCAATAAAGAGTAAATTAAAATAATAACTGGGAGCTATT 605097 v vv v iv ii vv viv v vi v i i vi i L1M1_orf2#LIN 1194 AGACATTACAACTGATACCGCAGAAATTCAAAGGATCATTAGTGGCTACT 1243 chr3qtel1M 605098 TTGCCCAACCGTGTGCCAATAAATCTGACAGTCTAAGTGAAATAGATGAA 605147 v vv ii i iv v i iiv i ii L1M1_orf2#LIN 1244 ATGAGCAACTATATGCCAATAAATTGGAAAATCTAGAAGAAATGGACAAA 1293 chr3qtel1M 605148 TATTTACAAAAATAAAAATTGCC-AGATTAGA----GAAGAAATAAAATA 605192 vii v v v v vi i - ii ---- vv v L1M1_orf2#LIN 1294 TTCCTAGACACATACAACCTACCAAGATTGAACCATGAAGAAATCCAAAA 1343 chr3qtel1M 605193 CTTAAATAACCCCATTTTAGACAAAGAAATTAAGCAAGCCATCGATAAA- 605241 i i i iv v vvi iii v i ii--- i -i - L1M1_orf2#LIN 1344 CCTGAACAGACCAATAACAAGTAACGAGATCG---AAGCCGT-AATAAAA 1389 chr3qtel1M 605242 ---CTCCC--TAAGAAAGAACCTTCAGGACCAGATAG------------A 605274 --- -- ii i i -- i v i ------------ L1M1_orf2#LIN 1390 AGTCTCCCAGTAAAGAAAAGCC--CGGGACCCGATGGCTTCACTGCTGAA 1437 chr3qtel1M 605275 TTCTACCAAACATTGAAAGAACAATAAATTCCAATATTATATAAACTATT 605324 v v iv v vi ivi L1M1_orf2#LIN 1438 TTCTACCAAACATTTAAAGAAGAACTAATACCAATCCTACTCAAACTATT 1487 chr3qtel1M 605325 -TGAAAAAGAATGAGCAAAGAAGGAGTTCCA--------CCACAA----- 605360 -i v iv iivi i i iv v -------- i i ----- L1M1_orf2#LIN 1488 CCGAAAAATAGAGGAGGAGGGAATACTTCCAAACTCATTCTACGAGGCCA 1537 chr3qtel1M 605361 --ATGGTGCCGATACCTATATCAGGAAAAGCCAAAACAGAGAAAGAAAAT 605408 -- viiv i v v i iv v v v i i i L1M1_orf2#LIN 1538 GTATTACCCTGATACCAAAACCAGACAAAGACACATCAAAAAAAGAAAAC 1587 chr3qtel1M 605409 TACAGACCAAACTCCTTAATGAATATTGATGCAAAAA 605445 i vv ii i L1M1_orf2#LIN 1588 TACAGGCCAATATCTCTGATGAATATTGATGCAAAAA 1624 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 40.69 CpG sites = 154, Kimura (unadjusted) = 41.64 Transitions / transversions = 1.12 (154/137) Gap_init rate = 0.06 (60 / 967), avg. gap size = 1.83 (110 / 60) 841 30.95 6.43 2.56 chr3qtel1M 604598 605499 (394501) L1M5_orf2#LINE/L1 741 1676 (1618) m_b152s551i3 5687 chr3qtel1M 604598 AACTAATTGAACATTAAACAATCTAATCCTAAAGCATTCCAAACAAGAAT 604647 v v i v ivi v i vv ii ----- v ii L1M5_orf2#LIN 741 AAATATTTGGAAATTAAACAACACACTTCTAAATAACCC-----ATGGGT 785 chr3qtel1M 604648 CAATAAAACAATCAAAAC---AAATAAACAATTTCATACAAGAGAAGGCC 604694 vi iv v ?--- v i v v iv i- vv v v? L1M5_orf2#LIN 786 CAAAGAAGAAATCACAANGGAAATTAGAAAATATTTTG-AACTGAATGAN 834 chr3qtel1M 604695 AATACTGAGACAAACGTACCAAAATTTATGGGATGCAGCCAAAGCAATTG 604744 ivvi v - i i i i i vv L1M5_orf2#LIN 835 AATGAAAATACAA-CATATCAAAATTTGTGGGATGCAGCTAAAGCAGTGC 883 chr3qtel1M 604745 TTAGGAGAAATTTTATATCTCTAAATGTTTACATGAGTAAAAAAGAGAAA 604794 ii i v v ?i i? i v v i i ii L1M5_orf2#LIN 884 TTAGAGGGAAATTTATAGCNTTAAATGCNTATATTAGAAAAGAAGAAAGG 933 chr3qtel1M 604795 GAGGAGCTCAATGAATTGGGCCTGCAATTTAAAAAGCTAGAA----AAGA 604840 vvvi iv vi ii i v vi i ---- L1M5_orf2#LIN 934 CTTAAAATCAATGATCTAAGCTTCCACCTTAAGAAGCTAGAAAAAGAAGA 983 chr3qtel1M 604841 ACAAATTAAGAATTCCCAATTAAATACCAAATTAGAAAAT-CTAAAACTA 604889 i i---i v v? i -v ivv i -v iv L1M5_orf2#LIN 984 GCAAATTAAA---CCCAAAGNAAGTA-GAAGGAAGGAAATAATAAAGATA 1029 chr3qtel1M 604890 AAAGGAGAAATCAGTAAAATTAAAAGTAA----ACTGCTGAACTAATGAA 604935 i v i i vi ii ---- viiv ivv v L1M5_orf2#LIN 1030 AGAGCAGAAATCAATGAAATAGAAAACAAANANACAATAGAGAAAATCAA 1079 chr3qtel1M 604936 TAAAACTAAGAACTGGTTTAATGAGGGAAAAAAACAATAAAATAGATAAA 604985 ii i i i i ivv ---- i v v L1M5_orf2#LIN 1080 CGAAGCCAAAAGCTGGTTCTTT----GAAAAGATCAATAAAATTGATAAA 1125 chr3qtel1M 604986 ACTTT-----GACTCATTGACTTTAAAAAATGAAATAT-CAAATTACCAG 605029 v i ----- v ii vvvv i vii v i- i L1M5_orf2#LIN 1126 CCTCTAGCNAGACTGATCAAGAAAAAAAGAGAGAAGACACAAATTACCAA 1175 chr3qtel1M 605030 TATCAAAAATGAAAAAGGTGAATTGATCACCAA---TAAAGAGTAAATTA 605076 ii v vv v ii vi --- v --- v L1M5_orf2#LIN 1176 TATCAGGAATGAAAAAGGAGACATCACTACAGATCCTACAG---ACATTA 1222 chr3qtel1M 605077 AAATAATAACTGGGAGCTATTTTGCCCAACCGTGTGCCAATAAATCTGAC 605126 vi ivi iiiv v vv iv i i ? L1M5_orf2#LIN 1223 AAAGGATAATAAGAGAATATTATGAACAACTTTATGCCAATAAATTTGAN 1272 chr3qtel1M 605127 AGTCTAAGTGAAATAGATGAATATTTACAAAAATAAAAATTGCCA----- 605171 iii ii i ii vii vv i v ? i ----- L1M5_orf2#LIN 1273 AACTTAGATGAAATGGACAAATTCCTTGAAAAACACAANTTACCAAAACT 1322 chr3qtel1M 605172 GATTAGAGAAGAAATAAAATACTTAAATAACCCCATTTTAGACAAAGAAA 605221 i?vi i v ii i i i v ivivi L1M5_orf2#LIN 1323 GACNCAAGAAGAAATAGAAAATCTGAATAGCCCTATATCTATTAAAGAAA 1372 chr3qtel1M 605222 TTAAGCAAGCCATCGATAAACTCCCTAAGAAAGAACCTTCAGGACCAGAT 605271 i iivv iv ii v v i i vi ii v i v L1M5_orf2#LIN 1373 TTGAATTTGTAATTAAAAACCTTCCCACAAAGAAAACTCCAGGCCCAGAT 1422 chr3qtel1M 605272 AG------------ATTCTACCAAACATTGAAAGAACAATAAATTCCAAT 605309 i ------------ v i v vv v L1M5_orf2#LIN 1423 GGCTTCACTGGTGAATTCTACCAAACATTTAAGGAAGAAATAATACCAAT 1472 chr3qtel1M 605310 ATTATATAAACTATTTGAAAAAGAATGAGCAAAGAAGGAG----TTCCAC 605355 v i i v iv i -- iiiv i i---- i v L1M5_orf2#LIN 1473 CTTACACAAACTCTTCCAGAA--AATAGAAAAAGAGGGAACACTTCCCAA 1520 chr3qtel1M 605356 CACA---AATGGTGCC-----------GATACCTATATCAGGAAAAGCCA 605391 v ---v iv ----------- v v i ? iv v L1M5_orf2#LIN 1521 CTCATTTTATGAGGCCAGCATNACCCTGATACCAAAACCNGACAAAGACA 1570 chr3qtel1M 605392 AAACAGAGAAAGAAAATTACAGACCAAACTCCTTAATGAATATTGATGCA 605441 vv iii vv i v i v - L1M5_orf2#LIN 1571 TTACAAGAAAAGAAAATTACAGACCAATATCCCTCATGAACATAGATGC- 1619 chr3qtel1M 605442 AAAAAAAATTTTT--TAAGATATTGACAAAGAAATTATAGCAAATTATCA 605489 --- ii ?--i i ii vvi v vi vv v L1M5_orf2#LIN 1620 ---AAAAATCCTNAACAAAATATTAGCAAATCGAATCCAGCAATATATAA 1666 chr3qtel1M 605490 TCGGGATAAT 605499 vvi L1M5_orf2#LIN 1667 AAAGGATAAT 1676 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 41.06 CpG sites = 148, Kimura (unadjusted) = 41.48 Transitions / transversions = 1.19 (148/124) Gap_init rate = 0.04 (37 / 901), avg. gap size = 2.22 (82 / 37) 13 12.43 2.44 7.69 chr3qtel1M 606488 606528 (393472) (GCAGG)n#Simple_repeat 1 39 (0) m_b152s252i4 5690 chr3qtel1M 606488 GCAGGGCAGGAGCACCCGAGGGTCAGGAGCA-GGCAGGGCAG 606528 - vvvv - - - (GCAGG)n#Simp 1 GCAGGGCAGG-GCAGGGCAGGG-CAGG-GCAGGGCAGGGCAG 39 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.10 (4 / 40), avg. gap size = 1.00 (4 / 4) 281 26.43 4.84 2.36 chr3qtel1M 607323 607446 (392554) MIR1_Amn#SINE/MIR 3 129 (101) m_b152s601i3 5691 chr3qtel1M 607323 GGGAGCCGGTGTGGAATGGTGGTTAGAGCCGTAGTCCCAGAGACAGGAAG 607372 v i vv i v vv i v ivi vv i ii MIR1_Amn#SINE 3 GGGAGGCAGTGTGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGAGA 52 chr3qtel1M 607373 CCTGGGCTTCCCACCCAGGCTC--CCATT----GGCTGAGGGACGCAGGC 607416 - ?v?i v -- i ----? ? v viv v MIR1_Amn#SINE 53 CCTGGG-TTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGG 101 chr3qtel1M 607417 CCAATGACTTCCCCTCTCTGAGATCTTCAG 607446 v i v ?v ? -- i MIR1_Amn#SINE 102 CAAGTCACTTNACCTCTCTGNG--CCTCAG 129 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.58 CpG sites = 13, Kimura (unadjusted) = 34.85 Transitions / transversions = 0.68 (13/19) Gap_init rate = 0.04 (5 / 123), avg. gap size = 1.80 (9 / 5) 620 28.21 3.41 1.44 chr3qtel1M 607983 608187 (391813) C MIRc#SINE/MIR (57) 211 3 m_b152s601i4 5692 chr3qtel1M 607983 ACATATTGTATCATTAGTTCTTCACAACAACCCT---AG--AGTGAGTGC 608027 i i i v v v i --- -- vv v C MIRc#SINE/MIR 211 ATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGC 162 chr3qtel1M 608028 TCGCATTATCA-CCCCACTTTACAGATGAGAAAGCTCAGTCCAAAAGAGA 608076 vv i i - i i i v v iv i - C MIRc#SINE/MIR 161 AGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAG- 113 chr3qtel1M 608077 AGGAAAGATACTTGTCCAGAATTAAACAGCTGGTAAGTATCTGAGGTAGG 608126 - vv vv i iii i v i iv v vii C MIRc#SINE/MIR 112 -GTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGG 64 chr3qtel1M 608127 ACTTGAATTCAGCTCTCTCCTCACTTTCAGGTCAGTGAGCTGCCCATTGA 608176 i ii v - v iiv vi vv vi i v C MIRc#SINE/MIR 63 ACTCGAACCCAGGTCT-TCCTGACTCCAAGTCCAGTGCTCTTTCCACTGC 15 chr3qtel1M 608177 ACTAC-CTGGCT 608187 i - v C MIRc#SINE/MIR 14 ACCACACTGCCT 3 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.24 CpG sites = 29, Kimura (unadjusted) = 35.85 Transitions / transversions = 1.04 (29/28) Gap_init rate = 0.03 (7 / 204), avg. gap size = 1.43 (10 / 7) 551 37.54 9.47 1.43 chr3qtel1M 608671 609124 (390876) L2#LINE/L2 2390 2879 (203) m_b152s601i5 5693 chr3qtel1M 608671 ATGCAACTCGACCTCCAC-ACATCTCAAACAGGATGGCCAGGAGGCTTCT 608719 v --i v v - v viv v i iv v L2#LINE/L2 2390 ATCCAACT--GCCTACTCGACATCTCCACTTGGATGTCTAATAGGCATCT 2437 chr3qtel1M 608720 TAGACTCAACATGCCCAAAGTCAGGCTCTTCATCTTTCTCCCAGGACC-- 608767 i i i i iiiiii i v i i ivii -- L2#LINE/L2 2438 CAAACTTAACATGTCCAAAACTGAACTCCTGATCTTCCCCCTCAAACCTG 2487 chr3qtel1M 608768 --CTTCCTG-------CCCTATTACTGTGGAGGGCAACATCATGCCCCTC 608808 -- i i ------- i iv v ?i v vi v ii iv L2#LINE/L2 2488 CTCCTCCCGCAGTCTTCCCCATCTCAGTNAATGGCAACTCCATCCTTCCA 2537 chr3qtel1M 608809 ATCCTTCACACTTCCGATACAGAAGTCATCCTGGATTTCTCACTATTTCT 608858 i ivi vi ivvvi iviv i v i i v v i L2#LINE/L2 2538 GTTGCTCAGGCCAAAAACCTTGGAGTCATCCTTGACTCCTCTCTTTCTCT 2587 chr3qtel1M 608859 CACCCATCCAGAGCCAATCAATACGGTGCCAGGCCTGTTAATTTCACCTC 608908 v -i v v v - i-- v iv iiii ii i L2#LINE/L2 2588 CACAC-CCCACATCCAATCCAT-CA--GCAAATCCTGTCGGCTCTACCTT 2633 chr3qtel1M 608909 CACA--GTATCC-----CTGGTCAAT----GTCACCTTTGCTG----CAT 608943 v --i ----- i ii v ----ii iii ---- i L2#LINE/L2 2634 CAAAATATATCCAGAATCCGACCACTTCTCACCACCTCCACTGCCACCAC 2683 chr3qtel1M 608944 CTCTGCCCATTTCAC-----TCTCTGCACC---ATCTCTG--------GT 608977 iiv i vvi ----- - i --- iv --------vi L2#LINE/L2 2684 CCTGGTCCAAGCCACCATCATCTCT-CGCCTGGATTACTGCAATAGCCTC 2732 chr3qtel1M 608978 CCATTTCATCTGCCAGCTTCAAGTCTCCACCTAATCTAGTCCATATTCTA 609027 i vi vi v v v vi ivv ivv ?i i vi v L2#LINE/L2 2733 CTAACTGGTCTCCCTGCTTCCACCCTTGCCCCCCTNCAGTCTATTCTCAA 2782 chr3qtel1M 609028 CTTAGCCACCAAAATGGTTTTCCTAAAGCATGGGCTTGAATATGTCACTC 609077 vi vi i i i ii ii i i ii iiv vi L2#LINE/L2 2783 CACAGCAGCCAGAGTGATCCTTTTAAAACGTAAGTCAGATCATGTCACTC 2832 chr3qtel1M 609078 CCATATTCAATAAACACCAGTGGCTCCCTATCATTTCCAGGATCAAA 609124 iv ii v vv v i i i vivii ii v L2#LINE/L2 2833 CTCTGCTCAAAACCCTCCAATGGCTTCCCATCTCACTCAGAGTAAAA 2879 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 53.13 CpG sites = 104, Kimura (unadjusted) = 55.72 Transitions / transversions = 1.62 (104/64) Gap_init rate = 0.04 (18 / 453), avg. gap size = 2.78 (50 / 18) 189 33.30 6.25 3.03 chr3qtel1M 609224 609319 (390681) C L2a_3end#LINE/L2 (2) 515 417 m_b152s601i7 5694 chr3qtel1M 609224 TCATTCAATTAATCAACATTTATTAAGCATCCACTGTGA---AGCTTCTG 609270 v i iv i i ii i i v--- viv C L2a_3end#LINE 515 TCATTCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTG 466 chr3qtel1M 609271 ACCCTCAGGACGCTGAGGACTCAG-GGT--ACAAGTAAAAAGAAGAGCCC 609317 ---i vi i i iv -i -- ivv i vi iiv C L2a_3end#LINE 465 ---TTCTAGGCGCTGGGGATACAGCAGTGAACAAAACAGACAAAAGTCCC 419 chr3qtel1M 609318 TG 609319 C L2a_3end#LINE 418 TG 417 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.40 CpG sites = 20, Kimura (unadjusted) = 46.49 Transitions / transversions = 1.82 (20/11) Gap_init rate = 0.06 (6 / 95), avg. gap size = 1.50 (9 / 6) 200 27.59 7.59 3.66 chr3qtel1M 609224 609302 (390698) C L2b_3end#LINE/L2 (2) 464 383 m_b152s601i6 5694 chr3qtel1M 609224 TCATTCAATTAATCAACATTTATTAAGCATCCACTGTGAAGCTTCTGACC 609273 v i iv i i i ii i vi---i v i ? C L2b_3end#LINE 464 TCATTCATTCAACAAATATTTACTGAGCGCCTACTGTGTG---CCAGGCN 418 chr3qtel1M 609274 CT---CAGGACGCTGAGGACTCAG-GGT--ACAAG 609302 --- vi i i iv - -- C L2b_3end#LINE 417 CTGTGCTAGGCGCTGGGGATACAGCGGTGAACAAG 383 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.80 CpG sites = 15, Kimura (unadjusted) = 37.06 Transitions / transversions = 2.50 (15/6) Gap_init rate = 0.08 (6 / 78), avg. gap size = 1.50 (9 / 6) 393 20.68 2.27 1.12 chr3qtel1M 609914 610001 (389999) C MIR3#SINE/MIR (38) 170 82 m_b152s601i8 5695 chr3qtel1M 609914 CTTAGACATCATCAAGTCCAAAGC--TCCTTTTTCAGATGAGAAAGCTGA 609961 v v vv -- v v i i C MIR3#SINE/MIR 170 CTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGA 121 chr3qtel1M 609962 GCCCCTAGACAGAGGAAGTGACCTGCCTGGGGTCACATGG 610001 v - v iv i iii ii C MIR3#SINE/MIR 120 GGCCC-AGAGAGGTGAAGTGACTTGCCCAAGGTCACACAG 82 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 24.37 CpG sites = 9, Kimura (unadjusted) = 24.37 Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.02 (2 / 87), avg. gap size = 1.50 (3 / 2) 15 12.92 2.78 2.78 chr3qtel1M 611434 611469 (388531) (GGCCCG)n#Simple_repeat 1 36 (0) m_b152s252i5 5696 chr3qtel1M 611434 GGGCCGGCACCGGG-GCGGGCCCGGAGCCCGGGCCCG 611469 v vv -v - (GGCCCG)n#Sim 1 GGCCCGGGCCCGGGCCCGGGCCCGG-GCCCGGGCCCG 36 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 14 21.08 7.25 2.78 chr3qtel1M 612801 612869 (387131) (GAAGAGT)n#Simple_repeat 1 72 (0) m_b152s252i6 5697 chr3qtel1M 612801 GAAGAGTAATGGGTGAAG-GTG-GGAGTTGGAAGAGTGATGAG-CAAATG 612847 i v i - -i - - v -v iv (GAAGAGT)n#Si 1 GAAGAGTGAAGAGTGAAGAGTGAAGAG-T-GAAGAGTGAAGAGTGAAGAG 48 chr3qtel1M 612848 TG-AGAG-CCAGAAGGAAGAGTGA 612869 - -vv iv (GAAGAGT)n#Si 49 TGAAGAGTGAAGAGTGAAGAGTGA 72 Matrix = Unknown Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.10 (7 / 68), avg. gap size = 1.00 (7 / 7) 13 29.14 3.12 1.54 chr3qtel1M 616807 616870 (383130) (CCTCCTT)n#Simple_repeat 1 65 (0) m_b152s252i7 5698 chr3qtel1M 616807 CCTCCCTCCTCCTTCCCCATCCCTGCAGCCGCACTGACT-GAGCCTCCCT 616855 i i v i v vv v - vv -vvv i (CCTCCTT)n#Si 1 CCTCCTTCCTCCTTCCTCCTTCCTCCTTCCTC-CTTCCTCCTTCCTCCTT 49 chr3qtel1M 616856 CCTCCTTCC-CCATCC 616870 - v (CCTCCTT)n#Si 50 CCTCCTTCCTCCTTCC 65 Matrix = Unknown Transitions / transversions = 0.36 (4/11) Gap_init rate = 0.05 (3 / 63), avg. gap size = 1.00 (3 / 3) 192 23.67 11.11 1.85 chr3qtel1M 618020 618118 (381882) L2#LINE/L2 2155 2262 (820) m_b152s601i9 5699 chr3qtel1M 618020 CCCAGCTCCCTGCCAGCCCCTTCTCAGTCTCCTTGGCGGGGTTTTCCT-- 618067 i v v v v i v v v ii -- L2#LINE/L2 2155 CCTACCTCACTGGCCGCTCCTTCTCAGTCTCCTTTGCTGGTTCCTCCTCA 2204 chr3qtel1M 618068 -------GCCCTCT-AACCTGGGTGTCCCTCAGGACTC-GCCCTGGGCGA 618108 ------- v - v v v v i i - i v -- L2#LINE/L2 2205 TCTCCCCGACCTCTNAACGTTGGAGTGCCCCAGGGCTCAGTCCTTG--GA 2252 chr3qtel1M 618109 CCCTCTCTCT 618118 iii L2#LINE/L2 2253 CCTCTTCTCT 2262 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.59 CpG sites = 10, Kimura (unadjusted) = 28.59 Transitions / transversions = 0.77 (10/13) Gap_init rate = 0.06 (6 / 98), avg. gap size = 2.17 (13 / 6) 11 27.88 3.28 3.28 chr3qtel1M 618802 618862 (381138) (GTCCAGG)n#Simple_repeat 1 61 (0) m_b152s252i8 5700 chr3qtel1M 618802 GTGCAGGGTCTACGGGCTCCAGAACCCA-AGTACAGGGTCCAGAACCCAA 618850 v i - - iii -i v iii i (GTCCAGG)n#Si 1 GTCCAGGGTCCA-GGG-TCCAGGGTCCAGGGTCCAGGGTCCAGGGTCCAG 48 chr3qtel1M 618851 GG-GCAGGTTCCA 618862 -v v (GTCCAGG)n#Si 49 GGTCCAGGGTCCA 61 Matrix = Unknown Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.07 (4 / 60), avg. gap size = 1.00 (4 / 4) 208 30.30 6.06 0.00 chr3qtel1M 621927 621992 (378008) MIR1_Amn#SINE/MIR 86 155 (75) m_b152s601i10 5701 chr3qtel1M 621927 GCTGGGCAGCATGGTGGAAGGCGCCTC----CCCTAAGCCTCAGCTCTCC 621972 ? iii v v v v v i i ?---- i i? i ii i MIR1_Amn#SINE 86 GCTGNGTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCT 135 chr3qtel1M 621973 TGTCTGTAAAGTAGGGATAA 621992 ii i i MIR1_Amn#SINE 136 CATCTGTAAAATGGGGATAA 155 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.87 CpG sites = 15, Kimura (unadjusted) = 44.87 Transitions / transversions = 3.00 (15/5) Gap_init rate = 0.02 (1 / 65), avg. gap size = 4.00 (4 / 1) 294 31.56 6.00 4.95 chr3qtel1M 621951 622050 (377950) MIRb#SINE/MIR 115 215 (53) m_b152s601i12 5701 chr3qtel1M 621951 CTCCCCTAAGCCTCAGCTCTCCTGTCTGTAAAGTAGGGATAAATCTGTAG 622000 ii i i i ii iii i i ----- i MIRb#SINE/MIR 115 CCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAA-----TAA 159 chr3qtel1M 622001 GACTTGCTTCACAGGGCTGGTCTGGGGCTCA------ATAAGGCGTCTTG 622044 v i i i i i v v i v i ------ v i v vi MIRb#SINE/MIR 160 TACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAA 209 chr3qtel1M 622045 AGTGCT 622050 i MIRb#SINE/MIR 210 AGCGCT 215 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.68 CpG sites = 23, Kimura (unadjusted) = 44.80 Transitions / transversions = 3.29 (23/7) Gap_init rate = 0.06 (6 / 99), avg. gap size = 1.83 (11 / 6) 303 31.71 4.88 0.00 chr3qtel1M 621951 622032 (377968) MIRc#SINE/MIR 112 197 (71) m_b152s601i11 5701 chr3qtel1M 621951 CTCCCCTAAGCCTCAGCTCTCCTGTCTGTAAAGTAGGGATAA----ATCT 621996 ii i i i ii iii i i ---- i MIRc#SINE/MIR 112 CCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCT 161 chr3qtel1M 621997 GTAGGACTTGCTTCACAGGGCTGGTCTGGGGCTCAA 622032 ivvvi i i i i v v i v MIRc#SINE/MIR 162 GCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAA 197 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.12 CpG sites = 20, Kimura (unadjusted) = 45.12 Transitions / transversions = 3.33 (20/6) Gap_init rate = 0.01 (1 / 81), avg. gap size = 4.00 (4 / 1) 37 16.53 0.00 0.00 chr3qtel1M 624725 624787 (375213) (G)n#Simple_repeat 1 63 (0) m_b152s252i9 5702 chr3qtel1M 624725 GGCGGGGGGAGGGGAAGGGGGGGGGGAGGGGGGGGGGGGGGGGGGAAGGG 624774 v i ii i ii (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 50 chr3qtel1M 624775 GGGAAGGGGGGGG 624787 ii (G)n#Simple_r 51 GGGGGGGGGGGGG 63 Matrix = Unknown Transitions / transversions = 8.00 (8/1) Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0) 195 26.44 10.14 1.33 chr3qtel1M 625321 625389 (374611) L2a_3end#LINE/L2 423 497 (20) m_b152s601i13 5703 chr3qtel1M 625321 CCTCTGTCTGCCTTGGTTTCCT--TGGTTCC-----ACTTAGCACGGAGC 625363 i i ii - iv -- vv -----i i v i v L2a_3end#LINE 423 CTTTTGTCTGTTTTG-TTCACTGCTGTATCCCCAGCGCCTAGAACAGTGC 471 chr3qtel1M 625364 CTGGCACACAGTAGGTGCTCCATGGA 625389 i i v ii L2a_3end#LINE 472 CTGGCACATAGTAGGCGCTCAATAAA 497 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.42 CpG sites = 12, Kimura (unadjusted) = 33.95 Transitions / transversions = 2.00 (12/6) Gap_init rate = 0.04 (3 / 68), avg. gap size = 2.67 (8 / 3) 231 18.97 10.34 0.00 chr3qtel1M 625326 625383 (374617) L2b_3end#LINE/L2 377 440 (26) m_b152s601i14 5703 chr3qtel1M 625326 GTCTGCCTTGGTTTCC-TTGGTTCC-----ACTTAGCACGGAGCCTGGCA 625369 i v iv -i vv -----i i i ? L2b_3end#LINE 377 GTCTGTCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCA 426 chr3qtel1M 625370 CACAGTAGGTGCTC 625383 i L2b_3end#LINE 427 CACAGTAGGCGCTC 440 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 18.34 CpG sites = 7, Kimura (unadjusted) = 22.76 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.04 (2 / 57), avg. gap size = 3.00 (6 / 2) 278 24.00 5.38 7.03 chr3qtel1M 627321 627450 (372550) C MIR1_Amn#SINE/MIR (101) 129 2 m_b152s601i16 5704 chr3qtel1M 627321 CTGAGGC--AGTTGGGGTTAAGTGACTTAC--AGGGTCACACAGCCAGGA 627366 -- v- i ? i -- i ? ?i -- C MIR1_Amn#SINE 129 CTGAGGCNCAGA-GAGGTNAAGTGACTTGCCCAAGGTCACNCAGCNGG-- 83 chr3qtel1M 627367 AGTGTAAGTGTCTGAGGCCAGATTTGAACTGAGGGCCTCCCGACTTCAGG 627416 ----i? v v v vi ? ? iv -i v i vi C MIR1_Amn#SINE 82 ----CNAGTGGCAGAGCCGGGANTNGAACCCAGG-TCTCCCGAGTCCCAG 38 chr3qtel1M 627417 GCTGGTG-GCTATT--TTAAACCAAACTTGCTTTCTT 627450 v ii -v i--i i v - i i i C MIR1_Amn#SINE 37 TCCAGTGCTCTATCCACTAGACCACAC-TGCCTCCCT 2 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.58 CpG sites = 18, Kimura (unadjusted) = 31.58 Transitions / transversions = 1.64 (18/11) Gap_init rate = 0.10 (13 / 129), avg. gap size = 1.23 (16 / 13) 337 22.62 3.64 7.55 chr3qtel1M 627321 627430 (372570) C MIRc#SINE/MIR (141) 127 22 m_b152s601i15 5704 chr3qtel1M 627321 CTGAGGC--AGTTGGGGTTAAGTGACTTAC--AGGGTCACACAGCCAGGA 627366 -- v- i i -- i i -- C MIRc#SINE/MIR 127 CTGAGGCTCAGA-GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG-- 81 chr3qtel1M 627367 AGTGTAAGTGTCTGAGGCCAGATTTGAACTGAGGGCCTCCCGACTTCAGG 627416 ---- v v v vi i i iv v i i i i C MIRc#SINE/MIR 80 ----TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr3qtel1M 627417 GCTGGTGGCTATTT 627430 v ii - v C MIRc#SINE/MIR 34 TCCAGT-GCTCTTT 22 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.02 CpG sites = 14, Kimura (unadjusted) = 27.38 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.09 (10 / 109), avg. gap size = 1.20 (12 / 10) 1039 32.73 4.20 1.19 chr3qtel1M 628461 629032 (370968) C L1ME5_3end#LINE/L1 (297) 644 56 m_b152s551i4 5705 chr3qtel1M 628461 TCCTGGTTCT-GCTCATTTCCCTCAGCAGCA-GTTCGTGTAAG-TCTCTC 628507 i v -i iv v vi - -- v - iv C L1ME5_3end#LI 644 TTCTGTTTCTTACTTTTTTCACTCAGCACTATGTT--TTTAAGATCCATC 597 chr3qtel1M 628508 CAGGTCTTTCTGAAATCATCCCGTTGGTCATTTCTTACAGAACAATAATA 628557 v ivi v vivv iv iv iii v v vvvv i C L1ME5_3end#LI 596 CATGTTGCTATGTGTACATCTAGTCCGTTGCTTCTAACTGCTGCATAGTA 547 chr3qtel1M 628558 TTCCATAA----CATTCA--------GATTCAGCCATTCTCCAATTGATG 628595 i ii---- i --------v iii v i v v C L1ME5_3end#LI 546 CTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCAGTGATG 497 chr3qtel1M 628596 GGCATCCATTTAATTTCCAGTTTCTGGCCACTACCAAGAGGGCTGCCACA 628645 i i vv viii ii i iv i v v iv v ii C L1ME5_3end#LI 496 GACACCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCTGCAATG 447 chr3qtel1M 628646 AACATTTTTGTACCTGTGGCTTCCTTTCTCTCCTTTAAGATCTGTTTGGG 628695 ii i v vv i iv vvvi viv v ii i v C L1ME5_3end#LI 446 AACATCCTCGTACATGTCCCCTTATGGACCTGTGTGAGAATTTCTTTGGG 397 chr3qtel1M 628696 GTATAAGCCCAGTAGAAACACTGCTGGATCAAAGGGGATGCACAATTTGG 628745 i vi v viiv i i v v ii vvi -- C L1ME5_3end#LI 396 ATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATGCGTATACT-- 349 chr3qtel1M 628746 TAACTTTTTGAGCA--TAGTTCTAAATTGCTCTCCAGAAGGCTTGGATCA 628793 --- vi -- v v i i v vi v i C L1ME5_3end#LI 348 TAA---TTTGACTAAGTACTGCCAGATTGCTCTCCAGAATGGCTGCACCA 302 chr3qtel1M 628794 GTTCACAGTTCCATCAACAATGCATCAGTGTCCCGGTTTTCCTGCATCCC 628843 ii v i i i i v v i vi ? i ii i C L1ME5_3end#LI 301 GTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATCCT 252 chr3qtel1M 628844 CTCCAACATTCATCATTATCTTTTCCTGTTATCTTGGCCAATCTGAGAGG 628893 v i iiv ivviii v v i v i i v C L1ME5_3end#LI 251 CGCCAACACTTGGCATTATCCAGCTTTCTAATTTTTGCCAGTCTAATAGG 202 chr3qtel1M 628894 TGTGTAGTGGTATCTCAGAGTTATCTTAATTTGTATTTCTCTGATCAATA 628943 iv i vv i i i i v C L1ME5_3end#LI 201 TGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATTTCTCTGATTACTA 152 chr3qtel1M 628944 ATGATTTAGAGCA---CCTTATATGATTAGAAATGGTTTTAATTTCTTCA 628990 v v --- i i v ivv iivv ivii i v C L1ME5_3end#LI 151 ATGAGTTTGAGCATCTCTTCATATGCTTGTTAGCCTTTCGGGTTTCCTCT 102 chr3qtel1M 628991 TCTGAAAAT----TGTTCATAAACTTTGACCATTTATCAATTGGAG 629032 v ---- vv v v v i C L1ME5_3end#LI 101 TCTGTAAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGGGG 56 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 42.75 CpG sites = 97, Kimura (unadjusted) = 44.01 Transitions / transversions = 1.10 (97/88) Gap_init rate = 0.03 (15 / 571), avg. gap size = 2.07 (31 / 15) 1085 29.52 1.99 2.81 chr3qtel1M 628555 629056 (370944) C L1ME3G_3end#LINE/L1 (395) 529 32 m_b152s551i5 5705 chr3qtel1M 628555 ATATTCCATAACATTCAGATTCAGCCATTCTCCAATTGATGGGCATCCAT 628604 v iv ---- i i i v i ii v C L1ME3G_3end#L 529 ATATACCATAATTT----ATTTAACCATTCCCCTATTGATGGACATTTAG 484 chr3qtel1M 628605 TTAATTTCCAGTTTCTGGCCACTACCAAGAGGGCTGCCACAAACATTTTT 628654 v vi i i v i i v v iv v ii ii C L1ME3G_3end#L 483 GTTGTTTCCAATTTTTCGCTATTACAAACAATGCTGCAATGAACATCCTT 434 chr3qtel1M 628655 GTACCTGTGGCTTCCTTTCTCTCCTTT---AAGATCTGTTTGGGGTATAA 628701 v --- ? viv v v v --- iv i v ? i i v v C L1ME3G_3end#L 433 GTACATG---CNTCCTTGTGCACATGTGCGAGTATTTCTNTAGGATAGAT 387 chr3qtel1M 628702 GCCCAGTAGAAACACTGCTGGATCAAAGGGGATGCACAATTTGGTAACTT 628751 ? ? v viiv i i v i v --- v C L1ME3G_3end#L 386 NCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGCATTTT---AAATT 340 chr3qtel1M 628752 TTTGAGCATAGTTCTAAATTGCTCTCCAGAAGGCTTGGATCAGTTCACAG 628801 viviv v v i i i ? vi v i i i v C L1ME3G_3end#L 339 TTAATAGATACTGCCAAATTGCCCTCCAAAANGGCTGTACCAATTTACAC 290 chr3qtel1M 628802 TTCCATCAACAATGCATCAGTGTCCCGGTTTTCCTGCATCCCCTCCAACA 628851 i i i i i v v v v i ii i i v C L1ME3G_3end#L 289 TCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCACACCCTCGCCAACA 240 chr3qtel1M 628852 TTCATCATTATCTTTTCCTGTTATCTTGGCCAATCTGAGAGGTGTGTAGT 628901 i ?ivi vv?iii vvv i v vi viv i C L1ME3G_3end#L 239 CTNGATATTATCAANCTTTTAAATTTTTGCCAATCTGATGGGTGAAAAAT 190 chr3qtel1M 628902 GGTATCTCAGAGTTATCTTAATTTGTATTTCTCTGATCAATAATGATTTA 628951 vv i i i i i v i vv v C L1ME3G_3end#L 189 GGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGATTACTAGTGAGGTT 140 chr3qtel1M 628952 GAGCACCTT---ATATGATTAGAAATGGTTTTAATTTCTTCATCTGAAAA 628998 i --- v vviiivi vv i v vi C L1ME3G_3end#L 139 GAGCATCTTTTCATATGTTTATTGGCCATTTGTATTTCCTCTTCTGTGAA 90 chr3qtel1M 628999 T----TGTTCATAAACTTTGACCATTTATCAATTGGAGAATGGCTTGGAT 629044 ---- vv v v v iv-- v v-- C L1ME3G_3end#L 89 TTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGGGT--TGTCTTT--T 44 chr3qtel1M 629045 TCTTATAAATTT 629056 vi C L1ME3G_3end#L 43 TCTTATTGATTT 32 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 38.32 CpG sites = 71, Kimura (unadjusted) = 38.66 Transitions / transversions = 0.97 (71/73) Gap_init rate = 0.03 (17 / 501), avg. gap size = 1.41 (24 / 17) 275 36.72 0.00 1.27 chr3qtel1M 629049 629208 (370792) C L1ME4c_3end#LINE/L1 (242) 588 431 m_b152s551i6 5706 chr3qtel1M 629049 ATAAATTTCAGTCAATTATCATTTCTTATAGTACAATAATATCCCATTAC 629098 ivi --i i v i ivvv i iiv C L1ME4c_3end#L 588 ATAGTCTTCA--TAATTATCATTTTTAATGGCTGCATAATATTCCATCGA 541 chr3qtel1M 629099 CTTCACTTATCACAATTTATTCAATCATTCCCCAGCTATTGTGCATCCCC 629148 v ?v iv i i i i i vii i vi iivv C L1ME4c_3end#L 540 GTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAG 491 chr3qtel1M 629149 TCAGTTTCCAGCTCCTTGCCATCACAGAAAGGCCTGCCACAAACATTTTT 629198 viv ii ii i i i i i v ivv v ii i i C L1ME4c_3end#L 490 GTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTC 441 chr3qtel1M 629199 GCGCATGTGG 629208 i i i C L1ME4c_3end#L 440 GTGCATATAG 431 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 50.56 CpG sites = 39, Kimura (unadjusted) = 55.02 Transitions / transversions = 2.05 (39/19) Gap_init rate = 0.01 (2 / 159), avg. gap size = 1.00 (2 / 2) 275 34.96 0.00 0.00 chr3qtel1M 629084 629206 (370794) C L1ME3F_3end#LINE/L1 (438) 552 430 m_b152s551i7 5706 chr3qtel1M 629084 ATAATATCCCATTACCTTCACTTATCACAATTTATTCAATCATTCCCCAG 629133 i iiv vv iv i i vi i v C L1ME3F_3end#L 552 ATAATATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTCCTG 503 chr3qtel1M 629134 CTATTGTGCATCCCCTCAGTTTCCAGCTCCTTGCCATCACAGAAAGGCCT 629183 iiiv vi iivvviv i ii i i ii v vv C L1ME3F_3end#L 502 TCGATGGACATTTGGGTTGTTTCCAGTTTTTTGCTATTACGAACAGTGCT 453 chr3qtel1M 629184 GCCACAAACATTTTTGCGCATGT 629206 i ii i ii C L1ME3F_3end#L 452 GCTATGAACATTCTTGTACATGT 430 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 46.51 CpG sites = 28, Kimura (unadjusted) = 50.04 Transitions / transversions = 1.87 (28/15) Gap_init rate = 0.00 (0 / 122), avg. gap size = 0.0 (0 / 0) 199 36.29 9.47 3.96 chr3qtel1M 629212 629475 (370525) L2#LINE/L2 2801 3078 (4) m_b152s601i17 5707 chr3qtel1M 629212 CCTTTGCCTAAAGCACAGGAATGACCATGTAATTCCTCCCACTCCATTAA 629261 --- i ii i vvv i v i i-i v vvvv L2#LINE/L2 2801 CCTTT---TAAAACGTAAGTCAGATCATGTCACTCCTCT-GCTCAAAACC 2846 chr3qtel1M 629262 GTAAAGTAGCTCTCTATCACCTCCAGGAACCAAAGACCGAATCCGAATCC 629311 v vv i i ii i v vii -- vi ii i -----i L2#LINE/L2 2847 CTCCAATGGCTTCCCATCTCACTCAG--AGTAAAAGCCAAA-----GTCC 2889 chr3qtel1M 629312 TCTGCTTGGCATTCGAAGTCCTTCCTGACCTTTTC-------AGTCTTCT 629354 ivvvv v v i i i v v i vv ------- viii L2#LINE/L2 2890 TTACAATGGCCTACAAGGCCCTACATGATCTGGTCCCCCGTTACCTCTCT 2939 chr3qtel1M 629355 GATCCCTTCTCCTTTCCCTGGCCTCCA-ACTC--TCTGATTCAGTCACAC 629401 i i v vi v vv i v-i -- i v i i L2#LINE/L2 2940 GACCTCATCTCCTACCACTCTCCCCCTCGCTCACTCCGCTCCAGCCACAC 2989 chr3qtel1M 629402 TGGCCTTCGTGCTGTTCCTC--AC---CCATAGACTCCTTTTCTCCAG-- 629444 i v -- --- viv v iiiiv ii -- L2#LINE/L2 2990 TGGCCTCCTTGCTGTTCCTCGAACACGCCAGGCACGCTCCCGCCTCAGGG 3039 chr3qtel1M 629445 --------CCAGCTGTCCCTCATGCCCAGAACACTCTCC 629475 -------- iv i iiv ii i i L2#LINE/L2 3040 CCTTTGCACTTGCTGTTCCCTCTGCCTGGAACGCTCTTC 3078 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 47.64 CpG sites = 52, Kimura (unadjusted) = 51.60 Transitions / transversions = 1.30 (52/40) Gap_init rate = 0.07 (18 / 263), avg. gap size = 2.00 (36 / 18) 188 34.43 5.32 4.21 chr3qtel1M 629234 629421 (370579) L2#LINE/L2 2820 3009 (73) m_b153s601i0 5707 chr3qtel1M 629234 GACCATGTAATTCCTCCCACTCCATTAAGTAAAGTAGCTCTCTATCACCT 629283 i v i i-i v vvvvv vv i i ii i v vi L2#LINE/L2 2820 GATCATGTCACTCCTCT-GCTCAAAACCCTCCAATGGCTTCCCATCTCAC 2868 chr3qtel1M 629284 CCAGGAACCAAAGACCGAATCCGAATCCTCTGCTTGGCATTCGAAGTCCT 629333 i -- vi ii i -----i ivvvv v v i i i L2#LINE/L2 2869 TCAG--AGTAAAAGCCAAA-----GTCCTTACAATGGCCTACAAGGCCCT 2911 chr3qtel1M 629334 TCCTGACCT---TTTCAGT---CT-TCTGATCCCTTCTCCTTTCCCTGGC 629376 v v i ---iii v --- - i i v vi v vv L2#LINE/L2 2912 ACATGATCTGGTCCCCCGTTACCTCTCTGACCTCATCTCCTACCACTCTC 2961 chr3qtel1M 629377 CTCCA-ACTC--TCTGATTCAGTCACACTGGCCTTCGTGCTGTTCCTC 629421 i v-i -- i v i i i v L2#LINE/L2 2962 CCCCTCGCTCACTCCGCTCCAGCCACACTGGCCTCCTTGCTGTTCCTC 3009 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 45.16 CpG sites = 33, Kimura (unadjusted) = 47.24 Transitions / transversions = 1.14 (33/29) Gap_init rate = 0.07 (13 / 187), avg. gap size = 1.38 (18 / 13) 653 34.12 10.17 1.34 chr3qtel1M 629336 629748 (370252) L2b_3end#LINE/L2 10 458 (8) m_b152s601i18 5707 chr3qtel1M 629336 CTGACCTTTTCAGTCTTCTGATCCCTTCTCCTTTCCCTGGCCTCCAACTC 629385 i iivii viii i ii i v vi v vv i ivi L2b_3end#LINE 10 CTGGCCCCGCTACCTCTCCGGCCTCATCTCCTACCACTCTCCCCTTGCTC 59 chr3qtel1M 629386 --TCTGATTCAGTCACACTGGCCTTCGTGCTGTTCCTCACCCAT---AGA 629430 -- v i i i v ivv i--- ?i L2b_3end#LINE 60 ACTCTGCTCCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACACGCCANG 109 chr3qtel1M 629431 CTCCTTTTCTCC--AG----------CCAGCTGTCCCTCATGCCCAGAAC 629468 ?i ii v -- ---------- ?v i iiv ii L2b_3end#LINE 110 CTCNCTCCCGCCTCAGGGCCTTTGCACNTGCTGTTCCCTCTGCCTGGAAC 159 chr3qtel1M 629469 ACTCT---CCATCTTGGTCTCTTGATT--TCCCCGGTCAAC-TTCAGAAT 629512 i i --- i iv- v i iii--ii iiv v - ivi L2b_3end#LINE 160 GCCCTTCCCCACCTCT-TCGCCTGGCCAACTCCTACTCATCCTTCAGGTC 208 chr3qtel1M 629513 CCAGCTAAAATCTCACCTTGTGCAGGAAGCCCTTCCTAGTCTCTC---TT 629559 i v v iv v i i iii i i ---ii L2b_3end#LINE 209 TCAGCTCAAATGTCACCTCCTCCGGGAAGCCCTCCCTGACCCCCCAGGCC 258 chr3qtel1M 629560 AGTTCCAGTGCCTTCTCTCAGGGAATTCTCTCTCA--TGTATCCTGCCTC 629607 i v vi i i - v ---- i i i --iv i v L2b_3end#LINE 259 GGGTCAGGCGCCCTC-CTCTGGG----CCCCCCCAGTCCTACCCTGCCAC 303 chr3qtel1M 629608 T------TAT--TTGTCTCTCTGCTTGCCT---TCCCTTATGAGCGCGGG 629646 ------ -- v?i i v i --- ii iv vvi v L2b_3end#LINE 304 TCTGGGTTATNATTGTCTGNTTACATGTCTGTCTCCCCCACTAGACTGTG 353 chr3qtel1M 629647 AGCTCCTCAAAAGCAGGAACTGTGTTTTCCTTTTTCTT---TATTTCCTC 629693 vii ii i i ? i vi v vi--- i v i L2b_3end#LINE 354 AGCTCCGTGAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTGTATCCCC 403 chr3qtel1M 629694 AACACATAGTACGGTGCCTGACACACAAGAGACTATTAATAAATGCTTAT 629743 i i v i i ? i iv i vv i i ii i L2b_3end#LINE 404 AGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTTGT 453 chr3qtel1M 629744 TGAGT 629748 i L2b_3end#LINE 454 TGAAT 458 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.82 CpG sites = 95, Kimura (unadjusted) = 49.99 Transitions / transversions = 2.16 (95/44) Gap_init rate = 0.05 (19 / 412), avg. gap size = 2.53 (48 / 19) 779 30.04 2.56 0.42 chr3qtel1M 633162 633395 (366605) MIRb#SINE/MIR 16 254 (14) m_b153s601i2 5708 chr3qtel1M 633162 GCACAGTGAATAGAGTACTTGCTT--GATTCAATAAGACCCAAGTTCAAA 633209 ii i v i vv -- v ivv iii i MIRb#SINE/MIR 16 GTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCGAA 65 chr3qtel1M 633210 GTCAGCCTCAGCTACTATATT--TTGTATGACCCTGAGCAAGTCACATAG 633257 vi v v v i - i --i i i i i v i MIRb#SINE/MIR 66 TCCCGGCTCTGCCACT-TACTAGCTGTGTGACCTTGGGCAAGTTACTTAA 114 chr3qtel1M 633258 CTTCTGTCTACTTCAGGTTCTTCGATTGTAAAAT-GGGATAACAGCAACT 633306 i v vvi i v i ivi - i ii v MIRb#SINE/MIR 115 CCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCT 164 chr3qtel1M 633307 CCCTCCTAGAGTTGTTGTGAAGCTCAGGAG-GAGCATATCTGTAAAATGC 633355 v vi i i v i iiv - vv iiv ii MIRb#SINE/MIR 165 ACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCGC 214 chr3qtel1M 633356 TTAGCGCAGGGCATGGCACATGGTAGGCACTCAGTGCATG 633395 i v v i i i i iv MIRb#SINE/MIR 215 TTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAAATG 254 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 37.57 CpG sites = 43, Kimura (unadjusted) = 39.77 Transitions / transversions = 1.59 (43/27) Gap_init rate = 0.02 (5 / 233), avg. gap size = 1.40 (7 / 5) 12 13.14 2.70 5.56 chr3qtel1M 633682 633718 (366282) (CGGCTCC)n#Simple_repeat 1 36 (0) m_b153s252i0 5709 chr3qtel1M 633682 CGGCTGCCGGC-CCCGGGTCCCAGCACCCTGCGCTCCC 633718 v - v i v - - (CGGCTCC)n#Si 1 CGGCTCCCGGCTCCCGGCTCCCGGCTCCC-G-GCTCCC 36 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.08 (3 / 36), avg. gap size = 1.00 (3 / 3) 200 20.75 5.66 0.00 chr3qtel1M 634185 634237 (365763) MIR1_Amn#SINE/MIR 104 159 (71) m_b153s601i3 5710 chr3qtel1M 634185 AATCGCTTAATCTCGTT-TGCCTCAGTTTCCTTCTCTGT--AATGGAGAA 634231 i i ? i vi -? iv -- i v MIR1_Amn#SINE 104 AGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGGAT 153 chr3qtel1M 634232 AGAGAT 634237 iv MIR1_Amn#SINE 154 AATGAT 159 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 26.03 CpG sites = 7, Kimura (unadjusted) = 26.03 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.50 (3 / 2) 194 23.81 0.00 0.00 chr3qtel1M 635557 635598 (364402) L2b_3end#LINE/L2 413 454 (12) m_b153s601i4 5711 chr3qtel1M 635557 CATCGAGCCTGGCACTCGGCAGGCGCTTCATAAATACTGGTT 635598 iv ? v i i ivi i v L2b_3end#LINE 413 CACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTTGTT 454 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 30.16 CpG sites = 6, Kimura (unadjusted) = 30.16 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 33 26.12 2.42 4.10 chr3qtel1M 636167 636290 (363710) (GGA)n#Simple_repeat 1 122 (0) m_b153s252i1 5712 chr3qtel1M 636167 GGAGGAGAAAGGAGGAGGATGGGGAAGAGGATAAAAAAAAGAGAGGAAGA 636216 -i v i i vi ii ii - - i (GGA)n#Simple 1 GGAGGAG-GAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG-GAGG-AGG 47 chr3qtel1M 636217 AGGAAAAGG-GGAGAAAG-GGAGGAAGA-GAAGAGGAGGAAGAAGGAAGA 636263 ii - i i - i - i - i i (GGA)n#Simple 48 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGG-AGGAGGAGGA 96 chr3qtel1M 636264 GGAGACAGGAGGAGGGGAAAGAAGAGG 636290 -v i i i i (GGA)n#Simple 97 GGAG-GAGGAGGAGGAGGAGGAGGAGG 122 Matrix = Unknown Transitions / transversions = 7.00 (21/3) Gap_init rate = 0.07 (8 / 123), avg. gap size = 1.00 (8 / 8) 257 24.37 24.12 3.43 chr3qtel1M 636837 637006 (362994) MIRc#SINE/MIR 49 252 (16) m_b153s601i6 5713 chr3qtel1M 636837 GGCCTAGAGTTCCGATTCTGCCTCCGACACTTACCCAGCTGTATAACC-- 636884 i i - vii i i v i v i- i i -- MIRc#SINE/MIR 49 GACCTGG-GTTCGAGTCCCGGCTCTGCCACTTACT-AGCTGTGTGACCTT 96 chr3qtel1M 636885 ------ACCATCTA-----------CTTCAGGTTCCTCATCTATGAAATG 636917 ------ii ii ----------- i v i i MIRc#SINE/MIR 97 GGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATG 146 chr3qtel1M 636918 GGGGTA---------GC---GCCAGCCTCGCATGGTTTTGAGAAGAATAA 636955 i --------- --- vi i v v vivi i v MIRc#SINE/MIR 147 GGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCA 196 chr3qtel1M 636956 AATGGAAAGATAA--CATGTGGATGCCCCT----ATCTGT---GTG-TAC 636995 --- --i i v v i ---- v --- - i MIRc#SINE/MIR 197 AATG---AGATAATGTATGTGAAAGCGCTTTGTAAACTGTAAAGTGCTAT 243 chr3qtel1M 636996 ACACCAATGTA 637006 -- MIRc#SINE/MIR 244 ACA--AATGTA 252 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 29.89 CpG sites = 27, Kimura (unadjusted) = 30.81 Transitions / transversions = 2.08 (27/13) Gap_init rate = 0.09 (16 / 169), avg. gap size = 3.00 (48 / 16) 308 24.89 17.52 3.21 chr3qtel1M 636837 636973 (363027) MIRb#SINE/MIR 52 207 (61) m_b153s601i5 5713 chr3qtel1M 636837 GGCCTAGAGTTCCGATTCTGCCTCCGACACTTACCCAGCTGTATAACC-- 636884 i i - vi i i v i v i- i i -- MIRb#SINE/MIR 52 GACCTGG-GTTCGAATCCCGGCTCTGCCACTTACT-AGCTGTGTGACCTT 99 chr3qtel1M 636885 -------------ACCATCT----ACTTCAGGTTCCTCATCTATGAAATG 636917 ------------- v v ----i i v i i MIRb#SINE/MIR 100 GGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATG 149 chr3qtel1M 636918 GGG---GTAGCGCCAGCCTCGCATGGTTTTGAGAAGAATAAAATGGAAAG 636964 ---i iii vi v v vivi i v --- MIRb#SINE/MIR 150 GGGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATG---AG 196 chr3qtel1M 636965 ATAA--CATGT 636973 -- MIRb#SINE/MIR 197 ATAATGCATGT 207 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 30.18 CpG sites = 21, Kimura (unadjusted) = 31.32 Transitions / transversions = 1.75 (21/12) Gap_init rate = 0.07 (10 / 136), avg. gap size = 2.90 (29 / 10) 202 39.46 8.05 0.00 chr3qtel1M 637934 638194 (361806) C L2b_3end#LINE/L2 (13) 453 172 m_b153s601i7 5714 chr3qtel1M 637934 ATAAACATTTAACAGGCAACTAGGATGTACCACTCACTGTGCTAAGTTCT 637983 i i viii iv vvi i vv ? i iv C L2b_3end#LINE 453 ACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCT 404 chr3qtel1M 637984 GGAAA---AGCTAAGAA-AAACTAAAACCAGGCCCTTTCTTCAAGAAGCT 638029 ii --- viv - ivi i v? i v vi i v i C L2b_3end#LINE 403 GGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGGAGCT 354 chr3qtel1M 638030 TAGATCCTCACAAGG-----AAACATGTAAATACATACAAACAAGGTACA 638074 i v vi viiii ----- i ?i v i vv? i vvi v C L2b_3end#LINE 353 CACAGTCTAGTGGGGGAGACAGACATGTAANCAGACAATNATAACCCAGA 304 chr3qtel1M 638075 --GGCTAAATAGGA--AATAATAAACAGAAGAAGAATCTAGAGTTAGC-- 638118 -- viii --iiviivivv i i ivv iv viii -- C L2b_3end#LINE 303 GTGGCAGGGTAGGACTGGGGGGGCCCAGAGGAGGGCGCCTGACCCGGCCT 254 chr3qtel1M 638119 -GAGGGTTTGGGAAAGCTTATTGTAGAAGGTGGGGTTTTAGTTGGGA--- 638164 - i iv ii vii v i ivi v i i --- C L2b_3end#LINE 253 GGGGGGTCAGGGAGGGCTTCCCGGAGGAGGTGACATTTGAGCTGAGACCT 204 chr3qtel1M 638165 GAAAGGT-ATAAGAAACTGGACA-GCCAAGAG 638194 i i - vv i ii v - v C L2b_3end#LINE 203 GAAGGATGAGTAGGAGTTGGCCAGGCGAAGAG 172 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 56.21 CpG sites = 62, Kimura (unadjusted) = 60.97 Transitions / transversions = 1.51 (62/41) Gap_init rate = 0.03 (8 / 260), avg. gap size = 2.62 (21 / 8) 262 37.20 6.74 2.49 chr3qtel1M 638232 638424 (361576) C L2#LINE/L2 (210) 2872 2672 m_b153s601i8 5714 chr3qtel1M 638232 CTGGAAGTGATGATGAGCCACTGAAGC-TTCTCCGGAAAGGAG-GTT--- 638276 iiv v ivi i i v- i vv v i - vi--- C L2#LINE/L2 2872 CTGAGTGAGATGGGAAGCCATTGGAGGGTTTTGAGCAGAGGAGTGACATG 2823 chr3qtel1M 638277 -TCAGCCCCGTGTCTTAGAAAAGTCACTTTGGTGGCCAGA--GAGGATTG 638323 - v v iiii i i iii i iv iivi-- i v C L2#LINE/L2 2822 ATCTGACTTACGTTTTAAAAGGATCACTCTGGCTGCTGTGTTGAGAATAG 2773 chr3qtel1M 638324 ACTGGACTGGGGAGACCCTGAAGGCAAGCAGACATCCCCAGTCGG----- 638368 ? vv vi vvv i i i v ----- ii ----- C L2#LINE/L2 2772 ACTGNAGGGGGGCAAGGGTGGAAGCAGGGAGAC-----CAGTTAGGAGGC 2728 chr3qtel1M 638369 TGTTGCAATAGCCTAGCTATGAGGTGATGAGGGTCTGTACCAGGGTGTGA 638418 i i ii i viiv i iv ii v vvi C L2#LINE/L2 2727 TATTGCAGTAATCCAGGCGAGAGATGATGGTGGCTTGGACCAGGGTGGTG 2678 chr3qtel1M 638419 GCAACG 638424 ii C L2#LINE/L2 2677 GCAGTG 2672 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 52.64 CpG sites = 44, Kimura (unadjusted) = 55.18 Transitions / transversions = 1.69 (44/26) Gap_init rate = 0.06 (11 / 192), avg. gap size = 1.64 (18 / 11) 487 34.87 1.03 0.00 chr3qtel1M 638589 638783 (361217) L1ME4a_3end#LINE/L1 238 434 (437) m_b153s551i5 5715 chr3qtel1M 638589 ATCTAATACTGGAGGGGAGGCGGGAAAGCTGGGACACTGACACATTGATG 638638 i i i ii v i iv i ?i i v v v v i i v L1ME4a_3end#L 238 ACCCAGTGTTGGCGAGGGTGTGGNGAAACGGGCACTCTCATACACTGCTG 287 chr3qtel1M 638639 GTGGAGTTGTGAACGGATCCAGCCGTTCTGGAGAGCAGTCTGGAGCTATG 638688 iiv i iv i v i v i i i viv L1ME4a_3end#L 288 GTGGGAGTGTAAATTGGTACAACCTTTCTGGAGGGCAATTTGGCAATATG 337 chr3qtel1M 638689 C-TC-AAAGTTATCAAACTGTGCGTACCCTCTGACCCAGCGGTGTTACTC 638736 i- - iiv v v ? i i iii vii i L1ME4a_3end#L 338 TATCAAAAGCCTTAAAAATGTNCATACCCTTTGACCCAGTAATTCCACTT 387 chr3qtel1M 638737 CTGGCCTTTTATCCCAAAGAGACCTTAAAGGAGGTGCAAGAACGTTT 638783 i vvv i i i ivv v ii v ? vi vi L1ME4a_3end#L 388 CTAGGAATTTATCCTAAGGAAATAATCAGAGATGTGNACAAAGATTT 434 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 50.44 CpG sites = 42, Kimura (unadjusted) = 50.44 Transitions / transversions = 1.62 (42/26) Gap_init rate = 0.01 (2 / 194), avg. gap size = 1.00 (2 / 2) 561 30.00 1.18 0.00 chr3qtel1M 638589 638758 (361242) L1ME4c_3end#LINE/L1 238 409 (421) m_b153s551i4 5715 chr3qtel1M 638589 ATCTAATACTGGAGGGGAGGCGGGAAAGCTGGGACACTGACACATTGATG 638638 i i i v i ?v vi i v ? v i v L1ME4c_3end#L 238 ACCCAATGCTGGCGAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTG 287 chr3qtel1M 638639 GTGGAGTTGTGAACGGATCCAGCCGTTCTGGAGAGCAGTCTGGAGCTATG 638688 vi? i iv i v i v i i i i viv i L1ME4c_3end#L 288 GTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACG 337 chr3qtel1M 638689 C-TCAA-AGTTATCAAACTGTGCGTACCCTCTGACCCAGCGGTGTTACTC 638736 i- - ii v v v i i iii vii i L1ME4c_3end#L 338 TATCAAGAGCCATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTT 387 chr3qtel1M 638737 CTGGCCTTTTATCCCAAAGAGA 638758 vvv i i i L1ME4c_3end#L 388 CTGGGAATTTATCCTAAGGAAA 409 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 39.75 CpG sites = 32, Kimura (unadjusted) = 40.81 Transitions / transversions = 1.68 (32/19) Gap_init rate = 0.01 (2 / 169), avg. gap size = 1.00 (2 / 2) 35 2.76 0.00 0.00 chr3qtel1M 639260 639296 (360704) (C)n#Simple_repeat 1 37 (0) c_b153s251i0 5716 chr3qtel1M 639260 CCCCCCGCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 639296 v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 37 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 14 25.59 0.00 0.00 chr3qtel1M 639560 639601 (360399) (GCCCCCC)n#Simple_repeat 1 42 (0) m_b153s252i2 5717 chr3qtel1M 639560 GCCCACGGCCCAGCGCCGGCTCCCCCCCGCCCCCCTCCCCCC 639601 v v vv vv iv v (GCCCCCC)n#Si 1 GCCCCCCGCCCCCCGCCCCCCGCCCCCCGCCCCCCGCCCCCC 42 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 16 9.26 0.00 0.00 chr3qtel1M 639581 639603 (360397) (C)n#Simple_repeat 1 23 (0) m_b153s252i3 5718 chr3qtel1M 639581 CCCCCCCGCCCCCCTCCCCCCCC 639603 v i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCC 23 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 12 10.36 0.00 11.43 chr3qtel1M 640178 640216 (359784) (GCGGGG)n#Simple_repeat 1 35 (0) m_b153s252i4 5719 chr3qtel1M 640178 GCGGGCGCGGGGGCCGGGAGGCGGCTGGGCTGGGGAGGG 640216 v - - -- v v (GCGGGG)n#Sim 1 GCGGGGGCGGGGG-CGGG-GGCGG--GGGCGGGGGCGGG 35 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.11 (4 / 38), avg. gap size = 1.00 (4 / 4) 11 12.84 8.82 0.00 chr3qtel1M 643248 643281 (356719) (GGCCGG)n#Simple_repeat 1 37 (0) m_b153s252i5 5720 chr3qtel1M 643248 GGCTGGGGATGGGGCC-GGGCCGGGG-C-GGCCCGGG 643281 i vi - - - v (GGCCGG)n#Sim 1 GGCCGGGGCCGGGGCCGGGGCCGGGGCCGGGGCCGGG 37 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.09 (3 / 33), avg. gap size = 1.00 (3 / 3) 15 24.62 3.39 1.67 chr3qtel1M 643259 643317 (356683) (GGGCC)n#Simple_repeat 1 60 (0) m_b153s252i6 5720 chr3qtel1M 643259 GGGCCGGGCCGGGGCGGCCCGGGCAGGAGGGGAGTCGGG-C-GGCCAGCT 643306 v v v - vv i i - - i vi (GGGCC)n#Simp 1 GGGCCGGGCCGGGCCGGGCCGGGCCGG-GCCGGGCCGGGCCGGGCCGGGC 49 chr3qtel1M 643307 CGGTGCGGGCC 643317 vv (GGGCC)n#Simp 50 CGGGCCGGGCC 60 Matrix = Unknown Transitions / transversions = 0.50 (4/8) Gap_init rate = 0.05 (3 / 58), avg. gap size = 1.00 (3 / 3) 15 22.67 2.90 5.97 chr3qtel1M 644767 644835 (355165) (CCCGC)n#Simple_repeat 1 67 (0) m_b153s252i7 5721 chr3qtel1M 644767 CCCGCCTGCCCCCCCGCCGCGGGCC-CCCCGCCCTGCCCACGGAGC-CCC 644814 -- v v vv - i - vvv - (CCCGC)n#Simp 1 CCCGCC--CCGCCCCGCCCCGCCCCGCCCCGCCCCGCCC-CGCCCCGCCC 47 chr3qtel1M 644815 GGCTCCTGCCCCGCGACGCCC 644835 v - i vv (CCCGC)n#Simp 48 CGC-CCCGCCCCGCCCCGCCC 67 Matrix = Unknown Transitions / transversions = 0.20 (2/10) Gap_init rate = 0.09 (6 / 68), avg. gap size = 1.00 (6 / 6) 227 24.49 17.86 1.54 chr3qtel1M 645432 645543 (354457) C MIR3#SINE/MIR (37) 171 42 m_b153s601i9 5722 chr3qtel1M 645432 CCCTGGA-ATGATCT-GTACAATTCCCCCATTTTCTAGAGAAGTAAGCTG 645479 i i - v - v ii i vi vi v i C MIR3#SINE/MIR 171 CCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTG 122 chr3qtel1M 645480 AGGCCCCAAAAAG-----------GCCTCAGGTC---CTGCAAG-TAGTG 645514 vi i i ----------- iv --- v ? - C MIR3#SINE/MIR 121 AGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTG 72 chr3qtel1M 645515 GCCCCGAGTCAGGG-GAGAACT--AGTCTCCT 645543 -- v i i i-v i--i C MIR3#SINE/MIR 71 G--CAGAGCCGGGACTAGAACCCAGGTCTCCT 42 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 29.55 CpG sites = 17, Kimura (unadjusted) = 30.92 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.08 (9 / 111), avg. gap size = 2.44 (22 / 9) 18 20.56 1.92 1.92 chr3qtel1M 645962 646013 (353987) (GGGAGCG)n#Simple_repeat 1 52 (0) m_b153s252i8 5723 chr3qtel1M 645962 GGGACCGATGCGCGGGGGAG-GGGGAGCGGGGGGCGGGGGGGGGGGGGGG 646010 v iv v - - i i v i v (GGGAGCG)n#Si 1 GGGAGCGGGGAGC-GGGGAGCGGGGAGCGGGGAGCGGGGAGCGGGGAGCG 49 chr3qtel1M 646011 GGG 646013 (GGGAGCG)n#Si 50 GGG 52 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.00 (2 / 2) 28 10.76 0.00 0.00 chr3qtel1M 645975 646014 (353986) (G)n#Simple_repeat 1 40 (0) m_b153s252i9 5723 chr3qtel1M 645975 GGGGGAGGGGGAGCGGGGGGCGGGGGGGGGGGGGGGGGGG 646014 i i v v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 40 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 202 20.04 4.29 7.35 chr3qtel1M 647049 647118 (352882) C MIR1_Amn#SINE/MIR (65) 165 98 m_b153s601i10 5724 chr3qtel1M 647049 GTCAGCAGCGATGTTTCC-TTTCACAGCCGAGGAAACTGAGGCAGCTCAG 647097 i v iv i ii - i vi --- ? C MIR1_Amn#SINE 165 GTCAGTATCATTATCCCCATTTTACAGATGAGGAAACTGAG---GCNCAG 119 chr3qtel1M 647098 ATTGGGGCAAA--GACTCGCCCA 647118 -- i i? -- i C MIR1_Amn#SINE 118 A--GAGGTNAAGTGACTTGCCCA 98 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 25.21 CpG sites = 10, Kimura (unadjusted) = 25.21 Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.10 (7 / 69), avg. gap size = 1.14 (8 / 7) 186 38.46 0.00 0.00 chr3qtel1M 647155 647219 (352781) MIR3#SINE/MIR 117 181 (27) m_b153s601i11 5725 chr3qtel1M 647155 GACGTCCGCTTTTCCATCTGCAAAACGGGTGGGCGAGACTAAAGGAGCTC 647204 i v v i iii i i i v ivi i v v MIR3#SINE/MIR 117 GGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTC 166 chr3qtel1M 647205 CTGGGTCTTCTCTGG 647219 ivi iii ii MIR3#SINE/MIR 167 TAAGGTCCCTTCCAG 181 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 60.23 CpG sites = 18, Kimura (unadjusted) = 60.23 Transitions / transversions = 2.57 (18/7) Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0) 13 27.47 2.08 0.00 chr3qtel1M 647369 647416 (352584) (GGGGCG)n#Simple_repeat 1 49 (0) m_b153s252i10 5726 chr3qtel1M 647369 GGGGCGGGAAC-AGGGCATGGTGGCGGGTGGGCCCGGGGGCGGGGGCGG 647416 ii -i iv vv v i vv (GGGGCG)n#Sim 1 GGGGCGGGGGCGGGGGCGGGGGCGGGGGCGGGGGCGGGGGCGGGGGCGG 49 Matrix = Unknown Transitions / transversions = 0.83 (5/6) Gap_init rate = 0.02 (1 / 47), avg. gap size = 1.00 (1 / 1) 16 5.20 0.00 0.00 chr3qtel1M 647670 647689 (352311) (A)n#Simple_repeat 1 20 (0) m_b153s252i11 5727 chr3qtel1M 647670 AACAAAAAAAAAAAAAAAAA 647689 v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAA 20 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 18 24.49 1.67 1.67 chr3qtel1M 648485 648544 (351456) (GGGTTA)n#Simple_repeat 1 60 (0) m_b153s252i12 5728 chr3qtel1M 648485 GGGTTCAGGACAGGTTTCGGGGGGAGGGTT-GGGTTGGGGTTGGGGTTAA 648533 vi vi v -i vv - i i i (GGGTTA)n#Sim 1 GGGTTAGGGTTAGGGTT-AGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAG 49 chr3qtel1M 648534 GGTTAGAGTTA 648544 i (GGGTTA)n#Sim 50 GGTTAGGGTTA 60 Matrix = Unknown Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.03 (2 / 59), avg. gap size = 1.00 (2 / 2) 261 27.72 1.01 5.26 chr3qtel1M 648804 648902 (351098) C MIR3#SINE/MIR (3) 205 111 m_b153s601i12 5729 chr3qtel1M 648804 TCGTGGAATTCGGGAACTCCAGACCTGGAGAGCAGGATCTTGCCTAGCCC 648853 i i ivvi ivi v - -- i iv-- vi C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGA-AG--GGACCTTAG--AGATC 161 chr3qtel1M 648854 AGGAGATGCAACCCCCTC-TCTTACAGGTGAAGAAATTGAGGGCCAGAGA 648902 vvvii v - i i i i v C MIR3#SINE/MIR 160 ATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGA 111 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 35.32 CpG sites = 15, Kimura (unadjusted) = 35.32 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.06 (6 / 98), avg. gap size = 1.00 (6 / 6) 41 0.00 0.00 0.00 chr3qtel1M 649553 649587 (350413) (TG)n#Simple_repeat 1 35 (0) c_b153s251i1 5730 chr3qtel1M 649553 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 649587 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 35 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 460 32.39 11.19 4.38 chr3qtel1M 649744 650279 (349721) C L1ME5_3end#LINE/L1 (339) 602 32 m_b153s551i6 5731 chr3qtel1M 649744 TCCTTCCATGTTTCTCTAAAATCACCAATTCCATCATTTCTCAACAG--- 649790 v v v ivivv i v v i iii - v --- C L1ME5_3end#LI 602 TCCATCCATGTTGCTATGTGTACATCTAGTCCGTTGCTTCT-AACTGCTG 554 chr3qtel1M 649791 --TAGCACTCCATCACAGTCCTTGATCACAGCTCACACCGGTACTC-CCC 649837 -- i viiivv v iv i vi i vivvvi - C L1ME5_3end#LI 553 CATAGTACTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCC 504 chr3qtel1M 649838 AGCTGATGGCTATTCCCGCAACTTCCAGCTCTTTGTCTCCACAAAGAGAG 649887 - vi ii vv ivi i i iii i v v iv C L1ME5_3end#LI 503 AG-TGATGGACACCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACG 455 chr3qtel1M 649888 CTGCCATATATGTTTTAGAATATATCCCTT------CCCCCATCA----- 649926 v iv ii ii v v i i i ------ ivii v ----- C L1ME5_3end#LI 454 CTGCAATGAACATCCTCGTACATGTCCCCTTATGGACCTGTGTGAGAATT 405 chr3qtel1M 649927 -CCTTGGGAAAT---------------------GGATCAAAAAGTTTG-- 649952 - i v --------------------- i v ii v -- C L1ME5_3end#LI 404 TCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATGCG 355 chr3qtel1M 649953 TACACACAGTTTGATAACCCCTGGGCCTAATTCCAGATT-TTTTCTGAAA 650001 i vi i ------ ii -- v v -i i iii C L1ME5_3end#LI 354 TATACTTAATTTGA------CTAAG--TACTGCCAGATTGCTCTCCAGAA 313 chr3qtel1M 650002 TGGTTGGATCATTTCACAGTTCCACCAACAGTGTATTAGTATGCCCATTT 650051 i v i v ii v i i i v vi v i ? C L1ME5_3end#LI 312 TGGCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATNT 263 chr3qtel1M 650052 TTCCATATCCCCTCCAACATTTGGGATTTTCCC-CTTTATCTTGTTAGCC 650100 ii i i v i v v v- v vv v v C L1ME5_3end#LI 262 CCCCACATCCTCGCCAACACTTGGCATTATCCAGCTTTCTAATTTTTGCC 213 chr3qtel1M 650101 ATCCAGATAGGTGTGA---GAA--------GTTGTTTTAATTTGCTTTTC 650139 vi vi i --- v-------- v C L1ME5_3end#LI 212 AGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATTTC 163 chr3qtel1M 650140 TCCAATCATTAAT---TTAGAGTAT-TTTTAATATGACTATATATAG--T 650183 ii i i --- v i - i v vi i --- -- C L1ME5_3end#LI 162 TCTGATTACTAATGAGTTTGAGCATCTCTTCATATGCTTGT---TAGCCT 116 chr3qtel1M 650184 TTTGATTTTTTTTCTTCCCAAAACTGTCTGTTTGTATCCTTTGATCACTT 650233 i i-v ii ivv i i ii vi i C L1ME5_3end#LI 115 TTCGG-GTTTCCTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCCATTT 67 chr3qtel1M 650234 ATAAACTAGGGAATGATTCATATTCTTTTTTTTTTTTTTTTAATTT 650279 v vv i i ----------- ?iiv i i v i C L1ME5_3end#LI 66 TTCTATTGGGG-----------TTNCCGTCTTTTTCTTGTTGATTT 32 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 42.82 CpG sites = 97, Kimura (unadjusted) = 44.26 Transitions / transversions = 1.41 (97/69) Gap_init rate = 0.07 (39 / 535), avg. gap size = 2.18 (85 / 39) 461 28.33 8.08 4.90 chr3qtel1M 649937 650233 (349767) C L1ME3G_3end#LINE/L1 (556) 368 63 m_b153s551i7 5731 chr3qtel1M 649937 TGGATCAAAAAGTTTGTACAC---ACAGTTTGATAACCCCTGGGCCTAAT 649983 i ii v ii i--- v v i iviv -- v C L1ME3G_3end#L 368 TGGGTCAAAGGGTATGCGCATTTTAAATTTTAATAGATACTG--CCAAAT 321 chr3qtel1M 649984 TCCAGATTTTTTCTGAAATGGTTGGATCATTTCACAGTTCCACCAACAGT 650033 v ------ii ii ? i v i v i v i i C L1ME3G_3end#L 320 TGC------CCTCCAAAANGGCTGTACCAATTTACACTCCCACCAGCAGT 277 chr3qtel1M 650034 GTATTAGTATGCCCATTTTTCCATATCCCCTCCAACATTTGGGATTTTC- 650082 v vi i i ii i i i v i ? iv v - C L1ME3G_3end#L 276 GTATGAGAGTACCCGTTTCCCCACACCCTCGCCAACACTNGATATTATCA 227 chr3qtel1M 650083 -CCCTTTATCTTGTTAGCCATCCAGATAGGTGTGAGAA------------ 650119 -? i vv v - vi v i -i i ------------ C L1ME3G_3end#L 226 ANCTTTTAAATTTTT-GCCAATCTGATGGGTG-AAAAATGGTATCTCATT 179 chr3qtel1M 650120 GTTGTTTTAATTTGCTTTTCTCCAATCATTAAT----TTAGAGTAT-TTT 650164 v i ii i i i ---- - i - C L1ME3G_3end#L 178 GTTGTTTTAATTTGCATTTCCCTGATTACTAGTGAGGTT-GAGCATCTTT 130 chr3qtel1M 650165 TAATATGACTATATATAGT--TTTGATTTTTTTTCTTCCCAAAACTGTCT 650212 v vi --- i i-- - v ii ivvi i i C L1ME3G_3end#L 129 TCATATGTTTAT---TGGCCATTTG-TATTTCCTCTTCTGTGAATTGCCT 84 chr3qtel1M 650213 GTTTGTATCCTTTGATCACTT 650233 ii vi i C L1ME3G_3end#L 83 GTTCATATCCTTTGCCCATTT 63 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 36.47 CpG sites = 53, Kimura (unadjusted) = 37.76 Transitions / transversions = 1.96 (53/27) Gap_init rate = 0.07 (21 / 296), avg. gap size = 1.86 (39 / 21) 514 28.14 7.63 1.52 chr3qtel1M 649985 650233 (349767) C L1ME3Cz_3end#LINE/L1 (671) 326 63 m_b153s551i8 5731 chr3qtel1M 649985 CCAGATT-TTTTCTGAAATGGTTGGATCATTTCACAGTTCCACCAACAGT 650033 i -i i ii i v i v i v i i C L1ME3Cz_3end# 326 CCAAATTGCTCTCCAAAGTGGTTGTACCAATTTACACTCCCACCAGCAGT 277 chr3qtel1M 650034 GTATTAGTATGCCCATTTTTCCATATCCCCTCCAACATTTGGGATTTTC- 650082 v vi v i i i i v i v v - C L1ME3Cz_3end# 276 GTATGAGAGTTCCCGTTTCTCCACATCCTCGCCAACACTTGGTATTGTCA 227 chr3qtel1M 650083 -CCCTTTATCTTGTTAGCCATCCAGATAGGTGTGAGA-----------AG 650120 -v i vv v - vi v i i -----------v C L1ME3Cz_3end# 226 GACTTTTAAATTTTT-GCCAATCTGATGGGTGTGAAATGGTATCTCATTG 178 chr3qtel1M 650121 TTGTTTTAATTTGCTTTTCTCCAATCATTAAT----TTAGAGTAT-TTTT 650165 ? v i ii i i i ---- - i - C L1ME3Cz_3end# 177 TNGTTTTAATTTGCATTTCCCTGATTACTAGTGAGGTT-GAGCATCTTTT 129 chr3qtel1M 650166 AATATGACTATATATAGTTTTGATTTTTTTTCTTCCCAAAACTGTCTGTT 650215 v vi vviivi iv i-- ii ivvi i i C L1ME3Cz_3end# 128 CATATGTTTATTGGCCATTCGGG--TTTCCTCTTCTGTGAATTGCCTGTT 81 chr3qtel1M 650216 TGTATCCTTTGATCACTT 650233 ii vi i C L1ME3Cz_3end# 80 CATATCCTTTGCCCATTT 63 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 35.36 CpG sites = 43, Kimura (unadjusted) = 36.71 Transitions / transversions = 1.65 (43/26) Gap_init rate = 0.04 (10 / 248), avg. gap size = 2.30 (23 / 10) 841 32.78 1.37 1.37 chr3qtel1M 650749 651113 (348887) C L1ME4c_3end#LINE/L1 (191) 639 275 m_b153s551i9 5732 chr3qtel1M 650749 TCCTGCTCATTTCACTCAGCATCAGTTCGTGTAAGTCTCTCCAGGCCTTT 650798 i iv i i i vv i iv vi i - v iivi C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATAAACATTT-TCCATGTTGCT 591 chr3qtel1M 650799 CTGAAATCATCCTGTTGGTCATTTCTTACAGA-ACAGTAATATTCCATAA 650847 viiv i v v iv vi i v ii v-i - vi C L1ME4c_3end#L 590 ACATAGTCTTCATAATTATCATTTTTAATGGCTGCA-TAATATTCCATCG 542 chr3qtel1M 650848 TTTTCATATACCACAATTTATTCAGCCATTCTCCAACTGATGGACATCCA 650897 vv ?v i i i i i i v i v ii C L1ME4c_3end#L 541 AGTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTA 492 chr3qtel1M 650898 TTCAGTTTCCAGTTTCTAGCCACTACAAAAAGGGCTGCCACAAACATTCG 650947 vviv i i v i i i v iv v ii iiv C L1ME4c_3end#L 491 GGTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTT 442 chr3qtel1M 650948 TGCACATACAGGTCCCTTTCCCTTCTTT---ATAATCTCTTTGGGATATA 650994 i ii i --- i i --- v i i i v C L1ME4c_3end#L 441 CGTGCATATAG---CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAA 395 chr3qtel1M 650995 AGCCCAGTAGTAACACTGCTGGATCAAAGGGTATGCACAGTTTGATAACT 651044 vv v iiv i i i v v v ii C L1ME4c_3end#L 394 TTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCT 345 chr3qtel1M 651045 TTTTGAGCATAGATCCAAACTACTCTCCAAAATGGTTGGATTCGTTCACA 651094 i vivi i vvv i i i v v iivi i C L1ME4c_3end#L 344 CTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACA 295 chr3qtel1M 651095 ACTCCACCAACAATG-ATGA 651113 ?iv i - C L1ME4c_3end#L 294 NTGCCACCAGCAATGTATGA 275 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 43.57 CpG sites = 71, Kimura (unadjusted) = 45.15 Transitions / transversions = 1.51 (71/47) Gap_init rate = 0.02 (8 / 364), avg. gap size = 1.25 (10 / 8) 477 32.90 8.04 2.90 chr3qtel1M 651135 652677 (347323) C L1M5_orf2#LINE/L1 (129) 3165 1546 m_b153s551i10 5732 chr3qtel1M 651135 TTTATATGTTTGAAATATG---CCTTTATCAGAGAATTGGTCTATAAATA 651181 i ivii i --- i v vv v?i ii C L1M5_orf2#LIN 3165 TTTATATATTCTGGATACGAGTCCTTTGTCAGATATATGTNTTGCAAATA 3116 chr3qtel1M 651182 ATTAGCTTCCCCTAATTTTCTGCTTTCCTTCTAATTTTGGCTACGTTGAT 651231 v ---- i i ? i viv v i v vviv v vi C L1M5_orf2#LIN 3115 TTT----TCTCCCANTCTGTGGCTTGCCTTTTCATTTTCTTAACGGTGTC 3070 chr3qtel1M 651232 TTTTATTTATGCAACCCCTTTTTAATCTAAAGTAACCAAAATGATCTACT 651281 iv?v - ivvvi v v i i v ? ii v v v v i C L1M5_orf2#LIN 3069 TTTTGANGA-GCAGAAGTTTTTAATTTTGATGNAGTCCAATTTATCAATT 3021 chr3qtel1M 651282 TTATCTACTTTATTTACTTCTATGCTCTCTATTTCATGTTTATTGATCAA 651331 v -- --iv ?-i i i i v v --- vv C L1M5_orf2#LIN 3020 TTTTCT--TTTAT--GGTTN-GTGCTTTTTGTGTCCTGTTTA---AGAAA 2979 chr3qtel1M 651332 TTGTTTTCTTATCCATAAATCTGATAGGTA-------ATGTGCTTCTCTA 651374 i- v i ? vv ii vviv i ------- vi ii C L1M5_orf2#LIN 2978 TC-TTTGCCTANCCCAAGGTCACGAAGATATTCTCCTATGTTTTCTTCTA 2930 chr3qtel1M 651375 AA---TTTACTTATGCTAT-TTTTATGTCTAAATC-ATGCATCCATTTTA 651419 i --- - vi vi ?- ii i ii - - i ?i C L1M5_orf2#LIN 2929 GAAGTTTTA-TAGTTTTANCTTTTACATTTAGGTCTATG-ATCCATCTNG 2882 chr3qtel1M 651420 ATATTCCCTTGGCGGATGGTGTAAGATATTAGTCTATACCCAATTTCTGT 651469 vv vvii v i v i i vvi v v?ii v i vi C L1M5_orf2#LIN 2881 AATTAATTTTTGTGTATGGTGTGAGGTAGGGGTCGAGNTTCATTTTTTTC 2832 chr3qtel1M 651470 CAGATGGTTTTCTAGTTTTCCTAACA----TTGTCA-------------- 651501 v v v i i v i i i ---- ii-------------- C L1M5_orf2#LIN 2831 CATATGGATATCCAATTGTTCCAGCACCATTTGTTGAAAAGACTATCCTT 2782 chr3qtel1M 651502 TCCCCA---AAT---CTTAA-ATCTTTA-CATTTATCAATT------ATA 651537 --- ---? ii- i i- vvv ? ------ C L1M5_orf2#LIN 2781 TCCCCACTGAATTGCNTTGGCACCTTTGTCAAAAATCAANTGNCCATATA 2732 chr3qtel1M 651538 TGAGTA---CTAT------AATCATT-TCCTATTCCTCTGACCCATT-AT 651576 v i--- ------ v vi - i i vi i i -i C L1M5_orf2#LIN 2731 TGTGTGGGTCTATTTCTGGACTCTCTATTCTGTTCCATTGATCTATTTGT 2682 chr3qtel1M 651577 CT-TTCTTA-ACCAGTACCAGATAGTTCTGAAAATAACTGCCTTATCATA 651624 - i -i i v iv ii vv iviiv i v C L1M5_orf2#LIN 2681 CTATCCTTACGCCAATACCACACTGTCTTGATTACTGTAGCTTTATAATA 2632 chr3qtel1M 651625 CAGTTTAAGATCTGGTAATGCTGAACCTCC---TTCATTTACATTTTTAT 651671 vivi i ? ? i iviiv --- ii iviv vv C L1M5_orf2#LIN 2631 AGTCTTGANATCNGGTAGTGTAAGTCCTCCAACTTTGTTCTTCTTTTTCA 2582 chr3qtel1M 651672 TAATTCCTTTG-TTATTTTTGATTTTTGGTTCATCCAAATGAATGTTATT 651720 vi vi -i i ? i ii v iviv v i v vv C L1M5_orf2#LIN 2581 AGATTGTTTTGGCTATTCTNGGTCCTTTGCATTTCCATATAAATTTTAGA 2532 chr3qtel1M 651721 ATT--TTTAT--AGCTCAATAAAATAATTT-TTAGTAGTTTAACTGAGAT 651765 i--i i -- vi v i v ii -i i v v i i i C L1M5_orf2#LIN 2531 ATCAGCTTGTCAATTTCTACAAAAAAACCTGCTGGGATTTTGATTGGGAT 2482 chr3qtel1M 651766 GGCACTGGAT-----AAGTAAATTAGGTAGAACTGTCATTTTTATTACAT 651810 v i i -----i vi v i v i v i ? iv i C L1M5_orf2#LIN 2481 TGCATTGAATCTATAGATCAATTTGGGGAGAATTGACATCTTNACAATAT 2432 chr3qtel1M 651811 TGGTTCTGCTTACTCATGAACAATTAT-TATTTCTCCATTTATTTAAATA 651859 iv v iv ii - vi - i ii v C L1M5_orf2#LIN 2431 TGAGTCTTCCAATCCATGAACA-TGGTATATCTCTCCATTTATTTAGGTC 2383 chr3qtel1M 651860 T-----GACTTCATATAAAAAGTATCTCATAATTATGTTCATT---TAGA 651901 -----i i - v v iv i i i ii i --- v ---? i C L1M5_orf2#LIN 2382 TTCTTTAATTTC-TCTCAGCAATGTTTTGTAGTT---TTCAGTGTANAGG 2337 chr3qtel1M 651902 TCCCGGTTTTGGCTTGGCAGGCATACTTTTAAGTGTTTTATATTGTCTGT 651951 ii vviv ?vi vi iiv i ii i ? i v i v C L1M5_orf2#LIN 2336 TCTTGCACATNTTTTGTTAGATTTATTCCTAAGTATTTNATGTTTTTTGA 2287 chr3qtel1M 651952 GGTTATTTTAAATGAAATGTGGCTTACTATCTCTTCTTGCAGGGCATTGT 652001 v i v iv vvvvi ?vv i v i v ivvvv C L1M5_orf2#LIN 2286 TGCTATTGTAAATGGTATTGTTTTTNAAATTTCATTTTCCAATTGTTTGT 2237 chr3qtel1M 652002 TAGTGTTATATACAAATGTTAATGTTTACTTTATAGGATTATAGTTAAGG 652051 iv iv v iiv v v -- i ---- v ------ C L1M5_orf2#LIN 2236 TGCTAGTATATAGAAATACAATTGATT--TTTGTA----TATTG------ 2199 chr3qtel1M 652052 ATTACTTTATATCCTACTATTTTGCTAAAATTATTAGTTATTTCTACTAT 652101 --- i i ?i v ii v i i vi v v v C L1M5_orf2#LIN 2198 ---ACCTTGTATCCNGCGACCTTGCTAAATTCACTTATTAGTTCTAGTAG 2152 chr3qtel1M 652102 TTTTAAAGTTGAATCTCTAGGGTTTTCCAAGTATACCAT-ATATCATCTG 652150 ?vvv v v i ? i i v ? v - i C L1M5_orf2#LIN 2151 TTTNTTTGTAGATTCTTTNGGATTTTCTACGTANACAATCATGTCATCTG 2102 chr3qtel1M 652151 CAAAAGGAGATAGTTGTATTGCCTCATTGCCCAATCTG-ATTCCTTCCAT 652199 i vii? i v v i v -i v- v ii C L1M5_orf2#LIN 2101 CGAATAANGACAGTTTTATTTCTTCCTT-TCCAATCTTTATGCCTTTTAT 2053 chr3qtel1M 652200 TTCTTTTTCTTCACTTACTGCTATTGTTAGCATTTCTATTACAATATTGA 652249 vv i vv v i v ii i v i C L1M5_orf2#LIN 2052 TTCTTTTTCTTGCCTTATTGCACTGGCTAGGACCTCCAGTACAATGTTGA 2003 chr3qtel1M 652250 GTAATATTAGTGATAATGGTCATCCTTGTTTGACTCCTAATGTTATTGGT 652299 i iv v i ? ii v i vii ii v vv v C L1M5_orf2#LIN 2002 ATAGAAGTGGTGANAGCGGACATCCTTGTCTTGTTCCCGATCTTAGGGGG 1953 chr3qtel1M 652300 AAGTCTTCTAGCTTATTCCCATTACAAATAATACTTGCTGATGGCTTTAG 652349 iv ? ii i? v iv viv i ii ? vv i vv C L1M5_orf2#LIN 1952 AAAGCNTTCAGTNTTTCACCATTAAGTATGATGTTNGCTGTAGGTTTTTC 1903 chr3qtel1M 652350 GGAGATGCTTCTAATCATCTCTAACGAAAAATCCATTC-ATACCTTTTCT 652398 v iii v vv - i - i iv v - v vv i C L1M5_orf2#LIN 1902 GTAGATGCCCTTTATCAGGT-TGA-GGAAGTTCCCTTCTATTCCTAGTTT 1855 chr3qtel1M 652399 TTCAAAATTTTAAAATAGAAATGGGAGTTGTATTTTGCCAAGTGCCTTTT 652448 viii i v vv vi vi v v i i i C L1M5_orf2#LIN 1854 GCTGAGAGTTTTTATCATGAATGGGTGTTGAATTTTGTCAAATGCTTTTT 1805 chr3qtel1M 652449 CTG----TATTGATATAATCATATGATTTTAAACTCTTC-TTATTC---- 652489 ---- v i ---- i - ---- C L1M5_orf2#LIN 1804 CTGCATCTATTGAGATGATCATATGATTTT----TCTCCTTTATTCTGTT 1759 chr3qtel1M 652490 -ATGTAATCAATTATGATAATAGCTTTT----TTTT-------TTTTCTA 652527 - i ii v iiv i v v ---- v -------ii vi C L1M5_orf2#LIN 1758 AATATGGTGAATTACATTGATTGATTTTCGAATGTTAAACCAACCTTGCA 1709 chr3qtel1M 652528 T---TGAGGCAAGCCTGAATTCTTAGT-ATGGT--------CTCAGTGTA 652565 --- i ii i iv --- i - i -------- ivv i C L1M5_orf2#LIN 1708 TTCCTGGGATAAACCCCA---CTTGGTCATGATGTATTATCCTTTTTATA 1662 chr3qtel1M 652566 TATTGCTATAGTCCCCTAGCTAGTATTTTATTTAGGATTTTTGCAATGAT 652615 iv v vvi v i i ? viv C L1M5_orf2#LIN 1661 TATTGCTGGATTCGATTTGCTAATATTTTGTTNAGGATTTTTGCATCTAT 1612 chr3qtel1M 652616 ATTTATTCGTGAAATTGCTCTCGT--TTTATTTCTATTTTCA---CTCTT 652660 i i vv v v v - -- vi i v v v --- i v C L1M5_orf2#LIN 1611 GTTCATGAGGGATATTGGTCT-GTAATTTTCTTTTCTTGTAATGTCTTTG 1563 chr3qtel1M 652661 CCTGCTTTAGGTAACAG 652677 i ? v v v C L1M5_orf2#LIN 1562 TCNGGTTTTGGTATCAG 1546 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 44.92 CpG sites = 264, Kimura (unadjusted) = 45.69 Transitions / transversions = 1.15 (264/229) Gap_init rate = 0.06 (88 / 1542), avg. gap size = 1.94 (171 / 88) 736 34.03 5.77 2.58 chr3qtel1M 651555 652646 (347354) C L1MC_orf2#LINE/L1 (590) 2704 1579 m_b153s551i11 5732 chr3qtel1M 651555 TCCTATTCCTCTGACCCATT-ATCT-TTCTTA-ACCAGTACCAGATAGTT 651601 i i vi i i -i - v-i i v iv i C L1MC_orf2#LIN 2704 TTCTGTTCCATTGATCTATTTGTCTATTCTTTCGCCAATACCACACTGTC 2655 chr3qtel1M 651602 CTGAAAATAACTGCCTTATCATACAGTTTAAGATCTGGTAATGCTGAACC 651651 i vv iviiv i vi vivi i ii v i iiiiv C L1MC_orf2#LIN 2654 TTGATTACTGTAGCTTTATAGTAAGTCTTGAAGTCGGGTAGTGTCAGTCC 2605 chr3qtel1M 651652 TCC---TTCATT-TACATTTTTATTAATTCCTTTGTTATTTTTGATTTTT 651697 --- ii - v vii i v v viv v i i v i i C L1MC_orf2#LIN 2604 TCCGACTTTGTTCTTCTCCTTCAATATTGTGTTGGCTATTCTGGGTCTTT 2555 chr3qtel1M 651698 GGTTCATCCAAATGAATGTTATTATT--TTTAT--AGCTCAATAAAATAA 651743 v iiiv v i iv vv i-- i -- vv v i C L1MC_orf2#LIN 2554 TGCCTCTCCATATAAACTTTAGAATCAGTTTGTCGATATCCACAAAATAA 2505 chr3qtel1M 651744 TTT-TTAGTAGTTTAACTGAGATGGCACTGGAT-----AAGTAAATTAGG 651787 i -i i v v i i i v i i -----i vi i i C L1MC_orf2#LIN 2504 CTTGCTGGGATTTTGATTGGGATTGCATTGAATCTATAGATCAAGTTGGG 2455 chr3qtel1M 651788 TAGAACTGTCATTTTTATTACATTGGTTCTGCTTACTCATGAACAATTAT 651837 v v i v iv i iv v i ii vvv v C L1MC_orf2#LIN 2454 AAGAACTGACATCTTGACAATATTGAGTCTTCCTATCCATGAACATGGAA 2405 chr3qtel1M 651838 TATTTCTCCATTTATTTAAATAT-----GACTTCATATAAAAAGTATCTC 651882 i i? v ----- i v - v vv vi i i C L1MC_orf2#LIN 2404 TATCTCTCCATTTATTTAGNTCTTCTTTGATTTCTT-TCATCAGAGTTTT 2356 chr3qtel1M 651883 ATAATTATGTTCATTTAGATCCCGGTTTTGGCTTGGCAGGCATACTTTTA 651932 i i v vi v ii vviv ivi vi iiv ivii C L1MC_orf2#LIN 2355 GTAGTTTTCCTCATATAGATCTTGTACATATTTTGTTAGATTTATACCTA 2306 chr3qtel1M 651933 AGTGTTTTATATTGTCTGTGG---TTATTTTAAATGAAATGTGGCTTACT 651979 i i v --- v ---i v v iv vvv i viv C L1MC_orf2#LIN 2305 AGTATTTCATTTT---TGGGGGTGCTAATGTAAATGGTATTGTGTTTTTA 2259 chr3qtel1M 651980 ATCTC---TTCTTGCAGGGCATTGTTAGTGTTATATACAAATGTTAATGT 652026 i --- iv?iv vv i i --- vi v iv v - C L1MC_orf2#LIN 2258 ATTTCAAATTCCANTTGTTCATTGCTGGT---ATATAGGAAAGCGATTG- 2213 chr3qtel1M 652027 TTACTTTATAGGATTATAGTTAAGGATTACTTTATATCCTACTATTTTGC 652076 -- - i---- - ------ i i i v ii C L1MC_orf2#LIN 2212 --ACTTT-TG----TATA-TTAA------CCTTGTATCCTGCAACCTTGC 2177 chr3qtel1M 652077 TAAAATTATTAGTTATTTCTACTATTTTTAAAGTTGAATCTCTAGGGTTT 652126 v iii vi v i vv v vvv i v i v i C L1MC_orf2#LIN 2176 TATAATCGCTTATTAGTTCCAGGAGTTTTTTTGTCGATTCTTTCGGATTT 2127 chr3qtel1M 652127 TCCAAGTATACCAT-ATATCATCTGCAAAAGGAGATAGTTGTATTGCCTC 652175 i vi v v - i i vii i v v i C L1MC_orf2#LIN 2126 TCTACATAGACAATCATGTCATCTGCGAACAAAGACAGTTTTATTTCTTC 2077 chr3qtel1M 652176 ATTGCCCAATCTG-ATTCCTTCCATTTCTTTTTCTTCACTTACTGCTATT 652224 v - - v ii i vv i vv v C L1MC_orf2#LIN 2076 CTT-CCCAATCTGTATACCTTTTATTTCCTTTTCTTGTCTTATTGCATTA 2028 chr3qtel1M 652225 GTTAGCATTTCTATTACAATATTGAGTAATATTAGTGATAATGGTCATCC 652274 i v i i v i i iv iv v i v iv v C L1MC_orf2#LIN 2027 GCTAGGACTTCCAGTACGATGTTGAAAAGGAGTGGTGAGAGGGGACATCC 1978 chr3qtel1M 652275 TTGTTTGACTCCTAATGTTATTGGTAAGTCTTCTAGCTTATTCCCATTAC 652324 ii vii i v vi v iv ? i v iv v C L1MC_orf2#LIN 1977 TTGCCTTGTTCCTGATCTTAGCGGGAAAGCTTCNAGTTTCTCACCATTAA 1928 chr3qtel1M 652325 AAATAATACTTGCTGATGGCTTTAGGGAGATGCTTCTAATCATCTCTAAC 652374 iv i ii v vv i vv v i ii v vv - i v C L1MC_orf2#LIN 1927 GTATGATGTTAGCTGTAGGTTTTTTGTAGATGTTCTTTATCAAGT-TGAG 1879 chr3qtel1M 652375 GAAAAATCCATTCATACCTTTTCTTTCAAAATTTTAAAATAGAAATGGGA 652424 ivvi v ii v vv i viii i v vv vi vi v C L1MC_orf2#LIN 1878 GAAGTTCCCCTCTATTCCTAGTTTGCTGAGAGTTTTTATCATGAATGGGT 1829 chr3qtel1M 652425 GTTGTATTTTGCCAAGTGCCTTTTCTG----TATTGATATAATCATATGA 652470 v i i i ---- i i C L1MC_orf2#LIN 1828 GTTGGATTTTGTCAAATGCTTTTTCTGCATCTATTGATATGATCATGTGA 1779 chr3qtel1M 652471 TTTTAAACTCTTCT------TATTCATGTAATCAATTATGATAATAGCTT 652514 ---- ------ i v i vi iiv v v C L1MC_orf2#LIN 1778 TTTT----TCTTCTTTAGCCTGTTGATGTGATGGATTACATTAATTGATT 1733 chr3qtel1M 652515 TTT---TTTTTTTCTATTGAGGCAAGCCTG----AATTCTTAGTATGGTC 652557 i--- v vvv i vivvv vi ---- v ii v - C L1MC_orf2#LIN 1732 TTCGAATGTTGAACCAGCCTTGCATACCTGGGATAAATCCCACT-TGGTC 1684 chr3qtel1M 652558 TCAGTGTAT--------------ATTGCTATAGTCCCCTAGCTAGTATTT 652593 vii -------------- i iv v vvi v i C L1MC_orf2#LIN 1683 GTGGTGTATAATTCTTTTTATACATTGTTGGATTCGATTTGCTAATATTT 1634 chr3qtel1M 652594 TATTTAGGATTTTTGCAATGATATTTATTCGTGAAATTG--CTCTCGTTT 652641 i v viv i i vv v v -- v v C L1MC_orf2#LIN 1633 TGTTGAGGATTTTTGCATCTATGTTCATGAGAGATATTGGTCTGTAGTTT 1584 chr3qtel1M 652642 TATTT 652646 v C L1MC_orf2#LIN 1583 TCTTT 1579 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 45.07 CpG sites = 186, Kimura (unadjusted) = 46.47 Transitions / transversions = 1.06 (186/176) Gap_init rate = 0.04 (49 / 1091), avg. gap size = 1.88 (92 / 49) 226 36.69 10.08 0.71 chr3qtel1M 652938 653066 (346934) L2d2_3end#LINE/L2 415 555 (0) m_b153s601i13 5733 chr3qtel1M 652938 TTGTGTGCTGTCTTTCCCATGAAACTGAGAGGTTCTGAAAAGCAGA---- 652983 i vi ii v iv i i vi v i vi ii i---- L2d2_3end#LIN 415 TTATGTCTTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACC 464 chr3qtel1M 652984 ----CTTTTTCATTTTAGTATTCCC----ATGTTTAACACAGGACCTAGC 653025 ---- v v v i v i ----ii ii i vi v L2d2_3end#LIN 465 ATGTCTTATACTTCTTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTGC 514 chr3qtel1M 653026 ATGTAGTAGGTGCTTCATGAACAACTGACTGA-CAGATTTAA 653066 iii i iv i i vi -i -iv i L2d2_3end#LIN 515 ACACAGTAGGCGCTCAATAAATATTTG-TTGATTTGATTTGA 555 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 51.14 CpG sites = 32, Kimura (unadjusted) = 54.69 Transitions / transversions = 2.13 (32/15) Gap_init rate = 0.04 (5 / 128), avg. gap size = 2.80 (14 / 5) 257 34.62 12.50 0.00 chr3qtel1M 652945 653048 (346952) L2b_3end#LINE/L2 332 448 (18) m_b153s601i14 5733 chr3qtel1M 652945 CTGTCTTTCCCATGAAACTGAGAGGTTCTGAAAAGCAGA----------- 652983 ii iv i v v i vvi ii i----------- L2b_3end#LINE 332 CTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTG 381 chr3qtel1M 652984 -CTTTTTCATTTTAGTATTCCCA-TGTTTAACACAGGACCTAGCATGTAG 653031 - v iiviv i -i ii i ?i i iii L2b_3end#LINE 382 TCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAG 431 chr3qtel1M 653032 TAGGTGCTTCATGAACA 653048 i ivi i i L2b_3end#LINE 432 TAGGCGCTCAGTAAATA 448 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 45.76 CpG sites = 27, Kimura (unadjusted) = 52.09 Transitions / transversions = 3.00 (27/9) Gap_init rate = 0.03 (3 / 103), avg. gap size = 4.33 (13 / 3) 277 32.36 6.85 2.63 chr3qtel1M 653695 653840 (346160) L2d2_3end#LINE/L2 381 532 (23) m_b153s601i15 5734 chr3qtel1M 653695 TAAATGCTTGTTTCTTTCCTTCCCTCCCC----GTCTGCGCCTCCGCTCT 653740 - v iv vi vv iii ---- i ii i ivv i L2d2_3end#LIN 381 TAAAT-CTTGTATTGTTATTTAACTTTTCACGTGTTTATGTCTTGTCTCC 429 chr3qtel1M 653741 CCATTTTGGCGGGGAGTTCCTTGGAAGCAGGGAC--TGACTT-TGCCGGT 653787 vi v iiv vi i iii -- v - i --- L2d2_3end#LIN 430 CCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATAC---T 476 chr3qtel1M 653788 TCTTTGTACTCC---CAGCACTTAACACGGTTTCTGGCACATAGTAGAAG 653834 ii --- i i i i vi v i iv L2d2_3end#LIN 477 TCTTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAGTAGGCG 526 chr3qtel1M 653835 CGTAAT 653840 vi L2d2_3end#LIN 527 CTCAAT 532 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 43.35 CpG sites = 30, Kimura (unadjusted) = 44.69 Transitions / transversions = 1.88 (30/16) Gap_init rate = 0.06 (8 / 145), avg. gap size = 1.75 (14 / 8) 295 32.69 3.85 0.00 chr3qtel1M 653737 653840 (346160) L2b_3end#LINE/L2 336 443 (23) m_b153s601i16 5734 chr3qtel1M 653737 CTCTCCATTTTGGCGGGGAGTTCCTTGGAAGCAGGGACTGACTTTGCCG- 653785 i vvi v i v v i v iii i ?v i i v- L2b_3end#LINE 336 CTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCTT 385 chr3qtel1M 653786 GTTCTT---TGTACTCCCAGCACTTAACACGGTTTCTGGCACATAGTAGA 653832 vi--- ii i i i i ?vi i i L2b_3end#LINE 386 GTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGG 435 chr3qtel1M 653833 AGCGTAAT 653840 v vi i L2b_3end#LINE 436 CGCTCAGT 443 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 42.76 CpG sites = 22, Kimura (unadjusted) = 46.52 Transitions / transversions = 1.83 (22/12) Gap_init rate = 0.02 (2 / 103), avg. gap size = 2.00 (4 / 2) 12 21.03 5.88 1.89 chr3qtel1M 654218 654268 (345732) (GCCCGGC)n#Simple_repeat 1 53 (0) m_b153s252i13 5735 chr3qtel1M 654218 GCCACGGTGCCCAGCGCCTTGCG-GCGGCCCTCGGC-CGCGGC-CCCCGC 654264 - i i iv -v v i - v - v (GCCCGGC)n#Si 1 GCC-CGGCGCCCGGCGCCCGGCGCCCGGCGCCCGGCGCCCGGCGCCCGGC 49 chr3qtel1M 654265 GCCC 654268 (GCCCGGC)n#Si 50 GCCC 53 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.08 (4 / 50), avg. gap size = 1.00 (4 / 4) 15 12.74 0.00 8.11 chr3qtel1M 654313 654352 (345648) (CAG)n#Simple_repeat 1 37 (0) m_b153s252i14 5736 chr3qtel1M 654313 CAGCGGCAGCACCAGCAGCAGGAGGCAGGCGGCCAGCAGC 654352 i v v - - i - (CAG)n#Simple 1 CAGCAGCAGCAGCAGCAGCAGCA-GCA-GCAG-CAGCAGC 37 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.08 (3 / 39), avg. gap size = 1.00 (3 / 3) 12 9.37 5.00 7.69 chr3qtel1M 655044 655083 (344917) (GGGGT)n#Simple_repeat 1 39 (0) m_b153s252i15 5737 chr3qtel1M 655044 GGGGTGGGGTGGGG-GGCG-GGGGAGGCCGGAGCGGGTGGGG 655083 - v - v -- v - (GGGGT)n#Simp 1 GGGGTGGGGTGGGGTGGGGTGGGGTGG--GGTG-GGGTGGGG 39 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.13 (5 / 39), avg. gap size = 1.00 (5 / 5) 190 17.65 0.00 0.00 chr3qtel1M 655829 655862 (344138) C MIRb#SINE/MIR (20) 248 215 m_b153s601i17 5738 chr3qtel1M 655829 TTAGGCTCCTACTATGGGCCAGGCACTGGGCTAA 655862 ii v i v v C MIRb#SINE/MIR 248 TTGAGCGCTTACTATGTGCCAGGCACTGTGCTAA 215 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 20.23 CpG sites = 3, Kimura (unadjusted) = 20.23 Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 344 31.92 12.93 3.17 chr3qtel1M 656398 656714 (343286) L2b_3end#LINE/L2 114 460 (6) m_b153s601i18 5739 chr3qtel1M 656398 CTTCCACTCCAGGGG-TTTCCAGTGGCTGGCTGCCAGGCCTGGGATGTAC 656446 i i ii v- v v?v viiv ivv i i i-- L2b_3end#LINE 114 CTCCCGCCTCAGGGCCTTTGCACNTGCTGTTCCCTCTGCCTGGAACGC-- 161 chr3qtel1M 656447 TCCCTCCTCACCTTCACTTC--CTGGTCACTTCCCTGGCTTCCTTTAATT 656494 - i i --- -- i vi ivvv v i iv L2b_3end#LINE 162 -CCTTCCCCACCT---CTTCGCCTGGCCAACTCCTACTCATCCTTCAGGT 207 chr3qtel1M 656495 CCCAATTAAGATCCCAGCTGCTGCTGGAAGCCTTTCTCCATCCCCC---T 656541 i ii v i vi v v v v i i iiv i ---i L2b_3end#LINE 208 CTCAGCTCAAATGTCACCTCCTCCGGGAAGCCCTCCCTGACCCCCCAGGC 257 chr3qtel1M 656542 TGATCCTGACGCCCT-CTCTGACGTCATGTCCAGGTCACTGCATCTACAA 656590 i ivi v i - -- v vivi - - i -i i v L2b_3end#LINE 258 CGGGTCAGGCGCCCTCCTCTG--GGCCCCCCCA-GTC-CTAC-CCTGCCA 302 chr3qtel1M 656591 CTTT--TTGGTCAGTGTTTATTTCCATGTTT-TCTCCACT-TTAGGCTAT 656636 i --v vi ? v i i? v i - v i-i i i L2b_3end#LINE 303 CTCTGGGTTATNATTGTCTGNTTACATGTCTGTCTCCCCCACTAGACTGT 352 chr3qtel1M 656637 GAATTCT-TGAAGGCA--------TTTTGTCT--TTC------------- 656662 ii i- i --------v i -- ------------- L2b_3end#LINE 353 GAGCTCCGTGAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTGTATCCC 402 chr3qtel1M 656663 ------TTTGCACAATGCCCAGCATACAGTAGGCGCTTAATGGATGCTTG 656706 ------i v i? ii i i i ii ii L2b_3end#LINE 403 CAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTTG 452 chr3qtel1M 656707 CTGACTGA 656714 i v L2b_3end#LINE 453 TTGAATGA 460 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 42.19 CpG sites = 63, Kimura (unadjusted) = 44.68 Transitions / transversions = 1.80 (63/35) Gap_init rate = 0.07 (23 / 316), avg. gap size = 2.26 (52 / 23) 444 31.25 14.95 0.94 chr3qtel1M 656434 656714 (343286) L2c_3end#LINE/L2 153 472 (6) m_b153s601i19 5739 chr3qtel1M 656434 GCCTGGGATGTACTCCCTCCTCACCTTCACTTCCTGGTCACTTCCCTGGC 656483 i iv i i iiv i i --- ii vi ivvv L2c_3end#LINE 153 GCCTGGAATGCTCTTCCCCCCTCCTTCCAC---CTGGCTAACTCCTACTC 199 chr3qtel1M 656484 TTCCTTTAATTCCCAATTAAGATCCCAGCTGCTGCTGGAAGCCTTTCTCC 656533 v i v? i ii v vi v v v v i iiv L2c_3end#LINE 200 ATCCTTCAAGNCTCAGCTCAGATGTCACCTCCTCCGGGAAGCCTTCCCTG 249 chr3qtel1M 656534 ATCCCCC----TTGATCCTGACGCCCTC-TCTG----------ACGTCAT 656568 i ----i ii iv ii - ----------i ii v L2c_3end#LINE 250 ACCCCCCAAGNCTAGTCTAGGTGCCCTCCTCTGTGCTCCCATAGCACCCT 299 chr3qtel1M 656569 GTCCAGGT---CACT---GCATCTAC----AACTTTT-TGGTCAGTGTTT 656607 i vii--- i --- ii i---- v - v v v i L2c_3end#LINE 300 GTCTATACTCCCATTATAGCACTTATCATTAACTTGTATTGTAATTGTCT 349 chr3qtel1M 656608 ATTTCCATGTTT-TCTCCACT-TTAGGCTATGAATTC-TTGAAGGCA--- 656651 i v ? i - v i-i i i ii - i --- L2c_3end#LINE 350 GTTTACNTGTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGG 399 chr3qtel1M 656652 -TTTTGTCTT-----TCTTTGCA----CAATGCCCAGCATACAGTAGGCG 656691 -iiv ----- i ---- ii ii i i L2c_3end#LINE 400 ACCGTGTCTTATTCATCTTTGTATCCCCAGCGCCTGGCACATAGTAGGCG 449 chr3qtel1M 656692 CTTAATGGATGCTTGCTGACTGA 656714 i ii i i v L2c_3end#LINE 450 CTCAATAAATGTTTGTTGAATGA 472 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 42.25 CpG sites = 61, Kimura (unadjusted) = 43.64 Transitions / transversions = 2.35 (61/26) Gap_init rate = 0.06 (17 / 280), avg. gap size = 2.65 (45 / 17) 345 36.18 4.41 2.60 chr3qtel1M 656772 656998 (343002) C L3#LINE/CR1 (756) 3343 3113 m_b153s601i20 5740 chr3qtel1M 656772 ACATTTACTCTGAGTCCAAGTCATGTGGGTGGGTTTTGCTCGT-GTTCTA 656820 ii iviv vv vv v v v v iv i i - i C L3#LINE/CR1 3343 ACATTTATCCCTGTTAAATTTCATCTTGTTGGTTTCGGCCCATCGTTCCA 3294 chr3qtel1M 656821 GCCTGCCCGGGTCTTTGTCCATCCTGAGACTCGCCCTATAT-GTGTCTGT 656869 i vi i ? v vv i vv - i v vi ?- i iv i C L3#LINE/CR1 3293 GCCTGTCGAGATCNTTTTGAATCTTGATTCT-GTCATCCANCGTATTAGC 3245 chr3qtel1M 656870 TGTTCCTCCCGACT---TGTCCCCTGGAGATTGGAGGCAGACGGCATCTC 656916 i i ii --- vi v i v viviv i v v v C L3#LINE/CR1 3244 TATCCCTCCCAGCTTTGTGTCATCTGCAAATTTGATAAGCATGCCTTCTA 3195 chr3qtel1M 656917 TGCTTTTATTTGGA--ACTGGACAAAACGGTGAACAGGAAAAAGC--AGG 656962 ii i iiiii-- i ivv i v v ii -- C L3#LINE/CR1 3194 TGTCTTCATCCAAGTCATTGATAAAAATGTTGAACAGGACAGGGCCAAGG 3145 chr3qtel1M 656963 ACAGACACAGATCCCG-GCCATTCCACTGGAGGCCTC 656998 -----ii i - v iv i i C L3#LINE/CR1 3144 ACAGA-----GCCCTGTGGCACGCCACTAGAGACCTC 3113 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 50.04 CpG sites = 45, Kimura (unadjusted) = 51.92 Transitions / transversions = 1.29 (45/35) Gap_init rate = 0.05 (12 / 226), avg. gap size = 1.33 (16 / 12) 20 11.13 0.00 0.00 chr3qtel1M 657304 657332 (342668) (G)n#Simple_repeat 1 29 (0) m_b153s252i16 5741 chr3qtel1M 657304 GGGAGTGGGGGGGGGCGGGGGGGGGGGGG 657332 i v v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG 29 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 282 20.00 12.31 0.00 chr3qtel1M 657939 658003 (341997) C MIR3#SINE/MIR (27) 181 109 m_b153s601i21 5742 chr3qtel1M 657939 CTGGAAGGGGCCTTCGGGCTAACCT--------CCTCTCTTGTTATAGAT 657980 i v i v v i -------- i v v i C MIR3#SINE/MIR 181 CTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGAT 132 chr3qtel1M 657981 GGAGAAACTGAGGCCCAGAGAAG 658003 ii i C MIR3#SINE/MIR 131 GAGGAAACTGAGGCCCAGAGAGG 109 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 23.69 CpG sites = 8, Kimura (unadjusted) = 23.69 Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.02 (1 / 64), avg. gap size = 8.00 (8 / 1) 13 15.40 5.56 0.00 chr3qtel1M 658381 658416 (341584) (GACAGG)n#Simple_repeat 1 38 (0) m_b153s252i17 5743 chr3qtel1M 658381 GACAGGCACAGGCAGAGGAACTGGG--AGGGACAGGGA 658416 v v v i v -- (GACAGG)n#Sim 1 GACAGGGACAGGGACAGGGACAGGGACAGGGACAGGGA 38 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.03 (1 / 35), avg. gap size = 2.00 (2 / 1) 251 35.87 6.09 2.07 chr3qtel1M 659444 659722 (340278) C L1ME4c_3end#LINE/L1 (191) 639 350 m_b153s551i12 5744 chr3qtel1M 659444 TCCTGCTCACTTCCTTTTGCATCAGCTCATATAAGTCTTCCCATATTTCT 659493 i ivi vi vi i vv v vi i - i v C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATAAACATTTTCC-ATGTTGCT 591 chr3qtel1M 659494 G--TGATCCTT----TCTTCATTTTTTAAGGACAATAGATAGTATTCTCT 659537 i-- ii i i---- iv - v i -- iv i iv C L1ME4c_3end#L 590 ACATAGTCTTCATAATTATCATTTTT-AATGGC--TGCATAATATTCCAT 544 chr3qtel1M 659538 CACAACCATGT--CACAGCTTGTTCAGCTATTCCCCAGTTAATGGGCATC 659585 iviv?v -- i ii ii i i i vi iv i i C L1ME4c_3end#L 543 CGAGTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATT 494 chr3qtel1M 659586 CTC-TCATTTCCAATACACTGTCACCACAAAAAGAACTTCTAAAAATAGT 659634 ivv- ii vivii ii ii i v ivi v v vi i vi C L1ME4c_3end#L 493 TAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATC 444 chr3qtel1M 659635 TTTGTACATAGTTAATTTTCTC-----TTTAAAAAATCTCTTTAGGATAC 659679 i i -- ii i ----- i vv i i v C L1ME4c_3end#L 443 TTCGTGCATA--TAGCTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAA 396 chr3qtel1M 659680 AGACCTAA---TGGTATTGCTGAGTCAAAGGGAATGCATAATTTTA 659722 vv i i--- v i i v v i v C L1ME4c_3end#L 395 ATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTA 350 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 48.94 CpG sites = 62, Kimura (unadjusted) = 52.05 Transitions / transversions = 1.72 (62/36) Gap_init rate = 0.04 (12 / 278), avg. gap size = 1.92 (23 / 12) 320 32.70 6.05 0.44 chr3qtel1M 659502 659716 (340284) C L1MC4a_3end#LINE/L1 (2055) 574 348 m_b153s551i13 5744 chr3qtel1M 659502 TTCTTCATTTTTTAAGGACAATAG-ATAGTATTCTCTCACAACCATGT-- 659548 i i v-vv iiv - i iv iiiivvv -- C L1MC4a_3end#L 574 TTCCTCATTCTTTT-TTACAGCTGCATAGTACTCCATTGTGTGGATGTAC 526 chr3qtel1M 659549 CACAGCTTGTTCAGCTATTCCCCAGTTAATGGGCATCCTC-TCATTTCCA 659597 i i i i i ? i vi ?? iivv- ii C L1MC4a_3end#L 525 CATAGTTTATTCAACCANTCTCCTATNNATGGGCATTTAGGTTGTTTCCA 476 chr3qtel1M 659598 ATACACTGTCACCACAAAAAGAACTTCTAAAAATAGTTTTGTACATAGTT 659647 ivi iv ii v ivi v v vi iii i vv C L1MC4a_3end#L 475 ATATTTTGCAATTACAAACAATGCTGCAATGAATAACCTTGTGCATATGT 426 chr3qtel1M 659648 AATTTT----CTCTTTAAAAAATCTCTTTAGGATACAGACCT---AATGG 659690 ? ----v v vi iivi v i i v vv --- i C L1MC4a_3end#L 425 NATTTTGTACATGTTGGAGGTGTATCTTCAGGGTAAATTCCTAGAAGTGG 376 chr3qtel1M 659691 TATTGCTGAGTCAAAGGG--AATGCATA 659716 v i -- C L1MC4a_3end#L 375 GATTGCTGGGTCAAAGGGTAAATGCATA 348 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 45.68 CpG sites = 41, Kimura (unadjusted) = 45.68 Transitions / transversions = 1.41 (41/29) Gap_init rate = 0.03 (7 / 214), avg. gap size = 2.00 (14 / 7) 18 19.41 0.00 0.00 chr3qtel1M 659736 659776 (340224) (AGAAA)n#Simple_repeat 1 41 (0) m_b153s252i18 5745 chr3qtel1M 659736 AGAACAGAAAAGAGAAAAACAGAAAAGGAAATAAAACAAAA 659776 v i i v i v v (AGAAA)n#Simp 1 AGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAA 41 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 44 34.43 0.56 1.69 chr3qtel1M 660010 660188 (339812) (AT)n#Simple_repeat 1 177 (0) m_b153s252i19 5746 chr3qtel1M 660010 ATATATATATATATAGAGAGAGAGACATATATATATGTCTATATATACAT 660059 v v v v v i i v i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr3qtel1M 660060 ACACATATATTCATACCCACTCACATACATATATCTATATACACACATAG 660109 i i vi ivi - - i i v i i i v (AT)n#Simple_ 51 ATATATATATATATATATA-T-ATATATATATATATATATATATATATAT 98 chr3qtel1M 660110 AGTA-ACATGAATACATATCTACATATATTCAGATACACACAAATATACA 660158 - - i iv i v i vi v i i i v i (AT)n#Simple_ 99 A-TATATATATATATATATATATATATATATATATATATATATATATATA 147 chr3qtel1M 660159 TGCATTTACCCATATGTAAACATATATCTA 660188 ii v ivi i v i v (AT)n#Simple_ 148 TATATATATATATATATATATATATATATA 177 Matrix = Unknown Transitions / transversions = 1.47 (28/19) Gap_init rate = 0.02 (4 / 178), avg. gap size = 1.00 (4 / 4) 483 25.98 5.24 0.84 chr3qtel1M 660827 661055 (338945) C L1ME5_3end#LINE/L1 (702) 239 1 m_b153s551i14 5747 chr3qtel1M 660827 GTATTTTCC--TTTTCTGTCATATTAGCCAATCTAATAGATGTGAAGCAG 660874 i v --i i-- v v i i i iii C L1ME5_3end#LI 239 GCATTATCCAGCTTTCTA--ATTTTTGCCAGTCTAATAGGTGTAAAGTGA 192 chr3qtel1M 660875 TATCTCAAAGTTGTTTTATTTTGCATTTTTCTAATCAATAGTGATTTAGA 660924 vv v i i i v i v v C L1ME5_3end#LI 191 TATCTCATTGTTGTTTTAATTTGCATTTCTCTGATTACTAATGAGTTTGA 142 chr3qtel1M 660925 GCA--TTTTTATATTATAGAAAGCTTT---GATT---TCTTCTGAAAACT 660966 -- i i vv v vv i --- i --- v i C L1ME5_3end#LI 141 GCATCTCTTCATATGCTTGTTAGCCTTTCGGGTTTCCTCTTCTGTAAATT 92 chr3qtel1M 660967 GCCTATTAATATCTTTTGATGATTTTTCAATTGGGG--AATGACTTGTTC 661014 i v i viv v --?vi v v C L1ME5_3end#LI 91 GCCTGTTCATATCCTTTGCCCATTTTTCTATTGGGGTTNCCGTCTTTTTC 42 chr3qtel1M 661015 CTATAAATTTGGTGCAATTATCTATATATTAGAGATATGAA 661055 i i vi vv v i vii i vv v C L1ME5_3end#LI 41 TTGTTGATTTGCAGGAGTTCCTTGTATATTCTAGATATTAA 1 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 31.73 CpG sites = 29, Kimura (unadjusted) = 32.38 Transitions / transversions = 0.97 (29/30) Gap_init rate = 0.03 (7 / 228), avg. gap size = 2.00 (14 / 7) 254 32.61 3.38 4.26 chr3qtel1M 660949 661185 (338815) C L1M1_orf2#LINE/L1 (41) 3253 3019 m_b153s551i15 5747 chr3qtel1M 660949 TGATTTCTTCTGAAAACTGCCTATTAATATCTTTTGATGATTTTTCAATT 660998 vi i i v i v v viv i i C L1M1_orf2#LIN 3253 TGTCTTCTTTTGAGAAATGTCTATTCAGATCTTTTGCCCATTTTTTAATC 3204 chr3qtel1M 660999 GGGGAAT--GACTTGTTCCTATAAATTTGGTGCAATTATCTATATATTAG 661046 ivv -- i v i v v vv ii vii vv C L1M1_orf2#LIN 3203 GGATTATTAGATTTTTTCCTATAGAGTTGTTTGAGCTCCTTATATATTCT 3154 chr3qtel1M 661047 AGATATGAAGCTTTTATCAAA---GAAACATAAAATTCCTCTCTCTCCTC 661093 i v v v ii i i --- v iiv iv v vi i i v i C L1M1_orf2#LIN 3153 GGTTATTAATCCCTTGTCAGATGGGTAGTTTGCAAATATTTTCTCCCATT 3104 chr3qtel1M 661094 ACCCAGCTTTTGGCTTTC-CTTCTAAACTTGGCTGTATTGGTTTTGTT-- 661140 ------ v v i v - --- v i - v iiv -- C L1M1_orf2#LIN 3103 ------CTGTGGGTTGTCTCTTC---ACTTTGTTG-ATTGTTTCCTTTGC 3064 chr3qtel1M 661141 TGTGCAAAACTTTTTAAATTTAGTGCAATTCAAATTATCCATTTT 661185 i vi v i ii ii i v v i C L1M1_orf2#LIN 3063 TGTGCAGAAGCTTTTTAACTTGATGTGATCCCATTTGTCCATTTT 3019 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 42.87 CpG sites = 39, Kimura (unadjusted) = 43.66 Transitions / transversions = 1.11 (39/35) Gap_init rate = 0.06 (13 / 236), avg. gap size = 1.38 (18 / 13) 265 36.25 2.71 2.71 chr3qtel1M 661458 662268 (337732) C L1M5_orf2#LINE/L1 (587) 2707 1897 m_b153s551i16 5747 chr3qtel1M 661458 CTAATCTATTCGACTAATTCACCTATTT---CTTA-GCCAGCAGGAGATT 661503 v i v i i ii ii i i --- - ii vv v i C L1M5_orf2#LIN 2707 CTATTCTGTTCCATTGATCTATTTGTCTATCCTTACGCCAATACCACACT 2658 chr3qtel1M 661504 GCTTTGTTGATTACCACTTTGTAGTACAATTTGAGATTTAATACAACTAG 661553 ii v v i iivi i i vivi ? i?ii vviiv C L1M5_orf2#LIN 2657 GTCTTGATTACTGTAGCTTTATAATAAGTCTTGANATCNGGTAGTGTAAG 2608 chr3qtel1M 661554 GCTACCTTCTTTCATATTCTCCCTCTCCCCCACATTAGTTCCCTTGATAT 661603 v iv vv ---i i i i i v-- v iv --- v v C L1M5_orf2#LIN 2607 TCCTCCAACTTT---GTTCTTCTTTTTCA--AGATTGTTT---TGGCTAT 2566 chr3qtel1M 661604 TCTTGACCATTTTTTCTTTCGGATGAAATGTGTTATT--TTTTTCTAGCT 661651 ? ii v vivi i iv i v v ivv i--i v v vi C L1M5_orf2#LIN 2565 TCTNGGTCCTTTGCATTTCCATATAAATTTTAGAATCAGCTTGTCAATTT 2516 chr3qtel1M 661652 CTACAATAAACACTTTTTTTTGGGGGGGGGGGATGGTATACCACTGAATA 661701 - v i vi ---- ivvvv iv v vv i v C L1M5_orf2#LIN 2515 CTACAA-AAAAACCTGCT----GGGATTTTGATTGGGATTGCATTGAATC 2471 chr3qtel1M 661702 AGTAGATTAATATAAGTTGTATTTTCATTTTTGTTTTATTGGCTCATTCT 661751 vi i v ii vv v vv i ?iivv iv v i v C L1M5_orf2#LIN 2470 TATAGATCAATTTGGGGAGAATTGACATCTTNACAATATTGAGTCTTCCA 2421 chr3qtel1M 661752 ATTCATGAGCAATTAATGTTTCTCTAATTTTTAAGGACTGTCTTTA-TTT 661800 i i vvvv i i i v v v v - - C L1M5_orf2#LIN 2420 ATCCATGAACATGGTATATCTCTCCATTTATTTAGGTCT-TCTTTAATTT 2372 chr3qtel1M 661801 GTATGAAAAGAGTTTTATAATTGTACTCATATAATCTCTGGATTTGTCTT 661850 v v v iv iv i i v vvvii ? iviii v iv ? i C L1M5_orf2#LIN 2371 CTCTCAGCAATGTTTTGTAGTTTTCAGTGTANAGGTCTTGCACATNTTTT 2322 chr3qtel1M 661851 GTCAGCTAGGCTCCCAAGTATTTTATATTGTCTACAGTTATTTTAAGTGC 661900 i v vvii i ? i v i ivv i v i v C L1M5_orf2#LIN 2321 GTTAGATTTATTCCTAAGTATTTNATGTTTTTTGATGCTATTGTAAATGG 2272 chr3qtel1M 661901 AGTTTTTATTTCTATTTCTTTCTGCCAGACTTTGTTGGTAATATGGAGAA 661950 vi v v ?vv v i v v vvv v i iv C L1M5_orf2#LIN 2271 TATTGTTTTTNAAATTTCATTTTCCAATTGTTTGTTGCTAGTATATAGAA 2222 chr3qtel1M 661951 ATGTTGATGATTTATGTGGGCT-TCTTTATATGCTGCAATTTAGCTGAAG 661999 iiviv v ivii -v i i v ? i ii v i v C L1M5_orf2#LIN 2221 ATACAATTGATTTTTGTATATTGACCTTGTATCCNGCGACCTTGCTAAAT 2172 chr3qtel1M 662000 CTGTTAATTATTTCAAGTAATTTAAAATTTTT---TTTTCTGGGATTCTC 662046 iiii v v v i ---? v --- i i ? i C L1M5_orf2#LIN 2171 TCACTTATTAGTTCTAGTAGTTT---NTTTGTAGATTCTTTNGGATTTTC 2125 chr3qtel1M 662047 TAGCTGTACTGTCATAGCATCTGTTAAAAATGATGTTTTTGTTCCCTCAT 662096 vv i? vi iv iv v ? iiv i i i v C L1M5_orf2#LIN 2124 TACGTANACAATCATGTCATCTGCGAATAANGACAGTTTTATTTCTTCCT 2075 chr3qtel1M 662097 TTTCTAT-TCTAAG----TAATTTCTTTTTCTTCATTTAT--CATTAAAG 662139 i v - i v ---- v vvi -- i --i C L1M5_orf2#LIN 2074 TTCCAATCTTTATGCCTTTTATTTCTTTTTCTTGCCTTATTGCACT--GG 2027 chr3qtel1M 662140 TTGGCATTGCTAATATAAGATTGAATA-TAGTGGTGATAATTCATAT-CT 662187 i i v iiv i i i vi -v ? iivv i - C L1M5_orf2#LIN 2026 CTAGGACCTCCAGTACAATGTTGAATAGAAGTGGTGANAGCGGACATCCT 1977 chr3qtel1M 662188 TGCTTTG-TCATGATCTTATTGGGAAGGTTTTTTTAGCTTATTCA-TGTT 662235 ii - vi vv i --i? i i? - -ii C L1M5_orf2#LIN 1976 TGTCTTGTTCCCGATCTTAGGGGGAAAG--CNTTCAGTNT-TTCACCATT 1930 chr3qtel1M 662236 ACAGACAATGCTTGTTGATGGTTTTAGATAGAT 662268 viv ii i ? i vv vvi C L1M5_orf2#LIN 1929 AAGTATGATGTTNGCTGTAGGTTTTTCGTAGAT 1897 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 51.09 CpG sites = 149, Kimura (unadjusted) = 52.40 Transitions / transversions = 1.09 (149/137) Gap_init rate = 0.04 (35 / 810), avg. gap size = 1.26 (44 / 35) 27 21.41 4.29 0.00 chr3qtel1M 662436 662505 (337495) (AT)n#Simple_repeat 1 73 (0) m_b153s252i20 5748 chr3qtel1M 662436 ATACATGTAAATATGTTAAAATATATATATATATATAT-TATA-AAATCC 662483 i i v i vv v - - v vi (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr3qtel1M 662484 A-ATATATGTATACATATTTATA 662505 - i i v (AT)n#Simple_ 51 ATATATATATATATATATATATA 73 Matrix = Unknown Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.04 (3 / 69), avg. gap size = 1.00 (3 / 3) 616 34.39 0.69 1.05 chr3qtel1M 662738 663025 (336975) L1ME4c_3end#LINE/L1 353 639 (191) m_b153s551i17 5749 chr3qtel1M 662738 AACTGTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGCTTATATTCC 662787 v v i i i vii v vv v i i L1ME4c_3end#L 353 AAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCT 402 chr3qtel1M 662788 AAAGAGAT--TTTAAAGAAGGGAAAAAGACCTGTATGTGCAAGAATGTTT 662835 i i -- i ii i -- i ii i ii i L1ME4c_3end#L 403 AAGGAAATAATTCAAAAGAAGGAAAAAG--CTATATGCACGAAGATGTTC 450 chr3qtel1M 662836 GTGGCAGCCCTTTTTATAGTGGGCAGAAACTGGAAACTGAGTGGATGCCC 662885 i v vi v i i vv i i vivv ii i L1ME4c_3end#L 451 ATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCC 500 chr3qtel1M 662886 ATCAAGTGGAAAATGGCTGAATAAATTGTGGTTTATGAACATTATGGAAT 662935 v vv ii i i i i vi v? viv L1ME4c_3end#L 501 AACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAAT 550 chr3qtel1M 662936 ATTATTGTTCTGTAAGAAATGACCAACAGGATGATTTCAGAAAGGCCTGG 662985 vvvv ii v i iv vi v v i viiv ivii v L1ME4c_3end#L 551 ATTATGCAGCCATTAAAAATGATAATTATGAAGACTATGTAGCAACATGG 600 chr3qtel1M 662986 AGAGACTTACATGAACTGATGCTGAGTGAAATGAGGAGGA 663025 - i iv vi vv i i i vi v i L1ME4c_3end#L 601 A-AAATGTTTATGATATAATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 46.60 CpG sites = 57, Kimura (unadjusted) = 47.98 Transitions / transversions = 1.39 (57/41) Gap_init rate = 0.01 (4 / 287), avg. gap size = 1.25 (5 / 4) 473 31.57 8.76 4.67 chr3qtel1M 663429 664707 (335293) C L1M5_orf2#LINE/L1 (1380) 1914 586 m_b153s551i18 5747 chr3qtel1M 663429 TGTAAGTTTCTCCAAGCTTCTCTCTAGATATTACTATCTTAAGGAAAGCT 663478 i i vv v v i ------- ii vv i ivii C L1M5_orf2#LIN 1914 TGTAGGTTTTTCGTAGATGCCCT-------TTATCAGGTTGAGGAAGTTC 1872 chr3qtel1M 663479 CTAGTTATTCCTGGGCTTTCTGGG-GTTTTTAATACAAATGAGT--TGTA 663525 ivvi i -i v i - vi ii i -- v C L1M5_orf2#LIN 1871 CCTTCTATTCCTAG-TTTGCTGAGAGTTTTTATCATGAATGGGTGTTGAA 1823 chr3qtel1M 663526 TTTTGTCAAAAGCCTTTTCTACATTGATTGAAATAATAATTTGATTTTTG 663575 v i i iv i i v v v C L1M5_orf2#LIN 1822 TTTTGTCAAATGCTTTTTCTGCATCTATTGAGATGATCATATGATTTTTC 1773 chr3qtel1M 663576 TTGTTTCTGTTATTGAAATGATCAATTATGCTGAGAG-TTTTC--AGGTT 663622 iv v vi i i v i v iii vv - -- v C L1M5_orf2#LIN 1772 TCCTTTATTCTGTTAATATGGTGAATTACATTGATTGATTTTCGAATGTT 1723 chr3qtel1M 663623 GAACTAGTACTACATTC-------------------------ATGTATGA 663647 i i iivi i ------------------------- v C L1M5_orf2#LIN 1722 AAACCAACCTTGCATTCCTGGGATAAACCCCACTTGGTCATGATGTATTA 1673 chr3qtel1M 663648 TCTTTTTGATATATATATATCTGTAATTACCTTGTTAGTATTTTATTAAA 663697 i ---- vv v v iivi i i i ? i C L1M5_orf2#LIN 1672 TCCTTTT----TATATATTGCTGGATTCGATTTGCTAATATTTTGTTNAG 1627 chr3qtel1M 663698 AATTTTTGCATCAGTAGTCATTAGAGAAATTAGTCTAGAGTTTTCTTTCT 663747 i vi iv v i v i iv i ii C L1M5_orf2#LIN 1626 GATTTTTGCATCTATGTTCATGAGGGATATTGGTCTGTAATTTTCTTTTC 1577 chr3qtel1M 663748 CTGTTTTAGCTCTTCCTGGTTTAGGTAGTAGCACCTTATTTGTATTGTGA 663797 i vv iv i vi ? v vi vii?v ii v iv ii i C L1M5_orf2#LIN 1576 TTGTAATGTCTTTGTCNGGTTTTGGTATCAGGGTNATGCTGGCCTCATAA 1527 chr3qtel1M 663798 GAGAAATTTTGTAGGACTCCTTCTTTGCTTATTTGCCCAAATAGCTTTTA 663847 i vi i vv v vii i vii v ivi v i v i C L1M5_orf2#LIN 1526 AATGAGTTGGGAAGTGTTCCCTCTTTTTCTATTTTCTGGAAGAGTTTGTG 1477 chr3qtel1M 663848 TAATATTGGAATTAATACTTCCTTAAATG--------------CCTGTGA 663883 v v v v -------------- v C L1M5_orf2#LIN 1476 TAAGATTGGTATTATTTCTTCCTTAAATGTTTGGTAGAATTCACCAGTGA 1427 chr3qtel1M 663884 ATTTATCTGATTCTGGGGATTTCTTCTTGTGGTCTGTTCATTTTCTTTAA 663933 vii ivi i v -- vvv v -- vv v C L1M5_orf2#LIN 1426 AGCCATCTGGGCCTGGAGTTTTCT--TTGTGGGAAGGT--TTTTAATTAC 1381 chr3qtel1M 663934 AAAAAAAA------AAAAAAAGATAGGGTCATTTAAAAATTCTATTTCCT 663977 vvv ------v v i v ii i i vv i C L1M5_orf2#LIN 1380 AAATTCAATTTCTTTAATAGATATAGGGCTATTCAGATTTTCTATTTCTT 1331 chr3qtel1M 663978 CTTCTGTTAATCTAGACAATATATATTTTTATAAATAGTGATTCCTTTCA 664027 v? i i i v ii ?v i i vv iiv v vi i v C L1M5_orf2#LIN 1330 CTTGNGTCAGTTTTGGTAANTTGTGTTTTTCAAGGAATTTGTCCATTTCA 1281 chr3qtel1M 664028 --------CTTGGATTTATAGGCATATGATTGGACAAAATA-ACACTTAA 664068 --------? iii v vii vv v -v v v C L1M5_orf2#LIN 1280 TCTAAGTTNTCAAATTTATTGGCATAAAGTTGTTCATAATATTCTCTTAT 1231 chr3qtel1M 664069 AATTGACTTAATTATTTCCTCT----TCATTGGTGATGAATTCATTCTTT 664114 v i-- -- v vi v ---- vv i --- viii C L1M5_orf2#LIN 1230 TATC--CTT--TTAATGTCTGTAGGATCTGTAGTGATG---TCTCCTTTT 1188 chr3qtel1M 664115 TCATTTTTGATATTGATAATTTG-GTTTTCTTTTTTTTTTT-----TAAA 664158 ii i - i i i ----- v i C L1M5_orf2#LIN 1187 TCATTCCTGATATTGGTAATTTGTGTCTTCTCTCTTTTTTTCTTGATCAG 1138 chr3qtel1M 664159 TCAAG-TAATGATTTATCTCTTTTATTGTCCTTTCCCCACAAAATAGCTC 664207 v? - iv i vv vi -i v vi vi i C L1M5_orf2#LIN 1137 TCTNGCTAGAGGTTTATCAATTTTATTGATCTTT-TCAAAGAACCAGCTT 1089 chr3qtel1M 664208 AATTGTATTTATTAAT----TCAATGGTTCACTTACATTCAACCTTACTT 664253 -- vv ii i ---- v v ?i?i iiv v ii i i - C L1M5_orf2#LIN 1088 --TTGGCTTCGTTGATTTTCTCTATTGTNTNTTTGTTTTCTATTTCATT- 1042 chr3qtel1M 664254 TAGAATTTCTAATTTAATATTTA--ATTGAC--------AATT------- 664286 ---i iv i v v -- vv -------- v ------- C L1M5_orf2#LIN 1041 ---GATTTCTGCTCTTATCTTTATTATTTCCTTCCTTCTACTTNCTTTGG 995 chr3qtel1M 664287 -TTTAATTTG---TTCTTTCCCTA-CTTTT--AGATGCATGCCCAATTCA 664329 - --- ii - i -- i v v ii iv C L1M5_orf2#LIN 994 GTTTAATTTGCTCTTCTTTTTCTAGCTTCTTAAGGTGGAAGCTTAGATCA 945 chr3qtel1M 664330 TTGATCT---ACTCTTTTTCTATTTTATTGATGCAACTGTTTAAAGATAT 664376 i ---i ii i v i --- ii ?vii ? v C L1M5_orf2#LIN 944 TTGATTTTAAGCCTTTCTTCTTTTCTA---ATATANGCATTTAANGCTAT 898 chr3qtel1M 664377 AAATTTTCCTCTATAGACTGCTTTGTGTGAATCCCATAAATCTTGGTATG 664426 i viv ivv v i i i C L1M5_orf2#LIN 897 AAATTTCCCTCTAAGCACTGCTTTAGCTGCATCCCACAAATTTTGATATG 848 chr3qtel1M 664427 TTGTCTCATTATTTTGATTATAGTTAAGAAAACTGTTTTTTTTTTAATTT 664476 v iv i ? v -i v i ------- v i C L1M5_orf2#LIN 847 TTGTATTTTCATTNTCATT-CAGTTCAAAA-------TATTTTCTAATTT 806 chr3qtel1M 664477 GTTCTTTGATTTTTTTTCCTTTCTTTAGGATTCTTCAGGATTATATGAAC 664526 vi?i v i i iivvi iv - i v i i v i i ---- C L1M5_orf2#LIN 805 CCNTTGTGATTTCTTCTTTGACCCAT-GGGTTATTTAGAAGTGTGT---- 761 chr3qtel1M 664527 CCCCCCCCCCCCATTT--TTTCCCAATAATTTAAAATCTGTTTCCA--TG 664572 -----------ii -- v v viii --- i -- i C L1M5_orf2#LIN 760 -----------TGTTTAATTTCCAAATATTTGGGGAT---TTTCTAGNTA 725 chr3qtel1M 664573 GCCCTTTATTA--AATTTGGGTTTT--TTGCATTATAATCCCAAAAAGAT 664618 v ii i --i vviv -- v i ii - vi i v C L1M5_orf2#LIN 724 TCTTTTTGTTATTGATTTCTAATTTAATTCCATTGTGGT-CAGAGAACAT 676 chr3qtel1M 664619 GCATTTAATATTTCTGCTTTTTTTAATTCAATTGTGA--GATTTTATGCC 664666 i vi vv iv iiiv ii ? v iv v --vi v C L1M5_orf2#LIN 675 ACTCTGTATGATTTCAATCCTTTNAAATTTATTGAGACTTGTTTTATGGC 626 chr3qtel1M 664667 CTAATATATGGTCAATTTTTGTTTATGTGCCATGTATCACT 664707 i i? v i v vv v i- C L1M5_orf2#LIN 625 CCAGNATATGGTCTATCTTGGTAAATGTTCCATGTG-CACT 586 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 42.48 CpG sites = 212, Kimura (unadjusted) = 42.81 Transitions / transversions = 1.23 (212/173) Gap_init rate = 0.07 (88 / 1278), avg. gap size = 1.98 (174 / 88) 631 33.08 7.44 0.87 chr3qtel1M 663459 663888 (336112) C L1M1_orf2#LINE/L1 (1403) 1891 1434 m_b153s551i19 5747 chr3qtel1M 663459 TTACTATCTTAAGGAAAGCTCTAGTTATTCCTGGGCTTTCTGGGGTTTTT 663508 i v i v v i ivvi v ii vi ivi C L1M1_orf2#LIN 1891 TTATTATGTTGAGGTATGTTCCTTCTATACCCAGTTTTTTGAGGGTTTTT 1842 chr3qtel1M 663509 AATACAAATGA--GTTGTATTTTGTCAAAAGCCTTTTCTACATTGATTGA 663556 vi ii v i-- v i v i vi ii C L1M1_orf2#LIN 1841 ATCATGAAGGGATGTTGAATTTTATCAAATGCTTTTTCAGCATCAATTGA 1792 chr3qtel1M 663557 AATAATAATTTGATTTTTGTTGTTTCTGTTATTGAAATGATCAATTATGC 663606 i v v i iv iv vi i v vv i iii C L1M1_orf2#LIN 1791 AATGATCATATGGTTTTTGTCCTTCATTCTGTTGATATGATGTATCACAT 1742 chr3qtel1M 663607 TGAGAGTTTT---CAGGTTGAACTAGTACTACATTC-------------- 663639 vv v ---i v i vivi i i -------------- C L1M1_orf2#LIN 1741 TGATTGATTTGCGTATGTTGAACCATCCTTGCATCCCNGGGATAAATCCC 1692 chr3qtel1M 663640 -----------ATGTATGATCTTTTTGATATATATATATCTGTAATTACC 663678 ----------- v i i --- i - v v iivi C L1M1_orf2#LIN 1691 ACTTGGTCATGATGAATGATCTTTTTAATGTAT---TGT-TGAATTCGGT 1646 chr3qtel1M 663679 TTGTTAGTATTTTATTAAAAATTTTTGCATCAGTAGTCATTAGAGAAATT 663728 i i i ii i v i v C L1M1_orf2#LIN 1645 TTGCTAGTATTTTGTTGAGGATTTTTGCATCAATATTCATCAGAGATATT 1596 chr3qtel1M 663729 AGTCTAGAGTTTTCTTTCTCTGTTTTAGCTCTTCCTGGTTTAGGTAGTAG 663778 i i iv i i v v iv i vi v vi C L1M1_orf2#LIN 1595 GGCCTGTAGTTTTCTTTTTTTGATGTGTCTTTGTCTGGTTTTGGTATCAG 1546 chr3qtel1M 663779 CACCTTATTTGTATTGTGAGAGAAATTTTGTAGGACTCCTTCTTTGCTTA 663828 viivv i v iv i iii vi i v v v i i i ivii C L1M1_orf2#LIN 1545 GGTAATACTGGCCTCGTAGAATGAGTTTGGAAGTATTCCCTCCTCCTCTA 1496 chr3qtel1M 663829 TTTGCCCAAATAGCTTTTATAATATTGGAATTAATACTTCCTTAAATGCC 663878 vi vi i vvi iv v i v i ii C L1M1_orf2#LIN 1495 TTTTTCGGAATAGTTTGAGTAGGATTGGTATTAGTTCTTCTTTAAATGTT 1446 chr3qtel1M 663879 TG--TGAATTTA 663888 --v i C L1M1_orf2#LIN 1445 TGGTAGAATTCA 1434 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 44.32 CpG sites = 83, Kimura (unadjusted) = 45.26 Transitions / transversions = 1.43 (83/58) Gap_init rate = 0.02 (9 / 429), avg. gap size = 4.00 (36 / 9) 15 15.40 4.26 4.26 chr3qtel1M 665083 665129 (334871) (ATAC)n#Simple_repeat 1 47 (0) m_b153s252i21 5750 chr3qtel1M 665083 ATACATCCACTACAT-GTTACATA-ATACAAAGATATACTACATACATA 665129 v - -vv - v v i - (ATAC)n#Simpl 1 ATACATACA-TACATACATACATACATACATACATACA-TACATACATA 47 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.09 (4 / 46), avg. gap size = 1.00 (4 / 4) 18 27.16 0.00 0.00 chr3qtel1M 666463 666504 (333496) (TA)n#Simple_repeat 1 42 (0) m_b154s252i0 5751 chr3qtel1M 666463 TATATATTTATATATACACACACACATATATATACACACATA 666504 v i i i i i i i i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATA 42 Matrix = Unknown Transitions / transversions = 8.00 (8/1) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 17 29.91 0.00 0.00 chr3qtel1M 666968 667016 (332984) (TA)n#Simple_repeat 1 49 (0) m_b154s252i1 5752 chr3qtel1M 666968 TAGATCTATTTTTATATATAGGTAAATGTGCATATATGTATATATGTAT 667016 v v v v vi v i ii i i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATAT 49 Matrix = Unknown Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 32 29.78 3.95 1.94 chr3qtel1M 667418 667569 (332431) (TGTATG)n#Simple_repeat 1 155 (0) m_b154s252i2 5753 chr3qtel1M 667418 TGTGTGTGAATGTGCATGTATATGTATATATGTATGTCTAAGCATATGTG 667467 i v i i i i v v ii - (TGTATG)n#Sim 1 TGTATGTGTATGTGTATGTGTATGTGTATGTGTATGTGTATGTGTATGT- 49 chr3qtel1M 667468 GGATATGTACACATGTA-G-GACTATGTATGTGTGCATATAGGTATATGT 667515 - - ii ii - - vv i iii i v i (TGTATG)n#Sim 50 -G-TATGTGTATGTGTATGTGTATGTGTATGTGTATGTGTATGTGTATGT 97 chr3qtel1M 667516 GTATGTG--TGTGGATCTGT-GGTGGATATGAATATATATGTGTGTATAC 667562 -- v v -v v i v i i i i ii (TGTATG)n#Sim 98 GTATGTGTATGTGTATGTGTATGTGTATGTGTATGTGTATGTGTATGTGT 147 chr3qtel1M 667563 AT-TGTAT 667569 - (TGTATG)n#Sim 148 ATGTGTAT 155 Matrix = Unknown Transitions / transversions = 2.18 (24/11) Gap_init rate = 0.05 (8 / 151), avg. gap size = 1.12 (9 / 8) 21 18.08 3.45 1.69 chr3qtel1M 667834 667891 (332109) (TTTTA)n#Simple_repeat 1 59 (0) m_b154s252i3 5754 chr3qtel1M 667834 TTTTGTTTTATTTTATTTTTATTTTCCTTT-TATGACTTTCTTTT-TTCT 667881 i - vi - v v i v - i (TTTTA)n#Simp 1 TTTTATTTTATTTTA-TTTTATTTTATTTTATTTTATTTTATTTTATTTT 49 chr3qtel1M 667882 ATTTTCTTTT 667891 v (TTTTA)n#Simp 50 ATTTTATTTT 59 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.05 (3 / 57), avg. gap size = 1.00 (3 / 3) 18 16.09 1.85 5.77 chr3qtel1M 667839 667892 (332108) (TTTTCT)n#Simple_repeat 1 52 (0) m_b154s252i4 5754 chr3qtel1M 667839 TTTTAT-TTTATTTTTATTTTCCTTTTATGACTTTCTTTTTTCTATTTTC 667887 v - v v i - vvi - - (TTTTCT)n#Sim 1 TTTTCTTTTTCTTTTTCTTTTTCTTTT-TCTTTTTC-TTTTTCT-TTTTC 47 chr3qtel1M 667888 TTTTT 667892 (TTTTCT)n#Sim 48 TTTTT 52 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.08 (4 / 53), avg. gap size = 1.00 (4 / 4) 467 23.21 0.81 9.65 chr3qtel1M 667906 668029 (331971) C MIRc#SINE/MIR (153) 115 2 m_b154s601i0 5755 chr3qtel1M 667906 GGGGTTAAATGACTTGCCCAGGATCATGCAGCTAGGAAAAATTAAGCGTC 667955 i i i i ii ------- i v C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGC 73 chr3qtel1M 667956 TGAGATTGGATTTGAACTCAGATCCTCCTGATTCCAGAGTCAAG-GATCT 668004 v viv i i i i i i - v - v C MIRc#SINE/MIR 72 AGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCA-AGTCCAGTGCTCT 24 chr3qtel1M 668005 ATCCACTGTGTCATGTAGCTGCCTC 668029 v iii i---i C MIRc#SINE/MIR 23 TTCCACTGCACCAC---ACTGCCTC 2 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 26.12 CpG sites = 19, Kimura (unadjusted) = 28.70 Transitions / transversions = 2.71 (19/7) Gap_init rate = 0.10 (12 / 123), avg. gap size = 1.00 (12 / 12) 18 27.49 1.49 1.49 chr3qtel1M 668369 668435 (331565) (AAGAAA)n#Simple_repeat 1 67 (0) m_b154s252i5 5756 chr3qtel1M 668369 AAGAAAAATCAGATCAAAAATGAGAAAG-AAAACAAAAAGCAAGCAAACA 668417 vv i vv - i - v v ivi v (AAGAAA)n#Sim 1 AAGAAAAAGAAAAAGAAAAA-GAAAAAGAAAAAGAAAAAGAAAAAGAAAA 49 chr3qtel1M 668418 AGAACAAAAAAATGAAAA 668435 v i v (AAGAAA)n#Sim 50 AGAAAAAGAAAAAGAAAA 67 Matrix = Unknown Transitions / transversions = 0.50 (5/10) Gap_init rate = 0.03 (2 / 66), avg. gap size = 1.00 (2 / 2) 1362 26.63 1.66 2.99 chr3qtel1M 668666 669207 (330793) C L1ME4c_3end#LINE/L1 (294) 536 2 m_b154s551i0 5757 chr3qtel1M 668666 ATGTACCATAATATATTCAGCCATTCTCCAATTGATGGACATCCACTCAG 668715 v i i i i v v ii vviv C L1ME4c_3end#L 536 ATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAGGTTG 487 chr3qtel1M 668716 TTTCCAGTTTCTGGCCACTACAAGAAGGGCTGCCACAAACATTTT--TGC 668763 i i v i i i iv iv v ii i -- C L1ME4c_3end#L 486 TTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTCGTGC 437 chr3qtel1M 668764 ATATGTGAGTCCTTTTCCCTCCTTTAAGATCTCTTAAGATTTCTTTGGGA 668813 --- - i i i i i----- --- i i C L1ME4c_3end#L 436 ATAT---AG-CTTTTTCCTTCTTTTGAA-----TTA---TTTCCTTAGGA 399 chr3qtel1M 668814 TACAAGCCCAGTAAAAATATTTGTGGGATCACAGGGTATGCATATTTTGA 668863 v vv v iviiv vv - v v i v C L1ME4c_3end#L 398 TAAATTCCCAGAAGTGGAATTACTGGG-TCAAAGGGTATGAACATTTTTA 350 chr3qtel1M 668864 TAGCCCTTTGGGCATAGTTCCAAATTGCTCTCCAGAATGATTGGATCAAG 668913 i i vivi i v v i i v i v i v C L1ME4c_3end#L 349 TGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAAT 300 chr3qtel1M 668914 TT-CACTACT-CCACCAATGTTTGAGGGTGCCAGTTTTCCCACATCCCCT 668961 - ? i i- v v ? i iv i ? i v C L1ME4c_3end#L 299 TTACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCG 250 chr3qtel1M 668962 CCAACATTTATCATTATC--TTTTTCTATCATCTTAGCCAATATGACAGG 669009 i vivi -- iv -- i v i v i i C L1ME4c_3end#L 249 CCAGCATTGGGTATTATCAATTTTTTAA--ATTTTTGCTAATTTAATAGG 202 chr3qtel1M 669010 TGTGTAGTGGTACCTCAAAGTTGTCTCAATTTGCATTTCTC--ATCAATA 669057 i iv i i vv ii i i-- i v C L1ME4c_3end#L 201 CGTAAAATGGTATCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACTA 152 chr3qtel1M 669058 GTGATTTAGAACATTTTTTAATATGACTAGAAATAGTTTCAATTTCTTCA 669107 i vv v iv i vi ivvv ivi? vv i v C L1ME4c_3end#L 151 GCGAGGTTGAACATTTTTCCATGTGTTTGTTTACTANTTGTATTTCCTCT 102 chr3qtel1M 669108 TCTGAAAATTGTTTGTTCATATCCTTTGACCATTTATCAATTGGAGAATG 669157 ? vi i i v v i vv v C L1ME4c_3end#L 101 TNTGTGAATTGTCTGTTCATGTCCTTTGCCCATTTATCTATTGGGGTCTT 52 chr3qtel1M 669158 GCTTGTATTCTTATCAAATTTGACTCAATTCTCTATATATTTTAGA-ATT 669206 v ?v v - v v ii i ? v? - C L1ME4c_3end#L 51 GATNTTTTTCTTATC-AATTTGAATGAGCTCTTTATATANTANAGATATT 3 chr3qtel1M 669207 A 669207 C L1ME4c_3end#L 2 A 2 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 32.86 CpG sites = 75, Kimura (unadjusted) = 34.04 Transitions / transversions = 1.15 (75/65) Gap_init rate = 0.04 (22 / 541), avg. gap size = 1.14 (25 / 22) 284 30.81 2.12 2.12 chr3qtel1M 669059 669247 (330753) C L1P4_orf2#LINE/L1 (0) 3294 3106 m_b154s551i1 5757 chr3qtel1M 669059 TGATTTAGAACATTTTTTAATATGACTAGAAATAGTTTCAATTTCTTCAT 669108 v v i v vi ivviiiv i vv v v C L1P4_orf2#LIN 3294 TGATGTTGAGCATTTTTTCATATGTTTGTTGGCCGCTTGTATGTCTTCTT 3245 chr3qtel1M 669109 CTGAAAATTGTTTGTTCATATCCTTTGACCATTTATCAATTGGAGAATGG 669158 i i v i i v i v i v ivv -- C L1P4_orf2#LIN 3244 TTGAGAAGTGTCTGTTCATGTCCTTTGCCCACTTTTTAATGGGGTTAT-- 3197 chr3qtel1M 669159 CTTGTATT---CTTATCAAATTTGACTCAATTCTCTATATATTTTAGA-A 669204 - v --- i i-i ? vi v i ii v i i - C L1P4_orf2#LIN 3196 -TTGTTTTTTGCTTGTT-GANTTGTTTAAGTTCCTTATAGATTCTGGATA 3149 chr3qtel1M 669205 TTAGGCCTTTATCAGAACCCTTGCATACAAAAATTTTTTCCCA 669247 i i i vv v v iv i i v i C L1P4_orf2#LIN 3148 TTAGACCTTTGTCGGATGCATAGTTTGCGAATATTTTCTCCCA 3106 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 38.87 CpG sites = 30, Kimura (unadjusted) = 40.70 Transitions / transversions = 1.11 (30/27) Gap_init rate = 0.03 (6 / 188), avg. gap size = 1.33 (8 / 6) 331 23.95 5.33 5.33 chr3qtel1M 669098 669247 (330753) C L1P3_orf2#LINE/L1 (39) 3255 3106 m_b154s551i2 5757 chr3qtel1M 669098 AATTTCTTCATCTGAAAATTGTTTGTTCATATCCTTTGACCATTTATCAA 669147 v v i i v i i v i v ii C L1P3_orf2#LIN 3255 AATGTCTTCTTTTGAGAAGTGTCTGTTCATATCCTTCGCCCACTTTTTGA 3206 chr3qtel1M 669148 TTGGAGAATGGCTTGTATTCTTAT--CAAATTTGACTCAATTCTCTATAT 669195 v ---i v i v i v --i vi v i ii i v C L1P3_orf2#LIN 3205 TGGG---GTTGTTTGTTTTTTTCTTGTAAATTTGTTTAAGTTCCTTGTAG 3159 chr3qtel1M 669196 ATTTTAGA-ATTAGGCCTTTATCAGAACCCTTGCATA-----CAAAAATT 669239 i i - v i ----- v ----- C L1P3_orf2#LIN 3158 ATTCTGGATATTAGCCCTTTGTCAGA-----TGGATAGATTGCAAAAATT 3114 chr3qtel1M 669240 TTTTCCCA 669247 i C L1P3_orf2#LIN 3113 TTCTCCCA 3106 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 28.40 CpG sites = 20, Kimura (unadjusted) = 29.42 Transitions / transversions = 1.43 (20/14) Gap_init rate = 0.07 (11 / 149), avg. gap size = 1.45 (16 / 11) 12 20.03 0.00 2.86 chr3qtel1M 669902 669937 (330063) (ATTTTT)n#Simple_repeat 1 35 (0) m_b154s252i6 5758 chr3qtel1M 669902 ATTTCTTCCTTTTATTATTATTATAGTTTTTATTTT 669937 - vi v v vi (ATTTTT)n#Sim 1 ATTT-TTATTTTTATTTTTATTTTTATTTTTATTTT 35 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) 676 24.99 3.11 1.92 chr3qtel1M 670290 670546 (329454) L1ME5_3end#LINE/L1 4 263 (678) m_b154s551i3 5759 chr3qtel1M 670290 ATTTCTAAAACATATAAAGAATTGACTG-AAATTTGTAAGAATAAAAGCC 670338 v i i i i i v- - ivii -- v L1ME5_3end#LI 4 ATATCTAGAATATACAAGGAACTC-CTGCAAATCAACAAGAA--AAAGAC 50 chr3qtel1M 670339 ATT--CCCCAATTGATAAATGGTCAAAGGATATGAACAAACAATGTTCAG 670386 iv?-- v v v ii v v L1ME5_3end#LI 51 GGNAACCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAG 100 chr3qtel1M 670387 ATGAAGGAATT--AAAGCCATATATAGTCATATGAAAAAATGCTCTAAAT 670434 v i i ii-- v - - i iv i i v v L1ME5_3end#LI 101 AAGAGGAAACCCGAAAGGC-TA-ACAAGCATATGAAGAGATGCTCAAACT 148 chr3qtel1M 670435 CATTATTGATTAGAGAAATGTATATTAAAACAACTCTGAAGTATCACTTC 670484 v i i i v vv ii i L1ME5_3end#LI 149 CATTAGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTT 198 chr3qtel1M 670485 ACACCTATCAGATTGGTGAAGATGACAAGA--AAAT-ATGATAAATGTTA 670531 i i ii i v v ii--ii - vi i i L1ME5_3end#LI 199 ACACCTATTAGACTGGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTG 248 chr3qtel1M 670532 GAGGGAATGTAGGGA 670546 v i i i L1ME5_3end#LI 249 GCGAGGATGTGGGGA 263 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 30.87 CpG sites = 40, Kimura (unadjusted) = 31.47 Transitions / transversions = 1.74 (40/23) Gap_init rate = 0.04 (10 / 256), avg. gap size = 1.30 (13 / 10) 303 30.04 6.44 8.10 chr3qtel1M 670729 671054 (328946) L1PA7_3end#LINE/L1 232 552 (349) m_b154s551i4 5760 chr3qtel1M 670729 GGAAATAAGAGTGATGC--AAGAAAAT-TATAAAAAGAGAGTCAACACTA 670775 i v -- --i ii - iv i v i--- i v L1PA7_3end#LI 232 GGAAACAACAG--ATGCTGGAGAGGATGTGGAGAAATAGG---AACGCTT 276 chr3qtel1M 670776 ATACATTGTTGATGG-AGTGGTGAACTGATTCAACCACTCTGGAGAACAA 670824 v i i - - i i ii i v ii i L1PA7_3end#LI 277 TTACACTGTTGGTGGGAGTG-TAAATTAGTTCAACCATTGTGGAAGACAG 325 chr3qtel1M 670825 T-TGGAACTATGCCCAAAGGGCTATAAAACTGTGTATACTACTTTGATCC 670873 - -- v v iv i- v i iiviv i - i L1PA7_3end#LI 326 TGTGG--CGATTCCTCAAGGA-TCTAGAACCAGAAATACCA-TTTGACCC 371 chr3qtel1M 670874 AGCAGTGATACTACTGGGTCTGTATCCTAAAGA----AAA-CAT------ 670912 i vvi i v i i v i ---- - ------ L1PA7_3end#LI 372 AGCAATCCCATTACTGGGTATATACCCAAAGGATTATAAATCATTCTACT 421 chr3qtel1M 670913 -TAAAGAGGGGAAAGGACCCACATGTACAAAAATGTTTGTAGCAGTTCTT 670961 - ------------ i viv i v i iv v L1PA7_3end#LI 422 ATAAAGA------------CACATGCACACGTATGTTTATTGCGGCACTG 459 chr3qtel1M 670962 TTTGTGGTGGCAACGAATTGGAAATTGGGTAGATGCTCATCAATTGGGGA 671011 iiiii i v v vivivvi i i ---- L1PA7_3end#LI 460 TTCACAATAGCAAAGACTTGGAACCAACCCAAATGCCCATCAAT----GA 505 chr3qtel1M 671012 AAGGCTGAATAAGT----TATGGTATATTAAAGTAATGGAATATTAT 671054 v i i iv---- i i i vv viiv i L1PA7_3end#LI 506 TAGACTGGATAAAGAAAATGTGGCACATATACACCATGGAATACTAT 552 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 38.14 CpG sites = 57, Kimura (unadjusted) = 39.88 Transitions / transversions = 1.73 (57/33) Gap_init rate = 0.11 (35 / 325), avg. gap size = 1.34 (47 / 35) 595 28.79 1.87 5.52 chr3qtel1M 670770 671144 (328856) L1ME3G_3end#LINE/L1 267 628 (296) m_b154s551i6 5760 chr3qtel1M 670770 ACACTAATACATTGTTGATGG-AGTGGTGAACTGATTCAACCACTCTGGA 670818 v v i i i - - i i i v i ?i i L1ME3G_3end#L 267 ACTCTCATACACTGCTGGTGGGAGTG-TAAATTGGTACAGCCNTTTTGGA 315 chr3qtel1M 670819 GAACAATT-GGAACTATGC-CCAAAGGGCTATAAAACTGTGTATACTACT 670866 ii - v v vi-ii i--- v - i i i- L1ME3G_3end#L 316 GGGCAATTTGGCAGTATCTATTAAAA---TTTAAAA-TGCGCATACC-CT 360 chr3qtel1M 670867 TTGATCCAGCAGTGATACTACTGGGTCTGTATCCTAAAGAAA-ACATTAA 670915 i i vvi v ? ?v v ? - - iiv L1ME3G_3end#L 361 TTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAGAAATAC-TCGC 409 chr3qtel1M 670916 AGAGGGG--AAAGGACCCACATGTACAAAAATGTTTGTAGCAGTTCTTTT 670963 v v v --v --?i ii ii v ivi v L1ME3G_3end#L 410 ACATGTGCACAAGGA--NGCATGTACAAGGATGTTCATTGCAGCATTGTT 457 chr3qtel1M 670964 TGTGGTGGCAACGAATTGGAAATTGGGTAGATGCTCATCAATTGGGGAAA 671013 ii i i vi ivivv i ii v v L1ME3G_3end#L 458 TGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCAATAGGGGAAT 507 chr3qtel1M 671014 GGCTGAATAAGTTATGGTATATTAAAGTAATGGAATATTATTGTTCTATT 671063 i i i iv viiv i vvvv ?i L1ME3G_3end#L 508 GGTTAAATAAATTATGGTATATCCATACTATGGAATACTATGCAGCNGTT 557 chr3qtel1M 671064 AGAAAAAAAAAAAAGATAAACCGGCTGATTTTAGAAAGGTCTGGAAAGAT 671113 --- i vi i i i vi----- v iv vv iiv L1ME3G_3end#L 558 ---AAAAAGAATGAGGTAGATCTA-----TATGTACTGACATGGAAAGAT 599 chr3qtel1M 671114 TTCCATGA-ATTTCCATGCTGAGTGAAACAAG 671144 i v - v --- i v L1ME3G_3end#L 600 CTCCAAGACATAT---TGTTGAGTGAAAAAAG 628 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 36.54 CpG sites = 59, Kimura (unadjusted) = 38.00 Transitions / transversions = 1.37 (59/43) Gap_init rate = 0.07 (26 / 374), avg. gap size = 1.04 (27 / 26) 785 29.78 1.05 1.05 chr3qtel1M 670770 671054 (328946) L1ME4c_3end#LINE/L1 271 555 (275) m_b154s551i5 5760 chr3qtel1M 670770 ACACTAATACATTGTTGATGGAGTGGTGAACTGATTCAACCACTCTGGAG 670819 ? v i i vi?v i i i v vi i i L1ME4c_3end#L 271 ACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAA 320 chr3qtel1M 670820 AACAATT-GGAACTATGCCCAAAGGGCTATAAAACTGTGTATACTACTTT 670868 i - v v i iviv i i v vi i- L1ME4c_3end#L 321 AGCAATTTGGCAATACGTATCAAGAGCCATAAAAATGTTCATACC-CTTT 369 chr3qtel1M 670869 GATCCAGCAGTGATACTACTGGGTCTGTATCCTAAAGAAAACATT--AAA 670916 i i i vvi v vv v i vv -- L1ME4c_3end#L 370 GACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAA 419 chr3qtel1M 670917 GAGGGGAAAGGACCCACATGTACAAAAATGTTTGTAGCAGTTCTTTTTGT 670966 i i i -- i i i i i ii v ivi v i L1ME4c_3end#L 420 GAAGGAAAAAG--CTATATGCACGAAGATGTTCATTGCAGCGTTATTTAT 467 chr3qtel1M 670967 GGTGGCAACGAATTGGAAATTGGGTAGATGCTCATCAATTGGGGAAAGGC 671016 ii i i vi ivivv i ii v v v i L1ME4c_3end#L 468 AATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAATGGT 517 chr3qtel1M 671017 TGAATAAGTTATGGTATATTAAAGTAATGGAATATTAT 671054 i i i i i? vvii L1ME4c_3end#L 518 TAAGTAAATTATGGTACATCNACTCGATGGAATATTAT 555 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 36.91 CpG sites = 53, Kimura (unadjusted) = 40.05 Transitions / transversions = 1.71 (53/31) Gap_init rate = 0.02 (5 / 284), avg. gap size = 1.20 (6 / 5) 15 10.11 6.25 0.00 chr3qtel1M 673082 673113 (326887) (TTG)n#Simple_repeat 1 34 (0) m_b154s252i8 5761 chr3qtel1M 673082 TTGTTGTTGTT-TTCTTGTT-TTGTGTTTGTTGT 673113 - v - vv (TTG)n#Simple 1 TTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGT 34 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.06 (2 / 31), avg. gap size = 1.00 (2 / 2) 15 14.23 6.00 3.92 chr3qtel1M 673081 673130 (326870) (TTTGTA)n#Simple_repeat 1 51 (0) m_b154s252i7 5762 chr3qtel1M 673081 TTTGTTGTTGTTTTCTTGT-TTTGTGTTTGT-TGTGTATCT-TATTTGTA 673127 vv - v - - i - v i - (TTTGTA)n#Sim 1 TTTGTATTTG-TAT-TTGTATTTGTATTTGTATTTGTATTTGTATTTGTA 48 chr3qtel1M 673128 TTT 673130 (TTTGTA)n#Sim 49 TTT 51 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.10 (5 / 49), avg. gap size = 1.00 (5 / 5) 19 0.00 0.00 0.00 chr3qtel1M 673402 673422 (326578) (T)n#Simple_repeat 1 21 (0) m_b154s252i9 5763 chr3qtel1M 673402 TTTTTTTTTTTTTTTTTTTTT 673422 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTT 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 20 13.87 0.00 0.00 chr3qtel1M 673459 673490 (326510) (T)n#Simple_repeat 1 32 (0) m_b154s252i10 5763 chr3qtel1M 673459 TTTTTATTTTTTTTTATTTTTTATTTTTTATT 673490 v v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 32 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 13 4.70 0.00 4.35 chr3qtel1M 673575 673598 (326402) (CCCT)n#Simple_repeat 1 23 (0) m_b154s252i11 5764 chr3qtel1M 673575 CCCTCCCTCCCTCCATCCCCTCCC 673598 v - (CCCT)n#Simpl 1 CCCTCCCTCCCTCCCT-CCCTCCC 23 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 231 31.71 1.59 2.40 chr3qtel1M 674743 674868 (325132) C L1ME3Cz_3end#LINE/L1 (429) 568 444 m_b154s551i7 5765 chr3qtel1M 674743 TCATTTTTTTAAAATAGTATAATAATACTC--TTCTACAATCATATACCA 674790 iv v v iv i - i i -- v ii -- C L1ME3Cz_3end# 568 TCATTCATTTTAACTGCTGTA-TAGTATTCCATTGTATGA--ATATACCA 522 chr3qtel1M 674791 TAGTTGGTTTAGCCATTCCTCAATTGGTGGGCATCCCTTTGATTTCTGAT 674840 i i vi v i v i i iivvv vi ii C L1ME3Cz_3end# 521 CAATTTATTTATCCATTCCCCTATTGATGGACATTTAGGTTGTTTCCAAT 472 chr3qtel1M 674841 TCTTAGCCACCACAAAAAGAGCTGCTAT 674868 i v i ii v iv v C L1ME3Cz_3end# 471 TTTTCGCTATTACAAACAATGCTGCAAT 444 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 42.60 CpG sites = 23, Kimura (unadjusted) = 42.60 Transitions / transversions = 1.44 (23/16) Gap_init rate = 0.03 (4 / 125), avg. gap size = 1.25 (5 / 4) 247 31.07 2.83 2.83 chr3qtel1M 674763 674868 (325132) C L1MC3_3end#LINE/L1 (1979) 553 448 m_b154s551i8 5765 chr3qtel1M 674763 AATAATACTCTTCTACAATCATATACCATAGTTGGTTTAGCCATTCCTCA 674812 i ivi ii vvv i i v v vi v C L1MC3_3end#LI 553 AATAATATTCCATTGTATGGATGTACCACAGTTTGTTTATCCATTCACCT 504 chr3qtel1M 674813 ATTGGTGGGCATCCCTTTGATT---TCTGATTCTTAGCCACCACAAAAAG 674859 iv i --- i --- iii i i v ii ii v i C L1MC3_3end#LI 503 ATTGAAGGACATC---TTGGTTGCTTCCAGTTTTTGGCGATTATGAATAA 457 chr3qtel1M 674860 AGCTGCTAT 674868 C L1MC3_3end#LI 456 AGCTGCTAT 448 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 42.14 CpG sites = 21, Kimura (unadjusted) = 42.14 Transitions / transversions = 1.91 (21/11) Gap_init rate = 0.04 (4 / 105), avg. gap size = 1.50 (6 / 4) 284 31.40 0.00 0.00 chr3qtel1M 674783 674868 (325132) C L1ME1_3end#LINE/L1 (393) 533 448 m_b154s551i9 5765 chr3qtel1M 674783 ATATACCATAGTTGGTTTAGCCATTCCTCAATTGGTGGGCATCCCTTTGA 674832 i i v v vi ?i i i iivvv vi C L1ME1_3end#LI 533 ATATACCACAATTTGTTTATCCATTCACCNGTTGATGGACATTTGGGTTG 484 chr3qtel1M 674833 TTTCTGATTCTTAGCCACCACAAAAAGAGCTGCTAT 674868 iii i i i ii i v i C L1ME1_3end#LI 483 TTTCCAGTTTTTGGCTATTACGAATAAAGCTGCTAT 448 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 41.91 CpG sites = 19, Kimura (unadjusted) = 44.17 Transitions / transversions = 2.38 (19/8) Gap_init rate = 0.00 (0 / 85), avg. gap size = 0.0 (0 / 0) 558 32.56 3.24 0.45 chr3qtel1M 676575 676790 (323210) C MIRc#SINE/MIR (0) 268 47 m_b154s601i1 5766 chr3qtel1M 676575 AAAAATAATAAGAACTAGCATTTACATGGTGATGTAATGCTTGCAAAGCA 676624 v v?v vi ii i iiv v vv i i i C MIRc#SINE/MIR 268 AATAATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCG 219 chr3qtel1M 676625 AATGGGACAAATAATGTCTTATTTGATCTTCTCATTGACCCTGGGAAGCA 676674 v- vvv v i v i i i v vii v i i C MIRc#SINE/MIR 218 C-TTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTA 170 chr3qtel1M 676675 GT---GAC---TAT-ACAAGCTCCATTGTGCAGATGAGAAACCTTATGCA 676717 v--- i --- - iv v i v i i v v v v C MIRc#SINE/MIR 169 GGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCT 120 chr3qtel1M 676718 GGAATAGATTAAGTGACTTGCCCAGGGTAACTCAGCCAGTAAACATCAGA 676767 vii v i i v v i iiiv C MIRc#SINE/MIR 119 CAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGA 70 chr3qtel1M 676768 GCCCAAATTTCAACTAGGGTTTT 676790 vii i iv ivi i C MIRc#SINE/MIR 69 GCCGGGACTCGAACCCAGGTCTT 47 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 42.22 CpG sites = 37, Kimura (unadjusted) = 43.88 Transitions / transversions = 1.12 (37/33) Gap_init rate = 0.02 (4 / 215), avg. gap size = 2.00 (8 / 4) 187 27.80 0.00 6.15 chr3qtel1M 676762 676830 (323170) C X24_LINE#LINE/L2 (110) 204 140 m_b154s601i2 5767 chr3qtel1M 676762 ATCAGAGCCCAAATTTCAACTAGGGTTTTATGGATGGAGGGACAACCTAT 676811 i i --i vv i i vi i v- viv C X24_LINE#LINE 204 ACCAGGGCCCAAA--CCATATAGGGCTTTATAGATTAAAGT-CAACACCT 158 chr3qtel1M 676812 TCATTTGCCACCCGGCAGC 676830 v v - i v C X24_LINE#LINE 157 TGAATTG-CACTCGGAAGC 140 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 34.95 CpG sites = 9, Kimura (unadjusted) = 34.95 Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.06 (4 / 68), avg. gap size = 1.00 (4 / 4) 279 33.29 8.29 1.83 chr3qtel1M 677703 677907 (322093) L2a_3end#LINE/L2 289 506 (11) m_b154s601i3 5768 chr3qtel1M 677703 CTTCCAGTCCCCTTTACCCT----TCCTTCTCTTGACTAGCTCCCATCG- 677747 i vi i ---- vi i iv - v ii i- L2a_3end#LINE 289 CTCCCTATCCCCCTTACCCTGCTTTATTTTTCTCCA-TAGCACTTATCAC 337 chr3qtel1M 677748 -ATCCTGTAGACAGCAGAGTTCACATAATTGA--GCCCAT-GT-TATCTC 677792 - ivii v vii v v i v v iv-- iii - - i L2a_3end#LINE 338 CATCTGACATACTATATATTTTACTTATTTATTTGTTTATTGTCTGTCTC 387 chr3qtel1M 677793 TCCCAA-GAGCCTGTGAGCTCCTTGAGGGCAGGGAAA---GCCCCTTCCT 677838 i v -v vv i v vv--- i iv iiv L2a_3end#LINE 388 CCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTCTGTTTTG 437 chr3qtel1M 677839 CTC-CTTCT--ATCCCTGGGGCTTGGTACCAAAGGGATGGGTACACAGGA 677885 i - v -- ii v i i v --- v viv i i v L2a_3end#LINE 438 TTCACTGCTGTATCCCCAGCGCCTAGAAC---AGTGCCTGGCACATAGTA 484 chr3qtel1M 677886 GGCATTTAATAAATGCTTGTTG 677907 ii i ii L2a_3end#LINE 485 GGCGCTCAATAAATATTTGTTG 506 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 44.70 CpG sites = 39, Kimura (unadjusted) = 45.64 Transitions / transversions = 1.39 (39/28) Gap_init rate = 0.07 (14 / 204), avg. gap size = 1.50 (21 / 14) 356 29.89 3.52 5.76 chr3qtel1M 677766 677907 (322093) L2d2_3end#LINE/L2 406 544 (11) m_b154s601i4 5768 chr3qtel1M 677766 TTCACATAATTGAGCCCATGTTATCTCTCCCAAGAGCCTGTGAGCTCCTT 677815 i iv iv i ---- i i v vv vi i L2d2_3end#LIN 406 TTCACGTGTTTATGTC----TTGTCTCCCCAACTAGATTGTAAGCTCCTT 451 chr3qtel1M 677816 GAGGGCAGGGA--AAGCCCCTTCCTCTCCTTCTATCCC---TGGGGCTTG 677860 -- v i iiv v - i v ---ii v i i L2d2_3end#LIN 452 GAGGGCAGGGACCATGTCTTATACT-TCTTTGTATCCCCCACAGCGCCTA 500 chr3qtel1M 677861 GTACCAAAGGGATGGGTACACAGGAGGCATTTAATAAATGCTTGTTG 677907 i --- v vivv i v ii i ii L2d2_3end#LIN 501 GCAC---AGTGCCTTGCACACAGTAGGCGCTCAATAAATATTTGTTG 544 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 36.78 CpG sites = 24, Kimura (unadjusted) = 39.29 Transitions / transversions = 1.50 (24/16) Gap_init rate = 0.07 (10 / 141), avg. gap size = 1.30 (13 / 10) 430 25.19 4.76 2.33 chr3qtel1M 677782 677907 (322093) L2b_3end#LINE/L2 327 455 (11) m_b154s601i5 5768 chr3qtel1M 677782 CATGT-TATCTCTCCCAAGAGCCTGTGAGCTCCTTGAGGGCAGGGA--AA 677828 - i i vv v v --i? L2b_3end#LINE 327 CATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGN 376 chr3qtel1M 677829 GCC--CCTTCCTCTCC-TTCTATCCCTGGGGCTTGGTACCAAAGGGATGG 677875 i --i vi v -i v ii v i i i --- ? viv L2b_3end#LINE 377 GTCTGTCTTGTTCACCGCTGTATCCCCAGCGCCTAGCAC---AGNGCCTG 423 chr3qtel1M 677876 GTACACAGGAGGCATTTAATAAATGCTTGTTG 677907 i v ii i i ii L2b_3end#LINE 424 GCACACAGTAGGCGCTCAGTAAATATTTGTTG 455 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 29.87 CpG sites = 20, Kimura (unadjusted) = 32.38 Transitions / transversions = 1.82 (20/11) Gap_init rate = 0.06 (7 / 125), avg. gap size = 1.29 (9 / 7) 393 24.13 4.27 0.83 chr3qtel1M 678050 678166 (321834) C MIRc#SINE/MIR (117) 151 31 m_b154s601i6 5769 chr3qtel1M 678050 ATCCTTCATTTTACAGATGAAGAGCCTGAGGTTC--AGAGGTTCAGCGAG 678097 i- i iv i -- v i v C MIRc#SINE/MIR 151 ATCCC-CATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGAC 103 chr3qtel1M 678098 GTGCCCAGGATCTCACTGCCA-CAAGAGCCTGAAAAGGGATTCCAAGCCA 678146 v i i v v i -i v v v ivv i v v C MIRc#SINE/MIR 102 TTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCA 53 chr3qtel1M 678147 GTTC-TCCTG-CCCCAGGCCCA 678166 v - - i i i C MIRc#SINE/MIR 52 GGTCTTCCTGACTCCAAGTCCA 31 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 29.38 CpG sites = 14, Kimura (unadjusted) = 29.38 Transitions / transversions = 1.00 (14/14) Gap_init rate = 0.04 (5 / 116), avg. gap size = 1.20 (6 / 5) 584 30.10 1.41 4.85 chr3qtel1M 678340 678552 (321448) MIRb#SINE/MIR 14 219 (49) m_b154s601i8 5770 chr3qtel1M 678340 TAGGACAGTAGAGAG-TCCTGGGCTT-GGAGTCAGGAAATGCAGAGTTCC 678387 i vi i i -v vi - iv ivv v i v MIRb#SINE/MIR 14 TGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCG 63 chr3qtel1M 678388 AGTCTGGCCCCAGATACTTG-GGGCCATATGCTCATGGGGAAGTCAGTTA 678436 i iv v i v vi i-vi ii i vi v v i v MIRb#SINE/MIR 64 AATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTA 113 chr3qtel1M 678437 ATCTCTCTTTGCCTCAGTTTCCTCAACTATCAAATGGGGATAATGATGGC 678486 i vv v i v i --- MIRb#SINE/MIR 114 ACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAAT--- 160 chr3qtel1M 678487 ACCCACACCAAAAGGTGGTTGTGAGGGTCAAGGGAGACTATGGCTCACTA 678536 i vi iv i v i i iv iv ------i MIRb#SINE/MIR 161 ACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATG------CA 204 chr3qtel1M 678537 TGTATATATACTTAGC 678552 - viii MIRb#SINE/MIR 205 TGTA-AAGCGCTTAGC 219 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 36.76 CpG sites = 34, Kimura (unadjusted) = 39.29 Transitions / transversions = 1.26 (34/27) Gap_init rate = 0.06 (13 / 212), avg. gap size = 1.00 (13 / 13) 676 26.98 4.76 0.00 chr3qtel1M 678340 678528 (321472) MIRc#SINE/MIR 11 208 (60) m_b154s601i7 5770 chr3qtel1M 678340 TAGGACAGTAGA--GAGTCCTGGGCTTGGAGTCAGGAAATGCAGAGTTCC 678387 i vi i -- iv i ivv v i v MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr3qtel1M 678388 AGTCTGGCCCCAGATACTTG-GGGCCATATGCTCATGGGGAAGTCAGTTA 678436 iv v i v vi i-vi ii i vi v v v MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTA 110 chr3qtel1M 678437 ATCTCTCTTTGCCTCAGTTTCCTCAACTATCAAATGGGGATAATGATG-- 678484 i vv v i v i i-- MIRc#SINE/MIR 111 ACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACC 160 chr3qtel1M 678485 -GC---ACCCACACCAAAAGGTGGTTGTGAGGGTCAAGGGAGACTATG 678528 - ---i i vi v i v i iv iv MIRc#SINE/MIR 161 TGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATG 208 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 33.94 CpG sites = 27, Kimura (unadjusted) = 33.94 Transitions / transversions = 1.12 (27/24) Gap_init rate = 0.03 (5 / 188), avg. gap size = 1.80 (9 / 5) 273 31.77 3.87 4.55 chr3qtel1M 678657 678811 (321189) L3#LINE/CR1 3866 4019 (80) m_b154s601i9 5771 chr3qtel1M 678657 CAGTGAGCTACAGATTTATCCTTTTTTTAATGAAAAGAACATTCTAAAGA 678706 v --i vvv ivv v v -- v vi L3#LINE/CR1 3866 CAGGGAG--GCAGATTTCGGCTCAATATAAGGAA--GAACTTTCTAACAA 3911 chr3qtel1M 678707 -CAAAACAGTTTCCCAAGAGCAAGAAGG---GCCTTAGGAAGAAGGGGGT 678752 - i i v --- i iiiii v --- ii? i v v i i L3#LINE/CR1 3912 TCAGAGCTGT---CCAAAAATGGAATGGGCTGCCTCGNGAGGTAGTGAGC 3958 chr3qtel1M 678753 TCCCT-TCATTGCACAT-TGCAAAGAGAAGCTGCATGATCAATTTTCAGA 678800 i- i v vi - v iv i v i v v i L3#LINE/CR1 3959 TCCCCGTCACTGGAGGTGTTCAAGCAGAGGCTGGATGACCACTTGTCAGG 4008 chr3qtel1M 678801 GATTTTGCAAA 678811 v i i L3#LINE/CR1 4009 GATGTTGTAGA 4019 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 40.07 CpG sites = 25, Kimura (unadjusted) = 42.54 Transitions / transversions = 1.14 (25/22) Gap_init rate = 0.07 (11 / 154), avg. gap size = 1.18 (13 / 11) 256 31.86 5.63 2.74 chr3qtel1M 679171 679312 (320688) C MIR3#SINE/MIR (31) 177 32 m_b154s601i10 5772 chr3qtel1M 679171 AAGGCACATTTCAGATTCAATTTGGTCCAATACTCATCTATTTACAGA-- 679218 v v vv i-- i i iv i - vv -- C MIR3#SINE/MIR 177 AAGGGACCTTAGAGATC--ATCTAGTCCAACCCCC-TCATTTTACAGATG 131 chr3qtel1M 679219 AGGGAACTGAAGCATGGAAA-----AGGGATCTGCTCAAAGGTCAGACCT 679263 i i vii i ----- v ii i - v vv C MIR3#SINE/MIR 130 AGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAA-GGTCACACAG 82 chr3qtel1M 679264 TTC-TAAGTGTCAGAGCCAACACTTTAATTCTAGTCACATCAAGTCCAGT 679312 i?v- v v iiv vv ii vi v v v vvi C MIR3#SINE/MIR 81 CNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGTCTCCTGACTCCCAGT 32 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 41.04 CpG sites = 20, Kimura (unadjusted) = 42.26 Transitions / transversions = 0.83 (20/24) Gap_init rate = 0.05 (7 / 141), avg. gap size = 1.71 (12 / 7) 276 26.70 13.73 0.87 chr3qtel1M 679211 679312 (320688) C MIRc#SINE/MIR (125) 143 29 m_b154s601i11 5772 chr3qtel1M 679211 TTTACAGA--AGGGAACTGAAGCATGGAAA-----AGGGATCTGCTCAAA 679253 -- i i vii i ----- v ii i - C MIRc#SINE/MIR 143 TTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAA- 95 chr3qtel1M 679254 GGTCAGACCTTTC-TAAGTGTCAGAGCCAACACTTTAATTCTAGTC---- 679298 v vvi v- v iiv iv ii vi ---- C MIRc#SINE/MIR 94 GGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCC 45 chr3qtel1M 679299 --ACATCAAGTCCAGT 679312 -- vi C MIRc#SINE/MIR 44 TGACTCCAAGTCCAGT 29 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 30.86 CpG sites = 16, Kimura (unadjusted) = 33.88 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.06 (6 / 101), avg. gap size = 2.50 (15 / 6) 12 15.85 0.00 3.45 chr3qtel1M 680971 681000 (319000) (GGAGG)n#Simple_repeat 1 29 (0) m_b154s252i12 5773 chr3qtel1M 680971 GGAGGGAGGGGGCTGGGAGGGGAGTGGGAG 681000 ii vv - (GGAGG)n#Simp 1 GGAGGGGAGGGGAGGGGAGGGGAG-GGGAG 29 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 264 26.21 7.77 0.00 chr3qtel1M 681666 681768 (318232) C L1MD1_3end#LINE/L1 (436) 553 443 m_b154s551i10 5774 chr3qtel1M 681666 AATAATATTCCCTAATATTCCTGTACCACAGTTTATTCCGCCATTCTCC- 681714 i i v ii vvv i ivi v - C L1MD1_3end#LI 553 AGTAGTATTCCATGGTATGGATGTACCACAGTTTGTTTAACCATTCACCC 504 chr3qtel1M 681715 -----AGG-CATCCGCGCACTTTCCA-TTTCTGGCCACTACAAAGAGACC 681757 ----- - i v ivv - i i i i v i v C L1MD1_3end#LI 503 GTTGAAGGACATCTGGGTTGTTTCCAGTTTTTGGCTATTACGAATAAAGC 454 chr3qtel1M 681758 TGCCACAAACA 681768 i i C L1MD1_3end#LI 453 TGCTATAAACA 443 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 31.55 CpG sites = 16, Kimura (unadjusted) = 33.03 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.04 (4 / 102), avg. gap size = 2.00 (8 / 4) 299 34.38 7.64 1.81 chr3qtel1M 682479 682635 (317365) C MIR3#SINE/MIR (21) 187 22 m_b154s601i12 5775 chr3qtel1M 682479 TCAGGGCGGGAAGGGATC------ACCCAC-AGTCCAATCTC--CATTTT 682519 i v i ------ i vv - i i -- C MIR3#SINE/MIR 187 TCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTT 138 chr3qtel1M 682520 AGAGATGACTGAATGGAGAGGCACAGAGAT---GTTGCTCATCCAGAGTT 682566 v vvi iv ivv v i --- vi iii ii i C MIR3#SINE/MIR 137 ACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTC 88 chr3qtel1M 682567 ATAATATAGTAAGAGAGGATCTGAGGCTGGATTTGAACCCAAGGCTTCTC 682616 --- i i i? vv viv v v v i v i v i v C MIR3#SINE/MIR 87 ---ACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGTCTCCTG 41 chr3qtel1M 682617 AACTCTAAACCTTGTTCCC 682635 vii i iv v i i C MIR3#SINE/MIR 40 ACTCCCAGTCCGTGCTCTC 22 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 47.80 CpG sites = 29, Kimura (unadjusted) = 47.80 Transitions / transversions = 1.21 (29/24) Gap_init rate = 0.04 (7 / 156), avg. gap size = 2.14 (15 / 7) 312 30.77 4.88 4.88 chr3qtel1M 682509 682631 (317369) C MIRc#SINE/MIR (117) 151 29 m_b154s601i13 5775 chr3qtel1M 682509 ATCTCCATTTTAGAGATGACTGAATGGAGAGGCACAGAGATGTT-----G 682553 i v vvi iv-- v v -----i C MIRc#SINE/MIR 151 ATCCCCATTTTACAGATGAGGAAACT--GAGGCTCAGAGAGGTTAAGTGA 104 chr3qtel1M 682554 CTCATCCAGAGTTATA-ATATAGTAAGAGAGGATCTGAGGCTGGATTTGA 682602 iii ii i i - vv v i---- v v v i i C MIRc#SINE/MIR 103 CTTGCCCAAGGTCACACAGCTAGTAAGTGG----CAGAGCCGGGACTCGA 58 chr3qtel1M 682603 ACCCAAGGCTTCTCAACTCTAAACCTTGT 682631 i v iii i ii iv C MIRc#SINE/MIR 57 ACCCAGGTCTTCCTGACTCCAAGTCCAGT 29 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 39.57 CpG sites = 22, Kimura (unadjusted) = 41.07 Transitions / transversions = 1.57 (22/14) Gap_init rate = 0.07 (8 / 122), avg. gap size = 1.50 (12 / 8) 547 18.97 5.04 8.96 chr3qtel1M 682736 682874 (317126) MIRc#SINE/MIR 2 135 (133) m_b154s601i14 5776 chr3qtel1M 682736 GGGGCAGCGAGGTGGTGCAGTGGATAGAGCACCAGTCCTGAAGTAAGGAG 682785 i i --- v ii v i i v i MIRc#SINE/MIR 2 GAGGCAGTG---TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr3qtel1M 682786 AACATGAGTTCAAATCC--AATCTAGACACTTAATAGCTTCCTAGTTGTG 682833 i v i i i --iv - v -------- i MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCT-GCCACTTA--------CTAGCTGTG 89 chr3qtel1M 682834 TGACCCTGGGCAAGTCACTTAACCT-----AACCCCAATTACCTCA 682874 i ----- i i i v MIRc#SINE/MIR 90 TGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCA 135 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 21.38 CpG sites = 17, Kimura (unadjusted) = 22.41 Transitions / transversions = 2.43 (17/7) Gap_init rate = 0.10 (14 / 138), avg. gap size = 1.36 (19 / 14) 436 29.53 12.55 5.08 chr3qtel1M 682892 683130 (316870) C MIRc#SINE/MIR (3) 265 10 m_b154s601i15 5777 chr3qtel1M 682892 AATCATAAGAGCTGGTATGTACATAGTGACTTAATGATTGCAAAGTACTT 682941 v v?v vii v ii iivi vv v i ii C MIRc#SINE/MIR 265 AATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCGCTT 216 chr3qtel1M 682942 G-ACAAATAATGTCTCATTTGAACCTTTCA-------TGT---------- 682973 v- v i v i v iv ------- ---------- C MIRc#SINE/MIR 215 TCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCA 166 chr3qtel1M 682974 -------TAT-ATTAGCTC-ATTCTACAGATGGGGAAACTGAGGAAGAAA 683014 ------- - v i - i i vvv i C MIRc#SINE/MIR 165 GGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGA 116 chr3qtel1M 683015 TAGGTTACATGACTTATGTAGCTTGTGTGGCCAGGGTCACA--GCTGGTA 683062 v vi ----- -------- i -- i C MIRc#SINE/MIR 115 GAGGTTAAGTGACTT-----GC--------CCAAGGTCACACAGCTAGTA 79 chr3qtel1M 683063 GGCAGCAGAACCTAAATTTGAACTTAGGTCTTATGGA-TTGAGGGACAGT 683111 i ii i vii i i ii viv - iv i vv C MIRc#SINE/MIR 78 AGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGT 29 chr3qtel1M 683112 CCTCTATCTATTCTGTCAC 683130 v v i i viii C MIRc#SINE/MIR 28 GCTCTTTCCACTGCACCAC 10 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 37.32 CpG sites = 38, Kimura (unadjusted) = 38.88 Transitions / transversions = 1.31 (38/29) Gap_init rate = 0.09 (21 / 238), avg. gap size = 2.05 (43 / 21) 694 27.00 5.63 3.83 chr3qtel1M 684553 684783 (315217) MIRb#SINE/MIR 4 238 (30) m_b154s601i16 5778 chr3qtel1M 684553 AGAGGAAGCTAGGTGGTCCAGT----AGACCA---ATGTTAGATATCAGA 684595 i v --- v ---- v ---iiv i -i MIRb#SINE/MIR 4 AGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGA-GTCAGA 49 chr3qtel1M 684596 CAGACCTGAGTTCAAATTCAGCCTCAAACACTGACTAGCTCTAGGACATT 684645 i i i v v viv v v iv v MIRb#SINE/MIR 50 CAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTT 99 chr3qtel1M 684646 GGGAAAACCACAGTACTTCTTTG--CCTCAGTTT----ATCTGAAAAGCA 684689 v iii vvv i i -- ---- v iii MIRb#SINE/MIR 100 GGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATG 149 chr3qtel1M 684690 GAGCTAACAAGAACATCTATTTCCCAGAGTTGTTGAGAGGATCAAACGAG 684739 i v i ---i i ii v i v i i MIRb#SINE/MIR 150 GGGATAATAA---TACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAG 196 chr3qtel1M 684740 ACGATATTTGTAAAACTCTCAGCACACAGTAGGTGCCACATAAT 684783 ii iiv i v i -- ivv v i MIRb#SINE/MIR 197 ATAATGCATGTAAAGCGCTTAG--CACAGTGCCTGGCACATAGT 238 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 33.60 CpG sites = 35, Kimura (unadjusted) = 34.30 Transitions / transversions = 1.40 (35/25) Gap_init rate = 0.06 (13 / 230), avg. gap size = 1.69 (22 / 13) 282 32.97 8.66 7.43 chr3qtel1M 685724 686162 (313838) L2#LINE/L2 1712 2155 (927) m_b154s601i17 5779 chr3qtel1M 685724 TCCCCCCTTGATCACCCTCCATTTACCCACTAATTCTGAATCTCTGTCTA 685773 i ivv -i v ----- ii i --- i v L2#LINE/L2 1712 TCTCCCCTCTCTC-TCCTGCAT-----CATCAATTTT---TCCCTCTCTA 1752 chr3qtel1M 685774 ATAGTTCCTCCCC-TCACTTCACAAATA--CAACCCTGTCTCCACAACGT 685820 v i v v i - vivi i -- vii?v v - v v L2#LINE/L2 1753 CTGGATCATTCCCATCAGCATACAAACATGCTGTNATTTCTCC-CATCTT 1801 chr3qtel1M 685821 ------ATAAAAACTCACTCA-GTCCCTTCCTCCCCATGTAGGT--TGTC 685861 ------ i i v i v- v iv ? v vi v --i i L2#LINE/L2 1802 TAAAAAACAAAAATTCTCCCTTGACCCCACNTCCCCCTCCAGCTACCGCC 1851 chr3qtel1M 685862 CTACAGCTTCCCAGC--CCTTTTCTGGCCAAACAACT----GGAGCTGGC 685905 i i--- i v -- i vii v vv ----i i -- L2#LINE/L2 1852 CCAT---TTCTCTGCTCCCCTTTACAGCAAAACTCCTCGAAAGAGTTG-- 1896 chr3qtel1M 685906 CTCCACA---ACTGTCGCCATCCCTTCCTTTCCTTTTAATTTCTTCAGAA 685952 - i i ---i v ---v i iii v i iiv L2#LINE/L2 1897 -TCTATACTCGCTGTCTCCA---ATTCCTCTCCTCCCATTCTCTCTTGAA 1942 chr3qtel1M 685953 CTCGG--CACTCTGGTTCCCAGCTTCACGATTCAACTGAAAAAGCTCTTT 686000 i iv-- v v i ii iv ii v i v i vv v L2#LINE/L2 1943 CCCACTCCAATCAGGCTTTCGTCCCCACCACTCCACCGAAACTGCTCTTG 1992 chr3qtel1M 686001 TCAGAGTGACCAACGATCTCCAAATCACTAAAACCAAAGACATCTGCTCG 686050 ii v i i vi ii v ------- v i L2#LINE/L2 1993 TCAAGGTCACCAATGACCTCCACGTTGCTAAATCCAA-------TGGTCA 2035 chr3qtel1M 686051 ATCCTCTGCCCTC-TTTT--TTA---TGTC-------TCTGAAACGGTCT 686087 i v i - i -- i--- ? ------- i v i iv L2#LINE/L2 2036 ATTCTCAGTCCTCATCTTACTTGACCTNTCAGCAGCATTTGACACAGTTG 2085 chr3qtel1M 686088 ATCATCCCCTTTTCCTT--AGTCCTCTCTTCTCTTCCCTCTAAGTTTTTG 686135 ii ii i -- iiv i v -------i i iii L2#LINE/L2 2086 ATCACTCCCTCCTTCTTGAAACACTTTCTTCACTT-------GGCTTCCA 2128 chr3qtel1M 686136 AGATGCTACTTTCTCCTGGCACTCCTC 686162 i ii i vi ivi L2#LINE/L2 2129 GGACACCACACTCTCCTGGTTTTCCTC 2155 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 43.68 CpG sites = 84, Kimura (unadjusted) = 46.06 Transitions / transversions = 1.68 (84/50) Gap_init rate = 0.11 (47 / 438), avg. gap size = 1.51 (71 / 47) 277 32.25 9.71 3.67 chr3qtel1M 686829 687034 (312966) L2a_3end#LINE/L2 289 506 (11) m_b154s601i18 5779 chr3qtel1M 686829 CTTCCAGTCCCCTTTACCCT----TCCTTCTCTTGACTGGCTCCCATCG- 686873 i vi i ---- vi i iv - i v ii i- L2a_3end#LINE 289 CTCCCTATCCCCCTTACCCTGCTTTATTTTTCTCCA-TAGCACTTATCAC 337 chr3qtel1M 686874 -ATCCTGTAGACAGCAGAGTTCACATAATTGA--GCCCAT-GT-TATCTC 686918 - ivii v vii v v i v v iv-- iii - - i L2a_3end#LINE 338 CATCTGACATACTATATATTTTACTTATTTATTTGTTTATTGTCTGTCTC 387 chr3qtel1M 686919 TCCC-AGGAGCCTGTGAGCTCCTTGAGGGCAGGGAAAGCCCCTTGCCTCT 686967 i - vv vv i v ---- ii i v L2a_3end#LINE 388 CCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGA----CTTTTGTCTGT 433 chr3qtel1M 686968 CCT--TC-------TATCCCTGGGGCTTGGTACCAAAGGGATGGGTACAC 687008 ii -- ------- ii v i i v --- v viv i i L2a_3end#LINE 434 TTTGTTCACTGCTGTATCCCCAGCGCCTAGAAC---AGTGCCTGGCACAT 480 chr3qtel1M 687009 AGGAGGCATTTAATAAATGCTTGTTG 687034 v ii i ii L2a_3end#LINE 481 AGTAGGCGCTCAATAAATATTTGTTG 506 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 43.24 CpG sites = 40, Kimura (unadjusted) = 44.19 Transitions / transversions = 1.67 (40/24) Gap_init rate = 0.08 (17 / 205), avg. gap size = 1.65 (28 / 17) 354 33.14 2.10 5.04 chr3qtel1M 686892 687034 (312966) L2d2_3end#LINE/L2 406 544 (11) m_b154s601i19 5779 chr3qtel1M 686892 TTCACATAATTGAGCCCATGTTATCTCTCCCAGGAGCCTGTGAGCTCCTT 686941 i iv iv i ---- i i v vv vi i L2d2_3end#LIN 406 TTCACGTGTTTATGTC----TTGTCTCCCCAACTAGATTGTAAGCTCCTT 451 chr3qtel1M 686942 GAGGGCAGGGAAAGCCCCTTGCCTCTCCTTCTATCCC---TGGGGCTTGG 686988 vviivi iivii i v ---ii v i i L2d2_3end#LIN 452 GAGGGCAGGGACCATGTCTTATACTTCTTTGTATCCCCCACAGCGCCTAG 501 chr3qtel1M 686989 TACCAAAGGGATGGGTACACAGGAGGCATTTAATAAATGCTTGTTG 687034 i --- v vivv i v ii i ii L2d2_3end#LIN 502 CAC---AGTGCCTTGCACACAGTAGGCGCTCAATAAATATTTGTTG 544 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 42.89 CpG sites = 28, Kimura (unadjusted) = 45.67 Transitions / transversions = 1.65 (28/17) Gap_init rate = 0.06 (8 / 142), avg. gap size = 1.25 (10 / 8) 426 27.41 3.94 2.33 chr3qtel1M 686908 687034 (312966) L2b_3end#LINE/L2 327 455 (11) m_b154s601i20 5779 chr3qtel1M 686908 CATGT-TATCTCTCCCAGGAGCCTGTGAGCTCCTTGAGGGCAGGGA--AA 686954 - i i vv v v --i? L2b_3end#LINE 327 CATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGN 376 chr3qtel1M 686955 GCC--CCTTGCCTCTCCTTCTATCCCTGGGGCTTGGTACCAAAGGGATGG 687002 i --i iiivi vi v ii v i i i --- ? viv L2b_3end#LINE 377 GTCTGTCTTGTTCACCGCTGTATCCCCAGCGCCTAGCAC---AGNGCCTG 423 chr3qtel1M 687003 GTACACAGGAGGCATTTAATAAATGCTTGTTG 687034 i v ii i i ii L2b_3end#LINE 424 GCACACAGTAGGCGCTCAGTAAATATTTGTTG 455 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 33.76 CpG sites = 23, Kimura (unadjusted) = 36.45 Transitions / transversions = 2.09 (23/11) Gap_init rate = 0.05 (6 / 126), avg. gap size = 1.33 (8 / 6) 412 23.27 4.27 0.83 chr3qtel1M 687177 687293 (312707) C MIRc#SINE/MIR (117) 151 31 m_b154s601i21 5780 chr3qtel1M 687177 ATCCTTCATTTTACAGATGAAGAGCCTGAGGTTC--AGAGGTTCAGCGAG 687224 i- i iv i -- v i v C MIRc#SINE/MIR 151 ATCCC-CATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGAC 103 chr3qtel1M 687225 GTGCCCAGGATCTCACTGCCA-CAAGAGCCTGAAAAGGGATTCCAAGCCA 687273 v i i v v i -i v v v ivv i v v C MIRc#SINE/MIR 102 TTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCA 53 chr3qtel1M 687274 GTTC-TCCTG-CTCCAGGCCCA 687293 v - - i i C MIRc#SINE/MIR 52 GGTCTTCCTGACTCCAAGTCCA 31 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 28.05 CpG sites = 13, Kimura (unadjusted) = 28.05 Transitions / transversions = 0.93 (13/14) Gap_init rate = 0.04 (5 / 116), avg. gap size = 1.20 (6 / 5) 628 27.13 5.32 0.00 chr3qtel1M 687467 687654 (312346) MIRc#SINE/MIR 11 208 (60) m_b154s601i22 5781 chr3qtel1M 687467 TGGGACAGCAGA--GAGCCCTGGGCT-GGAGTCAGGAAATGCAGAGTTCC 687513 vi ii -- v i - ivv v i v MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr3qtel1M 687514 AGTCTGGCCCCAGATACTTG-GGGCCATATGCTCACGGGGAAGTCAGTTA 687562 iv v i v vi i-vi ii i vi vi v v MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTA 110 chr3qtel1M 687563 ATCTCTCTTTGCCTCAGTTTCCTCAACTATCAAATGGGGATAATGATG-- 687610 i vv v i v i i-- MIRc#SINE/MIR 111 ACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACC 160 chr3qtel1M 687611 -GC---ACCCACACCAAAAGGTGGTTGTGAGGGTCAAGGGAGACTATG 687654 - ---i i vi v i v i iv iv MIRc#SINE/MIR 161 TGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATG 208 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 34.17 CpG sites = 27, Kimura (unadjusted) = 34.17 Transitions / transversions = 1.12 (27/24) Gap_init rate = 0.03 (6 / 187), avg. gap size = 1.67 (10 / 6) 50 9.12 0.00 0.00 chr3qtel1M 688767 688836 (311164) (AC)n#Simple_repeat 1 70 (0) c_b154s251i0 5782 chr3qtel1M 688767 ACACACACACACACACACACACACACACACACACACACTCGCAGATACAC 688816 v i v i (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50 chr3qtel1M 688817 ACTCGCACACACACACACAC 688836 v i (AC)n#Simple_ 51 ACACACACACACACACACAC 70 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0) 22 23.77 1.85 0.00 chr3qtel1M 688840 688893 (311107) (CA)n#Simple_repeat 1 55 (0) m_b154s252i13 5783 chr3qtel1M 688840 CACAGACACGTACATGCACACACACACTC-CCCCCCCCCACACACACACA 688888 v ii ii v - v v v v (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 chr3qtel1M 688889 CAGAC 688893 v (CA)n#Simple_ 51 CACAC 55 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.02 (1 / 53), avg. gap size = 1.00 (1 / 1) 22 3.81 0.00 0.00 chr3qtel1M 690458 690484 (309516) (T)n#Simple_repeat 1 27 (0) m_b154s252i14 5784 chr3qtel1M 690458 TTGTTTTTTTTTTTTTTTTTTTTTTTT 690484 v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTT 27 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 15 12.03 0.00 0.00 chr3qtel1M 691505 691531 (308469) (TTG)n#Simple_repeat 1 27 (0) m_b154s252i15 5785 chr3qtel1M 691505 TTATTTTTGTTGTTGTTGTTGTTTTTG 691531 i v v (TTG)n#Simple 1 TTGTTGTTGTTGTTGTTGTTGTTGTTG 27 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 413 26.46 0.85 6.31 chr3qtel1M 691532 691648 (308352) C MIRc#SINE/MIR (141) 127 17 m_b154s601i23 5786 chr3qtel1M 691532 CTGAGGC-AATTGGGATTAAGTGACTTGCCAAAGGTCATAAAGCTAGGAA 691580 -v vv i i v i v --- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG--- 81 chr3qtel1M 691581 AAATCAAGTGTCTGAGGCTATATTTGAACTCAAGTCCTCCTGACTTCAGG 691630 ----i v v v viv i i i i i i i C MIRc#SINE/MIR 80 ----TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr3qtel1M 691631 GTTGGTACTCTATGCACT 691648 viii i v v C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACT 17 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 31.68 CpG sites = 16, Kimura (unadjusted) = 33.05 Transitions / transversions = 1.23 (16/13) Gap_init rate = 0.07 (8 / 116), avg. gap size = 1.00 (8 / 8) 659 33.16 3.48 4.02 chr3qtel1M 692057 692498 (307502) L1ME4c_3end#LINE/L1 4 446 (384) m_b154s551i11 5787 chr3qtel1M 692057 ATATTTCTCAAATATATAGAGAATGGAGTCGAGTTTATAGGAATACAAGT 692106 i ? -- ? i iivv v i i v i v v? vi L1ME4c_3end#L 4 ATATCTNT--ANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATC 51 chr3qtel1M 692107 CATTTCTCAACTGACAAATGGTCAAAGTAGATGAACA--CAGTTTTCATG 692154 v vvi i iv i v v v -- i iv ?i L1ME4c_3end#L 52 AAGACCCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANA 101 chr3qtel1M 692155 CGAAGAAAT-CAAA-GGTATCTGTGTTCATATGGGATAAAAAAAAAGTAC 692202 v i - ?-i vviivi-- i ------ v v L1ME4c_3end#L 102 AGAGGAAATACAANTAGTAAACAAA--CACATGG------AAAAATGTTC 143 chr3qtel1M 692203 TAAATCACTACTGATTAGAAAAATACAAATTAAAACAGTTCTGAGGTACC 692252 v vv i v i i i i i i iivv i L1ME4c_3end#L 144 AACCTCGCTAGTAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACC 193 chr3qtel1M 692253 ACCTCACATTTATCAGATTAACTAATAAGCCAGAAAATTAA-AATAGCAA 692301 ii i iii i i i v - vii i i - v v L1ME4c_3end#L 194 ATTTTACGCCTATTAAATTAGCAAA-AATTTAAAAAATTGATAATACCCA 242 chr3qtel1M 692302 ATATTGGTGGCAATTCGGGAAAACTGGAACAATAATGCACTGTTTGTGGA 692351 ii i ivi? v vi v ?v v i i i v v L1ME4c_3end#L 243 ATGCTGGCGAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGC 292 chr3qtel1M 692352 ATTGTGAACTGATTCAACTGTTCTGAACAGCAATTTGGAACTATAAACAA 692401 ? i i i v iv i i v v v iiv iv L1ME4c_3end#L 293 ANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCA 342 chr3qtel1M 692402 AAGACTATCAAACTGTGCA------TTGACCCAGCAATATCACTAATAGA 692445 iii i v v v ------ i vi vv i i L1ME4c_3end#L 343 AGAGCCATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGG 392 chr3qtel1M 692446 GCTGTACCCCAAAGAGATTTTTTTTTTGCTAAAAAGGGGAAAAGACTTAT 692495 iv v i i i i vv ------ v i i i --i L1ME4c_3end#L 393 AATTTATCCTAAGGAAATAATT------CAAAAGAAGGAAAAAG--CTAT 434 chr3qtel1M 692496 CTG--------- 692498 v --------- L1ME4c_3end#L 435 ATGCACGAAGAT 446 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 44.32 CpG sites = 106, Kimura (unadjusted) = 46.45 Transitions / transversions = 1.36 (79/58) Gap_init rate = 0.06 (25 / 441), avg. gap size = 1.56 (39 / 25) 40 0.00 0.00 0.00 chr3qtel1M 692499 692532 (307468) (CA)n#Simple_repeat 1 34 (0) c_b154s251i1 5788 chr3qtel1M 692499 CACACACACACACACACACACACACACACACACA 692532 (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACA 34 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 659 33.16 3.48 4.02 chr3qtel1M 692533 692664 (307336) L1ME4c_3end#LINE/L1 447 574 (256) m_b154s551i11 5787 chr3qtel1M 692533 TTTATAGCAGCTCTTTTGGAGGTGGCAAAGATTTAGAAATTGAGGAGACT 692582 i v vi v vivii i i i v i ivivvv i iv L1ME4c_3end#L 447 TTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATG 496 chr3qtel1M 692583 TCTATCAATGGGAGAATGGCTGAGGAAATTGTAGTGCATGTGTGTTTATG 692632 i v i i i i v i i i ---i?vi -i L1ME4c_3end#L 497 TCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACAT---CNACT-CG 542 chr3qtel1M 692633 ATGGAATACTATTGTGATATAAAAAATGACAA 692664 i vvv vi v i L1ME4c_3end#L 543 ATGGAATATTATGCAGCCATTAAAAATGATAA 574 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 44.32 CpG sites = 106, Kimura (unadjusted) = 46.45 Transitions / transversions = 1.42 (27/19) Gap_init rate = 0.03 (4 / 131), avg. gap size = 1.00 (4 / 4) 16 0.00 0.00 0.00 chr3qtel1M 692678 692695 (307305) (A)n#Simple_repeat 1 18 (0) m_b154s252i16 5789 chr3qtel1M 692678 AAAAAAAAAAAAAAAAAA 692695 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAA 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 563 38.22 4.85 0.93 chr3qtel1M 693139 693447 (306553) C L3#LINE/CR1 (1340) 2759 2439 m_b154s601i24 5790 chr3qtel1M 693139 AGTTTATTGGCCTGCAACTTATAGGTTCCATTCTCTTCCCTTTTTTGAAA 693188 i ii i i ii ?i iv ii i i i i C L3#LINE/CR1 2759 AGCTTACCGGTCTGTAGTTTNCAGAATCCATCTTTTTTCCCTTTTTAAAA 2710 chr3qtel1M 693189 ATGAGGATG---TTGGCTTTTCTCCAGGCC-ATGGTGTTTCTCCTTTACT 693234 ? ii ? i?--- v iiv v i-v iiii i iv v C L3#LINE/CR1 2709 NTAGGNACNACATTTGCCCGTCTCCAGTCTTCTGGCACCTCTTCCGTTCT 2660 chr3qtel1M 693235 CCTTAACCATTCAAATGTCCTCGGCATC--TTCT-CAATCACATCTATCA 693281 v i iivi vi ivi i v -- i- i iiv C L3#LINE/CR1 2659 CCGTGATTTCTCAAAGATTACCGACAGCGGTTCCGCGATCACATCTGCAA 2610 chr3qtel1M 693282 GTCCTTTCAGGACCCAAAGATGCCATCTGTTTAGGTTAGATGATCTAAAC 693331 i v vii iv ii i i iiv iv ii i C L3#LINE/CR1 2609 GTTCTTTCAGTACCCTGGGATGTAATTCGTCTGGGCCTGGAGACTTGAAC 2560 chr3qtel1M 693332 TTATCAGAGGCAAAAAGAGGCTCTCTTATTATATTCCCTTACTAATTCCT 693381 i ivi i iivv iv i v -- i iv iiiv C L3#LINE/CR1 2559 TCATTTAAAGCGGCTAGGTGCTCTCTTACTATCT--CCTCACCTATCTTG 2512 chr3qtel1M 693382 GACACC-ATTTCATC------ATTTTCGTTTTGTTTGTTAATAGGC-AAA 693423 i vi - i v ------ v i i iiiiv -vi v -i C L3#LINE/CR1 2511 GGCTTCAATTCCCTCTTAACGATGTTTGTTCTACCCTTT-CCAGTCTGAA 2463 chr3qtel1M 693424 GGTTGCTGTTCTTGGCAGAGAAAA 693447 i iii v i ii i C L3#LINE/CR1 2462 GATCATTCTCCTTGATAGAGAAGA 2439 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 55.28 CpG sites = 85, Kimura (unadjusted) = 61.22 Transitions / transversions = 2.66 (85/32) Gap_init rate = 0.03 (10 / 308), avg. gap size = 1.80 (18 / 10) 186 30.93 1.41 4.35 chr3qtel1M 693500 693570 (306430) C L3#LINE/CR1 (1655) 2444 2376 m_b154s601i25 5790 chr3qtel1M 693500 AGAAAACAGAAG-AAAATAAAAATGGAGCAATTCTATTAATTCTCTGTTG 693548 i i - ii i v i i ii vvi ii C L3#LINE/CR1 2444 AGAAGACGGAAGCAAAATAGGAGTTGAGTAGTTCTGCTTTCTCTCTGTCA 2395 chr3qtel1M 693549 CTAATTATCATATATACACCAT 693570 iivi v --- i C L3#LINE/CR1 2394 TCTGTTAACAT---TACGCCAT 2376 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 37.76 CpG sites = 16, Kimura (unadjusted) = 43.25 Transitions / transversions = 3.20 (16/5) Gap_init rate = 0.06 (4 / 70), avg. gap size = 1.00 (4 / 4) 210 19.55 6.38 2.04 chr3qtel1M 693592 693638 (306362) L2a_3end#LINE/L2 465 513 (4) m_b154s601i26 5791 chr3qtel1M 693592 ACAATGCCTGGGACA---TAGATGCTTAATCAACGTTTGCTGAATTGAAT 693638 i v --- ii i v ii i - L2a_3end#LINE 465 ACAGTGCCTGGCACATAGTAGGCGCTCAATAAATATTTGTTGAA-TGAAT 513 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 20.73 CpG sites = 7, Kimura (unadjusted) = 23.65 Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.04 (2 / 46), avg. gap size = 2.00 (4 / 2) 532 23.14 6.42 7.57 chr3qtel1M 694996 695182 (304818) MIR1_Amn#SINE/MIR 18 202 (28) m_b154s601i27 5792 chr3qtel1M 694996 CCAGCAGATCGAGTGCTGG----GAAC------AATCTGAGTTCAAATCT 695035 i ii v ii ---- i ------i i i ? ? i MIR1_Amn#SINE 18 CTAGTGGATAGAGCACTGGACTGGGACTCGGGAGACCTGGGTTCNANTCC 67 chr3qtel1M 695036 AGCCCCAGACATTTTCTAGCTGTGTGACCTTGGGTAAGTCATTTAATCTC 695085 v v i v v i ?v i? ? i i ? i MIR1_Amn#SINE 68 CGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGTCACTTNACCTC 117 chr3qtel1M 695086 TGCTTGCCTCAGGTTCCTTAAATGTAAAATGGGGATAATAACAATACGTA 695135 viv? v i vv ---i vv MIR1_Amn#SINE 118 TCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGGATAAT---GATACTGA 164 chr3qtel1M 695136 CCTCTCAGGATTGTTGTAA--TGATCAAATGAGATCATATTTGTAAAAA 695182 ii------- -- v i--- - i vi i MIR1_Amn#SINE 165 CCTCCT-------TTGTAAAGTGCTT---TGAGATC-TACTGATGAAAA 202 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 29.83 CpG sites = 25, Kimura (unadjusted) = 29.83 Transitions / transversions = 1.67 (25/15) Gap_init rate = 0.09 (17 / 186), avg. gap size = 1.53 (26 / 17) 825 21.38 0.00 0.00 chr3qtel1M 695022 695180 (304820) MIR#SINE/MIR 48 206 (56) m_b154s601i28 5792 chr3qtel1M 695022 CTGAGTTCAAATCTAGCCCCAGACATTTTCTAGCTGTGTGACCTTGGGTA 695071 i i iv v i v v i v i MIR#SINE/MIR 48 CTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 97 chr3qtel1M 695072 AGTCATTTAATCTCTGCTTGCCTCAGGTTCCTTAAATGTAAAATGGGGAT 695121 i i i viv v i vv MIR#SINE/MIR 98 AGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGAT 147 chr3qtel1M 695122 AATAACAATACGTACCTCTCAGGATTGTTGTAATGATCAAATGAGATCAT 695171 i i v vi i i v i v v MIR#SINE/MIR 148 AATAATAGTACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAAT 197 chr3qtel1M 695172 ATTTGTAAA 695180 iv MIR#SINE/MIR 198 ACATGTAAA 206 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 24.59 CpG sites = 18, Kimura (unadjusted) = 25.42 Transitions / transversions = 1.12 (18/16) Gap_init rate = 0.00 (0 / 158), avg. gap size = 0.0 (0 / 0) 486 32.35 9.72 1.16 chr3qtel1M 695329 695647 (304353) L2#LINE/L2 1917 2262 (820) m_b154s601i29 5793 chr3qtel1M 695329 TTGCTTTGTTCTTGCTCTCTTTTTAAGCCTTAATAATCTGGATTTTGACT 695378 v i vi iiii i v v vivvi v v i v i L2#LINE/L2 1917 TTCCTCTCCTCCCATTCTCTCTTGAACCCACTCCAATCAGGCTTTCGTCC 1966 chr3qtel1M 695379 TGAT---TCCACCTAAATGACTTTCTCCAAAGTTTCTAACGATCTCTTAG 695425 iv i--- v ivi i ivi i iv i i i ivv L2#LINE/L2 1967 CCACCACTCCACCGAAACTGCTCTTGTCAAGGTCACCAATGACCTCCACG 2016 chr3qtel1M 695426 TAGCCAAATCCAGTGG-CTTTTCTTAGTCGTCAGACT-CTTGATCTCTCT 695473 v i i - vv i v vvi - i ? v L2#LINE/L2 2017 TTGCTAAATCCAATGGTCAATTCTCAGTCCTCATCTTACTTGACCTNTCA 2066 chr3qtel1M 695474 GCTATTTTGGACACTGTGGGTCACTCC-TCC-----AGAACAC------A 695511 viiv v v v i - -----ii ------v L2#LINE/L2 2067 GCAGCATTTGACACAGTTGATCACTCCCTCCTTCTTGAAACACTTTCTTC 2116 chr3qtel1M 695512 ACCTAGGTTTTT---------TTCTCTCTTGGATGTCCCCCTCCCTCTCT 695552 i - i ii---------iv i v v i v v L2#LINE/L2 2117 ACTT-GGCTTCCAGGACACCACACTCTCCTGGTTTTCCTCCTACCTCACT 2165 chr3qtel1M 695553 GACTATTCCTTCT--GTCTCCTTTGCTGGATCCTCCTCCAAATCCTTC-- 695598 i iii -- v --- iii -- L2#LINE/L2 2166 GGCCGCTCCTTCTCAGTCTCCTTTGCTGGTTCCTCCTC---ATCTCCCCG 2212 chr3qtel1M 695599 -CTTCTAACCATAGGTGTCCCTGCGGGTTTTATCCTGGGCCCCCTCCGCT 695647 - i ? v i v v v ivv i ivi v v i i v L2#LINE/L2 2213 ACCTCTNAACGTTGGAGTGCCCCAGGGCTCAGTCCTTGGACCTCTTCTCT 2262 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 42.07 CpG sites = 56, Kimura (unadjusted) = 43.84 Transitions / transversions = 1.22 (56/46) Gap_init rate = 0.04 (14 / 318), avg. gap size = 2.50 (35 / 14) 14 27.09 2.78 4.23 chr3qtel1M 698282 698353 (301647) (CCCTGC)n#Simple_repeat 1 71 (0) m_b154s252i17 5794 chr3qtel1M 698282 CCCTGCCCCTCTGGCT-CCCCTGACCCCTCAGCCCCCACCCCTGCTCCAG 698330 vivv - - -- ii i v (CCCTGC)n#Sim 1 CCCTGCCCCTGCCCCTGCCCCTG-CCCCT--GCCCCTGCCCCTGCCCCTG 47 chr3qtel1M 698331 TCACCCCTCCT-CCTCTCCCCCTG 698353 i v iv i - i v (CCCTGC)n#Sim 48 CCCCTGCCCCTGCCCCTGCCCCTG 71 Matrix = Unknown Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.07 (5 / 71), avg. gap size = 1.00 (5 / 5) 21 17.57 1.89 1.89 chr3qtel1M 698298 698350 (301650) (CCCCTCA)n#Simple_repeat 1 53 (0) m_b154s252i18 5795 chr3qtel1M 698298 CCCCTGACCCCTCAGCCCCCACCCCTGCTCCAGTCACCCCTC-CTCCTCT 698346 v v i - v vv - i v (CCCCTCA)n#Si 1 CCCCTCACCCCTCACCCCTCACCCCT-CACCCCTCACCCCTCACCCCTCA 49 chr3qtel1M 698347 CCCC 698350 (CCCCTCA)n#Si 50 CCCC 53 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.00 (2 / 2) 220 31.15 1.64 0.00 chr3qtel1M 700896 700956 (299044) C L2c_3end#LINE/L2 (0) 478 417 m_b154s601i30 5796 chr3qtel1M 700896 ACTCATTCATTCTACGAGCACTTGGCAAATACCTGCCGTGGGCC-GGCTC 700944 i v i i i ivii iii i ii v - v C L2c_3end#LINE 478 ATTCATTCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGC 429 chr3qtel1M 700945 TGAGGATACTAA 700956 i v C L2c_3end#LINE 428 TGGGGATACAAA 417 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 39.96 CpG sites = 14, Kimura (unadjusted) = 43.41 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.02 (1 / 60), avg. gap size = 1.00 (1 / 1) 16 9.75 2.86 2.86 chr3qtel1M 701933 701967 (298033) (CTTCCT)n#Simple_repeat 1 35 (0) m_b154s252i19 5797 chr3qtel1M 701933 CTGCCTCTTCCTCCTCC-CTTCCCTCTTCCTCCTCC 701967 v i - - i (CTTCCT)n#Sim 1 CTTCCTCTTCCTCTTCCTCTT-CCTCTTCCTCTTCC 35 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 194 30.16 13.11 5.19 chr3qtel1M 701974 702690 (297310) L2#LINE/L2 2312 3082 (0) m_b154s601i31 5798 chr3qtel1M 701974 TGAATGACCATCTCTCTGCTGCTAATTCTCAATTCTACCTTTTCCTGCCC 702023 i - v v v i i i v i iv i - v L2#LINE/L2 2312 TAAAT-ACCATCTATATGCTGATGACTCCCAAATTTATATCT-CCAGCCC 2359 chr3qtel1M 702024 CAAATTCTGC--TGA-CTC-AGTTTC-CATTTCCAAAGGCCT-TTCACAC 702067 vi vi v -- - - vi -i v vv -i i- L2#LINE/L2 2360 GGACCTCTCCCCTGAACTCCAGACTCGTATATCCAACTGCCTACTCG-AC 2408 chr3qtel1M 702068 ACCTTGAACTGGATGTCTAGAGGAGATTTTAAACTCAACACGTTCAAAAC 702117 i iv vi ivi iv i i i i i L2#LINE/L2 2409 ATCTCCACTTGGATGTCTAATAGGCATCTCAAACTTAACATGTCCAAAAC 2458 chr3qtel1M 702118 --GATTTGTGATCTTTCCTCT--AACCC-CTCCCCCT----TCTTCCCGG 702158 --i i iv i i -- i- i i---- vi L2#LINE/L2 2459 TGAACTCCTGATCTTCCCCCTCAAACCTGCTCCTCCCGCAGTCTTCCCCA 2508 chr3qtel1M 702159 TCCTA-TCACTAGAGAAGGGACCC--CCAG--GCTC---CCATG---CTC 702197 ii - ? v i vi vvvv i -- -- --- vi--- i L2#LINE/L2 2509 TCTCAGTNAATGGCAACTCCATCCTTCCAGTTGCTCAGGCCAAAAACCTT 2558 chr3qtel1M 702198 GGAAACATCCTGGGCTGCTCAC--ACTCTCACCCTGCAAATCCA--CCAT 702243 iv v i v v --v v iv v -- L2#LINE/L2 2559 GGAGTCATCCTTGACTCCTCTCTTTCTCTCACACCCCACATCCAATCCAT 2608 chr3qtel1M 702244 GGTGTCAAGATTTGCCATGTCACCTCTGCTCCGTCCCCCTCCGCGTCACC 702293 --iiv - --- - iv i--------- i i---- vv L2#LINE/L2 2609 --CAGCAA-AT---CC-TGTCGGCTCTA---------CCTTCA----AAA 2638 chr3qtel1M 702294 TCTGCTCCGTCTCCAACAGCCCTTTTCTCTTCTGACCCAGCCCCCATCCT 702343 v iii v vv i -- v i v iv ivv v v v i L2#LINE/L2 2639 TATATCCAGAATCCGAC--CACTTCTCACCACCTCCACTGCCACCACCCT 2686 chr3qtel1M 702344 GGAGAAGGCCCTCATCACTCCCCACCGGG---ACTGCCA----------- 702379 vvv i vi iii i i v --- v ----------- L2#LINE/L2 2687 GGTCCAAGCCACCATCATCTCTCGCCTGGATTACTGCAATAGCCTCCTAA 2736 chr3qtel1M 702380 -TGGGCCGCCTGCCTCTAATCT--CCCCCCTCCGTCCTCCCTTCAAC-CA 702425 - v iv i i vi -- ? ivi viii - L2#LINE/L2 2737 CTGGTCTCCCTGCTTCCACCCTTGCCCCCCTNCAGTCTATTCTCAACACA 2786 chr3qtel1M 702426 ----CCAAAGTAA--CTTTTC-----TAAG--AGACCCTGTCAC-CCCCT 702461 ---- i i -- v----- -- i v - i L2#LINE/L2 2787 GCAGCCAGAGTGATCCTTTTAAAACGTAAGTCAGATCATGTCACTCCTCT 2836 chr3qtel1M 702462 GCTC----CCCCATTTCCAGTGGC-TCTCACTGCTTCCAGGAGCAAATAC 702506 ---- ---- i - i iiv vii iivv vv L2#LINE/L2 2837 GCTCAAAACCC----TCCAATGGCTTCCCATCTCACTCAGAGTAAAAGCC 2882 chr3qtel1M 702507 AAAATGCTT------GCCTTCGAAGCCTTTCGC-ACCT-GTGCCCTGCAC 702548 i v ------ v i i i v ii- i - v i ivv L2#LINE/L2 2883 AAAGTCCTTACAATGGCCTACAAGGCCCTACATGATCTGGTCCCCCGTTA 2932 chr3qtel1M 702549 CCTTCCTG----CAT------CCAAG-GCCCCCAGGCTCCTTCTGTTCCA 702587 ii ---- ------ vv-v vv vi i i - L2#LINE/L2 2933 CCTCTCTGACCTCATCTCCTACCACTCTCCCCCTCGCTCACTCCGCTCC- 2981 chr3qtel1M 702588 TAGCCTGAGCCTGAGCATTTCCT--CTGGTCCTCCCCCAGGCCTGGGAGG 702635 - -- vv - --i -- v vvv v v v v L2#LINE/L2 2982 -AGCC--ACACTG-GC--CTCCTTGCTGTTCCTCGAACACGCCAGGCACG 3025 chr3qtel1M 702636 CTCCTCCTTCTGTGC---TACAACTACTGACCTCCCTGGCTTCCTCCAA- 702681 iv i v v --- i vi i --i -- v vv - L2#LINE/L2 3026 CTCCCGCCTCAGGGCCTTTGCACTTGCTG--TTCCCT--CTGCCTGGAAC 3071 chr3qtel1M 702682 --TCTCCCCCC 702690 -- i L2#LINE/L2 3072 GCTCTTCCCCC 3082 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 37.65 CpG sites = 107, Kimura (unadjusted) = 39.59 Transitions / transversions = 1.09 (107/98) Gap_init rate = 0.11 (78 / 716), avg. gap size = 1.72 (134 / 78) 59 26.22 6.51 0.44 chr3qtel1M 703134 703348 (296652) (AG)n#Simple_repeat 1 228 (0) m_b154s252i21 5799 chr3qtel1M 703134 AGAGAGAGAGAGAG-GAGAGGGA-AGGGGAAGAG-GAGAGGAAGAGAG-G 703179 - i - i ii - ii - (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr3qtel1M 703180 AGGGAAAGGGA-AGGGAGA-AGAGAGGGAAGGAAGGGGAGATGAGAAAG- 703226 i i i - i - i ii ii i - i - (AG)n#Simple_ 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA-GAGAGAGA 99 chr3qtel1M 703227 GAGGGA-AAAGATA-AGAAAAAG-GGGAG-GGGAGAGGAAGGGGGAAAGA 703272 i - i v - i i - i - i ii i i i (AG)n#Simple_ 100 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 149 chr3qtel1M 703273 AAGGAAAAGGGAG-GAAAGA-AGAATGAGAGAGAGACACACACAGAGAGA 703320 i ii i i - i - iv v v v v (AG)n#Simple_ 150 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 199 chr3qtel1M 703321 CACAGAGAGAGAGAGAGAGGAAGAG-GAG 703348 v v ii - (AG)n#Simple_ 200 GAGAGAGAGAGAGAGAGAGAGAGAGAGAG 228 Matrix = Unknown Transitions / transversions = 4.62 (37/8) Gap_init rate = 0.07 (15 / 214), avg. gap size = 1.00 (15 / 15) 29 26.74 1.39 8.15 chr3qtel1M 703147 703290 (296710) (GGAAG)n#Simple_repeat 1 135 (0) m_b154s252i22 5799 chr3qtel1M 703147 GGAGAGGGAAGGGGAAGAGGAGAGGAAGAG-A-GGAGGGAAAGGGAAGGG 703194 - - - ii i - - i i (GGAAG)n#Simp 1 GGA-AGGGAA-GGGAAG-GGAAGGGAAGGGAAGGGAAGGGAAGGGAAGGG 47 chr3qtel1M 703195 AGAAGAGAGGGAAGGAAGGGGAGATGAGAAAGGAGGGAAAAGATAAGAAA 703244 - i ii i i - - i i i -i iv -ii (GGAAG)n#Simp 48 A-AGGGAAGGGAAGGGAAGGGA-A-GGGAAGGGAAGG-GAAGGGAAG-GG 92 chr3qtel1M 703245 AAGGGGAGGGGAGAGGAAGGGGGAAAGAAAGGAAAAGGGAGGAAAG 703290 i i - -- i i i i i i (GGAAG)n#Simp 93 AAGGGAAGGGAAG-GGAA--GGGAAGGGAAGGGAAGGGAAGGGAAG 135 Matrix = Unknown Transitions / transversions = 25.00 (25/1) Gap_init rate = 0.09 (13 / 143), avg. gap size = 1.00 (13 / 13) 15 25.45 4.00 4.00 chr3qtel1M 703692 703766 (296234) (GTCT)n#Simple_repeat 1 75 (0) m_b155s252i2 5800 chr3qtel1M 703692 GTCTTTCTGTCTGTCTCTCACTGTCT-TC-GTCTCCCCTTTGTGTCTGTC 703739 v v -- - - -vi v v (GTCT)n#Simpl 1 GTCTGTCTGTCTGTCTGT--CTGTCTGTCTGTCT-GTCTGTCTGTCTGTC 47 chr3qtel1M 703740 TCT-TCTCCCTTTCTCCGTCTCTCTTTC 703766 v - v iv i v i v v (GTCT)n#Simpl 48 TGTCTGTCTGTCTGTCTGTCTGTCTGTC 75 Matrix = Unknown Transitions / transversions = 0.36 (4/11) Gap_init rate = 0.08 (6 / 74), avg. gap size = 1.00 (6 / 6) 13 15.85 0.00 7.89 chr3qtel1M 703735 703775 (296225) (CTTTCC)n#Simple_repeat 1 38 (0) m_b155s252i3 5801 chr3qtel1M 703735 CTGTCTCTTCTCCCTTTCTCCGTCTCTCTTTCCCTTGCCCT 703775 v i - - - i i v (CTTTCC)n#Sim 1 CTTTCCCTT-TCCCTTTC-CC-TTTCCCTTTCCCTTTCCCT 38 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.07 (3 / 40), avg. gap size = 1.00 (3 / 3) 21 13.26 0.00 0.00 chr3qtel1M 706383 706415 (293585) (G)n#Simple_repeat 1 33 (0) m_b155s252i4 5802 chr3qtel1M 706383 GGGGGGGGCGGGGGGAGGGGGTGGGGGGAGGGG 706415 v i v i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 33 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 13 37.39 0.00 0.00 chr3qtel1M 706775 706832 (293168) (CCCC)n#Simple_repeat 1 58 (0) m_b155s252i5 5803 chr3qtel1M 706775 CCCTCCCCCCCCACCCCCTTCCCTCTTTCTCCCTCCCCCCGCCCTTCCTG 706824 i v ii i iii i i v ii iv (CCCC)n#Simpl 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 50 chr3qtel1M 706825 TCCCCCCC 706832 i (CCCC)n#Simpl 51 CCCCCCCC 58 Matrix = Unknown Transitions / transversions = 4.33 (13/3) Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0) 16 15.11 6.82 0.00 chr3qtel1M 707377 707420 (292580) (GCCCTGC)n#Simple_repeat 1 47 (0) m_b155s252i6 5804 chr3qtel1M 707377 GCCC-GCGCACAG-GGCCTGCTCTCTGCG-CCTGCGCCCTGCTCCCT 707420 - v v - v v i - v (GCCCTGC)n#Si 1 GCCCTGCGCCCTGCGCCCTGCGCCCTGCGCCCTGCGCCCTGCGCCCT 47 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.07 (3 / 43), avg. gap size = 1.00 (3 / 3) 385 38.78 4.99 2.11 chr3qtel1M 709192 709652 (290348) C MamRTE1#LINE/RTE-BovB (610) 3202 2729 m_b155s601i0 5805 chr3qtel1M 709192 GTCCAGGTTTCACAGGCATACCACAATGAGGTCAGTACCATGGTTCTACA 709241 i v i ?viv ivvv v ?ii i v i ii C MamRTE1#LINE/ 3202 GTCCAGGTCTCACAGCCGTANAGAAGGTTGGACANCGCTATCGCTCTGTA 3153 chr3qtel1M 709242 GACCTTCAGTTTGGT----AGTCTGA---CACTTTTCCTCTCCCACACTT 709284 i ---- ii --- v vv v --- i C MamRTE1#LINE/ 3152 GACCTTTAGTTTGGTCTGGAGCTTGATGCCACGTTGGCGC---CACACTC 3106 chr3qtel1M 709285 TCCTTTAGAACCTTCCAAACCCTGAGCTAGCTCTGCCAATCTGTGTGCCA 709334 vii vvv i i vvviiv i ii viii ii vv vi v C MamRTE1#LINE/ 3105 TGTCTGCCAGCCTCCCAAAGGACATGCTGGCCTTCTTGATTCGGTTTTCT 3056 chr3qtel1M 709335 ATTTCATTATCAGTGTGTATATCCCTGGAAAGCGCGCTGCCAAGGTAAGT 709384 i v i ?i vv ii vi v i v ivv C MamRTE1#LINE/ 3055 ACTTCTTTGTCNATCAGTGCATCATTGGACAGCGTGCTGCCTAGGTAGCA 3006 chr3qtel1M 709385 GAACTTATCCACAGCATTCAAAACTTCTCCATTTTC--TG-CAACCAGTG 709431 i iiviv v i---i vi vi -- -v i vv C MamRTE1#LINE/ 3005 GAATTCGGTGACAGCTTTCAG---CTCTGTATTGCCGATGAAAATCTTTG 2959 chr3qtel1M 709432 GCTCCACATATGG-TGATATGGTACTGGCCAATAGAGCAGACAT--GTTT 709478 v iii v - vviv i v iii v v-- v -- i C MamRTE1#LINE/ 2958 GCTGCGTGTAGGGTTTCCCTGGTGCAGGCTGGTACAT--GACCTCGGTCT 2911 chr3qtel1M 709479 TCTGGA----TGTCATTAGGGCAAAATGA-GCACAAACAGCAGAGAATGG 709523 vv ---- i i i vv iv ii v- ii vi vviiv i ii C MamRTE1#LINE/ 2910 TCTTCAGGCTTATCGTCAGTCCGTAGCGCTGTGCTGACTCTGCAAAGCGG 2861 chr3qtel1M 709524 ATCCGTACTTTGTTGTATATCACTTTG-GAGGCTGCATC-AGTGCACAAT 709571 - i iv iv?i i i vii - v vv i v - v i C MamRTE1#LINE/ 2860 -TCCATGATCANCTGCATGTCTTCTTGCGCGTGTACTTCAAGAGCACAGT 2812 chr3qtel1M 709572 TACCTACAAACAGAA--TCATGCACCAACACTCCCTA-AACTTTCGTTTT 709618 i i vi v v -- v v -ii vv i v -i v vv C MamRTE1#LINE/ 2811 CATCGGCATACAGCAGTTCCTGGA-TGACTGTCTCAAGGACTTTCGATGA 2763 chr3qtel1M 709619 GGCTTGTAGCCTGTTCAAGTCAATGATTTTACCA 709652 v i v iv vi v v v C MamRTE1#LINE/ 2762 TGCTCGTAGCCTGTTGAGTTGGAAGAGTTTCCCA 2729 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 52.01 CpG sites = 89, Kimura (unadjusted) = 56.80 Transitions / transversions = 1.03 (89/86) Gap_init rate = 0.05 (22 / 460), avg. gap size = 1.50 (33 / 22) 341 37.60 3.20 0.00 chr3qtel1M 709771 710020 (289980) C MamRTE2#LINE/RTE-BovB (1223) 329 72 m_b155s551i0 5806 chr3qtel1M 709771 ATCCATTGTACAGAACCCAGGCAAGCTTGCCATCACGAAACTGATGGATT 709820 iivv i vvv vv v i i iii i v ii vv C MamRTE2#LINE/ 329 ATCCATTACTGAGGACCACTGCTCGCATACCGTCATAGAGCAGGCGGAGA 280 chr3qtel1M 709821 ATACTGATGAGCTTCTCTGGGAAACCAACTTTTAACATACTTTTCCATCA 709870 iv i ii ivv v v vvi i iv v v ii iv C MamRTE2#LINE/ 279 ATGGTGACGAATTTTGGTGGGCATCCATACTTCAGAAGAATCCTCCACAA 230 chr3qtel1M 709871 GCCCTTG----TGACCGTGTCAAAGGCCTTGGTCAGGTCTACAA---TTG 709913 vv i ii---- v v vv v ? v vi ---iii C MamRTE2#LINE/ 229 TGCTTCACGACTGACAGAGTCAAAGGCCTTCCTGANGTCGAGGAAGGCCA 180 chr3qtel1M 709914 TATAAAGACCTCTGTTCTGCTCCTGACATTTCTGCTGGAGTTGTGGAGCA 709963 vv i i vi i i i i v ? i vv C MamRTE2#LINE/ 179 TATAAAGAGGTTTATGTTGTTCTTGGCATTTTTCCTGNAGCTGGCGAGCA 130 chr3qtel1M 709964 GCACACACAGTAGCAATTGTTCCTCAGCCCCCTCTGAAACCACACTG-GC 710012 iiv v v v i iv v?vviv i v i - v C MamRTE2#LINE/ 129 GTGAAGACCGTATCAGTTGCGCCTCTNGATGCTCTAAACCCACGCTGAGA 80 chr3qtel1M 710013 TCTCGGGA 710020 ii C MamRTE2#LINE/ 79 TTCCGGGA 72 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 50.09 CpG sites = 46, Kimura (unadjusted) = 54.13 Transitions / transversions = 0.96 (46/48) Gap_init rate = 0.01 (3 / 249), avg. gap size = 2.67 (8 / 3) 190 13.79 0.00 0.00 chr3qtel1M 710043 710071 (289929) MIRc#SINE/MIR 14 42 (226) m_b155s601i1 5807 chr3qtel1M 710043 TGCAATGGAGAGAGCTCTGGACTTGGAAT 710071 i i v i MIRc#SINE/MIR 14 TGCAGTGGAAAGAGCACTGGACTTGGAGT 42 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 15.60 CpG sites = 3, Kimura (unadjusted) = 15.60 Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 289 32.29 2.06 4.21 chr3qtel1M 710091 710187 (289813) MIR#SINE/MIR 90 184 (78) m_b155s601i2 5808 chr3qtel1M 710091 CTTAGATAAGCCACTTGTGTCTTTCCAGGCTACTTCAGTTTCCTCATCTG 710140 i ii ii i-ii i ii--- i i MIR#SINE/MIR 90 CTTGGGCAAGTTACTTA-ACCTCTCTG---TGCCTCAGTTTCCTCATCTG 135 chr3qtel1M 710141 CAGAGTGAGTGTGACAGCAGCACTCACCTCCTA--GTCGGTGAGAGGAT 710187 i i i i vi i i ii i ii v -- i v v MIR#SINE/MIR 136 TAAAATGGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGGAT 184 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 48.33 CpG sites = 26, Kimura (unadjusted) = 48.33 Transitions / transversions = 6.50 (26/4) Gap_init rate = 0.05 (5 / 96), avg. gap size = 1.20 (6 / 5) 14 15.33 4.26 4.26 chr3qtel1M 715310 715356 (284644) (TAAATTA)n#Simple_repeat 1 47 (0) m_b155s252i7 5809 chr3qtel1M 715310 TAAAATATCAATTA-AAATTTTAAA-AATAAGTCTATCAAATTATAGAT 715356 v v - v -v i - - i (TAAATTA)n#Si 1 TAAATTATAAATTATAAATTATAAATTATAAAT-TAT-AAATTATAAAT 47 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.09 (4 / 46), avg. gap size = 1.00 (4 / 4) 13 15.67 2.50 5.13 chr3qtel1M 715617 715656 (284344) (CTTCCT)n#Simple_repeat 1 39 (0) m_b155s252i8 5810 chr3qtel1M 715617 CTTCCTTTTTCTCTTCCTACTTAACTCTT-CTCTTTCCCTT 715656 i i - -v - i i (CTTCCT)n#Sim 1 CTTCCTCTTCCTCTTCCT-CTT-CCTCTTCCTCTTCCTCTT 39 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.08 (3 / 39), avg. gap size = 1.00 (3 / 3) 13 19.74 0.00 6.98 chr3qtel1M 716351 716396 (283604) (AACACAA)n#Simple_repeat 1 43 (0) m_b155s252i9 5811 chr3qtel1M 716351 AACACAACAGACAGACAAGTCACAAACACAGAACACAAATTACAAA 716396 - - v v vv - i vi (AACACAA)n#Si 1 AACACAA-A-ACACAAAACACA-AAACACAAAACACAAAACACAAA 43 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.07 (3 / 45), avg. gap size = 1.00 (3 / 3) 272 32.58 10.88 1.42 chr3qtel1M 717543 717735 (282265) L2#LINE/L2 1969 2179 (903) m_b155s601i3 5812 chr3qtel1M 717543 ACCAGTTCCCTGACACTGTTCTTTACAAAGTGATCAATGATCTCT-TAGT 717591 v i v i v i vv i v i i i-iiv L2#LINE/L2 1969 ACCACTCCACCGAAACTGCTCTTGTCAAGGTCACCAATGACCTCCACGTT 2018 chr3qtel1M 717592 GTCAAGTTCAGTGACCTGAAAGGTCAGTC-------TCCTTGACCTTTCT 717634 ii i i i ii -- vvv ------- v ? v L2#LINE/L2 2019 GCTAAATCCAATGGTC--AATTCTCAGTCCTCATCTTACTTGACCTNTCA 2066 chr3qtel1M 717635 GCATTCTTGGTCACTATGGATCATCCTCTCCCTTTTG--TTCCCCTCCTC 717682 viv v v vi v ii i i i --viv ii i L2#LINE/L2 2067 GCAGCATTTGACACAGTTGATCACTCCCTCCTTCTTGAAACACTTTCTTC 2116 chr3qtel1M 717683 TGTAGGTTTCCAGG-------ATTCT----GTCTCCTTTCTGCCTCCTTG 717721 vv v i ------- i ---- i i i i i vi L2#LINE/L2 2117 ACTTGGCTTCCAGGACACCACACTCTCCTGGTTTTCCTCCTACCTCACTG 2166 chr3qtel1M 717722 GCTGGCTCTTCCTC 717735 i- i i L2#LINE/L2 2167 GCC-GCTCCTTCTC 2179 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 41.93 CpG sites = 38, Kimura (unadjusted) = 44.98 Transitions / transversions = 1.58 (38/24) Gap_init rate = 0.04 (8 / 192), avg. gap size = 3.00 (24 / 8) 200 30.01 9.82 3.07 chr3qtel1M 717620 717894 (282106) L2#LINE/L2 2097 2389 (693) m_b155s601i4 5812 chr3qtel1M 717620 CTCCTTGAC---CTTTCTGCATTCTTGGTCACTATGG-ATCATCCTCTCC 717665 i v--- v -- iiv i v i- i iv L2#LINE/L2 2097 CTTCTTGAAACACTTTCTTCA--CTTGGCTTCCAGGACACCACACTCTCC 2144 chr3qtel1M 717666 CTTTTGTTCCCCT-CCTCTGTAG--GTTTCCAGGATTCT--GTCTCCTTT 717710 ivv v i i - vv i -- i i ----- -- L2#LINE/L2 2145 TGGTTTTCCTCCTACCTCACTGGCCGCTCC-----TTCTCAGTCTCCTTT 2189 chr3qtel1M 717711 -CTG---CCTCCTTGGCTGGCTCTTCCTCTAAATAATGGC---CCTCAGG 717753 - --- iiv v- i vv ? iiv v--- i L2#LINE/L2 2190 GCTGGTTCCTCCTCATCTC-CCCGACCTCTNAACGTTGGAGTGCCCCAGG 2238 chr3qtel1M 717754 GTTCTATCCT-GGCCCTTTTTTCCTTCTTTA-CTAT-----TTCCCTTAG 717796 i vi - v i i - i - i-----i ?i L2#LINE/L2 2239 GCTCAGTCCTTGGACCTCTTCTC-TTCTCTATCTACACTCACTCCCTNGG 2287 chr3qtel1M 717797 AGATCTCATCAGCTCCCATGGATTTAGTGATCATCTCTGT----AAAATT 717842 v viv i v ivv i v i ---- vi i L2#LINE/L2 2288 TGATCTCATCCAGTCTCATGGCTTTAAATACCATCTATATGCTGATGACT 2337 chr3qtel1M 717843 CCCAAATCTATTTTCCCTGCCCTTCTCATTCTGCTGACTTCCAACTTCTC 717892 i v ii v vvvi vi iv vi ivi vi L2#LINE/L2 2338 CCCAAATTTATATCTCCAGCCCGGACCTCTCCCCTGAACTCCAGACTCGT 2387 chr3qtel1M 717893 AT 717894 L2#LINE/L2 2388 AT 2389 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 38.97 CpG sites = 44, Kimura (unadjusted) = 39.68 Transitions / transversions = 1.22 (44/36) Gap_init rate = 0.08 (21 / 274), avg. gap size = 1.71 (36 / 21) 1606 31.88 2.89 1.25 chr3qtel1M 719058 719921 (280079) L1P4_orf2#LINE/L1 1939 2816 (478) m_b155s551i1 5813 chr3qtel1M 719058 AAACTGCAACCATTTCCAATAAGATCAGCAGTGAAACAAGGTTGCCCACT 719107 i v v i vv i v v v iii i v L1P4_orf2#LIN 1939 AAGCTGGAAGCATTCCCCTTGAGAACTGGAACAAGACAAGGATGCCCACT 1988 chr3qtel1M 719108 ATCATCGTTACTATTCAATATTGCATTAGAAATGCTAGCTTTGGCAATAA 719157 v i ii v i v i i i i v ivvi v L1P4_orf2#LIN 1989 CTCACCACTCCTATTCAACATAGTACTGGAAGTCCTAGCCAGAGCAATCA 2038 chr3qtel1M 719158 GAGTTGAGAAAGAGATTAAAGGAATTAGAGTAGGCAATGAGGAAACCAAT 719207 ivvv i v v ivi i v v i ii v L1P4_orf2#LIN 2039 GGCAAGAGAAAGAAATAAAAGGCATCCAAATAGGAAAAGAAGAAGTCAAA 2088 chr3qtel1M 719208 TTATCACTCTTTGCTGATGATATGATGGTATACCTAGAGAACCCCAGAGA 719257 i v i i vv i i i L1P4_orf2#LIN 2089 CTATCTCTCTTCGCTGACGATATGATTCTATACCTAGAAAACCCTAAAGA 2138 chr3qtel1M 719258 TTCTACTAAAAAGCTATTAGAAATAATCCACACCTTTAGCAAAGTTGCAG 719307 i ii i i vi v i vv iv i i v L1P4_orf2#LIN 2139 CTCCGCCAAAAGGCTCCTAGAACTGATAAACGACTTCAGTAAAGTTTCAG 2188 chr3qtel1M 719308 GATACAAAATAAACCCACATAAATCATCCGCTTTCTTATATATCACTAAC 719357 v ivi v viv v ii i i v L1P4_orf2#LIN 2189 GATACAAAATCAATGTACAAAAATCAGTAGCATTTCTATACACCAATAAC 2238 chr3qtel1M 719358 AAAATCCAACAGTT-AGAGTTACA--AAGA--GAAATTTCATTTAAAATA 719402 i--- i -- i - ii v -- -- v ii v L1P4_orf2#LIN 2239 G---TTCAA--GCTGAGAGCCAAATCAAGAACGCAATCCCATTTACAATA 2283 chr3qtel1M 719403 ACTACTGATAGTATAAAATACTTAGGAATCTATCTGCCAAAGGAAAATCA 719452 i i vi v iv i vi iv v iivvv L1P4_orf2#LIN 2284 GCCACAAAAAAAATAAAATACCTAGGAATACATCTAACCAAGGAGGTGAA 2333 chr3qtel1M 719453 GAAACTTTATGAGCAAAACTACAAAACACTTTCCACATAAATTAAGTCTG 719502 ii v i ii v i viiv v v i ?ivv L1P4_orf2#LIN 2334 AGATCTCTACAAGGAGAACTACAAAACACTGCTGAAAGAAATCANAGATG 2383 chr3qtel1M 719503 ATTTAACCAACTGGGAAAATATTAAATGCTCTTGGATTGGGCGAACAAAT 719552 ivi v v i i vv v iv iv L1P4_orf2#LIN 2384 ACACAAACAAATGGAAAAACATTCCATGCTCATGGATTGGAAGAATCAAT 2433 chr3qtel1M 719553 ATAATAAAGATGACAATACTACCTAAACTATTCT----ATTTAGTGCTAT 719598 vi v i i v i i vi v ---- i ii L1P4_orf2#LIN 2434 ATCGTTAAAATGGCCATACTGCCCAAAGCAATCTACAGATTCAACGCTAT 2483 chr3qtel1M 719599 ACCAATCAGACTCCTAAAAAACTATTTTAATGATCTAGAAAAAAATAACA 719648 v v i v i vivvv v i vv vi v - iv L1P4_orf2#LIN 2484 TCCTATCAAACTACCAACGTCATTTTTCACAGAATTAGAAAAAACT-ATT 2532 chr3qtel1M 719649 ACAAAGTTCATATGGAAAAACAAAAGA----------TCAAAAGAAT--T 719686 vi i vv v ----------i iv -- L1P4_orf2#LIN 2533 CTAAAATTCATATGGAACCAAAAAAGAGCCCGAATAGCCAAAGCAATCCT 2582 chr3qtel1M 719687 AATGAAAAAAATCAAATGAAGGTGGCCTAGCTGTACCAGATCTAAAATTA 719736 vv i v - vv v v vi vv v ii v i L1P4_orf2#LIN 2583 AAGCAAAAAGAACAAA-GCCGGAGGCATCACATTACCCGACTTCAAACTA 2631 chr3qtel1M 719737 TATTATAAAGCAATGGTTACTAAAACCATTTGGTATTGGCTAAGAAACAG 719786 i i i v ii v i viiv i ivv i L1P4_orf2#LIN 2632 TACTACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAG 2681 chr3qtel1M 719787 ACTAGTTGATCAATGGAATAGGTTAG---GTTCAAAGGACAAAACAGACA 719833 vvi v i i iv ---iii i -i i i v --v L1P4_orf2#LIN 2682 ACACATAGACCAATGGAACAGAATAGAGAACCCAGA-AATAAAGCCG--C 2728 chr3qtel1M 719834 ATAACTTTAATAATCTAGTGTTTGACAAACCCAA-AGACCCCAGTTTTTG 719882 i v vi iv ii v i vi i - i vviv ivv v L1P4_orf2#LIN 2729 ACACCTACAACCATCTGATCTTCGACAAAGTCGACAAAAATAAGCAATGG 2778 chr3qtel1M 719883 GGATAAGAACTCACTATTTGACAAAAATTGCTGGGAAAA 719921 - i v ii i viv v L1P4_orf2#LIN 2779 GGA-AAGGACTCCCTATTCAATAAATGGTGCTGGGATAA 2816 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 40.33 CpG sites = 142, Kimura (unadjusted) = 42.37 Transitions / transversions = 1.09 (142/130) Gap_init rate = 0.02 (19 / 863), avg. gap size = 1.89 (36 / 19) 12 11.25 6.90 0.00 chr3qtel1M 720567 720595 (279405) (TCCCC)n#Simple_repeat 1 31 (0) m_b155s252i10 5814 chr3qtel1M 720567 TCCCC-CTCCTTCCCT-CCATCCCCTCCCCT 720595 - i i - v (TCCCC)n#Simp 1 TCCCCTCCCCTCCCCTCCCCTCCCCTCCCCT 31 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.07 (2 / 28), avg. gap size = 1.00 (2 / 2) 1336 28.08 2.59 2.40 chr3qtel1M 721009 721548 (278452) C L1ME3G_3end#LINE/L1 (380) 544 4 m_b155s551i2 5815 chr3qtel1M 721009 TATTCCAAAACATTCATATATTACAATTTACCCAGCCATTCTCCAATTGA 721058 v ii vv ii i iii i i v C L1ME3G_3end#L 544 TATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTATTGA 495 chr3qtel1M 721059 TGGGCATCCATTCAATTTCCAGTTTTTAGCCATTGCAAAAGGAGCTGCCA 721108 i ii vvivi i v i i viiv v C L1ME3G_3end#L 494 TGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCTGCAA 445 chr3qtel1M 721109 CAAACATTCTTGCACATACAGGTCCCTTTCCC----TTCAA-TCTCTCTT 721153 ii i i i ?-- i v v v---- v i - v i ? C L1ME3G_3end#L 444 TGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATTTCTN 397 chr3qtel1M 721154 TGGGATATAAGCCCAGTAGTAACACTGCTGAATCAAAATGTATGCAGAGT 721203 i v v? ? v iiv i ii iv iv v C L1ME3G_3end#L 396 TAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGCATT 347 chr3qtel1M 721204 TTGACAACTTTTTGAGCAGAG--TTCCAAATTGCTCTCCAGAATGGTTGG 721251 --- v -- ii v-- v i i ? i v C L1ME3G_3end#L 346 TT---AAATTTT--AATAGATACTGCCAAATTGCCCTCCAAAANGGCTGT 302 chr3qtel1M 721252 ATCCATGCACAACTCCACCCACAATGCATCAGTGTCCCAGTTTCCCCGCA 721301 i v vi vii vi i i v v v v i C L1ME3G_3end#L 301 ACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCACA 252 chr3qtel1M 721302 TCCCCTCTCCCCCAAT--ATCTTTTC---CTGTCA--TCTTAGCCAATCT 721344 -- v vv v -- v v --- v i -- i v C L1ME3G_3end#L 251 --CCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATCT 204 chr3qtel1M 721345 GAGAGGTGTGTAGTGGTATCTCAGAATTAGTTTAATTTGCATTTCTCTGA 721394 vi viv i vvi iv i C L1ME3G_3end#L 203 GATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGA 154 chr3qtel1M 721395 TCAATAGTGATTTGGAACACCCTTTCATGTGAGTAGAAATAGTTTCCATT 721444 i v vv v i i i i vv vviiivi vi C L1ME3G_3end#L 153 TTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGTATT 104 chr3qtel1M 721445 TCATCATCTGAAAATTGTCTGTTCCTATCCTTTGACCATTTATCAATTGG 721494 v v vi i v v v v C L1ME3G_3end#L 103 TCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGG 54 chr3qtel1M 721495 AGAATGGCTTGATTTCTTATAAATTTGAGTCAGTTCTCTATTTATTTTGG 721544 iv-- v -- vi vivv i v i C L1ME3G_3end#L 53 GT--TGTCTT--TTTCTTATTGATTTGTAGGAGTTCTTTATATATTCTGG 8 chr3qtel1M 721545 AGAT 721548 v C L1ME3G_3end#L 7 ATAT 4 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 35.43 CpG sites = 74, Kimura (unadjusted) = 36.03 Transitions / transversions = 1.00 (74/74) Gap_init rate = 0.04 (19 / 539), avg. gap size = 1.42 (27 / 19) 346 29.15 2.63 2.18 chr3qtel1M 721402 721629 (278371) C L1M5_orf2#LINE/L1 (0) 3294 3066 m_b155s551i3 5815 chr3qtel1M 721402 TGATTTGGAACACCCTTTCATGTGAGTAGAAATAGTTTCCATTTCATCAT 721451 ?v v i i i vv vviiivi v? v v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr3qtel1M 721452 CTGAAAATTGTCTGTTCCTATCCTTTGACCATTTATCAATTGGA--GAAT 721499 i vi v vvi i v v ?v i-- vv C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTT 3195 chr3qtel1M 721500 GGCTTGATTTCTTATAAATTTGAGTCAGTTCTCTATTTATTTTGGAGATG 721549 v -- ? vi ? vivv i v i v i C L1M5_orf2#LIN 3194 GTCTT--TTTNTTATTGANTTGTAGGAGTTCTTTATATATTCTGGATACG 3147 chr3qtel1M 721550 AGGTCTTTATCAAA-ACCTTTAACTGTAAAGATGTTTTCCCAGTTTATTG 721598 vi i i - iv v -?i i v v i ? i i v C L1M5_orf2#LIN 3146 AGTCCTTTGTCAGATATATGT-NTTGCAAATATTTTCTCCCANTCTGTGG 3098 chr3qtel1M 721599 CTTCCCTTCTAATCTTTTTTTAATAG---CTTTT 721629 v i v -- i ii --- C L1M5_orf2#LIN 3097 CTTGCCTTTTCA--TTTTCTTAACGGTGTCTTTT 3066 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 37.22 CpG sites = 30, Kimura (unadjusted) = 38.77 Transitions / transversions = 0.86 (30/35) Gap_init rate = 0.04 (8 / 227), avg. gap size = 1.38 (11 / 8) 180 36.49 0.00 0.00 chr3qtel1M 722189 722262 (277738) L2#LINE/L2 2658 2731 (351) m_b155s601i5 5816 chr3qtel1M 722189 CTTCTCTTCTCAGACATTGCTCCTGCCTTAGTCTAGGCCCTTATCACCTC 722238 vi v vvv i iv ii i i i i vii i L2#LINE/L2 2658 CTTCTCACCACCTCCACTGCCACCACCCTGGTCCAAGCCACCATCATCTC 2707 chr3qtel1M 722239 ATACACAGATTCATGCAATAGCCT 722262 vii vii vv L2#LINE/L2 2708 TCGCCTGGATTACTGCAATAGCCT 2731 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 49.20 CpG sites = 16, Kimura (unadjusted) = 52.32 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.00 (0 / 73), avg. gap size = 0.0 (0 / 0) 31 0.00 0.00 0.00 chr3qtel1M 722618 722646 (277354) (T)n#Simple_repeat 1 29 (0) c_b155s251i0 5817 chr3qtel1M 722618 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 722646 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 334 31.58 20.53 0.00 chr3qtel1M 723922 724111 (275889) L3#LINE/CR1 3690 3918 (181) m_b155s601i6 5818 chr3qtel1M 723922 CCAGGCCATGTGAGAATTGCTTGAAAGAAATGGGCAGATTTCGCCTAGAG 723971 v i i i vi v i v v vi v i L3#LINE/CR1 3690 CCATGTCATATGAGGAACGGTTGAAGGAACTGGGGATGTTTAGCCTGGAG 3739 chr3qtel1M 723972 AAGAG-----TTGGAGGCAACTGGAGAGCTGCGTTCACAGATT------- 724009 ----- i vi vv v iv v v ------- L3#LINE/CR1 3740 AAGAGAAGACTTAGAGGAGACATGATAGCTGTCTTCAAATATTTGAAGGG 3789 chr3qtel1M 724010 ------------GGAGGGATCAATCTTGTTCTGCTTGAGTTCAGAAAGTA 724047 ------------i i iv i iv iv i ii i L3#LINE/CR1 3790 CTGTCATGTGGAAGAGGGATTAGACTTATTCTGTGTGGCTCCAGAGGGCA 3839 chr3qtel1M 724048 CAG---------------GGAAGGTGCAAGGAGACCAATGTAACCTCCAT 724082 v i--------------- v i i i vi v viv v L3#LINE/CR1 3840 GAACTAGGACCAATGGGTGGAAGTTACAGGGAGGCAGATTTCGGCTCAAT 3889 chr3qtel1M 724083 GTCCAGAAAAGCTTCCTAACCATGACAGC 724111 i vvi i i i v v v L3#LINE/CR1 3890 ATAAGGAAGAACTTTCTAACAATCAGAGC 3918 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 39.91 CpG sites = 31, Kimura (unadjusted) = 41.70 Transitions / transversions = 1.07 (31/29) Gap_init rate = 0.02 (4 / 189), avg. gap size = 9.75 (39 / 4) 211 15.48 9.84 4.69 chr3qtel1M 725976 726036 (273964) MIR#SINE/MIR 79 142 (120) m_b155s601i7 5819 chr3qtel1M 725976 AGCCCTGTGACCT-GAGCCAG---CTGA--CTCTCTAGACTGCCTCAGTT 726019 iv - i v --- v -- i--- MIR#SINE/MIR 79 AGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTG---TGCCTCAGTT 125 chr3qtel1M 726020 TCTGTATCTGTAAAATG 726036 ivi MIR#SINE/MIR 126 TCCTCATCTGTAAAATG 142 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 17.52 CpG sites = 5, Kimura (unadjusted) = 17.52 Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.10 (6 / 60), avg. gap size = 1.50 (9 / 6) 20 8.02 0.00 0.00 chr3qtel1M 727874 727900 (272100) (G)n#Simple_repeat 1 27 (0) m_b155s252i11 5820 chr3qtel1M 727874 GGGGGGGGGGGGGGGGGGGGGAGGAGG 727900 i i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGG 27 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 30 0.00 0.00 0.00 chr3qtel1M 729240 729267 (270733) (GAG)n#Simple_repeat 1 28 (0) c_b155s251i1 5821 chr3qtel1M 729240 GAGGAGGAGGAGGAGGAGGAGGAGGAGG 729267 (GAG)n#Simple 1 GAGGAGGAGGAGGAGGAGGAGGAGGAGG 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 15 13.81 4.76 2.33 chr3qtel1M 731039 731080 (268920) (GGCAGGG)n#Simple_repeat 1 43 (0) m_b155s252i12 5822 chr3qtel1M 731039 GGCA-GCGG-AGGGTCCTGGGGGCAGGGGTGCTGGGGGCAGGGG 731080 - v - vv v - v (GGCAGGG)n#Si 1 GGCAGGGGGCAGGGGGCAGGGGGCAGGGG-GCAGGGGGCAGGGG 43 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.07 (3 / 41), avg. gap size = 1.00 (3 / 3) 13 28.87 0.00 1.96 chr3qtel1M 731091 731142 (268858) (CCGCC)n#Simple_repeat 1 51 (0) m_b155s252i13 5823 chr3qtel1M 731091 CCGCACCGCCCCTCCCCCGCAGGGCCTGGCCCCTCCCCGCCTCGAGCCGT 731140 v -v vvv iv v i vv i (CCGCC)n#Simp 1 CCGCCCCGCCCC-GCCCCGCCCCGCCCCGCCCCGCCCCGCCCCGCCCCGC 49 chr3qtel1M 731141 CC 731142 (CCGCC)n#Simp 50 CC 51 Matrix = Unknown Transitions / transversions = 0.33 (3/9) Gap_init rate = 0.02 (1 / 51), avg. gap size = 1.00 (1 / 1) 61 24.09 0.55 3.41 chr3qtel1M 731888 732068 (267932) (TCTCTG)n#Simple_repeat 1 176 (0) m_b155s252i14 5824 chr3qtel1M 731888 TCTCTGTCGCTGTC-CTGTTTCGCTCTCTGTTTCTCTGTGTGTGTTTCTT 731936 v - i vv -- v v i v (TCTCTG)n#Sim 1 TCTCTGTCTCTGTCTCTGTCTCTGTCTCTG--TCTCTGTCTCTGTCTCTG 48 chr3qtel1M 731937 TTTGCCTGCCTCTCTGTGTGTCTCTTCCTCTGCCTCTGTGTCTGTCTTTC 731986 i -- i v v v vi i v -- (TCTCTG)n#Sim 49 TCT--CTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTC--TC 94 chr3qtel1M 731987 TGTGTGTGTCTGTGTCTCTGTCTCTCCGTGTGTCTCTTCCTCTGCCTCTC 732036 v v v viv v vi i v (TCTCTG)n#Sim 95 TGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTG 144 chr3qtel1M 732037 TCTGGGTCTGTTTCTCTGTCTCTTTGTCTATC 732068 vv v v v v i (TCTCTG)n#Sim 145 TCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTC 176 Matrix = Unknown Transitions / transversions = 0.40 (10/25) Gap_init rate = 0.04 (7 / 180), avg. gap size = 1.00 (7 / 7) 38 9.86 0.00 0.00 chr3qtel1M 732335 732389 (267611) (GT)n#Simple_repeat 1 55 (0) c_b155s251i2 5825 chr3qtel1M 732335 GTGTGAGTGTGTGTGTGTGTGTGTGTGTGCATGTGCGTGTGTGTGCGTGT 732384 v ii i i (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50 chr3qtel1M 732385 GTGTG 732389 (GT)n#Simple_ 51 GTGTG 55 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 196 33.87 6.56 0.78 chr3qtel1M 733638 733759 (266241) C L2b_3end#LINE/L2 (211) 255 127 m_b155s601i8 5826 chr3qtel1M 733638 CTGGGGGATTCAGAAAGTTTTCCTGTAGAAGCTGACACTCCTGCTGAGAC 733687 i ivi i i vi i v i v i ivv C L2b_3end#LINE 255 CTGGGGGGTCAGGGAGGGCTTCCCGGAGGAGGTGACATTTGAGCTGAGAC 206 chr3qtel1M 733688 ATGAAAAGGGAGAAGG--------GGGAGGAGGGATGGAGCAGCGAGTAC 733729 v iiiv v --------i v i i i i v v v v C L2b_3end#LINE 205 CTGAAGGATGAGTAGGAGTTGGCCAGGCGAAGAGGTGGGGAAGGGCGTTC 156 chr3qtel1M 733730 AGAGGCAGAGGCAGAGACATGCACAGAGGC 733759 v- v ivii ? ii i C L2b_3end#LINE 155 C-AGGCAGAGGGAACAGCANGTGCAAAGGC 127 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 45.73 CpG sites = 24, Kimura (unadjusted) = 47.34 Transitions / transversions = 1.41 (24/17) Gap_init rate = 0.02 (2 / 121), avg. gap size = 4.50 (9 / 2) 35 21.11 2.30 0.00 chr3qtel1M 733762 733848 (266152) (AGAGAC)n#Simple_repeat 1 89 (0) m_b155s252i16 5827 chr3qtel1M 733762 AGAAACAGAGACAGATAC--ACACACACACAGAAACAGAGATAGAGACAG 733809 i v -- v v v i i (AGAGAC)n#Sim 1 AGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAG 50 chr3qtel1M 733810 AGACAGAAACACAGAGAAAGAGACACACAAAGAAAGAGA 733848 i v v i v v v i v (AGAGAC)n#Sim 51 AGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGA 89 Matrix = Unknown Transitions / transversions = 0.60 (6/10) Gap_init rate = 0.01 (1 / 86), avg. gap size = 2.00 (2 / 1) 502 24.14 1.68 2.54 chr3qtel1M 734625 734743 (265257) MIRc#SINE/MIR 24 141 (127) m_b155s601i9 5828 chr3qtel1M 734625 AGAGCACTGGGCTTAGTGCCAGGAAGTCCCGGATTCAAATCCAGCCTCAG 734674 i i v i v i i i i v v v MIRc#SINE/MIR 24 AGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTG 73 chr3qtel1M 734675 ACATTTACTAGTCCTGTGAATGTAAGTAAATCGCTTAATTTCTCATTTAA 734724 v i iiv viv ii i i i ii --- i MIRc#SINE/MIR 74 CCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTC---TGA 120 chr3qtel1M 734725 --CTCAGTTTCCTCATCTGTA 734743 -- MIRc#SINE/MIR 121 GCCTCAGTTTCCTCATCTGTA 141 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 28.90 CpG sites = 19, Kimura (unadjusted) = 30.19 Transitions / transversions = 2.11 (19/9) Gap_init rate = 0.03 (4 / 118), avg. gap size = 1.25 (5 / 4) 333 28.45 6.16 1.31 chr3qtel1M 734758 734903 (265097) L1ME4c_3end#LINE/L1 299 451 (379) m_b155s551i4 5829 chr3qtel1M 734758 AATTAGTTCAGCCTTTTTTGGAAAGAAACTTGG--ATCTATTCCCAG-GC 734804 i v i i - v i -- vii vi v - L1ME4c_3end#L 299 AATTGGTACAACCCTTTT-GGAAAGCAATTTGGCAATACGTATCAAGAGC 347 chr3qtel1M 734805 CACTAAACTGTTCATCCCTTTTCACCCAGCAATCCCACTATTAGTCATAT 734854 iv v v i v i i vi i vv v L1ME4c_3end#L 348 CATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTT 397 chr3qtel1M 734855 AACCCATGGGGA----TCAAAGAAAGAAAAGGGTTCCTATGCAC--AGAT 734898 v i v ii ---- ii i ii i -v -- L1ME4c_3end#L 398 ATCCTAAGGAAATAATTCAAAAGAAGGAAAAAGCT-ATATGCACGAAGAT 446 chr3qtel1M 734899 ACTTA 734903 ii i L1ME4c_3end#L 447 GTTCA 451 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 35.67 CpG sites = 25, Kimura (unadjusted) = 36.94 Transitions / transversions = 1.56 (25/16) Gap_init rate = 0.04 (6 / 145), avg. gap size = 1.83 (11 / 6) 19 8.38 5.00 2.44 chr3qtel1M 735822 735861 (264139) (AAAG)n#Simple_repeat 1 41 (0) m_b155s252i17 5830 chr3qtel1M 735822 AAATAAAGGAAGGAAAGAAAG-AAGGAAGAAAG-AAGAAAGA 735861 v - i - i - (AAAG)n#Simpl 1 AAAGAAA-GAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA 41 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.08 (3 / 39), avg. gap size = 1.00 (3 / 3) 265 17.02 0.00 0.00 chr3qtel1M 737375 737421 (262579) L2a_3end#LINE/L2 465 511 (6) m_b155s601i10 5831 chr3qtel1M 737375 ACAGTGTCTGGCACATAGTAAGTGATTAATAAATATTTATTGACTAA 737421 i i i v i i v i L2a_3end#LINE 465 ACAGTGCCTGGCACATAGTAGGCGCTCAATAAATATTTGTTGAATGA 511 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 17.25 CpG sites = 6, Kimura (unadjusted) = 19.91 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 314 33.74 4.97 0.60 chr3qtel1M 737570 737730 (262270) C L3#LINE/CR1 (869) 3230 3063 m_b155s601i11 5832 chr3qtel1M 737570 TTGTGCTAT-TGGAAATTTGA----CATTTTATCTATGCCTTCATGCAAG 737614 ii - v ---- viiv i v C L3#LINE/CR1 3230 TTGTGTCATCTGCAAATTTGATAAGCATGCCTTCTATGTCTTCATCCAAG 3181 chr3qtel1M 737615 TCAGTGACAAAAATATCAAATCT--CTGTGATGAAGGAGATTCCCCCA-G 737661 v i i ii ivv-- v - iiv v vvv ii- C L3#LINE/CR1 3180 TCATTGATAAAAATGTTGAACAGGACAG-GGCCAAGGACAGAGCCCTGTG 3132 chr3qtel1M 737662 GCACTATCTTAGAGACTACCTTCCCTGCTGAAATTGAACCATAGATGGTT 737711 vvivi iv i vv i v i v vi vivi C L3#LINE/CR1 3131 GCACGCCACTAGAGACCTCCCTCCAGGTTGACATCGATCCATTAATCAAC 3082 chr3qtel1M 737712 GCTTTTTGGTTCTGGCCAT 737730 i i v v i i i C L3#LINE/CR1 3081 ACCTTTTGGGTATAGTCGT 3063 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 43.49 CpG sites = 28, Kimura (unadjusted) = 45.75 Transitions / transversions = 1.08 (28/26) Gap_init rate = 0.03 (5 / 160), avg. gap size = 1.80 (9 / 5) 302 25.24 14.56 0.00 chr3qtel1M 737731 737833 (262167) C L3#LINE/CR1 (1105) 2994 2877 m_b155s601i12 5832 chr3qtel1M 737731 ATATTATAATGGGCTTGACCAAACACTTCA-TGAAATCCAGGTA-ACCCT 737778 i i vi i vii ii i ii- i - i? C L3#LINE/CR1 2994 ATATCATGAGAGACTTTGTCAAATGCCTTGCTGAAATCCAGATACACTNT 2945 chr3qtel1M 737779 GTC-----CATTA-------CTGCTAGTCTATT-ATCCTATCAAGAAAGA 737815 ----- v------- i i v - i i i C L3#LINE/CR1 2944 GTCTACGGCATTCCCCTGATCTACCAGTCTAGTAACCCTATCAAAAAAGG 2895 chr3qtel1M 737816 AAATGAGGTTCACTTGAC 737833 vii i C L3#LINE/CR1 2894 AAATGAGGTTAGTTTGGC 2877 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 33.46 CpG sites = 21, Kimura (unadjusted) = 33.46 Transitions / transversions = 4.20 (21/5) Gap_init rate = 0.05 (5 / 102), avg. gap size = 3.00 (15 / 5) 16 24.17 0.00 2.17 chr3qtel1M 738069 738115 (261885) (GTAG)n#Simple_repeat 1 46 (0) m_b155s252i18 5833 chr3qtel1M 738069 GTAAGTAGATAAGGTAGAAAGGTAAATAGGTAGGTAGCTAGATGGGT 738115 i i - iv ii v i i (GTAG)n#Simpl 1 GTAGGTAGGT-AGGTAGGTAGGTAGGTAGGTAGGTAGGTAGGTAGGT 46 Matrix = Unknown Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.02 (1 / 46), avg. gap size = 1.00 (1 / 1) 682 26.89 12.00 0.80 chr3qtel1M 738183 738407 (261593) C MIRb#SINE/MIR (6) 262 13 m_b155s601i13 5834 chr3qtel1M 738183 AAAGCTAACATTTCTGTGGCACCTACTATGTAC------------TAAGG 738220 i v v vvi i i i ------------ v C MIRb#SINE/MIR 262 AGAGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGC 213 chr3qtel1M 738221 ACTTTACAAATATT-TTTTAATTGATCTTCCTAACTACTCTGGAAAGTCA 738269 i vii - i i v i i vi v i vi i vi C MIRb#SINE/MIR 212 GCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAG 163 chr3qtel1M 738270 GTGCTATTATCCCCATTTTACAAATGA------------TCAGAGAGGTT 738307 ii i ------------ C MIRb#SINE/MIR 162 GTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTT 113 chr3qtel1M 738308 AAATGACATGGCCAGAATCATACAAATAGCGAGTGTCTAAGGTCAAATTT 738357 i i v v iii i iv ii v vi vivii i C MIRb#SINE/MIR 112 AAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTC 63 chr3qtel1M 738358 GAACTCAGGTCT-CCTGACTCC-AGGCCCTTGTACTCTATGTACTGCTCC 738405 i -i - i -- i v vi v C MIRb#SINE/MIR 62 GAACCCAGGTCTGTCTGACTCCAAAGCCC--GTGCTCTTTCCACTGCACC 15 chr3qtel1M 738406 AC 738407 C MIRb#SINE/MIR 14 AC 13 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 31.06 CpG sites = 39, Kimura (unadjusted) = 34.56 Transitions / transversions = 1.86 (39/21) Gap_init rate = 0.03 (7 / 224), avg. gap size = 4.14 (29 / 7) 27 7.18 4.35 2.13 chr3qtel1M 738416 738461 (261539) (GA)n#Simple_repeat 1 47 (0) m_b155s252i19 5835 chr3qtel1M 738416 GAGAGAGAGAAAGA-AGAGAGACAGAGAGATGA-AGAGAGAGAGAAAG 738461 i - v - - i (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGA-GAGAGAGAGAGAGAGAG 47 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.07 (3 / 45), avg. gap size = 1.00 (3 / 3) 344 26.67 3.67 3.67 chr3qtel1M 739133 739241 (260759) MIR#SINE/MIR 133 241 (21) m_b155s601i14 5836 chr3qtel1M 739133 CTGTAAAAT----ATCATACTATCATCTCTCTCTCAGCATTATTGTGAAT 739178 ---- v v vi i vi vi vi i iv MIR#SINE/MIR 133 CTGTAAAATGGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGG 182 chr3qtel1M 739179 ATTAAATGAGTTAATAAGTTTTTGTAAAGTCCTCAGCATAGTGTCTGACA 739228 ----iv iv i v i i i MIR#SINE/MIR 183 ATTAAATGAGTTAATA----CATGTAAAGCGCTTAGAACAGTGCCTGGCA 228 chr3qtel1M 739229 TATCGTAGATGCT 739241 i v iii MIR#SINE/MIR 229 CATAGTAAGCGCT 241 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 30.95 CpG sites = 17, Kimura (unadjusted) = 33.86 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.05 (5 / 108), avg. gap size = 1.60 (8 / 5) 15 24.40 0.00 0.00 chr3qtel1M 739266 739299 (260701) (CT)n#Simple_repeat 1 34 (0) m_b155s252i20 5837 chr3qtel1M 739266 CTCTCTCTGAATTTCTTTCTTTCTCTCTCCCTCT 739299 vvv i i i i (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 34 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 181 23.31 0.00 16.98 chr3qtel1M 739468 739529 (260471) MIR3#SINE/MIR 125 177 (31) m_b155s601i15 5838 chr3qtel1M 739468 TTTCTCCAGTTGTAAAAAGGCGGGTGGAGAAGGTTGGAGTAGATAGCCTC 739517 ii vi --------v ii v iii MIR3#SINE/MIR 125 TTTCCTCATCTGTAAAA--------TGAGGGGGTTGGACTAGATGATCTC 166 chr3qtel1M 739518 TTGAGGTCCCTT 739529 - i MIR3#SINE/MIR 167 -TAAGGTCCCTT 177 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 28.23 CpG sites = 9, Kimura (unadjusted) = 28.23 Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.15 (9 / 61), avg. gap size = 1.00 (9 / 9) 306 38.19 3.89 1.08 chr3qtel1M 740910 741089 (258911) L3#LINE/CR1 3912 4096 (3) m_b156s601i1 5839 chr3qtel1M 740910 TCAGAAACTGTCAGGACAGAGGATC--CTGTCCCAAGATGGAATGGATTG 740957 i- vii v vi i v-- i i i? v v i iii v L3#LINE/CR1 3912 TCAGAG-CTGTCCAAAAATGGAATGGGCTGCCTCGNGAGGTAGTGAGCTC 3960 chr3qtel1M 740958 TCC-TTGCTAGGAGACTTCCAAGAGTAGGCCAAGAGAACACTTCTTGGGT 741006 i - ii - iiv i viv iiiiv v v ii v L3#LINE/CR1 3961 CCCGTCACT-GGAGGTGTTCAAGCAGAGGCTGGATGACCACTTGTCAGGG 4009 chr3qtel1M 741007 CAGTTCTTGTGAAGATTCCTCTTCAGGATGGGAG--TAGATTGGGCTGCT 741054 vv v v viii viviv -- i i i iivi i L3#LINE/CR1 4010 ATGTTGTAGAAGGGATTCCTGCATTGGATGGGAGGTTGGACTAGATGACC 4059 chr3qtel1M 741055 CCTGAGGTTCTTTTCAATTC--AAACTCTGTGATTCT 741089 i i i i i i -- i i L3#LINE/CR1 4060 TCTAAGGTCCCTTCCAACTCTGAGATTCTGTGATTCT 4096 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 57.00 CpG sites = 45, Kimura (unadjusted) = 58.39 Transitions / transversions = 1.96 (45/23) Gap_init rate = 0.03 (6 / 179), avg. gap size = 1.50 (9 / 6) 27 13.72 0.00 0.00 chr3qtel1M 741703 741750 (258250) (CACACA)n#Simple_repeat 1 48 (0) m_b156s252i1 5840 chr3qtel1M 741703 CACAAGCACACAGACACACACAGACACACACAGACACACACACTCACA 741750 vi v v v v (CACACA)n#Sim 1 CACACACACACACACACACACACACACACACACACACACACACACACA 48 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 708 38.96 2.43 3.31 chr3qtel1M 742805 743749 (256251) C Tigger5#DNA/TcMar-Tigger (945) 1461 525 m_b156s502i0 5841 chr3qtel1M 742805 GCGAGCTCCTCCCACGACTCGGAGATGTTGTACACGGCATTGAGGATGTT 742854 i vi i i viv i v viiv ii v i C Tigger5#DNA/T 1461 GTGACTTCTTCCCATGCTGCAGCGATGTTCCGGATAGCATTTAGAATGTT 1412 chr3qtel1M 742855 GTAGTTCCGCCAGAACTCCCGGATCGTGCCCTTGTCGTCCCTGTGGGCTC 742904 iv iiiiiv i i v ------- v vvi vviv C Tigger5#DNA/T 1411 AAAACCTTTCCAAAACTCTCGGAGCGT-------TCGGCCAGATTCAGTC 1369 chr3qtel1M 742905 TCTGCTGCAGCAGATGGAAGACCCTC--CGCAGGTAGCAAGCCTTGAAGG 742952 v v vi vvii v - vi i-- i ii i v i v C Tigger5#DNA/T 1368 GCTTCAACAGCCTGCGCAA-ACGTTTGGCGTAAATAGTATGCTTTGAACG 1320 chr3qtel1M 742953 TGGCGATCACGCCTTGGTTCATGGGCTGGATCAGGGACGTGGTGTTCTTG 743002 ii v ii i v i i v v vv v vvv C Tigger5#DNA/T 1319 CAGCTATTGCGCCTTGGTCCATTGGTTGAATGAGTGCGGTTGTGTTCGGC 1270 chr3qtel1M 743003 GGGAGGTACTCCACTCGCACGTTGTCGGA--CAGGTCGTCTAGGTTTCCC 743050 v ii v v iivi i ii-- -- v ii v vi viivi C Tigger5#DNA/T 1269 GGCAAATACACAACCTTTACATCA--GGATGCATGTCACCGATATGCTGT 1222 chr3qtel1M 743051 GGGTGGCCCGGGGCGCTGTCCAGGATCAGCAGCGCCTTGTTGGGGAGGTT 743100 i v i i ii i i v vii vvv v C Tigger5#DNA/T 1221 GGATGCCCTGGAGCATTGTCTAAGATCAGAAGAATCTTGAATGGGATGTT 1172 chr3qtel1M 743101 GTTCTGGGCGCAGTATTTCTCCACGGCCGGGCAAAAAAAGTGCACGAACC 743150 i vvii i iiiiii vvv ivv v v vi C Tigger5#DNA/T 1171 GTTTTGCCTACAATATTCTCTTGCCTGCGGAATAAAACAGTTCAAAAACC 1122 chr3qtel1M 743151 ACTCCTGGAA-GAGGCTCATGGTCACCCAGGCCTTTTTGTGGGAGCGCCA 743199 v i vi -i v v - i i i vivi vi C Tigger5#DNA/T 1121 AGTCTTCAAACAATGCTGAT-GTCATCCAGGCTTTCTTGTTATGGCGATA 1073 chr3qtel1M 743200 GATCACCGGCAGGT-TGGGCTTGGAGAAACCCTTGAGGGCGCGGGGGCTC 743248 - v v v i i- iv vvv v ii iv v vi i C Tigger5#DNA/T 1072 -ATAAACGGGAAGCGTATGCTTGCTCACATTCTTGAATGCTCTAGGGTTC 1024 chr3qtel1M 743249 TCCGAATGGTAGACCAGCAGCGGCTTGAGCTTGAAGTCGCCTGCGGCATT 743298 i ii v iv v ii ---v ii C Tigger5#DNA/T 1023 TCCGAGTGGTAGATTAGGAAAGGCTTTAATTTGAA---CCCTGCAACATT 977 chr3qtel1M 743299 GCCCCCCAGGAGGAGAGTCAGAAGGTCCCTGGCTGCCTTAAAGCCGGATG 743348 v v ii v vi i v v ii iv i v v iii C Tigger5#DNA/T 976 TCCACCCAAAAGCAGCATTACACGGTCTTTGAATGCCTTGAATCCTGGCA 927 chr3qtel1M 743349 CGGTTTT---CTCCTCCACCGAGATGAAGGT---CCTG-TCGGGCAGGCG 743391 iv i --- i ------- v ---iv - v vi C Tigger5#DNA/T 926 TTGTCTTGGACTCTT-------GATGAATGTATGTATGCTCCGGCATACG 884 chr3qtel1M 743392 CTTCCAGAAGAGCCCCATCTCGTCCACATTGAACACCTGCTGGGGTGTGT 743441 v iv i i i i v i i ii i vv iivi C Tigger5#DNA/T 883 CTTCCAGAACAAGCTCGTTTCATCGACATTAAATATTTGTTCTGGCAAAT 834 chr3qtel1M 743442 AGCCTCCCTCCTGGATGACCTTCCTCAGCGCCTC--GGGGTACTTGGCCG 743489 viiii v vvi v i i viv v i --viiivi -- v C Tigger5#DNA/T 833 ATTTCTCATCCACAATTATCCTATGCAGCTCTTCCTTAAAAGCTT--CGG 786 chr3qtel1M 743490 CAGCTTCTGGATCTGTGCTGACTGTTTCGCTGCTAGTGCCCAGGTTGGGC 743539 v v v v ii vi ii i i iiivii vi iv v C Tigger5#DNA/T 785 CACCTTCAGTATCGGCACTTGCTGCCTCACCGCTGACCTTCACATTATGA 736 chr3qtel1M 743540 AGGCTGTGGCGGGCTTTGAACC--TGGTAAACCAGCCGCGGCTGGCTCCG 743587 iii i i vvi v -- -- v ii i v vii C Tigger5#DNA/T 735 AAATTATGACGCCTTTTGAAGCGTTGG--AACCACCCATGACTTGCTATA 688 chr3qtel1M 743588 AAGGTCT-CG---GCCTCAGCACTTTGGCCCTGCTCCCGCTTCAGGTCCT 743633 vi i - ---i v vi vv v i v - ---i i vviv C Tigger5#DNA/T 687 AACATTTGCGTATACGTAGGATCATCGGCAC-GCTC---TTTTAGCGTAT 642 chr3qtel1M 743634 GGAATAGGCTCTTGGCCTTGTCCTGGATGGTGGAGACGTTGACTGGCACC 743683 v v i ii v iv v viiv v i i vi i -i C Tigger5#DNA/T 641 CGAAAAGACTTCTTGCCTTAGCCTGGATCGTCAGTAGGCTAAGCGGTA-T 593 chr3qtel1M 743684 CCGCGTTGGT-TCTGGTCCTCGATCCAGACGCTCAGTAGCCGCTCCATGT 743732 v v iv - i v vii viv iiivi i C Tigger5#DNA/T 592 GCGCTTCTGTATCTGGTCTTCCATCCACGTGACAAGTAATTTTTCCATAT 543 chr3qtel1M 743733 TCTCCATC-ACCAGGCTC 743749 iv v -i vi C Tigger5#DNA/T 542 CATCAATCGGCCCAGCTC 525 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 55.16 CpG sites = 197, Kimura (unadjusted) = 57.14 Transitions / transversions = 1.24 (197/159) Gap_init rate = 0.05 (44 / 944), avg. gap size = 1.23 (54 / 44) 770 36.16 1.99 2.50 chr3qtel1M 742849 743452 (256548) C Tigger3#DNA/TcMar-Tigger (1427) 1602 1002 m_b156s502i1 5841 chr3qtel1M 742849 GATGTTGTAGTTCCGCCAGAACTCCCGGATCGTGCCCTTGTCGTCCCTGT 742898 i i iv i v --- iv----- v i v C Tigger3#DNA/T 1602 GATGTTGTAATCCTTCCAGAATTGC---ATCAG-----TGTCTTCTCAGT 1561 chr3qtel1M 742899 GGGCTC-TCTGCTGCAGCAGATGG--------AAGACCCTCCGCAGGTAG 742939 vvi - v i - i -------- ii v C Tigger3#DNA/T 1560 GTCTTCCTCAGTTGCAGCA-ATAGCCTGGGCAAAGGTCCTCCTCAGGTAG 1512 chr3qtel1M 742940 CAAGCCTTGAAGGTGGCGATCACGCCTTGGTTCATGGGCTGGATCAGGGA 742989 i i i i iv v v v i i v i ii C Tigger3#DNA/T 1511 TAGGCCTTAAAAGCTGCTATAACTCCTTGATCCATTGGTTGGATCAAAGA 1462 chr3qtel1M 742990 CGTGGTGTTCTTGGGGAGGTACTCCACTCGCACGTTGTCGGAC--AGGTC 743037 v ivvi iv v ivv ii -- i-- i C Tigger3#DNA/T 1461 GGTGGTGTTTGGAGGGAGAAACACCACTTTGATATTG--GGATGAAGATC 1414 chr3qtel1M 743038 GTCTAGGTTTCCCGGGTGGCCCGGGGCGCTGTCCAGGATCAGCAGCGCCT 743087 ii v vivvvvvv i vv v i ii i v vi v ivii C Tigger3#DNA/T 1413 ACCAATAAAAGGAGGATGTGCGGGAGCATTATCAACAATAAGCAAAATCT 1364 chr3qtel1M 743088 TGTTGGGGAGGTTGTTCTGGGCGCAGTATTTCTCCACGGC-CGGGCAAAA 743136 vvi v v i vvivi i ivv - v v i C Tigger3#DNA/T 1363 TGAAAGGTATGTTATTCTCCAAACAGTACTTCTCCATTTCGCTGGCATAG 1314 chr3qtel1M 743137 AAAGTGCACGAACCACTCCTGGAAGAGGCTCATGGTCACCCAGGCCTTTT 743186 v v - v ivvvv i vv vv i v v i C Tigger3#DNA/T 1313 CAATT-CAGGAGGGCATCTTGGAAGAGGAGCTGGGTCATCCATGACTTCT 1265 chr3qtel1M 743187 TGTGGGAGCGCCAGATCACCGGCAGGTTGGGCTTGGAGAAACCCTTGAGG 743236 i v vvv vvi vv i vv v ivv v iv i C Tigger3#DNA/T 1264 TATTGCTCCTGTAGTACACTGGCAGTGTGTGCTTATTGATATGCTTGAAG 1215 chr3qtel1M 743237 GCGCGGGGGCTCTCCGAATGGTAGACCAGCAGCGGCTTGAGCTTGAAGTC 743286 v v i vvvi vi i vv iv i v ii --- v C Tigger3#DNA/T 1214 GCCCTGGGGTTCTCACTGTGCCAGATCACAAAGGGTTTCAATTT---GTA 1168 chr3qtel1M 743287 GCCTGCGGCATTGCCCCCCAGGAGGAGAGTCAGAAGGTCCCTGGCTGCCT 743336 ii v v i vv i vvvv i iivv C Tigger3#DNA/T 1167 GCCTGCAACATTGCCCCCAAGCAAGACTGTTATCCTGTCCTTAAAAGCCT 1118 chr3qtel1M 743337 TAAAGCCGGATGCGGTTTTCTCCTCCACCGAGATGAAGGTCCTGTCGGGC 743386 i i v iiiiv vi vv vivvi i v i C Tigger3#DNA/T 1117 TGAAACCTGGCATTGACTTGGCCTCCTTATGGATGAAAGTCCTTTCAGGC 1068 chr3qtel1M 743387 AGGCGCTTCCAGAAGAGCCCCATCTCGTCCACATTGAACACCTGCTGGGG 743436 vv i v vvvvi i i i v ii vv C Tigger3#DNA/T 1067 ATCCGTTTCCAGAATAGGGAGGTTTCATCCATATTGAAGATTTGCTCTGG 1018 chr3qtel1M 743437 TGTGTAGCCTCCCTCC 743452 iiv iii i C Tigger3#DNA/T 1017 CAAGTAATTTTCCTCC 1002 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 49.88 CpG sites = 97, Kimura (unadjusted) = 49.88 Transitions / transversions = 0.84 (97/116) Gap_init rate = 0.03 (19 / 603), avg. gap size = 1.42 (27 / 19) 910 38.47 1.16 1.16 chr3qtel1M 742937 743712 (256288) C Tigger1#DNA/TcMar-Tigger (957) 1461 686 m_b156s502i2 5841 chr3qtel1M 742937 TAGCAAGCCTTGAAGGTGGCGATCACGCCTTGGTTCATGGGCTGGATCAG 742986 ii v i v vi i v i i v vv v C Tigger1#DNA/T 1461 TAATAAGACTTGAAAGTCGAAATTACTCCTTGATCCATGGGCTGCAGAAT 1412 chr3qtel1M 742987 GGACGTGGTGTTCTTGGGGAGGTACTCCACTCGCACGTTGTCGGACAGGT 743036 i v vvii v v v vv v vivv iv iv i v vv C Tigger1#DNA/T 1411 GGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCTTGTACATCT 1362 chr3qtel1M 743037 CGTCTAGGTTTCCCGGGTGGCCCGGGGCGCTGTCCAGGATCAGCAGCGCC 743086 vvii ivi ii i v v ii v v v i iiiii C Tigger1#DNA/T 1361 CCATCAGAGCTCTTGGGTGACCAGGTGCATTGTCAATGAGCAGTAATATT 1312 chr3qtel1M 743087 TTGTTGGGGAGGTTGTTCTGGGCGCAGTATTTCTCCACGGCCGGGCAAAA 743136 vvi i vv v i vv v vv v i i- vv C Tigger1#DNA/T 1311 TTGAAAGGAATCTTTTTTTCTGAGCAGTAGGTCTCAACAGT-GGGCTTAA 1263 chr3qtel1M 743137 AAAGTGCA-CGAACCACTCCTGGAAG-AGGCTCATGGTCACCCAGGCCTT 743184 vi v -ii - v v i- iiviiiv i i C Tigger1#DNA/T 1262 AATATTCAGTAAACCA-TGCTGTAAACAGATGTGCTGTCATCCAGGCTTT 1214 chr3qtel1M 743185 TTTGTGGGAGCGCCAGATCACCGGCAGGTTGGGCTTGGAGAAACCCTTGA 743234 v vvv vivvi v v iv i ii i viv ii i C Tigger1#DNA/T 1213 GTTGTTCCATTTATAGAGCACAGGCAGAGTAGATTTAGCATAATTCTTAA 1164 chr3qtel1M 743235 GGGCGCGGGGGCTCTCCGAATGGTAGACCAGCAGCGGCTTGAGCTTGAAG 743284 v vi ii i v i iv vi v i i C Tigger1#DNA/T 1163 GGGCCCTAGGATTTTCGGAATGGTAAATGAGCATTGGCTTCAACTTAAAG 1114 chr3qtel1M 743285 TCGCCTGCGGCATTGCCCCCCAGGAGGAGAGTCAGAAGGTCCCTGGCTGC 743334 i v v iv i iv i vvv i v vv C Tigger1#DNA/T 1113 TCACCAGCTGCATTAGCCCCTAACAAGAGAGTCAGCCTGTCCTTTGAAGC 1064 chr3qtel1M 743335 CTTAAAGCCGGATGCGGTTTTCTCCTCCACCGAGATGAAGGTCCTGTCGG 743384 i i i iiiiv vi iviv vv i ivvv C Tigger1#DNA/T 1063 TTTGAAGCCAGGCATTGACTTCTCCTCTCTAGCTATGAAAGTCCTAGATG 1014 chr3qtel1M 743385 GCAGGCGCTTCCAGAAGAGCCCCATCTCGTCCACATTGAACACCTGCTGG 743434 vviv iv ivv ii i i v i i v C Tigger1#DNA/T 1013 GCATCTTCTTCCAATAGAAGGCTGTTTCGTCTACATTGAAAATCTGTTGT 964 chr3qtel1M 743435 GGTGTGTAGCCTCCCTCCTGGATGACCTTCCTCAGCGCCTCGGGGTACTT 743484 vvv v i v vi i vvii vv i v i vi C Tigger1#DNA/T 963 TTAGTGTAGCCACCTTCATCAATGATCTTAGCTAGATCTTCTGGATAACT 914 chr3qtel1M 743485 GGCCGCAGCTTCTGGATCTGTGCTGACTGTTTCGCTGCTAGTGC--CCAG 743532 v i iv v ii vi i i -- v ii --ii v C Tigger1#DNA/T 913 TGCTGCAGCTTCTACATCAGCACTTGCTGCTTCAC--CTTGCACTTTTAT 866 chr3qtel1M 743533 GTTGGGCAGGCTGTGGCGGGCTTTGAACCTGGTAAACCAGCCGCGGCTGG 743582 iv v i v ivv vvv i i vi i i v v i C Tigger1#DNA/T 865 GTTATGGAGACGGCTTCTTTCCTTAAACCTCATGAACCAACCTCTGCTAG 816 chr3qtel1M 743583 CTCCGAAGGTCTCGGCCTCAGCACTTTGGCCCTGCTCCCGCTTCAGGTCC 743632 i i vv i vv iv viii vi iiv vvv vivvv C Tigger1#DNA/T 815 CTTCAAACTTTTCTTCTGCAGCTTCCTCACCTCTCTCAGCCTTCATAGAA 766 chr3qtel1M 743633 TGGAATAGGCTCTTGGCCTTGTCCTGGATGGTGGAGACGTTGACT----G 743678 v v iv ivv ii ----v i v i ---- C Tigger1#DNA/T 765 TTGAAGAGAGTTAGGGCCTTGCTCTGGAT----TAGGCTTTGGCTTAAGG 720 chr3qtel1M 743679 GCACCCCGC-GTTGGTTCTGGTCCTCGATCCAGAC 743712 v ivii i- i - i i v C Tigger1#DNA/T 719 GAATGTTGTGGCTGGTT-TGATCTTCTATCCAGAC 686 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 54.98 CpG sites = 144, Kimura (unadjusted) = 54.98 Transitions / transversions = 0.95 (144/151) Gap_init rate = 0.02 (14 / 775), avg. gap size = 1.29 (18 / 14) 248 8.33 0.00 0.00 chr3qtel1M 744238 744273 (255727) C Tigger23a#DNA/TcMar-Tigger (150) 623 588 m_b156s502i3 5842 chr3qtel1M 744238 AAAGTCACACTTCAGAATGCAGCAAACCTTTTGAAA 744273 i v i C Tigger23a#DNA 623 AAAATCACACTTAAGAATGCAGCAAACCTTTTAAAA 588 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 8.91 CpG sites = 2, Kimura (unadjusted) = 8.91 Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 270 35.69 5.95 1.55 chr3qtel1M 744699 744883 (255117) C L3#LINE/CR1 (55) 4044 3852 m_b156s601i2 5843 chr3qtel1M 744699 CCTGCCCTCCAGTGAAGGAGCCCCTGCTTGAAGCTCCCTGAGAAGGGCTG 744748 v v i v ii v vv vv v v v v C L3#LINE/CR1 4044 CCTCCCATCCAATGCAGGAATCCCTTCTACAACATCCCTGACAAGTGGTC 3995 chr3qtel1M 744749 GTCTAAGCCTGGGTGTGGAGACCTCTC-TGACTAGGCAGCCCTCCATCCT 744797 i i- vv iv i v iv- -i v i v i i ii C L3#LINE/CR1 3994 ATCC-AGCCTCTGCTTGAACACCTCCAGTGAC-GGGGAGCTCACTACCTC 3947 chr3qtel1M 744798 CGAAGGTGACCCCTTCCCTGGTGGGAAA---------GTGAGAACATT-T 744837 ?vi iii v v vv v v --------- v vi - C L3#LINE/CR1 3946 NCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGATTGTTAGAAAGTTCT 3897 chr3qtel1M 744838 CCCTTAAATTCAGATTGAAACTGGTATCTTGACAACCTCCCTCCAT 744883 i v v -ii iiv iv iivii i vi C L3#LINE/CR1 3896 TCCTTATATTGAG-CCGAAATCTGCCTCCCTGTAACTTCCACCCAT 3852 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 46.49 CpG sites = 31, Kimura (unadjusted) = 49.57 Transitions / transversions = 0.91 (31/34) Gap_init rate = 0.03 (6 / 184), avg. gap size = 2.33 (14 / 6) 313 35.00 10.71 0.00 chr3qtel1M 745642 745781 (254219) C L3#LINE/CR1 (13) 4086 3932 m_b156s601i3 5844 chr3qtel1M 745642 AACCCCAGAGT-GGAAAGGACCCCAGGGATC--------CA-----CAAT 745677 i i - i ii i i -------- ----- v C L3#LINE/CR1 4086 AATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCAACCTCCCAT 4037 chr3qtel1M 745678 TCGGGG-AGGAACCCTCTCTGCAGGAACCTTACCAGATGGTCATTGAGCT 745726 i iiv - i ii i iv v i iv ii iv i C L3#LINE/CR1 4036 CCAATGCAGGAATCCCTTCTACAACATCCCTGACAAGTGGTCATCCAGCC 3987 chr3qtel1M 745727 CTTCCTTGAAAGTTTCTGGAACTGGGGAGCTCTCTACCTCATAGAACAAA 745776 ii v viii ii vivi v ?iiiii iv C L3#LINE/CR1 3986 TCTGCTTGAACACCTCCAGTGACGGGGAGCTCACTACCTCNCGAGGCAGC 3937 chr3qtel1M 745777 CCACT 745781 i C L3#LINE/CR1 3936 CCATT 3932 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 49.49 CpG sites = 37, Kimura (unadjusted) = 52.95 Transitions / transversions = 3.08 (37/12) Gap_init rate = 0.03 (4 / 139), avg. gap size = 3.75 (15 / 4) 18 0.00 0.00 0.00 chr3qtel1M 746199 746221 (253779) (GGA)n#Simple_repeat 1 23 (0) m_b156s252i2 5845 chr3qtel1M 746199 GGAGGAGGAGGAGGAGGAGGAGG 746221 (GGA)n#Simple 1 GGAGGAGGAGGAGGAGGAGGAGG 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 16 5.20 0.00 0.00 chr3qtel1M 746954 746973 (253027) (AC)n#Simple_repeat 1 20 (0) m_b156s252i3 5846 chr3qtel1M 746954 ACAAACACACACACACACAC 746973 v (AC)n#Simple_ 1 ACACACACACACACACACAC 20 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 210 23.40 0.00 0.00 chr3qtel1M 747295 747341 (252659) L2b_3end#LINE/L2 395 441 (25) m_b156s601i4 5847 chr3qtel1M 747295 TGTATTCTCGCGGCTCAGCACGGTGCCTGGCACACAGTCGGGGCTTA 747341 i i ivv ii i ? v v i L2b_3end#LINE 395 TGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCA 441 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 29.60 CpG sites = 7, Kimura (unadjusted) = 29.60 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 249 32.74 0.88 2.70 chr3qtel1M 747353 747465 (252535) L3b_3end#LINE/CR1 448 558 (648) m_b156s601i5 5848 chr3qtel1M 747353 AGTTCTATACTTAAGTCTCCAAAAGTCAATTTTGTGGCTACAA-ATGGAG 747401 i ii ii - v i? ivi i iv i- i L3b_3end#LINE 448 AGTCCTGCACTTGGGT-TCAAAAAANCAATCGCGCGAGTACAGGATGGGG 496 chr3qtel1M 747402 GGAAGTAGGGTTAAAGGCAGACACTGCCTGAGAAAGATCTGGGATTGTGG 747451 ii vvv v ivi v?vv -- i i iv v vi L3b_3end#LINE 497 GAGACGCGGCTTAGCAGCAGCNCATG--TGAAAAAGACCTGGGGGTTTTA 544 chr3qtel1M 747452 GTGGACCCCAAGCT 747465 v v L3b_3end#LINE 545 GTTGACCGCAAGCT 558 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 40.39 CpG sites = 20, Kimura (unadjusted) = 45.33 Transitions / transversions = 1.25 (20/16) Gap_init rate = 0.04 (4 / 112), avg. gap size = 1.00 (4 / 4) 32 27.61 6.49 1.86 chr3qtel1M 748306 748459 (251541) (GGAGA)n#Simple_repeat 1 161 (0) m_b156s252i4 5849 chr3qtel1M 748306 GGAGTGGGGAAGAGAGAAGAGGA-AGGAGA-AAGGGGGGAAGGGA-AAGA 748352 v i i i - -i i i i i -i (GGAGA)n#Simp 1 GGAGAGGAGAGGAGAGGAGAGGAGAGGAGAGGAGAGGAGAGGAGAGGAGA 50 chr3qtel1M 748353 GAAG-GGGGA-AAGAAGAGAGG-GACGGA-AGAAGAAAAAGAGG-GGGAA 748397 i - i -i i - - - i - ii - i i (GGAGA)n#Simp 51 GGAGAGGAGAGGAGAGGAGAGGAGA-GGAGAGGAG-AGGAGAGGAGAGGA 98 chr3qtel1M 748398 GGGGAAAGGAGGGGAAAGAGGAGGGGAAGAGA-GAAAAGTGGGGAGGGGA 748446 i i i i ii i i - i i v i i (GGAGA)n#Simp 99 GAGGAGAGGAGAGGAGAGGAGAGGAGAGGAGAGGAGAGGAGAGGAGAGGA 148 chr3qtel1M 748447 GAGGA-AGGCAGAG 748459 - - (GGAGA)n#Simp 149 GAGGAGAGG-AGAG 161 Matrix = Unknown Transitions / transversions = 15.00 (30/2) Gap_init rate = 0.08 (13 / 153), avg. gap size = 1.00 (13 / 13) 14 27.29 1.72 3.51 chr3qtel1M 749181 749238 (250762) (TGCA)n#Simple_repeat 1 57 (0) m_b156s252i5 5850 chr3qtel1M 749181 TGCTTGCGGGCATGTTTGACATGTATGTATACATGCATTGCATG-GTGCA 749229 v iv iv - i i i - -i (TGCA)n#Simpl 1 TGCATGCATGCATGCATG-CATGCATGCATGCATGCA-TGCATGCATGCA 48 chr3qtel1M 749230 CACATGTAT 749238 ii i (TGCA)n#Simpl 49 TGCATGCAT 57 Matrix = Unknown Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.05 (3 / 57), avg. gap size = 1.00 (3 / 3) 17 28.50 6.61 2.38 chr3qtel1M 749292 749412 (250588) (CATGTG)n#Simple_repeat 1 126 (0) m_b156s252i6 5851 chr3qtel1M 749292 CATTTGTATTGTGTAGGTGCACATCTCTGTGCTCTGTGCGTTCACACGTG 749341 v i - i v ii viv -v i vii i (CATGTG)n#Sim 1 CATGTGCA-TGTGCATGTGCATGTGCATGTGC-ATGTGCATGTGCATGTG 48 chr3qtel1M 749342 CGTGTGCATG-GCA--TGCAGGTGCA---CCATGTACATGTGTGTGTTGT 749385 i - -- v ---v i ii - i (CATGTG)n#Sim 49 CATGTGCATGTGCATGTGCATGTGCATGTGCATGTGCATGTGCATG-TGC 97 chr3qtel1M 749386 GTGTGGGTGTTCATGTG--TGTGCCTGTG 749412 i vi v -- v (CATGTG)n#Sim 98 ATGTGCATGTGCATGTGCATGTGCATGTG 126 Matrix = Unknown Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.06 (7 / 120), avg. gap size = 1.57 (11 / 7) 30 13.63 1.67 3.39 chr3qtel1M 749374 749433 (250567) (TG)n#Simple_repeat 1 59 (0) m_b156s252i7 5852 chr3qtel1M 749374 TGTGTGTGT-TGTGTGTGGGTGTTCATGTGTGTGCCTGTGTGCTGTACTG 749422 - v vii iv - -v (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG-TGT-GTG 48 chr3qtel1M 749423 TGTGTGTGTGT 749433 (TG)n#Simple_ 49 TGTGTGTGTGT 59 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.05 (3 / 59), avg. gap size = 1.00 (3 / 3) 250 22.86 8.57 0.00 chr3qtel1M 749495 749564 (250436) C MIR3#SINE/MIR (63) 145 70 m_b156s601i6 5853 chr3qtel1M 749495 CTCATTTTACAGGTCAGGAAAC---GGGTTGGGGAG---AAGGGTCTTGC 749538 i v --- viii i --- v v C MIR3#SINE/MIR 145 CTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGC 96 chr3qtel1M 749539 CCAGAGTCACACAGAACCTCAGTGAC 749564 ii v?vv i i C MIR3#SINE/MIR 95 CCAAGGTCACACAGCNAGTTAGTGGC 70 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 28.17 CpG sites = 9, Kimura (unadjusted) = 28.17 Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.03 (2 / 69), avg. gap size = 3.00 (6 / 2) 188 28.58 3.88 4.90 chr3qtel1M 749879 749981 (250019) C MIR3#SINE/MIR (33) 175 74 m_b156s601i7 5854 chr3qtel1M 749879 GGGATCTCAGAAGGCATCATATATGCCCCCCTCATGTGA---AAGAAGTC 749925 i i iiv vvi viiv v v --- v i vv C MIR3#SINE/MIR 175 GGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGAA 126 chr3qtel1M 749926 ACTGAAGCAGCCAAAAGCTGTAAAGGGACTGG-CCAAAGTCACACGAGTC 749974 ---i v i vv i v v - i - - C MIR3#SINE/MIR 125 ACTGA---GGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACAC-AG-C 81 chr3qtel1M 749975 AAGTCAG 749981 ? i C MIR3#SINE/MIR 80 NAGTTAG 74 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 36.72 CpG sites = 13, Kimura (unadjusted) = 36.72 Transitions / transversions = 0.87 (13/15) Gap_init rate = 0.07 (7 / 102), avg. gap size = 1.29 (9 / 7) 413 30.27 1.90 5.92 chr3qtel1M 749969 750126 (249874) C L2d2_3end#LINE/L2 (1) 554 403 m_b156s601i8 5855 chr3qtel1M 749969 CGAGTCAAGTCAGCATGCACAAATTAAGTACCTACTGAATGCCAGGCACA 750018 i i i i vii ivv i ii vi v v C L2d2_3end#LIN 554 CAAATCAAATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACT 505 chr3qtel1M 750019 ATGCTAAGCATTG---AAGATATAAAAGAAAGGCAAAAAACAGTCCCTGC 750065 i i ii ---ii i - ivii i v ii C L2d2_3end#LIN 504 GTGCTAGGCGCTGTGGGGGATACAAA-GAAGTATAAGACATGGTCCCTGC 456 chr3qtel1M 750066 CCTCAAGGAGCTCACAGTCTAATGAAGGAAACATAAAAACAAGCTGTAGA 750115 i i i vii i --- i ----- i C L2d2_3end#LIN 455 CCTCAAGGAGCTTACAATCTAGTTGGGGAGAC---AAGACA-----TAAA 414 chr3qtel1M 750116 CATATATAAAG 750126 ii iv C L2d2_3end#LIN 413 CACGTGAAAAG 403 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 38.06 CpG sites = 35, Kimura (unadjusted) = 42.10 Transitions / transversions = 3.50 (35/10) Gap_init rate = 0.06 (10 / 157), avg. gap size = 1.20 (12 / 10) 325 31.36 14.79 4.09 chr3qtel1M 749991 750389 (249611) C L2b_3end#LINE/L2 (23) 443 4 m_b156s601i10 5855 chr3qtel1M 749991 ATTAAGTACCTACTGAATGCCAGGCACAATGCTAAGCATTGAAGATATAA 750040 i i ii vi ? vi i ii ii i i C L2b_3end#LINE 443 ACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGGGATACAG 394 chr3qtel1M 750041 ----AAGAAAGGCAAAAAACAGTCCCTGCCCTCAAGGAGCTCACAGTCTA 750086 ----i iv i i v?- i v C L2b_3end#LINE 393 CGGTGAACAAGACAGACN-CGGTCCCTGCCCTCACGGAGCTCACAGTCTA 345 chr3qtel1M 750087 ATGAAGGAAACATAAAAACAAGCTGTAGACATATATAA---AGAAC---- 750129 i ii i v v vii ? --- vv? --- ii---- C L2b_3end#LINE 344 GTGGGGGAGACAGACATGTAANC---AGACAATNATAACCCAGAGTGGCA 298 chr3qtel1M 750130 CTGTA-GAC-----AGATCAAATAGTAAATAACGAACTCTGGACCTAAGA 750173 vv - -----i ii v ivi viiiiiv vi i -- i ii i C L2b_3end#LINE 297 GGGTAGGACTGGGGGGGCCCAGAGGAGGGCGCCTGACCC--GGCCTGGGG 250 chr3qtel1M 750174 GCCATGGAGGAAGGCT----GTAGAAGGTGGAGTTTTAGTTGAAACCTCA 750219 --i vii i ---- v i ivi v i i v C L2b_3end#LINE 249 G--GTCAGGGAGGGCTTCCCGGAGGAGGTGACATTTGAGCTGAGACCTGA 202 chr3qtel1M 750220 AGGAACTTGGGAAGGTTAG-TGGTCA---GAAGAGA-GGAGAACAGCATT 750264 --- i v -- - i --- i- i vi i C L2b_3end#LINE 201 AGGA---TGAGTAGG--AGTTGGCCAGGCGAAGAGGTGGGGAAGGGCGTT 157 chr3qtel1M 750265 ATAGGCCTGGGGGA------------------TGATAAGGAAGTGCTCAT 750296 vi vvi i ------------------ viv i ? vv ? C L2b_3end#LINE 156 CCAGGCAGAGGGAACAGCANGTGCAAAGGCCCTGAGGCGGGAGNGAGCNT 107 chr3qtel1M 750297 GG-----------GACAGCCAGGAGACCAGGGACACTGGATGGAAGAGAA 750335 -----------i v i v ---- v iv i C L2b_3end#LINE 106 GGCGTGTTCGAGGAACAGCAAGGAGGCCAGTG----TGGCTGGAGCAGAG 61 chr3qtel1M 750336 TGTGCCAAGGAGTGAGATGTTGAAAAC----CTGGAAAGGTGAGAGGGGC 750381 v - i v vv v i i i---- i i iivi v C L2b_3end#LINE 60 TGAG-CAAGGGGAGAGTGGTAGGAGATGAGGCCGGAGAGGTAGCGGGGCC 12 chr3qtel1M 750382 AGGTGATG 750389 i vi C L2b_3end#LINE 11 AGATCGTG 4 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 39.78 CpG sites = 77, Kimura (unadjusted) = 43.77 Transitions / transversions = 1.79 (77/43) Gap_init rate = 0.08 (30 / 398), avg. gap size = 2.57 (77 / 30) 346 30.38 3.41 4.60 chr3qtel1M 749991 750166 (249834) C L2a_3end#LINE/L2 (23) 494 321 m_b156s601i9 5855 chr3qtel1M 749991 ATTAAGTACCTACTGAATGCCAGGCACAATGCTAAGCATTGAAGATATAA 750040 i ii ivi vi v i ii ii i i C L2a_3end#LINE 494 ATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGCGCTGGGGATACAG 445 chr3qtel1M 750041 AAGA----AAGGCAAAAAACAGTCCCTGCCCTCAAGGAGCTCACAGTCTA 750086 v v---- ii i v v v i v C L2a_3end#LINE 444 CAGTGAACAAAACAGACAAAAGTCCCTGCCCTCATGGAGCTTACATTCTA 395 chr3qtel1M 750087 ATGAAGGAAACATAAAAACAAGCTGTAGACATATATAA--AGAACCTGTA 750134 i ii i i--- v i -- iv v v v -- i iv i C L2a_3end#LINE 394 GTGGGGGGAG---ACAGACAA--TAAACAAATAAATAAGTAAAATATATA 350 chr3qtel1M 750135 GACAGATCAAATAGTAAATAACGAACTCTGGA 750166 -i vi i i -i - vi v C L2a_3end#LINE 349 G-TATGTCAGATGGT-GATAA-GTGCTATGGA 321 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 38.47 CpG sites = 33, Kimura (unadjusted) = 40.69 Transitions / transversions = 1.83 (33/18) Gap_init rate = 0.06 (10 / 175), avg. gap size = 1.40 (14 / 10) 971 35.32 7.10 4.86 chr3qtel1M 750289 751556 (248444) C L2#LINE/L2 (67) 3015 1721 m_b156s601i11 5855 chr3qtel1M 750289 GTGCTCATGGGACAGCCAGGAGACCAGGGACACTGGATGGAAGAGAATGT 750338 i iv i v i v ---- v ivi i v C L2#LINE/L2 3015 GTGTTCGAGGAACAGCAAGGAGGCCAGTG----TGGCTGGAGCGGAGTGA 2970 chr3qtel1M 750339 GCCAAGGAGTGAGATGTTGAAAAC----CTGGAAAGGTGAGAGGGG--CA 750382 v i i v vv v i i i----iii i i vi -- C L2#LINE/L2 2969 GCGAGGGGGAGAGTGGTAGGAGATGAGGTCAGAGAGGTAACGGGGGACCA 2920 chr3qtel1M 750383 GGTGATG-AGGGCTTTGAATGGCAG-ATAGAGCATTTTGA-TTTTACTCC 750429 i v - i v v v v-i - v i i- - C L2#LINE/L2 2919 GATCATGTAGGGCCTTGTAGGCCATTGTA-AGGACTTTGGCTTTTACTC- 2872 chr3qtel1M 750430 TGCAAGTGAGA--GGAAGATACTGGAGGTTACTTAGCA-AGGAGCTAAAA 750476 -- -- vi i v vi v - - i v C L2#LINE/L2 2871 TG--AGTGAGATGGGAAGCCATTGGAGGGTTTTGAGCAGAGGAG-TGACA 2825 chr3qtel1M 750477 TGGTCACACCTGCACTGTAAAAAAAAATTCCCTTGGTGACTGAATGGAGA 750526 i vv i i ii v ii -- iv ii ivi vi v C L2#LINE/L2 2824 TGATCTGACTTACGTTTTAAAAGGA--TCACTCTGGCTGCTGTGTTGAGA 2777 chr3qtel1M 750527 AAGGATTGAAATGGGGAGATGCCCAAGCCAGGGAGAACA----------- 750565 vi i ? iv vi v vivi iv v ----------- C L2#LINE/L2 2776 ATAGACTGNAGGGGGGCAAGGGTGGAAGCAGGGAGACCAGTTAGGAGGCT 2727 chr3qtel1M 750566 -------TCAACTAAGCCTGAGAAGACAAGGGTGTGTGCCAGAGTGGGGA 750608 ------- v v i i vv v iiiv iv vi i v i C L2#LINE/L2 2726 ATTGCAGTAATCCAGGCGAGAGATGATGGTGGCTTGGACCAGGGTGGTGG 2677 chr3qtel1M 750609 CAGTGTCAGGGGAGATAAGGGGGCATAATTGAGAGATGGTGCAAAGATGA 750658 vvi v v v v v iv v ivi v iv vii i ii C L2#LINE/L2 2676 CAGTGGAGGTGGTGAGAAGTGGTCGGATTCTGGATATATTTTGAAGGTAG 2627 chr3qtel1M 750659 AATGGACCAGAGACGCTGCAGAGGTGAGATGATGGACTATGGCGCCATAT 750708 iiv vi vvi -------------------- ------ C L2#LINE/L2 2626 AGCCGACAGGATTTGCTG--------------------ATGG------AT 2603 chr3qtel1M 750709 TAGATATGAAATGTGAGAGAGAGCAAGGAGTCCGGGGAAATTCTTGGGCT 750758 i i iii i vi vi ivi i ivi i C L2#LINE/L2 2602 TGGATGTGGGGTGTGAGAGAAAGAGAGGAGTCAAGGATGACTCCAAGGTT 2553 chr3qtel1M 750759 GGGATCCTAAGGGCCTTGGAGGATGGA---CCCATTT-CTGTATTACCAA 750804 vvviv i viv v i ---v ?- viv ivvi C L2#LINE/L2 2552 TTTGGCCTGAGCAACTGGAAGGATGGAGTTGCCATTNACTGAGATGGGGA 2503 chr3qtel1M 750805 AGAAAGTGGGAGGTGGGAAGAGTTTG-GGGGTGAGATAATGAGTTTGGTT 750853 vv i -- i v - - vi v v ii C L2#LINE/L2 2502 AGACTGCGGGAG--GAGCAG-GTTTGAGGGGGAAGATCAGGAGTTCAGTT 2456 chr3qtel1M 750854 TTGGGTGTGATGAGTTTAAGATGTCAACCTGGACATCCGGGTAGAGAACT 750903 iii v i i i v -i i ii i -- C L2#LINE/L2 2455 TTGGACATGTTAAGTTTGAGATGCCTA-TTAGACATCCAAGTGGAGA--T 2409 chr3qtel1M 750904 GT-GAAT-GGCCACTGCTGATGAGAGATTCGAGGTTCA---GAGTGATTG 750948 - i - vii vvv iv - ii ii --- v i iv C L2#LINE/L2 2408 GTCGAGTAGGCAGTTGGATATACGAG-TCTGGAGTTCAGGGGAGAGGTCC 2360 chr3qtel1M 750949 GGGCAGGATGAGTAGATCTGAGACTCCTCAGAATAAAAACTGTCACGAAA 750998 v vivi i i i v v v v i iv vviv C L2#LINE/L2 2359 GGGCTGGAGATATAAATTTGGGAGTCATCAGCATATAGATGGTATTTAAA 2310 chr3qtel1M 750999 TCCACATGAGA--GAATGAGATCCTCAAGTGAAACAATAGGGCAGGAGAA 751046 v -- -- i vi ? v ivv i ivi vvi C L2#LINE/L2 2309 GC--CATGAGACTGGATGAGATCACCNAGGGAGTGAGTGTAGATAGAGAA 2262 chr3qtel1M 751047 GAAAGTCTTGAGAGCCCAGGATAGAACACAAG---ACGCCGAAGGTTAGA 751093 i i---- iv v iv i v vi --- v i v v ? C L2#LINE/L2 2261 GAGAA----GAGGTCCAAGGACTGAGCCCTGGGGCACTCCAACGTTNAGA 2216 chr3qtel1M 751094 GGGC------ATGACCTGGAAGAGCGAGCCAGAAAGGCAGAGAAGGAATA 751137 v ------ --- i i v v iii i v iii C L2#LINE/L2 2215 GGTCGGGGAGATGA---GGAGGAACCAGCAAAGGAGACTGAGAAGGAGCG 2169 chr3qtel1M 751138 ATCAGAGAGG-GGGAGGGGAACAAGGAGAGACT-GTCCCCCAAACGCAAA 751185 ii v -i ii v vv - vi iii v v C L2#LINE/L2 2168 GCCAGTGAGGTAGGAGGAAAACCAGGAGAGTGTGGTGTCCTGGAAGCCAA 2119 chr3qtel1M 751186 GGGAAGCAGGAATCT--AGGAGGAAAGGATGATTGGCAGT-----ATACC 751228 v v i vi i -- i ii ii iii v ----- i i C L2#LINE/L2 2118 GTGAAGAAAGTGTTTCAAGAAGGAGGGAGTGATCAACTGTGTCAAATGCT 2069 chr3qtel1M 751229 -CAGAGA-GTCAAGGAGAATGAGGTCTGAGAAAAGG-CATTGGATCTGGC 751275 - v ? - v ii v vv i- i i C L2#LINE/L2 2068 GCTGANAGGTCAAGTAAGATGAGGACTGAGAATTGACCATTGGATTTAGC 2019 chr3qtel1M 751276 CAC-TAAGGGACAGCTGCTCACTTTGGTTACCA-AGCT----TGGAATGA 751319 v - iii v -i v v i iiv vvi- i ---- i i C L2#LINE/L2 2018 AACGTGGAGGTCA-TTGGTGACCTTGACAAGAGCAGTTTCGGTGGAGTGG 1970 chr3qtel1M 751320 TTAAGTCAAAATGCAGACTAA---GGAATTAAGA---AGTGAAAGGAGAG 751363 vii v i vv v i ii--- iv i --- i ii C L2#LINE/L2 1969 TGGGGACGAAAGCCTGATTGGAGTGGGTTCAAGAGAGAATGGGAGGAGAG 1920 chr3qtel1M 751364 AAAGCAGAGGCCCTGCTCATCCATAGCCTTTGCAAG----TTCAC---AA 751406 i vii i vvi vvi vv i i ii v i ---- ii --- C L2#LINE/L2 1919 GAATTGGAGACAGCGAGTATAGACAACTCTTTCGAGGAGTTTTGCTGTAA 1870 chr3qtel1M 751407 AGAGCAGAAGGAATCTAGGACAATAGTGAGCAGAGATGGAAAGGTCAAGT 751456 i v v ii vv i i ii ivi vi i iv? vii v C L2#LINE/L2 1869 AGGGGAGCAGAGAAATGGGGCGGTAGCTGGAGGGGGANGTGGGGTCAAGG 1820 chr3qtel1M 751457 GAGG------GCATTTTGAAGATAGGGCAGACATAGGCATGTC--TATGC 751498 i------ iv i i iv i i?vvi i-- C L2#LINE/L2 1819 GAGAATTTTTGTTTTTTAAAGATGGGAGAAATNACAGCATGTTTGTATGC 1770 chr3qtel1M 751499 TTATAGGCGACTGAAAGAGCTGGAGGCAAGGGGAGGACTGAAGAGGTCCC 751548 v i ------ v v ii vi vi i ii i v v --- C L2#LINE/L2 1769 TGATGG------GAATGATCCAGTAGAGAGGGAAAAATTGATGATG---C 1729 chr3qtel1M 751549 AGGACAGA 751556 v C L2#LINE/L2 1728 AGGAGAGA 1721 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 48.10 CpG sites = 242, Kimura (unadjusted) = 49.95 Transitions / transversions = 1.32 (242/184) Gap_init rate = 0.08 (97 / 1267), avg. gap size = 1.58 (153 / 97) 180 29.82 0.00 0.00 chr3qtel1M 752030 752086 (247914) L3#LINE/CR1 3816 3872 (227) m_b156s601i12 5856 chr3qtel1M 752030 TGTCCTGTCTGACCCCAGACGGCCAAACTAGGGCCAGTGAGGGGGAGGGA 752079 i i v i i v vi i i i v i vv L3#LINE/CR1 3816 TATTCTGTGTGGCTCCAGAGGGCAGAACTAGGACCAATGGGTGGAAGTTA 3865 chr3qtel1M 752080 GAGTGAG 752086 v v L3#LINE/CR1 3866 CAGGGAG 3872 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 38.69 CpG sites = 9, Kimura (unadjusted) = 38.69 Transitions / transversions = 1.12 (9/8) Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0) 11 9.73 8.57 2.70 chr3qtel1M 752200 752234 (247766) (AGGAAGG)n#Simple_repeat 1 37 (0) m_b156s252i8 5857 chr3qtel1M 752200 AGGAA-CAGTGAAGGAGGGA-G-GGAAGGAGGAAGAAG 752234 -v - i - - i (AGGAAGG)n#Si 1 AGGAAGGAG-GAAGGAGGAAGGAGGAAGGAGGAAGGAG 37 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.12 (4 / 34), avg. gap size = 1.00 (4 / 4) 182 28.00 8.00 0.00 chr3qtel1M 752442 752491 (247509) L2c_3end#LINE/L2 412 465 (13) m_b156s601i13 5858 chr3qtel1M 752442 TCAGCTTTGT----CAAGTGCCTGGCCCAGAACAGGCGTCTAATAAGCAC 752487 v ---- v i v v ii iii iiii L2c_3end#LINE 412 TCATCTTTGTATCCCCAGCGCCTGGCACATAGTAGGCGCTCAATAAATGT 461 chr3qtel1M 752488 TTGT 752491 L2c_3end#LINE 462 TTGT 465 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 33.71 CpG sites = 10, Kimura (unadjusted) = 37.06 Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.02 (1 / 49), avg. gap size = 4.00 (4 / 1) 185 26.32 0.00 0.00 chr3qtel1M 752454 752491 (247509) L2a_3end#LINE/L2 467 504 (13) m_b156s601i14 5858 chr3qtel1M 752454 AGTGCCTGGCCCAGAACAGGCGTCTAATAAGCACTTGT 752491 v v ii iii ii i L2a_3end#LINE 467 AGTGCCTGGCACATAGTAGGCGCTCAATAAATATTTGT 504 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 34.87 CpG sites = 8, Kimura (unadjusted) = 34.87 Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 321 23.08 16.15 0.00 chr3qtel1M 752737 752866 (247134) C MIR#SINE/MIR (3) 259 109 m_b156s601i15 5859 chr3qtel1M 752737 AATAGCTAATCCTGATGCAGC-CTGACTCCATGCCAGGCACT--TATA-- 752781 ivi v vv - v vii -- v -- C MIR#SINE/MIR 259 AATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAG 210 chr3qtel1M 752782 --CT---CATGCCTT---TC-TTTGAGCCTCCC--CTGTCCCGTGAGGTG 752820 -- --- iv --- - i v v -- vii ii i C MIR#SINE/MIR 209 CGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGGTA 160 chr3qtel1M 752821 GATGCTATTAT----CCCATTTCACAGCTGAGGAAGCTAAGCCA-AGAGG 752865 i i ---- i v i i v - i C MIR#SINE/MIR 159 GGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGA 110 chr3qtel1M 752866 G 752866 C MIR#SINE/MIR 109 G 109 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 28.01 CpG sites = 17, Kimura (unadjusted) = 28.01 Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.08 (10 / 129), avg. gap size = 2.10 (21 / 10) 184 22.22 0.00 0.00 chr3qtel1M 753648 753692 (246308) L2#LINE/L2 2707 2751 (331) m_b156s601i16 5860 chr3qtel1M 753648 CTCACTGGGATTTCTGCCAAGGCCTCCCGACTCGTCTCCCTGCTT 753692 i iv v v vi ii v L2#LINE/L2 2707 CTCGCCTGGATTACTGCAATAGCCTCCTAACTGGTCTCCCTGCTT 2751 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 23.64 CpG sites = 5, Kimura (unadjusted) = 26.56 Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 461 17.17 3.33 7.83 chr3qtel1M 754053 754172 (245828) Charlie1b#DNA/hAT-Charlie 401 515 (8) m_b156s502i4 5861 chr3qtel1M 754053 TTTAAATTTCTATTACAGTA----CTGACAGACATAACCCACACAAACAA 754098 v v i ----ii i i i Charlie1b#DNA 401 TTTTAATTTCTAATACGGTAAATATCGATAGATATAACCCACATAAACAA 450 chr3qtel1M 754099 ATGCTCTTTGAGGGAGGGTCCTCAATTTTATTTAAGAGTGTAAAAGTCCC 754148 v ----- vv v i ---- Charlie1b#DNA 451 AAGCTCTTTG-----GGGTCCTCAATAATTTTTAAGAGTGTAAAGG---- 491 chr3qtel1M 754149 TACCCAGGGACTAAAAAGTTTGAG 754172 vii v i i Charlie1b#DNA 492 GGTCCTGAGACCAAAAAGTTTGAG 515 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 17.47 CpG sites = 11, Kimura (unadjusted) = 19.65 Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.08 (10 / 119), avg. gap size = 1.30 (13 / 10) 185 24.49 4.08 0.00 chr3qtel1M 755248 755296 (244704) L2c_3end#LINE/L2 417 467 (11) m_b156s601i17 5860 chr3qtel1M 755248 TTTGTAACCCTAGAAGTTGGCACAAAGCAGGCGCTT--TTAAAGTTTGCT 755295 v i vivi v i i-- v v i L2c_3end#LINE 417 TTTGTATCCCCAGCGCCTGGCACATAGTAGGCGCTCAATAAATGTTTGTT 466 chr3qtel1M 755296 G 755296 L2c_3end#LINE 467 G 467 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 27.09 CpG sites = 6, Kimura (unadjusted) = 29.91 Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.02 (1 / 48), avg. gap size = 2.00 (2 / 1) 16 15.86 0.00 0.00 chr3qtel1M 755538 755565 (244435) (G)n#Simple_repeat 1 28 (0) m_b156s252i9 5862 chr3qtel1M 755538 GGGGCCGGGGAGTGGGGGGGGGGGGGGG 755565 vv i v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGG 28 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 203 22.67 25.33 0.00 chr3qtel1M 757351 757425 (242575) C L2b_3end#LINE/L2 (33) 433 340 m_b156s601i18 5863 chr3qtel1M 757351 TACCGTACGCCAGGCAGCCTGCTAAGCACTGGGAATACAG----GAA--- 757393 i ii ?viv i i i ---- --- C L2b_3end#LINE 433 TACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGGGATACAGCGGTGAACAA 384 chr3qtel1M 757394 ------------TCCTGGCCGCAGGGAGCTCACGATCTCATGGG 757425 ------------i v v v ii vi C L2b_3end#LINE 383 GACAGACNCGGTCCCTGCCCTCACGGAGCTCACAGTCTAGTGGG 340 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 26.28 CpG sites = 11, Kimura (unadjusted) = 28.19 Transitions / transversions = 1.83 (11/6) Gap_init rate = 0.04 (3 / 74), avg. gap size = 6.33 (19 / 3) 191 30.10 10.81 1.23 chr3qtel1M 757718 757791 (242209) C L2d2_3end#LINE/L2 (24) 531 451 m_b156s601i19 5864 chr3qtel1M 757718 TTCAGCGCCTGCTG--------GCTTTGGGCCAAGCACCGAGGAGACATT 757759 v i -------- vi v i i i i v i i- v C L2d2_3end#LIN 531 TTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGTGGGGG-ATA 483 chr3qtel1M 757760 CAAAGACACATGTGGGATGGTCCCTGCTTTCA 757791 vii iv iv ii C L2d2_3end#LIN 482 CAAAGAAGTATAAGACATGGTCCCTGCCCTCA 451 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 37.79 CpG sites = 14, Kimura (unadjusted) = 40.16 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.03 (2 / 73), avg. gap size = 4.50 (9 / 2) 31 38.67 1.94 3.45 chr3qtel1M 757803 758008 (241992) (GT)n#Simple_repeat 1 203 (0) m_b156s252i10 5865 chr3qtel1M 757803 GTGCGTGTGTATGTGTATGTGCACATGCATGTGCTGTGTGTGCAGTGCCC 757852 i i i iiii ii - -v ivi (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG-TGTGTGTG-TGTGTGT 48 chr3qtel1M 757853 ATGTAT-TGTGTGTACAT-TGCTGTGTGCACACATGCATGTGTGCAT-TG 757899 i i - iii - - iiiiii ii ii - (GT)n#Simple_ 49 GTGTGTGTGTGTGTGTGTGTG-TGTGTGTGTGTGTGTGTGTGTGTGTGTG 97 chr3qtel1M 757900 TGCGCTGCATGTGTCTGTGTGCAGTGCTGTGCGCATGTGTGTGCTTTGTG 757949 i - ii v -v - i ii - v (GT)n#Simple_ 98 TGTG-TGTGTGTGTGTGTGTG-TGTG-TGTGTGTGTGTGTGTG-TGTGTG 143 chr3qtel1M 757950 TGGGCATGTGTGTGTGTGCACATGTATGTTCACGTGTGTAT-TGTTATTG 757998 v ii iiii i viii i - vvv (GT)n#Simple_ 144 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 193 chr3qtel1M 757999 CCTGTGTGTG 758008 iv (GT)n#Simple_ 194 TGTGTGTGTG 203 Matrix = Unknown Transitions / transversions = 4.00 (44/11) Gap_init rate = 0.05 (11 / 205), avg. gap size = 1.00 (11 / 11) 338 27.96 5.04 0.81 chr3qtel1M 758872 758990 (241010) L3#LINE/CR1 3261 3384 (715) m_b156s601i20 5866 chr3qtel1M 758872 ACAGAATTGGGATCCAAAAAGA---CAACTGAC---AATATTAGGCAAAT 758915 iii i ? --- i v i --- iiv i vi v L3#LINE/CR1 3261 ACAGAATCAAGATTCAAAANGATCTCGACAGGCTGGAACGATGGGCCGAA 3310 chr3qtel1M 758916 GTTAATACAATGAAATTTAATAGAAATAGATATAGAGTCTTACTCTTAGA 758965 iii i vi i ii i i i i i vi i L3#LINE/CR1 3311 ACCAACAAGATGAAATTTAACAGGGATAAATGTAAAGTCCTGCATTTAGG 3360 chr3qtel1M 758966 TTCAAAAAGTCCAACTTCACAAGTA 758990 i - v L3#LINE/CR1 3361 TTCAAAAAAT-CAACTGCACAAGTA 3384 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 33.66 CpG sites = 26, Kimura (unadjusted) = 38.27 Transitions / transversions = 3.71 (26/7) Gap_init rate = 0.03 (3 / 118), avg. gap size = 2.33 (7 / 3) 1045 31.91 7.18 1.07 chr3qtel1M 760534 761062 (238938) C L1ME4c_3end#LINE/L1 (191) 639 79 m_b156s551i0 5867 chr3qtel1M 760534 TCCTGCTCATTTCACTCAACATCAGTTCATGTAAGTCTCTCTAGGTGTTT 760583 i iv i i vv iv vi i - i v vvi C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATAAACATTT-TCCATGTTGCT 591 chr3qtel1M 760584 CTGAAATCATCCTGCTGGTCCTTCTTACAGAACA-ATAATATTCCATAAA 760632 viiv i v v iv vi v i vv ivii- vi C L1ME4c_3end#L 590 ACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCGA 541 chr3qtel1M 760633 ATTCATACACCATAATTTATTCAGCCATTTGCCAGCTGATGGGCAT---- 760678 i ?v ii i i i iv vii v i ---- C L1ME4c_3end#L 540 GTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAG 491 chr3qtel1M 760679 -------CCACTC------------AAAGAGGGCTGCCACAAACATTTTG 760709 ------- v i------------ v iv v ii i v C L1ME4c_3end#L 490 GTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTC 441 chr3qtel1M 760710 GCACATACAGGTCCCTTTCCCTCCTTTAAG--ATCTCTTTGGGATAAAAG 760757 ii i -- ii i i i i-- i i i vv C L1ME4c_3end#L 440 GTGCATATAG--CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAATT 393 chr3qtel1M 760758 CCCAGTAGAAACTCTGCTGGATCAAAGGGTATGCACAGCTTGATAATTTT 760807 v viivvi i i v vi v iii i C L1ME4c_3end#L 392 CCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTCT 343 chr3qtel1M 760808 TTGAGCATAGTTCCAAATTGCTCTCCAGAATAGTTGGATGCATTCACAAC 760857 vivi i v v i i vi v ivv i ?i C L1ME4c_3end#L 342 TGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACANT 293 chr3qtel1M 760858 TCCACCAACAATGCATCAGTGTCCCAGTTTTCCCACATCCCCTCCAACAT 760907 v i i v ? v iv i ? i v i C L1ME4c_3end#L 292 GCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGCAT 243 chr3qtel1M 760908 TCATCATTATCTTTTCCTGCCATCTTAGCCAATCTGACAGGC-------- 760949 vivi vv ii vvv i v i i i i -------- C L1ME4c_3end#L 242 TGGGTATTATCAATTTTTTAAATTTTTGCTAATTTAATAGGCGTAAAATG 193 chr3qtel1M 760950 ATATTTCAGAGTTGTCTTAATTTTCATTTCTCTGATCAATAGTGATTTAG 760999 i i vv ii v i i v i vv v C L1ME4c_3end#L 192 GTATCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACTAGCGAGGTTG 143 chr3qtel1M 761000 AGCACCTTTTCA----TTTGACTAGAAATGGTTCAATTTCTTCATCTGAA 761045 i ii i ---- vi vv ? v --- i v ? vi C L1ME4c_3end#L 142 AACATTTTTCCATGTGTTTGTTTACTANTTGT---ATTTCCTCTTNTGTG 96 chr3qtel1M 761046 AAATGTCTGTTCATATC 761062 v i C L1ME4c_3end#L 95 AATTGTCTGTTCATGTC 79 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 42.11 CpG sites = 95, Kimura (unadjusted) = 43.50 Transitions / transversions = 1.32 (95/72) Gap_init rate = 0.02 (13 / 528), avg. gap size = 3.38 (44 / 13) 216 14.49 9.23 4.41 chr3qtel1M 762997 763061 (236939) MIR3#SINE/MIR 100 167 (41) m_b156s601i22 5868 chr3qtel1M 762997 GTCACTCAAGCTCCTCTG--CCTCAGTTTCCTCATTTCTAAAATGA---- 763040 iv v - -- i v ---- MIR3#SINE/MIR 100 GTCACTTCACCTC-TCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGG 148 chr3qtel1M 763041 GCTGGACATTCCAGGATCTCT 763061 i -- vv v MIR3#SINE/MIR 149 GTTGGAC--TAGATGATCTCT 167 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 16.13 CpG sites = 3, Kimura (unadjusted) = 16.13 Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.08 (5 / 64), avg. gap size = 1.80 (9 / 5) 230 15.56 2.22 0.00 chr3qtel1M 762997 763041 (236959) MIR#SINE/MIR 99 144 (118) m_b156s601i21 5868 chr3qtel1M 762997 GTCACTCAAGCTC-CTCTGCCTCAGTTTCCTCATTTCTAAAATGAG 763041 i i v - v i v i MIR#SINE/MIR 99 GTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGG 144 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 17.59 CpG sites = 4, Kimura (unadjusted) = 17.59 Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 13 0.00 0.00 9.09 chr3qtel1M 763292 763315 (236685) (GAG)n#Simple_repeat 1 22 (0) m_b156s252i11 5869 chr3qtel1M 763292 GAGGAGGAGGAGGAGCTGAGGAGG 763315 -- (GAG)n#Simple 1 GAGGAGGAGGAGGAG--GAGGAGG 22 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.09 (2 / 23), avg. gap size = 1.00 (2 / 2) 909 37.59 2.42 2.10 chr3qtel1M 764839 765789 (234211) C Tigger3#DNA/TcMar-Tigger (1351) 1678 725 m_b156s502i5 5870 chr3qtel1M 764839 TCTTCCTCCACACGGCGTTCATGGTCGCCGGCTTGAGCTCCTGCCAGGAC 764888 i v i v i ivv v vvvv vv viv i v C Tigger3#DNA/T 1678 TCTTCTTCCAGATGCCATTCATACACTCCTTGGTGACATCACCCCAAGCC 1629 chr3qtel1M 764889 TCGGCGATGTTGTCCACGGCCGTCAT-GATGTTGTAGCTGCGCCAGAACT 764937 ivi i v v iv i - v - iiiviv -- C Tigger3#DNA/T 1628 CAAGCAAGGTTCTTGATG-CAGTCATAGATGTTGTAATCCTTCCAGAA-- 1582 chr3qtel1M 764938 CTCGGATGCTGGGCTTCTC---GTCCCCGTCGGTCTCCTGGAGCAGCT-- 764982 - i v vvvv v --- ii v i - v v v ii i-- C Tigger3#DNA/T 1581 -TTGCATCAGTGTCTTCTCAGTGTCTTCCTCAGT-TGCAGCAATAGCCTG 1534 chr3qtel1M 764983 GACAGAGCGTCCTCTTCAGGTAAAAGGCCTTGAAGGTGGCGATCACCCCT 765032 i i - i iv i i iv v v i C Tigger3#DNA/T 1533 GGCAAAG-GTCCTCCTCAGGTAGTAGGCCTTAAAAGCTGCTATAACTCCT 1485 chr3qtel1M 765033 TGGTTCATGGGCTGGATCAAGGCTGATGTGTTTTTGGGCAGAAACTCCAC 765082 i i v i i vv vv vvi v v C Tigger3#DNA/T 1484 TGATCCATTGGTTGGATCAAAGAGGTGGTGTTTGGAGGGAGAAACACCAC 1435 chr3qtel1M 765083 CCTGATGTTGGCGGAGAGGTCGTCCAGGTGGGCCGGATG-GCACGGGGCG 765131 ii i vivii i ii v vivii vv - i- i i C Tigger3#DNA/T 1434 TTTGATATTGGGATGAAGATCACCAATAAAAGGAGGATGTGCG-GGAGCA 1386 chr3qtel1M 765132 CTGTCCAGGATCAGCAGGGCCTTGTGGGGCAGCTGATTCTCAGCACAGTG 765181 i i v vi v iiii vii i vv v viv i C Tigger3#DNA/T 1385 TTATCAACAATAAGCAAAATCTTGAAAGGTATGTTATTCTCCAAACAGTA 1336 chr3qtel1M 765182 CCTCTCCACAGCG-GGACAGAAGAAATTGGTGAACCACTCCTGGAAGATG 765230 i ivv -v i v iv v ii viiiv - i v C Tigger3#DNA/T 1335 CTTCTCCATTTCGCTGGCATAGCAATTCAGGAGGGCA-TCTTGGAAGAGG 1287 chr3qtel1M 765231 CTCATGGTCACCCAGTCGTTGCGGTTGGACCTCCAGATCACAGGCAGGCT 765280 vv vv i vvvv vivi vv vi vv v vv C Tigger3#DNA/T 1286 AGCTGGGTCATCCATGACTTCTTATTGCTCCTGTAGTACACTGGCAGTGT 1237 chr3qtel1M 765281 GGGCTTGGAGCAGCCCTTCAGGGCCCGTGGGTTCTCCGAGGGATACACCA 765330 v ivv vviiv v i vv vvv v vi v i C Tigger3#DNA/T 1236 GTGCTTATTGATATGCTTGAAGGCCCTGGGGTTCTCACTGTGCCAGATCA 1187 chr3qtel1M 765331 GCAGAGGCTTCAGCTTGCAGTCCCCGGCAGCATTACCCCCCAGGAGCAAG 765380 vv ii i ii i --- v i i ---i C Tigger3#DNA/T 1186 CAAAGGGTTTCAATTTGTAG---CCTGCAACATTGCCCCC---AAGCAAG 1143 chr3qtel1M 765381 ---GTCAGGTGGTCCTTGGAGGCCTTGAAGCCTGGC-CCGGCTCGGTCCT 765426 --- i vviv ii i i -ii i i - C Tigger3#DNA/T 1142 ACTGTTATCCTGTCCTTAAAAGCCTTGAAACCTGGCATTGACTTGG-CCT 1094 chr3qtel1M 765427 CCAGAGACACGAACGTCCTTTCAGGCAAGCGCTTCCAAAAGAGCCCCGTC 765476 vv viv i v vv i i v vvvv i C Tigger3#DNA/T 1093 CCTTATGGATGAAAGTCCTTTCAGGCATCCGTTTCCAGAATAGGGAGGTT 1044 chr3qtel1M 765477 TCATCGATGTTGAAAACCTGCTGTGGGGTGTACCCGCCATCGGCTATGAT 765526 v i i ii v viv viivi v vi v v v C Tigger3#DNA/T 1043 TCATCCATATTGAAGATTTGCTCTGGCAAGTAATTTTCCTCCACAATCAG 994 chr3qtel1M 765527 CTTTCTCAGCGTGTCCGGGTA-CCTGCGCGCTGCTTCCGTGTCTGCCACG 765575 viii v v iiiv -i v i- i i iii v vviv C Tigger3#DNA/T 993 CTTATCTAGAGTTTCCAAAAATTCTTCA-GCTGCCTTCACATCAGCACTC 945 chr3qtel1M 765576 GCGGGCTCGTCAGTCAGGAGCACGTTGTGC---------CGAGCCTTGAA 765616 i i ii v vvvv i i i--------- vi C Tigger3#DNA/T 944 GCAGACTCACCACTCACTTTCACATTATGTAATGAATAACGATTCTTGAA 895 chr3qtel1M 765617 CCGGGCAAACCAGCCATTGCTGGCTCCGAAGGTCTCCGCCTGCGCGCTC- 765665 i vvi v vv i vvii ---- i iv vv iiv - C Tigger3#DNA/T 894 TCGTTTAAACCACCCAGAGCTAGCAGTAAA----TTCAACATCGTAGTCG 849 chr3qtel1M 765666 TCCCCATGCTCCTGCTTCAGGGCCTCAAACAGGCTCTTGGCTTTCTCCTG 765715 vvi vv ii vi ivii v ii i v vv vv C Tigger3#DNA/T 848 GGTCCAGCCTTTTCTTTCAACATCGCAAACAAACTTTTTGCTTTGGCCGT 799 chr3qtel1M 765716 GATGAGCATGGTGTTGATGGGCAGCTGCTGCTGCTTCTGGTCCTCGATCC 765765 viv i vi v vvi v iv i i C Tigger3#DNA/T 798 GATCGTCATGGTGCTGAGAGGGATACGCTTCTGTGTCTGGTCTTCAATCC 749 chr3qtel1M 765766 ACAGGCTCAGCAGCCTCTCCATGT 765789 vivvv i v ii i C Tigger3#DNA/T 748 AGGTCATTAGAAGTTTCTCCATAT 725 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 52.39 CpG sites = 168, Kimura (unadjusted) = 53.04 Transitions / transversions = 0.92 (168/182) Gap_init rate = 0.03 (29 / 950), avg. gap size = 1.48 (43 / 29) 206 31.94 2.78 0.00 chr3qtel1M 766393 766464 (233536) L2d_3end#LINE/L2 432 505 (11) m_b156s601i23 5871 chr3qtel1M 766393 ACCTTTCTTTCGATCCC--CAGTACTTAGCAGAGGGCCTGGCAAACAGCA 766440 i? i ? v -- ii i v v ivi v i i L2d_3end#LINE 432 ACTNTTTTNTCGTTCCCCACAGCGCCTAGCACAGTGCTGAGCACATAGTA 481 chr3qtel1M 766441 GCTGCCTAATCAATTCTTACTAAT 766464 vi ii v v ii i L2d_3end#LINE 482 GGCGCTCAATAAATACTTGTTGAT 505 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 40.02 CpG sites = 15, Kimura (unadjusted) = 45.63 Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.01 (1 / 71), avg. gap size = 2.00 (2 / 1) 244 28.81 0.00 0.00 chr3qtel1M 766405 766463 (233537) L2b_3end#LINE/L2 398 456 (10) m_b156s601i24 5871 chr3qtel1M 766405 ATCCCCAGTACTTAGCAGAGGGCCTGGCAAACAGCAGCTGCCTAATCAAT 766454 ii i v ? v i vi ii i v L2b_3end#LINE 398 ATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAAT 447 chr3qtel1M 766455 TCTTACTAA 766463 vi ii i L2b_3end#LINE 448 ATTTGTTGA 456 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 33.23 CpG sites = 12, Kimura (unadjusted) = 39.39 Transitions / transversions = 2.40 (12/5) Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.0 (0 / 0) 17 14.07 0.00 7.14 chr3qtel1M 767927 767971 (232029) (CCTCCC)n#Simple_repeat 1 42 (0) m_b156s252i12 5872 chr3qtel1M 767927 CCTGCCTCCGCCCCTCCCCCCTCCCCCTTGGCCCCTCCCCCTCCC 767971 - i v ii - -v (CCTCCC)n#Sim 1 CCT-CCCCCTCCCCCTCCCCCTCCCCC-T-CCCCCTCCCCCTCCC 42 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.07 (3 / 44), avg. gap size = 1.00 (3 / 3) 396 23.58 7.55 0.00 chr3qtel1M 770270 770375 (229625) MIRc#SINE/MIR 2 115 (153) m_b156s601i25 5873 chr3qtel1M 770270 GGGGCAGCCAGGTACAGTGGATAGAGCATCAGCCCTGAAGTCAGGAGGAC 770319 i ivv i v iii v i i i MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr3qtel1M 770320 C-AAATATG-----TGACACC-CCACTTCCTAGCTGTGTGACCCT-GGCA 770361 -iii vi -----i i v i- v i - MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 101 chr3qtel1M 770362 AGTCACTTAACCCC 770375 i MIRc#SINE/MIR 102 AGTCACTTAACCTC 115 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 26.78 CpG sites = 18, Kimura (unadjusted) = 29.56 Transitions / transversions = 2.57 (18/7) Gap_init rate = 0.04 (4 / 105), avg. gap size = 2.00 (8 / 4) 212 27.17 19.35 2.07 chr3qtel1M 773319 773442 (226558) C MIRc#SINE/MIR (104) 164 20 m_b156s601i26 5874 chr3qtel1M 773319 GGCAGGTATTATCATAATACCTATTTTACAGTGTGGGAAAATGAGGC--- 773365 i v--- i vvvi v --- C MIRc#SINE/MIR 164 GGCAGGTATTATTATC---CCCATTTTACAGATGAGGAAACTGAGGCTCA 118 chr3qtel1M 773366 ---GGGTGAAGC--TTTGGGC---GTTGTAGAGCTGGTGA---------- 773397 ---i v i--i vv --- iii v i i ---------- C MIRc#SINE/MIR 117 GAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGC 68 chr3qtel1M 773398 --GGATCTGAGCTCAGGTTTTCGTGCCTCCAGGCCCCG-GCACTCTCC 773442 -- iii i i i v v i i v - v i C MIRc#SINE/MIR 67 CGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCC 20 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 33.56 CpG sites = 20, Kimura (unadjusted) = 34.86 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.07 (9 / 123), avg. gap size = 3.00 (27 / 9) 261 35.33 3.36 2.50 chr3qtel1M 774708 774945 (225055) L1PREC2_orf2#LINE/L1 2583 2822 (472) m_b156s551i1 5875 chr3qtel1M 774708 AAAAAAAAAACACAAAGAATGGTGGCTTAGCCATACCAAACCTAAAACTA 774757 iv iv v- v v vi vv vi i v L1PREC2_orf2# 2583 AAGCAAAAAGAACAAAGC-TGGAGGCATCACGCTACCCGACTTCAAACTA 2631 chr3qtel1M 774758 TATTATAAAACAGCAGTCATCGAAACCATTTGGTACTGGCTAAGAAACAG 774807 i i iii vi v i i viiv ivv i L1PREC2_orf2# 2632 TACTACAGGGCTACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAG 2681 chr3qtel1M 774808 AAGGGTTGACTAGTGGAACAAGTTAG-GATCGCAGTTCAATATAGTCA-A 774855 vivi v i i iiv - v v --v vi i i- L1PREC2_orf2# 2682 ACACATAGACCAATGGAACAGAATAGAGAGCCCAG--AAATAAGGCCGCA 2729 chr3qtel1M 774856 TGACTATAGCAATTTAGGGTT----AGAGTTCCCAAAGACCCCAGCTTTT 774901 iiv i i v i iivv ---- i i vv i -- v vv v L1PREC2_orf2# 2730 CACCTACAACCATCTGATCTTCGACAAAGCTGACAAAAA--CAAGCAATG 2777 chr3qtel1M 774902 GGGATAAGAACTCACTGTTTGACAAAAACTGCTGGA--AACTAGTT 774945 - i v i ii i viv i-- i i L1PREC2_orf2# 2778 GGGA-AAGGACTCCCTATTCAATAAATGGTGCTGGGATAACTGGCT 2822 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 47.56 CpG sites = 45, Kimura (unadjusted) = 49.24 Transitions / transversions = 1.22 (45/37) Gap_init rate = 0.04 (10 / 237), avg. gap size = 1.40 (14 / 10) 263 32.26 0.00 0.81 chr3qtel1M 774709 774833 (225167) L1M3_orf2#LINE/L1 2578 2701 (587) m_b156s551i2 5875 chr3qtel1M 774709 AAAAAAAAACACAAAGAATGGTGGCTTAGCCATACCAAACCTAAAACTAT 774758 i i iv v- v v vi vv v vi ii v v L1M3_orf2#LIN 2578 AGAAAGAAGAACAAAGC-TGGAGGCATCACACTTCCTGATTTCAAAATAT 2626 chr3qtel1M 774759 ATTATAAAACAGCAGTCATCGAAACCATTTGGTACTGGCTAAGAAACAGA 774808 i i vi v i vi v vv i L1M3_orf2#LIN 2627 ATTACAAAGCTACAGTAATCAAAACAGTATGGTACTGGCATAAAAACAGA 2676 chr3qtel1M 774809 AGGGTTGACTAGTGGAACAAGTTAG 774833 vivi v i i iiv L1M3_orf2#LIN 2677 CATATAGACCAATGGAACAGAATAG 2701 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 42.63 CpG sites = 19, Kimura (unadjusted) = 42.63 Transitions / transversions = 0.90 (19/21) Gap_init rate = 0.01 (1 / 124), avg. gap size = 1.00 (1 / 1) 242 32.34 9.24 1.15 chr3qtel1M 775360 775922 (224078) L1M1_orf2#LINE/L1 1239 1846 (1448) m_b156s551i3 5876 chr3qtel1M 775360 CTGTTGTGCCCAATTATATGCCAACAAA------ACTCATAAATGAGAGA 775403 ii i vv i i ------ v - i v i vi L1M1_orf2#LIN 1239 CTACTATGAGCAACTATATGCCAATAAATTGGAAAATC-TAGAAGAAATG 1287 chr3qtel1M 775404 GATGAATGCTTACAAAAATAAAA--TACCTAG-------CAT-AAG---- 775439 ii v i v v v v -- v ------- - ---- L1M1_orf2#LIN 1288 GACAAATTCCTAGACACATACAACCTACCAAGATTGAACCATGAAGAAAT 1337 chr3qtel1M 775440 -TACAATCTCAAAAAA--AAAAAAAAAAAAAAAAATCTGAACCATAA--A 775484 -i v i v v i -- v v iv vi i vi i i -- L1M1_orf2#LIN 1338 CCAAAACCTGAACAGACCAATAACAAGTAACGAGATCGAAGCCGTAATAA 1387 chr3qtel1M 775485 GAAATCCCCAAAGGTGGAGAGAAGGGTTTACAAGTGAATGGATTTTCAGG 775534 i i i v ---- v i ii iiiivi vivi v iv v v L1M1_orf2#LIN 1388 AAAGTCTCCCA----GTAAAGAAAAGCCCGGGACCCGATGGCTTCACTGC 1433 chr3qtel1M 775535 TGAATTCTATCAAACATTGAAAGAATAAATCACTCCAATACTATGTAAAT 775584 i v v v v iv v ivi i L1M1_orf2#LIN 1434 TGAATTCTACCAAACATTTAAAGAAGAACTAATACCAATCCTACTCAAAC 1483 chr3qtel1M 775585 TATTT----AAAAGGAGGGGGAAAGCATCCTAGCAAA---AACCTATGAA 775627 i---- vi i ii v v vv --- vi i i L1M1_orf2#LIN 1484 TATTCCGAAAAATAGAGGAGGAGGGAATACTTCCAAACTCATTCTACGAG 1533 chr3qtel1M 775628 ATAACTGTGGCCCTGATAACTTAAAGCAAA-AAAGAGAGG--AGAAAATG 775674 iiv v i vi - iv v i - v vi-- i v L1M1_orf2#LIN 1534 GCCAGTATTACCCTGAT-ACCAAAACCAGACAAAGACACATCAAAAAAAG 1582 chr3qtel1M 775675 AAATTTAAAGATTACTATCTACAAAGGATATTGAGGCCAAAATATTGAAT 775724 vi v iii v vii v i v v vi v i L1M1_orf2#LIN 1583 AAAACTACAGGCCAATATCTCTGATGAATATTGATGCAAAAATCCTCAAC 1632 chr3qtel1M 775725 AAAATATAAGCAAAGAGGCTACAGTAATATACT-----GATCAATTACTA 775769 iv vv iv v ii i i ----- v i ii L1M1_orf2#LIN 1633 AAAATACTAGCAAACCGAATTCAACAATACATTAAAAAGATCATTCATCA 1682 chr3qtel1M 775770 TAGCTAGGTCAGATTTATACCAGGAATGCTA-GTTGGTTTAATATTAGCA 775818 ii i i vi v ? i v - v i i vv L1M1_orf2#LIN 1683 TGACCAAGTGGGATTTATCCCNGGGATGCAAGGATGGTTCAACATACGCA 1732 chr3qtel1M 775819 AAACTATAAATA-GA-ACAACATA--AACTATAAT-ATTAATAGCAACCA 775863 v v v i- - v -- - v - vvi i iv L1M1_orf2#LIN 1733 AATCAATCAATGTGATACATCATATCAAC-AGAATGAAGGACAAAAACCA 1781 chr3qtel1M 775864 -GTAA--ATATTAAATGATGTATAAAAAGCTTTTGACAGAATATAATA-- 775908 -i i -- v i v ivv v i i vi i -- L1M1_orf2#LIN 1782 TATGATCATTTCAATTGATGCTGAAAAAGCATTTGATAAAATTCAACATC 1831 chr3qtel1M 775909 CATTTA-GGTAAAAA 775922 v i - i L1M1_orf2#LIN 1832 CCTTCATGATAAAAA 1846 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 41.74 CpG sites = 95, Kimura (unadjusted) = 43.35 Transitions / transversions = 1.12 (95/85) Gap_init rate = 0.05 (28 / 562), avg. gap size = 2.11 (59 / 28) 264 30.61 7.52 3.63 chr3qtel1M 775522 776026 (223974) L1MD_orf2#LINE/L1 1421 1944 (1350) m_b156s551i5 5876 chr3qtel1M 775522 ATGGATTTTCAGGTGAATTCTATCAAACATTGAAAGAATAAATCACTCCA 775571 v iv v v i i v v v v v L1MD_orf2#LIN 1421 ATGGTTTCACTGGAGAATTCTACCAAACGTTTAAAGAAGAATTAACACCA 1470 chr3qtel1M 775572 ATACTATGTAAATTATT--------TAAAAGGAGGGGGAAAGCATCCTAG 775613 v iii vi v -------- i ii i vi v i i L1MD_orf2#LIN 1471 ATTCTACACAATCTCTTCCAGAAAATAGAAGAGGAGGGAACACTTCCCAA 1520 chr3qtel1M 775614 CAAAAACCTATGAAATAACTGTGGCCCTGATAACTTAAAGCAAA-AAAGA 775662 -vv vii iiiv v i vi - iv v i - L1MD_orf2#LIN 1521 C-TCATTTTATGAGGCCAGTATTACCCTGAT-ACCAAAACCAGACAAAGA 1568 chr3qtel1M 775663 GAGG--AGAAAATGAAATTTAAAGATTACTATCTACAAAGGATATTGAGG 775710 v v-- i v vi v ii v iviv v i i v v L1MD_orf2#LIN 1569 CAGTACAAAAAAAGAAAACTACAGACCAATATCCCTCATGAACATAGACG 1618 chr3qtel1M 775711 CCAAAATATTGAATAAAATATAAGCAAAGAGGCTACAGTAATATACTGAT 775760 v vi v i v v? iv v i ivi v L1MD_orf2#LIN 1619 CAAAAATCCTCAACAAAATATTAGCAAATNGAATTCAGCAATATATAAAA 1668 chr3qtel1M 775761 C-AATT----ACTATAGCTAGGTCAGATTTATACCAGGAATGCTA-GTTG 775804 v- ---- i ii i i vi i v ? v - i L1MD_orf2#LIN 1669 AGAATTATACACCATGACCAAGTGGGGTTTATTCCAGGNATGCAAGGCTG 1718 chr3qtel1M 775805 GTTTAATATTAGCAAAACTATAAATAGAACAACATAAACTATAATATTAA 775854 i -- i -- v ---- ii v i iv L1MD_orf2#LIN 1719 GTTCAATATT--CGAAA--ATCAAT----CAATGTAATCCACCATATTAA 1760 chr3qtel1M 775855 TAG------------CAACCA-GTAA--ATATTAAATGATGTATAAAAAG 775889 i ------------v i -i i -- i v i v L1MD_orf2#LIN 1761 CAGGCTAAAGAAGAAAAATCACATGATCATATCAATTGATGCAGAAAAAG 1810 chr3qtel1M 775890 CTTTTGACAGAATATAATA--CATTTA-GGTAAAAAAAAAAAAAAAAAGC 775936 v i vi i -- i - i vvvvv i? ---- L1MD_orf2#LIN 1811 CATTTGACAAAATTCAACACCCATTCATGATAAAAACTCTCAGNAA---- 1856 chr3qtel1M 775937 CCACTAAGAATAAACAG--ACTT-TTCATAATGGCAAATGAAATCTATCA 775983 -- i i vi -- -i vvv ii viiv iv L1MD_orf2#LIN 1857 --ACTAGGAATAGAGGGGAACTTCCTCAACTTGATAAAGAGCATCTACAA 1904 chr3qtel1M 775984 AAAATTTGAAACTAACATCCATAATTATCACAATAAAATACTG 776026 ii iv i - v -- iii i v L1MD_orf2#LIN 1905 AAAACCTACAGCTAACAT-CATACTTA--ATGGTGAAAGACTG 1944 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 39.84 CpG sites = 80, Kimura (unadjusted) = 40.55 Transitions / transversions = 1.16 (80/69) Gap_init rate = 0.06 (32 / 504), avg. gap size = 1.78 (57 / 32) 334 32.08 6.82 0.99 chr3qtel1M 775522 775902 (224098) L1PB_orf2#LINE/L1 1421 1823 (1471) m_b156s551i4 5876 chr3qtel1M 775522 ATGGATTTTCAGGTGAATTCTATCAAACATTGAAAGAATAAATCACTCCA 775571 i iv v? i i v v v viiv L1PB_orf2#LIN 1421 ACGGATTCACAGCNGAATTCTACCAGACATTCAAAGAAGAATTGGTACCA 1470 chr3qtel1M 775572 ATACTATGTAAATTATTTAAAAGGAGGGGGAAA----GCATCCTAGCAAA 775617 v vv v i iv v i vi i ---- v vv v L1PB_orf2#LIN 1471 ATCCTATTGACACTATTCCACAAGATAGAGAAAGAGGGAATCCTCCCTAA 1520 chr3qtel1M 775618 AAC---CTATGAAATAACTGTGGCCCTGATAACTTAAAGCAAAAAAG--- 775661 v --- iiv v i vi i - iv v ii --- L1PB_orf2#LIN 1521 ATCATTCTATGAAGCCAGTATCACCCTAAT-ACCAAAACCAGGAAAGGAC 1569 chr3qtel1M 775662 AGAGGAGAAAATGAAATTTAAAGATTACTATCTACAAAGGATATTGAGGC 775711 v iv?i v vi v ii v ivii v i i v v L1PB_orf2#LIN 1570 ATAACNAAAAAAGAAAACTACAGACCAATATCCCTGATGAACATAGATGC 1619 chr3qtel1M 775712 CAAAATATTGAATAAAATATAAGCAAAGAGGCTACAGTAATATACT---- 775757 ? vi v i iv v vv iv v ii ii ii---- L1PB_orf2#LIN 1620 NAAAATCCTCAACAAAATACTAGCTAACCGAATCCAACAGCATATCAAAA 1669 chr3qtel1M 775758 -GATCAATTACTATAGCTAGGTCAGATTTATACCAGGAATGC-TAGTTGG 775805 - v vii i iiii i vi v i i -vi v L1PB_orf2#LIN 1670 AGATAATCCACCATGATCAAGTGGGTTTCATACCAGGGATGCAGGGATGG 1719 chr3qtel1M 775806 TTTAATATTAGCAAAACTATAAATA-GA---ACAACATAAACTATAATAT 775851 i vv iv v i- --- v --- iv L1PB_orf2#LIN 1720 TTTAACATACGCAAGTCAATAAATGTGATACACCACATAAAC---AGAAT 1766 chr3qtel1M 775852 TAATAGCAACCAGTAAAT-ATTA----AAT-GATGTATAAAAAGCTTTTG 775895 v i vv vi v - i ---- - i v v L1PB_orf2#LIN 1767 TAAAAACAAAAATCACATGATCATCTCAATAGATGCAGAAAAAGCATTTG 1816 chr3qtel1M 775896 ACAGAAT 775902 i L1PB_orf2#LIN 1817 ACAAAAT 1823 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 42.48 CpG sites = 60, Kimura (unadjusted) = 42.95 Transitions / transversions = 0.98 (60/61) Gap_init rate = 0.04 (15 / 380), avg. gap size = 2.00 (30 / 15) 240 32.24 1.10 4.55 chr3qtel1M 776620 776710 (223290) L2d2_3end#LINE/L2 457 544 (11) m_b156s601i27 5877 chr3qtel1M 776620 CAGGTGGCCATGCTTCCTTCCTTTTTCTTGTGGCTTGTACA-CACTTAGC 776668 - i ii iv v i i --- iv iivi - i i L2d2_3end#LIN 457 CAGG-GACCATGTCTTATACTTCTTT---GTATCCCCCACAGCGCCTAGC 502 chr3qtel1M 776669 ACAGCATCTGGCACATATTAAGCTCTTGATAGATGTTTGTTG 776710 iii v i v i v ii i i L2d2_3end#LIN 503 ACAGTGCCTTGCACACAGTAGGCGCTCAATAAATATTTGTTG 544 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 43.49 CpG sites = 21, Kimura (unadjusted) = 45.80 Transitions / transversions = 3.00 (21/7) Gap_init rate = 0.06 (5 / 90), avg. gap size = 1.00 (5 / 5) 241 26.00 0.00 0.00 chr3qtel1M 776661 776710 (223290) L2b_3end#LINE/L2 406 455 (11) m_b156s601i28 5877 chr3qtel1M 776661 CACTTAGCACAGCATCTGGCACATATTAAGCTCTTGATAGATGTTTGTTG 776710 i i ?ii i v i v iii i i L2b_3end#LINE 406 CGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTTGTTG 455 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 32.30 CpG sites = 11, Kimura (unadjusted) = 35.78 Transitions / transversions = 5.50 (11/2) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 559 33.44 1.59 1.92 chr3qtel1M 778498 778811 (221189) L1ME4c_3end#LINE/L1 342 654 (176) m_b157s551i0 5878 chr3qtel1M 778498 AAGGGCCATCAAAGTCTCCAAAGCCTTTGACCCAGCAGTGTTTCTGCTGG 778547 i v i v i v v i i viiv v L1ME4c_3end#L 342 AAGAGCCATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGG 391 chr3qtel1M 778548 GCTTACATCCCAAAGAGATCTT---AAAGGAGGAAAAGGGACCCACATGT 778594 vv vi i i i vv --- i i --- i i i L1ME4c_3end#L 392 GAATTTATCCTAAGGAAATAATTCAAAAGAAGGAAAAAG---CTATATGC 438 chr3qtel1M 778595 GCAAAAATGTTTGTGGCAGCCCTTTTTGTAGAGGCAAAATACTGGAAACT 778644 i i i ii v vi v i ivi i v i v L1ME4c_3end#L 439 ACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACA 488 chr3qtel1M 778645 GAGTGGAAGCCCATCAATTGGAGAATGGCTGAACAAGTTATGGTATATGA 778694 ivv ii v i v v i i i ii i i v? L1ME4c_3end#L 489 ACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCN 538 chr3qtel1M 778695 ATGTTACGGAATATTATTGTTCTGTAAGAAATGACCAGCAGGAAGA-TAT 778743 iviv i vvvv ii v i iv vi v - L1ME4c_3end#L 539 ACTCGATGGAATATTATGCAGCCATTAAAAATGATAATTATGAAGACTAT 588 chr3qtel1M 778744 CAGAGAGGCCTGGAGAGACTGACAGAACTGATGTTAAATGAAATGAGCAG 778793 -iv vii v i ivv vvvv vv i i vi L1ME4c_3end#L 589 -GTAGCAACATGGAAAATGTTTATGATATAATGTTAAGTGAAAAAAGCAG 637 chr3qtel1M 778794 AAC-CAGATCATTGTACAT 778811 i- i -- i? L1ME4c_3end#L 638 AATACAAA--ATTGTATNT 654 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 44.12 CpG sites = 57, Kimura (unadjusted) = 45.94 Transitions / transversions = 1.24 (57/46) Gap_init rate = 0.03 (9 / 313), avg. gap size = 1.22 (11 / 9) 226 29.68 9.80 0.90 chr3qtel1M 779908 780009 (219991) C MIRb#SINE/MIR (33) 235 125 m_b157s601i1 5879 chr3qtel1M 779908 ATGTGCCAGGCACTGGGCT-GGTAACTCATGAGAGTTA-CTC----GATC 779951 v -i iivi i iiv vi - ----i C MIRb#SINE/MIR 235 ATGTGCCAGGCACTGTGCTAAGCGCTTTACATGCATTATCTCATTTAATC 186 chr3qtel1M 779952 TTTACCACAGACTTGAGAGGC-GCTCATCTTATCC---TTTCACAGATGA 779997 i i v iv i v i- v vv v --- i C MIRb#SINE/MIR 185 CTCACAACAACCCTGCGAGGTAGGTATTATTATCCCCATTTTACAGATGA 136 chr3qtel1M 779998 AGTAGGCTGGGG 780009 i - ii i C MIRb#SINE/MIR 135 GG-AAACTGAGG 125 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.45 CpG sites = 19, Kimura (unadjusted) = 39.34 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.06 (6 / 101), avg. gap size = 1.83 (11 / 6) 467 17.65 0.00 6.59 chr3qtel1M 781043 781139 (218861) MIRb#SINE/MIR 107 197 (71) m_b157s601i2 5880 chr3qtel1M 781043 TTACTTAAACTGGGCCTCCCACTGCCTCAGTCTCTTCATTTGTAAAATGG 781092 ------ i vvv i i i MIRb#SINE/MIR 107 TTACTTAA------CCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGG 150 chr3qtel1M 781093 GGATAATAGCACCTACCTCCCACGGTTGTTGTAAGGATCAAACAAAA 781139 ii v v i i ii i MIRb#SINE/MIR 151 GGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGA 197 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 20.51 CpG sites = 11, Kimura (unadjusted) = 20.51 Transitions / transversions = 2.20 (11/5) Gap_init rate = 0.06 (6 / 96), avg. gap size = 1.00 (6 / 6) 443 28.11 0.00 3.51 chr3qtel1M 781199 781316 (218684) C MIRb#SINE/MIR (150) 118 5 m_b157s601i3 5879 chr3qtel1M 781199 GGGACTAGGTGACTTGTCCAGGGTCACAAAGCTAATGATGTACCTGAGGA 781248 i ii i i i i v i i - iv v vv C MIRb#SINE/MIR 118 GAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAA-GTGGCAGAGCC 70 chr3qtel1M 781249 TGGATTTGAGCTTGGGTCCTTCTGACTCCAGGGCTGGCGCTCTATCCACT 781298 v i i iii iv ii iv i v C MIRb#SINE/MIR 69 GGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACT 20 chr3qtel1M 781299 GTACTATCCAGCTGCCCC 781316 i i i--- C MIRb#SINE/MIR 19 GCACCAC---GCTGCCCC 5 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.27 CpG sites = 23, Kimura (unadjusted) = 37.23 Transitions / transversions = 2.56 (23/9) Gap_init rate = 0.03 (4 / 117), avg. gap size = 1.00 (4 / 4) 185 30.63 13.51 0.00 chr3qtel1M 781348 781458 (218542) C L2d_3end#LINE/L2 (39) 477 352 m_b157s601i4 5881 chr3qtel1M 781348 ATGTGCCAGGCACGATTCTATGTGCT--------CAAAATAAAAAGGCAA 781389 ivi vi v v i -------- i ? v ? ivii C L2d_3end#LINE 477 ATGTGCTCAGCACTGTGCTAGGCGCTGTGGGGAACGANAAAANAGTATAA 428 chr3qtel1M 781390 AAGCTAGGCCCTGCCCACAAGGAGCTCCGGCTCT--TTGGTGGG---AAA 781434 i vv i v v ivviv -- v i --- i C L2d_3end#LINE 427 GACATGGTCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGGAGACAAGA 378 chr3qtel1M 781435 CTAGCAAACAAGCTACAA--AGAGGA 781458 i v v vv -- i C L2d_3end#LINE 377 CTAACACACATGAAACAATTAGAGAA 352 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.75 CpG sites = 16, Kimura (unadjusted) = 40.71 Transitions / transversions = 0.89 (16/18) Gap_init rate = 0.04 (4 / 110), avg. gap size = 3.75 (15 / 4) 220 22.23 17.35 3.60 chr3qtel1M 781348 781445 (218555) C L2a_3end#LINE/L2 (37) 480 370 m_b157s601i5 5881 chr3qtel1M 781348 ATGTGCCAGGCACGATTCTATGTGCT-------CA-----AAATAAAA-A 781384 vi v i ------- -----i i - C L2a_3end#LINE 480 ATGTGCCAGGCACTGTTCTAGGCGCTGGGGATACAGCAGTGAACAAAACA 431 chr3qtel1M 781385 GGCAAAAGCTAGGCCCTGCCCACAAGGAGCTCCGGCTCTT-TGGTGGGAA 781433 i i---- v v ivvii v- v i C L2a_3end#LINE 430 GACAAAAGT----CCCTGCCCTCATGGAGCTTACATTCTAGTGGGGGGAG 385 chr3qtel1M 781434 AC---TAGCAAACAA 781445 ---i ii C L2a_3end#LINE 384 ACAGACAATAAACAA 370 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 25.63 CpG sites = 13, Kimura (unadjusted) = 27.11 Transitions / transversions = 1.62 (13/8) Gap_init rate = 0.09 (9 / 97), avg. gap size = 2.33 (21 / 9) 186 23.86 22.73 0.00 chr3qtel1M 781522 781609 (218391) C L2a_3end#LINE/L2 (345) 172 65 m_b157s601i6 5881 chr3qtel1M 781522 GAGGAAGAGGGTTCCAGGCATGAGGAACAGCCAG---AGAAACCAT---- 781564 i v vii v --- i ii v ---- C L2a_3end#LINE 172 GGGGAAGAGCGTTCCAGGCAGAGGGAACAGCAAGTGCAAAGGCCCTGAGG 123 chr3qtel1M 781565 CTGGAGC-------------CCAGAGAACTGCAAGGAGGCGAGTGTCGCT 781601 v -------------i iii v v v C L2a_3end#LINE 122 CGGGAGCGTGCCTGGCGTGTTCGAGGAACAGCAAGGAGGCCAGTGTGGCT 73 chr3qtel1M 781602 GGGTTGGA 781609 ivi C L2a_3end#LINE 72 GGAGCGGA 65 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.05 CpG sites = 12, Kimura (unadjusted) = 29.22 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.03 (3 / 87), avg. gap size = 6.67 (20 / 3) 339 27.10 4.50 3.57 chr3qtel1M 781634 781744 (218256) C L2d2_3end#LINE/L2 (9) 546 435 m_b157s601i7 5882 chr3qtel1M 781634 ATCACTAAGCATTTATTAAGTGCCTACTGGATGCAT-GCACGATGTGTGC 781682 vi ii i i vi v- ---- C L2d2_3end#LIN 546 ATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCAC----TGTGC 501 chr3qtel1M 781683 TAAGTGC--TGGGGAAGCCACAGAAAGATATGACC--GTTTCTGAGTTTG 781728 i i -- i vv v iv v v-- ii vvi ii C L2d2_3end#LIN 500 TAGGCGCTGTGGGGGATACAAAGAAGTATAAGACATGGTCCCTGCCCTCA 451 chr3qtel1M 781729 TGGAGCTTACCACCTA 781744 v v i C L2d2_3end#LIN 450 AGGAGCTTACAATCTA 435 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.42 CpG sites = 16, Kimura (unadjusted) = 34.24 Transitions / transversions = 1.23 (16/13) Gap_init rate = 0.06 (7 / 110), avg. gap size = 1.29 (9 / 7) 21 0.00 0.00 0.00 chr3qtel1M 782101 782123 (217877) (G)n#Simple_repeat 1 23 (0) m_b157s252i0 5883 chr3qtel1M 782101 GGGGGGGGGGGGGGGGGGGGGGG 782123 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGG 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 30 25.29 8.06 0.75 chr3qtel1M 782299 782422 (217578) (GA)n#Simple_repeat 1 133 (0) m_b157s252i1 5884 chr3qtel1M 782299 GAGAGAG-GGGAAAG-GAGAGAGAGGGAGGGAGAAAAATGGAGAGGGA-A 782345 - i i - i i i i vi i - (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr3qtel1M 782346 GGGAAGGAGACACCAAAG-GATGGAGAGAGAG-GAGAGAAAAAGAAAG-G 782392 i ii v -v i - vi - i i i - (GA)n#Simple_ 51 GAGAGAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 99 chr3qtel1M 782393 AGGGA-AGAG-GAAAAAAAGA-AGAG-GAGGGAG 782422 i - - i i i - - i (GA)n#Simple_ 100 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 133 Matrix = Unknown Transitions / transversions = 5.25 (21/4) Gap_init rate = 0.09 (11 / 123), avg. gap size = 1.00 (11 / 11) 15 22.57 2.90 5.97 chr3qtel1M 784112 784180 (215820) (CCCCT)n#Simple_repeat 1 67 (0) m_b157s252i2 5885 chr3qtel1M 784112 CCCCGCCCCTCCCCTCCTCCCTCCCAT-CACTCCGGAGTCCCTGCCCCT- 784159 v - - v - v --vv iv - (CCCCT)n#Simp 1 CCCCTCCCCTCCCCT-C-CCCTCCCCTCCCCTCC--CCTCCCCTCCCCTC 46 chr3qtel1M 784160 CCTTCCTCTCCACTGCACTCC 784180 i i v v v (CCCCT)n#Simp 47 CCCTCCCCTCCCCTCCCCTCC 67 Matrix = Unknown Transitions / transversions = 0.33 (3/9) Gap_init rate = 0.09 (6 / 68), avg. gap size = 1.00 (6 / 6) 181 25.93 3.70 0.00 chr3qtel1M 784213 784266 (215734) MIRc#SINE/MIR 120 175 (93) m_b157s601i8 5886 chr3qtel1M 784213 AGCCTCAGTTTCCTCAGTTCTGAAATAGGAATCATGCT--CAGCCCTCCC 784260 vi v i i i v iv -- v v MIRc#SINE/MIR 120 AGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCC 169 chr3qtel1M 784261 CCCCCC 784266 iv i MIRc#SINE/MIR 170 TACCTC 175 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.13 CpG sites = 7, Kimura (unadjusted) = 32.13 Transitions / transversions = 1.00 (7/7) Gap_init rate = 0.02 (1 / 53), avg. gap size = 2.00 (2 / 1) 196 21.74 2.17 0.00 chr3qtel1M 784214 784259 (215741) MIR1_Amn#SINE/MIR 123 169 (61) m_b157s601i9 5886 chr3qtel1M 784214 GCCTCAGTTTCCTCAGTTCTGAAATAGGAATCATGCT-CAGCCCTCC 784259 vi v i i i v v - v v MIR1_Amn#SINE 123 GCCTCAGTTTCCTCATCTGTAAAATGGGGATAATGATACTGACCTCC 169 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 25.70 CpG sites = 4, Kimura (unadjusted) = 25.70 Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1) 192 31.35 1.45 2.94 chr3qtel1M 785599 785667 (214333) C L2d2_3end#LINE/L2 (1) 554 487 m_b157s601i10 5887 chr3qtel1M 785599 CAAGTTAA-TCCACAAGCACCTATTAGGGACCGACTGTGCGCTGGGCACG 785647 i i - v ii ii ii vi v i vi v C L2d2_3end#LIN 554 CAAATCAAATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACT 505 chr3qtel1M 785648 CAGCCAGACTCTCCGTGGGG 785667 vv i i v -- C L2d2_3end#LIN 504 GTGCTAGGCGCT--GTGGGG 487 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.58 CpG sites = 13, Kimura (unadjusted) = 42.23 Transitions / transversions = 1.62 (13/8) Gap_init rate = 0.04 (3 / 68), avg. gap size = 1.00 (3 / 3) 23 18.68 0.00 0.00 chr3qtel1M 786780 786828 (213172) (AGAGAG)n#Simple_repeat 1 49 (0) m_b157s252i3 5888 chr3qtel1M 786780 AGCGAGAGAGAAAGAGGGAGAGGGAGAGAGAGATAGAGTAAGAAAGAGA 786828 v i i i v vi i (AGAGAG)n#Sim 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 49 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 13 25.68 2.17 0.00 chr3qtel1M 786865 786910 (213090) (GGCGGG)n#Simple_repeat 1 47 (0) m_b157s252i5 5889 chr3qtel1M 786865 GGAGGGGGCGGGACCGAGAGCGGCCGCCGGGCAGGGGGC-GGGGCGG 786910 v iv i i vv v vv - (GGCGGG)n#Sim 1 GGCGGGGGCGGGGGCGGGGGCGGGGGCGGGGGCGGGGGCGGGGGCGG 47 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1) 17 0.00 0.00 0.00 chr3qtel1M 787403 787421 (212579) (C)n#Simple_repeat 1 19 (0) m_b157s252i6 5890 chr3qtel1M 787403 CCCCCCCCCCCCCCCCCCC 787421 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCC 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 13 19.66 2.78 0.00 chr3qtel1M 788164 788199 (211801) (GGGAAGG)n#Simple_repeat 1 37 (0) m_b157s252i7 5891 chr3qtel1M 788164 GGGGAGGGGGGAGGCGG-AGAAGGAAGGGGGAAAGGG 788199 i i v - ii i (GGGAAGG)n#Si 1 GGGAAGGGGGAAGGGGGAAGGGGGAAGGGGGAAGGGG 37 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) 53 36.82 0.74 1.49 chr3qtel1M 788756 789025 (210975) (TGGA)n#Simple_repeat 1 268 (0) m_b157s252i8 5892 chr3qtel1M 788756 TGGATAGAGGGCT-GAAGGAAGGAACGGCAGGATTGACTGATGAATGGAT 788804 i v v - v v - i vv v iv i (TGGA)n#Simpl 1 TGGATGGATGGATGGATGGATGG-ATGGATGGATGGATGGATGGATGGAT 49 chr3qtel1M 788805 AGATGGAGGGACAAATGAATGGAAACACTAG-TGGAGGGAGGGACAAATG 788853 i v iii i viv - i - v v iii (TGGA)n#Simpl 50 GGATGGATGGATGGATGGATGGATGGA-TGGATGGATGGATGGATGGATG 98 chr3qtel1M 788854 GGTGGAAAGATTAATGGAGGGACTGATGGATGGGTGGAAGGAAGGAAGGA 788903 i vi vi v iv i v v v (TGGA)n#Simpl 99 GATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGA 148 chr3qtel1M 788904 GAGAGGGAAGGACAGACAAGGAGAAATTGATGGAGGGATACATAGATGGA 788953 vi v v -v -v v vii v v iv i (TGGA)n#Simpl 149 TGGATGGATGGA-TG-GATGGATGGATGGATGGATGGATGGATGGATGGA 196 chr3qtel1M 788954 TGAATGCATACACGGAGGAACTGATGGACAGATAAAGGGGTGGAAGGAGA 789003 i v iv i v i iv ii ii v i v vi (TGGA)n#Simpl 197 TGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATG 246 chr3qtel1M 789004 GATGGAGGGAGCGGTGGATGGA 789025 v vv i (TGGA)n#Simpl 247 GATGGATGGATGGATGGATGGA 268 Matrix = Unknown Transitions / transversions = 0.90 (36/40) Gap_init rate = 0.02 (6 / 269), avg. gap size = 1.00 (6 / 6) 18 7.52 0.00 0.00 chr3qtel1M 789212 789239 (210761) (GGAC)n#Simple_repeat 1 28 (0) m_b157s252i9 5893 chr3qtel1M 789212 GGGCGGTCGGACGGACGGACGGACGGAC 789239 i v (GGAC)n#Simpl 1 GGACGGACGGACGGACGGACGGACGGAC 28 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 18 20.83 3.51 1.72 chr3qtel1M 790142 790198 (209802) (CCCCT)n#Simple_repeat 1 58 (0) m_b157s252i10 5894 chr3qtel1M 790142 CCCCTCCCC-ATTCTACCCTCCCAGCCCCGCCCCGCCCCGCCCCTCGCCC 790190 -vii v vv v v v - (CCCCT)n#Simp 1 CCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTC-CCC 49 chr3qtel1M 790191 T-ACCTCCC 790198 -v (CCCCT)n#Simp 50 TCCCCTCCC 58 Matrix = Unknown Transitions / transversions = 0.25 (2/8) Gap_init rate = 0.05 (3 / 56), avg. gap size = 1.00 (3 / 3) 16 22.67 2.17 0.00 chr3qtel1M 790363 790408 (209592) (GGGGAG)n#Simple_repeat 1 47 (0) m_b157s252i12 5895 chr3qtel1M 790363 GGGCAGGGGCCAGAGGAGGGGGACGGGCA-GGGGCGGGGAAGGGGGA 790408 v vvi i v v - v i (GGGGAG)n#Sim 1 GGGGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGGA 47 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1) 14 11.56 3.57 0.00 chr3qtel1M 791385 791412 (208588) (GGA)n#Simple_repeat 1 29 (0) m_b157s252i13 5896 chr3qtel1M 791385 GGGGGACGAGGAGGACGAGGAGGA-GAGG 791412 i v v - (GGA)n#Simple 1 GGAGGAGGAGGAGGAGGAGGAGGAGGAGG 29 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 12 17.40 0.00 5.88 chr3qtel1M 794090 794125 (205875) (CCCCA)n#Simple_repeat 1 34 (0) m_b157s252i15 5897 chr3qtel1M 794090 CCCCAGCCCTGCCACACCCAGCCCCCACCCCACCCC 794125 - ii v -vv (CCCCA)n#Simp 1 CCCCA-CCCCACCCCACCC-CACCCCACCCCACCCC 34 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 15 22.11 3.51 3.51 chr3qtel1M 794088 794144 (205856) (ACCCAC)n#Simple_repeat 1 57 (0) m_b157s252i14 5898 chr3qtel1M 794088 ACCCCCAGCC-CTGCCACACCCAGCCCCCAC-CCCACCCCCTCTTCCCAC 794135 v v - vv - v - v v -v (ACCCAC)n#Sim 1 ACCCACACCCACACCCACACCCA-CACCCACACCCACACCCAC-ACCCAC 48 chr3qtel1M 794136 TCCCTCACC 794144 v v (ACCCAC)n#Sim 49 ACCCACACC 57 Matrix = Unknown Transitions / transversions = 0.00 (0/10) Gap_init rate = 0.07 (4 / 56), avg. gap size = 1.00 (4 / 4) 16 15.75 0.00 8.70 chr3qtel1M 796237 796286 (203714) (CGCCC)n#Simple_repeat 1 46 (0) m_b157s252i16 5899 chr3qtel1M 796237 CGCCCCTCCCCCGCCCGGCCCCTCCCCGCGCTCACCCGCGCCATCGCCCC 796286 -v v v - i i - -i (CGCCC)n#Simp 1 CGCCCC-GCCCCGCCCCGCCCCGCCCCGC-CCCGCCC-CGCC-CCGCCCC 46 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.08 (4 / 49), avg. gap size = 1.00 (4 / 4) 36 28.45 2.19 2.19 chr3qtel1M 796483 796619 (203381) (GGC)n#Simple_repeat 1 137 (0) m_b157s252i17 5900 chr3qtel1M 796483 GGCGGCGCCCGAGGCGGCGGCGGCGGACCCGGAGGCGCCCGAAGCCGAGG 796532 v v v vvv v v v vi v v (GGC)n#Simple 1 GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGG 50 chr3qtel1M 796533 CGGCGGCGGCCGCGGGCCCCGAAGGC-GCCCCGGCTGACGAC-GAGGCTG 796580 v - vv iv - vv - i i - v v (GGC)n#Simple 51 CGGCGGCGGCGGC-GGCGGCGGCGGCGGCGGCGGC-GGCGGCGGCGGCGG 98 chr3qtel1M 796581 CGGCGGACGAAGCGGCGGAGGCCGCGGACGAC-GCGGCGG 796619 vv vi v v - i - (GGC)n#Simple 99 CGGCGGCGGCGGCGGCGGCGGCGGCGG-CGGCGGCGGCGG 137 Matrix = Unknown Transitions / transversions = 0.24 (6/25) Gap_init rate = 0.04 (6 / 136), avg. gap size = 1.00 (6 / 6) 19 15.85 14.29 0.00 chr3qtel1M 797124 797207 (202793) (GCGCGA)n#Simple_repeat 1 96 (0) m_b157s252i18 5901 chr3qtel1M 797124 GCCCGA-CGC-AG-GCGA-TGGGATCGCG-GC-CGAGC-CGCGC-CGAG- 797164 v - - - -i v v - - - v - - (GCGCGA)n#Sim 1 GCGCGAGCGCGAGCGCGAGCGCGAGCGCGAGCGCGAGCGCGAGCGCGAGC 50 chr3qtel1M 797165 GCGAACGGGAGCAGGAGCGCGAGTGGGAGCG-G-GAG-GAGCGCGA 797207 i v iv i v - - v - (GCGCGA)n#Sim 51 GCGAGCGCGAGCGCGAGCGCGAGCGCGAGCGCGAGCGCGAGCGCGA 96 Matrix = Unknown Transitions / transversions = 0.50 (4/8) Gap_init rate = 0.14 (12 / 83), avg. gap size = 1.00 (12 / 12) 26 24.82 1.28 1.28 chr3qtel1M 797172 797249 (202751) (GGAGCA)n#Simple_repeat 1 78 (0) m_b157s252i19 5902 chr3qtel1M 797172 GGAGCAGGAGCGCGAGTGGGAGCGGGAGGA-GCGCGAAGAGCAGACGCTA 797220 iv ii i v - v - i iv vi (GGAGCA)n#Sim 1 GGAGCAGGAGCAGGAGCAGGAGCAGGAGCAGGAGC-AGGAGCAGGAGCAG 49 chr3qtel1M 797221 GAGCAGGAGCAGGAGACGGAGGAGGGGCA 797249 vv v i (GGAGCA)n#Sim 50 GAGCAGGAGCAGGAGCAGGAGCAGGAGCA 78 Matrix = Unknown Transitions / transversions = 1.00 (8/8) Gap_init rate = 0.03 (2 / 77), avg. gap size = 1.00 (2 / 2) 181 28.75 2.44 2.44 chr3qtel1M 797824 797905 (202095) C MIR#SINE/MIR (173) 89 8 m_b157s601i11 5903 chr3qtel1M 797824 GTCACCCAACTCCTACGGGGGCAAGGCTGGG-TTGGAACCCCGGGCTTCT 797872 v i vv -i v ii i - v v vvv C MIR#SINE/MIR 89 GTCACACAGCTAGTA-AGTGGCAGAGCCGGGATTCGAACCCAGGCAGTCT 41 chr3qtel1M 797873 GGACTCCAGATCCGGTGTCCCGAGTCACC-TGCT 797905 - v v ii iv ii i- C MIR#SINE/MIR 40 GG-CTCCAGAGCCCGTGCTCTTAACCACTATGCT 8 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.67 CpG sites = 11, Kimura (unadjusted) = 36.59 Transitions / transversions = 0.92 (11/12) Gap_init rate = 0.05 (4 / 81), avg. gap size = 1.00 (4 / 4) 213 29.42 1.45 1.45 chr3qtel1M 797824 797892 (202108) C MIRc#SINE/MIR (175) 93 25 m_b157s601i12 5903 chr3qtel1M 797824 GTCACCCAACTCCTACGGGGGCAAGGCTGGG-TTGGAACCCCGGGCTTCT 797872 v i vv -i v ii i -i v v v i C MIRc#SINE/MIR 93 GTCACACAGCTAGTA-AGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCC 45 chr3qtel1M 797873 GGACTCCAGATCCGGTGTCC 797892 v ii i ii C MIRc#SINE/MIR 44 TGACTCCAAGTCCAGTGCTC 25 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.07 CpG sites = 12, Kimura (unadjusted) = 38.51 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.03 (2 / 68), avg. gap size = 1.00 (2 / 2) 26 0.00 0.00 0.00 chr3qtel1M 798089 798113 (201887) (C)n#Simple_repeat 1 25 (0) c_b157s251i0 5904 chr3qtel1M 798089 CCCCCCCCCCCCCCCCCCCCCCCCC 798113 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCC 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 47 35.24 1.34 2.25 chr3qtel1M 799350 799573 (200427) (GA)n#Simple_repeat 1 222 (0) m_b157s252i20 5905 chr3qtel1M 799350 GAGGGAAAGGGA-AGAGAAAAAGTCAGAATGACAGAGAG-GAGAGAGACA 799397 i i i - i i vv iv v - v (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr3qtel1M 799398 GAAACTGAGAAAGGCAGAGAAATGGGGGAGAGAGGCAGAGACAGAAATGG 799447 i vv i iv i - i i iv v i - i (GA)n#Simple_ 51 GAGAGAGAGAGAGAGAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGA-GA 98 chr3qtel1M 799448 GGGAAAGAAATGGGAGAGAGGGGCAGAGAAATGGAGAGAGGCAGACAGAG 799497 i i i - i i iv i vi iv v (GA)n#Simple_ 99 GAGAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 147 chr3qtel1M 799498 AAATGGGAGAGAGAGGTAGACAAATGGAGAGAGGCAGAGACA-AAAGGGG 799546 i - i iv v i vi iv v - i i i (GA)n#Simple_ 148 AGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 196 chr3qtel1M 799547 GAAAGAAATGGGAGAGCGGGTCAGAGA 799573 i i - i v i vv (GA)n#Simple_ 197 GAGAGAGA-GAGAGAGAGAGAGAGAGA 222 Matrix = Unknown Transitions / transversions = 1.68 (37/22) Gap_init rate = 0.04 (8 / 223), avg. gap size = 1.00 (8 / 8) 215 27.62 20.00 0.00 chr3qtel1M 801158 801262 (198738) C MIR3#SINE/MIR (17) 191 66 m_b157s601i13 5906 chr3qtel1M 801158 AATGTCCAAGCC--CTGGGACCTTCCGGAGCCTCTT------CCTCCTCT 801199 vi i--vv vvi v v v------ i v C MIR3#SINE/MIR 191 AATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCA 142 chr3qtel1M 801200 TTTTC----TGAAGGAGTTGAGG---------GTAAAATGACTTGTCCAG 801236 v---- i i ii --------- i i i i C MIR3#SINE/MIR 141 TTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAA 92 chr3qtel1M 801237 GATCACACAGCTCCTGCGTGTCCGAG 801262 i ?vv vv v v C MIR3#SINE/MIR 91 GGTCACACAGCNAGTTAGTGGCAGAG 66 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.06 CpG sites = 13, Kimura (unadjusted) = 35.06 Transitions / transversions = 0.81 (13/16) Gap_init rate = 0.04 (4 / 104), avg. gap size = 5.25 (21 / 4) 283 34.94 6.57 3.37 chr3qtel1M 801635 803506 (196494) C L1M5_orf2#LINE/L1 (681) 2613 684 m_b157s551i1 5907 chr3qtel1M 801635 TATATGTCCACCC-CTTCATCCTT-TTTGCCATCACTTTCCTTGATGTTC 801682 i v v v- ii i - vi vv i v ii v v i C L1M5_orf2#LIN 2613 TGTAAGTCCTCCAACTTTGTTCTTCTTTTTCAAGATTGTTTTGGCTATTC 2564 chr3qtel1M 801683 TGTATCTTTTGT-TTTTCATTTAAAATTT-------GCTGAGCAAATT-T 801723 ?vi i i- i v v ------- viv v - C L1M5_orf2#LIN 2563 TNGGTCCTTTGCATTTCCATATAAATTTTAGAATCAGCTTGTCAATTTCT 2514 chr3qtel1M 801724 ATAAAGCATCCCTTTGCTACTTTGGTTAGTATTGCATTAAAAGTGTAAAT 801773 i iv v ivi vv i i i v i vv i i C L1M5_orf2#LIN 2513 ACAAAAAAACCTGCTGGGATTTTGATTGGGATTGCATTGAATCTATAGAT 2464 chr3qtel1M 801774 TAATTTAAGTGGTATTATTGTTTTCATTATGTTGACATGACCTAGCC-TG 801822 i ii vi v ivii i ? iv i vvivv v v - C L1M5_orf2#LIN 2463 CAATTTGGGGAGAATTGACATCTTNACAATATTGAGTCTTCCAATCCATG 2414 chr3qtel1M 801823 AGCACAGAAT-TTTCTCCAGTT-CTCAGGTGATTTCTTGTTTCTTTACCT 801870 i ii v - i v -i i vv i i vi ---- C L1M5_orf2#LIN 2413 AACATGGTATATCTCTCCATTTATTTAGGTCTTCTTTAATTTCT----CT 2368 chr3qtel1M 801871 TAGACAGTATATTGTAACTGAATCTAG---ACAAGTTTTTGGTGCACTTT 801917 i - i i v ii --- ii --- ? i i vviiii?i C L1M5_orf2#LIN 2367 CAG-CAATGTTTTGTAGTT---TTCAGTGTANAGGTCTTGCACATNTTTT 2322 chr3qtel1M 801918 AGGAGGCTGATCGCTATATATTTCATGTATTTTGTCACTTATTTGGAGTA 801967 ivv ii v iv vi ? v vii - vvi i i C L1M5_orf2#LIN 2321 GTTAGATTTATTCCTAAGTATTTNATGTTTTTTGATGC-TATTGTAAATG 2273 chr3qtel1M 801968 GGATTCCTTCCA-----TTATTGTTCC--TTGTGTTGGGTTATTTTCTAG 802010 v vi ii?----- i - -- v vvv i v v v C L1M5_orf2#LIN 2272 GTATTGTTTTTNAAATTTCATT-TTCCAATTGTTTGTTGCTAGTATATAG 2224 chr3qtel1M 802011 AAATGCTATTTATTGATTTTGAGGGGTATT--TTTGGTAGCTTCTAATTT 802058 i ----v --v vi --ii v v i?vii ii C L1M5_orf2#LIN 2223 AAATAC----AATTGATTTT--TGTATATTGACCTTGTATCCNGCGACCT 2180 chr3qtel1M 802059 TAGGAAAGCTTTTAAATTTTTTTAATTGTTGCCTTTGCTGATTCCTTAGG 802108 ivv viivi v v vv i i v -i? iv i ? C L1M5_orf2#LIN 2179 TGCTAAATTCACTTATTAGTTCTAGTAGTT-TNTTTGTAGATTCTTTNGG 2131 chr3qtel1M 802109 GTTTTCAAAGTAAACCATCCCATGATCAACATGTAGGAATAGGCTTATTT 802158 i v v ? v vii v vi ivi i?i i vi C L1M5_orf2#LIN 2130 ATTTTCTACGTANACAATCATGTCATCTGCGAATAANGACAGTTTTATTT 2081 chr3qtel1M 802159 -----ATTCCAGTCGTT-----CTTTA----TTATTGTTGTGTTATTGGT 802194 -----v i v -----i ---- v v iv - i C L1M5_orf2#LIN 2080 CTTCCTTTCCAATCTTTATGCCTTTTATTTCTTTTTCTTGCCTTATT-GC 2032 chr3qtel1M 802195 GCT-GCTAGCATTTCCAAAATCTTATCAAATGATAATGGGGAGACTGGG- 802242 i - v ii iv ivv i ii iiv i v ? vi i- C L1M5_orf2#LIN 2031 ACTGGCTAGGACCTCCAGTACAATGTTGAATAGAAGTGGTGANAGCGGAC 1982 chr3qtel1M 802243 ATCCTTGCTTCATTCCTGCATTTATTTGAAAAGGTTCCCAAGTATCTTCA 802292 ii ii i vvi vvv i v? i viv? v vi C L1M5_orf2#LIN 1981 ATCCTTGTCTTGTTCCCGATCTTAGGGGGAAAGCNTTCAGTNTTTCACCA 1932 chr3qtel1M 802293 TTGTATATGAGACTTGCTTTTGGTTTTAGATAGATGCTTTTTATGATATA 802342 ivi vii ? v v vvi ii v vi v C L1M5_orf2#LIN 1931 TTAAGTATGATGTTNGCTGTAGGTTTTTCGTAGATGCCCTTTATCAGGTT 1882 chr3qtel1M 802343 ATAGAAGGTCCTTTTGTATCCATACATTA--GAGGATTTTTGTTGTTGTC 802390 ivi v i i- i v vv i-- ii --- i ii v C L1M5_orf2#LIN 1881 GAGGAAGTTCCCTTC-TATTCCTAGTTTGCTGAGAGTTT---TTATCATG 1836 chr3qtel1M 802391 AACAAGACTGTTGAACAACATCAAAGGTTTTTTTTTTTACTTCTATTGAG 802440 iii -- ivvii v ---i i i v C L1M5_orf2#LIN 1835 AATGGG--TGTTGAATTTTGTCAAATG---CTTTTTCTGCATCTATTGAG 1791 chr3qtel1M 802441 GCATTCATGTGGTTTGGAATATTGATTGTTATTAACATGA-AAATAATGT 802489 iiiv i i vvvviv v -i i i i-i v ii C L1M5_orf2#LIN 1790 ATGATCATATGATTTTTCTCCTTTATT-CTGTTAATATGGTGAATTACAT 1742 chr3qtel1M 802490 TGATTGTTTTTCAAATTTTGAACCATTCCTGTATCCTTGGTATAAAACCT 802539 v i v i vi i i i i v v i C L1M5_orf2#LIN 1741 TGATTGATTTTCGAATGTTAAACCAACCTTGCATTCCTGGGATAAACCCC 1692 chr3qtel1M 802540 CTTTGTTCAGAGTGAATAATTTCTTTTGTAAATTGTTGTA----GTGTGT 802585 vi v vii v v iii i v i v ----i v i C L1M5_orf2#LIN 1691 ACTTGGTCATGATGTATTATCCTTTTTATATATTGCTGGATTCGATTTGC 1642 chr3qtel1M 802586 TAGAATTTTGTTTAGAACTTTTTAGCCAGTATTCATGAATGATTCCGGCC 802635 iv ? i i vvii vi i iv vii i C L1M5_orf2#LIN 1641 TAATATTTTGTTNAGGATTTTTGCATCTATGTTCATGAGGGATATTGGTC 1592 chr3qtel1M 802636 TATAGTTTTCCTTCTATGTTTTATCCTTCCCCAGTTTAAGCATGAAGACT 802685 i i i iiv vv i i vi ?i vi i v i ii? C L1M5_orf2#LIN 1591 TGTAATTTTCTTTTCTTGTAATGTCTTTGTCNGGTTTTGGTATCAGGGTN 1542 chr3qtel1M 802686 ATATTTGTCACATAAAG-GATTCTAGTAGGGTGCTTTCTTTTTCAATGTT 802734 ii v i v i- v ivi v v v ii v v C L1M5_orf2#LIN 1541 ATGCTGGCCTCATAAAATGAGTTGGGAAGTGTTCCCTCTTTTTCTATTTT 1492 chr3qtel1M 802735 -TG--AGAATTTGCTTAAG-------------------TAAATGTTTGAT 802762 - -- i iv ------------------- i C L1M5_orf2#LIN 1491 CTGGAAGAGTTTGTGTAAGATTGGTATTATTTCTTCCTTAAATGTTTGGT 1442 chr3qtel1M 802763 AAAATCTTCTCTGCTCATCAGGATGAGGAGCCCCTCCCCCCTCCCACTTT 802812 i --------- i -- i ---------- v ivivii C L1M5_orf2#LIN 1441 AGAAT---------TCACCAG--TGAAG----------CCATCTGGGCCT 1413 chr3qtel1M 802813 GATATTTCTTTTATACCCAGATCT----------ATTTATTTTTTT---C 802849 ivi ii i ivvv i i ---------- i v i ---i C L1M5_orf2#LIN 1412 GGAGTTTTCTTTGTGGGAAGGTTTTTAATTACAAATTCAATTTCTTTAAT 1363 chr3qtel1M 802850 TGAAACTGAGTTATTTAGGATTTTTTTTTTTTTTTGA--CAGTTTGGGCA 802897 v v iv i i i iv i v i i ?-- v i C L1M5_orf2#LIN 1362 AGATATAGGGCTATTCAGATTTTCTATTTCTTCTTGNGTCAGTTTTGGTA 1313 chr3qtel1M 802898 TTTTATATTTTTGAAGTTATTTCCCTATTTCTTTTGTATTCTTAGTTTGG 802947 v? i i v vv vi i v i ivi ? i iv vi C L1M5_orf2#LIN 1312 ANTTGTGTTTTTCAAGGAATTTGTCCATTTCATCTAAGTTNTCAAATTTA 1263 chr3qtel1M 802948 TTAACATAGAACTATGAATAATGT--TCAGATTATTCTTTT-TTGTTCCT 802994 ii i ii i vv i -- vv i -v iiv C L1M5_orf2#LIN 1262 TTGGCATAAAGTTGTTCATAATATTCTCTTATTATCCTTTTAATGTCTGT 1213 chr3qtel1M 802995 CCAATTTTGCTGTGATTTTACCTTGGTTATTTGCTATTCTATTAATTTG- 803043 vvi - i iv v iv vv i iviv vi iv - C L1M5_orf2#LIN 1212 AGGA-TCTGTAGTGATGTCTCCTTTTTCATTCCTGATATTGGTAATTTGT 1164 chr3qtel1M 803044 ----ATTTTGTTTTCTTTTTAATAAGATGAGTTAAGGATTTTTCAATTTT 803089 ----vi i v i i i v viv? i ii i v C L1M5_orf2#LIN 1163 GTCTTCTCTCTTTTTTTCTTGATCAGTCTNGCTAGAGGTTTATCAATTTT 1114 chr3qtel1M 803090 A-TGAGGTTCCCCTTCCCAGACACAGCTTTTAGTTTTATTGATCATTTCT 803138 - vv ---- vv vv i i ii iv i C L1M5_orf2#LIN 1113 ATTGATCTT----TTCAAAGAACCAGCTTTTGGCTTCGTTGATTTTCTCT 1068 chr3qtel1M 803139 GT----TTTTTGTTTCCACTTTT----ATTTCCCCTCTAATTTTTAATAT 803180 i ---- ? i vv i---- iv v i v C L1M5_orf2#LIN 1067 ATTGTNTNTTTGTTTTCTATTTCATTGATTTCTGCTCTTATCTTTATTAT 1018 chr3qtel1M 803181 CTTC-TCCT--TGATTATTTTACACTAGATTATTTCTTGGTATTTTGA-- 803225 i i - -- iv ?i ivii vi vvi vv v i ii-- C L1M5_orf2#LIN 1017 TTCCTTCCTTCTACTTNCTTTGGGTTTAATTTGCTCTTCTTTTTCTAGCT 968 chr3qtel1M 803226 TTTTAAAATAATACACATTCAGTTCATTTATCTT---TTTTTTTTCTTAT 803272 i ii ii--- vii i v v i ---ii i v C L1M5_orf2#LIN 967 TCTTAAGGTGG---AAGCTTAGATCATTGATTTTAAGCCTTTCTTCTTTT 921 chr3qtel1M 803273 CTGGCAGTATATGTTTGAAAGATTATGATTTTTCCTGTAAAGACTACTTT 803322 --- i ? iv vv ?ii i v i v iv i C L1M5_orf2#LIN 920 CT---AATATANGCATTTAANGCTATAAATTTCCCTCTAAGCACTGCTTT 874 chr3qtel1M 803323 AACAGCATTCTAGAAATTTTGGCATGCTGTTTCATGATTATAATTTTTTT 803372 i v i i v ii i v iv v ? v ivv C L1M5_orf2#LIN 873 AGCTGCATCCCACAAATTTTGATATGTTGTATTTTCATTNTCATTCAGTT 824 chr3qtel1M 803373 TAACATGCTTA-TCATTTC---TATGCTTTGTTTATCGACCCCCTAATTA 803418 i v ii v- v --- i v v iv i vivii C L1M5_orf2#LIN 823 CAAAATATTTTCTAATTTCCNTTGTGATTTCTTCTTTGACCCATGGGTTA 774 chr3qtel1M 803419 TTTAACATTCCCTTGTTAAGTCTCC----ATTTGG---TTGTCTATCTTG 803461 iv v viv v i i ---- --- v v? vv C L1M5_orf2#LIN 773 TTTAGAAGTGTGTTGTTTAATTTCCAAATATTTGGGGATTTTCTAGNTAT 724 chr3qtel1M 803462 TTTGTAGTCCTTGAACCAATTACTATTTTTATTGCCTTGTAGTCA 803506 i v v iv ----- v v v v v i C L1M5_orf2#LIN 723 CTTTTTGTTATTG-----ATTTCTAATTTAATTCCATTGTGGTCA 684 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 49.00 CpG sites = 356, Kimura (unadjusted) = 49.81 Transitions / transversions = 1.29 (356/276) Gap_init rate = 0.06 (107 / 1871), avg. gap size = 1.76 (188 / 107) 485 35.59 4.73 2.67 chr3qtel1M 801641 802740 (197260) C L1MD_orf2#LINE/L1 (687) 2607 1486 m_b157s551i2 5907 chr3qtel1M 801641 TCCACCC-CTTCATCCTT-TTTGCCATCACTTTCCTTGATGTTCTGTATC 801688 v - i i - vi vv i v ii v v i ivv C L1MD_orf2#LIN 2607 TCCTCCCACTTTATTCTTCTTTTTCAAAATTGTTTTAGCTATTCTAGTTC 2558 chr3qtel1M 801689 TTTTGTTTTTC-ATTTAAAATTTG--CTGAGC------AAATTTATAAAG 801729 i ii - v v i--v i ? ------ v i i i C L1MD_orf2#LIN 2557 CTTTGCCTTTCCATATAAATTTTAGAATAANCTTGTCTATATCTACAAAA 2508 chr3qtel1M 801730 CATCCCTTTGCTACTTTGGTTAGTATTGCATTAAAAGTGTAAATTAATTT 801779 v iivi vv i i vi v i vv ? i C L1MD_orf2#LIN 2507 AATCTTGCTGGGATTTTGATAGGAATTGCGTTAAACCTGTANATCAATTT 2458 chr3qtel1M 801780 AAGTGGTATTATTGTTTTCATTATGTTGACATGACCTAGCC-TGAGCACA 801828 ii vi v ivii i i i vvivv v v - i i C L1MD_orf2#LIN 2457 GGGGAGAATTGACATCTTTACTATGTTGAGTCTTCCAATCCATGAACACG 2408 chr3qtel1M 801829 GAAT-TTTCTCCAGTT-CTCAGGTGATTTCTTGTTTCTTTACCTTAGACA 801876 v - i v -i i i vv i i vi - v ---- C L1MD_orf2#LIN 2407 GTATGTCTCTCCATTTATTTAGATCTTCTTTGATTTCTTT-CAT----CA 2363 chr3qtel1M 801877 GTATATTGTAACTGAATCTAG---ACAAGTTTTTGGTGCAC--TTTAGGA 801921 ii v ii --- ii --- ii -- i i-- ivv C L1MD_orf2#LIN 2362 GCGTTTTGTAGTT---TTCAGCATACAAGTCCT--GTACATGTTTTGTTA 2318 chr3qtel1M 801922 GGCTGATCGCTATATATTTCATGTATTTTGTCACTTATTTGGAGTAGGAT 801971 ii v vv vi v - v v viv vvi i i v C L1MD_orf2#LIN 2317 GATTTATACCTAAGTATTTCATTT-TTTTTTGAGCGATTGTAAATGGTAT 2269 chr3qtel1M 801972 T--CCTTCCATTATTG--TTCCTTGTGTTGG--GTTATTTTCTAGAAATG 802015 --vi ii v v i -- vi vi-- i v v v i C L1MD_orf2#LIN 2268 TGTATTTTTAATTTCGGTTTCCACGTGTTCATTGCTAGTATATAGAAATA 2219 chr3qtel1M 802016 CTATTTATTGATTTTGAGGGGTATTTTTGGTAGCTTCTAATTTTAGGAAA 802065 v v --- viv v ?v i - v i vii ii ivvi C L1MD_orf2#LIN 2218 CAATTGATT---TTTGTATGTTNATCTTG-TATCCTGCGACCTTGCTGAA 2173 chr3qtel1M 802066 ---GCTTTTAAATTTTTTTAATTGTTGCCTTTGCTGATTCCTTAGGGTTT 802112 ---i v v i i vvv i v ---- iv i i C L1MD_orf2#LIN 2172 CTCACTTATTAGTTCTAGGAGTTTTT----TTGTAGATTCCTTGGGATTT 2127 chr3qtel1M 802113 TCAAAGTAAACCATCCCATGATCAACATGTAGGAATAGGCTTATTT---- 802158 v v i v vii v vi vi i i vi ---- C L1MD_orf2#LIN 2126 TCTACGTAGACAATCATGTCATCTGCAAATAGGGACAGTTTTATTTCTTC 2077 chr3qtel1M 802159 -ATTCCAGTC-----GTTCTTTATTA----TTGTTGTGTTATTGGTGCTG 802198 -v i ----- iii v---- v iv -ii C L1MD_orf2#LIN 2076 CTTTCCAATCTGTATGCCTTTTATTTCCTTTTCTTGCCTTATTG-CACTG 2028 chr3qtel1M 802199 -CTAGCATTTCCAAAATCTTATCAAATGATAATGGGGAGACTGGG-ATCC 802246 - v i iv iiv i ii i v i v vi i- C L1MD_orf2#LIN 2027 GCTAGAACTTCCAGTACTATGTTGAATAAGAGTGGTGAGAGCGGACATCC 1978 chr3qtel1M 802247 TTGCTTCATTCCTGCATTTATTTGAAAAGGTTCCCAAGTATCTTCATTGT 802296 i ii i vvi vvv i vv i vivv v vi iv C L1MD_orf2#LIN 1977 TTGCCTTGTTCCCGATCTTAGGGGGAAAGCATTCAGTCTTTCACCATTAA 1928 chr3qtel1M 802297 ATATGAGACTTGCTTTTGGTTTTAGATAGATGCTTTTTATGATATAATAG 802346 i vii v v v vvi i v vi vivi C L1MD_orf2#LIN 1927 GTATGATGTTAGCTGTAGGTTTTTTGTAGATGCTCTTTATCAAGTTGAGG 1878 chr3qtel1M 802347 AAGGTCCTTTTGTATCCATACATTA--GAGGATTTTTGTTGTTGTCAACA 802394 v ii i- i v vv ?-- ii i ii v--- ii C L1MD_orf2#LIN 1877 AAGTTCCCCTC-TATTCCTAGTTTNCTGAGAGTTTTTATCATG---AATG 1832 chr3qtel1M 802395 AGACTGTTGAACAACATCAAAGGTTTTTTTTTTTACTTCTATTGAGGCAT 802444 i -- ivvii v i i ---i v v viiiv C L1MD_orf2#LIN 1831 GG--TGTTGAATTTTGTCAAATGCTTTTTCT---GCATCAATTGATATGA 1787 chr3qtel1M 802445 TCATGTGGTTTGGAATATTGATTGTTATTAACATGA-AAATAATGTTGAT 802493 i vvvv v v vi-i i i i-ii v ii C L1MD_orf2#LIN 1786 TCATGTGATTTTTCTTCTTTAGC-CTGTTAATATGGTGGATTACATTGAT 1738 chr3qtel1M 802494 TGTTTTTCAAATTTTGAACCATTCCTGTATCCTTGGTATAAAACCTCTTT 802543 v i v vi i i ? i v v ivi C L1MD_orf2#LIN 1737 TGATTTTCGAATATTGAACCAGCCTTGCATNCCTGGAATAAACCCCACTT 1688 chr3qtel1M 802544 GTTCAGAGTGAATAATTTCTTTTGTAAATTGTTG----TAGTGTGTTAGA 802589 v vi v ii i v i ----i?i v i iv C L1MD_orf2#LIN 1687 GGTCATGGTGTATAATTCTTTTTATATATTGCTGAATTCNATTTGCTAAT 1638 chr3qtel1M 802590 ATTTTGTTTAGAACTTTTTAGCCAGTATTCATGAATGATTCCGGCCTATA 802639 v i i vv i vi i iv vii i i C L1MD_orf2#LIN 1637 ATTTTGTTGAGGATTTTTGCGTCTATGTTCATGAGGGATATTGGTCTGTA 1588 chr3qtel1M 802640 GTTTTCCTTCTATGTTTTATCCTTCCCCAGTTTAAGCATGAAGACTATAT 802689 i i v vi i i vi ii vi i v i iiv i C L1MD_orf2#LIN 1587 GTTTTCTTTTTTTGTACTGTCTTTGTCTGGTTTTGGTATCAGGGTAATAC 1538 chr3qtel1M 802690 TTGTCACATAAAG-GATTCTAGTAGGGTGCTTTCTTTTTCAATGTTTGAG 802738 v i v i- v ivi v v v ii i i v v ivi C L1MD_orf2#LIN 1537 TGGCCTCATAAAATGAGTTGGGAAGTGTTCCCTCCTCTTCTATTTTCTGG 1488 chr3qtel1M 802739 AA 802740 C L1MD_orf2#LIN 1487 AA 1486 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 48.32 CpG sites = 210, Kimura (unadjusted) = 50.23 Transitions / transversions = 1.23 (210/171) Gap_init rate = 0.05 (54 / 1099), avg. gap size = 1.52 (82 / 54) 12 22.36 7.69 0.00 chr3qtel1M 803507 803558 (196442) (TTGCTG)n#Simple_repeat 1 56 (0) m_b157s252i21 5908 chr3qtel1M 803507 TTTCTGCTG-TGTCTCTGTTGCTGTTACTG-TCCT-TGGCTACTGC-GTT 803552 v i - iv i - v - v ii - (TTGCTG)n#Sim 1 TTGCTGTTGCTGTTGCTGTTGCTGTTGCTGTTGCTGTTGCTGTTGCTGTT 50 chr3qtel1M 803553 TCTGTT 803558 v (TTGCTG)n#Sim 51 GCTGTT 56 Matrix = Unknown Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.08 (4 / 51), avg. gap size = 1.00 (4 / 4) 15 13.32 0.00 5.71 chr3qtel1M 803869 803905 (196095) (TTTG)n#Simple_repeat 1 35 (0) m_b157s252i22 5909 chr3qtel1M 803869 TTGGTTTGGGTTTTTAGATTTGTTTGTTTGTTTGTTT 803905 v - v v v - (TTTG)n#Simpl 1 TTTGTTT-GTTTGTTTG-TTTGTTTGTTTGTTTGTTT 35 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 14 16.38 2.94 0.00 chr3qtel1M 806744 806777 (193223) (TTTAAA)n#Simple_repeat 1 35 (0) m_b157s252i23 5910 chr3qtel1M 806744 TTGAAATTTAAATTT-AGTTTAAATTTTGTTTTAA 806777 v - i viv (TTTAAA)n#Sim 1 TTTAAATTTAAATTTAAATTTAAATTTAAATTTAA 35 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 17 28.07 1.92 1.92 chr3qtel1M 807677 807728 (192272) (TA)n#Simple_repeat 1 52 (0) m_b157s252i24 5911 chr3qtel1M 807677 TATA-ATATATATATATAAGTGTGTGTGTGTGTGTATGTGTATAGTATAT 807725 - vi i i i i i i i i i - (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATA-TATAT 49 chr3qtel1M 807726 ATA 807728 (TA)n#Simple_ 50 ATA 52 Matrix = Unknown Transitions / transversions = 10.00 (10/1) Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.00 (2 / 2) 16 18.35 0.00 2.56 chr3qtel1M 807686 807725 (192275) (TATGTG)n#Simple_repeat 1 39 (0) m_b157s252i25 5912 chr3qtel1M 807686 TATATATAAGTGTGTGTGTGTGTGTATGTGTATAGTATAT 807725 i i v i i - i (TATGTG)n#Sim 1 TATGTGTATGTGTATGTGTATGTGTATGTGTAT-GTGTAT 39 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1) 18 18.50 4.08 0.00 chr3qtel1M 807727 807775 (192225) (TAACCC)n#Simple_repeat 1 51 (0) m_b157s252i26 5913 chr3qtel1M 807727 TAACCCTAACGCTGACCCT--CCCGACTCCGGACTCTAACCCTAACCCTA 807774 v i -- v vi vi i (TAACCC)n#Sim 1 TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA 50 chr3qtel1M 807775 A 807775 (TAACCC)n#Sim 51 A 51 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.02 (1 / 48), avg. gap size = 2.00 (2 / 1) 182 20.44 4.62 9.68 chr3qtel1M 809281 809345 (190655) OldhAT1#DNA/hAT-Ac 2332 2393 (449) m_b157s601i14 5914 chr3qtel1M 809281 CTGATGGCATCCGAGTGATACAGACACAGGAACCACTGCCTG--GCTGCC 809328 i ----- v v i i - i i-- v OldhAT1#DNA/h 2332 CTGGTGGCAT-----TGTTACAGACAGAAGGACC-CTGCTTAGTGCAGCC 2375 chr3qtel1M 809329 AA-GCTAAGAGCCTCACT 809345 i- i i v OldhAT1#DNA/h 2376 AGTGTTGAGCGCCTCACT 2393 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 24.34 CpG sites = 8, Kimura (unadjusted) = 24.34 Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.12 (8 / 64), avg. gap size = 1.12 (9 / 8) 20 0.00 0.00 0.00 chr3qtel1M 810329 810350 (189650) (T)n#Simple_repeat 1 22 (0) m_b157s252i27 5915 chr3qtel1M 810329 TTTTTTTTTTTTTTTTTTTTTT 810350 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTT 22 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 262 26.37 4.40 0.00 chr3qtel1M 810918 811008 (188992) MamGyp-int#LTR/Gypsy 2416 2510 (2592) m_b157s551i3 5916 chr3qtel1M 810918 GATGCCCAGG-CTTCTCG---GGCAGCCCCTGGTTTTCAGTCCTGGATTG 810963 v - v i --- v i vv vi v MamGyp-int#LT 2416 GATGCCCTGGACTGCTTGCTAGGGAGTCAGTGGTTTTCAGTGTTGGATTT 2465 chr3qtel1M 810964 GCAGAGTGGATACTACCAGGGTTCTAGGTTTGAGGAAGACCAAGA 811008 vi i i i ivvi v vi ? i v MamGyp-int#LT 2466 GAGGAGTGGGTATTATCAGATACCTATGGCTGANGAGGACAAAGA 2510 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 33.15 CpG sites = 11, Kimura (unadjusted) = 33.15 Transitions / transversions = 0.85 (11/13) Gap_init rate = 0.02 (2 / 90), avg. gap size = 2.00 (4 / 2) 323 31.68 6.40 1.53 chr3qtel1M 811131 811255 (188745) MIR#SINE/MIR 124 254 (8) m_b157s601i15 5917 chr3qtel1M 811131 TTTTCTCATTTACCAAAATGGGGGGTAACAATAGCTCTTTCCTGCCAGGA 811180 i i ii- i- i iv i v vvi i MIR#SINE/MIR 124 TTTCCTCATCTGT-AAAATGGGGA-TAATAATAGTACCTACCTCATAGGG 171 chr3qtel1M 811181 CTGTTGTGAGGCTCAGATGAGCCGGTGATTGCTGAATGGTTAGCCCGG-G 811229 i v i i iiii ivv ivi ii v vv i - MIR#SINE/MIR 172 TTGTTGTGAGGATTAAATGAGTTAATACATGTAAAGCGCTTAGAACAGTG 221 chr3qtel1M 811230 TTTGGCACATATTA-------TATAAATGTCAG 811255 ii v -------v i MIR#SINE/MIR 222 CCTGGCACATAGTAAGCGCTCAATAAATGTTAG 254 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.00 CpG sites = 26, Kimura (unadjusted) = 43.52 Transitions / transversions = 2.00 (26/13) Gap_init rate = 0.03 (4 / 124), avg. gap size = 2.50 (10 / 4) 183 23.92 0.00 2.17 chr3qtel1M 812121 812167 (187833) MIRc#SINE/MIR 121 166 (102) m_b157s601i16 5918 chr3qtel1M 812121 GCCTCAGTTTCCCCATCTGTATAAATCATGGCACCCATATCTGTCCT 812167 i - viv ii viv i i MIRc#SINE/MIR 121 GCCTCAGTTTCCTCATCTGTA-AAATGGGGATAATAATACCTGCCCT 166 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.60 CpG sites = 7, Kimura (unadjusted) = 29.60 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.02 (1 / 46), avg. gap size = 1.00 (1 / 1) 390 28.92 7.28 3.85 chr3qtel1M 812557 812707 (187293) C MIRc#SINE/MIR (110) 158 3 m_b157s601i17 5919 chr3qtel1M 812557 TATGATGATCCTAGTTTTTACAGATGGGGAAACTGAGAC----GGAGCCC 812602 v v ivi - i i ----i vii C MIRc#SINE/MIR 158 TATTATTATCCCCATTTT-ACAGATGAGGAAACTGAGGCTCAGAGAGGTT 110 chr3qtel1M 812603 AAATA----GTCCAGGAT--CATAGTTCATAATTGTTTTAGGCTGGA-TT 812645 i i---- i i i -- i i vi v vivv v v - i C MIRc#SINE/MIR 109 AAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTC 60 chr3qtel1M 812646 GCATTCGGGTCCTCCTGACTCCAGACCCAATGTGCTCTACCCACTATGCC 812695 v ii i i iii -- vi iii C MIRc#SINE/MIR 59 GAACCCAGGTCTTCCTGACTCCAAGTCCA--GTGCTCTTTCCACTGCACC 12 chr3qtel1M 812696 ACTCAGCTGCCT 812707 ---i C MIRc#SINE/MIR 11 AC---ACTGCCT 3 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.37 CpG sites = 29, Kimura (unadjusted) = 38.57 Transitions / transversions = 2.23 (29/13) Gap_init rate = 0.07 (10 / 150), avg. gap size = 1.70 (17 / 10) 205 20.00 2.22 0.00 chr3qtel1M 812966 813010 (186990) MIR#SINE/MIR 97 142 (120) m_b157s601i18 5920 chr3qtel1M 812966 AGGCTACTTCACC-CTGTGTGCCTCAGTTTCCTTCTATAGAAAATG 813010 i i v - v iv v iv MIR#SINE/MIR 97 AAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATG 142 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 23.33 CpG sites = 4, Kimura (unadjusted) = 23.33 Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 19 0.00 0.00 0.00 chr3qtel1M 813228 813248 (186752) (GT)n#Simple_repeat 1 21 (0) m_b157s252i28 5921 chr3qtel1M 813228 GTGTGTGTGTGTGTGTGTGTG 813248 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTG 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 15 20.38 3.64 3.64 chr3qtel1M 813435 813489 (186511) (TCCCTT)n#Simple_repeat 1 55 (0) m_b157s252i29 5922 chr3qtel1M 813435 TCCCTCCCCCATTCCC-TTATCTTT-CTTTTCTCTTTGCCCTTTCCCATT 813482 ii v - vi - i i - - (TCCCTT)n#Sim 1 TCCCTTTCCCTTTCCCTTTCCCTTTCCCTTTCCCTTT-CCCTTTCCC-TT 48 chr3qtel1M 813483 TATCTTT 813489 vi (TCCCTT)n#Sim 49 TCCCTTT 55 Matrix = Unknown Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.07 (4 / 54), avg. gap size = 1.00 (4 / 4) 14 11.25 3.45 0.00 chr3qtel1M 813798 813826 (186174) (TTTA)n#Simple_repeat 1 30 (0) m_b157s252i30 5923 chr3qtel1M 813798 TTTACTTATTTATTT-TTTACTAATTTATT 813826 i - i v (TTTA)n#Simpl 1 TTTATTTATTTATTTATTTATTTATTTATT 30 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1) 200 36.64 5.19 2.53 chr3qtel1M 814345 814498 (185502) L2#LINE/L2 2358 2515 (567) m_b158s601i0 5924 chr3qtel1M 814345 CCAAACTTTCTGCCTCAAATTCTGACT------TCCAATTCTCGTCTCCA 814388 ii i iiiv v v i v ------ i --- i v - L2#LINE/L2 2358 CCGGACCTCTCCCCTGAACTCCAGACTCGTATATCCAACT---GCCTAC- 2403 chr3qtel1M 814389 TTGGCCTTTCCAACTGGATGTGCAGTTGACACCTTAAACTCGGCGCATGC 814438 i i v i vi vi i v i i i iii iii v L2#LINE/L2 2404 TCGACATCTCCACTTGGATGTCTAATAGGCATCTCAAACTTAACATGTCC 2453 chr3qtel1M 814439 AACACCGAGCTCACGATGTTTGCCCGTAGACCTCCCCCCCCCCC--CCCC 814486 v i i vi v iv vi i v i i v --i ii L2#LINE/L2 2454 AAAACTGAACTCCTGATCTTCCCCCTCAAACCTGCTCCTCCCGCAGTCTT 2503 chr3qtel1M 814487 CCCCGCCTCCGT 814498 ii v L2#LINE/L2 2504 CCCCATCTCAGT 2515 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 51.36 CpG sites = 37, Kimura (unadjusted) = 54.37 Transitions / transversions = 2.06 (37/18) Gap_init rate = 0.04 (6 / 153), avg. gap size = 2.00 (12 / 6) 19 22.11 0.00 0.00 chr3qtel1M 816641 816687 (183313) (CGGCCA)n#Simple_repeat 1 47 (0) m_b158s252i3 5925 chr3qtel1M 816641 CGACCTCGGCGGCGGCCACGGCCTCGGCCTCGGCCTCGGCGGCGGCC 816687 i v vi v v v vi (CGGCCA)n#Sim 1 CGGCCACGGCCACGGCCACGGCCACGGCCACGGCCACGGCCACGGCC 47 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 23 27.27 1.43 0.00 chr3qtel1M 817414 817483 (182517) (GGA)n#Simple_repeat 1 71 (0) m_b158s252i4 5926 chr3qtel1M 817414 GGA-GATGGGGCGGAGGAGGAAGAGGATGACGACGAGGACGACGACGAGG 817462 - v i v i v v v v v v (GGA)n#Simple 1 GGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGG 50 chr3qtel1M 817463 ATGGGGCTGAGGAAGAAGAGG 817483 v i vv i i (GGA)n#Simple 51 AGGAGGAGGAGGAGGAGGAGG 71 Matrix = Unknown Transitions / transversions = 0.45 (5/11) Gap_init rate = 0.01 (1 / 69), avg. gap size = 1.00 (1 / 1) 17 5.00 0.00 0.00 chr3qtel1M 819493 819513 (180487) (T)n#Simple_repeat 1 21 (0) m_b158s252i5 5927 chr3qtel1M 819493 TTTTTTTTTTTTTTTTCTTTT 819513 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTT 21 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 19 8.18 0.00 0.00 chr3qtel1M 819545 819570 (180430) (T)n#Simple_repeat 1 26 (0) m_b158s252i6 5927 chr3qtel1M 819545 TTTTTATTTTTATTTTTTTTTTTTTT 819570 v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 481 22.75 7.26 0.76 chr3qtel1M 820151 820274 (179726) L2a_3end#LINE/L2 384 515 (2) m_b158s601i1 5928 chr3qtel1M 820151 TCTCCTTCTGCTAGAATGTGAGCTC---GAGGGCAGACA---TTGTCT-T 820193 ii ii i --- iv --- - L2a_3end#LINE 384 TCTCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTCTGT 433 chr3qtel1M 820194 TTTGCTTGTATCTGTAAACCCAGTGCGTAG--TAGTGCCTGGAACGTAGG 820241 i iiivv vv i v --i v i v L2a_3end#LINE 434 TTTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACATAGT 483 chr3qtel1M 820242 AGGCAATTTAATAAATGCTTGTTGACTGACTGA 820274 -ii i ii v v L2a_3end#LINE 484 AGGC-GCTCAATAAATATTTGTTGAATGAATGA 515 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 25.57 CpG sites = 18, Kimura (unadjusted) = 27.86 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.04 (5 / 123), avg. gap size = 2.00 (10 / 5) 253 25.00 0.00 0.00 chr3qtel1M 820283 820338 (179662) C L3#LINE/CR1 (92) 4007 3952 m_b158s601i2 5929 chr3qtel1M 820283 CCGACAAATGGTGGAACGGCCTCTGCTTGAAGACTTCCAAGAAAGGGGAG 820332 i i vivv i v i ivi v C L3#LINE/CR1 4007 CTGACAAGTGGTCATCCAGCCTCTGCTTGAACACCTCCAGTGACGGGGAG 3958 chr3qtel1M 820333 CTCTCT 820338 v C L3#LINE/CR1 3957 CTCACT 3952 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 30.69 CpG sites = 7, Kimura (unadjusted) = 30.69 Transitions / transversions = 1.00 (7/7) Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0) 228 29.29 12.14 0.00 chr3qtel1M 820468 820607 (179393) L3#LINE/CR1 3600 3756 (343) m_b158s601i3 5930 chr3qtel1M 820468 TTCAGTTCAGGGCACCACA-TTCAGGACGGACACTGGGAAGCTAGGGAGC 820516 v i - i i v i iv i i i v L3#LINE/CR1 3600 TTCAGTTCTGGGCGCCACATTTTAAGAGGGACATTGACAAACTGGAGCGC 3649 chr3qtel1M 820517 --CCAG-GGAGGCCCATCGGGAT-GTGGAAGGT----ACACCAGGCCAT- 820557 -- - iv v i i - i i ---- v v i - L3#LINE/CR1 3650 GTCCAGAGGAGAGCGACCAGGATGGTGAAGGGTCTGGAAACCATGTCATA 3699 chr3qtel1M 820558 --AGCGAT-GCCCAAGGCACAG----TGCTAGAGCTGGAAGAGAGCAGAT 820600 -- vi i- iiv v v ---- i viiv ii v i L3#LINE/CR1 3700 TGAGGAACGGTTGAAGGAACTGGGGATGTTTAGCCTGGAGAAGAGAAGAC 3749 chr3qtel1M 820601 TTGGGGG 820607 i i L3#LINE/CR1 3750 TTAGAGG 3756 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 36.18 CpG sites = 26, Kimura (unadjusted) = 38.59 Transitions / transversions = 1.73 (26/15) Gap_init rate = 0.06 (8 / 139), avg. gap size = 2.12 (17 / 8) 186 22.22 2.22 0.00 chr3qtel1M 820796 820840 (179160) L3#LINE/CR1 3965 4010 (89) m_b158s601i4 5930 chr3qtel1M 820796 TCTCTGGAGGCTTTTAAGCTCAAGATGGA-GGCCCCTTGTCAGGGA 820840 v iv i vv i v - i v L3#LINE/CR1 3965 TCACTGGAGGTGTTCAAGCAGAGGCTGGATGACCACTTGTCAGGGA 4010 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 26.39 CpG sites = 4, Kimura (unadjusted) = 26.39 Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 13 11.53 3.23 3.23 chr3qtel1M 820942 820972 (179028) (GGGGA)n#Simple_repeat 1 31 (0) m_b158s252i7 5931 chr3qtel1M 820942 GGGGAGGGGA-GGGAGGGAAGGAAGAGAGGAG 820972 - i -i i (GGGGA)n#Simp 1 GGGGAGGGGAGGGGAGGGGAGG-GGAGGGGAG 31 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2) 406 21.60 6.14 2.54 chr3qtel1M 821225 821338 (178662) MIRb#SINE/MIR 137 254 (14) m_b158s601i5 5932 chr3qtel1M 821225 CATCTGAATAATGGGGATCAGAGCGTTACCTCCCGCCTAGGGTTGT---G 821271 v v v v i--- v v vi --- MIRb#SINE/MIR 137 CATCTGTAAAATGGGGATAATAA---TACCTACCTCGCAGGGTTGTTGTG 183 chr3qtel1M 821272 AAGTTCGAATTTGATGAT---TGTAAAGCCCTCAGCTC-GTGGCTGGCAC 821317 i v ii vv i --- v i v - v MIRb#SINE/MIR 184 AGGATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCAC 233 chr3qtel1M 821318 ACATTAGGCGCTTAATAAATG 821338 i v i i MIRb#SINE/MIR 234 ATAGTAAGCGCTCAATAAATG 254 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 25.55 CpG sites = 10, Kimura (unadjusted) = 25.55 Transitions / transversions = 0.71 (10/14) Gap_init rate = 0.05 (6 / 113), avg. gap size = 1.67 (10 / 6) 13 16.63 2.17 6.82 chr3qtel1M 821456 821501 (178499) (GGGCGG)n#Simple_repeat 1 44 (0) m_b158s252i8 5933 chr3qtel1M 821456 GGGC-GGAGCGAGAGCGAGGGGCGGGTTTGGGGGGGCGGGGGGGGGG 821501 - i i i - --v v v (GGGCGG)n#Sim 1 GGGCGGGGGCGGGGGCG-GGGGCGGG--GGCGGGGGCGGGGGCGGGG 44 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.09 (4 / 45), avg. gap size = 1.00 (4 / 4) 15 20.03 0.00 0.00 chr3qtel1M 821473 821501 (178499) (G)n#Simple_repeat 1 29 (0) m_b158s252i9 5933 chr3qtel1M 821473 GGGGCGGGTTTGGGGGGGCGGGGGGGGGG 821501 v vvv v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG 29 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 15 31.50 0.00 3.12 chr3qtel1M 821826 821891 (178109) (CCT)n#Simple_repeat 1 64 (0) m_b158s252i10 5934 chr3qtel1M 821826 CCTCTGCTTCTTCCACCTCCTTCCTTCTCCTCTCCCTGCCTCCTGCTGGA 821875 iv i i v - i ii - v vvv (CCT)n#Simple 1 CCTCCTCCTCCTCCTCCTCC-TCCTCCTCCTCCTCCT-CCTCCTCCTCCT 48 chr3qtel1M 821876 CCCCCTCCGCAACCTC 821891 i v vv (CCT)n#Simple 49 CCTCCTCCTCCTCCTC 64 Matrix = Unknown Transitions / transversions = 0.78 (7/9) Gap_init rate = 0.03 (2 / 65), avg. gap size = 1.00 (2 / 2) 294 29.29 8.09 2.08 chr3qtel1M 823185 823320 (176680) MIRc#SINE/MIR 108 251 (17) m_b158s601i6 5935 chr3qtel1M 823185 TTGATCTGTCTCATCTGTCTCAGTTCTCTGCCCTGTAAAATGGGCATCAG 823234 i i v v --- i ii vvi v v v MIRc#SINE/MIR 108 TTAACCTCTCTGA---GCCTCAGTTTCCTCATCTGTAAAATGGGGATAAT 154 chr3qtel1M 823235 AGCAGCT--TCTGCCT--CCCAGAGGG--GCTGTGAGGATCTGGAAAGAC 823278 ii v --i -- i v -- i viivi i MIRc#SINE/MIR 155 AATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGAT 204 chr3qtel1M 823279 -GTGTCTGTGGGA-CAC---GGACATTGCAAAGTGCATTATAGATGT 823320 -i v ii - i --- v v i i vv i i MIRc#SINE/MIR 205 AATGTATGTGAAAGCGCTTTGTAAACTGTAAAGTGCTATACAAATGT 251 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 37.01 CpG sites = 23, Kimura (unadjusted) = 38.26 Transitions / transversions = 1.44 (23/16) Gap_init rate = 0.07 (9 / 135), avg. gap size = 1.56 (14 / 9) 264 33.35 0.00 2.22 chr3qtel1M 823965 824056 (175944) MIR#SINE/MIR 119 208 (54) m_b158s601i7 5936 chr3qtel1M 823965 CTTAGTTTCCTTCCTTTTTAAACGGAGATAAATCATAGCATCTCCCTCTC 824014 i ivii v v i i - v i i v vi MIR#SINE/MIR 119 CTCAGTTTCCTCATCTGTAAAATGGGGAT-AATAATAGTACCTACCTCAT 167 chr3qtel1M 824015 GGGGTGATTGCAAGGGTCAAGCTGCATCAAGGCCTGTCAAGC 824056 i vi ii i i i- vi i vi v v MIR#SINE/MIR 168 AGGGTTGTTGTGAGGATTAAA-TGAGTTAATACATGTAAAGC 208 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 46.32 CpG sites = 19, Kimura (unadjusted) = 46.32 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.02 (2 / 91), avg. gap size = 1.00 (2 / 2) 430 25.00 0.00 0.00 chr3qtel1M 824467 824550 (175450) MIR#SINE/MIR 76 159 (103) m_b158s601i8 5937 chr3qtel1M 824467 ACCAATTATGTAAGCCTGGACAAGTCATTTAATCTCTGTGTGCCTAAGTT 824516 i ii i i v i i i i i v v MIR#SINE/MIR 76 ACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTT 125 chr3qtel1M 824517 TCTTCAATTGTGAAATGGGGATCATAAGGGCACC 824550 i vi i v vi i MIR#SINE/MIR 126 TCCTCATCTGTAAAATGGGGATAATAATAGTACC 159 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 31.83 CpG sites = 15, Kimura (unadjusted) = 31.83 Transitions / transversions = 2.50 (15/6) Gap_init rate = 0.00 (0 / 83), avg. gap size = 0.0 (0 / 0) 213 29.54 7.53 2.61 chr3qtel1M 825476 825621 (174379) L2b_3end#LINE/L2 270 422 (44) m_b158s601i9 5938 chr3qtel1M 825476 CCTTCTCTG--CCATTTC--CTCTATCCTGGCCCTTCCTTGGTCACTACT 825521 i -- viii --ii i v v -- v i i? i L2b_3end#LINE 270 CCTCCTCTGGGCCCCCCCAGTCCTACCCTGCCACT--CTGGGTTATNATT 317 chr3qtel1M 825522 GCCCATGTAGAT---TGTCTCCCCCTTTAAGAGTGGAAGCTTC-TGAGAG 825567 i ii?v v --- vi - v vi i - - L2b_3end#LINE 318 GTCTGNTTACATGTCTGTCTCCCCCACTA-GACTGTGAGCTCCGTGAG-G 365 chr3qtel1M 825568 GCAGGGGCTGC-TTGAGCTTTTGTAC--CTATAGCCACATCCATTAGCCC 825614 i i ?- iviv v vi -- i v v v vvi v L2b_3end#LINE 366 GCAGGGACCGNGTCTGTCTTGTTCACCGCTGTATCCCCAGCGCCTAGCAC 415 chr3qtel1M 825615 AGTGCCT 825621 ? L2b_3end#LINE 416 AGNGCCT 422 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 38.67 CpG sites = 23, Kimura (unadjusted) = 39.89 Transitions / transversions = 1.21 (23/19) Gap_init rate = 0.07 (10 / 145), avg. gap size = 1.50 (15 / 10) 184 36.36 4.35 4.35 chr3qtel1M 826529 826643 (173357) L2d_3end#LINE/L2 144 258 (258) m_b158s601i10 5939 chr3qtel1M 826529 CATTTCCCCCATGCTTAAAATGTATTTCCTTCTCGACTCT-GCTGCTTAA 826577 i i -- i ii ivi iii vv -v iiii L2d_3end#LINE 144 CGTTCCCCCC--GCCTGGAATGCCCTTCCCCTTCCTCTCTCTCTATCCAA 191 chr3qtel1M 826578 TTTTTTT---TCCTTCAGAATTTAGCTCAAGCACTATCTCCTCTTACACA 826624 v ii vi--- iiiiii iv i i --- i L2d_3end#LINE 192 ATCCTACCCATCCTTCAAGGCCCAGCTCAAGTCCCACCTCCTC---CACG 238 chr3qtel1M 826625 AAACA-TCCCTGATTGTTCC 826643 i v- iiii L2d_3end#LINE 239 AAGCCTTCCCTGACCACTCC 258 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 52.55 CpG sites = 32, Kimura (unadjusted) = 57.07 Transitions / transversions = 4.00 (32/8) Gap_init rate = 0.07 (8 / 114), avg. gap size = 1.25 (10 / 8) 493 29.84 11.63 5.49 chr3qtel1M 827278 827621 (172379) C L2c_3end#LINE/L2 (5) 473 110 m_b158s601i11 5940 chr3qtel1M 827278 TTAAGTCACCAAACTTTTATTAAGTACTTGCCATGTGTCAGACACCGTGT 827327 v v v v i ii i i i i --------- C L2c_3end#LINE 473 TTCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAG--------- 433 chr3qtel1M 827328 TAAGTGCTGGGGATTCAAAGCCAA--AAGACA--GTCCTTGCATTTAAGT 827373 --- i v vii -- -- i vi i v C L2c_3end#LINE 432 ---GCGCTGGGGATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGG 386 chr3qtel1M 827374 ATCTTGCAGCCTAATGAAGGAAACA-ACACG-A---AGATCGTTGGATGA 827418 v ii i i i i - ? - --- ivi -- ii C L2c_3end#LINE 385 AGCTCACAGTCTAGTGGAGGAGACAGACANGTAAACAGACAATT--ACAA 338 chr3qtel1M 827419 -ACAAACTATAGATAA-------AAT-------TAACCAGATTATCA--- 827450 - ii vv ------- ------- iv iv iii --- C L2c_3end#LINE 337 TACAAGTTAATGATAAGTGCTATAATGGGAGTATAGACAGGGTGCTATGG 288 chr3qtel1M 827451 ----ACAGAGGAAAGGAACTTAGAATTAA----GAAGGGTTGGGGAACAC 827492 ---- - i v i - i i---- ii ii vi C L2c_3end#LINE 287 GAGCACAGAGG-AGGGCACCTAG-ACTAGNCTTGGGGGGTCAGGGAAGGC 240 chr3qtel1M 827493 TTCCTGTA-GAAATGGAATTTTAGCAGGGACTTGCAGGA-AACCAGGGA- 827539 i v - ii iv i v v i ? v -i vi ii- C L2c_3end#LINE 239 TTCCCGGAGGAGGTGACATCTGAGCTGAGNCTTGAAGGATGAGTAGGAGT 190 chr3qtel1M 827540 -GGTCAATGTTCAAAGTGGAGGAGTGAA-AGCTTCCCAGGCATGGTGGCC 827587 -i i i- vv --- i v - v i vi v iv C L2c_3end#LINE 189 TAGCCAG-GTGGAA---GGAGGGGGGAAGAGCATTCCAGGCAGAGGGAAC 144 chr3qtel1M 827588 AGCCAGAGACAATGCCCAGAATCAGGAGAGGATT 827621 vv v vv v ? i iv i i i C L2c_3end#LINE 143 AGCATGTGCAAAGGCNCGGAGGCAGGAAAGAACT 110 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 38.01 CpG sites = 61, Kimura (unadjusted) = 40.23 Transitions / transversions = 1.69 (61/36) Gap_init rate = 0.10 (35 / 343), avg. gap size = 1.71 (60 / 35) 376 36.95 7.36 0.40 chr3qtel1M 827668 827898 (172102) C L2#LINE/L2 (367) 2715 2469 m_b158s601i12 5940 chr3qtel1M 827668 CCAGATATGAGGAGATGAAGGCTTGCATCGAAGTGACAGCAGTGCCAG-- 827715 iiiv iv iv v i iii iii vvi -- C L2#LINE/L2 2715 CCAGGCGAGAGATGATGGTGGCTTGGACCAGGGTGGTGGCAGTGGAGGTG 2666 chr3qtel1M 827716 ---AGAAGATGT-GAATT---GCTATC------AAGTAGAAACAATAGAA 827752 --- vv - i --- v v------ i iv i i i C L2#LINE/L2 2665 GTGAGAAGTGGTCGGATTCTGGATATATTTTGAAGGTAGAGCCGACAGGA 2616 chr3qtel1M 827753 TTTGTCAATTAATTGAATATGCAAGATGAGAGAAAGTGAGGAGTTGATGA 827802 iii vi i i viivi v ii v C L2#LINE/L2 2615 TTTGCTGATGGATTGGATGTGGGGTGTGAGAGAAAGAGAGGAGTCAAGGA 2566 chr3qtel1M 827803 TGACCCTACAA-TTAGAGCCTAGATAGCTGGGAAGTATGGGGGCATCCTC 827851 i i vii- vvi iiii i - v i viii v i C L2#LINE/L2 2565 TGACTCCAAGGTTTTTGGCCTGAGCAACT-GGAAGGATGGAGTTGCCATT 2517 chr3qtel1M 827852 TACAGTAAGAGGGAAGTTAGGAAGAAGGTTAGGTCTG-GGGAAAAGAT 827898 ? v vi vi viv vii i ivi i - ii C L2#LINE/L2 2516 NACTGAGATGGGGAAGACTGCGGGAGGAGCAGGTTTGAGGGGGAAGAT 2469 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 52.04 CpG sites = 56, Kimura (unadjusted) = 55.12 Transitions / transversions = 1.93 (56/29) Gap_init rate = 0.03 (8 / 230), avg. gap size = 2.25 (18 / 8) 295 25.26 3.09 2.04 chr3qtel1M 828714 828810 (171190) C L2#LINE/L2 (948) 2134 2037 m_b158s601i13 5940 chr3qtel1M 828714 GTGTCCCAACAACCTGGAGAGAAGAGAACATT--AAGGAGGAGAGGGTGA 828761 iiiv i --i v i iii -- i i i C L2#LINE/L2 2134 GTGTCCTGGAAGCC--AAGTGAAGAAAGTGTTTCAAGAAGGAGGGAGTGA 2087 chr3qtel1M 828762 TCA-CAGTGTCTGAGGCTGCAGAAAGGTCCAGAAGAATGAAGACTGAGAA 828810 - v vi v v ? v v ii i C L2#LINE/L2 2086 TCAACTGTGTCAAATGCTGCTGANAGGTCAAGTAAGATGAGGACTGAGAA 2037 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 32.38 CpG sites = 16, Kimura (unadjusted) = 32.38 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.04 (4 / 96), avg. gap size = 1.25 (5 / 4) 298 25.32 1.27 0.00 chr3qtel1M 828747 828825 (171175) C AmnL2-1#LINE/L2 (1197) 1416 1337 m_b158s601i14 5940 chr3qtel1M 828747 AGGAGGAGAGGGTGATC-ACAGTGTCTGAGGCTGCAGAAAGGTCCAGAAG 828795 vi ii i - vi vvi v i C AmnL2-1#LINE/ 1416 AGGAGGATGGAATGGTCCACAGTGTCGAAGGCTGCACTGAGGTCAAGGAG 1367 chr3qtel1M 828796 AATGAAGACTGAGAAAAAGTCATCAGTAAC 828825 i vv i i ? vi i C AmnL2-1#LINE/ 1366 AATGAGGAAGGAGAAAGAGCCNTCATCAGC 1337 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 32.14 CpG sites = 12, Kimura (unadjusted) = 32.14 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.01 (1 / 78), avg. gap size = 1.00 (1 / 1) 17 20.00 3.70 1.82 chr3qtel1M 829128 829181 (170819) (CTCTCC)n#Simple_repeat 1 55 (0) m_b158s252i11 5941 chr3qtel1M 829128 CTCGCTCCCTCCCTCTCCCTCTCGCTCACCCTCTTTCCT-TTCTTC-CCC 829175 v i i v v - i - i i - (CTCTCC)n#Sim 1 CTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTC-TCCCTCTCCCTCTCCC 49 chr3qtel1M 829176 TCCCCC 829181 i (CTCTCC)n#Sim 50 TCTCCC 55 Matrix = Unknown Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.06 (3 / 53), avg. gap size = 1.00 (3 / 3) 24 9.47 0.00 0.00 chr3qtel1M 829237 829270 (170730) (T)n#Simple_repeat 1 34 (0) m_b158s252i13 5942 chr3qtel1M 829237 TTTTTTTTTTTTTTTGTTTTGTTTTGTTTTTTTT 829270 v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 34 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 34 0.00 0.00 0.00 chr3qtel1M 830172 830200 (169800) (AG)n#Simple_repeat 1 29 (0) c_b158s251i0 5943 chr3qtel1M 830172 AGAGAGAGAGAGAGAGAGAGAGAGAGAGA 830200 (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGA 29 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 23 34.25 0.00 3.67 chr3qtel1M 831453 831565 (168435) (CCCT)n#Simple_repeat 1 109 (0) m_b158s252i14 5944 chr3qtel1M 831453 CCCTCCCTACTTCCTGCCGCTTTCTTCATTCTTTCCTCCCTCTCCTTCCT 831502 v i iv - ii i v i i i - i (CCCT)n#Simpl 1 CCCTCCCTCCCTCCCTCC-CTCCCTCCCTCCCTCCCTCCCTC-CCTCCCT 48 chr3qtel1M 831503 CCCTCTCTTCTTTCCTTCCTCCCATTCTTCCTCTCCTCTTTGCGCTCCAT 831552 i i i i i vii i - ii - v v (CCCT)n#Simpl 49 CCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTC-CCTCCCT-CCCTCCCT 96 chr3qtel1M 831553 CCATCCATTCCTC 831565 v v i (CCCT)n#Simpl 97 CCCTCCCTCCCTC 109 Matrix = Unknown Transitions / transversions = 2.50 (20/8) Gap_init rate = 0.04 (4 / 112), avg. gap size = 1.00 (4 / 4) 31 0.00 0.00 0.00 chr3qtel1M 831635 831663 (168337) (G)n#Simple_repeat 1 29 (0) c_b158s251i1 5945 chr3qtel1M 831635 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG 831663 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG 29 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 544 30.08 6.18 2.10 chr3qtel1M 832218 832492 (167508) C L2#LINE/L2 (893) 2189 1904 m_b158s601i15 5946 chr3qtel1M 832218 AAAGAAAAATCAGAATAAAAGGGGGCAGAGAGCCAGGAGGAGAACCAGGA 832267 i i v v --ii v v v vi i C L2#LINE/L2 2189 AAAGGAGACTGAGAA--GGAGCGGCCAGTGAGGTAGGAGGAAAACCAGGA 2142 chr3qtel1M 832268 GAGGG-GTTGTTCCCAGAACCGGGAGAGAAGAGAGTATCCCCGGGAGGAG 832316 v - v i ivii i i-- v i i ii vi i C L2#LINE/L2 2141 GAGTGTGGTGTCCTGGAAGCCA--AGTGAAGAAAGTGTTTCAAGAAGGAG 2094 chr3qtel1M 832317 --AGTGACCGGCAGCCTCTCCAAGGCTGCAGAGAGGTCCAGGA------- 832357 -- i ii v -- v v v v ? v v ------- C L2#LINE/L2 2093 GGAGTGATCAACTG--TGTCAAATGCTGCTGANAGGTCAAGTAAGATGAG 2046 chr3qtel1M 832358 GACTGAGAAAAGACCTTTGGATCTGGTCCCTAGGTGACCAGTGGTCGCTT 832407 vv v i i ivv vv v ii v vi i C L2#LINE/L2 2045 GACTGAGAATTGACCATTGGATTTAGCAACGTGGAGGTCATTGGTGACCT 1996 chr3qtel1M 832408 TGGAGAGGCCAGTTTTGATGGAGTGGTGAGGTCAGAAGCTGGATTATAGT 832457 ivi iv i i i v ii iv iv C L2#LINE/L2 1995 TGACAAGAGCAGTTTCGGTGGAGTGGTGGGGACGAAAGCCTGATTGGAGT 1946 chr3qtel1M 832458 G---TTAAGAGGCGA-GAAAGGAGAAG---TGGAGGCACTGA 832492 --- i ivi - ii i --- i vi C L2#LINE/L2 1945 GGGTTCAAGAGAGAATGGGAGGAGAGGAATTGGAGACAGCGA 1904 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 37.80 CpG sites = 46, Kimura (unadjusted) = 39.68 Transitions / transversions = 1.31 (46/35) Gap_init rate = 0.04 (11 / 274), avg. gap size = 2.09 (23 / 11) 183 29.64 21.25 3.49 chr3qtel1M 833570 833936 (166064) C L2#LINE/L2 (2224) 858 429 m_b158s601i16 5946 chr3qtel1M 833570 TGGAGGTGAACAGGTGGAAGAATAGAGAGGCTTGGGTGTCGGAA------ 833613 v iv vi i iv iv i i ------ C L2#LINE/L2 858 TGGAGGAGAGGAGGTCAAGGAACTGAGAGGCCAGGGTATTGGAAGGATCA 809 chr3qtel1M 833614 -CT------ATA-TGAAGTCCCC------TGTGCATGAGGGCAGTCTTGG 833649 - ------ - i v ------ i - iii i i v C L2#LINE/L2 808 TCTACGTGGATATTGAAATCACCAAGAATTATG-ACAGGAGTAGTGTTGG 760 chr3qtel1M 833650 GAAGCAGAGAAAGGCTGTGAGAGCCAGGTAATTAATTTATTC-AGGAA-- 833696 ----- iv i v -- - ii vv v - -- C L2#LINE/L2 759 -----AGAGAGTGACAGT--GAGCCAGG-AGCTAAAATCTTCAAGGAATG 718 chr3qtel1M 833697 ---GAGAGTGTCCTGGAGGTGTCTGTAGAT---TTTAAT----------- 833729 --- i v i -- v --- vi i----------- C L2#LINE/L2 717 AGGGGGAGTGACCCGGAG--GTCGGTAGATGACTGCAACAAGGAGGGGTA 670 chr3qtel1M 833730 -TGGGTGATAGA-TATGAACAGCATGAACCTTTTGAGAGCTCA-----TT 833772 -i i v - v - iii iv--- v i vi----- C L2#LINE/L2 669 GCGGGTGGTATAGTCTG-ATGACATGAGA---TTCAAAGCTGGGGTGTTT 624 chr3qtel1M 833773 GAGTGATGAAGG-GGAAGAA---GCCAGATATGACCCTGGGGAGCAGGGA 833818 v v v i - i ---v ii vii i vv i i C L2#LINE/L2 623 TAGGGAGGAGGGAGGGAGAATGGTCTGGAAGCGGCAATGAGGAGCAAGGA 574 chr3qtel1M 833819 GGGT-----TCCCACTTCT--------TGG-----AGAGTGAGTGAAGGG 833850 ii-----i i i-------- -----i i? v v ii i C L2#LINE/L2 573 GGACACCTACCCCACCTCCAGGCCCAGTGGTACGAGGGNTGTGGGAGAGA 524 chr3qtel1M 833851 AA--AGTCATTGCTGAAGAGGGCAACCTGGGTGAC--TGTCGTTA-GGGA 833895 -- i iii vi vi vv vii -- v i - C L2#LINE/L2 523 AAACAGCCACCACTTGAGAGGGCTGCAGGGGAAGCAGTGTCCTCAGGGGA 474 chr3qtel1M 833896 AAGCCAAGTTTCTTTAAGAGC----TGGTGATGGGGGCAGCTAGA 833936 i i ?v v ----v v ii ivii C L2#LINE/L2 473 GAGCCAGGTTTCNGTTAGAGCAAGAAGGTGAAGGGAACGTTCAGA 429 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 37.78 CpG sites = 65, Kimura (unadjusted) = 39.74 Transitions / transversions = 1.62 (65/40) Gap_init rate = 0.10 (35 / 366), avg. gap size = 2.66 (93 / 35) 244 22.48 7.14 4.65 chr3qtel1M 834321 834404 (165596) C MIRc#SINE/MIR (32) 236 151 m_b158s601i17 5947 chr3qtel1M 834321 TTTAAGGTTTGCAAAGATGTGTC-CATAGGTGATCTCATTTGACCCTC-- 834367 vi i vvv v - vi v i -- C MIRc#SINE/MIR 236 TTTACAGTTTACAAAGCGCTTTCACATACATTATCTCATTTGATCCTCAC 187 chr3qtel1M 834368 -ACAATCCTCTAAGGTAGATTGGCATAGTAG--ATTAGTA 834404 - i v i ---- vi i -- v C MIRc#SINE/MIR 186 AACAACCCTGTGAGGTA----GGCAGGGCAGGTATTATTA 151 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 26.84 CpG sites = 8, Kimura (unadjusted) = 26.84 Transitions / transversions = 0.80 (8/10) Gap_init rate = 0.10 (8 / 83), avg. gap size = 1.25 (10 / 8) 314 27.11 16.27 0.00 chr3qtel1M 834430 834595 (165405) C MIRc#SINE/MIR (0) 268 76 m_b158s601i18 5948 chr3qtel1M 834430 AAGAAAAATAATA----ACATTT--ATAGC-CTTTACA-TCTGGAAAACA 834471 v v i?---- -- - - i iv i i C MIRc#SINE/MIR 268 AATAATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCG 219 chr3qtel1M 834472 TTTTGTGATG-ATAATCTCATTT-----------TAACCCTTGGAGATGT 834509 i vvv i- v -----------i vv i iv C MIRc#SINE/MIR 218 CTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAG 169 chr3qtel1M 834510 GCTTAG-AAATATT------CCCATATAACAATTGAGGAAACTAAGGCAG 834552 vvi - ii ------ v v iv i vv C MIRc#SINE/MIR 168 GCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC 119 chr3qtel1M 834553 GCAGAAGTGAATTAATTTGTCCAAGGTCTCAGAGTTAATGAGT 834595 iv i v v i i i v v i i i C MIRc#SINE/MIR 118 AGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGT 76 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 33.40 CpG sites = 23, Kimura (unadjusted) = 34.32 Transitions / transversions = 1.05 (23/22) Gap_init rate = 0.05 (8 / 165), avg. gap size = 3.38 (27 / 8) 367 26.78 2.65 0.87 chr3qtel1M 834483 834595 (165405) C MIR#SINE/MIR (76) 186 72 m_b158s601i19 5948 chr3qtel1M 834483 TAATC-TCATTTTAACCCTTGGAGAT--GTGCTTAGAAATATTCCCATAT 834529 - ivvi vv i -- i - vv v i v C MIR#SINE/MIR 186 TAATCCTCACAACAACCCTATGAGGTAGGTACT-ATTATTATCCCCATTT 138 chr3qtel1M 834530 AACAATTGAGGAAACTAAGGCAGGCAGAAGTGAATTAATTTGTCCAAGGT 834579 v iv i viv i v v i i C MIR#SINE/MIR 137 TACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGT 88 chr3qtel1M 834580 CTCAGAGTTAATGAGT 834595 v v i i i C MIR#SINE/MIR 87 CACACAGCTAGTAAGT 72 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 33.36 CpG sites = 14, Kimura (unadjusted) = 33.36 Transitions / transversions = 0.88 (14/16) Gap_init rate = 0.03 (3 / 112), avg. gap size = 1.33 (4 / 3) 261 33.86 3.94 0.00 chr3qtel1M 834658 834784 (165216) L2#LINE/L2 2470 2601 (481) m_b158s601i20 5949 chr3qtel1M 834658 TTTTTTCTTTTGGACTCTCCCCTCTCCTTATTTTCCCTGTTGGTGTAGAG 834707 i ii ii iii iiv i i vivi i ii ivvv ?i v L2#LINE/L2 2470 TCTTCCCCCTCAAACCTGCTCCTCCCGCAGTCTTCCCCATCTCAGTNAAT 2519 chr3qtel1M 834708 GATATCTCCATCCTCCCATTTCCTCAGACTCCCAACC-AGGAGTTATCCT 834756 ii v i v v i ivvv -v i L2#LINE/L2 2520 GGCAACTCCATCCTTCCAGTTGCTCAGGCCAAAAACCTTGGAGTCATCCT 2569 chr3qtel1M 834757 GGACTCCTC----ACTCTCACACCCTCCATCC 834784 v ----v iv L2#LINE/L2 2570 TGACTCCTCTCTTTCTCTCACACCCCACATCC 2601 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 47.52 CpG sites = 26, Kimura (unadjusted) = 47.52 Transitions / transversions = 1.53 (26/17) Gap_init rate = 0.02 (2 / 126), avg. gap size = 2.50 (5 / 2) 218 34.43 0.00 0.00 chr3qtel1M 835031 835091 (164909) L2#LINE/L2 2674 2734 (348) m_b158s601i21 5949 chr3qtel1M 835031 CTGCTCCCATCTGAGTACAAGCCCTTAACACCTTATACCTGGACTATTAC 835080 iv i ivi v vii v i ivii i i i L2#LINE/L2 2674 CTGCCACCACCCTGGTCCAAGCCACCATCATCTCTCGCCTGGATTACTGC 2723 chr3qtel1M 835081 AATAGCTTCTT 835091 i i L2#LINE/L2 2724 AATAGCCTCCT 2734 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 46.23 CpG sites = 15, Kimura (unadjusted) = 50.08 Transitions / transversions = 2.50 (15/6) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 206 32.91 0.00 0.00 chr3qtel1M 835282 835360 (164640) L2b_3end#LINE/L2 67 145 (321) m_b158s601i22 5949 chr3qtel1M 835282 TCCAGTGACACTGACCCCCTTATTGTTTCTTACGCATCCCATTTTATCTT 835331 iv i i ii i iivi iv ?vi v? i L2b_3end#LINE 67 TCCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACACGCCANGCTCNCTC 116 chr3qtel1M 835332 CCCTCTCCACACATTTGCACTGGCTGTCC 835360 vi vivi v ?v i L2b_3end#LINE 117 CCGCCTCAGGGCCTTTGCACNTGCTGTTC 145 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 42.56 CpG sites = 16, Kimura (unadjusted) = 47.85 Transitions / transversions = 1.60 (16/10) Gap_init rate = 0.00 (0 / 78), avg. gap size = 0.0 (0 / 0) 17 12.53 0.00 0.00 chr3qtel1M 836432 836457 (163543) (T)n#Simple_repeat 1 26 (0) m_b158s252i15 5950 chr3qtel1M 836432 TTCTTTTTTTTTTTTTTTTATTATTT 836457 i v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 459 29.16 3.65 3.65 chr3qtel1M 836923 837196 (162804) C L1ME4a_3end#LINE/L1 (232) 639 366 m_b158s551i0 5951 chr3qtel1M 836923 CCTGCTCATTTCACTCAGCATCAATTCATGTAAGTCTCTCCAGGCCTTTC 836972 iv i i i vv vivi i ii v i v - C L1ME4a_3end#L 639 CCTGCTTTTTTCACTTAACATTATATCATGAGCATTTTCCCATGTCATT- 591 chr3qtel1M 836973 TGAAATTATCCTGTTGG-----TCATTTCTTACAGA-ACAGTAATATTCC 837016 -- - i - i i----- ? i v ii v-i - C L1ME4a_3end#L 590 --AAAT-ATTCT-TCGAAAACATNATTTTTAATGGCTGCA-TAATATTCC 546 chr3qtel1M 837017 ATAATTTTCATATACCACAATTTATTCAACCATTCTCCAACTGATGGACA 837066 v? v vv i i i ? i v i v C L1ME4a_3end#L 545 ATTNTATGGATGTACCATAATTTATTTAACCANTCCCCTATTGTTGGACA 496 chr3qtel1M 837067 TCCATTCAGTTTCCAGTTTTTAGCCACTACAAAAAGGCCTGCCACAAACA 837116 ii vviv i v i i i v ivv v ii C L1ME4a_3end#L 495 TTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAATGCTGCGATGAACA 446 chr3qtel1M 837117 TTCGTGCACATACAGTGACCTTT---CCCTTCTTT-ATAATCTCTTTGGG 837162 i v i ----i i --- v v i - v i i i C L1ME4a_3end#L 445 TCCTTGTACATA----AATCTTTGTNCACATCTCTGATTATTTCCTTAGG 400 chr3qtel1M 837163 ATATAATCCCAGTAGTAACACTGCTGGATCAAAG 837196 v v i v iiv i i i C L1ME4a_3end#L 399 ATAAATTCCTAGAAGTGGAATTACTGGGTCAAAG 366 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 38.00 CpG sites = 46, Kimura (unadjusted) = 38.64 Transitions / transversions = 1.48 (46/31) Gap_init rate = 0.05 (14 / 273), avg. gap size = 1.43 (20 / 14) 541 26.09 2.65 2.65 chr3qtel1M 837008 837196 (162804) C L1ME4c_3end#LINE/L1 (276) 554 366 m_b158s551i1 5951 chr3qtel1M 837008 TAATATTCCATAATTTTCATATACCACAATTTATTCAACCATTCTCCAAC 837057 vivv ?v i i i i i v i C L1ME4c_3end#L 554 TAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTAT 505 chr3qtel1M 837058 TGATGGACATCCATTCAGTTTCCAGTTTTTAGCCACTACAAAAAGGCCTG 837107 v ii vviv i v i i i v ivv C L1ME4c_3end#L 504 TGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCTG 455 chr3qtel1M 837108 CCACAAACA--TTCGTGCACATACAGTGACCTTTCCCTTCTTT---ATAA 837152 v ii -- i -----i i i --- v C L1ME4c_3end#L 454 CAATGAACATCTTCGTGCATATA-----GCTTTTTCCTTCTTTTGAATTA 410 chr3qtel1M 837153 TCTCTTTGGGATATAATCCCAGTAGTAACACTGCTGGATCAAAG 837196 i i i v v v iiv i i i C L1ME4c_3end#L 409 TTTCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAG 366 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 32.28 CpG sites = 29, Kimura (unadjusted) = 33.12 Transitions / transversions = 1.53 (29/19) Gap_init rate = 0.04 (7 / 188), avg. gap size = 1.43 (10 / 7) 319 25.51 12.50 2.00 chr3qtel1M 838139 838274 (161726) C MIR1_Amn#SINE/MIR (80) 150 1 m_b158s601i23 5952 chr3qtel1M 838139 CTCATTTTACAGATGAAT-ATCTGAGGCAAACAGA-GTGAA-TGA-TGGC 838184 i iv- v ?v v - ? - - v C MIR1_Amn#SINE 150 CCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGC 101 chr3qtel1M 838185 TCTGGATCACCCAGTAG---------AAAGTCTTGAA---GACTCAACT- 838221 i vi i ? i? --------- i i vv ?---i i iv - C MIR1_Amn#SINE 100 CCAAGGTCACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAACCCAGGTC 51 chr3qtel1M 838222 TTCTGGTTCCCAGCCCCATGCTCCATCCAGTGGACCACCCAACTGCTCTC 838271 i i iv i vi i v i --- iii C MIR1_Amn#SINE 50 TCCCGAGTCCCAGTCCAGTGCTCTATCCACTAGACCAC---ACTGCCTCC 4 chr3qtel1M 838272 TTA 838274 i C MIR1_Amn#SINE 3 CTA 1 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 32.72 CpG sites = 22, Kimura (unadjusted) = 33.96 Transitions / transversions = 1.83 (22/12) Gap_init rate = 0.07 (10 / 135), avg. gap size = 2.00 (20 / 10) 186 27.08 2.08 0.00 chr3qtel1M 838291 838338 (161662) C L2c_3end#LINE/L2 (66) 412 364 m_b158s601i24 5953 chr3qtel1M 838291 AATGAGCTTCAGTTC-TGCCCTCGTGGAGATCATGGTCTAAAGGAGGAG 838338 i viv i i - iv v ii iv C L2c_3end#LINE 412 AATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAGTGGAGGAG 364 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 31.38 CpG sites = 8, Kimura (unadjusted) = 34.61 Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.02 (1 / 47), avg. gap size = 1.00 (1 / 1) 14 5.00 0.00 0.00 chr3qtel1M 839247 839267 (160733) (CTC)n#Simple_repeat 1 21 (0) m_b158s252i16 5954 chr3qtel1M 839247 CTCCTCCTCCTCCTCCTTCTC 839267 i (CTC)n#Simple 1 CTCCTCCTCCTCCTCCTCCTC 21 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 19 0.00 0.00 0.00 chr3qtel1M 839404 839424 (160576) (G)n#Simple_repeat 1 21 (0) m_b158s252i17 5955 chr3qtel1M 839404 GGGGGGGGGGGGGGGGGGGGG 839424 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGG 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 17 24.18 0.00 3.85 chr3qtel1M 840138 840191 (159809) (TCCC)n#Simple_repeat 1 52 (0) m_b158s252i18 5956 chr3qtel1M 840138 TCCTTCCTTGCCCTCTTCTCCCTCCCTCCCTCCCTTCTTTCCTTCTACCC 840187 i i - -i i i i i iv (TCCC)n#Simpl 1 TCCCTCCCT-CCCTC-CCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCC 48 chr3qtel1M 840188 ACCC 840191 v (TCCC)n#Simpl 49 TCCC 52 Matrix = Unknown Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.04 (2 / 53), avg. gap size = 1.00 (2 / 2) 14 0.00 0.00 0.00 chr3qtel1M 840492 840509 (159491) (GGA)n#Simple_repeat 1 18 (0) m_b158s252i19 5957 chr3qtel1M 840492 GGAGGAGGAGGAGGAGGA 840509 (GGA)n#Simple 1 GGAGGAGGAGGAGGAGGA 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 380 27.48 6.09 14.55 chr3qtel1M 840779 841008 (158992) MIRb#SINE/MIR 42 254 (14) m_b158s601i25 5958 chr3qtel1M 840779 GAGT-GGACAGAGTGCTGGGCTTGGAGTCGGG----GAGACTC-CTAGCT 840822 -i v-- i i i vi v ---- vv i- MIRb#SINE/MIR 42 GAGTCAGACAGAC--CTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCT 89 chr3qtel1M 840823 GGGTGACCCTAGT--AGTCCCTTCACTTCT----ACCTCAGTTTCCTCAG 840866 v i i v-- iv v i ----i v MIRb#SINE/MIR 90 GTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCAT 139 chr3qtel1M 840867 CTGTAACTGTAAAACTGTACCTATAAAATGGAGATTAAAAACACTTTCCT 840916 -------------------- i - v i i v MIRb#SINE/MIR 140 CTGTA--------------------AAATGGGGAT-AATAATACCTACCT 168 chr3qtel1M 840917 TCCTAAGTTGTTATTAC-ATCATACATGTATGTTACATCATATTTGTAAG 840965 iv vii i v v- -- v ------ v v iiv i MIRb#SINE/MIR 169 CGCAGGGTTGTTGTGAGGAT--TAAATG------AGATAATGCATGTAAA 210 chr3qtel1M 840966 GTGCCTGGTCTAGT-TCTGGTACATAGTAGGTACTTAATATATG 841008 i i i ivi -i i i ii i v MIRb#SINE/MIR 211 GCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAAATG 254 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 31.37 CpG sites = 32, Kimura (unadjusted) = 34.54 Transitions / transversions = 1.45 (32/22) Gap_init rate = 0.17 (38 / 229), avg. gap size = 1.18 (45 / 38) 207 26.53 2.04 0.00 chr3qtel1M 840966 841014 (158986) L2d_3end#LINE/L2 453 502 (14) m_b158s601i26 5959 chr3qtel1M 840966 GTGCCTGGTCTAGTTCTG-GTACATAGTAGGTACTTAATATATGCTTATT 841014 i i ivi v - i ii i v i i L2d_3end#LINE 453 GCGCCTAGCACAGTGCTGAGCACATAGTAGGCGCTCAATAAATACTTGTT 502 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 28.13 CpG sites = 10, Kimura (unadjusted) = 34.95 Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.02 (1 / 48), avg. gap size = 1.00 (1 / 1) 16 23.91 5.36 1.72 chr3qtel1M 841313 841368 (158632) (TA)n#Simple_repeat 1 58 (0) m_b158s252i20 5960 chr3qtel1M 841313 TATATGT-TAAATATAGTAGAAATATATGT-TGTCCA-ATATATGCATAT 841359 i - v - v v i - i vi - ii (TA)n#Simple_ 1 TATATATATATATATA-TATATATATATATATATATATATATATATATAT 49 chr3qtel1M 841360 ATATTTATA 841368 v (TA)n#Simple_ 50 ATATATATA 58 Matrix = Unknown Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.07 (4 / 55), avg. gap size = 1.00 (4 / 4) 770 28.66 5.11 4.65 chr3qtel1M 841783 842232 (157768) C L1ME4c_3end#LINE/L1 (372) 458 7 m_b158s551i2 5961 chr3qtel1M 841783 GCTGCCACAAACATTTTTGCACATGTGGGTCCTTTTCCCTTTTTTT--AT 841830 v ii i i ii i i --- i i -- C L1ME4c_3end#L 458 GCTGCAATGAACATCTTCGTGCATATAG---CTTTTTCCTTCTTTTGAAT 412 chr3qtel1M 841831 GATCTAATTTGGATACAGACCCAATAGTGAAACTGCTGGATCAAAAAGTA 841880 v i vv v v vv iv i i i i ii C L1ME4c_3end#L 411 TATTTCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTA 362 chr3qtel1M 841881 T----AGTTTTGTAGTCCCATGG-GCAGAGTTCCAAATTGCTCTCCAGAA 841925 ---- v i i - i v i-i iv v v i i C L1ME4c_3end#L 361 TGAACATTTTTATGG-CTCTTGATACGTATTGCCAAATTGCTTTCCAAAA 313 chr3qtel1M 841926 CAATCCAGATCCAGAACTGGATCTGTTCACAACTCCACCAATGATGCATT 841975 ------------- iii v i vi i ?iv iii i v C L1ME4c_3end#L 312 -------------GGGTTGTACCAATTTACANTGCCACCAGCAATGTATG 276 chr3qtel1M 841976 AATGTTCCTCTTTTCCCACATCCCCGCCAGCATT------TATC--TTTT 842017 i? v vv iv i ? i ------ -- C L1ME4c_3end#L 275 AGNGTACCAGTTTCACCGCANCCTCGCCAGCATTGGGTATTATCAATTTT 226 chr3qtel1M 842018 TCCATTATCTTAGTCAATCTGAGAGATGTGAAAAAGTACCTCAAGAGTTG 842067 iv -- i v ii i i v ii i vi i vv- C L1ME4c_3end#L 225 TTAA--ATTTTTGCTAATTTAATAGGCGTAAAATGGTATCTCATT-GTTG 179 chr3qtel1M 842068 TCTTAATTTGCATTTCTCTAATCAATAGTGATTTAGAGCATTTTTTCATG 842117 ii i i i v i vv v i i C L1ME4c_3end#L 178 CTTTAATTTGCATTTCTTTGATTACTAGCGAGGTTGAACATTTTTCCATG 129 chr3qtel1M 842118 AGACTACAAATAGCTTTAATTTCATCATCTGATAATTGTCTGTTCTTTTC 842167 v vi iivv ivi? vv v v ? vv v v C L1ME4c_3end#L 128 TGTTTGTTTACTANTTGTATTTCCTCTTNTGTGAATTGTCTGTTCATGTC 79 chr3qtel1M 842168 CTTTGACCATTTATCAACTGAAG----AATGATTTGTATTATGCATTTGA 842213 v v i ii ----i -? v v vv C L1ME4c_3end#L 78 CTTTGCCCATTTATCTATTGGGGTCTTGAT-NTTTTTCTTATCAATTTGA 30 chr3qtel1M 842214 ATCAA----TTATATATTTTAGA 842232 v i---- ? v? C L1ME4c_3end#L 29 ATGAGCTCTTTATATANTANAGA 7 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 35.98 CpG sites = 70, Kimura (unadjusted) = 37.92 Transitions / transversions = 1.32 (70/53) Gap_init rate = 0.06 (28 / 449), avg. gap size = 1.57 (44 / 28) 468 32.35 7.12 2.75 chr3qtel1M 842096 842896 (157104) C L1M2_orf2#LINE/L1 (0) 3291 2457 m_b158s551i3 5961 chr3qtel1M 842096 TGATTTAGAGCATTTTTTCATGAGACTACAAATAGC--TTTA-ATTTCAT 842142 v v iviv ii--- i -- i- v v C L1M2_orf2#LIN 3291 TGATGTTGAGCATTTTTTCATATACCTGT---TGGCCATTTGTATGTCTT 3245 chr3qtel1M 842143 CATCTGATAATTGTCTGTTCTTTTCCTTTGACCATTTATCAACTGAAGAA 842192 v i v v i vvv v v ? ii i --- C L1M2_orf2#LIN 3244 CTTTTGAGAAATGTCTATTCAGGTCCTTTGCCCATTTTTNAATCGGA--- 3198 chr3qtel1M 842193 TGATTTGTATTAT-GC---------ATTTGAATCAATTATATATTTTAGA 842232 v v v - ---------i i ivv i i C L1M2_orf2#LIN 3197 TTATTTGTTTTTTTGCTGTTGAGTTGTTTGAGTTCCTTATATATTCTGGA 3148 chr3qtel1M 842233 AAGGAGGCCTTTACCAGAAGCACTGGCTGTAAAAAATGTTCCTAGTTTTC 842282 v vv iv i ii v ? iv vi i v v v ii ivi i v C L1M2_orf2#LIN 3147 TATTAATCCCTTGTCAGATGNATAGTTTGCAAATATTTTCTCCCATTCTG 3098 chr3qtel1M 842283 TA--CTTTCCTTCTAATCT--TGGCAGTGTTGGTTTGTTTGTGCAAAAAC 842328 --i v ii ii v -- iiv - vv i - i i C L1M2_orf2#LIN 3097 TAGGTTGTCTCTTCACTCTGTTGATTGT-TTCCTTTGCT-GTGCAGAAGC 3050 chr3qtel1M 842329 TTTTGAATTTAATATAATCAGAATGAGCCATTTTTCATTTCATAA--TGT 842376 v i i i vv v viv i vv ii vi-- C L1M2_orf2#LIN 3049 TTTTTAGTTTGATGTAATCCCATTTGTCTATTTTTGCTTTTGTTGCCTGT 3000 chr3qtel1M 842377 TCTCTTG---TCCTTTGGCCATAAATTCCTT-CCTTCCCCACAGATCTGA 842422 v i --- -- i? v v i - ivvv vv vi C L1M2_orf2#LIN 2999 GCTTTTGAGGTC--TTANCCAAAAAATCTTTGCCCAGACCAATGTCCTGA 2952 chr3qtel1M 842423 GAGGTAGACTATCCCT---TGTTCTCCTA--AGTTGCTTATAGTATCACC 842467 iiv ---- vi --- v i -- -- v ivv C L1M2_orf2#LIN 2951 AGCGT----TTCCCCTATGTTTTCTTCTAGTAGTT--TTATAGTTTCGGG 2908 chr3qtel1M 842468 CTTTATGTCTAAATCATGAACCCATTTCAATCTTATCTTGGTATATGGTG 842517 ii ii i i v v i ii vi v i v C L1M2_orf2#LIN 2907 TCTTACATTTAAGTCTTTAATCCATTTTGAGTTGATTTTTGTATATGGTG 2858 chr3qtel1M 842518 TTAGTTGTGGATC-AATGCCTAGTTTCTGCCATACCAGTTTCTAATTTTC 842566 vv v iv i - i vi vvvi - ivii v i i C L1M2_orf2#LIN 2857 AGAGATAGGGGTCTAGTTTCATTCTTCTGC-ATATGGATATCCAGTTTTC 2809 chr3qtel1M 842567 CCAGCAGTTTTTGTCAAATA----GTTCTTATCCCGGAAGCTGGGGTCTT 842612 viv i ii v ---- i vi -- ?vv iv v C L1M2_orf2#LIN 2808 CCAGCACCATTTATTGAAGAGACTGTCCTTTCCCC--ANTGTATGTTCTT 2761 chr3qtel1M 842613 TGGG--TTTGTCGAACACTAGATTGCTATAG--GTATTGATTATTGTGTC 842658 v v -- v ii v v i i-- ii v -- i v C L1M2_orf2#LIN 2760 GGCGCCTTTGTCGAAAATCAGTTGGCTGTAAATGCGTGGAT--TTATTTC 2713 chr3qtel1M 842659 TGTGTAC-CCAAGCTATTCCACTGATCCATTACTTTGTTTCTTAGCCAGT 842707 v v - i vv i i i i vvv i i vv C L1M2_orf2#LIN 2712 TGGGTTCTCTATTCTGTTCCATTGGTCTATGTGTCTGTTTTTATGCCAGT 2663 chr3qtel1M 842708 AGCAGAGGATTTTGATGACTGCCACTTTATAGTATAGTTTTAGGCCA--- 842754 v vivvi i v iivi i v v i i --- C L1M2_orf2#LIN 2662 ACCATGCTGTTTTGGTTACTATAGCTTTGTAGTATATTTTGAAGTCAGGT 2613 chr3qtel1M 842755 ---------CTTTC--CTTTGTATGTTTTCTTTCA----TTCTTTTGATA 842789 --------- i i -- - v ivi ---- v v v C L1M2_orf2#LIN 2612 AGTGTGATGCCTCCAGCTTTGT-TCTTTTTGCTCAGGATTGCTTTGGCTA 2564 chr3qtel1M 842790 TTCGTGACCTTTTGTTCTTCTAGATGGATTTTGTTATTATGTTTTCCAGT 842839 v ii vv i v i i ivv ? v i v C L1M2_orf2#LIN 2563 TTCGGGGTCTTTTGTGGTTCCATACGAATTTTAGGATTNTTTTTTCTATT 2514 chr3qtel1M 842840 TCTATAAAGTAATTTT-TTGGTAGTTTGATCGGTATGGAACTGAATAAGT 842888 i i - v i- v v v v v i vv C L1M2_orf2#LIN 2513 TCTGTGAAG-AATGTCATTGGTATTTTGATAGGGATTGCATTGAATCTGT 2465 chr3qtel1M 842889 AGATTGTT 842896 i i C L1M2_orf2#LIN 2464 AGATCGCT 2457 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 42.23 CpG sites = 124, Kimura (unadjusted) = 43.37 Transitions / transversions = 0.97 (124/128) Gap_init rate = 0.06 (44 / 800), avg. gap size = 1.82 (80 / 44) 982 32.11 1.69 0.48 chr3qtel1M 845298 845710 (154290) C L1ME4c_3end#LINE/L1 (227) 603 186 m_b158s551i4 5962 chr3qtel1M 845298 TTTTCATGTGTTTCTAGAGTCATCCTGCTTGTCATTTCCTATAGA---AT 845344 i vvi vi v v v iv i iiv i v--- C L1ME4c_3end#L 603 TTTCCATGTTGCTACATAGTCTTCATAATTATCATTTTTAATGGCTGCAT 554 chr3qtel1M 845345 AGTATTCCATAATATTCATATACCATAACTTATTCAGCCATTCTCCAATT 845394 i vivi ?v i i i i i i v C L1ME4c_3end#L 553 AATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTATT 504 chr3qtel1M 845395 GATGGGCATCCACTCACTTTCCAGTTTTTTGCCACTGCAAAGAGGGCTGC 845444 v i ii vvivv i i i i ii v iv C L1ME4c_3end#L 503 GTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGC 454 chr3qtel1M 845445 CACAAACATTTTTGCATATGTGGGTCCCTTTCCCTCATTTAA--TATCTC 845492 v ii i i iii i i -- ii i v i -- i C L1ME4c_3end#L 453 AATGAACATCTTCGTGCATATAG--CTTTTTCCTTCTTTTGAATTATTTC 406 chr3qtel1M 845493 TTTAGGATACAAGCCTAGTAGGAACACTGCTGGGTTAAAGGGTAT--ACA 845540 i v vv i v viiv i i i -- C L1ME4c_3end#L 405 CTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACA 356 chr3qtel1M 845541 ATTTGATAGCCTTTTGGGCCTACTTCCAAATGACTCTCCAGAATGGTTGG 845590 v v i ii vivi v i v vi i i v v C L1ME4c_3end#L 355 TTTTTATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGT 306 chr3qtel1M 845591 ATCCATGCACAGTTCCAACAACAATGTATCAGTGTCCCAGTTTTCCCACA 845640 i v vi ? v v i v ? v iv i C L1ME4c_3end#L 305 ACCAATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCA 256 chr3qtel1M 845641 TCCCCTCCAACATTTGTCATTATCTTTTCCTGTCATCTTAACCAATCTCA 845690 ? i v i v vi vv ii vvv i vi i i v C L1ME4c_3end#L 255 NCCTCGCCAGCATTGGGTATTATCAATTTTTTAAATTTTTGCTAATTTAA 206 chr3qtel1M 845691 GAGGTGTGAAGTAGTGTCTC 845710 v i i i i i C L1ME4c_3end#L 205 TAGGCGTAAAATGGTATCTC 186 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 41.68 CpG sites = 77, Kimura (unadjusted) = 43.90 Transitions / transversions = 1.40 (77/55) Gap_init rate = 0.01 (5 / 412), avg. gap size = 1.80 (9 / 5) 1008 28.57 1.59 1.86 chr3qtel1M 845343 845720 (154280) C L1ME3G_3end#LINE/L1 (376) 548 172 m_b158s551i5 5962 chr3qtel1M 845343 ATAGTATTCCATAATATTCATATACCATAACTTATTCAGCCATTCTCCAA 845392 i vv i i i i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr3qtel1M 845393 TTGATGGGCATCCACTCACTTTCCAGTTTTTTGCCACTGCAAAGAGGGCT 845442 i ii vvivv i i i i i v iv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr3qtel1M 845443 GCCACAAACATTTTTGCATATGTGGGTCCCTTTCCCTCATTT---AATAT 845489 v ii ii i i i---?i viv v v --- i C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACATGC---NTCCTTGTGCACATGTGCGAGTAT 402 chr3qtel1M 845490 CTCTTTAGGATACAAGCCTAGTAGGAACACTGCTGGGTTAAAGGGTATAC 845539 i ? v v? ? v viiv i i i C L1ME3G_3end#L 401 TTCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGC 352 chr3qtel1M 845540 A-ATTTGATAGCCTTT--TGGGCCTACTTCCAAATGACTCTCCAGAATGG 845586 i- -- ivi -- i i-- v vi i i ? C L1ME3G_3end#L 351 GCATTT--TAAATTTTAATAGA--TACTGCCAAATTGCCCTCCAAAANGG 306 chr3qtel1M 845587 TTGGATCCATGCACAGTTCCAACAACAATGTATCAGTGTCCCAGTTTTCC 845636 i v i v vi v i v i i v v v v i C L1ME3G_3end#L 305 CTGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCC 256 chr3qtel1M 845637 CACATCCCCTCCAACATTTGTCATTATCTTTTCCTGTCATCTTAACCAAT 845686 i i v i ? vi vv?iii vvv i vi C L1ME3G_3end#L 255 CACACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAAT 206 chr3qtel1M 845687 CTCAGAGGTGTGAAGTAGTGTCTCCGAGTTGTCT 845720 v vi vi i i i vvv i C L1ME3G_3end#L 205 CTGATGGGTGAAAAATGGTATCTCATTGTTGTTT 172 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 36.89 CpG sites = 61, Kimura (unadjusted) = 37.80 Transitions / transversions = 1.36 (61/45) Gap_init rate = 0.03 (10 / 377), avg. gap size = 1.30 (13 / 10) 11 14.43 7.50 2.38 chr3qtel1M 845890 845929 (154071) (ATATGT)n#Simple_repeat 1 42 (0) m_b158s252i21 5963 chr3qtel1M 845890 ATATGTTAAAGTATATGT-TA--AATACGATATATGTATATGT 845929 vv v - --v i - (ATATGT)n#Sim 1 ATATGTATATGTATATGTATATGTATATG-TATATGTATATGT 42 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.08 (3 / 39), avg. gap size = 1.33 (4 / 3) 1134 28.70 2.61 2.26 chr3qtel1M 846216 846789 (153211) C L1MC4_3end#LINE/L1 (2156) 633 58 m_b158s551i6 5964 chr3qtel1M 846216 GCTCATTTCACTCAGCATCAGTTCATGTAAGTCTC-TCCAGGCCTTTCTG 846264 iv i v? - v v vi - v ii? vi C L1MC4_3end#LI 633 GCTTCTTTCACTTAGCAANA-TGCATTTAAGATTCATCCATGTTNTTGCG 585 chr3qtel1M 846265 -AAATCATCCTGCTGGTCATTTCTT---ACCAAACAATAATATTCCATAA 846310 -i? ---- iv v i --- i ivvv i i vi C L1MC4_3end#LI 584 TGNATCA----GTAGTTCATTCCTTTTTATCGCTGAGTAGTATTCCATTG 539 chr3qtel1M 846311 CATTCAGATACCACAATTTATTCAGCCATTCTCCCATTGATGGGCAT-TC 846359 i vv vi i i i v v ii v i - ? C L1MC4_3end#LI 538 TATGGATGTACCACAGTTTGTTTATCCATTCACCTGTTGAAGGACATCTN 489 chr3qtel1M 846360 ATTCATTTTCTAGTTTCTGGCCCTTACAAAGAAGGCTGCCACAAACATTC 846409 iv ii i - ? i ?v ii v i i i C L1MC4_3end#LI 488 GGTTGTTTCC-AGNTTTTGGCNATTATGAATAAAGCTGCTATAAACATTC 440 chr3qtel1M 846410 TTGCACA----TATACGTCCCTTTCCCTTCTTTAAAATCTCTTTGGGGTA 846455 v i ---- v ii vvviv v?v -- v ?v ? -- C L1MC4_3end#LI 439 GTGTACAGGTTTTTGTGTGGACATANGTT--TTCANTTCNCTT--GGGTA 394 chr3qtel1M 846456 TAAGCCCAGTAGTAACACTGCTGGATCAAAGAGTATGCACAATTTGATAA 846505 v vi i v i?v i i v vi v?iii vv -- i C L1MC4_3end#LI 393 AATACCTAGGAGTGNGATTGCTGGGTCATATGGTAANTGTATGTT--TAG 346 chr3qtel1M 846506 CTGTTTGAGCATAGTTCCAAATTGCTTTCCAGAATGGCTGGATGTATTCA 846555 v ? i v - v v i i i i v ivvv ii C L1MC4_3end#LI 345 CTTTNTAAGAA-ACTGCCAAACTGTTTTCCAAAGTGGCTGTACCATTTTG 297 chr3qtel1M 846556 CAATTCCACCAACAATGTATCAGTGT--CCGTTTTCCCACATCCCCTCCA 846603 v i i v v -- ? vii i v C L1MC4_3end#LI 296 CATTCCCACCAGCAATGTATGAGAGTTCCNGTTGCTCCACATCCTCGCCA 247 chr3qtel1M 846604 ACATTTG---TCATCATTTCCTGTCATCTTAGCCAATCTGAGAGGTGTGT 846650 i --- ii v ?ii v v i v i v C L1MC4_3end#LI 246 GCATTTGGTATTGTCAGTNTTTTTGATTTTAGCCATTCTAATAGGTGTGT 197 chr3qtel1M 846651 AGTGGTATCTCAGAGTTGACTTAATTTGCATTTCGCTGATCAATAATGAT 846700 vv v vi v i v v? C L1MC4_3end#LI 196 AGTGGTATCTCATTGTGGTTTTAATTTGCATTTCCCTAATGACNAATGAT 147 chr3qtel1M 846701 ATGGAGCACCTTTTCATGTGAGTAGAAATGGTTTCAATTTCTTCATCTGA 846750 i v i vv vvviivi i vv v v iv v C L1MC4_3end#LI 146 GTTGAGCATCTTTTCATGTGCTTATTTGCCATCTGTATATCTTCTTTGGT 97 chr3qtel1M 846751 AAATTGTCTGTTCATATCCTTTGACCATTTATCAATTGG 846789 i v v i v v i C L1MC4_3end#LI 96 GAAATGTCTGTTCAAATCTTTTGCCCATTTTTTAATTGG 58 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 37.27 CpG sites = 78, Kimura (unadjusted) = 37.85 Transitions / transversions = 0.94 (78/83) Gap_init rate = 0.03 (20 / 573), avg. gap size = 1.40 (28 / 20) 1502 25.87 1.62 1.21 chr3qtel1M 846297 846789 (153211) C L1ME3G_3end#LINE/L1 (376) 548 54 m_b158s551i7 5964 chr3qtel1M 846297 ATAATATTCCATAACATTCAGATACCACAATTTATTCAGCCATTCTCCCA 846346 i ii vv v i i i i i C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr3qtel1M 846347 TTGATGGGCATTCATTCATTTTCTAGTTTCTGGCCCTTACAAAGAAGGCT 846396 i i vvivv i i i v iv v v C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr3qtel1M 846397 GCCACAAACATTCTTGCACATATACGTCCCTTT-CCCTTCTTTAAA-ATC 846444 v ii i i i-- ? i v - v v v vii i- i C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACATG--CNTCCTTGTGCACATGTGCGAGTATT 401 chr3qtel1M 846445 TCTTTGGGGTATAAGCCCAGTAGTAACACTGCTGGATCAAAGAGTATGCA 846494 ? i i v v? ? v iiv i i i i C L1ME3G_3end#L 400 TCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCG 351 chr3qtel1M 846495 CAATTTGATAACTGTTTGA-GCATAGTTCCAAATTGCTTTCCAGAATGGC 846543 - -- v - i -iv v v ii i ? C L1ME3G_3end#L 350 CA-TTT--TAAAT-TTTAATAGATACTGCCAAATTGCCCTCCAAAANGGC 305 chr3qtel1M 846544 TGGATGTATTCACAATTCCACCAACAATGTATCAGTGT--CCGTTTTCCC 846591 v ivv i v i i i v v -- i C L1ME3G_3end#L 304 TGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCC 255 chr3qtel1M 846592 ACATCCCCTCCAACATTTGTCATCATT--TCCTGTCA-TCTTAGCCAATC 846638 i i v i ? vi i i--? i v v - i v C L1ME3G_3end#L 254 ACACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATC 205 chr3qtel1M 846639 TGAGAGGTGTGTAGTGGTATCTCAGAGTTGACTTAATTTGCATTTCGCTG 846688 vi viv i vv vi v C L1ME3G_3end#L 204 TGATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTG 155 chr3qtel1M 846689 ATCAATAATGATATGGAGCACCTTTTCATGTGAGTAGAAATGGTTTCAAT 846738 i v i vi v i i vv vviiivi vv C L1ME3G_3end#L 154 ATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGTAT 105 chr3qtel1M 846739 TTCTTCATCTGAAAATTGTCTGTTCATATCCTTTGACCATTTATCAATTG 846788 i v vi i v v v C L1ME3G_3end#L 104 TTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTG 55 chr3qtel1M 846789 G 846789 C L1ME3G_3end#L 54 G 54 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 32.15 CpG sites = 68, Kimura (unadjusted) = 32.81 Transitions / transversions = 1.17 (68/58) Gap_init rate = 0.02 (12 / 492), avg. gap size = 1.17 (14 / 12) 1519 31.04 2.99 3.90 chr3qtel1M 846697 848067 (151933) C L1M5_orf2#LINE/L1 (0) 3294 1936 m_b158s551i8 5964 chr3qtel1M 846697 TGATATGGAGCACCTTTTCATGTGAGTAGAAATGGTTTCAATTTCTTCAT 846746 ?i v i vv vviiivi v? v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr3qtel1M 846747 CTGAAAATTGTCTGTTCATATCCTTTGACCATTTATCAATTGGA--GAAT 846794 i vi v vi i v v ?v i-- vv C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTT 3195 chr3qtel1M 846795 GGCTTGAACTATTATAAATTTG----AGTCAATTATATCTGTTAGAAATG 846840 v v--i ? vi ? ---- ivv v vi i v i C L1M5_orf2#LIN 3194 GTCTTT--TTNTTATTGANTTGTAGGAGTTCTTTATATATTCTGGATACG 3147 chr3qtel1M 846841 AGGTCTTTATCAGA---ACCTTTGGATGTAAAAATGTTTTCCCAGTTTAT 846887 vi i --- iv ? --- i v v i ? i i C L1M5_orf2#LIN 3146 AGTCCTTTGTCAGATATATGTNT---TGCAAATATTTTCTCCCANTCTGT 3100 chr3qtel1M 846888 GGCTTCCCTTCTAATCTTGTCTGCATTAGTTTTGTTTGTACGAA---AAC 846934 v i v i v i--- vii v iv - ? i--- v C L1M5_orf2#LIN 3099 GGCTTGCCTTTTCATTTTCTT---AACGGTGTCTTTTG-ANGAGCAGAAG 3054 chr3qtel1M 846935 TTTTTAACTT-AATATAATCAAAATTATCTATTTTATGATCAGTAATGAT 846983 i -i i? i v v v - -- vv v i C L1M5_orf2#LIN 3053 TTTTTAATTTTGATGNAGTCCAATTTATCAATTTT-T--TCTTTTATGGT 3007 chr3qtel1M 846984 CTCTAGTTTTTCT---TTGGTCACAAATTCTTT-CCTCCTCCACAGGTCT 847029 i?v iv v ---i v i vi v - v?i - - C L1M5_orf2#LIN 3006 TNGTGCTTTTTGTGTCCTGTTTAAGAAATCTTTGCCTANCCCA-AGGTC- 2959 chr3qtel1M 847030 AAGAGGTAAACTATCCTATGTT--CCTCTAGTTTATTTATAATCTCATTC 847077 v i - v i v -- i vvvv i i i ?ii C L1M5_orf2#LIN 2958 ACGAAG-ATATTCTCCTATGTTTTCTTCTAGAAGTTTTATAGTTTTANCT 2910 chr3qtel1M 847078 TTTATGTCTAGAT-TATGAACCCATTTTGACCTTATCTTGCTATACAGTG 847126 ii i i - -i i ? vi v i vv i ii C L1M5_orf2#LIN 2909 TTTACATTTAGGTCTATGA-TCCATCTNGAATTAATTTTTGTGTATGGTG 2861 chr3qtel1M 847127 TTAGGTGTGGGTCAGTACCTAGTTTCTGCCATACTGATTTCCAATTTTCT 847176 v iv iiv?iii v i v iv v v ii C L1M5_orf2#LIN 2860 TGAGGTAGGGGTCGAGNTTCATTTTTTTCCATATGGATATCCAATTGTTC 2811 chr3qtel1M 847177 CAGCAGTTTTTGTCAAACAGTGAATTCTTATCCCAAAAGCTGGG--GTTT 847224 viv ii v vvv i vi ---- ii-- i? C L1M5_orf2#LIN 2810 CAGCACCATTTGTTGAAAAGACTATCCTTTCCCCA----CTGAATTGCNT 2765 chr3qtel1M 847225 TGGGG--TTTGTCAAAGGGTAGATTATTAAAGTTAT-TGA--CTATTTTG 847269 vi-- iivi i? v?ii v vv i - i-- i- C L1M5_orf2#LIN 2764 TGGCACCTTTGTCAAAAATCAANTGNCCATATATGTGTGGGTCTATTTC- 2716 chr3qtel1M 847270 TCCTGTGAAC---CTAACCTATTCCACTGATCAACTAATCTATTTCCTA- 847315 ----- i --- vi i i v i vi i- i - C L1M5_orf2#LIN 2715 -----TGGACTCTCTATTCTGTTCCATTGATCTATTTGTCTATC-CTTAC 2672 chr3qtel1M 847316 GCCAATACCAAATGGTTTTGGTGACTGCTGCTTTATAATACAGTTTT-AG 847364 v iv i i v iv - i - ? C L1M5_orf2#LIN 2671 GCCAATACCACACTGTCTTGATTACTGTAGCTTTATAATA-AGTCTTGAN 2623 chr3qtel1M 847365 ATCTGGTACAGCTAGGTCACTTTGATTTGTTTTTTTTTTTTTGTTTTTTT 847414 ? vv - i - iii i ------------- i i C L1M5_orf2#LIN 2622 ATCNGGTAGTG-TAAGTC-CTCCAACTT-------------TGTTCTTCT 2588 chr3qtel1M 847415 TTTTTTTAAATTAATTCCCTTGAAATTCTTGACCTTTTGTTTTTCCAGAA 847464 iv- i iv --- v vv ? ii i iv v v C L1M5_orf2#LIN 2587 TTTTCA-AGATTGTTT---TGGCTATTCTNGGTCCTTTGCATTTCCATAT 2542 chr3qtel1M 847465 GAATTTTGTTGTTATTTTTTCTAGTTCAGTAAAATAACTTCTTGGGACTC 847514 i ivvi i vi v v v vii v i vi i i C L1M5_orf2#LIN 2541 AAATTTTAGAATCAGCTTGTCAATTTCTACAAAAAAACCTGCTGGGATTT 2492 chr3qtel1M 847515 TGATTGGTATAGCACTAAATAAATAAA---GTTTAGGTAGTATTGTCATT 847561 v v i i vv i ---i i v v v i C L1M5_orf2#LIN 2491 TGATTGGGATTGCATTGAATCTATAGATCAATTTGGGGAGAATTGACATC 2442 chr3qtel1M 847562 TTTATTATATTTGCTTGACTTAACCGAGAGCACTTGATATTTTTCTAATT 847611 ? iv viv ivv iv v iv i ivvv i i i v C L1M5_orf2#LIN 2441 TTNACAATATTGAGTCTTCCAATCCATGAACATGGTATATCTCTCCATTT 2392 chr3qtel1M 847612 ACTTAGATCTGACTTTATTTGTGTGGAAAGTGTTTTGTAGTTTTGCTCAG 847661 i i vvi v v v viiv i --- C L1M5_orf2#LIN 2391 ATTTAGGTCTTCTTTAATTTCTCTCAGCAATGTTTTGTAGTTT---TCAG 2345 chr3qtel1M 847662 ---ATAGTTCCTGACCTTCTCTTGGCAGATAGATTCCCAAATATTTTATA 847708 --- ? v i vv v ? i vi vv i i ? i C L1M5_orf2#LIN 2344 TGTANAGGTCTTGCACATNTTTTGTTAGATTTATTCCTAAGTATTTNATG 2295 chr3qtel1M 847709 CTATCGACTGTTGTTTTAAATGGAATTTCTCTTTGTATCTC---TTGCTG 847755 i v iviv i i v v vi i ?iv i --- v vi C L1M5_orf2#LIN 2294 TTTTTTGATGCTATTGTAAATGGTATTGTTTTTNAAATTTCATTTTCCAA 2245 chr3qtel1M 847756 TTGGATTTTGTTAGTGATGTATAAAAATGCTGAGGATTTATGTGGATTTA 847805 --- iv ii i i i vivv v iv v C L1M5_orf2#LIN 2244 TTG---TTTGTTGCTAGTATATAGAAATACAATTGATTTTTGTATATTGA 2198 chr3qtel1M 847806 TTTTGAATCCTGCAACTTTGATAAAGTTGTGGATTATTCCTAATAGCTTT 847855 ii v ? i i v v iiivv v i i i ? C L1M5_orf2#LIN 2197 CCTTGTATCCNGCGACCTTGCTAAATTCACTTATTAGTTCTAGTAGTTTN 2148 chr3qtel1M 847856 TTAGGTGTTTCTCTGGGGTTCTCTAAGTACACCATCATATCTTCAGCAAA 847905 v vv v i ? i i v ? v i v v i C L1M5_orf2#LIN 2147 TTTGTAGATTCTTTNGGATTTTCTACGTANACAATCATGTCATCTGCGAA 2098 chr3qtel1M 847906 GAGTAACAATTTGGTTTCCTCATGACCTATTCTAATTCCTTTAATTTCTT 847955 v i?i i vi i v vv v ii v v v C L1M5_orf2#LIN 2097 TAANGACAGTTTTATTTCTTCCTTTCCAATCTTTATGCCTTTTATTTCTT 2048 chr3qtel1M 847956 TTTCTTCTCTTATTGCCAAATCTAGCATTTCTGATTCGATATTGAATAGC 848005 vi vvviv v ii iii v i i v C L1M5_orf2#LIN 2047 TTTCTTGCCTTATTGCACTGGCTAGGACCTCCAGTACAATGTTGAATAGA 1998 chr3qtel1M 848006 AATGGTGATGGTGGGCAACCTTGTTTCACTCCTGAGCTTATTGGAAATGG 848055 i ?i i i v i iii i v vv i v v C L1M5_orf2#LIN 1997 AGTGGTGANAGCGGACATCCTTGTCTTGTTCCCGATCTTAGGGGGAAAGC 1948 chr3qtel1M 848056 TTCCAGTTTATC 848067 ? i ? v C L1M5_orf2#LIN 1947 NTTCAGTNTTTC 1936 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 41.27 CpG sites = 215, Kimura (unadjusted) = 42.22 Transitions / transversions = 1.11 (215/194) Gap_init rate = 0.05 (71 / 1370), avg. gap size = 1.32 (94 / 71) 18 0.00 6.25 3.03 chr3qtel1M 848715 848746 (151254) (CTCTTC)n#Simple_repeat 1 33 (0) m_b158s252i22 5965 chr3qtel1M 848715 CTCTTCCTCTTCCTCTTCCTC-T-CTCTTGCCTC 848746 - - - (CTCTTC)n#Sim 1 CTCTTCCTCTTCCTCTTCCTCTTCCTCTT-CCTC 33 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.10 (3 / 31), avg. gap size = 1.00 (3 / 3) 21 7.66 4.44 4.44 chr3qtel1M 852002 852046 (147954) (ATT)n#Simple_repeat 1 45 (0) m_b159s252i0 5966 chr3qtel1M 852002 ATTATTATTA-TATTATATATTA-CATTATTATTATAGATTTTTATT 852046 - - -i -v v (ATT)n#Simple 1 ATTATTATTATTATTAT-TATTATTATTATTATTAT-TATTATTATT 45 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4) 14 29.61 0.00 3.39 chr3qtel1M 852241 852301 (147699) (AGAA)n#Simple_repeat 1 59 (0) m_b159s252i1 5967 chr3qtel1M 852241 AGAAAAAAAGAAAAAAACCTGAGAAAGAAAACAAAAATGCAAGCAAACAA 852290 i i -vvi iv i v v - v (AGAA)n#Simpl 1 AGAAAGAAAGAAAGAAA-GAAAGAAAGAAAGAAAGAAAGAAAG-AAAGAA 48 chr3qtel1M 852291 TAACAGAAAGA 852301 vi v (AGAA)n#Simpl 49 AGAAAGAAAGA 59 Matrix = Unknown Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.03 (2 / 60), avg. gap size = 1.00 (2 / 2) 1550 27.02 1.65 2.21 chr3qtel1M 852556 853100 (146900) C L1ME3G_3end#LINE/L1 (376) 548 7 m_b159s551i0 5968 chr3qtel1M 852556 ATAATATTCCATAGAATTCATACACCACAATTTATTCAGCCATTCTCCAA 852605 i v vv i i i i i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr3qtel1M 852606 TTGATGGGCATCCACTTGGTTTCCAGTTTCTTGCCACTACAAAAAGGGCT 852655 i ii vv v i i i i i v iv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr3qtel1M 852656 GCCCCAAACATTTTTGCACATGTGGGTCCCTTTTCTTCCTCTGAGA---T 852702 vvii ii i i?---i v viv v v v --- C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACATGCN---TCCTTGTGCACATGTGCGAGTAT 402 chr3qtel1M 852703 CTCTTTGGAATATAAGCCCAGTAGAAACACTGCTGGGTCAAAGGGTATGC 852752 i ? i i v v? ? v viiv i C L1ME3G_3end#L 401 TTCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGC 352 chr3qtel1M 852753 ACAGTGTGATAACTTTTTTAAT--ATAGTTTCAAATTGCTCTCCAGAATG 852800 i v v i - ---- -- v vi i i ? C L1ME3G_3end#L 351 GCATTTTAA-A----TTTTAATAGATACTGCCAAATTGCCCTCCAAAANG 307 chr3qtel1M 852801 ATTGGATTTATTCATAATTCTACCAACAGTGTATCAGTGTCCCAGTTTTC 852850 ii v iiv i i v i i i v v v v i C L1ME3G_3end#L 306 GCTGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCC 257 chr3qtel1M 852851 CCACA---TCTCCAACATTCGTCATTATTTTTTCCTGTCATTTTAGCCAA 852897 --- v i ? vi ivv?iii vvv v C L1ME3G_3end#L 256 CCACACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAA 207 chr3qtel1M 852898 TCTGAGAGGTGTATAGTGGTATCTCAGAATTGTCTTAATTTG-ATTTCTC 852946 vi v v i vvi i - i C L1ME3G_3end#L 206 TCTGATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCC 157 chr3qtel1M 852947 TGATCAATAGTAATTTGGAGCACCTTTTCATGTGGCTACAGATAGTTTCA 852996 i v i vv v i i vi iv iivi vv C L1ME3G_3end#L 156 TGATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGT 107 chr3qtel1M 852997 ATTTCTTTATCTGAAAATTGTCTGTTTATGTCCTTTGACCATTTATCAAT 853046 i iv vi i i i v v v C L1ME3G_3end#L 106 ATTTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTAT 57 chr3qtel1M 853047 GGGAGAATGACTTGATTTCTTATAAATTTGAATCAATTCTCTGTATAATT 853096 v iv-- v -- vi v vv i i i v i C L1ME3G_3end#L 56 TGGGT--TGTCTT--TTTCTTATTGATTTGTAGGAGTTCTTTATATATTC 11 chr3qtel1M 853097 TGGA 853100 C L1ME3G_3end#L 10 TGGA 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.98 CpG sites = 76, Kimura (unadjusted) = 34.56 Transitions / transversions = 1.12 (76/68) Gap_init rate = 0.03 (16 / 544), avg. gap size = 1.31 (21 / 16) 521 32.07 5.16 3.38 chr3qtel1M 852964 853602 (146398) C L1M5_orf2#LINE/L1 (7) 3287 2638 m_b159s551i1 5968 chr3qtel1M 852964 GAGCACCTTTTCATGTGGCTACAGATAGTTTCAATTTCTTTATCTGAAAA 853013 i vi iv iivi v? v iv i vi C L1M5_orf2#LIN 3287 GAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTTTTGTGAA 3238 chr3qtel1M 853014 TTGTCTGTTTATGTCCTTTGACCATTTATCAATGGGA--GAATGACTTGA 853061 v i v i v v ?v v i-- vv v -- C L1M5_orf2#LIN 3237 GTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTTGTCTT-- 3190 chr3qtel1M 853062 TTTCTTATAAATTTGAATCAATTCTCTGTATAATTTGGAAATGAGGTCTT 853111 ? vi ? v vv i i i v i v i vi C L1M5_orf2#LIN 3189 TTTNTTATTGANTTGTAGGAGTTCTTTATATATTCTGGATACGAGTCCTT 3140 chr3qtel1M 853112 TATCAGAACCCTTGAATGTAAAAACGTTTCCCCAGTTTATTGCTTCTCTT 853161 i vviv vv?v i v iv ii ? i i v vi C L1M5_orf2#LIN 3139 TGTCAGATATATGTNTTGCAAATATTTTCTCCCANTCTGTGGCTTGCCTT 3090 chr3qtel1M 853162 CTAATCTTGTCTGCATTAGTTTTGTTTGTACAAAAACTTTTA-------- 853203 i v i v ivi iv ivi vvv? vi i ii -------- C L1M5_orf2#LIN 3089 TTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTTTAATTTTGAT 3040 chr3qtel1M 853204 -TAATCAAAATTATC-----TCTATTTTGTGATCAATAATGATCTTTAGT 853247 -? i v v ----- i v i i --- ?i v i - C L1M5_orf2#LIN 3039 GNAGTCCAATTTATCAATTTTTTCTTTTATGGT---TNGTGCTTTTT-GT 2994 chr3qtel1M 853248 TAGTCTTTGGTCACAAATTCCTT-CCT-CCTCAA-ATCTGAAAGGTAAAC 853294 -- -i v i vi v i - -? i -i vvi i -- i C L1M5_orf2#LIN 2993 --GTC-CTGTTTAAGAAATCTTTGCCTANCCCAAGGTCACGAAGAT--AT 2949 chr3qtel1M 853295 TATCCTATA--TTCTTCTAATTTATTTATAATCTTATTCTTTATGTCTAG 853342 v i-- ivvvv i i ?ii ii i C L1M5_orf2#LIN 2948 TCTCCTATGTTTTCTTCTAGAAGTTTTATAGTTTTANCTTTTACATTTAG 2899 chr3qtel1M 853343 ATC-ATGACCCATTTCGACCTTATCTTGGTATACGGTGTTAAGTATGGGT 853391 i - i i ? vi v i v i i v i v C L1M5_orf2#LIN 2898 GTCTATGATCCATCTNGAATTAATTTTTGTGTATGGTGTGAGGTAGGGGT 2849 chr3qtel1M 853392 CAATGCCTAGTTTCAACCATGCTGATTTCCAATTTTTCCTGCAGTTTTTG 853441 i v?iii v ivv iiv v v v viv C L1M5_orf2#LIN 2848 CGAGNTTCATTTTTTTCCATATGGATATCCAATTGTTCCAGCACCATTTG 2799 chr3qtel1M 853442 TCAAATAATGAATTCTTATCCCAAAAGCTGGGGT-CTTTGG---GTTTGT 853487 ii v ivvv i vi ---- iiv - ? ---v C L1M5_orf2#LIN 2798 TTGAAAAGACTATCCTTTCCCCA----CTGAATTGCNTTGGCACCTTTGT 2753 chr3qtel1M 853488 CAAACACTAGATTGCTATAGTCATTT---TCTATTTTGTTCTGTGAAC-- 853532 v ii i? v? i vvii v --- i------ i -- C L1M5_orf2#LIN 2752 CAAAAATCAANTGNCCATATATGTGTGGGTCTATTTC------TGGACTC 2709 chr3qtel1M 853533 -CTAACTTATTCCAGTCTTCAACTAGTTTATTTCTTA-GCCAATACCAAA 853580 - vii i v vv v i v i - i - v C L1M5_orf2#LIN 2708 TCTATTCTGTTCCATTGATCTATTTGTCTA-TCCTTACGCCAATACCACA 2660 chr3qtel1M 853581 TGGTTTTGATGACCACTGCTTT 853602 iv i v iiiv C L1M5_orf2#LIN 2659 CTGTCTTGATTACTGTAGCTTT 2638 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.14 CpG sites = 105, Kimura (unadjusted) = 44.33 Transitions / transversions = 1.13 (105/93) Gap_init rate = 0.06 (37 / 638), avg. gap size = 1.49 (55 / 37) 476 27.04 2.49 2.49 chr3qtel1M 854106 854306 (145694) C L1MC4_3end#LINE/L1 (2156) 633 433 m_b159s551i2 5969 chr3qtel1M 854106 GCTCATTTCACTCAGCATCAGTTCGTGTAAGTCTC-TCCAGGCCTTTCTG 854154 iv i v? - v i v vi - v ii? vi C L1MC4_3end#LI 633 GCTTCTTTCACTTAGCAANA-TGCATTTAAGATTCATCCATGTTNTTGCG 585 chr3qtel1M 854155 -AAATCATCCTGTTGGTCATTTCTT---ACAGAACAGTAATATTCCATAA 854200 -i? ---- v v i --- iv vvv i vi C L1MC4_3end#LI 584 TGNATCA----GTAGTTCATTCCTTTTTATCGCTGAGTAGTATTCCATTG 539 chr3qtel1M 854201 TATTCATATACCACAATTTATTCAGCCATTCTCCAACTGAAGGACATCCA 854250 vv i i i i v v vii i? C L1MC4_3end#LI 538 TATGGATGTACCACAGTTTGTTTATCCATTCACCTGTTGAAGGACATCTN 489 chr3qtel1M 854251 TTCAGTTTCCAGTTTCTAGCCACTACAAAAAGGGCTGCCACAAACATTCG 854300 vviv ? i i ? i ii v ii i i C L1MC4_3end#LI 488 GGTTGTTTCCAGNTTTTGGCNATTATGAATAAAGCTGCTATAAACATTCG 439 chr3qtel1M 854301 TGCACA 854306 i C L1MC4_3end#LI 438 TGTACA 433 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.81 CpG sites = 30, Kimura (unadjusted) = 35.64 Transitions / transversions = 1.30 (30/23) Gap_init rate = 0.04 (8 / 200), avg. gap size = 1.25 (10 / 8) 248 30.21 4.23 2.07 chr3qtel1M 854186 854327 (145673) C L1MB2_3end#LINE/L1 (365) 553 409 m_b159s551i4 5969 chr3qtel1M 854186 AGTAATATTCCATAATATTCATATACCACAATTTATTCAGCCATTC-TCC 854234 i vi vi v i i v - C L1MB2_3end#LI 553 AATAATATTCCATTGTATGTATATACCACATTTTGTTTATCCATTCATCC 504 chr3qtel1M 854235 AACTGAAGGACATCCATTCAGTTTCCAGTTTCTAGCCACTACAAAAAGGG 854284 iv - v iiiivviv i vi ii i i i iii v iv C L1MB2_3end#LI 503 GTC-GATGGACACTTGGGTTGCTTCCACCTCTTGGCTATTGTGAATAATG 455 chr3qtel1M 854285 CTGCCACAAACAT--TCGTGCACATA---CAGCGATGACCACTGCTTT 854327 i ii --vi v --- vv - - C L1MB2_3end#LI 454 CTGCTATGAACATGGGTGTGCAAATATCTCTTCGA-GACC-CTGCTTT 409 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.88 CpG sites = 26, Kimura (unadjusted) = 40.13 Transitions / transversions = 1.62 (26/16) Gap_init rate = 0.04 (6 / 141), avg. gap size = 1.50 (9 / 6) 523 25.62 0.00 0.00 chr3qtel1M 854186 854306 (145694) C L1MD1_3end#LINE/L1 (436) 553 433 m_b159s551i3 5969 chr3qtel1M 854186 AGTAATATTCCATAATATTCATATACCACAATTTATTCAGCCATTCTCCA 854235 i ii vv i i i i i v v C L1MD1_3end#LI 553 AGTAGTATTCCATGGTATGGATGTACCACAGTTTGTTTAACCATTCACCC 504 chr3qtel1M 854236 ACTGAAGGACATCCATTCAGTTTCCAGTTTCTAGCCACTACAAAAAGGGC 854285 ii iivviv i i i i i v ii C L1MD1_3end#LI 503 GTTGAAGGACATCTGGGTTGTTTCCAGTTTTTGGCTATTACGAATAAAGC 454 chr3qtel1M 854286 TGCCACAAACATTCGTGCACA 854306 i i i C L1MD1_3end#LI 453 TGCTATAAACATTCGTGTACA 433 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 30.48 CpG sites = 23, Kimura (unadjusted) = 33.10 Transitions / transversions = 2.88 (23/8) Gap_init rate = 0.00 (0 / 120), avg. gap size = 0.0 (0 / 0) 519 30.23 4.79 2.34 chr3qtel1M 854313 854688 (145312) C L1PB_orf2#LINE/L1 (642) 2652 2268 m_b159s551i5 5970 chr3qtel1M 854313 GATGACCACTGCTTTATAAAATAGTTTTAGGTCTGCTACAGCTGGGCCAC 854362 i i iv i iv v i v v v--- v vii C L1PB_orf2#LIN 2652 GGTGACTATGGCCTTATAGTATAGTTTGAAGTCGGGTAA---TGTGATGC 2606 chr3qtel1M 854363 CTTCA--TTTGATTTTTTTTTCCATTAGT--TCCCTTGAA-ATTCTTGAC 854407 i -- -- i v - -- v i iv- v vv vi C L1PB_orf2#LIN 2605 CTCCAGATTTG--TTCTTTTTGC-TTAGTCTTGCTTTGGCTATGCGGGCT 2559 chr3qtel1M 854408 CTTTTGTTCTTCCATATGAATTTTGTTGTTATTTTTTCTAGATTAGTAAA 854457 v vv ivvi i v iv i C L1PB_orf2#LIN 2558 CTTTTTTGGTTCCATATGAATTTTAGGATTGTTTTTTCTAGTTCTGTGAA 2509 chr3qtel1M 854458 ATAGTTTTTTGGTAGTTTGATTGGGATAGCATTAAATAAATAGATTAGTT 854507 iv vvv vv v v i v i vvi iv C L1PB_orf2#LIN 2508 GAATGATGGTGGTATTTTGATGGGAATTGCATTGAATTTGTAGATTGCTT 2459 chr3qtel1M 854508 TAGGTAGTATTGTCATCTTTATTATATTCACTTGACCTATCCAAGAGCGC 854557 v i v i i iv v i iv i v ii C L1PB_orf2#LIN 2458 TTGGCAGTATGGTCATTTTCACAATATTGATTCTACCCATCCATGAGCAT 2409 chr3qtel1M 854558 TTAATAT-TTTTCAAATGTTTAGATCTGACT-TGATTT---------GTG 854596 vvi i - i vv ivi - v - --------- C L1PB_orf2#LIN 2408 GGGATGTGTTTCCATTTGTTTGTGTC-GTCTATGATTTCTTTCAGCAGTG 2360 chr3qtel1M 854597 TTTTGTAGTTTTGCTCATATAGTTC-CTGACTTTCCCTTGG-CAGATGGA 854644 v ii v v -i v i -- -i i iv C L1PB_orf2#LIN 2359 TTTTGTAGTTTTCCTTGTAGAGGTCTTTCACCT--CCTTGGTTAGGTATA 2312 chr3qtel1M 854645 TTTCCAGATATTTTATACTATCGACAGGTACTTTAAATGGAATT 854688 i i ii vi v ivi v i v v ii C L1PB_orf2#LIN 2311 TTCCTAAGTATTTTATTTTTTTTGCAGCTATTGTAAAAGGGGTT 2268 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.15 CpG sites = 54, Kimura (unadjusted) = 39.15 Transitions / transversions = 0.95 (54/57) Gap_init rate = 0.05 (17 / 375), avg. gap size = 1.59 (27 / 17) 17 11.59 0.00 0.00 chr3qtel1M 854748 854776 (145224) (CTCC)n#Simple_repeat 1 29 (0) m_b159s252i2 5971 chr3qtel1M 854748 CTCCTTCTCTTCCTCCCTCCCTCCCTCCC 854776 i i i (CTCC)n#Simpl 1 CTCCCTCCCTCCCTCCCTCCCTCCCTCCC 29 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 17 19.31 4.26 0.00 chr3qtel1M 854892 854938 (145062) (AGAA)n#Simple_repeat 1 49 (0) m_b159s252i3 5972 chr3qtel1M 854892 AGAAAGAAAGAAA-AAA-AAGGAAACAAACAACAAAATAAAGATAAAAA 854938 - - i v v vi v v i (AGAA)n#Simpl 1 AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 49 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.04 (2 / 46), avg. gap size = 1.00 (2 / 2) 237 29.33 1.33 0.00 chr3qtel1M 855395 855469 (144531) C L1PA4_3end#LINE/L1 (580) 322 247 m_b159s551i6 5973 chr3qtel1M 855395 ACTTGCA-AATAGAGGGATCATTTCATAGCTCCACCAACAATGCATTAGT 855443 v - i vv i ii v i i ii i i vv C L1PA4_3end#LI 322 ACTTCCACAATGGTTGAACTAGTTTACAGTCCCACCAACAGTGTAAAAGT 273 chr3qtel1M 855444 GTCCCAGTTTTCCCACATCTTCTCCA 855469 i vi ii i C L1PA4_3end#LI 272 GTTCCTATTTCTCCACATCCTCTCCA 247 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.16 CpG sites = 15, Kimura (unadjusted) = 39.16 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.01 (1 / 74), avg. gap size = 1.00 (1 / 1) 60 0.00 0.00 0.00 chr3qtel1M 855999 856049 (143951) (TA)n#Simple_repeat 1 51 (0) c_b159s251i0 5974 chr3qtel1M 855999 TATATATATATATATATATATATATATATATATATATATATATATATATA 856048 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr3qtel1M 856049 T 856049 (TA)n#Simple_ 51 T 51 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 294 30.18 18.12 1.56 chr3qtel1M 856754 857029 (142971) C L2c_3end#LINE/L2 (10) 468 148 m_b159s601i0 5975 chr3qtel1M 856754 TCAGCAA-CAT--ATTCAACAGCTGCTTGTGTTTTAGGTGATGGGGAC-C 856799 i - -- v i iv i -i vii i v i- C L2c_3end#LINE 468 TCAACAAACATTTATTGAGCGCCTACT-ATGTGCCAGGCGCTGGGGATAC 420 chr3qtel1M 856800 AAAAAGGTA-AAAACACAGCACCTTGTCCTCAAGAACCTCATGATCGAAT 856848 i v v - i i i- i i i v iii v i C L2c_3end#LINE 419 AAAGATGAATAAGACACGGT-CCCTGCCCTCAAGGAGCTCACAGTCTAGT 371 chr3qtel1M 856849 GAGGAAAACA-----GTGGGCTAGCAATTATAA-ACAAGGTACATG--CA 856890 ii i i ----- iii vii i - v - --v C L2c_3end#LINE 370 GGAGGAGACAGACANGTAAACAGACAATTACAATACAAGTTA-ATGATAA 322 chr3qtel1M 856891 G-GGTA-AATTGGAG-------ATGATGTT----------AGAAGAAAGA 856921 - v - v ------- v i i ---------- i ii v C L2c_3end#LINE 321 GTGCTATAATGGGAGTATAGACAGGGTGCTATGGGAGCACAGAGGAGGGC 272 chr3qtel1M 856922 TCCTCG--CAG---TGGAGGGAACTGAGGAAGGCTTCTTGCAGGAGGTGG 856966 v v --i --- i --iiii ii v i C L2c_3end#LINE 271 ACCTAGACTAGNCTTGGGGGG--TCAGGGAAGGCTTCCCGGAGGAGGTGA 224 chr3qtel1M 856967 GATTT--GC--AGTATTCAGGG--GAACAAGG-------AGGTGAAGGTG 857003 v i -- -- ?v v i -- ii i i------- i i vi C L2c_3end#LINE 223 CATCTGAGCTGAGNCTTGAAGGATGAGTAGGAGTTAGCCAGGTGGAAGGA 174 chr3qtel1M 857004 AGGAGGGAGAACATTTTAGGCAAAGG 857029 i i i i ii i C L2c_3end#LINE 173 GGGGGGAAGAGCATTCCAGGCAGAGG 148 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.03 CpG sites = 60, Kimura (unadjusted) = 41.77 Transitions / transversions = 2.73 (60/22) Gap_init rate = 0.08 (22 / 275), avg. gap size = 2.50 (55 / 22) 310 29.63 3.70 0.00 chr3qtel1M 857168 857275 (142725) MIRc#SINE/MIR 3 114 (154) m_b159s601i1 5976 chr3qtel1M 857168 AGGTAG-ATGGTGCACTGGATAGAGCTCTGGCCCTGGGGTCA-GAGGACC 857215 i -i v v v v i i - i MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chr3qtel1M 857216 TGAGTTCAAATGTGATCCCAGATGCTTCCTGGCTGTGGGACAACAAGTGA 857265 i i i viviv i v vii v i v vviii ii MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 102 chr3qtel1M 857266 GTCAC--AACCT 857275 -- MIRc#SINE/MIR 103 GTCACTTAACCT 114 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.78 CpG sites = 19, Kimura (unadjusted) = 38.84 Transitions / transversions = 1.46 (19/13) Gap_init rate = 0.03 (3 / 107), avg. gap size = 1.33 (4 / 3) 341 34.65 3.33 2.20 chr3qtel1M 857332 857511 (142489) C L2#LINE/L2 (212) 2870 2689 m_b159s601i2 5975 chr3qtel1M 857332 GAGTTA-ATGGAGCCTCATTGAAACTTTCTGACTAGGGAGAGCAACATCA 857380 v - iivvi i ivv i vi i - ii v C L2#LINE/L2 2870 GAGTGAGATGGGAAGCCATTGGAGGGTTTTGAGCAGAG-GAGTGACATGA 2822 chr3qtel1M 857381 TTAAACTTTCCTGTGAGATAGATGACCTTGGCTGGTGGGTGAAGGATGAA 857430 ivi v v v v i vi v ii v v vi i ii C L2#LINE/L2 2821 TCTGACTTACGTTTTAAAAGGATCACTCTGGCTGCTGTGTTGAGAATAGA 2772 chr3qtel1M 857431 CT----GGAGTTAAGGGTGCTTGAAGTAGGAAGATGACTCAGCAGGCTAT 857476 ---- i vi --- i i iv v i v C L2#LINE/L2 2771 CTGNAGGGGGGCAAGGGTG---GAAGCAGGGAGACCAGTTAGGAGGCTAT 2725 chr3qtel1M 857477 TGGGACAA-CCAGGTGTGAAGTGATAAAGGCCCAGA 857511 viii - i v ii iiv iii C L2#LINE/L2 2724 TGCAGTAATCCAGGCGAGAGATGATGGTGGCTTGGA 2689 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 47.51 CpG sites = 37, Kimura (unadjusted) = 48.65 Transitions / transversions = 1.54 (37/24) Gap_init rate = 0.04 (7 / 179), avg. gap size = 1.43 (10 / 7) 282 33.88 12.19 3.16 chr3qtel1M 857488 857807 (142193) C L2#LINE/L2 (416) 2666 2319 m_b159s601i3 5975 chr3qtel1M 857488 GGTGTGAAGTGATAAAGGCCCAGAGA-AGTTAGGAGTCAAGCCCCATAGA 857536 v i viiivi ii v - v v i vi iiv v i i C L2#LINE/L2 2666 GGTGAGAAGTGGTCGGATTCTGGATATATTTTGAAGGTAGAGCCGACAGG 2617 chr3qtel1M 857537 ACTTGGTAATAGGTTGGCTATTGGGGTGGTGGTGAAGGAGAGTGAGCAGT 857586 i v i i i v i - ---- ii i v v C L2#LINE/L2 2616 ATTTGCTGATGGATTGGATGT-GGGGTG----TGAGAGAAAGAGAGGAGT 2572 chr3qtel1M 857587 TGAGAATGAAGTCCAAG---------CTG--TAAGTG--AGGATGGGTGT 857623 ii i v- --------- --i v -- ivv C L2#LINE/L2 2571 CAAGGATGAC-TCCAAGGTTTTTGGCCTGAGCAACTGGAAGGATGGAGTT 2523 chr3qtel1M 857624 GCTCTCAACTTCCTTAATAGGGAA--TTTAGGAGGGAGT-GGT-----GG 857665 iv i? vv---i i --i vv ii i- ----- C L2#LINE/L2 2522 GCCATTNACTGA---GATGGGGAAGACTGCGGGAGGAGCAGGTTTGAGGG 2476 chr3qtel1M 857666 TGAAGA-----------ATTTGGGA--TGCTGAATTTGAAACAGCTG--- 857699 v -----------i v -- i i i i iiv i--- C L2#LINE/L2 2475 GGAAGATCAGGAGTTCAGTTTTGGACATGTTAAGTTTGAGATGCCTATTA 2426 chr3qtel1M 857700 GACTGGCCCAGTTGAAGATGTTTAATAGACAGCTGGTTCT-CAAGACTAG 857748 --ii iv i iv i i i v v - i v i C L2#LINE/L2 2425 GAC--ATCCAAGTGGAGATGTCGAGTAGGCAGTTGGATATACGAGTCTGG 2378 chr3qtel1M 857749 AGGCTGGGAAAGAGATTAATGCTAGATAAATGAATTTGAAGATCATCTTT 857798 viii ii i iviv i v v i iiii vvi C L2#LINE/L2 2377 AGTTCAGGGGAGAGGTCCGGGCTGGAGATATAAATTTGGGAGTCATCAGC 2328 chr3qtel1M 857799 ATAGAGATG 857807 v C L2#LINE/L2 2327 ATATAGATG 2319 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 45.38 CpG sites = 67, Kimura (unadjusted) = 47.96 Transitions / transversions = 1.76 (67/38) Gap_init rate = 0.07 (22 / 319), avg. gap size = 2.27 (50 / 22) 217 30.07 7.26 0.76 chr3qtel1M 857893 858016 (141984) C L2#LINE/L2 (917) 2165 2034 m_b159s601i4 5975 chr3qtel1M 857893 AGAGAGGGAAGAGGGAAATCGGGAGAA---AGCACCCTGAAAACCTAGAG 857939 v v i i i i i---i iii i i v v C L2#LINE/L2 2165 AGTGAGGTAGGAGGAAAACCAGGAGAGTGTGGTGTCCTGGAAGCCAAGTG 2116 chr3qtel1M 857940 AGAAGAG-ATCTCA----GAAGTGGGTAATTCAC-ATGGCAAAGGCTATG 857983 ii i -i i ---- i v i i iv -i v v iiv C L2#LINE/L2 2115 AAGAAAGTGTTTCAAGAAGGAGGGAGTGATCAACTGTGTCAAATGCTGCT 2066 chr3qtel1M 857984 GAGAGGTCAAGAAAGAGGAGGATTTAAAAATTG 858016 ? v v -i i i C L2#LINE/L2 2065 GANAGGTCAAGTAAGATGAGGA-CTGAGAATTG 2034 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.30 CpG sites = 26, Kimura (unadjusted) = 41.30 Transitions / transversions = 2.36 (26/11) Gap_init rate = 0.04 (5 / 123), avg. gap size = 2.00 (10 / 5) 223 27.24 19.63 3.17 chr3qtel1M 858041 858203 (141797) MIRb#SINE/MIR 7 195 (73) m_b159s601i5 5977 chr3qtel1M 858041 GGCAGCTAGGTG--GCTGAGTGAGTG-GCTCTTTTGAGTCTGGAAGTTCT 858087 vv -- iv iv ii- vv v v iv vi MIRb#SINE/MIR 7 GGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCT 56 chr3qtel1M 858088 GAGTTTTTGAATCCTATTT--------TAATAGCTGTGGGACT----ATA 858125 i i-- iivi -------- v v i----ii MIRb#SINE/MIR 57 GGGTTC--GAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 104 chr3qtel1M 858126 A--TGCTTA----------GCCTCAGTTTCCTTATCTTTAAAATGCTAAT 858163 -- i ---------- i v vvi MIRb#SINE/MIR 105 AGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGAT 154 chr3qtel1M 858164 GACAGCACCTA-----TGGGGATGTTCAAATGAAGGATTAGATAA 858203 i i ii -----ii v ---i - i i MIRb#SINE/MIR 155 AATAATACCTACCTCGCAGGGTTGTT---GTG-AGGATTAAATGA 195 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.93 CpG sites = 26, Kimura (unadjusted) = 35.05 Transitions / transversions = 1.53 (26/17) Gap_init rate = 0.08 (13 / 162), avg. gap size = 2.92 (38 / 13) 254 16.36 11.27 5.33 chr3qtel1M 858133 858203 (141797) MIR#SINE/MIR 117 191 (71) m_b159s601i6 5977 chr3qtel1M 858133 GCCTCAGTTTCCTTATCTTTAAAATGC---TAATGACAGCACCT-----A 858174 i v v--- i i i ----- MIR#SINE/MIR 117 GCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTCA 166 chr3qtel1M 858175 TGGGGATGTTCAAATGAAGGATTAGATAA 858203 i v ---i - i i MIR#SINE/MIR 167 TAGGGTTGTT---GTG-AGGATTAAATGA 191 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 19.02 CpG sites = 8, Kimura (unadjusted) = 19.02 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.09 (6 / 70), avg. gap size = 2.00 (12 / 6) 14 17.23 2.44 2.44 chr3qtel1M 858318 858358 (141642) (AAAAAAG)n#Simple_repeat 1 41 (0) m_b159s252i4 5978 chr3qtel1M 858318 AAGAAAG-AATAAGCAAAAAGAAAAACAGAAAAACAAAAGAA 858358 i - v v - vi i (AAAAAAG)n#Si 1 AAAAAAGAAAAAAGAAAAAAGAAAAA-AGAAAAAAGAAAAAA 41 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 258 17.39 0.00 0.00 chr3qtel1M 860034 860079 (139921) C HERV35I#LTR/ERV1 (36) 6882 6837 m_b159s701i0 5979 chr3qtel1M 860034 GGGGGCAGGGGCAATGATCTCATCTTCTGAAACTTCTTCCTGCTGA 860079 i iv v i v i v C HERV35I#LTR/E 6882 GGAGAAAGGGCCGAAGATCTCATCTTCTGAAGCTACTTCCTGCTGA 6837 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 17.31 CpG sites = 4, Kimura (unadjusted) = 19.89 Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 250 20.78 0.00 3.77 chr3qtel1M 860042 860096 (139904) C MER83A-int#LTR/ERV1 (41) 4225 4173 m_b159s701i1 5979 chr3qtel1M 860042 GGGCAATGATCTCATCTTCTGAAACTTCTTCCTGCTGAGAATGGGCATAG 860091 ii v i i-- v vv v i C MER83A-int#LT 4225 GGGTGAAGGTCTCATCTTCC--AACTGCTTCCTGCTGACCAGGGGCGTAG 4178 chr3qtel1M 860092 AGCTG 860096 i C MER83A-int#LT 4177 AGTTG 4173 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 22.13 CpG sites = 6, Kimura (unadjusted) = 24.57 Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.04 (2 / 54), avg. gap size = 1.00 (2 / 2) 228 24.32 22.52 0.00 chr3qtel1M 863354 863464 (136536) C MIRb#SINE/MIR (46) 222 87 m_b159s601i7 5980 chr3qtel1M 863354 TATGCTAAACACTTT---TGCA----ATCATGTGATCTTCATGATAACAA 863396 i i i --- ----v v i i ii i vv C MIRb#SINE/MIR 222 TGTGCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCC 173 chr3qtel1M 863397 T-C--------TATTATT-TCTC---TTTACAAATCAGAAAACTGAG--- 863430 - -------- - i --- i v i --- C MIRb#SINE/MIR 172 TGCGAGGTAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCT 123 chr3qtel1M 863431 CAGAGA--TAAAATGATTTGCCATAAATTACATAAC 863464 -- v i i i vv ii i i i C MIRb#SINE/MIR 122 CAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGC 87 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.28 CpG sites = 19, Kimura (unadjusted) = 30.65 Transitions / transversions = 2.38 (19/8) Gap_init rate = 0.07 (8 / 110), avg. gap size = 3.12 (25 / 8) 14 17.22 5.13 0.00 chr3qtel1M 865786 865824 (134176) (ATCAT)n#Simple_repeat 1 41 (0) m_b159s252i5 5981 chr3qtel1M 865786 ATCA-ATCTTAT-ATTTTATATCATATCTTATTATATCCTA 865824 - v - v i v i v (ATCAT)n#Simp 1 ATCATATCATATCATATCATATCATATCATATCATATCATA 41 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2) 14 15.31 2.63 2.63 chr3qtel1M 865790 865827 (134173) (ATCTTAT)n#Simple_repeat 1 38 (0) m_b159s252i6 5981 chr3qtel1M 865790 ATCTTATATTTTATATCATATCTTATTATATCCTA-ATC 865827 i v -v v i - (ATCTTAT)n#Si 1 ATCTTATATCTTATATCTTAT-ATCTTATATCTTATATC 38 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 16 0.00 0.00 0.00 chr3qtel1M 867077 867094 (132906) (T)n#Simple_repeat 1 18 (0) m_b159s252i7 5982 chr3qtel1M 867077 TTTTTTTTTTTTTTTTTT 867094 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTT 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 648 29.69 2.18 0.00 chr3qtel1M 867737 867965 (132035) C L1M5_orf2#LINE/L1 (1099) 2195 1962 m_b159s551i7 5983 chr3qtel1M 867737 TTATATCTTGCAGTTTTGGTAGAGCTACGAGTTGTTTCCAATAGGTTTTT 867786 i i? iiii v i vii vvi iv i i v ? C L1M5_orf2#LIN 2195 TTGTATCCNGCGACCTTGCTAAATTCACTTATTAGTTCTAGTAGTTTNTT 2146 chr3qtel1M 867787 GGATGATTTTCTTGGATTCTCTAAGTATATCATCATATCATTTGGAAAGA 867836 v vv i i ? i v ? iv i i vi v C L1M5_orf2#LIN 2145 TGTAGATTCTTTNGGATTTTCTACGTANACAATCATGTCATCTGCGAATA 2096 chr3qtel1M 867837 ACGATAGTTTTATTTTCTCATTGCCTGTTCTAATTCC-----TTTATTTT 867881 ? i ii v v vi ii v v ----- v C L1M5_orf2#LIN 2095 ANGACAGTTTTATTTCTTCCTTTCCAATCTTTATGCCTTTTATTTCTTTT 2046 chr3qtel1M 867882 TCTTTTCTTATTGCTAAAGCCAACATTTCTAGTACAATACTGAATAATAG 867931 vi vvvi i iv ii i ii iv C L1M5_orf2#LIN 2045 TCTTGCCTTATTGCACTGGCTAGGACCTCCAGTACAATGTTGAATAGAAG 1996 chr3qtel1M 867932 TGATGATAATGGACATCCTTGTTTCATTCCTGAT 867965 i ? ii i ii i C L1M5_orf2#LIN 1995 TGGTGANAGCGGACATCCTTGTCTTGTTCCCGAT 1962 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.67 CpG sites = 43, Kimura (unadjusted) = 40.78 Transitions / transversions = 1.72 (43/25) Gap_init rate = 0.00 (1 / 228), avg. gap size = 5.00 (5 / 1) 20 30.77 2.74 0.00 chr3qtel1M 867970 868042 (131958) (TTTC)n#Simple_repeat 1 75 (0) m_b159s252i8 5984 chr3qtel1M 867970 TTCCTTCCTTTC-TCCCTCCCTCCCTCCCTTCCTTC-TTCTTTCTTCCTT 868017 i i - i i i i i i i i i - i (TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 50 chr3qtel1M 868018 CCTCTATTCCTCTCTTTCTTTCTTT 868042 i i v i i (TTTC)n#Simpl 51 TCTTTCTTTCTTTCTTTCTTTCTTT 75 Matrix = Unknown Transitions / transversions = 16.00 (16/1) Gap_init rate = 0.03 (2 / 72), avg. gap size = 1.00 (2 / 2) 225 24.15 8.60 2.02 chr3qtel1M 870631 870723 (129277) C MIRc#SINE/MIR (4) 264 166 m_b159s601i8 5985 chr3qtel1M 870631 ATACTAATAACTAATATTTCTA-AAAATTTTAAAGTTTTACAAAGTACTT 870679 v i?v v i v - iv i v - ii C MIRc#SINE/MIR 264 ATAATAACNCCTTACATTTGTATAGCACTTTACAGTTT-ACAAAGCGCTT 216 chr3qtel1M 870680 T-ACAGAT------TCATTTGATTCTCACAAACAAATCTAGAAGGTAGAT 870722 - v i------ i - vi ivi ii C MIRc#SINE/MIR 215 TCACATACATTATCTCATTTGATCCTCAC-AACAACCCTGTGAGGTAGGC 167 chr3qtel1M 870723 A 870723 C MIRc#SINE/MIR 166 A 166 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.42 CpG sites = 13, Kimura (unadjusted) = 30.20 Transitions / transversions = 1.44 (13/9) Gap_init rate = 0.05 (5 / 92), avg. gap size = 2.00 (10 / 5) 232 21.64 9.84 1.52 chr3qtel1M 870672 870732 (129268) C MIR#SINE/MIR (50) 212 147 m_b159s601i9 5985 chr3qtel1M 870672 AAGTACTTTACA------GATTCATTTGATTCTCACAAACAAATCTAGAA 870715 ii ------i i i i - vi vi C MIR#SINE/MIR 212 AAGCGCTTTACATGTATTAACTCATTTAATCCTCACAA-CAACCCTATGA 164 chr3qtel1M 870716 GGTAGATATTATTTTTA 870732 i i v C MIR#SINE/MIR 163 GGTAGGTACTATTATTA 147 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 24.17 CpG sites = 10, Kimura (unadjusted) = 26.81 Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.03 (2 / 60), avg. gap size = 3.50 (7 / 2) 15 28.44 1.64 1.64 chr3qtel1M 870881 870941 (129059) (AAAAT)n#Simple_repeat 1 61 (0) m_b159s252i9 5986 chr3qtel1M 870881 AAAACATAATTACATGCAGATTAAATAAATGAAAGAAAAATAAAATAAAA 870930 i v v v -v i v vv iv (AAAAT)n#Simp 1 AAAATAAAATAAAAT-AAAATAAAATAAAATAAAATAAAATAAAATAAAA 49 chr3qtel1M 870931 -AATAAAAAGTA 870941 - v v i (AAAAT)n#Simp 50 TAAAATAAAATA 61 Matrix = Unknown Transitions / transversions = 0.40 (4/10) Gap_init rate = 0.03 (2 / 60), avg. gap size = 1.00 (2 / 2) 17 22.52 0.00 0.00 chr3qtel1M 870903 870938 (129062) (A)n#Simple_repeat 1 36 (0) m_b159s252i10 5986 chr3qtel1M 870903 AAATAAATGAAAGAAAAATAAAATAAAAAATAAAAA 870938 v vi i v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 36 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 1372 31.06 1.93 1.28 chr3qtel1M 872105 872727 (127273) C L1ME4c_3end#LINE/L1 (192) 638 12 m_b159s551i8 5987 chr3qtel1M 872105 TCTGCTCATTTCACTTAGCATCAGTTCATGTAAATCTCTCCAAACCTCTC 872154 iv i i vv iv v i - viiiv v C L1ME4c_3end#L 638 TCTGCTTTTTTCACTTAACATTATATCATAAACATTT-TCCATGTTGCTA 590 chr3qtel1M 872155 TGTATTCATCCTGCTGGTCATTTCTTACAGAACAATAATATTCCATAACA 872204 ii v v v iv vi i v ii vvvv vivi C L1ME4c_3end#L 589 CATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCGAG 540 chr3qtel1M 872205 TTTGTATACCACAATTTACCCAATAATTCTCC-ATTGATGGGCATCCATT 872253 ?vi i i ii iv i - v i ii vv C L1ME4c_3end#L 539 TNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAGG 490 chr3qtel1M 872254 CATTTTCCAATTTCTAGCCACTACAAACAGGGCTGCCACAAACATTTTGG 872303 ivv i v i i i i iv v ii i v C L1ME4c_3end#L 489 TTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTCG 440 chr3qtel1M 872304 CACACACAGGTCCCTATCCCTTCTTTAG---TATCTCTTTGGGGTAAAAG 872350 ii i i --- i v i v --- i i i i vv C L1ME4c_3end#L 439 TGCATATAG---CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAATT 393 chr3qtel1M 872351 CCCAGTAGTAGCACTGCTGGATCAAAGGGTATGCACAGTTTGATAACTTT 872400 v i v i i i v v v ii i C L1ME4c_3end#L 392 CCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTCT 343 chr3qtel1M 872401 TTGAGCATAGTTCCAAATTGCTCTCCAGAATGGCTGGGT--GTTCACAAT 872448 vivi i v v i i v i vii--i i ? C L1ME4c_3end#L 342 TGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACANT 293 chr3qtel1M 872449 TCCACCAACAATGTATCAGTGTCTCTGTTTTCCCACATCCCCTCCAATGT 872498 v i v ? vi v iv i ? i v iii C L1ME4c_3end#L 292 GCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGCAT 243 chr3qtel1M 872499 TCCATATTATCTTTCCCTGTCATTCTAGCCAATCTGACAGGTGTGTAGTG 872548 vvi vv iii vvv i v i i i i i iv i C L1ME4c_3end#L 242 TGGGTATTATCAATTTTTTAAATTTTTGCTAATTTAATAGGCGTAAAATG 193 chr3qtel1M 872549 GTATCTCAGAGTTGTCTTAATTTGCATTTCTCTGATTAATAATAACTTGA 872598 vv ii i v iii vv vi C L1ME4c_3end#L 192 GTATCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACTAGCGAGGTTG 143 chr3qtel1M 872599 AACATATTTTCACATGGCTAGAAATAGGTTCAATTTCTTCATCTGAGAA- 872647 v i ii vi ivvv ivi? vv i v ? v - C L1ME4c_3end#L 142 AACATTTTTCCATGTGTTTGTTTACTANTTGTATTTCCTCTTNTGTGAAT 93 chr3qtel1M 872648 -ATCTATTCATATCCTTTGACCATTTATCAATTGGAGAATGGCTTGATTT 872696 -i i i v v i---- v ? C L1ME4c_3end#L 92 TGTCTGTTCATGTCCTTTGCCCATTTATCTATTGGG----GTCTTGATNT 47 chr3qtel1M 872697 T----TTACAAATTAGAGTCAATTCTCTATATATT 872727 ---- iv v i v ii i ? C L1ME4c_3end#L 46 TTTTCTTATCAATTTGAATGAGCTCTTTATATANT 12 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.44 CpG sites = 108, Kimura (unadjusted) = 41.91 Transitions / transversions = 1.30 (108/83) Gap_init rate = 0.02 (14 / 622), avg. gap size = 1.43 (20 / 14) 1499 28.23 1.29 1.66 chr3qtel1M 872189 872732 (127268) C L1ME3G_3end#LINE/L1 (376) 548 7 m_b159s551i9 5987 chr3qtel1M 872189 ATAATATTCCATAACATTTGTATACCACAATTTACCCAATAATTCTCC-A 872237 i ii vvi i iii iv i - C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr3qtel1M 872238 TTGATGGGCATCCATTCATTTTCCAATTTCTAGCCACTACAAACAGGGCT 872287 i ii vvivv i v i i iv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr3qtel1M 872288 GCCACAAACATTTTGGCACACACAGGTCCCTATCC-CTTCTTT-AGTATC 872335 v ii ii v i ii ?-- i i v - v v vi- i C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATT 401 chr3qtel1M 872336 TCTTTGGGGTAAAAGCCCAGTAGTAGCACTGCTGGATCAAAGGGTATGCA 872385 ? i i i v? ? v i v i i i C L1ME3G_3end#L 400 TCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCG 351 chr3qtel1M 872386 CAGTTTGATAACTTTTTGAGCATAGTTCCAAATTGCTCTCCAGAATGGCT 872435 v i -- i vvv - v v i i ? C L1ME3G_3end#L 350 CATTTTAA--ATTTTAATAG-ATACTGCCAAATTGCCCTCCAAAANGGCT 304 chr3qtel1M 872436 GGGT--GTTCACAATTCCACCAACAATGTATCAGTGTCTCTGTTTTCCCA 872483 vii--i i v i i i v v vi i i C L1ME3G_3end#L 303 GTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCA 254 chr3qtel1M 872484 CATCCCCTCCAATGTTCCATATTATCTTTCCCTGTCATTCTAGCCAATCT 872533 i i v iii ?v vv? ii vvv i v C L1ME3G_3end#L 253 CACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATCT 204 chr3qtel1M 872534 GACAGGTGTGTAGTGGTATCTCAGAGTTGTCTTAATTTGCATTTCTCTGA 872583 ii viv i vv i i C L1ME3G_3end#L 203 GATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGA 154 chr3qtel1M 872584 TTAATAATAACTTGAAACATATTTTCACATGGCTAGAAATAGGTTCAATT 872633 v i i vv vi i v i vi vviiiviv vv C L1ME3G_3end#L 153 TTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGTATT 104 chr3qtel1M 872634 TCTTCATCTGAGAA--ATCTATTCATATCCTTTGACCATTTATCAATTGG 872681 i v v --ii i v v v C L1ME3G_3end#L 103 TCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGG 54 chr3qtel1M 872682 AGAATGGCTTGATTTTTTACAAATTAGAGTCAATTCTCTATATATTTTGG 872731 iv-- v -- i ivi v vivv i i i C L1ME3G_3end#L 53 GT--TGTCTT--TTTCTTATTGATTTGTAGGAGTTCTTTATATATTCTGG 8 chr3qtel1M 872732 A 872732 C L1ME3G_3end#L 7 A 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.94 CpG sites = 86, Kimura (unadjusted) = 36.85 Transitions / transversions = 1.32 (86/65) Gap_init rate = 0.03 (14 / 543), avg. gap size = 1.14 (16 / 14) 350 27.69 3.31 1.96 chr3qtel1M 872630 872780 (127220) C L1P3_orf2#LINE/L1 (39) 3255 3103 m_b159s551i10 5987 chr3qtel1M 872630 AATTTCTTCATCTGAGAAAT--CTATTCATATCCTTTGACCATTTATCAA 872677 v v i i -- i i v i v ii C L1P3_orf2#LIN 3255 AATGTCTTCTTTTGAGAAGTGTCTGTTCATATCCTTCGCCCACTTTTTGA 3206 chr3qtel1M 872678 TTGGAGAATGGCTTGATTTT---TTACAAATTAGAGTCAATTCTCTATAT 872724 - i -- v i v --- ii v vv v i ii i v C L1P3_orf2#LIN 3205 -TGGGG--TTGTTTGTTTTTTTCTTGTAAATTTGTTTAAGTTCCTTGTAG 3159 chr3qtel1M 872725 ATTTTGGAAATGAGGCCTTTATCAGAACCTTTGACTGTAAAAATGTTTTC 872774 i v v v i vvvv v i i v i C L1P3_orf2#LIN 3158 ATTCTGGATATTAGCCCTTTGTCAGATGGATAGATTGCAAAAATTTTCTC 3109 chr3qtel1M 872775 CCAATC 872780 v C L1P3_orf2#LIN 3108 CCATTC 3103 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.89 CpG sites = 20, Kimura (unadjusted) = 34.91 Transitions / transversions = 0.95 (20/21) Gap_init rate = 0.03 (5 / 150), avg. gap size = 1.60 (8 / 5) 34 4.44 2.04 2.04 chr3qtel1M 874037 874085 (125915) (TTCC)n#Simple_repeat 1 49 (0) c_b159s251i1 5988 chr3qtel1M 874037 TTCCTTCCTCCCTTCCTTCCTCCCTT-CTTCCCTTCCTTCCTTCCTTCCT 874085 i i - - (TTCC)n#Simpl 1 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTT-CCTTCCTTCCTTCCTTCCT 49 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.04 (2 / 48), avg. gap size = 1.00 (2 / 2) 458 22.87 1.65 6.03 chr3qtel1M 874087 874207 (125793) C MIRc#SINE/MIR (142) 126 11 m_b159s601i10 5985 chr3qtel1M 874087 TAAGGC-AAGTGGGATTAAGTGACTTGCCCAGGATCACACAGCTAAGAAG 874135 i -v v i i i i iv C MIRc#SINE/MIR 126 TGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAG 77 chr3qtel1M 874136 TGTTAAGTATCTGAGGATGGATTTGAACTCAAGTCCTCCTGACTCCAGG- 874184 ---- i --- vvv i i i i i i - C MIRc#SINE/MIR 76 TG----GCA---GAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGT 34 chr3qtel1M 874185 CTGGTATTCTATCCCCAGCACCA 874207 ii ii v v v C MIRc#SINE/MIR 33 CCAGTGCTCTTTCCACTGCACCA 11 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.72 CpG sites = 17, Kimura (unadjusted) = 27.97 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.07 (9 / 120), avg. gap size = 1.00 (9 / 9) 261 17.18 12.30 4.58 chr3qtel1M 876202 876323 (123677) MIR3#SINE/MIR 74 204 (4) m_b159s601i11 5989 chr3qtel1M 876202 CTGACCTTCTGT-TGACATGTGGTCAAGTCACTT---CTCTCTGGGCAT- 876246 i i?v - v - v --- v - MIR3#SINE/MIR 74 CTAACTNGCTGTGTGACCT-TGGGCAAGTCACTTCACCTCTCTGGGCCTC 122 chr3qtel1M 876247 -GTTTTCTCCATC----AACTGAGGGTGATTATA-TGGA-GA-CTCCAAT 876288 - i - ---- v - i iv - i - - i v MIR3#SINE/MIR 123 AGTTTCCT-CATCTGTAAAATGAGGG-GGTTGGACTAGATGATCTCTAAG 170 chr3qtel1M 876289 CTCCCTTTCTACAGCT-TGATG-CCTATGATCCTATG 876323 v i--- - ii-i i MIR3#SINE/MIR 171 GTCCCTTC---CAGCTCTGACATTCTATGATTCTATG 204 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 20.05 CpG sites = 12, Kimura (unadjusted) = 20.05 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.13 (16 / 121), avg. gap size = 1.31 (21 / 16) 230 29.67 3.18 1.25 chr3qtel1M 876449 876605 (123395) L1M1_orf2#LINE/L1 2144 2303 (991) m_b159s551i11 5990 chr3qtel1M 876449 CTAAAAAATGAGTGGAAGCAATCAATAATTTTGGCAAAGTAGCAGAATAT 876498 ? iv v i vii v i v ii i v i i L1M1_orf2#LIN 2144 CNAAAAAACTATTAGAACTGATAAACAAATTCAGTAAAGTTGCAGGATAC 2193 chr3qtel1M 876499 AAAATAAACCCATTTAAATCATCAGCATTTCTCTACATCACCAACAAA-A 876547 v vi ivv vi v iii v iii - L1M1_orf2#LIN 2194 AAAATCAACATACAAAAATCAGTAGCATTTCTATATGCCAACAGTGAACA 2243 chr3qtel1M 876548 CTTTGCAAGAAGAGAT--AAGATGTACT-CCACTTAAAGTAATGATAACA 876594 v i - i i -- i v v - i v i iiv i - L1M1_orf2#LIN 2244 ATCTG-AAAAAGAAATCAAAAAAGTAATCCCATTTACAATAGCCACAA-A 2291 chr3qtel1M 876595 TAAAA-TAAATA 876605 - L1M1_orf2#LIN 2292 TAAAATTAAATA 2303 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.40 CpG sites = 28, Kimura (unadjusted) = 39.40 Transitions / transversions = 1.56 (28/18) Gap_init rate = 0.04 (6 / 156), avg. gap size = 1.17 (7 / 6) 23 7.03 0.00 0.00 chr3qtel1M 876755 876784 (123216) (TA)n#Simple_repeat 1 30 (0) m_b159s252i11 5991 chr3qtel1M 876755 TAAATTTATATATATATATATATATATATA 876784 v v (TA)n#Simple_ 1 TATATATATATATATATATATATATATATA 30 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 chr3qtel1M 877097 877114 (122886) (T)n#Simple_repeat 1 18 (0) m_b159s252i12 5992 chr3qtel1M 877097 TTTTTTTTTTTTTTTTTT 877114 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTT 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 12 12.45 0.00 6.90 chr3qtel1M 878471 878501 (121499) (CTT)n#Simple_repeat 1 29 (0) m_b159s252i13 5993 chr3qtel1M 878471 CTTCTTGCTCTTTCTTCTTTTTCTTCATTCT 878501 - ii i - (CTT)n#Simple 1 CTTCTT-CTTCTTCTTCTTCTTCTTC-TTCT 29 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2) 368 36.68 6.77 6.54 chr3qtel1M 879657 880114 (119886) C MamRTE1#LINE/RTE-BovB (1180) 2632 2174 m_b159s601i12 5994 chr3qtel1M 879657 ACACAACCTTGTTTCACTCCAGTGGTAACTAGGAAAT---CTGGAGAG-- 879701 i i i i v i - i i ---ii v -- C MamRTE1#LINE/ 2632 ACGCAATCCTGCTTCACTCCATTGGTGA-TGGGGAATGGGTCGGACAGGA 2584 chr3qtel1M 879702 CATCGTTCATTATT-CAGAACCCAGGCAAAGGTGCCATCATGAA--ACTC 879748 ii iv i v v- ivi -- v --- i i -- vi C MamRTE1#LINE/ 2583 CGCCGTCAACTCTGACGCGACC--GGCCA---TACCATCATGGAGTAGCC 2539 chr3qtel1M 879749 ATGGACAATACTGATGACCTCATCCAGGCA--CTAACTTTTGCCATGATT 879796 v i i-- vi i v iv vi -- v vivivi iii C MamRTE1#LINE/ 2538 TTAGG--ATCTTGGTGAACTTCTCAGGGCAGCCAAACTTGCTTAGTAGCT 2491 chr3qtel1M 879797 TCC----CACAAGTCTTCATTACCAACATTATCAAAGGTCTTCATTAGAT 879842 v ---- v i ----- ii iivii v ii ii v i C MamRTE1#LINE/ 2490 GCCAGAGCCCAGGTCT-----ACTGATGGCGTCAAATGCTTTTGTAAGGT 2446 chr3qtel1M 879843 TAACAAACATTATGTACAGACCTCTGTTCTGCTCCTTGACAATTCTCTTG 879892 ii ii i ivi i v ii ivi vi i i - iv i i C MamRTE1#LINE/ 2445 CGATGAATACAGTGCAGAGGTCTTGATGTTGTTCCCTG-CGCTTTTCCTG 2397 chr3qtel1M 879893 T-TTTGTCAAGAGGCAAACACCATATCGATTATTCCTCAGATCTTTCTGA 879941 - i v v v? v i ii vii ? v v ivvv vvi i C MamRTE1#LINE/ 2396 TATCTGACATGCNGCAAAGATCACGTCCGCTNTACCGCGCTGCGGCCTAA 2347 chr3qtel1M 879942 AGCCACACTG----TCAGATAGATAACTATCTTCTAGATGAAG--GATCA 879985 i ---- v iv vvv vi i----- i v -- v C MamRTE1#LINE/ 2346 AGCCACATTGCGATTCCGGGAGCGCACGGTT-----GACGATGTTGTTCA 2302 chr3qtel1M 879986 T--GTTTTTATAG-AGTACTCTGGCAAGAACCTTGTCAGGAATG----AC 880028 v-- iivv vi - v v i i i v ----i C MamRTE1#LINE/ 2301 GTAGCCGATCCAGAAGGACTCTGGCCAGGATCTTGCCAGCAATGGAGAGC 2252 chr3qtel1M 880029 TAAGAGACTGCTGCCTTCCCTGATGATTGTCCCAAGATAACTTATATCTC 880078 vi? - i ------- ii i v - vi i - v v C MamRTE1#LINE/ 2251 AGNGAGA-TGCCGC-------GATAGTTGCCGC-AGTCAGCTT-TCTCGC 2212 chr3qtel1M 880079 TGTCCTTTATAGAGATGGACAATGA-AAT--CATCTTTG 880114 iv i iv ii -ii - i -- C MamRTE1#LINE/ 2211 CTTTCTTCTTGAAGATGG-TGATGATAGTGGCATCTTTG 2174 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 46.70 CpG sites = 96, Kimura (unadjusted) = 53.69 Transitions / transversions = 1.57 (96/61) Gap_init rate = 0.10 (44 / 457), avg. gap size = 1.39 (61 / 44) 195 19.61 15.69 0.00 chr3qtel1M 880114 880164 (119836) MIRb#SINE/MIR 173 231 (37) m_b159s601i13 5995 chr3qtel1M 880114 GGGTTGTTGAGAGGA-------ACATAAAGT-TATGAAGTTCTTAACACA 880155 v ------- v v i- i i iv i MIRb#SINE/MIR 173 GGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGCACA 222 chr3qtel1M 880156 ATGCCTGGC 880164 i MIRb#SINE/MIR 223 GTGCCTGGC 231 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 20.58 CpG sites = 6, Kimura (unadjusted) = 23.09 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.04 (2 / 50), avg. gap size = 4.00 (8 / 2) 401 30.58 6.82 0.43 chr3qtel1M 883652 883871 (116129) C L1M4_orf2#LINE/L1 (1733) 1561 1328 m_b159s551i12 5996 chr3qtel1M 883652 CTGGTTTAGGTATCAGCACCATATCTGTGTCATAAAAGGAATTTGGTAGG 883701 v viiv iiv iv i v i v v v C L1M4_orf2#LIN 1561 CTGGTTTTGGTATCAGGGTAATACTGGCCTCATAGAATGAGTTGGGAAGT 1512 chr3qtel1M 883702 ACTCCTTCTTCACCTATTTTTCCAATTACTTTAAATAAATATTGGAATTA 883751 ii i i vi ivi vv v ivi- iv vi C L1M4_orf2#LIN 1511 GTTCCCTCCTCTTCTATTTTTTGGAAGAGTTTGTG-AAGGATTGGTGTTA 1463 chr3qtel1M 883752 A-----CTTTAAATGT-----AGAATTATTTTGTGAATCCATCTGGCCTT 883791 ----- ----- vviiv v ? i C L1M4_orf2#LIN 1462 ATTCTTCTTTAAATGTTTGGTAGAATTCACCAGTGAAGCCATCTGGNCCT 1413 chr3qtel1M 883792 GGAGATTTTTTCTTGTGAAGTTCATTGATGGCTTGTTCAATTTCTTTTTC 883841 ivv i iv v iv vi vi i vii C L1M4_orf2#LIN 1412 GGGCTTTTCTTTGTGGGAAGTTTTTTGATTACTAATTCAATCTCTTTACT 1363 chr3qtel1M 883842 TAAAATGAGACTAT-----TTCTGTATTTCTTCTT 883871 ivv ii v ----- i v C L1M4_orf2#LIN 1362 TGTTATAGGTCTATTCAGATTTTCTATTTCTTCTT 1328 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.13 CpG sites = 34, Kimura (unadjusted) = 40.13 Transitions / transversions = 1.03 (34/33) Gap_init rate = 0.02 (4 / 219), avg. gap size = 4.00 (16 / 4) 392 26.50 7.19 0.56 chr3qtel1M 883892 884058 (115942) C L1M1_orf2#LINE/L1 (2369) 925 748 m_b159s551i13 5997 chr3qtel1M 883892 CTTTTTT--TGTAAATATTCATCCATATAAAATTTCCCCTAAGAACTGCT 883939 -- iii i i vvv v i i v v C L1M1_orf2#LIN 925 CTTTTTTGATGTAGGCACTTATAGCTATAAACTTCCCTCTTAGTACTGCT 876 chr3qtel1M 883940 TTAGCTGAATCCTATAAATTTTGGTACATTGTCTT---ATCATCATTCAC 883986 v v i ii ii v --- i iii C L1M1_orf2#LIN 875 TTTGCTGTATCCCATAGGTTTTGGTATGTTGTGTTTCCATTATCATTTGT 826 chr3qtel1M 883987 TTGGATGAAATTATT--GTTTC-----TGATTTGGTGTTTGACCCACTCA 884029 vi - v --i ----- i vv vv vi C L1M1_orf2#LIN 825 TTCAA-GAAATTTTTCAATTTCCTTCTTAATTTCTTCATTGACCCACTGG 777 chr3qtel1M 884030 TTCTTTAGGATTAGATTATTTAGTTTCCA 884058 iv i vi v i i C L1M1_orf2#LIN 776 TCATTCAGGAGCATATTGTTTAATTTCCA 748 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.36 CpG sites = 25, Kimura (unadjusted) = 33.36 Transitions / transversions = 1.32 (25/19) Gap_init rate = 0.03 (5 / 166), avg. gap size = 2.60 (13 / 5) 545 32.06 6.33 2.40 chr3qtel1M 883915 884435 (115565) C L1PREC2_orf2#LINE/L1 (2394) 900 360 m_b159s551i14 5997 chr3qtel1M 883915 TATAAAATTTCCCCTAAGAACTGCTTTAGCTGAATCCTATAAATTTTGGT 883964 v i i v iv i vi i v i i C L1PREC2_orf2# 900 TATAAATTTCCCTCTTAACACTGCCTTAGCTGTGTCCCAGAGATTCTGGT 851 chr3qtel1M 883965 ACATTGT---CTTATCATCATTCACTTGGATGAAATTATTG-TTTCTG-- 884008 ii ---i i iv vii vi v v v - -- C L1PREC2_orf2# 850 ATGTTGTATCTTTGTTCTCATTAGTTTCAAAGAACTTCTTGATTTCTGCC 801 chr3qtel1M 884009 ---ATTTGGTGTTTGACCCA---CTCATTCTTTAGGATTAGATTATTTAG 884052 --- vi vv v ---v --- vi i i i C L1PREC2_orf2# 800 TTAATTTCATTATTTACCCAAAAGTCATTC---AGGAGCAGGTTGTTTAA 754 chr3qtel1M 884053 TTTCCAATTAAGTTT-TGGTTT---ATGATTTTCCATGGCCCTTTATTGA 884098 vv v v - ---ii i- i i - v -- C L1PREC2_orf2# 753 TTTCCATGTAATTGTATGGTTTTGAGCGATTTTCT-TAGTC-TTGATT-- 708 chr3qtel1M 884099 ATGTATTTTTTATTGTGTCATAATCTGAAAATGATATCTTTGAT---ATT 884145 - v - i iii ii i i i? --- v i --- C L1PREC2_orf2# 707 -TCTATTT-TTATTGCGCTGTGGTCCGAGAGNG---TGTTTGGTATGATT 663 chr3qtel1M 884146 TCTGTCTTTCTGCATTTGATTGTGAAGTTTTTAATACCCCAATACATGGT 884195 v ii i -i v i v v v ii v v ii C L1PREC2_orf2# 662 TCGGTTCTTTTGCATTTG-CTGAGGATTGTTTTATGTCCGATTATGTGGT 614 chr3qtel1M 884196 CAACTTT-GTATAGGTGTCATGTACCACTGTGAAAAATATATATTCCTTT 884244 i i - vi v i iv iv v i i iv C L1PREC2_orf2# 613 CGATTTTAGAGTATGTGCCATGTGGCGATGAGAAGAATGTATATTCTGTT 564 chr3qtel1M 884245 TTATCCACATTCAATTTTTTCCAAAGGTCTATCATACTCAACTTTTCTA- 884293 v v i?ivi vv ivv i vi i v viii vi vv i - C L1PREC2_orf2# 563 GTTTTNGGGTGGAGAGTTCTGTAGATGTCTATCAGGTCCATTTGGTCCAG 514 chr3qtel1M 884294 ----AAATTCACCTCCTTAACTTTTTTGCTTATTT--TGTTTTTA-GATT 884336 ----i i vv v iv i i v -- ii iv - i C L1PREC2_orf2# 513 TGTTGAGTTCAGGTCCTGAATATCTTTGTTAATTTTCTGCCTCGATGATC 464 chr3qtel1M 884337 TATCTAGTTCTGATAGAAGGATGTTGAGCTCCCCCATTAGTATACTTTTG 884386 i i v vi vi i iv i i v vv v v C L1PREC2_orf2# 463 TGTCTAATACTGTCAGTGGGGTGTTGAAGTCTCCCACTATTATTGTGTGG 414 chr3qtel1M 884387 ----CTATTTCTTCTTGCAACTCACTTA-AATTTACTCTAAGAATTTAGA 884431 ---- vv ii ? iv v v - i i i v i i i C L1PREC2_orf2# 413 GAGTCTAAGTCTCTTTGNAGGTCTCTAAGAACTTGCTTTATGAATCTGGG 364 chr3qtel1M 884432 TGCT 884435 C L1PREC2_orf2# 363 TGCT 360 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.29 CpG sites = 92, Kimura (unadjusted) = 43.41 Transitions / transversions = 1.30 (92/71) Gap_init rate = 0.05 (28 / 520), avg. gap size = 1.64 (46 / 28) 232 12.50 2.50 0.00 chr3qtel1M 884949 884988 (115012) MIR#SINE/MIR 83 123 (139) m_b159s601i14 5998 chr3qtel1M 884949 GTGTGACCTTGGGCTAGTTACTTAACCCCATT-TGCCTTAG 884988 v i vi - i MIR#SINE/MIR 83 GTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAG 123 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 13.79 CpG sites = 3, Kimura (unadjusted) = 13.79 Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1) 17 0.00 0.00 0.00 chr3qtel1M 884991 885009 (114991) (A)n#Simple_repeat 1 19 (0) m_b159s252i14 5999 chr3qtel1M 884991 AAAAAAAAAAAAAAAAAAA 885009 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAA 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 315 19.44 4.17 0.00 chr3qtel1M 886006 886077 (113923) C MIRc#SINE/MIR (39) 229 155 m_b159s601i15 6000 chr3qtel1M 886006 TTTACAAAGAGCTT-CGAACACA--ATCACATTGGATCCTCACACCACAC 886052 v - iv i -- v v v vv C MIRc#SINE/MIR 229 TTTACAAAGCGCTTTCACATACATTATCTCATTTGATCCTCACAACAACC 180 chr3qtel1M 886053 CTGTGAAATAGGTAGGGCTGGCATT 886077 ii i v i C MIRc#SINE/MIR 179 CTGTGAGGTAGGCAGGGCAGGTATT 155 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 22.55 CpG sites = 6, Kimura (unadjusted) = 22.55 Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.03 (2 / 71), avg. gap size = 1.50 (3 / 2) 751 31.97 2.11 2.54 chr3qtel1M 889376 889850 (110150) C HERVK14#LTR/ERVK (2931) 3165 2693 m_b160s701i0 6001 chr3qtel1M 889376 ACAGTATATCATCCATATAATGTAGTATCATGGCA----TGAAGCCACAC 889421 v i v - vi ii ---- v i ii--- C HERVK14#LTR/E 3165 ACAGAATATCATCCATGTAATGGA-TAATATAACATTTTTTAAACTG--- 3120 chr3qtel1M 889422 CTTTCTAATTAGCTCTAGGACTTGTGCTACATACACCTGACACAAGGTGG 889471 i i i i iv vii viv v viii v vi v C HERVK14#LTR/E 3119 TTCTCTAACTGGCTTAATAGCTTTCCCGACATAAGTTTGACAAATAGTCG 3070 chr3qtel1M 889472 GGCTACAACACATCTCTTGGGAGAGAATTTTCCATTGGTAGC-GTAGATC 889520 ivvvi vi v iv v i v v - vvi- C HERVK14#LTR/E 3069 GGCTATTTAGCATGCCTTGTGGTAGTACTTTCCAATGGTATCTGTCCG-C 3021 chr3qtel1M 889521 AGGCCCTGCATTGTTTACAGAGGGAATGGTAAAAGAAAATCTTTTTCTTA 889570 v ii vi i ii v ii v -- v C HERVK14#LTR/E 3020 TGGTTCTTTATTATTTATGGCGGGAACAGTAAAAGCAAA--TTTTTCATA 2973 chr3qtel1M 889571 TCCTCTGGG--GCCAGAGGGATAGAGAAGAAACAATCTTGTATGTCTGTT 889618 vi - -- i i i i vi i i i v vi i i C HERVK14#LTR/E 2972 ATCT-TGGGCAGCTAAAGGAATGGTAAAAAAGCAATCCTTTAGATCTATC 2924 chr3qtel1M 889619 ACTGTAACTGGCCAGTAAGTGGGTACCAGATTAGGAGATGGCTTGCCAGG 889668 i i vv vv v v i vvv v i v vvv v C HERVK14#LTR/E 2923 ACTATGAGAGGCCAGTATTTTGGGATCATTGTTGGGGAGGGCAGCCCTGG 2874 chr3qtel1M 889669 CTGTAGGGCTCCCATAGGTTCAATAGTATCATTAATGGCCCTAAGGTCCA 889718 i i v v i v vii v ii v ii ii C HERVK14#LTR/E 2873 TTGCAGTGCACCCATGGGTTGAATCACAGCATTAACAGCCCTTAAATCTG 2824 chr3qtel1M 889719 CTAGTATTCTGAATTTTCCAGATTTTTTTCTTTATGATAAATACAGGGCT 889768 i ii vv i v - v i ivv C HERVK14#LTR/E 2823 TTAACATTCTCCATTTCCCTGA-TTTTTTCTTAATGACAAATACAGGAGA 2775 chr3qtel1M 889769 ATTCCATGGGCTGGACATTGGTGCTTTATGTCTGGCCTT---CAACTGTT 889815 v vv i vi v iv v --- --- i C HERVK14#LTR/E 2774 ATTCCAAGGGGAGAAAGTAGGCTCTATATGTC---CCTTTTGCAATTGTT 2728 chr3qtel1M 889816 GTTGCACAATTTCATTTAAGGCTTGGGCTTTTTCC 889850 vi v v v i i vviv C HERVK14#LTR/E 2727 CCTGCACCAGTTCTTTTAAAGCCTCCAGTTTTTCC 2693 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.90 CpG sites = 74, Kimura (unadjusted) = 42.28 Transitions / transversions = 1.00 (74/74) Gap_init rate = 0.03 (16 / 474), avg. gap size = 1.38 (22 / 16) 17 26.26 0.00 1.82 chr3qtel1M 890469 890524 (109476) (TTTTATT)n#Simple_repeat 1 55 (0) m_b160s252i0 6002 chr3qtel1M 890469 TTTCATCTTATTATTCTTAATTCATTATAATTTGATTTTTATATTTTATT 890518 i - v i v iv vv iv v (TTTTATT)n#Si 1 TTTTAT-TTTTTATTTTTTATTTTTTATTTTTTATTTTTTATTTTTTATT 49 chr3qtel1M 890519 ATTTAT 890524 v (TTTTATT)n#Si 50 TTTTAT 55 Matrix = Unknown Transitions / transversions = 0.50 (4/8) Gap_init rate = 0.02 (1 / 55), avg. gap size = 1.00 (1 / 1) 12 8.85 4.17 0.00 chr3qtel1M 891715 891738 (108262) (ATTA)n#Simple_repeat 1 25 (0) m_b160s252i1 6003 chr3qtel1M 891715 ATT-ATTAATTAAATGATTAATTAA 891738 - v i (ATTA)n#Simpl 1 ATTAATTAATTAATTAATTAATTAA 25 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 1027 31.41 1.54 1.89 chr3qtel1M 892535 893118 (106882) C L1ME4c_3end#LINE/L1 (191) 639 58 m_b160s551i0 6004 chr3qtel1M 892535 TTCTGCTTATTTCACTTAGCATCAATTCATGTAAGTCTTTCCAGGCCTCT 892584 v i i vv iv vi - v iiv C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATAAACAT-TTTCCATGTTGCT 591 chr3qtel1M 892585 CTGAAATCATCCTGTTGGTCATTTCTTACAGAACAATAATATTCCATAAC 892634 viiv i v v iv vi i v ii vvvv viv C L1ME4c_3end#L 590 ACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCGA 541 chr3qtel1M 892635 ATTCATATACCACAATTTATTCAGCCATTCTTCAATTGATGGGCATCCA- 892683 i ?v i i i i i ii v v i ii - C L1ME4c_3end#L 540 GTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAG 491 chr3qtel1M 892684 -CTGTTTCCAATTTCTAGCCACTACAAAAAGGGCTGCTACAAAAATTTTT 892732 -i i v i i i v iv v ii v i i C L1ME4c_3end#L 490 GTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTC 441 chr3qtel1M 892733 GCACATGTGGGGCTCTTTCCTTCTTT--AAG-AGCTCTTTGGAATATAAA 892779 ii i i -- i -- v- vi i i i v vv C L1ME4c_3end#L 440 GTGCATATAG--CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAATT 393 chr3qtel1M 892780 CTGAGTAGTAACACTGCTGGATCAAAGGGT-TGCACAGTTTGATAATTTT 892828 iv v iiv i i i - v v v iii i C L1ME4c_3end#L 392 CCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTCT 343 chr3qtel1M 892829 TCAAGCATAGTTCCAAATTCCTCTCCAGAATGGTTGGATTTGTTCAAAAT 892878 v vi i v v v i i v v iivi i v ? C L1ME4c_3end#L 342 TGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACANT 293 chr3qtel1M 892879 TCCACCAACAATGTATCAGTGCCCCAGTTTTCCCACACGCCCTCCAACAT 892928 v i v ? iv iv i ?v i v i C L1ME4c_3end#L 292 GCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGCAT 243 chr3qtel1M 892929 TCGTCATTGTCT-TTTTCTGTCTTCTTAGCCAATCTGAGAGGTGTGTTGT 892977 v vi i v- i ivv i - i i i v i ivvi C L1ME4c_3end#L 242 TGGGTATTATCAATTTTTTAAATTTTT-GCTAATTTAATAGGCGTAAAAT 194 chr3qtel1M 892978 GATATCTAAAAGTTGTCTTAATTTGCATTTGCCTGATCAATAATTATTTG 893027 i v vv ii vii i v iiv vv v C L1ME4c_3end#L 193 GGTATCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACTAGCGAGGTT 144 chr3qtel1M 893028 GAGCACCTTTTCATATGACTAGAAATAGTTT--CAGTTTTTTTTTTTTAT 893075 i ii i i vi ------- --i ? v v ii iv C L1ME4c_3end#L 143 GAACATTTTTCCATGTGTTT-------GTTTACTANTTGTATTTCCTCTT 101 chr3qtel1M 893076 CTGAAAATTGTCTGTTCATATTCTTTGACCATATATCAATTGG 893118 ? vi i i v v v C L1ME4c_3end#L 100 NTGTGAATTGTCTGTTCATGTCCTTTGCCCATTTATCTATTGG 58 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.53 CpG sites = 101, Kimura (unadjusted) = 42.38 Transitions / transversions = 1.28 (101/79) Gap_init rate = 0.03 (18 / 583), avg. gap size = 1.11 (20 / 18) 1188 26.97 4.26 3.87 chr3qtel1M 892620 893159 (106841) C L1ME3Cz_3end#LINE/L1 (449) 548 7 m_b160s551i1 6004 chr3qtel1M 892620 ATAATATTCCATAACATTCATATACCACAATTTATTCAGCCATTCTTCAA 892669 i vii vv i v ii v C L1ME3Cz_3end# 548 ATAGTATTCCATTGTATGAATATACCACAATTTATTTATCCATTCCCCTA 499 chr3qtel1M 892670 TTGATGGGCATCCA--CTGTTTCCAATTTCTAGCCACTACAAAAAGGGCT 892717 i ii --i i v i i v iv C L1ME3Cz_3end# 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr3qtel1M 892718 GCTACAAAAATTTTTGCACATGTGGGGCTCTTTC----CTTCTTTAAGAG 892763 v ii v ii i ---- i v---- v v vii C L1ME3Cz_3end# 448 GCAATGAACATCCTTGTACATGT----CTCCTTGTGCACATGTGCGAGAG 403 chr3qtel1M 892764 CT-CTTTGGAATATAAACTGAGTAGTAACACTGCTGGATCAAAGGGT-TG 892811 i - i i ii v iv v iiv i i iv - C L1ME3Cz_3end# 402 TTTCTCTAGGGTATATACCTAGAAGTGGAATTGCTGGGTCGTAGGGTATG 353 chr3qtel1M 892812 CACAGTTTGATAATTTTTCAAGCATAGTTCCAAATTCCTCTCCAGAATGG 892861 i vi --i i v v - v v v i i C L1ME3Cz_3end# 352 CGCATCTT--CAACTTTACTAG-ATATTGCCAAATTGCTCTCCAAAGTGG 306 chr3qtel1M 892862 TTGGATTTGTTCAAAATTCCACCAACAATGTATCAGTGCCCCAGTTTTCC 892911 v iivi i v v i i i v v ii v ii C L1ME3Cz_3end# 305 TTGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTTCCCGTTTCTC 256 chr3qtel1M 892912 CACACGCCCTCCAACATTCGTCATTGTC---TTTTTCTGTCTTCTTAGCC 892958 iv i v i i vi ---i vvi i i--- C L1ME3Cz_3end# 255 CACATCCTCGCCAACACTTGGTATTGTCAGACTTTTAAATTTTT---GCC 209 chr3qtel1M 892959 AATCTGAGAGGTGTGTTGTGATATCTAAAAGTTGTCTTAATTTGCATTTG 893008 vi vvi i v vv ? i v C L1ME3Cz_3end# 208 AATCTGATGGGTGTGAAATGGTATCTCATTGTNGTTTTAATTTGCATTTC 159 chr3qtel1M 893009 CCTGATCAATAATTATTTGGAGCACCTTTTCATATGACTAGAAATAGT-- 893056 i v i v vv v i vi v--- i i-- C L1ME3Cz_3end# 158 CCTGATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTAT---TGGCCA 112 chr3qtel1M 893057 TTCAGTTTTTTTTTTTTATCTGAAAATTGTCTGTTCATATTCTTTGACCA 893106 i v ii i ---- vi i i v C L1ME3Cz_3end# 111 TTCGGGTTTCCTCT----TCTGTGAATTGCCTGTTCATATCCTTTGCCCA 66 chr3qtel1M 893107 TATATCAATTGGAAAATGGCTCAATTTC--------TTGTA--AATTCTC 893146 v v v --iv v i-- -------- -- i i C L1ME3Cz_3end# 65 TTTTTCTATTGG--GTTGTCTT--TTTCTTATTGATTTGTAGGAGTTCTT 20 chr3qtel1M 893147 TATATATTTTGGA 893159 i C L1ME3Cz_3end# 19 TATATATTCTGGA 7 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 33.04 CpG sites = 81, Kimura (unadjusted) = 34.27 Transitions / transversions = 1.37 (81/59) Gap_init rate = 0.05 (29 / 539), avg. gap size = 1.52 (44 / 29) 316 31.16 6.41 3.32 chr3qtel1M 893028 893495 (106505) C L1M5_orf2#LINE/L1 (7) 3287 2806 m_b160s551i2 6004 chr3qtel1M 893028 GAGCACCTTTTCATATGACTAGAAATAGTTTCAGTTTTTTTTTTTTATCT 893077 i i vi vviiivi v?i v i i v--- C L1M5_orf2#LIN 3287 GAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTTTTG---T 3241 chr3qtel1M 893078 GAAAATTGTCTGTTCATATTCTTTGACCATATATCAATTGGAAAATGGCT 893127 i-- vi ii v v v ?v ivvi vvv C L1M5_orf2#LIN 3240 GAAG--TGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTTGT 3193 chr3qtel1M 893128 CAATTTCTT--------GTA--AATTCTCTATATATTTTGGAAATGAGGC 893167 vv ? -------- -- i i i v i v C L1M5_orf2#LIN 3192 CTTTTTNTTATTGANTTGTAGGAGTTCTTTATATATTCTGGATACGAGTC 3143 chr3qtel1M 893168 CTTTATCAGA---ACCTTTGAATGTAAAAATGTTTTCTCAGTTTATTGCT 893214 i --- iv ? --- i v v i i ? i i v C L1M5_orf2#LIN 3142 CTTTGTCAGATATATGTNT---TGCAAATATTTTCTCCCANTCTGTGGCT 3096 chr3qtel1M 893215 TCCTTTCTAATCTTGTCTGCATTTTGTTTGTATGAA---AACTTTTTAAC 893261 v i i v i v ivi iv v v vv ? i--- v i C L1M5_orf2#LIN 3095 TGCCTTTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTTTAAT 3046 chr3qtel1M 893262 ---AATATAATCAAA-------ATTTTCTATTTTGTGATCAATAATGATC 893301 ---i i? i v ------- i v i i --- ?i v i C L1M5_orf2#LIN 3045 TTTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGGT---TNGTGCTT 2999 chr3qtel1M 893302 TCCAGTTCTTTGCTTACAAATTCTTT-CCTCGTCCACAGGTCTGAGAGGT 893350 ii- viii i vi v - v?i - vvii i C L1M5_orf2#LIN 2998 TTT-GTGTCCTGTTTAAGAAATCTTTGCCTANCCCA-AGGTCACGAAGAT 2951 chr3qtel1M 893351 AAACTATCCTATGTT--CTTCTAATTTATTTATAATCTCATTCTTTATGT 893398 --i v -- ivvvv i i i ?ii ii C L1M5_orf2#LIN 2950 A--TTCTCCTATGTTTTCTTCTAGAAGTTTTATAGTTTTANCTTTTACAT 2903 chr3qtel1M 893399 CTAGATC-ATGAACCCATTTCGACCTTATCTTGGTATATGGTGTTAAGTG 893447 i i - -i i ? vi v i v i v i i C L1M5_orf2#LIN 2902 TTAGGTCTATGA-TCCATCTNGAATTAATTTTTGTGTATGGTGTGAGGTA 2854 chr3qtel1M 893448 TGGGTTAATGCCTAGTTTCTGCCATATTAGTTTCCAATTTTCCCAGCA 893495 v ii v?iii v i v vii v v i C L1M5_orf2#LIN 2853 GGGGTCGAGNTTCATTTTTTTCCATATGGATATCCAATTGTTCCAGCA 2806 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.41 CpG sites = 81, Kimura (unadjusted) = 43.08 Transitions / transversions = 1.35 (81/60) Gap_init rate = 0.05 (25 / 467), avg. gap size = 1.84 (46 / 25) 40 0.00 0.00 0.00 chr3qtel1M 893550 893586 (106414) (T)n#Simple_repeat 1 37 (0) c_b160s251i0 6005 chr3qtel1M 893550 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 893586 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 37 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 3152 29.89 5.66 3.31 chr3qtel1M 893748 896079 (103921) C L1M4_orf2#LINE/L1 (871) 2423 39 m_b160s551i3 6004 chr3qtel1M 893748 CCTATCCAAGAGCACTTAATATTTTTCCAATTGTTTAGATCTGACTTTAT 893797 v v i ivvi i i v i i vvi v C L1M4_orf2#LIN 2423 CCAATCCATGAACATGGGATGTCTTTCCATTTATTTAGGTCTTCTTTAAT 2374 chr3qtel1M 893798 TTGTGTGGAAAGTGTTTTGTAGTTTTGCTCATATAGTTCCTGATTTTCCC 893847 v v vi v i vvvii i iv i vvi ii C L1M4_orf2#LIN 2373 TTCTTTCAACAATGTTTTGTAGTTTTCAGTGTACAAGTCTTGCACTTCTT 2324 chr3qtel1M 893848 TTGGTAGATAGATTCCCAAATATTTTATA--TTATCAAGTTATTTTAAAT 893895 v i vv i i v-- v v v i v C L1M4_orf2#LIN 2323 TTGTTAAATTTATTCCTAAGTATTTTATTCTTTTTGATGCTATTGTAAAT 2274 chr3qtel1M 893896 GGAATT--TCTCTTTATATCTCTTGCTCTTGGATT--TTGTTGGTGATAT 893941 -- i v v vi ---- i -- ii v ii i C L1M4_orf2#LIN 2273 GGAATTGTTTTCTTAATTTCATTT----TCGGATTGTTCATTGCTAGTGT 2228 chr3qtel1M 893942 ATAAAAATAATGAGGATTTAAGTGGATTTATTTTGTATCTTGTAACTTTG 893991 i vvivv vv iv v i i i i C L1M4_orf2#LIN 2227 ATAGAAATACAATTGATTTTTGTATATTGATCTTGTATCCTGCAACCTTG 2178 chr3qtel1M 893992 CCAAAGTTGTAGATTATTTCTAATAGCTTTTTAGTTGATTCTCTGGAGTT 894041 ii v i vv v i ? v ii i ii C L1M4_orf2#LIN 2177 CTGAACTCGTTTATTAGTTCTAATAGTTTTTTNGTGGATTCCTTAGGATT 2128 chr3qtel1M 894042 CTCTAAGTATACCAG--CATATCATCTGT--AGAGTGCTAATTTGGTTTC 894087 i -- v -- i i-- v v v i vii C L1M4_orf2#LIN 2127 TTCTA--TATACAAGATCATGTCATCTGCGAATAGAGATAGTTTTACTTC 2080 chr3qtel1M 894088 TTCATTACCTACTCTA-ATTCCTTTAATCTCTTTTTCATCTCTAATTGCC 894136 v v - v i- v v i v vi C L1M4_orf2#LIN 2079 TTCCTTTCC-AATCTGGATGCCTTTTATTTCTTTTTCTTGCCTAATTGCC 2031 chr3qtel1M 894137 CAAATTAGCATTTATAATACAATATTGAATAATAATGGTAATAATGGGCA 894186 viii v ii vi i i iv i ii v ii i C L1M4_orf2#LIN 2030 CTGGCTAGAACCTCCAGTACAATGTTGAATAGAAGTGGCGAGAGCGGACA 1981 chr3qtel1M 894187 ACATTGTTTCACTCCTGATTTTATTGGGAATGGTTCCAGTTTATCTCCAT 894236 v v i iii i vv v v? i i v v C L1M4_orf2#LIN 1980 TCCTTGTCTTGTTCCTGATCTTAGGGGGAAAGCNTTCAGTCTTTCACCAT 1931 chr3qtel1M 894237 TACATATGATGCTTACTGATGGTTTTAAATAGATGC----TACTATTTTA 894282 vi i vi vv vvi ---- ii vv i C L1M4_orf2#LIN 1930 TAAGTATGATGTTAGCTGTGGGTTTTTCGTAGATGCCCTTTATCAGGTTG 1881 chr3qtel1M 894283 AGGAAAAGTCCATTTCTTCCTATACTCTCTAGTGTTTTTTAATAGGAATG 894332 ivvi v i v vvi v iv - vi v v C L1M4_orf2#LIN 1880 AGGAAGTTCCCTTCTATTCCTAGTTTGTTGAGTGTTTTT-ATCATGAAAG 1832 chr3qtel1M 894333 GATGTTGGATTTTATCAAATGCTTTTTCTGCATCTATTGAGATGGCCATA 894382 i i i ii i C L1M4_orf2#LIN 1831 GGTGTTGGATTTTGTCAAATGCTTTTTCTGCGTCTATTGAGATGATCATG 1782 chr3qtel1M 894383 TGGTTTTAGTTAGTTTAAT-TAGTGATGTAGTCAATTATGTTAATAGTTT 894431 v iv- v - v i i i vv ii i v v C L1M4_orf2#LIN 1781 TGGTTTTTGTCC-TTTATTCTATTAATATGGTGTATTACATTGATTGATT 1733 chr3qtel1M 894432 TCCTCATATTGAACCAGCCCTGCATTCCTGGTATAAATCCTACTTGGTCA 894481 i v? i i i v i C L1M4_orf2#LIN 1732 TTCGNATGTTGAACCAACCTTGCATTCCTGGGATAAATCCCACTTGGTCA 1683 chr3qtel1M 894482 TGGTGTATTATCCTGAGGATGATTTTCTGTAATCTCTTTGCTAATATTTT 894531 v vvvv ivv v v v vv i C L1M4_orf2#LIN 1682 TGGTGTATAATCCTTTTTATATGTTGCTGGATTCGGTTTGCTAGTATTTT 1633 chr3qtel1M 894532 ATTTAAGATTTTTGCATCAATATTCATTAGGGAGATTCATCTATAATTTT 894581 i v i v v v vi i i C L1M4_orf2#LIN 1632 GTTGAGGATTTTTGCATCTATATTCATAAGGGATATTGGTCTGTAGTTTT 1583 chr3qtel1M 894582 CTTTCTCTGT----TTTTAACCTACCTGGTTTAGATATCAACACCATGTC 894627 iii ---- i ---- ii v i iviiv iii C L1M4_orf2#LIN 1582 CTTTTCTTGTGATGTCTT----TGTCTGGTTTTGGTATCAGGGTAATACT 1537 chr3qtel1M 894628 TGTGTCATAAAAGGAATTCTGTGGGACTCCTTCCTTCCCTATTTTTTCAA 894677 v iv i v i vv vi vii i iii vi C L1M4_orf2#LIN 1536 GGCCTCATAGAATGAGTTGGGAAGTGTTCCCTCCTCTTCTATTTTTTGGA 1487 chr3qtel1M 894678 ACAATTTATATAGTATTGGGGTTAATTGTT---TAAATGTTTGGTAGAAT 894724 v i i iv v v v --- C L1M4_orf2#LIN 1486 AGAGTTTGTGAAGGATTGGTGTTAATTCTTCTTTAAATGTTTGGTAGAAT 1437 chr3qtel1M 894725 TCACATGTAAAACCATCTCGTCCTGGAATTTTTTTTTTTTTTTTTTTAGG 894774 vv i i v ? iv i v ---------- C L1M4_orf2#LIN 1436 TCACCAGTGAAGCCATCTGGNCCTGGGCTTTTCTTTGT----------GG 1397 chr3qtel1M 894775 GA-----TTTGATTAATAGCTTGCTCTATTT-CTTTTTCTAAAATGGGAT 894818 ----- v ii iiv v - v ----- i vi C L1M4_orf2#LIN 1396 GAAGTTTTTTGATTACTAATTCAATCTCTTTACTTGTT-----ATAGGTC 1352 chr3qtel1M 894819 TATTTAAA----CAATACCTCCTCT---GTTAATCTGGGCAGCCTATATT 894861 i i ---- -- ii i --- i i i v i ii i i i C L1M4_orf2#LIN 1351 TATTCAGATTTTC--TATTTCTTCTTGAGTCAGTTTCGGTAGTTTGTGTC 1304 chr3qtel1M 894862 TTTGGAGGTAGTCATTCATTTCACTTAGATTATCAAATTTATTGGCATAA 894911 vv v v ii i ii i v i v C L1M4_orf2#LIN 1303 TTTCTAGGAATTTGTCCATTTCATCTAGGTTATCTAATTTGTTGGCATAC 1254 chr3qtel1M 894912 AGTTGGACAAAGTAACTCCTAATTACTGCTTTAATTTCCTCTTCATCAGT 894961 i vv v vii v v iivi v ivivvvi i C L1M4_orf2#LIN 1253 AATTGTTCATAGTATTCCCTTATAATCCTTTTTATTTCTGTAAGGTCGGT 1204 chr3qtel1M 894962 GGAAAGTTCTCCCTTTTCATTTTTAAGACTAACAATTTGATTTTCCTTTC 895011 i v vv i ii ii i vvi ii v i i i C L1M4_orf2#LIN 1203 AGTAATGTCCCCTCTTTCATTCCTGATTTTAGTAATTTGAGTCTTCTCTC 1154 chr3qtel1M 895012 TTTTTT--CTGATCAAATTTACCAAAGATTTATCCATCTTGTTGGTTTTT 895059 --i i ivi vi i i i v i i i C L1M4_orf2#LIN 1153 TTTTTTTCTTGGTCAGTCTAGCTAAAGGTTTGTCAATTTTGTTGATCTTT 1104 chr3qtel1M 895060 TCATAAAACCAAATTTTTATTTATTTATTTATTAATTCAATAGTTTTTTT 895109 v i v vi ------- ii i ------ i i v C L1M4_orf2#LIN 1103 TCAAAGAACCAACTTTTGGT-------TTCGTTGATT------TTCTCTA 1067 chr3qtel1M 895110 TTTTTTTTTTACTTTTAATTTTATTAACCTTTCCTTTTGT-TTTAGAATT 895158 v i i i iv i v ii iiv i vi - vv C L1M4_orf2#LIN 1066 TTGTTTTTCTATTCTCTATTTCATTTATTTCCGCTCTAATCTTTATTATT 1017 chr3qtel1M 895159 TCAAGTTTAGCATTTGATTTGGGGTTTTTAATTTGC---TCTTTTTCTAG 895205 vvvii vviii v --- i --- C L1M4_orf2#LIN 1016 TCCTTCCTTCTGCTTGCTTTGGG---TTTAGTTTGCTCTTCTTTTTCTAG 970 chr3qtel1M 895206 CTTTTTTAGTTGCAGGCCCAGTTCATTGATC-----TCTTTATTTTATGT 895250 i i v v v i vii v i i----- v i v v C L1M4_orf2#LIN 969 TTTCTTAAGGTGGAAGGTTAGGTTATTGATTTGAGATCTTTCTTCTTTTT 920 chr3qtel1M 895251 GA--GTAAGCCTCTAGAAATATAAAAATACCCCTTATTACTGCTTTGGCT 895298 v --i i v i v iv vv v i v vi ? C L1M4_orf2#LIN 919 TAATATAGGCATTTACAGCTATAAATTTCCCTCTAAGCACTGCTTTNGCT 870 chr3qtel1M 895299 GCATCCCA-AAATATGGGTATGTTGTCTCATTATTGTCATTC-TCTTGGA 895346 - i v v v iv ii v - i--- C L1M4_orf2#LIN 869 GCATCCCATAAGTTTTGGTATGTTGTGTTTTCGTTTTCATTCATCTC--- 823 chr3qtel1M 895347 TGAAATTATTGTGT--------CTATGATTTGCTATTTCACCCATTCATT 895388 -- v v v --------i i vi v v vi C L1M4_orf2#LIN 822 --AAAGTATTTTCTAATTTCCCTTGTGATTTCTTCTTTGACCCATTGGTT 775 chr3qtel1M 895389 CTTTAGGATGAAGTTATTTAGTTTCCAATTAGGTTTTGGTCTATTTTCC- 895437 v vviv i i vv ---- v vv i - C L1M4_orf2#LIN 774 ATTTAGGAGTGTGTTGTTTAATTTCCACATA----TTTGTGAATTTCCCA 729 chr3qtel1M 895438 -----CCTGGCTTTTTATTGAATGTAGTTTTTATTGCTTTGTGATCTGGA 895482 ----- --ii v v viviv i v v i - C L1M4_orf2#LIN 728 AATTTCCT--TCTGTTATTGATTTCTAATTTCATTCCATTGTGGTC-GGA 682 chr3qtel1M 895483 AAGAATGCATT-TACTATTTCTGCCTTTCTGCATTTGATTTTGAG----G 895527 i iv i v - iv vii i i iv i--- ---- C L1M4_orf2#LIN 681 GAACATACTTTGTATGATTTCAATCCTTTTAAATTTA---TTGAGACTTG 635 chr3qtel1M 895528 TCTTTATGTCCTAACATATGATCAATTTTTGTATATGTTCTATGAACTGC 895577 - v i v ii v viv i vi vvi C L1M4_orf2#LIN 634 T-TTTATGGCCTAACATATGGTCTATCCTGGAGAATGTTCCATGTGCACT 586 chr3qtel1M 895578 TGAAAAGAAAGTGTACTC--CTGT--CTCCATTCAGTTTTCTCCAAAAAT 895623 i v i -- --i vvi vv v vi i vi C L1M4_orf2#LIN 585 TGAGAAGAATGTGTATTCTGCTGTTGTTGGGTGGAGTGTTCTATAGATGT 536 chr3qtel1M 895624 CTATCATCCCTAACT--TTTCTAATATTCTATTTATCTCTT-TAATTTCT 895670 i i vvi ii -- v i i -- i i vv - v i C L1M4_orf2#LIN 535 CTGTTAGGTCTAGTTGGTTTATAGTGT--TGTTCAAGTCTTCTATTTCCT 488 chr3qtel1M 895671 TATTTATTTTGTGGT---TTGATTTACCTAATTCTGATAGTGCAAGGTTG 895717 i v i v vi--- v i i i v vi v viivi C L1M4_orf2#LIN 487 TGTTGATCTTCTGTCTAGTTGTTCTATCCATTATTGAAAGTGGGGTATTG 438 chr3qtel1M 895718 AGATCTCCCACTATTATTATTATATTGCTGTCTATTTCTTCTTGTAGCTC 895767 ii v i iv --- i i vi ii C L1M4_orf2#LIN 437 AAGTCTCCAACTATTATTGTTGAAT---TGTCTATTTCTCCCTTCAATTC 391 chr3qtel1M 895768 TCTTAACTTCCCCTTTAGGAATTTAGATGCTATACCACTTGGTGCATATA 895817 v i ii iiv i v v v iv v iiiii v C L1M4_orf2#LIN 390 TGTCAGTTTTTGCTTCATGTATTTTGGGGCTCTGTTGTTAGGTGCATATA 341 chr3qtel1M 895818 TGTTTA---------------------GTATTGA------TATTACTTTA 895840 --------------------- v ------ i i v C L1M4_orf2#LIN 340 TGTTTATAATTGTTATATCTTCCTGATGGATTGACCCTTTTATCATTATA 291 chr3qtel1M 895841 AAGTGCCCTTCCTTATCTGTTTTAATTACATAGATTTTTGCTTT------ 895884 i i i i --- i i v ---? ii ------ C L1M4_orf2#LIN 290 AAATGTCCTTCTTTGTC---TCTAGTAACA---NTTTTTGTCTTAAAGTC 247 chr3qtel1M 895885 TGCTTGATTTGAGATCAGGATGGCTACCCCTG--CTTTTTTGACTTCACC 895932 ii vi i v i v i i i v -- i i-- i i C L1M4_orf2#LIN 246 TATTTTGTCTGATATTAGTATAGCCACTCCAGCTCTCTTTTGG--TTACT 199 chr3qtel1M 895933 TGTAGCATAGTAGATTATGCTCCAACTCTCTATCTATCACCCTGCTTC-- 895980 vv v i v iv vi v ii i - v v ii v-- C L1M4_orf2#LIN 198 GTTTGCATGGTATATCTTTTTCCATCCTTTTA-CTTTCAACCTATTTGTG 150 chr3qtel1M 895981 ------------AAGTGTGTTTCCTGTAAACAACATATTGTAGGATTCTG 896018 ------------ i i i i v v iv C L1M4_orf2#LIN 149 TCTTTGAATCTAAAGTGTGTCTCTTGTAGACAGCATATAGTTGGATCATG 100 chr3qtel1M 896019 GCTTTTAATCCAGTCTGCTA---TCTGCCTTTGCTTTATGGAAGAGTTTA 896065 vi v v i --- --- v v i v C L1M4_orf2#LIN 99 TTTTTTTATCCATTCTGCCAATCTCTGCCTT---TTGATTGGAGTGTTTA 53 chr3qtel1M 896066 CCTCATTCACATTT 896079 vii i C L1M4_orf2#LIN 52 ATCCATTTACATTT 39 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.29 CpG sites = 370, Kimura (unadjusted) = 39.13 Transitions / transversions = 1.22 (370/304) Gap_init rate = 0.05 (117 / 2331), avg. gap size = 1.80 (211 / 117) 275 27.00 7.41 2.01 chr3qtel1M 895975 896163 (103837) C L1MEd_5end#LINE/L1 (7) 2217 2019 m_b160s551i5 6004 chr3qtel1M 895975 TGCTTCAAGTGTGTTTCCTGTAAACAACATATTGTAGGATTCTGGCTTTT 896024 i i i i i i v iv ivvvi C L1MEd_5end#LI 2217 TGTTTTAGGTGTGTCTCTTGTAAACAGCATATAGCTGGATTTGTTTTTTT 2168 chr3qtel1M 896025 AATCCAGTCTGCTA---TCTGCCTTTGCTTTATGGAAGAGTTTACCTCAT 896071 i vi --- i --- v iv i? vii C L1MEd_5end#LI 2167 AATCCAATCTGACAATCTCTGTCTT---TTAACTGGNGAGTTTAGTCCAT 2121 chr3qtel1M 896072 TCACATTTGCAGTTAAAACT-ATGAATTT---TCTATTTCCTACCATCT- 896116 i iiv v vv - iv --- i - - C L1MEd_5end#LI 2120 TTACATTTATTGTGATTACTGATATATTTGGATTTATTT-CTACCATCTT 2072 chr3qtel1M 896117 -TCTTATCC---CCA--GGTTATATTTTTCTCTTTCCTTTCTGCCTTACC 896160 - i i v --- i --v v v i ii i vi i C L1MEd_5end#LI 2071 ATTTTGTGCTTTCTATTTGTTCTATGTTTCTTTTTCTCTCCTTTCTTGCC 2022 chr3qtel1M 896161 CTC 896163 i C L1MEd_5end#LI 2021 TTC 2019 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.79 CpG sites = 31, Kimura (unadjusted) = 34.79 Transitions / transversions = 1.63 (31/19) Gap_init rate = 0.06 (11 / 188), avg. gap size = 1.64 (18 / 11) 374 20.40 6.08 3.97 chr3qtel1M 895975 896122 (103878) C L1MEh_5end#LINE/L1 (7) 2228 2078 m_b160s551i4 6004 chr3qtel1M 895975 TGCTTCAAGTGTGTTTCCTGTAAACAACATATTGTAGGATTCTGGCTTTT 896024 i i i i i i v i vi ? C L1MEh_5end#LI 2228 TGTTTTAAGTGTGTCTCTTGTAGACAGCATATTGTTGGATTTTGTTTTTN 2179 chr3qtel1M 896025 AATCCAGTCTGCTA---TCTGCCTTTGCTTTATGGAAGAGTTTACCTCAT 896071 i v? --- i --- v v iv v i C L1MEh_5end#LI 2178 AATCCAATCTGANAATCTCTGTCTT---TTAATTGGTGAGTTTAACCCAT 2132 chr3qtel1M 896072 TCACAT---TTGCAGTTAAAACTATGAATTT---TCTATTTCCTACCATC 896115 i --- i i vvi? -- ?---ii - i C L1MEh_5end#LI 2131 TTACATTTATTGTAATTACTGNTAT--ATTNGGACTTATTT-CTGCCATC 2085 chr3qtel1M 896116 TTCTTAT 896122 v C L1MEh_5end#LI 2084 TTATTAT 2078 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 25.29 CpG sites = 19, Kimura (unadjusted) = 25.29 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.06 (9 / 147), avg. gap size = 1.67 (15 / 9) 14 15.94 2.70 2.70 chr3qtel1M 896836 896872 (103128) (TTGT)n#Simple_repeat 1 37 (0) m_b160s252i2 6006 chr3qtel1M 896836 TTGTTTGTTTGTTT-TCTGGCTGTTTGTTATATTTTTT 896872 - i vi - i v (TTGT)n#Simpl 1 TTGTTTGTTTGTTTGTTTGTTTGTTTGTT-TGTTTGTT 37 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 246 32.02 4.58 2.24 chr3qtel1M 900696 900826 (99174) C MIRc#SINE/MIR (52) 216 83 m_b160s601i0 6007 chr3qtel1M 900696 TTCAGGCACA--ATTTCATTGGATCCTGACCATAAGTATGTGAA--AAAC 900741 vii -- i v v v i viv i-- ii C MIRc#SINE/MIR 216 TTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGC 167 chr3qtel1M 900742 AGGAATTGGCTTCATTCTCATTATATGTACAACTCAGGCCA-TGAG-CTT 900789 i-iv iv i v vii - v iv v vv - - i C MIRc#SINE/MIR 166 AGGG-CAGGTATTATTATCCCCAT-TTTACAGATGAGGAAACTGAGGCTC 119 chr3qtel1M 900790 AGAATGGCTGAGTGACTTAACCCAAATCCCAGCAGCT 900826 iv i i iv v ii v - C MIRc#SINE/MIR 118 AGAGAGGTTAAGTGACTTGCCCAAGGTCACA-CAGCT 83 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.69 CpG sites = 22, Kimura (unadjusted) = 42.69 Transitions / transversions = 1.16 (22/19) Gap_init rate = 0.05 (7 / 130), avg. gap size = 1.29 (9 / 7) 298 35.45 0.81 5.98 chr3qtel1M 902365 902487 (97513) C MIR#SINE/MIR (140) 122 6 m_b160s601i1 6008 chr3qtel1M 902365 TGAGACA-ATTGGGAATAAATAACTTGCCTAGGGTCACACAGCTAATTAG 902413 i - vv i iv i i i i v C MIR#SINE/MIR 122 TGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAG 73 chr3qtel1M 902414 AGTTAGGTATCTGAAGTCAGATTTGAATTCAGGTCTTCCTTCTTTAGGAT 902463 v vi -- v i -----i i ii ivv ivv ii iii C MIR#SINE/MIR 72 TGGCAG--AGCCG-----GGATTCGAACCCAGGCAGTCTGGCTCCAGAGC 30 chr3qtel1M 902464 CCACGTTCTTATCTCCTGCACCAT 902487 ii i v iv iii i C MIR#SINE/MIR 29 CCGTGCTCTTAACCACTATGCTAT 6 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 46.08 CpG sites = 28, Kimura (unadjusted) = 51.52 Transitions / transversions = 2.15 (28/13) Gap_init rate = 0.07 (8 / 122), avg. gap size = 1.00 (8 / 8) 343 28.04 0.84 10.09 chr3qtel1M 902380 902498 (97502) C MIRb#SINE/MIR (155) 113 5 m_b160s601i2 6008 chr3qtel1M 902380 TAAATAACTTGCCTAGGGTCACACAGCTAATTAGAGTTAGGTATCTGAAG 902429 i i i i v v vi -- v i --- C MIRb#SINE/MIR 113 TAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAG--AGCCG--- 69 chr3qtel1M 902430 TCAGATTTGAATTCAGGTCTTCCTT-CTTTAGGATCCACGTTCTTATCTC 902478 --i i ii vi v- ii iiii ii i - iv C MIRb#SINE/MIR 68 --GGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTT-TCCA 22 chr3qtel1M 902479 CTGCACCATCTAGCAGCCCC 902498 i--- v C MIRb#SINE/MIR 21 CTGCACCAC---GCTGCCCC 5 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.80 CpG sites = 22, Kimura (unadjusted) = 36.85 Transitions / transversions = 2.75 (22/8) Gap_init rate = 0.10 (12 / 118), avg. gap size = 1.00 (12 / 12) 751 31.69 0.82 1.09 chr3qtel1M 902582 902948 (97052) L1ME4c_3end#LINE/L1 274 639 (191) m_b160s551i6 6009 chr3qtel1M 902582 CTGATGCATTGTTGGTGGAGTTGTGAATGAATCCAACCATTCTGGAGAGC 902631 v i i vi? i vii v v i i L1ME4c_3end#L 274 CTCATACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGC 323 chr3qtel1M 902632 AATCTGAAATTATATCCCAAAAGCTATCAATCTGTGTATACACTTTGATC 902681 i iv v ii vi i i v vv vi v i L1ME4c_3end#L 324 AATTTGGCAATACGTATCAAGAGCCATAAAAATGTTCATACCCTTTGACC 373 chr3qtel1M 902682 CAGCAGTGTTACTGCTGGGCTTATATCCCAAAGAGATACT---AAAGAAG 902728 i i vii v vv v i i i v --- L1ME4c_3end#L 374 CAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAAGAAG 423 chr3qtel1M 902729 GGAAAGGGACGTGTATGTGCCAAAATGTTTGTGGCAGCCCTTTTTGTGGT 902778 i i v--- i ii v i ii v vi v i ii L1ME4c_3end#L 424 GAAAAAGC---TATATGCACGAAGATGTTCATTGCAGCGTTATTTATAAT 470 chr3qtel1M 902779 GGCTAGAAACTGGAAAATGAATGGATGCCCAACAATTGGAGAATGGTTGG 902828 i v i i vvivv ii i v i ii L1ME4c_3end#L 471 AGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAATGGTTAA 520 chr3qtel1M 902829 GTAAATTGTGGTATATGAATGCTATGGAATATTATTGTTCTGCAAGAAAT 902878 i i v? iv v vvvv iiiv i L1ME4c_3end#L 521 GTAAATTATGGTACATCNACTCGATGGAATATTATGCAGCCATTAAAAAT 570 chr3qtel1M 902879 GACCAGCAGAATGAATAGAGAGAGACTTGGAAAAACTTACATGAACTGAT 902928 iv vi vi v v viv vi v vv -i vv i L1ME4c_3end#L 571 GATAATTATGAAGACTATGTAGCAACATGGAAAATGTT-TATGATATAAT 619 chr3qtel1M 902929 GCTGAGTGAAATGAGCAGAA 902948 i i vi L1ME4c_3end#L 620 GTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.92 CpG sites = 63, Kimura (unadjusted) = 42.46 Transitions / transversions = 1.21 (63/52) Gap_init rate = 0.01 (5 / 366), avg. gap size = 1.40 (7 / 5) 12 28.69 0.00 0.00 chr3qtel1M 903202 903243 (96757) (ATATATA)n#Simple_repeat 1 42 (0) m_b160s252i3 6010 chr3qtel1M 903202 ATATATTGTATCTAGGATATACTATAAGATATTTAACATATA 903243 vi v iv v vi v i (ATATATA)n#Si 1 ATATATAATATATAATATATAATATATAATATATAATATATA 42 Matrix = Unknown Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 15 13.87 0.00 0.00 chr3qtel1M 903370 903393 (96607) (A)n#Simple_repeat 1 24 (0) m_b160s252i4 6011 chr3qtel1M 903370 AAAAAAAAAAACCAAAAACAAAAA 903393 vv v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAA 24 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 523 32.90 8.94 0.39 chr3qtel1M 904060 904294 (95706) MIR#SINE/MIR 1 255 (7) m_b160s601i3 6012 chr3qtel1M 904060 ACAATATGGC-TGGTGGTACAGTGGATTGATT----AATCATGAAGACCT 904104 i i - i vv v v iv ii ---- ii - vvi MIR#SINE/MIR 1 ACAGTATAGCATAGTGGTTAAGAGCACGGGCTCTGGAGCCA-GACTGCCT 49 chr3qtel1M 904105 GAATTCCAATTCCACTTTAGAAATTTGCTAGTCCTGCGACCCTAGATTAG 904154 ii v i ivi iv vv i i iiv i i i iiv MIR#SINE/MIR 50 GGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAG 99 chr3qtel1M 904155 T--CCTGGGACCTCTGCAACT--GTTTCTTTATCTGTAACATGGGAATAA 904200 -- i iivvi iiv -- i i v i MIR#SINE/MIR 100 TTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAA 149 chr3qtel1M 904201 TAATAACACTTACCTCCTAAGATTCTCCTGAGGATAAGATTAG--ACCAC 904248 ii i v i i v iv v i v -- vi MIR#SINE/MIR 150 TAATAGTACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATAC 199 chr3qtel1M 904249 ATTTA------T----ACAGTGCATGAGACATAACAAAAACTATATAAAT 904288 v ------ ---- v iv ii ivi vv MIR#SINE/MIR 200 ATGTAAAGCGCTTAGAACAGTGCCTGGCACATAGTAAGCGCTCAATAAAT 249 chr3qtel1M 904289 GCTAGC 904294 i MIR#SINE/MIR 250 GTTAGC 255 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.75 CpG sites = 47, Kimura (unadjusted) = 45.15 Transitions / transversions = 1.57 (47/30) Gap_init rate = 0.03 (8 / 234), avg. gap size = 2.75 (22 / 8) 195 21.54 16.67 7.14 chr3qtel1M 904462 904551 (95449) L2a_3end#LINE/L2 406 503 (14) m_b160s601i4 6013 chr3qtel1M 904462 CTCCATGAGAACAAGGGCTATCCCTTGTGTCTCTTTATGTTC-CTGCTGA 904510 ii i i------ v v - - v L2a_3end#LINE 406 CTCCATGAGGGCAGGGA------CTTTTGTCTGTTT-TGTTCACTGCTGT 448 chr3qtel1M 904511 TTCTCC-----------CAGGGCCTGTCATGTAGCAGGCATT---TAAAT 904546 v i ----------- v v ii i ii --- L2a_3end#LINE 449 ATCCCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGGCGCTCAATAAAT 498 chr3qtel1M 904547 GTCTG 904551 i i L2a_3end#LINE 499 ATTTG 503 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.66 CpG sites = 12, Kimura (unadjusted) = 26.33 Transitions / transversions = 2.00 (12/6) Gap_init rate = 0.11 (10 / 89), avg. gap size = 2.20 (22 / 10) 333 22.73 4.55 0.00 chr3qtel1M 904655 904742 (95258) C MIR3#SINE/MIR (6) 202 111 m_b160s601i5 6014 chr3qtel1M 904655 TAGGATCATAG---GTGACCTCTGGAAGGGAGCTAACAGGCCATGT-GTC 904700 i --- v vvv v v v ii v - C MIR3#SINE/MIR 202 TAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTC 153 chr3qtel1M 904701 CAACGCCCTCATTTTATAGAGGGCGAAACTGAGATTCAGTGA 904742 v i v iv iii v C MIR3#SINE/MIR 152 CAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGA 111 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.11 CpG sites = 8, Kimura (unadjusted) = 27.11 Transitions / transversions = 0.67 (8/12) Gap_init rate = 0.02 (2 / 87), avg. gap size = 2.00 (4 / 2) 409 22.92 0.00 0.00 chr3qtel1M 905426 905521 (94479) MIR#SINE/MIR 103 198 (64) m_b160s601i6 6015 chr3qtel1M 905426 CTTAAGCTCTATTTCCCTCAGTTTCCTCAACTTTCAAATGGGGAGGATAC 905475 v v v v v v v vi v MIR#SINE/MIR 103 CTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAA 152 chr3qtel1M 905476 GATTATCTAACTTGGAAGGTTGTTGTGAGGATAAAGTGACATAATA 905521 v v i v iiv i v i vv MIR#SINE/MIR 153 TAGTACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATA 198 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.38 CpG sites = 6, Kimura (unadjusted) = 27.38 Transitions / transversions = 0.38 (6/16) Gap_init rate = 0.00 (0 / 95), avg. gap size = 0.0 (0 / 0) 214 19.76 1.64 8.77 chr3qtel1M 905879 905939 (94061) MIRb#SINE/MIR 198 254 (14) m_b160s601i7 6016 chr3qtel1M 905879 TAATGTATTGTAAAGAAACCACTTAGCACAATACTTGGCAAATAATGGGC 905928 i - ---- i i i i v i ii MIRb#SINE/MIR 198 TAATGCAT-GTAAAG----CGCTTAGCACAGTGCCTGGCACATAGTAAGC 242 chr3qtel1M 905929 GA-AAATAAATG 905939 v-v MIRb#SINE/MIR 243 GCTCAATAAATG 254 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 21.18 CpG sites = 8, Kimura (unadjusted) = 23.55 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.10 (6 / 60), avg. gap size = 1.00 (6 / 6) 36 31.11 4.74 1.38 chr3qtel1M 907093 907206 (92794) (TGAGTG)n#Simple_repeat 1 115 (103) m_b160s252i5 6017 chr3qtel1M 907093 TGAGTGTATGTGTGTATTG-GAGTGTACATATGTATGTGTATGTGAGTGT 907141 iv - v - ivi i vi vi (TGAGTG)n#Sim 1 TGAGTGTGAGTGTG-AGTGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTGT 49 chr3qtel1M 907142 -A-TATGTGTGTGAGTATGTG-CTGAGTCTGTGTATCAGTATCCGAGTGA 907188 - - i v i v -v v v i v i vv v (TGAGTG)n#Sim 50 GAGTGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTGTGA 99 chr3qtel1M 907189 GTGAGATGCATTGAGTGC 907206 v - -vv i (TGAGTG)n#Sim 100 GTGTGA-G-TGTGAGTGT 115 Matrix = Unknown Transitions / transversions = 0.65 (11/17) Gap_init rate = 0.06 (7 / 113), avg. gap size = 1.00 (7 / 7) 31 9.47 0.00 0.00 chr3qtel1M 907207 907251 (92749) (GT)n#Simple_repeat 1 45 (0) c_b160s251i1 6018 chr3qtel1M 907207 GTGTCTGTGTATGTGTGAGAGTGTGTGTGTGTGTGTGTGTGTGTG 907251 v i v v (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 45 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 36 31.11 4.74 1.38 chr3qtel1M 907252 907347 (92653) (TGAGTG)n#Simple_repeat 116 217 (1) m_b160s252i5 6019 chr3qtel1M 907252 A--ATGAATTTGAGTTAGAATGGGTATGTGAGTGT--GTGTGAACATATA 907297 --i i v vv i v vi -- iii ivi (TGAGTG)n#Sim 116 AGTGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTGTGAG 165 chr3qtel1M 907298 TATGTATGTGAGTGTGTGTGAGATTGT-A-TGTGTGTGTGTGTGTGTGTG 907345 i vi v v v - - v v v (TGAGTG)n#Sim 166 TGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTG 215 chr3qtel1M 907346 TG 907347 (TGAGTG)n#Sim 216 TG 217 Matrix = Unknown Transitions / transversions = 0.85 (11/13) Gap_init rate = 0.04 (4 / 95), avg. gap size = 1.50 (6 / 4) 24 15.58 2.00 0.00 chr3qtel1M 908173 908222 (91778) (TTAT)n#Simple_repeat 1 51 (0) m_b160s252i6 6020 chr3qtel1M 908173 TTATTTCCTTTTTTTTTTTTTTTTTTAATT-TTTATTTATTTATTTATTT 908221 vi v v v v v - (TTAT)n#Simpl 1 TTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTT 50 chr3qtel1M 908222 A 908222 (TTAT)n#Simpl 51 A 51 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.02 (1 / 49), avg. gap size = 1.00 (1 / 1) 932 26.41 1.92 2.91 chr3qtel1M 908765 909076 (90924) C L1ME3Cz_3end#LINE/L1 (449) 548 240 m_b160s551i7 6021 chr3qtel1M 908765 ATAATATTCCATAATATTCATATACCACAATTTATTCAGCCATTCTCCAA 908814 i vi vv i v i v C L1ME3Cz_3end# 548 ATAGTATTCCATTGTATGAATATACCACAATTTATTTATCCATTCCCCTA 499 chr3qtel1M 908815 CTGATGGGCATCCACTCAGTTTCCAGTTTCTGGCCACTACAAAAAGGGCT 908864 i i ii vviv i i v i i v iv C L1ME3Cz_3end# 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr3qtel1M 908865 GCCACAAACATTTGTGCACATACAGGTCCCTTTCCCTGC---TTTATGA- 908910 v ii iiv i ---- i i --v --- v ii - C L1ME3Cz_3end# 448 GCAATGAACATCCTTGTACAT----GTCTCCTT--GTGCACATGTGCGAG 405 chr3qtel1M 908911 --TCTCTTTGGGATATAAGCCCAGTAGTAACACTGCTGGATCAAAGGGTA 908958 -- i i i i vi i v iiv i i iv C L1ME3Cz_3end# 404 AGTTTCTCTAGGGTATATACCTAGAAGTGGAATTGCTGGGTCGTAGGGTA 355 chr3qtel1M 908959 TGCACAGTTTGATAACTTTTTGAGCATAGTTCCAAATTGCTCTCCAGAAT 909008 i vi --i viv - v v i i C L1ME3Cz_3end# 354 TGCGCATCTT--CAACTTTACTAG-ATATTGCCAAATTGCTCTCCAAAGT 308 chr3qtel1M 909009 GGTTGGATGTATTCACAGTTCCACTAGCAATGTATTAGTGTTCCTGTTTT 909058 v ivv i v i i i v v i i C L1ME3Cz_3end# 307 GGTTGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTTCCCGTTTC 258 chr3qtel1M 909059 CCCACATCCCCTCCAACA 909076 i i v C L1ME3Cz_3end# 257 TCCACATCCTCGCCAACA 240 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 31.43 CpG sites = 49, Kimura (unadjusted) = 33.46 Transitions / transversions = 1.58 (49/31) Gap_init rate = 0.04 (12 / 311), avg. gap size = 1.25 (15 / 12) 16 10.97 4.65 4.65 chr3qtel1M 909153 909195 (90805) (GGAG)n#Simple_repeat 1 43 (0) m_b160s252i8 6022 chr3qtel1M 909153 GGA-GGAGAGAGGGAGGGAGGCA-GTAGGGAGGGTCAGGCAGGGA 909195 - i v - v -- v (GGAG)n#Simpl 1 GGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGG--AGGGAGGGA 43 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.10 (4 / 42), avg. gap size = 1.00 (4 / 4) 348 32.91 8.06 3.61 chr3qtel1M 910796 910981 (89019) C L3#LINE/CR1 (166) 3933 3740 m_b160s601i8 6023 chr3qtel1M 910796 TTCCACTTTGGAACAGCTCTAATTTCTAGGAAGTTTCCTCTTAT------ 910839 i v i i vi i iiii ------ C L3#LINE/CR1 3933 TTCCATTTTTGGACAGCTCTGATTGTTAGAAAGTTCTTCCTTATATTGAG 3884 chr3qtel1M 910840 CTGAAACCTATGTCTCCA-AACGTTCACCAGCTGCTCTTGATTCCGCCCT 910888 i i iiv i ii- v i vii v i ii i C L3#LINE/CR1 3883 CCGAAATCTGCCTCCCTGTAACTTCCACCCATTGGTCCTAGTTCTGCCCT 3834 chr3qtel1M 910889 ATGGAACAGAGCAATGTACTTGTAAATCTTCCTCTATGAGACTATGAGAG 910938 v i vivi ivi vv v vi i i i ------i v C L3#LINE/CR1 3833 CTGGAGCCACACAGAATAAGTCTAATCCCTCTTCCA------CATGACAG 3790 chr3qtel1M 910939 TCCT-----TGTTCTCAGAGATC---CATATCTCCTATTAATTCTTTTCT 910980 i ----- i ivv v v --- i -i v i C L3#LINE/CR1 3789 CCCTTCAAATATTTGAAGACAGCTATCATGTCTCCT-CTAAGTCTTCTCT 3741 chr3qtel1M 910981 T 910981 C L3#LINE/CR1 3740 T 3740 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.87 CpG sites = 39, Kimura (unadjusted) = 45.97 Transitions / transversions = 1.95 (39/20) Gap_init rate = 0.06 (11 / 185), avg. gap size = 2.00 (22 / 11) 396 26.81 5.14 2.70 chr3qtel1M 911232 911484 (88516) C L1PREC2_orf2#LINE/L1 (686) 2608 2350 m_b160s551i8 6024 chr3qtel1M 911232 TACCTCC--TTTTGAATTTTTTCATTA--ATTCCCTTGAGATACT-GGAC 911276 i --i vvi vv -- v - v i - i C L1PREC2_orf2# 2608 TGCCTCCAGCTTTGTTCTTTTTGCTTAGGATTGCCTTG-GCTATTCGGGC 2560 chr3qtel1M 911277 CTTTTGTTCATCCTG-ATAAATTTTGGTATTATTGTTTTCTAGTTCTATG 911325 ii v vi i ii- i iiv vi - i C L1PREC2_orf2# 2559 TCTTTTTTGGTTCCATATGAATTTTAAAATAGTT-TTTTCTAGTTCTGTG 2511 chr3qtel1M 911326 AAAAATTT--TTGGTAGTTTGATTGGTATGGCTCTGAATAAGTAAATTAA 911373 i v -- v v i vi vv iv C L1PREC2_orf2# 2510 AAGAATGTCATTGGTAGTTTGATAGGAATAGCATTGAATCTGTAAATTGC 2461 chr3qtel1M 911374 TTTAGATAGAATTGTCATTTTTATTACATTAGTTCAACCTACTCAGGAGC 911423 i ii v v i v iv i ii vv ii v C L1PREC2_orf2# 2460 TTTGGGCAGTATGGCCATTTTAACGATATTGATTCTTCCTATCCATGAGC 2411 chr3qtel1M 911424 AAGTGATGTTTTCCCAATTATT-----CAGATCTGAATTTATTTGTGTAA 911468 v vi i v i ----- vv - v v i i C L1PREC2_orf2# 2410 ATGGAATGTTTTTCCATTTGTTTGTGTCATCTCTGA-TTTCTTTGAGCAG 2362 chr3qtel1M 911469 AACATGTTTTGTAATT 911484 ---- C L1PREC2_orf2# 2361 ----TGTTTTGTAATT 2350 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 33.07 CpG sites = 35, Kimura (unadjusted) = 33.69 Transitions / transversions = 1.13 (35/31) Gap_init rate = 0.05 (13 / 252), avg. gap size = 1.54 (20 / 13) 390 26.22 4.96 8.03 chr3qtel1M 912108 912248 (87752) MIRc#SINE/MIR 2 138 (130) m_b160s601i9 6025 chr3qtel1M 912108 GGGGCATCATAGTGCA-TGCAA----CACTGGGCTTGGAATCAGGAAGTA 912152 i vii i - v ---- i i -- MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAG-- 49 chr3qtel1M 912153 TTAGCTTCAAAAGTTCAAATATTGCCTCAGTTATTTATTGGGTATGTTAA 912202 -- v ----ii i i vii v v ii i i i v i v v MIRc#SINE/MIR 50 --ACCT----GGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGAC 93 chr3qtel1M 912203 CCTGGCCAAGTCACTTAACACTATTT--GTCTCAGTTCTCTGTCATCT 912248 i v - v i -- i ii -- MIRc#SINE/MIR 94 CTTGGGCAAGTCACTTAAC-CTCTCTGAGCCTCAGTTTCC--TCATCT 138 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.08 CpG sites = 23, Kimura (unadjusted) = 33.49 Transitions / transversions = 2.09 (23/11) Gap_init rate = 0.10 (14 / 140), avg. gap size = 1.29 (18 / 14) 188 27.49 4.82 3.57 chr3qtel1M 913740 913822 (86178) C L3#LINE/CR1 (2013) 2086 2003 m_b160s601i10 6023 chr3qtel1M 913740 ACCATTTGTGAAGAAAGTCAGAGGTTTGTTGTTCAAAATACTTTCTAAGC 913789 i i vviv iv ii - i i -i i i ?- C L3#LINE/CR1 2086 ATCATTTGTAATTGTAGTCAGAATTTCATT-TTTAAGA-GCTTCCCAN-C 2040 chr3qtel1M 913790 TCTCTT-AGTCTCCTCCTTTTTTGAG---CTGGCCAT 913822 i - i vi iii --- ? C L3#LINE/CR1 2039 CCTCTTGAGCCATCTTTCTTTTTGAGTCTCNGGCCAT 2003 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.09 CpG sites = 17, Kimura (unadjusted) = 38.09 Transitions / transversions = 3.40 (17/5) Gap_init rate = 0.06 (5 / 82), avg. gap size = 1.40 (7 / 5) 329 31.64 3.24 10.00 chr3qtel1M 914145 914453 (85547) C L1ME4c_3end#LINE/L1 (246) 584 295 m_b160s551i9 6026 chr3qtel1M 914145 TCTTCATATTCACTGTTTTTCATGGC---ACAATGTTCCAGAATGTTCAT 914191 v i iii v --- i i vviv ?v C L1ME4c_3end#L 584 TCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCGAGTNGAT 535 chr3qtel1M 914192 GTACCACAATTTATTGAGGAATCCCCCCACTGAAAAGCATCTATTTTGTT 914241 i i v ivv i i i vviii i vv C L1ME4c_3end#L 534 GTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAGGTTGTT 485 chr3qtel1M 914242 TCTTTCTTGTATCTGCTTCATTTTTTGCAACAACAACATCAACAAAAACA 914291 i---------------v i --------i i vv v i C L1ME4c_3end#L 484 TCC---------------AATTTTTCGC--------TATTATAAATAACG 458 chr3qtel1M 914292 CAGCAATGAATACTTTGGTATAGGTAGGACTTTTCTTTCTCTGA----CT 914337 v i ii v ii vi vvi i ii i ----i C L1ME4c_3end#L 457 CTGCAATGAACATCTTCGTGCATATAGCTTTTTCCTTCTTTTGAATTATT 408 chr3qtel1M 914338 TCCTTAGAGTTTATGCCTTGCAGTGGGATCTCTGGGTCATAAAGTATGGA 914387 ii vv v iv v i iv v ii i C L1ME4c_3end#L 407 TCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAA 358 chr3qtel1M 914388 GATTTGGTCAT--CTTTTAATAAATCATGATTA-CGAATAACTTTCTGGA 914434 v -- i -- i i vi ---- i- i vi iii C L1ME4c_3end#L 357 CATTT--TTATGGCTCTTGATACGT----ATTGCCAAATTGCTTTCCAAA 314 chr3qtel1M 914435 ATAGTTGGACCAATTCACA 914453 vi v i C L1ME4c_3end#L 313 AGGGTTGTACCAATTTACA 295 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.98 CpG sites = 54, Kimura (unadjusted) = 42.55 Transitions / transversions = 1.59 (54/34) Gap_init rate = 0.11 (33 / 308), avg. gap size = 1.18 (39 / 33) 315 33.78 8.12 3.18 chr3qtel1M 914565 915044 (84956) L1M2_orf2#LINE/L1 1627 2129 (1162) m_b160s551i10 6027 chr3qtel1M 914565 AACAAAGTCCTTTCAAAACAAAT---ACAGGGTATTATCTAAGAAATTAT 914611 i v vv v i --- vii --- i i ? L1M2_orf2#LIN 1627 AACAAAATACTAGCAAACCGAATTCAACAGCACATTA---AAAAGATNAT 1673 chr3qtel1M 914612 TTATTCTGATCAAGGGGGAGTTATGCCAGAGGTGCAAAGATAGTTCAACT 914661 ?i iiv v v v i i i i v L1M2_orf2#LIN 1674 NCACCATGATCAAGTGGGATTTATCCCAGGGATGCAAGGATGGTTCAACA 1723 chr3qtel1M 914662 TTAGGGAAACAATGAACATA----ATCACATT--CTGAACCAAAG-CATC 914704 vv vi v i i i---- i-- v iv i - -- L1M2_orf2#LIN 1724 TACGCAAATCAATAAACGTGATACATCACATCAACAGAATGAAGGACA-- 1771 chr3qtel1M 914705 TAAGACCACACAGTCCTTTCAATAGATGAAGAGATTATTCTGGACTAAGC 914754 - i i iii v i v i vviivi v iv ii L1M2_orf2#LIN 1772 -AAAACCATATGATCATCTCAATAGATGCAGAAAAAGCATTTGATAAAAT 1820 chr3qtel1M 914755 AC-ACTTATCTATTGTGGTAAAAATTT------AATTAGAGTATAGGCCT 914797 v - v vi - ii i i i------ - i--- L1M2_orf2#LIN 1821 TCAACATCCCT-TCATGATAAAAACTCTCAACAAATTAG-GTATAGA--- 1865 chr3qtel1M 914798 GATGGGGCCAT-TTTCAATGTGATGAAATATATATATTTAAAACCAAAAG 914846 ---i iv i -ii iiii i ivvi vvv v v L1M2_orf2#LIN 1866 ---AGGAACGTACCTCAACACAATAAAGGCCATATATGACAAACCCACAG 1912 chr3qtel1M 914847 ----TATCACATAAAATGGGGTTACATCAGAACTTTTTCCAATAAATGTA 914892 ----i i ivi vv vi iii vii vv iv?iv L1M2_orf2#LIN 1913 CTAACATCATACTGAATGGGGAAAAGTTGAAAGCCTTTCCTCTAAGANCT 1962 chr3qtel1M 914893 GGATTGAAGCAAAGATGGTTATTCTTCCTACTCTTA-------------T 914929 vii ii i vii i i iv i ii ------------- L1M2_orf2#LIN 1963 GGAACAAGACAAGGATGCCCACTTTCACCACTTCTATTCAACATAGTACT 2012 chr3qtel1M 914930 GGAAATGCTAGCAATAGCA---AAATGACAGGAAGCGATTCAAAGAATAA 914976 i v v v --- iiii v i vi vv i v vv L1M2_orf2#LIN 2013 GGAAGTCCTAGCCAGAGCAATTAGGCAAGAGAAAGAAATAAAAGGCATCC 2062 chr3qtel1M 914977 AGACAGGTAAAGAGGAGCTCAAACTATTCCTGTTTGCTGATGATAGGATG 915026 i iv v i iv i i i v i v - L1M2_orf2#LIN 2063 AAATTGGAAAGGAGGAAGTCAAATTGTCCCTGTTTGCAGATGACATGAT- 2111 chr3qtel1M 915027 GCTTACCTG-AAAAAACCC 915044 - iv ?- i ? L1M2_orf2#LIN 2112 -CTTATATNTAGAAAANCC 2129 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 46.40 CpG sites = 95, Kimura (unadjusted) = 47.69 Transitions / transversions = 1.53 (95/62) Gap_init rate = 0.06 (27 / 479), avg. gap size = 2.04 (55 / 27) 325 26.08 2.59 0.85 chr3qtel1M 914929 915044 (84956) L1PB_orf2#LINE/L1 2015 2132 (1162) m_b160s551i11 6027 chr3qtel1M 914929 TGGAAATGCTAGCAATAGCAA---AATGACAGGAAGCGATTCAAAGAATA 914975 i v v v ---i ii v i vi vv ii v v L1PB_orf2#LIN 2015 TGGAAGTCCTAGCCAGAGCAATCAGACAAGAGAAAGAAATAAAGGGCATC 2064 chr3qtel1M 914976 AAGACAGGTAAAGAGGAGCTCAAACTATTCCTGTTTGCTGATGATAGGAT 915025 v i iv iv i iv v L1PB_orf2#LIN 2065 CAAATCGGTAAAGAGGAAGTCAAACTGTCGCTGTTTGCTGATGATATGAT 2114 chr3qtel1M 915026 GGCTTACCTGAAAAAACCC 915044 v i? - i L1PB_orf2#LIN 2115 CGTNTACCT-AGAAAACCC 2132 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 31.45 CpG sites = 15, Kimura (unadjusted) = 32.74 Transitions / transversions = 1.00 (15/15) Gap_init rate = 0.02 (2 / 115), avg. gap size = 2.00 (4 / 2) 306 31.37 2.46 3.31 chr3qtel1M 916144 916265 (83735) MIRb#SINE/MIR 145 265 (3) m_b160s601i11 6028 chr3qtel1M 916144 AGATGGTGGTATTGATGACAATCTTTTAGGGTTTGCTGTAAGGATCAGG- 916192 i v i v i iv v i ivi - i i i ii- MIRb#SINE/MIR 145 AAATGGGGATAATAATACCTACCTCGCAGGGTT-GTTGTGAGGATTAAAT 193 chr3qtel1M 916193 GGGAT--TGTCAGTAAGGTACTGAACACAGTGCCTGGCACTTACTAAATG 916240 i -- ivv i ii v i v v ii MIRb#SINE/MIR 194 GAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCG 243 chr3qtel1M 916241 CTACATAACAAATGCTGGTTTTCTT 916265 ---i i v i i i v MIRb#SINE/MIR 244 CT---CAATAAATGGTAGCTCTATT 265 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.19 CpG sites = 25, Kimura (unadjusted) = 42.95 Transitions / transversions = 2.08 (25/12) Gap_init rate = 0.05 (6 / 121), avg. gap size = 1.17 (7 / 6) 419 32.36 0.73 0.73 chr3qtel1M 919257 919393 (80607) MIRc#SINE/MIR 2 138 (130) m_b160s601i12 6029 chr3qtel1M 919257 GAGGAACTGGTAGTACAATGAAGAGAGACCTGGGCATAGAATCAGAAGTG 919306 v v - i i i i i vv i v i i i ivi MIRc#SINE/MIR 2 GAGGCAGTG-TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA 50 chr3qtel1M 919307 CTTGAGCTTAAATCAAGCTTCAGACAGTTCCTAGCTCTGCACCCCTTAGC 919356 i i i ii i vv vi v v v v v iiv i vi MIRc#SINE/MIR 51 CCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGC 100 chr3qtel1M 919357 AAGT-ACGTAAACTCTATTTGCCTCAGTTTCCTCACCT 919393 - v v v vv i MIRc#SINE/MIR 101 AAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCT 138 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.73 CpG sites = 23, Kimura (unadjusted) = 43.16 Transitions / transversions = 1.10 (23/21) Gap_init rate = 0.01 (2 / 136), avg. gap size = 1.00 (2 / 2) 340 21.92 1.37 0.00 chr3qtel1M 920324 920396 (79604) MIR#SINE/MIR 111 184 (78) m_b160s601i13 6030 chr3qtel1M 920324 CTCCAT-CCCCAGTTTCCTCAGCACTTAAATGGGGAGAATAATATTACCT 920372 ii - i v vv v v v MIR#SINE/MIR 111 CTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCT 160 chr3qtel1M 920373 AACTTGGAAGGTTATTGTGAAGAT 920396 v iiv i i i MIR#SINE/MIR 161 ACCTCATAGGGTTGTTGTGAGGAT 184 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.12 CpG sites = 8, Kimura (unadjusted) = 26.12 Transitions / transversions = 1.00 (8/8) Gap_init rate = 0.01 (1 / 72), avg. gap size = 1.00 (1 / 1) 319 23.41 0.00 3.90 chr3qtel1M 920330 920409 (79591) MIRb#SINE/MIR 125 201 (67) m_b160s601i14 6030 chr3qtel1M 920330 CCCCAGTTTCCTCAGCACTTAAATGGGGAGAATAATATTACCTAACTTGG 920379 i v vv v --- v v i v MIRb#SINE/MIR 125 CCTCAGTTTCCTCATCTGTAAAATGGGGA---TAATAATACCTACCTCGC 171 chr3qtel1M 920380 AAGGTTATTGTGAAGATAAGGCAACATAAT 920409 i i i v iiii v MIRb#SINE/MIR 172 AGGGTTGTTGTGAGGATTAAATGAGATAAT 201 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.48 CpG sites = 9, Kimura (unadjusted) = 28.25 Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.04 (3 / 79), avg. gap size = 1.00 (3 / 3) 503 28.80 1.35 3.81 chr3qtel1M 923651 923946 (76054) HERVK14C#LTR/ERVK 2953 3241 (4193) m_b160s701i1 6031 chr3qtel1M 923651 GCTTTACATCAATTAGTACAAGAACAATTAGAATTAGGACATATTGAGGA 923700 i vv vv ?vv i ? vv HERVK14C#LTR/ 2953 GCCTTACAGGAATTAGTCAAAGAACAATTAGANAAAGGACACATNGAGCC 3002 chr3qtel1M 923701 AACAAATAGCCCATGAAAGTAGTCCCCTATATGTGTTCTAAAGAAAAAAA 923750 v vv vvi ? i v --- ? vi i v vv ? - HERVK14C#LTR/ 3003 CACATTTTCTCCNTGGAATT---CNCCAGTGTTTGTAATNAAGAAAAAA- 3048 chr3qtel1M 923751 ATCTATTAAATGGAGAATGCTAACAGATTTGAGATGAGTAAACTCAATCT 923800 - iivi i v ? v i iv vvv v iv i v HERVK14C#LTR/ 3049 -TCCGGCAGATGGCGNATGCTAACCGACTTACGAGCCGTCAATGCAGTCA 3097 chr3qtel1M 923801 TGAAAGACATGGGTTCTTTACAATCAGGTTTGCCATGCCCAAACATCATC 923850 ?v vv? vv ?i i ii vi ? v viv v i HERVK14C#LTR/ 3098 TNCAACCNATGGGGGCNCTGCAGCCAGGGCTGCCNTCCCCCGCCATGATT 3147 chr3qtel1M 923851 CCCAGGGAATGGCCCTTATGGATAATAGATATTAAGGATTGTTTTTACTC 923900 i i v ? vvii v v v i i i viv HERVK14C#LTR/ 3148 CCTAGAGACTGGCCNTTAATAGTTATAGATTTGAAGGACTGCTTCTTTAC 3197 chr3qtel1M 923901 TATCCCTCTTCACCCTGAAGACAGG----GATAAATTTGCTTTCTTACTA 923946 i -- v --ii v ? i---- v -- HERVK14C#LTR/ 3198 TATTCCTCT--AGC--AGAGCCNGATTTTGAAAAATTTGCTT--TTACTA 3241 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.27 CpG sites = 33, Kimura (unadjusted) = 38.46 Transitions / transversions = 0.67 (33/49) Gap_init rate = 0.04 (12 / 295), avg. gap size = 1.25 (15 / 12) 325 33.40 6.91 2.01 chr3qtel1M 924014 924346 (75654) HERVK#LTR/ERVK 4856 5204 (2332) m_b160s701i2 6032 chr3qtel1M 924014 TATAGCAAATGGATATTACACATATG---------GGAAAAA---CACAA 924051 i i i i i i--------- i v--- i?v HERVK#LTR/ERV 4856 TATGGCAAATGGATGTCACGCATGTACCTTCATTTGGAAGATTGTCATNT 4905 chr3qtel1M 924052 ATTTGTGTTACAATGGACACTTATTCAGGCTTTATATCTGTATCCTCTTA 924101 i iii v i v i vii i vv i v vii HERVK#LTR/ERV 4906 GTCCATGTAACAGTTGATACTTATTCACATTTCATATGGGCAACCTGCCA 4955 chr3qtel1M 924102 -ATGAGAGCAAGCTTA-TTCACATGTAATAAATCACCCATTTCATTGTTT 924149 - iii v -- - v v v v iii viv HERVK#LTR/ERV 4956 GACAGGAGAAAG--TACTTCCCATGTTAAAAAACATTTATTATCTTGTTT 5003 chr3qtel1M 924150 TGTCTCTATAGTA-TCCCACACACCATTAAGACTGATAATGAGCCCTCAT 924198 iivii i v - i v v vv i i i vvv HERVK#LTR/ERV 5004 TGCTGTCATGGGAGTTCCAGAAAAAATTAAAACTGACAATGGGCCAGGAT 5053 chr3qtel1M 924199 ATACCTCTAAAATATTAAAACAATTCTTATA-----GGAATTCTTTATAT 924243 ivvivv ii? vv v v ----- vvi vi i HERVK#LTR/ERV 5054 ACTGTAGTAAAGCNTTCCAAAAATTCTTAAATCAGTGGAAAATTACACAT 5103 chr3qtel1M 924244 ATCATATTTTTGGGATTCCTCACAATCCTACAGGACAGGCCATTGTAGAA 924293 iv i ----- i i i i ivv v v HERVK#LTR/ERV 5104 ACAACA-----GGAATTCCTTATAATTCCCAAGGACAGGCCATAGTTGAA 5148 chr3qtel1M 924294 AGGACTAATCAGACCCTCAAG---TGATTTATCAAAAAACAAAAACAGTG 924340 i vii v i---ii vi i v v i vi v HERVK#LTR/ERV 5149 AGAACTAATAGAACACTCAAAGCTCAATTGGTTAAACAAAAAGAAGGGGG 5198 chr3qtel1M 924341 AGATAG 924346 i HERVK#LTR/ERV 5199 AGACAG 5204 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 45.39 CpG sites = 61, Kimura (unadjusted) = 45.97 Transitions / transversions = 1.27 (61/48) Gap_init rate = 0.04 (14 / 332), avg. gap size = 2.14 (30 / 14) 11 24.76 0.00 2.56 chr3qtel1M 925137 925176 (74824) (TTGAAA)n#Simple_repeat 1 39 (0) m_b161s252i0 6033 chr3qtel1M 925137 TTGGAATTGTATACTGAAATTGAAAATGAGACTGTATTTG 925176 i - v i v i i v v (TTGAAA)n#Sim 1 TTGAAATTG-AAATTGAAATTGAAATTGAAATTGAAATTG 39 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1) 22 29.52 0.00 0.00 chr3qtel1M 926413 926482 (73518) (GTCT)n#Simple_repeat 1 70 (0) m_b161s252i1 6034 chr3qtel1M 926413 GTCTGTTTTTCAGTCTCTCTGTCAATCTCTCTCTCTCTTTTCCCATCTGT 926462 i v v v vi v v v i vi ii (GTCT)n#Simpl 1 GTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGT 50 chr3qtel1M 926463 CTGTCTGTTTATATGTCTGT 926482 i i v (GTCT)n#Simpl 51 CTGTCTGTCTGTCTGTCTGT 70 Matrix = Unknown Transitions / transversions = 0.89 (8/9) Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0) 745 34.06 3.81 2.79 chr3qtel1M 927379 927982 (72018) C L1PB1_3end#LINE/L1 (288) 610 1 m_b161s551i0 6035 chr3qtel1M 927379 TCTTTAAGTCTCTCCAGGCCTCTCTGAA-ATCATCCTGCTGATTGTTTCT 927427 ii v iv i v vi -ii iv?-i v vi i C L1PB1_3end#LI 610 TCTCCAATTCCATCCAGGTCGCTGCGAATGCCATTAN-TTCATTCCTTTT 562 chr3qtel1M 927428 TACAGAACAATACTATTCCGTAACATTCATATACCATAACTAATCCAGCC 927477 ii vvv i v i iii vi i ?i vv ii v C L1PB1_3end#LI 561 TATGGCTGAGTAGTATTCCATGGTATATATATACCACANTTTCTTTATCC 512 chr3qtel1M 927478 ATTCCCCAACTGATGGGCATTCACTCAGTTTCCA-GTATTTGCCACTACA 927526 i viii i iivv v v -i v v i i i C L1PB1_3end#LI 511 ACTCGTTGATTGATGGGCATTTGGGCTGGTTCCATATTTTTGCAATTGCG 462 chr3qtel1M 927527 AAAAGGGCTGCCACAAACCTTTTTGCACATTTGGGTCCCTTTTTCTCATT 927576 vv v i i v viv ii ----i vi --i v C L1PB1_3end#LI 461 AATTGTGCTGCTATAAACATGCGTGTGCA----AGTATCTTTTTC--GTA 418 chr3qtel1M 927577 TAA-GA------TTACTTTGGAAATAAGTCCAATAGAAACACTGCTGGAT 927619 - ------ v i iv v vii i viiv i C L1PB1_3end#LI 417 TAATGACTTCTTTTCCTCTGGGTAGATACCCAGTAGTGGGATTGCTGGAT 368 chr3qtel1M 927620 AAAAAAGGATATGCACATTTTGATAGCCCTTTGGGCATAGTTCCAAATTG 927669 v vi v vv vi -- -- ii ii v - vi v i C L1PB1_3end#LI 367 CAAATGGTAGTTCTAC--TTT--TAGTTCTTTAAGGA-ATCTCCACACTG 323 chr3qtel1M 927670 CTCTCCACAATGGTTGAATCAGTTCATAGCTGCACCAACAATGTATTAGT 927719 i i i i v ii i i viiv i i vv C L1PB1_3end#LI 322 TTTTCCATAGTGGTTGTACTAGTTTACATTCCCACCAGCAGTGTAGAAGT 273 chr3qtel1M 927720 GTCCCAGTTTTCCCACATTCCTTCCAACTTTTGTAATTTTTT--TTTTGT 927767 i vv iv i i viv v i i v -- v C L1PB1_3end#LI 272 GTTCCCTTTTCACCGCATCCACGCCAACATCTATTATTTTTTGATTTTTT 223 chr3qtel1M 927768 CATCTTAGACAT------GAGAGTTATGTAGTGGTACCTCAGAGTTGTCT 927811 v iv i v ------ii v ---i i v vv v i C L1PB1_3end#LI 222 GATTATGGCCATTCTTGCAGGAGTAA---GGTGGTATCGCATTGTGGTTT 176 chr3qtel1M 927812 TAATTTACATTTCTCTGATCAATAGTGATTTAGAGCACCTTTTCATATGA 927861 i i i v v v ii v C L1PB1_3end#LI 175 TGATTTGCATTTCCCTGATCATTAGTGATGTTGAGCATTTTTTCATATGT 126 chr3qtel1M 927862 GTGGAAATGGTTTTAATTTCTTCATTTGAAAATTG----TTCATATCCTT 927907 v vviiivi vv v v i ---- i C L1PB1_3end#LI 125 TTGTTGGCCATTTGTATATCTTCTTTTGAGAATTGTCTATTCATGTCCTT 76 chr3qtel1M 927908 TGGCCATTTATCAATTGGA--GAATGGTCTCAATTCTTATAAATTTAAGT 927955 v v i v ii v -- vv v i i-- iivi ivv C L1PB1_3end#LI 75 AGCCCACTTTTTGATGGGATTGTTTGTTTTT--TTCTTGCTGATTTGTTT 28 chr3qtel1M 927956 CAGTTCTCTATATATTTTAGAAATGAG 927982 v ?i i v i i v v C L1PB1_3end#LI 27 GAGTTCNTTGTAGATTCTGGATATTAG 1 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 45.02 CpG sites = 108, Kimura (unadjusted) = 46.94 Transitions / transversions = 1.17 (108/92) Gap_init rate = 0.04 (25 / 603), avg. gap size = 1.60 (40 / 25) 1151 27.46 4.63 4.24 chr3qtel1M 927437 927976 (72024) C L1ME3G_3end#LINE/L1 (376) 548 7 m_b161s551i1 6035 chr3qtel1M 927437 ATACTATTCCGTAACATTCATATACCATAACTAATCCAGCCATTCCCCAA 927486 v i ii vv i v ii i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr3qtel1M 927487 CTGATGGGCATTCACTCAGTTTCCAGTATTT-GCCACTACAAAAAGGGCT 927535 i i i vviv i v - i i v iv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr3qtel1M 927536 GCCACAAACCTTTTTGCACATTTGGGTCCCTTTTTCTCATTTAAGATTAC 927585 v ii v ii i --- v?i v v v v iv v i C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACAT---GCNTCCTTGTGCACATGTGCGAGTAT 402 chr3qtel1M 927586 TTT----GGAAATAAGTCCAATAGAAACACTGCTGGATAAAAAAGGATAT 927631 i---- v v v?i ? iv viiv i i v -- i C L1ME3G_3end#L 401 TTCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAA--GGGTAT 354 chr3qtel1M 927632 GCACATTTTGATAGCCCTTTGG-GCATAGTTCCAAATTGCTCTCCACAAT 927680 i i ----vi ii-iv v v i v ? C L1ME3G_3end#L 353 GCGCATTTTAA----ATTTTAATAGATACTGCCAAATTGCCCTCCAAAAN 308 chr3qtel1M 927681 GGTTGAATCAGTTCATAGCTGCACCAACAATGTATTAGTGTCCCAGTTTT 927730 i v i i i i viiv i i v v v v i C L1ME3G_3end#L 307 GGCTGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTC 258 chr3qtel1M 927731 CCCACATTCCTTCCAACTTTTG-------TAATTTTT----TTTTTGTC- 927768 ii iiv vi ? -------i ?i ---- i - C L1ME3G_3end#L 257 CCCACACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCA 208 chr3qtel1M 927769 ATCTTAGACATGAGAGTTATGTAGTGGTACCTCAGAGTTGTCTTAATTTA 927818 v vivi i ------- i i vv i i C L1ME3G_3end#L 207 ATCTGATGGGTGAAA-------AATGGTATCTCATTGTTGTTTTAATTTG 165 chr3qtel1M 927819 CATTTCTCTGATCAATAGTGATTTAGAGCACCTTTTCATATG---AGTGG 927865 i i v vv v i --- v C L1ME3G_3end#L 164 CATTTCCCTGATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGG 115 chr3qtel1M 927866 AAATGGTTTTAATTTCTTCATTTGAAAAT----TGTTCATATCCTTTGGC 927911 vv -- v - i v i vi ---- v C L1ME3G_3end#L 114 CCAT--TTGT-ATTTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCC 68 chr3qtel1M 927912 CATTTATCAATTGGAGAATGGTCTCAATTCTTATAAATTTAAGTCAGTTC 927961 v v ---i v i-v vi ivivv C L1ME3G_3end#L 67 CATTTTTCTATTGG---GTTGTCTT-TTTCTTATTGATTTGTAGGAGTTC 22 chr3qtel1M 927962 TCTATATATTTTAGA 927976 i i i C L1ME3G_3end#L 21 TTTATATATTCTGGA 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.71 CpG sites = 77, Kimura (unadjusted) = 35.32 Transitions / transversions = 1.18 (77/65) Gap_init rate = 0.06 (31 / 539), avg. gap size = 1.55 (48 / 31) 303 26.81 5.19 3.27 chr3qtel1M 927837 928106 (71894) C L1M4_orf2#LINE/L1 (0) 3294 3020 m_b161s551i2 6035 chr3qtel1M 927837 TGATTTAGAGCACCTTTTCATATG---AGTGGAAATGGTTTTAATTTCTT 927883 v v i i --- v vv -- v - v C L1M4_orf2#LIN 3294 TGATGTTGAGCATCTTTTCATGTGCTTATTGGCCAT--TTGTA-TATCTT 3248 chr3qtel1M 927884 CATTTGAAAATTGT----TCATATCCTTTGGCCATTTATCAATTGGAGAA 927929 v v i v ---- v v v ? ivv C L1M4_orf2#LIN 3247 CTTTGGAGAAATGTCTATTCAAATCCTTTGCCCATTTTTNAATTGGGTTA 3198 chr3qtel1M 927930 TG-GTCTCAATTCTTAT-AAATT-TAAGTCAGTTCTCTATATATTTTAGA 927976 v- iv- v i -i i - -- i i i C L1M4_orf2#LIN 3197 TTTGTCTTT-TTATTGTTGAGTTGTAAG--AGTTCTTTATATATTCTGGA 3151 chr3qtel1M 927977 AATGAGGCCTTTATTAGAACCTTTATATGTAAAAATGTTTTCCTAGTTTA 928026 v i? v i i vviv v v i v v i i v i i C L1M4_orf2#LIN 3150 TACNAGTCCCTTATCAGATATATGATTTGCAAATATTTTCTCCCATTCTG 3101 chr3qtel1M 928027 TTGCTTCCCTTCTAACTTGTCAGCACTAGTTTTGTTT---GTACAAAAAT 928073 v v vi i v - vvv - v iv --- i i C L1M4_orf2#LIN 3100 TGGGTTGTCTTTTCACTT-TCTTGA-TAGTGTCCTTTGAAGCACAAAAGT 3053 chr3qtel1M 928074 GTTTTAA-CTTAATATAATCAAAGTTATCTAGTT 928106 - -i i iv i v v v C L1M4_orf2#LIN 3052 -TTTTAATTTTGATGAAGTCCAATTTATCTATTT 3020 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.60 CpG sites = 29, Kimura (unadjusted) = 33.60 Transitions / transversions = 0.71 (29/41) Gap_init rate = 0.06 (16 / 269), avg. gap size = 1.44 (23 / 16) 315 25.61 6.25 4.25 chr3qtel1M 927837 928044 (71956) C L1M5_orf2#LINE/L1 (0) 3294 3083 m_b161s551i3 6035 chr3qtel1M 927837 TGATTTAGAGCACCTTTTCATATG---AGTGGAAATGGTTTTAATTTCTT 927883 ?v v i i --- v vv --- v? v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCAT---TTGNATATCTT 3248 chr3qtel1M 927884 CATTTG-AAAAT---TGTTCATATCCTTTGGCCATTTATCAATTGGAGAA 927929 v -i i --- vi i v v ?v ivvi C L1M5_orf2#LIN 3247 CTTTTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTG 3198 chr3qtel1M 927930 TG-GTCTCAATTCTTATAAATTTAAGTCAGTTCTCTATATATTTTAGAAA 927978 v- iv- ? vi ? ivivv i i i v C L1M5_orf2#LIN 3197 TTTGTCTTT-TTNTTATTGANTTGTAGGAGTTCTTTATATATTCTGGATA 3149 chr3qtel1M 927979 TGAGGCCTTTATTAGAACCTTTATATGT-----AAAAATGTTTTCCTAGT 928023 i v i i ----- ----- v v i i ? C L1M5_orf2#LIN 3148 CGAGTCCTTTGTCAGA-----TATATGTNTTGCAAATATTTTCTCCCANT 3104 chr3qtel1M 928024 TTATTGCTTCCCTTCTAACTT 928044 i i v v i v i C L1M5_orf2#LIN 3103 CTGTGGCTTGCCTTTTCATTT 3083 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.05 CpG sites = 24, Kimura (unadjusted) = 32.81 Transitions / transversions = 0.89 (24/27) Gap_init rate = 0.07 (14 / 207), avg. gap size = 1.57 (22 / 14) 563 32.05 3.30 3.30 chr3qtel1M 928322 928776 (71224) C L1P1_orf2#LINE/L1 (492) 2802 2348 m_b161s551i4 6036 chr3qtel1M 928322 TTTGGTAAATACTGAATTTTTATCCCCAAAACTTGGGTCTTTT-GGTTTG 928370 iv vv ii - vvi vv i i i- C L1P1_orf2#LIN 2802 TTTATTAAATAGGGAATCCTT-TCCCCATTGCTTGTTTTTCTCAGGTTTG 2754 chr3qtel1M 928371 GCAAACACTAGGTTATTGTAGTCATTGACTATTTTGTCTTGTGAATGTCA 928420 v v ii i vi vi --i viiv i - v iv i-- C L1P1_orf2#LIN 2753 TCAAAGATCAGATAGTTGTAGATAT--GCGGCGTTAT-TTCTGAGGGC-- 2709 chr3qtel1M 928421 TCTATTCC--TCTGTGGGACTA---CTCTATTTCTTAG--CCAATACCAA 928463 i i-- ii v iv --- i -- i -- i v C L1P1_orf2#LIN 2708 TCTGTTCTGTTCCATTGATCTATATCTCTGTTT--TGGTACCAGTACCAT 2661 chr3qtel1M 928464 ATAGTTTTGATGACCATTGCTTTGTAATATACTTTTAAGTC---TAGCAC 928510 iiv i v ii v i i v v --- ii C L1P1_orf2#LIN 2660 GCTGTTTTGGTTACTGTAGCCTTGTAGTATAGTTTGAAGTCAGGTAGCGT 2611 chr3qtel1M 928511 AACTAGGCCAACTTCATTTGCGTTTTTTTTCATTA--ATTCCCTTGA-AA 928557 i i--- --- i vi vi i vvv -- vv i-i C L1P1_orf2#LIN 2610 GAT---GCC---TCCAGCTTTGTTCTTTTGGCTTAGGATTGACTTGGCGA 2567 chr3qtel1M 928558 TTCTTGACCTTTTGTTCTTCCAGATGAACTTTGTTAGTA-TTTTTTATAG 928606 v vv vi v vv v i-v - vi i C L1P1_orf2#LIN 2566 TGCGGGCTCTTTTTTGGTTCCATATGAACTTTA-AAGTAGTTTTTTCCAA 2518 chr3qtel1M 928607 ATCTGTAAAATAATTTCTTGGGAGTTTGGTTGGTATGGCACTGAATAAGT 928656 v i iv v iv v i i v v i vvi C L1P1_orf2#LIN 2517 TTCTGTGAAGAAAGTCATTGGTAGCTTGATGGGGATGGCATTGAATCTAT 2468 chr3qtel1M 928657 AGATAAATTTAGGTATTATTATTATTTTTATTATATTCATTCTGCTTACC 928706 i v vi i i v viii i iv v v i C L1P1_orf2#LIN 2467 AAATTACCTTGGGCAGTATGGCCATTTTCACGATATTGATTCTTCCTACC 2418 chr3qtel1M 928707 CAGGAGCACTTGATATTTTTCCCATTGGTTAGATCCGACTTTATTTTTGT 928756 v ivvi i i vv v iv vvi i?v C L1P1_orf2#LIN 2417 CATGAGCATGGAATGTTCTTCCATTTGTTTGTATCCTCTTTTATTTCNTT 2368 chr3qtel1M 928757 GAAAAGTGATTTGTACTTCT 928776 iv i v C L1P1_orf2#LIN 2367 GAGCAGTGGTTTGTAGTTCT 2348 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.11 CpG sites = 73, Kimura (unadjusted) = 42.69 Transitions / transversions = 1.07 (73/68) Gap_init rate = 0.05 (23 / 454), avg. gap size = 1.30 (30 / 23) 46 13.55 0.00 0.00 chr3qtel1M 930681 930753 (69247) (A)n#Simple_repeat 1 73 (0) m_b161s252i2 6037 chr3qtel1M 930681 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAGAAAGAA 930730 i i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr3qtel1M 930731 AAGAAAACAAACAATGAAATAAA 930753 i v v vi v (A)n#Simple_r 51 AAAAAAAAAAAAAAAAAAAAAAA 73 Matrix = Unknown Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.00 (0 / 72), avg. gap size = 0.0 (0 / 0) 25 11.47 0.00 0.00 chr3qtel1M 930774 930811 (69189) (GT)n#Simple_repeat 1 38 (0) m_b161s252i3 6038 chr3qtel1M 930774 GTGTGTGTGTGTGTGTGTGTGTGTCTCTGTCTGTCTGT 930811 v v v v (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 38 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 427 30.30 9.50 4.29 chr3qtel1M 932389 932588 (67412) MIRb#SINE/MIR 17 226 (42) m_b161s601i0 6039 chr3qtel1M 932389 TACAGTGGATAGACTGGGGATAGTCCCTTAAATCAGGAAGACTGGGGTTT 932438 i v ---- v ii v ii vi i iv iv i MIRb#SINE/MIR 17 TGCAGTGGAAAGA----GCACGGGCTTTGGAGTCAGACAGACCTGGGTTC 62 chr3qtel1M 932439 TAATCCCACCTCAGAAGCTTGCTAGT--------------CAAGTTATAG 932474 v iv v vvi i i-------------- ivv MIRb#SINE/MIR 63 GAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTT 112 chr3qtel1M 932475 GACTTCTGTTTGATTCAGTTTTCTTTAACTGTAAAATGGGCTTAATGATA 932524 i i v vv vi i i- v vv i MIRb#SINE/MIR 113 AACCTCTCTGAGCCTCAGTTTCCTC-ATCTGTAAAATGGGGATAATAATA 161 chr3qtel1M 932525 TTTGCAAAGTCCTCTGGTTGTCATGAGGATAAAATAAGACAATGCCATGT 932574 ii i v--- vivv ii v i i - MIRb#SINE/MIR 162 CCTACC---TCGCAGGGTTGTTGTGAGGATTAAATGAGATAATG-CATGT 207 chr3qtel1M 932575 ATGAC-----ACACAGTGC 932588 vii -----i MIRb#SINE/MIR 208 AAAGCGCTTAGCACAGTGC 226 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.10 CpG sites = 32, Kimura (unadjusted) = 39.80 Transitions / transversions = 1.23 (32/26) Gap_init rate = 0.06 (11 / 199), avg. gap size = 2.55 (28 / 11) 216 31.32 6.47 3.50 chr3qtel1M 932715 932853 (67147) L2d_3end#LINE/L2 364 506 (10) m_b161s601i1 6040 chr3qtel1M 932715 TTCATAGTTGTTGGGGTAGTTTCTGCCCCATCATTTGGTGACCTCCATGA 932764 ivv i vv v i -- v ii vv v i v v L2d_3end#LINE 364 TTCATGTGTGTTAGTCTTGTCTC--CCCAACTAGATTGTAAGCTCCTTGA 411 chr3qtel1M 932765 GAGCAGGGGATACCCTG-CTTATATCACTTTAT-GTTCC---TGGTACTC 932809 i --- v - ii?i ? - ---ii ii ii L2d_3end#LINE 412 GGGCAGGG---ACCATGTCTTATACTNTTTTNTCGTTCCCCACAGCGCCT 458 chr3qtel1M 932810 ACCCTAGGGCTG-CCATGTACCAGGCACTTAAT---TATTTACTGATT 932853 v vi v -v ii vi i i --- i ii L2d_3end#LINE 459 AGCACAGTGCTGAGCACATAGTAGGCGCTCAATAAATACTTGTTGATT 506 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.03 CpG sites = 25, Kimura (unadjusted) = 42.87 Transitions / transversions = 1.47 (25/17) Gap_init rate = 0.07 (10 / 138), avg. gap size = 1.40 (14 / 10) 230 36.28 5.60 0.76 chr3qtel1M 932736 932860 (67140) L2b_3end#LINE/L2 335 465 (1) m_b161s601i2 6040 chr3qtel1M 932736 TCTGCCCCATCATTTGGTGACCTCCATGAGAGCAGGGGATAC-CCTG-CT 932783 v ii vviv v i i ivii?-i - L2b_3end#LINE 335 TCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCT 384 chr3qtel1M 932784 TATATCACT-TTATGTTCCTGGTACTCACCCTAGGG-CTGCCATGTACCA 932831 i - i-i i i i ii ii ii v vi ? - v iii vi L2b_3end#LINE 385 TGT-TCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTA 433 chr3qtel1M 932832 GGCACTTAAT---TATTTACTGATTAGAAGAA 932860 i i i --- ii v ii v L2b_3end#LINE 434 GGCGCTCAGTAAATATTTGTTGAATGAATGAA 465 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 46.79 CpG sites = 33, Kimura (unadjusted) = 56.47 Transitions / transversions = 2.75 (33/12) Gap_init rate = 0.05 (6 / 124), avg. gap size = 1.33 (8 / 6) 231 28.89 5.56 0.00 chr3qtel1M 932922 933011 (66989) C MIR3#SINE/MIR (5) 203 109 m_b161s601i3 6041 chr3qtel1M 932922 ATAGGATCACAGA-TG--AGCACTGAAAGGGACCTACTGGGCCATGGAAT 932968 i i - -- vi i vvvi ii vv i C MIR3#SINE/MIR 203 ATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGT 154 chr3qtel1M 932969 GTGAACCACTCATTTTATAGATG-GGAAACCGA-ATTCACAGGGG 933011 vii v v i - i -iii v i C MIR3#SINE/MIR 153 CCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGG 109 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.71 CpG sites = 16, Kimura (unadjusted) = 37.71 Transitions / transversions = 1.60 (16/10) Gap_init rate = 0.04 (4 / 89), avg. gap size = 1.25 (5 / 4) 299 34.20 7.41 2.53 chr3qtel1M 933662 933850 (66150) MIRc#SINE/MIR 12 209 (59) m_b161s601i4 6042 chr3qtel1M 933662 GATAAAGTAGA--GAATCCTGGACAT--AGTCAGCTATACTCTGAGTTTG 933707 i iv i -- iiv v -- vv v - i i MIRc#SINE/MIR 12 GGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC-CTGGGTTCG 60 chr3qtel1M 933708 AAGGAAACCTTGAAGATTTACT----GTGTTCTTCTGGGCAAGTCAAGTA 933753 ivvvviv ivivv i ---- vviii vv MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTA 110 chr3qtel1M 933754 CATTCTGGTAATTTGCCTCAGTTTCCTCAGCTCTCAAATGGGGATAACTA 933803 vvi v- i --- v v v iv MIRc#SINE/MIR 111 ACCTCTC-TGA---GCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAA 156 chr3qtel1M 933804 TATC------ACCTAACTTGGAAAATTAAGATAAGGTTAAAGTGATACCA 933847 i ------i v iiv iii ivvi i v v i v iv MIRc#SINE/MIR 157 TACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAA 206 chr3qtel1M 933848 TGT 933850 MIRc#SINE/MIR 207 TGT 209 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 44.37 CpG sites = 30, Kimura (unadjusted) = 46.31 Transitions / transversions = 0.91 (30/33) Gap_init rate = 0.05 (9 / 188), avg. gap size = 2.11 (19 / 9) 316 29.42 1.74 5.41 chr3qtel1M 933728 933842 (66158) MIR#SINE/MIR 81 191 (71) m_b161s601i5 6042 chr3qtel1M 933728 CTGTGTTCTTCTGGGCAAGTCAAGTA--CATTCTGGTAATTTGCCTCAGT 933775 vviii i vv -- vi ------ MIR#SINE/MIR 81 CTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTG------TGCCTCAGT 124 chr3qtel1M 933776 TTCCTCAGCTCTCAAATGGGGATAACTATATCACCTAACTTGGAAAATTA 933825 v v v iv vi v iiv iii i MIR#SINE/MIR 125 TTCCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTCATAGGGTTG 174 chr3qtel1M 933826 AGATAAGGTTAAAGTGA 933842 vvi i v v i MIR#SINE/MIR 175 TTGTGAGGATTAAATGA 191 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.71 CpG sites = 16, Kimura (unadjusted) = 37.71 Transitions / transversions = 1.00 (16/16) Gap_init rate = 0.06 (7 / 114), avg. gap size = 1.14 (8 / 7) 26 16.35 6.33 2.44 chr3qtel1M 934034 934112 (65888) (TACA)n#Simple_repeat 1 82 (0) m_b161s252i5 6043 chr3qtel1M 934034 TACATAGAAATATATATAGATAGATAAATA-ATA-A-ACATACACACAGA 934080 v v i i v v v - - - i -- (TACA)n#Simpl 1 TACATACATACATACATACATACATACATACATACATACATACATAC--A 48 chr3qtel1M 934081 TGCATATATACAT--ATACACACATACATACATA 934112 i i -- i (TACA)n#Simpl 49 TACATACATACATACATACATACATACATACATA 82 Matrix = Unknown Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.08 (6 / 78), avg. gap size = 1.17 (7 / 6) 278 27.23 8.82 2.78 chr3qtel1M 934922 935057 (64943) C MIR3#SINE/MIR (1) 207 64 m_b161s601i6 6044 chr3qtel1M 934922 AATCA-AAAATCTTAAGATGT-GGAGCTGAAAG--ACCTTTCAGA-ATTG 934966 - i v ii -i i -- -- - ii C MIR3#SINE/MIR 207 AATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTT--AGAGATCA 160 chr3qtel1M 934967 AAGAGTTTAACCTGCTTCAATTTTTAG--GAGGAAATTGCAGCACAGA-- 935012 vvv ii i- i v vi -- i vi v -- C MIR3#SINE/MIR 159 TCTAGTCCAACCC-CCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGA 111 chr3qtel1M 935013 ---GAAGGGATTTCCCCAAAGGTCATAGACTTTATGAGTGTCCAAGTC 935057 --- v i v - i v vi?vi v v vi i C MIR3#SINE/MIR 110 GGTGAAGTGACTTGCCC-AAGGTCACACAGCNAGTTAGTGGCAGAGCC 64 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.89 CpG sites = 20, Kimura (unadjusted) = 34.89 Transitions / transversions = 1.25 (20/16) Gap_init rate = 0.08 (11 / 135), avg. gap size = 1.45 (16 / 11) 51 0.00 0.00 0.00 chr3qtel1M 937088 937131 (62869) (GT)n#Simple_repeat 1 44 (0) c_b161s251i0 6045 chr3qtel1M 937088 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 937131 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 44 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 14 24.01 1.89 3.85 chr3qtel1M 939364 939416 (60584) (TCCT)n#Simple_repeat 1 52 (0) m_b161s252i6 6046 chr3qtel1M 939364 TCCATCTCTTCCTTCCCTCTCTTCCCTCCCACACTCGTCCCCTCC-TCCT 939412 v - i - i iv vi v i i - (TCCT)n#Simpl 1 TCCTTC-CTTCCTTCCTTC-CTTCCTTCCTTCCTTCCTTCCTTCCTTCCT 48 chr3qtel1M 939413 TCCT 939416 (TCCT)n#Simpl 49 TCCT 52 Matrix = Unknown Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.06 (3 / 52), avg. gap size = 1.00 (3 / 3) 214 33.04 4.10 3.25 chr3qtel1M 939864 939985 (60015) L2d2_3end#LINE/L2 412 534 (21) m_b161s601i7 6047 chr3qtel1M 939864 TGTTAGTGTATTGTCTGCTCCAGCC-GTCTGTAATTTCCATGAGAGCAGG 939912 vi v - i i i- vi vi v i L2d2_3end#LIN 412 TGTTTATGTCTTGTCT-CCCCAACTAGATTGTAAGCTCCTTGAGGGCAGG 460 chr3qtel1M 939913 ATTTGTCCCTTGCACCTCCTTTTGATAC----TGGTGCTTAGCCCAGGGC 939958 iviii vi ii i i v - v ----ii i i v v L2d2_3end#LIN 461 GACCATGTCTTATACTTCTTTGT-ATCCCCCACAGCGCCTAGCACAGTGC 509 chr3qtel1M 939959 CTGGCATTCAGTGTTTGCATTCAATGA 939985 v iv i--v ii i L2d2_3end#LIN 510 CTTGCACACAGTA--GGCGCTCAATAA 534 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.63 CpG sites = 25, Kimura (unadjusted) = 45.86 Transitions / transversions = 1.79 (25/14) Gap_init rate = 0.05 (6 / 121), avg. gap size = 1.50 (9 / 6) 20 0.00 0.00 0.00 chr3qtel1M 940375 940396 (59604) (T)n#Simple_repeat 1 22 (0) m_b161s252i7 6048 chr3qtel1M 940375 TTTTTTTTTTTTTTTTTTTTTT 940396 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTT 22 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 285 28.57 3.57 0.00 chr3qtel1M 940511 940594 (59406) C MIR3#SINE/MIR (3) 205 119 m_b161s601i8 6049 chr3qtel1M 940511 TTATAGGATCATAGATGATCA---CTAGAAGGGACCTACCAGGCCATAGA 940557 i i vvi --- i vvv ii vv C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTA 156 chr3qtel1M 940558 ATGTAACTCCCTCTTTTTAGGGATCAGAAAACTTAAG 940594 i vi i v vi v i v i C MIR3#SINE/MIR 155 GTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGG 119 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.39 CpG sites = 12, Kimura (unadjusted) = 36.39 Transitions / transversions = 1.00 (12/12) Gap_init rate = 0.01 (1 / 83), avg. gap size = 3.00 (3 / 1) 16 0.00 0.00 0.00 chr3qtel1M 942253 942270 (57730) (A)n#Simple_repeat 1 18 (0) m_b161s252i8 6050 chr3qtel1M 942253 AAAAAAAAAAAAAAAAAA 942270 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAA 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 18 15.81 0.00 0.00 chr3qtel1M 942900 942935 (57065) (AGACTTC)n#Simple_repeat 1 36 (0) m_b161s252i9 6051 chr3qtel1M 942900 AGACTTCAGGATCCAGATTTCAGACTCCAGACTTCA 942935 iv i i i (AGACTTC)n#Si 1 AGACTTCAGACTTCAGACTTCAGACTTCAGACTTCA 36 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 542 29.40 5.02 1.49 chr3qtel1M 943708 943966 (56034) C L1M1_orf2#LINE/L1 (1567) 1727 1460 m_b161s551i6 6052 chr3qtel1M 943708 ATATTGAAACAGCTCTACATTCCTGACATAACTCCTACTTGGTCATGGTG 943757 i v v ii i i ? iv v i i C L1M1_orf2#LIN 1727 ATGTTGAACCATCCTTGCATCCCNGGGATAAATCCCACTTGGTCATGATG 1678 chr3qtel1M 943758 TATTAA---TTTGCTGTAATGTT--------TTTGCTAACATTTTGTTTA 943796 v v v--- iv v -------- ii v C L1M1_orf2#LIN 1677 AATGATCTTTTTAATGTATTGTTGAATTCGGTTTGCTAGTATTTTGTTGA 1628 chr3qtel1M 943797 AGATTTTTGCATTAATATTTATTAGAAAAAAATTGGCATATAATTTTCTT 943846 i i i i -- i v v i i C L1M1_orf2#LIN 1627 GGATTTTTGCATCAATATTCATCAG--AGATATTGGCCTGTAGTTTTCTT 1580 chr3qtel1M 943847 TCTCTGTTTTGACCCCACATGGTTTAGGTATCAATACCATATTTGTGT-- 943894 i i v v v iiiiiv v iviiv i v iv -- C L1M1_orf2#LIN 1579 TTTTTGATGTGTCTTTGTCTGGTTTTGGTATCAGGGTAATACTGGCCTCG 1530 chr3qtel1M 943895 TATAATGGGGATTTGTTAGCACTTCTACTTTCCTTAATTTTCCCAATTGT 943944 v i -- vv i i i iv i i ii v vv v C L1M1_orf2#LIN 1529 TAGAATGAG--TTTGGAAGTATTCCCTCCTCCTCTATTTTTCGGAATAGT 1482 chr3qtel1M 943945 TTACATAATATTGGAATTTGTT 943966 ivi iv v v C L1M1_orf2#LIN 1481 TTGAGTAGGATTGGTATTAGTT 1460 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.39 CpG sites = 42, Kimura (unadjusted) = 38.39 Transitions / transversions = 1.27 (42/33) Gap_init rate = 0.03 (7 / 258), avg. gap size = 2.43 (17 / 7) 563 24.69 6.40 1.10 chr3qtel1M 943708 943879 (56121) C L1M2_orf2#LINE/L1 (1567) 1724 1544 m_b161s551i5 6052 chr3qtel1M 943708 ATATTGAAACAGCTCTACATTCCTGACATAACTCCTACTTGGTCATGGTG 943757 i v v ii i i iv v i i C L1M2_orf2#LIN 1724 ATGTTGAACCATCCTTGCATCCCTGGGATAAATCCCACTTGATCATGGTG 1675 chr3qtel1M 943758 TA--------TTAATTTGCTGTAATGTT---TTTGCTAACATTTTGTTTA 943796 ? -------- v vivi --- ii v C L1M2_orf2#LIN 1674 NATNATCTTTTTAATGTGCTGTTGAATTCGGTTTGCTAGTATTTTGTTGA 1625 chr3qtel1M 943797 AGATTTTTGCATTAATATTTATTAGAAAAAAATTGGCATATAATTTTCTT 943846 i iv i i i --ii v v i i C L1M2_orf2#LIN 1624 GGATTTTTGCATCTATGTTCATCAG--GGATATTGGCCTGTAGTTTTCTT 1577 chr3qtel1M 943847 TCTCTGTTTTGACCCCACATGGTTTAGGTATCA 943879 i i v v iiiiv v C L1M2_orf2#LIN 1576 TTTTTGTTGTGTCCTTGTCTGGTTTTGGTATCA 1544 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 31.12 CpG sites = 27, Kimura (unadjusted) = 31.12 Transitions / transversions = 1.80 (27/15) Gap_init rate = 0.02 (4 / 171), avg. gap size = 3.25 (13 / 4) 180 20.64 3.08 3.08 chr3qtel1M 944120 944184 (55816) C X7D_LINE#LINE/CR1 (34) 125 61 m_b161s601i9 6053 chr3qtel1M 944120 CAAGTTC-CTTTGCTTTTGGAATACCAGATTCCATACCCTTTATTCATTT 944168 ? v - v i i vi v vi vv i C X7D_LINE#LINE 125 CANGTACTCTATACTTTTGGGATAATATATTCCATACATTTTTATCATCT 76 chr3qtel1M 944169 A-AAGTGAAAGTTAGTA 944184 -i - - C X7D_LINE#LINE 75 ACGAGT-AAAG-TAGTA 61 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 22.64 CpG sites = 6, Kimura (unadjusted) = 24.70 Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.06 (4 / 64), avg. gap size = 1.00 (4 / 4) 26 0.00 0.00 0.00 chr3qtel1M 944423 944447 (55553) (T)n#Simple_repeat 1 25 (0) c_b161s251i1 6054 chr3qtel1M 944423 TTTTTTTTTTTTTTTTTTTTTTTTT 944447 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 21 23.33 0.00 0.00 chr3qtel1M 944483 944527 (55473) (T)n#Simple_repeat 1 45 (0) m_b161s252i10 6054 chr3qtel1M 944483 TTTTCTTCTATTTTCTTCATTTTTTTTTTTTTTTTGGTTTTGTTT 944527 i i v i iv vv v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 45 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 15 16.97 2.38 2.38 chr3qtel1M 947205 947246 (52754) (AAATTCT)n#Simple_repeat 1 42 (0) m_b161s252i11 6055 chr3qtel1M 947205 AAATTAT-TATTAAAAATTCTAAATTCTATTTTCTTAAATTCT 947246 v -v vv vv - (AAATTCT)n#Si 1 AAATTCTAAATTCTAAATTCTAAATTCTAAATTC-TAAATTCT 42 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.05 (2 / 41), avg. gap size = 1.00 (2 / 2) 241 27.83 5.83 9.77 chr3qtel1M 947432 947654 (52346) C L1M2_orf2#LINE/L1 (3007) 284 70 m_b161s551i7 6056 chr3qtel1M 947432 CCTTCCTTATCTCTTTAAATTACATCTATTTTTGGTTT-----TGCTTTT 947476 i i --- ---i ii -----ivv C L1M2_orf2#LIN 284 CCTTCTTTGTCTCTTT---TTACA---GTTTTTGACTTAAAGTCTATTTT 241 chr3qtel1M 947477 ATCTGAGATCAGGGTCACTACCACTGCTTTTTTTTTTTTTTTAAATTTCA 947526 v v vi vi iv i?i --------ii v C L1M2_orf2#LIN 240 ATCTGATATAAGTATAGCTACTCCTGCTCNCTTTT--------GGTTTCC 199 chr3qtel1M 947527 GCTGATGCAT--AATATTTTGCTCCAGCCTTTTACCATTACTCTGTATGT 947574 i -- -- i vi v i i iv i v i i C L1M2_orf2#LIN 198 GTT--TGCATGGAATATCTTTTTCCATCCCTTCACTTTCAGTCTATGTGT 151 chr3qtel1M 947575 AT-----CAGGCTGCTTTAAATGTGTTTTTTGTAAATAGTATATTGTAGG 947619 i ----- - ---- i v i iii i v v C L1M2_orf2#LIN 150 GTCTTTACAGG-TG----AAGTGAGTTTCTTGTAGGCAGCATATAGTTGG 106 chr3qtel1M 947620 CTTCTGTCTTTTAATCTAGTCTGTTA-TCTACTTCT 947654 v ii i v i v v ii - iv C L1M2_orf2#LIN 105 GTCTTGTTTTTTTATCCATTCAGCCANTCTATGTCT 70 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.15 CpG sites = 36, Kimura (unadjusted) = 36.15 Transitions / transversions = 1.80 (36/20) Gap_init rate = 0.11 (25 / 222), avg. gap size = 1.36 (34 / 25) 247 31.53 1.80 0.00 chr3qtel1M 947532 947642 (52358) C L1MEc_5end#LINE/L1 (48) 2479 2367 m_b161s551i8 6056 chr3qtel1M 947532 TGCATA--ATATTTTGCTCCAGCCTTTTACCATTACTCTGTATGTATCAG 947579 i-- i vi v iv vi i v i vv C L1MEc_5end#LI 2479 TGCATGGTATATCTTTTTCCATCCTTTTACTTTTAACCTATTTGTGTCTT 2430 chr3qtel1M 947580 GCTGCTTTAAATGTGTTTTTTGTAAATAGTATATTGTAGGCTTCTGTCTT 947629 vv ii v i ? i iii i v v v ii ii C L1MEc_5end#LI 2429 TATATTTAAAGTGNGTTTCTTGTAGGCAGCATATAGTTGGGTCTTGCTTT 2380 chr3qtel1M 947630 TTAATCTAGTCTG 947642 v i i C L1MEc_5end#LI 2379 TTTATCCAATCTG 2367 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 42.92 CpG sites = 21, Kimura (unadjusted) = 42.92 Transitions / transversions = 1.50 (21/14) Gap_init rate = 0.01 (1 / 110), avg. gap size = 2.00 (2 / 1) 275 21.31 0.00 0.00 chr3qtel1M 947582 947642 (52358) C L1MEh_5end#LINE/L1 (7) 2228 2168 m_b161s551i9 6056 chr3qtel1M 947582 TGCTTTAAATGTGTTTTTTGTAAATAGTATATTGTAGGCTTCTGTCTTTT 947631 i i i i i i i v v i i ? C L1MEh_5end#LI 2228 TGTTTTAAGTGTGTCTCTTGTAGACAGCATATTGTTGGATTTTGTTTTTN 2179 chr3qtel1M 947632 AATCTAGTCTG 947642 i i C L1MEh_5end#LI 2178 AATCCAATCTG 2168 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 27.27 CpG sites = 11, Kimura (unadjusted) = 27.27 Transitions / transversions = 5.50 (11/2) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 12 21.16 0.00 2.94 chr3qtel1M 948002 948036 (51964) (TACA)n#Simple_repeat 1 34 (0) m_b161s252i12 6057 chr3qtel1M 948002 TAAATCCAGTATATGCATACATATATGCATACATA 948036 v v - i i i i (TACA)n#Simpl 1 TACATACA-TACATACATACATACATACATACATA 34 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 17 22.00 3.23 3.23 chr3qtel1M 952719 952780 (47220) (AAAAG)n#Simple_repeat 1 62 (0) m_b161s252i13 6058 chr3qtel1M 952719 AAAAGAAAA-AAATGTTAAAGAAAACAAAATGAAAGTAAACATAAACCAA 952767 - v -v v vi v v - vv (AAAAG)n#Simp 1 AAAAGAAAAGAAAAG-AAAAGAAAAGAAAAGAAAAGAAAAGA-AAAGAAA 48 chr3qtel1M 952768 AG-AATGAAAATAA 952780 - v v (AAAAG)n#Simp 49 AGAAAAGAAAAGAA 62 Matrix = Unknown Transitions / transversions = 0.10 (1/10) Gap_init rate = 0.07 (4 / 61), avg. gap size = 1.00 (4 / 4) 17 0.00 0.00 0.00 chr3qtel1M 953723 953741 (46259) (T)n#Simple_repeat 1 19 (0) m_b161s252i14 6059 chr3qtel1M 953723 TTTTTTTTTTTTTTTTTTT 953741 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 32 0.00 0.00 0.00 chr3qtel1M 953802 953831 (46169) (T)n#Simple_repeat 1 30 (0) c_b161s251i2 6059 chr3qtel1M 953802 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 953831 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 30 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 11 27.58 0.00 0.00 chr3qtel1M 954443 954481 (45519) (TAATACA)n#Simple_repeat 1 39 (0) m_b161s252i15 6060 chr3qtel1M 954443 TAAGACATAAGAGGAAACTCATAGTACAAAATACATAAT 954481 v v viv iv i v (TAATACA)n#Si 1 TAATACATAATACATAATACATAATACATAATACATAAT 39 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 15 15.31 0.00 5.26 chr3qtel1M 960648 960687 (39313) (TGTATGT)n#Simple_repeat 1 38 (0) m_b161s252i16 6061 chr3qtel1M 960648 TGTATGTTGTATGTTGTCTCCTGTCTGTTTTTTATGTTGT 960687 v vi v -- v (TGTATGT)n#Si 1 TGTATGTTGTATGTTGTATGTTGTATG--TTGTATGTTGT 38 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 16 24.30 5.66 0.00 chr3qtel1M 961488 961540 (38460) (TA)n#Simple_repeat 1 56 (0) m_b161s252i17 6062 chr3qtel1M 961488 TATATAT-TAAACATGTTAAAATATGT-TAAATTTA-ACATATATATATA 961534 - v i i vv v i - v v - i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr3qtel1M 961535 TTTATA 961540 v (TA)n#Simple_ 51 TATATA 56 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.06 (3 / 52), avg. gap size = 1.00 (3 / 3) 14 21.54 6.12 0.00 chr3qtel1M 962429 962477 (37523) (ATAT)n#Simple_repeat 1 52 (0) m_b162s252i1 6063 chr3qtel1M 962429 ATACATGT-TAAATATGT-TAAATACA-ATATATGTATATATATATTTGT 962475 i i - v i - v i - i v i (ATAT)n#Simpl 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr3qtel1M 962476 AT 962477 (ATAT)n#Simpl 51 AT 52 Matrix = Unknown Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.06 (3 / 48), avg. gap size = 1.00 (3 / 3) 1390 29.34 1.82 2.95 chr3qtel1M 962838 963385 (36615) C L1ME3Cz_3end#LINE/L1 (449) 548 7 m_b162s551i0 6064 chr3qtel1M 962838 ATAATATTCCATAATATTCACATGCCACAATTTATTCAGCCATTCTCCAA 962887 i vi vv i i i v i v C L1ME3Cz_3end# 548 ATAGTATTCCATTGTATGAATATACCACAATTTATTTATCCATTCCCCTA 499 chr3qtel1M 962888 TTGATGGGCATCCATTCAATTTCCAGTTTCTAGGCACTACAAAAAAGTCT 962937 i ii vvivi i i v vi i v vv C L1ME3Cz_3end# 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr3qtel1M 962938 GCCACAAACATTTTCGCACATATAGGTCCCTTT---CCCTTTTTTAAGA- 962983 v ii ii i i ---- i i --- v v v vii - C L1ME3Cz_3end# 448 GCAATGAACATCCTTGTACAT----GTCTCCTTGTGCACATGTGCGAGAG 403 chr3qtel1M 962984 --TCTCTGGGATATAAGCCCAGTAGTAACACTGCTGGATCAAAGAGTATG 963031 -- i i vi i v iiv i i iv i C L1ME3Cz_3end# 402 TTTCTCTAGGGTATATACCTAGAAGTGGAATTGCTGGGTCGTAGGGTATG 353 chr3qtel1M 963032 CACAGTTTGATAATTTTTTGAACATAGTTCCAAATTGCTCTCCAGAATGG 963081 i vi --i i viv i- v v i i C L1ME3Cz_3end# 352 CGCATCTT--CAACTTTACTAG-ATATTGCCAAATTGCTCTCCAAAGTGG 306 chr3qtel1M 963082 TTGGATCACTTCACAACTCCACCAACAATGTATCCGTGTCCCTAGTTTTC 963131 v i v i vii i i vv v i i- ii C L1ME3Cz_3end# 305 TTGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTTCCC-GTTTCT 257 chr3qtel1M 963132 CCAGATCCCCTCCAATATTCGTCATTATC---TTTTTCTGTCATCTTAGC 963178 v i v i i i vi i ---i v---v i v C L1ME3Cz_3end# 256 CCACATCCTCGCCAACACTTGGTATTGTCAGACTTTTA---AATTTTTGC 210 chr3qtel1M 963179 CAATCTGAGAGGTGTGTAATGGTACCTCAGAATTGTTTTAATTTACATTT 963228 vi v i vvi ? i C L1ME3Cz_3end# 209 CAATCTGATGGGTGTGAAATGGTATCTCATTGTNGTTTTAATTTGCATTT 160 chr3qtel1M 963229 CTTGTATCAATAGTGATTTAGAGCACCTTTTAATATGACTAGAAATAGTT 963278 iivv i v vv v i v vi vviiivi C L1ME3Cz_3end# 159 CCCTGATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATT 110 chr3qtel1M 963279 TTAGTTTTATCATCTGAAAAGTGCCTGTTTATATGCTTTGACCATTTACC 963328 ivi iv v vi v i v v vi C L1ME3Cz_3end# 109 CGGGTTTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTC 60 chr3qtel1M 963329 AACTGGAGAATTG-CTTGAATTCTTATAAATTTGAGTCACTTCTCTATAT 963377 v i ---i - v-- vi vivv v i C L1ME3Cz_3end# 59 TATTGG---GTTGTCTTT--TTCTTATTGATTTGTAGGAGTTCTTTATAT 15 chr3qtel1M 963378 ATTTTAGA 963385 i i C L1ME3Cz_3end# 14 ATTCTGGA 7 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.54 CpG sites = 87, Kimura (unadjusted) = 38.11 Transitions / transversions = 1.26 (87/69) Gap_init rate = 0.04 (21 / 547), avg. gap size = 1.24 (26 / 21) 257 25.87 7.45 7.45 chr3qtel1M 963242 963429 (36571) C L1MC_orf2#LINE/L1 (0) 3294 3107 m_b162s551i2 6064 chr3qtel1M 963242 TGATTTAGAGCACCTTTTAATATGACTAGAAATAGTTTTAGTTT---TAT 963288 v ? i v - ----- v vivi i --- C L1MC_orf2#LIN 3294 TGATGTNGAGCATCTTTTCATATG-CT-----TATTTGCCATCTGTATAT 3251 chr3qtel1M 963289 CATCT---GAAAAGTGCCTGTTTATATGCTTTGACCATTTACCAACTGGA 963335 v --- vi i i i vi vi v vi? ii i C L1MC_orf2#LIN 3250 CTTCTTTGGTGAGGTGTCTGTTCAGGTCTTTTGCCCATTTTTNAATCGGG 3201 chr3qtel1M 963336 GAATTGCTTGAATTCTTATAAATTTGAGTC-----ACTTCTCTATATATT 963380 --- i vv vi-- i----- v i i C L1MC_orf2#LIN 3200 ---TTGTTTGTTTTCTTATTG--TTGAGTTTTAAGAGTTCTTTGTATATT 3156 chr3qtel1M 963381 TTAGAAGTGAGTCCTTTATCAGA---ATCTTTGAAAGTAAAAATGTTTTC 963427 i vivv ---i v--- i v v i C L1MC_orf2#LIN 3155 TTGGATAACAGTCCTTTATCAGATATGTCTTTT---GCAAATATTTTCTC 3109 chr3qtel1M 963428 CC 963429 C L1MC_orf2#LIN 3108 CC 3107 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 31.77 CpG sites = 24, Kimura (unadjusted) = 32.64 Transitions / transversions = 1.14 (24/21) Gap_init rate = 0.10 (18 / 187), avg. gap size = 1.56 (28 / 18) 269 25.82 6.79 6.79 chr3qtel1M 963242 963403 (36597) C L1M4_orf2#LINE/L1 (0) 3294 3133 m_b162s551i1 6064 chr3qtel1M 963242 TGATTTAGAGCACCTTTTAATATG---ACTAGAAATAGTTTTAGTTTTAT 963288 v v i v i --- i i vv -- v ---- C L1M4_orf2#LIN 3294 TGATGTTGAGCATCTTTTCATGTGCTTATTGGCCAT--TTGTA----TAT 3251 chr3qtel1M 963289 CATCT---GAAAAGTGCCTGTTTATATGCTTTGACCATTTACCAACTGGA 963335 v --- i i i i i v v v vi? i i C L1M4_orf2#LIN 3250 CTTCTTTGGAGAAATGTCTATTCAAATCCTTTGCCCATTTTTNAATTGGG 3201 chr3qtel1M 963336 GAATTGCTTGAATTCTTATAAATTTGAGTC-----ACTTCTCTATATATT 963380 --- ii vv i vi-- i----- v i C L1M4_orf2#LIN 3200 ---TTATTTGTCTTTTTATTG--TTGAGTTGTAAGAGTTCTTTATATATT 3156 chr3qtel1M 963381 TTAGAAGTGAGTCCTTTATCAGA 963403 i i vii? i C L1M4_orf2#LIN 3155 CTGGATACNAGTCCCTTATCAGA 3133 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 32.95 CpG sites = 23, Kimura (unadjusted) = 32.95 Transitions / transversions = 1.44 (23/16) Gap_init rate = 0.09 (14 / 161), avg. gap size = 1.57 (22 / 14) 272 32.94 2.45 4.58 chr3qtel1M 963288 963532 (36468) C L1P3_orf2#LINE/L1 (46) 3248 3009 m_b162s551i3 6064 chr3qtel1M 963288 TCATCTGAAAAGTGCCTGTTTATATGCTTTGACCATTTACCAACTGGAGA 963337 v i i i i v i v i viii - i - C L1P3_orf2#LIN 3248 TCTTTTGAGAAGTGTCTGTTCATATCCTTCGCCCACTTTTTGA-TGGGG- 3201 chr3qtel1M 963338 ATTGCTTGAATT---CTTATAAATTTGAGTCACTTCTCTATATATTTTAG 963384 - i vv --- i vv v v ii i v i i C L1P3_orf2#LIN 3200 -TTGTTTGTTTTTTTCTTGTAAATTTGTTTAAGTTCCTTGTAGATTCTGG 3152 chr3qtel1M 963385 AAGTGAGTCCTTTATCAGAATCTTTGAAAGTAAAAATGTTTTCCCTAACC 963434 vi v i i vvvv v vv i v i vvv i C L1P3_orf2#LIN 3151 ATATTAGCCCTTTGTCAGATGGATAGATTGCAAAAATTTTCTCCCATTCT 3102 chr3qtel1M 963435 A-AAATTGTCTATTTTGGGTCCAATAATGATTTCTAATTTTTCTTTGGCC 963483 i- ii i i i--iv ii i ii --- v v -- C L1P3_orf2#LIN 3101 GTAGGTTGCCTGTTC--ACTCTGATGATAGTTTC---TTTTGCTGTG--C 3059 chr3qtel1M 963484 ACAAATTTCTTCCATTTCCTTAGATCTGAGAGGTCAATTAT--CCTTTGT 963531 v i-i ivi vv iv vvv v -- i C L1P3_orf2#LIN 3058 AGAAG-CTCTTTAGTTTAATTAGATCCCATTTGTCAATTTTGGCTTTTGT 3010 chr3qtel1M 963532 T 963532 C L1P3_orf2#LIN 3009 T 3009 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 43.51 CpG sites = 41, Kimura (unadjusted) = 44.28 Transitions / transversions = 1.14 (41/36) Gap_init rate = 0.06 (14 / 244), avg. gap size = 1.21 (17 / 14) 291 23.53 4.67 4.67 chr3qtel1M 963297 963403 (36597) C L1MD_orf2#LINE/L1 (55) 3239 3133 m_b162s551i4 6064 chr3qtel1M 963297 AAGTGCCTGTTTATATGCTTTGACCATTTACCAACTGGAGAATTGCTTGA 963346 i i ? i i vi v v i i --- i v C L1MD_orf2#LIN 3239 AAATGTCTNTTCATGTCTTTTGCCCATTTTCTAATTGGA---TTGTTTGT 3193 chr3qtel1M 963347 ATTCTTA----TAAATTT-GAGTCACTTCTCTATATATTTTAGAAGTGAG 963391 v i ---- i i - -- v i i vii? C L1MD_orf2#LIN 3192 TTTTTTACTGTTGAGTTTTGAG--AGTTCTTTATATATTCTAGATACNAG 3145 chr3qtel1M 963392 TCCTTTATCAGA 963403 i i C L1MD_orf2#LIN 3144 TCCTTTGTCGGA 3133 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 28.65 CpG sites = 17, Kimura (unadjusted) = 30.15 Transitions / transversions = 2.43 (17/7) Gap_init rate = 0.07 (7 / 106), avg. gap size = 1.43 (10 / 7) 233 30.79 6.55 4.27 chr3qtel1M 963557 964014 (35986) C L1M2_orf2#LINE/L1 (387) 2904 2437 m_b162s551i5 6065 chr3qtel1M 963557 TATGTCTAAATCATGAACCCATTTTGACTTTATCTTGGTATAAGGTGCTA 963606 ii i i v v i v v i v v vv C L1M2_orf2#LIN 2904 TACATTTAAGTCTTTAATCCATTTTGAGTTGATTTTTGTATATGGTGAGA 2855 chr3qtel1M 963607 GCTGTAGGTC-AATGTCTAGTTTCTGCCATATTACT-TTCAATTTTTCCA 963654 v ivi - i v vvvi - viv - i i i C L1M2_orf2#LIN 2854 GATAGGGGTCTAGTTTCATTCTTCTGC-ATATGGATATCCAGTTTTCCCA 2806 chr3qtel1M 963655 GGA--GTTTTTTGTCAAAAAATGAGTTCTTATTCTAAAGACTGGAATCTT 963702 v --i v -- i i iv- i vii i ?v vv v-- C L1M2_orf2#LIN 2805 GCACCATTTATTG--AAGAGACT-GTCCTTTCCCCANTGTATGT--TCTT 2761 chr3qtel1M 963703 TGGG--TTTGT-GAAA--CAATAGGTTACTATAGTCATTGATT-ATTTT- 963745 v v -- - -- i v i i- v vv i v - i- C L1M2_orf2#LIN 2760 GGCGCCTTTGTCGAAAATCAGTTGGCTG-TAAATGCGTGGATTTATTTCT 2712 chr3qtel1M 963746 --GTCCTGCGCAATTAATCTGTTCTTCTCATTGAT-TAC---TCTGCTTC 963789 -- i ------i v ---- i - i--- i i C L1M2_orf2#LIN 2711 GGGTTCT------CTATTCTGTTC----CATTGGTCTATGTGTCTGTTTT 2672 chr3qtel1M 963790 TCAGCCAGTATCAAATGGTTTTGATAACTGCTGCTTTATAATATATTTTT 963839 vv i viiv i v iiv i i v C L1M2_orf2#LIN 2671 TATGCCAGTACCATGCTGTTTTGGTTACTATAGCTTTGTAGTATATTTTG 2622 chr3qtel1M 963840 AGGTCTAGTACAGCTAGGCCTTCTTCATTTG--CATTTTCTTCATTAATT 963887 i vi vv iv v i vv - -- v vi vv v v C L1M2_orf2#LIN 2621 AAGTCAGGTAGTGTGATGCCTCCAGC-TTTGTTCTTTTTGCTCAGGATTG 2573 chr3qtel1M 963888 CTCTTAAAATTCTTGACCTTTTTCTCTTCTAGCTGAACTTTATTATTATT 963937 i vivv vv ii vivv i vvi i vv ? C L1M2_orf2#LIN 2572 CTTTGGCTATTCGGGGTCTTTTGTGGTTCCATACGAATTTTAGGATTNTT 2523 chr3qtel1M 963938 TTTTTCTAGATCTATATAAAAATTTC-TTGGTGT----ATAGC--TCG-- 963978 - vv i i- i v - i ---- v-- i -- C L1M2_orf2#LIN 2522 T-TTTCTATTTCTGTG-AAGAATGTCATTGGTATTTTGATAGGGATTGCA 2475 chr3qtel1M 963979 --GAATAAGTAGATTGATTTACGTAATATTGTCATTTT 964014 -- vv i v iv i v ? C L1M2_orf2#LIN 2474 TTGAATCTGTAGATCGCTTTGGGTAGTATGGNCATTTT 2437 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 39.25 CpG sites = 62, Kimura (unadjusted) = 40.38 Transitions / transversions = 0.85 (62/73) Gap_init rate = 0.08 (37 / 457), avg. gap size = 1.35 (50 / 37) 22 13.04 0.00 0.00 chr3qtel1M 964039 964072 (35928) (A)n#Simple_repeat 1 34 (0) m_b162s252i2 6066 chr3qtel1M 964039 AAAAGAAAAAAAAAACAGAAAAAAAAAGAAAAAA 964072 i v i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 34 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 817 30.48 6.16 3.72 chr3qtel1M 964243 964794 (35206) C L1ME3_3end#LINE/L1 (257) 652 88 m_b162s551i7 6067 chr3qtel1M 964243 ATGTATTCCT--GGTTCTG-CTTGTTTTGCTCAGCATCA---CTGTGCAA 964286 i i -- vv - v i i ? --- - i C L1ME3_3end#LI 652 ATGTACTCTTTTGTGTCTGGCTTCTTTCGCTCAACATNATGTCTGTG-AG 604 chr3qtel1M 964287 ATTTTTCCAGGCCTTTTTAAA---ATCAAGTTGCTCATCATTTTTAATAG 964333 iv v -- v ivi--- ? - v i i iv v v C L1ME3_3end#LI 603 ATTCATCCATG--TTGTTGCGTGTANCA-GTAGTTCGTTCTTTTTTATTG 557 chr3qtel1M 964334 AATAATAACATTCCATTGCTTTCATATATCATAACTTCTTCAGCCATTTC 964383 vvvvi ii iv vv i i i v i v ii C L1ME3_3end#LI 556 CTGTGTAGTATTCCATTGTATGAATATACCACAATTTATTTATCCATTCT 507 chr3qtel1M 964384 CCAACTGATGGGCATCTACTCCTTTTCCAATTCTTTTCCAGCACAAAAAG 964433 ? vii i i ivviiv i i ?vv i vi ii v i C L1ME3_3end#LI 506 NCTGTTGATGGACATTTGGGTTGTTTCCAGTTTTNGGCTATTATGAATAA 457 chr3qtel1M 964434 AGCTGCTACAAA-ATTTTTCCACATGTG----GGT---CCTTTCCCCTCT 964475 ii - i vi v---- --- v v v v - C L1ME3_3end#LI 456 AGCTGCTATGAACATTCTTGTACATGTCTTTTGGTGGACATATGCACTC- 408 chr3qtel1M 964476 TTTATTATTTCCTTAGGATACAGATCCAGTAATGGCACTGCTGGATCAAA 964525 ------ ii v i i v i i v i v i i v C L1ME3_3end#LI 407 ------ATTTCTCTTGGGTATATACCTAGGAGTGGAATTGCTGGGTCATA 364 chr3qtel1M 964526 GTCTATGCACA-GTTTTATAGCCCTTTGG-GCATAATTCCAAATTGCTCT 964573 vv v ii - --- -- i -iv v v iv i i C L1ME3_3end#LI 363 GGGTAGGCGTATGTTT---AGC--TTTAGTAGATACTGCCAAACAGTTTT 319 chr3qtel1M 964574 CCAGAATGGTTGGATCATTTCACAACTCCACCAACAATGCATTATTGTCC 964623 i i v i v i vii i i v vv i C L1ME3_3end#LI 318 CCAAAGTGGTTGTACCAATTTACACTCCCACCAGCAATGTATGAGAGTTC 269 chr3qtel1M 964624 CAATTTTCCCACATCCCCTCTAACATTTATCATTATCTTTTCTTGTTATC 964673 i vii i v i i ivi i vv ii v v i C L1ME3_3end#LI 268 CAGTTGCTCCACATCCTCGCCAACACTTGGTATTGTCAGTCTTTTTAATT 219 chr3qtel1M 964674 TCAGCCA---------ATATGAAGTGGTACCTCAGAGTTGTTTTAATTTA 964714 i ---------i i v i vv v i C L1ME3_3end#LI 218 TTAGCCATTCTGGTGGGTGTGTAGTGGTATCTCATTGTGGTTTTAATTTG 169 chr3qtel1M 964715 AATTTCTCTAATCAATAATGACTTAGAGAATTTTTTCATATGACTATAGA 964764 v i i v v iv v v ii vi --- C L1ME3_3end#LI 168 CATTTCCCTGATGACTAATGATGTTGAGCACCTTTTCATATGCTTAT--- 122 chr3qtel1M 964765 TGGC--TTTAATGAAATA----TTTGTAAAGTGCTT 964794 -- i-- v v---- i i C L1ME3_3end#LI 121 TGGCCATTTG--GATATCCTCTTTTGTGAAGTGCCT 88 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 39.21 CpG sites = 90, Kimura (unadjusted) = 40.50 Transitions / transversions = 1.25 (90/72) Gap_init rate = 0.06 (33 / 551), avg. gap size = 1.67 (55 / 33) 1119 30.44 2.73 0.45 chr3qtel1M 964318 964756 (35244) C L1ME4c_3end#LINE/L1 (255) 575 127 m_b162s551i8 6067 chr3qtel1M 964318 TCATCATTTTTAATAGAATAATAACATTCCATTGCTTTCATATATCATAA 964367 i i vvvv i i vv ?v i i C L1ME4c_3end#L 575 TTATCATTTTTAATGGCTGCATAATATTCCATCGAGTNGATGTACCATAA 526 chr3qtel1M 964368 CTTCTTCAGCCATTTCCCAACTGATGGGCATCTACTCCTTTTCCAATTCT 964417 i vi i i i v i v i i vviiv i C L1ME4c_3end#L 525 TTTACTTAACCATTCCCCTATTGTTGGACATTTAGGTTGTTTCCAATTTT 476 chr3qtel1M 964418 TTTCCAGCACAAAAAGAGCTGCTACAAA-ATTTTTCCACATGTGGGTCCT 964466 iv i vi i v iv v ii - i ivii i i -- i C L1ME4c_3end#L 475 TCGCTATTATAAATAACGCTGCAATGAACATCTTCGTGCATATAG--CTT 428 chr3qtel1M 964467 TTCCCCTCTTTT--ATTATTTCCTTAGGATACAGATCCAGTAATGGCACT 964514 i i -- v vvi v i v i C L1ME4c_3end#L 427 TTTCCTTCTTTTGAATTATTTCCTTAGGATAAATTCCCAGAAGTGGAATT 378 chr3qtel1M 964515 GCTGGATCAAAGTCTATGCACAGTTTTATAGCCCTTTGGGCATAATTCCA 964564 i i vv v v i i vivi i v v C L1ME4c_3end#L 377 ACTGGGTCAAAGGGTATGAACATTTTTATGGCTCTTGATACGTATTGCCA 328 chr3qtel1M 964565 AATTGCTCTCCAGAATGGTTGGATCATTTCACAACTCCACCAACAATGCA 964614 i i v v i v i ?iv i i C L1ME4c_3end#L 327 AATTGCTTTCCAAAAGGGTTGTACCAATTTACANTGCCACCAGCAATGTA 278 chr3qtel1M 964615 TTATTGTCCCAATTTTCCCACATCCCCTCTAACAT------TTATCATTA 964658 v v? v i iv i ? i v i i ------ v v C L1ME4c_3end#L 277 TGAGNGTACCAGTTTCACCGCANCCTCGCCAGCATTGGGTATTATCAATT 228 chr3qtel1M 964659 TCTT---TTCTTGTTATCTCAGCCAATATGAAGTGGTACCTCAGAGTTGT 964705 i --- i i vi i iiviiii i i i vv i C L1ME4c_3end#L 227 TTTTAAATTTTTGCTAATTTAATAGGCGTAAAATGGTATCTCATTGTTGC 178 chr3qtel1M 964706 TTTAATTTAAATTTCTCTAATCAATAATGACTTAGAGAATTTTTTCATAT 964755 iv i i i v ii vv v iv i i C L1ME4c_3end#L 177 TTTAATTTGCATTTCTTTGATTACTAGCGAGGTTGAACATTTTTCCATGT 128 chr3qtel1M 964756 G 964756 C L1ME4c_3end#L 127 G 127 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 38.05 CpG sites = 80, Kimura (unadjusted) = 40.87 Transitions / transversions = 1.51 (80/53) Gap_init rate = 0.01 (6 / 438), avg. gap size = 2.33 (14 / 6) 36 26.22 2.94 0.00 chr3qtel1M 965689 965790 (34210) (AT)n#Simple_repeat 1 105 (0) m_b162s252i3 6068 chr3qtel1M 965689 ATATATATAT-TATATACATATGCATTTGTCTACATACATATATGTTGGT 965737 - i ii v i v i i i vvi (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr3qtel1M 965738 ATATATACATGTACA-ATACATATGCATATATGTATATAACTATATATTT 965786 i i i - i ii i vv v (AT)n#Simple_ 51 ATATATATATATATATATATATATATATATATATATATATATATATATAT 100 chr3qtel1M 965787 A-ATA 965790 - (AT)n#Simple_ 101 ATATA 105 Matrix = Unknown Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.03 (3 / 101), avg. gap size = 1.00 (3 / 3) 13 18.91 0.00 0.00 chr3qtel1M 966269 966298 (33702) (CAAAC)n#Simple_repeat 1 30 (0) m_b162s252i4 6069 chr3qtel1M 966269 CAAACTTAAAAAAACCAAACCAAAACAAAC 966298 iv vv v (CAAAC)n#Simp 1 CAAACCAAACCAAACCAAACCAAACCAAAC 30 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 332 27.65 10.53 2.08 chr3qtel1M 966434 966566 (33434) MIR3#SINE/MIR 4 147 (61) m_b162s601i0 6070 chr3qtel1M 966434 GTATAGTGGTGGAAAAGAAAG-GAACTTTGGAATGAGAGTCAGCAAACCT 966482 i v iv iv i - v --- v i v i MIR3#SINE/MIR 4 GCAGAGTGGCTGAGCAGAGAGAGCAC---GGACTGGGAGTCAGGAGACCT 50 chr3qtel1M 966483 GCTTTC-AGTAATATTTCTGA---TAATTAGCCCTGTTATGCTGGGCCAG 966528 vv - vviivi v--- i ? iv v ivi v MIR3#SINE/MIR 51 GGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAG 100 chr3qtel1M 966529 TCACTTAACTACTTTGG---------TCTTCATCTGTAGAATTAGGG 966566 v iv i --------- i i v MIR3#SINE/MIR 101 TCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGG 147 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 33.88 CpG sites = 17, Kimura (unadjusted) = 35.18 Transitions / transversions = 0.89 (17/19) Gap_init rate = 0.05 (7 / 132), avg. gap size = 2.43 (17 / 7) 248 32.26 0.00 0.00 chr3qtel1M 967178 967239 (32761) MIRc#SINE/MIR 44 105 (163) m_b162s601i1 6071 chr3qtel1M 967178 AGGAAGACCTAGGTTCAAATCATGCCTTTGCTTCATAATGTCTATATTAC 967227 i i i vi v i iv v v iv i i v MIRc#SINE/MIR 44 AGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGAC 93 chr3qtel1M 967228 CCTGAACAAATC 967239 i ii i MIRc#SINE/MIR 94 CTTGGGCAAGTC 105 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 38.54 CpG sites = 13, Kimura (unadjusted) = 44.39 Transitions / transversions = 1.86 (13/7) Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0) 203 34.56 2.44 1.20 chr3qtel1M 967182 967263 (32737) MIRb#SINE/MIR 51 133 (135) m_b162s601i2 6071 chr3qtel1M 967182 AGACCTAGGTTCAAATCATGCCTTTGCTTCATAATGTCTATATTACCCTG 967231 i i vi v i iv v v iv i i v i MIRb#SINE/MIR 51 AGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTG 100 chr3qtel1M 967232 AACAAAT--CTTATACTATTTTAACTCTGATTTT 967263 ii i -- - ivi i i vi v v MIRb#SINE/MIR 101 GGCAAGTTACTTA-ACCTCTCTGAGCCTCAGTTT 133 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 43.70 CpG sites = 17, Kimura (unadjusted) = 48.47 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.02 (2 / 81), avg. gap size = 1.50 (3 / 2) 50 2.04 0.00 0.00 chr3qtel1M 967438 967487 (32513) (T)n#Simple_repeat 1 50 (0) c_b162s251i0 6072 chr3qtel1M 967438 TTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 967487 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 16 13.08 0.00 0.00 chr3qtel1M 967582 967606 (32394) (C)n#Simple_repeat 1 25 (0) m_b162s252i5 6073 chr3qtel1M 967582 CCCCACCCCCCCCCACCCCCTCCCC 967606 v v i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCC 25 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 1452 29.69 2.76 2.41 chr3qtel1M 967960 968539 (31461) C L1ME5_3end#LINE/L1 (304) 637 56 m_b162s551i9 6074 chr3qtel1M 967960 TCCTGCTCATTTCACTTAGCATCA-GTTCATGTAAG-TCTCTCCAGGC-- 968005 i i iv i ii - -- v - iv v i-- C L1ME5_3end#LI 637 TCTTACTTTTTTCACTCAGCACTATGTT--TTTAAGATCCATCCATGTTG 590 chr3qtel1M 968006 CTTTCTGAAATCATCCTGTTGGTCATTTCTTACAGA-ACAGTAATATTCC 968054 v v v -- iv iv iii v v v-i - i i C L1ME5_3end#LI 589 CTATGTGTA--CATCTAGTCCGTTGCTTCTAACTGCTGCA-TAGTACTCC 543 chr3qtel1M 968055 ATAATTTTCATATACCACAATTTATTCAGCCATTCTCCAACTGATGGACA 968104 ii v v vi v iii v i v v C L1ME5_3end#LI 542 ATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCAGTGATGGACA 493 chr3qtel1M 968105 TCCAT-TCAGTTTCAGTTTCTAGCCACTACAAA-AGGGCTGCCACAAACA 968152 i v- iivi i ii i iv i - iv v ii C L1ME5_3end#LI 492 CCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCTGCAATGAACA 443 chr3qtel1M 968153 TTCGTGCACATACAGGTCCCTTTC----CCTTCTTTATAATCTCTTTGGG 968198 i vi i ---- i v---- viv v v i C L1ME5_3end#LI 442 TCCTCGTACAT----GTCCCCTTATGGACCTGTGTGAGAATTTCTTTGGG 397 chr3qtel1M 968199 ATATAATCCCAGTAGTAACACTGCTGGATCAAAGGGTATGCACAGTTTGA 968248 vv v iiiv i i v ii vvi -- C L1ME5_3end#LI 396 ATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATGCGTATACT-- 349 chr3qtel1M 968249 TAACTT--TTGAGCATAGTTCAAACTACTCTCCAAAATGGTTGGATTCGT 968296 i --i i i iv i- i i i i i v iiv C L1ME5_3end#LI 348 TAATTTGACTAAGTACTGC-CAGATTGCTCTCCAGAATGGCTGCACCAGT 300 chr3qtel1M 968297 TCACAACTCCACCAACAATGAATCAATGTCCCAGTTTTCCCACATCCCCT 968346 ii vii i i v v iv i vi ? i i v C L1ME5_3end#LI 299 CTACACTCCCACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATCCTCG 250 chr3qtel1M 968347 CCAACAATCATCATTATTT--TTTCCTGTCATCTTAGCCAATCTGACAGG 968394 v iiv ii--i i i-- i v i i i C L1ME5_3end#LI 249 CCAACACTTGGCATTATCCAGCTTTCTA--ATTTTTGCCAGTCTAATAGG 202 chr3qtel1M 968395 TGTGTAGTGGTATCTTAGAGTTGTCTTAATTTGCATCTCTCTGATCAACA 968444 iv i i vv i i i vi C L1ME5_3end#LI 201 TGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATTTCTCTGATTACTA 152 chr3qtel1M 968445 ATGACTTGGAGCATCTTTTCATATGACTAGAAATATTTTCAATTTCTTCA 968494 v v i vi ivv iiv ivii i v C L1ME5_3end#LI 151 ATGAGTTTGAGCATCTCTTCATATGCTTGTTAGCCTTTCGGGTTTCCTCT 102 chr3qtel1M 968495 TCTGAGAATTGTCTGTTCATATCCTTTGACCA-TTTTCAATTGGAG 968539 vi i v - v i C L1ME5_3end#LI 101 TCTGTAAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGGGG 56 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 38.01 CpG sites = 104, Kimura (unadjusted) = 39.25 Transitions / transversions = 1.62 (104/64) Gap_init rate = 0.04 (24 / 579), avg. gap size = 1.25 (30 / 24) 1460 27.91 1.29 1.85 chr3qtel1M 968046 968589 (31411) C L1ME3G_3end#LINE/L1 (377) 547 7 m_b162s551i10 6074 chr3qtel1M 968046 TAATATTCCATAATTTTCATATACCACAATTTATTCAGCCATTCTCCAAC 968095 i i v vv i i i i v i C L1ME3G_3end#L 547 TAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTAT 498 chr3qtel1M 968096 TGATGGACATCCATTCAGTTTC-AGTTTCTAGCCACTACAAA-AGGGCTG 968143 ii vviv - i i v i i - iv C L1ME3G_3end#L 497 TGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCTG 448 chr3qtel1M 968144 CCACAAACATTCGTGCACATACAGGTCCCTTTCC-CTTCTTT-ATAATCT 968191 v ii i v i i ?-- i v v - v v vi- vv i C L1ME3G_3end#L 447 CAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATTT 400 chr3qtel1M 968192 CTTTGGGATATAATCCCAGTAGTAACACTGCTGGATCAAAGGGTATGCAC 968241 ? i v v? ? v iiv i i i C L1ME3G_3end#L 399 CTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGC 350 chr3qtel1M 968242 AGTTTGATAACTTTTGA-GCATAGT-TCAAACTACTCTCCAAAATGGTTG 968289 v --- v i -iv v -i i i i ? i C L1ME3G_3end#L 349 ATTTT---AAATTTTAATAGATACTGCCAAATTGCCCTCCAAAANGGCTG 303 chr3qtel1M 968290 GATTCGTTCACAACTCCACCAACAATGAATCAATGTCCCAGTTTTCCCAC 968339 v iivi i vii i i v v iv v v i C L1ME3G_3end#L 302 TACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCAC 253 chr3qtel1M 968340 ATCCCCTCCAACAATCATCATTATTTTTTCCTGTCATCTTAGCCAATCTG 968389 i i v v ?ivi ivv?iii vvv i v C L1ME3G_3end#L 252 ACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATCTG 203 chr3qtel1M 968390 ACAGGTGTGTAGTGGTATCTTAGAGTTGTCTTAATTTGCATCTCTCTGAT 968439 ii viv i i vv i i i C L1ME3G_3end#L 202 ATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGAT 153 chr3qtel1M 968440 CAACAATGACTTGGAGCATCTTTTCATATGACTAGAAATATTTTCAATTT 968489 i vi i vv v vi vviiivv vv C L1ME3G_3end#L 152 TACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGTATTT 103 chr3qtel1M 968490 CTTCATCTGAGAATTGTCTGTTCATATCCTTTGACCA-TTTTCAATTGGA 968538 i v v i v - v - C L1ME3G_3end#L 102 CCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGG- 54 chr3qtel1M 968539 GAATGAGCTTGATTTTTTATAAATTAGAGTTAATTCTCTATATATTTTGG 968588 --i viv -- i vi v vivv i i i C L1ME3G_3end#L 53 --GTTGTCTT--TTTCTTATTGATTTGTAGGAGTTCTTTATATATTCTGG 8 chr3qtel1M 968589 A 968589 C L1ME3G_3end#L 7 A 7 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 35.50 CpG sites = 80, Kimura (unadjusted) = 36.10 Transitions / transversions = 1.16 (80/69) Gap_init rate = 0.03 (17 / 543), avg. gap size = 1.00 (17 / 17) 1101 30.44 3.39 3.27 chr3qtel1M 968446 969301 (30699) C L1M5_orf2#LINE/L1 (0) 3294 2438 m_b162s551i11 6074 chr3qtel1M 968446 TGACTTGGAGCATCTTTTCATATGACTAGAAATATTTTCAATTTCTTCAT 968495 ?v v i vi vviiivv v? v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr3qtel1M 968496 CTGAGAATTGTCTGTTCATATCCTTTGACCATTTTCA-ATTGGAGAATGA 968544 i v v vi i v i?- ivvi vv C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTT 3195 chr3qtel1M 968545 G-CTTGATTTTTTAT-AAATTAGAGTTAATTCTCTATATATTTTGGAAAT 968592 - -- ? -i ? iv v- i i i v i C L1M5_orf2#LIN 3194 GTCTT--TTTNTTATTGANTTGTAGG-AGTTCTTTATATATTCTGGATAC 3148 chr3qtel1M 968593 GAGGCCTTTATCAGAACCTTTG-ACTGTAAA-ATATTTTCCCAGTTTATT 968640 v i -iv v -?i i - v i ? i i v C L1M5_orf2#LIN 3147 GAGTCCTTTGTCAGA-TATATGTNTTGCAAATATTTTCTCCCANTCTGTG 3099 chr3qtel1M 968641 GCTTCCCTTCTAATCTTGTCTGCATTAGTTTTGTTTGTACAAAAACTTTT 968690 v i v i v ivi iv ivi vvv? vi i ii C L1M5_orf2#LIN 3098 GCTTGCCTTTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTTT 3049 chr3qtel1M 968691 CAGTTTGGTATAATCGAA-------ATTTTCTATTTTGTGATCAGTAATG 968733 v v i i? i v ------- i v i i i? i--- C L1M5_orf2#LIN 3048 AATTTTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGGTTNGTG--- 3002 chr3qtel1M 968734 ATCTCTAGTTCTGCTTTGGTCATAAAAACCTTCCCCT-TCCACAGATCTG 968782 -- i -- v iii v i - i i iv -? vv i vv C L1M5_orf2#LIN 3001 --CTTT--TTGTGTCCTGTTTA-AGAAATCTTTGCCTANCCCAAGGTCAC 2957 chr3qtel1M 968783 AGAGGTAAACTATCCTATGTT--CCTCTAATTTATTAATAATTTCATTCT 968830 ii i --i v -- i ivvvv v i i ?ii C L1M5_orf2#LIN 2956 GAAGATA--TTCTCCTATGTTTTCTTCTAGAAGTTTTATAGTTTTANCTT 2909 chr3qtel1M 968831 TTATGCCTAGGTC-ATGAACCCATTTTGACCTTATCTTGGTGTACGGCGT 968879 iiii - -i i ? vi v i v i i C L1M5_orf2#LIN 2908 TTACATTTAGGTCTATGA-TCCATCTNGAATTAATTTTTGTGTATGGTGT 2860 chr3qtel1M 968880 TAAGTATGGATCAATGCCTAGTTTCTGCCATATTAGTTTCCAATTTTCCC 968929 v i v i i v?iii v i v vii v v i C L1M5_orf2#LIN 2859 GAGGTAGGGGTCGAGNTTCATTTTTTTCCATATGGATATCCAATTGTTCC 2810 chr3qtel1M 968930 AGCAATTTTTATCAAACAGTAAGTTCTTATCCCAAAAGCTGGGAT-CTTT 968978 viv i ii v vvvi i vi ---- iiv - ? C L1M5_orf2#LIN 2809 AGCACCATTTGTTGAAAAGACTATCCTTTCCCCA----CTGAATTGCNTT 2764 chr3qtel1M 968979 GGG---TTTGTCAAAGACTAGGTTGCTATATTTGT-TGACTGTTTTATCC 969024 v--- i ii i? v? i v - --- v i ii C L1M5_orf2#LIN 2763 GGCACCTTTGTCAAAAATCAANTGNCCATATATGTGTG---GGTCTATTT 2717 chr3qtel1M 969025 CTTGAAC---CTAATCTATTCCACTGATCAACTAATCTATTCCTTA-GCC 969070 - i --- v i i v i vi - - C L1M5_orf2#LIN 2716 CT-GGACTCTCTATTCTGTTCCATTGATCTATTTGTCTAT-CCTTACGCC 2669 chr3qtel1M 969071 AATACCAAATAGTTTTGGTAACTGCTGCTCTATAGTATAGTTTT-AGATC 969119 v iv i i v iv i i - i - ? C L1M5_orf2#LIN 2668 AATACCACACTGTCTTGATTACTGTAGCTTTATAATA-AGTCTTGANATC 2620 chr3qtel1M 969120 TGGTACAGCTAAG-CCACCATCATTTGAT-TTTTTTTTCATTAATTCCCT 969167 ? vv - - v v - v - i -vi vii C L1M5_orf2#LIN 2619 NGGTAGTG-TAAGTCCTCCAAC-TTTGTTCTTCTTTTTCA-AGATTGTTT 2573 chr3qtel1M 969168 TGAA-ATTCTTGACCTTTTGTTTTTCCATATGAACTTTGTTGTTATTTTT 969216 iv- ? ii i iv i i ivvi i vi v C L1M5_orf2#LIN 2572 TGGCTATTCTNGGTCCTTTGCATTTCCATATAAATTTTAGAATCAGCTTG 2523 chr3qtel1M 969217 TCTAGGTCATTAAAATAGTTTTTTGGGAGTCTGATTGGTATAGCGCTAAA 969266 v vv vvi v iii vi v i v v ii i C L1M5_orf2#LIN 2522 TCAATTTCTACAAAAAAACCTGCTGGGATTTTGATTGGGATTGCATTGAA 2473 chr3qtel1M 969267 TAAATAGATTAGTTTAGGTAGCCTATACATTTTCA 969301 vv i i i v vv vv i ? C L1M5_orf2#LIN 2472 TCTATAGATCAATTTGGGGAGAATTGACATCTTNA 2438 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 40.49 CpG sites = 139, Kimura (unadjusted) = 41.35 Transitions / transversions = 1.23 (139/113) Gap_init rate = 0.05 (46 / 855), avg. gap size = 1.24 (57 / 46) 391 34.46 0.56 0.56 chr3qtel1M 970472 970649 (29351) C L1MD1_3end#LINE/L1 (361) 628 451 m_b162s551i12 6075 chr3qtel1M 970472 TTTCACTCAGCATCAGTTCGTGTAAGTCTCTCCAGGCCTTTCTGAA-ATC 970520 v v iiv v ii iiv iiv vi vi- C L1MD1_3end#LI 628 TTTCACTCAGCATAATTCTCTGGAGATTCATCCAGGTTGTTGCGTGTATC 579 chr3qtel1M 970521 ATCCTGTTGGTCATTTCTTACAGAACAGTAATATTCCATAATATACATAT 970570 viv- v ivi i iv vvv i ii iv i C L1MD1_3end#LI 578 AATA-GTTCGTTCCTTTTTATTGCTGAGTAGTATTCCATGGTATGGATGT 530 chr3qtel1M 970571 ACCACAATTTATTCAGCCATTCTCCAACTGATGGGCATCCATTCAGTTTC 970620 i i i i v vii v i iivviv C L1MD1_3end#LI 529 ACCACAGTTTGTTTAACCATTCACCCGTTGAAGGACATCTGGGTTGTTTC 480 chr3qtel1M 970621 CAGTTTCTAGCCACTACAAAAAGGGCTGC 970649 i i i i i v ii C L1MD1_3end#LI 479 CAGTTTTTGGCTATTACGAATAAAGCTGC 451 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 44.94 CpG sites = 37, Kimura (unadjusted) = 48.24 Transitions / transversions = 1.54 (37/24) Gap_init rate = 0.01 (2 / 177), avg. gap size = 1.00 (2 / 2) 430 24.75 0.00 0.00 chr3qtel1M 970549 970649 (29351) C L1ME3G_3end#LINE/L1 (377) 547 447 m_b162s551i13 6075 chr3qtel1M 970549 TAATATTCCATAATATACATATACCACAATTTATTCAGCCATTCTCCAAC 970598 i i iv i i i i v i C L1ME3G_3end#L 547 TAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTAT 498 chr3qtel1M 970599 TGATGGGCATCCATTCAGTTTCCAGTTTCTAGCCACTACAAAAAGGGCTG 970648 i ii vviv i i v i i v iv C L1ME3G_3end#L 497 TGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCTG 448 chr3qtel1M 970649 C 970649 C L1ME3G_3end#L 447 C 447 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 31.19 CpG sites = 17, Kimura (unadjusted) = 31.19 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.00 (0 / 100), avg. gap size = 0.0 (0 / 0) 494 25.96 2.44 3.70 chr3qtel1M 970730 970893 (29107) C L1ME4c_3end#LINE/L1 (387) 443 282 m_b162s551i14 6076 chr3qtel1M 970730 TTCGTGCACATACAGGTCCCTTTCCCTTCTTT---ATGATCTCTTTGGGA 970776 i v----- i i --- v i i i C L1ME4c_3end#L 443 TTCGTGCATATAG-----CTTTTTCCTTCTTTTGAATTATTTCCTTAGGA 399 chr3qtel1M 970777 TATAAGCCCAGTAGTAACACTGCTGGGTCAGAGGGTATGCACAGTTTGAT 970826 v vv v iiv i i i v v v C L1ME4c_3end#L 398 TAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTAT 349 chr3qtel1M 970827 AAGTTTTTGA-GCATAATTCCAAACTACTCTCCAAAATGGTTGGATTCGT 970875 -i i i -i i v v i i i v v iivi C L1ME4c_3end#L 348 -GGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAAT 300 chr3qtel1M 970876 TCACAACTCCACCAACAA 970893 i ?iv i C L1ME4c_3end#L 299 TTACANTGCCACCAGCAA 282 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 31.99 CpG sites = 25, Kimura (unadjusted) = 32.97 Transitions / transversions = 1.56 (25/16) Gap_init rate = 0.05 (8 / 163), avg. gap size = 1.25 (10 / 8) 180 27.12 16.95 0.00 chr3qtel1M 973940 973998 (26002) MIR#SINE/MIR 184 252 (10) m_b162s601i3 6077 chr3qtel1M 973940 TCAAATAGGATAATATTTGTAAAACACTTAGAACAA----------ATAA 973979 i ii v iv i i i---------- i MIR#SINE/MIR 184 TTAAATGAGTTAATACATGTAAAGCGCTTAGAACAGTGCCTGGCACATAG 233 chr3qtel1M 973980 TAGGTACTTGATAAATGCT 973998 i ii ii i MIR#SINE/MIR 234 TAAGCGCTCAATAAATGTT 252 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 31.11 CpG sites = 14, Kimura (unadjusted) = 37.27 Transitions / transversions = 7.00 (14/2) Gap_init rate = 0.02 (1 / 58), avg. gap size = 10.00 (10 / 1) 15 12.16 0.00 0.00 chr3qtel1M 974032 974058 (25942) (ATTC)n#Simple_repeat 1 27 (0) m_b162s252i6 6078 chr3qtel1M 974032 ATTCATTCATTCACTCAGTCATCCATT 974058 i v i (ATTC)n#Simpl 1 ATTCATTCATTCATTCATTCATTCATT 27 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 19 11.17 2.44 2.44 chr3qtel1M 974218 974258 (25742) (TAGTAAG)n#Simple_repeat 1 41 (0) m_b162s252i7 6079 chr3qtel1M 974218 TAGTAAGTAGTAAGTAGTTGGGTAGTAAGTAG-AAATATTAA 974258 - ii - i v (TAGTAAG)n#Si 1 TAGTAAGTAGTAAGTAG-TAAGTAGTAAGTAGTAAGTAGTAA 41 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 14 20.09 5.66 1.82 chr3qtel1M 974529 974581 (25419) (AAATATA)n#Simple_repeat 1 55 (0) m_b162s252i8 6080 chr3qtel1M 974529 AAATA-AAAATAATAAAGTCAAAAGAATGAAA-A-AAAGAAGAAAATATA 974575 - - i vv iv i - - iv v (AAATATA)n#Si 1 AAATATAAAAT-ATAAAATATAAAATATAAAATATAAAATATAAAATATA 49 chr3qtel1M 974576 AAATAT 974581 (AAATATA)n#Si 50 AAATAT 55 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.08 (4 / 52), avg. gap size = 1.00 (4 / 4) 29 21.97 0.99 6.25 chr3qtel1M 975112 975212 (24788) (AAAT)n#Simple_repeat 1 96 (0) m_b162s252i9 6081 chr3qtel1M 975112 AAAT-AATAAATAAATAAATGAACAAACAAACAAATAAACAAAATAGAAA 975160 - i i i i -v - v (AAAT)n#Simpl 1 AAATAAATAAATAAATAAATAAATAAATAAATAAATAAA-TAAATA-AAT 48 chr3qtel1M 975161 AGAAGAATCATTAAATGAATATGAATTTTTAAAATAGAGTAAACAAATAA 975210 i vi v v - - i vvv - - i i (AAAT)n#Simpl 49 AAATAAATAAATAAAT-AA-ATAAATAAAT-AAATA-AATAAATAAATAA 94 chr3qtel1M 975211 AT 975212 (AAAT)n#Simpl 95 AT 96 Matrix = Unknown Transitions / transversions = 1.12 (9/8) Gap_init rate = 0.07 (7 / 100), avg. gap size = 1.00 (7 / 7) 14 21.12 2.90 7.58 chr3qtel1M 979772 979840 (20160) (TATAT)n#Simple_repeat 1 66 (0) m_b162s252i10 6082 chr3qtel1M 979772 TATATT-TACTTCAAATGTATGTCATCAATATTTTA-ATTAGTATTTTTT 979819 - - - v - i i - v v - - v v (TATAT)n#Simp 1 TATATTATA-TT-ATAT-TATATTAT-ATTATATTATATTA-TATTATAT 45 chr3qtel1M 979820 TATATTATGTCAGATTAAATT 979840 i i v v (TATAT)n#Simp 46 TATATTATATTATATTATATT 66 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.10 (7 / 68), avg. gap size = 1.00 (7 / 7) 33 0.00 0.00 2.86 chr3qtel1M 980225 980260 (19740) (TTAAT)n#Simple_repeat 1 35 (0) c_b162s251i1 6083 chr3qtel1M 980225 TTAATTTAATTTAATTTAATTTAATTTTAATTTAAT 980260 - (TTAAT)n#Simp 1 TTAATTTAATTTAATTTAATTTAA-TTTAATTTAAT 35 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) 460 29.74 6.92 0.59 chr3qtel1M 980853 981011 (18989) MIR1_Amn#SINE/MIR 3 171 (59) m_b162s601i4 6084 chr3qtel1M 980853 GAAAGGCAGTGTGGAGTAGTAGGATA-AATGCTACATTTGAAATCAGTGG 980901 ii vv - - iii iv i v i v i vi MIR1_Amn#SINE 3 GGGAGGCAGTGTGGTCTAGT-GGATAGAGCACTGGACTGGGACTCGGGAG 51 chr3qtel1M 980902 ACTTGGATTCACATACTGACTTTGCTAC-------CTATATGAC--TGGG 980942 i i ?v? v i i i i ------- i?i -- MIR1_Amn#SINE 52 ACCTGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGG 101 chr3qtel1M 980943 TAATTCAGTTGAACTTTCTATACTACTGTTTACTTATCTTTAAAATGAAG 980992 i v v ? v i i?i iv v v i v ii MIR1_Amn#SINE 102 CAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGG 151 chr3qtel1M 980993 GTGAT-ATACTAAATGCCTT 981011 i i - i viv MIR1_Amn#SINE 152 ATAATGATACTGACCTCCTT 171 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 38.95 CpG sites = 30, Kimura (unadjusted) = 41.27 Transitions / transversions = 1.76 (30/17) Gap_init rate = 0.03 (5 / 158), avg. gap size = 2.40 (12 / 5) 387 32.93 12.99 0.50 chr3qtel1M 980857 981033 (18967) MIR3#SINE/MIR 3 201 (7) m_b162s601i5 6084 chr3qtel1M 980857 GGCAGTGTGGAGTAGTAGGATAAATGCTACATTTGAAATCAGTGGACTTG 980906 v vvv i iivi iii -iv i v i i vi i MIR3#SINE/MIR 3 GGCAGAGTGGCTGAGCAGAGAGAGCAC-GGACTGGGAGTCAGGAGACCTG 51 chr3qtel1M 980907 GATTCACATACTGACTTTGCTAC-------CTATATGAC--TGGGTAATT 980947 i vvi v i i i i ------- i i -- i v MIR3#SINE/MIR 52 GGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGT 101 chr3qtel1M 980948 CAGTTGAACTTTCTATACTACTGTTTACTTATCTTTAAAATGAAGGTGAT 980997 v v v i ivi iv v v i v i v v MIR3#SINE/MIR 102 CACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTT 151 chr3qtel1M 980998 ATACTAAATG------------CCTTCTAGCTCTAAA--TCTAAGATACT 981033 iv i ------------ i i v-- v v MIR3#SINE/MIR 152 GGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCT 201 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 42.51 CpG sites = 32, Kimura (unadjusted) = 44.56 Transitions / transversions = 1.23 (32/26) Gap_init rate = 0.03 (5 / 176), avg. gap size = 4.80 (24 / 5) 24 27.62 1.52 0.00 chr3qtel1M 981114 981179 (18821) (TA)n#Simple_repeat 1 67 (0) m_b162s252i11 6085 chr3qtel1M 981114 TAAATACATATATATTTGCATATCTATATGTAAGTATGTGTATAT-TAAA 981162 v i v ii v i vi i i - v (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr3qtel1M 981163 TATTTACATGTATATAT 981179 v i i (TA)n#Simple_ 51 TATATATATATATATAT 67 Matrix = Unknown Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.02 (1 / 65), avg. gap size = 1.00 (1 / 1) 250 36.13 1.23 10.00 chr3qtel1M 981219 981381 (18619) MIRb#SINE/MIR 1 150 (118) m_b162s601i6 6086 chr3qtel1M 981219 CAGAGGGATGACCTAATGTCTTAGTAGATATAGGAGCTAGCCTTGGAGTT 981268 iiii v ii i--- i v v v - vi i i MIRb#SINE/MIR 1 CAGAGGGGCAGCGTGGTGC---AGTGGAAAGAGCA-CGGGCTTTGGAGTC 46 chr3qtel1M 981269 AGAATGGTCTATTGTATTGAAGTCTGTTTTCTGATACATGCTAAATCTAT 981318 vv ii iv- - i vi i vi - vi v i iv v i MIRb#SINE/MIR 47 AGACAGACCTGG-GT-TCGAATCCCGGCT-CTGCCACTTACTAGCTGTGT 93 chr3qtel1M 981319 GACTATAGGCAAGTCATTTAACTACTC--AGTTTTCAAAGAATTTCTTTA 981366 iv i i i iv -- ii i----- i i i- MIRb#SINE/MIR 94 GACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTC-----AGTTTCCTC- 137 chr3qtel1M 981367 AAATTTGTAGAACAG 981381 -- i i ii MIRb#SINE/MIR 138 --ATCTGTAAAATGG 150 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 49.92 CpG sites = 37, Kimura (unadjusted) = 52.93 Transitions / transversions = 2.31 (37/16) Gap_init rate = 0.10 (16 / 162), avg. gap size = 1.06 (17 / 16) 275 33.55 5.39 5.39 chr3qtel1M 981241 981407 (18593) MIRc#SINE/MIR 17 183 (85) m_b162s601i7 6086 chr3qtel1M 981241 AGTAGATATAGGAGCTAGCCTTGGAGTTAGAATGGTCTATTGTATTGAAG 981290 i v v v - i v i i v ii --- vi vi MIRc#SINE/MIR 17 AGTGGAAAGAGCA-CTGGACTTGGAGTCAGGAAGACCT---GGGTTCGAG 62 chr3qtel1M 981291 TCTGTTTTCTGATACATGCTAAATCTATGACTATAGGCAAGTCATTTAAC 981340 ivvvi vi v i iv v i iv i i MIRc#SINE/MIR 63 TCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAAC 112 chr3qtel1M 981341 T--------ACTCAGTTTTCAAAGAATTTCTTTAAAATTTGTAGAACAGT 981382 i--------v i vv ----- v vv v v i i MIRc#SINE/MIR 113 CTCTCTGAGCCTCAGTTTCCTCA-----TCTGTAAAATGGGGATAATAAT 157 chr3qtel1M 981383 TGTTGGTCTGCAT-TTTCAGAGGGTT 981407 vvi vi v -ii v MIRc#SINE/MIR 158 ACCTGCCCTGCCTACCTCACAGGGTT 183 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 43.86 CpG sites = 25, Kimura (unadjusted) = 44.97 Transitions / transversions = 0.89 (25/28) Gap_init rate = 0.07 (11 / 166), avg. gap size = 1.64 (18 / 11) 30 0.00 0.00 0.00 chr3qtel1M 981467 981492 (18508) (AC)n#Simple_repeat 1 26 (0) c_b162s251i2 6087 chr3qtel1M 981467 ACACACACACACACACACACACACAC 981492 (AC)n#Simple_ 1 ACACACACACACACACACACACACAC 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 20 6.99 3.33 0.00 chr3qtel1M 981493 981522 (18478) (GA)n#Simple_repeat 1 31 (0) m_b162s252i12 6088 chr3qtel1M 981493 GAGAGAGAGAGAGAGA-AGAGAAAGACAGAG 981522 - i v (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 31 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 30 13.49 9.59 0.00 chr3qtel1M 981738 981810 (18190) (AT)n#Simple_repeat 1 80 (0) m_b162s252i13 6089 chr3qtel1M 981738 ATATCTTTATAT-TAT-TATAT-TAATTATAT-TATATACACATATATAT 981783 v v - - - vv - i i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr3qtel1M 981784 A-AAATATATAAATTTATAT-TAT-TATAT 981810 - v v v - - (AT)n#Simple_ 51 ATATATATATATATATATATATATATATAT 80 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.10 (7 / 72), avg. gap size = 1.00 (7 / 7) 822 31.36 3.81 0.00 chr3qtel1M 981940 982175 (17825) MIRb#SINE/MIR 14 258 (10) m_b162s601i8 6090 chr3qtel1M 981940 TGGTGTAGTAGATAGAGTGCCAGGTCTAACATGAGGAAAAC-----TCCA 981984 i i v ii vi v i iivi v iv i ----- i i MIRb#SINE/MIR 14 TGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCG 63 chr3qtel1M 981985 AATCTAGCCTCAGCCATTTATTTATCATTTGATCCTGGACAACTCACCTA 982034 iv v v i i viiii v i i i v i i MIRb#SINE/MIR 64 AATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTA 113 chr3qtel1M 982035 ACTCTGCTT-GCCTCAGTTTCCTAATCTGTAAAGTGGTGATAATAGGACC 982083 iiiv v- v i v iv MIRb#SINE/MIR 114 ACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACC 163 chr3qtel1M 982084 TATCTCCCAGGATTACAGTGCAGATTAAATGAGATA---TCTGAAAGATA 982130 i v i iiv vi ---iv v iiii MIRb#SINE/MIR 164 TACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCG 213 chr3qtel1M 982131 CTTAATATAGTACTTTGCACATAGTAAGTGCTATGTAAATATTAG 982175 ii i i i v i vvi iv MIRb#SINE/MIR 214 CTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAAATGGTAG 258 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 40.21 CpG sites = 48, Kimura (unadjusted) = 42.60 Transitions / transversions = 1.85 (48/26) Gap_init rate = 0.01 (3 / 235), avg. gap size = 3.00 (9 / 3) 207 26.45 0.00 3.77 chr3qtel1M 982131 982185 (17815) L2d2_3end#LINE/L2 497 549 (6) m_b162s601i9 6091 chr3qtel1M 982131 CTTAATATAGTACTTTGCACATAGTAAGTGCTATGTAAATATTAGTAATT 982180 i ii i i i i i i vvi v -- v L2d2_3end#LIN 497 CCTAGCACAGTGCCTTGCACACAGTAGGCGCTCAATAAATATTTGT--TG 544 chr3qtel1M 982181 ATTTG 982185 L2d2_3end#LIN 545 ATTTG 549 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 31.23 CpG sites = 10, Kimura (unadjusted) = 34.24 Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.04 (2 / 54), avg. gap size = 1.00 (2 / 2) 29 15.63 7.53 3.09 chr3qtel1M 982274 982366 (17634) (AGAAG)n#Simple_repeat 1 97 (0) m_b162s252i14 6092 chr3qtel1M 982274 AGAATGAG-AGGGAGTGAGAAGAGAGGA-AAGAAAAGGGAGGAGAGGAGA 982321 - - i -v i - i i i i (AGAAG)n#Simp 1 AGAA-GAGAAGAGA-AGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGA 48 chr3qtel1M 982322 AGAG--GGGAA-ATAAGGGAAGTGGAAGGGAAGAGAAGAG-AG-GAAGAG 982366 -- i - v i -i i - - (AGAAG)n#Simp 49 AGAGAAGAGAAGAGAAGAGAAG-AGAAGAGAAGAGAAGAGAAGAGAAGAG 97 Matrix = Unknown Transitions / transversions = 5.00 (10/2) Gap_init rate = 0.10 (9 / 92), avg. gap size = 1.11 (10 / 9) 1487 29.15 2.68 3.17 chr3qtel1M 983027 983660 (16340) C L1ME5_3end#LINE/L1 (304) 637 7 m_b162s551i15 6093 chr3qtel1M 983027 TCCTGCTCATTTCACTCAGC-CTCAGTTTATGTAAG-TCTCTCCAGGC-- 983072 i i iv - vv --v - iv v i-- C L1ME5_3end#LI 637 TCTTACTTTTTTCACTCAGCACTATGTTT--TTAAGATCCATCCATGTTG 590 chr3qtel1M 983073 CTTTCTGAAATCATCTTGCTGGTAATTTCTTACTGAACAATAATGTTCCA 983122 v v v -- v iiv vii v vvvv i ii C L1ME5_3end#LI 589 CTATGTGTA--CATCTAGTCCGTTGCTTCTAACTGCTGCATAGTACTCCA 542 chr3qtel1M 983123 TAATATTCATATACCACAATTTATTCAGCCATTCTCCAATTGATGGGCAT 983172 ii i v vi v iii v i v v i i C L1ME5_3end#LI 541 TGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCAGTGATGGACAC 492 chr3qtel1M 983173 CCACTCAGTTTCCAGTTTCTGGCCACTACAAAGAGACCTGCCACAAACAT 983222 vviv ii ii i iv i v ivv v ii C L1ME5_3end#LI 491 CCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCTGCAATGAACAT 442 chr3qtel1M 983223 TTGTGCACATACAGGTCCCTTTC----CCTTCTTTAGTATCTCTTTGGGA 983268 i---- v i v i v---- viv v v i C L1ME5_3end#LI 441 C----CTCGTACATGTCCCCTTATGGACCTGTGTGAGAATTTCTTTGGGA 396 chr3qtel1M 983269 TATAAGCCCAGTAGTAATACTGCTGAATCAAAGGGTATGTACAGTTTGAT 983318 vi v iiiv i ii v i--- --- C L1ME5_3end#LI 395 TATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATGC---GT---AT 352 chr3qtel1M 983319 AACTT--TTTGAGCA--TAATTCCAAATTGCTCTCCAGAATGGCTGGATG 983364 - -- vi -- v v i v iv C L1ME5_3end#LI 351 A-CTTAATTTGACTAAGTACTGCCAGATTGCTCTCCAGAATGGCTGCACC 303 chr3qtel1M 983365 TATTCACAATTCCTCCAACAATGTATTAGTGTCCCTGTTTTCCCACATCC 983414 vi ii v i v i i i v v i i ? i C L1ME5_3end#LI 302 AGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATCC 253 chr3qtel1M 983415 CCTCCAACATTCTGCGTTATTTTCCCCTGTCATTCTAGCCAATCTGACCG 983464 i v i iv i iivv ii v v i v i i iv C L1ME5_3end#LI 252 TCGCCAACACTTGGCATTATCCAGCTTTCTAATTTTTGCCAGTCTAATAG 203 chr3qtel1M 983465 ATGTGTAGTGGTATCTCAGAGTTGTCTTAATTGGCATTTCTCTGATTAAT 983514 i iv i vv i v v C L1ME5_3end#LI 202 GTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATTTCTCTGATTACT 153 chr3qtel1M 983515 AATGACATGGAGCATCTTTTCATATGGGTAGAAATAG--TTTCAA-TTTC 983561 vv v i vv iv--- -- ii- C L1ME5_3end#LI 152 AATGAGTTTGAGCATCTCTTCATATGCTTGT---TAGCCTTTCGGGTTTC 106 chr3qtel1M 983562 TTTGTATGAGAATTGTCTGTTCATATCCTTTGACCATTTATCAATTGGAG 983611 i iv v vi i v v v i C L1ME5_3end#LI 105 CTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGGGG 56 chr3qtel1M 983612 --AATGGCTTGATTTCTTATAAATTAGAGTCAATTCTCTATACATTTTGG 983659 --?vi v -- i vi v vivv i ii i i i i C L1ME5_3end#LI 55 TTNCCGTCTT--TTTCTTGTTGATTTGCAGGAGTTCCTTGTATATTCTAG 8 chr3qtel1M 983660 A 983660 C L1ME5_3end#LI 7 A 7 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.36 CpG sites = 95, Kimura (unadjusted) = 37.71 Transitions / transversions = 1.13 (95/84) Gap_init rate = 0.05 (29 / 633), avg. gap size = 1.28 (37 / 29) 1652 27.42 0.36 1.66 chr3qtel1M 983112 983660 (16340) C L1ME3G_3end#LINE/L1 (376) 548 7 m_b162s551i16 6093 chr3qtel1M 983112 ATAATGTTCCATAATATTCATATACCACAATTTATTCAGCCATTCTCCAA 983161 i i i vv i i i i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr3qtel1M 983162 TTGATGGGCATCCACTCAGTTTCCAGTTTCTGGCCACTACAAAGAGACCT 983211 i ii vviv i i v i i v ivv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr3qtel1M 983212 GCCACAAACATTTGTGCACATACAGGTCCCTTTCC-CTTCTTT-AGTATC 983259 v ii iiv i i ?-- i v v - v v vi- i C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATT 401 chr3qtel1M 983260 TCTTTGGGATATAAGCCCAGTAGTAATACTGCTGAATCAAAGGGTATGTA 983309 ? i v v? ? v iiv i ii ii C L1ME3G_3end#L 400 TCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCG 351 chr3qtel1M 983310 CAGTTTGATAACTTTTTGAGCATAATTCCAAATTGCTCTCCAGAATGGCT 983359 v i -- i vvv - v v i i ? C L1ME3G_3end#L 350 CATTTTAA--ATTTTAATAG-ATACTGCCAAATTGCCCTCCAAAANGGCT 304 chr3qtel1M 983360 GGATGTATTCACAATTCCTCCAACAATGTATTAGTGTCCCTGTTTTCCCA 983409 v ivv i v i v i i v v v i i C L1ME3G_3end#L 303 GTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCA 254 chr3qtel1M 983410 CATCCCCTCCAACATTCTGCGTTATTTTCCCCTGTCATTCTAGCCAATCT 983459 i i v i ?viii ivv? ii vvv i v C L1ME3G_3end#L 253 CACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATCT 204 chr3qtel1M 983460 GACCGATGTGTAGTGGTATCTCAGAGTTGTCTTAATTGGCATTTCTCTGA 983509 iv i viv i vv i v i C L1ME3G_3end#L 203 GATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGA 154 chr3qtel1M 983510 TTAATAATGACATGGAGCATCTTTTCATATGGGTAGAAATAGTTTCAATT 983559 v i vi v vv vviiivi vv C L1ME3G_3end#L 153 TTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGTATT 104 chr3qtel1M 983560 TCTTTGTATGAGAATTGTCTGTTCATATCCTTTGACCATTTATCAATTGG 983609 i iv v v i v v v C L1ME3G_3end#L 103 TCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGG 54 chr3qtel1M 983610 AGAATGGCTTGATTTCTTATAAATTAGAGTCAATTCTCTATACATTTTGG 983659 iv-- v -- vi v vivv i i i i C L1ME3G_3end#L 53 GT--TGTCTT--TTTCTTATTGATTTGTAGGAGTTCTTTATATATTCTGG 8 chr3qtel1M 983660 A 983660 C L1ME3G_3end#L 7 A 7 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 34.23 CpG sites = 76, Kimura (unadjusted) = 35.13 Transitions / transversions = 1.06 (76/72) Gap_init rate = 0.02 (11 / 548), avg. gap size = 1.00 (11 / 11) 371 24.58 6.25 4.62 chr3qtel1M 983517 983708 (16292) C L1MC_orf2#LINE/L1 (0) 3294 3100 m_b162s551i17 6093 chr3qtel1M 983517 TGACATGGAGCATCTTTTCATATGGGTA---GAAATAGTTTCAATTTCTT 983563 ii ? vv --- vv vvv vi vi C L1MC_orf2#LIN 3294 TGATGTNGAGCATCTTTTCATATGCTTATTTGCCATCTGTATATCTTCTT 3245 chr3qtel1M 983564 TGTATGAGAATTGTCTGTTCATATCCTTTGACCATTTATCAATTGGAGAA 983613 -i i-- vi i v v ? i ---i C L1MC_orf2#LIN 3244 TG-GTGAGG--TGTCTGTTCAGGTCTTTTGCCCATTTTTNAATCGG---G 3201 chr3qtel1M 983614 TGGCTTGATTTCTTATAAATTAGAGTCAA---TTCTCTATACATTTTGG- 983659 v i v viv v vv i --- i i i - C L1MC_orf2#LIN 3200 TTGTTTGTTTTCTTATTGTTGAGTTTTAAGAGTTCTTTGTATATTTTGGA 3151 chr3qtel1M 983660 -AAGAGGCCTTTATCAGA---ACCTTTGACTGTAAAAATGTT-TTCCAGT 983704 - v v ---ii --- i v v - i C L1MC_orf2#LIN 3150 TAACAGTCCTTTATCAGATATGTCTTT---TGCAAATATTTTCTCCCAGT 3104 chr3qtel1M 983705 TTAT 983708 i i C L1MC_orf2#LIN 3103 CTGT 3100 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 29.66 CpG sites = 22, Kimura (unadjusted) = 30.45 Transitions / transversions = 0.96 (22/23) Gap_init rate = 0.08 (15 / 191), avg. gap size = 1.40 (21 / 15) 368 30.65 2.29 4.21 chr3qtel1M 984234 984451 (15549) C L2b_3end#LINE/L2 (243) 223 10 m_b162s601i10 6094 chr3qtel1M 984234 TGAC-TTTTAGCTGGAACTTGGAGGAAGCCAG-GGGAGCTAGG-AGGCAG 984280 - v ii i i v -- -i i i v- ii C L2b_3end#LINE 223 TGACATTTGAGCTGAGACCTGAAGGATG--AGTAGGAGTTGGCCAGGCGA 176 chr3qtel1M 984281 AGATGAAAGGAGAGCTCATTCCATGCATAGGGAACAGTTGAAGAAAAGGA 984330 v vii - vv i v v iv?iv v v C L2b_3end#LINE 175 AGAGGTGGGGA-AGGGCGTTCCAGGCAGAGGGAACAGCANGTGCAAAGGC 127 chr3qtel1M 984331 CCATATTTGGGAGATGAAGTGTCGTGTTTTAGGAACAGCAAGGAGTCCAT 984380 vv vvi ?viiv? v iv v v C L2b_3end#LINE 126 CCTGAGGCGGGAGNGAGCNTGGCGTGTTCGAGGAACAGCAAGGAGGCCAG 77 chr3qtel1M 984381 TAGCACTAGATCTCACAGAGT--ATAAGGCCAGGAGTGTGTAAGGTATAA 984428 ivvi i ----i --ii vv - - i iv i C L2b_3end#LINE 76 TGTGGCTGGA----GCAGAGTGAGCAAGGGGA-GAGTG-GTAGGAGATGA 33 chr3qtel1M 984429 GACAGGTAAGATGGGAAGGCCAG 984451 i v vi i i vii C L2b_3end#LINE 32 GGCCGGAGAGGTAGCGGGGCCAG 10 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 36.81 CpG sites = 33, Kimura (unadjusted) = 40.78 Transitions / transversions = 1.06 (33/31) Gap_init rate = 0.06 (13 / 217), avg. gap size = 1.08 (14 / 13) 304 32.67 6.33 7.01 chr3qtel1M 984285 984600 (15400) C L2#LINE/L2 (0) 3082 2769 m_b162s601i11 6094 chr3qtel1M 984285 GAAAGGAGAGCTCATTCCATGCATAGGGAACAGTTGAAGAAAAGGACCAT 984334 iii i --i v v iviiv v v vv C L2#LINE/L2 3082 GGGGGAAGAGC--GTTCCAGGCAGAGGGAACAGCAAGTGCAAAGGCCCTG 3035 chr3qtel1M 984335 ATTTGGGAG-ATGAAGTGTCGTGTTTTAGGAACAGCAAGGAGTCCATTAG 984383 vvi -i v-v v iv v v iv C L2#LINE/L2 3034 AGGCGGGAGCGTGC-CTGGCGTGTTCGAGGAACAGCAAGGAGGCCAGTGT 2986 chr3qtel1M 984384 CACTAGATCTCACAGAGT--ATAAGGCCAGGAGTGTGTAAGGTATAAGA- 984430 vi i ----i i --iii vvii - i iv i i- C L2#LINE/L2 2985 GGCTGGA----GCGGAGTGAGCGAGGGGGAGAGTG-GTAGGAGATGAGGT 2941 chr3qtel1M 984431 CAGGTAAG--ATGGGAAGGCCAGG--ATATGAAGCCATATCTG--ATGAC 984474 iv i -- i -i i i-- i iii v i vv -- vii C L2#LINE/L2 2940 CAGAGAGGTAACGGG-GGACCAGATCATGTAGGGCCTTGTAGGCCATTGT 2892 chr3qtel1M 984475 AAGCAGA---TGAC-TTTATCCTGGAAGTAATAGCCACTGGAATTTATTG 984520 -- --- i - ii -- i ----v iv vii C L2#LINE/L2 2891 AAG--GACTTTGGCTTTTACTCTG--AGTGA----GATGGGAAGCCATTG 2850 chr3qtel1M 984521 AGGGATTTTGAGGAGGGGGAGGGAGTGATGTGGTCAAATGTAC--TTTAG 984568 ii i v -----i ii i vi iv -- i C L2#LINE/L2 2849 GAGGGTTTTGAGCAG-----AGGAGTGACATGATCTGACTTACGTTTTAA 2805 chr3qtel1M 984569 GA-GATCATTTTGAAAGCTG-ATT--GGATAGATTG 984600 i - i i ivv -i -- i i C L2#LINE/L2 2804 AAGGATCACTCTGGCTGCTGTGTTGAGAATAGACTG 2769 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 40.62 CpG sites = 62, Kimura (unadjusted) = 45.12 Transitions / transversions = 1.82 (62/34) Gap_init rate = 0.11 (34 / 315), avg. gap size = 1.24 (42 / 34) 269 17.68 0.00 8.77 chr3qtel1M 985160 985221 (14779) DNM1r#Unknown 2495 2551 (2111) m_b162s502i0 6095 chr3qtel1M 985160 TGTGTGTGTGTGTGTGTATACATATTGTATATATATGTATATATACACAC 985209 i i i----- i i i ii DNM1r#Unknown 2495 TGTGTGTATATGTGTGTATG-----TGTGTATATATGTGTATATATACGT 2539 chr3qtel1M 985210 ATACATACAACA 985221 ?i v DNM1r#Unknown 2540 ATNTATAGAACA 2551 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 19.26 CpG sites = 9, Kimura (unadjusted) = 21.63 Transitions / transversions = 9.00 (9/1) Gap_init rate = 0.08 (5 / 61), avg. gap size = 1.00 (5 / 5) 308 26.43 2.25 2.25 chr3qtel1M 985225 985313 (14687) C L2a_3end#LINE/L2 (3) 514 426 m_b162s601i12 6096 chr3qtel1M 985225 CATTCAGGTCAACAAACATTTATTCAGTAGCCTACTATGTGCTAATCACT 985274 v- i v i- i iv C L2a_3end#LINE 514 CATTCAT-TCAACAAATATTTATTGAGC-GCCTACTATGTGCCAGGCACT 467 chr3qtel1M 985275 GTGTTAAATTCTGATGGTGCAA-AG-AAAGGAAACAAGCAA 985313 vi iiiv iv i i i- -i vi ii C L2a_3end#LINE 466 GTTCTAGGCGCTGGGGATACAGCAGTGAACAAAACAGACAA 426 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 30.51 CpG sites = 16, Kimura (unadjusted) = 34.12 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.05 (4 / 88), avg. gap size = 1.00 (4 / 4) 243 21.43 0.00 0.00 chr3qtel1M 985585 985626 (14374) C L2d_3end#LINE/L2 (3) 513 472 m_b162s601i13 6097 chr3qtel1M 985585 ATCAATTAATTAATAAACATTTATTAAGTACCTACTGTGTGC 985626 i i i ii i ii i C L2d_3end#LINE 513 ATCAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGC 472 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 23.98 CpG sites = 9, Kimura (unadjusted) = 27.98 Transitions / transversions = 1.00 (9/0) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 219 25.53 0.00 0.00 chr3qtel1M 985586 985632 (14368) C L2a_3end#LINE/L2 (2) 515 469 m_b162s601i14 6097 chr3qtel1M 985586 TCAATTAATTAATAAACATTTATTAAGTACCTACTGTGTGCCATACA 985632 v i v i i i i ii i vi C L2a_3end#LINE 515 TCATTCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCA 469 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 29.31 CpG sites = 9, Kimura (unadjusted) = 33.02 Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 262 34.94 7.34 6.12 chr3qtel1M 985680 986115 (13885) C L2c_3end#LINE/L2 (22) 456 16 m_b162s601i15 6097 chr3qtel1M 985680 TAATAAGTATCTACTATATGGCAGGTATTGTGCTAATTACAAGTACAAAT 985729 v i iii i v iii v --i - iv ii C L2c_3end#LINE 456 TATTGAGCGCCTACTATGTGCCAGGCGCTGGG--GAT-ACAAAGATGAAT 410 chr3qtel1M 985730 AAGGGGGGGGGGGAATGCC---AAGAAGCTTACAAACTAATGGGGG-GA- 985774 iviv vvvv-- --- i i iv i i - - C L2c_3end#LINE 409 AAGACACGGTCCC--TGCCCTCAAGGAGCTCACAGTCTAGTGGAGGAGAC 362 chr3qtel1M 985775 AAACAG----ACAGACAATTATGTAAAAACATGATATATTA-AAGTATCA 985819 i ?---- i--- v v v - v - iii C L2c_3end#LINE 361 AGACANGTAAACAGACAATTAC---AATACAAGTTA-ATGATAAGTGCTA 316 chr3qtel1M 985820 TA-TACAACTATATACAAAACA-TATAAATTAGAGACAATAAATAAAGAA 985867 - ivi v v iiiii- ------ i vv i i vi i iv C L2c_3end#LINE 315 TAATGGGAGTATAGACAGGGTGCTAT------GGGAGCACAGAGGAGGGC 272 chr3qtel1M 985868 AAC---ATTAGCATTAGGGGGATAAGAGAAAGCTTTCTA-AGACAGTTAG 985913 v --- i ?v i - v i i i ii- ivi v v C L2c_3end#LINE 271 ACCTAGACTAGNCTTGGGGGG-TCAGGGAAGGCTTCCCGGAGGAGGTGAC 223 chr3qtel1M 985914 ATTGTATCCAAGATCTAAAGGA--AGTAGGGAAATCAGA-AGATAGAGAT 985960 ivv v ii ?ii i -- -- i i v- i i - v C L2c_3end#LINE 222 ATCTGAGCTGAGNCTTGAAGGATGAGTAGG--AGTTAGCCAGGTGGA-AG 176 chr3qtel1M 985961 GAGGAGGGT-GAAAATTCCAGGCATGAGACACAGCCAGTGCTACTACATA 986009 i v- iv vii iv vv v vvi ?ii C L2c_3end#LINE 175 GAGGGGGGAAGAGCATTCCAGGCAGAGGGAACAGCATGTGCAAAGGCNCG 126 chr3qtel1M 986010 GAGTTGTG------TTGGGGTATTTTGTGTGAGGAACATTAAAAGGGTAA 986053 viiv ------i v ii--- v i ii-i i?i v v C L2c_3end#LINE 125 GAGGCAGGAAAGAACTGCGGCG---TGTTTGGGGAATG-CAAGNAGTTCA 80 chr3qtel1M 986054 GTGTAACTAGCTCACAAATTATTTGTGAAGAGGAGAATGTCAGA----AA 986099 ii i vv i ----i vv i i i i vvi ---- i C L2c_3end#LINE 79 GTGTGGCTGGAGCATA----GTGGGCGAGGAGGGGAGTGGAGGAGATGAG 34 chr3qtel1M 986100 ACTGGAAAG--AGGAAGG 986115 i i -- v C L2c_3end#LINE 33 GCTGGAGAGGTAGGCAGG 16 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 47.05 CpG sites = 88, Kimura (unadjusted) = 50.35 Transitions / transversions = 1.60 (88/55) Gap_init rate = 0.10 (42 / 435), avg. gap size = 1.40 (59 / 42) 274 35.00 6.14 4.76 chr3qtel1M 985881 986108 (13892) C L2b_3end#LINE/L2 (213) 253 23 m_b162s601i16 6097 chr3qtel1M 985881 GGGGGATAAGAGAAAGCTTTCTA-AGACAGTTAGATTGTATCCAAGATCT 985929 i v i ii i ii- ivi v v vv v ii i C L2b_3end#LINE 253 GGGGGGTCAGGGAGGGCTTCCCGGAGGAGGTGACATTTGAGCTGAGACCT 204 chr3qtel1M 985930 AAAGGA--AGTAGGGA--AATCAGAAGATAGAGATGAGGA-GGGTGAAAA 985974 i -- ii--iii iv - i i - i ---- C L2b_3end#LINE 203 GAAGGATGAGTAGGAGTTGGCCAGGCGA-AGAGGTGGGGAAGGGCG---- 159 chr3qtel1M 985975 TTCCAGGCATGAGACACAGCCAGTGCTACTACATAGAGTTGTGTTGGGGT 986024 vii iv v? v vvi viv vi v vv? i i C L2b_3end#LINE 158 TTCCAGGCAGAGGGAACAGCANGTGCAAAGGCCCTGAGGCGGGAGNGAGC 109 chr3qtel1M 986025 ATTTTGTGT--GAGGAACATTAAAAGGGTAAGTGTAACTAGCTCACAAAT 986072 ? vvi -- vi iii iv ii i vv v i-- C L2b_3end#LINE 108 NTGGCGTGTTCGAGGAACAGCAAGGAGGCCAGTGTGGCTGGAGCAGAG-- 61 chr3qtel1M 986073 TATTTGTG-AAGAGGAGAATGTCAGAAAA-----CTGGAAAG 986108 ---- v - i i vi i i ----- i i C L2b_3end#LINE 60 ----TGAGCAAGGGGAGAGTGGTAGGAGATGAGGCCGGAGAG 23 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 45.84 CpG sites = 47, Kimura (unadjusted) = 50.66 Transitions / transversions = 1.62 (47/29) Gap_init rate = 0.08 (18 / 227), avg. gap size = 1.39 (25 / 18) 507 38.34 7.37 2.64 chr3qtel1M 985963 986613 (13387) C L2#LINE/L2 (0) 3082 2402 m_b162s601i17 6097 chr3qtel1M 985963 GGAGGGTGAAAATTCCAGGCATGAGACACAGCCAGTGCTACTACATAGAG 986012 i iv ivi vii iv v v vvi viv C L2#LINE/L2 3082 GGGGGAAGAGCGTTCCAGGCAGAGGGAACAGCAAGTGCAAAGGCCCTGAG 3033 chr3qtel1M 986013 TTGTGTTGGGGTATTTTGTGTG----AGGAACATTAAAAGGGTAAGTGTA 986058 vi v --i v iii v i ---- vi iii iv i C L2#LINE/L2 3032 GCGGG--AGCGTGCCTGGCGTGTTCGAGGAACAGCAAGGAGGCCAGTGTG 2985 chr3qtel1M 986059 ACTAGCTCACAAATTATTTGTGAAGAGGAGAATGTCAGAAAACTGG---A 986105 i i vv i-i i v --- i i i i vi i i ivi --- C L2#LINE/L2 2984 GCTGGAGCG-GAGTGA---GCGAGGGGGAGAGTGGTAGGAGATGAGGTCA 2939 chr3qtel1M 986106 AAGAGG-----------AAGGTTATGAAGAGACTTAGAAGGCA--AACAG 986142 i -----------v i i v i v iv i v --ivv C L2#LINE/L2 2938 GAGAGGTAACGGGGGACCAGATCATGTAGGGCCTTGTAGGCCATTGTAAG 2889 chr3qtel1M 986143 AATTTTACAGTTAATTTTGAGGATAATAAGGAGACTCTCAAGTATAATGA 986192 i i ivvv v i i vivi ii i v vi vi vi vv C L2#LINE/L2 2888 GACTTTGGCTTTTACTCTGAGTGAGATGGGAAGCCATTGGAGGGTTTTGA 2839 chr3qtel1M 986193 ATATTCAGATGACATGGTCTGACTTCCATTTCAGAAGA-------TGACA 986235 ii vvviii i v i i i i------- i v C L2#LINE/L2 2838 GCAGAGGAGTGACATGATCTGACTTACGTTTTAAAAGGATCACTCTGGCT 2789 chr3qtel1M 986236 GCTGAAGGGAGAAGGATCTAGAGTGAG--AAGGACTTAATACAAGAAGAC 986283 vivv viiv i? v i -- i- vi vi i i C L2#LINE/L2 2788 GCTGTGTTGAGAATAGACTGNAGGGGGGCAAGGG-TGGAAGCAGGGAGAC 2740 chr3qtel1M 986284 CAACCAGTGAAG-TATTACAGTAATTCGGCTGTGCGATGGTAAGGCCCTG 986332 iii - i - i i i vi v v i iiv v i C L2#LINE/L2 2739 CAGTTAG-GAGGCTATTGCAGTAATCCAGGCGAGAGATGATGGTGGCTTG 2691 chr3qtel1M 986333 TATCAGAATGTCAGCAGTCTCAGA-GTAAAGAAAGAATACAAAGAATACA 986381 v i ii vii ---i - iiv i - i ivvvi v vii C L2#LINE/L2 2690 GACCAGGGTGGTGGCAGT---GGAGGTGGTGAGA-AGTGGTCGGATTCTG 2645 chr3qtel1M 986382 GTCCCAGAGATGTTGAAGGTTGAGTTGGCAAGGCTTTGCAGAT-GATTGA 986430 ---- v v v v ii i - v v - i C L2#LINE/L2 2644 G----ATATATTTTGAAGGTAGAGCCGAC-AGGATTTGCTGATGGATTGG 2600 chr3qtel1M 986431 TTCTAGGGAATGAGGGAGAATGGGGAGTTGAGGATAA---TAAATACATT 986477 v v i vi i i iv i ii i ---i ivviv C L2#LINE/L2 2599 ATGTGGGGTGTGAGAGAAAGAGAGGAGTCAAGGATGACTCCAAGGTTTTT 2550 chr3qtel1M 986478 G---TGAGC--CTG--AGGATTATGGTGCCCTTGCATTAATA---GGAAA 986517 --- -- -- viv v v -? i i v --- i C L2#LINE/L2 2549 GGCCTGAGCAACTGGAAGGATGGAGTTGCCATT-NACTGAGATGGGGAAG 2501 chr3qtel1M 986518 ATTA-AAAAGAGGAAAATGTG-GGGTAAAGA-AATGAGTTTAAATTTGAA 986564 i i-iii ii v ii v - vi -v v i iv i C L2#LINE/L2 2500 ACTGCGGGAGGAGCAGGTTTGAGGGGGAAGATCAGGAGTTCAGTTTTGGA 2451 chr3qtel1M 986565 TACAATGAGTCTAAGATGTCTATATTACATTAAATTTGAGCTGTCTAAT 986613 i iiv i i i i vvv iv v v v v i C L2#LINE/L2 2450 CATGTTAAGTTTGAGATGCCTATTAGACATCCAAGTGGAGATGTCGAGT 2402 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 53.36 CpG sites = 144, Kimura (unadjusted) = 56.92 Transitions / transversions = 1.45 (144/99) Gap_init rate = 0.05 (35 / 650), avg. gap size = 1.89 (66 / 35) 597 27.86 9.05 2.55 chr3qtel1M 986631 986851 (13149) C MIR#SINE/MIR (0) 262 28 m_b162s601i18 6098 chr3qtel1M 986631 AATAATAGCTAACATTTATGTAGGAAACACCATGTGACAG---------- 986670 vv vivvi i v ---------- C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCT 213 chr3qtel1M 986671 --GTGTTTTATAAGTAT---CTCATTTATTTCCTACAGCAACCC-ATAAG 986714 -- i i i v --- v i ii i - i C MIR#SINE/MIR 212 AAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAG 163 chr3qtel1M 986715 AGTAGATGCTGTTATC-TTCCTATTTTATAGAGGGTGAAGACAAGGCAAA 986763 - i i i i- i i i v iv ivii v C MIR#SINE/MIR 162 -GTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACA 114 chr3qtel1M 986764 CAGAAAGT--GCAACTGTGTCCAGGTTCTTCACGCATCTAGCAAATGATT 986811 v iiv -- i - i i ---v i v i i iiv C MIR#SINE/MIR 113 GAGAGGTTAAGTAACT-TGCCCAAG---GTCACACAGCTAGTAAGTGGCA 68 chr3qtel1M 986812 GAGGTAGGATTTGAACCTGGATCTTTCTGGTTTCAG-GCCC 986851 vii i ii i- vv i i - C MIR#SINE/MIR 67 GAGCCGGGATTCGAACCCAGG-CAGTCTGGCTCCAGAGCCC 28 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 33.31 CpG sites = 40, Kimura (unadjusted) = 36.43 Transitions / transversions = 2.00 (40/20) Gap_init rate = 0.06 (13 / 220), avg. gap size = 2.00 (26 / 13) 313 31.65 2.13 5.88 chr3qtel1M 986726 986866 (13134) C MIR1_Amn#SINE/MIR (75) 155 20 m_b162s601i19 6098 chr3qtel1M 986726 TTATCTTCCTATTTTATAGAGGGTGAAGACAAGGCAAACAGAAAGTGCAA 986775 -- i i v iv ivii ?-- i vv? C MIR1_Amn#SINE 155 TTATC--CCCATTTTACAGATGAGGAAACTGAGGCN--CAGAGAGGTNAA 110 chr3qtel1M 986776 CTG---TGTCCAGGTTCTTCACGCATCTAGCAAATGATTGAGGTAGGATT 986822 v --- i i v --- ? v ?i ? i iiv vii ? C MIR1_Amn#SINE 109 GTGACTTGCCCAAGGTC---ACNCAGCNGGCNAGTGGCAGAGCCGGGANT 63 chr3qtel1M 986823 TGAACCTGGATCTTTCTGGTTTCAGGCCCAATGTAACATTTACT 986866 ? ii i ii vi ii - i i ivvi ii C MIR1_Amn#SINE 62 NGAACCCAGGTCTCCCGAGTCCCA-GTCCAGTGCTCTATCCACT 20 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 45.44 CpG sites = 29, Kimura (unadjusted) = 47.23 Transitions / transversions = 2.23 (29/13) Gap_init rate = 0.06 (9 / 140), avg. gap size = 1.22 (11 / 9) 19 23.93 2.04 0.00 chr3qtel1M 988447 988495 (11505) (GT)n#Simple_repeat 1 50 (0) m_b162s252i15 6099 chr3qtel1M 988447 GTTTGTGTATGTATGTGTGTGTTTGTTTGGGGGGGAG-GGGTGTGTGTGT 988495 v i i v v v v v v - v (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50 Matrix = Unknown Transitions / transversions = 0.25 (2/8) Gap_init rate = 0.02 (1 / 48), avg. gap size = 1.00 (1 / 1) 548 30.68 3.61 2.55 chr3qtel1M 988914 989107 (10893) MIR3#SINE/MIR 3 198 (10) m_b162s601i20 6100 chr3qtel1M 988914 GACAGTATAGACCTAAGGAAA-AGATGACGGATTTAGAAACAA-AGTCCT 988961 i vi i -- i v i - vv i vi iv i- v MIR3#SINE/MIR 3 GGCAGAGTGG--CTGAGCAGAGAGAGCACGGACTGGGAGTCAGGAGACCT 50 chr3qtel1M 988962 GGGTTTCAAATCCTGACTCTACCATTTAATAGATCTATGTGATTTTGAGC 989011 - v i i i i i v v ? -- i ii i MIR3#SINE/MIR 51 GGGTT-CTAGTCCCGGCTCTGCCACTAACTNG--CTGTGTGACCTTGGGC 97 chr3qtel1M 989012 AAGTTATTAAAGCTATC--AGACTCAGTTTTCTCATTTG-AAAAAGAGAA 989058 i i vv v v --i v i i - v ii MIR3#SINE/MIR 98 AAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGG 147 chr3qtel1M 989059 AATTGACCTAAGGAATCTATAACGTCCCACTCGATTCTA--ATTCTATGA 989106 ii iv iivi v v vii iii i-- MIR3#SINE/MIR 148 GGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGA 197 chr3qtel1M 989107 T 989107 MIR3#SINE/MIR 198 T 198 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 40.55 CpG sites = 37, Kimura (unadjusted) = 41.51 Transitions / transversions = 1.76 (37/21) Gap_init rate = 0.05 (10 / 193), avg. gap size = 1.20 (12 / 10) 12 4.77 4.55 0.00 chr3qtel1M 989333 989354 (10646) (CCCT)n#Simple_repeat 1 23 (0) m_b162s252i16 6101 chr3qtel1M 989333 CCCTCCCTCTCTCCC-CCCTCCC 989354 i - (CCCT)n#Simpl 1 CCCTCCCTCCCTCCCTCCCTCCC 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.05 (1 / 21), avg. gap size = 1.00 (1 / 1) 328 32.03 5.29 8.42 chr3qtel1M 989719 989926 (10074) L4_C_Mam#LINE/RTE-X 2845 3046 (2092) m_b162s551i18 6102 chr3qtel1M 989719 TGGGATTAGTTGACAAGAATAATACTAAATGCAGATATGGG-ATATTGTT 989767 v ii v i ivi vii v - i L4_C_Mam#LINE 2845 TGGGCTTAGCCGTCAGGGCCAATAACGAATGCAGATTTGGGGACATTGTT 2894 chr3qtel1M 989768 GTCCACAGAATGATACCTGTGAGGGAAATTTTATAAGTATCACAG---TC 989814 i ii v iivi ii i i iv v --- i--- L4_C_Mam#LINE 2895 GCCCATGGTATGGCTTCTGCAAGAGGAATCGTAGAAG---CACAAATTTC 2941 chr3qtel1M 989815 TACTGATGACTAAGTTTAAAAAAACAAAAATA-TTCAGTACAGT----AG 989859 iii ii i-----------i iv - ?v vv v ---- L4_C_Mam#LINE 2942 CGTTGATGACTGGGC-----------GAGTTATTTCNCTCGACTTTACAG 2980 chr3qtel1M 989860 TACTATTATAGTCCCTCTATCATATTTAAT--ATTCTAGGGATCTGTCTA 989907 v iv ii i --- i vi -- i iv vi L4_C_Mam#LINE 2981 TCCTACGATGATCTCTC---CGTATTTTGTAGATTCCAGGACTCTCCCTA 3027 chr3qtel1M 989908 ATTAGGATCCATTAATTCC 989926 ii i v i L4_C_Mam#LINE 3028 GCTGGGATCCAGTAACTCC 3046 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 37.41 CpG sites = 41, Kimura (unadjusted) = 44.39 Transitions / transversions = 2.05 (41/20) Gap_init rate = 0.11 (22 / 207), avg. gap size = 1.27 (28 / 22) 440 34.37 5.43 3.03 chr3qtel1M 990087 990344 (9656) C L2#LINE/L2 (564) 2518 2255 m_b162s601i21 6103 chr3qtel1M 990087 TTGACAGAAATAAG-----TTGGAAGAGATGTAGATTTGGAGGGCAAAGT 990131 ? v i ii -----i vii iv i i ii v --- C L2#LINE/L2 2518 TTNACTGAGATGGGGAAGACTGCGGGAGGAGCAGGTTTGAGGGGGAA--- 2472 chr3qtel1M 990132 GAGATAATGAGTTTAGCTTTTGAT-TATTCAATTTTGAAGTATCTGT-GG 990179 -- v v i i v i- i - v ii ii i -i C L2#LINE/L2 2471 --GATCAGGAGTTCAGTTTTGGACATGTT-AAGTTTGAGATGCCTATTAG 2425 chr3qtel1M 990180 ACTTTCACAAGTTAA-ATATCCAATAGGCAATTAGTAGTGTAGGTCTAAA 990228 v i -- vi - i v i i i vvi iiii ii C L2#LINE/L2 2424 ACATCCA--AGTGGAGATGTCGAGTAGGCAGTTGGATATACGAGTCTGGA 2377 chr3qtel1M 990229 GTTCAGAGGAGAGATTGCAACTGGATATAAAGAATTGTGAGTTATCTGCC 990278 i i ivvii v v i v v i v v C L2#LINE/L2 2376 GTTCAGGGGAGAGGTCCGGGCTGGAGATATAAATTTGGGAGTCATCAGCA 2327 chr3qtel1M 990279 TAAAAATTACATTT-AATCTATGGAAGTTGATGAGGTGGCAAAAACA--- 990324 v i vii - v i ii v v i vi v? iiv --- C L2#LINE/L2 2326 TATAGATGGTATTTAAAGCCATGAGACTGGATGAGATCACCNAGGGAGTG 2277 chr3qtel1M 990325 --TGTAGACAAAGACATAAAGA 990344 -- i i vivi C L2#LINE/L2 2276 AGTGTAGATAGAGAAGAGAAGA 2255 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 47.48 CpG sites = 55, Kimura (unadjusted) = 49.22 Transitions / transversions = 1.77 (55/31) Gap_init rate = 0.06 (15 / 257), avg. gap size = 1.47 (22 / 15) 17 29.82 1.30 2.63 chr3qtel1M 990565 990641 (9359) (AAAATA)n#Simple_repeat 1 76 (0) m_b162s252i17 6104 chr3qtel1M 990565 AAAATACATTTTACAATAACCACATTATAATGAAAA-CAGAACAAAAATA 990613 v vv v v -- v v v i -v i i (AAAATA)n#Sim 1 AAAATAAAAATAAAAATAA--AAATAAAAATAAAAATAAAAATAAAAATA 48 chr3qtel1M 990614 ATAAGAAAAATAAAATTCAAAAAAAGAA 990641 v v v v v i (AAAATA)n#Sim 49 AAAATAAAAATAAAAATAAAAATAAAAA 76 Matrix = Unknown Transitions / transversions = 0.29 (4/14) Gap_init rate = 0.04 (3 / 76), avg. gap size = 1.00 (3 / 3) 244 33.34 0.00 1.55 chr3qtel1M 990904 991034 (8966) C L1ME4b_3end#LINE/L1 (342) 550 422 m_b162s551i20 6105 chr3qtel1M 990904 AGTATTCCATTACAATTATATACCACAACCTCTTCAGCCAATTCCCAATT 990953 ii vvv i i ii v i i i i v C L1ME4b_3end#L 550 AGTATTCCATTGTATGGATGTACCATAATTTATTTAACCAGTCCCCTATT 501 chr3qtel1M 990954 TATAGTCATTTCCTCAATTTTGAATTCTTTGCTACCACAAAAAGAGCTGC 991003 v i v vvvivi iv ii ii v iv C L1ME4b_3end#L 500 GATGGACATTTAGGTTGTTTCCAATCTTTTGCTATTACAAACAATGCTGC 451 chr3qtel1M 991004 TCTTAATATTTTTGTATGGATAGGCCCTTTC 991034 vv v vii i-- v i v C L1ME4b_3end#L 450 AATGAATAACCTTGTAC--ATACGTCATTTC 422 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 45.11 CpG sites = 23, Kimura (unadjusted) = 45.11 Transitions / transversions = 1.15 (23/20) Gap_init rate = 0.02 (2 / 130), avg. gap size = 1.00 (2 / 2) 260 31.90 0.00 0.00 chr3qtel1M 990904 991019 (8981) C L1ME3Cz_3end#LINE/L1 (451) 546 431 m_b162s551i19 6105 chr3qtel1M 990904 AGTATTCCATTACAATTATATACCACAACCTCTTCAGCCAATTCCCAATT 990953 ii vvv ii v i v v i v C L1ME3Cz_3end# 546 AGTATTCCATTGTATGAATATACCACAATTTATTTATCCATTCCCCTATT 497 chr3qtel1M 990954 TATAGTCATTTCCTCAATTTTGAATTCTTTGCTACCACAAAAAGAGCTGC 991003 v i v vvvivi iv i i ii v iv C L1ME3Cz_3end# 496 GATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCTGC 447 chr3qtel1M 991004 TCTTAATATTTTTGTA 991019 vv v i ii C L1ME3Cz_3end# 446 AATGAACATCCTTGTA 431 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 40.60 CpG sites = 18, Kimura (unadjusted) = 42.06 Transitions / transversions = 0.95 (18/19) Gap_init rate = 0.00 (0 / 115), avg. gap size = 0.0 (0 / 0) 91 40.36 0.80 2.24 chr3qtel1M 991736 992233 (7767) (CTC)n#Simple_repeat 1 491 (0) m_b162s252i18 6106 chr3qtel1M 991736 CTCCTCCTCCATCTCCTCCTCCTCCTTCATTTTCTTTCTTTTTCTCCTAC 991785 vi - v ii i i ii i - (CTC)n#Simple 1 CTCCTCCTCCTCCTCCTCCTCCTCC-TCCTCCTCCTCCTCCTCCTCCT-C 48 chr3qtel1M 991786 TTCTTTTTCTTGCAATTTTCTCCTTCTTTTCTTTCTCCTCCTCCT-CTTC 991834 i i ii i - vvii i i ii i i - i (CTC)n#Simple 49 CTCCTCCTCCT-CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC 97 chr3qtel1M 991835 TCTTCCTTCTCCTTCTTGCAATTCTTCTTCTCTTTTTCTTCTTCCTGAAA 991884 i i i ivivv i i i i ii i i --vv (CTC)n#Simple 98 TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT--CC 145 chr3qtel1M 991885 TTCTTCTTCTCTTTCTCCT-ATTTTTCTTTTATTCTTTCTCCTTTTATTC 991933 i i i i i -v ii i ii vi i i ii vi (CTC)n#Simple 146 TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC 195 chr3qtel1M 991934 CTTCTCCTTTTCCTCTTTCTGCATCTCCTTCTCTTTCTACTTTTTTCTCC 991983 i ii i i v vi i i i - i ii i (CTC)n#Simple 196 CTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT-CCTCCTCCTCC 244 chr3qtel1M 991984 TTCTCCTTCTTCCTGCAATTCTTCTTTGCAATTCTTCTCCTTCTCTTTCT 992033 i - i v vvi i i ivivv i i i i i (CTC)n#Simple 245 TCCTCC-TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT 293 chr3qtel1M 992034 TCTTCTCCCCTTCCTCTTCCTCCTTTCTTTTCCT-CTCTTCCTTCTTTCT 992082 i i i i i - i ii - i - i i (CTC)n#Simple 294 CCTCCTCCTCCTCCTCCTCCTCC-TCCTCCTCCTCCTCCTCC-TCCTCCT 341 chr3qtel1M 992083 CCTCCTCCTCCTTTTCCTTCTTCTTCTCCTCCTTTTCCTCCTCCTTTCTC 992132 ii i i i ii - i (CTC)n#Simple 342 CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC-TCCTC 390 chr3qtel1M 992133 TTTCT-CTTCTGCTTCTTATTCTCCTTCTCCTTCTTTCTCTTCCTCCTCT 992181 i i - i v i iv i i - i i i i (CTC)n#Simple 391 CTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC-TCCTCCTCCTCCTCCTCC 439 chr3qtel1M 992182 TCTTCAACTTCTTCCTCCTCCTCTTCCTTTTCCTCCCCCTCTTTCTCCTC 992231 i vv i i i ii i i i (CTC)n#Simple 440 TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC 489 chr3qtel1M 992232 CT 992233 (CTC)n#Simple 490 CT 491 Matrix = Unknown Transitions / transversions = 4.79 (115/24) Gap_init rate = 0.03 (15 / 497), avg. gap size = 1.00 (15 / 15) 42 6.89 6.58 0.00 chr3qtel1M 992455 992530 (7470) (TC)n#Simple_repeat 1 81 (0) c_b162s251i3 6107 chr3qtel1M 992455 TCTCTCTCTGTCTCTGTCTCTGTCTCTCTCTCTCTC-CT-TCT-TCT-TC 992500 v v v - - - - (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr3qtel1M 992501 TCCCTCTCCCTCTCTCTCTCT-TCTCTCTCT 992530 i i - (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 81 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.07 (5 / 75), avg. gap size = 1.00 (5 / 5) 36 27.68 0.85 1.71 chr3qtel1M 992642 992759 (7241) (CTCCTT)n#Simple_repeat 1 117 (0) m_b162s252i19 6108 chr3qtel1M 992642 CTCCTTTTCCAGCTCATTCTCCTCCTTCATTTTCCTTCTCTTTCTCCTTC 992691 i vv v i - v i i (CTCCTT)n#Sim 1 CTCCTTCTCCTTCTCCTTCTCCTTC-TCCTTCTCCTTCTCCTTCTCCTTC 49 chr3qtel1M 992692 TCCCTTTTCTTGCAATTTTTCTTCCTGC-AATTCTTCTCCTCTTCTTTCT 992740 - i i v vvi i i i v -vv i ii i (CTCCTT)n#Sim 50 T-CCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCT 98 chr3qtel1M 992741 CCTTCTCCTCCTTCTTCTC 992759 i i (CTCCTT)n#Sim 99 CCTTCTCCTTCTCCTTCTC 117 Matrix = Unknown Transitions / transversions = 1.60 (16/10) Gap_init rate = 0.03 (3 / 117), avg. gap size = 1.00 (3 / 3) 455 19.38 2.44 7.69 chr3qtel1M 994341 994463 (5537) C MIRc#SINE/MIR (141) 127 11 m_b162s601i22 6109 chr3qtel1M 994341 CTGAGGCAATTGGAG---TTAAGTGACTTGCTCAGGGTCACATATCTAGG 994387 -- ii --- i i i v v C MIRc#SINE/MIR 127 CTGAGGC--TCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGT 80 chr3qtel1M 994388 AAGTTTTCAGAGTCTGAGGCCAGATTTGACCTCAGGTCCTCCTGACTTCA 994437 vv- i --- --- i i v i i i C MIRc#SINE/MIR 79 AAGTGG-CAGAGCC---GG---GACTCGAACCCAGGTCTTCCTGACTCCA 37 chr3qtel1M 994438 GGGCTGGTGCTCTGTCCACTGTACCA 994463 i v ii v i C MIRc#SINE/MIR 36 AGTCCAGTGCTCTTTCCACTGCACCA 11 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 21.74 CpG sites = 15, Kimura (unadjusted) = 22.90 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.08 (10 / 122), avg. gap size = 1.20 (12 / 10) 14 11.31 7.50 2.38 chr3qtel1M 994912 994951 (5049) (AATTA)n#Simple_repeat 1 42 (0) m_b162s252i20 6110 chr3qtel1M 994912 AATTTAATTAAA-GAAATAAAACTTAAATTAAA--AAATTGAA 994951 v -v v - -- i (AATTA)n#Simp 1 AATTAAATTAAATTAAATTAAA-TTAAATTAAATTAAATTAAA 42 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.08 (3 / 39), avg. gap size = 1.33 (4 / 3) 214 31.00 2.27 7.14 chr3qtel1M 995011 995142 (4858) MIRb#SINE/MIR 5 130 (138) m_b162s601i23 6111 chr3qtel1M 995011 GGGCCAGCTAGGTGGCACCAATGACCAGTG-ATCAGCCCTGAAGAGAGGA 995059 v vv ---- i ivv v - ivi ii i vv iv MIRb#SINE/MIR 5 GGGGCAGCGTGGTG----CAGTGGAAAGAGCACGGGCTTTGGAGTCAGAC 50 chr3qtel1M 995060 GGTTCTGAGTTCAAATCTGCACTCAGAGACAACACTTTCTAGCCCTGTGA 995109 i vi i i ivvi v --- -- v iv MIRb#SINE/MIR 51 AGACCTGGGTTCGAATCCCGGCTCTG---C--CACTTACTAGCTGTGTGA 95 chr3qtel1M 995110 CCCTAGGCAAGTCAATTAACCCAACT--GCCTCAG 995142 i i i v ivv -- MIRb#SINE/MIR 96 CCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAG 130 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 37.71 CpG sites = 19, Kimura (unadjusted) = 40.36 Transitions / transversions = 1.00 (19/19) Gap_init rate = 0.08 (11 / 131), avg. gap size = 1.09 (12 / 11) 271 26.42 2.08 5.38 chr3qtel1M 995047 995142 (4858) MIRc#SINE/MIR 35 127 (141) m_b162s601i24 6111 chr3qtel1M 995047 CCTGAAGAGAGGAGGTTCTGAGTTCAAATCTGCACTCAGAGACAACACTT 995096 i i vv i vi i i i ivvi v --- -- MIRc#SINE/MIR 35 CTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTG---C--CACTT 79 chr3qtel1M 995097 TCTAGCCCTGTGACCCTAGGCAAGTCAATTAACCCAACT--GCCTCAG 995142 v iv i i v ivv -- MIRc#SINE/MIR 80 ACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 31.37 CpG sites = 13, Kimura (unadjusted) = 33.01 Transitions / transversions = 1.18 (13/11) Gap_init rate = 0.06 (6 / 95), avg. gap size = 1.17 (7 / 6) 21 4.17 0.00 0.00 chr3qtel1M 996919 996943 (3057) (T)n#Simple_repeat 1 25 (0) m_b162s252i21 6112 chr3qtel1M 996919 TTTTTCTTTTTTTTTTTTTTTTTTT 996943 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 288 23.53 12.83 4.08 chr3qtel1M 997442 997667 (2333) C L1ME3F_3end#LINE/L1 (439) 551 307 m_b162s551i21 6113 chr3qtel1M 997442 TAATATTCCTTTTTC---ATATACCACAATTTATTCAGCCATTCTCC-AA 997487 v v v--- i v -iv C L1ME3F_3end#L 551 TAATATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTCCTGT 502 chr3qtel1M 997488 CG-TGGACTCCATTCA----GTTTCCAGTTTCTAACCACTACAAAGA--G 997530 - --- ii---- i vi i i i v -- C L1ME3F_3end#L 501 CGATGGA---CATTTGGGTTGTTTCCAGTTTTTTGCTATTACGAACAGTG 455 chr3qtel1M 997531 CT-CCACAAACATTCTGCACATACAGGTC-CCT--TTCCCTTCTTTAAA- 997575 - i ii ---ii v - -- v v v v vi i- C L1ME3F_3end#L 454 CTGCTATGAACATTCT---TGTACATGTCTCCTGGTGCACATGTGCAAGA 408 chr3qtel1M 997576 --TTCTTTTGGG-ATATAATCCCAGTAT-----CCTCTGGATC--AAAAT 997615 -- i - -- i v v-----iiv i -- iii C L1ME3F_3end#L 407 GTTTCTCTTGGGTATATA--CCTAGGAGTGGAATTGCTGGGTCGTAGGGT 360 chr3qtel1M 997616 ATGCAAAT-TTGATAACTTTTTGACATAGT-TCAAACT-CTCTCCAAAAT 997662 i - --i vi v i -i i -i i i C L1ME3F_3end#L 359 ATGCGAATGTT--CAACTTTACGAGATAATGCCAAATTGTTTTCCAAAGT 312 chr3qtel1M 997663 GGTTG 997667 C L1ME3F_3end#L 311 GGTTG 307 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 27.18 CpG sites = 33, Kimura (unadjusted) = 29.18 Transitions / transversions = 1.83 (33/18) Gap_init rate = 0.12 (26 / 225), avg. gap size = 1.50 (39 / 26) 230 17.28 0.00 5.17 chr3qtel1M 998831 998891 (1109) C L1M3_orf2#LINE/L1 (613) 2675 2618 m_b162s551i22 6114 chr3qtel1M 998831 CTGTTTCTTTGCCAGTACCAAATGGCTTTGATGAACTGATGCTTTATAAT 998880 i v v iv i v- vv i C L1M3_orf2#LIN 2675 CTGTTTTTATGCCAGTACCATACTGTTTTGATT-ACTGTAGCTTTGTAAT 2627 chr3qtel1M 998881 ATAGTTTTTGA 998891 -- C L1M3_orf2#LIN 2626 ATA--TTTTGA 2618 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 19.61 CpG sites = 4, Kimura (unadjusted) = 19.61 Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.05 (3 / 60), avg. gap size = 1.00 (3 / 3) 14 7.42 6.90 0.00 chr3qtel1M 999094 999122 (878) (TCTG)n#Simple_repeat 1 31 (0) m_b162s252i22 6115 chr3qtel1M 999094 TCTATCTG-CT-TTTGTCTGTCTGTCTGTCT 999122 i - - i (TCTG)n#Simpl 1 TCTGTCTGTCTGTCTGTCTGTCTGTCTGTCT 31 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.07 (2 / 28), avg. gap size = 1.00 (2 / 2) 15 13.67 0.00 0.00 chr3qtel1M 999187 999210 (790) (A)n#Simple_repeat 1 24 (0) m_b162s252i23 6116 chr3qtel1M 999187 AAAAAAAAAAAGAAAACAAATAAA 999210 i v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAA 24 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 54 0.00 0.00 0.00 chr3qtel1M 999632 999677 (323) (TC)n#Simple_repeat 1 46 (0) c_b162s251i4 6117 chr3qtel1M 999632 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 999677 (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 46 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 14 20.54 0.00 0.00 chr4ptel1M 47 80 (999920) (ATATCT)n#Simple_repeat 1 34 (0) m_b163s252i0 6118 chr4ptel1M 47 ATATGTGTGTGTGTATCTATATCTATGTCTATAT 80 v i i v i i (ATATCT)n#Sim 1 ATATCTATATCTATATCTATATCTATATCTATAT 34 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 298 28.95 1.48 3.00 chr4ptel1M 872 1074 (998926) C LTR90B#LTR (445) 351 152 m_b163s502i0 6119 chr4ptel1M 872 CATTT-AAATCACATTGATTTAGTTTCTATAATTTGAAATTTGTAGAGTT 920 - vii ii v v ii - i iv iv?vi C LTR90B#LTR 351 CATTTCAAATCCTGTTAGTTTATTTTGTATAGCT-GAAACTCCTGTNCCT 303 chr4ptel1M 921 TTTACAGATTAGGTTTTGAACTTGGGTTGGACATTTTTGTAGATTTTTTT 970 iiv iv i iv v --- i ? v iv v? v C LTR90B#LTR 302 TTTGTTGATTAATTCTTGAGATTGGTTTGGA---TCTTGNATACATANTG 256 chr4ptel1M 971 TTCTTAAATGATTAAA--ATATTCATATCTGCTCACTCCAGGTTGAATTG 1018 i - v -- vi? i - i v i i ?i v i ? v C LTR90B#LTR 255 TTCTCAA-TCATTAAAGAAGGNTTA-ATTTGGTTATTCNGGGATGGANTC 208 chr4ptel1M 1019 CATAATGATTTCCAAAATTTTTATACTTTTCAAATTCATTCAGAAACTGT 1068 vv v v? v iv i v i v C LTR90B#LTR 207 CATTCTGTTTTCCAAATNTATTACCCTTCTCAATTTCATCCAGAAACTGG 158 chr4ptel1M 1069 AAATCT 1074 iv C LTR90B#LTR 157 AAGGCT 152 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.86 CpG sites = 29, Kimura (unadjusted) = 38.86 Transitions / transversions = 1.04 (29/28) Gap_init rate = 0.04 (8 / 202), avg. gap size = 1.12 (9 / 8) 309 31.26 12.73 4.15 chr4ptel1M 1830 2096 (997904) C L2#LINE/L2 (496) 2586 2298 m_b163s601i0 6120 chr4ptel1M 1830 GAGAATGGGA--AGTTAAAGAGAACTCCTAGGGTGCAAATATGAATGACC 1877 v i -- i i vi v v viviiiv iii i C L2#LINE/L2 2586 GAGAAAGAGAGGAGTCAAGGATGACTCCAAGGTTTTTGGCCTGAGCAACT 2537 chr4ptel1M 1878 ATAAGGATGG---------TAACAAAAATAGGTAAG--TACAGAAGGGAA 1916 iv --------- ? vi i i v -- i i i -- C L2#LINE/L2 2536 GGAAGGATGGAGTTGCCATTNACTGAGATGGGGAAGACTGCGGGAGG--A 2489 chr4ptel1M 1917 TTAAGTTTTCAGCAAAGTAAAAT---GATATCTGTTT--AACACATTGGG 1961 vi i --- viii v i --- vv v --i ii ii C L2#LINE/L2 2488 GCAGGTTT---GAGGGGGAAGATCAGGAGTTCAGTTTTGGACATGTTAAG 2442 chr4ptel1M 1962 TTTGGGTTGTCTATAACTAGACA--CAGTTCAAATTACCCAACAGGCAGT 2009 i v i --- -- iv vi iv ii v ii C L2#LINE/L2 2441 TTTGAGATGCCTAT---TAGACATCCAAGTGGAGATGTCGAGTAGGCAGT 2395 chr4ptel1M 2010 TGTTAATCTAGAAG--TGGAGCTCAGGAGAGAGTCTCGGGC--------T 2049 --i v vi -- i i vii -------- C L2#LINE/L2 2394 TG--GATATACGAGTCTGGAGTTCAGGGGAGAGGTCCGGGCTGGAGATAT 2347 chr4ptel1M 2050 AACTTTT---ATCGTCTG-ATGAGAGATGATAATTGAATCCATGGAAACT 2095 v v---i i v - - v i v i v - i C L2#LINE/L2 2346 AAATTTGGGAGTCATCAGCAT-ATAGATGGTATTTAAAGCCAT-GAGACT 2299 chr4ptel1M 2096 G 2096 C L2#LINE/L2 2298 G 2298 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.16 CpG sites = 50, Kimura (unadjusted) = 42.59 Transitions / transversions = 1.67 (50/30) Gap_init rate = 0.08 (22 / 266), avg. gap size = 2.09 (46 / 22) 22 11.88 2.70 0.00 chr4ptel1M 2103 2139 (997861) (TA)n#Simple_repeat 1 38 (0) m_b163s252i1 6121 chr4ptel1M 2103 TATATATATATATATATATATACACAAGTAT-TATATA 2139 i i vi - (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATA 38 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 408 20.48 8.94 0.75 chr4ptel1M 2623 2745 (997255) Charlie4#DNA/hAT-Charlie 3231 3363 (15) m_b163s502i1 6122 chr4ptel1M 2623 TGATCATTAAATTTCCATATAATTAATTTCCTTTGTAATCCAACATATTT 2672 v i v v ii v ii Charlie4#DNA/ 3231 TGATAACTATATTTCAATATAATTGGTTTCCTTTGTAATCCTATGTATTT 3280 chr4ptel1M 2673 TATTTTATATATTTTATAAACTTCATTCTGAGAAA-----CAT----TTT 2713 ii - v v i i----- ---- i Charlie4#DNA/ 3281 TATTTTATGCA-TTTAAAAACATTATTCTGAGAAGGGGTCCATAGGCTTC 3329 chr4ptel1M 2714 GCCTGATTTCC--AGAGGTACATGACGTAAAAAA 2745 i v i v -- i v i ii Charlie4#DNA/ 3330 ACCAGACTGCCAAAGGGGTCCATGGCACAAAAAA 3363 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 24.47 CpG sites = 16, Kimura (unadjusted) = 24.47 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.03 (4 / 122), avg. gap size = 3.00 (12 / 4) 16 9.26 0.00 0.00 chr4ptel1M 4688 4710 (995290) (A)n#Simple_repeat 1 23 (0) m_b163s252i2 6123 chr4ptel1M 4688 AAATAAAAAAAAAAAAAAAGAAA 4710 v i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAA 23 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 16 16.82 0.00 0.00 chr4ptel1M 5190 5217 (994783) (A)n#Simple_repeat 1 28 (0) m_b163s252i3 6124 chr4ptel1M 5190 AAAAAAAAAAGAAAGAAAGAAAAGAAAA 5217 i i i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA 28 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 17 26.98 3.23 0.00 chr4ptel1M 5597 5658 (994342) (TTTTA)n#Simple_repeat 1 64 (0) m_b163s252i4 6125 chr4ptel1M 5597 TTTTTTTCTATATAATGTT-TAATATTTTTTTATATTTGATTCTA-TTTA 5644 v i v v v - vv v v v i - (TTTTA)n#Simp 1 TTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTA 50 chr4ptel1M 5645 TTTTATATAACTTT 5658 v v i (TTTTA)n#Simp 51 TTTTATTTTATTTT 64 Matrix = Unknown Transitions / transversions = 0.27 (3/11) Gap_init rate = 0.03 (2 / 61), avg. gap size = 1.00 (2 / 2) 17 17.24 0.00 2.50 chr4ptel1M 7252 7292 (992708) (CAATACA)n#Simple_repeat 1 40 (0) m_b163s252i5 6126 chr4ptel1M 7252 CAATTACACAATTCACAATGCACAATGCACAAAATACATTA 7292 - v i i v i v (CAATACA)n#Si 1 CAA-TACACAATACACAATACACAATACACAATACACAATA 40 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 283 30.61 7.51 1.87 chr4ptel1M 7615 7867 (992133) C L1MD_orf2#LINE/L1 (1464) 1830 1564 m_b163s551i0 6127 chr4ptel1M 7615 GTGTTTTATCTTGTTAAAAGCTTTTTCTGCATCTACTGATATAGTTATAT 7664 vv i i v v i ii i i C L1MD_orf2#LIN 1830 GTGTTGAATTTTGTCAAATGCTTTTTCTGCATCAATTGATATGATCATGT 1781 chr4ptel1M 7665 GATTTTGGGTTCTTAGC---------------ATTATTTTCATAATTCTC 7699 vvv ii --------------- iv v viv i i C L1MD_orf2#LIN 1780 GATTTTTCTTCTTTAGCCTGTTAATATGGTGGATTACATTGATTGATTTT 1731 chr4ptel1M 7700 CTAATTTTAAACTAAC--TACATTTTTTTTAATAAAATCCAATCTGGCTG 7747 v v i i i -- i - ?ii vv vi v - iii C L1MD_orf2#LIN 1730 CGAATATTGAACCAGCCTTGCA-TNCCTGGAATAAACCCCACT-TGGTCA 1683 chr4ptel1M 7748 TAGTGTATAATATTTATGATTTGTTTCTGTACTCTCCTTGCTAATATTTT 7797 i vi v v v i v v i ?vi C L1MD_orf2#LIN 1682 TGGTGTATAATTCTTTTTATATATTGCTGAATTCNATTTGCTAATATTTT 1633 chr4ptel1M 7798 ATTTTAAATATTTAT-TCAGTTTTCACTCAAGATGCTAATCTGTAATTTT 7846 i vvii v ii- vi v ivvii ii ii i C L1MD_orf2#LIN 1632 GTTGAGGATTTTTGCGTCTATGTTCATGAGGGATATTGGTCTGTAGTTTT 1583 chr4ptel1M 7847 CTCTTTGTTTTG-ACTATCCTT 7867 i --- - i i C L1MD_orf2#LIN 1582 CTTT---TTTTGTACTGTCTTT 1564 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.40 CpG sites = 45, Kimura (unadjusted) = 41.11 Transitions / transversions = 1.45 (45/31) Gap_init rate = 0.04 (9 / 252), avg. gap size = 2.67 (24 / 9) 27 0.00 2.33 7.32 chr4ptel1M 8833 8875 (991125) (TCTGGT)n#Simple_repeat 1 41 (0) c_b163s251i0 6128 chr4ptel1M 8833 TCTGGTTCTGGTTCTGGTTCTGGTTATTCTGGTTCT-GTTCTGG 8875 --- - (TCTGGT)n#Sim 1 TCTGGTTCTGGTTCTGGTTCTGG---TTCTGGTTCTGGTTCTGG 41 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.10 (4 / 42), avg. gap size = 1.00 (4 / 4) 15 29.46 1.56 1.56 chr4ptel1M 8927 8990 (991010) (TATATGT)n#Simple_repeat 1 64 (0) m_b163s252i6 6129 chr4ptel1M 8927 TATGTGTTATATGTTTAATGTTGTA-ACTGTGTGTTCTATGTTCTGTGTG 8975 i vv i -ii i i v v i v (TATATGT)n#Si 1 TATATGTTATATGTTATATGTTATATGTTATATGTTATATGTTATATGTT 50 chr4ptel1M 8976 ATTTGTCTGTCTGTT 8990 v - i v (TATATGT)n#Si 51 ATATGT-TATATGTT 64 Matrix = Unknown Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.03 (2 / 63), avg. gap size = 1.00 (2 / 2) 16 9.32 0.00 0.00 chr4ptel1M 9052 9074 (990926) (TG)n#Simple_repeat 1 23 (0) m_b163s252i7 6130 chr4ptel1M 9052 TGTGTGTCTGTGTGTGTCTGTGT 9074 v v (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGT 23 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 55 0.00 0.00 0.00 chr4ptel1M 9158 9204 (990796) (TG)n#Simple_repeat 1 47 (0) c_b163s251i1 6131 chr4ptel1M 9158 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 9204 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 47 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 677 31.09 2.98 2.98 chr4ptel1M 10065 10568 (989432) L1M5_orf2#LINE/L1 2791 3294 (0) m_b163s551i1 6132 chr4ptel1M 10065 CTGTTTGATAAAAATTGCTGGGAAAATTGGAAACTAATATGGCAGAAACT 10114 v ii i viv i v v iiv v i v L1M5_orf2#LIN 2791 CTTTTCAACAAATGGTGCTGGAACAATTGGATATCCATATGGAAAAAAAT 2840 chr4ptel1M 10115 AGGCATTGATCCATACTTAACGCCGTACACCAAGATAAGGTCAAAATGGG 10164 iii?v i i v i v i i v i v iv ? i i L1M5_orf2#LIN 2841 GAANCTCGACCCCTACCTCACACCATACACAAAAATTAATTCNAGATGGA 2890 chr4ptel1M 10165 TTCAT-GACCTAGGCATAAAGAATGAAATTATTAATAAATTAGAGGAA-- 10211 - - iiii ii? i i v vvvvi i -- L1M5_orf2#LIN 2891 T-CATAGACCTAAATGTAAAAGNTAAAACTATAAAACTTCTAGAAGAAAA 2939 chr4ptel1M 10212 CATAGGATAGTTTACCTCTCAGACCTGTGGA-AGGGGAAGGTTTTTATGA 10260 v i -- i iivv vv ?- vi i i - i L1M5_orf2#LIN 2940 CATAGGAGAAT--ATCTTCGTGACCTTGGGNTAGGCAAAGATTTCT-TAA 2986 chr4ptel1M 10261 CCAAAGCAGAACTAGAGATCATTACTGATCACAAAATAGAAAATT----- 10305 v iii v -- i -----i ?i i i v i ----- L1M5_orf2#LIN 2987 ACAGGACACAA--AAAG-----CACNAACCATAAAAGAAAAAATTGATAA 3029 chr4ptel1M 10306 --TCGATTATACCAAACTGAAAAGTTTTTGTACAAACAAAACTAATGCAG 10353 -- v i ?i i v v ii i iv ?vvv ivi vi ivi L1M5_orf2#LIN 3030 ATTGGACTNCATCAAAATTAAAAACTTCTGCTCNTCAAAAGACACCGTTA 3079 chr4ptel1M 10354 ACAAGATTAGAAGGGAAGCAATAAACTGGGAAAATATTTTTACAGTCAAA 10403 v i v i v v i i ? i v v i i?- v L1M5_orf2#LIN 3080 AGAAAATGAAAAGGCAAGCCACAGANTGGGAGAAAATATTTGCAAN-ACA 3128 chr4ptel1M 10404 GGT-TCTGATAAAGGCCTCATTTCCAAAATATATAGAGAATTAACTCTAA 10452 vi - i v i v i i i v- vi L1M5_orf2#LIN 3129 TATATCTGACAAAGGACTCGTATCCAGAATATATAAAGAACTC-CTACAA 3177 chr4ptel1M 10453 TTTA-TAAAAAATCAAGCCATTC--TCCAATTGAAAAATGGTCAAAGGAT 10499 ? i - ? -- v vv --i v? v i i L1M5_orf2#LIN 3178 NTCAATAANAAA--AAGACAAACAACCCAATANAAAAATGGGCAAAAGAC 3225 chr4ptel1M 10500 ATGAACAGACAATTCTCAGATGAAGAAATTGAAACTATTTCTAGTTATAT 10549 v v v i v v ?v iviiivv ivi i L1M5_orf2#LIN 3226 TTGAACAGACACTTCACAAAAGAAGATATNCAAATGGCCAATAAGCACAT 3275 chr4ptel1M 10550 GAAAAGATGCTCCAAGTCA 10568 v v? L1M5_orf2#LIN 3276 GAAAAGATGCTCAACNTCA 3294 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.35 CpG sites = 85, Kimura (unadjusted) = 42.84 Transitions / transversions = 1.27 (85/67) Gap_init rate = 0.05 (23 / 503), avg. gap size = 1.30 (30 / 23) 1472 27.75 3.48 3.80 chr4ptel1M 10425 11057 (988943) L1ME5_3end#LINE/L1 7 637 (304) m_b163s551i3 6132 chr4ptel1M 10425 TCCAAAATATATAGAGAATTAACTCTAATTTATAAAAAATCAAGCCATT- 10473 i i i ii i vviv v iv i i -- v iv?- L1ME5_3end#LI 7 TCTAGAATATACAAGGAACTCCTGCAAATCAACAAGAAA--AAGACGGNA 54 chr4ptel1M 10474 -CTCCAATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGA 10522 - i v v i iv v L1ME5_3end#LI 55 ACCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGA 104 chr4ptel1M 10523 AGAAA-TTGAAA--CTATTTCTAGTTATATGAAAAGATGCTCCAAGTCAT 10569 i -ii -- --v v -i i v v L1ME5_3end#LI 105 GGAAACCCGAAAGGCTA--ACAAG-CATATGAAGAGATGCTCAAACTCAT 151 chr4ptel1M 10570 TATTAATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACA 10619 v i vv i i vi L1ME5_3end#LI 152 TAGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACA 201 chr4ptel1M 10620 CCTGTCAGATTGGCTAAGATGACAGGAA---AAATAATGATGATTGTTAA 10666 i i i v i --i i ---ii vii v ii L1ME5_3end#LI 202 CCTATTAGACTGGCAAAAAT--TAGAAAGCTGGATAATGCCAAGTGTTGG 249 chr4ptel1M 10667 -GGGGATGTGGGAAAACTGGGACATTGATTCATTGTTGGTGGAGTTGTGA 10715 - i i ? iv i vi v v i i iiv ii L1ME5_3end#LI 250 CGAGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAG 299 chr4ptel1M 10716 ACGAATCCAACCATTTTGGAAGAGTAGTTTGGAACTA--TGCTCAAA--A 10761 vii v i i - i i i v v -- iv -- L1ME5_3end#LI 300 ACTGGTGCAGCCATTCTGG-AGAGCAATCTGGCAGTACTTAGTCAAATTA 348 chr4ptel1M 10762 AGTTATCAAACTGTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGAT 10811 - --- --- v i i viii v vv L1ME5_3end#LI 349 AG-TAT---AC---GCATACCCTATGACCCAGCAATTCCGCTCCTGGGTA 391 chr4ptel1M 10812 TATATCCCAAAGAGATTATAAAGAAGG----GAAAGGGACCTGTATGTGC 10857 i v v viv ----v i ---- i L1ME5_3end#LI 392 TATATCCCAAAGAAATTCTCACACAGGTCCATAAGGGGAC----ATGTAC 437 chr4ptel1M 10858 ACGAATGTTTGTGGCAGCCCTTTTTGTAGTGGCTAGAAACTGGAAACTGA 10907 iv i ii v vi v i vi i ii ii viv L1ME5_3end#LI 438 GAGGATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAAC 487 chr4ptel1M 10908 ATGGATGTCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATATGAAA 10957 v i v v i v iii v iv v v L1ME5_3end#LI 488 CTGGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCAC 537 chr4ptel1M 10958 ATTATGGAATATTACTGT-TCTGTAAGAAATGACCAACAGGATGATTTCA 11006 ii i i - i-v v v iii vi vi -- v L1ME5_3end#LI 538 ACCATGGAGTACTA-TGCAGCAGTTAGAAGCAACGGACTAGATG--TACA 584 chr4ptel1M 11007 GAAAG--GCCTGGAGAGA-CTTACACGAAC-TGATGCTAAGTGAAATGAG 11052 v v --i v vi - v -- - ii i vi L1ME5_3end#LI 585 CATAGCAACATGGATGGATCTTAAA--AACATAGTGCTGAGTGAAAAAAG 632 chr4ptel1M 11053 CAGGA 11057 i i L1ME5_3end#LI 633 TAAGA 637 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.64 CpG sites = 100, Kimura (unadjusted) = 35.72 Transitions / transversions = 1.45 (100/69) Gap_init rate = 0.06 (37 / 632), avg. gap size = 1.24 (46 / 37) 1548 27.19 0.73 1.85 chr4ptel1M 10425 10971 (989029) L1ME3G_3end#LINE/L1 7 547 (377) m_b163s551i2 6132 chr4ptel1M 10425 TCCAAAATATATAGAGAATTAACTCTAATTTATAAAAAATCAAGCCATTC 10474 i i i vviv v iv i -- v --v L1ME3G_3end#L 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAA--AAGACA--A 52 chr4ptel1M 10475 TCCAATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGAAG 10524 i v v i v v i L1ME3G_3end#L 53 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chr4ptel1M 10525 AAATTGAAACTATTTCTAGTTATATGAAAAGATGCTCCAAGTCATTATTA 10574 vv iviiivv ivi v vv i v L1ME3G_3end#L 103 AAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTA 152 chr4ptel1M 10575 ATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACACCTGT 10624 i i vv i i viv ii L1ME3G_3end#L 153 ATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCAT 202 chr4ptel1M 10625 CAGATTGGCTAAGA-TGACAGGAAAAATAATGATGATTGTTAA-GGGGAT 10672 v i - v v i ?vvi ivi? v ii- i i L1ME3G_3end#L 203 CAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGT 252 chr4ptel1M 10673 GTGGGAAAACTGGGACATTGATTCATTGTTGGTGGAGTTGTGAACGAATC 10722 i v v vi v v i i iiv i ivii v L1ME3G_3end#L 253 GTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTA 302 chr4ptel1M 10723 CAACCATTTTGGAAGAGTAGTTTGGAACTATGCTCAAAAAGTTATCAAAC 10772 i ? - i i i v v - vvv i -- i v L1ME3G_3end#L 303 CAGCCNTTTTGG-AGGGCAATTTGGCAGTAT-CTATTAAAAT--TTAAAA 348 chr4ptel1M 10773 TGTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGATTATATCCCAAA 10822 i i i vii v ? ?v v i ? L1ME3G_3end#L 349 TGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANA 398 chr4ptel1M 10823 GAGATTAT-AAAGAAG-GGAAAGGGACCTGTATGTGCACGAATGTTTGTG 10870 i vv -iv v v - v v i --? i i v i ii v L1ME3G_3end#L 399 GAAATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTCATT 446 chr4ptel1M 10871 GCAGCCCTTTTTGTAGTGGCTAGAAACTGGAAACTGAATGGATGTCCATC 10920 vi v i i v i i vivv ii L1ME3G_3end#L 447 GCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATC 496 chr4ptel1M 10921 AGTTGGAGAATGGCTGAATAAATTGTGGTATATGAAAATTATGGAATATT 10970 i v i i i i vv v i i L1ME3G_3end#L 497 AATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACT 546 chr4ptel1M 10971 A 10971 L1ME3G_3end#L 547 A 547 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.26 CpG sites = 77, Kimura (unadjusted) = 34.84 Transitions / transversions = 1.12 (77/69) Gap_init rate = 0.03 (14 / 546), avg. gap size = 1.00 (14 / 14) 33 20.04 2.41 1.19 chr4ptel1M 11509 11591 (988409) (AAATAA)n#Simple_repeat 1 84 (0) m_b163s252i9 6133 chr4ptel1M 11509 AAATAAAAAAAATAAATAAAAAT-TAAA-AAAAATAAAAATAAAAATAAT 11556 v - -v - v (AAATAA)n#Sim 1 AAATAAAAATAA-AAATAAAAATAAAAATAAAAATAAAAATAAAAATAAA 49 chr4ptel1M 11557 TCTACTCCTTAAAAAAAAAAAAAAAAAAAAAAGAA 11591 vv vvvv v v v v v (AAATAA)n#Sim 50 AATAAAAATAAAAATAAAAATAAAAATAAAAATAA 84 Matrix = Unknown Transitions / transversions = 0.00 (0/14) Gap_init rate = 0.04 (3 / 82), avg. gap size = 1.00 (3 / 3) 230 29.07 1.16 0.00 chr4ptel1M 14493 14578 (985422) L1MB7_3end#LINE/L1 492 578 (353) m_b163s551i4 6134 chr4ptel1M 14493 ATGCCCATCATTTGAGGAATGC-TCAACAAGTTGTAGTATATGATTTTGA 14541 i vi v v- v iv i vvv vii L1MB7_3end#LI 492 ATGTCCATCAACTGATGAATGGATAAACAAAATGTGGTATATCCATACAA 541 chr4ptel1M 14542 TGGAATATTATTGTGCTATAAGAAATGATAAGATACT 14578 vv i i ivi i ii L1MB7_3end#LI 542 TGGAATATTATTCGGCCATAAAAAGGAATGAAGTACT 578 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.34 CpG sites = 13, Kimura (unadjusted) = 37.34 Transitions / transversions = 1.08 (13/12) Gap_init rate = 0.01 (1 / 85), avg. gap size = 1.00 (1 / 1) 49 0.00 0.00 0.00 chr4ptel1M 14895 14936 (985064) (TA)n#Simple_repeat 1 42 (0) c_b163s251i2 6135 chr4ptel1M 14895 TATATATATATATATATATATATATATATATATATATATATA 14936 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATA 42 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 218 36.85 7.31 0.86 chr4ptel1M 15291 15509 (984491) C L2c_3end#LINE/L2 (16) 462 230 m_b163s601i1 6136 chr4ptel1M 15291 AACATTTATTCAAACACTACAGT-----AAATGCTGGATATACAAAGATA 15335 v ivvv vi ----- iii iv i C L2c_3end#LINE 462 AACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGATACAAAGATG 413 chr4ptel1M 15336 AA--GCGTATAGTCCCTGACCTAAATGAGCTTTAAATTTATGAGAGGAGA 15383 --ivii ii v v v ivv i i vvi C L2c_3end#LINE 412 AATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAGTGGAGGAGA 363 chr4ptel1M 15384 CA-ACATCAATATAAGTAATTAAAA-ACAAAATAAATACAGGAAATGTGG 15431 - ?vv v i iii v - iv vv i i viv i ii C L2c_3end#LINE 362 CAGACANGTAAACAGACAATTACAATACAAGTTAATGATAAGTGCTATAA 313 chr4ptel1M 15432 GAGGAGTGAAAACACTAGAAGTTG-GGGAAT-CAGA--AGAGTCCTTATA 15477 vi iv i --i iv i i- ii- -- i iv i v C L2c_3end#LINE 312 TGGGAGTATAGACA--GGGTGCTATGGGAGCACAGAGGAGGGCACCTAGA 265 chr4ptel1M 15478 CAAG---TGATGACGCAAGAAAGCTTTCAAGGAAG 15509 v --- iv ivv i i vi vv i C L2c_3end#LINE 264 CTAGNCTTGGGGGGTCAGGGAAGGCTTCCCGGAGG 230 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 50.97 CpG sites = 45, Kimura (unadjusted) = 53.01 Transitions / transversions = 1.29 (45/35) Gap_init rate = 0.05 (10 / 218), avg. gap size = 1.80 (18 / 10) 12 28.17 1.89 1.89 chr4ptel1M 16154 16206 (983794) (TAAAAA)n#Simple_repeat 1 53 (0) m_b163s252i10 6137 chr4ptel1M 16154 TAAAAATAAAAACACATACTTAATATTAAAA-AATACTTAAAGTCAAAAC 16202 i - v v v v v - v v v i v i (TAAAAA)n#Sim 1 TAAAAATAAAAATA-AAAATAAAAATAAAAATAAAAATAAAAATAAAAAT 49 chr4ptel1M 16203 AAAA 16206 (TAAAAA)n#Sim 50 AAAA 53 Matrix = Unknown Transitions / transversions = 0.33 (3/9) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.00 (2 / 2) 219 26.56 3.12 0.00 chr4ptel1M 17430 17493 (982507) MIRc#SINE/MIR 196 261 (7) m_b163s601i2 6138 chr4ptel1M 17430 AAATGAGTTGATATATACAAAA-CACTTTGTAAAC-ACAAAGGGCCATAT 17477 v i i iii - i -ii v i i MIRc#SINE/MIR 196 AAATGAGATAATGTATGTGAAAGCGCTTTGTAAACTGTAAAGTGCTATAC 245 chr4ptel1M 17478 GAACATAAGCTATTAT 17493 i ii v?i MIRc#SINE/MIR 246 AAATGTAAGGNGTTAT 261 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.64 CpG sites = 14, Kimura (unadjusted) = 36.37 Transitions / transversions = 4.67 (14/3) Gap_init rate = 0.03 (2 / 63), avg. gap size = 1.00 (2 / 2) 21 4.00 0.00 0.00 chr4ptel1M 17928 17953 (982047) (CA)n#Simple_repeat 1 26 (0) m_b163s252i11 6139 chr4ptel1M 17928 CACACACACACATACACACACACACA 17953 i (CA)n#Simple_ 1 CACACACACACACACACACACACACA 26 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 510 33.01 1.49 2.50 chr4ptel1M 18699 18900 (981100) C MIRb#SINE/MIR (67) 201 2 m_b163s601i3 6140 chr4ptel1M 18699 ATTATGTTACCTTGCCTTCACAATGACTTTCCAATTTAGCTGATATTATT 18748 v i ii vii i ii ii v i vv ---i C MIRb#SINE/MIR 201 ATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAG---GTATTATT 155 chr4ptel1M 18749 CTCCTCATTTAAGAATTGAGGAAACTGAGGC--AAACAGATTTAATTACA 18796 v i v v iv -- i v i v i v v C MIRb#SINE/MIR 154 ATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACT 105 chr4ptel1M 18797 TGCCAAGGGGCACAAAGCTAGGAACTGTCTGAAGCTTGATTTAAACTCAG 18846 v i v v v v v v iv vv ii i C MIRb#SINE/MIR 104 TGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAG 55 chr4ptel1M 18847 TCACTTCTGATTCC-AGGCCAGATTTCTCTTCATTGTATTACCATCTCCC 18895 viviv i - i v vvi i i i i ii --v v C MIRb#SINE/MIR 54 GTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCACCAC--GCTGCC 7 chr4ptel1M 18896 CTTCT 18900 i C MIRb#SINE/MIR 6 CCTCT 2 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.46 CpG sites = 34, Kimura (unadjusted) = 44.36 Transitions / transversions = 1.10 (34/31) Gap_init rate = 0.03 (7 / 201), avg. gap size = 1.14 (8 / 7) 27 26.56 0.00 0.00 chr4ptel1M 19285 19356 (980644) (TTT)n#Simple_repeat 1 72 (0) m_b163s252i13 6141 chr4ptel1M 19285 TTTTTGTTGTTGTTTGCTTGCTTGCTTTTTTTTTTTTCTCTTTTTTCTTC 19334 v v v vi vi vi i i i i (TTT)n#Simple 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr4ptel1M 19335 TTTTTATTGTTTTTTTTCTTTT 19356 v v i (TTT)n#Simple 51 TTTTTTTTTTTTTTTTTTTTTT 72 Matrix = Unknown Transitions / transversions = 1.00 (8/8) Gap_init rate = 0.00 (0 / 71), avg. gap size = 0.0 (0 / 0) 358 25.58 3.49 0.00 chr4ptel1M 19976 20061 (979939) MIR3#SINE/MIR 115 203 (5) m_b163s601i4 6142 chr4ptel1M 19976 TGAATCTAAATTTCCCTATCTATAAAATGAGGGGATTGCACTCTATGGCC 20025 iii v i ii i i v vv ii MIR3#SINE/MIR 115 TGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATC 164 chr4ptel1M 20026 TGGTAGGTCCTTTCCAG---TGATCATCTATGATCCTAT 20061 vvv i --- ivv i MIR3#SINE/MIR 165 TCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTAT 203 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.00 CpG sites = 13, Kimura (unadjusted) = 32.00 Transitions / transversions = 1.44 (13/9) Gap_init rate = 0.01 (1 / 85), avg. gap size = 3.00 (3 / 1) 238 29.97 11.57 0.75 chr4ptel1M 20141 20261 (979739) C L2b_3end#LINE/L2 (0) 466 333 m_b163s601i5 6143 chr4ptel1M 20141 ATTTCTTCAAGTCAGCAAATATTTA---AGTGTCCAGGAAATGCCAGGCC 20187 iv -v i --- i i i vvivi ? C L2b_3end#LINE 466 ATTCATTCA-TTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCN 418 chr4ptel1M 20188 CTGCACCAAGAGCAAAAG-----GAGGT--ACGAG--TGATAC--TCCTT 20226 ii i i v viii ----- v -- i --v i? -- i C L2b_3end#LINE 417 CTGTGCTAGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCT 368 chr4ptel1M 20227 CCTCTCATCGAGGTCACAGATTGGCGGGGTAGACA 20261 v i iv v vi i i v C L2b_3end#LINE 367 GCCCTCACGGAGCTCACAGTCTAGTGGGGGAGACA 333 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.68 CpG sites = 22, Kimura (unadjusted) = 40.59 Transitions / transversions = 1.57 (22/14) Gap_init rate = 0.05 (6 / 120), avg. gap size = 2.50 (15 / 6) 362 26.45 3.97 3.97 chr4ptel1M 24106 24231 (975769) C MIRb#SINE/MIR (0) 268 143 m_b163s601i6 6144 chr4ptel1M 24106 AAGAAGAAAACTGGCATTTATTATAAGGCACCTCCTAAGTGCCAGACATC 24155 v v i i iv i---i i i v v i - C MIRb#SINE/MIR 268 AATAATAGAGCTACCATTTATTG---AGCGCTTACTATGTGCCAGGCA-C 223 chr4ptel1M 24156 TTTA--AAGCACCTTA---GCAGTAGCTCCCCATGTCCTCATAACAAACC 24200 v i-- i i --- v v viivvi i - C MIRb#SINE/MIR 222 TGTGCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAA-CC 174 chr4ptel1M 24201 CTAAAAAGTAGATATTATTATCCCTATTTTA 24231 ivi i i i C MIRb#SINE/MIR 173 CTGCGAGGTAGGTATTATTATCCCCATTTTA 143 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.84 CpG sites = 20, Kimura (unadjusted) = 33.61 Transitions / transversions = 1.67 (20/12) Gap_init rate = 0.06 (7 / 125), avg. gap size = 1.43 (10 / 7) 15 24.89 0.00 0.00 chr4ptel1M 24563 24596 (975404) (TG)n#Simple_repeat 1 34 (0) m_b163s252i14 6145 chr4ptel1M 24563 TGTATGTGGGTGTGTGTGTTCATGCATGTGTGTG 24596 i v vii ii (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 34 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 259 30.00 3.38 3.38 chr4ptel1M 26726 26932 (973068) C L1M2_orf2#LINE/L1 (1465) 1826 1620 m_b163s551i5 6146 chr4ptel1M 26726 TGTTGTACTTTATACAACATATTCTCTTTATAGATTGAATTGACTGTGTG 26775 v i vv iiiv i vi vv iv iii i C L1M2_orf2#LIN 1826 TGTTGAATTTTATCAAATGCTTTTTCTGCATCTATTGAGATGATCATATG 1777 chr4ptel1M 26776 GTTTTGCATGT--TTGAGTTTAG-AATGTGATTAATTATGTTCATTTTTT 26822 --- -- v v i iv-i vv i i i vv C L1M2_orf2#LIN 1776 GTTTT---TGTCCTTCATTCTGTTGATGTGATGTATCACGTTTATTGATT 1730 chr4ptel1M 26823 CCCCTAATGTTGAAATGTCCTGCCA-GCCTGGTAAAAATCCCACTTGATT 26871 iv v - vii vv -v v v i C L1M2_orf2#LIN 1729 TGCGTA-TGTTGAACCATCCTTGCATCCCTGGGATAAATCCCACTTGATC 1681 chr4ptel1M 26872 ATAATGAATGGTTTTTTGGATAATTTATTGTGG---TTGTTTTGATAGGA 26918 ii ? ?i i --- v ii v --- i v v v C L1M2_orf2#LIN 1680 ATGGTGNATNATCTTTT---TAATGTGCTGTTGAATTCGGTTTGCTAGTA 1634 chr4ptel1M 26919 CTTTGTTTAAAATT 26932 i v ii C L1M2_orf2#LIN 1633 TTTTGTTGAGGATT 1620 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.78 CpG sites = 31, Kimura (unadjusted) = 39.44 Transitions / transversions = 1.07 (31/29) Gap_init rate = 0.05 (11 / 206), avg. gap size = 1.27 (14 / 11) 325 29.48 9.29 0.66 chr4ptel1M 28546 28685 (971315) MIR3#SINE/MIR 50 201 (7) m_b163s601i7 6147 chr4ptel1M 28546 TGAGTGCAATTCCTAGTT-TAACATCAAC---ATGTGTAAAATTTGGCAA 28591 i v v v ii i - iv ii ---v i vv v MIR3#SINE/MIR 50 TGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAA 99 chr4ptel1M 28592 ATCCCTTC-----TCTGTGTTTCATTTTCCTC--CCATAAATTGAAGGGG 28634 i v ----- v ii v -- ii v - MIR3#SINE/MIR 100 GTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGA-GGGG 148 chr4ptel1M 28635 GTTGGACTCTTTAATCCCAAAGG-GTCTTTCAGCCCC-ATATCTTATGAC 28682 vvv i i v -vi i i i- i ii i MIR3#SINE/MIR 149 GTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGAT 198 chr4ptel1M 28683 TTT 28685 i MIR3#SINE/MIR 199 TCT 201 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.20 CpG sites = 24, Kimura (unadjusted) = 38.53 Transitions / transversions = 1.41 (24/17) Gap_init rate = 0.05 (7 / 139), avg. gap size = 2.00 (14 / 7) 29 0.00 0.00 0.00 chr4ptel1M 29494 29518 (970482) (TA)n#Simple_repeat 1 25 (0) c_b163s251i3 6148 chr4ptel1M 29494 TATATATATATATATATATATATAT 29518 (TA)n#Simple_ 1 TATATATATATATATATATATATAT 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 481 29.10 4.06 4.06 chr4ptel1M 29700 29896 (970104) C MIRb#SINE/MIR (67) 201 5 m_b163s601i8 6149 chr4ptel1M 29700 ATTGTATCGCTCTATCTTCATCCTCACTTTCCAAGTTAGGTTATATTGTT 29749 i v ii iv i ivviv ii v i v --- i C MIRb#SINE/MIR 201 ATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGT---ATTATT 155 chr4ptel1M 29750 ATCCCCATTTAAGAGTTGAGGAAACTGAGGCAAACTAACAGAGTTTAAAT 29799 v v v ---- v v v i C MIRb#SINE/MIR 154 ATCCCCATTTTACAGATGAGGAAACTGAGG----CTCAGAGAGGTTAAGT 109 chr4ptel1M 29800 GACTTGCCCAGAGGT-----AGGCAGTAACTGTCCAAGTCTTAATTGAAA 29844 i - ----- vi v v vi i vvi vi C MIRb#SINE/MIR 108 AACTTGCCCA-AGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAA 60 chr4ptel1M 29845 CCCCGATATACCTGACTAT-ATGCCCAGGA-CTCTCCAGTGTACTAC-CG 29891 v i v ii vi- v iv v- i v i i - v C MIRb#SINE/MIR 59 CCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCACCACGCT 10 chr4ptel1M 29892 GCTCC 29896 i C MIRb#SINE/MIR 9 GCCCC 5 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.77 CpG sites = 27, Kimura (unadjusted) = 37.23 Transitions / transversions = 0.96 (27/28) Gap_init rate = 0.06 (12 / 196), avg. gap size = 1.33 (16 / 12) 501 24.51 4.40 5.06 chr4ptel1M 29731 29889 (970111) C MIRc#SINE/MIR (101) 167 10 m_b163s601i9 6149 chr4ptel1M 29731 CAAGTTAGGTTATATTGTTATCCCCATTTAAGAGTTGAGGAAACTGAGGC 29780 i vi --- i v v v - C MIRc#SINE/MIR 167 CAGGGCAGGT---ATTATTATCCCCATTTTACAGATGAGGAAACTGAGG- 122 chr4ptel1M 29781 AAACTAACAGAGTTTAAATGACTTGCCCAGAGGT-----AGGCAGTAACT 29825 --- v v v i - ----- vi v C MIRc#SINE/MIR 121 ---CTCAGAGAGGTTAAGTGACTTGCCCA-AGGTCACACAGCTAGTAAGT 76 chr4ptel1M 29826 GTCCAAGTCTTAATTGAAACCCCGATATACCTGACTATATGCCCAGGACT 29875 v vi i vvi i vi v i v v vi v i vi C MIRc#SINE/MIR 75 GGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCT 26 chr4ptel1M 29876 C--TCCAGTGTACTAC 29889 -- v i i C MIRc#SINE/MIR 25 CTTTCCACTGCACCAC 10 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.85 CpG sites = 16, Kimura (unadjusted) = 29.76 Transitions / transversions = 0.76 (16/21) Gap_init rate = 0.06 (10 / 158), avg. gap size = 1.50 (15 / 10) 20 20.67 0.00 0.00 chr4ptel1M 30377 30415 (969585) (T)n#Simple_repeat 1 39 (0) m_b163s252i15 6150 chr4ptel1M 30377 TTTATTGTTTGTTATTATTGTCTTTTTTTTTTTTTTTTT 30415 v v v v v v i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 39 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 16 9.55 0.00 0.00 chr4ptel1M 32429 32451 (967549) (G)n#Simple_repeat 1 23 (0) m_b163s252i16 6151 chr4ptel1M 32429 GGGGGGGGGGGGGGAGAGGGGGG 32451 i i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGG 23 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 272 29.98 6.31 0.85 chr4ptel1M 32539 32649 (967351) C L2d2_3end#LINE/L2 (33) 522 406 m_b163s601i10 6152 chr4ptel1M 32539 TGCTGTGTGTCAGATACCA-G--AATCTTTGCTAGGAATACAAAGA--CA 32583 i iv ii ii- -- iv vi ivi i --i C L2d2_3end#LIN 522 TACTGTGTGCAAGGCACTGTGCTAGGCGCTGTGGGGGATACAAAGAAGTA 473 chr4ptel1M 32584 AAAGTGAGGGTCTCT--TCTAAGGGAGCTTCCAATCTATCTGGGAATACA 32631 v vv v i --i v i v vi i v C L2d2_3end#LIN 472 TAAGACATGGTCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGGAGACA 423 chr4ptel1M 32632 ACACATATAGCAAATGAA 32649 v - i vi C L2d2_3end#LIN 422 AGACATA-AACACGTGAA 406 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.82 CpG sites = 19, Kimura (unadjusted) = 39.35 Transitions / transversions = 1.36 (19/14) Gap_init rate = 0.05 (5 / 110), avg. gap size = 1.60 (8 / 5) 23 0.00 0.00 0.00 chr4ptel1M 34750 34774 (965226) (A)n#Simple_repeat 1 25 (0) m_b163s252i17 6153 chr4ptel1M 34750 AAAAAAAAAAAAAAAAAAAAAAAAA 34774 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAA 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 14 6.98 0.00 11.76 chr4ptel1M 34797 34834 (965166) (AATA)n#Simple_repeat 1 34 (0) m_b163s252i18 6154 chr4ptel1M 34797 AATAAAAAAGTTATAATAATAGTAAATAAATAAATAAA 34834 v -v - - - (AATA)n#Simpl 1 AATAAATAA-ATA-AATAA-A-TAAATAAATAAATAAA 34 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.11 (4 / 37), avg. gap size = 1.00 (4 / 4) 396 31.97 7.07 1.74 chr4ptel1M 35751 36132 (963868) L2#LINE/L2 2005 2406 (676) m_b163s601i11 6155 chr4ptel1M 35751 ATGATCCTCTCTTT-CTGAGACCAGGGAGCTCTCCCCAGTGCTCATTTTT 35799 i ii v v - i iv iv iv vv i i v i v L2#LINE/L2 2005 ATGACCTCCACGTTGCTAAATCCAATGGTCAATTCTCAGTCCTCATCTTA 2054 chr4ptel1M 35800 CTCAACCTTTCCCCAGCCTTTGACACAGATCACCCCTCTCTCCTTCCTGA 35849 ii ? vv v v v i v i i L2#LINE/L2 2055 CTTGACCTNTCAGCAGCATTTGACACAGTTGATCACTCCCTCCTTCTTGA 2104 chr4ptel1M 35850 G--ACTCTCTTCTCTACAGTTTTAGCACAGGACTCTCTCCAGGCTCTCCT 35897 i-- i v vviv ii v vv v v i i L2#LINE/L2 2105 AACACTTTCTTCACTTGGCTTCCAGGACACCACACTCTCCTGGTTTTCCT 2154 chr4ptel1M 35898 GCTCCCTTTCTGACC---CCTTACCTGTCTTCTGAACTGAAACTTCCCCC 35944 v v iv i --- vi v i vvi i--- i L2#LINE/L2 2155 CCTACCTCACTGGCCGCTCCTTCTCAGTCTCCTTTGCTGG---TTCCTCC 2201 chr4ptel1M 35945 AGAT---CACATCCTCTAATCACAGATATCCCCC----C----TCCTGGC 35983 vv --- v iv ? v iiv ivi v ---- ---- v v L2#LINE/L2 2202 TCATCTCCCCGACCTCTNAACGTTGGAGTGCCCCAGGGCTCAGTCCTTGG 2251 chr4ptel1M 35984 TCCTCCTCTTTTCTCCCTCTATACTAA------TG--GATCTCAT-CAGT 36024 v i i iv i v ------? -- - L2#LINE/L2 2252 ACCTCTTCTCTTCTCTATCTACACTCACTCCCTNGGTGATCTCATCCAGT 2301 chr4ptel1M 36025 TGCCATGCATTTAATCACTATTTCTGGGCTAATAATTGGCAAATTCTTCC 36074 i-i vv vi i i v iv i i i vv -- vi L2#LINE/L2 2302 C-TCATGGCTTTAAATACCATCTATATGCTGATGACTCCCAAAT--TTAT 2348 chr4ptel1M 36075 CTCTCCTGCCCTAATTTCTCTGCTGACTTTCAGGCCTGCAT-CCCTACTG 36123 v v vi ii iv vi i i ii i -i v L2#LINE/L2 2349 ATCTCCAGCCCGGACCTCTCCCCTGAACTCCAGACTCGTATATCCAACTG 2398 chr4ptel1M 36124 ACCTGCCTG 36132 - i ii L2#LINE/L2 2399 -CCTACTCG 2406 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.08 CpG sites = 62, Kimura (unadjusted) = 42.94 Transitions / transversions = 1.07 (62/58) Gap_init rate = 0.04 (17 / 381), avg. gap size = 2.00 (34 / 17) 220 29.97 12.95 3.97 chr4ptel1M 36173 36311 (963689) L2b_3end#LINE/L2 232 382 (84) m_b163s601i12 6155 chr4ptel1M 36173 GGAAAGCCTTCTTTAACTCCTCTTACT---TCTTATGCTTTCC------C 36213 i i ii i i i vvi i--- vvii ii ------ L2b_3end#LINE 232 GGGAAGCCCTCCCTGACCCCCCAGGCCGGGTCAGGCGCCCTCCTCTGGGC 281 chr4ptel1M 36214 TCTTCTAATTATTTCCTATTTCAC-CTG---TACAAAGTTGGCTATTTAC 36259 i ii i i iv vi ii-- - --- i? -- v i? L2b_3end#LINE 282 CCCCCCAGTCCTACCCTGC--CACTCTGGGTTATNA--TTGTCTGNTTAC 327 chr4ptel1M 36260 ATA---GTCTCCTC-ATTCAACTGTAAGCTC-GTGGAGGGCAGAGACTGT 36304 i--- i - i vi i - - i i - L2b_3end#LINE 328 ATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGTG-AGGGCAGGGACCG- 375 chr4ptel1M 36305 AGTGTGT 36311 ? v L2b_3end#LINE 376 NGTCTGT 382 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.85 CpG sites = 31, Kimura (unadjusted) = 43.23 Transitions / transversions = 3.44 (31/9) Gap_init rate = 0.09 (13 / 138), avg. gap size = 1.85 (24 / 13) 263 20.34 6.78 0.00 chr4ptel1M 36246 36304 (963696) L2c_3end#LINE/L2 342 404 (74) m_b163s601i13 6155 chr4ptel1M 36246 AGTTGGCTATTTACATA---GTCTCCTC-ATTCAACTGTAAGCTCGTGGA 36291 i v i ? i--- - i vi i v v L2c_3end#LINE 342 AATTGTCTGTTTACNTGTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGA 391 chr4ptel1M 36292 GGGCAGAGACTGT 36304 i i L2c_3end#LINE 392 GGGCAGGGACCGT 404 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 22.54 CpG sites = 8, Kimura (unadjusted) = 24.85 Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.03 (2 / 58), avg. gap size = 2.00 (4 / 2) 13 14.83 2.44 5.00 chr4ptel1M 36781 36821 (963179) (ATGAAAA)n#Simple_repeat 1 40 (0) m_b163s252i19 6156 chr4ptel1M 36781 ATGAAATAATTGAACAAAG-AAAATAAAACATGAAATATGAA 36821 - - v v - i v v (ATGAAAA)n#Si 1 ATGAAA-AA-TGAAAAATGAAAAATGAAAAATGAAAAATGAA 40 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.07 (3 / 40), avg. gap size = 1.00 (3 / 3) 15 13.99 8.16 1.92 chr4ptel1M 37288 37336 (962664) (AATAA)n#Simple_repeat 1 52 (0) m_b163s252i20 6157 chr4ptel1M 37288 AATAAAATATAAT--AATTAAAT-AAA-AAAATGAAAGCAATTATAAATA 37333 v -- v - - i vv v - (AATAA)n#Simp 1 AATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATA-AAATA 49 chr4ptel1M 37334 AAA 37336 (AATAA)n#Simp 50 AAA 52 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.08 (4 / 48), avg. gap size = 1.25 (5 / 4) 286 23.33 8.18 2.59 chr4ptel1M 39122 39231 (960769) MIR3#SINE/MIR 92 207 (1) m_b164s601i0 6158 chr4ptel1M 39122 TTTGGCAAATCCCTTC-----TCTGTGTTTCATTTTCCTC--CCATAAAT 39164 v i v ----- v ii v -- ii v MIR3#SINE/MIR 92 TTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAA 141 chr4ptel1M 39165 TGAAGGGGGTTGGACTCTTCAATCCCAAAGG-ATCTTTCAGCCCC-ACAT 39212 - vvvii i v -vi i i i- MIR3#SINE/MIR 142 TGA-GGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACAT 190 chr4ptel1M 39213 CTTATGACTTCTGATGGTT 39231 ii - - i MIR3#SINE/MIR 191 TCTATGA-TTCT-ATGATT 207 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.58 CpG sites = 15, Kimura (unadjusted) = 28.58 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.06 (7 / 109), avg. gap size = 1.71 (12 / 7) 15 17.16 6.52 0.00 chr4ptel1M 40181 40226 (959774) (GGTCTGC)n#Simple_repeat 1 49 (0) m_b164s252i1 6159 chr4ptel1M 40181 GGTCTGCCGCCCGAGGTC-G-GGTCTGTGGTC-GTGGTCTGCGGTCAGC 40226 v i i v - - i - i v (GGTCTGC)n#Si 1 GGTCTGCGGTCTGCGGTCTGCGGTCTGCGGTCTGCGGTCTGCGGTCTGC 49 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.07 (3 / 45), avg. gap size = 1.00 (3 / 3) 12 17.65 5.00 2.44 chr4ptel1M 42322 42361 (957639) (ACAAA)n#Simple_repeat 1 41 (0) m_b164s252i2 6160 chr4ptel1M 42322 ACAAAACAAAAC--CACAAAACAAATAAGAAAGAAATTAAAA 42361 --v - vi v vi (ACAAA)n#Simp 1 ACAAAACAAAACAAAACAAAACAAA-ACAAAACAAAACAAAA 41 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.50 (3 / 2) 1277 28.47 13.04 1.89 chr4ptel1M 42424 44471 (955529) L1PB_orf2#LINE/L1 568 2839 (455) m_b164s551i0 6161 chr4ptel1M 42424 GAATATACTTT---TCCAGCAGTTCATGGAACCTATTCAAAAAT---TAA 42467 v --- i ? iv ? vi v i ---iv L1PB_orf2#LIN 568 GAATATACATTCTATTCANCAGCGCATGGAACNTTCTCCAAGATAGACCA 617 chr4ptel1M 42468 TAT--TAGGACATAAAA-GACCTTTAA-------AGGAAAGCAGAAA--- 42504 -- v i - v i i ------- i iiv --- L1PB_orf2#LIN 618 TATGATAGGCCACAAAACGAGCCTCAATAAATTTAAGAAAATCGAAATTA 667 chr4ptel1M 42505 -AGTAAATGCCTTTTCAGATCA--ATGCAATAAAACTACAT-TCAAC--- 42547 - vi iii ii i i --i v iv v- --- L1PB_orf2#LIN 668 TATCAAGCACTCTCTCAGACCACAGTGGAATAAAACTGGAAATCAACTCC 717 chr4ptel1M 42548 AAAAAGTGAGGGGAA-----AAGACCA---AAAGA-ATGGAAAC-AAACA 42587 ------- ----- i --- v - i- i L1PB_orf2#LIN 718 AAAA-------GGAACCCTCAAAACCATGCAAATACATGGAAATTAAATA 760 chr4ptel1M 42588 ATCTCATCTTAAAAGAATGATTGG--TAAGCAC-AAATTAA-----ACAA 42629 i vv i i v - v --i ?v i- i ----- v v L1PB_orf2#LIN 761 ACCTGCTCCTGAATGA-TCATTGGGTCAANAATGAAATCAAGATGGAAAT 809 chr4ptel1M 42630 TTAATAACCCTAAGA---TAATGACAATAG---AACATCATACCAAAATT 42673 ? v ii vv ---v i ---v v v i ii L1PB_orf2#LIN 810 TNAAAAATTCTTCGAACTGAACGACAATAGTGACACAACCTATCAAAACC 859 chr4ptel1M 42674 TG-GGGATGCAGCCAAAGCGGTAATAAGAGGGAATTTTATATCCTTAGAG 42722 v- i v i iv i v i v i i v L1PB_orf2#LIN 860 TCTGGGATACAGCAAAGGCGGTGCTAAGAGGAAAGTTCATAGCCCTAAAT 909 chr4ptel1M 42723 GCTTTACTTGAATAAAACAGAGAAAGAAAAGATTAATGAATTGGGCTTGC 42772 i - v v v iv v i i v v i ivi ii vi ii v ii L1PB_orf2#LIN 910 GCCT-ACATCAAAAAGTCTGAAAGAGCACAAACAGACAATCTAAGGTCAC 958 chr4ptel1M 42773 AACT-AAAAAACTAAAAAAA----GACAAATTAAAACC----CCAACAAA 42813 v - ii i i ----i ii v ---- i i L1PB_orf2#LIN 959 ACCTCAAGGAACTAGAGAAACAAGAACAAACCAAACCCAAACCCAGCAGA 1008 chr4ptel1M 42814 TACTAAATCGGAAAT--TTAAAATTAAA--AGGA------GAAATTAAAA 42853 ---- i vv --ii i i i -- i ------ i L1PB_orf2#LIN 1009 ----AGAAAGGAAATAACCAAGATCAGAGCAGAACTAAATGAAATTGAAA 1054 chr4ptel1M 42854 TTTAAGAAAAAAACTATTGAAC-TAATTTAAAACTAAGGTTGGTTCTATG 42902 i-- iv v ivi v- v v vvv i i v L1PB_orf2#LIN 1055 C--AAACAAAAAAATACAAAAGATAAATGAAACAAAAAGCTGGTTCTTTG 1102 chr4ptel1M 42903 AAAAGCCAA-TAAAA-----AGATCCCTTTTAAAACTGATTA-GAAAAGG 42945 vi - ----- i vi vvii i i i ii - i L1PB_orf2#LIN 1103 AAAAGATAAATAAAATTGATAGACCATTAGCGAGATTAACCAAGAAAAGA 1152 chr4ptel1M 42946 AGGGAGGAAAATGAAATTAGTGTCTTAA---AAAATGAAAAGGGAGA-AT 42991 i i i viv v --- i ---i i v - L1PB_orf2#LIN 1153 AGAGAGAAGATCCAAATAAG---CTCAATTAGAAACGAAACGGGAGATAT 1199 chr4ptel1M 42992 TTCCACCAATGA-AGAGGAA-ATTAGAAATAAT----GAGTTTTTTGCTC 43035 v v i iiv- v i - iv i i v ---- iv vi v vv L1PB_orf2#LIN 1200 TACAACCGACACCACAGAAATACAAAAGATCATTCAAGGCTACTATGAAC 1249 chr4ptel1M 43036 AACTTTTATGCCAATAAATTTGATAACCTAAAGAA-ATGGATGACTACCC 43084 - i i vv i v v i i - i v v i L1PB_orf2#LIN 1250 A-CCTTTACGCGCATAAACTAGAAAACCTAGAGGAGATGGATAAATTCCT 1298 chr4ptel1M 43085 AAAAA----------TC--AGTTTAACAAAGAGGAGGAAGTAAAT---TT 43119 ii ---------- -- ? -- vv i ? i ?---i L1PB_orf2#LIN 1299 GGAAANATACAACCCTCCTAGNTTAA--ATCAGGAAGAANTAGANACCCT 1346 chr4ptel1M 43120 GAATAC-CCTTTCAGAAAAAGAAA---TGAACAGG-AATTAAACAATC-C 43163 i v- vv v v iv vi --- vv - ? v i- L1PB_orf2#LIN 1347 GAACAGACCAATAACAAGCAGCGAGATTGAAATGGTAATTNAAAAATTAC 1396 chr4ptel1M 43164 CAAGAAAAAATCCCCCAGGACCAGATGG-TTTACAG--GAATTC-ACCAA 43209 v vvvi i - i -- - i L1PB_orf2#LIN 1397 CAACAAAAAAAAGTCCAGGACCAGACGGATTCACAGCNGAATTCTACCAG 1446 chr4ptel1M 43210 ACATTTAAA-AACAATTGGCCCCAATGCATAT--AAATTATTTGATAAAA 43256 i - v iv v - -- v i iv i i L1PB_orf2#LIN 1447 ACATTCAAAGAAGAATTGGTACCAATCC-TATTGACACTATTCCACAAGA 1495 chr4ptel1M 43257 TAGGGAAAA--GGAGTCCTACC-AAACC-TTCTATGACACAGACATGGTA 43302 i i-- i v - i - --- v -- L1PB_orf2#LIN 1496 TAGAGAAAGAGGGAATCCTCCCTAAATCATTCTATGA---AGCCA--GTA 1540 chr4ptel1M 43303 T------GATACCTAAACCAGGA--GGCTGAAAACAGAAAAAAAAA---- 43340 ------i v -- viiv v? i i ---- L1PB_orf2#LIN 1541 TCACCCTAATACCAAAACCAGGAAAGGACATAACNAAAAAAGAAAACTAC 1590 chr4ptel1M 43341 GGACCAAT-TCCC-AATGAATATTGATGCTAAAATCTTAAATAAGATATT 43388 i - -i i v ? i v i i i L1PB_orf2#LIN 1591 AGACCAATATCCCTGATGAACATAGATGCNAAAATCCTCAACAAAATACT 1640 chr4ptel1M 43389 GA--AAAAGA---CTACAGAAAATCACTCCAAGATAATACAC-ATGATCA 43432 ii-- vv --- v v v v--v v - L1PB_orf2#LIN 1641 AGCTAACCGAATCCAACAGCATATCAA--AAAGATAATCCACCATGATCA 1688 chr4ptel1M 43433 AGTATGATTT--TACCAGGAATGCAGGGCTGGTTCAAATTAGGAAAA-CT 43479 i- i -- i v i vv v v i- v L1PB_orf2#LIN 1689 AGTG-GGTTTCATACCAGGGATGCAGGGATGGTTTAACATACGCAAGTCA 1737 chr4ptel1M 43480 ATCAATATAATTGGCCATTTTAACCAAATTAAAAAC--------CATAAT 43521 v i i vvi iv v vi -------- i L1PB_orf2#LIN 1738 ATAAATGTGATACACCACATAAACAGAATTAAAAACAAAAATCACATGAT 1787 chr4ptel1M 43522 CATCTCAATAGATGC-GAAAAAGCATTTGATAAAATCCAACATCCATTCC 43570 - i i ---- L1PB_orf2#LIN 1788 CATCTCAATAGATGCAGAAAAAGCATTTGACAAAATCCAGCATC----CC 1833 chr4ptel1M 43571 TTTA-----AAAACACTTGAGAGTATGGA---AAAATGGACTTTTCCTTA 43612 ----- v iiiv iv v i--- ? v -v v L1PB_orf2#LIN 1834 TTTATGATTAAAACCCTCAGCAAAATCGGCATANAAGGGAC-ATACCTTA 1882 chr4ptel1M 43613 AAA-AATCAGAATCATTTA----AAACCATCAG-TAAGATCATATGTAAT 43656 ?i- v i ii i ---- vv -i v ? ivv L1PB_orf2#LIN 1883 ANGTAATAAAAGCCATCTATGACAAACCCACAGCCAACATNATACTGAAT 1932 chr4ptel1M 43657 -GGGACAAACTGCAACCATTCCCAATAAGATCTGGAGTGAAACAAGG--- 43702 - v ii v v vv i v iii i --- L1PB_orf2#LIN 1933 GGGGAAAAGTTGAAAGCATTCCCCCTGAGAACTGGAACAAGACAAGGATG 1982 chr4ptel1M 43703 ----TTTACACCATTACTATT-----TAATAATGAAA--CCTAGCTATA- 43740 ----i iv i v ? ----- i v i -- i v - L1PB_orf2#LIN 1983 CCCACTCTCACCACTTCTNTTCAACATAGTACTGGAAGTCCTAGCCAGAG 2032 chr4ptel1M 43741 -AATAAGA-GCTAGAAAGAGATTAAAGGAATAAGAATAGG--AATGGGAA 43786 - v -ivv i v i v vvi v -- vi L1PB_orf2#LIN 2033 CAATCAGACAAGAGAAAGAAATAAAGGGCATCCAAATCGGTAAAGAGGAA 2082 chr4ptel1M 43787 G--AAATTATCACTCTTTTGCCGATGACATGATGGT-TGCTTA-AGAACC 43832 -- i i i -v i i v - i i - i L1PB_orf2#LIN 2083 GTCAAACTGTCGCT-GTTTGCTGATGATATGATCGTNTACCTAGAAAACC 2131 chr4ptel1M 43833 CCAAA---TTCTTTAAAAAGTTATTAGAAATAAT-CCCAACTTTA--AAA 43876 i --- i ii i i vi v i -vv?i v i -- L1PB_orf2#LIN 2132 CTAAAGACTCCTCCAGAAAGCTCCTAGAACTGATAAANGAATTCAGCAAA 2181 chr4ptel1M 43877 GTT---GTTTATAAAATAAACCC-CATAAGTCA-TAATTCT--TATATAT 43919 --- vv i v ivi- i i - ii -- i i L1PB_orf2#LIN 2182 GTTTCNGGATACAAAATTAATGTACACAAATCAGTAGCTCTNCTATACAC 2231 chr4ptel1M 43920 CAA-AAAAACCAACAGTCAGAGTTACAA--AAGA----AATTTCATTTAA 43962 - ivi -iv v i i - -- ---- iii v v L1PB_orf2#LIN 2232 CAACAGCGACCAA-GCTGAGAATCA-AATCAAGAACTCAACCCCTTTTAC 2279 chr4ptel1M 43963 AGTAACTACTGATAATATAAAAATATTTA-GAATCTATTGAA--GGGAAA 44009 i i i vi v v - i - v iiv --ii i i L1PB_orf2#LIN 2280 AATAGCTGCAAAAAAAAT-AAAATACTTAGGAATATACCTAACCAAGGAG 2328 chr4ptel1M 44010 ATCAGAAA-CTTTATGAGCAAAATTACAGACCACT-TTCACACAAAT--T 44055 i v i i - i ii v i i v -i v v v -- L1PB_orf2#LIN 2329 GTGAAAGACCTCTACAAGGAAAACTACAAAACACTGCTGAAAGAAATCAT 2378 chr4ptel1M 44056 AAGTTAT-CTAACCAATTGAAAAATATTAAATGCTC--GGATAGGGCGAG 44102 iiiv i- v v v v i ivv -- i vv i L1PB_orf2#LIN 2379 AGACGACACAAACAAATGGAAACACATCCCATGCTCATGGATGGGTAGAA 2428 chr4ptel1M 44103 CAAATATAATAAAGATGACAA-ATTACCTAAACTAATCTATTTATTTA-- 44149 iv vi i i v - i i v vi ivv i -- L1PB_orf2#LIN 2429 TCAATATTGTGAAAATGACCATACTGCCAAAAGCAATCTACAAATTCAAT 2478 chr4ptel1M 44150 GCTATACCAATCAGACTCCCAAAAAC-TATTTTAATGACCTAGAAAAATA 44198 v v v i v v vv v - vi i vv v -- L1PB_orf2#LIN 2479 GCAATTCCCATCAAAATACCACCATCATTCTTCACAGAACTAGAAAA--A 2526 chr4ptel1M 44199 ACAA---CAAAGTTCATATGG----AAAAAAAAGTCAAAAT-TTCAAGGG 44240 ---i i ---- i i viv -vi i v L1PB_orf2#LIN 2527 ACAATCCTAAAATTCATATGGAACCAAAAAAGAGCCCGCATAGCCAAAGC 2576 chr4ptel1M 44241 A--ATTAATGAAAAAAATCAAA--TGATGG--TTACTGTACCAGACTT-- 44282 -- i vv i v -- iv -- i vv v -- L1PB_orf2#LIN 2577 AAGACTAAGCAAAAAGAACAAATCTGGAGGCATCACATTACCCGACTTCA 2626 chr4ptel1M 44283 ----------TAAAGACGCAGTTACCAAAACATT-TGGTATTGGCTAAGG 44321 ---------- i v ii i vi- i i-- vi L1PB_orf2#LIN 2627 AACTATACTATAAGGCCATAGTCACCAAAACAGCATGGTACTGGT--ATA 2674 chr4ptel1M 44322 AAAATTAG----TTGATCAGTGGAATAGATTAGGT--TCAAGGGAAAAAC 44365 vi ---- v i i i v iv--i v ii v L1PB_orf2#LIN 2675 AAAATAGGCACATAGACCAATGGAACAGAATAGAGAACCCAGAAATAAAC 2724 chr4ptel1M 44366 GTCAACAAATATAGCAACCTAGTCTTT-ACAAACC---CAAAGATCCCA- 44410 viv i vv i v v ii i- v --- i iviv - L1PB_orf2#LIN 2725 CCAAATACTTACAGCCAACTGATCTTCGACAAAGCAAACAAAAACATAAA 2774 chr4ptel1M 44411 -CGGGATAAGAAC-TTATGTTTGATAAAAATTGCTGGGAAAATTGG-AAA 44457 -i iv i -iiv i ii i viv v - i L1PB_orf2#LIN 2775 GTGGGGAAAGGACACCCTATTCAACAAATGGTGCTGGGATAATTGGCAAG 2824 chr4ptel1M 44458 CTA-ATATGGCAGAA 44471 i - i i v L1PB_orf2#LIN 2825 CCACATGTAGGAGAA 2839 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.96 CpG sites = 319, Kimura (unadjusted) = 37.02 Transitions / transversions = 1.26 (319/253) Gap_init rate = 0.08 (158 / 2047), avg. gap size = 1.96 (310 / 158) 2143 27.13 10.78 1.83 chr4ptel1M 42643 44906 (955094) L1M5_orf2#LINE/L1 832 3294 (0) m_b164s551i1 6161 chr4ptel1M 42643 GATAATGACAATAGAACATCATACCAAAATTTG-GGGATGCAGCCAAAGC 42691 ? v v --- i - i L1M5_orf2#LIN 832 GANAATGAAAATACAACAT---ATCAAAATTTGTGGGATGCAGCTAAAGC 878 chr4ptel1M 42692 GGTAATAAGAGGGAATTTTATATCCTTAGAGGCTT-TACTTGAATAAAAC 42740 i iv v v v ? i v ? - i v - i - L1M5_orf2#LIN 879 AGTGCTTAGAGGGAAATTTATAGCNTTAAATGCNTATATTAGAA-AAGA- 926 chr4ptel1M 42741 AGAGAAAGAA--AAGATTAATGAATTGGGCTTGCAAC-TAAAAAACTAAA 42787 -- iv-- i i vi ii v v - i i i L1M5_orf2#LIN 927 --AGAAAGGCTTAAAATCAATGATCTAAGCTTCCACCTTAAGAAGCTAGA 974 chr4ptel1M 42788 AAAAGA----CAAATTAAAACCCCAACAAATACTAAATCGGAAAT-TTAA 42832 ---- v vv i? i vv iivv -v L1M5_orf2#LIN 975 AAAAGAAGAGCAAATTAAACCCAAAGNAAGTAGAAGGAAGGAAATAATAA 1024 chr4ptel1M 42833 AATTAAAAGGAGAAAT---TAAAATTTAAG--AAAAAAACTATTGAACTA 42877 iv i v --- i vv i-- ? ? v v ivv L1M5_orf2#LIN 1025 AGATAAGAGCAGAAATCAATGAAATAGAAAACAAANANACAATAGAGAAA 1074 chr4ptel1M 42878 ATT--TAAAACT-AAGGTTGGTTCTATGAAAAG-CCAATAAAA-----AG 42918 i--ii i i- i i v -i ----- i L1M5_orf2#LIN 1075 ATCAACGAAGCCAAAAGCTGGTTCTTTGAAAAGATCAATAAAATTGATAA 1124 chr4ptel1M 42919 ATCCCTTTTAAAACTGATT-AGAAAAGGAGGGAGGAAAATGAAATTAGTG 42967 i i vvi? i i- ii i i i vvv vii L1M5_orf2#LIN 1125 ACCTCTAGCNAGACTGATCAAGAAAAAAAGAGAGAAGACACAAATTACCA 1174 chr4ptel1M 42968 TCTTAAAAAATGAAAAGGGAGA-ATTTCCACCAATGAAGAGGAAATTAGA 43016 viv v ii i - iv i vi vvvivi v i L1M5_orf2#LIN 1175 ATATCAGGAATGAAAAAGGAGACATCACTACAGATCCTACAGACATTAAA 1224 chr4ptel1M 43017 A--ATAAT----GAGTTTTTTGCTCAACTTTTATGCCAATAAATTTGATA 43060 -- ---- i v v vv - ? L1M5_orf2#LIN 1225 AGGATAATAAGAGAATATTATGAACAAC-TTTATGCCAATAAATTTGANA 1273 chr4ptel1M 43061 ACCTAAA-GAAATGGATGACTACCC--AAAAAT-CAGTTTAACAAAG--- 43103 i i - ii v v i-- i- i? v i--- L1M5_orf2#LIN 1274 ACTTAGATGAAATGGACAAATTCCTTGAAAAACACAANTTACCAAAACTG 1323 chr4ptel1M 43104 ----AGGAGGAAGT---AAATTTGAATACCCTT---TCAGAAAAAGAAA- 43142 ---- i i i --- i v i --- vivv - L1M5_orf2#LIN 1324 ACNCAAGAAGAAATAGAAAATCTGAATAGCCCTATATCTATTAAAGAAAT 1373 chr4ptel1M 43143 TGAA-CAGGAATTAAACAATC--CCAAGAAAAAATCCCCCAGGACCAGAT 43189 -iv v - i -- v v i vv i v L1M5_orf2#LIN 1374 TGAATTTGTAATTAAA-AACCTTCCCACAAAGAAAACTCCAGGCCCAGAT 1422 chr4ptel1M 43190 GG-TTTACAG--GAATTC-ACCAAACATTTAA-AAACAATTGGCCCCAAT 43234 - i v -- - -i v v iiiv L1M5_orf2#LIN 1423 GGCTTCACTGGTGAATTCTACCAAACATTTAAGGAAGAAATAATACCAAT 1472 chr4ptel1M 43235 G-CATATAAATTATTTGATAAAATAGGGAA--AAGGAGTCCTACCAAACC 43281 v-i i i i v iv v ii -- i iiv v v i L1M5_orf2#LIN 1473 CTTACACAAACTCTTCCAGAAAATAGAAAAAGAGGGAACACTTCCCAACT 1522 chr4ptel1M 43282 --TTCTATGACACAGACATGG-TATGATACCTAAACCAGGAGGCTGAAAA 43328 -- i vi vii ?i-iv v ? i----ii i L1M5_orf2#LIN 1523 CATTTTATGAGGCCAGCATNACCCTGATACCAAAACCNGA----CAAAGA 1568 chr4ptel1M 43329 C------AGAAAAAAAAA----GGACCAAT-TCCC-AATGAATATTGATG 43366 ------ i ----i - -v i v L1M5_orf2#LIN 1569 CATTACAAGAAAAGAAAATTACAGACCAATATCCCTCATGAACATAGATG 1618 chr4ptel1M 43367 CTAAAATCTTAAATAAGATATTGAAAAA--GACTACAGAAA---ATCACT 43411 v i ? i i iiv -- v v v --- v -- L1M5_orf2#LIN 1619 CAAAAATCCTNAACAAAATATTAGCAAATCGAATCCAGCAATATATAA-- 1666 chr4ptel1M 43412 CCAAGATAATACA-CATGATCAAGTATGATTT-TACCAGGAATGCAGGGC 43459 vv i - i iv i - v i i L1M5_orf2#LIN 1667 AAAGGATAATACATCATGACCAAGTGGGGTTTATCCCAGGAATGCAAGGT 1716 chr4ptel1M 43460 TGGTTCAA-ATTAGGAAAACTATCAATATAATTGGCCATTTTAACCAAAT 43508 i - v i v v i vi v vi L1M5_orf2#LIN 1717 TGGTTTAACATTCGAAAATCAATCAATGTAATTCACCATATTAACAGAAT 1766 chr4ptel1M 43509 ------TAAAAACCATA--ATCATCTCAATAGATGC-GAAAAAGCATTTG 43549 ------v i -- - L1M5_orf2#LIN 1767 AAAGGAGAAAAATCATATGATCATCTCAATAGATGCAGAAAAAGCATTTG 1816 chr4ptel1M 43550 ATAAAATCCAACATCCATTCCTT-TAAAAACACTTG--AGAGTATGGAAA 43596 i i i v v- v ii-- i v v i v L1M5_orf2#LIN 1817 ACAAAATTCAACACCCATTCATGATAAAAACTCTCAGCAAACTAGGAATA 1866 chr4ptel1M 43597 AATGGACTTTTCCTTAAAA-AATCAGAATCATTT----AAAACCATCAG- 43640 i v ivvi i vv-i v iiiv i ---- vv - L1M5_orf2#LIN 1867 GAAGGGAACTTCCTCAACCTGATAAAGGGCATCTACGAAAAACCTACAGC 1916 chr4ptel1M 43641 TAAGATCATATGTAATGG-GACAAACTGCAACCATTCCCAATAAGATCTG 43689 ? v iv - v ? v ?v v vv v L1M5_orf2#LIN 1917 NAACATCATACTTAATGGTGAAANACTGAANGCTTTCCCCCTAAGATCGG 1966 chr4ptel1M 43690 GAGTGAAACAAG-------GTTTACACCATTACTATTTAA-----TAATG 43727 iii i ------- i ?v i v i ----- v L1M5_orf2#LIN 1967 GAACAAGACAAGGATGTCCGCTNTCACCACTTCTATTCAACATTGTACTG 2016 chr4ptel1M 43728 AAA--CCTAGCTA-TA-AATAAGAGCTAG--AAAGAGATTAAAGGAATAA 43771 i i-- i - i- - v -- i v v L1M5_orf2#LIN 2017 GAGGTCCTAGCCAGTGCAATAAG-GCAAGAAAAAGAAATAAAAGGCATAA 2065 chr4ptel1M 43772 GAATAGGAATGGGAAGAAAT-----TATCACTCTTTTGCCGATGACATGA 43816 ii v -i ----- i ?i v- i v L1M5_orf2#LIN 2066 AGATTGGAA-AGGAAGAAATAAAACTGTCNTTA-TTCGCAGATGACATGA 2113 chr4ptel1M 43817 TGGT-TGCTTA-AGAACCCCAAAT--TCTTTAAA-AAGTTATTAGAAATA 43861 v - i v - i i ? v-- vi - ii i v L1M5_orf2#LIN 2114 TTGTNTACGTAGAAAATCCNAAAGAATCTACAAANAAACTACTAGAACTA 2163 chr4ptel1M 43862 AT-CCCAACTTTA--AAAGTTGTT---TATAAAATAAAC-CCCATAAGTC 43904 -vvii v -- i i i?--- i ii v i-iv v i L1M5_orf2#LIN 2164 ATAAGTGAATTTAGCAAGGTCGCNGGATACAAGGTCAATATACAAAAATC 2213 chr4ptel1M 43905 A--TA-ATTCTTATATATCAAAAAAACCAACAGTCAG-------AGTTAC 43944 -- i- ii ii-- iv v i ii ------- i v? L1M5_orf2#LIN 2214 AATTGTATTTCTATATACT--AGCAACAAACAATTGGAAAATGAAATTTN 2261 chr4ptel1M 43945 AAAAGAAATTTCATTTAAAGTAACTACTGATAATATAAAAATATTTA-GA 43993 iv vi v i i vv vi v i -? i - L1M5_orf2#LIN 2262 AAAAACAATACCATTTACAATAGCATCAAAAAACAT-NAAATACTTAGGA 2310 chr4ptel1M 43994 ATCTATTGAAGGGAAAAT---CAGAAACTTTATGAGCAAAATTACAGACC 44040 vv iv vii ? --- ii v ? iivvv i i v L1M5_orf2#LIN 2311 ATAAATCTAACAAAANATGTGCAAGACCTNTACACTGAAAACTACAAAAC 2360 chr4ptel1M 44041 ACT-TTCACACAAATTAAGT--TATCT-AACCAATTGAAAAATATTAAAT 44086 i -i v v v iv--v i - iv v i i vvv L1M5_orf2#LIN 2361 ATTGCTGAGAGAAATTAAAGAAGACCTAAATAAATGGAGAGATATACCAT 2410 chr4ptel1M 44087 GCTC--GGATAGGGCGAGCAAATATAATAAAGATGACAAAT-TACCTAAA 44133 i -- v iv viv vi ? v v - v i L1M5_orf2#LIN 2411 GTTCATGGATTGGAAGACTCAATATTGTNAAGATGTCAATTCTCCCCAAA 2460 chr4ptel1M 44134 CTAATCTATTTATTTA--GCTATACCAATCAGACTCCCAAAAACTATTTT 44181 i i vv i -- v v i v iv iv v L1M5_orf2#LIN 2461 TTGATCTATAGATTCAATGCAATCCCAATCAAAATCCCAGCAGGTTTTTT 2510 chr4ptel1M 44182 AATGACCTAGAAAAATAACAA--------CAAAGTTCATATGGAAA---A 44220 -- --- - v i --------i i i --- L1M5_orf2#LIN 2511 --TG---TAG-AAATTGACAAGCTGATTCTAAAATTTATATGGAAATGCA 2554 chr4ptel1M 44221 AAAAGTCAAAATT--TCAAGGGAA--TTAATGAAAAAAATCAAA--TGAT 44264 iiii ? i v --i iiv -- i vi i i v -- iv L1M5_orf2#LIN 2555 AAGGACCNAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA 2604 chr4ptel1M 44265 GG--TTACTGTACC--------AGACTT----TAAAGACGCAGTTACCAA 44300 -- vv -------- ---- vii v i L1M5_orf2#LIN 2605 GGACTTACACTACCNGATNTCAAGACTTATTATAAAGCTACAGTAATCAA 2654 chr4ptel1M 44301 AACA-TTTGGTATTGGC-TAAGGA-AAATTAGTTGATCAGTGGAATAGAT 44347 i - v - - i iv i v i i v L1M5_orf2#LIN 2655 GACAGTGTGGTATTGGCGTAAGGATAGACAAATAGATCAATGGAACAGAA 2704 chr4ptel1M 44348 TAG---GTTCAAGGGAAAAACGTCA-ACAAATATAGCAACCTAGTCTTT- 44392 --- i - ii v i -i - v i ?v ?i ii i - L1M5_orf2#LIN 2705 TAGAGAGTCC-AGAAATAGAC-CCACACATATATGGNCANTTGATTTTTG 2752 chr4ptel1M 44393 ACAAA---CCCAAAG--ATCCCACGGGATAAGAA----CTTATGTTTGAT 44433 ---v ? -- i vii iv i ---- --- ii i L1M5_orf2#LIN 2753 ACAAAGGTGCCAANGCAATTCAGTGGGGAAAGGATAGTCTT---TTCAAC 2799 chr4ptel1M 44434 AAAAATTGCTGGGAAAATTGGAAACTAATATGGCAGAAACTAGGCATTGA 44483 viv i v v iiv v i v iii?v i L1M5_orf2#LIN 2800 AAATGGTGCTGGAACAATTGGATATCCATATGGAAAAAAATGAANCTCGA 2849 chr4ptel1M 44484 -TCCTACTTAACGCCG-ACACCAAGATAAAGGTCAAATGGGTTCAT-GAC 44530 -i i v i i- v i v vvi? i i- - L1M5_orf2#LIN 2850 CCCCTACCTCACACCATACACAAAAATTAATTCNAGATGGA-TCATAGAC 2898 chr4ptel1M 44531 CTAGGCATAAAAGAACGAAATTATTAA-----TAAATTAGAGGACCAAGG 44575 iiii -?ii i v ----- i -- ii vv L1M5_orf2#LIN 2899 CTAAATGTAAAAG-NTAAAACTATAAAACTTCTAGA--AGAAAACATAGG 2945 chr4ptel1M 44576 ---ATGTTTTCCCTGCCGTGGA--AGGGAAGGG--TCTTAG-------AC 44611 --- i i vivi v i-- v i i-- i------- L1M5_orf2#LIN 2946 AGAATATCTTCGTGACCTTGGGNTAGGCAAAGATTTCTTAAACAGGACAC 2995 chr4ptel1M 44612 AAAGAGAACTAGAGATCAAATATGATCCAAAATAGAAAATTTCGATTATA 44661 i v ? ivv v --- --v v v v v i ?i L1M5_orf2#LIN 2996 AAAAAGCACNAACCATAAAA---GA--AAAAATTGATAAATTGGACTNCA 3040 chr4ptel1M 44662 CC-AAACTGAAAAGTTTTGTACAAACAAAACTAATGCAGACAAGATTAGA 44710 i - i i v i iv ?vvv ivi vi ivi v i v i L1M5_orf2#LIN 3041 TCAAAATTAAAAACTTCTGCTCNTCAAAAGACACCGTTAAGAAAATGAAA 3090 chr4ptel1M 44711 AGGGAAGCAATAAACTGGGAAAATATTTTTACAGT-CAAAGGTTCGATAA 44759 v v i i ? i v v i i?- v vi ii i L1M5_orf2#LIN 3091 AGGCAAGCCACAGANTGGGAGAAAATATTTGCAANACATATATCTGACAA 3140 chr4ptel1M 44760 AGGCCT-ATTTCCAAAATATATAGAGAATTAACCT--AATTT-ATAAAAA 44805 v -i v i i i -- -- ? i- ? L1M5_orf2#LIN 3141 AGGACTCGTATCCAGAATATATAAAGAACT--CCTACAANTCAATAANAA 3188 chr4ptel1M 44806 TCAAGCCATTC--TCCAATTGAAAAATGGTCAAAGGATATGAACAGACAA 44853 -v v vv --i v? v i iv v L1M5_orf2#LIN 3189 -AAAGACAAACAACCCAATANAAAAATGGGCAAAAGACTTGAACAGACAC 3237 chr4ptel1M 44854 CT--CAGATGAAGAAATTAAACATTTCTAGT---CATATGAAAAGATGCT 44898 i -- i v v ?v - vv i i --- i L1M5_orf2#LIN 3238 TTCACAAAAGAAGATATNCAA-ATGGCCAATAAGCACATGAAAAGATGCT 3286 chr4ptel1M 44899 CCAAGTCA 44906 v v? L1M5_orf2#LIN 3287 CAACNTCA 3294 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.79 CpG sites = 335, Kimura (unadjusted) = 35.23 Transitions / transversions = 1.25 (335/268) Gap_init rate = 0.07 (155 / 2263), avg. gap size = 1.86 (289 / 155) 869 23.84 12.28 3.66 chr4ptel1M 44769 45273 (954727) L1MD1_3end#LINE/L1 7 553 (436) m_b164s551i2 6161 chr4ptel1M 44769 TCCAAAATATATAGAGAATT-----AACCTAAT-TTATAAAAATCAAGCC 44812 i i i i ----- ii i-v v - i v L1MD1_3end#LI 7 TCTAGAATATATAAAGAACTCTCAAAACTCAACAGTAAAAAAA-CAAACA 55 chr4ptel1M 44813 ATTCTCCAATTGAAAAATGGTCAAAGGATATGAACAGACAACTCA--GAT 44860 --- ii v i i v vi -- v L1MD1_3end#LI 56 AT---CCAATTAGAAAATGGGCAAAAGACATGAAGAGACATTTCACCGAA 102 chr4ptel1M 44861 GAAGAAATTAAACATTTC---TAGTCATATGAAAAGATGCTCCAAGTCAT 44907 i v - v v vv --- iv i i v vi L1MD1_3end#LI 103 GAGGATAT-ACAGATGGCAAATAAGCACATGAAAAGATGTTCAACATCAT 151 chr4ptel1M 44908 TAATCA----AGAAATGCAAATTAAGA----AATTTAAGAT---AATATA 44946 ii ----i i ---- -- i --- v i L1MD1_3end#LI 152 TAGCCATTAGGGAAATGCAAATTAAAACCACAA--TGAGATATCACTACA 199 chr4ptel1M 44947 CACCTGTCAGATTGGCTAAGATGACAGGACAAAATAATGATGAT------ 44990 i v i i ------ i ii i------ L1MD1_3end#LI 200 CACCTATCAGAATGGCTAAAATAA------AAAATAGTGACAACACCAAA 243 chr4ptel1M 44991 TGTTG--GGGGATGGGGA-AAACTGGG-AATTGATGC-TTGTTGG-GGAG 45034 i -- i v - i-v i v i - i - ii L1MD1_3end#LI 244 TGCTGGCGAGGATGCGGAGAAACTGGATCACTCATACATTGCTGGTGGGA 293 chr4ptel1M 45035 GTTTAAGA--ATCCAACCATTTTGGA----AGTTTGGAACTATGCTCAAA 45078 i v i --i v i i i ---- v v - v i L1MD1_3end#LI 294 ATGTAAAATGGTACAGCCACTCTGGAAAACAGTTTGGCAGT-TTCTTAAA 342 chr4ptel1M 45079 AAATCAAAC-TGTA--TACC---CGATCCAGAGGTTA----CTTGGG-AT 45117 ii - i -- --- i vii i---- i - L1MD1_3end#LI 343 AAACTAAACATGCAACTACCATACGACCCAGCAATTGCACTCCTGGGCAT 392 chr4ptel1M 45118 TATATCCCCAAAGAGATTATAAAGAAGG------GAAAGACCTGTATGTG 45161 - - i i v v vvv v ------v i ---- L1MD1_3end#LI 393 T-TAT-CCCAGAGAAATGAAAACTTATGTTCACACAAAAACCTGTA---- 436 chr4ptel1M 45162 CACGAATGTTTGTGGCAGCCCT-TTTGTAGTGG-TAAAAACTGGAAACGA 45209 i i ii - i i i -i i L1MD1_3end#LI 437 CACGAATGTTTATAGCAGCTTTATTCGTAATAGCCAAAAACTGGAAACAA 486 chr4ptel1M 45210 -ATGGATGTCCATCAGTTGGAGAATGGTTGAATAAATTGTGGTATA--AA 45256 -vii v iiv v i i i i --v L1MD1_3end#LI 487 CCCAGATGTCCTTCAACGGGTGAATGGTTAAACAAACTGTGGTACATCCA 536 chr4ptel1M 45257 AATTATGGAATATTACT 45273 v ii i L1MD1_3end#LI 537 TACCATGGAATACTACT 553 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 29.14 CpG sites = 77, Kimura (unadjusted) = 29.75 Transitions / transversions = 1.97 (77/39) Gap_init rate = 0.09 (45 / 504), avg. gap size = 1.82 (82 / 45) 22 0.00 0.00 0.00 chr4ptel1M 45782 45805 (954195) (A)n#Simple_repeat 1 24 (0) m_b164s252i3 6162 chr4ptel1M 45782 AAAAAAAAAAAAAAAAAAAAAAAA 45805 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAA 24 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 558 26.93 3.68 4.23 chr4ptel1M 46241 46430 (953570) C MIRb#SINE/MIR (67) 201 13 m_b164s601i1 6163 chr4ptel1M 46241 ATTGTATCATTTTATCCTCATCTTAACTTTCCAAGTTAGGTTATATTGTT 46290 i v v ivvi ii v i v --- i C MIRb#SINE/MIR 201 ATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGT---ATTATT 155 chr4ptel1M 46291 ATCCCCATTTAAGAGTTGAGGAAACTGAGGCAAAGTAACAAAATTTAAAT 46340 v v v ---- v v i iv i C MIRb#SINE/MIR 154 ATCCCCATTTTACAGATGAGGAAACTGAGGC----TCAGAGAGGTTAAGT 109 chr4ptel1M 46341 GACTTGCCCAGAGGT-----AGGCAGTAACTGTCCAAGTCTTAATTGAAA 46385 i - ----- vi v v vi i vvi vi C MIRb#SINE/MIR 108 AACTTGCCCA-AGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAA 60 chr4ptel1M 46386 TCCTGATATACCTGACTAT-ATGCCCATGA-ATTTCCACTGTACTAC 46430 i v i v ii vi- v i v-v i i C MIRb#SINE/MIR 59 CCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCACCAC 13 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.25 CpG sites = 24, Kimura (unadjusted) = 33.66 Transitions / transversions = 0.96 (24/25) Gap_init rate = 0.06 (11 / 189), avg. gap size = 1.36 (15 / 11) 225 30.59 4.71 0.00 chr4ptel1M 47070 47154 (952846) MIR3#SINE/MIR 115 203 (5) m_b164s601i2 6164 chr4ptel1M 47070 TGAATCTCCATTTCC-CATCTATGAAAGGGGAAGATTGCACTCCATGGCC 47118 iii vi - i i v i ii i v vv ii MIR3#SINE/MIR 115 TGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATC 164 chr4ptel1M 47119 CCGTAGATCCCTTCCAGTGCT--CA-TCTGGGATGCTAT 47154 i vv i iv -- - iv v MIR3#SINE/MIR 165 TCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTAT 203 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.78 CpG sites = 16, Kimura (unadjusted) = 40.78 Transitions / transversions = 1.60 (16/10) Gap_init rate = 0.04 (3 / 84), avg. gap size = 1.33 (4 / 3) 206 37.09 2.40 9.40 chr4ptel1M 47246 47370 (952630) C L2c_3end#LINE/L2 (1) 477 361 m_b164s601i3 6165 chr4ptel1M 47246 TTCTTCTAGTCAGTAAACA---ATTAAGTGCCTTCTACATGGCAGCCCTA 47292 v ii v ii --- i i v ii v ----- C L2c_3end#LINE 477 TTCATTCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAG----- 433 chr4ptel1M 47293 GGCCGAGCACCAGGAACATAAAGAAATGTAAGGGACATCCTCCACTCTCA 47342 ------ i ii i i i vivi iv ivi i ii i C L2c_3end#LINE 432 ------GCGCTGGGGATACAAAGATGAATAAGACACGGTCCCTGCCCTCA 389 chr4ptel1M 47343 TGAAGGTCACAGAATGGCCGGGAAGGCA 47370 v i v vv i iv i i i C L2c_3end#LINE 388 AGGAGCTCACAGTCTAGTGGAGGAGACA 361 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 49.31 CpG sites = 29, Kimura (unadjusted) = 55.22 Transitions / transversions = 2.23 (29/13) Gap_init rate = 0.10 (12 / 124), avg. gap size = 1.17 (14 / 12) 281 29.45 15.07 0.00 chr4ptel1M 47506 47651 (952349) C MIR#SINE/MIR (3) 259 92 m_b164s601i4 6166 chr4ptel1M 47506 AATAGCTGGTATTTATACAGC----ACTATGTGTCA-----TATTC---- 47542 iii vv ---- i ----- i ---- C MIR#SINE/MIR 259 AATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAG 210 chr4ptel1M 47543 CGCCT----TGT-----CTTATTTTATCTTCAGGAGAATCTGAGGACTTA 47583 i ---- ----- i v i vi v i iv v vv C MIR#SINE/MIR 209 CGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGGTA 160 chr4ptel1M 47584 GCTGCTCTTATTATACATATTTTACATACAAACAAAATGAATCCAACAGA 47633 v i v v vi v ii iv v iv vv v C MIR#SINE/MIR 159 GGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGA 110 chr4ptel1M 47634 GGTCCTATAACTTGACTA 47651 ivvi v i C MIR#SINE/MIR 109 GGTTAAGTAACTTGCCCA 92 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.70 CpG sites = 20, Kimura (unadjusted) = 37.70 Transitions / transversions = 0.87 (20/23) Gap_init rate = 0.03 (5 / 145), avg. gap size = 4.40 (22 / 5) 270 32.68 11.41 3.54 chr4ptel1M 47517 47700 (952300) C MIRc#SINE/MIR (39) 229 32 m_b164s601i5 6166 chr4ptel1M 47517 TTTATACAGCACTATGTGTCATATTCCGCCTTGTCTTATTTTATCTTCAG 47566 i v i ----v i ---i v i i v i v C MIRc#SINE/MIR 229 TTTACAAAGCGCT----TTCACAT---ACATTATCTCATTTGATCCTCAC 187 chr4ptel1M 47567 GAGAATC---TGAGG---ACTTAGCTGCTCTTATTATACATATTTTACAT 47610 i v i --- ---i vvi v v v v vi v C MIRc#SINE/MIR 186 AACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAG 137 chr4ptel1M 47611 ACAAACAAAATGAATCCAACAGAGGTCCTATAACTTG------------- 47647 ii iv v iv iv v ivvi i ------------- C MIRc#SINE/MIR 136 ATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACAC 87 chr4ptel1M 47648 -ACTAGCAAGTTTCTGAGGGAGGATTAAAACACCAGTCTTCCTG-CTATA 47695 -i i vv v vvi i vi v vi - vi C MIRc#SINE/MIR 86 AGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCA 37 chr4ptel1M 47696 AGGCC 47700 v C MIRc#SINE/MIR 36 AGTCC 32 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.65 CpG sites = 27, Kimura (unadjusted) = 43.50 Transitions / transversions = 0.87 (27/31) Gap_init rate = 0.07 (12 / 183), avg. gap size = 2.33 (28 / 12) 231 30.82 2.01 2.01 chr4ptel1M 50414 50562 (949438) L1M3_orf2#LINE/L1 3013 3161 (127) m_b164s551i3 6167 chr4ptel1M 50414 AAAATAGAAAATTTTGATTATATCAAATTGAAAAGTTTTTGTACA---AA 50460 v v vv i i i i i i i --- L1M3_orf2#LIN 3013 AAAATAGACAAGTGGGACTACATCAAACTAAAAAGCTTCTGCACAGCAAA 3062 chr4ptel1M 50461 CAAAACTAATGCAGACAAGATTAGAAGGGAAACAATAAACTGGGAAAACA 50510 vi - - - iii v i v v v iii v i v L1M3_orf2#LIN 3063 GGAAAC-AAT-CA-ACAGAGTGAAAAGGCAACCTACGGAATGGGAGAAAA 3109 chr4ptel1M 50511 GTTTTACAGTCAAAGGTTCTGATCAAGGTCTTATTTCCAAAATATATAGA 50560 vv i iv v vivv v i vi v v ii L1M3_orf2#LIN 3110 TATTTGCAAACCATATATCTGATAAGGGGTTAATATCCAAAATATATAAG 3159 chr4ptel1M 50561 GA 50562 L1M3_orf2#LIN 3160 GA 3161 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.04 CpG sites = 23, Kimura (unadjusted) = 40.31 Transitions / transversions = 1.05 (23/22) Gap_init rate = 0.03 (4 / 148), avg. gap size = 1.50 (6 / 4) 255 16.67 0.00 0.00 chr4ptel1M 50607 50654 (949346) L1ME5_3end#LINE/L1 135 182 (759) m_b164s551i4 6168 chr4ptel1M 50607 GATATGTTCCAAATCATTATTAATCAGAGAAATGCAAATTAAGATGAC 50654 v i v v v i ii L1ME5_3end#LI 135 GAGATGCTCAAACTCATTAGTAATCAGAGAAATGCAAATTAAAACAAC 182 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 18.94 CpG sites = 4, Kimura (unadjusted) = 18.94 Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 916 29.36 4.04 4.23 chr4ptel1M 54250 54818 (945182) HERVK14#LTR/ERVK 2597 3164 (2932) m_b164s701i0 6169 chr4ptel1M 54250 ATTTTTAGGAGGGATGAGTGCTG---CTGCAGCTTCCACCACTCCTAAAA 54296 v iiv v i --- v i i iiv i ---- HERVK14#LTR/E 2597 ATTTTTAGGAGCGGCCATTGTTGAGCCTCCGGCTCCCATTCCTCTT---- 2642 chr4ptel1M 54297 TGAGTTGGACTA-CTGACACACAAGTATGGGTGGACCAATGGCCCCTGAC 54345 --- v i - v v vi v v v v HERVK14#LTR/E 2643 ---GTTTGGCTAACTGCCAAACCGGTTTGGGTGGAGCAATGGCCGCTGAA 2689 chr4ptel1M 54346 TACAGAAAAAAC-AGCCACTCTACATCAATTAGTACAAGGACAAT---AA 54391 - i -i vvi i v vv i i i i i --- HERVK14#LTR/E 2690 -ACAGGAAAAACTGGAGGCTTTAAAAGAACTGGTGCAGGAACAATTGCAA 2738 chr4ptel1M 54392 GAGTTAGGACATGTTGAGGAAACAAACAGTCTGTGGAATTCCCTTATATT 54441 i --- i v vvv vvv vvi iv i i i HERVK14#LTR/E 2739 AAG---GGACATATAGAGCCTACTTTCTCCCCTTGGAATTCTCCTGTATT 2785 chr4ptel1M 54442 TGTTATAACAAAAAAAAATCTGGTAAATGGAGAATGTTAACAGATTTGAG 54491 i --i i v v i HERVK14#LTR/E 2786 TGTCAT--TAAGAAAAAATCAGGGAAATGGAGAATGTTAACAGATTTAAG 2833 chr4ptel1M 54492 ACAAGTAAATTCAATCCTGGAAGACATGGTTTCTGTACTG---GTAGATT 54538 ivvv v v vi vv vv vv ---v i ---vi ivi HERVK14#LTR/E 2834 GGCTGTTAATGCTGTGATTCAACCCATGG---GTGCACTGCAACCAGGGC 2880 chr4ptel1M 54539 TGCCAT-CCAAAC-TTGATCACCAGGGAATGGCC-CTTATGGATAATAGA 54585 v - v -v v v iiv v - i i - i HERVK14#LTR/E 2881 TGCCCTCCCCAACAATGATCCCAAAATACTGGCCTCTCATAG-TGATAGA 2929 chr4ptel1M 54586 TATTAAGGACTGCTTTTATTCTATCCCCCTTTATC--CTGAGGACGGGGA 54633 v v i v v i --i v -- iv i iviv HERVK14#LTR/E 2930 TCTAAAGGATTGCTTTTTTACCAT--TCCTTTAGCTGCCCAAGATTATGA 2977 chr4ptel1M 54634 TAAATTTGCTTTTTCAG-TACCAACATAATTTTCAAAG-ACCTGTGAAGA 54681 v v v - v iv v vvi - v i i v HERVK14#LTR/E 2978 AAAATTTGCTTTTACTGTTCCCGCCATAAATAATAAAGAACCAGCGGACA 3027 chr4ptel1M 54682 -AGGTCATATGGAAGGTATTGCCACAAGGTATGAAAAATAGTTCTTCCAT 54730 - vii - i i i i vv ii vv i HERVK14#LTR/E 3028 GATACCAT-TGGAAAGTACTACCACAAGGCATGCTAAATAGCCCGACTAT 3076 chr4ptel1M 54731 ATGCCAATGATATGTTGATAAAGCTATT-AGAAAGATAAAGAAACACAAC 54779 v i vvv i iv - vv v i --- ii HERVK14#LTR/E 3077 TTGTCAAACTTATGTCGGGAAAGCTATTAAGCCAGTTAGAGA---ACAGT 3123 chr4ptel1M 54780 ---ACAGATGCAGTCATCCTCCATTACCTGGATGATATCTTG 54818 --- v i ivi - iv v ii HERVK14#LTR/E 3124 TTAAAAAATGTTAT-ATTATCCATTACATGGATGATATTCTG 3164 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.08 CpG sites = 73, Kimura (unadjusted) = 37.50 Transitions / transversions = 0.84 (73/87) Gap_init rate = 0.07 (38 / 568), avg. gap size = 1.24 (47 / 38) 350 32.15 7.67 3.69 chr4ptel1M 55600 55964 (944036) HERVK#LTR/ERVK 4822 5200 (2336) m_b164s701i1 6170 chr4ptel1M 55600 GGGACTAACCCCAGAGGTGACAGGCCAAATGATATATGGTAGGTAGATGT 55649 iii i vvvv v v vvv i ii i HERVK#LTR/ERV 4822 GGAGTTAATCCCAGAGGTCTGTGTCCTAATGCGTTATGGCAAATGGATGT 4871 chr4ptel1M 55650 TACACATATAG--------GGAAAA----CATGAGTTCATATTACAGTTG 55687 i i i v-------- i ---- ?v i i v HERVK#LTR/ERV 4872 CACGCATGTACCTTCATTTGGAAGATTGTCATNTGTCCATGTAACAGTTG 4921 chr4ptel1M 55688 ACATATGTTCCGGCTT--TGTGGTCGCATCCTCTC-TACAAAAAGAAG-- 55732 i iv i vvii -- i -- v vi -v ii ii -- HERVK#LTR/ERV 4922 ATACTTATTCACATTTCATATGG--GCAACCTGCCAGACAGGAGAAAGTA 4969 chr4ptel1M 55733 CTGCCTCATGTGATCAAGCACTCATTTCACTGTTTTGCCTCTATGCGTAG 55782 v - v vv i i i vivi ivii v viv HERVK#LTR/ERV 4970 CTTCC-CATGTTAAAAAACATTTATTATCTTGTTTTGCTGTCATGGGAGT 5018 chr4ptel1M 55783 CCCACACACCATCAAGACTGATAATATGCCTTTATACACCTCAAAAGTAT 55832 i v v vv i i i iv vvv vvivvv i? HERVK#LTR/ERV 5019 TCCAGAAAAAATTAAAACTGACAATGGGCCAGGATACTGTAGTAAAGCNT 5068 chr4ptel1M 55833 TAAAACAGTTCTTA---CAG----GAATTCTCCCTACATCATATTTTTGG 55875 vv v i --- ----i viv v v ------- HERVK#LTR/ERV 5069 TCCAAAAATTCTTAAATCAGTGGAAAATTACACATACAACA-------GG 5111 chr4ptel1M 55876 AATCCCTTACAACCCCACAGGACAGGCCACTGTAGAAAGGACTGATCAGA 55925 i i ii vv iv v i i vii HERVK#LTR/ERV 5112 AATTCCTTATAATTCCCAAGGACAGGCCATAGTTGAAAGAACTAATAGAA 5161 chr4ptel1M 55926 CACTGAAGAG----ATTCATCAAAAATCAGAAAGAGGGAGGAG 55964 v - ---- vi i --- i i i HERVK#LTR/ERV 5162 CACTCAA-AGCTCAATTGGTTAAA---CAAAAAGAAGGGGGAG 5200 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 42.63 CpG sites = 58, Kimura (unadjusted) = 43.13 Transitions / transversions = 1.05 (58/55) Gap_init rate = 0.06 (22 / 364), avg. gap size = 1.91 (42 / 22) 16 17.42 0.00 0.00 chr4ptel1M 58603 58636 (941364) (GGGGTG)n#Simple_repeat 1 34 (0) m_b164s252i4 6171 chr4ptel1M 58603 GGGGCGGGGGTGGGGATGGAGGTGGGGATGGAGG 58636 i i i i i (GGGGTG)n#Sim 1 GGGGTGGGGGTGGGGGTGGGGGTGGGGGTGGGGG 34 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 19 9.47 5.88 0.00 chr4ptel1M 58944 58977 (941023) (CT)n#Simple_repeat 1 36 (0) m_b164s252i5 6172 chr4ptel1M 58944 CTCTCTGCCTCTCTCCCT-TCT-TCTCTCTCTCTCT 58977 vi i - - (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 36 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2) 16 16.12 0.00 0.00 chr4ptel1M 62088 62115 (937885) (T)n#Simple_repeat 1 28 (0) m_b164s252i6 6173 chr4ptel1M 62088 TTTTTGTTTTGTTTTGTTTTGTTTTTTT 62115 v v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 28 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 19 3.81 0.00 0.00 chr4ptel1M 62089 62115 (937885) (TTTTG)n#Simple_repeat 1 27 (0) m_b164s252i7 6173 chr4ptel1M 62089 TTTTGTTTTGTTTTGTTTTGTTTTTTT 62115 v (TTTTG)n#Simp 1 TTTTGTTTTGTTTTGTTTTGTTTTGTT 27 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 14 12.69 0.00 0.00 chr4ptel1M 63334 63359 (936641) (TTGT)n#Simple_repeat 1 26 (0) m_b164s252i9 6174 chr4ptel1M 63334 TTCTTTGTTTTTTTGTTTCTTTGTTT 63359 v v v (TTGT)n#Simpl 1 TTGTTTGTTTGTTTGTTTGTTTGTTT 26 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 13 22.07 4.08 2.00 chr4ptel1M 63334 63382 (936618) (TTCT)n#Simple_repeat 1 50 (0) m_b164s252i8 6175 chr4ptel1M 63334 TTCTTTGTTTTTTTGTTTCTTTGTTTTATTTC-TACTTT-TTCCTCTGTT 63381 v i v -i v - v - i i v (TTCT)n#Simpl 1 TTCTTTCTTTCTTTCTTTCTTT-CTTTCTTTCTTTCTTTCTTTCTTTCTT 49 chr4ptel1M 63382 T 63382 (TTCT)n#Simpl 50 T 50 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.06 (3 / 48), avg. gap size = 1.00 (3 / 3) 295 28.77 11.67 1.52 chr4ptel1M 64008 64127 (935873) C L3#LINE/CR1 (183) 3916 3785 m_b164s601i6 6176 chr4ptel1M 64008 TCTAATTGGTTTGAAA--TCTATTCTTACATCAAGACTTAATTGACTTTT 64055 i - v -- - i i ii v vv ivi i ii C L3#LINE/CR1 3916 TCTGATTG-TTAGAAAGTTCT-TCCTTATATTGAGCCGAAATCTGCCTCC 3869 chr4ptel1M 64056 TTGCAATTTCCACTGATTGCTCCTACTTCTGGGTTCTGGGACTA------ 64099 i i i iv v v vvi ii i ------ C L3#LINE/CR1 3868 CTGTAACTTCCACCCATTGGTCCTAGTTCTGCCCTCTGGAGCCACACAGA 3819 chr4ptel1M 64100 --AAGTCTAA----TCTTTCATATGATAACTTTT 64127 -- ---- i i i i ii C L3#LINE/CR1 3818 ATAAGTCTAATCCCTCTTCCACATGACAGCCCTT 3785 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.46 CpG sites = 24, Kimura (unadjusted) = 38.46 Transitions / transversions = 2.40 (24/10) Gap_init rate = 0.05 (6 / 119), avg. gap size = 2.67 (16 / 6) 1445 29.02 3.07 4.35 chr4ptel1M 64544 65195 (934805) C L1ME5_3end#LINE/L1 (291) 650 7 m_b164s551i5 6177 chr4ptel1M 64544 ATCTC---CTGGTTCT-GCTGATTTCACTCAGCATCA-GTTCATGTAAG- 64587 --- v -i vv ii - -- v - C L1ME5_3end#LI 650 ATCTCATTCTGTTTCTTACTTTTTTCACTCAGCACTATGTT--TTTAAGA 603 chr4ptel1M 64588 TCTTTCCAAGCCTCTCTGTATTCATCCTGCTGGTCATTTCTTACAAAACA 64637 iv v iiv v i v iv iiv iii v vivvvv C L1ME5_3end#LI 602 TCCATCCATGTTGCTATGTGTACATCTAGTCCGTTGCTTCTAACTGCTGC 553 chr4ptel1M 64638 ATAATATTCCATAACATTCATATACCACAGTTTACCCATCCATTCTCCAA 64687 i i iiii v vi v i i v C L1ME5_3end#LI 552 ATAGTACTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCA 503 chr4ptel1M 64688 TTTATGGGCATCCATTCATTTTTCAGTTTCTAGCCACTACAAAAAGTGCT 64737 v v i i vvivvii i ii i iv i v ii C L1ME5_3end#LI 502 GTGATGGACACCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCT 453 chr4ptel1M 64738 GCCACAAACATTTTGGCACTTTGGAAAGGCAGGTCCCTTTC----CCTTC 64783 v ii ii v i ----------- v i v---- vi C L1ME5_3end#LI 452 GCAATGAACATCCTCGTAC-----------ATGTCCCCTTATGGACCTGT 414 chr4ptel1M 64784 TTTAGTATCAATTTGGGATATAAGCCCAGTAGTAACACTGCTGGATCAAA 64833 v v v ivv vi v iiiv i i v C L1ME5_3end#LI 413 GTGAGAATTTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATA 364 chr4ptel1M 64834 AGGTATGCACAGTTTGATAACTT--TTTGGGCA--TAATTCTGAATTGCT 64879 i --- --- - -- ivi -- v v iii C L1ME5_3end#LI 363 GGGTATGC---GT---ATA-CTTAATTTGACTAAGTACTGCCAGATTGCT 321 chr4ptel1M 64880 CTCCAGAATGGTTGGATTCATTCACAACTCCACCAACAATGCATCAGTGT 64929 i v iivi ii vii i i v v C L1ME5_3end#LI 320 CTCCAGAATGGCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGT 271 chr4ptel1M 64930 CCCAGTTTTCCCACATCCCCTCCAACATTCATCATTATTT-TTTTTCTTG 64978 i vi ? i i v i iiv ii-vi -- C L1ME5_3end#LI 270 TCCTATNTCCCCACATCCTCGCCAACACTTGGCATTATCCAGCTTTCT-- 223 chr4ptel1M 64979 TCATCTTAGCCAATCTGACAGGTGTGTAGTGATATCTCAGAGTTGTCTTA 65028 -v i v i i i iv vv i C L1ME5_3end#LI 222 -AATTTTTGCCAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTA 174 chr4ptel1M 65029 ATTTGCATTTCTCTGATCAATAGTGATTTGGAACACTCTTTCATATGAGT 65078 i v i v v i iiii vv C L1ME5_3end#LI 173 ATTTGCATTTCTCTGATTACTAATGAGTTTGAGCATCTCTTCATATGCTT 124 chr4ptel1M 65079 GAAAATAG--TTTCAA-TTTCATCATCTGAAAATTGTCTGTTCATATCCT 65125 v--- -- ii- v v v i C L1ME5_3end#LI 123 GT---TAGCCTTTCGGGTTTCCTCTTCTGTAAATTGCCTGTTCATATCCT 77 chr4ptel1M 65126 TTGACCATTTGTCAATTGGAG--AATGGCTTGGTTTCTTATAAATTAGAG 65173 v v v i --?vi v -- i vi v vi C L1ME5_3end#LI 76 TTGCCCATTTTTCTATTGGGGTTNCCGTCTT--TTTCTTGTTGATTTGCA 29 chr4ptel1M 65174 TCAATTCTCTATATATTTTAGA 65195 vv i ii i i C L1ME5_3end#LI 28 GGAGTTCCTTGTATATTCTAGA 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.59 CpG sites = 102, Kimura (unadjusted) = 37.67 Transitions / transversions = 1.29 (102/79) Gap_init rate = 0.06 (39 / 651), avg. gap size = 1.23 (48 / 39) 398 31.22 2.54 2.54 chr4ptel1M 65052 65327 (934673) C L1M1_orf2#LINE/L1 (0) 3294 3019 m_b164s551i6 6177 chr4ptel1M 65052 TGATTTGGAACACTCTTTCATATGAGTGAAAATAGTTTCAATTTCATCAT 65101 v v i ii vv vvviivi vv v v v C L1M1_orf2#LIN 3294 TGATGTTGAGCACCTTTTCATATGCCTGTTTGCCATTTGTATGTCTTCTT 3245 chr4ptel1M 65102 CTGAAAATTGTCTGTTCATATCCTTTGACCATTTGTCAATTGGAGAAT-- 65149 i i v i v i v v i i vv -- C L1M1_orf2#LIN 3244 TTGAGAAATGTCTATTCAGATCTTTTGCCCATTTTTTAATCGGATTATTA 3195 chr4ptel1M 65150 GGCTTGGTTTCTTATAAATTAGAGTCAATTCTCTATATATTTTAGAAATG 65199 ii -- i i v v vv v ii ii i i vv v C L1M1_orf2#LIN 3194 GATTT--TTTCCTATAGAGTTGTTTGAGCTCCTTATATATTCTGGTTATT 3147 chr4ptel1M 65200 AGACCTTTATCAGAACCTTTAACTGTAAAAATGTTTTCCCAGTTTGTTGC 65249 iv i i vvvv vivi i v v i v i v v C L1M1_orf2#LIN 3146 AATCCCTTGTCAGATGGGTAGTTTGCAAATATTTTCTCCCATTCTGTGGG 3097 chr4ptel1M 65250 TT--CCCTTCCAACCTTGTTTGCATTAGTTTTGTTTG---TACAAAGGCT 65294 -- i -- i - - - iv --- i i i C L1M1_orf2#LIN 3096 TTGTCTCTTC--ACTTTGTT-G-ATT-GTTTCCTTTGCTGTGCAGAAGCT 3052 chr4ptel1M 65295 TTTTAATTTGATATAATCAAAATTATCTATTTT 65327 i i i vv v i i C L1M1_orf2#LIN 3051 TTTTAACTTGATGTGATCCCATTTGTCCATTTT 3019 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.25 CpG sites = 41, Kimura (unadjusted) = 40.88 Transitions / transversions = 0.95 (41/43) Gap_init rate = 0.04 (10 / 275), avg. gap size = 1.40 (14 / 10) 609 32.94 4.15 3.65 chr4ptel1M 65091 65717 (934283) C L1P3_orf2#LINE/L1 (39) 3255 2626 m_b164s551i7 6177 chr4ptel1M 65091 AATTTCATCATCTGAAAATTGTCTGTTCATATCCTTTGACCATTTGTCAA 65140 v v v i i v i v i v ii C L1P3_orf2#LIN 3255 AATGTCTTCTTTTGAGAAGTGTCTGTTCATATCCTTCGCCCACTTTTTGA 3206 chr4ptel1M 65141 TTGGAGAATGGCTTG---GTTTCTTATAAATTAGAGTCAATTCTCTATAT 65187 - i -- v i ---v i v vv v i ii i v C L1P3_orf2#LIN 3205 -TGGGG--TTGTTTGTTTTTTTCTTGTAAATTTGTTTAAGTTCCTTGTAG 3159 chr4ptel1M 65188 ATTTTAGAAATGAGACCTTTATCAGAACCTTTAACTGTAAAAATGTTTTC 65237 i i v v v i vvvv vi i i v i C L1P3_orf2#LIN 3158 ATTCTGGATATTAGCCCTTTGTCAGATGGATAGATTGCAAAAATTTTCTC 3109 chr4ptel1M 65238 CCAGTTTGTTGCTTCCCTTCCAACCTTGTTTGCA-TTAGTTTTGTTTGTA 65286 v i v v v viiv ii v vii - vv -i i C L1P3_orf2#LIN 3108 CCATTCTGTAGGTTGCCTGTTCACTCTGATGATAGTTTCTTTTG-CTGTG 3060 chr4ptel1M 65287 CAAAGGCTTTTTAATTTGATATAATCAAAATTATCTATTTTG----TGAT 65332 i i i i i vvi vv v i v ---- vi C L1P3_orf2#LIN 3059 CAGAAGCTCTTTAGTTTAATTAGATCCCATTTGTCAATTTTGGCTTTTGT 3010 chr4ptel1M 65333 CAATAATGATCTCTAGTTCTTCTTTGGTCACAAATTCCTTCCTCCTCCAC 65382 iivi v -- i v v v -- i ii v i v i v v vi C L1P3_orf2#LIN 3009 TGCCATTG--CTTTTGGTGT--TTTAGTCATGAAGTCTTTGCCCATGCCT 2964 chr4ptel1M 65383 AAGT-CTGAGAGGTAAACTATCCTATG--TTCCTCTAATTTATTTATGAT 65429 v - iv --- vv v -- i ivv v i C L1P3_orf2#LIN 2963 ATGTCCTGAATGGTA---TTGCCTAGGTTTTCTTCTAGGGTTTTTATGGT 2917 chr4ptel1M 65430 CTCATTCTTTATGCCAAAATCATAGACCCATTTTGATCTTATCTTGGAGT 65479 i i vvii i iiv i v vi i i vi v i v vi C L1P3_orf2#LIN 2916 TTTAGGTCTTACGTTTAAGTCTTTAATCCATCTTGAGTTAATTTTTGTAT 2867 chr4ptel1M 65480 ACAGTGTTAAATGTGGGTCCATGCCTAA--TTTCTGCCATA---CTAATT 65524 vi v iiviv - ii v -- - --- i-- C L1P3_orf2#LIN 2866 AAGGTGTAAGGAAGGGGTCCA-GTTTCAGTTTTCTG-CATATGGCTAG-- 2821 chr4ptel1M 65525 TCCAGCTTTCCCACCAGTTTTTGTCAAATAATGAATTCTTATCCCAAAAG 65574 - i v viv i i iv i vi vviv C L1P3_orf2#LIN 2820 -CCAGTTTTCCCAACACCATTTATTAAATAGGGAATCCTTTCCCCATTGC 2772 chr4ptel1M 65575 TTGGGATCTTTG---GGTTTGTCAAACACTAGATTACAATAAATATA-GA 65620 --- i --- v ii viivi i i i- i C L1P3_orf2#LIN 2771 TTG---TTTTTGTCAGGTTTGTCAAAGATCAGATGGTTGTAGATGTGTGG 2725 chr4ptel1M 65621 CTTTTTTGTCCTGTGAAC-CTAACCTATTCCACTGATCAACTAATCTATT 65669 v v -- i v iv - ivi i i i v ivv i C L1P3_orf2#LIN 2724 CGTTAT--TTCTGAGGCCTCTGTTCTGTTCCATTGGTCTATATATCTGTT 2677 chr4ptel1M 65670 TAG---CCAAAATCCAATG--GTTTTGGTGACTGCTGCTTTATAATATAG 65714 v --- iv i -- -- v iv i i i C L1P3_orf2#LIN 2676 TTGGTACCAGTACC--ATGCTGTTTTGGTTACTGTAGCCTTGTAGTATAG 2629 chr4ptel1M 65715 TTT 65717 C L1P3_orf2#LIN 2628 TTT 2626 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.72 CpG sites = 105, Kimura (unadjusted) = 44.31 Transitions / transversions = 1.12 (105/94) Gap_init rate = 0.06 (35 / 626), avg. gap size = 1.40 (49 / 35) 18 20.33 1.61 5.00 chr4ptel1M 66328 66389 (933611) (ATTTTT)n#Simple_repeat 1 60 (0) m_b164s252i10 6178 chr4ptel1M 66328 ATTATTATTTTTATTTTTATATACATATTTTTAAATTTCTTTTTTATGCT 66377 v - -iv - v iv vi (ATTTTT)n#Sim 1 ATTTTTATTTTTATTTTTAT-T-TTTATTTTT-ATTTTTATTTTTATTTT 47 chr4ptel1M 66378 T-TTCCTATTTTT 66389 - ii (ATTTTT)n#Sim 48 TATTTTTATTTTT 60 Matrix = Unknown Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.07 (4 / 61), avg. gap size = 1.00 (4 / 4) 13 9.02 2.33 10.00 chr4ptel1M 67285 67327 (932673) (ATATTT)n#Simple_repeat 1 40 (0) m_b164s252i11 6179 chr4ptel1M 67285 ATATCTGATCATTTATATTCTATATTTAT-CTGATATTTGATAT 67327 - v - - -i v - (ATATTT)n#Sim 1 ATAT-TTAT-ATTTATATT-TATATTTATATTTATATTT-ATAT 40 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.12 (5 / 42), avg. gap size = 1.00 (5 / 5) 215 20.63 6.35 0.00 chr4ptel1M 68474 68536 (931464) MIRc#SINE/MIR 165 231 (37) m_b164s601i7 6180 chr4ptel1M 68474 CTGCCTGTAACATAGGTTTGTTGTGAGTATCCAATG-GGT--TGTGTGTG 68520 iivv i v v v - i -- i MIRc#SINE/MIR 165 CTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTG 214 chr4ptel1M 68521 -AAGCTTTTTGTAAATT 68536 - vi i MIRc#SINE/MIR 215 AAAGCGCTTTGTAAACT 231 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 24.38 CpG sites = 7, Kimura (unadjusted) = 24.38 Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.05 (3 / 62), avg. gap size = 1.33 (4 / 3) 18 12.55 2.04 6.38 chr4ptel1M 69310 69358 (930642) (TTGAA)n#Simple_repeat 1 47 (0) m_b164s252i12 6181 chr4ptel1M 69310 TTGAGTTGGAATTTGAATAGAATTGAATT-AATTCAATAGGATTGGAATT 69358 i - - v - v v i - (TTGAA)n#Simp 1 TTGAATT-GAA-TTGAATTGAATTGAATTGAATTGAATTGAATT-GAATT 47 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.08 (4 / 48), avg. gap size = 1.00 (4 / 4) 312 32.39 6.00 5.30 chr4ptel1M 70784 71083 (928917) L1ME4c_3end#LINE/L1 253 554 (276) m_b164s551i8 6182 chr4ptel1M 70784 GGATGTGGAAAAACTGGTACATTGAT---TTGTTGATGGAATTACTAACT 70830 ? i vi ?i v --- i i v ? iiv i L1ME4c_3end#L 253 GGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATT 302 chr4ptel1M 70831 GATTCAGCCATTT--------ACTCTGGAATTATGTCCAAAGAGTTATTA 70872 i v i v -------- v i v v i viv ii v L1ME4c_3end#L 303 GGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAA 352 chr4ptel1M 70873 ACTTATTTGTTTCTACTTATACTCATTGACCCAGAAATATGATTATTAAG 70922 vv i i---------- i v v viv i vi ii L1ME4c_3end#L 353 AAATGTTC----------ATACCCTTTGACCCAGTAATTCCACTTCTGGG 392 chr4ptel1M 70923 --TCTATTTTCAA-AGATAATTAGGGGGAAAAGAAG--ACAGCCTATGTG 70967 -- i ii v i- i v----- -- v iv i L1ME4c_3end#L 393 AATTTATCCTAAGGAAATAATTC-----AAAAGAAGGAAAAAGCTATATG 437 chr4ptel1M 70968 TTATAAAATGTTT-TAGCAGCTTTCTTTATGGTTATAAAGACCTGAAAAT 71016 ivvv i i- v v v ii viii i vi i i L1ME4c_3end#L 438 CACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAAC 487 chr4ptel1M 71017 AGCAGAAATGCCCATCAATTGGGGAGTAGCTGGACAAGTTGTGGAATAT- 71065 i vv i v v i i i iiii i i v i - L1ME4c_3end#L 488 AACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATC 537 chr4ptel1M 71066 GATTGAGATGGAATATTA 71083 ? i v- L1ME4c_3end#L 538 NACTC-GATGGAATATTA 554 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 42.83 CpG sites = 55, Kimura (unadjusted) = 44.89 Transitions / transversions = 1.49 (55/37) Gap_init rate = 0.08 (23 / 299), avg. gap size = 1.48 (34 / 23) 312 30.36 0.89 0.00 chr4ptel1M 70974 71085 (928915) L1ME1_3end#LINE/L1 441 553 (373) m_b164s551i9 6182 chr4ptel1M 70974 AATGTTT-TAGCAGCTTTCTTTATGGTTATAAAGACCTGAAAATAGCAGA 71022 i- v ii ii viiv i v i i i vv L1ME1_3end#LI 441 AATGTTCATAGCAGCTTTATTCGTAATAGCCAAAAACTGGAAACAACCCA 490 chr4ptel1M 71023 AATGCCCATCAATTGGGGAGTAGCTGGACAAGTTGTGGAATATGATTGAG 71072 i i? v i i v ii i v vvv ivi L1ME1_3end#LI 491 AATGTCCATCAACNGGTGAATGGATAAACAAATTGTGGTATATCCATACA 540 chr4ptel1M 71073 ATGGAATATTACT 71085 i L1ME1_3end#LI 541 ATGGAATACTACT 553 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.13 CpG sites = 21, Kimura (unadjusted) = 40.88 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.01 (1 / 111), avg. gap size = 1.00 (1 / 1) 300 29.60 1.27 5.30 chr4ptel1M 71123 71279 (928721) L1ME3B_3end#LINE/L1 402 552 (437) m_b164s551i10 6183 chr4ptel1M 71123 AGGAAAACATGGAAAGATGCACAAGGAAACGGACCTGTATGTGCTAGAAT 71172 i vi i v v vi v ? -------- i v L1ME3B_3end#L 402 AGAAACGCGTGCACATGTGCACCAGGANAC--------ATGTACAAGAAT 443 chr4ptel1M 71173 GTTTGTGGCAGCCCTGTTTGTGGTGGCTAGAAACAGGAAAATGAATGGAT 71222 ii i vi i ii i i?i v vvivviii L1ME3B_3end#L 444 GTTCATAGCAGCATTGTTCGTAATAGCCNAAAACTGGAAACAACCCAAAT 493 chr4ptel1M 71223 GCCCATCAA-AG-AGAATGGTTGGGTAAATTATGGTAGATGAATGTTATG 71270 i - - v iii i v vv iiv L1ME3B_3end#L 494 GTCCATCAACAGTAGAATGGATAAATAAATTGTGGTATATTCATACAATG 543 chr4ptel1M 71271 GAATATTAT 71279 i L1ME3B_3end#L 544 GAATACTAT 552 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.13 CpG sites = 27, Kimura (unadjusted) = 39.56 Transitions / transversions = 1.59 (27/17) Gap_init rate = 0.06 (10 / 156), avg. gap size = 1.00 (10 / 10) 386 31.34 0.90 3.70 chr4ptel1M 71140 71361 (928639) L1ME3G_3end#LINE/L1 415 630 (294) m_b164s551i11 6183 chr4ptel1M 71140 TGCACAAGGAAACGGACCTGTATGTGCTAGAATGTTTGTGGCAGCCCTGT 71189 ?i -------- i v i ii v vi L1ME3G_3end#L 415 TGCACAAGGANGC--------ATGTACAAGGATGTTCATTGCAGCATTGT 456 chr4ptel1M 71190 TTGTGGTGGCTAGAAACAGGAAAATGAATGGATGCCCATCAA--AGAGAA 71237 ii i v i iv vvivv ii i --i i L1ME3G_3end#L 457 TTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCAATAGGGGAA 506 chr4ptel1M 71238 TGGTTGGGTAAATTATGGTAGATGAATGTTATGGAATATTATTGTTCTGT 71287 iii v vv ii i vvvv ? L1ME3G_3end#L 507 TGGTTAAATAAATTATGGTATATCCATACTATGGAATACTATGCAGCNGT 556 chr4ptel1M 71288 AAAAAATGACCAGCAGGATGAATACAGAGAGGCTTGGAGAGATTTACATG 71337 v vi iv vvi vv iiv vv i v i i v v L1ME3G_3end#L 557 TAAAAAGAATGAGGTAGATCTATATGTACTGACATGGAAAGATCTCCAAG 606 chr4ptel1M 71338 AACTGATGCTGAGTGAAATGAGCA 71361 vv iv i vi L1ME3G_3end#L 607 ACATATTGTTGAGTGAAAAAAGCA 630 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.68 CpG sites = 34, Kimura (unadjusted) = 41.68 Transitions / transversions = 1.03 (34/33) Gap_init rate = 0.04 (9 / 221), avg. gap size = 1.11 (10 / 9) 274 29.08 4.17 1.74 chr4ptel1M 72477 72644 (927356) L1MC_orf2#LINE/L1 2387 2558 (736) m_b164s551i12 6184 chr4ptel1M 72477 TAAATACAAGTGGAGAAATATTAATTGCTCATGCATAGACTCAGTCAATA 72526 -- i i vvv i v ivvv v L1MC_orf2#LIN 2387 TAAATA--AATGGAGAGATATTCCATGTTCATGGATAGGAAGACTCAATA 2434 chr4ptel1M 72527 TAATAAAAATGGCAAGTCTACCAAAATTAATCCAT----TCAGTTCTATC 72572 vi v i v iv v v v i i ---- i v v L1MC_orf2#LIN 2435 TTGTCAAGATGTCAGTTCTTCCCAACTTGATCTATAGATTCAATGCAATC 2484 chr4ptel1M 72573 CCAATCAAAGTACCAA-AAATTATTTTATAAAGCTTCTATAA--TAATAA 72619 i v i- i i ii -iv v i -- i vv L1MC_orf2#LIN 2485 CCAATCAAAATCCCAGCAAGTTATTTTGTGGA-TATCGACAAACTGATTC 2533 chr4ptel1M 72620 TAAAATTAATTTGGAAGAACAAAAG 72644 i v v iiii L1MC_orf2#LIN 2534 TAAAGTTTATATGGAGAGGCAAAAG 2558 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.26 CpG sites = 24, Kimura (unadjusted) = 37.26 Transitions / transversions = 1.00 (24/24) Gap_init rate = 0.04 (6 / 167), avg. gap size = 1.67 (10 / 6) 314 26.42 3.77 0.00 chr4ptel1M 72482 72587 (927413) L1P3_orf2#LINE/L1 2390 2499 (795) m_b164s551i13 6184 chr4ptel1M 72482 ACAAGTGGAGAAATATTAATTGCTCATGCATAGACTCAGTCAATATAATA 72531 i i i vvv v ivvv i vi i L1P3_orf2#LIN 2390 ACAAATGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTG 2439 chr4ptel1M 72532 AAAATGGCAAGTCTACCAAAATTAATCC----ATTCAGTTCTATCCCAAT 72577 v vv i v v ii---- i v v L1P3_orf2#LIN 2440 AAAATGGCCATACTGCCCAAAGTAATTTATAGATTCAATGCTATCCCCAT 2489 chr4ptel1M 72578 CAAAGTACCA 72587 iv L1P3_orf2#LIN 2490 CAAGCTACCA 2499 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 31.33 CpG sites = 12, Kimura (unadjusted) = 32.67 Transitions / transversions = 0.75 (12/16) Gap_init rate = 0.01 (1 / 105), avg. gap size = 4.00 (4 / 1) 234 32.77 0.00 0.00 chr4ptel1M 72680 72798 (927202) L1PREC2_orf2#LINE/L1 3132 3250 (44) m_b164s551i14 6185 chr4ptel1M 72680 ATCTGATAAAGATTATATTTCTCAAATATACAGAGAACTTAATCAAATTT 72729 i i ivv v iviv v i ii v L1PREC2_orf2# 3132 ATCTGACAAAGGTCTAATATCCAGCATCTATAAGGAACTTAAACAAATTT 3181 chr4ptel1M 72730 ATAAAAATATGAGTCATTTTCCAATTCATAATTGTTCAAAGGATATGAAC 72779 i i v vi vvv ivvi v v v v vv i L1PREC2_orf2# 3182 ACAAGAAAAAAACAAACAACCCCATTAAAAAGTGGGCAAAGGACATGAAC 3231 chr4ptel1M 72780 AGGCAATTTTCAGAGAAAG 72798 i v i ii L1PREC2_orf2# 3232 AGACACTTTTCAAAAGAAG 3250 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.48 CpG sites = 18, Kimura (unadjusted) = 43.48 Transitions / transversions = 0.86 (18/21) Gap_init rate = 0.00 (0 / 118), avg. gap size = 0.0 (0 / 0) 942 28.36 10.11 2.20 chr4ptel1M 72699 73163 (926837) L1ME5_3end#LINE/L1 7 507 (434) m_b164s551i15 6185 chr4ptel1M 72699 TCTCAAATATACAGAGAACTTAATCAAATTTATAAAAATATGA--GTCAT 72746 vi ii ivvv iv i i v v -- ?v i L1ME5_3end#LI 7 TCTAGAATATACAAGGAACTCCTGCAAATCAACAAGAAAAAGACGGNAAC 56 chr4ptel1M 72747 TTTCCAATTCATAATTGTTCAAAGGATATGAACAGGCAATTTTCAGA--- 72793 i-- vv v v vv v --- L1ME5_3end#LI 57 C--CCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGA 104 chr4ptel1M 72794 --------GAAAGG-----AATCTTATGAAAAAATGCTCTCAAAC--ACT 72828 -------- ----- v v i i -- -- i L1ME5_3end#LI 105 GGAAACCCGAAAGGCTAACAAGCATATGAAGAGATGCTC--AAACTCATT 152 chr4ptel1M 72829 ATTGATTAGAGAGAATGCTAATTAAAACAACACTGAGGTACCACTTCAAA 72878 v i i - v v i i i v L1ME5_3end#LI 153 AGTAATCAGAGA-AATGCAAATTAAAACAACAATGAGATATCACTTTACA 201 chr4ptel1M 72879 TCCATCAG------------------GTTTGTTAATGATAAACATTGGAG 72910 i i i ------------------ i v v vi iii v L1ME5_3end#LI 202 CCTATTAGACTGGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTGGCG 251 chr4ptel1M 72911 AAGATGTGAGCAAACTGAGATACTAATGTACTACTGATGGAATTGTAAAC 72960 i i v ? iv ii iv v i i i i v i L1ME5_3end#LI 252 AGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGAC 301 chr4ptel1M 72961 TAATGTAACCATTTTGGAGA--AATTTGGAGCTA--TCGCCAAAGGAA-T 73005 ii i i i -- i viv -- v i vv - L1ME5_3end#LI 302 TGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTAAGT 351 chr4ptel1M 73006 ATAAAACTCTCATACCCTTTGATCCATCAATACCACTGTTAGGTCTATAT 73055 ----- v v i v v i vi i v L1ME5_3end#LI 352 ATA-----CGCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATAT 396 chr4ptel1M 73056 CCCAAAGACGTTCAAAAGAAGG---A-GAGTGGATTTATACAAAGATATT 73101 vi vv viv --- -i v iv i i i i L1ME5_3end#LI 397 CCCAAAGAAATTCTCACACAGGTCCATAAGGGGACATGTACGAGGATGTT 446 chr4ptel1M 73102 TATAGTTGCTCTTTATGTGGTGGCTAAGAATTGAAAATCAAAAGGATGCT 73151 i v iv vi v v vii i i iiiv vvv i ii L1ME5_3end#LI 447 CATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGGGTGTC 496 chr4ptel1M 73152 CATCTATTGGAA 73163 - i i L1ME5_3end#LI 497 CATC-ACTGGGA 507 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.92 CpG sites = 71, Kimura (unadjusted) = 36.63 Transitions / transversions = 1.22 (71/58) Gap_init rate = 0.05 (22 / 464), avg. gap size = 2.64 (58 / 22) 210 29.23 0.00 0.00 chr4ptel1M 73870 73934 (926066) L3#LINE/CR1 2750 2814 (1285) m_b164s601i8 6186 chr4ptel1M 73870 CTGGTGAGGTTGACGTGGCTTCCTGGAAAAATCCCAGAAAGCATTTTGAA 73919 i i v v v i i v i i v v v v L3#LINE/CR1 2750 CCGGTAAGCTTGACGTCGATCCCCGGCAAAATTCTAGAACGGATTATTAA 2799 chr4ptel1M 73920 AGGGCTGATTAGTGA 73934 vi v i v L3#LINE/CR1 2800 ACAGATGGTTTGTGA 2814 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.64 CpG sites = 8, Kimura (unadjusted) = 37.17 Transitions / transversions = 0.73 (8/11) Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0) 400 31.31 10.56 3.29 chr4ptel1M 74106 74247 (925753) C MIRc#SINE/MIR (116) 152 1 m_b164s601i9 6187 chr4ptel1M 74106 TACTTTCATTTTTCAGATGAAGAAGCTAACTCCTTGGAGGAGTTAAGTAA 74155 iiii v i i i vv - ii ii i C MIRc#SINE/MIR 152 TATCCCCATTTTACAGATGAGGAAACTGAGGC-TCAGAGAGGTTAAGTGA 104 chr4ptel1M 74156 AGAACTCACTCAAAGCTTCACAGGTAGTTGGTAATGGAGTTGGGATCTGA 74205 ---- ii i i iiv v vi iiii ii iii C MIRc#SINE/MIR 103 ----CTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGA 58 chr4ptel1M 74206 ACCC----CTCCATGATCGCAAATA-----------CCACTGTACCACAC 74240 ---- i v iiv i v----------- i C MIRc#SINE/MIR 57 ACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACAC 8 chr4ptel1M 74241 TGCCTTG 74247 i C MIRc#SINE/MIR 7 TGCCTCG 1 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.49 CpG sites = 34, Kimura (unadjusted) = 44.80 Transitions / transversions = 3.78 (34/9) Gap_init rate = 0.05 (7 / 141), avg. gap size = 2.86 (20 / 7) 11 26.73 4.55 2.99 chr4ptel1M 75575 75640 (924360) (AAATGGA)n#Simple_repeat 1 67 (0) m_b165s252i0 6188 chr4ptel1M 75575 AAATGTGAAATGGAAAA-GGTAAA-GAACTACTAGGAAAACAGAATTTGT 75622 vi - v - i -v v - ii vv v (AAATGGA)n#Si 1 AAATGGAAAATGGAAAATGGAAAATGGA-AAAT-GGAAAATGGAAAATGG 48 chr4ptel1M 75623 GAATTGGAAAA-AGAAAAT 75640 i v -i (AAATGGA)n#Si 49 AAAATGGAAAATGGAAAAT 67 Matrix = Unknown Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.08 (5 / 65), avg. gap size = 1.00 (5 / 5) 13 34.49 0.00 0.00 chr4ptel1M 75786 75840 (924160) (TTTTT)n#Simple_repeat 1 55 (0) m_b165s252i1 6189 chr4ptel1M 75786 TTTTTTTTCTTTTTTAAGAACTTTATAATTTATTTTATTTTATTTATTTT 75835 i vvvvvi v vv v v v v (TTTTT)n#Simp 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr4ptel1M 75836 ATTTT 75840 v (TTTTT)n#Simp 51 TTTTT 55 Matrix = Unknown Transitions / transversions = 0.15 (2/13) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 21 6.16 2.94 0.00 chr4ptel1M 75808 75841 (924159) (TTTTA)n#Simple_repeat 1 35 (0) m_b165s252i2 6189 chr4ptel1M 75808 TTATAATTTATTTTATTTTA-TTTATTTTATTTTA 75841 v v - (TTTTA)n#Simp 1 TTTTATTTTATTTTATTTTATTTTATTTTATTTTA 35 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 12 16.31 2.78 2.78 chr4ptel1M 76094 76129 (923871) (AACAAAC)n#Simple_repeat 1 36 (0) m_b165s252i3 6190 chr4ptel1M 76094 AACAAACAACCAACCAACAAA-AACATTTAATAAACA 76129 - v - vvi i (AACAAAC)n#Si 1 AACAAACAA-CAAACAACAAACAACAAACAACAAACA 36 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 31 0.00 0.00 0.00 chr4ptel1M 76272 76300 (923700) (T)n#Simple_repeat 1 29 (0) c_b165s251i0 6191 chr4ptel1M 76272 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 76300 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 22 18.86 0.00 0.00 chr4ptel1M 76483 76524 (923476) (A)n#Simple_repeat 1 42 (0) m_b165s252i4 6192 chr4ptel1M 76483 AAAACCAAAAAAAAATAAAAAATGAAAAAAATAGAAAAAAAA 76524 vv v vi v i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 42 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 285 25.88 10.36 3.90 chr4ptel1M 77570 77762 (922238) L1MEi_5end#LINE/L1 2003 2207 (5) m_b165s551i0 6193 chr4ptel1M 77570 AAGGAGA---AAAGAAAAGAGAAAAGTGTAATGTGGGGATAA-------T 77609 --- ? - ?i i ivivi v ------- L1MEi_5end#LI 2003 AAGGAGAGAAAAAGNAAAGA-AAAAGNATGATAAACAGAAAACACAAAAT 2051 chr4ptel1M 77610 AAGATAGCAGGAAATA----CAGA---ATTAGTAGTTTTAATCATAAATG 77652 i i - ---- i --- i i i--- iv L1MEi_5end#LI 2052 AAGATGGTAG-AAATAAGTCCAAATATATCAGTAATC---ACAATAAATG 2097 chr4ptel1M 77653 TGATTGGGGTGAACTCTCTCATAAAGCAAAAGCAGA---TAGCAGACTGA 77699 i v iv i v ii v --- ii --- v i i L1MEi_5end#LI 2098 TAAATGGATTAAACTCACCTATTAA---AAGACAGAGATTATCAGATTGG 2144 chr4ptel1M 77700 ATTAAAAGCTAGAATCCTACAATATGCTGTTTGCAGGAAACACATTTAAA 77749 ivv i vi v i i i ii L1MEi_5end#LI 2145 ATTAAAAAAAAAAATCCAGCTATATGCTGTTTACAAGAGACACACCTAAA 2194 chr4ptel1M 77750 GCAGGGTGATACA 77762 i iiii i L1MEi_5end#LI 2195 ACAAAACGACACA 2207 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.15 CpG sites = 35, Kimura (unadjusted) = 34.05 Transitions / transversions = 2.69 (35/13) Gap_init rate = 0.07 (13 / 192), avg. gap size = 2.15 (28 / 13) 408 22.21 4.73 2.65 chr4ptel1M 77605 77752 (922248) L1MEh_5end#LINE/L1 2078 2228 (7) m_b165s551i1 6193 chr4ptel1M 77605 ATAATAAGATAGCAGGAAATA---CAGAAT-TAGTAGTTTTAATCATAAA 77650 i - --- v? - ?i vv v iv L1MEh_5end#LI 2078 ATAATAAGATGGCAG-AAATAAGTCCNAATATANCAGTAATTACAATAAA 2126 chr4ptel1M 77651 TGTGATTGGGGTGAACTCTCTCATAAAGCAAAAGCAGA---TAGCAGACT 77697 i v v i v iv v --- ii --- ?v i L1MEh_5end#LI 2127 TGTAAATGGGTTAAACTCACCAATTAA---AAGACAGAGATTNTCAGATT 2173 chr4ptel1M 77698 GAATTAAAAGCTAGAATCCTACAATATGCTGTTTGCAGGAAACACATTTA 77747 i ? ivi i v i i i i i L1MEh_5end#LI 2174 GGATTNAAAAACAAAATCCAACAATATGCTGTCTACAAGAGACACACTTA 2223 chr4ptel1M 77748 AAGCA 77752 i L1MEh_5end#LI 2224 AAACA 2228 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 27.79 CpG sites = 19, Kimura (unadjusted) = 27.79 Transitions / transversions = 1.46 (19/13) Gap_init rate = 0.05 (7 / 147), avg. gap size = 1.57 (11 / 7) 3968 30.41 4.78 3.56 chr4ptel1M 77647 80865 (919135) L1M5_orf2#LINE/L1 38 3294 (0) m_b165s551i2 6193 chr4ptel1M 77647 TAAATGTGATTGGGGTGAACTCTCTCATAAAGCAAAAGCAGA---TAGCA 77693 i v ?v i v iv v --- i --- iv L1M5_orf2#LIN 38 TAAATGTAAATGGNCTAAACACTCCAATTAA---AAGGCAGAGATTGTCA 84 chr4ptel1M 77694 GACTGAATTAAAAGCTAGAATCCTACAATATGCTGTTTGCAGGAAACACA 77743 i v ivi ii i v v i i i i i L1M5_orf2#LIN 85 GACTGGATAAAAAAACAAGACCCAACTATATGCTGTCTACAAGAGACGCA 134 chr4ptel1M 77744 TTTAAAGCAGGGTGATACATACAGAGTAAAGGTAAAAGGCTGAAGCAGAA 77793 i v ii viiv i v ? iv i i v i iv ii L1M5_orf2#LIN 135 CTTTAAATATAAAGACACAGANAGGTTGAAAGTAAAAGGATGGAAAAAGA 184 chr4ptel1M 77794 TCTATTATGCGTCAGGTAAAATAAAAAAAGCAGGGGTAGCCATCCTTATC 77843 v ii ivvviv ?vv i v ? i i vi v v L1M5_orf2#LIN 185 TATACCATGCAAACACTAANCAAAAGAAAGCTGGNGTGGCTATATTAATA 234 chr4ptel1M 77844 TCAGATCAAGCA------AAAGCAAAAATTCATCTAATTAAAAGAGATAA 77887 iv i ------ i i --- --- vv L1M5_orf2#LIN 235 TCAGACAAAGTAGACTTCAAGGCAAGAA---AT---ATTACCAGAGATAA 278 chr4ptel1M 77888 GGAAGGAAACTAAATCTTGCTAAA-GGGTAGCATAGATAATAAAGCAATA 77936 i i v i vv vv v - vi- vv v vi vv L1M5_orf2#LIN 279 AGAGGGACATTTCATAATGATAAAAGGGTCA-ATTCATCAAGAAGACATA 327 chr4ptel1M 77937 TCAATATTAAACACATATGCACCAAGTGGCATAGCATCTAAATTCCTAAA 77986 v vi iiii v i ii v v v v v i L1M5_orf2#LIN 328 ACAATCCTAAATGTGTATGCACCTAATAACAGAGCTTCAAAATACATGAA 377 chr4ptel1M 77987 GGAGAAGTTAAGAGAGGTGTAAGAAGAAATAGACAGCAAAACTATAAT-- 78034 v i ii i v iv iv i --- v i i -- L1M5_orf2#LIN 378 GCAAAAACTGACAGAACTAAAAGGAGAAATAGACA---AATCCACAATTA 424 chr4ptel1M 78035 -AGTAGGAGATCTCAACCTTGCACTTGCAG--ATTGAGATAAATCAAATC 78081 - ? i i vi?v v iv -- -- i v i v L1M5_orf2#LIN 425 TAGTNGGAGATTTTAACACNCCTCTCTCAGTAATTGA--TAGAACAAGTA 472 chr4ptel1M 78082 C-CAAAATAAATAATAAAGAAGTCAAAGAGGTAAATAAAA-TACCAGAAA 78129 v- - vi i i vi vi vv i i v - i ivv L1M5_orf2#LIN 473 GACAAAA-AATCAGTAAGGATATAGAAGATTTGAACAACACTATCAACCA 521 chr4ptel1M 78130 ATTAGATATGATAGATCTTTGGAGAAAACTGAATGGAGTCAGAAAGGAGT 78179 i v iv i v iv iv v ?v ivv iiv v?ivi i L1M5_orf2#LIN 522 ACTTGACCTAATTGACATTTATAGAACACTNCACCCAACAACNGCAGAAT 571 chr4ptel1M 78180 ACACTTTCTTTTTGACAGTTCATGGAACCTATACAAAAATTGACCATATA 78229 v ii vv iv v v v i v ? L1M5_orf2#LIN 572 ACACATTCTTTTCAAGTGCACATGGAACATTTACCAAGATAGACCATATN 621 chr4ptel1M 78230 TTAGGATATAAGGAC----CTCAAAATCAAATGCAGAAAGGAA-GAAATA 78274 i i vi i- ---- ---i vi?- v- v L1M5_orf2#LIN 622 CTGGGCCATAAA-ACAAGTCTCAA---TAAATTTN-AAAGGATTGAAATC 666 chr4ptel1M 78275 GTA---AATGCATTCTTT--TCAGATTATGATTCAAT-AAAAACTAACTT 78318 i --- i iii i --i v v ivi v - i ii i-- L1M5_orf2#LIN 667 ATACAGAGTATGTTCTCTGACCACAATGGAATTAAATTAGAAATCAAT-- 714 chr4ptel1M 78319 CAATAAAAAGACAGG-GGAAAATAGACCAAAAAGTAATTGGAAACTAAAT 78367 - i i ?v-i vv- --- v i i L1M5_orf2#LIN 715 -AACAAAAAGATANCTAGAAAATCC-CCAAA---TATTTGGAAATTAAAC 759 chr4ptel1M 78368 AATCTCA-TCCTAAAGAATGAATGGGTGAAACAGCAAATCA--------A 78408 - v - i v ivv v v iv -------- L1M5_orf2#LIN 760 AA-CACACTTCTAAATAACCCATGGGTCAAAGAAGAAATCACAANGGAAA 808 chr4ptel1M 78409 TT------CATCC--AAGAGAATGACAATAATGAGACAACATACCAAAAT 78450 ------i ii-- vv ? i vi v i L1M5_orf2#LIN 809 TTAGAAAATATTTTGAACTGAATGANAATGAAAATACAACATATCAAAAT 858 chr4ptel1M 78451 TTGTGGGATGCAGCCAAAGTGGTAATAAGGGGAAATTTTATATCTCCAGA 78500 i ii iv v i i v v ?ii i L1M5_orf2#LIN 859 TTGTGGGATGCAGCTAAAGCAGTGCTTAGAGGGAAATTTATAGCNTTAAA 908 chr4ptel1M 78501 GGCTTACTTGCATAAAATAAAGAAAG-----AGATCAATGAATTGGCCTT 78545 v ? iv -i v -i ----- i vi iiv L1M5_orf2#LIN 909 TGCNTATAT-TAGAAAA-GAAGAAAGGCTTAAAATCAATGATCTAAGCTT 956 chr4ptel1M 78546 GCAACTAAAAAAGCTAGAAAAGAAA---CAAATTAAAATCCCCTAATCAA 78592 v v v i ii --- --- v v? L1M5_orf2#LIN 957 CCACCTTAAGAAGCTAGAAAAAGAAGAGCAAATTAAA---CCCAAAGNAA 1003 chr4ptel1M 78593 ATACTAAACTTGAAATTTTAAAAATAAAAGGAGAGATTAATAATATTGAA 78642 i vv iivvv vv i i v i i i v v L1M5_orf2#LIN 1004 GTAGAAGGAAGGAAATAATAAAGATAAGAGCAGAAATCAATGAAATAGAA 1053 chr4ptel1M 78643 AGTAAAAAAAACTATTGAATTAATAAATAAAACTAACAAAACTAA---CT 78689 ii ? ? ----------i i v ii i i i --- L1M5_orf2#LIN 1054 AACAAANANA----------CAATAGAGAAAATCAACGAAGCCAAAAGCT 1093 chr4ptel1M 78690 GAA-----AAAAAAAACAACAAAATAGATAAACCTTTGGTAAATTTGATT 78734 iv-----i i v i v i i i? ivi i L1M5_orf2#LIN 1094 GGTTCTTTGAAAAGATCAATAAAATTGATAAACCTCTAGCNAGACTGATC 1143 chr4ptel1M 78735 AGAAAATGGAAAGAGAAAAATCAAATGGTTAGTCTTAAAAAGGAAAAAAG 78784 ii vii i i vv viii i v i ii v i L1M5_orf2#LIN 1144 AAGAAAAAAAGAGAGAAGACACAAATTACCAATATCAGGAATGAAAAAGG 1193 chr4ptel1M 78785 AGAACTTTCCACTAACAAA----GTGGAAATTAGAACAGTAATTAAGAGT 78830 vv --- - i ----iii v i vii - v L1M5_orf2#LIN 1194 AGACAT---CACTA-CAGATCCTACAGACATTAAAAGGATAAT-AAGAGA 1238 chr4ptel1M 78831 -TACTTTGCCCAACTTTATGCCAATAAATTTGATTACTTAAGTGAAATGA 78879 - i v vv ?v ii i L1M5_orf2#LIN 1239 ATATTATGAACAACTTTATGCCAATAAATTTGANAACTTAGATGAAATGG 1288 chr4ptel1M 78880 ATGAATACATACAAAAATATAGGTTGTTCAGATTAACAGAGGAGGAAGTA 78929 ii v v vv i i i? iiiv i i i ?v i i i L1M5_orf2#LIN 1289 ACAAATTCCTTGAAAAACACAANTTACCAAAACTGACNCAAGAAGAAATA 1338 chr4ptel1M 78930 AATTGCTTAACTAGTCCCATCTTAGAAAAAGAAATGAAAGAAGCTATTAA 78979 i vviii i v i i v ivivv vi vvv iv L1M5_orf2#LIN 1339 GAAAATCTGAATAGCCCTATATCTATTAAAGAAATTGAATTTGTAATTAA 1388 chr4ptel1M 78980 TCAACTCCCTAAAAAAAAAAAAATCCCCAGGACCAGATGGATTTATATGT 79029 vv v i i v i ---- i v v i ivv L1M5_orf2#LIN 1389 AAACCTTCCCACAAAGAAAA----CTCCAGGCCCAGATGGCTTCACTGGT 1434 chr4ptel1M 79030 GAATTCTACCAAACATTTAAAGAATGATTAGCCCCAATGCTATATAAATT 79079 i vi v iiv vi i i i L1M5_orf2#LIN 1435 GAATTCTACCAAACATTTAAGGAAGAAATAATACCAATCTTACACAAACT 1484 chr4ptel1M 79080 ATTTGAAAAAATAGAAAAAGAAGGAATCCTACCAAATTCCTTTTATGGCA 79129 v iv i i iv v v i v ivi L1M5_orf2#LIN 1485 CTTCCAGAAAATAGAAAAAGAGGGAACACTTCCCAACTCATTTTATGAGG 1534 chr4ptel1M 79130 CACACATGGTACTGATACCTAAACCAGGTAGGACAAAAACA------GAA 79173 vvi ?iiv v ? ----- i ------ L1M5_orf2#LIN 1535 CCAGCATNACCCTGATACCAAAACCNG-----ACAAAGACATTACAAGAA 1579 chr4ptel1M 79174 AAGGAAAATTATAGGCCAATCTCTGTAATGAATATTGATGCAAAAATCTT 79223 - i i v iv v i v i L1M5_orf2#LIN 1580 AAG-AAAATTACAGACCAATATCCCTCATGAACATAGATGCAAAAATCCT 1628 chr4ptel1M 79224 AAATAAAATATTAGCAAAAAGATTATAGAAAATCATCCCCAGAATAATAC 79273 ? i vv v vi v vvi vvvv i L1M5_orf2#LIN 1629 NAACAAAATATTAGCAAATCGAATCCAGCAATATATAAAAAGGATAATAC 1678 chr4ptel1M 79274 ACTATGACCAAGTAGGATTTATACCATGAATGTAGGGCTGGTTCAATATT 79323 ii i i v v i i i i i L1M5_orf2#LIN 1679 ATCATGACCAAGTGGGGTTTATCCCAGGAATGCAAGGTTGGTTTAACATT 1728 chr4ptel1M 79324 AGGAAAACTATTAGCATAATTGACTATATCAATA--ATCAAATTAACAAA 79371 v i v v i iii v i i i -- v i--i v L1M5_orf2#LIN 1729 CGAAAATCAATCAATGTAATTCACCATATTAACAGAATAAAG--GAGAAA 1776 chr4ptel1M 79372 AACCATATGATCATCTCAATAGATGAAGAAAAAGCATTTGATAAAATCCA 79421 i v i i L1M5_orf2#LIN 1777 AATCATATGATCATCTCAATAGATGCAGAAAAAGCATTTGACAAAATTCA 1826 chr4ptel1M 79422 ACACCCATTCCTATTAAAAACACT-AGAGAGTATAGGAATAAATGGACTT 79470 v iv v - vi ii- i v ivvi L1M5_orf2#LIN 1827 ACACCCATTCATGATAAAAACTCTCAGCAAAC-TAGGAATAGAAGGGAAC 1875 chr4ptel1M 79471 TTCCTTAAAATAGTA----GCATCTATTCAAAACCATCAGTAAGCATTAT 79516 i vv ii ---- ivv vv i? i i L1M5_orf2#LIN 1876 TTCCTCAACCTGATAAAGGGCATCTACGAAAAACCTACAGCNAACATCAT 1925 chr4ptel1M 79517 ATATAATGAGAATAAACTGGAACCATTCCCAATAATATCAGGGGTGAAGC 79566 iv ivi v ? i ?v v vv v i iiii ii L1M5_orf2#LIN 1926 ACTTAATGGTGAAANACTGAANGCTTTCCCCCTAAGATCGGGAACAAGAC 1975 chr4ptel1M 79567 AACATTGCCCACTCTCACCATTTCTATTCAATATTGTATTAGAAATGATA 79616 viv i i ? i i i i ii vv L1M5_orf2#LIN 1976 AAGGATGTCCGCTNTCACCACTTCTATTCAACATTGTACTGGAGGTCCTA 2025 chr4ptel1M 79617 GCTTTAGCAATAAGAGATGAAAAAAAGATTAAAGGAATAGAG--TAGA-- 79662 ivvv iv v i i v v i -- i -- L1M5_orf2#LIN 2026 GCCAGTGCAATAAGGCAAGAAAAAGAAATAAAAGGCATAAAGATTGGAAA 2075 chr4ptel1M 79663 --------TAA--TTATTATCTCTTTGCAAATGATATGATGCTATACCTA 79702 -------- --i i i? - v i i i vv ? v L1M5_orf2#LIN 2076 GGAAGAAATAAAACTGTCNT-TATTCGCAGATGACATGATTGTNTACGTA 2124 chr4ptel1M 79703 GAGAACCCCAGGGATTCTATTTAAAAGCTATTAGAAATAAT--------- 79743 i i ? ii v ivv ? i i v --------- L1M5_orf2#LIN 2125 GAAAATCCNAAAGAATCTACAAANAAACTACTAGAACTAATAAGTGAATT 2174 chr4ptel1M 79744 CCACAATTTTGCAGAATACAAAATAAATCCACAAAAATCATCAGCATTCT 79793 ivi vv i ? i ii v vi viv i ii L1M5_orf2#LIN 2175 TAGCAAGGTCGCNGGATACAAGGTCAATATACAAAAATCAATTGTATTTC 2224 chr4ptel1M 79794 TATATATCACTAACAAA--ATCCAAAAGCAAGAGATACAAAGAGAAATTC 79841 ii vi -- ivi -- v i vi? i iv v L1M5_orf2#LIN 2225 TATATACTAGCAACAAACAATTGGAAA--ATGAAATTTNAAAAACAATAC 2272 chr4ptel1M 79842 CATTTAAAATAACTGTTGATAATATAAAGTATTTGGGAATCTATCTGTCA 79891 v i vvivi v i ? i i i vv iv L1M5_orf2#LIN 2273 CATTTACAATAGCATCAAAAAACATNAAATACTTAGGAATAAATCTAACA 2322 chr4ptel1M 79892 AGGGAAAGTCAGGAACTATATGAGCAAAACTACAAAACACTTTCCACACA 79941 ii? vivv i v ? iivvv i viiv v v L1M5_orf2#LIN 2323 AAANATGTGCAAGACCTNTACACTGAAAACTACAAAACATTGCTGAGAGA 2372 chr4ptel1M 79942 AATAAAGTCAGATCTAAACAATTGGGAAAATATTAAGTGCTCCTAGATAG 79991 v ivv i i v ii i vvvi i v i v L1M5_orf2#LIN 2373 AATTAAAGAAGACCTAAATAAATGGAGAGATATACCATGTTCATGGATTG 2422 chr4ptel1M 79992 GTTGAGTGAATATAATAAAGATGACAATACT-----------TCTATTTA 80030 vv v v vi ? v v ----------- vv L1M5_orf2#LIN 2423 GAAGACTCAATATTGTNAAGATGTCAATTCTCCCCAAATTGATCTATAGA 2472 chr4ptel1M 80031 TTTAGTATTATACCAATCAAACTCCCAAGAAACTATCTTATTGACCTAAA 80080 i i iiv v v iv iii v i i v vv vi L1M5_orf2#LIN 2473 TTCAATGCAATCCCAATCAAAATCCCAGCAGGTTTTTTTGTAGAAATTGA 2522 chr4ptel1M 80081 AAAAATAACAACAAAATTCATCTGGAAGCCCCAAAAGTCAAGAAT-TTCA 80129 v iv i ivvi i v iiv v iiii ? -vi L1M5_orf2#LIN 2523 CAAGCTGATTCTAAAATTTATATGGAAATGCAAAGGACCNAGAATAGCCA 2572 chr4ptel1M 80130 AGGGAACTAAT----AAAAAAAAAATCAAA--TGAAGGTGGCCTA-ACTG 80172 --- - ---- i i v -- i -- i i - - L1M5_orf2#LIN 2573 A---AAC-AATCTTGAAAAAGAAGAACAAAGTTGGAG--GACTTACACT- 2615 chr4ptel1M 80173 AGCCTGATCT-AAGATTATATTATAAAGCAGCACTCATCAAAATAATTTG 80221 -i ? ? - i - vi v v i i i v L1M5_orf2#LIN 2616 -ACCNGATNTCAAGACT-TATTATAAAGCTACAGTAATCAAGACAGTGTG 2663 chr4ptel1M 80222 GTACTGGC-TAAGAAATATACTAGTTGATCAGTGGAATAGATTAGTTTCA 80270 i - -i v v i v i i v ---- L1M5_orf2#LIN 2664 GTATTGGCGTAAG-GATAGACAAATAGATCAATGGAACAGAATAG----A 2708 chr4ptel1M 80271 CAGGACA-AAATAG--TCA-ATAACTATAGCAATCTAGTGTTTAACAAAC 80316 v vv - --i - i vv i ?v ?i ii v i - L1M5_orf2#LIN 2709 GAGTCCAGAAATAGACCCACACATATATGGNCANTTGATTTTTGACAAA- 2757 chr4ptel1M 80317 TAACAATCTAGTGTAAACAAACAAAG-AACTCAGCTTTTGGGATAAGAAT 80365 ---------i i------- ? - i ---- iv i L1M5_orf2#LIN 2758 ---------GGTGC-------CAANGCAATTCAG----TGGGGAAAGGAT 2787 chr4ptel1M 80366 TCACTATTTGACAATAACTACTGGGAAAATTGGAAACTAGTATGACAGAA 80415 vvv v ii vviv i i v v iivi iv i L1M5_orf2#LIN 2788 AGTCTTTTCAACAAATGGTGCTGGAACAATTGGATATCCATATGGAAAAA 2837 chr4ptel1M 80416 ACTAGGCATTGACCC--------CACCATATACCAAGAAAAGGTCAAAAT 80457 v iii?v i -------- i v i vv iv ? i L1M5_orf2#LIN 2838 AATGAANCTCGACCCCTACCTCACACCATACACAAAAATTAATTCNAGAT 2887 chr4ptel1M 80458 AGGTTCAT-GATCTAGACATAAAGAACGAGATCATAAATAAATTAGAAG- 80505 - v - i i ii ii?ii i ii vvvvi - L1M5_orf2#LIN 2888 -GGATCATAGACCTAAATGTAAAAGNTAAAACTATAAAACTTCTAGAAGA 2936 chr4ptel1M 80506 -AACATAGAATAGTTTACCTCTCAGACCTGTGGA-AGAAAAAGGAATTTG 80553 - i v i-- i iivv vv ?- iv -- v L1M5_orf2#LIN 2937 AAACATAGGAGAA--TATCTTCGTGACCTTGGGNTAGGCAAAG--ATTTC 2982 chr4ptel1M 80554 TGACCAAAGAAGAACTAGAGATCATTATTGATCACAAAATAGAAAAT--- 80600 ---i v i vvi i i v i? --- i i v i --- L1M5_orf2#LIN 2983 T---TAAACAGGACACAAAAAGCACNA---ACCATAAAAGAAAAAATTGA 3026 chr4ptel1M 80601 ----TTCAATTATATC-AAGTTAAAAAAGTTTTTGTACAAACAAAACTAA 80645 ---- vi i ?i - i --i i iv ?vvv ivi v L1M5_orf2#LIN 3027 TAAATTGGACTNCATCAAAATTAAAAA--CTTCTGCTCNTCAAAAGACAC 3074 chr4ptel1M 80646 TGCAGACAAGATTAGAAGAGAAGCAATAAATTGGGAAAACATTTTTATAG 80695 i ivi v i v i iv v i i ? i v v ii i L1M5_orf2#LIN 3075 CGTTAAGAAAATGAAAAGGCAAGCCACAGANTGGGAGAAAATATTTGCAA 3124 chr4ptel1M 80696 T-CAAAGGTTCTGATAAAGGCCTCATTTCCAAAATATATAGAGAATTGAC 80744 ?- v vi- i v i v i i i vvi L1M5_orf2#LIN 3125 NACATATA-TCTGACAAAGGACTCGTATCCAGAATATATAAAGAACTCCT 3173 chr4ptel1M 80745 TTAAATTTATAAGAAATCAAGTCATTC--TCCAGTTGCTAAATGGTCAAA 80792 vi ? iv ? -- v vv --i i v?vv v L1M5_orf2#LIN 3174 ACAANTCAATAANAAA--AAGACAAACAACCCAATANAAAAATGGGCAAA 3221 chr4ptel1M 80793 GGATATGACTAGACTATTTTCAGATGAAGAAATTGAAACTATTTTTAGTC 80842 i iv vi vv iv i v v ?v iviiivv iv L1M5_orf2#LIN 3222 AGACTTGAACAGACACTTCACAAAAGAAGATATNCAAATGGCCAATAAGC 3271 chr4ptel1M 80843 ATATGAAAAGGTGCTCATCATTA 80865 i i v ? i L1M5_orf2#LIN 3272 ACATGAAAAGATGCTCAACNTCA 3294 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.31 CpG sites = 520, Kimura (unadjusted) = 40.93 Transitions / transversions = 1.23 (520/424) Gap_init rate = 0.05 (170 / 3218), avg. gap size = 1.59 (270 / 170) 670 27.92 6.74 0.71 chr4ptel1M 80716 80982 (919018) L1ME3A_3end#LINE/L1 1 283 (637) m_b165s551i3 6193 chr4ptel1M 80716 CTCATTTCCAAAATATATAGAGAATTGACTTAAATTTATAAGAAATCAAG 80765 v i i i vvivi iv -- L1ME3A_3end#L 1 CTCATATCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAA--AAG 48 chr4ptel1M 80766 TCATTC--TCCAGTTGCTAAATGGTCAAAGGATATGACTAGACTATTTTC 80813 v vv --i i v vv v i iv vi i vv iv L1ME3A_3end#L 49 ACAGACAACCCAATAGAAAAATGGGCAAAAGACTTGAACAGGCACTTCAC 98 chr4ptel1M 80814 AGATGAAGAAATTGAAACTATTTTTAGTCATATGAAAAGGTGCTCA---T 80860 i v i v iv iviiivv iv --- L1ME3A_3end#L 99 AAAAGAGGATATCCAAATGGCCAATAAACATATGAAAAGGTGCTCAACTT 148 chr4ptel1M 80861 CATTACTGATCAGAGAAATGCAAAT------------GAGATACCACTAC 80898 v v i ------------ ? L1ME3A_3end#L 149 CATTAGTCATCAGGGAAATGCAAATTAAAACCACAATGNGATACCACTAC 198 chr4ptel1M 80899 A-ACCTCTCAGAATGGCTAATATGACAGAAAAAGTTAATGACGAATGTTA 80947 - ivi v v i i v vi iv i i i L1ME3A_3end#L 199 ACACCCACCAGAATGGCTAAAATGAAAAAGACAGACAATACCAAGTGTTG 248 chr4ptel1M 80948 AAGGGGATGTGGGAAAACTGGGACACTGATACATT 80982 iv i iiv i i v v i L1ME3A_3end#L 249 GCGAGGATGTGGAGCAACCGGAACTCTCATACACT 283 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.98 CpG sites = 38, Kimura (unadjusted) = 35.56 Transitions / transversions = 1.06 (38/36) Gap_init rate = 0.02 (6 / 266), avg. gap size = 3.33 (20 / 6) 718 31.78 1.08 2.19 chr4ptel1M 81461 81830 (918170) L1ME3G_3end#LINE/L1 265 630 (294) m_b165s551i4 6193 chr4ptel1M 81461 GCACACTGATACATTGTTGATGGAATTATAAACTGATCCAACCATTCTAG 81510 i v v i i i i v i i i v i ? i i L1ME3G_3end#L 265 GTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTACAGCCNTTTTGG 314 chr4ptel1M 81511 AGAGCTATTTAGAATTATGCTCAAAAAAATTATCAAACTGTGTGTACCCT 81560 i v i v v - - vv --i v i ii L1ME3G_3end#L 315 AGGGCAATTTGGCAGTAT-CT-ATTAAAATT--TAAAATGCGCATACCCT 360 chr4ptel1M 81561 TTGATCCAGCAGTATTACTACTTGGATTATATCCCAAAGAGAT-CTTAAA 81609 i i vii v ? ?v v i ? i - iiv L1ME3G_3end#L 361 TTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAGAAATACTCGCA 410 chr4ptel1M 81610 GGAG-GGAAAAGGATCCAAATGGGCAAAAATATTTGTGGCAGCCCTTTTT 81658 viv - v v ?v -- vi ii i ii v vi v L1ME3G_3end#L 411 CATGTGCACAAGGANGC--ATGTACAAGGATGTTCATTGCAGCATTGTTT 458 chr4ptel1M 81659 GTAGTGGTTAGAAACTGGAAATTGAATGGATACCCATCAATTAGAAAATG 81708 i i iv i i ivivv ii ii vi ii L1ME3G_3end#L 459 GTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCAATAGGGGAATG 508 chr4ptel1M 81709 GCTGAATAAATTGTGGTATATGAATGTTATGGAATTTTATTGTTCTGTAA 81758 i i i vv ii vi vvvv ? v L1ME3G_3end#L 509 GTTAAATAAATTATGGTATATCCATACTATGGAATACTATGCAGCNGTTA 558 chr4ptel1M 81759 GAAATGACGAGCAGGATGATTTCAGGGA--GGCCTGGAGAGACTTACATG 81806 i vi i vvi --i vi v v -- i v i ii v v L1ME3G_3end#L 559 AAAAGAATGAGGTAGAT--CTATATGTACTGACATGGAAAGATCTCCAAG 606 chr4ptel1M 81807 AACTGATGCTGAGTGAAATAAGCA 81830 vv iv i v L1ME3G_3end#L 607 ACATATTGTTGAGTGAAAAAAGCA 630 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.90 CpG sites = 65, Kimura (unadjusted) = 43.47 Transitions / transversions = 1.30 (65/50) Gap_init rate = 0.03 (11 / 369), avg. gap size = 1.09 (12 / 11) 531 20.15 0.00 8.70 chr4ptel1M 83668 83792 (916208) MIRc#SINE/MIR 1 115 (153) m_b165s601i1 6194 chr4ptel1M 83668 CGGGGCAGCTGGGTGGTGCAGTGAGTAGAGCATCAGCCCTGAAGTCAGGA 83717 i i--- iiv iii v i i MIRc#SINE/MIR 1 CGAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGA 47 chr4ptel1M 83718 GGACCTGAGTTCAAGTCTAGTCTTAGACCCTTAACACTTCCTAGCTGTGT 83767 i i i iv v -------i iv v MIRc#SINE/MIR 48 AGACCTGGGTTCGAGTCCCGGCT-------CTGCCACTTACTAGCTGTGT 90 chr4ptel1M 83768 GACCATGGGCAAGTCACTTAACCCC 83792 v i MIRc#SINE/MIR 91 GACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 22.78 CpG sites = 16, Kimura (unadjusted) = 23.96 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.08 (10 / 124), avg. gap size = 1.00 (10 / 10) 35 0.00 5.00 0.00 chr4ptel1M 83810 83849 (916151) (AAAG)n#Simple_repeat 1 42 (0) c_b165s251i1 6195 chr4ptel1M 83810 AAAGAAAGAAA-AAA-AAAGAAAGAAAGAAAGAAAGAAAGAA 83849 - - (AAAG)n#Simpl 1 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAA 42 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 36 2.94 0.00 0.00 chr4ptel1M 85226 85260 (914740) (TG)n#Simple_repeat 1 35 (0) c_b165s251i2 6196 chr4ptel1M 85226 TGTGTGTGTATGTGTGTGTGTGTGTGTGTGTGTGT 85260 i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 35 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 13 32.72 0.00 1.72 chr4ptel1M 85937 85995 (914005) (ATGT)n#Simple_repeat 1 58 (0) m_b165s252i5 6197 chr4ptel1M 85937 ATGTATGGGTGTGAGGTGGGTGTGAGTGAGTGTATGTATCTACATACCTA 85986 vi - v iv i vi vi v ii iv (ATGT)n#Simpl 1 ATGTATGTATGT-ATGTATGTATGTATGTATGTATGTATGTATGTATGTA 49 chr4ptel1M 85987 TGTATGTAT 85995 (ATGT)n#Simpl 50 TGTATGTAT 58 Matrix = Unknown Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1) 31 17.57 5.26 3.09 chr4ptel1M 86240 86334 (913666) (TGTTT)n#Simple_repeat 1 97 (0) m_b165s252i6 6198 chr4ptel1M 86240 TGTTCTCTTTTG-TTT-TTTTGTTTTGCTTTATTTTGTTTTGTATTTCTT 86287 i v - - i i - v (TGTTT)n#Simp 1 TGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGT-TTTGTT 49 chr4ptel1M 86288 TTCAATTTTCTTTTTTTTTAATCACTTTT-TTTT-TTTT-TTTTTTTTTG 86334 --i v v iv ivv - - - v (TGTTT)n#Simp 50 TT--GTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTG 97 Matrix = Unknown Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.09 (8 / 94), avg. gap size = 1.00 (8 / 8) 238 17.39 2.17 0.00 chr4ptel1M 86335 86380 (913620) C MIR#SINE/MIR (139) 123 77 m_b165s601i2 6199 chr4ptel1M 86335 CTGAGGCA-ATTGGGGTTAAGTGACCTGTCTAGGGTCACACAGCTAG 86380 - vv i i i i i i C MIR#SINE/MIR 123 CTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAG 77 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 20.42 CpG sites = 6, Kimura (unadjusted) = 20.42 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1) 631 29.93 4.98 1.93 chr4ptel1M 86681 86881 (913119) MIRb#SINE/MIR 39 245 (23) m_b165s601i3 6200 chr4ptel1M 86681 TTGGAGTTGGGAAGATCTGCATTTAAATATGACTTCTGAACACTTACAAG 86730 ii iv i vi ii vivivi v- v MIRb#SINE/MIR 39 TTGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTCTGC-CACTTACTAG 87 chr4ptel1M 86731 TTGTGTGACCCTTAGAAATTCATCGAACCTTCATATGCCTCACTTTC-TC 86779 i i vi v v i iiv iiv iv v - MIRb#SINE/MIR 88 CTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTC 137 chr4ptel1M 86780 A-CTTTAAAATTGGAATTGCAATAGCACTTACCTCACAAGGTTATTATAA 86828 - v v i --- ii i i i i i i MIRb#SINE/MIR 138 ATCTGTAAAATGGGGAT---AATAATACCTACCTCGCAGGGTTGTTGTGA 184 chr4ptel1M 86829 AGACTAAATGAGAGAATATTTGCTAATCACTTAGCACA--------CATA 86870 i i v iiv iv v i -------- i MIRb#SINE/MIR 185 GGATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACA 234 chr4ptel1M 86871 TAGTAGACATT 86881 ii ii MIRb#SINE/MIR 235 TAGTAAGCGCT 245 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.64 CpG sites = 39, Kimura (unadjusted) = 40.08 Transitions / transversions = 1.95 (39/20) Gap_init rate = 0.04 (7 / 200), avg. gap size = 2.00 (14 / 7) 828 32.50 5.50 3.60 chr4ptel1M 87524 88123 (911877) C L1ME5_3end#LINE/L1 (275) 666 56 m_b165s551i5 6201 chr4ptel1M 87524 TGTTATTGCTGTGTATA-ATGTTCTCCTGGTTCT-ACTCACTTCACTCAG 87571 v - - - v iv i v - ivi C L1ME5_3end#LI 666 TGGTATTG-TGT-TATANATCTCATTCTGTTTCTTACTTTTTTCACTCAG 619 chr4ptel1M 87572 CATCA-GTTTATGTAGGTCTCTCCAGATCTCTCTGAAATTATCCTGCTGA 87620 ii - v i- i iv vi iv v vivvi iv iivi C L1ME5_3end#LI 618 CACTATGTTTTTA-AGATCCATCCATGTTGCTATGTGTACATCTAGTCCG 570 chr4ptel1M 87621 TTGTTTCTTA-TAAAACAATAATATCCCATAACATTCATATACTGTAACT 87669 i v - ivvi - i ii iiii v vi iii vi C L1ME5_3end#LI 569 TTGCTTCTAACTGCTGCA-TAGTACTCCATGGTGTGCATCCACCACATTT 521 chr4ptel1M 87670 TATTCAGCTACTCT-----------ACACTCAGTTT----CCAGTTTCTT 87704 iii v i ----------- i v ---- ii i ii C L1ME5_3end#LI 520 TACCTATCCACTCTCCCAGTGATGGACACCCAGGTTGCCTCCAACTCCCC 471 chr4ptel1M 87705 GCCACTACAAAAAGGGTTGCTACAAATATTTTTCCACATGTAGGTCCTTT 87754 i v iv i v ii i ii ivi v--i v C L1ME5_3end#LI 470 GCCACCACAAACAACGCTGCAATGAACATCCTCGTACATGTC--CCCTTA 423 chr4ptel1M 87755 T---CCTTTTTTATGATCCCTGTGTGATACATGCCCAGGAGAGACACTGC 87801 --- v v v vi ii v v i i v iv i C L1ME5_3end#LI 422 TGGACCTGTGTGAGAATTTCTTTGGGATATATACCCAGGAGCGGAATTGC 373 chr4ptel1M 87802 TGGATCAAAGGATATGTAGAGTTTGGTAGCCCTTTGGCCAGAGTTTT--- 87848 i v i iiv vvi -- i--- i i - vi --- C L1ME5_3end#LI 372 TGGGTCATAGGGTATGCGTATACT--TAA---TTTGACTA-AGTACTGCC 329 chr4ptel1M 87849 ATATTACTCTGTAGAATGGTTGGATCAGTTCACAAACTCATCAACAATGT 87898 v i vi i v i ii vv i i i i i C L1ME5_3end#LI 328 AGATTGCTCTCCAGAATGGCTGCACCAGTCTACACTCCCACCAGCAGTGC 279 chr4ptel1M 87899 ATTGGACCTCCCCTCCAATTTTCCC---TCCCCTCCAATA-TTGATAATT 87944 vi ivi i----- ? i --- i v i - ii - C L1ME5_3end#LI 278 ATGAGGGTTCCT-----ATNTCCCCACATCCTCGCCAACACTTGGCA-TT 235 chr4ptel1M 87945 ATCT---TTTCTTGACAATGTA-GTCGATCTAAAACATGTGTAGTGGTAA 87990 i--- ---- v v- i ii v vi iv i v C L1ME5_3end#LI 234 ATCCAGCTTTCT----AATTTTTGCCAGTCTAATAGGTGTAAAGTGATAT 189 chr4ptel1M 87991 CTCAGAGTTGTCTTAATTTGCATTTCTTTGATCAATAATGATTTAAATCA 88040 vv i i i v v vi v C L1ME5_3end#LI 188 CTCATTGTTGTTTTAATTTGCATTTCTCTGATTACTAATGAGTTTGAGCA 139 chr4ptel1M 88041 CCTTTTCATATGACTAGAAATGGTTTTAATTTCTTTCTCTGAAAATTGTC 88090 i i vi ivv iivv ivii i ii v i C L1ME5_3end#LI 138 TCTCTTCATATGCTTGTTAGCCTTTCGGGTTTCCTCTTCTGTAAATTGCC 89 chr4ptel1M 88091 TGTTCATTTCCTTTGACCATTTATCAACTGGAG 88123 v v v v i i C L1ME5_3end#LI 88 TGTTCATATCCTTTGCCCATTTTTCTATTGGGG 56 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 42.88 CpG sites = 115, Kimura (unadjusted) = 44.53 Transitions / transversions = 1.58 (115/73) Gap_init rate = 0.06 (34 / 599), avg. gap size = 1.62 (55 / 34) 836 32.73 4.95 2.23 chr4ptel1M 87638 88162 (911838) C L1ME4c_3end#LINE/L1 (275) 555 17 m_b165s551i6 6201 chr4ptel1M 87638 ATAATATCCCATAACATTCATATACTGTAACTTATTCAGCTACTCT---- 87683 i vivi ?v i ii i i i i i i i---- C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chr4ptel1M 87684 -------ACACTCAG----TTTCCAGTTTCTTGCCACTACAAAAAGGGTT 87722 ------- i i ---- i i i i i i v iv i C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCT 456 chr4ptel1M 87723 GCTACAAATATTTTTCCACATGTAGGTCCTTTTCCTTTTTT---ATGATC 87769 v ii i i ivii i -- i i --- v i C L1ME4c_3end#L 455 GCAATGAACATCTTCGTGCATATAG--CTTTTTCCTTCTTTTGAATTATT 408 chr4ptel1M 87770 CCTGTGTGATACATGCCCAGGAGAGACACTGCTGGATCAAAGGATATGTA 87819 i iv iv v v i v iv i i i i v C L1ME4c_3end#L 407 TCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAA 358 chr4ptel1M 87820 GAGTTTGGTAGCCCTTTGGCCAGAGTTTTATATTACTCTGTAGAATGGTT 87869 v v vi i i vivv iv v vii v i i vi i v C L1ME4c_3end#L 357 CATTTTTATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTT 308 chr4ptel1M 87870 GGATCAGTTCACAAACTCATCAACAATGTATTGGACCTCCCCTCCAATTT 87919 v i i i ?vvi i i - ii?v v ---- i C L1ME4c_3end#L 307 GTACCAATTTACANTGCCACCAGCAATGTAT-GAGNGTACC----AGTTT 263 chr4ptel1M 87920 TCCC---TCCCCTCCAATATTGATAATTATCTTTTCTTGACAATGTAGTC 87966 iv ---? i v ii ivv vv i v v v v v ii C L1ME4c_3end#L 262 CACCGCANCCTCGCCAGCATTGGGTATTATCAATTTTTTAAATTTTTGCT 213 chr4ptel1M 87967 GATCTAAAACATGTGTAGTGGTAACTCAGAGTTGTCTTAATTTGCATTTC 88016 i i v vii iv i v vv ii C L1ME4c_3end#L 212 AATTTAATAGGCGTAAAATGGTATCTCATTGTTGCTTTAATTTGCATTTC 163 chr4ptel1M 88017 TTTGATCAATAATGA-TTTAAATCACCTTTTCATATGACTAGAAATGGTT 88065 i v ii -v i - ii i i vi ivvv ivi? C L1ME4c_3end#L 162 TTTGATTACTAGCGAGGTTGAA-CATTTTTCCATGTGTTTGTTTACTANT 114 chr4ptel1M 88066 TTAATTTCTTTCTCTGAAAATTGTCTGTTCATTTCCTTTGACCATTTATC 88115 vv i ii ? vi v v C L1ME4c_3end#L 113 TGTATTTCCTCTTNTGTGAATTGTCTGTTCATGTCCTTTGCCCATTTATC 64 chr4ptel1M 88116 AACTGGAGAATGGCTTGAAA----TCTTATAAATTAGAGTCAATTCTCTA 88161 v i i---- v v?---- v v i v ii i C L1ME4c_3end#L 63 TATTGGG----GTCTTGATNTTTTTCTTATCAATTTGAATGAGCTCTTTA 18 chr4ptel1M 88162 T 88162 C L1ME4c_3end#L 17 T 17 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.39 CpG sites = 101, Kimura (unadjusted) = 45.61 Transitions / transversions = 1.51 (101/67) Gap_init rate = 0.04 (19 / 524), avg. gap size = 2.00 (38 / 19) 13 18.61 0.00 3.03 chr4ptel1M 88402 88435 (911565) (ATGAA)n#Simple_repeat 1 33 (0) m_b165s252i7 6202 chr4ptel1M 88402 ATGAAATGGAATGAAAATAGAATGAAATAGAATG 88435 i - ii ii (ATGAA)n#Simp 1 ATGAAATGAAATG-AAATGAAATGAAATGAAATG 33 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 459 28.01 9.86 1.96 chr4ptel1M 89433 89574 (910426) C MIRb#SINE/MIR (96) 172 20 m_b165s601i4 6203 chr4ptel1M 89433 TATGAAGTATGTGCTATTATTCTCCCCACTTTACTGTTGAGGAAATTGAG 89482 ii i v --- v i v v i C MIRb#SINE/MIR 172 TGCGAGGTAGGT---ATTATTATCCCCATTTTACAGATGAGGAAACTGAG 126 chr4ptel1M 89483 GCAGACAGAGGTGAAATGGCTTGC---------CATATTTAACAAGTGAC 89523 vv v v i ii --------- i vi ii i C MIRb#SINE/MIR 125 GCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGC 76 chr4ptel1M 89524 TGAAACTAGATTTGAACTCAGATCTTCCTGATTTCAG-----GTGTTCTC 89568 v iv vi i i i vi i i i----- i i C MIRb#SINE/MIR 75 AGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTT 26 chr4ptel1M 89569 TCTGCT 89574 ii C MIRb#SINE/MIR 25 TCCACT 20 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.32 CpG sites = 26, Kimura (unadjusted) = 36.70 Transitions / transversions = 2.00 (26/13) Gap_init rate = 0.04 (5 / 141), avg. gap size = 3.40 (17 / 5) 498 24.80 9.60 0.00 chr4ptel1M 89447 89571 (910429) C MIRc#SINE/MIR (110) 158 22 m_b165s601i5 6203 chr4ptel1M 89447 TATTATTCTCCCCACTTTACTGTTGAGGAAATTGAGGCAGACAGAGGTGA 89496 v i v v i vv v v C MIRc#SINE/MIR 158 TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTA 109 chr4ptel1M 89497 AATGGCTTGC---------CATATTTAACAAGTGACTGAAACTAGATTTG 89537 i i --------- i vi ii i v iv vi i i C MIRc#SINE/MIR 108 AGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCG 59 chr4ptel1M 89538 AACTCAGATCTTCCTGATTTCAGGT---GTTCTCTCT 89571 i i i i i --- v i C MIRc#SINE/MIR 58 AACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTT 22 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.69 CpG sites = 19, Kimura (unadjusted) = 30.87 Transitions / transversions = 1.58 (19/12) Gap_init rate = 0.02 (2 / 124), avg. gap size = 6.00 (12 / 2) 13 24.69 0.00 0.00 chr4ptel1M 90425 90459 (909541) (ATAC)n#Simple_repeat 1 35 (0) m_b165s252i8 6204 chr4ptel1M 90425 ATACACACGTACACACATACATATATGTATACTTA 90459 i i i i ii v (ATAC)n#Simpl 1 ATACATACATACATACATACATACATACATACATA 35 Matrix = Unknown Transitions / transversions = 6.00 (6/1) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 400 33.15 3.95 4.55 chr4ptel1M 90666 90842 (909158) MamSINE1#SINE/tRNA-RTE 16 191 (99) m_b165s601i6 6205 chr4ptel1M 90666 GCTAAGTAGACTAGAAGGTAGTACTAA-GAGGTACAAAGTTATGG--TTG 90712 v v ii iviii i - i- i i i -- i MamSINE1#SINE 16 GCTCAGTTGGTTAGAGCACGGTGCTAATGAGGC-CAAGGTCACGGGTTCG 64 chr4ptel1M 90713 GTCTAGGTATATGAGCTAGTTAGTGTGTTTCTTCTGTTTCATAGCCACAA 90762 i ivv i -- i i i--- vi i i i MamSINE1#SINE 65 ATCCCCGTGT--GGGCCAGTTAGC---TTTGCTCTGTTCCATGGCCACAG 109 chr4ptel1M 90763 A-TGCTATTGCTCAACC--ATTAAACATCTGGAAACCATGTACAGCTAGT 90809 - - iiv v v --iii iv i v v viii i v i i MamSINE1#SINE 110 ACTGC-ACCCCTAACCCCAGCCAGCCGTCTCGCAAATGCGTGCCGTTGGT 158 chr4ptel1M 90810 CACAAGAAGAATCAGGCA-AGAATGTAGAGGGCT 90842 ii i i - - i i v ? MamSINE1#SINE 159 CACAAGGGGGACC-GGCAGAGAGTGTGGATGGNT 191 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.89 CpG sites = 41, Kimura (unadjusted) = 47.98 Transitions / transversions = 2.73 (41/15) Gap_init rate = 0.07 (13 / 176), avg. gap size = 1.15 (15 / 13) 198 29.05 5.62 3.30 chr4ptel1M 91473 91561 (908439) MIR3#SINE/MIR 112 202 (6) m_b165s601i7 6206 chr4ptel1M 91473 CTCTGGGTTT--GTTTCCTCATTTTCTAAATGAAAGACATTGTCAAATAG 91520 ii -- i viv ii i-i --i v MIR3#SINE/MIR 112 CTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGG-GTTG--GACTAG 158 chr4ptel1M 91521 ACAACATCCAATGT-CTTTCCATCTCT--CAATCCATTGTTCCA 91561 ii iv i v - i v -- v i vi i MIR3#SINE/MIR 159 ATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTA 202 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.65 CpG sites = 17, Kimura (unadjusted) = 38.65 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.07 (6 / 88), avg. gap size = 1.33 (8 / 6) 231 30.65 1.61 0.00 chr4ptel1M 92061 92122 (907878) C MIR3#SINE/MIR (21) 187 125 m_b165s601i8 6207 chr4ptel1M 92061 TTAAAGCTGCAAGGC-CTTTAGAAAGTATCCAACCCAACCATTTCATTTT 92109 i i v v- i i vi i ii vii C MIR3#SINE/MIR 187 TCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTT 138 chr4ptel1M 92110 ATAGCTGGTAAAA 92122 i v ivi C MIR3#SINE/MIR 137 ACAGATGAGGAAA 125 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.67 CpG sites = 13, Kimura (unadjusted) = 41.67 Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.02 (1 / 61), avg. gap size = 1.00 (1 / 1) 22 3.12 2.86 2.86 chr4ptel1M 92372 92406 (907594) (ATG)n#Simple_repeat 1 35 (0) m_b165s252i9 6208 chr4ptel1M 92372 ATG-TGATGATAAATGATGATGATGATGATGATGAT 92406 - -i (ATG)n#Simple 1 ATGATGATGAT-GATGATGATGATGATGATGATGAT 35 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 31 0.00 0.00 0.00 chr4ptel1M 92432 92460 (907540) (T)n#Simple_repeat 1 29 (0) c_b165s251i3 6209 chr4ptel1M 92432 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 92460 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 507 21.99 0.72 7.75 chr4ptel1M 92461 92596 (907404) C MIRc#SINE/MIR (139) 129 3 m_b165s601i9 6210 chr4ptel1M 92461 GCTGAGGC-AATTGGGGTTAAGTGACTTGCTCAGGGTCACACAGCTAGGA 92509 i -v vv i i i -- C MIRc#SINE/MIR 129 ACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG-- 82 chr4ptel1M 92510 TATGTTGAGTGTTTGAGACCAGATTTGAACTCAAGTCCTCCTGACTTCAG 92559 ----- i viv v vi i i i i i i i C MIRc#SINE/MIR 81 -----TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAA 37 chr4ptel1M 92560 GGCTGGGGCTCTATCCACTGCACCACCTAGCTGCCCC 92596 v ii v v ---i i C MIRc#SINE/MIR 36 GTCCAGTGCTCTTTCCACTGCACCAC---ACTGCCTC 3 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 25.67 CpG sites = 18, Kimura (unadjusted) = 26.77 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.08 (11 / 135), avg. gap size = 1.00 (11 / 11) 326 30.24 4.10 2.42 chr4ptel1M 93284 93405 (906595) C L2d_3end#LINE/L2 (2) 514 391 m_b165s601i10 6211 chr4ptel1M 93284 AATGAAGGAATGATCAAACATTTATTAATCATTTACTATATGCTGAGCCC 93333 v vv v v ii i v iii i v v C L2d_3end#LINE 514 AATCAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCAC 465 chr4ptel1M 93334 CTTGCTGAGCAATA---GGAATAAAAATGCAGGCAGGTAAGACA--GTGC 93378 iv ii iv i--- ii ? vi? v---i -- v C L2d_3end#LINE 464 TGTGCTAGGCGCTGTGGGGAACGANAAAANAGT---ATAAGACATGGTCC 418 chr4ptel1M 93379 CTACTCTCAAGCAGTCTACATTCTAAT 93405 i i v ii v i C L2d_3end#LINE 417 CTGCCCTCAAGGAGCTTACAATCTAGT 391 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.34 CpG sites = 21, Kimura (unadjusted) = 40.80 Transitions / transversions = 1.40 (21/15) Gap_init rate = 0.04 (5 / 121), avg. gap size = 1.60 (8 / 5) 298 36.15 3.82 0.74 chr4ptel1M 93298 93428 (906572) C L2a_3end#LINE/L2 (14) 503 369 m_b165s601i11 6211 chr4ptel1M 93298 CAAACATTTATTAATCATTTACTATATGCTGAGCCCCTTGCTGAGCAATA 93347 i i v iii i iii v iv v ii iv i C L2a_3end#LINE 503 CAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGCGCTG 454 chr4ptel1M 93348 GGAATAAAAATGCAGGCAGGTAAGAC---AGTGCCTACTCTCAAGCAGTC 93394 i v ivv iiii iivv --- v i i v v ii C L2a_3end#LINE 453 GGGATACAGCAGTGAACAAAACAGACAAAAGTCCCTGCCCTCATGGAGCT 404 chr4ptel1M 93395 TACATTCTAATGAGCAATAAACAG-CAA-AAGCAGA 93428 i i -iiv i - - i i C L2a_3end#LINE 403 TACATTCTAGTGGG-GGGAGACAGACAATAAACAAA 369 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 50.36 CpG sites = 33, Kimura (unadjusted) = 53.84 Transitions / transversions = 2.36 (33/14) Gap_init rate = 0.03 (4 / 130), avg. gap size = 1.50 (6 / 4) 207 33.70 3.26 0.00 chr4ptel1M 94542 94633 (905367) L3#LINE/CR1 3968 4062 (37) m_b165s601i12 6212 chr4ptel1M 94542 CTGCAGATCTCCAAACCAAGATTCAGTGACCACTTGCCAGCTAGGCTCTA 94591 v i v i i vi ii vii i vv v i v L3#LINE/CR1 3968 CTGGAGGTGTTCAAGCAGAGGCTGGATGACCACTTGTCAGGGATGTTGTA 4017 chr4ptel1M 94592 TTA-GGATTCCTTTTCAGGATCG--GGTCAGAATAGATGGCCCCT 94633 vv - viviv v -- ii v i i L3#LINE/CR1 4018 GAAGGGATTCCTGCATTGGATGGGAGGTTGGACTAGATGACCTCT 4062 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 45.62 CpG sites = 16, Kimura (unadjusted) = 45.62 Transitions / transversions = 1.07 (16/15) Gap_init rate = 0.02 (2 / 91), avg. gap size = 1.50 (3 / 2) 240 35.51 2.80 0.00 chr4ptel1M 94782 94888 (905112) MIRc#SINE/MIR 65 174 (94) m_b165s601i13 6213 chr4ptel1M 94782 CCAGCTTTCACATTTACTGTCCATGTGGTCATAGGTAAGCCAATAGACTC 94831 i i vv i iv ii ii v i i i v vi ii MIRc#SINE/MIR 65 CCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCT 114 chr4ptel1M 94832 CTTTG-GCGTCAATCTCTCCATCTGTATCATGGTGACATCCAAACT--CC 94878 i - v i i ii vv v i viv v i-- MIRc#SINE/MIR 115 CTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCC 164 chr4ptel1M 94879 CTTCCTGCTT 94888 v i i MIRc#SINE/MIR 165 CTGCCTACCT 174 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 48.93 CpG sites = 24, Kimura (unadjusted) = 50.89 Transitions / transversions = 1.71 (24/14) Gap_init rate = 0.02 (2 / 106), avg. gap size = 1.50 (3 / 2) 242 35.63 1.15 0.00 chr4ptel1M 94782 94868 (905132) MIRb#SINE/MIR 68 155 (113) m_b165s601i14 6213 chr4ptel1M 94782 CCAGCTTTCACATTTACTGTCCATGTGGTCATAGGTAAGCCAATAGACTC 94831 i i vv i iv ii ii v i i ii v vi ii MIRb#SINE/MIR 68 CCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCT 117 chr4ptel1M 94832 CTTTG-GCGTCAATCTCTCCATCTGTATCATGGTGACA 94868 i - v i i ii vv v i MIRb#SINE/MIR 118 CTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATA 155 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 49.55 CpG sites = 21, Kimura (unadjusted) = 52.06 Transitions / transversions = 2.10 (21/10) Gap_init rate = 0.01 (1 / 86), avg. gap size = 1.00 (1 / 1) 247 25.18 25.90 0.00 chr4ptel1M 95566 95704 (904296) C L2d_3end#LINE/L2 (6) 510 336 m_b165s601i15 6214 chr4ptel1M 95566 AGTCAGGCAACAAGTATCCAGTAAGTGCCTACTATGTGCTGAACAT---- 95611 i iv ii v i i v i i---- C L2d_3end#LINE 510 AATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTGTG 461 chr4ptel1M 95612 CCAG-------AGAGAAGCAAAAAACA------------GTCCCTAGCCT 95642 i -------i i vv ? ? ------------ iv C L2d_3end#LINE 460 CTAGGCGCTGTGGGGAACGANAAAANAGTATAAGACATGGTCCCTGCCCT 411 chr4ptel1M 95643 CCAGAAGTT--CAGTCTAATAGGAGAAA------TAATATAC---AAACA 95681 v i i -- i i v i i ------ i i --- C L2d_3end#LINE 410 CAAGGAGCTTACAATCTAGTTGGGGAGACAAGACTAACACACATGAAACA 361 chr4ptel1M 95682 ACT--AGGACAGCAAAAGAGAATAT 95704 i -- i ii v v i C L2d_3end#LINE 360 ATTAGAGAACAATACAAGACAGTAT 336 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.60 CpG sites = 25, Kimura (unadjusted) = 32.75 Transitions / transversions = 2.50 (25/10) Gap_init rate = 0.05 (7 / 138), avg. gap size = 5.14 (36 / 7) 322 30.28 9.17 0.00 chr4ptel1M 95573 95681 (904319) C L2c_3end#LINE/L2 (11) 467 349 m_b165s601i16 6214 chr4ptel1M 95573 CAACAAGTATCCAGTAAGTGCCTACTATGTGC-------TGAACATCCAG 95615 ii ii v i i ------- iiv v i C L2c_3end#LINE 467 CAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGATACAA 418 chr4ptel1M 95616 AGAGAAGCAAAAAACAGTCCCTAGCCTCCAGAAGTT--CAGTCTAATAGG 95663 vi ii i v i iv v i i -- i i i C L2c_3end#LINE 417 AGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAGTGGA 368 chr4ptel1M 95664 AGAAATA-ATATACAAACA 95681 i i i - i ?ii C L2c_3end#LINE 367 GGAGACAGACANGTAAACA 349 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.44 CpG sites = 26, Kimura (unadjusted) = 42.99 Transitions / transversions = 3.71 (26/7) Gap_init rate = 0.03 (3 / 108), avg. gap size = 3.33 (10 / 3) 250 21.74 0.00 0.00 chr4ptel1M 95826 95871 (904129) C MIRc#SINE/MIR (138) 130 85 m_b165s601i17 6215 chr4ptel1M 95826 AAAATGTCACTTGAAGAGGTTAAGTGACTTACCCAGGATCACACAG 95871 v vvi iii i i i C MIRc#SINE/MIR 130 AAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAG 85 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.56 CpG sites = 7, Kimura (unadjusted) = 26.56 Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 227 19.51 0.00 0.00 chr4ptel1M 95840 95880 (904120) C MIR3#SINE/MIR (95) 113 73 m_b165s601i18 6216 chr4ptel1M 95840 AGAGGTTAAGTGACTTACCCAGGATCACACAGAGAATCAAT 95880 v i i i v? i i i C MIR3#SINE/MIR 113 AGAGGTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGT 73 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 24.17 CpG sites = 6, Kimura (unadjusted) = 24.17 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 206 24.18 21.98 0.00 chr4ptel1M 95874 95964 (904036) C L2d_3end#LINE/L2 (6) 510 400 m_b165s601i19 6217 chr4ptel1M 95874 AATCAATCAACTAGTATTTA-------CATACTA-------AACACTGTA 95909 v ------- v ------- i i C L2d_3end#LINE 510 AATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTGTG 461 chr4ptel1M 95910 ATAAGTAC--TGGAGACATACAAAAGAAT----GAAATACTCTGTACTCT 95953 v i ii -- i vvv ? ? i ---- v iv iv i i C L2d_3end#LINE 460 CTAGGCGCTGTGGGGAACGANAAAANAGTATAAGACATGGTCCCTGCCCT 411 chr4ptel1M 95954 CAAGGAATTTA 95964 ii C L2d_3end#LINE 410 CAAGGAGCTTA 400 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.81 CpG sites = 13, Kimura (unadjusted) = 30.63 Transitions / transversions = 1.44 (13/9) Gap_init rate = 0.04 (4 / 90), avg. gap size = 5.00 (20 / 4) 240 28.45 9.48 0.00 chr4ptel1M 97550 97665 (902335) L1ME3A_3end#LINE/L1 204 330 (590) m_b165s551i7 6218 chr4ptel1M 97550 CATCAGGTGGGCTAA--TAAGATAGAT-GATAATGATGAGTGCTAGTGGG 97596 i ivv -- i i v i- i ivii i i i i L1ME3A_3end#L 204 CACCAGAATGGCTAAAATGAAAAAGACAGACAATACCAAGTGTTGGCGAG 253 chr4ptel1M 97597 GATGTGGGAAAACAG--ACACTAATACACTGTTGGT-GGATTGTAAAC-- 97641 iiv v -- v v i - v i-- L1ME3A_3end#L 254 GATGTGGAGCAACCGGAACTCTCATACACTGCTGGTGGGAGTGTAAATTG 303 chr4ptel1M 97642 ---CATCCATTTAGGAGAAGCATTTGG 97665 --- v i v i vii L1ME3A_3end#L 304 GTACAACCACTTTGGAAAACTGTTTGG 330 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.69 CpG sites = 21, Kimura (unadjusted) = 37.12 Transitions / transversions = 1.75 (21/12) Gap_init rate = 0.05 (6 / 115), avg. gap size = 1.83 (11 / 6) 296 24.87 2.29 22.53 chr4ptel1M 97566 97783 (902217) L1ME4a_3end#LINE/L1 226 407 (464) m_b165s551i8 6218 chr4ptel1M 97566 AAGATAGATGATAATGATGAGTGCTAGTGGGGATGTGGGAAAACAGACAC 97615 --- iviv i i i i i ?i i i L1ME4a_3end#L 226 AAGAT---TGATAATACCCAGTGTTGGCGAGGGTGTGGNGAAACGGGCAC 272 chr4ptel1M 97616 TA--ATACACTGTTGGT-GGATTGTAAACCATCCATTTAGGAGAAGCATT 97662 v-- i - v --------------------- L1ME4a_3end#L 273 TCTCATACACTGCTGGTGGGAGTGTAAA---------------------T 301 chr4ptel1M 97663 TGGATCCTACCATTTAGGATCTAACTATTTAGGGGAACAATTTGGAACTA 97712 - v v v iv ------------ --- v v L1ME4a_3end#L 302 TGG-TACAACCTTTCTGG------------AGGG---CAATTTGGCAATA 335 chr4ptel1M 97713 TGC-CCAAAGGTCAACCAAAATGTGTATGTCCTTTGATCCAGTAA-TACA 97760 i-i i i -viv ?i ii i - v L1ME4a_3end#L 336 TGTATCAAAAGCC-TTAAAAATGTNCATACCCTTTGACCCAGTAATTCCA 384 chr4ptel1M 97761 CTATTAGGTCTGTATCTCAAAGA 97783 vi vv v ii i L1ME4a_3end#L 385 CTTCTAGGAATTTATCCTAAGGA 407 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 27.89 CpG sites = 25, Kimura (unadjusted) = 29.53 Transitions / transversions = 1.47 (25/17) Gap_init rate = 0.21 (45 / 217), avg. gap size = 1.02 (46 / 45) 304 22.83 8.70 0.00 chr4ptel1M 97574 97665 (902335) L1ME3G_3end#LINE/L1 227 326 (598) m_b165s551i9 6218 chr4ptel1M 97574 TGATAATGATGAGTGCTAGTGGGGATGTGGGAAAACAG--ACACTAATAC 97621 ivi? i i i i i i i -- v v L1ME3G_3end#L 227 TGATAATATCNAGTGTTGGCGAGGGTGTGGGGAAACGGGTACTCTCATAC 276 chr4ptel1M 97622 ACTGTTGGT-GGATTGTAAAC-----CATCCATTTAGGAGAAGCATTTGG 97665 i - v i----- v ? v iivv L1ME3G_3end#L 277 ACTGCTGGTGGGAGTGTAAATTGGTACAGCCNTTTTGGAGGGCAATTTGG 326 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 25.50 CpG sites = 13, Kimura (unadjusted) = 28.62 Transitions / transversions = 1.62 (13/8) Gap_init rate = 0.03 (3 / 91), avg. gap size = 2.67 (8 / 3) 268 31.49 2.34 0.77 chr4ptel1M 97685 97812 (902188) L1ME4c_3end#LINE/L1 308 437 (393) m_b165s551i10 6218 chr4ptel1M 97685 AACTATTTAGGGGAACAATTTGGAACTATGCCCAAAGGTCAACCAAAATG 97734 iv v ii i v v i iviv iv v iv L1ME4c_3end#L 308 AACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAAAATG 357 chr4ptel1M 97735 TGTATGTCCTTTGATCCAGTAA-TACACTATTAGGTCTGTATCTCAAAGA 97783 vi ii i - v vi i vv v ii i L1ME4c_3end#L 358 TTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGA 407 chr4ptel1M 97784 GAACAA--AAAAGGGAGGAAAGACCTATTTG 97812 - i --v i i i v v L1ME4c_3end#L 408 -AATAATTCAAAAGAAGGAAAAAGCTATATG 437 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.46 CpG sites = 22, Kimura (unadjusted) = 41.82 Transitions / transversions = 1.22 (22/18) Gap_init rate = 0.02 (3 / 127), avg. gap size = 1.33 (4 / 3) 339 35.46 3.10 6.39 chr4ptel1M 98218 98443 (901557) C MIRb#SINE/MIR (46) 222 4 m_b165s601i20 6219 chr4ptel1M 98218 TGTACCCAGCCCTTTACCAATATTATTTTGTTGGGAACTCACTACAACCT 98267 i iv v vvii i ii viivv v i C MIRb#SINE/MIR 222 TGTGCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCC 173 chr4ptel1M 98268 TGGCATACAGGAACTGTTGTTATCAATATGCATTTGAGGAAACTCAGGCC 98317 vv vii v i i i ivi v v i vv v i C MIRb#SINE/MIR 172 TGCGAGGTAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCT 123 chr4ptel1M 98318 AATAAATTTGAAATGACTAGCCCAATGTCTC------AGGAAGTGCCTGA 98361 v v i vv v i i v v v ------ v v v C MIRb#SINE/MIR 122 CAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGA 73 chr4ptel1M 98362 AGATAAATTAGAACTCGGTTCTCCATGTGCCTGAGGCTGAGTTCAAACTC 98411 ivvvii v i i v ------------ v v i vi C MIRb#SINE/MIR 72 GCCGGGATTCGAACCCAGGTCT------------GTCTGACTCCAAAGCC 35 chr4ptel1M 98412 AGTTCTCTCGACCTAGGGCACTA-GCTGCCTCT 98443 v v i--i i vv i - i C MIRb#SINE/MIR 34 CGTGCTCTT--TCCACTGCACCACGCTGCCCCT 4 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 48.32 CpG sites = 34, Kimura (unadjusted) = 48.32 Transitions / transversions = 0.83 (34/41) Gap_init rate = 0.07 (16 / 225), avg. gap size = 1.31 (21 / 16) 28 23.15 4.65 0.00 chr4ptel1M 99007 99092 (900908) (TAGA)n#Simple_repeat 1 90 (0) m_b165s252i10 6220 chr4ptel1M 99007 TAGATACATACTTAGATAGACAGAT-GATAGATAAATTAAT-GGTGGCTA 99054 v vv i - i vi - i i v (TAGA)n#Simpl 1 TAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATA 50 chr4ptel1M 99055 GAAAGAT-GATAGAT-GATAGATCTACAGGTAGACGGATA 99092 v - - vv i i ii (TAGA)n#Simpl 51 GATAGATAGATAGATAGATAGATAGATAGATAGATAGATA 90 Matrix = Unknown Transitions / transversions = 1.12 (9/8) Gap_init rate = 0.05 (4 / 85), avg. gap size = 1.00 (4 / 4) 20 17.70 0.00 5.56 chr4ptel1M 99019 99075 (900925) (TAGATGA)n#Simple_repeat 1 54 (0) m_b165s252i11 6221 chr4ptel1M 99019 TAGATAGACAGATGATAGATAAATTAATGGTGGCTAGAAAGATGATAGAT 99068 - i -i vi i i v - v (TAGATGA)n#Si 1 TAGAT-GATAGATGATAGAT-GATAGATGATAGAT-GATAGATGATAGAT 47 chr4ptel1M 99069 GATAGAT 99075 (TAGATGA)n#Si 48 GATAGAT 54 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.05 (3 / 56), avg. gap size = 1.00 (3 / 3) 28 23.15 4.65 0.00 chr4ptel1M 99007 99092 (900908) (TAGA)n#Simple_repeat 1 90 (0) m_b165s252i10 6220 chr4ptel1M 99007 TAGATACATACTTAGATAGACAGAT-GATAGATAAATTAAT-GGTGGCTA 99054 v vv i - i vi - i i v (TAGA)n#Simpl 1 TAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATA 50 chr4ptel1M 99055 GAAAGAT-GATAGAT-GATAGATCTACAGGTAGACGGATA 99092 v - - vv i i ii (TAGA)n#Simpl 51 GATAGATAGATAGATAGATAGATAGATAGATAGATAGATA 90 Matrix = Unknown Transitions / transversions = 1.12 (9/8) Gap_init rate = 0.05 (4 / 85), avg. gap size = 1.00 (4 / 4) 460 25.22 3.48 0.00 chr4ptel1M 99868 99982 (900018) C MIR#SINE/MIR (56) 206 88 m_b165s601i21 6222 chr4ptel1M 99868 TTGACATATATTACCCCATTTGATTCTCATATTGACACTATAA---AGAT 99914 v i v i i i i vii v i --- i C MIR#SINE/MIR 206 TTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGGTAGGT 157 chr4ptel1M 99915 GTTATTATTA-GCACATTTTTCAGATGAAGAAACTGAGGCTGGGAGCACT 99963 ii -v v v i vvi viv C MIR#SINE/MIR 156 ACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGT 107 chr4ptel1M 99964 TAAGTAACCTGTCCACAGT 99982 i i vi C MIR#SINE/MIR 106 TAAGTAACTTGCCCAAGGT 88 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.39 CpG sites = 17, Kimura (unadjusted) = 31.39 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.02 (2 / 114), avg. gap size = 2.00 (4 / 2) 372 20.27 17.36 2.16 chr4ptel1M 100008 100128 (899872) C MIRc#SINE/MIR (26) 242 104 m_b165s601i22 6223 chr4ptel1M 100008 TAGCACTT-ATATTGTACACAGC--------ATATGTTATCTCATTTGCC 100048 - i v v v -------- ii vi C MIRc#SINE/MIR 242 TAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATCTCATTTGAT 193 chr4ptel1M 100049 CTTCATAAC---CCTGT--------CAAGG-AGGTATTATTATTTTTACC 100086 i i --- -------- i - ii--- C MIRc#SINE/MIR 192 CCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCC---CC 146 chr4ptel1M 100087 ATTTTACAGAAGGAGAAATTGAGTCTGGGACAGATAAAGAGA 100128 v ii i v vi v i v v C MIRc#SINE/MIR 145 ATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGA 104 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 24.08 CpG sites = 14, Kimura (unadjusted) = 24.08 Transitions / transversions = 1.40 (14/10) Gap_init rate = 0.07 (8 / 120), avg. gap size = 3.00 (24 / 8) 374 25.53 3.09 3.09 chr4ptel1M 100029 100125 (899875) C MIRb#SINE/MIR (62) 206 110 m_b165s601i23 6223 chr4ptel1M 100029 CATATGTTATCTCATTTGCCCTTCATAAC---CCTGTCAAGGAGGTATTA 100075 iii ivi i i --- iv i v C MIRb#SINE/MIR 206 CATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTA 157 chr4ptel1M 100076 TTATTTTTACCATTTTACAGAAGGAGAAATTGAGTCTGGGACAGATAAAG 100125 ii--- v ii i v vi v i v C MIRb#SINE/MIR 156 TTATCC---CCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAG 110 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 30.74 CpG sites = 16, Kimura (unadjusted) = 32.38 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.04 (4 / 96), avg. gap size = 1.50 (6 / 4) 190 28.00 0.00 0.00 chr4ptel1M 100193 100242 (899758) C MIR1_Amn#SINE/MIR (81) 149 100 m_b165s601i25 6224 chr4ptel1M 100193 CCATCTTACAGATAAGGCAACTGAGGCAGCATGGGATGGAATGATTCTCC 100242 i i v ?vviv i i ?i i i iv C MIR1_Amn#SINE 149 CCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGCC 100 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.46 CpG sites = 9, Kimura (unadjusted) = 38.46 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 220 32.06 1.18 13.25 chr4ptel1M 100314 100482 (899518) MIR1_Amn#SINE/MIR 4 154 (76) m_b165s601i26 6225 chr4ptel1M 100314 GGAGGCAGAG--GACTGGAGAATGGGGCACTGAACTTCTCTGAGTAATAA 100361 v -- v i v i i i i ----- i - v -- MIR1_Amn#SINE 4 GGAGGCAGTGTGGTCTAGTGGATAGAGCACTGGACT-----GGG-ACT-- 45 chr4ptel1M 100362 ATGAGAAAACTAAGACCCCCCCATTCAGGTTCTCTGATTCTCAATTCTGT 100411 -i i i v ii ---ii ?v? i v -- ----- v i ?- i MIR1_Amn#SINE 46 -CGGGAGACCTGGG---TTCNANTCCCGG--CTCTG-----CCACTN-GC 83 chr4ptel1M 100412 TGATTGGATAACCCCAAACTGATCATTCCACTTGACTGGGCCTCAGTTTC 100461 i?ii ?i i iiiii vii i i? i vv ? MIR1_Amn#SINE 84 CNGCTGNGTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTC 133 chr4ptel1M 100462 CTGATCAGTAAAAGGAGGACA 100482 v v v i i MIR1_Amn#SINE 134 CTCATCTGTAAAATGGGGATA 154 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 45.49 CpG sites = 33, Kimura (unadjusted) = 46.93 Transitions / transversions = 2.36 (33/14) Gap_init rate = 0.12 (21 / 168), avg. gap size = 1.05 (22 / 21) 290 31.20 6.72 6.72 chr4ptel1M 100389 100522 (899478) MIR3#SINE/MIR 52 185 (23) m_b165s601i27 6225 chr4ptel1M 100389 GGTTCTCTGATTCTCAATTCTGT-------TGATTGGATAACCCCAAACT 100431 --- v i iii i------- ?ii vi i iiiii v MIR3#SINE/MIR 52 GGTTCT---AGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCA 98 chr4ptel1M 100432 GATCATTCCACTTGACTGGGCCTCAGTTTCCTGATCAGTAAAAGGAGGAC 100481 ii i i i vv v v v iv MIR3#SINE/MIR 99 AGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGG 148 chr4ptel1M 100482 ATCGGACCTTTCCATGTTAAAATCTAAAATCC--TCCAGTTTT 100522 i i --- vv --- vv ii -- i i MIR3#SINE/MIR 149 GTTGGAC---TAGATG---ATCTCTAAGGTCCCTTCCAGCTCT 185 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.52 CpG sites = 26, Kimura (unadjusted) = 43.02 Transitions / transversions = 2.00 (26/13) Gap_init rate = 0.08 (11 / 133), avg. gap size = 1.64 (18 / 11) 44 4.39 0.00 0.00 chr4ptel1M 101031 101077 (898923) (GT)n#Simple_repeat 1 47 (0) c_b165s251i4 6226 chr4ptel1M 101031 GTGTGTGTGAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGTG 101077 v i (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 47 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 262 31.03 1.15 0.00 chr4ptel1M 101621 101707 (898293) L1ME2z_3end#LINE/L1 439 526 (665) m_b165s551i11 6227 chr4ptel1M 101621 AGAATATTTCCAGTAGCTCTCTCTATAGTAGCAAAGAACTGGAAATTGTA 101670 i ivi i i v ii i v i iv iv L1ME2z_3end#L 439 AGAATGTTCATAGCAGCTTTATTCATAATAGCCAAAAACTGGAAACAGCC 488 chr4ptel1M 101671 GAGCTCCCCATCAACTGG-GAATGATTAAGTAAATTAT 101707 v v vi v - iv ii i i L1ME2z_3end#L 489 CAGGTGTCCATCAACAGGAGAATGGATAAACAAACTGT 526 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.77 CpG sites = 17, Kimura (unadjusted) = 41.77 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.01 (1 / 86), avg. gap size = 1.00 (1 / 1) 274 22.61 3.49 2.30 chr4ptel1M 102726 102811 (897189) C MIRc#SINE/MIR (6) 262 176 m_b165s601i28 6228 chr4ptel1M 102726 AATAATGACTAGAATTTCTCCAGCACTTTCAAGTTTATAAAGC---TTTA 102772 i?v viv v vi vv i --- i C MIRc#SINE/MIR 262 AATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCGCTTTCA 213 chr4ptel1M 102773 CTTATATTCACTCATTTGATCCCCACAGCACAACATTGT 102811 v i vv i -- vi C MIRc#SINE/MIR 212 CATACATTATCTCATTTGATCCTCACA--ACAACCCTGT 176 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 27.37 CpG sites = 8, Kimura (unadjusted) = 27.37 Transitions / transversions = 0.73 (8/11) Gap_init rate = 0.04 (3 / 85), avg. gap size = 1.67 (5 / 3) 287 18.46 3.08 0.00 chr4ptel1M 102914 102978 (897022) C MIR#SINE/MIR (120) 142 76 m_b165s601i29 6228 chr4ptel1M 102914 CATTTTACATTTGAGGAAACTGAGGCAAATAG-GGTTAAATGACTTG-CC 102961 vv v v - i i - C MIR#SINE/MIR 142 CATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCC 93 chr4ptel1M 102962 AAGGTAAAGGAATTAGT 102978 v viv ii C MIR#SINE/MIR 92 AAGGTCACACAGCTAGT 76 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 21.22 CpG sites = 5, Kimura (unadjusted) = 21.22 Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.03 (2 / 64), avg. gap size = 1.00 (2 / 2) 291 9.43 3.77 0.00 chr4ptel1M 102914 102966 (897034) C MIR1_Amn#SINE/MIR (82) 148 94 m_b165s601i30 6228 chr4ptel1M 102914 CATTTTACATTTGAGGAAACTGAGGCAAATAG-GGTTAAATGACTTG-CC 102961 vv ?v v - ? i - C MIR1_Amn#SINE 148 CATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGCCC 99 chr4ptel1M 102962 AAGGT 102966 C MIR1_Amn#SINE 98 AAGGT 94 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 10.52 CpG sites = 1, Kimura (unadjusted) = 10.52 Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.00 (2 / 2) 945 29.15 3.79 3.79 chr4ptel1M 103107 103819 (896181) L1M5_orf2#LINE/L1 2582 3294 (0) m_b165s551i12 6229 chr4ptel1M 103107 TGAAAAAAAA-ATCAAATGATGGTGG-CTTAGCTGTACCAGATCT-AAAA 103153 i - v - v v - - vv ? ? - i L1M5_orf2#LIN 2582 TGAAAAAGAAGAACAAA-GTTGGAGGACTTA-CACTACCNGATNTCAAGA 2629 chr4ptel1M 103154 TTATATTATAGAGCAGCAGTTACCAAAACTATTTGGTATTGGC-TAAGGA 103202 i - i vi v i i vi v - L1M5_orf2#LIN 2630 CT-TATTATAAAGCTACAGTAATCAAGACAGTGTGGTATTGGCGTAAGGA 2678 chr4ptel1M 103203 ATAGATTAGTTGATCAGTGGAATAGATTAG---GTTCAAGGGACAAAACA 103249 - iv i v i i v --- i - ii i i v - L1M5_orf2#LIN 2679 -TAGACAAATAGATCAATGGAACAGAATAGAGAGTCCA-GAAATAGACC- 2725 chr4ptel1M 103250 GTCA-ACAAATATAGCAACCTAGTCTTTGACAAAC---CCAAAG-ATCCC 103294 -- - v i ?v ?i ii i v--- ? - vii L1M5_orf2#LIN 2726 --CACACATATATGGNCANTTGATTTTTGACAAAGGTGCCAANGCAATTC 2773 chr4ptel1M 103295 AGCTTTTGGGATAAGAACTTACTGTTTGATAAAAATTGCTGGGAAAATTG 103344 ---- iv i ivvv v ii i viv i v L1M5_orf2#LIN 2774 AG----TGGGGAAAGGATAGTCTTTTCAACAAATGGTGCTGGAACAATTG 2819 chr4ptel1M 103345 GAAACTAATATGGCAGAAACTAGGCATTGATCCATACTTAACGCCGTACA 103394 v iiv v i v iii?v i i v i v i i L1M5_orf2#LIN 2820 GATATCCATATGGAAAAAAATGAANCTCGACCCCTACCTCACACCATACA 2869 chr4ptel1M 103395 CCAAGATAAGGTCAAAATGGGTTCAT-GACCTAGGCATAAAGAATGAAAT 103443 v i v iv ? i i - - iiii ii? i i L1M5_orf2#LIN 2870 CAAAAATTAATTCNAGATGGAT-CATAGACCTAAATGTAAAAGNTAAAAC 2918 chr4ptel1M 103444 TATTAATAAATTAGAGGAA--CATAGGATAGTTTACCTCTCAGACCTGTG 103491 v vvvvi i -- v i -- i iivv vv L1M5_orf2#LIN 2919 TATAAAACTTCTAGAAGAAAACATAGGAGAAT--ATCTTCGTGACCTTGG 2966 chr4ptel1M 103492 GA-AGGGGAAGGTCTTTATGACCAAAGCAGAACTAGAGATCATTACTGAT 103540 ?- vi i i i - i v iii v -- i -----i ?i i L1M5_orf2#LIN 2967 GNTAGGCAAAGATTTCT-TAAACAGGACACAA--AAAG-----CACNAAC 3008 chr4ptel1M 103541 CACAAAATAGAAAATT-------TCGATTATACCAAACTGAAAAGTTTTT 103583 i v i ------- v i ?i i v v ii i L1M5_orf2#LIN 3009 CATAAAAGAAAAAATTGATAAATTGGACTNCATCAAAATTAAAAACTTCT 3058 chr4ptel1M 103584 GTACAAACAAAACTAATGCAGACAAGATTAGAAGGGAAGCAATAAACTGG 103633 iv ?vvv ivi vi ivi v i v i v v i i ? L1M5_orf2#LIN 3059 GCTCNTCAAAAGACACCGTTAAGAAAATGAAAAGGCAAGCCACAGANTGG 3108 chr4ptel1M 103634 GAAAATATTTTTACAGTCAAAGGT-TCTGATAAAGGCCTCATTTCCAAAA 103682 i v v i i?- v vi - i v i v i L1M5_orf2#LIN 3109 GAGAAAATATTTGCAAN-ACATATATCTGACAAAGGACTCGTATCCAGAA 3157 chr4ptel1M 103683 TATATAGAGAATTAACTCTAATTTA-TAAAAAATCAAGCCATTC--TCCA 103729 i i v- vi ? i - ? -- v vv --i L1M5_orf2#LIN 3158 TATATAAAGAACTC-CTACAANTCAATAANAAA--AAGACAAACAACCCA 3204 chr4ptel1M 103730 ATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGAAGAAAT 103779 v? v i iv v v i v v L1M5_orf2#LIN 3205 ATANAAAAATGGGCAAAAGACTTGAACAGACACTTCACAAAAGAAGATAT 3254 chr4ptel1M 103780 TGAAACTATTTCTAGTCATATGAAAAGATGCTCCAAGTCA 103819 ?v iviiivv iv i v v? L1M5_orf2#LIN 3255 NCAAATGGCCAATAAGCACATGAAAAGATGCTCAACNTCA 3294 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.19 CpG sites = 112, Kimura (unadjusted) = 39.19 Transitions / transversions = 1.27 (112/88) Gap_init rate = 0.06 (42 / 712), avg. gap size = 1.29 (54 / 42) 1576 27.06 3.31 3.80 chr4ptel1M 103676 104309 (895691) L1ME5_3end#LINE/L1 7 637 (304) m_b165s551i14 6229 chr4ptel1M 103676 TCCAAAATATATAGAGAATTAACTCTAATTTATAAAAAATCAAGCCATT- 103724 i i i ii i vviv v iv i i -- v iv?- L1ME5_3end#LI 7 TCTAGAATATACAAGGAACTCCTGCAAATCAACAAGAAA--AAGACGGNA 54 chr4ptel1M 103725 -CTCCAATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGA 103773 - i v v i iv v L1ME5_3end#LI 55 ACCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGA 104 chr4ptel1M 103774 AGAAA-TTGAAA--CTATTTCTAGTCATATGAAAAGATGCTCCAAGTCAT 103820 i -ii -- --v v - i v v L1ME5_3end#LI 105 GGAAACCCGAAAGGCTA--ACAAG-CATATGAAGAGATGCTCAAACTCAT 151 chr4ptel1M 103821 TATTAATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACA 103870 v i vv i i vi L1ME5_3end#LI 152 TAGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACA 201 chr4ptel1M 103871 CCTGTCAGATTGGCTAAGATGACAGGAAA---AAATAATGATGATTGTTG 103917 i i i v i v --- ---ii vii v L1ME5_3end#LI 202 CCTATTAGACTGGCAAAAATTA---GAAAGCTGGATAATGCCAAGTGTTG 248 chr4ptel1M 103918 GAGGGGATGTGGGAAAACTGGGACATTGATTCATTGTTGGTGGAGTTGTG 103967 v i i ? iv i vi v v i i iiv i L1ME5_3end#LI 249 GCGAGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTA 298 chr4ptel1M 103968 AACGAATCCAACCATTTTGGAGAGTAGTTTGGAACTA--TGCTCAAA--A 104013 i vii v i i i i i v v -- iv -- L1ME5_3end#LI 299 GACTGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTA 348 chr4ptel1M 104014 AGTTATCAAACTGTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGAT 104063 - --- --- v i i viii v vv L1ME5_3end#LI 349 AG-TAT---AC---GCATACCCTATGACCCAGCAATTCCGCTCCTGGGTA 391 chr4ptel1M 104064 TATATCCCAAAGAGATTATAAAGAAGG----GAAAGGGACCTGTATGTGC 104109 i v v viv ----v i ---- i L1ME5_3end#LI 392 TATATCCCAAAGAAATTCTCACACAGGTCCATAAGGGGAC----ATGTAC 437 chr4ptel1M 104110 ACGAATGTTTGTGGCAGCCCTTTTTGTAGTGGCTAGAAACTGGAAACTGA 104159 iv i ii v vi v i vi i ii ii viv L1ME5_3end#LI 438 GAGGATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAAC 487 chr4ptel1M 104160 ATGGATGTCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATATGAAA 104209 v i v v i v iii v iv v v L1ME5_3end#LI 488 CTGGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCAC 537 chr4ptel1M 104210 ATTATGGAATATTACTGT-TCTGTAAGAAATGACCAACAGGATGATTTCA 104258 ii i i - i-v v v iii vi vi -- v L1ME5_3end#LI 538 ACCATGGAGTACTA-TGCAGCAGTTAGAAGCAACGGACTAGATG--TACA 584 chr4ptel1M 104259 GAAAG--GCCTGGAGAGA-CTTACACGAAC-TGATGCTGAGTGAAATGAG 104304 v v --i v vi - v -- - ii vi L1ME5_3end#LI 585 CATAGCAACATGGATGGATCTTAAA--AACATAGTGCTGAGTGAAAAAAG 632 chr4ptel1M 104305 CAGGA 104309 i i L1ME5_3end#LI 633 TAAGA 637 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.36 CpG sites = 94, Kimura (unadjusted) = 34.40 Transitions / transversions = 1.32 (94/71) Gap_init rate = 0.06 (36 / 633), avg. gap size = 1.25 (45 / 36) 1620 27.27 0.36 1.66 chr4ptel1M 103676 104223 (895777) L1ME3G_3end#LINE/L1 7 547 (377) m_b165s551i13 6229 chr4ptel1M 103676 TCCAAAATATATAGAGAATTAACTCTAATTTATAAAAAATCAAGCCATTC 103725 i i i vviv v iv i -- v --v L1ME3G_3end#L 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAA--AAGACA--A 52 chr4ptel1M 103726 TCCAATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGAAG 103775 i v v i v v i L1ME3G_3end#L 53 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chr4ptel1M 103776 AAATTGAAACTATTTCTAGTCATATGAAAAGATGCTCCAAGTCATTATTA 103825 vv iviiivv iv v vv i v L1ME3G_3end#L 103 AAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTA 152 chr4ptel1M 103826 ATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACACCTGT 103875 i i vv i i viv ii L1ME3G_3end#L 153 ATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCAT 202 chr4ptel1M 103876 CAGATTGGCTAAGATGACAGGAAAAAATAATGATGATTGTTGGAGGGGAT 103925 v i vvv iii?vvi ivi? v v i i L1ME3G_3end#L 203 CAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGT 252 chr4ptel1M 103926 GTGGGAAAACTGGGACATTGATTCATTGTTGGTGGAGTTGTGAACGAATC 103975 i v v vi v v i i iiv i ivii v L1ME3G_3end#L 253 GTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTA 302 chr4ptel1M 103976 CAACCATTTTGGAGAGTAGTTTGGAACTATGCTCAAAAAGTTATCAAACT 104025 i ? i i i v v - vvv i -- i v L1ME3G_3end#L 303 CAGCCNTTTTGGAGGGCAATTTGGCAGTAT-CTATTAAAAT--TTAAAAT 349 chr4ptel1M 104026 GTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGATTATATCCCAAAG 104075 i i i vii v ? ?v v i ? L1ME3G_3end#L 350 GCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAG 399 chr4ptel1M 104076 AGATTAT-AAAGAAG-GGAAAGGGACCTGTATGTGCACGAATGTTTGTGG 104123 i vv -iv v v - v v i --? i i v i ii v L1ME3G_3end#L 400 AAATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTCATTG 447 chr4ptel1M 104124 CAGCCCTTTTTGTAGTGGCTAGAAACTGGAAACTGAATGGATGTCCATCA 104173 vi v i i v i i vivv ii L1ME3G_3end#L 448 CAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCA 497 chr4ptel1M 104174 GTTGGAGAATGGCTGAATAAATTGTGGTATATGAAAATTATGGAATATTA 104223 i v i i i i vv v i i L1ME3G_3end#L 498 ATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACTA 547 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.35 CpG sites = 76, Kimura (unadjusted) = 34.93 Transitions / transversions = 1.07 (76/71) Gap_init rate = 0.02 (11 / 547), avg. gap size = 1.00 (11 / 11) 34 2.62 0.00 2.50 chr4ptel1M 104766 104806 (895194) (TAAA)n#Simple_repeat 1 40 (0) c_b165s251i5 6230 chr4ptel1M 104766 TAAATAAAAAAATAAATAAATAAATAAATAAATAAAATAAA 104806 v - (TAAA)n#Simpl 1 TAAATAAATAAATAAATAAATAAATAAATAAAT-AAATAAA 40 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 212 32.62 4.20 5.67 chr4ptel1M 104882 105024 (894976) C L2c_3end#LINE/L2 (6) 472 332 m_b165s601i31 6231 chr4ptel1M 104882 TCAATCAGTCAAACACTAAGCAGGCATCCATTACACTGTCA--TGATGGG 104929 v i- i v viii ii i i ii- i --i v C L2c_3end#LINE 472 TCATTCAA-CAAACATTTATTGAGCGCCTACTATG-TGCCAGGCGCTGGG 425 chr4ptel1M 104930 GATCCGA-GATCTAAACTAAAA---AGTCCTGGCCCTCCAGGACCTTATA 104975 v i - ---i v i ---i iv v v i i C L2c_3end#LINE 424 GATACAAAGAT---GAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACA 378 chr4ptel1M 104976 CTCTGCTTGGGGACCCAACATATTTGTGAAAAGAAATTTACAAGGCAAG 105024 v iv v i ---i v iv? i v v v vi C L2c_3end#LINE 377 GTCTAGTGGAGGA---GACAGACANGTAAACAGACAATTACAATACAAG 332 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.72 CpG sites = 26, Kimura (unadjusted) = 44.77 Transitions / transversions = 1.44 (26/18) Gap_init rate = 0.08 (11 / 142), avg. gap size = 1.27 (14 / 11) 224 20.75 7.59 2.41 chr4ptel1M 104952 105030 (894970) C L2d2_3end#LINE/L2 (92) 463 381 m_b165s601i32 6231 chr4ptel1M 104952 GTCCTGGCCCTCCAGGACCTTATACTCTGCTTGGGGACCCA--ACAT--A 104997 iv v v i v iv vv -- -- C L2d2_3end#LIN 463 GTCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGGAGACAAGACATAAA 414 chr4ptel1M 104998 TTTGTGAAAAG--AAATTTACAAGGCAAGCATTTA 105030 ivi -- - v vi - C L2d2_3end#LIN 413 CACGTGAAAAGTTAAA-TAACAATACAAG-ATTTA 381 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 22.73 CpG sites = 6, Kimura (unadjusted) = 24.34 Transitions / transversions = 0.60 (6/10) Gap_init rate = 0.06 (5 / 78), avg. gap size = 1.60 (8 / 5) 425 26.51 0.00 7.27 chr4ptel1M 105452 105569 (894431) MIR#SINE/MIR 2 111 (151) m_b165s601i33 6232 chr4ptel1M 105452 CAATACATCAAAACAGGCAAGGACACTGGGCCTGGAGTCAGGAGGATCTG 105501 i i v v iii vi ii v vi i - vvii MIR#SINE/MIR 2 CAGTATAGCATAGTGGTTAAGAGCACGGGCTCTGGAGCCAG-ACTGCCTG 50 chr4ptel1M 105502 AGTTCAAATCCTGATTCAGATGCTTAACATTTTCTAGCTGTGTGATCTTG 105551 i i i ii --- ---- i v i MIR#SINE/MIR 51 GGTTCGAATCCCGGCTC---TGC----CACTTACTAGCTGTGTGACCTTG 93 chr4ptel1M 105552 GGCAAGTCACTTAACCCC 105569 i i MIR#SINE/MIR 94 GGCAAGTTACTTAACCTC 111 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.32 CpG sites = 21, Kimura (unadjusted) = 34.24 Transitions / transversions = 2.62 (21/8) Gap_init rate = 0.07 (8 / 117), avg. gap size = 1.00 (8 / 8) 521 17.80 0.00 7.29 chr4ptel1M 105467 105569 (894431) MIRc#SINE/MIR 20 115 (153) m_b165s601i34 6232 chr4ptel1M 105467 GGCAAGGACACTGGGCCTGGAGTCAGGAGGATCTGAGTTCAAATCCTGAT 105516 v ii i i i i i i i i ii MIRc#SINE/MIR 20 GGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGC 69 chr4ptel1M 105517 TCAGATGCTTAACATTTTCTAGCTGTGTGATCTTGGGCAAGTCACTTAAC 105566 --- ---- i v i MIRc#SINE/MIR 70 TC---TGC----CACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAAC 112 chr4ptel1M 105567 CCC 105569 i MIRc#SINE/MIR 113 CTC 115 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 18.60 CpG sites = 15, Kimura (unadjusted) = 21.34 Transitions / transversions = 7.50 (15/2) Gap_init rate = 0.07 (7 / 102), avg. gap size = 1.00 (7 / 7) 233 12.87 1.06 0.00 chr4ptel1M 105577 105952 (894048) (AAGAAC)n#Simple_repeat 1 380 (0) m_b165s252i12 6233 chr4ptel1M 105577 AAGAAAAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAA 105626 v v v v v v v v (AAGAAC)n#Sim 1 AAGAACAAGAACAAGAACAAGAACAAGAACAAGAACAAGAACAAGAACAA 50 chr4ptel1M 105627 GAAGAACAACAACAACAACAACAACAACAACAACAACAACAACAACAAGA 105676 v v v v v v v v (AAGAAC)n#Sim 51 GAACAAGAACAAGAACAAGAACAAGAACAAGAACAAGAACAAGAACAAGA 100 chr4ptel1M 105677 ACAAGAAGAAGAACAAGAAGAACAAGAAGAACAAGAACAAGAACAAGAAC 105726 v v v v (AAGAAC)n#Sim 101 ACAAGAACAAGAACAAGAACAAGAACAAGAACAAGAACAAGAACAAGAAC 150 chr4ptel1M 105727 AAGAAGAACAAGAAGAAGAATAAGAAGAACAAGAACAAGAACAAGAACAA 105776 v v v v v v (AAGAAC)n#Sim 151 AAGAACAAGAACAAGAACAAGAACAAGAACAAGAACAAGAACAAGAACAA 200 chr4ptel1M 105777 GAACAAGAAGAACAAGAAGAAGAATAAGAAGAACAAGAACAAGAACAAGA 105826 v v v v v v (AAGAAC)n#Sim 201 GAACAAGAACAAGAACAAGAACAAGAACAAGAACAAGAACAAGAACAAGA 250 chr4ptel1M 105827 ACAAGAACAAGAAGAACAAGAAGAAGAATAAGAAGAACAAGAACAAGAAC 105876 v v v v v v (AAGAAC)n#Sim 251 ACAAGAACAAGAACAAGAACAAGAACAAGAACAAGAACAAGAACAAGAAC 300 chr4ptel1M 105877 AAGAACAAG---AAGAACAAGAACAAGAACAAGAACAAGAACAAGAAGAA 105923 --- v (AAGAAC)n#Sim 301 AAGAACAAGAACAAGAACAAGAACAAGAACAAGAACAAGAACAAGAACAA 350 chr4ptel1M 105924 CAAGAAGAACAAGAAGAAG-ACGACAACAA 105952 v v v - i v (AAGAAC)n#Sim 351 GAACAAGAACAAGAACAAGAACAAGAACAA 380 Matrix = Unknown Transitions / transversions = 0.02 (1/43) Gap_init rate = 0.01 (2 / 375), avg. gap size = 2.00 (4 / 2) 651 29.06 7.08 2.54 chr4ptel1M 106201 106426 (893574) MIRb#SINE/MIR 1 236 (32) m_b165s601i35 6234 chr4ptel1M 106201 CAAGGGAACATCACAGTGCA-TGGAA----CACTGGGCTAGGAGTCAGGA 106245 ii ii v iii - ---- v vi v iv MIRb#SINE/MIR 1 CAGAGGGGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGAC 50 chr4ptel1M 106246 AGACCTAAATTTAAACTTATTAGACAATTTAA-ACTTATTAGCTATGAGA 106294 iii ii iiiv--- i -- i iv- i i v MIRb#SINE/MIR 51 AGACCTGGGTTCGAATCCC---GGC--TCTGCCACTTACTAGCTGTGTGA 95 chr4ptel1M 106295 CATTGGACAAGTCATTTAGCTTCT----GTCTCTATTTCCCCACCTATGA 106340 v i i i i i ---- i vi i i i i MIRb#SINE/MIR 96 CCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAA 145 chr4ptel1M 106341 AATGGG-ATAAGAATAGC-ACCT----AGGTGGTGGTGAGGATCAAATGA 106384 - v v - ----i v v i MIRb#SINE/MIR 146 AATGGGGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGA 195 chr4ptel1M 106385 GTTCATGTGTGTAAAATGCTCTATATAAATGCCTGCTATATA 106426 v v ii ii ivii i- i vi i MIRb#SINE/MIR 196 GATAATGCATGTAAAGCGCTTAGCAC-AGTGCCTGGCACATA 236 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.64 CpG sites = 46, Kimura (unadjusted) = 39.12 Transitions / transversions = 2.56 (46/18) Gap_init rate = 0.06 (13 / 225), avg. gap size = 1.69 (22 / 13) 658 23.66 10.00 2.80 chr4ptel1M 106214 106413 (893587) MIRc#SINE/MIR 16 229 (39) m_b165s601i36 6234 chr4ptel1M 106214 CAGTGCATGGAACACTGGGCTAGGAGTCAGGAAGACCTAAATTTAAACTT 106263 v vi i i v iii ii iiii MIRc#SINE/MIR 16 CAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCC 65 chr4ptel1M 106264 ATTAGACAATTTAA-ACTTATTAGCTATGAGACATTGGACAAGTCATTTA 106312 v--- i -- i iv- i i v v i i MIRc#SINE/MIR 66 C---GGC--TCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTA 110 chr4ptel1M 106313 GCTTCT----GTCTCTATTTCCCCACCTATGAAAT-GGGATAAGAATA-- 106355 i i ---- i vi i i i i - v -- MIRc#SINE/MIR 111 ACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACC 160 chr4ptel1M 106356 -GC-------ACCT----AGGTGGTGGTGAGGATCAAATGAGTTCATGTG 106393 - ------- ----i v v v v i MIRc#SINE/MIR 161 TGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTA 210 chr4ptel1M 106394 TGTAAAATGCTCTATATAAA 106413 i - v v i MIRc#SINE/MIR 211 TGTGAAA-GCGCTTTGTAAA 229 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.64 CpG sites = 31, Kimura (unadjusted) = 29.48 Transitions / transversions = 2.07 (31/15) Gap_init rate = 0.07 (13 / 199), avg. gap size = 2.00 (26 / 13) 271 29.07 3.49 0.00 chr4ptel1M 106496 106581 (893419) MIR1_Amn#SINE/MIR 78 166 (64) m_b165s601i38 6235 chr4ptel1M 106496 ACATGTTGGCTGTATGATTCTGGGCAAATTCTTTAATCTC-ATGAACCTC 106544 v? ii? ?i iii i ivi ? i -v ?i MIR1_Amn#SINE 78 ACTNGCCNGCTGNGTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTC 127 chr4ptel1M 106545 GG-TTCCTCATCTGTTAAGTGAAAA-ACTGACTTTGATC 106581 i - v i iii - v ivi i MIR1_Amn#SINE 128 AGTTTCCTCATCTGTAAAATGGGGATAATGATACTGACC 166 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.19 CpG sites = 19, Kimura (unadjusted) = 43.19 Transitions / transversions = 3.17 (19/6) Gap_init rate = 0.04 (3 / 85), avg. gap size = 1.00 (3 / 3) 303 27.40 2.74 0.00 chr4ptel1M 106496 106568 (893432) MIRb#SINE/MIR 79 153 (115) m_b165s601i37 6235 chr4ptel1M 106496 ACATGTTGGCTGTATGATTCTGGGCAAATTCTTTAATCTC-ATGAACCTC 106544 v ii i i iii i vi i -v i MIRb#SINE/MIR 79 ACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTC 128 chr4ptel1M 106545 GG-TTCCTCATCTGTTAAGTGAAAA 106568 i - v i iii MIRb#SINE/MIR 129 AGTTTCCTCATCTGTAAAATGGGGA 153 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.88 CpG sites = 16, Kimura (unadjusted) = 36.88 Transitions / transversions = 4.00 (16/4) Gap_init rate = 0.03 (2 / 72), avg. gap size = 1.00 (2 / 2) 212 27.80 7.07 1.92 chr4ptel1M 106597 106695 (893305) L2c_3end#LINE/L2 363 466 (12) m_b165s601i39 6236 chr4ptel1M 106597 TCTCCCACATGAGAGTATGAGCTCCAT-ATGATAG---TC-TGGCTT-TT 106640 iv iv v i v - v ii ---i - v - L2c_3end#LINE 363 TCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATT 412 chr4ptel1M 106641 CCTGTTTGTGCCCCCAGGGCTT-ACACAGGAAGTAGCTACTTGATAAATT 106689 v v ii v i -i v-- vii ii v L2c_3end#LINE 413 CATCTTTGTATCCCCAGCGCCTGGCACAT--AGTAGGCGCTCAATAAATG 460 chr4ptel1M 106690 TTGGTT 106695 v L2c_3end#LINE 461 TTTGTT 466 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.51 CpG sites = 14, Kimura (unadjusted) = 35.27 Transitions / transversions = 1.08 (14/13) Gap_init rate = 0.07 (7 / 98), avg. gap size = 1.29 (9 / 7) 381 22.15 6.06 7.69 chr4ptel1M 107250 107381 (892619) MIRb#SINE/MIR 1 130 (138) m_b165s601i40 6237 chr4ptel1M 107250 CAGAGGGGCAGCTAGCTGGTGCAG-------AGTACCAGCCCTGAAGTCT 107292 -- - ------- i vi ii i v MIRb#SINE/MIR 1 CAGAGGGGCAGC--G-TGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCA 47 chr4ptel1M 107293 GGAGGGCCTGAGTTTAAATCTGGCCTCAGACACTTGACACTTCCTAGCTG 107342 ivi i i ii iv v ------- v v MIRb#SINE/MIR 48 GACAGACCTGGGTTCGAATCCCGGCTC-------TGCCACTTACTAGCTG 90 chr4ptel1M 107343 TGTGACCCTGGACAAGACACTTAACCCCAATT-GCCTCAG 107381 i i vi i vv v- MIRb#SINE/MIR 91 TGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAG 130 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 25.45 CpG sites = 16, Kimura (unadjusted) = 26.70 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.09 (12 / 131), avg. gap size = 1.50 (18 / 12) 393 24.37 0.91 6.73 chr4ptel1M 107272 107381 (892619) MIRc#SINE/MIR 24 127 (141) m_b165s601i41 6237 chr4ptel1M 107272 AGAGTACCAGCCCTGAAGTCTGGAGGGCCTGAGTTTAAATCTGGCCTCAG 107321 i ii v i i v i i i ii i iv v -- MIRc#SINE/MIR 24 AGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTC-- 71 chr4ptel1M 107322 ACACTTGACACTTCCTAGCTGTGTGACCCTGGACAAGACACTTAACCCCA 107371 ----- v v i i v i v MIRc#SINE/MIR 72 -----TGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCT 116 chr4ptel1M 107372 ATT-GCCTCAG 107381 v v- MIRc#SINE/MIR 117 CTGAGCCTCAG 127 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.41 CpG sites = 15, Kimura (unadjusted) = 29.98 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.07 (8 / 109), avg. gap size = 1.00 (8 / 8) 357 30.69 0.99 0.00 chr4ptel1M 107615 107715 (892285) C MIR3#SINE/MIR (18) 190 89 m_b165s601i42 6238 chr4ptel1M 107615 ATATTTGAGCCAGAAGGGACCTAAGAGAACATTGATTGCT-CTCCCTCAT 107663 i iv ii v v iv v v v- i C MIR3#SINE/MIR 190 ATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCAT 141 chr4ptel1M 107664 TTTTCAGGTGACAAAACTAACACCCAGGAGCATTAAGTGATCAGTCCAAA 107713 v i vi i vi iiivi v iiv i i C MIR3#SINE/MIR 140 TTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAG 91 chr4ptel1M 107714 GT 107715 C MIR3#SINE/MIR 90 GT 89 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.63 CpG sites = 18, Kimura (unadjusted) = 40.63 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.01 (1 / 100), avg. gap size = 1.00 (1 / 1) 12 12.84 8.82 0.00 chr4ptel1M 107871 107904 (892096) (CCTGCT)n#Simple_repeat 1 37 (0) m_b165s252i13 6239 chr4ptel1M 107871 CCTGC-CCTG-TCCAGCT-CTGTTCCAACTCCTGCTC 107904 - - v - i vi (CCTGCT)n#Sim 1 CCTGCTCCTGCTCCTGCTCCTGCTCCTGCTCCTGCTC 37 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.09 (3 / 33), avg. gap size = 1.00 (3 / 3) 755 34.49 13.71 1.77 chr4ptel1M 107905 108816 (891184) L2#LINE/L2 2034 3052 (30) m_b165s601i43 6240 chr4ptel1M 107905 CAGTTCTCAGCTTTGATCCTTCTTGACTTGTCTGGAACATCTGACATTA- 107953 i iii v i v i ? v v i i ivi- L2#LINE/L2 2034 CAATTCTCAGTCCTCATCTTACTTGACCTNTCAGCAGCATTTGACACAGT 2083 chr4ptel1M 107954 TAAGCACTTTCTCC-TCCTAAATCA-----TGCCCTGGGGATTTGGGG-G 107996 i v ii - i i v ----- v v v vv iii i-i L2#LINE/L2 2084 TGATCACTCCCTCCTTCTTGAAACACTTTCTTCACTTGGCTTCCAGGACA 2133 chr4ptel1M 107997 CCACAGTTCTCTCTAGGTGT---TCCTATCTGTCTGACC-CTTCCTCTCA 108042 --- iv v --- i vv i - i i L2#LINE/L2 2134 CCACA---CTCTCCTGGTTTTCCTCCTACCTCACTGGCCGCTCCTTCTCA 2180 chr4ptel1M 108043 GTCTCCCTTGCTGTATCATTTTCTATAT-CATGATCTATAACTG-CACAG 108090 i vv v ii - v - vi i v ? vi -iiv L2#LINE/L2 2181 GTCTCCTTTGCTGGTTCCTCCTC-ATCTCCCCGACCTCTNAACGTTGGAG 2229 chr4ptel1M 108091 TAATTCAAGGTTCTGTCCCAGAAC------------------AC-CTCA- 108120 ivii i i v iv i ------------------ - - L2#LINE/L2 2230 TGCCCCAGGGCTCAGTCCTTGGACCTCTTCTCTTCTCTATCTACACTCAC 2279 chr4ptel1M 108121 --GCTA-ATGATATCAGT---TCTCATGG--TTGAATTTTTTACAGCTAG 108162 --v ?-i v vi--- -- i viiv vi -- v L2#LINE/L2 2280 TCCCTNGGTGATCTCATCCAGTCTCATGGCTTTAAATACCATCTA--TAT 2327 chr4ptel1M 108163 GTAGATGATTCCCATATTAACACACTTGACCCTAG-----TCCCCCAGTC 108207 iv i v v i i- iv v ii ----- iiiv L2#LINE/L2 2328 GCTGATGACTCCCAAATTTATAT-CTCCAGCCCGGACCTCTCCCCTGAAC 2376 chr4ptel1M 108208 TCTAGTTCTCTGGACCTCCAACTTTCTTTTGGGCATCCCAAAATTGATG- 108256 i -v - v iv vi vi v i i v vv v - L2#LINE/L2 2377 TCCAG-ACTC-GTATATCCAACTGCCTACTCGACATCTCCACTTGGATGT 2424 chr4ptel1M 108257 --A--AAGTGTGTCAAATTCAATATGTCCCAAACAGAGCTCTTTATTTCT 108302 -- -- i ii v i i i v v i i v i - L2#LINE/L2 2425 CTAATAGGCATCTCAAACTTAACATGTCCAAAACTGAACTCCTGATCT-T 2473 chr4ptel1M 108303 CCCCCACAAGTC-----------CAAGCTTCCCTATTTCCATCAAGAGTA 108341 v ii ----------- iv i i vi ? vi i L2#LINE/L2 2474 CCCCCTCAAACCTGCTCCTCCCGCAGTCTTCCCCATCTCAGTNAATGGCA 2523 chr4ptel1M 108342 TCACCAAGTTTTCAATCACTTGGCTCACAA------GA-TCAACATTG-- 108382 v v vvi i i ii ii vi v ------ - v v -- L2#LINE/L2 2524 ACTCCATCCTTCCAGTTGCTCAGGCCAAAAACCTTGGAGTCATCCTTGAC 2573 chr4ptel1M 108383 ----------CTCTCAGCAACTCAC-TCTCATTCACC-CTAAATATT-TC 108419 ---------- - v i - iv i i -vi vi - L2#LINE/L2 2574 TCCTCTCTTTCTCTCA-CACCCCACATCCAATCCATCAGCAAATCCTGTC 2622 chr4ptel1M 108420 AGCTCTTACCTGACAACATCACACAG-ATGTGCTCCTTTCTCTCCAACTA 108468 i vv i v v i - iv - vi vi vi v v v L2#LINE/L2 2623 GGCTCTACCTTCAAAATAT-ATCCAGAATCCGACCACTTCTCACCACCTC 2671 chr4ptel1M 108469 CACAGCT-TTACCTTGGTTCGGATC--------------CCTGGTCTATC 108503 v i-ii i i iiii -------------- vi ii L2#LINE/L2 2672 CACTGCCACCACCCTGGTCCAAGCCACCATCATCTCTCGCCTGGATTACT 2721 chr4ptel1M 108504 ACAATATATTCCTAAGTGTTGCCTCTGGTTCAAATCTCTCCCCACTATTA 108553 i vvi v v vi i v v vi iv v ?ivi L2#LINE/L2 2722 GCAATAGCCTCCTAACTGGTCTCCCTGCTTCCACCCTTGCCCCCCTNCAG 2771 chr4ptel1M 108554 TCTGAACTTTAGACATTTGCCAAAGTGACTTTCCTAAAACACAGATCTGA 108603 ivv iv v viv i iii ii ii ii v L2#LINE/L2 2772 TCTATTCTCAACACAGCAGCCAGAGTGATCCTTTTAAAACGTAAGTCAGA 2821 chr4ptel1M 108604 CTGTGTTACTCA---G--CAGAA---TCCAGAGGCTCTATTATCTC---C 108642 iii i v--- -- i --- iv - vii --- L2#LINE/L2 2822 TCATGTCACTCCTCTGCTCAAAACCCTCCAATGGCT-TCCCATCTCACTC 2870 chr4ptel1M 108643 AGATTCAAATTCAAAATCCTTTCCCTGGTATCTAAAGCCATTTAGGGTTT 108692 v v vi i v vv iv vi i v vi v i i L2#LINE/L2 2871 AGAGTAAAAGCCAAAGTCCTTACAATGGCCTACAAGGCCCTACATGATCT 2920 chr4ptel1M 108693 GATCCAAATCTATCTTTCCAACCTTAT----TA-----CTCACCTTCATG 108733 i vvvvi i i ii i ---- ----- v i iiv L2#LINE/L2 2921 GGTCCCCCGTTACCTCTCTGACCTCATCTCCTACCACTCTCCCCCTCGCT 2970 chr4ptel1M 108734 TACTCTACAGCCCACTGCAGTGGACTCTTTTATTATTCCTTATACAGAGT 108783 i ii -v vi ii v v -i ii i iiv -v i L2#LINE/L2 2971 CACTCCGC-TCCAGCCACACTGGCCTC-CTTGCTGTTCCTCGAACA-CGC 3017 chr4ptel1M 108784 GATGCATCTACTCTCTGCT----GTCTTTGCAGTGGC 108816 v v --ii i vv ---- i v v L2#LINE/L2 3018 CAGGCA--CGCTCCCGCCTCAGGGCCTTTGCACTTGC 3052 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 46.05 CpG sites = 176, Kimura (unadjusted) = 48.32 Transitions / transversions = 1.32 (176/133) Gap_init rate = 0.06 (55 / 911), avg. gap size = 2.60 (143 / 55) 639 18.68 0.00 2.67 chr4ptel1M 108945 109098 (890902) Charlie4#DNA/hAT-Charlie 3214 3363 (15) m_b165s502i0 6241 chr4ptel1M 108945 TTTCTTTTTAAAATCAATTTTAATAACTATTATTTCAGTATAATTTGATT 108994 v - -- i - i v v Charlie4#DNA/ 3214 TTTGTTTTTAAA-T--ATTTTGATAACTAT-ATTTCAATATAATTGGTTT 3259 chr4ptel1M 108995 CCTTTGTAAACTTATGTGTTATATTTTACTCATTTAAAAATATTATTCTA 109044 v i i v iv i i Charlie4#DNA/ 3260 CCTTTGTAATCCTATGTATTTTATTTTATGCATTTAAAAACATTATTCTG 3309 chr4ptel1M 109045 AGAAGGAGATCCTCGATTTCCTAAGACTGTCAAAGGGGTCCATCAGAGAA 109094 i vi v v ii viv i viv v Charlie4#DNA/ 3310 AGAAGGGGTCCATAGGCTTCACCAGACTGCCAAAGGGGTCCATGGCACAA 3359 chr4ptel1M 109095 AAAA 109098 Charlie4#DNA/ 3360 AAAA 3363 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 21.59 CpG sites = 14, Kimura (unadjusted) = 21.59 Transitions / transversions = 1.00 (14/14) Gap_init rate = 0.03 (4 / 153), avg. gap size = 1.00 (4 / 4) 17 4.94 0.00 0.00 chr4ptel1M 109099 109119 (890881) (A)n#Simple_repeat 1 21 (0) m_b165s252i14 6242 chr4ptel1M 109099 AAAAAAAAAAAAAAAAAACAA 109119 v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAA 21 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 29 26.43 0.00 1.20 chr4ptel1M 109210 109293 (890707) (ATAG)n#Simple_repeat 1 83 (0) m_b165s252i15 6243 chr4ptel1M 109210 ATAGGTAGATGGGTAGATAGAGGGACAGACAGATAGGAAGAGTGGACAGA 109259 i i i vi i i iv - i i (ATAG)n#Simpl 1 ATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGA-TAGATAGA 49 chr4ptel1M 109260 CAGATCGCTAAATCGATAGATAGATAGAGATATA 109293 i v v i v v v (ATAG)n#Simpl 50 TAGATAGATAGATAGATAGATAGATAGATAGATA 83 Matrix = Unknown Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.01 (1 / 83), avg. gap size = 1.00 (1 / 1) 281 35.88 5.34 0.00 chr4ptel1M 109323 109453 (890547) L3#LINE/CR1 3847 3984 (115) m_b165s601i44 6244 chr4ptel1M 109323 GAACAACAGGCAGAAAGCACAGAGA--CAAATTGAGACTTAAGCTAAGGA 109370 v ii ii ivi i -- i vv i i vv L3#LINE/CR1 3847 GACCAATGGGTGGAAGTTACAGGGAGGCAGATTTCGGCTCAATATAAGGA 3896 chr4ptel1M 109371 AATGCTTTCTGATATTTTGAGCAGTTTAGAGGTATAAT----TGCTGCAG 109416 ivi i i v iv v ii i ii iv ---- iv i? L3#LINE/CR1 3897 AGAACTTTCTAACAATCAGAGCTGTCCAAAAATGGAATGGGCTGCCTCGN 3946 chr4ptel1M 109417 GAGCTCATGGGCTCTCAAT-AATGGAGGTCTTTGAACA 109453 v vi i i vi - v v ii i L3#LINE/CR1 3947 GAGGTAGTGAGCTCCCCGTCACTGGAGGTGTTCAAGCA 3984 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 49.16 CpG sites = 30, Kimura (unadjusted) = 52.44 Transitions / transversions = 1.76 (30/17) Gap_init rate = 0.02 (3 / 130), avg. gap size = 2.33 (7 / 3) 30 32.07 0.92 0.00 chr4ptel1M 109463 109571 (890429) (ATAT)n#Simple_repeat 1 110 (0) m_b165s252i17 6245 chr4ptel1M 109463 ATACATATATATGCCTATAAATTTCTGCATATGAAGATATATATGTATCT 109512 i iiv v v v ii iv v i v (ATAT)n#Simpl 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr4ptel1M 109513 GCATAAAAAGCT-TAGATATACATATACATACATATATATGTGTATGTAT 109561 ii v v vv - v i i i i i i (ATAT)n#Simpl 51 ATATATATATATATATATATATATATATATATATATATATATATATATAT 100 chr4ptel1M 109562 GTATATATAT 109571 i (ATAT)n#Simpl 101 ATATATATAT 110 Matrix = Unknown Transitions / transversions = 1.33 (16/12) Gap_init rate = 0.01 (1 / 108), avg. gap size = 1.00 (1 / 1) 21 32.43 3.28 2.44 chr4ptel1M 109459 109580 (890420) (ACATAT)n#Simple_repeat 1 123 (0) m_b165s252i16 6246 chr4ptel1M 109459 ACACATACATAT--ATATGCCTATAAATTTCTGCATATGAAGATATATAT 109506 i -- i v v -- v i iv v i (ACATAT)n#Sim 1 ACATATACATATACATATACATATACA--TATACATATACATATACATAT 48 chr4ptel1M 109507 GTATCTGCATAAAAAGCTTAGATATACATATAC--ATACATATATATGTG 109554 ii v i v v -iv v -- i i i (ACATAT)n#Sim 49 ACATATACATATACA-TATACATATACATATACATATACATATACATATA 97 chr4ptel1M 109555 TATGTATGTATATATATTCACACACA 109580 i i ii i v i i (ACATAT)n#Sim 98 CATATACATATACATATACATATACA 123 Matrix = Unknown Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.04 (5 / 121), avg. gap size = 1.40 (7 / 5) 204 28.97 12.15 0.00 chr4ptel1M 109596 109702 (890298) L2a_3end#LINE/L2 391 510 (7) m_b165s601i45 6240 chr4ptel1M 109596 CCAGTACAATGTAAGTTCCTTGA-GGCAG----TTTAGT---TTTTG-TC 109636 v v i v - ---- v --- - L2a_3end#LINE 391 CCACTAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTCTGTTTTGTTC 440 chr4ptel1M 109637 ATT-C--TATTCTTATCAGCTAAGACAGGGCCTTGCCCAGGGCA-GTATT 109682 i - -- i ii v iv ii v v v vi i - iii L2a_3end#LINE 441 ACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGGCGCT 490 chr4ptel1M 109683 TGATAAATGCCTCTTCAGTG 109702 ii iii v v i L2a_3end#LINE 491 CAATAAATATTTGTTGAATG 510 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.61 CpG sites = 19, Kimura (unadjusted) = 37.84 Transitions / transversions = 1.58 (19/12) Gap_init rate = 0.07 (7 / 106), avg. gap size = 1.86 (13 / 7) 506 35.37 9.68 0.59 chr4ptel1M 110854 111163 (888837) L3#LINE/CR1 3420 3757 (342) m_b165s601i46 6247 chr4ptel1M 110854 GTGAAGA-GATCTCATCATTTTA-TTAAGGGCAGGTTCAAT--GCACCTA 110899 i - i vivvi - i vv i i -- vi v L3#LINE/CR1 3420 GTGAAAAAGACCTAGGGGTTTTAGTTGACCGCAAGCTCAATATGAGCCAA 3469 chr4ptel1M 110900 C-------TATGACAGTCAGACTCACAACTGCAATCTTAGAATTCCTGGA 110942 ------- i i v i i vvvi v v iv v v vi L3#LINE/CR1 3470 CAGTGTGATGTGGCTGCCAAAAAAGCTAATGCAATCTTAGGCTGCATTAA 3519 chr4ptel1M 110943 --GAGGTATCATGTTCATGATTAAGAGGAGG-------------ATTCTT 110977 -- i vi i - ?i - -------------i v i L3#LINE/CR1 3520 TAGAAGTATAGTGTCCA-GANCAAG-GGAGGTAATAGTCCCGCTGTACTC 3567 chr4ptel1M 110978 TTCTCTGGTCAG-CCACATTTAGAGTACTGGCTTCAATTATAAACAATAC 111026 v v - i i i vv i v iii ivi L3#LINE/CR1 3568 TGCGCTGGTCAGACCACATCTGGAGTATTGCGTTCAGTTCTGGGCGCCAC 3617 chr4ptel1M 111027 TATTGAGGAAAGCCATTAATAAGCTAAAA-ATGTCCAGGAAAAAAATACA 111075 vv v i ii v i i i ii i-ii iii i ivv v L3#LINE/CR1 3618 ATTTTAAGAGGGACATTGACAAACTGGAGCGCGTCCAGAGGAGAGCGACC 3667 chr4ptel1M 111076 AGTAGGCCAAAAGGACTTATGTCCACGTCCTTTGGGGT-CTATTAAAG-A 111123 v v vii i v viviv i v v i v- vi i - L3#LINE/CR1 3668 AGGATGGTGAAGGGTCTGGAAACCATGTCATATGAGGAACGGTTGAAGGA 3717 chr4ptel1M 111124 CCCAAAGATGTTTAGTATGAAGAAGAGAAGACTCAAAAGA 111163 v iiii iv i i i i L3#LINE/CR1 3718 ACTGGGGATGTTTAGCCTGGAGAAGAGAAGACTTAGAGGA 3757 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 48.15 CpG sites = 64, Kimura (unadjusted) = 50.12 Transitions / transversions = 1.42 (64/45) Gap_init rate = 0.04 (12 / 309), avg. gap size = 2.67 (32 / 12) 253 30.43 1.45 0.00 chr4ptel1M 111164 111232 (888768) L3#LINE/CR1 3798 3867 (232) m_b165s601i47 6247 chr4ptel1M 111164 TAGAAGCAAGACTGGATTT-TCCTAATTGGCCACAGAGGGCAGAGCCAGA 111212 i vii i i i - i ivv iv i i i L3#LINE/CR1 3798 TGGAAGAGGGATTAGACTTATTCTGTGTGGCTCCAGAGGGCAGAACTAGG 3847 chr4ptel1M 111213 TGCAGTGGGTGGAAGATGCA 111232 vv i v i L3#LINE/CR1 3848 ACCAATGGGTGGAAGTTACA 3867 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.06 CpG sites = 14, Kimura (unadjusted) = 41.06 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.01 (1 / 68), avg. gap size = 1.00 (1 / 1) 394 31.30 5.92 1.70 chr4ptel1M 111406 111574 (888426) MIRc#SINE/MIR 92 267 (1) m_b165s601i48 6248 chr4ptel1M 111406 ACTTTATACAAGTCATTCAGTGTCTTTGACCCTGAGCTTTTTCACCTTCA 111455 i ivi i i iiv i v v i ii i vi MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTA 141 chr4ptel1M 111456 AAATGGAGATGATAGAACTTGGGATAATAACTTTACAAAGATTATTATAA 111505 i i iv i vvv iviv i i - i i i i i MIRc#SINE/MIR 142 AAATGGGGATAATAATACCTGCCCTGCCTACCTCAC-AGGGTTGTTGTGA 190 chr4ptel1M 111506 GG----AATG-GATTGTGTAAATCTCAAAGCACTATAGAAA-TGTAGA-T 111548 ---- - vi -- v v i v iv - i - MIRc#SINE/MIR 191 GGATCAAATGAGATAATGT--ATGTGAAAGCGCTTTGTAAACTGTAAAGT 238 chr4ptel1M 111549 ATTATATAAATG---GGACTTATTGTCAT 111574 ii i --- ?v i i MIRc#SINE/MIR 239 GCTATACAAATGTAAGGNGTTATTATTAT 267 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.09 CpG sites = 35, Kimura (unadjusted) = 43.23 Transitions / transversions = 2.06 (35/17) Gap_init rate = 0.05 (8 / 168), avg. gap size = 1.62 (13 / 8) 468 36.17 5.56 2.70 chr4ptel1M 111661 111984 (888016) L2#LINE/L2 2301 2633 (449) m_b166s601i3 6249 chr4ptel1M 111661 TTTCATG---TTAACTAACATTTATTAAACACCCAAGGATTCTCA----T 111703 i --- v v i --- ii i-i v i i ---- L2#LINE/L2 2301 TCTCATGGCTTTAAATACCATCTAT---ATGCT-GATGACTCCCAAATTT 2346 chr4ptel1M 111704 ATCTTTTCATATTGTCCTAACTTCTCTCCTGACTTCCAGTCTCACATTAC 111753 v i i ---- i vi i i vi v ii vv L2#LINE/L2 2347 ATATCTCCA----GCCCGGACCTCTCCCCTGAACTCCAGACTCGTATATC 2392 chr4ptel1M 111754 CAACTGC----TAGACATTTTGAACTGGATGTCCCATGGATATCTAAAGT 111799 ---- v i iv vi iv i ii v ii L2#LINE/L2 2393 CAACTGCCTACTCGACATCTCCACTTGGATGTCTAATAGGCATCTCAAAC 2442 chr4ptel1M 111800 TTAATTCAACAAACACAGAATTCATCTTCTCTCCTCCTAAACCCTCTCTT 111849 iviiv v v v i v vv ii i ii iv i L2#LINE/L2 2443 TTAACATGTCCAAAACTGAACTCCTGATCTTCCCCCTCAAACCTGCTCCT 2492 chr4ptel1M 111850 CCTACCACCTTTTCAATTCCTGTTGAGAGGA---CCA--CTAACA--TAC 111892 ii vii ii v ii v ?i vi v --- -- vv -- i L2#LINE/L2 2493 CCCGCAGTCTTCCCCATCTCAGTNAATGGCAACTCCATCCTTCCAGTTGC 2542 chr4ptel1M 111893 CCAGGCTCACAATTTTAGGTGTCACCTTCAACTTCTAACTTATACTCATA 111942 i iv v ii - v i i ii i vv viv i L2#LINE/L2 2543 TCAGGCCAAAAACCTT-GGAGTCATCCTTGACTCCTCTCTTTCTCTCACA 2591 chr4ptel1M 111943 CTATATATCCAAACTGCTGCTGAATTCTGTCTTTTCTAGCTT 111984 ivi i v iiiiivii i vvi v L2#LINE/L2 2592 CCCCACATCCAATCCATCAGCAAATCCTGTCGGCTCTACCTT 2633 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 51.03 CpG sites = 71, Kimura (unadjusted) = 52.48 Transitions / transversions = 1.65 (71/43) Gap_init rate = 0.05 (15 / 323), avg. gap size = 1.80 (27 / 15) 498 26.62 2.14 0.70 chr4ptel1M 112828 112967 (887033) MIRb#SINE/MIR 6 147 (121) m_b166s601i4 6250 chr4ptel1M 112828 GAGCAACTAGGTTGCACAGGAGAATGC-CAGGCTT-GAAGTCCAAAAGAC 112875 i i vv - vv i iv - i - i vi v MIRb#SINE/MIR 6 GGGCAGCGTGGT-GCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGAC 54 chr4ptel1M 112876 CTGAGTTCAAATGTGGCCTCAGATACTTACTACCTGTGTGACCCCAGGCA 112925 i i viv v v vi v iii MIRb#SINE/MIR 55 CTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 104 chr4ptel1M 112926 AGTGATTTCA-TTCTATTTGTCTCAGTTTAATCATCTGTAAAA 112967 v i v -i v vv i vv MIRb#SINE/MIR 105 AGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAA 147 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.00 CpG sites = 17, Kimura (unadjusted) = 33.07 Transitions / transversions = 0.85 (17/20) Gap_init rate = 0.03 (4 / 139), avg. gap size = 1.00 (4 / 4) 263 28.23 18.39 3.12 chr4ptel1M 113361 113583 (886417) L2#LINE/L2 1789 2044 (1038) m_b166s601i6 6251 chr4ptel1M 113361 TTTCTTCCATTTT----------AAATGTCTCCTTAGATCCTA--TCCCC 113398 i i ---------- - i v i i -- L2#LINE/L2 1789 TTTCTCCCATCTTTAAAAAACAAAAAT-TCTCCCTTGACCCCACNTCCCC 1837 chr4ptel1M 113399 CTACATTGCTTATTATCCTATCTATTTCTCCTGCCTTCCTCAGCCAAATG 113448 v -- - iiii i i --i v v i iiv v i- L2#LINE/L2 1838 CTCCA--GCT-ACCGCCCCATTT--CTCTGCTCCCCTTTACAGCAAAAC- 1881 chr4ptel1M 113449 TCTTCTAAAAAGATGTCCCTGTTCAATGCCTCCAGATACTCACTTCTCAT 113498 i v i v iv ii iv i iv v v i i L2#LINE/L2 1882 TCCTCGAAAGAGTTGTCTATACTCGCTGTCTCCAATTCCTCTCCTCCCAT 1931 chr4ptel1M 113499 TC--TCTT------------------CTT--GTC------ACTCAACTGA 113520 -- ------------------ -- ------ v i L2#LINE/L2 1932 TCTCTCTTGAACCCACTCCAATCAGGCTTTCGTCCCCACCACTCCACCGA 1981 chr4ptel1M 113521 AATTGGCCTTTCCAAAATTACCAATGATTCTTTA-GTTGCTGATTAAGAT 113569 i vi vi ii i -i ii - i v vvi L2#LINE/L2 1982 AACTGCTCTTGTCAAGGTCACCAATGA-CCTCCACGTTGCTAAATCCAAT 2030 chr4ptel1M 113570 GGCCTTTTCTCAAT 113583 i vv i L2#LINE/L2 2031 GGTCAATTCTCAGT 2044 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.76 CpG sites = 40, Kimura (unadjusted) = 37.16 Transitions / transversions = 1.90 (40/21) Gap_init rate = 0.07 (15 / 222), avg. gap size = 3.27 (49 / 15) 13 16.24 0.00 0.00 chr4ptel1M 113775 113802 (886198) (TGGT)n#Simple_repeat 1 28 (0) m_b166s252i0 6252 chr4ptel1M 113775 TGGTTGGTTGTTTGGTTAGCTGATTGGT 113802 v i i i (TGGT)n#Simpl 1 TGGTTGGTTGGTTGGTTGGTTGGTTGGT 28 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 12 9.24 0.00 4.17 chr4ptel1M 114195 114219 (885781) (TCCC)n#Simple_repeat 1 24 (0) m_b166s252i1 6253 chr4ptel1M 114195 TCCCTCCCACCCTCCACCCCCTCCC 114219 v - i (TCCC)n#Simpl 1 TCCCTCCCTCCCTCC-CTCCCTCCC 24 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 15 0.00 0.00 0.00 chr4ptel1M 114238 114254 (885746) (TA)n#Simple_repeat 1 17 (0) m_b166s252i2 6254 chr4ptel1M 114238 TATATATATATATATAT 114254 (TA)n#Simple_ 1 TATATATATATATATAT 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 285 32.47 0.00 0.00 chr4ptel1M 116376 116452 (883548) MIR3#SINE/MIR 105 181 (27) m_b166s601i7 6255 chr4ptel1M 116376 TTCCCTCCCCTAGGCATCAGTTTCCTTGAGTGTGAAATAAAGGTGCTGGA 116425 v ii i i v iivv i i i v i MIR3#SINE/MIR 105 TTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGA 154 chr4ptel1M 116426 TAAGGTGACTTCTAAAGTGTGTCCCAG 116452 iv i ii i viv i MIR3#SINE/MIR 155 CTAGATGATCTCTAAGGTCCCTTCCAG 181 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.25 CpG sites = 17, Kimura (unadjusted) = 45.25 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.00 (0 / 76), avg. gap size = 0.0 (0 / 0) 205 38.82 0.00 0.00 chr4ptel1M 116482 116566 (883434) MIR3#SINE/MIR 98 182 (26) m_b166s601i8 6256 chr4ptel1M 116482 AAGGGACTTCAGTCCTCAGGACCTTAATTCTGAAAGCTAGATAATGAGAG 116531 vv vii v i i i iivvv v iv v i MIR3#SINE/MIR 98 AAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGG 147 chr4ptel1M 116532 GATTACATGTGATGGCCTCTGAGCTCCTTCCTGGC 116566 i iv ivv ii i v i i ii MIR3#SINE/MIR 148 GGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGC 182 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 57.30 CpG sites = 19, Kimura (unadjusted) = 57.30 Transitions / transversions = 1.36 (19/14) Gap_init rate = 0.00 (0 / 84), avg. gap size = 0.0 (0 / 0) 247 29.51 21.31 0.00 chr4ptel1M 116609 116730 (883270) C MIRb#SINE/MIR (103) 165 18 m_b166s601i9 6257 chr4ptel1M 116609 TAGGCATTA--ATCTT-ATTTGATCAGCAAAGACATTGAGATTTAGAAAT 116655 i -- ii- v iviiii i v i ii i i v C MIRb#SINE/MIR 165 TAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAG 116 chr4ptel1M 116656 GATAA--AATTTACCCATATTCATGTATCGAATAAGT------------A 116691 v -- i i viv iii v v i ------------ C MIRb#SINE/MIR 115 GTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGA 66 chr4ptel1M 116692 TTTGAAC-----TCTGCCTGACTCCAAAGC----GCCCTCCCCTCTGC 116730 i ----- i ---- i ii v C MIRb#SINE/MIR 65 TTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGC 18 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.48 CpG sites = 26, Kimura (unadjusted) = 39.96 Transitions / transversions = 2.60 (26/10) Gap_init rate = 0.05 (6 / 121), avg. gap size = 4.33 (26 / 6) 19 10.01 0.00 0.00 chr4ptel1M 117945 117976 (882024) (TCCATA)n#Simple_repeat 1 32 (0) m_b166s252i3 6258 chr4ptel1M 117945 TCCATATCTTTATCCATATCCATATCCTTATC 117976 iv v (TCCATA)n#Sim 1 TCCATATCCATATCCATATCCATATCCATATC 32 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 265 29.82 7.33 3.87 chr4ptel1M 120574 120723 (879277) C MIR3#SINE/MIR (18) 190 36 m_b166s601i10 6259 chr4ptel1M 120574 ATGTCCAGGAACGGAAATGAGCTTGGAAGTCACTGAGTCCACTCCACTTC 120623 - iivi iv v i ii iiv vi v iv C MIR3#SINE/MIR 190 ATGTC-AGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCA 142 chr4ptel1M 120624 TTTTAACGGATAAGGAAA-TG-GGAACAGGGAGG----ATGCTCCACTCC 120667 - i i - - vv i ----i viiii i v C MIR3#SINE/MIR 141 TTTT-ACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCA 93 chr4ptel1M 120668 TGGTAACTCA---AG-TAGTATCAGAGTTGGGACATGACTGAACCC-GGT 120712 v v v --- - iv ii - i--- - C MIR3#SINE/MIR 92 AGGTCACACAGCNAGTTAGTGGCAGAGCCGGGAC-TA---GAACCCAGGT 47 chr4ptel1M 120713 CATCTATCTCC 120723 vi iv C MIR3#SINE/MIR 46 CTCCTGACTCC 36 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.16 CpG sites = 26, Kimura (unadjusted) = 39.35 Transitions / transversions = 1.53 (26/17) Gap_init rate = 0.08 (12 / 149), avg. gap size = 1.42 (17 / 12) 218 27.28 11.57 3.05 chr4ptel1M 120620 120740 (879260) C MIR#SINE/MIR (117) 145 15 m_b166s601i11 6259 chr4ptel1M 120620 CTTCTTTTAACGGATAAGGAAA-TG-GGAACAGGGAGGATGCTCCACT-- 120665 ii v v i i - - v i v ivviv -- C MIR#SINE/MIR 145 CCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTG 96 chr4ptel1M 120666 CCT--GGTAACTCA---AGT-AGTATCAGAGTTGGGACATGACTGAACCC 120709 i-- v v --- - iv ii i----ii C MIR#SINE/MIR 95 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGAT----TCGAACCC 50 chr4ptel1M 120710 GGTCA-TCTATCTCCAGAGTCAGCA---TTAACCA 120740 i v - iv i v ii--- C MIR#SINE/MIR 49 AGGCAGTCTGGCTCCAGAGCCCGTGCTCTTAACCA 15 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.25 CpG sites = 19, Kimura (unadjusted) = 34.91 Transitions / transversions = 1.46 (19/13) Gap_init rate = 0.10 (12 / 120), avg. gap size = 1.50 (18 / 12) 269 27.02 6.35 3.08 chr4ptel1M 120733 120858 (879142) L2d2_3end#LINE/L2 326 455 (100) m_b166s601i12 6260 chr4ptel1M 120733 ATTAACCATGT-CTTCCCCATGACACCTTTTTGGTTGCTTTCCTGAACAA 120781 i - v iii i i ivi i v i vi L2d2_3end#LIN 326 ATTAATCATGTACTGCCTTGTGACATCTCTTCTATTGTTGTCTTGAACTG 375 chr4ptel1M 120782 TTGTTCAACTCATGTATAATTCTGTTTAA---TTGATAGTGTT--TGTTT 120826 i i v v vi --i --- v i- -- i L2d2_3end#LIN 376 TTATTTAAATCTTGTATTGTT--ATTTAACTTTTCAC-GTGTTTATGTCT 422 chr4ptel1M 120827 TATTTCTCT-ACTGTGAGTG-AAGTTCTTTGAGG 120858 i i i i- i- v - i i L2d2_3end#LIN 423 TGTCTCCCCAACTA-GATTGTAAGCTCCTTGAGG 455 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.11 CpG sites = 24, Kimura (unadjusted) = 35.47 Transitions / transversions = 2.67 (24/9) Gap_init rate = 0.07 (9 / 125), avg. gap size = 1.33 (12 / 9) 267 32.73 6.14 0.83 chr4ptel1M 120984 121097 (878903) L2a_3end#LINE/L2 386 505 (12) m_b166s601i13 6261 chr4ptel1M 120984 TCTCCTGGTTAGATGGTACATTTC-TGTAGAGTAGTGACTCTC-TTTGTT 121031 i ivii vv vii i - - i i v i i- i L2a_3end#LINE 386 TCCCCCCACTAGAATGTAAGCTCCATG-AGGGCAGGGACTTTTGTCTGTT 434 chr4ptel1M 121032 TTTATTAAT--TATGTCCCCAGGGTTTAATAC---GCCTGGTACATAATA 121076 vv i v -- i i v ii iv --- i i L2a_3end#LINE 435 TTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACATAGTA 484 chr4ptel1M 121077 GGCATGTAATAAATCCTTATT 121097 iivi vi i L2a_3end#LINE 485 GGCGCTCAATAAATATTTGTT 505 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.01 CpG sites = 25, Kimura (unadjusted) = 45.75 Transitions / transversions = 2.08 (25/12) Gap_init rate = 0.04 (5 / 113), avg. gap size = 1.60 (8 / 5) 632 24.01 7.28 0.91 chr4ptel1M 121321 121526 (878474) MER121#DNA/hAT 100 318 (83) m_b166s502i0 6262 chr4ptel1M 121321 AGCACTTTTCTC-TTAATGTTTATGCCCTTGTGTATTTTAGGGGAAATAG 121369 i - v vi v i i vv MER121#DNA/hA 100 AGCACTTTTCCCCTTAATTTTTAAACCCATGTGTATTTCAAGGGAAATTT 149 chr4ptel1M 121370 ACTCCACATGGCCTTGATTCATTTACACTTAAATCATTAAAATACTGTTT 121419 v i viii v i ii MER121#DNA/hA 150 AATCCATATGTTTCTGATTCATTTACACTTAACTCATCAAAATGTTGTTT 199 chr4ptel1M 121420 TATAACAGCTGTCTCAATGTCT--GAGGCAGTGTTAGTTCTTTTTAT--- 121464 i v i - ii i-- i vv ? v iii ? --- MER121#DNA/hA 200 TGTAAGAGCTAT-TTGATGTCCAAGAAGCCTTNTGAGCCTTTTTNATAAG 248 chr4ptel1M 121465 ---------GTCTTTCTCCTTAAAAACAAGAAGACATTTACTGCCAGGAT 121505 --------- i i i i v iiv vi i v MER121#DNA/hA 249 CTTTTCTAAGCCTTTTTCCTTAGAAACAGGAAGTCGCGTTTTGCCAAGAG 298 chr4ptel1M 121506 TAAATGATATTCAAACACTAA 121526 i - i i v i MER121#DNA/hA 299 TAAACGA-ACTCGAACCCCAA 318 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 27.34 CpG sites = 32, Kimura (unadjusted) = 30.23 Transitions / transversions = 1.88 (32/17) Gap_init rate = 0.03 (6 / 205), avg. gap size = 2.83 (17 / 6) 376 20.00 1.25 0.00 chr4ptel1M 121838 121917 (878083) MIR3#SINE/MIR 122 202 (6) m_b166s601i14 6263 chr4ptel1M 121838 CAGTGACTTCATCTGTAAAATGAGGGGGTTGGACTAGCTGGCCTCTGATG 121887 vv i v ii i v MIR3#SINE/MIR 122 CAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGG 171 chr4ptel1M 121888 TCGCTTCCAGAAGTGA-GTCCTATGACCCTA 121917 v vvv -i i ii MIR3#SINE/MIR 172 TCCCTTCCAGCTCTGACATTCTATGATTCTA 202 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 23.41 CpG sites = 8, Kimura (unadjusted) = 23.41 Transitions / transversions = 1.00 (8/8) Gap_init rate = 0.01 (1 / 79), avg. gap size = 1.00 (1 / 1) 475 20.82 5.79 0.79 chr4ptel1M 122922 123042 (876958) C MIRc#SINE/MIR (18) 250 124 m_b166s601i15 6264 chr4ptel1M 122922 CATTTGTATGGCATCTCAAGGTTTACAAAGTACCTT-GCAAATATGATCT 122970 i ii i vi ii i -i v i v C MIRc#SINE/MIR 250 CATTTGTATAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATCT 201 chr4ptel1M 122971 CATTTGATCCTCCCCATCAATACTG----GTAGG-ACGGT-GCTGTTATT 123014 v v - iv ---- - v i- v i C MIRc#SINE/MIR 200 CATTTGATCCTCACAA-CAACCCTGTGAGGTAGGCAGGGCAGGTATTATT 152 chr4ptel1M 123015 ATGCTCATAATACAGATGAGGAAACTGA 123042 v i vv C MIRc#SINE/MIR 151 ATCCCCATTTTACAGATGAGGAAACTGA 124 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 23.50 CpG sites = 14, Kimura (unadjusted) = 24.72 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.04 (5 / 120), avg. gap size = 1.60 (8 / 5) 378 16.85 3.37 0.00 chr4ptel1M 123390 123478 (876522) Charlie4a#DNA/hAT-Charlie 356 447 (61) m_b166s502i1 6265 chr4ptel1M 123390 TATTTT-ATAATGGT--TTCAATAGAATTGATTTCCTTTGTAACCCTACC 123436 - iv -- v i i iv Charlie4a#DNA 356 TATTTTGATAACTGTATTTCAATATAATTGGTTTCCTTTGTAATCCTATG 405 chr4ptel1M 123437 TATTTTAATGGACACATTTAGAAATATTTTTCTGAGAAGGGG 123478 v vv ii i i v Charlie4a#DNA 406 TATTTTATTTTATGCATTTAAAAACATTATTCTGAGAAGGGG 447 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 19.23 CpG sites = 8, Kimura (unadjusted) = 19.23 Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.02 (2 / 88), avg. gap size = 1.50 (3 / 2) 384 17.11 0.00 0.00 chr4ptel1M 123403 123478 (876522) Charlie4#DNA/hAT-Charlie 3242 3317 (61) m_b166s502i2 6265 chr4ptel1M 123403 TTTCAATAGAATTGATTTCCTTTGTAACCCTACCTATTTTAATGGACACA 123452 v i i iv v vv ii Charlie4#DNA/ 3242 TTTCAATATAATTGGTTTCCTTTGTAATCCTATGTATTTTATTTTATGCA 3291 chr4ptel1M 123453 TTTAGAAATATTTTTCTGAGAAGGGG 123478 i i v Charlie4#DNA/ 3292 TTTAAAAACATTATTCTGAGAAGGGG 3317 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 19.57 CpG sites = 7, Kimura (unadjusted) = 19.57 Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.00 (0 / 75), avg. gap size = 0.0 (0 / 0) 274 29.63 7.44 2.36 chr4ptel1M 126034 126154 (873846) MIR1_Amn#SINE/MIR 3 129 (101) m_b166s601i16 6266 chr4ptel1M 126034 GAGGAGCAGCTGGTGGCGCAGTGGATACAGCACCAGCCCTGGAGTCAGGA 126083 i ii i-- ivi v ii v iv v i MIR1_Amn#SINE 3 GGGAGGCAGT--GTGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGA 50 chr4ptel1M 126084 AAGCCCGAATTCACTTAACACTTCT--------TTAGCTGTGTAACTCTG 126125 i - i ii ?v? vv ivi --------ii? ? i ii MIR1_Amn#SINE 51 GA-CCTGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTG 99 chr4ptel1M 126126 GGCTAGTCACTTAACC-CCAAATGCCTCAG 126154 v ? - ivvi? MIR1_Amn#SINE 100 GGCAAGTCACTTNACCTCTCTGNGCCTCAG 129 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.28 CpG sites = 23, Kimura (unadjusted) = 42.50 Transitions / transversions = 1.92 (23/12) Gap_init rate = 0.04 (5 / 120), avg. gap size = 2.40 (12 / 5) 381 27.33 7.41 1.75 chr4ptel1M 126036 126143 (873857) MIRc#SINE/MIR 2 115 (153) m_b166s601i17 6266 chr4ptel1M 126036 GGAGCAGCTGGTGGCGCAGTGGATACAGCACCAGCCCTGGAGTCAGGAAA 126085 ii i-- i v v ii v i i MIRc#SINE/MIR 2 GAGGCAGT--GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAG 49 chr4ptel1M 126086 GCCCGAATTCA---CTTAACACTTCT-----TTAGCTGTGTAACTCTGGG 126127 i i ii i--- iiii v v i-----i i ii MIRc#SINE/MIR 50 ACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGG 99 chr4ptel1M 126128 CTAGTCACTTAACCCC 126143 v i MIRc#SINE/MIR 100 CAAGTCACTTAACCTC 115 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.33 CpG sites = 23, Kimura (unadjusted) = 36.73 Transitions / transversions = 3.83 (23/6) Gap_init rate = 0.04 (4 / 107), avg. gap size = 2.50 (10 / 4) 268 27.80 2.66 4.32 chr4ptel1M 126177 126364 (873636) L1P1_orf2#LINE/L1 2372 2556 (738) m_b166s551i0 6267 chr4ptel1M 126177 AAATAAAATA--ATTTAAATAATTGGAGAAATATTAAATGACCATGGGTA 126224 v -- vi i v ii i vv vi L1P1_orf2#LIN 2372 AAATAAAAGAGGATACAAACAAATGGAAGAACATTCCATGCTCATGGGTA 2421 chr4ptel1M 126225 AGCAAAGCCAATATGATAAAAATGACAATTTTACCTAATGTAATTAATAT 126274 i v i ii vi i i v vi i i v v v L1P1_orf2#LIN 2422 GGAAGAATCAATATCGTGAAAATGGCCATACTGCCCAAGGTAATTTATAG 2471 chr4ptel1M 126275 ATTCAATTCCTTCCTTCCAAATTAAATTACCAAAAAAATGTATTTTACTA 126324 v v -- -- i ii -- vi iv vi i vi L1P1_orf2#LIN 2472 ATTCAATGCCATCC--CC--ATCAAGCTACC--AATGACTTTCTTCACAG 2515 chr4ptel1M 126325 AATTTGAAAAAATAAC---GAAATTCATTTGGAGGAACAAAAA 126364 v iv ---i i v -- v L1P1_orf2#LIN 2516 AATTGGAAAAAACTACTTTAAAGTTCATATGGA--ACCAAAAA 2556 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.42 CpG sites = 27, Kimura (unadjusted) = 35.29 Transitions / transversions = 1.17 (27/23) Gap_init rate = 0.05 (10 / 187), avg. gap size = 1.30 (13 / 10) 304 29.43 13.27 0.79 chr4ptel1M 127496 127608 (872392) MIRc#SINE/MIR 24 150 (118) m_b166s601i18 6268 chr4ptel1M 127496 AGATTATAGTACTTG-AGTCAGAAA-ATCTGGACTCTAATC-----TTTA 127538 vi iv v - i - i ii v i ----- i i MIRc#SINE/MIR 24 AGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTG 73 chr4ptel1M 127539 CCACTT--------TGTGATCTGGAAAGAAATCATTTTACCTCTTTGGAC 127580 -------- i v iiv- i i v i ii MIRc#SINE/MIR 74 CCACTTACTAGCTGTGTGACCTTGGGC-AAGTCACTTAACCTCTCTGAGC 122 chr4ptel1M 127581 CCCAGTAATCCCATTTGTGAAATGAAGA 127608 i vvi i i i ii MIRc#SINE/MIR 123 CTCAGTTTCCTCATCTGTAAAATGGGGA 150 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.94 CpG sites = 24, Kimura (unadjusted) = 39.94 Transitions / transversions = 2.67 (24/9) Gap_init rate = 0.04 (5 / 112), avg. gap size = 3.20 (16 / 5) 490 30.20 9.29 0.66 chr4ptel1M 127510 127649 (872351) MIR3#SINE/MIR 37 188 (20) m_b166s601i19 6268 chr4ptel1M 127510 GAGTCAGAAAATCTGGACTCTAATC-----TTTACCACT--------TTG 127546 i i i ii i ----- i i --------v MIR3#SINE/MIR 37 GAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTG 86 chr4ptel1M 127547 TGATCTGGAAAGAAATCATTTTACCTCTTTGGACCCCAGTAATCCCATTT 127596 i v iiv- i i i i i i vvi i i MIR3#SINE/MIR 87 TGACCTTGGGC-AAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCT 135 chr4ptel1M 127597 GTGAAATGAAGAGCTCAAGCTAGATGACTTCTTTAGTCTCTTTCATCTCT 127646 i i i v iiii ii vvi i i v MIR3#SINE/MIR 136 GTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCT 185 chr4ptel1M 127647 AAC 127649 i MIR3#SINE/MIR 186 GAC 188 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.25 CpG sites = 33, Kimura (unadjusted) = 42.25 Transitions / transversions = 3.67 (33/9) Gap_init rate = 0.02 (3 / 139), avg. gap size = 4.67 (14 / 3) 12 23.82 3.92 1.92 chr4ptel1M 127751 127801 (872199) (TAATAAA)n#Simple_repeat 1 52 (0) m_b166s252i4 6269 chr4ptel1M 127751 TAGTAAAT-AGACAAAATAAATAATAAGATACTTCAT-AGGAATCATAAA 127798 i - v v v - v vv - vi v (TAATAAA)n#Si 1 TAATAAATAATAAATAATAAATAATAA-ATAATAAATAATAAATAATAAA 49 chr4ptel1M 127799 TAA 127801 (TAATAAA)n#Si 50 TAA 52 Matrix = Unknown Transitions / transversions = 0.25 (2/8) Gap_init rate = 0.06 (3 / 50), avg. gap size = 1.00 (3 / 3) 220 22.22 0.00 0.00 chr4ptel1M 129251 129295 (870705) C L3b_3end#LINE/CR1 (19) 1187 1143 m_b166s601i20 6270 chr4ptel1M 129251 AGTATTGGAAGGGACCTCAGAAGCCAGCTAGCCCAGTTCTCCTCC 129295 v i i i v i vii ? i C L3b_3end#LINE 1187 AGAATTGGAAAGGACCTCAGAGGTCATCTAGTCCATCCCTNCCCC 1143 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.08 CpG sites = 7, Kimura (unadjusted) = 28.08 Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 277 26.91 22.41 0.71 chr4ptel1M 129363 129478 (870522) C MIRb#SINE/MIR (116) 152 12 m_b166s601i21 6271 chr4ptel1M 129363 CCTCACTTTTCAGACAGGAACAATTAAGGCTTTTGAAGGATAAGACATTT 129412 i i v iii i - i i ivvii v vv i C MIRb#SINE/MIR 152 CCCCATTTTACAGATGAGGA-AACTGAGGCTCAGAGAGGTTAAGTAACTT 104 chr4ptel1M 129413 GCCCAGCCTCACACTGGGAGTGAATGGC---------------------- 129440 ivv v vv i i ---------------------- C MIRb#SINE/MIR 103 GCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGG 54 chr4ptel1M 129441 ----TCTGACTCCAAACCCAGTCCTCTTTCAACTGCACCATG 129478 ---- v v v v i C MIRb#SINE/MIR 53 TCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCACCACG 12 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.52 CpG sites = 16, Kimura (unadjusted) = 33.83 Transitions / transversions = 1.07 (16/15) Gap_init rate = 0.03 (3 / 115), avg. gap size = 9.00 (27 / 3) 16 0.00 0.00 0.00 chr4ptel1M 129499 129515 (870485) (A)n#Simple_repeat 1 17 (0) m_b166s252i5 6272 chr4ptel1M 129499 AAAAAAAAAAAAAAAAA 129515 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 217 27.08 0.00 0.00 chr4ptel1M 129750 129797 (870203) C L2d_3end#LINE/L2 (4) 512 465 m_b166s601i22 6273 chr4ptel1M 129750 TCATTAAACTAACAAGCATTTATTGGGTACTTGCAATGGGCTTAGCAC 129797 v v ii i i ii i i v v i C L2d_3end#LINE 512 TCAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCAC 465 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.51 CpG sites = 9, Kimura (unadjusted) = 35.21 Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 632 20.39 2.58 1.92 chr4ptel1M 129801 129955 (870045) C MIR#SINE/MIR (27) 235 80 m_b166s601i23 6274 chr4ptel1M 129801 TACTCTGTGCC-TGCACTGTGCTTACCACTTTTACACATATGCCTTCATC 129849 v -v v v v i - ii vvvi i C MIR#SINE/MIR 235 TACTATGTGCCAGGCACTGTTCTAAGCGCTTT-ACATGTATTAACTCATT 187 chr4ptel1M 129850 CTACCATCACAACAACCCTGGGAGGGAGGTACTGTTATTATCTCCATTTT 129899 iv i v iv v i i C MIR#SINE/MIR 186 TAATCCTCACAACAACCCTATGAGGTAGGTACTATTATTATCCCCATTTT 137 chr4ptel1M 129900 ACGGTTGAGAGAACTAAGGGGAACA-AGAG--TAAGTACCTTGCCCAAGG 129946 i v ii i -- v - -- v C MIR#SINE/MIR 136 ACAGATGAGGAAACTGA--GGCACAGAGAGGTTAAGTAACTTGCCCAAGG 89 chr4ptel1M 129947 TCATCCAGC 129955 iv C MIR#SINE/MIR 88 TCACACAGC 80 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 23.09 CpG sites = 15, Kimura (unadjusted) = 23.93 Transitions / transversions = 0.94 (15/16) Gap_init rate = 0.04 (6 / 154), avg. gap size = 1.17 (7 / 6) 16 16.55 4.88 0.00 chr4ptel1M 130105 130145 (869855) (ATAT)n#Simple_repeat 1 43 (0) m_b166s252i6 6275 chr4ptel1M 130105 ATGTATGTATATATA-ATCTATATGTATATA-ATTCATATATA 130145 i i - v i - vi (ATAT)n#Simpl 1 ATATATATATATATATATATATATATATATATATATATATATA 43 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 662 25.97 10.50 0.00 chr4ptel1M 130147 130327 (869673) C MIRc#SINE/MIR (54) 214 15 m_b166s601i24 6276 chr4ptel1M 130147 CACATATAATATTTCATTTGATCCTCACA-TAACCTTATGAGGTAAG--- 130192 i v i -i i i i --- C MIRc#SINE/MIR 214 CACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAG 165 chr4ptel1M 130193 -AC---TATT-TTACCCTCATTATACAGATGTGAAAACTGAGGTTTAGA- 130236 -i --- - i i v v i i i - C MIRc#SINE/MIR 164 GGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAG 115 chr4ptel1M 130237 --------TGTCTTACCCAGAGTCAGATAGCTAGCTAGTAAGTGGGGCAG 130278 -------- v i ii v i iv iivv i v i C MIRc#SINE/MIR 114 AGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGG 65 chr4ptel1M 130279 GA-TGAAAGTCAGTTCTCTCCAACTCCAAGTTCAATACTTTAGCCATTAC 130327 - vi vi v ii ii i i i i vv i i C MIRc#SINE/MIR 64 GACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGC 15 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.62 CpG sites = 33, Kimura (unadjusted) = 33.37 Transitions / transversions = 2.36 (33/14) Gap_init rate = 0.04 (7 / 180), avg. gap size = 2.71 (19 / 7) 242 24.32 7.38 5.65 chr4ptel1M 130634 130755 (869245) Charlie4#DNA/hAT-Charlie 3253 3376 (2) m_b166s502i3 6277 chr4ptel1M 130634 TTGATTATTCTCTGTAATCCAATGTGCTT-ATTCTA-------AAACACG 130675 i - i i v ii - i ------- v i Charlie4#DNA/ 3253 TTGGTT-TCCTTTGTAATCCTATGTATTTTATTTTATGCATTTAAAAACA 3301 chr4ptel1M 130676 ATTTCTTCTAA-AAGAGCTGCAGTCATAGGCTGCTTCAGACTGCCAAGGG 130724 -- v i - i v ----i v vi i Charlie4#DNA/ 3302 --TTATTCTGAGAAGGGGT----CCATAGGCTTCACCAGACTGCCAAAGG 3345 chr4ptel1M 130725 GCTCAAGGATACCAACAAGGCTGAGAAGCCC 130755 v v v ii v v i i v Charlie4#DNA/ 3346 GGTCCATGGCACAAAAAAGGTTAAGAACCCC 3376 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 29.96 CpG sites = 16, Kimura (unadjusted) = 29.96 Transitions / transversions = 1.33 (16/12) Gap_init rate = 0.08 (10 / 121), avg. gap size = 1.60 (16 / 10) 420 13.02 12.77 1.92 chr4ptel1M 130930 131023 (868977) MIR3#SINE/MIR 95 198 (10) m_b166s601i25 6278 chr4ptel1M 130930 GGCAAGACCTACTTCACCCCATTGGGTCTCAGTTTCCTCATCTGC-AAAT 130978 v -- i vi i i- MIR3#SINE/MIR 95 GGCAAGTC--ACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAAT 142 chr4ptel1M 130979 GATGGAGTTGGA---------CTCTAAGGTCTCTTCTTCCTC-GA-ATTC 131017 v i --------- i ivv - - MIR3#SINE/MIR 143 GAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTC 192 chr4ptel1M 131018 TATGAT 131023 MIR3#SINE/MIR 193 TATGAT 198 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 14.44 CpG sites = 7, Kimura (unadjusted) = 14.44 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.06 (6 / 93), avg. gap size = 2.33 (14 / 6) 355 25.00 3.26 0.00 chr4ptel1M 131023 131114 (868886) MIR3#SINE/MIR 111 205 (3) m_b166s601i26 6279 chr4ptel1M 131023 TCTC-AAACCTCAGTTTCAATATCTGTAACATGATAGAGTTGGACTGCCT 131071 -iii vvi v vi i ivv MIR3#SINE/MIR 111 TCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGAT 160 chr4ptel1M 131072 GAGCCAGAAGGCCCCTTCCAGCTCTAAA--TCTATGACCCAATGA 131114 v ivv i i v-- ii v MIR3#SINE/MIR 161 GATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTATGA 205 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.77 CpG sites = 12, Kimura (unadjusted) = 30.77 Transitions / transversions = 1.09 (12/11) Gap_init rate = 0.02 (2 / 91), avg. gap size = 1.50 (3 / 2) 326 23.41 0.00 1.06 chr4ptel1M 133350 133444 (866556) Charlie4#DNA/hAT-Charlie 46 139 (3239) m_b166s502i4 6280 chr4ptel1M 133350 GACAGATTTCAGGATGTCTGTGAACTTGAATGGGAAAATAAATATACCTT 133399 i v iv i i - v i i Charlie4#DNA/ 46 GATAGAATTCAGGGGGTCCGTGAACTTGGATGGGAAAA-AATTACATCTT 94 chr4ptel1M 133400 TTTTTTGTATCCCTTGTAAGTGAAATTTGGCATTTACTTCCGTTA 133444 v vvv vv i v v i v vi Charlie4#DNA/ 95 TATTTTCACTAACCTCTAACTGAAATTTAGCATTTCCTTCAATTA 139 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 26.69 CpG sites = 9, Kimura (unadjusted) = 28.10 Transitions / transversions = 0.69 (9/13) Gap_init rate = 0.01 (1 / 94), avg. gap size = 1.00 (1 / 1) 199 30.00 1.67 0.00 chr4ptel1M 133537 133596 (866404) C MIRc#SINE/MIR (120) 148 88 m_b166s601i27 6281 chr4ptel1M 133537 CCCATTTTAGAAAAAGGGAGATTGAACCTCAGTG-CATTGAGTGATTTGA 133585 v i vii i i iv v -vi i i v C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr4ptel1M 133586 CATGGGTCACA 133596 vvi C MIRc#SINE/MIR 98 CCAAGGTCACA 88 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.18 CpG sites = 10, Kimura (unadjusted) = 39.18 Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.02 (1 / 59), avg. gap size = 1.00 (1 / 1) 25 0.00 0.00 0.00 chr4ptel1M 133643 133669 (866331) (A)n#Simple_repeat 1 27 (0) m_b166s252i7 6282 chr4ptel1M 133643 AAAAAAAAAAAAAAAAAAAAAAAAAAA 133669 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAA 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 17 4.35 0.00 0.00 chr4ptel1M 134638 134661 (865339) (GGAT)n#Simple_repeat 1 24 (0) m_b166s252i8 6283 chr4ptel1M 134638 GGATGGATGGACGGATGGATGGAT 134661 i (GGAT)n#Simpl 1 GGATGGATGGATGGATGGATGGAT 24 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 86 28.12 3.23 0.95 chr4ptel1M 135397 135706 (864294) (TCTGTC)n#Simple_repeat 1 317 (0) m_b166s252i9 6284 chr4ptel1M 135397 TCTTTCTCT-CCTGTGTCTCTCCGTGTGTGTTTTTCTCTCTCT-TGTCTC 135444 v -i v viv v v i v v - (TCTGTC)n#Sim 1 TCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTC 50 chr4ptel1M 135445 TGTCAGTGTGTGTGT-T-TGTGTGTGTTTGTGTGCACCGGCGC-GTGGGC 135491 vv v v - - v v i v - v i v v - vvvi (TCTGTC)n#Sim 51 TGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGT-CTCTGTCTCTGTCTCT 99 chr4ptel1M 135492 GTTTCTGTGTCTGTATGT-TCTGTCTGTCTGTCTCTGTCTCTGTCTCTCT 135540 i v v v - v v v v (TCTGTC)n#Sim 100 GTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGT 149 chr4ptel1M 135541 CTCTCTCTCTCTCGTGTGTTTCTGTGTCTCTCTGTGTTCTGTGTTTCTGT 135590 v v - v i v v v - v i (TCTGTC)n#Sim 150 CTCTGTCTCTGTC-TCTGTCTCTGTCTCTGTCTCTG-TCTCTGTCTCTGT 197 chr4ptel1M 135591 GTC--TCTCGGTCTGTCTATCTGTCTCTGTCTCTGTCTCTGT-ACTGTGT 135637 v -- v v v v -v v (TCTGTC)n#Sim 198 CTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCT 247 chr4ptel1M 135638 ATGTGCGTTTCTGTGTCTCTCCGTGTGTGTTTTTCTCTCTCT-TGTCTCT 135686 v viv v v viv v v i v v - (TCTGTC)n#Sim 248 CTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCT 297 chr4ptel1M 135687 GTCAGTGTGTGTGTTTGTGT 135706 vv v v i v (TCTGTC)n#Sim 298 GTCTCTGTCTCTGTCTCTGT 317 Matrix = Unknown Transitions / transversions = 0.22 (13/58) Gap_init rate = 0.04 (12 / 309), avg. gap size = 1.08 (13 / 12) 29 10.75 0.00 0.00 chr4ptel1M 135759 135808 (864192) (TCTGTC)n#Simple_repeat 1 50 (0) c_b166s251i0 6284 chr4ptel1M 135759 TCTGTCTCTGTCTCTGTCTCTCTCTCTCTCTCAATCTCTGTCTCTCTCTC 135808 v v vi v (TCTGTC)n#Sim 1 TCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTC 50 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 443 29.47 5.06 1.22 chr4ptel1M 136994 137151 (862849) C MIR3#SINE/MIR (7) 201 38 m_b166s601i28 6285 chr4ptel1M 136994 AGAACCA--GAACTTGAGAACTTGAAGAGAC-TCGAAGGTCATCTAACCT 137040 i -- iv v i v i - iii i ii i C MIR3#SINE/MIR 201 AGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCC 152 chr4ptel1M 137041 AACCCTG-AATTTTACTGATGAGAAAATTAAGGACT---GTGTTCAA-TT 137085 iv-v v i i i v i--- v v v - v C MIR3#SINE/MIR 151 AACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTG 102 chr4ptel1M 137086 ACTTGCCCAAAGTCATACTCAGGTAGTAAGAATCACAGGTGAGATTTGAA 137135 i i -- v? v viv v vi i i v C MIR3#SINE/MIR 101 ACTTGCCCAAGGTCACA--CAGCNAGTTAGTGGCAGAGCCGGGACTAGAA 54 chr4ptel1M 137136 TCCAAGTCCTCTATCT 137151 i i ii iv C MIR3#SINE/MIR 53 CCCAGGTCTCCTGACT 38 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.78 CpG sites = 27, Kimura (unadjusted) = 38.87 Transitions / transversions = 1.42 (27/19) Gap_init rate = 0.04 (7 / 157), avg. gap size = 1.43 (10 / 7) 398 24.56 4.31 5.22 chr4ptel1M 137049 137164 (862836) C MIRb#SINE/MIR (120) 148 34 m_b166s601i29 6285 chr4ptel1M 137049 ATTTTACTGATGAGAAAATTAAGGACT-----GTGTTCAATTACTTGCCC 137093 v i i i - -----iv v i v C MIRb#SINE/MIR 148 ATTTTACAGATGAGGAAACTGAGG-CTCAGAGAGGTTAAGTAACTTGCCC 100 chr4ptel1M 137094 AAAGTCATACTCAGGTAGTAAGAATCACAGGTGAGATTTGAATCCAAGTC 137143 i i -- v viv v vi i i i i -- C MIRb#SINE/MIR 99 AAGGTCACAC--AGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGG-- 54 chr4ptel1M 137144 CTCTATCTGGATTCAAATCCC 137164 - i iv i v C MIRb#SINE/MIR 53 -TCTGTCTGACTCCAAAGCCC 34 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.75 CpG sites = 16, Kimura (unadjusted) = 30.37 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.06 (7 / 115), avg. gap size = 1.57 (11 / 7) 18 24.80 1.69 1.69 chr4ptel1M 137287 137345 (862655) (AGAC)n#Simple_repeat 1 59 (0) m_b166s252i10 6286 chr4ptel1M 137287 AGACA-TCTGACAGACCGAAATGCACATACACAGCACAGACAGAGACAGA 137335 -v v v v vi v i v - v v v (AGAC)n#Simpl 1 AGACAGACAGACAGACAGACAGACAGACAGACAG-ACAGACAGACAGACA 49 chr4ptel1M 137336 GACAGACAGA 137345 (AGAC)n#Simpl 50 GACAGACAGA 59 Matrix = Unknown Transitions / transversions = 0.20 (2/10) Gap_init rate = 0.03 (2 / 58), avg. gap size = 1.00 (2 / 2) 15 28.34 1.89 1.89 chr4ptel1M 137323 137375 (862625) (AG)n#Simple_repeat 1 53 (0) m_b166s252i11 6287 chr4ptel1M 137323 AGACAGAGACAGAGACAGACAGAAAAATAAAGCGATGAGAGGGA-AAAAA 137371 v v v v i i v i v - i - i i (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA-GAGAGAGAGAGAGA 49 chr4ptel1M 137372 GAGA 137375 (AG)n#Simple_ 50 GAGA 53 Matrix = Unknown Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.00 (2 / 2) 48 0.00 0.00 0.00 chr4ptel1M 137466 137506 (862494) (TA)n#Simple_repeat 1 41 (0) c_b166s251i1 6288 chr4ptel1M 137466 TATATATATATATATATATATATATATATATATATATATAT 137506 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATAT 41 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 211 16.68 2.00 4.08 chr4ptel1M 137988 138037 (861963) C L2c_3end#LINE/L2 (1) 477 429 m_b166s601i30 6289 chr4ptel1M 137988 TTAATTCAATTCAATAATC-TTTATTAAAAGTCTGCTACTGTGCCAGGCG 138036 v - i v - i iv i i - C L2c_3end#LINE 477 TTCATTCA-TTCAACAAACATTTATTGAGCGCCTACTA-TGTGCCAGGCG 430 chr4ptel1M 138037 C 138037 C L2c_3end#LINE 429 C 429 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 19.13 CpG sites = 5, Kimura (unadjusted) = 19.13 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.06 (3 / 49), avg. gap size = 1.00 (3 / 3) 24 6.13 2.94 0.00 chr4ptel1M 138038 138071 (861929) (AC)n#Simple_repeat 1 35 (0) m_b166s252i12 6290 chr4ptel1M 138038 ACGCACACACACACA-ACACACACAAACACACACA 138071 i - v (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACA 35 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 71 8.29 1.96 0.00 chr4ptel1M 138071 138172 (861828) (AG)n#Simple_repeat 1 104 (0) m_b166s252i13 6291 chr4ptel1M 138071 AGTGAGAGAAAGAAAGAGAGAGAGAAAGAGAGAGAGAGAGAGAGAGAGAG 138120 v i i i (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr4ptel1M 138121 AGAGAGAGAGAGAGAGAGAGAGA-AGAGAGA-AGAGAGAGTGAGTGAGTG 138168 - - v v v (AG)n#Simple_ 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 100 chr4ptel1M 138169 TGAG 138172 v (AG)n#Simple_ 101 AGAG 104 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.02 (2 / 101), avg. gap size = 1.00 (2 / 2) 248 26.16 0.00 1.54 chr4ptel1M 138589 138654 (861346) C Tigger14a#DNA/TcMar-Tigger (5) 319 255 m_b166s502i5 6292 chr4ptel1M 138589 AATTCTTTGTAACCTATGCAGAGTCAGGACATGGAATACTCTGGTTAAGT 138638 i i v i ii- vi v ii ii vi C Tigger14a#DNA 319 AACTCTCTGTTATCCG-GCATGGTCAGGAAATGGGGTGTTCTGGTTAATC 271 chr4ptel1M 138639 GAATATTCTGGTTCAT 138654 i v C Tigger14a#DNA 270 AAATATTCTGGTTAAT 255 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 31.02 CpG sites = 12, Kimura (unadjusted) = 33.72 Transitions / transversions = 2.40 (12/5) Gap_init rate = 0.02 (1 / 65), avg. gap size = 1.00 (1 / 1) 18 23.27 0.00 0.00 chr4ptel1M 138714 138753 (861247) (T)n#Simple_repeat 1 40 (0) m_b166s252i14 6293 chr4ptel1M 138714 TTTTTCTTTTTTTTTTCTTTTTTATTATAGCTTTTTATTT 138753 i i v v vvi v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 40 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 14 21.98 2.38 0.00 chr4ptel1M 139154 139195 (860805) (ATAAAA)n#Simple_repeat 1 43 (0) m_b166s252i15 6294 chr4ptel1M 139154 ATAAATATAAAAATATAAAGATACGT-AAAACAAAGATAAAAA 139195 v v v v vi - i i (ATAAAA)n#Sim 1 ATAAAAATAAAAATAAAAATAAAAATAAAAATAAAAATAAAAA 43 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.02 (1 / 41), avg. gap size = 1.00 (1 / 1) 467 31.17 5.84 0.00 chr4ptel1M 139304 139457 (860543) MIR3#SINE/MIR 46 208 (0) m_b166s601i31 6295 chr4ptel1M 139304 GATATGGGTTCAAATCCCAGCTCAACCCTTTGCTTGCTGTGAGATCTTGA 139353 iv v i i vi vi vi ? v i i MIR3#SINE/MIR 46 GACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGG 95 chr4ptel1M 139354 GCAAGATGATTGA-------GCATCTCAATGTTCTCATCTGCAAAGTGAG 139396 viiv v ------- vii i v i i i MIR3#SINE/MIR 96 GCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAG 145 chr4ptel1M 139397 AGGAATGTACCAGCTGGTCCATGACAGCTCTTTCAGTTCTAA-ATT-TGC 139444 i iv v i v i iv i viv i i i i - - ii MIR3#SINE/MIR 146 GGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTAT 195 chr4ptel1M 139445 GATTTTATGTTTC 139457 i v MIR3#SINE/MIR 196 GATTCTATGATTC 208 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.17 CpG sites = 30, Kimura (unadjusted) = 42.35 Transitions / transversions = 1.67 (30/18) Gap_init rate = 0.02 (3 / 153), avg. gap size = 3.00 (9 / 3) 345 32.30 5.81 4.60 chr4ptel1M 139533 139704 (860296) C L2d_3end#LINE/L2 (3) 513 340 m_b166s601i32 6296 chr4ptel1M 139533 ATTGACCAATCTGCAAGCATTTATTAAGTGTTCACCATGTACGAGGCACT 139582 ii i vi i i i iii i i vvi C L2d_3end#LINE 513 ATCAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACT 464 chr4ptel1M 139583 GTGCTAAGCACTA-GGGAAACAAAGAAAAATT-TAGGAT-TAGGATTAGC 139629 i i i- i i ?i ? v - i i- i vviiv C L2d_3end#LINE 463 GTGCTAGGCGCTGTGGGGAACGANAAAANAGTATAAGACATGGTCCCTGC 414 chr4ptel1M 139630 CCTCAAAATATTTCCCGTCCTTAAGGAGTTAATGTGGGGAAAATAACATG 139679 iivii v vi i------ iiv v ivi i v -- C L2d_3end#LINE 413 CCTCAAGGAGCTTACAATCT------AGTTGGGGAGACAAGACTAACA-- 372 chr4ptel1M 139680 TACAT-AAATAATTAT------ATACAAGATA 139704 i - i v------ i C L2d_3end#LINE 371 CACATGAAACAATTAGAGAACAATACAAGACA 340 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.70 CpG sites = 38, Kimura (unadjusted) = 46.37 Transitions / transversions = 2.53 (38/15) Gap_init rate = 0.08 (13 / 171), avg. gap size = 1.38 (18 / 13) 43 4.48 0.00 0.00 chr4ptel1M 139738 139783 (860217) (GT)n#Simple_repeat 1 46 (0) c_b166s251i2 6297 chr4ptel1M 139738 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGTCTGTGTGTGT 139783 i v (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 46 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 398 25.20 8.41 3.57 chr4ptel1M 139882 140095 (859905) L1PA17_3end#LINE/L1 67 290 (623) m_b166s551i1 6298 chr4ptel1M 139882 AAATAGTCAAAGAATATGTCCAGGCATTTCTCAAAAGAAAAAATCCATGT 139931 i i v i i vv i i i v v v i L1PA17_3end#L 67 AAGTGGGCAAAGGACATGAACAGACACTTCTCAAAAGAAGACATACAAGC 116 chr4ptel1M 139932 GACCACCAGAACACTGTGGGGAGGAGATGCTC--CATTGTTAATAATTAA 139979 i v - - i --- ii i -- iii v i i L1PA17_3end#L 117 GGCCAACA-AACA-TAT---GAAAAAATGCTCAACATCACTAATCATCAG 161 chr4ptel1M 139980 AGAAATAAATATTGAAACAACTTTGAAGTTCCATCTTATACCAGT----- 140024 iv v ii v vv ii v i i ----- L1PA17_3end#L 162 AGAAATGCAAATCAAAACCACAATGAGATACCATCTCACACCAGTCAGAA 211 chr4ptel1M 140025 TGG--ATTAGTAAAAATGATTTTAAAAATGACA-ATGTTGGAAAGGCTAT 140071 -- v --- v iv i - vi ? ii L1PA17_3end#L 212 TGGCTATTATTAAAA---AGTCAAAAAATAACAGATGTTGGCGAGGNTGC 258 chr4ptel1M 140072 -GAGAAAATAG-------ATACATTGTTGTTG 140095 - vi ------- i v L1PA17_3end#L 259 GGAGAAAAGGGAACGCTTATACACTGTTGGTG 290 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 29.60 CpG sites = 32, Kimura (unadjusted) = 31.79 Transitions / transversions = 1.60 (32/20) Gap_init rate = 0.07 (14 / 213), avg. gap size = 1.86 (26 / 14) 296 22.23 0.00 2.22 chr4ptel1M 140148 140239 (859761) Charlie7#DNA/hAT-Charlie 2311 2400 (215) m_b166s502i6 6299 chr4ptel1M 140148 AAAAGCAATGAAGCATAATTTAATTATACTCTTCTTCCTAAAATATTGTT 140197 ii - i i i i vi iv i Charlie7#DNA/ 2311 AAAAATAATGAAGCATA-TTCAATCACATTGCTCTCACTAAAATATTATT 2359 chr4ptel1M 140198 ACTAATAATATTAGTGGAACCAAAAAGTTTTTGTGCCAATAA 140239 v - v ii v vv i v Charlie7#DNA/ 2360 AATAAT-ATTTTAGTGAGAGCAAAAATGTTTTGTACCATTAA 2400 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 26.86 CpG sites = 12, Kimura (unadjusted) = 26.86 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.02 (2 / 91), avg. gap size = 1.00 (2 / 2) 22 25.34 6.45 0.00 chr4ptel1M 140612 140704 (859296) (ACATTC)n#Simple_repeat 1 99 (0) m_b166s252i16 6300 chr4ptel1M 140612 ACATATACATTCAGATTC-C-TACATATTCAAATTCACA--CACCTATAC 140657 vi v - - v i v -- v vi (ACATTC)n#Sim 1 ACATTCACATTCACATTCACATTCACATTCACATTCACATTCACATTCAC 50 chr4ptel1M 140658 ATGCCCTCTCACACACACATTCAGATTTACA--CACATTCAGACACACA 140704 v v vi iv v i -- v iv (ACATTC)n#Sim 51 ATTCACATTCACATTCACATTCACATTCACATTCACATTCACATTCACA 99 Matrix = Unknown Transitions / transversions = 0.54 (7/13) Gap_init rate = 0.04 (4 / 92), avg. gap size = 1.50 (6 / 4) 19 33.02 0.00 0.00 chr4ptel1M 140645 140708 (859292) (CA)n#Simple_repeat 1 64 (0) m_b166s252i17 6300 chr4ptel1M 140645 CACACACCTATACATGCCCTCTCACACACACATTCAGATTTACACACATT 140694 vi i ii v v v iv v ivi iv (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 chr4ptel1M 140695 CAGACACACACACA 140708 v (CA)n#Simple_ 51 CACACACACACACA 64 Matrix = Unknown Transitions / transversions = 0.89 (8/9) Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0) 309 25.14 8.81 7.45 chr4ptel1M 141295 141453 (858547) MIR1_Amn#SINE/MIR 19 179 (51) m_b166s601i33 6301 chr4ptel1M 141295 TAGTGGATAGA---CTGTGACATGTACAGCTAGGAAGAATTGGATTCAAA 141341 --- - --- ivii v i vi i ? ? MIR1_Amn#SINE 19 TAGTGGATAGAGCACTG-GAC---TGGGACTCGGGAGACCTGGGTTCNAN 64 chr4ptel1M 141342 TCCTTTCTCAGGAGCTCACTAGCTGTATGTCCT-GGG--AATCACTTCAT 141388 ivv v vvi ?i i? ?i v - -- i ? i MIR1_Amn#SINE 65 TCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGTCACTTNAC 114 chr4ptel1M 141389 CTC-------ATCAGACTC-TGATCTGTAGAATGAGGGTTTAGGCTGGAT 141430 -------v vi - v i i i --------i MIR1_Amn#SINE 115 CTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGGAT--------AAT 156 chr4ptel1M 141431 GATTCTGAGGTCCTCTGCAGGGT 141453 v vv i i ii MIR1_Amn#SINE 157 GATACTGACCTCCTTTGTAAAGT 179 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.00 CpG sites = 22, Kimura (unadjusted) = 33.08 Transitions / transversions = 1.47 (22/15) Gap_init rate = 0.11 (17 / 158), avg. gap size = 1.53 (26 / 17) 319 24.74 11.29 2.22 chr4ptel1M 141296 141419 (858581) MIRc#SINE/MIR 17 151 (117) m_b166s601i34 6301 chr4ptel1M 141296 AGTGGATAGA---CTGTGACATGTACAGCTAGGAAGAATTGGATTCAAAT 141342 v --- - v v -- ii vi i i i MIRc#SINE/MIR 17 AGTGGAAAGAGCACTG-GACTTGGA--GTCAGGAAGACCTGGGTTCGAGT 63 chr4ptel1M 141343 CCTTTCTCAGGAGCTCACTAGCTGTATGTCC-TGGG--AATCACTTCATC 141389 ivv v vvi i i v - -- i v i MIRc#SINE/MIR 64 CCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACC 113 chr4ptel1M 141390 T-------CATCAGACT-CTGATCTGTAGAATGAGGGT 141419 ------- v vi - v i i i MIRc#SINE/MIR 114 TCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGAT 151 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.15 CpG sites = 16, Kimura (unadjusted) = 30.49 Transitions / transversions = 1.14 (16/14) Gap_init rate = 0.07 (8 / 123), avg. gap size = 2.12 (17 / 8) 383 26.70 9.85 0.69 chr4ptel1M 141319 141450 (858550) MIR3#SINE/MIR 38 181 (27) m_b166s601i35 6301 chr4ptel1M 141319 AGCTAGGAAGAATTGGATTCAAATCCTTTCTCAGGAGCTCACTAGCTGTA 141368 ii - vi i v i ivv v vvi v ? i MIR3#SINE/MIR 38 AGTCAGGA-GACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTG 86 chr4ptel1M 141369 TGTCCT-GGG--AATCACTTCATCTCATCAGACT--------CTGATCTG 141407 v - -- i i viii i i-------- v MIR3#SINE/MIR 87 TGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTG 136 chr4ptel1M 141408 TAGAATGA-GGGTTTAGGCTGGATGAT-TCTGAGGTCCTCTGCAG 141450 i - v i i i - i ii v MIR3#SINE/MIR 137 TAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAG 181 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.21 CpG sites = 22, Kimura (unadjusted) = 34.43 Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.05 (6 / 131), avg. gap size = 2.33 (14 / 6) 248 26.62 0.00 7.35 chr4ptel1M 141892 141964 (858036) MamRTE1#LINE/RTE-BovB 2046 2113 (1699) m_b166s601i36 6302 chr4ptel1M 141892 AACAATAAGGCTAGTGGACCTGATGGCATTCCAGCTGAGCTTTTTATTCA 141941 iii i vvi v v v i --- MamRTE1#LINE/ 2046 AATGGTAAAGCTCTCGGACCTGATGGCATACCTGCTGAGATTTTCA---A 2092 chr4ptel1M 141942 ACATCTTAAAAGGAGATGCTGTT 141964 i --vv ii i i MamRTE1#LINE/ 2093 GCA--GGAAGGGGAGACGCTGCT 2113 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.15 CpG sites = 11, Kimura (unadjusted) = 33.56 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.07 (5 / 72), avg. gap size = 1.00 (5 / 5) 226 30.58 25.62 0.00 chr4ptel1M 144358 144478 (855522) MIRc#SINE/MIR 1 152 (116) m_b166s601i37 6303 chr4ptel1M 144358 CAAGACACCATAGTGCAATGAAAGGAGTATTT--CCTGGGGTT------- 144398 i i vii i i i i i i v-- i i i------- MIRc#SINE/MIR 1 CGAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA 50 chr4ptel1M 144399 -CTGCATTCTAATCCTGCCCCAACTGCTT-CT--CTGCATGACCTT---- 144440 - vi v i i v i vi ii - -- ii ---- MIRc#SINE/MIR 51 CCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGC 100 chr4ptel1M 144441 -----------CCT---TGGGCCTCAATTTCCTCGCCTACAAAATGACAA 144476 ----------- --- i i ii ii ivi MIRc#SINE/MIR 101 AAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGA 150 chr4ptel1M 144477 TA 144478 MIRc#SINE/MIR 151 TA 152 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.19 CpG sites = 30, Kimura (unadjusted) = 43.41 Transitions / transversions = 4.29 (30/7) Gap_init rate = 0.06 (7 / 120), avg. gap size = 4.43 (31 / 7) 252 28.85 0.00 0.00 chr4ptel1M 144438 144489 (855511) MIR3#SINE/MIR 109 160 (48) m_b166s601i38 6303 chr4ptel1M 144438 CTTCCTTGGGCCTCAATTTCCTCGCCTACAAAATGACAATATTGGGTTAG 144487 i ii i ii ii viivi ii MIR3#SINE/MIR 109 CCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAG 158 chr4ptel1M 144488 AT 144489 MIR3#SINE/MIR 159 AT 160 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.66 CpG sites = 13, Kimura (unadjusted) = 40.66 Transitions / transversions = 6.50 (13/2) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 190 30.50 5.25 18.75 chr4ptel1M 145058 145400 (854600) C L2c_3end#LINE/L2 (7) 471 168 m_b166s601i40 6304 chr4ptel1M 145058 CAGTCAACAAGTATTTATTAAGCACTTACTGTGTGTAAGGCACTTTGTGC 145107 v ii i i i i iv i ------- C L2c_3end#LINE 471 CATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGC------- 429 chr4ptel1M 145108 AGCACCTTGGAGTGCACAAAGGC-----AGAACCAG-CCCTGCCCTAGAG 145151 ------- i -ii ii----- vv i - vi C L2c_3end#LINE 428 -------TGGGG-ATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAG 387 chr4ptel1M 145152 GAGTTCACATCCTACTG--GGGGATAAATAAGTAACTAAGTAACATGTGA 145199 i vi v -- i i i i ? vi iii ---- v C L2c_3end#LINE 386 GAGCTCACAGTCTAGTGGAGGAGACAGACANGTAAACAGACAA----TTA 341 chr4ptel1M 145200 CATGTAACAAGTAACAAGAAAATAAGTAGTGTAACTGTTTACATGAAAG- 145248 -i - v ---- vi iv i --------- ii - C L2c_3end#LINE 340 CA-AT-ACAAGTTA----ATGATAAGTGCTATA---------ATGGGAGT 306 chr4ptel1M 145249 ATAACAACAGAGTAG-ATGGGAGGTAACCTTACAGGGAAAGGAATGGCTG 145297 --i i iv- -------i i i i v i-- i C L2c_3end#LINE 305 ATA--GACAGGGTGCTATGGGAG-------CACAGAGGAGGGCAC--CTA 267 chr4ptel1M 145298 GATGTGGGAAAAGGTGCCGATGGAAGGAGAGGGAAGATCGCCAGCAGAGG 145347 i- i --------? i-- ii vv iiiv v v ii C L2c_3end#LINE 266 GAC-TAG--------NCT--TGGGGGGTCAGGGAAGGCTTCCCGGAGGAG 228 chr4ptel1M 145348 GTGGTATCTGAGTCCTAGCC----ACAGCCAG--GGAA--ACTCAGGGAG 145389 ii - iv ? ---- viiiv -- i-- vi vi C L2c_3end#LINE 227 GTGACATCTGAG-CTGAGNCTTGAAGGATGAGTAGGAGTTAGCCAGGTGG 179 chr4ptel1M 145390 AAAGAGAGGGG 145400 i i C L2c_3end#LINE 178 AAGGAGGGGGG 168 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.99 CpG sites = 61, Kimura (unadjusted) = 40.92 Transitions / transversions = 2.54 (61/24) Gap_init rate = 0.19 (65 / 342), avg. gap size = 1.15 (75 / 65) 340 26.79 9.27 12.24 chr4ptel1M 145058 145359 (854641) C L2a_3end#LINE/L2 (7) 510 217 m_b166s601i39 6304 chr4ptel1M 145058 CAGTCAACAAGTATTTATTAAGCACTTACTGTGTGTAAGGCACTTTGTGC 145107 v i i i i i iv v vivv C L2a_3end#LINE 510 CATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTA 461 chr4ptel1M 145108 AGCACCTTGG-------AGTGCACAAAGGCAGA-ACCAG-CCCTGCCCTA 145148 i i ivv ------- v -i - vv - v C L2a_3end#LINE 460 GGCGCTGGGGATACAGCAGTGAACAAA-ACAGACAAAAGTCCCTGCCCTC 412 chr4ptel1M 145149 GAGGAGTTCACATCCTACTGGGGG----------ATAAATAAGTAACTAA 145188 iv i i i v ---------- i i v C L2a_3end#LINE 411 ATGGAGCTTACATTCTAGTGGGGGGAGACAGACAATAAACAAATAAATAA 362 chr4ptel1M 145189 GTAACATGTGACATGTAACAAGTAACAAGAAAATAAGTAGTGTAACTGTT 145238 v ----- i ii v v v v ivi ------i i v C L2a_3end#LINE 361 GTAAAAT-----ATATAGTATGTCAGATGGTGATAAGT------GCTATG 323 chr4ptel1M 145239 TACATGAAAGATAACAACAGAGTAGATGGGAGGTAACCTTACAGGGAAAG 145288 v --- i - i i ------ ---------- v C L2a_3end#LINE 322 GA---GAAAAATAA-AGCAGGGTA------AGG----------GGGATAG 293 chr4ptel1M 145289 GAATGGCTGGATGTGGGAAAAGGTGC-CGAT--------GGAAGGAGAGG 145329 i vv ? ---- ?i i i- ? -------- iv vv C L2a_3end#LINE 292 GGAGTGNTGG----GGGNGAGGGTGTGCNATTTTAAATAGGGTGGTCAGG 247 chr4ptel1M 145330 GAAGATCGCCAGCAGAGGGTGGTATCTGAG 145359 ii v ?vvv i ii i C L2a_3end#LINE 246 GAAGGCCTCNCTGAGAAGGTGACATTTGAG 217 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.99 CpG sites = 38, Kimura (unadjusted) = 34.15 Transitions / transversions = 1.15 (38/33) Gap_init rate = 0.14 (42 / 301), avg. gap size = 1.52 (64 / 42) 482 26.28 3.85 8.54 chr4ptel1M 145059 145266 (854734) C L2d2_3end#LINE/L2 (8) 547 349 m_b166s601i41 6304 chr4ptel1M 145059 AGTCAACAAGTATTTATTAAGCACTTACTGTGTGTAAGGCACTTTGTGCA 145108 i i i i i i v ivvi C L2d2_3end#LIN 547 AATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAG 498 chr4ptel1M 145109 GCACCTTGGAGTGCACAAAGGCAGAACCAG-------CCCTGCCCTAGAG 145151 i iv i vii i- v iv ------- vi C L2d2_3end#LIN 497 GCGCTGTGGGGGATACAAAGA-AGTATAAGACATGGTCCCTGCCCTCAAG 449 chr4ptel1M 145152 GAGTTCACATCCTACTGGGGGATAAATAAGTAAC-TAAGTAACATGTGAC 145200 i i vi v v -- i i -- - --- i v C L2d2_3end#LIN 448 GAGCTTACAATCTAGTTGGGG--AGACAAG--ACATA---AACACGTGAA 406 chr4ptel1M 145201 ATGTAACAAGTAACAAGAAAATAAGTAGTGTAACTGTTTACATGAAAGAT 145250 v --i i v v v vv i-i v i------ i C L2d2_3end#LIN 405 AAGT--TAAATAACAATACAAGATTTAA-ATAACAGTTC------AAGAC 365 chr4ptel1M 145251 AACAACAGAGTAGATG 145266 i iv C L2d2_3end#LIN 364 AACAATAGAAGAGATG 349 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.64 CpG sites = 30, Kimura (unadjusted) = 33.01 Transitions / transversions = 1.50 (30/20) Gap_init rate = 0.09 (19 / 207), avg. gap size = 1.32 (25 / 19) 292 31.52 2.17 0.00 chr4ptel1M 145991 146082 (853918) C MIRb#SINE/MIR (138) 130 37 m_b166s601i42 6305 chr4ptel1M 145991 CTGGGGCCCAGGAAATTTAAGTCACCTTCCCAA-ATGACACAGGTTGTAC 146039 i i ii iv v i v -i v v v v C MIRb#SINE/MIR 130 CTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAA 81 chr4ptel1M 146040 ATTTCGTAAGTAGGATTTAAACCCAGATCC-TCTGACCCCAGAG 146082 i vv iv ivii ii i i- i i C MIRb#SINE/MIR 80 GTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAG 37 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.33 CpG sites = 18, Kimura (unadjusted) = 42.59 Transitions / transversions = 1.64 (18/11) Gap_init rate = 0.02 (2 / 91), avg. gap size = 1.00 (2 / 2) 301 35.48 4.41 2.16 chr4ptel1M 146382 146744 (853256) L1PB1_3end#LINE/L1 228 598 (300) m_b166s551i2 6306 chr4ptel1M 146382 ATGAAAGAACATTAGCTGTTGGAGAGGATGCCAGAAAATTGAAACACTAA 146431 v i i v v v v vivi vv i vv L1PB1_3end#LI 228 ATCAAAAAATAATAGATGTTGGCGTGGATGCGGTGAAAAGGGAACACTTC 277 chr4ptel1M 146432 TGCATTGTTGATGAAGTTGTGAACTGTCCCAGCTATTCTAGAAAGCATTT 146481 i i i i iiiv i iviv i i i v i i v v L1PB1_3end#LI 278 TACACTGCTGGTGGGAATGTAAACTAGTACAACCACTATGGAAAACAGTG 327 chr4ptel1M 146482 TGGAACTCTGCCCAAAGGGCTATAAAACTGTGCATACCCTTTGATCTAGC 146531 iv - v ii ii - iiv vi - v i L1PB1_3end#LI 328 TGGAGAT-TCCTTAAAGAACTA-AAAGTAGAAC-TACCATTTGATCCAGC 374 chr4ptel1M 146532 -----------TAGGTTTGTATCCC-----AAAGATATTATTAAAAGGGG 146565 ----------- i v v i v----- vi i v v ii- L1PB1_3end#LI 375 AATCCCACTACTGGGTATCTACCCAGAGGAAAAGAAGTCATTATACGAA- 423 chr4ptel1M 146566 GGAAAGACCCACATGCACAAAAATGTTGAGAGCAGCTTTCTTGGTGGTGG 146615 -- i-- v viv v v vivv v iii v L1PB1_3end#LI 424 --AAAGAT--ACTTGCACACGCATGTTTATAGCAGCACAATTCGCAATTG 469 chr4ptel1M 146616 CAAAGAACTGGAAATTGAGTGGATGTCCATCAATTGGGGAACGGCTAAAT 146665 i vv viv vviii i iiiv ii v v L1PB1_3end#LI 470 CAAAAATATGGAACCAGCCCAAATGCCCATCAATCAACGAGTGGATAAAG 519 chr4ptel1M 146666 AAATTGTGGTATGTGAATGTAATTGAATATTATTGTTCCATAAGAATGAT 146715 ? i iv iiv v i i vvv i v v L1PB1_3end#LI 520 AAANTGTGGTATATATATACCATGGAATACTACTCAGCCATAAAAAGGAA 569 chr4ptel1M 146716 TAAAAAGGCGGATTTCAGAAAGACCTAGA 146744 i ?viii vv iv iv i L1PB1_3end#LI 570 TGAANTAATGGCATTCGCAGCGACCTGGA 598 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 48.53 CpG sites = 66, Kimura (unadjusted) = 49.64 Transitions / transversions = 1.10 (66/60) Gap_init rate = 0.03 (10 / 362), avg. gap size = 2.40 (24 / 10) 738 30.82 3.77 0.00 chr4ptel1M 146398 146715 (853285) L1ME4c_3end#LINE/L1 244 573 (257) m_b166s551i3 6306 chr4ptel1M 146398 TGTTGGAGAGGATGCCAGAAAATTGAAACACTAATGCATTGTTGATGAAG 146447 i v ? vivi i iv ? v i i i ivi L1ME4c_3end#L 244 TGCTGGCGAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCA 293 chr4ptel1M 146448 TTGTGAACTGTCCCAGCTATTCTAGAAAGCATTTTGGAACTCTGCCCAAA 146497 ? i i viv i iv i i v v v vi iviv L1ME4c_3end#L 294 NTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAA 343 chr4ptel1M 146498 GGGCTATAAAACTGTGCATACCCTTTGATCTAG-----------CTAGGT 146536 i i v v i i ----------- i v L1ME4c_3end#L 344 GAGCCATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGA 393 chr4ptel1M 146537 TTGTATCCCAAAGATATTATTAAAAGGGGGGAAAGACCCACATGCACAAA 146586 v v i i v v v i ii i v i i i L1ME4c_3end#L 394 ATTTATCCTAAGGAAATAATTCAAAAGAAGGAAAAAGCTATATGCACGAA 443 chr4ptel1M 146587 AATGTTGAGAGCAGCTTTCTTGGTGGTGGCAAAGAACTGGAAATTGAGTG 146636 i v vv v v vi ii i i i i ivivv i L1ME4c_3end#L 444 GATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTA 493 chr4ptel1M 146637 GATGTCCATCAATTGGGGAACGGCTAAATAAATTGTGGTATGTGAATGTA 146686 i v v i i i i ii v? ivii L1ME4c_3end#L 494 AATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCG 543 chr4ptel1M 146687 ATTGAATATTATTGTTCCA-TAAGAATGAT 146715 v vvvv - i L1ME4c_3end#L 544 ATGGAATATTATGCAGCCATTAAAAATGAT 573 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.23 CpG sites = 56, Kimura (unadjusted) = 41.49 Transitions / transversions = 1.33 (56/42) Gap_init rate = 0.01 (2 / 317), avg. gap size = 6.00 (12 / 2) 200 28.53 1.25 8.00 chr4ptel1M 148648 148727 (851273) C MIRc#SINE/MIR (144) 124 50 m_b166s601i43 6307 chr4ptel1M 148648 AGCCTTATAGTGACTCAGAGACTTATCCAAGGTC-CAAGGTCATCCAGTG 148696 v i v v ii v v ii - ---- v i i C MIRc#SINE/MIR 124 AGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACA----CAGCTAGTA 79 chr4ptel1M 148697 AGTATATCCAAGCTGGGAATCAAAACCAGGT 148727 -- iv vi i v i v C MIRc#SINE/MIR 78 AG--TGGCAGAGCCGGGACTCGAACCCAGGT 50 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.08 CpG sites = 11, Kimura (unadjusted) = 36.20 Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.09 (7 / 79), avg. gap size = 1.00 (7 / 7) 34 20.33 0.00 0.00 chr4ptel1M 148863 148935 (851065) (GGAGTA)n#Simple_repeat 1 73 (0) m_b167s252i0 6308 chr4ptel1M 148863 GGAGTAGGAGTAGGAGTAGGACTAGGAAGGGGATGAGGATGAGGAGTAGC 148912 v ivi vv vv v (GGAGTA)n#Sim 1 GGAGTAGGAGTAGGAGTAGGAGTAGGAGTAGGAGTAGGAGTAGGAGTAGG 50 chr4ptel1M 148913 AGTATGAGTAGAAGTATAAGTAG 148935 v i vi (GGAGTA)n#Sim 51 AGTAGGAGTAGGAGTAGGAGTAG 73 Matrix = Unknown Transitions / transversions = 0.44 (4/9) Gap_init rate = 0.00 (0 / 72), avg. gap size = 0.0 (0 / 0) 21 23.14 0.00 3.23 chr4ptel1M 149372 149435 (850565) (CAAAAA)n#Simple_repeat 1 62 (0) m_b167s252i1 6309 chr4ptel1M 149372 CAAAGCCAAAAACAACTGTCTTAAATGATAAAAAAAAACAAAAACAAAAA 149421 iv -viv vv ii v v - (CAAAAA)n#Sim 1 CAAAAACAAAAACAA-AAACAAAAACAAAAACAA-AAACAAAAACAAAAA 48 chr4ptel1M 149422 CAAAAAAAAAAACA 149435 v (CAAAAA)n#Sim 49 CAAAAACAAAAACA 62 Matrix = Unknown Transitions / transversions = 0.50 (4/8) Gap_init rate = 0.03 (2 / 63), avg. gap size = 1.00 (2 / 2) 23 9.78 0.00 0.00 chr4ptel1M 149401 149433 (850567) (A)n#Simple_repeat 1 33 (0) m_b167s252i2 6310 chr4ptel1M 149401 AAAAAAAAACAAAAACAAAAACAAAAAAAAAAA 149433 v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 33 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 590 23.91 2.88 0.70 chr4ptel1M 149948 150086 (849914) C L2d2_3end#LINE/L2 (2) 553 412 m_b167s601i1 6311 chr4ptel1M 149948 AAGTCAA-TCAACAAGTATTTGTTTATCTCCTACTAAGTGTCAGGCAATA 149996 i - i i v v v iv iv v i C L2d2_3end#LIN 553 AAATCAAATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTG 504 chr4ptel1M 149997 TGCTAAGTGTTG---GGGATACAAAGAAAAGTAAAACCAGAGTCCCTGCT 150043 i i i --- ivi i - vi i C L2d2_3end#LIN 503 TGCTAGGCGCTGTGGGGGATACAAAGAAGTATAAGAC-ATGGTCCCTGCC 455 chr4ptel1M 150044 CTCAAAGAGCTCCCACTCTAATAGGGAAGACAGGATGCAAACA 150086 i iv v i v i i iii C L2d2_3end#LIN 454 CTCAAGGAGCTTACAATCTAGTTGGGGAGACAAGACATAAACA 412 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.69 CpG sites = 22, Kimura (unadjusted) = 29.76 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.02 (3 / 138), avg. gap size = 1.67 (5 / 3) 558 27.95 5.13 4.59 chr4ptel1M 149951 150145 (849855) C L2b_3end#LINE/L2 (6) 460 265 m_b167s601i2 6311 chr4ptel1M 149951 TCAATCAACAAGTATTTGTTTATCTCCTACTAAGTGTCAGGCAATATGCT 150000 v i ii v v v iv i ?v i C L2b_3end#LINE 460 TCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCT 411 chr4ptel1M 150001 AAGTGTTGGGGATACAAAGAAAAGTAAAAC---CAGAGTCCCTGCTCTCA 150047 i i i iv ivi ii i --- ?vi i C L2b_3end#LINE 410 AGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCA 361 chr4ptel1M 150048 AAGAGCTCCCACTCTAATAGGGAAGACAGG-ATGCAAACAACTGTGTACA 150096 vi v v i i i i- i ? i------ C L2b_3end#LINE 360 CGGAGCTCACAGTCTAGTGGGGGAGACAGACATGTAANCAG------ACA 317 chr4ptel1M 150097 ACAA-GATCTAGA----CAGAGTA-AATTAGAGATCATCTCAGAGAGAAA 150140 i? -i i i ---- i -i i i i i--iv i - ii C L2b_3end#LINE 316 ATNATAACCCAGAGTGGCAGGGTAGGACTGGGGG--GGCCCAGAG-GAGG 270 chr4ptel1M 150141 GCACC 150145 i C L2b_3end#LINE 269 GCGCC 265 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.70 CpG sites = 39, Kimura (unadjusted) = 38.51 Transitions / transversions = 3.00 (39/13) Gap_init rate = 0.07 (14 / 194), avg. gap size = 1.36 (19 / 14) 22 24.57 0.00 0.00 chr4ptel1M 152276 152324 (847676) (AT)n#Simple_repeat 1 49 (0) m_b167s252i3 6312 chr4ptel1M 152276 ATAGATAAAGACACACATGTATGTATGTATGTATATATATATATATATA 152324 v v v i i i i i i i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATA 49 Matrix = Unknown Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 19 24.47 0.00 1.85 chr4ptel1M 152292 152346 (847654) (ATGT)n#Simple_repeat 1 54 (0) m_b167s252i4 6312 chr4ptel1M 152292 ATGTATGTATGTATGTATATATATATATATATAATTTTTGCAAATATGTC 152341 i i i i - v v i vi v (ATGT)n#Simpl 1 ATGTATGTATGTATGTATGTATGTATGTATGT-ATGTATGTATGTATGTA 49 chr4ptel1M 152342 AGTAT 152346 v (ATGT)n#Simpl 50 TGTAT 54 Matrix = Unknown Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1) 213 23.39 23.86 2.83 chr4ptel1M 152364 152451 (847549) C L2c_3end#LINE/L2 (0) 478 373 m_b167s601i3 6313 chr4ptel1M 152364 ATCCATT-ATTTAATAATTAGCATTTATTGGGAAC-TACTAGATGCCAG- 152410 i - i i ---i i vi - vi - C L2c_3end#LINE 478 ATTCATTCATTCAACAA---ACATTTATTGAGCGCCTACTATGTGCCAGG 432 chr4ptel1M 152411 ---TAGAGATATAAAAATGA---------------TGTCCTTAGGGAGCT 152442 --- i i i i --------------- i i i C L2c_3end#LINE 431 CGCTGGGGATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCT 382 chr4ptel1M 152443 TGCACCCTA 152451 ii vi C L2c_3end#LINE 381 CACAGTCTA 373 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.56 CpG sites = 17, Kimura (unadjusted) = 30.40 Transitions / transversions = 5.67 (17/3) Gap_init rate = 0.09 (8 / 87), avg. gap size = 3.00 (24 / 8) 18 10.73 4.76 2.33 chr4ptel1M 152530 152571 (847429) (TTATGGA)n#Simple_repeat 1 43 (0) m_b167s252i5 6314 chr4ptel1M 152530 TTATGGATAAATGGATTA-GGGTTAGGGGTT-TGGATTATGGAT 152571 -v - i v i - (TTATGGA)n#Si 1 TTATGGAT-TATGGATTATGGATTATGGATTATGGATTATGGAT 43 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.07 (3 / 41), avg. gap size = 1.00 (3 / 3) 46 0.00 0.00 0.00 chr4ptel1M 152717 152755 (847245) (AC)n#Simple_repeat 1 39 (0) c_b167s251i0 6315 chr4ptel1M 152717 ACACACACACACACACACACACACACACACACACACACA 152755 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACA 39 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 307 30.34 4.49 0.00 chr4ptel1M 153212 153300 (846700) C MIR3#SINE/MIR (6) 202 110 m_b167s601i4 6316 chr4ptel1M 153212 TAGGACCATAAA--GCTAAAG--GAGAGGAATCTGAGAGGTTTTCTGGTC 153257 i i i -- ii i -- ii i i v i iv i C MIR3#SINE/MIR 202 TAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTC 153 chr4ptel1M 153258 TAATGCCCCCCTTTCAAAAATGGGTAAACTGAGACCCAGGGAG 153300 i iv i v i v i i v i i C MIR3#SINE/MIR 152 CAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAG 110 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 42.37 CpG sites = 21, Kimura (unadjusted) = 42.37 Transitions / transversions = 3.50 (21/6) Gap_init rate = 0.02 (2 / 88), avg. gap size = 2.00 (4 / 2) 180 28.26 0.00 0.00 chr4ptel1M 153264 153309 (846691) C MIRc#SINE/MIR (119) 149 104 m_b167s601i5 6316 chr4ptel1M 153264 CCCCCTTTCAAAAATGGGTAAACTGAGACCCAGGGAGAATCAATGA 153309 v i v i i v i i i iv v i C MIRc#SINE/MIR 149 CCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGA 104 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.62 CpG sites = 8, Kimura (unadjusted) = 36.62 Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 242 26.67 6.67 0.00 chr4ptel1M 153392 153466 (846534) C MIR3#SINE/MIR (2) 206 127 m_b167s601i6 6317 chr4ptel1M 153392 ATCAAAGA-TCATAG--TGCCAGGAATAGAAAGACCCTCCAAGTCCACCT 153438 v - -- i iiv i i iv ivi vi i C MIR3#SINE/MIR 206 ATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCT 157 chr4ptel1M 153439 AGTCCAGTGCCCTCATTTTGCAG--GAGAA 153466 iiv i -- i C MIR3#SINE/MIR 156 AGTCCAACCCCCTCATTTTACAGATGAGGA 127 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.55 CpG sites = 14, Kimura (unadjusted) = 34.55 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.04 (3 / 74), avg. gap size = 1.67 (5 / 3) 186 25.31 6.41 3.75 chr4ptel1M 153757 153834 (846166) C MIR1_Amn#SINE/MIR (67) 163 84 m_b167s601i7 6318 chr4ptel1M 153757 CAGCATCTTATTATACC-ATTTTACAAATAAGGAGAGGAAGATTCAGGAT 153805 i -- v - i i i vvi ii? iiv C MIR1_Amn#SINE 163 CAGTATC--ATTATCCCCATTTTACAGATGAGGAAACTGAGGCNCAGAGA 116 chr4ptel1M 153806 GGTAA----CCTTCCCCCAAATTACCCAAGCTG 153834 ? ----v v v ii i ? - ? C MIR1_Amn#SINE 115 GGTNAAGTGACTTGCCCAAGGTCACNC-AGCNG 84 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.18 CpG sites = 12, Kimura (unadjusted) = 34.18 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.06 (5 / 77), avg. gap size = 1.60 (8 / 5) 244 29.58 2.74 2.74 chr4ptel1M 153830 153902 (846098) MIRb#SINE/MIR 10 82 (186) m_b167s601i8 6319 chr4ptel1M 153830 AGC-TGATGCTGTAGAAAGAGCACTGATTCTGGAGCCAAA-GGACTGTTG 153877 - i v i v ii i i i -i --i MIRb#SINE/MIR 10 AGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGAC--CTG 57 chr4ptel1M 153878 GATTCATATCTGAGTCTTGACACTT 153902 i iv ivi iii v MIRb#SINE/MIR 58 GGTTCGAATCCCGGCTCTGCCACTT 82 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.58 CpG sites = 16, Kimura (unadjusted) = 40.61 Transitions / transversions = 3.20 (16/5) Gap_init rate = 0.06 (4 / 72), avg. gap size = 1.00 (4 / 4) 272 30.43 6.78 1.61 chr4ptel1M 155081 155257 (844743) MIR1_Amn#SINE/MIR 12 197 (33) m_b167s601i9 6320 chr4ptel1M 155081 TATGGCATAGTATCCAGTACATGATACTTGGAGTCAAGAAGACCTCATTC 155130 i iv ivvi vi iviv v v ii - viv i MIR1_Amn#SINE 12 TGTGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGA-GACCTGGGTT 60 chr4ptel1M 155131 CAAATCCA---TCT--CAGGGACTGGTTGTTTGATTCTGG--AAGTCACT 155173 ? ? v--- -- vv?i i? i ?v iii -- MIR1_Amn#SINE 61 CNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGTCACT 110 chr4ptel1M 155174 GGGCCATTCTGCGCTTCCATTTTCCTTTTCTGTAACAT-GAAAGAATCGA 155222 v?i vi ? i - v iv v - ii v - MIR1_Amn#SINE 111 TNACCTCTCTGNGCCT-CAGTTTCCTCATCTGTAAAATGGGGATAAT-GA 158 chr4ptel1M 155223 AATTA--CTGCTCTCTAAGTTGCTAT-AAATCTA-TGAT 155257 v i i-- v i v iv v - i - MIR1_Amn#SINE 159 TACTGACCTCCTTTGTAAAGTGCTTTGAGATCTACTGAT 197 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 41.04 CpG sites = 28, Kimura (unadjusted) = 42.08 Transitions / transversions = 1.12 (28/25) Gap_init rate = 0.06 (10 / 176), avg. gap size = 1.50 (15 / 10) 338 30.29 5.22 1.44 chr4ptel1M 155106 155239 (844761) MIR3#SINE/MIR 32 170 (38) m_b167s601i10 6320 chr4ptel1M 155106 ACTTGGAGTCAAGAAGACCTCA-TTCCAAATCCATCTCAGG----GACTG 155150 v i - vi- i ivi iv v v----i ? MIR3#SINE/MIR 32 ACTGGGAGTCAGGA-GACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTN 80 chr4ptel1M 155151 GTTGTTTGATTCTGG--AAGTCACTGGGCCATTCTGCGCTTCCATTTTCC 155198 i v iii -- vvi vi v i - v MIR3#SINE/MIR 81 GCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTC-AGTTTCC 129 chr4ptel1M 155199 TTTTCTGTAACATGAAAGAATCGAAATTACTGCTCTCTAAG 155239 iv v ii ii i i v viv v MIR3#SINE/MIR 130 TCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAG 170 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.80 CpG sites = 22, Kimura (unadjusted) = 40.09 Transitions / transversions = 1.22 (22/18) Gap_init rate = 0.04 (5 / 133), avg. gap size = 1.80 (9 / 5) 419 20.64 12.30 0.74 chr4ptel1M 155437 155558 (844442) MIR1_Amn#SINE/MIR 13 148 (82) m_b167s601i11 6321 chr4ptel1M 155437 GCGGCCCAGTGGATAAGGCAATGGCCCTGGAATTC---AGATCTGGCTTC 155483 i i i ii v -v i i --- i v MIR1_Amn#SINE 13 GTGGTCTAGTGGATAGAGCACTGG-ACTGGGACTCGGGAGACCTGGGTTC 61 chr4ptel1M 155484 AGAT---AG--------CTTACTAGCTGCAAGATTTAGGGCAACTCACTT 155522 ?i? ---i -------- ?i i? ?iv ii v v MIR1_Amn#SINE 62 NANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGTCACTT 111 chr4ptel1M 155523 TGCC-CTGTTTGCCTCAGTTTCTTCATCTGTAAAATG 155558 ?i - v v? i MIR1_Amn#SINE 112 NACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATG 148 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 25.52 CpG sites = 17, Kimura (unadjusted) = 26.76 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.04 (5 / 121), avg. gap size = 3.20 (16 / 5) 571 29.70 5.82 1.98 chr4ptel1M 155804 156095 (843905) L1ME3Cz_3end#LINE/L1 77 379 (618) m_b167s551i0 6322 chr4ptel1M 155804 TATGAATA--CAATTGTTTAGAA-AGGTCTCTTGAAT--CCAAGCAACCA 155848 i -- -ivi - vvv ii -- -i v L1ME3Cz_3end# 77 TATGAACAGGCAATT-CACAGAAGAGGAAACCCGAATGGCCAA-TAAACA 124 chr4ptel1M 155849 TATGAAAAAGTGTTCCAAGTCATAAATAATTAGAGAAATAAAAGTTCAAG 155898 ii i v vv iv i i i iv i v i L1ME3Cz_3end# 125 TATGAAAAGATGCTCAACCTCACTAGTAATCAGGGAAATGCAAATTAAAA 174 chr4ptel1M 155899 CAACTCTGAGGTTCCACCTCATATCCATCATATTGACAAAGATGACAAAA 155948 ? vv i v ii i i v i i v-i L1ME3Cz_3end# 175 CNACAATGAGATACCATTTCACACCCATCAGATTGGCAAAAATT-TAAAA 223 chr4ptel1M 155949 ATA-GAAAACAATAATTGCT-----GGATGCAGGAAAACAGACACACTAA 155992 i v- v i vi v i ----- ii ii i iv v v L1ME3Cz_3end# 224 GTCTGACAATACCAAGTGTTGGCGAGGATGTGGAGAAACGGGAACTCTCA 273 chr4ptel1M 155993 TGTACTGTTGATGGAATTATGAATTGGCCTAGGCATTCT-GAAAGCAATT 156041 ii i i i v i i ivi iv i i - i L1ME3Cz_3end# 274 TACACTGCTGGTGGGAGTGTAAATTGGTACAACCACTTTGGAGAGCAATT 323 chr4ptel1M 156042 TGG-GAT-TCTGCTCCAAAGTT---ATTGTGCAGACCTGTTTGACCCAGC 156086 -i - iv -- ---iv i v i- vi L1ME3Cz_3end# 324 TGGCAATATCTAGT--AAAGTTGAAGATGCGCATACCC-TACGACCCAGC 370 chr4ptel1M 156087 AATACTACT 156095 v i L1ME3Cz_3end# 371 AATTCCACT 379 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.17 CpG sites = 54, Kimura (unadjusted) = 39.58 Transitions / transversions = 1.74 (54/31) Gap_init rate = 0.05 (15 / 291), avg. gap size = 1.53 (23 / 15) 604 32.28 3.53 0.38 chr4ptel1M 155841 156095 (843905) L1ME5_3end#LINE/L1 121 383 (558) m_b167s551i1 6322 chr4ptel1M 155841 AGCAACCATATGAAAAAGTGTTCCAAGTCATAAATAATTAGAGAAATAAA 155890 i v i ii i v v v i i iv L1ME5_3end#LI 121 AACAAGCATATGAAGAGATGCTCAAACTCATTAGTAATCAGAGAAATGCA 170 chr4ptel1M 155891 AGTTCAAGCAACTCTGAGGTTCCACCTCATATCCATCATATTGACAAAGA 155940 i v i vv i vi i i i i i i v i i i L1ME5_3end#LI 171 AATTAAAACAACAATGAGATATCACTTTACACCTATTAGACTGGCAAAAA 220 chr4ptel1M 155941 TGACAAAAATAGAAAACAATAATTGCT-----GGATGCAGGAAAACAGAC 155985 v v iv i v iivi v i ----- ii i ? i iv L1ME5_3end#LI 221 TTAGAAAGCTGGATAATGCCAAGTGTTGGCGAGGATGTGGGGANATAGGA 270 chr4ptel1M 155986 ACACTAATGTACTGTTGATGGAATTATGAATTGGCCTAGGCATTCT-GAA 156034 v v i i i i v i ii i ivi v - i L1ME5_3end#LI 271 ACCCTCATGCACTGCTGGTGGGAGTGTAGACTGGTGCAGCCATTCTGGAG 320 chr4ptel1M 156035 AGCAATTTGGGATT-CTGCTCCAAAGTTATTGT--GCAGACCTGTTTGAC 156081 i v v - vvvi v v v i -- v i- v L1ME5_3end#LI 321 AGCAATCTGGCAGTACTTAGTCAAATTAAGTATACGCATACCC-TATGAC 369 chr4ptel1M 156082 CCAGCAATACTACT 156095 v ii L1ME5_3end#LI 370 CCAGCAATTCCGCT 383 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 43.21 CpG sites = 49, Kimura (unadjusted) = 44.03 Transitions / transversions = 1.48 (49/33) Gap_init rate = 0.02 (5 / 254), avg. gap size = 2.00 (10 / 5) 371 21.96 8.70 1.01 chr4ptel1M 156166 156257 (843743) C MIRc#SINE/MIR (135) 133 35 m_b167s601i12 6316 chr4ptel1M 156166 AGAAAAC--AGGC----AGAAGTAAAGTGACTTGTCCGGGGTCATACAGC 156209 i -- ---- i v i ii i C MIRc#SINE/MIR 133 AGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGC 84 chr4ptel1M 156210 TAGTAAATATCAAATGCC-ATATTTTAACTCAGATCTTCCTGA-TCTGAG 156257 i iv i - -iv i iv i i - ii C MIRc#SINE/MIR 83 TAGTAAGTGGCAGA-GCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 25.87 CpG sites = 16, Kimura (unadjusted) = 27.48 Transitions / transversions = 4.00 (16/4) Gap_init rate = 0.05 (5 / 91), avg. gap size = 1.80 (9 / 5) 242 32.59 0.00 3.97 chr4ptel1M 156331 156461 (843539) L1ME3_3end#LINE/L1 425 550 (359) m_b167s551i2 6323 chr4ptel1M 156331 AAAAGAATCCATGGGTGCAAAAATATTTATAGTAGTTCTTCCCATAATAG 156380 --- -- i i i i i i i vii L1ME3_3end#LI 425 AAAAGA---CATG--TACAAGAATGTTCATAGCAGCTTTATTCATAATAG 469 chr4ptel1M 156381 TCAAAACCCAGAAACTAAAGAGCTTCCCGTCTACTATAGAACAACAAAAC 156430 i ? v ii v vvv iv vi i v vi? iiivv i L1ME3_3end#LI 470 CCNAAAACTGGAAACAACCCAAATGTCCATCAACAGNAGAATGGATAAAT 519 chr4ptel1M 156431 AAATGGCAGCATTTGAATGCAATGGAATATT 156461 v ii i v vv i i L1ME3_3end#LI 520 AAATTGTGGTATATTCATACAATGGAATACT 550 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 45.45 CpG sites = 25, Kimura (unadjusted) = 45.45 Transitions / transversions = 1.56 (25/16) Gap_init rate = 0.04 (5 / 130), avg. gap size = 1.00 (5 / 5) 258 34.17 0.00 0.00 chr4ptel1M 156345 156464 (843536) L1MD3_3end#LINE/L1 434 553 (2189) m_b167s551i3 6323 chr4ptel1M 156345 GTGCAAAAATATTTATAGTAGTTCTTCCCATAATAGTCAAAACCCAGAAA 156394 i vi i i i i vii ? i ? ii L1MD3_3end#LI 434 GTACACGAATGTTTATAGCAGCTTTATTCATAATNGCCAAAANCTGGAAA 483 chr4ptel1M 156395 CTAAAGAGCTTCCCGTCTACTATAGAACAACAAAACAAATGGCAGCATTT 156444 v vv? v vi ? v vivv iiivv iv ii i iv L1MD3_3end#LI 484 CAACCNAGATGTCCNTCAACAGGTGAATGGATAAACAAACTGTGGTACAT 533 chr4ptel1M 156445 GAATGCAATGGAATATTGTT 156464 vv i i i L1MD3_3end#LI 534 CCATACAATGGAATACTATT 553 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 48.03 CpG sites = 24, Kimura (unadjusted) = 49.76 Transitions / transversions = 1.41 (24/17) Gap_init rate = 0.00 (0 / 119), avg. gap size = 0.0 (0 / 0) 469 31.15 2.53 3.51 chr4ptel1M 156979 157294 (842706) L1MC5a_3end#LINE/L1 324 636 (2141) m_b167s551i5 6324 chr4ptel1M 156979 AATTTGGAACTATGCTCAAAAAGTTATTAAACTGTGCAT--ACCCTTTGA 157026 v v - viv --- v - i -- L1MC5a_3end#L 324 AATTTGGCAATAT-CTAGCAAA---ATTACA-TATGCATTTACCCTTTGA 368 chr4ptel1M 157027 TCCAGCAGTGTTTCTACTGGGCTTATATCCCAAAGAGAT-CTT--AAAGA 157073 i i viiv v i vv v i v i- ?-- i L1MC5a_3end#L 369 CCCAGCAATCCCACTTCTAGGAATCTATCCCGAAGATACACTNGCAAAAA 418 chr4ptel1M 157074 GGGGAAAGGGACCTGTATGTGGACGAATGTTTGTGGCAGCCCTCTTTGTA 157123 viv -? -- iiv v iv i ii v vi v L1MC5a_3end#L 419 TACGAAA-NGAC--GTATGCACAAGGTTATTCATTGCAGCATTATTTGTA 465 chr4ptel1M 157124 GTGGCTAGAAACTGGAAACTGAGTGGATGCCCATCAGTTGGAGAGTGGCT 157173 i i v i i vivviii i i v i v i L1MC5a_3end#L 466 ATAGCAAAAGACTGGAAACAACCCAAATGTCCATCAATAGGGGACTGGTT 515 chr4ptel1M 157174 GAATAAATTGTGGTATATGAATGTTATGGAATATTATTATTCTCTAAGAA 157223 i i i vv iiiv i i vvvv v - L1MC5a_3end#L 516 GAATAAACTATGGTACATCCACACAATGGAGTACTATGCAGCTGTAA-AA 564 chr4ptel1M 157224 ATGACCAGCAGGAGGATTTC---AGAAAGGCCTGGAGAGACTTGCAGGAA 157270 v -- vv i i --- v vv ?iv v ii v v L1MC5a_3end#L 565 AGGA--ATGAGGAAGATCTCTATATACTGNTATGGAGTGATCTCCAGGAT 612 chr4ptel1M 157271 CTGATGTTGAGTGAAGTGAGCAGG 157294 v iv i ivi i L1MC5a_3end#L 613 ATATTGTTAAGTGAAAAAAGCAAG 636 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.84 CpG sites = 48, Kimura (unadjusted) = 41.40 Transitions / transversions = 1.02 (48/47) Gap_init rate = 0.05 (15 / 315), avg. gap size = 1.27 (19 / 15) 652 27.32 0.86 2.18 chr4ptel1M 156979 157210 (842790) L1ME3G_3end#LINE/L1 320 548 (376) m_b167s551i4 6324 chr4ptel1M 156979 AATTTGGAACTATGCTCAAAAAGTTATTAAACTGTGCATACCCTTTGATC 157028 v v - vvv i -- v i i L1ME3G_3end#L 320 AATTTGGCAGTAT-CTATTAAAATT--TAAAATGCGCATACCCTTTGACC 366 chr4ptel1M 157029 CAGCAGTGTTTCTACTGGGCTTATATCCCAAAGAGAT-CTTAAAGA-GGG 157076 i viiv v ? ?v v i ? i - iiv v - v L1ME3G_3end#L 367 CAGCAATTCCACTTCTNGGNATCTATCCTANAGAAATACTCGCACATGTG 416 chr4ptel1M 157077 GAAAGGGACCTGTATGTGGACGAATGTTTGTGGCAGCCCTCTTTGTAGTG 157126 v v i --? i iv v i ii v vi v i i L1ME3G_3end#L 417 CACAAGGA--NGCATGTACAAGGATGTTCATTGCAGCATTGTTTGTAATA 464 chr4ptel1M 157127 GCTAGAAACTGGAAACTGAGTGGATGCCCATCAGTTGGAGAGTGGCTGAA 157176 v i i vivv ii i i v i i i i L1ME3G_3end#L 465 GCGAAAAATTGGAAACAACCTAAATGTCCATCAATAGGGGAATGGTTAAA 514 chr4ptel1M 157177 TAAATTGTGGTATATGAATGTTATGGAATATTAT 157210 i vv ii i L1ME3G_3end#L 515 TAAATTATGGTATATCCATACTATGGAATACTAT 548 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.90 CpG sites = 34, Kimura (unadjusted) = 35.38 Transitions / transversions = 1.21 (34/28) Gap_init rate = 0.03 (7 / 231), avg. gap size = 1.00 (7 / 7) 17 8.02 0.00 0.00 chr4ptel1M 158127 158153 (841847) (CATGC)n#Simple_repeat 1 27 (0) m_b167s252i6 6325 chr4ptel1M 158127 CATGCCATGCTATGCCATGCTATGCCA 158153 i i (CATGC)n#Simp 1 CATGCCATGCCATGCCATGCCATGCCA 27 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 322 31.91 2.80 1.38 chr4ptel1M 159206 159348 (840652) L1ME2z_3end#LINE/L1 430 574 (617) m_b167s551i6 6326 chr4ptel1M 159206 ACTTATACAAAAATATTTATAGCAGCTTTTTGTGT-ATGGCTAAGAATTG 159254 i i i i v vii - i i i i L1ME2z_3end#L 430 ACTTGTACAAGAATGTTCATAGCAGCTTTATTCATAATAGCCAAAAACTG 479 chr4ptel1M 159255 GAAACTG---AAGAATGTTGATCAGTTGGAGATTGGCAGAACAACCTTTG 159301 v --- i -- iv iiv v vvi v v L1ME2z_3end#L 480 GAAACAGCCCAGG--TGTCCATCAACAGGAGAATGGATAAACAAACTGTG 527 chr4ptel1M 159302 CTATATTATTGTAATGAATCATTATTGTACTATAAGAAAAGACAAGC 159348 v vv ii i vi i i vvi v i iii i i L1ME2z_3end#L 528 GTATATTCATACAATGGAATACTACTCAGCAATAAAAAGGAACGAAC 574 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 42.05 CpG sites = 28, Kimura (unadjusted) = 43.36 Transitions / transversions = 1.65 (28/17) Gap_init rate = 0.03 (4 / 142), avg. gap size = 1.50 (6 / 4) 19 22.98 0.00 0.00 chr4ptel1M 159589 159626 (840374) (T)n#Simple_repeat 1 38 (0) m_b167s252i7 6327 chr4ptel1M 159589 TTTTTCTTTCTTTTTTTCTTTTTTCTCTTTCTTTCTTT 159626 i i i i i i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 38 Matrix = Unknown Transitions / transversions = 1.00 (7/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 390 29.49 7.84 2.48 chr4ptel1M 160874 161026 (838974) MIRc#SINE/MIR 20 180 (88) m_b167s601i13 6328 chr4ptel1M 160874 GGACAGAGGACTAGACC------CAAAAAGATCTGGATGGAAATCTCATC 160917 v v i i------ ii i i vvi i i iv MIRc#SINE/MIR 20 GGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGC 69 chr4ptel1M 160918 TTAAAAACACTTCCTAGCTGTACAACTTTGGCCAAATC-CCCAGACTTTC 160966 iviv-- v iii i v i - ii iv i MIRc#SINE/MIR 70 TCTGC--CACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTC 117 chr4ptel1M 160967 TGAGGAT---TTTCCTCATCTAGAAAATGGGGACCATAACACTGTTGGC- 161012 vv --- iv iv i --i v - MIRc#SINE/MIR 118 TGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAC--CTGCCC 165 chr4ptel1M 161013 -ACCTCCCTCAAAAG 161026 -i v v i MIRc#SINE/MIR 166 TGCCTACCTCACAGG 180 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.58 CpG sites = 27, Kimura (unadjusted) = 38.84 Transitions / transversions = 1.59 (27/17) Gap_init rate = 0.06 (9 / 152), avg. gap size = 1.78 (16 / 9) 197 32.25 4.17 3.09 chr4ptel1M 161055 161150 (838850) C L3#LINE/CR1 (2) 4097 4001 m_b167s601i14 6329 chr4ptel1M 161055 TAACATCGCAAAGTCCCAAAGCTGAAGGAGAACCTGCAGGGCCATCCAGT 161104 iv i i i i i i i i i - vvii i i C L3#LINE/CR1 4097 TAGAATCACAGAATCTCAGAGTTGGAAGGGA-CCTTAGAGGTCATCTAGT 4049 chr4ptel1M 161105 TTAACTGGTCCC--CGAAC-CACAACTCCCT-CTCTGACATTCTTGACAA 161150 ii i-- -- v i- vi v - vii i i C L3#LINE/CR1 4048 CCAACC--TCCCATCCAATGCAGGAATCCCTTCTACAACATCCCTGACAA 4001 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 46.26 CpG sites = 23, Kimura (unadjusted) = 46.26 Transitions / transversions = 3.29 (23/7) Gap_init rate = 0.06 (6 / 95), avg. gap size = 1.17 (7 / 6) 272 31.08 6.90 5.68 chr4ptel1M 161186 161359 (838641) L2b_3end#LINE/L2 281 456 (10) m_b167s601i15 6330 chr4ptel1M 161186 CTCCCCCA--TTTATCCTGTCTACTT---GTTGT--TGGAATG--TACTT 161226 i --ii i i - i--- i -- v vv -- v L2b_3end#LINE 281 CCCCCCCAGTCCTACCCTGCC-ACTCTGGGTTATNATTGTCTGNTTACAT 329 chr4ptel1M 161227 GTTTGTTTTTTCCCCATTGCAAAAAAGAGATCTTCCTGAAG-CAGACATT 161275 i i i-- i --- i vv v v i v i - iv ii L2b_3end#LINE 330 GTCTGTCTC--CCCCACT---AGACTGTGAGCTCCGTGAGGGCAGGGACC 374 chr4ptel1M 161276 GCTGTTGCCTT--TCTTTGTTGTATCCCCAGTGCTTTGTATGACACGCAT 161323 ?vvi i -- vii i i i v i--- - ?ii L2b_3end#LINE 375 GNGTCTGTCTTGTTCACCGCTGTATCCCCAGCGCCTAGC---ACA-GNGC 420 chr4ptel1M 161324 TAAGCAGACAGTGGGAGCTTAATAAATGTTTCTTGA 161359 ivi v i v i i i v L2b_3end#LINE 421 CTGGCACACAGTAGGCGCTCAGTAAATATTTGTTGA 456 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.48 CpG sites = 33, Kimura (unadjusted) = 42.83 Transitions / transversions = 1.83 (33/18) Gap_init rate = 0.09 (16 / 173), avg. gap size = 1.38 (22 / 16) 275 31.56 2.96 6.11 chr4ptel1M 161225 161359 (838641) L2a_3end#LINE/L2 377 507 (10) m_b167s601i16 6330 chr4ptel1M 161225 TTGTTTGTTTTTTCCCCATTGCAAAAAAGAGATCTTCCTGAAG-CAGACA 161273 i i ii- i --- i v vi v i v i - iv L2a_3end#LINE 377 TTGTCTGTCTCC-CCCCACT---AGAATGTAAGCTCCATGAGGGCAGGGA 422 chr4ptel1M 161274 TTGCTGT-TGCCTT--TCTTTGTTGTATCCCCAGTGCTTTGTATGACACG 161320 i vi - ii -- vi i i i v ---i - L2a_3end#LINE 423 CTTTTGTCTGTTTTGTTCACTGCTGTATCCCCAGCGCCTAG---AACA-G 468 chr4ptel1M 161321 CATTAAGCAGACAGTGGGAGCTTAATAAATGTTTCTTGA 161359 iiiivi v i i v i i v L2a_3end#LINE 469 TGCCTGGCACATAGTAGGCGCTCAATAAATATTTGTTGA 507 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 42.07 CpG sites = 28, Kimura (unadjusted) = 43.57 Transitions / transversions = 2.33 (28/12) Gap_init rate = 0.08 (11 / 134), avg. gap size = 1.09 (12 / 11) 269 23.39 3.70 5.00 chr4ptel1M 161288 161368 (838632) L2d2_3end#LINE/L2 475 554 (1) m_b167s601i17 6330 chr4ptel1M 161288 CTTTGTTGTATCCCC---AGTGCTTTGTATGACACGCATTAAGCAGACAG 161334 iv --- i i v i iiii-- v -- v L2d2_3end#LIN 475 CTTCTTTGTATCCCCCACAGCGCCTAGCACAGT--GCCTT--GCACACAG 520 chr4ptel1M 161335 TGGGAGCTTAATAAATGTTTCTTGATTTGACTTG 161368 i v i i v i L2d2_3end#LIN 521 TAGGCGCTCAATAAATATTTGTTGATTTGATTTG 554 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.04 CpG sites = 12, Kimura (unadjusted) = 28.92 Transitions / transversions = 2.00 (12/6) Gap_init rate = 0.06 (5 / 80), avg. gap size = 1.40 (7 / 5) 265 31.89 10.32 2.96 chr4ptel1M 161367 161492 (838508) C L3#LINE/CR1 (100) 3999 3865 m_b167s601i18 6329 chr4ptel1M 161367 TGGCCATTCAGCTTTTGTTTGAAGTCCTCCAAATGA--GAAAATTTTCCA 161414 i i i i i vv - i -- ii ii iv i C L3#LINE/CR1 3999 TGGTCATCCAGCCTCTGCTTGAACACCTCC-AGTGACGGGGAGCTCACTA 3951 chr4ptel1M 161415 CTTAGAGAGACAAATCATC----------ACACTTCTGATTGCTGCAAGG 161454 i v?v i ivi i---------- vi i --- i C L3#LINE/CR1 3950 CCTCNCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGATTGTT---AGA 3904 chr4ptel1M 161455 CAGTTCTTCCTTGTCTTAAGTC-AATTCTATACCTCTAT 161492 v i v i i - v iivi i i C L3#LINE/CR1 3903 AAGTTCTTCCTTATATTGAGCCGAAATCTGCCTCCCTGT 3865 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 45.36 CpG sites = 28, Kimura (unadjusted) = 45.36 Transitions / transversions = 2.55 (28/11) Gap_init rate = 0.06 (7 / 125), avg. gap size = 2.43 (17 / 7) 11 21.03 3.12 8.20 chr4ptel1M 162873 162936 (837064) (GTGTGTCT)n#Simple_repeat 1 61 (0) m_b167s252i8 6331 chr4ptel1M 162873 GTGTGATCAGTAT-TCTGTATGTCTTATATGTTAGATAGTCTAGTTGTGC 162921 - v i - i - i i iv vvv - - - (GTGTGTCT)n#S 1 GTGTG-TCTGTGTGTCTGTGTGTC-TGTGTGTCTGTGTGTCT-G-TGTG- 45 chr4ptel1M 162922 TCTGTGT-TCTGTGTG 162936 - (GTGTGTCT)n#S 46 TCTGTGTGTCTGTGTG 61 Matrix = Unknown Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.11 (7 / 63), avg. gap size = 1.00 (7 / 7) 13 15.51 5.56 0.00 chr4ptel1M 164261 164296 (835704) (TGTATA)n#Simple_repeat 1 38 (0) m_b167s252i9 6332 chr4ptel1M 164261 TGT-TATGTATATGCATATGGGTATG-ATTTGTATGTG 164296 - i vi - v i (TGTATA)n#Sim 1 TGTATATGTATATGTATATGTATATGTATATGTATATG 38 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 252 29.22 2.17 3.30 chr4ptel1M 165655 165746 (834254) C L3#LINE/CR1 (297) 3802 3712 m_b167s601i19 6333 chr4ptel1M 165655 TTCTAGAGGACAGCCTTTCAATAACTAGAGGATAATGGCTATCCCACCCC 165704 i v v i vv i v i i --- viii i C L3#LINE/CR1 3802 TTCCACATGACAGCCCTTCAAATATTTGAAGACA---GCTATCATGTCTC 3756 chr4ptel1M 165705 CA--AAGTCTTCTCTTGTCCAAGATCAACAGTCTCAGCTCTGTC 165746 v-- v i v v vi i i iv C L3#LINE/CR1 3755 CTCTAAGTCTTCTCTTCTCCAGGCTAAACATCCCCAGTTCCTTC 3712 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.70 CpG sites = 14, Kimura (unadjusted) = 37.70 Transitions / transversions = 1.17 (14/12) Gap_init rate = 0.04 (4 / 91), avg. gap size = 1.25 (5 / 4) 443 22.37 8.59 2.21 chr4ptel1M 166343 166470 (833530) C MIRc#SINE/MIR (123) 145 10 m_b167s601i20 6334 chr4ptel1M 166343 ATTTTATAGATGAGCAAACTGAGG--CAGACAGGATGGAATTCCATGCCC 166390 i v -- v - vi i vv v C MIRc#SINE/MIR 145 ATTTTACAGATGAGGAAACTGAGGCTCAGAGAGG-TTAAGTGACTTGCCC 97 chr4ptel1M 166391 TAGGTTACACAGTCAGTAAGTATCTAGAGTT-GGATTTGAACT---GACT 166436 v i ii iv - ii- i i i--- v C MIRc#SINE/MIR 96 AAGGTCACACAGCTAGTAAGTGGC-AGAGCCGGGACTCGAACCCAGGTCT 48 chr4ptel1M 166437 TCCTGACTC-----CTGGTGCTTTATCCCGCTTTACCAC 166470 ----- ii i - i i vi C MIRc#SINE/MIR 47 TCCTGACTCCAAGTCCAGTGCTCT-TTCCACTGCACCAC 10 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 25.07 CpG sites = 18, Kimura (unadjusted) = 27.30 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.06 (7 / 127), avg. gap size = 2.00 (14 / 7) 15 17.16 2.44 2.44 chr4ptel1M 166564 166604 (833396) (ATAG)n#Simple_repeat 1 41 (0) m_b167s252i10 6335 chr4ptel1M 166564 ATA-ATGGTTAGATGATATCTATAGATAGATAAATAGATAGA 166604 - i v - v vv i (ATAG)n#Simpl 1 ATAGATAGATAGAT-AGATAGATAGATAGATAGATAGATAGA 41 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 318 36.92 3.93 1.09 chr4ptel1M 166639 166816 (833184) C MIR3#SINE/MIR (4) 204 22 m_b167s601i21 6336 chr4ptel1M 166639 CATAAAGTCAGAGTATA-AATAGCTAAAAGAGACCT--GAGATTTATTTA 166685 i i v v i-v v ii i -- i- i C MIR3#SINE/MIR 204 CATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATC-ATCTA 156 chr4ptel1M 166686 ACAAAAACTGTTCTCTGTACACAGGAGTCAGCCCTAGCCCAAAGAACTAA 166735 iivv v ivi vi v v v vv i ivvi i iv i C MIR3#SINE/MIR 155 GTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGA 106 chr4ptel1M 166736 --TGACTCCTGTAAAATCGTGCAGTGGTTCACTAGCAAAGCTAAGACTGG 166783 -- ivivi ii iii i?iv i v i i iii i C MIR3#SINE/MIR 105 AGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAG 56 chr4ptel1M 166784 GTCTCAGACC-CCTGCCTCT-AATCCGGTGCTCTC 166816 iv i ii - v i- i - C MIR3#SINE/MIR 55 AACCCAGGTCTCCTGACTCCCAGTCCG-TGCTCTC 22 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 53.44 CpG sites = 42, Kimura (unadjusted) = 54.89 Transitions / transversions = 1.83 (42/23) Gap_init rate = 0.04 (7 / 177), avg. gap size = 1.29 (9 / 7) 239 31.86 9.63 5.74 chr4ptel1M 166919 167271 (832729) C L3#LINE/CR1 (225) 3874 3509 m_b167s601i22 6337 chr4ptel1M 166919 GCCTCACAGTAACTTCTACC--TTACTCATTTTTCT------TGAAGCCC 166960 v v i -- iv v vv ------ i v C L3#LINE/CR1 3874 GCCTCCCTGTAACTTCCACCCATTGGTCCTAGTTCTGCCCTCTGGAGCCA 3825 chr4ptel1M 166961 TA-AGA-TAA--TTGATCTGAAACTCTTCCTCCTGTCCCCGCCCCCAACA 167006 i - - --i i i---- v v ------------ C L3#LINE/CR1 3824 CACAGAATAAGTCTAATCC----CTCTTCCACATG------------ACA 3791 chr4ptel1M 167007 AACCCTCACATACTGGAAGACAACAGGCATTTTGTCCTC--AGTCTTCCC 167054 iv i v i v i viv v i- -- i C L3#LINE/CR1 3790 GCCCTTCAAATATTTGAAGACAGCTATCATGTC-TCCTCTAAGTCTTCTC 3742 chr4ptel1M 167055 TTCTCCAGGTTCCCCATCCCTCCCTCCTTCAGCCA--------GTGAAA- 167095 i vvv ivvi i i--------i v - C L3#LINE/CR1 3741 TTCTCCAGGCTAAACATCCCCAGTTCCTTCAACCGTTCCTCATATGACAT 3692 chr4ptel1M 167096 -GTTTCCCTGCCCC---CCTTCCTCTTCTCCTTTCTGTAATCACCCTCCA 167141 - vvi i--- v vv v ii i v iiv i v C L3#LINE/CR1 3691 GGTTTCCAGACCCTTCACCATCCTGGTCGCTCTCCTCTGGACGCGCTCCA 3642 chr4ptel1M 167142 GCTGATCGAATGTCTTCC--AGAATTTCAGCAGGTAGAATAGGAGACCTG 167189 i vi - iii -- i v -i ivvi iv i vi vvv C L3#LINE/CR1 3641 GTTTGTC-AATGTCCCTCTTAAAATGT-GGCGCCCAGAACTGAACGCAAT 3594 chr4ptel1M 167190 ACTCCAGGGATGG-CAGAGCCCCACTAAGGGCCAGTGGG-CCACC-CTTC 167236 ivi - v v vv i - ii vv i - i ii- i C L3#LINE/CR1 3593 ACTCCAGATGTGGTCTGACCAGCGC-AGAGTACAGCGGGACTATTACCTC 3545 chr4ptel1M 167237 CCTCCTTCTGG--GCTAGAATTCTGCATAGTATAGCC 167271 iv? --i v v ii- i ii C L3#LINE/CR1 3544 CCTTGNTCTGGACACTATACTTCTAT-TAATGCAGCC 3509 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.57 CpG sites = 57, Kimura (unadjusted) = 42.68 Transitions / transversions = 1.16 (57/49) Gap_init rate = 0.10 (36 / 352), avg. gap size = 1.53 (55 / 36) 227 33.34 2.54 3.42 chr4ptel1M 167438 167555 (832445) L2c_3end#LINE/L2 344 460 (18) m_b167s601i23 6338 chr4ptel1M 167438 TTGTTGCTTTACATTTTTATTACCCCCATTCAAAGGTGTGCTCCCC-AGG 167486 ivv ? v i i iv i i vi vv v ii- L2c_3end#LINE 344 TTGTCTGTTTACNTGTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGG 393 chr4ptel1M 167487 GCAGTGGGAATGAGTTTGGGTTTGATCT--GGAGACATAGTACCTGGCAC 167534 -- vi v i vi-- v -- v vv vi ii L2c_3end#LINE 394 GCAG--GGACCGTGTCTTA--TTCATCTTTGTATCCCCAGCGCCTGGCAC 439 chr4ptel1M 167535 ACGATAAGCGCTCACTGACTG 167555 iii i v i v L2c_3end#LINE 440 ATAGTAGGCGCTCAATAAATG 460 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 42.25 CpG sites = 20, Kimura (unadjusted) = 45.59 Transitions / transversions = 1.11 (20/18) Gap_init rate = 0.05 (6 / 117), avg. gap size = 1.17 (7 / 6) 21 0.00 0.00 0.00 chr4ptel1M 167785 167807 (832193) (C)n#Simple_repeat 1 23 (0) m_b167s252i11 6339 chr4ptel1M 167785 CCCCCCCCCCCCCCCCCCCCCCC 167807 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCC 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 187 17.61 5.66 14.29 chr4ptel1M 167833 167885 (832115) L2c_3end#LINE/L2 415 463 (15) m_b167s601i24 6340 chr4ptel1M 167833 TCTTTGGATCGCCATCTCTTAGCACTTGGCACATAGCAAGCACT---TAG 167879 v v ------- i i i i i --- i L2c_3end#LINE 415 TCTTTGTATCCCCA-------GCGCCTGGCACATAGTAGGCGCTCAATAA 457 chr4ptel1M 167880 ATGTTT 167885 L2c_3end#LINE 458 ATGTTT 463 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 15.09 CpG sites = 6, Kimura (unadjusted) = 20.42 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.15 (8 / 52), avg. gap size = 1.25 (10 / 8) 13 17.78 0.00 3.03 chr4ptel1M 167886 167919 (832081) (TTCA)n#Simple_repeat 1 33 (0) m_b167s252i12 6341 chr4ptel1M 167886 TTCCTTCATTGATTCATTGAATCAATCTATTCAT 167919 v v v v v - (TTCA)n#Simpl 1 TTCATTCATTCATTCATTCATTCATTC-ATTCAT 33 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 238 26.72 11.76 4.59 chr4ptel1M 167921 168022 (831978) C L2d2_3end#LINE/L2 (3) 552 444 m_b167s601i25 6342 chr4ptel1M 167921 AATAAACTTAATAAAAAGTCATCAATTAAGGATCTCCTACATGCCAGGCA 167970 v v i i ----i iv i vii v iii v C L2d2_3end#LIN 552 AATCAAATCAACAAA----TATTTATTGAGCGCCTACTGTGTGCAAGGCA 507 chr4ptel1M 167971 TTTTGCTAAGCATCTGTG-------CTAAGCAA---AAGACA--GTCCCT 168008 i v i i- ------- v v i--- -- C L2d2_3end#LIN 506 CTGTGCTAGGCG-CTGTGGGGGATACAAAGAAGTATAAGACATGGTCCCT 458 chr4ptel1M 168009 GTCCTCGAAGAGCT 168022 i i i C L2d2_3end#LIN 457 GCCCTCAAGGAGCT 444 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.19 CpG sites = 17, Kimura (unadjusted) = 34.42 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.08 (8 / 101), avg. gap size = 2.12 (17 / 8) 477 29.41 3.45 6.19 chr4ptel1M 168304 168535 (831465) MER121#DNA/hAT 1 226 (175) m_b167s502i0 6343 chr4ptel1M 168304 TGGGGATGGGCTGACTCCAGCCCC-CTTTGGGTTTAGTAAGTTCCTCAAG 168352 i - vi i v -i iivii iivi i i MER121#DNA/hA 1 TAGGGATGGGC-GAACCCGGCCGCGTTTTGGGTTCGTCGAACGTCTCGAA 49 chr4ptel1M 168353 ATATTTGCTGAATATTTGGAGTTTCATCAAACCCACTAA----GTTTTCC 168398 v viii ii v i iviiv -- ---- v MER121#DNA/hA 50 CTATTTTTCAAACGTTTTGGGTTCGGCAAAACCCA--AAACGCGTTTTGC 97 chr4ptel1M 168399 CAATGATTTTTCCCTTCATTTTTTAAAGT--TGCCTATTGCAAATGAAAT 168446 vv i i i v vi-- iv v iv MER121#DNA/hA 98 CAAGCACTTTTCCCCTTAATTTTTAAACCCATGTGTATTTCAAGGGAAAT 147 chr4ptel1M 168447 CTAATCCTCATGTTTCTCATTTTTTGAGTCATAAATCATCAACACACAAA 168496 i vi v iv v vv v v v ii---- MER121#DNA/hA 148 TTAATCCATATGTTTCTGATTCATTTACACTTAACTCATCAAAATG---- 193 chr4ptel1M 168497 ACCCCCCTGGTTTTGTTAGAACTA-TTGATGTCCATAAAG 168535 ------- v v i - vi MER121#DNA/hA 194 -------TTGTTTTGTAAGAGCTATTTGATGTCCAAGAAG 226 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 32.74 CpG sites = 35, Kimura (unadjusted) = 38.00 Transitions / transversions = 1.21 (35/29) Gap_init rate = 0.08 (18 / 231), avg. gap size = 1.22 (22 / 18) 20 0.00 0.00 0.00 chr4ptel1M 168711 168732 (831268) (A)n#Simple_repeat 1 22 (0) m_b167s252i13 6344 chr4ptel1M 168711 AAAAAAAAAAAAAAAAAAAAAA 168732 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAA 22 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 21 11.15 2.56 0.00 chr4ptel1M 168851 168889 (831111) (TTTTAT)n#Simple_repeat 1 40 (0) m_b167s252i15 6345 chr4ptel1M 168851 TTTTATATGTATTTTTATTTTTTATTTTA-TTTTATTTTT 168889 v v vv - (TTTTAT)n#Sim 1 TTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTT 40 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.03 (1 / 38), avg. gap size = 1.00 (1 / 1) 479 25.54 0.74 7.87 chr4ptel1M 168892 169027 (830973) C MIRc#SINE/MIR (141) 127 1 m_b167s601i26 6346 chr4ptel1M 168892 CTGAGGC-AATTGGGGTTAAATGACTTGCCTAGGGTCACACAGCTAGGAA 168940 -v vv i i i i --- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG--- 81 chr4ptel1M 168941 GTGTTAAGTGTCTGAGGTCAGATTGAAACTCAGGTCCTCTTGACTTCAGG 168990 ---- v v vivi i vi i i i i i C MIRc#SINE/MIR 80 ----TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr4ptel1M 168991 GCTGATTCTCTATCCACTGAACTACCTAGCTGCCCTG 169027 v iii v v v i ---i ii C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTGCACCAC---ACTGCCTCG 1 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.37 CpG sites = 20, Kimura (unadjusted) = 31.89 Transitions / transversions = 1.67 (20/12) Gap_init rate = 0.08 (11 / 135), avg. gap size = 1.00 (11 / 11) 251 20.29 8.70 0.00 chr4ptel1M 169786 169854 (830146) MIRb#SINE/MIR 110 184 (84) m_b167s601i27 6347 chr4ptel1M 169786 CTTAAGCCCTCTCGGCT---GTTTCCTCCTCTGTGAAATGGGG---CTAA 169829 v i vi i--- v i ---v MIRb#SINE/MIR 110 CTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAA 159 chr4ptel1M 169830 CACCTCCTTCTCAGGGTTGGTGCGA 169854 i v i v v i MIRb#SINE/MIR 160 TACCTACCTCGCAGGGTTGTTGTGA 184 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 23.81 CpG sites = 7, Kimura (unadjusted) = 23.81 Transitions / transversions = 1.00 (7/7) Gap_init rate = 0.03 (2 / 68), avg. gap size = 3.00 (6 / 2) 194 26.56 4.69 0.00 chr4ptel1M 170899 170962 (829038) L3#LINE/CR1 4022 4088 (11) m_b167s601i28 6348 chr4ptel1M 170899 GGAGTTCTGCCCCG--CGGGAA-TTGGGCTAGATGTCCGCCAAGGCTCCT 170945 v i vii --i i- i v v i ii L3#LINE/CR1 4022 GGATTCCTGCATTGGATGGGAGGTTGGACTAGATGACCTCTAAGGTCCCT 4071 chr4ptel1M 170946 TGCAACTTTCAGTTTCT 170962 v i v v L3#LINE/CR1 4072 TCCAACTCTGAGATTCT 4088 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.57 CpG sites = 10, Kimura (unadjusted) = 33.57 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.03 (2 / 63), avg. gap size = 1.50 (3 / 2) 199 25.37 5.26 6.67 chr4ptel1M 171611 171686 (828314) MIR1_Amn#SINE/MIR 29 103 (127) m_b167s601i29 6349 chr4ptel1M 171611 AGCTCTGGACCAAAACTAAATCAGGGAGACTTGCATTCAAATCTCACCTC 171660 v iiii ---- - i vi ? ? i iv MIR1_Amn#SINE 29 AGCACTGGACTGGGACT----C-GGGAGACCTGGGTTCNANTCCCGGCTC 73 chr4ptel1M 171661 AGACACTAGCTAG----ATGACCATAAGCA 171686 v v ? i? ----i v ii MIR1_Amn#SINE 74 TGCCACTNGCCNGCTGNGTGACCTTGGGCA 103 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.25 CpG sites = 12, Kimura (unadjusted) = 34.62 Transitions / transversions = 2.00 (12/6) Gap_init rate = 0.08 (6 / 75), avg. gap size = 1.50 (9 / 6) 182 11.11 0.00 0.00 chr4ptel1M 171832 171858 (828142) C L3#LINE/CR1 (857) 3242 3216 m_b167s601i30 6350 chr4ptel1M 171832 TCCCTTCCAGTTTTGTGTCATGTGCAA 171858 i i v C L3#LINE/CR1 3242 TCCCTCCCAGCTTTGTGTCATCTGCAA 3216 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 12.16 CpG sites = 2, Kimura (unadjusted) = 12.16 Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 459 25.00 1.83 0.91 chr4ptel1M 172909 173017 (826983) MIRc#SINE/MIR 35 144 (124) m_b167s601i31 6351 chr4ptel1M 172909 CCTGGAGTCAGGAAAGCCTGAGTATACATCTGACCTCAGACACTTGCTAG 172958 i ii i viivi iviv v v i MIRc#SINE/MIR 35 CTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAG 84 chr4ptel1M 172959 CTGTGTGACCATGAGGAAGTCACTTCATGCCATTT--GCCTCAGTTTTCT 173006 v i v v i- iv i -- i MIRc#SINE/MIR 85 CTGTGTGACCTTGGGCAAGTCACTTAAC-CTCTCTGAGCCTCAGTTTCCT 133 chr4ptel1M 173007 CACCGGTAAAA 173017 i v MIRc#SINE/MIR 134 CATCTGTAAAA 144 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.24 CpG sites = 16, Kimura (unadjusted) = 31.08 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.02 (2 / 108), avg. gap size = 1.50 (3 / 2) 48 24.98 3.79 0.00 chr4ptel1M 173662 173793 (826207) (AG)n#Simple_repeat 1 137 (0) m_b167s252i17 6352 chr4ptel1M 173662 AGAGGGAGA-ACAGAGAGAGACAGAATCAGAGAGGGGGGGAGGGA-AGA- 173708 i - v v ivv i i i i - - (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr4ptel1M 173709 AGAGAGAGAGGAAGAAAGTAAGAGAGAGAGAGAAACAGAGAGAGAGAGAG 173758 ii i vi i v (AG)n#Simple_ 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 100 chr4ptel1M 173759 GGGGGGGGGGGGGGGGA-AGGAAGA-AGAGAGAGAGA 173793 i i i i i i i i - ii - (AG)n#Simple_ 101 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 137 Matrix = Unknown Transitions / transversions = 3.50 (21/6) Gap_init rate = 0.04 (5 / 131), avg. gap size = 1.00 (5 / 5) 16 0.00 0.00 0.00 chr4ptel1M 173758 173774 (826226) (G)n#Simple_repeat 1 17 (0) m_b167s252i18 6353 chr4ptel1M 173758 GGGGGGGGGGGGGGGGG 173774 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGG 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 48 24.98 3.79 0.00 chr4ptel1M 173662 173793 (826207) (AG)n#Simple_repeat 1 137 (0) m_b167s252i17 6352 chr4ptel1M 173662 AGAGGGAGA-ACAGAGAGAGACAGAATCAGAGAGGGGGGGAGGGA-AGA- 173708 i - v v ivv i i i i - - (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr4ptel1M 173709 AGAGAGAGAGGAAGAAAGTAAGAGAGAGAGAGAAACAGAGAGAGAGAGAG 173758 ii i vi i v (AG)n#Simple_ 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 100 chr4ptel1M 173759 GGGGGGGGGGGGGGGGA-AGGAAGA-AGAGAGAGAGA 173793 i i i i i i i i - ii - (AG)n#Simple_ 101 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 137 Matrix = Unknown Transitions / transversions = 3.50 (21/6) Gap_init rate = 0.04 (5 / 131), avg. gap size = 1.00 (5 / 5) 475 32.33 2.98 0.58 chr4ptel1M 174382 174549 (825451) C MIR3#SINE/MIR (17) 191 20 m_b167s601i32 6354 chr4ptel1M 174382 AAAGTCAGA-CTGAAGGGAATCTTGGACATGGCCT---TCAAATCATTTA 174427 v - i i i i i v vii ---i vi vi i C MIR3#SINE/MIR 191 AATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCA 142 chr4ptel1M 174428 TTTAAAAAATGTGGGAACTGAATTTCAGAGATATTAA-TGGCTTCCCCAA 174476 v v i v i ivii vi v - i v C MIR3#SINE/MIR 141 TTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAA 92 chr4ptel1M 174477 AGTCACAGAGTTTTTGTGTAGCAGAGTTGGGATCTGAAGCCAGATTCCCT 174526 i v i?vv vv i ii iiv v i ii C MIR3#SINE/MIR 91 GGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGTCTCCT 42 chr4ptel1M 174527 GAATTCAAATCCAGTGTTATTTC 174549 v i v i - i v i C MIR3#SINE/MIR 41 GACTCCCAGTCC-GTGCTCTCTC 20 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 43.08 CpG sites = 32, Kimura (unadjusted) = 44.20 Transitions / transversions = 1.45 (32/22) Gap_init rate = 0.02 (4 / 167), avg. gap size = 1.50 (6 / 4) 516 29.58 2.11 0.00 chr4ptel1M 174427 174568 (825432) C MIRc#SINE/MIR (123) 145 1 m_b167s601i33 6354 chr4ptel1M 174427 ATTTAAAAAATGTGGGAACTGAATTTCAGAGATATTAA-TGGCTTCCCCA 174475 v v i v i ivi vi - i v C MIRc#SINE/MIR 145 ATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCA 96 chr4ptel1M 174476 AAGTCACAGAGTTTTTGTGTAGCAGAGTTGGGATCTGAAGCCAGAT-TCC 174524 i v i vv iv i ii iii v i - i C MIRc#SINE/MIR 95 AGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTC 46 chr4ptel1M 174525 CTGAATTCAAATCCAGTGTTATTTCC-CTATATTATAGTTTCTTG 174568 v i i i v - ii ii i v vi i C MIRc#SINE/MIR 45 CTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTGCCTCG 1 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.63 CpG sites = 27, Kimura (unadjusted) = 39.20 Transitions / transversions = 1.80 (27/15) Gap_init rate = 0.02 (3 / 141), avg. gap size = 1.00 (3 / 3) 22 10.17 2.27 2.27 chr4ptel1M 175886 175929 (824071) (ATTTTAA)n#Simple_repeat 1 44 (0) m_b167s252i19 6355 chr4ptel1M 175886 ATTTCTAAATTTTAAATTTCTATTTTTAAATTTT-AATTTTCAAT 175929 - iv v - v (ATTTTAA)n#Si 1 ATTT-TAAATTTTAAATTTTAAATTTTAAATTTTAAATTTTAAAT 44 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2) 14 12.84 5.88 0.00 chr4ptel1M 175980 176013 (823987) (TTATTT)n#Simple_repeat 1 36 (0) m_b167s252i20 6356 chr4ptel1M 175980 TTATTTTTATCATTA-TTTT-TCTTTCTTTTTATTT 176013 iv - - i v (TTATTT)n#Sim 1 TTATTTTTATTTTTATTTTTATTTTTATTTTTATTT 36 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2) 15 7.97 0.00 6.90 chr4ptel1M 176849 176879 (823121) (CTG)n#Simple_repeat 1 29 (0) m_b167s252i21 6357 chr4ptel1M 176849 CTGCTGATTGTTGCTGCTGACTGCTGCTGCT 176879 -i i - (CTG)n#Simple 1 CTGCTG-CTGCTGCTGCTG-CTGCTGCTGCT 29 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2) 870 33.79 5.79 2.90 chr4ptel1M 177532 178101 (821899) L3#LINE/CR1 3401 3986 (113) m_b167s601i34 6358 chr4ptel1M 177532 TGACTATAG-AGCAGTTTCTTTGAAAA-TATTAAGGAGTTTTCACTGGAT 177579 i - - iviv -v iiv i - v v i L3#LINE/CR1 3401 TGGCT-TAGCAGCAGTTCACGTGAAAAAGACCTAGGGGTTTT-AGTTGAC 3448 chr4ptel1M 177580 GATAAGATTGAGATGAGGAAATAATGGGATGTGAAATCCAAGAAAGCGAA 177629 vii v ii v vv i i v ivvv i v L3#LINE/CR1 3449 CGCAAGCTCAATATGAGCCAACAGTGTGATGTGGCTGCCAAAAAAGCTAA 3498 chr4ptel1M 177630 TGCCATTTATGGGAGCATTAAAAGAGTAATAGACTTGGGGTTGCAGGACA 177679 v i vv vv v ivv vv ivi i?iivi vi L3#LINE/CR1 3499 TGCAATCTTAGGCTGCATTAATAGAAGTATAGTGTCCAGANCAAGGGAGG 3548 chr4ptel1M 177680 TGAAGGCACTGTTGCACTCTGCTCTTAGGGGATCAC-TCTGGGGATGCTG 177728 i vi iv i i i v vivvi i - i - ii L3#LINE/CR1 3549 TAATAGTCCCGCTGTACTCTGCGCTGGTCAGACCACATCTGGAG-TATTG 3597 chr4ptel1M 177729 TGTTCA-------------CAATTTAGGAAGAAACTTGATGAGCTTGAAA 177765 i ------------- v i i i vv ii i v iv L3#LINE/CR1 3598 CGTTCAGTTCTGGGCGCCACATTTTAAGAGGGACATTGACAAACTGGAGC 3647 chr4ptel1M 177766 GTGTCCCCAGAAAGGCAAGGAGAATGGTGGAAGAATTCAATCTCCTG--G 177813 i vv i ii i vv i i i ivi vi vvi v --i L3#LINE/CR1 3648 GCGTCCAGAGGAGAGCGACCAGGATGGTGAAGGGTCTGGAAACCATGTCA 3697 chr4ptel1M 177814 TATGAAGAATAAGCTAAAAAGGGCACTGAGGATGTTTAACT--GA-AAGA 177860 i ii- i i --- v i i i-- - L3#LINE/CR1 3698 TATGAGGAACG-GTTGAA---GGAACTGGGGATGTTTAGCCTGGAGAAGA 3743 chr4ptel1M 177861 AAAAACTTGAGGGAATAAATGATATTTGTTTTTATGTATTTTAAGGGTTT 177910 i i - i i v v vi i i vi v i - L3#LINE/CR1 3744 GAAGACTT-AGAGGAGACATGATAGCTGTCTTCAAATATTTGAAGGGCT- 3791 chr4ptel1M 177911 GTCCC-TGGATTCAA-ATTGTACTTTTTTAAACTTGTTAACAGATAACAG 177958 vi- vvvii- iv v ivivv v i v- vii L3#LINE/CR1 3792 GTCATGTGGAAGAGGGATTAGACTTATTCTGTGTGGCTC-CAGAGGGCAG 3840 chr4ptel1M 177959 AACTAGAAC-AATGGGAAGAAGTTACAAAGGGGTGGATTTTCACACAATG 178007 i - vi ii i ii ivi v i L3#LINE/CR1 3841 AACTAGGACCAATGGGTGGAAGTTACAGGGAGGCAGATTTCGGCTCAATA 3890 chr4ptel1M 178008 TCATGAAAAGCTTCACAACAATTAGAGAAGTCCAACATTGGA-------G 178050 v v i i ivi i vv v v ------- L3#LINE/CR1 3891 TAAGGAAGAACTTTCTAACAATCAGAGCTGTCCAAAAATGGAATGGGCTG 3940 chr4ptel1M 178051 CTTAATAAAGAAGTGCA-TCCCC-TCCCTGGCTCATCTAGGAGTTATAGC 178098 i vi?i i v vi- - v ------- v vv L3#LINE/CR1 3941 CCTCGNGAGGTAGTGAGCTCCCCGTCACTGG-------AGGTGTTCAAGC 3983 chr4ptel1M 178099 AGA 178101 L3#LINE/CR1 3984 AGA 3986 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 43.41 CpG sites = 103, Kimura (unadjusted) = 46.45 Transitions / transversions = 1.23 (103/84) Gap_init rate = 0.05 (30 / 569), avg. gap size = 1.67 (50 / 30) 220 37.99 11.47 3.40 chr4ptel1M 179074 179291 (820709) L2b_3end#LINE/L2 220 454 (12) m_b167s601i35 6359 chr4ptel1M 179074 GTCACCTCCTCCTTGAAGCCTTTCCTGATTTCTCCAGCTA---CAAGTGC 179120 vv i i iii i vi ii--- i i L2b_3end#LINE 220 GTCACCTCCTCCGGGAAGCCCTCCCTGACCCCCCAGGCCGGGTCAGGCGC 269 chr4ptel1M 179121 CTCACCCAACAATGGA-CTTTGGGGTTTTTACTTGATTTATTTTCTATCT 179169 iiv i ----- i- iiivvi ii vv i --ii i i vvi - L2b_3end#LINE 270 CCTCCTC-----TGGGCCCCCCCAGTCCTACCCTG--CCACTCTGGGT-T 311 chr4ptel1M 179170 AT--TTGGATGCAAACAGGTTGATC-ATCCCA-TAGAATGTAAGATCCTT 179215 -- vv ?vv v ivi -vi - v i v v L2b_3end#LINE 312 ATNATTGTCTGNTTACATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGT 361 chr4ptel1M 179216 GAAGACAGAGACT-TATGTATCTTA-----------ATTTTCCACACTAA 179253 i i i i-?i v i i----------- iii vi i iv L2b_3end#LINE 362 GAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTGTATCCCCAGCGCCTA 411 chr4ptel1M 179254 GTACAGAACCTGA-----ATTAAGTACTTTATAAATGCTTATT 179291 i ?i i----- v i ii ivi ii i L2b_3end#LINE 412 GCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTTGTT 454 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 53.58 CpG sites = 55, Kimura (unadjusted) = 59.71 Transitions / transversions = 2.20 (55/25) Gap_init rate = 0.07 (16 / 217), avg. gap size = 2.06 (33 / 16) 419 23.17 3.91 5.56 chr4ptel1M 179308 179435 (820565) C MIRc#SINE/MIR (141) 127 2 m_b167s601i36 6360 chr4ptel1M 179308 CTGAGGC-AACTGGGATTAAGTGACTTCCCCAAGGTCACACCAGCTAGTA 179356 -v vv i i v - C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACA-CAGCTAGTA 79 chr4ptel1M 179357 AG-AATTAAGTGTCTGAGACCAGATTCCA--TC-TCCTGACTTCAGGGCT 179402 -iiivi --- i i iv vi -- - i i v i C MIRc#SINE/MIR 78 AGTGGCAGAG---CCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCC 32 chr4ptel1M 179403 GGTGCTCTATCCACTATACTACCTAGCTGCCCC 179435 i v ii i ---i i C MIRc#SINE/MIR 31 AGTGCTCTTTCCACTGCACCAC---ACTGCCTC 2 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.41 CpG sites = 19, Kimura (unadjusted) = 28.61 Transitions / transversions = 2.11 (19/9) Gap_init rate = 0.09 (11 / 127), avg. gap size = 1.09 (12 / 11) 15 13.23 3.03 0.00 chr4ptel1M 179447 179479 (820521) (ATTGA)n#Simple_repeat 1 34 (0) m_b167s252i22 6361 chr4ptel1M 179447 ATTGAATTTAAATGAATAGAATTGAA-TAAATTG 179479 v v v - i (ATTGA)n#Simp 1 ATTGAATTGAATTGAATTGAATTGAATTGAATTG 34 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 17 23.33 0.00 0.00 chr4ptel1M 179534 179578 (820422) (AGAG)n#Simple_repeat 1 45 (0) m_b167s252i24 6362 chr4ptel1M 179534 AGAGAAAGAGAGACAAAGTGACAGATAGAAGGAGACAGAGAGAGA 179578 i v i v v v ii v (AGAG)n#Simpl 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 45 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 19 19.07 5.80 2.82 chr4ptel1M 179532 179600 (820400) (ACAGAG)n#Simple_repeat 1 71 (0) m_b167s252i23 6363 chr4ptel1M 179532 ACAGAGA-A-AGAGAGACAAAGTGACAGATAGAAGGAGACAGAGAGAGAA 179579 - - v v v v -- vi v i (ACAGAG)n#Sim 1 ACAGAGACAGAGACAGAGACAGAGACAG--AGACAGAGACAGAGACAGAG 48 chr4ptel1M 179580 ACA-A-TCAGAGGCAGAGGCAGA 179600 - -v i i (ACAGAG)n#Sim 49 ACAGAGACAGAGACAGAGACAGA 71 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.09 (6 / 68), avg. gap size = 1.00 (6 / 6) 215 29.17 0.00 0.00 chr4ptel1M 179683 179730 (820270) L2b_3end#LINE/L2 410 457 (9) m_b167s601i37 6364 chr4ptel1M 179683 TAGCATAGTGTCTGGCACATAATGGTTACTTACTAAATGTTTACTAAA 179730 i ? i i i i vii i v i ii i L2b_3end#LINE 410 TAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTTGTTGAA 457 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.96 CpG sites = 12, Kimura (unadjusted) = 42.50 Transitions / transversions = 6.00 (12/2) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 1864 22.13 8.47 2.13 chr4ptel1M 180087 180617 (819383) Charlie7#DNA/hAT-Charlie 1899 2462 (153) m_b167s502i1 6365 chr4ptel1M 180087 TGAAAATAATCATGTCTATATACTGCTAAAACACCATCTAAAAA-AGTAT 180135 i ivv i ii i -i ---- ii ii - v Charlie7#DNA/ 1899 TAAAAACTCTCATATCTGCACACT-TTAAAA----ACTTGGAAACAGAAT 1943 chr4ptel1M 180136 TTTTCAACCTGTTTAAAAACCTTTCAAATGAAGAATTTCAGTAGTTTTTT 180185 ii i i i i v v Charlie7#DNA/ 1944 TTTCTAACCTGTTTAAAAATCTTCCAAATGAAGAGTTTCAGTGGGTTTTG 1993 chr4ptel1M 180186 AACTTCTTTGTTAAAACTATA-----------TCTTTTGATTAATTTGCA 180224 iiv v -----------i ii i Charlie7#DNA/ 1994 AACCCATTTGTTAAAAATATAAAAATGCAACACCTTCCGATTAGTTTGCA 2043 chr4ptel1M 180225 AGAATTACTCATTGATACCACGGAAGAAGGAAATTTACGGGCTGGATTTC 180274 iv v i i v v vi i i Charlie7#DNA/ 2044 AGAACAACTGATTGACATCAGGGAAGATGGAAATTTACTAGCCGAATTTC 2093 chr4ptel1M 180275 AACAAAAATCTCAGCATGATTAGTGGATGACATTG-GAAATAAATATCAT 180323 i iv i i iv -i i i Charlie7#DNA/ 2094 AACAAAAACCTTTGCATAATTGGTGGATGGGATTGAAAAATGAGTATCAT 2143 chr4ptel1M 180324 GATTTAGCCAGCACTTTTTGCGGTGCACTTCTTCCATTTTAATCTAGGTA 180373 iv i vviivi i vi v Charlie7#DNA/ 2144 GATTTAGTAAGCGCAGCCAACGATGCACTTCTTCCATTTGGATCTACGTA 2193 chr4ptel1M 180374 TCTTTGCATGATGTCTTTTTCAGTTCTGACCACAATTTAAACCACATATC 180423 iiv i i i v vi v v vi - Charlie7#DNA/ 2194 TCTTTGTGAGGTATCTTTTTCAGCTATGACAGCCATTAAAACCAAGTAT- 2242 chr4ptel1M 180424 CAACCCCAAACAAAC-AAATCTAGAACCTGACCTTTCA------GTATTA 180466 ----- v i -i ii v iv ------ i Charlie7#DNA/ 2243 -----CGAAATAAACTGAACTTAGAACCAGACCTTCGAATCGCTGTATCA 2287 chr4ptel1M 180467 CAAACT-------TAGGATC--------TGACTAAG-ATTTTCAATCACA 180500 v -------i i i-------- i iv - v Charlie7#DNA/ 2288 CAAAGTGTTAAACCAAGATTTTCAAAAATAATGAAGCATATTCAATCACA 2337 chr4ptel1M 180501 TTGCTCTTGCTAAAATGTTCTTAATAGCATTTTAGTGAGAATCAGAAGGC 180550 ii i v ii iiv i v i Charlie7#DNA/ 2338 TTGCTCTCACTAAAATATTATTAATAATATTTTAGTGAGAGCAAAAATGT 2387 chr4ptel1M 180551 TTTATGTTATTAATAAATAAAATA-----TATTTCCAAAATA----TTAT 180591 i iii ----- -i ---- Charlie7#DNA/ 2388 TTTGTACCATTAATAAATAAAATAAAAATTATTT-TAAAATATTGTTTAT 2436 chr4ptel1M 180592 TTCAACTTTCTCTCAAACTTTTAAAA 180617 v v vv Charlie7#DNA/ 2437 TTCATCTTTATCTCATCCTTTTAAAA 2462 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 25.93 CpG sites = 76, Kimura (unadjusted) = 27.02 Transitions / transversions = 1.95 (76/39) Gap_init rate = 0.04 (22 / 530), avg. gap size = 2.59 (57 / 22) 25 16.37 5.45 0.00 chr4ptel1M 180795 180849 (819151) (AT)n#Simple_repeat 1 58 (0) m_b167s252i25 6366 chr4ptel1M 180795 ATATATA-ATGTATTTGTATATATA-ATATATATGTATATCCA-ATATAT 180841 - i v i - i vi - (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr4ptel1M 180842 ATGTAGAT 180849 i v (AT)n#Simple_ 51 ATATATAT 58 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.06 (3 / 54), avg. gap size = 1.00 (3 / 3) 342 27.84 2.88 4.38 chr4ptel1M 180898 181036 (818964) Charlie7#DNA/hAT-Charlie 2477 2613 (2) m_b167s502i2 6367 chr4ptel1M 180898 TGTGTTTTGTCACAGACATAAT-TATTAGTTTGGTAGGATTTGCATATAA 180946 i i v iiv - vii v iv i Charlie7#DNA/ 2477 TATGTTTTATAATGTACATAATATATTAGTACAGTAGTACATGTATATAA 2526 chr4ptel1M 180947 CTGGTAAATAAGTAAATACATATATATATCGGGAATACATGCTCATTTTT 180996 i vi i ------ i i ii i vvv Charlie7#DNA/ 2527 TTTATAAATAAATA------TACATATATTGGGGGTGCATGCTCAAAATT 2570 chr4ptel1M 180997 TTTCCCCG--GAGGATGAGCAATT-CAACACTGTGTAGACCAC 181036 iv i -- i v i i-v v v v v Charlie7#DNA/ 2571 TTTTACTGATGGGGATGCGCGATCAAAAAAGTTTGGAGACCAC 2613 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 34.34 CpG sites = 21, Kimura (unadjusted) = 35.52 Transitions / transversions = 1.31 (21/16) Gap_init rate = 0.07 (9 / 138), avg. gap size = 1.11 (10 / 9) 209 19.65 7.94 3.03 chr4ptel1M 181661 181723 (818277) MIRc#SINE/MIR 8 73 (195) m_b167s601i38 6368 chr4ptel1M 181661 GTATGGAGCAAGT----AGTGCAGTGGACA-GGAGTCAGGATGACCTGAG 181705 i v - ---- v v v- v i MIRc#SINE/MIR 8 GTGTGGTGCA-GTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGG 56 chr4ptel1M 181706 TTTAAGTCTTCAGCCCTG 181723 ii -i i i MIRc#SINE/MIR 57 TTCGAGTC-CCGGCTCTG 73 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 18.81 CpG sites = 7, Kimura (unadjusted) = 23.14 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.06 (4 / 62), avg. gap size = 1.75 (7 / 4) 182 23.53 0.00 0.00 chr4ptel1M 182925 182958 (817042) C MIR3#SINE/MIR (148) 60 27 m_b167s601i39 6369 chr4ptel1M 182925 ACTAGAACTTGGACTTCCTGACTCCCAGCCCTTG 182958 iii iii i v C MIR3#SINE/MIR 60 ACTAGAACCCAGGTCTCCTGACTCCCAGTCCGTG 27 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.61 CpG sites = 7, Kimura (unadjusted) = 30.61 Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 198 37.61 1.69 0.84 chr4ptel1M 183097 183214 (816786) C MIR3#SINE/MIR (59) 149 31 m_b167s601i40 6370 chr4ptel1M 183097 CTCCCTCACTTTACTTAAGGGGAAAATAGGGACCGAATGGATTGAGGGAC 183146 i i vv v i v ii v ii vi i vi v C MIR3#SINE/MIR 149 CCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGAC 100 chr4ptel1M 183147 CTTTCCTGGA--GCTCAGACGGTTGGCAGCAGAGCAGAGACATGAAGCCT 183194 i vi vi i--i v v?i i ii v i vv v v C MIR3#SINE/MIR 99 TTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCA 50 chr4ptel1M 183195 AGTGGACTGGCTCTGCAATC 183214 i vvv i i- i C MIR3#SINE/MIR 49 GGTCTCCTGACTCC-CAGTC 31 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 54.69 CpG sites = 24, Kimura (unadjusted) = 54.69 Transitions / transversions = 1.20 (24/20) Gap_init rate = 0.02 (2 / 117), avg. gap size = 1.50 (3 / 2) 247 21.68 1.61 3.28 chr4ptel1M 184128 184189 (815811) L2c_3end#LINE/L2 372 432 (46) m_b167s601i41 6371 chr4ptel1M 184128 CTACACTGTCAGCTACTTGAGGGCAGGAACTGTCCCCT-TTCATTGCTGT 184176 v v v i i vi i - -- v L2c_3end#LINE 372 CTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCAT--CTTT 419 chr4ptel1M 184177 GAATTTCCAGCAC 184189 v ii i L2c_3end#LINE 420 GTATCCCCAGCGC 432 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 21.54 CpG sites = 7, Kimura (unadjusted) = 25.85 Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.05 (3 / 61), avg. gap size = 1.00 (3 / 3) 14 18.95 8.16 0.00 chr4ptel1M 184241 184289 (815711) (TGAAT)n#Simple_repeat 1 53 (0) m_b167s252i26 6372 chr4ptel1M 184241 TGAATCGAACTGACTTG-A-TGAACTGAATCGAACTGACTTG-A-TGAAC 184286 i i v - - i i i v - - i (TGAAT)n#Simp 1 TGAATTGAATTGAATTGAATTGAATTGAATTGAATTGAATTGAATTGAAT 50 chr4ptel1M 184287 TGA 184289 (TGAAT)n#Simp 51 TGA 53 Matrix = Unknown Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.08 (4 / 48), avg. gap size = 1.00 (4 / 4) 291 21.89 26.09 0.69 chr4ptel1M 184416 184530 (815470) MIRb#SINE/MIR 9 152 (116) m_b167s601i42 6373 chr4ptel1M 184416 CACCATGGTGCAGTGAAAA-----TGGGCCT-GCAGTC---CAAA---AG 184453 v i i -----i i - v --- i ---i MIRb#SINE/MIR 9 CAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGG 58 chr4ptel1M 184454 GTCC-AATCTTTGCCCTGCCATTTACTGGCCATGGGATCT---------- 184492 i - iiv i i i ii v i ---------- MIRb#SINE/MIR 59 GTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTT 108 chr4ptel1M 184493 -----ACCTCTTTCAGCC--AGTTTTCCCCAACTATAAAATGAGG 184530 ----- i v -- - i v i i MIRb#SINE/MIR 109 ACTTAACCTCTCTGAGCCTCAGTTT-CCTCATCTGTAAAATGGGG 152 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 23.45 CpG sites = 19, Kimura (unadjusted) = 27.17 Transitions / transversions = 3.17 (19/6) Gap_init rate = 0.08 (9 / 114), avg. gap size = 3.44 (31 / 9) 273 29.02 16.95 0.73 chr4ptel1M 184455 184572 (815428) MIR3#SINE/MIR 55 191 (17) m_b167s601i43 6373 chr4ptel1M 184455 TCCAATCTTTGCCCTGCCATTTACTGGCCATGGGATCT------------ 184492 i i iiv i i v ? ii v i ------------ MIR3#SINE/MIR 55 TCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCAC 104 chr4ptel1M 184493 ---ACCTCTTTCAGCC--AGTTTTCCCCAACTATAAAATGAGGGGACTAA 184537 --- i vi -- - i v i ii ii MIR3#SINE/MIR 105 TTCACCTCTCTGGGCCTCAGTTT-CCTCATCTGTAAAATGAGGGGGTTGG 153 chr4ptel1M 184538 ACAGAAGGGTCTT---GGTGCCTTCCCCCTGTAAAATT 184572 vii v i i--- v vv v i v MIR3#SINE/MIR 154 ACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATT 191 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.28 CpG sites = 22, Kimura (unadjusted) = 38.76 Transitions / transversions = 1.83 (22/12) Gap_init rate = 0.04 (5 / 117), avg. gap size = 4.20 (21 / 5) 47 22.98 2.52 0.00 chr4ptel1M 185063 185181 (814819) (GACA)n#Simple_repeat 1 122 (0) m_b167s252i27 6374 chr4ptel1M 185063 GATAGACAGACAAACAGACAGACTGATGGATAGAGAGAGAG-CAAACAGA 185111 i i v ii i v v - i (GACA)n#Simpl 1 GACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGA 50 chr4ptel1M 185112 TAAACAGACAAAAAGATAGACAGACTGACAGACAGAGAGGTAGAAAGATA 185161 i i i v i v v ii v i (GACA)n#Simpl 51 CAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACA 100 chr4ptel1M 185162 GAC--ACAGGTAGACAGATAGA 185181 -- ii i (GACA)n#Simpl 101 GACAGACAGACAGACAGACAGA 122 Matrix = Unknown Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.02 (2 / 118), avg. gap size = 1.50 (3 / 2) 212 24.61 0.00 10.81 chr4ptel1M 185677 185758 (814242) MIR#SINE/MIR 23 96 (166) m_b167s601i44 6375 chr4ptel1M 185677 AGCAGGGCCTCCTGGATAGAGCCTGCATGTGACTGAATTCAAGTCCTGTC 185726 v v - vvv v ------ ii i i i v MIR#SINE/MIR 23 AGCACGGGCTC-TGGAGCCAGACTGC------CTGGGTTCGAATCCCGGC 65 chr4ptel1M 185727 TCCGCCACTCACTAACATGTGGGAGCCTGGGC 185758 i i i - v v i MIR#SINE/MIR 66 TCTGCCACTTACTAGC-TGTGTGACCTTGGGC 96 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 25.97 CpG sites = 9, Kimura (unadjusted) = 29.66 Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.10 (8 / 81), avg. gap size = 1.00 (8 / 8) 231 22.46 0.00 2.04 chr4ptel1M 185709 185758 (814242) MIRc#SINE/MIR 52 100 (168) m_b167s601i45 6375 chr4ptel1M 185709 CTGAATTCAAGTCCTGTCTCCGCCACTCACTAACATGTGGGAGCCTGGGC 185758 ii i i v i i i - v v i MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGC-TGTGTGACCTTGGGC 100 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 22.13 CpG sites = 8, Kimura (unadjusted) = 27.80 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.02 (1 / 49), avg. gap size = 1.00 (1 / 1) 219 27.29 0.00 1.82 chr4ptel1M 186147 186202 (813798) MIRb#SINE/MIR 49 103 (165) m_b168s601i1 6376 chr4ptel1M 186147 ACAGCCCTAAATTCAAGTCCTGTCTCCATCACTTACTAAGCTGTGGGAGC 186196 v iii i i i v iii - v v MIRb#SINE/MIR 49 ACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACT-AGCTGTGTGACC 97 chr4ptel1M 186197 CTAGGC 186202 i i MIRb#SINE/MIR 98 TTGGGC 103 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 30.08 CpG sites = 11, Kimura (unadjusted) = 35.93 Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.02 (1 / 55), avg. gap size = 1.00 (1 / 1) 343 27.47 13.37 2.69 chr4ptel1M 186331 186532 (813468) L3#LINE/CR1 3775 3997 (102) m_b168s601i2 6377 chr4ptel1M 186331 CAAGTGTTGGAAGAGCTTTCA---GCAGGAGGGATTTGATTTGT---GTT 186374 i i v i v --- v i v i i --- v L3#LINE/CR1 3775 CAAATATTTGAAGGGCTGTCATGTGGAAGAGGGATTAGACTTATTCTGTG 3824 chr4ptel1M 186375 TAGTGCTGG-GGGCAGA-----GAC-----AGCAGAAATTGCAAAGAGAC 186413 i iv ii - ----- -----i ii i i ii i L3#LINE/CR1 3825 TGGCTCCAGAGGGCAGAACTAGGACCAATGGGTGGAAGTTACAGGGAGGC 3874 chr4ptel1M 186414 AAGTTTAGACTCAACAGGAGGAA-AACTGGGAGCTGCTGAAGA-CTGGGC 186461 ii v i i vi - ------ v i vi - v i L3#LINE/CR1 3875 AGATTTCGGCTCAATATAAGGAAGAACT------TTCTAACAATCAGAGC 3918 chr4ptel1M 186462 TG-----AAATGGAATGAGCTGCCCCAGG-GGCAGCG-GCTGCCTGTCCT 186504 ----- i i i? - i i - v i vi L3#LINE/CR1 3919 TGTCCAAAAATGGAATGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGTCAC 3968 chr4ptel1M 186505 CGGAGGTCTCCAAATAGGAG-TAGATGAC 186532 i v i ii ii - i L3#LINE/CR1 3969 TGGAGGTGTTCAAGCAGAGGCTGGATGAC 3997 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 35.02 CpG sites = 40, Kimura (unadjusted) = 36.77 Transitions / transversions = 2.86 (40/14) Gap_init rate = 0.08 (17 / 201), avg. gap size = 1.94 (33 / 17) 365 29.60 3.25 1.27 chr4ptel1M 186560 186713 (813287) L3#LINE/CR1 3942 4098 (1) m_b168s601i3 6378 chr4ptel1M 186560 CCCAGGGGGTAGTGAGCTCCCCATCCTTGGAGGTCTCCAAGCAGAATTGA 186609 i i? i i vi v i ivivi L3#LINE/CR1 3942 CTCGNGAGGTAGTGAGCTCCCCGTCACTGGAGGTGTTCAAGCAGAGGCTG 3991 chr4ptel1M 186610 GATGACCCCGTGTCCATGACCTCATGGTGGGCATC----CACTGGCAGTG 186655 v v viv iv ii i vi v i---- i vv v L3#LINE/CR1 3992 GATGACCACTTGTCAGGGATGTTGTAGAAGGGATTCCTGCATTGGATGGG 4041 chr4ptel1M 186656 TGGCTTGGATGCAGA-GGCCACTCAGGTTCCCTCCAATGCTAAGTTTCTG 186704 v - i-i - i v v i i iv i v L3#LINE/CR1 4042 AGG-TTGGAC-TAGATGACCTCTAAGGTCCCTTCCAACTCTGAGATTCTG 4089 chr4ptel1M 186705 GGATTCTGT 186713 v i L3#LINE/CR1 4090 TGATTCTAT 4098 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 36.66 CpG sites = 25, Kimura (unadjusted) = 38.84 Transitions / transversions = 1.25 (25/20) Gap_init rate = 0.03 (4 / 153), avg. gap size = 1.75 (7 / 4) 370 27.78 13.89 0.00 chr4ptel1M 187114 187293 (812707) MIR#SINE/MIR 46 250 (12) m_b168s601i4 6379 chr4ptel1M 187114 GCCCTGGTCCAAATCTGGTCTCAGACACTTGCTGGGTGTGTGA-CTTGAG 187162 iv i i iv v v v i i v - i MIR#SINE/MIR 46 GCCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGG 95 chr4ptel1M 187163 CAAGTCACC--ATCTGTAGCCCCCTCAGTTT-CTGAACGGCAGAATGGGG 187209 i i-- i v vvviv - v v v i i MIR#SINE/MIR 96 CAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGG 145 chr4ptel1M 187210 CTAATGTTAGCACTT-TCTCCCA-GATTATGGGGAGCCTCAGATATGCTA 187257 v iv i i -i vi - i i v v vv i i iv i MIR#SINE/MIR 146 ATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTA 195 chr4ptel1M 187258 ATA------------TT-------TGCCTGGCACATAGTAGGCACTTGAT 187288 ------------ ------- i i ii MIR#SINE/MIR 196 ATACATGTAAAGCGCTTAGAACAGTGCCTGGCACATAGTAAGCGCTCAAT 245 chr4ptel1M 187289 AAATG 187293 MIR#SINE/MIR 246 AAATG 250 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.67 CpG sites = 28, Kimura (unadjusted) = 35.41 Transitions / transversions = 1.27 (28/22) Gap_init rate = 0.04 (7 / 179), avg. gap size = 3.57 (25 / 7) 239 13.89 0.00 0.00 chr4ptel1M 187264 187299 (812701) L2c_3end#LINE/L2 431 466 (12) m_b168s601i5 6380 chr4ptel1M 187264 GCCTGGCACATAGTAGGCACTTGATAAATGCCTGTT 187299 i ii ii L2c_3end#LINE 431 GCCTGGCACATAGTAGGCGCTCAATAAATGTTTGTT 466 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 12.92 CpG sites = 5, Kimura (unadjusted) = 16.27 Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 222 25.59 16.77 1.69 chr4ptel1M 188783 188937 (811063) MIR3#SINE/MIR 10 187 (21) m_b168s601i6 6381 chr4ptel1M 188783 TGGCTGAG------GAGTCACGGGGCTCAGTGTCAGGGGGAGCTGAGTTC 188826 ------ - i- vi v i - v i MIR3#SINE/MIR 10 TGGCTGAGCAGAGAGAG-CACGGA-CTGGGAGTCAGGAG-ACCTGGGTTC 56 chr4ptel1M 188827 AAAACCTGCCACGGGTGCTTAACAATTCTG--ACCTTGGGCAAG---CT- 188870 v iv i v v v vii v vi?ii v -- --- - MIR3#SINE/MIR 57 TAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTT 106 chr4ptel1M 188871 --------TGGGACTCAGTTTCCCCTTCCCTAAAAGGAGGGAGTTTGGCT 188912 -------- v i v iv v i v i MIR3#SINE/MIR 107 CACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACT 156 chr4ptel1M 188913 ---TGACCACCA---TCCTCTCCTGCTCTAA 188937 --- i v i --- ii v i MIR3#SINE/MIR 157 AGATGATCTCTAAGGTCCCTTCCAGCTCTGA 187 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 31.05 CpG sites = 20, Kimura (unadjusted) = 32.02 Transitions / transversions = 1.05 (20/19) Gap_init rate = 0.06 (10 / 154), avg. gap size = 2.90 (29 / 10) 192 35.38 5.38 0.00 chr4ptel1M 189644 189773 (810227) L3#LINE/CR1 3948 4084 (15) m_b168s601i7 6382 chr4ptel1M 189644 AGTTAATAAAGTCCCT-TCACTCGTTGTCTTCAGACAAAG-CTGGGCACC 189691 v i i iv i- v vv v ii i - iiiv L3#LINE/CR1 3948 AGGTAGTGAGCTCCCCGTCACTGGAGGTGTTCAAGCAGAGGCTGGATGAC 3997 chr4ptel1M 189692 CGCTTATTGAGGA-GTTCTGGCAGGAA--CCTTCATTCAGGCAGAGATTG 189738 i i iii - v i v i -- v viivvi i L3#LINE/CR1 3998 CACTTGTCAGGGATGTTGTAGAAGGGATTCCTGCATTGGATGGGAGGTTG 4047 chr4ptel1M 189739 GCCTGGGGAGCCGCGAC--TCCCCTCCAACCCTCAGA 189773 v i ivii v v v-- i i v L3#LINE/CR1 4048 GACTAGATGACCTCTAAGGTCCCTTCCAACTCTGAGA 4084 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 48.31 CpG sites = 27, Kimura (unadjusted) = 49.87 Transitions / transversions = 1.42 (27/19) Gap_init rate = 0.04 (5 / 129), avg. gap size = 1.40 (7 / 5) 293 27.85 1.25 1.25 chr4ptel1M 189873 189952 (810048) C MIRc#SINE/MIR (87) 181 102 m_b168s601i8 6383 chr4ptel1M 189873 CCCTGTGAGGCAAATGCTGGC-GATATCATTATCTCTATTTTACATATGA 189921 i iiii-v - i i i i v C MIRc#SINE/MIR 181 CCCTGTGAGGTAGGCA-GGGCAGGTATTATTATCCCCATTTTACAGATGA 133 chr4ptel1M 189922 GGTAAATGAGGTTTGAAGGACTTAAGCAACT 189952 v v i iii iiv ii C MIRc#SINE/MIR 132 GGAAACTGAGGCTCAGAGAGGTTAAGTGACT 102 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 37.41 CpG sites = 17, Kimura (unadjusted) = 37.41 Transitions / transversions = 3.40 (17/5) Gap_init rate = 0.03 (2 / 79), avg. gap size = 1.00 (2 / 2) 307 26.03 4.08 2.00 chr4ptel1M 191291 191388 (808612) MIRc#SINE/MIR 49 148 (120) m_b168s601i9 6384 chr4ptel1M 191291 GACCTGAACTCAGATATGACCTCATGT-ACTTCCTAGTTGTGGAACCT-G 191338 iii iii viviv - i- v i vi - MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTC-TGCCACTTACTAGCTGTGTGACCTTG 97 chr4ptel1M 191339 GGCAAAGCACTGAATGCCATTTG--CCTCAGTTTCCTCATCTGTAAAATA 191386 iv v ivi - i -- i MIRc#SINE/MIR 98 GGCAAGTCACTTAACCTC-TCTGAGCCTCAGTTTCCTCATCTGTAAAATG 146 chr4ptel1M 191387 AG 191388 i MIRc#SINE/MIR 147 GG 148 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 30.10 CpG sites = 17, Kimura (unadjusted) = 33.33 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.05 (5 / 97), avg. gap size = 1.20 (6 / 5) 311 21.13 2.82 0.00 chr4ptel1M 191318 191388 (808612) MIR#SINE/MIR 72 144 (118) m_b168s601i10 6384 chr4ptel1M 191318 ACTTCCTAGTTGTGGAACCT-GGGCAAAGCACTGAATGCCATT-TGCCTC 191365 v i vi - ivi v ivi vi - MIR#SINE/MIR 72 ACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTC 121 chr4ptel1M 191366 AGTTTCCTCATCTGTAAAATAAG 191388 ii MIR#SINE/MIR 122 AGTTTCCTCATCTGTAAAATGGG 144 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 25.26 CpG sites = 9, Kimura (unadjusted) = 25.26 Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.03 (2 / 70), avg. gap size = 1.00 (2 / 2) 535 31.47 0.91 2.79 chr4ptel1M 192008 192226 (807774) MIR#SINE/MIR 21 235 (27) m_b168s601i11 6385 chr4ptel1M 192008 AGAGCGTCAGCTCTGGAGTTAACAAAGTCCGAGTTCGAATTCAGCCTCAG 192057 iivi ii i- vv i i i i v v v MIR#SINE/MIR 21 AGAGCACGGGCTCTGGAGCCAG-ACTGCCTGGGTTCGAATCCCGGCTCTG 69 chr4ptel1M 192058 ACA-TTCCTAGTTATGTGATCCTAGCGAGGCAAGCCCCATAAGCTCTGTT 192106 v - v i i i i i ---- iiv v v v v MIR#SINE/MIR 70 CCACTTACTAGCTGTGTGACCTTGG----GCAAGTTACTTAACCTCTCTG 115 chr4ptel1M 192107 TGCCTGCGCAACCTCATCTGTAAAGTGGAGACCAAAGCAGTCCTTACCCC 192156 vv ivv i i iv v ii v i i MIR#SINE/MIR 116 TGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTC 165 chr4ptel1M 192157 AAAGGATTGTTGTACAGATCCAACGAGACCGTTATCT-TAAAGCTCTTAG 192205 v i ivi iv i -iiiv iv - v MIR#SINE/MIR 166 ATAGGGTTGTTGTGAGGATTAAATGAG-TTAATACATGTAAAGCGCTTAG 214 chr4ptel1M 192206 CACGGTGTATGGTGCATCGTA 192226 v i iv ii v MIR#SINE/MIR 215 AACAGTGCCTGGCACATAGTA 235 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 41.08 CpG sites = 38, Kimura (unadjusted) = 41.90 Transitions / transversions = 1.31 (38/29) Gap_init rate = 0.04 (8 / 218), avg. gap size = 1.00 (8 / 8) 26 38.35 2.14 0.70 chr4ptel1M 192395 192534 (807466) (AGAA)n#Simple_repeat 1 142 (0) m_b168s252i1 6386 chr4ptel1M 192395 AGAAAAGAACAAAGGAATGAAGGGACAAAGAAAGGAGGAAGGAGAGGAAG 192444 ii v i vi ii v i i i i i (AGAA)n#Simpl 1 AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG 50 chr4ptel1M 192445 AAAGAAGGGAGGGAGCAAGGAAAGAAGGAGA-AAAGGAAGTACAGAAAGA 192493 i i i i iv i i i - i - v (AGAA)n#Simpl 51 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG-AAAGAAAGA 99 chr4ptel1M 192494 TGGGAGGGAGGGAGGGAGGAAA-AAGGGAAG-TAGAAAGATAG 192534 vi i i i i i i i i - i i -v v (AGAA)n#Simpl 100 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG 142 Matrix = Unknown Transitions / transversions = 3.88 (31/8) Gap_init rate = 0.03 (4 / 139), avg. gap size = 1.00 (4 / 4) 24 32.94 3.36 1.65 chr4ptel1M 192428 192546 (807454) (GGAG)n#Simple_repeat 1 121 (0) m_b168s252i2 6386 chr4ptel1M 192428 GGA-GGAAGGAGAGGAAGAAAGAAGGGAGGGA-GCAAGGAAAGAAGGAGA 192475 - i - i i i i - v i ii i i (GGAG)n#Simpl 1 GGAGGGAGGGAG-GGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGG 49 chr4ptel1M 192476 AAAGGAAGTACAGAAAGATGGGAGGGAGGGAGGGA-GGAAAAAGGGAAGT 192524 i i i v vi ii - - iii i v (GGAG)n#Simpl 50 GAGGGAGGGAGGGAGGGA-GGGAGGGAGGGAGGGAGGGAGGGAGGGAGGG 98 chr4ptel1M 192525 AGAAAGATA-GGAGAGAGGGAGG 192546 ii iv - i (GGAG)n#Simpl 99 AGGGAGGGAGGGAGGGAGGGAGG 121 Matrix = Unknown Transitions / transversions = 4.80 (24/5) Gap_init rate = 0.05 (6 / 118), avg. gap size = 1.00 (6 / 6) 192 25.00 0.00 0.00 chr4ptel1M 192547 192590 (807410) C L2d2_3end#LINE/L2 (12) 543 500 m_b168s601i12 6387 chr4ptel1M 192547 AGCAGGCATTTATGGAGCACCAACTATGTAAAAGGCCCTGTGCT 192590 i iii v i v i iv v C L2d2_3end#LIN 543 AACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCT 500 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 27.97 CpG sites = 7, Kimura (unadjusted) = 31.32 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 24 7.35 2.13 4.35 chr4ptel1M 193118 193164 (806836) (TTCC)n#Simple_repeat 1 46 (0) m_b168s252i3 6388 chr4ptel1M 193118 TTCCTTCCTTACTTCTTTTCTTCCTTCCTTCC-TCCTTCTCTGTCCTT 193164 v i i - - - (TTCC)n#Simpl 1 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC-CT-TCCTT 46 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.07 (3 / 46), avg. gap size = 1.00 (3 / 3) 324 33.57 2.22 5.99 chr4ptel1M 193431 193655 (806345) L3#LINE/CR1 3181 3397 (702) m_b168s601i13 6389 chr4ptel1M 193431 CTTGAATAAAACCCTCAGAGGG--TGAT-ATCAGAATTGAAGATGACATA 193477 i i iv v - i -- v - i v v i L3#LINE/CR1 3181 CTTGGATGAAGACAT-AGAAGGCATGCTTATCAAATTTGCAGATGACACA 3229 chr4ptel1M 193478 AAAGATTGAGGGGGAGGAGTGGGGCTGGCTGACAGGG-GCCTGACAGTAC 193526 i--i i i ---------- i i i v ?- vv v i L3#LINE/CR1 3230 AAG--CTGGGAGGGA----------TAGCTAATACGNTGGATGACAGAAT 3267 chr4ptel1M 193527 TGGGTTCCTGGAGCATCTCAGTAT-CTAGAGAGACAGACCAAATATAGTA 193575 iii v i vii ?v iii v- i iv ii i i vvi ii L3#LINE/CR1 3268 CAAGATTCAAAANGATCTCGACAGGCTGGAACGATGGGCCGAAACCAACA 3317 chr4ptel1M 193576 AGATTGAATTAGATAGTCATCAATGTAAACACTTGAACTCAGGACCAAAA 193625 vi vi i vv v vv i v i i vi L3#LINE/CR1 3318 AGATGAAATTTAACAGGGATAAATGTAAAGTCCTGCATTTAGGTTCAAAA 3367 chr4ptel1M 193626 AGTCAATTGTACGAATACAGGATGGAGGAG 193655 i i i i i ii L3#LINE/CR1 3368 AATCAACTGCACAAGTACAGGATGGAGAGG 3397 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 45.62 CpG sites = 46, Kimura (unadjusted) = 47.52 Transitions / transversions = 1.84 (46/25) Gap_init rate = 0.08 (17 / 224), avg. gap size = 1.06 (18 / 17) 317 20.53 17.59 0.79 chr4ptel1M 193782 193889 (806111) C MIRb#SINE/MIR (17) 251 126 m_b168s601i15 6390 chr4ptel1M 193782 TTATTAAGCACCCACTTTGT--CAGGCACTGTGCTGACTACTTTTACTAA 193829 i i ii v -- i vii - vvi C MIRb#SINE/MIR 251 TTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGC-TTTACATG 203 chr4ptel1M 193830 AACTACCTTATTTGATCTTCACAAAA-----GGGAGGTAGG-GT------ 193867 v i i i i i v ----- v -i ------ C MIRb#SINE/MIR 202 CATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATTAT 153 chr4ptel1M 193868 -----TTTTACAGTTGAGGAAACTGAG 193889 ----- v C MIRb#SINE/MIR 152 CCCCATTTTACAGATGAGGAAACTGAG 126 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 21.95 CpG sites = 14, Kimura (unadjusted) = 24.56 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.06 (6 / 107), avg. gap size = 3.33 (20 / 6) 206 28.00 12.00 0.00 chr4ptel1M 193889 193963 (806037) C MIRc#SINE/MIR (175) 93 10 m_b168s601i16 6391 chr4ptel1M 193889 GTCACACATCTAATTAGCAGCTGATGCTGGCTTTGAACTCAGGCCTTCCT 193938 v i v ii v vv v vi i i i C MIRc#SINE/MIR 93 GTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCT 44 chr4ptel1M 193939 G-----AGGCCCAGGACTTT----ATTACACCAC 193963 ----- i i vi i ---- i i C MIRc#SINE/MIR 43 GACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 34.05 CpG sites = 13, Kimura (unadjusted) = 36.19 Transitions / transversions = 1.62 (13/8) Gap_init rate = 0.03 (2 / 74), avg. gap size = 4.50 (9 / 2) 196 23.26 0.00 0.00 chr4ptel1M 193990 194032 (805968) L3#LINE/CR1 3546 3588 (511) m_b168s601i17 6389 chr4ptel1M 193990 AGGTGACAGTCCTACTGTACTCTGCCCAGCTCAGGTCAAATCT 194032 i i ii v v v ii v L3#LINE/CR1 3546 AGGTAATAGTCCCGCTGTACTCTGCGCTGGTCAGACCACATCT 3588 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 24.84 CpG sites = 6, Kimura (unadjusted) = 28.41 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 263 31.30 2.56 1.69 chr4ptel1M 194092 194208 (805792) L3#LINE/CR1 3623 3740 (359) m_b168s601i18 6389 chr4ptel1M 194092 AGGAAGGCCATTGATGAATTGAATGATGTC-AGAGAAAGTCAACCATAAT 194140 i i v ii i i vvii - i iiv i vi L3#LINE/CR1 3623 AAGAGGGACATTGACAAACTGGAGCGCGTCCAGAGGAGAGCGACCAGGAT 3672 chr4ptel1M 194141 GGTTAGAGAGTCTG-AAATTGTGGTA-GTCAGGAATCATTTGAAGAAACT 194188 v - i - iii vi -i v - iv i L3#LINE/CR1 3673 GGTGA-AGGGTCTGGAAACCATGTCATATGAGGAA-CGGTTGAAGGAACT 3720 chr4ptel1M 194189 GGGGATTTTTAACGCAAAGA 194208 v i viii L3#LINE/CR1 3721 GGGGATGTTTAGCCTGGAGA 3740 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 36.85 CpG sites = 25, Kimura (unadjusted) = 43.11 Transitions / transversions = 2.27 (25/11) Gap_init rate = 0.04 (5 / 116), avg. gap size = 1.00 (5 / 5) 183 22.19 4.71 9.88 chr4ptel1M 196265 196349 (803651) MIRc#SINE/MIR 5 85 (183) m_b168s601i19 6392 chr4ptel1M 196265 GCAG-GTGGTGCAATGGTTACAGC--TGCGCCTG-AGTCAGGAAGGCGCA 196310 - i vv v -- vi i - i --- MIRc#SINE/MIR 5 GCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC--- 51 chr4ptel1M 196311 TCTTCCTGGGTTCAAATCCAGCCTCAGACTCCTATTAGC 196349 ----- i i v v v v v i i MIRc#SINE/MIR 52 -----CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGC 85 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 24.58 CpG sites = 8, Kimura (unadjusted) = 26.28 Transitions / transversions = 0.89 (8/9) Gap_init rate = 0.13 (11 / 84), avg. gap size = 1.09 (12 / 11) 243 16.00 1.96 1.96 chr4ptel1M 196539 196589 (803411) MIR3#SINE/MIR 102 152 (56) m_b168s601i20 6393 chr4ptel1M 196539 CACTT-ACCTCCCCTGGGCCTCAGTTTCCTTCTCTGTAAAAAGAGAAAGG 196587 - i - iv v iii v MIR3#SINE/MIR 102 CACTTCACCTCTC-TGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGT 150 chr4ptel1M 196588 TG 196589 MIR3#SINE/MIR 151 TG 152 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 18.25 CpG sites = 5, Kimura (unadjusted) = 18.25 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.04 (2 / 50), avg. gap size = 1.00 (2 / 2) 217 27.14 7.14 0.00 chr4ptel1M 197079 197148 (802852) L2d2_3end#LINE/L2 476 550 (5) m_b168s601i21 6394 chr4ptel1M 197079 TTATTTATGTCTCT----GCTTCTAACACAGAGCCT-GCATACAGAAGGC 197123 v i i i i---- vi i v - i v L2d2_3end#LIN 476 TTCTTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAGTAGGC 525 chr4ptel1M 197124 ACTCAATGCATGCTTATTGCATTGA 197148 i iv ii i vv L2d2_3end#LIN 526 GCTCAATAAATATTTGTTGATTTGA 550 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 32.57 CpG sites = 12, Kimura (unadjusted) = 34.83 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.03 (2 / 69), avg. gap size = 2.50 (5 / 2) 219 27.42 3.23 0.00 chr4ptel1M 197084 197145 (802855) L2b_3end#LINE/L2 395 458 (8) m_b168s601i22 6394 chr4ptel1M 197084 TATGTCTCT-GCTTCTAACACAGAGCCT-GCATACAGAAGGCACTCAATG 197131 i i i i- vi i ? - i v i i i L2b_3end#LINE 395 TGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTA 444 chr4ptel1M 197132 CATGCTTATTGCAT 197145 v ii i v L2b_3end#LINE 445 AATATTTGTTGAAT 458 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 34.54 CpG sites = 13, Kimura (unadjusted) = 37.36 Transitions / transversions = 3.25 (13/4) Gap_init rate = 0.03 (2 / 61), avg. gap size = 1.00 (2 / 2) 183 18.33 16.67 0.00 chr4ptel1M 197168 197227 (802773) C MIRc#SINE/MIR (187) 81 12 m_b168s601i23 6395 chr4ptel1M 197168 GTAACTGGCAGGGC-AGGACTCAAACCCAGGT--------CTCCAAG-CC 197207 v i -i i -------- - C MIRc#SINE/MIR 81 GTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCC 32 chr4ptel1M 197208 AGCGTGCTTCCCAGCACACC 197227 i iv i vii C MIRc#SINE/MIR 31 AGTGCTCTTTCCACTGCACC 12 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 17.46 CpG sites = 8, Kimura (unadjusted) = 21.67 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.05 (3 / 59), avg. gap size = 3.33 (10 / 3) 16 5.20 0.00 0.00 chr4ptel1M 197547 197566 (802434) (TG)n#Simple_repeat 1 20 (0) m_b168s252i4 6396 chr4ptel1M 197547 TGTGTGAGTGTGTGTGTGTG 197566 v (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTG 20 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 255 16.58 3.72 3.72 chr4ptel1M 197567 197754 (802246) HERVIP10FH#LTR/ERV1 811 998 (4104) m_b168s701i0 6397 chr4ptel1M 197567 AGAAAGAGGCAGAAACAGAAACAGAGAGATAGAGACAGAGAGAGACAGAG 197616 i i - i v i v iv v v HERVIP10FH#LT 811 AGAGAGAAG-AGAGAGAGAGAGAGAGAGGAAGAGAGAGAGAGAGAAAGAG 859 chr4ptel1M 197617 AGATAGCAATAAACAGAGAGACAGAGAAAGAG--AAAGAGAGAGACACAC 197664 v viiv i v i ii -- v vi HERVIP10FH#LT 860 AGAGAGAGGGAGAGAGAGAGACAAAGAGGGAGTCAAAGAGAGAGAGAGGC 909 chr4ptel1M 197665 AGAGAGAAG-AGAGACAGAGAAGACAGAGAGATAGAGACGAGAGAGACAG 197713 i - - i --i v - v HERVIP10FH#LT 910 AGAGAGAGGAAGAGACAGAG-AGACAAAGAG--GGAGTC-AGAGAGAGAG 955 chr4ptel1M 197714 ATGGAGAGACAGAAAG----AGAGAGAAAGAGAGAGAGAGAGAGA 197754 -- ---- i v HERVIP10FH#LT 956 A--GAGAGACAGAAAGTCAAAGAGAGAAAGAAAGAGAGAGATAGA 998 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 18.86 CpG sites = 16, Kimura (unadjusted) = 18.86 Transitions / transversions = 1.14 (16/14) Gap_init rate = 0.05 (10 / 187), avg. gap size = 1.40 (14 / 10) 86 22.49 2.38 0.47 chr4ptel1M 197755 197964 (802036) (GAGA)n#Simple_repeat 1 214 (0) m_b168s252i5 6398 chr4ptel1M 197755 GACAGAGACAACGAGACAGAGATGAGAGAGAAAGAGACAG-GATACAGAG 197803 v v iv v - i v - v v (GAGA)n#Simpl 1 GAGAGAGAGAGAGAGAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGAG 49 chr4ptel1M 197804 AGAGAAAGAGA-AGAGAGA-AAAGAGAGAGAGA-AGACAGAGAGA-AGAG 197849 i - - i - v - (GAGA)n#Simpl 50 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 99 chr4ptel1M 197850 AGAGGGAGAAAAAGAGGGAGAGAGAAAGGGAAAGGGAGAGGGAGAGGGAG 197899 i i i i i i i i i i (GAGA)n#Simpl 100 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 149 chr4ptel1M 197900 AGGAAGGGAGGGAGGGAGAGGAAGGGAAAGAAGGAAAGAGGGGGAGGGAG 197949 ii i i i ii i i ii i i i i (GAGA)n#Simpl 150 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 199 chr4ptel1M 197950 GGAGGGAGAGAGAGA 197964 i i (GAGA)n#Simpl 200 AGAGAGAGAGAGAGA 214 Matrix = Unknown Transitions / transversions = 3.88 (31/8) Gap_init rate = 0.03 (6 / 209), avg. gap size = 1.00 (6 / 6) 31 5.80 0.00 0.00 chr4ptel1M 197969 198004 (801996) (GT)n#Simple_repeat 1 36 (0) c_b168s251i0 6399 chr4ptel1M 197969 GTGTGTGTGTGGGTGTGTGTGTGGGTGTGTGTGTGT 198004 v v (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 36 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 12 20.48 5.56 3.64 chr4ptel1M 198052 198105 (801895) (GTGA)n#Simple_repeat 1 55 (0) m_b168s252i7 6400 chr4ptel1M 198052 GTGAGTGTGTGAGCATGATTGAATGGCTCTGTGTGTGA--GAGGGAGTGA 198099 v -- v i iv vv v -- v (GTGA)n#Simpl 1 GTGAGTGAGTGAG--TGAGTGAGTGAGTGAGTGAGTGAGTGAGTGAGTGA 48 chr4ptel1M 198100 G-GAGTG 198105 - (GTGA)n#Simpl 49 GTGAGTG 55 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.08 (4 / 53), avg. gap size = 1.25 (5 / 4) 167 31.91 1.94 0.16 chr4ptel1M 198324 198941 (801059) (AGAG)n#Simple_repeat 1 629 (0) m_b168s252i8 6401 chr4ptel1M 198324 AGAGA-AGCCAGAG-GGGAGGGAGAGAGACAGAGACAGCGAAAGAGAAAA 198371 - vv - i i v v v i i i (AGAG)n#Simpl 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr4ptel1M 198372 ACAGAAACAGAGAAACATAGAGAGAGATAGAGACAGACACACACAGAGAG 198421 v i v i v v v v v v v v (AGAG)n#Simpl 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 100 chr4ptel1M 198422 ACAAAAACAGAGAGACAGGCGGACAGAGACAGA-AGGAAGGGGGGGAAAG 198470 v i i v v ivi v v - ii i i i i (AGAG)n#Simpl 101 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 150 chr4ptel1M 198471 AGAAACAGAAAGACAGAGACAGACACCGAGAGAGACAGAGAAAGATACAA 198520 i v i v v v vv v i v v i (AGAG)n#Simpl 151 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 200 chr4ptel1M 198521 ACAGACCAAAACAGAGAAACAGAGACA-AGAGGCAGAAACAGAGGGA-AG 198568 v vvi i v i v v - iv i v i - (AGAG)n#Simpl 201 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 250 chr4ptel1M 198569 GGGGAGAGAGAGGCAGAGTCAGACAGACAGACAGATACAGAGACAGAGAG 198618 i i iv vv v v v v v v (AGAG)n#Simpl 251 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 300 chr4ptel1M 198619 -GAGGAAAAGAGACAGAGAAGGAGAGAAAAACAGAAACATAGAGACACAG 198667 - ii i v ii i i v i v v v v (AGAG)n#Simpl 301 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 350 chr4ptel1M 198668 ACAGACAGAAACAGAGACAGACAAACCCACATAGAGACATACAGACAGAA 198717 v v i v v v i vvv v v v v v v i (AGAG)n#Simpl 351 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 400 chr4ptel1M 198718 AGAGAGAGAGGGA-AGGGGGAAAGAGAGAAACAGA-AGCACAGACAGAGA 198765 i - i i i i v - - v v (AGAG)n#Simpl 401 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG-AGAGAGAGAGA 449 chr4ptel1M 198766 TACAGAGAGAAACAAAGAGAGATACAGATGGACAGAAACAGAGAGACAGA 198815 v v i v i v v vi v i v v (AGAG)n#Simpl 450 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 499 chr4ptel1M 198816 GACA-AAAGACAGACAGAGATAGAGACAGAGGGAAGGGGAGAGAGAGAGA 198864 v - i v v v v i ii i (AGAG)n#Simpl 500 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 549 chr4ptel1M 198865 AAGA-AGGGGGGGGCAAAAAGACAGACAGACAGACACAGACACAGACACA 198913 i - i i i iv i i v v v v v v v v v (AGAG)n#Simpl 550 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 599 chr4ptel1M 198914 GAGACA-AGAGTCAGAG-GAGGGAGAGAGA 198941 v - vv - i (AGAG)n#Simpl 600 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 629 Matrix = Unknown Transitions / transversions = 0.65 (63/97) Gap_init rate = 0.02 (13 / 617), avg. gap size = 1.00 (13 / 13) 181 23.96 3.82 2.29 chr4ptel1M 198340 198941 (801059) (AGAGAC)n#Simple_repeat 1 611 (0) m_b168s252i9 6401 chr4ptel1M 198340 AGGGAGAGAGACAGAGACAGCGAAAGAGA-A-AAACAGAAACAGAGAAAC 198387 i v v v - - i i -- (AGAGAC)n#Sim 1 AGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAG--AC 48 chr4ptel1M 198388 ATAGAGAGAGATAGAGACAGACACACACAGAGAGACAAAAACAGAGAGAC 198437 v v i v v v v i i v v (AGAGAC)n#Sim 49 AGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAG 98 chr4ptel1M 198438 AGGC-G-GACAGAGACAGA-AGGAAGGGGGGGAAAGAGAAACAGA-A-AG 198482 i - - - vii ivi i v v v - - (AGAGAC)n#Sim 99 AGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAG 148 chr4ptel1M 198483 ACAGAGACAGACACCGAG--AGAGACAGAGAAAGATACA-A-ACAGA-CC 198527 v v -- v v - - -v (AGAGAC)n#Sim 149 ACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGAC 198 chr4ptel1M 198528 A-AAACAGAGAAACAGAGACAAGAGGCAGAAACAGAGGGA-AGGGGGAGA 198575 - i -- - i i iv - ivi (AGAGAC)n#Sim 199 AGAGACAGAG--ACAGAGAC-AGAGACAGAGACAGAGACAGAGACAGAGA 245 chr4ptel1M 198576 GAGAGGCAGAGTCAGACAGACAGACAGATACAGAGACAGAGAGGAGGAAA 198625 v i v v v v v -v ii v (AGAGAC)n#Sim 246 CAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGA-CAGAGAC 294 chr4ptel1M 198626 AGAGACAGAGAAGGAGAGAAAAACAGAAACATAGAGACACAGAC--AGAC 198673 vi v i i i -- v -- (AGAGAC)n#Sim 295 AGAGACAGAGACAGAGACAGAGACAGAGAC--AGAGACAGAGACAGAGAC 342 chr4ptel1M 198674 AGAAACAGAGAC--AGACAAACCCACATAGAGACATACAGACAGAAAGAG 198721 i -- i vv v v v v i v i v (AGAGAC)n#Sim 343 AGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAG 392 chr4ptel1M 198722 AGAGAGGGA-AGGGGGAAAGAGAGAAACAGAAGCACAGACAGAGATACAG 198770 v i - i iv i v i ii v i v (AGAGAC)n#Sim 393 AGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAG 442 chr4ptel1M 198771 AGAGAAACAAAGAGAGATACAGATGGACAGAAACAGAGAGACAGAGACA- 198819 v i i v v -- i -- - (AGAGAC)n#Sim 443 ACAGAGACAGAGACAGAGACAGA--GACAGAGAC--AGAGACAGAGACAG 488 chr4ptel1M 198820 AAAGACAGACAGAGATAGAGACAGAGGGAAGGGGAGAGAGAGAGAAAGAA 198869 i v v i iv ii iv v v - (AGAGAC)n#Sim 489 AGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAG-A 537 chr4ptel1M 198870 GGGGGGGGCA-A-AAAGACAGACAGACAGACACAGACACAGACACAGAGA 198917 ivi i i - - v v v v v v v (AGAGAC)n#Sim 538 GACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGA 587 chr4ptel1M 198918 CAAGAGTCAGAG-GAGGGAGAGAGA 198941 - v -v i v (AGAGAC)n#Sim 588 C-AGAGACAGAGACAGAGACAGAGA 611 Matrix = Unknown Transitions / transversions = 0.76 (51/67) Gap_init rate = 0.06 (34 / 601), avg. gap size = 1.09 (37 / 34) 197 9.38 0.00 0.00 chr4ptel1M 201420 201451 (798549) MIRb#SINE/MIR 116 147 (121) m_b168s601i24 6402 chr4ptel1M 201420 CTCTCTCAGCCTTAGTTTCCTCAACTGTAAAA 201451 v i v MIRb#SINE/MIR 116 CTCTCTGAGCCTCAGTTTCCTCATCTGTAAAA 147 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 10.01 CpG sites = 1, Kimura (unadjusted) = 10.01 Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 373 29.11 8.42 1.39 chr4ptel1M 202970 203171 (796829) L1ME4c_3end#LINE/L1 356 571 (259) m_b168s551i0 6403 chr4ptel1M 202970 TGTGCATACGCTTTGACCCA------CTAGGTCTG------TATCCCAAA 203007 v v ------ i vv ------ i i L1ME4c_3end#L 356 TGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAG 405 chr4ptel1M 203008 AATGTAA---AAAGGAAGGAAAGAGTCTATTTGAACAAAAATACTCATAG 203054 i vi --- i i - v v i i ii v L1ME4c_3end#L 406 GAAATAATTCAAAAGAAGGAAAAAG-CTATATGCACGAAGATGTTCATTG 454 chr4ptel1M 203055 CAGCTCTTTTTATGGTGGCTAAGAACTGAAAATCAAGGGGGTGCCCATCA 203104 vi v ii i v i i i iv vvviii i v L1ME4c_3end#L 455 CAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACA 504 chr4ptel1M 203105 AGTGGGGAAGAGCTGGAACAAGTTGTGGTATAT-GATTATCATGGAATAT 203153 vv vi i -i ii i i i -? i -iv L1ME4c_3end#L 505 ATAGGGGAATGGTT-AAGTAAATTATGGTACATCNACT-CGATGGAATAT 552 chr4ptel1M 203154 TATTTTG-TATAAAAAATG 203171 viv -i v L1ME4c_3end#L 553 TATGCAGCCATTAAAAATG 571 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 36.64 CpG sites = 35, Kimura (unadjusted) = 38.32 Transitions / transversions = 1.52 (35/23) Gap_init rate = 0.04 (8 / 201), avg. gap size = 2.50 (20 / 8) 305 36.28 1.45 1.45 chr4ptel1M 203033 203239 (796761) L1MD1_3end#LINE/L1 430 636 (353) m_b168s551i2 6403 chr4ptel1M 203033 ATTTGAACAAAAATACTCATAGCAGCTCTTTTTATGGTGGCTAAGAACTG 203082 ii v vi ii i i v ii ii i i i L1MD1_3end#LI 430 ACCTGTACACGAATGTTTATAGCAGCTTTATTCGTAATAGCCAAAAACTG 479 chr4ptel1M 203083 AAAATCAAGGGGGTGCCCATCAAGTGGGGAAGAGCTGGAACAAGTTGTGG 203132 i iv vvvi i i v vv v vi i -i ii L1MD1_3end#LI 480 GAAACAACCCAGATGTCCTTCAACGGGTGAATGGTT-AAACAAACTGTGG 528 chr4ptel1M 203133 TATATGATTATCATGGAATATTATTTTGT-ATAAAAAATGGCTAGCAGGA 203181 i vvv i i i iv i- ivii v i --v L1MD1_3end#LI 529 TACATCCATACCATGGAATACTACTCAGCAATAAAAAGGAACGAAC--TA 576 chr4ptel1M 203182 TGGTTTCA-G-AAAAACCTGGAAAGATTTCCATAAAGCCATACAAAGTAA 203229 v v v - - v vii i v i iii i vi i L1MD1_3end#LI 577 TTGATACACGCAACAACCTGGATGAATCTCCAGAGAATTATGCTGAGTGA 626 chr4ptel1M 203230 AGTGAGCCGA 203239 ivi i L1MD1_3end#LI 627 AAAAAGCCAA 636 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 50.41 CpG sites = 47, Kimura (unadjusted) = 52.65 Transitions / transversions = 1.74 (47/27) Gap_init rate = 0.03 (6 / 206), avg. gap size = 1.00 (6 / 6) 393 30.37 0.74 0.74 chr4ptel1M 203033 203168 (796832) L1ME2z_3end#LINE/L1 430 565 (626) m_b168s551i1 6403 chr4ptel1M 203033 ATTTGAACAAAAATACTCATAGCAGCTCTTTTTATGGTGGCTAAGAACTG 203082 i v i ii i v i ii i i i L1ME2z_3end#L 430 ACTTGTACAAGAATGTTCATAGCAGCTTTATTCATAATAGCCAAAAACTG 479 chr4ptel1M 203083 AAAATCAAGGGGGTGCCCATCAAGTGGGGAAGAGCTGGAACAAGTTGTGG 203132 i ivivvvi i vv i vi v -i ii L1ME2z_3end#L 480 GAAACAGCCCAGGTGTCCATCAACAGGAGAATGGAT-AAACAAACTGTGG 528 chr4ptel1M 203133 TATATGATTATCATGGAATATTATTTTGT-ATAAAAA 203168 vvv iv i i iv i- L1ME2z_3end#L 529 TATATTCATACAATGGAATACTACTCAGCAATAAAAA 565 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 40.57 CpG sites = 26, Kimura (unadjusted) = 40.57 Transitions / transversions = 1.73 (26/15) Gap_init rate = 0.01 (2 / 135), avg. gap size = 1.00 (2 / 2) 494 21.12 4.76 3.36 chr4ptel1M 204390 204536 (795464) C MIR1_Amn#SINE/MIR (80) 150 2 m_b168s601i25 6404 chr4ptel1M 204390 CTCATTTTACAGATGAGGAAACTGAGGCAAACAG-GGTGAAGTGACTTGC 204438 i ?v v - ? C MIR1_Amn#SINE 150 CCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGC 101 chr4ptel1M 204439 CTAGGGTCACACAGCTGGGAAGT------ATCTGAATTTGAACTCAGGTC 204482 i i ? ? v? ------ii v i ? ? i C MIR1_Amn#SINE 100 CCAAGGTCACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAACCCAGGTC 51 chr4ptel1M 204483 TTCCCAATGTAGGCCTGACCCTCCATGCCCTGAGCCACTTCACTTGCCCT 204532 i v i vivi i iiiiv i v v iii --- - - C MIR1_Amn#SINE 50 TCCCGAGTCCCAGTCCAGTGCTCTATCCACTAGACCA---CAC-TG-CCT 6 chr4ptel1M 204533 CCCT 204536 C MIR1_Amn#SINE 5 CCCT 2 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 27.14 CpG sites = 20, Kimura (unadjusted) = 27.14 Transitions / transversions = 2.00 (20/10) Gap_init rate = 0.05 (7 / 146), avg. gap size = 1.71 (12 / 7) 272 26.85 5.50 0.88 chr4ptel1M 205347 205455 (794545) C L3#LINE/CR1 (5) 4094 3981 m_b168s601i26 6405 chr4ptel1M 205347 AAACACAGAATTTGAGGGTTGCAGGG--TCTCTGTAGTGAGTGAGTGTAA 205394 v i v i v i --i iv vi v viv vi C L3#LINE/CR1 4094 AATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCAA 4045 chr4ptel1M 205395 ACCACACACTAAAGGCAAG----CCTGGTAGAACAGACCTGACAAGTGGT 205440 - v v iiv v i ---- vv v vv C L3#LINE/CR1 4044 -CCTCCCATCCAATGCAGGAATCCCTTCTACAACATCCCTGACAAGTGGT 3996 chr4ptel1M 205441 CATCCAGCCTCTGCT 205455 C L3#LINE/CR1 3995 CATCCAGCCTCTGCT 3981 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.27 CpG sites = 11, Kimura (unadjusted) = 33.27 Transitions / transversions = 0.61 (11/18) Gap_init rate = 0.03 (3 / 108), avg. gap size = 2.33 (7 / 3) 251 26.92 0.00 0.00 chr4ptel1M 205677 205728 (794272) L2b_3end#LINE/L2 396 447 (19) m_b168s601i27 6406 chr4ptel1M 205677 GTGTCCCCAGCATTTAGCTCAGTGTCTGGCATGAAGTAAGCACTTAATAA 205726 i iii v ? i iiv i i i i L2b_3end#LINE 396 GTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAA 445 chr4ptel1M 205727 GT 205728 i L2b_3end#LINE 446 AT 447 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 30.96 CpG sites = 12, Kimura (unadjusted) = 37.69 Transitions / transversions = 6.00 (12/2) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 344 21.97 6.82 0.00 chr4ptel1M 206494 206625 (793375) HERVIP10FH#LTR/ERV1 891 1031 (4071) m_b168s701i1 6407 chr4ptel1M 206494 GTGAGAGAGAGAGAGAGACAGAGAAAAACAGAGACATAGAGCCAGAGAGA 206543 v i i i iiv v v i i HERVIP10FH#LT 891 GTCAAAGAGAGAGAGAGGCAGAGAGAGGAAGAGACAGAGAGACAAAGAGG 940 chr4ptel1M 206544 TAG--AGAAAGAGAAAGACAGACTGACAGTCAGAGAGACAGAGACTGAGA 206591 v -- i i v v v i v i vv HERVIP10FH#LT 941 GAGTCAGAGAGAGAGAGAGAGACAGAAAGTCAAAGAGAGAAAGAAAGAGA 990 chr4ptel1M 206592 AAG-T----GT-GTAAAAAATAAATA-TACACCCTATACCT 206625 i - ---- - i v i - ii v HERVIP10FH#LT 991 GAGATAGAAGTAGTAAAGAAAAAACAGTGTACCCTATTCCT 1031 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 26.33 CpG sites = 16, Kimura (unadjusted) = 26.33 Transitions / transversions = 1.23 (16/13) Gap_init rate = 0.04 (5 / 131), avg. gap size = 1.80 (9 / 5) 288 22.91 7.91 13.69 chr4ptel1M 206893 207069 (792931) C MIR3#SINE/MIR (21) 187 20 m_b168s601i28 6408 chr4ptel1M 206893 TCAGAGCTAGGAAG-ACCTTAGTGATCACCCAG----ACCCCCTCA---T 206934 i i i - v i i ---- --- C MIR3#SINE/MIR 187 TCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTT 138 chr4ptel1M 206935 AAAGGGGGCCCAAGAAAGGCCCCCTGTAAAGAAAGGCCCA-AAAAGTCCA 206983 v iv ---- i ------ ------- - i i vv C MIR3#SINE/MIR 137 ACAGATG----AGGAAA------CTG-------AGGCCCAGAGAGGTGAA 105 chr4ptel1M 206984 TTACCTGGTCCAGGGGTCACACAGTC--TTAAAAATGGAGATGGGATTCA 207031 v iv v i -i i?-- iviiii vi i vi C MIR3#SINE/MIR 104 GTGACTTGCCCA-AGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAG 56 chr4ptel1M 207032 AACCCAGGTTCTCCTGACT---GGTCCTTGAATGCTCTTTC 207069 - ---i ----i i C MIR3#SINE/MIR 55 AACCCAGG-TCTCCTGACTCCCAGTCC----GTGCTCTCTC 20 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 26.36 CpG sites = 24, Kimura (unadjusted) = 28.24 Transitions / transversions = 2.18 (24/11) Gap_init rate = 0.16 (29 / 176), avg. gap size = 1.28 (37 / 29) 317 24.53 6.09 4.27 chr4ptel1M 206968 207082 (792918) C MIRc#SINE/MIR (144) 124 8 m_b168s601i29 6408 chr4ptel1M 206968 AGGCCCAAAAAG-TCCATTACCTGGTCCAGGGGTCACACAGTCTTAAAAA 207016 i i i - iv v iv v i i - - viv i C MIRc#SINE/MIR 124 AGGCTCAGAGAGGTTAAGTGACTTGCCCAAGG-TCACACAG-CTAGTAAG 77 chr4ptel1M 207017 TGG---AGATGGGATTCAAACCCAGGTTCTCCTGACT---GGTCCTTGAA 207060 --- vi i i ii ---i --- i C MIRc#SINE/MIR 76 TGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCC---AG 30 chr4ptel1M 207061 TGCTCTTTCCTCTACATCTCAC 207082 v i i v C MIRc#SINE/MIR 29 TGCTCTTTCCACTGCACCACAC 8 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 28.08 CpG sites = 18, Kimura (unadjusted) = 30.77 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.07 (8 / 114), avg. gap size = 1.50 (12 / 8) 19 26.71 0.00 3.12 chr4ptel1M 209775 209840 (790160) (TAA)n#Simple_repeat 1 64 (0) m_b168s252i10 6409 chr4ptel1M 209775 TAATAATACCACTACTAATCATGAATACTAAAGAGATCCACAAATAATAA 209824 vi v v v - v vi v -vi vv (TAA)n#Simple 1 TAATAATAATAATAATAATAAT-AATAATAATAATA-ATAATAATAATAA 48 chr4ptel1M 209825 CAATAATAATAATAAT 209840 i (TAA)n#Simple 49 TAATAATAATAATAAT 64 Matrix = Unknown Transitions / transversions = 0.40 (4/10) Gap_init rate = 0.03 (2 / 65), avg. gap size = 1.00 (2 / 2) 254 32.17 0.70 4.35 chr4ptel1M 209851 209993 (790007) L1ME4c_3end#LINE/L1 413 550 (280) m_b168s551i3 6410 chr4ptel1M 209851 TTTAAAAAAAGGAAAATGACCTATATGTACAAAAAATATTCCTAGTAACT 209900 i i -- v i i i - i v v i i v L1ME4c_3end#L 413 TTCAAAAGAAGGAAAA--AGCTATATGCACGAAGA-TGTTCATTGCAGCG 459 chr4ptel1M 209901 CTCTTCTCAA-GGCAAAAATATACTGGAAATTAAGGGAATGCCTATCAGT 209949 i v ivi -i i --- i iv vvvi i i v i L1ME4c_3end#L 460 TTATTTATAATAGCGAAAA---ATTGGAAACAACCTAAATGTCCAACAAT 506 chr4ptel1M 209950 TGGGGAATGGCTCAATAAACTATTGTGTGTGTTTGTGATGGAAT 209993 v i v i i v iii v?vivi L1ME4c_3end#L 507 AGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAAT 550 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 40.12 CpG sites = 27, Kimura (unadjusted) = 44.11 Transitions / transversions = 1.59 (27/17) Gap_init rate = 0.05 (7 / 142), avg. gap size = 1.00 (7 / 7) 15 17.23 2.44 2.44 chr4ptel1M 211855 211895 (788105) (ATCCTA)n#Simple_repeat 1 41 (0) m_b168s252i11 6411 chr4ptel1M 211855 ATCCTAACCCTAAATGTGCACCCTAATCCTAATCCTAA-CCT 211895 i - vivv i - (ATCCTA)n#Sim 1 ATCCTAATCCT-AATCCTAATCCTAATCCTAATCCTAATCCT 41 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 272 29.20 12.70 2.16 chr4ptel1M 212145 212270 (787730) C L2d2_3end#LINE/L2 (3) 552 414 m_b168s601i30 6412 chr4ptel1M 212145 AATCAAGTTAATAAGCATTCATTAAGCATCTATTGTTTTCCAGACATTCG 212194 i i i ii i i ii i v v v i i - C L2d2_3end#LIN 552 AATCAAATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACT-G 504 chr4ptel1M 212195 TACTAAATTC---AGGAGATAC---------TAAAAAATAATCTTTTTCC 212232 i iiiv ---i i --------- i v ii ii vi C L2d2_3end#LIN 503 TGCTAGGCGCTGTGGGGGATACAAAGAAGTATAAGACATGGTCCCTGCCC 454 chr4ptel1M 212233 TCAAGGAGCTTAC---CCA-TTAGGCAGAGAGCAGATACAAA 212270 --- i - i -- vv i i C L2d2_3end#LIN 453 TCAAGGAGCTTACAATCTAGTTGGG--GAGACAAGACATAAA 414 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 37.25 CpG sites = 28, Kimura (unadjusted) = 40.22 Transitions / transversions = 3.50 (28/8) Gap_init rate = 0.06 (7 / 125), avg. gap size = 2.71 (19 / 7) 205 28.53 8.27 5.11 chr4ptel1M 212152 212284 (787716) C L2c_3end#LINE/L2 (10) 468 332 m_b168s601i31 6412 chr4ptel1M 212152 TTAATAAGCATTCATTAAGCATCTATTGTTTTCCAGACATTCGTACTAAA 212201 i i i i i ii i i v v i ii v ----ii C L2c_3end#LINE 468 TCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGG----GGA 423 chr4ptel1M 212202 TTCAGGAGAT-ACTAAAAAATAATCTTTTTCCTCAAGGAGCTTAC---CC 212247 v i- - v i v iii ii vi i --- i C L2c_3end#LINE 422 TACAA-AGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCT 374 chr4ptel1M 212248 ATTAG-GCAGAGAG-CAGAT--ACA---AATTACAATGGACAAG 212284 v i - v v - ?i -- --- -- C L2c_3end#LINE 373 AGTGGAGGAGACAGACANGTAAACAGACAATTACAAT--ACAAG 332 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 34.36 CpG sites = 26, Kimura (unadjusted) = 38.62 Transitions / transversions = 2.60 (26/10) Gap_init rate = 0.10 (13 / 132), avg. gap size = 1.38 (18 / 13) 252 17.65 3.92 0.00 chr4ptel1M 213709 213759 (786241) C MIRc#SINE/MIR (120) 148 96 m_b168s601i32 6413 chr4ptel1M 213709 CTCATTTTACAGCTGTGAAAACTGAGG--CAAATGGGTTAAGGGACTTGC 213756 i v v i -- i vi v C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr4ptel1M 213757 TCA 213759 i C MIRc#SINE/MIR 98 CCA 96 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 20.31 CpG sites = 5, Kimura (unadjusted) = 20.31 Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.02 (1 / 50), avg. gap size = 2.00 (2 / 1) 47 0.00 0.00 0.00 chr4ptel1M 214568 214607 (785393) (TA)n#Simple_repeat 1 40 (0) c_b168s251i1 6414 chr4ptel1M 214568 TATATATATATATATATATATATATATATATATATATATA 214607 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATA 40 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 17 18.81 0.00 0.00 chr4ptel1M 214733 214763 (785237) (A)n#Simple_repeat 1 31 (0) m_b168s252i12 6415 chr4ptel1M 214733 AAAAAAAGAATAAAAAAGAAAGGAAAAAAAA 214763 i v i ii (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 31 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 19 22.64 0.00 0.00 chr4ptel1M 215852 215892 (784108) (T)n#Simple_repeat 1 41 (0) m_b168s252i13 6416 chr4ptel1M 215852 TTTTTCCTTTTTTTTTTTTTTTTAATTATAGTTTTTTATTT 215892 ii vv v vv v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 41 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 563 33.84 1.81 1.81 chr4ptel1M 219900 220230 (779770) C L1ME4c_3end#LINE/L1 (191) 639 309 m_b168s551i4 6417 chr4ptel1M 219900 TCCTGCTTATTTCACTCAGCATCAGTTCATATAAGTCTCTCCAGGCCTTT 219949 i v i i i vv v vi i - v iivi C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATAAACATTT-TCCATGTTGCT 591 chr4ptel1M 219950 CTGAAATCATCCTGCTGGTCATTTCTTACAGAACAATAATATTCCATAAC 219999 viiv i v v iv vi i v ii vvvv viv C L1ME4c_3end#L 590 ACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCGA 541 chr4ptel1M 220000 ATTCATAAACCACAATTTATTCAGCTGTTCTCCAATTGATGGGCATCCAC 220049 i ?v iv i i i i ii i v v i ii v C L1ME4c_3end#L 540 GTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAG 491 chr4ptel1M 220050 TCAGTTTCCATTTTCTGGCCCCTACAAAACATTCTGCCACAAACATTCAT 220099 viv v i v ivi i vv iv v ii iivi C L1ME4c_3end#L 490 GTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTC 441 chr4ptel1M 220100 GCACATACAGGTCTTTTTCCCTTCTTTAAA--ATCCCTTTGGGATATAAG 220147 ii i -- i ii i -- ii i i v vv C L1ME4c_3end#L 440 GTGCATATAG--CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAATT 393 chr4ptel1M 220148 CCCAGTAGTAATACTGCTGGATCAAAGGGTATGCACAGTTTGATAACTTT 220197 v iiv i i i v v v ii i C L1ME4c_3end#L 392 CCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTCT 343 chr4ptel1M 220198 T--TGAGTATTAAAAAGAGATT--TTTCCAAGAGTGT 220230 -- iv ivv --- -- i v C L1ME4c_3end#L 342 TGATACGTATTGCCAA---ATTGCTTTCCAAAAGGGT 309 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 44.98 CpG sites = 63, Kimura (unadjusted) = 46.74 Transitions / transversions = 1.34 (63/47) Gap_init rate = 0.03 (9 / 330), avg. gap size = 1.33 (12 / 9) 568 28.92 0.97 0.97 chr4ptel1M 219985 220190 (779810) C L1ME3G_3end#LINE/L1 (376) 548 343 m_b168s551i5 6417 chr4ptel1M 219985 ATAATATTCCATAACATTCATAAACCACAATTTATTCAGCTGTTCTCCAA 220034 i ii vv v i i i ii i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr4ptel1M 220035 TTGATGGGCATCCACTCAGTTTCCATTTTCTGGCCCCTACAAAACATTCT 220084 i ii vviv v i v ivi vv v C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr4ptel1M 220085 GCCACAAACATTCATGCACATACAGGTCTTTTTCC-CTTCTTTAAA-ATC 220132 v ii i v i i ?-- i v v - v v vii i- i C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATT 401 chr4ptel1M 220133 CCTTTGGGATATAAGCCCAGTAGTAATACTGCTGGATCAAAGGGTATGCA 220182 i ? i v v? ? v iiv i i i C L1ME3G_3end#L 400 TCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCG 351 chr4ptel1M 220183 CAGTTTGA 220190 v i C L1ME3G_3end#L 350 CATTTTAA 343 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 36.72 CpG sites = 34, Kimura (unadjusted) = 38.47 Transitions / transversions = 1.36 (34/25) Gap_init rate = 0.02 (4 / 205), avg. gap size = 1.00 (4 / 4) 14 11.59 3.45 0.00 chr4ptel1M 220271 220299 (779701) (AGAT)n#Simple_repeat 1 30 (0) m_b168s252i14 6418 chr4ptel1M 220271 AGGTAGGTAGATAGATAGATA-ATAGACAG 220299 i i - i (AGAT)n#Simpl 1 AGATAGATAGATAGATAGATAGATAGATAG 30 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1) 186 16.67 11.90 0.00 chr4ptel1M 220303 220344 (779656) C MIR#SINE/MIR (3) 259 213 m_b168s601i33 6419 chr4ptel1M 220303 AATAG--AACATTTATTAAGCATTCA---TATGCCAGATACTGTTCT 220344 -- i ii i --- i ii C MIR#SINE/MIR 259 AATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCT 213 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 17.16 CpG sites = 7, Kimura (unadjusted) = 20.27 Transitions / transversions = 1.00 (7/0) Gap_init rate = 0.05 (2 / 41), avg. gap size = 2.50 (5 / 2) 230 24.82 5.32 10.00 chr4ptel1M 220308 220401 (779599) C L2c_3end#LINE/L2 (16) 462 373 m_b168s601i34 6420 chr4ptel1M 220308 AACATTTATTAAGCATTCA---TATGCCAGATACTGTTCTGGGGATACAA 220354 i iiii --- i iii ----- C L2c_3end#LINE 462 AACATTTATTGAGCGCCTACTATGTGCCAGGCGCTG-----GGGATACAA 418 chr4ptel1M 220355 ATACAAGTGAATAAGACA--GTCTATTTTTTCAAGGATTTTACATTTTA 220401 v ---- -- iv viii vi i v i C L2c_3end#LINE 417 AGA----TGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTA 373 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 27.89 CpG sites = 16, Kimura (unadjusted) = 31.70 Transitions / transversions = 3.20 (16/5) Gap_init rate = 0.12 (11 / 93), avg. gap size = 1.27 (14 / 11) 35 18.40 1.28 1.28 chr4ptel1M 220415 220492 (779508) (CTTC)n#Simple_repeat 1 78 (0) m_b168s252i15 6421 chr4ptel1M 220415 CTTCCATCTTTCCCTTCTTTCCTCCCTCCCTTCCTTTCTTCCTTCTTTCC 220464 v i - i i i i i (CTTC)n#Simpl 1 CTTCCTTCCTT-CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 49 chr4ptel1M 220465 TTTTTTTCTTCCTTCCAT-CTTTCTTCCT 220492 ii i v - i (CTTC)n#Simpl 50 TTCCTTCCTTCCTTCCTTCCTTCCTTCCT 78 Matrix = Unknown Transitions / transversions = 5.00 (10/2) Gap_init rate = 0.03 (2 / 77), avg. gap size = 1.00 (2 / 2) 24 24.91 2.35 3.57 chr4ptel1M 220421 220505 (779495) (TCTT)n#Simple_repeat 1 84 (0) m_b168s252i16 6421 chr4ptel1M 220421 TCTTTCCCTTCTTTCCTCCCTCCCTTCCTTTC-TTCCTTCTTTCCTTTTT 220469 - i - ii ii i - i - i (TCTT)n#Simpl 1 TCTTT-CTTTCTTT-CTTTCTTTCTTTCTTTCTTTCTTTCTTT-CTTTCT 47 chr4ptel1M 220470 TTC-TTCCTTCCATCTTTCTTCCTCTTTTTTTTTGTT 220505 - i iv i i i i v (TCTT)n#Simpl 48 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 84 Matrix = Unknown Transitions / transversions = 7.00 (14/2) Gap_init rate = 0.06 (5 / 84), avg. gap size = 1.00 (5 / 5) 462 22.97 14.74 2.29 chr4ptel1M 220902 221057 (778943) C MIRc#SINE/MIR (25) 243 69 m_b168s601i35 6422 chr4ptel1M 220902 ATAGCCTTTTAAGGTTTGTAAAGTACTTT-----ACA------CATGTGA 220940 vi vi ii ii ----- ------ v C MIRc#SINE/MIR 243 ATAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATCTCATTTGA 194 chr4ptel1M 220941 --------ACAACCCTATAAGATAGTATAAAGTAAGTCTTAGTATTCTCC 220982 -------- i i i -ii ii i i --- v v C MIRc#SINE/MIR 193 TCCTCACAACAACCCTGTGAGGTAG-GCAGGGCAGG---TATTATTATCC 148 chr4ptel1M 220983 CCATTTTACAGAGAAGAAAAC--AGGCTGAGAAAAG--AAGTGATTTGTC 221028 vi i -- v i i -- i i C MIRc#SINE/MIR 147 CCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCC 98 chr4ptel1M 221029 CAAGATCATACAACTAATAAGTGATTGAG 221057 i i i i iiv C MIRc#SINE/MIR 97 CAAGGTCACACAGCTAGTAAGTGGCAGAG 69 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 27.89 CpG sites = 27, Kimura (unadjusted) = 28.98 Transitions / transversions = 3.38 (27/8) Gap_init rate = 0.06 (9 / 155), avg. gap size = 3.00 (27 / 9) 16 0.00 0.00 0.00 chr4ptel1M 221612 221629 (778371) (T)n#Simple_repeat 1 18 (0) m_b168s252i17 6423 chr4ptel1M 221612 TTTTTTTTTTTTTTTTTT 221629 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTT 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 20 4.30 0.00 0.00 chr4ptel1M 222435 222458 (777542) (G)n#Simple_repeat 1 24 (0) m_b168s252i18 6424 chr4ptel1M 222435 GGGGGGTGGGGGGGGGGGGGGGGG 222458 v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGG 24 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 324 23.94 2.82 0.00 chr4ptel1M 222725 222795 (777205) Charlie4#DNA/hAT-Charlie 1 73 (3305) m_b168s502i0 6425 chr4ptel1M 222725 CAGGAGTTCTTGACCTGGG-TCCATAGATCCTTAAGGA-CCCATGGATAG 222772 i i - ii i ii i-i i Charlie4#DNA/ 1 CAGGGGTTCTTAACCTGGGGTCCACGGACCCCCAAGGGGTCCGTGGATAG 50 chr4ptel1M 222773 ATTTCCCAGGGCCTTTGAACTTG 222795 v vvi i iv Charlie4#DNA/ 51 AATTCAGGGGGTCCGTGAACTTG 73 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 24.04 CpG sites = 13, Kimura (unadjusted) = 30.44 Transitions / transversions = 3.25 (13/4) Gap_init rate = 0.03 (2 / 70), avg. gap size = 1.00 (2 / 2) 412 27.54 6.29 1.81 chr4ptel1M 222802 222960 (777040) Charlie4a#DNA/hAT-Charlie 343 508 (0) m_b169s502i1 6426 chr4ptel1M 222802 TTTGTTTCTTAAATATTTTGCTAAATGTATTTCTTAACAAAAATTACTTT 222851 ? i v v v -- i- v iv Charlie4a#DNA 343 TTTGNTTTTTTAATATTTTGATAACTGTATTTC--AAT-ATAATTGGTTT 389 chr4ptel1M 222852 CTTTTGCTCTCCTAGGTGTTTT----------CCTAAAAATATTCTACAG 222891 i ivv v i ----------ii i v v v Charlie4a#DNA 390 CCTTTGTAATCCTATGTATTTTATTTTATGCATTTAAAAACATTATTCTG 439 chr4ptel1M 222892 GGAAAGGGACAGTAGACTGCAACACAGTGACAGAAAAGTTCAAGACATAG 222941 i i v vi i v v v v v i iii i v i i i Charlie4a#DNA 440 AGAAGGGGTCCATAGGCTTCACCAGACTGCCAAAGGGGTCCATGGCACAA 489 chr4ptel1M 222942 AAAAGGCCAAGAACTCCTG 222960 ii i Charlie4a#DNA 490 AAAAGGTTAAGAACCCCTG 508 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.34 CpG sites = 24, Kimura (unadjusted) = 35.34 Transitions / transversions = 1.26 (24/19) Gap_init rate = 0.03 (4 / 158), avg. gap size = 3.25 (13 / 4) 336 27.06 16.67 1.99 chr4ptel1M 223597 223728 (776272) MIR3#SINE/MIR 13 163 (45) m_b169s601i0 6427 chr4ptel1M 223597 CTGAGCTCAGATAGAGC-TGGGCTAGG---CAGGAGCACCCGAGTTCAAA 223642 -- v -i i i --- - i i v i MIR3#SINE/MIR 13 CTGAGC--AGAGAGAGCACGGACTGGGAGTCAGGAG-ACCTGGGTTCTAG 59 chr4ptel1M 223643 TCTCATCTCAGA----------------GACTTCTAGCAACTCACTGTGC 223676 i iv v v---------------- i ivi v vii MIR3#SINE/MIR 60 TCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCAC 109 chr4ptel1M 223677 TTCTATCTATCTCAGTTTCCTCATCTGTAAAAT--AGGGATGAAATGAGA 223724 i v vvii --i i vii iv MIR3#SINE/MIR 110 CTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGA 159 chr4ptel1M 223725 TAAT 223728 i MIR3#SINE/MIR 160 TGAT 163 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.34 CpG sites = 22, Kimura (unadjusted) = 34.78 Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.05 (7 / 131), avg. gap size = 3.57 (25 / 7) 385 19.23 17.95 2.22 chr4ptel1M 223606 223722 (776278) MIR1_Amn#SINE/MIR 24 158 (72) m_b169s601i1 6427 chr4ptel1M 223606 GATAGAGC--TGGGCTAGG---CAGGAGCACCCGAGTTCAAATCTCATCT 223650 -- i i --- i - i i ? ? i iv MIR1_Amn#SINE 24 GATAGAGCACTGGACTGGGACTCGGGAG-ACCTGGGTTCNANTCCCGGCT 72 chr4ptel1M 223651 C----------------AGAGACTTCTAGCAACTCACTGTGCTTCTATCT 223684 ----------------? v i ivi v v?i i v v? MIR1_Amn#SINE 73 CTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGTCACTTNACCTCTCTGN 122 chr4ptel1M 223685 ATCTCAGTTTCCTCATCTGTAAAATAGGGATGAAATGA 223722 ii i -- MIR1_Amn#SINE 123 GCCTCAGTTTCCTCATCTGTAAAATGGGGAT--AATGA 158 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 21.73 CpG sites = 15, Kimura (unadjusted) = 24.17 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.05 (6 / 116), avg. gap size = 4.00 (24 / 6) 323 12.24 0.00 0.00 chr4ptel1M 223712 223760 (776240) MIRb#SINE/MIR 185 233 (35) m_b169s601i2 6428 chr4ptel1M 223712 GGATGAAATGAGATAATATATGAAAAGCACTTAGCACAGCGCCTGGCAC 223760 v ii v i i MIRb#SINE/MIR 185 GGATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCAC 233 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 11.29 CpG sites = 4, Kimura (unadjusted) = 13.54 Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 271 34.26 0.93 0.00 chr4ptel1M 223812 223919 (776081) C L3#LINE/CR1 (702) 3397 3289 m_b169s601i3 6429 chr4ptel1M 223812 CCTCACCATCCTGGATTGACAAACTTGAATTTTTGAAACCAAGTGTCGGA 223861 v v i viiiv v v v i i iv C L3#LINE/CR1 3397 CCTCTCCATCCTGTACTTGTGCAGTTGATTTTTTGAACCTAAATGCAGGA 3348 chr4ptel1M 223862 ATTTACAATAACCCCTGGTAAATATGCTTTT-CTACCTCTAGGCTACGAT 223910 v v v i v v vv i -i ivi iii v i ivi C L3#LINE/CR1 3347 CTTTACATTTATCCCTGTTAAATTTCATCTTGTTGGTTTCGGCCCATCGT 3298 chr4ptel1M 223911 TCCAACCTG 223919 i C L3#LINE/CR1 3297 TCCAGCCTG 3289 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.15 CpG sites = 19, Kimura (unadjusted) = 46.68 Transitions / transversions = 1.06 (19/18) Gap_init rate = 0.01 (1 / 107), avg. gap size = 1.00 (1 / 1) 508 21.74 2.61 0.00 chr4ptel1M 224120 224234 (775766) C Charlie1b#DNA/hAT-Charlie (6) 517 400 m_b169s502i2 6430 chr4ptel1M 224120 TTCTCCAGCCTTC-GGTCTTGGGGTCTCTCAAGACTCATAAAAGTTATTG 224168 v i i i- ii ii i iv v v i C Charlie1b#DNA 517 TTCTCAAACTTTTTGGTCTCAGGACCCCTTTACACTCTTAAAAATTATTG 468 chr4ptel1M 224169 AGGACCTCA--GAGCTTTTGTTTATGTGGGTGGTTTCCATCAGTATTTAC 224216 i -- vi v i ii C Charlie1b#DNA 467 AGGACCCCAAAGAGCTTTTGTTTATGTGGGTTATATCTATCGATATTTAC 418 chr4ptel1M 224217 TCTATTAGGAATTAGAAC 224234 iv i i C Charlie1b#DNA 417 CGTATTAGAAATTAAAAC 400 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 24.22 CpG sites = 18, Kimura (unadjusted) = 26.66 Transitions / transversions = 2.57 (18/7) Gap_init rate = 0.02 (2 / 114), avg. gap size = 1.50 (3 / 2) 189 18.88 0.00 8.33 chr4ptel1M 224637 224688 (775312) L3#LINE/CR1 2019 2066 (2033) m_b169s601i4 6431 chr4ptel1M 224637 AAAGAACAGTTAATGGTCTAGGAGGAATGGGAAGCTTTCACAAATTAAAT 224686 - --- iii i i? i i v v L3#LINE/CR1 2019 AAAGAA-AG---ATGGCTCAAGAGGGNTGGGAAGCTCTTAAAAATGAAAT 2064 chr4ptel1M 224687 TC 224688 L3#LINE/CR1 2065 TC 2066 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 23.03 CpG sites = 7, Kimura (unadjusted) = 23.03 Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.08 (4 / 51), avg. gap size = 1.00 (4 / 4) 182 20.00 0.00 0.00 chr4ptel1M 224860 224889 (775111) L3#LINE/CR1 3552 3581 (518) m_b169s601i5 6431 chr4ptel1M 224860 TAGTCCTACTGCACTCTGTGCTAGCCAGAC 224889 ii i i i i L3#LINE/CR1 3552 TAGTCCCGCTGTACTCTGCGCTGGTCAGAC 3581 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 15.96 CpG sites = 6, Kimura (unadjusted) = 25.54 Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 214 25.00 0.00 0.00 chr4ptel1M 225175 225214 (774786) C MIRb#SINE/MIR (178) 90 51 m_b169s601i6 6432 chr4ptel1M 225175 CAGATAATAAGTACCAGAGTTGGGATTTAAATCCAGTTCT 225214 v i iv ii ii i v C MIRb#SINE/MIR 90 CAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCT 51 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 24.09 CpG sites = 7, Kimura (unadjusted) = 31.73 Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 291 32.81 7.12 1.90 chr4ptel1M 225860 226210 (773790) L1MA10_3end#LINE/L1 205 573 (508) m_b169s551i0 6433 chr4ptel1M 225860 GTTAAGAATTAGCTA--GTTAGAAAAGGAAAA--TTACAAGTATTGGAGG 225905 i -- i --i i i iv -- v i v i L1MA10_3end#L 205 GTTAGGA--TGGCTATTATCAAAAAAACAAAAGATAACAAGTGTTGGCGA 252 chr4ptel1M 225906 GGATGTGGGAAAAACTGAGAGCTT------TGTTGCTAGAGTTGTGAATT 225949 ii ??v ivv ------ v i iiv i ? L1MA10_3end#L 253 GGATGTGGAGAAANNGGAACCCTTGTACACTGTTGGTGGGAATGTAAANT 302 chr4ptel1M 225950 GATTCAACCAC--TCGAGAGCAATTTGGAACTATGTGCAAAGGGCTATAA 225997 i v i -- v i i i v iv - viv iiii - L1MA10_3end#L 303 GGTGCAGCCACTATGGAAAACAGTATGGAGGT-TCCTCAAAAAATTA-AA 350 chr4ptel1M 225998 AACTGGGCATACCCTTTGGTCCAGCAATACTACTACTAAGTCTGTATCCT 226047 iv ii - v v i v i v ii v i - L1MA10_3end#L 351 AATAGAAC-TACCATATGATCCAGCAATCCCACTTCTGGGTATATATCC- 398 chr4ptel1M 226048 TAAAGAAATCAA---AGGA----AAAGGAATTATATATATGAAACTATTG 226090 v v v --- ----i ii - v ii ivvvvv i v L1MA10_3end#L 399 AAAAGAATTGAAATCAGGATCTCGAAGAGA-TATCTGCACTCCCATGTTC 447 chr4ptel1M 226091 ATTGCATCTTTTTT--CAGTAGATAAGAATTGGAGATTGTGGGATTGCCC 226138 v v v -- i vi vv i iviivvi v i L1MA10_3end#L 448 ATTGCAGCATTATTCACAATAGCCAAGATATGGAAACAACCTAAATGTCC 497 chr4ptel1M 226139 ATCAATTACGGAATGACTGAAG--GCTGTGATATATGATTGTAATGAAAT 226186 i ivivv iv i --iv i ivv ii i L1MA10_3end#L 498 ATCGACGGATGAATGGATAAAGAAAATGTGGTATATACATACAATGGAAT 547 chr4ptel1M 226187 ATTACT--GTGTTTAAAAAAAAGCAA 226210 i -- iv v i v L1MA10_3end#L 548 ATTATTCAGCCTTAAAAAAGAAGGAA 573 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.36 CpG sites = 63, Kimura (unadjusted) = 44.97 Transitions / transversions = 1.26 (63/50) Gap_init rate = 0.05 (16 / 350), avg. gap size = 2.00 (32 / 16) 509 29.72 7.72 2.88 chr4ptel1M 225893 226190 (773810) L1ME3Cz_3end#LINE/L1 236 547 (450) m_b169s551i1 6433 chr4ptel1M 225893 CAAGTATTGGAGGGGATGTGGGAAAAACTGAGAGCTTT--------GTTG 225934 i v i - i - i i i -------- i L1ME3Cz_3end# 236 CAAGTGTTGGCGAGGATGTGG-AGAAAC-GGGAACTCTCATACACTGCTG 283 chr4ptel1M 225935 CTAGAGTTGTGAATTGATTCAACCACTC--GAGAGCAATTTGGAACTATG 225982 v i iiv i i v i-- v v v L1ME3Cz_3end# 284 GTGGGAGTGTAAATTGGTACAACCACTTTGGAGAGCAATTTGGCAATATC 333 chr4ptel1M 225983 T-GCAAAGGGCTATAAAACTGGGCATACCCTTTGGTCCAGCAATACTACT 226031 - i v---- i iv v vi ii v i L1ME3Cz_3end# 334 TAGTAAAGT----TGAAGATGCGCATACCCTACGACCCAGCAATTCCACT 379 chr4ptel1M 226032 ACTAAGTCTGTATCCTTAAAGAAA---TCAAA-----GGAAAAGGAATTA 226073 v i v i - i i --- iv ----- v v ivi L1ME3Cz_3end# 380 TCTAGGTATATA-CCCTAGAGAAACTCTCGCACATGTGCACAAGGAGACA 428 chr4ptel1M 226074 TATATATGAAACTATTGATTGCATC--TTTTTTCAGTAGATAAGAATTGG 226121 i i v i -- i v v -- v vi i vv i L1ME3Cz_3end# 429 TGTACAAGGA--TGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGG 476 chr4ptel1M 226122 AGATTGTGGGATTGCCCATCAATTACGGAATGACTGA--AGGCTGTGATA 226169 i iviivvi v i viv iv i -- iii i L1ME3Cz_3end# 477 AAACAACCTAAATGTCCATCAATAGGGGAATGGATAAATAAATTGTGGTA 526 chr4ptel1M 226170 TATGATTGTAATGAAATATTA 226190 vvv ii i i L1ME3Cz_3end# 527 TATTCATACAATGGAATACTA 547 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.89 CpG sites = 51, Kimura (unadjusted) = 39.06 Transitions / transversions = 1.46 (51/35) Gap_init rate = 0.05 (16 / 297), avg. gap size = 2.00 (32 / 16) 511 31.15 4.96 0.73 chr4ptel1M 225929 226190 (773810) L1ME4c_3end#LINE/L1 282 554 (276) m_b169s551i2 6433 chr4ptel1M 225929 TTGTTGCTAGAGTTGTGAATTGATTCAACCACTC--GAGAGCAATTTGGA 225976 i v i vi? i i v vi i-- i v L1ME4c_3end#L 282 TTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGGC 331 chr4ptel1M 225977 ACTATGTGCAAAGGGCTATAAAACTGGGCATACCCTTTGGTCCAGCAATA 226026 v i iiv i i v vv ii i v L1ME4c_3end#L 332 AATACGTATCAAGAGCCATAAAAATGTTCATACCCTTTGACCCAGTAATT 381 chr4ptel1M 226027 CTACTACTAAGTCTGTATCCTTAAAGAAA----TCAAAGGAA--AAGGAA 226070 i v ii vv v - i ---- i -- ii i L1ME4c_3end#L 382 CCACTTCTGGGAATTTATCC-TAAGGAAATAATTCAAAAGAAGGAAAAAG 430 chr4ptel1M 226071 TTATATATATGAAACTATTGATTGCATCTTT-TTT-CAGTAGATAAGAAT 226118 i ii i iv i v v v - -i i vv i L1ME4c_3end#L 431 CTATATGCACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAAT 480 chr4ptel1M 226119 TGGAGATTGTGGGATTGCCCATCAATTACGGAATGACTGA--AGGCTGTG 226166 i iviivvi v i v viv ii i -- iii i L1ME4c_3end#L 481 TGGAAACAACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATG 530 chr4ptel1M 226167 ATATAT-GATTGTAATGAAATATTA 226190 i i -? i -ii i L1ME4c_3end#L 531 GTACATCNACT-CGATGGAATATTA 554 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.54 CpG sites = 53, Kimura (unadjusted) = 42.75 Transitions / transversions = 1.89 (53/28) Gap_init rate = 0.03 (9 / 261), avg. gap size = 1.67 (15 / 9) 17 18.82 0.00 2.33 chr4ptel1M 227872 227915 (772085) (TTCAAAT)n#Simple_repeat 1 43 (0) m_b169s252i1 6434 chr4ptel1M 227872 TTCAATTTTTAATTTCCAAACTACAAATTTCAGAATTTCAACTT 227915 v i v i i v - v (TTCAAAT)n#Si 1 TTCAAATTTCAAATTTCAAATTTCAAATTTCA-AATTTCAAATT 43 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.02 (1 / 43), avg. gap size = 1.00 (1 / 1) 220 30.79 11.48 1.49 chr4ptel1M 227968 228089 (771911) C MIR3#SINE/MIR (56) 152 19 m_b169s601i7 6435 chr4ptel1M 227968 CGACTGTCTCACTTTCCTGAAGAGGAAACAGAGATCTAGAGA----AAGT 228013 i ivi i v v v v ii i ---- C MIR3#SINE/MIR 152 CAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGT 103 chr4ptel1M 228014 AACTGGCTC---GT-ATGCAGTGA-----TGACAGAGACTTGAATCAAAG 228054 i v i --- - ii i? ----- i v vv v vi v C MIR3#SINE/MIR 102 GACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAAC 53 chr4ptel1M 228055 CCAAAT-TCATTTTTGCCAGATTCCATAGTCTCACT 228089 ii - v vvi v -- i iv v C MIR3#SINE/MIR 52 CCAGGTCTCCTGACTCCCAG--TCCGTGCTCTCTCT 19 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.40 CpG sites = 19, Kimura (unadjusted) = 40.81 Transitions / transversions = 1.06 (19/18) Gap_init rate = 0.06 (7 / 121), avg. gap size = 2.29 (16 / 7) 220 35.53 2.56 2.56 chr4ptel1M 228172 228249 (771751) L2c_3end#LINE/L2 363 440 (38) m_b169s601i8 6436 chr4ptel1M 228172 TTTCTTTCAGTTGATTACAAGCTCTTTGAGGATTAGGA--ATGTTTTATT 228219 i i i v v i iii i iivi --i i - L2c_3end#LINE 363 TCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTAT- 411 chr4ptel1M 228220 GTTGTCTTTGAATTTCTAGCATCTAACCCA 228249 - ii v ii i ii ii v L2c_3end#LINE 412 -TCATCTTTGTATCCCCAGCGCCTGGCACA 440 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 49.01 CpG sites = 22, Kimura (unadjusted) = 55.27 Transitions / transversions = 4.40 (22/5) Gap_init rate = 0.04 (3 / 77), avg. gap size = 1.33 (4 / 3) 242 28.71 6.74 2.15 chr4ptel1M 228184 228272 (771728) L2d2_3end#LINE/L2 437 529 (26) m_b169s601i9 6436 chr4ptel1M 228184 GATTACAAGCTCTTTGAGGATTAGGA--ATGTTTTATTGTTGTCTTTGAA 228231 ii i iivi -- i vv -- v L2d2_3end#LIN 437 GATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACT--TCTTTGTA 484 chr4ptel1M 228232 TTTC---TAGCATCTAACCCAGTGCCTCCC-CATAATATCCCCTC 228272 ii ---i ii i v iv - i i vv v L2d2_3end#LIN 485 TCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAGTAGGCGCTC 529 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.74 CpG sites = 16, Kimura (unadjusted) = 37.66 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.06 (5 / 88), avg. gap size = 1.60 (8 / 5) 223 30.91 6.36 0.00 chr4ptel1M 228269 228378 (771622) C L3#LINE/CR1 (149) 3950 3834 m_b169s601i10 6437 chr4ptel1M 228269 CCTCTTCAGTCTGGCCATTCCATTTTGAGATTGCACCAACTTT-----AA 228313 ?iv v v v vi iv v ii i v ----- i C L3#LINE/CR1 3950 CCTCNCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGATTGTTAGAAAG 3901 chr4ptel1M 228314 TTTTTCCCTACTATAAGCTTAAA-CTGGC-ACCTGCAACTCCCACCCATT 228361 i i ivv i iv - v -v i i C L3#LINE/CR1 3900 TTCTTCCTTATATTGAGCCGAAATCTGCCTCCCTGTAACTTCCACCCATT 3851 chr4ptel1M 228362 GTTCATTATCTTGCCTT 228378 v v vi ii i C L3#LINE/CR1 3850 GGTCCTAGTTCTGCCCT 3834 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.04 CpG sites = 18, Kimura (unadjusted) = 41.10 Transitions / transversions = 1.12 (18/16) Gap_init rate = 0.03 (3 / 109), avg. gap size = 2.33 (7 / 3) 16 5.27 0.00 0.00 chr4ptel1M 228467 228486 (771514) (A)n#Simple_repeat 1 20 (0) m_b169s252i2 6438 chr4ptel1M 228467 AAAAAAAAAAAAAAAGAAAA 228486 i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAA 20 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 26 26.88 6.04 2.60 chr4ptel1M 228819 228967 (771033) (TCTTCA)n#Simple_repeat 1 154 (0) m_b169s252i3 6439 chr4ptel1M 228819 TCTT-ATCTATAATATTCAT-ATGATTCTCATCCTTC-TCTTC-T-TTCA 228863 - - v v -v v ii - - - - (TCTTCA)n#Sim 1 TCTTCATCT-TCATCTTCATCTTCATCTTCAT-CTTCATCTTCATCTTCA 48 chr4ptel1M 228864 TCTTCCTTCTCTTCCTCTTCTTCATCTTCCTTTTCCTCCTCCACCTCTTC 228913 v ii v i v v i v i vv i v (TCTTCA)n#Sim 49 TCTTCATCTTCATCTTCATCTTCATCTTCATCTTCATCTTCATCTTCATC 98 chr4ptel1M 228914 TATCATCTTCTTTGTCTTCCTTC-TTTTCCCCAACATCCTCCTTTTC--C 228960 - v iv v - - i vi vv i v i -- (TCTTCA)n#Sim 99 T-TCATCTTCATCTTCAT-CTTCATCTTCATCTTCATCTTCATCTTCATC 146 chr4ptel1M 228961 TTC-TCTT 228967 - (TCTTCA)n#Sim 147 TTCATCTT 154 Matrix = Unknown Transitions / transversions = 0.68 (13/19) Gap_init rate = 0.08 (12 / 148), avg. gap size = 1.08 (13 / 12) 27 36.60 0.00 1.67 chr4ptel1M 228844 228965 (771035) (CTC)n#Simple_repeat 1 120 (0) m_b169s252i4 6440 chr4ptel1M 228844 CTCATCCTTCTCTTCTTTCATCTTCCTTCTCTTCCTCTTCTTCATCTTCC 228893 v i i -i v i i i i i v i (CTC)n#Simple 1 CTCCTCCTCCTCCTC-CTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC 49 chr4ptel1M 228894 TTTTCCTCCTCCACCTCTTCTATCATCTTCTTTGTCTTCCTTCTTTTCCC 228943 ii v i -v v i i iv i i ii i (CTC)n#Simple 50 TCCTCCTCCTCCTCCTCCTC-CTCCTCCTCCTCCTCCTCCTCCTCCTCCT 98 chr4ptel1M 228944 CAACATCCTCCTTTTCCTTCTC 228965 vv v ii i (CTC)n#Simple 99 CCTCCTCCTCCTCCTCCTCCTC 120 Matrix = Unknown Transitions / transversions = 2.30 (23/10) Gap_init rate = 0.02 (2 / 121), avg. gap size = 1.00 (2 / 2) 338 34.09 5.68 3.33 chr4ptel1M 229236 229411 (770589) C MIRc#SINE/MIR (75) 193 14 m_b169s601i11 6441 chr4ptel1M 229236 TCTTTAAAAATACTCTCTGAGGAAGGCAGCCAAGA----ATTTTCTTCAT 229281 i i v vv i v v vvv i---- v ii C MIRc#SINE/MIR 193 TCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCAT 144 chr4ptel1M 229282 TTTACAAATAAGGAAAAATAAAACTCAAAATCAGGGTTAAATAAGTTTCC 229331 i i - v i ii i ---ii i i v --v C MIRc#SINE/MIR 143 TTTACAGATGAGG-AAACTGAGGCTCAGA---GAGGTTAAGTGACTT--G 100 chr4ptel1M 229332 CCCAATGTCATATAA--AGTAAGTGGTGAGACAAAGATTCAAGGAGAATT 229379 v i i i-- iiiii vii i i ivvv iv C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGT 50 chr4ptel1M 229380 CTTACTG----CACATGCTGTGCTATGTCAATGGCA 229411 v ---- vi v v v v v iv C MIRc#SINE/MIR 49 CTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCA 14 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 44.62 CpG sites = 32, Kimura (unadjusted) = 46.82 Transitions / transversions = 1.23 (32/26) Gap_init rate = 0.05 (9 / 175), avg. gap size = 1.78 (16 / 9) 417 33.06 0.00 0.83 chr4ptel1M 229860 229981 (770019) C MIRc#SINE/MIR (141) 127 7 m_b169s601i12 6442 chr4ptel1M 229860 CTGAATCACTAATAGTTTAAGAGACTCGTGCAGGGTCACTCAGGCAATAT 229909 iv v vi v v v i iv i v vi i v C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAA 78 chr4ptel1M 229910 GGGTCAGAGGCAAAACTTGGATTCAAGTTTTCTCTGACTCCAAGGTCAGT 229959 v v v iii i i ii i i - vi C MIRc#SINE/MIR 77 GTGGCAGAGCCGGGACTCGAACCCAGGTCTTC-CTGACTCCAAGTCCAGT 29 chr4ptel1M 229960 TCATTCTCTACTATACCATATT 229981 v vi i i ii i i C MIRc#SINE/MIR 28 GCTCTTTCCACTGCACCACACT 7 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.25 CpG sites = 24, Kimura (unadjusted) = 45.32 Transitions / transversions = 1.50 (24/16) Gap_init rate = 0.01 (1 / 121), avg. gap size = 1.00 (1 / 1) 216 32.81 0.00 11.27 chr4ptel1M 230245 230323 (769677) MIR3#SINE/MIR 115 185 (23) m_b169s601i13 6443 chr4ptel1M 230245 TGAATCTTAGTTTCTTCACCTGGAAAATGGGAAAATGGGGAAAATGATTG 230294 iii i i i v i iiii v ------- i - MIR3#SINE/MIR 115 TGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTG-------GACT- 156 chr4ptel1M 230295 AGATGGCCCATAGAGCCCCTTCAAGCTTT 230323 ii iv ii i v i MIR3#SINE/MIR 157 AGATGATCTCTAAGGTCCCTTCCAGCTCT 185 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 47.76 CpG sites = 19, Kimura (unadjusted) = 47.76 Transitions / transversions = 4.75 (19/4) Gap_init rate = 0.10 (8 / 78), avg. gap size = 1.00 (8 / 8) 180 33.33 0.00 0.00 chr4ptel1M 230828 230875 (769125) MIRc#SINE/MIR 38 85 (183) m_b169s601i14 6444 chr4ptel1M 230828 GAAGCTAAGAAGACCCGAGTTCAAATCCTGCCTCAGATGCATACTGGC 230875 i ii i i i i i i v v vii v i MIRc#SINE/MIR 38 GGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGC 85 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.06 CpG sites = 12, Kimura (unadjusted) = 48.33 Transitions / transversions = 3.00 (12/4) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 267 33.54 12.01 4.39 chr4ptel1M 231142 231799 (768201) C L2#LINE/L2 (1159) 1923 1218 m_b169s601i15 6445 chr4ptel1M 231142 AGAGGGAGTGACAGCAATGAATGTGGGCAAAT--TTCAACTAGCTT-GTT 231188 i v ivii ii i i i i v -- i vv i - i C L2#LINE/L2 1923 AGAGGAATTGGAGACAGCGAGTATAGACAACTCTTTCGAGGAGTTTTGCT 1874 chr4ptel1M 231189 AATGAAGGGAAG--GAGAAATGGGGGGTGTAGCTGGATGAGAATGGAGTA 231236 i- i i -- v - v i i ? vi vi C L2#LINE/L2 1873 G-TAAAGGGGAGCAGAGAAATGGGGCG-GTAGCTGGAGGGGGANGTGGGG 1826 chr4ptel1M 231237 TCAAAAGAAAA-----GTATTTTAA----GGGAGATACTTAAGCA-G--- 231273 ii i ----- v ---- v i?vv - --- C L2#LINE/L2 1825 TCAAGGGAGAATTTTTGTTTTTTAAAGATGGGAGAAATNACAGCATGTTT 1776 chr4ptel1M 231274 --ATGCAAAAGAGCAAAAAAAAAAAAAAAAAAAAAAA--GCAGATGCAAA 231319 -- vi v i v vi vvv iv i i iii -- vv ii C L2#LINE/L2 1775 GTATGCTGATGGGAATGATCCAGTAGAGAGGGAAAAATTGATGATGCAGG 1726 chr4ptel1M 231320 AGAGCCTCTCGCAATGCACAAGAAAAAGACCCTGGATCTTGATGCAAAAG 231369 ------------- v i ii i iviv v -- i----- C L2#LINE/L2 1725 AGAG-------------AGAGGGGAGAATTGCTGGAGC--GATGT----- 1696 chr4ptel1M 231370 CCTGGAGGAGATAGAAGAGGATGGTTTAAAGGATGTGAGTAGAGGGATTA 231419 v v iiiii i vv vv viiiii i i i C L2#LINE/L2 1695 CCTTGAGTAGGCGAGAGGGGATGGGATCTAGTGCACAAGTGGAGGGGTTG 1646 chr4ptel1M 231420 GCCTCA-ATA--ACGACTGACATGTGTTCTTTCCTTGAAGACACAAGGGA 231466 i - -- vv v --- v i v v v - vi C L2#LINE/L2 1645 GCCTTAGATAGGAGCACGGACA---GTTCATCCGTAGTA-ACAGGAGGGA 1600 chr4ptel1M 231467 ---CAGAGGAGAGGAGGACAAATGGTGATAGAGTTTCAAATTCTGGAGGT 231513 --- v viv i v i vv i - vvvv iv v v C L2#LINE/L2 1599 AGGCAGAGTATGTGGGCACAGATGCAGGTAG-GTGGGTAGATGTGGTGGT 1551 chr4ptel1M 231514 -CAAGGATGAGGAA---TGCTGCTGTACTG-TCCTAGCGTTCTCAGTGA- 231557 -vi ?? v ---iv v - i - i -iv - C L2#LINE/L2 1550 GGGAGNNTGTGGAAGTTCTCTTCTG-ATTGCTTCTA-TTTTCTCAGTGAA 1503 chr4ptel1M 231558 -----AAGCTAGTTCACTTTCTACATATTAAGGGTAGAA----------T 231592 ----- v v iivv i- v v i i ii---------- C L2#LINE/L2 1502 ATAGGAAGCAAGGTCATCAGCTG-AGAGTGAGGATAGGGGAGGAGGTGTT 1454 chr4ptel1M 231593 GTAG--TTAAT--GAGAGCAGAAACTGCCCAAAGGTTCCTCT------GT 231632 v -- i v-- v iv -iv viv v ------ C L2#LINE/L2 1453 GGAGGTTTGAGGAGAGAGGAGAAGGTG-TGAAATAGTCGTCTAGGAGAGT 1405 chr4ptel1M 231633 GGGGAAGT-AGT-GAC---AGAAG---AGAAGGATTGACAAGCTGCCAGA 231674 ii - i - ---i i--- v ? v ii v vvv C L2#LINE/L2 1404 GGGAGAGTGAATGGACTAGGGAAATGTAGTANGATTGCCGGGCAGCATTA 1355 chr4ptel1M 231675 AGAGCCTAATGGAAGTTATTCATCATACATTTATAGTCAGCAAAATCAAC 231724 i i v v i ?v vi iv v v vvv i i C L2#LINE/L2 1354 AGGGCCCACTTGAGGTTNGTGGTCATGAATTTAAAGTGAGACCAGTCAGC 1305 chr4ptel1M 231725 TTAATTCGGTGACTTTTTCTAGCAACACACAGTAACCCAAG----GTCAC 231770 v ii vv vi i i v iiv ivi ? ii ---- v i C L2#LINE/L2 1304 ATGGTTGTGTGTTTTTCTCCAGCCACGTTCAGCTGCNCGGGTGCAGGCGC 1255 chr4ptel1M 231771 TGAAT-GGCAGAGG-------TTAACCAGAGTGGAAG 231799 v i - i i------- i v ?i C L2#LINE/L2 1254 GGAGTAGGCGGAGAGTTGGATTTAACCAGGGTTGNGG 1218 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 44.08 CpG sites = 111, Kimura (unadjusted) = 46.47 Transitions / transversions = 1.11 (111/100) Gap_init rate = 0.09 (58 / 657), avg. gap size = 1.90 (110 / 58) 29 0.00 0.00 0.00 chr4ptel1M 233979 234005 (765995) (ATA)n#Simple_repeat 1 27 (0) c_b169s251i0 6446 chr4ptel1M 233979 ATAATAATAATAATAATAATAATAATA 234005 (ATA)n#Simple 1 ATAATAATAATAATAATAATAATAATA 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 570 18.48 2.46 2.46 chr4ptel1M 234006 234127 (765873) C MIRb#SINE/MIR (9) 259 138 m_b169s601i16 6447 chr4ptel1M 234006 GCTAACTTTTACTAAGCATCTAAAAT-TGCCAGGCACTGTGCTAAGCCCT 234054 v v i i iii vv - v C MIRb#SINE/MIR 259 GCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCT 210 chr4ptel1M 234055 T--CATACATTATCTCATTTGATCCTCATGACAACCCTGGGAAGGAAATG 234102 -- i i ii v i v --- C MIRb#SINE/MIR 209 TTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTA---G 163 chr4ptel1M 234103 CTATTGTTAGCTCCATTTTAGAGAT 234127 v i v i v C MIRb#SINE/MIR 162 GTATTATTATCCCCATTTTACAGAT 138 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 20.38 CpG sites = 12, Kimura (unadjusted) = 21.42 Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.04 (5 / 121), avg. gap size = 1.20 (6 / 5) 422 32.00 1.13 1.13 chr4ptel1M 234269 234445 (765555) L1ME4c_3end#LINE/L1 397 573 (257) m_b169s551i3 6448 chr4ptel1M 234269 TATTCCGAAGAGATCATT--AAAAAAGGGAAAGGACCTATATGAGCAAAA 234316 i ii i i v -- i i i -- vi i i L1ME4c_3end#L 397 TATCCTAAGGAAATAATTCAAAAGAAGGAAAAAG--CTATATGCACGAAG 444 chr4ptel1M 234317 ATGTTTGTGGCAGCCCTTTTTATAGCGGCAAGTAACTGGAAGCTGACTGG 234366 ii v vi v iii i iv i i viv ii L1ME4c_3end#L 445 ATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAA 494 chr4ptel1M 234367 ACGTCCATCAGTTGGAGAATGGCTGAATAAGTCATGTTATATGAATGTAA 234416 i v i v i i i i i i v i v? ivii L1ME4c_3end#L 495 ATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGA 544 chr4ptel1M 234417 TGGAATATTATTATTCTATAAGAAATGAT 234445 vvvv i v i L1ME4c_3end#L 545 TGGAATATTATGCAGCCATTAAAAATGAT 573 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.26 CpG sites = 38, Kimura (unadjusted) = 44.65 Transitions / transversions = 2.11 (38/18) Gap_init rate = 0.02 (3 / 176), avg. gap size = 1.33 (4 / 3) 295 31.61 1.83 3.24 chr4ptel1M 234301 234519 (765481) L1MC4_3end#LINE/L1 430 645 (2144) m_b169s551i4 6448 chr4ptel1M 234301 ACCTATATGAGCAAAAATGTTTGTGGCAGCCCTTTTTATAGCGGCAAGTA 234350 i ---- vi i i ii v i ii? v iv L1MC4_3end#LI 430 ACCTGTA----CACGAATGTTTATAGCAGCTTTATTCATAATNGCCAAAA 475 chr4ptel1M 234351 ACTGGAAGCTGACTGGACGTCCATCAGTTGGAGAATGGCTGAATAAGTCA 234400 ? i viv ?i i v iiv v v i i iiii L1MC4_3end#LI 476 NCTGGAAACAACCNAGATGTCCTTCAACAGGTGAATGGATAAACAAACTG 525 chr4ptel1M 234401 TGTTATATGAATGTAATGGAATATTATTATTCTATAAGAAATGATGAGCA 234450 v i vv ii i i vvv v i ivi i - L1MC4_3end#LI 526 TGGTACATCCATACAATGGAATACTACTCAGCGATAAAAAGGAATGAAC- 574 chr4ptel1M 234451 GATTGGTTT-CAGAAAAGCCTGGA-AAGACTTATGTGAATTGATGCTAAA 234498 v i i ?i- iv ? i v -i iv vi v ?v- i L1MC4_3end#LI 575 TACTGATNCACGCAANAACATGGATGAATCTTAAATGCATNT-TGCTAAG 623 chr4ptel1M 234499 TGAACTGAA--CAGAACCAAAAG 234519 v- -- ?v?? L1MC4_3end#LI 624 TGAAA-GAAGCCAGNCNNAAAAG 645 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.33 CpG sites = 40, Kimura (unadjusted) = 45.17 Transitions / transversions = 1.48 (40/27) Gap_init rate = 0.05 (10 / 218), avg. gap size = 1.10 (11 / 10) 15 11.22 0.00 3.33 chr4ptel1M 234687 234717 (765283) (TTGT)n#Simple_repeat 1 30 (0) m_b169s252i5 6449 chr4ptel1M 234687 TTTTTTGTTATTGTTGTTTGTTTGTTTGTTT 234717 v - vv (TTGT)n#Simpl 1 TTGTTTGTT-TGTTTGTTTGTTTGTTTGTTT 30 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.03 (1 / 30), avg. gap size = 1.00 (1 / 1) 291 35.45 1.82 0.00 chr4ptel1M 235147 235256 (764744) C L3#LINE/CR1 (75) 4024 3913 m_b169s601i17 6450 chr4ptel1M 235147 TCCCCCATACAACATCTCAAAGAAGCCATCATCTAGCCTTTATTTGACAA 235196 iiv i vi v ivi i i ii vv C L3#LINE/CR1 4024 TCCCTTCTACAACATCCCTGACAAGTGGTCATCCAGCCTCTGCTTGAACA 3975 chr4ptel1M 235197 ACTTCAGAGA--GAGAATCCTCTGCTTCCTGTGACCGACAGTTCTACTTT 235244 v i v -- i iii v i i ?i v i v v vi i i C L3#LINE/CR1 3974 CCTCCAGTGACGGGGAGCTCACTACCTCNCGAGGCAGCCCATTCCATTTT 3925 chr4ptel1M 235245 GGGGTACCTCTG 235256 v ii v C L3#LINE/CR1 3924 TGGACAGCTCTG 3913 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 49.26 CpG sites = 24, Kimura (unadjusted) = 51.18 Transitions / transversions = 1.60 (24/15) Gap_init rate = 0.01 (1 / 109), avg. gap size = 2.00 (2 / 1) 185 28.39 0.00 10.98 chr4ptel1M 237001 237091 (762909) MIR#SINE/MIR 100 181 (81) m_b169s601i19 6451 chr4ptel1M 237001 TTACTTTTTCTCTCCAAGGCTCAGCTTCCTTTCTTCTCTGTTAGGTGGGG 237050 vvi iiv v i ---- iv v ii MIR#SINE/MIR 100 TTACTTAACCTCTCTGTGCCTCAGTTTC----CTCATCTGTAAAATGGGG 145 chr4ptel1M 237051 CAAATACTTATAATACCTACCACCTTTAAGATGGTTGAAAG 237091 --- v v i v v-- i i v vi MIR#SINE/MIR 146 ---ATAATAATAGTACCTACCTCA--TAGGGTTGTTGTGAG 181 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.43 CpG sites = 11, Kimura (unadjusted) = 35.43 Transitions / transversions = 0.92 (11/12) Gap_init rate = 0.10 (9 / 90), avg. gap size = 1.00 (9 / 9) 186 20.21 0.00 16.39 chr4ptel1M 237001 237071 (762929) MIRb#SINE/MIR 107 167 (101) m_b169s601i18 6451 chr4ptel1M 237001 TTACTTTTTCTCTCCAAGGCTCAGCTTCCTTTCTTCTCTGTTAGGTGGGG 237050 vvi ii v i ---- iv v ii MIRb#SINE/MIR 107 TTACTTAACCTCTCTGAGCCTCAGTTTC----CTCATCTGTAAAATGGGG 152 chr4ptel1M 237051 CAAATACTTATAATACCTACC 237071 --- --- MIRb#SINE/MIR 153 ---ATA---ATAATACCTACC 167 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 23.14 CpG sites = 7, Kimura (unadjusted) = 23.14 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.14 (10 / 70), avg. gap size = 1.00 (10 / 10) 368 23.75 7.50 0.00 chr4ptel1M 237437 237516 (762484) MIRc#SINE/MIR 42 127 (141) m_b169s601i20 6452 chr4ptel1M 237437 TCAGGAAGACCTGAGTTCAAATCC------TGCCTTTTATGAGTTGTGCA 237480 i i i ------ vi iv i ii MIRc#SINE/MIR 42 TCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTG 91 chr4ptel1M 237481 GCTATGGGCAAGAACCTTAACTTCTCTGAGCTTTAG 237516 i iv vvv i i i MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 27.76 CpG sites = 13, Kimura (unadjusted) = 29.60 Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.01 (1 / 79), avg. gap size = 6.00 (6 / 1) 407 30.91 1.80 0.89 chr4ptel1M 237623 237733 (762267) C MIR3#SINE/MIR (0) 208 97 m_b169s601i21 6453 chr4ptel1M 237623 GGATCACAAGACCAT-GAAT-TTGGAGTTACAAGGGGTCCACAAAAACTA 237670 i i ii i - - ii i iv i- vi i i ii C MIR3#SINE/MIR 208 GAATCATAGAATCATAGAATGTCAGAGCTGGAAGGGA-CCTTAGAGATCA 160 chr4ptel1M 237671 TCTAATCCAGCCCTTTCATTTTACAGATGAGGAAACTGAATTTTAGGGAA 237720 i i ii iviii i i C MIR3#SINE/MIR 159 TCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAG 110 chr4ptel1M 237721 GCATTGTGATCTG 237733 iivv ii C MIR3#SINE/MIR 109 GTGAAGTGACTTG 97 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 44.90 CpG sites = 29, Kimura (unadjusted) = 44.90 Transitions / transversions = 5.80 (29/5) Gap_init rate = 0.03 (3 / 110), avg. gap size = 1.00 (3 / 3) 253 34.31 4.90 0.00 chr4ptel1M 238523 238624 (761376) MamSINE1#SINE/tRNA-RTE 41 147 (143) m_b169s601i22 6454 chr4ptel1M 238523 AAAGAAGGCAAGACCAAGGGTTC-ATTCAATTCTA--TTA-TTAACTT-A 238567 v i v ii v - i vvv v i--ii - i -i MamSINE1#SINE 41 AATGAGGCCAAGGTCACGGGTTCGATCCCCGTGTGGGCCAGTTAGCTTTG 90 chr4ptel1M 238568 TTCCATTCCATAGCCATAGCATGTATTCCTAATTCCAGGCTTGCATCTCA 238617 i ii i i vv i ii ii v vvv i i MamSINE1#SINE 91 CTCTGTTCCATGGCCACAGACTGCACCCCTAACCCCAGCCAGCCGTCTCG 140 chr4ptel1M 238618 CAAATAC 238624 i MamSINE1#SINE 141 CAAATGC 147 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 44.42 CpG sites = 22, Kimura (unadjusted) = 48.27 Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.04 (4 / 101), avg. gap size = 1.25 (5 / 4) 14 15.26 0.00 0.00 chr4ptel1M 239413 239441 (760559) (TGTC)n#Simple_repeat 1 29 (0) m_b169s252i6 6455 chr4ptel1M 239413 TGTCTGTCTGTCTGTCTCTGTCTCTATCT 239441 v v v i (TGTC)n#Simpl 1 TGTCTGTCTGTCTGTCTGTCTGTCTGTCT 29 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 51 0.00 0.00 0.00 chr4ptel1M 239442 239485 (760515) (CA)n#Simple_repeat 1 44 (0) c_b169s251i1 6456 chr4ptel1M 239442 CACACACACACACACACACACACACACACACACACACACACACA 239485 (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACA 44 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 37 17.24 5.93 3.31 chr4ptel1M 239873 239990 (760010) (ACAGAG)n#Simple_repeat 1 121 (0) m_b169s252i7 6457 chr4ptel1M 239873 ACAGA-AGAGAGAGAAAGACAGATACAGAGAAGCTGAGACAGA-A-AGAG 239919 - v v i v - - v - - (ACAGAG)n#Sim 1 ACAGAGACAGAGACAGAGACAGAGACAGAG-A-CAGAGACAGAGACAGAG 48 chr4ptel1M 239920 ATAGGAGA-GGGGAAAGACAAAGAGACAAAGACCAAAG-CAGA-A-AGAG 239965 i - -i i v v v i - i - - - (ACAGAG)n#Sim 49 ACA-GAGACAGAGACAGAGACAGAGACAGAGA-CAGAGACAGAGACAGAG 96 chr4ptel1M 239966 ACAGAGACAGACATAGACACAAAGA 239990 v i v i (ACAGAG)n#Sim 97 ACAGAGACAGAGACAGAGACAGAGA 121 Matrix = Unknown Transitions / transversions = 0.89 (8/9) Gap_init rate = 0.09 (11 / 117), avg. gap size = 1.00 (11 / 11) 21 29.17 2.78 3.74 chr4ptel1M 240245 240352 (759648) (ACAT)n#Simple_repeat 1 107 (0) m_b169s252i8 6458 chr4ptel1M 240245 ACACATATACATACTTACATACATTCATATATATAGTTTCATACATAAAT 240294 i i v v i i -- v v (ACAT)n#Simpl 1 ACATACATACATACATACATACATACATACATACA--TACATACATACAT 48 chr4ptel1M 240295 ACGCCCATATGTGCA-ACATTC-T-CATGCATTCACATTCAATCACACAC 240341 iiv ii i - v - - i - - v vv i i (ACAT)n#Simpl 49 ACATACATACATACATACATACATACATACA-T-ACATACATACATACAT 96 chr4ptel1M 240342 CCACACACACA 240352 v i i (ACAT)n#Simpl 97 ACATACATACA 107 Matrix = Unknown Transitions / transversions = 1.40 (14/10) Gap_init rate = 0.07 (7 / 107), avg. gap size = 1.00 (7 / 7) 15 5.48 0.00 0.00 chr4ptel1M 240335 240353 (759647) (CA)n#Simple_repeat 1 19 (0) m_b169s252i9 6459 chr4ptel1M 240335 CACACACCCACACACACAC 240353 v (CA)n#Simple_ 1 CACACACACACACACACAC 19 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 3678 28.52 2.84 3.05 chr4ptel1M 240516 242486 (757514) C L1M5_orf2#LINE/L1 (587) 2707 741 m_b169s551i5 6460 chr4ptel1M 240516 CTACCTTATTCTACTGATCAACTTTTCTATTTCTTA-ACCAGTATTAAAT 240564 iii i i i v i v i- -i i ii v i C L1M5_orf2#LIN 2707 CTATTCTGTTCCATTGATCTATTTGTCTATC-CTTACGCCAATACCACAC 2659 chr4ptel1M 240565 GGTTTTGATGACCACTGCTTTATAATATAGTTTT-ATATCTGGCACAGGT 240613 v i v iiiv - i - ? ? i -iv C L1M5_orf2#LIN 2658 TGTCTTGATTACTGTAGCTTTATAATA-AGTCTTGANATCNGGTA-GTGT 2611 chr4ptel1M 240614 AGGTCCTCCCA-TTTGCTTTTCTCTTCATTAATTCCTTTGAA-ATTATTG 240661 i v - i i i ivvvi vi iv- v ? C L1M5_orf2#LIN 2610 AAGTCCTCCAACTTTGTTCTTCTTTTTCAAGATTGTTTTGGCTATTCTNG 2561 chr4ptel1M 240662 ACCTTTTGTTCTTCCAGATGAATTTTG--------TTGTTATTTTTTTCC 240703 ii i ivi v i i-------- i v ---- C L1M5_orf2#LIN 2560 GTCCTTTGCATTTCCATATAAATTTTAGAATCAGCTTGTCAATTT----C 2515 chr4ptel1M 240704 TAGATCAGTAAAAGTTTCTTGGGAGTCTGATTGGTATAACACTAAATAAA 240753 --- i- iii vi v i v vi i i vv C L1M5_orf2#LIN 2514 TA---CAA-AAAAACCTGCTGGGATTTTGATTGGGATTGCATTGAATCTA 2469 chr4ptel1M 240754 TAGATTACTTTAGGGAGTATTGTCATCTTTATTATATTTGCTTGAGT--- 240800 i v i v v ? iv ----- --- C L1M5_orf2#LIN 2468 TAGATCAATTTGGGGAGAATTGACATCTTNACAATA-----TTGAGTCTT 2424 chr4ptel1M 240801 --GATCCAAGAGCACTTAATATTTTACCAATTGTTTAGATCTGACTTTAT 240848 --i v i ivvv i iv v i i vvi v C L1M5_orf2#LIN 2423 CCAATCCATGAACATGGTATATCTCTCCATTTATTTAGGTCTTCTTTAAT 2374 chr4ptel1M 240849 TTGTGTGGAAAGTGTTTTGTAGTTTTGCTCATATAGTTCCT-CACTTTCC 240897 v v viiv i vvvii ? v i - -v ?i C L1M5_orf2#LIN 2373 TTCTCTCAGCAATGTTTTGTAGTTTTCAGTGTANAGGTCTTGCAC-ATNT 2325 chr4ptel1M 240898 CTTGGTAGATGGATTCCCAAATATTTTATACTATCAACAATTATTTTAAA 240947 i v vv i i ? ii v ivivvii v C L1M5_orf2#LIN 2324 TTTGTTAGATTTATTCCTAAGTATTTNATGTTTTTTGATGCTATTGTAAA 2275 chr4ptel1M 240948 TGGAATTTCTCTTTTGTATC---TTTTGCTGTTGGATTTTGTTAGTGATA 240994 v - v i ?iv i--- v vi --- iv ii C L1M5_orf2#LIN 2274 TGGTA-TTGTTTTTNAAATTTCATTTTCCAATTG---TTTGTTGCTAGTA 2229 chr4ptel1M 240995 TATAAAAATTCTA-TGATTTTTGTGGATTTATTTTGGATCTTGCAACTTT 241043 i v v - iv v ii v i? i i C L1M5_orf2#LIN 2228 TATAGAAATACAATTGATTTTTGTATATTGACCTTGTATCCNGCGACCTT 2179 chr4ptel1M 241044 GCTAAAATTG-TGATTATTTCTAATAGTTTTTCAATTGATTCTCTAGGGT 241092 v ii- v v i ? ivi v i ? i C L1M5_orf2#LIN 2178 GCTAAATTCACTTATTAGTTCTAGTAGTTTNTTTGTAGATTCTTTNGGAT 2129 chr4ptel1M 241093 TCTTGAAGTATATCATCATATCCTTTGCAGCAAGTAATAATTTGGTTTCA 241142 i iv v ? iv i v i iivv i?i i i vi v C L1M5_orf2#LIN 2128 TTTCTACGTANACAATCATGTCATCTGCGAATAANGACAGTTTTATTTCT 2079 chr4ptel1M 241143 TGACCTATTCTAATT------CCTTTAATTTCTTTGCCTTCTCTTATTGC 241186 -- - i i------ v vi vi C L1M5_orf2#LIN 2078 T--CCT-TTCCAATCTTTATGCCTTTTATTTCTTTTTCTTGCCTTATTGC 2032 chr4ptel1M 241187 CAAAGCTAGCATTTCTAATACAATACTGAATAGTAATGGTGACAGTGAGC 241236 vvvi v ii i i ii v i ? i ii C L1M5_orf2#LIN 2031 ACTGGCTAGGACCTCCAGTACAATGTTGAATAGAAGTGGTGANAGCGGAC 1982 chr4ptel1M 241237 AACCTTGCTTCACCTTTGATCTTATTGGAAATAGTTCCAGTTCATCTCCA 241286 v ii iiiiiii vv i viv? i ?iv v C L1M5_orf2#LIN 1981 ATCCTTGTCTTGTTCCCGATCTTAGGGGGAAAGCNTTCAGTNTTTCACCA 1932 chr4ptel1M 241287 TTACATATGATGCTTGCTGATGGTTTTAAATAGATGCTGATTGTT---TT 241333 vi i ? vv vvi ivv i i--- C L1M5_orf2#LIN 1931 TTAAGTATGATGTTNGCTGTAGGTTTTTCGTAGATGCCCTTTATCAGGTT 1882 chr4ptel1M 241334 AAGGAAAAGTCCACT--TATTCCTATATTCTCT-AGTGTTTTTATTAGAA 241380 i -- i v -- -i iv - v i vi C L1M5_orf2#LIN 1881 GAGG--AAGTTCCCTTCTATTCCTA-GTTTGCTGAGAGTTTTTATCATGA 1835 chr4ptel1M 241381 ATAGGTGTTGAATTTTATCAAATGCTTTTTTTGCATCTATTGAGATAATC 241430 i i i i C L1M5_orf2#LIN 1834 ATGGGTGTTGAATTTTGTCAAATGCTTTTTCTGCATCTATTGAGATGATC 1785 chr4ptel1M 241431 ATATGGTTTTT---GTTAATTTGGTTATCGATATAGTCAATTATGCTAAT 241477 i ---v v iv --- i v iii i C L1M5_orf2#LIN 1784 ATATGATTTTTCTCCTTTATTCTGTTA---ATATGGTGAATTACATTGAT 1738 chr4ptel1M 241478 AATTTTCCTAATATTGAATCAGCCCTGCATTCCTGGCATAAATACTACTT 241527 viv i v i i i i i v iv i C L1M5_orf2#LIN 1737 TGATTTTCGAATGTTAAACCAACCTTGCATTCCTGGGATAAACCCCACTT 1688 chr4ptel1M 241528 GGTCATGGTGTATTATCCTGGGGATGATTTTCTATAATCTCTTTGCTATT 241577 i vvvv ivv v iv v vv v C L1M5_orf2#LIN 1687 GGTCATGATGTATTATCCTTTTTATATATTGCTGGATTCGATTTGCTAAT 1638 chr4ptel1M 241578 ATTTTATTTAAGATTTTTGCATTAATATTCATTAGGGAGATTAGGGAGAT 241627 i ? i iv i -- ------- v C L1M5_orf2#LIN 1637 ATTTTGTTNAGGATTTTTGCATCTATGTTCAT--G-------AGGGATAT 1597 chr4ptel1M 241628 TGGCCTATAATTTTCTTTCTCTGT--TTTCATCCTACCTGGTTCCGTTAT 241675 i i iii -- v v -- ii ? ii v C L1M5_orf2#LIN 1596 TGGTCTGTAATTTTCTTTTCTTGTAATGTCTT--TGTCNGGTTTTGGTAT 1549 chr4ptel1M 241676 CGTTACCATATCTGTGTCATAAAAGGAATTTGGTAGAAGTCCTTCTTTCC 241725 ivvii? iiiv iv v i v v viv i ii C L1M5_orf2#LIN 1548 CAGGGTNATGCTGGCCTCATAAAATGAGTTGGGAAGTGTTCCCTCTTTTT 1499 chr4ptel1M 241726 CTATTTTTTTCAAATAGTTTATAAAGTATTGGAGTTAATTGTTCTTTAAA 241775 - i vi v i iv iv vi v v i C L1M5_orf2#LIN 1498 CTA-TTTTCTGGAAGAGTTTGTGTAAGATTGGTATTATTTCTTCCTTAAA 1450 chr4ptel1M 241776 TGTTTGGTAGAATTCACATGTAAATCCATCTGGTCCTGGGGATTTTTTTT 241825 vv i v v i --- i C L1M5_orf2#LIN 1449 TGTTTGGTAGAATTCACCAGTGAAGCCATCTGGGCCTGGAG---TTTTCT 1403 chr4ptel1M 241826 TTTTAGGAAGTTGATTAATAGCTTGTTCTATTTCTTTTTCTGAAATGGGA 241875 v i v vv vi vvi v vviv v i i C L1M5_orf2#LIN 1402 TTGTGGGAAGGTTTTTAATTACAAATTCAATTTCTTTAATAGATATAGGG 1353 chr4ptel1M 241876 TTATTTAAGTAATTTATTTCCTCTTCTATTAATCTGGGCAATCTATATTT 241925 i i ii vv i i v?i i i i v i ?i i i C L1M5_orf2#LIN 1352 CTATTCAGATTTTCTATTTCTTCTTGNGTCAGTTTTGGTAANTTGTGTTT 1303 chr4ptel1M 241926 TTGTAGATAGTTCTCCATTTCACTTAGGTCATCAAATTTATTGGCATAAA 241975 vv iv v v ii i i? C L1M5_orf2#LIN 1302 TTCAAGGAATTTGTCCATTTCATCTAAGTTNTCAAATTTATTGGCATAAA 1253 chr4ptel1M 241976 GTTGGGCAAAGTA-ACTCTTAATAATTGCTCTAAGTTCCTCT----TCAT 242020 vv v i -v v -- v i v i vi v ---- vv C L1M5_orf2#LIN 1252 GTTGTTCATAATATTCTCTTATTA--TCCTTTTAATGTCTGTAGGATCTG 1205 chr4ptel1M 242021 TGGTGGATAGTTCTCCCTTTTCATTTGTGAGACTAACAATTTGATTTTCC 242070 i - i-- i iv v i iii vv i i C L1M5_orf2#LIN 1204 TAGT-GATG--TCTCCTTTTTCATTCCTGATATTGGTAATTTGTGTCTTC 1158 chr4ptel1M 242071 TCTTTCCTTTTTCTAATCAAATTAACTAAAGGTTTATCTATTTTTGTTGG 242120 i ii ii i ivi ?i i - v i - C L1M5_orf2#LIN 1157 TCTCTTTTTTTCTTGATCAGTCTNGCTAGAGGTTTATC-AATTTTATT-G 1110 chr4ptel1M 242121 ATTTTTTCATAAGACCAAC--TCAGTTTTATTTACTTATTCAATAGATTG 242168 i v ii i -- ii i ii v i vi v v v? ? C L1M5_orf2#LIN 1109 ATCTTTTCAAAGAACCAGCTTTTGGCTTCGTTGATTTTCTCTATTGTNTN 1060 chr4ptel1M 242169 TTTAGTTTCCATTTTATTGATCTCT--TTTGATTTTTAGAATTGCAAGTT 242216 iv i i i -- i v i vv v vvvii C L1M5_orf2#LIN 1059 TTTGTTTTCTATTTCATTGATTTCTGCTCTTATCTTTATTATTTCCTTCC 1010 chr4ptel1M 242217 TGGTATTTGA-TTGAGTTTTTAAAATTTG---TTCTTTTTCTAGCTTTTT 242262 vv i ?v- i ---- --- - i C L1M5_orf2#LIN 1009 TTCTACTTNCTTTGGGTTT----AATTTGCTCTTCTTTTTCTAGC-TTCT 965 chr4ptel1M 242263 TTAGTTGCAAGACCAATTCACTGATCTT--TTCATTCTCCATTTTATGCA 242310 v v v vii iv i i --vi v i - v i- C L1M5_orf2#LIN 964 TAAGGTGGAAGCTTAGATCATTGATTTTAAGCCTTTCTTC-TTTTCTA-A 917 chr4ptel1M 242311 AGTAAGCCTCTAGAAATATAAAATTTCCCTTT-ATTACTGCTTTGGCAGC 242359 vi ? v i i?iv - i - vi i v C L1M5_orf2#LIN 916 TATANGCATTTAANGCTAT-AAATTTCCCTCTAAGCACTGCTTTAGCTGC 868 chr4ptel1M 242360 ATCCCACAAATTTTGGTATGTTGTCTCATTATTGTCATTCTCTTGGATGA 242409 i v iv i ? vv vi viv C L1M5_orf2#LIN 867 ATCCCACAAATTTTGATATGTTGTATTTTCATTNTCATTCAGTTCAAAAT 818 chr4ptel1M 242410 AATTATTAATTGTGTCTATGATTTGTTGTTTCACCCATTCATTCTTTAGG 242459 v vi viv?i i v v v vvi v i C L1M5_orf2#LIN 817 ATTTTCTAATTTCCNTTGTGATTTCTTCTTTGACCCATGGGTTATTTAGA 768 chr4ptel1M 242460 ATAAGATTATTTAGTTTTCAATTACTT 242486 vvivi i i i v i C L1M5_orf2#LIN 767 AGTGTGTTGTTTAATTTCCAAATATTT 741 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.86 CpG sites = 307, Kimura (unadjusted) = 37.48 Transitions / transversions = 1.29 (307/238) Gap_init rate = 0.04 (85 / 1970), avg. gap size = 1.36 (116 / 85) 407 32.90 3.54 3.11 chr4ptel1M 242584 243063 (756937) L1M5_orf2#LINE/L1 2806 3287 (7) m_b169s551i6 6461 chr4ptel1M 242584 TGCTGGGAAAATTGGAAACTAGTATGGCAGAAAGTAGGCATATACCCAGA 242633 i v v iivi v i i iii?v vv vv L1M5_orf2#LIN 2806 TGCTGGAACAATTGGATATCCATATGGAAAAAAATGAANCTCGACCCCTA 2855 chr4ptel1M 242634 TCTAACACT---TACCAAGATAAGGTTGAAATGGGTTCATGG-TCTAGAC 242679 i v i---i v i v iv i? i i - i -i i i L1M5_orf2#LIN 2856 CCTCACACCATACACAAAAATTAATTCNAGATGGAT-CATAGACCTAAAT 2904 chr4ptel1M 242680 ATAAAGAATGGTATTATAAACAAATT----AAAAGAACATAGGATAGTTT 242725 i ii? iiv i -- v ---- i i v i v L1M5_orf2#LIN 2905 GTAAAAGNTAAAACTATAAA--ACTTCTAGAAGAAAACATAGGAGAATAT 2952 chr4ptel1M 242726 GCCTCTTAGATTTGTGGATGAGGAAGGAATTTGTAACCAAAGCAGAACTA 242775 - i v iivi - ? ii v i v iv v iii v vv L1M5_orf2#LIN 2953 -CTTCGTGACCTTG-GGNTAGGCAAAGATTTCTTAAACAGGACACAAAAA 3000 chr4ptel1M 242776 GAGATCATTATTGATCACAAAATAGATAATTTTGATTATATTAAGTTTAA 242825 viv?v ii vi vv v v v v i ?i i iv L1M5_orf2#LIN 3001 GCACNAACCATAAAAGAAAAAATTGATAAATTGGACTNCATCAAAATTAA 3050 chr4ptel1M 242826 AAGATTTTTGTACCAACAAAACTAATGCAG--AAAAAAATTAGAAGGGAA 242873 - i i i-i ?v --i ii v -- i v i v L1M5_orf2#LIN 3051 AA-ACTTCTGC-TCNTCAAAA--GACACCGTTAAGAAAATGAAAAGGCAA 3096 chr4ptel1M 242874 GCAATAAACTGGGAGAACACTTTTATATCCAAAGGATCTGATAAAGGCCT 242923 v i i ? v iv ii v?vv viv i v L1M5_orf2#LIN 3097 GCCACAGANTGGGAGAAAATATTTGCAANACATATATCTGACAAAGGACT 3146 chr4ptel1M 242924 CATTTTTAAAATATATAGAGAACTGACTCAAATTTACAATAGTTCAAGCC 242973 i v ii i i vviv ? iv i ? i--v v L1M5_orf2#LIN 3147 CGTATCCAGAATATATAAAGAACTCCTACAANTCAATAANAA--AAAGAC 3194 chr4ptel1M 242974 ATTC--TCCAATTGATAAATGGTCAAAGCATATGAATAGACAATTTTCAG 243021 vv --i v? v v iv iv i v iv i L1M5_orf2#LIN 3195 AAACAACCCAATANAAAAATGGGCAAAAGACTTGAACAGACACTTCACAA 3244 chr4ptel1M 243022 ATGAAGAAATTTAACTATATG-----TAGTCACATGAAAAGGTGTTC 243063 v v ?i ---- ----- iv i i L1M5_orf2#LIN 3245 AAGAAGATATNCAA----ATGGCCAATAAGCACATGAAAAGATGCTC 3287 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 45.84 CpG sites = 84, Kimura (unadjusted) = 46.26 Transitions / transversions = 1.22 (84/69) Gap_init rate = 0.04 (21 / 479), avg. gap size = 1.52 (32 / 21) 601 27.51 2.54 2.98 chr4ptel1M 242928 243163 (756837) L1ME5_3end#LINE/L1 7 241 (700) m_b169s551i7 6461 chr4ptel1M 242928 TTTAAAATATATAGAGAACTGACTCAAATTTACAATAGTTCAAGCCATT- 242976 i i i ii vviv iv v i--v v iv?- L1ME5_3end#LI 7 TCTAGAATATACAAGGAACTCCTGCAAATCAACAAGAA--AAAGACGGNA 54 chr4ptel1M 242977 -CTCCAATTGATAAATGGTCAAAGCATATGAATAGACAATTTTCAGATGA 243025 - i v v v v i i v v L1ME5_3end#LI 55 ACCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGA 104 chr4ptel1M 243026 AGAAATTTAA----CTATATGTAGTCACATGAAAAGGTGTTCCAAATAAG 243071 i iiii ---- ---ii iv i i i i v v v v L1ME5_3end#LI 105 GGAAACCCGAAAGGCTA---ACAAGCATATGAAGAGATGCTCAAACTCAT 151 chr4ptel1M 243072 TATTGATCAGAGAAATGCAAATTAAGACAACTCTGAGTTACCACTACACA 243121 v i i vv v i vi L1ME5_3end#LI 152 TAGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACA 201 chr4ptel1M 243122 CCTTTCAAACTGGCTAAGATGACAGAACAATGAACAATGCCA 243163 v i i v i --i viv i i L1ME5_3end#LI 202 CCTATTAGACTGGCAAAAAT--TAGAAAGCTGGATAATGCCA 241 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.70 CpG sites = 35, Kimura (unadjusted) = 35.14 Transitions / transversions = 1.25 (35/28) Gap_init rate = 0.04 (10 / 235), avg. gap size = 1.30 (13 / 10) 384 20.92 0.74 11.48 chr4ptel1M 244090 244224 (755776) C Charlie4a#DNA/hAT-Charlie (0) 508 387 m_b169s502i3 6462 chr4ptel1M 244090 CAGAGACTTTGAACCTTTTTTGTGAGTTCTGGATCCCTTTGGTTGTAGGT 244139 i ii i v --iiv i i----i C Charlie4a#DNA 508 CAGGGGTTCTTAACCTTTTTTGTG--CCATGGACCCCTTTGGC----AGT 465 chr4ptel1M 244140 TTAGGTGAAACTTATGAACCCCTGTCCAAAAAATATGTTTTTAA-TGCAT 244188 i - i i i vii i v - - C Charlie4a#DNA 464 CT-GGTGAAGCCTATGGACCCCTTCTCAGAATA-ATGTTTTTAAATGCAT 417 chr4ptel1M 244189 AAAGTGCAAAATATCACAAAGGCTAATGAAAGGAAA 244224 i -- --- v v v i- C Charlie4a#DNA 416 AAAAT--AAAAT---ACATAGGATTAC-AAAGGAAA 387 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 25.03 CpG sites = 18, Kimura (unadjusted) = 25.03 Transitions / transversions = 2.57 (18/7) Gap_init rate = 0.11 (15 / 134), avg. gap size = 1.00 (15 / 15) 324 23.80 3.74 1.83 chr4ptel1M 244190 244296 (755704) C Charlie4a#DNA/hAT-Charlie (396) 112 4 m_b169s502i4 6462 chr4ptel1M 244190 AAGTGCAAAATATCA--CAAAGGCTAATGAAAGGAAAGAATTTCATTTCT 244237 i v v --i i i i iv - v v i C Charlie4a#DNA 112 AAATGCTAAATTTCAGTTAGAGGTTAGTGAAAATAAAGA-TGTAATTTTT 64 chr4ptel1M 244238 T--CCCATCAAAGTTAATGGACCCCCTGAAATCTATGCACTGATTAAGAG 244285 -- v v i v v v ii-vv C Charlie4a#DNA 63 TTCCCCATCCAAGTTCACGGACCCCCTGAATTCTATCCACGGACC-CCAG 15 chr4ptel1M 244286 ATTAAAAATCC 244296 i i i C Charlie4a#DNA 14 GTTAAGAACCC 4 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 27.63 CpG sites = 13, Kimura (unadjusted) = 28.95 Transitions / transversions = 1.08 (13/12) Gap_init rate = 0.04 (4 / 106), avg. gap size = 1.50 (6 / 4) 353 20.45 2.25 1.11 chr4ptel1M 244190 244278 (755722) C Charlie4#DNA/hAT-Charlie (3249) 129 40 m_b169s502i5 6462 chr4ptel1M 244190 AAGTGCAAAATATCA--CAAAGGCTAATGAAAGGAAAGAATTTCATTTCT 244237 i v v --i i i i iv - v v i C Charlie4#DNA/ 129 AAATGCTAAATTTCAGTTAGAGGTTAGTGAAAATAAAGA-TGTAATTTTT 81 chr4ptel1M 244238 TCCCATCAAAGTTAATGGACCCCCTGAAATCTATGCACTGA 244278 v v i v v v C Charlie4#DNA/ 80 TCCCATCCAAGTTCACGGACCCCCTGAATTCTATCCACGGA 40 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 22.52 CpG sites = 8, Kimura (unadjusted) = 23.96 Transitions / transversions = 0.80 (8/10) Gap_init rate = 0.02 (2 / 88), avg. gap size = 1.50 (3 / 2) 561 25.42 10.60 5.73 chr4ptel1M 244917 245133 (754867) C MIR#SINE/MIR (2) 260 34 m_b169s601i23 6463 chr4ptel1M 244917 TAATGGCTAGCATTTACATAAAGCCTACTATGTCCCAGGCACT------- 244959 i i ivv iv i v ------- C MIR#SINE/MIR 260 TAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAA 211 chr4ptel1M 244960 -----TTACAAATATTATCTTAATTAATTTTCATAATAACTTTGCAATGT 245004 ----- vi v i v ii i i ii iii v C MIR#SINE/MIR 210 GCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGGT 161 chr4ptel1M 245005 TGATTGCCCCCATTAAACCTACATAAGCCCCATTTTGAAGTTGAGAAAAC 245054 v i ----v i -------- v v iv v i C MIR#SINE/MIR 160 AGGT----ACTATTA--------TTATCCCCATTTTACAGATGAGGAAAC 123 chr4ptel1M 245055 TGAG--ACAGACAAAGTTAAGTAACTTGTCCAAAATCAT----CCAGTCA 245098 -- -i i i ii i---- i v C MIR#SINE/MIR 122 TGAGGCACAGA-GAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAA 74 chr4ptel1M 245099 GTGTCTGAGCT---ATTCTAGGCTCAGCAGTCTA--TCCA 245133 v v i--- v iv ivi i-- C MIR#SINE/MIR 73 GTGGCAGAGCCGGGATTCGAACCCAGGCAGTCTGGCTCCA 34 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.24 CpG sites = 32, Kimura (unadjusted) = 31.99 Transitions / transversions = 1.60 (32/20) Gap_init rate = 0.09 (19 / 216), avg. gap size = 1.89 (36 / 19) 22 0.00 0.00 0.00 chr4ptel1M 245288 245311 (754689) (CA)n#Simple_repeat 1 24 (0) m_b169s252i10 6464 chr4ptel1M 245288 CACACACACACACACACACACACA 245311 (CA)n#Simple_ 1 CACACACACACACACACACACACA 24 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 406 36.13 9.31 3.59 chr4ptel1M 245372 245661 (754339) C L2b_3end#LINE/L2 (10) 456 151 m_b169s601i25 6465 chr4ptel1M 245372 TCAATAAACATTTA---AGTATCTACTATGTGCCAATCACTGTGCTAAGT 245418 i i --- iii i iv ? i i C L2b_3end#LINE 456 TCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGC 407 chr4ptel1M 245419 GCTAAAGATATAAAAAAGGAGGCAA---AAACCCAGTCTC--CCCTTGAG 245463 iii i iviiv i -- --- i ? i i -- iiv C L2b_3end#LINE 406 GCTGGGGATACAGCGGTGAA--CAAGACAGACNCGGTCCCTGCCCTCACG 359 chr4ptel1M 245464 GAGCTTACAGATTAATGGAGGCACCAAGTAAATATGTACAAAGAAGCTC- 245512 i vi i i ---- iii i i v?v viv ?- C L2b_3end#LINE 358 GAGCTCACAGTCTAGTGGGGG----AGACAGACATGTAANCAGACAATNA 313 chr4ptel1M 245513 ---TCTACAA-GTTAGATAAGAAATAATAAA---CAGAGG-GAATA---A 245551 ---i i v i- vi ivv i v iiviii--- - iiii---i C L2b_3end#LINE 312 TAACCCAGAGTGGCAGGGTAGGACTGGGGGGGCCCAGAGGAGGGCGCCTG 263 chr4ptel1M 245552 ATTGGAATTGAGAGGAGTTGAAGAAGGCTTCCTGTAGGAAGTAGAATTTT 245601 iiv ivi i -- i iiii i i v i iiv v C L2b_3end#LINE 262 ACCCGGCCTGGG--GGGTCAGGGAGGGCTTCCCGGAGGAGGTGACATTTG 215 chr4ptel1M 245602 AGTTGCAATTTAAAGGA--AACA-AAG--GGC--AGTGAGGGGGCATGGG 245644 i vi ii i -- ii -i -- --i i i i -- C L2b_3end#LINE 214 AGCTGAGACCTGAAGGATGAGTAGGAGTTGGCCAGGCGAAGAGG--TGGG 167 chr4ptel1M 245645 AAAGAAGAGTTCCCAGC 245661 i -i v vi C L2b_3end#LINE 166 GAAG-GGCGTTCCAGGC 151 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 50.85 CpG sites = 78, Kimura (unadjusted) = 57.20 Transitions / transversions = 3.39 (78/23) Gap_init rate = 0.08 (24 / 289), avg. gap size = 1.58 (38 / 24) 413 28.75 8.15 2.10 chr4ptel1M 245372 245506 (754494) C L2d2_3end#LINE/L2 (10) 545 403 m_b169s601i24 6465 chr4ptel1M 245372 TCAATAAACATTTA---AGTATCTACTATGTGCCAATCACTGTGCTAAGT 245418 i i --- iii i v iv i i C L2d2_3end#LIN 545 TCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGC 496 chr4ptel1M 245419 GCT---AAAGATATAAAAAAGGAGGCAAAAACCCAGTCTC--CCCTTGAG 245463 ---iii i i v v--- i vii i -- ii C L2d2_3end#LIN 495 GCTGTGGGGGATACAAAGAAGTAT---AAGACATGGTCCCTGCCCTCAAG 449 chr4ptel1M 245464 GAGCTTACAGATTAATGGAGGCACCAAG---TAAATATGTACAAAG 245506 ivi i v i viv --- i i iv C L2d2_3end#LIN 448 GAGCTTACAATCTAGTTGGGGAGACAAGACATAAACACGTGAAAAG 403 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.69 CpG sites = 28, Kimura (unadjusted) = 38.76 Transitions / transversions = 2.80 (28/10) Gap_init rate = 0.05 (7 / 134), avg. gap size = 2.00 (14 / 7) 422 26.73 1.29 8.28 chr4ptel1M 245626 245780 (754220) MIRc#SINE/MIR 4 148 (120) m_b169s601i26 6466 chr4ptel1M 245626 GGCAGTGAGGGGGCATGGGAAAGAAGAGTTCCCAGCTTGGAATCAGGAAG 245675 -v v vv iv --- ivii i MIRc#SINE/MIR 4 GGCAGTG-TGGTGCAGTGGAAAGAGCA---CTGGACTTGGAGTCAGGAAG 49 chr4ptel1M 245676 ATTCATCTTCCCAAATTCAAAACCAGCCTCAGACACTTCCTAGCCATGTT 245725 -------- iiii i iv v v v v v ii v MIRc#SINE/MIR 50 A--------CCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTG 91 chr4ptel1M 245726 GCCCTAGA-AAGTCACTTCACC-CTGTTTGCCTCAGGTTCTTCATCTATA 245773 i i i i- v - v vv v i i MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTA 141 chr4ptel1M 245774 AAATGAG 245780 i MIRc#SINE/MIR 142 AAATGGG 148 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.21 CpG sites = 20, Kimura (unadjusted) = 33.26 Transitions / transversions = 1.11 (20/18) Gap_init rate = 0.09 (14 / 154), avg. gap size = 1.00 (14 / 14) 31 0.00 0.00 0.00 chr4ptel1M 245824 245852 (754148) (AAAT)n#Simple_repeat 1 29 (0) c_b169s251i2 6467 chr4ptel1M 245824 AAATAAATAAATAAATAAATAAATAAATA 245852 (AAAT)n#Simpl 1 AAATAAATAAATAAATAAATAAATAAATA 29 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 43 0.00 0.00 0.00 chr4ptel1M 246263 246301 (753699) (AAG)n#Simple_repeat 1 39 (0) c_b169s251i3 6468 chr4ptel1M 246263 AAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAG 246301 (AAG)n#Simple 1 AAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAG 39 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 37 0.00 2.86 0.00 chr4ptel1M 246613 246647 (753353) (AT)n#Simple_repeat 1 36 (0) c_b169s251i4 6469 chr4ptel1M 246613 ATATATATATATATATATATATATATATATA-ATAT 246647 - (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATAT 36 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 758 29.09 5.00 0.00 chr4ptel1M 247064 247283 (752717) C MIRc#SINE/MIR (1) 267 37 m_b169s601i27 6470 chr4ptel1M 247064 ATAATGATAATATTTTATATTTACGTAATGCTAGGTGCTTTGCTAAGCAT 247113 i i?ii i iii iii vviiiv i v ii C MIRc#SINE/MIR 267 ATAATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCGC 218 chr4ptel1M 247114 TTT-ACAATTATTATCTCATTCATTCCTCACAACAACCCTGGAAGGTGGG 247162 - vvi iiv vi i C MIRc#SINE/MIR 217 TTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGG 168 chr4ptel1M 247163 T---GC---TAGTAGGATCCCCATTTTACACATGAAGAAAATGGGGCAAC 247206 i--- --- v vv v i v i vvv C MIRc#SINE/MIR 167 CAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCA 118 chr4ptel1M 247207 CAAAAGTCAAATGATTTTTCAGGGGTCACA----TAGTAAGTGTTGGAGG 247252 v i i i i i vi vii ---- vii v C MIRc#SINE/MIR 117 GAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGC 68 chr4ptel1M 247253 CTGGATTTGAGCTCAGGGCTTTCTGATTCCA 247283 v i i i i v i i C MIRc#SINE/MIR 67 CGGGACTCGAACCCAGGTCTTCCTGACTCCA 37 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.98 CpG sites = 41, Kimura (unadjusted) = 38.54 Transitions / transversions = 1.78 (41/23) Gap_init rate = 0.02 (4 / 219), avg. gap size = 2.75 (11 / 4) 818 24.87 2.08 1.55 chr4ptel1M 247092 247283 (752717) C MIRb#SINE/MIR (36) 232 40 m_b169s601i28 6470 chr4ptel1M 247092 TGCTAGGTGCTTTGCTAAGCATTTTACAATTATTATCTCATTCATTCCTC 247141 i ii v ii vvi i v C MIRb#SINE/MIR 232 TGCCAGGCACTGTGCTAAGCGCTTTACATGCATTATCTCATTTAATCCTC 183 chr4ptel1M 247142 ACAACAACCCTGGAAGGTGGGTGCTAGTAGGATCCCCATTTTACACATGA 247191 vi i ii v --- v C MIRb#SINE/MIR 182 ACAACAACCCTGCGAGGTAGGTATTATT---ATCCCCATTTTACAGATGA 136 chr4ptel1M 247192 AGAAAATGGGGCAACCAAAAGTCAAATGATTTTTCAGGGGTCACA----T 247237 i v i vvvv i i i i i i vi vii ---- C MIRb#SINE/MIR 135 GGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCT 86 chr4ptel1M 247238 AGTAAGTGTTGGAGGCTGGATTTGAGCTCAGGGCTTTCTGATTCCA 247283 vii v v i i i v v i C MIRb#SINE/MIR 85 AGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCA 40 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.58 CpG sites = 28, Kimura (unadjusted) = 30.89 Transitions / transversions = 1.47 (28/19) Gap_init rate = 0.02 (4 / 191), avg. gap size = 1.75 (7 / 4) 274 15.03 4.76 12.82 chr4ptel1M 248080 248163 (751837) C MIRb#SINE/MIR (83) 185 108 m_b169s601i29 6471 chr4ptel1M 248080 CTCTCAACCACCTTG-AAGGCAGGTATTATAAGTATCTGCCCCATTTAAC 248128 v v i -i i --- --- v C MIRb#SINE/MIR 185 CTCACAACAACCCTGCGAGGTAGGTATTAT---TATC---CCCATTTTAC 142 chr4ptel1M 248129 AGAGAAGGAAGGAAGCCGAGGCTTAGAGAG---AAGTA 248163 vi i---- i i --- C MIRb#SINE/MIR 141 AGATGAGGAAA----CTGAGGCTCAGAGAGGTTAAGTA 108 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 15.21 CpG sites = 7, Kimura (unadjusted) = 16.80 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.14 (12 / 83), avg. gap size = 1.17 (14 / 12) 278 23.73 1.69 0.00 chr4ptel1M 248266 248324 (751676) Plat_L3#LINE/CR1 3514 3573 (0) m_b169s551i8 6472 chr4ptel1M 248266 GGGATTGACCTAAGTGACCTTT-GAGCTCCCTTCCAACTATGAGACTCTA 248314 ii iv i ii i - v i v i? i Plat_L3#LINE/ 3514 GGGGCTGGACCAGATGACCTCTCGAGGTCCCTTCCAGCTCTANGATTCTA 3563 chr4ptel1M 248315 TGATTCTATG 248324 i Plat_L3#LINE/ 3564 TGATTCTACG 3573 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 28.27 CpG sites = 11, Kimura (unadjusted) = 30.93 Transitions / transversions = 3.67 (11/3) Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1) 692 29.10 3.72 2.03 chr4ptel1M 248336 248577 (751423) MIRc#SINE/MIR 23 268 (0) m_b169s601i30 6473 chr4ptel1M 248336 AAGAACATTGGAATTGGACTCATGATGACCTGATTTCAAATCCCACCTGA 248385 i i v v v v iv i i iv vv MIRc#SINE/MIR 23 AAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCT 72 chr4ptel1M 248386 GACACTAATTAAGTTCCTGATCCAGGATGAATCACTTAGTTTTTCTCAGA 248435 v v i iv viv i iv iii i iii i v v MIRc#SINE/MIR 73 GCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGC 122 chr4ptel1M 248436 TTCAGTTGGTCC-CATCCACAAAATGGGAATTTTAATA---GC---ACCT 248478 i -- - iii i vv --- ---i MIRc#SINE/MIR 123 CTCAGTT--TCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCT 170 chr4ptel1M 248479 AGTTCACAGGATGGTTGTGAGGATCTGTTGGGACAATAAACAT-ACAATG 248527 vi i v viv i i iv ii - v ii MIRc#SINE/MIR 171 ACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCG 220 chr4ptel1M 248528 CATTGCAAACCA-AAAGGACTATAGAAATGATCACTGTTGTTATTATCAT 248576 v i ii- vi v - v -- v? i MIRc#SINE/MIR 221 CTTTGTAAACTGTAAAGTGCTATACAAATG-TAA--GGNGTTATTATTAT 267 chr4ptel1M 248577 T 248577 MIRc#SINE/MIR 268 T 268 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.95 CpG sites = 40, Kimura (unadjusted) = 38.03 Transitions / transversions = 1.38 (40/29) Gap_init rate = 0.04 (10 / 241), avg. gap size = 1.40 (14 / 10) 458 22.30 6.56 0.78 chr4ptel1M 248927 249048 (750952) C MIR3#SINE/MIR (2) 206 78 m_b169s601i31 6474 chr4ptel1M 248927 ATCACAAGATTACAGA--TTTAGAGTTACAAAGGAACCTCAGGGCTCAA- 248973 i ii i i --v i i i-i i i i v v- C MIR3#SINE/MIR 206 ATCATAGAATCATAGAATGTCAGAGCTG-GAAGGGACCTTAGAGATCATC 158 chr4ptel1M 248974 -AGTCAA--CCTTTCATTTTACAGATGAGGAAACTGAGTCCCAGGGAGGT 249020 - v -- ii v i C MIR3#SINE/MIR 157 TAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGT 108 chr4ptel1M 249021 TA--TGACATGCCACAGATCACAGAGTAAG 249048 v -- v vv i v i? C MIR3#SINE/MIR 107 GAAGTGACTTGCCCAAGGTCACACAGCNAG 78 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 27.40 CpG sites = 17, Kimura (unadjusted) = 27.40 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.05 (6 / 121), avg. gap size = 1.50 (9 / 6) 522 34.32 11.11 4.19 chr4ptel1M 249704 250576 (749424) L2#LINE/L2 2152 3082 (0) m_b169s601i32 6475 chr4ptel1M 249704 CCTTCT-CCTCCATGTTCTCTCTTTTCCAGGTTTTCATGGCTGGTTCATC 249752 i - vv vi v i ii - i i v v v L2#LINE/L2 2152 CCTCCTACCTCACTGGCCGCTCCTTCTCAG-TCTCCTTTGCTGGTTCCTC 2200 chr4ptel1M 249753 ACCCACATCAGTCACTATC---AC-TCGGTCTTCCCCAGGATTCTATCCC 249798 - i iv vviv i- --- - i vv v ii vi i L2#LINE/L2 2201 -CTCATCTCCCCGACC-TCTNAACGTTGGAGTGCCCCAGGGCTCAGTCCT 2248 chr4ptel1M 249799 AGGTATTTTTCCCTTTTCCTTCTATACTCATTCCCTTGGTAACCTCTTTG 249848 v vvi i i i iv i i ? i i v iv L2#LINE/L2 2249 TGGACCTCTTCTCTTCTCTATCTACACTCACTCCCTNGGTGATCTCATCC 2298 chr4ptel1M 249849 GTTCCCACGAATTTAACCATCATCTCTATTCAGAT-ACTGCTATGTCTAT 249897 iv i i iv vi i v v v - v i vi i L2#LINE/L2 2299 AGTCTCATGGCTTTAAATACCATCTATATGCTGATGACTCCCAAATTTAT 2348 chr4ptel1M 249898 ACATCCATCTCCAGTCTATCCTTTGAG-TTGAGGTTC--ACATCAAAATG 249944 iv v i viii v ii i- iv ii -- i v v L2#LINE/L2 2349 ATCTCCAGCCCGGACCTCTCCCCTGAACTCCAGACTCGTATATCCAACTG 2398 chr4ptel1M 249945 CTTGTTGGATATTTCAAACTGGAGGTTCTAGAGTCACTTCCAACTCCAC- 249993 i ii v i i v vi v iiv v v ii v iv - L2#LINE/L2 2399 CCTACTCGACATCTCCACTTGGATGTCTAATAGGCATCTCAAACTTAACA 2448 chr4ptel1M 249994 ---CTAAA--TAA--TCC----CTTCCTC--AAAATCTTCCCCTCTTCTA 250030 --- i -- i -- ---- i --v i v i iivi L2#LINE/L2 2449 TGTCCAAAACTGAACTCCTGATCTTCCCCCTCAAACCTGCTCCTCCCGCA 2498 chr4ptel1M 250031 AATGTTGCTATTTCTGTCACAAGTAGGACAATCCTTCTGGGTTCCCAGGT 250080 iviv iv i i v ? vvi i ivv v ii v v i i L2#LINE/L2 2499 GTCTTCCCCATCTCAGTNAATGGCAACTCCATCCTTCCAGTTGCTCAGGC 2548 chr4ptel1M 250081 TTATAAC----GAGT-ATTCTTCAGTACTTCTCCCTCTCCCTTGCCCCGT 250125 iv v ---- - i -- - i i i i ii v vi L2#LINE/L2 2549 CAAAAACCTTGGAGTCATCCTT--G-ACTCCTCTCTTTCTCTCACACCCC 2595 chr4ptel1M 250126 ACAGCCAA-CCA--AG----------------TACCTTC--------TCT 250148 v - -- ---------------- -------- i L2#LINE/L2 2596 ACATCCAATCCATCAGCAAATCCTGTCGGCTCTACCTTCAAAATATATCC 2645 chr4ptel1M 250149 TGCATCTGATCCCTTCTGTCCTCTCACACAGCTACCTCCTTAATTCAGCC 250198 v v i i v vv v iiv v i v i ii i iv L2#LINE/L2 2646 AGAATCCGACCACTTCTCACCACCTCCACTGCCACCACCCTGGTCCAAGC 2695 chr4ptel1M 250199 CCTTATCATG-GTTGCCTGGATTTTTTACAAGCACCACCAGTTTTTATAC 250247 vii v-v i - vi i vvi v -------- v L2#LINE/L2 2696 CACCATCATCTCTCGCCTGGA-TTACTGCAATAGCCTCC--------TAA 2736 chr4ptel1M 250248 CTGTTCTCCTTGCCTCAGATTTCTCCCTACTTGGGTCTATCCTTCACCCT 250297 v i i vivii iv iv ?vi i iv v v L2#LINE/L2 2737 CTGGTCTCCCTGCTTCCACCCTTGCCCCCCTNCAGTCTATTCTCAACACA 2786 chr4ptel1M 250298 GCTGCCAAAGTAATTTTCCTTAAATG-----CAGAT-GTAGCAC------ 250335 v i i ii ii v i ----- -i iv ------ L2#LINE/L2 2787 GCAGCCAGAGTGATCCTTTTAAAACGTAAGTCAGATCATGTCACTCCTCT 2836 chr4ptel1M 250336 -----AATCAGTCCAGAGATTTTCTATCATCTCTCTTCAAATGGTAACAG 250380 ----- v vv iv ii i --- v - i -- v L2#LINE/L2 2837 GCTCAAAACCCTCCAATGGCTTCC---CATCTCAC-TCAGA--GTAAAAG 2880 chr4ptel1M 250381 C---ACCGCTGA-----GCTTTTAAAGTCGTA---AAGCTG--CCCCAGC 250417 --- viv v ----- i vi i i v ---i v -- v i L2#LINE/L2 2881 CCAAAGTCCTTACAATGGCCTACAAGGCCCTACATGATCTGGTCCCCCGT 2930 chr4ptel1M 250418 CGAACTTTTCAGTCTCATTGGCCATGACTCT--CCCTCCCTCATTCTGCT 250465 i- v i iiiii ivv i iv -- v i i - L2#LINE/L2 2931 T-ACCTCTCTGACCTCATCTCCTACCACTCTCCCCCTCGCTCACTCCGC- 2978 chr4ptel1M 250466 ATCTAGCCAAACAAGATTCCCCCCCCCCTTTTTTTTTTTTTTTTTTTTAC 250515 - i v vi vi -------------- vi v ii ivv L2#LINE/L2 2979 -TCCAGCCACACTGGCCTCC--------------TTGCTGTTCCTCGAAC 3013 chr4ptel1M 250516 ACAC--AGCAC---TCCACCT--GTGCC-TTGCACTGGCC-TTCCCACAT 250556 i --i ---i i -- v - v i- v - L2#LINE/L2 3014 ACGCCAGGCACGCTCCCGCCTCAGGGCCTTTGCACTTGCTGTTCCCTC-T 3062 chr4ptel1M 250557 GCCTGGGATGTTTTTCCTTC 250576 i i i i ii L2#LINE/L2 3063 GCCTGGAACGCTCTTCCCCC 3082 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 45.62 CpG sites = 165, Kimura (unadjusted) = 47.94 Transitions / transversions = 1.35 (165/122) Gap_init rate = 0.08 (72 / 872), avg. gap size = 1.89 (136 / 72) 218 33.20 6.46 10.67 chr4ptel1M 250410 250672 (749328) L2c_3end#LINE/L2 13 265 (213) m_b169s601i33 6475 chr4ptel1M 250410 GCCCCAGCCGAACTTTTCAGTCTCATTGGCCATGACTCTCC--CTCCCTC 250457 v v v i i i iv- viv i -- v i L2c_3end#LINE 13 GCCCCTGCCTACCTCTCCAGCCTCATCT-CCTCCACTCCCCTCCTCGCCC 61 chr4ptel1M 250458 ATTCTGCTATCTAGCCAAACAAGATTCCCCCCCCCCTTTTTTTTTTTTTT 250507 i v -- i v vii i ? --------------- viv L2c_3end#LINE 62 ACTATGCT--CCAGCCACACTGAACTNC---------------TTGCATT 94 chr4ptel1M 250508 TTTTTTACACACAGCA--------CTCCACCTGTGCCTT-GCAC-TGGCC 250547 iiiivv i v -------- v vi i ? - - viv L2c_3end#LINE 95 CCCCAAACACGCCGCAGTTCTTTCCTGCCTCCGNGCCTTTGCACATGCTG 144 chr4ptel1M 250548 TTCCCACATGCCTGGGATGTTTTTCCTTCTTACTTCTGTTTCAAAGAATG 250597 v - i i i ii i v iiii ---- iv i L2c_3end#LINE 145 TTCCCTC-TGCCTGGAATGCTCTTCCCCCCTCCTTCCACCT----GGCTA 189 chr4ptel1M 250598 ACT----TTCATTCTTTAATAATGTACAGCTCAAGCACCATATGTTCC-T 250642 ----i i i v?v --- iiiii iv vi -v L2c_3end#LINE 190 ACTCCTACTCATCCTTCAAGNCT---CAGCTCAGATGTCACCTCCTCCGG 236 chr4ptel1M 250643 GAAGCTTTTCTCAATCTCCCAAATTCTAGT 250672 i i iii i i i-? L2c_3end#LINE 237 GAAGCCTTCCCTGACCCCCCAAG-NCTAGT 265 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 45.51 CpG sites = 51, Kimura (unadjusted) = 47.22 Transitions / transversions = 1.89 (51/27) Gap_init rate = 0.13 (33 / 262), avg. gap size = 1.33 (44 / 33) 277 21.62 1.33 1.33 chr4ptel1M 251154 251228 (748772) L1MC4a_3end#LINE/L1 490 564 (2065) m_b169s551i9 6476 chr4ptel1M 251154 ATGCCCATCGGTTGGAGAACGGCTGAATAAGTTGTGGTATATGAACATTA 251203 ??i v ?i i ii i i vv iv L1MC4a_3end#L 490 ATGCCCATNNATAGGAGANTGGTTGAATAAACTATGGTACATCCACACAA 539 chr4ptel1M 251204 TGGAATATTATTGC-TCTGTAAGAAA 251228 i i - -v i L1MC4a_3end#L 540 TGGAGTACTA-TGCAGCTGTAAAAAA 564 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 27.72 CpG sites = 11, Kimura (unadjusted) = 27.72 Transitions / transversions = 2.20 (11/5) Gap_init rate = 0.03 (2 / 74), avg. gap size = 1.00 (2 / 2) 302 19.67 0.00 0.00 chr4ptel1M 251154 251214 (748786) L1ME3F_3end#LINE/L1 492 552 (438) m_b169s551i10 6476 chr4ptel1M 251154 ATGCCCATCGGTTGGAGAACGGCTGAATAAGTTGTGGTATATGAACATTA 251203 i iiv i v i i vv iv L1ME3F_3end#L 492 ATGTCCATCGACAGGAGAATGGATAAATAAATTGTGGTATATTCACACAA 541 chr4ptel1M 251204 TGGAATATTAT 251214 L1ME3F_3end#L 542 TGGAATATTAT 552 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 23.14 CpG sites = 7, Kimura (unadjusted) = 23.14 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 13 32.90 0.00 0.00 chr4ptel1M 251466 251518 (748482) (TTTT)n#Simple_repeat 1 53 (0) m_b169s252i11 6477 chr4ptel1M 251466 TTTTTGTTGTTTGCTTGCATTTTGTTTTCTTTCTCATTTTTTTTTCCTTT 251515 v v vi viv v i i iv ii (TTTT)n#Simpl 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr4ptel1M 251516 TTT 251518 (TTTT)n#Simpl 51 TTT 53 Matrix = Unknown Transitions / transversions = 1.00 (7/7) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 18 0.00 0.00 0.00 chr4ptel1M 251722 251741 (748259) (A)n#Simple_repeat 1 20 (0) m_b169s252i12 6478 chr4ptel1M 251722 AAAAAAAAAAAAAAAAAAAA 251741 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAA 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 212 18.73 0.00 6.78 chr4ptel1M 251754 251816 (748184) C L3#LINE/CR1 (1114) 2985 2927 m_b169s601i34 6479 chr4ptel1M 251754 GATACTTTGTGCAACTCTGCCTCACTTAAATCCAGTTCACAGCATGTCTA 251803 v - v -- ii v v - vi? C L3#LINE/CR1 2985 GAGACTTTGT-CAAAT--GCCTTGCTGAAATCCAGAT-ACACTNTGTCTA 2940 chr4ptel1M 251804 AGACATTACCCTG 251816 v i v C L3#LINE/CR1 2939 CGGCATTCCCCTG 2927 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 21.87 CpG sites = 4, Kimura (unadjusted) = 21.87 Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.06 (4 / 62), avg. gap size = 1.00 (4 / 4) 20 8.35 5.00 0.00 chr4ptel1M 251867 251882 (748118) (ATGT)n#Simple_repeat 1 18 (24) m_b169s252i13 6480 chr4ptel1M 251867 ATATATATATG-A-GTAT 251882 i i - - (ATGT)n#Simpl 1 ATGTATGTATGTATGTAT 18 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.13 (2 / 15), avg. gap size = 1.00 (2 / 2) 29 0.00 0.00 0.00 chr4ptel1M 251883 251907 (748093) (AC)n#Simple_repeat 1 25 (0) c_b169s251i5 6481 chr4ptel1M 251883 ACACACACACACACACACACACACA 251907 (AC)n#Simple_ 1 ACACACACACACACACACACACACA 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 20 8.35 5.00 0.00 chr4ptel1M 251908 251930 (748070) (ATGT)n#Simple_repeat 19 41 (1) m_b169s252i13 6482 chr4ptel1M 251908 TATATATGTATGTATGTATGTAT 251930 i (ATGT)n#Simpl 19 TATGTATGTATGTATGTATGTAT 41 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 392 25.55 15.33 0.00 chr4ptel1M 251934 252070 (747930) L2a_3end#LINE/L2 350 507 (10) m_b169s601i35 6475 chr4ptel1M 251934 TATATATTTTACTT------TTACTTATTTTCT-----TCCTGATTAGAA 251972 ------ ii v -----i iv i L2a_3end#LINE 350 TATATATTTTACTTATTTATTTGTTTATTGTCTGTCTCCCCCCACTAGAA 399 chr4ptel1M 251973 TATAAGTTCCTTGAGAGAAA------TTATTTAATTC-TTGGCATTTATA 252015 i i v i v i------ i i iv i- vi vvi i L2a_3end#LINE 400 TGTAAGCTCCATGAGGGCAGGGACTTTTGTCTGTTTTGTTCACTGCTGTA 449 chr4ptel1M 252016 GGCCCAGCACCTAGGTCAGTGCCTGACACATAGTAAA---TAAATAAATA 252062 vv i iv i ii--- v L2a_3end#LINE 450 TCCCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGGCGCTCAATAAATA 499 chr4ptel1M 252063 CATGTTGA 252070 iv L2a_3end#LINE 500 TTTGTTGA 507 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.05 CpG sites = 22, Kimura (unadjusted) = 32.16 Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.04 (5 / 136), avg. gap size = 4.20 (21 / 5) 21 37.48 1.87 0.93 chr4ptel1M 253724 253830 (746170) (TA)n#Simple_repeat 1 108 (0) m_b169s252i14 6483 chr4ptel1M 253724 TATAT-TAGTTATGTTTATAAATACATGTGTTTATGTGTATATATACCTG 253772 - vv i v v i i i v i i iv i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr4ptel1M 253773 TTTATATATTTATGCACATGTGTTTGTATACAGTGCATATATA-ATGTGT 253821 v v ii i i i v i i - ii - i i (TA)n#Simple_ 51 TATATATATATATATATATATATATATATATA-TATATATATATATATAT 99 chr4ptel1M 253822 GTATATTTA 253830 i v (TA)n#Simple_ 100 ATATATATA 108 Matrix = Unknown Transitions / transversions = 2.00 (20/10) Gap_init rate = 0.03 (3 / 106), avg. gap size = 1.00 (3 / 3) 448 26.58 1.52 3.08 chr4ptel1M 254069 254200 (745800) C L2a_3end#LINE/L2 (15) 502 373 m_b169s601i36 6484 chr4ptel1M 254069 AAGCATTTATTAAAGACTAACTGTATGCCAGGCACTGTGCTAAGGTCAGG 254118 ii i ivi iv i i v i vv v C L2a_3end#LINE 502 AAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGCGCTGG 453 chr4ptel1M 254119 GAGTAAAACTATGCACAAAA-AGAAGACAGTCCCTCCCTCCTCTCAAGAA 254167 ii v i vi v - vi v v ---- v i C L2a_3end#LINE 452 GGATACAGCAGTGAACAAAACAGACAAAAGTCCCTGCC----CTCATGGA 407 chr4ptel1M 254168 GCTTACATTTTAATGGAGGAAGAAATAC-ATAAA 254200 i i i i v v - C L2a_3end#LINE 406 GCTTACATTCTAGTGGGGGGAGACAGACAATAAA 373 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.22 CpG sites = 19, Kimura (unadjusted) = 33.40 Transitions / transversions = 1.27 (19/15) Gap_init rate = 0.05 (6 / 131), avg. gap size = 1.00 (6 / 6) 372 27.48 5.69 2.36 chr4ptel1M 254616 254738 (745262) MIRb#SINE/MIR 5 131 (137) m_b169s601i37 6485 chr4ptel1M 254616 GGGGCAGCTGGATGGCACAGTGGGTAGAGCACCAGCCCTGAAGTCTG-CA 254664 ---i ii iv vi ii i v - MIRb#SINE/MIR 5 GGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACA 51 chr4ptel1M 254665 AATGTGACCTTAGACACT-----TAACACTTCCTAGCTGTGTGACCCTAG 254709 i iv ivi iii iv i----- iv v i i MIRb#SINE/MIR 52 GACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 101 chr4ptel1M 254710 GCAAGCCACTTAACCTCAATT-GCCTCAGT 254738 ii vv v- MIRb#SINE/MIR 102 GCAAGTTACTTAACCTCTCTGAGCCTCAGT 131 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.59 CpG sites = 22, Kimura (unadjusted) = 35.72 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.05 (6 / 122), avg. gap size = 1.67 (10 / 6) 219 20.93 0.00 0.00 chr4ptel1M 254757 254799 (745201) L3#LINE/CR1 3829 3871 (228) m_b169s601i38 6486 chr4ptel1M 254757 TTCAGAGGTCAATACTAGGACCGATGGCTAGAACTTGCAGGGA 254799 i v iv i v i v i L3#LINE/CR1 3829 TCCAGAGGGCAGAACTAGGACCAATGGGTGGAAGTTACAGGGA 3871 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 24.84 CpG sites = 5, Kimura (unadjusted) = 24.84 Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 12 23.14 6.90 1.64 chr4ptel1M 255599 255656 (744344) (TATA)n#Simple_repeat 1 61 (0) m_b169s252i15 6487 chr4ptel1M 255599 TATAAATATGTATACATATAT-TGTATTTA-ACATATACTTTA-ACATAT 255645 v i i - i v - i - v - i (TATA)n#Simpl 1 TATATATATATATATATATATATATATATATATATATA-TATATATATAT 49 chr4ptel1M 255646 TTA-ACATGTAT 255656 v - i i (TATA)n#Simpl 50 ATATATATATAT 61 Matrix = Unknown Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.09 (5 / 57), avg. gap size = 1.00 (5 / 5) 320 27.78 2.53 6.58 chr4ptel1M 256194 256351 (743649) L2c_3end#LINE/L2 327 478 (0) m_b169s601i39 6488 chr4ptel1M 256194 ATTATCTTCTATT-TCCTTATCTGCTTCCATGTTATATGCCCCCCCATGC 256242 v v - vv i i v ? i- i - i i -- L2c_3end#LINE 327 ATTAACTTGTATTGTAATTGTCTGTTTACNTGTC-TGT-CTCCTCCA--C 372 chr4ptel1M 256243 CAAGATGTCACAGTTCCTTTAGGAAAGGAACTGAATGTTTT-TAGATCAC 256291 i iiv v -- i v iv i i -- i - vv vi L2c_3end#LINE 373 TAGACTGTGA--GCTCCTTGAGGGCAGGGACCG--TGTCTTATTCATCTT 418 chr4ptel1M 256292 CGTA-CACCAGAGCCTA-CACAAAGTAAAGGCTCAATAAATGCTCATTGG 256339 i - v v i- v iiv i ii i L2c_3end#LINE 419 TGTATCCCCAGCGCCTGGCACATAGTAGGCGCTCAATAAATGTTTGTTGA 468 chr4ptel1M 256340 ATTGGAGTAAAT 256351 -- i i L2c_3end#LINE 469 AT--GAATGAAT 478 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.84 CpG sites = 25, Kimura (unadjusted) = 35.94 Transitions / transversions = 1.56 (25/16) Gap_init rate = 0.09 (14 / 157), avg. gap size = 1.00 (14 / 14) 369 26.76 10.26 1.78 chr4ptel1M 256874 257029 (742971) MIR3#SINE/MIR 37 205 (3) m_b169s601i41 6489 chr4ptel1M 256874 GAATCAG-AGATTCGGAGTTCGAGTCTCATCTCTGATACACACTAATGCT 256922 i - iii - v i iv vi vv ?-- MIR3#SINE/MIR 37 GAGTCAGGAGACCTGG-GTTCTAGTCCCGGCTCTGCCACTAACTN--GCT 83 chr4ptel1M 256923 AAGTGAT-TTAAGGGAGTCACT-AACCTCTCTAGGTCTTTGTTTCCTGAC 256970 iv i- ii vi -v i i iv v i MIR3#SINE/MIR 84 GTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCAT 133 chr4ptel1M 256971 CTG-ACAATAA--GGGTTGGAATAG-----CT-----GCCCCATCTAGAT 257007 - v i -- v ----- ----- i v i v MIR3#SINE/MIR 134 CTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCT 183 chr4ptel1M 257008 CTATGACCCTTTGATCCCATGA 257029 ivv ii v i i MIR3#SINE/MIR 184 CTGACATTCTATGATTCTATGA 205 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.20 CpG sites = 24, Kimura (unadjusted) = 34.23 Transitions / transversions = 1.41 (24/17) Gap_init rate = 0.06 (10 / 155), avg. gap size = 1.90 (19 / 10) 408 28.12 3.82 2.26 chr4ptel1M 256874 257004 (742996) MIRc#SINE/MIR 39 171 (97) m_b169s601i40 6489 chr4ptel1M 256874 GAATCAG--AGATTCGGAGTTCGAGTCTCATCTCTGATACACACTAATGC 256921 i -- iii - i iv vi vi -- MIRc#SINE/MIR 39 GAGTCAGGAAGACCTGG-GTTCGAGTCCCGGCTCTGCCACTTACTA--GC 85 chr4ptel1M 256922 TAAGTGAT-TTAAGGGAGTCACT-AACCTCTCTAGGTCTTTGTTTCCTGA 256969 iv i- ii vi - ii i iv v MIRc#SINE/MIR 86 TGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCA 135 chr4ptel1M 256970 CCTG-ACAATAAGGGTTGGAATAGCTGCCCCATCTA 257004 i - v ii i viv v iii MIRc#SINE/MIR 136 TCTGTAAAATGGGGATAATAATACCTGCCCTGCCTA 171 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.76 CpG sites = 25, Kimura (unadjusted) = 37.08 Transitions / transversions = 2.27 (25/11) Gap_init rate = 0.05 (7 / 130), avg. gap size = 1.14 (8 / 7) 219 26.39 12.26 3.48 chr4ptel1M 257058 257163 (742837) MIRb#SINE/MIR 81 195 (73) m_b169s601i42 6490 chr4ptel1M 257058 TCACTAATGGTGGGTGACCTTGGG-AAGCTATTTTATCTCTCTAAGACTC 257106 i -- v v - i i v i i v MIRb#SINE/MIR 81 TTACTA--GCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTC 128 chr4ptel1M 257107 AG---GAGCATCAGAAGTATGG---------TACTTGTTTTGTGAGGTTC 257144 ---vvv v v iv --------- i iii i iii v MIRb#SINE/MIR 129 AGTTTCCTCATCTGTAAAATGGGGATAATAATACCTACCTCGCAGGGTTG 178 chr4ptel1M 257145 TTATGAGGATGAATCATGA 257163 i v -- MIRb#SINE/MIR 179 TTGTGAGGATTAA--ATGA 195 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.76 CpG sites = 15, Kimura (unadjusted) = 33.24 Transitions / transversions = 1.25 (15/12) Gap_init rate = 0.07 (7 / 105), avg. gap size = 2.43 (17 / 7) 227 20.00 6.00 0.00 chr4ptel1M 257059 257108 (742892) MIR3#SINE/MIR 72 124 (84) m_b169s601i43 6490 chr4ptel1M 257059 CACTAA--TGGTGGGTGACCTTGGG-AAGCTATTTTATCTCTCTAAGACT 257105 --? v v - ii i i i ii v MIR3#SINE/MIR 72 CACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCT 121 chr4ptel1M 257106 CAG 257108 MIR3#SINE/MIR 122 CAG 124 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 24.57 CpG sites = 7, Kimura (unadjusted) = 24.57 Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.04 (2 / 49), avg. gap size = 1.50 (3 / 2) 336 31.82 9.09 0.00 chr4ptel1M 257178 257309 (742691) C MIR3#SINE/MIR (3) 205 62 m_b169s601i44 6491 chr4ptel1M 257178 TCATGAGACCATAGA--TTTAGATCTGAAAGTGAACTTGGGGGT------ 257219 iii i --v i v i v v i i i ------ C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTA 156 chr4ptel1M 257220 -TCTAATTCCCCCATTTTAAAGATGAGGAACCCGAGA-CAAGCAAAATGA 257267 - i ii i v v i i- v vi ii C MIR3#SINE/MIR 155 GTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGA 106 chr4ptel1M 257268 AGTGATGTTTCTAGAAT--GACAGCGGGCAAGTGTCTGAGTCAG 257309 iv vi i iii --v ?i iv v v i i C MIR3#SINE/MIR 105 AGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGG 62 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.77 CpG sites = 28, Kimura (unadjusted) = 44.23 Transitions / transversions = 2.00 (28/14) Gap_init rate = 0.04 (5 / 131), avg. gap size = 2.40 (12 / 5) 209 17.81 23.29 0.00 chr4ptel1M 257766 257838 (742162) L3#LINE/CR1 3159 3248 (851) m_b169s601i45 6492 chr4ptel1M 257766 TGCTTAGCATTTTGATCAGTGAC----ATGAAGACATA-------TG--T 257802 i i i v i ---- ------- -- L3#LINE/CR1 3159 TGTTCAACATTTTTATCAATGACTTGGATGAAGACATAGAAGGCATGCTT 3208 chr4ptel1M 257803 CTTAAAACAGCAGGTGT----GAGCTGGGAGGGATAGCTA 257838 v i viv i v----i L3#LINE/CR1 3209 ATCAAATTTGCAGATGACACAAAGCTGGGAGGGATAGCTA 3248 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 20.64 CpG sites = 8, Kimura (unadjusted) = 20.64 Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.06 (4 / 72), avg. gap size = 4.25 (17 / 4) 302 34.92 2.38 0.00 chr4ptel1M 257918 258043 (741957) C MIRb#SINE/MIR (138) 130 2 m_b169s601i46 6493 chr4ptel1M 257918 CTGGAGCACTCAGAAATTAAATGATTGACCCA--GTCAAGAAATTAATGC 257965 ii v vv ii i i i vi -- viv ii i iv C MIRb#SINE/MIR 130 CTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAA 81 chr4ptel1M 257966 TTGCCAGCAGCAGGATCTGAACCCAGACTTCTTT-ACTACAACGCCAGCT 258014 v v viv i ii iii v i - v v v iv C MIRb#SINE/MIR 80 GTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTG 31 chr4ptel1M 258015 CTCTATCCAGTGGGCCACCCTGTCCCTCT 258043 v v vi v i C MIRb#SINE/MIR 30 CTCTTTCCACTGCACCACGCTGCCCCTCT 2 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 45.33 CpG sites = 24, Kimura (unadjusted) = 48.34 Transitions / transversions = 1.20 (24/20) Gap_init rate = 0.02 (2 / 125), avg. gap size = 1.50 (3 / 2) 321 24.17 13.60 0.71 chr4ptel1M 258886 259010 (740990) Tigger19b#DNA/TcMar-Tigger 405 545 (5) m_b169s601i47 6494 chr4ptel1M 258886 CTAGAATATCAGACACATTCATATTTAAA--CAAACAC-AAATCATATTC 258932 i i ii i --i ii - v i Tigger19b#DNA 405 CCAGAACATCAGACACACCCATATTCAAATGTAAGTACAAAAACACATTC 454 chr4ptel1M 258933 CAATGGCGAATAGAAAATGG-TTTTGGATTATCTG-AATCTTTGAT---- 258976 v v i v- i- i -vi i v ---- Tigger19b#DNA 455 CAAAGCCAAATAT-AAATGATTTTTGGATTATCCGCCGTTTTGGATTATC 503 chr4ptel1M 258977 ------ACT--TCCTTTCCACTCTCACTGAAAATCAAGATTT 259010 ------? -- ii i vv i v v i v Tigger19b#DNA 504 CACGCCNCTGCTCCCCTCCATTAGCGCGGATAATCGAGAGTT 545 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 25.69 CpG sites = 19, Kimura (unadjusted) = 30.33 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.06 (8 / 124), avg. gap size = 2.25 (18 / 8) 362 24.51 1.94 0.96 chr4ptel1M 259673 259775 (740225) C Charlie4a#DNA/hAT-Charlie (0) 508 405 m_b169s502i6 6495 chr4ptel1M 259673 CAAAGGGTCTTCACCATTTTTGTGTCAAGTACCTGTTTGGTAGTCTGGAA 259722 ii v v v i v v iv i vi C Charlie4a#DNA 508 CAGGGGTTCTTAACCTTTTTTGTGCCATGGACCCCTTTGGCAGTCTGGTG 459 chr4ptel1M 259723 GAAACTA-GGCCCCCTTCTTAAGAATTATGTTTTCAAA-GTATTAGAGGA 259770 i iv - v i- v i - i v i vi C Charlie4a#DNA 458 AAGCCTATGGACCCCTTCTC-AGAATAATGTTTTTAAATGCATAAAATAA 410 chr4ptel1M 259771 AATAC 259775 C Charlie4a#DNA 409 AATAC 405 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 30.01 CpG sites = 13, Kimura (unadjusted) = 30.01 Transitions / transversions = 1.08 (13/12) Gap_init rate = 0.03 (3 / 102), avg. gap size = 1.00 (3 / 3) 364 21.26 0.00 1.25 chr4ptel1M 259762 259842 (740158) C Charlie4a#DNA/hAT-Charlie (388) 120 41 m_b170s502i1 6495 chr4ptel1M 259762 ATTAGAGGAAATACTTTATTTCAGTTAGAGATTGAGGAAAATAAAGATGT 259811 ii i vv i iiv C Charlie4a#DNA 120 ATTGAAGGAAATGCTAAATTTCAGTTAGAGGTTAGTGAAAATAAAGATGT 71 chr4ptel1M 259812 AATTTTTTTTTCTTATCCAAATTGGGGGGCC 259842 - i ii i viv i C Charlie4a#DNA 70 AATTT-TTTTCCCCATCCAAGTTCACGGACC 41 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 25.85 CpG sites = 12, Kimura (unadjusted) = 25.85 Transitions / transversions = 2.40 (12/5) Gap_init rate = 0.01 (1 / 80), avg. gap size = 1.00 (1 / 1) 223 30.78 0.00 11.39 chr4ptel1M 260089 260176 (739824) C L2b_3end#LINE/L2 (189) 277 199 m_b170s601i1 6496 chr4ptel1M 260089 AAAGAATGGCACCAATTGCCCAGCTTGATGACCCAGCCCAACTAGAGGGC 260138 i i v i -- vi i i iv ivi -------i C L2b_3end#LINE 277 AGAGGAGGGCGCC--TGACCCGGCCTGGGGGGTCAG-------GGAGGGC 237 chr4ptel1M 260139 CTCCTGCAGAAGGTGACTCTTGGGCTGAGCCTTGAAAG 260176 i i v i vi i v i i C L2b_3end#LINE 236 TTCCCGGAGGAGGTGACATTTGAGCTGAGACCTGAAGG 199 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.83 CpG sites = 17, Kimura (unadjusted) = 41.47 Transitions / transversions = 2.43 (17/7) Gap_init rate = 0.10 (9 / 87), avg. gap size = 1.00 (9 / 9) 530 35.49 11.22 1.11 chr4ptel1M 260308 260797 (739203) C L2#LINE/L2 (219) 2863 2325 m_b170s601i2 6496 chr4ptel1M 260308 ATAGGAAGCCCCTAAAG---TTCAGTCAGTAGAAATGGACATGGCCAGAC 260354 i vi ii --- iiiv - i i - ii v C L2#LINE/L2 2863 ATGGGAAGCCATTGGAGGGTTTTGAGCAG-AGGAGTG-ACATGATCTGAC 2816 chr4ptel1M 260355 CTGAACTTTAGGAAAATCACTTTGGCAACTGTGT-------------GAG 260391 i ivii ii ii i vi -------------? C L2#LINE/L2 2815 TTACGTTTTAAAAGGATCACTCTGGCTGCTGTGTTGAGAATAGACTGNAG 2766 chr4ptel1M 260392 GAGGG-AGGAGTAGTGAGAGGGAGA--AGCT-TGACCCCATTGGA----- 260432 i - i i i viiv -- i -v vv i v ----- C L2#LINE/L2 2765 GGGGGCAAGGGTGGAAGCAGGGAGACCAGTTAGGAGGCTATTGCAGTAAT 2716 chr4ptel1M 260433 --AAGCAATTGAGATGATGAAGGTCTGTCCCATGGTGGGGGCTGCATTGG 260480 -- i i -- iv ii vv v v v iivv C L2#LINE/L2 2715 CCAGGCGA--GAGATGATGGTGGCTTGGACCAGGGTGGTGGCAGTGGAGG 2668 chr4ptel1M 260481 TGGGGAGAAG-GCTCATATTCAAGAAAT--------------GCC---AT 260512 v - v iv vi v -------------- --- v C L2#LINE/L2 2667 TGGTGAGAAGTGGTCGGATTCTGGATATATTTTGAAGGTAGAGCCGACAG 2618 chr4ptel1M 260513 TATTTGGCAATTAATGGGACATCTGAGATAAGCAAGAGTTGGGAGTCAAG 260562 v vii vi v ii vv ivi i vi i vvi C L2#LINE/L2 2617 GATTTGCTGATGGATTGGATGTGGGGTGTGAGAGAAAGAGAGGAGTCAAG 2568 chr4ptel1M 260563 GATGAAACCAAGGTTCA-AGTCTGGATAA-----AAAATGGTGGTGCCCT 260606 vv iv-i i iii ----- ii v v v C L2#LINE/L2 2567 GATGACTCCAAGGTTTTTGGCCTGAGCAACTGGAAGGATGGAGTTGCCAT 2518 chr4ptel1M 260607 AAAGAATAACAGGGAAATTCATAAAGGGAG-AAGTCTAAGCAGGGAGGAA 260655 v? vvivi ii iviiiiiiii - i i i -i i - C L2#LINE/L2 2517 TNACTGAGATGGGGAAGACTGCGGGAGGAGCAGGTTTGAG-GGGGAAGA- 2470 chr4ptel1M 260656 TAATAAGTTCTGTTTTATCCATGTGGAGTTGGAAATGCCTACTGGACACT 260705 v vi v ivv vi v i i i ii C L2#LINE/L2 2469 TCAGGAGTTCAGTTTTGGACATGTTAAGTTTGAGATGCCTATTAGACATC 2420 chr4ptel1M 260706 CACTTCAGAAAGACCAACAGGAAGTTGG-TG-AAGAA-CTACAGCTTAGG 260752 vv viii v v v ii v - i- v i- iv i i C L2#LINE/L2 2419 CAAGTGGAGATGTCGAGTAGGCAGTTGGATATACGAGTCTGGAGTTCAGG 2370 chr4ptel1M 260753 AGAGTGACTAGGGCTGGGTCAGTAGATCTGAGAATCACCGGCATA 260797 i v iiiv ivvvi i i i i i i C L2#LINE/L2 2369 GGAGAGGTCCGGGCTGGAGATATAAATTTGGGAGTCATCAGCATA 2325 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 49.12 CpG sites = 105, Kimura (unadjusted) = 50.89 Transitions / transversions = 1.57 (105/67) Gap_init rate = 0.04 (22 / 489), avg. gap size = 2.77 (61 / 22) 449 34.85 3.09 2.39 chr4ptel1M 261025 261315 (738685) C L2#LINE/L2 (746) 2336 2044 m_b170s601i3 6496 chr4ptel1M 261025 GTCATTTGCAGGCAAATAG------AATCTATGGGAGCTGAA--AAATTA 261066 iv vii i i ------ v i i - i -- i i C L2#LINE/L2 2336 GTCATCAGCATATAGATGGTATTTAAAGCCATGAGA-CTGGATGAGATCA 2288 chr4ptel1M 261067 CCATGTGAGAGAGCACAAATAAGAAAAAGAAGATGGTCCAATG-CAGAGA 261115 ?v v v iii i iii i - v - v v C L2#LINE/L2 2287 CCNAGGGAGTGAGTGTAGATAGAGAAGAGAAGA-GGTCCAAGGACTGAGC 2239 chr4ptel1M 261116 TTTGATGGACACCCATACTTAGTGGTCCATCAAATGAATGAGGTCCAGTC 261165 ii iv v v v iii ? v vivv i ivii iv iv C L2#LINE/L2 2238 CCTGGGGCACTCCAACGTTNAGAGGTCGGGGAGATGAGGAGGAACCAGCA 2189 chr4ptel1M 261166 AAAGAGACTGAGAATGAACTCTCAGGCAGGTAGTGGGTAGAAACAAGAGA 261215 i v i vvi vv - i v i v i C L2#LINE/L2 2188 AAGGAGACTGAGAAGGAGCGGCCAGTGAGGTAG-GAGGAAAACCAGGAGA 2140 chr4ptel1M 261216 GAGCAAGTTACAAAAACCCAGAAAGAAGAGAGCATTGAGAAGAAAGAGAA 261265 v iiivv v vii v - iv i ii v-v i ii C L2#LINE/L2 2139 GTGTGGTGTCCTGGAAGCCA-AGTGAAGAAAGTGTTT-CAAGAAGGAGGG 2092 chr4ptel1M 261266 TGTGGTCAATAATGTTGAATACTGCAGTTAGGAGTCAAGGAGGATGCAGA 261315 v i ivi ii i v v? -- v i vi C L2#LINE/L2 2091 AGTGATCAACTGTGTCAAATGCTGCTGANAG--GTCAAGTAAGATGAGGA 2044 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 48.59 CpG sites = 57, Kimura (unadjusted) = 49.38 Transitions / transversions = 1.36 (57/42) Gap_init rate = 0.03 (10 / 290), avg. gap size = 1.60 (16 / 10) 617 30.72 1.20 0.60 chr4ptel1M 262578 262744 (737256) MIRb#SINE/MIR 6 173 (95) m_b170s601i4 6497 chr4ptel1M 262578 GGCCAAC-TGGCACAGTGGAAAGAGTTGCAGCCCTGGAATCAGGAAAGCC 262626 v i - ii ivvvi ii i iv ii MIRb#SINE/MIR 6 GGGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACC 55 chr4ptel1M 262627 CAAGTTCAAATCTCACCTCAGACACTTACTAACTGTATAATACTGGGAAA 262676 iii i i iv v v i i i ivi v MIRb#SINE/MIR 56 TGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 105 chr4ptel1M 262677 ATCACTTAATCTCCATG-GCCTCAGTTTTCTCAACTGCAGAATGAGAGTA 262725 i i i iv - i v i i i ii MIRb#SINE/MIR 106 GTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATA 155 chr4ptel1M 262726 CCATTATCCTATTTTACAG 262744 vi v - ii ii MIRb#SINE/MIR 156 ATAATA-CCTACCTCGCAG 173 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.92 CpG sites = 37, Kimura (unadjusted) = 42.38 Transitions / transversions = 2.64 (37/14) Gap_init rate = 0.02 (3 / 166), avg. gap size = 1.00 (3 / 3) 629 28.37 0.71 0.00 chr4ptel1M 262585 262725 (737275) MIRc#SINE/MIR 11 152 (116) m_b170s601i5 6497 chr4ptel1M 262585 TGGCACAGTGGAAAGAGTTGCAGCCCTGGAATCAGGAAAGCCCAAGTTCA 262634 ii ivvii v i i ii iii i MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr4ptel1M 262635 AATCTCACCTCAGACACTTACTAACTGTATAATACTGGGAAAATCACTTA 262684 i i iv v v i i i ivi v i MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTA 110 chr4ptel1M 262685 ATCTCCATG-GCCTCAGTTTTCTCAACTGCAGAATGAGAGTA 262725 i iv - i v i i i ii MIRc#SINE/MIR 111 ACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATA 152 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.66 CpG sites = 30, Kimura (unadjusted) = 38.13 Transitions / transversions = 3.00 (30/10) Gap_init rate = 0.01 (1 / 140), avg. gap size = 1.00 (1 / 1) 527 31.83 4.76 3.42 chr4ptel1M 262649 262879 (737121) C MIRb#SINE/MIR (25) 243 10 m_b170s601i6 6498 chr4ptel1M 262649 CACTTACTAACTGTATAATACTGGGAAAATCACTTAATCTCCATGGCCTC 262698 i vv ivviii v vv v i v iv v vii C MIRb#SINE/MIR 243 CGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACATGCATTATCTC 194 chr4ptel1M 262699 AGTT--TTCTCAA-------CTGCAGAATGAGAGTACCATTATCCT-ATT 262738 v -- i v------- iiii - - ii i- C MIRb#SINE/MIR 193 ATTTAATCCTCACAACAACCCTGCGAGGT-AG-GTATTATTATCCCCATT 146 chr4ptel1M 262739 TTACAGATGAAGAAACTGAGGCAGGCAATAGTCAAGGGACTTGTCCAAGT 262788 i vviv ivi i vi i v C MIRb#SINE/MIR 145 TTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGG 96 chr4ptel1M 262789 ATATACACCTAGTAAA-GATATGAAGGAAGGAGTCAAATTCAGGTCTACC 262837 vi i v i- ii --i vvi v i ii ii C MIRb#SINE/MIR 95 TCACACAGCTAGTAAGTGGCA--GAGCCGGGATTCGAACCCAGGTCTGTC 48 chr4ptel1M 262838 TGATTCTAGACCCAGTGCTCTACTCTATACTATAGCCACGTT 262879 i i i v v -i --i ii - i C MIRb#SINE/MIR 47 TGACTCCAAAGCCCGTGCTCT-TTC--CACTGCA-CCACGCT 10 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.18 CpG sites = 44, Kimura (unadjusted) = 43.18 Transitions / transversions = 1.63 (44/27) Gap_init rate = 0.05 (12 / 230), avg. gap size = 1.58 (19 / 12) 542 26.86 1.47 1.47 chr4ptel1M 262723 262858 (737142) C MIRc#SINE/MIR (109) 159 24 m_b170s601i7 6498 chr4ptel1M 262723 GTACCATTATCCT-ATTTTACAGATGAAGAAACTGAGGCAGGCAATAGTC 262771 ii i- i vviv ivi i C MIRc#SINE/MIR 159 GTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTT 110 chr4ptel1M 262772 AAGGGACTTGTCCAAGTATATACACCTAGTAAA-GATATGAAGGAAGGAG 262820 v i vvi i v i- ii --i vvi v C MIRc#SINE/MIR 109 AAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCA--GAGCCGGGAC 62 chr4ptel1M 262821 TCAAATTCAGGTCTACCTGATTCTAGACCCAGTGCTCT 262858 i ii v i i iii C MIRc#SINE/MIR 61 TCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCT 24 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.25 CpG sites = 24, Kimura (unadjusted) = 34.62 Transitions / transversions = 2.00 (24/12) Gap_init rate = 0.03 (4 / 135), avg. gap size = 1.00 (4 / 4) 305 21.34 0.00 7.58 chr4ptel1M 262890 262960 (737040) C L2d_3end#LINE/L2 (0) 516 451 m_b170s601i8 6499 chr4ptel1M 262890 TCAATTAGTCAATCAACAAGTTTTTATTATTTTGTATCTACTATGTGTCA 262939 i i v i---v iii iiv C L2d_3end#LINE 516 TCAATCAATCAATCAACAAGTATTTATTG---AGCGCCTACTATGTGCTC 470 chr4ptel1M 262940 AGCACTATATACTAGGTGCTG 262960 -- i i i C L2d_3end#LINE 469 AGCAC--TGTGCTAGGCGCTG 451 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 21.76 CpG sites = 11, Kimura (unadjusted) = 26.19 Transitions / transversions = 3.67 (11/3) Gap_init rate = 0.07 (5 / 70), avg. gap size = 1.00 (5 / 5) 261 24.41 0.00 7.14 chr4ptel1M 262894 262968 (737032) C L2a_3end#LINE/L2 (2) 515 446 m_b170s601i9 6499 chr4ptel1M 262894 TTAGTCAATCAACAAGTTTTTATTATTTTGTATCTACTATGTGTCAAGCA 262943 i v v i v iv--- iii i i C L2a_3end#LINE 515 TCATTCATTCAACAAATATTTATTGA---GCGCCTACTATGTGCCAGGCA 469 chr4ptel1M 262944 CTATATACTAGGTGCTGGATATATA 262968 i - - i iv i C L2a_3end#LINE 468 CTGT-T-CTAGGCGCTGGGGATACA 446 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.17 CpG sites = 12, Kimura (unadjusted) = 30.60 Transitions / transversions = 2.40 (12/5) Gap_init rate = 0.07 (5 / 74), avg. gap size = 1.00 (5 / 5) 315 25.12 16.11 1.17 chr4ptel1M 262998 263146 (736854) MIR1_Amn#SINE/MIR 15 185 (45) m_b170s601i10 6500 chr4ptel1M 262998 GGCCTGATCCATAGGGCTCTGGCCCTGGAAACCGAGAGATCTGAGTTTGA 263047 i ii vv i v v - i vi i i i i? MIR1_Amn#SINE 15 GGTCTAGTGGATAGAGCACTGGAC-TGGGACTCGGGAGACCTGGGTTCNA 63 chr4ptel1M 263048 AT------TCTGCCTCAGACACTATTGGGTGATC-TGGACACGTCACTGG 263090 ? ------ v v?i - ?ii ? i - i v v? MIR1_Amn#SINE 64 NTCCCGGCTCTGCCACTNGC-CNGCTGNGTGACCTTGGGCAAGTCACTTN 112 chr4ptel1M 263091 GCTTCGGTAAACCTCA---TCCTCATC-GACAAATGAAG-TAAT------ 263129 i i vv i?i --- - vv ii - ------ MIR1_Amn#SINE 113 ACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATGATACT 162 chr4ptel1M 263130 ------TTTGGTAAAATGCTTTG 263146 ------i v i MIR1_Amn#SINE 163 GACCTCCTTTGTAAAGTGCTTTG 185 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.56 CpG sites = 23, Kimura (unadjusted) = 33.56 Transitions / transversions = 1.64 (23/14) Gap_init rate = 0.06 (9 / 148), avg. gap size = 2.89 (26 / 9) 12 10.73 6.67 0.00 chr4ptel1M 263726 263755 (736245) (CACAGG)n#Simple_repeat 1 32 (0) m_b170s252i0 6501 chr4ptel1M 263726 CACAGG-AAAAGCCCAGGC-CAGGCACAGGCA 263755 - v i v - (CACAGG)n#Sim 1 CACAGGCACAGGCACAGGCACAGGCACAGGCA 32 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.07 (2 / 29), avg. gap size = 1.00 (2 / 2) 15 3.43 5.88 5.88 chr4ptel1M 263739 263772 (736228) (CAGG)n#Simple_repeat 1 34 (0) m_b170s252i1 6501 chr4ptel1M 263739 CAGGCCAGGCA--CAGGCAGGCAGGTAGGCAGAGCA 263772 - -- i - (CAGG)n#Simpl 1 CAGG-CAGGCAGGCAGGCAGGCAGGCAGGCAG-GCA 34 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.09 (3 / 33), avg. gap size = 1.33 (4 / 3) 17 20.12 0.00 0.00 chr4ptel1M 264600 264633 (735367) (A)n#Simple_repeat 1 34 (0) m_b170s252i2 6502 chr4ptel1M 264600 AAAACTAAAAAAAATGAAAAAAATAGAAAAAAAA 264633 vv vi v i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 34 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 775 30.79 5.59 4.08 chr4ptel1M 265535 266428 (733572) L1PREC2_orf2#LINE/L1 2348 3254 (40) m_b170s551i0 6503 chr4ptel1M 265535 AAAACTACAAAACGCCACACAAATAAAGTCAGATCT-----AAACAACTG 265579 i i i ii v v - vv ----- v L1PREC2_orf2# 2348 AGAATTACAAAACACTGCTCAAAGAAA-TCAGAGATGACACAAACAAATG 2396 chr4ptel1M 265580 GAAAAATATCAAGTGCTCTTGGATAAACCAAGTGAATATAATAAAGATGA 265629 i ivvi v iivvi i v vi v i i L1PREC2_orf2# 2397 GAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTTAAAATGG 2446 chr4ptel1M 265630 TAATACTAGCTAAACTAATCTATTTATTTAGTGCTATACCAATCAAACTC 265679 iv iv i vi i ivv i i v v v L1PREC2_orf2# 2447 CCATACTGCCCAAAGCAATTTACAGATTCAATGCTATTCCTATCAAACTA 2496 chr4ptel1M 265680 CCAA-GAAACTATTTTACTGATCTAGAAAAAA------TAACATTCATCT 265722 - v i -i i v v ------ v v L1PREC2_orf2# 2497 CCAATGACATT-CTTCACAGAACTAGAAAAAACTATTTTAAAATTCATAT 2545 chr4ptel1M 265723 GGAAAAATAAAAGGTCAAGAAT-TTCAAGGGAA--CTGA-TAAAAAAAAC 265768 vv v iv vv -vi v -- i -i i L1PREC2_orf2# 2546 GGAACCAAAAAAGAGCCCGAATAGCCAAGGCAATCCTAAGCAAAAAGAAC 2595 chr4ptel1M 265769 CAA--TGAAGGTAGCCTAGCTGTACCAGACCTAAAATTATATTAGAAAGC 265816 v -- i i v vi- -- v i v i i v ii L1PREC2_orf2# 2596 AAAGCTGGAGGCATCAC-GC--TACCCGACTTCAAACTATACTACAGGGC 2642 chr4ptel1M 265817 AGAAGTCACCAAAACCATTTGGTATTGGCTAAGAAATAGACTAGCTGATC 265866 viv v viiv i ivv i i vviiv i L1PREC2_orf2# 2643 TACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGACACATAGACC 2692 chr4ptel1M 265867 AGTGGAATAGCTTAG-GTTCACAGGAAAAAATAA--TCG-ACAACTATAG 265912 i i vv - vv v ---- --i - v i i L1PREC2_orf2# 2693 AATGGAACAGAATAGAGAGCCCAG----AAATAAGGCCGCACACCTACAA 2738 chr4ptel1M 265913 CAATCAAATGTTTGACAAACC---CAAAGACCCCAGTTTTTGAGATAAGA 265959 v vi v i v --- i -- v ivv v i - i L1PREC2_orf2# 2739 CCATCTGATCTTCGACAAAGCTGACAAAAA--CAAGCAATGGGGA-AAGG 2785 chr4ptel1M 265960 ATTCACTATTTGATAAAAACTGCTGGGAAAATTGGAAACTAG---TATGG 266006 i v ii viv v i --- --- - L1PREC2_orf2# 2786 ACTCCCTATTCAATAAATGGTGCTGGGATAACTGG---CTAGCCATAT-G 2831 chr4ptel1M 266007 CAGAAACTAAGCATTGG---CCTACACTTAACACCATATACCAAGATAAG 266053 iv viiv i --- v - - v i v i L1PREC2_orf2# 2832 CAGAAGATTGAAACTGGACCCCTTC-CTT-ACACCATATACAAAAATCAA 2879 chr4ptel1M 266054 GTTACCAAAATGGGTTCATGGTCTAGGCATCAAGAATGAAATTATAAATA 266103 v --- i i v v iii iiii v ivvii i v L1PREC2_orf2# 2880 CT---CAAGATGGATTAAAGACTTAAATGTAAAACCCAAAACTATAAAAA 2926 chr4ptel1M 266104 AATTAGAAG--AACATAGGATAATTTACCTCTC-AGACCTATGGAGGATG 266150 vvi i -- v -i -- vi -i v v i v ivv L1PREC2_orf2# 2927 CCCTGGAAGACAACCTAGG-CAA--TACCATTCTGGACATAGGAACGGGC 2973 chr4ptel1M 266151 AAGGAATTTGTGACCAAAGAAGAATTAGAGATCATTATTG-------ATC 266193 i v ii ---- vvivi i v -- ------- v L1PREC2_orf2# 2974 AAAGATTTCATGAC----GAAGACGCCAAAAGCA--ATTGCAACAAAAGC 3017 chr4ptel1M 266194 ATAAAATAGATAATTTTGA-CTATATCATGTTAAA-AGGTTTTGTACAGA 266241 - v i v vv - - i vii - v i i - L1PREC2_orf2# 3018 A-AAAATTGACAAATGGGATCTA-ATTAAACTAAAGAGCTTCTGCACAG- 3064 chr4ptel1M 266242 CAAAACTAA-TGCAGACAAGATTAGAAGGGAAGCAATAAACTGGACAAAT 266290 vv - iivi iii v iv iv v v i i v ivi v L1PREC2_orf2# 3065 CAAAAGAAACTATCAACAGAGTAAACAGACAACCTACAGAATGGGAGAAA 3114 chr4ptel1M 266291 ATTTTTACAGTCAGAT---TCTGATAAAGGTCTCATTTCCAGATTATACA 266337 ? i iv -v --- i v v vv v i L1PREC2_orf2# 3115 ATNTTTGCAAAC-TATGCATCTGACAAAGGTCTAATATCCAGCATCTATA 3163 chr4ptel1M 266338 GAGAATCAACTCATATTTATAAG---AAATCAAACCCTTCTCCAATTGAT 266384 ii iiv vv v i --- v vv-- i - i v L1PREC2_orf2# 3164 AGGAACTTAAACAAATTTACAAGAAAAAAACAAACAA--CCCC-ATTAAA 3210 chr4ptel1M 266385 AAATGGTCAAAGGATATGAATAGAAAATTTTCGATTGAAGAAAT 266428 i v i i v v i vv v L1PREC2_orf2# 3211 AAGTGGGCAAAGGACATGAACAGACACTTTTCAAAAGAAGACAT 3254 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.64 CpG sites = 130, Kimura (unadjusted) = 40.22 Transitions / transversions = 0.97 (130/134) Gap_init rate = 0.06 (58 / 893), avg. gap size = 1.50 (87 / 58) 298 30.40 4.76 3.62 chr4ptel1M 266196 266468 (733532) L1M3_orf2#LINE/L1 3013 3288 (0) m_b170s551i1 6503 chr4ptel1M 266196 AAAATAGATAATTTTGACTATATCATGTTAAAAGGTTT-TGTACAG---A 266241 i v vv i vii i i - i --- L1M3_orf2#LIN 3013 AAAATAGACAAGTGGGACTACATCAAACTAAAAAGCTTCTGCACAGCAAA 3062 chr4ptel1M 266242 CAAAACTAATGCAGACAAGATTAGAAGGGAAGCAATAAACTGGAC--AAA 266289 vi - - - iii v i v v v iii v iv-- L1M3_orf2#LIN 3063 GGAAAC-AAT-CA-ACAGAGTGAAAAGGCAACCTACGGAATGGGAGAAAA 3109 chr4ptel1M 266290 TATTTTTACAGTCAGAT-TCTGATAAAGGTCTCATTTCCAGATTATACAG 266338 vi - ii v - i vi v v i v i i L1M3_orf2#LIN 3110 TATTTGCA-AACCATATATCTGATAAGGGGTTAATATCCAAAATATATAA 3158 chr4ptel1M 266339 AGAAT-----CAACTC-ATATTTATAAGAAATCAAACCCTTCTCCAATTG 266382 i i----- - ---ii i v --- vvi i ? L1M3_orf2#LIN 3159 GGAACTCNTACAACTCAATA---GCAAAAAAACAAA---TAACCCGATTN 3202 chr4ptel1M 266383 ATAAATGGTCAAAGGATATGAATAGAAAATTTTCGATTGAAGAAATTGAA 266432 v v iv v v i v vv v vv L1M3_orf2#LIN 3203 AAAAATGGGCAAAGGACCTGAATAGACATTTCTCCAAAGAAGACATACAA 3252 chr4ptel1M 266433 ACTATTTCTAGTCATATGACAAGGTACTTCAAATCA 266468 iviiivvi vi v i i iv v L1M3_orf2#LIN 3253 ATGGCCAACAGGTATATGAAAAGATGCTCAACATCA 3288 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.56 CpG sites = 42, Kimura (unadjusted) = 39.90 Transitions / transversions = 1.11 (42/38) Gap_init rate = 0.06 (16 / 272), avg. gap size = 1.44 (23 / 16) 1268 29.74 2.76 2.95 chr4ptel1M 266325 266868 (733132) L1ME3C_3end#LINE/L1 7 549 (321) m_b170s551i2 6503 chr4ptel1M 266325 TCCAGATTATACAGAGAA-TCAACT-CATATTTATAAGAAATCAAACCCT 266372 v i i - -- - v iv v i vvi L1ME3C_3end#L 7 TCCAGAATATATAAAGAACTC--CTACAAATCAATAAGAAAACAGACAAC 54 chr4ptel1M 266373 TCTCCAATTGATAAATGGTCAAAGGATATGAATAGAAAATTTTCGATTGA 266422 --- v v v i i iv iv iivv L1ME3C_3end#L 55 ---CCAATAGAAAAATGGGCAAAAGATATGAACAGGCAATTCACAGAAGA 101 chr4ptel1M 266423 AGAAATTGAAACTATTTCTAGTCATATGACAAGGTACTTCAAATCATTAT 266472 i i?vi iviiivv iv v i i iv vv i v L1ME3C_3end#L 102 GGAAACNCGAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAG 151 chr4ptel1M 266473 TGATCAGAGAAATACAAACTAAGAAAACTCTGAGATACCACTACACACCT 266522 i i i i i v? vv i v i L1ME3C_3end#L 152 TAATCAGGGAAATGCAAATTAAAACNACAATGAGATACCATTTCACACCC 201 chr4ptel1M 266523 GTCAGACTGGCTAAGATGACAGGAAAAA----ATAATGATGAAAGTTGGA 266568 i i v i v----v i---- i ivii iv v L1ME3C_3end#L 202 ATCAGATTGGCAAAAATT----TAAAAGTCTGACAATACCAAGTGTTGGC 247 chr4ptel1M 266569 G-GGATGTGGGAAAACTGGGACACTGATACTTTGTTGGAGGAATTGTGAA 266617 - iiv v i v v vi i v i v i L1ME3C_3end#L 248 GAGGATGTGGAGCAACGGGAACTCTCATACACTGCTGGTGGGAGTGTAAA 297 chr4ptel1M 266618 TGGATCCAACCATTCTGGAGAGCAATTTGG-AATATGCTCAAAAAGTTGT 266666 v i v i i - - viv - L1ME3C_3end#L 298 TTGGTACAACCACTTTGGAGAGCAATTTGGCAATAT-CTAGTAAAGTTG- 345 chr4ptel1M 266667 CAAACTGTGTATACCCTTTGATCCAGCAGTGCTATTATTGGACTTATATT 266716 - iv i i vi i i v i i vi i iiv ii L1ME3C_3end#L 346 -AAGATGCGCATACCCTACGACCCAGCAATTCCACTCCTAGGTATATACC 394 chr4ptel1M 266717 CCAAAGAGA-TCTTAAAGGT------AAGGGGACCCATATGTGCAAAAAT 266759 i i i - iiv v ------ i ---- i i L1ME3C_3end#L 395 CTAGAGAAACTCTCGCACGTGTGCACAAGGAGAC----ATGTACAAGAAT 440 chr4ptel1M 266760 GTCTGTGTCAGCCCTTTTTGTAGTGGCCAGAAACTGGAAATTGAATGGAT 266809 iii vv vi v i i v i i ivivv ii L1ME3C_3end#L 441 GTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAAT 490 chr4ptel1M 266810 GCCCATCAATTGGAAAATGGCTGAATAAATTATGGTATATGAATGTGATA 266859 i iv i v i i vv iii i L1ME3C_3end#L 491 GTCCATCAACAGGAGAATGGATAAATAAATTGTGGTATATTCATACAATG 540 chr4ptel1M 266860 GAATATTAT 266868 i L1ME3C_3end#L 541 GAATACTAT 549 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.94 CpG sites = 94, Kimura (unadjusted) = 39.27 Transitions / transversions = 1.49 (94/63) Gap_init rate = 0.04 (23 / 543), avg. gap size = 1.35 (31 / 23) 936 32.31 2.98 1.73 chr4ptel1M 266376 266945 (733055) L1MC5a_3end#LINE/L1 58 634 (2143) m_b170s551i3 6503 chr4ptel1M 266376 CCAATTGATAAATGGTCAAAGGATATGAATAGAAAATTTTCGATTGAAGA 266425 v v v i i v i iv iivvi L1MC5a_3end#L 58 CCAATAGAAAAATGGGCAAAAGATATGAACAGACAGTTCACAGAAAAAGA 107 chr4ptel1M 266426 AATTGAAACTATTTCTAGTCATATGACAAGGTACTTCAAATCATTATTGA 266475 vv iviiiii iv v i i iv vv i vv i L1MC5a_3end#L 108 AATGCAAATGGCCCTTAAACATATGAAAAGATGCTCAACCTCACTCATAA 157 chr4ptel1M 266476 TCAGAGAAATACAAACTAAGAAAACTCTGAGATACCACTACACACCTGTC 266525 v i i i vv v i v v i L1MC5a_3end#L 158 TAAGAGAAATGCAAATTAAAACTACACTGAGATACCATTTCTCACCTATC 207 chr4ptel1M 266526 AGACTGGCTAAGAT--GACAG---GAAAAAATAATGATGAAAGTTGGAG- 266569 i v i --i v --- v v v v- ---- v - L1MC5a_3end#L 208 AGATTGGCAAAAATCCAAAAGTTTGACAACATACTC-TG----TTGGCGA 252 chr4ptel1M 266570 GGATGTGGGAAAACTGGGACACTGATACTTTGTTGGAGGAATTGTGAATG 266619 v i v v v v v i v i v ii vv L1MC5a_3end#L 253 GGCTGTGGGGAAACAGGCACTCTCATACATTGCTGGTGGGAATGCAAAAT 302 chr4ptel1M 266620 GATCCAACCATTCTGGAGAGCAATTTGG-AATATGCTCAAAAAGTTGTCA 266668 i v vi v i v - - viv i i- L1MC5a_3end#L 303 GGTACAACCCCTATGGAGGGGAATTTGGCAATAT-CTAGCAAAATTA-CA 350 chr4ptel1M 266669 AACTGTGTATACCCTTTGATCCAGCAGTGCTATTATTGGACTTATATTCC 266718 v - ii v i i v i i vi i ivv v i L1MC5a_3end#L 351 TA-TGCATTTACCCTTTGACCCAGCAATCCCACTTCTAGGAATCTATCCC 399 chr4ptel1M 266719 AAAGAGAT-CTT--AAAGGTAAGGGGACCCATATGTGCAAAAATGTCTGT 266765 i v i- ?-- ii v iii?vv i ii iiv i iii L1MC5a_3end#L 400 GAAGATACACTNGCAAAAATACGAAANGACGTATGCACAAGGTTATTCAT 449 chr4ptel1M 266766 GTCAGCCCTTTTTGTAGTGGCCAGAAACTGGAAATTGAATGGATGCCCAT 266815 vv vi v i i v i i ivivviii i L1MC5a_3end#L 450 TGCAGCATTATTTGTAATAGCAAAAGACTGGAAACAACCCAAATGTCCAT 499 chr4ptel1M 266816 CAATTGGAAAATGGCTGAATAAATTATGGTATATGAATGTGATAGAATAT 266865 v ii v i i i vv iiii i i i L1MC5a_3end#L 500 CAATAGGGGACTGGTTGAATAAACTATGGTACATCCACACAATGGAGTAC 549 chr4ptel1M 266866 TATTGTTCTGTAAGAATGACCAGCAGGAGGATTTC---AGAAAGGCCTGG 266912 vvvv i v -- vv i i --- v vv ?iv L1MC5a_3end#L 550 TATGCAGCTGTAAAAAGGA--ATGAGGAAGATCTCTATATACTGNTATGG 597 chr4ptel1M 266913 AGAGA----CAGGAACTGATGCTGAGTGAAATGAGCA 266945 v ---- vv iv i i vi L1MC5a_3end#L 598 AGTGATCTCCAGGATATATTGTTAAGTGAAAAAAGCA 634 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 42.81 CpG sites = 95, Kimura (unadjusted) = 43.44 Transitions / transversions = 1.10 (95/86) Gap_init rate = 0.03 (18 / 569), avg. gap size = 1.50 (27 / 18) 15 20.59 6.90 1.64 chr4ptel1M 267227 267284 (732716) (TATA)n#Simple_repeat 1 61 (0) m_b170s252i3 6504 chr4ptel1M 267227 TATAAATATGTATACATATAT-TGTATTTA-ACATATACTTTA-ACATAT 267273 v i i - i v - i - v - i (TATA)n#Simpl 1 TATATATATATATATATATATATATATATATATATATA-TATATATATAT 49 chr4ptel1M 267274 TTA-ATATGTAT 267284 v - i (TATA)n#Simpl 50 ATATATATATAT 61 Matrix = Unknown Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.09 (5 / 57), avg. gap size = 1.00 (5 / 5) 29 30.17 3.31 1.63 chr4ptel1M 267705 267825 (732175) (TA)n#Simple_repeat 1 123 (0) m_b170s252i4 6505 chr4ptel1M 267705 TATGTATA-ATATATA-ATCTACTTAGATATAGATGATATTGATAGAGAT 267752 i - - v iv v v - vv v v (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATAT-ATATATATATATAT 49 chr4ptel1M 267753 GTAAATATAGACA-ATATAAAGTACATATATATACATAAATATGCACGAA 267801 i v v i - v - i i v ii iiv (TA)n#Simple_ 50 ATATATATATATATATATATA-TATATATATATATATATATATATATATA 98 chr4ptel1M 267802 CTTATGCATATAT-TAAACATATAT 267825 iv ii - v i (TA)n#Simple_ 99 TATATATATATATATATATATATAT 123 Matrix = Unknown Transitions / transversions = 0.93 (14/15) Gap_init rate = 0.05 (6 / 120), avg. gap size = 1.00 (6 / 6) 211 33.33 1.59 0.00 chr4ptel1M 268236 268298 (731702) C L2d2_3end#LINE/L2 (0) 555 492 m_b170s601i11 6506 chr4ptel1M 268236 TCACATCAAGTTAGCAAGCATT-ACTGAACATCTACTGCGCACCAAGGAT 268284 v i i i ii - i i ii i ii v i v i C L2d2_3end#LIN 555 TCAAATCAAATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCAC 506 chr4ptel1M 268285 TGGGTTAAGAGCTG 268298 v i i v C L2d2_3end#LIN 505 TGTGCTAGGCGCTG 492 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 45.23 CpG sites = 16, Kimura (unadjusted) = 48.57 Transitions / transversions = 3.20 (16/5) Gap_init rate = 0.02 (1 / 62), avg. gap size = 1.00 (1 / 1) 364 30.64 5.66 5.66 chr4ptel1M 268829 269499 (730501) L1M5_orf2#LINE/L1 2617 3287 (7) m_b170s551i4 6507 chr4ptel1M 268829 CCAGATCT-AAAACTATATGATAAAGTCACAGTCATCCATACTATTTGGT 268877 ? ? - i - v ii v v v vi v L1M5_orf2#LIN 2617 CCNGATNTCAAGACT-TATTATAAAGCTACAGTAATCAAGACAGTGTGGT 2665 chr4ptel1M 268878 ACTGCC-TAAGAAATAGAGTAGTCAATCAGTGGAATAGGTTAGGTTTGTG 268926 i v - i - vv i vi i i iv i----- L1M5_orf2#LIN 2666 ATTGGCGTAAGGA-TAGACAAATAGATCAATGGAACAGAATAGA-----G 2709 chr4ptel1M 268927 AGAT--AAAATAGTCAATGACTACAACAACCTAGGGTTGGATAAACC--- 268971 vi--i v ----- i - -iv v ?ii?v i vii--- L1M5_orf2#LIN 2710 AGTCCAGAAATAGAC-----CCACA-CA-TATATGGNCANTTGATTTTTG 2752 chr4ptel1M 268972 -CAAAGGTCCCAAC----TTC--TGGGACAAAAATTCACTACTTGACAAA 269014 - v ?---- -- iv ii vvv vi ii L1M5_orf2#LIN 2753 ACAAAGGTGCCAANGCAATTCAGTGGGGAAAGGATAGTCTTTTCAACAAA 2802 chr4ptel1M 269015 AAGTACTAGAAAAATTGGAAATTAGTATGGCAGAAACTAGGTATTGACCA 269064 vi i i v v ivi v i v iii?v i v L1M5_orf2#LIN 2803 TGGTGCTGGAACAATTGGATATCCATATGGAAAAAAATGAANCTCGACCC 2852 chr4ptel1M 269065 ACACCTAACATCCTATACCAAGATAAAGTCAAAATGGGTTCAT-GATTTA 269113 vi v i v i v i v v ? i i - - ii L1M5_orf2#LIN 2853 CTACCTCACACCATACACAAAAATTAATTCNAGATGGAT-CATAGACCTA 2901 chr4ptel1M 269114 GACATAAAGAATGATACTATAAGCAAATT--AGAA--AAACTTAGGCTAG 269159 i ii ii? i v -- v -- -- v vv i L1M5_orf2#LIN 2902 AATGTAAAAGNTAAAACTATAA--AACTTCTAGAAGAAAACATAGGAGAA 2949 chr4ptel1M 269160 TTTACCTCACATCTGTAGAGAAGGTGAA--TTTATGGTCAAAGAAGA-AC 269206 v - i iiiv iv i i?v ii -- v ---i v i - L1M5_orf2#LIN 2950 TAT-CTTCGTGACCTTGGGNTAGGCAAAGATTTCT---TAAACAGGACAC 2995 chr4ptel1M 269207 TAGA-GTAC--ATTATGAAATGCAAAATGAATAATTTTGATTATATTAAG 269253 v i - i -- ii i viv vi v v i ?i i i L1M5_orf2#LIN 2996 AAAAAGCACNAACCATAAAAGAAAAAATTGATAAATTGGACTNCATCAAA 3045 chr4ptel1M 269254 TTTAAAAGTTTTTG---TTCAAACAAAACCAATGCAGGCAAGATTAGAAG 269300 v ii i ---? vi v iv i- -- i v i L1M5_orf2#LIN 3046 ATTAAAAACTTCTGCTCNTCAAAAGACACCGTTA-AG--AAAATGAAAAG 3092 chr4ptel1M 269301 GGCAGCAGTAAACTGGGAAAAAA-ATTTACATCCAAGGGTTCTGATAAAC 269349 vv vii i ? i - i v?vv vivv i - L1M5_orf2#LIN 3093 GCAAGCCACAGANTGGGAGAAAATATTTGCAANACATATATCTGACAAA- 3141 chr4ptel1M 269350 CCTTGGTTCTGATTTCTAAAATACATAAAGAACT-----GACTCAAATTT 269394 ---- v- vi v i i i -----i ? -- v L1M5_orf2#LIN 3142 ----GGA-CTCGTATCCAGAATATATAAAGAACTCCTACAANTCAA--TA 3184 chr4ptel1M 269395 ATAAGAATACAAGTTATTTTCTAATTGACAAATGGTCAAAGAATATGAAT 269444 ? i v iiv ---i i v? v v ii iv i L1M5_orf2#LIN 3185 ANAAAAAGACAAACAA---CCCAATANAAAAATGGGCAAAAGACTTGAAC 3231 chr4ptel1M 269445 AGACAATTT-TAGATGAAGAAATTAAAATCATGTCTAGT---CATATGAA 269490 v i-i i v v ?v --- v i i --- i L1M5_orf2#LIN 3232 AGACACTTCACAAAAGAAGATATNCAA---ATGGCCAATAAGCACATGAA 3278 chr4ptel1M 269491 AAAATTCTC 269499 i v L1M5_orf2#LIN 3279 AAGATGCTC 3287 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.83 CpG sites = 110, Kimura (unadjusted) = 41.97 Transitions / transversions = 1.31 (110/84) Gap_init rate = 0.09 (57 / 670), avg. gap size = 1.33 (76 / 57) 839 31.35 4.22 4.22 chr4ptel1M 269369 269984 (730016) L1MC5a_3end#LINE/L1 12 627 (2150) m_b170s551i6 6507 chr4ptel1M 269369 AATACATAAAGAACTGACTC---AAATTTATAAGAATACAAGTTATTTTC 269415 i i --- --- v v v vi viv ivvi L1MC5a_3end#L 12 AATATATAAAGAGCT---TCTAAAAATTGAGAAGAAAAAGACCAACAACC 58 chr4ptel1M 269416 TAATTGACAAATGGTCAAAGAATATGAATAGACAATTT-TAGATGAAGAA 269464 i v v v ii i i i-i vi L1MC5a_3end#L 59 CAATAGAAAAATGGGCAAAAGATATGAACAGACAGTTCACAGAAAAAGAA 108 chr4ptel1M 269465 ATTAAAATCATGTCTAGTCATATGAAAAAATTCTCTAAATTACTATTGCT 269514 vv viivii iv i v v vv i vv iv L1MC5a_3end#L 109 ATGCAAATGGCCCTTAAACATATGAAAAGATGCTCAACCTCACTCATAAT 158 chr4ptel1M 269515 CAGAGAAATGCATATTAAACCAACTCTGAGATACCACTGCACACCT-TCA 269563 v v v v v i v v - L1MC5a_3end#L 159 AAGAGAAATGCAAATTAAAACTACACTGAGATACCATTTCTCACCTATCA 208 chr4ptel1M 269564 AATTGGCTAAGATGACGGGGAAAGATAATGATAAAA------GTTGGGGG 269607 i v i -- --vi v -- i v ------ v i L1MC5a_3end#L 209 GATTGGCAAAAAT--C--CAAAAGTT--TGACAACATACTCTGTTGGCGA 252 chr4ptel1M 269608 GAGTGTGGGGAAACTGGGAATCCAATACATTGTTGGTGGATTCGTGTACT 269657 iv v v v iv i ivvi iiv v L1MC5a_3end#L 253 GGCTGTGGGGAAACAGGCACTCTCATACATTGCTGGTGGGAATGCAAAAT 302 chr4ptel1M 269658 GATCCAACTATTCTGAAGAGCAATATGGAACTATGCC--CAAAGGACTAC 269705 i v ivi v i i v v v v - i-- -- i L1MC5a_3end#L 303 GGTACAACCCCTATGGAGGGGAATTTGGCAATAT-CTAGCAAA--ATTAC 349 chr4ptel1M 269706 CAAACTGTGCATATA--CTTTGTTCCAGCAATATCCCTATCGAGCTTGTA 269753 ----v i v -- vi vi v viiii vv v L1MC5a_3end#L 350 ----ATATGCATTTACCCTTTGACCCAGCAATCCCACTTCTAGGAATCTA 395 chr4ptel1M 269754 TCCTAAGGAGATCATTA--AGGAAT--GAAAGGGACCCACAGGTGCAAAA 269799 ii i v - i ?-- ii -- ? i--- ii v ii ii L1MC5a_3end#L 396 TCCCGAAGATA-CACTNGCAAAAATACGAAANGA---CGTATGCACAAGG 441 chr4ptel1M 269800 CTGTTTGTGGCAGCCCCATTTGTAGTGGCAAGAAACTGGGAACTGAGTGG 269849 i i ii v vii i i i i i vivviii L1MC5a_3end#L 442 TTATTCATTGCAGCATTATTTGTAATAGCAAAAGACTGGAAACAACCCAA 491 chr4ptel1M 269850 GTGCCCATC-ATTGGGGAATGGCTGAATAAGTCATGGTCTATGAATGTTA 269898 i i - v v i iii vi vv iiiv L1MC5a_3end#L 492 ATGTCCATCAATAGGGGACTGGTTGAATAAACTATGGTACATCCACACAA 541 chr4ptel1M 269899 TGGAATATTATT--GTTTT-ATAAGAAATGATCAGCAGGAGGATTTC--- 269942 i i v-- i v - v i ------ i i --- L1MC5a_3end#L 542 TGGAGTACTATGCAGCTGTAAAAAGGAATG------AGGAAGATCTCTAT 585 chr4ptel1M 269943 AGAGAGGCCTGGAGAGACTTACAGGAACTGATGCTAAATGAA 269984 v vv ?iv v ii v vv iv i i L1MC5a_3end#L 586 ATACTGNTATGGAGTGATCTCCAGGATATATTGTTAAGTGAA 627 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.11 CpG sites = 99, Kimura (unadjusted) = 41.73 Transitions / transversions = 1.15 (99/86) Gap_init rate = 0.06 (38 / 615), avg. gap size = 1.37 (52 / 38) 1186 30.01 2.03 1.47 chr4ptel1M 269369 269909 (730091) L1ME4a_3end#LINE/L1 12 555 (316) m_b170s551i5 6507 chr4ptel1M 269369 AATACATAAAGAACTGACT--CAAATTTATAAGAATACAAGTTATTTTCT 269416 i i -- -- iv v vi vvv ivii i L1ME4a_3end#L 12 AATATATAAAGAGCT--CTTACAAATCAATAAGAAAAAGACGAACACCCC 59 chr4ptel1M 269417 AATTGACAAATGGTCAAAGAATATGAATAGACAATTT-TAGATGAAGAAA 269465 v v v i i i i-i i v L1ME4a_3end#L 60 AATAGAAAAATGGGCAAAGGACATGAACAGACAATTCACAAAAGAAGAAA 109 chr4ptel1M 269466 TTAAAATCATGTCTAGT---CATATGAAAAAATTCTCTAAATTACTATTG 269512 - v -- v i i --- ? vi v vv i v i L1ME4a_3end#L 110 T-ACAA--ATGGCCAATAAACATATGAAAANATGTTCAACCTCACTAGTA 156 chr4ptel1M 269513 CTCAGAGAAATGCATATTAAACCAACTCTGAGATACCACTGCACACCT-T 269561 v i v v vv i viv - L1ME4a_3end#L 157 ATCAAAGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCTAT 206 chr4ptel1M 269562 CAAATTGGCTAAGATGACGGGGAAAGATAATGATAAAAGTTGGGGGGAGT 269611 v vvviii vv iviv iv v i i L1ME4a_3end#L 207 CAAATTGGCAAAGATTTAAAAGATTGATAATACCCAGTGTTGGCGAGGGT 256 chr4ptel1M 269612 GTGGGGAAACTGGGAATCCAATACATTGTTGGTGGATTCGTGTACTGATC 269661 ? v v v iv i i ivvi iv i i v L1ME4a_3end#L 257 GTGGNGAAACGGGCACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTA 306 chr4ptel1M 269662 CAACTATTCTGAAGAGCAATATGGAACTATGC-CCAAAGGACTACCAAAC 269710 iv i i v v v i-i i v -iv v L1ME4a_3end#L 307 CAACCTTTCTGGAGGGCAATTTGGCAATATGTATCAAAAGCCT-TAAAAA 355 chr4ptel1M 269711 TGTGCATATACTTTGTTCCAGCAATATCCCTATCGAGCTTGTATCCTAAG 269760 ? iv vi i vi v viiii vv v L1ME4a_3end#L 356 TGTNCATACCCTTTGACCCAGTAATTCCACTTCTAGGAATTTATCCTAAG 405 chr4ptel1M 269761 GAGATCATTAAGGA-ATGAA-AGGGACCCACAGGTGCAAAACTGTTTGTG 269808 i v i ii -i ? - ii iii i-- i iiv ii v L1ME4a_3end#L 406 GAAATAATCAGAGATGTGNACAAAGATTTAT--GTACAAGGATGTTCATC 453 chr4ptel1M 269809 GCAGCCCCATTTGTAGTGGCAAGAAACTGGGAACTGAGTGGGTGCCCATC 269858 vii i i i i i i i vivv iii i v L1ME4a_3end#L 454 GCAGCATTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAAC 503 chr4ptel1M 269859 -ATTGGGGAATGGCTGAATAAGTCATGGTCTATGAATGTTATGGAATATT 269907 - v ? i i i i vi vv i?v L1ME4a_3end#L 504 AATAGGGGANTGGTTAAATAAATTATGGTACATCCATANAATGGAATATT 553 chr4ptel1M 269908 AT 269909 L1ME4a_3end#L 554 AT 555 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.51 CpG sites = 89, Kimura (unadjusted) = 39.83 Transitions / transversions = 1.25 (89/71) Gap_init rate = 0.03 (16 / 540), avg. gap size = 1.19 (19 / 16) 22 33.87 0.00 0.00 chr4ptel1M 270153 270226 (729774) (TT)n#Simple_repeat 1 74 (0) m_b170s252i5 6508 chr4ptel1M 270153 TTTTTCTCTTTTTTGTTGTTATTGTTTGCTTGGTTTTTTTTTATTTTATT 270202 i i v v v v vi vv v v (TT)n#Simple_ 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr4ptel1M 270203 TTCTCTCTCATTTTTCTCCTTTTT 270226 i i i iv i ii (TT)n#Simple_ 51 TTTTTTTTTTTTTTTTTTTTTTTT 74 Matrix = Unknown Transitions / transversions = 1.00 (10/10) Gap_init rate = 0.00 (0 / 73), avg. gap size = 0.0 (0 / 0) 271 34.01 1.74 5.41 chr4ptel1M 271100 271214 (728786) C L2c_3end#LINE/L2 (6) 472 362 m_b170s601i12 6506 chr4ptel1M 271100 TCAATCAGCGAGGATTCTCTAAACCCTCATTATCTGTTAGTCACCATACT 271149 v i i iv ivi i i v ii i v ii v i ----- C L2c_3end#LINE 472 TCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGC-----T 428 chr4ptel1M 271150 AAGAATACAAAGAAAAGGCAAAAC-TAGCCCCCGAGCTCAAGAAGCTTAT 271198 ii i vi -ii i -ii i i vv i i i C L2c_3end#LINE 427 GGGGATACAAAGATGA-ATAAGACACGGTCCCTGCCCTCAAGGAGCTCAC 379 chr4ptel1M 271199 AGTCTAATGG-GGAGAC 271214 i - C L2c_3end#LINE 378 AGTCTAGTGGAGGAGAC 362 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 45.73 CpG sites = 28, Kimura (unadjusted) = 49.87 Transitions / transversions = 3.11 (28/9) Gap_init rate = 0.07 (8 / 114), avg. gap size = 1.00 (8 / 8) 465 27.16 3.12 7.94 chr4ptel1M 272012 272235 (727765) MIR1_Amn#SINE/MIR 13 226 (4) m_b170s601i14 6509 chr4ptel1M 272012 GTGGTACAGTGAATGGAATAATGGGGCAGGACTCAGGAAGACATCTTCCC 272061 vi i i ii v ivii i - ------ i MIR1_Amn#SINE 13 GTGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGA-GAC------CT 55 chr4ptel1M 272062 TAGTTCAAATCTGGCCTCAGATATCTCCTAGTTGTGTAACCCTGGGCAAA 272111 vi ? ? iv v v vi ii?v i? i ? i i i MIR1_Amn#SINE 56 GGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAG 105 chr4ptel1M 272112 TGATTTAA-CTCTATTTTCCTCAGTTTCCTCATCTGTAAAAATGAGTTGG 272160 v i ? - v v?v - i--- MIR1_Amn#SINE 106 TCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGT-AAAATGG---GG 151 chr4ptel1M 272161 AGAAGGA-AATGGCCAACCCCTCCAATAT-CTCTGTTGAGAACAACTG-- 272206 v v - v i -v ii vi vi - --- v v -- MIR1_Amn#SINE 152 ATAATGATACTGACC-TCCTTTGTAAAGTGCT---TTGAGATCTACTGAT 197 chr4ptel1M 272207 --AGAGTACTGAACAACAACAACAGGTATTA 272235 -- i i iv i v i --i MIR1_Amn#SINE 198 GAAAAGTGCTACATAAGAGC--TAGGTATTA 226 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.17 CpG sites = 33, Kimura (unadjusted) = 35.97 Transitions / transversions = 1.43 (33/23) Gap_init rate = 0.10 (22 / 223), avg. gap size = 1.09 (24 / 22) 514 26.90 0.71 4.44 chr4ptel1M 272012 272151 (727849) MIRc#SINE/MIR 10 144 (124) m_b170s601i13 6509 chr4ptel1M 272012 GTGGTACAGTGAATGGAATAATGGGGCAGGACTCAGGAAGACATCTTCCC 272061 i i vi ii v iviv v ------ i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC------CT 53 chr4ptel1M 272062 TAGTTCAAATCTGGCCTCAGATATCTCCTAGTTGTGTAACCCTGGGCAAA 272111 vi i i iv v v vi ii v i i i i MIRc#SINE/MIR 54 GGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAG 103 chr4ptel1M 272112 TGATTTAA-CTCTATTTTCCTCAGTTTCCTCATCTGTAAAA 272151 v i - v vvv MIRc#SINE/MIR 104 TCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAA 144 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.74 CpG sites = 20, Kimura (unadjusted) = 33.88 Transitions / transversions = 1.25 (20/16) Gap_init rate = 0.05 (7 / 139), avg. gap size = 1.00 (7 / 7) 229 33.51 6.32 5.76 chr4ptel1M 272235 272424 (727576) L3b_3end#LINE/CR1 947 1137 (69) m_b170s601i15 6510 chr4ptel1M 272235 AGAGGAA-TGAGACGCTGAGACAGCAGCGGAATCGGCTTAAGTCTTAGTG 272283 - i --- v i v ivi vv ii i ------- L3b_3end#LINE 947 AGAGGAAATGGG---CTTAAACTGCAGCATGAGGGATTTAGGT------- 986 chr4ptel1M 272284 TGGATGAAAAGAAAAAATTTTTAACAATTGGAGCTGCCAAGAAATGAAAT 272333 i iv i i v ii i i vi i ii iv v i L3b_3end#LINE 987 TAGATATAAGGAAGAACTTCCTGACAGTGAGAGTTGTTAAACACTGGAAT 1036 chr4ptel1M 272334 CGGCTGTCTTGGGAGG-TACTG--TCCCCTTC-CAGGAGAA-----AAAC 272374 v i ii vv - i v -- i - v i----- v L3b_3end#LINE 1037 GGGTTACCGAGGGAGGTTGCGGAATCTCCTTCTCTGGAGAGNCTTTAAAA 1086 chr4ptel1M 272375 AAAGATCGCATGGTCATTCATTAAGGATGAG--GAAGGTACGTCCTACTT 272422 v v v vv iii ivi v--i i - i i L3b_3end#LINE 1087 ATAGAACGGATTCTCATCTGTCTGGGATGACTTAAAGGCA-GTCCTGCCT 1135 chr4ptel1M 272423 GG 272424 i L3b_3end#LINE 1136 AG 1137 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 46.46 CpG sites = 37, Kimura (unadjusted) = 46.46 Transitions / transversions = 1.61 (37/23) Gap_init rate = 0.09 (17 / 189), avg. gap size = 1.35 (23 / 17) 441 26.88 8.90 0.63 chr4ptel1M 272291 272436 (727564) L3#LINE/CR1 3892 4049 (50) m_b170s601i16 6510 chr4ptel1M 272291 AAAGAAAAAATTTTTAACAATTGGAGCTGCCAAGAAATGAAATCGGCTGT 272340 i i v i ii i v i i v i L3#LINE/CR1 3892 AAGGAAGAACTTTCTAACAATCAGAGCTGTCCAAAAATGGAATGGGCTGC 3941 chr4ptel1M 272341 CTTGGGAGGTACTG---TCCCCTTC-CAGGAGA----AAAACAAAGATCG 272382 i ? v --- v - v i----v i i iii L3#LINE/CR1 3942 CTCGNGAGGTAGTGAGCTCCCCGTCACTGGAGGTGTTCAAGCAGAGGCTG 3991 chr4ptel1M 272383 CATGGTCATTCATTAAGGA---TGAGGAAGGTACGTCCTAC-TTGGTTGT 272428 v ii i ii i i --- vi v i- i - v v L3#LINE/CR1 3992 GATGACCACTTGTCAGGGATGTTGTAGAAGGGAT-TCCTGCATTGGATGG 4040 chr4ptel1M 272429 G-GATTGGA 272436 - i L3#LINE/CR1 4041 GAGGTTGGA 4049 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.07 CpG sites = 27, Kimura (unadjusted) = 35.21 Transitions / transversions = 2.25 (27/12) Gap_init rate = 0.05 (7 / 145), avg. gap size = 2.00 (14 / 7) 186 18.72 2.13 9.09 chr4ptel1M 272785 272831 (727169) C MamGypsy2-LTR#LTR/Gypsy (38) 145 102 m_b170s601i17 6511 chr4ptel1M 272785 CAAGCCTCCAAAAGAGCCATCAGTTCTTTATTGCT-TAAAACTGCTCT 272831 i i v i i ---- i -i i C MamGypsy2-LTR 145 CAGGCCTTCAACAAAAC----AGTCCTTTATTGCTGCAAAACTACTCT 102 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 22.64 CpG sites = 7, Kimura (unadjusted) = 22.64 Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.11 (5 / 46), avg. gap size = 1.00 (5 / 5) 21 0.00 0.00 0.00 chr4ptel1M 272861 272883 (727117) (T)n#Simple_repeat 1 23 (0) m_b170s252i6 6512 chr4ptel1M 272861 TTTTTTTTTTTTTTTTTTTTTTT 272883 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTT 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 337 16.93 2.99 2.99 chr4ptel1M 272897 272963 (727037) EuthAT-N1a#DNA/hAT-Tip100 112 178 (80) m_b170s502i2 6513 chr4ptel1M 272897 AATAATTAACTAAAATAGGAAATTACCA--CTGCAGGCACATTGTTAATA 272944 ii ii --iv -- i EuthAT-N1a#DN 112 AATAATTAGTTAAAATAGGAAGCTACCAGATGGC--GCGCATTGTTAATA 159 chr4ptel1M 272945 ATGTCCATCTATGAGCCAC 272963 iii i EuthAT-N1a#DN 160 ACACCCATCTGTGAGCCAC 178 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 18.29 CpG sites = 10, Kimura (unadjusted) = 20.29 Transitions / transversions = 10.00 (10/1) Gap_init rate = 0.05 (3 / 66), avg. gap size = 1.33 (4 / 3) 269 28.41 5.38 5.38 chr4ptel1M 273003 273095 (726905) C L2b_3end#LINE/L2 (7) 459 367 m_b170s601i18 6514 chr4ptel1M 273003 CATTTGACAGACATTTATTAAATAAAGGCTTACTGTGTATCAGGCACTGG 273052 ii i i i i ii---- i ii ? v C L2b_3end#LINE 459 CATTCAACAAATATTTACTGAGC----GCCTACTGTGTGCCAGGCNCTGT 414 chr4ptel1M 273053 GCTAAGAGCTACAGAT-----GGAGATATCAGATTGAAACATTCCCTG 273095 i v ivi ----- v - iv iv v? iv C L2b_3end#LINE 413 GCTAGGCGCTGGGGATACAGCGGTGA-ACAAGACAGACNCGGTCCCTG 367 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.72 CpG sites = 17, Kimura (unadjusted) = 38.65 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.07 (6 / 92), avg. gap size = 1.67 (10 / 6) 201 32.64 13.21 5.57 chr4ptel1M 273129 273446 (726554) C L2c_3end#LINE/L2 (137) 341 1 m_b170s601i20 6514 chr4ptel1M 273129 ACAATATATAATTAATAATATAAATGCCATAATAGTAAAAATAAAAAAGT 273178 i - i i -- i i i -i iv i v i - C L2c_3end#LINE 341 ACAATACA-AGTTAATGATA--AGTGCTATAATGG-GAGTATAGACAGG- 297 chr4ptel1M 273179 CAAATCAGTCATTTGGGGATAGAAGATA----TTAG--CAG-CTGGAAGT 273221 ---i -- ii vv i v i i vi----i --i - v ii v C L2c_3end#LINE 296 ---GT--GCTATGGGAGCACAGAGGAGGGCACCTAGACTAGNCTTGGGGG 252 chr4ptel1M 273222 TTCAGAAAAGCTTTTCTGTAGATGGTGAC--CTGGGGCTAAGTCTTGAAG 273269 v ii vi i i v iv -- i - i ? C L2c_3end#LINE 251 GTCAGGGAAGGCTTCCCGGAGGAGGTGACATCTGAG-CTGAGNCTTGAAG 203 chr4ptel1M 273270 AA-AAGTAATAATT--CCAAAATATGGA--GACGAGGATAGAGTTCTGCA 273314 i -i iv i -- ii--- -- v i iv ----- C L2c_3end#LINE 202 GATGAGTAGGAGTTAGCCAGG---TGGAAGGAGGGGGGAAGAG-----CA 161 chr4ptel1M 273315 CTCTAGGAAAGCAGAACAGTCAGTGCAAAGG-ATGGAGATAAG--AGAA- 273360 i i v iivi ivv -?i ii i -- - C L2c_3end#LINE 160 TTCCAGGCAGAGGGAACAGCATGTGCAAAGGCNCGGAGGCAGGAAAGAAC 111 chr4ptel1M 273361 ------------GGAGCAAGCAAGTCAGCCAGTGGGGCTGGA-------- 273390 ------------ i v v ?vivi v -------- C L2c_3end#LINE 110 TGCGGCGTGTTTGGGGAATGCAAGNAGTTCAGTGTGGCTGGAGCATAGTG 61 chr4ptel1M 273391 --CAAGAACGT--ATGGAAAAAAGGAGATTCTGGATGCAGGAAGGGATTT 273436 -- i i v v--i ii i v ii vvi v i v iiiv C L2c_3end#LINE 60 GGCGAGGAGGGGAGTGGAGGAGATGAGGCTGGAGAGGTAGGCAGGGGCCA 11 chr4ptel1M 273437 GGTCAAGAAG 273446 i iv ? C L2c_3end#LINE 10 GATCGTGNAG 1 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.88 CpG sites = 65, Kimura (unadjusted) = 46.54 Transitions / transversions = 1.97 (65/33) Gap_init rate = 0.10 (32 / 317), avg. gap size = 1.91 (61 / 32) 202 36.62 2.92 5.56 chr4ptel1M 273129 273368 (726632) C L2d_3end#LINE/L2 (174) 342 109 m_b170s601i19 6514 chr4ptel1M 273129 ACAATATATAATTAA-TAATATAAATGCCATAATAGTAAAAA-TAAAAAA 273176 i - iv - v ----i i v i - v iv C L2d_3end#LINE 342 ACAGTATATAATTAAGTGCTA-AATTGC----GTGGTACAGACTATAAGT 298 chr4ptel1M 273177 GTCAAATCAGTCATTTGGGGATAGAAGATATTAGCA---GCTGGAAGTTT 273223 ii v vv --- ii i vi i v i ii--- ivvv C L2d_3end#LINE 297 GCTATAGGAGT---TCAGAGAAGGGAGAGATCAGTGTGGGCTGGAGTGGT 251 chr4ptel1M 273224 CAGAAAAGCTTTTCTGTAGATGGTGAC-CTGGGGCTAAGTCTTGAAGAA- 273271 ii vi iv v iv iv- v i ii i i - C L2d_3end#LINE 250 CAGGGAAGGCTTCGTGGAGGAGGTGGGACTTGAGCTGGGCCTTGAAGGAT 201 chr4ptel1M 273272 AAGTAATAATTCCAAAATATGGAGACGAGGATAGAGTTCTGCACTCTAGG 273321 ii iv v ---ii vi - vi i vvvv i i C L2d_3end#LINE 200 GGGTAGGATTT---GGATAGAGAGA-GAGGAAGGGGAAGGGCATTCCAGG 155 chr4ptel1M 273322 AAAGCAGAACAGTCAGTGCAAAGGATGGAGATAAGAGAAGGAGCAAG 273368 vii vi i ivv v -i v viv i v v C L2d_3end#LINE 154 CGGGGGGAACGGCGTGAGCAAAGG-CGCAGAGGCGGGAATGCGCAAG 109 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 46.63 CpG sites = 46, Kimura (unadjusted) = 51.86 Transitions / transversions = 1.24 (46/37) Gap_init rate = 0.08 (18 / 239), avg. gap size = 1.11 (20 / 18) 373 34.21 1.96 0.65 chr4ptel1M 273632 273784 (726216) MIR3#SINE/MIR 51 205 (3) m_b170s601i21 6515 chr4ptel1M 273632 GGGTTCTGACCTCTGTTCTGGTACTG-CTACTTGTGTGACTGTCAGCGAG 273680 iii i v i vi i- ?vi iv vi i MIR3#SINE/MIR 51 GGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAG 100 chr4ptel1M 273681 TCACTTAATTCCCCTATTGCCACAGCTTTCTCATCTGTAAAAATTAGGAG 273730 v iii i iv- v i i vvvi i MIR3#SINE/MIR 101 TCACTTCACCTCTCTGG-GCCTCAGTTTCCTCATCTGTAAAATGAGGGGG 149 chr4ptel1M 273731 TCAAACTATCTGGCCCCCAGGGTGCAGAACAACTCTACCACTCTCC--TT 273778 iii vv ii i i i v vvvv i iv i vi-- MIR3#SINE/MIR 150 TTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATT 199 chr4ptel1M 273779 CTATGA 273784 MIR3#SINE/MIR 200 CTATGA 205 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 48.32 CpG sites = 32, Kimura (unadjusted) = 48.32 Transitions / transversions = 1.60 (32/20) Gap_init rate = 0.02 (3 / 152), avg. gap size = 1.33 (4 / 3) 348 29.78 3.38 6.99 chr4ptel1M 274904 275051 (724949) C L2d2_3end#LINE/L2 (1) 554 412 m_b170s601i22 6516 chr4ptel1M 274904 CAAATCAAGTCAACAAGCATTTATAAAGTGCCTA--ATGAGCCAAATATT 274951 i ii vi i --i v v iii i C L2d2_3end#LIN 554 CAAATCAAATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACT 505 chr4ptel1M 274952 GTACTAAGCTCT---GGATATGCAAAGAAAGAAAAAACCAGAACTTCCTA 274998 i i v --- iv i iv v i --------- v i C L2d2_3end#LIN 504 GTGCTAGGCGCTGTGGGGGATACAAAGAAGTATAAGA---------CATG 464 chr4ptel1M 274999 GTCCCACATCTCAAGTAGTTAATAATCTAAGGGAGGGAGACAACATGCAA 275048 vvvi v i v i - vvi v iii C L2d2_3end#LIN 463 GTCCCTGCCCTCAAGGAGCTTACAATCT-AGTTGGGGAGACAAGACATAA 415 chr4ptel1M 275049 ATA 275051 i C L2d2_3end#LIN 414 ACA 412 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.89 CpG sites = 25, Kimura (unadjusted) = 39.12 Transitions / transversions = 1.56 (25/16) Gap_init rate = 0.08 (12 / 147), avg. gap size = 1.25 (15 / 12) 44 0.00 0.00 0.00 chr4ptel1M 275069 275106 (724894) (GT)n#Simple_repeat 1 38 (0) c_b170s251i0 6517 chr4ptel1M 275069 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 275106 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 38 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 409 33.93 8.15 0.69 chr4ptel1M 275107 275376 (724624) C Charlie7#DNA/hAT-Charlie (1953) 662 373 m_b170s502i3 6518 chr4ptel1M 275107 ATAGACAAATAAAGTAAGGTTCTTTGTTAGTGACAGTGGTTATAAAATCA 275156 v vv ii ii v i ii i v i vi C Charlie7#DNA/ 662 ATATACACTTAGGGCGAGGTTCATCGTTAACGATAGTGGATGTAAATCCA 613 chr4ptel1M 275157 TATCTCAAGGA---TTCTTAATTTTTTTTTAATTTAAGGAGCCAGTTTCT 275203 i iv --- i vv iv- vvvvi iii C Charlie7#DNA/ 612 TATTTCAAATAGTCTTCTTGATAATTTCG-AATTTTTTTGGCCGACTTCT 564 chr4ptel1M 275204 TGTCCAATTTCATTATATCTTCCTTGTTTTTAACCTGAAAATATGGTCAA 275253 vi i v v v v - viv i iii C Charlie7#DNA/ 563 TGTCAGATCTGATTAGATCGTCATTGTTTTT-ACCTCGTAATGTGGCTGA 515 chr4ptel1M 275254 AAAAGCACTCATCCACAGAG----------AGCCATAC---------ATT 275284 vi vi i v vvi ---------- iv i ---------i C Charlie7#DNA/ 514 CGAAGAGCTCGTACTAGGAGTAGAAGTGTCAGCTCTGCCATTTTCTTGTT 465 chr4ptel1M 275285 GTCTCCTCATGCTTAGATAATTAATATTTTCCTTTGTGTCCAATGCCTTT 275334 iiv ii iv v i v i ivi viv ii vi C Charlie7#DNA/ 464 GTTCGCTTGTGCTTGCATTATTAGTATTATCTTCAATCCGCGGTTTCTTT 415 chr4ptel1M 275335 GCAGTAGTGTTTGGAAATCATTTGTACATTTGGTGAGAGTTA 275376 v i v vv ii i v v i C Charlie7#DNA/ 414 GCAGGAATCTTTTTAAGCCACTTGTCCATTTTGTGAGGGTTA 373 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.16 CpG sites = 50, Kimura (unadjusted) = 46.47 Transitions / transversions = 1.22 (50/41) Gap_init rate = 0.02 (5 / 269), avg. gap size = 4.80 (24 / 5) 255 29.47 4.04 4.04 chr4ptel1M 275480 275578 (724422) C MIRc#SINE/MIR (152) 116 18 m_b170s601i23 6519 chr4ptel1M 275480 AGAAGTGAAGTTGCCCACTCAGAATGATGAGACAG--AGATAAGTTG--G 275525 i v vi iii i i--- i v v -- - v -- C MIRc#SINE/MIR 116 AGAGGTTAAGTGACTTGCCCAA---GGTCACACAGCTAG-TAAGTGGCAG 71 chr4ptel1M 275526 GGGCAGAATTAGAACCCAGGCCTTCTTGATGCCGAGTTCAGTAATCTATC 275575 i v i i i v i i iv i i iv v C MIRc#SINE/MIR 70 AGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTC 21 chr4ptel1M 275576 CAC 275578 C MIRc#SINE/MIR 20 CAC 18 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.21 CpG sites = 18, Kimura (unadjusted) = 39.01 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.06 (6 / 98), avg. gap size = 1.33 (8 / 6) 415 29.62 9.45 0.92 chr4ptel1M 275579 275779 (724221) C Charlie7#DNA/hAT-Charlie (2214) 401 184 m_b170s502i4 6518 chr4ptel1M 275579 TAAGCCACTCTGCTCTCTTTTGTGAGGATCCATTT-CTGAAAACTAGACA 275627 - - iv i ivi -v v i C Charlie7#DNA/ 401 TAAGCCACT-TG-TCCATTTTGTGAGGGTTAGTTTAGTTAAAACTAGATA 354 chr4ptel1M 275628 ATATCATCCATAA---CA---AGTCCTGTAC-C---AACCGTGACATGTC 275667 v i --- --- ii vv i - --- i ii i i C Charlie7#DNA/ 353 ATATAATCCGTAAATCCACTTAACCGGGCACACGTAAACTGCAATACGTC 304 chr4ptel1M 275668 ACAACATACTGAAATAGAACAAACTAGTGAGGAAATAACGCTTGACCCCT 275717 i i ii vv i v iviiv vv ii C Charlie7#DNA/ 303 GCAATACGCTGAAAGCGAACGAACGAGTGAGGGCGCCACTGTCAACCCCT 254 chr4ptel1M 275718 CCCTCTTGTTG--------CTTTTACTTCAGGAAACATCAATTATCAACC 275759 viv v -------- i v i v v ivv i ivvi C Charlie7#DNA/ 253 CCGCGTTGTGGAACTCCCACTCTTCCCTCAGGATACCTCGCGTACCGCAT 204 chr4ptel1M 275760 CTGACAAGTGACTGTTTGAC 275779 v v i i C Charlie7#DNA/ 203 GTGACACGTGACCGTCTGAC 184 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 30.74 CpG sites = 33, Kimura (unadjusted) = 38.60 Transitions / transversions = 1.27 (33/26) Gap_init rate = 0.04 (8 / 200), avg. gap size = 2.62 (21 / 8) 355 23.17 0.00 0.00 chr4ptel1M 276583 276664 (723336) L1ME3A_3end#LINE/L1 185 266 (654) m_b170s551i7 6520 chr4ptel1M 276583 TGAGATACCACTACATACCTGTCAGATTGGCTAGAATGACAAGGAAAGAA 276632 ? i iii v i v i v v L1ME3A_3end#L 185 TGNGATACCACTACACACCCACCAGAATGGCTAAAATGAAAAAGACAGAC 234 chr4ptel1M 276633 AATGCAGAATGTTGGAGGGGATGTGGGAAAAC 276664 i vi i v i iiv L1ME3A_3end#L 235 AATACCAAGTGTTGGCGAGGATGTGGAGCAAC 266 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 28.87 CpG sites = 12, Kimura (unadjusted) = 28.87 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.00 (0 / 81), avg. gap size = 0.0 (0 / 0) 676 32.46 3.78 3.00 chr4ptel1M 276701 277097 (722903) L1ME5_3end#LINE/L1 251 650 (291) m_b170s551i8 6521 chr4ptel1M 276701 GAGGAT-CAGGGTTA-GGGGACACTGATACATTGTTGATGGAATTGTGAA 276748 -ii v? -i i v v i i i i i v ii L1ME5_3end#LI 251 GAGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGA 300 chr4ptel1M 276749 TACCTCCAGCCATTCTGGAAAGCAATTTGGAACTATGCTCCAAAAGTTA- 276797 ivvv v i i v v -- i---- i - L1ME5_3end#LI 301 CTGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTA--CTT----AGTCAA 344 chr4ptel1M 276798 -TCAAAC-TGTGCATCCCCTTTGATCCAGCAGTGTTTCTACTGGGCTTAT 276845 - i ii- ii v v i i viiv v iv L1ME5_3end#LI 345 ATTAAGTATACGCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATAT 394 chr4ptel1M 276846 ATCCCAAAGAGATCTTAAGGAAGG----GAAAGGGACCTGTATGTGCCAA 276891 i ii v viv ----v i v i ---- i L1ME5_3end#LI 395 ATCCCAAAGAAATTCTCACACAGGTCCATAAGGGGACATGTACG----AG 440 chr4ptel1M 276892 AATGTTTGTGGCAGCCCTGTTTGCAGTGGCCAGAAACTGGAAACTGAATG 276941 i ii v vi ii vi i ii ii vivv L1ME5_3end#LI 441 GATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTG 490 chr4ptel1M 276942 GATGCCCATCAACTGGAGAATGGGTGGGTAAATAGTGGTATATGAATGTT 276991 i i viv i i i vv iv v iiii L1ME5_3end#LI 491 GGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACACC 540 chr4ptel1M 276992 ATGGAATATTATTGTTCTGTAGGAAATGACCAGCAGGATGAATACAGAGA 277041 i i vvvv v vi iii vii vi v i v v L1ME5_3end#LI 541 ATGGAGTACTATGCAGCAGTTAGAAGCAACGGACTAGATGTACACATAGC 590 chr4ptel1M 277042 GGATTGGAGAGA-CTGACAGGAAC-TGATGCTGAGTGAAATGAGC-AGAA 277088 iivv vi - v v -- - ii vi i- L1ME5_3end#LI 591 AACATGGATGGATCTTAAA--AACATAGTGCTGAGTGAAAAAAGTAAGAA 638 chr4ptel1M 277089 CCAG---GAGAT 277097 v --- L1ME5_3end#LI 639 ACAGAATGAGAT 650 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 42.79 CpG sites = 74, Kimura (unadjusted) = 44.23 Transitions / transversions = 1.45 (74/51) Gap_init rate = 0.06 (22 / 396), avg. gap size = 1.23 (27 / 22) 798 29.48 1.04 1.04 chr4ptel1M 276716 277003 (722997) L1ME4c_3end#LINE/L1 268 555 (275) m_b170s551i9 6521 chr4ptel1M 276716 GGGACACTGATACATTGTTGATGGAATTGTGAATACCTCCAGCCATTCTG 276765 v ? v i i v ? i vvv v i v i L1ME4c_3end#L 268 GGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTG 317 chr4ptel1M 276766 GAAAGCAATTTGGAACTATGCTCCAAAAGTTATCAAACTGTGCATCCCCT 276815 v v i ivi i ii v v v v L1ME4c_3end#L 318 GAAAGCAATTTGGCAATACGTATCAAGAGCCATAAAAATGTTCATACCCT 367 chr4ptel1M 276816 TTGATCCAGCAGTGTTTCTACTGGGCTTATATCCCAAAGAGAT-CTT--A 276862 i i i viiv v vv v i i i -v -- L1ME4c_3end#L 368 TTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAA 417 chr4ptel1M 276863 AGGAAGGGAAAGGGACCTGTATGTGCCAAAATGTTTGTGGCAGCCCTGTT 276912 i i i --- i ii v i ii v vi i L1ME4c_3end#L 418 AAGAAGGAAAAAG---CTATATGCACGAAGATGTTCATTGCAGCGTTATT 464 chr4ptel1M 276913 TGCAGTGGCCAGAAACTGGAAACTGAATGGATGCCCATCAACTGGAGAAT 276962 ii i i v i i vivv ii i v iv i L1ME4c_3end#L 465 TATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAAT 514 chr4ptel1M 276963 GGGTGGGTAAATAGTGGTATATGAATGTTATGGAATATTAT 277003 v ii vi i v? iviv L1ME4c_3end#L 515 GGTTAAGTAAATTATGGTACATCNACTCGATGGAATATTAT 555 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.75 CpG sites = 48, Kimura (unadjusted) = 38.93 Transitions / transversions = 1.33 (48/36) Gap_init rate = 0.02 (5 / 287), avg. gap size = 1.20 (6 / 5) 226 23.00 1.30 4.00 chr4ptel1M 277649 277725 (722275) C L1ME3G_3end#LINE/L1 (376) 548 474 m_b170s551i10 6522 chr4ptel1M 277649 ATAGCATTTCATAACATTCATATTCCATAATTTCTTTTGCTATTTCTCAA 277698 i i ii vv v v vi i i i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr4ptel1M 277699 TTGATGGATACTCTCTA-GTTGTTTACA 277725 i --- i - v C L1ME3G_3end#L 498 TTGATGGACA---TTTAGGTTGTTTCCA 474 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 27.94 CpG sites = 10, Kimura (unadjusted) = 27.94 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.05 (4 / 76), avg. gap size = 1.00 (4 / 4) 37 0.00 0.00 0.00 chr4ptel1M 279076 279107 (720893) (CT)n#Simple_repeat 1 32 (0) c_b170s251i1 6523 chr4ptel1M 279076 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 279107 (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 32 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 391 23.01 5.04 8.70 chr4ptel1M 279115 279233 (720767) C MIRb#SINE/MIR (150) 118 4 m_b170s601i24 6524 chr4ptel1M 279115 GGAGTTAAATGACTTGCCCAGGGTCACACAGCTAGGAAGTGTTAAGTGTC 279164 ii i i i ------- v C MIRb#SINE/MIR 118 GAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGC 76 chr4ptel1M 279165 TGAGACCAGATTTGAACTTGGGAACCTCTGACTTCA------GGGTTCTA 279208 v v vi i iii vviv i ------ v i v C MIRb#SINE/MIR 75 AGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTT 26 chr4ptel1M 279209 TCCACTATGCCACCTCGCTGCCCTT 279233 i--- v i C MIRb#SINE/MIR 25 TCCACTG---CACCACGCTGCCCCT 4 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.64 CpG sites = 15, Kimura (unadjusted) = 27.93 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.09 (11 / 118), avg. gap size = 1.45 (16 / 11) 267 21.82 10.23 1.04 chr4ptel1M 279219 279306 (720694) MIR3#SINE/MIR 107 202 (6) m_b170s601i25 6525 chr4ptel1M 279219 CACCTCGCTGC-CCTTA-TTTCCTCATTTTTAAA-TGAAAAGATTGGGCT 279265 v v- i - i v - iii i i MIR3#SINE/MIR 107 CACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACT 156 chr4ptel1M 279266 A--TGGTTTCT----TCCAGTTTTAAGTCTATCATTCTATGATTCTA 279306 -- i i ---- v- ii iv iv MIR3#SINE/MIR 157 AGATGATCTCTAAGGTCCC-TTCCAGCTCTGACATTCTATGATTCTA 202 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.64 CpG sites = 13, Kimura (unadjusted) = 26.64 Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.07 (6 / 87), avg. gap size = 1.67 (10 / 6) 296 33.91 0.83 2.52 chr4ptel1M 280071 280191 (719809) MIRc#SINE/MIR 2 120 (148) m_b170s601i26 6526 chr4ptel1M 280071 GAAGCAGTCAGCCATAATG-AAAGAGGCCTGGCCTCAGAGTCAGGAAAAA 280119 i vv viii i - vv v ii i v MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr4ptel1M 280120 CTGAGTTCAAATCCTACCTTTTGACACATTTGTGCTTGGAGACCCCATGG 280169 i i i iiv - i v v vivv vv v i-- MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGC-TCTGCCACTTACTAGCTGTGTGACCT--TGG 98 chr4ptel1M 280170 GCAACCCACTTATTTTCCTTAA 280191 vi vii ii i MIRc#SINE/MIR 99 GCAAGTCACTTAACCTCTCTGA 120 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.08 CpG sites = 22, Kimura (unadjusted) = 46.37 Transitions / transversions = 1.22 (22/18) Gap_init rate = 0.03 (4 / 120), avg. gap size = 1.00 (4 / 4) 594 33.14 1.70 0.56 chr4ptel1M 280283 280458 (719542) C MIR3#SINE/MIR (2) 206 29 m_b170s601i27 6527 chr4ptel1M 280283 ATCATAGATCCATAGA---TTTAAATTAGAAAAGGGCTTAGAAGCCATCA 280329 vi --- ivi ii i ii iv iii v C MIR3#SINE/MIR 206 ATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCT 157 chr4ptel1M 280330 AGTCCAACCCTTTTGTTATATAAATGACAAAACCAAGACACAGAAAGAAT 280379 ii ii v i i vi ii i v i ivv C MIR3#SINE/MIR 156 AGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTG 107 chr4ptel1M 280380 AAGTGAGTTGTCTAGAGTCACACAACCAGGAAGCATCTGGAGCAGGATTT 280429 v i i ii i ? vv iiv v iiv i i v C MIR3#SINE/MIR 106 AAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTA 57 chr4ptel1M 280430 GAACTCCAGGCTTCTTGACTTTGAGTCTG 280458 - ii i iiv i C MIR3#SINE/MIR 56 GAAC-CCAGGTCTCCTGACTCCCAGTCCG 29 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 45.17 CpG sites = 41, Kimura (unadjusted) = 47.51 Transitions / transversions = 2.41 (41/17) Gap_init rate = 0.01 (2 / 175), avg. gap size = 2.00 (4 / 2) 21 0.00 0.00 0.00 chr4ptel1M 280712 280734 (719266) (AC)n#Simple_repeat 1 23 (0) m_b170s252i7 6528 chr4ptel1M 280712 ACACACACACACACACACACACA 280734 (AC)n#Simple_ 1 ACACACACACACACACACACACA 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 511 34.47 12.63 0.00 chr4ptel1M 280753 281045 (718955) L3#LINE/CR1 3456 3785 (314) m_b170s601i28 6529 chr4ptel1M 280753 TTAAT-TAAATCAATGTTATGTCATGGCAGCCACAAAA-TGAATGCTGTC 280800 i - i ii iiv i vii v v -iv vi L3#LINE/CR1 3456 TCAATATGAGCCAACAGTGTGATGTGGCTGCCAAAAAAGCTAATGCAATC 3505 chr4ptel1M 280801 TTAGGCTGCTTTGAGGGA--TCTAAGATCCAAAATAAGC-AGGT------ 280841 v i vi -- v ivi i ?i v- ------ L3#LINE/CR1 3506 TTAGGCTGCATTAATAGAAGTATAGTGTCCAGANCAAGGGAGGTAATAGT 3555 chr4ptel1M 280842 ----TTGTAACCCATGTTA-------CATGTCTAGA-TCCTATGTCC--T 280877 ----i vi iii i i------- ii i - vi ii i -- L3#LINE/CR1 3556 CCCGCTGTACTCTGCGCTGGTCAGACCACATCTGGAGTATTGCGTTCAGT 3605 chr4ptel1M 280878 T------GTCAGAC---AAAACAGACACTGACAAGCCAAAAAGTGTCCAG 280918 ------ i v i--- i vi i i iii iv i L3#LINE/CR1 3606 TCTGGGCGCCACATTTTAAGAGGGACATTGACAAACTGGAGCGCGTCCAG 3655 chr4ptel1M 280919 AAGAGAACAATCGAGGTGATGAAAGGATT-GAAGTCCTGCTGTTTGGGGA 280967 i i i i ii i i i vi - ii v iii v i L3#LINE/CR1 3656 AGGAGAGCGACCAGGATGGTGAAGGGTCTGGAAACCATGTCATATGAGGA 3705 chr4ptel1M 280968 ATAGTGGAAGGAACTAATGACCAGGAGTCTGGATAAGAGAAGACTTAAGA 281017 ii v iiv ivvvv i v iii L3#LINE/CR1 3706 ACGGTTGAAGGAACTGGGGATGTTTAGCCTGGAGAAGAGAAGACTTAGAG 3755 chr4ptel1M 281018 GGGA-ATCCTACCT-TCTCCTCATATTTAA 281045 i - vv v - i vv i L3#LINE/CR1 3756 GAGACATGATAGCTGTCTTCAAATATTTGA 3785 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 46.35 CpG sites = 70, Kimura (unadjusted) = 50.02 Transitions / transversions = 2.26 (70/31) Gap_init rate = 0.05 (14 / 292), avg. gap size = 2.64 (37 / 14) 219 26.21 8.55 7.14 chr4ptel1M 281081 281232 (718768) L2b_3end#LINE/L2 269 422 (44) m_b170s601i29 6530 chr4ptel1M 281081 CCATCCCCTG--CTCCTCAAGTACCTTCCCTCTCTTCACCCCACCTTTCA 281128 v i -- i i v - v vi --- i iivv vi? L2b_3end#LINE 269 CCCTCCTCTGGGCCCCCCCAGT-CCTACCCTGCC---ACTCTGGGTTATN 314 chr4ptel1M 281129 ATTTTCC-TTTGCATGT-TGTCTTCCTCTCTTCTTATATTACACTAAACT 281176 v i-? i - i i v ---- v i i--- i i L2b_3end#LINE 315 ATTGTCTGNTTACATGTCTGTCTCCCCCACT----AGACTG---TGAGCT 357 chr4ptel1M 281177 CCATAAGGGCAGGGAC--------TCTT-TTAAAATCTGTATCTCCAGGA 281217 i i -------- - v vvv i vi L2b_3end#LINE 358 CCGTGAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTGTATCCCCAGCG 407 chr4ptel1M 281218 CTGAGCACAGTGCCT 281232 iv ? L2b_3end#LINE 408 CCTAGCACAGNGCCT 422 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.66 CpG sites = 21, Kimura (unadjusted) = 33.86 Transitions / transversions = 1.31 (21/16) Gap_init rate = 0.11 (16 / 151), avg. gap size = 1.50 (24 / 16) 264 26.53 11.34 2.86 chr4ptel1M 281136 281232 (718768) L2a_3end#LINE/L2 369 473 (44) m_b170s601i30 6530 chr4ptel1M 281136 TTTGCATGTTGTCTTCCTCTCTTC-TTATATTACACTAAACTCCATAAGG 281184 iv i vi i ii -i v v i--- i i L2a_3end#LINE 369 TTTGTTTATTGTCTGTCTCCCCCCACTAGAATG---TAAGCTCCATGAGG 415 chr4ptel1M 281185 GCAGGGACTCTT----------TTAAAATCTGTATCTCCAGGACTGAGCA 281224 i ---------- v vvv i vi iv v L2a_3end#LINE 416 GCAGGGACTTTTGTCTGTTTTGTTCACTGCTGTATCCCCAGCGCCTAGAA 465 chr4ptel1M 281225 CAGTGCCT 281232 L2a_3end#LINE 466 CAGTGCCT 473 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.85 CpG sites = 14, Kimura (unadjusted) = 33.46 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.05 (5 / 96), avg. gap size = 2.80 (14 / 5) 704 30.48 13.20 1.48 chr4ptel1M 281482 281784 (718216) L3#LINE/CR1 3758 4095 (4) m_b170s601i31 6531 chr4ptel1M 281482 GAAATGATGATTGTCTCCAAGTATTTGACAGACTGTTATGTGAAAGACAG 281531 v iii i i vi i i i vi L3#LINE/CR1 3758 GACATGATAGCTGTCTTCAAATATTTGAAGGGCTGTCATGTGGAAGAGGG 3807 chr4ptel1M 281532 ATTAAGCTTGCTCTTCTTAGCCCCGGAAGGTAGAATTAGAAGCTATGGGT 281581 ii ii viv i i i i i i i v v L3#LINE/CR1 3808 ATTAGACTTATTCTGTGTGGCTCCAGAGGGCAGAACTAGGACCAATGGGT 3857 chr4ptel1M 281582 AAAATTTGAAAGCAGGTATATTTAGGCTTTTTGGAAAGAA-AATTGTCTG 281630 ii v iv i v i v v ivv iv i - i v i L3#LINE/CR1 3858 GGAAGTTACAGGGAGGCAGATTTCGGCTCAATATAAGGAAGAACTTTCTA 3907 chr4ptel1M 281631 ATCAATTAGAGC---------ATGGAACAAGATCCCTTAGGAGCTATTGG 281671 - i --------- iii v v ii? v v i L3#LINE/CR1 3908 A-CAATCAGAGCTGTCCAAAAATGGAATGGGCTGCCTCGNGAGGTAGTGA 3956 chr4ptel1M 281672 GTTCTCTGGTCTTTGGTAGT-------------CTGGATGACTATTTGGC 281708 i i i- vi vi ------------- i i v L3#LINE/CR1 3957 GCTCCCC-GTCACTGGAGGTGTTCAAGCAGAGGCTGGATGACCACTTGTC 4005 chr4ptel1M 281709 TGG-----------AGATATTCATTCA---GGT--CAGATCAGGCTAGAT 281742 v ----------- iv v v --- i --v i ii i L3#LINE/CR1 4006 AGGGATGTTGTAGAAGGGATTCCTGCATTGGATGGGAGGTTGGACTAGAT 4055 chr4ptel1M 281743 GGCTGCCTCT-TGGTCTTTTCCCATCCTGAAATTTTTTCATTC 281784 ---i -v ii v ii i i v v L3#LINE/CR1 4056 G---ACCTCTAAGGTCCCTTCCAACTCTGAGATTCTGTGATTC 4095 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.96 CpG sites = 59, Kimura (unadjusted) = 41.23 Transitions / transversions = 1.84 (59/32) Gap_init rate = 0.04 (12 / 302), avg. gap size = 3.75 (45 / 12) 463 35.63 2.11 1.04 chr4ptel1M 281803 281992 (718008) MIR3#SINE/MIR 17 208 (0) m_b170s601i32 6532 chr4ptel1M 281803 GTAGAAAAGCCATGAGATGTGGAGTCCAGAGGACCAGAATTACAATTCTA 281852 i i iiv i iiv - - ii v ii vi i i ii MIR3#SINE/MIR 17 GCAGAGAGAGCACGGACTG-GGAGTC-AGGAGACCTGGGTTCTAGTCCCG 64 chr4ptel1M 281853 TTTCCACCATTTG-TGACTATCTGAGCTTCAGGTAGTCACTGAAATTGTA 281901 vi ii i vi- ?i i v v vi vv vv vi v v MIR3#SINE/MIR 65 GCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTC 114 chr4ptel1M 281902 TGAGCCTCAGTCAGCTCATCTAGAAAATGAAGAGTTCGGTCTAGAAGAGC 281951 i ivv iv i i v i v v v MIR3#SINE/MIR 115 TGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATC 164 chr4ptel1M 281952 TTGAAGGTCTTTTCCAGCTCAAA---TCAATGACCTCACGATCC 281992 iv ii vi --- v iiii i i MIR3#SINE/MIR 165 TCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTATGATTC 208 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 48.88 CpG sites = 41, Kimura (unadjusted) = 51.23 Transitions / transversions = 1.58 (41/26) Gap_init rate = 0.02 (4 / 189), avg. gap size = 1.50 (6 / 4) 346 41.49 6.22 0.00 chr4ptel1M 282015 282255 (717745) L3#LINE/CR1 3807 4062 (37) m_b170s601i33 6529 chr4ptel1M 282015 GATTTGATTTGTTCTCCTTGGACACAG-GGACAGAGATAAAAATGACTGG 282063 v i i viv viv - i iv ii vii iv L3#LINE/CR1 3807 GATTAGACTTATTCTGTGTGGCTCCAGAGGGCAGAACTAGGACCAATGGG 3856 chr4ptel1M 282064 CAGAAACTGAAAAGGGGCAGAATTTACCTTGAGATAAGGA-GTATCACCT 282112 ii ii iv ii i v iiv ii v - v iivi L3#LINE/CR1 3857 TGGAAGTTACAGGGAGGCAGATTTCGGCTCAATATAAGGAAGAACTTTCT 3906 chr4ptel1M 282113 AATGCTTGTCGTGATCTCAAAGTGCAGTTGATTGCTTTA-----TCCTTA 282157 iiv iivv ivi iv i v i v ii i ii----- vv v L3#LINE/CR1 3907 AACAATCAGAGCTGTCCAAAAATGGAATGGGCTGCCTCGNGAGGTAGTGA 3956 chr4ptel1M 282158 ACTATT--TCTCTAA----TCCCAAGTGGAAGTTGAATATCTGATTGTCA 282201 i vii-- v ii----vii ii i i i iv iiv L3#LINE/CR1 3957 GCTCCCCGTCACTGGAGGTGTTCAAGCAGAGGCTGGATGACCACTTGTCA 4006 chr4ptel1M 282202 GAGATGTGGTAAAGGAGATTTCT--ATGCAATCATGGACTGGATTAGATG 282249 i v i i i i -- vvi vivi ii i L3#LINE/CR1 4007 GGGATGTTGTAGAAGGGATTCCTGCATTGGATGGGAGGTTGGACTAGATG 4056 chr4ptel1M 282250 ACCTCT 282255 L3#LINE/CR1 4057 ACCTCT 4062 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 64.06 CpG sites = 66, Kimura (unadjusted) = 66.65 Transitions / transversions = 1.94 (66/34) Gap_init rate = 0.03 (6 / 240), avg. gap size = 2.50 (15 / 6) 180 36.00 13.98 1.66 chr4ptel1M 282278 282599 (717401) C L2b_3end#LINE/L2 (67) 399 39 m_b170s601i34 6533 chr4ptel1M 282278 ATAAATCAATCAACAAGTGAG--GTAATCCCTGTCATCAAGGATCCCACA 282325 v v ii v vv --?iii i v v v i C L2b_3end#LINE 399 ATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGGAGCTCACA 350 chr4ptel1M 282326 TTCTCTTGGA--AAACAGAAATGTTCACAGATA------------AGTAG 282361 v vv i-- i v vv? i ------------ i C L2b_3end#LINE 349 GTCTAGTGGGGGAGACAGACATGTAANCAGACAATNATAACCCAGAGTGG 300 chr4ptel1M 282362 ----ATAT-ACAGCAAGTGCCTAC----TGACACTAGATTCATAACTGGG 282402 ----i v- v vii v i v----v i i iv ii i-iv C L2b_3end#LINE 299 CAGGGTAGGACTGGGGGGGCCCAGAGGAGGGCGCCTGACCCG-GCCTGGG 251 chr4ptel1M 282403 GGAGGCAGGAAAAACCTCTTGAAGA---TGGCAATTGAGCTAAGCCTGGA 282449 - v i iii i ii i i--- i v i v iv C L2b_3end#LINE 250 GG-GTCAGGGAGGGCTTCCCGGAGGAGGTGACATTTGAGCTGAGACCTGA 202 chr4ptel1M 282450 AAG--GAGCTAGGGATT--CCTGGAAATGATATTGAGGATGAGCCTCTCA 282495 i -- - ii -- v vi v -iv i v i v ii C L2b_3end#LINE 201 AGGATGAG-TAGGAGTTGGCCAGGCGAAGA-GGTGGGGAAGGGCGTTCCA 154 chr4ptel1M 282496 GCCATGGAGGAATAA-AGCCACAAGGG---TGGATCGGGA-CTATCCTAG 282540 v - ii i i- ?vii i --- iiv -?v v ? i C L2b_3end#LINE 153 GGCA-GAGGGAACAGCANGTGCAAAGGCCCTGAGGCGGGAGNGAGCNTGG 105 chr4ptel1M 282541 CAATAT------AGCAGCCCAGAAACCAGGTCTGCCAAAACACAGGGTAC 282584 -i i ------ i vvi ii vviv iii i v v vi C L2b_3end#LINE 104 C-GTGTTCGAGGAACAGCAAGGAGGCCAGTGTGGCTGGAGCAGAGTGAGC 56 chr4ptel1M 282585 ATGAG--GAGTAGTAAG 282599 v i -- i i C L2b_3end#LINE 55 AAGGGGAGAGTGGTAGG 39 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 48.04 CpG sites = 68, Kimura (unadjusted) = 52.77 Transitions / transversions = 1.48 (68/46) Gap_init rate = 0.06 (20 / 321), avg. gap size = 2.55 (51 / 20) 248 28.53 9.52 7.25 chr4ptel1M 282303 282491 (717509) C L2c_3end#LINE/L2 (78) 400 208 m_b170s601i35 6533 chr4ptel1M 282303 TCCCTGTCATCAAGGATCCCACATTCTCTTGGA--AAACAGAAATGTTCA 282350 i v v i v vv -- i v ? vv C L2c_3end#LINE 400 TCCCTGCCCTCAAGGAGCTCACAGTCTAGTGGAGGAGACAGACANGTAAA 351 chr4ptel1M 282351 CAGATAAGTAGATATACAGCAAGTGCCTACTGACACTAGATTCATAACTG 282400 i v v - --- --- v i -- vvii - C L2c_3end#LINE 350 CAGACAATTACA-ATA---CAAGT---TAATGATA--AGTGCTATAA-TG 311 chr4ptel1M 282401 GGGG---AGGCAGGA------AAAACCTCTTGAAGATGGCAATTGAGCTA 282441 i --- i i------iii v v -v i v vi iii C L2c_3end#LINE 310 GGAGTATAGACAGGGTGCTATGGGAGCAC-AGAGGAGGGCACCTAGACTA 262 chr4ptel1M 282442 AGCCTGGAAAGGAGCTAGGGA----TTCCT---GGAAATGATATTGAGGA 282484 i? i --- i ii ---- i--- ii i ivii v C L2c_3end#LINE 261 GNCTTGG---GGGGTCAGGGAAGGCTTCCCGGAGGAGGTGACATCTGAGC 215 chr4ptel1M 282485 TGAGCCT 282491 ? C L2c_3end#LINE 214 TGAGNCT 208 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.93 CpG sites = 30, Kimura (unadjusted) = 37.90 Transitions / transversions = 1.50 (30/20) Gap_init rate = 0.10 (19 / 188), avg. gap size = 1.68 (32 / 19) 184 29.02 8.06 5.51 chr4ptel1M 282386 282509 (717491) C L2c_3end#LINE/L2 (209) 269 143 m_b170s601i36 6533 chr4ptel1M 282386 CTAGATTCATAACTGGGGGAGGCAGGAAAAACCTCTTGAAGA---TGGCA 282432 i vi?-- v i v i ii i ii i i--- i C L2c_3end#LINE 269 CTAGACTAGN--CTTGGGGGGTCAGGGAAGGCTTCCCGGAGGAGGTGACA 222 chr4ptel1M 282433 ATTGAGCTAAGCCTGGAAAG--GAGCTAGGGATT--CC---TGGAAATGA 282475 vi i ? v i -- - ii -- --- i- C L2c_3end#LINE 221 TCTGAGCTGAGNCTTGAAGGATGAG-TAGGAGTTAGCCAGGTGGAAG-GA 174 chr4ptel1M 282476 TATTGAGGATGAGCCTCTCAGCCATGGAGGAATA 282509 vi-- i v v ii v - ii i C L2c_3end#LINE 173 GG--GGGGAAGAGCATTCCAGGCA-GAGGGAACA 143 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.65 CpG sites = 25, Kimura (unadjusted) = 40.23 Transitions / transversions = 2.78 (25/9) Gap_init rate = 0.09 (11 / 123), avg. gap size = 1.55 (17 / 11) 567 15.92 4.32 5.07 chr4ptel1M 282961 283099 (716901) C MER63D#DNA/hAT-Tip100 (590) 471 334 m_b170s502i5 6534 chr4ptel1M 282961 CATGACACACATTTAAAAGTTTAATCTACATTA---ACATTCTCCCCATT 283007 i v -- i --- i i - C MER63D#DNA/hA 471 CACGACACACTTTTAA--GTTTAATCTGCATTATTAACATTTTCTCCAT- 425 chr4ptel1M 283008 AACACTTTCTTAAGCCTGGCCAATAAACAAAACAACAGATCCAGCCCTGA 283057 -- i i v v i i v C MER63D#DNA/hA 424 --CACTTTCTTAAGTCTAGACAATCAACAAAACAATAAATCAAGCCCTGA 377 chr4ptel1M 283058 TTTGTAGAGTTAGC---TTTCTCTGGATTATAAATTCTCATGCCA 283099 v v --- iv -- i v vii C MER63D#DNA/hA 376 TTTGTAGCGTTTGCCGATTTCCGTGG--TGTAAATACTCCCACCA 334 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 16.26 CpG sites = 12, Kimura (unadjusted) = 18.05 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.07 (9 / 138), avg. gap size = 1.44 (13 / 9) 224 35.38 0.83 3.42 chr4ptel1M 283229 283348 (716652) C L2#LINE/L2 (560) 2522 2406 m_b170s601i37 6533 chr4ptel1M 283229 GTCATTGAACGGAAAGAGGTTGGTTA-GAAAGAGACATGGGTTTAAGTGA 283277 i ? vi ii v i vv ii i- ii iii -- i v i C L2#LINE/L2 2522 GCCATTNACTGAGATGGGGAAGACTGCGGGAGGAGCA--GGTTTGAGGGG 2475 chr4ptel1M 283278 AAAGACAATGAATTTTGTTGGAAACATATATAGAGTTTTAGATGCCTATG 283327 i iv v i iv vvii i - - v v C L2#LINE/L2 2474 GAAGATCAGGAGTTCAGTTTTGGACATGT-TA-AGTTTGAGATGCCTATT 2427 chr4ptel1M 283328 GATTATCTAAGTGGCAATGTC 283348 iivi i vi C L2#LINE/L2 2426 AGACATCCAAGTGGAGATGTC 2406 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 51.71 CpG sites = 27, Kimura (unadjusted) = 51.71 Transitions / transversions = 1.93 (27/14) Gap_init rate = 0.04 (5 / 119), avg. gap size = 1.00 (5 / 5) 325 39.33 5.98 0.52 chr4ptel1M 283396 283579 (716421) C L3#LINE/CR1 (3322) 777 584 m_b170s601i38 6535 chr4ptel1M 283396 TTGTACCAACATGAATTACCAAAAGTAGGCAGAAGTCATTCAGTTTG-TG 283444 i v v i i v ii i i vi ivivi - C L3#LINE/CR1 777 TCGTTCCCACGTGAATCAGCAGGAGTGGGTAGCGGTCGGCGGGTTTGATG 728 chr4ptel1M 283445 AG------CAG-TTCTCTTTCATGACTTTAATTAATATCTAAGGACAATT 283487 ------ -i iv i v ivi vv iiiiiv vi iv C L3#LINE/CR1 727 AGTCTTGGCAGGCTCTCCGTCACGTCTCGGATACACGCTCCAGGAAGACA 678 chr4ptel1M 283488 GTA-ATCTCTTTACT-GTTATTTTCGTGTCAACAAATAACTGCATTAGTG 283535 i - i iiv i - ii iv iv - vi v iii i v iv i C L3#LINE/CR1 677 GCACACCTCCCGATTAGCCACGTCAG-GTCTGCATACGGCCGCCTCCGTA 629 chr4ptel1M 283536 CTCCTCAGGGGTGAGTAACCAACT-CCACAATTCTTTTCTTCTTC 283579 ii v v v i- i iv v i i C L3#LINE/CR1 628 TCCCTCAGCGGGGAGTCACCAACCACCACGACGCGTCTCTTCCTC 584 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.53 CpG sites = 46, Kimura (unadjusted) = 60.11 Transitions / transversions = 1.77 (46/26) Gap_init rate = 0.04 (7 / 183), avg. gap size = 1.71 (12 / 7) 539 30.58 8.54 1.41 chr4ptel1M 283766 283964 (716036) MIRb#SINE/MIR 42 254 (14) m_b170s601i39 6536 chr4ptel1M 283766 GAGTCACAAAAGACCAGAGTTCAAATCTTGCTTCAGATATTTCCTA---- 283811 -i v v i i ii vi v vi i v ---- MIRb#SINE/MIR 42 GAGTCA-GACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTG 90 chr4ptel1M 283812 --TG----TGGGCAATTCACTCAACTGTTATCTTCCTTAGCTTCCTCAAC 283855 -- ---- v i i ivi v vvv i i v MIRb#SINE/MIR 91 TGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATC 140 chr4ptel1M 283856 TTTAAAGTGGGCATGATAAAGCCTCTTCCTAACAGAGTTGTTATGATACT 283905 v i v i vi v-- vi i i viv MIRb#SINE/MIR 141 TGTAAAATGGGGATAATAATACCTA--CCTCGCAGGGTTGTTGTGAGGAT 188 chr4ptel1M 283906 CAAATAAGGTAATTTTTATTAGATGCTTAATACAGCATCTG-------GT 283948 i i i viv i v iii ii iii ------- MIRb#SINE/MIR 189 TAAATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGT 238 chr4ptel1M 283949 CAGTGCTTAATAAATG 283964 v i i MIRb#SINE/MIR 239 AAGCGCTCAATAAATG 254 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.36 CpG sites = 36, Kimura (unadjusted) = 40.67 Transitions / transversions = 1.50 (36/24) Gap_init rate = 0.04 (7 / 198), avg. gap size = 2.86 (20 / 7) 443 33.94 8.26 0.00 chr4ptel1M 284070 284287 (715713) C L2#LINE/L2 (498) 2584 2349 m_b170s601i40 6537 chr4ptel1M 284070 GAGAGTGAAAATTTGAGAATGAGTC--AGGTGCCAAACCTAGGTAACTGA 284117 i v ii v ii i v -- viivii ii i i C L2#LINE/L2 2584 GAAAGAGAGGAGTCAAGGATGACTCCAAGGTTTTTGGCCTGAGCAACTGG 2535 chr4ptel1M 284118 GAGAATGGTGGTACCCTTGCCAGTAATAGGGAAG-TT-----AAGAGAAG 284161 i i v v i v ?v v vi i -i ----- i v C L2#LINE/L2 2534 AAGGATGGAGTTGCCATTNACTGAGATGGGGAAGACTGCGGGAGGAGCAG 2485 chr4ptel1M 284162 ATTTTGCAGGAAAGAGAATGAATGAAATTTTGGACATAATGAATTTGAGA 284211 i vivi i vv v i vv i iv i i C L2#LINE/L2 2484 GTTTGAGGGGGAAGATCAGGAGTTCAGTTTTGGACATGTTAAGTTTGAGA 2435 chr4ptel1M 284212 TGCCTGTGGGATA----------GATGTTGAGGTAGCAATTTGATATACA 284251 i vi i ---------- i vvi i v i C L2#LINE/L2 2434 TGCCTATTAGACATCCAAGTGGAGATGTCGAGTAGGCAGTTGGATATACG 2385 chr4ptel1M 284252 AAACTGGAACCCCAGACAGAGATGAGGGCTGGATAT 284287 iv iii vi iv i vv v C L2#LINE/L2 2384 AGTCTGGAGTTCAGGGGAGAGGTCCGGGCTGGAGAT 2349 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 45.54 CpG sites = 44, Kimura (unadjusted) = 47.33 Transitions / transversions = 1.47 (44/30) Gap_init rate = 0.02 (4 / 217), avg. gap size = 4.50 (18 / 4) 17 7.81 0.00 0.00 chr4ptel1M 284702 284728 (715272) (TATG)n#Simple_repeat 1 27 (0) m_b170s252i8 6538 chr4ptel1M 284702 TATATATCTATGTATGTATGTATGTAT 284728 i v (TATG)n#Simpl 1 TATGTATGTATGTATGTATGTATGTAT 27 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 246 26.34 10.24 1.67 chr4ptel1M 285482 285647 (714353) L1M3_orf2#LINE/L1 1113 1292 (1996) m_b170s551i11 6539 chr4ptel1M 285482 CAAAAT-GACAAACCTTTAGCCTATCTAGTGAAAAAGAAGATGAC----A 285526 - iviv ivi ii v ---- L1M3_orf2#LIN 1113 CAAAATTGACAAACCTTTAGCTAGACTAAGAAAAAAAGAGAAGACTCAAA 1162 chr4ptel1M 285527 TAAATCAAAT---GAAT-AAGGTGAAATCATCCCAAAATCAGATGC---- 285568 v ---i - i v i iv iv --- v ---- L1M3_orf2#LIN 1163 TAAATAAAATCAGAAATGAAAGAGGAGACATTACAA---CTGATGCCACA 1209 chr4ptel1M 285569 --AATAAAAAGAATAATAAAAACCTGCTAT--ATAGTTATATGCTAATAA 285614 -- i v i iv i -- i i i i i L1M3_orf2#LIN 1210 GAAATAAAAAGGATCATAAGAGACTACTATGAACAATTATACGCCAACAA 1259 chr4ptel1M 285615 ATCTAAGAACACAGAATAATTTGATGATTACCT 285647 ivi v vi v v v i v v L1M3_orf2#LIN 1260 ATTGGATAACCTAGAAGAAATGGATAAATTCCT 1292 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.18 CpG sites = 24, Kimura (unadjusted) = 33.11 Transitions / transversions = 1.26 (24/19) Gap_init rate = 0.06 (10 / 165), avg. gap size = 2.00 (20 / 10) 19 26.68 0.00 0.00 chr4ptel1M 285701 285749 (714251) (AG)n#Simple_repeat 1 49 (0) m_b170s252i9 6540 chr4ptel1M 285701 AGAGAGAGATGGAGACACAGCAATGGAGAGAGACGGAGAGAGACAGAGA 285749 vi v v vi vi vi v (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 49 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 11 21.01 5.13 0.00 chr4ptel1M 286518 286556 (713444) (AAAGTGA)n#Simple_repeat 1 41 (0) m_b170s252i10 6541 chr4ptel1M 286518 AAAGT-TAAAGTTAAAAGATTTAA-TCAAAAGTGAAAAGTG 286556 -v v vvvv - v (AAAGTGA)n#Si 1 AAAGTGAAAAGTGAAAAGTGAAAAGTGAAAAGTGAAAAGTG 41 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2) 28 15.64 7.04 0.00 chr4ptel1M 286790 286860 (713140) (TAC)n#Simple_repeat 1 76 (0) m_b170s252i11 6542 chr4ptel1M 286790 TACTTATTCTACTATTA-TTCTACTACT-CTACT-CTACT-CTACTACTA 286835 vv v i - v - - - (TAC)n#Simple 1 TACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTA 50 chr4ptel1M 286836 -TTCTACTACTTATTCTACTATTACT 286860 - v vv v i (TAC)n#Simple 51 CTACTACTACTACTACTACTACTACT 76 Matrix = Unknown Transitions / transversions = 0.25 (2/8) Gap_init rate = 0.07 (5 / 70), avg. gap size = 1.00 (5 / 5) 12 22.59 0.00 2.70 chr4ptel1M 287037 287074 (712926) (TTAAA)n#Simple_repeat 1 37 (0) m_b170s252i12 6543 chr4ptel1M 287037 TTAAAAAAATAATAAATTTAATCATTTTAAATTAAATT 287074 vv - v v i vv (TTAAA)n#Simp 1 TTAAATTAA-ATTAAATTAAATTAAATTAAATTAAATT 37 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 410 31.50 6.06 3.81 chr4ptel1M 287968 288198 (711802) L3#LINE/CR1 3559 3794 (305) m_b170s601i41 6544 chr4ptel1M 287968 GCCGTCTTCTGTCTAGGTCACAGAACACCAGGAGCAGTATGTACCAACTG 288017 i vi iviv v vv i v i v ii -i --- L3#LINE/CR1 3559 GCTGTACTCTGCGCTGGTCAGACCACATCTGGAGTATTGCGT-TCA---G 3604 chr4ptel1M 288018 TCCTGAGCAGCCCAGTTTAGGGAGCTCGTTGGTAAGATGGAGAGCATTCA 288067 i i iv v v i ii vv i ii iv v i i L3#LINE/CR1 3605 TTCTGGGCGCCACATTTTAAGAGGGACATTGACAAACTGGAGCGCGTCCA 3654 chr4ptel1M 288068 GCAGAAGGTGACCAGC-TTGTGAAGGACC---ACCCCATCCCCACCATAT 288113 vi ii i v- v ii --- vv ----ii L3#LINE/CR1 3655 GAGGAGAGCGACCAGGATGGTGAAGGGTCTGGAAACCAT----GTCATAT 3700 chr4ptel1M 288114 GA-GAATGATTTCAGGAACTCTGGTTGCTAATTCTG-----GAAAAGACT 288157 - i i vv vv v i v vi ----- i L3#LINE/CR1 3701 GAGGAACGGTTGAAGGAACTGGGGATGTTTAGCCTGGAGAAGAGAAGACT 3750 chr4ptel1M 288158 CCAGAGGGGA---AATAGTTGTCTACAAGTATAAGAA-GTCTGTC 288198 -i i ---i i v i vv - v L3#LINE/CR1 3751 -TAGAGGAGACATGATAGCTGTCTTCAAATATTTGAAGGGCTGTC 3794 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.39 CpG sites = 39, Kimura (unadjusted) = 41.95 Transitions / transversions = 1.26 (39/31) Gap_init rate = 0.07 (15 / 230), avg. gap size = 1.53 (23 / 15) 23 8.12 2.56 0.00 chr4ptel1M 288753 288791 (711209) (AAAAG)n#Simple_repeat 1 40 (0) m_b170s252i13 6545 chr4ptel1M 288753 AAAAAAAAAGAAAAGAAAAGAAAAGAAAA-ACAAGAATAG 288791 i - v v (AAAAG)n#Simp 1 AAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAG 40 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.03 (1 / 38), avg. gap size = 1.00 (1 / 1) 22 7.42 0.00 0.00 chr4ptel1M 288814 288842 (711158) (A)n#Simple_repeat 1 29 (0) m_b170s252i15 6546 chr4ptel1M 288814 AAAAAAAAAAAAAAAAAAAAAAAGAAGAA 288842 i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA 29 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 543 30.53 16.67 0.36 chr4ptel1M 288860 289099 (710901) L3#LINE/CR1 3814 4092 (7) m_b170s601i42 6544 chr4ptel1M 288860 CTTTTTCTCTTTGACCCCAGAGGACAGATCCAAGATCATCAGGTTGAAGT 288909 v v v i i i v i i i vii v L3#LINE/CR1 3814 CTTATTCTGTGTGGCTCCAGAGGGCAGAACTAGGACCAATGGGTGGAAGT 3863 chr4ptel1M 288910 GACATGGAAAC----TTTGGCTTGATGTCAGGAAAAAACAT-TAATAATT 288954 v v ii ---- i ii i v i viv - i i L3#LINE/CR1 3864 TACAGGGAGGCAGATTTCGGCTCAATATAAGGAAGAACTTTCTAACAATC 3913 chr4ptel1M 288955 GAAGCCTTTCCAATTTGGAGTATATTGCCCTGGGAAGAAAGTAGCT---- 289000 ii iv i v vv i ivii ii ? i v ivv ---- L3#LINE/CR1 3914 AGAGCTGTCCAAAAATGGAATGGGCTGCCTCGNGAGGTAGTGAGCTCCCC 3963 chr4ptel1M 289001 -------------TTTAAACAGCGCCTTGGATGACCACCTGTTGGGTATG 289037 ------------- i i v v - i ii v L3#LINE/CR1 3964 GTCACTGGAGGTGTTCAAGCAGAGGC-TGGATGACCACTTGTCAGGGATG 4012 chr4ptel1M 289038 TT-TAGTGGGAATTTTTGC-TCAG--GGAAGGT--------------TTT 289069 - vi i ii - ii -- i -------------- i L3#LINE/CR1 4013 TTGTAGAAGGGATTCCTGCATTGGATGGGAGGTTGGACTAGATGACCTCT 4062 chr4ptel1M 289070 GCAATACCTTCCAACTCTGAAATTCTCTGA 289099 ivii v i v L3#LINE/CR1 4063 AAGGTCCCTTCCAACTCTGAGATTCTGTGA 4092 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.74 CpG sites = 47, Kimura (unadjusted) = 41.24 Transitions / transversions = 1.81 (47/26) Gap_init rate = 0.04 (9 / 239), avg. gap size = 4.56 (41 / 9) 22 17.23 3.08 4.69 chr4ptel1M 289329 289393 (710607) (TTTG)n#Simple_repeat 1 64 (0) m_b170s252i16 6547 chr4ptel1M 289329 TTTGTTTGGTTTGGTTTTTTGTGGAGGGGGTTGTTTTTGTTTGTTTGTTT 289378 - v v -vv vvv - v (TTTG)n#Simpl 1 TTTGTTT-GTTTGTTTGTTTGT-TTGTTTGTT-TGTTTGTTTGTTTGTTT 47 chr4ptel1M 289379 G-TT-TTTGTTTTTTTG 289393 - - v (TTTG)n#Simpl 48 GTTTGTTTGTTTGTTTG 64 Matrix = Unknown Transitions / transversions = 0.00 (0/9) Gap_init rate = 0.08 (5 / 64), avg. gap size = 1.00 (5 / 5) 17 20.59 0.00 0.00 chr4ptel1M 289359 289392 (710608) (T)n#Simple_repeat 1 34 (0) m_b170s252i17 6548 chr4ptel1M 289359 TTGTTTTTGTTTGTTTGTTTGTTTTTGTTTTTTT 289392 v v v v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 34 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 554 18.95 0.00 6.60 chr4ptel1M 289405 289517 (710483) C MIRc#SINE/MIR (153) 115 10 m_b170s601i43 6549 chr4ptel1M 289405 GGGGTTAAGTGATTTGCCCAGAGTCACACAGCTAGGAAGTGTTAAGTGTC 289454 i i ii ------- v C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGC 73 chr4ptel1M 289455 TGAGGCTGGATTTGAACTCAGGTCCTCCTGATTTCAGGGCTGGTACTCTA 289504 v v v i i i i i i i v ii i v C MIRc#SINE/MIR 72 AGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTT 23 chr4ptel1M 289505 TCCACTGCACCAC 289517 C MIRc#SINE/MIR 22 TCCACTGCACCAC 10 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 21.11 CpG sites = 14, Kimura (unadjusted) = 22.34 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.06 (7 / 112), avg. gap size = 1.00 (7 / 7) 14 28.81 0.00 0.00 chr4ptel1M 290057 290102 (709898) (AAA)n#Simple_repeat 1 46 (0) m_b170s252i18 6550 chr4ptel1M 290057 AAAAAAAAAAAAGGTAAATAACTTAATTAAAAAAAAAAGAAGAAAA 290102 iiv v vvv vv i i (AAA)n#Simple 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 46 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 621 26.30 7.51 1.09 chr4ptel1M 290246 290418 (709582) MIR3#SINE/MIR 23 206 (2) m_b170s601i44 6551 chr4ptel1M 290246 AGAGCACTGATTTTGGAAGT-AGATGACCCAAGTTCAAATACTGGCTCTG 290294 v i -- i - iv iii v i v i MIR3#SINE/MIR 23 AGAGCACGGACT--GGGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTG 70 chr4ptel1M 290295 TCACTTACTATCTG----------GGTAAATCAACTCACTTCTTTGGAAC 290334 i v ?v ---------- i i vi i i iv MIR3#SINE/MIR 71 CCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCC 120 chr4ptel1M 290335 TCTGTTTCCTTATATGTAAAATCAGTTAGTTGGACTGGGTGACCTCTGTA 290384 v i v v vvi i i i ivi MIR3#SINE/MIR 121 TCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAG 170 chr4ptel1M 290385 GTTCATTTCACCTCTAAA--TCTATGGTCTTATGAT 290418 i v i v i v-- i ii MIR3#SINE/MIR 171 GTCCCTTCCAGCTCTGACATTCTATGATTCTATGAT 206 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.71 CpG sites = 28, Kimura (unadjusted) = 33.63 Transitions / transversions = 1.65 (28/17) Gap_init rate = 0.03 (5 / 172), avg. gap size = 3.00 (15 / 5) 42 14.86 1.08 4.44 chr4ptel1M 290765 290857 (709143) (AAGG)n#Simple_repeat 1 90 (0) m_b170s252i19 6552 chr4ptel1M 290765 AAGGAAGGAAGAAAAGAAGGAAAGAAGGAAAGGAGGGAGGAAGAGAAGGA 290814 i i i i i i - (AAGG)n#Simpl 1 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG-GAAGGA 49 chr4ptel1M 290815 A-GAAGAGAGAGAGAGGGAAGGAGGGAAGGAGGGAGGGAGGGAA 290857 - - - - i i i i i (AAGG)n#Simpl 50 AGGAAG-GA-AG-GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 90 Matrix = Unknown Transitions / transversions = 1.00 (11/0) Gap_init rate = 0.05 (5 / 92), avg. gap size = 1.00 (5 / 5) 27 15.27 0.00 0.00 chr4ptel1M 291059 291102 (708898) (A)n#Simple_repeat 1 44 (0) m_b170s252i20 6553 chr4ptel1M 291059 AAAAAAAAAAAAAAAAAAGAAAGAAAAGAAAAGAAAATTAAAAA 291102 i i i i vv (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 44 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 529 25.58 3.10 0.00 chr4ptel1M 291133 291261 (708739) MIR3#SINE/MIR 46 178 (30) m_b170s601i45 6554 chr4ptel1M 291133 GACCTGGACTCAGATCCTGCCTCTGACACCAACTT----TATGATCTTGG 291178 ii vii i v v i ?---- i i MIR3#SINE/MIR 46 GACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGG 95 chr4ptel1M 291179 GGAAATCCCTTAGCTTTCTTGGGCCTCAGTTTCCTCTTCTGTCAAATAAA 291228 v i v vi i iii v v i i MIR3#SINE/MIR 96 GCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAG 145 chr4ptel1M 291229 AGCCTGGGGCTAGTTAACCTCTGAGGTCCCTTC 291261 i vv v i v i i i MIR3#SINE/MIR 146 GGGGTTGGACTAGATGATCTCTAAGGTCCCTTC 178 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.39 CpG sites = 21, Kimura (unadjusted) = 32.59 Transitions / transversions = 1.75 (21/12) Gap_init rate = 0.01 (1 / 128), avg. gap size = 4.00 (4 / 1) 59 5.89 0.00 0.00 chr4ptel1M 291660 291730 (708270) (AGAGAC)n#Simple_repeat 1 71 (0) c_b170s251i2 6555 chr4ptel1M 291660 AGAGACAGAGTCAGAGACAGAGACAGAGTCAGAGACAGAGACAGAGTCAG 291709 v v v (AGAGAC)n#Sim 1 AGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAG 50 chr4ptel1M 291710 AGACAGAGTCAGAGACAGAGA 291730 v (AGAGAC)n#Sim 51 AGACAGAGACAGAGACAGAGA 71 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0) 289 26.92 3.85 0.00 chr4ptel1M 292666 292743 (707257) C L2d_3end#LINE/L2 (42) 474 394 m_b170s601i46 6556 chr4ptel1M 292666 TGCTGGGCACTAT-CTGGGGGCTGGGGAAAAC--CAAAACAACATAAAAT 292712 vi i - i v v ii --? ? ii i i C L2d_3end#LINE 474 TGCTCAGCACTGTGCTAGGCGCTGTGGGGAACGANAAAANAGTATAAGAC 425 chr4ptel1M 292713 ACAGCCTTTGCTCTCAAGGTGCTTAAATTCT 292743 ii i ii i v v v C L2d_3end#LINE 424 ATGGTCCCTGCCCTCAAGGAGCTTACAATCT 394 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.39 CpG sites = 15, Kimura (unadjusted) = 36.39 Transitions / transversions = 2.50 (15/6) Gap_init rate = 0.03 (2 / 77), avg. gap size = 1.50 (3 / 2) 22 5.72 5.41 0.00 chr4ptel1M 293361 293397 (706603) (AAAT)n#Simple_repeat 1 39 (0) m_b170s252i21 6557 chr4ptel1M 293361 AAATAAGCAAA-AAATAAATAAATAAATAAA-AAATAAA 293397 ii - - (AAAT)n#Simpl 1 AAATAAATAAATAAATAAATAAATAAATAAATAAATAAA 39 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 25 16.07 6.94 1.32 chr4ptel1M 293481 293552 (706448) (AATAA)n#Simple_repeat 1 76 (0) m_b170s252i22 6558 chr4ptel1M 293481 AAAAAAATATAATAAAAACAAATATAAATAAAAT--AATAAATAAAAATT 293528 v v vv - -- vv v (AATAA)n#Simp 1 AATAAAATAAAATAAAATAAAATA-AAATAAAATAAAATAAAATAAAATA 49 chr4ptel1M 293529 TAA-AAAAT-ATATAAAA-AATATAAA 293552 v - - v - v (AATAA)n#Simp 50 AAATAAAATAAAATAAAATAAAATAAA 76 Matrix = Unknown Transitions / transversions = 0.00 (0/10) Gap_init rate = 0.07 (5 / 71), avg. gap size = 1.20 (6 / 5) 15 9.12 0.00 0.00 chr4ptel1M 293863 293886 (706114) (GAT)n#Simple_repeat 1 24 (0) m_b170s252i23 6559 chr4ptel1M 293863 GATAATGATGATGGTGATGATGAT 293886 i i (GAT)n#Simple 1 GATGATGATGATGATGATGATGAT 24 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 183 12.21 4.55 6.98 chr4ptel1M 294451 294494 (705506) C L3#LINE/CR1 (267) 3832 3790 m_b170s601i47 6560 chr4ptel1M 294451 TGGAGCCACAGCCAGGGTAAGATTTAATA--TCTTCCACATGAAAG 294494 -- ii - i v-- v C L3#LINE/CR1 3832 TGGAGCCACA--CAGAATAAG-TCTAATCCCTCTTCCACATGACAG 3790 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 13.42 CpG sites = 3, Kimura (unadjusted) = 13.42 Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.09 (4 / 43), avg. gap size = 1.25 (5 / 4) 433 31.68 3.42 2.72 chr4ptel1M 295015 295306 (704694) C L1MC5a_3end#LINE/L1 (2131) 646 353 m_b170s551i12 6561 chr4ptel1M 295015 TCTCCTG-ATCCTGCTCATTTCACTCAGCATCAGTTCGTGTAAGTCTCTC 295063 ? i - i i iv i i vi vv v v ii v C L1MC5a_3end#L 646 TNTTCTGCACCTTGCTTTTTTCACTTAACAATATATCCTGGAGATCACTC 597 chr4ptel1M 295064 CAGACCTTTCT---GAAATCATCCTGTTGAGTCATTTCTTACAGAACAAT 295110 v ? vv v --- i v v--- v v - vvvv C L1MC5a_3end#L 596 CATANCAGTATATAGAGATCTTCCTC---ATTCCTTT-TTACAGCTGCAT 551 chr4ptel1M 295111 AATATTCCATAATATTCATATATCACAATTTATTCAGCCATTCTCTAATT 295160 i i vi i vv i i i i i v i iv C L1MC5a_3end#L 550 AGTACTCCATTGTGTGGATGTACCATAGTTTATTCAACCAGTCCCCTATT 501 chr4ptel1M 295161 GATGGGCATCCACTCAGTCTCCAGTTTCTGGCCATTACAAAGAGAGTTGT 295210 i iiivviv i i i v i v iv i i C L1MC5a_3end#L 500 GATGGACATTTGGGTTGTTTCCAGTCTTTTGCTATTACAAATAATGCTGC 451 chr4ptel1M 295211 TGTAAACA--TTTGTGCACATACAGGTCCCTTTCCCTTCTT-TAAG-ATT 295256 vi i i --i -- -- ?i iviv i -i? -i v C L1MC5a_3end#L 450 AATGAATAACCTTGTGCA--TAC--GTCNTTTCGTATTTTTGCNAGTGTA 405 chr4ptel1M 295257 TCTTTGGGATATAAGTCCAGTAGAAACACTGCTGGATCAAAGGGT--ATG 295304 i v vvi i v viiv i i -- C L1MC5a_3end#L 404 TCTTCGGGATAGATTCCTAGAAGTGGGATTGCTGGGTCAAAGGGTAAATG 355 chr4ptel1M 295305 CA 295306 C L1MC5a_3end#L 354 CA 353 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.80 CpG sites = 50, Kimura (unadjusted) = 43.07 Transitions / transversions = 1.25 (50/40) Gap_init rate = 0.05 (14 / 291), avg. gap size = 1.29 (18 / 14) 404 29.15 3.87 6.08 chr4ptel1M 295026 295361 (704639) C L1MC4a_3end#LINE/L1 (1997) 632 304 m_b170s551i13 6561 chr4ptel1M 295026 TGCTCATTTCACTCAGCATCAGTTCGTGTAAGTCTCTCCAGACC--TTTC 295073 iv i i vi vv v v i v v i -- iv C L1MC4a_3end#L 632 TGCTTTTTTCACTTAACAATATATCCTGGAAATCACTCCATATCAGTTCA 583 chr4ptel1M 295074 T-GAAATCATCCTGTTGAGTCATTTCTTACAGAACAATAATATTCCATAA 295122 - i v v--- v - i vvvv i i vi C L1MC4a_3end#L 582 TAGAGATCTTCCTC---ATTC-TTTTTTACAGCTGCATAGTACTCCATTG 537 chr4ptel1M 295123 TATTCATATATCACAATTTATTCAGCCATTCTCTAATTGATGGGCATCCA 295172 i vv i i i i i ? iv ?? ii C L1MC4a_3end#L 536 TGTGGATGTACCATAGTTTATTCAACCANTCTCCTATNNATGGGCATTTA 487 chr4ptel1M 295173 CTCAGTCTCCAGTTTCTGGCCATTACAAAGAGAGTTGTTGTAAACA--TT 295220 vviv i i v i v v v iv i ivi i i --i C L1MC4a_3end#L 486 GGTTGTTTCCAATATTTTGCAATTACAAACAATGCTGCAATGAATAACCT 437 chr4ptel1M 295221 TGTGCACATACAGGTCCCTTTCC-CTTCTTTAAGATT--TCTTTGGGATA 295267 i ---- ?vi vi- v v vi i v-- ii i C L1MC4a_3end#L 436 TGTGCATAT----GTNATTTTGTACATGTTGGAGGTGTATCTTCAGGGTA 391 chr4ptel1M 295268 TAAGTCCAGTAGAAAC---ACTGCTGGATCAAAGGGT--ATGCACAGTTT 295312 - v -- ii--- i i -- i --- C L1MC4a_3end#L 390 -AATTCC--TAGAAGTGGGATTGCTGGGTCAAAGGGTAAATGCATA---T 347 chr4ptel1M 295313 GATACCTTTTTGAGCATAGTTCCAGATTGCTCTTGAGACAGAATGGTTG 295361 - vi v v - v v i v i i---- ? v C L1MC4a_3end#L 346 G-TAGTTTTGTTAG-ATATTGCCAAATTCCCCTC----CANAAGGGTTG 304 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.29 CpG sites = 49, Kimura (unadjusted) = 38.29 Transitions / transversions = 1.14 (49/43) Gap_init rate = 0.08 (27 / 335), avg. gap size = 1.22 (33 / 27) 638 28.66 1.13 3.88 chr4ptel1M 295109 295373 (704627) C L1ME3G_3end#LINE/L1 (376) 548 291 m_b170s551i14 6561 chr4ptel1M 295109 ATAATATTCCATAATATTCATATATCACAATTTATTCAGCCATTCTCTAA 295158 i i vv i i i i i iv C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr4ptel1M 295159 TTGATGGGCATCCACTCAGTCTCCAGTTTCTGGCCATTACAAAGAGAGTT 295208 i ii vviv i i i v i v iv i C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr4ptel1M 295209 GTTGTAAACATTTGTGCACATACAGGTCCCTTTCC-CTTCTTTAAG-ATT 295256 ivi i iiv i i ?-- i v v - v v vii - C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATT 401 chr4ptel1M 295257 TCTTTGGGATATAAGTCCAGTAGAAACACTGCTGGATCAAAGGGTATGCA 295306 ? i v v?i ? v viiv i i i C L1ME3G_3end#L 400 TCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCG 351 chr4ptel1M 295307 CAGTTTGATACCTTTTTGA-GCATAGTTCCAGATTGCTCTTGAGACAGAA 295355 v i - --- i -iv v v i i i---- i C L1ME3G_3end#L 350 CATTTTAA-A---TTTTAATAGATACTGCCAAATTGCCCTC----CAAAA 309 chr4ptel1M 295356 TGGTTGGATGTATTCACA 295373 ? i v ivv i C L1ME3G_3end#L 308 NGGCTGTACCAATTTACA 291 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.85 CpG sites = 45, Kimura (unadjusted) = 38.27 Transitions / transversions = 1.61 (45/28) Gap_init rate = 0.05 (13 / 264), avg. gap size = 1.00 (13 / 13) 262 24.44 2.17 2.17 chr4ptel1M 295693 295784 (704216) L1MC_orf2#LINE/L1 104 195 (3099) m_b170s551i15 6562 chr4ptel1M 295693 ATCCAACAATATGTTGTTTATAAGAAACACATTTGTGATACTAAGAATTA 295742 i v i i v i vvi iv --i L1MC_orf2#LIN 104 ACCCAACTATATGTTGTCTACAAGAAACCCACTTTAAATATAAAGA--CA 151 chr4ptel1M 295743 CACAAAG-TTAAAA-TACAGAGCTGGAGAAGAATCTATTATGCT 295784 i v - - v ?i v ii v ii L1MC_orf2#LIN 152 CATATAGATTAAAAGTAAANGGATGGAGAAAGATATACCATGCT 195 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 30.63 CpG sites = 13, Kimura (unadjusted) = 30.63 Transitions / transversions = 1.44 (13/9) Gap_init rate = 0.04 (4 / 91), avg. gap size = 1.00 (4 / 4) 681 32.92 4.35 2.97 chr4ptel1M 295964 296561 (703439) L1PB1_3end#LINE/L1 25 630 (268) m_b170s551i16 6563 chr4ptel1M 295964 CTCAAATTCAAAT--GTATAAAAATAAGAGTCAATCCTCAATTGATAAGT 296011 -- -- i vi v v iv i-- ii v L1PB1_3end#LI 25 CTCAAA--CAAATCAGCAAGAAAAAAACAAACAATCCC--ATCAAAAAGT 70 chr4ptel1M 296012 AGCCAAAGGATAGGAGTAAACAGTTGTTAGAAGAATAAATCAAAGCAATC 296061 i v v i v i i i v i i v v vv iiiii L1PB1_3end#LI 71 GGGCTAAGGACATGAATAGACAATTCTCAAAAGAAGATATACAAATGGCC 120 chr4ptel1M 296062 AATAGTCACAGGAAAAAATGCTCTAAATCACTATTGATTAGAGAAATGAA 296111 i iv i v v v v i i v L1PB1_3end#LI 121 AACAAACATATGAAAAAATGCTCAACATCACTAATGATCAGGGAAATGCA 170 chr4ptel1M 296112 AATCAAAACAACTCGAAGGTACTACCTCACAAATATTGGAATGGCTAGCA 296161 v vvviv i i i vvv iivi --- L1PB1_3end#LI 171 AATCAAAACCACAATGCGATACCACCTTACTCCTGCAAGAATGGC---CA 217 chr4ptel1M 296162 TGA-CAGAAAA--AGAAAATGACAAATGCTGAAGGGGATGTGGCAAATTA 296208 i - i -- i i i i i iv v i ii vvi L1PB1_3end#LI 218 TAATCAAAAAATCAAAAAATAATAGATGTTGGCGTGGATGCGGTGAAAAG 267 chr4ptel1M 296209 AGTACCCTAATGCACTTTTGGT--GAATAGTAAACTGGTCCAGCCATTCT 296256 i v v vv i vi -- - i v i i v L1PB1_3end#LI 268 GGAACACTTCTACACTGCTGGTGGGAAT-GTAAACTAGTACAACCACTAT 316 chr4ptel1M 296257 GGAGAACAATTTGAAACTATGCCCAAAGGGTCATGAAACTGGA--TACCC 296304 i i v i i-- v iv i iv - i v i -- v L1PB1_3end#LI 317 GGAAAACAGTGTGGAG--ATTCCTTAAAGAAC-TAAAAGTAGAACTACCA 363 chr4ptel1M 296305 ATTGCTCTAGAAATACCACTAGTAGGTCTGAATCCCAGACAGATCAAAGA 296354 v v i v v v i v vv - -i -- L1PB1_3end#LI 364 TTTGATCCAGCAATCCCACTACTGGGTATCTA-CCCAGA-GGA--AAAGA 409 chr4ptel1M 296355 A----------AAGTAAGGTCCACTTACACAAAAACATTTATAGCAACAA 296394 ----------i iv i -- i viv ii i v L1PB1_3end#LI 410 AGTCATTATACGAAAAAGAT--ACTTGCACACGCATGTTTATAGCAGCAC 457 chr4ptel1M 296395 TTTTTGTGGTATCAAGGAATTAGAAATGAAGGAGATGCCCATCAATTGGA 296444 vv i iii vv ii vv i viiivvv i iiiv L1PB1_3end#LI 458 AATTCGCAATTGCAAAAATATGGAACCAGCCCAAATGCCCATCAATCAAC 507 chr4ptel1M 296445 AAATGACTGAACAAGCT---GTATATGATTATTATGGATTACTGCTGTGC 296491 i i iv i v i? --- ivv ii v i vv L1PB1_3end#LI 508 GAGTGGATAAAGAAANTGTGGTATATATATACCATGGAATACTACTCAGC 557 chr4ptel1M 296492 TACAAGGAATAATGAGCAGGATGGT-TTCAGAAAAACCTGGAAAGACTTA 296540 i i ii iv i-?vi i- iv ivi vi v i L1PB1_3end#LI 558 CATAAAAAGGAATGAA-NTAATGGCATTCGCAGCGACCTGGATGGAATTG 606 chr4ptel1M 296541 TGAACTGTTA---CAAGAGAAGTA 296561 vii i ---i v L1PB1_3end#LI 607 GAGACTATTATTCTAAGTGAAGTA 630 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 42.67 CpG sites = 108, Kimura (unadjusted) = 44.88 Transitions / transversions = 1.30 (108/83) Gap_init rate = 0.05 (27 / 597), avg. gap size = 1.63 (44 / 27) 881 31.86 3.34 1.94 chr4ptel1M 295998 296506 (703494) L1MB7_3end#LINE/L1 57 572 (359) m_b170s551i17 6563 chr4ptel1M 295998 CTCAATTGATAAGTAGCCAAAGGATAGGAGTAAACAGTTGTTAGAAGAAT 296047 i ? v i i v vv i i v v ivi v L1MB7_3end#LI 57 CCCAATTNAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAG 106 chr4ptel1M 296048 AAATCAAAGCAATCAATAGTCACAGGAAAAAATGCTCTAAATCACTATTG 296097 v vv iiiii iv v i v v i v v L1MB7_3end#LI 107 ATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCATTAGTC 156 chr4ptel1M 296098 ATTAGAGAAATGAAAATCAAAACAACTCGAAGGTACTACCTCACAAATAT 296147 i v v vvvi i i i vvi i L1MB7_3end#LI 157 ATTAGGGAAATGCAAATCAAAACCACAATGAGATACCACTTCACACCCAC 206 chr4ptel1M 296148 TGGAATGGCTAGCATGACAGAAAAAGAAAATGACAAATGCTGAAGGGGAT 296197 i i vv ? v i i v v i i i iv i L1MB7_3end#LI 207 TAGGATGGCTATAATNAAAAAGACAGACAATAACAAGTGTTGGCGAGGAT 256 chr4ptel1M 296198 GTGGCAAATTAAGTACCCTAATGCACTTTTGGT--GAATAGTAAACTGGT 296245 vi v vi v v i i vi -- - v L1MB7_3end#LI 257 GTGGAGAAATTGGAACCCTCATACATTGCTGGTGGGAAT-GTAAAATGGT 305 chr4ptel1M 296246 CCAGCCATTCTGGAGAACAATTTGAAACTATGCCCAAAGGGTCATGAAAC 296295 v ii i i i iv v - v i ii i--- L1MB7_3end#LI 306 GCAGCCGCTTTGGAAAACAGTTTGGCAGT-TCCTCAAAAAGTT---AAAC 351 chr4ptel1M 296296 -TGGA--TACCCAT-TGCTCTAGAAATACCACTAGTAGGTCTGAATCCCA 296341 - i -- - - vi i v v vv v iv i v L1MB7_3end#LI 352 ATAGAGTTA-CCATATGACCCAGCAATTCCACTCCTAGGTATATACCCAA 400 chr4ptel1M 296342 GACAGATCAAAGAAAAGTAAGGTCC--------ACTTACACAAAAACATT 296383 v i? ---- vvv v -------- ii vi ii L1MB7_3end#LI 401 GAGAANT----GAAAACATATGTCCACACAAAAACTTGTACACGAATGTT 446 chr4ptel1M 296384 TATAGCAACAATTTTTGTGGTATCAAGGAATTAGAAATGAAGGAGATGCC 296433 i i v v ii ii v v ii v i ii vvv i i L1MB7_3end#LI 447 CATAGCAGCATTATTCATAATAGCCAAAAAGTGGAAACAACCCAAATGTC 496 chr4ptel1M 296434 CATCAATTGGAAAATGACTGAACAA---GCTGTATATGATTATTATGGAT 296480 i ivi iv i --- iv vvv iv v L1MB7_3end#LI 497 CATCAACTGATGAATGGATAAACAAAATGTGGTATATCCATACAATGGAA 546 chr4ptel1M 296481 TACTGCTGTGCTACAAGGAATAATGA 296506 i ii vv i i ii iv L1MB7_3end#LI 547 TATTATTCGGCCATAAAAAGGAATGA 572 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 42.01 CpG sites = 85, Kimura (unadjusted) = 42.72 Transitions / transversions = 1.15 (85/74) Gap_init rate = 0.03 (16 / 508), avg. gap size = 1.69 (27 / 16) 14 23.55 4.76 3.12 chr4ptel1M 296899 296961 (703039) (TAAA)n#Simple_repeat 1 64 (0) m_b171s252i0 6564 chr4ptel1M 296899 TAACATAAATAAATGGATATATAAAGATAAT-AGGAAATATAGAATTTAA 296947 - ii v v - - iv v v v v (TAAA)n#Simpl 1 TAA-ATAAATAAATAAATAAATAAATA-AATAAATAAATAAATAAATAAA 48 chr4ptel1M 296948 -AAAGAGA-AAATAAA 296961 - v i - (TAAA)n#Simpl 49 TAAATAAATAAATAAA 64 Matrix = Unknown Transitions / transversions = 0.50 (4/8) Gap_init rate = 0.08 (5 / 62), avg. gap size = 1.00 (5 / 5) 502 35.70 4.50 0.93 chr4ptel1M 297014 297324 (702676) L2#LINE/L2 2554 2875 (207) m_b171s601i0 6565 chr4ptel1M 297014 ATCTTAGGAGCCATCCTAGATTCCTCACTATCTCTCACACCCCAAGTCCA 297063 i - i v i v v vi L2#LINE/L2 2554 ACCTT-GGAGTCATCCTTGACTCCTCTCTTTCTCTCACACCCCACATCCA 2602 chr4ptel1M 297064 ATATGGTGCCAATACCTGTTATTTC-ACCTGCTCAGCCCCTTGTAAATAT 297112 viiviiv vv iivi - v vv iiviv ivvi vi L2#LINE/L2 2603 ATCCATCAGCAAATCCTGTCGGCTCTACCTTCAAAATATATCCAGAATCC 2652 chr4ptel1M 297113 -ACCGCTTTCTCAGACAACGACACT--------CCTGGCTCAGACCTTCA 297153 - i - v- v vv -------- ii ii vi L2#LINE/L2 2653 GACCACTT-CTCAC-CACCTCCACTGCCACCACCCTGGTCCAAGCCACCA 2700 chr4ptel1M 297154 TCATCTCCCACCTGGAATATTGCAATGGG-TGCAGAGAGGTCTACCTGCC 297202 i i v i i v- v vi vv v i L2#LINE/L2 2701 TCATCTCTCGCCTGGATTACTGCAATAGCCTCCTAACTGGTCTCCCTGCT 2750 chr4ptel1M 297203 TCAGATCTCTCTATCCTCCAAGTCACCCTCCAATCAACCACTAAAGCAAT 297252 vivi iv ivi ? ivii ii v vv i vi i i ii L2#LINE/L2 2751 TCCACCCTTGCCCCCCTNCAGTCTATTCTCAACACAGCAGCCAGAGTGAT 2800 chr4ptel1M 297253 CTAACTAAAATGCAGATCCAACTATGTCACCCCATTACTCAAA---TTTC 297299 ivvi i i ii vi ii i vi i ---i i L2#LINE/L2 2801 CCTTTTAAAACGTAAGTCAGATCATGTCACTCCTCTGCTCAAAACCCTCC 2850 chr4ptel1M 297300 AGTGACTCCCCATCACCTCCAGGGT 297324 i i i v vii i L2#LINE/L2 2851 AATGGCTTCCCATCTCACTCAGAGT 2875 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 48.15 CpG sites = 65, Kimura (unadjusted) = 50.88 Transitions / transversions = 1.44 (65/45) Gap_init rate = 0.03 (8 / 310), avg. gap size = 2.12 (17 / 8) 320 26.70 3.37 17.95 chr4ptel1M 297790 297967 (702033) L2c_3end#LINE/L2 319 474 (4) m_b171s601i1 6565 chr4ptel1M 297790 CACTTATCCTGAATATAACTTACTTTGTA----CATATTTGCTTGT-TCT 297834 v ----- iiv ----iv i i ? - v L2c_3end#LINE 319 CACTTATCAT-----TAACTTGTATTGTAATTGTCTGTTTACNTGTCTGT 363 chr4ptel1M 297835 CTCCTCTATTAATCTGTGAGCTTCTAGAGAACATGGATTGTCTTTTACTT 297884 i i iv i v ii v ii v i i i L2c_3end#LINE 364 CTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTC 413 chr4ptel1M 297885 -TTTTTGTGTCTCTAACAATGAACACTTTGCATAGTGCTCAGCACATAGT 297933 - i i i -------------------i i iii L2c_3end#LINE 414 ATCTTTGTATCCC-------------------CAGCGCCTGGCACATAGT 444 chr4ptel1M 297934 AGGAACTTAAGTTTATTTATTTATTGAATTGAAT 297967 vi i --- vv i i - L2c_3end#LINE 445 AGGCGCTCAA---TAAATGTTTGTTGAA-TGAAT 474 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.67 CpG sites = 28, Kimura (unadjusted) = 33.86 Transitions / transversions = 2.55 (28/11) Gap_init rate = 0.18 (31 / 177), avg. gap size = 1.10 (34 / 31) 429 29.66 1.25 5.19 chr4ptel1M 297811 297970 (702030) L2d2_3end#LINE/L2 402 555 (0) m_b171s601i2 6565 chr4ptel1M 297811 ACTTTGTACATATTTGCTTGTTCTCTCCTCTATTAATCTGTGAGCTTCTA 297860 vi i i iiv v v i v i ivi i i v L2d2_3end#LIN 402 ACTTTTCACGTGTTTATGTCTTGTCTCCCCAACTAGATTGTAAGCTCCTT 451 chr4ptel1M 297861 GAGAACATGGAT--TGTCTTTTACTTTTTTTGTGTCTCTAACAATGAACA 297908 ii v i-- v i - i i iv ii ---- L2d2_3end#LIN 452 GAGGGCAGGGACCATGTCTTATACTTCTTT-GTATCCCCCACAGCG---- 496 chr4ptel1M 297909 CTTTGCATAGTGCTCAGCACATAGTAGGAACTTAAGTTTATTTATTTATT 297958 i v i iiv i vi i --- vv i L2d2_3end#LIN 497 CCTAGCACAGTGCCTTGCACACAGTAGGCGCTCAA---TAAATATTTGTT 543 chr4ptel1M 297959 GAATTGAATTGA 297970 v v L2d2_3end#LIN 544 GATTTGATTTGA 555 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.75 CpG sites = 28, Kimura (unadjusted) = 39.05 Transitions / transversions = 1.65 (28/17) Gap_init rate = 0.06 (9 / 159), avg. gap size = 1.11 (10 / 9) 184 30.39 1.90 16.67 chr4ptel1M 298328 298485 (701515) C L2d_3end#LINE/L2 (36) 480 343 m_b171s601i3 6566 chr4ptel1M 298328 ATTAAATGCCCA-CATTAGGTTGGGCAGCAGCAGGGACTGCAACCCAAAG 298376 i vi i - i iv i i - v ii --i i ?vv ?i C L2d_3end#LINE 480 ACTATGTGCTCAGCACTGTGCTAGGC-GCTGTGGGGA--ACGANAAAANA 434 chr4ptel1M 298377 ACA-AAGACAAATTAGTTCCTGTCCTCAAGTGGTTTGCATTCTACCAATC 298425 ii - --- i i i vi i i-------- C L2d_3end#LINE 433 GTATAAGACA---TGGTCCCTGCCCTCAAGGAGCTTA--------CAATC 395 chr4ptel1M 298426 TATCTGGGAGGA-AAGAGTAGAGAACATTTACATCTAAAATGTTTAGAAA 298474 vi ii - v ---- ---- iv i iiv i C L2d_3end#LINE 394 TAGTTGGGGAGACAAGACT----AAC----ACACATGAAACAATTAGAGA 353 chr4ptel1M 298475 GCAAATGCAAG 298485 i - i C L2d_3end#LINE 352 AC-AATACAAG 343 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.03 CpG sites = 30, Kimura (unadjusted) = 41.43 Transitions / transversions = 3.00 (30/10) Gap_init rate = 0.17 (26 / 157), avg. gap size = 1.00 (26 / 26) 72 0.00 0.00 0.00 chr4ptel1M 299233 299296 (700704) (C)n#Simple_repeat 1 64 (0) c_b171s251i0 6567 chr4ptel1M 299233 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 299282 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 50 chr4ptel1M 299283 CCCCCCCCCCCCCC 299296 (C)n#Simple_r 51 CCCCCCCCCCCCCC 64 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0) 248 32.40 10.68 3.32 chr4ptel1M 299411 299691 (700309) L2b_3end#LINE/L2 165 465 (1) m_b171s601i4 6568 chr4ptel1M 299411 TCTTCATCCCTAGGTGCCCAGCAGGCTCTTCCTCCTCCTTTCTGCCTCAG 299460 ii i i --vi ii vii i v v ivv i L2b_3end#LINE 165 TCCCCACCTCT--TCGCCTGGCCAACTCCTACTCATCCTTCAGGTCTCAG 212 chr4ptel1M 299461 ---AACCTTTGCTTT-----GGAGGCCCAATCAGGTACCACCT----CGG 299498 --- viv ii i i----- i vvi v -- v i---- L2b_3end#LINE 213 CTCAAATGTCACCTCCTCCGGGAAGCCCTCCCTG--ACCCCCCAGGCCGG 260 chr4ptel1M 299499 AGAAAAAGCCTTC-TCTACAGTCTCCTC---TCTGCCCTGGGATTCCCTT 299544 ivv iiv i - i-i i i i ---i i vv i --- L2b_3end#LINE 261 GTCAGGCGCCCTCCTCTG-GGCCCCCCCAGTCCTACCCTGCCACTC---T 306 chr4ptel1M 299545 GTGTTGTT-CCCTTTGCCTCCAT-TCTGTC-CCTCCAGGAGACTGTGAAC 299591 v i ?-iiv i ?i v - - i vv i L2b_3end#LINE 307 GGGTTATNATTGTCTGNTTACATGTCTGTCTCCCCCACTAGACTGTGAGC 356 chr4ptel1M 299592 CCCCAGAGGGCCTGGGC-GTG---ATGCTGT-CACC-TTGTTATCCCCAG 299635 i vv vv i - ? ---i vi - -i - L2b_3end#LINE 357 TCCGTGAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTGT-ATCCCCAG 405 chr4ptel1M 299636 GGCC-----CAGAGACTTGCACACAGAAAGCATTTGAGAAATGTCTGCAG 299680 v ----- ? v v v i ii iiiv i i iv L2b_3end#LINE 406 CGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTTGTTG 455 chr4ptel1M 299681 AACGGAATGGA 299691 i- i L2b_3end#LINE 456 AAT-GAATGAA 465 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.02 CpG sites = 55, Kimura (unadjusted) = 45.45 Transitions / transversions = 1.67 (55/33) Gap_init rate = 0.08 (23 / 280), avg. gap size = 1.74 (40 / 23) 274 25.42 5.33 8.22 chr4ptel1M 299542 299691 (700309) L2c_3end#LINE/L2 332 477 (1) m_b171s601i5 6568 chr4ptel1M 299542 CTTGTGTTGT-----TCCCTTTGCCTCCATTCTGTC-CCTCCAGGAGACT 299585 i ----- iv i ? v--- - vv L2c_3end#LINE 332 CTTGTATTGTAATTGTCTGTTTACNTG---TCTGTCTCCTCCACTAGACT 378 chr4ptel1M 299586 GTGAACCCCCAGAGGGCCTGGGC-GTGATGCTGT-CACCTTGTTATCCCC 299633 i i iv vv i - - vi i - i vv L2c_3end#LINE 379 GTGAGCTCCTTGAGGGCAGGGACCGTG-TCTTATTCATCTTTGTATCCCC 427 chr4ptel1M 299634 AGGGCCCAGAGACTTGCACACAGAAAGCATTTGAGAAATGTCTGCAGAAC 299683 v ------- v i v i ii ii v i iv i L2c_3end#LINE 428 AGCGCC-------TGGCACATAGTAGGCGCTCAATAAATGTTTGTTGAAT 470 chr4ptel1M 299684 GGAATGGA 299691 - i L2c_3end#LINE 471 -GAATGAA 477 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.76 CpG sites = 20, Kimura (unadjusted) = 31.84 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.11 (16 / 149), avg. gap size = 1.25 (20 / 16) 335 24.73 5.38 0.00 chr4ptel1M 299741 299833 (700167) MIR3#SINE/MIR 111 208 (0) m_b171s601i6 6569 chr4ptel1M 299741 TCCCTGGGCCTCGATTTCCTCACCTGTGAAAGGAGAGGGTTGGGTGAGA- 299789 i ii i i v i iiv - MIR3#SINE/MIR 111 TCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGAT 160 chr4ptel1M 299790 -GTCTCTGAGGTACCCACCAGTTC--ACCCTCTAAGA-CCCATAATCC 299833 -i i v iv i -- vi v -i i i i MIR3#SINE/MIR 161 GATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTATGATTC 208 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.57 CpG sites = 17, Kimura (unadjusted) = 31.57 Transitions / transversions = 2.83 (17/6) Gap_init rate = 0.04 (4 / 92), avg. gap size = 1.25 (5 / 4) 373 22.22 10.10 0.00 chr4ptel1M 300738 300836 (699164) C L2c_3end#LINE/L2 (6) 472 364 m_b171s601i7 6570 chr4ptel1M 300738 TCAATCTATAAACATTAATGAAGCTCCTACTATGTGCCAAGCACCG---- 300783 v v i v vi v i i i ---- C L2c_3end#LINE 472 TCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGA 423 chr4ptel1M 300784 TGCTAAG-----CAAG-CACAATCCCTGCCCTCAAGGAGCTGACAATCTA 300827 i v -----i - ii v i C L2c_3end#LINE 422 TACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTA 373 chr4ptel1M 300828 ACTAAGCAG 300836 iivi v C L2c_3end#LINE 372 GTGGAGGAG 364 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.09 CpG sites = 13, Kimura (unadjusted) = 26.83 Transitions / transversions = 1.44 (13/9) Gap_init rate = 0.03 (3 / 98), avg. gap size = 3.33 (10 / 3) 270 22.55 3.12 7.61 chr4ptel1M 301060 301155 (698845) MIRb#SINE/MIR 5 96 (172) m_b171s601i8 6571 chr4ptel1M 301060 GGGGCTGCCAGGTGGTGGCTCAGTGGACAGAGTGCTGGATCTGGAG-CAG 301108 v --- --- v ii v v i - MIRb#SINE/MIR 5 GGGGCAGC---GTGGTG---CAGTGGAAAGAGCACGGGCTTTGGAGTCAG 48 chr4ptel1M 301109 CAAGACCGGAGTTCAAATCTTACCTC--ATACTTACCAGGCTGTGCGAC 301155 vv v i i iiiv --vi i - i MIRb#SINE/MIR 49 ACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTA-GCTGTGTGAC 96 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 23.89 CpG sites = 11, Kimura (unadjusted) = 27.06 Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.09 (9 / 95), avg. gap size = 1.11 (10 / 9) 319 24.68 3.66 1.19 chr4ptel1M 301074 301155 (698845) MIRc#SINE/MIR 10 93 (175) m_b171s601i9 6571 chr4ptel1M 301074 GTGGCTCAGTGGACAGAGTGCTGGATCTGGAG-CAGCAAGACCGGAGTTC 301122 iv v ii ii - v v i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr4ptel1M 301123 AAATCTTACCTC--ATACTTACCAGGCTGTGCGAC 301155 i i iiiv --vi i - i MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTA-GCTGTGTGAC 93 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.34 CpG sites = 14, Kimura (unadjusted) = 31.22 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.04 (3 / 81), avg. gap size = 1.33 (4 / 3) 308 27.62 9.52 0.00 chr4ptel1M 301465 301569 (698431) L2d2_3end#LINE/L2 440 554 (1) m_b171s601i10 6572 chr4ptel1M 301465 TGTGAGCTCCTTGAGGGCAGGAGG---GGCTT-----TCTTTAGATCCC- 301505 i iiv--- v ----- iv - L2d2_3end#LIN 440 TGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACTTCTTTGTATCCCC 489 chr4ptel1M 301506 -GAAGCACTCAGCACAATGGCCAGAACTTAGCAGGTGCTTAATAAATGCT 301554 -iv i ii i v iv v vi i i i ii L2d2_3end#LIN 490 CACAGCGCCTAGCACAGTGCCTTGCACACAGTAGGCGCTCAATAAATATT 539 chr4ptel1M 301555 TGGTGCCTGGATCTG 301569 v vi v i L2d2_3end#LIN 540 TGTTGATTTGATTTG 554 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.54 CpG sites = 18, Kimura (unadjusted) = 35.55 Transitions / transversions = 1.64 (18/11) Gap_init rate = 0.04 (4 / 104), avg. gap size = 2.50 (10 / 4) 232 27.59 1.72 0.00 chr4ptel1M 301568 301625 (698375) MIRc#SINE/MIR 19 77 (191) m_b171s601i11 6573 chr4ptel1M 301568 TGGATAGAGAGCTG-ACCTAGGGCCAGGAAGACCCGAGTTCAAGCCTTGC 301616 v vi - i i i i i i i i ii v MIRc#SINE/MIR 19 TGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGG 68 chr4ptel1M 301617 TTCTGACAC 301625 i v MIRc#SINE/MIR 69 CTCTGCCAC 77 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.01 CpG sites = 12, Kimura (unadjusted) = 36.67 Transitions / transversions = 3.00 (12/4) Gap_init rate = 0.02 (1 / 57), avg. gap size = 1.00 (1 / 1) 599 22.20 14.53 0.51 chr4ptel1M 302174 302345 (697655) MIRc#SINE/MIR 28 223 (45) m_b171s601i12 6574 chr4ptel1M 302174 CACTGG---TGGTG-CAGGAAGAATCGAGTGGAAATCTAG--------AT 302211 --- v - vii i vvi i iv -------- i MIRc#SINE/MIR 28 CACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCAC 77 chr4ptel1M 302212 TTACTAGCTGTGTCACTCTGG-CAAGTTCCTTAACTCTGTCTG--CCTTG 302258 v ii - iv - v -- ii MIRc#SINE/MIR 78 TTACTAGCTGTGTGACCTTGGGCAAGTCACTTAAC-CTCTCTGAGCCTCA 126 chr4ptel1M 302259 ACTTTCTCATCTGTAAAATGGGGATAATAACA---GC---ACATACTTCA 302302 ii i i --- ---i v i MIRc#SINE/MIR 127 GTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCA 176 chr4ptel1M 302303 TAGA---GTTGTGGGAATCAAATAAGATAACATACAC-AAAGTGCTT 302345 i i--- i i i ii iii- i MIRc#SINE/MIR 177 CAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTT 223 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.94 CpG sites = 29, Kimura (unadjusted) = 27.64 Transitions / transversions = 3.22 (29/9) Gap_init rate = 0.06 (10 / 171), avg. gap size = 2.60 (26 / 10) 820 20.13 3.14 0.00 chr4ptel1M 302210 302368 (697632) MIR#SINE/MIR 72 235 (27) m_b171s601i13 6574 chr4ptel1M 302210 ATTTACTAGCTGTGTCACTCTGG-CAAGTTCCTTAAC-TCTGTCTGCCTT 302257 i v ii - v - v v i MIR#SINE/MIR 72 ACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTC 121 chr4ptel1M 302258 GACTTTCTCATCTGTAAAATGGGGATAATAACAGCACATACTTCATAGA- 302306 iii i i i v i i- MIR#SINE/MIR 122 AGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTCATAGGG 171 chr4ptel1M 302307 --GTTGTGGGAATCAAATAAGATAACATACACAAAGTGCTTAACACAGTG 302354 -- i i i i v i i iii i iv MIR#SINE/MIR 172 TTGTTGTGAGGATTAAATGAGTTAATACATGTAAAGCGCTTAGAACAGTG 221 chr4ptel1M 302355 CCTGGCACAAAATA 302368 v i MIR#SINE/MIR 222 CCTGGCACATAGTA 235 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 23.49 CpG sites = 24, Kimura (unadjusted) = 24.36 Transitions / transversions = 3.00 (24/8) Gap_init rate = 0.03 (4 / 158), avg. gap size = 1.25 (5 / 4) 185 25.64 0.00 0.00 chr4ptel1M 302336 302374 (697626) L2d2_3end#LINE/L2 490 528 (27) m_b171s601i14 6575 chr4ptel1M 302336 CAAAGTGCTTAACACAGTGCCTGGCACAAAATAGAAACT 302374 v i i i v v i ivi L2d2_3end#LIN 490 CACAGCGCCTAGCACAGTGCCTTGCACACAGTAGGCGCT 528 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.87 CpG sites = 6, Kimura (unadjusted) = 32.14 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 786 31.66 20.78 0.18 chr4ptel1M 302866 303327 (696673) C L3#LINE/CR1 (1) 4098 3542 m_b171s601i15 6576 chr4ptel1M 302866 ATAGGATCACAGAATTTAAGGGTTGAAAGGAAGCTCAGTGGCCATCTGCT 302915 i i v i i i v i v i iv C L3#LINE/CR1 4098 ATAGAATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGT 4049 chr4ptel1M 302916 TCAA------GTC--ATATAAGAAT-------AAAACATATTCAACAAGT 302950 i ------i -- ii i ------- v viiii C L3#LINE/CR1 4048 CCAACCTCCCATCCAATGCAGGAATCCCTTCTACAACATCCCTGACAAGT 3999 chr4ptel1M 302951 AGTCATC-AACCTTTGCTCAAAAACTAC-----ATAGGTAGGTAGGTAGC 302994 i - i i ii v iv ----- ii v v viv - C L3#LINE/CR1 3998 GGTCATCCAGCCTCTGCTTGAACACCTCCAGTGACGGGGAGCTCACTA-C 3950 chr4ptel1M 302995 CTCTGGGGTCTATACTTTCCATT--------------------GGGAAGT 303024 ?v i v viiv v --------------------i i C L3#LINE/CR1 3949 CTCNCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGATTGTTAGAAAGT 3900 chr4ptel1M 303025 TTTTCCTGGTATCAAGCTAAAATA-GCCTCTTT-----TTGCA------- 303061 i vi ii ii v- ii ----- v ------- C L3#LINE/CR1 3899 TCTTCCTTATATTGAGCCGAAATCTGCCTCCCTGTAACTTCCACCCATTG 3850 chr4ptel1M 303062 -------TTCTTCCCGCTAGGACCAAATGGAAAAA----------TCCTC 303094 ------- v v i ii v ii v ---------- i C L3#LINE/CR1 3849 GTCCTAGTTCTGCCCTCTGGAGCCACACAGAATAAGTCTAATCCCTCTTC 3800 chr4ptel1M 303095 CATATGACAAGCCTTCTCAGACTTGAAGG-AGACATCGT-TTTTCACTGA 303142 i iv vv v i i- vi i - i i v i C L3#LINE/CR1 3799 CACATGACAGCCCTTCAAATATTTGAAGACAGCTATCATGTCTCCTCTAA 3750 chr4ptel1M 303143 GTCTTCTCTTCTTCAG---------------TTCATTCAAA-GATGCTCG 303176 i --------------- v v- v v i C L3#LINE/CR1 3749 GTCTTCTCTTCTCCAGGCTAAACATCCCCAGTTCCTTCAACCGTTCCTCA 3700 chr4ptel1M 303177 TAGGACATG--CACAAAAGCCTTCATGATCGTGGTCGC-CTCCTCCAGAC 303223 v --iv v i v iv v - ii C L3#LINE/CR1 3699 TATGACATGGTTTCCAGACCCTTCACCATCCTGGTCGCTCTCCTCTGGAC 3650 chr4ptel1M 303224 AC--TTGGGTTTATTGATGTTCTTCTTAGGCCATGGTACCCACAACATAG 303271 i -- ivi i ii i i iivii ii v vv i C L3#LINE/CR1 3649 GCGCTCCAGTTTGTCAATGTCCCTCTTAAAATGTGGCGCCCAGAACTGAA 3600 chr4ptel1M 303272 CACAGTATTCCAGAGAAGGATTAATGAAGATCAAATGTAACGAGTTGAT- 303320 i i i viv vi i iv iviivi i ii i i viv - C L3#LINE/CR1 3599 CGCAATACTCCAGATGTGGTCTGACCAGCGCAGAGTACAGCGGGACTATT 3550 chr4ptel1M 303321 -CCTCCCT 303327 - C L3#LINE/CR1 3549 ACCTCCCT 3542 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.69 CpG sites = 93, Kimura (unadjusted) = 43.20 Transitions / transversions = 1.75 (93/53) Gap_init rate = 0.05 (21 / 461), avg. gap size = 4.62 (97 / 21) 244 35.72 14.39 0.32 chr4ptel1M 303090 303367 (696633) C L3b_3end#LINE/CR1 (300) 906 590 m_b171s601i16 6576 chr4ptel1M 303090 TCCTCCATATGACAAGCCTTCTCAGACTTGAAGG-AGACATC--GTTTTT 303136 i ii i i v vi v i-? vi i-- i?ii C L3b_3end#LINE 906 TCCTCTACGTAATAACCCTTCATATACTTGAAGACNGTTATTAAGTCNCC 857 chr4ptel1M 303137 CACTGAGTCTTCTCTTCT---------------TCAGTTCATTCAAAG-A 303170 - v i ---------------i v i vv-v C L3b_3end#LINE 856 C-CTCAGCCTTCTCTTCTCCAGGCTGAATAATCCCAGTTCCTTTAACCTT 808 chr4ptel1M 303171 TGCTCGTAGG--ACATGCACAAAAGCCTTCATGATCGTGGTCGC-CTCCT 303217 v i --v viv v ivv i v v iv v i - C L3b_3end#LINE 807 TCCTCATAGGTCCCATTTTCCAGCCCTTTAATCATTTTTGTTGCTCTCCT 758 chr4ptel1M 303218 CCAGA--CACTTGGGTTTATTGATGTTCTTCTTAGGCCATGGTACCCACA 303265 iii -- v ivii? v iv i i i i ii?ii ?i v C L3b_3end#LINE 757 CTGAACTCTCTCCAANTTCTCCACGTCCCTTTTAAANTGTGGNGCCCAGA 708 chr4ptel1M 303266 ACATAGCACAGTATTCCAGAGAAGGATTAATGAAGATCAAATGTAACGAG 303315 vv i i i ?vi? vi i iv iviivi i iv i i C L3b_3end#LINE 707 ACTGAACGCAGTACTCCAGNTGNGGCCTGACCAGCGCAGAGTAGAGCGGG 658 chr4ptel1M 303316 TTGAT--CCTCCCT---------GGCAG-----CTGCTGAGGAAGCCCCA 303349 v?? -- --------- ii----- i i v v v C L3b_3end#LINE 657 ANNATCACCTCCCTTGNTCTGTCGGCGATNCTTCTGTTAATGCAGCCCAA 608 chr4ptel1M 303350 GATGACCTGATTTTTTTT 303367 vi v v vi C L3b_3end#LINE 607 GATCGCATTAGCTTTTTT 590 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 48.48 CpG sites = 58, Kimura (unadjusted) = 53.20 Transitions / transversions = 1.41 (58/41) Gap_init rate = 0.04 (11 / 277), avg. gap size = 3.73 (41 / 11) 19 15.40 5.66 1.82 chr4ptel1M 303411 303463 (696537) (TAATCC)n#Simple_repeat 1 55 (0) m_b171s252i1 6577 chr4ptel1M 303411 TAATTCATAATCCTAATCCCAATCCTAACCCTAAT--TAACTGTAACCCT 303458 - v i i -- iiv i (TAATCC)n#Sim 1 TAA-TCCTAATCCTAATCCTAATCCTAATCCTAATCCTAATCCTAATCCT 49 chr4ptel1M 303459 AA-CCT 303463 - (TAATCC)n#Sim 50 AATCCT 55 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.06 (3 / 52), avg. gap size = 1.33 (4 / 3) 208 37.50 5.77 0.00 chr4ptel1M 303466 303569 (696431) C L3b_3end#LINE/CR1 (585) 621 512 m_b171s601i17 6576 chr4ptel1M 303466 TCAACGTAACCTAAAATGATATTAGCTTTTTTTGT--TTGC--CGAATCA 303511 i i i i i i vii v i--ii -- v iii C L3b_3end#LINE 621 TTAATGCAGCCCAAGATCGCATTAGCTTTTTTGGCAGCCGCGTCGCACTG 572 chr4ptel1M 303512 TCAACTCATATCAAACTTATATTCCA-TGAAATCCCCA-TTTTCCCTCAG 303559 iii ii i iiiv v - i i -v i iii v C L3b_3end#LINE 571 CTGACTCATATTGAGCTTGCGGTCAACTAAAACCCCCAGGTCTTTTTCAC 522 chr4ptel1M 303560 ATAAACTGTT 303569 i?i i C L3b_3end#LINE 521 ATGNGCTGCT 512 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 54.04 CpG sites = 32, Kimura (unadjusted) = 62.10 Transitions / transversions = 4.57 (32/7) Gap_init rate = 0.04 (4 / 103), avg. gap size = 1.50 (6 / 4) 380 21.72 11.72 2.88 chr4ptel1M 304599 304726 (695274) L2c_3end#LINE/L2 334 472 (6) m_b171s601i18 6578 chr4ptel1M 304599 TGTTTTGTA--TGTCTAGTCATTTACATGTCTGTC----CCATTATAGTA 304642 v -- i---- ? ---- i v v i L2c_3end#LINE 334 TGTATTGTAATTGTCTG----TTTACNTGTCTGTCTCCTCCACTAGACTG 379 chr4ptel1M 304643 TGAGCTTCTTGAGGCTAAGGCCTGT-TTTTATC--TTATTGAATCCTTAG 304689 i vi i v i - i i-- iv v ii L2c_3end#LINE 380 TGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTATCCCCAG 429 chr4ptel1M 304690 TGGCTAGCAC--AGTAAA----CAGTAAATGCTTGTTGATTGA 304726 i v i -- ii---- i i v L2c_3end#LINE 430 CGCCTGGCACATAGTAGGCGCTCAATAAATGTTTGTTGAATGA 472 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.47 CpG sites = 18, Kimura (unadjusted) = 26.73 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.08 (10 / 127), avg. gap size = 1.90 (19 / 10) 13 19.09 0.00 0.00 chr4ptel1M 305301 305330 (694670) (AAAGA)n#Simple_repeat 1 30 (0) m_b171s252i2 6579 chr4ptel1M 305301 AAAAACAAGAAAGGAAAAGAAATAAAAAGA 305330 i v i vi (AAAGA)n#Simp 1 AAAGAAAAGAAAAGAAAAGAAAAGAAAAGA 30 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 538 23.62 0.78 0.78 chr4ptel1M 305676 305803 (694197) MIR1_Amn#SINE/MIR 21 148 (82) m_b171s601i19 6580 chr4ptel1M 305676 GTAGATAGAAAGCTGGGTCGAGACTCAAGGAGACCTGCATTCAAATTCAG 305725 i ivi iii i i- vi ? ? i v MIR1_Amn#SINE 21 GTGGATAGAGCACTGGACTGGGACTCG-GGAGACCTGGGTTCNANTCCCG 69 chr4ptel1M 305726 TCTCAGATACTTACTAACCAGGTGACCATGGGCAAGGCA-TTAAACTCTG 305774 v v vi ?i i?i ii? v v - ? v v MIR1_Amn#SINE 70 GCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGTCACTTNACCTCTC 119 chr4ptel1M 305775 CTTCCTTCAGTTTCCTCATCTGTAAAATG 305803 iv?v i MIR1_Amn#SINE 120 TGNGCCTCAGTTTCCTCATCTGTAAAATG 148 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.89 CpG sites = 18, Kimura (unadjusted) = 31.12 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.02 (2 / 127), avg. gap size = 1.00 (2 / 2) 292 31.00 3.00 0.00 chr4ptel1M 305953 306052 (693948) MIRc#SINE/MIR 164 266 (2) m_b171s601i20 6581 chr4ptel1M 305953 CTTTCCTGCTTCACAGAAATTTTCTGAGAATTAAATAAGATAATATTTGT 306002 i v i i iiv v v i i i i v MIRc#SINE/MIR 164 CCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGT 213 chr4ptel1M 306003 -AGAGTATTTTGCAAACCTTAAAGCATTCTATTA--GGCAGCTGCTATTA 306049 - i iii i iv iii v iv -- vv v? i MIRc#SINE/MIR 214 GAAAGCGCTTTGTAAACTGTAAAGTGCTATACAAATGTAAGGNGTTATTA 263 chr4ptel1M 306050 TTA 306052 MIRc#SINE/MIR 264 TTA 266 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.44 CpG sites = 20, Kimura (unadjusted) = 42.48 Transitions / transversions = 1.82 (20/11) Gap_init rate = 0.02 (2 / 99), avg. gap size = 1.50 (3 / 2) 305 25.33 4.00 0.00 chr4ptel1M 306159 306233 (693767) C L2d2_3end#LINE/L2 (2) 553 476 m_b171s601i21 6582 chr4ptel1M 306159 AAATCAA-TCAATCAACATTTATTAAGTTTCCCTTGTGTGTTAGGCACTG 306207 - iv i i ivi ivi iv C L2d2_3end#LIN 553 AAATCAAATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTG 504 chr4ptel1M 306208 CTCTAGGTGC--TAGGGAAGCCAAAGAA 306233 iv i -- i i vv C L2d2_3end#LIN 503 TGCTAGGCGCTGTGGGGGATACAAAGAA 476 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.90 CpG sites = 12, Kimura (unadjusted) = 31.83 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.03 (2 / 74), avg. gap size = 1.50 (3 / 2) 281 28.41 2.27 0.00 chr4ptel1M 306323 306410 (693590) C L3#LINE/CR1 (325) 3774 3685 m_b171s601i22 6583 chr4ptel1M 306323 AAGATAATCATCATGTGTCCCCTGTGTCTTATGTTCTCCAGGCTATCTAT 306372 i iii v i iv v v vvi C L3#LINE/CR1 3774 AAGACAGCTATCATGTCTCCTCTAAGTCTTCTCTTCTCCAGGCTAAACAT 3725 chr4ptel1M 306373 -CTCATTTCTTTCAAATGATTCCCCTATAA-AGGGCTTCC 306410 - i v i vi v i i v i - v i C L3#LINE/CR1 3724 CCCCAGTTCCTTCAACCGTTCCTCATATGACATGGTTTCC 3685 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.66 CpG sites = 14, Kimura (unadjusted) = 36.47 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.02 (2 / 87), avg. gap size = 1.00 (2 / 2) 18 27.34 2.78 1.37 chr4ptel1M 307100 307171 (692829) (ATAA)n#Simple_repeat 1 73 (0) m_b171s252i3 6584 chr4ptel1M 307100 ATAAA-AAAAATATTCAT-AAGAACTGCACAAATAAATAAAAGAAATAAA 307147 - v v vv - v v iv i - v (ATAA)n#Simpl 1 ATAAATAAATAAATAAATAAATAAATAAATAAATAAAT-AAATAAATAAA 49 chr4ptel1M 307148 ACAAAAAGTAAAAAATTAAATAAA 307171 vv v i v v (ATAA)n#Simpl 50 TAAATAAATAAATAAATAAATAAA 73 Matrix = Unknown Transitions / transversions = 0.23 (3/13) Gap_init rate = 0.04 (3 / 71), avg. gap size = 1.00 (3 / 3) 12 11.68 10.81 0.00 chr4ptel1M 307179 307215 (692785) (GAAGTA)n#Simple_repeat 1 41 (0) m_b171s252i4 6585 chr4ptel1M 307179 GAAGTAGAAGTAG-ATTA-AA-TA-AATTAGAAGAGGAAGT 307215 - v - - - v vi (GAAGTA)n#Sim 1 GAAGTAGAAGTAGAAGTAGAAGTAGAAGTAGAAGTAGAAGT 41 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.11 (4 / 36), avg. gap size = 1.00 (4 / 4) 507 24.81 5.41 1.96 chr4ptel1M 307941 308088 (691912) L2d2_3end#LINE/L2 398 550 (5) m_b171s601i23 6586 chr4ptel1M 307941 TTCAACTTTCT-----TTTATATATTGTCTTCTTCCATTACATTGTAAGT 307985 i ii----- i v i i- v i v i L2d2_3end#LIN 398 TTTAACTTTTCACGTGTTTATGTCTTGTCTCCC-CAACTAGATTGTAAGC 446 chr4ptel1M 307986 TCCTTGAGGGCAGAGACTACTTTTCTTTTTCTTATTTGTCTCCTT---AG 308032 i i -- v v v v v ii--- L2d2_3end#LIN 447 TCCTTGAGGGCAGGGACCA--TGTCTTATACTTCTTTGTATCCCCCACAG 494 chr4ptel1M 308033 CAATTAGCATACTGCCTGATACATAGTAGTCACATAATAAATGTTTATTG 308082 ivi i v vii i v i vi i i L2d2_3end#LIN 495 CGCCTAGCACAGTGCCTTGCACACAGTAGGCGCTCAATAAATATTTGTTG 544 chr4ptel1M 308083 AATTGA 308088 v L2d2_3end#LIN 545 ATTTGA 550 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.88 CpG sites = 22, Kimura (unadjusted) = 30.91 Transitions / transversions = 1.57 (22/14) Gap_init rate = 0.03 (5 / 147), avg. gap size = 2.20 (11 / 5) 13 25.56 0.00 0.00 chr4ptel1M 308645 308681 (691319) (AAA)n#Simple_repeat 1 37 (0) m_b171s252i5 6587 chr4ptel1M 308645 AAATAAAAAGCTATAATAATAAAAAAAAAAAAAGAAA 308681 v ivv v v v i (AAA)n#Simple 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 37 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 200 25.81 4.84 0.00 chr4ptel1M 308921 308982 (691018) C L2#LINE/L2 (882) 2200 2136 m_b171s601i24 6582 chr4ptel1M 308921 GATGATCCAGTAAAGGAAACT---AAAGAGTGCTCAGACATGTAGGAGAA 308967 v v i i --- i i vi vv v i C L2#LINE/L2 2200 GAGGAACCAGCAAAGGAGACTGAGAAGGAGCGGCCAGTGAGGTAGGAGGA 2151 chr4ptel1M 308968 GATCCAGGAGAAAGT 308982 i v iv C L2#LINE/L2 2150 AAACCAGGAGAGTGT 2136 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.63 CpG sites = 8, Kimura (unadjusted) = 31.94 Transitions / transversions = 1.00 (8/8) Gap_init rate = 0.02 (1 / 61), avg. gap size = 3.00 (3 / 1) 18 23.41 0.00 0.00 chr4ptel1M 308983 309022 (690978) (A)n#Simple_repeat 1 40 (0) m_b171s252i6 6588 chr4ptel1M 308983 AAAAAAAAAAAAAAAAAATACAAAGAAGAGATGAAAATAA 309022 v v i i i vi v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 40 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 409 33.14 0.57 0.00 chr4ptel1M 310963 311137 (688863) L1ME4a_3end#LINE/L1 244 419 (452) m_b171s551i4 6589 chr4ptel1M 310963 TATTGATGGGAATGTGGAAAAACTGAGACACTATTGCATTATTGGTGGAG 311012 i ii i ii ?i v iv v vv i i ii ii L1ME4a_3end#L 244 TGTTGGCGAGGGTGTGGNGAAACGGGCACTCTCATACACTGCTGGTGGGA 293 chr4ptel1M 311013 TTGTGAAATAATCCAGCGTT-CTGGAGAGCAATTGGGAATTATGCCCAAA 311061 v i v ii v i v - i v v v iviv L1ME4a_3end#L 294 GTGTAAATTGGTACAACCTTTCTGGAGGGCAATTTGGCAATATGTATCAA 343 chr4ptel1M 311062 AGGTCATAAAACTGCACGTAACCTTTCATCCAGCAGTTTCACTGCTAGAT 311111 i i v v i? i v v i i i i v iv L1ME4a_3end#L 344 AAGCCTTAAAAATGTNCATACCCTTTGACCCAGTAATTCCACTTCTAGGA 393 chr4ptel1M 311112 TTATATCCCAAAGAGATCATAAAAGA 311137 v v i i i v v i L1ME4a_3end#L 394 ATTTATCCTAAGGAAATAATCAGAGA 419 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 44.97 CpG sites = 34, Kimura (unadjusted) = 46.07 Transitions / transversions = 1.42 (34/24) Gap_init rate = 0.01 (1 / 174), avg. gap size = 1.00 (1 / 1) 742 29.47 5.05 1.96 chr4ptel1M 311152 311646 (688354) L1MA10_3end#LINE/L1 124 633 (448) m_b171s551i5 6590 chr4ptel1M 311152 AGTTATAAGAAAAGGTGCTCTAAATCACTATTGATCAGAGAAATGCAAAT 311201 v v v v v v i L1MA10_3end#L 124 AGGTATATGAAAAGGTGCTCAACATCACTAATCATCAGGGAAATGCAAAT 173 chr4ptel1M 311202 TAAGACAACTCTGACATACCACTCTCAGACTGGCTAAGACAGC------- 311244 i i v vv v i - v iv i i ii ------- L1MA10_3end#L 174 CAAAACCACAATGAGATATCAC-CTCACACCTGTTAGGATGGCTATTATC 222 chr4ptel1M 311245 -----AGGAAAAGATAACA-------GAGGGGATGTGGGGAAACTGGAAC 311282 ----- iv ------- v i i ?? L1MA10_3end#L 223 AAAAAAACAAAAGATAACAAGTGTTGGCGAGGATGTGGAGAAANNGGAAC 272 chr4ptel1M 311283 ACTAATACTTAGTTGGTGAATTTGTGAATGGTTCCAGCCATTCTGGAAAG 311332 v vi viv iivv i ?v v v i v i L1MA10_3end#L 273 CCTTGTACACTGTTGGTGGGAATGTAAANTGGTGCAGCCACTATGGAAAA 322 chr4ptel1M 311333 CAATTTGGAACTATGCTCAAAAAGTTATCAAATTGCCCATACCTTTTGAT 311382 i v iv - v i -v v vv - v v L1MA10_3end#L 323 CAGTATGGAGGT-TCCTCAAAAAATTA-AAAATAGAAC-TACCATATGAT 369 chr4ptel1M 311383 CCAGCAGTATTTCTATTGGGCTTATATCCCAAAAAGATCTTAAAGGAGAG 311432 i viiv vi iv -- vi v vv ii L1MA10_3end#L 370 CCAGCAATCCCACTTCTGGGTATATATCC--AAAAGAATTGAAATCAGGA 417 chr4ptel1M 311433 ACAGGAACCCACATGTGCAAAAC--TGTTTATGGCAGCCCTCTTTGTAGT 311480 v vv vvv i v vvv -- i v vi v iii i L1MA10_3end#L 418 TCTCGAAGAGATATCTGCACTCCCATGTTCATTGCAGCATTATTCACAAT 467 chr4ptel1M 311481 GG-CAAGAAATTGGAAACTGAGTGGATGCCCATCAGTTGGA-GAATGACT 311528 i - v - vivv ii i - vi - iv L1MA10_3end#L 468 AGCCAAGATA-TGGAAACAACCTAAATGTCCATC-GACGGATGAATGGAT 515 chr4ptel1M 311529 AAATAAATTATGGTATACGAATGTGATGGAATATTATT--GTTCTATAAG 311576 v v i iiv iii -- iii v i L1MA10_3end#L 516 AAAGAAAATGTGGTATATACATACAATGGAATATTATTCAGCCTTAAAAA 565 chr4ptel1M 311577 AAACGATCATCAGGATGATTTCAGAGAGGCCTGGAGAGACTTGCAGAAAC 311626 i v ivv vv -iv vv v -i v vii i v i vv L1MA10_3end#L 566 AGAAGGAAATCCTG-CCATTTGCGACA-ACATGGATGAACCTGGAGGACA 613 chr4ptel1M 311627 TGATGCTGAGTGAAATGAGC 311646 v i i L1MA10_3end#L 614 TTATGCTAAGTGAAATAAGC 633 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.66 CpG sites = 64, Kimura (unadjusted) = 37.99 Transitions / transversions = 0.81 (64/79) Gap_init rate = 0.03 (17 / 494), avg. gap size = 2.06 (35 / 17) 923 27.65 4.88 1.18 chr4ptel1M 311156 311565 (688435) L1ME3G_3end#LINE/L1 124 548 (376) m_b171s551i6 6590 chr4ptel1M 311156 ATAAGAAAAGGTGCTCTAAATCACTATTGATCAGAGAAATGCAAATTAAG 311205 v i v vv v i i i L1ME3G_3end#L 124 ATATGAAAAGATGCTCAACCTCACTAGTAATCAGGGAAATGCAAATTAAA 173 chr4ptel1M 311206 ACAACTCTGACATACCACTCT--------CAGACTGGCTAAGAC-----A 311242 vv v i i -------- i v i i----- L1ME3G_3end#L 174 ACAACAATGAGATACCATTTTTCACCCATCAGATTGGCAAAAATTTAAAA 223 chr4ptel1M 311243 GCAGGAAAAGATAA-----CAGAGGGGATGTGGGGAAACTGGAACACTAA 311287 ?vv v v v?-----ii v i i v v v v L1ME3G_3end#L 224 GNTTGATAATATCNAGTGTTGGCGAGGGTGTGGGGAAACGGGTACTCTCA 273 chr4ptel1M 311288 TACTTAGTTGGTGAATTTGTGAATGGTTCCAGCCATTCTGGAAAGCAATT 311337 viv i iivv i v v v ? i ii L1ME3G_3end#L 274 TACACTGCTGGTGGGAGTGTAAATTGGTACAGCCNTTTTGGAGGGCAATT 323 chr4ptel1M 311338 TGGAACTATGCTCAAAAAGTTATCAAATTGCCCATACCTTTTGATCCAGC 311387 v v viviv v -- - v i i L1ME3G_3end#L 324 TGGCAGTATCTATTAAAATTTA--AAAT-GCGCATACCCTTTGACCCAGC 370 chr4ptel1M 311388 AGTATTTCTATTGGGCTTATATCCCAAAAAGAT-CTTAAAGGAGAG-ACA 311435 i viiv vi ? ?v v i ? i i - iiv viv v - L1ME3G_3end#L 371 AATTCCACTTCTNGGNATCTATCCTANAGAAATACTCGCACATGTGCACA 420 chr4ptel1M 311436 GGAACCCACATGTGCAAAACTGTTTATGGCAGCCCTCTTTGTAGTGGCAA 311485 i i ?--i i iiv i v vi v i i i L1ME3G_3end#L 421 AGGAN--GCATGTACAAGGATGTTCATTGCAGCATTGTTTGTAATAGCGA 468 chr4ptel1M 311486 GAAATTGGAAACTGAGTGGATGCCCATCAGTTGGAGAATGACTAAATAAA 311535 i vivv ii i i v i ii L1ME3G_3end#L 469 AAAATTGGAAACAACCTAAATGTCCATCAATAGGGGAATGGTTAAATAAA 518 chr4ptel1M 311536 TTATGGTATACGAATGTGATGGAATATTAT 311565 ivv iiv i L1ME3G_3end#L 519 TTATGGTATATCCATACTATGGAATACTAT 548 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.99 CpG sites = 59, Kimura (unadjusted) = 35.82 Transitions / transversions = 1.11 (59/53) Gap_init rate = 0.02 (10 / 409), avg. gap size = 2.50 (25 / 10) 274 35.90 1.71 0.00 chr4ptel1M 313295 313411 (686589) C L2#LINE/L2 (1070) 2012 1894 m_b171s601i25 6582 chr4ptel1M 313295 GAGATAATTGGTCATCTTAGAAAGAACAACTTCAGTTAAGAGGTGAGT-T 313343 i v v i iiv i ii i vi v i v-i C L2#LINE/L2 2012 GAGGTCATTGGTGACCTTGACAAGAGCAGTTTCGGTGGAGTGGTGGGGAC 1963 chr4ptel1M 313344 GGAAACTAGATTCAAG-GGATTGAAAAGTGAATAAGAATGGGGGAGGTAG 313392 i i iv vi - i v i v ii ivi i iv i C L2#LINE/L2 1962 GAAAGCCTGATTGGAGTGGGTTCAAGAGAGAATGGGAGGAGAGGAATTGG 1913 chr4ptel1M 313393 AGGCAATAAATCTAGACAA 313411 i iii i v C L2#LINE/L2 1912 AGACAGCGAGTATAGACAA 1894 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 47.22 CpG sites = 29, Kimura (unadjusted) = 52.96 Transitions / transversions = 2.23 (29/13) Gap_init rate = 0.02 (2 / 116), avg. gap size = 1.00 (2 / 2) 203 25.42 11.86 0.00 chr4ptel1M 313432 313490 (686510) C L2a_3end#LINE/L2 (55) 462 397 m_b171s601i26 6591 chr4ptel1M 313432 TAGGTGATGGATGTACAA----AACCAAAAC---CAAAAGTCTCTATCCT 313474 i v ivi i----i v --- i ii C L2a_3end#LINE 462 TAGGCGCTGGGGATACAGCAGTGAACAAAACAGACAAAAGTCCCTGCCCT 413 chr4ptel1M 313475 CAAGAGCCTTACATTC 313490 v iiv C L2a_3end#LINE 412 CATGGAGCTTACATTC 397 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.62 CpG sites = 10, Kimura (unadjusted) = 32.20 Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.03 (2 / 58), avg. gap size = 3.50 (7 / 2) 16 13.14 2.70 5.56 chr4ptel1M 314412 314448 (685552) (AT)n#Simple_repeat 1 36 (0) m_b171s252i7 6592 chr4ptel1M 314412 ATATCATATA-ACATAGAGATATAAATATAGTATATAT 314448 - - i v v v - (AT)n#Simple_ 1 ATAT-ATATATATATATATATATATATATA-TATATAT 36 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.08 (3 / 36), avg. gap size = 1.00 (3 / 3) 200 36.92 15.38 0.00 chr4ptel1M 314845 315104 (684896) L2d2_3end#LINE/L2 2 301 (254) m_b171s601i27 6593 chr4ptel1M 314845 TCCTTGACCTTTTGCCAACCTGTCTTTCCATCCCTGCTTCATATTAATCC 314894 vi i vviv ?i v i iii vi i v L2d2_3end#LIN 2 TCCACGATCTGGCCCCAACCTNCCTTTCCAGCCTTATCTCCCACTATTCC 51 chr4ptel1M 314895 CT---------CTTTTGCTTAGTCTAGAC------ATTCACTTTTTCACA 314929 i--------- i ii iviv i i ------ i v ii v i L2d2_3end#LIN 52 CCTNCACGAACCCTCCGCTCCAGCCAAACTGGTCTACTCACTGTCCCCCG 101 chr4ptel1M 314930 AACACAACAT-CACTTTTGCTTTTCTACGCCCT-GTTCA-G--ATTC--- 314971 iv v - i ? iv vii i i - i - --i --- L2d2_3end#LIN 102 AACACGCCTTGCGCNTTCCCGCCTCTGCGCCTTTGCTCACGCCGTTCCCC 151 chr4ptel1M 314972 ----------TGCTCTCCCGATCAC---CCAGTT-TTGAAAGCCCATCCT 315007 ---------- i i vv iv --- vi - iv v i i v L2d2_3end#LIN 152 CCGCCTGGAATGCCCTTCCCCTTCCTCTCCACCTATCCAAATCCTACCCA 201 chr4ptel1M 315008 TCCTCAAAGACCCATCTTGAATGATACCT---CCATAAAGTTTCCCATGG 315054 iv i v ii ?vi --- i i ii i v i L2d2_3end#LIN 202 TCCTTCAAGGCCCAGCTCAAATNCCACCTCCTCCGTGAAGCCTTCCCTGA 251 chr4ptel1M 315055 TTCCTTCACTCAACAATGGCCATTTCCTTCCCAGGACTCACAGAGCACTT 315104 iiv i vi vi? i ii vi i i i v i vi v ? L2d2_3end#LIN 252 CCACTCCAGCCCGNAGTGATCTCTCCCTCCTCTGAACTCCTATAGCANTT 301 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 49.35 CpG sites = 63, Kimura (unadjusted) = 56.33 Transitions / transversions = 1.91 (63/33) Gap_init rate = 0.04 (11 / 259), avg. gap size = 3.64 (40 / 11) 200 22.07 4.17 5.63 chr4ptel1M 315239 315310 (684690) C MIR#SINE/MIR (148) 114 44 m_b171s601i28 6594 chr4ptel1M 315239 AGAGAA-TAAAGGAACCTGCCCAAGTTCAAATATCC--TAGATGAGCAGA 315285 i- v v i v v i v i-- ii - C MIR#SINE/MIR 114 AGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTG-GCAGA 66 chr4ptel1M 315286 AGGCTGGACTTTGACACCCAGGCAG 315310 -- i iv i - C MIR#SINE/MIR 65 --GCCGGGATTCGA-ACCCAGGCAG 44 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 22.69 CpG sites = 9, Kimura (unadjusted) = 26.62 Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.08 (6 / 71), avg. gap size = 1.17 (7 / 6) 308 30.57 11.70 0.53 chr4ptel1M 315538 315708 (684292) C MER119#DNA/hAT-Charlie (393) 190 1 m_b171s502i0 6595 chr4ptel1M 315538 CATCATCAAATGAATTGTGGGGTGATTCCATGT-GAAACTG--AAGTGCC 315584 i i v i v i v i iiv - -- v i C MER119#DNA/hA 190 CGTCATCGAAAGGAATGTAGCGCGATCTAATGTTGAAACTGTGAACTACC 141 chr4ptel1M 315585 TTGTGCTAGT------------CCCCTACAGATGCTAAGAA---CAAGAA 315619 i v ------------vi v iii v --- viviv C MER119#DNA/hA 140 TCGAGCTAGTAGTTCGCGCGGTGTCCGACAGATGTCGAGTATCGCTGTGT 91 chr4ptel1M 315620 TTGCATTGAAAAATTTAAATCTCCC-CGGTGCCT-TATAAGTTTGCTGTG 315667 v v i v v v - i i- i i i i C MER119#DNA/hA 90 TTCCCTCGAAAATTTAAAATATCCCGCGGCGCCCCTGTGAGTTCGCTGCG 41 chr4ptel1M 315668 GTGCCCCCAGGGCATCTCAGTAAATACTTTGGGAATCAGGG 315708 i -i ii i iiv i v i iv C MER119#DNA/hA 40 GCGCCCC-GGGGCGCCTCGGCGCACAGTTTGGGAACCGCGG 1 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 26.95 CpG sites = 32, Kimura (unadjusted) = 40.78 Transitions / transversions = 1.60 (32/20) Gap_init rate = 0.04 (7 / 170), avg. gap size = 3.00 (21 / 7) 204 23.08 7.69 0.00 chr4ptel1M 316503 316554 (683446) MIRc#SINE/MIR 7 62 (206) m_b171s601i29 6596 chr4ptel1M 316503 AATATGGTGTGTTGGGTAGACTAC--G--TTGGAGTCAAGAAGACCTGGA 316548 i i iiv iv vi -- -- i i MIRc#SINE/MIR 7 AGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGG 56 chr4ptel1M 316549 TTCAAG 316554 i MIRc#SINE/MIR 57 TTCGAG 62 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.11 CpG sites = 9, Kimura (unadjusted) = 28.93 Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.04 (2 / 51), avg. gap size = 2.00 (4 / 2) 272 28.57 2.56 1.27 chr4ptel1M 316766 316843 (683157) C L2c_3end#LINE/L2 (41) 437 359 m_b171s601i30 6597 chr4ptel1M 316766 GCCAGGCAC-AGGGATACAGGGACAAAATGGGAAATATTCCTTTTCCTCA 316814 i -i ii ii - ii v iiv i vi C L2c_3end#LINE 437 GCCAGGCGCTGGGGATACAAAGATGAA-TAAGACACGGTCCCTGCCCTCA 389 chr4ptel1M 316815 AGAAGCTTACATTC-AATAGGGGAGAGAGA 316843 i i v - i i i v C L2c_3end#LINE 388 AGGAGCTCACAGTCTAGTGGAGGAGACAGA 359 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.02 CpG sites = 17, Kimura (unadjusted) = 38.79 Transitions / transversions = 3.40 (17/5) Gap_init rate = 0.04 (3 / 77), avg. gap size = 1.00 (3 / 3) 245 39.56 5.84 2.64 chr4ptel1M 316874 317130 (682870) C L2d2_3end#LINE/L2 (289) 266 2 m_b171s601i31 6597 chr4ptel1M 316874 TTCAGGAGGGAGCGGTTACTAACTAGACATGCCATAGGAGAGAATGCCTA 316923 ? i vv i i vvi -- i v vv iv ivii?iii i C L2d2_3end#LIN 266 TNCGGGCTGGAGTGGTCAGGGA--AGGCTTCACGGAGGAGGTGGNATTTG 219 chr4ptel1M 316924 AGTTGAGCCTTGAAGGAACCCACCTA---TCTTAAGAGGCACAGAAACAG 316970 i i ---iivv --- i vi v iiv iiv C L2d2_3end#LIN 218 AGCTGGGCCTTGAAGGA---TGGGTAGGATTTGGATAGGTGGAGAGGAAG 172 chr4ptel1M 316971 GGGAGGGAT-TTCCAGGCAGGAGACACACCCCTGGCAAAGACACAGAAGG 317019 i ii- i i iv iv vivi i i i v C L2d2_3end#LIN 171 GGGAAGGGCATTCCAGGCGGGGGGAACGGCGTGAGCAAAGGCGCAGAGGC 122 chr4ptel1M 317020 GGGAAACAGAATAGTG-ATTAGCTGAACAGCAA--AAA--------GCTG 317058 ?vv v vi i -i v vv i ii -- i -------- C L2d2_3end#LIN 121 GGGAANGCGCAAGGCGTGTTCGGGGGACAGTGAGTAGACCAGTTTGGCTG 72 chr4ptel1M 317059 GAATATATAATACATAAATGGGAGTCATGTAAAAAGAAAGTGTGGAAAGA 317108 iiiv vii v i i? v i vi -ii i v i i- i C L2d2_3end#LIN 71 GAGCGGAGGGTTCGTGNAGGGGAATAGTG-GGAGATAAGGC-TGGAAAGG 24 chr4ptel1M 317109 TAAGATAGAACTAGATTATGAA 317130 ? i v i ii i ii i C L2d2_3end#LIN 23 NAGGTTGGGGCCAGATCGTGGA 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 54.15 CpG sites = 65, Kimura (unadjusted) = 63.47 Transitions / transversions = 1.91 (65/34) Gap_init rate = 0.05 (12 / 256), avg. gap size = 1.83 (22 / 12) 257 40.75 7.07 2.02 chr4ptel1M 316970 317252 (682748) C L2#LINE/L2 (2) 3080 2784 m_b171s601i32 6597 chr4ptel1M 316970 GGGGAGGGATTTCCAGGCAGGAGACACACCCCTGGCAAAGACACAGAAGG 317019 i i vv ii iv v vvvv i v v i v C L2#LINE/L2 3080 GGGAAGAGCGTTCCAGGCAGAGGGAACAGCAAGTGCAAAGGCCCTGAGGC 3031 chr4ptel1M 317020 GGGAAACAGAATAGTG-ATTAGCTGAACAGCAAAAAG----------CTG 317058 ivvv vv i i -i v vv ii ---------- C L2#LINE/L2 3030 GGGAGCGTGCCTGGCGTGTTCGAGGAACAGCAAGGAGGCCAGTGTGGCTG 2981 chr4ptel1M 317059 GAATATATAATACATAAATGGGAGTCATGTAAAAAGAAAGTGTGGAAAGA 317108 iiiv --i iviii iv vvvv ii iivi vvii i i C L2#LINE/L2 2980 GAGCGGA--GTGAGCGAGGGGGAGAGTGGTAGGAGATGAGGTCAGAGAGG 2933 chr4ptel1M 317109 TAAGATAGAACTAGATTATGAAAAGGCCTCAATTCCCAGC-CAAGGAGTT 317157 vivi i i i v i- iivvvv vi-i v C L2#LINE/L2 2932 TAACGGGGGACCAGATCATGTAG-GGCCTTGTAGGCCATTGTAAGGACTT 2884 chr4ptel1M 317158 TA-----TATTTTAAATTAGATAGGGAGTCACTGAAGATCTTTGAGCAGC 317202 i----- i i i i v i i i i i ivi v C L2#LINE/L2 2883 TGGCTTTTACTCTGAGTGAGATGGGAAGCCATTGGAGGGTTTTGAGCAGA 2834 chr4ptel1M 317203 AAAAAGAAGTGGTCCCACATGTGCTTT---TGAGTTATTCAATTGGCAGC 317249 ii iv vi i iv v ii i ---v ii i i --- v C L2#LINE/L2 2833 GGAGTGACATGATCTGACTTACGTTTTAAAAGGATCACTC---TGGCTGC 2787 chr4ptel1M 317250 TGT 317252 C L2#LINE/L2 2786 TGT 2784 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 57.74 CpG sites = 66, Kimura (unadjusted) = 62.32 Transitions / transversions = 1.40 (66/47) Gap_init rate = 0.04 (11 / 282), avg. gap size = 2.36 (26 / 11) 192 17.73 6.15 4.55 chr4ptel1M 317326 317390 (682610) C L3#LINE/CR1 (912) 3187 3122 m_b171s601i33 6598 chr4ptel1M 317326 ATCTATATC-TTGATAAACGTGT-GAACTAACTCAGGGCCAAGCAGAGAT 317373 i vi - vi - - ivv v v v C L3#LINE/CR1 3187 ATCCAAGTCATTGATAAAAATGTTGAAC-AGGACAGGGCCAAGGACAGAG 3139 chr4ptel1M 317374 CCC--TGGCACGCTCCACT 317390 -- -- C L3#LINE/CR1 3138 CCCTGTGGCACG--CCACT 3122 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 20.25 CpG sites = 4, Kimura (unadjusted) = 20.25 Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.09 (6 / 64), avg. gap size = 1.17 (7 / 6) 245 26.09 4.35 0.00 chr4ptel1M 317399 317467 (682533) C Charlie4#DNA/hAT-Charlie (1) 3377 3306 m_b171s502i1 6599 chr4ptel1M 317399 AGGAATTCTCAGC---TTTTGGATCCTGCCCCTCTCTGGCAGTTTGGTAA 317445 ii i i --- vii v vv i i i i C Charlie4#DNA/ 3377 AGGGGTTCTTAACCTTTTTTGTGCCATGGACCCCTTTGGCAGTCTGGTGA 3328 chr4ptel1M 317446 AGTCCATGGAGCCCTTCTCGGA 317467 i i v i C Charlie4#DNA/ 3327 AGCCTATGGACCCCTTCTCAGA 3306 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 33.74 CpG sites = 13, Kimura (unadjusted) = 33.74 Transitions / transversions = 2.60 (13/5) Gap_init rate = 0.01 (1 / 68), avg. gap size = 3.00 (3 / 1) 369 24.30 0.00 1.87 chr4ptel1M 317480 317588 (682412) C Charlie4#DNA/hAT-Charlie (3238) 140 34 m_b171s502i2 6599 chr4ptel1M 317480 ATAATTTCAAGAAACACTAAATCACAGCTCTAGGTTGGTGAAAATAAAGA 317529 vv i ii iv i vv i C Charlie4#DNA/ 140 ATAATTGAAGGAAATGCTAAATTTCAGTTAGAGGTTAGTGAAAATAAAGA 91 chr4ptel1M 317530 TGTAGATTTTTAGCCATGTTAACTTCATAGATCCATTGAAATCTATCCAA 317579 - vv -ii v ii i vi v v C Charlie4#DNA/ 90 TGTA-ATTTTTTCCCAT-CCAAGTTCACGGACCCCCTGAATTCTATCCAC 43 chr4ptel1M 317580 GGCCCTTTT 317588 v ii C Charlie4#DNA/ 42 GGACCCCTT 34 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 28.29 CpG sites = 14, Kimura (unadjusted) = 29.76 Transitions / transversions = 1.17 (14/12) Gap_init rate = 0.02 (2 / 108), avg. gap size = 1.00 (2 / 2) 274 33.93 16.10 2.76 chr4ptel1M 317680 318064 (681936) C L3#LINE/CR1 (1066) 3033 2599 m_b171s601i34 6598 chr4ptel1M 317680 CCATCATGTAGCCCATCACTCTCTATCTTTCCCACAAGCAGAGCAAGAGA 317729 i vi vvi i vi v v v v C L3#LINE/CR1 3033 CTATCATCCAGCCCATATTTCTCCATCTTGTCCACAAGGATATCATGAGA 2984 chr4ptel1M 317730 GATTTCACTCAGAT--TTAGCAAAGAACTTGAT------CGTCT------ 317765 i ii- i --i v vi i v iv ------i ------ C L3#LINE/CR1 2983 GACTTTG-TCAAATGCCTTGCTGAAATCCAGATACACTNTGTCTACGGCA 2935 chr4ptel1M 317766 ---CCTTGCCCTACCAGTCT-GAAAGCCTGTCCAAAAAGGTGGGAAAGGA 317811 --- i vi - v v i v ---- v C L3#LINE/CR1 2934 TTCCCCTGATCTACCAGTCTAGTAACCCTATCAAAAAA----GGAAATGA 2889 chr4ptel1M 317812 GCGGAAAGGAACAAGGC-TATCATTAGTTAGTC--TGC---------ATG 317849 vvv ivvvii v i - i iv v ii -- ---------i C L3#LINE/CR1 2888 GGTTAGTTTGGCATGACTTGTTCTTAGTGAACCCATGCTGGCTCCTAGTG 2839 chr4ptel1M 317850 ATC-TAACATCCTTTTCTTGAAGT------------TTTGTTCCTATAAT 317886 -ivi v -- ------------ i ---- C L3#LINE/CR1 2838 ATCACCGCTTCCTTTTCT--AAGTGCTCACAAACCATCTGTT----TAAT 2795 chr4ptel1M 317887 AATACATTCTGGAATGTTAATAGAAATGGTGATCAAATGGATTGGACAAT 317936 v i i v ivii ii v vvi iivv ii v vi C L3#LINE/CR1 2794 AATCCGTTCTAGAATTTTGCCGGGGATCGACGTCAAGCTTACCGGTCTGT 2745 chr4ptel1M 317937 AGCTTACA-ACTCTGTTCTCTTCACCCTATT---ACCAGGT----CCTTC 317978 i ? - v ii ii i iv i v --- ?i ?---- v i C L3#LINE/CR1 2744 AGTTTNCAGAATCCATCTTTTTTCCCTTTTTAAAANTAGGNACNACATTT 2695 chr4ptel1M 317979 ACCC--TTGGGGAATTCT-ACATTGTTTTCTCTTTCCCTGGGCTCTCAAG 318025 i --i vvi vv -i iivi i vi i v ivi i C L3#LINE/CR1 2694 GCCCGTCTCCAGTCTTCTGGCACCTCTTCCGTTCTCCGTGATTTCTCAAA 2645 chr4ptel1M 318026 GA--------AGTAGCCTCGTCATTCACATCATCAAAGTCCTTCAGT 318064 -------- ii iii iv - vv iv i C L3#LINE/CR1 2644 GATTACCGACAGCGGTTCCGCGA-TCACATCTGCAAGTTCTTTCAGT 2599 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.83 CpG sites = 73, Kimura (unadjusted) = 47.51 Transitions / transversions = 1.35 (73/54) Gap_init rate = 0.07 (28 / 384), avg. gap size = 2.64 (74 / 28) 186 16.22 0.00 0.00 chr4ptel1M 318128 318164 (681836) C L3#LINE/CR1 (1612) 2487 2451 m_b171s601i35 6598 chr4ptel1M 318128 TTTCTTCTATTCTTTCCAATCTGAAAATCATTCTTCT 318164 v ii i i i C L3#LINE/CR1 2487 TTTGTTCTACCCTTTCCAGTCTGAAGATCATTCTCCT 2451 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 19.03 CpG sites = 5, Kimura (unadjusted) = 19.03 Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 39 32.78 1.85 2.48 chr4ptel1M 319020 319181 (680819) (AAG)n#Simple_repeat 1 161 (0) m_b171s252i9 6600 chr4ptel1M 319020 AAGAAAAACTAAAAAAAGGAGGAGAAAGAGGAAGAGAGGGGAAGAAGAGG 319069 i vv i i i i - i - ii i (AAG)n#Simple 1 AAGAAGAAGAAGAAGAAGAAGAAG-AAGAAGAAGA-AGAAGAAGAAGAAG 48 chr4ptel1M 319070 AAG-GGGAGAGGAAGAGGGGAAAGAGAGGAGAAGGAGGAGGAGGAGAGAA 319118 -i i i i iii - i i i i i ii (AAG)n#Simple 49 AAGAAGAAGAAGAAGAAGAAGAAGA-AGAAGAAGAAGAAGAAGAAGAAGA 97 chr4ptel1M 319119 AGAAG-AGTAG-GGGAGGAGAGGAAGGAGAAAGAAGAAAAAGAGGAGGAG 319166 - v -i i i i i - i i i i (AAG)n#Simple 98 AGAAGAAGAAGAAGAAGAAGAAGAAGAAG-AAGAAGAAGAAGAAGAAGAA 146 chr4ptel1M 319167 GAGGAGGAGGAAGAA 319181 i i i (AAG)n#Simple 147 GAAGAAGAAGAAGAA 161 Matrix = Unknown Transitions / transversions = 11.67 (35/3) Gap_init rate = 0.04 (7 / 161), avg. gap size = 1.00 (7 / 7) 59 19.21 4.83 0.66 chr4ptel1M 319036 319180 (680820) (AGG)n#Simple_repeat 1 151 (0) m_b171s252i10 6600 chr4ptel1M 319036 AGGAGGAGAAAGAGGAAGA-GAGG-GGAAGAAGAGGAAGGGGA-GAGGAA 319082 i i i - - i i i i - i (AGG)n#Simple 1 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG 50 chr4ptel1M 319083 GAGGGGAAAGA-GAGGAGAAGGAGGAGGAGGA-GAGAAAGAAGAGTAGG- 319129 i i i - i - i i i v - (AGG)n#Simple 51 GAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA 100 chr4ptel1M 319130 GGAGGA-GAGGAAGGAGAAAGAAGAAAAAGAGGAGGAGGAGGAGGAGGAA 319178 - - i i i ii i i (AGG)n#Simple 101 GGAGGAGGAGG-AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG 149 chr4ptel1M 319179 GA 319180 (AGG)n#Simple 150 GA 151 Matrix = Unknown Transitions / transversions = 22.00 (22/1) Gap_init rate = 0.06 (8 / 144), avg. gap size = 1.00 (8 / 8) 21 30.41 0.00 0.00 chr4ptel1M 319239 319296 (680704) (TT)n#Simple_repeat 1 58 (0) m_b171s252i12 6601 chr4ptel1M 319239 TTCTTTTTTTTTTTTTTTTTAATACTCACTTTTTTTTTTCTTTCCCCCTT 319288 i vv vi ivi i iiiii (TT)n#Simple_ 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr4ptel1M 319289 TTTTTTTT 319296 (TT)n#Simple_ 51 TTTTTTTT 58 Matrix = Unknown Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0) 18 8.72 0.00 0.00 chr4ptel1M 320646 320670 (679330) (A)n#Simple_repeat 1 25 (0) m_b171s252i13 6602 chr4ptel1M 320646 AAAAAAAAAAAAAAAAAAAGAAGAA 320670 i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAA 25 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 211 29.44 10.29 4.89 chr4ptel1M 321956 322130 (677870) C MIRb#SINE/MIR (81) 187 4 m_b171s601i36 6603 chr4ptel1M 321956 TCCTGGCGAAGACACTGCAGTGGTGGCCATTCCCTTCTCCGGCTGATCTT 322005 vi i vi v - v i vi viiv i ----- i C MIRb#SINE/MIR 187 TCCTCACAACAACCCTGC-GAGGTAGGTATTATTATCCCC-----ATTTT 144 chr4ptel1M 322006 ACAGATAAGGAAACTGAGGC-AAACGAG--TAAAAGACTCGGCCAGTGCC 322052 i -v iv -- ivi i v iv i C MIRb#SINE/MIR 143 ACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTC 94 chr4ptel1M 322053 ACCCAGCTA------GGCAAGGTCTGGGGCTGATGAA--CGGATC--CCC 322092 v ------ ii - i ii --i -- i i --i i C MIRb#SINE/MIR 93 ACACAGCTAGTAAGTGGCAGAG-CCGGGATT--CGAACCCAGGTCTGTCT 47 chr4ptel1M 322093 GATTCCAGGTCCCGCGCTCT----GC-GCACTACGGCGTCCCT 322130 i iiv i ----i - i vi i C MIRb#SINE/MIR 46 GACTCCAAAGCCCGTGCTCTTTCCACTGCACCACGCTGCCCCT 4 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.52 CpG sites = 34, Kimura (unadjusted) = 39.64 Transitions / transversions = 2.27 (34/15) Gap_init rate = 0.09 (16 / 174), avg. gap size = 1.69 (27 / 16) 280 26.71 3.33 7.64 chr4ptel1M 322001 322150 (677850) C MIR1_Amn#SINE/MIR (83) 147 4 m_b171s601i38 6603 chr4ptel1M 322001 ATCTTACAGATAAGGAAACTGAGG--CAAACGAGTAAAA-GACTCGGCCA 322047 i i -- i vii ? i- i v C MIR1_Amn#SINE 147 ATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGCCCA 98 chr4ptel1M 322048 GTGCCACCCAGCTAGGCAAGGTCTGGGGCTGATGAACGGATCCCCGA--T 322095 iv i ? -? ? vvvii i i i- ?i? v v i-- C MIR1_Amn#SINE 97 AGGTCACNCAGC-NGGCNAGTGGCAGAGCCGG-GANTNGAACCCAGGTCT 50 chr4ptel1M 322096 TCCAGGTCCCGCGCTCTGCGCACTACGGCGTCCCTTAGAGGTCCGCACTG 322145 i ii i- ii v i v ----- vi --- i C MIR1_Amn#SINE 49 CCCGAGTCCCA-GTCCAGTGCTCTA-----TCCACTAGA---CCACACTG 9 chr4ptel1M 322146 CCTTC 322150 i C MIR1_Amn#SINE 8 CCTCC 4 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.11 CpG sites = 26, Kimura (unadjusted) = 36.61 Transitions / transversions = 2.36 (26/11) Gap_init rate = 0.09 (14 / 149), avg. gap size = 1.14 (16 / 14) 294 24.53 10.74 2.29 chr4ptel1M 322001 322121 (677879) C MIRc#SINE/MIR (123) 145 15 m_b171s601i37 6603 chr4ptel1M 322001 ATCTTACAGATAAGGAAACTGAGGC-AAACGAG--TAAAAGACTCGGCCA 322047 i i -v iv -- iv i v C MIRc#SINE/MIR 145 ATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCA 96 chr4ptel1M 322048 GTGCCACCCAGCTA------GGCAAGGTCTGGGGCTGATGAA--CGGATC 322089 iv i v ------ ii - i i --i -- i i C MIRc#SINE/MIR 95 AGGTCACACAGCTAGTAAGTGGCAGAG-CCGGGACT--CGAACCCAGGTC 49 chr4ptel1M 322090 --CCCGATTCCAGGTCCCGCGCTCTGCGCACTAC 322121 -- i i i v i viv i C MIRc#SINE/MIR 48 TTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGC 15 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.42 CpG sites = 20, Kimura (unadjusted) = 30.97 Transitions / transversions = 2.22 (20/9) Gap_init rate = 0.07 (8 / 120), avg. gap size = 2.00 (16 / 8) 25 23.57 3.49 2.30 chr4ptel1M 322950 323035 (676965) (AGGAGG)n#Simple_repeat 1 87 (0) m_b171s252i14 6604 chr4ptel1M 322950 AGGAGGGGGGGGAAGAGGGGAAGGAGG-GGAGTCAAGAAGGAGGAAAAGG 322998 i i i i i - --i i ii (AGGAGG)n#Sim 1 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG--GAGGAGGAGGAGGAGG 48 chr4ptel1M 322999 -GGTCAAGAAGGGGGAGGAGGGGGAGGAGG-GCAGGAGG 323035 - vvi i i i - v (AGGAGG)n#Sim 49 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGG 87 Matrix = Unknown Transitions / transversions = 4.33 (13/3) Gap_init rate = 0.06 (5 / 85), avg. gap size = 1.00 (5 / 5) 191 18.75 0.00 0.00 chr4ptel1M 323405 323436 (676564) C MIR#SINE/MIR (12) 250 219 m_b171s601i39 6605 chr4ptel1M 323405 CATTTATTAAGCACTTAATGTGTGCCAAGAAC 323436 i i v i i v C MIR#SINE/MIR 250 CATTTATTGAGCGCTTACTATGTGCCAGGCAC 219 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 18.14 CpG sites = 4, Kimura (unadjusted) = 22.07 Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 329 31.69 1.38 4.26 chr4ptel1M 323680 323824 (676176) L2d2_3end#LINE/L2 170 310 (245) m_b171s601i40 6606 chr4ptel1M 323680 CTCTTTATTTCCATTTGTGGATAATCTTTTTTTTCCTTCAAGACCCAGCA 323729 i iv i ii i vv - i viiiv i v L2d2_3end#LIN 170 CCCTTCCTCTCCACCTATCCA-AATCCTACCCATCCTTCAAGGCCCAGCT 218 chr4ptel1M 323730 GAGGAGCTGCCTTCTCCATGAAGGCTTTGCTGATTTCCCTCTGCCAAAAG 323779 v iiv? ii i i v iv iiv i - v vi? L2d2_3end#LIN 219 CAAATNCCACCTCCTCCGTGAAGCCTTCCCTGACCACTC-CAGCCCGNAG 267 chr4ptel1M 323780 GAATTTCTCCCTCCTC--AGCTTTTCCTAGAGCATTCTGTCATTTGT 323824 vi i -- i --- v ? - i ii i L2d2_3end#LIN 268 TGATCTCTCCCTCCTCTGAAC---TCCTATAGCANT-TATTGTCTGT 310 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.93 CpG sites = 29, Kimura (unadjusted) = 44.71 Transitions / transversions = 1.93 (29/15) Gap_init rate = 0.05 (7 / 144), avg. gap size = 1.14 (8 / 7) 483 28.56 4.17 0.81 chr4ptel1M 323908 324027 (675973) C L2b_3end#LINE/L2 (8) 458 335 m_b171s601i41 6607 chr4ptel1M 323908 ATTAAATAAACATCAATTAAGGACCTACTATACACTAGGCACTGTGTTAA 323957 v i i iv i i vi i iii i ? i i C L2b_3end#LINE 458 ATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAG 409 chr4ptel1M 323958 GCTCTAGGAATACAAAGA-----AAGGCAAAAGTTAGTCCCTGCCCTGAT 324002 v i i iv i----- i - i v?ii v i C L2b_3end#LINE 408 GCGCTGGGGATACAGCGGTGAACAAGAC-AGACNCGGTCCCTGCCCTCAC 360 chr4ptel1M 324003 GGGACTCACAATCTAATGGGAGAGA 324027 ii i i i C L2b_3end#LINE 359 GGAGCTCACAGTCTAGTGGGGGAGA 335 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.26 CpG sites = 27, Kimura (unadjusted) = 40.03 Transitions / transversions = 3.86 (27/7) Gap_init rate = 0.02 (2 / 119), avg. gap size = 3.00 (6 / 2) 194 27.66 0.00 0.00 chr4ptel1M 324473 324519 (675481) C MIRb#SINE/MIR (8) 260 214 m_b171s601i42 6608 chr4ptel1M 324473 AGTCAGCATTTATTAAGTAGCTACAATGTGCCTGGAACTGTGTAAAG 324519 ii v i iivi v v v iv C MIRb#SINE/MIR 260 AGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAG 214 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.51 CpG sites = 7, Kimura (unadjusted) = 35.09 Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 308 27.94 4.38 5.93 chr4ptel1M 324480 324616 (675384) C L2d2_3end#LINE/L2 (19) 536 402 m_b171s601i43 6609 chr4ptel1M 324480 ATTTATTAAGTAGCTACAATGTGCCTGGAACTGTGTAAAGTTC---AGGA 324526 i iiv vi vv v iv i iv ---i i C L2d2_3end#LIN 536 ATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGTGGGG 487 chr4ptel1M 324527 TATACAAAGAAAGAGCCCCAAGAAAGGG--CCTGCCCTCAAGAAGCAAAC 324574 v iv ----i v v -- i vv C L2d2_3end#LIN 486 GATACAAAGAAGTA----TAAGACATGGTCCCTGCCCTCAAGGAGCTTAC 441 chr4ptel1M 324575 CATCTCA-TAGGGAGACAAATCAGAATTTTCCATGTGCAAAAT 324616 v vi- i iv v ----v i v i C L2d2_3end#LIN 440 AATCTAGTTGGGGAGACAAGACATAA----ACACGTGAAAAGT 402 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.62 CpG sites = 17, Kimura (unadjusted) = 35.18 Transitions / transversions = 0.89 (17/19) Gap_init rate = 0.08 (11 / 136), avg. gap size = 1.27 (14 / 11) 326 36.50 8.85 1.93 chr4ptel1M 324727 325212 (674788) C L2#LINE/L2 (0) 3082 2564 m_b171s601i44 6609 chr4ptel1M 324727 GGGGGAGAGGCAGTGGGAGAAAGGAGGAACTTCGAGATCCAAGA----GA 324772 iii - vvv iv ii vv i vv v i---- C L2#LINE/L2 3082 GGGGGAAGAGC-GTTCCAGGCAGAGGGAACAGCAAGTGCAAAGGCCCTGA 3034 chr4ptel1M 324773 GGCCGG-GAGTGCT----GTGTGGAAAGATCAACCAGAAGACAAGGCTCA 324817 v - v i---- vvi i v i v i i v vv vi C L2#LINE/L2 3033 GGCGGGAGCGTGCCTGGCGTGTTCGAGGAACAGCAAGGAGGCCAGTGTGG 2984 chr4ptel1M 324818 CTGGATTACAGAGTG--CATGGAGGACCATGAGATGTAAGAA--GACTGT 324863 --i i -- iv i ---- vv i i-- vvvi C L2#LINE/L2 2983 CTGGA--GCGGAGTGAGCGAGGGGGA----GAGTGGTAGGAGATGAGGTC 2940 chr4ptel1M 324864 AAAGAGAGAA---GGGGCCACATTATGCAAGGCTTTAAATATCAA-GCAA 324909 i iv --- i v i i i i iv vii v- i C L2#LINE/L2 2939 AGAGAGGTAACGGGGGACCAGATCATGTAGGGCCTTGTAGGCCATTGTAA 2890 chr4ptel1M 324910 GAGGTTTGA-TTTCATTCTGGAGCTA-ATCAGGAGCTGT-GGGGGATTAT 324956 iiv i- i i - iv - vi i ii - i i - C L2#LINE/L2 2889 GGACTTTGGCTTTTACTCTG-AGTGAGATGGGAAGCCATTGGAGGGTT-T 2842 chr4ptel1M 324957 CAAACAGGGGA-CAATAAAGACAGACCTGTATTTTAGGAG-ATCAGTTTG 325004 ii i i -ii i viiv v i iii ii - v i C L2#LINE/L2 2841 TGAGCAGAGGAGTGACATGATCTGACTTACGTTTTAAAAGGATCACTCTG 2792 chr4ptel1M 325005 ACACCAGAGAAGAGGATGGACTGAAGAGGGGAAAGAATTGAAGCAGAGGG 325054 i vv v v vv i i ? i v ii v i i C L2#LINE/L2 2791 GCTGCTGTGTTGAGAATAGACTGNAGGGGGGCAAGGGTGGAAGCAGGGAG 2742 chr4ptel1M 325055 ATGAATCAGCAGGTTATT--------------AAGGG--GATGAGAGTCT 325088 iv i i v i --------------i i -- ivi ii C L2#LINE/L2 2741 ACCAGTTAGGAGGCTATTGCAGTAATCCAGGCGAGAGATGATGGTGGCTT 2692 chr4ptel1M 325089 G---CAGGGCAGTAATGGTATGACAGGAGAGAA--GGCGGGATCCAAGAA 325133 --- ii iiii iviivv v -- iv i vi v C L2#LINE/L2 2691 GGACCAGGGTGGTGGCAGTGGAGGTGGTGAGAAGTGGTCGGATTCTGGAT 2642 chr4ptel1M 325134 ATGCTACAAAGGTGGAAACAACAGGATTCAACTACTGATCCCACGTGGGA 325183 ii vii i iv i iiviv iv ivv i i C L2#LINE/L2 2641 ATATTTTGAAGGTAGAGCCGACAGGATTTGCTGATGGATTGGATGTGGGG 2592 chr4ptel1M 325184 GGCTGAGAGACAGTGAGGAGCTGAGGGTG 325212 v - v v iii i C L2#LINE/L2 2591 TG-TGAGAGAAAGAGAGGAGTCAAGGATG 2564 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 50.50 CpG sites = 109, Kimura (unadjusted) = 53.29 Transitions / transversions = 1.68 (109/65) Gap_init rate = 0.05 (26 / 485), avg. gap size = 2.04 (53 / 26) 309 20.69 0.00 0.00 chr4ptel1M 325249 325306 (674694) MIRb#SINE/MIR 197 254 (14) m_b171s601i45 6610 chr4ptel1M 325249 ATAATATTTGTAAAGTCCTTAGTACAGTGCCTGGCACATTTTAGAAGTTC 325298 iiv iv i vv iiv i MIRb#SINE/MIR 197 ATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTC 246 chr4ptel1M 325299 AATAAATG 325306 MIRb#SINE/MIR 247 AATAAATG 254 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 22.32 CpG sites = 7, Kimura (unadjusted) = 24.58 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0) 309 24.75 17.82 0.00 chr4ptel1M 325344 325444 (674556) C L2#LINE/L2 (576) 2506 2388 m_b171s601i46 6609 chr4ptel1M 325344 GGAAAGGTTA--GGAGGA--AGG-----GGAAGAAGATAATGAGTTCAAT 325384 i ii i-- -- ----- ii v v i C L2#LINE/L2 2506 GGGAAGACTGCGGGAGGAGCAGGTTTGAGGGGGAAGATCAGGAGTTCAGT 2457 chr4ptel1M 325385 TTTAGACATGTTGAATTTAAAATATTTA---------CAATTCAAGATGT 325425 i i i i i iii --------- v vi C L2#LINE/L2 2456 TTTGGACATGTTAAGTTTGAGATGCCTATTAGACATCCAAGTGGAGATGT 2407 chr4ptel1M 325426 CCAACAGGCAATTGGACAT 325444 v ii i i C L2#LINE/L2 2406 CGAGTAGGCAGTTGGATAT 2388 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.09 CpG sites = 20, Kimura (unadjusted) = 32.09 Transitions / transversions = 4.00 (20/5) Gap_init rate = 0.04 (4 / 100), avg. gap size = 4.50 (18 / 4) 186 31.88 0.00 4.55 chr4ptel1M 325633 325701 (674299) C L2#LINE/L2 (2461) 621 556 m_b171s601i47 6609 chr4ptel1M 325633 GGGTGAAGGAACTAGGAAAAGCCTGGAAATGGGGATGGGAAGTGAGGAGT 325682 v i i vvii vi i ii vi i i ii v C L2#LINE/L2 621 GGGAGGAGGGAGGGAGAATGGTCTGGAAGCGGCAATGAGGAGCAAGGAGG 572 chr4ptel1M 325683 ATTCTACCTCCCCCACCTC 325701 ---i v C L2#LINE/L2 571 A---CACCTACCCCACCTC 556 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.92 CpG sites = 14, Kimura (unadjusted) = 43.74 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.04 (3 / 68), avg. gap size = 1.00 (3 / 3) 282 34.11 2.55 6.62 chr4ptel1M 325962 326118 (673882) AmnSINE2#SINE/tRNA-Deu 96 246 (112) m_b171s601i48 6611 chr4ptel1M 325962 CTTCATTTTAATGTGACAGATGAGTAGCTTGCCAGGAAATTTACTCTGTA 326011 ii vvi v ii i i v vv ? v v i v - AmnSINE2#SINE 96 CTTCATCCTTCCGAGGTAGATAAATTGAGTNCCACGCAGTTTACTGTGT- 144 chr4ptel1M 326012 CAAACTGGAGAGTTTCT---ATAAAAGTTTCAGTAACTGAGGTCTGATGG 326058 ------- ? i i i --- i i vi v i- ii i i ivi vv AmnSINE2#SINE 145 -------GNGGGTCTTTCGGATGAGACCTTAAA-AACCAAAGCCCTGTCT 186 chr4ptel1M 326059 GCTCTGGGCAGACATTAACAATCCCATTGGCCCTTTTCCTAACTGTAGAG 326108 v ii vi i- v v vv i AmnSINE2#SINE 187 GCTCTGCGTGGACATTAAAGATCCCG-TGGCGCTTTTCGTAAGAGTAGGG 235 chr4ptel1M 326109 A-TGGTCCCAG 326118 i- v i i AmnSINE2#SINE 236 GTTTGCCCCGG 246 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.97 CpG sites = 29, Kimura (unadjusted) = 47.90 Transitions / transversions = 1.38 (29/21) Gap_init rate = 0.08 (12 / 156), avg. gap size = 1.17 (14 / 12) 600 26.92 0.64 0.64 chr4ptel1M 326642 326798 (673202) C MIRb#SINE/MIR (73) 195 39 m_b171s601i49 6608 chr4ptel1M 326642 TCATTTTACAGCTATAACAATACTGGTAGGATGCTATTATTATTCCCATT 326691 v ivvii i iv vv vv v i C MIRb#SINE/MIR 195 TCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATTATCCCCATT 146 chr4ptel1M 326692 TTACAGATGAGG-AATTAAGGCTGAGAGACATTAAGCAACTTGACCAAGG 326740 - i i v vi i v C MIRb#SINE/MIR 145 TTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGG 96 chr4ptel1M 326741 CCACACATCTTATTAAATATCAGAAGCAAAATTTGAAAGCACATCTTCTT 326790 i v - v i iv iv iii i vv vi vii C MIRb#SINE/MIR 95 TCACACAGC-TAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCT 47 chr4ptel1M 326791 CACTCCAA 326798 v C MIRb#SINE/MIR 46 GACTCCAA 39 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.81 CpG sites = 21, Kimura (unadjusted) = 33.70 Transitions / transversions = 1.00 (21/21) Gap_init rate = 0.01 (2 / 156), avg. gap size = 1.00 (2 / 2) 616 23.88 1.48 0.74 chr4ptel1M 326666 326800 (673200) C MIRc#SINE/MIR (99) 169 34 m_b171s601i50 6608 chr4ptel1M 326666 GGTAGGAT-GCTATTATTATTCCCATTTTACAGATGAGGAA-TTAAGGCT 326713 i ii- v i -i i C MIRc#SINE/MIR 169 GGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCT 120 chr4ptel1M 326714 GAGAGACATTAAGCAACTTGACCAAGGCCACACATCTTATTAAATATCAG 326763 v vi ii v i v - v i iv C MIRc#SINE/MIR 119 CAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGC-TAGTAAGTGGCAG 71 chr4ptel1M 326764 AAGCAAAATTTGAAAGCACATCTTCTTCACTCCAAGT 326800 iv iii i i vv vi i v C MIRc#SINE/MIR 70 AGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGT 34 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.34 CpG sites = 20, Kimura (unadjusted) = 29.49 Transitions / transversions = 1.67 (20/12) Gap_init rate = 0.02 (3 / 134), avg. gap size = 1.00 (3 / 3) 17 20.15 2.08 2.08 chr4ptel1M 327281 327328 (672672) (AAATAT)n#Simple_repeat 1 48 (0) m_b171s252i15 6612 chr4ptel1M 327281 AAAAATTAATAT-TATTTAATAAATAAATATATATATATATATATATAT 327328 v v -v v - v v v v (AAATAT)n#Sim 1 AAATATAAATATAAATATAA-ATATAAATATAAATATAAATATAAATAT 48 Matrix = Unknown Transitions / transversions = 0.00 (0/8) Gap_init rate = 0.04 (2 / 47), avg. gap size = 1.00 (2 / 2) 26 17.37 5.08 0.00 chr4ptel1M 327289 327347 (672653) (AT)n#Simple_repeat 1 62 (0) m_b171s252i16 6612 chr4ptel1M 327289 ATAT-TATTTA-ATAAATAAATATATATATATATATATATATTTA-AAAG 327335 - v - v v v - v v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr4ptel1M 327336 ATATTGCTATAT 327347 vvv (AT)n#Simple_ 51 ATATATATATAT 62 Matrix = Unknown Transitions / transversions = 0.00 (0/9) Gap_init rate = 0.05 (3 / 58), avg. gap size = 1.00 (3 / 3) 479 25.75 11.95 2.30 chr4ptel1M 329186 329344 (670656) C MIR3#SINE/MIR (21) 187 14 m_b171s601i51 6613 chr4ptel1M 329186 TTAGAGATGAAAAGGGCCTTAGAGGTCATTAAGTCTAACTAC-TCACTTT 329234 i v i i i i iv i iv - i C MIR3#SINE/MIR 187 TCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTT 138 chr4ptel1M 329235 ACAGAGAGGGAAACTGAGGCATGGAGAGGTTAA--GA--TGT----GGTT 329276 vii vii v -- -- i---- i C MIR3#SINE/MIR 137 ACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTC 88 chr4ptel1M 329277 ATTCAGCTA---AGTAA-------ATGACTAGAATTCACATCTTCCTGAC 329316 iv ? --- ii-------iv ii vi - C MIR3#SINE/MIR 87 ACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGTC-TCCTGAC 39 chr4ptel1M 329317 CCCAAGCCCAATCCACTTTTTCTCCTCA 329344 i v i i---ii i i v C MIR3#SINE/MIR 38 TCCCAGTCCG---TGCTCTCTCTGCTCA 14 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.49 CpG sites = 29, Kimura (unadjusted) = 33.57 Transitions / transversions = 2.64 (29/11) Gap_init rate = 0.06 (10 / 158), avg. gap size = 2.30 (23 / 10) 13 16.35 7.32 0.00 chr4ptel1M 330988 331028 (668972) (AAATATT)n#Simple_repeat 1 44 (0) m_b171s252i17 6614 chr4ptel1M 330988 AAATATTAAATA--AAATATT-CATAATCACTATCAATTATTAA 331028 -- -v v v v i v (AAATATT)n#Si 1 AAATATTAAATATTAAATATTAAATATTAAATATTAAATATTAA 44 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.50 (3 / 2) 16 31.00 0.00 1.89 chr4ptel1M 331147 331200 (668800) (TA)n#Simple_repeat 1 53 (0) m_b171s252i18 6615 chr4ptel1M 331147 TATATTTATAAAAATATATAAAAATATATAAACTTCATATTGATATTTTT 331196 v v v v v v - vi vv v v (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATA-TATATATATATATATAT 49 chr4ptel1M 331197 AAAT 331200 v (TA)n#Simple_ 50 ATAT 53 Matrix = Unknown Transitions / transversions = 0.08 (1/12) Gap_init rate = 0.02 (1 / 53), avg. gap size = 1.00 (1 / 1) 339 26.19 8.33 0.00 chr4ptel1M 332805 332888 (667112) C MIRc#SINE/MIR (158) 110 20 m_b171s601i52 6616 chr4ptel1M 332805 TAAATGACTTGCCCAAGGTCACAC------TAAGCA-TGGAGGTGAGATT 332847 i ------ ii-ii vi i i C MIRc#SINE/MIR 110 TAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACT 61 chr4ptel1M 332848 AGAACTCAGGTTTTCCTGATTCCTGGCTCCGTTTCCCTTCC 332888 v i i i vi ii v vii i C MIRc#SINE/MIR 60 CGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCC 20 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.42 CpG sites = 17, Kimura (unadjusted) = 34.38 Transitions / transversions = 3.40 (17/5) Gap_init rate = 0.02 (2 / 83), avg. gap size = 3.50 (7 / 2) 299 19.40 7.46 0.00 chr4ptel1M 332938 333004 (666996) C MIR3#SINE/MIR (24) 184 113 m_b171s601i53 6617 chr4ptel1M 332938 GAGCTAGAA----CCTCAGAGACCCTCAAGGCTAACCTT-TCTTCTTACA 332982 i ---- i i v v v i ii- v i C MIR3#SINE/MIR 184 GAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACA 135 chr4ptel1M 332983 GTTGAAGAAACTGAGGCCCAGA 333004 v i C MIR3#SINE/MIR 134 GATGAGGAAACTGAGGCCCAGA 113 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 22.84 CpG sites = 8, Kimura (unadjusted) = 22.84 Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.03 (2 / 66), avg. gap size = 2.50 (5 / 2) 251 26.54 11.72 2.88 chr4ptel1M 333099 333226 (666774) L3#LINE/CR1 3958 4096 (3) m_b171s601i54 6618 chr4ptel1M 333099 CCCACCATTACTGCCGAAAGTCA-GCA-AGGGTGGATAACCACATATTGG 333146 i v i i vv iviv - - v i v i ii L3#LINE/CR1 3958 CTCCCCGTCACTGGAGGTGTTCAAGCAGAGGCTGGATGACCACTTGTCAG 4007 chr4ptel1M 333147 GTATGTGGTAGAAGAGCCTCTCATGCA---GATACAAAATGTG---TAGG 333190 v v i vi i-- --- ivi ii - --- i L3#LINE/CR1 4008 GGATGTTGTAGAAGGGATTCC--TGCATTGGATGGGAGGT-TGGACTAGA 4054 chr4ptel1M 333191 TTGATCTC-AAGG----ATCCAATTCTGTGGTTC--TGATTCT 333226 - i - ----v i v i -- L3#LINE/CR1 4055 -TGACCTCTAAGGTCCCTTCCAACTCTGAGATTCTGTGATTCT 4096 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.51 CpG sites = 20, Kimura (unadjusted) = 33.76 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.09 (11 / 127), avg. gap size = 1.73 (19 / 11) 13 21.89 2.27 2.27 chr4ptel1M 334193 334236 (665764) (TTTTG)n#Simple_repeat 1 44 (0) m_b172s252i0 6619 chr4ptel1M 334193 TTTTGTTTTGTTTT-CTTGGGGTTGATTTTTTTTGCTCTTGTCTT 334236 -i v vv v v - i i (TTTTG)n#Simp 1 TTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTG-TTTTGTTTT 44 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2) 15 5.56 0.00 0.00 chr4ptel1M 334546 334564 (665436) (TC)n#Simple_repeat 1 19 (0) m_b172s252i1 6620 chr4ptel1M 334546 TCTCTCTCTCCCTCTCTCT 334564 i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCT 19 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 42 0.00 0.00 0.00 chr4ptel1M 334566 334601 (665399) (AC)n#Simple_repeat 1 36 (0) c_b172s251i0 6621 chr4ptel1M 334566 ACACACACACACACACACACACACACACACACACAC 334601 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACAC 36 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 12 25.56 0.00 0.00 chr4ptel1M 334990 335026 (664974) (AAAG)n#Simple_repeat 1 37 (0) m_b172s252i2 6622 chr4ptel1M 334990 AAAGAAAGAAATTCAAAGATAAAGAAAGATAGATAGA 335026 vvv i i v v v (AAAG)n#Simpl 1 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA 37 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 222 25.86 11.61 3.31 chr4ptel1M 335548 335659 (664341) L2d_3end#LINE/L2 393 513 (3) m_b172s601i4 6623 chr4ptel1M 335548 TAGAATTTGAGTTCCTGGAGAGT-GGGACTAT--CTTTTTCTATCT---- 335590 v v i i v i i- i -- v v ? i ---- L2d_3end#LINE 393 TAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACTNTTTTNTC 442 chr4ptel1M 335591 GTACCTC-CAGCACTTGGT---GTACTGATTTGCACAT--CAGGCATTGA 335634 v i - i i i i--- i --- --i ii v L2d_3end#LINE 443 GTTCCCCACAGCGCCTAGCACAGTGCTGA---GCACATAGTAGGCGCTCA 489 chr4ptel1M 335635 ATAAATGCATTAGTCATTAATTTAT 335659 i - iv v i v L2d_3end#LINE 490 ATAAATAC-TTGTTGATTGATTGAT 513 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.40 CpG sites = 18, Kimura (unadjusted) = 33.27 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.09 (10 / 111), avg. gap size = 1.70 (17 / 10) 236 26.40 4.26 11.36 chr4ptel1M 335548 335641 (664359) L2c_3end#LINE/L2 373 460 (18) m_b172s601i3 6623 chr4ptel1M 335548 TAGAATTTGAGTTCCTGGAGAGT-GGGAC--TATCTTTTTC-TATCTGTA 335593 v v i v i i- -- i v - v i L2c_3end#LINE 373 TAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTA 422 chr4ptel1M 335594 CCTCCAGCACTTGGTGTACTGATTTGCACATCAGGCATTGAATAAATG 335641 i i i i ii---------- i vi ii v L2c_3end#LINE 423 TCCCCAGCGCCTGGCA----------CATAGTAGGCGCTCAATAAATG 460 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.90 CpG sites = 15, Kimura (unadjusted) = 33.59 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.14 (13 / 93), avg. gap size = 1.08 (14 / 13) 454 31.30 7.94 5.08 chr4ptel1M 335839 336279 (663721) L1ME4c_3end#LINE/L1 102 554 (276) m_b172s551i0 6624 chr4ptel1M 335839 AAAGGAATTGCAAAGATTCA-CAATCATATG-AATGATGTTCTAAATAAT 335886 i v i ?v v v - v i - vi ----- i L1ME4c_3end#L 102 AGAGGAAATACAANTAGTAAACAAACACATGGAAAAATGTTC-----AAC 146 chr4ptel1M 335887 AACACTAATTATTACAAAAATTTAAATCAAAACAACCCTAAGAT-----T 335931 vv i i v i v i vi i i vv i ----- L1ME4c_3end#L 147 CTCGCTAGTAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATT 196 chr4ptel1M 335932 TCACACATGTTCTGGGAATTAGGAGGAAAGAGGAAAATGACCAAAAGTGG 335981 i i v i ----i v --------- vvvv v i L1ME4c_3end#L 197 TTACGCCTATT----AAATTAGCA---------AAAATTTAAAAAATTGA 233 chr4ptel1M 335982 CAAT--TCAATTTTGGAGGGATTGTGGAAAAGATA--ACACTT-----TT 336022 i --i vi v i i? i vi iv i-- ? i----- L1ME4c_3end#L 234 TAATACCCAATGCTGGCGAGGNTGCGGTGAAACTGGTACNCTCATACATT 283 chr4ptel1M 336023 GTTGGTGGAGCTGTGAAATGACATGATCATTTTGGAAAGCAAATTGGAAT 336072 i vi? i v ii ii i v v v v L1ME4c_3end#L 284 GCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGGCAA 333 chr4ptel1M 336073 TATGCAAATAAAGTAACCAAAATGTCCATTTTTTTTTTGAATCAGAGGTT 336122 i i vvv i iv iv i viii -- vi vii L1ME4c_3end#L 334 TACGTATCAAGAGCCATAAAAATGTTCATACCCTTT--GACCCAGTAATT 381 chr4ptel1M 336123 AGGCTTCT----------CCTCAA-AAGTAA-------GGGGGGAAAAGT 336154 vvi ---------- v i- i ------- ii i - L1ME4c_3end#L 382 CCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAAGAAGGAAAAAG- 430 chr4ptel1M 336155 CCCTAGATACTCCAAAATATTTATAGCAGCACTTTTTGTGATAGCAAAAT 336204 -- v i v v i i i v ii v i i i v L1ME4c_3end#L 431 --CTATATGCACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAA 478 chr4ptel1M 336205 ATTGGAAACAAGGAATATGTCCATTGATTAATGAATGGATAA-TAAATTA 336253 vvv v vii viiv v - L1ME4c_3end#L 479 ATTGGAAACAACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTA 528 chr4ptel1M 336254 CAATGCATGAATGCAATAGAATATTA 336279 iii i v? iv i i L1ME4c_3end#L 529 TGGTACATCNACTCGATGGAATATTA 554 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.43 CpG sites = 74, Kimura (unadjusted) = 42.37 Transitions / transversions = 1.30 (74/57) Gap_init rate = 0.07 (33 / 440), avg. gap size = 1.76 (58 / 33) 361 28.46 3.85 0.00 chr4ptel1M 336170 336299 (663701) L1MB7_3end#LINE/L1 441 575 (356) m_b172s551i1 6624 chr4ptel1M 336170 AATATTTATAGCAGCACTTTTTGTGATAGCAAAATATTGGAAACAAGGAA 336219 i i i v ii i v v v vvv L1MB7_3end#LI 441 AATGTTCATAGCAGCATTATTCATAATAGCCAAAAAGTGGAAACAACCCA 490 chr4ptel1M 336220 TATGTCCATTGATTAATGAATGGAT-AATAAATTACAATGCATGAATGCA 336268 v ii i i - i v iiii ii vv i L1MB7_3end#LI 491 AATGTCCATCAACTGATGAATGGATAAACAAAATGTGGTATATCCATACA 540 chr4ptel1M 336269 ATAGAATATTACTGTGTT----AAAGAAATGATGT 336299 i i vv ii---- i v L1MB7_3end#LI 541 ATGGAATATTATTCGGCCATAAAAAGGAATGAAGT 575 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.02 CpG sites = 23, Kimura (unadjusted) = 37.02 Transitions / transversions = 1.64 (23/14) Gap_init rate = 0.02 (2 / 129), avg. gap size = 2.50 (5 / 2) 15 25.32 0.00 0.00 chr4ptel1M 337167 337208 (662792) (AAA)n#Simple_repeat 1 42 (0) m_b172s252i3 6625 chr4ptel1M 337167 AAAAAAAAAAAAAAAAACCACTGAATAAAAAACCAAAAAGAA 337208 vv vvi v vv i (AAA)n#Simple 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 42 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 4320 29.71 3.94 2.55 chr4ptel1M 337907 340697 (659303) L1M5_orf2#LINE/L1 360 3188 (106) m_b172s551i2 6626 chr4ptel1M 337907 AGCCTCCAAATTCCTAGAG---AAGTTGAGAGAGAATACAAGAAGAAATA 337953 i v v v ii --- ii v - v v i L1M5_orf2#LIN 360 AGCTTCAAAATACATGAAGCAAAAACTGACAGA-ACTAAAAGGAGAAATA 408 chr4ptel1M 337954 GGCA---TCAAAACTATACTAGTAGGGGATCTCAACCTTGCTCTCTCAG- 337999 i ---i v i --- ? i i i vi?v - L1M5_orf2#LIN 409 GACAAATCCACAATTATA---GTNGGAGATTTTAACACNCCTCTCTCAGT 455 chr4ptel1M 338000 AATTAGATAAATGGAACCACAAAATAAATGAGAAAAGTTA-AGTAGGT-- 338046 - i -iv vi v v v v v i v - v i -- L1M5_orf2#LIN 456 AATT-GATAGA-ACAAGTAGACAAAAAATCAGTAAGGATATAGAAGATTT 503 chr4ptel1M 338047 -AACCAAAATATTAGAAAAGTTAGGTGTGATAGATCTTTGGAGAAAAGTG 338095 - v v v i ivv v - iiv i v iv iv v v ? L1M5_orf2#LIN 504 GAACAACACTATCAACCAACTT-GACCTAATTGACATTTATAGAACACTN 552 chr4ptel1M 338096 AATGGAG--ACAGAAAGGAGTTTACTTTTTTCTCAATGGTTTATGGAACT 338143 v ivv i-- ? v -- i vi v i i vv ivi v L1M5_orf2#LIN 553 CACCCAACAACNGCA--GAATACACATTCTTTTCAAGTGCACATGGAACA 600 chr4ptel1M 338144 TATACAAAAATTGACCATGTATTAGGACATAAAA---ACCTCAAAATCAA 338190 v v i v i ?i i v ---ii ---i L1M5_orf2#LIN 601 TTTACCAAGATAGACCATATNCTGGGCCATAAAACAAGTCTCAA---TAA 647 chr4ptel1M 338191 ATGCAGAAAGGCAGAAATAGTAAGTACATTAT-TTTTCAGATCATGATGC 338239 vi?i i iiv vi --i v v - i v i ii v L1M5_orf2#LIN 648 ATTTNAAAGGATTGAAATCATA--CAGAGTATGTTCTCTGACCACAATGG 695 chr4ptel1M 338240 AATTAAA-----AATCACATTTAATATAAGGCCAGG-AGAAAATAGACCA 338283 ----- v--- i v i vi ?v- vv- L1M5_orf2#LIN 696 AATTAAATTAGAAATCAA---TAACAAAAAGATANCTAGAAAATCC-CCA 741 chr4ptel1M 338284 AAATTTAATTGGAAATTAAATAACCTAATCCTAAAGAATAAATGGATGAA 338333 --- v i vi v i v ivv i v L1M5_orf2#LIN 742 AA---TATTTGGAAATTAAACAACACACTTCTAAATAACCCATGGGTCAA 788 chr4ptel1M 338334 ACAGCAAATCATA---GACACCATCAATAATTTCATCCAAGAGAATGACA 338380 v iv i --- v ii vv vv ii--- vv ? L1M5_orf2#LIN 789 AGAAGAAATCACAANGGAAATTAGAAAATATTTTG---AACTGAATGANA 835 chr4ptel1M 338381 ATAATGAGACAACATACCAAAATTTGTGGGATACAACCAAAGCAGT-TAT 338429 i vi v i i i i -iv L1M5_orf2#LIN 836 ATGAAAATACAACATATCAAAATTTGTGGGATGCAGCTAAAGCAGTGCTT 885 chr4ptel1M 338430 AATGGGAAATTTTATATCTCTCAATGTTTAC-TT-GCATAAAATAAAGAG 338477 iv - v ?i v i? i- - v v i v iv L1M5_orf2#LIN 886 AGAGGGAAATTT-ATAGCNTTAAATGCNTATATTAGAAAAGAAGAAAGGC 934 chr4ptel1M 338478 --AAGATCAATTAATTGAGCTTACAACTAAAAAAGCTAGAAAAAGAA--- 338522 -- i v vi i v v v i --- L1M5_orf2#LIN 935 TTAAAATCAATGATCTAAGCTTCCACCTTAAGAAGCTAGAAAAAGAAGAG 984 chr4ptel1M 338523 CAAATTAAAAACCC---TTAAATACCAAATTTGAAATTCTGAAAATGCAA 338569 -- ---v? i vv iivvv vv i i -- L1M5_orf2#LIN 985 CAAATTAAA--CCCAAAGNAAGTAGAAGGAAGGAAATAATAAAGAT--AA 1030 chr4ptel1M 338570 GGG-GGAGATTAATAAAGTTGAAAATAAGAAAACTATTGAATTAATAAAT 338618 i -i i i i i v i i? ? v v ivv v i L1M5_orf2#LIN 1031 GAGCAGAAATCAATGAAATAGAAAACAAANANACAATAGAGAAAATCAAC 1080 chr4ptel1M 338619 AAAACTGA--GTTGGTTTTATGAAAA-ACCCATAAAATAGATAAACCTTT 338665 i i ii -- i i v - i v v i L1M5_orf2#LIN 1081 GAAGCCAAAAGCTGGTTCTTTGAAAAGATCAATAAAATTGATAAACCTCT 1130 chr4ptel1M 338666 GGTTAATTTGATTA-GAAAAGAAGAAAGAAGAAAACCAAATTGTTAGTCT 338714 i i? ivi i - i i v -- iii i v L1M5_orf2#LIN 1131 AGCNAGACTGATCAAGAAAAAAAGAGAGAAGACA--CAAATTACCAATAT 1178 chr4ptel1M 338715 CAAAAATGAAAAGGGAGAACTTTCCACCAATGAAGAGGAAATTAGAGCAA 338764 ii i vv iv i vi vvvivi v i ivi L1M5_orf2#LIN 1179 CAGGAATGAAAAAGGAGACATCACTACAGATCCTACAGACATTAAAAGGA 1228 chr4ptel1M 338765 TAATTAGGAGCTATTTTGCCCAACTTTATGCCAACACATTTGATAATCTA 338814 v iiiv v vv i v ? ii L1M5_orf2#LIN 1229 TAATAAGAGAATATTATGAACAACTTTATGCCAATAAATTTGANAACTTA 1278 chr4ptel1M 338815 AATTAAATGGAAGAATATCTACAAAAATATAGATTGCTCAGGTTAACAGA 338864 i v vi vi vv i i i? i iv iii i ?v L1M5_orf2#LIN 1279 GATGAAATGGACAAATTCCTTGAAAAACACAANTTACCAAAACTGACNCA 1328 chr4ptel1M 338865 AGAGGAAATAACTTATTTAAATAATCCAAT-TTTAGAAAAAGAAATAGAA 338913 i ivvv i i ii v - i vv - v L1M5_orf2#LIN 1329 AGAAGAAATAGAAAATCTGAATAGCCCTATATCTATTAAA-GAAATTGAA 1377 chr4ptel1M 338914 AAAGACATTAATCAACCCCCTAAGAAAAAAATCTCCAGGGCCAGATGGAT 338963 vvv vv -v ii iv v i v v v L1M5_orf2#LIN 1378 TTTGTAATTAA-AAACCTTCCCACAAAGAAAACTCCAGGCCCAGATGGCT 1426 chr4ptel1M 338964 TTATATGTGAATTCTACCAAGCATTCAAGGAACAATTAATTACAATACTA 339013 i ivv i i v v vv vi L1M5_orf2#LIN 1427 TCACTGGTGAATTCTACCAAACATTTAAGGAAGAAATAATACCAATCTTA 1476 chr4ptel1M 339014 TATAAACTATTTGAAAAAATAGGAAAAGAAGGAGTCTTACCAAATTCCTT 339063 i i v iv i i i iivi v v i v L1M5_orf2#LIN 1477 CACAAACTCTTCCAGAAAATAGAAAAAGAGGGAACACTTCCCAACTCATT 1526 chr4ptel1M 339064 TTATAATACAGATATGGTGTTGACAACTAAACCAGGTAGGGTGAAAACAG 339113 i vi viii ?iivi i v v ? ii ii vv vv i L1M5_orf2#LIN 1527 TTATGAGGCCAGCATNACCCTGATACCAAAACCNGACAAAGACATTACAA 1576 chr4ptel1M 339114 AGAAAGAAAATTATAGACCAATTTCCCTAATGTATATTGATGCAAAAATC 339163 ii i v v v i v L1M5_orf2#LIN 1577 GAAAAGAAAATTACAGACCAATATCCCTCATGAACATAGATGCAAAAATC 1626 chr4ptel1M 339164 TTAAATAAAATATTAGCAATGAGATTTCAGAAAGTCATCCCCAGGATAAT 339213 i ? i vvv v i v vvi vvvv L1M5_orf2#LIN 1627 CTNAACAAAATATTAGCAAATCGAATCCAGCAATATATAAAAAGGATAAT 1676 chr4ptel1M 339214 ACACCACAACCAAGTAGAATTTATATCAGGAATGCAGGGCTGGTTCAATA 339263 i ii i ii vi i i i i L1M5_orf2#LIN 1677 ACATCATGACCAAGTGGGGTTTATCCCAGGAATGCAAGGTTGGTTTAACA 1726 chr4ptel1M 339264 GTAGGAAAACTATTAGCATAATTGACTATATCAATA-ACCAAACTAACAA 339312 v v i v v i iii v i i i - vi v-i v L1M5_orf2#LIN 1727 TTCGAAAATCAATCAATGTAATTCACCATATTAACAGAATAAAG-GAGAA 1775 chr4ptel1M 339313 AAATCATATGATTATCTCAATAGATGCAGAAAAAGCATTTGATAAAATCC 339362 i i i L1M5_orf2#LIN 1776 AAATCATATGATCATCTCAATAGATGCAGAAAAAGCATTTGACAAAATTC 1825 chr4ptel1M 339363 AACATCCATTCTTATTAAAAAC---------ACTAGAGAGTATA--GGAA 339401 i v iv --------- - i v -- L1M5_orf2#LIN 1826 AACACCCATTCATGATAAAAACTCTCAGCAAACTAG-GAATAGAAGGGAA 1874 chr4ptel1M 339402 TTTCCTTAACATGATCAGTAGCATCTATTTAAAACCATCAGCAAGCATCA 339451 i i v v ivi ivv vv ? i L1M5_orf2#LIN 1875 CTTCCTCAACCTGATAAAGGGCATCTACGAAAAACCTACAGCNAACATCA 1924 chr4ptel1M 339452 TATGTAATGGGGACAAACTAGAACCATTCCCAATAAAATCAGAAGTGAAA 339501 iv v v ? ii ?v v vv i i i iii i L1M5_orf2#LIN 1925 TACTTAATGGTGAAANACTGAANGCTTTCCCCCTAAGATCGGGAACAAGA 1974 chr4ptel1M 339502 CAAGGCTGTCCACTATCACCATTACTATTCAATATTGTATTAGAAATGCT 339551 v i ? i v i i i ii v L1M5_orf2#LIN 1975 CAAGGATGTCCGCTNTCACCACTTCTATTCAACATTGTACTGGAGGTCCT 2024 chr4ptel1M 339552 TGCTTG-GCAATCAAAGG--GGGAAAAGA--TTAAAGG------AATT-- 339588 v iv - -- --i i -- v ------i -- L1M5_orf2#LIN 2025 AGCCAGTGCAAT--AAGGCAAGAAAAAGAAATAAAAGGCATAAAGATTGG 2072 chr4ptel1M 339589 ATAGTAAGTAAACCAAATTATCACTCT--GCAGATGAAATA----TTTAC 339632 v v - iv i i ?i v -- v i---- ? L1M5_orf2#LIN 2073 AAAGGAAG-AAATAAAACTGTCNTTATTCGCAGATGACATGATTGTNTAC 2121 chr4ptel1M 339633 ----AGAATCCTAGAGAATCAACCAAAAAACTACTAGAAACAATTCACAA 339678 ---- i ? i v v ? vi vviii L1M5_orf2#LIN 2122 GTAGAAAATCCNAAAGAATCTACAAANAAACTACTAGAACTAATAAGTGA 2171 chr4ptel1M 339679 CTTTAGGAAAGTTGCAAGATACAAAATAAATCCACATTAATCAAC---AT 339725 v v i i ?i ii v vi vv i--- L1M5_orf2#LIN 2172 ATTTAGCAAGGTCGCNGGATACAAGGTCAATATACAAAAATCAATTGTAT 2221 chr4ptel1M 339726 TTTTATACATTGCCAACAAAGTCTAGCAGCAAGAGATACAAAAAGAAATT 339775 i i i iv vvv v v iv v i vi? iv v L1M5_orf2#LIN 2222 TTCTATATACTAGCAACAAACAATTGGAAAATGAAATTTNAAAAACAATA 2271 chr4ptel1M 339776 CCATTCAAAATAACTGTTCATAGTATAAAATATTCCGGAATCTATCTGCC 339825 i v i vvivv v ii ? i iv vv iv L1M5_orf2#LIN 2272 CCATTTACAATAGCATCAAAAAACATNAAATACTTAGGAATAAATCTAAC 2321 chr4ptel1M 339826 AAGGGAAAGTCAGGAACTATACAAACACAACTACAAAACACTTTCCACAT 339875 ii? vivv i v ? vvv v i viiv v v L1M5_orf2#LIN 2322 AAAANATGTGCAAGACCTNTACACTGAAAACTACAAAACATTGCTGAGAG 2371 chr4ptel1M 339876 AAATAAAGTCAGATCTAATCAATTGGAAAAATATCAAATGCTCTTGGATA 339925 v ivv i vi v i i vvv i v v L1M5_orf2#LIN 2372 AAATTAAAGAAGACCTAAATAAATGGAGAGATATACCATGTTCATGGATT 2421 chr4ptel1M 339926 GGCAGAAAGAATATAATAAAAATGACAACACTACCTAAATTAATCTACTT 339975 v vvv vi ? i v iv v i i ivv L1M5_orf2#LIN 2422 GGAAGACTCAATATTGTNAAGATGTCAATTCTCCCCAAATTGATCTATAG 2471 chr4ptel1M 339976 GTTTGATACCATACCAATCAAACTCCCAAGAAATTATTTTCCAGATCTAG 340025 i ii i v v v iv ii v vi ----- L1M5_orf2#LIN 2472 ATTCAATGCAATCCCAATCAAAATCCCAGCAGGTTTTTTTGTAGA----- 2516 chr4ptel1M 340026 AAAAAAAAAAATAGTAACAAAGTTCATCTGGAAGAATAAAAGGTCAAGAA 340075 vvi v iv ii vvi i i v ivii i ii ? L1M5_orf2#LIN 2517 AATTGACAAGCTGATTCTAAAATTTATATGGAAATGCAAAGGACCNAGAA 2566 chr4ptel1M 340076 T-TTCAAGGGAATTAATGAAAAAAAAATGCTAA--TGAAGATGGCTTAGC 340122 -vi iiv iv- i ivi v -- i -- i - L1M5_orf2#LIN 2567 TAGCCAAAACAATCT-TGAAAAAGAAGAACAAAGTTGGAG--GACTTA-C 2612 chr4ptel1M 340123 TGTGCCAGATCT-AAAACTATATTATAAAGCAGCAGTCACCAAAACCATT 340171 vv i ? ? - i - vi v i i vi v L1M5_orf2#LIN 2613 ACTACCNGATNTCAAGACT-TATTATAAAGCTACAGTAATCAAGACAGTG 2661 chr4ptel1M 340172 TGGTTCTGGC-TAAGAAATAGGTTGGT-GATAGTTGGAATAGATTAG-GA 340218 vi - i - iivii - viv i v - L1M5_orf2#LIN 2662 TGGTATTGGCGTAAGGA-TAGACAAATAGATCAATGGAACAGAATAGAGA 2710 chr4ptel1M 340219 TCACAGGACAAAATAG--TCA-ATAACTATAGCAATCTAGTGTTTGACAA 340265 viv ---- --i - i vv i ?v ?i ii v L1M5_orf2#LIN 2711 GTCCAG----AAATAGACCCACACATATATGGNCANTTGATTTTTGACAA 2756 chr4ptel1M 340266 A---CCCAAAG-AGTCCAACTTTTGGGATAAGAACTCACTATTTGACAAA 340311 ---v ? - i i i---- iv i ivvv v ii L1M5_orf2#LIN 2757 AGGTGCCAANGCAATTCAG----TGGGGAAAGGATAGTCTTTTCAACAAA 2802 chr4ptel1M 340312 AACTTCTGGGAAAATTGGAAATTAGTGTGGACAAAATTAGGACTCGACCC 340361 viv v i v v ivi i v v iii? L1M5_orf2#LIN 2803 TGGTGCTGGAACAATTGGATATCCATATGGAAAAAAATGAANCTCGACCC 2852 chr4ptel1M 340362 ACATCTAACACCACATATAAAGATAAGATCTAAATGAGTTCAT-GATTTA 340410 vi i v i i i i v iv ? i - v - ii L1M5_orf2#LIN 2853 CTACCTCACACCATACACAAAAATTAATTCNAGATG-GATCATAGACCTA 2901 chr4ptel1M 340411 GACATAAACTGTTATATTATAAGCAAAT--TAGA--GAAACAT--GAGAT 340454 i ii vv? v v i -- v -- --i -- v L1M5_orf2#LIN 2902 AATGTAAAAGNTAAAACTATAA--AACTTCTAGAAGAAAACATAGGAGAA 2949 chr4ptel1M 340455 TGTTTGTTTCTCA-AATCTGAGGAAAAGGAAGGAATTTGTGTCCA----- 340498 i i ----- i-i i vi ?v i v i v iv ivv ----- L1M5_orf2#LIN 2950 TATCT-----TCGTGACCTTGGGNTAGGCAAAGATTTCTTAAACAGGACA 2994 chr4ptel1M 340499 -AAGAAGAACTGGAACTCATAATTGAACACCAAATAGATAATTTTGATTA 340547 - i v --? - --- v vv v v v i ? L1M5_orf2#LIN 2995 CAAAAAGCAC--NAAC-CATAA---AAGAAAAAATTGATAAATTGGACTN 3038 chr4ptel1M 340548 TATTAAGTTAAAAAGGTTTTGTATAAGCAAAAC-TAATGAAAACAAGATC 340596 i i iv v iv i i- v?v v-i vi vv v i v L1M5_orf2#LIN 3039 CATCAAAATTAAAAACTTCTGC-TCNTCAAAAGACACCGTTAAGAAAATG 3087 chr4ptel1M 340597 AGAAGGGAAGCAATAAATTGGGAAATCATTTTTACATTTAAGGGATCTGA 340646 i v v i i ? i vv v i v?vv viv L1M5_orf2#LIN 3088 AAAAGGCAAGCCACAGANTGGGAGAAAATATTTGCAANACATATATCTGA 3137 chr4ptel1M 340647 TAAAGGCTTTCTTTCTAAAATATATAGAGAATTGACTCAAATTTATAAGA 340696 i vi iv v i i i i vviv ? iv ? L1M5_orf2#LIN 3138 CAAAGGACTCGTATCCAGAATATATAAAGAACTCCTACAANTCAATAANA 3187 chr4ptel1M 340697 A 340697 L1M5_orf2#LIN 3188 A 3188 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.91 CpG sites = 418, Kimura (unadjusted) = 39.41 Transitions / transversions = 1.07 (418/390) Gap_init rate = 0.04 (124 / 2790), avg. gap size = 1.47 (182 / 124) 960 31.67 3.12 4.58 chr4ptel1M 340660 341301 (658699) L1ME4c_3end#LINE/L1 7 639 (191) m_b172s551i3 6626 chr4ptel1M 340660 TCTAAAATATATAGAGAATTGACTCAAATTTATAAGAAT----TCAAGCC 340705 ?v ? i ii v i v v---- v L1ME4c_3end#L 7 TCTNTANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAAGAC 56 chr4ptel1M 340706 ATTCTCCAATTGATAAATTGGAGATAAATTGATAAAATTGATAAAAGAAT 340755 ----i ----------- v ii i-- i v-- i L1ME4c_3end#L 57 ----CCCAAT-----------AGATAAATGGGCAAAG--GACAT--GAAC 87 chr4ptel1M 340756 ATGAACAATTTTTAGATGAAGAAATTAAAACTATTTC-TAATCTTATGAG 340804 --i ivi ? v i - v ? v vv-i v vi ii L1ME4c_3end#L 88 A--GACAATTCACANAAGAGGAAAT-ACAANTAGTAAACAAACACATGGA 134 chr4ptel1M 340805 AAGGTGCTCTAAATCTCTATTGATCAGAAAAATGCAAATTAAGACAACTC 340854 ii i v vv v v i i i ii vv L1ME4c_3end#L 135 AAAATGTTCAACCTCGCTAGTAATCAAAGAAATGCAAATTAAAGCAACAA 184 chr4ptel1M 340855 TGAGATACCACTACACATCTCTCAGATTGGCTAAAATGACAGGAAAAGAC 340904 i vi ii v i i i v vvv ii vv i L1ME4c_3end#L 185 TGAGATACCATTTTACGCCTATTAAATTAGCAAAAATTTAAAAAATTGAT 234 chr4ptel1M 340905 AAAGATAAATGTTAG--GGGAAGTAGGAAAACTGGGACAC-CAT-TATTG 340950 viviv i i --i ?v ii vi v ? - -i L1ME4c_3end#L 235 AATACCCAATGCTGGCGAGGNTGCGGTGAAACTGGTACNCTCATACATTG 284 chr4ptel1M 340951 TTGGTAGAGTTGAGAATGGATCCAACCATTCTGGAAAACAATTTGGACCT 341000 i i vi? vi v i v v i i vvv L1ME4c_3end#L 285 CTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGGCAAT 334 chr4ptel1M 341001 ATGTTCAAAAAGTTATCAAATTGTGTATACTATTTGACCCAGTAATGTTT 341050 i viv i ii v v vi iv viiv L1ME4c_3end#L 335 ACGTATCAAGAGCCATAAAAATGTTCATACCCTTTGACCCAGTAATTCCA 384 chr4ptel1M 341051 CTACTGGGCTTATATCCCAAAGAAAT--CTTAAAGGAGGGGAAGGGACCC 341098 v vv v i i --i i i i i ii -- i L1ME4c_3end#L 385 CTTCTGGGAATTTATCCTAAGGAAATAATTCAAAAGAAGGAAAAAG--CT 432 chr4ptel1M 341099 ACGTGTACAAAAAATGTT--TGGCAGCACTTTTCATAGTGTCAAGAAACT 341146 ii i -i i -- v ii v i i iv i i i L1ME4c_3end#L 433 ATATGCAC-GAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATT 481 chr4ptel1M 341147 GGAAAGAATTGAGTGGATGTCCATCAAT-------TGGCTGAATAAATTA 341189 v ii--- ii v ------- i i i L1ME4c_3end#L 482 GGAAACAACC---TAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTA 528 chr4ptel1M 341190 TGATATATGAATATTATGGAATATTATTGTTCTGTAAGAAATGATCAACA 341239 i i v? iviv vvvv ii v i v vi L1ME4c_3end#L 529 TGGTACATCNACTCGATGGAATATTATGCAGCCATTAAAAATGATAATTA 578 chr4ptel1M 341240 GGATGATTTCCGAGAGGCCTGGAGAGACTTACAGGAACTGATGCTGAGTG 341289 v v i vivv vii v i ivv -i v vv i i i L1ME4c_3end#L 579 TGAAGACTATGTAGCAACATGGAAAATGTT-TATGATATAATGTTAAGTG 627 chr4ptel1M 341290 AAATGAGCAGAA 341301 vi L1ME4c_3end#L 628 AAAAAAGCAGAA 639 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.96 CpG sites = 110, Kimura (unadjusted) = 43.04 Transitions / transversions = 1.31 (110/84) Gap_init rate = 0.06 (37 / 641), avg. gap size = 1.32 (49 / 37) 1014 28.16 4.81 2.66 chr4ptel1M 340739 341216 (658784) L1ME3G_3end#LINE/L1 61 548 (376) m_b172s551i4 6626 chr4ptel1M 340739 AAAATTGATAAAAGAATATGAACA----ATTTTTAGATGAAGAAATTAAA 340784 v ivv i ---- ivi v i vv L1ME3G_3end#L 61 AAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGGAAATACAA 110 chr4ptel1M 340785 ACTATTTCTAATCTTATGAGAAGGTGCTCTAAATCTCTATTGATCAGAAA 340834 iviiivv v v i i v vv v v i ii L1ME3G_3end#L 111 ATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTAATCAGGGA 160 chr4ptel1M 340835 AATGCAAATTAAGACAACTCTGAGATACCACTACACATCTCTCAGATTGG 340884 i vv i viv i iv L1ME3G_3end#L 161 AATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCATCAGATTGG 210 chr4ptel1M 340885 CTAAAATGACAGGAAAAGACAAA-GATA---AATGTTAG--GGGAAGTAG 340928 v v----v ?ivi -i --- i i --i iv i L1ME3G_3end#L 211 CAAAAATT----TAAAAGNTTGATAATATCNAGTGTTGGCGAGGGTGTGG 256 chr4ptel1M 340929 GAAAACTGGGACAC-CAT-TATTGTTGGTAGAGTTGAGAATGGATCCAAC 340976 i v v v - -i i i i iiv vi v i v i L1ME3G_3end#L 257 GGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTACAGC 306 chr4ptel1M 340977 CATTCTGGAAAACAATTTGGACCTATGTTCAAAAAGTTATCAAATTGTGT 341026 ? i iii vvv v viv v -- - i i L1ME3G_3end#L 307 CNTTTTGGAGGGCAATTTGGCAGTATCTATTAAAATTTA--AAAT-GCGC 353 chr4ptel1M 341027 ATACTATTTGACCCAGTAATGTTTCTACTGGGCTTATATCCCAAAGAAAT 341076 iv i viiv v ? ?v v i ? L1ME3G_3end#L 354 ATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAGAAAT 403 chr4ptel1M 341077 -CTTAAAGGAGGGGA-AGGGACCCACGTGTACAAAAAATGTT--TGGCAG 341122 - iiv viv v v - i ?v -- ii - -- v L1ME3G_3end#L 404 ACTCGCACATGTGCACAAGGANGCA--TGTACAAGGA-TGTTCATTGCAG 450 chr4ptel1M 341123 CACTTTTCATAGTGTCAAGAAACTGGAAAGAATTGAGTGGATGTCCATCA 341172 i v ii i iv i i i v ii--- ii L1ME3G_3end#L 451 CATTGTTTGTAATAGCGAAAAATTGGAAACAACC---TAAATGTCCATCA 497 chr4ptel1M 341173 AT-------TGGCTGAATAAATTATGATATATGAATATTATGGAATATTA 341215 ------- i i i vv i i L1ME3G_3end#L 498 ATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACTA 547 chr4ptel1M 341216 T 341216 L1ME3G_3end#L 548 T 548 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 35.54 CpG sites = 72, Kimura (unadjusted) = 36.62 Transitions / transversions = 1.22 (72/59) Gap_init rate = 0.05 (23 / 477), avg. gap size = 1.57 (36 / 23) 234 10.65 0.00 4.26 chr4ptel1M 341636 341684 (658316) LTR81C#LTR/Gypsy 884 930 (223) m_b172s502i0 6627 chr4ptel1M 341636 TGCCATCTAGGAGAGGGGGTAGGGGGAAGGAGGAGAAAATCTGAAACAC 341684 v i -i - i v LTR81C#LTR/Gy 884 TGCCATCTTGGAGAGGAG-CAGGGGGA-GGAGGAGGAAATCTGAAAGAC 930 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 11.55 CpG sites = 3, Kimura (unadjusted) = 11.55 Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.04 (2 / 48), avg. gap size = 1.00 (2 / 2) 62 24.55 0.63 1.27 chr4ptel1M 342525 342682 (657318) (CTCTCT)n#Simple_repeat 1 157 (0) m_b172s252i4 6628 chr4ptel1M 342525 CTCTCTCTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCACTCTCACTCTCA 342574 i v v v (CTCTCT)n#Sim 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chr4ptel1M 342575 CTCTCACTCT-TCCCGTCCCTCTCCCCTTCTTTTCCTCTCCCTCTCTCCT 342623 v - i - i i ii i ii i ii (CTCTCT)n#Sim 51 CTCTCTCTCTCTCTC-TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 99 chr4ptel1M 342624 TCTTCCCCTCCCATCTTTCCCTCCCTTTCTCTCTGTCCTTCCCTCCATCT 342673 ii i i - i i i i v ii i iv (CTCTCT)n#Sim 100 TCTCTCTCTCTC-TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 148 chr4ptel1M 342674 CTCCCTCTC 342682 i (CTCTCT)n#Sim 149 CTCTCTCTC 157 Matrix = Unknown Transitions / transversions = 4.17 (25/6) Gap_init rate = 0.02 (3 / 157), avg. gap size = 1.00 (3 / 3) 405 24.37 6.35 2.29 chr4ptel1M 343420 343545 (656455) C L2b_3end#LINE/L2 (44) 422 292 m_b172s601i6 6629 chr4ptel1M 343420 AGGCACTGTGCTAAGTGCTAGAGATATAAAG---AACTACAAAAACCTGG 343466 ? i i i i i iv --- v v v i ?i C L2b_3end#LINE 422 AGGCNCTGTGCTAGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGG 373 chr4ptel1M 343467 TCTCTGTCCTCAGTGAGCTCACATTCTAATACAGGAGACA-ACTTG---C 343512 i i vv v i ivi - v ---? C L2b_3end#LINE 372 TCCCTGCCCTCACGGAGCTCACAGTCTAGTGGGGGAGACAGACATGTAAN 323 chr4ptel1M 343513 CA-ACAATTATACAGCAAGATAAATGCAGAGTAG 343545 - ? vvv iii i--- i C L2b_3end#LINE 322 CAGACAATNATAACCCAGAGTG---GCAGGGTAG 292 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.98 CpG sites = 18, Kimura (unadjusted) = 31.45 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.06 (7 / 125), avg. gap size = 1.57 (11 / 7) 412 21.83 3.41 1.11 chr4ptel1M 343420 343507 (656493) C L2d2_3end#LINE/L2 (44) 511 422 m_b172s601i5 6629 chr4ptel1M 343420 AGGCACTGTGCTAAGTGCTA---GAGATATAAAGAACTACAAAAACCTGG 343466 i i i--- i i v i i - v C L2d2_3end#LIN 511 AGGCACTGTGCTAGGCGCTGTGGGGGATACAAAGAAGTATAAGA-CATGG 463 chr4ptel1M 343467 TCTCTGTCCTCAGTGAGCTCACATTCTAATACAGGAGACAA 343507 i i iv i v i vvi C L2d2_3end#LIN 462 TCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGGAGACAA 422 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 25.03 CpG sites = 13, Kimura (unadjusted) = 26.64 Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.02 (2 / 87), avg. gap size = 2.00 (4 / 2) 378 28.68 9.04 3.54 chr4ptel1M 345016 345203 (654797) C MIRc#SINE/MIR (68) 200 3 m_b172s601i7 6630 chr4ptel1M 345016 CATCTGACTCTCACAAGAAGCCTTTCAGGTTGCTACTCCAGGTATTGGAA 345065 i ii v v v v v vi vvv ivv C MIRc#SINE/MIR 200 CATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTA 151 chr4ptel1M 345066 CCTGCATCT----GA-GCAGAAAC--AGGCTCAGG----------GACCC 345098 i iv i ---- - vi -- i---------- ii C MIRc#SINE/MIR 150 TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTT 101 chr4ptel1M 345099 GCCCATGGAAACAGAGCAAGTAAGTGGAACCAGTTGGAAGGAAGTTTGAA 345148 v vv v v v -v ii i -----i i C MIRc#SINE/MIR 100 GCCCAAGGTCACACAGCTAGTAAGTGGCA-GAGCCGGGA-----CTCGAA 57 chr4ptel1M 345149 GCCAGTTCTCTCTGGACTCCAGGTACAAAGCACTTTCCATTAAAGCCCAT 345198 v v ii - i v iv v i iv v v i C MIRc#SINE/MIR 56 CCCAGGTCTTCCT-GACTCCAAGTCCAGTGCTCTTTCCACTGCACCACAC 8 chr4ptel1M 345199 TGCCT 345203 C MIRc#SINE/MIR 7 TGCCT 3 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.80 CpG sites = 24, Kimura (unadjusted) = 36.48 Transitions / transversions = 0.86 (24/28) Gap_init rate = 0.06 (11 / 187), avg. gap size = 2.18 (24 / 11) 270 26.39 5.56 0.00 chr4ptel1M 346479 346550 (653450) MIR3#SINE/MIR 49 124 (84) m_b172s601i8 6631 chr4ptel1M 346479 CTCAGTTCTCAGCCCAGCTTAGTCACT----TGCTGTGTGATCTCTGACA 346524 vi viv i iv i ----? i iv i MIR3#SINE/MIR 49 CTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCA 98 chr4ptel1M 346525 AATCACTGAAGCTCTCCAGGCCTCAG 346550 i vv v ii MIR3#SINE/MIR 99 AGTCACTTCACCTCTCTGGGCCTCAG 124 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.69 CpG sites = 11, Kimura (unadjusted) = 33.84 Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.01 (1 / 71), avg. gap size = 4.00 (4 / 1) 271 23.33 6.67 0.00 chr4ptel1M 346491 346550 (653450) MIRc#SINE/MIR 64 127 (141) m_b172s601i9 6631 chr4ptel1M 346491 CCCAGCTTAGTCACTT----GCTGTGTGATCTCTGACAAATCACTGAAGC 346536 i iv i ---- i iv i i v v MIRc#SINE/MIR 64 CCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACC 113 chr4ptel1M 346537 TCTCCAGGCCTCAG 346550 iii MIRc#SINE/MIR 114 TCTCTGAGCCTCAG 127 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 26.68 CpG sites = 10, Kimura (unadjusted) = 29.12 Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.02 (1 / 59), avg. gap size = 4.00 (4 / 1) 218 28.08 4.44 1.08 chr4ptel1M 348105 348194 (651806) MIR3#SINE/MIR 111 203 (5) m_b172s601i10 6631 chr4ptel1M 348105 TCTCTGGACCTCAGTTTCCTGCTTGGGCAAGTGAGTGGGCTGGGCT--CT 348152 i vv iv vv i v i i --v MIR3#SINE/MIR 111 TCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGAT 160 chr4ptel1M 348153 GCTTTGTCCACATCCTTTCCAAGTCTA--ATGCCATGAGTCTAT 348194 v i v -v vi i iv i-- v i v MIR3#SINE/MIR 161 GATCTCT-AAGGTCCCTTCCAGCTCTGACATTCTATGATTCTAT 203 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.36 CpG sites = 11, Kimura (unadjusted) = 35.36 Transitions / transversions = 0.79 (11/14) Gap_init rate = 0.03 (3 / 89), avg. gap size = 1.67 (5 / 3) 290 31.78 0.93 0.00 chr4ptel1M 348782 348888 (651112) L3#LINE/CR1 1618 1725 (2374) m_b172s601i11 6632 chr4ptel1M 348782 TAATGCTCTCATTAAATGCAATGGAAAGCTCGC-CAGACACAAGAGCGGG 348830 i i v v v iiv v iv i v - vi v?vi L3#LINE/CR1 1618 TGATGCTTTCCTGATACAGATTACAAAACTGGCACAGAGGCAAGATNCAG 1667 chr4ptel1M 348831 GTATGAAGGCAAGCTTCTTCTACCCAGACATCTGATAGAGGTCTCATTCT 348880 vvi v viii vv i i v i i ? L3#LINE/CR1 1668 TAGTGATGGGGGACTTCAACTATCCGGACATCTGCTGGAAGTCTCATTCN 1717 chr4ptel1M 348881 GCTGAAAG 348888 i L3#LINE/CR1 1718 GCTAAAAG 1725 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 41.39 CpG sites = 17, Kimura (unadjusted) = 43.03 Transitions / transversions = 1.00 (17/17) Gap_init rate = 0.01 (1 / 106), avg. gap size = 1.00 (1 / 1) 296 23.76 1.03 8.89 chr4ptel1M 348922 349018 (650982) C MIR3#SINE/MIR (9) 199 110 m_b172s601i12 6633 chr4ptel1M 348922 AGTCCTGAAATTTCACTGCTTAGAAGAGAGTCCTCAGAGACCATCTAACA 348971 i v ii v vv -i i -- i i --- C MIR3#SINE/MIR 199 AATCATAGAATGTCAGAGCT-GGAAGGGA--CCTTAGAGATCATCTA--- 156 chr4ptel1M 348972 GAGACCAACATCCTCAGTTTATA-ATGAGAAAACTGAGGTCGAGGGGG 349018 -- v vi v i - i i v i i C MIR3#SINE/MIR 155 --GTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAG 110 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.02 CpG sites = 13, Kimura (unadjusted) = 29.02 Transitions / transversions = 1.62 (13/8) Gap_init rate = 0.09 (9 / 96), avg. gap size = 1.00 (9 / 9) 277 19.44 18.06 0.00 chr4ptel1M 349141 349212 (650788) L3#LINE/CR1 1786 1870 (2229) m_b172s601i13 6632 chr4ptel1M 349141 GGAAGCAATAAGGGGA-CTCCTGTTCT-----------TAATCAACAAGA 349178 ii - v ii ----------- i i i L3#LINE/CR1 1786 GGAAGCAACGAGGGGAACTGCTACTCTGGACTTAATTCTGACCAACAAGG 1835 chr4ptel1M 349179 AAGAACTAGCTGGTGAAGT-GAAGGCAACAGAAAC 349212 i i - v i i i L3#LINE/CR1 1836 AAGAACTGGTTGGTGAAGTGGAAGTCGATAGGAAC 1870 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 19.86 CpG sites = 12, Kimura (unadjusted) = 23.83 Transitions / transversions = 6.00 (12/2) Gap_init rate = 0.04 (3 / 71), avg. gap size = 4.33 (13 / 3) 487 31.38 4.76 0.51 chr4ptel1M 349408 349596 (650404) C MIRc#SINE/MIR (63) 205 9 m_b172s601i14 6634 chr4ptel1M 349408 TAGTTTATTTGATCCACACAGT--CCCTGTGATGTCGGT---GCTATTAT 349452 vi i v ii-- v v i--- viv C MIRc#SINE/MIR 205 TATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTAT 156 chr4ptel1M 349453 TATTATTCCCCTTTTACAAATGGGGAAACTGGAGCAGACAAATGTTGA-C 349501 i v i i ii vv v i v i -i C MIRc#SINE/MIR 155 TATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGT 106 chr4ptel1M 349502 GACTCCCTCAATG--ACACAGTGAGGCAGTATCTAAAGCC-TAATTCAGA 349548 iv i v -- iv vv iv - i -vi i ii C MIRc#SINE/MIR 105 GACTTGCCCAAGGTCACACAGCTAGTAAGTGGC-AGAGCCGGGACTCGAA 57 chr4ptel1M 349549 GTCAGGTCTTTTGGACTCTTGATCGTTCCCTCTCTCCACAAAACCACA 349596 vi iiv ivii vvviv i viv C MIRc#SINE/MIR 56 CCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACA 9 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 40.63 CpG sites = 32, Kimura (unadjusted) = 41.55 Transitions / transversions = 1.19 (32/27) Gap_init rate = 0.03 (6 / 188), avg. gap size = 1.67 (10 / 6) 383 26.47 6.67 2.40 chr4ptel1M 349855 349974 (650026) C L2a_3end#LINE/L2 (12) 505 381 m_b172s601i15 6635 chr4ptel1M 349855 AGCAAATATTTATTATGTTCCTTCCCCACACAAAGCCCTGTGCCAGGCAC 349904 i iv iv v iviiii v i v v i i C L2a_3end#LINE 505 AACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGCGC 456 chr4ptel1M 349905 TGGGGATAC--------ACAAAGCAGAACAAGAGGATCCCTGACCTCAGG 349946 -------- i - i -- v v C L2a_3end#LINE 455 TGGGGATACAGCAGTGAACAAAACAG-ACAAAAG--TCCCTGCCCTCATG 409 chr4ptel1M 349947 GAGCGTGCATCTTCTTGGAAGGAGGCAG 349974 v i ii vv ii i C L2a_3end#LINE 408 GAGCTTACATTCTAGTGGGGGGAGACAG 381 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.00 CpG sites = 19, Kimura (unadjusted) = 33.61 Transitions / transversions = 1.58 (19/12) Gap_init rate = 0.03 (4 / 119), avg. gap size = 2.75 (11 / 4) 465 26.23 17.78 0.47 chr4ptel1M 351717 351896 (648104) C MIRb#SINE/MIR (14) 254 44 m_b172s601i16 6636 chr4ptel1M 351717 CATTTATTCAGTGCTTCCTATGCCCCAGGTACCCTGCCAAGTATTTTACA 351766 v i v iv i iv i iii C MIRb#SINE/MIR 254 CATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACA 205 chr4ptel1M 351767 ---ATTAATCTTGCTTAATATTTTTAA--------------AAATATT-- 351797 --- - iii vi ivi -------------- ii -- C MIRb#SINE/MIR 204 TGCATTA-TCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTAT 156 chr4ptel1M 351798 ---------TTTAAAGTTGAGGAAACTGAGGCAAGGAGAGGTGAACTGCC 351838 --------- v v vvi v v iv C MIRb#SINE/MIR 155 TATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAAC 106 chr4ptel1M 351839 TTATCCAAGATCCCA-AGC---TAAGTGTCTGAGGCTAGATTTGACCTCA 351884 ii i v - --- v v v vi i v i C MIRb#SINE/MIR 105 TTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCA 56 chr4ptel1M 351885 GGCCCTACTGAC 351896 i ivv C MIRb#SINE/MIR 55 GGTCTGTCTGAC 44 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.31 CpG sites = 26, Kimura (unadjusted) = 32.88 Transitions / transversions = 1.24 (26/21) Gap_init rate = 0.03 (6 / 179), avg. gap size = 5.50 (33 / 6) 384 23.83 8.40 0.71 chr4ptel1M 351797 351927 (648073) C MIR3#SINE/MIR (67) 141 1 m_b172s601i18 6636 chr4ptel1M 351797 TTTTAAAGTTGAGGAAACTGAGGCAAGGAGAGGTGAACTGCCTTATCCAA 351846 v v vvi v v ii C MIR3#SINE/MIR 141 TTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAA 92 chr4ptel1M 351847 GATCCCA-AGCTA---AGTGTCTGAGGCTAGATTTGACCTCAGGCCCTAC 351892 i v - ? --- v v v vi i v v i -i v C MIR3#SINE/MIR 91 GGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGG-TCTCC 43 chr4ptel1M 351893 TGA--CACAG---GTGCATTGCCTGCT--GCCCCGCTATCAG 351927 -- v --- vi vi -- v v ii C MIR3#SINE/MIR 42 TGACTCCCAGTCCGTGCTCTCTCTGCTCAGCCACTCTGCCAG 1 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.00 CpG sites = 12, Kimura (unadjusted) = 29.00 Transitions / transversions = 0.63 (12/19) Gap_init rate = 0.05 (6 / 130), avg. gap size = 2.00 (12 / 6) 395 24.78 4.42 0.00 chr4ptel1M 351797 351909 (648091) C MIRc#SINE/MIR (124) 144 27 m_b172s601i17 6636 chr4ptel1M 351797 TTTTAAAGTTGAGGAAACTGAGGCAAGGAGAGGTGAACTGCCTTATCCAA 351846 v v vvi v v v ii C MIRc#SINE/MIR 144 TTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAA 95 chr4ptel1M 351847 GATCCCA-AGC---TAAGTGTCTGAGGCTAGATTTGACCTCAGGCCCTAC 351892 i v - --- v v v vi i i v i i i v C MIRc#SINE/MIR 94 GGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCC 45 chr4ptel1M 351893 TGAC-ACAGGTGCATTGC 351909 -v i v v C MIRc#SINE/MIR 44 TGACTCCAAGTCCAGTGC 27 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.91 CpG sites = 11, Kimura (unadjusted) = 30.11 Transitions / transversions = 0.65 (11/17) Gap_init rate = 0.03 (3 / 112), avg. gap size = 1.67 (5 / 3) 275 26.15 1.03 5.38 chr4ptel1M 352236 352332 (647668) C MIRc#SINE/MIR (165) 103 11 m_b172s601i19 6637 chr4ptel1M 352236 CCTGCTCCAGGTCCCAGGGTCAGCAGGTGTCAGAGGCAGCCCTGGAACCC 352285 i i v v vi ii i i v v i vv v C MIRc#SINE/MIR 103 CTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCC 54 chr4ptel1M 352286 TGGTCTTTTTAAGTATCTCCAAGGCCAGC-TTCTTATCCACTTCACCA 352332 v ii i ---- v i-i - v C MIRc#SINE/MIR 53 AGGTCTTCCTGA----CTCCAAGTCCAGTGCTCTT-TCCACTGCACCA 11 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.94 CpG sites = 13, Kimura (unadjusted) = 32.56 Transitions / transversions = 1.18 (13/11) Gap_init rate = 0.06 (6 / 96), avg. gap size = 1.00 (6 / 6) 337 30.83 8.51 3.38 chr4ptel1M 352691 352831 (647169) L2b_3end#LINE/L2 317 464 (2) m_b172s601i20 6638 chr4ptel1M 352691 TATTTGTTTGCATGC--GATTTCTCCGTCGGACTGTGAGCTCTTTGCAGA 352738 i i ? i i-- vi i i iiii iv vi i L2b_3end#LINE 317 TGTCTGNTTACATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGG 366 chr4ptel1M 352739 CAGGGACTGTTTTTTGGCTGCTTTTTTC-------TTTTTTTGGCACTTA 352781 i ?----- v ii v ------- v iiiii i i L2b_3end#LINE 367 CAGGGACCGN-----GTCTGTCTTGTTCACCGCTGTATCCCCAGCGCCTA 411 chr4ptel1M 352782 GCACAGTGTCTAG--CACAGTCAGTACTTACTAAATGTTGATTG-ATTAA 352828 ? i i -- vi ii i v i vi - v L2b_3end#LINE 412 GCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTTGTTGAATGAA 461 chr4ptel1M 352829 TGA 352831 L2b_3end#LINE 462 TGA 464 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.81 CpG sites = 32, Kimura (unadjusted) = 44.71 Transitions / transversions = 3.20 (32/10) Gap_init rate = 0.06 (9 / 140), avg. gap size = 1.89 (17 / 9) 309 29.48 1.04 1.04 chr4ptel1M 353340 353435 (646565) MIRc#SINE/MIR 90 185 (83) m_b172s601i21 6639 chr4ptel1M 353340 TAACTTAGAGAAAGTCACTGAATCTCTCTGACCCCCAGTTTCTTCAGCTC 353389 i i v i v v i v i i v v MIRc#SINE/MIR 90 TGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTG 139 chr4ptel1M 353390 T-CAATGAGAAAAATTATGCTTTTTACCACCTCTCTCACAAGCTTGT 353435 -v i i v v i i vii- ii vi i v MIRc#SINE/MIR 140 TAAAATGGGGATAATAATACCTGCC-CTGCCTACCTCACAGGGTTGT 185 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.38 CpG sites = 16, Kimura (unadjusted) = 38.38 Transitions / transversions = 1.33 (16/12) Gap_init rate = 0.02 (2 / 95), avg. gap size = 1.00 (2 / 2) 217 28.25 12.96 1.67 chr4ptel1M 353826 353933 (646067) MIRc#SINE/MIR 34 153 (115) m_b172s601i22 6640 chr4ptel1M 353826 ACTCTGAGTGAGGAAGAGAGAGAAGCTCTGGTTCCACCTCAGAGATTTCC 353875 iv v vvvi -- i vi i iv v vv i v MIRc#SINE/MIR 34 ACTTGGAGTCAGGAAGACCTGG--GTTCGAGTCCCGGCTCTGCCACTTAC 81 chr4ptel1M 353876 TAACTGAGTG-CTCTGGCCAAGTCACT---------TGAA--TCAGCTTC 353913 i v - ii v --------- i-- i MIRc#SINE/MIR 82 TAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTC 131 chr4ptel1M 353914 TTCCTCTGTTAA--GAGGACAA 353933 i v v -- i i MIRc#SINE/MIR 132 CTCATCTGTAAAATGGGGATAA 153 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.49 CpG sites = 15, Kimura (unadjusted) = 35.95 Transitions / transversions = 1.00 (15/15) Gap_init rate = 0.06 (6 / 107), avg. gap size = 2.67 (16 / 6) 181 12.77 2.04 4.17 chr4ptel1M 353952 354000 (646000) C MamRTE1#LINE/RTE-BovB (3224) 588 541 m_b172s601i23 6641 chr4ptel1M 353952 ATAGCATC-TGATGTCCCTTGAGGCAAGGGTTATTTTGTTCTTGTCTTTG 354000 i - i v v v v -- ?? ? C MamRTE1#LINE/ 588 ATAGCGTCCTGATGTTCCATGACGCAATGGTTATTTTCT--TTGTNNTNG 541 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 12.61 CpG sites = 2, Kimura (unadjusted) = 15.05 Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.06 (3 / 48), avg. gap size = 1.00 (3 / 3) 276 26.98 0.00 0.00 chr4ptel1M 354065 354127 (645873) C MIRc#SINE/MIR (159) 109 47 m_b172s601i24 6642 chr4ptel1M 354065 AAATTGTTTGCCCAGGGCTGCATAGCAGCTAAGTGTCAGAGGCAGGACTC 354114 i vii i iii i viv v v i C MIRc#SINE/MIR 109 AAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTC 60 chr4ptel1M 354115 GAACACAGGCCTT 354127 v i C MIRc#SINE/MIR 59 GAACCCAGGTCTT 47 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.16 CpG sites = 11, Kimura (unadjusted) = 34.67 Transitions / transversions = 1.83 (11/6) Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0) 409 34.10 12.32 1.92 chr4ptel1M 354139 354422 (645578) C L3#LINE/CR1 (3) 4096 3784 m_b172s601i25 6643 chr4ptel1M 354139 AGAACCTCAGAGAACCTCAGAGCTGGCAGGGTTCCTCAGAAGACGTCTCA 354188 -- v i i v v- i i v i vi C L3#LINE/CR1 4096 AGAA--TCACAGAATCTCAGAGTTGGAAGGGA-CCTTAGAGGTCATCTAG 4050 chr4ptel1M 354189 TCCAGCCGGTGCC-TGGAAAATAG---TCTCTTCTATGGCACAGTTATCG 354234 i -- v - vv vii --- i iii ivvi iv i C L3#LINE/CR1 4049 TCCAACC--TCCCATCCAATGCAGGAATCCCTTCTACAACATCCCTGACA 4002 chr4ptel1M 354235 AGTGGTCATCCAGATATCATCTCACTGTCTCCAGGGAAGGATGGCCTGTG 354284 viviiiii v viii v v ivi iiiiv C L3#LINE/CR1 4001 AGTGGTCATCCAGCCTCTGCTTGAACACCTCCAGTGACGGGGAGCTCACT 3952 chr4ptel1M 354285 ACTTCC----GCA--CCA----------GGACCGCTCAAATTGCTGGGCA 354318 i ?---- -- ---------- v vi i i iv C L3#LINE/CR1 3951 ACCTCNCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGATTGTTAGAAA 3902 chr4ptel1M 354319 GATTCTCCTTAAATCAAGGCTAA-----TTTTTTGGGCACTTTCCTCCTT 354363 v ii v ii v v -----ii iiiv vv i vi v C L3#LINE/CR1 3901 GTTCTTCCTTATATTGAGCCGAAATCTGCCTCCCTGTAACTTCCACCCAT 3852 chr4ptel1M 354364 TGACTGCTAGTCCTGTCCTCCAAGGCCA---AGGACAAGT-------CTC 354403 i- v i i iiii --- i i ------- C L3#LINE/CR1 3851 TGG-TCCTAGTTCTGCCCTCTGGAGCCACACAGAATAAGTCTAATCCCTC 3803 chr4ptel1M 354404 CTCCACAGAACAGTCTTTC 354422 i vi i i C L3#LINE/CR1 3802 TTCCACATGACAGCCCTTC 3784 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 48.45 CpG sites = 61, Kimura (unadjusted) = 48.45 Transitions / transversions = 1.79 (61/34) Gap_init rate = 0.05 (14 / 283), avg. gap size = 2.93 (41 / 14) 204 21.43 0.00 0.00 chr4ptel1M 355082 355123 (644877) C L2d2_3end#LINE/L2 (13) 542 501 m_b172s601i26 6644 chr4ptel1M 355082 ACAAGTATTTACTAAGCACCTCGTGTGAGCAAGCCACTGGGC 355123 i i i i vv v v v C L2d2_3end#LIN 542 ACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGC 501 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 22.31 CpG sites = 4, Kimura (unadjusted) = 25.32 Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 294 34.34 9.22 1.59 chr4ptel1M 355237 355529 (644471) C L3b_3end#LINE/CR1 (741) 465 151 m_b172s601i27 6645 chr4ptel1M 355237 GAAATCAAGGACAGAGCTTCCCATTTGTTCCTAGTAAATGGAACACTGTT 355286 vi vi ii iv i i i iv i vvv ivi C L3b_3end#LINE 465 GAACCCAAGTGCAGGACTTTACGTTTATCCCTGTTGAATTTCATCTTGTT 416 chr4ptel1M 355287 CAAATTGGCCCATCTTTTTCATCTTTTGG--TCCCTTT---CCCCCACTT 355331 vi?v i i? v i vi v i i-- vi ---i iv i C L3b_3end#LINE 415 GGNTTCGGCCCGNCGTTCTAGTCTGTCGAGATCGTTTTGGATCCTGATTT 366 chr4ptel1M 355332 ---AACCAGCATGTTTGCTGCCCATCCCAGCTT-TGCCAT------ATTT 355371 --- v i i i v i i vv - i------ C L3b_3end#LINE 365 TGCATCCAACGTATTAGCCGTCGCTCCCAGCTTCTGCCACTNGCAAATTT 316 chr4ptel1M 355372 AA-AAGCATTCCATCCACATACAACCTGATCCAAGTCCCTGATCCGATGT 355420 i - - v iv ii ---- i v vi v i vv C L3b_3end#LINE 315 GATAAGC-TGCTTTCCGTAT----CTTCATCCAAGTCATTGATACAAATT 271 chr4ptel1M 355421 TGGACAG--CCAGACTAAGGAGGGATCCC-ACAG-ATGCTCCCCGTGAC- 355465 ii -- v i i vi v -i i - i iv iv v - C L3b_3end#LINE 270 CAGACAGGACAAGGCCAAGGACAGAGCCCTGCGGCACGCCACTAGAGACT 221 chr4ptel1M 355466 --CTC-AGGATGAGG--GGTCCAATC-TGACTGAACTCTGGGTTCATTCA 355509 -- - v vi-- i? v ?- v vi vv i ? iv ii C L3b_3end#LINE 220 CCCTCCAGGTTGACATCGANCCATTNATCAACGTCCTTTGGGTNCGGTTG 171 chr4ptel1M 355510 TTTAACTAGTGCCGAATGCC 355529 i i ivv? i C L3b_3end#LINE 170 TTCAACCAGCTANGAATGTC 151 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 41.82 CpG sites = 57, Kimura (unadjusted) = 49.12 Transitions / transversions = 1.36 (57/42) Gap_init rate = 0.07 (19 / 292), avg. gap size = 1.68 (32 / 19) 193 19.15 6.38 0.00 chr4ptel1M 355681 355727 (644273) L2d2_3end#LINE/L2 476 525 (30) m_b172s601i28 6646 chr4ptel1M 355681 TTCTTGGTATCCCC---AGCACCTGCCACAGTGGCTAGCACAGAATCGGC 355727 v --- i iv v v v i v L2d2_3end#LIN 476 TTCTTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAGTAGGC 525 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 19.60 CpG sites = 3, Kimura (unadjusted) = 22.11 Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.02 (1 / 46), avg. gap size = 3.00 (3 / 1) 196 19.51 0.00 0.00 chr4ptel1M 355687 355727 (644273) L2b_3end#LINE/L2 396 436 (30) m_b172s601i29 6646 chr4ptel1M 355687 GTATCCCCAGCACCTGCCACAGTGGCTAGCACAGAATCGGC 355727 i iv ? v i v i v L2b_3end#LINE 396 GTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGC 436 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 20.30 CpG sites = 4, Kimura (unadjusted) = 23.41 Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 241 26.01 8.67 5.16 chr4ptel1M 356457 356606 (643394) MIR3#SINE/MIR 1 155 (53) m_b172s601i30 6647 chr4ptel1M 356457 CTGGTCTGGTGGCTCAGGGGATAGAACCCCCCCATCAAGAGTCAGGAAGT 356506 ivvi v vi v i v vv-- iiii - v MIR3#SINE/MIR 1 CTGGCAGAGTGGCTGAGCAGAGAGAGCACGG--ACTGGGAGTCAGGA-GA 47 chr4ptel1M 356507 CCCGAGTGCAAGTCCAG--TCGGACCAC------G-TGTGCGGCCAGCTG 356547 i i v v v -- v - ------ - i i --i MIR3#SINE/MIR 48 CCTGGGTTCTAGTCCCGGCTCTG-CCACTAACTNGCTGTGTGACC--TTG 94 chr4ptel1M 356548 GACAGATCCCATCCCCTCTT---GCCTCAGTT-CATCATCTGTAAAATGA 356593 i ii v v v i--- - v MIR3#SINE/MIR 95 GGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGA 144 chr4ptel1M 356594 GCCGGAGAAGGAC 356606 -- i vv MIR3#SINE/MIR 145 G--GGGGTTGGAC 155 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.28 CpG sites = 18, Kimura (unadjusted) = 32.28 Transitions / transversions = 0.95 (18/19) Gap_init rate = 0.09 (13 / 149), avg. gap size = 1.62 (21 / 13) 247 28.30 9.23 2.16 chr4ptel1M 356465 356594 (643406) MIRc#SINE/MIR 10 148 (120) m_b172s601i31 6647 chr4ptel1M 356465 GTGGCTCAGGGGATAGAACCCCCCCATCAAGAGTCAGGAAGTCCCGAGTG 356514 iv v v i v ivv- iivi v i i v MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGG-ACTTGGAGTCAGGAAGACCTGGGTT 58 chr4ptel1M 356515 CAAGTCCAG--TCGG------ACCACGTGTGCGGCCAGCTGGACAGATCC 356556 i v -- v ------ i vv i i --i i ii v MIRc#SINE/MIR 59 CGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACC--TTGGGCAAGTCA 106 chr4ptel1M 356557 CATCCCCTCTT---GCCTCAG-TTCATCATCTGTAAAATGAG 356594 v vv i--- - v i MIRc#SINE/MIR 107 CTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.80 CpG sites = 18, Kimura (unadjusted) = 36.02 Transitions / transversions = 1.00 (18/18) Gap_init rate = 0.05 (7 / 129), avg. gap size = 2.14 (15 / 7) 339 27.79 20.00 1.05 chr4ptel1M 356769 356928 (643072) C MIRc#SINE/MIR (44) 224 35 m_b172s601i32 6648 chr4ptel1M 356769 AAAACTCTTTTGCATTCATTCTCCCATTTGAGCC---CAGCAGGATCCTC 356815 i v ii v v i v --- i -- i v C MIRc#SINE/MIR 224 AAAGCGCTTTCACATACATTATCTCATTTGATCCTCACAACA--ACCCTG 177 chr4ptel1M 356816 TGGGACAAG-------AGTATT--TCCTCCCATTC-----ATAGGGA--- 356848 i ii i -------i -- vii i----- ii --- C MIRc#SINE/MIR 176 TGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAAC 127 chr4ptel1M 356849 -----CT-------GTTTAATGACTTGCCCAGGGTCACGTAGCTAGAGAA 356886 ----- ------- v i i ii vi i C MIRc#SINE/MIR 126 TGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAG 77 chr4ptel1M 356887 TGTCTGTGGCGGAATCTGAGCCCAGGTGTTCCCTACTCTGAG 356928 v v v v i iii i v iv ii C MIRc#SINE/MIR 76 TGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.41 CpG sites = 30, Kimura (unadjusted) = 36.47 Transitions / transversions = 2.14 (30/14) Gap_init rate = 0.06 (9 / 159), avg. gap size = 3.78 (34 / 9) 204 21.28 6.38 0.00 chr4ptel1M 357078 357124 (642876) C MIRc#SINE/MIR (195) 73 24 m_b172s601i33 6649 chr4ptel1M 357078 CAGAAGCAGCACTTGAACCCAGATCTTTCTG-TTCCAAG--GAGGGCTCT 357124 iv i v i i i -i --v v C MIRc#SINE/MIR 73 CAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCT 24 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 19.98 CpG sites = 6, Kimura (unadjusted) = 25.47 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.04 (2 / 46), avg. gap size = 1.50 (3 / 2) 334 31.51 6.22 7.89 chr4ptel1M 358119 358311 (641689) MIR#SINE/MIR 23 212 (50) m_b172s601i34 6650 chr4ptel1M 358119 AACATAGACCCTGGATTCGGATCTGCCACAGACTC----CCCAGCTCCGG 358164 i ii i i vi i - -ii ii ---- i i - MIR#SINE/MIR 23 AGCACGGGCTCTGGAGCCAGA-CTGCC-TGGGTTCGAATCCCGGCTCTG- 69 chr4ptel1M 358165 GGCAAGTCACTGAAGCTGTGTGAGGCCATATCCCCAGGCCA------TAA 358208 -- v v i -- -------- iii v ------ MIR#SINE/MIR 70 --CCACTTACT--AGCTGTGTGA--------CCTTGGGCAAGTTACTTAA 107 chr4ptel1M 358209 CCTCT--GACCCTCAGCTCTCTCACCTGCACAATGGGGATAATAAGGGCA 358256 -- vv i ii i i v vi i MIR#SINE/MIR 108 CCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTA 157 chr4ptel1M 358257 TCTTCATCACAGAGTAACGGCAAGGACCCAATAAGATGGCACGTACAAAA 358306 i v v i i viiv ii iiv i v iii i ii i MIR#SINE/MIR 158 CCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATACATGTAAAG 207 chr4ptel1M 358307 TGCTT 358311 i MIR#SINE/MIR 208 CGCTT 212 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 40.88 CpG sites = 42, Kimura (unadjusted) = 44.27 Transitions / transversions = 3.00 (42/14) Gap_init rate = 0.09 (18 / 192), avg. gap size = 1.50 (27 / 18) 534 27.20 1.06 6.15 chr4ptel1M 358391 358578 (641422) MIR3#SINE/MIR 3 181 (27) m_b172s601i35 6651 chr4ptel1M 358391 GGCAGCCAAGTGGCTGAGCAGGTAATGCACTGATCCTGGACTCACCAAGA 358440 --- iv iv v - iv v v-i MIR3#SINE/MIR 3 GGCAG---AGTGGCTGAGCAGAGAGAGCACGGA-CTGGGAGTCAG-GAGA 47 chr4ptel1M 358441 CTTGAGTTCAAATTTACCCTCAGACATCTACTAGCTACATGACCATGGGC 358490 i i v i iivvv v v iiv ? iii v MIR3#SINE/MIR 48 CCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGC 97 chr4ptel1M 358491 AAGTCACTGTGCC-CTGTTTGCCTCAGTTTCCTCACCTATAAAATGAGCT 358539 vii - v vv i i vv MIR3#SINE/MIR 98 AAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGG 147 chr4ptel1M 358540 GG-AGAAAGAAATGATGAACCACTCTAGGACCTCTGCCAG 358578 -v i vv i ------ i ii i v MIR3#SINE/MIR 148 GGTTGGACTAGATGAT------CTCTAAGGTCCCTTCCAG 181 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.27 CpG sites = 24, Kimura (unadjusted) = 34.27 Transitions / transversions = 1.00 (24/24) Gap_init rate = 0.07 (13 / 187), avg. gap size = 1.00 (13 / 13) 18 12.00 8.70 0.00 chr4ptel1M 358884 358929 (641071) (TGTACA)n#Simple_repeat 1 50 (0) m_b172s252i5 6652 chr4ptel1M 358884 TGTACATGTACATG--GATGTGCATGTGCATGT-C-TATACATGTATATG 358929 --v i i - - i i (TGTACA)n#Sim 1 TGTACATGTACATGTACATGTACATGTACATGTACATGTACATGTACATG 50 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.07 (3 / 45), avg. gap size = 1.33 (4 / 3) 15 19.86 0.00 0.00 chr4ptel1M 358935 358969 (641031) (GACAGA)n#Simple_repeat 1 35 (0) m_b172s252i6 6653 chr4ptel1M 358935 GACTGAGGAAAAGGCAGAGACAGAGACAAAGACAG 358969 v iv i i i (GACAGA)n#Sim 1 GACAGAGACAGAGACAGAGACAGAGACAGAGACAG 35 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 229 13.04 15.22 0.00 chr4ptel1M 359896 359941 (640059) MIR3#SINE/MIR 92 144 (64) m_b172s601i36 6654 chr4ptel1M 359896 TTGGGCAAGCCACTTT-----TTTG--CCTCAGTTTCCTCATCTGTGGAA 359938 i i----- i -- ii MIR3#SINE/MIR 92 TTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAA 141 chr4ptel1M 359939 CGA 359941 i MIR3#SINE/MIR 142 TGA 144 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 15.11 CpG sites = 6, Kimura (unadjusted) = 15.11 Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.04 (2 / 45), avg. gap size = 3.50 (7 / 2) 342 30.49 5.00 1.61 chr4ptel1M 360378 360497 (639503) C L2d_3end#LINE/L2 (14) 502 379 m_b172s601i37 6655 chr4ptel1M 360378 AATAAATTTTTATTATGTGCTTACCATGT--TTAACTCTGTTCTTAATGC 360425 i i v iv i i i -- i i v v viii C L2d_3end#LINE 502 AACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTGTGCTAGGCGC 453 chr4ptel1M 360426 T---AGAAATAGCAAGAAAGGCAAAACCATGGTCTCTACCCT-AAGAAGT 360471 ---i i iii? i ? vvv iv i i - i i C L2d_3end#LINE 452 TGTGGGGAACGANAAAANAGTATAAGACATGGTCCCTGCCCTCAAGGAGC 403 chr4ptel1M 360472 TCACAGTCTAATTTAGGGGGGAAAAG 360497 i i i -- i v C L2d_3end#LINE 402 TTACAATCTAGTT--GGGGAGACAAG 379 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.03 CpG sites = 26, Kimura (unadjusted) = 42.96 Transitions / transversions = 2.60 (26/10) Gap_init rate = 0.04 (5 / 119), avg. gap size = 1.60 (8 / 5) 322 13.21 1.89 0.00 chr4ptel1M 360627 360679 (639321) C MIR3#SINE/MIR (52) 156 103 m_b172s601i38 6656 chr4ptel1M 360627 AGTCCAACCCCCTCATTTTACAG-TGAGAAAACTGAAGCCCAAGGAAGAC 360675 - i i ii i vv C MIR3#SINE/MIR 156 AGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTG 107 chr4ptel1M 360676 AAGT 360679 C MIR3#SINE/MIR 106 AAGT 103 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 14.80 CpG sites = 5, Kimura (unadjusted) = 14.80 Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.02 (1 / 52), avg. gap size = 1.00 (1 / 1) 302 30.78 2.68 6.25 chr4ptel1M 360673 360821 (639179) MIRc#SINE/MIR 98 241 (27) m_b172s601i39 6657 chr4ptel1M 360673 GACAAGTCAGAAGACCTAGTTTGAAAGTCCCAATTCTAATTCCTCATCTG 360722 i vvvi v- i -- i i i ----- MIRc#SINE/MIR 98 GGCAAGTCACTTAACCTC-TCTGA--GCCTCAGTT-----TCCTCATCTG 139 chr4ptel1M 360723 CCTAATGGAGGCAGTAACATTTGCAGTATCTCCTTCACAAGGACTGTTGA 360772 ivv i ii i i ii vv ii v i - ii v MIRc#SINE/MIR 140 TAAAATGGGGATAATAATACCTGCCCTGCCTACCTCAC-AGGGTTGTTGT 188 chr4ptel1M 360773 GAAGATCAAA--AGACAGT-CATTACTCAGTGCTTAGTAAAC-ATAGAGT 360818 i -- i i -i vvvvv i v -i i MIRc#SINE/MIR 189 GAGGATCAAATGAGATAATGTATGTGAAAGCGCTTTGTAAACTGTAAAGT 238 chr4ptel1M 360819 ACT 360821 i MIRc#SINE/MIR 239 GCT 241 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.88 CpG sites = 27, Kimura (unadjusted) = 41.15 Transitions / transversions = 1.69 (27/16) Gap_init rate = 0.08 (12 / 148), avg. gap size = 1.08 (13 / 12) 456 21.60 20.13 0.56 chr4ptel1M 360830 360978 (639022) C MIR#SINE/MIR (0) 262 85 m_b172s601i40 6658 chr4ptel1M 360830 AAGAATAACTGACATTTATAGAGCACTT--TAAGTGTCA--------TC- 360868 v i i v i -- v i -------- - C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCT 213 chr4ptel1M 360869 AAGTGCTTTATA------AAC-------ATTCTCCCAATAACTCTCATGT 360905 i i ------ ------- i v i i - v C MIR#SINE/MIR 212 AAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCT-ATGA 164 chr4ptel1M 360906 TGT------TTTTACCATTCCCATTTTACAAAGGAGGAAACTGAGGCAAA 360949 v ------ v ii i i v v C MIR#SINE/MIR 163 GGTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACA 114 chr4ptel1M 360950 GAGAAATCAAGTGACTTGTTGAGAGCCAC 360978 ii i i iiv ii i C MIR#SINE/MIR 113 GAGAGGTTAAGTAACTTGCCCAAGGTCAC 85 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 24.45 CpG sites = 22, Kimura (unadjusted) = 26.33 Transitions / transversions = 2.20 (22/10) Gap_init rate = 0.05 (7 / 148), avg. gap size = 4.43 (31 / 7) 545 25.61 16.09 1.52 chr4ptel1M 361018 361247 (638753) C MIRc#SINE/MIR (3) 265 3 m_b172s601i41 6659 chr4ptel1M 361018 AATAACAATGGCTCATATTTATGCAGCACCC-ACTCTGTTCTAGGTGATT 361066 i i?v i i i ii ii- vv v v v i i v C MIRc#SINE/MIR 265 AATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCGCTT 216 chr4ptel1M 361067 T---ATAAAACATCTCATTTGATCTT--------------------GG-A 361092 --- v vi i -------------------- - C MIRc#SINE/MIR 215 TCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCA 166 chr4ptel1M 361093 AGGCAGGTGCTATTACCTCCACT--------GAAGTAACTGAGGCAGGTA 361134 i ii i i i -------- i v vviv C MIRc#SINE/MIR 165 GGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGA 116 chr4ptel1M 361135 GTGGTAAAGTGACCTTCCCAGAGTCAC-CACCTAATAAGCAGCTGAGGCT 361183 v v i v ii - v i ii v v v C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 66 chr4ptel1M 361184 GGATTTAAACTCA--TCTTTCTGACTCCACAGT-CAATGATCTACCCTCT 361230 i ii i -- i - - i v vi v C MIRc#SINE/MIR 65 GGACTCGAACCCAGGTCTTCCTGACTCCA-AGTCCAGTGCTCTTTCCACT 17 chr4ptel1M 361231 GTGCCACCTCACTGCCT 361247 --- v C MIRc#SINE/MIR 16 G---CACCACACTGCCT 3 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.88 CpG sites = 34, Kimura (unadjusted) = 32.29 Transitions / transversions = 1.42 (34/24) Gap_init rate = 0.05 (12 / 229), avg. gap size = 3.42 (41 / 12) 552 31.93 3.06 2.54 chr4ptel1M 361460 361655 (638345) C L3#LINE/CR1 (109) 3990 3794 m_b172s601i42 6660 chr4ptel1M 361460 AGCCTCT-CCAGAACTACTCCCAATGAGGGAAAGCTCCCTATTTTCCATA 361508 - iv - ii i v ii v ii i? ivi C L3#LINE/CR1 3990 AGCCTCTGCTTGAAC-ACCTCCAGTGACGGGGAGCTCACTACCTCNCGAG 3942 chr4ptel1M 361509 GTAACTCAGGCCACTCTGAAGCAACTTAAAGTCATTAG----TTCC-CCT 361553 i i i vv i i viii i ivi - ii ---- i- C L3#LINE/CR1 3941 GCAGCCCATTCCATTTTTGGACAGCTCTGA-TTGTTAGAAAGTTCTTCCT 3893 chr4ptel1M 361554 CACATCAAACTGAAATTTGCTTCTTTACAATTTCTATCCATTGCGACTAG 361603 i i ii i i i i ii ii i i i vvv C L3#LINE/CR1 3892 TATATTGAGCCGAAATCTGCCTCCCTGTAACTTCCACCCATTGGTCCTAG 3843 chr4ptel1M 361604 TTCTGACCTCTGAAGCCAGGCAAAATCAGCCATCCAAGCTCTCTTCCAAA 361653 v i vi i v --- i v i v C L3#LINE/CR1 3842 TTCTGCCCTCTGGAGCCACACAGAATAAG---TCTAATCCCTCTTCCACA 3796 chr4ptel1M 361654 TG 361655 C L3#LINE/CR1 3795 TG 3794 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 43.32 CpG sites = 45, Kimura (unadjusted) = 45.42 Transitions / transversions = 2.81 (45/16) Gap_init rate = 0.04 (8 / 195), avg. gap size = 1.38 (11 / 8) 261 26.07 0.00 4.11 chr4ptel1M 361835 361910 (638090) MIRc#SINE/MIR 2 74 (194) m_b172s601i43 6661 chr4ptel1M 361835 GAGGCAGCTAGGTGGGGCAGTGGATAGATCACCAGCCCTGAAGAGAGGAA 361884 i--- v v v ii v i i vv MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr4ptel1M 361885 GACCTGAGTTCAAATTTGGCCTCAGC 361910 i i i iiv v v MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGC 74 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.39 CpG sites = 10, Kimura (unadjusted) = 32.39 Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.04 (3 / 75), avg. gap size = 1.00 (3 / 3) 336 35.01 1.23 1.65 chr4ptel1M 361914 362157 (637843) L1ME4c_3end#LINE/L1 397 639 (191) m_b172s551i5 6662 chr4ptel1M 361914 TAGCCCAAAAAGATA-TT--AAAGAAGGGAAAGGGACCTGTTAGTGCAAA 361960 v i ii i - -- i i --- i vv ii i L1ME4c_3end#L 397 TATCCTAAGGAAATAATTCAAAAGAAGGAAAAAG---CTATATGCACGAA 443 chr4ptel1M 361961 AATGTTTGTGACAGGTCTCTTTGTAGTGGCCAGAAAATGGAAACTGAGTG 362010 i ii vi vvi v i i i v i v vivv i L1ME4c_3end#L 444 GATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTA 493 chr4ptel1M 362011 GATGCCCATCAATTGGAGAATGGCTGAATAAATTGGGGTATATGAATATT 362060 i i v v i i i i iv i v? iviv L1ME4c_3end#L 494 AATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCG 543 chr4ptel1M 362061 ATGGAATATTATTGTTCTGTAAGAAATGACCAGCAGGAGGATTTCAGAGA 362110 vvvv ii v i iv vi v i i viiv v L1ME4c_3end#L 544 ATGGAATATTATGCAGCCATTAAAAATGATAATTATGAAGACTATGTAGC 593 chr4ptel1M 362111 GGCCTGGAGTGACTTATATGAACTGATGCTGAGTGAAATGAGCAGAA 362157 ii v i-i iv v vv i i i vi L1ME4c_3end#L 594 AACATGGAA-AATGTTTATGATATAATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 47.65 CpG sites = 49, Kimura (unadjusted) = 49.32 Transitions / transversions = 1.40 (49/35) Gap_init rate = 0.02 (6 / 243), avg. gap size = 1.17 (7 / 6) 430 29.17 0.00 0.00 chr4ptel1M 361954 362073 (637927) L1ME2z_3end#LINE/L1 434 553 (638) m_b172s551i6 6662 chr4ptel1M 361954 GTGCAAAAATGTTTGTGACAGGTCTCTTTGTAGTGGCCAGAAAATGGAAA 362003 i i ii ii v i v ii i i i v L1ME2z_3end#L 434 GTACAAGAATGTTCATAGCAGCTTTATTCATAATAGCCAAAAACTGGAAA 483 chr4ptel1M 362004 CTGAGTGGATGCCCATCAATTGGAGAATGGCTGAATAAATTGGGGTATAT 362053 v vvii i i iv v i i i v L1ME2z_3end#L 484 CAGCCCAGGTGTCCATCAACAGGAGAATGGATAAACAAACTGTGGTATAT 533 chr4ptel1M 362054 GAATATTATGGAATATTATT 362073 vv iv i i L1ME2z_3end#L 534 TCATACAATGGAATACTACT 553 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.60 CpG sites = 23, Kimura (unadjusted) = 38.60 Transitions / transversions = 1.92 (23/12) Gap_init rate = 0.00 (0 / 119), avg. gap size = 0.0 (0 / 0) 348 27.71 4.66 4.66 chr4ptel1M 361961 362153 (637847) L1MC3_3end#LINE/L1 441 633 (1899) m_b172s551i7 6662 chr4ptel1M 361961 AATGTTTGTGACAGGTCTCTTTGTAGTGGCCAGAAAATGGAA---ACTGA 362007 i ii v i v ii i v i v --- ii L1MC3_3end#LI 441 AATGTTTATAGCAGCTTTATTCATAATCGCCAAAAACTGGAAGCAACCAA 490 chr4ptel1M 362008 GTGGATGCCCATCAATTGGAGAATGGCTGAATAAATTGGGGTATATGAAT 362057 --- i v v v v i i i v i vv L1MC3_3end#LI 491 G---ATGTCCTTCAATAGGTGAATGGATAAACAAACTGTGGTACATCCAT 537 chr4ptel1M 362058 ATTATGGAATATTATTGTTCTGT---AAGAAATGA-CCAGCAGGAGGATT 362103 iv vvv vi --- - i v i ----ii L1MC3_3end#LI 538 ACAATGGAATATTATTCAGCGATAAAAAGAAATGAGCTATCAAG----CC 583 chr4ptel1M 362104 TCAGAGAGGCCTGGAGTGA--CTTATATGAACTGATGCTGAGTGAAATGA 362151 v ii i i v - -- v v - iv i vi L1MC3_3end#LI 584 ACGAAAAGACATGGA-TGAATCTTAAATGCA-TATTGCTAAGTGAAAGAA 631 chr4ptel1M 362152 GC 362153 L1MC3_3end#LI 632 GC 633 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 34.39 CpG sites = 28, Kimura (unadjusted) = 35.24 Transitions / transversions = 1.22 (28/23) Gap_init rate = 0.07 (13 / 192), avg. gap size = 1.38 (18 / 13) 283 13.73 1.96 0.00 chr4ptel1M 362605 362655 (637345) MIR#SINE/MIR 72 123 (139) m_b172s601i44 6663 chr4ptel1M 362605 ACTTCCTGGCTGTGTGACCCTGGGCAAGTCACTTAACCCCAAT-TGCCTC 362653 v i i i i vv - MIR#SINE/MIR 72 ACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTC 121 chr4ptel1M 362654 AG 362655 MIR#SINE/MIR 122 AG 123 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 15.28 CpG sites = 4, Kimura (unadjusted) = 15.28 Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.02 (1 / 50), avg. gap size = 1.00 (1 / 1) 465 18.18 0.00 1.01 chr4ptel1M 363152 363251 (636749) Charlie4#DNA/hAT-Charlie 3218 3316 (62) m_b172s502i1 6664 chr4ptel1M 363152 TTCTTGGATATTTTGAATAGCTTTATTTCAATAGAACTGGCTTCCTTGGT 363201 i ii - i v v i i v Charlie4#DNA/ 3218 TTTTTAAATATTTTGA-TAACTATATTTCAATATAATTGGTTTCCTTTGT 3266 chr4ptel1M 363202 AAGGATTTGTGTTTTACTTTGTGCATTTAAAAACAAGATTCTGAGAAGGG 363251 vvv v i i i vv Charlie4#DNA/ 3267 AATCCTATGTATTTTATTTTATGCATTTAAAAACATTATTCTGAGAAGGG 3316 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 20.94 CpG sites = 9, Kimura (unadjusted) = 20.94 Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.01 (1 / 99), avg. gap size = 1.00 (1 / 1) 630 24.36 6.75 1.75 chr4ptel1M 363938 364100 (635900) C Charlie4a#DNA/hAT-Charlie (3) 505 335 m_b172s502i2 6665 chr4ptel1M 363938 GAGTTCTTGATCTCTGTTGTGTTCTGGATCCC-----------AATGTAG 363976 i i i i v iiv i -----------ii v C Charlie4a#DNA 505 GGGTTCTTAACCTTTTTTGTGCCATGGACCCCTTTGGCAGTCTGGTGAAG 456 chr4ptel1M 363977 CCTAAGGATCTCTTCTCAGAATCATGTTCTAAAATGGGTGGGATAAAATA 364026 v i i v i v vi iii C Charlie4a#DNA 455 CCTATGGACCCCTTCTCAGAATAATGTTTTTAAATGCATAAAATAAAATA 406 chr4ptel1M 364027 CATGGGATTGCAAATGAAGCCAATTACACTGAAATGCTGTTATCACAATA 364076 i i v i i i i v v C Charlie4a#DNA 405 CATAGGATTACAAAGGAAACCAATTATATTGAAATACAGTTATCAAAATA 356 chr4ptel1M 364077 TTTTTAAAAGAATAAGCTCATGGT 364100 --- i ?i ii ii i C Charlie4a#DNA 355 ---TTAAAAAANCAAATTTGTGAT 335 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 31.26 CpG sites = 29, Kimura (unadjusted) = 31.26 Transitions / transversions = 2.90 (29/10) Gap_init rate = 0.02 (4 / 162), avg. gap size = 3.50 (14 / 4) 201 23.09 2.94 4.48 chr4ptel1M 364143 364210 (635790) C MIRc#SINE/MIR (155) 113 47 m_b172s601i45 6666 chr4ptel1M 364143 GATTAAGTGATTTGTCCAGAGTTACAAAGCTTGATAGGT-TCCCAGCT-G 364190 i i i ii i v v - i -v vv i- C MIRc#SINE/MIR 113 GGTTAAGTGACTTGCCCAAGGTCACACAGCTAG-TAAGTGGCAGAGCCGG 65 chr4ptel1M 364191 GACTCTGAAGCCAGAGTTTT 364210 - v - i C MIRc#SINE/MIR 64 GACTC-GAACCCAG-GTCTT 47 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 25.99 CpG sites = 9, Kimura (unadjusted) = 28.14 Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.07 (5 / 67), avg. gap size = 1.00 (5 / 5) 18 24.06 0.00 2.22 chr4ptel1M 365461 365506 (634494) (GA)n#Simple_repeat 1 45 (0) m_b172s252i7 6667 chr4ptel1M 365461 GAGAGAGTGAGATGACAGAGATACAAAGAGAGAGGAAGGGAGGGAG 365506 v - v v v i ii i i (GA)n#Simple_ 1 GAGAGAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 45 Matrix = Unknown Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1) 273 16.67 0.00 0.00 chr4ptel1M 365755 365796 (634204) C EuthAT-N1#DNA/hAT-Tip100 (141) 194 153 m_b172s502i3 6668 chr4ptel1M 365755 ATTATTCTTGCTAATTAGGTGCCAGATCCAGTTGTTTCTATG 365796 i i iiii i C EuthAT-N1#DNA 194 ATTATTCTTGCTAACTAGGTGCTAAGCTCAGTTGTTTCTACG 153 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 17.16 CpG sites = 7, Kimura (unadjusted) = 20.27 Transitions / transversions = 1.00 (7/0) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 352 33.33 0.00 0.00 chr4ptel1M 366128 366223 (633777) C L2b_3end#LINE/L2 (5) 461 366 m_b172s601i46 6669 chr4ptel1M 366128 TTCATTAAACAAAGATTTATTAAGCATCTGCCCTGTGTAAAGCACTGCAC 366177 v v i i ii i iv iv i ? ii C L2b_3end#LINE 461 TTCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGC 412 chr4ptel1M 366178 TAGGTACTGAGAATACAGTGACAAAAAGGTAAGTTTCAATCATTGC 366223 ii i i i iii v i vv vi? ii vi C L2b_3end#LINE 411 TAGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGC 366 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 40.61 CpG sites = 23, Kimura (unadjusted) = 49.30 Transitions / transversions = 2.56 (23/9) Gap_init rate = 0.00 (0 / 95), avg. gap size = 0.0 (0 / 0) 17 16.14 0.00 0.00 chr4ptel1M 367487 367515 (632485) (T)n#Simple_repeat 1 29 (0) m_b172s252i8 6670 chr4ptel1M 367487 TTTCTTTTTTCTTTTTTTTCTTCTTTTTT 367515 i i i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 502 23.86 0.00 8.77 chr4ptel1M 367531 367654 (632346) C MIRb#SINE/MIR (150) 118 5 m_b172s601i47 6671 chr4ptel1M 367531 GGAGCTAAGTGACTTGTCCAGAGTCACACAGCTAGGAAGTGTTAAGTGTC 367580 ii i i i ii ------- v C MIRb#SINE/MIR 118 GAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGC 76 chr4ptel1M 367581 TGAAGTCAGATTTGAACTCAGGTCCTCCTGACTTCAGGGTTCATGCTCTA 367630 v ivivi i i ivi i ii ii i v C MIRb#SINE/MIR 75 AGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTT 26 chr4ptel1M 367631 TCCACTGCACAACCTAGCTGCCCC 367654 v --- C MIRb#SINE/MIR 25 TCCACTGCACCAC---GCTGCCCC 5 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 25.98 CpG sites = 20, Kimura (unadjusted) = 29.85 Transitions / transversions = 2.86 (20/7) Gap_init rate = 0.08 (10 / 123), avg. gap size = 1.00 (10 / 10) 226 25.42 3.39 0.00 chr4ptel1M 367782 367840 (632160) C L3b_3end#LINE/CR1 (227) 979 919 m_b172s601i48 6672 chr4ptel1M 367782 TCCCACAGG--GCACTTTAAGCTTATTTCCTCTTGCCTTGTTCTCCAAAG 367829 v v -- v ii iii i vivi C L3b_3end#LINE 979 TCCCTCATGCTGCAGTTTAAGCCCATTTCCTCTTGTTCTGTCCTCAGTGG 930 chr4ptel1M 367830 AGCTGGAGCAC 367840 v v C L3b_3end#LINE 929 AGATGGAGAAC 919 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.47 CpG sites = 8, Kimura (unadjusted) = 31.47 Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.02 (1 / 58), avg. gap size = 2.00 (2 / 1) 184 31.12 11.00 5.21 chr4ptel1M 368059 368258 (631742) L2a_3end#LINE/L2 40 250 (267) m_b172s601i49 6673 chr4ptel1M 368059 TCTAACCACATTCCCCCACACCTCAGCTCGCTTAAGTCCCGTAACATGGA 368108 iv vi v i - vii iv i ----- iv i L2a_3end#LINE 40 TCCTACCACTCTCCCCCTCGC-TCACTCCGCTCCAGCC-----ACACTGG 83 chr4ptel1M 368109 CCTCCTGGCTATTCTCTGAACAAG--AGCCTCCATTGCTTGCCTCCAATT 368156 v i iii v -- v -v ii - ii viivi L2a_3end#LINE 84 CCTCCTTGCTGTTCCTCGAACACGCCAGGC-ACGCT-CCCGCCTCAGGGC 131 chr4ptel1M 368157 ATTTTCTCTGGCTGACTTCCATT--CCTGGGAAGCTCTTGCTCC-----T 368199 v v v v -- v i-- i v v i ----- L2a_3end#LINE 132 CTTTGCACTTGCTG--TTCCCTCTGCCTGGAACGCTCTTCCCCCAGATAT 179 chr4ptel1M 368200 CCTC-TG-----------CATTTCCTTTAAGTA-TCAATTAAATCTCCAC 368236 v - ----------- ii i i v- iiv i v - L2a_3end#LINE 180 CCGCATGGCTCGCTCCCTCACCTCCTTCAGGTCTTTGCTCAAATGT-CAC 228 chr4ptel1M 368237 CTTCTTCAAGCTGCCTTTCCTG 368258 ivi? vv i L2a_3end#LINE 229 CTTCTCAGNGAGGCCTTCCCTG 250 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.08 CpG sites = 33, Kimura (unadjusted) = 41.70 Transitions / transversions = 1.27 (33/26) Gap_init rate = 0.09 (17 / 199), avg. gap size = 1.94 (33 / 17) 190 32.42 2.86 7.46 chr4ptel1M 368059 368198 (631802) L2#LINE/L2 2949 3082 (0) m_b172s601i50 6673 chr4ptel1M 368059 TCTAACCACATTCCCCCACACCTCAGCTCGCTTAAGTCCCGTAACATGGA 368108 iv vi v i - vii iv i ----- iv i L2#LINE/L2 2949 TCCTACCACTCTCCCCCTCGC-TCACTCCGCTCCAGCC-----ACACTGG 2992 chr4ptel1M 368109 CCTCCTGGCTATTCTCTGAACAAG--AGCCTCCATTGCTTGCCTCCAATT 368156 v i iii v -- v -v ii - ii viivi L2#LINE/L2 2993 CCTCCTTGCTGTTCCTCGAACACGCCAGGC-ACGCT-CCCGCCTCAGGGC 3040 chr4ptel1M 368157 ATTTTCTCTGGCTGACTTCCATT--CCTGGGAAGCTCTTGCTCC 368198 v v v v -- v i-- i v v i L2#LINE/L2 3041 CTTTGCACTTGCTG--TTCCCTCTGCCTGGAACGCTCTTCCCCC 3082 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.05 CpG sites = 23, Kimura (unadjusted) = 43.30 Transitions / transversions = 1.21 (23/19) Gap_init rate = 0.09 (12 / 139), avg. gap size = 1.17 (14 / 12) 69 8.29 1.96 0.00 chr4ptel1M 368277 368378 (631622) (AC)n#Simple_repeat 1 104 (0) c_b172s251i1 6674 chr4ptel1M 368277 ACACACACACACACACACACTCAC-CACATTGACACACACACACACTCAC 368325 v - ivv v (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50 chr4ptel1M 368326 -CACACATACACATTCACACACACACACACACACACACACACACACACAC 368374 - i iv (AC)n#Simple_ 51 ACACACACACACACACACACACACACACACACACACACACACACACACAC 100 chr4ptel1M 368375 ACAC 368378 (AC)n#Simple_ 101 ACAC 104 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.02 (2 / 101), avg. gap size = 1.00 (2 / 2) 204 31.61 3.92 15.22 chr4ptel1M 369074 369226 (630774) MIRb#SINE/MIR 5 142 (126) m_b172s601i51 6675 chr4ptel1M 369074 GAAGCAGTGGAATGCAATGGAGTGTGCA---GCTTTATAGGCA-ATGGAC 369119 ii i vii i iv v --- iv v - ii MIRb#SINE/MIR 5 GGGGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGAC 54 chr4ptel1M 369120 CTTTGGG--CAAAGCCCAGCTTTGGTCCTATCAACCAGGAGCGAGGGGTC 369167 -- -- i v i i --- i iiv i vv i ----- - MIRb#SINE/MIR 55 CT--GGGTTCGAATCCCGGCTCTG---CCACTTACTAGCTGTG-----T- 93 chr4ptel1M 369168 GGGGAGGGCAGACTTTGGGCAAGTTATCTCCCTTCCCTGGGATACACATT 369217 ---------- i ii vv i i i viv vv MIRb#SINE/MIR 94 ----------GACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTT 133 chr4ptel1M 369218 CCCCATCTG 369226 i MIRb#SINE/MIR 134 CCTCATCTG 142 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.88 CpG sites = 26, Kimura (unadjusted) = 41.87 Transitions / transversions = 1.73 (26/15) Gap_init rate = 0.16 (24 / 152), avg. gap size = 1.12 (27 / 24) 340 31.37 0.98 0.00 chr4ptel1M 369178 369279 (630721) MIR3#SINE/MIR 88 190 (18) m_b172s601i52 6675 chr4ptel1M 369178 GACTTTGGGCAAGTTATCTCCCTTCCCTGGGATACACATTCCCCATCTGG 369227 i i ii v i i viv vv i v MIR3#SINE/MIR 88 GACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGT 137 chr4ptel1M 369228 ACAACAACAGAATTGGGCTACAAGAACCCCTAAGTCCTTTCT-GCTCTGA 369276 v ii vi ii i v v v i iv i i i- MIR3#SINE/MIR 138 AAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGA 187 chr4ptel1M 369277 AAT 369279 v MIR3#SINE/MIR 188 CAT 190 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 42.01 CpG sites = 19, Kimura (unadjusted) = 42.01 Transitions / transversions = 1.46 (19/13) Gap_init rate = 0.01 (1 / 101), avg. gap size = 1.00 (1 / 1) 632 21.73 2.16 0.71 chr4ptel1M 369522 369660 (630340) C MIR#SINE/MIR (51) 211 71 m_b172s601i53 6676 chr4ptel1M 369522 AGCTCTTTACAAATATGACCTCATTTGATCTTCACACTAACCTTA-GAG- 369569 v vi v v i i vi i - - C MIR#SINE/MIR 211 AGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGG 162 chr4ptel1M 369570 -AGATGCTATTATTATCCCCACTTGACAGATAAGGAAATTGAGGCTGAGA 369618 - i i i v i i vv C MIR#SINE/MIR 161 TAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGA 112 chr4ptel1M 369619 GAGGTTGTGTGCTCTTTCCAGAGTCACACAGATAAGTAAATG 369660 iv ivii vi ii v - i C MIR#SINE/MIR 111 GAGGTTAAGTAACTTGCCCAAGGTCACACAGCT-AGTAAGTG 71 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 26.15 CpG sites = 18, Kimura (unadjusted) = 26.15 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.03 (4 / 138), avg. gap size = 1.00 (4 / 4) 364 23.76 11.88 0.00 chr4ptel1M 369782 369882 (630118) C MIRc#SINE/MIR (154) 114 2 m_b172s601i54 6677 chr4ptel1M 369782 AGGTTAAGTGACTTGTTTAGGTTCACACAGTTAGT--GTCTAAGA-CCAA 369828 iii i v i -- vvv - ii C MIRc#SINE/MIR 114 AGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGG 65 chr4ptel1M 369829 GAT--AAACC-------TCCTGACTCCAAGGCTGGTATTATATCCACTGA 369869 i--i ------- v ii ii v v v C MIRc#SINE/MIR 64 GACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGC 15 chr4ptel1M 369870 ACCACTTAGCCTC 369882 viv C MIRc#SINE/MIR 14 ACCACACTGCCTC 2 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 26.34 CpG sites = 14, Kimura (unadjusted) = 29.12 Transitions / transversions = 1.40 (14/10) Gap_init rate = 0.04 (4 / 100), avg. gap size = 3.00 (12 / 4) 249 33.64 6.36 0.00 chr4ptel1M 370640 370749 (629251) C L2a_3end#LINE/L2 (6) 511 395 m_b173s601i1 6678 chr4ptel1M 370640 TCACTC--TAAGTCTTTATTAAAGACTTACTGTATGACAGGGATTCATC- 370686 i --i i v i ivi i i i v v i vv - C L2a_3end#LINE 511 TCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCT 462 chr4ptel1M 370687 AGGTGCTGGGAGAACAAAGATAAA-AATGCAATCA---TTCCCTACTTTC 370732 i iiv ivii i - vi iv ---v i ii C L2a_3end#LINE 461 AGGCGCTGGGGATACAGCAGTGAACAAAACAGACAAAAGTCCCTGCCCTC 412 chr4ptel1M 370733 AGTGAGCTTCCATTCCA 370749 vv v i C L2a_3end#LINE 411 ATGGAGCTTACATTCTA 395 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 43.29 CpG sites = 23, Kimura (unadjusted) = 46.77 Transitions / transversions = 1.64 (23/14) Gap_init rate = 0.04 (4 / 109), avg. gap size = 1.75 (7 / 4) 321 33.25 7.64 9.03 chr4ptel1M 370652 370965 (629035) C L2c_3end#LINE/L2 (20) 458 149 m_b173s601i2 6678 chr4ptel1M 370652 TTTATTAAAGACTTACTGTATGACAGGGATTCATCAGGTGCTGGGAGAAC 370701 i ivi i i i -----------i i iiv C L2c_3end#LINE 458 TTTATTGAGCGCCTACTATGTG-----------CCAGGCGCTGGGGATAC 420 chr4ptel1M 370702 AAAGATAAA-AATGCAATCATTCCCTACTTTCAGTGAGCTTCCATTCCAA 370750 i - vi -- iv i ii iv iv v i i C L2c_3end#LINE 419 AAAGATGAATAAGACA--CGGTCCCTGCCCTCAAGGAGCTCACAGTCTAG 372 chr4ptel1M 370751 AGCTCCATTCTAGTAGGGACAATGCCGTGAGCAT----TTCCCATATAAA 370796 ---------- i vi i ivvv? i i v---- v v i i C L2c_3end#LINE 371 ----------TGGAGGAGACAGACANGTAAACAGACAATTACAATACAAG 332 chr4ptel1M 370797 TGA--GATAAAGACAA-AATAAATGAATACATATAATTCT--GGAAG--- 370838 v -- ivi v - iiiv v v i vii v -- i --- C L2c_3end#LINE 331 TTAATGATAAGTGCTATAATGGGAGTATAGACAGGGTGCTATGGGAGCAC 282 chr4ptel1M 370839 ---GGAAGGCAC-TAG-CAGGTGGAAGAGGATTAGGAAAAGGCTCACATT 370883 --- i - - vi ?vvvi i i i i i vi v ivv C L2c_3end#LINE 281 AGAGGAGGGCACCTAGACTAGNCTTGGGGGGTCAGGGAAGGCTTCCCGGA 232 chr4ptel1M 370884 GAAGATGGCATTGGAGCTAAGTTTTGGAGGA-AACCAGGTGTT--CTAAG 370930 i i i iv i ?i i -i vi v -- i i C L2c_3end#LINE 231 GGAGGTGACATCTGAGCTGAGNCTTGAAGGATGAGTAGGAGTTAGCCAGG 182 chr4ptel1M 370931 ---AATGAGGATGAAGAAGCACAGCATTCTAGGCAGAG 370965 --- v -- ii --- i C L2c_3end#LINE 181 TGGAAGGAGG--GGGGAAG---AGCATTCCAGGCAGAG 149 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 44.18 CpG sites = 61, Kimura (unadjusted) = 46.93 Transitions / transversions = 1.79 (61/34) Gap_init rate = 0.13 (40 / 313), avg. gap size = 1.30 (52 / 40) 206 32.47 5.65 3.15 chr4ptel1M 370858 370981 (629019) C L2a_3end#LINE/L2 (259) 258 132 m_b173s601i3 6678 chr4ptel1M 370858 AAGAGGATTAGGAAAAGGCTCACATTGAAGATGGCATTGGAGCTAAGTTT 370907 i iv i i i i v ? vvv i i v v vii C L2a_3end#LINE 258 AGGGTGGTCAGGGAAGGCCTCNCTGAGAAGGTGACATTTGAGCAAAGACC 209 chr4ptel1M 370908 TGGAGGAAACCAGGTGTTCTAAGAATGAGGAT-----GAAGAAGCACAGC 370952 i iiiv - vv v ivv v ----- ii --- C L2a_3end#LINE 208 TGAAGGAGGTGAGG-GAGCGAGCCATGCGGATATCTGGGGGAAG---AGC 163 chr4ptel1M 370953 ATTCTAGGCAGA--GACTCCCCAGTGCAAAG 370981 i i -- vivv v C L2a_3end#LINE 162 GTTCCAGGCAGAGGGAACAGCAAGTGCAAAG 132 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 42.38 CpG sites = 20, Kimura (unadjusted) = 43.86 Transitions / transversions = 1.05 (20/19) Gap_init rate = 0.05 (6 / 123), avg. gap size = 1.83 (11 / 6) 259 32.84 0.00 0.00 chr4ptel1M 372115 372181 (627819) C MIRc#SINE/MIR (45) 223 157 m_b173s601i4 6679 chr4ptel1M 372115 AAGCACTTTCAAATATGCTATCTCCTTCAGACCTCACAGAAGTCCCACAA 372164 i v iii v iiiv iv ii iiii C MIRc#SINE/MIR 223 AAGCGCTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGA 174 chr4ptel1M 372165 GGCAGATAGGGCAGATA 372181 i ii i C MIRc#SINE/MIR 173 GGTAGGCAGGGCAGGTA 157 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 45.39 CpG sites = 18, Kimura (unadjusted) = 48.62 Transitions / transversions = 4.50 (18/4) Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.0 (0 / 0) 20 19.03 4.84 1.56 chr4ptel1M 373475 373536 (626464) (TTATA)n#Simple_repeat 1 64 (0) m_b173s252i0 6680 chr4ptel1M 373475 TTATATTATATAATACTATAAAAT-TTGTATTTATATTACATAATGCTAT 373523 v i vv - i - i v ii (TTATA)n#Simp 1 TTATATTATATTATATTATATTATATTATA-TTATATTATATTATATTAT 49 chr4ptel1M 373524 A-TATA-CATATTAT 373536 - -i (TTATA)n#Simp 50 ATTATATTATATTAT 64 Matrix = Unknown Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.07 (4 / 61), avg. gap size = 1.00 (4 / 4) 648 35.31 1.81 2.74 chr4ptel1M 373717 374048 (625952) L1ME5_3end#LINE/L1 185 513 (428) m_b173s551i0 6681 chr4ptel1M 373717 TGGGAGATCATGTCATACCCATCAGACTGG-ATAAGGTGGCAGGAAAAAT 373765 i v iv i i i i - v iv i v i vvii L1ME5_3end#LI 185 TGAGATATCACTTTACACCTATTAGACTGGCAAAAATTAGAAAGCTGGAT 234 chr4ptel1M 373766 AATGATAAATGTTGAAAGGGATGTAGGAAAACTGGAACATTAATACATTG 373815 vi i ivii i i ? iv vi v i i L1ME5_3end#LI 235 AATGCCAAGTGTTGGCGAGGATGTGGGGANATAGGAACCCTCATGCACTG 284 chr4ptel1M 373816 TTGGTGGAGTTGTGAACATATCCAGCCATTCTGTAGAGCAATTTGGAACT 373865 i iiv ii vvi v v i v v L1ME5_3end#LI 285 CTGGTGGGAGTGTAGACTGGTGCAGCCATTCTGGAGAGCAATCTGGCAGT 334 chr4ptel1M 373866 A--TGCCCAAAGGGCTATCAATCTGTGTATATCCTTTGATTCAGCAGAGT 373913 -- ivi ---i -- i v ii i i v ii ivvi L1ME5_3end#LI 335 ACTTAGTCAAA---TTA--AGTATACGCATACCCTATGACCCAGCAATTC 379 chr4ptel1M 373914 CACTACTGACTCTATACCCCAAAGACATCATTTAAAAAGA---AAAAAGG 373960 i v iv v i v i-i i v v i--- v i L1ME5_3end#LI 380 CGCTCCTGGGTATATATCCCAAAGAAATT-CTCACACAGGTCCATAAGGG 428 chr4ptel1M 373961 ATTCATGTGTGCAAAAATGTTTCTAGCAGCTCTTTTTGTGATGGCAAGGA 374010 i--- ii i i ii iv v vi v i ii L1ME5_3end#LI 429 G---ACATGTACGAGGATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGA 475 chr4ptel1M 374011 ATTGAAAATTGAGTGGATGCGCATCAACAAGGGAATGG 374048 i i iiivivv i iv viii i i L1ME5_3end#LI 476 GTTGGAGGCAACCTGGGTGTCCATCACTGGGAGAGTGG 513 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 47.73 CpG sites = 74, Kimura (unadjusted) = 50.98 Transitions / transversions = 1.85 (74/40) Gap_init rate = 0.04 (12 / 331), avg. gap size = 1.25 (15 / 12) 663 33.79 1.71 1.02 chr4ptel1M 373760 374052 (625948) L1ME4c_3end#LINE/L1 226 520 (310) m_b173s551i1 6681 chr4ptel1M 373760 AAAAATAATGATA---AATGTTGAAAGGGATGTAGGAAAACTGGAACATT 373806 v i i --- i ivii ? ii vi v ?i L1ME4c_3end#L 226 AAAATTGATAATACCCAATGCTGGCGAGGNTGCGGTGAAACTGGTACNCT 275 chr4ptel1M 373807 AATACATTGTTGGTGGAGTTGTGAACATATCCAGCCATTCTGTAGAGCAA 373856 v i vi? i ivvi v i v i v i L1ME4c_3end#L 276 CATACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGCAA 325 chr4ptel1M 373857 TTTGGAACTATGCCCAAAGGGCTATCAATCTGTGTATATCCTTTGATTCA 373906 v v i iviv i i v vv vi i ii L1ME4c_3end#L 326 TTTGGCAATACGTATCAAGAGCCATAAAAATGTTCATACCCTTTGACCCA 375 chr4ptel1M 373907 GCAGAGTCACTACTGACTCTATACCCCAAAGACATCATTTAAA--AAGAA 373954 i ivvi v ivvv v i i i v v i -- i L1ME4c_3end#L 376 GTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAAGAAGGA 425 chr4ptel1M 373955 AAAAGGATTCATGTGTGCAAAAATGTTTCTAGCAGCTCTTTTTGTGATGG 374004 ---ii i ii i i iv v vi v i i i L1ME4c_3end#L 426 AAAAG---CTATATGCACGAAGATGTTCATTGCAGCGTTATTTATAATAG 472 chr4ptel1M 374005 CAAGGAATTGAAAATTGAGTGGATGCGCATCAACAAGGGAATGGCTGA 374052 i ii i ivivv ii iv v i i i i L1ME4c_3end#L 473 CGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAATGGTTAA 520 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 44.36 CpG sites = 61, Kimura (unadjusted) = 47.83 Transitions / transversions = 1.65 (61/37) Gap_init rate = 0.02 (5 / 292), avg. gap size = 1.60 (8 / 5) 2500 28.39 7.19 3.17 chr4ptel1M 374059 375728 (624272) L1M5_orf2#LINE/L1 1525 3259 (35) m_b173s551i2 6682 chr4ptel1M 374059 TTTTATGATACAGACATGGTACTGATACCTAAACCAGTTGGATGAAA--A 374106 vi vii ?iiv v ? viii - v -- L1M5_orf2#LIN 1525 TTTTATGAGGCCAGCATNACCCTGATACCAAAACCNGACAAA-GACATTA 1573 chr4ptel1M 374107 CAGAGAAAGAAAAGTATAGCTCAATCTCCCTAATGAATGTTGATGAAAAA 374156 iii v i vi v v ii v v L1M5_orf2#LIN 1574 CAAGAAAAGAAAATTACAGACCAATATCCCTCATGAACATAGATGCAAAA 1623 chr4ptel1M 374157 CTCTTAAATAAAATATTAGCAAAGAGATTATAGAAAATCATCTCCAA--G 374204 v i ? i vv v vi v --i v vv -- L1M5_orf2#LIN 1624 ATCCTNAACAAAATATTAGCAAATCGAATCCAGCAA--TATATAAAAAGG 1671 chr4ptel1M 374205 ATAATACACCACAACCAAGTAGGATTTTTACTAGGAATTCAGGGCTGGTT 374254 i ii i i v v i v i i L1M5_orf2#LIN 1672 ATAATACATCATGACCAAGTGGGGTTTATCCCAGGAATGCAAGGTTGGTT 1721 chr4ptel1M 374255 CAATATTAGAAAAACTATTAGCATAATTGACTATATCAATA-ACTAAATT 374303 i i v v v i iii v i i i - v v- L1M5_orf2#LIN 1722 TAACATTCGAAAATCAATCAATGTAATTCACCATATTAACAGAATAAAG- 1770 chr4ptel1M 374304 AACAAAAATCATATGATTATCTCATTAGATGCAGAAAAAGCATTTGATAA 374353 i v i v i L1M5_orf2#LIN 1771 GAGAAAAATCATATGATCATCTCAATAGATGCAGAAAAAGCATTTGACAA 1820 chr4ptel1M 374354 AATCCAACACCCATTCCTAATTAAAAT-------------GGACT----- 374385 i v i v i------------- v ----- L1M5_orf2#LIN 1821 AATTCAACACCCATTCATGATAAAAACTCTCAGCAAACTAGGAATAGAAG 1870 chr4ptel1M 374386 ----TTTCCTTAAAATAGTCAATATCATCTATTTAAAACCATCAACAAGC 374431 ----i i vv ii v viv ivv vv i ? i L1M5_orf2#LIN 1871 GGAACTTCCTCAACCTGATAAAGGGCATCTACGAAAAACCTACAGCNAAC 1920 chr4ptel1M 374432 ATCATATGTAATGAGGATAAACTGGAACCATTCCCAATAAGATCAGGGGT 374481 iv iv v ? i ?v v vv i iii L1M5_orf2#LIN 1921 ATCATACTTAATGGTGAAANACTGAANGCTTTCCCCCTAAGATCGGGAAC 1970 chr4ptel1M 374482 GAAACAAGGTTG----------CCATTACTCTCCAACATTGTATTAGAAA 374521 i i v ---------- i v v i i i ii L1M5_orf2#LIN 1971 AAGACAAGGATGTCCGCTNTCACCACTTCTATTCAACATTGTACTGGAGG 2020 chr4ptel1M 374522 TGCTAGCTTTAGCAATAAGAGAAAAAAAAGAAATTAAAGGAATTAGAATA 374571 v ivvv iv i v v v ii v L1M5_orf2#LIN 2021 TCCTAGCCAGTGCAATAAGGCAAGAAAAAGAAATAAAAGGCATAAAGATT 2070 chr4ptel1M 374572 GGTAATGAGGAAACTAAATTATCATTCCTTGCAGATAATATGATGGTATA 374621 v v i iv i i ? vi i i i v ? L1M5_orf2#LIN 2071 GGAAAGGAAGAAATAAAACTGTCNTTATTCGCAGATGACATGATTGTNTA 2120 chr4ptel1M 374622 CTTAGAGAACCCCAGAGAATCAATTAAAAACCTATTAGAAATAATCCACA 374671 v i i ? i v iv ? v i v vviii L1M5_orf2#LIN 2121 CGTAGAAAATCCNAAAGAATCTACAAANAAACTACTAGAACTAATAAGTG 2170 chr4ptel1M 374672 ACTTTAGCAAAGTTGCAGGATACAAAATAAATCCACATAAATCATCAGCA 374721 v i i ? ii v vi v viv i L1M5_orf2#LIN 2171 AATTTAGCAAGGTCGCNGGATACAAGGTCAATATACAAAAATCAATTGTA 2220 chr4ptel1M 374722 TTTTTATATATCATTAACAAAATCCAACAGCAA---GAGATACAAAGAGA 374768 i ii vi --- iv v --- i vi? i iv L1M5_orf2#LIN 2221 TTTCTATATACTAGCAACAAA---CAATTGGAAAATGAAATTTNAAAAAC 2267 chr4ptel1M 374769 AGTGCCATTTAAAATAACTGTTGATAGCATAAAATGTCTGCCAAGGGA-A 374817 i i v i vvivi v i ? iii ---- i - L1M5_orf2#LIN 2268 AATACCATTTACAATAGCATCAAAAAACATNAAATACTT----AGGAATA 2313 chr4ptel1M 374818 AATC-AGTAATTATATGAGC---------------AAAACTACAAAAGAC 374851 - ii -v ? v --------------- v i L1M5_orf2#LIN 2314 AATCTAACAA-AANATGTGCAAGACCTNTACACTGAAAACTACAAAACAT 2362 chr4ptel1M 374852 TTTCCACACAAATAAAGTCATATCTAAGCAATTGGAGAA--ATACCAAGT 374899 viiv v v v ivv v i ii v i-- -- L1M5_orf2#LIN 2363 TGCTGAGAGAAATTAAAGAAGACCTAAATAAATGGAGAGATATACCA--T 2410 chr4ptel1M 374900 GTTCTTGGATAGATTGAGCAAATATAATAAAGATGACAAT---------A 374940 v v ivv viv vi ? v --------- L1M5_orf2#LIN 2411 GTTCATGGATTGGAAGACTCAATATTGTNAAGATGTCAATTCTCCCCAAA 2460 chr4ptel1M 374941 T--ATTT----ATTTAGTGCTATACCAATCAAACTCCCAAGAAACTATTT 374984 -- i ---- i i v v v iv iii v L1M5_orf2#LIN 2461 TTGATCTATAGATTCAATGCAATCCCAATCAAAATCCCAGCAGGTTTTTT 2510 chr4ptel1M 374985 TGCTGACCTAGAAAAAATAA---CAAAATTCATCTGGAAGAACAAAAGGT 375031 iv vv v v iv i ---i i v ivi i ii L1M5_orf2#LIN 2511 TGTAGAAATTGACAAGCTGATTCTAAAATTTATATGGAAATGCAAAGGAC 2560 chr4ptel1M 375032 TAAAAAT-TTCAAAGGAA--TTAATGAAAAGAAAATCAAA--TGAAGGTG 375076 i? i -vi iv -- i -- i v -- i -- L1M5_orf2#LIN 2561 CNAGAATAGCCAAAACAATCTTGA--AAAAGAAGAACAAAGTTGGAG--G 2606 chr4ptel1M 375077 GCCCAGCTGTACCAGATCT-AAAACTATGTTATAAAACAGTGGTCATCAA 375125 i ii - vv ? ? - i - i i viii v L1M5_orf2#LIN 2607 ACTTA-CACTACCNGATNTCAAGACT-TATTATAAAGCTACAGTAATCAA 2654 chr4ptel1M 375126 AAACATTTGGTACTGGC-TAAGAAATAGAGAAGTTGATCAGTAGAATTGC 375174 i vvi v i - -i v i v i i ----- L1M5_orf2#LIN 2655 GACAGTGTGGTATTGGCGTAAG-GATAGACAAATAGATCAATGGA----- 2698 chr4ptel1M 375175 TTAAGTTCACAAAACAGAAA----AAAAATA---TCATCTATGATGATAG 375217 -------- i i i ---- i ---i ivi - - i L1M5_orf2#LIN 2699 --------ACAGAATAGAGAGTCCAGAAATAGACCCACACAT-AT-ATGG 2738 chr4ptel1M 375218 TAATCTAATATTTGACAAACCTA--AAGGCTCCTTTAGGCCTTAGGAACT 375265 ?v ?i i v vv i-- ? -vv i --- vi vv L1M5_orf2#LIN 2739 NCANTTGATTTTTGACAAAGGTGCCAANGC-AATTCAG---TGGGGAAAG 2784 chr4ptel1M 375266 CA----CTATTTGACAAAAATTGCTGAGAAAACTGGAAACTAGTATGGCA 375311 v ---- v ii viv ii v i v iivi v L1M5_orf2#LIN 2785 GATAGTCTTTTCAACAAATGGTGCTGGAACAATTGGATATCCATATGGAA 2834 chr4ptel1M 375312 GAAAGTAGGCATAGACCCATACCTAACACCATATACCAAGAGAAGGTCAA 375361 i i iii?v v v v i v i vv iv ? L1M5_orf2#LIN 2835 AAAAATGAANCTCGACCCCTACCTCACACCATACACAAAAATTAATTCNA 2884 chr4ptel1M 375362 AATGGATTCAT-GATTTAGGAATAAAGAATGAGATTATAAACAAATTAGA 375410 i - - ii iivi ii? i i i vvvvi L1M5_orf2#LIN 2885 GATGGA-TCATAGACCTAAATGTAAAAGNTAAAACTATAAAACTTCTAGA 2933 chr4ptel1M 375411 AG--AACATAGGATAGTTTACATC-TCA-GATTTGTGGGAAAGG-AAGGA 375455 -- v ---- i - i- ii - ?v - i L1M5_orf2#LIN 2934 AGAAAACATAGGAGA----ATATCTTCGTGACCT-TGGGNTAGGCAAAGA 2978 chr4ptel1M 375456 ATTTGTAACCA----AAGAAGATCATTATTGATCACAAAACA-------G 375494 v iv v ---- vi i v i? --- i i v ------- L1M5_orf2#LIN 2979 TTTCTTAAACAGGACACAAAAAGCACNA---ACCATAAAAGAAAAAATTG 3025 chr4ptel1M 375495 ATAATTTTGATTATATT-AAGTTAAAAAGTTTT--TGTACAAACAAAACT 375541 v v i ?i i- i v i -- v?v vi v i L1M5_orf2#LIN 3026 ATAAATTGGACTNCATCAAAATTAAAAACTTCTGCTCNTCAAAAGACACC 3075 chr4ptel1M 375542 AATGCAGACAAGATTAGAAGGGAAGCAATAAACTGGGAAAACATTTTTAC 375591 iv ---i v i v i v v i i ? i v v i L1M5_orf2#LIN 3076 GTT---AAGAAAATGAAAAGGCAAGCCACAGANTGGGAGAAAATATTTGC 3122 chr4ptel1M 375592 -ATCCAAATGATCTGATAAAGGCCTCATTTCTAAAATATATAGAGAATTG 375640 - ?v v - i v i v i i i i v L1M5_orf2#LIN 3123 AANACATAT-ATCTGACAAAGGACTCGTATCCAGAATATATAAAGAACTC 3171 chr4ptel1M 375641 ACTCAAATTTATAATAGTTCAAGCCATTC--TCCAACTGATAAATGGTCA 375688 viv ? iv ? i--v v vv --i iv? v v L1M5_orf2#LIN 3172 CTACAANTCAATAANAA--AAAGACAAACAACCCAATANAAAAATGGGCA 3219 chr4ptel1M 375689 AAGGATATGAATAGACAATTTTCAGATGAAGAAATTGAAA 375728 i iv i v iv i v v ?v L1M5_orf2#LIN 3220 AAAGACTTGAACAGACACTTCACAAAAGAAGATATNCAAA 3259 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.69 CpG sites = 249, Kimura (unadjusted) = 37.41 Transitions / transversions = 1.19 (249/210) Gap_init rate = 0.05 (91 / 1669), avg. gap size = 1.92 (175 / 91) 877 31.86 4.48 2.10 chr4ptel1M 376337 376849 (623151) L1MB4_3end#LINE/L1 120 644 (283) m_b173s551i4 6682 chr4ptel1M 376337 CAGTAGCCACATGAAAAGGTGCTCCAAATCACTATTGATCAGGGAAATGC 376386 i iv i v v v v i L1MB4_3end#LI 120 CAATAAGCACATGAAAAGATGCTCAACATCACTAGTCATTAGGGAAATGC 169 chr4ptel1M 376387 AAATTAAGACAACTTTGAGATACCACTACATACCTGTCAGATTGGTTAGA 376436 i i v vv v i iiii iv i v? L1MB4_3end#LI 170 AAATCAAAACCACAATGAGATACCACTTCACACCCACTAGGATGGCTATN 219 chr4ptel1M 376437 ATGACAGGGAAAGATAATGCGGAATGTTGGAGGGGATATAGGAAAACTGG 376486 v v iii vi v ivvi i v i i i ii i L1MB4_3end#LI 220 ATCAAAAAAACGGAAAATAACAAGTGTTGGCGAGGATGTGGAGAAATTGG 269 chr4ptel1M 376487 GACATCAATACATTGTTGGT-GGAATG------GATCCAACCATTCTGGA 376529 i viivi i i - ------ i v i ii v L1MB4_3end#LI 270 AACCCTCGTGCATTGCTGGTGGGAATGTAAAATGGTGCAGCCGCTGTGGA 319 chr4ptel1M 376530 GAGCAGTTTGGAACTACACTCAAAAAGTTATCAAACTGTGCA-TATCCTT 376578 i i viv v - --- vvv v - i v v L1MB4_3end#LI 320 AAACAGTTTGGCGGTTC-CTCAAAAAGTT---AAACATAGAATTACCATA 365 chr4ptel1M 376579 TGACCCAACAGTGTTTCTACTGGGCTTGGATCCCAAAGAAATCTTAAAAG 376628 i i viiv v i iv iv i v --- i L1MB4_3end#LI 366 TGACCCAGCAATTCCACTCCTAGGTATATACCCAAAAGAA---TTGAAAG 412 chr4ptel1M 376629 GAGGGA---AAGGAGCCCACATGTGCAAAAATGTTTGTGGCAGCCCTTTT 376675 v --- iv -vi v i vv ii i - v v L1MB4_3end#LI 413 CAGGGACTCAAACAG-ATACTTGTACACCAATGTTCATAGCAG-CATTAT 460 chr4ptel1M 376676 TTGTAGGGGCAAAAAACTAGAAACTGAGTAGATGCCCATCAATTGGAGAA 376725 iii ivi v iv i vivvi ii i - iv iv L1MB4_3end#LI 461 TCACAATAGCCAAAAGGTGGAAACAACCCAAGTGTCCAT-AACAGATGAA 509 chr4ptel1M 376726 TGGCTGAATAAATTATGGTATATGAATGCTATGGGATTCTATT--GTTTT 376773 v i i v i iv i v i vi -- ii? L1MB4_3end#LI 510 TGGATAAACAAAATGTGGTATATACATACAATGGAATATTATTCAGCCNT 559 chr4ptel1M 376774 -ATAAGAAATGA----CCA--ACATG--ATGATTTCAGAGAGACCTGGAA 376814 - v i ---- ii-- -- ii iv -i vii v L1MB4_3end#LI 560 AAAAAGGAATGAAATTCTGATACATGCTACAACAT-GGATGAACCTTGAA 608 chr4ptel1M 376815 GAACTGATGCTGAGGGAAGTGAGCAGGAC-CAGAAG 376849 i vv v i v i i vi - i L1MB4_3end#LI 609 AACATTATGCTAAGTGAAATAAGCCAGACACAAAAG 644 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.62 CpG sites = 93, Kimura (unadjusted) = 43.06 Transitions / transversions = 1.39 (93/67) Gap_init rate = 0.04 (21 / 512), avg. gap size = 1.62 (34 / 21) 1307 26.54 2.55 2.08 chr4ptel1M 376337 376767 (623233) L1ME3G_3end#LINE/L1 116 548 (376) m_b173s551i3 6682 chr4ptel1M 376337 CAGTAGCCACATGAAAAGGTGCTCCAAATCACTATTGATCAGGGAAATGC 376386 i iv i i v vv v i L1ME3G_3end#L 116 CAATAAACATATGAAAAGATGCTCAACCTCACTAGTAATCAGGGAAATGC 165 chr4ptel1M 376387 AAATTAAGACAACTTTGAGATACCACTACATACCTGTCAGATTGGTTAGA 376436 i vv i vivi ii iv i L1ME3G_3end#L 166 AAATTAAAACAACAATGAGATACCATTTTTCACCCATCAGATTGGCAAAA 215 chr4ptel1M 376437 ATGACAGGGAAAGATAATGCGGAATGTTGGAGGGGATATAGGAAAACTGG 376486 vvv ii ?vv iiv? i v i i i i i v L1ME3G_3end#L 216 ATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGTGTGGGGAAACGGG 265 chr4ptel1M 376487 GACATCAATACATTGTTGGTGG-------AATGGATCCAACCATTCTGGA 376529 v viiv i i ------- v i v i ? i L1ME3G_3end#L 266 TACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTACAGCCNTTTTGGA 315 chr4ptel1M 376530 GAGCAGTTTGGAACTA--CACTCAAAAAGTTATCAAACTGTGCATATCCT 376577 i i v v --i i -- v --- v i i L1ME3G_3end#L 316 GGGCAATTTGGCAGTATCTATT--AAAATTT---AAAATGCGCATACCCT 360 chr4ptel1M 376578 TTGACCCAACAGTGTTTCTACTGGGCTTGGATCCCAAAGAAAT-CTTA-A 376625 i i viiv v ? ?v vv i ? - ii- L1ME3G_3end#L 361 TTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAGAAATACTCGCA 410 chr4ptel1M 376626 AAGGAGGGAAAGGAGCCCACATGTGCAAAAATGTTTGTGGCAGCCCTTTT 376675 v v v viv ---?i i ii ii v - v v L1ME3G_3end#L 411 CATGTGCACAAGGA---NGCATGTACAAGGATGTTCATTGCAG-CATTGT 456 chr4ptel1M 376676 TTGTAGGGGCAAAAAACTAGAAACTGAGTAGATGCCCATCAATTGGAGAA 376725 ivi i i i vivv i i v i L1ME3G_3end#L 457 TTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCAATAGGGGAA 506 chr4ptel1M 376726 TGGCTGAATAAATTATGGTATATGAATGCTATGGGATTCTAT 376767 i i vv i i v L1ME3G_3end#L 507 TGGTTAAATAAATTATGGTATATCCATACTATGGAATACTAT 548 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 32.96 CpG sites = 63, Kimura (unadjusted) = 34.12 Transitions / transversions = 1.29 (63/49) Gap_init rate = 0.03 (13 / 430), avg. gap size = 1.54 (20 / 13) 84 0.00 0.00 1.33 chr4ptel1M 377091 377166 (622834) (AT)n#Simple_repeat 1 75 (0) c_b173s251i0 6683 chr4ptel1M 377091 ATATATATATATATATATATATATATATATATATATATACTATATATATA 377140 - (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATA-TATATATATA 49 chr4ptel1M 377141 TATATATATATATATATATATATATA 377166 (AT)n#Simple_ 50 TATATATATATATATATATATATATA 75 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.01 (1 / 75), avg. gap size = 1.00 (1 / 1) 17 14.61 3.85 3.85 chr4ptel1M 377313 377347 (622653) (TAAA)n#Simple_repeat 1 35 (17) m_b173s252i1 6684 chr4ptel1M 377313 TAAAT-AA-AAATAAACAGATGAATGAATAGATAGAC 377347 - - i i i i i - - (TAAA)n#Simpl 1 TAAATAAATAAATAAATAAATAAATAAATAAATA-A- 35 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.12 (4 / 34), avg. gap size = 1.00 (4 / 4) 53 0.00 0.00 0.00 chr4ptel1M 377348 377392 (622608) (AG)n#Simple_repeat 1 45 (0) c_b173s251i1 6685 chr4ptel1M 377348 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 377392 (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 45 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 17 14.61 3.85 3.85 chr4ptel1M 377393 377408 (622592) (TAAA)n#Simple_repeat 36 51 (1) m_b173s252i1 6686 chr4ptel1M 377393 TGAATAAATAAATAAA 377408 i (TAAA)n#Simpl 36 TAAATAAATAAATAAA 51 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 15), avg. gap size = 0.0 (0 / 0) 44 0.00 0.00 0.00 chr4ptel1M 378127 378164 (621836) (GT)n#Simple_repeat 1 38 (0) c_b173s251i2 6687 chr4ptel1M 378127 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 378164 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 38 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 230 28.36 7.61 4.21 chr4ptel1M 378381 378472 (621528) L2d2_3end#LINE/L2 426 520 (35) m_b173s601i5 6688 chr4ptel1M 378381 CTTGCCCATTAGAGTATCATCTCCTTGAGAGCAGAGTTCTTCGTGCTCTT 378430 iv v i v i v v i i ---vi i - L2d2_3end#LIN 426 CTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGG---ACCATG-TCTT 471 chr4ptel1M 378431 G----TCTTGGTATCCC---CAAGACTCAACACAATGCCTTACTCAAAG 378472 i---- v --- ivi ii i i i v v L2d2_3end#LIN 472 ATACTTCTTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAG 520 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.91 CpG sites = 15, Kimura (unadjusted) = 36.75 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.07 (6 / 91), avg. gap size = 1.83 (11 / 6) 293 29.23 4.57 3.15 chr4ptel1M 379321 379539 (620461) C L1M4_orf2#LINE/L1 (2245) 1049 828 m_b173s551i5 6689 chr4ptel1M 379321 ATTTTATTGATCTCATCTTTAATTTTTAGGATTTCCAATTTAGTATTTAA 379370 i v i vv i i vv vvii vv ii iv C L1M4_orf2#LIN 1049 ATTTCATTTATTTCCGCTCTAATCTTTATTATTTCCTTCCTTCTGCTTGC 1000 chr4ptel1M 379371 CTGGAGATTTTTAATTTG---TCCTTTTTCTAGTTTGTTTAATTGCATGC 379417 i v i --- i --- i v v iv v v v C L1M4_orf2#LIN 999 TTTGGG---TTTAGTTTGCTCTTCTTTTTCTAGTTTCTTAAGGTGGAAGG 953 chr4ptel1M 379418 CCA----ATTGATCT--GCTCTTTCTCTATTTTATTGATGTAAGAATCTA 379461 ii ---- i -- v - v - i i i v i C L1M4_orf2#LIN 952 TTAGGTTATTGATTTGAGATCTTTCT-TCTTTT-TTAATATAGGCATTTA 905 chr4ptel1M 379462 GAGATAAAAAAATTTTCCTCTGATTTCAGCTTCTGCTGTATTGC-TAAGT 379510 v v -- v i i viv v i? i iv - C L1M4_orf2#LIN 904 CAGCT--ATAAATTTCCCTCTAAGCACTGCTTTNGCTGCATCCCATAAGT 857 chr4ptel1M 379511 TCTGAAATGTTGTCTCATCATTGTCATTC 379539 i iv v iv i v C L1M4_orf2#LIN 856 TTTGGTATGTTGTGTTTTCGTTTTCATTC 828 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.00 CpG sites = 31, Kimura (unadjusted) = 37.76 Transitions / transversions = 1.00 (31/31) Gap_init rate = 0.05 (11 / 218), avg. gap size = 1.55 (17 / 11) 210 20.69 1.69 1.69 chr4ptel1M 379565 379623 (620377) C MIR3#SINE/MIR (78) 130 72 m_b173s601i6 6690 chr4ptel1M 379565 AGGGAAC-ACGGCCAAGGGAGGAGAAGTGACTTGACCATGCTCACTTAGC 379613 i -iv v i v v v v vi C MIR3#SINE/MIR 130 AGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGC 81 chr4ptel1M 379614 ATAGTCAGTG 379623 -? i C MIR3#SINE/MIR 80 -NAGTTAGTG 72 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 24.75 CpG sites = 5, Kimura (unadjusted) = 24.75 Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.03 (2 / 58), avg. gap size = 1.00 (2 / 2) 547 30.91 5.63 2.04 chr4ptel1M 379787 380070 (619930) L1ME3Cz_3end#LINE/L1 255 548 (449) m_b173s551i6 6691 chr4ptel1M 379787 GGAAAAATGGAGCAGTATTATTACATTGTTGGTGGAATTATTAAGTAGGC 379836 i i - v v v i - i i i v i v v i vv L1ME3Cz_3end# 255 GGAGAAACGG-GAACTCTCAT-ACACTGCTGGTGGGAGTGTAAATTGGTA 302 chr4ptel1M 379837 CAACCATTTTGGAGAACAATTTGAAATTAT-------ACTCAAAG----G 379875 i i iv v ------- v ii ---- L1ME3Cz_3end# 303 CAACCACTTTGGAGAGCAATTTGGCAATATCTAGTAAAGTTGAAGATGCG 352 chr4ptel1M 379876 TATAGCCTTAGCTGCAACAATATCACCACTGGGTCTGCATCCCAAAGAAA 379925 i v vv viv i vi iv i v ii i i i L1ME3Cz_3end# 353 CATACCCTACGACCCAGCAATTCCACTTCTAGGTATATACCCTAGAGAAA 402 chr4ptel1M 379926 -TCAGAGAAAAG-GGAAAAGAACATAGATGTGCAAAAATAGTGATAGCAG 379973 - vviv v v - v v i v i -- i ii iv v v L1ME3Cz_3end# 403 CTCTCGCACATGTGCACAAGGAGACA--TGTACAAGGATGTTCATTGCAG 450 chr4ptel1M 379974 CTCTTTTTGTACTGGTAAAGAATTGGAATTGAAACC---ATGCTCATCAA 380020 vi v v i ii i vi-- --- ii L1ME3Cz_3end# 451 CATTGTTTGTAATAGCGAAAAATTGGAAAC--AACCTAAATGTCCATCAA 498 chr4ptel1M 380021 TCAGGGAATGACTGAACAAATTGTAGTATATGATTGTGATGGAATACTAT 380070 vi iv i i i vvv iii L1ME3Cz_3end# 499 TAGGGGAATGGATAAATAAATTGTGGTATATTCATACAATGGAATACTAT 548 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.88 CpG sites = 47, Kimura (unadjusted) = 40.78 Transitions / transversions = 1.21 (47/39) Gap_init rate = 0.04 (11 / 283), avg. gap size = 2.00 (22 / 11) 240 29.29 12.96 0.41 chr4ptel1M 380929 381144 (618856) L2a_3end#LINE/L2 264 506 (11) m_b173s601i7 6692 chr4ptel1M 380929 AAGTGGC-CTCCCTACCTGCTATTAGTATCTAACCCTCT----CTG-TTT 380972 i ? - v v? iv i ?i v vi v i ---- - L2a_3end#LINE 264 AAATNGCACACCCTCNCCCCCANCACTCCCTATCCCCCTTACCCTGCTTT 313 chr4ptel1M 380973 ACCTTTCATC----TACT-----CTATATG-CATTTTCTATATTT-ACCT 381011 ii vi ----i ----- i v - vi v - i L2a_3end#LINE 314 ATTTTTCTCCATAGCACTTATCACCATCTGACATACTATATATTTTACTT 363 chr4ptel1M 381012 ATTTG---GATTTTTACATATATTTACATA-TGGAATGTAAGTTCCTTGA 381057 i--- v v iiv i v iiv vi - i i v L2a_3end#LINE 364 ATTTATTTGTTTATTGTCTGTCTCCCCCCACTAGAATGTAAGCTCCATGA 413 chr4ptel1M 381058 GGTCAGGGACTATT-TTTGTTTT-TTC-TTA--ATCTCTTCAATATTTGT 381102 v v - i - -i i--i v ii iiiii iv L2a_3end#LINE 414 GGGCAGGGACTTTTGTCTGTTTTGTTCACTGCTGTATCCCCAGCGCCTAG 463 chr4ptel1M 381103 CACTGTGCCTGGCATCT-GT-GATGCTTCAATAAATGTTTCTTG 381144 v v iv - - ii - i v L2a_3end#LINE 464 AACAGTGCCTGGCACATAGTAGGCGC-TCAATAAATATTTGTTG 506 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.39 CpG sites = 38, Kimura (unadjusted) = 39.08 Transitions / transversions = 1.52 (38/25) Gap_init rate = 0.07 (16 / 215), avg. gap size = 1.81 (29 / 16) 293 28.07 4.35 0.84 chr4ptel1M 381039 381153 (618847) L2d2_3end#LINE/L2 435 553 (2) m_b173s601i8 6692 chr4ptel1M 381039 TGGAATGTAAGTTCCTTGAGGTCAGGGACTAT-TTTTGTTTTTTCTTA-A 381086 i v i v i - i i vi ii i- L2d2_3end#LIN 435 TAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACTTCTTTGTA 484 chr4ptel1M 381087 TCTCTT-CAATATTTGTCACTGTGCCTGGCAT-CTGT-GATGCTTCAATA 381133 i ii- iiiii iv v v i- v - ii - L2d2_3end#LIN 485 TCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAGTAGGCGC-TCAATA 533 chr4ptel1M 381134 AATGTTTCTTGGTTTGTTTT 381153 i v i v L2d2_3end#LIN 534 AATATTTGTTGATTTGATTT 553 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.11 CpG sites = 23, Kimura (unadjusted) = 37.23 Transitions / transversions = 2.56 (23/9) Gap_init rate = 0.05 (6 / 114), avg. gap size = 1.00 (6 / 6) 383 21.52 2.53 0.00 chr4ptel1M 381609 381687 (618313) MIR#SINE/MIR 44 124 (138) m_b173s601i9 6693 chr4ptel1M 381609 CTTCCAGAGTTCAAATCTGGACTCAGCCATTTACTAGCCGTGTGTCCCTG 381658 v v i i iv i v i i v i MIR#SINE/MIR 44 CTGCCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTG 93 chr4ptel1M 381659 GGCAAGTCACTTAACCTGATTGT--CTCAAT 381687 i vvi -- i MIR#SINE/MIR 94 GGCAAGTTACTTAACCTCTCTGTGCCTCAGT 124 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 24.09 CpG sites = 10, Kimura (unadjusted) = 25.79 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.01 (1 / 78), avg. gap size = 2.00 (2 / 1) 264 29.65 11.90 1.62 chr4ptel1M 381790 381957 (618043) C L2a_3end#LINE/L2 (2) 515 331 m_b173s601i10 6694 chr4ptel1M 381790 TTATTCAATTCAACAATCATTTGTGAAGTTATCTCTGGCATAGAGGGCAT 381839 i - vi i vi i-ii viviii ivvi i C L2a_3end#LINE 515 TCATTCA-TTCAACAAATATTTATTGAGC-GCCTACTATGTGCCAGGCAC 468 chr4ptel1M 381840 TGTGCTTGGCACTGAGAATATAG------ACCAAA-AGA-AGAAATCCCT 381881 v v i i i i ------ v - - i i C L2a_3end#LINE 467 TGTTCTAGGCGCTGGGGATACAGCAGTGAACAAAACAGACAAAAGTCCCT 418 chr4ptel1M 381882 GCTCTCAC-AAGCTTG-----TGGT-GAAGAAGATAGA-AATAAATTGAA 381923 i i-i i----- i - ii i i - -ii C L2a_3end#LINE 417 GCCCTCATGGAGCTTACATTCTAGTGGGGGGAGACAGACAATAAA-CAAA 369 chr4ptel1M 381924 AAGATAAGGAAAGC---TAGTTTG-AAGAGGATGATAA 381957 v i v ii--- v -v v i C L2a_3end#LINE 368 TAAATAAGTAAAATATATAGTATGTCAGATGGTGATAA 331 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.93 CpG sites = 35, Kimura (unadjusted) = 40.22 Transitions / transversions = 2.50 (35/14) Gap_init rate = 0.07 (12 / 167), avg. gap size = 1.92 (23 / 12) 248 28.81 3.39 0.00 chr4ptel1M 383254 383312 (616688) L1PA4_3end#LINE/L1 262 322 (580) m_b173s551i7 6695 chr4ptel1M 383254 GAGGTAGG--CATTCTTACACCATTGGTAGAACTGTAAACTGGTCTGATC 383301 ii -- i i ii i i i iii i L1PA4_3end#LI 262 GAAATAGGAACACTTTTACACTGTTGGTGGGACTGTAAACTAGTTCAACC 311 chr4ptel1M 383302 ATTCTAAAAAT 383312 v ii i L1PA4_3end#LI 312 ATTGTGGAAGT 322 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.83 CpG sites = 16, Kimura (unadjusted) = 41.83 Transitions / transversions = 16.00 (16/1) Gap_init rate = 0.02 (1 / 58), avg. gap size = 2.00 (2 / 1) 230 20.42 0.00 2.04 chr4ptel1M 384058 384107 (615893) MIR3#SINE/MIR 149 197 (11) m_b173s601i11 6696 chr4ptel1M 384058 GTTAGACTAGATTACTCCCCAAGGTCCCTTTGAGCTCTAAAATTGAATGA 384107 i v - i i iv i v vv MIR3#SINE/MIR 149 GTTGGACTAGATGA-TCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGA 197 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 23.98 CpG sites = 5, Kimura (unadjusted) = 23.98 Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.02 (1 / 49), avg. gap size = 1.00 (1 / 1) 487 20.65 6.98 6.15 chr4ptel1M 385826 385954 (614046) C MIRc#SINE/MIR (122) 146 17 m_b173s601i12 6697 chr4ptel1M 385826 CATTTTAGAGATCAGGAAATTGAGG---------ATTAAGCTACTTGCCC 385866 v v i ---------i iv C MIRc#SINE/MIR 146 CATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCC 97 chr4ptel1M 385867 AGGGTAATACAGCTACGAAGTGCCTCAGACTAGATATGAACTCAGAAAGA 385916 i v i vv v vv v vi ivi i ----- C MIRc#SINE/MIR 96 AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAG----- 52 chr4ptel1M 385917 AGAGTCTGCCTGACTCCAAGCCCAGTGCTCTATCTACT 385954 --- v i v i C MIRc#SINE/MIR 51 ---GTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACT 17 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 23.19 CpG sites = 11, Kimura (unadjusted) = 24.24 Transitions / transversions = 0.79 (11/14) Gap_init rate = 0.07 (9 / 128), avg. gap size = 1.89 (17 / 9) 16 10.03 0.00 0.00 chr4ptel1M 385994 386015 (613985) (T)n#Simple_repeat 1 22 (0) m_b173s252i2 6698 chr4ptel1M 385994 TTTTTTTTTCCTTTTTTTTTTT 386015 ii (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTT 22 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 388 24.19 12.90 0.00 chr4ptel1M 386718 386841 (613159) MIR#SINE/MIR 123 262 (0) m_b173s601i13 6699 chr4ptel1M 386718 GTTTCCTTTTCAATAAATAGAGGA-GATAATAGCACCTAACTCCCACGGT 386766 iv vi vv i -i i v vi v MIR#SINE/MIR 123 GTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTCATAGGGT 172 chr4ptel1M 386767 AGTTGTGAGAATCAAATGAGATAAT---TATAAAAC------------AC 386801 v i i v --- i i ------------i MIR#SINE/MIR 173 TGTTGTGAGGATTAAATGAGTTAATACATGTAAAGCGCTTAGAACAGTGC 222 chr4ptel1M 386802 CTGGCATAGAGTAAATACCATAGAACTGTTAGCTATTATT 386841 i v iii ivv v v MIR#SINE/MIR 223 CTGGCACATAGTAAGCGCTCAATAAATGTTAGCTATTATT 262 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.31 CpG sites = 16, Kimura (unadjusted) = 29.58 Transitions / transversions = 1.14 (16/14) Gap_init rate = 0.02 (3 / 123), avg. gap size = 5.33 (16 / 3) 409 19.39 21.43 0.00 chr4ptel1M 388057 388154 (611846) MIRc#SINE/MIR 28 146 (122) m_b173s601i14 6700 chr4ptel1M 388057 CACCGGGCTTGGAGTCAGAAAGACTCA---TCAAACCC------------ 388091 i i i iii--- i ii ------------ MIRc#SINE/MIR 28 CACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCAC 77 chr4ptel1M 388092 -----AGCTATGTGACTCTGGGCAAGTCACTTGACCCAGTTTA-CCTCAA 388135 ----- i ii i ivvi v - i MIRc#SINE/MIR 78 TTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAG 127 chr4ptel1M 388136 TTTCCTCATCTGTAAAATG 388154 MIRc#SINE/MIR 128 TTTCCTCATCTGTAAAATG 146 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 22.26 CpG sites = 16, Kimura (unadjusted) = 23.67 Transitions / transversions = 5.33 (16/3) Gap_init rate = 0.04 (4 / 97), avg. gap size = 5.25 (21 / 4) 288 34.82 4.40 2.47 chr4ptel1M 388470 388628 (611372) MIRc#SINE/MIR 32 193 (75) m_b173s601i15 6701 chr4ptel1M 388470 GGACTTGG-GT--GGACG--CCAAATTCAAACCTCACTTCGAACATTCAC 388514 - -- v -- iiii i ii i ivi viv i i MIRc#SINE/MIR 32 GGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTAC 81 chr4ptel1M 388515 ATAAAGTGCATGATCCTGGTCAA-TCCCTTTGCCTCACAAAGCCTCAGTA 388563 - iv- ii i i v - v vi v vi v MIRc#SINE/MIR 82 -TAGC-TGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTT 129 chr4ptel1M 388564 TATGTTTCTGTAAAA-GGGGCCAACATTACTTGTACCACCCATTTCCCTG 388612 viviv - vi i v i iv ii i ii v v MIRc#SINE/MIR 130 TCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAG 179 chr4ptel1M 388613 GGGATCATTGTAAGAA 388628 -- ii i i MIRc#SINE/MIR 180 GG--TTGTTGTGAGGA 193 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 47.06 CpG sites = 35, Kimura (unadjusted) = 49.72 Transitions / transversions = 1.84 (35/19) Gap_init rate = 0.06 (9 / 158), avg. gap size = 1.22 (11 / 9) 217 32.73 20.91 0.00 chr4ptel1M 389066 389175 (610825) MIR3#SINE/MIR 50 182 (26) m_b173s601i16 6702 chr4ptel1M 389066 TGTGTTCAAATCATGCCTCTGATACTTATTGCCCATCTCAATGTGGGCAG 389115 v v i vi v vi v i ?v ii v v viv i MIR3#SINE/MIR 50 TGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAA 99 chr4ptel1M 389116 ATCATTTGGCCACTTTGG-----------------------ATGAAAGAG 389142 i i vi v i ----------------------- ii i MIR3#SINE/MIR 100 GTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGG 149 chr4ptel1M 389143 CTGGACAAGATGGCTTTTCAGGTCCCTTCTAGC 389175 i v iii i v i MIR3#SINE/MIR 150 TTGGACTAGATGATCTCTAAGGTCCCTTCCAGC 182 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 43.35 CpG sites = 21, Kimura (unadjusted) = 45.05 Transitions / transversions = 1.40 (21/15) Gap_init rate = 0.01 (1 / 109), avg. gap size = 23.00 (23 / 1) 418 25.23 3.74 0.00 chr4ptel1M 389245 389351 (610649) MIRc#SINE/MIR 36 146 (122) m_b173s601i17 6703 chr4ptel1M 389245 TTGAAATCAGAGGTCCCTAGCTCCC--TTCCTGATCTGCCACTTACTACA 389292 i i iiivv i v i v-- i v v vv MIRc#SINE/MIR 36 TTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGC 85 chr4ptel1M 389293 TGTGTGACCCTAGGTGAGCCACTGAATCTGTCTCAAC--CAGTGTCCTCA 389340 i i ii i v i v v i -- v MIRc#SINE/MIR 86 TGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCA 135 chr4ptel1M 389341 TCTGTAAAATG 389351 MIRc#SINE/MIR 136 TCTGTAAAATG 146 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.27 CpG sites = 15, Kimura (unadjusted) = 31.27 Transitions / transversions = 1.25 (15/12) Gap_init rate = 0.02 (2 / 106), avg. gap size = 2.00 (4 / 2) 514 19.81 3.57 0.87 chr4ptel1M 390264 390375 (609625) Charlie4#DNA/hAT-Charlie 30 144 (3234) m_b173s502i0 6704 chr4ptel1M 390264 CTCCAAGGAACCTGTGACTAGATTTCAGGGA-CCCATGAACTTGGAAAGG 390312 i iii i iv v i-i i vi Charlie4#DNA/ 30 CCCCAAGGGGTCCGTGGATAGAATTCAGGGGGTCCGTGAACTTGGATGGG 79 chr4ptel1M 390313 AAAAA--TACATCTTCATTTT-ACTACCCTTTAGCTGAAATTTAGCACCA 390359 -- i - v i i ii- Charlie4#DNA/ 80 AAAAAATTACATCTTTATTTTCACTAACCTCTAACTGAAATTTAGCATT- 128 chr4ptel1M 390360 TCCTACAATTTTGGAT 390375 v v i Charlie4#DNA/ 129 TCCTTCAATTATGAAT 144 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 21.41 CpG sites = 16, Kimura (unadjusted) = 23.81 Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.04 (4 / 111), avg. gap size = 1.25 (5 / 4) 271 20.59 6.85 6.85 chr4ptel1M 390387 390459 (609541) Charlie4#DNA/hAT-Charlie 3304 3376 (2) m_b173s502i1 6705 chr4ptel1M 390387 ATTCTGAGAAA-----CACATGTTTCACCAGACTACAAAAGGAGTCCATG 390431 i----- i v i i v i Charlie4#DNA/ 3304 ATTCTGAGAAGGGGTCCATAGGCTTCACCAGACTGCCAAAGGGGTCCATG 3353 chr4ptel1M 390432 ATACACGCCAGAAAGGGTTACGAGGCCC 390459 ii ----- i i v iv Charlie4#DNA/ 3354 GCA-----CAAAAAAGGTTAAGAACCCC 3376 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 24.89 CpG sites = 10, Kimura (unadjusted) = 24.89 Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.08 (6 / 72), avg. gap size = 1.67 (10 / 6) 293 26.25 10.00 0.00 chr4ptel1M 390501 390580 (609420) C MIRc#SINE/MIR (120) 148 61 m_b173s601i18 6706 chr4ptel1M 390501 CTCATCTTACCAATGAGGAAACTGAGACTGAGAGA--------CATTTGT 390542 i i vi i v --------v i i C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr4ptel1M 390543 CCAAAGGCTTCTACCTAATAAGTTTCAGAGCAAGGACT 390580 i v vivi v i vv vi C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACT 61 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.89 CpG sites = 11, Kimura (unadjusted) = 32.73 Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.01 (1 / 79), avg. gap size = 8.00 (8 / 1) 340 23.19 26.04 3.42 chr4ptel1M 390669 390860 (609140) MIRc#SINE/MIR 18 251 (17) m_b173s601i19 6707 chr4ptel1M 390669 GTGGCACAGAACACTGGGATTAGAGTTAGAAAGATGGGAGTTCAAATTCT 390718 v - i iv i i i ivv i i i i i MIRc#SINE/MIR 18 GTGGAA-AGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCC 66 chr4ptel1M 390719 G--CCTGAGATTTTCTAGC----------TGGACAAGTCCCTT-ACCTCT 390755 --i vv i v ---------- i v - MIRc#SINE/MIR 67 GGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCT 116 chr4ptel1M 390756 ATTTGCCTCTATAGTTTTCCCAAGCATAAAATGGA-------------GC 390792 v vv --- i i vvii i------------- MIRc#SINE/MIR 117 CTGAGCCTC---AGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGC 163 chr4ptel1M 390793 CTTGTC---------GG--------GAGGGTCAAATGAGTGCAATAAT-- 390823 i i --------- -------- i ---- -- MIRc#SINE/MIR 164 CCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAG----ATAATGT 209 chr4ptel1M 390824 -TGTT-AAGTACTTACTACATT---AAGTGCTATATAAATGT 390860 - v- ii vv v i --- i MIRc#SINE/MIR 210 ATGTGAAAGCGCTTTGTAAACTGTAAAGTGCTATACAAATGT 251 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 26.23 CpG sites = 26, Kimura (unadjusted) = 28.61 Transitions / transversions = 1.53 (26/17) Gap_init rate = 0.09 (18 / 191), avg. gap size = 3.22 (58 / 18) 421 23.71 2.92 7.63 chr4ptel1M 390954 391090 (608910) C MIR1_Amn#SINE/MIR (82) 148 18 m_b173s601i21 6708 chr4ptel1M 390954 CATTTCACAGATGAGAAAACTGAGGCAAACAG-GATGAAATGACTTGTCA 391002 i i ?v v - i ? i i - C MIR1_Amn#SINE 148 CATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGCC- 100 chr4ptel1M 391003 CATAGTCACACATCTAATAAGTGTCTAAGGCTGTATTTGAACTCTGGAAG 391052 vi ? v ?iii? v vi v v v ? ? i ------ C MIR1_Amn#SINE 99 CAAGGTCACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAACCC------ 56 chr4ptel1M 391053 ATGAGACTTCTTGA-TCCCAGTCC--TACTATATTTATTAG 391090 --- iii ii - -- i v ii i C MIR1_Amn#SINE 55 ---AGGTCTCCCGAGTCCCAGTCCAGTGCTCTATCCACTAG 18 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.24 CpG sites = 20, Kimura (unadjusted) = 31.51 Transitions / transversions = 2.00 (20/10) Gap_init rate = 0.10 (13 / 136), avg. gap size = 1.08 (14 / 13) 422 20.65 2.46 8.70 chr4ptel1M 390954 391075 (608925) C MIRc#SINE/MIR (122) 146 32 m_b173s601i20 6708 chr4ptel1M 390954 CATTTCACAGATGAGAAAACTGAGG--CAAACAGGATGAAATGACTTGTC 391001 i i -- i v - v i i C MIRc#SINE/MIR 146 CATTTTACAGATGAGGAAACTGAGGCTCAGAGAGG-TTAAGTGACTTGCC 98 chr4ptel1M 391002 ACATAGTCACACATCTAATAAGTGTCTAAGGCTGTATTTGAACTCTGGAA 391051 - vi v i v vi v v v i i i ---- C MIRc#SINE/MIR 97 -CAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCC----A 53 chr4ptel1M 391052 GATGAGACTTCTTGA-TCCCAGTCC 391075 i ---- i - v C MIRc#SINE/MIR 52 GGT----CTTCCTGACTCCAAGTCC 32 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 23.14 CpG sites = 13, Kimura (unadjusted) = 24.31 Transitions / transversions = 1.30 (13/10) Gap_init rate = 0.10 (12 / 121), avg. gap size = 1.08 (13 / 12) 453 30.14 15.83 1.35 chr4ptel1M 391647 391905 (608095) C L3#LINE/CR1 (1) 4098 3803 m_b173s601i22 6709 chr4ptel1M 391647 ATAGAATGACAGAATATTCAG--TTAGAAGGGACCTCAATGGCCGTCTTC 391694 v -i -- i i iv i i vv C L3#LINE/CR1 4098 ATAGAATCACAGAAT-CTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAG 4050 chr4ptel1M 391695 TCCAGTCCACC-CCCAAAG-AAGAATCCTGACTAGGGTATATTGAACAA- 391741 ii iv -i v - i ivv viii viivi - C L3#LINE/CR1 4049 TCCAACCTCCCATCCAATGCAGGAATCCCTTCTACAACATCCCTGACAAG 4000 chr4ptel1M 391742 ---TCATCTGGTCTTTGTCTGAAAACTTCTAACGA-AGGAAGCCATCCAC 391787 --- ii i i ii v i i ii -i i ivv i C L3#LINE/CR1 3999 TGGTCATCCAGCCTCTGCTTGAACACCTCCAGTGACGGGGAGCTCACTAC 3950 chr4ptel1M 391788 CT-GTG-GGCAAAGC----------TAGAGCGCTCGGCTCATTAGAAGGA 391825 -?i - ivv ---------- i vv v v ii i v C L3#LINE/CR1 3949 CTCNCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGATTGTTAGAAAGT 3900 chr4ptel1M 391826 TCTT------------------TCTGCCTCTCTGCAGCTTTCTTCTGTTG 391857 ------------------ i i i i vi ii C L3#LINE/CR1 3899 TCTTCCTTATATTGAGCCGAAATCTGCCTCCCTGTAACTTCCACCCATTG 3850 chr4ptel1M 391858 CTCCTAGAT-TGTCCATCTGGGGTCAATCAGCTAACCAATC-AATCCCTC 391905 v v - i - i i vv -- iv i - C L3#LINE/CR1 3849 GTCCTAGTTCTGCCC-TCTGGAGCCACACAG--AATAAGTCTAATCCCTC 3803 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.24 CpG sites = 50, Kimura (unadjusted) = 40.63 Transitions / transversions = 1.85 (50/27) Gap_init rate = 0.06 (16 / 258), avg. gap size = 2.81 (45 / 16) 244 28.01 6.42 1.75 chr4ptel1M 391893 392001 (607999) C L2d_3end#LINE/L2 (1) 515 402 m_b173s601i23 6710 chr4ptel1M 391893 CAATCAATCCCTCAACAAGTATTCATTAAACACCCACTAAAT-----GAA 391937 vv i i i i i vi ----- v C L2d_3end#LINE 515 CAATCAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCA 466 chr4ptel1M 391938 CTCTGCTAGTCCCTA-GGTATCCAAAGAAAAAGTGAAAAACA-GAACCCA 391985 v v v i- vivv i ?i ? iv i - iv - C L2d_3end#LINE 465 CTGTGCTAGGCGCTGTGGGGAACGANAAAANAGTATAAGACATGGTCCC- 417 chr4ptel1M 391986 GAGTTTTCAAGAAGCT 392001 -v iii i C L2d_3end#LINE 416 -TGCCCTCAAGGAGCT 402 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.78 CpG sites = 17, Kimura (unadjusted) = 36.79 Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.05 (5 / 108), avg. gap size = 1.80 (9 / 5) 236 36.30 8.85 5.29 chr4ptel1M 391896 392279 (607721) C L2b_3end#LINE/L2 (2) 464 68 m_b173s601i24 6710 chr4ptel1M 391896 TCAATCCCTCAACAAGTATTCATTAAACACCCACTAAATG---AACTCTG 391942 v vi i i i i i i i ivi ---ii ? C L2b_3end#LINE 464 TCATTCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTG 415 chr4ptel1M 391943 --CTAGTCCCTAGGTATCCAAAGAAAAAGTGAA--AAACAGAACCCAGA- 391987 -- v v i v v iv ----- -- i - ? i v- C L2b_3end#LINE 414 TGCTAGGCGCTGGGGATACAGCG-----GTGAACAAGACAGA-CNCGGTC 371 chr4ptel1M 391988 ---GTTTTCAAGAAGCT-ATATTTTAACAAGAAA-ACCCACATGT---CT 392029 --- iii v i - i v i iiii ii - vv --- v C L2b_3end#LINE 370 CCTGCCCTCACGGAGCTCACAGTCTAGTGGGGGAGACAGACATGTAANCA 321 chr4ptel1M 392030 G-TAA--ATAGCCAAGGAGACGCAAGGGAATCTTAGAGG----TAAAGAA 392072 -i -- i v - vv i v ivvi i i ----i i i C L2b_3end#LINE 320 GACAATNATAACCCAG-AGTGGCAGGGTAGGACTGGGGGGGCCCAGAGGA 272 chr4ptel1M 392073 ACTAGCACCTCCCCCAGGTTGGAGGGGGAACCAGAAGAAGCCTCTTGAAG 392122 i--i i vv i vi i ----i iiiii i ii i C L2b_3end#LINE 271 G--GGCGCCTGACCCGGCCTGGGGGG----TCAGGGAGGGCTTCCCGGAG 228 chr4ptel1M 392123 ATGGAAG-GGCAGCCACCTTGCATAGAAAGCC-AAGAATTCTAAGAAATT 392170 --- i - i -----i viiv i v i- i vvvv i i C L2b_3end#LINE 227 ---GAGGTGACA-----TTTGAGCTGAGACCTGAAGGATGAGTAGGAGTT 186 chr4ptel1M 392171 G---AGATAAGGAGA--GAGAAAG-CAATCTAGGCAAGGGGCACGCCCAA 392214 --- iii i i-- i i - iv i ii v iv v?i C L2b_3end#LINE 185 GGCCAGGCGAAGAGGTGGGGAAGGGCGTTCCAGGCAGAGGGAACAGCANG 136 chr4ptel1M 392215 GGCAAAGACCCAGAGGTGAGAGACAGAGTTGGGGGT--AGGGATCTGCAA 392262 v i v i i ?v v? v v v --ii v v C L2b_3end#LINE 135 TGCAAAGGCCCTGAGGCGGGAGNGAGCNTGGCGTGTTCGAGGAACAGCAA 86 chr4ptel1M 392263 -CAGATGAGTCTGACTAG 392279 -v iiv v i i C L2b_3end#LINE 85 GGAGGCCAGTGTGGCTGG 68 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 48.83 CpG sites = 86, Kimura (unadjusted) = 54.37 Transitions / transversions = 1.87 (86/46) Gap_init rate = 0.10 (38 / 383), avg. gap size = 1.45 (55 / 38) 542 23.02 12.70 0.00 chr4ptel1M 392556 392681 (607319) MIRc#SINE/MIR 5 146 (122) m_b173s601i25 6711 chr4ptel1M 392556 GCAAAGTGGCACAGTGAATGGAGAATCAGCCCTGAAGTCAGAAGGACCCA 392605 iv ii i vi v iii v i i i i ii MIRc#SINE/MIR 5 GCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTG 54 chr4ptel1M 392606 AGTTCAAGTCTCA-----GACAC-TGCTAGCTGTGTGACCCTAGGCAAGT 392649 i i i i----- v - i i i MIRc#SINE/MIR 55 GGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGT 104 chr4ptel1M 392650 CACTTAA----------CTTTAGTTACCTCATCTGTAAAATG 392681 ---------- i i v MIRc#SINE/MIR 105 CACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATG 146 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 26.74 CpG sites = 23, Kimura (unadjusted) = 29.11 Transitions / transversions = 3.83 (23/6) Gap_init rate = 0.02 (3 / 125), avg. gap size = 5.33 (16 / 3) 207 28.67 10.68 1.79 chr4ptel1M 394130 394232 (605768) C L2#LINE/L2 (741) 2341 2230 m_b173s601i26 6710 chr4ptel1M 394130 TGAGAATCATCAGCACCAAGATGATCCTTGAATCCAC-----------AG 394168 i i ivv i vi i v i----------- C L2#LINE/L2 2341 TGGGAGTCATCAGCATATAGATGGTATTTAAAGCCATGAGACTGGATGAG 2292 chr4ptel1M 394169 ATCACCAAGTGAAGCAGTGAGGAGAGAGAACAGAACAGGGCTCAGCACAA 394218 ? v ivv vi v v v v iv v vi C L2#LINE/L2 2291 ATCACCNAGGGAGTGAGTGTAGATAGAGAAGAGAAGAGGTCCAAGGACTG 2242 chr4ptel1M 394219 AGTCCTACCGGACA 394232 i i-- i C L2#LINE/L2 2241 AGCCCTG--GGGCA 2230 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.02 CpG sites = 14, Kimura (unadjusted) = 37.02 Transitions / transversions = 0.93 (14/15) Gap_init rate = 0.03 (3 / 102), avg. gap size = 4.33 (13 / 3) 240 24.44 7.14 3.96 chr4ptel1M 394651 394748 (605252) C MER63D#DNA/hAT-Tip100 (597) 464 364 m_b173s502i2 6712 chr4ptel1M 394651 CACTTTAAATTCCATTCTG---TATCAACTTTCCATCTGTATCACACTAT 394697 v v ii v --- i v i-- vi vi v C MER63D#DNA/hA 464 CACTTTTAAGTTTAATCTGCATTATTAACATTT--TCTCCATCACTTTCT 417 chr4ptel1M 394698 TGATTGTCTAGACAATCAATAAAACAATA----AAGCTTCAGTTGCTAGC 394743 i -- i ---- iiiii vv C MER63D#DNA/hA 416 TAA--GTCTAGACAATCAACAAAACAATAAATCAAGCCCTGATTTGTAGC 369 chr4ptel1M 394744 ATTTG 394748 i C MER63D#DNA/hA 368 GTTTG 364 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 28.77 CpG sites = 14, Kimura (unadjusted) = 30.33 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.06 (6 / 97), avg. gap size = 1.83 (11 / 6) 11 17.30 7.69 0.00 chr4ptel1M 395315 395353 (604647) (TGGGGC)n#Simple_repeat 1 42 (0) m_b173s252i3 6713 chr4ptel1M 395315 TGGGAATGGGGCTGGGGCTGTGTCT---GCTGGGGCAGCGGC 395353 iv v v --- v v (TGGGGC)n#Sim 1 TGGGGCTGGGGCTGGGGCTGGGGCTGGGGCTGGGGCTGGGGC 42 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.03 (1 / 38), avg. gap size = 3.00 (3 / 1) 23 0.00 0.00 0.00 chr4ptel1M 395384 395408 (604592) (A)n#Simple_repeat 1 25 (0) m_b173s252i4 6714 chr4ptel1M 395384 AAAAAAAAAAAAAAAAAAAAAAAAA 395408 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAA 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 227 25.43 0.00 1.69 chr4ptel1M 395875 395934 (604066) L2d2_3end#LINE/L2 478 536 (19) m_b173s601i27 6715 chr4ptel1M 395875 CTTTTAACTCTCCATCTGGGTCCGGCCCAGAGTCTGGCACACAGTGGGCG 395924 vv ii i - v v i ii v v i v i L2d2_3end#LIN 478 CTTTGTATCCCCCA-CAGCGCCTAGCACAGTGCCTTGCACACAGTAGGCG 526 chr4ptel1M 395925 CTCAATAAAT 395934 L2d2_3end#LIN 527 CTCAATAAAT 536 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.47 CpG sites = 8, Kimura (unadjusted) = 31.47 Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.02 (1 / 59), avg. gap size = 1.00 (1 / 1) 245 18.44 0.00 6.12 chr4ptel1M 395883 395934 (604066) L2b_3end#LINE/L2 399 447 (19) m_b173s601i28 6715 chr4ptel1M 395883 TCTCCATCTGGGTCCGGCCCAGAGTCTGGCACACAGTGGGCGCTCAATAA 395932 i v --- i ii v ? i i i L2b_3end#LINE 399 TCCCCAGC---GCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAA 445 chr4ptel1M 395933 AT 395934 L2b_3end#LINE 446 AT 447 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 22.45 CpG sites = 7, Kimura (unadjusted) = 22.45 Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.00 (3 / 3) 252 13.16 0.00 0.00 chr4ptel1M 395900 395937 (604063) L2c_3end#LINE/L2 425 462 (16) m_b173s601i29 6715 chr4ptel1M 395900 CCCAGAGTCTGGCACACAGTGGGCGCTCAATAAATGCT 395937 v i i i i L2c_3end#LINE 425 CCCAGCGCCTGGCACATAGTAGGCGCTCAATAAATGTT 462 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 14.87 CpG sites = 4, Kimura (unadjusted) = 14.87 Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 65 19.37 2.02 6.32 chr4ptel1M 396001 396198 (603802) (GAG)n#Simple_repeat 1 190 (0) m_b173s252i5 6716 chr4ptel1M 396001 GAAGAGGATGTGAGGGATG-GGA-AAGGAGGAGAAAAAGAAAGAGGGATG 396048 i v v ii v - -i i ii i i - v (GAG)n#Simple 1 GAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA-GGAGG 49 chr4ptel1M 396049 GGCAGAAGAAGGAGGAAGGAGAAAGAGGGAGGAAGAAGGAGGAGAGAGGA 396098 i v i i - i i - - i - - (GAG)n#Simple 50 AGGAGGAGGAGGAGG-AGGAGGAGGA-GGAGG-AGGAGGAGGAG-GAGG- 94 chr4ptel1M 396099 AGAAGGAAAGAAGAGG-GG-GGAGGAGGGAGGAAGAGGAGGGAGGAAGAG 396146 i - i i - - - i - i (GAG)n#Simple 95 AGGAGG-AGGAGGAGGAGGAGGAGGA-GGAGGAGGAGGA-GGAGGAGGAG 141 chr4ptel1M 396147 GAAGAGGAGGAGGAAGAGGAGGGGGAGGAGGGAGGAAGGAAGAGGAGGGA 396196 i i i - - i - (GAG)n#Simple 142 GAGGAGGAGGAGGAGGAGGAGGAGGAGGA-GGAGG-AGGAGGAGGA-GGA 188 chr4ptel1M 396197 GG 396198 (GAG)n#Simple 189 GG 190 Matrix = Unknown Transitions / transversions = 4.80 (24/5) Gap_init rate = 0.08 (16 / 197), avg. gap size = 1.00 (16 / 16) 192 29.09 0.00 0.00 chr4ptel1M 396650 396704 (603296) C MIR1_Amn#SINE/MIR (71) 159 105 m_b173s601i30 6717 chr4ptel1M 396650 ATTCTTGTTCCCCTTCTACGGCTGAGGAAGCGGAGGCGCAGGGAAAAGAA 396699 iv i i v i i v i v ? i iiv? C MIR1_Amn#SINE 159 ATCATTATCCCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAA 110 chr4ptel1M 396700 ATCAC 396704 i v C MIR1_Amn#SINE 109 GTGAC 105 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 40.14 CpG sites = 10, Kimura (unadjusted) = 40.14 Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 40 24.82 3.90 2.56 chr4ptel1M 396957 397110 (602890) (GTTAGG)n#Simple_repeat 1 156 (0) m_b173s252i6 6718 chr4ptel1M 396957 GTTAGGGTTAGGG-GACATTTGGGGTTAGGAGGTA--TTTAGGATTAAGG 397003 -v viv i - v --v i i (GTTAGG)n#Sim 1 GTTAGGGTTAGGGTTAGGGTTAGGGTTAGG-GTTAGGGTTAGGGTTAGGG 49 chr4ptel1M 397004 TTAGGATTTAGGGTTAGGCTTTGGG-GGCATTTAGGGTTAGGGTTTGGG- 397051 -v v v -viviv v - (GTTAGG)n#Sim 50 TTAGG-GTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGT 98 chr4ptel1M 397052 GACATTTAGGGTTAGGG-GGCAGTTAGGGTTAGAGGCGCGAATTTAGGGT 397100 v viv -vivi - ivv -iv (GTTAGG)n#Sim 99 TAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAG-GGTTAG-GGTTAGGGT 146 chr4ptel1M 397101 TAGGGTTAGG 397110 (GTTAGG)n#Sim 147 TAGGGTTAGG 156 Matrix = Unknown Transitions / transversions = 0.55 (11/20) Gap_init rate = 0.06 (9 / 153), avg. gap size = 1.11 (10 / 9) 258 25.00 0.00 0.00 chr4ptel1M 397251 397306 (602694) L3#LINE/CR1 4043 4098 (1) m_b173s601i31 6719 chr4ptel1M 397251 GGTTGAACTCAATGACCCCTGAGTTTCCTTTCTACTTTGAAATTGTGGGA 397300 i vi i i v i i v i i v v L3#LINE/CR1 4043 GGTTGGACTAGATGACCTCTAAGGTCCCTTCCAACTCTGAGATTCTGTGA 4092 chr4ptel1M 397301 TTCTGT 397306 i L3#LINE/CR1 4093 TTCTAT 4098 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.36 CpG sites = 9, Kimura (unadjusted) = 31.36 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0) 12 18.13 3.12 0.00 chr4ptel1M 397895 397926 (602074) (GGAGAA)n#Simple_repeat 1 33 (0) m_b173s252i7 6720 chr4ptel1M 397895 GGAGCAGGAG-GGGAGAAAGAGAAGGGGAGGGA 397926 v -i i i i (GGAGAA)n#Sim 1 GGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGA 33 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 214 21.62 0.00 0.00 chr4ptel1M 398549 398585 (601415) MIRb#SINE/MIR 218 254 (14) m_b173s601i32 6721 chr4ptel1M 398549 GCACAGTGTCTGATACAAAGTAGGCACCTAATAAATG 398585 i ii v i i ii MIRb#SINE/MIR 218 GCACAGTGCCTGGCACATAGTAAGCGCTCAATAAATG 254 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 23.45 CpG sites = 7, Kimura (unadjusted) = 27.38 Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 202 26.32 0.00 0.00 chr4ptel1M 398552 398589 (601411) L2c_3end#LINE/L2 427 464 (14) m_b173s601i33 6722 chr4ptel1M 398552 CAGTGTCTGATACAAAGTAGGCACCTAATAAATGCCTG 398589 i i ii v i ii ii L2c_3end#LINE 427 CAGCGCCTGGCACATAGTAGGCGCTCAATAAATGTTTG 464 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.33 CpG sites = 9, Kimura (unadjusted) = 36.01 Transitions / transversions = 9.00 (9/1) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 474 33.89 8.16 2.69 chr4ptel1M 398595 398876 (601124) L3#LINE/CR1 3555 3851 (248) m_b173s601i34 6723 chr4ptel1M 398595 TCCTACT-TCCTCTGCTCTCATCAGACCTCAATTAAGGTACTATATTCAG 398643 ii - v v vi v vi iii i iii L3#LINE/CR1 3555 TCCCGCTGTACTCTGCGCTGGTCAGACCACATCTGGAGTATTGCGTTCAG 3604 chr4ptel1M 398644 ATCCGAGGGCTACAGTTTGAAAAGGCCCC---CAATCTGTGAGGAAACCC 398690 v i i v i v i i i v vi--- v - vivi-i L3#LINE/CR1 3605 TTCTGGGCGCCACATTTTAAGAGGGACATTGACAAACTG-GAGCGCG-TC 3652 chr4ptel1M 398691 CACCAAAGAATACCCAGGAGAGTGGAAGGAGGGCCTTGAGTCTATGTCAT 398740 vvii iiiv vi ---- i i v iv i L3#LINE/CR1 3653 CAGAGGAGAGCGACCAGGATGGT----GAAGGGTCTGGAAACCATGTCAT 3698 chr4ptel1M 398741 AGGAAGAGTATTTGATGGAATGGAGG--GTTTAGCCT--------AAAGA 398780 v i iiiv v iv i -- --------i L3#LINE/CR1 3699 ATGAGGAACGGTTGAAGGAACTGGGGATGTTTAGCCTGGAGAAGAGAAGA 3748 chr4ptel1M 398781 CCCAGAGAGGAACATCAGATCTGTCACCACCTTTAGGAAGGTC---CAC- 398826 ii - ii v v v vi vv v vv v --- i- L3#LINE/CR1 3749 CTTAGAG-GAGACATGATAGCTGTCTTCAAATATTTGAAGGGCTGTCATG 3797 chr4ptel1M 398827 TAGCTGAGGGACTACGTTTGTT-----TGATCCTGGAGGGCAGAATCAGA 398871 i vv i vii i ----- iii ii ii i L3#LINE/CR1 3798 TGGAAGAGGGATTAGACTTATTCTGTGTGGCTCCAGAGGGCAGAACTAGG 3847 chr4ptel1M 398872 AGCCA 398876 - L3#LINE/CR1 3848 A-CCA 3851 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 42.79 CpG sites = 57, Kimura (unadjusted) = 47.26 Transitions / transversions = 1.58 (57/36) Gap_init rate = 0.05 (15 / 281), avg. gap size = 2.07 (31 / 15) 289 14.34 29.46 6.62 chr4ptel1M 399080 399191 (600809) MIRc#SINE/MIR 11 146 (122) m_b173s601i35 6724 chr4ptel1M 399080 TGG-GCAGTAGATAGAGCACTGGAATCAGTGGGCTTGGAATCAGGAAGGC 399128 - i v --------- i i MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGA---------CTTGGAGTCAGGAAGAC 51 chr4ptel1M 399129 TCA--TTT----------TCCATCACTTACTAG-----------TG---- 399151 iii-- i---------- iii ----------- ---- MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 101 chr4ptel1M 399152 ----ACTTAACC-CTGTTTGCCTCAGTTTCCTCATCTGCAAAATG 399191 ---- - v vv i MIRc#SINE/MIR 102 AGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATG 146 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 15.41 CpG sites = 11, Kimura (unadjusted) = 16.57 Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.14 (16 / 111), avg. gap size = 2.62 (42 / 16) 190 26.19 0.00 0.00 chr4ptel1M 399337 399378 (600622) C L2d2_3end#LINE/L2 (10) 545 504 m_b173s601i36 6725 chr4ptel1M 399337 TCAATAAATAGTTGCAAAGTGACCACTGTGTGTAAGTCACTG 399378 i v iivi i v i i v C L2d2_3end#LIN 545 TCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTG 504 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.65 CpG sites = 7, Kimura (unadjusted) = 33.26 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 243 27.31 0.82 6.96 chr4ptel1M 399784 399905 (600095) C Charlie4a#DNA/hAT-Charlie (389) 119 5 m_b173s502i3 6726 chr4ptel1M 399784 TTGAAGGAATTGCTTCCTTTCTGTCAAAGG-GGGTGGAAAATAAGGGGTT 399832 v vvv v i i -vi - i ivv C Charlie4a#DNA 119 TTGAAGGAAATGCTAAATTTCAGTTAGAGGTTAGT-GAAAATAAAGATGT 71 chr4ptel1M 399833 GGTTTTGTTTCCCATTCACGCTCACGGAGCCGTGAAATTGGGCGCTCATG 399882 ii v i i v i v vivi ----- - v C Charlie4a#DNA 70 AATTTTTTTCCCCATCCAAGTTCACGGACCCCCTGAATT-----CT-ATC 27 chr4ptel1M 399883 GACCCACCCCAGCCTAAGGAACC 399905 v vv vi - C Charlie4a#DNA 26 CACGGACCCCAGGTTAA-GAACC 5 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.87 CpG sites = 13, Kimura (unadjusted) = 33.87 Transitions / transversions = 0.72 (13/18) Gap_init rate = 0.07 (9 / 121), avg. gap size = 1.00 (9 / 9) 225 22.09 13.95 0.00 chr4ptel1M 400278 400363 (599637) C MIR1_Amn#SINE/MIR (95) 135 38 m_b173s601i37 6727 chr4ptel1M 400278 AGGAGAC--AGGC----AAAACTTAAGTGACTTACCCAAGGTCACTCAAT 400321 i -- ---- i iv ? i ? ii C MIR1_Amn#SINE 135 AGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGCCCAAGGTCACNCAGC 86 chr4ptel1M 400322 TTGGGA-TGGCACAGACAGG-GCAAAACT---ATCTCCTG-GCCCTAG 400363 ?v v? - v v i -?i?i i---i i - i i C MIR1_Amn#SINE 85 NGGCNAGTGGCAGAGCCGGGANTNGAACCCAGGTCTCCCGAGTCCCAG 38 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 26.24 CpG sites = 14, Kimura (unadjusted) = 29.93 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.07 (6 / 85), avg. gap size = 2.00 (12 / 6) 288 35.00 8.72 1.72 chr4ptel1M 401500 401717 (598283) L2b_3end#LINE/L2 222 454 (12) m_b173s601i38 6728 chr4ptel1M 401500 CACCACTTCTGT--AGCCTTCTC-AACCTTGCAGAAGCAAGGTCCATCCC 401546 v i i v-- i i -i iiv -- vi viv v L2b_3end#LINE 222 CACCTCCTCCGGGAAGCCCTCCCTGACCCCCCAG--GCCGGGTCAGGCGC 269 chr4ptel1M 401547 TTCTCCTTTCTTTCTCCCC--CTCTACTC---CTTTTTGGGATCTC-TTC 401590 i- i vvvi i --ii i --- vi i v v ?- v L2b_3end#LINE 270 C-CTCCTCTGGGCCCCCCCAGTCCTACCCTGCCACTCTGGGTTATNATTG 318 chr4ptel1M 401591 TCT----ACA---CTGCCTTTCCCGTTGGAACAGAAGCTCCTTGGAATCA 401633 ---- --- i ii ii i viivi v iiiv L2b_3end#LINE 319 TCTGNTTACATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCA 368 chr4ptel1M 401634 GGGACTATCT-TGTATTTGTTT-TTATT-TATCCTTAGCACTCAGAACAG 401680 ii?v - -i i-iiii - ii i ii v L2b_3end#LINE 369 GGGACCGNGTCTGT-CTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAG 417 chr4ptel1M 401681 TTCCTGAGACAGAGCAAGAGCTTAATAAATACTCATT 401717 ?v iv v i i v i i i ii L2b_3end#LINE 418 NGCCTGGCACACAGTAGGCGCTCAGTAAATATTTGTT 454 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 46.67 CpG sites = 51, Kimura (unadjusted) = 51.91 Transitions / transversions = 2.12 (51/24) Gap_init rate = 0.06 (14 / 217), avg. gap size = 1.64 (23 / 14) 382 30.83 4.13 0.80 chr4ptel1M 401597 401717 (598283) L2a_3end#LINE/L2 381 505 (12) m_b173s601i39 6728 chr4ptel1M 401597 CTGCCTTTCCC-GTTGGAACAGAAGCTCCTTGGAATCAGGGACTATC--T 401643 i ii -ii i iiv v iiiv v i--i L2a_3end#LINE 381 CTGTCTCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTC 430 chr4ptel1M 401644 TGTATTTGTTT-TTATT-TATCCTTAGCACTCAGAACAGTTCCTGAGACA 401691 - i-i ii - ii i ii v iv L2a_3end#LINE 431 TGT-TTTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACA 479 chr4ptel1M 401692 GAGCAAGAGCTTAATAAATACTCATT 401717 v i i v i i ii L2a_3end#LINE 480 TAGTAGGCGCTCAATAAATATTTGTT 505 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 41.86 CpG sites = 29, Kimura (unadjusted) = 43.50 Transitions / transversions = 3.62 (29/8) Gap_init rate = 0.04 (5 / 120), avg. gap size = 1.20 (6 / 5) 68 19.95 1.99 0.65 chr4ptel1M 401718 401868 (598132) (TCCT)n#Simple_repeat 1 153 (0) m_b173s252i8 6729 chr4ptel1M 401718 TCCTTCCTCCATTCCCTCTTTCC-TGTTTCCCTCCCT-CTTCCTTCC-TC 401764 i v i i - vi i i - - (TCCT)n#Simpl 1 TCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC 50 chr4ptel1M 401765 CTTCCTTTCTTTCTTTCCTTCCTCCCTCCCTTCCTTCCTCCCTTCCTTTT 401814 - i i i i i ii (TCCT)n#Simpl 51 CTTCC-TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 99 chr4ptel1M 401815 TTCCTTCCTCCCTTCCTTCTTTCTTTGTTTCCTTTCCTCCTTTTTTTCTT 401864 i i i vi i i ii i (TCCT)n#Simpl 100 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 149 chr4ptel1M 401865 CCTT 401868 (TCCT)n#Simpl 150 CCTT 153 Matrix = Unknown Transitions / transversions = 7.33 (22/3) Gap_init rate = 0.03 (4 / 150), avg. gap size = 1.00 (4 / 4) 217 24.76 0.00 8.20 chr4ptel1M 401869 401934 (598066) MIR#SINE/MIR 108 168 (94) m_b173s601i41 6730 chr4ptel1M 401869 CCTTCCTGAGAATCTCAATTTCCTTATCAGTAAAATGAGGGCAAACTCAG 401918 ii v --i i i v i ii ---i i MIR#SINE/MIR 108 CCTCTCTGTG--CCTCAGTTTCCTCATCTGTAAAATGGGGATAA---TAA 152 chr4ptel1M 401919 TACCACCTACATCATA 401934 vi v MIR#SINE/MIR 153 TAGTACCTACCTCATA 168 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.29 CpG sites = 11, Kimura (unadjusted) = 31.29 Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.08 (5 / 65), avg. gap size = 1.00 (5 / 5) 220 17.99 0.00 5.13 chr4ptel1M 401869 401909 (598091) MIR3#SINE/MIR 109 147 (61) m_b173s601i40 6730 chr4ptel1M 401869 CCTTCCTGAGAATCTCAATTTCCTTATCAGTAAAATGAGGG 401909 ii i --i i i v MIR3#SINE/MIR 109 CCTCTCTGGG--CCTCAGTTTCCTCATCTGTAAAATGAGGG 147 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 21.59 CpG sites = 6, Kimura (unadjusted) = 21.59 Transitions / transversions = 6.00 (6/1) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 261 31.20 2.56 9.59 chr4ptel1M 402164 402319 (597681) C L2c_3end#LINE/L2 (11) 467 322 m_b173s601i42 6725 chr4ptel1M 402164 CAGCCAACACCTGTGATGTGCCTACTATGTGGCAGGCACTGTCCTAGGTG 402213 i v ii i viv i v i --------- C L2c_3end#LINE 467 CAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTG--------- 427 chr4ptel1M 402214 CTGGAATACAAATTCAAAAATGAATTGGTTACTTCCCTCAA--AGTTTAT 402261 -- i vvii v v vvi iv v -- i i i C L2c_3end#LINE 426 --GGGATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCAC 379 chr4ptel1M 402262 AGTCTATTGAGGAAGGAAACCCCATAGATCCAGA-AATGCATAA-ACACA 402309 v ii i iv iv v?i i -- - -i i - vi C L2c_3end#LINE 378 AGTCTAGTGGAGGAGACAGACANGTAAA--CAGACAAT-TACAATACAAG 332 chr4ptel1M 402310 TAGATGATAA 402319 vi C L2c_3end#LINE 331 TTAATGATAA 322 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.01 CpG sites = 26, Kimura (unadjusted) = 41.67 Transitions / transversions = 1.44 (26/18) Gap_init rate = 0.11 (17 / 155), avg. gap size = 1.06 (18 / 17) 250 28.20 9.76 6.30 chr4ptel1M 402181 402426 (597574) C L2d2_3end#LINE/L2 (28) 527 274 m_b173s601i45 6725 chr4ptel1M 402181 GTGCCTACTATGTGGCAGGCACTGTCCTAGGTGCT----GGAATACAAAT 402226 i i vv v i ---- i - C L2d2_3end#LIN 527 GCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGTGGGGGATACAAA- 479 chr4ptel1M 402227 TCAAAAAT--GAATTGGTTACTTCCCTCAA--AGTTTATAGTCTA-TTGA 402271 -v iv -- vv iv v -- i i i - i C L2d2_3end#LIN 478 -GAAGTATAAGACATGGTCCCTGCCCTCAAGGAGCTTACAATCTAGTTGG 430 chr4ptel1M 402272 GGAAGGAAACCCCATAGATCCA-GAAATGCATAAACACATAGATGATAAA 402320 iiv i--v i iv i- v i- i ----- ii v C L2d2_3end#LIN 429 GGAGACAAG--ACATAAACACGTGAAAAGT-TAAATA-----ACAATACA 388 chr4ptel1M 402321 GAATAGAAATGGTAG---AAAATAGAGATGATAG-ATAAATGAATCAATA 402366 ii vv iii --- i i --- ii - v i vvv vi C L2d2_3end#LIN 387 AGATTTAAATAACAGTTCAAGACA---ACAATAGAAGAGATGTCACAAGG 341 chr4ptel1M 402367 -AATACATG---AATGGGTGAATGAA---TACA---AATAAATACTGATA 402406 - i --- v vii --- --- ? i - C L2d2_3end#LIN 340 CAGTACATGATTAATTGCCAAATGAATGGTACAGACAATAANTGCT-ATA 292 chr4ptel1M 402407 GAAATCCTCAAAAAAGGAGG 402426 i i -- i ii ii C L2d2_3end#LIN 291 GGAGT--TCAGAGGAGGGAG 274 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.93 CpG sites = 42, Kimura (unadjusted) = 37.09 Transitions / transversions = 1.83 (42/23) Gap_init rate = 0.11 (27 / 245), avg. gap size = 1.48 (40 / 27) 295 26.91 6.01 6.59 chr4ptel1M 402181 402363 (597637) C L2a_3end#LINE/L2 (28) 489 308 m_b173s601i43 6725 chr4ptel1M 402181 GTGCCTACTATGTGGCAGGCACTGTCCTAGGTGCT-GGAATACAA-ATT- 402227 i v i i - i i- v - C L2a_3end#LINE 489 GCGCCTACTATGTGCCAGGCACTGTTCTAGGCGCTGGGGATACAGCAGTG 440 chr4ptel1M 402228 --CAAAA---ATGAATTGGTTACTTCCCTCA--AAGTTTATAGTCTATTG 402270 -- --- ii --i iv v --i i i v v C L2a_3end#LINE 439 AACAAAACAGACAAA--AGTCCCTGCCCTCATGGAGCTTACATTCTAGTG 392 chr4ptel1M 402271 AGGAAGGAAACCCCATAGATCCAGAAATGCATAAACACATAGATGATAAA 402320 i -- i ----- - v v iiv i vi i vv v C L2a_3end#LINE 391 GGG--GGAGAC-----AGA-CAATAAACAAATAAATAAGTAAAATATATA 350 chr4ptel1M 402321 GAATA-GAAATGGTAGAAAATAGAGATGATAGATAAATGAATCA 402363 v i-v i iiv i - vv i- v i v C L2a_3end#LINE 349 GTATGTCAGATGGTGATAAGT-GCTATGG-AGAAAAATAAAGCA 308 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.20 CpG sites = 26, Kimura (unadjusted) = 33.99 Transitions / transversions = 1.30 (26/20) Gap_init rate = 0.10 (19 / 182), avg. gap size = 1.21 (23 / 19) 356 22.31 9.38 1.94 chr4ptel1M 402181 402276 (597724) C L2b_3end#LINE/L2 (28) 438 336 m_b173s601i44 6725 chr4ptel1M 402181 GTGCCTACTATGTGGCAGGCACTGTCCTAGGTGCT-GGAATACA------ 402223 i i v ? v i - i ------ C L2b_3end#LINE 438 GCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGGGATACAGCGGTG 389 chr4ptel1M 402224 AATTCAAAAATGAATTGGTTACTTCCCTCA--AAGTTTATAGTCTATTGA 402271 -- i vv v?i iv v --i i i i v i C L2b_3end#LINE 388 AA--CAAGACAGACNCGGTCCCTGCCCTCACGGAGCTCACAGTCTAGTGG 341 chr4ptel1M 402272 GGAAG 402276 i C L2b_3end#LINE 340 GGGAG 336 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 23.39 CpG sites = 13, Kimura (unadjusted) = 27.84 Transitions / transversions = 1.62 (13/8) Gap_init rate = 0.05 (5 / 95), avg. gap size = 2.20 (11 / 5) 450 20.27 8.51 5.52 chr4ptel1M 402566 402706 (597294) C MIR3#SINE/MIR (43) 165 21 m_b173s601i46 6731 chr4ptel1M 402566 AGCTCACCTTCTCCAGCTCC----TTTTACAGATGAGGAAACTGAG--CC 402609 v i vv i i ---- -- C MIR3#SINE/MIR 165 AGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCC 116 chr4ptel1M 402610 AAACAGGATGAAGTGTCTTGCGCAGGGTCACACAGA----TAGTGTCTGA 402655 i v - v v i v---- v v - C MIR3#SINE/MIR 115 AGAGAGG-TGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAG- 68 chr4ptel1M 402656 AGCCAGAATT-GAACTCTGGAAGAAGCCTCTTGAC-CCCAGCCCACATTC 402703 i i i - i ------ i i i - i iiii C MIR3#SINE/MIR 67 AGCCGGGACTAGAACCC------AGGTCTCCTGACTCCCAGTCCGTGCTC 24 chr4ptel1M 402704 GCT 402706 v C MIR3#SINE/MIR 23 TCT 21 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 22.18 CpG sites = 17, Kimura (unadjusted) = 24.16 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.09 (13 / 140), avg. gap size = 1.54 (20 / 13) 184 21.79 16.88 4.65 chr4ptel1M 402752 402828 (597172) MIRc#SINE/MIR 31 116 (152) m_b173s601i47 6732 chr4ptel1M 402752 TGGAC--GAAGTCAGGAAG--------TCACATCCTGCCTGGGACACTTT 402791 -- i -------- ivi i v vv v v MIRc#SINE/MIR 31 TGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTA 80 chr4ptel1M 402792 CCAGCTGTGTGACTTCTCGAGCTTAAG---CTTAGTTTCT 402828 i -- i i -- --- iii MIRc#SINE/MIR 81 CTAGCTGTGTGAC--CTTGGGC--AAGTCACTTAACCTCT 116 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 22.82 CpG sites = 10, Kimura (unadjusted) = 26.51 Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.09 (7 / 76), avg. gap size = 2.43 (17 / 7) 441 33.45 5.88 3.28 chr4ptel1M 403156 403393 (596607) MIRc#SINE/MIR 25 268 (0) m_b173s601i48 6733 chr4ptel1M 403156 GGGCCCTGGCCTTGGAGTC-GACAG--CTTGGCTCAGGGCATGGTCCCTC 403202 i v v - iv -- v i ii v vi ii iv MIRc#SINE/MIR 25 GAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGC 74 chr4ptel1M 403203 CACT--------GGATAACTTTGGTGCAAAACACTCCATCTTCTTCTACC 403244 -------- vi i i - iv iv i iii vvi MIRc#SINE/MIR 75 CACTTACTAGCTGTGTGACCTTGG-GCAAGTCACTTAACCTCTCTGAGCC 123 chr4ptel1M 403245 TCAGTTTCCTCATTCACAAAAT-GGGATGATAACATGCGCAAGATCCCTC 403293 iiii - i i ivi ----i ivi MIRc#SINE/MIR 124 TCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGC----CCTGCC 169 chr4ptel1M 403294 TACCTTCACCCAGGGCTCTTCTGTGGCCCAAAAGAGAT--CCTAGATAGA 403341 --- v i v v v vi v --iv vi ii MIRc#SINE/MIR 170 TACCT---CACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAA 216 chr4ptel1M 403342 TGCATCTTAAAAAGCGTAAAGGGTTCCACATATGTTGGGTATTATTGTCG 403391 v iii iv vi v i vi v vi ?i i ii MIRc#SINE/MIR 217 AGCGCTTTGTAAACTGTAAAGTGCTATACAAATGTAAGGNGTTATTATTA 266 chr4ptel1M 403392 TT 403393 MIRc#SINE/MIR 267 TT 268 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 44.24 CpG sites = 48, Kimura (unadjusted) = 46.77 Transitions / transversions = 1.66 (48/29) Gap_init rate = 0.05 (13 / 237), avg. gap size = 1.69 (22 / 13) 344 31.30 3.05 0.00 chr4ptel1M 403901 404031 (595969) MIR1_Amn#SINE/MIR 2 136 (94) m_b173s601i49 6734 chr4ptel1M 403901 AGGAGAGCTGGGTGGAGCAGTGGGTAGGGAA--GGCCTGG-AGTCAGGAA 403947 iii v v vvi i i v -- v - v i i MIR1_Amn#SINE 2 AGGGAGGCAGTGTGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGAG 51 chr4ptel1M 403948 ACCTGAATTCAAATCCAATCTCAGAC-CTGACTAGCCATATGACCCTGAT 403996 ii ? ? viv v v - ?i i? ii?i i iv MIR1_Amn#SINE 52 ACCTGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGG 101 chr4ptel1M 403997 CAAGTCACTAAACTTCCTTCTTTCTTTCCTTCCTC 404031 v? i ii v?vi ivvi MIR1_Amn#SINE 102 CAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTC 136 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 42.19 CpG sites = 24, Kimura (unadjusted) = 45.15 Transitions / transversions = 1.41 (24/17) Gap_init rate = 0.02 (3 / 130), avg. gap size = 1.33 (4 / 3) 385 24.77 4.55 0.88 chr4ptel1M 403903 404012 (595988) MIRc#SINE/MIR 2 115 (153) m_b173s601i50 6734 chr4ptel1M 403903 GAGAGCTGGGTGGAGCAGTGGGTAGGGAA---GGCCTGGAGTCAGGAA-A 403948 - v v v iv i v --- i i - MIRc#SINE/MIR 2 GAG-GCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA 50 chr4ptel1M 403949 CCTGAATTCAAATCCAATCTCAGAC-CTGACTAGCCATATGACCCTGATC 403997 ii i i viv v v - v ii i i iv MIRc#SINE/MIR 51 CCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGC 100 chr4ptel1M 403998 AAGTCACTAAACTTC 404012 v i MIRc#SINE/MIR 101 AAGTCACTTAACCTC 115 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.93 CpG sites = 15, Kimura (unadjusted) = 30.55 Transitions / transversions = 1.25 (15/12) Gap_init rate = 0.04 (4 / 109), avg. gap size = 1.50 (6 / 4) 16 20.27 0.00 0.00 chr4ptel1M 404032 404067 (595933) (CCTC)n#Simple_repeat 1 36 (0) m_b173s252i9 6735 chr4ptel1M 404032 CCTCCCTCTCTTCTTTCCTTCCTCCCTCCCTTCCTC 404067 i i i i i i (CCTC)n#Simpl 1 CCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTC 36 Matrix = Unknown Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 12 16.33 5.71 0.00 chr4ptel1M 404200 404234 (595766) (CTGCCTC)n#Simple_repeat 1 37 (0) m_b173s252i10 6736 chr4ptel1M 404200 CTGCCTTCT-CCATCT-CTCCCTGCCTCCTGCCTCCT 404234 i - vi - ii (CTGCCTC)n#Si 1 CTGCCTCCTGCCTCCTGCCTCCTGCCTCCTGCCTCCT 37 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 239 36.49 1.37 8.03 chr4ptel1M 404396 404541 (595459) MIR3#SINE/MIR 51 187 (21) m_b173s601i51 6737 chr4ptel1M 404396 GAGTTCAAAACCTGCCTCCGTCACTTATCAGCTGGATGATTTCAGGGATT 404445 i v iv i v i i v ii? vi ii ii v -- MIR3#SINE/MIR 51 GGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCA-- 98 chr4ptel1M 404446 CTGATTGGTTGGAGATTGGCCTCCTTCAGCTCCAACTCCGGGATCTGTAA 404495 ------i iiv--- vi ii vi ii ii i vvv MIR3#SINE/MIR 99 ------AGTCAC---TTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAA 139 chr4ptel1M 404496 AA-GA-GGGGCAGGAACAGATGGTTCCTAAAGTTCCATCTAGCCCAGA 404541 - - iv vi i ii i i v i i v MIR3#SINE/MIR 140 AATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGA 187 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 52.45 CpG sites = 33, Kimura (unadjusted) = 54.15 Transitions / transversions = 2.06 (33/16) Gap_init rate = 0.09 (13 / 145), avg. gap size = 1.00 (13 / 13) 13 14.73 3.33 0.00 chr4ptel1M 405072 405101 (594899) (GGA)n#Simple_repeat 1 31 (0) m_b173s252i11 6738 chr4ptel1M 405072 GGAGGA-GAGGAGAATGAGGATGAGAAGGAG 405101 - i v v i (GGA)n#Simple 1 GGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG 31 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 307 35.88 1.16 1.74 chr4ptel1M 406242 406414 (593586) C MamRTE1#LINE/RTE-BovB (1187) 2625 2454 m_b173s601i52 6739 chr4ptel1M 406242 CCTGCTCTCACTTCACTGGTGACTGGGAAAGCGTGAGAGCATTGC-CCAT 406290 - i i iv v v vi - vvi - i C MamRTE1#LINE/ 2625 CCTGCT-TCACTCCATTGGTGATGGGGAATGGGTCGGA-CAGGACGCCGT 2578 chr4ptel1M 406291 CGCCCAGAACTTGGGCAAGCGTGACATCGTGGAACTGCCGTACAATACTG 406340 iv ivvi vi iv iiv i iv i iiv v vi vi C MamRTE1#LINE/ 2577 CAACTCTGACGCGACCGGCCATACCATCATGGAGTAGCCTTAGGATCTTG 2528 chr4ptel1M 406341 ATAAACTTCTCAGGGCTACCAAATTTTGACAGGATTTTCCATAAGCCCTT 406390 i i vi i vvvi v vi v -i vv C MamRTE1#LINE/ 2527 GTGAACTTCTCAGGGCAGCCAAACTTGCTTAGTAGCTGCCA-GAGCCCAG 2479 chr4ptel1M 406391 GT-GACTCAGAGCACCAAAGGCCTT 406414 -v v vi ii v i C MamRTE1#LINE/ 2478 GTCTACTGATGGCGTCAAATGCTTT 2454 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 44.38 CpG sites = 31, Kimura (unadjusted) = 49.84 Transitions / transversions = 1.03 (31/30) Gap_init rate = 0.03 (5 / 172), avg. gap size = 1.00 (5 / 5) 345 35.51 1.87 0.00 chr4ptel1M 407540 407646 (592354) MIR3#SINE/MIR 97 205 (3) m_b174s601i0 6740 chr4ptel1M 407540 CGAACCAACTCCCATCTCCAGATTTCAGTTTTCTCATCTATAAAATGAGC 407589 i ii vi v v ii iii i i v MIR3#SINE/MIR 97 CAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGG 146 chr4ptel1M 407590 AAATTGAATAGGAGAGTCTCT--GGTTCATTCCAAATCTAATATTCAGCG 407637 iii i ivi vii -- i v iv i i vii MIR3#SINE/MIR 147 GGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATG 196 chr4ptel1M 407638 ATTTCACAA 407646 ii ii MIR3#SINE/MIR 197 ATTCTATGA 205 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 53.80 CpG sites = 29, Kimura (unadjusted) = 53.80 Transitions / transversions = 3.22 (29/9) Gap_init rate = 0.01 (1 / 106), avg. gap size = 2.00 (2 / 1) 216 36.05 4.27 5.17 chr4ptel1M 407699 407815 (592185) C L2a_3end#LINE/L2 (0) 517 402 m_b174s601i1 6741 chr4ptel1M 407699 ATTTAATTTTTTAAAAAGCATTTATCAAGCACTTAATATGTGCAGAATTC 407748 i v iv i v ii ii i i v viiiiv C L2a_3end#LINE 517 ATTCATTCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCAC 468 chr4ptel1M 407749 CATCCTGGACACTGGAAAGACCCAACATTTAAACAAAAAAGAT-----TC 407793 ii i i i i ii v -- i -v i v i----- C L2a_3end#LINE 467 TGTTCTAGGCGCTGGGGATA--CAGCA-GTGAACAAAACAGACAAAAGTC 421 chr4ptel1M 407794 TTTGCTCTTTTCATAGCGTCTA 407815 ii i --- i v ii C L2a_3end#LINE 420 CCTGCCC---TCATGGAGCTTA 402 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 50.56 CpG sites = 30, Kimura (unadjusted) = 54.76 Transitions / transversions = 3.00 (30/10) Gap_init rate = 0.06 (7 / 116), avg. gap size = 1.57 (11 / 7) 183 35.09 0.00 0.00 chr4ptel1M 408717 408773 (591227) C MIRc#SINE/MIR (210) 58 2 m_b174s601i2 6742 chr4ptel1M 408717 AACCTGGGTCCTCCTGAGCTCGAGTGCAACGTGCTATCCACTGTGCAATA 408766 ii i vii i v ii iv v ii v i C MIRc#SINE/MIR 58 AACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACA 9 chr4ptel1M 408767 TCGCCCC 408773 ii i C MIRc#SINE/MIR 8 CTGCCTC 2 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 52.42 CpG sites = 15, Kimura (unadjusted) = 52.42 Transitions / transversions = 3.00 (15/5) Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0) 187 35.23 2.27 0.00 chr4ptel1M 408939 409026 (590974) C L2a_3end#LINE/L2 (6) 511 422 m_b174s601i3 6743 chr4ptel1M 408939 TCAGCCAATAAGCACTGATTAAACACCTCTTGGGTGCCAGGCACGGGACT 408988 vi i ii i v i i i vi iv v vv C L2a_3end#LINE 511 TCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCT 462 chr4ptel1M 408989 AAG-GTCAGAGATACAA-AGAGAGGGAAAAACCCAAACGT 409026 i - iii i i- v ivi v vv v C L2a_3end#LINE 461 AGGCGCTGGGGATACAGCAGTGAACAAAACAGACAAAAGT 422 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 47.19 CpG sites = 18, Kimura (unadjusted) = 49.44 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.02 (2 / 87), avg. gap size = 1.00 (2 / 2) 220 29.69 6.25 0.00 chr4ptel1M 408944 409007 (590993) C L2d2_3end#LINE/L2 (11) 544 477 m_b174s601i4 6743 chr4ptel1M 408944 CAATAAGCACTGATTAAACACCTCTTGGGTGCCAGGCACGGGACTAAG-- 408991 i ii i v i i i vi v v v vi i -- C L2d2_3end#LIN 544 CAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCG 495 chr4ptel1M 408992 --GTCAGAGATACAAAGA 409007 -- vi i C L2d2_3end#LIN 494 CTGTGGGGGATACAAAGA 477 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 36.63 CpG sites = 12, Kimura (unadjusted) = 39.29 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.03 (2 / 63), avg. gap size = 2.00 (4 / 2) 405 29.58 2.08 1.38 chr4ptel1M 410869 411012 (588988) MIR3#SINE/MIR 4 148 (60) m_b174s601i6 6744 chr4ptel1M 410869 GCAGAGAGGCTGCAGGGGAAAGAACAAGGTCTTTGGAGACCGAGGACCTG 410918 v - vi i i v v v- v v ii MIR3#SINE/MIR 4 GCAGAGTGGCTG-AGCAGAGAGAGCACGGACTG-GGAGTCAGGAGACCTG 51 chr4ptel1M 410919 GATTCAAATCCTGCCTCTGACA-TGGCCTTCTGTATGATCTCAGAAAAAC 410967 i v i i v v - ii i?v i i ii iv ii MIR3#SINE/MIR 52 GGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGT 101 chr4ptel1M 410968 TACTTAGCCTCTCTGGTACTCAGGGGC--CATCCCTAAAGAGAGGGG 411012 i vi vv vvv -- iv iv MIR3#SINE/MIR 102 CACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGG 148 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 37.43 CpG sites = 22, Kimura (unadjusted) = 38.59 Transitions / transversions = 1.10 (22/20) Gap_init rate = 0.03 (4 / 143), avg. gap size = 1.25 (5 / 4) 465 25.62 1.64 0.81 chr4ptel1M 410869 410990 (589010) MIRb#SINE/MIR 8 130 (138) m_b174s601i5 6744 chr4ptel1M 410869 GCAGAGAGGCTGCAGGGGAAAGAACAAGGTCTTTGGAGACCGA-GGACCT 410917 v v - v i v v v v -i MIRb#SINE/MIR 8 GCAGCGTGG-TGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCT 56 chr4ptel1M 410918 GGATTCAAATCCTGCCTCTGACATGGCCT-TCTGTATGATCTCAGAAAAA 410966 i i i v v ivvv -v i i ii iv i MIRb#SINE/MIR 57 GGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAG 106 chr4ptel1M 410967 CTACTTAGCCTCTCTGGTACTCAG 410990 i i ivv MIRb#SINE/MIR 107 TTACTTAACCTCTCTGAGCCTCAG 130 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.25 CpG sites = 15, Kimura (unadjusted) = 31.59 Transitions / transversions = 0.94 (15/16) Gap_init rate = 0.02 (3 / 121), avg. gap size = 1.00 (3 / 3) 190 19.65 1.85 5.77 chr4ptel1M 411022 411075 (588925) MIRb#SINE/MIR 40 91 (177) m_b174s601i7 6745 chr4ptel1M 411022 TAGACTCAGAGA-ACTTGGGTTTGAATCCTGCCTCTGACATGCTTCCTCA 411070 i v v - i i i v v -- v - MIRb#SINE/MIR 40 TGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTCTGCCA--CTTACT-A 86 chr4ptel1M 411071 TCTGT 411075 v MIRb#SINE/MIR 87 GCTGT 91 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 18.11 CpG sites = 4, Kimura (unadjusted) = 22.75 Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.08 (4 / 53), avg. gap size = 1.00 (4 / 4) 261 22.81 0.00 20.31 chr4ptel1M 411062 411138 (588862) MIR3#SINE/MIR 124 187 (21) m_b174s601i8 6744 chr4ptel1M 411062 GCTTCCTCATCTGTAAAAATAAAGGTGGAAGTGAAGGAATTAGATTAAAT 411111 i ------------- i ii i i i MIR3#SINE/MIR 124 GTTTCCTCATCTGTAAAA-------------TGAGGGGGTTGGACTAGAT 160 chr4ptel1M 411112 GAAGTCCAAGTTTGCTTCCAGCTCCGA 411138 vv i v iv i MIR3#SINE/MIR 161 GATCTCTAAGGTCCCTTCCAGCTCTGA 187 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 26.84 CpG sites = 10, Kimura (unadjusted) = 26.84 Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.17 (13 / 76), avg. gap size = 1.00 (13 / 13) 51 22.05 8.40 2.79 chr4ptel1M 411148 411385 (588615) (TA)n#Simple_repeat 1 251 (0) m_b174s252i0 6746 chr4ptel1M 411148 TATAAAAATAT-TATAAGTTTAT-TAT-TGTTGATAT-TAT-TATAT-TA 411191 v v - vi v - - i vv - - - (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr4ptel1M 411192 T-TTTATATATTAATATA-ATATATA-ATGTATATTAATATACTGTGT-T 411237 - v vv - - i vv - i i - (TA)n#Simple_ 51 TATATATATATATATATATATATATATATATATATATATATA-TATATAT 99 chr4ptel1M 411238 ACAT-TATTTATAAAT-TATGATGTGTA-ATGTAAAAATTTGT-TATAAA 411283 i - v v - - i i - i v v v i - v (TA)n#Simple_ 100 ATATATATATATATATATAT-ATATATATATATATATATATATATATATA 148 chr4ptel1M 411284 TATA-ATATATGACATACAT-TTTATATAATTATGTA-ACATAT-TATAT 411329 - - i i - v vv i - i - (TA)n#Simple_ 149 TATATATATAT-ATATATATATATATATATATATATATATATATATATAT 197 chr4ptel1M 411330 ATACTATAT-TCTATA-ATATAAAAATATGCTGTGATATTTCACATATAC 411377 - - v - v v -v i - v - i i (TA)n#Simple_ 198 ATA-TATATATATATATATATATATATAT-ATAT-ATATAT-ATATATAT 243 chr4ptel1M 411378 ATATACAT 411385 i (TA)n#Simple_ 244 ATATATAT 251 Matrix = Unknown Transitions / transversions = 0.72 (18/25) Gap_init rate = 0.11 (27 / 237), avg. gap size = 1.00 (27 / 27) 455 24.82 3.29 1.95 chr4ptel1M 412296 412447 (587553) C MIRc#SINE/MIR (110) 158 5 m_b174s601i9 6747 chr4ptel1M 412296 TGTTATCATCCCCCGTTTTACAGCTGAGGAAACTGAGG--CAGACGGGGC 412343 i i -i v -- - i i C MIRc#SINE/MIR 158 TATTATTATCCCC-ATTTTACAGATGAGGAAACTGAGGCTCAGA-GAGGT 111 chr4ptel1M 412344 CACAGTGCCTTGCCCCAGA-CAAGCAGCCAGTAAGGGGCTGGGCCTGGAT 412392 i - v v i- vi i v v i v i C MIRc#SINE/MIR 110 TA-AGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGAC 62 chr4ptel1M 412393 GTG-CCCTTGGGCTGCCCGACCCC-GGCTCAGCACTCTGTCCACTGCTCC 412440 vi -v iv v v i i -i ii ii v v C MIRc#SINE/MIR 61 TCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACC 12 chr4ptel1M 412441 ATCTTGC 412447 ivi C MIRc#SINE/MIR 11 ACACTGC 5 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.84 CpG sites = 22, Kimura (unadjusted) = 30.83 Transitions / transversions = 1.47 (22/15) Gap_init rate = 0.05 (7 / 151), avg. gap size = 1.14 (8 / 7) 23 0.00 0.00 0.00 chr4ptel1M 412784 412808 (587192) (A)n#Simple_repeat 1 25 (0) m_b174s252i1 6748 chr4ptel1M 412784 AAAAAAAAAAAAAAAAAAAAAAAAA 412808 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAA 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 48 0.00 0.00 0.00 chr4ptel1M 412905 412945 (587055) (TG)n#Simple_repeat 1 41 (0) c_b174s251i0 6749 chr4ptel1M 412905 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 412945 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 41 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 447 24.39 1.63 0.00 chr4ptel1M 413954 414076 (585924) C MER63D#DNA/hAT-Tip100 (597) 464 340 m_b174s502i0 6750 chr4ptel1M 413954 CAGTTTTAAGTT-ATTCTGCATTACTG-CAATTATTCAATCAATTTCTTA 414001 v - v i i- v vi v v C MER63D#DNA/hA 464 CACTTTTAAGTTTAATCTGCATTATTAACATTTTCTCCATCACTTTCTTA 415 chr4ptel1M 414002 AGCCTAAAATATTAACCAAATGATAAATTAAGCTCTGATTTGTAAAGTTT 414051 i i vv i v ii i i iv C MER63D#DNA/hA 414 AGTCTAGACAATCAACAAAACAATAAATCAAGCCCTGATTTGTAGCGTTT 365 chr4ptel1M 414052 ACTGATGTCCAAAGGATAAATGCTC 414076 i i v ivi vi i C MER63D#DNA/hA 364 GCCGATTTCCGTGGTGTAAATACTC 340 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 27.70 CpG sites = 17, Kimura (unadjusted) = 30.01 Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.02 (2 / 122), avg. gap size = 1.00 (2 / 2) 603 19.61 14.38 0.00 chr4ptel1M 414148 414300 (585700) C MIRc#SINE/MIR (0) 268 94 m_b174s601i10 6751 chr4ptel1M 414148 AATAGAAATAACTGC---CATTTGTATGGCTCTTTAAAGTTTGCAGAGAG 414194 iv ?v --- i v v i i v C MIRc#SINE/MIR 268 AATAATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCG 219 chr4ptel1M 414195 TTTT-GCAAGTATTATCTCATTTGATCACCACAACAACTTTGGGAAGGAG 414243 i -i vii vi ii v i v C MIRc#SINE/MIR 218 CTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAG 169 chr4ptel1M 414244 G------AGCTATTATTACCCCCATTTTACAGAGGC--------AGGC-- 414277 ------ v i v v-------- -- C MIRc#SINE/MIR 168 GCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC 119 chr4ptel1M 414278 --AGTAGTTAAGTGATTTGCTCAGG 414300 -- vi i i i C MIRc#SINE/MIR 118 AGAGAGGTTAAGTGACTTGCCCAAG 94 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 23.19 CpG sites = 17, Kimura (unadjusted) = 23.19 Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.04 (6 / 152), avg. gap size = 3.67 (22 / 6) 21 0.00 0.00 0.00 chr4ptel1M 416129 416151 (583849) (A)n#Simple_repeat 1 23 (0) m_b174s252i2 6752 chr4ptel1M 416129 AAAAAAAAAAAAAAAAAAAAAAA 416151 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAA 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 281 30.60 2.00 15.04 chr4ptel1M 416196 416345 (583655) C L2d2_3end#LINE/L2 (1) 554 422 m_b174s601i11 6753 chr4ptel1M 416196 CAAATCAAGTCAAAAAGCATTTACGAAGTGCCTACTGTAAGCTGGGCACT 416245 i v ii ivi i iv vi C L2d2_3end#LIN 554 CAAATCAAATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACT 505 chr4ptel1M 416246 GACTGCTACAAACT---GGAAATACAAAGAAAAGCAAAAAAAAAAAAAAA 416292 -- vivi --- ii ------------------ i C L2d2_3end#LIN 504 G--TGCTAGGCGCTGTGGGGGATACAAAG------------------AAG 475 chr4ptel1M 416293 AAAAAAAAAAAAGCCTTGTCCTCAAGTGGCTCTTAGTCTAATAGGGCAGA 416342 v v i v viiv i i vi ivi i i v v C L2d2_3end#LIN 474 TATAAGACATGGTCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGGAGA 425 chr4ptel1M 416343 TAA 416345 i C L2d2_3end#LIN 424 CAA 422 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 37.08 CpG sites = 24, Kimura (unadjusted) = 39.70 Transitions / transversions = 1.60 (24/15) Gap_init rate = 0.14 (21 / 149), avg. gap size = 1.10 (23 / 21) 200 32.69 0.00 0.00 chr4ptel1M 417167 417218 (582782) C L2a_3end#LINE/L2 (77) 440 389 m_b174s601i12 6753 chr4ptel1M 417167 GAACAGAAGAAAGTGGAGTCTTTGCCTTCGAGGAGTTTATATTCTAACAG 417216 i v i vvii ii i iv i i iii C L2a_3end#LINE 440 GAACAAAACAGACAAAAGTCCCTGCCCTCATGGAGCTTACATTCTAGTGG 391 chr4ptel1M 417217 GG 417218 C L2a_3end#LINE 390 GG 389 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 47.19 CpG sites = 13, Kimura (unadjusted) = 47.19 Transitions / transversions = 3.25 (13/4) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 417 24.55 0.73 7.81 chr4ptel1M 418221 418357 (581643) MIRb#SINE/MIR 2 129 (139) m_b174s601i13 6754 chr4ptel1M 418221 AGAGGGGCAGCTGGATGGCACAGTGGAAACAGCCCCTGCCCTGTAGTCAG 418270 ---i ii v v vv ii v MIRb#SINE/MIR 2 AGAGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAG 48 chr4ptel1M 418271 GAGGACCCGAGTTCAAATCCAGCCTCAGACACTAAACACTTCCTAACTTT 418320 ivi i i i v v v - ------ v i v MIRb#SINE/MIR 49 ACAGACCTGGGTTCGAATCCCGGCTCTG-C------CACTTACTAGCTGT 91 chr4ptel1M 418321 GTGACCCGGTGCAAGTCACTTAACTCCAAT-AACCTCA 418357 iv v i ii vv - i MIRb#SINE/MIR 92 GTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCA 129 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 27.64 CpG sites = 16, Kimura (unadjusted) = 29.84 Transitions / transversions = 1.07 (16/15) Gap_init rate = 0.08 (11 / 136), avg. gap size = 1.00 (11 / 11) 27 23.95 1.27 2.56 chr4ptel1M 418665 418743 (581257) (GGA)n#Simple_repeat 1 78 (0) m_b174s252i3 6755 chr4ptel1M 418665 GGAGGAGGAGGATGAGGAGGAAGAAGAGAAGGAGCAGAAGGGGAAAGGGG 418714 v i i i v i i i i i (GGA)n#Simple 1 GGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGG 50 chr4ptel1M 418715 A-GAGAGAGTGTGAATGGGGAGGAGGAAGA 418743 - - - v i v i i (GGA)n#Simple 51 AGGAG-GAG-GAGGAGGAGGAGGAGGAGGA 78 Matrix = Unknown Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.04 (3 / 78), avg. gap size = 1.00 (3 / 3) 15 9.72 0.00 8.33 chr4ptel1M 419015 419053 (580947) (ATTTAAA)n#Simple_repeat 1 36 (0) m_b174s252i4 6756 chr4ptel1M 419015 ATTTTTAATTTAAAAGTATTTTAAATTTAAAATTTAAAA 419053 vv - -- v (ATTTAAA)n#Si 1 ATTTAAAATTT-AAA--ATTTAAAATTTAAAATTTAAAA 36 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.08 (3 / 38), avg. gap size = 1.00 (3 / 3) 54 1.99 0.00 0.00 chr4ptel1M 419206 419256 (580744) (AC)n#Simple_repeat 1 51 (0) c_b174s251i1 6757 chr4ptel1M 419206 ACACACACACACACACACACACACACACAAACACACACACACACACACAC 419255 v (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50 chr4ptel1M 419256 A 419256 (AC)n#Simple_ 51 A 51 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 365 22.89 3.61 0.00 chr4ptel1M 419421 419503 (580497) C MIR3#SINE/MIR (7) 201 116 m_b174s601i14 6758 chr4ptel1M 419421 AGAATCAAAGA-T-TTAAAGCTTGTCGGGACCCT-GAAACCATTTAGTTC 419467 v - - i i v vv i - i i i i C MIR3#SINE/MIR 201 AGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCC 152 chr4ptel1M 419468 AACCTATTCTTTTTACAAGTGGGAAAACTGAGGCCC 419503 ivi v ii i i C MIR3#SINE/MIR 151 AACCCCCTCATTTTACAGATGAGGAAACTGAGGCCC 116 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 28.25 CpG sites = 13, Kimura (unadjusted) = 28.25 Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.04 (3 / 82), avg. gap size = 1.00 (3 / 3) 190 22.73 4.55 0.00 chr4ptel1M 419935 419978 (580022) MIR#SINE/MIR 206 251 (11) m_b174s601i15 6754 chr4ptel1M 419935 AGCGCTCAG--CAGTGTCTGGCACAGAATAAGAACTCTAGAAACAT 419978 i -- i v i vi v v ii MIR#SINE/MIR 206 AGCGCTTAGAACAGTGCCTGGCACATAGTAAGCGCTCAATAAATGT 251 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 24.50 CpG sites = 6, Kimura (unadjusted) = 27.62 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.02 (1 / 43), avg. gap size = 2.00 (2 / 1) 203 35.07 4.31 1.68 chr4ptel1M 420305 420420 (579580) C MIRc#SINE/MIR (141) 127 9 m_b174s601i16 6759 chr4ptel1M 420305 CCAAGACCCAGAAAG-TCAAGCCCTTTTCCCAGACTGCCTTAGCTGG--A 420351 ii i i i - i ivvi v iiv vv vi i -- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAA 78 chr4ptel1M 420352 GTGTCAGAAGCCAGA--TTGAACCTTAGGGCTTCCTAAGGCTGAGTGCAG 420399 v - i i-- i i- v i vv ii v C MIRc#SINE/MIR 77 GTGGCAGA-GCCGGGACTCGAACCC-AGGTCTTCCTGACTCCAAGTCCAG 30 chr4ptel1M 420400 CAGCCTTTCCCCCGAAATACA 420420 iivi v i v vi C MIRc#SINE/MIR 29 TGCTCTTTCCACTGCACCACA 9 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 45.97 CpG sites = 24, Kimura (unadjusted) = 49.45 Transitions / transversions = 1.50 (24/16) Gap_init rate = 0.04 (5 / 115), avg. gap size = 1.40 (7 / 5) 230 27.32 8.91 5.77 chr4ptel1M 421051 421151 (578849) L2c_3end#LINE/L2 370 473 (5) m_b174s601i17 6760 chr4ptel1M 421051 CACTACAGAATGCAAGCCCCTTAAGGGTGAGGGC---ACTTTAGTC---- 421093 -- v ii i i iii i ---iii v ---- L2c_3end#LINE 370 CACTA--GACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCT 417 chr4ptel1M 421094 -TATCTCCCCCACACCTAGCTCCACACTTGTGGCAGCT-AAGAAATATTT 421141 - i v vi i i --- - v i vv - v i L2c_3end#LINE 418 TTGTATCCCCAGCGCCTGGC---ACA-TAGTAGGCGCTCAATAAATGTTT 463 chr4ptel1M 421142 GTTGAATTAA 421151 v L2c_3end#LINE 464 GTTGAATGAA 473 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 33.68 CpG sites = 17, Kimura (unadjusted) = 35.38 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.10 (10 / 100), avg. gap size = 1.50 (15 / 10) 305 25.00 1.56 0.00 chr4ptel1M 421536 421599 (578401) C L2b_3end#LINE/L2 (7) 459 395 m_b174s601i18 6761 chr4ptel1M 421536 CATTCAACAAGCATTTATTAAGCACTTGCTGTAAGCCAGGAACTGTAC-A 421584 ii i i i i i iv v? i - C L2b_3end#LINE 459 CATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTA 410 chr4ptel1M 421585 AGCCCCAGGGATATA 421599 i v ii i C L2b_3end#LINE 409 GGCGCTGGGGATACA 395 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.76 CpG sites = 13, Kimura (unadjusted) = 33.34 Transitions / transversions = 4.33 (13/3) Gap_init rate = 0.02 (1 / 63), avg. gap size = 1.00 (1 / 1) 216 23.95 3.16 7.69 chr4ptel1M 422099 422193 (577807) C L2d2_3end#LINE/L2 (51) 504 414 m_b174s601i19 6762 chr4ptel1M 422099 GTGCTAGTC-CTCTGGGCTTTAAATACAATCAAAAGGA-AAGACA-GAAC 422145 v - v ----ii -- i v - - iv C L2d2_3end#LIN 504 GTGCTAGGCGCTGTGGG----GGATACAA--AGAAGTATAAGACATGGTC 461 chr4ptel1M 422146 CTTCCCTTCAAGGAGCTGATATTCTAAAGGAGGTAAACAACACACAAA 422193 i v i v i v ivv i - i v i C L2d2_3end#LIN 460 CCTGCCCTCAAGGAGCTTACAATCTAGTTGGGG-AGACAAGACATAAA 414 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.04 CpG sites = 11, Kimura (unadjusted) = 29.04 Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.11 (10 / 94), avg. gap size = 1.00 (10 / 10) 181 29.25 7.23 1.14 chr4ptel1M 422124 422206 (577794) C L2a_3end#LINE/L2 (73) 444 357 m_b174s601i20 6762 chr4ptel1M 422124 CAATCAAAAGGAAAGACAGAA--CCTTCCCTTCAAGGAGCTGATATTCTA 422171 i v v ii v i -- i v i v v i C L2a_3end#LINE 444 CAGTGAACAAAACAGACAAAAGTCCCTGCCCTCATGGAGCTTACATTCTA 395 chr4ptel1M 422172 ----AAGGAGGTAAACAACACACAAAATGGATCAGAAAA 422206 ----ii ii i i v - ii v v C L2a_3end#LINE 394 GTGGGGGGAGACAGACAATAAAC-AAATAAATAAGTAAA 357 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 38.47 CpG sites = 15, Kimura (unadjusted) = 38.47 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.04 (3 / 82), avg. gap size = 2.33 (7 / 3) 18 15.51 0.00 0.00 chr4ptel1M 423016 423045 (576955) (G)n#Simple_repeat 1 30 (0) m_b174s252i5 6763 chr4ptel1M 423016 GGGGGGGGGGGGGGGGGGAGAGGGAGAGGG 423045 i i i i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 30 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 194 31.88 7.29 1.98 chr4ptel1M 423250 423345 (576655) C L2c_3end#LINE/L2 (5) 473 373 m_b174s601i21 6764 chr4ptel1M 423250 TTCAGTCAAC------TCATCTGGCACTTACTAAGTGGCCATTAATGGCA 423293 v ------ i ivi i i v v viviiv vi C L2c_3end#LINE 473 TTCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGG 424 chr4ptel1M 423294 AT-CAAATCTGAAACTGAAAATTTGTCTCTGCCCTGAAAGAGCTCACTTT 423342 - vv -- i i vviv i v i vv C L2c_3end#LINE 423 ATACAAAGATGAA--TAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGT 376 chr4ptel1M 423343 CTA 423345 C L2c_3end#LINE 375 CTA 373 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 36.66 CpG sites = 14, Kimura (unadjusted) = 41.97 Transitions / transversions = 0.88 (14/16) Gap_init rate = 0.04 (4 / 95), avg. gap size = 2.25 (9 / 4) 15 32.19 3.33 3.33 chr4ptel1M 423368 423457 (576543) (GTAT)n#Simple_repeat 1 90 (0) m_b174s252i6 6765 chr4ptel1M 423368 GTGTGTATGTATGTACGTACATAGCTGCACATGTA-G-ATGAGTGTGTGT 423415 i i ii vv iiii - - vi i (GTAT)n#Simpl 1 GTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGT 50 chr4ptel1M 423416 A-GTATACATGTGTGTCTATATGGACATATATGTATCATATGT 423457 - ii i v i - -i i -i (GTAT)n#Simpl 51 ATGTATGTATGTATGTATGTAT-G-TATGTATGTAT-GTATGT 90 Matrix = Unknown Transitions / transversions = 4.25 (17/4) Gap_init rate = 0.07 (6 / 89), avg. gap size = 1.00 (6 / 6) 290 18.18 1.19 14.86 chr4ptel1M 423495 423578 (576422) Charlie4#DNA/hAT-Charlie 3304 3377 (1) m_b174s502i1 6766 chr4ptel1M 423495 ATTCGGAGAAGGGGGTCCGTAAGCTTCACTC-ACTGTCAGACGGGTCTAT 423543 v - i i iv- i i v i Charlie4#DNA/ 3304 ATTCTGAGAAGGGG-TCCATAGGCTTCACCAGACTGCCAAAGGGGTCCAT 3352 chr4ptel1M 423544 GGAACAACAACAACCAAAAAAGAGTAAAAACCTCT 423578 -------- -- iv i i Charlie4#DNA/ 3353 GG--------CA--CAAAAAAGGTTAAGAACCCCT 3377 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 20.83 CpG sites = 9, Kimura (unadjusted) = 20.83 Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.14 (12 / 83), avg. gap size = 1.00 (12 / 12) 19 8.35 0.00 0.00 chr4ptel1M 423699 423724 (576276) (A)n#Simple_repeat 1 26 (0) m_b174s252i7 6767 chr4ptel1M 423699 AAAAAAAAAAAAAAAAAAAAGGAAAA 423724 ii (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAA 26 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 17 9.64 2.63 5.41 chr4ptel1M 424200 424237 (575763) (GAG)n#Simple_repeat 1 37 (0) m_b174s252i8 6768 chr4ptel1M 424200 GAGGAAGAGAGAAGAGGAGGAGGAGGGAGAAGG-GGAGG 424237 i - i - i - (GAG)n#Simple 1 GAGGAGGAG-GAGGAGGAGGAGGA-GGAGGAGGAGGAGG 37 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.08 (3 / 37), avg. gap size = 1.00 (3 / 3) 13 28.03 0.00 0.00 chr4ptel1M 424202 424242 (575758) (GGGAGG)n#Simple_repeat 1 41 (0) m_b174s252i9 6768 chr4ptel1M 424202 GGAAGAGAGAAGAGGAGGAGGAGGGAGAAGGGGAGGGGTAG 424242 i i i i i i i i v (GGGAGG)n#Sim 1 GGGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGGAG 41 Matrix = Unknown Transitions / transversions = 8.00 (8/1) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 371 30.99 7.18 3.74 chr4ptel1M 424496 424676 (575324) C L3#LINE/CR1 (13) 4086 3900 m_b174s601i22 6769 chr4ptel1M 424496 AATGTCAATTAGGTGGAAAGG-CCTCAAAAGTTACCT-GT---ATC---C 424537 v i-- v i - i i i i i - --- i --- C L3#LINE/CR1 4086 AATCTCAG--AGTTGGAAGGGACCTTAGAGGTCATCTAGTCCAACCTCCC 4039 chr4ptel1M 424538 ACCCAA-ACCAAACTCTCCTCTAAAGTATCCCTGATG-GTAGTCAGCCAG 424585 i -i vii v i i v ii ii- i v C L3#LINE/CR1 4038 ATCCAATGCAGGAATCCCTTCTACAACATCCCTGACAAGTGGTCATCCAG 3989 chr4ptel1M 424586 CCTCTCTCTCTAGAAAAAGCTCTGATGATAGGGAGCCCCTTATGCCCAGA 424635 vii ----i v v iii ii i vi ivi ?v C L3#LINE/CR1 3988 CCTCTGCTT----GAACACCTCCAGTGACGGGGAGCTCACTACCTCNCGA 3943 chr4ptel1M 424636 G--AGTTCAATGCCA-TGATGGATAGATGTAATTATTAGCAAGT 424676 -- ii - v - vv i v v i i v C L3#LINE/CR1 3942 GGCAGCCC-ATTCCATTTTTGGACAGCTCTGATTGTTAGAAAGT 3900 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 41.36 CpG sites = 36, Kimura (unadjusted) = 42.56 Transitions / transversions = 2.00 (36/18) Gap_init rate = 0.08 (15 / 180), avg. gap size = 1.33 (20 / 15) 214 20.00 2.22 0.00 chr4ptel1M 424918 424962 (575038) C L3b_3end#LINE/CR1 (4) 1202 1157 m_b174s601i23 6770 chr4ptel1M 424918 AAACCAGAGAATTT-GGAGTTAGAATGGACTTCAGAGGTCAACTGG 424962 v i -i i i v i v i C L3b_3end#LINE 1202 AAACCATAGAATCTCAGAATTGGAAAGGACCTCAGAGGTCATCTAG 1157 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 23.85 CpG sites = 6, Kimura (unadjusted) = 23.85 Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 786 29.58 3.69 1.61 chr4ptel1M 424990 425233 (574767) MIRc#SINE/MIR 2 250 (18) m_b174s601i24 6771 chr4ptel1M 424990 GAAGCAGTTTAGGTGGCACAGTAATTAGAGTGCTGGGTCTGGAGTCAAGA 425039 i ---- ii iivv ii iii i MIRc#SINE/MIR 2 GAGGCAGT----GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGA 47 chr4ptel1M 425040 AAACCTGAATTCAAATTCAGCCTCAGATACTTCCTAGCTGTGTGCTTCAG 425089 i ii i i i v v v vi v viiiv MIRc#SINE/MIR 48 AGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTG 97 chr4ptel1M 425090 AGCAAGTCACTGCACCTCTACCTGCCTTGTTTTCCTCGCCTGTAAAAT-- 425137 i vv vivv iiv ii -- MIRc#SINE/MIR 98 GGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGG 147 chr4ptel1M 425138 -GACAATCCTACTAGCATTTCC-A----AAAGGGTTGTTGCAAGGATCAA 425181 - i vv iv vi v - ---- v ii MIRc#SINE/MIR 148 GGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAA 197 chr4ptel1M 425182 ATGGGACAATAATTGT-AAAACTCTTTGTCCACATTAACATGTTAGATTG 425230 i i ivv - i v vv vv vi i v ivi MIRc#SINE/MIR 198 ATGAGATAATGTATGTGAAAGCGCTTTGTAAACTGTAAAGTGCTATACAA 247 chr4ptel1M 425231 ATG 425233 MIRc#SINE/MIR 248 ATG 250 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 37.82 CpG sites = 40, Kimura (unadjusted) = 38.51 Transitions / transversions = 1.29 (40/31) Gap_init rate = 0.04 (9 / 243), avg. gap size = 1.44 (13 / 9) 53 0.00 0.00 0.00 chr4ptel1M 427219 427263 (572737) (AC)n#Simple_repeat 1 45 (0) c_b174s251i2 6772 chr4ptel1M 427219 ACACACACACACACACACACACACACACACACACACACACACACA 427263 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACA 45 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 214 20.00 4.00 0.00 chr4ptel1M 427988 428037 (571963) L3#LINE/CR1 3723 3774 (325) m_b174s601i25 6773 chr4ptel1M 427988 GGATGTTTAGCCAGCAGGAGAGAAACCTC--AGGAGTCATTCTAGCAGTC 428035 v v i iv i-- v vv v L3#LINE/CR1 3723 GGATGTTTAGCCTGGAGAAGAGAAGACTTAGAGGAGACATGATAGCTGTC 3772 chr4ptel1M 428036 TT 428037 L3#LINE/CR1 3773 TT 3774 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 23.27 CpG sites = 3, Kimura (unadjusted) = 23.27 Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.02 (1 / 49), avg. gap size = 2.00 (2 / 1) 223 30.91 0.00 0.00 chr4ptel1M 428039 428093 (571907) L2d_3end#LINE/L2 451 505 (11) m_b174s601i26 6774 chr4ptel1M 428039 CAGCCCTTAGCACAGTGCTAGGCACACAATAAGGGCCTCCTAAGGGCTTG 428088 v i ii i i i v iivv ivi L2d_3end#LINE 451 CAGCGCCTAGCACAGTGCTGAGCACATAGTAGGCGCTCAATAAATACTTG 500 chr4ptel1M 428089 CTAAT 428093 i i L2d_3end#LINE 501 TTGAT 505 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 42.48 CpG sites = 12, Kimura (unadjusted) = 42.48 Transitions / transversions = 2.40 (12/5) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 210 18.18 9.09 0.00 chr4ptel1M 428098 428141 (571859) L3#LINE/CR1 3773 3820 (279) m_b174s601i27 6773 chr4ptel1M 428098 TCCAAGCATTTGAAGGGCTGTCCTATGGA----GGATTAGTTTTGTTC 428141 i ii v i ---- vi i L3#LINE/CR1 3773 TTCAAATATTTGAAGGGCTGTCATGTGGAAGAGGGATTAGACTTATTC 3820 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 21.53 CpG sites = 6, Kimura (unadjusted) = 21.53 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.02 (1 / 43), avg. gap size = 4.00 (4 / 1) 256 28.55 6.48 2.68 chr4ptel1M 428184 428291 (571709) C MIRb#SINE/MIR (156) 112 1 m_b174s601i29 6775 chr4ptel1M 428184 AAGTGACTTGCCCACCATCACACAGCTGCTAAGTGTCTGAAATAGAAACT 428233 i vvi iv v v ivii i vii C MIRb#SINE/MIR 112 AAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTC 63 chr4ptel1M 428234 GAGCACAGTTCTTCCTGGCCCCAGGATGCCGACTGC-CGTGCCA--GCA- 428279 i v v vi i i iiii- -- - v v -- - C MIRb#SINE/MIR 62 GAACCCAGGTCTGTCTGACTCCAAAGC-CCG--TGCTCTTTCCACTGCAC 16 chr4ptel1M 428280 ---GCTGCCTCTCTG 428291 --- i C MIRb#SINE/MIR 15 CACGCTGCCCCTCTG 1 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 33.81 CpG sites = 18, Kimura (unadjusted) = 37.03 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.07 (7 / 107), avg. gap size = 1.43 (10 / 7) 310 28.00 0.00 0.00 chr4ptel1M 428184 428258 (571742) C MIRc#SINE/MIR (159) 109 35 m_b174s601i28 6775 chr4ptel1M 428184 AAGTGACTTGCCCACCATCACACAGCTGCTAAGTGTCTGAAATAGAAACT 428233 vvi iv v v ivii i vii C MIRc#SINE/MIR 109 AAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTC 60 chr4ptel1M 428234 GAGCACAGTTCTTCCTGGCCCCAGG 428258 i v v i i i C MIRc#SINE/MIR 59 GAACCCAGGTCTTCCTGACTCCAAG 35 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 31.52 CpG sites = 12, Kimura (unadjusted) = 35.85 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.00 (0 / 74), avg. gap size = 0.0 (0 / 0) 592 24.30 6.62 4.69 chr4ptel1M 428604 428875 (571125) Charlie1a#DNA/hAT-Charlie 1175 1451 (4) m_b174s502i2 6776 chr4ptel1M 428604 AGACTGACAAAAATCCGA--CAATGCCATTAT-----CTCAATTCGGTTT 428646 i vi vii -- i v ----- v i-- Charlie1a#DNA 1175 AGATTTGCAAAAATGTAAAACAATGCCACTCTTCTCACTAAATTT--TTT 1222 chr4ptel1M 428647 TGTTTTGTAAAGTTCAGTTATATT-CACACACACACA--AATTATGTCAA 428693 v i vi v - i v v i ii-- v i Charlie1a#DNA 1223 TGTTTTGGAAAATATAGTTATTTTTCATAAAAATATGTTATTTATGTTAA 1272 chr4ptel1M 428694 CATTTTACGGA---ATTATCATTTG-AAATGAACTAATTAACTTTTCAGT 428739 v v i i--- i v- i v iv i iv Charlie1a#DNA 1273 CATGTAATGGGTTTATTATTATTTTTAAATGAATTAATAAATATTTTAAA 1322 chr4ptel1M 428740 --TTTATCCATTTCAGTTTCGAAGGTGGTAAATGTCAA--GATATCTCAC 428785 -- v vi i i v vi i i -- vv v Charlie1a#DNA 1323 AATTTCTCAGTTTTAATTTCTAATATGGTAAATATCGATAGATATAACCC 1372 chr4ptel1M 428786 ACAGAAACAAAAGCTCTCGCGGAGTGGCGGGGGGAAGAGGGTAATTTTTA 428835 v i------ v vvvvv ----- Charlie1a#DNA 1373 ACATAAACAAAAGCTCTT------TGGGGTCCTCAA-----TAATTTTTA 1411 chr4ptel1M 428836 AAAGTGTAAAATGGTCCTTGGACCCAAAAGTTTGAGAACC 428875 i iv vi v Charlie1a#DNA 1412 AGAGTGTAAAGGGGTCCTGAGACCAAAAAGTTTGAGAACC 1451 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 29.06 CpG sites = 30, Kimura (unadjusted) = 29.60 Transitions / transversions = 0.91 (30/33) Gap_init rate = 0.08 (21 / 271), avg. gap size = 1.48 (31 / 21) 352 18.34 0.00 1.67 chr4ptel1M 429088 429148 (570852) C L2d2_3end#LINE/L2 (2) 553 494 m_b174s601i30 6777 chr4ptel1M 429088 AAATCAAGTCAAGGAACATTTTATTAAGTGCCTACTATGTGCCAAGCACT 429137 i vi i - i i i v i C L2d2_3end#LIN 553 AAATCAAATCAACAAATATTT-ATTGAGCGCCTACTGTGTGCAAGGCACT 505 chr4ptel1M 429138 GTGCTAAGCAC 429148 i i C L2d2_3end#LIN 504 GTGCTAGGCGC 494 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 17.69 CpG sites = 9, Kimura (unadjusted) = 22.00 Transitions / transversions = 4.50 (9/2) Gap_init rate = 0.02 (1 / 60), avg. gap size = 1.00 (1 / 1) 306 23.69 0.00 5.56 chr4ptel1M 429096 429171 (570829) C L2a_3end#LINE/L2 (10) 507 436 m_b174s601i31 6777 chr4ptel1M 429096 TCAAGGAACATTTTATTAAGTGCCTACTATGTGCCAAGCACTGTGCTAAG 429145 vi i - i i i v i C L2a_3end#LINE 507 TCAACAAATATTT-ATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGG 459 chr4ptel1M 429146 CACCAGAATCAATCAATCAGTTAACA 429171 i ii i---i vv v v C L2a_3end#LINE 458 CGCTGGG---GATACAGCAGTGAACA 436 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 25.25 CpG sites = 11, Kimura (unadjusted) = 29.18 Transitions / transversions = 1.83 (11/6) Gap_init rate = 0.05 (4 / 75), avg. gap size = 1.00 (4 / 4) 233 22.43 0.00 14.63 chr4ptel1M 429164 429257 (570743) C MIR#SINE/MIR (6) 256 175 m_b174s601i32 6778 chr4ptel1M 429164 AGTTAACATTTATTAAGCTCCTTCTATGGGCCAGGAATGGTGCTATGTAG 429213 i i v i v v v iv v --- C MIR#SINE/MIR 256 AGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTA---AG 210 chr4ptel1M 429214 TGCTAATTAATAAACACTTATTAAGCTCCACTGCATGCCCACAA 429257 i -- ----- iv - - i vv v i C MIR#SINE/MIR 209 CGCT--TT-----ACATGTATTAA-CT-CATTTAATCCTCACAA 175 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 24.48 CpG sites = 8, Kimura (unadjusted) = 26.06 Transitions / transversions = 0.80 (8/10) Gap_init rate = 0.13 (12 / 93), avg. gap size = 1.00 (12 / 12) 527 27.23 1.34 6.34 chr4ptel1M 429264 429412 (570588) MIRc#SINE/MIR 7 148 (120) m_b174s601i33 6779 chr4ptel1M 429264 AGTGCTGCTCAGGGGAGAGAGTGCTAGACCTGGAATCAGGAAGACTCTTT 429313 iv iv v i ii i i i ------ MIRc#SINE/MIR 7 AGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA------ 50 chr4ptel1M 429314 TTCCTGACTTCAAAT-CTGATTTCATATATTTTCTAGCTGTGGGATCCTA 429362 -- iv i i - i ii iiii-i i v v i i i MIRc#SINE/MIR 51 --CCTGGGTTCGAGTCCCGGCTCTGC-CACTTACTAGCTGTGTGACCTTG 97 chr4ptel1M 429363 GGTAAGTCACTTTACC-CTATTTGCCTCAGTTTCCTTATCAGTGAAATGA 429411 i v - v vv i v i i MIRc#SINE/MIR 98 GGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGG 147 chr4ptel1M 429412 G 429412 MIRc#SINE/MIR 148 G 148 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 33.14 CpG sites = 27, Kimura (unadjusted) = 35.48 Transitions / transversions = 2.45 (27/11) Gap_init rate = 0.07 (11 / 148), avg. gap size = 1.00 (11 / 11) 29 0.00 0.00 0.00 chr4ptel1M 430537 430561 (569439) (AC)n#Simple_repeat 1 25 (0) c_b174s251i3 6780 chr4ptel1M 430537 ACACACACACACACACACACACACA 430561 (AC)n#Simple_ 1 ACACACACACACACACACACACACA 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 267 27.40 2.67 2.67 chr4ptel1M 430974 431048 (568952) C L2d2_3end#LINE/L2 (4) 551 477 m_b174s601i34 6781 chr4ptel1M 430974 ATCAATAATCAAGAAGTATCTGTGAAGTACCTAGGGCATGCCAGGCACTG 431023 -- v i i i vi ii vv ii v C L2d2_3end#LIN 551 ATCAA--ATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTG 504 chr4ptel1M 431024 TGCTAAATGCCAAGAGG--TACAAAGA 431048 iii iiv i -- C L2d2_3end#LIN 503 TGCTAGGCGCTGTGGGGGATACAAAGA 477 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 31.19 CpG sites = 14, Kimura (unadjusted) = 35.83 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.04 (3 / 74), avg. gap size = 1.33 (4 / 3) 232 33.77 0.00 2.50 chr4ptel1M 430982 431063 (568937) C L2b_3end#LINE/L2 (10) 456 377 m_b174s601i35 6781 chr4ptel1M 430982 TCAAGAAGTATCTGTGAAGTACCTAGGGCATGCCAGGCACTGTGCTAAAT 431031 v i i iivi ii vv ii ? iii C L2b_3end#LINE 456 TCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGC 407 chr4ptel1M 431032 GCCAAGAGGTACAAAGAGCAAAAAAAGCAGAC 431063 i-i i i iv - ii v ii C L2b_3end#LINE 406 GCT-GGGGATACAGCG-GTGAACAAGACAGAC 377 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 45.11 CpG sites = 21, Kimura (unadjusted) = 50.89 Transitions / transversions = 3.50 (21/6) Gap_init rate = 0.02 (2 / 81), avg. gap size = 1.00 (2 / 2) 231 24.27 4.23 1.37 chr4ptel1M 431177 431247 (568753) HSAT5v1#Satellite 5208 5280 (618) m_b174s502i3 6782 chr4ptel1M 431177 ATGTGTGAATACAATGTGTGCGTG--TGTGGATACA-ATGTGTGCGTGTG 431223 i v i i --i i vi i i-ii i HSAT5v1#Satel 5208 ATGCGTGCATGCAATGTGTGTGTGCACGCGCGTGCGCGCGTGTGTGTGTG 5257 chr4ptel1M 431224 TGGATACAATGTGTGCGTGTGTGT 431247 ? ii -i i HSAT5v1#Satel 5258 TGNACGC-GTGTGTGCGCGTGTGT 5280 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 12.65 CpG sites = 15, Kimura (unadjusted) = 32.65 Transitions / transversions = 7.50 (15/2) Gap_init rate = 0.04 (3 / 70), avg. gap size = 1.33 (4 / 3) 16 27.94 0.00 2.08 chr4ptel1M 431735 431783 (568217) (AG)n#Simple_repeat 1 48 (0) m_b174s252i11 6783 chr4ptel1M 431735 AGAGCAGAAAAAGACACAGAGTGACACAGAGAGAAAAACAGAGACAGAG 431783 - i i v v v v v i i v v (AG)n#Simple_ 1 AGAG-AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 48 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.02 (1 / 48), avg. gap size = 1.00 (1 / 1) 304 28.23 3.59 10.90 chr4ptel1M 431789 431955 (568045) C L2b_3end#LINE/L2 (19) 447 292 m_b174s601i36 6784 chr4ptel1M 431789 ATTTTTCAGGGGTCTACCATGTGCCAGGCTT----CTAAGAGCTGGCAAT 431834 viiii v i ii ?i---- i v vi C L2b_3end#LINE 447 ATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGGGAT 398 chr4ptel1M 431835 ACAAGCAAAAACAGCAACAATAGCACACCGCAAGACAGTCT-TACCCTCA 431883 - iivi ----- v - v ?------ i i- i C L2b_3end#LINE 397 ACA-GCGGTGA-----ACAAGA-CAGACN------CGGTCCCTGCCCTCA 361 chr4ptel1M 431884 AGAAGCTTACAGTCTAATGGGGAGAAAGATAACACATAGAACGAGGTAA- 431932 v i i i ---i i i- iv ?v ii - C L2b_3end#LINE 360 CGGAGCTCACAGTCTAGTGGGG---GAGACAG-ACATGTAANCAGACAAT 315 chr4ptel1M 431933 AATGAAGGAGGGGGGCAAGGTAG 431955 ? i vvv i v i C L2b_3end#LINE 314 NATAACCCAGAGTGGCAGGGTAG 292 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 35.65 CpG sites = 28, Kimura (unadjusted) = 37.97 Transitions / transversions = 2.00 (28/14) Gap_init rate = 0.12 (20 / 166), avg. gap size = 1.15 (23 / 20) 360 22.44 6.80 9.03 chr4ptel1M 431789 431935 (568065) C L2a_3end#LINE/L2 (19) 498 355 m_b174s601i37 6784 chr4ptel1M 431789 ATTTTTCAGGGGTCTACCATGTGCCAGGC----TTCTAAGAGCTGGCAAT 431834 v iii v i i ---- i v vi C L2a_3end#LINE 498 ATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGCGCTGGGGAT 449 chr4ptel1M 431835 ACAAGCAA-AAACAGCAACAATAGCACACCGCAAGACAGTCT-TACCCTC 431882 - i-i i---- i - ------- v i- i C L2a_3end#LINE 448 ACA-GCAGTGAACAA----AACAG-ACA-------AAAGTCCCTGCCCTC 412 chr4ptel1M 431883 AAGAAGCTTACAGTCTAAT--GGGGAGAAAGATAAC--ACATAGAACGAG 431928 v i v i -- v i i-- v v vv i C L2a_3end#LINE 411 ATGGAGCTTACATTCTAGTGGGGGGAGACAGACAATAAACAAATAAATAA 362 chr4ptel1M 431929 GTAAAAT 431935 C L2a_3end#LINE 361 GTAAAAT 355 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 27.11 CpG sites = 18, Kimura (unadjusted) = 27.11 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.12 (18 / 146), avg. gap size = 1.28 (23 / 18) 385 24.60 15.87 0.00 chr4ptel1M 432297 432422 (567578) C L2b_3end#LINE/L2 (2) 464 319 m_b174s601i38 6785 chr4ptel1M 432297 TTAGTCAAGCAGCAAACTATTACTGAGCACCTACGATGTGCCAGGCAGTG 432346 i v vv i ivv i vi ?v C L2b_3end#LINE 464 TCATTCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTG 415 chr4ptel1M 432347 TGCTAAACATTAGGGATACA---------AAGAAAAACA-------TGTC 432380 ii ii i --------- v i ?------- i C L2b_3end#LINE 414 TGCTAGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCC 365 chr4ptel1M 432381 TTTAAGGAGCTCCCAGT---GTATGGGATAT-GACTTGTAAATAAA 432422 i i v v --- iv v i- v ?i i C L2b_3end#LINE 364 CTCACGGAGCTCACAGTCTAGTGGGGGAGACAGACATGTAANCAGA 319 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 28.97 CpG sites = 18, Kimura (unadjusted) = 31.34 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.03 (4 / 125), avg. gap size = 5.00 (20 / 4) 20 3.67 0.00 0.00 chr4ptel1M 432611 432638 (567362) (TTTGT)n#Simple_repeat 1 28 (0) m_b174s252i12 6786 chr4ptel1M 432611 TTTGTTTTTTTTTGTTTTGTTTTGTTTT 432638 v (TTTGT)n#Simp 1 TTTGTTTTGTTTTGTTTTGTTTTGTTTT 28 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 42 0.00 0.00 0.00 chr4ptel1M 433239 433274 (566726) (TA)n#Simple_repeat 1 36 (0) c_b174s251i4 6787 chr4ptel1M 433239 TATATATATATATATATATATATATATATATATATA 433274 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATA 36 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 748 27.63 6.78 4.50 chr4ptel1M 433655 434067 (565933) Charlie1b#DNA/hAT-Charlie 14 435 (88) m_b174s502i4 6788 chr4ptel1M 433655 AGTACAGTTCCCAGAGTCCTGCAAATCCCCAAGATCCTTTCTAGGTGT-- 433702 iii i vvi vi viii i i vi v -- Charlie1b#DNA 14 AGTGTGGTCCGGGGACCCCTGGGGGTCCCCGAGACCCTTTCAGGGGGTCC 63 chr4ptel1M 433703 AGGAGGCCAAAATTATTTGCCTATTAAAATACT---------CCTCCCCT 433743 iv i i v v v -- ---------ii v i Charlie1b#DNA 64 GCGAGGTCAAAACTATTTTCATAATAA--TACTAAGACGTTATTTGCCTT 111 chr4ptel1M 433744 TTCCAAGCACATATTTACAGGA------AGCCAGATTTTCTTCATATGCT 433787 i vv v vi iv v ------ iviii -- v v Charlie1b#DNA 112 TTTCACTCTCATTCTCTCACGAGTGTACAGTGGAGTTTTC--CAGAGGCT 159 chr4ptel1M 433788 TCAAGCAAAACAGCATAGCACAACAGACTAAAGGCAGAAGCAGATGGGAG 433837 v v -- viiivv v i i i v iv Charlie1b#DNA 160 ACATG--ACGTGTGATATCGCAACAGATTGAATGCAGAAGCAGATATGAG 207 chr4ptel1M 433838 AAGCTGGCCAGCCTTGTCCTTTTAAGTCAGTAATTAGAGAGATGTGTGCA 433887 ----v iv v i v i vv i -- v Charlie1b#DNA 208 AA----TCCAGCTGTCTTCTATTAAGCCAGACATTAAAGAGA--TTTGCA 251 chr4ptel1M 433888 AAAAAGATACAAATTGATACCCCTTTTCTCACTATTTTTTTTTTGTTTCA 433937 --- ii vii i v i -vv ii Charlie1b#DNA 252 AAA---ATGTAAAACAATGCCACTCTTCTCACTA-AATTTTTTTGTTTTG 297 chr4ptel1M 433938 GAA---CTAGTTCTTTTTC-T---AATGCTGCTATTTATGTTAATATGTG 433980 ---v v - --- i- i i i Charlie1b#DNA 298 GAAAATATAGTTATTTTTCATAAAAATA-TGTTATTTATGTTAACATGTA 346 chr4ptel1M 433981 GTGAGATTATTGGGTT-TTTTTTAATAAATTG--AGATAGTTTTAAAAGT 434027 i i v --i - v i i-- i v v v Charlie1b#DNA 347 ATGGGTTTATT--ATTATTTTTAAATGAATTAATAAATATTTTAAAAATT 394 chr4ptel1M 434028 GGTCA-TTTTAATTTCCAATACAGTAAACCTCCCCAGATAT 434067 vv - i i iv vvi Charlie1b#DNA 395 TCTCAGTTTTAATTTCTAATACGGTAAATATCGATAGATAT 435 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 33.12 CpG sites = 58, Kimura (unadjusted) = 35.06 Transitions / transversions = 1.14 (58/51) Gap_init rate = 0.07 (28 / 412), avg. gap size = 1.68 (47 / 28) 1233 20.81 4.46 3.59 chr4ptel1M 433709 434067 (565933) Charlie1#DNA/hAT-Charlie 2332 2693 (88) m_b174s502i5 6788 chr4ptel1M 433709 CCAAAATTATTTGC-----CTATTAAAATACTCCTCCCCTTTCCAAGCAC 433753 v i v----- i vi Charlie1#DNA/ 2332 CCACAATTATCTGAAAAGGCTATTAAAATACTCCTCCCTTTTCCAACTAC 2381 chr4ptel1M 433754 ATATTTACAGGAAGCCAGATTTTCTTCATATGCTTCAAGCAAAACAGCAT 433803 i iiiv i i i v i Charlie1#DNA/ 2382 ATATCTGTGTGAGGCCGGATTTTCTTCATATACTTCAACCAAAACAACAT 2431 chr4ptel1M 433804 AGCACAACAGACTAAAGGCAGAAGCAGATGGGAGAAGCTGGCCAGCCTTG 433853 v i i i v iv ----v iv v Charlie1#DNA/ 2432 ATCGCAACAGATTGAATGCAGAAGCAGATATGAGAA----TCCAGCTGTC 2477 chr4ptel1M 433854 TCCTTTTAAGTCAGTAATTAGAGAGATGTGTGCAAAAAAGATACAAATTG 433903 i v i vv i -- v --- ii vii Charlie1#DNA/ 2478 TTCTATTAAGCCAGACATTAAAGAGA--TTTGCAAAA---ATGTAAAACA 2522 chr4ptel1M 433904 ATACCCCTTTTCTCACTATTTTTTTTTTGTTTCAGAA---CTAGTTCTTT 433950 i v i -vv ii ---v v Charlie1#DNA/ 2523 ATGCCACTCTTCTCACTA-AATTTTTTTGTTTTGGAAAATATAGTTATTT 2571 chr4ptel1M 433951 TTC-T---AATGCTGCTATTTATGTTAATATGTGGTGAGATTATTGGGTT 433996 - --- i- i i ii i v --i Charlie1#DNA/ 2572 TTCATAAAAATA-TGTTATTTATGTTAACATGTAATGGGTTTATT--ATT 2618 chr4ptel1M 433997 -TTTTTTAATAAATTG--AGATAGTTTTAAAAGTGGTCA-TTTTAATTTC 434042 - v i i-- i v v v vv - Charlie1#DNA/ 2619 ATTTTTAAATGAATTAATAAATATTTTAAAAATTTCTCAGTTTTAATTTC 2668 chr4ptel1M 434043 CAATACAGTAAACCTCCCCAGATAT 434067 i i iv vvi Charlie1#DNA/ 2669 TAATACGGTAAATATCGATAGATAT 2693 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 23.56 CpG sites = 41, Kimura (unadjusted) = 24.71 Transitions / transversions = 1.32 (41/31) Gap_init rate = 0.06 (20 / 358), avg. gap size = 1.45 (29 / 20) 494 21.71 5.43 0.00 chr4ptel1M 434086 434214 (565786) MER63D#DNA/hAT-Tip100 330 465 (596) m_b174s502i6 6789 chr4ptel1M 434086 GCCA-GATGTGAGCTTTTATACCTCAGGAATCAGCAAA-GTTACAACACC 434133 - i v iv i v i i i - i vv v MER63D#DNA/hA 330 GCCATGGTGGGAGTATTTACACCACGGAAATCGGCAAACGCTACAAATCA 379 chr4ptel1M 434134 CGACTTTATGTATAGTTTTGT-GGTTGTCCAGACT--AAAAAGTAGTGGA 434180 v i v v v - i i -- i ii MER63D#DNA/hA 380 GGGCTTGATTTATTGTTTTGTTGATTGTCTAGACTTAAGAAAGTGATGGA 429 chr4ptel1M 434181 GACAATGTCAGTAA--CAGATTAAATTTAAAGGTGT 434214 v i i -- i i MER63D#DNA/hA 430 GAAAATGTTAATAATGCAGATTAAACTTAAAAGTGT 465 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 24.03 CpG sites = 17, Kimura (unadjusted) = 26.12 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.04 (5 / 128), avg. gap size = 1.40 (7 / 5) 300 19.48 14.29 0.00 chr4ptel1M 434277 434353 (565647) Charlie1#DNA/hAT-Charlie 2690 2777 (4) m_b174s502i7 6790 chr4ptel1M 434277 ATGTAACTCATCTAAATAAAAAGTCTTGGGTGTATTCAATAACTTTGAAG 434326 i i iv i iv v v vi i v Charlie1#DNA/ 2690 ATATAACCCACATAAACAAAAGCTCTTTGGGGTCCTCAATAATTTTTAAG 2739 chr4ptel1M 434327 AGT----------CTTGAGACC-AAAAGTTGGAGAACC 434353 ---------- i - v Charlie1#DNA/ 2740 AGTGTAAAGGGGTCCTGAGACCAAAAAGTTTGAGAACC 2777 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 22.76 CpG sites = 8, Kimura (unadjusted) = 22.76 Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.03 (2 / 76), avg. gap size = 5.50 (11 / 2) 20 4.35 0.00 0.00 chr4ptel1M 434461 434484 (565516) (T)n#Simple_repeat 1 24 (0) m_b174s252i14 6791 chr4ptel1M 434461 TTTTTTTTTTTCTTTTTTTTTTTT 434484 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTT 24 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 17 24.73 0.00 0.00 chr4ptel1M 435352 435392 (564608) (TTA)n#Simple_repeat 1 41 (0) m_b174s252i15 6792 chr4ptel1M 435352 TTATTATTGTTGCTACTGTTATTACTATCATTGTTATTATT 435392 i ii i i i i i (TTA)n#Simple 1 TTATTATTATTATTATTATTATTATTATTATTATTATTATT 41 Matrix = Unknown Transitions / transversions = 1.00 (8/0) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 23 23.69 0.00 0.00 chr4ptel1M 435393 435445 (564555) (GAG)n#Simple_repeat 1 53 (0) m_b174s252i16 6793 chr4ptel1M 435393 GAGGAAGAGGAGGAGAAGGAAAAGGAGGAAGAGAAAGAAGAGAAGAAGGA 435442 i i ii i i i i i i (GAG)n#Simple 1 GAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA 50 chr4ptel1M 435443 GGA 435445 (GAG)n#Simple 51 GGA 53 Matrix = Unknown Transitions / transversions = 1.00 (10/0) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 416 20.44 9.16 2.88 chr4ptel1M 435669 435799 (564201) C L2d_3end#LINE/L2 (4) 512 374 m_b174s601i39 6794 chr4ptel1M 435669 TCACTCAGCCAA-AAACATTTATTAAGC----ACTATGGTGCCCCAAGCA 435713 v ii - ii i ---- - i -- C L2d_3end#LINE 512 TCAATCAATCAACAAGTATTTATTGAGCGCCTACTATG-TGCTC--AGCA 466 chr4ptel1M 435714 CTGGGCTAAG---TGTGGGGATACAAAGAAAG-GCAAAAG---TAGTCCC 435756 v i --- - i ?i ?- i v --- i C L2d_3end#LINE 465 CTGTGCTAGGCGCTGTGGGGA-ACGANAAAANAGTATAAGACATGGTCCC 417 chr4ptel1M 435757 AGTCCTCCACAAGACTTCAATCTAATTGGGGAGACACAGCTAA 435799 v i v vi vi v i vii C L2d_3end#LINE 416 TGCCCTCAAGGAGCTTACAATCTAGTTGGGGAGACAAGACTAA 374 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 23.88 CpG sites = 17, Kimura (unadjusted) = 24.97 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.07 (9 / 130), avg. gap size = 1.78 (16 / 9) 441 24.11 5.36 0.00 chr4ptel1M 435681 435792 (564208) C L2d2_3end#LINE/L2 (15) 540 423 m_b174s601i40 6794 chr4ptel1M 435681 AAACATTTATTAAGCAC-TATGGTGCCCCAAGCACTGGGCTAAG---TGT 435726 i i i - iv iv v i v i --- C L2d2_3end#LIN 540 AAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGT 491 chr4ptel1M 435727 GGGG-ATACAAAGAAAGGCAAAA-GTAGTCCCAGTCCTCCACAAGACTTC 435774 - ivii i -i i v i v vi vi v C L2d2_3end#LIN 490 GGGGGATACAAAGAAGTATAAGACATGGTCCCTGCCCTCAAGGAGCTTAC 441 chr4ptel1M 435775 AATCTAATTGGGGAGACA 435792 i C L2d2_3end#LIN 440 AATCTAGTTGGGGAGACA 423 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 28.56 CpG sites = 17, Kimura (unadjusted) = 29.87 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.04 (4 / 111), avg. gap size = 1.50 (6 / 4) 359 28.87 0.00 1.03 chr4ptel1M 435970 436067 (563933) MIRc#SINE/MIR 28 124 (144) m_b174s601i41 6795 chr4ptel1M 435970 CACAGCACGTGGCATCCACAAGACCTGGGTTCAAGTCTGGGAACTGAAAC 436019 v v v vi viv i iv vv vv MIRc#SINE/MIR 28 CACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCAC 77 chr4ptel1M 436020 CTCCCAGTTGTATGACTGTTGGAGGAGCCATTTACCCTCTCTAAGCCT 436067 i v i i i i- ivi i i v i MIRc#SINE/MIR 78 TTACTAGCTGTGTGACC-TTGGGCAAGTCACTTAACCTCTCTGAGCCT 124 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 35.27 CpG sites = 14, Kimura (unadjusted) = 36.88 Transitions / transversions = 1.00 (14/14) Gap_init rate = 0.01 (1 / 97), avg. gap size = 1.00 (1 / 1) 188 18.18 4.55 0.00 chr4ptel1M 436272 436315 (563685) L3#LINE/CR1 3893 3938 (161) m_b174s601i42 6796 chr4ptel1M 436272 AGGAAGGACTTCCTCACCATAGGAGCTGTCCCAAA--GGAAAGGGC 436315 i i v v vi v -- v L3#LINE/CR1 3893 AGGAAGAACTTTCTAACAATCAGAGCTGTCCAAAAATGGAATGGGC 3938 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 20.83 CpG sites = 3, Kimura (unadjusted) = 20.83 Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.02 (1 / 43), avg. gap size = 2.00 (2 / 1) 433 18.90 6.14 2.54 chr4ptel1M 436482 436595 (563405) MER63D#DNA/hAT-Tip100 354 471 (590) m_b174s502i8 6797 chr4ptel1M 436482 CAGAAATAGGTAAATGTTACAA--CAGGACATGATTTAGTTTTCTTTTTT 436529 i v i i i -- i v --- v v MER63D#DNA/hA 354 CGGAAATCGGCAAACGCTACAAATCAGGGCTTGATTTA---TTGTTTTGT 400 chr4ptel1M 436530 T--TTTTCTAGACTTCCCAAA---ATAGAGAGGATATTCATAATGCAGAT 436574 -- v vvv --- i ii i v MER63D#DNA/hA 401 TGATTGTCTAGACTTAAGAAAGTGATGGAGAAAATGTTAATAATGCAGAT 450 chr4ptel1M 436575 TAAGCTTAAAAGTATGTCATG 436595 i i i MER63D#DNA/hA 451 TAAACTTAAAAGTGTGTCGTG 471 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 18.72 CpG sites = 12, Kimura (unadjusted) = 22.06 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.05 (6 / 113), avg. gap size = 1.67 (10 / 6) 244 15.56 2.22 0.00 chr4ptel1M 436599 436643 (563357) MER63C#DNA/hAT-Tip100 881 926 (4) m_b174s502i9 6798 chr4ptel1M 436599 ACTTTTTTCCCCA-AGAGCCAGCTGTTAAACACTTGCCAGAACCCC 436643 i - i i i i v v MER63C#DNA/hA 881 ATTTTTTTCCCCAGAGAGCCGGTTGTTAAACATTTACCAGCACACC 926 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 15.18 CpG sites = 5, Kimura (unadjusted) = 17.84 Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 192 33.19 2.63 6.85 chr4ptel1M 436689 436840 (563160) C MIRc#SINE/MIR (78) 190 45 m_b174s601i43 6799 chr4ptel1M 436689 TCCCAACAGCCATGTGGGACGGGC-GTGCAATATGTTCTCTACCCTCTCC 436737 v i v i iii - v i-i i v - --- i C MIRc#SINE/MIR 190 TCACAACAACCCTGTGAGGTAGGCAGGGCAG-GTATTAT-TA---TCCCC 146 chr4ptel1M 436738 GACTTCCAGATGAGAACAGGGAGGCTC--AGAGGTCAC-TGCTCTGCCAG 436784 ivi v i v vv -- i v- vii vi C MIRc#SINE/MIR 145 ATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCA 96 chr4ptel1M 436785 CAGTCCCCCAGCTCCAAGTCGGAGGGAGAATGGCAGACTACAAGTCCAGA 436834 vi v v --- vi v v iiv -i - i ii i C MIRc#SINE/MIR 95 AGGTCACACAGCT---AGTAAGTGGCAGAGCCG-GGACT-CGAACCCAGG 51 chr4ptel1M 436835 CTCTCC 436840 iii C MIRc#SINE/MIR 50 TCTTCC 45 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 44.02 CpG sites = 28, Kimura (unadjusted) = 45.34 Transitions / transversions = 1.47 (28/19) Gap_init rate = 0.09 (13 / 151), avg. gap size = 1.08 (14 / 13) 601 20.79 3.95 1.94 chr4ptel1M 437028 437179 (562821) C Charlie4#DNA/hAT-Charlie (14) 3364 3210 m_b174s502i10 6800 chr4ptel1M 437028 CCTCTTTGGGTTATGGACCCCTTCAGCATTCTGGTGGTGAGC----GGAA 437073 i i v ii ii v i-- ---- v C Charlie4#DNA/ 3364 CTTTTTTGTGCCATGGACCCCTTTGGCAGTCTGGTGA--AGCCTATGGAC 3317 chr4ptel1M 437074 CATTTCTTAAAATAATGTTTC-AAATG-ACAAAATAAAACGTCTAGGATT 437121 vi i i i- - i iiiv C Charlie4#DNA/ 3316 CCCTTCTCAGAATAATGTTTTTAAATGCATAAAATAAAATACATAGGATT 3267 chr4ptel1M 437122 ATAAAAGAAACCAGGTACATTGAAATATCTTGATCAAAATATTTTTGAAA 437171 i i iv i vv v - vi C Charlie4#DNA/ 3266 ACAAAGGAAACCAATTATATTGAAATATAGTTATCAAAATA-TTTAAAAA 3218 chr4ptel1M 437172 CAAGTTTG 437179 i C Charlie4#DNA/ 3217 CAAATTTG 3210 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 25.07 CpG sites = 21, Kimura (unadjusted) = 25.07 Transitions / transversions = 2.10 (21/10) Gap_init rate = 0.04 (6 / 151), avg. gap size = 1.50 (9 / 6) 438 23.64 7.30 4.26 chr4ptel1M 437935 438071 (561929) L2c_3end#LINE/L2 332 472 (6) m_b174s601i44 6801 chr4ptel1M 437935 CTTGTCTGTGCAAAGTTGTTTGT--GCGTGC---TCTCCCCCATTAGTAC 437979 v - i -- i --i ? i--- i i vvi L2c_3end#LINE 332 CTTGTAT-TGTAA--TTGTCTGTTTACNTGTCTGTCTCCTCCACTAGACT 378 chr4ptel1M 437980 ATGAGCCTCTCGAGGGCAGGGGCTGTCTTTTGGCTTTCAT-TTAGCA--- 438025 i ii i i i v i i--- - v i --- L2c_3end#LINE 379 GTGAGCTCCTTGAGGGCAGGGACCGTGTCTTA---TTCATCTTTGTATCC 425 chr4ptel1M 438026 -CAGTGCCCAGCACATAGTAGGTGCTTAATAAATGCATGCTGACTAA 438071 - i ii i i iv i v i L2c_3end#LINE 426 CCAGCGCCTGGCACATAGTAGGCGCTCAATAAATGTTTGTTGAATGA 472 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 26.87 CpG sites = 24, Kimura (unadjusted) = 30.35 Transitions / transversions = 3.43 (24/7) Gap_init rate = 0.08 (11 / 136), avg. gap size = 1.45 (16 / 11) 198 30.88 8.82 0.00 chr4ptel1M 438542 438609 (561391) C MIR1_Amn#SINE/MIR (148) 82 9 m_b174s601i45 6802 chr4ptel1M 438542 CCAGGGTCAGAGGTGAAACTTGAACCCAAATCTTCATGGCTCCAGT---- 438587 ? v v vi ii ? ? ii i vvi ii ---- C MIR1_Amn#SINE 82 CNAGTGGCAGAGCCGGGANTNGAACCCAGGTCTCCCGAGTCCCAGTCCAG 33 chr4ptel1M 438588 --CTCTGTTCTTCAGATGACACTG 438609 -- i i vii iv C MIR1_Amn#SINE 32 TGCTCTATCCACTAGACCACACTG 9 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 41.81 CpG sites = 14, Kimura (unadjusted) = 44.72 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.03 (2 / 67), avg. gap size = 3.00 (6 / 2) 220 25.93 3.70 0.00 chr4ptel1M 438544 438597 (561403) C MIRc#SINE/MIR (190) 78 23 m_b174s601i46 6802 chr4ptel1M 438544 AGGGTCAGAGGTGAAACTTGAACCCAAATCTTCATGGCTCC-AGTCTC-T 438591 v v vi ii i ii v i - iv- C MIRc#SINE/MIR 78 AGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGT 29 chr4ptel1M 438592 GTTCTT 438597 i C MIRc#SINE/MIR 28 GCTCTT 23 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 27.38 CpG sites = 9, Kimura (unadjusted) = 32.87 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.04 (2 / 53), avg. gap size = 1.00 (2 / 2) 798 23.63 5.63 4.72 chr4ptel1M 438837 439067 (560933) MIRc#SINE/MIR 35 267 (1) m_b174s601i47 6803 chr4ptel1M 438837 CCTGGAGTCAGCAAGACCTGAGTTTGAATTTTAGACCAGAAACATACCTA 438886 i v i i i iiii vi v vv v - MIRc#SINE/MIR 35 CTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTAC-TA 83 chr4ptel1M 438887 GCTGTATGAAGCTGGGCAAGTCACCTTACTTCT----GCCTCAGTTTCCT 438932 i vvi i v i ---- MIRc#SINE/MIR 84 GCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCT 133 chr4ptel1M 438933 CATTTGTAAAATGTATATCATAATG---GC---ACCTACCTCCCAGGATG 438976 i viv v i--- ---i v i v MIRc#SINE/MIR 134 CATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTT 183 chr4ptel1M 438977 GTTGGAAGGATCAGATAAGATAA--GATGT-AGAGTGCTTTGTCATCTGA 439023 vi i i --v - i i ------ MIRc#SINE/MIR 184 GTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTTTGT------A 227 chr4ptel1M 439024 AACCTTCAAATGTTACCTGTATAAATGCTGGATATTAGGATTAT 439067 iv v i i ---- i ivi i?i vv MIRc#SINE/MIR 228 AACTGTAAAGTGCTA----TACAAATGTAAGGNGTTATTATTAT 267 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 27.13 CpG sites = 31, Kimura (unadjusted) = 29.14 Transitions / transversions = 1.48 (31/21) Gap_init rate = 0.07 (16 / 230), avg. gap size = 1.50 (24 / 16) 215 33.52 8.02 0.57 chr4ptel1M 439176 439337 (560663) L3#LINE/CR1 3466 3639 (460) m_b174s601i48 6804 chr4ptel1M 439176 CCAACAGTCTAAGATGGCAGTCTGACAAGCTACTGGGATCTCAGGACTCA 439225 v i vi v i vi v v vi i viv L3#LINE/CR1 3466 CCAACAGTGTGATGTGGCTGCCAAAAAAGCTAATGCAATCTTAGGCTGCA 3515 chr4ptel1M 439226 TTAAGAAAAGTGAAG-GCTCGGTGCTAAAGAGGAGA---TCCCACC-TA- 439269 v i iv - ii i v? v ii vi --- i i- - L3#LINE/CR1 3516 TTAATAGAAGTATAGTGTCCAGANCAAGGGAGGTAATAGTCCCGCTGTAC 3565 chr4ptel1M 439270 -TTGC-CCAGCCCGGCC-CTGCTGAAGTGACCTCTGACA-TGCTGTGCTT 439315 -i - ii i v i - vv i - iiv vvv - v v vi L3#LINE/CR1 3566 TCTGCGCTGGTCAGACCACATCTGGAGT-ATTGCGTTCAGTTCTGGGCGC 3614 chr4ptel1M 439316 CATA---TAAGAGGGGCATTAAGAA 439337 i --- i i v L3#LINE/CR1 3615 CACATTTTAAGAGGGACATTGACAA 3639 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 44.78 CpG sites = 29, Kimura (unadjusted) = 45.94 Transitions / transversions = 1.16 (29/25) Gap_init rate = 0.06 (10 / 161), avg. gap size = 1.40 (14 / 10) 367 34.59 13.72 2.38 chr4ptel1M 439335 439713 (560287) L3#LINE/CR1 3676 4096 (3) m_b174s601i49 6804 chr4ptel1M 439335 GAAGGGGCTTCAAATCCCTGTCCTCTGAGGGTTAGTTGAAGGAATCACAG 439384 v vv - v v v ivii iiivi L3#LINE/CR1 3676 GAAGGGTCTGGAAA-CCATGTCATATGAGGAACGGTTGAAGGAACTGGGG 3724 chr4ptel1M 439385 GGGGGCAGGTTGAAGGGAGAGAATCTGTCTTGGGGG-GCCAGAGGGACTG 439433 iv vvi vi i i- --- v i i - v viivii L3#LINE/CR1 3725 ATGTTTAGCCTGGAGA-AGAGAA---GACTTAGAGGAGACATGATAGCTG 3770 chr4ptel1M 439434 TC-----ACATTTCTA----TGTCTTCTG----AGGG--------TGTTC 439462 ----- i vv ---- v v ---- -------- i L3#LINE/CR1 3771 TCTTCAAATATTTGAAGGGCTGTCATGTGGAAGAGGGATTAGACTTATTC 3820 chr4ptel1M 439463 TATTTGGCTCCAGA-------ACCCAGAGAAATGGACAGAAATAGCAAAG 439505 i v ------- ivi vv iii i vi ii L3#LINE/CR1 3821 TGTGTGGCTCCAGAGGGCAGAACTAGGACCAATGGGTGGAAGTTACAGGG 3870 chr4ptel1M 439506 AGGCCAATGTGGACTTGAGATCAGGAAAAGTCCTTC--ATGTTTAGGGCT 439553 vi v v i ii v v i i- i -- iiv i i L3#LINE/CR1 3871 AGGCAGATTTCGGCTCAATATAAGGAAGAA-CTTTCTAACAATCAGAGCT 3919 chr4ptel1M 439554 TTCCAAGCAGTG--AGGGATGGCCACCAGAAGCAGTAGGATCCCCCTGCC 439601 v i- i -- v iiv v v? i i ii v v --- L3#LINE/CR1 3920 GTCCAAA-AATGGAATGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGT--- 3965 chr4ptel1M 439602 CCCCAAAGGGCTTCAGACAAA--------------TT-TCA-GGAGACTG 439635 v iii vv ii i -------------- - - vii L3#LINE/CR1 3966 CACTGGAGGTGTTCAAGCAGAGGCTGGATGACCACTTGTCAGGGATGTTG 4015 chr4ptel1M 439636 GGGTGAGACTTTTTGC--CAGGTAAG-GGTTGGGATAGATGGTCACTGGG 439682 vi vii iv ii --ii i ii - iv ii v ii L3#LINE/CR1 4016 TAGAAGGGATTCCTGCATTGGATGGGAGGTTGGACTAGATGACCTCTAAG 4065 chr4ptel1M 439683 ATATCCTCCAACTGGGAAATTCTGGGATTCT 439713 i vi i vv i v L3#LINE/CR1 4066 GTCCCTTCCAACTCTGAGATTCTGTGATTCT 4096 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 48.22 CpG sites = 77, Kimura (unadjusted) = 48.83 Transitions / transversions = 1.51 (77/51) Gap_init rate = 0.06 (23 / 378), avg. gap size = 2.70 (62 / 23) 300 28.81 0.87 6.42 chr4ptel1M 440271 440385 (559615) L1ME2z_3end#LINE/L1 443 551 (640) m_b174s551i0 6805 chr4ptel1M 440271 TATTGAGAGCAATACTTT-TTCATGGTGGCGAAAAACTGGAAATGGGCCA 440319 i v v i-- - ii i v ii v L1ME2z_3end#L 443 TGTTCATAGCAG--CTTTATTCATAATAGCCAAAAACTGGAAACAGCCCA 490 chr4ptel1M 440320 AGTGCCCATTAGTGGGAGCATGGAGAAATGAGTTGTATTGCAGTATGTGC 440369 i i i iii v v ii ----- i ii i v L1ME2z_3end#L 491 GGTGTCCATCAACAGGAGAATGGATAAACAA-----ACTGTGGTATATTC 535 chr4ptel1M 440370 ATTTAATTGAGTATTA 440385 vi v i i L1ME2z_3end#L 536 ATACAATGGAATACTA 551 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 38.30 CpG sites = 22, Kimura (unadjusted) = 38.30 Transitions / transversions = 2.44 (22/9) Gap_init rate = 0.07 (8 / 114), avg. gap size = 1.00 (8 / 8) 37 6.53 0.00 0.00 chr4ptel1M 441077 441124 (558876) (CCCTAA)n#Simple_repeat 1 48 (0) c_b174s251i5 6806 chr4ptel1M 441077 CCCTAACCCTAATCCGAACCCTAACCCTAACCCTAACGCTAACCCTAA 441124 i v v (CCCTAA)n#Sim 1 CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA 48 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 208 36.07 0.00 0.00 chr4ptel1M 441303 441363 (558637) C MIRc#SINE/MIR (197) 71 11 m_b174s601i50 6807 chr4ptel1M 441303 GAGGCAAGATTTGGATCTGGATCTTGCAGACTGCAAGTCCAATACTTCCC 441352 v ii i i i i ii i v v v i i iiii C MIRc#SINE/MIR 71 GAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTT 22 chr4ptel1M 441353 ACACCGAACCA 441363 v i v C MIRc#SINE/MIR 21 CCACTGCACCA 11 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 46.97 CpG sites = 16, Kimura (unadjusted) = 54.25 Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 209 33.80 5.23 5.23 chr4ptel1M 441563 441715 (558285) L2b_3end#LINE/L2 280 432 (34) m_b174s601i51 6808 chr4ptel1M 441563 GTCCCTGCAGCGCTTTCTTCCTTCCCATCCCTGACTCTTCATTCTCTATT 441612 i iv ---- i v i v - i iv iv ? v i? L2b_3end#LINE 280 GCCCCCCCAG----TCCTACCCTGCCA-CTCTGGGTTATNATTGTCTGNT 324 chr4ptel1M 441613 TATGTG-CTGTCTTTTCCTATTTAATT-TAAGCCTCTTGAAGGCAGGAAC 441660 ii - - ii i i vi i - i ii v i i L2b_3end#LINE 325 TACATGTCTGTC-TCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGAC 373 chr4ptel1M 441661 TAT-CCTTCCTTCCGCTTGTATGTGTATCCCCAA-----AGCCCAATGTC 441704 ii?-i vi -- i iiivvv i----- v i? i L2b_3end#LINE 374 CGNGTCTGTCTT--GTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCC 421 chr4ptel1M 441705 TGATACAAAAT 441715 ii v i L2b_3end#LINE 422 TGGCACACAGT 432 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 49.10 CpG sites = 35, Kimura (unadjusted) = 50.82 Transitions / transversions = 2.50 (35/14) Gap_init rate = 0.08 (12 / 152), avg. gap size = 1.33 (16 / 12) 253 28.18 2.11 6.59 chr4ptel1M 441603 441697 (558303) L2c_3end#LINE/L2 343 433 (45) m_b174s601i52 6808 chr4ptel1M 441603 ATTCTCTATTTATGTG-CTGTCTTTTCCTATTTAATT-TAAGCCTCTTGA 441650 v i i? - ii - i vi i - i ii L2c_3end#LINE 343 ATTGTCTGTTTACNTGTCTGTCTCCTCC-ACTAGACTGTGAGCTCCTTGA 391 chr4ptel1M 441651 AGGCAGGAACTATCCTTCCTTCCGCTTGTATGTGTATCCCCAAAGCC 441697 i i ii vii iv vv ----- iv L2c_3end#LINE 392 GGGCAGGGACCGTGTCTTATTCATCTT-----TGTATCCCCAGCGCC 433 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 35.69 CpG sites = 18, Kimura (unadjusted) = 37.87 Transitions / transversions = 2.57 (18/7) Gap_init rate = 0.09 (8 / 94), avg. gap size = 1.00 (8 / 8) 240 31.79 7.14 1.69 chr4ptel1M 441604 441715 (558285) L2a_3end#LINE/L2 366 483 (34) m_b174s601i53 6808 chr4ptel1M 441604 TTCTCTATTTATGTG-CTGTCTTTTCCTATT-TAATTTAAGCCTCTTGAA 441651 v i i - - iii i i -v v ii v i L2a_3end#LINE 366 TTATTTGTTTAT-TGTCTGTCTCCCCCCACTAGAATGTAAGCTCCATGAG 414 chr4ptel1M 441652 GGCAGGAACTATCCTTCCTTCCGCTTGTATG-TGTATCCCCAAAGCC--- 441697 i v iv iiv ii i iii- - iv --- L2a_3end#LINE 415 GGCAGGGACTTTTGTCTGTTTTGTTCAC-TGCTGTATCCCCAGCGCCTAG 463 chr4ptel1M 441698 --CAATGTCTGATACAAAAT 441715 -- i i ii v i L2a_3end#LINE 464 AACAGTGCCTGGCACATAGT 483 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 44.90 CpG sites = 26, Kimura (unadjusted) = 44.90 Transitions / transversions = 2.89 (26/9) Gap_init rate = 0.06 (7 / 111), avg. gap size = 1.43 (10 / 7) 718 23.12 4.60 0.55 chr4ptel1M 441787 441960 (558040) MIRc#SINE/MIR 12 192 (76) m_b174s601i54 6809 chr4ptel1M 441787 GGCGCAGTGGATGCAGCATTGCAGCTGGGACCACGAAGATTTGGATTAAA 441836 i viv i v vi iii v ii i vi MIRc#SINE/MIR 12 GGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGA 61 chr4ptel1M 441837 ATCCAGCCCCAGACACTCCCTAGCTCTGGCATCCTGGGCAAGCCATTCAC 441886 i v v i v v iv v vv i i i i i v MIRc#SINE/MIR 62 GTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAA 111 chr4ptel1M 441887 CTTCTTCT--GCCTCAGTTTCCTCATCTGTAAAATGGGGACAATAACA-- 441932 i - -- i i -- MIRc#SINE/MIR 112 CCTC-TCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACC 160 chr4ptel1M 441933 -GCC---CCTACCTCCCTGGGTTGTTGTGAAG 441960 - --- v v i MIRc#SINE/MIR 161 TGCCCTGCCTACCTCACAGGGTTGTTGTGAGG 192 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 27.30 CpG sites = 23, Kimura (unadjusted) = 28.11 Transitions / transversions = 1.35 (23/17) Gap_init rate = 0.03 (5 / 173), avg. gap size = 1.80 (9 / 5) 279 26.32 3.95 0.00 chr4ptel1M 442491 442566 (557434) MIR#SINE/MIR 178 256 (6) m_b174s601i55 6809 chr4ptel1M 442491 TGAGG-CTACGTGA--TCATATGTCTAAAGCAGTTCACACAATCCCTGGC 442537 -i vi -- v ii v iv viv i v MIR#SINE/MIR 178 TGAGGATTAAATGAGTTAATACATGTAAAGCGCTTAGAACAGTGCCTGGC 227 chr4ptel1M 442538 ACACAGTAGGCACTCAATATATGCTTGCT 442566 i i i v i v MIR#SINE/MIR 228 ACATAGTAAGCGCTCAATAAATGTTAGCT 256 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.11 CpG sites = 11, Kimura (unadjusted) = 32.96 Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.03 (2 / 75), avg. gap size = 1.50 (3 / 2) 290 26.15 0.00 0.00 chr4ptel1M 442502 442566 (557434) MIRb#SINE/MIR 196 260 (8) m_b174s601i56 6809 chr4ptel1M 442502 GATCATATGTCTAAAGCAGTTCACACAATCCCTGGCACACAGTAGGCACT 442551 v iii v iv vi i v i i i MIRb#SINE/MIR 196 GATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCT 245 chr4ptel1M 442552 CAATATATGCTTGCT 442566 v v v MIRb#SINE/MIR 246 CAATAAATGGTAGCT 260 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 28.19 CpG sites = 9, Kimura (unadjusted) = 32.61 Transitions / transversions = 1.12 (9/8) Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0) 525 34.07 6.11 0.53 chr4ptel1M 443092 443271 (556729) L3#LINE/CR1 3909 4098 (1) m_b174s601i57 6810 chr4ptel1M 443092 CAGTCAGAGCTTTGCAGGAACGGGTGAGGGTATCTTAAGAAGTCCAGAGT 443141 i v v ii i ivvi v ii ii? i vvv i L3#LINE/CR1 3909 CAATCAGAGCTGTCCAAAAATGGAATGGGCTGCCTCGNGAGGTAGTGAGC 3958 chr4ptel1M 443142 TCTCTATCACAAGAGGTCTTCCAACAAAGGCTATATGGCCACTTGTGCAA 443191 i ii vi v v i i iv i vvii L3#LINE/CR1 3959 TCCCCGTCACTGGAGGTGTTCAAGCAGAGGCTGGATGACCACTTGTCAGG 4008 chr4ptel1M 443192 AATACCCTAGGGGAAATTCTCAGCTT----------TTAG-CTGGATGGC 443230 i iiiv ii ii iiivv ---------- i - i i L3#LINE/CR1 4009 GATGTTGTAGAAGGGATTCCTGCATTGGATGGGAGGTTGGACTAGATGAC 4058 chr4ptel1M 443231 TTCTGAAGTATCTTCCCACTTCTGAGATTCTGTGATCTTAT 443271 i i i vi v - ii L3#LINE/CR1 4059 CTCTAAGGTCCCTTCCAAC-TCTGAGATTCTGTGATTCTAT 4098 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 46.62 CpG sites = 42, Kimura (unadjusted) = 49.22 Transitions / transversions = 2.21 (42/19) Gap_init rate = 0.02 (3 / 179), avg. gap size = 4.00 (12 / 3) 367 27.55 1.01 1.01 chr4ptel1M 443269 443367 (556633) C MIRc#SINE/MIR (110) 158 60 m_b174s601i58 6811 chr4ptel1M 443269 TATTCTATCTCCTTATTTTACAGATGTGTAAACTGAGGCCCTG-GAAGTT 443317 v - v ii v v i v - i C MIRc#SINE/MIR 158 TATTAT-TATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTT 110 chr4ptel1M 443318 AATTGAATTATCCAAGGTCTCACTGGTACCAAGTAGCCACACTGAAATTC 443367 v v ii v v v vi i vivi i ii i C MIRc#SINE/MIR 109 AAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTC 60 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 33.25 CpG sites = 14, Kimura (unadjusted) = 34.80 Transitions / transversions = 1.08 (14/13) Gap_init rate = 0.02 (2 / 98), avg. gap size = 1.00 (2 / 2) 16 0.00 0.00 0.00 chr4ptel1M 444258 444274 (555726) (A)n#Simple_repeat 1 17 (0) m_b174s252i17 6812 chr4ptel1M 444258 AAAAAAAAAAAAAAAAA 444274 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 33 21.47 3.12 2.06 chr4ptel1M 444275 444370 (555630) (TTAT)n#Simple_repeat 1 97 (0) m_b174s252i18 6813 chr4ptel1M 444275 TTATTTATTTAATCTATTTATTTCAATCTTAATATTTTTCTTTA-ATCTT 444323 - i vvv v v v v v -v v (TTAT)n#Simpl 1 TTATTTATTT-ATTTATTTATTTATTTATTTATTTATTTATTTATTTATT 49 chr4ptel1M 444324 TATTTTATTT-TTAATTTA-TTATTTATTTTAATCTTTTTTTATTTATT 444370 - - v - vvv v v (TTAT)n#Simpl 50 TA-TTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATT 97 Matrix = Unknown Transitions / transversions = 0.06 (1/16) Gap_init rate = 0.05 (5 / 95), avg. gap size = 1.00 (5 / 5) 389 20.31 0.00 5.06 chr4ptel1M 444536 444618 (555382) C MIRb#SINE/MIR (91) 177 99 m_b174s601i59 6814 chr4ptel1M 444536 AATCCTGGGAGATAGGAAGGTGTTGGTATCCCCATTCTACAGATGATTAA 444585 i v i ---- i iv i vv C MIRb#SINE/MIR 177 AACCCTGCGAGGTAGG----TATTATTATCCCCATTTTACAGATGAGGAA 132 chr4ptel1M 444586 ATTGAGGCTCAGACAATTGAAGGAATTTGCCCA 444618 i v iv v v i C MIRb#SINE/MIR 131 ACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCA 99 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 23.76 CpG sites = 8, Kimura (unadjusted) = 23.76 Transitions / transversions = 1.00 (8/8) Gap_init rate = 0.05 (4 / 82), avg. gap size = 1.00 (4 / 4) 231 24.62 4.23 2.78 chr4ptel1M 445362 445432 (554568) C L2d2_3end#LINE/L2 (49) 506 435 m_b175s601i1 6815 chr4ptel1M 445362 CTGTGGTCTGAGCACC-TGGGGGCCACAAAGTTGCAAAAGACC--ATCCC 445408 -- ii i i- vi vv i v v--i C L2d2_3end#LIN 506 CTGTG--CTAGGCGCTGTGGGGGATACAAAGAAGTATAAGACATGGTCCC 459 chr4ptel1M 445409 TGCTCCTGAGGAGCTCACAATCTA 445432 i iii i C L2d2_3end#LIN 458 TGCCCTCAAGGAGCTTACAATCTA 435 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.97 CpG sites = 12, Kimura (unadjusted) = 31.18 Transitions / transversions = 2.40 (12/5) Gap_init rate = 0.06 (4 / 70), avg. gap size = 1.25 (5 / 4) 202 26.79 7.14 0.00 chr4ptel1M 445640 445695 (554305) L2d2_3end#LINE/L2 496 555 (0) m_b175s601i2 6816 chr4ptel1M 445640 GCTCAGCACAGTGCCTGGCAAATA----GCACTTTATAAGTGCCTGGTGC 445685 ii v v i ---- i iv i iii v v L2d2_3end#LIN 496 GCCTAGCACAGTGCCTTGCACACAGTAGGCGCTCAATAAATATTTGTTGA 545 chr4ptel1M 445686 CTTGATTTGA 445695 i L2d2_3end#LIN 546 TTTGATTTGA 555 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.66 CpG sites = 10, Kimura (unadjusted) = 34.49 Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.02 (1 / 55), avg. gap size = 4.00 (4 / 1) 324 18.65 0.00 1.69 chr4ptel1M 445691 445750 (554250) MIRc#SINE/MIR 116 174 (94) m_b175s601i3 6817 chr4ptel1M 445691 TTTGAACCTCTGTTTCCTCACCTGTAAAATAGAGATAAATAATGCCTGTG 445740 i i v i i i - i iv MIRc#SINE/MIR 116 TCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGAT-AATAATACCTGCC 164 chr4ptel1M 445741 GTACCTACCT 445750 v i MIRc#SINE/MIR 165 CTGCCTACCT 174 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 22.11 CpG sites = 8, Kimura (unadjusted) = 22.11 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.02 (1 / 59), avg. gap size = 1.00 (1 / 1) 185 17.02 6.38 0.00 chr4ptel1M 445940 445986 (554014) L2a_3end#LINE/L2 381 430 (87) m_b175s601i4 6818 chr4ptel1M 445940 CTGTCTCCCCC-ACTCGGATGTAAGCTCC--TAGGCCAAGGGCTGTTTTC 445986 - v i --v v i i v v L2a_3end#LINE 381 CTGTCTCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTC 430 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 19.31 CpG sites = 3, Kimura (unadjusted) = 19.31 Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.04 (2 / 46), avg. gap size = 1.50 (3 / 2) 209 24.59 8.20 0.00 chr4ptel1M 447282 447342 (552658) C MIR3#SINE/MIR (61) 147 82 m_b175s601i5 6819 chr4ptel1M 447282 CTTTCATTCGGCAGATAAGGAAACTGAGGCACAGA-AGACG----GATTT 447326 ii ivi i v - ii ---- i C MIR3#SINE/MIR 147 CCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTT 98 chr4ptel1M 447327 CCCCACAGACAAACAG 447342 v vi v v C MIR3#SINE/MIR 97 GCCCAAGGTCACACAG 82 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.47 CpG sites = 9, Kimura (unadjusted) = 30.47 Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.03 (2 / 60), avg. gap size = 2.50 (5 / 2) 201 29.98 6.59 1.04 chr4ptel1M 447286 447376 (552624) C MIR#SINE/MIR (120) 142 47 m_b175s601i6 6819 chr4ptel1M 447286 CATTCGGCAGATAAGGAAACTGAGGCACAGAAGACG------GATTTCCC 447329 ivi i - v ------i i v C MIR#SINE/MIR 142 CATTTTACAGATGAGGAAACTGAGGCACAG-AGAGGTTAAGTAACTTGCC 94 chr4ptel1M 447330 CACAGACAAACAGGTCGGAATCTTTAAAAGAGGGATTTGAAGCCGGG 447376 vi v v v v v vivvi i ivv i v i C MIR#SINE/MIR 93 CAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGG 47 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.80 CpG sites = 12, Kimura (unadjusted) = 38.54 Transitions / transversions = 0.80 (12/15) Gap_init rate = 0.02 (2 / 90), avg. gap size = 3.50 (7 / 2) 249 26.24 7.38 3.15 chr4ptel1M 447356 447477 (552523) MIRc#SINE/MIR 22 148 (120) m_b175s601i7 6820 chr4ptel1M 447356 AAAGAG----GGATTTGAAGCCGGGAAAGAGACCTGGGTTGGAGTCCCGG 447401 ---- i i i i --- v MIRc#SINE/MIR 22 AAAGAGCACTGGACTTGGAGTCAGGAA---GACCTGGGTTCGAGTCCCGG 68 chr4ptel1M 447402 AGTCGGTCCTCTACT--CCCTGGGAGCTGAGGGCAGTC---TCGCGTTTC 447446 -v v i vii -- iv v v vi vv --- vi v i MIRc#SINE/MIR 69 -CTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTC 117 chr4ptel1M 447447 CCGGACTCAGTTTCCTCCTCTGGGAAACGGG 447477 ivi v v vi i MIRc#SINE/MIR 118 TGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.61 CpG sites = 15, Kimura (unadjusted) = 32.61 Transitions / transversions = 0.94 (15/16) Gap_init rate = 0.06 (7 / 121), avg. gap size = 1.86 (13 / 7) 12 15.26 3.45 0.00 chr4ptel1M 447951 447979 (552021) (AGGGC)n#Simple_repeat 1 30 (0) m_b175s252i2 6821 chr4ptel1M 447951 AGGG-AGGGCAGGGCAGACCCGGGCTGGGC 447979 - iv v v (AGGGC)n#Simp 1 AGGGCAGGGCAGGGCAGGGCAGGGCAGGGC 30 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1) 17 9.12 0.00 0.00 chr4ptel1M 450078 450101 (549899) (A)n#Simple_repeat 1 24 (0) m_b175s252i3 6822 chr4ptel1M 450078 AAAAGAGAAAAAAAAAAAAAAAAA 450101 i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAA 24 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 36 19.89 1.23 1.23 chr4ptel1M 450149 450229 (549771) (AGGG)n#Simple_repeat 1 81 (0) m_b175s252i4 6823 chr4ptel1M 450149 AGAGAGGAAAAGAGGAAGGGGAGGGAGAAAGGAAGGAAGGGA-GGAAGGA 450197 i i ii i - ii i i - i (AGGG)n#Simpl 1 AGGGAGGGAGGGAGGGA-GGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGA 49 chr4ptel1M 450198 AGGAAGGAGAGAGGGAGGGAGGGAGGGAGGGA 450229 i i i (AGGG)n#Simpl 50 GGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGA 81 Matrix = Unknown Transitions / transversions = 1.00 (13/0) Gap_init rate = 0.03 (2 / 80), avg. gap size = 1.00 (2 / 2) 233 26.72 6.67 4.35 chr4ptel1M 450284 450373 (549627) C MIRc#SINE/MIR (94) 174 83 m_b175s601i8 6824 chr4ptel1M 450284 AGGGAAGCAGAACAAG-A--GTCATCTCCATTTTATGGATGAGATTCGAA 450330 v i ii i - --i i i ii ---- C MIRc#SINE/MIR 174 AGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAG----GAA 129 chr4ptel1M 450331 --TG-GATTCAGAAAAGGGAGGTGATTTGGCCAAGATGTCACAGTT 450373 -- - ii i i vv i i v i vv i C MIRc#SINE/MIR 128 ACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCT 83 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.04 CpG sites = 17, Kimura (unadjusted) = 35.04 Transitions / transversions = 2.83 (17/6) Gap_init rate = 0.09 (8 / 89), avg. gap size = 1.25 (10 / 8) 662 32.58 11.94 2.27 chr4ptel1M 450776 451378 (548622) L2#LINE/L2 2140 2799 (283) m_b175s601i9 6825 chr4ptel1M 450776 TCTCCTGGCTCTCCTACCACCTCTCTGACTA-TCCTTCTCGGTCTCCTTT 450824 i i v i v i ii- i L2#LINE/L2 2140 TCTCCTGGTTTTCCTCCTACCTCACTGGCCGCTCCTTCTCAGTCTCCTTT 2189 chr4ptel1M 450825 ATGAGATCCTCAGCCAGATCCCTAACC-CTAGATGTTC---CGCTCC--- 450867 iivi v v-i vv ii - ?i i v---i i --- L2#LINE/L2 2190 GCTGGTTCCTCC-TCATCTCCCCGACCTCTNAACGTTGGAGTGCCCCAGG 2238 chr4ptel1M 450868 -TTCTGTTCTGGG--CTCTCTTCTTCCCTATC------------CTTAGT 450902 -i v i v -- ii i ------------ ?i L2#LINE/L2 2239 GCTCAGTCCTTGGACCTCTTCTCTTCTCTATCTACACTCACTCCCTNGGT 2288 chr4ptel1M 450903 GATCTCAGC---TCCCATGGACTGAATGAAGATTCCTTCACTGATAATTC 450949 v --- i vi v vv vv iiv vii i i L2#LINE/L2 2289 GATCTCATCCAGTCTCATGGCTTTAAATACCATCTATATGCTGATGACTC 2338 chr4ptel1M 450950 TCAAATCTGCCCATCCAGCCTCAACTTCTCTGCTGACTTCCCATCTCCAG 450999 i i iiviv ivi i iv vi viv vvi L2#LINE/L2 2339 CCAAATTTATATCTCCAGCCCGGACCTCTCCCCTGAACTCCAGACTCGTA 2388 chr4ptel1M 451000 TCTCCAATTTGCCT-TTCAAG-----CACCTGGATGTCCAGAAAACACTT 451043 v i - -i i v----- i i iv ii ii L2#LINE/L2 2389 TATCCAACT-GCCTACTCGACATCTCCACTTGGATGTCTAATAGGCATCT 2437 chr4ptel1M 451044 GAAGTTCAATATGTCCAGAAGCAAACTCATTATCTTTTTTCTT-AGCCT- 451091 v ii i i i vii v v iiii i- i - L2#LINE/L2 2438 CAAACTTAACATGTCCAAAACTGAACTCCTGATCTTCCCCCTCAAACCTG 2487 chr4ptel1M 451092 -TCCTCCA-------TCATCATTACTGCCAAGGGTA---CCATCCTTCC- 451129 - v------- vi iv v i? v i --- - L2#LINE/L2 2488 CTCCTCCCGCAGTCTTCCCCATCTCAGTNAATGGCAACTCCATCCTTCCA 2537 chr4ptel1M 451130 ----CCCAGG------ACCTAGGTGTTACCTTGGACTCCTCATTGTCTCT 451169 ---- i ------ v v i i i v vi v L2#LINE/L2 2538 GTTGCTCAGGCCAAAAACCTTGGAGTCATCCTTGACTCCTCTCTTTCTCT 2587 chr4ptel1M 451170 TAGCCTCCATTTCCAA------GGTTGCTTCTGTTTGTATAATATTCTTT 451213 i vv i iv ------i iviv i iv ivi-- iii iv L2#LINE/L2 2588 CACACCCCACATCCAATCCATCAGCAAATCCTGTCGGCTC--TACCTTCA 2635 chr4ptel1M 451214 AAATACAACCTTCC--TCTCTGACCCGCCCTCCTGCTCCCCCCCACCACC 451261 i ---- --vv i --- v i vvi v i ii L2#LINE/L2 2636 AAATATA----TCCAGAATCCGAC---CACTTCTCACCACCTCCACTGCC 2678 chr4ptel1M 451262 ACCATGCT-GTGCAGGTCCACGATCATTTAT-ACCTGCATTTCTGCAACA 451309 iv - v i - v i v -i v v i L2#LINE/L2 2679 ACCACCCTGGTCCAAG-CCACCATCATCTCTCGCCTGGATTACTGCAATA 2727 chr4ptel1M 451310 GTTGC--AG--GGGCGTCTGGCTACCCAGAGTTTCTTCCCGCTCCAGTCC 451355 iiv -- i-- v vi iv v --- vii ivi v ? i L2#LINE/L2 2728 GCCTCCTAACTGGTCTCCCTGCTTCC---ACCCTTGCCCCCCTNCAGTCT 2774 chr4ptel1M 451356 ATCCT--ATTCAGTCACTAAAGTGA 451378 i -- iv ivi i i L2#LINE/L2 2775 ATTCTCAACACAGCAGCCAGAGTGA 2799 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 42.46 CpG sites = 117, Kimura (unadjusted) = 45.08 Transitions / transversions = 1.56 (117/75) Gap_init rate = 0.06 (39 / 602), avg. gap size = 2.23 (87 / 39) 344 35.28 7.05 4.77 chr4ptel1M 451519 451887 (548113) L2b_3end#LINE/L2 88 464 (2) m_b175s601i10 6825 chr4ptel1M 451519 GCTGTTCCATGAACAAGACCTTCTGCCCTTCAC-TCTGGACATTCTCTCG 451567 vi v v v?v v? iii i - v i v iv v ? L2b_3end#LINE 88 GCTGTTCCTCGAACACGCCANGCTCNCTCCCGCCTCAGGGCCTTTGCACN 137 chr4ptel1M 451568 GGCTGCCCTCCATGCCTGGAAGGCTCTCCCTC----CTCAGCTCAG---A 451610 v ii i iv v i i i ---- iv iii --- L2b_3end#LINE 138 TGCTGTTCCCTCTGCCTGGAACGCCCTTCCCCACCTCTTCGCCTGGCCAA 187 chr4ptel1M 451611 CTACTGACCTCACTTTAAATAAGAACAAAAAATAAATAAATAACAAAATA 451660 v i-- iii --- v iv vv ivvi i-- v v--- v L2b_3end#LINE 188 CTCCTA--CTCATCCT---TCAGGTCTCAGCTCAAATG--TCACC---TC 227 chr4ptel1M 451661 TTCTAGGAAGCCTGGCCCAATCCCT---GCTAATTCTAATGCCTTTGCCC 451707 i ii ivv ii i i--- iiiv viii i -- i L2b_3end#LINE 228 CTCCGGGAAGCCCTCCCTGACCCCCCAGGCCGGGTCAGGCGCCCT--CCT 275 chr4ptel1M 451708 CTGTTCATTGTT--TCCTATTGATCCTGTCTATAATTAGGATGTATTTGC 451755 vv viivii-- iivvv vv i-ii v? - i i ? L2b_3end#LINE 276 CTGGGCCCCCCCAGTCCTACCCTGCCACTCTG-GGTTATNAT-TGTCTGN 323 chr4ptel1M 451756 TT-CTTTCTTGTCTCACTCATTAGGTAATGAGCT-TGTGAAGGGCAAGGA 451803 - v vii v i i iivi -i - i L2b_3end#LINE 324 TTACATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGTG-AGGGCAGGGA 372 chr4ptel1M 451804 CTGTCTTTTGCCTCTTTTTTCCC-----ATTCCCAGTACTTAGCACAGGG 451848 i -?v i -- v iv ----- i ii i ? L2b_3end#LINE 373 CCG-NGTCTG--TCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNG 419 chr4ptel1M 451849 ACT-GCACAT-GTAGGAAT----TAATTGTTTATTGATTGATTGA 451887 v - i- vii---- v i i v v L2b_3end#LINE 420 CCTGGCACACAGTAGGCGCTCAGTAAATATTTGTTGAATGAATGA 464 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 45.99 CpG sites = 74, Kimura (unadjusted) = 51.44 Transitions / transversions = 1.48 (74/50) Gap_init rate = 0.08 (29 / 368), avg. gap size = 1.52 (44 / 29) 410 21.22 9.16 2.88 chr4ptel1M 451761 451891 (548109) L2d_3end#LINE/L2 378 516 (0) m_b175s601i11 6825 chr4ptel1M 451761 TCTTGTCTCACTCATTAGGTAATGAGCTTGTGAAGGGCAAGGAC--TGTC 451808 v iv i i vi i iv vi i -- L2d_3end#LINE 378 TCTTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTC 427 chr4ptel1M 451809 TTTTGCCTCTTTTTTCCCATTCC---CAGTACTTAGCACAGGGACT--GC 451853 v i--- ? ?i i --- ii i v - -- L2d_3end#LINE 428 TTATA---CTNTTTTNTCGTTCCCCACAGCGCCTAGCACAGTG-CTGAGC 473 chr4ptel1M 451854 ACAT-GTAGG-AATTAAT---TGTTTATTGATTGATTGATTGA 451891 - -iv i --- ii i L2d_3end#LINE 474 ACATAGTAGGCGCTCAATAAATACTTGTTGATTGATTGATTGA 516 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 22.94 CpG sites = 19, Kimura (unadjusted) = 26.37 Transitions / transversions = 2.38 (19/8) Gap_init rate = 0.08 (10 / 130), avg. gap size = 1.60 (16 / 10) 44 0.00 0.00 0.00 chr4ptel1M 452084 452121 (547879) (GT)n#Simple_repeat 1 38 (0) c_b175s251i0 6826 chr4ptel1M 452084 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 452121 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 38 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 277 15.69 3.95 2.79 chr4ptel1M 452124 452300 (547700) HERVIP10FH#LTR/ERV1 823 1001 (4101) m_b175s701i0 6827 chr4ptel1M 452124 GAGAGAGACAGAGAGACAGAGACAGAGAGACAGAGAGAGAGAGAGAGAGA 452173 v iv v v i i HERVIP10FH#LT 823 GAGAGAGAGAGAGAGGAAGAGAGAGAGAGAGAAAGAGAGAGAGAGGGAGA 872 chr4ptel1M 452174 GAGAGAGAGAGAGAGAGAGGCAGAGAGACAGAGAGAGACAGAAACAG--A 452221 v i i v i -- i i v -- HERVIP10FH#LT 873 GAGAGAGACAAAGAGGGAGTCAAAGAG--AGAGAGAGGCAGAGAGAGGAA 920 chr4ptel1M 452222 GAGACAGAG-GACAAAGAGAGAGAGAAAAGGGGGAGGGAGAGAGACAGAG 452270 - i vv i --- i i i HERVIP10FH#LT 921 GAGACAGAGAGACAAAGAGGGAGTCAGA---GAGAGAGAGAGAGACAGAA 967 chr4ptel1M 452271 A--CAGAAAGAG-AAGACAGAGAG-CATATAAGT 452300 -- i i - v -v v HERVIP10FH#LT 968 AGTCAAAGAGAGAAAGAAAGAGAGAGATAGAAGT 1001 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 17.76 CpG sites = 15, Kimura (unadjusted) = 17.76 Transitions / transversions = 1.25 (15/12) Gap_init rate = 0.06 (10 / 176), avg. gap size = 1.20 (12 / 10) 383 34.31 10.74 3.44 chr4ptel1M 453484 453809 (546191) L2#LINE/L2 2660 3008 (74) m_b175s601i12 6828 chr4ptel1M 453484 TCTCTTCATTCACACAGTCAATACTGGAGTCCGGAAGCC--CATC--CTG 453529 vi iiiv v i vi ivvi -- -- -- v L2#LINE/L2 2660 TCTCACCACCTCCACTGCCACCACCCTGGTCC--AAGCCACCATCATCTC 2707 chr4ptel1M 453530 TCACCTGGACTATTGTAATAACCTCCTAATGTGTCTCCTTGCCT-CAAAT 453578 i i i i i ivv i i - vvi L2#LINE/L2 2708 TCGCCTGGATTACTGCAATAGCCTCCTAACTGGTCTCCCTGCTTCCACCC 2757 chr4ptel1M 453579 TTGTCCCCAATCCAAGTCGTCCTCTAAACAACTGCCAAAGTGGTTTTCCT 453628 i -v ? iviii i v v i v i i ii ii L2#LINE/L2 2758 TTGCCCCC-CTNCAGTCTATTCTCAACACAGCAGCCAGAGTGATCCTTTT 2806 chr4ptel1M 453629 GATGCACAAGCTTGACCACATGGCCTTGCCTTCTCCCTGCTTAGTAAACT 453678 i vi ii iiv i -------- i viii i i iv vv L2#LINE/L2 2807 AAAACGTAAGTCAGATCA--------TGTCACTCCTCTGCTCAAAACCCT 2848 chr4ptel1M 453679 CAAGTGGCTGCCC-TTTCCCTCCAGAATCAAATAGAAATTCCTGA----- 453722 v i v - i v - i v vvv v v ----- L2#LINE/L2 2849 CCAATGGCTTCCCATCTCACT-CAGAGTAAAAGCCAAAGTCCTTACAATG 2897 chr4ptel1M 453723 GTCT---GGGAATGAAATGACTTAGACCCTT----CCTGTCT--TCTTAT 453763 i ---i vviv v ii i v ii---- v --i i L2#LINE/L2 2898 GCCTACAAGGCCCTACATGATCTGGTCCCCCGTTACCTCTCTGACCTCAT 2947 chr4ptel1M 453764 -GCCTTCCA-TGTTTCCTTCAC-------------GTCAAACTGGTCTTC 453798 -v v - v ii i i ------------- i v i i L2#LINE/L2 2948 CTCCTACCACTCTCCCCCTCGCTCACTCCGCTCCAGCCACACTGGCCTCC 2997 chr4ptel1M 453799 TTGCCATTTCT 453809 ii i L2#LINE/L2 2998 TTGCTGTTCCT 3008 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 46.00 CpG sites = 67, Kimura (unadjusted) = 48.54 Transitions / transversions = 1.63 (67/41) Gap_init rate = 0.07 (23 / 325), avg. gap size = 2.04 (47 / 23) 18 30.80 0.00 3.08 chr4ptel1M 454397 454463 (545537) (TA)n#Simple_repeat 1 65 (0) m_b175s252i5 6829 chr4ptel1M 454397 TACATACTTTATATAAGTGTACATATATATAAGTAAATATATTTACTTAT 454446 i - v vi i i vi v v iv (TA)n#Simple_ 1 TATATA-TATATATATATATATATATATATATATATATATATATATATAT 49 chr4ptel1M 454447 ATAAAGTAACTTTATAT 454463 v - vv v (TA)n#Simple_ 50 ATATA-TATATATATAT 65 Matrix = Unknown Transitions / transversions = 0.60 (6/10) Gap_init rate = 0.03 (2 / 66), avg. gap size = 1.00 (2 / 2) 558 24.81 16.29 3.41 chr4ptel1M 455541 455853 (544147) C X32_DNA#DNA/TcMar-Tc1 (0) 352 1 c_b175s401i0 6830 chr4ptel1M 455541 CAGGATCTAACATAAAGTGTTTATATAAA----AAAATTTAATAATTCAA 455586 i v- vi i ii iv---- v i i i C X32_DNA#DNA/T 352 CAGGGTCTT-CATAAAGTCCTTGTGCAGTTTTTAAACTTTAATAACTTAG 304 chr4ptel1M 455587 AGTTGAAGGTATTATAGGAAGAAAATCTATAAAAAGTATTTAGAAGTAAA 455636 - v v i v -- i vi i i i i C X32_DNA#DNA/T 303 -GTTGTAGGTATGATAGAAACAA--TCTGTAAATGGCATTTAAAGGCAAA 257 chr4ptel1M 455637 TGGATCTTTCTTCTTATAACTGATTTGGATTTCAATTATGTTAGTCAT-T 455685 v vi i i i v i v i i -v C X32_DNA#DNA/T 256 TTGAATTTTCTTCTCACAGCTGATATGGACTTCAATTCTGCTAGCCATAG 207 chr4ptel1M 455686 CATTCATTGGGTAATTACCTTCTTGTCTTATACAGGCATTTTTCATTTGT 455735 v iv v ------ i vvvii v C X32_DNA#DNA/T 206 GACACAGT------TTACCTTCTCGTCTACGGTAGCCATTTTTCATTTGT 163 chr4ptel1M 455736 CTCAGGAACTG-AATGGGAATGCA-------------------------G 455759 v v - ii i ------------------------- C X32_DNA#DNA/T 162 CACAGGATCTGAAATAAGAATACATTGTGTACAATTGTGTAATGTAGTTG 113 chr4ptel1M 455760 TCTTGATCCATAATTATTTTGCTTATAATTG------------TTTTTCT 455797 i i v iv v v v v ------------ v C X32_DNA#DNA/T 112 TCCTAAACTTTAATAAATTTGCTTTTAAATGCCATTTACAGATTGTTTCT 63 chr4ptel1M 455798 ATGAT------AACCTAAA--ATTTACATTTAAATATATCTCCGAGGACT 455839 v ------ i-- v vi vi i--iv i C X32_DNA#DNA/T 62 ATCATACCTACAACCTAAGTTATTAAAGTTTAAAAGTG--CACAAGGACT 15 chr4ptel1M 455840 TTGTGTAGACCCTG 455853 i v C X32_DNA#DNA/T 14 TTATGAAGACCCTG 1 Matrix = 18p41g.matrix Kimura (with divCpGMod) = 30.20 CpG sites = 40, Kimura (unadjusted) = 30.69 Transitions / transversions = 1.14 (40/35) Gap_init rate = 0.06 (19 / 312), avg. gap size = 3.32 (63 / 19) 291 28.28 3.98 9.58 chr4ptel1M 455859 456034 (543966) Charlie4z#DNA/hAT-Charlie 1 167 (0) m_b175s502i0 6831 chr4ptel1M 455859 CAGAGATTCTAAACCTGGAGTCTAAAAATATTTTTCTATAGTTTGATAAC 455908 i i v i i vii ivvi - vi --- i -- Charlie4z#DNA 1 CAGGGGTTCTTAACCTGGGGTCCATGGATGGGCTTC-AGGG---GGT--C 44 chr4ptel1M 455909 TGTTTGATTCCCTTTATAATATTATGTA---TTTTGT---TATATGCACT 455952 i -- vi i v - vv i --- --- i i Charlie4z#DNA 45 CGT--GAACCCCCTGA-AATTGTATGCAAAATTTTGTGCGTATGTGCATT 91 chr4ptel1M 455953 CAAACTACTCTGAGAAGAGT-TCTAGAGATTTCATCAGACAATCAAAGAG 456001 i------i i i v- i v v ivv i Charlie4z#DNA 92 T------TTCTGGGGAGAGGGTCCATAGCTTTCATCAGATTCTCAAAGGG 135 chr4ptel1M 456002 GTCCATAACACACACAAAAATGAAGAACTACTG 456034 i i - v v ii v i Charlie4z#DNA 136 GTCCGTGAC-CCCAAAAAGGTTAAGAACCACTG 167 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 34.41 CpG sites = 28, Kimura (unadjusted) = 36.44 Transitions / transversions = 1.65 (28/17) Gap_init rate = 0.11 (19 / 175), avg. gap size = 1.21 (23 / 19) 557 22.74 10.96 0.62 chr4ptel1M 455889 456034 (543966) Charlie4a#DNA/hAT-Charlie 348 508 (0) m_b175s502i1 6831 chr4ptel1M 455889 TTTTTCTATAGTTTGATAACTGT------------TTGATTCCCTTTATA 455926 iv v ------------ i i i Charlie4a#DNA 348 TTTTTTAATATTTTGATAACTGTATTTCAATATAATTGGTTTCCTTTGTA 397 chr4ptel1M 455927 ATATTATGTATTTTGTTATATGCACTCAAA----CTACTCTGAGAAGAGT 455972 vi i v i i ----i i i v Charlie4a#DNA 398 ATCCTATGTATTTTATTTTATGCATTTAAAAACATTATTCTGAGAAGGGG 447 chr4ptel1M 455973 TCTAGAGATTTCATCAGACAATCAAAGAGGTCCATAACACACACAAAAAT 456022 i v ii i vii i ii - v ii Charlie4a#DNA 448 TCCATAGGCTTCACCAGACTGCCAAAGGGGTCCATGGCACA-AAAAAGGT 496 chr4ptel1M 456023 GAAGAACTACTG 456034 v iv Charlie4a#DNA 497 TAAGAACCCCTG 508 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 28.12 CpG sites = 23, Kimura (unadjusted) = 28.12 Transitions / transversions = 2.30 (23/10) Gap_init rate = 0.02 (3 / 145), avg. gap size = 5.67 (17 / 3) 303 21.83 1.22 5.06 chr4ptel1M 456906 456987 (543013) L3#LINE/CR1 3842 3920 (179) m_b175s601i13 6832 chr4ptel1M 456906 ACTAGGACCACTGGGTCAAAGTAACAGTGAGGTAGACTTCTAGCTCAATC 456955 v vi v v i i -i v L3#LINE/CR1 3842 ACTAGGACCAATGGGTGGAAGTTACAGGGAGGCAGATTTC-GGCTCAATA 3890 chr4ptel1M 456956 TAAGCAAAAAC-ATCTAAATGTAGTTAAAACTG 456987 v i -v ---i i i i i L3#LINE/CR1 3891 TAAGGAAGAACTTTCTAA---CAATCAGAGCTG 3920 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 24.46 CpG sites = 10, Kimura (unadjusted) = 26.19 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.06 (5 / 81), avg. gap size = 1.00 (5 / 5) 40 12.51 0.00 0.00 chr4ptel1M 457474 457543 (542457) (TG)n#Simple_repeat 1 70 (0) c_b175s251i1 6833 chr4ptel1M 457474 TGTGTGTGTATGTGTGTATTTGTGTGTGTGTGTGTGTGTGTGTATGTATT 457523 i i v i i v (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr4ptel1M 457524 TGGGTGTGTGTATGTGTGTG 457543 v i (TG)n#Simple_ 51 TGTGTGTGTGTGTGTGTGTG 70 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0) 971 31.05 5.81 3.05 chr4ptel1M 458376 459046 (540954) C L1ME4c_3end#LINE/L1 (141) 689 1 m_b175s551i0 6834 chr4ptel1M 458376 CATAGCTAATTATCCTTACATCTTTGTTATTGTAA--TAGGT-CATTCTC 458422 vv ---i vv v ii i-- ?i - v i i C L1ME4c_3end#L 689 CATACGTAATT---TTTACATAGTTGTAATCATAGCGTANATACAATTTT 643 chr4ptel1M 458423 CTGTTCTGTGTAGTTCATTTTGCATCAGTTCATACAAGTCTTCCCAGGAT 458472 v i iv vv i vi i vv v vi i - v v C L1ME4c_3end#L 642 GTATTCTGCTTTTTTCACTTAACATTATATCATAAACATTTTCC-ATGTT 594 chr4ptel1M 458473 TTTCCAAAAACATCCTGCTCATCATTTCTTATAGCATAATAATATTTCAT 458522 vi v v iv v v iv i i v i vvv i C L1ME4c_3end#L 593 GCTACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCAT 544 chr4ptel1M 458523 CACAATC-ATATACCACAATTTGTTTGGCCATTTCCCAATTGTTGGGTAT 458571 i- i ?- i i ii ii i v ii C L1ME4c_3end#L 543 CG-AGTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACAT 495 chr4ptel1M 458572 CCGATTA---TGTTTTTAATTCTTAATCACCACAAAAAGAATTGCTACAG 458618 ---- --- ii i viii ii i v ivii v iii C L1ME4c_3end#L 494 ----TTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGA 449 chr4ptel1M 458619 ATATTTTTATACATATAGGTCTCCATATGTTCTTTCTTT-GA----TCTC 458663 i i ii i v i ------- i - ---- i C L1ME4c_3end#L 448 ACATCTTCGTGCATATAGCTTT-------TTCCTTCTTTTGAATTATTTC 406 chr4ptel1M 458664 CTTGGGGTACAGGCCTA--AGCAGAATTGCTGAGTCATTGGGAATACAAA 458711 i i v vv i -- ii i i vv v iv v C L1ME4c_3end#L 405 CTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACA 356 chr4ptel1M 458712 GTTTAAAAGTCTTTTAGT-TATAGTCCCAAATTACTTTCCAGAATGGTTG 458760 v v vi - i ii -ii v v i i v C L1ME4c_3end#L 355 TTTTTATGG-CTCTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTG 307 chr4ptel1M 458761 CACTAGTTCACA----------------ATTAGTGAACCTGTTCTCCTAC 458794 i i i i ---------------- v ? v v iiv ii C L1ME4c_3end#L 306 TACCAATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCACCGC 257 chr4ptel1M 458795 ATTCCCCCTAGAAT--GCCATTTTC--TTTTTTGGTCATCTTTGTTGATC 458840 ?i i v i v -- vi v -- ii-- i i i i C L1ME4c_3end#L 256 ANCCTCGCCAGCATTGGGTATTATCAATTTTTTAA--ATTTTTGCTAATT 209 chr4ptel1M 458841 TGAAAACTGTGAGATGATATCTGA--GTTGTTTTAATTTGCAATTTTCTA 458888 i v ivi i i i v -- i v i i i C L1ME4c_3end#L 208 TAATAGGCGTAAAATGGTATCTCATTGTTGCTTTAATTTGCATTTCTTTG 159 chr4ptel1M 458889 ATTATTAGTGA--TTCAGAACATTTTTTCATGTCACTATTGATAGGTTTG 458936 i i -- -- i vvi i v ivi? vv C L1ME4c_3end#L 158 ATTACTAGCGAGGTT--GAACATTTTTCCATGTGTTTGTTTACTANTTGT 111 chr4ptel1M 458937 ATTTCTTCCTCTGAAAACTGTCTTTTTATATCCTTTAACAATTTATTATT 458986 i i ? vi i v i i iv v ivv C L1ME4c_3end#L 110 ATTTCCTCTTNTGTGAATTGTCTGTTCATGTCCTTTGCCCATTTATCTAT 61 chr4ptel1M 458987 TGGGGAATTTCTCTTATTCTTGTAAATTTGACCCAGTTCACTATATATTT 459036 vv vv ? v i v viv i vi ? v C L1ME4c_3end#L 60 TGGGGTCTTGATNTTTTTCTTATCAATTTGAATGAGCTCTTTATATANTA 11 chr4ptel1M 459037 TAGAAATGAA 459046 ? v v C L1ME4c_3end#L 10 NAGATATTAA 1 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.89 CpG sites = 118, Kimura (unadjusted) = 42.18 Transitions / transversions = 1.40 (118/84) Gap_init rate = 0.05 (34 / 670), avg. gap size = 1.76 (60 / 34) 412 28.50 2.99 0.49 chr4ptel1M 458904 459104 (540896) C L1M4_orf2#LINE/L1 (7) 3287 3082 m_b175s551i1 6834 chr4ptel1M 458904 GAACATTTTTTCATGTCACTATTGATAGGTTTG-ATTTCTTCCTCTGAAA 458952 i i vvi ii-vi - v i iv i C L1M4_orf2#LIN 3287 GAGCATCTTTTCATGTGCTTATTGGC-CATTTGTATATCTTCTTTGGAGA 3239 chr4ptel1M 458953 ACTGTCTTTTTATATCCTTTAACAATTTATTATTTGGGGAATTTCTCTTA 459002 v v i v iv v v ? v vv v v C L1M4_orf2#LIN 3238 AATGTCTATTCAAATCCTTTGCCCATTTTTNAATTGGGTTATTTGTCTTT 3189 chr4ptel1M 459003 TTCTTGTAAATTTGACCCAGTTCACTATATATTTTAGAAATGAAGACTTT 459052 v vi v vvvv vi i i v i? ivv i C L1M4_orf2#LIN 3188 TTATTGTTGAGTTGTAAGAGTTCTTTATATATTCTGGATACNAGTCCCTT 3139 chr4ptel1M 459053 ATTAGATATGTCA----CAAAGATTTCCCCCCAGTTTCT-GGTTTTCTTA 459097 i i v ---- v i i v i v - v v C L1M4_orf2#LIN 3138 ATCAGATATATGATTTGCAAATATTTTCTCCCATTCTGTGGGTTGTCTTT 3089 chr4ptel1M 459098 TCATTTT 459104 i C L1M4_orf2#LIN 3088 TCACTTT 3082 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.44 CpG sites = 24, Kimura (unadjusted) = 36.44 Transitions / transversions = 0.73 (24/33) Gap_init rate = 0.02 (4 / 200), avg. gap size = 1.75 (7 / 4) 286 32.15 7.23 5.39 chr4ptel1M 460654 461054 (538946) C HERVK13#LTR/ERVK (2280) 5836 5429 m_b175s701i1 6835 chr4ptel1M 460654 TCAAGAAGTTGATAGTATAAAGAGCTAAATTTAGAAGTTCTCTAGGGTTA 460703 i i v vv v i i ivv vv viv iv C HERVK13#LTR/E 5836 TTAAGAAATTTAGTGTAAAAAGAGCCAGATTTAACTGAGCATGAGGAGTA 5787 chr4ptel1M 460704 TCTGTGGC-TCCCCCTTTCTTTT--------GTTTTTGGAGGAACATCTT 460744 --- i - ii -------- ?i i vvi- C HERVK13#LTR/E 5786 ---GCGGCATCCCCCTTCTTTTTAGTGTCCTGTTTNCGAAGTTG-ATCTT 5741 chr4ptel1M 460745 --AATGTCTCTGTTT-CTCCTCTCTACTATTGC-TGTCCTTGAGGATTAA 460790 -- i i - i v- v - i i vv - i ii v C HERVK13#LTR/E 5740 TGAGTGTTT-TATTGGCTCGT-TCCACCAAGGCCTGTCCTCGAGAGTTAT 5693 chr4ptel1M 460791 AGGGTATGCCAGTAGTGTGTAAAATCTTATCCTGTGCACAAAAGTGTGCA 460840 v v viv --------- v vivv v ii C HERVK13#LTR/E 5692 AGGGGATGCCAGTTGTGTGAGTAAT---------TGCCCATGTCTGAGTG 5652 chr4ptel1M 460841 AAATGTTTAGAAGTA---------TATGCAGGTCCATTATCTGTTTTTA- 460880 v v i i --------- vv i v i v - C HERVK13#LTR/E 5651 AACTTTTTAAAAGCAGCGCTAGTGTAGCCGGGGCCGTTATCAGTTTTTAG 5602 chr4ptel1M 460881 TTGCTTGTGGCACATCCATAATTGCAAATGCTTGTATGAGGAACTCGGTG 460930 v i v i -ii ii vi -i v? v v viv vv v v C HERVK13#LTR/E 5601 TTTCTCGGGACA-GCCCATAACCGAGAA-ACANGAAAGCATATGTCGTTT 5554 chr4ptel1M 460931 ACCAC---TCGGGTTGTCTCT--TTTG-CTGCTGGTATTGCAAAAGTGAA 460974 v i---i vii v i i-- - viv iviv vv i - C HERVK13#LTR/E 5553 AACATGAGCCGTACTTTCCCCCGTTTGACAAGTGGCCCAGATAAAATGA- 5505 chr4ptel1M 460975 TCCTGAAAAAGTGTCTACCACAACATGGATAAACGACAGATGACCAAAAG 461024 ---- i v iviiv v v v v vi C HERVK13#LTR/E 5504 ----GAAAAGGTGTCAATAGTTACATGTATAAAAGAAAGCTTGCCAAAAG 5459 chr4ptel1M 461025 ATTTATAATGGGTCACATCCATTTGCCAAA 461054 vvvv i i i C HERVK13#LTR/E 5458 CAGGATAATGAGTCACGTCCATTTGCCAGA 5429 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.23 CpG sites = 56, Kimura (unadjusted) = 42.72 Transitions / transversions = 0.85 (56/66) Gap_init rate = 0.08 (32 / 400), avg. gap size = 1.59 (51 / 32) 520 26.33 7.34 3.31 chr4ptel1M 460704 461139 (538861) C HERVK14C#LTR/ERVK (2322) 5112 4660 m_b175s701i2 6835 chr4ptel1M 460704 TCTGTGGCTCCCCCTTTCT----TTTGTTTTTGGAG--GAACATCTTAAT 460747 v i i ---- v i-- i?- i v C HERVK14C#LTR/ 5112 TCTCTGGTTCCCCCCTTCTGTCTTTTGTTTTTGTAATTGAGN-TTTTAAG 5064 chr4ptel1M 460748 GTCTCTGTT-TCTCCTCTCTACTATTGCT-GTCCTTGAGGATTAAAGGGT 460795 - vi -v v - v v v - ? i v v C HERVK14C#LTR/ 5063 GT-TCGATTAGCTCGT-TCAACAATGGCTTGNCCTTGAGAATTATAGGGG 5016 chr4ptel1M 460796 ATGCCAGTAGTGTG--TAAAATCTTATCCTGTGCACAAAAGTGTGCAAAA 460843 ? ? -- vi ?ii iv - v vi v i? ?i i C HERVK14C#LTR/ 5015 ATNCCAGTANTGTGTTTAATGTNCCATTGT-TGAAGGAACGCNTNTAAAG 4967 chr4ptel1M 460844 TGTTTAGAAGTATATGCAGGTCCATTATCTGTTTTTATTGCTTGTGGCAC 460893 -? vv ??i vv v v i ? v ?vi v i C HERVK14C#LTR/ 4966 -NTTTACTANNGTAGCCTGGGCCATTGTCNGTTTTAATNTTTTGTGGAAT 4918 chr4ptel1M 460894 ATCCATAATTGCAAATGCTTGTATGAGGAACTCGGTGACCACTCG-GGTT 460942 ii i i? i -i vv v v vii vv vv v v vv -i i? C HERVK14C#LTR/ 4917 GCCCATGACNGCGAA-ACAGGAAAGCAAATGTCTTTTAACACGAGCAGCN 4869 chr4ptel1M 460943 GTCTCTTTTGCTGCTGGTA--TTGC-----AAAAGTGAATCCTGAAAAAG 460985 i ?ii i -- i -- ? -----v i ----- i C HERVK14C#LTR/ 4868 GCCTCNCCTGTT--TGGCAAGTNGCCCANACAAAATGA-----GAAAAGG 4826 chr4ptel1M 460986 TGTCTACCACAACATGGATAAACGACAGATGACCAAA-AGATTTATAATG 461034 i vii? iiv ? ? v vv -i? vv i- C HERVK14C#LTR/ 4825 TATCTACAGTNACATGGACGTANGANAGTTTCCCAAATGNAGGTAC-ATG 4777 chr4ptel1M 461035 GGTCACATCCATTTGCCAAATTTCAGTGGATCTCAAACCATGAGGGTT-- 461082 ? i ? viv? v i i?vi v vi ? -- C HERVK14C#LTR/ 4776 GGTNACGTCCATTTGCCANAGCGNATTAGGNGCCAATCCTCGNGGGTTAA 4727 chr4ptel1M 461083 CT----TCCCTGGA---GTCAG-TGTAGGACAGTGGAAAGGAAGGCAA-G 461123 ?---- v --- v - v -v v v?? i - C HERVK14C#LTR/ 4726 CNCCAGTCCCTTGATGTGGCAGTTGTAGCAC-CTGGCACNNAGGGCAATG 4678 chr4ptel1M 461124 CTGGACA--GACTTTTAC 461139 i ? -- ? i ?i C HERVK14C#LTR/ 4677 TTGNACAATGNCCTTNGC 4660 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 34.11 CpG sites = 53, Kimura (unadjusted) = 36.11 Transitions / transversions = 0.91 (53/58) Gap_init rate = 0.07 (30 / 435), avg. gap size = 1.57 (47 / 30) 318 30.13 7.00 7.00 chr4ptel1M 462018 462274 (537726) C HERVK3#LTR/ERVK (3651) 3551 3295 m_b175s701i3 6835 chr4ptel1M 462018 GCTTCTTTTGTAAGCTGT-GTGGTGAGTTAAAAGCACTGTCTCCCCTTAA 462066 i v ? i i- i v i v ? v vvi iivi i C HERVK3#LTR/ER 3551 GCCTCTTTAGTNAGTTGCCGCGGGGAATTTAANGAAGAATCTCCTTGCAG 3502 chr4ptel1M 462067 AATGTCATAT-GATGATTGCAA-TTGATAGGTAGTCAAGCCTAACACTAG 462114 ii v vi v- -- i - iv vi i iii C HERVK3#LTR/ER 3501 GGTTTGGTAAAGATG--TGTAAGTTGATAGGTAGCAATACCTAGCATCGG 3454 chr4ptel1M 462115 ACACATCCATTGGATATCTCTTATCAATTTCTGAAAATCATTCAGTGTGT 462164 i i v v vi i i vi vi i iv v C HERVK3#LTR/ER 3453 GCGCAGCCAATTAATATCCCCTAATAATTGTTGAAAATCATTTAAAGTCT 3404 chr4ptel1M 462165 TTAGCTTCGCTGTTCTTAAGGACAGTTTTTGAACTGTTAGCACCTTAGG- 462213 v i ---- ii v -------- ii ---vi v - C HERVK3#LTR/ER 3403 GTAAC----CTGTCTTTACGGA--------GAACTACT---TTCTGAGGC 3369 chr4ptel1M 462214 -GTATACTTC-----------ATA--TCCTAAATATTGAAAAGGAGCATG 462249 - i ----------- -- i ? iv v i v vv C HERVK3#LTR/ER 3368 CGTACACTTCTCTCCGTAACAATAGTTCCTAAGTANTGGTATGGGGAAGT 3319 chr4ptel1M 462250 TCTTTGAATTTTTTTCTGGAGCTAT 462274 v v -ii i ? C HERVK3#LTR/ER 3318 TGTTTGCA-CCTTCTCTGGAGCNAT 3295 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.30 CpG sites = 42, Kimura (unadjusted) = 40.56 Transitions / transversions = 1.40 (42/30) Gap_init rate = 0.10 (25 / 256), avg. gap size = 1.44 (36 / 25) 1128 29.06 5.72 4.95 chr4ptel1M 462091 462912 (537088) C HERVK14C#LTR/ERVK (3762) 3672 2845 m_b175s701i4 6835 chr4ptel1M 462091 ATAGGTAGTCAAGCCTAACACTAGA-CACATCCATTGGATATCTCTTATC 462139 vv v - v i- iv v vi i i vi C HERVK14C#LTR/ 3672 ATAGGTAGGAATGCCTAA-AGTAGGTCGAATCCAATTAATATCCCCTAAT 3624 chr4ptel1M 462140 AATTTCTGAAAATCATTCAGTGTGTTTAGCTTCGCTGTTCTTAAGGACAG 462189 i i iv v i vvvvv v ---- i --- C HERVK14C#LTR/ 3623 AATTTTTGAAAATCATTTAAAGTTTTCAGAGAGTCTTTTC----GAA--- 3581 chr4ptel1M 462190 TTTTTGAACTGTTAGCACCTTAGGGTATACTT-----------CATATCC 462228 -- iv v ?iv iv- iiv ----------- - C HERVK14C#LTR/ 3580 --TTTGAACCTTTTGNGGCTTAAT-TGCCCTTTCCTGAACCTGCAT-TCC 3535 chr4ptel1M 462229 TAAATATTGAAAAGGAGCATGTCTTTGAATTTTTTTCTGGAGCTATGTGC 462278 i i i v?iv v - ? ? v? C HERVK14C#LTR/ 3534 CAAATATTGGAAAGGAGTAGNCGTTTGAATTTTAT-CNGGNGCTATGANC 3486 chr4ptel1M 462279 AATTTGCAGTTTCTTAGTATTTCTATGGTCTTTTGTAGACATGCTTCTAA 462328 i-- iv --i ----- ? iv i i i ii v--v C HERVK14C#LTR/ 3485 AATC--CAGCGTC--GG-----CNACCGCCTTCTGTAAATGTGA--ATAA 3447 chr4ptel1M 462329 CATTTG-----TT--CCTCAGGTGTTCATCC-----CAATATATCATCTT 462366 i v ----- --i ii - iv -----? i iv C HERVK14C#LTR/ 3446 CACTGGATAAGTTGGTCTCGAGT-TTCGGCCGCACANAATATGTCATCCA 3398 chr4ptel1M 462367 TGTAATATAATAACATAACT-TTTGGAAATGCTTTTCTTACTGGAGTAAG 462415 i i- i i ?vv- i ivvv i ? v vvv v C HERVK14C#LTR/ 3397 TATAATG-AATGATATANGAATCTGGAAACTGATCTCTNACAGGTTGAAT 3349 chr4ptel1M 462416 AGCAGCAGCAACATAA-TTTGACATATAGTAGTGATGTTTTTTATTCCCT 462464 vv?vv v ? - v ? ? viv i ivvi v C HERVK14C#LTR/ 3348 AGCCTNCCCCACANAAGTTTGACAAATNGTNGGACTATTCAACATGCCCT 3299 chr4ptel1M 462465 GTGGCAAAACTGTCCATTCATATCTTTTAAAAGGCTCAGCTAA--GTTAA 462512 i ? v v v ? vviviv? i -- vi-- v C HERVK14C#LTR/ 3298 GCGGCAANACTTTCCAATGATANCTGGCTGCNGGTTC--CTTGTTGTTCA 3251 chr4ptel1M 462513 CGCTGGGCATTGAAAAGGCAAATCTTTTCGTATCCTCCTTATCTAGAGGA 462562 iivii v v v i i iviv ?vv ivv C HERVK14C#LTR/ 3250 TAGCAGGAATAGTAAAAGCAAATTTTTCAAAATCNGGCTCTGCTAGAGGA 3201 chr4ptel1M 462563 ATAGAATAGGAATAATCCTTAATGTCTATAACCCAAAGAGGCCATTCTCT 462612 v v i ii i v vi ivvv i? v C HERVK14C#LTR/ 3200 ATAGTAAAGAAGCAGTCCTTCAAATCTATAACTATTAANGGCCAGTCTCT 3151 chr4ptel1M 462613 AGGCAA--ATGAGTAGGAGATGGAAGTCCAGGCTGAAGAGTTCCCGTAGT 462660 - -- - ii i ? v i v v ? ii i ? v C HERVK14C#LTR/ 3150 AGG-AATCATG-GCGGGGGANGGCAGCCCTGGCTGCAGNGCCCCCATNGG 3103 chr4ptel1M 462661 TTCCAT--CTGTTCATTTACCTTTCTTAAATCAGTCAACATCCTCCATTT 462708 v? -- -- v vvi v i i i i ? v i C HERVK14C#LTR/ 3102 TTGNATGACTG--CATTGACGGCTCGTAAGTCGGTTAGCATNCGCCATCT 3055 chr4ptel1M 462709 TCCAGGTTTCTTTCTTACAACAAATACTGGGGAATTCCAAGGA------- 462751 v i i i ii ? iv i ? ? ------- C HERVK14C#LTR/ 3054 GCCGGATTTTTTCTTNATTACAAACACTGGNGAATTCCANGGAGAAAATG 3005 chr4ptel1M 462752 ----CTTA----GTCCTTGGTCAAGTTGCTCCTGTACTATATCTAATAAG 462793 ---- i?---- v? v i i i vv vv ivi C HERVK14C#LTR/ 3004 TGGGCTCNATGTGTCCTTTNTCTAATTGTTCTTTGACTAATTCCTGTAAG 2955 chr4ptel1M 462794 GCCTGAATTTTATCACTAGCTAAGGACCACTGTTCTATCCACACTGGTGT 462843 ivv v v viv ?? iv i ? ? i v ? ?v C HERVK14C#LTR/ 2954 GCCCCCAGTTTTTCCTGAGNNAGCGGCCACTGNTCNACCCAAACNGGNTT 2905 chr4ptel1M 462844 ATCATTTTTCCATTGGATAGGAACAAGTGAAAGTGTTGGCAGACCTTCAA 462893 v viv i? vv vi i i -------? iv v i -- C HERVK14C#LTR/ 2904 TTGGGTCNTCCATTTTAAGGGAATAGG-------NTCTGGAGGC--TCAA 2864 chr4ptel1M 462894 CAGCAGCCCTGCCTAAAAA 462912 ii viv C HERVK14C#LTR/ 2863 CAGTGGCCGCCCCTAAAAA 2845 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.33 CpG sites = 109, Kimura (unadjusted) = 39.51 Transitions / transversions = 0.92 (109/118) Gap_init rate = 0.07 (54 / 821), avg. gap size = 1.63 (88 / 54) 49 18.79 5.30 1.92 chr4ptel1M 463303 463383 (536617) (AGTCGGG)n#Simple_repeat 1 83 (73) m_b175s252i6 6836 chr4ptel1M 463303 AGTCGGGAGTCGGGAGGC-GCATTTAGG-GTTAGG-GT-TAGAGTCGGGA 463348 v - v v ii - ii - -vi (AGTCGGG)n#Si 1 AGTCGGGAGTCGGGAGTCGGGAGTCGGGAGTCGGGAGTCGGGAGTCGGGA 50 chr4ptel1M 463349 GTCGGGAGGC-AGAGTCGGGAGTCGGGAGGCGCATT 463383 v -i v ---v (AGTCGGG)n#Si 51 GTCGGGAGTCGGGAGTCGGGAGTCGGGAGTCG---G 83 Matrix = Unknown Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.10 (8 / 80), avg. gap size = 1.00 (8 / 8) 44 0.00 0.00 0.00 chr4ptel1M 463384 463423 (536577) (TTAGGG)n#Simple_repeat 1 40 (0) c_b175s251i2 6837 chr4ptel1M 463384 TTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAG 463423 (TTAGGG)n#Sim 1 TTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAG 40 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 49 18.79 5.30 1.92 chr4ptel1M 463424 463492 (536508) (AGTCGGG)n#Simple_repeat 84 155 (1) m_b175s252i6 6838 chr4ptel1M 463424 AGTCGGGAGGC-GCATTTAGG-GT-TAGAGTCGGGAGGCGGGAGTCGGGA 463470 v - v v ii - -vi v (AGTCGGG)n#Si 84 AGTCGGGAGTCGGGAGTCGGGAGTCGGGAGTCGGGAGTCGGGAGTCGGGA 133 chr4ptel1M 463471 GGCAGGAGTCGGGAGGCGGGAG 463492 v i v (AGTCGGG)n#Si 134 GTCGGGAGTCGGGAGTCGGGAG 155 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.04 (3 / 68), avg. gap size = 1.00 (3 / 3) 18 9.77 6.25 4.08 chr4ptel1M 463598 463645 (536355) (ACCCTA)n#Simple_repeat 1 49 (0) m_b175s252i7 6839 chr4ptel1M 463598 ACTCTAACCCTAACCCTAAATGCCT--CCC-GACTCTAACCCTAACCCTA 463644 i - -v -- -i i (ACCCTA)n#Sim 1 ACCCTAACCCTAACCCT-AA-CCCTAACCCTAACCCTAACCCTAACCCTA 48 chr4ptel1M 463645 A 463645 (ACCCTA)n#Sim 49 A 49 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.09 (4 / 47), avg. gap size = 1.25 (5 / 4) 259 25.35 0.00 0.00 chr4ptel1M 464857 464927 (535073) C HERVK11#LTR/ERVK (6683) 1270 1200 m_b175s701i5 6840 chr4ptel1M 464857 AAATTCTGTAATAACATCTTAACATAAGATGATGTAGCTCAATAAAGAGT 464906 v i v i iv v vv v vv C HERVK11#LTR/E 1270 AAAGTTTGTAATACCATTTTAACATAAGGAGAAGTAGGACCATACTGAGT 1221 chr4ptel1M 464907 GCAAGCATTTTTCAGGTCTTT 464927 i ii v iv C HERVK11#LTR/E 1220 ACAAGCATCCTTAAATTCTTT 1200 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 30.97 CpG sites = 7, Kimura (unadjusted) = 30.97 Transitions / transversions = 0.64 (7/11) Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0) 245 19.70 6.06 0.00 chr4ptel1M 465820 465885 (534115) C L1P1_orf2#LINE/L1 (1447) 1847 1778 m_b175s551i2 6841 chr4ptel1M 465820 GCTTTTA--ATAATAGGTAGT-GTATTTCGTCAAAAGCCTATTCAGCTTC 465866 i -- i vi v - v i i v v v C L1P1_orf2#LIN 1847 GTTTTTAGCATGAAGGGTTGTTGAATTTTGTCAAAGGCCTTTTCTGCATC 1798 chr4ptel1M 465867 CATTGAAATAATCAT-TGGT 465885 i i - C L1P1_orf2#LIN 1797 TATTGAGATAATCATGTGGT 1778 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 23.07 CpG sites = 7, Kimura (unadjusted) = 23.07 Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.05 (3 / 65), avg. gap size = 1.33 (4 / 3) 235 32.37 8.55 4.20 chr4ptel1M 466564 466781 (533219) C L1PREC2_orf2#LINE/L1 (740) 2554 2341 m_b175s551i3 6842 chr4ptel1M 466564 TTTGATCCCCAAGATGAATTTTGTTCTAGTTTTTTCCCTAA--CTATAAA 466611 i i -- v ivvv -- i-- i i C L1PREC2_orf2# 2554 TTTGGTTCC--ATATGAATTTTAAAATAGTTTTTTC--TAGTTCTGTGAA 2509 chr4ptel1M 466612 GTAAT-TATTTGGAAGGCTGATTGATATGACATTGAAT----AAATTAAT 466656 - - vv v vi v iv ii ---- iv C L1PREC2_orf2# 2508 G-AATGTCATTGGTAGTTTGATAGGAATAGCATTGAATCTGTAAATTGCT 2460 chr4ptel1M 466657 TTAAGTAATACTTTTATTGTGTAATTTTTATTATAATGGCTTAGCTTAGC 466706 ii i i ------- - iv v iv v ii ivv i v C L1PREC2_orf2# 2459 TTGGGCAGTA-------TG-GCCATTTTAACGATATTGATTCTTCCTATC 2418 chr4ptel1M 466707 AATGAGTAATTAATATTTCTCTATTTAAATATGT----TTAGAT--CTTT 466750 v i vvv i i i ivv i ---- iv -- C L1PREC2_orf2# 2417 CATGAGCATGGAATGTTTTTCCATTTGTTTGTGTCATCTCTGATTTCTTT 2368 chr4ptel1M 466751 GTGCCAAGTGTTTTGTAATTCTGTTCAT-GTA 466781 v -- --- - C L1PREC2_orf2# 2367 GAGC--AGTGTTTTGTAATTCT---CATTGTA 2341 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 42.25 CpG sites = 86, Kimura (unadjusted) = 43.82 Transitions / transversions = 1.08 (28/26) Gap_init rate = 0.11 (24 / 217), avg. gap size = 1.33 (32 / 24) 263 31.46 10.46 3.05 chr4ptel1M 466719 466781 (533219) C L1MD_orf2#LINE/L1 (889) 2405 2330 m_b175s551i4 6842 chr4ptel1M 466719 ATATTTCTC----TATTTAAATATGTTTAGATCTTTGTGCCAAGTGTTTT 466764 i i ---- i v vi v i i v vviv i C L1MD_orf2#LIN 2405 ATGTCTCTCCATTTATTTAGATCTTCTTTGATTTCTTTCATCAGCGTTTT 2356 chr4ptel1M 466765 GTAATTCT----------GTTCATGTA 466781 i i ---------- i - C L1MD_orf2#LIN 2355 GTAGTTTTCAGCATACAAGTCC-TGTA 2330 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.61 CpG sites = 81, Kimura (unadjusted) = 42.42 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.05 (3 / 62), avg. gap size = 5.00 (15 / 3) 44 0.00 0.00 0.00 chr4ptel1M 466782 466819 (533181) (GT)n#Simple_repeat 1 38 (0) c_b175s251i3 6843 chr4ptel1M 466782 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 466819 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 38 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 263 31.46 10.46 3.05 chr4ptel1M 466820 467214 (532786) C L1MD_orf2#LINE/L1 (965) 2329 1915 m_b175s551i4 6842 chr4ptel1M 466820 TCGTGGTGCCAGGTAGATTCCCAAATATTT-ATACTGTTTCTAGATATTT 466868 vi vv ii i vv v i i - vi v iv vv v C L1MD_orf2#LIN 2329 ATGTTTTGTTAGATTTATACCTAAGTATTTCATTTTTTTTTGAGCGATTG 2280 chr4ptel1M 466869 TAA-TAGAATT-TATTTCTTCCTCCTCGATTT-----TGTTCAC----AA 466907 - i v - i vvi -- i ----- i---- i C L1MD_orf2#LIN 2279 TAAATGGTATTGTATTTTTAATT--TCGGTTTCCACGTGTTCATTGCTAG 2232 chr4ptel1M 466908 TATACAGAAATGGTGATGATTGGCGTGGGTTTATTTTATATACTGCCACT 466957 i ivviv vvi iv ? i i v v i C L1MD_orf2#LIN 2231 TATATAGAAATACAATTGATTTTTGTATGTTNATCTTGTATCCTGCGACC 2182 chr4ptel1M 466958 TTGCTGAAGTTGCCAATTGTTTCAATTAGTTTTTTTTTTAGTTGACTC-- 467005 v ii iv iv v vv ---- v i -- C L1MD_orf2#LIN 2181 TTGCTGAACTCACTTATTAGTTCTAGGAGTTTTTTT----GTAGATTCCT 2136 chr4ptel1M 467006 TAATGTTCTCTAGGGCAACTATCATATCACCTGTAAAAAGTG--AGTTTT 467053 iivi i v vvi v i i i v v -- C L1MD_orf2#LIN 2135 TGGGATTTTCTACGTAGACAATCATGTCATCTGCAAATAGGGACAGTTTT 2086 chr4ptel1M 467054 CTGTCCTC--TTC--ATCTGTTCAT-TCTTTCATGT-TTGTTCTTGTCTT 467097 v v i -- -- -- -i i v -i v i C L1MD_orf2#LIN 2085 ATTTCTTCCTTTCCAATCTGT--ATGCCTTTTATTTCCTTTTCTTGCCTT 2038 chr4ptel1M 467098 ATTGTTACTTATTGCTTA----TTTTACTGCAATATCAAAT---AGTAAT 467140 -----i i vi ---- ii v i v i ii --- ii C L1MD_orf2#LIN 2037 ATTG-----CACTGGCTAGAACTTCCAGTACTATGTTGAATAAGAGTGGT 1993 chr4ptel1M 467141 TATATCAGACATCCTTATTTCACCTTCTTTCTTCAAACAAAAAGC-TTTT 467189 v v v i iii iiiiii vv - iivii - iv C L1MD_orf2#LIN 1992 GAGAGCGGACATCCTTGCCTTGTTCCCGATCTT-AGGGGGAAAGCATTCA 1944 chr4ptel1M 467190 GTCCTT-ATCAT---GTATAATGCTTGCT 467214 i - i --- i i v C L1MD_orf2#LIN 1943 GTCTTTCACCATTAAGTATGATGTTAGCT 1915 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.61 CpG sites = 81, Kimura (unadjusted) = 42.42 Transitions / transversions = 1.35 (70/52) Gap_init rate = 0.08 (30 / 394), avg. gap size = 1.60 (48 / 30) 545 28.78 6.39 1.22 chr4ptel1M 467400 467712 (532288) C L1M4_orf2#LINE/L1 (1444) 1850 1522 m_b175s551i5 6844 chr4ptel1M 467400 AATGCTTTTA--ATAATAGG-TAGTGTATTTTGTCAAAAGCCTATTCAGC 467446 i i -- i v - iv v v i v v C L1M4_orf2#LIN 1850 AGTGTTTTTATCATGAAAGGGTGTTGGATTTTGTCAAATGCTTTTTCTGC 1801 chr4ptel1M 467447 TTCCATTGAAATAATCATGTGATTTT-----TTTGGATTATTGATGTGGT 467491 v i i i i ----- ivvi i i C L1M4_orf2#LIN 1800 GTCTATTGAGATGATCATGTGGTTTTTGTCCTTTATTCTATTAATATGGT 1751 chr4ptel1M 467492 CAGTTATGTTAATAGTTTTCCTAATACTGAATCAACCATATATTTGTGGT 467541 vvi ii i v v i v? ii i v ii iv v C L1M4_orf2#LIN 1750 GTATTACATTGATTGATTTTCGNATGTTGAACCAACCTTGCATTCCTGGG 1701 chr4ptel1M 467542 ACAAAATCCAACTTTTTCAT-GTGTATGAT-CTTCTGATAAATTTCTATA 467589 i- v vv - i - i v vi v iv C L1M4_orf2#LIN 1700 AT-AAATCCCACTTGGTCATGGTGTATAATCCTTTTTATATGTTGCTGGA 1652 chr4ptel1M 467590 ACC---TTGCC--TGTTTT-TTAAATTTTTTTGCATCAATAGTCATTAGG 467633 vi --- i-- i - i ivv v v v C L1M4_orf2#LIN 1651 TTCGGTTTGCTAGTATTTTGTTGAGGATTTTTGCATCTATATTCATAAGG 1602 chr4ptel1M 467634 AAAACTTGGATTATAGATTTCTTTCTGCTT----TGGCTCTCCCGGGCTT 467679 i v - vi i v i-- ---- v i vi v i C L1M4_orf2#LIN 1601 GATA-TTGGTCTGTAGTTTTCTTTT--CTTGTGATGTCTTTGTCTGGTTT 1555 chr4ptel1M 467680 AGGTGTCATGATCATATTTGTATCAAAGGAGGA 467712 v i v i v i v iv v i v C L1M4_orf2#LIN 1554 TGGTATCAGGGTAATACTGGCCTCATAGAATGA 1522 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.03 CpG sites = 46, Kimura (unadjusted) = 37.03 Transitions / transversions = 1.07 (46/43) Gap_init rate = 0.04 (13 / 312), avg. gap size = 1.85 (24 / 13) 12 26.38 6.78 0.00 chr4ptel1M 467892 467950 (532050) (TATA)n#Simple_repeat 1 63 (0) m_b175s252i8 6845 chr4ptel1M 467892 TATAGATATGTATACATATAT-TGTATTTA-ACATATAGTTTTA-ACATA 467938 v i i - i v - i vv v - i (TATA)n#Simpl 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr4ptel1M 467939 TTTA-ACATGTAT 467950 v - i i (TATA)n#Simpl 51 TATATATATATAT 63 Matrix = Unknown Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.07 (4 / 58), avg. gap size = 1.00 (4 / 4) 349 25.93 1.23 0.00 chr4ptel1M 468143 468223 (531777) MIRb#SINE/MIR 35 116 (152) m_b175s601i14 6846 chr4ptel1M 468143 GGCCCTGGAGTCAGAAGGACCTGAATTCAAATATGATCTCAGGCATTT-C 468191 ii vi ii i viviv v v i - MIRb#SINE/MIR 35 GGCTTTGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTAC 84 chr4ptel1M 468192 TAGCTGTGTGACTCGTGGCAACTTATTTAACC 468223 iivv v i MIRb#SINE/MIR 85 TAGCTGTGTGACCTTGGGCAAGTTACTTAACC 116 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.83 CpG sites = 12, Kimura (unadjusted) = 32.45 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.01 (1 / 80), avg. gap size = 1.00 (1 / 1) 26 0.00 0.00 0.00 chr4ptel1M 468234 468258 (531742) (ACA)n#Simple_repeat 1 25 (0) c_b175s251i4 6847 chr4ptel1M 468234 ACAACAACAACAACAACAACAACAA 468258 (ACA)n#Simple 1 ACAACAACAACAACAACAACAACAA 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 14 21.48 1.64 6.90 chr4ptel1M 468475 468535 (531465) (TTTCATT)n#Simple_repeat 1 58 (0) m_b175s252i9 6848 chr4ptel1M 468475 TTTCATTTCTTTATTGGTTGTGAATTTACGCTTTTCATTTTTGATTTTT- 468523 - i -- - v v v ii v - (TTTCATT)n#Si 1 TTTCATTT-TTCATT--TT-TCATTTTTCATTTTTCATTTTTCATTTTTC 46 chr4ptel1M 468524 TTTTTCCAATTT 468535 v i v (TTTCATT)n#Si 47 ATTTTTCATTTT 58 Matrix = Unknown Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.08 (5 / 60), avg. gap size = 1.00 (5 / 5) 23 9.78 0.00 0.00 chr4ptel1M 470518 470550 (529450) (T)n#Simple_repeat 1 33 (0) m_b175s252i10 6849 chr4ptel1M 470518 TTTTTTTTTTTTTTTTTTTTTTTTGCTCTTTTT 470550 vi i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 33 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 13 18.86 2.63 2.63 chr4ptel1M 471667 471704 (528296) (ATC)n#Simple_repeat 1 38 (0) m_b175s252i11 6850 chr4ptel1M 471667 ATCATTATCATCATCATCAATAATAATTAACACCA-CAT 471704 i - v v i v i - (ATC)n#Simple 1 ATCATCATCATCATCATC-ATCATCATCATCATCATCAT 38 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 12 22.59 0.00 2.70 chr4ptel1M 472204 472241 (527759) (AATTGTT)n#Simple_repeat 1 37 (0) m_b175s252i12 6851 chr4ptel1M 472204 AATTGTTTTATGCTATTTGTTTATTGTTAATCTGTAAA 472241 vvv i v v - v (AATTGTT)n#Si 1 AATTGTTAATTGTTAATTGTTAATTGTTAAT-TGTTAA 37 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 16 19.56 0.00 0.00 chr4ptel1M 474457 474486 (525514) (TA)n#Simple_repeat 1 30 (0) m_b175s252i13 6852 chr4ptel1M 474457 TATATATGTGTATATGTGTATATTTATATA 474486 i i i i v (TA)n#Simple_ 1 TATATATATATATATATATATATATATATA 30 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 203 18.35 20.51 2.17 chr4ptel1M 477684 477761 (522239) C MIRc#SINE/MIR (155) 113 22 m_b175s601i15 6853 chr4ptel1M 477684 GGTTAAGGGACTTGGCCATGGTTAACCAGGCTAAT--GTGTCAGGGGCAG 477731 v v v i vv - i -- v i v i C MIRc#SINE/MIR 113 GGTTAAGTGACTTGCCCAAGGTCACACA-GCTAGTAAGTGGCAGAGCCGG 65 chr4ptel1M 477732 A----------AGGTCTTCCT-ATTCCAAG---AATGACTCTTT 477761 i---------- - i --- i - C MIRc#SINE/MIR 64 GACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTG-CTCTTT 22 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 19.65 CpG sites = 7, Kimura (unadjusted) = 21.26 Transitions / transversions = 1.00 (7/7) Gap_init rate = 0.08 (6 / 77), avg. gap size = 3.00 (18 / 6) 404 17.02 3.09 3.09 chr4ptel1M 479113 479209 (520791) Charlie4a#DNA/hAT-Charlie 377 473 (35) m_b175s502i2 6854 chr4ptel1M 479113 ATATAATTGGCTTCCTTTGTAATCCTCTGTATTTTTCTTTAT--ATTTAA 479160 i v vi -- Charlie4a#DNA 377 ATATAATTGGTTTCCTTTGTAATCCTATGTATTTTATTTTATGCATTTAA 426 chr4ptel1M 479161 AACCATGACTCCATGAAGTGCTCTA-AGCCTTCTCTAGACCACTGCCAAA 479209 v v i iiv v v i - v v i --- Charlie4a#DNA 427 AAACATTATTCTGAGAAGGGGTCCATAGGCTTCACCAG---ACTGCCAAA 473 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 19.34 CpG sites = 7, Kimura (unadjusted) = 19.34 Transitions / transversions = 0.78 (7/9) Gap_init rate = 0.05 (5 / 96), avg. gap size = 1.20 (6 / 5) 570 32.49 0.00 2.60 chr4ptel1M 479337 479494 (520506) C L3#LINE/CR1 (121) 3978 3825 m_b175s601i16 6855 chr4ptel1M 479337 AAGACCTCTAGTGACAAGGAACTCCTCAGCTTTTGGGACAGCTTATTTCA 479386 v i ii i vii v i?i i i ii i C L3#LINE/CR1 3978 AACACCTCCAGTGACGGGGAGCTCACTACCTCNCGAGGCAGCCCATTCCA 3929 chr4ptel1M 479387 TTTTGGAACAACTCTAAATGTGAAGGCAGTTTTCTTTTATCCTGAGCTGA 479436 v i i i v v- iv i iii vi i C L3#LINE/CR1 3928 TTTTTGGACAGCTCTGATTGTT-AGAAAGTTCTTCCTTATATTGAGCCGA 3880 chr4ptel1M 479437 AATCCATCTCCCTTTAGCTTTTCTCCACTGGTTCCAGCTCTATTTTTAAT 479486 iii v i iivi i i i i iiii ---i C L3#LINE/CR1 3879 AATCTGCCTCCCTGTAACTTCCACCCATTGGTCCTAGTTCTGCCCT---C 3833 chr4ptel1M 479487 TGGAGTCA 479494 i C L3#LINE/CR1 3832 TGGAGCCA 3825 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 43.76 CpG sites = 40, Kimura (unadjusted) = 47.87 Transitions / transversions = 4.00 (40/10) Gap_init rate = 0.03 (4 / 157), avg. gap size = 1.00 (4 / 4) 209 26.50 0.00 5.66 chr4ptel1M 480629 480684 (519316) C MIRc#SINE/MIR (212) 56 4 m_b175s601i17 6856 chr4ptel1M 480629 CTCAAGTTTTCCTGACTCCAAGTCTGATGCTCTAATAACTACTCCATCTA 480678 i i i iii vviv i v i--- C MIRc#SINE/MIR 56 CCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC--- 10 chr4ptel1M 480679 GCTGCC 480684 i C MIRc#SINE/MIR 9 ACTGCC 4 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.24 CpG sites = 10, Kimura (unadjusted) = 34.24 Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.05 (3 / 55), avg. gap size = 1.00 (3 / 3) 304 29.15 1.87 3.81 chr4ptel1M 481896 482002 (517998) C MIRc#SINE/MIR (153) 115 11 m_b176s601i1 6857 chr4ptel1M 481896 GGGGTTAAATGACTTGCCAAGGGTCACAACAG--AGTGTCACATATCTGA 481943 i i v i - -- --- vi iv v C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACA-CAGCTAGT---AAGTGGCAGA 70 chr4ptel1M 481944 GGTTGAATTTGAACGCAGGCCCTCCCGACTCCAGGACTGGTGTTCCATAC 481993 viv i i i v i i i i v ii i iv v C MIRc#SINE/MIR 69 GCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCC 20 chr4ptel1M 481994 ACTGTGTCA 482002 iii C MIRc#SINE/MIR 19 ACTGCACCA 11 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 35.33 CpG sites = 20, Kimura (unadjusted) = 38.62 Transitions / transversions = 2.00 (20/10) Gap_init rate = 0.05 (5 / 106), avg. gap size = 1.20 (6 / 5) 231 27.65 6.32 1.00 chr4ptel1M 482480 482574 (517426) C MIR3#SINE/MIR (95) 113 14 m_b176s601i4 6858 chr4ptel1M 482480 AGAATTTAAGCAACTTGCCCA-GGTCTTGGAGGCAGTAAGTAGCAGAG-- 482526 iv v ii - viiv v? v i -- C MIR3#SINE/MIR 113 AGAGGTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCC 64 chr4ptel1M 482527 --GACTTGG-CCTAGGTCTTCTGTCCACTAAACCATGCTGTCATCTCCTT 482573 -- v i- i i v iv i iv i v - v i C MIR3#SINE/MIR 63 GGGACTAGAACCCAGGTCTCCTGACTCCCAGTCCGTGCTCTC-TCTGCTC 15 chr4ptel1M 482574 A 482574 C MIR3#SINE/MIR 14 A 14 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.91 CpG sites = 14, Kimura (unadjusted) = 35.58 Transitions / transversions = 1.17 (14/12) Gap_init rate = 0.05 (5 / 94), avg. gap size = 1.40 (7 / 5) 235 21.93 10.84 1.10 chr4ptel1M 482480 482562 (517438) C MIRb#SINE/MIR (149) 119 29 m_b176s601i3 6858 chr4ptel1M 482480 AGAATTTAAGCAACTTGCCC-AGGTCTTGGAGGCAGTAAGTAGCAGA--- 482525 iv i - viiv vi i --- C MIRb#SINE/MIR 119 AGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCC 70 chr4ptel1M 482526 -GGACTTG-GCCTAGGTCT-TCTGTCCACTAAA--CCATGCT 482562 - i i -i i - v i- i -- i C MIRb#SINE/MIR 69 GGGATTCGAACCCAGGTCTGTCTGACT-CCAAAGCCCGTGCT 29 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 23.59 CpG sites = 13, Kimura (unadjusted) = 27.00 Transitions / transversions = 2.60 (13/5) Gap_init rate = 0.09 (7 / 82), avg. gap size = 1.43 (10 / 7) 237 21.54 9.23 0.00 chr4ptel1M 482480 482544 (517456) C MIRc#SINE/MIR (152) 116 46 m_b176s601i2 6858 chr4ptel1M 482480 AGAATTTAAGCAACTTGCCC-AGGTCTTGGAGGCAGTAAGTAGCAGA--- 482525 iv ii - viiv vi i --- C MIRc#SINE/MIR 116 AGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCC 67 chr4ptel1M 482526 -GGACTTG-GCCTAGGTCTTC 482544 - i -i i C MIRc#SINE/MIR 66 GGGACTCGAACCCAGGTCTTC 46 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 24.18 CpG sites = 10, Kimura (unadjusted) = 26.32 Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.06 (4 / 64), avg. gap size = 1.50 (6 / 4) 15 15.90 0.00 5.41 chr4ptel1M 484537 484575 (515425) (CCTC)n#Simple_repeat 1 37 (0) m_b176s252i0 6859 chr4ptel1M 484537 CCTCCCTGCTTTGCTCCCTCCCTCCCTCCGGCTCCTTCC 484575 v i iv -- i (CCTC)n#Simpl 1 CCTCCCTCCCTCCCTCCCTCCCTCCCTCC--CTCCCTCC 37 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2) 191 18.80 9.59 5.26 chr4ptel1M 485723 485795 (514205) MIR3#SINE/MIR 112 187 (21) m_b176s601i5 6860 chr4ptel1M 485723 CTCTGGGCCT--GT---CTCATCTGTAGGAGGTTGAAGGTTGGACTCAAT 485767 -- --- ii v v- ii vi MIR3#SINE/MIR 112 CTCTGGGCCTCAGTTTCCTCATCTGTAAAATGA-GGGGGTTGGACTAGAT 160 chr4ptel1M 485768 --TCCCCAATCATGTCCCTGCCAGCTCTAA 485795 -- i i v--- v i MIR3#SINE/MIR 161 GATCTCTAAG---GTCCCTTCCAGCTCTGA 187 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 22.06 CpG sites = 8, Kimura (unadjusted) = 22.06 Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.10 (7 / 72), avg. gap size = 1.57 (11 / 7) 395 27.87 13.40 2.16 chr4ptel1M 487103 487311 (512689) MIRb#SINE/MIR 4 235 (33) m_b176s601i6 6861 chr4ptel1M 487103 AGAGGTAGTTAAGTGGCTCAGTGGATAGAGCAATGGGCCT-GGTGTCAGG 487151 i i i--- iv v -i i - v i MIRb#SINE/MIR 4 AGGGGCAGC---GTGGTGCAGTGGAAAGAGCA-CGGGCTTTGGAGTCAGA 49 chr4ptel1M 487152 AAGATCTGAGTTCAAGTTT-GACTT---CAGATATATAGCTTTGT-ATCT 487196 v i i i i ii- i i--- vv i- v - i MIRb#SINE/MIR 50 CAGACCTGGGTTCGAATCCCGGCTCTGCCACTTAC-TAGCTGTGTGACCT 98 chr4ptel1M 487197 TGAACATGTCACTT------------CATCCGTTTCCTCAATTCAAAAAA 487234 ii v i ------------ v v vi vv v MIRb#SINE/MIR 99 TGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAAT 148 chr4ptel1M 487235 AGAGATAA-GTCATCTCCCTC------CTATTAGGTGGATCAAATGAGAT 487277 i i -ivi i v ------i i iv v i MIRb#SINE/MIR 149 GGGGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGAT 198 chr4ptel1M 487278 AAT---TGTAAAATGTTTAGTCTAGTGTGTGGCAAAT 487311 --- ii i ivi iv v MIRb#SINE/MIR 199 AATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACAT 235 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.05 CpG sites = 36, Kimura (unadjusted) = 36.19 Transitions / transversions = 1.71 (36/21) Gap_init rate = 0.06 (13 / 208), avg. gap size = 2.54 (33 / 13) 267 32.01 4.52 1.25 chr4ptel1M 487626 487780 (512220) L2d2_3end#LINE/L2 89 248 (307) m_b176s601i7 6862 chr4ptel1M 487626 TCACTACCCTTCCAAATACTTCTCATAGTTTCCCAACTCTGAGCTTTTGC 487675 ii i- i i vi iiiiv? iv v i L2d2_3end#LIN 89 TCACTGTCCC-CCGAACACGCCTTGCGCNTTCCCGCCTCTGCGCCTTTGC 137 chr4ptel1M 487676 TCACATCATTGCCTCCTCCTAGAATTGTTCATCTCAATAGATACTA-CTA 487724 ii i v i v i - ii v i vv vvviv i - L2d2_3end#LIN 138 TCACGCCGTTCCCCCCGCCTGGAA-TGCCCTTCCCCTTCCTCTCCACCTA 186 chr4ptel1M 487725 T---AATTCTTTTCTTGCTTCAAGGTCCATCTCAGATGACACCT-TTCCC 487770 --- i vii v v i v i ?v -i v L2d2_3end#LIN 187 TCCAAATCCTACCCATCCTTCAAGGCCCAGCTCAAATNCCACCTCCTCCG 236 chr4ptel1M 487771 TG--GTCTTCTC 487780 -- i i L2d2_3end#LIN 237 TGAAGCCTTCCC 248 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 38.27 CpG sites = 30, Kimura (unadjusted) = 44.28 Transitions / transversions = 1.58 (30/19) Gap_init rate = 0.04 (6 / 154), avg. gap size = 1.50 (9 / 6) 280 33.34 1.41 2.86 chr4ptel1M 487818 487959 (512041) L2d_3end#LINE/L2 361 500 (16) m_b176s601i8 6862 chr4ptel1M 487818 TGTTTTATAGTTATGGGTCTCATTTCCCCCATTAGAGTATACATTCCTTT 487867 i ivv i vi ii i v i v i vii v L2d_3end#LINE 361 TGTTTCATGTGTGTTAGTCTTGTCTCCCCAACTAGATTGTAAGCTCCTTG 410 chr4ptel1M 487868 AAGGCTAGAATTAGGTCTGAT-TTATCTTCTTCTTTACCTCAAAGCTTAG 487916 i vi i ii v v -i ? i ? iv iv v iv i L2d_3end#LINE 411 AGGGCAGGGACCATGTCTTATACTNTTTTNTCGTTCCCCACAGCGCCTAG 460 chr4ptel1M 487917 TAAAGTAGCTT-GCATACAGTAGGTGATAAACATAAAATACATG 487959 i v - v- i i i v v i--- v L2d_3end#LINE 461 CACAGT-GCTGAGCACATAGTAGGCGCTCAAT---AAATACTTG 500 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 43.89 CpG sites = 27, Kimura (unadjusted) = 46.67 Transitions / transversions = 1.42 (27/19) Gap_init rate = 0.04 (6 / 141), avg. gap size = 1.00 (6 / 6) 311 33.62 3.45 0.00 chr4ptel1M 487834 487949 (512051) L2d2_3end#LINE/L2 419 538 (17) m_b176s601i9 6862 chr4ptel1M 487834 GTCTCATTTCCCCCATTAGAGTATACATTCCTTTAAGGCTAGAATTAGGT 487883 ii i v i v i vii v i vi i ii v L2d2_3end#LIN 419 GTCTTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGT 468 chr4ptel1M 487884 CTGATTTATCTTCTTCTTTACCTCAAAGCTTAGTAAAGTAGCTTGCATAC 487933 v viv iv v iiv v iv i i v iv i L2d2_3end#LIN 469 CTTATACTTCTTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCACAC 518 chr4ptel1M 487934 AGTAGGTG----ATAAACAT 487949 i ---- i L2d2_3end#LIN 519 AGTAGGCGCTCAATAAATAT 538 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 44.66 CpG sites = 23, Kimura (unadjusted) = 46.30 Transitions / transversions = 1.44 (23/16) Gap_init rate = 0.01 (1 / 115), avg. gap size = 4.00 (4 / 1) 236 29.68 4.93 7.04 chr4ptel1M 488870 489072 (510928) C L1ME4b_3end#LINE/L1 (234) 658 460 m_b176s551i0 6863 chr4ptel1M 488870 TGCTGTGTACAATGTTCT----CTTGGTTCTACTCATTTCACTTAACATC 488915 i i ii v ---- v i ------ vi C L1ME4b_3end#L 658 TACTATACACACTGTTCTGCACCTTGCTTTT------TTCACTTAACAAT 615 chr4ptel1M 488916 AGTTCATGTA-ATCTTTCCAAGCCTTTCTGAAATCAGCCTGCTCATCATT 488964 vv v v - ? vii vv viiv ?vv i v iv C L1ME4b_3end#L 614 ATATCTTGGAGATCNTTCCATATCAGTACATANAGAGCTTCCTCATTCTT 565 chr4ptel1M 488965 TCTTATGGAACAATAATATTCCATTACATT--TGTA---TAACTTATTCA 489009 i i vvvv i ii v-- --- i i C L1ME4b_3end#L 564 TTTTACGGCTGCATAGTATTCCATTGTATGGATGTACCATAATTTATTTA 515 chr4ptel1M 489010 GCCATTTCCCAACTGATGGACATCCACACATCCACTCAGCTTCCAGTTTC 489059 i v i v i ii vii- ------- i i i i C L1ME4b_3end#L 514 ACCAGTCCCCTATTGATGGACATTTAGGT-T-------GTTTCCAATCTT 473 chr4ptel1M 489060 TTGCCACTACAAA 489072 i i C L1ME4b_3end#L 472 TTGCTATTACAAA 460 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 38.31 CpG sites = 32, Kimura (unadjusted) = 39.22 Transitions / transversions = 1.33 (32/24) Gap_init rate = 0.09 (18 / 202), avg. gap size = 1.33 (24 / 18) 245 23.85 7.25 2.78 chr4ptel1M 488895 489032 (510968) C L1ME4a_3end#LINE/L1 (233) 638 495 m_b176s551i1 6863 chr4ptel1M 488895 CTACTCATTTCACTTAACATCAGTTCATGTA-ATCTTTCCAAGCCTTTCT 488943 i iv i vv vi- i i v i v -- C L1ME4a_3end#L 638 CTGCTTTTTTCACTTAACATTATATCATGAGCATTTTCCCATGTCATT-- 591 chr4ptel1M 488944 GAAATCAGCCTGCT----CATCATTTCTTATGGAACAATAATATTCCATT 488989 - - vi v v---- ? i v vvvv C L1ME4a_3end#L 590 -AAAT-ATTCTTCGAAAACATNATTTTTAATGGCTGCATAATATTCCATT 543 chr4ptel1M 488990 ACATT--TGT---ATAACTTATTCAGCCATTTCCCAACTGATGGACAT 489032 ?i v-- --- i i i ? i v i v C L1ME4a_3end#L 542 NTATGGATGTACCATAATTTATTTAACCANTCCCCTATTGTTGGACAT 495 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 29.73 CpG sites = 15, Kimura (unadjusted) = 29.73 Transitions / transversions = 0.88 (15/17) Gap_init rate = 0.06 (8 / 137), avg. gap size = 1.75 (14 / 8) 593 31.10 5.46 5.92 chr4ptel1M 489273 489730 (510270) L3#LINE/CR1 3302 3757 (342) m_b176s601i10 6864 chr4ptel1M 489273 TGGGCTGAATCTAGTAAGATGAAATTCAATAGGAATAAAAGTAATGTCTC 489322 i v i ii i i i v v ii L3#LINE/CR1 3302 TGGGCCGAAACCAACAAGATGAAATTTAACAGGGATAAATGTAAAGTCCT 3351 chr4ptel1M 489323 ACTCTAAGGTTTCAAAAATTCAATT-TGCAACTATAAGTTGGGGGAAGAA 489371 i vi v - v i -ii v i i v i -- i L3#LINE/CR1 3352 GCATTTAGG-TTCAAAAAATCAACTGCACAAGTACAGGATGGAG--AGGA 3398 chr4ptel1M 489372 --TGGCTGGTGAGCAGTTT-TGATTAAAAAATATCAAAGGATCTTAGTAA 489418 -- vivv i-i -- i v i v i i i vi L3#LINE/CR1 3399 TCTGGCTTAGCAGCAGTTCACG--TGAAAAAGACCTAGGGGTTTTAGTTG 3446 chr4ptel1M 489419 CCTGAAACTTCCCTTTAGGTCATTAA-GTGATAGGTCAGTCAAAGAAGCT 489467 v i v vi vv v ii i vi i- iv v v i i L3#LINE/CR1 3447 ACCGCAAGCTCAATATGAGCCAACAGTGTGATGTGGCTGCCAAAAAAGCT 3496 chr4ptel1M 489468 GATTGATGTCTTAGGCTTCAATGACAGAGTTCTGAC-TCTCAAGCACAGG 489516 i vv -i v v i i iv v iii- ivi ? - L3#LINE/CR1 3497 AATGCA-ATCTTAGGCTGCATTAATAGAAGTATAGTGTCCAGANCA-AGG 3544 chr4ptel1M 489517 AAGGTGACAGTCCTTCTGGTA-TCTGCCCTAATTAAAAAAAAAAAAAAAA 489565 i i i iv - - v ii i--------- i vv v L3#LINE/CR1 3545 GAGGTAATAGTCCCGCT-GTACTCTGCGCTGGTC---------AGACCAC 3584 chr4ptel1M 489566 ATCTCCAGTATTATGATCATTTCTGGGCCCTGACTGAAGTTT-ACAGAGA 489614 vv ii v v v i- --- v - v i L3#LINE/CR1 3585 ATCTGGAGTATTGCGTTCAGTTCTGGGCGCC-AC---ATTTTAAGAGGGA 3630 chr4ptel1M 489615 CCTCTGATAAACTGGGAATCATCCAGAATCAGAGTG-CAAAG--GGTGAA 489661 v - i iivv i i-v i - v i -- L3#LINE/CR1 3631 CAT-TGACAAACTGGAGCGCGTCCAGAG-GAGAGCGACCAGGATGGTGAA 3678 chr4ptel1M 489662 AGGGCTATGAGAAC---------TGAAGAAGAACTG--GGAACCCTGGGT 489700 i v -- ii --------- i viii -- -- v L3#LINE/CR1 3679 GGGTC--TGGAAACCATGTCATATGAGGAACGGTTGAAGGAA--CTGGGG 3724 chr4ptel1M 489701 AGA---AACCAGTAGGAGAGAAGCTTCAGGGGA 489730 vi--- i v v i vi i i L3#LINE/CR1 3725 ATGTTTAGCCTGGAGAAGAGAAGACTTAGAGGA 3757 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 38.37 CpG sites = 79, Kimura (unadjusted) = 41.58 Transitions / transversions = 1.44 (79/55) Gap_init rate = 0.09 (39 / 457), avg. gap size = 1.33 (52 / 39) 17 0.00 0.00 0.00 chr4ptel1M 490320 490338 (509662) (A)n#Simple_repeat 1 19 (0) m_b176s252i1 6865 chr4ptel1M 490320 AAAAAAAAAAAAAAAAAAA 490338 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAA 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 275 16.87 22.89 0.00 chr4ptel1M 491241 491323 (508677) C MIR#SINE/MIR (84) 178 77 m_b176s601i11 6866 chr4ptel1M 491241 ACAACAATCCTGAGAGGTAGGTGCTACTATGATCCCCATTT--CAGA--- 491285 i iv i i v -- --- C MIR#SINE/MIR 178 ACAACAACCCTATGAGGTAGGTACTATTATTATCCCCATTTTACAGATGA 129 chr4ptel1M 491286 --------ATGGATA---AGGTT---TGACCCGCCCAAGGTCACACAGTC 491321 -------- v v i --- --- i ii ii C MIR#SINE/MIR 128 GGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCT 79 chr4ptel1M 491322 AG 491323 C MIR#SINE/MIR 78 AG 77 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 19.60 CpG sites = 10, Kimura (unadjusted) = 19.60 Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.06 (5 / 82), avg. gap size = 3.80 (19 / 5) 232 25.92 3.61 2.38 chr4ptel1M 491418 491500 (508500) MIR#SINE/MIR 120 203 (59) m_b176s601i12 6867 chr4ptel1M 491418 TCGGTCTCTTCACCTGTAGAATGGAGACAATAGATGCCCCTACCACACCT 491467 i i i i i i i ivv iv v -- MIR#SINE/MIR 120 TCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTCA--T 167 chr4ptel1M 491468 TGAG-TGTT-TTAAGATCAAATAAGTTAGC-CATGT 491500 v i - - v i i i ii- MIR#SINE/MIR 168 AGGGTTGTTGTGAGGATTAAATGAGTTAATACATGT 203 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.40 CpG sites = 15, Kimura (unadjusted) = 33.40 Transitions / transversions = 2.50 (15/6) Gap_init rate = 0.06 (5 / 82), avg. gap size = 1.00 (5 / 5) 15 13.48 3.03 0.00 chr4ptel1M 493266 493298 (506702) (TTTCTC)n#Simple_repeat 1 34 (0) m_b176s252i2 6868 chr4ptel1M 493266 TTTCTC-TCATCTTTCTCTTTTTCTTTCTCTCTC 493298 - iv i i (TTTCTC)n#Sim 1 TTTCTCTTTCTCTTTCTCTTTCTCTTTCTCTTTC 34 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 16 16.04 0.00 3.33 chr4ptel1M 493268 493298 (506702) (TC)n#Simple_repeat 1 30 (0) m_b176s252i3 6868 chr4ptel1M 493268 TCTCTCATCTTTCTCTTTTTCTTTCTCTCTC 493298 - i i i i (TC)n#Simple_ 1 TCTCTC-TCTCTCTCTCTCTCTCTCTCTCTC 30 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.03 (1 / 30), avg. gap size = 1.00 (1 / 1) 215 30.36 7.81 2.22 chr4ptel1M 493618 493745 (506255) L2d_3end#LINE/L2 382 516 (0) m_b176s601i14 6869 chr4ptel1M 493618 GTTTCCTTAAC-AGAGTGTAAAC-CCTCAATG-CAGAGATGGGGTGACTT 493664 i ii - v i - ii v - i iviv -- L2d_3end#LINE 382 GTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGT--CTT 429 chr4ptel1M 493665 GAACT---TTGTCTCTCCTT----CACCTAGCACAGCGTCTGGAACATAT 493707 iv --- ? vi ii---- i i iivi v v L2d_3end#LINE 430 ATACTNTTTTNTCGTTCCCCACAGCGCCTAGCACAGTGCTGAGCACATAG 479 chr4ptel1M 493708 CATGCATTTAATAAAAGCTTGGAGGATTGCTTCATTGA 493745 i v ii i vi v-v v v L2d_3end#LINE 480 TAGGCGCTCAATAAATACTTGT-TGATTGATTGATTGA 516 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 38.00 CpG sites = 23, Kimura (unadjusted) = 40.78 Transitions / transversions = 1.53 (23/15) Gap_init rate = 0.06 (8 / 127), avg. gap size = 1.62 (13 / 8) 218 29.09 8.57 1.79 chr4ptel1M 493618 493722 (506278) L2d2_3end#LINE/L2 424 535 (20) m_b176s601i13 6869 chr4ptel1M 493618 GTTTCCTTAAC-AGAGTGTAAAC-CCTCAATG-CAGAGATGGGGTGACTT 493664 i ii - v i - ii v - i iviv -- L2d2_3end#LIN 424 GTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGT--CTT 471 chr4ptel1M 493665 GAACTT---TGTCTCTCCTTCA---CCTAGCACAGCGTCTGGAACATATC 493708 iv --- v i iv --- i i v v i vi L2d2_3end#LIN 472 ATACTTCTTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAGT 521 chr4ptel1M 493709 ATGCATTTAATAAA 493722 v ii i L2d2_3end#LIN 522 AGGCGCTCAATAAA 535 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 36.65 CpG sites = 19, Kimura (unadjusted) = 38.29 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.07 (7 / 104), avg. gap size = 1.57 (11 / 7) 211 30.53 6.36 1.74 chr4ptel1M 493790 493899 (506101) MIRc#SINE/MIR 89 203 (65) m_b176s601i15 6870 chr4ptel1M 493790 GTGGCCACTGGCAAAACA--TCATCTCTCCAACTGGGAGTTTCCTCACCT 493837 i viv iv -- v i ii vivvv i MIRc#SINE/MIR 89 GTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCT 138 chr4ptel1M 493838 GTAACGCGG-----ACAATGCCTGCAGCACCTAGCAGACAAGGTTTTTGG 493882 vii ----- i i vvii v vv i v v MIRc#SINE/MIR 139 GTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGT 188 chr4ptel1M 493883 GAAGATCTAACTTGAGA 493899 i v -- MIRc#SINE/MIR 189 GAGGATCAAA--TGAGA 203 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 39.68 CpG sites = 16, Kimura (unadjusted) = 39.68 Transitions / transversions = 0.94 (16/17) Gap_init rate = 0.04 (4 / 109), avg. gap size = 2.25 (9 / 4) 12 12.46 2.33 10.00 chr4ptel1M 494623 494665 (505335) (TTTTC)n#Simple_repeat 1 40 (0) m_b176s252i4 6871 chr4ptel1M 494623 TTTTCCTTTCTTTGTCTTATCACATTTTC-TTTCCCTTCTTTTC 494665 i - - -v - - ii (TTTTC)n#Simp 1 TTTTCTTTTCTTT-TCTT-T-TC-TTTTCTTTTCTTTTCTTTTC 40 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.12 (5 / 42), avg. gap size = 1.00 (5 / 5) 340 32.84 9.48 0.43 chr4ptel1M 495741 495951 (504049) MIR#SINE/MIR 32 261 (1) m_b176s601i16 6872 chr4ptel1M 495741 TCTGAAGTCCAGATGACCCAAGTTTGAATCTATCCTCAGAGAAGTATTAG 495790 i - ivi iii i ivvv v vv vv i MIR#SINE/MIR 32 TCTGGAG-CCAGACTGCCTGGGTTCGAATCCCGGCTCTGCCACTTACTAG 80 chr4ptel1M 495791 CTGAATGACC----ACAAGTCATT---CCCCTTT-TG-----GCTGCCTC 495827 vi ----i i i --- i i - ----- i v MIR#SINE/MIR 81 CTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTC 130 chr4ptel1M 495828 ATC-ATGAAACGGGGATCCTAATATCCCCTATCTCCCTGGATCATTGGGA 495876 -i i i vv viv i viv i ii v MIR#SINE/MIR 131 ATCTGTAAAATGGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTGA 180 chr4ptel1M 495877 AGACCGAATGAGAT-CTATTTGTCAAGCACTT-----ATTATCTGGCCCA 495920 i iii v -v iv v i ----- v ii v MIR#SINE/MIR 181 GGATTAAATGAGTTAATACATGTAAAGCGCTTAGAACAGTGCCTGGCACA 230 chr4ptel1M 495921 TTGGAGACACGACTTAAGTGTTAGCTGTGAT 495951 v v ii i vvvv i i v MIR#SINE/MIR 231 TAGTAAGCGCTCAATAAATGTTAGCTATTAT 261 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 41.81 CpG sites = 38, Kimura (unadjusted) = 44.37 Transitions / transversions = 1.23 (38/31) Gap_init rate = 0.04 (8 / 210), avg. gap size = 2.62 (21 / 8) 312 24.07 11.67 3.08 chr4ptel1M 496291 496410 (503590) C MIRc#SINE/MIR (62) 206 77 m_b176s601i17 6873 chr4ptel1M 496291 TTACCTAGCACTTGG-CATCACAAAAATC-TGTGAGATGTAC-------- 496330 i -- i i- v v i - i ivi -------- C MIRc#SINE/MIR 206 TTATCT--CATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGG 159 chr4ptel1M 496331 TATTCTCGTCTCCATTTTACAGAAGAGGAGAGTGGG----AGAAAAGTTA 496376 v ii i v i v i ---- i i C MIRc#SINE/MIR 158 TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTA 109 chr4ptel1M 496377 AATGAGCTATCCATGGTCACACAGTAATGGTAAG 496410 i vi ii v i-- i C MIRc#SINE/MIR 108 AGTGACTTGCCCAAGGTCACACAGC--TAGTAAG 77 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 30.41 CpG sites = 20, Kimura (unadjusted) = 30.41 Transitions / transversions = 2.50 (20/8) Gap_init rate = 0.07 (8 / 119), avg. gap size = 2.25 (18 / 8) 356 22.75 6.80 1.85 chr4ptel1M 496308 496410 (503590) C MIR#SINE/MIR (82) 180 73 m_b176s601i18 6873 chr4ptel1M 496308 TCACAAAAATC-TGTGAGAT--GTACTATTCTCGTCTCCATTTTACAGAA 496354 v i - i i -- v ii i v C MIR#SINE/MIR 180 TCACAACAACCCTATGAGGTAGGTACTATTATTATCCCCATTTTACAGAT 131 chr4ptel1M 496355 GAGGAGAGTGGG----AGAAAAGTTAAATGAGCTATCCATGGTCACACAG 496400 i v i ---- i i i i vi ii v C MIR#SINE/MIR 130 GAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAG 81 chr4ptel1M 496401 TAATGGTAAG 496410 i-- i C MIR#SINE/MIR 80 C--TAGTAAG 73 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 28.37 CpG sites = 17, Kimura (unadjusted) = 28.37 Transitions / transversions = 2.83 (17/6) Gap_init rate = 0.05 (5 / 102), avg. gap size = 1.80 (9 / 5) 314 8.05 6.25 3.03 chr4ptel1M 496469 496532 (503468) MIR3#SINE/MIR 79 144 (64) m_b176s601i19 6874 chr4ptel1M 496469 TAGCTGGATGACCT-GGGCCAGTCACTTCCCCT---TGGCTGCCTCAGTT 496514 ? vi - v v --- -- MIR3#SINE/MIR 79 TNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGG--GCCTCAGTT 126 chr4ptel1M 496515 TCCTCATCTGCAAAATGA 496532 i MIR3#SINE/MIR 127 TCCTCATCTGTAAAATGA 144 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 8.68 CpG sites = 2, Kimura (unadjusted) = 8.68 Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.06 (4 / 63), avg. gap size = 1.50 (6 / 4) 21 0.00 0.00 0.00 chr4ptel1M 497312 497334 (502666) (A)n#Simple_repeat 1 23 (0) m_b176s252i5 6875 chr4ptel1M 497312 AAAAAAAAAAAAAAAAAAAAAAA 497334 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAA 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 260 29.20 4.39 0.85 chr4ptel1M 498469 498582 (501418) MIR3#SINE/MIR 75 192 (16) m_b176s601i20 6876 chr4ptel1M 498469 TAGCTGGCTGAGTAAC--TAGGTAAGTCA-TCAACCTCTCTGGGATTCAG 498515 i ? v i -- i i - iv vi MIR3#SINE/MIR 75 TAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAG 124 chr4ptel1M 498516 -TTGCTCCTACAGAAAATCA-GAGATTAGGGTAGAGGACATCTAGAGTAC 498563 - v v viiv v - i i i iv v iv ii v MIR3#SINE/MIR 125 TTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCC 174 chr4ptel1M 498564 CTCTAGAGGCTTAACATTC 498582 - vv vii i MIR3#SINE/MIR 175 CT-TCCAGCTCTGACATTC 192 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 38.18 CpG sites = 18, Kimura (unadjusted) = 38.18 Transitions / transversions = 1.20 (18/15) Gap_init rate = 0.04 (5 / 113), avg. gap size = 1.20 (6 / 5) 672 28.21 2.33 6.94 chr4ptel1M 498912 499212 (500788) L1ME3G_3end#LINE/L1 255 542 (382) m_b176s551i2 6877 chr4ptel1M 498912 GGGAAAACTGGGACACTAATACATTGTGGGTAGAGTTGTAAATTGATCCA 498961 i v v v v i iv i iiv i v L1ME3G_3end#L 255 GGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTACA 304 chr4ptel1M 498962 ACTATTTTGTAGAGCAATTTGGAACTATGCCA--GAGATAGCAAACTACA 499009 i i? v i v v - i --i i -vi v i i L1ME3G_3end#L 305 GCCNTTTTGGAGGGCAATTTGGCAGTAT-CTATTAAAAT-TTAAAATGCG 352 chr4ptel1M 499010 CATGCCCTTTGATCTAGCAGTGTCACTACTGGGCTTGTATCCCAAAGAGA 499059 i i i i vi v ? ?v v i ? i L1ME3G_3end#L 353 CATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAGAAA 402 chr4ptel1M 499060 TATTAAAGGAGGGAAAGGGACCCACATGTGCAAAAGAAAAAA-AAAAAAA 499108 i ---------------- v v i ?iv -iv v i L1ME3G_3end#L 403 TACT----------------CGCACATGTGCACAAGGANGCATGTACAAG 436 chr4ptel1M 499109 AAAGTTCATAGCAGCCCTTCTTTTAGTGGCAAAGAACTGGAAA----TTG 499154 i v v vi vi v i i i i i ----i i L1ME3G_3end#L 437 GATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTA 486 chr4ptel1M 499155 AGTTGGCCTTCAGTTGGAGAATGGCTGAATAAAGTTATGGGATATAAATG 499204 i- v v i v i i i - v vv i L1ME3G_3end#L 487 AA-TGTCCATCAATAGGGGAATGGTTAAATAAA-TTATGGTATATCCATA 534 chr4ptel1M 499205 TTGTGGGA 499212 i i i L1ME3G_3end#L 535 CTATGGAA 542 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.90 CpG sites = 47, Kimura (unadjusted) = 37.08 Transitions / transversions = 1.47 (47/32) Gap_init rate = 0.08 (23 / 300), avg. gap size = 1.17 (27 / 23) 17 13.12 0.00 0.00 chr4ptel1M 499556 499581 (500419) (A)n#Simple_repeat 1 26 (0) m_b176s252i6 6878 chr4ptel1M 499556 AAAAAAAAAAAAAGAAAGAAAGAAAA 499581 i i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAA 26 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 249 28.19 5.00 2.44 chr4ptel1M 501401 501480 (498520) C UCON55#DNA/TcMar-Tigger (110) 82 1 m_b176s502i0 6879 chr4ptel1M 501401 CCTTAGATGGAGTTCAAGACACACCAACCTTATACTAACATCTACCCCAC 501450 i i i iv vi ii vv ii i i i C UCON55#DNA/Tc 82 CCTTGGATGGGGTCCAAGACGGACCCGCCTTATACCGAATTCCGCTCTAT 33 chr4ptel1M 501451 AACTAATACTGTGTT----TAAGATTCAAGTATA 501480 i v -- ---- i i v i C UCON55#DNA/Tc 32 AGCGAATA--GTGTTATAGTGAGGTTCCAGTGTA 1 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 28.87 CpG sites = 16, Kimura (unadjusted) = 37.57 Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.04 (3 / 79), avg. gap size = 2.00 (6 / 3) 256 26.25 10.92 0.76 chr4ptel1M 501628 501746 (498254) L2#LINE/L2 1950 2080 (1002) m_b176s601i21 6880 chr4ptel1M 501628 CAATCTGGCTTCCA--ACCACAATTC-----AAACTGCTCTTTCCCAAGT 501670 v i i--v v i ----- vi v i L2#LINE/L2 1950 CAATCAGGCTTTCGTCCCCACCACTCCACCGAAACTGCTCTTGTCAAGGT 1999 chr4ptel1M 501671 TA-GGATGGTCTCTCTAGTTGCCAAATTAAAAGGTC---TCTTAGTTCTC 501716 i -vi ii ivi- i iv v --- i i L2#LINE/L2 2000 CACCAATGACCTCCAC-GTTGCTAAATCCAATGGTCAATTCTCAGTCCTC 2048 chr4ptel1M 501717 ATCTCAAT--ACTTCTCTGAAGCATCCGACAC 501746 i v -- i ? v v ii L2#LINE/L2 2049 ATCTTACTTGACCTNTCAGCAGCATTTGACAC 2080 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 31.00 CpG sites = 19, Kimura (unadjusted) = 33.61 Transitions / transversions = 1.58 (19/12) Gap_init rate = 0.05 (6 / 118), avg. gap size = 2.33 (14 / 6) 292 25.35 0.00 0.00 chr4ptel1M 502311 502381 (497619) DNM1r#Unknown 2476 2546 (2116) m_b176s502i1 6881 chr4ptel1M 502311 ATATGTATAAGTGTATGTATGTATATATATGTGTGTGTATATATATATAT 502360 ii iv i i i i i i i DNM1r#Unknown 2476 ACGTGTATGTGTGTATATATGTGTGTATATGTGTGTATGTGTGTATATAT 2525 chr4ptel1M 502361 ATATATATACACACACACATA 502381 i i i ii i?i DNM1r#Unknown 2526 GTGTATATATACGTATNTATA 2546 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 30.23 CpG sites = 17, Kimura (unadjusted) = 35.38 Transitions / transversions = 17.00 (17/1) Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0) 262 16.38 6.45 1.54 chr4ptel1M 502332 502393 (497607) C DNM1r#Unknown (2116) 2546 2482 m_b176s502i2 6881 chr4ptel1M 502332 TATATATATGTGTGTGTATATATATATATATATATATACACA----CACA 502377 ? i i i i i i i i i i ---- C DNM1r#Unknown 2546 TATANATACGTATATATACACATATATACACACATACACACATATACACA 2497 chr4ptel1M 502378 CATATATACTACACAT 502393 - C DNM1r#Unknown 2496 CATATATAC-ACACAT 2482 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 18.07 CpG sites = 10, Kimura (unadjusted) = 20.27 Transitions / transversions = 1.00 (10/0) Gap_init rate = 0.03 (2 / 61), avg. gap size = 2.50 (5 / 2) 18 0.00 0.00 0.00 chr4ptel1M 503068 503087 (496913) (A)n#Simple_repeat 1 20 (0) m_b176s252i7 6882 chr4ptel1M 503068 AAAAAAAAAAAAAAAAAAAA 503087 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAA 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 535 30.67 4.64 5.08 chr4ptel1M 503358 503594 (496406) C MIRc#SINE/MIR (6) 262 27 m_b176s601i22 6883 chr4ptel1M 503358 AACACTGCTTGACATTTACATAATACCTTTAAGGTTTGCATAGTGTTTT- 503406 i vi? i v ii ii - vi i v i i - C MIRc#SINE/MIR 262 AATAACNCCTTACATTTGTATAGCAC-TTTACAGTTTACAAAGCGCTTTC 214 chr4ptel1M 503407 ATAGATATGATTTCATTTTACACTCACAACAAGCCTGGGAGGTAAATA-- 503454 i v i v i v iv v v iii -- C MIRc#SINE/MIR 213 ACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGG 164 chr4ptel1M 503455 -C---TGTTATCATTTACAGTATTTACAGATGAAGGTACTAAAG----GA 503496 - --- i i iiv v-- i iv i i ---- C MIRc#SINE/MIR 163 GCAGGTATTATTATCCCCAT--TTTACAGATGAGGAAACTGAGGCTCAGA 116 chr4ptel1M 503497 GATGTTCAATTATTTGTCTAAGACTCAAAGAGTCAAAAAACTTGTAAGCA 503546 v v i v i i i --------- v v i v ii C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAG---------GTCACACAGCTAGTAAGTG 75 chr4ptel1M 503547 TCTAAGGCAAGATTTGAACTCAGATCTTCTTGCCTTTAGGCCCAATGC 503594 v vi v ii i i i i i v ii i i i C MIRc#SINE/MIR 74 GCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGC 27 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 39.34 CpG sites = 46, Kimura (unadjusted) = 41.76 Transitions / transversions = 2.00 (46/23) Gap_init rate = 0.07 (17 / 236), avg. gap size = 1.35 (23 / 17) 16 0.00 0.00 0.00 chr4ptel1M 505525 505542 (494458) (A)n#Simple_repeat 1 18 (0) m_b176s252i8 6884 chr4ptel1M 505525 AAAAAAAAAAAAAAAAAA 505542 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAA 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 12 7.80 3.23 6.67 chr4ptel1M 509329 509359 (490641) (CGAGG)n#Simple_repeat 1 30 (0) m_b176s252i9 6885 chr4ptel1M 509329 CGAGGCGAGGCCCGAGGCGAGGCCCGG-GAGG 509359 -- vv - (CGAGG)n#Simp 1 CGAGGCGAGG--CGAGGCGAGGCGAGGCGAGG 30 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.10 (3 / 30), avg. gap size = 1.00 (3 / 3) 14 20.28 2.38 2.38 chr4ptel1M 509426 509467 (490533) (GCCG)n#Simple_repeat 1 42 (0) m_b176s252i10 6886 chr4ptel1M 509426 GCCTGCCGTCCGGCCTCGCGGCTCGGCCGGCCGG-GGGCCTGC 509467 v v vvv - -v v (GCCG)n#Simpl 1 GCCGGCCGGCCGGCCGGCCGGC-CGGCCGGCCGGCCGGCCGGC 42 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.05 (2 / 41), avg. gap size = 1.00 (2 / 2) 188 21.31 9.84 0.00 chr4ptel1M 510938 510998 (489002) C MIR3#SINE/MIR (52) 156 90 m_b176s601i23 6887 chr4ptel1M 510938 AGTCCAACCCC-TAAGGTTACAAAGAAGCAGACTGAGGCTTAGA----TG 510982 - v vv i vi v i ii ---- C MIR3#SINE/MIR 156 AGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTG 107 chr4ptel1M 510983 AGG-GACTTGCACAAAG 510998 i - v i C MIR3#SINE/MIR 106 AAGTGACTTGCCCAAGG 90 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 25.34 CpG sites = 7, Kimura (unadjusted) = 25.34 Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.05 (3 / 60), avg. gap size = 2.00 (6 / 3) 18 4.55 0.00 0.00 chr4ptel1M 511459 511481 (488519) (TA)n#Simple_repeat 1 23 (0) m_b176s252i11 6888 chr4ptel1M 511459 TATATATATATACATATATATAT 511481 i (TA)n#Simple_ 1 TATATATATATATATATATATAT 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 353 13.11 3.28 0.00 chr4ptel1M 511825 511885 (488115) MIR3#SINE/MIR 83 145 (63) m_b176s601i24 6889 chr4ptel1M 511825 TGTGTGACCCCAGGCAAGTCACTTGACCCATCTG--CCTCAGTTTCCTCA 511872 iii v iv -- MIR3#SINE/MIR 83 TGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCA 132 chr4ptel1M 511873 TCTGTAAAGTAAG 511885 i i MIR3#SINE/MIR 133 TCTGTAAAATGAG 145 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 14.73 CpG sites = 6, Kimura (unadjusted) = 14.73 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.02 (1 / 60), avg. gap size = 2.00 (2 / 1) 354 28.35 14.53 1.49 chr4ptel1M 514181 514359 (485641) C MIRb#SINE/MIR (27) 241 40 m_b176s601i25 6890 chr4ptel1M 514181 CCTGCTACATGGCAGGCTCTATGCTGGCTGCTTTATATATACT---TTAT 514227 i i ii v v i iivi i ii i --- i C MIRb#SINE/MIR 241 CTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACATGCATTATCTCAT 192 chr4ptel1M 514228 TTGGTCCTAGCAAAA-------GAGGTATGGTAT----ATCCCCATTTTA 514266 ii vi v ------- - ---- C MIRb#SINE/MIR 191 TTAATCCTCACAACAACCCTGCGAGGTA-GGTATTATTATCCCCATTTTA 143 chr4ptel1M 514267 CAGCTGGAGAAA--------TAGTGA---TAGGTGAGTGTCCCAGGGTCA 514305 v ii --------i v --- i i v vv i C MIRb#SINE/MIR 142 CAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCA 93 chr4ptel1M 514306 T-CAGGTAGTAAATGTTTAAGGTGTGGGATTCACATTCAAATCTTAATGA 514354 i- v i vivi --vi iv ii ii vvv C MIRb#SINE/MIR 92 CACAGCTAGTAAGTGGCAGAG--CCGGGATTCGAACCCAGGTCTGTCTGA 45 chr4ptel1M 514355 CTCCA 514359 C MIRb#SINE/MIR 44 CTCCA 40 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 34.29 CpG sites = 32, Kimura (unadjusted) = 37.08 Transitions / transversions = 1.78 (32/18) Gap_init rate = 0.05 (9 / 178), avg. gap size = 3.22 (29 / 9) 292 28.81 10.53 1.82 chr4ptel1M 514237 514388 (485612) C MIRc#SINE/MIR (100) 168 4 m_b176s601i26 6890 chr4ptel1M 514237 GCAAAAGAGGTATGGTATATCCCCATTTTACAGCTGGAGAAA-------- 514278 iiiv vi - v ii -------- C MIRc#SINE/MIR 168 GCAGGGCAGGTATTAT-TATCCCCATTTTACAGATGAGGAAACTGAGGCT 120 chr4ptel1M 514279 TAGTGA---TAGGTGAGTGTCCCAGGGTCAT-CAGGTAGTAAATGTTTAA 514324 i v --- i v vv i i- v i vivi C MIRc#SINE/MIR 119 CAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGA 70 chr4ptel1M 514325 GGTGTGGGATTCACATTCAAATCTTAATGACTCC-AGT-CAATATTCATT 514372 --vi i iv ii ii vv - - i ii v C MIRc#SINE/MIR 69 G--CCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTT 22 chr4ptel1M 514373 GTGCT-CCCCA-ACTACC 514388 vii - v - i C MIRc#SINE/MIR 21 CCACTGCACCACACTGCC 4 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 35.37 CpG sites = 26, Kimura (unadjusted) = 37.57 Transitions / transversions = 1.53 (26/17) Gap_init rate = 0.07 (10 / 151), avg. gap size = 1.90 (19 / 10) 13 17.85 4.17 4.17 chr4ptel1M 514882 514929 (485071) (GTGTTTT)n#Simple_repeat 1 48 (0) m_b176s252i12 6891 chr4ptel1M 514882 GTG-TTTGTGATTGTCGTGTTTGGTG-TTTGTGGGGTTTGTTTTCTGTTT 514929 - - - i v - vvv v v (GTGTTTT)n#Si 1 GTGTTTTGTG-TT-TTGTGTTTTGTGTTTTGTGTTTTGTGTTTTGTGTTT 48 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.09 (4 / 47), avg. gap size = 1.00 (4 / 4) 26 22.80 0.00 0.00 chr4ptel1M 515070 515125 (484875) (T)n#Simple_repeat 1 56 (0) m_b176s252i13 6892 chr4ptel1M 515070 TTTTTTTTTTTTTTTTTTTTAGGTCTTGTTTTTAACTTTTCTTTGTTTTT 515119 vvv i v vvi i v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr4ptel1M 515120 TTGTTT 515125 v (T)n#Simple_r 51 TTTTTT 56 Matrix = Unknown Transitions / transversions = 0.38 (3/8) Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0) 21 20.39 0.00 0.00 chr4ptel1M 515888 515927 (484073) (T)n#Simple_repeat 1 40 (0) m_b176s252i14 6893 chr4ptel1M 515888 TTTTTTTTTGTTTTTTGGGGTTTTTTTTGTTTGTTTTTTT 515927 v vvvv v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 40 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 21 29.15 1.16 1.16 chr4ptel1M 515970 516031 (483969) (TTTTTTG)n#Simple_repeat 1 61 (25) m_b176s252i15 6893 chr4ptel1M 515970 TTTTTAGGATATTGTTTGGGGTTGGTGGCTTTTTGTGTTTTTTTTTTTTT 516019 v vv v vvv vv v i - v v (TTTTTTG)n#Si 1 TTTTTTGTTTTTTGTTTTTTGTTTTTTGTTTTTTGT-TTTTTGTTTTTTG 49 chr4ptel1M 516020 TTTTTCGTTTTT 516031 i (TTTTTTG)n#Si 50 TTTTTTGTTTTT 61 Matrix = Unknown Transitions / transversions = 0.17 (2/12) Gap_init rate = 0.02 (1 / 61), avg. gap size = 1.00 (1 / 1) 24 17.54 0.00 0.00 chr4ptel1M 515999 516031 (483969) (T)n#Simple_repeat 1 33 (13) m_b176s252i16 6893 chr4ptel1M 515999 TTTTTGTGTTTTTTTTTTTTTTTTTTCGTTTTT 516031 v v iv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 33 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 44 0.00 0.00 0.00 chr4ptel1M 516032 516069 (483931) (TG)n#Simple_repeat 1 38 (0) c_b176s251i0 6894 chr4ptel1M 516032 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 516069 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 38 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 24 17.54 0.00 0.00 chr4ptel1M 516070 516081 (483919) (T)n#Simple_repeat 34 45 (1) m_b176s252i16 6895 chr4ptel1M 516070 GTTTTAATTTTT 516081 v vv (T)n#Simple_r 34 TTTTTTTTTTTT 45 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 11), avg. gap size = 0.0 (0 / 0) 21 29.15 1.16 1.16 chr4ptel1M 516070 516092 (483908) (TTTTTTG)n#Simple_repeat 62 85 (1) m_b176s252i15 6896 chr4ptel1M 516070 G-TTTTAATTTTTAAATTTTGGTT 516092 - vi viv v (TTTTTTG)n#Si 62 GTTTTTTGTTTTTTGTTTTTTGTT 85 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.05 (1 / 22), avg. gap size = 1.00 (1 / 1) 27 0.00 0.00 0.00 chr4ptel1M 519535 519560 (480440) (G)n#Simple_repeat 1 26 (0) c_b177s251i0 6897 chr4ptel1M 519535 GGGGGGGGGGGGGGGGGGGGGGGGGG 519560 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGG 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 12 17.32 0.00 5.71 chr4ptel1M 519649 519685 (480315) (GGGCCG)n#Simple_repeat 1 35 (0) m_b177s252i0 6898 chr4ptel1M 519649 GGACCAGGACCTGGTGGTCGTGGCCGGGGCCGGGGCC 519685 i i i - - i v (GGGCCG)n#Sim 1 GGGCCGGGGCC-GG-GGCCGGGGCCGGGGCCGGGGCC 35 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 186 23.50 0.00 6.38 chr4ptel1M 521313 521362 (478638) L2#LINE/L2 2298 2344 (738) m_b177s601i0 6899 chr4ptel1M 521313 CAGTCTTGTGGCTTCAGTAGTCACTATCTCTAAGCAGATGATTCTCAGAT 521362 ii i -- i - i v v v i i i L2#LINE/L2 2298 CAGTCTCATGGCTTTA--AAT-ACCATCTATATGCTGATGACTCCCAAAT 2344 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.31 CpG sites = 8, Kimura (unadjusted) = 29.31 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.06 (3 / 49), avg. gap size = 1.00 (3 / 3) 18 31.03 1.59 0.00 chr4ptel1M 521427 521489 (478511) (CTCC)n#Simple_repeat 1 64 (0) m_b177s252i1 6900 chr4ptel1M 521427 CTTCCTCCCTCCCTCCCTCCTTCCTTTCTTCTCGTTCTCTCTTTCCCCCT 521476 i i i i i i vii i ii i (CTCC)n#Simpl 1 CTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCT 50 chr4ptel1M 521477 CCCTTCC-CCCACC 521489 i - v (CTCC)n#Simpl 51 CCCTCCCTCCCTCC 64 Matrix = Unknown Transitions / transversions = 6.50 (13/2) Gap_init rate = 0.02 (1 / 62), avg. gap size = 1.00 (1 / 1) 16 9.55 0.00 0.00 chr4ptel1M 523572 523594 (476406) (A)n#Simple_repeat 1 23 (0) m_b177s252i2 6901 chr4ptel1M 523572 AAAAAAAAAAAAAAGAAAGAAAA 523594 i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAA 23 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 194 21.06 0.00 2.63 chr4ptel1M 524935 524973 (475027) C MIRc#SINE/MIR (151) 117 80 m_b177s601i1 6902 chr4ptel1M 524935 GAGAGTATTGAGTGGCTTTCCTTAAGTCACACAACTAGT 524973 -i i i v iv i i C MIRc#SINE/MIR 117 GAGAG-GTTAAGTGACTTGCCCAAGGTCACACAGCTAGT 80 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 25.76 CpG sites = 6, Kimura (unadjusted) = 25.76 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.03 (1 / 38), avg. gap size = 1.00 (1 / 1) 55 4.94 0.00 0.00 chr4ptel1M 530765 530827 (469173) (T)n#Simple_repeat 1 63 (0) c_b177s251i1 6903 chr4ptel1M 530765 TTTTTTTGTTTCTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 530814 v i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr4ptel1M 530815 TTTTTTTTTTTTT 530827 (T)n#Simple_r 51 TTTTTTTTTTTTT 63 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0) 13 19.79 4.00 4.00 chr4ptel1M 531325 531374 (468626) (TTGTT)n#Simple_repeat 1 50 (0) m_b177s252i3 6904 chr4ptel1M 531325 TTATTTTG-TTTGTTTTGGTTTGGGGGTTGTTTTGGGTT-TTTTTTTTTC 531372 i - - -v vv vv - v v (TTGTT)n#Simp 1 TTGTTTTGTTTTGTTTT-GTTT-TGTTTTGTTTTGTTTTGTTTTGTTTTG 48 chr4ptel1M 531373 TT 531374 (TTGTT)n#Simp 49 TT 50 Matrix = Unknown Transitions / transversions = 0.14 (1/7) Gap_init rate = 0.08 (4 / 49), avg. gap size = 1.00 (4 / 4) 19 24.53 0.00 0.00 chr4ptel1M 531486 531534 (468466) (TTTTT)n#Simple_repeat 1 49 (0) m_b177s252i4 6905 chr4ptel1M 531486 TTTTTTTGTTTTGTTTGGGTTGGGTTTTTTGTTTTTTTGTTTTTTTTTT 531534 v v vvv vvv v v (TTTTT)n#Simp 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 49 Matrix = Unknown Transitions / transversions = 0.00 (0/10) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 15 13.87 0.00 0.00 chr4ptel1M 532700 532723 (467277) (T)n#Simple_repeat 1 24 (0) m_b177s252i5 6906 chr4ptel1M 532700 TTTTTTTGTTGTTTTTTGTTTTTT 532723 v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTT 24 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 18 0.00 0.00 0.00 chr4ptel1M 532937 532956 (467044) (AT)n#Simple_repeat 1 20 (0) m_b177s252i6 6907 chr4ptel1M 532937 ATATATATATATATATATAT 532956 (AT)n#Simple_ 1 ATATATATATATATATATAT 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 15 5.56 0.00 0.00 chr4ptel1M 533773 533791 (466209) (T)n#Simple_repeat 1 19 (0) m_b177s252i7 6908 chr4ptel1M 533773 TTTTTTTTTTTTCTTTTTT 533791 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 18 4.00 0.00 3.70 chr4ptel1M 534974 535001 (464999) (CCT)n#Simple_repeat 1 27 (0) m_b177s252i8 6909 chr4ptel1M 534974 CCTCCTTCCTCTTCCTCCTCCTCCTCCT 535001 - i (CCT)n#Simple 1 CCTCC-TCCTCCTCCTCCTCCTCCTCCT 27 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 13 9.98 5.88 2.86 chr4ptel1M 536016 536049 (463951) (AGGAG)n#Simple_repeat 1 35 (0) m_b177s252i9 6910 chr4ptel1M 536016 AGGACAGG-GAGGAAAGGGAGAGGAGA-GTGAGGAG 536049 v - i - - v (AGGAG)n#Simp 1 AGGAGAGGAGAGGAGA-GGAGAGGAGAGGAGAGGAG 35 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.09 (3 / 33), avg. gap size = 1.00 (3 / 3) 233 31.01 0.00 2.82 chr4ptel1M 538972 539044 (460956) MIR#SINE/MIR 142 212 (50) m_b177s601i2 6911 chr4ptel1M 538972 GAAGATGAGAATAGCTCCTATCTCATAAAATTGCTGTGTGGATCAAAAGA 539021 ii i v iv i iii i v i v MIR#SINE/MIR 142 GGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGGATTAAATGA 191 chr4ptel1M 539022 GATCGATCACATAGACAGTGTCT 539044 - ii - iv v i ii MIR#SINE/MIR 192 G-TTAAT-ACATGTAAAGCGCTT 212 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 40.28 CpG sites = 16, Kimura (unadjusted) = 42.94 Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.03 (2 / 72), avg. gap size = 1.00 (2 / 2) 208 24.07 23.44 2.60 chr4ptel1M 539745 539872 (460128) L3#LINE/CR1 1636 1789 (2310) m_b177s601i3 6912 chr4ptel1M 539745 GATTGGAAACCTGGCACAGAGAGGGCCAGGCACAGTGG-GATGGGAGAC- 539792 iv v --- v ii? i - i - L3#LINE/CR1 1636 GATTACAAAACTGGCACAGAG---GCAAGATNCAGTAGTGATGGGGGACT 1682 chr4ptel1M 539793 -CAGC-------------------AG---CACTTT-CCAAAAGCAGAA-A 539817 - i ------------------- --- i i?- i i- L3#LINE/CR1 1683 TCAACTATCCGGACATCTGCTGGAAGTCTCATTCNGCTAAAAGCAGAGCA 1732 chr4ptel1M 539818 TGCTGCTA---TCTTCAACTGCCTTTGTGGCAATCTTGTCCTTCAAAAAC 539864 - v --- v vi vv i i ii ii i iv L3#LINE/CR1 1733 T-CTGATAAATTCTTGACTTGCCTTGCTGACAATTTCATCTCTCAGAAGG 1781 chr4ptel1M 539865 TGGAGGGA 539872 i i L3#LINE/CR1 1782 TAGAGGAA 1789 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 31.06 CpG sites = 21, Kimura (unadjusted) = 31.06 Transitions / transversions = 2.33 (21/9) Gap_init rate = 0.09 (12 / 127), avg. gap size = 2.83 (34 / 12) 346 24.35 3.80 1.23 chr4ptel1M 540241 540319 (459681) L2d2_3end#LINE/L2 462 542 (13) m_b177s601i4 6913 chr4ptel1M 540241 ATCTTGTGCTTGTGTTTCCTTGGGTCCCCCATA---CTTAGCACAGTGCC 540287 i v - i ii i vi i --- i L2d2_3end#LIN 462 ACCATGT-CTTATACTTCTTTGTATCCCCCACAGCGCCTAGCACAGTGCC 510 chr4ptel1M 540288 TGGTATACAGTAAGCACTTGATAAATGTGTGT 540319 v i i i i ii i v L2d2_3end#LIN 511 TTGCACACAGTAGGCGCTCAATAAATATTTGT 542 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.33 CpG sites = 15, Kimura (unadjusted) = 31.33 Transitions / transversions = 3.75 (15/4) Gap_init rate = 0.03 (2 / 78), avg. gap size = 2.00 (4 / 2) 343 30.86 0.00 0.00 chr4ptel1M 540249 540329 (459671) L2b_3end#LINE/L2 383 463 (3) m_b177s601i5 6913 chr4ptel1M 540249 CTTGTGTTTCCTTGGGTCCCCCATACTTAGCACAGTGCCTGGTATACAGT 540298 vivi vi vi viii i ? i i L2b_3end#LINE 383 CTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGT 432 chr4ptel1M 540299 AAGCACTTGATAAATGTGTGTGACATGAATG 540329 i i iii i v viv L2b_3end#LINE 433 AGGCGCTCAGTAAATATTTGTTGAATGAATG 463 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 38.04 CpG sites = 17, Kimura (unadjusted) = 42.80 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.00 (0 / 80), avg. gap size = 0.0 (0 / 0) 207 34.73 3.47 4.50 chr4ptel1M 540359 540560 (459440) L2c_3end#LINE/L2 222 421 (57) m_b177s601i6 6914 chr4ptel1M 540359 TGTTCCCTCTTCCAGAAAACCTTCCCTTCCCCCTCTCCCCAATTCAAAGG 540408 iv i i i i vv i vvv? v v v i v L2c_3end#LINE 222 TGTCACCTCCTCCGGGAAGCCTTCCCTGACCCCCCAAGNCTAGTCTAGGT 271 chr4ptel1M 540409 GATCTCACCCTCTGGTTTCTCATTGCACTTTGCTTTAACATCTTCCTATC 540458 vi --- vvi i v ii ii ---- vi i i L2c_3end#LINE 272 GCCCTC---CTCTGTGCTCCCATAGCACCCTGTCT----ATACTCCCATT 314 chr4ptel1M 540459 -T-GTCCCTATCTTC--CCTGTGTCTCAGTTACGGGGCCACAT-TCCGCT 540503 - - iv i v i-- i i ivi i iivv vii ? - i ii L2c_3end#LINE 315 ATAGCACTTATCATTAACTTGTATTGTAATTGTCTGTTTACNTGTCTGTC 364 chr4ptel1M 540504 TCCTCTCCAGTGGAGTCTAAGCCTATTGGGGGCAGGGATTTTGTCTT-TT 540552 -- v i v v i iiv i iiv - L2c_3end#LINE 365 TCCTC--CACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATT 412 chr4ptel1M 540553 C-TTTCTGT 540560 - i i L2c_3end#LINE 413 CATCTTTGT 421 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 47.49 CpG sites = 41, Kimura (unadjusted) = 49.62 Transitions / transversions = 1.58 (41/26) Gap_init rate = 0.07 (15 / 201), avg. gap size = 1.07 (16 / 15) 195 38.15 3.23 1.91 chr4ptel1M 541264 541418 (458582) MIRc#SINE/MIR 85 241 (27) m_b177s601i7 6915 chr4ptel1M 541264 CTATGTGGCCAGAGAGAAGTCATTGAATACGAGGAGGGCCTTCTCTTCCT 541313 i i vvi iv i v i- vvvvv i ivvi MIRc#SINE/MIR 85 CTGTGTGACCTTGGGCAAGTCACTTAAC-CTCTCTGAGCCTCAGTTTCCT 133 chr4ptel1M 541314 TGGGTCT-TAAGATGGATTCAACAAAATTAGCCTTACATAACTCACAGAT 541362 ii-- - i ivvi i v iiv i i v v iv MIRc#SINE/MIR 134 CA--TCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGG 181 chr4ptel1M 541363 TTATGCTGAGGGTAAAGCAAAATCAC-TGGGTCAAAG-ACTT--TAAGGT 541408 i vv i v iii i v i- iv v -i -- iv MIRc#SINE/MIR 182 TTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTTTGTAAACT 231 chr4ptel1M 541409 GGAAAGGACT 541418 v vi MIRc#SINE/MIR 232 GTAAAGTGCT 241 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 53.60 CpG sites = 31, Kimura (unadjusted) = 55.01 Transitions / transversions = 1.15 (31/27) Gap_init rate = 0.05 (7 / 154), avg. gap size = 1.14 (8 / 7) 16 0.00 0.00 0.00 chr4ptel1M 542525 542542 (457458) (A)n#Simple_repeat 1 18 (0) m_b177s252i10 6916 chr4ptel1M 542525 AAAAAAAAAAAAAAAAAA 542542 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAA 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 15 16.92 7.69 4.48 chr4ptel1M 544014 544078 (455922) (TCT)n#Simple_repeat 1 67 (0) m_b177s252i11 6917 chr4ptel1M 544014 TCTTC-TCTTCTTC-TATTC-GCTTCCGGGCTTCTTCTTCAGCCCTCCTC 544060 - - v -v - -vv -vi i i (TCT)n#Simple 1 TCTTCTTCTTCTTCTTCTTCTTCTT-C-TTCTTCTTCTTC-TTCTTCTTC 47 chr4ptel1M 544061 TTC-TCCTCTTC-TCTTCTT 544078 - i - (TCT)n#Simple 48 TTCTTCTTCTTCTTCTTCTT 67 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.12 (8 / 64), avg. gap size = 1.00 (8 / 8) 180 25.01 5.62 5.62 chr4ptel1M 544864 544952 (455048) L3#LINE/CR1 3736 3824 (275) m_b177s601i8 6918 chr4ptel1M 544864 GGAGCA-AGAAAACTT-GAGAA-ACAAAATTAGTTACTGTCAA-TATTCT 544909 v - i - i - vi - i iiiv - - L3#LINE/CR1 3736 GGAGAAGAGAAGACTTAGAGGAGACATGAT-AGCTGTCTTCAAATATT-T 3783 chr4ptel1M 544910 GAGGGGCTGCCACG-AGAATTCCAAGGGTAACCTTTATTCTGTG 544952 i i i -i ---v i i v vvi L3#LINE/CR1 3784 GAAGGGCTGTCATGTGGAA---GAGGGATTAGACTTATTCTGTG 3824 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 31.51 CpG sites = 14, Kimura (unadjusted) = 31.51 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.11 (10 / 88), avg. gap size = 1.00 (10 / 10) 191 29.18 15.89 5.53 chr4ptel1M 545503 545716 (454284) L2b_3end#LINE/L2 213 447 (19) m_b177s601i9 6919 chr4ptel1M 545503 CTTCAATCCCCCCTTCTATAGGAAGCCTTCCTTGATCCCTCTTAAATGCT 545552 iv vi v i vii i i i i ---- v i L2b_3end#LINE 213 CTCAAATGTCACCTCCTCCGGGAAGCCCTCCCTGACCCCCC----AGGCC 258 chr4ptel1M 545553 G---CAG---CCTTCCCTCTGGTACCTCCTG--CCTGCAGGTCCTGC-A- 545592 --- --- i - vv i ii-- i ---- - - L2b_3end#LINE 259 GGGTCAGGCGCCCTCC-TCTGGGCCCCCCCAGTCCTAC----CCTGCCAC 303 chr4ptel1M 545593 --TGGAATTGCTCTTCTCCAGGGATTTGCCCATTGTCCCTACCATTACAC 545640 -- i- ii?v v ii?vv iv i --- i iv i v L2b_3end#LINE 304 TCTGGG-TTATNATTGTCTGNTTACATGTC---TGTCTCCCCCACTAGAC 349 chr4ptel1M 545641 TGTAGACTTTTT-----CA----TC----CTTTCTT---------TGTAT 545668 iii iiv ----- ----i ---- v --------- L2b_3end#LINE 350 TGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTGTAT 399 chr4ptel1M 545669 CCCCGGCACTTAGGACAGCTCCTGGCACATGGGAGGCCCTTAATAAGT 545716 i i i v ?v ii v v i i i L2b_3end#LINE 400 CCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAAT 447 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 36.23 CpG sites = 39, Kimura (unadjusted) = 39.80 Transitions / transversions = 1.95 (39/20) Gap_init rate = 0.11 (23 / 213), avg. gap size = 2.04 (47 / 23) 249 28.40 3.37 1.10 chr4ptel1M 545648 545736 (454264) L2d_3end#LINE/L2 426 516 (0) m_b177s601i10 6919 chr4ptel1M 545648 TTTTTCATCCTTTCTTTGTATCCC-CGGCACTTAGGACAGCTCCTG-GCA 545695 i vi ii? i? i vi - i i i v - v - L2d_3end#LINE 426 TCTTATACTNTTTTNTCGTTCCCCACAGCGCCTAGCACAG-TGCTGAGCA 474 chr4ptel1M 545696 CATGGGAGGCCCTTAATAAGT-CTCAGTGACTGATTTACTGA 545736 i v v i i - iiv i v i L2d_3end#LINE 475 CATAGTAGGCGCTCAATAAATACTTGTTGATTGATTGATTGA 516 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 34.72 CpG sites = 17, Kimura (unadjusted) = 38.65 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.05 (4 / 88), avg. gap size = 1.00 (4 / 4) 271 22.86 4.11 4.11 chr4ptel1M 545659 545731 (454269) L2d2_3end#LINE/L2 476 548 (7) m_b177s601i11 6919 chr4ptel1M 545659 TTCTTTGTATCCC---CGGCACTTAGGACAGCTCCTGGCACATGGGAGGC 545705 --- i i i v iv v ii v L2d2_3end#LIN 476 TTCTTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAGTAGGC 525 chr4ptel1M 545706 CCTTAATAAGTCTCAGTGACTGATTT 545731 v i i v iv --- L2d2_3end#LIN 526 GCTCAATAAATATTTGT---TGATTT 548 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 25.71 CpG sites = 9, Kimura (unadjusted) = 27.67 Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.06 (4 / 72), avg. gap size = 1.50 (6 / 4) 296 20.75 0.00 0.00 chr4ptel1M 545664 545716 (454284) L2a_3end#LINE/L2 446 498 (19) m_b177s601i12 6919 chr4ptel1M 545664 TGTATCCCCGGCACTTAGGACAGCTCCTGGCACATGGGAGGCCCTTAATA 545713 i i i i iv i v v i L2a_3end#LINE 446 TGTATCCCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGGCGCTCAATA 495 chr4ptel1M 545714 AGT 545716 i L2a_3end#LINE 496 AAT 498 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 22.62 CpG sites = 8, Kimura (unadjusted) = 25.20 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 15 7.81 3.70 0.00 chr4ptel1M 545897 545923 (454077) (GGGA)n#Simple_repeat 1 28 (0) m_b177s252i12 6920 chr4ptel1M 545897 GGGAGGG-GGACGGGAGGGAGGGAGGGA 545923 - iv (GGGA)n#Simpl 1 GGGAGGGAGGGAGGGAGGGAGGGAGGGA 28 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 26), avg. gap size = 1.00 (1 / 1) 12 23.03 0.00 9.09 chr4ptel1M 546298 546357 (453643) (GAAAAAA)n#Simple_repeat 1 55 (0) m_b177s252i13 6921 chr4ptel1M 546298 GAACAAAGATAAATGCAGAGAAAAGTTAAAAGATTGGAAAAAAGAAAGAC 546347 v - --v i vv --ii i i v (GAAAAAA)n#Si 1 GAAAAAAGA-AAA--AAGAAAAAAGAAAAAAGA--AAAAAGAAAAAAGAA 45 chr4ptel1M 546348 AAAAGAAAAA 546357 (GAAAAAA)n#Si 46 AAAAGAAAAA 55 Matrix = Unknown Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.08 (5 / 59), avg. gap size = 1.00 (5 / 5) 192 10.41 4.08 2.00 chr4ptel1M 550349 550397 (449603) MIR1_Amn#SINE/MIR 91 140 (90) m_b177s601i13 6922 chr4ptel1M 550349 GTGACCCTGGGCAA-TC-CTTCACCTGTCCCTGCCTCAGTTTCCCACATC 550396 i - - ? v iv? i- MIR1_Amn#SINE 91 GTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCT-CATC 139 chr4ptel1M 550397 T 550397 MIR1_Amn#SINE 140 T 140 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 11.83 CpG sites = 3, Kimura (unadjusted) = 11.83 Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.06 (3 / 48), avg. gap size = 1.00 (3 / 3) 213 36.73 1.01 1.01 chr4ptel1M 551626 551724 (448276) C L2b_3end#LINE/L2 (169) 297 199 m_b177s601i14 6923 chr4ptel1M 551626 GGATGAGAGAGGGGAGGAC-AGAACAAAGTCCTCCTCCTAGCCAGAGGAA 551674 i ii vv i v - iv ii iv iivv ii v i ii C L2b_3end#LINE 297 GGGTAGGACTGGGGGGGCCCAGAGGAGGGCGCCTGACCCGGCCTGGGGGG 248 chr4ptel1M 551675 ATCTGAGAAGGCTTCATAGAGGTAGTGACGTCACAGCTGAGACCTGAAAG 551724 - v i i vii vi i ivv i C L2b_3end#LINE 247 -TCAGGGAGGGCTTCCCGGAGGAGGTGACATTTGAGCTGAGACCTGAAGG 199 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 46.85 CpG sites = 23, Kimura (unadjusted) = 53.78 Transitions / transversions = 1.77 (23/13) Gap_init rate = 0.02 (2 / 98), avg. gap size = 1.00 (2 / 2) 251 34.09 0.00 0.00 chr4ptel1M 551637 551724 (448276) C L2c_3end#LINE/L2 (189) 289 202 m_b177s601i15 6923 chr4ptel1M 551637 GGGAGGACAGAACAAAGTCCTCCTCCTAGCCAGAGGAAATCTGAGAAGGC 551686 v iv ii iv iivvv ? vvi iii v i C L2c_3end#LINE 289 GGGAGCACAGAGGAGGGCACCTAGACTAGNCTTGGGGGGTCAGGGAAGGC 240 chr4ptel1M 551687 TTCATAGAGGTAGTGACGTCACAGCTGAGACCTGAAAG 551724 vii vi i vv ? i i C L2c_3end#LINE 239 TTCCCGGAGGAGGTGACATCTGAGCTGAGNCTTGAAGG 202 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 46.04 CpG sites = 17, Kimura (unadjusted) = 48.54 Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.00 (0 / 87), avg. gap size = 0.0 (0 / 0) 265 21.82 17.27 0.00 chr4ptel1M 551794 551903 (448097) C MIR3#SINE/MIR (43) 165 37 m_b177s601i16 6924 chr4ptel1M 551794 AGGTCACCTAGAGCA------TCATTTTACAGATGAGGACCTCGAGGCTC 551837 i i vv ------ vvii i C MIR3#SINE/MIR 165 AGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCC 116 chr4ptel1M 551838 GCTGAGG----GGGAC-TGCCCA----CACA-AGC-ATTAAATGGCAAAG 551876 ivv ---- v - ---- - - v v i i C MIR3#SINE/MIR 115 AGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAG 66 chr4ptel1M 551877 CAGGGATTCGCACCCAG--CACCCAACTC 551903 v i v v -- v ii C MIR3#SINE/MIR 65 CCGGGACTAGAACCCAGGTCTCCTGACTC 37 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 25.89 CpG sites = 11, Kimura (unadjusted) = 25.89 Transitions / transversions = 0.85 (11/13) Gap_init rate = 0.06 (7 / 109), avg. gap size = 2.71 (19 / 7) 251 23.61 10.94 0.71 chr4ptel1M 551810 551937 (448063) C MIR1_Amn#SINE/MIR (82) 148 8 m_b177s601i18 6924 chr4ptel1M 551810 CATTTTACAGATGAGGACCTCGAGGCTCGCTGAGG----GGGAC-TGCCC 551854 vvii ? ivv ---- v - C MIR1_Amn#SINE 148 CATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGCCC 99 chr4ptel1M 551855 A----CACA-AGCA-TTAAATGGCAAAGCAGGGATTCGCACCCAG--CAC 551896 ---- ?- ?-vi? i i v ? ? v -- v C MIR1_Amn#SINE 98 AAGGTCACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAACCCAGGTCTC 49 chr4ptel1M 551897 CCAACTCGGATTCTCACCCTC-ATGCACAAAAACCATGCTGC 551937 i v vv v iviiv - v -v i ii C MIR1_Amn#SINE 48 CCGAGTCCCAGTCCAGTGCTCTATCCAC-TAGACCACACTGC 8 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.06 CpG sites = 13, Kimura (unadjusted) = 30.20 Transitions / transversions = 0.76 (13/17) Gap_init rate = 0.06 (8 / 127), avg. gap size = 1.88 (15 / 8) 313 16.67 13.10 0.00 chr4ptel1M 551810 551893 (448107) C MIRc#SINE/MIR (122) 146 52 m_b177s601i17 6924 chr4ptel1M 551810 CATTTTACAGATGAGGACCTCGAGGCTCGCTGAGG----GGGACT-GCCC 551854 vvii ivv ---- v - C MIRc#SINE/MIR 146 CATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCC 97 chr4ptel1M 551855 A----CACA-AGC-ATTAAATGGCAAAGCAGGGATTCGCACCCAG 551893 ---- - - v i i v i v C MIRc#SINE/MIR 96 AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAG 52 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 18.88 CpG sites = 6, Kimura (unadjusted) = 18.88 Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.06 (5 / 83), avg. gap size = 2.20 (11 / 5) 587 19.99 5.62 3.05 chr4ptel1M 554115 554274 (445726) Charlie4a#DNA/hAT-Charlie 345 508 (0) m_b177s502i0 6925 chr4ptel1M 554115 TGGTTCTCAAATAGTTCGATAACTGCATTTCAGCAACATGGGTTTCCTTT 554164 ? i iv v i i ii vv v Charlie4a#DNA 345 TGNTTTTTTAATATTTTGATAACTGTATTTCAATATAATTGGTTTCCTTT 394 chr4ptel1M 554165 GTAATCCTA--TACTTTCCCTTTTTAATTTCCTTCCAAAACATGATTCT- 554211 -- i v--- -- v v iv v - Charlie4a#DNA 395 GTAATCCTATGTATTTTA---TTTTA--TGCATTTAAAAACATTATTCTG 439 chr4ptel1M 554212 ---AAGGATCCATAGGCTTCCCCATACTACCAGA-GGGTCCATGACACAA 554257 --- i i v v i i - i Charlie4a#DNA 440 AGAAGGGGTCCATAGGCTTCACCAGACTGCCAAAGGGGTCCATGGCACAA 489 chr4ptel1M 554258 GAAC--CTGAGAACCTTTG 554274 i v--i i ii Charlie4a#DNA 490 AAAAGGTTAAGAACCCCTG 508 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 23.77 CpG sites = 18, Kimura (unadjusted) = 23.77 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.06 (10 / 159), avg. gap size = 1.40 (14 / 10) 19 3.81 0.00 0.00 chr4ptel1M 554981 555007 (444993) (CTCC)n#Simple_repeat 1 27 (0) m_b177s252i14 6926 chr4ptel1M 554981 CTACCTCCCTCCCTCCCTCCCTCCCTC 555007 v (CTCC)n#Simpl 1 CTCCCTCCCTCCCTCCCTCCCTCCCTC 27 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 215 16.67 2.33 2.33 chr4ptel1M 555307 555349 (444651) C L3#LINE/CR1 (103) 3996 3954 m_b177s601i19 6927 chr4ptel1M 555307 TCATCCTAGCC-CTATTTCAGGACCTCCAGTGATGGAGAGCTCA 555349 - - ii v iv i i C L3#LINE/CR1 3996 TCATCC-AGCCTCTGCTTGAACACCTCCAGTGACGGGGAGCTCA 3954 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 16.41 CpG sites = 5, Kimura (unadjusted) = 19.33 Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.00 (2 / 2) 245 26.97 11.88 0.89 chr4ptel1M 555753 555853 (444147) C L3#LINE/CR1 (703) 3396 3285 m_b178s601i1 6928 chr4ptel1M 555753 CTCTCTCATCT----CTTCTACAATGGATTTTGGGAACCAAAAGGTA--A 555796 - i---- v i i v vv v v i -- C L3#LINE/CR1 3396 CTCTC-CATCCTGTACTTGTGCAGTTGATTTTTTGAACCTAAATGCAGGA 3348 chr4ptel1M 555797 CTTCG---TTACTCCTATTGATTTCCATCCTA---GATCCGACCCAGCGT 555840 ii--- ii i i v i i i--- v i i v C L3#LINE/CR1 3347 CTTTACATTTATCCCTGTTAAATTTCATCTTGTTGGTTTCGGCCCATCGT 3298 chr4ptel1M 555841 GCCAGCCTTTCAA 555853 v v i C L3#LINE/CR1 3297 TCCAGCCTGTCGA 3285 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.76 CpG sites = 16, Kimura (unadjusted) = 34.32 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.05 (5 / 100), avg. gap size = 2.60 (13 / 5) 230 13.33 23.33 0.00 chr4ptel1M 556212 556271 (443729) MIR3#SINE/MIR 72 145 (63) m_b178s601i2 6929 chr4ptel1M 556212 CGCCAACTGCCT-TGTAACTCTGGGCAA---TCTTCACCTCT-------- 556249 i i ?v - i ii ---v -------- MIR3#SINE/MIR 72 CACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCT 121 chr4ptel1M 556250 --GTTTCCTCATCTGTAAAATGGG 556271 -- i MIR3#SINE/MIR 122 CAGTTTCCTCATCTGTAAAATGAG 145 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 15.30 CpG sites = 6, Kimura (unadjusted) = 15.30 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.07 (4 / 59), avg. gap size = 3.50 (14 / 4) 314 21.82 19.09 0.00 chr4ptel1M 556224 556333 (443667) MIRc#SINE/MIR 88 218 (50) m_b178s601i3 6929 chr4ptel1M 556224 TGTAACTCTGGGCAA---TCTTCACCTCT----------GTTTCCTCATC 556260 i ii ---v v ---------- MIRc#SINE/MIR 88 TGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATC 137 chr4ptel1M 556261 TGTAAAAT-GGGACAATAATAGC------ATCTA-CTCGAAGGGTCGAAG 556302 - i v ------ii - iv i vv MIRc#SINE/MIR 138 TGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTG 187 chr4ptel1M 556303 TGAGGATTGTGAGACAAAATGTTTGTAAAGG 556333 iiviv v v v i i MIRc#SINE/MIR 188 TGAGGATCAAATGAGATAATGTATGTGAAAG 218 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.08 CpG sites = 13, Kimura (unadjusted) = 26.08 Transitions / transversions = 1.18 (13/11) Gap_init rate = 0.05 (5 / 109), avg. gap size = 4.20 (21 / 5) 588 23.36 1.46 0.00 chr4ptel1M 556239 556375 (443625) MIR#SINE/MIR 112 250 (12) m_b178s601i4 6929 chr4ptel1M 556239 TCTTCACCTCTGTTTCCTCATCTGTAAAATGGG-ACAATAATAGCATCTA 556287 vii v - i i i MIR#SINE/MIR 112 TCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTA 161 chr4ptel1M 556288 C-TCGAAGGGTCGAAGTGAGGATTGTGAGACAAAATGTTTGTAAAGGGTT 556336 - iv i vv iviv vvv iiv v i MIR#SINE/MIR 162 CCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATACATGTAAAGCGCT 211 chr4ptel1M 556337 TAGGGCAGTTCCTGGCACATAGTAGGTGCTTAATATGTG 556375 ii v i i i vi MIR#SINE/MIR 212 TAGAACAGTGCCTGGCACATAGTAAGCGCTCAATAAATG 250 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.40 CpG sites = 18, Kimura (unadjusted) = 28.42 Transitions / transversions = 1.29 (18/14) Gap_init rate = 0.01 (2 / 136), avg. gap size = 1.00 (2 / 2) 284 31.25 7.81 0.00 chr4ptel1M 556955 557082 (442918) MIR3#SINE/MIR 56 193 (15) m_b178s601i5 6930 chr4ptel1M 556955 CCAGACCTGCCTTTGCCCTTTACTCTCCAAGTGATCAAGGAGAAGTCACT 557004 i v i v i vi v ?v iiv i vv iv MIR3#SINE/MIR 56 CTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACT 105 chr4ptel1M 557005 T---CTCTCTGGGCCT--GTTTTCTCATCAGTAAGAAAAAAAGACC--TC 557047 --- -- i v i vi iii iii--v MIR3#SINE/MIR 106 TCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGAC 155 chr4ptel1M 557048 CAG-TCATGTCTGAAGT-CCTGCTCGCCCCGA-GTTCT 557082 i - v v i i - v iv i i -i MIR3#SINE/MIR 156 TAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCT 193 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.90 CpG sites = 24, Kimura (unadjusted) = 42.31 Transitions / transversions = 1.50 (24/16) Gap_init rate = 0.05 (6 / 127), avg. gap size = 1.67 (10 / 6) 213 23.21 5.36 0.00 chr4ptel1M 558247 558302 (441698) C L2b_3end#LINE/L2 (1) 465 407 m_b178s601i6 6931 chr4ptel1M 558247 TTCTTTGAGTCAATGAGTATTTCAGTAGCACCT---GTGTGCCAGGCACT 558293 v v v ii i vvvv i --- ? C L2b_3end#LINE 465 TTCATTCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCT 416 chr4ptel1M 558294 GTGCTGAGC 558302 ii C L2b_3end#LINE 415 GTGCTAGGC 407 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.10 CpG sites = 6, Kimura (unadjusted) = 28.53 Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.02 (1 / 55), avg. gap size = 3.00 (3 / 1) 249 26.87 0.00 0.00 chr4ptel1M 559508 559574 (440426) Charlie4a#DNA/hAT-Charlie 434 500 (8) m_b178s502i0 6932 chr4ptel1M 559508 ATTCCAAGGAGAGGTCTCTCTATTTCCCCAGACGGACAAAGGGGTCCAAA 559557 ii i i iv vvii v v v vi Charlie4a#DNA 434 ATTCTGAGAAGGGGTCCATAGGCTTCACCAGACTGCCAAAGGGGTCCATG 483 chr4ptel1M 559558 GCCCAAAAAGGGTAAAG 559574 v i v Charlie4a#DNA 484 GCACAAAAAAGGTTAAG 500 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 33.61 CpG sites = 9, Kimura (unadjusted) = 33.61 Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.0 (0 / 0) 215 38.47 3.41 4.00 chr4ptel1M 561451 561626 (438374) C L2#LINE/L2 (2237) 845 671 m_b178s601i7 6933 chr4ptel1M 561451 GTGGAGTAGCTAGAAAGTTAGAGTGCTTGAGGGAGTATCAATATGGAGAT 561500 vi v i iii i ii i ii v i vi v ii v C L2#LINE/L2 845 GTCAAGGAACTGAGAGGCCAGGGTATTGGAAGGATCATCTACGTGGATAT 796 chr4ptel1M 561501 CAAAGGCCCC-----TTCTAACAGAGCCCAGGAG-GTGGGAAGGAGAGAA 561544 ii iv v ----- v i i---- v - v ii v v C L2#LINE/L2 795 TGAAATCACCAAGAATTATGACAGG----AGTAGTGTTGGAGAGAGTGAC 750 chr4ptel1M 561545 AGTCGGGAGCCCAGTCCTGAACTCGTGAAGGAAGGAACAAGCGCGTCCTG 561594 --- vi vv i v v v v ivii v i v i C L2#LINE/L2 749 AGT---GAGCCAGGAGCTAAAATCTTCAAGGAATGAGGGGGAGTGACCCG 703 chr4ptel1M 561595 GACACTGGGAGAGAACAGCATCTAGAACTGGT 561626 viii v vi v v v i vv C L2#LINE/L2 702 GAGGTCGGTAGATGACTGCAACAAGGAGGGGT 671 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 51.65 CpG sites = 34, Kimura (unadjusted) = 55.50 Transitions / transversions = 1.10 (34/31) Gap_init rate = 0.05 (9 / 175), avg. gap size = 1.44 (13 / 9) 463 31.56 2.08 2.62 chr4ptel1M 562541 562732 (437268) MIR#SINE/MIR 45 235 (27) m_b178s601i8 6934 chr4ptel1M 562541 TGGCCGGCATCAAATCCTGCCCAAGAAACTTCATCAACTGTGTGACTCTG 562590 v i vv i i v ivv vv - ii i ii MIR#SINE/MIR 45 TGCCTGGGTTCGAATCCCGGCTCTGCCACTT-ACTAGCTGTGTGACCTTG 93 chr4ptel1M 562591 GTC---TTAATTAATATCAGTCTCCTTCAGTCTCTTTAACAACTACACAA 562637 v --- v iv vv v v i i i --- v ii v MIR#SINE/MIR 94 GGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCT---CATCTGTAAAA 140 chr4ptel1M 562638 TGAGGATCACAATAGTACCT-CTTGCCAATGTAGTAATGAGGAGCAAAAG 562686 i v i - i vvi iv v vi vi v MIR#SINE/MIR 141 TGGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGGATTAAATG 190 chr4ptel1M 562687 AGGGATTACTTGTAAAACTCAGAGGCACAACGCCTGGCACATGGTA 562732 vv v v i v vv i- ii i MIR#SINE/MIR 191 AGTTAATACATGTAAAGCGCTTAGA-ACAGTGCCTGGCACATAGTA 235 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.52 CpG sites = 27, Kimura (unadjusted) = 41.27 Transitions / transversions = 0.84 (27/32) Gap_init rate = 0.04 (7 / 191), avg. gap size = 1.29 (9 / 7) 315 23.55 2.80 4.76 chr4ptel1M 564092 564198 (435802) C MIRc#SINE/MIR (69) 199 95 m_b178s601i9 6935 chr4ptel1M 564092 ATTTATTTCT-ACAGCACCTACTATGTGCCCTGGG-AGGGAAGTGTTATT 564139 iv i - i --- iv vvv i - v v-- C MIRc#SINE/MIR 199 ATTTGATCCTCACAACA---ACCCTGTGAGGTAGGCAGGGCAGG--TATT 155 chr4ptel1M 564140 ATTATCCCCAGTTC-CAACGGAGGAAGCAGAGGCCAACAGGGGATAAGTG 564188 v i- ivv i v iv v i v C MIRc#SINE/MIR 154 ATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTG 105 chr4ptel1M 564189 ACTTGCCCAA 564198 C MIRc#SINE/MIR 104 ACTTGCCCAA 95 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.30 CpG sites = 10, Kimura (unadjusted) = 28.30 Transitions / transversions = 0.71 (10/14) Gap_init rate = 0.08 (8 / 106), avg. gap size = 1.00 (8 / 8) 347 23.75 1.25 0.00 chr4ptel1M 564119 564198 (435802) C MIR#SINE/MIR (91) 171 91 m_b178s601i10 6935 chr4ptel1M 564119 CCCTGGGAGGGAAGTGTTATTATTATCCCCAGTTC-CAACGGAGGAAGCA 564167 iv v i ii v i- ivv i v C MIR#SINE/MIR 171 CCCTATGAGGTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACT 122 chr4ptel1M 564168 GAGGCCAACAGGGGATAAGTGACTTGCCCAA 564198 vv v i v i C MIR#SINE/MIR 121 GAGGCACAGAGAGGTTAAGTAACTTGCCCAA 91 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.73 CpG sites = 9, Kimura (unadjusted) = 28.73 Transitions / transversions = 0.90 (9/10) Gap_init rate = 0.01 (1 / 79), avg. gap size = 1.00 (1 / 1) 25 22.45 7.53 0.00 chr4ptel1M 565078 565170 (434830) (CGC)n#Simple_repeat 1 100 (0) m_b178s252i1 6936 chr4ptel1M 565078 CGCCGCTGCTGCC-CTG-CGCCGCCGCCGCCGCCGTGAACACC-CCTTGG 565124 i i - i - iviv i - viv (CGC)n#Simple 1 CGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCG 50 chr4ptel1M 565125 CCGCCGCCGGTGCCTCC-CCGCCCCCGCC-CCCCAGCC-CCG-GGCCGCC 565170 vi v - v - v v - -v (CGC)n#Simple 51 CCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCC 100 Matrix = Unknown Transitions / transversions = 0.80 (8/10) Gap_init rate = 0.08 (7 / 92), avg. gap size = 1.00 (7 / 7) 191 33.70 7.61 0.00 chr4ptel1M 566139 566230 (433770) C L2c_3end#LINE/L2 (6) 472 374 m_b178s601i12 6937 chr4ptel1M 566139 TCAGCCAAGAAGCATGTACCCAGTGCC--CTGTGTGTCAGACACTGGG-- 566184 vi v i v iiv i -- i i i i -- C L2c_3end#LINE 472 TCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGA 423 chr4ptel1M 566185 -ACAAG--TGCTGGGGACCCAGAAAGGGCCCTGGGGAAGCTCACAATCT 566230 - i-- vvvii v i vvvvv vii i i C L2c_3end#LINE 422 TACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCT 374 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.16 CpG sites = 17, Kimura (unadjusted) = 45.95 Transitions / transversions = 1.21 (17/14) Gap_init rate = 0.04 (4 / 91), avg. gap size = 1.75 (7 / 4) 237 27.69 3.08 0.00 chr4ptel1M 566139 566203 (433797) C L2b_3end#LINE/L2 (6) 460 394 m_b178s601i11 6937 chr4ptel1M 566139 TCAGCCAAGAAGCATGTACCCAGTGCC--CTGTGTGTCAGACACTGGGAC 566186 vi v ii v iv i -- i i ? v vi C L2b_3end#LINE 460 TCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCT 411 chr4ptel1M 566187 AAGTGCTGGGGACCCAG 566203 i i iv C L2b_3end#LINE 410 AGGCGCTGGGGATACAG 394 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.45 CpG sites = 11, Kimura (unadjusted) = 36.35 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.02 (1 / 64), avg. gap size = 2.00 (2 / 1) 91 20.99 1.42 0.94 chr4ptel1M 566519 566730 (433270) (AGGGTT)n#Simple_repeat 1 213 (0) m_b178s252i2 6938 chr4ptel1M 566519 AGGGTTAGGGTTAGATTTAGGGTTAGGGTTGAGATTCCAAGTTAGAGTCC 566568 iv - iv ivii i iv (AGGGTT)n#Sim 1 AGGGTTAGGGTTAGGGTTAGGGTTAGGGTT-AGGGTTAGGGTTAGGGTTA 49 chr4ptel1M 566569 GGAGGCA--TTTAGGGTTAGGGTTAAAGTTACCGTTAGGGTT-GTGTTAG 566615 - vi --v ii vv - v (AGGGTT)n#Sim 50 GG-GTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAG 98 chr4ptel1M 566616 GGTTAGGGTTAGGGTTATCGTTTGGTTTAATGTTAGAGTTAGGTTTAGGG 566665 vv v v iv i v (AGGGTT)n#Sim 99 GGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGG 148 chr4ptel1M 566666 TTGGGGTTAGGGTTAGGGTCAGGATTGGGGTTAGCGTCAGGCTTGGCGTT 566715 i i i i v i v i v (AGGGTT)n#Sim 149 TTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTT 198 chr4ptel1M 566716 AGGTTTAGGGTTCGG 566730 v v (AGGGTT)n#Sim 199 AGGGTTAGGGTTAGG 213 Matrix = Unknown Transitions / transversions = 0.90 (18/20) Gap_init rate = 0.02 (4 / 211), avg. gap size = 1.25 (5 / 4) 307 15.76 0.00 4.06 chr4ptel1M 567609 567813 (432187) HERVIP10FH#LTR/ERV1 802 998 (4104) m_b178s701i0 6939 chr4ptel1M 567609 AGAGAGAGAGAGAGAGAGAGAGAGAGAGACAGAGAGGGGAGACAGAGAGA 567658 - i - v i --- HERVIP10FH#LT 802 AGAGAG-GAAAGAGAGA-AGAGAGAGAGAGAGAGAGAGGA---AGAGAGA 846 chr4ptel1M 567659 GAGAGAGAGAGACACAGAGAGAGAGAGAGAGACACAGAGAGAGAGTCACA 567708 i v v i v i i v HERVIP10FH#LT 847 GAGAGAGAAAGAGAGAGAGAGGGAGAGAGAGAGACAAAGAGGGAGTCAAA 896 chr4ptel1M 567709 GAGAGAGAGGAGACAGAGACACAGAGAGAGACAGACAGACAGAGAGAAAA 567758 - i v -- ii v i ii i HERVIP10FH#LT 897 GAGAGAGAG-AGGCAGAGAGA--GGAAGAGACAGAGAGACAAAGAGGGAG 943 chr4ptel1M 567759 AGAGAGAGAGAGAGACAGAGACAGAGACAGAGAGAAAAAGAGAGAGAGAG 567808 vv v v v i v i i i HERVIP10FH#LT 944 TCAGAGAGAGAGAGAGAGACAGAAAGTCAAAGAGAGAAAGAAAGAGAGAG 993 chr4ptel1M 567809 AGAGA 567813 v HERVIP10FH#LT 994 ATAGA 998 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 17.80 CpG sites = 17, Kimura (unadjusted) = 17.80 Transitions / transversions = 1.21 (17/14) Gap_init rate = 0.04 (8 / 204), avg. gap size = 1.00 (8 / 8) 52 16.03 3.85 0.00 chr4ptel1M 567814 567917 (432083) (GA)n#Simple_repeat 1 108 (0) m_b178s252i3 6940 chr4ptel1M 567814 GAG-GAGACAGAGAGACACAGAGAGAGACAGATGGACAGAGAGAGACAGA 567862 - v v v v vi v v (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr4ptel1M 567863 GAGAGAGACAGAGACAGAGAG-GGGGGAGAAACAGAGAGACAGAGA-AGA 567910 v v - i i i v v - (GA)n#Simple_ 51 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 100 chr4ptel1M 567911 GAG-GAGA 567917 - (GA)n#Simple_ 101 GAGAGAGA 108 Matrix = Unknown Transitions / transversions = 0.36 (4/11) Gap_init rate = 0.04 (4 / 103), avg. gap size = 1.00 (4 / 4) 42 2.38 0.00 0.00 chr4ptel1M 568824 568866 (431134) (G)n#Simple_repeat 1 43 (0) c_b178s251i0 6941 chr4ptel1M 568824 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGAGGGG 568866 i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 43 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 13 8.48 4.00 0.00 chr4ptel1M 571778 571802 (428198) (TCCA)n#Simple_repeat 1 26 (0) m_b178s252i4 6942 chr4ptel1M 571778 TCCATCCATCCAT-CATTCATCCCTC 571802 - i v (TCCA)n#Simpl 1 TCCATCCATCCATCCATCCATCCATC 26 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 196 27.66 2.13 0.00 chr4ptel1M 572970 573016 (426984) C L2c_3end#LINE/L2 (20) 458 411 m_b178s601i13 6943 chr4ptel1M 572970 TTTAGGAAGCACCTGTTATGTGCCAGGCACCGAGGG-ACAAAAACAAA 573016 vvi i ii i i i i- i ii C L2c_3end#LINE 458 TTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGATACAAAGATGAA 411 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.69 CpG sites = 11, Kimura (unadjusted) = 37.96 Transitions / transversions = 5.50 (11/2) Gap_init rate = 0.02 (1 / 46), avg. gap size = 1.00 (1 / 1) 83 19.95 0.50 4.10 chr4ptel1M 573596 573797 (426203) (TTCC)n#Simple_repeat 1 195 (0) m_b178s252i5 6944 chr4ptel1M 573596 TTCCTTCCTTCACTT-CTTCCCTCCCTCCCTCTTTCCTTCCCTTCTTCCT 573644 - - i i i i i i (TTCC)n#Simpl 1 TTCCTTCCTTC-CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT 49 chr4ptel1M 573645 TCATTTCCTTCCTTTCCTCTCTCCCTCCATTCCTTTCTTCCCTCTCTTCC 573694 -i - ii i i v i i - (TTCC)n#Simpl 50 TC-CTTCCTTCC-TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC-CTTCC 96 chr4ptel1M 573695 TTCCTTTTCTCCTTCCCTTCCTTTCTTTTTTCCCTCCCTTCCTTTCTTCC 573744 iii - i ii - i i (TTCC)n#Simpl 97 TTCCTTCCTTCCTT-CCTTCCTTCCTTCCTT-CCTTCCTTCCTTCCTTCC 144 chr4ptel1M 573745 TTCCCTCCCTCCTTGCCCTCCTTCCTCCCTCCCTCCCCTCCCTCTCTTCT 573794 i i - i i i i i i - i (TTCC)n#Simpl 145 TTCCTTCCTTCCTT-CCTTCCTTCCTTCCTTCCTTCCTTCCTTC-CTTCC 192 chr4ptel1M 573795 TTC 573797 (TTCC)n#Simpl 193 TTC 195 Matrix = Unknown Transitions / transversions = 30.00 (30/1) Gap_init rate = 0.04 (9 / 201), avg. gap size = 1.00 (9 / 9) 12 9.24 0.00 4.17 chr4ptel1M 575680 575704 (424296) (TCCC)n#Simple_repeat 1 24 (0) m_b178s252i6 6945 chr4ptel1M 575680 TCCCTCCCACCCTCCACCCCCTCCC 575704 v - i (TCCC)n#Simpl 1 TCCCTCCCTCCCTCC-CTCCCTCCC 24 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 1685 30.33 0.47 0.63 chr4ptel1M 576022 576658 (423342) C L1ME4c_3end#LINE/L1 (191) 639 4 m_b178s551i0 6946 chr4ptel1M 576022 TTCTGCTCATTTCACTTAGCATCAGTTCATGTAATTCTCTCCAAGCTTCT 576071 iv i i vv i- ivi i v i v C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATA-AACATTTTCCATGTTGCT 591 chr4ptel1M 576072 CTGTATTCAGCTTGCTGGTCATTTCTTACAGAACAATAATATTCCATAAC 576121 vii v vv v iv vi i v ii vvvv viv C L1ME4c_3end#L 590 ACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCGA 541 chr4ptel1M 576122 ATTCATATACCACAATTTACCCAACCATTCTCCAATTGATGGGCAGCCAC 576171 i ?v i i ii i v v i vii v C L1ME4c_3end#L 540 GTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAG 491 chr4ptel1M 576172 TCAGTTTCCAGCTTCTGGCCACTACAAACAGGGCTGCCACAAACATTTTG 576221 viv ii i v i i i i iv v ii i v C L1ME4c_3end#L 490 GTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTC 441 chr4ptel1M 576222 GCACATACAGGTCCCTTTCCCTTCTTT---AGTATCTCCTTGGGGTATAA 576268 ii i --- i i --- v i i i v v C L1ME4c_3end#L 440 GTGCATATAG---CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAAT 394 chr4ptel1M 576269 GCCCAGTAGAAACACTGCTGGGTCAAAGGGTATGCACAGTTTGATAACTT 576318 v v viiv i i v v v ii i C L1ME4c_3end#L 393 TCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTC 344 chr4ptel1M 576319 TTTGGGCATAATTCCAGATTGCTCTCCAGAATGGTTGGATTCGTTCACAG 576368 vivi i v v i i i v v iivi i ? C L1ME4c_3end#L 343 TTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACAN 294 chr4ptel1M 576369 CTCCACCAACAATGTGTCAGTGTCCCAGTTTTCCCACATCCCCTTCAACA 576418 iv i i v ? v iv i ? i vi i C L1ME4c_3end#L 293 TGCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGCA 244 chr4ptel1M 576419 CTCATCATTATTTTTTCCTGTCATCTTAGCCAATCTGACAGGTGTGTAGT 576468 i vivi ivv ii vvv i v i i i i i iv i C L1ME4c_3end#L 243 TTGGGTATTATCAATTTTTTAAATTTTTGCTAATTTAATAGGCGTAAAAT 194 chr4ptel1M 576469 GGTATCTCAGAGTTGTCTTAATTTGCATTTCTCTGATTAATAATGATTTG 576518 vv ii i v ii vv v C L1ME4c_3end#L 193 GGTATCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACTAGCGAGGTT 144 chr4ptel1M 576519 GAACACTCTTTCATATGAGTGGTAATGATTTTAATTTCATCATCTGAAAA 576568 i i i i vv v v iv ? vv v v ? vi C L1ME4c_3end#L 143 GAACATTTTTCCATGTGTTTGTTTACTANTTGTATTTCCTCTTNTGTGAA 94 chr4ptel1M 576569 TTGTCTGTTCATATCCTTTGACCATTTATCAGTTGGAGAATAGCTTGGTT 576618 i v vi i vv v v ?vv C L1ME4c_3end#L 93 TTGTCTGTTCATGTCCTTTGCCCATTTATCTATTGGGGTCTTGATNTTTT 44 chr4ptel1M 576619 TCTTATAAATTAGAGTCAGCTCTCTATATATTTTGGAAAT 576658 v v i v i ? v?i v C L1ME4c_3end#L 43 TCTTATCAATTTGAATGAGCTCTTTATATANTANAGATAT 4 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 38.98 CpG sites = 101, Kimura (unadjusted) = 40.32 Transitions / transversions = 1.11 (101/91) Gap_init rate = 0.01 (5 / 636), avg. gap size = 1.40 (7 / 5) 438 32.03 2.92 2.46 chr4ptel1M 576512 576956 (423044) C L1M5_orf2#LINE/L1 (0) 3294 2848 m_b178s551i1 6946 chr4ptel1M 576512 TGATTTGGAACACTCTTTCATATGAGTGGTAATGATTTTAATTTCATCAT 576561 ?v v i iii i vv iv iiiv v? v v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr4ptel1M 576562 CTGAAAATTGTCTGTTCATATCCTTTGACCATTTATCAGTTGGA--GAAT 576609 i vi v vi i v v ?vi i-- vv C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTT 3195 chr4ptel1M 576610 AGCTTGGTTTCTTA-TAAATTAGAGTCAGCTCTCTATATATTTTGGAAAT 576658 iv -- ? - i ? iv -v i i i v i C L1M5_orf2#LIN 3194 GTCTT--TTTNTTATTGANTTGTAG-GAGTTCTTTATATATTCTGGATAC 3148 chr4ptel1M 576659 GAGGCCTTTATCAGAACCTTTAACTGTGAAGATGTTTTCCCAGTTTGTTG 576708 v i vviv vv?i ii v v i ? i v C L1M5_orf2#LIN 3147 GAGTCCTTTGTCAGATATATGTNTTGCAAATATTTTCTCCCANTCTGTGG 3098 chr4ptel1M 576709 CTTCCCTTCTAATCTTGTTTACATTAGTTTTGTTTGTACAGAAGCTTTTT 576758 v i v i v v iv ivi vvv? vi i v C L1M5_orf2#LIN 3097 CTTGCCTTTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTTTA 3048 chr4ptel1M 576759 AATTTGATGTAATCAA-------AATTTTCTATTTTGTGATCAATAGGTC 576801 v ? i v ------- i v i i i?i - v i C L1M5_orf2#LIN 3047 ATTTTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGGTTNGT-GCTT 2999 chr4ptel1M 576802 TCTAGTTCGTCTTTAGTCACAAATTTCTTCCTCTTCCACAAGTCTGAGAG 576851 i ivv v v --- v i i v v?i - i vvii C L1M5_orf2#LIN 2998 TTTGTGTCCTGTTTA---AGAAATCTTTGCCTANCCCA-AGGTCACGAAG 2953 chr4ptel1M 576852 ATAAACTATCCTATG--TTCCTCCAATTTGTTTATAATCTCGTTCTTTAT 576899 -- i v -- i i ivvvv i i ii?ii i C L1M5_orf2#LIN 2952 AT--ATTCTCCTATGTTTTCTTCTAGAAGTTTTATAGTTTTANCTTTTAC 2905 chr4ptel1M 576900 GTATAAATC-ATGAACCCATTTTGATCTTATCTTGGTATACGGTGTTACG 576948 i v ii - - i i ? vi v i v i i v v C L1M5_orf2#LIN 2904 ATTTAGGTCTATG-ATCCATCTNGAATTAATTTTTGTGTATGGTGTGAGG 2856 chr4ptel1M 576949 TGTGGGTC 576956 iv C L1M5_orf2#LIN 2855 TAGGGGTC 2848 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 43.09 CpG sites = 72, Kimura (unadjusted) = 44.36 Transitions / transversions = 1.07 (72/67) Gap_init rate = 0.04 (16 / 444), avg. gap size = 1.50 (24 / 16) 200 19.61 1.92 1.92 chr4ptel1M 578756 578807 (421193) MIR#SINE/MIR 71 122 (140) m_b178s601i14 6947 chr4ptel1M 578756 CACTTCCTAGTTGTGTGACCCCTGGGCAAGTCCCTTCACCCCAAC-TGCC 578804 v i - i iv v i vvi- MIR#SINE/MIR 71 CACTTACTAGCTGTGTGA-CCTTGGGCAAGTTACTTAACCTCTCTGTGCC 119 chr4ptel1M 578805 TCA 578807 MIR#SINE/MIR 120 TCA 122 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 22.87 CpG sites = 5, Kimura (unadjusted) = 22.87 Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.00 (2 / 2) 210 14.65 0.00 2.44 chr4ptel1M 578756 578797 (421203) MIRc#SINE/MIR 75 115 (153) m_b178s601i15 6947 chr4ptel1M 578756 CACTTCCTAGTTGTGTGACCCCTGGGCAAGTCCCTTCACCCC 578797 v i - i v v i MIRc#SINE/MIR 75 CACTTACTAGCTGTGTGA-CCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 16.35 CpG sites = 3, Kimura (unadjusted) = 16.35 Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.02 (1 / 41), avg. gap size = 1.00 (1 / 1) 75 1.42 0.00 0.00 chr4ptel1M 580300 580370 (419630) (C)n#Simple_repeat 1 71 (0) c_b178s251i1 6948 chr4ptel1M 580300 CCCCGCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 580349 v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 50 chr4ptel1M 580350 CCCCCCCCCCCCCCCCCCCCC 580370 (C)n#Simple_r 51 CCCCCCCCCCCCCCCCCCCCC 71 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0) 183 30.97 1.39 5.80 chr4ptel1M 581814 581885 (418115) L2c_3end#LINE/L2 394 462 (16) m_b178s601i16 6949 chr4ptel1M 581814 GCAGAAACTGCCTCCGACACAAACTTCT-CCCCCAGTGCTGTGCAGGCAC 581862 ii i iv iv iv vvi v -i i ---- v L2c_3end#LINE 394 GCAGGGACCGTGTCTTATTCATCTTTGTATCCCCAGCGC----CTGGCAC 439 chr4ptel1M 581863 ACAGCAGGTGCTTAATAAATGCT 581885 i i i i i L2c_3end#LINE 440 ATAGTAGGCGCTCAATAAATGTT 462 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.34 CpG sites = 14, Kimura (unadjusted) = 41.91 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.07 (5 / 71), avg. gap size = 1.00 (5 / 5) 196 23.81 2.38 0.00 chr4ptel1M 581844 581885 (418115) L2d_3end#LINE/L2 456 498 (18) m_b178s601i17 6949 chr4ptel1M 581844 CCCAGTGCTGTGCAG-GCACACAGCAGGTGCTTAATAAATGCT 581885 i ii v v - i i i i i L2d_3end#LINE 456 CCTAGCACAGTGCTGAGCACATAGTAGGCGCTCAATAAATACT 498 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.87 CpG sites = 8, Kimura (unadjusted) = 30.48 Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.02 (1 / 41), avg. gap size = 1.00 (1 / 1) 14 33.33 0.00 1.56 chr4ptel1M 583317 583381 (416619) (AAAAT)n#Simple_repeat 1 64 (0) m_b178s252i7 6950 chr4ptel1M 583317 AAAAGAAAGTAAAATAAAGTCAAATATGTGGGAAAAAAATTAAAATTTTA 583366 v i i v -ivivi v v vvv (AAAAT)n#Simp 1 AAAATAAAATAAAATAAAATAAAATA-AAATAAAATAAAATAAAATAAAA 49 chr4ptel1M 583367 AAAAAGAAAAAAAAA 583381 v v v (AAAAT)n#Simp 50 TAAAATAAAATAAAA 64 Matrix = Unknown Transitions / transversions = 0.42 (5/12) Gap_init rate = 0.02 (1 / 64), avg. gap size = 1.00 (1 / 1) 14 14.34 2.27 7.14 chr4ptel1M 584329 584372 (415628) (AGG)n#Simple_repeat 1 42 (0) m_b178s252i8 6951 chr4ptel1M 584329 AGGTGGAGGCGGGACCAGGGGGAGTGA-GAGGAGGAGGAGGGAGG 584372 v -i vv i - - - (AGG)n#Simple 1 AGGAGGAGG-AGGAGGAGGAGGAG-GAGGAGGAGGAGGA-GGAGG 42 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.09 (4 / 43), avg. gap size = 1.00 (4 / 4) 30 21.85 1.90 5.94 chr4ptel1M 590520 590624 (409376) (GGGAGAA)n#Simple_repeat 1 101 (0) m_b178s252i9 6952 chr4ptel1M 590520 GGGAGATGGGGGCAAGAAAAAGGGGGGAAGGAGGGGGAAGAAAGGAGTAA 590569 v i v i i i i i i ii i i - (GGGAGAA)n#Si 1 GGGAGAAGGGAGAAGGGAGAAGGGAGAAGGGAGAAGGGAGAAGGGAG-AA 49 chr4ptel1M 590570 GGGAAGAAGGGAGGGAGGGAG--GGAAGAAGAGAAGAAGGGAGGGAAAGG 590617 - - i -- i - i -- i (GGGAGAA)n#Si 50 GGG-AGAAGGGA-GAAGGGAGAAGGGAGAAG-GGAGAAGGGA--GAAGGG 94 chr4ptel1M 590618 AGAAGGG 590624 (GGGAGAA)n#Si 95 AGAAGGG 101 Matrix = Unknown Transitions / transversions = 7.50 (15/2) Gap_init rate = 0.07 (7 / 104), avg. gap size = 1.14 (8 / 7) 276 35.35 6.06 0.00 chr4ptel1M 590790 590888 (409112) C MIRc#SINE/MIR (163) 105 1 m_b178s601i18 6953 chr4ptel1M 590790 GATATATCCAGGGTCACCCTGTTAGGAGG-----AAGCTGG-ATTTGAAC 590833 iv ii i v v i v i -----i i - i i C MIRc#SINE/MIR 105 GACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAAC 56 chr4ptel1M 590834 TTGTGCCCTCCCAAGTCCAGGTCCAATGCTCTGTCCGTTGCCCTCCATGG 590883 iiiv i i ii v i i v ii v iv iv C MIRc#SINE/MIR 55 CCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTG 6 chr4ptel1M 590884 CCCTG 590888 ii C MIRc#SINE/MIR 5 CCTCG 1 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.74 CpG sites = 25, Kimura (unadjusted) = 52.22 Transitions / transversions = 2.50 (25/10) Gap_init rate = 0.02 (2 / 98), avg. gap size = 3.00 (6 / 2) 20 21.59 3.23 1.59 chr4ptel1M 591179 591240 (408760) (AAAAAGG)n#Simple_repeat 1 63 (0) m_b178s252i10 6954 chr4ptel1M 591179 AAAAAGGGGAGAGGAAAAAGG-AAAA-GAAAAAAGTAAAAGGAAGGAAGG 591226 ii i - - i v -i (AAAAAGG)n#Si 1 AAAAAGGAAAAAGGAAAAAGGAAAAAGGAAAAAGGAAAAAGGAA-AAAGG 49 chr4ptel1M 591227 GGAAAGACCAAAGG 591240 ii ivv (AAAAAGG)n#Si 50 AAAAAGGAAAAAGG 63 Matrix = Unknown Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.05 (3 / 61), avg. gap size = 1.00 (3 / 3) 14 28.98 2.90 2.90 chr4ptel1M 591181 591249 (408751) (AAAGGGG)n#Simple_repeat 1 69 (0) m_b178s252i11 6954 chr4ptel1M 591181 AAAGGGG--AGAGGAAAAAGGAAAAGAAAAAAGTAAAAGGAAGGAAGGGG 591228 -- i ii i ii i vi -i i (AAAGGGG)n#Si 1 AAAGGGGAAAGGGGAAAGGGGAAAGGGGAAAGGGGAAAGG-GGAAAGGGG 49 chr4ptel1M 591229 AAAGACCAAAGGGGGGAAGGG 591249 ivv - i (AAAGGGG)n#Si 50 AAAGGGGAAA-GGGGAAAGGG 69 Matrix = Unknown Transitions / transversions = 4.00 (12/3) Gap_init rate = 0.04 (3 / 68), avg. gap size = 1.33 (4 / 3) 13 26.08 3.33 3.33 chr4ptel1M 591182 591241 (408759) (AAAGGG)n#Simple_repeat 1 60 (0) m_b178s252i12 6954 chr4ptel1M 591182 AAGGGGAGAGGAAAAAGGAAAAGAAAAAAGTAAAAGG-AA-GGAAGGGGA 591229 i i -i i ii i v i - - i (AAAGGG)n#Sim 1 AAAGGGAAAGG-GAAAGGGAAAGGGAAAGGGAAAGGGAAAGGGAAAGGGA 49 chr4ptel1M 591230 AAGACCAAAGGG 591241 -vv (AAAGGG)n#Sim 50 AAG-GGAAAGGG 60 Matrix = Unknown Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.07 (4 / 59), avg. gap size = 1.00 (4 / 4) 300 24.33 15.97 1.52 chr4ptel1M 594024 594311 (405689) L1ME4b_3end#LINE/L1 44 372 (520) m_b179s551i0 6955 chr4ptel1M 594024 AAAAAATC--CCACCTAATT--AAAATTCCCAAAGGATATGAACAGA-AA 594068 i i -- v i v-- vvv - i L1ME4b_3end#L 44 AAAAGACCAACAACCCAATAGAAAAATGGGCAAAGGATATGAACAGACAG 93 chr4ptel1M 594069 TTCTCAGATGAAGAAATTGAACTATTTCT--ATCATAAGAAAA-ATGCTC 594115 v vi i vv v ivi -- v v - - L1ME4b_3end#L 94 TTCACAGAAAAGGAAATACAAATGGCTCTTAAACATATGAAAAGATGCT- 142 chr4ptel1M 594116 CAAGCT--TTTA-------AGAAATGCAAATTAAGAA-ACTCTAAGATAC 594155 v --i i ------- i v- v i L1ME4b_3end#L 143 CAACCTCACTCATAATAAGAGAAATGCAAATTAAAACTACACTGAGATAC 192 chr4ptel1M 594156 CAT-----AACGTCCAGATTT---AAGATGAAGGAAAAAATAATGATA-- 594195 ----- v vvi v--- v -- ivv i i i -- L1ME4b_3end#L 193 CATTTTTCACCTATCAGATTGGCAAAGATCAA--AAAGTTTGATAACACA 240 chr4ptel1M 594196 ----GTTGGAGGGGATTTGGGGAAAATGGGACT-TGATGCATTGTTGGTG 594240 ---- v i i v vv v - v i i L1ME4b_3end#L 241 CTGTGTTGGCGAGGGTGTGGGGAAACAGGCACTCTCATACATTGCTGGTG 290 chr4ptel1M 594241 GAGGGAACAATC----CAACATTT-TGGAGAG-AGTTTG-----AACTAT 594279 ii vivv i---- v i - i - i ----- v L1ME4b_3end#L 291 GGAGTGTAAATTGGTACAACCTCTATGGAGGGCAATTTGGCAATATCTAT 340 chr4ptel1M 594280 GCCGGTTATCAAACTGTAC--ACCCTTTGATCCA 594311 vvvii - - i -- i L1ME4b_3end#L 341 CAAAATTA-CAAA-TGCACATACCCTTTGACCCA 372 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 29.65 CpG sites = 32, Kimura (unadjusted) = 29.65 Transitions / transversions = 0.86 (32/37) Gap_init rate = 0.08 (23 / 287), avg. gap size = 2.22 (51 / 23) 16 0.00 0.00 0.00 chr4ptel1M 594937 594953 (405047) (A)n#Simple_repeat 1 17 (0) m_b179s252i0 6956 chr4ptel1M 594937 AAAAAAAAAAAAAAAAA 594953 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 660 32.05 9.74 1.40 chr4ptel1M 595462 595923 (404077) L1ME4c_3end#LINE/L1 56 555 (275) m_b179s551i1 6957 chr4ptel1M 595462 CTCCAACTGGGAAAGGGTCAAAGAACACGAACA----ATTTTCAAAAGAA 595507 i iv iv v v i i ---- iv ? i L1ME4c_3end#L 56 CCCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAG 105 chr4ptel1M 595508 ACTGAAACCCTTTCTAGT-------CATATGAAAAGATGATCA----CGA 595546 --- iv vv?- ------- i i i v ---- v L1ME4c_3end#L 106 ---GAAATACAAN-TAGTAAACAAACACATGGAAAAATGTTCAACCTCGC 151 chr4ptel1M 595547 CAG--ATCAGAGAAATGGAGATTAAGACAACTCTGAGGTACTGGCTCACG 595594 i -- i v i ii vv i iivi i L1ME4c_3end#L 152 TAGTAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACG 201 chr4ptel1M 595595 CCTCTCAGACCGGCTAAGATGACAGGAAAAGACAAGGATGAATGGGGGAG 595644 v i i iii v i vvv ii vv i viviv vv v L1ME4c_3end#L 202 CCTATTAAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGCTGGCG 251 chr4ptel1M 595645 AGGATG---------TGGGACACTGAGACATGGTTGGTGGAACTGTGAAC 595685 ? --------- v ? v v v i v ? i i L1ME4c_3end#L 252 AGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAAT 301 chr4ptel1M 595686 AGATTCAACCATTGTGGAGAGCAGTTTGGAAGTGTGCCCAAAGGGCCATT 595735 v i v v v i i v i ii iviv i v L1ME4c_3end#L 302 TGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATA 351 chr4ptel1M 595736 GAACCGTGCATATCCTCTGACCCAGCAGTGTTTA------------TATC 595773 i vi v i i i i - ii ------------ L1ME4c_3end#L 352 AAAATGTTCATACCCTTTGACCCAGTAAT-TCCACTTCTGGGAATTTATC 400 chr4ptel1M 595774 CCAAAGAGAT--CTTACAGGAAGGAAAGGGACCCACATGTGCCAAAATGC 595821 i i i --i i v i ii -- i i ii v i i L1ME4c_3end#L 401 CTAAGGAAATAATTCAAAAGAAGGAAAAAG--CTATATGCACGAAGATGT 448 chr4ptel1M 595822 ---CTGAGGCATCCTCTGTGATGGAGAAAAACTGGAAACTGAGGGAA-GC 595867 ---i vi i iv i i i i v i vivvvi - i L1ME4c_3end#L 449 TCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGT 498 chr4ptel1M 595868 CCATCACTGGGAGGACACTTGAATAAGTTATAGTGTAG-AATGCGATGGA 595916 v v i i i iiv i i i i ii v-? iv L1ME4c_3end#L 499 CCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGA 548 chr4ptel1M 595917 ATATTAT 595923 L1ME4c_3end#L 549 ATATTAT 555 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 43.62 CpG sites = 90, Kimura (unadjusted) = 44.46 Transitions / transversions = 1.61 (90/56) Gap_init rate = 0.04 (17 / 461), avg. gap size = 3.06 (52 / 17) 381 30.47 10.28 3.69 chr4ptel1M 595473 596007 (403993) L1MC4a_3end#LINE/L1 66 634 (1995) m_b179s551i2 6957 chr4ptel1M 595473 AAAGGGTCAAAGAACACGAACA----ATTTTCAAAA-GAAACTGAAA--- 595514 v v ii i ---- iv - ? iv? --- L1MC4a_3end#L 66 AAATGGGCAAAAGACATGAACAGACAATTCACAAAAAGANATANAAATGG 115 chr4ptel1M 595515 CCCTTTCTAGTCATATGAAAAGATGATCA-CGACA-----GATCAGAGAA 595558 --- iv v - vv -----i v L1MC4a_3end#L 116 CCCTT---AAACATATGAAAAGATGTTCAACCTCACTCATAATAAGAGAA 162 chr4ptel1M 595559 ATGGAGATTAAGACAACTCTGAGGTACTGGCTCACGCCTCTCAGACCGGC 595608 v i i v v i iivi v i v ii L1MC4a_3end#L 163 ATGCAAATTAAAACTACACTGAGATACCATTTCTCACCTATCAGATTGGC 212 chr4ptel1M 595609 TAAGATGACAGGAAAA---GACAAGGATGAATGGGGGAGAGGATGTGGG- 595654 v i v- -- i--- vivvvvv vv v v - L1MC4a_3end#L 213 AAAAATT-CA--AAAGTTTGACAACACACTCTGTTGGCGAGGCTGTGGGG 259 chr4ptel1M 595655 --------ACACTGAGACATGGTTGGTGGAACTGTGAACAGATTCAACCA 595696 -------- v v v v i i v ii ?v i v v L1MC4a_3end#L 260 AAACAGGCACTCTCATACATTGCTGGTGGGAATGCAAANTGGTACAACCC 309 chr4ptel1M 595697 TTGTGGAGAGCAGTTTGGAAGTGTGCC--CAAAGGGCCATTGAACCGTGC 595744 ? i v i v i i - i-- ivvv ------i L1MC4a_3end#L 310 TTNTGGAGGGGAATTTGGCAATAT-CTAACAAAACTACAT------ATGC 352 chr4ptel1M 595745 A--TATCCTCTGACCCAGCAGT-----GTTTA------TATCCCAAAGAG 595781 -- i i i -----v i ------ i ii v L1MC4a_3end#L 353 ATTTACCCTTTGACCCAGCAATCCCACTTCTAGGAATTTACCCTGAAGAT 402 chr4ptel1M 595782 A----TCTTACAGGAAGGAAAGGGACCCACATGTGC-CAAA---ATGC-C 595822 ---- iv v v vi -----i? i - i--- v -i L1MC4a_3end#L 403 ACACCTCCAACATGTACAAAA-----TNACATATGCACAAGGTTATTCAT 447 chr4ptel1M 595823 TGAGGCATCCTCTGTGATGGAGAAAAACTGGAAACTGAGGGAA-GCCCAT 595871 vi iv i i v vi v i vivvvi - L1MC4a_3end#L 448 TGCAGCATTGTTTGTAATTGCAAAATATTGGAAACAACCTAAATGCCCAT 497 chr4ptel1M 595872 CACTGGGAGGACACTTGAATAAGTTATAGTGTAG-AATGCGATGGAATAT 595920 ??v i i?iiv ii i ii v-v ii i i i L1MC4a_3end#L 498 NNATAGGAGANTGGTTGAATAAACTATGGTACATCCACACAATGGAGTAC 547 chr4ptel1M 595921 TATTGTTCTGTAAGAAATGAGCAGCAGGAGGATTTCAGAGA---GGCCTG 595967 vvvv i --- v vv i i viv --- iiv L1MC4a_3end#L 548 TATGCAGCTGTAAAAA---AGAATGAGGAAGATCTCTATGAACTGATATG 594 chr4ptel1M 595968 GAGAGACTGACAGAAACTGATGCTGAGTGAAGTGAGCAGA 596007 v i vv i vv iv i i ivi i L1MC4a_3end#L 595 GAGTGATTTCCAGGATATATTGTTAAGTGAAAAAAGCAAA 634 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 40.66 CpG sites = 80, Kimura (unadjusted) = 40.66 Transitions / transversions = 1.04 (80/77) Gap_init rate = 0.07 (40 / 534), avg. gap size = 1.90 (76 / 40) 258 29.75 0.00 7.20 chr4ptel1M 598266 598399 (401601) L1MB2_3end#LINE/L1 144 268 (650) m_b179s551i3 6958 chr4ptel1M 598266 AACATCATTATTGTTATTTAAAGTAATTCAGCAGCAAATTAAAACATTTC 598315 i --i i - ii v ------ i vvivv L1MB2_3end#LI 144 AACATCACTA--ATCATT-AGGGAAAT------GCAAATCAAAACCACAA 184 chr4ptel1M 598316 TCAGGTAGTACCTCAAACTTAACAGATTGCCTAATATGACAGAAAAAGAA 598365 v i vi v ii vi iv v v v v i v L1MB2_3end#LI 185 TGAGATATCACCTCACACCCATTAGGATGGCTACTATCAAAAAAACAGAA 234 chr4ptel1M 598366 AATGACAAATGCTGGGGGGGATGTGGGCAAACTG 598399 i i i v i iv i L1MB2_3end#LI 235 AATAACAAGTGTTGGCGAGGATGTGGAGAAATTG 268 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 38.38 CpG sites = 20, Kimura (unadjusted) = 38.38 Transitions / transversions = 1.18 (20/17) Gap_init rate = 0.07 (9 / 133), avg. gap size = 1.00 (9 / 9) 240 28.36 14.18 0.00 chr4ptel1M 598299 598432 (401568) L1MA8_3end#LINE/L1 168 320 (718) m_b179s551i4 6958 chr4ptel1M 598299 GCAAATTAAAACATTTCTCAGGTAGTACCTCAAACTTAACAGATTGCCTA 598348 vvivv v i vi v i ivi v v L1MA8_3end#LI 168 GCAAATTAAAACCACAATGAGATATCACCTCACACCTGTTAGAATGGCTA 217 chr4ptel1M 598349 ATATGACAGAAAAAGAAAATGACAAATGCTGGGGGGGATGTGG------- 598391 v v v i i vii i i i i v i ------- L1MA8_3end#LI 218 TTATCAAAAAGACGAAAGATAACAAGTGTTGGCGAGGATGTGGAGAAAAG 267 chr4ptel1M 598392 ---------GCAAACTGTTGGTAGAATTGTGAAT--GGAGAGCAATT-TG 598429 --------- v i i v i -- v v v - L1MA8_3end#LI 268 GGAACCCTTGCACACTGTTGGTGGGAATGTAAATTAGTACAGCCATTATG 317 chr4ptel1M 598430 GAA 598432 L1MA8_3end#LI 318 GAA 320 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 34.78 CpG sites = 18, Kimura (unadjusted) = 35.92 Transitions / transversions = 0.90 (18/20) Gap_init rate = 0.03 (4 / 133), avg. gap size = 4.75 (19 / 4) 263 31.68 0.00 0.00 chr4ptel1M 598299 598399 (401601) L1MB1_3end#LINE/L1 168 268 (647) m_b179s551i5 6958 chr4ptel1M 598299 GCAAATTAAAACATTTCTCAGGTAGTACCTCAAACTTAACAGATTGCCTA 598348 i vvivv v i vi v i ivi iv v L1MB1_3end#LI 168 GCAAATCAAAACCACAATGAGATATCACCTCACACCTGTTAGGATGGCTA 217 chr4ptel1M 598349 ATATGACAGAAAAAGAAAATGACAAATGCTGGGGGGGATGTGGGCAAACT 598398 v v v i v i i i i v i iv i L1MB1_3end#LI 218 TTATCAAAAAAACAAAAAATAACAAGTGTTGGCGAGGATGTGGAGAAATT 267 chr4ptel1M 598399 G 598399 L1MB1_3end#LI 268 G 268 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 41.77 CpG sites = 16, Kimura (unadjusted) = 41.77 Transitions / transversions = 1.00 (16/16) Gap_init rate = 0.00 (0 / 100), avg. gap size = 0.0 (0 / 0) 292 33.03 0.00 5.39 chr4ptel1M 598441 598616 (401384) L1ME3C_3end#LINE/L1 399 565 (305) m_b179s551i6 6959 chr4ptel1M 598441 AAAGACTATCAAACTGTGTGTACCCAAAAAAAACCTATTTGTACAAAAAT 598490 i i v iv - i --- ii i v ---- i L1ME3C_3end#L 399 AGAAACTCTCGCAC-GTGTGCAC---AAGGAGACAT----GTACAAGAAT 440 chr4ptel1M 598491 ATTGGTCACAGCTCTTTTTGTGATGACTAAGAATTGGAAATTGAGGGAAT 598540 i vi ii vi v i ii v i ivivvvi L1ME3C_3end#L 441 GTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAAT 490 chr4ptel1M 598541 GCCCATTAATTGGAGAACAGCTGAATAAAATGCAGCATATTATTTTGATG 598590 i i iv ii v i v ii i vv vii L1ME3C_3end#L 491 GTCCATCAACAGGAGAATGGATAAATAAATTGTGGTATATTCATACAATG 540 chr4ptel1M 598591 GAATATCATGGTGCTGTAAGAAATGA 598616 ii ivv v v - L1ME3C_3end#L 541 GAATACTATACAGCAGTTA-AAATGA 565 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 44.17 CpG sites = 34, Kimura (unadjusted) = 45.31 Transitions / transversions = 1.62 (34/21) Gap_init rate = 0.05 (9 / 175), avg. gap size = 1.00 (9 / 9) 327 36.36 0.00 0.00 chr4ptel1M 598466 598619 (401381) L1ME4c_3end#LINE/L1 422 575 (255) m_b179s551i7 6959 chr4ptel1M 598466 AAAAAAAACCTATTTGTACAAAAATATTGGTCACAGCTCTTTTTGTGATG 598515 ii v v i i i i vi ii vi v i i i L1ME4c_3end#L 422 AGGAAAAAGCTATATGCACGAAGATGTTCATTGCAGCGTTATTTATAATA 471 chr4ptel1M 598516 ACTAAGAATTGGAAATTGAGGGAATGCCCATTAATTGGAGAACAGCTGAA 598565 i v i ivivvvi i vi v i ii i i i L1ME4c_3end#L 472 GCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAATGGTTAAG 521 chr4ptel1M 598566 TAAAATGCAGCATATTATTTTGATGGAATATCATGGTGCTGTAAGAAATG 598615 v iii i i i?vi i i vv ii v i L1ME4c_3end#L 522 TAAATTATGGTACATCNACTCGATGGAATATTATGCAGCCATTAAAAATG 571 chr4ptel1M 598616 ATGA 598619 i L1ME4c_3end#L 572 ATAA 575 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 51.77 CpG sites = 39, Kimura (unadjusted) = 54.78 Transitions / transversions = 2.29 (39/17) Gap_init rate = 0.00 (0 / 153), avg. gap size = 0.0 (0 / 0) 12 27.92 0.00 2.22 chr4ptel1M 599141 599186 (400814) (GGAGGGG)n#Simple_repeat 1 45 (0) m_b179s252i1 6960 chr4ptel1M 599141 GGGGGTGGGGGGGCGGAGGGGAGAGGAGGGTAAGAGGGAGAGGAGA 599186 i v i v i - v i i i i (GGAGGGG)n#Si 1 GGAGGGGGGAGGGGGGAGGGGGGAGG-GGGGAGGGGGGAGGGGGGA 45 Matrix = Unknown Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1) 16 14.72 0.00 7.32 chr4ptel1M 599142 599185 (400815) (GGGGA)n#Simple_repeat 1 41 (0) m_b179s252i2 6960 chr4ptel1M 599142 GGGGTGGGGGGGCGGAGGGGAGAGGAGGGTAAGAGGGAGAGGAG 599185 v i - i -i - i (GGGGA)n#Simp 1 GGGGAGGGGAGG-GGAGGGGAGGGGAGGG-GAG-GGGAGGGGAG 41 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.07 (3 / 43), avg. gap size = 1.00 (3 / 3) 186 32.06 0.99 7.37 chr4ptel1M 600504 600604 (399396) MIR1_Amn#SINE/MIR 23 117 (113) m_b179s601i0 6961 chr4ptel1M 600504 GGATGGCACAGCGGAC-AGAATTCGGAGGACCGGAGCTCAGAGCTGACCT 600552 i vi vi -i i i ii v i i ?i?v iviv MIR1_Amn#SINE 23 GGATAGAGCACTGGACTGGGACTCGGGAGACCTGGGTTCNANTCCCGGCT 72 chr4ptel1M 600553 TGGACACTGAACGCTTTCTAGCTGTGCAGCCCTGGGCAAGTCACTTCGCC 600602 iv v ?i------- i? ? iii i ?i MIR1_Amn#SINE 73 CTGCCACTNG-------CCNGCTGNGTGACCTTGGGCAAGTCACTTNACC 115 chr4ptel1M 600603 CC 600604 i MIR1_Amn#SINE 116 TC 117 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 47.27 CpG sites = 22, Kimura (unadjusted) = 49.71 Transitions / transversions = 2.75 (22/8) Gap_init rate = 0.08 (8 / 100), avg. gap size = 1.00 (8 / 8) 190 28.25 2.22 9.52 chr4ptel1M 600515 600604 (399396) MIR3#SINE/MIR 29 112 (96) m_b179s601i1 6961 chr4ptel1M 600515 CGGAC-AGAATTCGGAGGACCGGAGCTC-AGAGCTGACCTTGGACACTGA 600562 -i i v i ii v i i - vv i i ii -v i MIR3#SINE/MIR 29 CGGACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTG-CCACTAA 77 chr4ptel1M 600563 ACGCTTTCTAGCTGTGCAGCCCTGGGCAAGTCACTTCGCCCC 600604 ------- ? iii i i i MIR3#SINE/MIR 78 -------CTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTC 112 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 36.37 CpG sites = 18, Kimura (unadjusted) = 38.57 Transitions / transversions = 3.60 (18/5) Gap_init rate = 0.11 (10 / 89), avg. gap size = 1.00 (10 / 10) 12 14.30 3.03 3.03 chr4ptel1M 603350 603382 (396618) (CCCGCC)n#Simple_repeat 1 33 (0) m_b179s252i3 6962 chr4ptel1M 603350 CCCGCCCGCGCCAGCAGCCCGCG-CCCCGCCCCC 603382 v -v v v - (CCCGCC)n#Sim 1 CCCGCCCCCGCC-CCCGCCCCCGCCCCCGCCCCC 33 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.06 (2 / 32), avg. gap size = 1.00 (2 / 2) 12 11.20 3.23 3.23 chr4ptel1M 603450 603480 (396520) (GAGGGG)n#Simple_repeat 1 31 (0) m_b179s252i4 6963 chr4ptel1M 603450 GAGGAGGGGGGGGGA-TGGGAGGGGGAGAGGG 603480 - i -v i (GAGGGG)n#Sim 1 GAGG-GGGAGGGGGAGGGGGAGGGGGAGGGGG 31 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2) 15 14.03 4.88 2.38 chr4ptel1M 605263 605303 (394697) (GGCCCC)n#Simple_repeat 1 42 (0) m_b179s252i5 6964 chr4ptel1M 605263 GGCCCCTTCTCCCGGGCCCGGCCTC--CCCCGGCCCCGCCCCC 605303 vv - v i -- v (GGCCCC)n#Sim 1 GGCCCCGGC-CCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCC 42 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.50 (3 / 2) 262 25.71 1.43 0.00 chr4ptel1M 608583 608652 (391348) C MIRc#SINE/MIR (21) 247 177 m_b179s601i2 6965 chr4ptel1M 608583 TTGTAGACGGCTTTAAGGTTTGCAAAGTGCTTT-ACAACTATTGTCTCAT 608631 v vvi vi i i - vvi i C MIRc#SINE/MIR 247 TTGTATAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATCTCAT 198 chr4ptel1M 608632 TCAATGCTCACAAGTACCTTG 608652 ii v vv i C MIRc#SINE/MIR 197 TTGATCCTCACAACAACCCTG 177 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 29.75 CpG sites = 9, Kimura (unadjusted) = 31.80 Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.01 (1 / 69), avg. gap size = 1.00 (1 / 1) 185 32.95 1.12 1.12 chr4ptel1M 609119 609207 (390793) C MIRb#SINE/MIR (178) 90 2 m_b179s601i3 6966 chr4ptel1M 609119 CAGCCAGTATGCATCCAAGGCAACACTTGAACCCAGCTATTTCTG-CTCT 609167 i v iiv vi v iiv i i v v v - i C MIRb#SINE/MIR 90 CAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCC 41 chr4ptel1M 609168 AGAAGCCAGCTTCCTGTTCACTACACCCACCTGCTCCTCT 609207 - v ivii v i i vvv i C MIRb#SINE/MIR 40 A-AAGCCCGTGCTCTTTCCACTGCACCACGCTGCCCCTCT 2 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 40.30 CpG sites = 15, Kimura (unadjusted) = 44.23 Transitions / transversions = 1.07 (15/14) Gap_init rate = 0.02 (2 / 88), avg. gap size = 1.00 (2 / 2) 226 30.58 0.82 8.85 chr4ptel1M 610796 610917 (389083) C MIRc#SINE/MIR (155) 113 1 m_b179s601i4 6965 chr4ptel1M 610796 GGTGAAGTGACG-ACTCAGGGTCATAGAACTATTGAGCCAGGTGCCTGAG 610844 v v-i i i i v i v i ----- v v C MIRc#SINE/MIR 113 GGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAG-----TGGCAGAG 69 chr4ptel1M 610845 GCCGTATTGGACCTCCAGTGCTCCCAACTCCAGGGCTGGTGCTCCACCCA 610894 v v v i v v i vi vi ii i v ii ivi C MIRc#SINE/MIR 68 CCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCA 19 chr4ptel1M 610895 GCTGCCCCACATCCTCTGCCTTG 610917 - v ---- i C MIRc#SINE/MIR 18 -CTGCACCACA----CTGCCTCG 1 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 38.14 CpG sites = 18, Kimura (unadjusted) = 39.62 Transitions / transversions = 1.12 (18/16) Gap_init rate = 0.09 (11 / 121), avg. gap size = 1.00 (11 / 11) 285 23.26 2.25 3.41 chr4ptel1M 611567 611655 (388345) C Charlie7#DNA/hAT-Charlie (440) 2175 2088 m_b179s502i0 6967 chr4ptel1M 611567 AGAAATGCAGGGCAGG-TGTGAATACTAAAGCCAGATACTCATTCTTCAA 611615 i vv iv - i vv v vv i C Charlie7#DNA/ 2175 AGAAGTGCATCGTTGGCTGCGCTTACTAAATCATGATACTCATTTTTCAA 2126 chr4ptel1M 611616 TCCCAT-CACTCAGCACGCAGAAGTTTGTCTTGTTGCAATT 611655 - iv vi i i i --- v C Charlie7#DNA/ 2125 TCCCATCCACCAATTATGCAAAGGTTT---TTGTTGAAATT 2088 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 26.40 CpG sites = 9, Kimura (unadjusted) = 27.95 Transitions / transversions = 0.82 (9/11) Gap_init rate = 0.06 (5 / 88), avg. gap size = 1.00 (5 / 5) 15 20.36 0.00 0.00 chr4ptel1M 611876 611904 (388096) (C)n#Simple_repeat 1 29 (0) m_b179s252i6 6968 chr4ptel1M 611876 CCCCTCCTTCCCCCCCACCCCCCTCCCCC 611904 i ii v i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC 29 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 1028 27.55 2.72 2.98 chr4ptel1M 612290 612693 (387307) C L1ME3G_3end#LINE/L1 (521) 403 1 m_b179s551i8 6969 chr4ptel1M 612290 ATCTCTTTGGGATATAAGCCCAGTAGAAACACTGCTGGGTCAAGGGGTAT 612339 i ? i v v? ? v viiv i i C L1ME3G_3end#L 403 ATTTCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTAT 354 chr4ptel1M 612340 GCACAGTTTGATCATTTGATCATTGGAGCATAGTGTCAAACTGCTCTCCA 612389 i v i -- v -- v ---- v i i i C L1ME3G_3end#L 353 GCGCATTTTAA--ATTTTA--ATAG----ATACTGCCAAATTGCCCTCCA 312 chr4ptel1M 612390 AAATGGTTGGATCCGTTCTCAGTTCTACCAACAATGTACCAGTGTCCCAG 612439 ? i v i vi iv v i i i i iv v v v C L1ME3G_3end#L 311 AAANGGCTGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCG 262 chr4ptel1M 612440 GTTCCCCATATCCCCTCTAACATTCATCATTATCTTTCCCTGTCATTCTA 612489 v i i i v i i ?ivi vv? ii vvv i v C L1ME3G_3end#L 261 TTTCCCCACACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTT 212 chr4ptel1M 612490 GCCAATCTGACAGGTG----------TCTCAGAGTTGTCTTAATTTGCAT 612529 ii ---------- vv i C L1ME3G_3end#L 211 GCCAATCTGATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCAT 162 chr4ptel1M 612530 TTCTCTGATCAATAGTGATTTACAGCACTTTTTCATATGACTAGAAATGG 612579 i i v vv vv ii vi vviiivi C L1ME3G_3end#L 161 TTCCCTGATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCA 112 chr4ptel1M 612580 TTTTAATTTCTTCATCTGAAAATTGTCTGTTGATATCCTTTG-ACATTTA 612628 vv i v vi i v -v v C L1ME3G_3end#L 111 TTTGTATTTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTT 62 chr4ptel1M 612629 TCAATTGGAGAATGGCTTGAATTCTTATAAATTGGAGTCAATTCTCTCTA 612678 v iv-- v v-- vi v vivv i i v C L1ME3G_3end#L 61 TCTATTGGGT--TGTCTTT--TTCTTATTGATTTGTAGGAGTTCTTTATA 16 chr4ptel1M 612679 TATTTTAGAAATGAA 612693 i i v v C L1ME3G_3end#L 15 TATTCTGGATATTAA 1 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 34.94 CpG sites = 52, Kimura (unadjusted) = 35.33 Transitions / transversions = 0.93 (52/56) Gap_init rate = 0.03 (14 / 403), avg. gap size = 1.64 (23 / 14) 732 34.16 4.37 3.22 chr4ptel1M 612553 613535 (386465) C L1P3_orf2#LINE/L1 (8) 3286 2293 m_b179s551i9 6969 chr4ptel1M 612553 AGCACTTTTTCATATGACTAGAAATGGTTTTAATTTCTTCATCTGAAAAT 612602 vi vi ivviiiv iv v v v i i v C L1P3_orf2#LIN 3286 AGCTTTTTTTCATATGTTTGTTGGCCGCATAAATGTCTTCTTTTGAGAAG 3237 chr4ptel1M 612603 TGTCTGTTGATATCCTTTGAC-ATTTATCAATTGGAGAATGGCTTGAATT 612651 v i v - i v ii v ivvi vvv vvv C L1P3_orf2#LIN 3236 TGTCTGTTCATATCCTTCGCCCACTTTTTGATGGGGTTGTTTGTTTTTTT 3187 chr4ptel1M 612652 CTTATAAATTGGAGTCAATTCTCTCTATATTTTAGAAATGAAACCTTTAT 612701 i v vv v i ii v v i i v v iv i C L1P3_orf2#LIN 3186 CTTGTAAATTTGTTTAAGTTCCTTGTAGATTCTGGATATTAGCCCTTTGT 3137 chr4ptel1M 612702 CAGAACCCTTAAATGTAAAAATGTTTTCCCAGCTTACTGCTTCCCTTCTA 612751 vvvv vi v i v i vii iiv v v vi v C L1P3_orf2#LIN 3136 CAGATGGATAGATTGCAAAAATTTTCTCCCATTCTGTAGGTTGCCTGTTC 3087 chr4ptel1M 612752 ATCTTGTCTGCAT--TAGTTTTGTTTA---TACAAAAACCTGTTAGCTTA 612796 i---- - -- iv i--- i i i iiv i C L1P3_orf2#LIN 3086 AC----TCTG-ATGATAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTA 3042 chr4ptel1M 612797 ATATAATCAACATTC-TCTACTTGGGGTTCAATTATGAGTTCCAGTTCTT 612845 vvi v- i- v i v v ivi iiv v v ivv vv v C L1P3_orf2#LIN 3041 ATTAGATCC-CATTTGTCAATTTTGGCTTTTGTTGCCATTGCTTTTGGTG 2993 chr4ptel1M 612846 CTTTGGCCACAAATTCCT--CCCTTCTCCACAGATCTGAGAGGTA--GAC 612891 i i i ii v i -- v vi i i- vi iv -- v C L1P3_orf2#LIN 2992 TTTTAGTCATGAAGTCTTTGCCCATGCCTAT-GTCCTGAATGGTATTGCC 2944 chr4ptel1M 612892 TACCTTTT--------GTTTTTTTAGTTTGCTTATATCACTCTTTATATC 612933 vv -------- v i --- vi ----- ii i C L1P3_orf2#LIN 2943 TAGGTTTTCTTCTAGGGTTTTTATGGTTT---TAGGTC-----TTACGTT 2902 chr4ptel1M 612934 TAAATCATGAACCCATTTTGACCTTATTTTTGTATACGATGTTAGGTGTG 612983 i v v i i vi v v i v viv C L1P3_orf2#LIN 2901 TAAGTCTTTAATCCATCTTGAGTTAATTTTTGTATAAGGTGTAAGGAAGG 2852 chr4ptel1M 612984 GGTC-AATGCCTAGTTTCTGCCATA---CTAGGTTCCAATTTTCCCAAAA 613029 - i vi viv - --- --- i v C L1P3_orf2#LIN 2851 GGTCCAGTTTCAGTTTTCTGC-ATATGGCTAG---CCAGTTTTCCCAACA 2806 chr4ptel1M 613030 GTTTTTGTCGAATAGTGAGTTCTTATCCCAAAAGCTTGGTCTTTG---GG 613076 viv i ii v i i - v vv - i --- C L1P3_orf2#LIN 2805 CCATTTATTAAATAGGGAATCCTT-TCCCCATTGCTTG-TTTTTGTCAGG 2758 chr4ptel1M 613077 TTTGTAAAACACTAGATTGCTATAGTCAT-TGCC--TATTTTGTCCTGTG 613123 v v ii v i i vii - v -- ---- v C L1P3_orf2#LIN 2757 TTTGTCAAAGATCAGATGGTTGTAGATGTGTGGCGTTATTT----CTGAG 2712 chr4ptel1M 613124 ATC-CTAACCTATTCCACTGATCAACTAT-TCTATTTCTTAGCCGGTACC 613171 ii - ivi i i i v - - i ivvvi i C L1P3_orf2#LIN 2711 GCCTCTGTTCTGTTCCATTGGTCTA-TATATCTGTTTTGGTACCAGTACC 2663 chr4ptel1M 613172 AAATGATTTTGATGATTGCTGCTTTATGATATAGTTTTAGGTCTGGCACA 613221 viivi i v i iv i i ii v i ------ C L1P3_orf2#LIN 2662 ATGCTGTTTTGGTTACTGTAGCCTTGTAGTATAGTTTGAAGTC------A 2619 chr4ptel1M 613222 GGTAG-GCCATGTCTTCTATGGCATTTTTTTTCATTA--ATTCCCTTGAA 613268 - iv i i viivvii i vv -- vi iv C L1P3_orf2#LIN 2618 GGTAGCGTGATGCCTCCAGCTTTGTTCTTTTTGCTTAGGATTGTCTTGGC 2569 chr4ptel1M 613269 -ATTCTTGACCTTTTGTTCTTCCAGATGAATTTTATCAT--TTTTTTTTA 613315 - v vv vi v vv v v vvi -- i C L1P3_orf2#LIN 2568 TATACGGGCTCTTTTTTGGTTCCATATGAAATTTAAAGTAGTTTTTTCTA 2519 chr4ptel1M 613316 --TCTATAAAATAATTTCTTGGGAGTTTGGT----ATGGCATTAAATAAG 613359 -- i i iv v ivv v i i ---- i i vvi C L1P3_orf2#LIN 2518 ATTCTGTGAAGAAAGTCAATGGTAGCTTGATGGGGATAGCATTGAATCTA 2469 chr4ptel1M 613360 TAGATTAATTTAGATAATATTGTCATTTTTATTATATTTGCTCAGCCTAC 613409 i v i ii i v i i iv vii vv i C L1P3_orf2#LIN 2468 TAAATTACTTTGGGCAGTATGGCCATTTTCACGATATTGATTCTTCCTAT 2419 chr4ptel1M 613410 CCATGAGTACTTGATATTTTTCCACCTGATTAGGTCTGACTTTATTTATG 613459 i ivvi i ii v iv ivvii viv C L1P3_orf2#LIN 2418 CCATGAGCATGGAATGTTTTTCCATTTGTTTGTGTCCTCTCTTATTTCCT 2369 chr4ptel1M 613460 TGGAAAATGTTTTGTAGTTGTGTTCTTATAGTTCCTGACTTTCCCTTGGC 613509 iiv i v v vi ivv v v vvviv vv C L1P3_orf2#LIN 2368 TGAGCAGTGGTTTGTAGTTCTCCTTGAAGAGGTCCTTCACATCCCTTGTA 2319 chr4ptel1M 613510 AGATAGATTCCCAAATATTTTATACT 613535 v iv i ii v C L1P3_orf2#LIN 2318 AGTTGTATTCCTAGGTATTTTATTCT 2293 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 45.80 CpG sites = 163, Kimura (unadjusted) = 46.40 Transitions / transversions = 1.01 (163/162) Gap_init rate = 0.05 (52 / 982), avg. gap size = 1.44 (75 / 52) 283 28.15 0.00 3.12 chr4ptel1M 614301 614399 (385601) C Charlie7#DNA/hAT-Charlie (2056) 559 464 m_b179s502i1 6967 chr4ptel1M 614301 AGATGGGATTAGATCAGGATTGTTTGGACGGTGCCGTGTGGTTGATCAAG 614350 vv ivv vv vvi ivi i iv C Charlie7#DNA/ 559 AGATCTGATTAGATCGTCATTGTTTTTACCTCGTAATGTGGCTGACGAAG 510 chr4ptel1M 614351 AGCTCTTGCCAGGAGAAGGAGAAACGCCGGCTCTGCCATTGGCTTTTTG 614399 v i i --- v ii i i vv v C Charlie7#DNA/ 509 AGCTCGTACTAGG---AGTAGAAGTGTCAGCTCTGCCATTTTCTTGTTG 464 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 30.91 CpG sites = 12, Kimura (unadjusted) = 35.43 Transitions / transversions = 0.80 (12/15) Gap_init rate = 0.03 (3 / 98), avg. gap size = 1.00 (3 / 3) 406 26.77 2.04 3.45 chr4ptel1M 615062 615208 (384792) C Charlie7#DNA/hAT-Charlie (2177) 438 294 m_b179s502i2 6967 chr4ptel1M 615062 TTATCTG-AGTCTGTAGTTTCTCTGCAGGAATCTTCATGACTGTCCCCAA 615110 v- i i ii i iv i -- i v iv- C Charlie7#DNA/ 438 TTATCTTCAATCCGCGGTTTCTTTGCAGGAATCTTTTTAA--GCCACTT- 392 chr4ptel1M 615111 AGTCCCTTTTATGAGAGTTGGTTTAGGGAAATCCAGTTAATCTCATCCAT 615160 - v i i i vv v i v v v i C Charlie7#DNA/ 391 -GTCCATTTTGTGAGGGTTAGTTTAGTTAAAACTAGATAATATAATCCGT 343 chr4ptel1M 615161 AAATCCACTTCA-GGGGTAC-CAGAGACTGCAGCTAGGCTGCCACATGCT 615208 v -v i - iv i i- v ii v i i C Charlie7#DNA/ 342 AAATCCACTTAACCGGGCACACGTAAACTGCAA-TACGTCGCAATACGCT 294 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 27.55 CpG sites = 22, Kimura (unadjusted) = 33.84 Transitions / transversions = 1.38 (22/16) Gap_init rate = 0.05 (8 / 146), avg. gap size = 1.00 (8 / 8) 215 33.33 0.00 0.00 chr4ptel1M 615278 615337 (384663) C L2a_3end#LINE/L2 (0) 517 458 m_b179s601i6 6970 chr4ptel1M 615278 ACTCCCTCAGTCAAGCAACATTTATTAGATGCCTGTTATGTGCCAGGTGT 615327 i vi v vv i iiii ii iii C L2a_3end#LINE 517 ATTCATTCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCAC 468 chr4ptel1M 615328 TCCACTAAGC 615337 viv i C L2a_3end#LINE 467 TGTTCTAGGC 458 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 44.04 CpG sites = 14, Kimura (unadjusted) = 47.39 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0) 232 27.45 0.00 0.00 chr4ptel1M 615278 615328 (384672) C L2c_3end#LINE/L2 (0) 478 428 m_b179s601i5 6970 chr4ptel1M 615278 ACTCCCTCAGTCAAGCAACATTTATTAGATGCCTGTTATGTGCCAGGTGT 615327 i vi v vv iiii ii i i C L2c_3end#LINE 478 ATTCATTCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGC 429 chr4ptel1M 615328 T 615328 C L2c_3end#LINE 428 T 428 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 29.81 CpG sites = 10, Kimura (unadjusted) = 36.07 Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 38 27.86 0.72 4.51 chr4ptel1M 615684 615821 (384179) (TTCT)n#Simple_repeat 1 133 (0) m_b179s252i7 6971 chr4ptel1M 615684 TTCTCTTTGTCATTTCTTTTTCTGTTTCTTTCCTTCTTTTCCTCCTTCCT 615733 i i v - i i v i - i i i (TTCT)n#Simpl 1 TTCTTTCTTTC-TTTCTTTCTTTCTTTCTTTCTTTC-TTTCTTTCTTTCT 48 chr4ptel1M 615734 TCCTCTTTTTTCTTTCTTCTCTTCCTTTCTCTCTCTTTCTCCTTCTCACT 615783 i - i - i i i i i i iv (TTCT)n#Simpl 49 TTCT-TTCTTTCTTTCTT-TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 96 chr4ptel1M 615784 GTATCCTCCTTTCTTCCTTCCTGTTTCTCTCT-TTTCTT 615821 - - i i i i v i i i - (TTCT)n#Simpl 97 -T-TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 133 Matrix = Unknown Transitions / transversions = 6.00 (24/4) Gap_init rate = 0.05 (7 / 137), avg. gap size = 1.00 (7 / 7) 232 17.95 0.00 0.00 chr4ptel1M 615840 615878 (384122) C 7SLRNA#SINE/Alu (63) 257 219 [m_b179s502i3] 6972 chr4ptel1M 615840 GCTATTCACAAGCCTGATCCCACTGCAGATCAACACAGG 615878 i vi i v i i C 7SLRNA#SINE/A 257 GCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGG 219 Matrix = 18p49g.matrix Kimura (with divCpGMod) = 14.83 CpG sites = 5, Kimura (unadjusted) = 21.09 Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 15 12.16 3.70 0.00 chr4ptel1M 616315 616341 (383659) (AG)n#Simple_repeat 1 28 (0) m_b179s252i8 6973 chr4ptel1M 616315 AGAGAGAGAGGGAGAGAGCAAGAG-GAG 616341 i vi - (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAG 28 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.04 (1 / 26), avg. gap size = 1.00 (1 / 1) 23 28.00 2.53 0.00 chr4ptel1M 616538 616616 (383384) (TACA)n#Simple_repeat 1 81 (0) m_b179s252i9 6974 chr4ptel1M 616538 TACATACATACATACATACATAGGT-GATACACATATAGATACCTATATG 616586 vi -v i i v v i i (TACA)n#Simpl 1 TACATACATACATACATACATACATACATACATACATACATACATACATA 50 chr4ptel1M 616587 CGTGTAAACATACACATGTATATA-AAACAT 616616 i ii v i ii i - v (TACA)n#Simpl 51 CATACATACATACATACATACATACATACAT 81 Matrix = Unknown Transitions / transversions = 2.00 (12/6) Gap_init rate = 0.03 (2 / 78), avg. gap size = 1.00 (2 / 2) 11 13.18 5.71 2.78 chr4ptel1M 618635 618669 (381331) (GCCCCC)n#Simple_repeat 1 36 (0) m_b179s252i10 6975 chr4ptel1M 618635 GCCCCCTGGCCCCGCCCCC-TCCGAG-CCCCGCCCCC 618669 - v -i vv - (GCCCCC)n#Sim 1 GCCCCC-GCCCCCGCCCCCGCCCCCGCCCCCGCCCCC 36 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.09 (3 / 34), avg. gap size = 1.00 (3 / 3) 24 7.37 4.65 0.00 chr4ptel1M 618892 618934 (381066) (CTCCCCT)n#Simple_repeat 1 45 (0) m_b179s252i11 6976 chr4ptel1M 618892 CTCCCCTCTCCCCTCTCCTTTCTCCCCTCT-CCCTC-CGCCTCTC 618934 ii - - v (CTCCCCT)n#Si 1 CTCCCCTCTCCCCTCTCCCCTCTCCCCTCTCCCCTCTCCCCTCTC 45 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.00 (2 / 2) 25 8.08 3.33 6.90 chr4ptel1M 618973 619032 (380968) (CTCC)n#Simple_repeat 1 58 (0) m_b179s252i12 6977 chr4ptel1M 618973 CTCGCTCCCCTCCTCCCTCTTCCTCCCTCCCT-CCTCCCTCTTCCTACCT 619021 v ii -- - -- v (CTCC)n#Simpl 1 CTCCCTCCCTCCCTCCCTC--CCTCCCTCCCTCCCTCCCTC--CCTCCCT 46 chr4ptel1M 619022 CCCT-CCTCCCT 619032 - (CTCC)n#Simpl 47 CCCTCCCTCCCT 58 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.10 (6 / 59), avg. gap size = 1.00 (6 / 6) 31 12.59 0.00 0.00 chr4ptel1M 618980 619032 (380968) (CCCTCCT)n#Simple_repeat 1 53 (0) m_b179s252i13 6977 chr4ptel1M 618980 CCCTCCTCCCTCTTCCTCCCTCCCTCCTCCCTCTTCCTACCTCCCTCCTC 619029 i ii i iv (CCCTCCT)n#Si 1 CCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTC 50 chr4ptel1M 619030 CCT 619032 (CCCTCCT)n#Si 51 CCT 53 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 31 22.48 3.19 2.11 chr4ptel1M 619411 619504 (380496) (CTCCC)n#Simple_repeat 1 95 (0) m_b179s252i14 6978 chr4ptel1M 619411 CTCCCTTTCCC-CCCCT-TCTTCCACCCCCCATCCCT-TCTTCCCTTCCT 619457 i i - -i i v i vi -i i i i (CTCCC)n#Simp 1 CTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCC 50 chr4ptel1M 619458 CTACTCCCTCCCCTCCCCTCTCCTCCCCCCCCCGCCCCGCCCTTCCC 619504 - - i i v v i (CTCCC)n#Simp 51 CT-C-CCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCC 95 Matrix = Unknown Transitions / transversions = 3.25 (13/4) Gap_init rate = 0.05 (5 / 93), avg. gap size = 1.00 (5 / 5) 37 4.88 0.00 0.00 chr4ptel1M 619537 619579 (380421) (GCG)n#Simple_repeat 1 43 (0) c_b179s251i0 6979 chr4ptel1M 619537 GCGGCAGCGGCAGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGG 619579 i i (GCG)n#Simple 1 GCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGG 43 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 23 24.85 4.00 2.97 chr4ptel1M 619596 619695 (380305) (GCGGGCC)n#Simple_repeat 1 101 (0) m_b179s252i15 6980 chr4ptel1M 619596 GCGAGACGTGGGCC-C-CGCCGTGGGCCGTGGGCCGTGGGCCGTGGCCGG 619643 i v i - -v i i i i -- v (GCGGGCC)n#Si 1 GCGGGCCGCGGGCCGCGGGCCGCGGGCCGCGGGCCGCGGGCCGCGG--GC 48 chr4ptel1M 619644 CGCTGGAGGCGGGGCCCGCGCAGCGCGGCGGC-GGCGGCGGGCCG-GAGC 619691 v vv v v v v - v - v - i (GCGGGCC)n#Si 49 CGCGGGCCGCGGGCCGCGGGCCGCG-GGCCGCGGGCCGCGGGCCGCGGGC 97 chr4ptel1M 619692 GGCG 619695 v (GCGGGCC)n#Si 98 CGCG 101 Matrix = Unknown Transitions / transversions = 0.54 (7/13) Gap_init rate = 0.07 (7 / 99), avg. gap size = 1.00 (7 / 7) 190 28.12 4.69 0.00 chr4ptel1M 621839 621902 (378098) C L2b_3end#LINE/L2 (3) 463 397 m_b179s601i7 6981 chr4ptel1M 621839 CGTTCAGTTAAAAAAAAGGT--TAAGCACCTGCTGC-TCTCAGGCCTTGT 621885 i v i v v vv -- i i i i- vi ?i C L2b_3end#LINE 463 CATTCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGT 414 chr4ptel1M 621886 CCCAGGCGCTGGCAATA 621902 v i vi C L2b_3end#LINE 413 GCTAGGCGCTGGGGATA 397 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 34.21 CpG sites = 10, Kimura (unadjusted) = 36.71 Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.03 (2 / 63), avg. gap size = 1.50 (3 / 2) 363 27.14 9.82 0.56 chr4ptel1M 623956 624118 (375882) MIRc#SINE/MIR 40 217 (51) m_b179s601i8 6982 chr4ptel1M 623956 AGTTAGGAAG-CCTGAGCTTGAGTTCAGTTCTTGCCTCGGA-TAACTGC- 624002 i - i i i i v viii v vv - i i- MIRc#SINE/MIR 40 AGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTG 89 chr4ptel1M 624003 TGA--GTGCGCCAGTC---CGCCCTGTCTG--CCTCGCCTTCCTCATCGT 624045 --v v v ---iiv v -- ivi vv MIRc#SINE/MIR 90 TGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTG 139 chr4ptel1M 624046 TAAAATGGGGACAGCCATAGCGGCC------ACCTCCCAGGGTTGTGGCA 624089 i iiv v v ------ v v ii MIRc#SINE/MIR 140 TAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTG 189 chr4ptel1M 624090 AGGACCACATGAGACCCCCGTATGTCAAA 624118 i v -ivvi v MIRc#SINE/MIR 190 AGGATCAAATGAGA-TAATGTATGTGAAA 217 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 33.16 CpG sites = 22, Kimura (unadjusted) = 34.09 Transitions / transversions = 1.00 (22/22) Gap_init rate = 0.05 (8 / 162), avg. gap size = 2.12 (17 / 8) 202 20.57 7.04 4.11 chr4ptel1M 625869 625939 (374061) L2d2_3end#LINE/L2 414 486 (69) m_b179s601i9 6983 chr4ptel1M 625869 TCTATGTGTTACCTTCCATCATCT-GA--GTAAGCTCCTTGAGGAGAGGG 625915 i v ii i -- v - -- iv L2d2_3end#LIN 414 TTTATGTCTTGTCTCCC--CAACTAGATTGTAAGCTCCTTGAGGGCAGGG 461 chr4ptel1M 625916 ACTGGCTCTTGTGAC--CTTTATATC 625939 iivv i - -- i L2d2_3end#LIN 462 ACCATGTCTTAT-ACTTCTTTGTATC 486 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 24.62 CpG sites = 9, Kimura (unadjusted) = 24.62 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.09 (6 / 70), avg. gap size = 1.33 (8 / 6) 248 35.71 3.54 0.86 chr4ptel1M 626909 627021 (372979) C L2d_3end#LINE/L2 (7) 509 394 m_b179s601i10 6984 chr4ptel1M 626909 ATCAGTCAGTAACCAGT-ATTAAGTACTTACTAGATGCCGGGCGCTGTGC 626957 i ii vi v - i ii i vi ivi i C L2d_3end#LINE 509 ATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTGTGC 460 chr4ptel1M 626958 TAAGTGCTAAAGGT--TCAAAAAGAAGCATGAGGCA-GCCCCCCTTTTTC 627004 i i ivi v--iv ? i? i i i - vi iviii C L2d_3end#LINE 459 TAGGCGCTGTGGGGAACGANAAAANAGTATAAGACATGGTCCCTGCCCTC 410 chr4ptel1M 627005 AGGGAAGCTCTCGGTCT 627021 i - iv ii C L2d_3end#LINE 409 AAGG-AGCTTACAATCT 394 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 49.05 CpG sites = 30, Kimura (unadjusted) = 55.60 Transitions / transversions = 3.00 (30/10) Gap_init rate = 0.04 (4 / 112), avg. gap size = 1.25 (5 / 4) 258 35.41 2.06 1.02 chr4ptel1M 626925 627021 (372979) C L2d2_3end#LINE/L2 (22) 533 436 m_b179s601i11 6984 chr4ptel1M 626925 TATTAAGTACTTACTAGATGCCGGGCGCTGTGCTAAGTGCTA-AAGGTTC 626973 i ii i ivi vi i i i i-ii vvi C L2d2_3end#LIN 533 TATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGTGGGGGAT 484 chr4ptel1M 626974 AAAAAGAAGCATGAGGCA-GCCCCCCTTTTTCAGGGAAGCTCTCGGTCT 627021 v i i i - vi iviii i - iv ii C L2d2_3end#LIN 483 ACAAAGAAGTATAAGACATGGTCCCTGCCCTCAAGG-AGCTTACAATCT 436 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 48.58 CpG sites = 26, Kimura (unadjusted) = 53.60 Transitions / transversions = 3.25 (26/8) Gap_init rate = 0.03 (3 / 96), avg. gap size = 1.00 (3 / 3) 315 28.93 0.00 0.00 chr4ptel1M 627851 627971 (372029) C L1PA6_3end#LINE/L1 (764) 137 17 m_b179s551i10 6985 chr4ptel1M 627851 TTTTTCATTTGACTACAGATAGCTTTAATTTCTTCATTTGAAAACTGCTT 627900 v v iiv iiv v v v v i v ii C L1PA6_3end#LI 137 TTTTTCATGTGTCTGTTGGCTGCATAAATGTCTTCTTTTGAGAAGTGTCT 88 chr4ptel1M 627901 GTTCATATCCTTTGCCCATTTATCGATTGGGGAATGACTCATATTCTTAT 627950 i v i v vvi vvv iv v i C L1PA6_3end#LI 87 GTTCATATCCTTTGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCTTGT 38 chr4ptel1M 627951 AAATTTGACTCAGTTCTCTAT 627971 vi v i i C L1PA6_3end#LI 37 AAATTTGTTTAAGTTCTTTGT 17 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 36.69 CpG sites = 15, Kimura (unadjusted) = 36.69 Transitions / transversions = 0.75 (15/20) Gap_init rate = 0.00 (0 / 120), avg. gap size = 0.0 (0 / 0) 359 22.34 0.00 0.00 chr4ptel1M 627878 627971 (372029) C L1ME4c_3end#LINE/L1 (720) 110 17 m_b179s551i11 6985 chr4ptel1M 627878 ATTTCTTCATTTGAAAACTGCTTGTTCATATCCTTTGCCCATTTATCGAT 627927 i v ? vi i ii i v C L1ME4c_3end#L 110 ATTTCCTCTTNTGTGAATTGTCTGTTCATGTCCTTTGCCCATTTATCTAT 61 chr4ptel1M 627928 TGGGGAATGACTCATATTCTTATAAATTTGACTCAGTTCTCTAT 627971 vv viv ?v v v v v i i C L1ME4c_3end#L 60 TGGGGTCTTGATNTTTTTCTTATCAATTTGAATGAGCTCTTTAT 17 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 27.29 CpG sites = 9, Kimura (unadjusted) = 27.29 Transitions / transversions = 0.75 (9/12) Gap_init rate = 0.00 (0 / 93), avg. gap size = 0.0 (0 / 0) 34 25.32 1.55 4.80 chr4ptel1M 628933 629061 (370939) (ATATAC)n#Simple_repeat 1 125 (0) m_b179s252i16 6986 chr4ptel1M 628933 ATTTACGTATACACATGTGTGTACATATATTCACTCATACATATAAATAT 628982 v i i iii i -- - - v (ATATAC)n#Sim 1 ATATACATATACATATACATATACATATA--CA-T-ATACATATACATAT 46 chr4ptel1M 628983 ATACTCATAGCTCTACCCATACATAT--ATCTATATACACATATACATAT 629030 i - - vv v vi -- v i i (ATATAC)n#Sim 47 ACA-T-ATACATATACATATACATATACATATACATATACATATACATAT 94 chr4ptel1M 629031 ACCTATATCCACCCATATACACATACACATA 629061 v ivi iv i i (ATATAC)n#Sim 95 ACATATACATATACATATACATATACATATA 125 Matrix = Unknown Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.05 (7 / 128), avg. gap size = 1.14 (8 / 7) 13 13.96 7.14 2.27 chr4ptel1M 629301 629342 (370658) (CCTTAT)n#Simple_repeat 1 44 (0) m_b179s252i17 6987 chr4ptel1M 629301 CCTTATCCTTATCTTCTCTCCCCAT-CTT-TCCCT-TCCTTATCC 629342 i - v ii - - i - (CCTTAT)n#Sim 1 CCTTATCCTTATCCT-TATCCTTATCCTTATCCTTATCCTTATCC 44 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.10 (4 / 41), avg. gap size = 1.00 (4 / 4) 20 9.69 0.00 0.00 chr4ptel1M 631002 631034 (368966) (TTTTG)n#Simple_repeat 1 33 (0) m_b180s252i2 6988 chr4ptel1M 631002 TTTTGTTTTGTTTTGTTTTGTTTTTATCTGTTT 631034 vv i (TTTTG)n#Simp 1 TTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTT 33 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 313 29.70 3.17 5.56 chr4ptel1M 631787 632007 (367993) L1PA13_3end#LINE/L1 6 221 (689) m_b180s551i0 6989 chr4ptel1M 631787 ATCCAGCATATATAAAAAATGGATCCAGACTTATAAGAATAAGAGCCATT 631836 v ii ivv vv i i i - i i v vi L1PA13_3end#L 6 ATCCAGCATCTATAAGGAACTTAAACAAATTTACAAGAA-AAAAACAAAC 54 chr4ptel1M 631837 --CCTCATTTGAGAGATGATCAAAAGGTATGAACAGGGAGTTTTTCAAAA 631884 -- i vi i - iv i ii iv -i L1PA13_3end#L 55 AACCCCATTAAAAAG-TGGGCAAAGGACATGAACAGACA-CTTTTCAAAA 102 chr4ptel1M 631885 GAAATCCTA---ACAG-CAATAACCTTGTGGGGGAATAAAAAAGCTTCAA 631930 iv v ---i i - i i v i i------ iv v L1PA13_3end#L 103 GAAGACATACATGCGGCCAACAATCATATGA------AAAAAAGCTCAAC 146 chr4ptel1M 631931 ATCACTAATAACTAAAGAAACTAAAAATAAGGGCAACTTTGAGGTTCCAT 631980 i v i i - iv v iii v vv i v L1PA13_3end#L 147 ATCACTGATCATTAGAGAAA-TGCAAATCAAAACCACAATGAGATACCAT 195 chr4ptel1M 631981 CTCCCACCTTAATTA-AGTATCTATTAT 632007 v -- i i - i iv L1PA13_3end#L 196 CTCACACC--AGTCAGAATGGCTATTAT 221 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 38.25 CpG sites = 38, Kimura (unadjusted) = 39.07 Transitions / transversions = 1.58 (38/24) Gap_init rate = 0.07 (16 / 220), avg. gap size = 1.19 (19 / 16) 736 29.18 3.81 0.46 chr4ptel1M 632010 632219 (367781) C MIRb#SINE/MIR (37) 231 15 m_b180s601i0 6990 chr4ptel1M 632010 GTCAGATATTATACTAAGCACTTTACATATATTATGTTATTTGATCCTCA 632059 i ii i i i i ii v i i C MIRb#SINE/MIR 231 GCCAGGCACTGTGCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCA 182 chr4ptel1M 632060 TAACAACTCTGGGACGGTGCTGTTATTATCTCTATTTTACAATTGAGGAA 632109 i i v v vv v i i i iv C MIRb#SINE/MIR 181 CAACAACCCTGCGAGGTAGGTATTATTATCCCCATTTTACAGATGAGGAA 132 chr4ptel1M 632110 ACTGAGGTAGAAAGTCATCAAGTGACTTGTTCAGAG----ATGATTAGTA 632155 ivv i vvi i i ii ii ---- iiii C MIRb#SINE/MIR 131 ACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTA 82 chr4ptel1M 632156 GGAGTCTGAGGCAGGATTTGAACATAGGTCT---TAATTCC-AGGCCCAT 632201 i v v v v i i vi --- i i - i i- C MIRb#SINE/MIR 81 AGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCG- 33 chr4ptel1M 632202 TGCTTTAACTACCACCCC 632219 i vv i ii v C MIRb#SINE/MIR 32 TGCTCTTTCCACTGCACC 15 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 35.68 CpG sites = 42, Kimura (unadjusted) = 38.96 Transitions / transversions = 2.21 (42/19) Gap_init rate = 0.02 (4 / 209), avg. gap size = 2.25 (9 / 4) 15 16.43 2.22 4.55 chr4ptel1M 632535 632579 (367421) (TTCACTT)n#Simple_repeat 1 44 (0) m_b180s252i3 6991 chr4ptel1M 632535 TTCACTTTTCAATATTTTCACTCTTCACCTTTCA-TCATCATTTTT 632579 - -v i i - iv i (TTCACTT)n#Si 1 TTCACTTTTC-A-CTTTTCACTTTTCACTTTTCACTTTTCACTTTT 44 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.07 (3 / 44), avg. gap size = 1.00 (3 / 3) 14 13.34 2.86 2.86 chr4ptel1M 633629 633663 (366337) (ATAGAA)n#Simple_repeat 1 35 (0) m_b180s252i4 6992 chr4ptel1M 633629 ATAGAATTATAATTGATAAATA-AAATAGAAATAGA 633663 v v v - v - (ATAGAA)n#Sim 1 ATAGAAATAGAAAT-AGAAATAGAAATAGAAATAGA 35 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 377 30.71 4.26 0.68 chr4ptel1M 634322 634462 (365538) MIR#SINE/MIR 117 262 (0) m_b180s601i1 6993 chr4ptel1M 634322 GCCATGGTTTTTTCTGCTGCACACTGGGGATCTTCATAGCTTTTTCCCTC 634371 vii ii vv i v v vv v - vii v MIR#SINE/MIR 117 GCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAG-TACCTACCTC 165 chr4ptel1M 634372 CCAGCATGATTGTG-GGATGGAATGAGAGAGT---TATAAAGAGCTTAG- 634416 vi vi vi - vi vv i --- i v - MIR#SINE/MIR 166 ATAGGGTTGTTGTGAGGATTAAATGAGTTAATACATGTAAAGCGCTTAGA 215 chr4ptel1M 634417 -CAGTATCTGGCACCCAGTAGGTGCTTAATGAGTGCAGGCAATTATT 634462 - ii vi i i i i i ivi v MIR#SINE/MIR 216 ACAGTGCCTGGCACATAGTAAGCGCTCAATAAATGTTAGCTATTATT 262 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 39.09 CpG sites = 23, Kimura (unadjusted) = 40.29 Transitions / transversions = 1.15 (23/20) Gap_init rate = 0.04 (5 / 140), avg. gap size = 1.40 (7 / 5) 17 0.00 0.00 0.00 chr4ptel1M 636786 636804 (363196) (G)n#Simple_repeat 1 19 (0) m_b180s252i5 6994 chr4ptel1M 636786 GGGGGGGGGGGGGGGGGGG 636804 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGG 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 330 27.83 12.17 0.00 chr4ptel1M 638947 639061 (360939) C MIRc#SINE/MIR (124) 144 16 m_b180s601i2 6995 chr4ptel1M 638947 TTTTACAGTTGGGGAAGCTGAGGC------AGGC--AGTGG--GGC---- 638982 v i i ------ i-- i--v ---- C MIRc#SINE/MIR 144 TTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAA 95 chr4ptel1M 638983 GGTTACTCAGCTAATCAGAGTCTGAGGTTAGCTTTGAACTCAGACCTCCC 639032 i v i v v v v vivi vi i i ii i C MIRc#SINE/MIR 94 GGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCC 45 chr4ptel1M 639033 CAACTCCAGACCCGGTACTCTATCCACTG 639061 ii iii i i v C MIRc#SINE/MIR 44 TGACTCCAAGTCCAGTGCTCTTTCCACTG 16 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 33.38 CpG sites = 21, Kimura (unadjusted) = 36.20 Transitions / transversions = 1.91 (21/11) Gap_init rate = 0.04 (4 / 114), avg. gap size = 3.50 (14 / 4) 184 27.68 1.89 8.00 chr4ptel1M 641486 641591 (358409) L3#LINE/CR1 1063 1162 (2937) m_b180s601i3 6996 chr4ptel1M 641486 GGGAACTCACTGATC--ATCTGAGAGGAGCCCCAAAATGGAAGTTCTGGG 641533 ii i i i -- -i - iii v i v vv L3#LINE/CR1 1063 GGAGACTCGCCGACCTGATC-AAGAGGA-CTTTAAACTGAAATTTGAGGG 1110 chr4ptel1M 641534 AACTAGGAAAGAAAGTGTCCAGAAAGCAGCTGGAGCACCGGGTCGCTGCG 641583 -- i i i v i- i v iv i -i ii L3#LINE/CR1 1111 AA--AGGAAAAAAAATGCCCAGATAA-AACTGTAAAACCGGAT-ACTATG 1156 chr4ptel1M 641584 GTCAGGAT 641591 -- L3#LINE/CR1 1157 G--AGGAT 1162 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 33.10 CpG sites = 20, Kimura (unadjusted) = 36.51 Transitions / transversions = 2.86 (20/7) Gap_init rate = 0.09 (9 / 105), avg. gap size = 1.11 (10 / 9) 13 27.49 0.00 5.08 chr4ptel1M 645091 645152 (354848) (GGCGGCG)n#Simple_repeat 1 59 (0) m_b180s252i6 6997 chr4ptel1M 645091 GGCGGAGGGCGGCGGCGCGCCGAGCGGTGGTGGGGCCACCTGCTTGGCCA 645140 v - v i i - v viv v -v vi (GGCGGCG)n#Si 1 GGCGGCGGGCGGCGG-GCGGCGGGCGGCGG-GCGGCGGGCGGC-GGGCGG 47 chr4ptel1M 645141 GGGGCGGCGGGC 645152 v (GGCGGCG)n#Si 48 CGGGCGGCGGGC 59 Matrix = Unknown Transitions / transversions = 0.44 (4/9) Gap_init rate = 0.05 (3 / 61), avg. gap size = 1.00 (3 / 3) 69 1.53 0.00 0.00 chr4ptel1M 645355 645420 (354580) (G)n#Simple_repeat 1 66 (0) c_b180s251i0 6998 chr4ptel1M 645355 GGGGGGGGGGGGGGGGGGGGGTGGGGGGGGGGGGGGGGGGGGGGGGGGGG 645404 v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 50 chr4ptel1M 645405 GGGGGGGGGGGGGGGG 645420 (G)n#Simple_r 51 GGGGGGGGGGGGGGGG 66 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0) 193 25.00 0.00 0.00 chr4ptel1M 646640 646679 (353321) C L2c_3end#LINE/L2 (10) 468 429 m_b180s601i4 6999 chr4ptel1M 646640 TCAGCCAGCGTTTATTAAGCATCTACTCTGTGCCAGCTGC 646679 i v i i i ii v vi C L2c_3end#LINE 468 TCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGC 429 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 24.46 CpG sites = 7, Kimura (unadjusted) = 31.73 Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 260 14.58 4.17 0.00 chr4ptel1M 646938 646985 (353015) C MIR1_Amn#SINE/MIR (78) 152 103 m_b180s601i5 7000 chr4ptel1M 646938 TTTCTATTTTACAGATGAGGAAACTGAGG--CAGACGAGTAGAGTGACTT 646985 ii i -- vii ?i C MIR1_Amn#SINE 152 TCCCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTT 103 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 17.28 CpG sites = 6, Kimura (unadjusted) = 17.28 Transitions / transversions = 6.00 (6/1) Gap_init rate = 0.02 (1 / 47), avg. gap size = 2.00 (2 / 1) 282 25.75 16.26 2.14 chr4ptel1M 648718 648840 (351160) MIR3#SINE/MIR 13 152 (56) m_b180s601i6 7001 chr4ptel1M 648718 CTGAGAACACAGAGCGCCAGCCTTGAAGTCAGGAGACCCGTGGGTTCAAA 648767 v v v i -i v v i -- v i MIR3#SINE/MIR 13 CTGAGCAGAGAGAGCAC-GGACTGGGAGTCAGGAGACC--TGGGTTCTAG 59 chr4ptel1M 648768 TCTC----------------TGCTGTGCATCCC----CAGGTCATGTAAA 648797 i ----------------? iiv i---- i iv v v MIR3#SINE/MIR 60 TCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCAC 109 chr4ptel1M 648798 CTCTGCCTGCCTCAGTGCTCTCATCTATAAAATGGGGCTGTTG 648840 vivv vii i i vv MIR3#SINE/MIR 110 CTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTG 152 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 31.05 CpG sites = 15, Kimura (unadjusted) = 32.26 Transitions / transversions = 0.94 (15/16) Gap_init rate = 0.04 (5 / 122), avg. gap size = 4.60 (23 / 5) 307 21.85 19.63 1.59 chr4ptel1M 648728 648834 (351166) MIRc#SINE/MIR 24 149 (119) m_b180s601i7 7001 chr4ptel1M 648728 AGAGCGCCAGCCTTGAAGTCAGGA-GACCCGTGGGTTCAAATC-----TC 648771 i ii v i - -- i i ----- MIRc#SINE/MIR 24 AGAGCACTGGACTTGGAGTCAGGAAGACC--TGGGTTCGAGTCCCGGCTC 71 chr4ptel1M 648772 TGC-----------TGTGCATCCC----CAGGTCATGTAAACTCTGCCTG 648806 ----------- iiv i---- i iv v vivv MIRc#SINE/MIR 72 TGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAG 121 chr4ptel1M 648807 CCTCAGTGCTCTCATCTATAAAATGGGG 648834 vii i MIRc#SINE/MIR 122 CCTCAGTTTCCTCATCTGTAAAATGGGG 149 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 25.27 CpG sites = 15, Kimura (unadjusted) = 26.60 Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.06 (6 / 106), avg. gap size = 3.83 (23 / 6) 273 27.03 0.00 0.00 chr4ptel1M 649016 649089 (350911) C MIR#SINE/MIR (119) 143 70 m_b180s601i8 7002 chr4ptel1M 649016 CCTTTTTACAGATGGGGAAATTGAGGCAGGCAGCAGGGAAGGGTCTTGCC 649065 v i i viv vi vv viv C MIR#SINE/MIR 143 CCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCC 94 chr4ptel1M 649066 AAAGGCCTCGCAGCTAAGGAGTGG 649089 v i v i ivi C MIR#SINE/MIR 93 CAAGGTCACACAGCTAGTAAGTGG 70 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 33.69 CpG sites = 9, Kimura (unadjusted) = 33.69 Transitions / transversions = 0.82 (9/11) Gap_init rate = 0.00 (0 / 73), avg. gap size = 0.0 (0 / 0) 22 3.85 0.00 0.00 chr4ptel1M 650848 650874 (349126) (G)n#Simple_repeat 1 27 (0) m_b180s252i7 7003 chr4ptel1M 650848 GGGGGGGGGGGGGGGGGGGGGGGGAGG 650874 i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGG 27 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 18 8.48 0.00 0.00 chr4ptel1M 653321 653345 (346655) (C)n#Simple_repeat 1 25 (0) m_b180s252i8 7004 chr4ptel1M 653321 CCCGCCCCCTCCCCCCCCCCCCCCC 653345 v i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCC 25 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 298 35.13 14.29 0.43 chr4ptel1M 655268 655470 (344530) C MIR#SINE/MIR (6) 256 26 m_b180s601i9 7005 chr4ptel1M 655268 AGCGAGCATACATTAAACATCTGCTGTGTGCCAGGCCCCGAGCTAAGTGC 655317 v i vi i i iii i i v i vv i C MIR#SINE/MIR 256 AGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGCGC 207 chr4ptel1M 655318 CTGA-------TGGCT-------TCCT---GGTCACCCTGGGGGGAAGGT 655350 i v ------- ii ------- ---iiiv iv i v C MIR#SINE/MIR 206 TTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGGTAGGT 157 chr4ptel1M 655351 GCTGGCTTGGCTCCCATTTTACAAGGGTGACAACTGAGGCAAGCAGCAGA 655400 i iviv viii iiv v iv viv vi v C MIR#SINE/MIR 156 ACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGT 107 chr4ptel1M 655401 CAAG-----TGCC-----TCATCTGG--ATTTAGTGTCCAAGACAGGATT 655438 i ----- ----- ivii -- v v v vi v i C MIR#SINE/MIR 106 TAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATT 57 chr4ptel1M 655439 CAAACTCAGGGCTTCCTGGCTTCAGGCTCCAT 655470 i i - vvi i ivi i C MIR#SINE/MIR 56 CGAACCCA-GGCAGTCTGGCTCCAGAGCCCGT 26 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 44.79 CpG sites = 43, Kimura (unadjusted) = 49.66 Transitions / transversions = 1.54 (43/28) Gap_init rate = 0.03 (7 / 202), avg. gap size = 4.29 (30 / 7) 16 30.11 1.89 0.00 chr4ptel1M 656696 656748 (343252) (TG)n#Simple_repeat 1 54 (0) m_b180s252i9 7006 chr4ptel1M 656696 TGTATGTGTTTATGTGCAAGTGTG-GTCTGGGTGTGCATGAGAGTATGTG 656744 i v i iiv - v v ii v v i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr4ptel1M 656745 TGTG 656748 (TG)n#Simple_ 51 TGTG 54 Matrix = Unknown Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.02 (1 / 52), avg. gap size = 1.00 (1 / 1) 53 29.56 0.00 1.27 chr4ptel1M 659116 659275 (340725) (TGGA)n#Simple_repeat 1 158 (0) m_b180s252i10 7007 chr4ptel1M 659116 TGGGTGGGTGGATCCACAAATGGATGGATGGAAGGTTAGATGGAGGGACG 659165 i i vv iii v v i v i (TGGA)n#Simpl 1 TGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATG 50 chr4ptel1M 659166 GATGGATGGGATGGACGGACAGACGAATGGATGAATGGATGGAAGGATGG 659215 - i ii i i i v (TGGA)n#Simpl 51 GATGGAT-GGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGG 99 chr4ptel1M 659216 TCAGATAGATGGGAGGAATGGAAGGATGGACGGACGTGTAGACAGGTGGC 659265 vii i - v i v i i vi i ii i v (TGGA)n#Simpl 100 ATGGATGGAT-GGATGGATGGATGGATGGATGGATGGATGGATGGATGGA 148 chr4ptel1M 659266 TGGACGGGTG 659275 i i (TGGA)n#Simpl 149 TGGATGGATG 158 Matrix = Unknown Transitions / transversions = 2.36 (26/11) Gap_init rate = 0.01 (2 / 159), avg. gap size = 1.00 (2 / 2) 407 37.92 7.77 2.97 chr4ptel1M 661712 662097 (337903) C L3#LINE/CR1 (2997) 1102 699 m_b180s601i10 7008 chr4ptel1M 661712 TTTGACTTTAAAGCTCTTTTGTTTGTAGTTGCAAGTAT-CAGCCAAAGAC 661760 v v ii i v iiviviv i v - ? ? v C L3#LINE/CR1 1102 TTTCAGTTTAAAGTCCTCTTGATCAGGTCGGCGAGTCTCCNGNCAAACAC 1053 chr4ptel1M 661761 ATCCTTGCTGGCCTGGCTCAAGGGTCCTCCGATCCTAACCAGGGGTCCCT 661810 i i v i i vvv v iiv iv vi ?i i i v C L3#LINE/CR1 1052 GTTCTTCCCGGTCTTCGTGAGATGCACTCCGTCCCTNGCCAGGAGCCCAT 1003 chr4ptel1M 661811 TGTGCTTATAT------------TTCCGAAGCCCAGATTCCATTTTCCCA 661848 i v vi ------------ i v iv i i ii i i v C L3#LINE/CR1 1002 CGTTCTGGTATCNTAAGCCATGGTCCAGAAAACCAAATCCTGTTCTTCGA 953 chr4ptel1M 661849 CA-CATCCCATTAACGATCCGTGATCTTTCCACATCTAACGGTTGCTGTG 661897 - ivvv i v v i vvv i i ivv -- v v v C L3#LINE/CR1 952 CACCATCTACGTAGCCAGCTGTTCACTTCCCATATCCTCC--TTTCTCTT 905 chr4ptel1M 661898 GTA---TCTCTTCCTTTCCAACGAGAAGGAGACCCAGTGCGGGC----CC 661940 vi --- v vv -- vi i ---ii viii ---- C L3#LINE/CR1 904 CCAAAGTCACGACCTT--CAACTGGAAGAAGA---GATGAAAACACCACC 860 chr4ptel1M 661941 TG----CCGATGTC---CAACTTCTGGTCGCAGACCTTACAATCTTTGGC 661983 ---- v v --- ii iv i vvi i i v i vi i v C L3#LINE/CR1 859 TGTGCCCCCAAGTCCTTCAGTTTCCTGCCCAGGACTTCAAAGTCACTAGA 810 chr4ptel1M 661984 AGC-CTTTTGAGGTGCTTTTTAGCAGAATCATTTCTCAGTGTCCCTGACA 662032 iii- v iv vii i ii v vi iv ----- vviii C L3#LINE/CR1 809 GATGCATTCCAGGTTTCTTCTGACTGTGTCATTCGT-----TCCCACGTG 765 chr4ptel1M 662033 AATCGCCAGAGGTGGGCAGCGAGCAGC-TGTGAGATAAGCCTGAGCAGGC 662081 iv ii i iv i -v vv i i vi C L3#LINE/CR1 764 AATCAGCAGGAGTGGGTAGCGGTCGGCGGGTTTGATGAGTCTTGGCAGGC 715 chr4ptel1M 662082 TCTCTGTTACGTCTTG 662097 i i i C L3#LINE/CR1 714 TCTCCGTCACGTCTCG 699 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 49.99 CpG sites = 79, Kimura (unadjusted) = 55.65 Transitions / transversions = 1.25 (79/63) Gap_init rate = 0.05 (21 / 385), avg. gap size = 2.00 (42 / 21) 12 16.31 2.78 2.78 chr4ptel1M 663109 663144 (336856) (AGGTTAT)n#Simple_repeat 1 36 (0) m_b180s252i11 7009 chr4ptel1M 663109 AGGTAAGTAGGTTAAGGGTTA-AGGCTATTGGTTATA 663144 v - vi - i v (AGGTTAT)n#Si 1 AGGTTA-TAGGTTATAGGTTATAGGTTATAGGTTATA 36 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 16 0.00 0.00 0.00 chr4ptel1M 664079 664095 (335905) (T)n#Simple_repeat 1 17 (0) m_b180s252i12 7010 chr4ptel1M 664079 TTTTTTTTTTTTTTTTT 664095 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTT 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 12 11.13 6.90 0.00 chr4ptel1M 664286 664314 (335686) (TATAT)n#Simple_repeat 1 31 (0) m_b180s252i13 7011 chr4ptel1M 664286 TATATTATTATATATTATA-TACATTA-ATT 664314 vv - i - (TATAT)n#Simp 1 TATATTATATTATATTATATTATATTATATT 31 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.07 (2 / 28), avg. gap size = 1.00 (2 / 2) 36 0.00 0.00 0.00 chr4ptel1M 664324 664354 (335646) (TA)n#Simple_repeat 1 31 (0) c_b180s251i1 7012 chr4ptel1M 664324 TATATATATATATATATATATATATATATAT 664354 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATAT 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 15 3.83 0.00 10.00 chr4ptel1M 664986 665018 (334982) (GAAAA)n#Simple_repeat 1 30 (0) m_b180s252i14 7013 chr4ptel1M 664986 GAAAGAGAGAAGGAAAAGAAAAGAAAATGAAAA 665018 - - i - (GAAAA)n#Simp 1 GAAA-AGA-AAAGAAAAGAAAAGAAAA-GAAAA 30 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.09 (3 / 32), avg. gap size = 1.00 (3 / 3) 495 21.61 1.63 5.93 chr4ptel1M 665821 665943 (334057) MIRc#SINE/MIR 10 127 (141) m_b180s601i11 7014 chr4ptel1M 665821 GTGGGGCAGTGAAGAGAGCATCAGCCCTGAAGTCAGGAGGATCTAG-TTC 665869 v i i iii v i i i i i - MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr4ptel1M 665870 AAATCTGGTCTCAGACACTTAACGCCTCCTAACTGTGTGACCCTGGGCAA 665919 i i iv v v v ------- i i MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTGACCTTGGGCAA 102 chr4ptel1M 665920 GTCACTTAACCCCAAT-TGCCTCAG 665943 i vv -v MIRc#SINE/MIR 103 GTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 24.83 CpG sites = 16, Kimura (unadjusted) = 26.02 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.07 (9 / 122), avg. gap size = 1.00 (9 / 9) 472 30.43 6.21 5.32 chr4ptel1M 668338 668691 (331309) C L1ME3G_3end#LINE/L1 (561) 363 7 m_b181s551i0 7015 chr4ptel1M 668338 CAAAGGATATG-G-ATTTTGGTGACTTTT--TGGGCACAGTTCCAAATTG 668383 i - - i--- v -- i ii -- v C L1ME3G_3end#L 363 CAAAGGGTATGCGCATTTTA---AATTTTAATAGATAC--TGCCAAATTG 319 chr4ptel1M 668384 TTTTCCAAAATGGCTGCACCAATTCACAACCTTACCAACAGTGTGTCAAT 668433 iii ? i i vi ii i i v iv C L1ME3G_3end#L 318 CCCTCCAAAANGGCTGTACCAATTTACACTCCCACCAGCAGTGTATGAGA 269 chr4ptel1M 668434 ATAGTTACTTCCAGACAGTCTCTCCAATATTTCTCATTTTCA--TTTTTA 668481 i viiii vv vi v i i ?vvi v --i C L1ME3G_3end#L 268 GTACCCGTTTCCCCACACCCTCGCCAACACTNGATATTATCAANCTTTTA 219 chr4ptel1M 668482 TTACTTCTGTTAAACTGATGGGT---------------ATTAGTCATTTT 668516 -v i i ii v --------------- - ii C L1ME3G_3end#L 218 -AATTTTTGCCAATCTGATGGGTGAAAAATGGTATCTCATT-GTTGTTTT 171 chr4ptel1M 668517 AATTTTATTTTTCTCTAATTATTAGTAAAGGACTAGTATTTTTAAAAAAT 668566 - iiv i i i -i viv i i -----vi C L1ME3G_3end#L 170 AA-TTTGCATTTCCCTGATTACTAGT-GAGGTTGAGCATCTTT-----TC 128 chr4ptel1M 668567 ATATTGTTATTGACAGCTTGGATTTCTTC-CCTGGAAACATATCAGTTCA 668615 vv i vii v i -i vi i- ii v C L1ME3G_3end#L 127 ATATGTTTATTGGCCATTTGTATTTCCTCTTCTGTGAAT-TGCCTGTTCA 79 chr4ptel1M 668616 CATTCTCTGACCATTTATCAGTTAAAGAATAGTTCTCATTCTTCTAAGTT 668665 i i i v v vi --- ii v - iv v vii C L1ME3G_3end#L 78 TATCCTTTGCCCATTTTTCTATT---GGGTTG-TCTTTTTCTTATTGATT 33 chr4ptel1M 668666 TGAAGATATCCCTTGCATATCTTGGA 668691 v ivi i i ii ii C L1ME3G_3end#L 32 TGTAGGAGTTCTTTATATATTCTGGA 7 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 40.82 CpG sites = 68, Kimura (unadjusted) = 41.43 Transitions / transversions = 2.00 (68/34) Gap_init rate = 0.07 (25 / 353), avg. gap size = 1.64 (41 / 25) 474 30.22 6.01 4.69 chr4ptel1M 668376 668691 (331309) C L1ME3Cz_3end#LINE/L1 (671) 326 7 m_b181s551i1 7015 chr4ptel1M 668376 CCAAATTGTTTTCCAAAATGGCTGCACCAATTCACAACCTTACCAACAGT 668425 i i i i i i vi ii i C L1ME3Cz_3end# 326 CCAAATTGCTCTCCAAAGTGGTTGTACCAATTTACACTCCCACCAGCAGT 277 chr4ptel1M 668426 GTGTCAATATAGTTAC---TTCCAGACAGTCTCTCCAATATTTCTCATTT 668472 i v i--- v --- ivv vi v i i vvi v C L1ME3Cz_3end# 276 GTATGAG---AGTTCCCGTTTCTCCACATCCTCGCCAACACTTGGTATTG 230 chr4ptel1M 668473 TC--ATTTTTATTACTTCTGTTAAACTGATGGGTAT----TAG----TCA 668512 -- i -v i i ii v i ---- i ---- C L1ME3Cz_3end# 229 TCAGACTTTTA-AATTTTTGCCAATCTGATGGGTGTGAAATGGTATCTCA 181 chr4ptel1M 668513 TTTTAATTTT-ATT----TTTCTCTAATTATTAGTAAAGGACTAGTATTT 668557 v ?i - ---- i i i -i viv i i C L1ME3Cz_3end# 180 TTGTNGTTTTAATTTGCATTTCCCTGATTACTAGT-GAGGTTGAGCATCT 132 chr4ptel1M 668558 TTAAAAAATATATTGTTATTGACAGCTTGGATTTCTTC-CCTGGAAACAT 668606 -----vi vv i vii i i i -i vi i- C L1ME3Cz_3end# 131 TT-----TCATATGTTTATTGGCCATTCGGGTTTCCTCTTCTGTGAAT-T 88 chr4ptel1M 668607 ATCAGTTCACATTCTCTGACCATTTATCAGTTAAAGAATAGTTCTCATTC 668656 ii v i i i v v vi --- ii v - iv C L1ME3Cz_3end# 87 GCCTGTTCATATCCTTTGCCCATTTTTCTATT---GGGTTG-TCTTTTTC 42 chr4ptel1M 668657 TTCTAAGTTTGAAGATATCCCTTGCATATCTTGGA 668691 v vii v ivi i i ii ii C L1ME3Cz_3end# 41 TTATTGATTTGTAGGAGTTCTTTATATATTCTGGA 7 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 40.30 CpG sites = 61, Kimura (unadjusted) = 40.91 Transitions / transversions = 2.03 (61/30) Gap_init rate = 0.07 (22 / 315), avg. gap size = 1.55 (34 / 22) 15 19.06 9.33 2.50 chr4ptel1M 669730 669804 (330196) (ATATT)n#Simple_repeat 1 80 (0) m_b181s252i0 7016 chr4ptel1M 669730 ATATTTTATTTTAATATACTATA-TATAATCCCTATATAATATAATTAGA 669778 v v v i - v viv - v - v (ATATT)n#Simp 1 ATATTATATTATATTATATTATATTATATTATAT-TATATTAT-ATTATA 48 chr4ptel1M 669779 -TAT-TTA-ATT-T-TTATATCATTTTA-ATT 669804 - - - - - i v - (ATATT)n#Simp 49 TTATATTATATTATATTATATTATATTATATT 80 Matrix = Unknown Transitions / transversions = 0.33 (3/9) Gap_init rate = 0.12 (9 / 74), avg. gap size = 1.00 (9 / 9) 13 19.39 0.00 2.78 chr4ptel1M 670450 670486 (329514) (AAATAA)n#Simple_repeat 1 36 (0) m_b181s252i1 7017 chr4ptel1M 670450 AAATAAAAAGCTATAATAATAATAATAATAAAGATAA 670486 -iv v v v i (AAATAA)n#Sim 1 AAATAAAAA-TAAAAATAAAAATAAAAATAAAAATAA 36 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 18 10.73 0.00 0.00 chr4ptel1M 670462 670491 (329509) (ATA)n#Simple_repeat 1 30 (0) m_b181s252i2 7017 chr4ptel1M 670462 ATAATAATAATAATAATAAAGATAATCATA 670491 vi v (ATA)n#Simple 1 ATAATAATAATAATAATAATAATAATAATA 30 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 241 28.19 8.72 0.00 chr4ptel1M 670555 670703 (329297) C L1M1_orf2#LINE/L1 (1067) 2227 2066 m_b181s551i2 7018 chr4ptel1M 670555 ATAGTAATACTCATGACTTTTATGGACTCATTTTATAGTCTACATCCTTG 670604 v i vv i i ivii v i vi i v i i C L1M1_orf2#LIN 2227 ATAGAAATGCTACTGATTTTTGTATGTTGATTTTGTATCCTGCAACTTTA 2178 chr4ptel1M 670605 CTGAATT-GTTT--CAATT-----AAGTTTTTAATTGACTCTC-AAATTT 670645 - -- i ----- iv ?i v v i- ii C L1M1_orf2#LIN 2177 CTGAATTTGTTTATCAGTTCTAATAGTTTTTTNGTGGAGTCTTTAGGTTT 2128 chr4ptel1M 670646 CTCTAAGCAAACCATCATATCATCTGAAAAATACAATAATTT---TGCTT 670692 i i ii v vv v vv vi --- v C L1M1_orf2#LIN 2127 TTCCAAATATAAGATCATATCATCTGCAAACAAGGATAATTTGACTTCTT 2078 chr4ptel1M 670693 TCTCT-CAATTT 670703 i i - C L1M1_orf2#LIN 2077 CCTTTCCAATTT 2066 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 36.49 CpG sites = 24, Kimura (unadjusted) = 36.49 Transitions / transversions = 1.33 (24/18) Gap_init rate = 0.04 (6 / 148), avg. gap size = 2.17 (13 / 6) 233 30.61 5.31 1.71 chr4ptel1M 670991 671103 (328897) C L2d_3end#LINE/L2 (6) 510 394 m_b181s601i1 7019 chr4ptel1M 670991 AATCGGGCAAGAAGCATTTATGAAGCACCTGTTTTG---TTAGTACTGGG 671037 iiv v i vi i ii v --- i i v C L2d_3end#LINE 510 AATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTGTG 461 chr4ptel1M 671038 TCAAG-GGGGTAGGTATATAAGGAAAG-GTACAA-ATGTGATTCTTGCTC 671084 ii i - vv i v - ii ?i ?- i - ii i i i i C L2d_3end#LINE 460 CTAGGCGCTGTGGGGA-ACGANAAAANAGTATAAGACATGGTCCCTGCCC 412 chr4ptel1M 671085 TCAAAGTAGCTCACATTCT 671103 i - i v C L2d_3end#LINE 411 TCAAGG-AGCTTACAATCT 394 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 39.82 CpG sites = 25, Kimura (unadjusted) = 43.48 Transitions / transversions = 2.78 (25/9) Gap_init rate = 0.05 (6 / 112), avg. gap size = 1.33 (8 / 6) 16 37.27 0.00 0.00 chr4ptel1M 671104 671178 (328822) (TTT)n#Simple_repeat 1 75 (0) m_b181s252i3 7020 chr4ptel1M 671104 TTTTTTTTTTTTTTAACAATAGCTTTTTCTTTTCTTTTCTTTTATTATTA 671153 vvivv vvi i i i v v v (TTT)n#Simple 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr4ptel1M 671154 TTATTATTATTATAGCTTTTTATTT 671178 v v v v vvi v (TTT)n#Simple 51 TTTTTTTTTTTTTTTTTTTTTTTTT 75 Matrix = Unknown Transitions / transversions = 0.38 (6/16) Gap_init rate = 0.00 (0 / 74), avg. gap size = 0.0 (0 / 0) 18 8.72 0.00 0.00 chr4ptel1M 671243 671267 (328733) (C)n#Simple_repeat 1 25 (0) m_b181s252i4 7021 chr4ptel1M 671243 CCCCTCCTCCCCCCCCCCCCCCCCC 671267 i i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCC 25 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 1626 27.11 2.05 2.70 chr4ptel1M 671619 672251 (327749) C L1ME3G_3end#LINE/L1 (292) 632 4 m_b181s551i3 7022 chr4ptel1M 671619 CCTGCTTGTTTCACTCAGCATCAGTTCATGTAAGTCTCTCCAGGCCTTTC 671668 i v i vi vv v v ii i v i vv v C L1ME3G_3end#L 632 CTTGCTTTTTTCACTCAACAATATGTCTTGGAGATCTTTCCATGTCAGTA 583 chr4ptel1M 671669 TG---AAATCATCCTGTTGGTCGTTTTTTACAGAACAATAGTATTCCAGG 671715 ii--- i vv vv -- - v ? vvvv vi C L1ME3G_3end#L 582 CATATAGATCTACCTCAT--TC-TTTTTAACNGCTGCATAGTATTCCATA 536 chr4ptel1M 671716 GCATTCATATACCACAATTTATTCAGCCATTCTCCAATTGATGGATCCAC 671765 i vv i i i i v -- i C L1ME3G_3end#L 535 GTATGGATATACCATAATTTATTTAACCATTCCCCTATTGATGGA--CAT 488 chr4ptel1M 671766 TCAG----TTTCTAGTTTCTGGCCACTATAAAGAGACCTGCCACAAACAT 671811 i ---- i i i v i i i v ivv v ii C L1ME3G_3end#L 487 TTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCTGCAATGAACAT 438 chr4ptel1M 671812 TCTTGCTCATACAGGCTCCTTT---CCCTTCTTTAAG-ATCTCTTTGGGA 671857 i ---- v ?i i --- v v v vii - i ? i C L1ME3G_3end#L 437 CCTTG----TACATGCNTCCTTGTGCACATGTGCGAGTATTTCTNTAGGA 392 chr4ptel1M 671858 TATA-ACCCAGTAGTAGCATTGCTGGATCAAAGGGTATACACAGTTTGAT 671906 v -? ? v i v i i i v i - C L1ME3G_3end#L 391 TAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGCATTTTAA- 343 chr4ptel1M 671907 AACTTTTTGAGCATAGTTTCAAATTGCTCTCCAGAATGGTTGGATTCGTT 671956 - i vvv - v vi i i ? i v iivi C L1ME3G_3end#L 342 -ATTTTAATAG-ATACTGCCAAATTGCCCTCCAAAANGGCTGTACCAATT 295 chr4ptel1M 671957 CACAGCTCCACCAACAATGTATCAGTGTCCCAGTTTTCCCGCATCCCCTC 672006 i vii i i v v v v i i i i v C L1ME3G_3end#L 294 TACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCACACCCTCGC 245 chr4ptel1M 672007 CAACATTCCGCATTATCTTTCCCTGTCATTCTAGCCCATCT-ATGAGGTA 672055 i ?vii vv? ii vvv i v v - - i C L1ME3G_3end#L 244 CAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATCTGATG-GGTG 196 chr4ptel1M 672056 TGTAGTGGTATCTCAGAGTTGTCTTAATTTGCATTTCGCTGATTAATAAT 672105 viv i vv i v v i C L1ME3G_3end#L 195 AAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGATTACTAGT 146 chr4ptel1M 672106 GACTTGGAGCATCTTTTCATATGGCTAGAAATAGTTTCAATTTCTTTGTC 672155 vv v vi vviiivi vv i iv C L1ME3G_3end#L 145 GAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGTATTTCCTCTTC 96 chr4ptel1M 672156 TGAGAATTGTCTGTTCATATCCTTTGACCATTTCTCAATTGGAGAATGGC 672205 v i v i v iv-- v C L1ME3G_3end#L 95 TGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGGGT--TGTC 48 chr4ptel1M 672206 TTGATTTCTTATAAATTAGAGTCAATTCTCTATATATTTTGGAAAT 672251 -- vi v vivv i i i v C L1ME3G_3end#L 47 TT--TTTCTTATTGATTTGTAGGAGTTCTTTATATATTCTGGATAT 4 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 34.02 CpG sites = 82, Kimura (unadjusted) = 34.54 Transitions / transversions = 0.96 (82/85) Gap_init rate = 0.04 (23 / 632), avg. gap size = 1.30 (30 / 23) 1665 26.65 1.65 2.40 chr4ptel1M 671703 672248 (327752) C L1ME3Cz_3end#LINE/L1 (449) 548 7 m_b181s551i4 7022 chr4ptel1M 671703 ATAGTATTCCAGGGCATTCATATACCACAATTTATTCAGCCATTCTCCAA 671752 vv i vv i v i v C L1ME3Cz_3end# 548 ATAGTATTCCATTGTATGAATATACCACAATTTATTTATCCATTCCCCTA 499 chr4ptel1M 671753 TTGATGGATCCACTCAG----TTTCTAGTTTCTGGCCACTATAAAGAGAC 671798 -- i i ---- i i i v i i i v ivv C L1ME3Cz_3end# 498 TTGATGGA--CATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATG 451 chr4ptel1M 671799 CTGCCACAAACATTCTTGCTCATACAGGCTCCTTT--CCCTTCTTTAAGA 671846 v ii i iv --- v v-- v v v vii C L1ME3Cz_3end# 450 CTGCAATGAACATCCTTGTACAT---GTCTCCTTGTGCACATGTGCGAGA 404 chr4ptel1M 671847 -TCTCTTTGGGATATA-ACCCAGTAGTAGCATTGCTGGATCAAAGGGTAT 671894 - i i i i - i v i v i iv C L1ME3Cz_3end# 403 GTTTCTCTAGGGTATATACCTAGAAGTGGAATTGCTGGGTCGTAGGGTAT 354 chr4ptel1M 671895 ACACAGTTTGATAACTTTTTGAGCATAGTTTCAAATTGCTCTCCAGAATG 671944 i i vi --i viv - v vi i i C L1ME3Cz_3end# 353 GCGCATCTT--CAACTTTACTAG-ATATTGCCAAATTGCTCTCCAAAGTG 307 chr4ptel1M 671945 GTTGGATTCGTTCACAGCTCCACCAACAATGTATCAGTGTCCCAGTTTTC 671994 v iivi i vii i i v v i v ii C L1ME3Cz_3end# 306 GTTGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTTCCCGTTTCT 257 chr4ptel1M 671995 CCGCATCCCCTCCAACATTCCGCATTATCTTTCCCTGTCATTCTAGCCCA 672044 i i v i iv i i vvv ii vvv i v v C L1ME3Cz_3end# 256 CCACATCCTCGCCAACACTTGGTATTGTCAGACTTTTAAATTTTTGCCAA 207 chr4ptel1M 672045 TCT-ATGAGGTATGTAGTGGTATCTCAGAGTTGTCTTAATTTGCATTTCG 672093 - - i v i vv ? i v C L1ME3Cz_3end# 206 TCTGATG-GGTGTGAAATGGTATCTCATTGTNGTTTTAATTTGCATTTCC 158 chr4ptel1M 672094 CTGATTAATAATGACTTGGAGCATCTTTTCATATGGCTAGAAATAGTTTC 672143 v i vv v vi vviiivi iv C L1ME3Cz_3end# 157 CTGATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTCG 108 chr4ptel1M 672144 AATTTCTTTGTCTGAGAATTGTCTGTTCATATCCTTTGACCATTTCTCAA 672193 ii i iv v i v i v C L1ME3Cz_3end# 107 GGTTTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTA 58 chr4ptel1M 672194 TTGGAGAATGGCTTGATTTCTTATAAATTAGAGTCAATTCTCTATATATT 672243 iv-- v -- vi v vivv i i C L1ME3Cz_3end# 57 TTGGGT--TGTCTT--TTTCTTATTGATTTGTAGGAGTTCTTTATATATT 12 chr4ptel1M 672244 TTGGA 672248 i C L1ME3Cz_3end# 11 CTGGA 7 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 32.33 CpG sites = 76, Kimura (unadjusted) = 33.49 Transitions / transversions = 1.15 (76/66) Gap_init rate = 0.03 (18 / 545), avg. gap size = 1.22 (22 / 18) 395 29.38 1.83 2.45 chr4ptel1M 672112 672275 (327725) C L1P3_orf2#LINE/L1 (7) 3287 3125 m_b181s551i5 7022 chr4ptel1M 672112 GAGCATCTTTTCATATGGCTAGAAATAGTTTCAATTTCTTTGTCTGAGAA 672161 v i vi ivviiiv iv v v iv i C L1P3_orf2#LIN 3287 GAGCTTTTTTTCATATGTTTGTTGGCCGCATAAATGTCTTCTTTTGAGAA 3238 chr4ptel1M 672162 TTGTCTGTTCATATCCTTTGACCATTTCTCAATTGGAGAATGGCTTG--- 672208 v i v i i ii - i -- v i --- C L1P3_orf2#LIN 3237 GTGTCTGTTCATATCCTTCGCCCACTTTTTGA-TGGGG--TTGTTTGTTT 3191 chr4ptel1M 672209 ATTTCTTATAAATTAGAGTCAATTCTCTATATATTTTGGAAATGAGGCCT 672258 v i v vv v i ii i v i v v v C L1P3_orf2#LIN 3190 TTTTCTTGTAAATTTGTTTAAGTTCCTTGTAGATTCTGGATATTAGCCCT 3141 chr4ptel1M 672259 TTATCAGAATAAATAAA 672275 i - ii i C L1P3_orf2#LIN 3140 TTGTCAG-ATGGATAGA 3125 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 37.05 CpG sites = 26, Kimura (unadjusted) = 38.08 Transitions / transversions = 1.24 (26/21) Gap_init rate = 0.03 (5 / 163), avg. gap size = 1.40 (7 / 5) 274 22.24 3.53 4.76 chr4ptel1M 673139 673223 (326777) C HERV4_I#LTR/ERV1 (2954) 3585 3502 m_b181s701i0 7023 chr4ptel1M 673139 ACCTTGTATTCCCTAGAGGGCAGAAAATTAAGAGTTTTTATAGCTGCATC 673188 i i ivvv v i v i --- i i C HERV4_I#LTR/E 3585 ACTTTGTATCCCCTGTCTGCCAGGAAATTCAAAGTTTTTATA---GTATT 3539 chr4ptel1M 673189 TAGG---GAAGCCTCTAGGGTGGGGCTGCAGATCAAGA 673223 v --- iv v i v - C HERV4_I#LTR/E 3538 TTGGTCAGAAGCCTCCTGGGTTGGGCTACACA-CAAGA 3502 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 26.56 CpG sites = 9, Kimura (unadjusted) = 26.56 Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.06 (5 / 84), avg. gap size = 1.40 (7 / 5) 355 34.84 1.65 2.21 chr4ptel1M 674627 674808 (325192) C LTR43-int#LTR/ERV1 (2239) 2559 2379 m_b181s701i1 7023 chr4ptel1M 674627 GCAGCAGCTAAAATTTGGGACTGTTCTCTATTTCTCACTTTAACTCTGTG 674676 i??i i v vi v i ii i i i v ivv i v C LTR43-int#LTR 2559 GCGNNGGCCAACAACTGGGCCCGTCTTTTGTCTCTCTCTTCTTCCCTTTG 2510 chr4ptel1M 674677 GTCTTCCT---CCTCTGCTGCAGTTTGGTCCCTATTATTAAAGACTCCAA 674723 i i ii? --- -- v v i - i vi i i C LTR43-int#LTR 2509 ATTTCTNTGTGCCTCT--TTCACTCTG-TCTCGGTTATTGAAGACCCCAA 2463 chr4ptel1M 674724 GAGGTGTTTTTAATAGCTGAGTTGGAGAAGTTTAAGGACCCAAAACTGGC 674773 i v iiv i i v v ivv ii ii vii i i C LTR43-int#LTR 2462 AAGCTACATTTAGTAGTTCATTTATTGGGGTTTGGGGACCCATGGCTAGT 2413 chr4ptel1M 674774 TCCAGCATCTTCCTCTGTATATCTGGGGCAGACCG 674808 ii- iiv i ivv i C LTR43-int#LTR 2412 TTT-GTGACTTTCTCCTAATATCTGGGGCAGACTG 2379 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 49.12 CpG sites = 42, Kimura (unadjusted) = 51.59 Transitions / transversions = 2.10 (42/20) Gap_init rate = 0.03 (5 / 181), avg. gap size = 1.40 (7 / 5) 31 3.53 10.34 0.00 chr4ptel1M 675834 675891 (324109) (TTTTC)n#Simple_repeat 1 64 (0) m_b181s252i5 7024 chr4ptel1M 675834 TTGTCCTTT-TTTTCTTTTCTTTTCTTTTCTTTTC-TTTC-TTTC-TTTC 675879 v i - - - - (TTTTC)n#Simp 1 TTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTC 50 chr4ptel1M 675880 TTTT-TTTT-TTTT 675891 - - (TTTTC)n#Simp 51 TTTTCTTTTCTTTT 64 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.11 (6 / 57), avg. gap size = 1.00 (6 / 6) 444 30.81 6.58 5.51 chr4ptel1M 676783 677177 (322823) MamRTE1#LINE/RTE-BovB 346 744 (3068) m_b181s601i2 7025 chr4ptel1M 676783 GGAAACAGCATGGGATTCAGC----CCCTGGGTGTTGGAGAAGCCTT-TT 676827 v i iv -- i ----? iv v i - MamRTE1#LINE/ 346 GGCAGCAGCACCG--TTCGGCAGCGNCCTGGGTGTCTGAGCAGCCCTGTT 393 chr4ptel1M 676828 AAGGGCTACATTGCTCACCTTCTGACCTGAGGAAGGGTCTAGAAAAGGTA 676877 v i?ii ii -- i v- i ? i MamRTE1#LINE/ 394 TAGGANCGCGCTGCTCAC--TCCGAA-TGGGGAAGGGNCTAGAAAAGGTG 440 chr4ptel1M 676878 CCCTAACAATTGTCTGTTT------ACCCAACCCTGG----CCTGTTTCC 676917 vvi i ii ------ ?i v? ---- v v vi MamRTE1#LINE/ 441 CCCTAAACGTTGCCTGCCTCGCCAAANTCAAANCTGGCTCACCAGATTAT 490 chr4ptel1M 676918 CACAGCAGGTAGGGATCCTACGC-TGTGGTTGAAACACAAAAAAGGTACA 676966 i iv v -- i ii ?v - i vv v? ----- -i MamRTE1#LINE/ 491 CGCGTCTGGT--GGGTTTTANTCTTGCGGTGCAAAANCAAA-----TA-G 532 chr4ptel1M 676967 AAAACTTCTG----CAAAGATGAT-TCCACT-CACCACTGGTACATGGAC 677010 v i?---- vi -v i - ii - v ---- MamRTE1#LINE/ 533 AAAACTACCNANNACAAAGAAAATAACCATTGCGTCA-TGGAACAT---- 577 chr4ptel1M 677011 TAATACACT-TACAGATAACACAAAATTCATCAGACTT---GAAAGATGA 677056 i iv i - i - i ivi --- v v v --- v MamRTE1#LINE/ 578 CAGGACGCTATGC-GATGACGAGAA---CAGCAGTCGTCCAGAAAGAAGA 623 chr4ptel1M 677057 ACTATTCCTGTTGCAAGAGAACTCAGCTGGTCTCACATCTAAATAGCAGC 677106 viiv ii i v v vvv v i vivivi v v v v MamRTE1#LINE/ 624 ACGGCACTCGTCGCACGTGAACTGTCCAGATACGGAGTCGACATCGCCGC 673 chr4ptel1M 677107 CCTGAGGGAAATAAGGCTGACAAATAAAGGTCAGCTTCCCAAAACTGGAG 677156 v v iv i vv vi i v iv vi i v v MamRTE1#LINE/ 674 ACTGAGCGAAACCAGACTTCCTGATGAAGGACAGCTCACGGAGACAGGTG 723 chr4ptel1M 677157 CTGGATTCAGGCTTTTCTGGA 677177 i ? v ivvi i MamRTE1#LINE/ 724 CCGGNTACGCCTTCTTCTGGA 744 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 34.57 CpG sites = 58, Kimura (unadjusted) = 41.64 Transitions / transversions = 1.02 (58/57) Gap_init rate = 0.08 (32 / 394), avg. gap size = 1.50 (48 / 32) 454 35.85 5.48 2.83 chr4ptel1M 677310 677619 (322381) MamRTE1#LINE/RTE-BovB 878 1195 (2617) m_b181s601i3 7025 chr4ptel1M 677310 AAAATGCCATACCACCATCCACCAGTGCCTGTGCTCCCACCGTGACAAAC 677359 ii i? i i - i i v i i i i i MamRTE1#LINE/ 878 AAAGCGCTNTGCCACCGTC-ATCAGCGCATATGCCCCCACCATGACGAAT 926 chr4ptel1M 677360 CCTGAAGAGGTCAAAGAAAAATCTTATGAAGACCTGGAGACCTTTATCAT 677409 v i v vv i ii ii i i v vvi i ii MamRTE1#LINE/ 927 ACCGATGAGGAGAAAGAAAGATTCTACAAGGATCTGGACAGACTCATCGC 976 chr4ptel1M 677410 TGATGTGCCCGAAGAGGACAAGCATATAATT-CTGGTGACTTTAATGCTA 677458 v vv i viv vvv vv vi i- v v i i i vv MamRTE1#LINE/ 977 AGCGGTACCAACATCTGACAAGCTGATCGTCACGGGAGATTTCAACGCAC 1026 chr4ptel1M 677459 GAGTAAGCTCCTA-GCTAGGGCGAGGAGGA---------------ATGGA 677492 v vi vv v - iiiii v i --------------- i i MamRTE1#LINE/ 1027 GTGTCGGCAGCGATGCCGAAACGTGGAGAAAAGTCATCGGACCNCACGGG 1076 chr4ptel1M 677493 GTTGGAAACAGCAATAGCAATGGTCCCTTAGTACTGAAGAGTTGTGCATC 677542 i vvv? i ivi vv i v iviiv vvv MamRTE1#LINE/ 1077 ATTGGAAAGCTNAACAGCAATGGTCTACTCCTGCTCAGCGAATGTGCCAA 1126 chr4ptel1M 677543 TCATGATCTTCTCATCACCAACACTGTGTTCCATTTACCTAAAGCAAAAA 677592 v v v iv v ii v iii ------ i v MamRTE1#LINE/ 1127 GCATCAGCTCGTAATCACCAACACCATCTTCCGCCTAC------CGAATA 1170 chr4ptel1M 677593 AAAAAAAAAAATCTGATGGATGCACTC 677619 i i i v -- i MamRTE1#LINE/ 1171 AGAGAAAGACATC--ATGGATGCACCC 1195 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 41.44 CpG sites = 59, Kimura (unadjusted) = 50.81 Transitions / transversions = 1.20 (59/49) Gap_init rate = 0.04 (12 / 309), avg. gap size = 2.17 (26 / 12) 27 25.27 0.00 0.00 chr4ptel1M 677868 677937 (322063) (AAAA)n#Simple_repeat 1 70 (0) m_b181s252i7 7026 chr4ptel1M 677868 AAAAACACAAGGAAGAAAGAAAAAAACAGGCAAACAAACAATAACTAAAA 677917 v v ii i i v iiv v v v vv (AAAA)n#Simpl 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr4ptel1M 677918 AAAAAAAAAAAAAAAAAAAA 677937 (AAAA)n#Simpl 51 AAAAAAAAAAAAAAAAAAAA 70 Matrix = Unknown Transitions / transversions = 0.67 (6/9) Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0) 207 33.39 2.34 5.42 chr4ptel1M 679375 679545 (320455) MamRTE1#LINE/RTE-BovB 2047 2212 (1600) m_b181s601i4 7025 chr4ptel1M 679375 ATGGCAAAGCATTTGGTGCCAATTCTATTCCAGTTGAGATTTATGAGGTG 679424 i vi i vv ii vvi v v i - v i ii MamRTE1#LINE/ 2047 ATGGTAAAGCTCTCGGACCTGATGGCATACCTGCTGAGATTT-TCAAGCA 2095 chr4ptel1M 679425 GGGGGTAGGGTGGTCCAGTGCTCATACTAAAGCTGAATGAAGTTTTCCAG 679474 ii -- v iiv -- i v ---iv v iiiv ivv MamRTE1#LINE/ 2096 GGAAG--GGGAGACGC--TGCTTAGAC---GTCTGCATAGGCTTTTCTTC 2138 chr4ptel1M 679475 ATAATATGG-GTAA-GAGGTTATCCCTCAGAATTTCAAGGATGCTTCCAT 679522 vv - v- vv v v i i iv i MamRTE1#LINE/ 2139 AGCATATGGAGTACCGAGGAAATGCCGCAGGATTTCAAAGATGCCACTAT 2188 chr4ptel1M 679523 TGT--CCATCTCTAAAATAAAAAGG 679545 ii -- ii i - i MamRTE1#LINE/ 2189 CATCACCATCTTCAAGA-AGAAAGG 2212 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 41.98 CpG sites = 30, Kimura (unadjusted) = 45.33 Transitions / transversions = 1.25 (30/24) Gap_init rate = 0.07 (12 / 170), avg. gap size = 1.08 (13 / 12) 21 7.96 5.00 0.00 chr4ptel1M 679974 680013 (319987) (ATGTTTT)n#Simple_repeat 1 42 (0) m_b181s252i8 7027 chr4ptel1M 679974 ATGTTTTATGTTTT-TGTTTT-TGTTTTAAGTATGATGTTTT 680013 - - v v v (ATGTTTT)n#Si 1 ATGTTTTATGTTTTATGTTTTATGTTTTATGTTTTATGTTTT 42 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 208 25.59 6.02 1.15 chr4ptel1M 680534 680616 (319384) MamRTE1#LINE/RTE-BovB 3138 3224 (588) m_b181s601i5 7025 chr4ptel1M 680534 ACCAAGCTGAAGGTCTACAGA--GACTGTGCTGATCTCA-TTACTGTACG 680580 i i -- iv i ? - iv -i v ? MamRTE1#LINE/ 3138 ACCAAACTAAAGGTCTACAGAGCGATAGCGNTG-TCCAACCTTCTNTACG 3186 chr4ptel1M 680581 CCTGAGAAACCTGGAC--AGTACAAGCGCCACGCCAGG 680616 v v i --ivi ii i ii v MamRTE1#LINE/ 3187 GCTGTGAGACCTGGACCTGCCACAGACGTCACATCCGG 3224 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 31.62 CpG sites = 14, Kimura (unadjusted) = 33.58 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.05 (4 / 82), avg. gap size = 1.50 (6 / 4) 250 20.64 9.68 6.25 chr4ptel1M 680891 681014 (318986) C HERVK14C#LTR/ERVK (2009) 5425 5298 m_b181s701i2 7028 chr4ptel1M 680891 TTCTTGGGTCTTTTCCTT---CTTGGGTTGTCTCTCTGATGGACAAGGCA 680937 ivi i--- i v vv -- - vi v C HERVK14C#LTR/ 5425 TTCCGAGGTCTTTTCCTCTTCCTTGGATTCTGGCTC--ATGG-CACAGCT 5379 chr4ptel1M 680938 -AACATGGCTCGTTGGCACCCAT--------CTGATTTCTTTTCCATCTG 680978 -? v v i v i v-------- i-- i --- C HERVK14C#LTR/ 5378 TNAGATGTCTTGTGGGTACCCAGACAGGAAGCTGATTC--TCTCC---TG 5334 chr4ptel1M 680979 TAGAGATACAAGCAAACCCTCTGCCCCAAGTAGTTA 681014 v? i ? i v ?i ? C HERVK14C#LTR/ 5333 GNGAGACACAAGCAAANCCTCTACCCCATGTNATNA 5298 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 24.51 CpG sites = 12, Kimura (unadjusted) = 25.69 Transitions / transversions = 1.00 (12/12) Gap_init rate = 0.09 (11 / 123), avg. gap size = 1.82 (20 / 11) 447 28.47 8.41 7.41 chr4ptel1M 681134 681668 (318332) C HERVK3#LTR/ERVK (2185) 5017 4478 m_b181s701i3 7028 chr4ptel1M 681134 CTGTCTGCCAGAGTCAGTGCATCTTTGTCAAAAATC-AAGAAATTAATAG 681182 v ii vvvv iv ii ii i - i v v C HERVK3#LTR/ER 5017 CTTTCTGCTGGAGTCTTACCATCCGTACCAGGAGTCNAAAAAATTTAAAG 4968 chr4ptel1M 681183 TATAACGAG-CTAGATTTAGAAGTTCT--CTAGGGT--TACCTGTGGCTC 681227 - ii - i v --- i --i ii -- vi - v C HERVK3#LTR/ER 4967 TA-AATAAGGCTAAATGTAG---TTTTGATTGAGGTGGTAGTTG-GCCTC 4923 chr4ptel1M 681228 C----CCCTTTCTTTTGTTTGTGGAGGA-GCGTCTTGATATTTC-TGTTT 681271 ---- ?iiii v vv iv - iv i i v- vi C HERVK3#LTR/ER 4922 CTATACCNCCCTTTTTGTTTTTTCAACATGCGTTGTAATGTTTGATGTGC 4873 chr4ptel1M 681272 CTCCTCTCGACTATTGCCT-GTCCTTAAGGATTAAAAGGTATGCCAGTGG 681320 iv v--- v - iv v v v v vv C HERVK3#LTR/ER 4872 CCGCTCTA---TAATGCCTTGTCCTCTAGGATTATAAGGAATTCCTGTTT 4826 chr4ptel1M 681321 TGTG---TAAAATCTGATACTGTGCACAAAAGTGTGCAAA--ATGTTTAG 681365 i --- v ii ii vi -- vi v v v -- vi C HERVK3#LTR/ER 4825 TATGGGTTATAGCCCAAAGCTGT--AAGAAATTTTGAAAAGCATGACTAG 4778 chr4ptel1M 681366 AAGCATATGCAGGTCCATTATCTGTTTTTA-TTGCTTGTGGCACATCCAT 681414 ---i v i i v - i i- i ivi C HERVK3#LTR/ER 4777 ---TATAAGCGGGTCCATTGTCAGTTTTTAATTGTTTA-GGTATCCCCAT 4732 chr4ptel1M 681415 AATTGCAAATGCTTGTATAAGGAAC----TCA------GTGACCACTCGG 681454 vvv ----- i vii ---- i------i ----- C HERVK3#LTR/ER 4731 ATGAGCAAATG-----ATGACAGACAATGTCGCCGTACATGACCA----- 4692 chr4ptel1M 681455 GCTGTCTCTTTTGCTGCTGGTAT------TGCAAAA-GTGAATCCTGAAA 681497 vii i -- i ------ iv -i ----- v C HERVK3#LTR/ER 4691 GCTGTCTCACCTGTT--TGGCATGTAGCATGCAGCATATGA-----GAAT 4649 chr4ptel1M 681498 AAGTATCTAT----CACA--ACATGGATAAAAGACAGATGACCAAAAGAT 681541 i ---- -- i v ------ v vi i v C HERVK3#LTR/ER 4648 AAGTGTCTATAGNTCACAGAACATAGCTAA------GCTTGCCAAAGGCT 4605 chr4ptel1M 681542 -TTATAATGGGTCACATCCATTTGCCAAATTTCATTGGGTCTCAAACCAT 681590 -i i- v v i v vvi vi C HERVK3#LTR/ER 4604 GCTATG-TGTGTAACATCCATTTGCCAGATTTCATTTGGAGCCAAACCTC 4556 chr4ptel1M 681591 GAGGGTT-CTTCCTTGGAGTCA-GTGTAGGACAGTGGAAAGGAAGGCAAG 681638 v - v? vv -- - ii v? viv v v vv C HERVK3#LTR/ER 4555 GTGGGTTACANCCTTCTA--CAGGTGCGGCNCCAGGGACATGCTGGCAAG 4508 chr4ptel1M 681639 CTGGACAGACTTTTACTATGCTCCTGGCTT 681668 iv i v ? ivi i C HERVK3#LTR/ER 4507 TAGGACAGGCTTGTACNATAGCCCTAGCTT 4478 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 34.75 CpG sites = 72, Kimura (unadjusted) = 36.69 Transitions / transversions = 1.04 (72/69) Gap_init rate = 0.11 (60 / 534), avg. gap size = 1.42 (85 / 60) 498 31.17 7.28 2.97 chr4ptel1M 681168 681620 (318380) C HERVK#LTR/ERVK (2270) 5266 4795 m_b181s701i4 7028 chr4ptel1M 681168 TCAAGAAATTAATAGTATAACGAGCTAGATTTAGAAGTT-C-TCTAGGG- 681214 i i v v iv v --- - - i - C HERVK#LTR/ERV 5266 TTAAAAAATTTAAAGTATAGAGTGCTAGATT---AAGTTGCATCTGGGGA 5220 chr4ptel1M 681215 ---TTAC--------CTGTGGCTCCCCCTTTCTTTTGTTTGTGGAGGAGC 681253 ---? -------- -- ii ivvv ivv v C HERVK#LTR/ERV 5219 GTGNTACACTCCTTACTGT--CTCCCCCTTCTTTTTGTTTAACCAATTGA 5172 chr4ptel1M 681254 GTCTTGATATTTCTGTTTCTCCTCTCGACTATTGCCTGTCCTTAAGGATT 681303 ii vvv i vv i i i v ii i C HERVK#LTR/ERV 5171 GCTTTGAGTGTTCTATTAGTTCTTTCAACTATGGCCTGTCCTTGGGAATT 5122 chr4ptel1M 681304 AAAAGGTATGCCAGTGGTGTGTAAAATCTGATACTGTGCACAAAAGTGTG 681353 v v v v v i iv i vvi -iivi i i v v C HERVK#LTR/ERV 5121 ATAAGGAATTCCTGTTGTATGTGTAATTTTCCACTG-ATTTAAGAATTTT 5073 chr4ptel1M 681354 CAAAATG-TTTAGAAGCATATGCAGGTCCATTATCTGTTTTTATTGCTTG 681402 iii ? - vv vvi v v i i v v vi v C HERVK#LTR/ERV 5072 TGGAANGCTTTACTACAGTATCCTGGCCCATTGTCAGTTTTAATTTTTTC 5023 chr4ptel1M 681403 TGGCACATCCATAATTGCAAATGCTTGTATAAGGAACTCAGTGACC---- 681448 v vi i iv ------- i iv v v i vii---- C HERVK#LTR/ERV 5022 TGGAACTCCCATGACAGCAAA-------ACAAGATAATAAATGTTTTTTA 4980 chr4ptel1M 681449 ACTCGGGCTGTCTCTTTTGCTG-CTGGTA--TTGCAAAAGTGAATCCTGA 681495 vi vv vii i v - i -- vv vi viv C HERVK#LTR/ERV 4979 ACATGGGAAGTACTTTCTCCTGTCTGGCAGGTTGCCCATATGAAATGTGA 4930 chr4ptel1M 681496 AAAAGTATCTATCACAACATGGATAAAAGACAGATGACCAAAAG-ATTTA 681544 v v iiiiv i ? v ivivv v - vv C HERVK#LTR/ERV 4929 ATAAGTATCAACTGTTACATGGACANATGACAATCTTCCAAATGAAGGTA 4880 chr4ptel1M 681545 TAATGGGTCACATCCATTTGCCAAATTTCATTGGGTCTCAAACCATGAGG 681594 i- v v v viv i v v i vivi C HERVK#LTR/ERV 4879 C-ATGCGTGACATCCATTTGCCATAACGCATTAGGACACAGACCTCTGGG 4831 chr4ptel1M 681595 GTT-----CTTCCT-TGGAGT---CA-GTGTAGGAC 681620 i ----- v - v --- - C HERVK#LTR/ERV 4830 ATTAACTCCTGCCTCTTGAGTGGGCAGGTGTAGGAC 4795 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 40.64 CpG sites = 62, Kimura (unadjusted) = 41.02 Transitions / transversions = 0.83 (62/75) Gap_init rate = 0.06 (28 / 452), avg. gap size = 1.68 (47 / 28) 563 26.99 7.80 3.98 chr4ptel1M 681219 681654 (318346) C HERVK14C#LTR/ERVK (2323) 5111 4660 m_b181s701i5 7028 chr4ptel1M 681219 CTGTGGCTCCCCCTTTCT----TTTGTTTGTGGAGGAGCGTCTTGATATT 681264 v i i ---- v v ivv v ?i v viv C HERVK14C#LTR/ 5111 CTCTGGTTCCCCCCTTCTGTCTTTTGTTTTTGTAATTGAGNTTTTAAGGT 5062 chr4ptel1M 681265 TCTGTT-TCTCCTCTCGACTATTGCCTGTCCTTAAGGATTAAAAGGTATG 681313 vi -v v - i v v i ? i i v i v ? C HERVK14C#LTR/ 5061 TCGATTAGCTCGT-TCAACAATGGCTTGNCCTTGAGAATTATAGGGGATN 5013 chr4ptel1M 681314 CCAGTGGTGTGTAAAATCTGATACTG-TGCACAAAAGTGTGCAAAATGTT 681362 i? vv v ?vi i - v vi v i? ?i i-? C HERVK14C#LTR/ 5012 CCAGTANTGTGTTTAATGTNCCATTGTTGAAGGAACGCNTNTAAAG-NTT 4964 chr4ptel1M 681363 TAGAAGCATATGCAGGTCCATTATCTGTTTTTATTGCTTGTGGCACATCC 681412 vv ??i vv v v i ? v ?vi v iii C HERVK14C#LTR/ 4963 TACTANNGTAGCCTGGGCCATTGTCNGTTTTAATNTTTTGTGGAATGCCC 4914 chr4ptel1M 681413 ATAATTGCAAATGCTTGTATAAGGAACTCAGTGACC----ACTCG---GG 681455 i i? i ------- i i i viv i v i---- v ---i C HERVK14C#LTR/ 4913 ATGACNGCGAA-------ACAGGAAAGCAAATGTCTTTTAACACGAGCAG 4871 chr4ptel1M 681456 CTGTCTCTTTTGCTGCTGGTA--TTGC-----AAAAGTGAATCCTGAAAA 681498 ? i ?ii i -- i -- ? -----v i ----- C HERVK14C#LTR/ 4870 CNGCCTCNCCTGTT--TGGCAAGTNGCCCANACAAAATGA-----GAAAA 4828 chr4ptel1M 681499 AGTATCTATCACAACATGGATAAAAGACAGATGACCAAA-AGATTTATAA 681547 i ivii? iiv ? ? v vv -i? vv i- C HERVK14C#LTR/ 4827 GGTATCTACAGTNACATGGACGTANGANAGTTTCCCAAATGNAGGTAC-A 4779 chr4ptel1M 681548 TGGGTCACATCCATTTGCCAAATTTCATTGGGTCTCAAACCATGAGGGTT 681597 ? i ? viv? i ?vi v vi ? C HERVK14C#LTR/ 4778 TGGGTNACGTCCATTTGCCANAGCGNATTAGGNGCCAATCCTCGNGGGTT 4729 chr4ptel1M 681598 --C-----TTCCTTGGAGT--CAG-TGTAGGACAGTGGAAAGGAAGGCAA 681637 -- ----- i iv -- - v -v v v?? i C HERVK14C#LTR/ 4728 AACNCCAGTCCCTTGATGTGGCAGTTGTAGCAC-CTGGCACNNAGGGCAA 4680 chr4ptel1M 681638 -GCTGGACA--GACTTTTAC 681654 - i ? -- ? i ?i C HERVK14C#LTR/ 4679 TGTTGNACAATGNCCTTNGC 4660 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.36 CpG sites = 59, Kimura (unadjusted) = 37.44 Transitions / transversions = 1.09 (59/54) Gap_init rate = 0.07 (32 / 435), avg. gap size = 1.62 (52 / 32) 567 32.44 1.99 1.99 chr4ptel1M 681278 681579 (318421) C HERVK11#LTR/ERVK (2674) 5279 4978 m_b181s701i6 7028 chr4ptel1M 681278 TCGACTATTGCCTGTCCTTAAGGATTAAAAGGTATGCCAGTGGTGTGTAA 681327 v i iv i i iv v v i ii i vi C HERVK11#LTR/E 5279 TCCACCACAGCCTGTCCCTGAGGATTGTAAGGGATTCCGGTAATATGGGA 5230 chr4ptel1M 681328 AATCTGATACTGT-GCACAAA--AGTGTGCAAAATGTTTAGAAGCATATG 681374 iivvi - i -- i --- vvi vv i v C HERVK11#LTR/E 5229 AATTCCCCACTGTTGCATAAATAAAT---CAAAAGCCTTACTAACATATC 5183 chr4ptel1M 681375 CAGGTCCATTATCTGTTTTTATTGCTTGTGGCACATCCATAATTGCAAAT 681424 vv i i i vvv i v vvi i - C HERVK11#LTR/E 5182 CAGGGGCGTTGTCTGTCTTTATTTGATATGGAAGCCCCATAACTGCAAA- 5134 chr4ptel1M 681425 GCTTGTATAAGGAACTCAGTGACCACTCGGGCTGTCTCTTTTGCTGCT-G 681473 vv v vi vv ivv v v i-- i vi iiv i - C HERVK11#LTR/E 5133 GCAAGAATACAGATGTTTTTTAACAT--GGGCCGTGCCTTCCCCTGTTTG 5086 chr4ptel1M 681474 GTA--TTGCAAAAGTGAATCCTGAAAAAGTATCTATCACAACATGGATAA 681521 i -- v vv ii i v i i iviv v i v C HERVK11#LTR/E 5085 GCAAGTAGCCCAGATAAAACCTGAGAAGGTATCTACAGAAACATGCACAT 5036 chr4ptel1M 681522 AAGACAGATGACCAAAAGATTTATAATGGGTCACATCCATTTGCCAAATT 681571 v ? vivi i vi vv i v vv C HERVK11#LTR/E 5035 ATGANAGTCTGCCAAAGGAGCTAACATGAGTCACATCCATTTGCCATAAA 4986 chr4ptel1M 681572 TCATTGGG 681579 ? i C HERVK11#LTR/E 4985 NCATTAGG 4978 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 41.63 CpG sites = 46, Kimura (unadjusted) = 43.38 Transitions / transversions = 0.92 (46/50) Gap_init rate = 0.03 (10 / 301), avg. gap size = 1.20 (12 / 10) 1118 30.18 3.95 6.37 chr4ptel1M 682589 683423 (316577) C HERVK14#LTR/ERVK (2683) 3413 2598 m_b181s701i7 7028 chr4ptel1M 682589 GCCTAACACTAGATGCATCCATTGGATATCTCCTATCAATTTCGGAAAGT 682638 vii i i v v vi i vi iv i i C HERVK14#LTR/E 3413 GCCTAAAGTTGGACGAATCCAATTAATGTCTCCTAATAATTTTTGGAAAT 3364 chr4ptel1M 682639 CATTTAAGGTGTTTAACTTCTCTGTTCTTAAAGAAAGTTTTTGTATTGTA 682688 v v v v vv vvvi vi viviv C HERVK14#LTR/E 3363 CATTTAAGGTTTTTAAATTATCTCTTCGAATTTGAACCTTTTGAGGCTTA 3314 chr4ptel1M 682689 A--GCACCTTAGGGTATAC-TTCATATCCTAAATATTGAAAAGGAGTATG 682735 -- i -- v v - - i i vi C HERVK14#LTR/E 3313 ATAGCACTTT--GTTCTACCTTCAT-TCCTAGATATTGAAAGGGAGTAGA 3267 chr4ptel1M 682736 TCTTTGAATTTTTTCTGGAGCTTTGTACAATTTGTAATTCCTTAGTGTTT 682785 vv i v v i ---- i --- -- i ivi iv C HERVK14#LTR/E 3266 AGTTTGGATTTTATCGGGGGCT----ATAATT---AA--CCCTGCCGCAT 3226 chr4ptel1M 682786 CTATGGTCTTTTGTAGACATCCTTCTA-----ACAT---TTGCTCC---- 682823 i ii i v - - vi v ----- --- vi ---- C HERVK14#LTR/E 3225 TTACAGCCTTTTCTA-AC-TGTTTGTAGCACAACATCAATTCTTCCCTAG 3178 chr4ptel1M 682824 --TCAGTTGCACATCCCAATATATCATCCATGTAATGTAACAACATAA-- 682869 -- i --- iv -i i i -- C HERVK14#LTR/E 3177 TTTCAGCTGCACA---CAGAATATCATCCATGTAATG-GATAATATAACA 3132 chr4ptel1M 682870 TTTTTGGGAATGCTTTTCTTA--GGAGTAAGAGCAGCAGCAATATACATT 682917 vii v - i v -- vv v vvivv i i vi C HERVK14#LTR/E 3131 TTTTTTAAACTG-TTCTCTAACTGGCTTAATAGCTTTCCCGACATAAGTT 3083 chr4ptel1M 682918 TGACACATAGCAGGGCTATTTTTCATTCCTTGTGGGGGGGAAAAAACTAT 682967 v iv vv v v------ iv v C HERVK14#LTR/E 3082 TGACAAATAGTCGGGCTATTTAGCATGCCTTGTGGT------AGTACTTT 3039 chr4ptel1M 682968 CCATTCATATCTTTTAAAAGG--CTTAGTTAAATTAACATTGGGCACTGA 683015 v vi v ivivv -- vi -- v iivi v v v C HERVK14#LTR/E 3038 CCAATGGTATCTGTCCGCTGGTTCTTTATTA--TTTATGGCGGGAACAGT 2991 chr4ptel1M 683016 AAAGGCAAATCTTTTCATA-TCCTCCTTATCCAGAGGGATACAATAGAAA 683064 i - - i vvvi v i i i ivv v i i C HERVK14#LTR/E 2990 AAAAGCAAAT-TTTTCATAATCTTGGGCAGCTAAAGGAATGGTAAAAAAG 2942 chr4ptel1M 683065 CAATCCCTAATGTCTATAATGCAAAGAGGCCATTCTCTAGGCA--GTTGA 683112 i v vi v ivvvi v v i v v --i - C HERVK14#LTR/E 2941 CAATCCTTTAGATCTATCACTATGAGAGGCCAGTATTTTGGGATCATTG- 2893 chr4ptel1M 683113 GTAGGAGATGGAAGTCCAGGGTGAAGAGTTTCCATAGTTTCCATCTT-TC 683161 - v i v v i v v v v ivi i v vv vi-v C HERVK14#LTR/E 2892 -TTGGGGAGGGCAGCCCTGGTTGCAGTGCACCCATGGGTTGAATCACAGC 2844 chr4ptel1M 683162 ATTTACTCTTCTTAAATCAGTCAACATCCTCCATTTTCCAGATTTCTTTT 683211 v vvii v i i i v i i C HERVK14#LTR/E 2843 ATTAACAGCCCTTAAATCTGTTAACATTCTCCATTTCCCTGATTTTTTCT 2794 chr4ptel1M 683212 TTACAAGAAATACAGGGGAATTCCAAGAACTTAGAGAAAGT------TGT 683255 v ii v i i----i ------ i C HERVK14#LTR/E 2793 TAATGACAAATACAGGAGAATTCCAAGG----GGAGAAAGTAGGCTCTAT 2748 chr4ptel1M 683256 AAGTGTGTTTGGTCAAGTTGCTCTTGCATTATATCTAATAAGGCCTGAAT 683305 v viv v - - i i ii vv vv i vv v C HERVK14#LTR/E 2747 ATGTCCCTTTTG-CAA-TTGTTCCTGCACCAGTTCTTTTAAAGCCTCCAG 2700 chr4ptel1M 683306 TTTTTTTTTTTTTACTAGCTAAAGGCCACTGTTCTTTCTACCCACACTGG 683355 ii v ---i ---- i ----i i v i C HERVK14#LTR/E 2699 TTTTTCCTGTTT---CAGC----GGCCATTG----CTCCACCCAAACCGG 2661 chr4ptel1M 683356 TGTATCAGTTTTCCATTGAATGGGAACAGGTAAAAGTACAGGCCTTCAAC 683405 v iv vv vvv vi ii --- iviiv -- C HERVK14#LTR/E 2660 TTTGGCAGTTAGCCAAACAAGAGGAATGGG---AGCCGGAGGC--TCAAC 2616 chr4ptel1M 683406 AGCAGCCCTGCCTAAAAA 683423 iii viv C HERVK14#LTR/E 2615 AATGGCCGCTCCTAAAAA 2598 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 37.43 CpG sites = 110, Kimura (unadjusted) = 38.87 Transitions / transversions = 0.87 (110/126) Gap_init rate = 0.08 (64 / 834), avg. gap size = 1.33 (85 / 64) 14 14.64 0.00 3.23 chr4ptel1M 685289 685320 (314680) (CTC)n#Simple_repeat 1 31 (0) m_b181s252i9 7029 chr4ptel1M 685289 CTGCTCCTCCTATTCCTCCTCCTCCCTCCACC 685320 v vi - v (CTC)n#Simple 1 CTCCTCCTCCTCCTCCTCCTCCT-CCTCCTCC 31 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 529 28.01 4.28 2.63 chr4ptel1M 686644 686830 (313170) MIRc#SINE/MIR 18 207 (61) m_b181s601i6 7030 chr4ptel1M 686644 GTAGATGGAGCAATAGA--TACAGTGCTGAGATACCCAAGTTCAAATCCA 686691 i vi v i -- iv - v ii v iii i i v MIRc#SINE/MIR 18 GTGGAAAGAGCACTGGACTTGGAGT-CAGGAAGACCTGGGTTCGAGTCCC 66 chr4ptel1M 686692 GTTTCAGATATTTACAAACTGGTTGATCTTGGTCAAGTCATTTGATCTAT 686741 vi v vi i v i vv i v i i i v MIRc#SINE/MIR 67 GGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCT 116 chr4ptel1M 686742 GTGTGCCTCAGTATCCTCCTCTATAAAATGGAAATTGTAATA---GC--- 686785 v v v v i ii vi --- --- MIRc#SINE/MIR 117 CTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCT 166 chr4ptel1M 686786 ATCCACTTTCCAGGGTGGTTGTGAGGATATCTCACATGGGATAAT 686830 ii i i iv v ---- v i MIRc#SINE/MIR 167 GCCTACCTCACAGGGTTGTTGTGAGGA----TCAAATGAGATAAT 207 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 35.00 CpG sites = 29, Kimura (unadjusted) = 35.87 Transitions / transversions = 1.32 (29/22) Gap_init rate = 0.04 (8 / 186), avg. gap size = 1.62 (13 / 8) 705 25.35 4.31 1.87 chr4ptel1M 686674 686882 (313118) MIR#SINE/MIR 45 258 (4) m_b181s601i7 7030 chr4ptel1M 686674 TACCCAAGTTCAAATCCAGTTTCAGATATTTACAAACTGGTTGATCTTGG 686723 i iii i v vi v vi i v i vv i MIR#SINE/MIR 45 TGCCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 94 chr4ptel1M 686724 TCAAGTCATTTGATCTATGTGTGCCTCAGTATCCTCCTCTATAAAATGGA 686773 v i i i i v v v v i i MIR#SINE/MIR 95 GCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGG 144 chr4ptel1M 686774 AATTGTAATAGCATCCACTTTCCAGGGTGGTTGTGAGGATATCTCACATG 686823 i vi i i i i ivi v ---- i v MIR#SINE/MIR 145 GATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGGA----TTAAATG 190 chr4ptel1M 686824 GGATAAT-CA--TAAAATGCTTACTGCAGTGACTGG--CATAGTAGGCGC 686868 i v - -- ii vvi v -- i MIR#SINE/MIR 191 AGTTAATACATGTAAAGCGCTTAGAACAGTGCCTGGCACATAGTAAGCGC 240 chr4ptel1M 686869 ----TACATATTAGCTAT 686882 ---- v i MIR#SINE/MIR 241 TCAATAAATGTTAGCTAT 258 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 30.23 CpG sites = 31, Kimura (unadjusted) = 31.68 Transitions / transversions = 1.48 (31/21) Gap_init rate = 0.04 (8 / 208), avg. gap size = 1.62 (13 / 8) 14 12.94 2.63 5.41 chr4ptel1M 689628 689665 (310335) (GGGA)n#Simple_repeat 1 37 (0) m_b181s252i10 7031 chr4ptel1M 689628 GGGAGGGGAGAAGACGG-GAGAGGAAGGGAGGGAGGGAG 689665 - -i v - i i (GGGA)n#Simpl 1 GGGA-GGGAG-GGAGGGAGGGAGGGAGGGAGGGAGGGAG 37 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.08 (3 / 37), avg. gap size = 1.00 (3 / 3) 531 23.95 2.07 2.07 chr4ptel1M 691659 691803 (308197) MIR#SINE/MIR 108 252 (10) m_b181s601i8 7032 chr4ptel1M 691659 CCTCTCTGCCTACCTTAGCTTCTTCCTCTGTAAAAT-GAGATAATAAGAA 691707 -- i i i i v - i v- MIR#SINE/MIR 108 CCTCTCTG--TGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAAT-A 154 chr4ptel1M 691708 GCACCCACCTCCCAGGG-TGTTGTGAGTGTCAAATGAAATCCCATTTGTA 691756 i i vi - vi i iv vvi iv MIR#SINE/MIR 155 GTACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATACATGTA 204 chr4ptel1M 691757 AAGTACTTGACAC-CTGCTTGGCACAGAGTAGGTACTTAATAAGTGTT 691803 ii iiv -v i v i ii i i MIR#SINE/MIR 205 AAGCGCTTAGAACAGTGCCTGGCACATAGTAAGCGCTCAATAAATGTT 252 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 27.57 CpG sites = 23, Kimura (unadjusted) = 29.87 Transitions / transversions = 2.09 (23/11) Gap_init rate = 0.04 (6 / 144), avg. gap size = 1.00 (6 / 6) 203 19.44 0.00 0.00 chr4ptel1M 691772 691807 (308193) L2c_3end#LINE/L2 431 466 (12) m_b181s601i9 7033 chr4ptel1M 691772 GCTTGGCACAGAGTAGGTACTTAATAAGTGTTTATT 691807 i v ii i i i L2c_3end#LINE 431 GCCTGGCACATAGTAGGCGCTCAATAAATGTTTGTT 466 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 19.66 CpG sites = 6, Kimura (unadjusted) = 23.83 Transitions / transversions = 6.00 (6/1) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 21 0.00 0.00 0.00 chr4ptel1M 692356 692378 (307622) (T)n#Simple_repeat 1 23 (0) m_b181s252i11 7034 chr4ptel1M 692356 TTTTTTTTTTTTTTTTTTTTTTT 692378 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTT 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 chr4ptel1M 693137 693153 (306847) (T)n#Simple_repeat 1 17 (0) m_b181s252i12 7035 chr4ptel1M 693137 TTTTTTTTTTTTTTTTT 693153 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTT 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 16 16.57 0.00 0.00 chr4ptel1M 693222 693248 (306752) (T)n#Simple_repeat 1 27 (0) m_b181s252i13 7036 chr4ptel1M 693222 TTTCTTTTTTCTTTTAATTTTTTTTTT 693248 i i vv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTT 27 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 257 32.05 5.47 4.33 chr4ptel1M 693697 693970 (306030) C L1MA10_3end#LINE/L1 (436) 645 369 m_b181s551i6 7037 chr4ptel1M 693697 CTCCTGTTCCTG-CTCATTTCACTCAGCATCAGTTCCTGTAAGTCTCTCC 693745 i v? - i i v vv vi i iiv C L1MA10_3end#L 645 CTTCTGTGNCTGGCTTATTTCACTTAGCATAATGTCCTCCAGGTTCATCC 596 chr4ptel1M 693746 AGG-----GCACTTTGAA--ATCCTCCTGCTGATCATTTCTTACAGAACA 693788 v ----- vv v v -- i- v ------ i vi vvv C L1MA10_3end#L 595 ATGTTGTCGCAAATGGCAGGATT-TCCTTCT------TTTTTAAGGCTGA 553 chr4ptel1M 693789 ATAATATTCCATTACATTCATATACCACAACTTATTCAGCCATTTTCCAA 693838 ii vi vi v i v ivi vi C L1MA10_3end#L 552 ATAATATTCCATTGTATGTATATACCACATTTTCTTTATCCATTCATCCG 503 chr4ptel1M 693839 TTGATGGGCATTCA-TTCGTTTTCCAGTTTCTAGCCACTACAAAAAGGGC 693887 i i i -v i - vv ii i i i iii v iv C L1MA10_3end#L 502 TCGATGGACATTTAGGTTG-TTTCCATATCTTGGCTATTGTGAATAATGC 454 chr4ptel1M 693888 TGCATCAAACATTT--TTGCACATAGGGGTCCCTTT----CCCTTCTTTA 693931 vii vv--v v ---- i i----i vv v C L1MA10_3end#L 453 TGCAATGAACATGGGAGTGCAGATA----TCTCTTCGAGATCCTGATTTC 408 chr4ptel1M 693932 AGATCTCTGTGATATAAGCCCGGTAGTCACACTGCTGGA 693970 iv i vv vi i v viv i C L1MA10_3end#L 407 AATTCTTTTGGATATATACCCAGAAGTGGGATTGCTGGA 369 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 40.71 CpG sites = 42, Kimura (unadjusted) = 42.67 Transitions / transversions = 1.00 (42/42) Gap_init rate = 0.07 (18 / 273), avg. gap size = 1.50 (27 / 18) 433 29.85 1.95 1.95 chr4ptel1M 693705 693909 (306091) C L1ME3G_3end#LINE/L1 (292) 632 428 m_b181s551i7 7037 chr4ptel1M 693705 CCTGCTCATTTCACTCAGCATCAGTTCCTGTAAGTCTCTCCAGG---GCA 693751 i iv i vi vv i v ii i v --- i C L1ME3G_3end#L 632 CTTGCTTTTTTCACTCAACAATATGTCTTGGAGATCTTTCCATGTCAGTA 583 chr4ptel1M 693752 CTTTGAAATCCTCCTGCTGATCATTTCTTACAGAACAATAATATTCCATT 693801 v vv i iv - -- iv i v ? vvvv i v C L1ME3G_3end#L 582 CATATAGATCTACCT-C--ATTCTTTTTAACNGCTGCATAGTATTCCATA 536 chr4ptel1M 693802 ACATTCATATACCACAACTTATTCAGCCATTTTCCAATTGATGGGCATTC 693851 ii vv i i i i ii v i i C L1ME3G_3end#L 535 GTATGGATATACCATAATTTATTTAACCATTCCCCTATTGATGGACATTT 486 chr4ptel1M 693852 A-TTCGTTTTCCAGTTTCTAGCCACTACAAAAAGGGCTGCATCAAACATT 693900 -v i - i i v i i v iv vii i C L1ME3G_3end#L 485 AGGTTG-TTTCCAATTTTTCGCTATTACAAACAATGCTGCAATGAACATC 437 chr4ptel1M 693901 TTTGCACAT 693909 i i C L1ME3G_3end#L 436 CTTGTACAT 428 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 39.41 CpG sites = 35, Kimura (unadjusted) = 39.41 Transitions / transversions = 1.40 (35/25) Gap_init rate = 0.03 (6 / 204), avg. gap size = 1.33 (8 / 6) 310 31.62 4.37 3.24 chr4ptel1M 693788 693970 (306030) C L1MB2_3end#LINE/L1 (365) 553 369 m_b181s551i8 7037 chr4ptel1M 693788 AATAATATTCCATTACATTCATATACCACAACTTATTCAGCCATTTTCCA 693837 ii vi vi i i v ivi v C L1MB2_3end#LI 553 AATAATATTCCATTGTATGTATATACCACATTTTGTTTATCCATTCATCC 504 chr4ptel1M 693838 ATTGATGGGCATTCATTCGTT--TTCCAGTTTCTAGCCACTACAAAAAGG 693885 i i i i -- vv -- vi ii i i i iii v iv C L1MB2_3end#LI 503 GTCGATGGACACT--TGGGTTGCTTCCACCTCTTGGCTATTGTGAATAAT 456 chr4ptel1M 693886 GCTGCATCAAACAT--TTTTGCACATAGGGGTCCCTTT----CCCTTCTT 693929 vvii --v v v ---- i i---- v C L1MB2_3end#LI 455 GCTGCTATGAACATGGGTGTGCAAATA----TCTCTTCGAGACCCTGCTT 410 chr4ptel1M 693930 TAAGATCTCTGTGATATAAGCCCGGTAGTCACACTGCTGGA 693970 v iv i vv vi i v viv i C L1MB2_3end#LI 409 TCAATTCTTTTGGATATATACCCAGAAGTGGGATTGCTGGA 369 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 39.34 CpG sites = 32, Kimura (unadjusted) = 42.28 Transitions / transversions = 1.33 (32/24) Gap_init rate = 0.05 (9 / 182), avg. gap size = 1.56 (14 / 9) 488 23.33 0.83 0.83 chr4ptel1M 693789 693909 (306091) C L1ME3C_3end#LINE/L1 (321) 549 429 m_b181s551i9 7037 chr4ptel1M 693789 ATAATATTCCATTACATTCATATACCACAACTTATTCAGCCATTTTCCAA 693838 i ii vv i i v i vi C L1ME3C_3end#L 549 ATAGTATTCCATTGTATGAATATACCACAATTTATTTATCCATTCTCCTG 500 chr4ptel1M 693839 TTGATGGGCATTCA-TTCGTTTTCCAGTTTCTAGCCACTACAAAAAGGGC 693887 i i -v i - i i v i i v iv C L1ME3C_3end#L 499 TTGATGGACATTTAGGTTG-TTTCCAATTTTTCGCTATTACAAACAATGC 451 chr4ptel1M 693888 TGCATCAAACATTTTTGCACAT 693909 vii i i C L1ME3C_3end#L 450 TGCAATGAACATTCTTGTACAT 429 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 28.91 CpG sites = 19, Kimura (unadjusted) = 28.91 Transitions / transversions = 2.11 (19/9) Gap_init rate = 0.02 (2 / 120), avg. gap size = 1.00 (2 / 2) 200 30.91 0.00 2.94 chr4ptel1M 693996 694065 (305935) MIRb#SINE/MIR 194 261 (7) m_b181s601i10 7038 chr4ptel1M 693996 GAGATCATAGTTGTAGAAAATACTTAGCCCAATCCCTGGCACCTGGTAGG 694045 v ivv -- iii v i v v i i MIRb#SINE/MIR 194 GAGATAATGCATGTA--AAGCGCTTAGCACAGTGCCTGGCACATAGTAAG 241 chr4ptel1M 694046 TGCTGTATAAGTGCTGATTC 694065 i vv i v iii MIRb#SINE/MIR 242 CGCTCAATAAATGGTAGCTC 261 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 35.74 CpG sites = 12, Kimura (unadjusted) = 40.90 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.03 (2 / 69), avg. gap size = 1.00 (2 / 2) 280 26.08 18.92 1.54 chr4ptel1M 696059 696280 (303720) C L3b_3end#LINE/CR1 (664) 542 283 m_b181s601i11 7039 chr4ptel1M 696059 AGACCCCCACGTCTTTTT-GCATGCA-TCCTGCT-------------CCC 696093 i v -i ?i- v ------------- C L3b_3end#LINE 542 AAACCCCCAGGTCTTTTTCACATGNGCTGCTGCTAAGCCGCGTCTCCCCC 493 chr4ptel1M 696094 AGCTTTCACTTCGCAGGCTTGTTTTTGT-AATCCAACT-TAGAACT---- 696137 v i vi - iv v ? v - i v -i i ---- C L3b_3end#LINE 492 ATCCTGTACT-CGCGCGATTGNTTTTTTGAACCCAAGTGCAGGACTTTAC 444 chr4ptel1M 696138 ----------GTTCAATTTTATTTGATTAGATTGGGTCTTATATTCCAGC 696177 ---------- v i i vi i ? v i iv?ii i i C L3b_3end#LINE 443 GTTTATCCCTGTTGAATTTCATCTTGTTGGNTTCGGCCCGNCGTTCTAGT 394 chr4ptel1M 696178 CTGTCAGGACCTTTTTGGAACTTGTCTGTGTCATCTCAAAACATAAGC-- 696225 ii i v v i vi v - - vii v -- C L3b_3end#LINE 393 CTGTCGAGATCGTTTTGGATCCTGATTTTG-CATC-CAACGTATTAGCCG 346 chr4ptel1M 696226 -AGCTTTGAGTTTT-----CT-GCAAATTCATTCAACGTGATTTC--TAC 696266 -v iiv i i----- - iiv v i - v -- i C L3b_3end#LINE 345 TCGCTCCCAGCTTCTGCCACTNGCAAATTTGATAAGC-TGCTTTCCGTAT 297 chr4ptel1M 696267 CTTCATCCAAGTCA 696280 C L3b_3end#LINE 296 CTTCATCCAAGTCA 283 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 30.13 CpG sites = 34, Kimura (unadjusted) = 33.74 Transitions / transversions = 1.48 (34/23) Gap_init rate = 0.07 (16 / 221), avg. gap size = 2.88 (46 / 16) 458 26.58 7.47 0.54 chr4ptel1M 696136 696309 (303691) C L3#LINE/CR1 (766) 3333 3148 m_b181s601i12 7039 chr4ptel1M 696136 CTGTTCAATTTTATTTGATTAGATTGGGTCTTATATTCCAGCCTGTCAGG 696185 v i i vi i v v i ivvii ii C L3#LINE/CR1 3333 CTGTTAAATTTCATCTTGTTGGTTTCGGCCCATCGTTCCAGCCTGTCGAG 3284 chr4ptel1M 696186 ACCTTTTTGGAACTTGTCTGTGTCATCTCAAAACATAAG----------C 696225 i ? i v vi v - ?vii v ---------- C L3#LINE/CR1 3283 ATCNTTTTGAATCTTGATTCTGTCATC-CANCGTATTAGCTATCCCTCCC 3235 chr4ptel1M 696226 AGCTTTGAGTTTTCTGCAAATTCATTCAACGTGATTTCTA--CCTTCATC 696273 v iv iiv v i i vi --i C L3#LINE/CR1 3234 AGCTTTGTGTCATCTGCAAATTTGATAAGCATGCCTTCTATGTCTTCATC 3185 chr4ptel1M 696274 CAAGTCAGT-AGAAAAATGTTGTTAATGACAAGGGCA 696309 v - v vvv v i v C L3#LINE/CR1 3184 CAAGTCATTGATAAAAATGTTGAACAGGACAGGGCCA 3148 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 31.00 CpG sites = 23, Kimura (unadjusted) = 33.67 Transitions / transversions = 1.00 (23/23) Gap_init rate = 0.02 (4 / 173), avg. gap size = 3.50 (14 / 4) 236 34.10 2.27 2.27 chr4ptel1M 696520 696651 (303349) C L3#LINE/CR1 (1083) 3016 2885 m_b181s601i13 7039 chr4ptel1M 696520 TCTCTTCATATT-TTTATGAGTGTAGCATGAAGGACTTTTTTAAAAGCTG 696568 i i v - ii ii vi v ii v i v iv C L3#LINE/CR1 3016 TTTCTCCATCTTGTCCACAAGGATATCATGAGAGACTTTGTCAAATGCCT 2967 chr4ptel1M 696569 GGCTTAAATATAGTCA-ACATTGCTAAGGACACGACTACTTTCCTCTGCC 696617 v v vi vi - v? iiv v i --- i v ii vv i C L3#LINE/CR1 2966 TGCTGAAATCCAGATACACTNTGTCTACGGC---ATTCCCCTGATCTACC 2920 chr4ptel1M 696618 AATCTAGT-ACCCTGTTGGAAAAGGAAACAAGTTT 696651 i - i iii ii v C L3#LINE/CR1 2919 AGTCTAGTAACCCTATCAAAAAAGGAAATGAGGTT 2885 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 48.17 CpG sites = 27, Kimura (unadjusted) = 48.17 Transitions / transversions = 1.59 (27/17) Gap_init rate = 0.05 (6 / 131), avg. gap size = 1.00 (6 / 6) 367 22.87 12.24 1.85 chr4ptel1M 698759 698905 (301095) MIRc#SINE/MIR 69 230 (38) m_b181s601i14 7040 chr4ptel1M 698759 CTCTGGTGCTT--TGACTGCGTGACTTTGGGTCAGTCATTTCACCTC--- 698803 vii -- ii i i iv i v --- MIRc#SINE/MIR 69 CTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCT 118 chr4ptel1M 698804 -AGACTCATTTTCTTCATCTGCAAAAATGAAAATAATAATA---GCACTT 698849 - v v i i- iii --- v v MIRc#SINE/MIR 119 GAGCCTCAGTTTCCTCATCTGT-AAAATGGGGATAATAATACCTGCCCTG 167 chr4ptel1M 698850 CCTGC----CAAGGCTGTAGTACAGG--CAAA--AGGTGAT-TATGGGTA 698890 i ---- i i v i- -- -- i i - v - MIRc#SINE/MIR 168 CCTACCTCACAGGGTTGTTGTG-AGGATCAAATGAGATAATGTATGTG-A 215 chr4ptel1M 698891 AAGGACCTCGAAAAC 698905 vi i i v MIRc#SINE/MIR 216 AAGCGCTTTGTAAAC 230 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 27.20 CpG sites = 22, Kimura (unadjusted) = 28.20 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.08 (11 / 146), avg. gap size = 1.91 (21 / 11) 19 3.81 0.00 0.00 chr4ptel1M 699114 699140 (300860) (GGGTG)n#Simple_repeat 1 27 (0) m_b181s252i14 7041 chr4ptel1M 699114 GGGTGGTGTGGGGTGGGGTGGGGTGGG 699140 v (GGGTG)n#Simp 1 GGGTGGGGTGGGGTGGGGTGGGGTGGG 27 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 19 14.37 0.00 0.00 chr4ptel1M 699252 699282 (300718) (A)n#Simple_repeat 1 31 (0) m_b181s252i15 7042 chr4ptel1M 699252 AAATAAAAAAAAAAAAATTAAAAAAAAATAA 699282 v vv v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 31 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 557 27.78 0.69 0.00 chr4ptel1M 700380 700523 (299477) MIRc#SINE/MIR 4 148 (120) m_b181s601i15 7043 chr4ptel1M 700380 GGCTGGATGGCTCAATGGAGAGAGTATCGAGTCTGGAATCAGAAAAACTT 700429 v vi iv i i i ii iiii i i i i MIRc#SINE/MIR 4 GGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCT 53 chr4ptel1M 700430 GGGCTCAAATGTGGCCTCAGACACTTCCTAGCTGGGTGACTATGGAAAAG 700479 i i i viv v v v v v iv iv MIRc#SINE/MIR 54 GGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAG 103 chr4ptel1M 700480 TCATTTTACC-CTGTTTGCCTCAGTTTCCTCATCTGTAGAATGAG 700523 i v - v vv i i MIRc#SINE/MIR 104 TCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 34.56 CpG sites = 24, Kimura (unadjusted) = 35.67 Transitions / transversions = 1.50 (24/16) Gap_init rate = 0.01 (1 / 143), avg. gap size = 1.00 (1 / 1) 16 16.52 0.00 0.00 chr4ptel1M 700837 700863 (299137) (T)n#Simple_repeat 1 27 (0) m_b181s252i16 7044 chr4ptel1M 700837 TTTTTTTTTTTTAATTTTCTTTATTTT 700863 vv i v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTT 27 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 388 14.81 7.41 0.00 chr4ptel1M 701306 701386 (298614) C MIRc#SINE/MIR (53) 215 129 m_b181s601i16 7045 chr4ptel1M 701306 TTACAAATCTTATCTCCTTTGATCCTCACAACAACCCTGGGAGGTAG--- 701352 i v iv v v --- C MIRc#SINE/MIR 215 TCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCA 166 chr4ptel1M 701353 GGGC---TACAATGATACCTATTTTACAGATGAGAAA 701386 --- iv v v i i C MIRc#SINE/MIR 165 GGGCAGGTATTATTATCCCCATTTTACAGATGAGGAA 129 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 16.52 CpG sites = 5, Kimura (unadjusted) = 16.52 Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.03 (2 / 80), avg. gap size = 3.00 (6 / 2) 263 33.60 2.40 0.00 chr4ptel1M 702263 702387 (297613) C L1MC5_3end#LINE/L1 (2116) 578 451 m_b181s551i10 7046 chr4ptel1M 702263 TGTTCCTCATTTC-TTTTAGAAC--AATAATATTCCATTACTTTTGTATA 702309 i i - v i --v i i iiv vvi i C L1MC5_3end#LI 578 TATTCCTCATTCCTTTTTACAGCTGCATAGTACTCCATTGTGTGGATGTA 529 chr4ptel1M 702310 TCATAACATATTCAGCCATTCCCCAACTGAGGGGCATCCACTCAATTTTC 702359 i iiv i v v i v i iiivvivi i C L1MC5_3end#LI 528 CCATAGTTTATTCAACCAGTCCCCTATTGATGGACATTTGGGTTGTTTCC 479 chr4ptel1M 702360 AATTCTTTACCATCACAAAAAGAACTGC 702387 i ii i i i v vi C L1MC5_3end#LI 478 AGTCTTTTGCTATTACAAATAGTGCTGC 451 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 47.39 CpG sites = 28, Kimura (unadjusted) = 47.39 Transitions / transversions = 2.00 (28/14) Gap_init rate = 0.02 (2 / 124), avg. gap size = 1.50 (3 / 2) 26 13.98 0.00 0.00 chr4ptel1M 703010 703050 (296950) (T)n#Simple_repeat 1 41 (0) m_b181s252i17 7047 chr4ptel1M 703010 TTTCTTTCTTTCTTTTCTTTTCTTTTTTTTTTTTTTTTTTT 703050 i i i i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 41 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 376 31.37 3.63 2.56 chr4ptel1M 703542 703734 (296266) C L1MC5_3end#LINE/L1 (2129) 565 371 m_b182s551i1 7046 chr4ptel1M 703542 TTCTTACAGAACAATAATATTCCATAACATTCATATACTGCAATTTACCC 703591 i vvvv i i viii vv i iii i ii C L1MC5_3end#LI 565 TTTTTACAGCTGCATAGTACTCCATTGTGTGGATGTACCATAGTTTATTC 516 chr4ptel1M 703592 AACCATTCTCCAATTGATGGGCATCCA--TTCATTTTCCAGTGTCTAGCC 703639 v i v i iii-- v-- v i v i C L1MC5_3end#LI 515 AACCAGTCCCCTATTGATGGACATTTGGGTTG--TTTCCAGTCTTTTGCT 468 chr4ptel1M 703640 ACTATAAACAGGGCTGCCACAAATA-TTTTGCCACATACAGGTCTCTTTC 703688 i i i v v ii -ii i-i -- i iv C L1MC5_3end#LI 467 ATTACAAATAGTGCTGCAATGAATAGCCTTGT-GCATAC--GTCTTTTCG 421 chr4ptel1M 703689 CCTTCTT--TAGTATGTCTTTGGGGTATAAGCCCAGTAGTTG--TTGCTG 703734 iv i --i i i i v vv i v v -- C L1MC5_3end#LI 420 TATTTTTGCCAGTGTATCTTTGGGATAGATTCCTAGAAGTGGGATTGCTG 371 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.62 CpG sites = 38, Kimura (unadjusted) = 42.60 Transitions / transversions = 1.81 (38/21) Gap_init rate = 0.05 (9 / 192), avg. gap size = 1.33 (12 / 9) 435 28.75 2.91 2.91 chr4ptel1M 703555 703726 (296274) C L1ME4c_3end#LINE/L1 (275) 555 384 m_b182s551i2 7046 chr4ptel1M 703555 ATAATATTCCATAACATTCATATACTGCAATTTACCCAACCATTCTCCAA 703604 vivi ?v i iii ii i v C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chr4ptel1M 703605 TTGATGGGCATCCA--TTCATTTTCCAGTGTCTAGCCACTATAAACAGGG 703652 v i ii -- v-- i v i v i i i iv C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTG--TTTCCAATTTTTCGCTATTATAAATAACG 458 chr4ptel1M 703653 CTGCCACAAATATTTTGCCACATACAGGTCTCTTTCCCTTCTTT---AGT 703699 v ii i i vvii i v --- i --- v C L1ME4c_3end#L 457 CTGCAATGAACATCTTCGTGCATATAGCT---TTTTCCTTCTTTTGAATT 411 chr4ptel1M 703700 ATGTCTTTGGGGTATAAGCCCAGTAGT 703726 v i i i v vv v C L1ME4c_3end#L 410 ATTTCCTTAGGATAAATTCCCAGAAGT 384 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.67 CpG sites = 29, Kimura (unadjusted) = 37.67 Transitions / transversions = 1.53 (29/19) Gap_init rate = 0.04 (7 / 171), avg. gap size = 1.43 (10 / 7) 281 13.64 0.00 0.00 chr4ptel1M 703867 703910 (296090) hAT-4b_Ther#DNA/hAT-Tip100 1151 1194 (69) m_b182s502i0 7048 chr4ptel1M 703867 TTTTTCTTTCATGATTTATGAGATCATGTACATGGAATGGTATG 703910 i i ii i v hAT-4b_Ther#D 1151 TTTTTCTTTCATGATTCATGAGATTATGTATGTGGGATGGGATG 1194 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 15.55 CpG sites = 5, Kimura (unadjusted) = 15.55 Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 400 30.71 9.29 0.00 chr4ptel1M 705682 705821 (294179) MIRb#SINE/MIR 55 207 (61) m_b182s601i0 7049 chr4ptel1M 705682 CTGGGCCTGGAATCAGTCCCCCACACTTAGTAGTTCTGTAATCTTGGACA 705731 iii i vi v v i ivv v i v i i i MIRb#SINE/MIR 55 CTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 104 chr4ptel1M 705732 AGTTACTTAATTTCTGCTTGCCTCTGGTTCTTTAATTGTAGAATGAAGA- 705780 ii vivv v v i i vi i ii - MIRb#SINE/MIR 105 AGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGAT 154 chr4ptel1M 705781 ------------CTCCCAGGGTGGTTGTGAGGATCAGATAATGTCTGGCA 705818 ------------ v v i i i vi vvv MIRb#SINE/MIR 155 AATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCA 204 chr4ptel1M 705819 TGT 705821 MIRb#SINE/MIR 205 TGT 207 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.26 CpG sites = 24, Kimura (unadjusted) = 40.48 Transitions / transversions = 1.26 (24/19) Gap_init rate = 0.01 (2 / 139), avg. gap size = 6.50 (13 / 2) 284 33.33 1.06 1.06 chr4ptel1M 705945 706038 (293962) C MIRc#SINE/MIR (128) 140 47 m_b182s601i1 7050 chr4ptel1M 705945 ACAGATGAGGACACTAAGA-TAAATAAAATGGGGTGACTTGTCCAGGACC 705993 v i i- v ivi ii vii i i ii C MIRc#SINE/MIR 140 ACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTC 91 chr4ptel1M 705994 ACACTGTTAGTATGTATTTGAGACCCATATTAGAACTCAGATCCT 706038 v i v iviv - viv i v i i i C MIRc#SINE/MIR 90 ACACAGCTAGTAAGTGGCAGAG-CCGGGACTCGAACCCAGGTCTT 47 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 46.49 CpG sites = 20, Kimura (unadjusted) = 46.49 Transitions / transversions = 1.82 (20/11) Gap_init rate = 0.02 (2 / 93), avg. gap size = 1.00 (2 / 2) 378 26.31 3.65 2.90 chr4ptel1M 707086 707222 (292778) MIRb#SINE/MIR 8 145 (123) m_b182s601i2 7051 chr4ptel1M 707086 GCAGCTAAGTGAGTGTAGTAGAGTGC-CACGG---CTGGAGTCAGAATGA 707131 --- - i i iv v- ---i vv MIRb#SINE/MIR 8 GCAGC---GTG-GTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGA 53 chr4ptel1M 707132 CCTTGGTTGACATGTGGCCTCAGACCCTTAGTAGTTGTGTGATCTTGGAC 707181 v viv viv v v v v v i i i MIRb#SINE/MIR 54 CCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGC 103 chr4ptel1M 707182 AAGTCATTTTACC-CTGTTTGCCTCTGTTTTTTAATCCATAA 707222 i i v - v vv v ii v ii MIRb#SINE/MIR 104 AAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAA 145 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.45 CpG sites = 15, Kimura (unadjusted) = 32.52 Transitions / transversions = 0.75 (15/20) Gap_init rate = 0.05 (7 / 136), avg. gap size = 1.29 (9 / 7) 252 33.60 5.93 1.63 chr4ptel1M 707748 707865 (292135) MIR1_Amn#SINE/MIR 27 149 (81) m_b182s601i3 7052 chr4ptel1M 707748 AGAACATTGTGCTATA--TTAGAAGGCTAAGCTTTGATCTTCCAGCTCTT 707795 i i vi ivi-- ii i i ivi v i? ?- i i v MIR1_Amn#SINE 27 AGAGCACTGGACTGGGACTCGGGAGACCTGGGTTCNAN-TCCCGGCTCTG 75 chr4ptel1M 707796 CT-TTTCTTACCTAAGTGACCCTGGATGAGTCA----ACTTCTTTTGAAT 707840 i-i ?vii?v i? i iii ---- i i - ?ii MIR1_Amn#SINE 76 CCACTNGCCNGCTGNGTGACCTTGGGCAAGTCACTTNACCTCTCT-GNGC 124 chr4ptel1M 707841 CTCAGTTGCCTCAATTGAAAAGTGG 707865 v vi v i MIR1_Amn#SINE 125 CTCAGTTTCCTCATCTGTAAAATGG 149 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 48.83 CpG sites = 29, Kimura (unadjusted) = 53.16 Transitions / transversions = 2.90 (29/10) Gap_init rate = 0.04 (5 / 117), avg. gap size = 1.80 (9 / 5) 276 31.15 8.53 2.94 chr4ptel1M 707764 707892 (292108) MIR3#SINE/MIR 40 175 (33) m_b182s601i4 7052 chr4ptel1M 707764 TTAGAAGGC-TAAGCTTTGATCTTCCAGCTCTTCTTTT--CTTACCTAAG 707810 i i i - ii i i ii -- i v ivi -- ?i - iv MIR3#SINE/MIR 40 TCAGGAGACCTGGGTTCTAGTC--CCGGCTCTGCCACTAACTNGC-TGTG 86 chr4ptel1M 707811 TGACCCTGGATGAGTCAACTTC----TTTTGAATCTCAGTTGCCTCAATT 707856 i iii - ----i i iii v vi MIR3#SINE/MIR 87 TGACCTTGGGCAAGTCA-CTTCACCTCTCTGGGCCTCAGTTTCCTCATCT 135 chr4ptel1M 707857 GAAAAGT----GGTTTGGAATAGATTATCTTGAACATCTC 707892 v i ---- v v v iv vi i MIR3#SINE/MIR 136 GTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCC 175 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 42.19 CpG sites = 28, Kimura (unadjusted) = 43.74 Transitions / transversions = 2.55 (28/11) Gap_init rate = 0.06 (8 / 128), avg. gap size = 1.88 (15 / 8) 217 21.15 14.71 2.63 chr4ptel1M 709221 709322 (290678) L2c_3end#LINE/L2 332 445 (33) m_b182s601i5 7053 chr4ptel1M 709221 CTTGT-TTGTG-TTAT-TGTTTGCATAT-TGTCTC----AACAGACTGAA 709262 - i- i - i ? i - ---- vi vi L2c_3end#LINE 332 CTTGTATTGTAATTGTCTGTTTACNTGTCTGTCTCCTCCACTAGACTGTG 381 chr4ptel1M 709263 ACCTTCCTGAGTGCAGGGGCT-TGGTTTATTC-TC-----ACCCCTAGGC 709305 v i i v i i- vi - ----- i i - L2c_3end#LINE 382 AGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTATCCCCA-GC 430 chr4ptel1M 709306 ACAGTTGGCACATGGTA 709322 i --i i L2c_3end#LINE 431 GC--CTGGCACATAGTA 445 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 23.53 CpG sites = 16, Kimura (unadjusted) = 26.40 Transitions / transversions = 3.20 (16/5) Gap_init rate = 0.11 (11 / 101), avg. gap size = 1.64 (18 / 11) 754 25.61 1.83 3.72 chr4ptel1M 711390 711608 (288392) C MIRb#SINE/MIR (14) 254 40 m_b182s601i6 7054 chr4ptel1M 711390 CATTTATGTAGGGCCTACTATGTGCCAGA-ACTGTGCTCAGCACTTTTAC 711438 vv v i i- v i - C MIRb#SINE/MIR 254 CATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTT-AC 206 chr4ptel1M 711439 CAATAGATAAGCTCATCTTATCCTTGCAACAACTTTGAGAGCCAGGTGCT 711488 -- iv v v i v ii ii v vi ii C MIRb#SINE/MIR 205 --ATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATT 158 chr4ptel1M 711489 GCTGTTACCTCTGTTTGGTACTTGAGAAAACTGAGGC--AGATAGCTTAA 711536 i--- i i ii vii vv i -- v v C MIRb#SINE/MIR 157 A---TTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAA 111 chr4ptel1M 711537 ATGACTTGTCCAGAGTTACTTAGCTAGTAAGTATC-CAGTGGGCTAATTC 711585 i i i ii i vi iv -v iv --i C MIRb#SINE/MIR 110 GTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGG--GATTC 63 chr4ptel1M 711586 CAAATCAGGTCTCCCTGACTCCA 711608 v vi vi C MIRb#SINE/MIR 62 GAACCCAGGTCTGTCTGACTCCA 40 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.31 CpG sites = 32, Kimura (unadjusted) = 32.02 Transitions / transversions = 1.45 (32/22) Gap_init rate = 0.05 (11 / 218), avg. gap size = 1.09 (12 / 11) 464 27.74 8.70 2.04 chr4ptel1M 712022 712205 (287795) C L3#LINE/CR1 (694) 3405 3210 m_b182s601i7 7055 chr4ptel1M 712022 AGCCACAGCTTCTCT-TTGGGTA--TGTGCAGTTGGTTTTGAAAGCC--A 712066 v v i i- ivv -- i vvi i -- C L3#LINE/CR1 3405 AGCCAGATCCTCTCCATCCTGTACTTGTGCAGTTGATTTTTTGAACCTAA 3356 chr4ptel1M 712067 ATACAGGACTTTTATGTTTACCTGTATTAAATTTTATCTTGTCAAACTTG 712116 i - ii i iv i i iiivi i C L3#LINE/CR1 3355 ATGCAGGACTTT-ACATTTATCCCTGTTAAATTTCATCTTGTTGGTTTCG 3307 chr4ptel1M 712117 ACCCA--G---GAG-TTATCATGATTAACAATTTAAGT-----TTCCGTC 712155 i -- ---v -i i iv --- ?v i i ----- i C L3#LINE/CR1 3306 GCCCATCGTTCCAGCCTGTCGAGAT---CNTTTTGAATCTTGATTCTGTC 3260 chr4ptel1M 712156 ACTTGGCATCTTCACTCTCCTTCCCAGCTTCAGGTCATCTGTAAATTTGA 712205 iiii? i v vi v i iiv i C L3#LINE/CR1 3259 ATCCANCGTATTAGCTATCCCTCCCAGCTTTGTGTCATCTGCAAATTTGA 3210 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.25 CpG sites = 35, Kimura (unadjusted) = 37.07 Transitions / transversions = 2.33 (35/15) Gap_init rate = 0.06 (11 / 183), avg. gap size = 1.82 (20 / 11) 11 27.41 2.00 2.00 chr4ptel1M 715772 715821 (284179) (TATTTAC)n#Simple_repeat 1 50 (0) m_b182s252i1 7056 chr4ptel1M 715772 TATTTACTTTGTATCTTTTTGCT-TTTAATATTTTCTAACATCTATTAAC 715820 v v - v i - v v vivv v (TATTTAC)n#Si 1 TATTTACTATTTA-CTATTTACTATTTACTATTTACTATTTACTATTTAC 49 chr4ptel1M 715821 T 715821 (TATTTAC)n#Si 50 T 50 Matrix = Unknown Transitions / transversions = 0.22 (2/9) Gap_init rate = 0.04 (2 / 49), avg. gap size = 1.00 (2 / 2) 20 4.30 0.00 0.00 chr4ptel1M 716113 716136 (283864) (A)n#Simple_repeat 1 24 (0) m_b182s252i2 7057 chr4ptel1M 716113 AATAAAAAAAAAAAAAAAAAAAAA 716136 v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAA 24 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 214 23.40 0.00 0.00 chr4ptel1M 716355 716401 (283599) MIR#SINE/MIR 206 252 (10) m_b182s601i9 7058 chr4ptel1M 716355 AGCACTTTGTACAGTGCCTGGCATGTTGGAAGTGCTTAATATGTGTT 716401 i v v ii v v i i vi MIR#SINE/MIR 206 AGCGCTTAGAACAGTGCCTGGCACATAGTAAGCGCTCAATAAATGTT 252 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 22.76 CpG sites = 6, Kimura (unadjusted) = 28.43 Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 224 21.95 0.00 0.00 chr4ptel1M 716355 716395 (283605) MIRb#SINE/MIR 210 250 (18) m_b182s601i8 7058 chr4ptel1M 716355 AGCACTTTGTACAGTGCCTGGCATGTTGGAAGTGCTTAATA 716395 i v i ii v v i i MIRb#SINE/MIR 210 AGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATA 250 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 20.25 CpG sites = 6, Kimura (unadjusted) = 26.73 Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 357 25.89 5.52 10.40 chr4ptel1M 716846 717026 (282974) X4b_DNA#DNA/TcMar-Tigger 475 647 (0) m_b182s502i1 7059 chr4ptel1M 716846 CTTCTCTTTACTTGCTAATTATCTGTCCGGTTTGCAGACATG--GAACTT 716893 i i vv i--------- v v -- ii v X4b_DNA#DNA/T 475 CTTCTTTTCACTTGCTAATTCACTA---------CAGAGAGGCTGGGCAT 515 chr4ptel1M 716894 GCAATTTTGCTTC-TAACCA----CTGCAGGCCAGGAATGTGATTTCTAA 716938 - i i i - vv ---- i ii i X4b_DNA#DNA/T 516 -CAGTTCTGTTTCATCTCCAGNTCCTGCAGACTGGGAATGTGATTTCTAG 564 chr4ptel1M 716939 CCACCTA---ACTGCAACAAAATTCTACTGGAATAGGGAAGAAATTTTTT 716985 v iv --- i vi i i iv i --i v ----- X4b_DNA#DNA/T 565 CAATGTATTCATTTTAACAAAATTCCATTACAACA--AAACAA-----TT 607 chr4ptel1M 716986 TAGATGCTGCATGGGAATTCGTTGTAATGGGATTTGACTTG 717026 i iiv - i ii i v i X4b_DNA#DNA/T 608 TGGATGTCCCAT-GGAGTTTATTATAATGGGATTTTACCTG 647 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 32.77 CpG sites = 28, Kimura (unadjusted) = 32.77 Transitions / transversions = 2.00 (28/14) Gap_init rate = 0.12 (22 / 180), avg. gap size = 1.27 (28 / 22) 34 3.03 0.00 0.00 chr4ptel1M 717211 717244 (282756) (CA)n#Simple_repeat 1 34 (0) c_b182s251i0 7060 chr4ptel1M 717211 CACACACACACACACACACACACACACATACACA 717244 i (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACA 34 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 21 10.85 0.00 0.00 chr4ptel1M 717303 717332 (282668) (T)n#Simple_repeat 1 30 (0) m_b182s252i3 7061 chr4ptel1M 717303 TTTTTTTTTTTTGTGATTTTTTTTTTTTTT 717332 v vv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 30 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 188 32.35 0.00 0.00 chr4ptel1M 721656 721723 (278277) MIRc#SINE/MIR 98 165 (103) m_b182s601i11 7062 chr4ptel1M 721656 GGCAAGCTAGTTTGCTGTCCTATGCCTCGGTTTACTGCTCTGTAAAATGG 721705 ii v vi ivii iv i v vv MIRc#SINE/MIR 98 GGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGG 147 chr4ptel1M 721706 GGAGTATTGTGTCTTCCC 721723 vv vi ii v MIRc#SINE/MIR 148 GGATAATAATACCTGCCC 165 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 42.98 CpG sites = 11, Kimura (unadjusted) = 42.98 Transitions / transversions = 1.00 (11/11) Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0) 231 24.53 0.00 0.00 chr4ptel1M 721656 721708 (278292) MIR#SINE/MIR 94 146 (116) m_b182s601i10 7062 chr4ptel1M 721656 GGCAAGCTAGTTTGCTGTCCTATGCCTCGGTTTACTGCTCTGTAAAATGG 721705 i v vi ivii i i v vv MIR#SINE/MIR 94 GGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGG 143 chr4ptel1M 721706 GGA 721708 MIR#SINE/MIR 144 GGA 146 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.11 CpG sites = 7, Kimura (unadjusted) = 30.11 Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 337 31.08 6.67 0.79 chr4ptel1M 722028 722147 (277853) C MIRb#SINE/MIR (118) 150 24 m_b182s601i12 7063 chr4ptel1M 722028 CCATTTTACAGATGAGAAGACTGAGCCTT---GAGGTTAA-TGACTTGTC 722073 i i v i--- - i i C MIRb#SINE/MIR 150 CCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCC 101 chr4ptel1M 722074 T-AGCTCACCCAAGTAGCAGAGAGTACAAATGGGGGTTTGAATCT-GGCC 722121 i- v v iv i iivi i -i iiv i i i i- i C MIRb#SINE/MIR 100 CAAGGTCACACAGCTAGTAAGTGGCA-GAGCCGGGATTCGAACCCAGGTC 52 chr4ptel1M 722122 CATT--ATGCCAAAGCCAGCACCCCCTC 722147 ii i-- iv v ii i ii C MIRb#SINE/MIR 51 TGTCTGACTCCAAAGCCCGTGCTCTTTC 24 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 42.38 CpG sites = 29, Kimura (unadjusted) = 44.05 Transitions / transversions = 3.62 (29/8) Gap_init rate = 0.05 (6 / 119), avg. gap size = 1.50 (9 / 6) 16 9.32 0.00 0.00 chr4ptel1M 722200 722222 (277778) (TA)n#Simple_repeat 1 23 (0) m_b182s252i4 7064 chr4ptel1M 722200 TATTTCTATATATATATATATAT 722222 v v (TA)n#Simple_ 1 TATATATATATATATATATATAT 23 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 31 0.00 0.00 0.00 chr4ptel1M 722232 722260 (277740) (T)n#Simple_repeat 1 29 (0) c_b182s251i1 7065 chr4ptel1M 722232 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 722260 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 314 32.56 4.82 3.02 chr4ptel1M 722607 722834 (277166) C L1ME4c_3end#LINE/L1 (257) 573 342 m_b182s551i3 7066 chr4ptel1M 722607 ATTGTTTCTTATGGCACGGTAATATTCCATCAGAATC-ATCTGCC-T--C 722652 ii i v vvvi - i ?- v i - --i C L1ME4c_3end#L 573 ATCATTTTTAATGGCTGCATAATATTCCATC-GAGTNGATGTACCATAAT 525 chr4ptel1M 722653 TTGTTCAGCCATTCCTTCATTGACGAGCGTCCCTTTGGTTTCCAATTCTT 722702 ii i i iii vi ii i iivvv v i C L1ME4c_3end#L 524 TTACTTAACCATTCCCCTATTGTTGGACATTTAGGTTGTTTCCAATTTTT 475 chr4ptel1M 722703 AGCCACCACAAA-AGAGCTGCTGGGGATATTTTTGTATGGAAATGGGTCC 722751 v i ii i - iv viv i i i i -- v v i -- i C L1ME4c_3end#L 474 CGCTATTATAAATAACGCTGCAATGAACATCTTCG--TGCATATAG--CT 429 chr4ptel1M 722752 TTTTCCCTCTTTGGGGCTG--TCTTTGCAACA----CCTGGCAGTGGGAT 722795 i v iii i-- i ivi i ---- ii v i C L1ME4c_3end#L 428 TTTTCCTTCTTTTGAATTATTTCCTTAGGATAAATTCCCAGAAGTGGAAT 379 chr4ptel1M 722796 CGCTGGATCAGAGGGTGTGCACAGTTTTTTGTAGCTCTT 722834 ii i i i v -- i i C L1ME4c_3end#L 378 TACTGGGTCAAAGGGTATGAACA--TTTTTATGGCTCTT 342 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 45.55 CpG sites = 52, Kimura (unadjusted) = 46.48 Transitions / transversions = 2.60 (52/20) Gap_init rate = 0.06 (13 / 227), avg. gap size = 1.38 (18 / 13) 247 19.66 4.76 3.12 chr4ptel1M 722873 722935 (277065) MIR3#SINE/MIR 81 144 (64) m_b182s601i13 7067 chr4ptel1M 722873 GCTCTGTGACCCTGGG--ATTC-CTCTGAATTTCTAGGCAGCTCAGCTTC 722919 v i -- v - iiivv i i -- i MIR3#SINE/MIR 81 GCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGC--CTCAGTTTC 128 chr4ptel1M 722920 CTCATTTGTAAAATGA 722935 i MIR3#SINE/MIR 129 CTCATCTGTAAAATGA 144 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 23.38 CpG sites = 8, Kimura (unadjusted) = 23.38 Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.06 (4 / 62), avg. gap size = 1.25 (5 / 4) 13 15.33 5.26 2.56 chr4ptel1M 723848 723885 (276115) (TGC)n#Simple_repeat 1 39 (0) m_b182s252i5 7068 chr4ptel1M 723848 TGCTGCTGCTGCT-CTCCTGCTCGCTTC-ACGGCTCCTGC 723885 - v - v -i v v (TGC)n#Simple 1 TGCTGCTGCTGCTGCTGCTGCT-GCTGCTGCTGCTGCTGC 39 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.08 (3 / 37), avg. gap size = 1.00 (3 / 3) 408 26.82 1.61 0.80 chr4ptel1M 726187 726310 (273690) MIRb#SINE/MIR 128 252 (16) m_b182s601i14 7069 chr4ptel1M 726187 CAGTTTTCTCATCTGTAAATTGGGCACAAGAACGGC-ACCTT-CTGAATG 726234 i v v i v iiv - i- v ii v MIRb#SINE/MIR 128 CAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTACCTCGCAGGGTT 177 chr4ptel1M 726235 GTATGTGAGGATCAAATGGGGTAGCGATTGTAAAGCACCGGGCAGTGTGT 726284 - i i i ii vv i ivi vv i MIRb#SINE/MIR 178 GT-TGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAGTGC 226 chr4ptel1M 726285 CTGGCACCTAGTAGGAGCTGGATAGA 726310 v i v vi i MIRb#SINE/MIR 227 CTGGCACATAGTAAGCGCTCAATAAA 252 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.46 CpG sites = 19, Kimura (unadjusted) = 33.93 Transitions / transversions = 1.36 (19/14) Gap_init rate = 0.02 (3 / 123), avg. gap size = 1.00 (3 / 3) 233 36.75 0.00 2.04 chr4ptel1M 726666 726765 (273235) L2#LINE/L2 2672 2769 (313) m_b182s601i15 7070 chr4ptel1M 726666 CATTGCCACCATCACAGATCAGACCCTTCTGGTCTCTCACCTGGATTGTT 726715 i i vii vi ii viiv vi i ii L2#LINE/L2 2672 CACTGCCACCACCCTGGTCCAAGCCACCATCATCTCTCGCCTGGATTACT 2721 chr4ptel1M 726716 GGGGAAGTTCCCTAATGGGTCTTCCTGCTGTGGGTCTCTCGTCCCCCCTC 726765 viiv iii iv i vivi-- i i i i? L2#LINE/L2 2722 GCAATAGCCTCCTAACTGGTCTCCCTGCTTCCA--CCCTTGCCCCCCTNC 2769 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 54.23 CpG sites = 26, Kimura (unadjusted) = 56.74 Transitions / transversions = 2.60 (26/10) Gap_init rate = 0.02 (2 / 99), avg. gap size = 1.00 (2 / 2) 201 25.00 0.00 0.00 chr4ptel1M 727357 727392 (272608) C L2c_3end#LINE/L2 (18) 460 425 m_b182s601i16 7071 chr4ptel1M 727357 CATTTATGAAGTACCTGCTGTGTGTCAAGCACTGGG 727392 vi ii i i i i i C L2c_3end#LINE 460 CATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGG 425 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 24.27 CpG sites = 8, Kimura (unadjusted) = 33.38 Transitions / transversions = 8.00 (8/1) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 198 27.61 1.67 3.39 chr4ptel1M 727358 727417 (272583) C L2d2_3end#LINE/L2 (19) 536 478 m_b182s601i17 7071 chr4ptel1M 727358 ATTTATGAAGTACCTGCTGTGTGTCAAGCACTGGGTTGCGCAACCTGAAG 727407 vi ii i iv i v i iv i-- vi C L2d2_3end#LIN 536 ATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCG--CTGTGG 489 chr4ptel1M 727408 GGGA-ACCAAG 727417 - v C L2d2_3end#LIN 488 GGGATACAAAG 478 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.92 CpG sites = 10, Kimura (unadjusted) = 35.53 Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.05 (3 / 59), avg. gap size = 1.00 (3 / 3) 318 25.67 6.31 1.72 chr4ptel1M 728587 728697 (271303) C L1ME4c_3end#LINE/L1 (441) 389 274 m_b182s551i4 7072 chr4ptel1M 728587 AAAAACGGAATT-----GTCAAAGGAGAGGCACAGTTTGATAGCCCTTT- 728630 i ii ----- iv v v v v i i v- C L1ME4c_3end#L 389 AGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTCTTGA 340 chr4ptel1M 728631 TA-GTATGGTTCCATATTGCTCTCCAGAATGGTTGGATCAGTTTGCAACT 728679 - v -- v i i v v i i i ?iv C L1ME4c_3end#L 339 TACGTATTG--CCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACANTG 292 chr4ptel1M 728680 TTACCAACAATGCATTAG 728697 ii i i v C L1ME4c_3end#L 291 CCACCAGCAATGTATGAG 274 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 32.45 CpG sites = 16, Kimura (unadjusted) = 32.45 Transitions / transversions = 1.33 (16/12) Gap_init rate = 0.05 (5 / 110), avg. gap size = 1.80 (9 / 5) 292 28.99 0.00 0.00 chr4ptel1M 728641 728709 (271291) C L1ME5_3end#LINE/L1 (611) 330 262 m_b182s551i5 7072 chr4ptel1M 728641 CCATATTGCTCTCCAGAATGGTTGGATCAGTTTGCAACTTTACCAACAAT 728690 v i v i i i viiii i i C L1ME5_3end#LI 330 CCAGATTGCTCTCCAGAATGGCTGCACCAGTCTACACTCCCACCAGCAGT 281 chr4ptel1M 728691 GCATTAGACTCTTTACTTC 728709 v iv iii i? C L1ME5_3end#LI 280 GCATGAGGGTTCCTATNTC 262 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.13 CpG sites = 15, Kimura (unadjusted) = 40.13 Transitions / transversions = 3.00 (15/5) Gap_init rate = 0.00 (0 / 68), avg. gap size = 0.0 (0 / 0) 228 29.49 1.28 0.00 chr4ptel1M 729942 730019 (269981) C L1ME1_3end#LINE/L1 (400) 526 448 m_b182s551i6 7073 chr4ptel1M 729942 ACAACTTGTC-AGGCATTCTCCAGTTGATGGGTGTCCCCTCGGTTTCCAA 729990 i i- vv v ? iii iivvviv i C L1ME1_3end#LI 526 ACAATTTGTTTATCCATTCACCNGTTGATGGACATTTGGGTTGTTTCCAG 477 chr4ptel1M 729991 TTTGTGGCCACCACAAAGAGAGCTGCTAT 730019 v i ii i v i C L1ME1_3end#LI 476 TTTTTGGCTATTACGAATAAAGCTGCTAT 448 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.20 CpG sites = 14, Kimura (unadjusted) = 39.40 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.01 (1 / 77), avg. gap size = 1.00 (1 / 1) 233 29.23 0.00 0.00 chr4ptel1M 729955 730019 (269981) C L1ME2z_3end#LINE/L1 (679) 512 448 m_b182s551i7 7073 chr4ptel1M 729955 CATTCTCCAGTTGATGGGTGTCCCCTCGGTTTCCAATTTGTGGCCACCAC 730004 v iiii ivvv v i v i ii i C L1ME2z_3end#L 512 CATTCTCCTGTTGATGGACACCTGGGCTGTTTCCAGTTTTTGGCTATTAT 463 chr4ptel1M 730005 AAAGAGAGCTGCTAT 730019 i v i C L1ME2z_3end#L 462 GAATAAAGCTGCTAT 448 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.47 CpG sites = 12, Kimura (unadjusted) = 38.47 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0) 23 16.81 0.00 0.00 chr4ptel1M 731668 731707 (268293) (T)n#Simple_repeat 1 40 (0) m_b182s252i6 7074 chr4ptel1M 731668 TTTTTTTTTTTTCTTTTATTTATTTATTTATTTTTTATTT 731707 i v v v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 40 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 524 27.71 2.27 3.21 chr4ptel1M 732147 732366 (267634) C L1ME1_3end#LINE/L1 (271) 655 438 m_b182s551i8 7075 chr4ptel1M 732147 AGTATATAATGATCTCCTG-GTCCTGCTCATTTCACTCAGCATCA-GTTT 732194 i ? --- ii - iv iv v - ? C L1ME1_3end#LI 655 AGTATGTANT---CTTTTGTGTCTGGCTTCTTTCACTCAGCATAATGNTT 609 chr4ptel1M 732195 GTGTAAGTCTCTCCAGGCCTTTCTGAA-ATCATCCTGTTGGTCATTTCTT 732243 v - ii iiv v iiv vi vi- viv- v ivi i C L1ME1_3end#LI 608 TTG-AGATTCATCCATGTTGTTGCGTGTATCAGTA-GTTCGTTCCTTTTT 561 chr4ptel1M 732244 ACAGAACAGTAATATTCCATAATATTCATATACCACAATTTATTCAGCCA 732293 iv vvv i vi vv i i v C L1ME1_3end#LI 560 ATTGCTGAGTAGTATTCCATTGTATGGATATACCACAATTTGTTTATCCA 511 chr4ptel1M 732294 TTCTCTAACTGATGGACATCC--ATTCAGTTTCCAGTTTTTAGCCACTAC 732341 v i?ii ii--i -- i i i C L1ME1_3end#LI 510 TTCACCNGTTGATGGACATTTGGGTT--GTTTCCAGTTTTTGGCTATTAC 463 chr4ptel1M 732342 GAAAAGGGCTGCCACAAACATTCGT 732366 v ii i ii C L1ME1_3end#LI 462 GAATAAAGCTGCTATGAACATTCGT 438 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 35.51 CpG sites = 36, Kimura (unadjusted) = 36.29 Transitions / transversions = 1.57 (36/23) Gap_init rate = 0.05 (11 / 219), avg. gap size = 1.09 (12 / 11) 527 30.05 1.53 1.53 chr4ptel1M 732171 732366 (267634) C L1MD1_3end#LINE/L1 (356) 633 438 m_b182s551i9 7075 chr4ptel1M 732171 GCTCATTTCACTCAGCATCAGTTTGTGTAAGTCTCTCCAGGCCTTTCTGA 732220 iv v v i v v ii iiv iiv vi v C L1MD1_3end#LI 633 GCTTTTTTCACTCAGCATAATTCTCTGGAGATTCATCCAGGTTGTTGCGT 584 chr4ptel1M 732221 A-ATCATCCTGTTGGTCATTTCTTACAGAACAGTAATATTCCATAATATT 732269 i- viv- v ivi i iv vvv i ii v C L1MD1_3end#LI 583 GTATCAATA-GTTCGTTCCTTTTTATTGCTGAGTAGTATTCCATGGTATG 535 chr4ptel1M 732270 CATATACCACAATTTATTCAGCCATTCTCTAACTGATGGACATCCA--TT 732317 v i i i i i v ivii v ii-- C L1MD1_3end#LI 534 GATGTACCACAGTTTGTTTAACCATTCACCCGTTGAAGGACATCTGGGTT 485 chr4ptel1M 732318 CAGTTTCCAGTTTTTAGCCACTACGAAAAGGGCTGCCACAAACATTCGT 732366 -- i i i v ii i i C L1MD1_3end#LI 484 --GTTTCCAGTTTTTGGCTATTACGAATAAAGCTGCTATAAACATTCGT 438 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.91 CpG sites = 35, Kimura (unadjusted) = 39.68 Transitions / transversions = 1.52 (35/23) Gap_init rate = 0.03 (5 / 195), avg. gap size = 1.20 (6 / 5) 414 23.85 1.52 4.69 chr4ptel1M 732253 732384 (267616) C L1ME4a_3end#LINE/L1 (317) 554 427 m_b182s551i10 7075 chr4ptel1M 732253 TAATATTCCATAATATTCATATACCACAATTTATTCAGCCATTCTCTAAC 732302 v? vv i i i i ? i iv i C L1ME4a_3end#L 554 TAATATTCCATTNTATGGATGTACCATAATTTATTTAACCANTCCCCTAT 505 chr4ptel1M 732303 TGATGGACATCCA--TTCAGTTTCCAGTTTTTAGCCACTACGAAAAGGGC 732350 v ii -- -- i v i i ii v iv C L1ME4a_3end#L 504 TGTTGGACATTTAGGTT--GTTTCCAATTTTTCGCTATTATAAATAATGC 457 chr4ptel1M 732351 TGCCACAAACATTCGTTAAAGCAAATAAATCTTT 732384 v ii i v ---- i v C L1ME4a_3end#L 456 TGCGATGAACATCCTT----GTACATAAATCTTT 427 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 30.02 CpG sites = 19, Kimura (unadjusted) = 30.02 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.05 (7 / 131), avg. gap size = 1.14 (8 / 7) 619 27.82 7.59 6.61 chr4ptel1M 732926 733360 (266640) C L1MB8_3end#LINE/L1 (360) 565 127 m_b182s551i11 7076 chr4ptel1M 732926 TTCTTATAGTACAATGATATTCCGTTAGT---CATATAC-ACAGCTTATT 732971 i v ivv i i - ---v - vi C L1MB8_3end#LI 565 TTTTTATTGCCGAATAATATTCCATT-GTATGGATATACCACATTTTATT 517 chr4ptel1M 732972 CAGCCATTCCTCAG---ATGGGCCTCCCCCTCGATTTCCAATTCATAGCC 733018 i v v --- i v iivvv i - v iv i i C L1MB8_3end#LI 516 TATCCATTCATCAGTTGATGGACATTTGGGTTG-TTTCCACTTTTTGGCT 468 chr4ptel1M 733019 ACCAC-AATAAGGGCTGCTATAATTATTTTTGTACAAATAAGTAGTTGTC 733067 ii i- v - i vi iv i ----------- C L1MB8_3end#LI 467 ATTATGAATAATG-CTGCTATGAACATTCGTGTACAAGT----------- 430 chr4ptel1M 733068 ATTTTCCCTCCTCACTCCCTCCTCCATTTTAAGAATCTTTTGGGGATACA 733117 - viv vvv ivivi -- i ------- i v i C L1MB8_3end#LI 429 -TTTTGTGTGGACATATGTT--TTCATTT-------CTCTTGGGTATATA 390 chr4ptel1M 733118 GACCTAGGAATGATATTGCTGGATCAAA-GG-------ATGTTTATAGCC 733159 -- i iv i v - ------- --i C L1MB8_3end#LI 389 --CCTAGGAGTGGAATTGCTGGGTCATATGGTAACTCTATGTTTA--ACC 344 chr4ptel1M 733160 TTTTGAATATAGTTTCAGATTGTTCTCCAGAATGGGTGC-CTGACTTACA 733208 iv - v vi i i i ii v - iivi C L1MB8_3end#LI 343 TTTTGAGGA-ACTGCCAGACTGTTTTCCAAAGCGGCTGCACCATTTTACA 295 chr4ptel1M 733209 AGTCCACTAACAGGGTATTAGTGTGTCAGTTTTCCCACATCCTCCCCAAC 733258 vvi i i v v v vi i ii v C L1MB8_3end#LI 294 TTCCCACCAGCAGTGTATGAGGGTTCCAATTTCTCCACATCCTCGCCAAC 245 chr4ptel1M 733259 ----------ATCCAGCTTTTT--TTTTTTCTATATTAGTTATTGTGAAT 733296 ---------- iiv -- v vv i vi viv v C L1MB8_3end#LI 244 ACTTGTTATTATCTGTCTTTTTGATTATAGCCATCCTAGTGGGTGTGAAG 195 chr4ptel1M 733297 AGGTA--TCA--GTTGTTTTAATTTTCATTTCTCTGATCAGTATTGATTT 733342 v -- -- v i v i v v v v C L1MB8_3end#LI 194 TGGTATCTCATTGTGGTTTTGATTTGCATTTCCCTGATGACTAATGATGT 145 chr4ptel1M 733343 AAAGCACTTTTTCATATG 733360 vi ii i C L1MB8_3end#LI 144 TGAGCATCTTTTCATGTG 127 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 34.52 CpG sites = 59, Kimura (unadjusted) = 35.28 Transitions / transversions = 1.09 (59/54) Gap_init rate = 0.09 (40 / 434), avg. gap size = 1.55 (62 / 40) 781 25.09 8.71 0.35 chr4ptel1M 733097 733360 (266640) C L1ME5_3end#LINE/L1 (529) 412 127 m_b182s551i12 7076 chr4ptel1M 733097 TAAGAATCTTTTGGGGATACAGACCTAGGAATGATATTGCTGGATCAAAG 733146 i i i v i v i ii iv i v C L1ME5_3end#LI 412 TGAGAATTTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAG 363 chr4ptel1M 733147 G--ATGTTTATAGCCT--TTTGAATA--TAGTTTCAGATTGTTCTCCAGA 733190 -- iv - i -- v -- v vi i C L1ME5_3end#LI 362 GGTATGCGTATA-CTTAATTTGACTAAGTACTGCCAGATTGCTCTCCAGA 314 chr4ptel1M 733191 ATGGGTGC-CTGACTTACAAGTCCACTAACAGGGTATTAGTGTGTCAGTT 733239 v - iiiii vvi i i v i v v vi vi ? C L1ME5_3end#LI 313 ATGGCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATN 264 chr4ptel1M 733240 TTCCCACATCCTCCCCAACA----------TCCAGCTTTTT--TTTTTTC 733277 i v ---------- i -- v C L1ME5_3end#LI 263 TCCCCACATCCTCGCCAACACTTGGCATTATCCAGCTTTCTAATTTTTGC 214 chr4ptel1M 733278 TATATTAGTTATTGTGAATAGGTATC--A--GTTGTTTTAATTTTCATTT 733323 i vvi i viv i vv i -- -- v C L1ME5_3end#LI 213 CAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATTT 164 chr4ptel1M 733324 CTCTGATCAGTATTGATTTAAAGCACTTTTTCATATG 733360 i v v v vi ii i C L1ME5_3end#LI 163 CTCTGATTACTAATGAGTTTGAGCATCTCTTCATATG 127 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 30.11 CpG sites = 37, Kimura (unadjusted) = 31.23 Transitions / transversions = 1.28 (37/29) Gap_init rate = 0.03 (9 / 263), avg. gap size = 2.67 (24 / 9) 413 30.94 1.28 6.76 chr4ptel1M 733562 733717 (266283) MIRc#SINE/MIR 6 153 (115) m_b182s601i18 7077 chr4ptel1M 733562 CAGTGGTTGGAGTAGTTGTTGGAGTACCAAGTTGAGAGTTGGGAAGACTC 733611 -- v i v vvi i iiiii vi ii i- MIRc#SINE/MIR 6 CAGTG--TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC- 52 chr4ptel1M 733612 ATCTTTTTGAATTCAAATCTGGTCTCAGA-GTTTACTAGCTGAGTGACCC 733660 ------- ii i i iv v v v-ii v i MIRc#SINE/MIR 53 -------TGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCT 95 chr4ptel1M 733661 CAGACAAGTCATGCAA-CTCTATTTGCCTCAGTTTCCTCACCAGTAAAGT 733709 ii i ivi - v vv i v i MIRc#SINE/MIR 96 TGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAAT 145 chr4ptel1M 733710 GCGAAGAA 733717 v i v MIRc#SINE/MIR 146 GGGGATAA 153 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 40.07 CpG sites = 28, Kimura (unadjusted) = 41.29 Transitions / transversions = 1.65 (28/17) Gap_init rate = 0.08 (12 / 155), avg. gap size = 1.00 (12 / 12) 243 31.38 5.56 4.83 chr4ptel1M 735154 735297 (264703) MIR1_Amn#SINE/MIR 2 146 (84) m_b182s601i19 7078 chr4ptel1M 735154 AGAGAGGAATTGTGCTATGG-GGAAAGAGCATTGATGCCCCTAGAAC--- 735199 i v v v v i - v i i----v i i --- MIR1_Amn#SINE 2 AGGGAGGCAGTGTGGTCTAGTGGATAGAGCACTGG----ACTGGGACTCG 47 chr4ptel1M 735200 --AGATCCAGCTTAGGTGGCTGGCTTCAG-ACTTGTGTGATCTGGGGCAA 735246 -- i ii v v?i?vv i iiiv- ? iv? -- ? -ii MIR1_Amn#SINE 48 GGAGACCTGGGTTCNANTCCCGGCTCTGCCACTNGCCNG--CTGNG-TGA 94 chr4ptel1M 735247 GTCAGGGCAAGTCATCTTGCTTCCC-AGATCTCAGTTTCTTCATTTGTAA 735295 viiv ii ?i i i -i?ii i i MIR1_Amn#SINE 95 CCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAA 144 chr4ptel1M 735296 AA 735297 MIR1_Amn#SINE 145 AA 146 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 44.89 CpG sites = 29, Kimura (unadjusted) = 46.42 Transitions / transversions = 2.07 (29/14) Gap_init rate = 0.08 (12 / 143), avg. gap size = 1.25 (15 / 12) 340 26.58 2.53 0.00 chr4ptel1M 735251 735329 (264671) MIR3#SINE/MIR 94 174 (34) m_b182s601i20 7078 chr4ptel1M 735251 GGGCAAGTCATCTTGCTTCCC-AGATCTCAGTTTCTTCATTTGTAAAACA 735299 ii ii i i -i ii i i ii MIR3#SINE/MIR 94 GGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATG 143 chr4ptel1M 735300 TGGTGGTTTGACTAGA-GAGCCTTCAAGTCC 735329 v v v - v ii v i MIR3#SINE/MIR 144 AGGGGGTTGGACTAGATGATCTCTAAGGTCC 174 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.97 CpG sites = 16, Kimura (unadjusted) = 34.97 Transitions / transversions = 3.20 (16/5) Gap_init rate = 0.03 (2 / 78), avg. gap size = 1.00 (2 / 2) 17 13.12 0.00 0.00 chr4ptel1M 737822 737847 (262153) (T)n#Simple_repeat 1 26 (0) m_b182s252i7 7079 chr4ptel1M 737822 TTTTTTTTTCCTTTTTCTTTTTTTTT 737847 ii i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 242 33.54 4.37 5.52 chr4ptel1M 738159 738341 (261659) L3#LINE/CR1 2448 2628 (1471) m_b182s601i21 7080 chr4ptel1M 738159 TCATGAGGAATGA-CTTTGGACTTAAAAGATGGAACGGAAGAAAGCTCAC 738207 v ii - ii vi -- v -- v vv ii L3#LINE/CR1 2448 TCAAGGAGAATGATCTTCAGACTGGAAAG--GGTA--GAACAAACATCGT 2493 chr4ptel1M 738208 TA----GGACTTCCAGCCCCAGAGAAGCTGAGTGG-TATTATTAGAGCAC 738252 ---- v vv v v i - vi - v vv L3#LINE/CR1 2494 TAAGAGGGAATTGAAGCCCAAGATAGG-TGAGGAGATAGTAAGAGAGCAC 2542 chr4ptel1M 738253 CCCGCTGTCCTCGGTGAATTTTTTTTTTTACTGTGACCACAGA--AATGA 738300 iv i iii vii i ivvv i ii ---- i - -- v L3#LINE/CR1 2543 CTAGCCGCTTTAAATGAGTTCAAGTCTCCA----GGCC-CAGACGAATTA 2587 chr4ptel1M 738301 TGTCCTCAAGTACCAAAAGCAGGAGCAGATGTGCTCATGGA 738341 ii ivii ii v vvv v ii L3#LINE/CR1 2588 CATCCCAGGGTACTGAAAGAACTTGCAGATGTGATCGCGGA 2628 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 41.37 CpG sites = 31, Kimura (unadjusted) = 45.48 Transitions / transversions = 1.15 (31/27) Gap_init rate = 0.08 (14 / 182), avg. gap size = 1.29 (18 / 14) 200 31.25 4.00 4.00 chr4ptel1M 738423 738522 (261478) L3#LINE/CR1 2843 2942 (1157) m_b182s601i22 7080 chr4ptel1M 738423 AGGAGTAAGCAGTGAGGACTTCTCCAA-AGCGGCTCGTTCCAGGCTAACT 738471 iv - i --- v i - i iiv i v ii i L3#LINE/CR1 2843 AGGAGCCAGCA-TGGG---TTCACTAAGAACAAGTCATGCCAAACTAACC 2888 chr4ptel1M 738472 CCCTTTCCTTGTTC--CCAGGCTGTTAGACTGCTAAGTCA-GGGAATGAT 738518 i v v i--ivi i ii v ii - vi L3#LINE/CR1 2889 TCATTTCCTTTTTTGATAGGGTTACTAGACTGGTAGATCAGGGGAATGCC 2938 chr4ptel1M 738519 GTGG 738522 i L3#LINE/CR1 2939 GTAG 2942 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 41.11 CpG sites = 21, Kimura (unadjusted) = 43.08 Transitions / transversions = 2.33 (21/9) Gap_init rate = 0.07 (7 / 99), avg. gap size = 1.14 (8 / 7) 13 20.95 0.00 0.00 chr4ptel1M 738740 738772 (261228) (TTGTTT)n#Simple_repeat 1 33 (0) m_b182s252i8 7081 chr4ptel1M 738740 TTGTTTTTGTTTTCTTGTTTGTATTTCTTTGTG 738772 iv v v v v (TTGTTT)n#Sim 1 TTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTG 33 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 26 11.47 0.00 0.00 chr4ptel1M 739738 739775 (260225) (T)n#Simple_repeat 1 38 (0) m_b182s252i9 7082 chr4ptel1M 739738 TTTTTTTTTTATTTTTTTTATTTTTTTATTTTTTATTT 739775 v v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 38 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 18 0.00 0.00 0.00 chr4ptel1M 740452 740471 (259529) (T)n#Simple_repeat 1 20 (0) m_b183s252i1 7083 chr4ptel1M 740452 TTTTTTTTTTTTTTTTTTTT 740471 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTT 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 301 24.23 8.49 2.68 chr4ptel1M 741914 742019 (257981) MIRc#SINE/MIR 16 127 (141) m_b183s601i0 7084 chr4ptel1M 741914 CAATGGCACAGAGTACTGGCCCTGGAGTCGGGA-------GGTTC-AGAT 741955 i v - i v i i ------- - vi MIRc#SINE/MIR 16 CAGTGGAA-AGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTC 64 chr4ptel1M 741956 GTGACATTTCATACTTCCTAGCTGTGTGACTCTGAGTAAAGTCATTTAAC 742005 vi i - i vvi v ii i i- i MIRc#SINE/MIR 65 CCGGC-TCTGCCACTTACTAGCTGTGTGACCTTGGGC-AAGTCACTTAAC 112 chr4ptel1M 742006 CCCAAT-TGCCTCAG 742019 i vv -v MIRc#SINE/MIR 113 CTCTCTGAGCCTCAG 127 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 28.57 CpG sites = 15, Kimura (unadjusted) = 29.98 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.06 (6 / 105), avg. gap size = 2.00 (12 / 6) 338 16.42 3.33 12.05 chr4ptel1M 744374 744463 (255537) C Charlie4a#DNA/hAT-Charlie (0) 508 426 m_b183s502i0 7085 chr4ptel1M 744374 CAGGAGTTCTTAAACCTTACTCTTTCTTTTGTGCCATGGGCCCCTTCAGC 744423 i - -------- i ii C Charlie4a#DNA 508 CAGGGGTTCTTAA-CCTT--------TTTTGTGCCATGGACCCCTTTGGC 468 chr4ptel1M 744424 AGTT---TGAAACCTCCAGGCCTCTTCTCAGAAAAAATATTTT 744463 i--- i vii i i - v i C Charlie4a#DNA 467 AGTCTGGTGAAGCCTATGGACCCCTTCTCAG-AATAATGTTTT 426 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 19.12 CpG sites = 11, Kimura (unadjusted) = 19.12 Transitions / transversions = 5.50 (11/2) Gap_init rate = 0.12 (11 / 89), avg. gap size = 1.18 (13 / 11) 383 28.10 15.03 0.00 chr4ptel1M 746744 746896 (253104) MIR#SINE/MIR 83 258 (4) m_b183s601i1 7086 chr4ptel1M 746744 GTGTGACTCTGGGTGAGCC-CTTC-CCCCGCT-TGCCTCAGTTTCCTCAG 746790 ii ii ii- v- i v - v MIR#SINE/MIR 83 GTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCAT 132 chr4ptel1M 746791 TTGTCACATGGAGATCGTTATAGCCTTTACTTCCCAGGGTGGTGGTG--- 746837 i v v i vi v ivii i vi v v --- MIR#SINE/MIR 133 CTGTAAAATGGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGG 182 chr4ptel1M 746838 -----------------CTGCCAAGGGCTTAGTACAGTGCCTGGTACTCA 746870 -----------------v iv v v i vi MIR#SINE/MIR 183 ATTAAATGAGTTAATACATGTAAAGCGCTTAGAACAGTGCCTGGCACATA 232 chr4ptel1M 746871 GCAGCTGCTGGATGAATGCTGGCTAT 746896 i ivi vi i i i MIR#SINE/MIR 233 GTAAGCGCTCAATAAATGTTAGCTAT 258 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 35.05 CpG sites = 25, Kimura (unadjusted) = 36.10 Transitions / transversions = 1.39 (25/18) Gap_init rate = 0.03 (5 / 152), avg. gap size = 4.60 (23 / 5) 270 23.33 17.21 5.15 chr4ptel1M 747463 747584 (252416) MIRb#SINE/MIR 16 151 (117) m_b183s601i2 7087 chr4ptel1M 747463 GTTCACTGGGCAGCGAAGAGGCTT-GGAGTCGGGAAGACCCCTCTTCCGA 747511 v v iv v v vi - i iv i------- i MIRb#SINE/MIR 16 GTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCT-------GG 58 chr4ptel1M 747512 GTTCAAATATGGCCTCAGGTGCTTCCTAGATGTGTGA------------- 747548 i viv v v vii v v ------------- MIRb#SINE/MIR 59 GTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTT 108 chr4ptel1M 747549 -----ACCTGTTTG--CCTCAGTTTCCTTATCTGTAAAATGGG 747584 ----- v i -- i MIRb#SINE/MIR 109 ACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 151 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 25.95 CpG sites = 12, Kimura (unadjusted) = 28.27 Transitions / transversions = 0.80 (12/15) Gap_init rate = 0.09 (11 / 121), avg. gap size = 2.55 (28 / 11) 290 19.63 19.42 6.03 chr4ptel1M 747482 747584 (252416) MIRc#SINE/MIR 33 148 (120) m_b183s601i3 7087 chr4ptel1M 747482 GGCTTGGAGTCGGGAAGACCCCTCTTCCGAGTTCAAATATGGCCTCAGGT 747531 i i i------- i i i viv v v vi MIRc#SINE/MIR 33 GACTTGGAGTCAGGAAGACCT-------GGGTTCGAGTCCCGGCTCTGCC 75 chr4ptel1M 747532 GCTTCCTAGATGTGTGA------------------ACCTGTTTG--CCTC 747561 i v v ------------------ v i -- MIRc#SINE/MIR 76 ACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTC 125 chr4ptel1M 747562 AGTTTCCTTATCTGTAAAATGGG 747584 i MIRc#SINE/MIR 126 AGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 21.95 CpG sites = 11, Kimura (unadjusted) = 23.29 Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.09 (9 / 102), avg. gap size = 3.00 (27 / 9) 11 32.77 0.00 0.00 chr4ptel1M 747856 747904 (252096) (CCCTGG)n#Simple_repeat 1 49 (0) m_b183s252i2 7088 chr4ptel1M 747856 CCCGGGCCCTTCCCCTGCAGCAGGCTTCCGCTCTGGCCCTGGCTCTGGC 747904 v vv vvv v iiiv i i (CCCTGG)n#Sim 1 CCCTGGCCCTGGCCCTGGCCCTGGCCCTGGCCCTGGCCCTGGCCCTGGC 49 Matrix = Unknown Transitions / transversions = 0.62 (5/8) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 39 0.00 0.00 0.00 chr4ptel1M 750423 750458 (249542) (G)n#Simple_repeat 1 36 (0) c_b183s251i0 7089 chr4ptel1M 750423 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 750458 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 36 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 18 4.55 0.00 0.00 chr4ptel1M 751023 751045 (248955) (GT)n#Simple_repeat 1 23 (0) m_b183s252i3 7090 chr4ptel1M 751023 GTGCGTGTGTGTGTGTGTGTGTG 751045 i (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTG 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 14 23.39 1.85 3.77 chr4ptel1M 751027 751080 (248920) (GTGAGT)n#Simple_repeat 1 53 (0) m_b183s252i4 7090 chr4ptel1M 751027 GTGTGTGTGTGTGTGTGTGAGAGAGAGAGAGAGAGATATGCAG-GTGAGG 751075 v v v v v v v v - i - - v (GTGAGT)n#Sim 1 GTGAGTGTGAGTGTGAGTGTGAGTGTGAGTGTGAG-TGTG-AGTGTGAGT 48 chr4ptel1M 751076 GTGAG 751080 (GTGAGT)n#Sim 49 GTGAG 53 Matrix = Unknown Transitions / transversions = 0.11 (1/9) Gap_init rate = 0.06 (3 / 53), avg. gap size = 1.00 (3 / 3) 16 0.00 0.00 0.00 chr4ptel1M 751045 751062 (248938) (GA)n#Simple_repeat 1 18 (0) m_b183s252i5 7091 chr4ptel1M 751045 GAGAGAGAGAGAGAGAGA 751062 (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGA 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 18 4.55 0.00 0.00 chr4ptel1M 751023 751045 (248955) (GT)n#Simple_repeat 1 23 (0) m_b183s252i3 7090 chr4ptel1M 751023 GTGCGTGTGTGTGTGTGTGTGTG 751045 i (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTG 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 14 23.39 1.85 3.77 chr4ptel1M 751027 751080 (248920) (GTGAGT)n#Simple_repeat 1 53 (0) m_b183s252i4 7090 chr4ptel1M 751027 GTGTGTGTGTGTGTGTGTGAGAGAGAGAGAGAGAGATATGCAG-GTGAGG 751075 v v v v v v v v - i - - v (GTGAGT)n#Sim 1 GTGAGTGTGAGTGTGAGTGTGAGTGTGAGTGTGAG-TGTG-AGTGTGAGT 48 chr4ptel1M 751076 GTGAG 751080 (GTGAGT)n#Sim 49 GTGAG 53 Matrix = Unknown Transitions / transversions = 0.11 (1/9) Gap_init rate = 0.06 (3 / 53), avg. gap size = 1.00 (3 / 3) 17 6.78 3.03 3.03 chr4ptel1M 752758 752790 (247210) (GGGA)n#Simple_repeat 1 33 (0) m_b183s252i6 7092 chr4ptel1M 752758 GGGAGTGGAGGCAGGGAGGGA-GGAGTGAGGGAG 752790 - v - v (GGGA)n#Simpl 1 GGGAG-GGAGGGAGGGAGGGAGGGAGGGAGGGAG 33 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.06 (2 / 32), avg. gap size = 1.00 (2 / 2) 197 17.97 1.64 8.77 chr4ptel1M 753986 754046 (245954) MIR1_Amn#SINE/MIR 107 163 (67) m_b183s601i4 7093 chr4ptel1M 753986 CACTCATCAGCTTTGTGAAC-TCAGCTTACTCATCTGTTAAATGGGGATT 754034 -- ? v i v ?i - i v v - MIR1_Amn#SINE 107 CACT--TNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGGAT- 153 chr4ptel1M 754035 GGAATGGCATTG 754046 -- ii i MIR1_Amn#SINE 154 --AATGATACTG 163 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 21.58 CpG sites = 6, Kimura (unadjusted) = 21.58 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.10 (6 / 60), avg. gap size = 1.00 (6 / 6) 499 21.24 9.38 0.72 chr4ptel1M 753996 754123 (245877) MIRb#SINE/MIR 116 254 (14) m_b183s601i5 7093 chr4ptel1M 753996 CTTTGTGAAC-TCAGCTTACTCATCTGTTAAATGGGGATTGGAATG---- 754040 i v i - i v v viv i---- MIRb#SINE/MIR 116 CTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTA 165 chr4ptel1M 754041 ----GCA---TTGTTGCGAGCATCCAATGAGATTATATTTGCAAAGACAC 754083 ---- --- i v iv v iiv i - i MIRb#SINE/MIR 166 CCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAG-CGC 214 chr4ptel1M 754084 TTAGCACAGTGCCTGGCACACAGCCGGTGCTTACTAAATG 754123 i ivi i i v MIRb#SINE/MIR 215 TTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAAATG 254 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 23.33 CpG sites = 16, Kimura (unadjusted) = 25.42 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.04 (5 / 127), avg. gap size = 2.60 (13 / 5) 194 25.64 0.00 0.00 chr4ptel1M 754090 754128 (245872) L2c_3end#LINE/L2 427 465 (13) m_b183s601i6 7094 chr4ptel1M 754090 CAGTGCCTGGCACACAGCCGGTGCTTACTAAATGCTCAT 754128 i i iv i i v i ii L2c_3end#LINE 427 CAGCGCCTGGCACATAGTAGGCGCTCAATAAATGTTTGT 465 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 25.75 CpG sites = 8, Kimura (unadjusted) = 33.66 Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 180 22.45 6.12 0.00 chr4ptel1M 754140 754188 (245812) C MIRc#SINE/MIR (1) 267 216 m_b183s601i7 7095 chr4ptel1M 754140 ATAAAAATAAGCC---ACATTTCTGTCGTGCTTTAAGGTTTGCAAAGCAC 754186 v v? --- v i v ii vi i i C MIRc#SINE/MIR 267 ATAATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCGC 218 chr4ptel1M 754187 TT 754188 C MIRc#SINE/MIR 217 TT 216 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 24.88 CpG sites = 6, Kimura (unadjusted) = 27.70 Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.02 (1 / 48), avg. gap size = 3.00 (3 / 1) 210 40.26 0.00 0.00 chr4ptel1M 757119 757195 (242805) MIR3#SINE/MIR 112 188 (20) m_b183s601i8 7096 chr4ptel1M 757119 CTTTGAGCCTCGCCTGCCCTCTTGATCAAGCGAGGGAGATGAGCTAGAAA 757168 i i ivi v iiv ivi v ii i v ii vi MIR3#SINE/MIR 112 CTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATG 161 chr4ptel1M 757169 ACTTGCAAGGTGTCTCCTGGTTCTGAC 757195 ii vi vi i ii i MIR3#SINE/MIR 162 ATCTCTAAGGTCCCTTCCAGCTCTGAC 188 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 64.94 CpG sites = 22, Kimura (unadjusted) = 64.94 Transitions / transversions = 2.44 (22/9) Gap_init rate = 0.00 (0 / 76), avg. gap size = 0.0 (0 / 0) 252 36.21 8.39 1.57 chr4ptel1M 758464 758940 (241060) C L1MC4a_3end#LINE/L1 (1995) 634 126 m_b183s551i0 7097 chr4ptel1M 758464 TCTGCTCATTTCCCTCAGCATCGGTTCCTGTCAGTCTCTCCAGGCC---T 758510 i iv v i i viivv vv i v vii --- C L1MC4a_3end#L 634 TTTGCTTTTTTCACTTAACAATATATCCTGGAAATCACTCCATATCAGTT 585 chr4ptel1M 758511 CTCTGACATCCTCCTGCTGGTCATTTCTTACAGAACAATAATATTCCCTC 758560 viv v i vv -- - i vvvv i i v i C L1MC4a_3end#L 584 CATAGAGATCTTCCTCAT--TC-TTTTTTACAGCTGCATAGTACTCCATT 538 chr4ptel1M 758561 ACCTTCATATCCCATAACTTACTCAGCCACTCTCCGGGTGATGGGC--TC 758608 iiv vv i v ii i i ? viv?? -- i C L1MC4a_3end#L 537 GTGTGGATGTACCATAGTTTATTCAACCANTCTCCTATNNATGGGCATTT 488 chr4ptel1M 758609 AG----TTTCCA-----------CTACAAA-AGGGCTGCCACAAACA--- 758639 ---- -----------i - iv v ii i --- C L1MC4a_3end#L 487 AGGTTGTTTCCAATATTTTGCAATTACAAACAATGCTGCAATGAATAACC 438 chr4ptel1M 758640 TGGGGCACACGTGGGTCCCTTCCCCTCCTTTAGG---ATCTCTGGGATAT 758686 v v i i ?iv iiv --v v vi vv --- iii i v C L1MC4a_3end#L 437 TTGTGCATATGTNATTTTGT--ACATGTTGGAGGTGTATCTTCAGGGTAA 390 chr4ptel1M 758687 GAGCCCGGTGGAAGCACTGCTGGGTCAGAGGGGAGGCACG-GCCTGATGA 758735 ivv ii vi vi v i i v iiii i-iiv ii vv C L1MC4a_3end#L 389 ATTCCTAGAAGTGGGATTGCTGGGTCAAAGGGTAAATGCATATGTAGTTT 340 chr4ptel1M 758736 CGCTGGCCATAGTTCACAACTGCTCTCCCCAACGGCTGGATCCGTTCACA 758785 i i i -- v v vv i v i v? v i v i v? ii C L1MC4a_3end#L 339 TGTTAG--ATATTGCCAAATTCCCCTCCANAAGGGTTGTACCANTTTGCA 292 chr4ptel1M 758786 GTCCC--CTACAATGTGTCAG--TGCCCCGTTTCCCACATCCTCTCCAAC 758831 v -- vi i v -- ivv i v v C L1MC4a_3end#L 291 TTCCCACCAGCAATGTATGAGAGTGCCTGTTTCCCCACAGCCTCGCCAAC 242 chr4ptel1M 758832 ACTGCTCCTCACCA--TTTCCGGA-----GCCAGTGGGACAGGTGTGGGC 758874 vv iviv iii --i ii i ----- i vv i v iiv C L1MC4a_3end#L 241 AGAGTGTGTTGTCAAACTTTTGAATTTTTGCCAATCTGATAGGTGAGAAA 192 chr4ptel1M 758875 TGG-GTCTCATGAGTTGTCTTCCTTTGCATTTCTCTGAGCAGTAGTGACT 758923 -i - v v i vv v vi vv vv C L1MC4a_3end#L 191 TGGTATCTCA-GTGTAGTTTTAATTTGCATTTCTCTTATTATGAGTGAGG 143 chr4ptel1M 758924 TGGAGCCCCTGTTCACA 758940 v i vi v i C L1MC4a_3end#L 142 TTGAACATCTTTTCATA 126 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 51.59 CpG sites = 87, Kimura (unadjusted) = 51.59 Transitions / transversions = 1.05 (87/83) Gap_init rate = 0.04 (21 / 476), avg. gap size = 2.29 (48 / 21) 490 32.16 9.92 1.89 chr4ptel1M 758548 758940 (241060) C L1ME5_3end#LINE/L1 (389) 552 129 m_b183s551i1 7097 chr4ptel1M 758548 ATAATATTCCCTCACCTTCATATCCCATAACTTACTCAGCCACTCTCCGG 758597 i i v viiv v viv i vi ii v vi C L1ME5_3end#LI 552 ATAGTACTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCA 503 chr4ptel1M 758598 GTGATGGGC--TCAGTTT---------------CCACTACAAA-AGGGCT 758629 i --i v --------------- i - iv C L1ME5_3end#LI 502 GTGATGGACACCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCT 453 chr4ptel1M 758630 GCCACAAACATGGG-GCACACGTGGGTCCCTTCC---CCTCCTTTAGGAT 758675 v ii vvv- i i ---i vi--- viv v i C L1ME5_3end#LI 452 GCAATGAACATCCTCGTACATGT---CCCCTTATGGACCTGTGTGAGAAT 406 chr4ptel1M 758676 CTCT--GGGATATGAGCCCGGTGGAAGCACTGCTGGGTCAGAGGGGAGGC 758723 i -- ivi i vi vi v i v v v C L1ME5_3end#LI 405 TTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATGC 356 chr4ptel1M 758724 ACG-GCCTGATGACGCTGGCCA--TAGTTCACAACTGCTCTCCCCAACGG 758770 iii-i i i ----i i i -- v v vvi i vv i C L1ME5_3end#LI 355 GTATACTTAAT----TTGACTAAGTACTGCCAGATTGCTCTCCAGAATGG 310 chr4ptel1M 758771 CTGGATCCGTTCACAGTCCC--CTACAATGTGTCAGTGCCCCG--TTTCC 758816 v i v ii v -- vi i ii v v ii v--? i C L1ME5_3end#LI 309 CTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATNTCCC 260 chr4ptel1M 758817 CACATCCTCTCCAACACTGCTCCTCA-CCA-TTTCCGGA-----GCCAGT 758859 v vvv v i - -i i vi ----- C L1ME5_3end#LI 259 CACATCCTCGCCAACACTTGGCATTATCCAGCTTTCTAATTTTTGCCAGT 210 chr4ptel1M 758860 GGGACAGGTGTGGGCTGG-GTCTCATGAGTTGTCTTCCTTTGCATTTCTC 758908 vvi i iiiv i-i v- i vv C L1ME5_3end#LI 209 CTAATAGGTGTAAAGTGATATCTCATT-GTTGTTTTAATTTGCATTTCTC 161 chr4ptel1M 758909 TGAGCAGTAGTGACTTGGAGCCCCTGTTCACA 758940 vi v i v v vi v i C L1ME5_3end#LI 160 TGATTACTAATGAGTTTGAGCATCTCTTCATA 129 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 42.28 CpG sites = 67, Kimura (unadjusted) = 43.20 Transitions / transversions = 1.18 (67/57) Gap_init rate = 0.06 (22 / 392), avg. gap size = 2.14 (47 / 22) 14 10.68 0.00 6.25 chr4ptel1M 761283 761316 (238684) (GGGGAA)n#Simple_repeat 1 32 (0) m_b183s252i7 7098 chr4ptel1M 761283 GGAGAAGAGGGAGAGGGGAAGGGGAACGTGAAGG 761316 i - - v v (GGGGAA)n#Sim 1 GGGGAAG-GGGA-AGGGGAAGGGGAAGGGGAAGG 32 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2) 204 25.00 12.50 0.00 chr4ptel1M 762092 762163 (237837) MIRc#SINE/MIR 112 192 (76) m_b183s601i9 7099 chr4ptel1M 762092 CCTCTCCCGGCCTCCGTTTTCCCGTCTGACAAATGGGGATGAGAAT-CTT 762140 ivi v i i i vv i v - i MIRc#SINE/MIR 112 CCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCT 161 chr4ptel1M 762141 GGTCCGCCC-TCTCAT-------TTGTGAGG 762163 vi i i-i i------- MIRc#SINE/MIR 162 GCCCTGCCTACCTCACAGGGTTGTTGTGAGG 192 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 31.51 CpG sites = 12, Kimura (unadjusted) = 31.51 Transitions / transversions = 2.00 (12/6) Gap_init rate = 0.04 (3 / 71), avg. gap size = 3.00 (9 / 3) 207 23.91 0.00 0.00 chr4ptel1M 762092 762137 (237863) MIRb#SINE/MIR 115 160 (108) m_b183s601i10 7099 chr4ptel1M 762092 CCTCTCCCGGCCTCCGTTTTCCCGTCTGACAAATGGGGATGAGAAT 762137 ivi v i i i vv i v MIRb#SINE/MIR 115 CCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAAT 160 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 29.20 CpG sites = 6, Kimura (unadjusted) = 29.20 Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 19 11.71 2.70 0.00 chr4ptel1M 764026 764062 (235938) (AATA)n#Simple_repeat 1 38 (0) m_b183s252i8 7100 chr4ptel1M 764026 AATAAATAAATAAATAAACAAATAGAT-AAGAAAGAAA 764062 i i - v v (AATA)n#Simpl 1 AATAAATAAATAAATAAATAAATAAATAAATAAATAAA 38 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 394 27.72 13.46 0.57 chr4ptel1M 764074 764229 (235771) MIR3#SINE/MIR 30 205 (3) m_b183s601i11 7101 chr4ptel1M 764074 GGACTTGGAGT-AAGAACCCTGGGTTTGGATCCCGACTCTGCTATT-TTT 764121 v - i iv ivii i i i -vi MIR3#SINE/MIR 30 GGACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACT 79 chr4ptel1M 764122 GGCTTTCGT---TCTGGACAAATTGCTTCCCCTCTGTGGG--TCAGCTTC 764166 ? v - ---ii i i ii v v -- i MIR3#SINE/MIR 80 NGCTGT-GTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTC 128 chr4ptel1M 764167 CTTGTCTACAAAGTCCAGCGGTTAGACCA-------------GTTCC-TC 764202 ii ii i vvi v i i ------------- i - MIR3#SINE/MIR 129 CTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTC 178 chr4ptel1M 764203 CATCCCTGACATTTCCTAATTTTAGGA 764229 v i iiv i i v MIR3#SINE/MIR 179 CAGCTCTGACATTCTATGATTCTATGA 205 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 36.75 CpG sites = 30, Kimura (unadjusted) = 36.75 Transitions / transversions = 2.31 (30/13) Gap_init rate = 0.05 (7 / 155), avg. gap size = 3.14 (22 / 7) 14 17.13 0.00 7.14 chr4ptel1M 764479 764523 (235477) (AAATTAA)n#Simple_repeat 1 42 (0) m_b183s252i9 7102 chr4ptel1M 764479 AAATTAATAAATAAATCTTAATTAGTTAATAAAATTAAAAATTAA 764523 v v vv -v i - - (AAATTAA)n#Si 1 AAATTAAAAATTAAAAATTAA-AAATT-A-AAAATTAAAAATTAA 42 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.07 (3 / 44), avg. gap size = 1.00 (3 / 3) 442 23.53 12.59 1.90 chr4ptel1M 764978 765120 (234880) MIRb#SINE/MIR 45 202 (66) m_b183s601i12 7103 chr4ptel1M 764978 TCCAACAGACTCA--TTCAAATTCAGCC----CCACGTACTGG--ATACG 765019 vi iii-- i i v v ---- v i --i ii MIRb#SINE/MIR 45 TCAGACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTG 94 chr4ptel1M 765020 ATCCTGGGCAAATCACTCAACCTCT----GCCTCCATTTCCGCATCTGTC 765065 i i i i i ---- vi v v MIRb#SINE/MIR 95 ACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTA 144 chr4ptel1M 765066 AAATGGGAATCATAGCAGTACGTATCTT-TAGGGCTGTTGGGAGG----- 765109 i v --- i v i i-i i v ----- MIRb#SINE/MIR 145 AAATGGGGATAAT---AATACCTACCTCGCAGGGTTGTTGTGAGGATTAA 191 chr4ptel1M 765110 ATGAGTTAATG 765120 v MIRb#SINE/MIR 192 ATGAGATAATG 202 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 27.15 CpG sites = 22, Kimura (unadjusted) = 29.22 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.06 (9 / 142), avg. gap size = 2.33 (21 / 9) 528 22.00 12.67 0.00 chr4ptel1M 765004 765153 (234847) MIRc#SINE/MIR 74 242 (26) m_b183s601i13 7103 chr4ptel1M 765004 CCACGTACTGG--ATACGATCCTGGGCAAATCACTCAACCTCT----GCC 765047 v i --i ii i i i i ---- MIRc#SINE/MIR 74 CCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCC 123 chr4ptel1M 765048 TCCATTTCCGCATCTGTCAAATGGGAATCATA------GCAGTACGTATC 765091 vi v v i v ------ vv i v i MIRc#SINE/MIR 124 TCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACC 173 chr4ptel1M 765092 TT-TAGGGCTGTTGGGAGG-----ATGAGTTAATGT-TTTGGAGGTCCTT 765134 i-i i v ----- v - v i i iv MIRc#SINE/MIR 174 TCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTT 223 chr4ptel1M 765135 TGTCAAGTGTAAGGTGCTA 765153 v v i MIRc#SINE/MIR 224 TGTAAACTGTAAAGTGCTA 242 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 25.54 CpG sites = 19, Kimura (unadjusted) = 26.45 Transitions / transversions = 1.36 (19/14) Gap_init rate = 0.04 (6 / 149), avg. gap size = 3.17 (19 / 6) 285 28.41 4.55 0.00 chr4ptel1M 765486 765573 (234427) C MER63D#DNA/hAT-Tip100 (612) 449 358 m_b183s502i1 7104 chr4ptel1M 765486 TCTGCATTCCCAAAGTCCTCTCCATCACTTA---GAGTCCCAATGAGCCA 765532 vii vi ii v---i ivi ii v v C MER63D#DNA/hA 449 TCTGCATTATTAACATTTTCTCCATCACTTTCTTAAGTCTAGACAATCAA 400 chr4ptel1M 765533 CAAAACAGTACATTAAGCCTTGACTT-TGGGGTTTACTGATT 765573 i v i i i - i v i i C MER63D#DNA/hA 399 CAAAACAATAAATCAAGCCCTGATTTGTAGCGTTTGCCGATT 358 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 35.53 CpG sites = 17, Kimura (unadjusted) = 37.45 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.02 (2 / 87), avg. gap size = 2.00 (4 / 2) 210 31.37 0.00 0.00 chr4ptel1M 767285 767335 (232665) C L2b_3end#LINE/L2 (2) 464 414 m_b183s601i14 7105 chr4ptel1M 767285 TCACTCACCTAGGAAGCATCTATTAAGCACCTGCTATGTGCCAGGTTCAG 767334 i iii iv ii i i i i i i i? v C L2b_3end#LINE 464 TCATTCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTG 415 chr4ptel1M 767335 T 767335 C L2b_3end#LINE 414 T 414 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 43.59 CpG sites = 14, Kimura (unadjusted) = 47.90 Transitions / transversions = 7.00 (14/2) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 236 24.44 0.00 0.00 chr4ptel1M 767285 767329 (232671) C L2c_3end#LINE/L2 (2) 476 432 m_b183s601i15 7105 chr4ptel1M 767285 TCACTCACCTAGGAAGCATCTATTAAGCACCTGCTATGTGCCAGG 767329 i iii iv i i i i i C L2c_3end#LINE 476 TCATTCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGG 432 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 28.95 CpG sites = 10, Kimura (unadjusted) = 32.57 Transitions / transversions = 10.00 (10/1) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 222 29.41 0.00 0.00 chr4ptel1M 767335 767385 (232615) C L2b_3end#LINE/L2 (2) 464 414 m_b183s601i16 7105 chr4ptel1M 767335 TCACTCACCTAGGAAGCATCTATTAAGCACCTGCTGTGTGCCAGGTTCAG 767384 i iii iv ii i i i i i i? v C L2b_3end#LINE 464 TCATTCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTG 415 chr4ptel1M 767385 T 767385 C L2b_3end#LINE 414 T 414 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 39.20 CpG sites = 13, Kimura (unadjusted) = 43.13 Transitions / transversions = 6.50 (13/2) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 224 26.67 0.00 0.00 chr4ptel1M 767335 767379 (232621) C L2c_3end#LINE/L2 (2) 476 432 m_b183s601i17 7105 chr4ptel1M 767335 TCACTCACCTAGGAAGCATCTATTAAGCACCTGCTGTGTGCCAGG 767379 i iii iv i i i i i i C L2c_3end#LINE 476 TCATTCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGG 432 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 32.99 CpG sites = 11, Kimura (unadjusted) = 36.92 Transitions / transversions = 11.00 (11/1) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 180 31.91 0.00 0.00 chr4ptel1M 767389 767435 (232565) C L2b_3end#LINE/L2 (6) 460 414 m_b183s601i18 7105 chr4ptel1M 767389 TCACCTAGGAAGCATCTATTAATCACCTGCTGTGTGCCAGGTTCAGT 767435 iii iv ii i i i v i i i? v C L2b_3end#LINE 460 TCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGT 414 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 43.18 CpG sites = 12, Kimura (unadjusted) = 47.70 Transitions / transversions = 4.00 (12/3) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 183 29.27 0.00 0.00 chr4ptel1M 767389 767429 (232571) C L2c_3end#LINE/L2 (6) 472 432 m_b183s601i19 7105 chr4ptel1M 767389 TCACCTAGGAAGCATCTATTAATCACCTGCTGTGTGCCAGG 767429 iii iv i i i v i i i C L2c_3end#LINE 472 TCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGG 432 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 36.50 CpG sites = 10, Kimura (unadjusted) = 41.02 Transitions / transversions = 5.00 (10/2) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 221 27.66 0.00 0.00 chr4ptel1M 767439 767485 (232515) C L2b_3end#LINE/L2 (6) 460 414 m_b183s601i20 7105 chr4ptel1M 767439 TCACCTAGCAAGCATCTATTAAGCACCTGCTGTGTGCCAGGTTCAGT 767485 iii i ii i i i i i i? v C L2b_3end#LINE 460 TCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGT 414 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 36.21 CpG sites = 12, Kimura (unadjusted) = 40.32 Transitions / transversions = 12.00 (12/1) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 223 24.39 0.00 0.00 chr4ptel1M 767439 767479 (232521) C L2c_3end#LINE/L2 (6) 472 432 m_b183s601i21 7105 chr4ptel1M 767439 TCACCTAGCAAGCATCTATTAAGCACCTGCTGTGTGCCAGG 767479 iii i i i i i i i C L2c_3end#LINE 472 TCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGG 432 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 29.34 CpG sites = 10, Kimura (unadjusted) = 33.45 Transitions / transversions = 1.00 (10/0) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 202 29.79 0.00 0.00 chr4ptel1M 767489 767535 (232465) C L2b_3end#LINE/L2 (6) 460 414 m_b183s601i22 7105 chr4ptel1M 767489 TCACCTAGGAAGCATCTATTAAGCACCTGCTGTGTGCCAGGTTCAGT 767535 iii iv ii i i i i i i? v C L2b_3end#LINE 460 TCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGT 414 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 39.61 CpG sites = 12, Kimura (unadjusted) = 43.92 Transitions / transversions = 6.00 (12/2) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 204 26.83 0.00 0.00 chr4ptel1M 767489 767529 (232471) C L2c_3end#LINE/L2 (6) 472 432 m_b183s601i23 7105 chr4ptel1M 767489 TCACCTAGGAAGCATCTATTAAGCACCTGCTGTGTGCCAGG 767529 iii iv i i i i i i C L2c_3end#LINE 472 TCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGG 432 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 32.83 CpG sites = 10, Kimura (unadjusted) = 37.14 Transitions / transversions = 10.00 (10/1) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 180 31.91 0.00 0.00 chr4ptel1M 767539 767585 (232415) C L2b_3end#LINE/L2 (6) 460 414 m_b183s601i24 7105 chr4ptel1M 767539 TCACCTAGGAAGCATCTATTAATCACCTGCTGTGTGCCAGGTTCAGT 767585 iii iv ii i i i v i i i? v C L2b_3end#LINE 460 TCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGT 414 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 43.18 CpG sites = 12, Kimura (unadjusted) = 47.70 Transitions / transversions = 4.00 (12/3) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 183 29.27 0.00 0.00 chr4ptel1M 767539 767579 (232421) C L2c_3end#LINE/L2 (6) 472 432 m_b183s601i25 7105 chr4ptel1M 767539 TCACCTAGGAAGCATCTATTAATCACCTGCTGTGTGCCAGG 767579 iii iv i i i v i i i C L2c_3end#LINE 472 TCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGG 432 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 36.50 CpG sites = 10, Kimura (unadjusted) = 41.02 Transitions / transversions = 5.00 (10/2) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 202 29.79 0.00 0.00 chr4ptel1M 767589 767635 (232365) C L2b_3end#LINE/L2 (6) 460 414 m_b183s601i26 7105 chr4ptel1M 767589 TCACCTAGGAAGCATCTATTAAGCACCTGCTGTGTGCCAGGTTCAGT 767635 iii iv ii i i i i i i? v C L2b_3end#LINE 460 TCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGT 414 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 39.61 CpG sites = 12, Kimura (unadjusted) = 43.92 Transitions / transversions = 6.00 (12/2) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 204 26.83 0.00 0.00 chr4ptel1M 767589 767629 (232371) C L2c_3end#LINE/L2 (6) 472 432 m_b183s601i27 7105 chr4ptel1M 767589 TCACCTAGGAAGCATCTATTAAGCACCTGCTGTGTGCCAGG 767629 iii iv i i i i i i C L2c_3end#LINE 472 TCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGG 432 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 32.83 CpG sites = 10, Kimura (unadjusted) = 37.14 Transitions / transversions = 10.00 (10/1) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 180 31.91 0.00 0.00 chr4ptel1M 767639 767685 (232315) C L2b_3end#LINE/L2 (6) 460 414 m_b183s601i28 7105 chr4ptel1M 767639 TCACCTAGGAAGCATCTATTAATCACCTGCTGTGTGCCAGGTTCAGT 767685 iii iv ii i i i v i i i? v C L2b_3end#LINE 460 TCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGT 414 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 43.18 CpG sites = 12, Kimura (unadjusted) = 47.70 Transitions / transversions = 4.00 (12/3) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 183 29.27 0.00 0.00 chr4ptel1M 767639 767679 (232321) C L2c_3end#LINE/L2 (6) 472 432 m_b183s601i29 7105 chr4ptel1M 767639 TCACCTAGGAAGCATCTATTAATCACCTGCTGTGTGCCAGG 767679 iii iv i i i v i i i C L2c_3end#LINE 472 TCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGG 432 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 36.50 CpG sites = 10, Kimura (unadjusted) = 41.02 Transitions / transversions = 5.00 (10/2) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 248 30.86 2.44 1.20 chr4ptel1M 767681 767762 (232238) C L2d_3end#LINE/L2 (0) 516 434 m_b183s601i30 7106 chr4ptel1M 767681 TCAGTCTCTCACCTAGGAAGCATCTATTAAGCACCTGCTGTGTGCCAGGC 767730 i vv vii iv i i i i i i ivi C L2d_3end#LINE 516 TCAATCAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGC 467 chr4ptel1M 767731 ACTGTATTATGCAGCTGCAAG--ACTAGAAGACA 767762 ii v - iii -- v ? i ? C L2d_3end#LINE 466 ACTGTGCTAGGC-GCTGTGGGGAACGANAAAANA 434 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 41.73 CpG sites = 18, Kimura (unadjusted) = 44.17 Transitions / transversions = 2.57 (18/7) Gap_init rate = 0.02 (2 / 81), avg. gap size = 1.50 (3 / 2) 257 25.86 0.00 1.72 chr4ptel1M 767689 767747 (232253) C L2b_3end#LINE/L2 (6) 460 403 m_b183s601i31 7106 chr4ptel1M 767689 TCACCTAGGAAGCATCTATTAAGCACCTGCTGTGTGCCAGGCACTGTATT 767738 iii iv ii i i i i i ? ii C L2b_3end#LINE 460 TCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCT 411 chr4ptel1M 767739 ATGCAGCTG 767747 v - C L2b_3end#LINE 410 AGGC-GCTG 403 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 32.60 CpG sites = 13, Kimura (unadjusted) = 35.61 Transitions / transversions = 6.50 (13/2) Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1) 252 24.35 0.00 8.06 chr4ptel1M 767698 767764 (232236) C L2d2_3end#LINE/L2 (15) 540 479 m_b183s601i32 7106 chr4ptel1M 767698 AAGCATCTATTAAGCACCTGCTGTGTGCCAGGCACTGTATTATGCAGCTG 767747 ii i i i i v ii v - C L2d2_3end#LIN 540 AAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGC-GCTG 492 chr4ptel1M 767748 CAAGACTAGAAGACAAA 767764 iii ---- i v C L2d2_3end#LIN 491 TGGG----GGATACAAA 479 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 28.63 CpG sites = 12, Kimura (unadjusted) = 31.13 Transitions / transversions = 4.00 (12/3) Gap_init rate = 0.08 (5 / 66), avg. gap size = 1.00 (5 / 5) 185 32.79 12.15 1.69 chr4ptel1M 767844 768057 (231943) L3#LINE/CR1 3642 3877 (222) m_b183s601i33 7107 chr4ptel1M 767844 TGGAAAGTGTGTAGAGGGG-GCAGCCAGGA----GGAGGGACATTAGGTC 767888 iv i vi i - ii ---- i v - viiiv L3#LINE/CR1 3642 TGGAGCGCGTCCAGAGGAGAGCGACCAGGATGGTGAAGGGTC-TGGAAAC 3690 chr4ptel1M 767889 CCTGACATAGGAGGATAAACTGA-GGATCTGGGGGAGGCAGAGCCTGGAT 767937 v v v vviii - v - v ivv v L3#LINE/CR1 3691 CATGTCATATGAGGAACGGTTGAAGGAACTGGGG-ATGTTTAGCCTGGAG 3739 chr4ptel1M 767938 TAGAGCCAATTCCAAC---CCATGAGGACAGTCTTCAAGGATTTAAAGG- 767983 v vvi i ivi v---v vii v iv i - L3#LINE/CR1 3740 AAGAGAAGACTTAGAGGAGACATGATAGCTGTCTTCAAATATTTGAAGGG 3789 chr4ptel1M 767984 -CGGCCTCT----------CCAGA---AACCAGTTTGGC-CCAG-GGGCA 768017 -i v v v ----------ii --- vi v v - - L3#LINE/CR1 3790 CTGTCATGTGGAAGAGGGATTAGACTTATTCTGTGTGGCTCCAGAGGGCA 3839 chr4ptel1M 768018 GAGCTAGGGCTTGTGGGTAAAATTCAGGCTGGAAATCAGA 768057 i i ivi ii v i -- v i iv L3#LINE/CR1 3840 GAACTAGGACCAATGGGTGGAAGTTA--CAGGGAGGCAGA 3877 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 41.48 CpG sites = 35, Kimura (unadjusted) = 43.97 Transitions / transversions = 1.03 (35/34) Gap_init rate = 0.07 (14 / 213), avg. gap size = 2.14 (30 / 14) 335 20.85 7.09 1.34 chr4ptel1M 768255 768395 (231605) C Charlie7#DNA/hAT-Charlie (238) 2377 2229 m_b183s502i2 7108 chr4ptel1M 768255 TCTCA-TAAAAAAAAAAAATTAATGCTTTTAGTGAGAGCAGTGTAATTGA 768303 - v vv vv v i- i i C Charlie7#DNA/ 2377 TCTCACTAAAATATTATTAATAATA-TTTTAGTGAGAGCAATGTGATTGA 2329 chr4ptel1M 768304 ------TTCATTATTTTTGAATATCATGTTCTTCATACTTTGGTAGATGG 768347 ------ v v v - v i vv v ii C Charlie7#DNA/ 2328 ATATGCTTCATTATTTTTGAAAATCTTGGT-TTAACACTTTGTGATACAG 2280 chr4ptel1M 768348 TGATTCAAATGTCTGGTTTTACATTCAATTTCTTTCAAAACT---TTTTA 768394 i i v i vi i v i v --- C Charlie7#DNA/ 2279 CGATTCGAAGGTCTGGTTCTAAGTTCAGTTTATTTCGATACTTGGTTTTA 2230 chr4ptel1M 768395 A 768395 C Charlie7#DNA/ 2229 A 2229 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 21.81 CpG sites = 12, Kimura (unadjusted) = 24.49 Transitions / transversions = 0.71 (12/17) Gap_init rate = 0.04 (5 / 140), avg. gap size = 2.40 (12 / 5) 1151 23.36 9.19 1.03 chr4ptel1M 768521 768879 (231121) C Charlie7#DNA/hAT-Charlie (463) 2152 1765 m_b183s502i3 7108 chr4ptel1M 768521 TGCTAAATCATAATATTCTTTTTTCAGGCCC-TCCTCCAAGTTAGGCAAA 768569 i i i v iv - v - v C Charlie7#DNA/ 2152 TACTAAATCATGATACTCATTTTTCAATCCCATCCACCAA-TTATGCAAA 2104 chr4ptel1M 768570 GATCTGTGCTGAATTT--GCT--------TC--TTTCCCCTCTTGTCAAT 768607 i i v i v -- -------- -- i i vv C Charlie7#DNA/ 2103 GGTTTTTGTTGAAATTCGGCTAGTAAATTTCCATCTTCCCTGATGTCAAT 2054 chr4ptel1M 768608 C---TGATCTTATAAATTCAGGGTAGGATGATGATGCACTTTGACGTTTT 768654 --- v ii i v --- v v i v i v ii C Charlie7#DNA/ 2053 CAGTTGTTCTTGCAAACTAA---TCGGAAGGTGTTGCATTTTTATATTTT 2007 chr4ptel1M 768655 TAACATGCGGGTCCAAAGCC-GCCGGAAGTCTCCATTTAGAAGATTTGTC 768703 vii i i -i i i v i i v v C Charlie7#DNA/ 2006 TAACAAATGGGTTCAAAACCCACTGAAACTCTTCATTTGGAAGATTTTTA 1957 chr4ptel1M 768704 ACCGAGTTGGGAAATTCTGTTTCCAGGTTTTCCCAATCTGTGGGTAGAAG 768753 v ii i i i ivv i v ii i vi C Charlie7#DNA/ 1956 AACAGGTTAGAAAATTCTGTTTCCAAGTTTTTAAAGTGTGCAGATATGAG 1907 chr4ptel1M 768754 AGTTTTTATGGGGGCCACACTGAGGGTGCTTTTG----------CACCT- 768792 i v v i v vivi i i ---------- v - C Charlie7#DNA/ 1906 AGTTTTTATAGGTGACACATTTACATCGTTTTCGGCAACAAAATCACATA 1857 chr4ptel1M 768793 -CGATGGGAACA-CTCCAAACTT--GTTTTCAAAA-GCTCTCTTCACAGC 768837 - i -i v -- - i i C Charlie7#DNA/ 1856 ACGATGGAAACATTTCCAAACATCCGTTTTCAAAATGCTCTCTCCATAGC 1807 chr4ptel1M 768838 CGGAGTTTCTTCTGAAAAGCAGTTACTTCCTCCCTCATTATT 768879 vv ii i v i C Charlie7#DNA/ 1806 ACGAGTTTCTTTCGAAAAGCAGTTACTTTCTCACTCATTGTT 1765 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 27.41 CpG sites = 50, Kimura (unadjusted) = 28.61 Transitions / transversions = 1.52 (50/33) Gap_init rate = 0.04 (16 / 358), avg. gap size = 2.31 (37 / 16) 13 21.97 9.52 0.00 chr4ptel1M 771335 771397 (228603) (CTCGGC)n#Simple_repeat 1 69 (0) m_b183s252i10 7109 chr4ptel1M 771335 CTAGGACTCGGCCTCGGCCTC--CCCGGGCCCCCAGCTC--CCTCGGCCT 771380 v v -- iv i viv -- (CTCGGC)n#Sim 1 CTCGGCCTCGGCCTCGGCCTCGGCCTCGGCCTCGGCCTCGGCCTCGGCCT 50 chr4ptel1M 771381 C--CCTGGGCCCCCGGCTC 771397 -- v i v v (CTCGGC)n#Sim 51 CGGCCTCGGCCTCGGCCTC 69 Matrix = Unknown Transitions / transversions = 0.50 (4/8) Gap_init rate = 0.05 (3 / 62), avg. gap size = 2.00 (6 / 3) 252 31.52 2.17 0.00 chr4ptel1M 773791 773882 (226118) C CR1-3_Croc#LINE/CR1 (1706) 1899 1806 m_b183s551i2 7110 chr4ptel1M 773791 TAGACACCCTGTCAAAGA-GGAAATGAAATCAGTGTGGGATGATTTGTTC 773839 vi ii - i v i iv v iv i i C CR1-3_Croc#LI 1899 TAGTTACTTTGTCAAAGAAGGAGATCAAGTTTGTTTGACACGATTTGTTT 1850 chr4ptel1M 773840 CTCATAAATCCTCGC-GGAGGTGAGGGAACACCTTCTTCTCCTC 773882 i i vi - vv ivv v v v i i i C CR1-3_Croc#LI 1849 TTCGTAAATCCATGCTGGCTGCTTGTGATCAGCCTTTCCTCCTC 1806 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 38.20 CpG sites = 16, Kimura (unadjusted) = 41.89 Transitions / transversions = 1.23 (16/13) Gap_init rate = 0.02 (2 / 91), avg. gap size = 1.00 (2 / 2) 558 33.12 7.63 1.49 chr4ptel1M 774137 774516 (225484) L2#LINE/L2 2089 2491 (591) m_b183s601i34 7111 chr4ptel1M 774137 ACTCTCTCCTGGCTGATCTCTTCTCTTCA---GGCTCTGGGGAACACCG- 774182 i vvi vvivi i --- iivi - i- L2#LINE/L2 2089 ACTCCCTCCTTCTTGAAACACTTTCTTCACTTGGCTTCCAGGA-CACCAC 2137 chr4ptel1M 774183 GCTCTTGTGGTTTTCTTCCCACCTGGCTAACCTTTCCT----AG------ 774222 i iv i i vi ii vi ---- ------ L2#LINE/L2 2138 ACTCTCCTGGTTTTCCTCCTACCTCACTGGCCGCTCCTTCTCAGTCTCCT 2187 chr4ptel1M 774223 -----GGGCCCTCCTGCAGACCCTGCTCTGTAACCCTCGGTGTGCCTCGG 774267 ----- vi vvvvv i vi v ? v v i v i i L2#LINE/L2 2188 TTGCTGGTTCCTCCTCATCTCCCCGACCTCTNAACGTTGGAGTGCCCCAG 2237 chr4ptel1M 774268 GG-TCAGGCC-----CCTCCTCTCTTCTCCCTTTGTACTGCTTCGCTTAG 774311 - v ----- i iv i ii vvi v ?i L2#LINE/L2 2238 GGCTCAGTCCTTGGACCTCTTCTCTTCTCTATCTACACTCACTCCCTNGG 2287 chr4ptel1M 774312 TGACCTCAGCAGCTGCCATGGATTTAATGGCCATCTCTATGCCGTTAGTT 774361 i v viv vi v vvi v i v iii L2#LINE/L2 2288 TGATCTCATCCAGTCTCATGGCTTTAAATACCATCTATATGCTGATGACT 2337 chr4ptel1M 774362 CTCCGACCTCCCTTTTC--CCGGGGCCAGTCTCTCAGCCAACCTTCAATC 774409 i vi ii viv i i -- v i -- i -- ii v i iv L2#LINE/L2 2338 CCCAAATTTATATCTCCAGCCCGGACC--TCTCCC--CTGAACTCCAGAC 2383 chr4ptel1M 774410 TCTCTCTCCCCAACTGCCTTTCAGACACCTCAAACTGAATGTCCAGTGGA 774459 -v v vi viiv i v vi i i i i i L2#LINE/L2 2384 TC-GTATATCCAACTGCCTACTCGACATCTCCACTTGGATGTCTAATAGG 2432 chr4ptel1M 774460 CATCTTGCACCCCATGTGTCCAAAACGGAG-TCATGGCCTTTCCCCT-AA 774507 iiv iiv ii v i- v ii i - L2#LINE/L2 2433 CATCTCAAACTTAACATGTCCAAAACTGAACTCCTGATCTTCCCCCTCAA 2482 chr4ptel1M 774508 ACCTTCCCC 774516 v i L2#LINE/L2 2483 ACCTGCTCC 2491 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 45.11 CpG sites = 72, Kimura (unadjusted) = 45.62 Transitions / transversions = 1.38 (72/52) Gap_init rate = 0.04 (16 / 379), avg. gap size = 2.19 (35 / 16) 551 28.17 11.74 0.00 chr4ptel1M 775055 775267 (224733) C MIRc#SINE/MIR (22) 246 9 m_b183s601i35 7112 chr4ptel1M 775055 TGTATGGCTCTTGGAGGTTCCTGAAGCGCCGT-GCAAATATTATATCA-- 775101 i v vivi ivii iv -i v i v -- C MIRc#SINE/MIR 246 TGTATAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATCTCATT 197 chr4ptel1M 775102 -GATTCTTACTACAACTCTATGAGGGAGGT------GCTATCGTTCTTTG 775144 - i i v i i v i------ v ii v iiv C MIRc#SINE/MIR 196 TGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCC 147 chr4ptel1M 775145 CATTTTAAAGTT-AGGAA---GAGGGCCAGGGAG---CAGGGA------- 775180 v v - --- vi i ---v v ------- C MIRc#SINE/MIR 146 CATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCC 97 chr4ptel1M 775181 -AGGTCACACAGCTGGTAAGAGTTTGAGGATGGATTTGAACTCAGGCCTT 775229 - i v viv vvv i i i i C MIRc#SINE/MIR 96 AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTT 47 chr4ptel1M 775230 CCTGCCTCCAGCTCTGGAGTTCTAGCCCCTGCATCACA 775267 v iv ii v i vv v i C MIRc#SINE/MIR 46 CCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACA 9 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 35.08 CpG sites = 31, Kimura (unadjusted) = 35.81 Transitions / transversions = 1.07 (31/29) Gap_init rate = 0.04 (9 / 212), avg. gap size = 2.78 (25 / 9) 183 35.25 1.85 2.80 chr4ptel1M 775603 775710 (224290) L3#LINE/CR1 3615 3721 (378) m_b183s601i36 7113 chr4ptel1M 775603 CACATCCCTGGAGGAAGCAGCTGGTAAGATAAAAATGCTTCCAAAGAAG- 775651 iiivi i - -i ii - ivii ii v i i - L3#LINE/CR1 3615 CACATTTTAAGAGGGA-CA-TTGACAA-ACTGGAGCGCGTCCAGAGGAGA 3661 chr4ptel1M 775652 GCGATCTGGATGGTAAATGGTTTGAAGA-AATGCAAAAGGAAGCTCAGTT 775700 i v i v i i i -v iv v v i vv i L3#LINE/CR1 3662 GCGACCAGGATGGTGAAGGGTCTGGAAACCATGTCATATGAGGAACGGTT 3711 chr4ptel1M 775701 GAAAGAGCCG 775710 i i i L3#LINE/CR1 3712 GAAGGAACTG 3721 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 47.58 CpG sites = 26, Kimura (unadjusted) = 51.69 Transitions / transversions = 2.36 (26/11) Gap_init rate = 0.05 (5 / 107), avg. gap size = 1.00 (5 / 5) 363 33.50 10.68 0.00 chr4ptel1M 775706 775911 (224089) L3#LINE/CR1 3766 3993 (106) m_b183s601i37 7113 chr4ptel1M 775706 AGCCGTCTTCAGGGGCTGGAAGGACGGTCACCGAAGGGAATGAGAAGACT 775755 i iivii v i v ivviiii iv vv L3#LINE/CR1 3766 AGCTGTCTTCAAATATTTGAAGGGCTGTCATGTGGAAGAGGGATTAGACT 3815 chr4ptel1M 775756 TGCTTTGTTTTCGGCCTGAGGAAAGAATGACAGTCAAAGAAATGAA--TA 775803 ii i v vvvv v iv iv viii v iivv -- L3#LINE/CR1 3816 TATTCTGTGTGGCTCCAGAGGGCAGAACTAGGACCAATGGGTGGAAGTTA 3865 chr4ptel1M 775804 TAAG-AGGCAAA--------------AAGGAAGAACTTCC-AGCTGT-AC 775836 i i - i -------------- i - i vi - v L3#LINE/CR1 3866 CAGGGAGGCAGATTTCGGCTCAATATAAGGAAGAACTTTCTAACAATCAG 3915 chr4ptel1M 775837 TCCAGTCCAGA--TGCAACAGGCTGCCTCAGAAAAGAGTGAATTCTCC-T 775883 vv v i -- v ii i?i iiv ii i - L3#LINE/CR1 3916 AGCTGTCCAAAAATGGAATGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGT 3965 chr4ptel1M 775884 CACAGAAGGTCTTCAAGCAAAGGCTGGA 775911 v i v i L3#LINE/CR1 3966 CACTGGAGGTGTTCAAGCAGAGGCTGGA 3993 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 45.32 CpG sites = 40, Kimura (unadjusted) = 46.25 Transitions / transversions = 1.38 (40/29) Gap_init rate = 0.03 (7 / 205), avg. gap size = 3.14 (22 / 7) 54 16.01 2.31 3.91 chr4ptel1M 775924 776053 (223947) (TTAGGG)n#Simple_repeat 1 128 (0) m_b183s252i11 7114 chr4ptel1M 775924 TTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGAGTCGGGAGTCGGG-- 775971 i ii iv v -- (TTAGGG)n#Sim 1 TTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTT 50 chr4ptel1M 775972 AGGCGAATTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGAGTCGGGA 776021 - --- i ii - (TTAGGG)n#Sim 51 AGG-G---TTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGG- 95 chr4ptel1M 776022 GGCGAATTTAGGGTTAGAGTT-GGGTTAGAGTT 776053 viiiiv i - i (TTAGGG)n#Sim 96 GTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTT 128 Matrix = Unknown Transitions / transversions = 3.25 (13/4) Gap_init rate = 0.05 (7 / 129), avg. gap size = 1.14 (8 / 7) 15 11.16 3.33 0.00 chr4ptel1M 776077 776106 (223894) (ACCCTA)n#Simple_repeat 1 31 (0) m_b183s252i12 7115 chr4ptel1M 776077 ACTCTAACCCTAACCC-GACTCTAACCCTAA 776106 i -i i (ACCCTA)n#Sim 1 ACCCTAACCCTAACCCTAACCCTAACCCTAA 31 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 359 32.63 6.75 3.26 chr4ptel1M 776245 776659 (223341) L1PB_orf2#LINE/L1 2508 2936 (358) m_b183s551i3 7116 chr4ptel1M 776245 CTTCACAGAACTAGGAAAAATAATCACCAAGTTCATCTGGAGAACAAAAT 776294 i i viv i v - v v L1PB_orf2#LIN 2508 CTTCACAGAACTAGAAAAAACAATCCTAAAATTCATATGGA-ACCAAAAA 2556 chr4ptel1M 776295 --------TATGG----GGCA---TTAATGAAAAAATGCTAATGAAGATG 776329 --------i i ----i ---i vv ivi v vvi - L1PB_orf2#LIN 2557 AGAGCCCGCATAGCCAAAGCAAGACTAAGCAAAAAGAACAAATCTGGA-G 2605 chr4ptel1M 776330 GCCTAGCTGTACCAGAGTGCAAACTATATTATAAAGCTGTGGTCAGCAAA 776379 v vi vv v v v i i ii i v L1PB_orf2#LIN 2606 GCATCACATTACCCGACTTCAAACTATACTATAAGGCCATAGTCACCAAA 2655 chr4ptel1M 776380 ACCATTCGGTATTTGGTA-AGAAATAGAGTAGTCGATCAGGGGAATAGGT 776428 viivi -i - i ivvvi v i iv i iv L1PB_orf2#LIN 2656 ACAGCATGGTA-CTGGTATAAAAATAGGCACATAGACCAATGGAACAGAA 2704 chr4ptel1M 776429 TAG-GTTCACAGGACAAAATCTCAATAACTTTAATAATCTAGTGTTTGAC 776477 - vv v i vv i iv vi vi iiv v ii v i L1PB_orf2#LIN 2705 TAGAGAACCCAGAAATAAACCCAAATACTTACAGCCAACTGATCTTCGAC 2754 chr4ptel1M 776478 A---CACTCAAAGACACAAGCTTTTGGGATAAGAATGCACTATTTGACAA 776524 --- vv i i i---v iv i ii v ii L1PB_orf2#LIN 2755 AAAGCAAACAAAAACATAAA---GTGGGGAAAGGACACCCTATTCAACAA 2801 chr4ptel1M 776525 AAATTGCTGGACAAATTGG-AAATTA---GTATGGCA--GAAACTAGGCA 776568 viv ivv - iii --- v iv -- i -- L1PB_orf2#LIN 2802 ATGGTGCTGGGATAATTGGCAAGCCACATGTAGGAGAATGAAACTGG--A 2849 chr4ptel1M 776569 TTGACTCATACCTAACACTGTATACCAAGATAAAGTTGAAATGGATTCAT 776618 i-- vi -- iv v i v v ii i iv v L1PB_orf2#LIN 2850 TC--CTCATCTCT--CACCTTATACAAAAATCAACTCAAGATGGATCAAG 2895 chr4ptel1M 776619 GATTTAGTCATAAAGGGTGATATTCTAAGCAAAT--TAGAAGA 776659 i iviv iivv v iiv -- -- L1PB_orf2#LIN 2896 GACTTAAATCTAAGACCTGAAACCATAA--AAATTCTAGAAGA 2936 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 43.34 CpG sites = 69, Kimura (unadjusted) = 43.78 Transitions / transversions = 1.11 (69/62) Gap_init rate = 0.06 (24 / 414), avg. gap size = 1.75 (42 / 24) 909 31.88 5.02 2.04 chr4ptel1M 776867 777484 (222516) L1ME4c_3end#LINE/L1 4 639 (191) m_b184s551i3 7117 chr4ptel1M 776867 ATTTCTAAAATAGAGGGAGAATTGACTCAAATTTATAAGAAT----TCAA 776912 v ?v ? v vii ii v i v v---- L1ME4c_3end#L 4 ATATCTNTANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAA 53 chr4ptel1M 776913 GCCATTTTCCAACTAATAAATAGTCAAAGGATATGCACA----ATTTTCA 776958 v ----i ivi i v i v ---- iv L1ME4c_3end#L 54 GAC----CCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACA 99 chr4ptel1M 776959 GATGAAGAAATTAAAACCATTTTTAGTCATATGAAAAAATGCTCTAGATC 777008 ? v i vv ?ivi vvvi iv i i i v vv L1ME4c_3end#L 100 NAAGAGGAAATACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTC 149 chr4ptel1M 777009 ACTACCGATCAAAGAAATGCAA-TTAAGGCAACTCTGAGATA-----TTA 777052 i vii - i vv ----- L1ME4c_3end#L 150 GCTAGTAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTA 199 chr4ptel1M 777053 C-----TCAGATTGGTTAAGATGACAGGCAAA--GACAATAATGAATATT 777095 ----- i i i iv i vvv i-- -- i viv ii L1ME4c_3end#L 200 CGCCTATTAAATTAGCAAAAATTTAAA--AAATTGATAATACCCAATGCT 247 chr4ptel1M 777096 GGAGGGTATGTGGGAAAACTGGGACAGCAATACATTGTTGGTGGAATTGT 777145 v i v? i vi v ?viv i v ? L1ME4c_3end#L 248 GGCGAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGT 297 chr4ptel1M 777146 AAACTTGTCTAGCCATTCTGGAGAGCAATTTGGAAGTA--TACCCAAAGG 777193 i v vi i v i i v i -- i -- i L1ME4c_3end#L 298 AAATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATC--AAGA 345 chr4ptel1M 777194 GCTACCAAAG---GCACACCCTTTGATCCAACACTATTC--CCACTGGGC 777238 i iv i---v i i ii -- -- iv v L1ME4c_3end#L 346 GCCATAAAAATGTTCATACCCTTTGACCCAGTA--ATTCCACTTCTGGGA 393 chr4ptel1M 777239 TTATATCCCAAAGAGATCAT--AAAGGAGAGGAAGGGACTCACATGTGCA 777286 v v i i i v -- i - iiii - i ii i L1ME4c_3end#L 394 ATTTATCCTAAGGAAATAATTCAAAAGA-AGGAAAAAGCT-ATATGCACG 441 chr4ptel1M 777287 AAATTGTTTTTGGCAGCCCTTTTTGCAGTGGCAAGGAACTGGAACGCGCG 777336 iv iv v vi v ii i i i ii i vvvi v L1ME4c_3end#L 442 AAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACC 491 chr4ptel1M 777337 TGGATGCCCATGAGTTGGAGAATGGCTGAATAAGTTATGATCTATGAATG 777386 ii i vv i v i i i i i i vi v? iv L1ME4c_3end#L 492 TAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACT 541 chr4ptel1M 777387 TTTTGGAATAGTATTGTTCTGTAAGAAAAGATCAGCAGGAGGATTTCAGA 777436 ivv v vvvv ii v i v v vi v i i viiv L1ME4c_3end#L 542 CGATGGAATATTATGCAGCCATTAAAAATGATAATTATGAAGACTATGTA 591 chr4ptel1M 777437 G-AGTCTGGAAAGATTTACATGAACTGATGCTGAGGGAAGTGAGCAGAA 777484 - iiv - v vi vv i i i v ivi L1ME4c_3end#L 592 GCAACATGGAAA-ATGTTTATGATATAATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 41.91 CpG sites = 107, Kimura (unadjusted) = 43.40 Transitions / transversions = 1.24 (107/86) Gap_init rate = 0.04 (24 / 617), avg. gap size = 1.83 (44 / 24) 1050 31.26 4.72 2.71 chr4ptel1M 776867 777481 (222519) L1ME3G_3end#LINE/L1 4 630 (294) m_b183s551i4 7117 chr4ptel1M 776867 ATTTCTAAAATAGAGGGAGAATTGACTCAAATTTATAAGAATTCAAGCCA 776916 v i i v vii i vviv iv --v v L1ME3G_3end#L 4 ATATCCAGAATATATAAAGAACTCCTACAAATCAATAAGAA--AAAGACA 51 chr4ptel1M 776917 TTTTCCAACTAATAAATAGTCAAAGGATATGCACA----ATTTTCAGATG 776962 vi-- ivi v i v v ---- iv v L1ME3G_3end#L 52 AC--CCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAG 99 chr4ptel1M 776963 AAGAAATTAAAACCATTTTTAGTCATATGAAAAAATGCTCTAGATCACTA 777012 i vv iviiivv iv i v vv L1ME3G_3end#L 100 AGGAAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTA 149 chr4ptel1M 777013 CCGATCAAAGAAATGCAA-TTAAGGCAACTCTGAGATA-------TTAC- 777053 vii ii - ii vv ------- i - L1ME3G_3end#L 150 GTAATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACC 199 chr4ptel1M 777054 --TCAGATTGGTTAAGA--TGACAGGCAAAGACAATAATGAATATTGGAG 777099 -- iv i -- i v ?i--v i vi? i i v L1ME3G_3end#L 200 CATCAGATTGGCAAAAATTTAAAAGNT--TGATAATATCNAGTGTTGGCG 247 chr4ptel1M 777100 GGTATGTGGGAAAACTGGGACAGCAATACATTGTTGGTGGAATTGTAAAC 777149 i vi i v v vviv i i i v i L1ME3G_3end#L 248 AGGGTGTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAAT 297 chr4ptel1M 777150 TTGTCTAGCCATTCTGGAGAGCAATTTGGAAGTATACCCAAAGGGCTACC 777199 v vi ? i i v viviv iivi vv L1ME3G_3end#L 298 TGGTACAGCCNTTTTGGAGGGCAATTTGGCAGTATCTATTAAAATTTAAA 347 chr4ptel1M 777200 AAAGGCACACCCTTTGATCCAACACTATTC--CCACTGGGCTTATATCCC 777247 viv i i i -- -- iv ? ?v v i L1ME3G_3end#L 348 ATGCGCATACCCTTTGACCCAGCA--ATTCCACTTCTNGGNATCTATCCT 395 chr4ptel1M 777248 AAAGAGA---TCATAAAGGAGAGGAAGGGACTCACATGTGCAAAATTGTT 777294 ? i --- ii v v v viv i---?i i iiv L1ME3G_3end#L 396 ANAGAAATACTCGCACATGTGCACAAGGA---NGCATGTACAAGGATGTT 442 chr4ptel1M 777295 TTTGGCAGCCCTTTTTGCAGTGGCAAGGAACTGGAACGCGCGTGGATGCC 777344 iv v vi v i i i i ii i vvvi v ii i L1ME3G_3end#L 443 CATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTC 492 chr4ptel1M 777345 CATGAGTTGGAGAATGGCTGAATAAGTTATGATCTATGAATGTTTTGGAA 777394 v i v i i i i i v vv ii v L1ME3G_3end#L 493 CATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAA 542 chr4ptel1M 777395 TAGTATTGTTCTGTAAGAAAAGATCAGCAGGAGGATTT-------CAGAG 777437 v vvvv ? v i ii ---v vi i ------- v v L1ME3G_3end#L 543 TACTATGCAGCNGTTAAAAAGAAT---GAGGTAGATCTATATGTACTGAC 589 chr4ptel1M 777438 AGTCTGGAAAGATTTACATGAACTGATGCTGAGGGAAGTGAGCA 777481 --- i v v vv iv i v ivi L1ME3G_3end#L 590 A---TGGAAAGATCTCCAAGACATATTGTTGAGTGAAAAAAGCA 630 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 41.30 CpG sites = 96, Kimura (unadjusted) = 41.89 Transitions / transversions = 1.05 (96/91) Gap_init rate = 0.04 (26 / 614), avg. gap size = 1.77 (46 / 26) 224 10.11 0.31 0.00 chr4ptel1M 779509 779832 (220168) (TCCACCC)n#Simple_repeat 1 325 (0) m_b184s252i0 7118 chr4ptel1M 779509 TCCATCCTCCATCCCCCATCCTCCACCCTCCACCCTCCACCCTCCATCCT 779558 i i i i i (TCCACCC)n#Si 1 TCCACCCTCCACCCTCCACCCTCCACCCTCCACCCTCCACCCTCCACCCT 50 chr4ptel1M 779559 CCACCCTCCACCC-CCACCCTCCATCCCCCACCCTCCACCCTCCACCCTC 779607 - i i (TCCACCC)n#Si 51 CCACCCTCCACCCTCCACCCTCCACCCTCCACCCTCCACCCTCCACCCTC 100 chr4ptel1M 779608 TACCCCCCACCCTCCACCCTCCACCCTCCATCCCCCACCCTCCATCCTCC 779657 i i i i i (TCCACCC)n#Si 101 CACCCTCCACCCTCCACCCTCCACCCTCCACCCTCCACCCTCCACCCTCC 150 chr4ptel1M 779658 ATCCTCCCCCCTCCACCCTCCATCCCCCACCCTCCATCCTCCACCCTCCA 779707 i v i i i (TCCACCC)n#Si 151 ACCCTCCACCCTCCACCCTCCACCCTCCACCCTCCACCCTCCACCCTCCA 200 chr4ptel1M 779708 CCCTCCACCCTCCATCCCCCACCCTCCATCCTCCACCCTCCACCCCCCAT 779757 i i i i i (TCCACCC)n#Si 201 CCCTCCACCCTCCACCCTCCACCCTCCACCCTCCACCCTCCACCCTCCAC 250 chr4ptel1M 779758 CCTCCCCCCTCCACCCTCCATCCCCCACCCTCCACCCTCCAACCCCCACC 779807 v i i v i (TCCACCC)n#Si 251 CCTCCACCCTCCACCCTCCACCCTCCACCCTCCACCCTCCACCCTCCACC 300 chr4ptel1M 779808 CTCCACCCTCCATCCTCCATCATCC 779832 i i v (TCCACCC)n#Si 301 CTCCACCCTCCACCCTCCACCCTCC 325 Matrix = Unknown Transitions / transversions = 6.50 (26/4) Gap_init rate = 0.00 (1 / 323), avg. gap size = 1.00 (1 / 1) 233 21.43 0.00 0.00 chr4ptel1M 781869 781910 (218090) C L2c_3end#LINE/L2 (3) 475 434 m_b184s601i0 7119 chr4ptel1M 781869 CACTCAGTCAATGAACATTTAGTAAGCGCCTACTGAGTGCTA 781910 i v ii v i iv i C L2c_3end#LINE 475 CATTCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCA 434 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 25.95 CpG sites = 6, Kimura (unadjusted) = 25.95 Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 556 25.76 10.77 0.47 chr4ptel1M 783195 783389 (216611) C MIRc#SINE/MIR (0) 268 54 m_b184s601i1 7120 chr4ptel1M 783195 AATGATAATAGCAGTGCACATTTTCATAGTGCGAGGC-GCTTA---ACCA 783240 i i ?vivi vi ii vvvi - i --- v i C MIRc#SINE/MIR 268 AATAATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCG 219 chr4ptel1M 783241 CTTT-ACAAATATCACCTCATTTAATCCTCCTAATG-CCCCGTGAAGCAG 783288 - v i i i i vi ii- i i i C MIRc#SINE/MIR 218 CTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAG 169 chr4ptel1M 783289 GTA---C---TATTATTATCCCCATTTTACAGTTGAGGAAACTCAGG-TA 783331 i --- --- v v - v C MIRc#SINE/MIR 168 GCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC 119 chr4ptel1M 783332 GGCGATGACT--GTGACTCGCCC-AGGTCACAAGACT-----GTGTCTGA 783373 i v - ii -- i - vii ----- v v C MIRc#SINE/MIR 118 AGAGA-GGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGA 70 chr4ptel1M 783374 GGTCAGATTTGAACTC 783389 vivi i i i C MIRc#SINE/MIR 69 GCCGGGACTCGAACCC 54 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.44 CpG sites = 32, Kimura (unadjusted) = 32.82 Transitions / transversions = 1.78 (32/18) Gap_init rate = 0.06 (11 / 194), avg. gap size = 2.00 (22 / 11) 668 21.68 8.38 0.56 chr4ptel1M 783223 783389 (216611) C MIR#SINE/MIR (33) 229 50 m_b184s601i2 7120 chr4ptel1M 783223 GTGCGAGGCGCT----TAACCACTTTACAAATATCACCTCATTTAATCCT 783268 v i ---- v i vi i v C MIR#SINE/MIR 229 GTGCCAGGCACTGTTCTAAGCGCTTTACATGTATTAACTCATTTAATCCT 180 chr4ptel1M 783269 CCTAATG-CCCCGTGAAGCAGGTACTATTATTATCCCCATTTTACAGTTG 783317 vi ii- ii i i v C MIR#SINE/MIR 179 CACAACAACCCTATGAGGTAGGTACTATTATTATCCCCATTTTACAGATG 130 chr4ptel1M 783318 AGGAAACTCAGGTA-GGCGATGACT--GTGACTCGCCC-AGGTCACAAGA 783363 v i -i v - ii -- i i - vii C MIR#SINE/MIR 129 AGGAAACTGAGGCACAGAGA-GGTTAAGTAACTTGCCCAAGGTCACACAG 81 chr4ptel1M 783364 CT-----GTGTCTGAGGTCAGATTTGAACTC 783389 ----- v v vivi i i C MIR#SINE/MIR 80 CTAGTAAGTGGCAGAGCCGGGATTCGAACCC 50 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 23.75 CpG sites = 23, Kimura (unadjusted) = 26.22 Transitions / transversions = 1.77 (23/13) Gap_init rate = 0.04 (7 / 166), avg. gap size = 2.14 (15 / 7) 380 19.98 9.09 0.76 chr4ptel1M 783283 783403 (216597) C MIR1_Amn#SINE/MIR (59) 171 41 m_b184s601i3 7120 chr4ptel1M 783283 AAGCAGGT-ACTATTATTATCCCCATTTTACAGTTGAGGAAACTCAGG-- 783329 v - v i v v -- C MIR1_Amn#SINE 171 AAGGAGGTCAGTATCATTATCCCCATTTTACAGATGAGGAAACTGAGGCN 122 chr4ptel1M 783330 TAG-GCGATGACTGTGACTCGCCC-AGGTCACA----AGACT-GTGTCTG 783372 i - v i ? v- i - ?----? i ?- v v C MIR1_Amn#SINE 121 CAGAGAGGTNAA-GTGACTTGCCCAAGGTCACNCAGCNGGCNAGTGGCAG 73 chr4ptel1M 783373 AGGTCAGATTTGAACTC-TATCCTCTGAGCCC 783403 vivi ? ? i -vi ii i i C MIR1_Amn#SINE 72 AGCCGGGANTNGAACCCAGGTCTCCCGAGTCC 41 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 22.70 CpG sites = 13, Kimura (unadjusted) = 24.98 Transitions / transversions = 1.18 (13/11) Gap_init rate = 0.07 (8 / 120), avg. gap size = 1.50 (12 / 8) 246 31.09 13.33 0.35 chr4ptel1M 784022 784276 (215724) C L1ME3G_3end#LINE/L1 (579) 345 58 m_b184s551i4 7121 chr4ptel1M 784022 TAATTTTTACTAAGTACTTTCCAAG-GCTCTGCAGAAAGATTGTGTGAGT 784070 v v ii vi v v- i v i ? ii iiv i C L1ME3G_3end#L 345 TAAATTTTAATAGATACTGCCAAATTGCCCTCCAAAANGGCTGTACCAAT 296 chr4ptel1M 784071 TTGCAATTCCACTGACAATGAACGAGTGTGCCAGCCTCCCCACA------ 784114 i v i iii i v i v i v ii ------ C L1ME3G_3end#L 295 TTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCACACCCTCG 246 chr4ptel1M 784115 --AACAC-AGA-GTTCTGCACC--TGGAATTGTTG-----ATGA-GGGT- 784151 -- -? -i v vv ? -- vi v -----v - - C L1ME3G_3end#L 245 CCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATCTGATGGGTG 196 chr4ptel1M 784152 --------TACTTTAAGGTTACACAAATTTGCA--TCTCTGATAAATGAG 784191 -------- ii i vv iiviv -- i v v - C L1ME3G_3end#L 195 AAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGATTACT-AG 147 chr4ptel1M 784192 TAAGGTTATG-ACCTCTGACTA--ATTATCAGCCCTCTCTGTTTCCCCTT 784238 i iv - i i vvv --v ii v i v i i C L1ME3G_3end#L 146 TGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGTATTTCCTCTT 97 chr4ptel1M 784239 TTGAGATTTGCC-ATTCCTATTGCTTGGCCATTTATCCA 784276 i v v -i v ivi v v i C L1ME3G_3end#L 96 CTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTA 58 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 41.73 CpG sites = 43, Kimura (unadjusted) = 41.73 Transitions / transversions = 1.19 (43/36) Gap_init rate = 0.06 (14 / 254), avg. gap size = 2.50 (35 / 14) 279 28.41 2.25 1.11 chr4ptel1M 784026 784114 (215886) C L1MC4a_3end#LINE/L1 (2287) 342 253 m_b184s551i5 7121 chr4ptel1M 784026 TTTTACTAAGTACTTTCCAAGG--CTCTGCAGAAAGATTGTGTGAGTTTG 784073 ii ii - v iv-- i v ? i i iiv ? C L1MC4a_3end#L 342 TTTTGTTAGATA-TTGCCAAATTCCCCTCCANAAGGGTTGTACCANTTTG 294 chr4ptel1M 784074 CAATTCCACTGACAATGAACGAGTGTGCCAGCCTCCCCACA 784114 v i iii v i v v ii C L1MC4a_3end#L 293 CATTCCCACCAGCAATGTATGAGAGTGCCTGTTTCCCCACA 253 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 38.65 CpG sites = 17, Kimura (unadjusted) = 38.65 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.02 (2 / 88), avg. gap size = 1.50 (3 / 2) 570 19.28 17.84 1.87 chr4ptel1M 784634 784818 (215182) C MIRc#SINE/MIR (45) 223 10 m_b184s601i4 7122 chr4ptel1M 784634 AAGTGCTTTTACAAACATGATCTCATTTGATCCTGG-----ACCCTGGAA 784678 i i v v vi----- vi C MIRc#SINE/MIR 223 AAGCGCTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGA 174 chr4ptel1M 784679 GGGAGGT-------GCGTTATGATCCCCATTTTACAGATGAGGAAAC--A 784719 v i------- ii v -- C MIRc#SINE/MIR 173 GGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGA 124 chr4ptel1M 784720 GG--CAGGCAGCGCT---TCCCTTGCTCAGGGTCCTACAAGTAGTAAGCT 784764 -- iv - i --- vv i i vi iv -- C MIRc#SINE/MIR 123 GGCTCAGAGAG-GTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAG-- 77 chr4ptel1M 784765 TTG--AGGAC--AGACTGGAAATCA---C------ATTCCGAGTCCA-TG 784800 - -- ii --i v vi --- ------ i i - C MIRc#SINE/MIR 76 -TGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTG 28 chr4ptel1M 784801 CTCTACCCGCTGCACCAC 784818 vi i C MIRc#SINE/MIR 27 CTCTTTCCACTGCACCAC 10 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 22.00 CpG sites = 21, Kimura (unadjusted) = 22.71 Transitions / transversions = 1.50 (21/14) Gap_init rate = 0.08 (14 / 184), avg. gap size = 2.64 (37 / 14) 269 18.60 16.28 0.00 chr4ptel1M 785010 785095 (214905) MIR3#SINE/MIR 70 169 (39) m_b184s601i5 7123 chr4ptel1M 785010 GCCAC-ACCCACCTGGGTGACCTTGG---AGTCACTTCA--------GGA 785047 - v i?v v --- -------- v MIR3#SINE/MIR 70 GCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGC 119 chr4ptel1M 785048 CTCAGTTTCTCCAAATGGACCATGA-GGGGTCAGAGTAGATGGT-TCTAA 785095 ii vv v vv - ii v i - MIR3#SINE/MIR 120 CTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAA 169 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 21.68 CpG sites = 6, Kimura (unadjusted) = 21.68 Transitions / transversions = 0.60 (6/10) Gap_init rate = 0.06 (5 / 85), avg. gap size = 2.80 (14 / 5) 189 24.39 0.00 0.00 chr4ptel1M 785138 785178 (214822) MIRc#SINE/MIR 11 51 (217) m_b184s601i6 7124 chr4ptel1M 785138 TGATGCAGTGGCTAGAGCAGCAGGCTTAGAGTCTAGAAGAC 785178 i vv vii i i vi MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.16 CpG sites = 6, Kimura (unadjusted) = 30.16 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 297 10.42 4.17 0.00 chr4ptel1M 785187 785234 (214766) MIR3#SINE/MIR 96 145 (63) m_b184s601i7 7125 chr4ptel1M 785187 GCAAGTCACTTCACCCGTTTG--CCTCAGTTTCCTGATCTGTAATATGAG 785234 iv i -- v v MIR3#SINE/MIR 96 GCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAG 145 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 11.22 CpG sites = 2, Kimura (unadjusted) = 11.22 Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.02 (1 / 47), avg. gap size = 2.00 (2 / 1) 243 24.57 0.00 1.75 chr4ptel1M 786057 786114 (213886) L2d2_3end#LINE/L2 478 534 (21) m_b184s601i8 7126 chr4ptel1M 786057 CTTTCTATCCCTACCCAGCACCTGACCCAGTGCCTTGCATAGTGTAGATT 786106 v i- v i ii v i vv iiv L2d2_3end#LIN 478 CTTTGTATCCCC-CACAGCGCCTAGCACAGTGCCTTGCACACAGTAGGCG 526 chr4ptel1M 786107 CTTAATAA 786114 i L2d2_3end#LIN 527 CTCAATAA 534 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 25.40 CpG sites = 8, Kimura (unadjusted) = 30.29 Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.02 (1 / 57), avg. gap size = 1.00 (1 / 1) 14 15.60 0.00 0.00 chr4ptel1M 786804 786832 (213168) (GTTT)n#Simple_repeat 1 29 (0) m_b184s252i1 7127 chr4ptel1M 786804 GTTTGTTTACTTGTTTGTTTTTTTGTCTG 786832 ii v i (GTTT)n#Simpl 1 GTTTGTTTGTTTGTTTGTTTGTTTGTTTG 29 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 473 29.16 2.49 7.85 chr4ptel1M 786893 787093 (212907) C MIRc#SINE/MIR (56) 212 22 m_b184s601i9 7128 chr4ptel1M 786893 CATAGCATATAT-TCACTTGAACCTCCTAACAACC-TGTCAGGTTATTAT 786940 - - - i v vi - v vivi v C MIRc#SINE/MIR 212 CATA-CAT-TATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAG 165 chr4ptel1M 786941 AACAACTGCAAGATTGCTTGTCTCCTTTTTACAGAAGAATAAACTCAGGT 786990 ii iv ----- i- i i v v iv v i C MIRc#SINE/MIR 164 GGCAGGT-----ATTA-TTATCCCCATTTTACAGATGAGGAAACTGAGGC 121 chr4ptel1M 786991 TCAGAA--TTTAGGAAATTTGCCCACGTTTGTGCAGCTGGCCCATGTCAG 787038 i--v i vi i v v iiii i ivvi v C MIRc#SINE/MIR 120 TCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAG 71 chr4ptel1M 787039 AGACAGGATTGGAACTCAGGCCCTGTGGCCTCCTG-CCCCAGGTCCAGGA 787087 v i i v i i------- i - i i vi C MIRc#SINE/MIR 70 AGCCGGGACTCGAACCCAGGT-------CTTCCTGACTCCAAGTCCAGTG 28 chr4ptel1M 787088 CTTCTT 787093 ii C MIRc#SINE/MIR 27 CTCTTT 22 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 37.03 CpG sites = 33, Kimura (unadjusted) = 37.93 Transitions / transversions = 1.57 (33/21) Gap_init rate = 0.10 (19 / 200), avg. gap size = 1.05 (20 / 19) 34 19.38 2.83 4.81 chr4ptel1M 787603 787708 (212292) (TTCCC)n#Simple_repeat 1 104 (0) m_b184s252i2 7129 chr4ptel1M 787603 TTCTCCTCTCCTACCC-TCCATTCTTCTCCCTTCCTCTTCCCTTCCCTTC 787651 - ii v - v iii - (TTCCC)n#Simp 1 TTC-CCTTCCCTTCCCTTCCCTTCCCTTCCCTTCC-CTTCCCTTCCCTTC 48 chr4ptel1M 787652 CCCTCTC-TCCCTCCCATTCCCCTCCCCTCCCCT-CCTTCTCCTTTCTTC 787699 i i - i v i i i - - i i - (TTCCC)n#Simp 49 CCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTC-CCTTCCCT- 96 chr4ptel1M 787700 TCTCCTTCC 787708 - (TTCCC)n#Simp 97 TC-CCTTCC 104 Matrix = Unknown Transitions / transversions = 4.33 (13/3) Gap_init rate = 0.08 (8 / 105), avg. gap size = 1.00 (8 / 8) 16 17.57 0.00 0.00 chr4ptel1M 788108 788134 (211866) (T)n#Simple_repeat 1 27 (0) m_b184s252i3 7130 chr4ptel1M 788108 TTCTTCTTCTTTTTTTTTTTTTTCTTT 788134 i i i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTT 27 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 208 34.51 5.31 0.00 chr4ptel1M 789331 789443 (210557) L2#LINE/L2 2406 2524 (558) m_b184s601i10 7131 chr4ptel1M 789331 GACATCTC---TCAAATGTCCCCAAAATACCTCAAACTTATCAAGTCCAA 789377 --- iii ivvv iii i v v L2#LINE/L2 2406 GACATCTCCACTTGGATGTCTAATAGGCATCTCAAACTTAACATGTCCAA 2455 chr4ptel1M 789378 AAGAGAATTCCTCCTCCT-CTCCTC-AGTGTCCCCTTCCTTCCATGTT-T 789424 vv i vv i - i - iiv v i i iv vi v -i L2#LINE/L2 2456 AACTGAACTCCTGATCTTCCCCCTCAAACCTGCTCCTCCCGCAGTCTTCC 2505 chr4ptel1M 789425 CTATTTCTGTGGAGGGTGA 789443 i i v ?i v ii L2#LINE/L2 2506 CCATCTCAGTNAATGGCAA 2524 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 46.97 CpG sites = 23, Kimura (unadjusted) = 48.74 Transitions / transversions = 1.44 (23/16) Gap_init rate = 0.04 (4 / 112), avg. gap size = 1.50 (6 / 4) 18 12.96 0.00 0.00 chr4ptel1M 790909 790942 (209058) (AAACAA)n#Simple_repeat 1 34 (0) m_b184s252i4 7132 chr4ptel1M 790909 AAACAAAAACAAAAACAAAAACTAATTCAAATAC 790942 v vv v (AAACAA)n#Sim 1 AAACAAAAACAAAAACAAAAACAAAAACAAAAAC 34 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 13 20.77 3.57 5.45 chr4ptel1M 791745 791800 (208200) (GAGGAAG)n#Simple_repeat 1 55 (0) m_b184s252i5 7133 chr4ptel1M 791745 GAGGAATGAGGAGGGATATAGGGAGAGAAGGA--AAGTGAAAAAATAGGA 791792 v i -iv i - -- - ii iv (GAGGAAG)n#Si 1 GAGGAAGGAGGAAGGA-GGAAGGAG-GAAGGAGGAAG-GAGGAAGGAGGA 47 chr4ptel1M 791793 AGGAGGAA 791800 (GAGGAAG)n#Si 48 AGGAGGAA 55 Matrix = Unknown Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.07 (4 / 55), avg. gap size = 1.25 (5 / 4) 18 31.12 1.59 0.00 chr4ptel1M 791904 791966 (208034) (GA)n#Simple_repeat 1 64 (0) m_b184s252i7 7134 chr4ptel1M 791904 GAAAGAGAGAAAGAGA-AGACAGAGACAGAAAAAGACTGAGCAACACACA 791952 i i - v v i i vv vi v v v (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr4ptel1M 791953 GAAACAAAGAGAGA 791966 i v i (GA)n#Simple_ 51 GAGAGAGAGAGAGA 64 Matrix = Unknown Transitions / transversions = 0.78 (7/9) Gap_init rate = 0.02 (1 / 62), avg. gap size = 1.00 (1 / 1) 223 31.04 0.00 7.41 chr4ptel1M 793575 793661 (206339) MIR#SINE/MIR 104 184 (78) m_b184s601i11 7135 chr4ptel1M 793575 TTAATCTGTCTGTGTCTGAGAGCTTTCTCTTCCGTAAAGAGGCGGGGGAT 793624 i v i v --i i v i i----v MIR#SINE/MIR 104 TTAACCTCTCTGTGCCTCAG--TTTCCTCATCTGTAAAA----TGGGGAT 147 chr4ptel1M 793625 AATTGTAGCACCTCTCTAGCAAGGTCTTGGTAAACAT 793661 vi i vi vii i iv v i iv MIR#SINE/MIR 148 AATAATAGTACCTACCTCATAGGGTTGTTGTGAGGAT 184 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 41.13 CpG sites = 15, Kimura (unadjusted) = 41.13 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.07 (6 / 86), avg. gap size = 1.00 (6 / 6) 299 24.35 12.41 4.05 chr4ptel1M 793699 793835 (206165) C MER63D#DNA/hAT-Tip100 (585) 476 329 m_b184s502i0 7136 chr4ptel1M 793699 ACAAAAACTAACAGACTTTTAAGTTTAATCTG---------CATTTCCCT 793739 i v -i v --------- i ii C MER63D#DNA/hA 476 ACAGACAC-GACACACTTTTAAGTTTAATCTGCATTATTAACATTTTCTC 428 chr4ptel1M 793740 CATCACTTTCCAAAGCCTAGA-AATCAACAGATTTGTAGTT-----TTTG 793783 iv i - i vivi iv -----ii C MER63D#DNA/hA 427 CATCACTTTCTTAAGTCTAGACAATCAACAAAACAATAAATCAAGCCCTG 378 chr4ptel1M 793784 ATCTGTA--GTCTGCCTCTTTCTGAGAGTAGAAATGCTTGCATTGAAAAT 793831 i -- i vv i v - iv i iv ii---- C MER63D#DNA/hA 377 ATTTGTAGCGTTTGCCGATTTCCGTG-GTGTAAATACTCCCACC----AT 333 chr4ptel1M 793832 GGCC 793835 C MER63D#DNA/hA 332 GGCC 329 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 28.26 CpG sites = 21, Kimura (unadjusted) = 30.52 Transitions / transversions = 1.91 (21/11) Gap_init rate = 0.07 (10 / 136), avg. gap size = 2.30 (23 / 10) 234 36.51 7.62 0.89 chr4ptel1M 793906 794010 (205990) L3#LINE/CR1 3277 3388 (711) m_b184s601i12 7137 chr4ptel1M 793906 AAAGGATCCCAATAGGCTGGGGTGACAGGTCAAATCTAACCGAACAAGGT 793955 ? i i i iii ii i i v i vii ii ii L3#LINE/CR1 3277 AAANGATCTCGACAGGCTGGAACGATGGGCCGAAACCAACAAGATGAAAT 3326 chr4ptel1M 793956 C------GAGTAAATGGAATGTTCTGCA--CAAATTTGAAAAATTGTCTC 793997 i------ ii v v i --i ii ii iiv v L3#LINE/CR1 3327 TTAACAGGGATAAATGTAAAGTCCTGCATTTAGGTTCAAAAAATCAACTG 3376 chr4ptel1M 793998 CGCCAAATTTAGG 794010 i- i vi L3#LINE/CR1 3377 CA-CAAGTACAGG 3388 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 51.70 CpG sites = 31, Kimura (unadjusted) = 59.07 Transitions / transversions = 4.43 (31/7) Gap_init rate = 0.03 (3 / 104), avg. gap size = 3.00 (9 / 3) 12 25.52 0.00 0.00 chr4ptel1M 795712 795748 (204252) (TTTCTCT)n#Simple_repeat 1 37 (0) m_b184s252i8 7138 chr4ptel1M 795712 TTTCTCTTTTCTATATTACATTTTCACCTTCCTCTTT 795748 v v viv v i i (TTTCTCT)n#Si 1 TTTCTCTTTTCTCTTTTCTCTTTTCTCTTTTCTCTTT 37 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 332 29.11 20.00 0.99 chr4ptel1M 795842 796011 (203989) MIRc#SINE/MIR 15 216 (52) m_b184s601i13 7139 chr4ptel1M 795842 GCAGTGAGACGGGTG-TGGGCTTGAAGCCAGGAAAAGCTGTCTCCAAGTC 795890 ii v i ii- i i i i v vv i i MIRc#SINE/MIR 15 GCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTC 64 chr4ptel1M 795891 C----TCTG------ACT-----------CTTG----------TTAACCC 795909 ---- ------ ----------- ---------- i MIRc#SINE/MIR 65 CCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCT 114 chr4ptel1M 795910 CTC--AGTCTCATTGTCCTCACCTTTTGCCTGGGGATAATTATATCCAGA 795957 -- i v v i v vivv v i iivv MIRc#SINE/MIR 115 CTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCC 164 chr4ptel1M 795958 ATGCCCCCTTCATACGGTTGTTTTGAAGCTCCATTAGAAAAAAATATATA 796007 v iv i i v v i v v -- vi i v i i MIRc#SINE/MIR 165 CTGCCTACCTCACAGGGTTGTTGTGAGGATCAA--ATGAGATAATGTATG 212 chr4ptel1M 796008 TAGA 796011 ii MIRc#SINE/MIR 213 TGAA 216 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 36.87 CpG sites = 28, Kimura (unadjusted) = 37.85 Transitions / transversions = 1.33 (28/21) Gap_init rate = 0.05 (8 / 169), avg. gap size = 4.50 (36 / 8) 237 29.34 2.15 1.06 chr4ptel1M 796485 796577 (203423) C L1ME3F_3end#LINE/L1 (467) 523 430 m_b184s551i6 7140 chr4ptel1M 796485 ATTTGGTTAGCCATTCCGCAGTCTATAGATAATTCCTTTGTTTCTGAGTC 796534 iv v iv v v i i v vvv i- i C L1ME3F_3end#L 523 ATTTATTTATCCATTCTCCTGTCGATGGACATTTGGGTTGTTTCC-AGTT 475 chr4ptel1M 796535 TTT--CTCTCACAGAAAGTGCTGCCATAAATATTTTGGTGTATGT 796577 -- v i ii v i i i i v ii C L1ME3F_3end#L 474 TTTTGCTATTACGAACAGTGCTGCTATGAACATTCTTGTACATGT 430 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 36.28 CpG sites = 15, Kimura (unadjusted) = 38.05 Transitions / transversions = 1.25 (15/12) Gap_init rate = 0.02 (2 / 92), avg. gap size = 1.50 (3 / 2) 273 31.64 3.77 0.61 chr4ptel1M 796729 796887 (203113) C L1ME2z_3end#LINE/L1 (971) 220 57 m_b184s551i7 7140 chr4ptel1M 796729 TTTTAGTCATTTTTATCAATCTGCA-----ACTTCAG-GTTGTTTTGATT 796772 i i vi vii v i ----- ii v- v i C L1ME2z_3end#L 220 TTTTAGCCATTCTGGTGGGTGTGTAGTGGTATCTCATTGTGGTTTTAATT 171 chr4ptel1M 796773 TGCATTTCTATTTATTATTAGTGATTTGGACCATTATTTTATGTGGTTGT 796822 i-i v v i i v v v i v i v i C L1ME2z_3end#L 170 TGCATTTCC-CTGATGACTAATGATGTTGAGCACTTTTTCATGTGCTTAT 122 chr4ptel1M 796823 AAATACTTTGCAATTCTTCTTTTGAGAAATGTTTGTTCACATCCTTTGAC 796872 viiivv i i vv i v i i v i v C L1ME2z_3end#L 121 TGGCCATTCGTATATCTTCCTTTGTGAAGTGTCTGTTCAAATCTTTTGCC 72 chr4ptel1M 796873 CACTTCTCTACTGGG 796887 i i iv i C L1ME2z_3end#L 71 CATTTTTTAATTGGG 57 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 41.26 CpG sites = 29, Kimura (unadjusted) = 42.38 Transitions / transversions = 1.38 (29/21) Gap_init rate = 0.02 (3 / 158), avg. gap size = 2.33 (7 / 3) 357 27.28 0.00 1.95 chr4ptel1M 796761 796917 (203083) C L1PA14_3end#LINE/L1 (726) 182 29 m_b184s551i9 7140 chr4ptel1M 796761 GTTGTTTTGATTTGCATTTCTATTTATTATTAGTGATTTGGACCATTATT 796810 v -i v v i v v v v v C L1PA14_3end#L 182 GTGGTTTTGATTTGCATTTCT-CTAATGATCAGTGATATTGAGCTTTTTT 134 chr4ptel1M 796811 TTATGTGGTTGTAAATACTTTGCAATTCTTCTTTTGAGAAATGTTTGTTC 796860 i i v viiivviv i vv i i C L1PA14_3end#L 133 TCATATGCTTGTTGGCCGCATGTATGTCTTCTTTTGAGAAGTGTCTGTTC 84 chr4ptel1M 796861 ACATCCTTTGACCACTTCTCTACTGGGGAATGGCTATTACTCTTCAGTAT 796910 ii v - i v -v vi i vi iiv v C L1PA14_3end#L 83 ATGTCCTTTGCCCACTT-TTTAATGGGG-TTGTTTGTTTTTCTCTTGTAA 36 chr4ptel1M 796911 ATTTATT 796917 i C L1PA14_3end#L 35 ATTTGTT 29 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 34.17 CpG sites = 20, Kimura (unadjusted) = 34.17 Transitions / transversions = 0.91 (20/22) Gap_init rate = 0.02 (3 / 156), avg. gap size = 1.00 (3 / 3) 455 22.84 0.00 0.79 chr4ptel1M 796761 796888 (203112) C L1ME4a_3end#LINE/L1 (689) 182 56 m_b184s551i8 7140 chr4ptel1M 796761 GTTGTTTTGATTTGCATTTCTATTTATTATTAGTGATTTGGACCATTATT 796810 i - v i vv v v ?v C L1ME4a_3end#L 182 GTTGTTTTAATTTGCATTTCT-TTGATTACTAGTGAGGTTGAACATNTTT 134 chr4ptel1M 796811 TTATGTGGTTGTAAATACTTTGCAATTCTTCTTTTGAGAAATGTTTGTTC 796860 i i v i viiivv i v v v i C L1ME4a_3end#L 133 TCATATGTTTATTGGCCATTTGTATTTCTTCTTTTGTGAATTGTCTGTTC 84 chr4ptel1M 796861 ACATCCTTTGACCACTTCTCTACTGGGG 796888 ii v i i i C L1ME4a_3end#L 83 ATGTCCTTTGCCCATTTTTCTATTGGGG 56 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 27.76 CpG sites = 15, Kimura (unadjusted) = 27.76 Transitions / transversions = 1.07 (15/14) Gap_init rate = 0.01 (1 / 127), avg. gap size = 1.00 (1 / 1) 232 30.82 7.84 0.70 chr4ptel1M 796794 797061 (202939) C L1M2_orf2#LINE/L1 (0) 3291 3005 m_b184s551i11 7140 chr4ptel1M 796794 TGATTTGGACCATTATTTTATGTGGTTGTAAATACTTTGCAATTCTTCTT 796843 v v v v i i ivi viiivv i vv C L1M2_orf2#LIN 3291 TGATGTTGAGCATTTTTTCATATACCTGTTGGCCATTTGTATGTCTTCTT 3242 chr4ptel1M 796844 TTGAGAAATGTTTGTTCACATCCTTTGACCACTTCTCTACTGGGGAAT-- 796891 i i vi v i i ?v ii ivv -- C L1M2_orf2#LIN 3241 TTGAGAAATGTCTATTCAGGTCCTTTGCCCATTTTTNAATCGGATTATTT 3192 chr4ptel1M 796892 -GGCTATTACTCTTCAGTATATTT--ATTGTTTATCTGTTTTGGATTCCA 796938 -vvi v i v v - i --i vi v i i vii C L1M2_orf2#LIN 3191 GTTTTTTTGCTGTTGAGT-TGTTTGAGTTCCTTATATATTCTGGATATTA 3143 chr4ptel1M 796939 AATCCTTCTCAGA-GA--AATTTG---ATGATTTTAGCAC-TTCTTT--- 796978 vi v - ?-- i --- - vv v - v --- C L1M2_orf2#LIN 3142 ATCCCTTGTCAGATGNATAGTTTGCAAAT-ATTTTCTCCCATTCTGTAGG 3094 chr4ptel1M 796979 TCTTATCTTAACTGCATTAA-TGTTGT-----CTGTACCGAAACTTTTCA 797022 iv v v vii i - vi----- i v i i C L1M2_orf2#LIN 3093 TTGTCTCTTCACTCTGTTGATTGTTTCCTTTGCTGTGCAGAAGCTTTTTA 3044 chr4ptel1M 797023 GTTTCAGGTAACCAGAATTATTTATTTATTTTTTTGCTG 797061 v v i vv v i i v vi i C L1M2_orf2#LIN 3043 GTTTGATGTAATCCCATTTGTCTATTTTTGCTTTTGTTG 3005 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.95 CpG sites = 40, Kimura (unadjusted) = 40.58 Transitions / transversions = 0.95 (40/42) Gap_init rate = 0.04 (12 / 267), avg. gap size = 1.92 (23 / 12) 243 27.43 5.70 3.09 chr4ptel1M 796794 796951 (203049) C L1M5_orf2#LINE/L1 (0) 3294 3133 m_b184s551i10 7140 chr4ptel1M 796794 TGATTTGGACCATTATTTTATGTGGTTGTAAATACTTTGCAATTCTTCTT 796843 ?v v v iv i v i viiivv ? vv C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr4ptel1M 796844 TTGAGAAATGTTTGTTCACATCCTTTGACCACTTCTCTACTGGGGAATGG 796893 v i i vi i v i i ? i v-- v C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGT--TGT 3197 chr4ptel1M 796894 CTATTACTCTTCAGTAT--ATTT------ATTGTTTATCTGTTTTGGATT 796935 i i -- i i?v -- ? ------i v v i i - C L1M5_orf2#LIN 3196 TTGT--CTTTTTNTTATTGANTTGTAGGAGTTCTTTATATATTCTGGA-T 3150 chr4ptel1M 796936 CCAAATCCTTC-TCAGA 796951 v i i i- C L1M5_orf2#LIN 3149 ACGAGTCCTTTGTCAGA 3133 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 35.26 CpG sites = 23, Kimura (unadjusted) = 36.34 Transitions / transversions = 1.21 (23/19) Gap_init rate = 0.05 (8 / 157), avg. gap size = 1.75 (14 / 8) 257 20.45 4.23 10.45 chr4ptel1M 797070 797140 (202860) C MIRc#SINE/MIR (153) 115 49 m_b184s601i14 7141 chr4ptel1M 797070 GGGGTTAAATGATTT-CCCAGAGTCACACAGCTAAGCAGTGTTAAGTGTC 797118 i i i - ii i------- v C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGC 73 chr4ptel1M 797119 AT-GCC-AAATTTGAACTCAGGTC 797140 v- -ii i i i C MIRc#SINE/MIR 72 AGAGCCGGGACTCGAACCCAGGTC 49 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 22.91 CpG sites = 11, Kimura (unadjusted) = 25.11 Transitions / transversions = 5.50 (11/2) Gap_init rate = 0.14 (10 / 70), avg. gap size = 1.00 (10 / 10) 52 12.33 1.10 1.10 chr4ptel1M 797311 797401 (202599) (TTCC)n#Simple_repeat 1 91 (0) m_b184s252i9 7142 chr4ptel1M 797311 TTCATTACTTCCTCCCTCCCTTCCTTCCTTCCTTCCTT-CTTCCTTCCCT 797359 v v i i - i (TTCC)n#Simpl 1 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 50 chr4ptel1M 797360 CCTTCCCTCCCTCCCTCCCTTCCTTGCTTCCTTCCTTCTTTC 797401 - i i i v i (TTCC)n#Simpl 51 CCTT-CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC 91 Matrix = Unknown Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.02 (2 / 90), avg. gap size = 1.00 (2 / 2) 334 30.12 9.67 2.86 chr4ptel1M 797420 797812 (202188) C L1PREC2_orf2#LINE/L1 (484) 2810 2392 m_b184s551i12 7140 chr4ptel1M 797420 CAGCAGCTTTTATGAAAGAGAGAG--CTTTTCCC-TCGGTAATTTATGGT 797466 v v vi v i -- i - i v vi v vi C L1PREC2_orf2# 2810 CAGCACCATTTATTGAATAGGGAGTCCTTTCCCCATTGCTTGTTTTTGTC 2761 chr4ptel1M 797467 A------TCAAATACCAGATTATTG--AGTTT----CATTATTTCTGATT 797504 ------ i v i vi --i v ---- v i-- C L1PREC2_orf2# 2760 AGCTTTGTCGAAGATCAGATGGTTGTAGGTGTGCGGCCTTATTTCTGG-- 2713 chr4ptel1M 797505 TGCCCTTGTTTAGTATGTTCCATTGATCTATCTCTCTATACTTTAATTAA 797554 - i i--- v v i v v i vi vv ii i C L1PREC2_orf2# 2712 -GCTCTC---TATTCTGTTCCATTGGTCTATGTGTCTGTTTTTGTACCAG 2667 chr4ptel1M 797555 TACTAGATGACTTTGATGATTACTGCTTCAAAATATAGTTTCAAGT---G 797601 i viivii i v i iiv iiiiv i v --- C L1PREC2_orf2# 2666 TACCATGCTGTTTTGGTTACTGTAGCCCTGTAGTATAGTTTGAAGTCGGG 2617 chr4ptel1M 797602 TAGATGTGTTATTTCC--CTTTAGCTCTACTTCCTTAATATT--CTAGAT 797647 -i v iii -- - i vi v iv -- v ii C L1PREC2_orf2# 2616 TAG-CGTGATGCCTCCAGCTTT-GTTCTTTTTGCTTAGGATTGCCTTGGC 2569 chr4ptel1M 797648 CTTTTG----CTTTTT---TTCCAAATTACTTTT---ATTATTTTCTCAA 797687 iv i ---- --- v v v --- vi i v C L1PREC2_orf2# 2568 TATTCGGGCTCTTTTTTGGTTCCATATGAATTTTAAAATAGTTTTTTCTA 2519 chr4ptel1M 797688 GTTCTATAAAG--TATCCCTGGATAATCTGATTGGTATAGCATTAAAG-T 797734 i i -- i vi - i i v v i v- C L1PREC2_orf2# 2518 GTTCTGTGAAGAATGTCATTGG-TAGTTTGATAGGAATAGCATTGAATCT 2470 chr4ptel1M 797735 GTAAATTAATTTTGTCAATATTGTCATTTTTATTACCTTG--TCAAAGTC 797782 iv v v i v i v iv iv -- ---v C L1PREC2_orf2# 2469 GTAAATTGCTTTGGGCAGTATGGCCATTTTAACGATATTGATTC---TTC 2423 chr4ptel1M 797783 CAATCC-CACACACTGAATATTCTTCCATTT 797812 v -iivi iv i i C L1PREC2_orf2# 2422 CTATCCATGAGCATGGAATGTTTTTCCATTT 2392 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 37.77 CpG sites = 64, Kimura (unadjusted) = 39.52 Transitions / transversions = 1.25 (64/51) Gap_init rate = 0.07 (27 / 392), avg. gap size = 1.85 (50 / 27) 21 10.46 0.00 0.00 chr4ptel1M 797841 797871 (202129) (TG)n#Simple_repeat 1 31 (0) m_b184s252i10 7143 chr4ptel1M 797841 TGTGTGTGTATGTGTGTGTCTATGTGTGTGT 797871 i v i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 31 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 13 29.85 3.03 0.00 chr4ptel1M 797876 797906 (202094) (GAGACA)n#Simple_repeat 1 31 (37) m_b184s252i11 7144 chr4ptel1M 797876 GAGACAGAGAAATACAGAAAGAGAAAGAGGG 797906 v v v v i v i vi (GAGACA)n#Sim 1 GAGACAGAGACAGAGACAGAGACAGAGACAG 31 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 31 0.00 0.00 0.00 chr4ptel1M 797907 797933 (202067) (AC)n#Simple_repeat 1 27 (0) c_b184s251i0 7145 chr4ptel1M 797907 ACACACACACACACACACACACACACA 797933 (AC)n#Simple_ 1 ACACACACACACACACACACACACACA 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 13 29.85 3.03 0.00 chr4ptel1M 797934 797967 (202033) (GAGACA)n#Simple_repeat 32 67 (1) m_b184s252i11 7146 chr4ptel1M 797934 GACAGAAACACACCCACA-A-AGAAACAGAGATAGA 797967 i v vv v - - i i (GAGACA)n#Sim 32 GACAGAGACAGAGACAGAGACAGAGACAGAGACAGA 67 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2) 53 3.85 0.00 0.00 chr4ptel1M 798036 798089 (201911) (GA)n#Simple_repeat 1 54 (0) c_b184s251i1 7147 chr4ptel1M 798036 GAGAGAGAGAGAGAAAGAGAGAGAGAGAGAGAGAAAGAGAGAGAGAGAGA 798085 i i (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr4ptel1M 798086 GAGA 798089 (GA)n#Simple_ 51 GAGA 54 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 33 3.13 0.00 0.00 chr4ptel1M 798163 798195 (201805) (AC)n#Simple_repeat 1 33 (0) c_b184s251i2 7148 chr4ptel1M 798163 ACACACATACACACACACACACACACACACACA 798195 i (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACA 33 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 347 32.76 2.56 0.84 chr4ptel1M 799696 799812 (200188) C MIR3#SINE/MIR (49) 159 41 m_b184s601i15 7149 chr4ptel1M 799696 TTTAATACGGCCCTGTTATTTTTCAGTGAAGGAGACTAAAACT---GGAG 799742 i i v ii iv i v vvi i i ii i---i C MIR3#SINE/MIR 159 TCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAG 110 chr4ptel1M 799743 GTCAAGTAATTTGACCTGGGTGACACAGATAATTAAATGCCTGAGATGGG 799792 v i i v vi v v? i - i v v vi C MIR3#SINE/MIR 109 GTGAAGTGACTTGCCCAAGGTCACACAGCNAGTT-AGTGGCAGAGCCGGG 61 chr4ptel1M 799793 GTTTGAACCCAGGTCCTTTG 799812 ii v iii C MIR3#SINE/MIR 60 ACTAGAACCCAGGTCTCCTG 41 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 44.04 CpG sites = 24, Kimura (unadjusted) = 45.71 Transitions / transversions = 1.71 (24/14) Gap_init rate = 0.02 (2 / 116), avg. gap size = 2.00 (4 / 2) 360 25.52 3.16 1.03 chr4ptel1M 799713 799807 (200193) C MIRb#SINE/MIR (120) 148 52 m_b184s601i16 7149 chr4ptel1M 799713 ATTTTTCAGTGAAGGAGACTAAAACT---GGAGGTCAAGTAATTTGACCT 799759 v vvi i i ii ---i i i v v C MIRb#SINE/MIR 148 ATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCA 99 chr4ptel1M 799760 GGGTGACACAGATAATTAAATGCCTGAGATGGGGTTTGAACCCAGGTC 799807 i v v i- i v v vi i i C MIRb#SINE/MIR 98 AGGTCACACAGCTAG-TAAGTGGCAGAGCCGGGATTCGAACCCAGGTC 52 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 28.76 CpG sites = 14, Kimura (unadjusted) = 31.88 Transitions / transversions = 1.40 (14/10) Gap_init rate = 0.02 (2 / 94), avg. gap size = 2.00 (4 / 2) 459 32.78 7.29 1.48 chr4ptel1M 801335 801526 (198474) MIRc#SINE/MIR 41 243 (25) m_b184s601i17 7150 chr4ptel1M 801335 GTGAAGAAGACCTGAGTTCCAATTCTGATTCTGACCCAGCCCAACTATAA 801384 v i i v i i i ii v v vvv i i i iv MIRc#SINE/MIR 41 GTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGT 90 chr4ptel1M 801385 GAGCACAGACTGATCACT--GCTTTCTTGAGCTTTAGCAGTCCTATCTGT 801432 v vii i vii --i i iii i i ivvi ii MIRc#SINE/MIR 91 GACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGT 140 chr4ptel1M 801433 AAAATGGGGACAGTAATGTTAGTTCT------CTTACATGGTTGTTAGTG 801476 i i iiiv ii ------ i v - MIRc#SINE/MIR 141 AAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTT-GTG 189 chr4ptel1M 801477 AG--TAAAATGGTGGATGAGGT---TCCAAGCTCTATATAAA-TGTGAAC 801520 -- v --i i v --- vv v v i - i v MIRc#SINE/MIR 190 AGGATCAAATG--AGATAATGTATGTGAAAGCGCTTTGTAAACTGTAAAG 237 chr4ptel1M 801521 TACTAT 801526 i MIRc#SINE/MIR 238 TGCTAT 243 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 44.39 CpG sites = 40, Kimura (unadjusted) = 45.42 Transitions / transversions = 1.82 (40/22) Gap_init rate = 0.04 (8 / 191), avg. gap size = 2.12 (17 / 8) 539 21.99 13.58 4.55 chr4ptel1M 801709 801870 (198130) MIRb#SINE/MIR 79 254 (14) m_b184s601i18 7151 chr4ptel1M 801709 ATTTACTAGCTGCATGACCTTGAGCAAGTCAGTTAACCTCTGTCTCCCTT 801758 i ii i i v v vvv i MIRb#SINE/MIR 79 ACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTC 128 chr4ptel1M 801759 AGTTTCTTCAATTATAAAAAAAAAATGGGGCTGACAACATCT--CT---- 801802 i vi i ------ v i i i i -- ---- MIRb#SINE/MIR 129 AGTTTCCTCATCTGT------AAAATGGGGATAATAATACCTACCTCGCA 172 chr4ptel1M 801803 GGATTGCTGTGAAGATCAAATGAGCT---------------TTTTGCATA 801837 i i i i v ---------------i v i MIRb#SINE/MIR 173 GGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGCACA 222 chr4ptel1M 801838 GTGGCTGGTACATAGTAC-CATTAATAATAAATG 801870 v i v- ii --i MIRb#SINE/MIR 223 GTGCCTGGCACATAGTAAGCGCT--CAATAAATG 254 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 26.05 CpG sites = 23, Kimura (unadjusted) = 26.97 Transitions / transversions = 2.09 (23/11) Gap_init rate = 0.07 (12 / 161), avg. gap size = 2.50 (30 / 12) 340 28.85 11.68 1.32 chr4ptel1M 802165 802301 (197699) MIRc#SINE/MIR 7 157 (111) m_b184s601i19 7152 chr4ptel1M 802165 AGTGTGGTAGAGTGGA-------CTGAATCTT--AGTCA---AAACATGG 802202 iv ------- i - -- --- i v MIRc#SINE/MIR 7 AGTGTGGTGCAGTGGAAAGAGCACTGGA-CTTGGAGTCAGGAAGACCTGG 55 chr4ptel1M 802203 GAGTTGAACCTTGCCTCAG--AC--ACCAGCTGCATGACCATAGACAGGT 802248 -v i ii ii v v -- -- i ii v i i i MIRc#SINE/MIR 56 G-TTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGT 104 chr4ptel1M 802249 CATGGAATTTCTTGGGGTCTCAGTTTTATTCTCTGTGCAGCGGGGATGAA 802298 ivv ii iv i i iv iv iv ii i v MIRc#SINE/MIR 105 CACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAAT 154 chr4ptel1M 802299 AAT 802301 MIRc#SINE/MIR 155 AAT 157 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 35.68 CpG sites = 26, Kimura (unadjusted) = 38.19 Transitions / transversions = 2.00 (26/13) Gap_init rate = 0.05 (7 / 136), avg. gap size = 2.57 (18 / 7) 319 28.38 0.00 0.00 chr4ptel1M 803280 803353 (196647) MIRc#SINE/MIR 168 241 (27) m_b184s601i20 7152 chr4ptel1M 803280 CTTGCTTCCCGAGGTTGTTGGGAAGTTCAAATGAGAACCTCTATGCAAGA 803329 i i i v ii v i v vvv v ii i MIRc#SINE/MIR 168 CCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAA 217 chr4ptel1M 803330 ATGCTTTGCAAACTTTGAAGTGCT 803353 ii i v i MIRc#SINE/MIR 218 GCGCTTTGTAAACTGTAAAGTGCT 241 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 34.65 CpG sites = 13, Kimura (unadjusted) = 36.85 Transitions / transversions = 1.62 (13/8) Gap_init rate = 0.00 (0 / 73), avg. gap size = 0.0 (0 / 0) 990 18.79 10.55 1.16 chr4ptel1M 803416 803652 (196348) C MIRc#SINE/MIR (0) 268 10 m_b184s601i21 7153 chr4ptel1M 803416 AATAACAATAAAG---TACATTTATATAATGTTTTAAAGTTTGCAAAATG 803462 i v?--- i iiii v i ii C MIRc#SINE/MIR 268 AATAATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCG 219 chr4ptel1M 803463 CTTT-ACAAACATTGCCTCATTTGATCCTCACAATAGCCCT---AGGT-- 803506 - v ii i i --- -- C MIRc#SINE/MIR 218 CTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAG 169 chr4ptel1M 803507 ----GGTAGGTGTTAAGATGCCCATTTTACAGATGAAGAAACTGAGG--C 803550 ---- i i vv v i -- C MIRc#SINE/MIR 168 GCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC 119 chr4ptel1M 803551 AGGCCGAGGCTAAAGTGAATTG-CCAGGGTCATACATCTAGGAA----CA 803595 i-- i - v - i i v v ---- C MIRc#SINE/MIR 118 AGA--GAGGTT-AAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCA 72 chr4ptel1M 803596 -AGTTTGGGTT----CTCTGGTCTTCCTGATTCCAAACCCAGTCCTCTAT 803640 - iiv ii ---- i v i ii v v C MIRc#SINE/MIR 71 GAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTT 22 chr4ptel1M 803641 CCATTGAGCCAC 803652 i vi C MIRc#SINE/MIR 21 CCACTGCACCAC 10 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 21.19 CpG sites = 30, Kimura (unadjusted) = 22.31 Transitions / transversions = 2.14 (30/14) Gap_init rate = 0.06 (13 / 236), avg. gap size = 2.15 (28 / 13) 213 30.48 17.71 0.89 chr4ptel1M 804637 804732 (195268) C L2b_3end#LINE/L2 (1) 465 354 m_b184s601i22 7154 chr4ptel1M 804637 TTTATCCAGTCAGCAAGCATGTTCTCAACG---------TGCCAGGCACT 804677 i i v i ii v v v i --------- ? C L2b_3end#LINE 465 TTCATTCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCT 416 chr4ptel1M 804678 GTACTAGCCACTGAG-----AGTGAGAGACAAAAATGGA---GATCCCCG 804719 i v i i ----- i ivii - i ii --- i i C L2b_3end#LINE 415 GTGCTAGGCGCTGGGGATACAGCGGTGAAC-AAGACAGACNCGGTCCCTG 367 chr4ptel1M 804720 CTCTCCAGGAATT 804732 i vv ii C L2b_3end#LINE 366 CCCTCACGGAGCT 354 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 38.69 CpG sites = 21, Kimura (unadjusted) = 42.62 Transitions / transversions = 2.62 (21/8) Gap_init rate = 0.04 (4 / 95), avg. gap size = 4.50 (18 / 4) 220 29.41 8.82 0.00 chr4ptel1M 804666 804733 (195267) C L2d2_3end#LINE/L2 (39) 516 443 m_b184s601i23 7154 chr4ptel1M 804666 GTGCCAGGCACTGTACTAGCCACTGAGAGTGAGAGACAAAAATGGA---- 804711 v i v i v i v v v v i i iv ---- C L2d2_3end#LIN 516 GTGCAAGGCACTGTGCTAGGCGCTGTGGGGGATACAAAGAAGTATAAGAC 467 chr4ptel1M 804712 --GATCCCCGCTCTCCAGGAATTT 804733 -- i i i v ii C L2d2_3end#LIN 466 ATGGTCCCTGCCCTCAAGGAGCTT 443 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 35.74 CpG sites = 11, Kimura (unadjusted) = 38.12 Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.03 (2 / 67), avg. gap size = 3.00 (6 / 2) 244 29.37 10.58 1.77 chr4ptel1M 806387 806490 (193510) MIR3#SINE/MIR 89 201 (7) m_b184s601i24 7155 chr4ptel1M 806387 ACCTAAGTTAGGCCATTTCTCCTCTTGGGGGCCCCCAG-------A---G 806426 vi vi i i i v iv -- i ------- --- MIR3#SINE/MIR 89 ACCTTGGGCAAGTCACTTCACCTCTCTGGG--CCTCAGTTTCCTCATCTG 136 chr4ptel1M 806427 TAAAGTGAATGAGATGAGCTAGCTGATCCATCAGTCCTTCTCCAGCTCTC 806476 i iv i v ii v iv v vi iii v MIR3#SINE/MIR 137 TAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTG 186 chr4ptel1M 806477 AGA-TCTAGGATTCT 806490 v - v MIR3#SINE/MIR 187 ACATTCTATGATTCT 201 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 38.24 CpG sites = 17, Kimura (unadjusted) = 38.24 Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.05 (5 / 103), avg. gap size = 2.60 (13 / 5) 201 28.91 9.82 4.24 chr4ptel1M 807706 807817 (192183) MIRc#SINE/MIR 3 120 (148) m_b184s601i25 7156 chr4ptel1M 807706 AGTCAGGATGGGGTGGTAGGTAGAGCACT-GCCTTGGAGTCCCCAAAGCC 807754 v vi v ii i iv - v vvv ii MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chr4ptel1M 807755 CTTAACCTCCCTGAGGCCCGGTTCTCTCAT-------CTATGAGACCTTG 807797 -- iivi --- v i vi i------- i v MIRc#SINE/MIR 53 --TGGGTTC---GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTG 97 chr4ptel1M 807798 TG---GTCCCTGAAGATCTCTGA 807817 v --- v v vv MIRc#SINE/MIR 98 GGCAAGTCACTTAACCTCTCTGA 120 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 36.84 CpG sites = 14, Kimura (unadjusted) = 36.84 Transitions / transversions = 0.82 (14/17) Gap_init rate = 0.07 (8 / 111), avg. gap size = 2.00 (16 / 8) 202 25.24 0.00 9.62 chr4ptel1M 807736 807792 (192208) MIRc#SINE/MIR 93 144 (124) m_b184s601i26 7156 chr4ptel1M 807736 CCTTGGAGTCCCCAAAGCCCTTAACCTCCCTGAGGCCCGGTTCTCTCATC 807785 i----- iv v i v i i ii MIRc#SINE/MIR 93 CCTTGGG-----CAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATC 137 chr4ptel1M 807786 TATGAGA 807792 i i i MIRc#SINE/MIR 138 TGTAAAA 144 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 32.26 CpG sites = 10, Kimura (unadjusted) = 32.26 Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.09 (5 / 56), avg. gap size = 1.00 (5 / 5) 438 23.39 4.03 0.00 chr4ptel1M 808867 808990 (191010) C MIR1_Amn#SINE/MIR (80) 150 22 m_b184s601i27 7157 chr4ptel1M 808867 CTTATTTTCCAGGTGAGGAA-CTGAGGCA-AGTAGGGGGAAGTGCCTTGC 808914 ii v i - ?- vii v? v C MIR1_Amn#SINE 150 CCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGC 101 chr4ptel1M 808915 CCAGGGTCACCCAGCCAGCAAGCATCTGAGGCCAAATTTGAACTCAGGGC 808964 i ? ?i ? iiv v v vii ? ? i v C MIR1_Amn#SINE 100 CCAAGGTCACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAACCCAGGTC 51 chr4ptel1M 808965 TCAC--ATTGCA-TCCACTTCTCCATCTA 808990 v --i iv - v v i i C MIR1_Amn#SINE 50 TCCCGAGTCCCAGTCCAGTGCTCTATCCA 22 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.56 CpG sites = 16, Kimura (unadjusted) = 30.56 Transitions / transversions = 1.23 (16/13) Gap_init rate = 0.03 (4 / 123), avg. gap size = 1.25 (5 / 4) 192 20.40 4.00 1.96 chr4ptel1M 809222 809271 (190729) L2b_3end#LINE/L2 335 385 (81) m_b184s601i28 7158 chr4ptel1M 809222 TCTTCCCCGAGGAGAAGGTGAGCTTCCTGAGGGCAGGGACTGA--CTACC 809269 i - vv vv i v i ?-- ii L2b_3end#LINE 335 TCTCCCCC-ACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTC 383 chr4ptel1M 809270 TT 809271 L2b_3end#LINE 384 TT 385 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 21.92 CpG sites = 5, Kimura (unadjusted) = 24.58 Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.04 (2 / 49), avg. gap size = 1.50 (3 / 2) 204 19.51 0.00 0.00 chr4ptel1M 809222 809262 (190738) L2a_3end#LINE/L2 384 424 (93) m_b184s601i29 7158 chr4ptel1M 809222 TCTTCCCCGAGGAGAAGGTGAGCTTCCTGAGGGCAGGGACT 809262 i v vv v i i v L2a_3end#LINE 384 TCTCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGACT 424 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 22.61 CpG sites = 3, Kimura (unadjusted) = 22.61 Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 183 27.06 10.67 6.41 chr4ptel1M 809680 809754 (190246) MIRc#SINE/MIR 22 99 (169) m_b184s601i30 7159 chr4ptel1M 809680 AGAGAGCAGTGGCCAGAACCTGGGCCCA--AAGACC------CGAGTCTG 809721 i v ----- i ivi -- ------ iv MIRc#SINE/MIR 22 AAAGAGCACTGG-----ACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCC 66 chr4ptel1M 809722 AGCTCTGCCATTCACTAACTAGGGAACTCTGAG 809754 i i i i iv vi ii i MIRc#SINE/MIR 67 GGCTCTGCCACTTACTAGCTGTGTGACCTTGGG 99 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 33.36 CpG sites = 14, Kimura (unadjusted) = 35.73 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.09 (7 / 74), avg. gap size = 1.86 (13 / 7) 215 24.44 4.44 0.00 chr4ptel1M 809855 809899 (190101) L2c_3end#LINE/L2 411 457 (21) m_b184s601i31 7160 chr4ptel1M 809855 TTTGTCTTTGTATCCT--GTGCCTAACACACAGTTGGTACTTAATAA 809899 ii i-- i ii i v ii i L2c_3end#LINE 411 TTCATCTTTGTATCCCCAGCGCCTGGCACATAGTAGGCGCTCAATAA 457 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 25.22 CpG sites = 10, Kimura (unadjusted) = 32.57 Transitions / transversions = 10.00 (10/1) Gap_init rate = 0.02 (1 / 44), avg. gap size = 2.00 (2 / 1) 234 21.69 3.75 7.79 chr4ptel1M 810548 810627 (189373) MIRc#SINE/MIR 115 191 (77) m_b184s601i32 7159 chr4ptel1M 810548 CTCTGA-CCTCAGTTTCCTCATCTGCAAAATGTCCATGATA--ACCTTGA 810594 - i vvv i -- --- MIRc#SINE/MIR 115 CTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCT--- 161 chr4ptel1M 810595 GCCATAGCTCCTGTGCCCCAGGGACACTGTGAG 810627 v i--- iivi v viii MIRc#SINE/MIR 162 GCCCTG---CCTACCTCACAGGGTTGTTGTGAG 191 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 25.86 CpG sites = 9, Kimura (unadjusted) = 25.86 Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.10 (8 / 79), avg. gap size = 1.12 (9 / 8) 259 14.63 0.00 0.00 chr4ptel1M 810809 810849 (189151) C EutTc1-N1#DNA/TcMar-Tc1 (5) 583 543 m_b184s502i1 7161 chr4ptel1M 810809 TGTCCCCAAAGTCTTGGTGCAGTTGGAAGCTTTGGTAACTT 810849 v vv ii i C EutTc1-N1#DNA 583 TGTCCCAAAAGTCTTGGTGCAGTTTTAAGCTTTAATAACCT 543 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 16.35 CpG sites = 3, Kimura (unadjusted) = 16.35 Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 50 23.80 0.87 0.00 chr4ptel1M 810858 810972 (189028) (TG)n#Simple_repeat 1 116 (0) m_b184s252i13 7162 chr4ptel1M 810858 TGTGAGTGTGTGTGTGTGTGTGTGTATCAGTGTGCTTATGTGTATATTTG 810907 v i vv iv i i i v (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr4ptel1M 810908 TGTATGTGTATGTGTGTATATGTATGTATGTG-GTATATAAGTGTGTCTA 810956 i i i i i i - i i iv v i (TG)n#Simple_ 51 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 100 chr4ptel1M 810957 TGAGTGTGTGTGTGTG 810972 v (TG)n#Simple_ 101 TGTGTGTGTGTGTGTG 116 Matrix = Unknown Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.01 (1 / 114), avg. gap size = 1.00 (1 / 1) 193 36.23 0.00 0.00 chr4ptel1M 810973 811041 (188959) L2a_3end#LINE/L2 446 514 (3) m_b184s601i33 7158 chr4ptel1M 810973 TGTGTTTCTAGCCTTTAGCACAGTGACTTAAGCATGGAAAGTGTTTTATA 811022 i ii i vii v v vivi i v i i i iv L2a_3end#LINE 446 TGTATCCCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGGCGCTCAATA 495 chr4ptel1M 811023 AATACTAGTGGACTGACTG 811041 i v v v v L2a_3end#LINE 496 AATATTTGTTGAATGAATG 514 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 48.33 CpG sites = 14, Kimura (unadjusted) = 51.24 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.00 (0 / 68), avg. gap size = 0.0 (0 / 0) 197 27.59 3.33 3.33 chr4ptel1M 810982 811041 (188959) L2d_3end#LINE/L2 452 511 (5) m_b184s601i34 7158 chr4ptel1M 810982 AGCCTTTAGCACAGTGACTTAAG--CATGGAAAGTGTTTTATAAATACTA 811029 vii --i i -- i v i i i iv v L2d_3end#LINE 452 AGCGCCTAGCACAGTG--CTGAGCACATAGTAGGCGCTCAATAAATACTT 499 chr4ptel1M 811030 GTGGACTGACTG 811041 v i i L2d_3end#LINE 500 GTTGATTGATTG 511 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 33.23 CpG sites = 11, Kimura (unadjusted) = 36.05 Transitions / transversions = 2.20 (11/5) Gap_init rate = 0.05 (3 / 59), avg. gap size = 1.33 (4 / 3) 246 26.86 6.32 2.02 chr4ptel1M 811038 811132 (188868) MIRc#SINE/MIR 29 127 (141) m_b184s601i35 7163 chr4ptel1M 811038 ACTGTAGTGGGGGGCA--AAGACCTGGGTTCAAATCTTGTCTCTGATGGA 811085 v v v i v -- i i ii v viivv MIRc#SINE/MIR 29 ACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACT 78 chr4ptel1M 811086 TGCTAACCAGGGTGACCAGAGGC-AGTCACTCA---TTTCTCAGCTCTCA 811131 i i i- v vvi - i --- i v - MIRc#SINE/MIR 79 TACTAGCT-GTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGC-CTCA 126 chr4ptel1M 811132 G 811132 MIRc#SINE/MIR 127 G 127 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.56 CpG sites = 13, Kimura (unadjusted) = 33.73 Transitions / transversions = 1.08 (13/12) Gap_init rate = 0.05 (5 / 94), avg. gap size = 1.60 (8 / 5) 365 35.82 6.32 0.54 chr4ptel1M 811136 811309 (188691) MIR3#SINE/MIR 2 185 (23) m_b184s601i36 7164 chr4ptel1M 811136 TGGTGAGGCAGCACAGCAGACAGAGCGCTGGACTTGGAGCCTGGGGTACC 811185 iiii ii vv v i - v i v i vv i MIR3#SINE/MIR 2 TGGCAGAGTGGCTGAGCAGAGAGAGCAC-GGACTGGGAGTCAGGAGACCT 50 chr4ptel1M 811186 GAGTTCAAATTCTGCCTC---AACGTGTTGGCTAAGTCCTCCTGGACAAG 811232 i v i i i v ---v vvii ? iv vvi i i MIR3#SINE/MIR 51 GGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAG 100 chr4ptel1M 811233 TCATTTCTCCT-TCTCAGCTTTGGTTTCCTTGTCTGGAA-------GGGC 811274 i v - vi i ii ii v ------- i MIR3#SINE/MIR 101 TCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGT 150 chr4ptel1M 811275 TGAATAGGACAGCCTTTGAGGCTCCTTCTGCCTTT 811309 i ivi iiii i i ii iiv i MIR3#SINE/MIR 151 TGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCT 185 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 51.71 CpG sites = 42, Kimura (unadjusted) = 53.02 Transitions / transversions = 2.10 (42/20) Gap_init rate = 0.02 (4 / 173), avg. gap size = 3.00 (12 / 4) 399 29.77 7.63 0.00 chr4ptel1M 811140 811270 (188730) MIRc#SINE/MIR 2 142 (126) m_b184s601i37 7164 chr4ptel1M 811140 GAGGCAGCA-----CAGCAGACAGAGCGCTGGACTTGGAGCCTGGGGTAC 811184 ii----- ii v i i v iiv MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr4ptel1M 811185 C-GAGTTCAAATTCTGCCT---CAACGTGTTGGCTAAGTCCTCCTGGACA 811230 - i i i i i v --- v v ii i iv vvi i i MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 101 chr4ptel1M 811231 AGTCATTTCTCCT-TCTCAGCTTTGGTTTCCTTGTCTGGAA 811270 i vv - v i ii ii v MIRc#SINE/MIR 102 AGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAA 142 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 37.15 CpG sites = 26, Kimura (unadjusted) = 39.81 Transitions / transversions = 2.00 (26/13) Gap_init rate = 0.03 (4 / 130), avg. gap size = 2.50 (10 / 4) 16 28.66 2.67 2.67 chr4ptel1M 811687 811761 (188239) (CTCT)n#Simple_repeat 1 75 (0) m_b184s252i14 7165 chr4ptel1M 811687 CTGTCTCTATCGTCCATTTGTCTCTCTC-CCCTGTCTCTCTGTCTGCCTC 811735 v v - iv i v - i v v vi (CTCT)n#Simpl 1 CTCTCTCTCTC-TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 49 chr4ptel1M 811736 TGTCTGCTTTC-CTGTCCGTCTGTCTC 811761 v - i - v iv v (CTCT)n#Simpl 50 TCTCT-CTCTCTCTCTCTCTCTCTCTC 75 Matrix = Unknown Transitions / transversions = 0.55 (6/11) Gap_init rate = 0.05 (4 / 74), avg. gap size = 1.00 (4 / 4) 32 15.34 0.00 0.00 chr4ptel1M 812349 812406 (187594) (TGTG)n#Simple_repeat 1 58 (0) m_b184s252i15 7166 chr4ptel1M 812349 TGAGTGTGAGTGTGTGTGAGTGACTGTGAGTGTGTATGTGTGTGTGTGTG 812398 v v v vv v i (TGTG)n#Simpl 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr4ptel1M 812399 AGTGTGTG 812406 v (TGTG)n#Simpl 51 TGTGTGTG 58 Matrix = Unknown Transitions / transversions = 0.14 (1/7) Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0) 190 27.64 8.42 0.98 chr4ptel1M 812746 812840 (187160) C MIR3#SINE/MIR (101) 107 6 m_b184s601i38 7167 chr4ptel1M 812746 GAATTG-CTTGTTCCGGGTCCCACAGCAAGTGTGTGTCAGGAGCGGAACG 812794 v - ii vi v ? vv v iiv i v C MIR3#SINE/MIR 107 GAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACT 58 chr4ptel1M 812795 TGAACACGGGTCTT---ACTGCCTAG---GGCCTCTCCATGC-CGCTCAC 812837 v v i i--- - i --- vv iv - ivi C MIR3#SINE/MIR 57 AGAACCCAGGTCTCCTGACT-CCCAGTCCGTGCTCTCTCTGCTCAGCCAC 9 chr4ptel1M 812838 TCT 812840 C MIR3#SINE/MIR 8 TCT 6 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 35.22 CpG sites = 12, Kimura (unadjusted) = 35.22 Transitions / transversions = 0.86 (12/14) Gap_init rate = 0.05 (5 / 94), avg. gap size = 1.80 (9 / 5) 221 29.69 0.00 0.00 chr4ptel1M 812752 812815 (187185) C MIRc#SINE/MIR (165) 103 40 m_b184s601i39 7167 chr4ptel1M 812752 CTTGTTCCGGGTCCCACAGCAAGTGTGTGTCAGGAGCGGAACGTGAACAC 812801 ii vi v v iv v iiv i vi v C MIRc#SINE/MIR 103 CTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCC 54 chr4ptel1M 812802 GGGTCTTACTGCCT 812815 i v v C MIRc#SINE/MIR 53 AGGTCTTCCTGACT 40 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 35.70 CpG sites = 9, Kimura (unadjusted) = 38.14 Transitions / transversions = 0.90 (9/10) Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0) 529 23.06 6.02 2.17 chr4ptel1M 813367 813499 (186501) C Charlie4a#DNA/hAT-Charlie (11) 497 360 m_b184s502i2 7168 chr4ptel1M 813367 AACTTTCATAATGCCCTAGATCCCGCTGGTAGCAGTTTAATGAAACGTGT 813416 i iv vi v i i vi --- i ii i v i C Charlie4a#DNA 497 AACCTTTTTTGTGCCATGGACCCCTTTGG---CAGTCTGGTGAAGCCTAT 451 chr4ptel1M 813417 GGAGCCCTTCTTGGAAAAATGCTTTTAAATGT-----ATAAAATACATGG 813461 v ii v i i----- i C Charlie4a#DNA 450 GGACCCCTTCTCAGAATAATGTTTTTAAATGCATAAAATAAAATACATAG 401 chr4ptel1M 813462 AATTACGAAGGAAACTAGTTATGCTGAAAT---GTTGTCAA 813499 i i i i ii --- i C Charlie4a#DNA 400 GATTACAAAGGAAACCAATTATATTGAAATACAGTTATCAA 360 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 29.04 CpG sites = 23, Kimura (unadjusted) = 29.04 Transitions / transversions = 3.29 (23/7) Gap_init rate = 0.04 (5 / 132), avg. gap size = 2.20 (11 / 5) 31 29.49 0.74 4.58 chr4ptel1M 813590 813725 (186275) (AGAA)n#Simple_repeat 1 131 (0) m_b184s252i17 7169 chr4ptel1M 813590 AGAGAGAAAGAAAAAAAAGAAGTTA-ATAGAGACAGTGAAAGAGAGAGAG 813638 i i ii vv - v i v iv i i (AGAA)n#Simpl 1 AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG 50 chr4ptel1M 813639 AGATTGACAAAGAAAGAAAGAAACAGACACACAGAGAGAAAGAGAGGGGT 813688 i vvi v - - v v v i - -i iv (AGAA)n#Simpl 51 AAAGAAAGAAAGAAAGAAAG-AA-AGAAAGAAAGAAAGAAAGA-A-AGAA 96 chr4ptel1M 813689 AGAGAGAGAGAGAGAGAGAAAGAGAGAGAGAGAAAGA 813725 i i i i - - i (AGAA)n#Simpl 97 AGAAAGAAAGAAAGAAAGAAAGA-A-AGAAAGAAAGA 131 Matrix = Unknown Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.05 (7 / 135), avg. gap size = 1.00 (7 / 7) 54 21.16 0.00 0.00 chr4ptel1M 813617 813725 (186275) (AG)n#Simple_repeat 1 109 (0) m_b184s252i18 7169 chr4ptel1M 813617 AGAGACAGTGAAAGAGAGAGAGAGATTGACAAAGAAAGAAAGAAACAGAC 813666 v v i vv v i i i i v v (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr4ptel1M 813667 ACACAGAGAGAAAGAGAGGGGTAGAGAGAGAGAGAGAGAGAAAGAGAGAG 813716 v v i i iv i (AG)n#Simple_ 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 100 chr4ptel1M 813717 AGAGAAAGA 813725 i (AG)n#Simple_ 101 AGAGAGAGA 109 Matrix = Unknown Transitions / transversions = 1.00 (10/10) Gap_init rate = 0.00 (0 / 108), avg. gap size = 0.0 (0 / 0) 397 21.20 11.05 1.01 chr4ptel1M 813922 814102 (185898) L2#LINE/L2 2140 2338 (744) m_b184s601i40 7170 chr4ptel1M 813922 TCTCCTGGTTCTCCCCCTCCTTCTCTGACCTCTTCTTTCTCACT-TCCTT 813970 i i v i v i v i - v - L2#LINE/L2 2140 TCTCCTGGTTTTCCTCCTACCTCACTGGCCGCTCCTT-CTCAGTCTCCTT 2188 chr4ptel1M 813971 TGCCGGATCCTCCTC------CAGATC-----ACCCT----TTCCCCAGG 814005 i v ------ v i ----- vi ---- v L2#LINE/L2 2189 TGCTGGTTCCTCCTCATCTCCCCGACCTCTNAACGTTGGAGTGCCCCAGG 2238 chr4ptel1M 814006 GCTCTGTCCTGG---CCCTTCTCTTCTCCCTCTAGA-TAACTTCCCTTGC 814051 v v --- i iv v - v - ? v L2#LINE/L2 2239 GCTCAGTCCTTGGACCTCTTCTCTTCTCTATCTACACTCAC-TCCCTNGG 2287 chr4ptel1M 814052 TGACCTCATCCACTTCCATGGATTTCATGACCATCTCTACACCGATAATT 814101 i v ii v v vv v ii i i i L2#LINE/L2 2288 TGATCTCATCCAGTCTCATGGCTTTAAATACCATCTATATGCTGATGACT 2337 chr4ptel1M 814102 C 814102 L2#LINE/L2 2338 C 2338 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 25.25 CpG sites = 18, Kimura (unadjusted) = 25.25 Transitions / transversions = 0.90 (18/20) Gap_init rate = 0.04 (8 / 180), avg. gap size = 2.75 (22 / 8) 850 33.12 15.14 1.32 chr4ptel1M 814384 815050 (184950) L2#LINE/L2 2325 3082 (0) m_b185s601i1 7170 chr4ptel1M 814384 TAGGATGATAATTCTTAAATCTATCTTTCCTGCCCCAGCTGATTTGCTGA 814433 v v i i ii i v i v vii ivv iiv L2#LINE/L2 2325 TATGCTGATGACTCCCAAATTTATATCTCCAGCCCGGACCTCTCCCCTGA 2374 chr4ptel1M 814434 TCTCCAGTCTCACACTTCTGCCTGCCTTTCCAACATTTCAAACTGGACAC 814483 v v ii iv iiv vii i i v vi iii L2#LINE/L2 2375 ACTCCAGACTCGTATATCCAACTGCCTACTCGACATCTCCACTTGGATGT 2424 chr4ptel1M 814484 CCAGTAGGTGTCTTAAACTCAACATGTCTGAAACAAAACCCC-------- 814525 i i ii i i ii vi i -------- L2#LINE/L2 2425 CTAATAGGCATCTCAAACTTAACATGTCCAAAACTGAACTCCTGATCTTC 2474 chr4ptel1M 814526 --------GCCTGCTCCTCC------CTTCCCTTTTGCTG-GAAGGGGAA 814560 --------i ------ iv iv v -? v v L2#LINE/L2 2475 CCCCTCAAACCTGCTCCTCCCGCAGTCTTCCCCATCTCAGTNAATGGCAA 2524 chr4ptel1M 814561 CCACACC---CCAGTGTCCCAGGATTACCACCTAGAAGTCATTCTGGATT 814607 iv i --- vv i viv vv v i i v i L2#LINE/L2 2525 CTCCATCCTTCCAGTTGCTCAGGCCAAAAACCTTGGAGTCATCCTTGACT 2574 chr4ptel1M 814608 CCTCACTTCCAGATCCACCC--CATCAAATTCACCTTTATAGCA---TCG 814652 v i vvviv -- v i i ----- ---i v L2#LINE/L2 2575 CCTCTCTTTCTCTCACACCCCACATCCAATCCATC-----AGCAAATCCT 2619 chr4ptel1M 814653 ATCAGCTACACCCCC---TTCTGCCC----TCAGA-----TATTGCTACC 814690 i i vi ii ---v v ii ---- v ----- v ii i L2#LINE/L2 2620 GTCGGCTCTACCTTCAAAATATATCCAGAATCCGACCACTTCTCACCACC 2669 chr4ptel1M 814691 TCCTC-----CCACCCCG---CAGACCCACGTTCCCTCACTCCGGAACTA 814732 v ----- i --- ii vv i ivi v v v i i L2#LINE/L2 2670 TCCACTGCCACCACCCTGGTCCAAGCCACCATCATCTCTCGCCTGGATTA 2719 chr4ptel1M 814733 CTGCATTAAGCTGT--AGGGG-------ACTTCAAGTCTT--TCTCCTCC 814771 v iv vi-- vv -------i v vi --i i ? L2#LINE/L2 2720 CTGCAATAGCCTCCTAACTGGTCTCCCTGCTTCCACCCTTGCCCCCCTNC 2769 chr4ptel1M 814772 AGTCCATCCTCCATTCAGGTACCAAAG-GATTTTTCTAAAGCATAGGTCC 814820 i i v iv vvi i - ii i i i i v L2#LINE/L2 2770 AGTCTATTCTCAACACAGCAGCCAGAGTGATCCTTTTAAAACGTAAGTCA 2819 chr4ptel1M 814821 CATTATGCCATTCCCCTGC-----------------CTTCCCGTCTTCTC 814853 v i i i i ----------------- i ivii L2#LINE/L2 2820 GATCATGTCACTCCTCTGCTCAAAACCCTCCAATGGCTTCCCATCTCACT 2869 chr4ptel1M 814854 CAGGAGTAATAG--AAAATGCTCTGC-TTGGTGTTCAAAGCCCTTCATAG 814900 - v -- i v - i -v iv v i v ii L2#LINE/L2 2870 CA-GAGTAAAAGCCAAAGTCCT-TACAATGGCCTACAAGGCCCTACATGA 2917 chr4ptel1M 814901 CCCAATCCGCTCCTGTCTTTCC--CATCATCTTTTA--ACTTACTTCCTA 814946 i iii v ivi ii i i-- v ii -- iv ii v L2#LINE/L2 2918 TCTGGTCCCCCGTTACCTCTCTGACCTCATCTCCTACCACTCTCCCCCTC 2967 chr4ptel1M 814947 ATACACTTTAATCCAGGGACACACTGGCCTCCTGGATGTTCCATGGATA- 814995 iiv iiiv -- v v v vi i i - L2#LINE/L2 2968 GCTCACTCCGCTCCA--GCCACACTGGCCTCCTTGCTGTTCCTCGAACAC 3015 chr4ptel1M 814996 ---AG--ACGGTCCATGTTTCAG---CTTTGGGCT-----CTCCCCAGAT 815032 --- -- v -i ii --- vi -----i ivvii L2#LINE/L2 3016 GCCAGGCACGCTCC-CGCCTCAGGGCCTTTGCACTTGCTGTTCCCTCTGC 3064 chr4ptel1M 815033 TTGGAACATTCTCCCTCC 815050 i ii i i L2#LINE/L2 3065 CTGGAACGCTCTTCCCCC 3082 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 43.04 CpG sites = 134, Kimura (unadjusted) = 45.95 Transitions / transversions = 1.60 (134/84) Gap_init rate = 0.05 (36 / 666), avg. gap size = 3.08 (111 / 36) 200 34.32 9.51 5.77 chr4ptel1M 814830 815197 (184803) AmnL2-1#LINE/L2 2170 2550 (63) m_b185s601i2 7170 chr4ptel1M 814830 ATTCCCCTGCCTTCCCGTCTTCTCCAGGAGT-AATAGAAAATGCTCTGCT 814878 i v v i i iivi i vi- i vv vvi v i AmnL2-1#LINE/ 2170 ACTCCACTGGCTCCCCATTCATTTCAGGATCCAGTTCAAAATTGCCTTCC 2219 chr4ptel1M 814879 TGGTGTTCAAAGCCCTTCATAGCCCAATCCGCTCCTGTCTTTCCCA---- 814924 v v i i i i ---- iii v i vi i ---- AmnL2-1#LINE/ 2220 TTGTTTTTAAAACCCTCCATGG----ACTTGCTCCAGCCTACCTCACGGA 2265 chr4ptel1M 814925 -----TCATCTTTTAACTTACTTCCTAATACACTTTA---ATCCAGGGAC 814966 ----- - i iv iv i iviiv v iii---i i ---- AmnL2-1#LINE/ 2266 CCTTGTC-TCTCTCTACTCCCCTCCCCGCTCCCTCCGCTCGTCTAG---- 2310 chr4ptel1M 814967 ACACTGGCCTCCTGGATGTTCCATGG-ATAAG------ACGGTCCATGTT 815009 - i vvv i v vi- i v------ v ivi iv AmnL2-1#LINE/ 2311 -CACCGGCCTCCTCTCTGTCCCTTCACACAATCTCGCCACTGTTGGTGCG 2359 chr4ptel1M 815010 TCAGCTTTGGGCTCT----CCCCAG--ATTTGGAACATTCTCCCTCCTCC 815053 vv i vvv ---- i v -- i vi i vivi AmnL2-1#LINE/ 2360 AGAGCCTTCTCCTCTGCAGCTCCTGCCATCTGGAACAGCCTTCCTGTATC 2409 chr4ptel1M 815054 TCTTCAACT-ATTGACCTTCCCGATCTCCTTT-AAGTCTCAACTAAAATC 815101 i iv - i ii -- ? - i ? i v AmnL2-1#LINE/ 2410 TCTCCGCCTCATCGACTCTCC--ATCTCNTTTCAAATCTCANCTGAAAAC 2457 chr4ptel1M 815102 ACACATTCTACAGGAAACCTTCCCTACCATTCTGTATTTCAGTGCTTTTC 815151 i iv i vi-----v v ivvi vv ---v i i AmnL2-1#LINE/ 2458 ATATCTTTTCT-----CCCTTGCCTATACCTCTTAATTTC---TCTCTCC 2499 chr4ptel1M 815152 TTCTGTGAATTATTTCCTATTTA--TCTG-----GTATATAGCTCATTTT 815194 i iv- vi -- ----- - vi v i i AmnL2-1#LINE/ 2500 CTCTGCT-ATTATTTATTATTTAACTCTGTAACTGTAT-TATTTAACTCT 2547 chr4ptel1M 815195 GTA 815197 AmnL2-1#LINE/ 2548 GTA 2550 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 44.09 CpG sites = 68, Kimura (unadjusted) = 48.01 Transitions / transversions = 1.33 (68/51) Gap_init rate = 0.09 (34 / 367), avg. gap size = 1.68 (57 / 34) 769 28.55 9.28 4.09 chr4ptel1M 814900 815341 (184659) L2b_3end#LINE/L2 3 466 (0) m_b185s601i3 7170 chr4ptel1M 814900 GCCCAATCCGCTCCTGT---CTTTCC--CATCATCTTTTA--ACTTACTT 814942 v i i vi i i--- i -- v ii -- iv ii L2b_3end#LINE 3 GCACGATCTGGCCCCGCTACCTCTCCGGCCTCATCTCCTACCACTCTCCC 52 chr4ptel1M 814943 CCTAATACACTTTAATCCAGGGACACACTGGCCTCCTGGATGTTCCATGG 814992 i iv - i iv v-- v v vi i L2b_3end#LINE 53 CTTGCT-CACTCTGCTCCAGC--CACACTGGCCTCCTTGCTGTTCCTCGA 99 chr4ptel1M 814993 ATAAG--ACGGTCCAT---GTTTCAG---CTTTG----GGCT-CTCCCCA 815029 i v -- ? v ?v --- ii --- ----v -i iv L2b_3end#LINE 100 ACACGCCANGCTCNCTCCCGCCTCAGGGCCTTTGCACNTGCTGTTCCCTC 149 chr4ptel1M 815030 GATTTGGAACATTCTCCCTCCTCCTCTTCAACTATTGACC--TTCCCGAT 815077 viii iii i - v iv --- i --i iiv L2b_3end#LINE 150 TGCCTGGAACGCCCTTCC-CCACCTCTTCGCCT---GGCCAACTCCTACT 195 chr4ptel1M 815078 C-TCCTTTAAGTCTCAACTAAAATCACACATTCTACAGGAAACCTTCCCT 815126 - i i i v vv v i v i i i L2b_3end#LINE 196 CATCCTTCAGGTCTCAGCTCAAATGTCACCTCCTCCGGGAAGCCCTCCCT 245 chr4ptel1M 815127 -ACCATTCTG--TATTTCAGTGC-TTTTCTTCTGTGAATTATT--TCCTA 815170 - vii v --iivv - -iii i v vviivii-- L2b_3end#LINE 246 GACCCCCCAGGCCGGGTCAG-GCGCCCTCCTCTGGGCCCCCCCAGTCCTA 294 chr4ptel1M 815171 TTTATCTGGTA-TATAGCTCATTTTGTATATATTTGTTTGCATAT-TGTC 815218 ii--- vi - v i v i ?---- - i i ? i i - L2b_3end#LINE 295 CC---CTGCCACTCTGGGTTATN----AT-TGTCTGNTTACATGTCTGTC 336 chr4ptel1M 815219 TCCCCCATTTAGATTGAAAGCTACATGGGGGCAGGGA-----TTTCCCTT 815263 i - i vi v i i ----- i vi L2b_3end#LINE 337 TCCCCCACT-AGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCTT 385 chr4ptel1M 815264 --TCGCCTCTTTATGT---GCCCTTAGCACACAGCCTGACACACAGTAGG 815308 -- i v v vi--- v i v? i L2b_3end#LINE 386 GTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGG 435 chr4ptel1M 815309 AGCTTAATAAATGTTAGTTGAATTGAATTGAAT 815341 v i i i v - - L2b_3end#LINE 436 CGCTCAGTAAATATTTGTTGAA-TGAA-TGAAT 466 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 34.73 CpG sites = 76, Kimura (unadjusted) = 37.93 Transitions / transversions = 1.69 (76/45) Gap_init rate = 0.09 (38 / 441), avg. gap size = 1.58 (60 / 38) 19 19.22 0.00 0.00 chr4ptel1M 815703 815738 (184262) (T)n#Simple_repeat 1 36 (0) m_b185s252i2 7171 chr4ptel1M 815703 TTTGTTCTTGTTTTCTCTCTTTTTTTTTTTTTTTTT 815738 v i v i i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 36 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 190 24.34 5.06 6.41 chr4ptel1M 816061 816139 (183861) L2d2_3end#LINE/L2 378 455 (100) m_b185s601i4 7172 chr4ptel1M 816061 ATTTAAATCT-GC-TTAACTTAGTGAACCCATCACGCCAGGGATATGTC- 816107 - i- i-- v v iiv i--- vv - L2d2_3end#LIN 378 ATTTAAATCTTGTATTG--TTATTTAACTTTTCACGT---GTTTATGTCT 422 chr4ptel1M 816108 -ATCTCCTCTGCTAGAGGGGAAGTTCCTTGAGG 816139 -i i vi vv v i L2d2_3end#LIN 423 TGTCTCCCCAACTAGATTGTAAGCTCCTTGAGG 455 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 29.66 CpG sites = 9, Kimura (unadjusted) = 29.66 Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.12 (9 / 78), avg. gap size = 1.00 (9 / 9) 18 15.81 0.00 0.00 chr4ptel1M 816269 816304 (183696) (TGGAGTC)n#Simple_repeat 1 36 (0) m_b185s252i3 7173 chr4ptel1M 816269 TGGAACCTGGACTCTGGAGTCTGGAGCCTGAAGTCT 816304 ii v i i (TGGAGTC)n#Si 1 TGGAGTCTGGAGTCTGGAGTCTGGAGTCTGGAGTCT 36 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 25 29.99 5.48 1.32 chr4ptel1M 816674 816819 (183181) (TCCTC)n#Simple_repeat 1 152 (0) m_b185s252i4 7174 chr4ptel1M 816674 TCCCCTCCT-TCCT-TCATCAGCTGT-CTCTCCT-TCCTCTCCTTTTC-C 816718 i - - v vv v - - i i - (TCCTC)n#Simp 1 TCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTC 50 chr4ptel1M 816719 CCTTCCCCAGTCCCCCATTTTCCTGTGGTATCCTGGGATTTCCATCTCAT 816768 i i i vv i ivi i v vv v vvvv i - v (TCCTC)n#Simp 51 TCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCC-TCTCCT 99 chr4ptel1M 816769 -ACCTCTTC-CTCCTCCCCCTTCATCCTCCTCTCC-CTCCTTTCCTCCCC 816815 -v i - i ii v - - i i (TCCTC)n#Simp 100 CTCCTCTCCTCTCCTCTCCTCTCCT-CTCCTCTCCTCTCCTCTCCTCTCC 148 chr4ptel1M 816816 TCTC 816819 (TCCTC)n#Simp 149 TCTC 152 Matrix = Unknown Transitions / transversions = 0.94 (17/18) Gap_init rate = 0.07 (10 / 145), avg. gap size = 1.00 (10 / 10) 11 17.39 2.86 2.86 chr4ptel1M 816699 816733 (183267) (TCCCCT)n#Simple_repeat 1 35 (0) m_b185s252i5 7175 chr4ptel1M 816699 TCTCCTTCCTC-TCCTTTTCCCCTTCCCCAGTCCCC 816733 i i - ii -v (TCCCCT)n#Sim 1 TCCCCTTCCCCTTCCCCTTCCCCTTCCCC-TTCCCC 35 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 25 29.99 5.48 1.32 chr4ptel1M 816674 816819 (183181) (TCCTC)n#Simple_repeat 1 152 (0) m_b185s252i4 7174 chr4ptel1M 816674 TCCCCTCCT-TCCT-TCATCAGCTGT-CTCTCCT-TCCTCTCCTTTTC-C 816718 i - - v vv v - - i i - (TCCTC)n#Simp 1 TCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTC 50 chr4ptel1M 816719 CCTTCCCCAGTCCCCCATTTTCCTGTGGTATCCTGGGATTTCCATCTCAT 816768 i i i vv i ivi i v vv v vvvv i - v (TCCTC)n#Simp 51 TCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCC-TCTCCT 99 chr4ptel1M 816769 -ACCTCTTC-CTCCTCCCCCTTCATCCTCCTCTCC-CTCCTTTCCTCCCC 816815 -v i - i ii v - - i i (TCCTC)n#Simp 100 CTCCTCTCCTCTCCTCTCCTCTCCT-CTCCTCTCCTCTCCTCTCCTCTCC 148 chr4ptel1M 816816 TCTC 816819 (TCCTC)n#Simp 149 TCTC 152 Matrix = Unknown Transitions / transversions = 0.94 (17/18) Gap_init rate = 0.07 (10 / 145), avg. gap size = 1.00 (10 / 10) 22 16.73 3.39 3.39 chr4ptel1M 816770 816828 (183172) (CCT)n#Simple_repeat 1 59 (0) m_b185s252i6 7176 chr4ptel1M 816770 CCTCTTCCTCCTCCCCCTTCATCCTCCTCTCCCTCCT-TTCCTCC-CCTC 816817 i i - v ii -i - (CCT)n#Simple 1 CCTCCTCCTCCTCCTCC-TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC 49 chr4ptel1M 816818 TCTCCCCCCCC 816828 - i i (CCT)n#Simple 50 -CTCCTCCTCC 59 Matrix = Unknown Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.07 (4 / 58), avg. gap size = 1.00 (4 / 4) 474 17.35 1.02 0.00 chr4ptel1M 817426 817523 (182477) Charlie4a#DNA/hAT-Charlie 370 468 (40) m_b185s502i1 7177 chr4ptel1M 817426 TATTTCAATATAATTGCTGTCCTTTGTAATCCCTTGCATTTTATTTTATG 817475 v v iv i Charlie4a#DNA 370 TATTTCAATATAATTGGTTTCCTTTGTAATCCTATGTATTTTATTTTATG 419 chr4ptel1M 817476 CCTTTAAAAGCATGGTTCTCAG-AGGGGACGACTGGCTTCATGAGATTG 817523 v i vi v - v v iv iv i Charlie4a#DNA 420 CATTTAAAAACATTATTCTGAGAAGGGGTCCATAGGCTTCACCAGACTG 468 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 19.75 CpG sites = 7, Kimura (unadjusted) = 19.75 Transitions / transversions = 0.70 (7/10) Gap_init rate = 0.01 (1 / 97), avg. gap size = 1.00 (1 / 1) 593 18.42 1.75 0.00 chr4ptel1M 817635 817748 (182252) MER63D#DNA/hAT-Tip100 344 459 (602) m_b185s502i2 7178 chr4ptel1M 817635 ATTTCTGCCCCATAAATCAGCAAACACTACAGGTCAGGGCTTGATTTATT 817684 vii v iv i i ii MER63D#DNA/hA 344 ATTTACACCACGGAAATCGGCAAACGCTACAAATCAGGGCTTGATTTATT 393 chr4ptel1M 817685 GCTTTGTTGATGGTCTAGACTTGAAAAAGTGATGGAG--AATGGTCACAA 817732 i v i i -- v v i MER63D#DNA/hA 394 GTTTTGTTGATTGTCTAGACTTAAGAAAGTGATGGAGAAAATGTTAATAA 443 chr4ptel1M 817733 GTCAGCTTAAACTCAA 817748 vv v i MER63D#DNA/hA 444 TGCAGATTAAACTTAA 459 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 18.16 CpG sites = 12, Kimura (unadjusted) = 21.38 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.01 (1 / 113), avg. gap size = 2.00 (2 / 1) 408 10.45 0.00 0.00 chr4ptel1M 819566 819632 (180368) MER63D#DNA/hAT-Tip100 399 465 (596) m_b185s502i3 7179 chr4ptel1M 819566 GTTGATTGTCTAGACTTAATAAAGTGATGGAGAAGAAGTGGATAATGCAA 819615 v i v vi i MER63D#DNA/hA 399 GTTGATTGTCTAGACTTAAGAAAGTGATGGAGAAAATGTTAATAATGCAG 448 chr4ptel1M 819616 ATTAAGCTTAAAAGTGT 819632 i MER63D#DNA/hA 449 ATTAAACTTAAAAGTGT 465 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 11.31 CpG sites = 4, Kimura (unadjusted) = 11.31 Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.0 (0 / 0) 237 23.30 2.20 5.68 chr4ptel1M 819774 819864 (180136) C L2c_3end#LINE/L2 (222) 256 169 m_b185s601i5 7180 chr4ptel1M 819774 GAAGGGTCAGGAAAAGTTTTG-GGAGGATGTGAC-TCTGAGCTCAGCCCT 819821 ii i i i iv- v - v ? i C L2c_3end#LINE 256 GGGGGGTCAGGGAAGGCTTCCCGGAGGAGGTGACATCTGAGCTGAGNCTT 207 chr4ptel1M 819822 GAAGGAAGTGAAGTTGAAGATTGAGTCAGAGCTGAGGAGGGAG 819864 -- - -- i v v i ivvvi i C L2c_3end#LINE 206 GAAGGA--TG-AGT--AGGAGTTAGCCAGGTGGAAGGAGGGGG 169 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 28.83 CpG sites = 12, Kimura (unadjusted) = 28.83 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.08 (7 / 90), avg. gap size = 1.00 (7 / 7) 370 32.77 1.68 0.00 chr4ptel1M 820462 820580 (179420) C MIR3#SINE/MIR (34) 174 54 m_b185s601i6 7181 chr4ptel1M 820462 GAACC--AGAGGTCTTCCAGTCCAGCCTCCTCTTTCCACACATAGGGAAA 820509 i -- i v i i i v ii v ii C MIR3#SINE/MIR 174 GGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAA 125 chr4ptel1M 820510 CCGAGGCTCAGAGAAGTAATTTGATCCGGCCACGATCATGGAGGTAACAG 820559 i i i i vv iii v v i iiv v? iivi C MIR3#SINE/MIR 124 CTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTA 75 chr4ptel1M 820560 GCGGCCGAAGCGTGGCTAGGA 820580 i v iv v i i C MIR3#SINE/MIR 74 GTGGCAGAGCCGGGACTAGAA 54 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 46.24 CpG sites = 26, Kimura (unadjusted) = 46.24 Transitions / transversions = 2.00 (26/13) Gap_init rate = 0.01 (1 / 118), avg. gap size = 2.00 (2 / 1) 284 34.91 1.89 0.00 chr4ptel1M 820487 820592 (179408) C MIRc#SINE/MIR (118) 150 43 m_b185s601i7 7181 chr4ptel1M 820487 TCCTCTTTCCACACATAGGGAAACCGAGGCTCAGAGAAGTAATTTGATCC 820536 i v ii v ii i i v vv iii C MIRc#SINE/MIR 150 TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTT 101 chr4ptel1M 820537 GGCCACGATCATGGAGGTAACAGGCGGCCGAAGCGTGGCTAGGA--GGAG 820584 v v i iiv v ii i i v iv v i v i --vii C MIRc#SINE/MIR 100 GCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGG 51 chr4ptel1M 820585 TCCTCCTG 820592 i C MIRc#SINE/MIR 50 TCTTCCTG 43 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 49.41 CpG sites = 23, Kimura (unadjusted) = 49.41 Transitions / transversions = 1.64 (23/14) Gap_init rate = 0.01 (1 / 105), avg. gap size = 2.00 (2 / 1) 264 22.41 0.00 0.00 chr4ptel1M 822362 822419 (177581) L2a_3end#LINE/L2 382 439 (78) m_b185s601i8 7182 chr4ptel1M 822362 TGTTTTCCCCCATTAGAATGAAAGCACCTTGAGGACAGGGGCTGTTTTTT 822411 i i i v v v i i v v i L2a_3end#LINE 382 TGTCTCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTCT 431 chr4ptel1M 822412 TTTTTTTT 822419 v v L2a_3end#LINE 432 GTTTTGTT 439 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 26.75 CpG sites = 6, Kimura (unadjusted) = 26.75 Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0) 21 30.59 4.35 1.05 chr4ptel1M 822442 822533 (177467) (TC)n#Simple_repeat 1 95 (0) m_b185s252i7 7183 chr4ptel1M 822442 TCCCTCTCTCTCTCTCAC-CTCCCCATCCCCCTCT-TCCTTCTCATCTCT 822489 i v - i iv i i - ii - (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TCTCT 49 chr4ptel1M 822490 TTCTCCCCAGCTATCTCT-TTTCTCT-TGATTTTCTCTCCCTCCCT 822533 i i ivv v - i - vvi i i i (TC)n#Simple_ 50 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 95 Matrix = Unknown Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.05 (5 / 91), avg. gap size = 1.00 (5 / 5) 449 23.89 2.61 1.72 chr4ptel1M 823198 823312 (176688) MIRc#SINE/MIR 12 127 (141) m_b185s601i9 7184 chr4ptel1M 823198 GGCGCAGCGGATAGAGCCCCAGCC--GAAGTCAGGAGGACCTGAATTCAA 823245 i i v v ii v -- i i ii i MIRc#SINE/MIR 12 GGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGA 61 chr4ptel1M 823246 ATGTGATCTCAGACACTTTTCCTGGCTGTGTGACCCTGGGCAAGTCACTT 823295 i viviv v v --v i i MIRc#SINE/MIR 62 GTCCCGGCTCTGCCACTT--ACTAGCTGTGTGACCTTGGGCAAGTCACTT 109 chr4ptel1M 823296 AACCCCAATT-GCCTCAG 823312 i vv v- MIRc#SINE/MIR 110 AACCTCTCTGAGCCTCAG 127 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 26.73 CpG sites = 15, Kimura (unadjusted) = 29.20 Transitions / transversions = 1.25 (15/12) Gap_init rate = 0.04 (4 / 114), avg. gap size = 1.25 (5 / 4) 231 34.93 3.51 12.60 chr4ptel1M 823363 823647 (176353) C L2c_3end#LINE/L2 (16) 462 201 m_b185s601i10 7185 chr4ptel1M 823363 AGCACGTATTGAGCCCCTCCGAGCCGGACATTATGCTAAGTGCTGGA-AT 823411 i iv v v v --------- i i i i i- C L2c_3end#LINE 462 AACATTTATTGAGCGCCTACTA---------TGTGCCAGGCGCTGGGGAT 422 chr4ptel1M 823412 ACAAAAAGAAGCAAAAGAGGGCTCCTGCCCTCCAAGGGCTCAGAG----- 823456 i vi ii i v v ii v i i v ----- C L2c_3end#LINE 421 ACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAG 372 chr4ptel1M 823457 -GGAGGAGCCAG-TGTGCAAACATATA--TACAAAGCAAGCCAGAGAGGG 823502 - v -ii? i v i -- vi ii --- v i C L2c_3end#LINE 371 TGGAGGAGACAGACANGTAAACAGACAATTACAATACAAGTTA---ATGA 325 chr4ptel1M 823503 GGAGAGAGAAAACAATGAACTAGTCTATATGAAAAGCCATGTACGGGACA 823552 vi v vv--- i ii-- v v iiiiiv ---- i vv C L2c_3end#LINE 324 TAAGTGCT---ATAATGGG--AGTATAGACAGGGTGC----TATGGGAGC 284 chr4ptel1M 823553 ATTAAGAAAGACTAAATGGAGGGAAGGCACCGGAGGTCATAGGAGTTCAG 823602 ivi i i i --- ivv ivv ? viv i ---------i C L2c_3end#LINE 283 ACAGAGGAGGGC---ACCTAGACTAGNCTTGGGGGGTCA---------GG 246 chr4ptel1M 823603 GAGGATTTCCTGTAGAAGGTGGGATTTTAGGTGGGACTTGAGGAA 823647 i ii i v i iv i v v i ? i i C L2c_3end#LINE 245 GAAGGCTTCCCGGAGGAGGTGACATCTGAGCTGAGNCTTGAAGGA 201 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 47.83 CpG sites = 54, Kimura (unadjusted) = 49.47 Transitions / transversions = 1.64 (54/33) Gap_init rate = 0.13 (38 / 284), avg. gap size = 1.13 (43 / 38) 246 29.17 11.28 2.07 chr4ptel1M 823369 823501 (176499) C L2b_3end#LINE/L2 (22) 444 300 m_b185s601i11 7185 chr4ptel1M 823369 TATTGAGCCCCTCC---GAGCCGGACATTATGCTAAGTGCTGGA-ATACA 823414 i v v --- v i i ?i i i i i- C L2b_3end#LINE 444 TACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGGGATACA 395 chr4ptel1M 823415 AAAAGAAGCAAAAGAG----GGCTCCTGCCCTCCAAGGGCTCAGAG---- 823456 iviivi i i v ---- ii vvi i v ---- C L2b_3end#LINE 394 GCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGGAGCTCACAGTCTA 345 chr4ptel1M 823457 --GGAGGAGCCAG-TGTGCAAACATATATACAAAGCAAGCCAGAGAGG 823501 -- i v -ii i ? v i - i? --i v v C L2b_3end#LINE 344 GTGGGGGAGACAGACATGTAANCAGACA-ATNA--TAACCCAGAGTGG 300 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 35.94 CpG sites = 25, Kimura (unadjusted) = 39.99 Transitions / transversions = 1.92 (25/13) Gap_init rate = 0.07 (9 / 132), avg. gap size = 2.00 (18 / 9) 268 24.05 10.59 2.17 chr4ptel1M 823369 823453 (176547) C L2d2_3end#LINE/L2 (22) 533 442 m_b185s601i12 7185 chr4ptel1M 823369 TATTGAGCCCCTCC---GAGCCGGACATTATGCTAAGTGCTG----GAAT 823411 v v --- v vi i i i i i ---- i C L2d2_3end#LIN 533 TATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGTGGGGGAT 484 chr4ptel1M 823412 ACAAAAAGAAGCAAAAGA--GGGCTCCTGCCCTCCAAGGGCTCA 823453 -- i v --v ii v i i i C L2d2_3end#LIN 483 ACAAA--GAAGTATAAGACATGGTCCCTGCCCTCAAGGAGCTTA 442 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 28.19 CpG sites = 13, Kimura (unadjusted) = 29.96 Transitions / transversions = 1.86 (13/7) Gap_init rate = 0.06 (5 / 84), avg. gap size = 2.20 (11 / 5) 19 0.00 0.00 0.00 chr4ptel1M 823820 823843 (176157) (CCCT)n#Simple_repeat 1 24 (0) m_b185s252i8 7186 chr4ptel1M 823820 CCCTCCCTCCCTCCCTCCCTCCCT 823843 (CCCT)n#Simpl 1 CCCTCCCTCCCTCCCTCCCTCCCT 24 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 387 30.11 3.31 5.41 chr4ptel1M 824407 824557 (175443) L2c_3end#LINE/L2 330 477 (1) m_b185s601i13 7187 chr4ptel1M 824407 AATTTACCTTGTACATAGTTCCTTT---TGTC-ACTTCCCTCATCAGAGT 824452 i iiv - v iiv --- -iii ii ii v L2c_3end#LINE 330 AACTTGTATTGTA-ATTGTCTGTTTACNTGTCTGTCTCCTCCACTAGACT 378 chr4ptel1M 824453 GGGAATTTCTTGAGGGCAGGAGCTTT-TCTTTTTTAACTTCCTTTGTATA 824501 v ii i ii iv - v i ----i v L2c_3end#LINE 379 GTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCA----TCTTTGTATC 424 chr4ptel1M 824502 CATAGTGCATGGCACAGAACAGATCCTTAACAAATAATGTTTGTTGACTG 824551 vi i v v ii iiv i i --- v L2c_3end#LINE 425 CCCAGCGCCTGGCACATAGTAGGCGCTCAATA---AATGTTTGTTGAATG 471 chr4ptel1M 824552 ACTAAA 824557 v i L2c_3end#LINE 472 AATGAA 477 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 36.79 CpG sites = 29, Kimura (unadjusted) = 40.46 Transitions / transversions = 2.07 (29/14) Gap_init rate = 0.07 (11 / 150), avg. gap size = 1.18 (13 / 11) 194 24.05 16.46 0.00 chr4ptel1M 824980 825058 (174942) C L2d2_3end#LINE/L2 (51) 504 413 m_b185s601i15 7188 chr4ptel1M 824980 GCGTCAAGCACTA---GAGATACAAA--AGTC--AGA--TCGTCCGTGCC 825020 i ii i i i--- i -- v-- -- v v C L2d2_3end#LIN 504 GTGCTAGGCGCTGTGGGGGATACAAAGAAGTATAAGACATGGTCCCTGCC 455 chr4ptel1M 825021 CTCAAAGAGCCTATATTCTACT--ATAAGACA--ACATAGAC 825058 i i i v v --ivi -- i C L2d2_3end#LIN 454 CTCAAGGAGCTTACAATCTAGTTGGGGAGACAAGACATAAAC 413 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 28.20 CpG sites = 13, Kimura (unadjusted) = 30.08 Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.08 (6 / 78), avg. gap size = 2.17 (13 / 6) 235 28.99 8.70 0.00 chr4ptel1M 824980 825048 (174952) C L2c_3end#LINE/L2 (39) 439 365 m_b185s601i14 7188 chr4ptel1M 824980 GCGTCAAGCACTAGAGATACAAA----AGTCAGATC--GTCCGTGCCCTC 825023 i i i i i i ---- i v iv-- v C L2c_3end#LINE 439 GTGCCAGGCGCTGGGGATACAAAGATGAATAAGACACGGTCCCTGCCCTC 390 chr4ptel1M 825024 AAAGAGCCTATATTCTACTATAAGA 825048 i ii i v v iv i C L2c_3end#LINE 389 AAGGAGCTCACAGTCTAGTGGAGGA 365 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 36.21 CpG sites = 14, Kimura (unadjusted) = 38.71 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.03 (2 / 68), avg. gap size = 3.00 (6 / 2) 340 25.07 2.91 7.07 chr4ptel1M 825481 825583 (174417) MIRb#SINE/MIR 4 102 (166) m_b185s601i16 7189 chr4ptel1M 825481 AGAGGCACTTTGCTTGGTGAAACATTGGATAAAGGACAGACTTGGGAGTT 825530 i ---- v --- v v i v i i v i MIRb#SINE/MIR 4 AGGGGCA----GCGTGGTG---CAGTGGAAAGAGCACGGGCTTTGGAGTC 46 chr4ptel1M 825531 AGGAGAACCTGAGTTCAAATTCAGCCTCAGACACT---TAGTTGTGTGAC 825577 ivii i i i v v v v --- i MIRb#SINE/MIR 47 AGACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGAC 96 chr4ptel1M 825578 CCTAGG 825583 i i MIRb#SINE/MIR 97 CTTGGG 102 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 28.02 CpG sites = 14, Kimura (unadjusted) = 31.04 Transitions / transversions = 1.40 (14/10) Gap_init rate = 0.08 (8 / 102), avg. gap size = 1.25 (10 / 8) 343 27.67 4.35 2.56 chr4ptel1M 825497 825611 (174389) MIRc#SINE/MIR 10 126 (142) m_b185s601i17 7189 chr4ptel1M 825497 GTGAAACATTGGATAAAGGAC-AGACTTGGGAGTTAGGAGAACCTGAGTT 825545 ivi v v i v -i - i ii i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGG-AGTCAGGAAGACCTGGGTT 58 chr4ptel1M 825546 CAAATTCAGCCTCAGACACT---TAGTTGTGTGACCCTAGGAATAGCCCT 825592 i i i v v v v --- i i i v viv v MIRc#SINE/MIR 59 CGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACT 108 chr4ptel1M 825593 T-ACCGGACTGTAAGCCCCA 825611 - v-- v i i MIRc#SINE/MIR 109 TAACCT--CTCTGAGCCTCA 126 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 33.79 CpG sites = 17, Kimura (unadjusted) = 35.17 Transitions / transversions = 1.21 (17/14) Gap_init rate = 0.05 (6 / 114), avg. gap size = 1.33 (8 / 6) 226 25.97 6.10 6.10 chr4ptel1M 825589 825670 (174330) L2b_3end#LINE/L2 338 419 (47) m_b185s601i18 7190 chr4ptel1M 825589 CCCTTACCGGACTGTAAGCCCCATGAAGGCAGGAATCCTAGTTTCCCTAA 825638 ii ii i i i i i - v? i vi vi L2b_3end#LINE 338 CCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGA-CCGNGTCTGTCTTG 386 chr4ptel1M 825639 GCCTTTCACCTCT-----CCCAGGGTCTAGCCCAAAG 825670 ---- v ----- v i v i? L2b_3end#LINE 387 ----TTCACCGCTGTATCCCCAGCGCCTAGCACAGNG 419 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 32.41 CpG sites = 14, Kimura (unadjusted) = 34.55 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.07 (6 / 81), avg. gap size = 1.67 (10 / 6) 211 30.34 2.36 6.56 chr4ptel1M 825879 826005 (173995) L2c_3end#LINE/L2 354 475 (3) m_b185s601i19 7191 chr4ptel1M 825879 ATCTCTCTGTCCCCTCCTTTT--TTGATAATTTTGATGAGGATAGTGACT 825926 i? v i vi v--i - i vi ivv ii v i L2c_3end#LINE 354 ACNTGTCTGTCTCCTCCACTAGACTG-TGAGCTCCTTGAGGGCAGGGACC 402 chr4ptel1M 825927 GATAGGCTGACTC-TCTATCTATTCCATCAAGCTGCCTCTGCATGCAGCA 825975 - - v v i - v v i -- - - v- iii i L2c_3end#LINE 403 G-T-GTCTTATTCATCTTTGTATCCC--CA-GC-GCCTG-GCACATAGTA 445 chr4ptel1M 825976 AACACTTAATAAATGTTTATTGAACTGATG 826005 ii i i i ivi L2c_3end#LINE 446 GGCGCTCAATAAATGTTTGTTGAATGAATG 475 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 37.92 CpG sites = 23, Kimura (unadjusted) = 40.88 Transitions / transversions = 1.77 (23/13) Gap_init rate = 0.08 (10 / 126), avg. gap size = 1.10 (11 / 10) 215 24.45 0.00 2.22 chr4ptel1M 825959 826004 (173996) L2d2_3end#LINE/L2 507 551 (4) m_b185s601i20 7191 chr4ptel1M 825959 TGCCTCTGCATGCAGCAAACACTTAATAAATGTTTATTGAACTGAT 826004 - ii i ii i i i i vi L2d2_3end#LIN 507 TGCCT-TGCACACAGTAGGCGCTCAATAAATATTTGTTGATTTGAT 551 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 28.95 CpG sites = 10, Kimura (unadjusted) = 32.57 Transitions / transversions = 10.00 (10/1) Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1) 589 26.87 13.43 0.00 chr4ptel1M 826438 826638 (173362) C MIRc#SINE/MIR (2) 266 39 m_b185s601i21 7192 chr4ptel1M 826438 TACTAATAATGGCT-ATGTTTATACAGC-CCCCACCATGTGCCAGGTGC- 826484 v i?v - ii i i - iii vi v i v i i - C MIRc#SINE/MIR 266 TAATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCGCT 217 chr4ptel1M 826485 ---ACAATTATTATCTCACTGGATCCACACAACAACGCTGGGAGG----- 826526 --- vvi i v v v v ----- C MIRc#SINE/MIR 216 TTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGC 167 chr4ptel1M 826527 --GGCA---ACTGTCACTCTTATTTTACAGATGAGGACATTGAGGC---- 826567 -- --- i i i ii ii v i ---- C MIRc#SINE/MIR 166 AGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAG 117 chr4ptel1M 826568 -------AAGAACCTTGGCCTGGGTCTCAAAGCTAGTAAGTGTTTGAGGC 826610 ------- viv v vi v v viv v C MIRc#SINE/MIR 116 AGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCC 67 chr4ptel1M 826611 CAGATTTGAAGTCAGTTCTTCCTGTCTC 826638 vi i i vi v v C MIRc#SINE/MIR 66 GGGACTCGAACCCAGGTCTTCCTGACTC 39 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 32.48 CpG sites = 29, Kimura (unadjusted) = 34.00 Transitions / transversions = 1.16 (29/25) Gap_init rate = 0.04 (7 / 200), avg. gap size = 3.86 (27 / 7) 290 23.19 1.43 1.43 chr4ptel1M 826648 826717 (173283) C MIR#SINE/MIR (100) 162 93 m_b185s601i22 7193 chr4ptel1M 826648 GTGAGTGATATCGTTGTCTCCCATTTTAGTGATGAGAAAACTGAGGCACA 826697 ii iv ii i - vv i C MIR#SINE/MIR 162 GTAGGTACTATTATTATC-CCCATTTTACAGATGAGGAAACTGAGGCACA 114 chr4ptel1M 826698 GATC-CTTGAATAACTGGCCC 826717 vv-v i i v C MIR#SINE/MIR 113 GAGAGGTTAAGTAACTTGCCC 93 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 28.17 CpG sites = 9, Kimura (unadjusted) = 28.17 Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.03 (2 / 69), avg. gap size = 1.00 (2 / 2) 635 26.23 8.74 0.00 chr4ptel1M 826802 826984 (173016) MIRc#SINE/MIR 52 250 (18) m_b185s601i23 7194 chr4ptel1M 826802 CTGAGTTCCAGTGCCAGTCCTG-----TACAAG--AAGCGGCCTAAGG-A 826843 i v v i ii ----- v --iv i i vi - MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 101 chr4ptel1M 826844 AATCACTTAATGTCTCCTGACCTCAGATTTTTCATCTGTAAAATGGAGAA 826893 i iv ivii v ii i v MIRc#SINE/MIR 102 AGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGAT 151 chr4ptel1M 826894 AATCAT---TGC---AATTCCCTTTCAGGGTTGATGTGAGAATCAAACGA 826937 v --- ---ivi v iv v i i MIRc#SINE/MIR 152 AATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGA 201 chr4ptel1M 826938 GATCATATTTGTAAAAAGAC--TGTGAACCCCAAAGTGCTACATAAATG 826984 v i v i ivi -- i ivi i i MIRc#SINE/MIR 202 GATAATGTATGTGAAAGCGCTTTGTAAACTGTAAAGTGCTATACAAATG 250 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 31.57 CpG sites = 30, Kimura (unadjusted) = 33.25 Transitions / transversions = 1.67 (30/18) Gap_init rate = 0.03 (6 / 182), avg. gap size = 2.67 (16 / 6) 225 30.36 3.65 1.43 chr4ptel1M 827082 827218 (172782) C AmnL2-1#LINE/L2 (322) 2291 2152 m_b185s601i24 7195 chr4ptel1M 827082 GGGGATGGGGAGGAGGTGAGGGGTA--GTGCA-AAGGCAGGCTGGAGCGG 827128 - v i- i ii -- v i-i i ii C AmnL2-1#LINE/ 2291 GGGGA-GGGGAGTAGA-GAGAGACAAGGTCCGTGAGGTAGGCTGGAGCAA 2244 chr4ptel1M 827129 TATCATG-AGGGCTTTCAACTCAGGCCAGGGAGTTTAGAGTTG-ATTCTA 827176 vvi - i v vv i vv v i v ii - i i C AmnL2-1#LINE/ 2243 GTCCATGGAGGGTTTTAAAAACAAGGAAGGCAATTTTGAACTGGATCCTG 2194 chr4ptel1M 827177 GAGGCAATGGGGAGCCACTGAAGTTTACTGAGTAACAGGGTG 827218 i ivv v i vvi v vvi C AmnL2-1#LINE/ 2193 AAATGAATGGGGAGCCAGTGGAGTTGTTTGAGGATGGGGGTG 2152 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 38.46 CpG sites = 22, Kimura (unadjusted) = 39.69 Transitions / transversions = 1.16 (22/19) Gap_init rate = 0.04 (6 / 136), avg. gap size = 1.17 (7 / 6) 356 25.09 4.58 8.73 chr4ptel1M 827554 827684 (172316) MIRb#SINE/MIR 4 129 (139) m_b185s601i25 7196 chr4ptel1M 827554 AGAGGCACTTTGCTTGGTGAAACAGTGGATAAAGGACAGACTTGGGAGTT 827603 i ---- v --- v i v i i v i MIRb#SINE/MIR 4 AGGGGCA----GCGTGGTG---CAGTGGAAAGAGCACGGGCTTTGGAGTC 46 chr4ptel1M 827604 AGGAGAACCTGAGTTCAAATTCAGCCTCAGACACT---TAGTTGTATGAC 827650 ivii i i i v v v v --- i i MIRb#SINE/MIR 47 AGACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGAC 96 chr4ptel1M 827651 CCTAGGAATAGCCCTTACTGGA---CTGTAAGCCCCA 827684 i i v - --- vi --- v i i MIRb#SINE/MIR 97 CTTGGGCA-AG---TTACTTAACCTCTCTGAGCCTCA 129 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 28.68 CpG sites = 18, Kimura (unadjusted) = 31.12 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.10 (13 / 130), avg. gap size = 1.31 (17 / 13) 245 24.68 6.10 6.10 chr4ptel1M 827662 827743 (172257) L2b_3end#LINE/L2 338 419 (47) m_b185s601i26 7197 chr4ptel1M 827662 CCCTTACTGGACTGTAAGCCCCATGAAGGCAGGAATCCTAGTTTCCCTAA 827711 ii i i i i i i - v? i vi vi L2b_3end#LINE 338 CCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGA-CCGNGTCTGTCTTG 386 chr4ptel1M 827712 GCCTTTCACCTCT-----CCCAGGGTCTAGCCCAAAG 827743 ---- v ----- v i v i? L2b_3end#LINE 387 ----TTCACCGCTGTATCCCCAGCGCCTAGCACAGNG 419 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 30.12 CpG sites = 13, Kimura (unadjusted) = 32.17 Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.07 (6 / 81), avg. gap size = 1.67 (10 / 6) 203 28.77 4.71 5.95 chr4ptel1M 827839 828008 (171992) C L2#LINE/L2 (781) 2301 2134 m_b185s601i27 7188 chr4ptel1M 827839 ACTGGAGCTGAGGGCGCGGAGCCAGTGATTA-AGCCCTTGGGAAGTGGTG 827887 -- iv i v? vv v i- v-- v i v iv C L2#LINE/L2 2301 ACTGGA--TGAGATCACCNAGGGAGTGAGTGTAGA--TAGAGAAGAGAAG 2256 chr4ptel1M 827888 AGATCACCAAGAC-GATCCCTCAG-----CCAA-GTCCACAGATAGGGGT 827930 i - v i - v vi ----- - i? v i v v C L2#LINE/L2 2255 AGGTC-CAAGGACTGAGCCCTGGGGCACTCCAACGTTNAGAGGTCGGGGA 2207 chr4ptel1M 827931 GCAATATGGATGATATTGTGTCAAAGGGGACTAAGAAGTAGAGATCAGAG 827980 -- iv v vviv --- i i v v ii v C L2#LINE/L2 2206 G--ATGAGGAGGAACCAG---CAAAGGAGACTGAGAAGGAGCGGCCAGTG 2162 chr4ptel1M 827981 GGACAGGAAGACAACCAGGAGGGAGTGG 828008 i ii i v i v C L2#LINE/L2 2161 AGGTAGGAGGAAAACCAGGAGAGTGTGG 2134 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 37.10 CpG sites = 21, Kimura (unadjusted) = 37.10 Transitions / transversions = 0.84 (21/25) Gap_init rate = 0.08 (14 / 169), avg. gap size = 1.29 (18 / 14) 15 16.14 0.00 0.00 chr4ptel1M 828184 828212 (171788) (TTC)n#Simple_repeat 1 29 (0) m_b185s252i9 7198 chr4ptel1M 828184 TTCTCCTTCTTCTTCTTCTTTTTTTTTTT 828212 i i i i (TTC)n#Simple 1 TTCTTCTTCTTCTTCTTCTTCTTCTTCTT 29 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 12 29.56 0.00 5.00 chr4ptel1M 828411 828473 (171527) (ACAAAAA)n#Simple_repeat 1 60 (0) m_b185s252i10 7199 chr4ptel1M 828411 ACAAGAAAAATCAAATCAAAAAGGAAAAATGAAAAAAGAAAATAAAATGT 828460 - vvv v iv vv v - v -iv (ACAAAAA)n#Si 1 ACAA-AAAACAAAAAACAAAAAACAAAAAACAAAAAACAAAA-AACA-AA 47 chr4ptel1M 828461 AAGCAAACAACAA 828473 i v (ACAAAAA)n#Si 48 AAACAAAAAACAA 60 Matrix = Unknown Transitions / transversions = 0.27 (3/11) Gap_init rate = 0.05 (3 / 62), avg. gap size = 1.00 (3 / 3) 17 11.47 5.26 0.00 chr4ptel1M 828415 828452 (171548) (GAAAAAT)n#Simple_repeat 1 40 (0) m_b185s252i11 7199 chr4ptel1M 828415 GAAAAAT--CAAATCAAAAAGGAAAAATGAAAAAAGAAAA 828452 --v v v v (GAAAAAT)n#Si 1 GAAAAATGAAAAATGAAAAATGAAAAATGAAAAATGAAAA 40 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.03 (1 / 37), avg. gap size = 2.00 (2 / 1) 12 18.88 7.14 0.00 chr4ptel1M 828417 828458 (171542) (AAAAT)n#Simple_repeat 1 45 (0) m_b185s252i12 7199 chr4ptel1M 828417 AAAATCAAATCAAA-AAGGAAAAAT-GAA-AAAAGAAAATAAAAT 828458 v v - iiv -i - v (AAAAT)n#Simp 1 AAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAAT 45 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.07 (3 / 41), avg. gap size = 1.00 (3 / 3) 704 28.32 5.57 1.58 chr4ptel1M 828474 828778 (171222) C L1ME3_3end#LINE/L1 (592) 317 1 m_b185s551i1 7200 chr4ptel1M 828474 CAGAATGGTTGAATCAGTTCACAA-CTCACCAACAATGCATTGGTGTCCC 828522 i i v i i i v- i i i vi v i C L1ME3_3end#LI 317 CAAAGTGGTTGTACCAATTTACACTCCCACCAGCAATGTATGAGAGTTCC 268 chr4ptel1M 828523 AGTTTTCCCACATCCCTTCCAACATTTATCATTGTCTTTCCCTGTCATCT 828572 vii iiv i ivi vv ii v v i C L1ME3_3end#LI 267 AGTTGCTCCACATCCTCGCCAACACTTGGTATTGTCAGTCTTTTTAATTT 218 chr4ptel1M 828573 TAGCCAATCTGAGAGGTGTGTAGTAGTGTCTCAGAGTTTTCTTAATTTGC 828622 v ivi i i vv vv i C L1ME3_3end#LI 217 TAGCCATTCTGGTGGGTGTGTAGTGGTATCTCATTGTGGTTTTAATTTGC 168 chr4ptel1M 828623 ATTTCTCTGATCAATAATGATTTGGAGCATCTTTTTATATG---ATTGG- 828668 i v v v v i i --- - C L1ME3_3end#LI 167 ATTTCCCTGATGACTAATGATGTTGAGCACCTTTTCATATGCTTATTGGC 118 chr4ptel1M 828669 -----AAATAGTTTAATTTCTGAAAATTGTCTCGTCATATCCTTTGACTA 828713 -----ii vii vv v i-- i vv vi i v i C L1ME3_3end#LI 117 CATTTGGATATCCTCTTTTGTGAAG--TGCCTGTTCAAGTCTTTTGCCCA 70 chr4ptel1M 828714 ----TCAATTGGAGAATGGTTTGAA---TTCTTATAAATTTGAGTCAATT 828756 ---- i ---i v vv--- vi vivv i C L1ME3_3end#LI 69 TTTTTTAATTGG---GTTGTTTGTCTTTTTCTTATTGATTTGTAGGAGTT 23 chr4ptel1M 828757 CTCTCTAAATTTTAGAAATGAG 828778 i v v i i v i C L1ME3_3end#LI 22 CTTTATATATTCTGGATACGAG 1 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 35.17 CpG sites = 46, Kimura (unadjusted) = 36.22 Transitions / transversions = 1.18 (46/39) Gap_init rate = 0.04 (11 / 304), avg. gap size = 2.00 (22 / 11) 766 26.56 3.32 0.00 chr4ptel1M 828474 828714 (171286) C L1ME5_3end#LINE/L1 (624) 317 69 m_b185s551i0 7200 chr4ptel1M 828474 CAGAATGGTTGAATCAGTTCACAA-CTCACCAACAATGCATTGGTGTCCC 828522 i v i ii v- i i i vi v i C L1ME5_3end#LI 317 CAGAATGGCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCC 268 chr4ptel1M 828523 AGTTTTCCCACATCCCTTCCAACATTTATCATTGTCTTTCCCTGTCATCT 828572 vi ? i iiv i iv i ivv ii v v i C L1ME5_3end#LI 267 TATNTCCCCACATCCTCGCCAACACTTGGCATTATCCAGCTTTCTAATTT 218 chr4ptel1M 828573 TAGCCAATCTGAGAGGTGTGTAGTAGTGTCTCAGAGTTTTCTTAATTTGC 828622 v i i v iv ii i vv v i C L1ME5_3end#LI 217 TTGCCAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGC 168 chr4ptel1M 828623 ATTTCTCTGATCAATAATGATTTGGAGCATCTTTTTATATGATTGGAAAT 828672 i v v v i i v vv ii C L1ME5_3end#LI 167 ATTTCTCTGATTACTAATGAGTTTGAGCATCTCTTCATATGCTTGTTAGC 118 chr4ptel1M 828673 ------AGTTTAAT-TTCTGAAAATTGTCTCGTCATATCCTTTGACTAT 828714 ------i vv - v i vv v i C L1ME5_3end#LI 117 CTTTCGGGTTTCCTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCCAT 69 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 32.88 CpG sites = 35, Kimura (unadjusted) = 33.51 Transitions / transversions = 1.21 (35/29) Gap_init rate = 0.01 (3 / 240), avg. gap size = 2.67 (8 / 3) 756 32.62 4.60 2.85 chr4ptel1M 828640 829879 (170121) C L1M5_orf2#LINE/L1 (0) 3294 2034 m_b185s551i2 7200 chr4ptel1M 828640 TGATTTGGAGCATCTTTTTATATG---ATTGG------AAATAGTTTAAT 828680 ?v v i i --- ------i? vi vv C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr4ptel1M 828681 TTCTGAAAATTGTCTCGTCATATCCTTTGACTAT----CAATTGGAGAAT 828726 v i-- vv vi i v i ----?v i--- C L1M5_orf2#LIN 3244 TTGTGAAG--TGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGG---T 3200 chr4ptel1M 828727 GGTTTGAATTCTTATAAATTTGAGTC-----AATTCTCTCTAAATTTTAG 828771 v vv i ? v -- ? i----- i i v v i i C L1M5_orf2#LIN 3199 TGTTTGTCTTTTTNTTA--TTGANTTGTAGGAGTTCTTTATATATTCTGG 3152 chr4ptel1M 828772 AAATGAGGCCTTTAGCAGAAATTTTGAATGCAAAAATATTTTACTAGTTT 828821 v i v iv v v vv?v v v i v i ? i C L1M5_orf2#LIN 3151 ATACGAGTCCTTTGTCAGATATATGTNTTGCAAATATTTTCTCCCANTCT 3102 chr4ptel1M 828822 ATTGCTTCCTTCCTAATCTTGTCTGCATTAGTTTTTTTCC------AACT 828865 i v v i ii v i v ivi iv - i vv?------ v C L1M5_orf2#LIN 3101 GTGGCTTGCCTTTTCATTTTCTTAACGGT-GTCTTTTGANGAGCAGAAGT 3053 chr4ptel1M 828866 TTTTAACTT-AACATAATCAAAATCATATAGTTTGTGTTCAATAATGAAT 828914 i -i ii? i v v i vv v v v iv ii v?i C L1M5_orf2#LIN 3052 TTTTAATTTTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGGTTNGT 3003 chr4ptel1M 828915 TCCAATT----CTTCTTTGCCACAAATTCCTTCTTTCTCCACACATCTGA 828960 v ivv ---- i v i-- v iii v i v?i - vi vvi C L1M5_orf2#LIN 3002 GCTTTTTGTGTCCTGTTTA--AGAAATCTTTGCCTANCCCA-AGGTCACG 2956 chr4ptel1M 828961 GAGGTAAACTATCCTTTGTC--CTTCTAG---TTTACTTAAAATATCATT 829005 i i --i v v i-- --- --- v i v i ?i C L1M5_orf2#LIN 2955 AAGATA--TTCTCCTATGTTTTCTTCTAGAAGTTT---TATAGTTTTANC 2911 chr4ptel1M 829006 CTTTATGTCTAGATCATA-AACCCATTTCAACTTTGTATTGAT-TATAGT 829053 i ii i i - -i i i ?i v vi v vi - i C L1M5_orf2#LIN 2910 TTTTACATTTAGGTC-TATGATCCATCTNGAATTAATTTTTGTGTATGGT 2862 chr4ptel1M 829054 ATTAGGTATGGGTCAATGCCTAGTTTCTGCCATACTAGCT-TCCAATTTT 829102 i v v i v?iii v i v - i v - v C L1M5_orf2#LIN 2861 GTGAGGTAGGGGTCGAGNTTCATTTTTTTCCATA-TGGATATCCAATTGT 2813 chr4ptel1M 829103 CTCAGAAGTTTTTGTCAAATGGTGAATTCTTATCCCAAAAGCTGGGGT-C 829151 ii v viv ii vi vvv i vi ---- iiv - C L1M5_orf2#LIN 2812 TCCAGCACCATTTGTTGAAAAGACTATCCTTTCCCCA----CTGAATTGC 2767 chr4ptel1M 829152 TTTGGG---TTTGTCAAACACTAGATTACTATAGTCAT-TGA--CTATTT 829195 ? v--- v ii i? v? i vvii - i-- C L1M5_orf2#LIN 2766 NTTGGCACCTTTGTCAAAAATCAANTGNCCATATATGTGTGGGTCTATTT 2717 chr4ptel1M 829196 TGTCTGGTGAGCCTAACCTATTCCACTGATTGACTACTCTATTGCTTA-G 829244 --- vvvvi vi i i iv i vv i- - C L1M5_orf2#LIN 2716 ---CTGGACTCTCTATTCTGTTCCATTGATCTATTTGTCTATC-CTTACG 2671 chr4ptel1M 829245 CCAATACCAAATGGTTTTAATGACCGCTGCTTTATAATATAGTTTT-AGG 829293 v iv i i v i iv - i - ?i C L1M5_orf2#LIN 2670 CCAATACCACACTGTCTTGATTACTGTAGCTTTATAATA-AGTCTTGANA 2622 chr4ptel1M 829294 TCTGGCCCAGCAAGGTCACCTTCA--TTTGC-ATTTTGTTTCATTAATTC 829340 ? ivvv i v--- i -- i-v i v v-i v C L1M5_orf2#LIN 2621 TCNGGTAGTGTAAGT---CCTCCAACTTTGTTCTTCTTTTTCAA-GATTG 2576 chr4ptel1M 829341 CCTTGAA-ATTCTTGACCTTTTGTTCTTCCAGATGAACTTTA---TTATT 829386 ii iv- ? ii i ivi v i i --- i vi C L1M5_orf2#LIN 2575 TTTTGGCTATTCTNGGTCCTTTGCATTTCCATATAAATTTTAGAATCAGC 2526 chr4ptel1M 829387 TTTTCTAAATCTGTAATATAGTTTTTGGGGAGTCTGATTGGTATAGCGTT 829436 v v vv ii v v iii viv v i v v i C L1M5_orf2#LIN 2525 TTGTCAATTTCTACAAAAAAACCTGCTGGGATTTTGATTGGGATTGCATT 2476 chr4ptel1M 829437 GAATAAGTAGATGTATTTAGGTAGTATTGTCATTTTTATTATATTTGCTT 829486 vvi vv i v v v i ? iv viv i C L1M5_orf2#LIN 2475 GAATCTATAGATCAATTTGGGGAGAATTGACATCTTNACAATATTGAGTC 2426 chr4ptel1M 829487 GGCCTACCCATGAACAATTG--ATATTTTTCCAACTGATTAGAGCTGAGG 829534 vv v i -- -- i i vi iv iv vvvv C L1M5_orf2#LIN 2425 TTCCAATCCATGAACA--TGGTATATCTCTCCATTTATTTAGGTCTTCTT 2378 chr4ptel1M 829535 TTATTTGTGTGGAAAGTGTTTTGTGGTGGTGCTCATATAGTTCCTGACTT 829584 v v v viiv i i vv vvvii ? v i vviv C L1M5_orf2#LIN 2377 TAATTTCTCTCAGCAATGTTTTGTAGTTTTCAGTGTANAGGTCTTGCACA 2328 chr4ptel1M 829585 TCCCTCGGCAGATGGATTCCCAAATATTTTATATTATCAACAGTTATTTT 829634 ?ii i vi vv i i ? i v ivivv i v C L1M5_orf2#LIN 2327 TNTTTTGTTAGATTTATTCCTAAGTATTTNATGTTTTTTGATGCTATTGT 2278 chr4ptel1M 829635 ACATGGAATTTCTCTTTGTATCTC--TTGCTGCTGGACTTTGTTGGTGAT 829682 v v vi i ?iv i -- v iiv v -- v ii C L1M5_orf2#LIN 2277 AAATGGTATTGTTTTTNAAATTTCATTTTCCAATTG--TTTGTTGCTAGT 2230 chr4ptel1M 829683 GTATAAAAATGCTGATGATTTATGTGGATTTATTTTGTATCCTGCAACTT 829732 i i i viv v iv v ii ? i i C L1M5_orf2#LIN 2229 ATATAGAAATACAATTGATTTTTGTATATTGACCTTGTATCCNGCGACCT 2180 chr4ptel1M 829733 TGCTAAAGTTGTGAATTATTTCTAATAGGTTTTTTAGTTGATTCTCTAGG 829782 v iiivv v i v ? - v i ? C L1M5_orf2#LIN 2179 TGCTAAATTCACTTATTAGTTCTAGTAGTTTNTTT-GTAGATTCTTTNGG 2131 chr4ptel1M 829783 GTAATCTAAGTATACCATCATATCATCTGCAAAGAGTGATAATTTGGTTT 829832 i vv v ? v i i v i? i i vi C L1M5_orf2#LIN 2130 ATTTTCTACGTANACAATCATGTCATCTGCGAATAANGACAGTTTTATTT 2081 chr4ptel1M 829833 CCTCCTTATCTCTTCTAATTCCTTTAATCTCCTTTTCTTCTGTTATT 829879 i vi vv ii v v v i i viv C L1M5_orf2#LIN 2080 CTTCCTTTCCAATCTTTATGCCTTTTATTTCTTTTTCTTGCCTTATT 2034 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 44.18 CpG sites = 198, Kimura (unadjusted) = 45.09 Transitions / transversions = 1.02 (198/195) Gap_init rate = 0.05 (60 / 1239), avg. gap size = 1.55 (93 / 60) 1010 32.90 2.55 2.19 chr4ptel1M 829008 829871 (170129) C L1P4_orf2#LINE/L1 (386) 2908 2042 m_b185s551i3 7200 chr4ptel1M 829008 TTATGTCTAGATCATAAACCCATTTCAACTTTGTATTGAT-TATAGTATT 829056 ii i ii v v i i ii v vi v vi - i ivv C L1P4_orf2#LIN 2908 TTACATTTAAGTCTTTAATCCATCTTGAGTTAATTTTTGTATATGGTGAA 2859 chr4ptel1M 829057 AGGTATGGGTC-AATGCCTAGTTTCTGCCATACTAGCT-TCCAATTTTCT 829104 v - i vi vvvi - - i -v i v i C L1P4_orf2#LIN 2858 AGGTAGGGGTCCAGTTTCATTCTTCTGC-ATA-TGGCTAGCCAGTTATCC 2811 chr4ptel1M 829105 CAGAAGTTTTTGTCAAATGGTGAATTCTTATCCCAAAAGCTGGGGTCT-T 829153 v viv i ii i v i i - v vv vivv i - C L1P4_orf2#LIN 2810 CAGCACCATTTATTGAATAGGGAGTCCTT-TCCCCATTGCTTATTTTTGT 2762 chr4ptel1M 829154 TGGGTTTGTCAAACACTAGATTACTATAGTCAT-TGACTATTTTGTCTGG 829202 i iv i v ii vii i vii -i i - v v C L1P4_orf2#LIN 2761 CGACTTTGTCGAAGATCAGATGGTTGTAGGTGTGCGGCT-TTATTTCTGG 2713 chr4ptel1M 829203 TGAGCCTAACCTATTCCACTGATTGACTACTCTATTGCTTAGCCAATACC 829252 vvvvi vi i i i iv ivvv i vi vvi i C L1P4_orf2#LIN 2712 GTTCTCTATTCTGTTCCATTGGTCTATGTGTCTGTTTTTGTACCAGTACC 2663 chr4ptel1M 829253 AAATGGTTTTAATGACCGCTGCTTTATAATATAGTTTTAGGTCTGGCCCA 829302 viiv ii v i iv i i i v i v i--- C L1P4_orf2#LIN 2662 ATGCTGTTTTGGTTACTGTAGCCTTGTAGTATAGTTTGAAGTCGGGT--- 2616 chr4ptel1M 829303 GCAAGGTCA--CCTTCATTTGCATTTTGTTTCATTA--ATTCCCTTGAA- 829347 -- v v -- i ivi vii i v vv -- v i iv- C L1P4_orf2#LIN 2615 --AATGTGATGCCTCCGGCTTTGTTCTTTTTGCTTAGGATTGCTTTGGCT 2568 chr4ptel1M 829348 ATTCTTGACCTTTTGTTCTTCCAGATGAACTTTA---TTATTTTTTCTAA 829394 vv vi v vv v i --- vi C L1P4_orf2#LIN 2567 ATTCGGGCTCTTTTTTGGTTCCATATGAATTTTAGAATAGTTTTTTCTAA 2518 chr4ptel1M 829395 ATCTGT--AATATAGTTTTTGGGGAGTCTGATTGGTATAGCGTTGAATAA 829442 v -- v iiiv -- v i v v vv C L1P4_orf2#LIN 2517 TTCTGTGAAAAATGACGTT--GGTAGTTTGATAGGAATAGCGTTGAATCT 2470 chr4ptel1M 829443 GTAGATGTATTTAGGTAGTATTGTCATTTTTATTATATT--TGCTTGGCC 829490 vvv i i v i v iv -- v -- C L1P4_orf2#LIN 2469 GTAGATTGCTTTGGGCAGTATGGCCATTTTAACGATATTGATTCTT--CC 2422 chr4ptel1M 829491 TACCCATGAACAATTGATATTTTTCCAACTGATTAGAGCTGAGGTTATTT 829540 v i i vvvi i vi v iviv vvvv? v C L1P4_orf2#LIN 2421 AATCCATGAGCATGGAATGTTTTTCCATTTGTTTGTGTCATCTNTGATTT 2372 chr4ptel1M 829541 GTGTGGAAAGTGTTTTGTGGTGGTGCTCATATAGTTCCTGACTTTCCCTC 829590 v v viiv i vv v ii v v i vvvii i v C L1P4_orf2#LIN 2371 CTTTCAGCAGTGTTTTGTAGTTCTCCTTGTAGAGATCTTTCACCTCCTTG 2322 chr4ptel1M 829591 GGCAGATGGATTCCCAAATATTTTATATTATCAACAGTTATTTTACATGG 829640 vi v i ii v v iviii i v v C L1P4_orf2#LIN 2321 GTTAGATGTATTCCTAGGTATTTTATTTTTTTTGTGGCTATTGTAAATGG 2272 chr4ptel1M 829641 AATTTC--TCTT--TGTATCTCTT-GCTGCTGGACTTTGTTGGTGATGTA 829685 i v -- -- v iv i- -- i v i --- C L1P4_orf2#LIN 2271 GATTGCGTTCTTGATTTGGCTCTCAGCT--TGAACGTTATTGGTG---TA 2227 chr4ptel1M 829686 TAAAAATGCTGATGATTTATGTGGATTTATTTTGTATCCTGCAACTTTGC 829735 i iv v iv v v i C L1P4_orf2#LIN 2226 TAGAAATGCTACTGATTTTTGTACATTGATTTTGTATCCTGAAACTTTAC 2177 chr4ptel1M 829736 TAAAGTTGTGAATTATTTCTAATAGGTTTTTTAGTTGATTCTCTAGGGTA 829785 i i vv i v iv - ii i iv v i v C L1P4_orf2#LIN 2176 TGAAGTCGTTTATCAGTTCTAGGA-GCCTTTTGGCGGAGTCTTTAGGGTT 2128 chr4ptel1M 829786 ATCTAAGTATACCATCATATCATCTGCAAAGAGTGATAATTTGGTTTCCT 829835 v i vv i v i v i ii i C L1P4_orf2#LIN 2127 TTCTAGGTATAGAATCATATCGTCAGCGAAGAGAGATAGTTTGACTTCTT 2078 chr4ptel1M 829836 CCTTATCTCTTCTAATTCCTTTAATCTCCTTTTCTT 829871 i vi v ivi v v i i i C L1P4_orf2#LIN 2077 CTTTTCCTATTTGGATGCCTTTTATTTCTTTCTCTT 2042 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 41.97 CpG sites = 138, Kimura (unadjusted) = 44.03 Transitions / transversions = 0.99 (138/140) Gap_init rate = 0.04 (32 / 863), avg. gap size = 1.28 (41 / 32) 428 23.14 3.97 3.97 chr4ptel1M 830007 830132 (169868) C MIR1_Amn#SINE/MIR (59) 171 46 m_b185s601i28 7201 chr4ptel1M 830007 AAGGAGGTGGCCATTTCCTTCTCCAGCTCATTTTACAAATGAGGAAACTG 830056 -- vi v v v ---i i C MIR1_Amn#SINE 171 AAGGAGGT--CAGTATCATTATCC---CCATTTTACAGATGAGGAAACTG 127 chr4ptel1M 830057 AGG--CAGA---ATAAAGTGACTGGGCCAGGGTCACACAGCCATTATATG 830101 -- ---i ? v v i ? ?ivi?vi C MIR1_Amn#SINE 126 AGGCNCAGAGAGGTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNAGTG 77 chr4ptel1M 830102 TCTGAGGCCAGATTTACATTCAGGCCTTCTG 830132 v v v vi ? ?iv ii i i i C MIR1_Amn#SINE 76 GCAGAGCCGGGANTNGAACCCAGGTCTCCCG 46 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 28.59 CpG sites = 15, Kimura (unadjusted) = 29.82 Transitions / transversions = 1.15 (15/13) Gap_init rate = 0.06 (7 / 125), avg. gap size = 1.43 (10 / 7) 454 20.74 5.61 0.89 chr4ptel1M 830033 830139 (169861) C MIR3#SINE/MIR (63) 145 34 m_b185s601i29 7201 chr4ptel1M 830033 CTCATTTTACAAATGAGGAAACTGAGG--CAGA---ATAAAGTGACTGGG 830077 i -- ---i i v v C MIR3#SINE/MIR 145 CTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGC 96 chr4ptel1M 830078 CCAGGGTCACACAGCCA-TTATATGTCTGAGGCCAGATTTACATTCAGGC 830126 i ? - -i v v v vi i viv ii i C MIR3#SINE/MIR 95 CCAAGGTCACACAGCNAGTTA-GTGGCAGAGCCGGGACTAGAACCCAGGT 47 chr4ptel1M 830127 CTTCTGTCTACCA 830139 i v v C MIR3#SINE/MIR 46 CTCCTGACTCCCA 34 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 24.85 CpG sites = 12, Kimura (unadjusted) = 24.85 Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.04 (4 / 106), avg. gap size = 1.75 (7 / 4) 218 31.64 5.69 2.36 chr4ptel1M 830176 830298 (169702) MIRc#SINE/MIR 19 145 (123) m_b185s601i30 7202 chr4ptel1M 830176 TGAGAAGGGTATTGAAGGAAGAGG-AGGATGACCTGCCTTTGAATACTG- 830223 ii i i i i vvvi v- v vv i i v i - MIRc#SINE/MIR 19 TGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGG 68 chr4ptel1M 830224 -TCTGCCAAGACCGCCTTGGTGTCTCCTCTTGGATGAATCTCTTGAACAC 830272 - --- ivv v v v vvi iii i v i v v MIRc#SINE/MIR 69 CTCTGCC---ACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 chr4ptel1M 830273 TCTGTG-CTCA-TTTCATGATC--TAAAAT 830298 v - - v v -- MIRc#SINE/MIR 116 TCTGAGCCTCAGTTTCCTCATCTGTAAAAT 145 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 38.73 CpG sites = 17, Kimura (unadjusted) = 41.42 Transitions / transversions = 0.81 (17/21) Gap_init rate = 0.07 (9 / 122), avg. gap size = 1.11 (10 / 9) 267 34.68 3.96 2.94 chr4ptel1M 830821 830921 (169079) C L2c_3end#LINE/L2 (11) 467 366 m_b185s601i31 7203 chr4ptel1M 830821 CAATAAGCACTTATCAGGTGCTTACTGTGTGTCACACAGCGAGGATGCAA 830870 i i i iii i i i i vi ivi i i C L2c_3end#LINE 467 CAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGATACAA 418 chr4ptel1M 830871 AGAAAGGCAAAGGACAGTTCCTGTTTCCATTAAGTAG-GCAC---TTAAT 830916 viiii iiv i i --- v i v -v ---i i C L2c_3end#LINE 417 AGATGAATAAGACACGGTCCCTG---CCCTCAAGGAGCTCACAGTCTAGT 371 chr4ptel1M 830917 GAAGG 830921 i C L2c_3end#LINE 370 GGAGG 366 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 45.74 CpG sites = 27, Kimura (unadjusted) = 52.56 Transitions / transversions = 3.86 (27/7) Gap_init rate = 0.05 (5 / 100), avg. gap size = 1.40 (7 / 5) 390 26.83 8.93 4.57 chr4ptel1M 831044 831211 (168789) MIR#SINE/MIR 3 177 (85) m_b185s601i32 7204 chr4ptel1M 831044 AGTAGTAACACTGGTGGCTCA-AGCACCAGACTTGGAGCCCTAAAGT-CT 831091 - i - i i v - vi vii -- i v - i MIR#SINE/MIR 3 AGTA-TAGCA-TAGTGGTTAAGAGCACGGGCTCTGGAGCC--AGACTGCC 48 chr4ptel1M 831092 TGAGTTCAAATCCAG------CCACT--CT-GCTACGTGGCTCTGGGAAA 831132 i i v ------ -- - ii i ii v MIR#SINE/MIR 49 TGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 98 chr4ptel1M 831133 GTCA----ACTTCTGTCTACCTCAGTTTCCTGCTCTGTGCAATGATAAAA 831178 i ---- i v v i vv iv ----ii MIR#SINE/MIR 99 GTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATG----GG 144 chr4ptel1M 831179 GAAAGGAACAGTCCCTCTCTCTTGGATTTGTTG 831211 v iv i v vi v i iv MIR#SINE/MIR 145 GATAATAATAGTACCTACCTCATAGGGTTGTTG 177 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 33.21 CpG sites = 26, Kimura (unadjusted) = 34.19 Transitions / transversions = 1.53 (26/17) Gap_init rate = 0.08 (14 / 167), avg. gap size = 1.64 (23 / 14) 539 31.61 5.50 1.32 chr4ptel1M 832107 832324 (167676) C MIRc#SINE/MIR (25) 243 17 m_b185s601i33 7205 chr4ptel1M 832107 ATGACATTTCAAAGTTTGGAAATCACTTT-ATATACATGACCTTATTCCT 832155 ii i i v iv v i - i v i i ivv C MIRc#SINE/MIR 243 ATAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATCTCATTTGA 194 chr4ptel1M 832156 ACCTCACACATAATGCTG-------GGCCCATCAACTATTA--GACGCCA 832196 v - i iv ------- vviv iv --iv v C MIRc#SINE/MIR 193 TCCTCACA-ACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCA 145 chr4ptel1M 832197 TTTCATAGATGAAGAGATGGAGGCTTCTGAAGGCTAA-TGTCTTGCCCTG 832245 i i i i iv ivvii i - v -- C MIRc#SINE/MIR 144 TTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCC-- 97 chr4ptel1M 832246 ATAATTCCCCAGCTCGGAAGCGGT-GAGATCGCTTTGGAAGCCAGGTCTT 832294 vii iv v v v i i- viv vvi v v C MIRc#SINE/MIR 96 AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTT 47 chr4ptel1M 832295 CCTGGCTCCAAGTTTAGCTCTCTGTTCTCT 832324 i ii iv v i v C MIRc#SINE/MIR 46 CCTGACTCCAAGTCCAGTGCTCTTTCCACT 17 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 40.29 CpG sites = 36, Kimura (unadjusted) = 41.89 Transitions / transversions = 1.12 (36/32) Gap_init rate = 0.04 (8 / 217), avg. gap size = 1.88 (15 / 8) 253 24.14 5.17 0.00 chr4ptel1M 832361 832418 (167582) L2d_3end#LINE/L2 455 515 (1) m_b185s601i34 7206 chr4ptel1M 832361 GCCTAGAATAGTGCTAGACATCTGGTAGACACT---TAAATGCTTTTTGA 832407 v i iii iv i i i --- i v L2d_3end#LINE 455 GCCTAGCACAGTGCTGAGCACATAGTAGGCGCTCAATAAATACTTGTTGA 504 chr4ptel1M 832408 TTGGTAGATTG 832418 i v L2d_3end#LINE 505 TTGATTGATTG 515 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 27.84 CpG sites = 10, Kimura (unadjusted) = 30.41 Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.02 (1 / 57), avg. gap size = 3.00 (3 / 1) 23 25.02 4.26 3.16 chr4ptel1M 832857 832950 (167050) (GAGG)n#Simple_repeat 1 95 (0) m_b185s252i13 7207 chr4ptel1M 832857 GAGGGATGGAGAGGAAGGCAGGGAAGGGGAGGGGGA-GGAAGG-GGGAGG 832904 - - i v i i i i - i - (GAGG)n#Simpl 1 GAGGGA-GG-GAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGG 48 chr4ptel1M 832905 AAAAAAGGG-GCAAGGAAAGGTAGGGA-GGAGAGAGAGAGAGAGGGAG 832950 i iii - vi -i v - i i i (GAGG)n#Simpl 49 GAGGGAGGGAGGGAGG-GAGGGAGGGAGGGAGGGAGGGAGGGAGGGAG 95 Matrix = Unknown Transitions / transversions = 5.00 (15/3) Gap_init rate = 0.08 (7 / 93), avg. gap size = 1.00 (7 / 7) 185 23.14 0.00 5.13 chr4ptel1M 833035 833075 (166925) C L2a_3end#LINE/L2 (12) 505 467 m_b185s601i35 7208 chr4ptel1M 833035 AGCAAGTATTTATTAAACTCCCATTATGTGCCGTTGACACT 833075 i i i i v i i i-- i C L2a_3end#LINE 505 AACAAATATTTATTGAGCGCCTACTATGTGCCA--GGCACT 467 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 29.94 CpG sites = 8, Kimura (unadjusted) = 29.94 Transitions / transversions = 8.00 (8/1) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 373 15.79 1.28 2.60 chr4ptel1M 833063 833140 (166860) MIR1_Amn#SINE/MIR 74 150 (80) m_b185s601i36 7209 chr4ptel1M 833063 TGCCGTTGACACTAGCTGTATGACCTTGTGTAAGTGACTTAACC-CTATT 833111 ii ?i --i? ?i v i v ? - v v MIR1_Amn#SINE 74 TGCCACTNGC--CNGCTGNGTGACCTTGGGCAAGTCACTTNACCTCTCTG 121 chr4ptel1M 833112 TGCCTCAGTTTCCTCATCTGTAAAAAGAG 833140 ? v i MIR1_Amn#SINE 122 NGCCTCAGTTTCCTCATCTGTAAAATGGG 150 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 19.37 CpG sites = 7, Kimura (unadjusted) = 19.37 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.04 (3 / 77), avg. gap size = 1.00 (3 / 3) 432 11.76 1.47 0.00 chr4ptel1M 833073 833140 (166860) MIR#SINE/MIR 76 144 (118) m_b185s601i37 7209 chr4ptel1M 833073 ACTAGCTGTATGACCTTGTGTAAGTGACTTAACC-CTATTTGCCTCAGTT 833121 i v i v - v v MIR#SINE/MIR 76 ACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTT 125 chr4ptel1M 833122 TCCTCATCTGTAAAAAGAG 833140 v i MIR#SINE/MIR 126 TCCTCATCTGTAAAATGGG 144 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 12.80 CpG sites = 3, Kimura (unadjusted) = 12.80 Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.01 (1 / 67), avg. gap size = 1.00 (1 / 1) 180 36.42 0.00 4.04 chr4ptel1M 833876 833978 (166022) L3#LINE/CR1 1634 1732 (2367) m_b185s601i38 7210 chr4ptel1M 833876 CAGATCACGTGTCTGGAGCATACGGGGGATGCGCCAGGGATGGGGGTTAT 833925 i iviv vi v v vii ? ivi v viv L3#LINE/CR1 1634 CAGATTACAAAACTGGCACAGAGGCAAGATNCAGTAGTGATGGGGGACTT 1683 chr4ptel1M 833926 CCATTATCTGCTGGGGAGTCTGCTGGAGGCTCCATGCTGCCCAGGACAAA 833975 v i i ---- ivi i iii v ? iv iii i L3#LINE/CR1 1684 CAACTATCCG----GACATCTGCTGGAAGTCTCATTCNGCTAAAAGCAGA 1729 chr4ptel1M 833976 GCA 833978 L3#LINE/CR1 1730 GCA 1732 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 51.82 CpG sites = 22, Kimura (unadjusted) = 54.07 Transitions / transversions = 1.57 (22/14) Gap_init rate = 0.04 (4 / 102), avg. gap size = 1.00 (4 / 4) 12 22.37 4.76 0.00 chr4ptel1M 836221 836262 (163738) (AAAAC)n#Simple_repeat 1 44 (0) m_b185s252i14 7211 chr4ptel1M 836221 AAAACAAAACCAAA-AGAATGAAA-AAAAGAAGACAATATAAAA 836262 v - i ii - v i v i (AAAAC)n#Simp 1 AAAACAAAACAAAACAAAACAAAACAAAACAAAACAAAACAAAA 44 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.05 (2 / 41), avg. gap size = 1.00 (2 / 2) 245 22.97 1.35 0.00 chr4ptel1M 836482 836555 (163445) HAL1ME#LINE/L1 1445 1519 (946) m_b185s551i4 7212 chr4ptel1M 836482 CCTGGA-ATATTATAGCTAAATTCCAGAACTCCCAGGTCAAGGAGCAAAT 836530 i - i i? ? iv i ? v vi i v HAL1ME#LINE/L 1445 CCTAGACACATCNTNGTGAAATTTCAGAACNCCAAGGATAAAGAGAAAAT 1494 chr4ptel1M 836531 ACTGCAAGCATCCAGAAAGAAACAA 836555 v iv v i v HAL1ME#LINE/L 1495 CCTAAAAGCTTCCAGAGAGAAAAAA 1519 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 29.18 CpG sites = 9, Kimura (unadjusted) = 29.18 Transitions / transversions = 1.12 (9/8) Gap_init rate = 0.01 (1 / 73), avg. gap size = 1.00 (1 / 1) 284 26.14 11.11 0.00 chr4ptel1M 837417 837569 (162431) L1ME4c_3end#LINE/L1 2 171 (659) m_b185s551i5 7213 chr4ptel1M 837417 TAATTTCTCAAAGATGTAGAGAACTAAGTCAAATTTGTAAAATCCAGAGC 837466 v ?v ?v i i i v v vi i vvv ? v L1ME4c_3end#L 2 TAATATCTNTANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATC 51 chr4ptel1M 837467 CATTCCCCAATTGATAAATGACCAAAAGATATGA----GCAATTTTCAGA 837512 v vv v iv i i ----i iv ? L1ME4c_3end#L 52 AAGACCCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANA 101 chr4ptel1M 837513 TAAGG---------TAGT---CAAACATAT-GAAAAATACTTTAACTCAC 837549 vi --------- --- i - ii iv v i L1ME4c_3end#L 102 AGAGGAAATACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGC 151 chr4ptel1M 837550 TATTGATTGGAGAAATGCAA 837569 v i iii L1ME4c_3end#L 152 TAGTAATCAAAGAAATGCAA 171 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 32.58 CpG sites = 20, Kimura (unadjusted) = 33.58 Transitions / transversions = 1.00 (20/20) Gap_init rate = 0.03 (4 / 152), avg. gap size = 4.25 (17 / 4) 338 28.80 1.57 1.57 chr4ptel1M 837568 837569 (162431) L1ME2z_3end#LINE/L1 439 440 (751) m_b185s551i6 7213 chr4ptel1M 837568 AA 837569 i L1ME2z_3end#L 439 AG 440 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 37.70 CpG sites = 21, Kimura (unadjusted) = 37.70 Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 1), avg. gap size = 0.0 (0 / 0) 49 4.08 0.00 0.00 chr4ptel1M 837570 837620 (162380) (AT)n#Simple_repeat 1 51 (0) c_b185s251i0 7214 chr4ptel1M 837570 ATATATATATGTATATATATATATGTATATATATATATATATATATATAT 837619 i i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr4ptel1M 837620 A 837620 (AT)n#Simple_ 51 A 51 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 338 28.80 1.57 1.57 chr4ptel1M 837621 837744 (162256) L1ME2z_3end#LINE/L1 441 564 (627) m_b185s551i6 7213 chr4ptel1M 837621 ATGTTTATAGCAGCTTTTTTTCTCAGGGCAAAGCACTGGAAACTGAGGGG 837670 i v iv v vi v iv v vvvi L1ME2z_3end#L 441 ATGTTCATAGCAGCTTTATTCATAATAGCCAAAAACTGGAAACAGCCCAG 490 chr4ptel1M 837671 ATGCTCATCAATTGAGGAATAGCTGAACAAATTGTGGTATATGATCAT-- 837718 i ii iv ii i v i i -- -- L1ME2z_3end#L 491 GTGTCCATCAACAGGAGAATGGATAAACAAACTGTGGTATAT--TCATAC 538 chr4ptel1M 837719 GATAAAATATTATTGTGCTATAAGAA 837744 i ii i i vv v i L1ME2z_3end#L 539 AATGGAATACTACTCAGCAATAAAAA 564 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 37.70 CpG sites = 21, Kimura (unadjusted) = 37.70 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.02 (3 / 123), avg. gap size = 1.33 (4 / 3) 12 34.76 0.00 0.00 chr4ptel1M 837867 837920 (162080) (TTT)n#Simple_repeat 1 54 (0) m_b185s252i15 7215 chr4ptel1M 837867 TTTTTACCTTTTGTTGTTGTTGTTGACTTGCTTTTTTTTTTTTTTTCTCA 837916 vii v v v v vvi vi i iv (TTT)n#Simple 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr4ptel1M 837917 TTTT 837920 (TTT)n#Simple 51 TTTT 54 Matrix = Unknown Transitions / transversions = 0.67 (6/9) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 16 34.03 0.00 1.35 chr4ptel1M 837868 837942 (162058) (TTTTTC)n#Simple_repeat 1 74 (0) m_b185s252i16 7215 chr4ptel1M 837868 TTTTACCTTTTGTTGTTGTTGTTGACTTGCTTTTTTTTTTTTTTTCTCAT 837917 v i v v v v vvi v i i i - (TTTTTC)n#Sim 1 TTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTC-T 49 chr4ptel1M 837918 TTTCCCTTTTGATCTGATTTTTCTT 837942 i i vv i vv (TTTTTC)n#Sim 50 TTTTCTTTTTCTTTTTCTTTTTCTT 74 Matrix = Unknown Transitions / transversions = 0.67 (8/12) Gap_init rate = 0.01 (1 / 74), avg. gap size = 1.00 (1 / 1) 232 30.51 1.69 0.00 chr4ptel1M 838228 838286 (161714) L2d2_3end#LINE/L2 496 555 (0) m_b185s601i39 7216 chr4ptel1M 838228 GTCTAGCACAGTGCCTTGCATATAGCAGGTCTGTAAGAAATG-CTATCAA 838276 i i i i ivivi v i-i i ii L2d2_3end#LIN 496 GCCTAGCACAGTGCCTTGCACACAGTAGGCGCTCAATAAATATTTGTTGA 545 chr4ptel1M 838277 GCTGAGTTGA 838286 vi v L2d2_3end#LIN 546 TTTGATTTGA 555 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 38.79 CpG sites = 13, Kimura (unadjusted) = 41.91 Transitions / transversions = 2.60 (13/5) Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1) 325 35.31 11.93 4.69 chr4ptel1M 838824 839242 (160758) C L3#LINE/CR1 (1) 4098 3651 m_b185s601i40 7217 chr4ptel1M 838824 ATCGAATCACAAAGTGTCAGAGTTGAAAGTTGCCT-AAAAGCTGCCTTAT 838872 v i i v i vvi - i i iiii vi C L3#LINE/CR1 4098 ATAGAATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGT 4049 chr4ptel1M 838873 TGAAG-TGTTATCTGAAAAAGCCGTCTTTTCTACCACAAACTCATCTGGG 838921 iv v- vii ii viv vvi ii v vv iiiv vi v C L3#LINE/CR1 4048 CCAACCTCCCATCCAATGCAGGAATCCCTTCTACAACATCCCTGACAAGT 3999 chr4ptel1M 838922 GGTCTTCCCGCCATTGCCAGAAGACCCCCA-TG-CGCAGA-------ACC 838962 v v vi iv v i - - vi ------- C L3#LINE/CR1 3998 GGTCATCCAGCCTCTGCTTGAACACCTCCAGTGACGGGGAGCTCACTACC 3949 chr4ptel1M 838963 --------CAGCCC---CC--TTGGGAATACTTCCGACAGTCATTAAGAT 838999 -------- --- -- vv i i vi i iv i vv v C L3#LINE/CR1 3948 TCNCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGATTGTTAGAAAGTT 3899 chr4ptel1M 839000 GTTCCTGACATCAAGCCCAAATTCTACCTCTTCTTCTTCCTTCTCCTCTT 839049 v v i ii v - i -- i v vv iv i v C L3#LINE/CR1 3898 CTTCCTTATATTGAGCCGAAA-TCTGCCTC--CCTGTAACTTCCACCCAT 3852 chr4ptel1M 839050 CCTCTTCTGGCCCCTACTCTCATGATGCTCTGGGGC--CACAGA------ 839091 ------- i ivii ----iiv i -- ------ C L3#LINE/CR1 3851 -------TGGTCCTAGTTCT----GCCCTCTGGAGCCACACAGAATAAGT 3813 chr4ptel1M 839092 CCAATTTAT------CAAAAGGGTCCTTCAAAGGCTTGAAAAGAGCCAGC 839135 i iiv ------ vi vi i vii i v i v C L3#LINE/CR1 3812 CTAATCCCTCTTCCACATGACAGCCCTTCAAATATTTGAAGACAGCTATC 3763 chr4ptel1M 839136 ACATTTCTGCTCAATATTCTTTCTTTC---CT-----CCTCCAGTTTTTT 839177 ii i iv v i v i ii i --- -----i i ii C L3#LINE/CR1 3762 ATGTCTCCTCTAAGTCTTCTCTTCTCCAGGCTAAACATCCCCAGTTCCTT 3713 chr4ptel1M 839178 CTCCTTAATTTCT----TCAAATGGTTGTCCTACTTGTAACTTTAACATC 839223 vv i--i i ---- v v vi vv i----- i v C L3#LINE/CR1 3712 CAACC--GTTCCTCATATGACATGGTTTCCAGACC-----CTTCACCATC 3670 chr4ptel1M 839224 TTGGCATTCCTCCTCTGGA 839242 i ivvii C L3#LINE/CR1 3669 CTGGTCGCTCTCCTCTGGA 3651 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 49.20 CpG sites = 81, Kimura (unadjusted) = 49.77 Transitions / transversions = 1.35 (81/60) Gap_init rate = 0.08 (34 / 418), avg. gap size = 2.09 (71 / 34) 403 29.21 12.21 0.68 chr4ptel1M 839284 839545 (160455) C L2#LINE/L2 (893) 2189 1898 m_b185s601i41 7218 chr4ptel1M 839284 AAATGAGTCTGAAAAGTAGTAGT--GTGACAGGTAAGAGGAAAACCAA-- 839329 v v i v ii i-- -- i i-- C L2#LINE/L2 2189 AAAGGAGACTGAGAAGGAGCGGCCAGTGA--GGTAGGAGGAAAACCAGGA 2142 chr4ptel1M 839330 --------TGCCCTAGA------GAGAAGAGA-TGGT-CAAGAAGAAGG- 839362 -------- i i ------ v i - v - i - C L2#LINE/L2 2141 GAGTGTGGTGTCCTGGAAGCCAAGTGAAGAAAGTGTTTCAAGAAGGAGGG 2092 chr4ptel1M 839363 --TGATCAGGGGTGTCCGAGGCTGCAGAGAGGGCCAGAAGGATGAAGACT 839410 -- ivv vi v v ? v v v i i C L2#LINE/L2 2091 AGTGATCAACTGTGTCAAATGCTGCTGANAGGTCAAGTAAGATGAGGACT 2042 chr4ptel1M 839411 GAGGAAAGGCCATTAGCTATGGTGATTAAGAGATCACTGGCAACTCTGGA 839460 i vv i i v v i ii ivvi i i ii ii iv C L2#LINE/L2 2041 GAGAATTGACCATTGGATTTAGCAACGTGGAGGTCATTGGTGACCTTGAC 1992 chr4ptel1M 839461 CAGAGAAGTTTCTGT-TAAT-GTAAGATCAGAAGCAAGACAAGAGAGAGT 839508 v v v -v i - ii iv ii vv ivi v i C L2#LINE/L2 1991 AAGAGCAGTTTCGGTGGAGTGGTGGGGACGAAAGCCTGATTGGAGTGGGT 1942 chr4ptel1M 839509 T-AAG---GGGTG---GGGGAGGAAGTGTAGACATTGATTGTAG 839545 - --- ii --- i v v vi v i C L2#LINE/L2 1941 TCAAGAGAGAATGGGAGGAGAGGAATTGGAGACAGCGAGTATAG 1898 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 35.54 CpG sites = 43, Kimura (unadjusted) = 38.11 Transitions / transversions = 1.30 (43/33) Gap_init rate = 0.05 (14 / 261), avg. gap size = 2.43 (34 / 14) 18 27.78 1.27 3.90 chr4ptel1M 839872 839950 (160050) (TTGTT)n#Simple_repeat 1 77 (0) m_b185s252i17 7219 chr4ptel1M 839872 TTATTTTCATTTTTTTTTGGTTTTGTTTTCATTTGTCTTGTTTTCTCTTT 839921 i -i v - vv i v - (TTGTT)n#Simp 1 TTGTTTT-GTTTTGTTTT-GTTTTGTTTTGTTTTGTTTTGTTTTGT-TTT 47 chr4ptel1M 839922 CTCATGATTT-TCCCCTTTTGTTCTGATTT 839950 v iv v - iiiv i v (TTGTT)n#Simp 48 GTTTTGTTTTGTTTTGTTTTGTTTTGTTTT 77 Matrix = Unknown Transitions / transversions = 0.89 (8/9) Gap_init rate = 0.05 (4 / 78), avg. gap size = 1.00 (4 / 4) 190 19.15 2.08 2.08 chr4ptel1M 840028 840075 (159925) L2#LINE/L2 2229 2276 (806) m_b185s601i42 7220 chr4ptel1M 840028 GTCCCTCAAGGTTCAGTC-TTGGACCCTCCTATCTTCTCTTTCTATATT 840075 v i i i - - i v v i i L2#LINE/L2 2229 GTGCCCCAGGGCTCAGTCCTTGGACC-TCTTCTCTTCTCTATCTACACT 2276 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 22.63 CpG sites = 6, Kimura (unadjusted) = 22.63 Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.04 (2 / 47), avg. gap size = 1.00 (2 / 2) 210 36.78 5.42 3.69 chr4ptel1M 840477 840716 (159284) L2#LINE/L2 2433 2676 (406) m_b185s601i43 7220 chr4ptel1M 840477 CATCTTAAACTCAGCTTGACCCAAACTGAAGGCTCC--ATCTTTCCTTCC 840524 i i i v v v -- -- i iii L2#LINE/L2 2433 CATCTCAAACTTAACATGTCCAAAACTGAA--CTCCTGATCTTCCCCCTC 2480 chr4ptel1M 840525 AAGGC--CTCCTTCCTT-TTTTTTTTTTTCCTGGTGAA-GGTGCCATCTT 840570 iv -- i vi-v i iiiiv iii ? - iiv vi v L2#LINE/L2 2481 AAACCTGCTCCTCCCGCAGTCTTCCCCATCTCAGTNAATGGCAACTCCAT 2530 chr4ptel1M 840571 CCTCCTAATGAGCAAGGATCCTGACCTAGAACCGGTCCT---CTCACTCT 840617 i i i viviv vivvvi v i vivi --- - L2#LINE/L2 2531 CCTTCCAGTTGCTCAGGCCAAAAACCTTGGAGTCATCCTTGACTC-CTCT 2579 chr4ptel1M 840618 CCCCCTCCCCCACCC--CATCCAGCCCATTGCCGAGATGTGCCAGTTTTA 840665 iii i v -- ii iiv i iviv i i i i L2#LINE/L2 2580 CTTTCTCTCACACCCCACATCCAATCCATCAGCAAATCCTGTCGGCTCTA 2629 chr4ptel1M 840666 CCTCCATGACATATATTTTTTTGGTATTTGTTCA--TCTCATTTTCTCCT 840713 i -- v ---- iii v ii vi -- iivi v L2#LINE/L2 2630 CCTTCA--AAATATA----TCCAGAATCCGACCACTTCTCACCACCTCCA 2673 chr4ptel1M 840714 CTG 840716 L2#LINE/L2 2674 CTG 2676 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 52.75 CpG sites = 56, Kimura (unadjusted) = 54.74 Transitions / transversions = 1.93 (56/29) Gap_init rate = 0.07 (16 / 239), avg. gap size = 1.38 (22 / 16) 20 7.03 3.33 0.00 chr4ptel1M 841110 841139 (158861) (TG)n#Simple_repeat 1 31 (0) m_b185s252i18 7221 chr4ptel1M 841110 TGTG-GAGTGTGTGTGTGTGTGTGTGTTTGT 841139 - v v (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 31 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 281 31.13 5.69 0.78 chr4ptel1M 841282 841404 (158596) C L3b_3end#LINE/CR1 (350) 856 728 m_b185s601i44 7222 chr4ptel1M 841282 CCTCAGC-----ATTCTCCAGGCCAGGAT-ATTCCAGATCTTTTAGAGTC 841325 -----v i- i - i v i ivv i C L3b_3end#LINE 856 CCTCAGCCTTCTCTTCTCCAGGCT-GAATAATCCCAGTTCCTTTAACCTT 808 chr4ptel1M 841326 TTAATAAAAGTCCAATTTGCCAACACTTTGGTAACCTTGGTGACTCTCC- 841374 ivvi v i v v i v ii v ii v vi - C L3b_3end#LINE 807 TCCTCATAGGTCCCATTTTCCAGCCCTTTAATCATTTTTGTTGCTCTCCT 758 chr4ptel1M 841375 CTAGATCCTCTCCCAGTTCTGTTTGCCCCT 841404 ii ii v ? vivi i C L3b_3end#LINE 757 CTGAACTCTCTCCAANTTCTCCACGTCCCT 728 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 40.47 CpG sites = 22, Kimura (unadjusted) = 41.92 Transitions / transversions = 1.38 (22/16) Gap_init rate = 0.03 (4 / 122), avg. gap size = 2.00 (8 / 4) 294 25.35 4.23 0.00 chr4ptel1M 842315 842385 (157615) L2d2_3end#LINE/L2 477 550 (5) m_b185s601i45 7223 chr4ptel1M 842315 TCTTTGTATTCTC---AGTAATAAGCTCAGTGCCTGGTACATAGTAGGAG 842361 i i --- iiviv v v i i v L2d2_3end#LIN 477 TCTTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAGTAGGCG 526 chr4ptel1M 842362 CTGAATAAATGCTTGCTTACTTGA 842385 v ii i v i L2d2_3end#LIN 527 CTCAATAAATATTTGTTGATTTGA 550 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 29.42 CpG sites = 11, Kimura (unadjusted) = 31.74 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.01 (1 / 70), avg. gap size = 3.00 (3 / 1) 28 8.13 0.00 0.00 chr4ptel1M 842498 842537 (157463) (ATC)n#Simple_repeat 1 40 (0) c_b185s251i1 7224 chr4ptel1M 842498 ATCATCATCATCATCATCATCATCACCGCCATCATCATCA 842537 i ii (ATC)n#Simple 1 ATCATCATCATCATCATCATCATCATCATCATCATCATCA 40 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 206 31.35 0.00 1.49 chr4ptel1M 842563 842630 (157370) C MIRb#SINE/MIR (46) 222 156 m_b185s601i46 7225 chr4ptel1M 842563 TGTTCAGAACGCTTCATATGGCGCTGGCTCCCTTGAGCCTCCCAAGAACC 842612 v vi i i i - ii iv vi i v v v C MIRb#SINE/MIR 222 TGTGCTAAGCGCTTTACATG-CATTATCTCATTTAATCCTCACAACAACC 174 chr4ptel1M 842613 CCTTGAGGGGGGTATTAT 842630 ivi vi C MIRb#SINE/MIR 173 CTGCGAGGTAGGTATTAT 156 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 39.16 CpG sites = 12, Kimura (unadjusted) = 41.74 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.01 (1 / 67), avg. gap size = 1.00 (1 / 1) 220 24.00 2.00 0.00 chr4ptel1M 842865 842914 (157086) MIR#SINE/MIR 162 212 (50) m_b185s601i47 7226 chr4ptel1M 842865 CCTC-TCAGGTTGTTGAGAGGACCCAAGAAGTTAACATATGAAAAGTGCT 842913 - vi v iiv vi i i v i MIR#SINE/MIR 162 CCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATACATGTAAAGCGCT 211 chr4ptel1M 842914 T 842914 MIR#SINE/MIR 212 T 212 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 26.66 CpG sites = 7, Kimura (unadjusted) = 29.48 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.02 (1 / 49), avg. gap size = 1.00 (1 / 1) 335 31.10 6.00 7.80 chr4ptel1M 843342 843641 (156359) L2#LINE/L2 2755 3049 (33) m_b185s601i48 7227 chr4ptel1M 843342 CCCTTGTCCCATTCCTACTCCAGTCCATCATCTACTCTGCAGTCAAAATG 843391 i ---- -- ? i iv v v v i i i L2#LINE/L2 2755 CCCTTGCCCC----C--CTNCAGTCTATTCTCAACACAGCAGCCAGAGTG 2798 chr4ptel1M 843392 ATCTTCCTAAAATGCATGTC--ATC----CCCTCTCCTACTTGACAAACT 843435 i ii i i v -- ---- v ii i ii v vv L2#LINE/L2 2799 ATCCTTTTAAAACGTAAGTCAGATCATGTCACTCCTCTGCTCAAAACCCT 2848 chr4ptel1M 843436 CCAGTGGCTCCCTATTACTTCCAGTATCAAGTATATAATCCTGTT--TGA 843483 i i i iv vii vi v ivvi v i vvi-- i L2#LINE/L2 2849 CCAATGGCTTCCCATCTCACTCAGAGTAAAAGCCAAAGTCCTTACAATGG 2898 chr4ptel1M 843484 CATTCAGGTCTCCTTAAGGA---GGTCCCTTCCCACCTTTCCAGTCTTTA 843530 v v i v - vv v --- iivii i i- v i i L2#LINE/L2 2899 CCTACAAGGC-CCTACATGATCTGGTCCCCCGTTACCTCTCT-GACCTCA 2946 chr4ptel1M 843531 TCCATCTTACC-CTCTCCCTGT--CTCACCCCATAGTCTTTAATGCACTG 843577 -- i - iv -- i i---- ii -- - -- L2#LINE/L2 2947 TC--TCCTACCACTCTCCCCCTCGCTCACTCCG----CTCCA--GC-C-- 2985 chr4ptel1M 843578 ACACTGGCCTCCTGGCTGTTCTTAAAAGA----AGACACTTCATTTCCTG 843623 v i vi v ---- i ----vi i L2#LINE/L2 2986 ACACTGGCCTCCTTGCTGTTCCTCGAACACGCCAGGCAC----GCTCCCG 3031 chr4ptel1M 843624 ACTCAATGTCAGTGCATT 843641 v iv i vv i L2#LINE/L2 3032 CCTCAGGGCCTTTGCACT 3049 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 38.47 CpG sites = 51, Kimura (unadjusted) = 41.61 Transitions / transversions = 1.46 (51/35) Gap_init rate = 0.10 (30 / 299), avg. gap size = 1.37 (41 / 30) 453 31.99 8.98 3.23 chr4ptel1M 843673 843995 (156005) L2b_3end#LINE/L2 124 464 (2) m_b185s601i49 7227 chr4ptel1M 843673 AGGGCATTC---CAGGCTGTGTCTCATGACTGGAATGCCCTCCCTC---- 843715 v i--- ?v vi iiv v i i i ---- L2b_3end#LINE 124 AGGGCCTTTGCACNTGCTGTTCCCTCTGCCTGGAACGCCCTTCCCCACCT 173 chr4ptel1M 843716 CTTAGC-TG--CACCTCCTGGCT--TTCTTCAAATCCAAGCAAAAATCCC 843760 v - -- v i- -- i ii iv vv vi L2b_3end#LINE 174 CTTCGCCTGGCCAACTCCTA-CTCATCCTTCAGGTCTCAGCTCAAATGTC 222 chr4ptel1M 843761 ACTTTTTACAAGAAGCCTTCCC-AATTCCCT--TTCATTTCAGTGATTTT 843807 i ii v ii i -i ii i--vi ivv vviiii L2b_3end#LINE 223 ACCTCCTCCGGGAAGCCCTCCCTGACCCCCCAGGCCGGGTCAGGCGCCCT 272 chr4ptel1M 843808 TCTACTGATTATTTCCCA--CTTATCTT----TTCTAGACCTTGTTTGTC 843851 i - ivi-iii -- i i i ----i i iiiv ?v L2b_3end#LINE 273 CCT-CTGGGC-CCCCCCAGTCCTACCCTGCCACTCTGGGTTATNATTGTC 320 chr4ptel1M 843852 TACATTTGTTTACCTGTC-GTCTCCCA-ATTAGATTTTGAGTTTCTTGTG 843899 ------ ? v - v- i i v i i v v L2b_3end#LINE 321 T------GNTTACATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGTGAG 364 chr4ptel1M 843900 CAC-GGGCCC---TCTATTTTACCTTTCTTTTGTATCCTTCATGCTTAGC 843945 vi - v --- i i ii- iv ivi iivii i L2b_3end#LINE 365 GGCAGGGACCGNGTCTGTCTTGT-TCACCGCTGTATCCCCAGCGCCTAGC 413 chr4ptel1M 843946 ACAGTTCCTGGCACCTAGTAAGTGCTTCA--AAATGTTTATTGACCGATT 843993 ?v vi i i - -- i i vi v L2b_3end#LINE 414 ACAGNGCCTGGCACACAGTAGGCGC-TCAGTAAATATTTGTTGAATGAAT 462 chr4ptel1M 843994 GA 843995 L2b_3end#LINE 463 GA 464 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 40.70 CpG sites = 66, Kimura (unadjusted) = 44.95 Transitions / transversions = 1.94 (66/34) Gap_init rate = 0.08 (25 / 322), avg. gap size = 1.60 (40 / 25) 478 17.55 4.41 3.65 chr4ptel1M 844170 844305 (155695) MIR1_Amn#SINE/MIR 12 148 (82) m_b185s601i50 7228 chr4ptel1M 844170 TATAGTCTA-TGTAT-TAGCAGCTAGA-TGGCACAGTGGGTAGATTTGAG 844216 i i - v -v - i - v -- v v ii i MIR1_Amn#SINE 12 TGTGGTCTAGTGGATAGAGCA-CTGGACTGGGAC--TCGGGAGACCTGGG 58 chr4ptel1M 844217 TTCAAATCAGCC--CTCAGACACTTACTAGCTGTGTGATCCTGCACAAGT 844264 ? ? -- -- v v ?i i? ? i i vi MIR1_Amn#SINE 59 TTCNANTC--CCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGT 106 chr4ptel1M 844265 CACTTAA-CTATGTTTGCCTCAGTTTCCTCATCTGCAAAATG 844305 ? - v v v? i MIR1_Amn#SINE 107 CACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATG 148 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 21.46 CpG sites = 12, Kimura (unadjusted) = 21.46 Transitions / transversions = 1.09 (12/11) Gap_init rate = 0.07 (10 / 135), avg. gap size = 1.10 (11 / 10) 493 20.86 4.24 2.50 chr4ptel1M 844205 844322 (155678) MIRc#SINE/MIR 45 164 (104) m_b185s601i51 7228 chr4ptel1M 844205 GGTAGATTTGAGTTCAAATCAGCC--CTCAGACACTTACTAGCTGTGTGA 844252 v ii i i i -- -- v v MIRc#SINE/MIR 45 GGAAGACCTGGGTTCGAGTC--CCGGCTCTGCCACTTACTAGCTGTGTGA 92 chr4ptel1M 844253 TCCTGCACAAGTCACTTAACTATGTTT--GCCTCAGTTTCCTCATCTGCA 844300 i i vi i- v i -- i MIRc#SINE/MIR 93 CCTTGGGCAAGTCACTTAACC-TCTCTGAGCCTCAGTTTCCTCATCTGTA 141 chr4ptel1M 844301 AAATGACTCCAAT-ATATTTGTC 844322 ivvvi - ii i MIRc#SINE/MIR 142 AAATGGGGATAATAATACCTGCC 164 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 23.93 CpG sites = 16, Kimura (unadjusted) = 25.12 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.05 (6 / 117), avg. gap size = 1.33 (8 / 6) 494 17.34 3.96 2.94 chr4ptel1M 844205 844305 (155695) MIRb#SINE/MIR 48 149 (119) m_b185s601i52 7228 chr4ptel1M 844205 GGTAGATTTGAGTTCAAATCAGCC--CTCAGACACTTACTAGCTGTGTGA 844252 ii ii i i -- -- v v MIRb#SINE/MIR 48 GACAGACCTGGGTTCGAATC--CCGGCTCTGCCACTTACTAGCTGTGTGA 95 chr4ptel1M 844253 TCCTGCACAAGTCACTTAACTATGTTT--GCCTCAGTTTCCTCATCTGCA 844300 i i vi i i- v i -- i MIRb#SINE/MIR 96 CCTTGGGCAAGTTACTTAACC-TCTCTGAGCCTCAGTTTCCTCATCTGTA 144 chr4ptel1M 844301 AAATG 844305 MIRb#SINE/MIR 145 AAATG 149 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 19.10 CpG sites = 13, Kimura (unadjusted) = 20.40 Transitions / transversions = 3.25 (13/4) Gap_init rate = 0.05 (5 / 100), avg. gap size = 1.40 (7 / 5) 246 16.72 7.00 10.31 chr4ptel1M 844433 844532 (155468) L2c_3end#LINE/L2 332 428 (50) m_b185s601i53 7229 chr4ptel1M 844433 CTTGT-CTGTATTTATTTGTTTGTTTGT-TATCTCC-CCA-GAAACAACT 844478 -i v i i ii? - i - -v i ---- L2c_3end#LINE 332 CTTGTATTGTAATTGTCTGTTTACNTGTCTGTCTCCTCCACTAGAC---- 377 chr4ptel1M 844479 TTTTGTGAGCTCTTTGAGGGCATGGAT--TGTCTTTGGACTC-TTTTTGT 844525 --- i v i-- --- i - i L2c_3end#LINE 378 ---TGTGAGCTCCTTGAGGGCAGGGACCGTGTCTT---ATTCATCTTTGT 421 chr4ptel1M 844526 ATCTCCA 844532 i L2c_3end#LINE 422 ATCCCCA 428 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 19.82 CpG sites = 12, Kimura (unadjusted) = 19.82 Transitions / transversions = 4.00 (12/3) Gap_init rate = 0.16 (16 / 99), avg. gap size = 1.06 (17 / 16) 21 18.44 0.00 0.00 chr4ptel1M 844714 844751 (155249) (T)n#Simple_repeat 1 38 (0) m_b185s252i20 7230 chr4ptel1M 844714 TTTTTCTTTTTTCTTTTCTTTTCTTTTTTTTTACTTTT 844751 i i i i vi (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 38 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 69 1.61 0.00 0.00 chr4ptel1M 844997 845059 (154941) (TC)n#Simple_repeat 1 63 (0) c_b185s251i2 7231 chr4ptel1M 844997 TCTCTCTCCCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 845046 i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr4ptel1M 845047 TCTCTCTCTCTCT 845059 (TC)n#Simple_ 51 TCTCTCTCTCTCT 63 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0) 536 29.33 5.91 1.03 chr4ptel1M 845224 845409 (154591) C MIRc#SINE/MIR (17) 251 57 m_b185s601i54 7232 chr4ptel1M 845224 ACATCTGTATTATGCTTTAAAGCTGGCAAAATACTTG-ATATTCACTA-C 845271 i viii v i vi iii v- i v i - C MIRc#SINE/MIR 251 ACATTTGTATAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATC 202 chr4ptel1M 845272 TTATTTGAGTTTCACAACAATCTTGAGA-------AGAATATGC-TTATT 845313 i vii i i v ------- iii v i- C MIRc#SINE/MIR 201 TCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATT 152 chr4ptel1M 845314 -TTGCCACTTTACAGATCAGGAAACTGAGTCACAAAGTGAATTAAGTGTC 845362 - iv i v v v i v -i v C MIRc#SINE/MIR 151 ATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAG-GTTAAGTGAC 103 chr4ptel1M 845363 TCGTCCAAGGGTCTGCATCTGGTGAGTGTCTAGAGAAAGGATTCAAA 845409 i i vivii v i i v - vvi i i C MIRc#SINE/MIR 102 TTGCCCAAGGTCACACAGCTAGTAAGTGGC-AGAGCCGGGACTCGAA 57 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 35.82 CpG sites = 34, Kimura (unadjusted) = 38.66 Transitions / transversions = 1.70 (34/20) Gap_init rate = 0.04 (7 / 185), avg. gap size = 1.86 (13 / 7) 587 18.05 6.25 3.03 chr4ptel1M 845620 845779 (154221) Charlie4a#DNA/hAT-Charlie 343 507 (1) m_b185s502i4 7233 chr4ptel1M 845620 TTTGTTTTTTAACAATCCATCTTGATAATTGCATTTTAAAATAATTGGTT 845669 ? --i -- i i i i v Charlie4a#DNA 343 TTTGNTTTTT--TAAT--ATTTTGATAACTGTATTTCAATATAATTGGTT 388 chr4ptel1M 845670 TCCTTCTAAAGTTTTA---ATTTTATTTTTTGCATTTAAAAACATCATTG 845716 - iv i ii --- v i v Charlie4a#DNA 389 TCCTT-TGTAATCCTATGTATTTTATTTTATGCATTTAAAAACATTATTC 437 chr4ptel1M 845717 GAAGAAAGGGCCTACCGGATT------GCTGGCAAAGGGGTCTATGGCAC 845760 vi i i i iv v ------i v i Charlie4a#DNA 438 TGAGAAGGGGTCCATAGGCTTCACCAGACTGCCAAAGGGGTCCATGGCAC 487 chr4ptel1M 845761 AATAAAGGCTAAG-ACTCCT 845779 v i - i Charlie4a#DNA 488 AAAAAAGGTTAAGAACCCCT 507 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 21.31 CpG sites = 19, Kimura (unadjusted) = 21.31 Transitions / transversions = 2.11 (19/9) Gap_init rate = 0.05 (8 / 159), avg. gap size = 1.88 (15 / 8) 580 25.00 0.75 0.75 chr4ptel1M 845784 845916 (154084) C MIR3#SINE/MIR (51) 157 25 m_b185s601i55 7234 chr4ptel1M 845784 TAGTTGAACCCCTTCATTTTTCAGATGAGGAAACTGGGGCCCAGGGAAGG 845833 iv i v i i i v C MIR3#SINE/MIR 157 TAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGT 108 chr4ptel1M 845834 AGAGTG-CCTGCTTCTGGTCGCACAAACACTAAGGGGCAGAAACAGGACT 845882 ii - i iivv i iv? v v v iv i C MIR3#SINE/MIR 107 GAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACT 58 chr4ptel1M 845883 TAAACCCCGGCTGTCTGGTTCCCAGTCACGTGCT 845916 vi v iivi ii - C MIR3#SINE/MIR 57 AGAACCCAGGTCTCCTGACTCCCAGTC-CGTGCT 25 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 30.31 CpG sites = 20, Kimura (unadjusted) = 31.46 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.02 (2 / 132), avg. gap size = 1.00 (2 / 2) 467 29.79 1.40 1.40 chr4ptel1M 845795 845937 (154063) C MIRb#SINE/MIR (116) 152 10 m_b185s601i56 7234 chr4ptel1M 845795 CTTCATTTTTCAGATGAGGAAACTGGGGCCCAGGGAAGGAGAGT-GCCTG 845843 ii v i i i i vvi -i i C MIRb#SINE/MIR 152 CCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTG 103 chr4ptel1M 845844 CTTCTGGTCGCACAAACACTAAGGGGCAGAAACAGGACTTAAACCCCGG- 845892 iivv i ivi v v iv i i ii v - C MIRb#SINE/MIR 102 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGT 53 chr4ptel1M 845893 CTGTCTGGTTCCCAGTCACGTGCTAACATTCCTCGGTTCTAGGCT 845937 ii v iv v -- v v v iv i v C MIRb#SINE/MIR 52 CTGTCTGACTCCAAAGCCCGTGCT--CTTTCCACTGCACCACGCT 10 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 36.46 CpG sites = 24, Kimura (unadjusted) = 38.93 Transitions / transversions = 1.33 (24/18) Gap_init rate = 0.03 (4 / 142), avg. gap size = 1.00 (4 / 4) 361 27.68 12.81 1.49 chr4ptel1M 846817 847058 (152942) C L2#LINE/L2 (576) 2506 2238 m_b185s601i57 7235 chr4ptel1M 846817 GGGAAG-CTGGGAGGAGGAG-AGACTTTGGGGGAAAGATAACGAGCTCTT 846864 - v - - ii vi i v v i vv C L2#LINE/L2 2506 GGGAAGACTGCG-GGAGGAGCAGGTTTGAGGGGGAAGATCAGGAGTTCAG 2458 chr4ptel1M 846865 CTTTGGCCATGT-GTGCCTGAGACAC-TAATGGCTCTCCTCGTCTGAGG- 846911 i v -iv ii ii - v i viv vv v- i- C L2#LINE/L2 2457 TTTTGGACATGTTAAGTTTGAGATGCCTATTAGACATCCAAGTG-GAGAT 2409 chr4ptel1M 846912 GTCAGAAGGGCGAGTTGG------GAGC---GAGCTCAAAG-------CT 846945 iiivi - ------ i--- i ii ------- i C L2#LINE/L2 2408 GTCGAGTAGGC-AGTTGGATATACGAGTCTGGAGTTCAGGGGAGAGGTCC 2360 chr4ptel1M 846946 G--CAGGAGA---ACAGCTGAGAATCATTTGCTTAGAGATGGTCACTGAA 846990 -- v --- v vi i i iv v v vvi i C L2#LINE/L2 2359 GGGCTGGAGATATAAATTTGGGAGTCATCAGCATATAGATGGTATTTAAA 2310 chr4ptel1M 846991 GCCATGGGCATTAA--GAGATCACCAAGGGAGAGAATGTGGAAGGAGAAG 847038 i - i ii-- ? v i i vi C L2#LINE/L2 2309 GCCATGAG-ACTGGATGAGATCACCNAGGGAGTGAGTGTAGATAGAGAAG 2261 chr4ptel1M 847039 AAAAG-GATCT--GGGCAGAGCC 847058 i - i i-- i v C L2#LINE/L2 2260 AGAAGAGGTCCAAGGACTGAGCC 2238 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 34.48 CpG sites = 40, Kimura (unadjusted) = 35.84 Transitions / transversions = 1.54 (40/26) Gap_init rate = 0.07 (17 / 241), avg. gap size = 2.06 (35 / 17) 227 32.77 8.40 0.00 chr4ptel1M 847302 847420 (152580) MIR3#SINE/MIR 39 167 (41) m_b185s601i58 7236 chr4ptel1M 847302 GTTGGGAAACGTAGG----AGTTTAAGCTTCACTTGTGACTAGACATGT- 847346 ii i v i ---- iivi iii ivv i ? vii - MIR3#SINE/MIR 39 GTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTG 88 chr4ptel1M 847347 ATCT-GAGCAAGTCACTCCACCACGGTGGCTCTCACTT--CTGATCAACC 847393 i - i i v vv vi v -- v viiv MIR3#SINE/MIR 89 ACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTA 138 chr4ptel1M 847394 AAATG-GGAGCTAGGAGT-GTTGATCCCT 847420 - i v v v - v i MIR3#SINE/MIR 139 AAATGAGGGGGTTGGACTAGATGATCTCT 167 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 43.32 CpG sites = 22, Kimura (unadjusted) = 44.88 Transitions / transversions = 1.29 (22/17) Gap_init rate = 0.05 (6 / 118), avg. gap size = 1.67 (10 / 6) 258 25.27 6.52 5.38 chr4ptel1M 847603 847694 (152306) C L3b_3end#LINE/CR1 (591) 615 523 m_b185s601i59 7237 chr4ptel1M 847603 CAGCCC--GATTGTGGAAGCGTTT--GGGGGCTGCCAGAAGTTGCA--GC 847646 -- i iivv v -- vi i ----- i -- C L3b_3end#LINE 615 CAGCCCAAGATCGCATTAGCTTTTTTGGCAGCCGC-----GTCGCACTGC 571 chr4ptel1M 847647 TGACTCGTATTGAGCTTGCAGCCTGCCCAAGTGCCCAGATCTTTTCCA 847694 i i i vi iv iiv i i C L3b_3end#LINE 570 TGACTCATATTGAGCTTGCGGTCAACTAAAACCCCCAGGTCTTTTTCA 523 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 25.35 CpG sites = 15, Kimura (unadjusted) = 32.08 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.09 (8 / 91), avg. gap size = 1.38 (11 / 8) 374 26.40 17.20 1.10 chr4ptel1M 848624 848780 (151220) MIRc#SINE/MIR 69 250 (18) m_b185s601i60 7238 chr4ptel1M 848624 CTCTGACCCTTCTTAGCTGGGCGATCTTGGACAGATCACTCGGCCTCTCT 848673 v v vi v i i i ii iii MIRc#SINE/MIR 69 CTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCT 118 chr4ptel1M 848674 GCAGCCTCAGGTTCCT-ATATGT----------------TCCCCCCACCA 848706 - v - v ---------------- v iv v ii MIRc#SINE/MIR 119 G-AGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTG 167 chr4ptel1M 848707 CC-ACCC--CAGGGATTCTGTGAAGCTCAAATGGGAGAAC-------AAA 848746 - i-- v vi i v i v i------- MIRc#SINE/MIR 168 CCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAA 217 chr4ptel1M 848747 GTGCTTTGCAAAACTGAAAGACCCTGTGCAGGTG 848780 i i- v iiiv i i ii MIRc#SINE/MIR 218 GCGCTTTGT-AAACTGTAAAGTGCTATACAAATG 250 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 32.67 CpG sites = 26, Kimura (unadjusted) = 33.68 Transitions / transversions = 1.73 (26/15) Gap_init rate = 0.04 (7 / 156), avg. gap size = 4.14 (29 / 7) 16 18.91 0.00 0.00 chr4ptel1M 848867 848896 (151104) (G)n#Simple_repeat 1 30 (0) m_b185s252i21 7239 chr4ptel1M 848867 GGGGTGGGGGGTGGGAGGGTGGGGTGGGGG 848896 v v i v v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 30 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 19 14.33 4.17 2.04 chr4ptel1M 848868 848915 (151085) (GGGT)n#Simple_repeat 1 49 (0) m_b185s252i22 7239 chr4ptel1M 848868 GGGTGGG-GGGTGGGAGGGTGGGGTGGG-GGATGTGTGTGTGTGGGGGTG 848915 - v - - i v v v v (GGGT)n#Simpl 1 GGGTGGGTGGGTGGGTGGGT-GGGTGGGTGGGTGGGTGGGTGGGTGGGTG 49 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.06 (3 / 47), avg. gap size = 1.00 (3 / 3) 221 32.47 6.10 2.35 chr4ptel1M 849729 849892 (150108) C L3#LINE/CR1 (62) 4037 3868 m_b185s601i61 7240 chr4ptel1M 849729 TCCGAT-CAGAAAATGGCTCTTCCCCAAC---CCCGACAAGTGGCGATTC 849774 i - i ---v i iv --- i iv i C L3#LINE/CR1 4037 TCCAATGCAGGAA---TCCCTTCTACAACATCCCTGACAAGTGGTCATCC 3991 chr4ptel1M 849775 GGCCTCCG--GGCAGACGTCCCGAGA-AGGGA-CCCGCTGCATCCCGGAG 849820 i i --v v v v v v -i - i i i v ? ii C L3#LINE/CR1 3990 AGCCTCTGCTTGAACACCTCCAGTGACGGGGAGCTCACTACCTCNCGAGG 3941 chr4ptel1M 849821 AGACGCCTTCGACTTTGGGGC--CCCGTGAGTGCGGGGAAGTTTCTCCTC 849868 vii v v v i v i -- i - v ivi i ii i C L3#LINE/CR1 3940 CAGCCCATTCCATTTTTGGACAGCTC-TGATTGTTAGAAAGTTCTTCCTT 3892 chr4ptel1M 849869 CCGCTGAGTTGGGAGCTGCCTCCC 849892 viii ii ii v C L3#LINE/CR1 3891 ATATTGAGCCGAAATCTGCCTCCC 3868 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 42.69 CpG sites = 33, Kimura (unadjusted) = 45.07 Transitions / transversions = 1.74 (33/19) Gap_init rate = 0.06 (10 / 163), avg. gap size = 1.40 (14 / 10) 266 30.81 6.25 4.39 chr4ptel1M 849927 850038 (149962) C L3#LINE/CR1 (231) 3868 3755 m_b185s601i62 7240 chr4ptel1M 849927 CTGTGACCCGCACTGAGGGGTCCT-GCTCACGCCTTTGGGGCCAAACAGA 849975 i iiv iv vv - i vvv i i v C L3#LINE/CR1 3868 CTGTAACTTCCACCCATTGGTCCTAGTTCTGCCCTCTGGAGCCACACAGA 3819 chr4ptel1M 849976 ACAAATCT-----CTTTTTCAAGTGACCATGTCTCAAATATCTGAACCAG 850020 i i ----- i i vi viivii i ---- C L3#LINE/CR1 3818 ATAAGTCTAATCCCTCTTCCACATGACAGCCCTTCAAATATTTGAA---- 3773 chr4ptel1M 850021 CAACGGCT-TCGGGTCTTC 850038 -i i - iv i C L3#LINE/CR1 3772 -GACAGCTATCATGTCTCC 3755 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 41.48 CpG sites = 21, Kimura (unadjusted) = 41.48 Transitions / transversions = 1.75 (21/12) Gap_init rate = 0.07 (8 / 111), avg. gap size = 1.50 (12 / 8) 474 15.58 11.71 1.64 chr4ptel1M 850394 850504 (149496) C MIRc#SINE/MIR (99) 169 48 m_b185s601i63 7241 chr4ptel1M 850394 GGAAGGG-AGGGACTATCGTATCCCTACTTTACAGAGGAGGAAACGGAGG 850442 v - v i -- i i v v C MIRc#SINE/MIR 169 GGCAGGGCAGGTATTAT--TATCCCCATTTTACAGATGAGGAAACTGAGG 122 chr4ptel1M 850443 --CAGAGAGGTGAAGTGACTTGCC----------CAGCTAGGAAGTATCT 850480 -- v ---------- v iv v C MIRc#SINE/MIR 121 CTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCA 72 chr4ptel1M 850481 GAGGCTGAACTTGAACTCAGGTCT 850504 v v i i i C MIRc#SINE/MIR 71 GAGCCGGGACTCGAACCCAGGTCT 48 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 16.45 CpG sites = 7, Kimura (unadjusted) = 17.50 Transitions / transversions = 0.70 (7/10) Gap_init rate = 0.05 (5 / 110), avg. gap size = 3.00 (15 / 5) 257 28.43 10.26 0.78 chr4ptel1M 850815 850931 (149069) C L3b_3end#LINE/CR1 (1056) 150 23 m_b185s601i64 7237 chr4ptel1M 850815 TAAGTGAATACTCATTTAGCC-ACATCTCTCCATCTTTTCCACAAG---- 850859 v vi i ?- ii - i i v i ---- C L3b_3end#LINE 150 TAACTGACCATTN-TCCAGCCCACATTTCTCCGTCTTGTCCACGAGGATA 102 chr4ptel1M 850860 --ACAA-ACAC---ATCAAATGCTTTGCTTGAGGGTGGGCAAACTG-GTC 850902 -- i - v ---i i vi ivvvi ii v i- C L3b_3end#LINE 101 TCACGAGAGACTTTGTCAAATGCCTTGCTGAAATCAAGATACACTATGTC 52 chr4ptel1M 850903 CCTGGGATTCCCCGGGCCTGGCAGGATAG 850931 iv ? v ii vi v? C L3b_3end#LINE 51 TATGGNATTCCCCTGATCTGCTAGTNTAG 23 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 33.88 CpG sites = 20, Kimura (unadjusted) = 38.19 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.06 (7 / 116), avg. gap size = 1.86 (13 / 7) 252 32.09 11.19 0.00 chr4ptel1M 850826 850959 (149041) C L3#LINE/CR1 (1069) 3030 2882 m_b185s601i65 7237 chr4ptel1M 850826 TCATTTAGCC-ACATCTCTCCATCTTTTCCACAAGAC-------AAACAC 850867 ii - i i v iv------- i v C L3#LINE/CR1 3030 TCATCCAGCCCATATTTCTCCATCTTGTCCACAAGGATATCATGAGAGAC 2981 chr4ptel1M 850868 ---ATCAAATGCTTTGCTTGAGGGTGGGCAAACTG-GTCCCTGGGATTCC 850913 ---i i vi ivvii ii v ?- ivi v C L3#LINE/CR1 2980 TTTGTCAAATGCCTTGCTGAAATCCAGATACACTNTGTCTACGGCATTCC 2931 chr4ptel1M 850914 CCGGGCCTGGCAGGATAGGAGACT--GCAAAGGA-GAGAGGAGGCTGGT 850959 v ii iv vv v iv i--v ii - i v i i C L3#LINE/CR1 2930 CCTGATCTACCAGTCTAGTAACCCTATCAAAAAAGGAAATGAGGTTAGT 2882 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 42.57 CpG sites = 26, Kimura (unadjusted) = 43.95 Transitions / transversions = 1.53 (26/17) Gap_init rate = 0.05 (6 / 133), avg. gap size = 2.50 (15 / 6) 547 15.69 4.90 0.00 chr4ptel1M 853033 853134 (146866) MIRc#SINE/MIR 40 146 (122) m_b186s601i3 7242 chr4ptel1M 853033 AGTCAGGAGGACCTGAGTTCAAATCCAACCTTAG--AC--ATTAGCTGGG 853078 i i i i viv iv -- -- i v MIRc#SINE/MIR 40 AGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTG 89 chr4ptel1M 853079 TGACCCTGGGCAAGTCACTTCACC-CTGTTTGCCTCAGTTTCCTCATCTG 853127 i v - v vv MIRc#SINE/MIR 90 TGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTG 139 chr4ptel1M 853128 TAAAATG 853134 MIRc#SINE/MIR 140 TAAAATG 146 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 15.42 CpG sites = 8, Kimura (unadjusted) = 17.68 Transitions / transversions = 1.00 (8/8) Gap_init rate = 0.03 (3 / 101), avg. gap size = 1.67 (5 / 3) 15 24.06 5.56 2.70 chr4ptel1M 853619 853690 (146310) (AGGG)n#Simple_repeat 1 74 (0) m_b186s252i0 7243 chr4ptel1M 853619 AGAGAAGG-GGGTGGGATAGAGAGGGAGGGAGGGACGGAGCCAGAGCCAG 853667 i i - v -- i v vv i vvi (AGGG)n#Simpl 1 AGGGAGGGAGGGAGGGA--GGGAGGGAGGGAGGGAGGGAGGGAGGGAGGG 48 chr4ptel1M 853668 A-GGTGGG-GGGAGGG-GGAAGGAAG 853690 - v - - i i (AGGG)n#Simpl 49 AGGGAGGGAGGGAGGGAGGGAGGGAG 74 Matrix = Unknown Transitions / transversions = 1.00 (7/7) Gap_init rate = 0.08 (6 / 71), avg. gap size = 1.00 (6 / 6) 21 30.90 0.93 4.85 chr4ptel1M 853620 853726 (146274) (GAGAGG)n#Simple_repeat 1 103 (0) m_b186s252i1 7243 chr4ptel1M 853620 GAGAAGGGGGTGGGATAGAGAGGGAGGGAGGGACGGAGCCAGAGCCAGAG 853669 - i v v i i i i -- vv vv (GAGAGG)n#Sim 1 GAG-AGGGAGAGGGAGAGGGAGAGGGAGAGGGA--GAGGGAGAGGGAGAG 47 chr4ptel1M 853670 GTGGGGGGAGGGGGA-AGGAAGAAAGAATGGGGGAGAAGGAGAAGGAGAA 853718 vi i i - i - i i - i i i i (GAGAGG)n#Sim 48 GGAGAGGGAGAGGGAGAGGGAG-AGGGA-GAGGGAGAGGGAGAGGGAGAG 95 chr4ptel1M 853719 AGAAAGGG 853726 i i (GAGAGG)n#Sim 96 GGAGAGGG 103 Matrix = Unknown Transitions / transversions = 2.43 (17/7) Gap_init rate = 0.06 (6 / 106), avg. gap size = 1.00 (6 / 6) 56 5.17 2.38 2.38 chr4ptel1M 854031 854114 (145886) (ACAGAG)n#Simple_repeat 1 84 (0) c_b186s251i0 7244 chr4ptel1M 854031 ACAGAGACAGAGACAGAGAGAGAGAGACAAAGAGAGAGACAGAG--AGAG 854078 -- v i v -- (ACAGAG)n#Sim 1 ACAGAGACAGAGAC--AGAGACAGAGACAGAGACAGAGACAGAGACAGAG 48 chr4ptel1M 854079 ACAGAGACAGAGACAGAGGCAGAGACAGAGACAGAG 854114 i (ACAGAG)n#Sim 49 ACAGAGACAGAGACAGAGACAGAGACAGAGACAGAG 84 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.04 (3 / 83), avg. gap size = 1.33 (4 / 3) 13 20.20 6.12 1.96 chr4ptel1M 854410 854458 (145542) (CTCTCCT)n#Simple_repeat 1 51 (0) m_b186s252i2 7245 chr4ptel1M 854410 CTCTCCTCTCT-CTCTCCTCTTTCTTCCT-TTTCCTCCCCCCT-TCCCAT 854456 - ii i - - i i i - i v (CTCTCCT)n#Si 1 CTCTCCTCTCTCCTCTCTCCTCTC-TCCTCTCTCCTCTCTCCTCTCTCCT 49 chr4ptel1M 854457 CT 854458 (CTCTCCT)n#Si 50 CT 51 Matrix = Unknown Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.08 (4 / 48), avg. gap size = 1.00 (4 / 4) 15 21.90 0.00 2.33 chr4ptel1M 854463 854506 (145494) (TTTTTAT)n#Simple_repeat 1 43 (0) m_b186s252i3 7246 chr4ptel1M 854463 TTTTTATTTTTTATTTTTCTTTATTCATCTGGCTATTTTTTTTT 854506 iv v i - vvi v (TTTTTAT)n#Si 1 TTTTTATTTTTTATTTTTTATTTTTTAT-TTTTTATTTTTTATT 43 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.02 (1 / 43), avg. gap size = 1.00 (1 / 1) 215 29.75 4.60 3.41 chr4ptel1M 855352 855438 (144562) MIR#SINE/MIR 114 201 (61) m_b186s601i4 7247 chr4ptel1M 855352 TGTACCT--GCTGTTTTATTT--AAAATGACCATGGTGACAGCACCTCCC 855397 i -- i vii i i -- ivv ii i i i v MIR#SINE/MIR 114 TGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTACC 163 chr4ptel1M 855398 CTCAGGGGGGGTTGTTGTGAGGATCCAATGGTCTCATCCAT 855438 - vi -- iv ivi v v MIR#SINE/MIR 164 -TCATAGGG--TTGTTGTGAGGATTAAATGAGTTAATACAT 201 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 39.51 CpG sites = 16, Kimura (unadjusted) = 39.51 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.06 (5 / 86), avg. gap size = 1.40 (7 / 5) 224 24.68 12.38 3.51 chr4ptel1M 855615 855719 (144281) C MIR#SINE/MIR (126) 136 23 m_b186s601i5 7248 chr4ptel1M 855615 ACAGTTGTGGGGGTTGTAGTCACAGA-----TGAATAACCTG----AGGT 855655 v v iiii - v ----- i i i ---- C MIR#SINE/MIR 136 ACAGATGAGGAAACTG-AGGCACAGAGAGGTTAAGTAACTTGCCCAAGGT 88 chr4ptel1M 855656 C---CAGAGAGGTTATGGTAGAGGCTCCGAGACTTGAACTCAGGCC-CCT 855701 --- vv vvvi i --- i i i i v-i C MIR#SINE/MIR 87 CACACAGCTAGTAAGTGGCAGAG---CCGGGATTCGAACCCAGGCAGTCT 41 chr4ptel1M 855702 GCCTCCAGAGCCCGGGCT 855719 v v C MIR#SINE/MIR 40 GGCTCCAGAGCCCGTGCT 23 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.11 CpG sites = 14, Kimura (unadjusted) = 30.54 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.08 (8 / 104), avg. gap size = 2.12 (17 / 8) 324 29.44 5.84 5.16 chr4ptel1M 858572 858725 (141275) L3b_3end#LINE/CR1 459 613 (593) m_b186s601i6 7249 chr4ptel1M 858572 TGAACTCAAAAAACCCCACTC-CATGAGTACAAGATGGGGGAAGCACGGC 858620 iii ? -- v - ii i ii i L3b_3end#LINE 459 TGGGTTCAAAAAANC--AATCGCGCGAGTACAGGATGGGGGAGACGCGGC 506 chr4ptel1M 858621 TC-----CAGTGCATTGGGAATAAGGACTAGACATCCATTCA---GACTG 858662 i----- i? - v v iv i ivi --- i --- i L3b_3end#LINE 507 TTAGCAGCAGCNCA-TGTGAAAAAGACCTGGGGGT---TTTAGTTGACCG 552 chr4ptel1M 858663 CAAGCTTGATCTGGGCGAACAGGTCGACACGGCATCCAAGGAGGGTGCCA 858712 ii v i iv i vv i vv ii i v i-- L3b_3end#LINE 553 CAAGCTCAATATGAGTCAGCAGTGCGACGCGGCTGCCAAAAAAGCTA--A 600 chr4ptel1M 858713 GCCAGTCTTGGGC 858725 vv ii L3b_3end#LINE 601 TGCGATCTTGGGC 613 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 33.07 CpG sites = 29, Kimura (unadjusted) = 40.06 Transitions / transversions = 2.07 (29/14) Gap_init rate = 0.07 (11 / 153), avg. gap size = 1.55 (17 / 11) 185 20.92 2.27 2.27 chr4ptel1M 859813 859856 (140144) L2a_3end#LINE/L2 390 433 (84) m_b186s601i7 7250 chr4ptel1M 859813 CCCATGAGAACCTAAGCTTCCTGAGGGTAGGGGACCTTT-CCTGT 859856 iv iv i v i - i -i L2a_3end#LINE 390 CCCACTAGAATGTAAGCTCCATGAGGGCA-GGGACTTTTGTCTGT 433 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 25.21 CpG sites = 6, Kimura (unadjusted) = 25.21 Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2) 456 24.79 8.11 1.91 chr4ptel1M 859861 860008 (139992) C L3#LINE/CR1 (126) 3973 3817 m_b186s601i8 7251 chr4ptel1M 859861 CTCCA-TGGCGGGGGACACGTAGAACCTCCTGAGGAAGCCCCATTTATTT 859909 - i ii v -- vv ?i v vv ii C L3#LINE/CR1 3973 CTCCAGTGACGGGGAGCTC--ACTACCTCNCGAGGCAGCCCATTCCATTT 3926 chr4ptel1M 859910 CTGAATTGCTCTGATTGTTGAGACAATT-TTCCTT-CATCCAGCCGAAAC 859957 i i iv - v i - -i iv i C L3#LINE/CR1 3925 TTGGACAGCTCTGATTGTT-AGAAAGTTCTTCCTTATATTGAGCCGAAAT 3877 chr4ptel1M 859958 GAGCCTCTCTGGCACTTCC---------TCCCAGTCCTGTTCTCTGGGGT 859998 vv i vv --------- i i ii i i C L3#LINE/CR1 3876 CTGCCTCCCTGTAACTTCCACCCATTGGTCCTAGTTCTGCCCTCTGGAGC 3827 chr4ptel1M 859999 CACATGCAAT 860008 iiv C L3#LINE/CR1 3826 CACACAGAAT 3817 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.14 CpG sites = 22, Kimura (unadjusted) = 31.18 Transitions / transversions = 1.57 (22/14) Gap_init rate = 0.05 (7 / 147), avg. gap size = 2.14 (15 / 7) 17 18.38 0.00 0.00 chr4ptel1M 860428 860458 (139542) (T)n#Simple_repeat 1 31 (0) m_b186s252i4 7252 chr4ptel1M 860428 TTATTTGTTTTTTCTTTCTTTTTTCTTTTTT 860458 v v i i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 31 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 306 23.01 0.00 4.92 chr4ptel1M 860493 860556 (139444) C L2d_3end#LINE/L2 (0) 516 456 m_b186s601i9 7253 chr4ptel1M 860493 TTAATCAATAGCCAGCTAATAAGCATTTATTAAGTGCCTACTATATGCCA 860542 i --- iii i i i i i iv C L2d_3end#LINE 516 TCAATCAAT---CAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTC 470 chr4ptel1M 860543 GGCAGTGTGCTAAG 860556 i v i C L2d_3end#LINE 469 AGCACTGTGCTAGG 456 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 26.96 CpG sites = 12, Kimura (unadjusted) = 29.47 Transitions / transversions = 6.00 (12/2) Gap_init rate = 0.05 (3 / 63), avg. gap size = 1.00 (3 / 3) 254 12.82 0.00 0.00 chr4ptel1M 861013 861051 (138949) C MER58D#DNA/hAT-Charlie (347) 39 1 m_b186s502i0 7254 chr4ptel1M 861013 GCCGAATCTGGCCCGCGGGCCATAGTTTGAGGACCCCTG 861051 i i i vv C MER58D#DNA/hA 39 GCCGGATTTGGCCCGCGGGCCGTAGTTTGCCGACCCCTG 1 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 11.36 CpG sites = 3, Kimura (unadjusted) = 14.18 Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 369 29.42 0.00 1.18 chr4ptel1M 861081 861166 (138834) Charlie1b#DNA/hAT-Charlie 1 85 (438) m_b186s502i1 7255 chr4ptel1M 861081 CAGTAGTTCTCAAAGTCTGGTCCAGAGCATCCTGGGAATCTCTGAAATCC 861130 ii v i i vvi ii i i i i Charlie1b#DNA 1 CAGCGGTTCTCAAAGTGTGGTCCGGGGACCCCTGGGGGTCCCCGAGACCC 50 chr4ptel1M 861131 TTTCAGAGAGTCTACAAATTCATAATTGGTTTTTAT 861166 i i ii i iv v i -i i Charlie1b#DNA 51 TTTCAGGGGGTCCGCGAGGTCAAAACT-ATTTTCAT 85 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 30.26 CpG sites = 20, Kimura (unadjusted) = 40.82 Transitions / transversions = 4.00 (20/5) Gap_init rate = 0.01 (1 / 85), avg. gap size = 1.00 (1 / 1) 510 16.94 4.96 2.42 chr4ptel1M 861159 861279 (138721) Charlie1a#DNA/hAT-Charlie 1332 1455 (0) m_b186s502i2 7256 chr4ptel1M 861159 GTTTTTATTTTTAATGTGATCAATATCTATAACTATAACCCACAGAAACA 861208 v i i i v v iv v Charlie1a#DNA 1332 GTTTTAATTTCTAATATGGTAAATATCGATAGATATAACCCACATAAACA 1381 chr4ptel1M 861209 AAA---CTTTGGACAGATCCTCAATCATTTTTAATAGGATAAA--GATAT 861253 --- --- i v v vi -- i vi Charlie1a#DNA 1382 AAAGCTCTTTGG---GGTCCTCAATAATTTTTAAGAGTGTAAAGGGGTCC 1428 chr4ptel1M 861254 TGAGAAC-AAAAGTTTGAGGACCACTG 861279 v - i i Charlie1a#DNA 1429 TGAGACCAAAAAGTTTGAGAACCGCTG 1455 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 18.30 CpG sites = 10, Kimura (unadjusted) = 19.31 Transitions / transversions = 1.00 (10/10) Gap_init rate = 0.05 (6 / 120), avg. gap size = 1.50 (9 / 6) 306 26.12 19.89 3.24 chr4ptel1M 862163 862348 (137652) C L2b_3end#LINE/L2 (19) 447 232 m_b186s601i10 7253 chr4ptel1M 862163 ATTTATTAAGCACCTACTGTGCTCTGGGCACTG----AG---CTGGGGAT 862205 i i i iv ii ? ---- --- C L2b_3end#LINE 447 ATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGGGAT 398 chr4ptel1M 862206 ----------------------CAGTTCCCGGTCTTGGGGAGCTCTCAGT 862233 ---------------------- i i i vi iiv v C L2b_3end#LINE 397 ACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGGAGCTCACAGT 348 chr4ptel1M 862234 TCCAATGGGGGAGAC-GACGTGCAAGCA-ACTGTGTAGAAACAAGCTGTG 862281 - i i - i i ? - vi ?- v v v v--- C L2b_3end#LINE 347 -CTAGTGGGGGAGACAGACATGTAANCAGACAATN-ATAACCCAGA---G 303 chr4ptel1M 862282 TGCCAGGCCCTGGAACTGAGAG----CAGGGAAGGCTTTCTG--TGGACC 862325 v v-- i i i i ---- i i vivi --iv i C L2b_3end#LINE 302 TGGCAGGG--TAGGACTGGGGGGGCCCAGAGGAGGGCGCCTGACCCGGCC 255 chr4ptel1M 862326 GGGGGGATCAAGAAAGGCTTCTC 862348 v i i i i i C L2b_3end#LINE 254 TGGGGGGTCAGGGAGGGCTTCCC 232 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 31.75 CpG sites = 32, Kimura (unadjusted) = 34.46 Transitions / transversions = 2.13 (32/15) Gap_init rate = 0.08 (14 / 185), avg. gap size = 3.14 (44 / 14) 244 26.71 5.83 1.87 chr4ptel1M 862775 862877 (137123) L1M2_orf2#LINE/L1 2203 2309 (982) m_b186s551i0 7257 chr4ptel1M 862775 CAGAAATCACCAGCATTTTTATGTAAAATCAATAAAACCCAGCAGGAAGA 862824 i vi i iiivv v ii -- i v v i i L1M2_orf2#LIN 2203 CAAAAATCAGTAGCATTTCTATACGCCAACAACGAA--CTATCTGAAAAA 2250 chr4ptel1M 862825 GAAA------GAGAAATCCTATTTAAAATAATTACAAAAAATATAAGATA 862868 ------i v i v ii v i L1M2_orf2#LIN 2251 GAAATCAAGAAAGCAATCCCATTTACAATAGCTACAAAAAAAATAAAATA 2300 chr4ptel1M 862869 CCTGGGCAT 862877 i v L1M2_orf2#LIN 2301 CCTAGGAAT 2309 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 30.73 CpG sites = 17, Kimura (unadjusted) = 34.12 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.03 (3 / 102), avg. gap size = 2.67 (8 / 3) 235 37.78 0.00 0.00 chr4ptel1M 863305 863439 (136561) L1P1_orf2#LINE/L1 2776 2910 (384) m_b186s551i1 7258 chr4ptel1M 863305 TGGGGTAAGGATTCACCATCTTACAAAAACTGCTGGGAAAATGGGACAGT 863354 v v i i v i viv iv vi i L1P1_orf2#LIN 2776 TGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGC 2825 chr4ptel1M 863355 AGGATGAAGGAAATCAGATTTAGATCAACACCTCATACCTGACATCAAGA 863404 viv v i iiiii vi i vviv i i v i iv i L1P1_orf2#LIN 2826 CATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAA 2875 chr4ptel1M 863405 TGAACCCCCAATGGATACATGACCCAAATGTTAAA 863439 v ii vvi vv v ii i i L1P1_orf2#LIN 2876 TTAATTCAAGATGGATTAAAGACTTAAACGTTAGA 2910 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 53.15 CpG sites = 29, Kimura (unadjusted) = 54.76 Transitions / transversions = 1.32 (29/22) Gap_init rate = 0.00 (0 / 134), avg. gap size = 0.0 (0 / 0) 574 26.28 4.43 4.43 chr4ptel1M 863501 863703 (136297) MIR3#SINE/MIR 2 204 (4) m_b186s601i11 7259 chr4ptel1M 863501 TGACAGCATAGGCTGG--AGGTAGAGCACTGGGTAAAGCGATAGGAAGAC 863548 i vi - i-- iv - iivii v vi - MIR3#SINE/MIR 2 TGGCAGAGT-GGCTGAGCAGAGAGAGCAC-GGACTGGGAGTCAGGA-GAC 48 chr4ptel1M 863549 CTGGGTTCAAATGTGCCAGAT-----AATTACTAGTT-TGTGGCCCTGGG 863592 v -- v i v ----- v v ? i - i i MIR3#SINE/MIR 49 CTGGGTTCTA--GTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGG 96 chr4ptel1M 863593 CAAGCCCTTTAATCTCTCTAGGCCTCAGTTT-CTCATTTTGGCAAAATGG 863641 i vi v i i - i -- i i MIR3#SINE/MIR 97 CAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCT--GTAAAATGA 144 chr4ptel1M 863642 GGGAGTTAGATTTGATGACTCCCAAAGTCTGTGCAATTTTCCAATTAATC 863691 i i i v iii i i iv v v -vi ii -i v MIR3#SINE/MIR 145 GGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCA-GCTCTGA-CATTC 192 chr4ptel1M 863692 TATGATTCTATG 863703 MIR3#SINE/MIR 193 TATGATTCTATG 204 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 32.91 CpG sites = 33, Kimura (unadjusted) = 33.73 Transitions / transversions = 1.83 (33/18) Gap_init rate = 0.06 (13 / 202), avg. gap size = 1.38 (18 / 13) 183 25.84 5.17 9.91 chr4ptel1M 863741 863856 (136144) L2d2_3end#LINE/L2 361 471 (84) m_b186s601i12 7260 chr4ptel1M 863741 TATTGTCTTCATTTGGTAG--GAAT--TGTATT-TTCTTTGTTTCGTCTC 863785 i v vi v v--i -- - v ivi iv v L2d2_3end#LIN 361 TGTTGTCTTGAACTGTTATTTAAATCTTGTATTGTTATTTAACTTTTCAC 410 chr4ptel1M 863786 ATATTTATGCCACTCTCTGCACACATCTCCCTTGATAGAAT-TAAGCCCC 863834 i i ---- - ------ iviv v - i L2d2_3end#LIN 411 GTGTTTATG----TCT-TG------TCTCCCCAACTAGATTGTAAGCTCC 449 chr4ptel1M 863835 TTGAGAGCAGAGGCCATCTCCT 863856 i i i v i L2d2_3end#LIN 450 TTGAGGGCAGGGACCATGTCTT 471 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.62 CpG sites = 15, Kimura (unadjusted) = 32.03 Transitions / transversions = 1.25 (15/12) Gap_init rate = 0.13 (15 / 115), avg. gap size = 1.13 (17 / 15) 202 24.08 2.13 11.63 chr4ptel1M 863763 863856 (136144) L2d_3end#LINE/L2 344 429 (87) m_b186s601i13 7260 chr4ptel1M 863763 TTGTATT-TTCTTTGTTTCGTCTCATATTTATGCCACTCTCTGCACACAT 863811 - i iv - i i --i ii v - ------ L2d_3end#LINE 344 TTGTATTGTTCTCTAATT-GTTTCATGT--GTGTTAGTCT-TG------T 383 chr4ptel1M 863812 CTCCCTTGATAGAAT-TAAGCCCCTTGAGAGCAGAGGCCATCTCCT 863856 iviv v - i i i i v i L2d_3end#LINE 384 CTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTT 429 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.79 CpG sites = 14, Kimura (unadjusted) = 29.79 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.13 (12 / 93), avg. gap size = 1.00 (12 / 12) 189 32.76 1.72 0.00 chr4ptel1M 863811 863868 (136132) L2c_3end#LINE/L2 363 421 (57) m_b186s601i14 7260 chr4ptel1M 863811 TCTCCCTTGATAGAAT-TAAGCCCCTTGAGAGCAGAGGCCATCTCCTTTT 863859 iiiiv v - i i i i i i v i v L2c_3end#LINE 363 TCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATT 412 chr4ptel1M 863860 TGCCTTAGT 863868 iii v L2c_3end#LINE 413 CATCTTTGT 421 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 43.33 CpG sites = 14, Kimura (unadjusted) = 46.81 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.02 (1 / 57), avg. gap size = 1.00 (1 / 1) 265 31.03 1.14 1.14 chr4ptel1M 863901 863988 (136012) C MIR3#SINE/MIR (76) 132 45 m_b186s601i15 7261 chr4ptel1M 863901 TGAGGTGAAGGATGCCTTAAGGAGGGGAAAGGATTTCCTCAAAATTGTCC 863950 vi vv v i- ii v iv i v i ii iiiv C MIR3#SINE/MIR 132 TGAGGAAACTGAGGCCC-AGAGAGGTGAAGTGACTTGCCCAAGGTCACAC 84 chr4ptel1M 863951 AGCTAGTTAA-GGCCGAACCGGGACTGCAACTGAGGTCT 863988 ? i- v i iv iv C MIR3#SINE/MIR 83 AGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGTCT 45 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 42.04 CpG sites = 16, Kimura (unadjusted) = 42.04 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.02 (2 / 87), avg. gap size = 1.00 (2 / 2) 253 34.50 2.61 1.72 chr4ptel1M 863916 864030 (135970) C MIRc#SINE/MIR (147) 121 6 m_b186s601i16 7261 chr4ptel1M 863916 CTTAAGGAGGGGAAAGGATTTCCTCAAAATTGTCCAGCTAGTTAA-GGCC 863964 i ii vv iv i v i ii iiiv v i- v C MIRc#SINE/MIR 121 CTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCA 72 chr4ptel1M 863965 GAACCGGGACTGCAACTGAGGTCTAACC--CTCCACCAGGTTGGTGGTAT 864012 i vv iv vv i-- -- viii v v C MIRc#SINE/MIR 71 GAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCA--AGTCCAGTGCTCT 24 chr4ptel1M 864013 TTCCTCAGACCCAGATTG 864030 v v vv v i C MIRc#SINE/MIR 23 TTCCACTGCACCACACTG 6 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 46.93 CpG sites = 19, Kimura (unadjusted) = 46.93 Transitions / transversions = 0.95 (19/20) Gap_init rate = 0.04 (4 / 114), avg. gap size = 1.25 (5 / 4) 200 31.58 2.11 0.00 chr4ptel1M 864496 864590 (135410) C L3#LINE/CR1 (146) 3953 3857 m_b186s601i17 7262 chr4ptel1M 864496 CCACCTCCCCAGA-AGCCCCTTCCTCTTTTGAGAAGCTCTCATTGGAGGG 864544 i ? v i- v vi iiv v vvi i C L3#LINE/CR1 3953 CTACCTCNCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGATTGTTAGA 3904 chr4ptel1M 864545 AAGGTTTTCTTGATCTAGAGCCTCCTTTTG-CTCCTTATTCCTCCCA 864590 v i i v v v vvvv i - i i vv i C L3#LINE/CR1 3903 AAGTTCTTCCTTATATTGAGCCGAAATCTGCCTCCCTGTAACTTCCA 3857 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 41.80 CpG sites = 13, Kimura (unadjusted) = 41.80 Transitions / transversions = 0.76 (13/17) Gap_init rate = 0.02 (2 / 94), avg. gap size = 1.00 (2 / 2) 486 19.51 13.82 0.00 chr4ptel1M 864594 864716 (135284) Charlie4#DNA/hAT-Charlie 1 140 (3238) m_b186s502i3 7263 chr4ptel1M 864594 CAGGGATTCT--GTCTGAGATCC--TGAACCCCAAAAGGTTTGTAGATA- 864638 i --ii i i --v v ii ii i - Charlie4#DNA/ 1 CAGGGGTTCTTAACCTGGGGTCCACGGACCCCCAAGGGGTCCGTGGATAG 50 chr4ptel1M 864639 AATTTAGA-----CGC---CTCGGGTAG----AAATTACACCTTTTTTTT 864676 i i----- i--- i i i ---- i v Charlie4#DNA/ 51 AATTCAGGGGGTCCGTGAACTTGGATGGGAAAAAATTACATCTTTATTTT 100 chr4ptel1M 864677 CACCAACCTCTTCCTGAAATTTAGCATTTCCTTCAGTTAT 864716 i vv i Charlie4#DNA/ 101 CACTAACCTCTAACTGAAATTTAGCATTTCCTTCAATTAT 140 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 22.52 CpG sites = 19, Kimura (unadjusted) = 23.63 Transitions / transversions = 3.80 (19/5) Gap_init rate = 0.05 (6 / 122), avg. gap size = 2.83 (17 / 6) 258 19.05 0.00 0.00 chr4ptel1M 864762 864803 (135197) MIRc#SINE/MIR 70 111 (157) m_b186s601i18 7264 chr4ptel1M 864762 TTTAACACTTCTTAGCTGTGTGACCCTGGGTAAATCACTTAA 864803 i iv vi i i i MIRc#SINE/MIR 70 TCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAA 111 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 22.78 CpG sites = 6, Kimura (unadjusted) = 22.78 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 296 29.76 0.00 0.00 chr4ptel1M 864828 864911 (135089) Charlie4a#DNA/hAT-Charlie 425 508 (0) m_b186s502i4 7265 chr4ptel1M 864828 AAAAAGACGATTCTGAGTCCAGATTTTCTGGGTTCTCCTGATTTCCAAAG 864877 v iv vvvi i iiviv v v v i v Charlie4a#DNA 425 AAAAACATTATTCTGAGAAGGGGTCCATAGGCTTCACCAGACTGCCAAAG 474 chr4ptel1M 864878 GGGTCCATGACACAAGAAAGATTAAAAGTCGCTG 864911 i i i i ii v Charlie4a#DNA 475 GGGTCCATGGCACAAAAAAGGTTAAGAACCCCTG 508 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 38.52 CpG sites = 13, Kimura (unadjusted) = 38.52 Transitions / transversions = 1.08 (13/12) Gap_init rate = 0.00 (0 / 83), avg. gap size = 0.0 (0 / 0) 276 31.08 0.00 0.00 chr4ptel1M 864912 864985 (135015) C L3#LINE/CR1 (264) 3835 3762 m_b186s601i19 7262 chr4ptel1M 864912 CTCTAGGATCAAACAGAACAAATCTAACCATTTTCCCACAAGGCAGCCCT 864961 i iii v i i i vi i i v i C L3#LINE/CR1 3835 CTCTGGAGCCACACAGAATAAGTCTAATCCCTCTTCCACATGACAGCCCT 3786 chr4ptel1M 864962 GCGAATACTTCATGCTAGTTACCA 864985 v i i v v vi i i C L3#LINE/CR1 3785 TCAAATATTTGAAGACAGCTATCA 3762 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 42.68 CpG sites = 16, Kimura (unadjusted) = 42.68 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.00 (0 / 73), avg. gap size = 0.0 (0 / 0) 18 4.77 0.00 0.00 chr4ptel1M 865026 865047 (134953) (AT)n#Simple_repeat 1 22 (0) m_b186s252i5 7266 chr4ptel1M 865026 ATATATATATATATATACATAT 865047 i (AT)n#Simple_ 1 ATATATATATATATATATATAT 22 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 508 25.98 7.09 0.00 chr4ptel1M 865149 865275 (134725) C MIRc#SINE/MIR (123) 145 10 m_b186s601i20 7267 chr4ptel1M 865149 ATTTTACAGATATGAAAACTGAGGC--AGAGAGA--AAAAGACTGGTTCA 865194 iv i -- i-- iv v ii C MIRc#SINE/MIR 145 ATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCA 96 chr4ptel1M 865195 GGGTGACACAGCTAGTAATTATCAGAGGTAGGATCTGAACACAGGTCCTC 865244 i v v iv vii iii v i C MIRc#SINE/MIR 95 AGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTC 46 chr4ptel1M 865245 TTAACT-----TCTCATGCCATATCCATCGTACCAC 865275 i i ----- ivi iv v ii i C MIRc#SINE/MIR 45 CTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.56 CpG sites = 22, Kimura (unadjusted) = 33.13 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.02 (3 / 126), avg. gap size = 3.00 (9 / 3) 356 23.00 20.00 0.00 chr4ptel1M 866104 866203 (133797) MIRc#SINE/MIR 25 144 (124) m_b186s601i21 7268 chr4ptel1M 866104 GAGTGATAGGCCTGGAGGCAAGAAAACCTGAGTTC-AGATCTACCTCAGA 866152 iiv i i i v i i i - vi iiv v v MIRc#SINE/MIR 25 GAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGC 74 chr4ptel1M 866153 CACTGACTAGCTGTGTGAC-----------------ACCCTTTT--GCCA 866183 v ----------------- ii i -- v MIRc#SINE/MIR 75 CACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCT 124 chr4ptel1M 866184 CAGTTTCCTCATTTGTAAAA 866203 i MIRc#SINE/MIR 125 CAGTTTCCTCATCTGTAAAA 144 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 26.67 CpG sites = 15, Kimura (unadjusted) = 28.26 Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.03 (3 / 99), avg. gap size = 6.67 (20 / 3) 182 30.91 1.82 0.00 chr4ptel1M 866378 866432 (133568) MIRb#SINE/MIR 201 256 (12) m_b186s601i22 7269 chr4ptel1M 866378 TGCACAGTAGGCACTT-GTGCAGTGCCTGTCACACCGTAGGCACTTGTTA 866426 iivv i i - ii v iv i i iiv MIRb#SINE/MIR 201 TGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATA 250 chr4ptel1M 866427 ACTGGT 866432 v MIRb#SINE/MIR 251 AATGGT 256 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 35.47 CpG sites = 11, Kimura (unadjusted) = 41.73 Transitions / transversions = 1.83 (11/6) Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1) 354 21.92 0.00 1.37 chr4ptel1M 866975 867048 (132952) C L2a_3end#LINE/L2 (2) 515 443 m_b186s601i23 7270 chr4ptel1M 866975 TCAATAAATCAGCAAGCATTTATTAAGCATTTACTACATCCCAGGCACTG 867024 v v v i ii i iii ii v C L2a_3end#LINE 515 TCATTCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTG 466 chr4ptel1M 867025 TGCTATGCGATGGGGATACCAGCA 867048 v v v - C L2a_3end#LINE 465 TTCTAGGCGCTGGGGATA-CAGCA 443 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 24.45 CpG sites = 9, Kimura (unadjusted) = 26.29 Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.01 (1 / 73), avg. gap size = 1.00 (1 / 1) 204 32.25 7.75 1.46 chr4ptel1M 867129 867257 (132743) C L2d_3end#LINE/L2 (232) 284 148 m_b186s601i24 7271 chr4ptel1M 867129 AAAGAAATGAAAAGTAATAGTAGTGATGGGGGAATCAGGGAAGGTCTCAT 867178 i iv i ii v vv i - v i vii ii i C L2d_3end#LINE 284 AGAGAAGGGAGAGATCAGTGTGG-GCTGGAGTGGTCAGGGAAGGCTTCGT 236 chr4ptel1M 867179 GTAGGAGGAAGCATTTGAGGTGAGTTTTAAAAGAAGCCAGGGATTCTAAA 867228 v vi v i v i ii i i v vvvi - ii C L2d_3end#LINE 235 GGAGGAGGTGGGACTTGAGCTGGGCCTTGAAGGATGGGTAGGATT-TGGA 187 chr4ptel1M 867229 T-GA-------GAAGGG--AGCACATTCCAGGCACAGGG 867257 - ------- -- vi ivi C L2d_3end#LINE 186 TAGAGAGAGAGGAAGGGGAAGGGCATTCCAGGCGGGGGG 148 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 41.06 CpG sites = 25, Kimura (unadjusted) = 43.92 Transitions / transversions = 1.56 (25/16) Gap_init rate = 0.04 (5 / 128), avg. gap size = 2.40 (12 / 5) 262 33.06 7.97 1.36 chr4ptel1M 867154 867291 (132709) C L2a_3end#LINE/L2 (257) 260 114 m_b186s601i25 7271 chr4ptel1M 867154 ATGGGGGAATCAGGGAAGGTCTCATGTAGGAGGAAGCATTTGAGGTGAGT 867203 i vii i ?ivv i vii vvi v C L2a_3end#LINE 260 ATAGGGTGGTCAGGGAAGGCCTCNCTGAGAAGGTGACATTTGAGCAAAGA 211 chr4ptel1M 867204 TTTAAAAGAAGCCAGGG--------ATTCTAA-ATGAGAAGGGAGCACAT 867244 ii i i i iv -------- v vi - vv ii i vi i C L2a_3end#LINE 210 CCTGAAGGAGGTGAGGGAGCGAGCCATGCGGATATCTGGGGGAAGAGCGT 161 chr4ptel1M 867245 TCCAGGCACAGGG-GTAGCCAATGCAAAAGTACCTTGAGA-GAGAATGT 867291 v -ii v i i -- i i- i ii C L2a_3end#LINE 160 TCCAGGCAGAGGGAACAGCAAGTGCAAAGG--CCCTGAGGCGGGAGCGT 114 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 43.92 CpG sites = 30, Kimura (unadjusted) = 46.83 Transitions / transversions = 2.00 (30/15) Gap_init rate = 0.04 (6 / 137), avg. gap size = 2.17 (13 / 6) 322 26.88 9.17 0.77 chr4ptel1M 867157 867276 (132724) C L2c_3end#LINE/L2 (222) 256 127 m_b186s601i26 7271 chr4ptel1M 867157 GGGGAATCAGGGAAGGTCTCATGTAGGAGGAAGCATTTGAGGTGAGTTTT 867206 ii ii vi v vii i v ?i C L2c_3end#LINE 256 GGGGGGTCAGGGAAGGCTTCCCGGAGGAGGTGACATCTGAGCTGAGNCTT 207 chr4ptel1M 867207 AAAAGA--AGCCAGGGATT--CTAAATG--AGAAGGG----AGCACATTC 867246 i i -- -i ii -- i ii -- i ---- vi C L2c_3end#LINE 206 GAAGGATGAG-TAGGAGTTAGCCAGGTGGAAGGAGGGGGGAAGAGCATTC 158 chr4ptel1M 867247 CAGGCACAGGG-GTAGCCAATGCAAAAGTAC 867276 v -ii vvi i i? C L2c_3end#LINE 157 CAGGCAGAGGGAACAGCATGTGCAAAGGCNC 127 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 34.79 CpG sites = 24, Kimura (unadjusted) = 36.24 Transitions / transversions = 3.00 (24/8) Gap_init rate = 0.05 (6 / 119), avg. gap size = 2.00 (12 / 6) 247 23.91 0.00 0.00 chr4ptel1M 867297 867342 (132658) C L2c_3end#LINE/L2 (1) 477 432 m_b186s601i27 7272 chr4ptel1M 867297 TTCAATCACTCAACAAGCCTTCATTGAGTGCTTACTATATATCGGG 867342 v i i v i i i i ii i C L2c_3end#LINE 477 TTCATTCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGG 432 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 27.45 CpG sites = 9, Kimura (unadjusted) = 30.80 Transitions / transversions = 4.50 (9/2) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 255 30.80 10.60 1.27 chr4ptel1M 867401 867617 (132383) L1P3_orf2#LINE/L1 2267 2503 (791) m_b186s551i2 7273 chr4ptel1M 867401 AAGTTCCACTTAAAATAACTACAAAAGGTATAAAATATTTGGGAGCTTA- 867449 v i i i v vi ii v ii i iivi - L1P3_orf2#LIN 2267 AACTCCCATTCACAATTGCTACAAAGAGAATAAAATACCTAGGAATACAA 2316 chr4ptel1M 867450 CTTACAAAAGATACACAGCA----TTATATGAACATTATCACAAAATACT 867495 ii iiiv v ---- vv v iv i --- vi L1P3_orf2#LIN 2317 CTTACAAGGGATGTGAAGGACCTCTTCAAGGAGAACTA---CAAACCACT 2363 chr4ptel1M 867496 -CT----GAGGTAAGAGAGGTT-TAAATAATTGCAGAAATATTAATTGCT 867539 - ---- ii vi-i i v v i i vvv L1P3_orf2#LIN 2364 GCTCAAGGAAATAAGAGAGGACACAAACAAATGGAAAAACATTCCATGCT 2413 chr4ptel1M 867540 CATGGATGGATTGAACCAACATTGTAAACAGGATAATACCACC-----TA 867584 i ivv i i i i v v iiv ii ----- L1P3_orf2#LIN 2414 CATGGATAGGAAGAATCAATATCGTGAAAATGGCCATACTGCCCAAAGTA 2463 chr4ptel1M 867585 ACTTA---ATTCAAT----TCCACATCAATCAACTATTAA 867617 i --- ---- v v v i i L1P3_orf2#LIN 2464 ATTTATAGATTCAATGCTATCCCCATCAAGCTACCATTGA 2503 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 40.33 CpG sites = 40, Kimura (unadjusted) = 41.15 Transitions / transversions = 1.54 (40/26) Gap_init rate = 0.05 (11 / 216), avg. gap size = 2.36 (26 / 11) 14 22.98 1.59 6.67 chr4ptel1M 867800 867862 (132138) (TTTA)n#Simple_repeat 1 60 (0) m_b186s252i6 7274 chr4ptel1M 867800 TTTTTTCATTTATAATATCTTTTTTA-TTATATATATATATATATTATTA 867848 v i -v - v - v v v - - (TTTA)n#Simpl 1 TTTATTTATTTAT-TTAT-TTATTTATTTATTTATTTATTTAT-TTATT- 46 chr4ptel1M 867849 TAGCTTCTTATTTA 867862 vi vi (TTTA)n#Simpl 47 TATTTATTTATTTA 60 Matrix = Unknown Transitions / transversions = 0.38 (3/8) Gap_init rate = 0.08 (5 / 62), avg. gap size = 1.00 (5 / 5) 19 9.78 11.36 0.00 chr4ptel1M 867807 867850 (132150) (AT)n#Simple_repeat 1 49 (0) m_b186s252i7 7275 chr4ptel1M 867807 ATTTATA-ATATCT-TTTTTAT-TATATATATATATATAT-TAT-TATA 867850 v - v - v v - - - (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATA 49 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.12 (5 / 43), avg. gap size = 1.00 (5 / 5) 14 22.98 1.59 6.67 chr4ptel1M 867800 867862 (132138) (TTTA)n#Simple_repeat 1 60 (0) m_b186s252i6 7274 chr4ptel1M 867800 TTTTTTCATTTATAATATCTTTTTTA-TTATATATATATATATATTATTA 867848 v i -v - v - v v v - - (TTTA)n#Simpl 1 TTTATTTATTTAT-TTAT-TTATTTATTTATTTATTTATTTAT-TTATT- 46 chr4ptel1M 867849 TAGCTTCTTATTTA 867862 vi vi (TTTA)n#Simpl 47 TATTTATTTATTTA 60 Matrix = Unknown Transitions / transversions = 0.38 (3/8) Gap_init rate = 0.08 (5 / 62), avg. gap size = 1.00 (5 / 5) 668 30.66 2.84 2.84 chr4ptel1M 868288 868569 (131431) C L1ME5_3end#LINE/L1 (304) 637 356 m_b186s551i3 7276 chr4ptel1M 868288 TCCTGCTCCTTTCACTCAGCATCA-GTTCATGTAAG-TCTCTCCAGGC-- 868333 i i ii ii - -- v - iv v i-- C L1ME5_3end#LI 637 TCTTACTTTTTTCACTCAGCACTATGTT--TTTAAGATCCATCCATGTTG 590 chr4ptel1M 868334 CTTTCTGAAATCATCCTGCTGGTCATTTCTTACAGAACAATAATATTCCA 868383 v v v -- iv iiv iii v v vvvv i i C L1ME5_3end#LI 589 CTATGTGTA--CATCTAGTCCGTTGCTTCTAACTGCTGCATAGTACTCCA 542 chr4ptel1M 868384 TAATATTCATATACCACAGTTTATTCAGCCATTCTCCAACTGATGGGCAG 868433 ii i v vi v iii v i v v i v C L1ME5_3end#LI 541 TGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCAGTGATGGACAC 492 chr4ptel1M 868434 CCAATTAGTTTCCAGTTTCTGGTCACTACAAAGAGGGCTGCCACAAACAT 868483 iv v ii ii i iv i i v iv v ii C L1ME5_3end#LI 491 CCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCTGCAATGAACAT 442 chr4ptel1M 868484 TCTTGCACCTACAGGTCCCTTTCC---CTTCTTTAAGA-TCTCTTTGGGA 868529 i i ---- v i vi--- i v v i - i C L1ME5_3end#LI 441 CCTCG----TACATGTCCCCTTATGGACCTGTGTGAGAATTTCTTTGGGA 396 chr4ptel1M 868530 TATAAGCCCAGTAGTAACACTGCTGGGTCAAAGGGTATGC 868569 vi v iiiv i v C L1ME5_3end#LI 395 TATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATGC 356 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.26 CpG sites = 49, Kimura (unadjusted) = 40.59 Transitions / transversions = 1.40 (49/35) Gap_init rate = 0.05 (13 / 281), avg. gap size = 1.23 (16 / 13) 654 31.19 1.89 1.89 chr4ptel1M 868289 868605 (131395) C L1ME4a_3end#LINE/L1 (232) 639 323 m_b186s551i4 7276 chr4ptel1M 868289 CCTGCTCCTTTCACTCAGCATCAGTTCATGTAAGTCTCTCCAGGCCTTTC 868338 ii i i i vv vivi i ii v i v - C L1ME4a_3end#L 639 CCTGCTTTTTTCACTTAACATTATATCATGAGCATTTTCCCATGTCATT- 591 chr4ptel1M 868339 TGAAATCATCCTGCTGG----TCATTTCTTACAGAACAATAATATTCCAT 868384 -- - i v vii---- ? i v ii vvvv C L1ME4a_3end#L 590 --AAAT-ATTCTTCGAAAACATNATTTTTAATGGCTGCATAATATTCCAT 544 chr4ptel1M 868385 AATATTCATATACCACAGTTTATTCAGCCATTCTCCAACTGATGGGCAGC 868434 v? vv i i i i i ? i v i v i vi C L1ME4a_3end#L 543 TNTATGGATGTACCATAATTTATTTAACCANTCCCCTATTGTTGGACATT 494 chr4ptel1M 868435 CAATTAGTTTCCAGTTTCTGGTCACTACAAAGAGGGCTGCCACAAACATT 868484 i iv v i i v ii i i v iv v ii i C L1ME4a_3end#L 493 TAGGTTGTTTCCAATTTTTCGCTATTATAAATAATGCTGCGATGAACATC 444 chr4ptel1M 868485 CTTGCACCTACAGGTCCCT-TTCCCTTCTTTAAG-ATCTCTTTGGGATAT 868532 i v v -- ii - ? v v i i v- i i i v C L1ME4a_3end#L 443 CTTGTACATAAA--TCTTTGTNCACATCTCTGATTATTTCCTTAGGATAA 396 chr4ptel1M 868533 AAGCCCAGTAGTAACACTGCTGGGTCAAAGGGTATGCAGAATTTGATGGC 868582 vv i v iiv i i ? v v v v C L1ME4a_3end#L 395 ATTCCTAGAAGTGGAATTACTGGGTCAAAGGGTATGNACATTTTTAAGGC 346 chr4ptel1M 868583 TTTTTGAGTATAGTTCCAAATTG 868605 vivii v v C L1ME4a_3end#L 345 TTTTGATACATATTGCCAAATTG 323 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 42.26 CpG sites = 54, Kimura (unadjusted) = 42.26 Transitions / transversions = 1.26 (54/43) Gap_init rate = 0.03 (9 / 316), avg. gap size = 1.33 (12 / 9) 699 25.79 2.15 3.48 chr4ptel1M 868373 868605 (131395) C L1ME3F_3end#LINE/L1 (438) 552 323 m_b186s551i5 7276 chr4ptel1M 868373 ATAATATTCCATAATATTCATATACCACAGTTTATTCAGCCATTCTCCAA 868422 vi i vv i i v vi C L1ME3F_3end#L 552 ATAATATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTCCTG 503 chr4ptel1M 868423 CTGATGGGCAGCCAATTAGTTTCCAGTTTCTGGTCACTACAAAGAGGGCT 868472 ii i viiiiv v i v ii i i v v C L1ME3F_3end#L 502 TCGATGGACATTTGGGTTGTTTCCAGTTTTTTGCTATTACGAACAGTGCT 453 chr4ptel1M 868473 GCCACAAACATTCTTGCACCTACAGGTC-CCT--TTCCCTTCTTTAAGA- 868518 i ii ---- v - -- v v v v vi - C L1ME3F_3end#L 452 GCTATGAACATTCTTG----TACATGTCTCCTGGTGCACATGTGCAAGAG 407 chr4ptel1M 868519 TCTCTTTGGGATATAAGCCCAGTAGTAACACTGCTGGGTCAAAGGGTATG 868568 i i v i vi i v iiv i iv C L1ME3F_3end#L 406 TTTCTCTTGGGTATATACCTAGGAGTGGAATTGCTGGGTCGTAGGGTATG 357 chr4ptel1M 868569 CAGAAT-TTGATGGCTTTTTGAGTATAGTTCCAAATTG 868605 - - v --i vi - i v C L1ME3F_3end#L 356 C-GAATGTTCA--ACTTTACGAG-ATAATGCCAAATTG 323 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 29.58 CpG sites = 33, Kimura (unadjusted) = 32.20 Transitions / transversions = 1.32 (33/25) Gap_init rate = 0.05 (12 / 232), avg. gap size = 1.08 (13 / 12) 241 29.48 4.94 3.66 chr4ptel1M 868678 868839 (131161) L1PREC2_orf2#LINE/L1 2728 2891 (403) m_b186s551i6 7277 chr4ptel1M 868678 CACACCTAGAA--ACCTAGTGTTCAATAA-TCT--CAAAGACCCAAGTTA 868722 v -- i ii v i i -v -- i -- iv L1PREC2_orf2# 2728 CACACCTACAACCATCTGATCTTCGACAAAGCTGACAAAAAC--AAGCAA 2775 chr4ptel1M 868723 CTGGGAGTAAAAACTCACTATTCAACAAAAACTGCTGGGAAAATTGGAAA 868772 iv -- ii v i viv v i vv L1PREC2_orf2# 2776 TGGGGA--AAGGACTCCCTATTCAATAAATGGTGCTGGGATAACTGGCTA 2823 chr4ptel1M 868773 GCAATCTGCAGAA-ATTACATTTTGATAAACATT--TTATACCATATGTC 868819 v v - iv vi v i--v v -- i iiv L1PREC2_orf2# 2824 GCCATATGCAGAAGATTGAAACTGGAC--CCCTTCCTTACACCATATACA 2871 chr4ptel1M 868820 AGGATTGGCTCCAAATGTAT 868839 ii iii v i v L1PREC2_orf2# 2872 AAAATCAACTCAAGATGGAT 2891 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 37.15 CpG sites = 25, Kimura (unadjusted) = 38.20 Transitions / transversions = 1.19 (25/21) Gap_init rate = 0.07 (11 / 161), avg. gap size = 1.27 (14 / 11) 229 30.33 1.89 2.53 chr4ptel1M 869054 869212 (130788) L1PA10_3end#LINE/L1 19 176 (739) m_b186s551i8 7277 chr4ptel1M 869054 AAAGAATTGATTCAAATGTATAAGAATTAGAACTATCA--TCCATTTGAT 869101 i i v vv v i v- i v v --i vi v L1PA10_3end#L 19 AAGGAACTTAAACAAATTTACAAGAAA-AAAACAAACAACCCCATTAAAA 67 chr4ptel1M 869102 GGATGGCAAAAGG-ATGAGGCCAGGCAGTTGTCAAAAGAAGAAATCTAAG 869150 i vv i i- i-- i v v v i v L1PA10_3end#L 68 AGTGGGCAAAGGACATGAA--CAGACACTTCTCAAAAGAAGACATTTATG 115 chr4ptel1M 869151 CTATCCGCAGCCATATGAAAAAAATGCTCCAAATCATTACTATTTAGAAA 869200 vii vi iv - v v i iv vv i L1PA10_3end#L 116 CGGCCAACAAACATATGAAAAAAA-GCTCAACATCACTGATCATTAGAGA 164 chr4ptel1M 869201 GTTAAAAATTAA 869212 iv iv i L1PA10_3end#L 165 AATGCAAATCAA 176 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.19 CpG sites = 22, Kimura (unadjusted) = 39.19 Transitions / transversions = 0.88 (22/25) Gap_init rate = 0.04 (6 / 158), avg. gap size = 1.17 (7 / 6) 273 27.31 1.45 4.48 chr4ptel1M 869054 869191 (130809) L1PA6_3end#LINE/L1 19 152 (749) m_b186s551i7 7277 chr4ptel1M 869054 AAAGAATTGATTCAAATGTATAAGAATTAGAACTATCA--TCCATTTGAT 869101 i v vv v i v- i v v --i ivi v L1PA6_3end#LI 19 AAAGAACTTAAACAAATTTACAAGAAA-AAAACAAACAACCCCATCAAAA 67 chr4ptel1M 869102 GGATGGCAAAAGGATGAGGCCAGGCAGTTGTCAAAAGAAGAAATCTAAGC 869151 i - vv iv iv i v v v i v L1PA6_3end#LI 68 AG-TGGGCAAAGGATATGAACAGACACTTCTCAAAAGAAGACATTTATGC 116 chr4ptel1M 869152 TATCCGCAGCCATATGAAAAAAATGCTCCAAATCATTACT 869191 vii vi v i - --- i L1PA6_3end#LI 117 AGCCAACAGACACATG-AAAAAATGCTC---ATCATCACT 152 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 34.06 CpG sites = 16, Kimura (unadjusted) = 34.06 Transitions / transversions = 0.80 (16/20) Gap_init rate = 0.05 (7 / 137), avg. gap size = 1.14 (8 / 7) 268 26.94 0.93 2.86 chr4ptel1M 869106 869212 (130788) L1PB4_3end#LINE/L1 72 176 (727) m_b186s551i9 7277 chr4ptel1M 869106 GGCAAAAGG-ATGAGGCCAGGCAGTTGTCAAAAGAAGAAATCTAAGCTAT 869154 i i- i-- i v v v vi vii L1PB4_3end#LI 72 GGCAAAGGACATGAA--CAGACATTTTTCAAAAGAAGACATACAAGCGGC 119 chr4ptel1M 869155 CCGCAGCCATATGAAAAAAATGCTCCAAATCATTACTATTTAGAAAGTTA 869204 vi iv - v v i v vv i i iv i L1PB4_3end#LI 120 CAACAAACATATG-AAAAAATGCTCAACATCACTAATCATCAGAGAAATG 168 chr4ptel1M 869205 AAAATTAA 869212 v L1PB4_3end#LI 169 CAAATTAA 176 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 33.70 CpG sites = 14, Kimura (unadjusted) = 33.70 Transitions / transversions = 1.00 (14/14) Gap_init rate = 0.04 (4 / 106), avg. gap size = 1.00 (4 / 4) 16 13.08 0.00 0.00 chr4ptel1M 869871 869895 (130105) (A)n#Simple_repeat 1 25 (0) m_b186s252i8 7278 chr4ptel1M 869871 AAAAAAAAAATAAAATAAAAAGAAA 869895 v v i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAA 25 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 17 12.81 2.94 0.00 chr4ptel1M 870123 870156 (129844) (ATT)n#Simple_repeat 1 35 (0) m_b186s252i9 7279 chr4ptel1M 870123 ATTATTAAT-TTCCTATTTTTATTATTATTATTAT 870156 v - vi v (ATT)n#Simple 1 ATTATTATTATTATTATTATTATTATTATTATTAT 35 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 318 20.76 6.41 1.22 chr4ptel1M 870159 870236 (129764) C MIRc#SINE/MIR (110) 158 77 m_b186s601i28 7280 chr4ptel1M 870159 TATTATTATCCTATTTTTACAAATAAGGAAATTGAG--TCAGATCAGATG 870206 ivv i i i -- -v i v C MIRc#SINE/MIR 158 TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGA-GAGGTT 110 chr4ptel1M 870207 AAGTGACTTGCTTGA---CACATAAATAGTAGG 870236 iii --- i iv i C MIRc#SINE/MIR 109 AAGTGACTTGCCCAAGGTCACACAGCTAGTAAG 77 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 25.07 CpG sites = 11, Kimura (unadjusted) = 25.07 Transitions / transversions = 2.20 (11/5) Gap_init rate = 0.04 (3 / 77), avg. gap size = 2.00 (6 / 3) 181 22.16 0.00 9.76 chr4ptel1M 870215 870259 (129741) L2a_3end#LINE/L2 469 509 (8) m_b186s601i29 7281 chr4ptel1M 870215 TGCTTGACACATAAATAGTAGGAGCTTAATCCACACTTGTTGAGT 870259 i i ---- v i vv i i i L2a_3end#LINE 469 TGCCTGGCACATA----GTAGGCGCTCAATAAATATTTGTTGAAT 509 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 26.73 CpG sites = 6, Kimura (unadjusted) = 26.73 Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4) 31 26.63 2.22 3.76 chr4ptel1M 870357 870378 (129622) (TCTC)n#Simple_repeat 1 20 (113) m_b186s252i10 7282 chr4ptel1M 870357 TCTCTCTCTGCAGATCTTTCTT 870378 - -vv i i (TCTC)n#Simpl 1 TCTCTCTCT-C-TCTCTCTCTC 20 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.10 (2 / 21), avg. gap size = 1.00 (2 / 2) 40 10.19 2.67 0.00 chr4ptel1M 870379 870453 (129547) (TCTA)n#Simple_repeat 1 77 (0) c_b186s251i1 7283 chr4ptel1M 870379 TCTAT-TATCTATCTATCTATCTATCTATC-ACCCATCTATCCATCCATC 870426 - - i i i i (TCTA)n#Simpl 1 TCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATC 50 chr4ptel1M 870427 CATCCATCTATCTATCAATCTATCTAT 870453 i i v (TCTA)n#Simpl 51 TATCTATCTATCTATCTATCTATCTAT 77 Matrix = Unknown Transitions / transversions = 6.00 (6/1) Gap_init rate = 0.03 (2 / 74), avg. gap size = 1.00 (2 / 2) 31 26.63 2.22 3.76 chr4ptel1M 870454 870565 (129435) (TCTC)n#Simple_repeat 21 132 (1) m_b186s252i10 7284 chr4ptel1M 870454 GTCTGTTTTTCTGTTTGCT-TATCTATCTC-CTCTCTCTCTGTTTTTCTG 870501 v v i i v i - - v v - v i i v (TCTC)n#Simpl 21 CTCTCTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 69 chr4ptel1M 870502 TCTCCTTATCTATCTC-CTATCTCTCTATCTCTCTCTCTATCTATCATGT 870550 ii v v - v v v v - v (TCTC)n#Simpl 70 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TCT 118 chr4ptel1M 870551 CTGGTTTATCTCTCT 870565 -v i v (TCTC)n#Simpl 119 CT-CTCTCTCTCTCT 132 Matrix = Unknown Transitions / transversions = 0.50 (8/16) Gap_init rate = 0.05 (6 / 111), avg. gap size = 1.00 (6 / 6) 16 13.08 0.00 0.00 chr4ptel1M 870759 870783 (129217) (C)n#Simple_repeat 1 25 (0) m_b186s252i11 7285 chr4ptel1M 870759 CCCCCCCCTCCCCACCCCCGCCCCC 870783 i v v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCC 25 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 249 32.39 0.00 0.00 chr4ptel1M 872053 872123 (127877) C MIR3#SINE/MIR (41) 167 97 m_b186s601i30 7286 chr4ptel1M 872053 AGAGCTTTTTTAGTCCAACCCTCTCGTTTCACAGATGACAAGGAGGAGTC 872102 v iv i i i i vi iivv v C MIR3#SINE/MIR 167 AGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGC 118 chr4ptel1M 872103 CCTGGGGAGTCACAGGATTTG 872123 v i ii v viv i C MIR3#SINE/MIR 117 CCAGAGAGGTGAAGTGACTTG 97 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 43.64 CpG sites = 13, Kimura (unadjusted) = 43.64 Transitions / transversions = 1.30 (13/10) Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0) 243 27.42 1.61 0.00 chr4ptel1M 872189 872250 (127750) C L3#LINE/CR1 (127) 3972 3910 m_b186s601i31 7287 chr4ptel1M 872189 TCCAAGGCCAGGGAAGCCCCT-CCTGTCAAGGCAATCTATCCCCTTCTTG 872237 iv v i ivi v - v? i ii i i v i C L3#LINE/CR1 3972 TCCAGTGACGGGGAGCTCACTACCTCNCGAGGCAGCCCATTCCATTTTTG 3923 chr4ptel1M 872238 GACAGCTCTAATT 872250 i C L3#LINE/CR1 3922 GACAGCTCTGATT 3910 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 31.02 CpG sites = 11, Kimura (unadjusted) = 36.19 Transitions / transversions = 1.83 (11/6) Gap_init rate = 0.02 (1 / 61), avg. gap size = 1.00 (1 / 1) 465 31.78 11.08 7.31 chr4ptel1M 872398 872767 (127233) C L3#LINE/CR1 (413) 3686 3304 m_b186s601i32 7287 chr4ptel1M 872398 CTGGACTCTCCACCACAGTGTTCATCATCTTCTAGACAC--TCC----TC 872441 ii i i ivv v iiiv i i i -- ---- v C L3#LINE/CR1 3686 CCAGACCCTTCACCATCCTGGTCGCTCTCCTCTGGACGCGCTCCAGTTTG 3637 chr4ptel1M 872442 TCC-TGGCTATCTGGCTATCTGGTATCCA------ACCGTGATACTCTAT 872484 v- v iv vivv v iii ------ v ii i v C L3#LINE/CR1 3636 TCAATGTCCCTCTTAAAATGTGGCGCCCAGAACTGAACGCAATACTCCAG 3587 chr4ptel1M 872485 CT----TCTGAGAAG---AGAGTATGATGGGGTTATCCCCTTCCTGTCCC 872527 v ---- vv --- iiii ii iv i vv?i C L3#LINE/CR1 3586 ATGTGGTCTGACCAGCGCAGAGTACAGCGGGACTATTACCTCCCTTGNTC 3537 chr4ptel1M 872528 TGGAAGCTTTGGCTCTG--AGTGCAGCCCAAGGTCACGT--GCTATTTTT 872573 vi v ivi i-- i i i ii i -- - C L3#LINE/CR1 3536 TGGACACTATACTTCTATTAATGCAGCCTAAGATTGCATTAGCT-TTTTT 3488 chr4ptel1M 872574 AATGTACATAATGTACCATATTGCACTGGAGACTCCTATTGAACTTGCAG 872623 ii---- ------i i ii vv i v i i C L3#LINE/CR1 3487 GG----CA------GCCACATCACACTGTTGGCTCATATTGAGCTTGCGG 3448 chr4ptel1M 872624 TCCACTAAAACATCTTTTTTTTTTTTTTCAGAACAAGTGCTATATACATA 872673 v vi vvv i ivivv viv -------- C L3#LINE/CR1 3447 TCAACTAAAACCCCTAGGTCTTTTTCACGTGAACTGCTGCTA-------- 3406 chr4ptel1M 872674 TATAGACAGATATTCCCCCAACCCCCTTTATACTTGTGAAGTTGATTTTT 872723 --- v vi i -- i ---- i v C L3#LINE/CR1 3405 ---AGCCAGATCCTCTCC--ATCC----TGTACTTGTGCAGTTGATTTTT 3365 chr4ptel1M 872724 TGTCCC----------------CATTTATCTC-ATGAAATTATATCTTAC 872756 vv ---------------- i -i v vi ii C L3#LINE/CR1 3364 TGAACCTAAATGCAGGACTTTACATTTATCCCTGTTAAATTTCATCTTGT 3315 chr4ptel1M 872757 AAGATTCAGTC 872767 vi v i i C L3#LINE/CR1 3314 TGGTTTCGGCC 3304 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 39.39 CpG sites = 64, Kimura (unadjusted) = 43.06 Transitions / transversions = 1.42 (64/45) Gap_init rate = 0.10 (38 / 369), avg. gap size = 1.82 (69 / 38) 238 28.91 5.99 4.73 chr4ptel1M 872921 873087 (126913) C L2#LINE/L2 (496) 2586 2418 m_b186s601i33 7288 chr4ptel1M 872921 GGGGAAGCAAAGAGACAGAAGGATGACTCCTAAGT----GAAACCCTGAG 872966 i i vi i v -- v i ---- i--- C L2#LINE/L2 2586 GAGAAAGAGAGGAGTCA--AGGATGACTCCAAGGTTTTTGG---CCTGAG 2542 chr4ptel1M 872967 GTGACAGGAATGATTGGGAAAT-CCTTGAAATTAG--GAGGGAAATTAGG 873013 -ii v v -- iv - v v? v v -- i i i i iv C L2#LINE/L2 2541 -CAACTGGAAGGAT--GGAGTTGCCATTNACTGAGATGGGGAAGACTGCG 2495 chr4ptel1M 873014 AAGGGGGCAGGCTTGAGGG--AAGATCATGGGTTCCATTTGGGGCAAGCA 873061 iii i i -- v i vi v i v iv C L2#LINE/L2 2494 GGAGGAGCAGGTTTGAGGGGGAAGATCAGGAGTTCAGTTTTGGACATGTT 2445 chr4ptel1M 873062 GAGAGTGAG-TAACTATGGGACATCCA 873087 i vv - iv vi C L2#LINE/L2 2444 AAGTTTGAGATGCCTATTAGACATCCA 2418 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 37.71 CpG sites = 26, Kimura (unadjusted) = 37.71 Transitions / transversions = 1.30 (26/20) Gap_init rate = 0.08 (13 / 166), avg. gap size = 1.38 (18 / 13) 193 34.29 1.43 0.00 chr4ptel1M 873094 873163 (126837) L2d_3end#LINE/L2 443 513 (3) m_b186s601i34 7289 chr4ptel1M 873094 GTTCCCTAGCTCTCTTAGCACAGCCCTTGGCACA-AATATGCACTGGGTG 873142 i vvv v i iv vi - i v i vii i L2d_3end#LINE 443 GTTCCCCACAGCGCCTAGCACAGTGCTGAGCACATAGTAGGCGCTCAATA 492 chr4ptel1M 873143 AAAATTTACTGACTTGTTGAT 873163 v i ii i vi L2d_3end#LINE 493 AATACTTGTTGATTGATTGAT 513 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 44.81 CpG sites = 14, Kimura (unadjusted) = 47.55 Transitions / transversions = 1.40 (14/10) Gap_init rate = 0.01 (1 / 69), avg. gap size = 1.00 (1 / 1) 218 24.58 1.69 3.45 chr4ptel1M 873096 873154 (126846) L2b_3end#LINE/L2 399 456 (10) m_b186s601i35 7289 chr4ptel1M 873096 TCCCTAGCTCTCTTAGCACAGCCCTTGGCACA-AATATGCACTGGGTGAA 873144 i v i-- ?v i - i v i vi i L2b_3end#LINE 399 TCCCCAGCGCC--TAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAA 446 chr4ptel1M 873145 AATTTACTGA 873154 v ii L2b_3end#LINE 447 TATTTGTTGA 456 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 28.70 CpG sites = 9, Kimura (unadjusted) = 31.36 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.05 (3 / 58), avg. gap size = 1.00 (3 / 3) 42 10.40 0.00 0.00 chr4ptel1M 873196 873258 (126742) (TG)n#Simple_repeat 1 63 (0) c_b186s251i2 7290 chr4ptel1M 873196 TGTGTGTGTGTGTGTGTGTGTATGTGTGTGTGTGAATGTGCACGTGTGTG 873245 i vi iii (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr4ptel1M 873246 TGTGTGTGTGTGT 873258 (TG)n#Simple_ 51 TGTGTGTGTGTGT 63 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0) 23 15.50 0.00 0.00 chr4ptel1M 874106 874148 (125852) (TGAA)n#Simple_repeat 1 43 (0) m_b186s252i12 7291 chr4ptel1M 874106 TGAATGAAAGAAGAAATGAATGAATGGATGAGTGAAGGAATGA 874148 v vi i i v (TGAA)n#Simpl 1 TGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGA 43 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 372 35.84 8.09 0.00 chr4ptel1M 874656 874828 (125172) C L3#LINE/CR1 (3) 4096 3910 m_b186s601i36 7292 chr4ptel1M 874656 AGAATTAGAGAATGTCCAAGGTGGAAGGGATCGTAGTGACCCCCAAGTCC 874705 i v v vi v i v v ii vi v C L3#LINE/CR1 4096 AGAATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCC 4047 chr4ptel1M 874706 AGCCTGT-GT---GTGAAAGAGTCCTCAGCACAATACATTTGACAAGTGA 874751 i vi-i ---i v i i iivvi i ivii i C L3#LINE/CR1 4046 AACCTCCCATCCAATGCAGGAATCCCTTCTACAACATCCCTGACAAGTGG 3997 chr4ptel1M 874752 -CATTTAGGCTTT---------TCTCCAGGGAAGGAAAATCCCCTGAAAA 874791 - ii v i ---------i v v ii iii v ivvvv C L3#LINE/CR1 3996 TCATCCAGCCTCTGCTTGAACACCTCCAGTGACGGGGAGCTCACTACCTC 3947 chr4ptel1M 874792 CTAAGCCAGCCAGTTCCACTTTTGAATAACTCTATTT 874828 ?ii v vi i i i i iv C L3#LINE/CR1 3946 NCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGATT 3910 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 50.35 CpG sites = 38, Kimura (unadjusted) = 51.72 Transitions / transversions = 1.58 (38/24) Gap_init rate = 0.02 (4 / 172), avg. gap size = 3.50 (14 / 4) 307 35.39 10.49 0.56 chr4ptel1M 875484 875645 (124355) C L3#LINE/CR1 (84) 4015 3838 m_b186s601i37 7293 chr4ptel1M 875484 CAGCCCCCCCAACAAGTGGTCAATCAGTCTTT-----AATGCCTTCTACC 875528 i vi ii vi i i ----- ii i - vi C L3#LINE/CR1 4015 CAACATCCCTGACAAGTGGTCATCCAGCCTCTGCTTGAACACCTCC-AGT 3967 chr4ptel1M 875529 AAGGGAGATCT-GCTACTTCACAAGATTTTCTTTTCCACTTTAGGGGAGT 875577 i v i v -i i ? i iivvi iv i v iv i C L3#LINE/CR1 3966 GACGGGGAGCTCACTACCTCNCGAGGCAGCCCATTCCATTTTTGGACAGC 3917 chr4ptel1M 875578 GCTCATTTTTGAGAAGGTTTTCCTTCCAT----------TTTACCCCTCT 875617 v v v iii v i vi ---------- i i i i C L3#LINE/CR1 3916 TCTGATTGTTAGAAAGTTCTTCCTTATATTGAGCCGAAATCTGCCTCCCT 3867 chr4ptel1M 875618 ATAA-TTTCAGTCATAAAGCCTAGATTTG 875645 i - i vi viiv v i C L3#LINE/CR1 3866 GTAACTTCCACCCATTGGTCCTAGTTCTG 3838 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 50.45 CpG sites = 38, Kimura (unadjusted) = 51.82 Transitions / transversions = 2.00 (38/19) Gap_init rate = 0.03 (5 / 161), avg. gap size = 3.60 (18 / 5) 425 24.43 4.44 6.02 chr4ptel1M 875748 875882 (124118) C MIRc#SINE/MIR (120) 148 16 m_b186s601i38 7294 chr4ptel1M 875748 CTCATTTTATAGATGGGGAAACTGAGAC-CA-AGTAGTT--GTGACTTGG 875793 i i i i - - vi -- v C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr4ptel1M 875794 TCAGGGTCACCCATCTAGTAAGTGTCTGAAGCCAGATGTAAACTCAGGAA 875843 i i v v v v - i -----i -- C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAG-AGCCGG-----GACTC--GAA 57 chr4ptel1M 875844 CATGAGATTGCTTGACTTCAGGCTCAGGACTA--TCCATTG 875882 viii vi v i i i ii vi v-- i C MIRc#SINE/MIR 56 CCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTG 16 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.26 CpG sites = 20, Kimura (unadjusted) = 30.43 Transitions / transversions = 1.82 (20/11) Gap_init rate = 0.09 (12 / 134), avg. gap size = 1.17 (14 / 12) 357 31.76 8.87 2.31 chr4ptel1M 876111 876313 (123687) C L3#LINE/CR1 (677) 3422 3207 m_b186s601i39 7293 chr4ptel1M 876111 CGCATGAACT-CTGATTTTGCTAACTTTCCCTCATCTTTAACTAATAGAG 876159 i i - -i vv i iv iii ii i vv vi iv C L3#LINE/CR1 3422 CACGTGAACTGCTG-CTAAGCCAGATCCTCTCCATCCTGTACTTGTGCAG 3374 chr4ptel1M 876160 TTTATTTTGGAGATCTGATAGCAGGACTTTACACTTATT----TTA---T 876202 v vvii i i vv i i---- --- C L3#LINE/CR1 3373 TTGATTTTTTGAACCTAAATGCAGGACTTTACATTTATCCCTGTTAAATT 3324 chr4ptel1M 876203 TCA---------TTTTGGCCAATTCTTCTAGTCAGTTGCTGCTATTTTTC 876243 --------- i v iv i i --- ii vv i? i C L3#LINE/CR1 3323 TCATCTTGTTGGTTTCGGCCCATCGTTCCAGCC---TGTCGAGATCNTTT 3277 chr4ptel1M 876244 TGGATCCCAATTTTGATCATCCACTCAGTTGGCTATTTCT-TCATCTTTA 876292 i iii i - ?ivvi i ii -i v i C L3#LINE/CR1 3276 TGAATCTTGATTCTG-TCATCCANCGTATTAGCTATCCCTCCCAGCTTTG 3228 chr4ptel1M 876293 TGCCTTTTACAAGTTTGATAA 876313 i v i i i C L3#LINE/CR1 3227 TGTCATCTGCAAATTTGATAA 3207 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 39.86 CpG sites = 43, Kimura (unadjusted) = 44.62 Transitions / transversions = 2.15 (43/20) Gap_init rate = 0.05 (10 / 202), avg. gap size = 2.30 (23 / 10) 254 29.73 9.84 0.75 chr4ptel1M 877133 877254 (122746) C MIR3#SINE/MIR (23) 185 53 m_b186s601i40 7295 chr4ptel1M 877133 AGAGTTGGAAAGGGACCTTTGAGGCCATTTATACCATCACTTCCATTTCA 877182 i - v ii i vv v v iii i C MIR3#SINE/MIR 185 AGAGCTGGAA-GGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTA 137 chr4ptel1M 877183 TGAAGGAGGGAGATAAGTGCCAGAGA----------CTTAGC-AAGGCCA 877221 iii v i iv i vv ---------- iv - i C MIR3#SINE/MIR 136 CAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCA 87 chr4ptel1M 877222 -ACAGGAAAGAAGGGGCAGAGGAGGGATTCAAAC 877254 - v? ivv v vv i vi C MIR3#SINE/MIR 86 CACAGCNAGTTAGTGGCAGAGCCGGGACTAGAAC 53 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 38.98 CpG sites = 19, Kimura (unadjusted) = 38.98 Transitions / transversions = 1.12 (19/17) Gap_init rate = 0.03 (4 / 121), avg. gap size = 3.25 (13 / 4) 244 30.23 14.73 0.00 chr4ptel1M 877164 877292 (122708) C MIRc#SINE/MIR (110) 158 11 m_b186s601i41 7295 chr4ptel1M 877164 TACCATCACTTCCATTTCATGAAGGAGGGAGATAAGTGCCAGAGA----- 877208 ii i iii i iii v i iv i vvi ----- C MIRc#SINE/MIR 158 TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTA 109 chr4ptel1M 877209 -----CTTAGC-AAGGCCA-ACAGGAAAGAAGGGGCAGAGGAGGGATTCA 877251 ----- iv - i - vv iv v vv i i C MIRc#SINE/MIR 108 AGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCG 59 chr4ptel1M 877252 AACT--GCTCTGC--GAC---AAATCCAGCCCACTTTCGATTGCACCA 877292 i-- v v -- --- i iv v v i C MIRc#SINE/MIR 58 AACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCA 11 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 38.56 CpG sites = 23, Kimura (unadjusted) = 39.88 Transitions / transversions = 1.44 (23/16) Gap_init rate = 0.05 (7 / 128), avg. gap size = 2.71 (19 / 7) 274 29.21 4.44 1.08 chr4ptel1M 877891 877980 (122020) C MIRc#SINE/MIR (163) 105 13 m_b186s601i42 7296 chr4ptel1M 877891 GAATTGCCCAGATATTA-ATAATCAGTTTGTGTCAGG--TGGGATTTGAA 877937 v - vi i - i iii vv v i--i i i C MIRc#SINE/MIR 105 GACTTGCCCA-AGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAA 57 chr4ptel1M 877938 CTCAGGTCTT-CTGGCTTTAAGGACAGCTTTCTATCCACTACAC 877980 i - i ii vv ivi v i C MIRc#SINE/MIR 56 CCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCAC 13 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 34.88 CpG sites = 17, Kimura (unadjusted) = 38.65 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.04 (4 / 89), avg. gap size = 1.25 (5 / 4) 199 29.42 13.47 8.42 chr4ptel1M 878290 878482 (121518) C L2c_3end#LINE/L2 (0) 478 277 m_b186s601i43 7297 chr4ptel1M 878290 ATTCAATTCAACTCAACAAATATTTGATTGGAT-TTTATGATGGGTCAAG 878338 - -i i - iii-ii iv v i i C L2c_3end#LINE 478 ATTCA-TTCA-TTCAACAAACATTT-ATTGAGCGCCTACTATGTGCCAGG 432 chr4ptel1M 878339 CAGTACATTGAGTTGTGAGAGCAGAAAGGTGAGCAAATCATTGTACTCAG 878388 ---------- i - i -i v i ii iv iv - i v C L2c_3end#LINE 431 C----------GCTG-GGGA-TACAAAGATGAATAAGACACGGT-CCCTG 395 chr4ptel1M 878389 CCTT----GAGCTTTCAGCCTTGTGGAGCAAGGAGGGTGTGTGGACAGGT 878434 i ---- iv i v -i ivi iii? ii ii C L2c_3end#LINE 394 CCCTCAAGGAGCTCACAGTCTAGTGGAG-GAGACAGACANGTAAACAGAC 346 chr4ptel1M 878435 GGT---AACAGAAG------------GCCATA-----AGTG-ACACAGAG 878463 ii --- i v ------------ i ----- i- v i C L2c_3end#LINE 345 AATTACAATACAAGTTAATGATAAGTGCTATAATGGGAGTATAGACAGGG 296 chr4ptel1M 878464 TGCCATGGGAGCATAGGGG 878482 i i i C L2c_3end#LINE 295 TGCTATGGGAGCACAGAGG 277 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 39.11 CpG sites = 41, Kimura (unadjusted) = 41.26 Transitions / transversions = 3.73 (41/11) Gap_init rate = 0.12 (23 / 192), avg. gap size = 1.87 (43 / 23) 192 28.99 5.80 0.00 chr4ptel1M 878577 878645 (121355) L3#LINE/CR1 904 976 (3123) m_b186s601i44 7298 chr4ptel1M 878577 GAGGAGAAAAATAGATTTGAGAAGTGAATAGCTAGCTA---AAATGTCAT 878623 i iivi v i i i --- i vii L3#LINE/CR1 904 GAAGAGAAAGGAGGATATGGGAAGTGAACAGCTGGCTACGTAGATGGTGT 953 chr4ptel1M 878624 CCAA-AATTGCAGTTAGATTTCT 878645 v - iv v v i v L3#LINE/CR1 954 CGAAGAACAGGATTTGGTTTTCT 976 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 37.75 CpG sites = 12, Kimura (unadjusted) = 37.75 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.03 (2 / 68), avg. gap size = 2.00 (4 / 2) 243 29.84 3.68 1.44 chr4ptel1M 878646 878781 (121219) L1ME3C_3end#LINE/L1 41 179 (691) m_b186s551i10 7299 chr4ptel1M 878646 AGAAAATACAAAAATGAGTATGATGAATGGTTAAAGGATATGAACAGGTA 878695 i v v viv i - vi vi i i L1ME3C_3end#L 41 AGAAAACAGACAACCCAATA-GAAAAATGGGCAAAAGATATGAACAGGCA 89 chr4ptel1M 878696 GTTTCCCAAGGGAAACAATTCAAA-----AATAGCCATGTGGACAAATTC 878740 i - v iii iiv i? i ----- iv i i v i v L1ME3C_3end#L 90 ATT-CACAGAAGAGGAAACNCGAATGGCCAATAAACATATGAAAAGATGC 138 chr4ptel1M 878741 TCCAAATCAATAATAATTAGAAAAATCCAAATTAAAGCAAC 878781 v vv v i i ii v i ? L1ME3C_3end#L 139 TCAACCTCACTAGTAATCAGGGAAATGCAAATTAAAACNAC 179 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 38.80 CpG sites = 24, Kimura (unadjusted) = 40.11 Transitions / transversions = 1.50 (24/16) Gap_init rate = 0.02 (3 / 135), avg. gap size = 2.33 (7 / 3) 319 26.36 4.50 0.87 chr4ptel1M 878671 878781 (121219) L1ME5_3end#LINE/L1 68 182 (759) m_b186s551i11 7299 chr4ptel1M 878671 AATGGTTAAAGGATATGAACAGGTAGTTTCCCAAGGGAAACAATTCAAAA 878720 vi i i v vi i iii - ii i L1ME5_3end#LI 68 AATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAGGA-AACCCGAAA 116 chr4ptel1M 878721 A--TAGC---CATGTGGACAAATTCTCCAAATCAATAATAATTAGAAAAA 878765 i-- i --- i i v i v v v v i i i L1ME5_3end#LI 117 GGCTAACAAGCATATGAAGAGATGCTCAAACTCATTAGTAATCAGAGAAA 166 chr4ptel1M 878766 TCCAAATTAAAGCAAC 878781 v i L1ME5_3end#LI 167 TGCAAATTAAAACAAC 182 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 32.49 CpG sites = 20, Kimura (unadjusted) = 33.95 Transitions / transversions = 2.22 (20/9) Gap_init rate = 0.03 (3 / 110), avg. gap size = 2.00 (6 / 3) 219 25.00 1.92 0.00 chr4ptel1M 879514 879565 (120435) MIR#SINE/MIR 71 123 (139) m_b186s601i46 7300 chr4ptel1M 879514 CAATTGCTTACTGTGTGACCCTGGACAAGTCACTTAATA-CCAAATGCCT 879562 v i vi i i i iv- ivvi MIR#SINE/MIR 71 CACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCT 120 chr4ptel1M 879563 CAG 879565 MIR#SINE/MIR 121 CAG 123 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 31.20 CpG sites = 8, Kimura (unadjusted) = 31.20 Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.02 (1 / 51), avg. gap size = 1.00 (1 / 1) 234 16.22 0.00 0.00 chr4ptel1M 879514 879550 (120450) MIRc#SINE/MIR 75 111 (157) m_b186s601i45 7300 chr4ptel1M 879514 CAATTGCTTACTGTGTGACCCTGGACAAGTCACTTAA 879550 v i vi i i MIRc#SINE/MIR 75 CACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAA 111 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 18.61 CpG sites = 4, Kimura (unadjusted) = 18.61 Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 249 26.92 17.53 0.44 chr4ptel1M 880360 880553 (119447) L2#LINE/L2 2115 2341 (741) m_b186s601i47 7301 chr4ptel1M 880360 TCTCTGGGTTTTCATGATGTTGCTTTCTCCTGCTTTGCCTC-TACCT-AT 880407 v v i i v iiiii vi v v - - i L2#LINE/L2 2115 TCACTTGGCTTCCAGGACACCACACTCTCCTGGTTTTCCTCCTACCTCAC 2164 chr4ptel1M 880408 GGGCCTGCTCCTTCTTGGGCTCC---ACTGGGGCGT----ATCTTCC--A 880448 v - ii v ---i vv v ---- i -- L2#LINE/L2 2165 TGGCC-GCTCCTTCTCAGTCTCCTTTGCTGGTTCCTCCTCATCTCCCCGA 2213 chr4ptel1M 880449 TGTCCCAAC---------CCCCAGA--TCCATCCT--GATCT-TCCTCCT 880484 iv i? --------- i-- vi -- i - i i L2#LINE/L2 2214 CCTCTNAACGTTGGAGTGCCCCAGGGCTCAGTCCTTGGACCTCTTCTCTT 2263 chr4ptel1M 880485 TTCTCTCAACACTC-TTCCC--GGTGACCACATCAGGT------GTTTTG 880525 i v v -i -- i v vi ------ i i L2#LINE/L2 2264 CTCTATCTACACTCACTCCCTNGGTGATCTCATCCAGTCTCATGGCTTTA 2313 chr4ptel1M 880526 GGGAGCATCTCTGTGCATGTGACTCCCA 880553 iiv v v i vvi L2#LINE/L2 2314 AATACCATCTATATGCTGATGACTCCCA 2341 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 34.36 CpG sites = 30, Kimura (unadjusted) = 34.36 Transitions / transversions = 1.36 (30/22) Gap_init rate = 0.07 (13 / 193), avg. gap size = 2.69 (35 / 13) 316 35.71 11.88 2.26 chr4ptel1M 880671 881074 (118926) C L2#LINE/L2 (77) 3005 2564 m_b186s601i48 7297 chr4ptel1M 880671 AACAGCAAGTTGGTCAGGATGGCTGGATC--ATCAAGGGACAGGAAAGAT 880718 vv i vi v -- vii v vi i iii C L2#LINE/L2 3005 AACAGCAAGGAGGCCAGTGTGGCTGGAGCGGAGTGAGCGAGGGGGAGAGT 2956 chr4ptel1M 880719 GTGTACAA----AGACTGGAAAGGGAG-GAAGAACCAGGCTACAGAGG-- 880761 - vi ---- iiii i v i- ii i iii iiv -- C L2#LINE/L2 2955 G-GTAGGAGATGAGGTCAGAGAGGTAACGGGGGACCAGATCATGTAGGGC 2907 chr4ptel1M 880762 -----AGAGT-TTATAA-----TTGA-TTTTA----GAA-GCAATAGGGA 880794 ----- ivi- i ----- i- ---- i- vi i i C L2#LINE/L2 2906 CTTGTAGGCCATTGTAAGGACTTTGGCTTTTACTCTGAGTGAGATGGGAA 2857 chr4ptel1M 880795 GCCCCTGGAGG----CGAGGGGAAGGGTAGTGAGGAGTCAGCAGTCCTAC 880840 vi ----i vi i --- vi-- v v v v i C L2#LINE/L2 2856 GCCATTGGAGGGTTTTGAGCAGAGG---AGTGACA--TGATCTGACTTAC 2812 chr4ptel1M 880841 ACTTGAGGAAAATCCTTTTGACAGCTGTGGCGAAGATGG---GCGAGAGA 880887 ii v ii ii vi i i v vi ii i --- ?ii i i C L2#LINE/L2 2811 GTTTTAAAAGGATCACTCTGGCTGCTGTGTTGAGAATAGACTGNAGGGGG 2762 chr4ptel1M 880888 GCAGAGA--GATCCAGG-AGATCTGTTTGGAGGCTCTTGACATAAGTTAG 880934 ii i-- vv - i v v v vvi vii C L2#LINE/L2 2761 GCAAGGGTGGAAGCAGGGAGACCAGTTAGGAGGCTATTGCAGTAATCCAG 2712 chr4ptel1M 880935 ACAAGAGATGCCAAAGGCCTGAACTCGGGCGGTCACTGCGGGAGCAGCCA 880984 i i viiiv i i iv i vi v i ii ii iv C L2#LINE/L2 2711 GCGAGAGATGATGGTGGCTTGGACCAGGGTGGTGGCAGTGGAGGTGGTGA 2662 chr4ptel1M 880985 GAGTGGGACTGATCCAAGAGCCGTCTGGAAGGTAGAGGCGA---GGTTTG 881031 ivv v v i vi vvii i v v --- i C L2#LINE/L2 2661 GAAGTGGTCGGATTCTGGATATATTTTGAAGGTAGAGCCGACAGGATTTG 2612 chr4ptel1M 881032 GGAACTGGTGAATAAAA---------TGAGTGAAGCTGAGGGGTCAAGGA 881072 ---- i i vii --------- v ivv i C L2#LINE/L2 2611 ----CTGATGGATTGGATGTGGGGTGTGAGAGAAAGAGAGGAGTCAAGGA 2566 chr4ptel1M 881073 TG 881074 C L2#LINE/L2 2565 TG 2564 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 50.86 CpG sites = 91, Kimura (unadjusted) = 51.96 Transitions / transversions = 1.82 (91/50) Gap_init rate = 0.06 (26 / 403), avg. gap size = 2.23 (58 / 26) 371 31.32 11.23 1.66 chr4ptel1M 881068 881343 (118657) C L2#LINE/L2 (548) 2534 2233 m_b186s601i49 7297 chr4ptel1M 881068 AAGGATGCTAGCTGCACCCTTGACGGCAATGGGGAAGGCTG--------- 881108 v- i -- v ? v vi i --------- C L2#LINE/L2 2534 AAGGATGG-AGTTGC--CATTNACTGAGATGGGGAAGACTGCGGGAGGAG 2488 chr4ptel1M 881109 -------GAAGGGGGAGA-CAGCAATCTCTATTTTGGAT-TGTAACCTTT 881149 ------- i i - v i - vi i- v vv C L2#LINE/L2 2487 CAGGTTTGAGGGGGAAGATCAGGAGT-TCAGTTTTGGACATGTTAAGTTT 2439 chr4ptel1M 881150 GAAATACCTACAGGACA---------AG-TGTCCAA-AGGCA-CTGGTGA 881187 i i ivi --------- - v i- -i vv C L2#LINE/L2 2438 GAGATGCCTATTAGACATCCAAGTGGAGATGTCGAGTAGGCAGTTGGATA 2389 chr4ptel1M 881188 TGCTGGATTGGGGCTCGGGAGAAAGACTGGGCCTGGATGGGGAAATCTGG 881237 i vi vi i i i i i iiiv v viviv i C L2#LINE/L2 2388 TACGAGTCTGGAGTTCAGGGGAGAGGTCCGGGCTGGAGATATAAATTTGG 2339 chr4ptel1M 881238 GGCTTACTTACATAGAGATGCGAATCGAACCCATGGAGGTTGAGGAGATG 881287 iv i iivi v vv v ii v iiiv v v v C L2#LINE/L2 2338 GAGTCATCAGCATATAGATGGTATTTAAAGCCATGAGACTGGATGAGATC 2289 chr4ptel1M 881288 GCTGAAAGAGGGGTGTGTGGGGACAAAAGAGAAGGTGCCCA-GAACAGAG 881336 i i? ii v i- i iv v i iv i - i v C L2#LINE/L2 2288 ACCNAGGGAGTGA-GTGTAGATAGAGAAGAGAAGAGGTCCAAGGACTGAG 2240 chr4ptel1M 881337 CCCTGGG 881343 C L2#LINE/L2 2239 CCCTGGG 2233 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 42.26 CpG sites = 49, Kimura (unadjusted) = 42.26 Transitions / transversions = 1.36 (49/36) Gap_init rate = 0.05 (14 / 275), avg. gap size = 2.57 (36 / 14) 295 27.22 14.87 7.69 chr4ptel1M 881467 881661 (118339) MIR1_Amn#SINE/MIR 13 220 (10) m_b186s601i50 7302 chr4ptel1M 881467 GTAGCTTGCTGGATACAATACTGGATT-----TCAAG----------TTA 881501 i ii iv v ii i ----- ii ---------- i? MIR1_Amn#SINE 13 GTGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGAGACCTGGGTTCN 62 chr4ptel1M 881502 AATCCCTGC-CT--CACACATTTACTATATGACCCTGGGGGAAAGACATT 881548 ? v - -- v?iii?i i?i i v-- v i MIR1_Amn#SINE 63 ANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGC--AAGTCACT 110 chr4ptel1M 881549 TAAC---TGGAAGCCTCAGTTTCCTTATCTATGATATGGGTTTCATAGTA 881595 ? --- vvi? i i i v ---v i i MIR1_Amn#SINE 111 TNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGG---GATAATG 157 chr4ptel1M 881596 GCACCTACCTTACAGATCACATATATAAAGTACTTCATAAAATTT----- 881640 ii iv --------- v v i i -- i i i ----- MIR1_Amn#SINE 158 ATACTGACCT---------CCTTTGTAAAGTGCTT--TGAGATCTACTGA 196 chr4ptel1M 881641 ---AAAGTGCTCTATAAATGCTAG 881661 --- vi iv MIR1_Amn#SINE 197 TGAAAAGTGCTACATAAGAGCTAG 220 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 36.73 CpG sites = 34, Kimura (unadjusted) = 37.73 Transitions / transversions = 2.27 (34/15) Gap_init rate = 0.12 (23 / 194), avg. gap size = 1.96 (45 / 23) 365 23.64 23.27 1.55 chr4ptel1M 881499 881657 (118343) MIRc#SINE/MIR 58 250 (18) m_b186s601i51 7302 chr4ptel1M 881499 TTAAATCCCTGCCTCACACATTTACTA----TATGACCCTGGGGGAAAGA 881544 ii i v iiii - i ---- i i v-- v MIRc#SINE/MIR 58 TCGAGTCCCGGCTCTGC-CACTTACTAGCTGTGTGACCTTGGGC--AAGT 104 chr4ptel1M 881545 CATTTAAC---TGGAAGCCTCAGTTTCCTTATCTATGATATGGGTTTCAT 881591 i --- vvi i i i v vv v MIRc#SINE/MIR 105 CACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAAT 154 chr4ptel1M 881592 AGTA---GC---ACCTACCTTACA-------------GATCACAT----- 881617 i --- ---i i ------------- v ----- MIRc#SINE/MIR 155 AATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGAT 204 chr4ptel1M 881618 -ATAT-----AAAGTACTTCATAAAATTTAAAGTGCTCTATAAATG 881657 - i ----- ii ii v v v i MIRc#SINE/MIR 205 AATGTATGTGAAAGCGCTTTGTAAACTGTAAAGTGCTATACAAATG 250 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 27.29 CpG sites = 24, Kimura (unadjusted) = 29.36 Transitions / transversions = 1.85 (24/13) Gap_init rate = 0.07 (11 / 158), avg. gap size = 3.64 (40 / 11) 386 30.49 2.78 2.07 chr4ptel1M 882112 882255 (117745) L3#LINE/CR1 3867 4011 (88) m_b186s601i52 7303 chr4ptel1M 882112 AGGGAGACA--TTTTCCCATAATATTTAATGTTGAATTGCTT--TGATTA 882157 i -- ivv vi -- v vv i vii --ii i L3#LINE/CR1 3867 AGGGAGGCAGATTTCGGCTCAATAT--AAGGAAGAACTTTCTAACAATCA 3914 chr4ptel1M 882158 GAGCCCTCCCAGGGAAGAAGGGGCTGCCTCAGGCGCCAGTGGGGTCCCCT 882207 iv v iiivi v i? v vi i v v L3#LINE/CR1 3915 GAGCTGTCCAAAAATGGAATGGGCTGCCTCGNGAGGTAGTGAGCTCCCCG 3964 chr4ptel1M 882208 TCCCTGGAAGACTCCAAGCAAAGGCTGGGTGACCCCCTGGTCAGAAAT 882255 v i vv i i i v i - ii L3#LINE/CR1 3965 TCACTGGAGGTGTTCAAGCAGAGGCTGGATGACCACTT-GTCAGGGAT 4011 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 38.07 CpG sites = 24, Kimura (unadjusted) = 40.48 Transitions / transversions = 1.26 (24/19) Gap_init rate = 0.03 (5 / 143), avg. gap size = 1.40 (7 / 5) 13 14.91 3.33 0.00 chr4ptel1M 882628 882657 (117343) (TTCAC)n#Simple_repeat 1 31 (0) m_b186s252i13 7304 chr4ptel1M 882628 TTCCCTTCCCTTCACTTCAGTGC-CTTCACT 882657 v v v v - (TTCAC)n#Simp 1 TTCACTTCACTTCACTTCACTTCACTTCACT 31 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 16 21.68 3.64 1.79 chr4ptel1M 884576 884630 (115370) (CACTT)n#Simple_repeat 1 56 (0) m_b186s252i14 7305 chr4ptel1M 884576 CACTTTTCTAGACTT-ATTTCATATCACTTTAATT-ACATCACTTCACTT 884623 iv vv - i iv i v - v (CACTT)n#Simp 1 CACTTCACTTCACTTCACTTCACTTCACTTCACTTCACTTCACTTCACTT 50 chr4ptel1M 884624 CATCTTC 884630 - (CACTT)n#Simp 51 CA-CTTC 56 Matrix = Unknown Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.06 (3 / 54), avg. gap size = 1.00 (3 / 3) 192 34.25 15.38 4.75 chr4ptel1M 884667 884991 (115009) L2a_3end#LINE/L2 155 512 (5) m_b186s601i53 7306 chr4ptel1M 884667 CCTGGGATGGATTTCCCC------TCTCCAGGGTCTCTCTTCCCTTTTGA 884710 i i vvi ------ iv v - v i --- iiv L2a_3end#LINE 155 CCTGGAACGCTCTTCCCCCAGATATCCGCATGG-CTCGCTCCC---TCAC 200 chr4ptel1M 884711 TTTCTTGAAGTCCCT-CTGAAAAGCCCCTTCTTCCATGAAGCCTTCCTTA 884759 i i v i ii - v v i v i ii vi? i i i L2a_3end#LINE 201 CTCCTTCAGGTCTTTGCTCAAATGTCACCTTCTCAGNGAGGCCTTCCCTG 250 chr4ptel1M 884760 ATCAGC---TGGAAAATATTGCTCTCTCTCCTGATTTCTCCCAGCAC-AT 884805 i v --- vv ?vii v i ? -------- ? -vi L2a_3end#LINE 251 ACCACCCTATTTAAAATNGCACACCCTCNCC--------CCCANCACTCC 292 chr4ptel1M 884806 TTATAGATCTTACTTTTGCATTGTTTTCCAGTTCATGGCACAGGT----A 884851 i vvvi -ii v i i -- i i vvi ---- L2a_3end#LINE 293 CTATCCCCCTTAC-CCTGCTTTATTTTTC--TCCATAGCACTTATCACCA 339 chr4ptel1M 884852 TCTG-TGT-CTATATCTTCTAC------ATTCG----------------- 884876 -ii - v i ------ i ----------------- L2a_3end#LINE 340 TCTGACATACTATATATTTTACTTATTTATTTGTTTATTGTCTGTCTCCC 389 chr4ptel1M 884877 ---ATTAGATTGTAAGATTCTT------AAAGACTTATTTCTGTCTCATT 884917 --- i v v i v ------ ii v v i ii L2a_3end#LINE 390 CCCACTAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTCTGTTTTGTT 439 chr4ptel1M 884918 TCTACT-TTGGGTCTCCGGTATCTGCTATAGCTCATCACGCATAGTGGAT 884966 --i -i vi i i iii ivv i iv v vi i i ii L2a_3end#LINE 440 --CACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGGC 487 chr4ptel1M 884967 GGTTAGAAAGCATTGATTCAGTGAA 884991 v i iv ii vi v i L2a_3end#LINE 488 GCTCAATAAATATTTGTTGAATGAA 512 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 46.76 CpG sites = 67, Kimura (unadjusted) = 49.50 Transitions / transversions = 1.72 (67/39) Gap_init rate = 0.09 (29 / 324), avg. gap size = 2.31 (67 / 29) 274 24.71 9.41 0.00 chr4ptel1M 885027 885111 (114889) Charlie4#DNA/hAT-Charlie 1 93 (3285) m_b186s502i5 7307 chr4ptel1M 885027 CAGGCATTCTTAACC-GGGCCCCACAGATT------GGGTCCACAGCAAG 885069 vi - vi i ii------ iii vv Charlie4#DNA/ 1 CAGGGGTTCTTAACCTGGGGTCCACGGACCCCCAAGGGGTCCGTGGATAG 50 chr4ptel1M 885070 ATTGCAGGGGGTTCCTGAATATGGAAGGG-AAAAACTGCATCT 885111 v v i v iv v - i i Charlie4#DNA/ 51 AATTCAGGGGGTCCGTGAACTTGGATGGGAAAAAATTACATCT 93 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 27.17 CpG sites = 12, Kimura (unadjusted) = 30.52 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.04 (3 / 84), avg. gap size = 2.67 (8 / 3) 626 17.78 0.00 4.84 chr4ptel1M 885235 885364 (114636) C Charlie4a#DNA/hAT-Charlie (2) 506 383 m_b186s502i6 7308 chr4ptel1M 885235 GGCATTTTTAATCTTTTTGGGTGTCATGGACCCCTTGGGCAGACAGCCCG 885284 vi i i v - i v ----i i C Charlie4a#DNA 506 GGGGTTCTTAACCTTTTTTG-TGCCATGGACCCCTTTGGCAG----TCTG 462 chr4ptel1M 885285 GTGACCCCCTTGGACTCCTGTCTTAGAATAATGTTTTTAAATGCATAAAA 885334 vv iv i - i C Charlie4a#DNA 461 GTGAAGCCTATGGACCCCT-TCTCAGAATAATGTTTTTAAATGCATAAAA 413 chr4ptel1M 885335 TCATATCTGAAGGATTGCAAAGGAAACCAA 885364 v v viiv i C Charlie4a#DNA 412 TAAAATACATAGGATTACAAAGGAAACCAA 383 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 20.42 CpG sites = 12, Kimura (unadjusted) = 20.42 Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.05 (6 / 129), avg. gap size = 1.00 (6 / 6) 185 24.51 20.87 7.75 chr4ptel1M 885946 886060 (113940) C L2d2_3end#LINE/L2 (3) 552 424 m_b186s601i54 7309 chr4ptel1M 885946 AGTCAAA--AATAAACATTCTTTTAAAAATTGAGGACCTACTGTGTGCAA 885993 i -- i i i-------- vi C L2d2_3end#LIN 552 AATCAAATCAACAAATATTT--------ATTGAGCGCCTACTGTGTGCAA 511 chr4ptel1M 885994 AGTA--------------GTGGAAAATGCAAAGAAAAATCCAACAATATG 886029 i i -------------- iii i iv vvi - i- C L2d2_3end#LIN 510 GGCACTGTGCTAGGCGCTGTGGGGGATACAAAGAAGTATAAGAC-ATG-G 463 chr4ptel1M 886030 TGTCTGCC----AGAAATTTATAAT----TTGGAGAAAC 886060 vi ---- i ii i ---- i i C L2d2_3end#LIN 462 TCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGGAGAC 424 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.65 CpG sites = 21, Kimura (unadjusted) = 32.18 Transitions / transversions = 4.20 (21/5) Gap_init rate = 0.12 (14 / 114), avg. gap size = 2.43 (34 / 14) 242 37.07 1.71 0.85 chr4ptel1M 886447 886563 (113437) C L2b_3end#LINE/L2 (38) 428 311 m_b186s601i55 7310 chr4ptel1M 886447 TGTGTGAGGTATTATGGCCAACACTGGGGATACACAGATGGG-AAAAT-G 886494 iv i?i i vivii i vv i ii- i i- C L2b_3end#LINE 428 TGTGCCAGGCNCTGTGCTAGGCGCTGGGGATACAGCGGTGAACAAGACAG 379 chr4ptel1M 886495 CTCCAGTTCTTGCCCACAGTAAGCTTTTACTCTGCTAGAAGGAACACACA 886544 vi? i i i v vvi ivi v iv i ii ii v C L2b_3end#LINE 378 ACNCGGTCCCTGCCCTCACGGAGCTCACAGTCTAGTGGGGGAGACAGACA 329 chr4ptel1M 886545 GTGTGCTCAGAGAAACATA 886563 - iv? v v? C L2b_3end#LINE 328 -TGTAANCAGACAATNATA 311 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 53.34 CpG sites = 27, Kimura (unadjusted) = 57.45 Transitions / transversions = 1.69 (27/16) Gap_init rate = 0.03 (3 / 116), avg. gap size = 1.00 (3 / 3) 219 30.86 10.33 7.94 chr4ptel1M 886456 886726 (113274) C L2c_3end#LINE/L2 (33) 445 169 m_b186s601i56 7310 chr4ptel1M 886456 TATTATG-GCCAA-CACTGGGGATACACAGATGGGAAAATGCTCCAGTTC 886503 i - i- i v -- v v viv i i C L2c_3end#LINE 445 TACTATGTGCCAGGCGCTGGGGATACAAAGAT--GAATAAGACACGGTCC 398 chr4ptel1M 886504 TTGCCCACAGTAAGCTTTTACTCTGCTAGAAGGAACACACAGTGTGCTCA 886553 i v ivi ivi v iv i i ii v -? ivv C L2c_3end#LINE 397 CTGCCCTCAAGGAGCTCACAGTCTAGTGGAGGAGACAGACA-NGTAAACA 349 chr4ptel1M 886554 GAGAA--AC-ATATGATGTCAT--TGGGTG---TAATG---GTGTCCACT 886592 v -- - ii vv v -- ii --- --- i vv v C L2c_3end#LINE 348 GACAATTACAATACAAGTTAATGATAAGTGCTATAATGGGAGTATAGACA 299 chr4ptel1M 886593 GGGAGCAATCTGTACCTGGAAGGACTGGGGAAGGCATC-AGA-------- 886633 v ------ -- i v v i i i - -------- C L2c_3end#LINE 298 GGGTGC------TA--TGGGAGCACAGAGGAGGGCACCTAGACTAGNCTT 257 chr4ptel1M 886634 GAGAAGTCA-CCAAGCCTTGTGTGACTGCAAATAGCAT----GTTGAGTC 886678 i ii -vv v vivv -- v ii ii ---- i ? C L2c_3end#LINE 256 GGGGGGTCAGGGAAGGCTTCCCGGA--GGAGGTGACATCTGAGCTGAGNC 209 chr4ptel1M 886679 -TGAGGGATAATCAGCAATCGTCACTGGCTAAAATCTAGAAGGAGGAGG 886726 - i i vi v i ------ i i ii--- i i C L2c_3end#LINE 208 TTGAAGGATGAGTAGGAGT------TAGCCAGG---TGGAAGGAGGGGG 169 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 40.13 CpG sites = 45, Kimura (unadjusted) = 41.55 Transitions / transversions = 1.41 (45/32) Gap_init rate = 0.13 (34 / 270), avg. gap size = 1.47 (50 / 34) 16 4.12 0.00 3.85 chr4ptel1M 888158 888184 (111816) (TTTTC)n#Simple_repeat 1 26 (0) m_b187s252i0 7311 chr4ptel1M 888158 TTTTCTTTTTCTTTTCTTTTCTTGTCT 888184 - v (TTTTC)n#Simp 1 TTTTC-TTTTCTTTTCTTTTCTTTTCT 26 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.04 (1 / 26), avg. gap size = 1.00 (1 / 1) 213 33.89 11.71 1.64 chr4ptel1M 888625 888735 (111265) C L3#LINE/CR1 (5) 4094 3973 m_b187s601i1 7312 chr4ptel1M 888625 AACCCCAGGCTCATGAAGCTGCAAAGGATCTTGGGG-------AGATCA- 888666 i v iv viii i v i i i i ------- vi - C L3#LINE/CR1 4094 AATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCAA 4045 chr4ptel1M 888667 --TTGCGTCTGGTGTCAGGAG---CTTCTGATGCCATCCTGGGTAAAGGA 888711 -- iv i iii - i--- - iiv iv ii iv i C L3#LINE/CR1 4044 CCTCCCATCCAATG-CAGGAATCCCTTCT-ACAACATCCCTGACAAGTGG 3997 chr4ptel1M 888712 TCATCCAGCCTCTAGTTAAATACC 888735 iv i i C L3#LINE/CR1 3996 TCATCCAGCCTCTGCTTGAACACC 3973 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 49.30 CpG sites = 27, Kimura (unadjusted) = 49.30 Transitions / transversions = 2.70 (27/10) Gap_init rate = 0.05 (6 / 110), avg. gap size = 2.50 (15 / 6) 232 33.89 1.30 6.12 chr4ptel1M 888862 889015 (110985) C L3#LINE/CR1 (771) 3328 3182 m_b187s601i2 7312 chr4ptel1M 888862 AAGTTGTCATGTTGTCCAGCTTTCAGCCCATCCCACTGAACGGCCACAAT 888911 i - v i-- v i viv iiiv v i ivi C L3#LINE/CR1 3328 AAATT-TCATCTTGTT--GGTTTCGGCCCATCGTTCCAGCCTGTCGAGAT 3282 chr4ptel1M 888912 CTTTCTCAATCCTGATTCCAGCGCCCAGAGTATTGGCTCCTCCTTCCGAA 888961 ? i v i iiv ii ?v i vii i iiv C L3#LINE/CR1 3281 CNTTTTGAATCTTGATTCTGTCATCCANCGTATTAGCTATCCCTCCCAGC 3232 chr4ptel1M 888962 TTAGTTTCCTCCCCACCAGAAAAAGTCACACCCACACTTTCTC--TCTTC 889009 v v v i------ v vv v i vv ii i v-- C L3#LINE/CR1 3231 TTTGTGTCATCT------GCAAATTTGATAAGCATGCCTTCTATGTCTTC 3188 chr4ptel1M 889010 ATCCAA 889015 C L3#LINE/CR1 3187 ATCCAA 3182 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 44.48 CpG sites = 27, Kimura (unadjusted) = 47.10 Transitions / transversions = 1.23 (27/22) Gap_init rate = 0.07 (10 / 153), avg. gap size = 1.10 (11 / 10) 743 31.31 5.72 0.00 chr4ptel1M 889097 889393 (110607) C L3#LINE/CR1 (1107) 2992 2679 m_b187s601i3 7312 chr4ptel1M 889097 ATCAC-AGAGAGGCTGTCATGGGCCTTCCTGAAATCGGCACCCACCATTT 889145 i- vvi viv v viv iv i? v C L3#LINE/CR1 2992 ATCATGAGAGACTTTGTCAAATGCCTTGCTGAAATCCAGATACACTNTGT 2943 chr4ptel1M 889146 CTCTGGCCTTCCTTTCATCCGCCAGCCTCGTCACAGCCCCAAAAAGGGAA 889195 vi v ii v ii i v v vvivi i C L3#LINE/CR1 2942 CTACGGCATTCCCCTGATCTACCAGTCTAGTAACCCTATCAAAAAAGGAA 2893 chr4ptel1M 889196 ATGGGGCTAGACTGGTCTGA----TTCATGGTGAACCTTCAATGGCTTGT 889241 i i vi iv ---- v i iviiv iv C L3#LINE/CR1 2892 ATGAGGTTAGTTTGGCATGACTTGTTCTTAGTGAACCCATGCTGGCTCCT 2843 chr4ptel1M 889242 ATTGATTACTGCTTTC--ATCGAAGCGCTTA-AAATTGTCTTTTAAATAC 889288 v i i i --v v i i - iii v v v C L3#LINE/CR1 2842 AGTGATCACCGCTTCCTTTTCTAAGTGCTCACAAACCATCTGTTTAATAA 2793 chr4ptel1M 889289 TGTGTTCCTTGATCTTATCAGGAACCGACATCCTCCTTACTGGTCTGTAG 889338 vi ivvi i ii i i i i vvv i C L3#LINE/CR1 2792 TCCGTTCTAGAATTTTGCCGGGGATCGACGTCAAGCTTACCGGTCTGTAG 2743 chr4ptel1M 889339 TTT------TCCA--GTCTCTGCCTTTGGAAAGCT-GGGACATTGTGTGG 889379 ------ --v i i v vv i? - ? ?vii v v C L3#LINE/CR1 2742 TTTNCAGAATCCATCTTTTTTCCCTTTTTAAAANTAGGNACNACATTTGC 2693 chr4ptel1M 889380 CCAACTCCAGGCTT 889393 iv v C L3#LINE/CR1 2692 CCGTCTCCAGTCTT 2679 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 38.07 CpG sites = 49, Kimura (unadjusted) = 42.07 Transitions / transversions = 1.11 (49/44) Gap_init rate = 0.02 (7 / 296), avg. gap size = 2.43 (17 / 7) 303 30.63 8.20 3.66 chr4ptel1M 889485 889667 (110333) C L3#LINE/CR1 (1617) 2482 2292 m_b187s601i4 7312 chr4ptel1M 889485 TCCATTCCCTCTTGTCTAAAGAACATTCTCCTTACT---GAAGACAAAAG 889531 i ii ii iv i v iv --- ii C L3#LINE/CR1 2482 TCTACCCTTTCCAGTCTGAAGATCATTCTCCTTGATAGAGAAGACGGAAG 2433 chr4ptel1M 889532 CCAAAGAGGAATCAGGGATTTTTCCTTTC---CAATTTTCTCTTGCCACA 889578 v v i iii v v i v --- vi iv v iv iv C L3#LINE/CR1 2432 CAAAATAGGAGTTGAGTAGTTCTGCTTTCTCTCTGTCATCTGTTAACATT 2383 chr4ptel1M 889579 ACCCGCTCTGCTC---------GACTCATCTCTTCCTTATTCAGCTCTGA 889619 v vv i --------- i iii ? i v -vi - C L3#LINE/CR1 2382 ACGCCATCTGCCCCAAGCAGCGGGCCTGTCNCTTTCTTTTTC-CTTCTG- 2335 chr4ptel1M 889620 ACTCCCTCAATATTCAATTTTTCAAAGGCTGTTTTTTGTTGTCCCTGG 889667 - --v i -- ii vv v v? i i C L3#LINE/CR1 2334 -CTCC--GAACAT--AGCTTTGAAAAGCCTTNTTTTTGTTGTCCTTAG 2292 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 40.20 CpG sites = 31, Kimura (unadjusted) = 41.20 Transitions / transversions = 1.35 (31/23) Gap_init rate = 0.05 (10 / 182), avg. gap size = 2.20 (22 / 10) 328 27.07 1.15 2.33 chr4ptel1M 890770 890856 (109144) C MIR3#SINE/MIR (52) 156 71 m_b187s601i5 7313 chr4ptel1M 890770 AGGCCAATTCTTCATTAATTTGCAGATAGGAAAACTGAGGCTCAAAGAGG 890819 v ii ii-- i v i ii i i i C MIR3#SINE/MIR 156 AGTCCAACCCCC--TCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGG 109 chr4ptel1M 890820 TGAAATGACTATCCTAGGATCATATAGCTCA-TAGTGG 890856 i vv i i i i i ?vi- C MIR3#SINE/MIR 108 TGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGG 71 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 36.65 CpG sites = 18, Kimura (unadjusted) = 36.65 Transitions / transversions = 3.60 (18/5) Gap_init rate = 0.03 (3 / 86), avg. gap size = 1.00 (3 / 3) 355 17.94 10.99 2.02 chr4ptel1M 890941 891031 (108969) MIR#SINE/MIR 44 142 (120) m_b187s601i6 7314 chr4ptel1M 890941 CTTCTTGAGTTCAAATCTGATCTCAGACACTTCCTAGCTGTGTGAC---- 890986 v i i i iviv v v v ---- MIR#SINE/MIR 44 CTGCCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTG 93 chr4ptel1M 890987 ---AAGTCGCTT---CTTCCTGTTTGCCTCAGTTTCCTCATTTGTAAAAT 891030 --- ii --- ii -- i MIR#SINE/MIR 94 GGCAAGTTACTTAACCTCTCTGT--GCCTCAGTTTCCTCATCTGTAAAAT 141 chr4ptel1M 891031 G 891031 MIR#SINE/MIR 142 G 142 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 18.12 CpG sites = 10, Kimura (unadjusted) = 20.90 Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.06 (5 / 90), avg. gap size = 2.40 (12 / 5) 186 31.94 6.12 0.97 chr4ptel1M 894781 894878 (105122) C L2a_3end#LINE/L2 (35) 482 380 m_b187s601i7 7315 chr4ptel1M 894781 CTATTTG--AGGCACTGCCCTGGGTACTCGGG-CACAATCCCCTCCCAAG 894827 v -- ii i ii v -i i- vvivvv i C L2a_3end#LINE 482 CTATGTGCCAGGCACTGTTCTAGGCGCTGGGGATACAG-CAGTGAACAAA 434 chr4ptel1M 894828 AGGGACA---GTTGTTGCCCTCAAGGAGCCTCCATTCTCCTGGCGAATGG 894874 vi --- ivi v i v vv v iiv i C L2a_3end#LINE 433 ACAGACAAAAGTCCCTGCCCTCATGGAGCTTACATTCTAGTGGGGGGAGA 384 chr4ptel1M 894875 CAGA 894878 C L2a_3end#LINE 383 CAGA 380 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 40.42 CpG sites = 16, Kimura (unadjusted) = 42.38 Transitions / transversions = 1.07 (16/15) Gap_init rate = 0.04 (4 / 97), avg. gap size = 1.75 (7 / 4) 54 6.53 0.00 0.00 chr4ptel1M 896273 896336 (103664) (GT)n#Simple_repeat 1 64 (0) c_b187s251i0 7316 chr4ptel1M 896273 GTGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTTGTGTGTGTGT 896322 i v (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50 chr4ptel1M 896323 GAGTGTGAGTGTGT 896336 v v (GT)n#Simple_ 51 GTGTGTGTGTGTGT 64 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0) 190 11.01 0.00 2.02 chr4ptel1M 897615 897917 (102083) (AAGG)n#Simple_repeat 1 297 (0) m_b187s252i1 7317 chr4ptel1M 897615 AAGAAAGGAAGGAAGGAAAGAAGGAAGGAAGGAAGGAAGGAAAGAAGGAA 897664 i i i (AAGG)n#Simpl 1 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 50 chr4ptel1M 897665 TGAAGGAAGGAAGGAAGGAAGAAAAAGAAGGAAGGAAAGAAGAAAAAGAA 897714 v -i i i -i i (AAGG)n#Simpl 51 GGAAGGAAGGAAGGAAGGAAG-GAAGGAAGGAAGGAAGGAAG-GAAGGAA 98 chr4ptel1M 897715 GGAAGGAAGGAAGGAAGGAAGGAAGGAAAGAAGGAATGAAGGAAGGAAGA 897764 i v - (AAGG)n#Simpl 99 GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG- 147 chr4ptel1M 897765 AAAAGAAGGAAGGAAGGAAGGAAAAGAAGGAAAGAAGGAAGGAAGGAAAG 897814 i i - i i i (AAGG)n#Simpl 148 GAAGGAAGGAAGGAAGGAAGG-AAGGAAGGAAGGAAGGAAGGAAGGAAGG 196 chr4ptel1M 897815 AAGGAAGGAAGGAAGAAAAAGAAGGAAGGAAGGAAGAAAAAGAAGGAAGG 897864 -i i -i i (AAGG)n#Simpl 197 AAGGAAGGAAGGAAG-GAAGGAAGGAAGGAAGGAAG-GAAGGAAGGAAGG 244 chr4ptel1M 897865 AAGGAAGGAAGGAAGGGAGGGAGGGAGGGAGGGAGGAAAGAAAGAAAGAA 897914 i i i i i i i i (AAGG)n#Simpl 245 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 294 chr4ptel1M 897915 AGA 897917 i (AAGG)n#Simpl 295 GGA 297 Matrix = Unknown Transitions / transversions = 13.50 (27/2) Gap_init rate = 0.02 (6 / 302), avg. gap size = 1.00 (6 / 6) 40 9.10 2.70 2.70 chr4ptel1M 898013 898086 (101914) (TCTCTG)n#Simple_repeat 1 74 (0) m_b187s252i2 7318 chr4ptel1M 898013 TCTCTGTCACTGCCTCTGTCTCTGTCTATCTCTGCCTGTCTCTGTCTC-- 898060 v i v v -- -- (TCTCTG)n#Sim 1 TCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCT--CTGTCTCTGTCTCTG 48 chr4ptel1M 898061 TCTCTGTCTCTGTGTCTGTCTCTCTC 898086 v v (TCTCTG)n#Sim 49 TCTCTGTCTCTGTCTCTGTCTCTGTC 74 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.04 (3 / 73), avg. gap size = 1.33 (4 / 3) 13 15.91 0.00 0.00 chr4ptel1M 899261 899288 (100712) (TGAC)n#Simple_repeat 1 28 (0) m_b187s252i3 7319 chr4ptel1M 899261 TGATTGCCTGCCTAACTGACTGACTGAC 899288 i v v i (TGAC)n#Simpl 1 TGACTGACTGACTGACTGACTGACTGAC 28 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 11 16.38 5.88 0.00 chr4ptel1M 899747 899780 (100220) (ATGTGT)n#Simple_repeat 1 36 (0) m_b187s252i4 7320 chr4ptel1M 899747 ATGTTTTTCTG-AT-TGTGTGTGTATGTGTGTGTGT 899780 v v v - - i i (ATGTGT)n#Sim 1 ATGTGTATGTGTATGTGTATGTGTATGTGTATGTGT 36 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2) 18 4.77 0.00 0.00 chr4ptel1M 899760 899781 (100219) (TG)n#Simple_repeat 1 22 (0) m_b187s252i5 7320 chr4ptel1M 899760 TGTGTGTGTATGTGTGTGTGTG 899781 i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTG 22 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 64 15.40 4.73 1.31 chr4ptel1M 899786 899933 (100067) (AGAGAC)n#Simple_repeat 1 153 (0) m_b187s252i6 7321 chr4ptel1M 899786 AGAGACAGAGA-TG-GAGGGAGACAGACACAAACACAGAAAGACAGAGAC 899833 -v - vi v i v -- (AGAGAC)n#Sim 1 AGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAG--AGACAGAGAC 48 chr4ptel1M 899834 ACAGAGAGAGAGACAGAAAGAGAGAGAGA-A-TGAGAGACAGAGAGACAA 899881 v v v v v v - -v v v v i (AGAGAC)n#Sim 49 AGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAG 98 chr4ptel1M 899882 AGA-AGAGACAGAGAC--AGACAGAGAGAGACACAGAGACAGAGACAGAG 899928 - -- v v (AGAGAC)n#Sim 99 AGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAG 148 chr4ptel1M 899929 AGAGA 899933 v (AGAGAC)n#Sim 149 ACAGA 153 Matrix = Unknown Transitions / transversions = 0.18 (3/17) Gap_init rate = 0.05 (8 / 147), avg. gap size = 1.12 (9 / 8) 18 16.00 3.77 3.77 chr4ptel1M 899980 900032 (99968) (TCTG)n#Simple_repeat 1 53 (0) m_b187s252i7 7322 chr4ptel1M 899980 TCTGTCT-T-TCTCTCTCTGTCTGTCTCTCTCTCCCTGTGTGTGTCTCTG 900027 - - v v v v -- v v v (TCTG)n#Simpl 1 TCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGT--CTGTCTGTCTGTCTG 48 chr4ptel1M 900028 TCTGT 900032 (TCTG)n#Simpl 49 TCTGT 53 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.08 (4 / 52), avg. gap size = 1.00 (4 / 4) 215 20.00 7.27 0.00 chr4ptel1M 900151 900205 (99795) C MIR#SINE/MIR (25) 237 179 m_b187s601i8 7323 chr4ptel1M 900151 CCTACTGTGCGCCAGGC-CCATT-TAAGGACTTTACAAATATT--CTCAT 900196 i i i - ii - vi vi -- C MIR#SINE/MIR 237 CTTACTATGTGCCAGGCACTGTTCTAAGCGCTTTACATGTATTAACTCAT 188 chr4ptel1M 900197 TTGATTCTC 900205 i i C MIR#SINE/MIR 187 TTAATCCTC 179 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 21.98 CpG sites = 9, Kimura (unadjusted) = 24.49 Transitions / transversions = 4.50 (9/2) Gap_init rate = 0.06 (3 / 54), avg. gap size = 1.33 (4 / 3) 55 0.00 0.00 0.00 chr4ptel1M 901540 901586 (98414) (TA)n#Simple_repeat 1 47 (0) c_b187s251i1 7324 chr4ptel1M 901540 TATATATATATATATATATATATATATATATATATATATATATATAT 901586 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATAT 47 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 28 29.40 3.15 2.34 chr4ptel1M 901589 901715 (98285) (TAGA)n#Simple_repeat 1 128 (0) m_b187s252i8 7325 chr4ptel1M 901589 TAGAAAGAT-GATAAGCATAGGTAGGTAGATAGATAGATAACCAGACAGA 901637 v - - - i i ivi i (TAGA)n#Simpl 1 TAGATAGATAGAT-AG-ATAGATAGATAGATAGATAGATAGATAGATAGA 48 chr4ptel1M 901638 CAGACAGACAAACACACACACACACAG-GAGACACAGTAAATAGACAGAT 901686 i i i i i v i v i v i -v i v - i i (TAGA)n#Simpl 49 TAGATAGATAGATAGATAGATAGATAGATAGATAGA-TAGATAGATAGAT 97 chr4ptel1M 901687 GGACTGA-AGCTAGATTGAGAGAT-GATAGA 901715 i iv - v v v - (TAGA)n#Simpl 98 AGATAGATAGATAGATAGATAGATAGATAGA 128 Matrix = Unknown Transitions / transversions = 1.64 (18/11) Gap_init rate = 0.06 (7 / 126), avg. gap size = 1.00 (7 / 7) 187 28.71 6.52 5.38 chr4ptel1M 902892 902983 (97017) L2d2_3end#LINE/L2 459 551 (4) m_b187s601i10 7326 chr4ptel1M 902892 GGGACTGC-TTTTGCCTTTCTTTGTATCCC---CAATGCTTAGCACAGAG 902937 iii- i iivi --- ii i v L2d2_3end#LIN 459 GGGACCATGTCTTATACTTCTTTGTATCCCCCACAGCGCCTAGCACAGTG 508 chr4ptel1M 902938 GCTGGCTGGCATTTAGATACTC--TAAATGCTCCTTGACGATTTTGAT 902983 v v vvi -v iii -- ii iv ---- L2d2_3end#LIN 509 CCTTGCACACA-GTAGGCGCTCAATAAATATTTGTTGA----TTTGAT 551 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 33.99 CpG sites = 17, Kimura (unadjusted) = 38.04 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.09 (8 / 91), avg. gap size = 1.38 (11 / 8) 228 27.14 8.54 1.14 chr4ptel1M 902892 902973 (97027) L2b_3end#LINE/L2 369 456 (10) m_b187s601i9 7326 chr4ptel1M 902892 GGGACTGCTTTTGCCTT-----TCTTTGTATCCCCAATGCTTAGCACAGA 902936 i ?v i i -----i vi ii i ? L2b_3end#LINE 369 GGGACCGNGTCTGTCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGN 418 chr4ptel1M 902937 GGCTGGCTGGCATTTAGATACTC--TAAATGCTCCTTGA 902973 v vvi -v iii -- ii iv L2b_3end#LINE 419 GCCTGGCACACA-GTAGGCGCTCAGTAAATATTTGTTGA 456 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 30.21 CpG sites = 15, Kimura (unadjusted) = 36.47 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.04 (3 / 81), avg. gap size = 2.67 (8 / 3) 333 33.22 5.56 5.92 chr4ptel1M 904427 904714 (95286) L2b_3end#LINE/L2 178 464 (2) m_b187s601i11 7327 chr4ptel1M 904427 GCCTGGAACGCTCTCCCTCCTCCGCTTCGAATC-CAGCTAAAATTCCACC 904475 vvvi iiv v -- iii - v vi L2b_3end#LINE 178 GCCTGGCCAACTCCTACTCATCC--TTCAGGTCTCAGCTCAAATGTCACC 225 chr4ptel1M 904476 TCCTGCAGGAAGTCCTCCCCAAGCCCTCTTAATTC---CCCGGCTTCTTT 904522 v i i ii v i -- ivi ---i v vi i i L2b_3end#LINE 226 TCCTCCGGGAAGCCCTCCCTGACCCCCC--AGGCCGGGTCAGGCGCCCTC 273 chr4ptel1M 904523 CTGTTCGTTATCCCCTGTTTT-CTCTGTAGAGAGCCTGGATTGTACATAC 904571 v vv ii-i v ii - i iv--- vi i ---- ?v L2b_3end#LINE 274 CTCTGGGCC-CCCCCAGTCCTACCCTGCC---ACTCTGGGTT----ATNA 315 chr4ptel1M 904572 CGGTCTGCCGCCGTCACCCTCCCCTTCCCCACGTTAGATTGTGAGCTTTG 904621 iv ?ivv i vv iv --- i -- i ii L2b_3end#LINE 316 TTGTCTGNTTACATGTCTGTC---TCCCCCAC--TAGACTGTGAGCTCCG 360 chr4ptel1M 904622 -GGGGGCAGGGACGTCCTTTGCCTCTTTC-----CGTAGCCCCAAAACTT 904665 - i vv?v i i iv -----i v ivi i L2b_3end#LINE 361 TGAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTGTATCCCCAGCGCCT 410 chr4ptel1M 904666 AGCCCAGAGCTCGGCGCTTTGTCAACGTTTATTG---ATTTG--AAGTGA 904710 v ? ii i viv vii i i v i--- --i i L2b_3end#LINE 411 AGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTTGTTGAATGA 460 chr4ptel1M 904711 ATGA 904714 L2b_3end#LINE 461 ATGA 464 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 44.46 CpG sites = 54, Kimura (unadjusted) = 46.61 Transitions / transversions = 1.50 (54/36) Gap_init rate = 0.08 (24 / 287), avg. gap size = 1.38 (33 / 24) 211 21.05 0.00 0.00 chr4ptel1M 905633 905670 (94330) C L2c_3end#LINE/L2 (13) 465 428 m_b187s601i12 7328 chr4ptel1M 905633 ATAATCATTTATGAAATGCCTACTGTGTGCCAGGCACT 905670 i v vi ii i i C L2c_3end#LINE 465 ACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCT 428 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 18.77 CpG sites = 6, Kimura (unadjusted) = 25.76 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 281 19.63 16.77 14.56 chr4ptel1M 905638 905792 (94208) C MIR#SINE/MIR (12) 250 93 m_b187s601i13 7329 chr4ptel1M 905638 CATTTATGAAATGCCTACTGTGTGCCAGGCACT-------------TAGA 905674 vi ii i i ------------- v C MIR#SINE/MIR 250 CATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGCGCTTTACA 201 chr4ptel1M 905675 T----------AATGGATCCTCACAACCTCCCTGGAAGGGCGGTTACTGT 905714 ---------- v vi vv ivi vv - i C MIR#SINE/MIR 200 TGTATTAACTCATTTAATCCTCACAACAACCCTATGAGGTAGGT-ACTAT 152 chr4ptel1M 905715 TGCTATCTCCATTTTACTGTTACTATCTCTGTTTAACAATGGAGGAAACT 905764 ii i v v -------------------- C MIR#SINE/MIR 151 TATTATCCCCATTTTACAGAT--------------------GAGGAAACT 122 chr4ptel1M 905765 GAGGCAGCAGCAGAG---AAGTGACCTGTCC 905792 - - --- i i i C MIR#SINE/MIR 121 GAGGCA-CAG-AGAGGTTAAGTAACTTGCCC 93 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 22.18 CpG sites = 15, Kimura (unadjusted) = 23.16 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.17 (26 / 154), avg. gap size = 1.88 (49 / 26) 17 25.96 1.92 1.92 chr4ptel1M 906051 906102 (93898) (GT)n#Simple_repeat 1 52 (0) m_b187s252i9 7330 chr4ptel1M 906051 GTGTCTCTGGGTGTGTGCATGTCTTCGTGTGCTGAGTGTGTCTGGGT-TG 906099 v v v ii v vi - v v v - (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG-TGTGTGTGTGTGTGTGTG 49 chr4ptel1M 906100 TGT 906102 (GT)n#Simple_ 50 TGT 52 Matrix = Unknown Transitions / transversions = 0.38 (3/8) Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.00 (2 / 2) 14 20.23 0.00 0.00 chr4ptel1M 909202 909235 (90765) (GAATT)n#Simple_repeat 1 34 (0) m_b187s252i10 7331 chr4ptel1M 909202 GAACTGAGTTGAGTTGAAGTGAATTTAAGTGAAT 909235 i i i v v v (GAATT)n#Simp 1 GAATTGAATTGAATTGAATTGAATTGAATTGAAT 34 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 230 25.79 4.69 3.08 chr4ptel1M 909351 909414 (90586) C DNM1r#Unknown (2106) 2556 2492 m_b187s502i0 7332 chr4ptel1M 909351 TGCCTTGT---ATGCATGTGTGTATACACGTATGCATGCACATGTGGACA 909397 i --- i? ii i i ii ii i ii -- C DNM1r#Unknown 2556 TGCCCTGTTCTATANATACGTATATATACACATATATACACACAT--ACA 2509 chr4ptel1M 909398 CACACACATACACATAT 909414 i i i C DNM1r#Unknown 2508 CACATATACACACATAT 2492 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 34.17 CpG sites = 16, Kimura (unadjusted) = 37.18 Transitions / transversions = 1.00 (16/0) Gap_init rate = 0.05 (3 / 63), avg. gap size = 1.67 (5 / 3) 283 33.00 6.09 2.52 chr4ptel1M 909636 909750 (90250) C LTR90B#LTR (10) 786 668 m_b187s502i1 7333 chr4ptel1M 909636 AGTGGTGGGGTTTGAAAACCCTGCCTGTTGGAA-------AGGTTTTTGT 909678 iv v i iiv --- i ------- iv i vi C LTR90B#LTR 786 AGCTGTGGTGTCTGAAAATTAT---TGCTGGAATATCTGGAATTCTTAAT 740 chr4ptel1M 909679 AGGTGCTTCAGGAAGCCCAGAGACTTTTGATCAGCAAATAAAAATCCAAG 909728 iivii i i i i i iv v ivi ii C LTR90B#LTR 739 AAAAATTCCAGGAAGCCCGGGGGCTTCTGGGCAGCATATGTGAATTTAAG 690 chr4ptel1M 909729 GTGAAAGAAACATCCTCTCTCC 909750 v i i iv i C LTR90B#LTR 689 GGGAAAGAAATATTCCATCTTC 668 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 45.00 CpG sites = 26, Kimura (unadjusted) = 46.80 Transitions / transversions = 2.36 (26/11) Gap_init rate = 0.04 (4 / 114), avg. gap size = 2.50 (10 / 4) 413 27.18 6.29 4.83 chr4ptel1M 910870 911012 (88988) L2a_3end#LINE/L2 369 513 (4) m_b187s601i14 7334 chr4ptel1M 910870 TCTGTGTATTAGCCGTCACCTTCCTTTCAGGAGAGGGATGGCAGCTCCTT 910919 i v iv i ---- iii vv --- vv v L2a_3end#LINE 369 TTTGTTTATTGTCTGTC----TCCCCCCACTAGA---ATGTAAGCTCCAT 411 chr4ptel1M 910920 GGGGGTGGGGGTTTCTTTCTGTCT---------CTGTATGCCCAGGGCTT 910960 i ii ii i v i --------- v v i L2a_3end#LINE 412 GAGGGCAGGGACTTTTGTCTGTTTTGTTCACTGCTGTATCCCCAGCGCCT 461 chr4ptel1M 910961 TGCACAATGCCTGGCACATAGAAAGAGCTTAACAGATGTTTATTGATCGA 911010 v v i v i v i i i i i vi L2a_3end#LINE 462 AGAACAGTGCCTGGCACATAGTAGGCGCTCAATAAATATTTGTTGAATGA 511 chr4ptel1M 911011 AT 911012 L2a_3end#LINE 512 AT 513 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 34.67 CpG sites = 22, Kimura (unadjusted) = 34.67 Transitions / transversions = 1.47 (22/15) Gap_init rate = 0.06 (8 / 142), avg. gap size = 2.00 (16 / 8) 536 29.33 5.91 1.03 chr4ptel1M 911038 911223 (88777) MIRc#SINE/MIR 57 251 (17) m_b187s601i15 7335 chr4ptel1M 911038 TTTGAGCTTCTTTTTTGTTACTCTCCTATACT-TGGAATCCCGAAAATGT 911086 i iii vvi i ii - v -i - vi i ii iiv v MIRc#SINE/MIR 57 TTCGAGTCCCGGCTCTGCCACT-TACTA-GCTGTGTGACCTTGGGCAAGT 104 chr4ptel1M 911087 CACTTCATCTCTGCCTGCCTCAGTTTCTTCACCTGTAAAATGGGAATAGT 911136 v i vivv i i i i MIRc#SINE/MIR 105 CACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAAT 154 chr4ptel1M 911137 AATA------CTACCCACCCTGCAGGGTTGTTGAGAGGCTCAAATAAGAT 911180 ------ i i iii v v i MIRc#SINE/MIR 155 AATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGAT 204 chr4ptel1M 911181 A---TTTGT-ATCGTGCCCCGAAGAGCTTCAAATGCTATATAAATGT 911223 --- v - vv i iii v i viv v i i MIRc#SINE/MIR 205 AATGTATGTGAAAGCGCTTTGTAAACTGTAAAGTGCTATACAAATGT 251 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 36.98 CpG sites = 35, Kimura (unadjusted) = 38.84 Transitions / transversions = 1.84 (35/19) Gap_init rate = 0.03 (6 / 185), avg. gap size = 2.17 (13 / 6) 24 3.54 0.00 0.00 chr4ptel1M 911317 911345 (88655) (G)n#Simple_repeat 1 29 (0) m_b187s252i11 7336 chr4ptel1M 911317 GGGGCGGGGGGGGGGGGGGGGGGGGGGGG 911345 v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG 29 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 193 27.78 0.00 1.85 chr4ptel1M 911366 911420 (88580) MIRc#SINE/MIR 81 134 (134) m_b187s601i16 7337 chr4ptel1M 911366 CTGGTCTTGTGACATGGAGCAAGTCCTTTCAATCTCTTTCAATTTCAGTT 911415 i iiv v v i vi - i i v iii MIRc#SINE/MIR 81 CTAGCTGTGTGACCTTGGGCAAGTCACTT-AACCTCTCTGAGCCTCAGTT 129 chr4ptel1M 911416 TCCTC 911420 MIRc#SINE/MIR 130 TCCTC 134 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 36.20 CpG sites = 10, Kimura (unadjusted) = 36.20 Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1) 61 0.00 0.00 0.00 chr4ptel1M 911560 911614 (88386) (TTCC)n#Simple_repeat 1 55 (0) c_b187s251i2 7338 chr4ptel1M 911560 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 911609 (TTCC)n#Simpl 1 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 50 chr4ptel1M 911610 CCTTC 911614 (TTCC)n#Simpl 51 CCTTC 55 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 265 26.23 3.16 7.69 chr4ptel1M 912066 912160 (87840) C HSAT5v1#Satellite (602) 5296 5206 m_b187s502i2 7339 chr4ptel1M 912066 TGGCCAGGAATGCCAGGAGATGCACACGCTCACAACACACATGCACGAGC 912115 ii v v i----- v - i i ? ivi C HSAT5v1#Satel 5296 TGGCCAGAGAAGCAAGA-----CACACGCGCACA-CACGCGTNCACACAC 5253 chr4ptel1M 912116 ACACATGGGTGCAT---TATGCACACACACATATACGTGTACATGTGT 912160 i v i i---ii - i i i iii C HSAT5v1#Satel 5252 ACACACGCGCGCACGCGCGTGCACACACACAT-TGCATGCACGCATGT 5206 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 22.64 CpG sites = 18, Kimura (unadjusted) = 34.92 Transitions / transversions = 3.60 (18/5) Gap_init rate = 0.09 (8 / 94), avg. gap size = 1.25 (10 / 8) 36 2.70 0.00 0.00 chr4ptel1M 912649 912686 (87314) (CTC)n#Simple_repeat 1 38 (0) c_b187s251i3 7340 chr4ptel1M 912649 CTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCTTCCT 912686 i (CTC)n#Simple 1 CTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT 38 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 219 29.72 7.26 2.31 chr4ptel1M 913473 913596 (86404) L2b_3end#LINE/L2 320 449 (17) m_b187s601i17 7341 chr4ptel1M 913473 CTGTTTACAAGT-TG---CCCCTGTTAAGACTG-GCACTCCCTGAGGGTG 913517 ? v - --- iii - - vi v ii L2b_3end#LINE 320 CTGNTTACATGTCTGTCTCCCCCACTA-GACTGTGAGCTCCGTGAGGGCA 368 chr4ptel1M 913518 TG---TGGGATGGTCTTTGGCCCTTCG-TGCATCTCCAGGACTTCCTGGA 913563 v ---i ? viv -- ii vi - i i vi i vviiv L2b_3end#LINE 369 GGGACCGNGTCTGTCTT--GTTCACCGCTGTATCCCCAGCGCCTAGCACA 416 chr4ptel1M 913564 GTTCCTGGCACATAGTAGGTGCTTAAGAACTGT 913596 ?v i i i iv v i L2b_3end#LINE 417 GNGCCTGGCACACAGTAGGCGCTCAGTAAATAT 449 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 36.28 CpG sites = 22, Kimura (unadjusted) = 40.59 Transitions / transversions = 1.57 (22/14) Gap_init rate = 0.07 (8 / 123), avg. gap size = 1.50 (12 / 8) 220 20.00 0.00 0.00 chr4ptel1M 913563 913602 (86398) MIR#SINE/MIR 218 257 (5) m_b187s601i18 7337 chr4ptel1M 913563 AGTTCCTGGCACATAGTAGGTGCTTAAGAACTGTCAGCCA 913602 v i i i v v i i MIR#SINE/MIR 218 AGTGCCTGGCACATAGTAAGCGCTCAATAAATGTTAGCTA 257 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 20.49 CpG sites = 5, Kimura (unadjusted) = 23.72 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 13 26.84 0.00 0.00 chr4ptel1M 916360 916399 (83601) (CCC)n#Simple_repeat 1 40 (0) m_b187s252i12 7342 chr4ptel1M 916360 CCCCCCCCCCCCGCCGCCTTTGCCCCCCCCTCCCGCCGCC 916399 v v iiiv i v v (CCC)n#Simple 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 40 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 212 17.59 1.26 0.00 chr4ptel1M 917405 917802 (82198) (AC)n#Simple_repeat 1 403 (0) m_b187s252i13 7343 chr4ptel1M 917405 ACACACACACACACACACACACACACACACACACATACATACACACACAC 917454 i i (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50 chr4ptel1M 917455 ACTCTTTCTCTCTCTCACACACACACACTCTCTCACACACACTC-CACAC 917503 v viv v v v v v v v v - (AC)n#Simple_ 51 ACACACACACACACACACACACACACACACACACACACACACACACACAC 100 chr4ptel1M 917504 ACACACTCATACACACTCTCTCTCACACACACACACACACACACACACAC 917553 v i v v v v (AC)n#Simple_ 101 ACACACACACACACACACACACACACACACACACACACACACACACACAC 150 chr4ptel1M 917554 ACCCCTACAC-CTCTCTCACACACACACTCTCTCACACACACACTCACAC 917602 v vi - v v v v v v v (AC)n#Simple_ 151 ACACACACACACACACACACACACACACACACACACACACACACACACAC 200 chr4ptel1M 917603 ACACCTACAC-CTCACAC-CACAC-CTCTCTCACCCACACTCACACACAC 917649 vi - v - - v v v v v (AC)n#Simple_ 201 ACACACACACACACACACACACACACACACACACACACACACACACACAC 250 chr4ptel1M 917650 TCACACACACACCCTCTCTCTCACACACACACTCACACACACACTCTCTC 917699 v v v v v v v v v v (AC)n#Simple_ 251 ACACACACACACACACACACACACACACACACACACACACACACACACAC 300 chr4ptel1M 917700 TCTCACACACACACACTCACACACACACTCACACACTCTCACACACACAC 917749 v v v v v v (AC)n#Simple_ 301 ACACACACACACACACACACACACACACACACACACACACACACACACAC 350 chr4ptel1M 917750 AATCACACACACACACACACACACTCACATACACACACCCTCACGCACAC 917799 vv v i v v i (AC)n#Simple_ 351 ACACACACACACACACACACACACACACACACACACACACACACACACAC 400 chr4ptel1M 917800 TCA 917802 v (AC)n#Simple_ 401 ACA 403 Matrix = Unknown Transitions / transversions = 0.15 (8/54) Gap_init rate = 0.01 (5 / 397), avg. gap size = 1.00 (5 / 5) 113 16.66 3.33 0.81 chr4ptel1M 918040 918279 (81721) (CTGT)n#Simple_repeat 1 246 (0) m_b187s252i15 7344 chr4ptel1M 918040 CTGTCTCTGTGTCTGTGTCTGTGTCTGTCCCTGTCACTGTCTGTCTGTCT 918089 v v v v v iv v vv (CTGT)n#Simpl 1 CTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCT 50 chr4ptel1M 918090 CTCTGTCTCTGTCTCTGTCAGTCTGTCCTGTCAGTCTGTC--TCTCTCTC 918137 v v v v v - v -- v v (CTGT)n#Simpl 51 GTCTGTCTGTCTGTCTGTCTGTCTGT-CTGTCTGTCTGTCTGTCTGTCTG 99 chr4ptel1M 918138 TCTGTCTCTCTGTCTGTCTCTCTGTCTGTCTCTCTGTCTGTC--TCTGTC 918185 v v v -- (CTGT)n#Simpl 100 TCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTC 149 chr4ptel1M 918186 AGTCTGTCTCTCTCTCTGTCTCTCTGTCTGTCTCTCTGTCTGTC--TCTG 918233 v v v v v -- (CTGT)n#Simpl 150 TGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTG 199 chr4ptel1M 918234 TCAGTCTGCCCTGTGAGTCTGTCGGTC--TCTGGCTCTCTCCCTGTCT 918279 v -i vv v -- v v vi (CTGT)n#Simpl 200 TCTGTCTG-TCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCT 246 Matrix = Unknown Transitions / transversions = 0.09 (3/32) Gap_init rate = 0.03 (6 / 239), avg. gap size = 1.67 (10 / 6) 56 15.00 8.33 6.64 chr4ptel1M 918035 918286 (81714) (TCTCCTG)n#Simple_repeat 1 256 (0) m_b187s252i14 7345 chr4ptel1M 918035 TCTCGCTGTCT-CTGTGT-CTGTGT-CTGTGT-CTGTC-CCTGTC-ACTG 918078 - - v - v - v - - -v (TCTCCTG)n#Si 1 TCTC-CTGTCTCCTGTCTCCTGTCTCCTGTCTCCTGTCTCCTGTCTCCTG 49 chr4ptel1M 918079 TCTGTCTGTCTCTCTGTCT-CTGTCT-CTGTC-AGTCTGTCCTGTCAGTC 918125 -i - - - -vv v v -vi (TCTCCTG)n#Si 50 TCT-CCTGTCTC-CTGTCTCCTGTCTCCTGTCTCCTGTCTCCTGTC-TCC 96 chr4ptel1M 918126 TGTCT-CTCTCTCTCTGTCT-CTCTGT-CTGTCTCTCTGTCTGTCTCTCT 918172 - v - - v v - - -i v (TCTCCTG)n#Si 97 TGTCTCCTGTCTC-CTGTCTCCTGTCTCCTGTCTC-CTGTCT-CCTGTCT 143 chr4ptel1M 918173 GTCTGTCT-CTGTCAGTCTGTCT-CTCTCT-CTGTCTCTCTGTCTGTCTC 918219 -i - -vi - v - - -i v (TCTCCTG)n#Si 144 -CCTGTCTCCTGTC-TCCTGTCTCCTGTCTCCTGTCTC-CTGTCT-CCTG 189 chr4ptel1M 918220 TCTGTCTGTCT-CTGTCAGTCTG-C-CCTGTGAGTCTGTCGGTCTCTGGC 918266 -i - -vi - - -vvi -- - v (TCTCCTG)n#Si 190 TCT-CCTGTCTCCTGTC-TCCTGTCTCCTGT-CTCCTGTC--TC-CTGTC 233 chr4ptel1M 918267 T-CTCTC-CCTGTCTCCT-TCTC 918286 - v - - (TCTCCTG)n#Si 234 TCCTGTCTCCTGTCTCCTGTCTC 256 Matrix = Unknown Transitions / transversions = 0.43 (9/21) Gap_init rate = 0.15 (38 / 251), avg. gap size = 1.00 (38 / 38) 16 0.00 0.00 0.00 chr4ptel1M 919382 919399 (80601) (G)n#Simple_repeat 1 18 (0) m_b187s252i16 7346 chr4ptel1M 919382 GGGGGGGGGGGGGGGGGG 919399 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGG 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 30 0.00 0.00 0.00 chr4ptel1M 919788 919815 (80185) (GAGACC)n#Simple_repeat 1 28 (0) c_b187s251i4 7347 chr4ptel1M 919788 GAGACCGAGACCGAGACCGAGACCGAGA 919815 (GAGACC)n#Sim 1 GAGACCGAGACCGAGACCGAGACCGAGA 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 252 30.20 4.12 1.00 chr4ptel1M 920056 920152 (79848) C L2d2_3end#LINE/L2 (31) 524 425 m_b187s601i19 7348 chr4ptel1M 920056 CCTGCTTTCTGACCAGGCACCGTCCTAGGCACAA--AGGGATGCAAAGAA 920103 i v v - v i v i vi--i i C L2d2_3end#LIN 524 CCTACTGTGTG-CAAGGCACTGTGCTAGGCGCTGTGGGGGATACAAAGAA 476 chr4ptel1M 920104 ACA-AGGAAACCTCTTCTGCTCTCAAGAAGCTTACCTTC-AACTGGACAG 920151 ii - i v ivviii i i vv - ii iv C L2d2_3end#LIN 475 GTATAAGACATGGTCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGGAG 426 chr4ptel1M 920152 A 920152 C L2d2_3end#LIN 425 A 425 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 38.33 CpG sites = 18, Kimura (unadjusted) = 40.13 Transitions / transversions = 1.64 (18/11) Gap_init rate = 0.04 (4 / 96), avg. gap size = 1.25 (5 / 4) 399 30.21 4.35 1.05 chr4ptel1M 920170 920353 (79647) MIR3#SINE/MIR 2 191 (17) m_b187s601i20 7349 chr4ptel1M 920170 TGGTTAGGTGGCCTAGACGAGAGACCCCTGGCTCTGGAGCCATAC--CCT 920217 ivii iv vv v v v i v- i viv-- MIR3#SINE/MIR 2 TGGCAGAGTGGCTGAGCAGAGAGAGCACGGACTG-GGAGTCAGGAGACCT 50 chr4ptel1M 920218 GAGTTCAAGTGCAACCTGGGATGCTAATTGTATGTGTGGCCTTGG-TAAG 920266 i v v viv vv vii i ?vv i -i MIR3#SINE/MIR 51 GGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAG 100 chr4ptel1M 920267 TCACT--AACACTCAGGACC-CTGTTTTCTCATCTCTAAAAGGAGGGGAT 920313 -- v v v i - v i v v i MIR3#SINE/MIR 101 TCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGT 150 chr4ptel1M 920314 GTGAACTC-TTGGCCTTTGAGAG-GCTTCCAACTGTGGCATT 920353 - i v-v ii i i iv-v i v i MIR3#SINE/MIR 151 -TGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATT 191 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 38.35 CpG sites = 25, Kimura (unadjusted) = 39.24 Transitions / transversions = 0.83 (25/30) Gap_init rate = 0.04 (8 / 183), avg. gap size = 1.25 (10 / 8) 306 22.54 11.58 1.92 chr4ptel1M 920678 920772 (79228) C MIR3#SINE/MIR (20) 188 85 m_b187s601i21 7350 chr4ptel1M 920678 GTCAGGGCACTGAAGGAAATGTAGACTTCATCCGGTTTAATTCCCCCCAT 920727 i -iv i viv vv ii ii i- i C MIR3#SINE/MIR 188 GTCAGAGC-TGGAAGGGACCTTAGAGATCATCTAGTCCAAC-CCCCTCAT 141 chr4ptel1M 920728 TTTACAGATGAAGAAACT-AGGCC--------TGA--TGATTTGCTCATG 920766 i - -------- -- i i v C MIR3#SINE/MIR 140 TTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAG 91 chr4ptel1M 920767 ACCACA 920772 ii C MIR3#SINE/MIR 90 GTCACA 85 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 27.93 CpG sites = 15, Kimura (unadjusted) = 27.93 Transitions / transversions = 2.50 (15/6) Gap_init rate = 0.05 (5 / 94), avg. gap size = 2.60 (13 / 5) 252 25.17 12.15 3.45 chr4ptel1M 920711 920817 (79183) C MIRc#SINE/MIR (108) 160 45 m_b187s601i22 7350 chr4ptel1M 920711 GGTTTAATTCCCCCCATTTTACAGATGAAGAAACT-AGGC-CTGA----- 920753 v v vi i - - v ----- C MIRc#SINE/MIR 160 GGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGT 111 chr4ptel1M 920754 ----TGATTTGCTCATGACCACAGCACCAGGAAATCTCAGG--CAGGTCT 920797 ---- i i v ii vvi i v i vv i-- i v C MIRc#SINE/MIR 110 TAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACT 61 chr4ptel1M 920798 CGGGTTAATGTAGTTCTTCC 920817 ---- ivi v C MIRc#SINE/MIR 60 CG----AACCCAGGTCTTCC 45 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 29.68 CpG sites = 13, Kimura (unadjusted) = 31.07 Transitions / transversions = 1.00 (13/13) Gap_init rate = 0.08 (9 / 106), avg. gap size = 1.89 (17 / 9) 225 30.50 5.09 1.34 chr4ptel1M 920827 921042 (78958) L1M5_orf2#LINE/L1 3007 3230 (64) m_b187s551i0 7351 chr4ptel1M 920827 ATCACAAAATAAAAAATT-------TTGATTGCATCAAATTAAAAAGCCT 920869 i i v ------- v i ? v v i i L1M5_orf2#LIN 3007 ACCATAAAAGAAAAAATTGATAAATTGGACTNCATCAAAATTAAAAACTT 3056 chr4ptel1M 920870 TTGTACAAACAAAACTAATGCAGATAAGATTAGAAGGGAAGCAACAAACT 920919 i iv ?vvv ivi vi ivi v i v i v v i ? L1M5_orf2#LIN 3057 CTGCTCNTCAAAAGACACCGTTAAGAAAATGAAAAGGCAAGCCACAGANT 3106 chr4ptel1M 920920 GGGAAAATAGCTTCACAGTTAAAGGTTCTGAGAAAGGCCTCATTTCCAAA 920969 i v vv ii i?vv vivv v v i v i L1M5_orf2#LIN 3107 GGGAGAAAATATTTGCAANACATATATCTGACAAAGGACTCGTATCCAGA 3156 chr4ptel1M 920970 ATATGTAGAGAATTGACTCTAATTT-ATAAGAAATCAAGCCATTC--TCC 921016 i i i -v vi ? i- ? -- v vv --i L1M5_orf2#LIN 3157 ATATATAAAGAACT-CCTACAANTCAATAANAAA--AAGACAAACAACCC 3203 chr4ptel1M 921017 AATTGAGAAAT-GTCAAAGGATATGAA 921042 v? i - v i iv L1M5_orf2#LIN 3204 AATANAAAAATGGGCAAAAGACTTGAA 3230 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 39.78 CpG sites = 31, Kimura (unadjusted) = 41.39 Transitions / transversions = 0.91 (31/34) Gap_init rate = 0.03 (7 / 215), avg. gap size = 2.00 (14 / 7) 1473 31.61 2.57 0.47 chr4ptel1M 920961 921583 (78417) L1ME4c_3end#LINE/L1 4 639 (191) m_b187s551i1 7351 chr4ptel1M 920961 ATTTCCAAAATATGTAGAGAATTGACTCTAATTTATAAGAAATCAAGCCA 921010 v i?v ? i i ii v i v v vv? v v L1ME4c_3end#L 4 ATATCTNTANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAA 53 chr4ptel1M 921011 TTCTCCAATTGAGAAATGT-CAAAGGATATGAA------ATTTTCAGAGG 921053 vv i v v v- i ------ iv ? i L1ME4c_3end#L 54 GACCCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAG 103 chr4ptel1M 921054 ATGAAATTGAAACTATTTCCACTCATATG--AAAGTGTTCCAAATCACTA 921101 v vv ?ivi vvv vv i -- i v vv i L1ME4c_3end#L 104 AGGAAATACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTA 153 chr4ptel1M 921102 TTGATCAGAGAAATGTAAATTAAGACAGCTCTGAGATACCACTACACCCC 921151 v i i i ii i vv i vi v L1ME4c_3end#L 154 GTAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCC 203 chr4ptel1M 921152 TGTCAGACTGGCTAAGATGACAGGAAAAAATAATGATGAGTGTTGGAGGG 921201 i i i i i v i vvv ii vvi iviv i i v i L1ME4c_3end#L 204 TATTAAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGCTGGCGAG 253 chr4ptel1M 921202 GATGTGGGAAAACTGGGACACTGATACATTGTTGGTGGAGCTGTGAACGA 921251 ? i vi v ? v i vi? i ivi L1ME4c_3end#L 254 GNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTG 303 chr4ptel1M 921252 ATCCAACCATTCTGGAGAGCAATCTGGAATTATGCCCCAAAAGTTATCAA 921301 i v v i i i v v i ivi i ii v L1ME4c_3end#L 304 GTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAA 353 chr4ptel1M 921302 ATTGTGCATACCCTTTGACCCAGCAGTGTTACTACTGGGCGTATACCCCA 921351 v v i i vii v vi v i i L1ME4c_3end#L 354 AATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTA 403 chr4ptel1M 921352 AAGAGATACT--AAAAAAGGGCAAGGGACCTGTCTGTGCCAAAATGTTTG 921399 i i v -- i i v ii -- i v ii v i ii L1ME4c_3end#L 404 AGGAAATAATTCAAAAGAAGGAAAAAG--CTATATGCACGAAGATGTTCA 451 chr4ptel1M 921400 TGGCGGCCCTGTTTGTAGTGGCTCAAAACTGGAAACTGAATGGATGCCCT 921449 v i vi i i i i vv i vivv ii i v L1ME4c_3end#L 452 TTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCA 501 chr4ptel1M 921450 TCAATTGGAGAATGGTTAGGTAAATGGTGGTATGTGAACGTTATGGAATA 921499 v v i i vi ii v? viv L1ME4c_3end#L 502 ACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATA 551 chr4ptel1M 921500 TAAT-----TGTAAGAAATGACCAGCAGGATGAATACAGAGAGGCTTGGA 921544 v -----ii v i iv vi v v v iiv vii v L1ME4c_3end#L 552 TTATGCAGCCATTAAAAATGATAATTATGAAGACTATGTAGCAACATGGA 601 chr4ptel1M 921545 GAGACTTACATGAACTGATGCTAAGTGAAATGAGCAGAA 921583 - i iv vi vv i i vi L1ME4c_3end#L 602 -AAATGTTTATGATATAATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 41.62 CpG sites = 105, Kimura (unadjusted) = 42.77 Transitions / transversions = 1.15 (105/91) Gap_init rate = 0.01 (8 / 622), avg. gap size = 2.38 (19 / 8) 282 20.72 13.92 2.27 chr4ptel1M 922138 922216 (77784) C MIRb#SINE/MIR (14) 254 167 m_b187s601i23 7352 chr4ptel1M 922138 CATTTAGTAAGCACCTATTGTGTATCAGGTACTGGGCTAAG------AC- 922180 v i i i i i ii i v ------ - C MIRb#SINE/MIR 254 CATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACA 205 chr4ptel1M 922181 ----TCATCTCATTTGGTCCTCTACAACATATCCTACAAG 922216 ---- i ii - - i i i C MIRb#SINE/MIR 204 TGCATTATCTCATTTAATCCTC-ACAACA-ACCCTGCGAG 167 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 22.33 CpG sites = 14, Kimura (unadjusted) = 26.02 Transitions / transversions = 7.00 (14/2) Gap_init rate = 0.06 (5 / 78), avg. gap size = 2.60 (13 / 5) 247 29.77 13.42 3.05 chr4ptel1M 922195 922343 (77657) C L3#LINE/CR1 (78) 4021 3858 m_b187s601i24 7353 chr4ptel1M 922195 CCTCTACAACATATCCTACAAGTGGTCATCGTGGCCGACACAGTTTGA-C 922243 i vi iv ---- v v v v i - C L3#LINE/CR1 4021 CTTCTACAACATCCCTGACAAGTGGTCATC----CAGCCTCTGCTTGAAC 3976 chr4ptel1M 922244 ATCTGC--------------CA-TCCTTTGCAAAGTGGCTCGTTCCATTT 922278 i v -------------- - v i i? i i ii i i C L3#LINE/CR1 3975 ACCTCCAGTGACGGGGAGCTCACTACCTCNCGAGGCAGCCCATTCCATTT 3926 chr4ptel1M 922279 GTGGATCATTCTCATTGACAGGAAGTTCTTTCCTCAC----AGCCTAAAC 922324 v ivii v vi i - i i---- v i C L3#LINE/CR1 3925 TTGGACAGCTCTGATTGTTAGAAAGTTC-TTCCTTATATTGAGCCGAAAT 3877 chr4ptel1M 922325 ATAGCTCTTTTCATCTTTC 922343 v iv ii vi v i C L3#LINE/CR1 3876 CTGCCTCCCTGTAACTTCC 3858 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 38.52 CpG sites = 26, Kimura (unadjusted) = 39.73 Transitions / transversions = 1.53 (26/17) Gap_init rate = 0.06 (9 / 148), avg. gap size = 2.78 (25 / 9) 237 20.62 6.25 1.49 chr4ptel1M 922347 922410 (77590) C L2a_3end#LINE/L2 (5) 512 446 m_b187s601i25 7354 chr4ptel1M 922347 TTCAGTTCAACA----TTTTTTAAGCACCCACTATGTGCAATGAACATTC 922392 - ---- v i i i v v v vv i C L2a_3end#LINE 512 TTCA-TTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTT 464 chr4ptel1M 922393 CTAGGCACTGGGGACCCA 922410 i iv C L2a_3end#LINE 463 CTAGGCGCTGGGGATACA 446 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 20.30 CpG sites = 6, Kimura (unadjusted) = 24.23 Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.03 (2 / 63), avg. gap size = 2.50 (5 / 2) 325 29.08 10.71 0.00 chr4ptel1M 922532 922727 (77273) L1ME4b_3end#LINE/L1 120 336 (556) m_b187s551i2 7355 chr4ptel1M 922532 TCATAATCACATGAAAGAATGCTCCAAGTTACTACTAAGAAGAGAAATGC 922581 v v i ii v vv i vv v L1ME4b_3end#L 120 TCTTAAACATATGAAAAGATGCTCAACCTCACTCATAATAAGAGAAATGC 169 chr4ptel1M 922582 AAA-GAAAACTACTCTGAAGTCTCAT-----GCCCAGAATATTAGCAAAG 922625 -v v ii vi -----i i vv v i L1ME4b_3end#L 170 AAATTAAAACTACACTGAGATACCATTTTTCACCTATCAGATTGGCAAAG 219 chr4ptel1M 922626 ATGGCAATAGTTGA----------TGTTG--GAGGGT-TATGGGAAGAGG 922662 viv viv ---------- -- - iv i v L1ME4b_3end#L 220 ATCAAAAAGTTTGATAACACACTGTGTTGGCGAGGGTGTGGGGAAACAGG 269 chr4ptel1M 922663 CACACAAGTGCATTGTTGGTGGAGTTGGGAAT--GAAGAACCATTTAAGA 922710 v vvi i i iiv vi -- v v vi vvi L1ME4b_3end#L 270 CACTCTCATACATTGCTGGTGGGAGTGTAAATTGGTACAACCTCTATGGA 319 chr4ptel1M 922711 AAGCAATTTAGAATTAT 922727 ii i v v L1ME4b_3end#L 320 GGGCAATTTGGCAATAT 336 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 36.98 CpG sites = 25, Kimura (unadjusted) = 36.98 Transitions / transversions = 0.78 (25/32) Gap_init rate = 0.03 (6 / 195), avg. gap size = 3.50 (21 / 6) 304 31.49 9.55 0.42 chr4ptel1M 922534 922753 (77247) L1ME3Cz_3end#LINE/L1 118 357 (640) m_b187s551i3 7355 chr4ptel1M 922534 ATAATCACATGAAAGAATGCTCCAAGTTACTACTAAGAAGAGAAATGCAA 922583 v i ii v vv i v vv i L1ME3Cz_3end# 118 ATAAACATATGAAAAGATGCTCAACCTCACTAGTAATCAGGGAAATGCAA 167 chr4ptel1M 922584 A-GAAAACTACTCTGAA-----GTCTCATGCCCAGAATATTAGCAAAGA- 922626 -v ? vv i-----i i ii vv v i i - L1ME3Cz_3end# 168 ATTAAAACNACAATGAGATACCATTTCACACCCATCAGATTGGCAAAAAT 217 chr4ptel1M 922627 ---------TGGCAATAGTTGATGTTGGAG-GGTTATGGGAAGA--GGCA 922664 --------- i vivii v - v i ii i -- v L1ME3Cz_3end# 218 TTAAAAGTCTGACAATACCAAGTGTTGGCGAGGATGTGGAGAAACGGGAA 267 chr4ptel1M 922665 CACAAGTGCATTGTTGGTGGAGTTGGGAAT--GAAGAACCATTTAAGAAA 922712 v vvi i i i iiv vi -- v v i vi i L1ME3Cz_3end# 268 CTCTCATACACTGCTGGTGGGAGTGTAAATTGGTACAACCACTTTGGAGA 317 chr4ptel1M 922713 GCAATTTAGAATTATGAAATGAATGCTTAATATACCCACAC 922753 i v v vv i i - i v v i v i L1ME3Cz_3end# 318 GCAATTTGGCAATATCTAGTAAA-GTTGAAGATGCGCATAC 357 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 41.87 CpG sites = 36, Kimura (unadjusted) = 41.87 Transitions / transversions = 1.09 (36/33) Gap_init rate = 0.04 (8 / 219), avg. gap size = 2.75 (22 / 8) 251 33.01 11.57 1.12 chr4ptel1M 923641 923882 (76118) C L3#LINE/CR1 (343) 3756 3490 m_b187s601i26 7353 chr4ptel1M 923641 CCACTAAGTCTTCTCTTCCCCAGAC-AAAAATCTCC---TCCTTCTTCAG 923686 v i i - v i --- vv v C L3#LINE/CR1 3756 CCTCTAAGTCTTCTCTTCTCCAGGCTAAACATCCCCAGTTCCTTCAACCG 3707 chr4ptel1M 923687 TTTAT-GCACGA-ATGGGAGCTTAGGGCTTGGCAGCCT-TTAACTGCCCA 923733 iv -ii i - --vi ivi i iivv v v -i iiii i v C L3#LINE/CR1 3706 TTCCTCATATGACATGG--TTTCCAGACCCTTCACCATCCTGGTCGCTCT 3659 chr4ptel1M 923734 CACATTGCAGGCTCTCCTGCTTCTCCGTGCTCTTCCTCAAAGGGAGTTCC 923783 - vi v v v v i v vi ii i i v v vi iv C L3#LINE/CR1 3658 C-CTCTGGACGCGCTCCAGTTTGTCAATGTCCCTCTTAAAATGTGGCGCC 3610 chr4ptel1M 923784 CAGAGCTAAATTCA--------------GTCTGACCAGGGCA-AGGAAAG 923818 i i iv -------------- v - v v C L3#LINE/CR1 3609 CAGAACTGAACGCAATACTCCAGATGTGGTCTGACCAGCGCAGAGTACAG 3560 chr4ptel1M 923819 CTGA---ATTTCCTCCTTGCAGCT-GACTCTGAGCCTCTCTT-ATGCATT 923863 v i--- v i vv?v - v ivi i v - vi C L3#LINE/CR1 3559 CGGGACTATTACCTCCCTTGNTCTGGACACTATACTTCTATTAATGCAGC 3510 chr4ptel1M 923864 CTAAGCTC-TATTTGCCTTT 923882 v i-i v i C L3#LINE/CR1 3509 CTAAGATTGCATTAGCTTTT 3490 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 42.37 CpG sites = 40, Kimura (unadjusted) = 44.58 Transitions / transversions = 1.03 (40/39) Gap_init rate = 0.06 (14 / 241), avg. gap size = 2.21 (31 / 14) 13 23.22 2.13 2.13 chr4ptel1M 924014 924060 (75940) (TGTTCTG)n#Simple_repeat 1 47 (0) m_b187s252i17 7356 chr4ptel1M 924014 TGTGCTGTGCTGTGTGTGC-CCGCTCTGTGTTTGTGTGCTCTGTGTTC 924060 v i v v -vi i - v i (TGTTCTG)n#Si 1 TGTTCTGTGTTCTGTGTTCTGTGTTCTGTG-TTCTGTGTTCTGTGTTC 47 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.04 (2 / 46), avg. gap size = 1.00 (2 / 2) 652 27.91 0.00 0.00 chr4ptel1M 925379 925593 (74407) C L1ME4b_3end#LINE/L1 (677) 215 1 m_b188s551i0 7357 chr4ptel1M 925379 GCCAATCTGACAGGTATGTAGTAGTATTTCAGAGTTGTCTTAATTTGAAT 925428 i iviv i i i v v i v C L1ME4b_3end#L 215 GCCAATCTGATAGGTGAAAAATGGTATCTCAGTGTAGTTTTAATTTGCAT 166 chr4ptel1M 925429 TTCTCTGATTAATAATGACTTGGAGCATCTTTTCATATGGCTAGAAATAG 925478 v vv i vv v vi ii iivi C L1ME4b_3end#L 165 TTCTCTTATTATGAGTGAGGTTGAGCATCTTTTCATATGTTTAAGAGCCA 116 chr4ptel1M 925479 TTTCAATTTCTTTGTCTGAGAACTGTCTGTTCATATCCTTTGACAATTTA 925528 vv i v v v v v C L1ME4b_3end#L 115 TTTGTATTTCCTTTTCTGTGAACTGTCTGTTCATATCCTTTGCCCATTTT 66 chr4ptel1M 925529 TCAATTGGAGAATGGCTTGATTTCTTATAAACCAGAGTCAATTCTCTATA 925578 v ivvi v v ivv vi iiv vivv ii i C L1ME4b_3end#L 65 TCTATTGGGTTGTTGGTCTTTTTCTTATTGATTTGTAGGAGCTCTTTATA 16 chr4ptel1M 925579 TATTTTGGAAATGAG 925593 vv v C L1ME4b_3end#L 15 TATTAGGGAAATTAG 1 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 35.00 CpG sites = 25, Kimura (unadjusted) = 35.00 Transitions / transversions = 0.71 (25/35) Gap_init rate = 0.00 (0 / 214), avg. gap size = 0.0 (0 / 0) 1331 33.24 3.36 2.05 chr4ptel1M 925444 926693 (73307) C L1M5_orf2#LINE/L1 (0) 3294 2029 m_b188s551i1 7357 chr4ptel1M 925444 TGACTTGGAGCATCTTTTCATATGGCTAGAAATAGTTTCAATTTCTTTGT 925493 ?v v i vi vviiivi v? v iv C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr4ptel1M 925494 CTGAGAACTGTCTGTTCATATCCTTTGACAATTTATCAATTGGA--GAAT 925541 i v v vi i v v v ?v i-- vv C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTT 3195 chr4ptel1M 925542 GGCTTGATTTCTTATAAACCAGAGTCAATTCTCTATATATTTTGGAAATG 925591 v -- ? vi ?iv vivv i i i v i C L1M5_orf2#LIN 3194 GTCTT--TTTNTTATTGANTTGTAGGAGTTCTTTATATATTCTGGATACG 3147 chr4ptel1M 925592 AGGCCTTTATCAGAACTTTTGACTGTAAAAATGTTTTCCCAGTTTATTGC 925641 v i vv v vv?i i v v i ? i i v C L1M5_orf2#LIN 3146 AGTCCTTTGTCAGATATATGTNTTGCAAATATTTTCTCCCANTCTGTGGC 3097 chr4ptel1M 925642 TTCCCTTATAATCTTGTCTGCATTAGTTTTGTTTGTACAAAAACTTTTCA 925691 v v v i v ivi iv ivi vvv? vi i ii v C L1M5_orf2#LIN 3096 TTGCCTTTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTTTAA 3047 chr4ptel1M 925692 ATTTGATATAATCAAA-------AATTTCTATTTTGTGATCAATAATGAT 925734 v i? i v ------- v i v i i --- ?i v C L1M5_orf2#LIN 3046 TTTTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGGT---TNGTGCT 3000 chr4ptel1M 925735 CTCTAGTTCTTCGGGCATAAATTCTTTCCTCTTTCACAGCTCTGAGAGGG 925784 i i ivv i vvvvv v ii v v?ii vi iivi i--- C L1M5_orf2#LIN 2999 TTTTGTGTCCTGTTTAAGAAATCTTTGCCTANCCCAAGGTCACGAA---G 2953 chr4ptel1M 925785 AAACTATCCTGT-TTTTCTAATTTA-----TTTATAATCTCATTCTTTAT 925828 v i v i - -- i ----- i i i ?ii i C L1M5_orf2#LIN 2952 ATATTCTCCTATGTTTTCT--TCTAGAAGTTTTATAGTTTTANCTTTTAC 2905 chr4ptel1M 925829 GCCTAGGTC-ATGAACCCATTTTGACTTTATCTTGGTGTACGGTGTTAAG 925877 iii - -i i ? v v i v i v i C L1M5_orf2#LIN 2904 ATTTAGGTCTATGA-TCCATCTNGAATTAATTTTTGTGTATGGTGTGAGG 2856 chr4ptel1M 925878 TGTGGGTTGATGCCTAGTTTCTGCCATACTAATTTCCAACTTTCCCAGCA 925927 iv i v?iii v i v ivi v i v i C L1M5_orf2#LIN 2855 TAGGGGTCGAGNTTCATTTTTTTCCATATGGATATCCAATTGTTCCAGCA 2806 chr4ptel1M 925928 ATTTTTGTCAAACAGTGAGTTCTTATCCCAAAAGCTGGGT--CTTTGGG- 925974 viv ii v vvvi i vi ---- ii -- ? v- C L1M5_orf2#LIN 2805 CCATTTGTTGAAAAGACTATCCTTTCCCCA----CTGAATTGCNTTGGCA 2760 chr4ptel1M 925975 --TTTGTCAAACACTAGGTTGTTAAAATTAT-TGACTGTTTTGTCCTTTG 926021 -- v ii i? v?ii v vv i - iv v v ---- i C L1M5_orf2#LIN 2759 CCTTTGTCAAAAATCAANTGNCCATATATGTGTGGGTCTATT----TCTG 2714 chr4ptel1M 926022 AAC---CTAACCTATTCCACTGATCAACTAGTCTATTTCTTA-GTCAATA 926067 i --- vi i i v i v i- - i C L1M5_orf2#LIN 2713 GACTCTCTATTCTGTTCCATTGATCTATTTGTCTATC-CTTACGCCAATA 2665 chr4ptel1M 926068 CCAAATGGTTTTGGTAACCGCTGCTTTATAAT-----TTTAGATCTGGTA 926112 v iv i i v i iv ----- v ? ? C L1M5_orf2#LIN 2664 CCACACTGTCTTGATTACTGTAGCTTTATAATAAGTCTTGANATCNGGTA 2615 chr4ptel1M 926113 CAGCTAGGCCACCTTCATTTGATTTTTGTTTTCATTAATTTCCTTGAAAT 926162 vv iv v v vv - v i iv vv v v ii v vv C L1M5_orf2#LIN 2614 GTGTAAGTCCTCCAAC-TTTGTTCTTCTTTTTCAAGATTGTTTTGGCTAT 2566 chr4ptel1M 926163 TCTTGACCTGTTTTTTTTTTTTAATATGAACTTTG---TTATTTTTTCTA 926209 ? ii i--- viv iv i i i--- i vi v v C L1M5_orf2#LIN 2565 TCTNGGTCC---TTTGCATTTCCATATAAATTTTAGAATCAGCTTGTCAA 2519 chr4ptel1M 926210 GTCAT-TAAAATAGTTTTGGGGGAGTCTGATTGGTATAGTGCTAAAT--- 926255 v iv -i v iii vvv v i v v iii i --- C L1M5_orf2#LIN 2518 TTTCTACAAAAAAACCTGCTGGGATTTTGATTGGGATTGCATTGAATCTA 2469 chr4ptel1M 926256 -AGATTAGTTTAAGTAGTATTGTCATCTTTATTATATTTGCTTGCCCTAT 926304 - i i ii v v v ? iv viv ivi v C L1M5_orf2#LIN 2468 TAGATCAATTTGGGGAGAATTGACATCTTNACAATATTGAGTCTTCCAAT 2419 chr4ptel1M 926305 CCAAGAGCATTTAATAATTTTCCAATTGGTCAGATCTGCTTTA-TTTGTG 926353 v i vvv vi i v iv i i v - v v C L1M5_orf2#LIN 2418 CCATGAACATGGTATATCTCTCCATTTATTTAGGTCTTCTTTAATTTCTC 2369 chr4ptel1M 926354 TGGAAAGTATTTTGTAGTTTTGCTCGTATAGTTCTTGACTTTCCTTTGGC 926403 viiv i i vvvi ? v vviv ?i vi C L1M5_orf2#LIN 2368 TCAGCAATGTTTTGTAGTTTTCAGTGTANAGGTCTTGCACATNTTTTGTT 2319 chr4ptel1M 926404 AGGCAGATTCCTAAATATTTTATACTATCAGTAGTTAGTTTAAATGAAAT 926453 iivv i ? ii v iv vv i v v iv C L1M5_orf2#LIN 2318 AGATTTATTCCTAAGTATTTNATGTTTTTTGATGCTATTGTAAATGGTAT 2269 chr4ptel1M 926454 TTCTCTTTGTAACTCTAATTGTTGGATT--TTGTTAGTGATATATAAGAA 926501 vi i ?-- v i v v ivi -- iv ii ii C L1M5_orf2#LIN 2268 TGTTTTTN--AAATTTCATTTTCCAATTGTTTGTTGCTAGTATATAGAAA 2221 chr4ptel1M 926502 TGCTGATGGCTTATGTGGGTTTATTTTGTATCCTGCAACTTTGTTAAAGG 926551 i viv ii v ivi v ii ? i i i vv C L1M5_orf2#LIN 2220 TACAATTGATTTTTGTATATTGACCTTGTATCCNGCGACCTTGCTAAATT 2171 chr4ptel1M 926552 TGTGGATTATTTCTAATAGCTTGTTAGTAGAATCTCTGGGGTTCTCTAAG 926601 iiivv v i i ? v v i ? i i v C L1M5_orf2#LIN 2170 CACTTATTAGTTCTAGTAGTTTNTTTGTAGATTCTTTNGGATTTTCTACG 2121 chr4ptel1M 926602 TATACCATCATGTCATCAGCAAAGAGTGATAATTTGGCTTCCTCATTACC 926651 ? v v i v i? i i vii i v v C L1M5_orf2#LIN 2120 TANACAATCATGTCATCTGCGAATAANGACAGTTTTATTTCTTCCTTTCC 2071 chr4ptel1M 926652 TACTCTAATTCCTTTAATCTCTTTCTCAACTCTTATTTTACT 926693 v iii v v v i i vvvi vi C L1M5_orf2#LIN 2070 AATCTTTATGCCTTTTATTTCTTTTTCTTGCCTTATTGCACT 2029 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 45.36 CpG sites = 206, Kimura (unadjusted) = 46.28 Transitions / transversions = 1.02 (206/201) Gap_init rate = 0.04 (44 / 1249), avg. gap size = 1.55 (68 / 44) 24 32.44 2.88 2.88 chr4ptel1M 927502 927640 (72360) (ATCC)n#Simple_repeat 1 139 (0) m_b188s252i0 7358 chr4ptel1M 927502 ATGCATCCATCCATCTGTCTGTCTAACTATTCATCCTTCCATTCATCCAT 927551 v ii ii i v i i v i (ATCC)n#Simpl 1 ATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCAT 50 chr4ptel1M 927552 CCTTCCATCTGTCTTTTTTTCCTTTCTTCCAT-CTTTTATCTCTCTCTCC 927600 v ii iv iiv v i v - v ii iv - vi (ATCC)n#Simpl 51 CCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATC-CATC 99 chr4ptel1M 927601 CATAC-TACAT--ATCTATCCACCCCACTTCATTCCATCCATC 927640 v - v -- i -i - i - (ATCC)n#Simpl 100 CATCCATCCATCCATCCATCCA-TCCA-TCCA-TCCATCCATC 139 Matrix = Unknown Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.05 (7 / 138), avg. gap size = 1.14 (8 / 7) 69 0.00 0.00 0.00 chr4ptel1M 927649 927709 (72291) (TTCC)n#Simple_repeat 1 61 (0) c_b188s251i0 7359 chr4ptel1M 927649 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 927698 (TTCC)n#Simpl 1 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 50 chr4ptel1M 927699 CCTTCCTTCCT 927709 (TTCC)n#Simpl 51 CCTTCCTTCCT 61 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 251 36.75 0.84 1.69 chr4ptel1M 927851 927969 (72031) L2#LINE/L2 2322 2439 (643) m_b188s601i0 7360 chr4ptel1M 927851 CTGTGTGCAGCTGACTCCCAGATCTCTATGTCTAGCCTTGGCC-CTTCCC 927899 i i v v i i v v i iv i - i L2#LINE/L2 2322 CTATATGCTGATGACTCCCAAATTTATATCTCCAGCCCGGACCTCTCCCC 2371 chr4ptel1M 927900 TGAGCCTTGGACTGCTGCATCTATAGCTTCCTGGTGGACTCCTGAAGCAG 927949 i iiii --i i v vi i v iv v vi vv viv L2#LINE/L2 2372 TGAACTCCAGACT--CGTATATCCAACTGCCTACTCGACATCTCCACTTG 2419 chr4ptel1M 927950 AATCCCTGACAAGCACCCCA 927969 i vi i i i i i L2#LINE/L2 2420 GATGTCTAATAGGCATCTCA 2439 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 49.90 CpG sites = 27, Kimura (unadjusted) = 53.59 Transitions / transversions = 1.69 (27/16) Gap_init rate = 0.03 (3 / 118), avg. gap size = 1.00 (3 / 3) 244 31.17 5.36 2.61 chr4ptel1M 929273 929384 (70616) C MIR3#SINE/MIR (48) 160 46 m_b188s601i1 7361 chr4ptel1M 929273 ATTTAATCTGCCCTCTTCCCCTTTTTATCGATGATGAAACGGAGGTACAG 929322 i i iiv i i v--- iv v v iv C MIR3#SINE/MIR 160 ATCTAGTCCAACCCCCTCA---TTTTACAGATGAGGAAACTGAGGCCCAG 114 chr4ptel1M 929323 AGAG--GAAATCACCTGCCTGAGCTTGTGCAGATAATAAAT--CA-AACC 929367 -- i v i ii v iiii v? i v i -- - i C MIR3#SINE/MIR 113 AGAGGTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCC 64 chr4ptel1M 929368 AGGA-GAGAAAGCAGATC 929384 i -v vv i C MIR3#SINE/MIR 63 GGGACTAGAACCCAGGTC 46 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 40.81 CpG sites = 21, Kimura (unadjusted) = 42.48 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.06 (7 / 111), avg. gap size = 1.29 (9 / 7) 352 30.43 5.07 0.00 chr4ptel1M 929289 929426 (70574) C MIRc#SINE/MIR (118) 150 6 m_b188s601i2 7361 chr4ptel1M 929289 TCCCCTTTTTATCGATGATGAAACGGAGGTACAGAGAGG--AAATCACCT 929336 v iv v v iv -- i v i C MIRc#SINE/MIR 150 TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTT 101 chr4ptel1M 929337 GCCTGAGCTTGTGCAGATAATAAAT--CA-AACCAGGA-GAGAAAGCAGA 929382 ii v iiii v i i -- - i i -vv vv i C MIRc#SINE/MIR 100 GCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGG 51 chr4ptel1M 929383 TCCT-TTACCAACAACTCAATTGCTCCTTCCATTGCATAATCCTG 929426 i -i iv vv v v v i i iv iv C MIRc#SINE/MIR 50 TCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTG 6 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 38.51 CpG sites = 22, Kimura (unadjusted) = 39.72 Transitions / transversions = 1.10 (22/20) Gap_init rate = 0.04 (5 / 137), avg. gap size = 1.40 (7 / 5) 266 34.20 1.74 0.86 chr4ptel1M 933122 933236 (66764) MIRc#SINE/MIR 2 117 (151) m_b188s601i3 7362 chr4ptel1M 933122 GAGGGGGTGTGATATAGTAGGCAGTGAACTCATCTTGGAGTTAGGAAGAT 933171 vi i ii i iv v v viv i i MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr4ptel1M 933172 CTGGGAAC-CGTCCTCTGTCAGACATATTCCTGGCTCTGAGATTCTGGG- 933219 vv -v ivvv v v i- v i v v iii - MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCAC-TTACTAGCTGTGTGACCTTGGGC 100 chr4ptel1M 933220 AAATGGCCCAACTTCCC 933236 i vi ii i i MIRc#SINE/MIR 101 AAGTCACTTAACCTCTC 117 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 45.21 CpG sites = 21, Kimura (unadjusted) = 46.85 Transitions / transversions = 1.17 (21/18) Gap_init rate = 0.03 (3 / 114), avg. gap size = 1.00 (3 / 3) 209 33.33 0.00 0.00 chr4ptel1M 933285 933341 (66659) C L3#LINE/CR1 (8) 4091 4035 m_b188s601i4 7363 chr4ptel1M 933285 CACGAAATCTCAGTATTTGGAGGGGTTTCGAGGGTCATCTGGTCAAACTC 933334 ii vi v i iii iiii i v ii C L3#LINE/CR1 4091 CACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCAACCT 4042 chr4ptel1M 933335 CACTTCC 933341 v v C L3#LINE/CR1 4041 CCCATCC 4035 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 48.07 CpG sites = 14, Kimura (unadjusted) = 48.07 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0) 528 25.81 0.81 0.00 chr4ptel1M 933595 933718 (66282) C MIRc#SINE/MIR (120) 148 24 m_b188s601i5 7364 chr4ptel1M 933595 CTCATTTTATAGTGGAGGAAACTGAGACAAACAGAG-TGAAGTGACCGGT 933643 i i vv i vv v - v iv i C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr4ptel1M 933644 CCAGGGTCACACAGGTGGTCAGTGACAGAGACCACCTTTAAACTCAGGTT 933693 i v i v i v vivvi ii i i C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTC 49 chr4ptel1M 933694 CCCTTGACTCCAAGGCCAGTCCTCT 933718 ii i v v C MIRc#SINE/MIR 48 TTCCTGACTCCAAGTCCAGTGCTCT 24 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 30.75 CpG sites = 17, Kimura (unadjusted) = 32.06 Transitions / transversions = 1.13 (17/15) Gap_init rate = 0.01 (1 / 123), avg. gap size = 1.00 (1 / 1) 23 26.04 0.00 3.17 chr4ptel1M 934962 935026 (64974) (AC)n#Simple_repeat 1 63 (0) m_b188s252i1 7365 chr4ptel1M 934962 ACACACATACATCTATAAACATACACACACACATATACACATATACACGT 935011 i - - i v i i i i i ii (AC)n#Simple_ 1 ACACACACACA-C-ACACACACACACACACACACACACACACACACACAC 48 chr4ptel1M 935012 ACACTCCTACACACA 935026 v vi (AC)n#Simple_ 49 ACACACACACACACA 63 Matrix = Unknown Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.03 (2 / 64), avg. gap size = 1.00 (2 / 2) 227 26.61 1.22 3.75 chr4ptel1M 935933 936014 (63986) C L1M8_5end#LINE/L1 (2275) 80 1 m_b188s551i2 7366 chr4ptel1M 935933 TGTTCTGTCTTTACTTTTTGTGGAGGAAATCTGG-AGAGCCTAAAGTTTT 935981 i v --- i i i v v - vi v ii v C L1M8_5end#LIN 80 TGCTCTGTCTGT---TTTTATGGGGGGATTCGGGGAGATTCAAAAACTAT 34 chr4ptel1M 935982 CTCACCTCCTCTGCCTTCTTCCCAGAGTCCTCC 936014 vi i v v i v i C L1M8_5end#LIN 33 GCCGCCGCCGCCGCCATCTTCCCAGAATCCTCC 1 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 29.57 CpG sites = 11, Kimura (unadjusted) = 33.26 Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.05 (4 / 81), avg. gap size = 1.00 (4 / 4) 13 4.76 0.00 4.35 chr4ptel1M 937908 937931 (62069) (CCCT)n#Simple_repeat 1 23 (0) m_b188s252i2 7367 chr4ptel1M 937908 CCCTCCCTCCCTCCACCCCCTCCC 937931 - i (CCCT)n#Simpl 1 CCCTCCCTCCCTCC-CTCCCTCCC 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 1590 31.14 1.59 0.63 chr4ptel1M 938244 938870 (61130) C L1ME4c_3end#LINE/L1 (191) 639 7 m_b188s551i3 7368 chr4ptel1M 938244 TTCTGCTCATTTCACTCAGCATCATTTCATGTAAGTCTCTCCAGGCCTTT 938293 iv i i i v iv vi i - v iivi C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATAAACATTT-TCCATGTTGCT 591 chr4ptel1M 938294 CTGTATTCATCCTGCTGGTCATTTCTTACAGAACAATAATATTCCGTAAC 938343 vii v v v iv vi i v ii vvvv i viv C L1ME4c_3end#L 590 ACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCGA 541 chr4ptel1M 938344 ATTCATATACCACCATTTATCCAACCATTCTCCATTTGATGGGCATCCAC 938393 i ?v i iv iii i vv v i ii v C L1ME4c_3end#L 540 GTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAG 491 chr4ptel1M 938394 TCAGTTTCCAGCTTCTAGCCACTACAAACAGGGCTGCCAGAAACATTTTG 938443 viv ii i v i i i i iv v vi i v C L1ME4c_3end#L 490 GTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTC 441 chr4ptel1M 938444 GCACATACAGGACCCTTTCCCTTCTTT---AGTATCTCCTTGGGGTATAA 938490 ii i --- i i --- v i i i v v C L1ME4c_3end#L 440 GTGCATATAG---CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAAT 394 chr4ptel1M 938491 GCTCAGCACTG------CTGGGTCAAAGGGTATGCACAGTTTGATAACTT 938534 v i v v ------ v v v ii i C L1ME4c_3end#L 393 TCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTC 344 chr4ptel1M 938535 TTGGGGCATAATTCCAGATTGCTCTCCAGAATGGTTGGATTCGTTCACAG 938584 ivi i v v i i i v v iivi i ? C L1ME4c_3end#L 343 TTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACAN 294 chr4ptel1M 938585 CTCCACCAACAATGTATCAGTGTCCCAGTTTTCCCGCATCCCCTCCAACA 938634 iv i v ? v iv ? i v i C L1ME4c_3end#L 293 TGCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGCA 244 chr4ptel1M 938635 TTCATCATTATTTTTTCCTGTCATCTTAGCCAATCTG-CAGGTCTGTAGT 938683 vivi ivv ii vvv i v i i i-i iv iv i C L1ME4c_3end#L 243 TTGGGTATTATCAATTTTTTAAATTTTTGCTAATTTAATAGGCGTAAAAT 194 chr4ptel1M 938684 GGTATCTCAGAGTTGTCTTAATTTGCATTTCTCTGATTAACAATGACTTG 938733 vv ii i vi ii vv v C L1ME4c_3end#L 193 GGTATCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACTAGCGAGGTT 144 chr4ptel1M 938734 GAGCATCTTTTCATATGACTAGAAATAGTTTCAATTTCTTCATCTGAGAA 938783 i i i i vi ivvv ivi? vv i v ? v C L1ME4c_3end#L 143 GAACATTTTTCCATGTGTTTGTTTACTANTTGTATTTCCTCTTNTGTGAA 94 chr4ptel1M 938784 TTGTCTGTTCATATCCTTTGACCATTTTTCAATGGGAGAATGGCTTGATT 938833 i v v v v i vv v v ?vv C L1ME4c_3end#L 93 TTGTCTGTTCATGTCCTTTGCCCATTTATCTATTGGGGTCTTGATNTTTT 44 chr4ptel1M 938834 TCTTATAAATTAGAGTCGATTCTCTATGTATTTTAGA 938870 v v i viii i i ? v? C L1ME4c_3end#L 43 TCTTATCAATTTGAATGAGCTCTTTATATANTANAGA 7 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 40.72 CpG sites = 103, Kimura (unadjusted) = 41.84 Transitions / transversions = 1.13 (103/91) Gap_init rate = 0.01 (7 / 626), avg. gap size = 2.00 (14 / 7) 551 31.79 5.25 3.05 chr4ptel1M 938727 939336 (60664) C L1M5_orf2#LINE/L1 (0) 3294 2672 m_b188s551i4 7368 chr4ptel1M 938727 TGACTTGGAGCATCTTTTCATATGACTAGAAATAGTTTCAATTTCTTCAT 938776 ?v v i vi vviiivi v? v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr4ptel1M 938777 CTGAGAATTGTCTGTTCATATCCTTTGACCATTTTTCAATGGGA--GAAT 938824 i v v vi i v ?v v i-- vv C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTT 3195 chr4ptel1M 938825 GGCTTGATTTCTTA-TAAATTAGAGTCGATTCTCTATGTATTTTAGAAAA 938873 v -- ? - i ? iv vv - i i i i v v C L1M5_orf2#LIN 3194 GTCTT--TTTNTTATTGANTTGTAGGAG-TTCTTTATATATTCTGGATAC 3148 chr4ptel1M 938874 GAGGCCTTTCTCAGAACCTTTAACTGTGAAGATGTTTTCCCAGTTTGTTG 938923 v v vviv vv?i ii v v i ? i v C L1M5_orf2#LIN 3147 GAGTCCTTTGTCAGATATATGTNTTGCAAATATTTTCTCCCANTCTGTGG 3098 chr4ptel1M 938924 CTTCCCTTCTAATCTTGTTTACATTAGTTTTTTTTGTACAGAAACTTTTT 938973 v i v i v v iv ivi vv? vi ii v C L1M5_orf2#LIN 3097 CTTGCCTTTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTTTA 3048 chr4ptel1M 938974 AATTTGATGTAATCAA-------AATTTTCTATTTTGTGATCAATAATGG 939016 v ? i v ------- i v i i --- ?i v C L1M5_orf2#LIN 3047 ATTTTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGGT---TNGTGC 3001 chr4ptel1M 939017 TCTCTAGTTCTTCTTTGGTCACAAATTTCTTCCTCCTCCACAAGTCTGAG 939066 i i ivv i v i--- v i i v v?i - i vvii C L1M5_orf2#LIN 3000 TTTTTGTGTCCTGTTTA---AGAAATCTTTGCCTANCCCA-AGGTCACGA 2955 chr4ptel1M 939067 ACATAAACTATCCCATG--TTCCTCT-GATTTATTTATAATCTCGTTCTT 939113 v -- i v i -- i - vv - i i ii?ii C L1M5_orf2#LIN 2954 AGAT--ATTCTCCTATGTTTTCTTCTAGAAGT-TTTATAGTTTTANCTTT 2908 chr4ptel1M 939114 TATGCCTAAATCATGGACCCATTTTGATCTTATCTTGGTATGCGGTGTTA 939163 iiii ii vvv i i ? vi v i v i ii v C L1M5_orf2#LIN 2907 TACATTTAGGTCTATGATCCATCTNGAATTAATTTTTGTGTATGGTGTGA 2858 chr4ptel1M 939164 AGTGTGGCTCCATGCCTAATTTCTGCCATACTAATTTCCAGTTATCCCAG 939213 i iv v v v?iii v i v ivi v i i i C L1M5_orf2#LIN 2857 GGTAGGGGTCGAGNTTCATTTTTTTCCATATGGATATCCAATTGTTCCAG 2808 chr4ptel1M 939214 CAATTTTTGTCAAATAATGAATTCTTATCCCA--AAAGTGAGGATCTTTG 939261 viv ii v ivvv i vi --i v ----- ? C L1M5_orf2#LIN 2807 CACCATTTGTTGAAAAGACTATCCTTTCCCCACTGAATTG-----CNTTG 2763 chr4ptel1M 939262 G--GTTTTGCTGTAGTT--ATTGACTAT-TTTGT---------CTTGTGA 939297 --vi iiiv iv -- ? ? i - v ---------i v i C L1M5_orf2#LIN 2762 GCACCTTTGTCAAAAATCAANTGNCCATATATGTGTGGGTCTATTTCTGG 2713 chr4ptel1M 939298 AC---CTAACCTGTTCCACTGATCAACTAGTCTACTTCTTAC 939336 --- vi i v i v - i C L1M5_orf2#LIN 2712 ACTCTCTATTCTGTTCCATTGATCTATTTGTCTA-TCCTTAC 2672 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 43.27 CpG sites = 98, Kimura (unadjusted) = 43.89 Transitions / transversions = 1.09 (98/90) Gap_init rate = 0.05 (30 / 609), avg. gap size = 1.70 (51 / 30) 510 29.92 0.00 0.00 chr4ptel1M 939415 939541 (60459) C MIR#SINE/MIR (15) 247 121 m_b188s601i6 7369 chr4ptel1M 939415 TTATGAGGCGCCCATTGTCTGCCAGGCCCTGTGCTTGGGCTTTTACAATT 939464 vii ii i i v v v vi vvi vv C MIR#SINE/MIR 247 TTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGCGCTTTACATGT 198 chr4ptel1M 939465 ATTAGCTCATCTGATACCTGTAACAACTCTGGGAGATAGGGGCTATTACT 939514 i i i v iiii i iv i vi i C MIR#SINE/MIR 197 ATTAACTCATTTAATCCTCACAACAACCCTATGAGGTAGGTACTATTATT 148 chr4ptel1M 939515 ACCTCCATTTTGTAACTGAGGAAACTG 939541 i i ii iv C MIR#SINE/MIR 147 ATCCCCATTTTACAGATGAGGAAACTG 121 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 39.99 CpG sites = 25, Kimura (unadjusted) = 39.99 Transitions / transversions = 1.92 (25/13) Gap_init rate = 0.00 (0 / 126), avg. gap size = 0.0 (0 / 0) 217 31.25 0.00 0.00 chr4ptel1M 939991 940054 (59946) C L2a_3end#LINE/L2 (2) 515 452 m_b188s601i7 7370 chr4ptel1M 939991 TCCCTTATTCTGCAGTCATTTGCTAAGGGCTAATTCTGTGCCAGGCACTG 940040 vi i vi ivi ii i v iv i v C L2a_3end#LINE 515 TCATTCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTG 466 chr4ptel1M 940041 TCCCAGCCCCTGGG 940054 i i v v C L2a_3end#LINE 465 TTCTAGGCGCTGGG 452 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 41.85 CpG sites = 12, Kimura (unadjusted) = 41.85 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0) 13 20.34 2.86 0.00 chr4ptel1M 942107 942141 (57859) (CCT)n#Simple_repeat 1 36 (0) m_b188s252i3 7371 chr4ptel1M 942107 CCTCCTCCTCCTCATCTTTCT-TTCCTTTTCCTCCT 942141 v i i -i ii (CCT)n#Simple 1 CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT 36 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 15 13.67 0.00 0.00 chr4ptel1M 943301 943324 (56676) (C)n#Simple_repeat 1 24 (0) m_b188s252i5 7372 chr4ptel1M 943301 CCCCGCCCCCTCCCCCCCCACCCC 943324 v i v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCC 24 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 16 27.25 0.00 4.69 chr4ptel1M 943297 943363 (56637) (CCCGC)n#Simple_repeat 1 64 (0) m_b188s252i4 7373 chr4ptel1M 943297 CCGGCCCCGCCCCCTCCCCCCCCACCCCGTGCATCCCTGGTCCCAGGCCC 943346 v vi v i iv vv -v - -v (CCCGC)n#Simp 1 CCCGCCCCGCCCCGCCCCGCCCCGCCCCGCCCCGCCC-CG-CCC-CGCCC 47 chr4ptel1M 943347 CCCCCCGCCGCGCCGCG 943363 v v v (CCCGC)n#Simp 48 CGCCCCGCCCCGCCCCG 64 Matrix = Unknown Transitions / transversions = 0.27 (3/11) Gap_init rate = 0.05 (3 / 66), avg. gap size = 1.00 (3 / 3) 254 23.28 4.05 1.32 chr4ptel1M 944717 944790 (55210) HSAT5v1#Satellite 5211 5286 (612) m_b188s502i0 7374 chr4ptel1M 944717 CGTGCAT-CAGTGTAAGCACACA-GTGTGTGCAAGTGTGCATGTGTGTGT 944764 - i iv iiii - i i iv i ii ? HSAT5v1#Satel 5211 CGTGCATGCAATGTGTGTGTGCACGCGCGTGCGCGCGTGTGTGTGTGTGN 5260 chr4ptel1M 944765 ACACATGTGTGCG-GTGTGGCTGTGCT 944790 i i - v - HSAT5v1#Satel 5261 ACGCGTGTGTGCGCGTGTGTCT-TGCT 5286 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 18.64 CpG sites = 14, Kimura (unadjusted) = 30.33 Transitions / transversions = 4.67 (14/3) Gap_init rate = 0.05 (4 / 73), avg. gap size = 1.00 (4 / 4) 248 24.37 5.88 3.45 chr4ptel1M 944811 944895 (55105) HSAT5v1#Satellite 5206 5292 (606) m_b188s502i1 7374 chr4ptel1M 944811 ACATGAGTG--TGCA---TGTGTGTACACAGGTGTGCGGTGTGGCTGTGC 944855 v -- --- i iv i -i i -- i HSAT5v1#Satel 5206 ACATGCGTGCATGCAATGTGTGTGTGCACGCGCGTGCG-CGCG--TGTGT 5252 chr4ptel1M 944856 ATGTGTGCACACACGAGTGTGCATGTGTGTAGCCCTTCTG 944895 i ? i ii v i i v v iii HSAT5v1#Satel 5253 GTGTGTGNACGCGTGTGTGCGCGTGTGTCTTGCTTCTCTG 5292 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 17.97 CpG sites = 15, Kimura (unadjusted) = 31.58 Transitions / transversions = 3.00 (15/5) Gap_init rate = 0.06 (5 / 84), avg. gap size = 1.60 (8 / 5) 1257 32.36 2.22 2.95 chr4ptel1M 945254 946380 (53620) L1M5_orf2#LINE/L1 2176 3294 (0) m_b188s551i5 7375 chr4ptel1M 945254 AGCAGGAGGGCAGGATACAAAATAAACCCACATAAGTCATCAGCATTCTT 945303 i ivv ? ii v ivi v i viv i ii L1M5_orf2#LIN 2176 AGCAAGGTCGCNGGATACAAGGTCAATATACAAAAATCAATTGTATTTCT 2225 chr4ptel1M 945304 ATATATCACTAACAAA--ATCCAACGGTCAGAGTTACAAAGAGAAATTCC 945351 ii vi -- ivi vii v i v ?-- i iv v L1M5_orf2#LIN 2226 ATATACTAGCAACAAACAATTGGAAAATGAAATTTN--AAAAACAATACC 2273 chr4ptel1M 945352 ATTTAAAGTAACTACTGACAGTATAAAATATTTAGGAATCTACCTGCCAA 945401 v i i vv vi v ii ? i vv i iv L1M5_orf2#LIN 2274 ATTTACAATAGCATCAAAAAACATNAAATACTTAGGAATAAATCTAACAA 2323 chr4ptel1M 945402 GGGAAAATCAGAAACTTTATGAGCAAAACTACAAAACACTTTCCACACAA 945451 ii? vivv ii v ? iivvv i viiv v v L1M5_orf2#LIN 2324 AANATGTGCAAGACCTNTACACTGAAAACTACAAAACATTGCTGAGAGAA 2373 chr4ptel1M 945452 ATTAAGTCTGATCTAACCAATTGGAAAAATATAATTAAATGCTCTTGGAT 945501 ivvv i vi v i i vi--- i v L1M5_orf2#LIN 2374 ATTAAAGAAGACCTAAATAAATGGAGAGATATACC---ATGTTCATGGAT 2420 chr4ptel1M 945502 TGGGCGAGCAAATATAATAAAGATGACAATACTGCCTAAACTAATCTATT 945551 iv viv vi ? v v v i i i v L1M5_orf2#LIN 2421 TGGAAGACTCAATATTGTNAAGATGTCAATTCTCCCCAAATTGATCTATA 2470 chr4ptel1M 945552 TGTTTAGCGCTATACCAATCAGACTCCTAAAAAACTTTTTTAATGATCTA 945601 vi i ii v v i v i iv iii ivv vv v L1M5_orf2#LIN 2471 GATTCAATGCAATCCCAATCAAAATCCCAGCAGGTTTTTTTGTAGAAATT 2520 chr4ptel1M 945602 GAAAAA-TAACAATGAAGTTCATATGGAAAAACAAAAGGTCAAGAATT-T 945649 v i- i ivv i i i vi i ii ? v-i L1M5_orf2#LIN 2521 GACAAGCTGATTCTAAAATTTATATGGAAATGCAAAGGACCNAGAATAGC 2570 chr4ptel1M 945650 CAAGGGAATTAATGAAAAAAAAAAATCAAATGCAGGTAGTCTACCTGTAC 945699 iiv iv- i i - - iv vi v vv vv L1M5_orf2#LIN 2571 CAAAACAATCT-TGAAAAAGAAGAA-CAAA-GTTGGAGGACTTACACTAC 2617 chr4ptel1M 945700 CAGATCT-AATATTATATTATAAAGTAGCGGTCACCAAAACCATTTGGTA 945748 ? ? - v i - ivi i v i i vi v L1M5_orf2#LIN 2618 CNGATNTCAAGACT-TATTATAAAGCTACAGTAATCAAGACAGTGTGGTA 2666 chr4ptel1M 945749 TTGGC-TAAGAAATAGACTAGTTGATCAATGGAATAGGTTAG---GTTCA 945794 - i - v i v i iv --- i L1M5_orf2#LIN 2667 TTGGCGTAAGGA-TAGACAAATAGATCAATGGAACAGAATAGAGAGTCCA 2715 chr4ptel1M 945795 AAGGACAAAACAGCCA-ATAACTTTAATAATCTAGTGTTTGACAAAC--- 945840 i ---- v v v - i vv v ii?v ?i ii v v--- L1M5_orf2#LIN 2716 GA----AATAGACCCACACATATATGGNCANTTGATTTTTGACAAAGGTG 2761 chr4ptel1M 945841 CCAAAGACCCCCAGTTT--TGGGGATAAGAATTCACTGTTTGACAAAAAT 945888 ? ----- i i-- - i vvv v ii viv L1M5_orf2#LIN 2762 CCAANG-----CAATTCAGTGGGGA-AAGGATAGTCTTTTCAACAAATGG 2805 chr4ptel1M 945889 TGCTGGGAAAATTGGAAATTAGTATGGCAGAAACTAGGCATTGACTCACA 945938 i v v ivi v i v iii?v i i vi L1M5_orf2#LIN 2806 TGCTGGAACAATTGGATATCCATATGGAAAAAAATGAANCTCGACCCCTA 2855 chr4ptel1M 945939 CTTAACACCATACACCAAGATAAGGTCAAAATATGGGGTTCAT-GATCTA 945987 i v v i v iv ? i ---- v - i L1M5_orf2#LIN 2856 CCTCACACCATACACAAAAATTAATTCNAGAT----GGATCATAGACCTA 2901 chr4ptel1M 945988 GGCATAAAGAATGAGATTATAAATAAATTGGAAGAG--CATAGGATAGTT 946035 iiii ii? i i i vvvvi i i-- v i - L1M5_orf2#LIN 2902 AATGTAAAAGNTAAAACTATAAAACTTCTAGAAGAAAACATAGGAGAAT- 2950 chr4ptel1M 946036 TACCTCTCAGACCTGTGGAAGAGG-AATGAATTTATAACCAA---AGAAG 946081 - i iivv - i?v - v v iv v i--- v i L1M5_orf2#LIN 2951 -ATCTTCGTGACCT-TGGGNTAGGCAAAGATTTCTTAAACAGGACACAAA 2998 chr4ptel1M 946082 AACTAGAGATCATTATTGATCATAAAATAGAAAAATTTGATTATATCAAA 946131 vi v?i i v vv v--- v v v i ?i L1M5_orf2#LIN 2999 AAGCACNAACCATAAAAGAA---AAAATTGATAAATTGGACTNCATCAAA 3045 chr4ptel1M 946132 TTGAAAAGTTTGTGTACAAGCAAAACTAATGCAGACAAGATTAGAAGGGA 946181 v v ii v iv ?vvv ivi vi ivi v i v i v L1M5_orf2#LIN 3046 ATTAAAAACTTCTGCTCNTCAAAAGACACCGTTAAGAAAATGAAAAGGCA 3095 chr4ptel1M 946182 AGCAATAAACTGGGAAAATATTTTTATAGTCAAAGGTTCTGATAAAGGCC 946231 v i i ? i v v ii i?vv vivv i v L1M5_orf2#LIN 3096 AGCCACAGANTGGGAGAAAATATTTGCAANACATATATCTGACAAAGGAC 3145 chr4ptel1M 946232 TCATTTCCAAAATATATAGAGAATTGACTCTAATTT-ATACGAAATCAAG 946280 i v i i i -v vi ? i- v? -- L1M5_orf2#LIN 3146 TCGTATCCAGAATATATAAAGAACT-CCTACAANTCAATAANAAA--AAG 3192 chr4ptel1M 946281 CCATTC--TCCAATTGATAAATGGTTAAAGGATTTGAATAGACAATTCTC 946328 v vv --i v? v vi i i i v v L1M5_orf2#LIN 3193 ACAAACAACCCAATANAAAAATGGGCAAAAGACTTGAACAGACACTTCAC 3242 chr4ptel1M 946329 AGATGAAGAAATTGAAATTATTTCTAGCCATATGAAAATATGCTCCAAAT 946378 i v v ?v viiivv iv i v v v? L1M5_orf2#LIN 3243 AAAAGAAGATATNCAAATGGCCAATAAGCACATGAAAAGATGCTCAACNT 3292 chr4ptel1M 946379 CA 946380 L1M5_orf2#LIN 3293 CA 3294 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 43.87 CpG sites = 181, Kimura (unadjusted) = 44.54 Transitions / transversions = 1.05 (181/173) Gap_init rate = 0.04 (48 / 1126), avg. gap size = 1.21 (58 / 48) 1076 32.38 3.20 4.21 chr4ptel1M 946234 946952 (53048) L1MA8_3end#LINE/L1 4 715 (323) m_b188s551i7 7375 chr4ptel1M 946234 ATTTCCAAAATATATAGAGAATTGACTCTAATTTA----TACGAAATCAA 946279 v ii i v vv - i i ----i v v L1MA8_3end#LI 4 ATATCCAAAATATATAAGGAACTCAAAC-AACTCAATAGCAAGAAAACAA 52 chr4ptel1M 946280 GCCATTCTCCAATTGATAAATGGTTAAAGGATTTGAATAGACAATTCTCA 946329 --- vvi i ? v vi ii v L1MA8_3end#LI 53 ---ATAACCCGATTNAAAAATGGGCAAAGGACCTGAATAGACATTTCTCA 99 chr4ptel1M 946330 GATGAAGAAATTGAAATTATTTCTAGCCATATGAAAATATGCTCCAAATC 946379 i v v vv viiivvi vi v v v L1MA8_3end#LI 100 AAAGAAGACATACAAATGGCCAACAGGTATATGAAAAAATGCTCAACATC 149 chr4ptel1M 946380 ATTATTAATCAGAGAAATGCAAAGT-AAGCAACTCTGAGATACCGCTACA 946428 i v v i v - i v vv i i iv L1MA8_3end#LI 150 ACTAATCATCAGGGAAATGCAAATTAAAACCACAATGAGATATCACCTCA 199 chr4ptel1M 946429 CACTTGTTGGACTGGCTAGAATGACAGG---GAAAGATAACGCGGAATAT 946475 i i v vv v v ii--- ---i i i L1MA8_3end#LI 200 CACCTGTTAGAATGGCTATTATCAAAAAGACGAAAGATAAC---AAGTGT 246 chr4ptel1M 946476 TGGAGGGGATGCGGGAAAACTGGGACACTGATACATTGTTGGTGGAATTG 946525 v i i ii vv i v vii i i v L1MA8_3end#LI 247 TGGCGAGGATGTGGAGAAAAGGGAACCCTTGCACACTGTTGGTGGGAATG 296 chr4ptel1M 946526 TGAATACCTCCAGCCATTCTGGAGAGCAATTTGGAACTATGCTCCAAAAG 946575 i vvv v v i i i v iv - v v i L1MA8_3end#LI 297 TAAATTAGTACAGCCATTATGGAAAACAGTATGGAGGT-TCCTCAAAAAA 345 chr4ptel1M 946576 TTATCAAACTGTGCATACCCTTTGATCCAGCAGTGCTACTACTGGGCTTA 946625 -- v ivivv v v i v i iv L1MA8_3end#LI 346 TTA--AAAATAGAACTACCATATGATCCAGCAATCCCACTACTGGGTATA 393 chr4ptel1M 946626 TA--CACCAGAGATATACTAAAGAAG--GGAAAGGGACCTGTATGTGCCA 946671 -- vvi i iv v v iv v -- i i iv i i i- v - L1MA8_3end#LI 394 TATCCAAAGGAAATGAAATCAGTATGTCGAAGAGATATCTGCAC-TCCC- 441 chr4ptel1M 946672 AAATGTTTGTGGCAGCTCTGTTTGTAGTGGACAGAAGCTGGAGACTGAGT 946721 -- ii v vi i iii i i v ii vv iv vivv L1MA8_3end#LI 442 --ATGTTCATTGCAGCATTATTCACAATAGCCAAGATATGGAATCAACCT 489 chr4ptel1M 946722 GGCTGCCCATCAGTTGGAGAATGGTTGGGTAAATTGTGATATATGAATGT 946771 iiv i iiv iv v iiiv v i iv iii L1MA8_3end#LI 490 AAGTGTCCATCAACGGATGAATGGATAAAGAAAATGTGGTATATATACAC 539 chr4ptel1M 946772 TATGGAATATTATTGTTCTGTAAGAAATGACCAGCAGGAGGAT------- 946814 v i vvv iv i ------ v -i ------- L1MA8_3end#LI 540 AATGGAATACTATTCAGCCTTAAAAA------AGAAGGA-AATCCTGTCA 582 chr4ptel1M 946815 TTCAGGAAGGCCTGGAGAGACTTACATGAACTGATGCTGAGTGAAATGAG 946864 iiv vii v vii i iv v vv v i i i L1MA8_3end#LI 583 TTTGCGACAACATGGATGAACCTGGAGGACATTATGTTAAGTGAAATAAG 632 chr4ptel1M 946865 -CAGAACCAGGAGATCATTATATACCTCAACAATGATAC-TGTATGAGGA 946912 - ivv i iiv --- v v - ii vvi - i ---- L1MA8_3end#LI 633 CCAGGCACAGAAAGAC---AAATACCGC-ATGATCTCACTTATATG---- 674 chr4ptel1M 946913 TGGAATCTGAAGGAAGTGGATTTCTTTGA--CAAAGAGAAGA 946952 - ii v vi v v -- i v L1MA8_3end#LI 675 TGGAATCT-AAAAAAGTCGAACTCATAGAAGCAGAGAGTAGA 715 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 42.67 CpG sites = 114, Kimura (unadjusted) = 43.18 Transitions / transversions = 1.05 (114/109) Gap_init rate = 0.05 (39 / 718), avg. gap size = 1.36 (53 / 39) 1559 31.43 0.94 0.94 chr4ptel1M 946234 946869 (53131) L1ME4c_3end#LINE/L1 4 639 (191) m_b188s551i6 7375 chr4ptel1M 946234 ATTTCCAAAATATATAGAGAATTGACTCTAATTTATACGAAATCAAGCCA 946283 v i?v ? i ii v i v v v vv? v v L1ME4c_3end#L 4 ATATCTNTANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAA 53 chr4ptel1M 946284 TTCTCCAATTGATAAATGGTTAAAGGATTTGAATAGACAATTCTCAGATG 946333 vv i v vi iv i v ? v L1ME4c_3end#L 54 GACCCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAG 103 chr4ptel1M 946334 AAGAAATTGAAATTATTTCTAGCCATATGAAAATATGCTCCAAATCATTA 946383 i vv ? vi vvvi iv i i v i v vv ii L1ME4c_3end#L 104 AGGAAATACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTA 153 chr4ptel1M 946384 TTAATCAGAGAAATGCAAAGTAA-GCAACTCTGAGATACCGCTACACACT 946432 v i v - vv ii vi i i L1ME4c_3end#L 154 GTAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCC 203 chr4ptel1M 946433 TGTTGGACTGGCTAGAATGACAGGGAAAGATAACGCGGAATATTGGAGGG 946482 i ii i i v i vvv iii vv ii vv ii v i L1ME4c_3end#L 204 TATTAAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGCTGGCGAG 253 chr4ptel1M 946483 GATGCGGGAAAACTGGGACACTGATACATTGTTGGTGGAATTGTGAATAC 946532 ? vi v ? v i v ? i vv L1ME4c_3end#L 254 GNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTG 303 chr4ptel1M 946533 CTCCAGCCATTCTGGAGAGCAATTTGGAACTATGCTCCAAAAGTTATCAA 946582 v v i v i i v v i ivi i ii v L1ME4c_3end#L 304 GTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAA 353 chr4ptel1M 946583 ACTGTGCATACCCTTTGATCCAGCAGTGCTACTACTGGGCTTATACACCA 946632 v v i i i v i v vv v iv i L1ME4c_3end#L 354 AATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTA 403 chr4ptel1M 946633 GAGATATACT---AAAGAAGGGAAAGGGACCTGTATGTGCCAAAATGTTT 946679 ii v v --- i i --- i ii v i i L1ME4c_3end#L 404 AGGAAATAATTCAAAAGAAGGAAAAAG---CTATATGCACGAAGATGTTC 450 chr4ptel1M 946680 GTGGCAGCTCTGTTTGTAGTGGACAGAAGCTGGAGACTGAGTGGCTGCCC 946729 i v vi i i i i vv i ii i vivv iiv i L1ME4c_3end#L 451 ATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCC 500 chr4ptel1M 946730 ATCAGTTGGAGAATGGTTGGGTAAATTGTGATATATGAATGTTATGGAAT 946779 v i v i ii i i i v? iviv L1ME4c_3end#L 501 AACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAAT 550 chr4ptel1M 946780 ATTATTGTTCTGTAAGAAATGACCAGCAGGAGGATTTCAGGAAG--GCCT 946827 vvvv ii v i iv vi v i i -- v v --i v L1ME4c_3end#L 551 ATTATGCAGCCATTAAAAATGATAATTATGAAGACT--ATGTAGCAACAT 598 chr4ptel1M 946828 GGAGAGACTTACATGAACTGATGCTGAGTGAAATGAGCAGAA 946869 - i iv vi vv i i i vi L1ME4c_3end#L 599 GGA-AAATGTTTATGATATAATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 41.17 CpG sites = 103, Kimura (unadjusted) = 42.28 Transitions / transversions = 1.08 (103/95) Gap_init rate = 0.01 (9 / 635), avg. gap size = 1.33 (12 / 9) 13 23.41 2.50 0.00 chr4ptel1M 947936 947975 (52025) (TCTT)n#Simple_repeat 1 41 (0) m_b188s252i6 7376 chr4ptel1M 947936 TCATTCATTTTTTCTTTCTTT-TTTTTTTGTTTTTGTTTTT 947975 v v i - i v i v i (TCTT)n#Simpl 1 TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT 41 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1) 17 14.91 2.70 0.00 chr4ptel1M 947939 947975 (52025) (TTCTTT)n#Simple_repeat 1 38 (0) m_b188s252i7 7376 chr4ptel1M 947939 TTCATTTTTTCTTTCTTTTT-TTTTTGTTTTTGTTTTT 947975 v i i - v v (TTCTTT)n#Sim 1 TTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTT 38 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 23 20.30 0.00 0.00 chr4ptel1M 947943 947987 (52013) (T)n#Simple_repeat 1 45 (0) m_b188s252i8 7376 chr4ptel1M 947943 TTTTTTCTTTCTTTTTTTTTTGTTTTTGTTTTTTAACTTTTTATT 947987 i i v v vvi v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 45 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 659 32.08 1.68 1.34 chr4ptel1M 948388 948684 (51316) C L1ME4c_3end#LINE/L1 (191) 639 342 m_b188s551i8 7377 chr4ptel1M 948388 TTCTGCTCATTTCACTTAGCATTAGTTCTTGTAAATCTCTCCAATCCT-C 948436 iv i -- v ii iv i i v vi - C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTA--TATCATAAACATTTTCCATGTTGC 592 chr4ptel1M 948437 TCTGTATTCATCCTGCTGGTCATTTCTTACAGAACAATAATATTCCATAA 948486 vii v v v iv vi i v ii vvvv vi C L1ME4c_3end#L 591 TACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCG 542 chr4ptel1M 948487 CATTCATATACCACAATTTACCCA-CCATTCTCCAACTGATGGGCAGCCA 948535 vi ?v i i ii - i v i v i vii C L1ME4c_3end#L 541 AGTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTA 492 chr4ptel1M 948536 CTCATTTTCCTGTTTCTAGCCACTACAAACAGGGCTGCCACAAACATTTT 948585 vvivv vi i v i i i i iv v ii i C L1ME4c_3end#L 491 GGTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTT 442 chr4ptel1M 948586 GGCCCATACAGGTCCTTTCCCTTTTTT---AGTATCTCCTTGGGGTATAA 948632 v iv i -- i i i --- v i i i v v C L1ME4c_3end#L 441 CGTGCATATAG--CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAAT 394 chr4ptel1M 948633 GCCCAGTAGTAGCACTGCTGGGTCAAAGGAGATGTACAGTTTGATAACTT 948682 v v i v i i iv v v v ii i C L1ME4c_3end#L 393 TCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTC 344 chr4ptel1M 948683 TT 948684 C L1ME4c_3end#L 343 TT 342 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 42.53 CpG sites = 52, Kimura (unadjusted) = 43.14 Transitions / transversions = 1.24 (52/42) Gap_init rate = 0.02 (7 / 296), avg. gap size = 1.29 (9 / 7) 267 34.58 7.92 2.88 chr4ptel1M 948472 948736 (51264) C L1MA10_3end#LINE/L1 (528) 553 276 m_b188s551i9 7377 chr4ptel1M 948472 AATAATATTCCATAACATTCATATACCACAATTTACCCA-CCATTCTCCA 948520 vii vi v viii - vi v C L1MA10_3end#L 553 AATAATATTCCATTGTATGTATATACCACATTTTCTTTATCCATTCATCC 504 chr4ptel1M 948521 ACTGATGGGCAGCCA-CTCATTTTCCTGTTTCTAGCCACTACAAACAGGG 948569 iii i vii -v ii i v i i - i i i iii i iv C L1MA10_3end#L 503 GTCGATGGACATTTAGGTTGTTTCCATATCT-TGGCTATTGTGAATAATG 455 chr4ptel1M 948570 CTGCCACAAACATTTTGGCCCATACAGGTCCTT----TCCCTTTTTTAGT 948615 v ii vvvi iv v i vv i i---- ivv i i C L1MA10_3end#L 454 CTGCAATGAACATGGGAGTGCAGATATCTCTTCGAGATCCTGATTTCAAT 405 chr4ptel1M 948616 ATCTCCTTGGGGTATAAGCCCAGTAGTAGCACTGCTGGGTCAAAGGAGAT 948665 --- i v i vi v i v i i v v iv v C L1MA10_3end#L 404 ---TCTTTTGGATATATACCCAGAAGTGGGATTGCTGGATCATATGGTAG 358 chr4ptel1M 948666 GTACAGTTTGATAACTTTTTGCAG---CTC---ATTATTTCTTAC----G 948705 v vi v -- i vi --- --- i i iii i---- C L1MA10_3end#L 357 TTCTATTTT--TAATTTTTTGAGGAACCTCCATACTGTTTTCCATAGTGG 310 chr4ptel1M 948706 CTGCAGCAGT-----CTTCCATCATGACTGTGTACA 948736 v ? -----i i i -- v C L1MA10_3end#L 309 CTGCACCANTTTACATTCCCACCA--ACAGTGTACA 276 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 46.70 CpG sites = 55, Kimura (unadjusted) = 49.05 Transitions / transversions = 1.62 (55/34) Gap_init rate = 0.06 (15 / 264), avg. gap size = 1.93 (29 / 15) 18 10.92 7.55 3.64 chr4ptel1M 949169 949221 (50779) (ATATATT)n#Simple_repeat 1 55 (0) m_b188s252i9 7378 chr4ptel1M 949169 ATATATT-TA-ATAATATATTA-ATATTAGCATGCTAATATATTATA-AT 949214 - - v - -i -v v - (ATATATT)n#Si 1 ATATATTATATATTATATATTATATATTA-TAT-ATTATATATTATATAT 48 chr4ptel1M 949215 TAGATAT 949221 v (ATATATT)n#Si 49 TATATAT 55 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.12 (6 / 52), avg. gap size = 1.00 (6 / 6) 14 12.33 2.56 5.26 chr4ptel1M 949483 949521 (50479) (GGAGGGA)n#Simple_repeat 1 38 (0) m_b188s252i10 7379 chr4ptel1M 949483 GGAGGGCGGAGGCA-GCGGGAGGCGGCGGAGGAGGGAGGA 949521 v v - v -i - (GGAGGGA)n#Si 1 GGAGGGAGGAGGGAGGAGGGAGG-AG-GGAGGAGGGAGGA 38 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.08 (3 / 38), avg. gap size = 1.00 (3 / 3) 310 36.02 1.86 0.00 chr4ptel1M 949555 949715 (50285) C Charlie7#DNA/hAT-Charlie (427) 2188 2025 m_b188s502i2 7380 chr4ptel1M 949555 AGACCCAG-CGGAAGGAGGCCAGGGACGGCGGCGCGTACCCCCTCCCGCT 949603 i i-i i vv vv vi v v ivvv vi v C Charlie7#DNA/ 2188 AGATCCAAATGGAAGAAGTGCATCGTTGGCTGCGCTTACTAAATCATGAT 2139 chr4ptel1M 949604 CCTTATTTC-CGCTCCCTTCCGTCGGTTCCGGAAAGACCGTTGTTAGAAT 949652 v i i- iv v ii ii vi v iiiv ii C Charlie7#DNA/ 2138 ACTCATTTTTCAATCCCATCCACCAATTATGCAAAGGTTTTTGTTGAAAT 2089 chr4ptel1M 949653 TCGGCCAATACATTTCCATCTTCCCGGGCGTTTGT-GGTCGCGCTCACAG 949701 i i v v ii ivi -i i iv ii i C Charlie7#DNA/ 2088 TCGGCTAGTAAATTTCCATCTTCCCTGATGTCAATCAGTTGTTCTTGCAA 2039 chr4ptel1M 949702 ACTGCTGGGAAGAT 949715 iv v i C Charlie7#DNA/ 2038 ACTAATCGGAAGGT 2025 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 51.22 CpG sites = 34, Kimura (unadjusted) = 51.22 Transitions / transversions = 1.42 (34/24) Gap_init rate = 0.02 (3 / 160), avg. gap size = 1.00 (3 / 3) 14 8.51 0.00 3.85 chr4ptel1M 952632 952658 (47342) (AGTC)n#Simple_repeat 1 26 (0) m_b188s252i11 7381 chr4ptel1M 952632 AGTCAGTCATTCAGTGAGTCAGTTCAG 952658 v v - (AGTC)n#Simpl 1 AGTCAGTCAGTCAGTCAGTCAG-TCAG 26 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.04 (1 / 26), avg. gap size = 1.00 (1 / 1) 253 30.11 3.23 0.00 chr4ptel1M 953944 954036 (45964) X11_DNA#DNA/TcMar-Tigger 143 238 (249) m_b188s502i3 7382 chr4ptel1M 953944 AGTCCAGGCTCAGTTTGGCGACTTTTTCAAATCACCGGTTCAGGAAATGA 953993 i v v iv ii iii i vv i i v X11_DNA#DNA/T 143 AATCCAGTCTAAAATCAGTAGCTTTTTCAAACCAAGGGCTCAAGAAATTA 192 chr4ptel1M 953994 AGTGTTCCT--AGGAAGGTTTCAAATTCTGGGGCTAG-AATTATTT 954036 vi -- iviv vi v v i - v X11_DNA#DNA/T 193 AGGATTCCTTCAACGTGCCTTCAACTTCTGGGTCCAGCAATTAATT 238 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 37.46 CpG sites = 15, Kimura (unadjusted) = 39.23 Transitions / transversions = 1.15 (15/13) Gap_init rate = 0.02 (2 / 92), avg. gap size = 1.50 (3 / 2) 12 24.01 0.00 2.50 chr4ptel1M 955415 955455 (44545) (TCTGGC)n#Simple_repeat 1 40 (0) m_b188s252i12 7383 chr4ptel1M 955415 TCTGCCTCTGTTTCAGACCCTGGCTTTTGCTCCTGGCTCTG 955455 v vi v i i i v - (TCTGGC)n#Sim 1 TCTGGCTCTGGCTCTGGCTCTGGCTCTGGCT-CTGGCTCTG 40 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 13 29.14 0.00 4.92 chr4ptel1M 957501 957564 (42436) (AGGGGGC)n#Simple_repeat 1 61 (0) m_b188s252i13 7384 chr4ptel1M 957501 AGGGAGCATGGGGCAGAGGTTCTTAGGGGGCAGGGGGCTTGCCCCAGGTT 957550 i v - vv -- vv vvv vv (AGGGGGC)n#Si 1 AGGGGGCAGGGGGCAG-GGGGC--AGGGGGCAGGGGGCAGGGGGCAGGGG 47 chr4ptel1M 957551 ACAGGGTGAAGGGG 957564 i v v (AGGGGGC)n#Si 48 GCAGGGGGCAGGGG 61 Matrix = Unknown Transitions / transversions = 0.17 (2/12) Gap_init rate = 0.05 (3 / 63), avg. gap size = 1.00 (3 / 3) 213 28.08 3.30 2.17 chr4ptel1M 963283 963373 (36627) L2b_3end#LINE/L2 355 446 (20) m_b189s601i0 7385 chr4ptel1M 963283 GCTTCCTGGGGAGCACGGGCTGC--CTGCCTTCCTC-CTGCTTGTATTCC 963329 i v i - v i i ?-- i vi - i - i L2b_3end#LINE 355 GCTCCGTGAGG-GCAGGGACCGNGTCTGTCTTGTTCACCGCT-GTATCCC 402 chr4ptel1M 963330 CAGCACTCATCAAGGCTGGGGGCACACACTAGGCGCATAGTTAA 963373 i ii v vi ?vvvv v vi v L2b_3end#LINE 403 CAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAA 446 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.55 CpG sites = 13, Kimura (unadjusted) = 36.77 Transitions / transversions = 1.08 (13/12) Gap_init rate = 0.04 (4 / 90), avg. gap size = 1.25 (5 / 4) 16 0.00 0.00 0.00 chr4ptel1M 966381 966397 (33603) (C)n#Simple_repeat 1 17 (0) m_b189s252i0 7386 chr4ptel1M 966381 CCCCCCCCCCCCCCCCC 966397 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCC 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 18 8.72 0.00 0.00 chr4ptel1M 973819 973843 (26157) (T)n#Simple_repeat 1 25 (0) m_b189s252i1 7387 chr4ptel1M 973819 TTTTTCTTTCTTTTTTTTTTTTTTT 973843 i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 22 15.09 4.55 4.55 chr4ptel1M 975126 975191 (24809) (TTTTC)n#Simple_repeat 1 66 (0) m_b189s252i2 7388 chr4ptel1M 975126 TTTTCTTTTC--TCCATTTCTTTTCTTTCCTCTTCTCTTTC-TTTCTTCC 975172 -- i v i i - - ii (TTTTC)n#Simp 1 TTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCT-TTTCTTTTCTTTT 49 chr4ptel1M 975173 CTCTTTCTTCTTCCCTTCT 975191 - - ii (TTTTC)n#Simp 50 CT-TTTCTT-TTCTTTTCT 66 Matrix = Unknown Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.08 (5 / 65), avg. gap size = 1.20 (6 / 5) 14 24.76 4.69 3.08 chr4ptel1M 975133 975196 (24804) (TTCTCCC)n#Simple_repeat 1 65 (0) m_b189s252i3 7388 chr4ptel1M 975133 TTCTCCATT-TCTTTTCTTTCCTCTTCTCTT-T-CTTTCTTCCCTCTTTC 975179 v - ii - i ii i - - i i i ii (TTCTCCC)n#Si 1 TTCTCCCTTCTCCCTTC-TCCCTTCTCCCTTCTCCCTTCTCCCTTCTCCC 49 chr4ptel1M 975180 TTCTTCCCTTCTCCCTT 975196 - (TTCTCCC)n#Si 50 TTC-TCCCTTCTCCCTT 65 Matrix = Unknown Transitions / transversions = 11.00 (11/1) Gap_init rate = 0.08 (5 / 63), avg. gap size = 1.00 (5 / 5) 217 29.41 1.47 0.00 chr4ptel1M 975952 976019 (23981) C L2b_3end#LINE/L2 (15) 451 383 m_b189s601i1 7389 chr4ptel1M 975952 AAGCGTTTACGATGTGCTTCCTGCATCCCGGGCTCTGTGCTTGGCCTTGG 976001 iii viv i i v ii v i ? v vi C L2b_3end#LINE 451 AAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGG 402 chr4ptel1M 976002 GGTGACA-CGGGTAACAAG 976019 vv - vv C L2b_3end#LINE 401 GGATACAGCGGTGAACAAG 383 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.18 CpG sites = 10, Kimura (unadjusted) = 38.55 Transitions / transversions = 1.00 (10/10) Gap_init rate = 0.01 (1 / 67), avg. gap size = 1.00 (1 / 1) 13 15.53 0.00 3.33 chr4ptel1M 976318 976348 (23652) (GGGGA)n#Simple_repeat 1 30 (0) m_b189s252i4 7390 chr4ptel1M 976318 GGGGAGAGGAGAGATGGGGAGGGGGAGGGGA 976348 i i iv - (GGGGA)n#Simp 1 GGGGAGGGGAGGGGAGGGGA-GGGGAGGGGA 30 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.03 (1 / 30), avg. gap size = 1.00 (1 / 1) 336 28.21 6.84 0.00 chr4ptel1M 977457 977573 (22427) MIRc#SINE/MIR 24 148 (120) m_b189s601i2 7391 chr4ptel1M 977457 AGAGTGTCGGGCCTGGAGCCGGGGAGCGTCGTGTTCTGCTGCGCCCTCAG 977506 iiii i i i i i vvii v viv v vvv v MIRc#SINE/MIR 24 AGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTG 73 chr4ptel1M 977507 ACACTGACTGGCCCTCTGACCCTGGGCCAGTCGCTG------TCTG--CC 977548 v v i iv v i v i v------ -- MIRc#SINE/MIR 74 CCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCC 123 chr4ptel1M 977549 TCAGTTTCCTCATCTGTGAAATGGG 977573 i MIRc#SINE/MIR 124 TCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.86 CpG sites = 17, Kimura (unadjusted) = 35.86 Transitions / transversions = 1.06 (17/16) Gap_init rate = 0.02 (2 / 116), avg. gap size = 4.00 (8 / 2) 18 4.77 0.00 0.00 chr4ptel1M 979733 979754 (20246) (T)n#Simple_repeat 1 22 (0) m_b189s252i5 7392 chr4ptel1M 979733 TTTTTTTTTTCTTTTTTTTTTT 979754 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTT 22 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 261 32.83 3.31 6.84 chr4ptel1M 980112 980232 (19768) C L2c_3end#LINE/L2 (18) 460 344 m_b189s601i3 7393 chr4ptel1M 980112 CATTTATTAAGCACTTACTGTATGCTTTGGCATC----ATGCTAAGTGCG 980157 i i i i i -iv iii---- i v -ii C L2c_3end#LINE 460 CATTTATTGAGCGCCTACTATGTGC-CAGGCGCTGGGGATACAAAG-ATG 413 chr4ptel1M 980158 GAGATGGCAAAGTCTCCGCTCTCCAGGGGCTCCCAGTGGAGTGGGGCGGG 980207 i v v i vi i i i v i v vv i - i C L2c_3end#LINE 412 AATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAGTGGAG-GAG 364 chr4ptel1M 980208 GCAAGAAGCATGTGTGGACAGGCAA 980232 i i----- ii? ii i C L2c_3end#LINE 363 ACAG-----ACANGTAAACAGACAA 344 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.36 CpG sites = 28, Kimura (unadjusted) = 47.80 Transitions / transversions = 3.11 (28/9) Gap_init rate = 0.07 (9 / 120), avg. gap size = 1.33 (12 / 9) 272 27.78 4.17 0.00 chr4ptel1M 980627 980698 (19302) C MIRb#SINE/MIR (3) 265 191 m_b189s601i4 7394 chr4ptel1M 980627 AAGAGAACAAGTGTTTATTAAGCACCTAGTGTGTGCCAGACTCTGCGCCC 980676 v i v vii i i i v i i v i iv C MIRb#SINE/MIR 265 AATAGAGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTA 216 chr4ptel1M 980677 AGAGCCATACA---GTTATCTCATT 980698 v iv ---i C MIRb#SINE/MIR 215 AGCGCTTTACATGCATTATCTCATT 191 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.47 CpG sites = 12, Kimura (unadjusted) = 35.67 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.01 (1 / 71), avg. gap size = 3.00 (3 / 1) 394 26.97 7.75 3.38 chr4ptel1M 984602 984743 (15257) C MIRb#SINE/MIR (117) 151 4 m_b189s601i5 7394 chr4ptel1M 984602 CTCATTTTACAGATGAGGAAATTGAGGCAAACGGGGGT---GT---TTGC 984645 i i vv vi i --- --- C MIRb#SINE/MIR 151 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGC 102 chr4ptel1M 984646 CCAGGCTCACATGTTTAG--AGTGGATCTGGGGCTGGATTTAAACTTGGG 984693 i v iivi -- -- v i v v ii iii C MIRb#SINE/MIR 101 CCAAGGTCACACAGCTAGTAAGTGG--CAGAGCCGGGATTCGAACCCAGG 54 chr4ptel1M 984694 TC---CTGACTTTGGGACCAGCGCTCCGTCCACCACTCCTCCATGGTACC 984740 --- iiiiii v i iv --- v v i v i C MIRb#SINE/MIR 53 TCTGTCTGACTCCAAAGCCCGTGCTCTTT---CCACTGCACCACGCTGCC 7 chr4ptel1M 984741 CCT 984743 C MIRb#SINE/MIR 6 CCT 4 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.28 CpG sites = 24, Kimura (unadjusted) = 34.72 Transitions / transversions = 1.85 (24/13) Gap_init rate = 0.06 (9 / 141), avg. gap size = 1.78 (16 / 9) 14 13.62 0.00 11.11 chr4ptel1M 985155 985204 (14796) (CCCCCGG)n#Simple_repeat 1 45 (0) m_b189s252i6 7395 chr4ptel1M 985155 CCCCTGGCCCTCGGCCTCCCCCTCCCCCGGCCCTCGGCCTTCCCCGGCCC 985204 i i - - vv i - -- (CCCCCGG)n#Si 1 CCCCCGGCCCCCGG-C-CCCCGGCCCCCGGCCCCCGG-C--CCCCGGCCC 45 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.10 (5 / 49), avg. gap size = 1.00 (5 / 5) 200 31.82 0.00 0.00 chr4ptel1M 985442 985507 (14493) C MIR1_Amn#SINE/MIR (56) 174 109 m_b189s601i6 7396 chr4ptel1M 985442 ACAAGAGAGGTTTGCCTTCTTCAGCTCCTTTTGTAGATGGGGAAACTGAG 985491 ii iv iv iv vvv i v ii i C MIR1_Amn#SINE 174 ACAAAGGAGGTCAGTATCATTATCCCCATTTTACAGATGAGGAAACTGAG 125 chr4ptel1M 985492 GCAAACAGTGTTTGAG 985507 ?v v v v ?i C MIR1_Amn#SINE 124 GCNCAGAGAGGTNAAG 109 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.65 CpG sites = 10, Kimura (unadjusted) = 43.65 Transitions / transversions = 0.91 (10/11) Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0) 191 23.81 0.00 0.00 chr4ptel1M 985498 985539 (14461) C MIRc#SINE/MIR (190) 78 37 m_b189s601i7 7397 chr4ptel1M 985498 AGTGTTTGAGGCCAGATTAGCACTCAGGTCTTCCTGACTCCA 985539 viv v vi i v v i C MIRc#SINE/MIR 78 AGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCA 37 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.69 CpG sites = 4, Kimura (unadjusted) = 28.69 Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 227 31.40 10.47 0.00 chr4ptel1M 985669 985754 (14246) MIRc#SINE/MIR 35 129 (139) m_b189s601i8 7398 chr4ptel1M 985669 CTTGGAGTCCAGAACGTCAGGACTTGATTCTCGTTACT----CTTAATAG 985714 vi vii v ii i v i viv ---- v MIRc#SINE/MIR 35 CTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAG 84 chr4ptel1M 985715 TGGTATGACTCTGGATAAATCACT-----TCTCTGAATCGCATTT 985754 iv i ii ii i ----- ii v v MIRc#SINE/MIR 85 CTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTT 129 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.35 CpG sites = 17, Kimura (unadjusted) = 42.45 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.02 (2 / 85), avg. gap size = 4.50 (9 / 2) 282 28.88 3.26 2.15 chr4ptel1M 985885 985976 (14024) C L2c_3end#LINE/L2 (9) 469 377 m_b189s601i9 7399 chr4ptel1M 985885 TTAAATAAACAGTGAGGGAATACTTATT--GTTCTGGGTGCTGGGGCCGC 985932 v i v v vv iii i i -- v ii i vii C L2c_3end#LINE 469 TTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGATAC 420 chr4ptel1M 985933 AAGGAAGAA-AAGCCCTGCGGTCCCTGCCCTCCAGGAGCGTGCAG 985976 i v - v --i v vii C L2c_3end#LINE 419 AAAGATGAATAAGAC--ACGGTCCCTGCCCTCAAGGAGCTCACAG 377 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.67 CpG sites = 15, Kimura (unadjusted) = 37.41 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.04 (4 / 91), avg. gap size = 1.25 (5 / 4) 191 35.92 1.71 7.21 chr4ptel1M 986886 987002 (12998) C L2c_3end#LINE/L2 (5) 473 363 m_b189s601i10 7400 chr4ptel1M 986886 TTCAGTTCAAGAACCCTTTAGTAGCCATTTTGTTGAACCCTGGCTTAGCC 986935 - v v v v iiv iii ------ iv vvii v C L2c_3end#LINE 473 TTCA-TTCAACAAACATTTATTGAGCGCCT------ACTATGTGCCAGGC 431 chr4ptel1M 986936 CCTGGTGGGTGCAAAGACAAAACCGCAACCGTTCCTGCCTATGAGGAGCT 986985 v - i i ii vvv vv v i ivii C L2c_3end#LINE 430 GCTGG-GGATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCT 382 chr4ptel1M 986986 --CAGTCTGCCGAGGGGGA 987002 -- ivi ii i C L2c_3end#LINE 381 CACAGTCTAGTGGAGGAGA 363 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 48.19 CpG sites = 21, Kimura (unadjusted) = 50.00 Transitions / transversions = 1.17 (21/18) Gap_init rate = 0.08 (9 / 116), avg. gap size = 1.11 (10 / 9) 216 34.32 3.65 2.16 chr4ptel1M 987103 987239 (12761) L2d_3end#LINE/L2 378 516 (0) m_b189s601i11 7401 chr4ptel1M 987103 TCTCGTCTTCCCCAGGGAGAGGGTGAGCTCCCTGAG--CTG---TCTTGT 987147 i - ivv vv i i -- v ---i v L2d_3end#LINE 378 TCTTGTCT-CCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGT 426 chr4ptel1M 987148 CTTTTTGCTTCTATTTACATTTCCAGGACTTCTCTCACCCTACCTGGTAC 987197 v -i ?i v ? vvv ii vii vi vv vv i ivi i L2d_3end#LINE 427 CTTAT-ACTNTTTTNTCGTTCCCCACAGCGCCTAGCACAGTGCTGAGCAC 475 chr4ptel1M 987198 ATAGTAGACACGCAATAAAGGATCTGTTTATCTATGCACTGA 987239 i i v -v ii v iv vv i L2d_3end#LINE 476 ATAGTAGGCGCTCAATAAA-TACTTGTTGATTGATTGATTGA 516 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.11 CpG sites = 22, Kimura (unadjusted) = 47.50 Transitions / transversions = 0.92 (22/24) Gap_init rate = 0.04 (5 / 136), avg. gap size = 1.60 (8 / 5) 262 31.01 5.88 2.44 chr4ptel1M 987107 987225 (12775) L2a_3end#LINE/L2 383 505 (12) m_b189s601i12 7401 chr4ptel1M 987107 GTCTTCCCCAGGGAGAGGGTGAGCTCCCTGAG--CTG----TCTTGTCT- 987149 i vivv iv i v -- v ---- i - L2a_3end#LINE 383 GTCTCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTCTG 432 chr4ptel1M 987150 TTTTGCTTCTATTTACATTTCCAGGACTTCTCTCACCCTACCTGGTACAT 987199 i ivivvi ii ii vi -- vvv vv i i L2a_3end#LINE 433 TTTTGTTCACTGCTGTATCCCCAGCGC--CTAGAACAGTGCCTGGCACAT 480 chr4ptel1M 987200 AGTAGACACGCAATAAAGGATCTGTT 987225 i i v -v i L2a_3end#LINE 481 AGTAGGCGCTCAATAAA-TATTTGTT 505 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.94 CpG sites = 19, Kimura (unadjusted) = 40.81 Transitions / transversions = 1.12 (19/17) Gap_init rate = 0.05 (6 / 118), avg. gap size = 1.67 (10 / 6) 145 30.07 3.00 2.83 chr4ptel1M 987251 987884 (12116) (ATCT)n#Simple_repeat 1 635 (0) m_b189s252i8 7402 chr4ptel1M 987251 ATCTATC-ACCATATCTGTGCCCATC-ACCCATCTATGTCATCCATCCAC 987298 - i - i -- i - i i v - i i i (ATCT)n#Simpl 1 ATCTATCTATC-TATCTAT--CTATCTATCTATCTATCT-ATCTATCTAT 46 chr4ptel1M 987299 TTGTCCATCCATC-ATGTACTTCCCTAGTCTCTATTTCTGTCTCCATTTC 987347 i i i i - v ii vi - v v v i viv v (ATCT)n#Simpl 47 CTATCTATCTATCTATCTATCTATCTA-TCTATCTATCTATCTATCTATC 95 chr4ptel1M 987348 TAT-AATCT-T-TAT-TATCCATTTATC-ATCATCTCTATCCAGCTCCCT 987392 -v - - - i i - - v i v vi (ATCT)n#Simpl 96 TATCTATCTATCTATCTATCTATCTATCTATC-TATCTATCTATCTATCT 144 chr4ptel1M 987393 GACCGA-CTATGTATCTATGTATCTGTCTGTCTGTCTGTCCGTCCATCTG 987441 - i v - v v i i i i ii i i (ATCT)n#Simpl 145 -ATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTA 193 chr4ptel1M 987442 TCCATCCATCTATCTATCTATCTGTTTTTGTTTACTTATTTATCTAGCCA 987491 i i i i v v v - - i v i (ATCT)n#Simpl 194 TCTATCTATCTATCTATCTATCTATCTATCTAT-C-TATCTATCTATCTA 241 chr4ptel1M 987492 TCTCTCTATCTGCTTTTCTGTCTGCCTGTCCTTCCATCCATCCATCCACC 987541 v iii v i ii i iv i i i i i (ATCT)n#Simpl 242 TCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATC 291 chr4ptel1M 987542 CACCTATCTATGTCTGTTTTTCTGTCTATCTATCTA-CTATCCATC-ATC 987589 i i -- i i v i - i - (ATCT)n#Simpl 292 TATCTATCTA--TCTATCTATCTATCTATCTATCTATCTATCTATCTATC 339 chr4ptel1M 987590 CATTTATTCATCTATATATTGATCTATCTAGTCTGTTTTTCTGTCTGCTT 987639 i i ii v iv - i i v i iii (ATCT)n#Simpl 340 TATCTATCTATCTATCTATCTATCTATCTA-TCTATCTATCTATCTATCT 388 chr4ptel1M 987640 ATCTAT-TATCCATCTATCTATATATCTGTATCTGT-TTTGTCT-GCT-T 987685 - i v i v v v - i i -v - (ATCT)n#Simpl 389 ATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTAT 438 chr4ptel1M 987686 ATCTCTATCTATCTACCTACCTATCTTATCTATCTAGCCTGTTTTCCTGT 987735 v v i i - -i i i vi i (ATCT)n#Simpl 439 CTATCTATCTATCTATCTATCTATC-TATCTATCTA-TCTATCTATCTAT 486 chr4ptel1M 987736 CTGCTTATCTAT-TATCTATCTATCCATCTATCTTTCTGTCTGTTTTTCT 987784 iii - i v i i i v (ATCT)n#Simpl 487 CTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCT 536 chr4ptel1M 987785 ATCTGCTTATCTATCT-CCTCTCTCTCTTTCTCTCAGTCTGTTTTTGTCT 987833 iii -i v v v v vi i i v v v (ATCT)n#Simpl 537 ATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTAT 586 chr4ptel1M 987834 CCTTATCTATCT-CCTGTCTATCTCTGCTTTTCTGCCTGCTTATCTAT-T 987881 - - -i i v - - v ii iii - (ATCT)n#Simpl 587 -C-TATCTATCTATCTATCTATCTAT-C-TATCTATCTATCTATCTATCT 632 chr4ptel1M 987882 ATC 987884 (ATCT)n#Simpl 633 ATC 635 Matrix = Unknown Transitions / transversions = 2.09 (98/47) Gap_init rate = 0.06 (37 / 633), avg. gap size = 1.00 (37 / 37) 233 34.84 6.02 0.71 chr4ptel1M 988154 988286 (11714) C L2#LINE/L2 (212) 2870 2731 m_b189s601i13 7400 chr4ptel1M 988154 GAGTCA-ACAGGAAGCCGCCGAAG--TCCTAAGACTGGGTGCTGCCCTGG 988200 v - ii iii i -- ii i - v i viv v v i C L2#LINE/L2 2870 GAGTGAGATGGGAAGCCATTGGAGGGTTTTGAG-CAGAGGAGTGACATGA 2822 chr4ptel1M 988201 TCCGAACTGCATTTCAGAGTG-TCACCATGGCAGCTGTGGTGG--ATGAT 988247 i vi i i i i iv - iv v v i-- iiv C L2#LINE/L2 2821 TCTGACTTACGTTTTAAAAGGATCACTCTGGCTGCTGTGTTGAGAATAGA 2772 chr4ptel1M 988248 TCGGAGAGTAG--AGACTGGAGTCAGGAAGACCAGTGAGGA 988286 ii ? i vi -- iv iv i v C L2#LINE/L2 2771 CTGNAGGGGGGCAAGGGTGGAAGCAGGGAGACCAGTTAGGA 2731 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 48.78 CpG sites = 30, Kimura (unadjusted) = 50.40 Transitions / transversions = 1.88 (30/16) Gap_init rate = 0.05 (6 / 132), avg. gap size = 1.50 (9 / 6) 225 28.05 13.91 0.77 chr4ptel1M 988451 988565 (11435) L3#LINE/CR1 3967 4096 (3) m_b189s601i14 7403 chr4ptel1M 988451 ACAGGAGAGTGTTGGGGAAGGGAGGGGCTGACTGCTTGCAAGGGCTGCTG 988500 v - vii v i ivv v ii iv v i L3#LINE/CR1 3967 ACTGGAG-GTGTTCAAGCAGAGGCTGGATGACCACTTGTCAGGGATGTTG 4015 chr4ptel1M 988501 GGGGCAGG-TCCCTG--TTGG---------TGG----GACGGCCTCTGTA 988534 vi ivi - i -- --------- ---- i i ivi L3#LINE/CR1 4016 TAGAAGGGATTCCTGCATTGGATGGGAGGTTGGACTAGATGACCTCTAAG 4065 chr4ptel1M 988535 GTCCCTTTCAGCGCTGAGATTCTGTCACTCT 988565 i i v v i L3#LINE/CR1 4066 GTCCCTTCCAACTCTGAGATTCTGTGATTCT 4096 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.12 CpG sites = 19, Kimura (unadjusted) = 36.12 Transitions / transversions = 1.46 (19/13) Gap_init rate = 0.04 (5 / 114), avg. gap size = 3.40 (17 / 5) 191 17.39 4.35 0.00 chr4ptel1M 989383 989428 (10572) MIR3#SINE/MIR 98 145 (63) m_b189s601i15 7404 chr4ptel1M 989383 AAGTCACTT-ACATCATTTG-CCTCAGTCTCCACATTTGCAAAATGAG 989428 - v vi v - i v i i MIR3#SINE/MIR 98 AAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAG 145 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 19.89 CpG sites = 4, Kimura (unadjusted) = 19.89 Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.04 (2 / 45), avg. gap size = 1.00 (2 / 2) 728 24.92 4.33 9.96 chr4ptel1M 989513 989766 (10234) C MIRb#SINE/MIR (0) 268 28 m_b189s601i16 7405 chr4ptel1M 989513 AATGACTGAACAACAACACACTAAGT-CCTACTACGTGCCCAACACTGCG 989561 i iv i v v ivi i i i- i i vii i C MIRb#SINE/MIR 268 AATAATAGAGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTG 219 chr4ptel1M 989562 CTGAGGACTTT-------TTAA-TCATTTAATCTTCACAACCATCCTATG 989603 i vi ------- v- i v i ii C MIRb#SINE/MIR 218 CTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCG 169 chr4ptel1M 989604 AGGTGCAGGTACTTTTAATCCCCATTTTACGGTTGAGGAAACTGA-ATTA 989652 -- i v - i v -ii v C MIRb#SINE/MIR 168 AGGT--AGGTATTATTA-TCCCCATTTTACAGATGAGGAAACTGAGGCTC 122 chr4ptel1M 989653 ACAGGAGTTAACAACAATGTAATTCACCTCAAGTGACTTGCTCAGAGTCA 989702 v ii --------------------- i i ii C MIRb#SINE/MIR 121 AGAGAGGTT---------------------AAGTAACTTGCCCAAGGTCA 93 chr4ptel1M 989703 CACAGCTAATAAATGTCTGAGGTTAGATTTGAACTCAGGTCTTCCTGACT 989752 i i v v vivi i i vi C MIRb#SINE/MIR 92 CACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACT 43 chr4ptel1M 989753 CC-AAGCCTTTACCC 989766 - iv i i C MIRb#SINE/MIR 42 CCAAAGCCCGTGCTC 28 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.39 CpG sites = 39, Kimura (unadjusted) = 31.27 Transitions / transversions = 2.17 (39/18) Gap_init rate = 0.11 (29 / 253), avg. gap size = 1.21 (35 / 29) 14 28.87 0.00 1.96 chr4ptel1M 989985 990036 (9964) (TACA)n#Simple_repeat 1 51 (0) m_b189s252i9 7406 chr4ptel1M 989985 TACATACCTACCTACGTACACACATACCCTTAAACACACAAACACTACTT 990034 v v i i vivi v i v - v (TACA)n#Simpl 1 TACATACATACATACATACATACATACATACATACATACATACA-TACAT 49 chr4ptel1M 990035 AC 990036 (TACA)n#Simpl 50 AC 51 Matrix = Unknown Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.02 (1 / 51), avg. gap size = 1.00 (1 / 1) 273 35.18 8.55 1.60 chr4ptel1M 990806 991273 (8727) L1ME4a_3end#LINE/L1 157 656 (215) m_b189s551i0 7407 chr4ptel1M 990806 ATAAGAAAAATGTAAATCCAAACAAC--------------TTGCACCTGG 990841 v i i i iv -------------- v iv L1ME4a_3end#L 157 ATCAAAGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCTAT 206 chr4ptel1M 990842 CCAGCTGTCAAACATGACAAAAAAATCAAAATAGTCAATGTTAGAGGGGT 990891 v ii v v v-i i v v v vi i i v i v L1ME4a_3end#L 207 CAAATTGGCAAAGATT-TAAAAGATTGATAATACCCAGTGTTGGCGAGGG 255 chr4ptel1M 990892 TATGGAAAAACAGGCCCACGGATACACGGTTGGTTGAGCTGGGAATTAGT 990941 i ?i i v v vv v i v iiv vi i L1ME4a_3end#L 256 TGTGGNGAAACGGGCACTCTCATACACTGCTGGTGGGAGTGTAAATTGGT 305 chr4ptel1M 990942 CCAAACATTTC----AATCAATTTGGAATTAT---TCAAAGGAGGTGAAT 990984 v v - ----iiv v v --- i vvv i - L1ME4a_3end#L 306 ACAACC-TTTCTGGAGGGCAATTTGGCAATATGTATCAAAAGCCTTAAA- 353 chr4ptel1M 990985 AAAATCTCCATATCCTTTGGTTAGGAAATCCCATTGCAATAGCATGTGCT 991034 -- v ? i iiivi v i i v v -i v v iii L1ME4a_3end#L 354 --AATGTNCATACCCTTTGACCCAGTAATTCCACTTCTA-GGAATTTATC 400 chr4ptel1M 991035 TCAAGGAAGTTGACA-AGA----AACAGAGGTCC-CATATAGG------- 991071 ii i viv - ----? i i ii-ii i i ------- L1ME4a_3end#L 401 CTAAGGAAATAATCAGAGATGTGNACAAAGATTTATGTACAAGGATGTTC 450 chr4ptel1M 991072 -CCGGAGCACTTTTTCCAGTAGAGAACCAT----ATCTAG-TAGATGTCT 991115 -i v i v vi i v vv ---- v v v- i i L1ME4a_3end#L 451 ATCGCAGCATTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCC 500 chr4ptel1M 991116 ATCAATTAGGGAATGGCTCAACATATTGTGATATGTTAATATAATGGATT 991165 v vi ? i v i v i i ii iv ? v L1ME4a_3end#L 501 AACAATAGGGGANTGGTTAAATAAATTATGGTACATCCATANAATGGAAT 550 chr4ptel1M 991166 ATTATGGTACCATTAGGAACAGTAAATATAAATAATTCATAGAAACAGAA 991215 vvi ii i?i ivv vii v viv ivi vii L1ME4a_3end#L 551 ATTATGCAGCCATTAAAAATNATGTTTTCGAAGAATATTTAATGACATGG 600 chr4ptel1M 991216 GAAGATTTATATGAACTTCTGCAGAGTGGAGTAAACAGAACTGGGAAAAC 991265 i vivi vv vv ivi i iv i i?i--iv L1ME4a_3end#L 601 GAAAATGCTCATGATATAATGTTAAGTGAAAAAAGCAGGNT--ACAAAAC 648 chr4ptel1M 991266 AATATACA 991273 vi i L1ME4a_3end#L 649 TGTATATA 656 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 49.10 CpG sites = 88, Kimura (unadjusted) = 50.02 Transitions / transversions = 1.19 (88/74) Gap_init rate = 0.04 (18 / 467), avg. gap size = 2.67 (48 / 18) 286 32.95 15.87 0.46 chr4ptel1M 991786 991974 (8026) L3#LINE/CR1 3259 3476 (623) m_b189s601i17 7408 chr4ptel1M 991786 TGACAGAATTA-GTGTCGAAATAATGTTGG-AGGCTGGAAAGCTCATCTA 991833 i - vv i ?i v i i- v v viv ii L3#LINE/CR1 3259 TGACAGAATCAAGATTCAAAANGATCTCGACAGGCTGGAACGATGGGCCG 3308 chr4ptel1M 991834 AAACCAACAACCTGACACCT-----------------AGTCTTGTGTTTC 991866 vv v ii ----------------- i ii v L3#LINE/CR1 3309 AAACCAACAAGATGAAATTTAACAGGGATAAATGTAAAGTCCTGCATTTA 3358 chr4ptel1M 991867 ACTTT-AAAAATCA--TGCATGA------GGTGG-GA-GACTTGCCTTGG 991905 iv i- -- ii ------ i - - ii v i L3#LINE/CR1 3359 GGTTCAAAAAATCAACTGCACAAGTACAGGATGGAGAGGATCTGGCTTAG 3408 chr4ptel1M 991906 CAGCTGCTGCTGTGAAAAACATGTGGGGAGATGTATTTGGCCAGGAGCCT 991955 v i vvi v iv i - v v v i ivi ii L3#LINE/CR1 3409 CAGCAGTTCACGTGAAAAAGACCTAGGG-GTTTTAGTTGACCGCAAGCTC 3457 chr4ptel1M 991956 GCCCCGAGACAGCGGTACG 991974 ivivi v i i ii L3#LINE/CR1 3458 AATATGAGCCAACAGTGTG 3476 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.43 CpG sites = 37, Kimura (unadjusted) = 45.47 Transitions / transversions = 1.48 (37/25) Gap_init rate = 0.05 (9 / 188), avg. gap size = 3.44 (31 / 9) 54 5.20 0.00 0.00 chr4ptel1M 992087 992146 (7854) (CA)n#Simple_repeat 1 60 (0) c_b189s251i0 7409 chr4ptel1M 992087 CACACACACACACACACACACACACACACACACACTCACACAGACACACT 992136 v v v (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 chr4ptel1M 992137 CACACACACA 992146 (CA)n#Simple_ 51 CACACACACA 60 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0) 277 30.58 5.08 3.91 chr4ptel1M 992845 993021 (6979) C L2b_3end#LINE/L2 (23) 443 265 m_b189s601i19 7410 chr4ptel1M 992845 ATTAGGAGCCTACGGTACCGGCGGCTCTGTGCCGGGCCCTGGGAACACAA 992894 i ii v v iivvvv ? ii v i i i C L2b_3end#LINE 443 ACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGGGATACAG 394 chr4ptel1M 992895 AGGGGTA-AAGA-----ACGGGCCCTGCTCTCACTGGGCTCACAGTCTAG 992938 v v v - -----? v i v i C L2b_3end#LINE 393 CGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGGAGCTCACAGTCTAG 344 chr4ptel1M 992939 CAGGACACGCAAGACA--CACGCGGGCAGGT-TAAAGAAAAGTGGCCAGA 992985 ii iv vi - --i v? i i iv?- vvv i --- C L2b_3end#LINE 343 TGGGGGAGAC-AGACATGTAANCAGACAATNATAACCCAGAGTGGC---A 298 chr4ptel1M 992986 GAGCAGAGCACGTGGAGCCGAGGCTGGGCGGGTGCC 993021 i i ii vv v i v ---i v i C L2b_3end#LINE 297 GGGTAGGACTGGGGGGGCCCAG---AGGAGGGCGCC 265 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.38 CpG sites = 28, Kimura (unadjusted) = 41.41 Transitions / transversions = 1.17 (28/24) Gap_init rate = 0.06 (11 / 176), avg. gap size = 1.45 (16 / 11) 348 29.85 5.97 0.00 chr4ptel1M 992845 992978 (7022) C L2d2_3end#LINE/L2 (23) 532 391 m_b189s601i18 7410 chr4ptel1M 992845 ATTAGGAGCCTACGGTACCGGCGGCTCTGTGCCGGGCCCTG---GGAACA 992891 ii v v iivviv v ii v --- i i C L2d2_3end#LIN 532 ATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGTGGGGGATA 483 chr4ptel1M 992892 CAAAGGGGTA-AAGA-ACGGGCCCTGCTCTCACTGGGCTCACAGTCTAGC 992939 ii - - i v i vv i i i i C L2d2_3end#LIN 482 CAAAGAAGTATAAGACATGGTCCCTGCCCTCAAGGAGCTTACAATCTAGT 433 chr4ptel1M 992940 AGGACACGCAAGACAC--ACGCG-GGCAGGTTAAAGAAAAGT 992978 v iv vi i-- i - iv i v v i C L2d2_3end#LIN 432 TGGGGAGACAAGACATAAACACGTGAAAAGTTAAATAACAAT 391 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.29 CpG sites = 24, Kimura (unadjusted) = 39.29 Transitions / transversions = 1.50 (24/16) Gap_init rate = 0.04 (5 / 133), avg. gap size = 1.60 (8 / 5) 29 19.01 0.00 0.00 chr4ptel1M 993625 993678 (6322) (GT)n#Simple_repeat 1 54 (0) m_b189s252i10 7411 chr4ptel1M 993625 GTATGTGTGTGTGTGGATATGTAAGTGTGTATGTGTGAGTGTGTGTGTGT 993674 i vi i iv i v (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50 chr4ptel1M 993675 GAGT 993678 v (GT)n#Simple_ 51 GTGT 54 Matrix = Unknown Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 370 23.69 10.00 1.54 chr4ptel1M 995454 995573 (4427) MIRc#SINE/MIR 4 133 (135) m_b189s601i20 7412 chr4ptel1M 995454 GGCACCGAGGTGC--TGCAGAGAGCAGTCTGGAGTCCAAGGCAGGAAAAG 995501 vi v -- v i -- v ivi v i v MIRc#SINE/MIR 4 GGCAGTGTGGTGCAGTGGAAAGAGCA--CTGGACTTGGAGTCAGGAAGAC 51 chr4ptel1M 995502 CTGGGTTCTAATCC---TCCTGACACTGAC------TGTGGCCACTGGCA 995542 v i ---ii v v ------ i viv MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 101 chr4ptel1M 995543 AGTCACCT-ACCTCTGTGAATTTCAGTGTCCT 995573 i - v iii v MIRc#SINE/MIR 102 AGTCACTTAACCTCTCTGAGCCTCAGTTTCCT 133 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.77 CpG sites = 14, Kimura (unadjusted) = 28.77 Transitions / transversions = 1.00 (14/14) Gap_init rate = 0.05 (6 / 119), avg. gap size = 2.33 (14 / 6) 15 18.54 0.00 2.63 chr4ptel1M 995793 995831 (4169) (ACCCTA)n#Simple_repeat 1 38 (0) m_b189s252i11 7413 chr4ptel1M 995793 ACTCTGACCCTAAATGCTAACCCTAACCCTGACCCTCAC 995831 i i - iv i v (ACCCTA)n#Sim 1 ACCCTAACCCT-AACCCTAACCCTAACCCTAACCCTAAC 38 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.03 (1 / 38), avg. gap size = 1.00 (1 / 1) 140 6.67 4.13 4.79 chr4ptel1M 995833 996147 (3853) (CCAT)n#Simple_repeat 1 313 (0) c_b189s251i1 7414 chr4ptel1M 995833 CCATCCATCCATCTC-CCCATCCATCCATCCATCCATCTCCT-CATCTAT 995880 - -i - v - i (CCAT)n#Simpl 1 CCATCCATCCATC-CATCCATCCATCCATCCATCCATC-CATCCATCCAT 48 chr4ptel1M 995881 CTATTTGCTCATCCATCTATCCATCTATCTC-CCCGTCCATCCATCCATC 995929 i -- - - i i - -i i (CCAT)n#Simpl 49 CCA--T-C-CATCCATCCATCCATCCATC-CATCCATCCATCCATCCATC 93 chr4ptel1M 995930 CATCCATCCATCTC-CCCATCCATCCATCCATCCATCTC-CCCATCCATC 995977 - -i - -i (CCAT)n#Simpl 94 CATCCATCCATC-CATCCATCCATCCATCCATCCATC-CATCCATCCATC 141 chr4ptel1M 995978 TC-CCCATCCATCCATCCATCTC-CCCATCCATCCATCCATCCCTCC--C 996023 - -i - -i v -- (CCAT)n#Simpl 142 -CATCCATCCATCCATCCATC-CATCCATCCATCCATCCATCCATCCATC 189 chr4ptel1M 996024 CATCCATCCATCCATCCATCTC-CCCATCCATCCATCCATCCATCTC-CC 996071 - -i - -i (CCAT)n#Simpl 190 CATCCATCCATCCATCCATC-CATCCATCCATCCATCCATCCATC-CATC 237 chr4ptel1M 996072 CATCCATCCATCCATCCATTCATCCATCTC-CCCATCCATCCATCCATCC 996120 i - -i (CCAT)n#Simpl 238 CATCCATCCATCCATCCATCCATCCATC-CATCCATCCATCCATCCATCC 286 chr4ptel1M 996121 ATCTC-CCCATCCATCCATCCATCCATC 996147 - -i (CCAT)n#Simpl 287 ATC-CATCCATCCATCCATCCATCCATC 313 Matrix = Unknown Transitions / transversions = 8.00 (16/2) Gap_init rate = 0.09 (27 / 314), avg. gap size = 1.04 (28 / 27) 15 27.87 0.00 0.00 chr4ptel1M 996151 996195 (3805) (CCAT)n#Simple_repeat 1 45 (0) m_b189s252i12 7414 chr4ptel1M 996151 CCATCCATCTCCCCATCTATCCATTTGCTCATCCATCCATCGATC 996195 ivi i iiiii v (CCAT)n#Simpl 1 CCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATC 45 Matrix = Unknown Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 300 23.10 18.97 2.99 chr4ptel1M 996423 996538 (3462) C MIRc#SINE/MIR (120) 148 15 m_b189s601i21 7415 chr4ptel1M 996423 CTCACTTTTCAGACAAGGAATCTAAG-CCCAGAAAAGTTAAGAGAT---C 996468 i i v ii v i - i i i v i--- C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr4ptel1M 996469 TCAAGGTCAC----CGGGTA------------GGGATTTGAACCCAGGCC 996502 i ---- vi ------------ i i i C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTC 49 chr4ptel1M 996503 TT--TGCCTGTAAATCAAATGCAGAGTCTTACTACTGC 996538 -- v vi i v i ---- v i C MIRc#SINE/MIR 48 TTCCTGACTCCAAGTCCAGTGC----TCTTTCCACTGC 15 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.50 CpG sites = 18, Kimura (unadjusted) = 28.80 Transitions / transversions = 2.25 (18/8) Gap_init rate = 0.08 (9 / 115), avg. gap size = 2.89 (26 / 9) 498 24.88 14.77 5.02 chr4ptel1M 996613 996849 (3151) C MIRc#SINE/MIR (0) 268 10 m_b189s601i22 7416 chr4ptel1M 996613 AATAATAATAATA---TGCATG---ATAGC---TCATATTTCCATGGAGT 996653 i?--- i v--- --- i i v i- iii i C MIRc#SINE/MIR 268 AATAATAATAACNCCTTACATTTGTATAGCACTTTACAGTTT-ACAAAGC 220 chr4ptel1M 996654 GTTTT---AGACAGGATCTTATTTGATCCTCACAAAGA---AGCAAG--A 996695 i --- v vv i vi ---v ii -- C MIRc#SINE/MIR 219 GCTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTA 170 chr4ptel1M 996696 GGCAGGG--GTTATTATCATCTCAAGTCTACAGATGAGGAAACTGAGG-- 996741 -- v i i v v i -- C MIRc#SINE/MIR 169 GGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCT 120 chr4ptel1M 996742 CAGA--------------TGTCCAGGGTCACACAGCTAAAATATGTCTGA 996777 -------------- i i iv vi v v C MIRc#SINE/MIR 119 CAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGA 70 chr4ptel1M 996778 GATTGGGTTTATAGCTAGATCTTTCTGATCCTGGATCTGATTCCAGACCC 996827 viv ii iiv v i i ------------i i iii C MIRc#SINE/MIR 69 GCCGGGACTCGAACCCAGGTCTT------------CCTGACTCCAAGTCC 32 chr4ptel1M 996828 TGTGCTCTATCCATTTCACAAC 996849 v v i v v C MIRc#SINE/MIR 31 AGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.27 CpG sites = 34, Kimura (unadjusted) = 31.34 Transitions / transversions = 1.55 (34/22) Gap_init rate = 0.09 (22 / 236), avg. gap size = 2.18 (48 / 22) 509 24.84 9.27 7.69 chr4ptel1M 996651 996855 (3145) C MIRb#SINE/MIR (53) 215 8 m_b189s601i23 7416 chr4ptel1M 996651 AGTGTTTTAGA--CAGGATCTTATTTGATCCTCACAAAGAAGCAA-GAGG 996697 i i v -- vv i i vi vv vi- C MIRb#SINE/MIR 215 AGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGG 166 chr4ptel1M 996698 CAGGGGTTATTATCATCTCAAGTCTACAGATGAGGAAACTGAGG--CAGA 996745 i --- i i v v i -- C MIRb#SINE/MIR 165 TAGG---TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGA 119 chr4ptel1M 996746 --------------TGTCCAGGGTCACACAGCTAAAATATGTCTGAGATT 996781 -------------- i i iv vi v v viv C MIRb#SINE/MIR 118 GAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 69 chr4ptel1M 996782 GGGTTTATAGCTAGATCTTTCTGATCCTGGATCTGATTCCAGACCCTGTG 996831 i iiv v i i ------------i i i v i C MIRb#SINE/MIR 68 GGATTCGAACCCAGGTCT------------GTCTGACTCCAAAGCCCGTG 31 chr4ptel1M 996832 CTCTATCCATTTCACAACTGCTAC 996855 v i v v - i C MIRb#SINE/MIR 30 CTCTTTCCACTGCACCAC-GCTGC 8 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.60 CpG sites = 26, Kimura (unadjusted) = 30.69 Transitions / transversions = 1.24 (26/21) Gap_init rate = 0.10 (20 / 204), avg. gap size = 1.75 (35 / 20) 429 32.21 3.28 4.56 chr4ptel1M 998401 998644 (1356) C MARNA#DNA/TcMar-Mariner (345) 241 1 m_b189s502i0 7417 chr4ptel1M 998401 AGATGTGACTGTCGAGCAATCGAGG--GCCTTTTTTTCATGGCTCATAAA 998448 i i vi i - i-- vi i vii C MARNA#DNA/TcM 241 AGGTGTGACTATAAAGTAAT-GAGACTGATTTTCTTGTGTGGCTCATAAA 193 chr4ptel1M 998449 CTGTCTTTGAAGATGAGG-AAAAAGAAGAAACCC-AAACCATTTTTAACA 998496 v i iii vv-v i ivi - vii v i C MARNA#DNA/TcM 192 CTGGCTCTGAAGGCAATTCCAAAAGAGGAGTTCCAAAAATGTTTTGAGCA 143 chr4ptel1M 998497 GTGATGATATCATTGAGATACATGATTGGCATCCCAAGCTGCCCGGCTTG 998546 i iiiii i ii vi vvii v v v iivi C MARNA#DNA/TcM 142 ATGGCAGCATCGTTGGAATAAGTGTACAGCCTCCCAAGGTGACTACTTTG 93 chr4ptel1M 998547 GAGGA-GACAGT-GTTTGGCTGGATAAAATTCTGGTAAATTGGTCGAAAA 998594 i -i v -i v v - i ivi v iv C MARNA#DNA/TcM 92 AAGGACAACACTCATTTGGATGTAT-AAGTTCTGGTGTGTTTGTTTAAAA 44 chr4ptel1M 998595 AAGAAAAAAGTGGGCTGTATTACTTGACAGTCACATCTC--ATACATATC 998642 --------- vi ivi v i i -- i ii C MARNA#DNA/TcM 43 A---------TCAGCCTCATTACTTTATAGTCACACCTCGTATACGTGCC 3 chr4ptel1M 998643 CA 998644 C MARNA#DNA/TcM 2 CA 1 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 42.67 CpG sites = 49, Kimura (unadjusted) = 44.30 Transitions / transversions = 1.88 (49/26) Gap_init rate = 0.07 (17 / 243), avg. gap size = 1.12 (19 / 17) 416 31.54 1.17 3.59 chr4ptel1M 999399 999569 (431) MIR3#SINE/MIR 2 168 (40) m_b189s601i24 7418 chr4ptel1M 999399 TGGCAGGGAGGAAAGAGCAGAAGGGAGATCTTCGATTCTGAAACTT-GAA 999447 i v vv- --- v viv -- ii v i- i MIR3#SINE/MIR 2 TGGCAGAGTGGCT-GAGCAGA---GAGAGCACGGA--CTGGGAGTCAGGA 45 chr4ptel1M 999448 GACCTGGGTTCAAATTCCAGCTGGAATACTTCTTGGATTTTTGAC-ATAG 999496 v i i i vvivi vvi ? v v v -v i MIR3#SINE/MIR 46 GACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGG 95 chr4ptel1M 999497 GCAAGACACTTGGTCTCCCTGGGTCTTAGTGTCCTTGTCTATAAAATAAG 999546 v vii i i i v ii i i MIR3#SINE/MIR 96 GCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAG 145 chr4ptel1M 999547 CATGTTTGATCAGACCGTGTCTA 999569 viv v ii ivi v MIR3#SINE/MIR 146 GGGGTTGGACTAGATGATCTCTA 168 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.88 CpG sites = 27, Kimura (unadjusted) = 41.95 Transitions / transversions = 1.08 (27/25) Gap_init rate = 0.05 (8 / 170), avg. gap size = 1.00 (8 / 8) 289 29.53 8.43 4.89 chr4qtel1M 111 288 (999712) L3#LINE/CR1 3819 4002 (97) m_b190s601i0 7419 chr4qtel1M 111 TCTGTCTG--TCCAGAG---AGAAC-AGGAACAGAGGCAGGA-----CAA 149 v -- --- - v iv vv ----- i L3#LINE/CR1 3819 TCTGTGTGGCTCCAGAGGGCAGAACTAGGACCAATGGGTGGAAGTTACAG 3868 chr4qtel1M 150 AGAGG--GATGTCCCATTTGGTCTGGGGAAGAAAGACCACCCCGATAAAT 197 i -- - i vii iii v ii ---- vii ii i vi L3#LINE/CR1 3869 GGAGGCAGAT-TTCGGCTCAATATAAGGAAGAA----CTTTCTAACAATC 3913 chr4qtel1M 198 GGAGTTGCCCCACG-TAGAACGTG-GGTCTCGGTTGGGAGAGGGCAGCAT 245 i i i v vi- i i v -v i ?vv v v i ---- L3#LINE/CR1 3914 AGAGCTGTCCAAAAATGGAATGGGCTGCCTCGNGAGGTAGTGAGC----T 3959 chr4qtel1M 246 CTTTCTCACTGGAGGTCTTCAAGCAAAGGCTGGATGTTCACTT 288 iiiv v i vi L3#LINE/CR1 3960 CCCCGTCACTGGAGGTGTTCAAGCAGAGGCTGGATGACCACTT 4002 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 38.12 CpG sites = 30, Kimura (unadjusted) = 39.13 Transitions / transversions = 1.50 (30/20) Gap_init rate = 0.09 (16 / 177), avg. gap size = 1.50 (24 / 16) 255 24.43 19.85 0.00 chr4qtel1M 317 447 (999553) C MIR3#SINE/MIR (0) 208 52 m_b190s601i1 7420 chr4qtel1M 317 GAATC-TAGAACCGTAG--CTTTAGGGACGGAAGAGACAGTAGA-ATGA- 361 - i i --iv i i vi i vv - v - C MIR3#SINE/MIR 208 GAATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCAT 159 chr4qtel1M 362 -------------CTCATTTTACAGAGGAGGGGAAT------CTGAGAAG 392 ------------- v ii v ------ v i C MIR3#SINE/MIR 158 CTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGG 109 chr4qtel1M 393 CGAGGTGACTC-CCCAAGGTTTC-CAGCTAGTTAAGCGGACAGCCAGGAA 440 i i i- iv - ? ivv v v i v C MIR3#SINE/MIR 108 TGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGAC 59 chr4qtel1M 441 TCCAACC 447 vv C MIR3#SINE/MIR 58 TAGAACC 52 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 29.02 CpG sites = 16, Kimura (unadjusted) = 30.10 Transitions / transversions = 1.00 (16/16) Gap_init rate = 0.06 (8 / 130), avg. gap size = 3.25 (26 / 8) 265 26.45 8.74 0.90 chr4qtel1M 362 464 (999536) C MIR#SINE/MIR (118) 144 34 m_b190s601i2 7420 chr4qtel1M 362 CTCATTTTACAGAGGAGGGGAAT------CTGAGAAGCGAGGTGACTC-C 404 i v ii v ------ v i iv i i i- C MIR#SINE/MIR 144 CCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGC 95 chr4qtel1M 405 CCAAGGTTTC-CAGCTAGTTAAGCGG-ACAGCCAGGAATCCAACCACGGC 452 iv - - i - v i v v vv C MIR#SINE/MIR 94 CCAAGGTCACACAGCTAG-TAAGTGGCAGAGCCGGGATTCGAACCCAGGC 46 chr4qtel1M 453 CGTTAGTTTCTA 464 v iv vi i C MIR#SINE/MIR 45 AGTCTGGCTCCA 34 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 31.61 CpG sites = 14, Kimura (unadjusted) = 33.06 Transitions / transversions = 1.08 (14/13) Gap_init rate = 0.05 (5 / 102), avg. gap size = 2.00 (10 / 5) 194 35.80 1.23 0.00 chr4qtel1M 808 888 (999112) C MIR3#SINE/MIR (15) 193 112 m_b190s601i3 7421 chr4qtel1M 808 AGGATCTAAGAGCTGGGAGGGAGCCCCCAGGCCCT-GAGTCCAAGACCCT 856 i v v i v iivv ii v -v vv C MIR3#SINE/MIR 193 AGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCT 144 chr4qtel1M 857 CACTTCATGAGGAAGAAAACCAAGGTCCAAGG 888 i i iiiivi i ii i ii C MIR3#SINE/MIR 143 CATTTTACAGATGAGGAAACTGAGGCCCAGAG 112 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 51.99 CpG sites = 19, Kimura (unadjusted) = 51.99 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.01 (1 / 80), avg. gap size = 1.00 (1 / 1) 16 21.58 5.56 4.11 chr4qtel1M 997 1068 (998932) (TGTGCA)n#Simple_repeat 1 73 (0) m_b190s252i0 7422 chr4qtel1M 997 TGTGCATGTACATGTGTGCATGTG--TGTTTATGTGTATGTGTGCATGCA 1044 i -- -- vi i iiii (TGTGCA)n#Sim 1 TGTGCATGTGCA--TGTGCATGTGCATGTGCATGTGCATGTGCATGTGCA 48 chr4qtel1M 1045 TCGT-C-TGTGCACATGTCTGTGCAT 1068 - - - ii iv (TGTGCA)n#Sim 49 T-GTGCATGTGCATGTGCATGTGCAT 73 Matrix = Unknown Transitions / transversions = 5.00 (10/2) Gap_init rate = 0.08 (6 / 71), avg. gap size = 1.17 (7 / 6) 16 16.93 0.00 0.00 chr4qtel1M 2177 2203 (997797) (T)n#Simple_repeat 1 27 (0) m_b190s252i1 7423 chr4qtel1M 2177 TTTTTTTTTTCTGTTTTTCTTTTTCTT 2203 i v i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTT 27 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 14 14.41 0.00 3.12 chr4qtel1M 2178 2210 (997790) (TTTTTC)n#Simple_repeat 1 32 (0) m_b190s252i2 7423 chr4qtel1M 2178 TTTTTTTTTCTGTTTTTCTTTTTCTTCCTTCTT 2210 i i v -i (TTTTTC)n#Sim 1 TTTTTCTTTTTCTTTTTCTTTTTCTT-TTTCTT 32 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 231 30.67 0.00 0.00 chr4qtel1M 2465 2539 (997461) C L1MA4_3end#LINE/L1 (481) 566 492 m_b190s551i0 7424 chr4qtel1M 2465 TTCCTGATAGCACAATAATATTCCATTATATTCATACGCCACAACTTGTT 2514 ii v i vv i i vi ii vi v C L1MA4_3end#LI 566 TTTTTTATGGCTGAATAATATTCCATTGTGTATATATACCACATTTTCTT 517 chr4qtel1M 2515 CAGCCATTCCCCGATGGATGGTCAC 2539 i v vi vi v v C L1MA4_3end#LI 516 TATCCATTCATCCGTTGATGGACAC 492 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 37.91 CpG sites = 12, Kimura (unadjusted) = 40.11 Transitions / transversions = 1.09 (12/11) Gap_init rate = 0.00 (0 / 74), avg. gap size = 0.0 (0 / 0) 788 27.79 10.89 2.38 chr4qtel1M 2479 2983 (997017) C L1ME3G_3end#LINE/L1 (376) 548 2 m_b190s551i1 7424 chr4qtel1M 2479 ATAATATTCCATTATATTCATACGCCACAACTTGTTCAGCCATTCCCCGA 2528 i vi vv ii i i i i i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr4qtel1M 2529 TGGATGGTCACCC-------CTCCGATTT----CCAATAAAAAGAGATGT 2567 v v iii-------i i ---- i v v v - i C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACA-ATGC 450 chr4qtel1M 2568 TACAATG----TTTTTGTACAGG------TGGG----TCTGTTACCATTT 2603 i ---- ii v ------ v ---- v iv vi C L1ME3G_3end#L 449 TGCAATGAACATCCTTGTACATGCNTCCTTGTGCACATGTGCGAGTATTT 400 chr4qtel1M 2604 TTTTAA-AT-GATCTCT-GAAATATAGTATACTAGATCAAAGGGTATGCA 2650 i ? i- - ?i ?- i iv i - i i i i C L1ME3G_3end#L 399 CTNTAGGATAGATNCCNAGAAGTGGAAT-TGCTGGGTCAAAGGGTATGCG 351 chr4qtel1M 2651 CATTTTGATTGCCTTTAGGGTATGGCTCCAAATTGCCCTCCAGAATGGTC 2700 i v --- iviv iviv i ? ii C L1ME3G_3end#L 350 CATTTTAAAT---TTTAATAGATACTGCCAAATTGCCCTCCAAAANGGCT 304 chr4qtel1M 2701 AGATCAGTTCACAACTCCACCTACAAT---------TACTC--------- 2732 iv i i i vii vi i --------- i --------- C L1ME3G_3end#L 303 GTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCA 254 chr4qtel1M 2733 ----CTCTCTAACATTTGTCATTTT---TCTTTTCTGTTTTATTAGCCAC 2775 ---- v i i ? vi v ---? vvi v--- v C L1ME3G_3end#L 253 CACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTT---GCCAA 207 chr4qtel1M 2776 TCTGATGAGTGTGAGGTGATAACTCAGAGCTGTTTTAATTTGCATTTCTC 2825 i vi ii i v vv i i C L1ME3G_3end#L 206 TCTGATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCC 157 chr4qtel1M 2826 TAATCAATAATGATTTAGAATAT-TTTTCATATGACTATAGACAGATTTA 2874 i i v i vv v ii - vi v i -v i C L1ME3G_3end#L 156 TGATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGC-CATTTG 108 chr4qtel1M 2875 -ATTTCTTTATCTGAAAATTGCCTGTTCTTATCCTTTGATCATTTATCAG 2923 - i iv vi v vi v vi C L1ME3G_3end#L 107 TATTTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTA 58 chr4qtel1M 2924 TTGGGGAATGACTTATATTCTCATATATTTGACTCACTTTTCTATATATT 2973 v-- v -- v i vv vvvv v i i C L1ME3G_3end#L 57 TTGGGT--TGTCT--TTTTCTTATTGATTTGTAGGAGTTCTTTATATATT 12 chr4qtel1M 2974 TGAGAAATCA 2983 ivi v i C L1ME3G_3end#L 11 CTGGATATTA 2 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 35.50 CpG sites = 78, Kimura (unadjusted) = 36.16 Transitions / transversions = 1.32 (78/59) Gap_init rate = 0.05 (27 / 504), avg. gap size = 2.52 (68 / 27) 496 22.48 0.81 5.98 chr4qtel1M 3028 3150 (996850) MIRc#SINE/MIR 11 127 (141) m_b190s601i4 7425 chr4qtel1M 3028 TGGCACAGTGGATAGAGCAGCAGCCCTGAAGTCAGGAGGACCTGAGTTCA 3077 ii v vii v i i i i i MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr4qtel1M 3078 AATCTAGCTTCAGACACTCAACACTTCCTAGCTGTGTGACTCTGGGCAAG 3127 i iv vi v v i ------- ii MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTGACCTTGGGCAAG 103 chr4qtel1M 3128 TCACTTAACCCCAAT-TGCCTCAG 3150 i vv -v MIRc#SINE/MIR 104 TCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 26.01 CpG sites = 16, Kimura (unadjusted) = 27.21 Transitions / transversions = 1.60 (16/10) Gap_init rate = 0.07 (8 / 122), avg. gap size = 1.00 (8 / 8) 189 34.29 0.00 1.43 chr4qtel1M 4039 4109 (995891) C L3#LINE/CR1 (1109) 2990 2921 m_b190s601i5 7426 chr4qtel1M 4039 CGTGAGGCATTTTGTCAAACGGTCTGCCAAAGTCTAGATGGATTCTATTC 4088 i iv i i vii ii i i iv i ? i- C L3#LINE/CR1 2990 CATGAGAGACTTTGTCAAATGCCTTGCTGAAATCCAGATACACTNTG-TC 2942 chr4qtel1M 4089 TTAGCCCTTGTCTTCATCTAC 4109 vv v v vi i v C L3#LINE/CR1 2941 TACGGCATTCCCCTGATCTAC 2921 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 49.20 CpG sites = 15, Kimura (unadjusted) = 49.20 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.01 (1 / 70), avg. gap size = 1.00 (1 / 1) 343 28.79 7.30 4.37 chr4qtel1M 4167 4344 (995656) L2#LINE/L2 2566 2748 (334) m_b190s601i6 7427 chr4qtel1M 4167 TTTTTCATTCTTCTCTTCCCTTCACATCCTCCCCCACATCCAATCCATCA 4216 ii v i i i ii ----- L2#LINE/L2 2566 TCCTTGACTCCTCTCTTTCTCTCACA-----CCCCACATCCAATCCATCA 2610 chr4qtel1M 4217 TCGA-----GTCACTTCTATCTTC------TTTCCATAACACTTCAATTA 4255 v i ----- ivi i ------ v v --- i i ii L2#LINE/L2 2611 GCAAATCCTGTCGGCTCTACCTTCAAAATATATCCAGAA---TCCGACCA 2657 chr4qtel1M 4256 -TCCTC-CCACCCACGTGGCCAGCACTCTGGTCCATACCCTGCTCATCTC 4303 - i - iv iiv v i vi vivv L2#LINE/L2 2658 CTTCTCACCACCTCCACTGCCACCACCCTGGTCCAAGCCACCATCATCTC 2707 chr4qtel1M 4304 TCACCTTGATTATGGCGATCACCACCTGGCAGATTGCTCTG 4344 i v iv i vi v ii v i iv i L2#LINE/L2 2708 TCGCCTGGATTACTGCAATAGCCTCCTAACTGGTCTCCCTG 2748 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 34.83 CpG sites = 31, Kimura (unadjusted) = 37.75 Transitions / transversions = 1.72 (31/18) Gap_init rate = 0.07 (12 / 177), avg. gap size = 1.75 (21 / 12) 75 15.72 4.40 2.70 chr4qtel1M 5103 5284 (994716) (AGGA)n#Simple_repeat 1 185 (0) m_b190s252i3 7428 chr4qtel1M 5103 AGGAAGGAAGGGAGAAAGGAAGGAAAAAAAGAAGGAAAGGAA-GCAGGAG 5151 i i ii i - - v i (AGGA)n#Simpl 1 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG-AAGGAAGGAAGGAA 49 chr4qtel1M 5152 AGAAGAAGGGAAGG-AGGTATGAGGGGAGAAAGAAAATGGAAGG-AGGAA 5199 i i i - v v i i i -i - - (AGGA)n#Simpl 50 GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG-GAA-GGAAGGAAGGAA 97 chr4qtel1M 5200 GGAAAG-AGGAA--AAGGAAGGAAGGCAGGAATGAAGGAACAAAGGAAGG 5246 i - -- v v vi (AGGA)n#Simpl 98 GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG 147 chr4qtel1M 5247 AAGGAAGGAA-GAAAAAAGGGAGG-AGGAACGGAAGAGAA 5284 - ii i - - - (AGGA)n#Simpl 148 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAA-GGAAG-GAA 185 Matrix = Unknown Transitions / transversions = 3.00 (18/6) Gap_init rate = 0.07 (12 / 181), avg. gap size = 1.08 (13 / 12) 19 21.43 4.50 8.41 chr4qtel1M 5176 5286 (994714) (GGAAAA)n#Simple_repeat 1 107 (0) m_b190s252i4 7428 chr4qtel1M 5176 GGAGAAAGAAAATG-GAAGGAGGAAGGAAAGAGGAAAAGG--AAGGAAGG 5222 i i v -i -i - -- -- (GGAAAA)n#Sim 1 GGAAAAGGAAAAGGAAAAGGA-AAAGGAAA-AGGAAAAGGAAAAGGAA-- 46 chr4qtel1M 5223 CAGGAATGAAGGAACAAAG-GAAGGAAGGAAGGAAGAAAAAAGGGAGGAG 5271 v -- - i -i -- i ii i ii (GGAAAA)n#Sim 47 AAGGAA--AAGGAA-AAGGAAAAGGAA--AAGGAAAAGGAAAAGGAAAAG 91 chr4qtel1M 5272 G-AACGGAAGAGAAAA 5286 - v i i (GGAAAA)n#Sim 92 GAAAAGGAAAAGGAAA 107 Matrix = Unknown Transitions / transversions = 4.67 (14/3) Gap_init rate = 0.12 (13 / 110), avg. gap size = 1.08 (14 / 13) 183 32.05 5.13 0.00 chr4qtel1M 5671 5748 (994252) C L2a_3end#LINE/L2 (7) 510 429 m_b190s601i7 7429 chr4qtel1M 5671 CAGTCAATAAGCATTTATTAAGCGCTTACTGTTGGCAACTCACACCTCAG 5720 v i ii i i i vv v vv vvi vi C L2a_3end#LINE 510 CATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTA 461 chr4qtel1M 5721 TGAGCTGGGA--CCATCAGTGG--AAAGTAGA 5748 v v i--v v i-- ii C L2a_3end#LINE 460 GGCGCTGGGGATACAGCAGTGAACAAAACAGA 429 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 42.29 CpG sites = 12, Kimura (unadjusted) = 42.29 Transitions / transversions = 0.92 (12/13) Gap_init rate = 0.03 (2 / 77), avg. gap size = 2.00 (4 / 2) 197 23.81 0.00 0.00 chr4qtel1M 5672 5713 (994287) C L2d2_3end#LINE/L2 (8) 547 506 m_b190s601i8 7429 chr4qtel1M 5672 AGTCAATAAGCATTTATTAAGCGCTTACTGTTGGCAACTCAC 5713 i i ii i i vv vv C L2d2_3end#LIN 547 AATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCAC 506 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 29.26 CpG sites = 6, Kimura (unadjusted) = 29.26 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 13 18.91 0.00 0.00 chr4qtel1M 5757 5786 (994214) (TGTG)n#Simple_repeat 1 30 (0) m_b190s252i5 7430 chr4qtel1M 5757 TGGGTGTGAATGAGTGTGTGAGTGTGTGTG 5786 v vi v v (TGTG)n#Simpl 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 30 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 91 31.46 3.29 0.29 chr4qtel1M 6333 6666 (993334) (CTGCTA)n#Simple_repeat 1 344 (0) m_b190s252i6 7431 chr4qtel1M 6333 CTGCTGCTGCTGCTGCCATTGCTA---CTATTACTACTGCGATTGTTACT 6379 i i i i --- i i v i i (CTGCTA)n#Sim 1 CTGCTACTGCTACTGCTACTGCTACTGCTACTGCTACTGCTACTGCTACT 50 chr4qtel1M 6380 GCTA---CTATTGCTACTGCTGCTGTTACTATTACTGCTGCTGTTGTTAC 6426 --- i i i ii i i ii i (CTGCTA)n#Sim 51 GCTACTGCTACTGCTACTGCTACTGCTACTGCTACTGCTACTGCTACTGC 100 chr4qtel1M 6427 TACTGCTACTGCTACTAATACTACTACTGCTATTGCTA-T--TATTGCTA 6473 iv i i - -- i (CTGCTA)n#Sim 101 TACTGCTACTGCTACTGCTACTGCTACTGCTACTGCTACTGCTACTGCTA 150 chr4qtel1M 6474 ATACTGCTGTTGCTGCTGTTACTATTGTTACTGTTACTACTGAGGTTGTT 6523 v i i i i ii i i i i i ivv i ii (CTGCTA)n#Sim 151 CTGCTACTGCTACTGCTACTGCTACTGCTACTGCTACTGCTACTGCTACT 200 chr4qtel1M 6524 ACTATTGCTGTTGCTACTATTGCTTGTA-T-TTACTGATGCTGCTGTTAC 6571 i i ii ii i vv - -i v i ii i (CTGCTA)n#Sim 201 GCTACTGCTACTGCTACTGCTACTGCTACTGCTACTGCTACTGCTACTGC 250 chr4qtel1M 6572 TATTGCTGTTGCTACTATTACTTCTACTTACTACTGCAGCTATTACTACT 6621 i ii ii v - i vi ii i (CTGCTA)n#Sim 251 TACTGCTACTGCTACTGCTACTGCTAC-TGCTACTGCTACTGCTACTGCT 299 chr4qtel1M 6622 ACTGCTATTGCTATTATTGCTAATACTGCTGTTGCTGCTGTTACT 6666 i i ii i iv ii i i (CTGCTA)n#Sim 300 ACTGCTACTGCTACTGCTACTGCTACTGCTACTGCTACTGCTACT 344 Matrix = Unknown Transitions / transversions = 6.27 (69/11) Gap_init rate = 0.02 (7 / 333), avg. gap size = 1.71 (12 / 7) 15 36.18 0.00 0.00 chr4qtel1M 6859 6925 (993075) (TAC)n#Simple_repeat 1 67 (0) m_b190s252i7 7432 chr4qtel1M 6859 TACTATTGTTACTGCTACTAATTTTACTATTTTTTCTAATTCTTCTTTTA 6908 i ii i v vi i vi v v v v vi (TAC)n#Simple 1 TACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTA 50 chr4qtel1M 6909 CTGGTATTACTACTACT 6925 iv i (TAC)n#Simple 51 CTACTACTACTACTACT 67 Matrix = Unknown Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.0 (0 / 0) 16 21.24 0.00 4.44 chr4qtel1M 8295 8341 (991659) (CTA)n#Simple_repeat 1 45 (0) m_b190s252i8 7433 chr4qtel1M 8295 CTACTATTACTTCTACTTACTACTGTGAACTACTACTGCTATAACTA 8341 i v - -vvv i iv (CTA)n#Simple 1 CTACTACTACTACTAC-TACTACT-ACTACTACTACTACTACTACTA 45 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.04 (2 / 46), avg. gap size = 1.00 (2 / 2) 479 25.81 4.84 0.00 chr4qtel1M 9115 9238 (990762) MIRc#SINE/MIR 19 148 (120) m_b190s601i9 7434 chr4qtel1M 9115 TGGGGAGAGCCCTGAGCCTGGGGTCAGGGAGATCCAAATTAAAATC--AG 9162 ii v ii i i i i iiii vi i --i MIRc#SINE/MIR 19 TGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGG 68 chr4qtel1M 9163 C-CTATC--TTCCTAGCCGTGTGACCCTGGGTAAGTCACTTAA-GTCTGT 9208 - ii -- v i i i -v v MIRc#SINE/MIR 69 CTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCT 118 chr4qtel1M 9209 TTGCCTCAATTTCCTTATCTGTCATATGAG 9238 vv i i v v i MIRc#SINE/MIR 119 GAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 30.69 CpG sites = 23, Kimura (unadjusted) = 33.23 Transitions / transversions = 2.56 (23/9) Gap_init rate = 0.03 (4 / 123), avg. gap size = 1.50 (6 / 4) 12 20.13 4.08 4.08 chr4qtel1M 9414 9462 (990538) (CCTGC)n#Simple_repeat 1 49 (0) m_b190s252i9 7435 chr4qtel1M 9414 CCAGCCCTCCCCGGCCCTTGCTCCTGTCCT--CCTGCCCCCCGCTGTCCT 9461 v v v - - i -- iv v i (CCTGC)n#Simp 1 CCTGCCCTGCCCTGCCC-TGC-CCTGCCCTGCCCTGCCCTGCCCTGCCCT 48 chr4qtel1M 9462 G 9462 (CCTGC)n#Simp 49 G 49 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.06 (3 / 48), avg. gap size = 1.33 (4 / 3) 217 30.91 0.00 0.00 chr4qtel1M 10195 10249 (989751) C L2b_3end#LINE/L2 (7) 459 405 m_b190s601i10 7436 chr4qtel1M 10195 CAGTCCATAAGCATTGTTTAAGCACTTACTGTATTCTAGGCCCTGTGCTA 10244 v v i ii vvi i i i i v i ? C L2b_3end#LINE 459 CATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTA 410 chr4qtel1M 10245 AATGC 10249 iii C L2b_3end#LINE 409 GGCGC 405 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 36.90 CpG sites = 12, Kimura (unadjusted) = 43.63 Transitions / transversions = 2.40 (12/5) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 311 25.82 22.34 1.69 chr4qtel1M 11246 11442 (988558) MIRb#SINE/MIR 18 254 (14) m_b190s601i11 7437 chr4qtel1M 11246 GCAGTGGGTGGAGACCCAGGCCT-GGAG--ACTCAGACTTGAATT-AAGT 11291 ivi - v i i - -- vv i ii -i i MIRb#SINE/MIR 18 GCAGTGGAAAGAG-CACGGGCTTTGGAGTCAGACAGACCTGGGTTCGAAT 66 chr4qtel1M 11292 CCC---TCCGACACTT--CAGCTGTATGAT----GCCAAGT--------- 11323 --- i v --i i i---- v --------- MIRb#SINE/MIR 67 CCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACC 116 chr4qtel1M 11324 -----GAGTCACATCATCCTCCACGGTAAAA-GGAGACCATAATAGCCCC 11367 ----- i v viv vv v - i iv --- MIRb#SINE/MIR 117 TCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATA---CC 163 chr4qtel1M 11368 CACTCCCCCGAATCATTGTGACAATAAAATGAG---------------CC 11402 i ii v v ii ii vi v --------------- v MIRb#SINE/MIR 164 TACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCG 213 chr4qtel1M 11403 CTGATCACA-TGCCTGGCACACAGTAGGTGCTGTATAAATG 11442 v v - i i i vv MIRb#SINE/MIR 214 CTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAAATG 254 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 30.06 CpG sites = 28, Kimura (unadjusted) = 32.36 Transitions / transversions = 1.27 (28/22) Gap_init rate = 0.08 (15 / 196), avg. gap size = 3.20 (48 / 15) 29 24.52 2.33 2.33 chr4qtel1M 12013 12098 (987902) (GA)n#Simple_repeat 1 86 (0) m_b190s252i10 7438 chr4qtel1M 12013 GAGTGAG-GTGAGAGAGAGAGAAAGAAACAGAGACAGAGAAGGGGAGAGT 12061 v - v i i v v ii i v (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr4qtel1M 12062 GAGCATGAGAGAAATAAAGAGAGA-AAAGAAAAATAGA 12098 - - i v i - i i i v (GA)n#Simple_ 51 GAG-A-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 86 Matrix = Unknown Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.05 (4 / 85), avg. gap size = 1.00 (4 / 4) 43 13.53 8.25 0.00 chr4qtel1M 12112 12208 (987792) (AT)n#Simple_repeat 1 105 (0) m_b190s252i11 7439 chr4qtel1M 12112 ATGTATATA-ATATATTTTAATGTATACACATATATA-ATATA-ATAAAT 12158 i - v vv i i i - - v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr4qtel1M 12159 GTATATA-AAATATAT-TTTATAT-TATAT-TATATATATCTATATATAT 12204 i - v - v - - v (AT)n#Simple_ 51 ATATATATATATATATATATATATATATATATATATATATATATATATAT 100 chr4qtel1M 12205 -TATA 12208 - (AT)n#Simple_ 101 ATATA 105 Matrix = Unknown Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.08 (8 / 96), avg. gap size = 1.00 (8 / 8) 17 19.96 0.00 0.00 chr4qtel1M 12208 12247 (987753) (AGAGGC)n#Simple_repeat 1 40 (0) m_b190s252i12 7440 chr4qtel1M 12208 AGAGGCAGAGGCCAAGAGAGATTCAGAGGCAGAGACAGAG 12247 vi iv vv i (AGAGGC)n#Sim 1 AGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAG 40 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 79 0.00 2.70 0.00 chr4qtel1M 12254 12327 (987673) (CA)n#Simple_repeat 1 76 (0) c_b190s251i0 7441 chr4qtel1M 12254 CACACACACACACACACACACAC-CACACACACACACACACACACACACA 12302 - (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 chr4qtel1M 12303 CACA-ACACACACACACACACACACA 12327 - (CA)n#Simple_ 51 CACACACACACACACACACACACACA 76 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.03 (2 / 73), avg. gap size = 1.00 (2 / 2) 239 32.71 5.22 4.31 chr4qtel1M 12451 12565 (987435) C L3b_3end#LINE/CR1 (183) 1023 908 m_b190s601i12 7442 chr4qtel1M 12451 ATGATTGTCAC-GTCAGGAAATTCCGGGATCTTCGTATCTGA----GACC 12495 ii i v - i i---- i ii i ----i i C L3b_3end#LINE 1023 ACAACTCTCACTGTCAGGAAGTTCT----TCCTTATATCTAACCTAAATC 978 chr4qtel1M 12496 CCACGTATCG-AGCTGGATCATCGTTTCCTCTCGTGGACCCATTGGCAAT 12544 v i iii - i vi v -i i i vvvvi v ii iiiv C L3b_3end#LINE 977 CCTCATGCTGCAGTTTAAGC-CCATTTCCTCTTGTTCTGTCCTCAGTGGA 929 chr4qtel1M 12545 GATGGAGAACAGCTGGTCACC 12565 C L3b_3end#LINE 928 GATGGAGAACAGCTGGTCACC 908 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 46.48 CpG sites = 26, Kimura (unadjusted) = 46.48 Transitions / transversions = 2.60 (26/10) Gap_init rate = 0.07 (8 / 114), avg. gap size = 1.38 (11 / 8) 249 20.45 16.67 1.03 chr4qtel1M 12606 12689 (987311) MIRc#SINE/MIR 52 148 (120) m_b190s601i13 7443 chr4qtel1M 12606 CTGGG--CGAGTGCCCGG----GACACTTAGTAGATGTGCAATCCTGGGC 12649 -- - ---- v v v ii i i MIRc#SINE/MIR 52 CTGGGTTCGAGT-CCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGC 100 chr4qtel1M 12650 AAGTCG--------CTCTGAGATTCAGTTTTCTATGCTGACAAATAGG 12689 i-------- vi i vvv vv i MIRc#SINE/MIR 101 AAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 24.03 CpG sites = 8, Kimura (unadjusted) = 24.03 Transitions / transversions = 0.89 (8/9) Gap_init rate = 0.05 (4 / 83), avg. gap size = 3.75 (15 / 4) 13 4.30 3.85 3.85 chr4qtel1M 12934 12959 (987041) (TCCC)n#Simple_repeat 1 26 (0) m_b190s252i13 7444 chr4qtel1M 12934 TCCCTCCCTCCCTCCCCTGCC-CCCTC 12959 - v - (TCCC)n#Simpl 1 TCCCTCCCTCCCT-CCCTCCCTCCCTC 26 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.08 (2 / 25), avg. gap size = 1.00 (2 / 2) 754 35.80 0.87 1.22 chr4qtel1M 13315 13891 (986109) C L1ME4c_3end#LINE/L1 (255) 575 1 m_b190s551i2 7445 chr4qtel1M 13315 TCATCAGTTCTTATAACACAACAGTATTCTATCATAATCATGGACCACAC 13364 i v i v ii vvv i i i iviv?v v i v C L1ME4c_3end#L 575 TTATCATTTTTAATGGCTGCATAATATTCCATCGAGTNGATGTACCATAA 526 chr4qtel1M 13365 CTTGTTTAACCATCCTCCACCTGATAGACATCCCCTCAATTTCTAATTTT 13414 i ii i i vvi v i iivvvivi i C L1ME4c_3end#L 525 TTTACTTAACCATTCCCCTATTGTTGGACATTTAGGTTGTTTCCAATTTT 476 chr4qtel1M 13415 TTGCCTCCACAAAATA--GCTAATATTTATATTTT-GTAGAAATAAGTCC 13461 i ivii i - -- ivv vv i i - iv v i-- i C L1ME4c_3end#L 475 TCGCTATTATAAA-TAACGCTGCAATGAACATCTTCGTGCATATAG--CT 429 chr4qtel1M 13462 TTTTCCTTTTCCTTTAAGAAAAATCTCTTT-GGATATAGACCCAGTTACG 13510 i -- -- vv i i - v vv vvii C L1ME4c_3end#L 428 TTTTCCTTCT--TTT--GAATTATTTCCTTAGGATAAATTCCCAGAAGTG 383 chr4qtel1M 13511 GTATTGCTGAGTAAAAGGGTATACGCAGTTTTATAGCCCTTCAGTCATAA 13560 v i i v ivi v i i v vv i v C L1ME4c_3end#L 382 GAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTCTTGATACGTAT 333 chr4qtel1M 13561 TTCCAAATTGCTCTCCAGCATAGTTGGGTCAGTTTACAACTCTACCAA-G 13609 v i iv vi vii i ?iv i i-i C L1ME4c_3end#L 332 TGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACANTGCCACCAGCA 283 chr4qtel1M 13610 ATGCATTGGGGTGTCAATTTTCCCACATCTTCTCCAAAAGTTTCCATTAT 13659 i vi ? ii i iv i ? i v iv v vvvi C L1ME4c_3end#L 282 ATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGCATTGGGTATTAT 233 chr4qtel1M 13660 CTTTTTTTGTCGCATTACCCAAATTGATAAATGTGAGAAAGTTCCTCAGT 13709 vv vvviiv vv i v i iii i i vi vi v C L1ME4c_3end#L 232 CAATTTTTTAAATTTTTGCTAATTTAATAGGCGTAAAATGGTATCTCATT 183 chr4qtel1M 13710 GTTGTTTTAATTTGCTTTTCTCTAATTAGTACTAATATAGATCATTTTAA 13759 i v i i v vii vi v v vv C L1ME4c_3end#L 182 GTTGCTTTAATTTGCATTTCTTTGATTACTAGCGAGGTTGAACATTTTTC 133 chr4qtel1M 13760 AATATGATTATGGATAGCTTTGGTTTTTCCATCTGAAAACTGCACGTCCA 13809 v i v i vv ivi? vvi iii v ? vi i ivi i C L1ME4c_3end#L 132 CATGTGTTTGTTTACTANTTGTATTTCCTCTTNTGTGAATTGTCTGTTCA 83 chr4qtel1M 13810 TATCCTTTGACCATCTGTTTATTGGAGAATGACTTATATTGTTATAAATT 13859 i v i i i i vv viv ?v v v v C L1ME4c_3end#L 82 TGTCCTTTGCCCATTTATCTATTGGGGTCTTGATNTTTTTCTTATCAATT 33 chr4qtel1M 13860 TGACATACTTTTCTAGATGTTTGAGAAATGAA 13891 vvv vi i i v i? v? v v C L1ME4c_3end#L 32 TGAATGAGCTCTTTATATANTANAGATATTAA 1 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 48.76 CpG sites = 105, Kimura (unadjusted) = 50.90 Transitions / transversions = 1.06 (105/99) Gap_init rate = 0.02 (11 / 576), avg. gap size = 1.09 (12 / 11) 822 32.72 2.19 3.22 chr4qtel1M 13335 13836 (986164) C L1ME5_3end#LINE/L1 (389) 552 56 m_b190s551i3 7445 chr4qtel1M 13335 ACAGTATTCTATCATAATCATGGACCACACCTTGTTTAACCATCCTCCAC 13384 i i i vi ivv vv ii iii v ii vv C L1ME5_3end#LI 552 ATAGTACTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCA 503 chr4qtel1M 13385 CTGATAGACATCCCCTCAATTTCTAATTTTTTGCCTCCACAAAATA-GCT 13433 v i i vvviviii i i iiii v vv - C L1ME5_3end#LI 502 GTGATGGACACCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCT 453 chr4qtel1M 13434 AATATTTATATTTT-GTAGAAATAAGTCCTTTTCCTTTT---CCTTTAAG 13479 ivv vv i ii - ----i v ---- v --- v iv C L1ME5_3end#LI 452 GCAATGAACATCCTCGTA----CATGTCC----CCTTATGGACCTGTGTG 411 chr4qtel1M 13480 AAAAATCTCTTTGG-ATATAGACCCAGTTACGGTATTGCTGAGTAAAAGG 13528 i - i - v vvi v i v v C L1ME5_3end#LI 410 AGAA-TTTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGG 362 chr4qtel1M 13529 GTATACGCAGTTTTATAGCCCTTCAGTCA-TAATTCCAAATTGCTCTCCA 13577 i i vvi ----vi v v v - v v i C L1ME5_3end#LI 361 GTATGCGTATACTTA----ATTTGACTAAGTACTGCCAGATTGCTCTCCA 316 chr4qtel1M 13578 GCATAGTTGGGTCAGTTTACAACTCTACCAAGA-TGCATTGGGGTGTCAA 13626 v i i vii i vii i iv - vi vi v C L1ME5_3end#LI 315 GAATGGCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTA 266 chr4qtel1M 13627 TTTTCCCACATCTTCTCCAAAAGTTTCCATTATCTTTTTTTGTCGCATTA 13676 ? i i v v v vv ivvi v viiv v C L1ME5_3end#LI 265 TNTCCCCACATCCTCGCCAACACTTGGCATTATCCAGCTTTCTAATTTTT 216 chr4qtel1M 13677 CCCAAATTGATAAATGTGAGAAAGTTCCTCAGTGTTGTTTTAATTTGCTT 13726 v ivi i ii i iivii vi v v C L1ME5_3end#LI 215 GCCAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCAT 166 chr4qtel1M 13727 TTCTCTAATTAGTACTAATATAGATCATTTTAAAATATGATTATGGATAG 13776 i v v i vv v v i ivvv v i --- C L1ME5_3end#LI 165 TTCTCTGATTACTAATGAGTTTGAGCATCTCTTCATATGCTTGT---TAG 119 chr4qtel1M 13777 CTTT---GGTTTTTCCATCTGAAAACTGCACGTCCATATCCTTTGACCAT 13823 i --- iii v v i vi i v C L1ME5_3end#LI 118 CCTTTCGGGTTTCCTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCCAT 69 chr4qtel1M 13824 CTGTTTATTGGAG 13836 i v i i C L1ME5_3end#LI 68 TTTTCTATTGGGG 56 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 43.53 CpG sites = 82, Kimura (unadjusted) = 43.90 Transitions / transversions = 1.06 (82/77) Gap_init rate = 0.05 (23 / 501), avg. gap size = 1.17 (27 / 23) 227 36.21 1.20 2.42 chr4qtel1M 14575 14741 (985259) L1MD1_3end#LINE/L1 491 655 (334) m_b190s551i4 7446 chr4qtel1M 14575 GATGCCCATCAATTGGAGAATAGTTGGGTAAATTGTGGTATATGAATGCT 14624 i v iv v i iiii i i vv i i L1MD1_3end#LI 491 GATGTCCTTCAACGGGTGAATGGTTAAACAAACTGTGGTACATCCATACC 540 chr4qtel1M 14625 ATGGAATATTATCGTTCTGTAAGAAATGACCAGCAGGATGATTT-CAGAA 14673 i iivvv vi i ivi v i viv- vi- iv L1MD1_3end#LI 541 ATGGAATACTACTCAGCAATAAAAAGGAACGAACTAT-TGATACACGCAA 589 chr4qtel1M 14674 AGTCCTGGAGAGACTTACATGAACTGATGCTGAGTGAAATGAG-CAGAAC 14722 viv vii ii v vii v v vi - ivv L1MD1_3end#LI 590 CAACCTGGATGAATCTCCAGAGAATTATGCTGAGTGAAAAAAGCCAATCC 639 chr4qtel1M 14723 CAAGAGATCATTATATACT 14741 i ---i i L1MD1_3end#LI 640 CAAAAG---GTTACATACT 655 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 48.91 CpG sites = 34, Kimura (unadjusted) = 51.42 Transitions / transversions = 1.36 (34/25) Gap_init rate = 0.04 (6 / 166), avg. gap size = 1.00 (6 / 6) 298 33.79 0.00 0.69 chr4qtel1M 14576 14721 (985279) L1ME4c_3end#LINE/L1 495 639 (191) m_b190s551i5 7446 chr4qtel1M 14576 ATGCCCATCAATTGGAGAATAGTTGGGTAAATTGTGGTATATGAATGCTA 14625 i v v i i ii i i v? iv v L1ME4c_3end#L 495 ATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGA 544 chr4qtel1M 14626 TGGAATATTATCGTTCTGTAAGAAATGACCAGCAGGATGATTTCAGAAAG 14675 vvvv ii v i iv vi v v i viiv ivi L1ME4c_3end#L 545 TGGAATATTATGCAGCCATTAAAAATGATAATTATGAAGACTATGTAGCA 594 chr4qtel1M 14676 TCCTGGAGAGACTTACATGAACTGATGCTGAGTGAAATGAGCAGAA 14721 v v - i iv vi vv i i i vi L1ME4c_3end#L 595 ACATGGA-AAATGTTTATGATATAATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 46.20 CpG sites = 25, Kimura (unadjusted) = 46.20 Transitions / transversions = 1.04 (25/24) Gap_init rate = 0.01 (1 / 145), avg. gap size = 1.00 (1 / 1) 15 27.69 0.00 0.00 chr4qtel1M 15123 15161 (984839) (AA)n#Simple_repeat 1 39 (0) m_b190s252i14 7447 chr4qtel1M 15123 AATAAAAAAATATACATTTAAAAAAAAAAAGAAAGAAAA 15161 v v v v vvv i i (AA)n#Simple_ 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 39 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 232 27.28 0.00 1.14 chr4qtel1M 16310 16398 (983602) C L3#LINE/CR1 (302) 3797 3710 m_b190s601i14 7448 chr4qtel1M 16310 CATGACCTCCCCTTCAAATCCTTGAAATCACGTCTCCCCCCACCCTCCAG 16359 vv - vi iv vv v vivi v iiiv C L3#LINE/CR1 3797 CATGACAGCCC-TTCAAATATTTGAAGACAGCTATCATGTCTCCTCTAAG 3749 chr4qtel1M 16360 GCTTCTCATCTCCAGACTAAACCTGTCCAGTTCCTTCAA 16398 v v i v vi C L3#LINE/CR1 3748 TCTTCTCTTCTCCAGGCTAAACATCCCCAGTTCCTTCAA 3710 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 33.92 CpG sites = 9, Kimura (unadjusted) = 33.92 Transitions / transversions = 0.60 (9/15) Gap_init rate = 0.01 (1 / 88), avg. gap size = 1.00 (1 / 1) 193 31.37 2.94 0.00 chr4qtel1M 16319 16420 (983580) C L3b_3end#LINE/CR1 (315) 891 787 m_b190s601i15 7448 chr4qtel1M 16319 CCCTTCAAATCCTTGAAATCACGTCTCCCCCCACCCTCCAGGCTTCTCAT 16368 v v iv ?vv v ivvvi ? ii v v C L3b_3end#LINE 891 CCCTTCATATACTTGAAGACNGTTATTAAGTCNCCCCTCAGCCTTCTCTT 842 chr4qtel1M 16369 CTCCAGACTAAACCTGTCCAGTTCCTTCAATGCATTGTCAT---TCCCAT 16415 i i ivvvi i iviv iv --- C L3b_3end#LINE 841 CTCCAGGCTGAATAATCCCAGTTCCTTTAACCTTTCCTCATAGGTCCCAT 792 chr4qtel1M 16416 TATTC 16420 v i C L3b_3end#LINE 791 TTTCC 787 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 41.97 CpG sites = 14, Kimura (unadjusted) = 41.97 Transitions / transversions = 0.78 (14/18) Gap_init rate = 0.01 (1 / 101), avg. gap size = 3.00 (3 / 1) 224 27.53 3.60 11.65 chr4qtel1M 16517 16627 (983373) L2c_3end#LINE/L2 374 476 (2) m_b190s601i16 7449 chr4qtel1M 16517 AGACTGCATACACCTTGGGGG-AGGGGTCATGTTTTTGCCTTTCTTTGTA 16565 iivi v i - ii i i -iiiiv L2c_3end#LINE 374 AGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTT-ATTCATCTTTGTA 422 chr4qtel1M 16566 TCTCCAGGCCTTCTCCAGACACATTCGTATCTGGAACATT---TAAATGT 16612 i ----- v v i - v -----ii ii --- L2c_3end#LINE 423 TCCCCAG-----CGCCTGGCACA-TAGTA-----GGCGCTCAATAAATGT 461 chr4qtel1M 16613 TTGTTGACTGGCTGA 16627 v iv L2c_3end#LINE 462 TTGTTGAATGAATGA 476 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 32.36 CpG sites = 19, Kimura (unadjusted) = 35.65 Transitions / transversions = 2.38 (19/8) Gap_init rate = 0.13 (14 / 110), avg. gap size = 1.14 (16 / 14) 20 41.52 0.00 0.00 chr4qtel1M 16841 16940 (983060) (CAGA)n#Simple_repeat 1 100 (0) m_b190s252i15 7450 chr4qtel1M 16841 CACACAAGCATATAGACAGACCGGCTGGTAGGCGGACAGACAGACAAGCA 16890 v ii v i v i v ii i i ii (CAGA)n#Simpl 1 CAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACA 50 chr4qtel1M 16891 GGCAGATGGGCAGATAGATGTGCTGGCCAACAGACAGACAAGCAGGCAGA 16940 i ii i i iivi v i vi ii i (CAGA)n#Simpl 51 GACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGA 100 Matrix = Unknown Transitions / transversions = 3.29 (23/7) Gap_init rate = 0.00 (0 / 99), avg. gap size = 0.0 (0 / 0) 83 2.38 1.16 0.00 chr4qtel1M 17244 17329 (982671) (TCCT)n#Simple_repeat 1 87 (0) c_b190s251i1 7451 chr4qtel1M 17244 TCCTTCCTTCCTTCCTTCCTTCCTCCCTTCCTCCCTTCC-TCCTTCCTTC 17292 i i - (TCCT)n#Simpl 1 TCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC 50 chr4qtel1M 17293 CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 17329 (TCCT)n#Simpl 51 CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 87 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.01 (1 / 85), avg. gap size = 1.00 (1 / 1) 354 34.69 12.24 0.00 chr4qtel1M 17806 18001 (981999) MIRc#SINE/MIR 48 267 (1) m_b190s601i17 7452 chr4qtel1M 17806 AGGCCTGAGTTCAGATCCT--CCCTAGCCCCTGCCAGTTGTATAAAGCTG 17853 i i iii i-- i iv v i i i i i i vvi MIRc#SINE/MIR 48 AGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTG 97 chr4qtel1M 17854 GGTAAGTCAGCTAATCTGTCT--TCCTCGGTTCCCCCAAGTGTAAAG--- 17898 i vi i v --v i i i vv i--- MIRc#SINE/MIR 98 GGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGG 147 chr4qtel1M 17899 ----------ACCCGC---ACCAACATCCCAGA---CTTGTGAGGATCTA 17932 ---------- i ---i v v v i---v v MIRc#SINE/MIR 148 GGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAA 197 chr4qtel1M 17933 CTGAGATTATATTTGT-ACAATATTTTGCAAGGCCAAAAAGGCCATATGA 17981 v v i v - v iiii i ivivv iv i ii MIRc#SINE/MIR 198 ATGAGATAATGTATGTGAAAGCGCTTTGTAAACTGTAAAGTGCTATACAA 247 chr4qtel1M 17982 GCACTAACTCTTATTACTAT 18001 iiiiv iv?v i MIRc#SINE/MIR 248 ATGTAAGGNGTTATTATTAT 267 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 46.29 CpG sites = 43, Kimura (unadjusted) = 49.52 Transitions / transversions = 1.72 (43/25) Gap_init rate = 0.04 (7 / 195), avg. gap size = 3.43 (24 / 7) 22 22.92 0.00 0.00 chr4qtel1M 19039 19084 (980916) (C)n#Simple_repeat 1 46 (0) m_b190s252i16 7453 chr4qtel1M 19039 CCCCCCCTGCACCTACCCCCTCCCCCCCCCCCCCCACCTCCCCTCC 19084 iv v iv i v i i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 46 Matrix = Unknown Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 22 21.54 3.03 1.49 chr4qtel1M 19041 19106 (980894) (CCCCCT)n#Simple_repeat 1 67 (0) m_b190s252i17 7453 chr4qtel1M 19041 CCCCCTGCACCTACCCCCTCCCCCCCCCCCCCCACCT-CCCCTCCTGC-A 19088 v v - i i v - iv -v (CCCCCT)n#Sim 1 CCCCCTCCCCCT-CCCCCTCCCCCTCCCCCTCCCCCTCCCCCTCCCCCTC 49 chr4qtel1M 19089 CCTCTCACTCTCCCCGTC 19106 i v i v (CCCCCT)n#Sim 50 CCCCTCCCCCTCCCCCTC 67 Matrix = Unknown Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.05 (3 / 65), avg. gap size = 1.00 (3 / 3) 136 11.89 0.00 0.47 chr4qtel1M 19538 19749 (980251) (CACACA)n#Simple_repeat 1 211 (0) m_b190s252i18 7454 chr4qtel1M 19538 CACTCACACAGACACACACACTCACACAGACACATATACTGACACAGACA 19587 v v v v i i vv v (CACACA)n#Sim 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 chr4qtel1M 19588 CACACACACAGACACACACACTCACACAGACACACACACTCACACAGACA 19637 v v v v v (CACACA)n#Sim 51 CACACACACACACACACACACACACACACACACACACACACACACACACA 100 chr4qtel1M 19638 CACACACAGACACACACTCACACAGACACATACACTGACACACACACACT 19687 v v v i vv v (CACACA)n#Sim 101 CACACACACACACACACACACACACACACACACACACACACACACACACA 150 chr4qtel1M 19688 CACACACACACTCACACACACACACACACACACACACACACACACACAAA 19737 v v (CACACA)n#Sim 151 CACACACACACACACACACACACACACACACACACACACACACACACACA 200 chr4qtel1M 19738 CACAGCACACAC 19749 - (CACACA)n#Sim 201 CACA-CACACAC 211 Matrix = Unknown Transitions / transversions = 0.15 (3/20) Gap_init rate = 0.00 (1 / 211), avg. gap size = 1.00 (1 / 1) 255 21.05 20.00 0.00 chr4qtel1M 20546 20640 (979360) C MIR3#SINE/MIR (7) 201 88 m_b190s601i18 7455 chr4qtel1M 20546 AGGATCATAGAG---CAGAG----GAGGGAGCCCAGATGTCCTGCAGTCC 20588 i i--- ----i v ii vi v vi C MIR3#SINE/MIR 201 AGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCC 152 chr4qtel1M 20589 A----CCTCA-----CAGATGAATACACTGAGGTCCAGGGTTGTGAAATG 20629 ---- ----- iv v i i vv i C MIR3#SINE/MIR 151 AACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTG 102 chr4qtel1M 20630 ACT---CCCAGGTC 20640 --- v C MIR3#SINE/MIR 101 ACTTGCCCAAGGTC 88 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 25.00 CpG sites = 11, Kimura (unadjusted) = 25.00 Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.05 (5 / 94), avg. gap size = 3.80 (19 / 5) 16 8.18 0.00 0.00 chr4qtel1M 20714 20739 (979261) (AGGGC)n#Simple_repeat 1 26 (0) m_b190s252i19 7456 chr4qtel1M 20714 AGGGCCGGCCAGGGCAGGGCAGGGCA 20739 v v (AGGGC)n#Simp 1 AGGGCAGGGCAGGGCAGGGCAGGGCA 26 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 232 29.69 1.56 0.00 chr4qtel1M 21135 21198 (978802) MIRb#SINE/MIR 107 171 (97) m_b190s601i20 7457 chr4qtel1M 21135 TCACTCAGCCCATGGGAGCCTTGGTTTCTTCATCCATAAAGTGGGGTTAA 21184 i i i iv vv ii i ii i v MIRb#SINE/MIR 107 TTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAA 156 chr4qtel1M 21185 CAGCAGCC-CCTCGC 21198 i ii v i- MIRb#SINE/MIR 157 TAATACCTACCTCGC 171 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 40.49 CpG sites = 14, Kimura (unadjusted) = 40.49 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.02 (1 / 63), avg. gap size = 1.00 (1 / 1) 236 26.92 0.00 0.00 chr4qtel1M 21135 21186 (978814) MIRc#SINE/MIR 104 155 (113) m_b190s601i19 7457 chr4qtel1M 21135 TCACTCAGCCCATGGGAGCCTTGGTTTCTTCATCCATAAAGTGGGGTTAA 21184 i i iv vv ii i ii i v MIRc#SINE/MIR 104 TCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAA 153 chr4qtel1M 21185 CA 21186 i MIRc#SINE/MIR 154 TA 155 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 35.13 CpG sites = 10, Kimura (unadjusted) = 35.13 Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 60 7.67 0.98 3.00 chr4qtel1M 21682 21783 (978217) (CACTCA)n#Simple_repeat 1 100 (0) c_b190s251i2 7458 chr4qtel1M 21682 CACTCACACTCACACTCACACACACTCACTCATACACACAATCACACTCA 21731 v -- i v v (CACTCA)n#Sim 1 CACTCACACTCACACTCACACTCA--CACTCACACTCACACTCACACTCA 48 chr4qtel1M 21732 CACTCACACACACTCTCACA-TACACACTCACACTCACACTCACTCTCAC 21780 v v - - v (CACTCA)n#Sim 49 CACTCACACTCACACTCACACT-CACACTCACACTCACACTCACACTCAC 97 chr4qtel1M 21781 ACT 21783 (CACTCA)n#Sim 98 ACT 100 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.04 (4 / 101), avg. gap size = 1.00 (4 / 4) 243 34.41 2.86 6.70 chr4qtel1M 22486 23429 (976571) L1M2_orf2#LINE/L1 2382 3291 (0) m_b190s551i6 7459 chr4qtel1M 22486 CACAGATAAGTCTAAAAAAAATCAGGTGCTCATGAGCAGACCGAGCTAAT 22535 i ? i v-i i v vvi iiiv ivv ii L1M2_orf2#LIN 2382 CACAAANAAATG-GAAAGATATCCCATGCTCATGGATTGGAAGAATTAAT 2430 chr4qtel1M 22536 ATCATAAAAATGACAATTCTACCTAAATCGGTCCAGTTGCTCAGTACGTC 22585 ii v ? v v i v i i ------ - i- L1M2_orf2#LIN 2431 ATTGTTAAAATGNCCATACTACCCAAAGCGATCTA------CAG-AT-TC 2472 chr4qtel1M 22586 GGTGACATAACAATCAAACTGCCCA-AATATTATTTTATGAAATGAGGAA 22634 ii vv vv v v i v -i i v ivvv - i L1M2_orf2#LIN 2473 AATGCAATCCCTATCAAAATACCAATGACATTCTTCACAGAAAT-AGAAA 2521 chr4qtel1M 22635 AAGTAATAACAAAATTCTTCTGGAAGAACAAAAAGTCAAGATTATCAAGA 22684 i? vvi v v vv iii vv v v v i L1M2_orf2#LIN 2522 AAANAATCCTAAAATTCGTATGGAACCACAAAAGACCCCGAATAGCCAAA 2571 chr4qtel1M 22685 GAATTAATGAG-AAAAAATACAAAGGAGGGGGGCTTAGGAGTACCAGACC 22733 v v vv - iv vv i vv i -v v v i L1M2_orf2#LIN 2572 GCAATCCTGAGCAAAAAGAACAAAGCTGGAGGCATCA-CACTACCTGACT 2620 chr4qtel1M 22734 TAAAACTCTATTCCAAAGC---AGCAGCCCCAA-AGCC--GTACTGGCTA 22777 v v v i v --- i i vv - v-- vv L1M2_orf2#LIN 2621 TCAAAATATACTACAAAGCTATAGTAACCAAAACAGCATGGTACTGGCAT 2670 chr4qtel1M 22778 AGAAACAG-CG-ATGGATCCGTGGAATAGCTTAGATACACATGACAAT-A 22824 i - i- i i vi i vv v - viiiv - L1M2_orf2#LIN 2671 AAAAACAGACACATAGACCAATGGAACAGAATAGAGA-ACCCAGAAATAA 2719 chr4qtel1M 22825 ATCAAGGC--CCACAGTAATCTAGTATTTGCTAAAG--CCCGAGCTCCAG 22870 v v --ii iv v ii v i vi --v i v-v v L1M2_orf2#LIN 2720 ATCCACGCATTTACAGCCAACTGATTTTCGACAAAGGCGCCAAGA-ACAT 2768 chr4qtel1M 22871 CTGCTGGAATAAGAACTCACTATTTGACAAACATTGCCAGGAAAACCGGA 22920 vii? iiv i vvv v ii i iiv ii i L1M2_orf2#LIN 2769 ACANTGGGGAAAGGACAGTCTCTTCAATAAATGGTGCTGGGAAAACTGGA 2818 chr4qtel1M 22921 AAAGAAGACGTCAGACACTTGACATTA-ACCTACATCTCATACCCCAGGC 22969 v vvv v i - vivv v i - ivi vi vi vi- L1M2_orf2#LIN 2819 TATCCATATG-CAGAAGAATGAAACTAGACCCCTATCTCTCACCATATA- 2866 chr4qtel1M 22970 CCAAAATAAGGTCAAAACGGGTACATGATTTGGGTCTAAAGGGGGATATC 23019 v v iv i i vv v i iii v iivvv v ii L1M2_orf2#LIN 2867 CAAAAATCAACTCAAAATGGATTAAAGACTTAAATGTAAGACCCGAAACT 2916 chr4qtel1M 23020 ATAAGCAAATTAGGAGAGAAAATTAGCATAAACAAATCAGGAGACCTGTC 23069 ivvv i i i v - viv ivv v iiv L1M2_orf2#LIN 2917 ATAAAACTACTAGAAGAAAACA-TAGGGGAAACGCTTCAGGACATTGGTC 2965 chr4qtel1M 23070 AGATCTTTGGAGAAGGGAAGAATTTATGATCAAGAAGACCCAAAAAACAT 23119 ------- iv ---- v v i?i--- iv i i L1M2_orf2#LIN 2966 -------TGGGCA----AAGATTTTTTGGNT---AAGACCTCAAAAGCAC 3001 chr4qtel1M 23120 TGTG----AAATGC-AAAACAGACAACTTGGGCTACGTCAAATTTAAAAA 23164 v - ---- v - i v v ii i -i L1M2_orf2#LIN 3002 AG-GCAACAAAAGCAAAAATAGACAAATGGGATTACATCAAA-CTAAAAA 3049 chr4qtel1M 23165 GGTTCATACA-AACAAAACCAAC-ACAAACAAGATGAAAAGGGAA-GTAC 23211 v - i - i ivv - iv iii i iv -v L1M2_orf2#LIN 3050 GCTTC-TGCACAGCAAAGGAAACAATCAACAGAGTGAAGAGACAACCTAC 3098 chr4qtel1M 23212 AAAACTGGGAAACAATTTTTATAGCCAGTAGTTCTGATAAAGGCCTCATT 23261 i - i v v ii iv vi ?vv i i vi v v L1M2_orf2#LIN 3099 AGAA-TGGGAGAAAATATTTGCAAACTATNCATCTGACAAGGGATTAATA 3147 chr4qtel1M 23262 TCTAAAATATAGTTTTATTTTATAAATAAAATTATATATATACATATTTA 23311 i i ----------- --ii i -----i v vv iv L1M2_orf2#LIN 3148 TCCAGAATA-----------TATAA--GGAACT-----CAAACAACTCAA 3179 chr4qtel1M 23312 TATTTATAAGGATACAAGTCATTCCCCAATTGATAAACCGTTAAAGGATA 23361 i ---ii ii v i v --- i ? v iv vi iv L1M2_orf2#LIN 3180 CA---GCAAAAAAACAAATAAT---CCGATTNAAAAATGGGCAAAGGACC 3223 chr4qtel1M 23362 TGAACAGACAATTTTCAGATGACGAAATGAAA---GCCATTTCTAGTCAC 23408 i v i i v v v iv --- ---vi vi i L1M2_orf2#LIN 3224 TGAATAGACATTTCTCAAAAGAAGACATACAAATGGCCA---ACAGGTAT 3270 chr4qtel1M 23409 ATGAAAAGATAATCTAAATCA 23429 i iv v v L1M2_orf2#LIN 3271 ATGAAAAAATGCTCAACATCA 3291 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 46.48 CpG sites = 149, Kimura (unadjusted) = 47.11 Transitions / transversions = 0.97 (149/154) Gap_init rate = 0.08 (78 / 943), avg. gap size = 1.13 (88 / 78) 596 32.26 0.36 0.36 chr4qtel1M 23292 23571 (976429) L1ME4c_3end#LINE/L1 12 291 (539) m_b190s551i7 7459 chr4qtel1M 23292 ATTATATATATA-CATATTTATATTTATAAGGATACAAGTCATTCCCCAA 23340 ? v v - vi i v v i v v? viv vv L1ME4c_3end#L 12 ANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAAGACCCCAA 61 chr4qtel1M 23341 TTGATAAACCGTTAAAGGATATGAACAGACAATTTTCAGATGACGAAATG 23390 v iv vi i iv ? v v i L1ME4c_3end#L 62 TAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAGGAAATA 111 chr4qtel1M 23391 AAAGCCATTTCTAGTCACATGAAAAGATAATCTAAATCAGTATTGATCAG 23440 v ?ivi vvvi iv i i iv v vv iv v i i L1ME4c_3end#L 112 CAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTAGTAATCAA 161 chr4qtel1M 23441 AGAAATGCAAATTAAGACAACTCTGAGGTATCACCTCACACCTCTCCGAT 23490 ii vv i i ii i i v ivi L1ME4c_3end#L 162 AGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCTATTAAAT 211 chr4qtel1M 23491 TGGCTAAAATGACAGGGAAAGACAATGATAAATGCTGGAGGGGATGTGGG 23540 i v vvv iii vv i iviv v i ? i v L1ME4c_3end#L 212 TAGCAAAAATTTAAAAAATTGATAATACCCAATGCTGGCGAGGNTGCGGT 261 chr4qtel1M 23541 AAAAGAGGGACACTGGCCGCATTGTTGGTGG 23571 i vv v ? vi-ii i L1ME4c_3end#L 262 GAAACTGGTACNCTCA-TACATTGCTGGTGG 291 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 42.05 CpG sites = 43, Kimura (unadjusted) = 43.94 Transitions / transversions = 0.91 (43/47) Gap_init rate = 0.01 (2 / 279), avg. gap size = 1.00 (2 / 2) 816 24.78 0.84 1.27 chr4qtel1M 23335 23571 (976429) L1ME5_3end#LINE/L1 56 291 (650) m_b190s551i8 7459 chr4qtel1M 23335 CCCCAATTGATAAACCGTTAAAGGATATGAACAGACAATTTTCAGATGAC 23384 v v iv vi i v v v L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chr4qtel1M 23385 GAAA--TGAAAGCCATTTCTAGTCACATGAAAAGATAATCTAAATCAGTA 23432 --i v - vv v - i i iv v v v L1ME5_3end#LI 106 GAAACCCGAAAGGC-TAACAAG-CATATGAAGAGATGCTCAAACTCATTA 153 chr4qtel1M 23433 TTGATCAGAGAAATGCAAATTAAGACAACTCTGAGGTATCACCTCACACC 23482 v i i vv i i i L1ME5_3end#LI 154 GTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACC 203 chr4qtel1M 23483 TCTCCGATTGGCTAAAATGACAGGGAAAGACAATGATAAATGCTGGAGGG 23532 v iv i v v v ii vvi i vi i i v i L1ME5_3end#LI 204 TATTAGACTGGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTGGCGAG 253 chr4qtel1M 23533 GATGTGGGAAAAGAGGGACACTGGCCGCATTGTTGGTGG 23571 i ? v i v vi-i i i L1ME5_3end#LI 254 GATGTGGGGANATAGGAACCCTCA-TGCACTGCTGGTGG 291 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 29.87 CpG sites = 28, Kimura (unadjusted) = 30.47 Transitions / transversions = 0.93 (28/30) Gap_init rate = 0.02 (4 / 236), avg. gap size = 1.25 (5 / 4) 22 10.38 0.00 0.00 chr4qtel1M 23574 23605 (976395) (T)n#Simple_repeat 1 32 (0) m_b190s252i20 7460 chr4qtel1M 23574 TTCTTTTTTTTTTTTTTTTTTCCTTTTTTTTT 23605 i ii (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 32 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 794 33.14 1.16 1.45 chr4qtel1M 24072 24417 (975583) C L1ME4c_3end#LINE/L1 (191) 639 295 m_b190s551i9 7461 chr4qtel1M 24072 TCCTGCTCATTTCACTCAGCATCAGTTCGTGTAAGTCTCTCCAGGCCTTT 24121 i iv i i i vv i iv vi i - v iivi C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATAAACATTT-TCCATGTTGCT 591 chr4qtel1M 24122 CTGAAATCATCCTGTTGGTCATTTCTTACAGA-ACAGTAATATTCCATAA 24170 viiv i v v iv vi i v ii v-i - vi C L1ME4c_3end#L 590 ACATAGTCTTCATAATTATCATTTTTAATGGCTGCA-TAATATTCCATCG 542 chr4qtel1M 24171 TTTTCATATACCACAATTTATTCAGCCATTCTCCAACTGATGGACATCCA 24220 vv ?v i i i i i i v i v ii C L1ME4c_3end#L 541 AGTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTA 492 chr4qtel1M 24221 TTCAGTTTCCAGTTTTTAGCCACTACAAAAAGGGCTGCCACAAACATTCG 24270 vviv i v i i i v iv v ii iiv C L1ME4c_3end#L 491 GGTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTT 442 chr4qtel1M 24271 TGCACATACAGGTCCCTTTCCCTTCTTT---ATAATCTCTTTGGGATATA 24317 i ii i --- i i --- v i i i v C L1ME4c_3end#L 441 CGTGCATATAG---CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAA 395 chr4qtel1M 24318 ATCCCAGTAGTAACACTCCTGGATCAAAGGGTATGCACAGTTTGATAACT 24367 v v iiv i v i v v v ii C L1ME4c_3end#L 394 TTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCT 345 chr4qtel1M 24368 TTTTGAGCATAGTTCCAAGCTACTCTCCAAAATGGTTGGATTCGTTCACA 24417 i vivi i v v ii i i v v iivi i C L1ME4c_3end#L 344 CTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACA 295 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 44.02 CpG sites = 68, Kimura (unadjusted) = 45.69 Transitions / transversions = 1.51 (68/45) Gap_init rate = 0.02 (7 / 345), avg. gap size = 1.29 (9 / 7) 599 33.67 4.43 2.56 chr4qtel1M 24405 24788 (975212) L1ME3G_3end#LINE/L1 263 653 (271) m_b190s551i10 7459 chr4qtel1M 24405 GGATTCGTTCACA-ACTGTTGGTGGAGTTCTGAAATGATCCAGCCCTTAT 24453 i v vi i - i iiv v i v i v ? v L1ME3G_3end#L 263 GGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTACAGCCNTTTT 312 chr4qtel1M 24454 GGGGAGTGATCTGGAATTGTGTCCA--AAGGGCAATAAAACTGTGCATAC 24501 i i ii i v -- i i -- i--- v v v i L1ME3G_3end#L 313 GGAGGGCAATTTGGCA--GTATCTATTAAA---ATTTAAAATGCGCATAC 357 chr4qtel1M 24502 CCTTTGACCCAGCAGTGCCATTACTGGGTCTGCATCCCAAGGAAA---TC 24548 i v i v ? ?v vi i ?i --- L1ME3G_3end#L 358 CCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAGAAATACTC 407 chr4qtel1M 24549 ATAAAGGAGGGAAAAGGACCCAGGTGAGCAAAACTGTTTGTAGCAGC--T 24596 ii v v -v v v ?v v --i iiv ii v -- L1ME3G_3end#L 408 GCACATG-TGCACAAGGANGCATGT--ACAAGGATGTTCATTGCAGCATT 454 chr4qtel1M 24597 CTTTGTGGTGGCAAAGAACTGGAAAAGGAGTGGATATCTATCGACTGGGG 24646 v ii i i i i viivv ii i i i iv L1ME3G_3end#L 455 GTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCAATAGGGG 504 chr4qtel1M 24647 AATGGCTGAACAAGCTGTGATACATGAAGGTAATGGACTATTAT-----T 24691 i i i ii i i i vv viiv v i -----? L1ME3G_3end#L 505 AATGGTTAAATAAATTATGGTATATCCATACTATGGAATACTATGCAGCN 554 chr4qtel1M 24692 GTTCTATAAAACG-GGCTGATCTG---AGAAAGGCCTGGAGAGATTTACA 24737 vv v i i - iv i---iv vv i v i i v L1ME3G_3end#L 555 GTTAAAAAGAATGAGGTAGATCTATATGTACTGACATGGAAAGATCTCCA 604 chr4qtel1M 24738 CAAACTGATGCTGAGCACAACAAGCAGGACCCGGAATACAGTGCACACAG 24787 vi vv iv i iiv v i viv i -- ii i ii L1ME3G_3end#L 605 AGACATATTGTTGAGTGAAAAAAGCAAGTTGCAGA--ACGATACGTACAG 652 chr4qtel1M 24788 T 24788 L1ME3G_3end#L 653 T 653 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 44.99 CpG sites = 75, Kimura (unadjusted) = 47.62 Transitions / transversions = 1.47 (75/51) Gap_init rate = 0.04 (17 / 383), avg. gap size = 1.59 (27 / 17) 766 32.15 1.75 0.69 chr4qtel1M 24406 24690 (975310) L1ME4c_3end#LINE/L1 268 555 (275) m_b190s551i11 7459 chr4qtel1M 24406 GATTCGTTCACA-ACTGTTGGTGGAGTTCTGAAATGATCCAGCCCTTATG 24454 i v ?i i - i i vi? v i v i v i v L1ME4c_3end#L 268 GGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTG 317 chr4qtel1M 24455 GGGAGTGATCTGGAATTGTGTCCAAAGGGCAATAAAACTGTGCATACCCT 24504 ii ii i v v ii viv i v v v L1ME4c_3end#L 318 GAAAGCAATTTGGCAATACGTATCAAGAGCCATAAAAATGTTCATACCCT 367 chr4qtel1M 24505 TTGACCCAGCAGTGCCATTACTGGGTCTGCATCCCAAGGAAATCAT--AA 24552 i i v i v vv vi i v -- L1ME4c_3end#L 368 TTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAA 417 chr4qtel1M 24553 AGGAGGGAAAAGGACCCAGGTGAGCAAAACTGTTTGTAGCAGC--TCTTT 24600 i i i -- i vi vi i iv ii v -- v L1ME4c_3end#L 418 AAGAAGGAAAAAG--CTATATGCACGAAGATGTTCATTGCAGCGTTATTT 465 chr4qtel1M 24601 GTGGTGGCAAAGAACTGGAAAAGGAGTGGATATCTATCGACTGGGGAATG 24650 i ii i i i i viivv ii i i v i iv L1ME4c_3end#L 466 ATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAATG 515 chr4qtel1M 24651 GCTGAACAAGCTGTGATACATGAAGGTAATGGACTATTAT 24690 i i ii ii i i v? vvii v L1ME4c_3end#L 516 GTTAAGTAAATTATGGTACATCNACTCGATGGAATATTAT 555 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 41.95 CpG sites = 58, Kimura (unadjusted) = 44.70 Transitions / transversions = 1.76 (58/33) Gap_init rate = 0.02 (5 / 284), avg. gap size = 1.40 (7 / 5) 13 18.22 0.00 0.00 chr4qtel1M 25041 25071 (974929) (ATAAAA)n#Simple_repeat 1 31 (0) m_b190s252i21 7462 chr4qtel1M 25041 ATAACCATAAAAATAAAGAAAACAATAAAAA 25071 vv i v v (ATAAAA)n#Sim 1 ATAAAAATAAAAATAAAAATAAAAATAAAAA 31 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 52 3.30 1.56 1.56 chr4qtel1M 30274 30337 (969663) (GCCTCCT)n#Simple_repeat 1 64 (0) c_b190s251i3 7463 chr4qtel1M 30274 GCCTCCTGCCGCCTGCCTCCTAACC-CCTGCCTCCTGCCTCCTGCCTCCT 30322 v -i - (GCCTCCT)n#Si 1 GCCTCCTGCCTCCTGCCTCCT-GCCTCCTGCCTCCTGCCTCCTGCCTCCT 49 chr4qtel1M 30323 GCCTCCTGCCTCCTG 30337 (GCCTCCT)n#Si 50 GCCTCCTGCCTCCTG 64 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.03 (2 / 63), avg. gap size = 1.00 (2 / 2) 321 10.25 0.39 2.57 chr4qtel1M 30795 31311 (968689) (AGGA)n#Simple_repeat 1 506 (0) m_b190s252i22 7464 chr4qtel1M 30795 AGGAAGGGAGGAAGGAAGGGAGGGAGAAAACAAGGGAGGGAAAAAGGAGG 30844 i i i i iv i i ii i (AGGA)n#Simpl 1 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG 50 chr4qtel1M 30845 GAGGAAAAGAGAGAGGGAGAGAAGGAAGGAAGGAAGGAAAGGAAGGAAGG 30894 i i i ii i ii - (AGGA)n#Simpl 51 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG-AAGGAAGGAAGG 99 chr4qtel1M 30895 AAGGAAGGAAGGAAGGAAGGAAAGAAGGAAGGAAGGAAGGAAGGAAGGAA 30944 i (AGGA)n#Simpl 100 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 149 chr4qtel1M 30945 GGAAGGAAGGAAGGAGAGAAAGGAAGGAAGGAGAGGAAGGAAGGAAGGAG 30994 - i - - (AGGA)n#Simpl 150 GGAAGGAAGGAAGGA-AGGAAGGAAGGAAGGA-AGGAAGGAAGGAAGGA- 196 chr4qtel1M 30995 AGAAAGGAAGGAAGGAAGGAGAGAAAGGAAGGAAGGAAGGAGAGAAAGGA 31044 i - i - i (AGGA)n#Simpl 197 AGGAAGGAAGGAAGGAAGGA-AGGAAGGAAGGAAGGAAGGA-AGGAAGGA 244 chr4qtel1M 31045 AGGAA-AAAGGAAAGGAAGGAAGGAAGGAAAGGAAGGAAGGAAGGAAGGA 31093 -i - - (AGGA)n#Simpl 245 AGGAAGGAAGG-AAGGAAGGAAGGAAGG-AAGGAAGGAAGGAAGGAAGGA 292 chr4qtel1M 31094 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG 31143 (AGGA)n#Simpl 293 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG 342 chr4qtel1M 31144 GAAGGAGAGAAAGGAAGGAAGGAGAGGAAGGAAGGAAGGAGAGAAAGGAA 31193 - i - - i (AGGA)n#Simpl 343 GAAGGA-AGGAAGGAAGGAAGGA-AGGAAGGAAGGAAGGA-AGGAAGGAA 389 chr4qtel1M 31194 GGAAGGAAGGGAGGGAGGGAGGGAGGAGAGAAAGGAAGGAAGAGAGGGAG 31243 i i i i - i ii i (AGGA)n#Simpl 390 GGAAGGAAGGAAGGAAGGAAGGAAGGA-AGGAAGGAAGGAAGGAAGGAAG 438 chr4qtel1M 31244 GGAGGGAGGGAGGAAGGGAGGAAGGAAGGAAGAGAGGGAGGGAAGG-AGG 31292 i i i i - i i - (AGGA)n#Simpl 439 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG-GAAGGAAGGAAGGAAGG 487 chr4qtel1M 31293 ACAGAAGGAAGCAGGCAAG 31311 vi v i v (AGGA)n#Simpl 488 AAGGAAGGAAGGAAGGAAG 506 Matrix = Unknown Transitions / transversions = 10.50 (42/4) Gap_init rate = 0.03 (15 / 516), avg. gap size = 1.00 (15 / 15) 21 25.24 0.00 0.00 chr4qtel1M 31796 31851 (968149) (AAAA)n#Simple_repeat 1 56 (0) m_b190s252i24 7465 chr4qtel1M 31796 AAAAATAAAAAGCTTTAATAAAGAAAAAAAGAAAGTAAAATAAAAAAAAA 31845 v ivvvv v i i iv v (AAAA)n#Simpl 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr4qtel1M 31846 AAAAAA 31851 (AAAA)n#Simpl 51 AAAAAA 56 Matrix = Unknown Transitions / transversions = 0.50 (4/8) Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0) 38 0.00 0.00 0.00 chr4qtel1M 32098 32132 (967868) (C)n#Simple_repeat 1 35 (0) c_b190s251i4 7466 chr4qtel1M 32098 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 32132 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 35 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 35 27.92 5.08 2.76 chr4qtel1M 32918 33094 (966906) (TCCT)n#Simple_repeat 1 181 (0) m_b190s252i25 7467 chr4qtel1M 32918 TCCCTCCCTCCTGTCCCTCTGTTCC--CCCTCCCT-CTTCCTTCCTTCCC 32964 i i - i -v -- i i - i (TCCT)n#Simpl 1 TCCTTCCTTCCT-TCCTTC-CTTCCTTCCTTCCTTCCTTCCTTCCTTCCT 48 chr4qtel1M 32965 TCCCT-CTTCCCTCCTTCCCTCCCTCCCTCC-TCTCTGCTTCCTTTC-TC 33011 i - i i i i - ii v i - (TCCT)n#Simpl 49 TCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC 98 chr4qtel1M 33012 TTTCTTTTATTTCTT-TTCCCTTCTTTTCCTTTCTTTCCTACATT--TTC 33058 i i iv i -i i -i - i v v -- (TCCT)n#Simpl 99 CTTCCTTCCTTCCTTCCTTCCTTC-CTTCC-TTCCTTCCTTCCTTCCTTC 146 chr4qtel1M 33059 TTTGTTTACTACCTAGTTTCTTTTCTTGCTTCACTT 33094 i vi v v vvi i i v - (TCCT)n#Simpl 147 CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC-CTT 181 Matrix = Unknown Transitions / transversions = 2.45 (27/11) Gap_init rate = 0.07 (12 / 176), avg. gap size = 1.17 (14 / 12) 16 9.55 0.00 0.00 chr4qtel1M 38796 38818 (961182) (AC)n#Simple_repeat 1 23 (0) m_b191s252i0 7468 chr4qtel1M 38796 ACACACACGCACGCACACACACA 38818 i i (AC)n#Simple_ 1 ACACACACACACACACACACACA 23 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 26 27.53 0.00 1.27 chr4qtel1M 38897 38976 (961024) (GAGA)n#Simple_repeat 1 79 (0) m_b191s252i2 7469 chr4qtel1M 38897 GAGAAAGAGAGATGAGTGAGAGACATACAGAGACAGAAACAGAGACACAG 38946 i - v v v v v i v v v (GAGA)n#Simpl 1 GAGAGAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 49 chr4qtel1M 38947 AGACAGAGACAGACAAAAAGGTAGATAGAG 38976 v v v i i iv v (GAGA)n#Simpl 50 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 79 Matrix = Unknown Transitions / transversions = 0.38 (5/13) Gap_init rate = 0.01 (1 / 79), avg. gap size = 1.00 (1 / 1) 334 32.95 3.01 4.91 chr4qtel1M 38979 39144 (960856) C L2b_3end#LINE/L2 (19) 447 285 m_b191s601i0 7470 chr4qtel1M 38979 ATTTACTAAGCATTTCGTATGTGCCAGGTTTTATGCTAAGTGCT-GGGAT 39027 i iii vv i i?i i i i - C L2b_3end#LINE 447 ATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGGGAT 398 chr4qtel1M 39028 ACAAATATCAACAA-ATGG---CAGCATCTGTCCTCAGGGGGCTTCCATT 39073 ivvi v - ii --- i ivi i v i iv v C L2b_3end#LINE 397 ACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGGAGCTCACAGT 348 chr4qtel1M 39074 CCCACAGGAAAGACCACACAAGACATAGACTTGGGAAGGGGCAAGACAGA 39123 iviii ii ------ iv v?ii iv iv?ii vv C L2b_3end#LINE 347 CTAGTGGGGGAGAC------AGACATGTAANCAGACAATNATAACCCAGA 304 chr4qtel1M 39124 GTGGTCAGAGTTTGAGCTGGG 39144 - i vv - C L2b_3end#LINE 303 GTGG-CAGGGTAGGA-CTGGG 285 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 43.31 CpG sites = 34, Kimura (unadjusted) = 47.07 Transitions / transversions = 1.89 (34/18) Gap_init rate = 0.07 (11 / 165), avg. gap size = 1.18 (13 / 11) 279 29.54 12.50 2.13 chr4qtel1M 39327 39454 (960546) MIRc#SINE/MIR 9 149 (119) m_b191s601i1 7471 chr4qtel1M 39327 TGTGGGGGAGCCAGATAAAGTTTTGGACTTGGAGTCAAGAAGGCCTGAGT 39376 v v i-i v i ivi i i i MIRc#SINE/MIR 9 TGTGGTGCAGT-GGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGT 57 chr4qtel1M 39377 TTGAATCCTACCACAGAGAC--AC-AGCTA-------------AAGTCAC 39410 i i iiv v v vv -- - i------------- -- MIRc#SINE/MIR 58 TCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGT--C 105 chr4qtel1M 39411 ACCTGGTCTCTACCTTCCTCAGTTTGCTTGTCTGTAAAATAAAG 39454 i iii vivvv v ii iii MIRc#SINE/MIR 106 ACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGG 149 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 36.20 CpG sites = 23, Kimura (unadjusted) = 39.04 Transitions / transversions = 1.64 (23/14) Gap_init rate = 0.05 (6 / 127), avg. gap size = 3.17 (19 / 6) 37 11.60 2.33 1.15 chr4qtel1M 39544 39629 (960371) (CAT)n#Simple_repeat 1 87 (0) c_b191s251i0 7472 chr4qtel1M 39544 CATCATCAACATCATCCTCACCATCATCATCATCA-CTATCATTATCATC 39592 v v i - - i (CAT)n#Simple 1 CATCATCATCATCATCATCATCATCATCATCATCATC-ATCATCATCATC 49 chr4qtel1M 39593 ACCATCATCTTCACCATCATTATCAACATC-TCATCAT 39629 i v i i v - (CAT)n#Simple 50 ATCATCATCATCATCATCATCATCATCATCATCATCAT 87 Matrix = Unknown Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.04 (3 / 85), avg. gap size = 1.00 (3 / 3) 572 25.20 1.42 0.35 chr4qtel1M 39659 41071 (958929) (TCA)n#Simple_repeat 1 1428 (0) m_b191s252i3 7473 chr4qtel1M 39659 TCATCATCCCCAACCCCATCATCATCATCATTACCACCACCATCATCATC 39708 vi v vi i i i i (TCA)n#Simple 1 TCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATC 50 chr4qtel1M 39709 ACCATCATCATC-TCATCATTGTTGTCATTGTCACTGTCATCATTATTAT 39757 i - ii ii ii iii i i (TCA)n#Simple 51 ATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCAT 100 chr4qtel1M 39758 CATCATTTCCATCCCCATCAACATCATCATCATCATTACTATCATCACCA 39807 ivi vi v i ii i (TCA)n#Simple 101 CATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCA 150 chr4qtel1M 39808 TCATTGTCACCATCATCCCCATCATCATCATCATCATCATCATCACCACC 39857 ii i vi i i (TCA)n#Simple 151 TCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATC 200 chr4qtel1M 39858 ATCATCTTCACCATCATCAACATC-TCATAATTGTGATCATTGTTATCAT 39906 v i v - v ii v ii i (TCA)n#Simple 201 ATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCAT 250 chr4qtel1M 39907 CATC-CCATCTCCATCATCATCAGCACCATCATCATTAACATCACCATCA 39955 -i vi v i i v i (TCA)n#Simple 251 CATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCA 300 chr4qtel1M 39956 TCATCATCATCACCACCATCATCTTCACCATCATCATCATC-TTATCATT 40004 i i v i - i i (TCA)n#Simple 301 TCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATC 350 chr4qtel1M 40005 GTTGCCATTGTCATTGTCCTCATTACTGTCATCATCCCTATCCCCATCAT 40054 i iii ii ii v i iii vii vi (TCA)n#Simple 351 ATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCAT 400 chr4qtel1M 40055 CATCATCATCATCACCATCATCACCATTATTACCATCATCATCATCATCA 40104 i i i i i (TCA)n#Simple 401 CATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCA 450 chr4qtel1M 40105 TC-TCATAATTGTTGTCATTGTCACTGTCATCATTGTTATTATCATCCCC 40153 - v ii ii ii iii ii i i vi (TCA)n#Simple 451 TCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATC 500 chr4qtel1M 40154 ATCATCATCATCATCATCATTGTTACCATCATCATCATCACCATCATCTT 40203 ii i i i v (TCA)n#Simple 501 ATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCAT 550 chr4qtel1M 40204 CACCATTATCAACATC-TCATTATTGTTGTCATTGTCATTGTGATCATTG 40252 i i v - i ii ii ii ii v ii (TCA)n#Simple 551 CATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCA 600 chr4qtel1M 40253 TTATCATCATCCTCATCCTCATCATCATCATCTTCACCATTATCATCACC 40302 i v v v i i i (TCA)n#Simple 601 TCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATC 650 chr4qtel1M 40303 ATCATCGTCATCAACATC-TCATCATTGTGGTCATTGTCATTGTCATCAC 40351 i v - ii vi ii ii i (TCA)n#Simple 651 ATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCAT 700 chr4qtel1M 40352 TGTTTTCACCATCTCCATCATCATCATCATCATCATCACCATCACCATCA 40401 ii iv i vi i i (TCA)n#Simple 701 CATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCA 750 chr4qtel1M 40402 TCACCATCATCTTCACCATCATCATCCTCAACATC-TCATCAT-TTTGTC 40449 i v i v v - -v ii (TCA)n#Simple 751 TCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATC 800 chr4qtel1M 40450 ATTGTCATTGTCATCATTGTTGTCATCATCCCCATCCCCATCATCATCAT 40499 ii ii ii ii vi vi (TCA)n#Simple 801 ATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCAT 850 chr4qtel1M 40500 CACCATCATCGTCGTCATCACCATCATCATCATCATCCCCATCACCATCA 40549 i i i i vi i (TCA)n#Simple 851 CATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCA 900 chr4qtel1M 40550 TCATCATCCCCATCATCATCATCATCATCATCGCCATCATTGTCATCATA 40599 vi ii ii - (TCA)n#Simple 901 TCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCAT- 949 chr4qtel1M 40600 GATC-TC-TCTGTAACTC-TCTGTAAT-ATTACCATCAGTTTCACCACCA 40645 v - - -i v - - -i v - i i viv i i (TCA)n#Simple 950 CATCATCATC-ATCA-TCATC-ATCATCATCATCATCATCATCATCATCA 996 chr4qtel1M 40646 CCACCACAATCATCATCATCATCATCAT-GTCATCATTGTTATCATCACC 40694 i i iv -i ii i i (TCA)n#Simple 997 TCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATC 1046 chr4qtel1M 40695 ATCATTATCATCATCCCCATCATCATCATCACCATCATCACCATAATTGT 40744 i vi i i v ii (TCA)n#Simple 1047 ATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCAT 1096 chr4qtel1M 40745 CCCCATCATTACCATCATCTTCACCATCATCATCATC-TTATCATGGTTG 40793 vi i i v i - i vi ii (TCA)n#Simple 1097 CATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCA 1146 chr4qtel1M 40794 TCATTGTCATTGTCATCATTGTTGTCATCATCCCTGTCCCCATCATCCTC 40843 ii ii ii ii viii vi v (TCA)n#Simple 1147 TCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATC 1196 chr4qtel1M 40844 ATCATCATCATCACTACCATTACCATCAGCTTCACCACCATCATCCTCAT 40893 ii i i i v v i i v (TCA)n#Simple 1197 ATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCAT 1246 chr4qtel1M 40894 CAACATC-TCATCATTGTTGCCATTGAT-ATTGTCATCATTGTTATCATC 40941 v - ii iii - v - ii ii i (TCA)n#Simple 1247 CATCATCATCATCATCATCATCA-TCATCATCATCATCATCATCATCATC 1295 chr4qtel1M 40942 ACCATCATTACCACCATTATCATCATCATC-TC-TCATCATTGTTGCTGT 40989 i i i i i - - ii iiiii (TCA)n#Simple 1296 ATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCAT 1345 chr4qtel1M 40990 TATCATTGTTATCATTATCCCCACCCCCATCCCCATTATCATCATCATCT 41039 i ii i i vi i vi vi i v (TCA)n#Simple 1346 CATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCA 1395 chr4qtel1M 41040 TCTTCATCATCATTACCATCATCCTC-TCATCA 41071 v i i v - (TCA)n#Simple 1396 TCATCATCATCATCATCATCATCATCATCATCA 1428 Matrix = Unknown Transitions / transversions = 3.59 (226/63) Gap_init rate = 0.02 (25 / 1412), avg. gap size = 1.00 (25 / 25) 30 8.86 3.23 1.59 chr4qtel1M 41090 41151 (958849) (TCA)n#Simple_repeat 1 63 (0) c_b191s251i1 7473 chr4qtel1M 41090 TCATCATTATCATC-CCATCCTCATCATCATCACCATCATCTTCA-CTAT 41137 i -i v i v - - (TCA)n#Simple 1 TCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATC-AT 49 chr4qtel1M 41138 CATCATCATCATCA 41151 (TCA)n#Simple 50 CATCATCATCATCA 63 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.05 (3 / 61), avg. gap size = 1.00 (3 / 3) 242 13.06 2.08 4.26 chr4qtel1M 42189 42236 (957764) C MIR3#SINE/MIR (54) 154 108 m_b191s601i2 7474 chr4qtel1M 42189 TCCCACTTCAGCTCATTTTACAGATGAGGAAACTGAGG-CAAAAAAGGT 42236 v ii -- - v i i C MIR3#SINE/MIR 154 TCCAACCCC--CTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGT 108 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 14.53 CpG sites = 4, Kimura (unadjusted) = 14.53 Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.06 (3 / 47), avg. gap size = 1.00 (3 / 3) 316 17.97 21.24 1.48 chr4qtel1M 42200 42312 (957688) C MIR#SINE/MIR (118) 144 10 m_b191s601i3 7474 chr4qtel1M 42200 CTCATTTTACAGATGAGGAAACTGAGGCAAAA------------------ 42231 i v i------------------ C MIR#SINE/MIR 144 CCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGC 95 chr4qtel1M 42232 --AAGGTCCCTCAGGTAGGAAGGGTGTGGAGCT-GGATTTGAACTCACAA 42278 -- v v v v v - ii i- i i viv C MIR#SINE/MIR 94 CCAAGGTCACACAGCTAGTAAGTG-GCAGAGCCGGGATTCGAACCCAGGC 46 chr4qtel1M 42279 AG-CTTGTTCCA-AGCCCAGTGCTC-TACCCACTGTG 42312 - v i - - - v i C MIR#SINE/MIR 45 AGTCTGGCTCCAGAGCCC-GTGCTCTTAACCACTATG 10 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 18.55 CpG sites = 10, Kimura (unadjusted) = 20.72 Transitions / transversions = 1.00 (10/10) Gap_init rate = 0.07 (8 / 112), avg. gap size = 3.25 (26 / 8) 53 15.11 0.00 0.00 chr4qtel1M 42540 42627 (957373) (AC)n#Simple_repeat 1 88 (0) m_b191s252i4 7475 chr4qtel1M 42540 ACACAGACACAGACACACACACACTCTCACACACACTCACACACACACAC 42589 v v v v v (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50 chr4qtel1M 42590 ACTCAGACACTCATACTGACACACACACACATACACAC 42627 v v v i vv i (AC)n#Simple_ 51 ACACACACACACACACACACACACACACACACACACAC 88 Matrix = Unknown Transitions / transversions = 0.20 (2/10) Gap_init rate = 0.00 (0 / 87), avg. gap size = 0.0 (0 / 0) 206 25.00 0.00 0.00 chr4qtel1M 42712 42755 (957245) C MIR#SINE/MIR (3) 259 216 m_b191s601i4 7476 chr4qtel1M 42712 AATGGCCAACACTTATTAAGCTCCTGCTGTGTGCCGGCCAGTGT 42755 i i i i v i i i i v v C MIR#SINE/MIR 259 AATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGT 216 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 31.93 CpG sites = 8, Kimura (unadjusted) = 31.93 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 189 20.04 2.90 5.97 chr4qtel1M 43680 43748 (956252) C MIR3#SINE/MIR (24) 184 118 m_b191s601i5 7477 chr4qtel1M 43680 GGGCTGGGAGCCAGGAGCCAAGGG--CAGCTAAGGCCAACTCCCTGATTT 43727 i i --- v iv i -- v - v i v C MIR3#SINE/MIR 184 GAGCTGGAAG---GGACCTTAGAGATCATCTA-GTCCAACCCCCTCATTT 139 chr4qtel1M 43728 CCCAGAAGAGGAAACTGAGGC 43748 iv v C MIR3#SINE/MIR 138 TACAGATGAGGAAACTGAGGC 118 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 23.35 CpG sites = 6, Kimura (unadjusted) = 23.35 Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.07 (5 / 68), avg. gap size = 1.20 (6 / 5) 425 31.61 5.00 1.94 chr4qtel1M 44365 44564 (955436) C MamRTE1#LINE/RTE-BovB (676) 3136 2931 m_b191s601i6 7478 chr4qtel1M 44365 TGGAGCCGGA-GCCGC-CCGACACCATATTTTGTCTGCTTGTCTCC--GA 44410 iv - i -ii i i i i i iv i --i C MamRTE1#LINE/ 3136 TGGAGCTTGATGCCACGTTGGCGCCACACTCTGTCTGCCAGCCTCCCAAA 3087 chr4qtel1M 44411 GGACAATGCCGGCTTTCTTCTTGGTCCTGGTTTCT-CCCCTTTGTCTGTT 44459 - i --- i i v v - ii ?i i C MamRTE1#LINE/ 3086 GGACA-TGCTGGC---CTTCTTGATTCGGTTTTCTACTTCTTTGTCNATC 3041 chr4qtel1M 44460 GGCGCCTCCCGGGACAGCGTGTCACCCAGGGAAGGGGGCTGGGGG----- 44504 i i v viv iii i v ivi iii v v ----- C MamRTE1#LINE/ 3040 AGTGCATCATTGGACAGCGTGCTGCCTAGGTAGCAGAATTCGGTGACAGC 2991 chr4qtel1M 44505 CTCCGGTCCCTTATTGCCAAGGAAAATATTTGGCTGGAACCGAGGTTTCC 44554 i i i ii iv i v v vivviii C MamRTE1#LINE/ 2990 TTTCAGCTCTGTATTGCCGATGAAAATCTTTGGCTGCGTGTAGGGTTTCC 2941 chr4qtel1M 44555 CTGGAGCGAG 44564 v ii C MamRTE1#LINE/ 2940 CTGGTGCAGG 2931 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 41.38 CpG sites = 44, Kimura (unadjusted) = 44.32 Transitions / transversions = 2.44 (44/18) Gap_init rate = 0.05 (9 / 199), avg. gap size = 1.56 (14 / 9) 265 25.54 18.90 1.34 chr4qtel1M 45106 45232 (954768) C L3#LINE/CR1 (1) 4098 3950 m_b191s601i7 7479 chr4qtel1M 45106 ACAGAATGACAGGATTTGGGGATTGGAAATGATCTCAGGAACCATCTGGG 45155 i v i i vi ii iv i i iiii i v C L3#LINE/CR1 4098 ATAGAATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGT 4049 chr4qtel1M 45156 CTAA---TCCACTCACT---------CCTT----AAC--CCC--ACAGAG 45185 i ---i ii v --------- ---- -- -- - C L3#LINE/CR1 4048 CCAACCTCCCATCCAATGCAGGAATCCCTTCTACAACATCCCTGACA-AG 4000 chr4qtel1M 45186 T--TCATCCAGCTTCTACCTGAAGCACAT--AATGAGGGAGAGCCCGCTA 45231 -- i i i - v -- i v i i i C L3#LINE/CR1 3999 TGGTCATCCAGCCTCTGCTTGAA-CACCTCCAGTGACGGGGAGCTCACTA 3951 chr4qtel1M 45232 C 45232 C L3#LINE/CR1 3950 C 3950 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 33.41 CpG sites = 25, Kimura (unadjusted) = 33.41 Transitions / transversions = 3.57 (25/7) Gap_init rate = 0.07 (9 / 126), avg. gap size = 2.89 (26 / 9) 219 24.39 2.57 0.50 chr4qtel1M 45322 45904 (954096) (CT)n#Simple_repeat 1 595 (0) m_b191s252i5 7480 chr4qtel1M 45322 CTCTCTGCT-TCCCCCT-TCTTTGTCTTTCTTTCTCTATGCTC-CCCTCT 45368 - - i i - i v i i v - - i (CT)n#Simple_ 1 CTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT-CTCTCTCTCT 48 chr4qtel1M 45369 CTCCCTCTCTGTCTTTCTCTC-CTCTTCCCCTTTCTCTTTCCCTCTCTTT 45417 i v i - ii i i i i i (CT)n#Simple_ 49 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 98 chr4qtel1M 45418 AT-TTTCCCCCCCAACTCTCTTTGTCTGTTTTTCTCCATCGATCTCCCTG 45466 v - i i i i -v i v v i i iv vv i v (CT)n#Simple_ 99 CTCTCTCTCTCTC-TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 147 chr4qtel1M 45467 TCTCTGTCTCTCTCTCTCTCTCCTTCTCTCTGGCTCTCTAAC-CTCTATC 45515 v ii vv vv - v (CT)n#Simple_ 148 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 197 chr4qtel1M 45516 TCTCTGTCTCTTTCTCTCTCT-TCTC-CCCTTTCTCCCTCTCTTTATCT- 45562 v i - - i i i i v - (CT)n#Simple_ 198 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 247 chr4qtel1M 45563 TCCCTCTTTCTCTCTCTCTAGCTTTCTCTGTCTCTGTTTTTCTCCATCTC 45612 i i vv i v v i i iv (CT)n#Simple_ 248 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 297 chr4qtel1M 45613 TCTATGTCTCTGTCTCTCTGTCTGTCTCTCTCTCTCTCTGTGTCTCTGTC 45662 v v v v v v v v (CT)n#Simple_ 298 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 347 chr4qtel1M 45663 TCTGTTTCTGTCTCTCTCTCTCTCTTTCTCTCTCTCTAGTTCTCTCTGTC 45712 v i v i vvi v (CT)n#Simple_ 348 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 397 chr4qtel1M 45713 TCTGTTTTTCTCCGTCTCTCTCTGTTTCTTTCTCTCTCTC-CTC-CCCTT 45760 v i i iv v i i - - i i (CT)n#Simple_ 398 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 447 chr4qtel1M 45761 TC-CCCCCTCTCTTTATTTTTC-CCCTTTCTCTCTCTCTAGCTTTCTCTG 45808 - i i i v i i - i i vv i v (CT)n#Simple_ 448 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 497 chr4qtel1M 45809 TCTCTGTTTTTCTCCATCTATCTCTCTGTCTCTGTCTCTGCCTCTCTCTG 45858 v i i iv v v v vi v (CT)n#Simple_ 498 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 547 chr4qtel1M 45859 GCTCTCTTCCTCTCCCTCTCT-TCTCCCTC-CTCCCTCTCCCCCCCTC 45904 v ii i - i - i i i i (CT)n#Simple_ 548 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 595 Matrix = Unknown Transitions / transversions = 1.29 (67/52) Gap_init rate = 0.03 (18 / 582), avg. gap size = 1.00 (18 / 18) 350 25.81 8.60 0.00 chr4qtel1M 46389 46481 (953519) L2b_3end#LINE/L2 361 461 (5) m_b191s601i8 7481 chr4qtel1M 46389 TGAGGACAGGGAC------TGTTTTGT--ATCGCTCTACCTCAAGCGCTT 46430 i ------ i -- i v i i v i L2b_3end#LINE 361 TGAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTGTATCCCCAGCGCCT 410 chr4qtel1M 46431 AGTATGTCTCCTTAAACATAGTAAGTACTTGATAAATACTTGTTGAATGA 46480 i iiv?v viv i i ii iii i L2b_3end#LINE 411 AGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTTGTTGAATGA 460 chr4qtel1M 46481 A 46481 L2b_3end#LINE 461 A 461 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 32.02 CpG sites = 18, Kimura (unadjusted) = 33.98 Transitions / transversions = 3.00 (18/6) Gap_init rate = 0.02 (2 / 92), avg. gap size = 4.00 (8 / 2) 415 32.73 3.04 1.72 chr4qtel1M 46969 47198 (952802) C L1ME4c_3end#LINE/L1 (246) 584 352 m_b191s551i0 7482 chr4qtel1M 46969 TCCTCATATGTGTTGTTTCTTATGGCACAATGATATTATGTTACACTCAG 47018 i vv i ii i v vvv i vii iivii?v v C L1ME4c_3end#L 584 TCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCGAGTNGAT 535 chr4qtel1M 47019 G--CCATAATTTATTCCATCATTTCCCAATCGTTGGGCAGCTACTTTATC 47066 -- i iv i i v i i vi vv i i C L1ME4c_3end#L 534 GTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAGGTTGTT 485 chr4qtel1M 47067 TGTATTTCTTTGCTCTTACAAAAAGTGCTACAATCAATATTTAGGTGTA- 47115 vi v i i v i v ii i v i i vv i - C L1ME4c_3end#L 484 TCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTCGTGCAT 435 chr4qtel1M 47116 AGAGGTCTTTTCCCTCCCTGTTGCTGACTTCTTGAGGATATATCCCGAGA 47165 v -- i i i v viv v i i v v i v - C L1ME4c_3end#L 434 ATAG--CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAATTCCCAG- 388 chr4qtel1M 47166 AAATGAAA----TGAGTCAGAAGGGCATATACATTTT 47198 i i ---- i - i iv C L1ME4c_3end#L 387 AAGTGGAATTACTGGGTCA-AAGGGTATGAACATTTT 352 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 42.23 CpG sites = 43, Kimura (unadjusted) = 44.76 Transitions / transversions = 1.39 (43/31) Gap_init rate = 0.03 (7 / 229), avg. gap size = 1.57 (11 / 7) 242 30.15 9.26 1.72 chr4qtel1M 47207 47314 (952686) DNM1r#Unknown 2431 2546 (2116) m_b191s502i0 7483 chr4qtel1M 47207 CAGAATGGTTGGACCAATTCACAGCTCTACAGGTCGTGTG------CGTA 47250 v i -- ii v v v iviv i ------ iii DNM1r#Unknown 2431 CAGCACGGT--GACTGATTCCCAGCGCTAGAGGCGAGGCGGTCGGCCACG 2478 chr4qtel1M 47251 TGTATGTGTGTGCATATG-GTATATACCTGCATATA---GTACATATACA 47296 ii - i iv ii i--- i iii DNM1r#Unknown 2479 TGTATGTGTGTATATATGTGTGTATATGTGTGTATGTGTGTATATATGTG 2528 chr4qtel1M 47297 TACACACACATATACATA 47314 i i i i ?i DNM1r#Unknown 2529 TATATATACGTATNTATA 2546 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 33.95 CpG sites = 25, Kimura (unadjusted) = 42.72 Transitions / transversions = 3.57 (25/7) Gap_init rate = 0.05 (5 / 107), avg. gap size = 2.40 (12 / 5) 229 22.37 0.00 8.33 chr4qtel1M 47270 47347 (952653) C DNM1r#Unknown (2116) 2546 2475 m_b191s502i1 7484 chr4qtel1M 47270 TATATACCTGCATATAGTACATATACATACACACACATATACATATACAT 47319 ? ivi i - i i i i i i C DNM1r#Unknown 2546 TATANATACGTATATA-TACACATATATACACACATACACACATATACAC 2498 chr4qtel1M 47320 ACATGTATGATATATGTGTATACAAGTG 47347 ----- iiiii v C DNM1r#Unknown 2497 ACAT-----ATATACACACATACACGTG 2475 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 26.76 CpG sites = 14, Kimura (unadjusted) = 28.91 Transitions / transversions = 7.00 (14/2) Gap_init rate = 0.08 (6 / 77), avg. gap size = 1.00 (6 / 6) 234 22.64 0.00 4.84 chr4qtel1M 47303 47367 (952633) DNM1r#Unknown 2475 2536 (2126) m_b191s502i2 7484 chr4qtel1M 47303 CACATATACATATACATACATGTATGATATATGTGTATACAAGTGTGTAT 47352 i i ii i ii i i - i i-- DNM1r#Unknown 2475 CACGTGTATGTGTGTATATATGTGTG-TATATGTGTGTAT--GTGTGTAT 2521 chr4qtel1M 47353 GTGTGTGTAAATATA 47367 i i v DNM1r#Unknown 2522 ATATGTGTATATATA 2536 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 26.90 CpG sites = 13, Kimura (unadjusted) = 29.41 Transitions / transversions = 13.00 (13/1) Gap_init rate = 0.05 (3 / 64), avg. gap size = 1.00 (3 / 3) 19 6.79 6.45 0.00 chr4qtel1M 48675 48705 (951295) (TA)n#Simple_repeat 1 33 (0) m_b191s252i6 7485 chr4qtel1M 48675 TATA-ATTTATA-AAATATATATATATATATAT 48705 - v - v (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATAT 33 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2) 18 4.50 0.00 0.00 chr4qtel1M 48861 48883 (951117) (TA)n#Simple_repeat 1 23 (0) m_b191s252i7 7486 chr4qtel1M 48861 TATATATATATATCTATATATAT 48883 v (TA)n#Simple_ 1 TATATATATATATATATATATAT 23 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 17 24.04 0.00 2.13 chr4qtel1M 48895 48942 (951058) (GGAA)n#Simple_repeat 1 47 (0) m_b191s252i8 7487 chr4qtel1M 48895 GGAAGGAAAGAAGGGAGGGAGGGAGACAAGAAAAGAGAGAAGGAAGGA 48942 i i i i -v i i ii (GGAA)n#Simpl 1 GGAAGGAAGGAAGGAAGGAAGGAAG-GAAGGAAGGAAGGAAGGAAGGA 47 Matrix = Unknown Transitions / transversions = 8.00 (8/1) Gap_init rate = 0.02 (1 / 47), avg. gap size = 1.00 (1 / 1) 315 30.00 10.83 0.00 chr4qtel1M 49135 49254 (950746) C L3#LINE/CR1 (75) 4024 3892 m_b191s601i9 7488 chr4qtel1M 49135 TCCTCTTTATAACATAC---ACAAGTGGTT--------TTTGCTTGAAGG 49173 ii i i v --- i-------- i vi C L3#LINE/CR1 4024 TCCCTTCTACAACATCCCTGACAAGTGGTCATCCAGCCTCTGCTTGAACA 3975 chr4qtel1M 49174 TCCTCAG-AAAGGGGGCCCCAAGGCCTCG-GGGGCAGCATGCTCCACTCT 49221 i ii -i v iv i vvi ?- i viii i i C L3#LINE/CR1 3974 CCTCCAGTGACGGGGAGCTCACTACCTCNCGAGGCAGCCCATTCCATTTT 3925 chr4qtel1M 49222 GGGATGGCTCCCCTTGTTAGGAAACTCTTCCTT 49254 v ii ivv i ii C L3#LINE/CR1 3924 TGGACAGCTCTGATTGTTAGAAAGTTCTTCCTT 3892 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 41.40 CpG sites = 26, Kimura (unadjusted) = 41.40 Transitions / transversions = 2.60 (26/10) Gap_init rate = 0.03 (4 / 119), avg. gap size = 3.25 (13 / 4) 296 28.57 1.10 0.00 chr4qtel1M 49420 49510 (950490) C Plat_L3#LINE/CR1 (296) 3277 3186 m_b191s551i1 7489 chr4qtel1M 49420 TCCTCTCTGTCCAAGCCCCTCAGACAGTAGGAGACAGTGATTATGTT-CC 49468 i ii vv i i v i v v i v v i- C Plat_L3#LINE/ 3277 TCCTCCCCATAAAAACCCTTCATATACTTGAAGACAGTTATTAAGTCACC 3228 chr4qtel1M 49469 TCCTGGTCTTCTCTTCTTGAGGGTAAACACTCCCTGTTCCTT 49510 i i i i iv v vi vi C Plat_L3#LINE/ 3227 CCTTAGCCTTCTCTTCTCCAGGCTAAACAACCCCAATTCCTT 3186 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 36.86 CpG sites = 15, Kimura (unadjusted) = 36.86 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.01 (1 / 90), avg. gap size = 1.00 (1 / 1) 221 24.63 0.00 5.26 chr4qtel1M 50050 50109 (949891) L2d2_3end#LINE/L2 497 553 (2) m_b191s601i10 7490 chr4qtel1M 50050 CCTAGCTGAAGAGCACATGGCACACAGCAGGGCTTTAATAAATGTTTATT 50099 --- v ii v v i vvi i i i L2d2_3end#LIN 497 CCTAGC---ACAGTGCCTTGCACACAGTAGGCGCTCAATAAATATTTGTT 543 chr4qtel1M 50100 GACTTTATTT 50109 i v L2d2_3end#LIN 544 GATTTGATTT 553 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 30.29 CpG sites = 8, Kimura (unadjusted) = 30.29 Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.05 (3 / 59), avg. gap size = 1.00 (3 / 3) 15 0.00 0.00 0.00 chr4qtel1M 50986 51004 (948996) (TAT)n#Simple_repeat 1 19 (0) m_b191s252i9 7491 chr4qtel1M 50986 TATTATTATTATTATTATT 51004 (TAT)n#Simple 1 TATTATTATTATTATTATT 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 313 27.98 9.52 0.73 chr4qtel1M 51831 51956 (948044) C L2b_3end#LINE/L2 (11) 455 319 m_b191s601i12 7492 chr4qtel1M 51831 CAACAAGCATTTATTGATCACCTGCTGTGTACCAGGAG-------AGACA 51873 ii i v i i i v?------- i i C L2b_3end#LINE 455 CAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCG 406 chr4qtel1M 51874 TTGGGGATATAGAG----ACAAAAGTGAAATAGTCCCTGCTTGCAGCAAG 51919 i i v ---- i vv v?ii iiv vvi C L2b_3end#LINE 405 CTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGGAG 356 chr4qtel1M 51920 TATCCATTCAATTGGGGAAGACA-CCATGTCATGCAGA 51956 iviv v v v i -v v -? C L2b_3end#LINE 355 CTCACAGTCTAGTGGGGGAGACAGACATGTAA-NCAGA 319 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 32.87 CpG sites = 19, Kimura (unadjusted) = 36.83 Transitions / transversions = 1.19 (19/16) Gap_init rate = 0.03 (4 / 125), avg. gap size = 3.25 (13 / 4) 363 30.90 0.00 4.67 chr4qtel1M 51831 51942 (948058) C L2c_3end#LINE/L2 (11) 467 361 m_b191s601i11 7492 chr4qtel1M 51831 CAACAAGCATTTATTGATCACCTGCTGTGTACCAGGAGAGACATTGGGGA 51880 i v i i i i ----- ii C L2c_3end#LINE 467 CAACAAACATTTATTGAGCGCCTACTATGTGCCAGG-----CGCTGGGGA 423 chr4qtel1M 51881 TATAGAGACAAAAGTGAAATAGTCCCTGCTTGCAGCAAGTATCCATTCAA 51930 i i ii viv v ii iiv ivi iviv v v C L2c_3end#LINE 422 TACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTA 373 chr4qtel1M 51931 TTGGGGAAGACA 51942 v i i C L2c_3end#LINE 372 GTGGAGGAGACA 361 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 36.72 CpG sites = 22, Kimura (unadjusted) = 41.83 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.05 (5 / 111), avg. gap size = 1.00 (5 / 5) 453 22.22 1.00 1.00 chr4qtel1M 52027 52126 (947874) MIRc#SINE/MIR 12 111 (157) m_b191s601i13 7493 chr4qtel1M 52027 GGTACAGTGGATTGAGTGCTGGACTTGGGGAAGGGAAGACCTGAATTCAA 52076 i vv ii i vvi ii i MIRc#SINE/MIR 12 GGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGA 61 chr4qtel1M 52077 ATCC-AGCTTTAGATACTTATTAGGTGTGTGATTCTGGGCAAGTCACTTA 52125 i -i i - vi i v iii MIRc#SINE/MIR 62 GTCCCGGCTCT-GCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTA 110 chr4qtel1M 52126 A 52126 MIRc#SINE/MIR 111 A 111 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 24.58 CpG sites = 16, Kimura (unadjusted) = 27.44 Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.02 (2 / 99), avg. gap size = 1.00 (2 / 2) 15 15.01 0.00 0.00 chr4qtel1M 52308 52337 (947663) (AATG)n#Simple_repeat 1 30 (0) m_b191s252i10 7494 chr4qtel1M 52308 AATGAATGAATCAGCAAATGAATGAATGAA 52337 v iii (AATG)n#Simpl 1 AATGAATGAATGAATGAATGAATGAATGAA 30 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 12 5.00 0.00 4.55 chr4qtel1M 52536 52558 (947442) (GGAG)n#Simple_repeat 1 22 (0) m_b191s252i11 7495 chr4qtel1M 52536 GGATGGGAGGGAGGGAGAGAGGG 52558 - i (GGAG)n#Simpl 1 GGA-GGGAGGGAGGGAGGGAGGG 22 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.05 (1 / 22), avg. gap size = 1.00 (1 / 1) 190 36.17 3.19 0.00 chr4qtel1M 53678 53771 (946229) C L3#LINE/CR1 (251) 3848 3752 m_b191s601i14 7496 chr4qtel1M 53678 TCTTAGCTCTTCTTCCTTGGGCCAAGGAAGCTAAGTC--ATACCCAGTCC 53725 i i v iii v i viv iiv -- v ivv C L3#LINE/CR1 3848 TCCTAGTTCTGCCCTCTGGAGCCACACAGAATAAGTCTAATCCCTCTTCC 3799 chr4qtel1M 53726 ACAGGGCAGCCCTCC-ATCACCAGGGGGCAGTTATGGGGTCTCCTTT 53771 v i i - vi iiv ii i i viv i C L3#LINE/CR1 3798 ACATGACAGCCCTTCAAATATTTGAAGACAGCTATCATGTCTCCTCT 3752 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 52.08 CpG sites = 21, Kimura (unadjusted) = 52.08 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.02 (2 / 93), avg. gap size = 1.50 (3 / 2) 617 26.91 2.46 2.97 chr4qtel1M 55248 55450 (944550) C MIRb#SINE/MIR (37) 231 30 m_b191s601i15 7497 chr4qtel1M 55248 GCCAGGCTCTGTGTTAAGTTCTTTAGAAACCTTCTCTCATTCGATCCCC- 55296 v i iv v vi v v ii i - C MIRb#SINE/MIR 231 GCCAGGCACTGTGCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCA 182 chr4qtel1M 55297 CAA-AAGCCTGGGAGGTAGGCGCTCTCAATCTCTCCATTTCACATCTGAG 55345 - v v iii v i --- i i vv C MIRb#SINE/MIR 181 CAACAACCCTGCGAGGTAGGTATTATTA---TCCCCATTTTACAGATGAG 135 chr4qtel1M 55346 AACTCTGAGGCCGACAGCGGTGACGTGATTTGTCCA--GTCCCACAGCTA 55393 i vv iv v v v v i i i -- v C MIRb#SINE/MIR 134 GAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTA 85 chr4qtel1M 55394 CTAAGGGTCTGAGCTCAGATTTGAATTCAAG-CTTCCTGACTTCTTCAGG 55442 v v v v ivi i ii i - vi --- i ii C MIRb#SINE/MIR 84 GTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGA---CTCCAAA 38 chr4qtel1M 55443 GCCTGTGC 55450 i C MIRb#SINE/MIR 37 GCCCGTGC 30 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 30.79 CpG sites = 28, Kimura (unadjusted) = 33.80 Transitions / transversions = 1.12 (28/25) Gap_init rate = 0.05 (10 / 202), avg. gap size = 1.10 (11 / 10) 205 26.24 0.00 1.64 chr4qtel1M 55653 55714 (944286) C L3#LINE/CR1 (1482) 2617 2557 m_b191s601i16 7498 chr4qtel1M 55653 ATCTATCAGTTCTTTCAGGACCCAGGGAGGCAGTTCATGTGGGGGCAGGT 55702 iiv v v v i i i v - v v v C L3#LINE/CR1 2617 ATCTGCAAGTTCTTTCAGTACCCTGGGATGTAATTCGTCT-GGGCCTGGA 2569 chr4qtel1M 55703 CCCCTGAACTCA 55714 vv i C L3#LINE/CR1 2568 GACTTGAACTCA 2557 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 30.04 CpG sites = 6, Kimura (unadjusted) = 32.30 Transitions / transversions = 0.60 (6/10) Gap_init rate = 0.02 (1 / 61), avg. gap size = 1.00 (1 / 1) 335 22.73 4.55 0.00 chr4qtel1M 55853 55962 (944038) C L3#LINE/CR1 (1751) 2348 2234 m_b191s601i17 7498 chr4qtel1M 55853 TCCTTTTCCTT-TAC-CCAAATATAACTTAGAAAACAATCATTTTTGTTG 55900 i - i - i i i v vvv i? C L3#LINE/CR1 2348 TCTTTTTCCTTCTGCTCCGAACATAGCTTTGAAAAGCCTTNTTTTTGTTG 2299 chr4qtel1M 55901 ACCTT--CACTTTTCTCT-CCAGCCTCCACTCAGTCAGAACTTCAGCACT 55947 v -- i i i - v vi v v ii i vi C L3#LINE/CR1 2298 TCCTTAGCATTTTTTTTTGCAAGCCTCAGCTCATTCTGGGCTTTAGCCTT 2249 chr4qtel1M 55948 CCTGACACTATTCCT 55962 i C L3#LINE/CR1 2248 CCTGACACTATTCTT 2234 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 26.64 CpG sites = 15, Kimura (unadjusted) = 27.93 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.04 (4 / 109), avg. gap size = 1.25 (5 / 4) 195 34.48 2.52 2.52 chr4qtel1M 56810 56928 (943072) C L3#LINE/CR1 (2023) 2076 1958 m_b191s601i18 7498 chr4qtel1M 56810 ATTGATAGCTTCAAAATGTCACTCTGAAAGGGTCCCCCACCC-CTTAAAT 56858 - -- i v i i v ii v i v? - i ii C L3#LINE/CR1 2076 ATTG-TAG--TCAGAATTTCATTTTTAAGAGCTTCCCANCCCTCTTGAGC 2030 chr4qtel1M 56859 GACTTCTTTGCTCAACTGTTCACCCATG--ACCACTCCTATTTCCTCTGA 56906 v ii i i vi ii v v i?iv -- i iv v i C L3#LINE/CR1 2029 CATCTTTCTTTTTGAGTCTCNGGCCATGGAATCATACCTCTTTTCTCTGA 1980 chr4qtel1M 56907 ACCATCTGAAATGTTCTCTTTC 56928 iiv i v v i i C L3#LINE/CR1 1979 ATTTTTTGAAATCTGCTTTTCC 1958 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 50.30 CpG sites = 26, Kimura (unadjusted) = 50.30 Transitions / transversions = 1.86 (26/14) Gap_init rate = 0.04 (5 / 118), avg. gap size = 1.20 (6 / 5) 12 13.67 0.00 0.00 chr4qtel1M 57758 57781 (942219) (AGC)n#Simple_repeat 1 24 (0) m_b191s252i12 7499 chr4qtel1M 57758 AGCTGCAAGAGCAGCAGCAGCAGC 57781 v iv (AGC)n#Simple 1 AGCAGCAGCAGCAGCAGCAGCAGC 24 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 446 20.96 5.36 6.31 chr4qtel1M 58835 58946 (941054) MIRc#SINE/MIR 3 113 (155) m_b191s601i19 7500 chr4qtel1M 58835 AGATAG-GTGGCACAGTGGAGAGAACATTAG-CTC----TCAAGAGAACC 58878 ii - ii i i i i - i---- i ii MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chr4qtel1M 58879 TGAGTTCAAATCCAGCCTCAGACACTTGACACTTGCTAGCTGTGTGACTC 58928 i i i v v ------- v i ii MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTC-------TGCCACTTACTAGCTGTGTGACCT 95 chr4qtel1M 58929 TGGACAAGTCACTTAACC 58946 i MIRc#SINE/MIR 96 TGGGCAAGTCACTTAACC 113 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 24.84 CpG sites = 19, Kimura (unadjusted) = 26.22 Transitions / transversions = 6.33 (19/3) Gap_init rate = 0.09 (10 / 111), avg. gap size = 1.30 (13 / 10) 331 21.86 5.84 9.85 chr4qtel1M 59057 59193 (940807) MIRb#SINE/MIR 6 137 (131) m_b191s601i20 7501 chr4qtel1M 59057 GGGCAGCTAGGTGACCCAGTAGATAGAGGAACAGAGCACTGGAATCAGAA 59106 vv --- i v v v-- i vi i v MIRb#SINE/MIR 6 GGGCAGCGTGGTG---CAGTGGAAAGAGCAC--GGGCTTTGGAGTCAGAC 50 chr4qtel1M 59107 AGATTCATCTTCCTGAGTTCAGATGGGACCTCAGACACTTACTAGCTGTG 59156 -------- i ii vvviv v v MIRb#SINE/MIR 51 AGA--------CCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTG 92 chr4qtel1M 59157 TGAC------CAAATCACTTCACC-CTATATGCCTCAG-TTCCTC 59193 ------ i i v - v iv - MIRb#SINE/MIR 93 TGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTC 137 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 23.71 CpG sites = 11, Kimura (unadjusted) = 25.76 Transitions / transversions = 0.69 (11/16) Gap_init rate = 0.12 (16 / 136), avg. gap size = 1.31 (21 / 16) 226 25.07 2.29 11.67 chr4qtel1M 59292 59422 (940578) L1MEi_5end#LINE/L1 2085 2204 (8) m_b191s551i3 7502 chr4qtel1M 59292 ATAACTATGAATGTGAATGGAATGAGCTCACCCAT---AAAACAGAAGTG 59338 v v i i v i i i --- i ii - L1MEi_5end#LI 2085 ATCACAATAAATGTAAATGGATTAAACTCACCTATTAAAAGACAGAGAT- 2133 chr4qtel1M 59339 GATAGCAGAATGGATTAAAAACCACAATCCTGCGATACATCATATGCGAT 59388 -- v v vv v v -------i vi L1MEi_5end#LI 2134 --TATCAGATTGGATTAAAAAAAAAAATCCAGC-------TATATGCTGT 2174 chr4qtel1M 59389 TTGAGACATAAAGATACATAGAGAGTAAAAGGAC 59422 --- - i i ivv i ii v L1MEi_5end#LI 2175 TT---ACA-AGAGACACACCTAAAACAAAACGAC 2204 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 30.56 CpG sites = 16, Kimura (unadjusted) = 30.56 Transitions / transversions = 1.23 (16/13) Gap_init rate = 0.12 (15 / 130), avg. gap size = 1.13 (17 / 15) 238 22.89 1.19 1.19 chr4qtel1M 59292 59375 (940625) L1M4c_5end#LINE/L1 2376 2459 (41) m_b191s551i2 7502 chr4qtel1M 59292 ATAACTATGAATGTGAATGGAATGAGCTCACCCATAAAACAGAAGTGGAT 59341 v v i i v i i v v v - vi?i L1M4c_5end#LI 2376 ATTACTTTAAATGTAAATGGATTAAACTCTCCAATCAAA-AGACANAGAT 2424 chr4qtel1M 59342 -AGCAGAATGGATTAAAAACCACAATCCTGCGATA 59375 -i ? v ?i vi v L1M4c_5end#LI 2425 TGGCNGAATGGATTAAAAAACANGATCCAACTATA 2459 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 28.73 CpG sites = 9, Kimura (unadjusted) = 28.73 Transitions / transversions = 0.90 (9/10) Gap_init rate = 0.02 (2 / 83), avg. gap size = 1.00 (2 / 2) 273 35.16 0.91 0.00 chr4qtel1M 59595 59813 (940187) L1ME3A_3end#LINE/L1 1 221 (699) m_b191s551i4 7503 chr4qtel1M 59595 CTTATTTCACAAATATATATGAAAGTGAACCAAATTTGTAAAAATAAGAG 59644 i v vvi vii v vvvv ivi i v v L1ME3A_3end#L 1 CTCATATCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAAAAGAC 50 chr4qtel1M 59645 CCTTTCCTCAAGTGATAAACGGTCAAAGGATATGAACAAGCAGTTTTCAG 59694 vvvivv i vv v i v i iv i v iv i L1ME3A_3end#L 51 AGACAACCCAATAGAAAAATGGGCAAAAGACTTGAACAGGCACTTCACAA 100 chr4qtel1M 59695 AAGAAGAAATCAAAATTATGTATAGTCACATAAAAA--TGCTCTAAATCA 59742 i v v viivv iv i i -- v vv L1ME3A_3end#L 101 AAGAGGATATCCAAATGGCCAATAAACATATGAAAAGGTGCTCAACTTCA 150 chr4qtel1M 59743 CTACTGATTAAAGAAATGGAAATTAAAACAATTCGGATGTACCACCTCCC 59792 i v v i ii v v ivvv ?vi iv v L1ME3A_3end#L 151 TTAGTCATCAGGGAAATGCAAATTAAAACCACAATGNGATACCACTACAC 200 chr4qtel1M 59793 ATCTACCAGAAATGTCAAAAT 59813 i i vv ii L1ME3A_3end#L 201 ACCCACCAGAATGGCTAAAAT 221 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 47.97 CpG sites = 32, Kimura (unadjusted) = 47.97 Transitions / transversions = 0.71 (32/45) Gap_init rate = 0.00 (1 / 218), avg. gap size = 2.00 (2 / 1) 421 29.91 12.28 0.31 chr4qtel1M 59625 59909 (940091) L1ME4a_3end#LINE/L1 31 349 (522) m_b191s551i5 7503 chr4qtel1M 59625 CAAATTTGTAAAAATAAGAGCCTTTCCTCAAGTGATAAACGGTCAAAGGA 59674 ivi i v vvvviv i vv v i v L1ME4a_3end#L 31 CAAATCAATAAGAAAAAGACGAACACCCCAATAGAAAAATGGGCAAAGGA 80 chr4qtel1M 59675 TATGAACAAGCAGTTTTCAGAAGAAGAAATCAAAATTATGTATAGTCACA 59724 i ii i iv i vv viivv iv i L1ME4a_3end#L 81 CATGAACAGACAATTCACAAAAGAAGAAATACAAATGGCCAATAAACATA 130 chr4qtel1M 59725 T--AAAAATGCTCTAAATCACTACTGATTAAAGAAATGGAAATTAAAACA 59772 -- ? i v vv v i i v L1ME4a_3end#L 131 TGAAAANATGTTCAACCTCACTAGTAATCAAAGAAATGCAAATTAAAACA 180 chr4qtel1M 59773 ATTCGGATGTACCACCTCCCATCTACCAGAAATGTCAAA----------- 59811 ivvv vi ii ii i i - v v ----------- L1ME4a_3end#L 181 ACAATGAGATACCATTTTTCACCTATCA-AATTGGCAAAGATTTAAAAGA 229 chr4qtel1M 59812 ---ATAG----------TGGAGGGATTGAAAGGAAATGAGGACATCAATG 59848 --- i---------- v i iv vii? i i v viiv i L1ME4a_3end#L 230 TTGATAATACCCAGTGTTGGCGAGGGTGTGGNGAAACGGGCACTCTCATA 279 chr4qtel1M 59849 CACTGT---TGGAAGTGTAAAT-----AAACCATTCTGGAGAGTATTTTG 59890 i--- i -----v v i i v L1ME4a_3end#L 280 CACTGCTGGTGGGAGTGTAAATTGGTACAACCTTTCTGGAGGGCAATTTG 329 chr4qtel1M 59891 G-AATAGTTCCCAAAGGGCT 59909 - vv vi i v L1ME4a_3end#L 330 GCAATATGTATCAAAAGCCT 349 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 38.51 CpG sites = 43, Kimura (unadjusted) = 39.09 Transitions / transversions = 1.02 (43/42) Gap_init rate = 0.03 (8 / 284), avg. gap size = 4.50 (36 / 8) 456 26.00 15.29 1.45 chr4qtel1M 59650 59891 (940109) L1ME5_3end#LINE/L1 56 330 (611) m_b191s551i6 7503 chr4qtel1M 59650 CCTCAAGTGATAAACGGTCAAAGGATATGAACAAGCAGTTTTCAGAAGAA 59699 i vv v i v i i v i L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chr4qtel1M 59700 GAAATC---AAAATTATGTATAGTCACAT--AAAAATGCTCTAAATCACT 59744 i --- iii --- i iv i -- i i v v i L1ME5_3end#LI 106 GAAACCCGAAAGGCTA---ACAAGCATATGAAGAGATGCTCAAACTCATT 152 chr4qtel1M 59745 ACTGATTAAAGAAATGGAAATTAAAACAATTCGGATGTACCACCTCCCAT 59794 v i i i v ivvv vi i i iv i L1ME5_3end#LI 153 AGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACAC 202 chr4qtel1M 59795 CTACCAGAAATGTCAAAA--TAG-----TGG--------AGGGATTGA-A 59828 ii - v v -- ----- -------- i vi i-i L1ME5_3end#LI 203 CTATTAG-ACTGGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTGGCG 251 chr4qtel1M 59829 AGGAAATGAGGACATCA--------ATGCACTGT---TGGAAGTGTAAAT 59867 vi i ? vi-------- i--- i i i L1ME5_3end#LI 252 AGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGAC 301 chr4qtel1M 59868 -----AAACCATTCTGGAGAGTATTTTGG 59891 -----v i i v i L1ME5_3end#LI 302 TGGTGCAGCCATTCTGGAGAGCAATCTGG 330 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 32.61 CpG sites = 40, Kimura (unadjusted) = 33.27 Transitions / transversions = 1.82 (40/22) Gap_init rate = 0.05 (13 / 241), avg. gap size = 3.15 (41 / 13) 21 26.63 1.47 2.99 chr4qtel1M 60452 60519 (939481) (TA)n#Simple_repeat 1 67 (0) m_b191s252i13 7504 chr4qtel1M 60452 TAAATTTATATACACACATATATATATACCATATATCATACCTATGTACC 60501 v v i i i -i - iv i iv (TA)n#Simple_ 1 TATATATATATATATATATATATATATA-TATATAT-ATATATATATATA 48 chr4qtel1M 60502 TATGCATGTA-ATATATAT 60519 ii i - (TA)n#Simple_ 49 TATATATATATATATATAT 67 Matrix = Unknown Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.04 (3 / 67), avg. gap size = 1.00 (3 / 3) 23 3.67 0.00 0.00 chr4qtel1M 62606 62633 (937367) (G)n#Simple_repeat 1 28 (0) m_b191s252i14 7505 chr4qtel1M 62606 GGGGGTGGGGGGGGGGGGGGGGGGGGGG 62633 v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGG 28 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 475 23.80 4.61 3.25 chr4qtel1M 62736 62887 (937113) C MIR3#SINE/MIR (32) 176 23 m_b191s601i21 7506 chr4qtel1M 62736 AGAGATCTTGGAGGAGCCATTTCCTTT--CCAGCTCATTTTACAGACTAG 62783 i i i i--i i vv ii-- vv iv C MIR3#SINE/MIR 176 AGGGACCTTAGAGA--TCATCTAGTCCAACCCCCTCATTTTACAGATGAG 129 chr4qtel1M 62784 GAAACTGAGGC--AAACAGGCCTGAAGTGACTTGCTCAGGATCACACAGT 62831 -- i v -- i i i i C MIR3#SINE/MIR 128 GAAACTGAGGCCCAGAGAGG--TGAAGTGACTTGCCCAAGGTCACACAGC 81 chr4qtel1M 62832 TAGCAAGT-ACTGAGGCTGAATTTGAATTCAGGTCTTCCTGGC-CCCGGA 62879 ? iv -i v v v i i v ii - i - i v C MIR3#SINE/MIR 80 NAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGTC-TCCTGACTCCCAGT 32 chr4qtel1M 62880 CC-TGCCCT 62887 - i C MIR3#SINE/MIR 31 CCGTGCTCT 23 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 29.80 CpG sites = 23, Kimura (unadjusted) = 29.80 Transitions / transversions = 1.92 (23/12) Gap_init rate = 0.07 (10 / 151), avg. gap size = 1.20 (12 / 10) 515 20.37 2.73 1.80 chr4qtel1M 62767 62876 (937124) C MIRc#SINE/MIR (120) 148 38 m_b191s601i22 7506 chr4qtel1M 62767 CTCATTTTACAGACTAGGAAACTGAGG--CAAACAGGCCTGAAGTGACTT 62814 i iv -- i v -- v C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGG--TTAAGTGACTT 101 chr4qtel1M 62815 GCTCAGGATCACACAGTTAGCAAGT-ACTGAGGCTGAATTTGAATTCAGG 62863 i i i i i -i v v v i i i ii C MIRc#SINE/MIR 100 GCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGG 51 chr4qtel1M 62864 TCTTCCTGGCCCC 62876 i i C MIRc#SINE/MIR 50 TCTTCCTGACTCC 38 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 23.36 CpG sites = 16, Kimura (unadjusted) = 24.63 Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.04 (4 / 109), avg. gap size = 1.25 (5 / 4) 208 24.10 12.05 0.00 chr4qtel1M 65118 65200 (934800) L2a_3end#LINE/L2 386 478 (39) m_b191s601i23 7507 chr4qtel1M 65118 TCCCCCCCTTAGAATCTAAGCTTCTTG-GGGC-GGGGCTCT----CATTG 65161 vi v i v - - i i ----ii v L2a_3end#LINE 386 TCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTCTGTTT 435 chr4qtel1M 65162 TGGCTGCTGTTGTAGCCCCAGAGC----AACAGGGCCAGGCGC 65200 viii i v v ---- v v i L2a_3end#LINE 436 TGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCAC 478 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 29.49 CpG sites = 11, Kimura (unadjusted) = 29.49 Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.05 (4 / 82), avg. gap size = 2.50 (10 / 4) 93 19.78 1.06 0.00 chr4qtel1M 65664 65852 (934148) (AGAG)n#Simple_repeat 1 191 (0) m_b191s252i15 7508 chr4qtel1M 65664 AGAGAGAGAGAGACAGAGAGAGACAGAGAGACAGAGACAGGGAGAGACAG 65713 v v v v i v (AGAG)n#Simpl 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr4qtel1M 65714 GGAGAGACAGAGATAGAGATAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 65763 i v v v (AGAG)n#Simpl 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 100 chr4qtel1M 65764 AGAGAGAGAGAGAGAGAGAGAGAGAGAAAGGAAGGAAGAAAAAG-GAAGG 65812 i ii ii i i - ii (AGAG)n#Simpl 101 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 150 chr4qtel1M 65813 AAGGAAGGAGAAAGAAAGAAGGAAAGA-AGGAAGGAAGAGA 65852 ii ii i i ii i - ii ii (AGAG)n#Simpl 151 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 191 Matrix = Unknown Transitions / transversions = 3.00 (24/8) Gap_init rate = 0.01 (2 / 188), avg. gap size = 1.00 (2 / 2) 253 22.56 0.00 2.89 chr4qtel1M 65874 66051 (933949) HERVIP10FH#LTR/ERV1 811 983 (4119) m_b191s701i0 7509 chr4qtel1M 65874 AGAGAGAGAGAGAGAGACAGAGAGAGATAAAGAGAGAGACAGAGACAGAG 65923 - v vi v v - HERVIP10FH#LT 811 AGAGAGA-AGAGAGAGAGAGAGAGAGAGGAAGAGAGAGAGAGAGAAAGA- 858 chr4qtel1M 65924 ACCGAGAGACAGAGAGAGACAGAGACAGAGACAGAGAGACAGAAAGAGAC 65973 --- v i v i vi vv v i v HERVIP10FH#LT 859 ---GAGAGAGAGGGAGAGAGAGAGACAAAGAGGGAGTCAAAGAGAGAGAG 905 chr4qtel1M 65974 AGGCACAGAAAGAAAAACACACAGAGATAGAAACAGAGATACAGAGACAG 66023 v i i i v v i i i vi vi v v HERVIP10FH#LT 906 AGGCAGAGAGAGGAAGAGACAGAGAGACAAAGAGGGAGTCAGAGAGAGAG 955 chr4qtel1M 66024 AGACAGACACACACACACAGAGGGAGAG 66051 v v v vv v i i HERVIP10FH#LT 956 AGAGAGACAGAAAGTCAAAGAGAGAAAG 983 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 26.83 CpG sites = 15, Kimura (unadjusted) = 26.83 Transitions / transversions = 0.62 (15/24) Gap_init rate = 0.03 (5 / 177), avg. gap size = 1.00 (5 / 5) 26 14.04 0.00 0.00 chr4qtel1M 66179 66225 (933775) (GTGT)n#Simple_repeat 1 47 (0) m_b191s252i17 7510 chr4qtel1M 66179 GTGGGTGTGTGAGTGAGTGTGAGTGTGTGTGTGAGTGTATGTGTGTG 66225 v v v v v i (GTGT)n#Simpl 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 47 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 12 15.72 6.52 4.26 chr4qtel1M 66534 66579 (933421) (CCT)n#Simple_repeat 1 47 (0) m_b191s252i18 7511 chr4qtel1M 66534 CCTCC-CCACCTCCTCCTTCACTGTGCCCCCTCCTCATCC-CC-CCTCC 66579 - v - - viv i v - - (CCT)n#Simple 1 CCTCCTCCTCCTCCTCC-TC-CTCCTCCTCCTCCTCCTCCTCCTCCTCC 47 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.11 (5 / 45), avg. gap size = 1.00 (5 / 5) 438 20.79 4.95 0.00 chr4qtel1M 66604 66704 (933296) C MIR3#SINE/MIR (4) 204 99 m_b191s601i24 7512 chr4qtel1M 66604 CAAAGGCTCATGGCA-GTCAGGGCTGGAAGGGACCTCGGAAA----CTAG 66648 v iv i v - i ii i ---- C MIR3#SINE/MIR 204 CATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAG 155 chr4qtel1M 66649 TCCATCCTCCTCGTTTTCCAGAGGGGGAAATGGAGGCCCAGAGAAATGCA 66698 v i i v v i iv ii v C MIR3#SINE/MIR 154 TCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAA 105 chr4qtel1M 66699 TTGACT 66704 v C MIR3#SINE/MIR 104 GTGACT 99 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 24.69 CpG sites = 12, Kimura (unadjusted) = 24.69 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.02 (2 / 100), avg. gap size = 2.50 (5 / 2) 36 8.66 0.00 0.00 chr4qtel1M 67216 67264 (932736) (AC)n#Simple_repeat 1 49 (0) c_b191s251i2 7513 chr4qtel1M 67216 ACACACACACACACACACACACACACACGCACTCGCAAACACACACACA 67264 i v i v (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACA 49 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 16 13.08 0.00 0.00 chr4qtel1M 67300 67324 (932676) (AC)n#Simple_repeat 1 25 (0) m_b191s252i19 7513 chr4qtel1M 67300 ACACACACTCATACACTCACACACA 67324 v i v (AC)n#Simple_ 1 ACACACACACACACACACACACACA 25 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 302 26.03 2.74 0.00 chr4qtel1M 68053 68125 (931875) L3#LINE/CR1 3899 3973 (126) m_b191s601i25 7514 chr4qtel1M 68053 AAGTTATTAACACTCGGAATTGTCCCAAAGTGAAA--AACTTCCATGGGG 68100 v vi v i ii v i i --ii v vi ? i L3#LINE/CR1 3899 AACTTTCTAACAATCAGAGCTGTCCAAAAATGGAATGGGCTGCCTCGNGA 3948 chr4qtel1M 68101 GGTAATGAGCTCCCCATTACTGGAG 68125 i i i L3#LINE/CR1 3949 GGTAGTGAGCTCCCCGTCACTGGAG 3973 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 29.64 CpG sites = 13, Kimura (unadjusted) = 33.95 Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.01 (1 / 72), avg. gap size = 2.00 (2 / 1) 217 37.10 1.61 0.00 chr4qtel1M 69334 69457 (930543) C MIRc#SINE/MIR (106) 162 37 m_b191s601i26 7515 chr4qtel1M 69334 CAGGGGTTATTGGCCCCGGTC-ACAGCTGGGCAGATCTCGGCG-AATGAG 69381 vi iv iv i- v i v i iivv v- iv C MIRc#SINE/MIR 162 CAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAG 113 chr4qtel1M 69382 GGTAAGTGTCTCGTCCAGCGTCACTCAGCTTCTGGAAGTCTGAGGCTAGA 69431 v v i i iv v vv iiiv v v v vi C MIRc#SINE/MIR 112 GTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGA 63 chr4qtel1M 69432 GTTTAATTTCAGTCTTCCTGATGCCA 69457 v iv iiivi iv C MIRc#SINE/MIR 62 CTCGAACCCAGGTCTTCCTGACTCCA 37 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 50.40 CpG sites = 22, Kimura (unadjusted) = 51.99 Transitions / transversions = 0.92 (22/24) Gap_init rate = 0.02 (2 / 123), avg. gap size = 1.00 (2 / 2) 33 7.51 0.00 0.00 chr4qtel1M 69507 69548 (930452) (AC)n#Simple_repeat 1 42 (0) c_b191s251i3 7516 chr4qtel1M 69507 ACACACACACTCACACATTCACACACACACACACACACACAC 69548 v iv (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACAC 42 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 269 34.07 2.22 0.00 chr4qtel1M 70723 70857 (929143) L3#LINE/CR1 3554 3691 (408) m_b191s601i27 7517 chr4qtel1M 70723 GTCCCTCGGCCCTCTGAGCAGGTCAGCCTCC--CCGCGGTCCTG-GCCCA 70769 v v iv v v v iv -- i vi vi - ii L3#LINE/CR1 3554 GTCCCGCTGTACTCTGCGCTGGTCAGACCACATCTGGAGTATTGCGTTCA 3603 chr4qtel1M 70770 GTTCTGAGTGTCCCCGTTGAGGAGGGACATCGACCTGCTGACACGTGTCC 70819 i i i v vv v i i vvi ivi i L3#LINE/CR1 3604 GTTCTGGGCGCCACATTTTAAGAGGGACATTGACAAACTGGAGCGCGTCC 3653 chr4qtel1M 70820 AGAGGAGAGCAAGCCCGTCAGGCAAGAGCTTGGACATC 70857 i v vv vii vv i ii v i L3#LINE/CR1 3654 AGAGGAGAGCGACCAGGATGGTGAAGGGTCTGGAAACC 3691 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 42.26 CpG sites = 23, Kimura (unadjusted) = 46.20 Transitions / transversions = 1.00 (23/23) Gap_init rate = 0.01 (2 / 134), avg. gap size = 1.50 (3 / 2) 21 21.59 0.00 0.00 chr4qtel1M 71241 71283 (928717) (T)n#Simple_repeat 1 43 (0) m_b191s252i20 7518 chr4qtel1M 71241 TTTTTTTTTTTTTTTTTTAAGTATTTCGTTTTGTTTGTTTTTT 71283 vvv v iv v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 43 Matrix = Unknown Transitions / transversions = 0.14 (1/7) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 17 3.56 0.00 9.38 chr4qtel1M 72125 72159 (927841) (GTTTT)n#Simple_repeat 1 32 (0) m_b191s252i21 7519 chr4qtel1M 72125 GTTTTGTTTTGGGTTTGTGTTTTGCTTTGTTTTGT 72159 -- - i (GTTTT)n#Simp 1 GTTTTGTTTT--GTTT-TGTTTTGTTTTGTTTTGT 32 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.09 (3 / 34), avg. gap size = 1.00 (3 / 3) 61 0.00 0.00 0.00 chr4qtel1M 72363 72417 (927583) (C)n#Simple_repeat 1 55 (0) c_b191s251i4 7520 chr4qtel1M 72363 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 72412 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 50 chr4qtel1M 72413 CCCCC 72417 (C)n#Simple_r 51 CCCCC 55 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 695 18.98 6.57 0.00 chr4qtel1M 74943 75079 (924921) MIR#SINE/MIR 117 262 (0) m_b192s601i0 7521 chr4qtel1M 74943 GTCGCAGTTCCCTCATCTGTAGAGTGGGGATAATGA-----CCCGTC--- 74984 i v i i i i ----- iii --- MIR#SINE/MIR 117 GCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTCA 166 chr4qtel1M 74985 -AGAGTCATTGTGAGAATCAAATGAGATCATATATGTAAAACACTTAGTA 75033 - i ii i i v v i i i v MIR#SINE/MIR 167 TAGGGTTGTTGTGAGGATTAAATGAGTTAATACATGTAAAGCGCTTAGAA 216 chr4qtel1M 75034 CAGTGCCTGGCACATAGTGGGCACGACATAAATGTTAGCTATTATT 75079 ii i vvv MIR#SINE/MIR 217 CAGTGCCTGGCACATAGTAAGCGCTCAATAAATGTTAGCTATTATT 262 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 20.69 CpG sites = 19, Kimura (unadjusted) = 22.60 Transitions / transversions = 2.71 (19/7) Gap_init rate = 0.02 (3 / 136), avg. gap size = 3.00 (9 / 3) 198 26.86 1.47 1.47 chr4qtel1M 76259 76326 (923674) L2#LINE/L2 1838 1905 (1177) m_b192s601i1 7522 chr4qtel1M 76259 CTCAAGGTACGCCTTCATGACTCACCTCCCTTTCTGGAGCAAA-CTCCTG 76307 v v vv ii vv vv i - iv - v L2#LINE/L2 1838 CTCCAGCTACCGCCCCATTTCTCTGCTCCCCTT-TACAGCAAAACTCCTC 1886 chr4qtel1M 76308 GTAAAAGTCATCTATACTC 76326 v i ii L2#LINE/L2 1887 GAAAGAGTTGTCTATACTC 1905 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.30 CpG sites = 7, Kimura (unadjusted) = 33.30 Transitions / transversions = 0.64 (7/11) Gap_init rate = 0.03 (2 / 67), avg. gap size = 1.00 (2 / 2) 17 14.21 0.00 0.00 chr4qtel1M 76431 76461 (923539) (TCC)n#Simple_repeat 1 31 (0) m_b192s252i0 7523 chr4qtel1M 76431 TCCTCCTCCTCCTCCTCTTTCTCAGCCTCCT 76461 i i vv (TCC)n#Simple 1 TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT 31 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 95 9.84 6.77 1.99 chr4qtel1M 77373 77564 (922436) (TG)n#Simple_repeat 1 201 (0) m_b192s252i1 7524 chr4qtel1M 77373 TGTGTGTGT-TGTGTGT-TGAGTGCTGTGTTTGTATATGT-TGTCTGTGT 77419 - - v - v i i - v (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTG-TGTGTGTGTGTGTGTGTGTGTGTGT 49 chr4qtel1M 77420 GT-TGTGAGTGT-TGTTTGTGTGTGATGTGTGT-TGTGTGTGT-TGAGTG 77465 - v - v - - - v (TG)n#Simple_ 50 GTGTGTGTGTGTGTGTGTGTGTGTG-TGTGTGTGTGTGTGTGTGTGTGTG 98 chr4qtel1M 77466 CTGTTTGTATATGT-TGTGTGTGTGT-TGTGAGTGT-TGTGTTTGTGTGA 77512 - v i i - - v - v - (TG)n#Simple_ 99 -TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG- 146 chr4qtel1M 77513 TGTGTGT-TGTATGTGTGTGAGTGTGTGTGTG-GTGCGAGTGT-TGTGTG 77559 - i v - i v - (TG)n#Simple_ 147 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 196 chr4qtel1M 77560 TGTGT 77564 (TG)n#Simple_ 197 TGTGT 201 Matrix = Unknown Transitions / transversions = 0.55 (6/11) Gap_init rate = 0.09 (17 / 191), avg. gap size = 1.00 (17 / 17) 16 5.27 0.00 0.00 chr4qtel1M 77989 78008 (921992) (G)n#Simple_repeat 1 20 (0) m_b192s252i2 7525 chr4qtel1M 77989 GGGGGGGGGGGGGGGGAGGG 78008 i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGG 20 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 18 9.47 2.94 0.00 chr4qtel1M 80769 80802 (919198) (CGGCCC)n#Simple_repeat 1 35 (0) m_b192s252i4 7526 chr4qtel1M 80769 CGGCCCAGGCCCCGCCCCCGG-CCCGCCCCCGGCC 80802 v v - v (CGGCCC)n#Sim 1 CGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCC 35 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 14 13.23 6.06 0.00 chr4qtel1M 80988 81020 (918980) (GCT)n#Simple_repeat 1 35 (0) m_b192s252i5 7527 chr4qtel1M 80988 GCTGCTGCTGCCGCTGCTCCT-CT-CGGCGGCTGC 81020 i v - - v v (GCT)n#Simple 1 GCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC 35 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.06 (2 / 32), avg. gap size = 1.00 (2 / 2) 20 11.75 8.77 1.64 chr4qtel1M 81055 81111 (918889) (CGGCG)n#Simple_repeat 1 61 (0) m_b192s252i6 7528 chr4qtel1M 81055 CGGCCCGGC-CAGTGGGGGGCGGCGGCGGAG-GGCGCGGCG-GGCGCGGC 81101 v - i i v v - v - - (CGGCG)n#Simp 1 CGGCGCGGCGCGGCGCGGCGCGGC-GCGGCGCGGCGCGGCGCGGCGCGGC 49 chr4qtel1M 81102 GCGG-G-GGCGC 81111 - - (CGGCG)n#Simp 50 GCGGCGCGGCGC 61 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.11 (6 / 56), avg. gap size = 1.00 (6 / 6) 18 19.25 2.38 0.00 chr4qtel1M 81069 81110 (918890) (GGC)n#Simple_repeat 1 43 (0) m_b192s252i7 7529 chr4qtel1M 81069 GGGGGCGGCGGCGGAGGGCGCGGCGGGCGCGGC-GCGGGGGCG 81110 v v vv vv - v (GGC)n#Simple 1 GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCG 43 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.02 (1 / 41), avg. gap size = 1.00 (1 / 1) 203 24.13 3.39 1.67 chr4qtel1M 81234 81292 (918708) C MIR3#SINE/MIR (61) 147 88 m_b192s601i2 7530 chr4qtel1M 81234 CTCTC-TTTTACCGAGAGGGACACTGAGG-CCGGAGCATGCGCAGTGACT 81281 i - v vii v - i - v i v C MIR3#SINE/MIR 147 CCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAG-AGGTGAAGTGACT 99 chr4qtel1M 81282 TTCCCAGAATC 81292 v iii C MIR3#SINE/MIR 98 TGCCCAAGGTC 88 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.64 CpG sites = 8, Kimura (unadjusted) = 29.64 Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.05 (3 / 58), avg. gap size = 1.00 (3 / 3) 14 22.70 5.17 1.67 chr4qtel1M 81536 81593 (918407) (GCCCC)n#Simple_repeat 1 60 (0) m_b192s252i8 7531 chr4qtel1M 81536 GCCCGGGCCC-CCCCGCGCC-CCCTTCCCCCCCACGCCCACGCCCC-CTC 81582 v v - v - iv v v - - i (GCCCC)n#Simp 1 GCCCCGCCCCGCCCCGCCCCGCCCCGCCCCGCCCCGCCC-CGCCCCGCCC 49 chr4qtel1M 81583 CGTCTCTCCCC 81593 i i v (GCCCC)n#Simp 50 CGCCCCGCCCC 60 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.07 (4 / 57), avg. gap size = 1.00 (4 / 4) 16 9.98 0.00 5.88 chr4qtel1M 83921 83956 (916044) (TGTCTC)n#Simple_repeat 1 34 (0) m_b192s252i9 7532 chr4qtel1M 83921 TGTCCTCTCTCTATGTCTCTGTCTCTGCCTCTTGTC 83956 - v v i - (TGTCTC)n#Sim 1 TGT-CTCTGTCTCTGTCTCTGTCTCTGTCTC-TGTC 34 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 182 30.55 2.70 2.70 chr4qtel1M 84289 84362 (915638) C MIR#SINE/MIR (108) 154 81 m_b192s601i3 7533 chr4qtel1M 84289 TAGTAGAGTCCTCTGTTTGCAAATGAGGAAGCCGAGGCAGGCAGTGACA- 84337 v vvi i vv i i i i -- v vi- C MIR#SINE/MIR 154 TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCA--CAGAGAGGT 107 chr4qtel1M 84338 GGATTCATTTGCCC-AGTTCATGCAG 84362 vi v v i - v ii C MIR#SINE/MIR 106 TAAGTAACTTGCCCAAGGTCACACAG 81 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.77 CpG sites = 11, Kimura (unadjusted) = 39.77 Transitions / transversions = 1.00 (11/11) Gap_init rate = 0.05 (4 / 73), avg. gap size = 1.00 (4 / 4) 196 31.81 3.33 5.68 chr4qtel1M 86709 86798 (913202) C MIR#SINE/MIR (134) 128 41 m_b192s601i5 7534 chr4qtel1M 86709 GGAAAGTGGGGCACAGAGA-ACTCAGTGACTTGGCCTGGGATCACAGAGA 86757 v i -ii v i - iii i v v C MIR#SINE/MIR 128 GGAAACTGAGGCACAGAGAGGTTAAGTAACTT-GCCCAAGGTCACACAGC 80 chr4qtel1M 86758 TGGGGTCTAA--AGCAGAATGAGGAGCCAAGTCTGGATAGTCT 86798 i ---- --i iivi vi i ii ii ii C MIR#SINE/MIR 79 TAG----TAAGTGGCAGAGCCGGGATTCGAACCCAGGCAGTCT 41 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.75 CpG sites = 21, Kimura (unadjusted) = 45.39 Transitions / transversions = 3.50 (21/6) Gap_init rate = 0.08 (7 / 89), avg. gap size = 1.14 (8 / 7) 198 30.00 0.00 0.00 chr4qtel1M 87225 87274 (912726) MIRb#SINE/MIR 21 70 (198) m_b192s601i6 7535 chr4qtel1M 87225 GTGCACGGAGCCCGGGTTTTGGAGCCGAGAAGGCTTTGATTCGAATCCTG 87274 v vi v i i iiiv i i v i i MIRb#SINE/MIR 21 GTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCGAATCCCG 70 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.76 CpG sites = 10, Kimura (unadjusted) = 40.24 Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 15 13.87 0.00 0.00 chr4qtel1M 87427 87450 (912550) (T)n#Simple_repeat 1 24 (0) m_b192s252i10 7536 chr4qtel1M 87427 TTTTTTTTTGTTGTGTTTTTTTTT 87450 v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTT 24 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 247 27.78 8.33 0.00 chr4qtel1M 89777 89848 (910152) C MIRb#SINE/MIR (92) 176 99 m_b192s601i7 7537 chr4qtel1M 89777 ACCACACGAGGCAGGTACCGCTGGCTCCATTTTACAGGTCAGCAAACCGA 89826 vii i iiii iv i i v v i C MIRb#SINE/MIR 176 ACCCTGCGAGGTAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGA 127 chr4qtel1M 89827 GG----GAGAGGC--GGTGACCTGCTCA 89848 ---- i--i i i i C MIRb#SINE/MIR 126 GGCTCAGAGAGGTTAAGTAACTTGCCCA 99 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.60 CpG sites = 16, Kimura (unadjusted) = 37.60 Transitions / transversions = 4.00 (16/4) Gap_init rate = 0.03 (2 / 71), avg. gap size = 3.00 (6 / 2) 15 5.48 0.00 0.00 chr4qtel1M 90619 90637 (909363) (C)n#Simple_repeat 1 19 (0) m_b192s252i11 7538 chr4qtel1M 90619 CCCCCCCCCCCCCCCCACC 90637 v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCC 19 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 16 6.72 0.00 8.82 chr4qtel1M 91153 91189 (908811) (CCCCTC)n#Simple_repeat 1 34 (0) m_b192s252i13 7539 chr4qtel1M 91153 CCCCTCCCCCATCTCCTCCTCCCCCTGCCCCCCCCCC 91189 - - - v i (CCCCTC)n#Sim 1 CCCCTCCCCC-TC-CC-CCTCCCCCTCCCCCTCCCCC 34 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.08 (3 / 36), avg. gap size = 1.00 (3 / 3) 69 22.77 3.12 2.06 chr4qtel1M 91272 91463 (908537) (AGGA)n#Simple_repeat 1 194 (0) m_b192s252i14 7540 chr4qtel1M 91272 AGAAAGAAAGGAAGGCAGGAA-GAAAGAA-GAAGAAAGAAAAAGAAAGAA 91319 i i v - i - i -i i i (AGGA)n#Simpl 1 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG-GAAGGAAGGAA 49 chr4qtel1M 91320 GGAAGGAAGGAGGAAAAGGAGGGAGGAAGGAGGGAGAGAGGGGAGGAA-G 91368 i i i i i i ii i i - (AGGA)n#Simpl 50 GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG 99 chr4qtel1M 91369 AAGGGGGGGAGGAA-GAAGGGGGGAGGGAGGGAGGGAGGGGAGAGGGAGG 91417 ii i - ii i i i -i - i (AGGA)n#Simpl 100 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA-AGGA-AGGAAGG 147 chr4qtel1M 91418 GAGGAAGG-AGGGAGGGAGGAAGG-AGGGAGGGAGGGAGGAATGGAAG 91463 i - i i - i i i - (AGGA)n#Simpl 148 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA-GGAAG 194 Matrix = Unknown Transitions / transversions = 33.00 (33/1) Gap_init rate = 0.05 (10 / 191), avg. gap size = 1.00 (10 / 10) 14 20.88 6.25 3.03 chr4qtel1M 92163 92226 (907774) (CCCTGC)n#Simple_repeat 1 66 (0) m_b192s252i15 7541 chr4qtel1M 92163 CCCT-CCCC-GCTCCT-CCCGCGCTCCGTGCCCCGGCCTCTGCCCC-GCA 92208 - - i - vi - v v i - v (CCCTGC)n#Sim 1 CCCTGCCCCTGCCCCTGCCCCTGC-CCCTGCCCCTGCCCCTGCCCCTGCC 49 chr4qtel1M 92209 GCTCCCGCCCGCCCCGGC 92226 v v - i v (CCCTGC)n#Sim 50 CCTGCC-CCTGCCCCTGC 66 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.10 (6 / 63), avg. gap size = 1.00 (6 / 6) 13 18.22 4.26 4.26 chr4qtel1M 93004 93050 (906950) (GCGGG)n#Simple_repeat 1 47 (0) m_b192s252i16 7542 chr4qtel1M 93004 GCGGTGCGAAGGGCGTGGCCGGG-AGCGCGGGGCCGGG-AGGGCGGGGC 93050 v -- v v -i v v -i (GCGGG)n#Simp 1 GCGGGGCG--GGGCGGGGCGGGGCGGGGCGGGGCGGGGCGGGGCGGGGC 47 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.09 (4 / 46), avg. gap size = 1.00 (4 / 4) 364 30.25 1.68 0.00 chr4qtel1M 94603 94721 (905279) MIRc#SINE/MIR 25 145 (123) m_b192s601i8 7543 chr4qtel1M 94603 GAGTTCCAAATTTGGAGTTAG-AGGCCCTGCCTTCGAATCCTGCCTTTGC 94651 iv iii i i - i v vv i i v i MIRc#SINE/MIR 25 GAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGC 74 chr4qtel1M 94652 CACTTATTTCCTGTGTGACCTCCAGGACGTCCCTTTATAT-TCTCCTTCT 94700 i vv ivi v v v v iv - vvvi MIRc#SINE/MIR 75 CACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCT 124 chr4qtel1M 94701 CAGTCTCCACATTTAGAAAAT 94721 i v i iv MIRc#SINE/MIR 125 CAGTTTCCTCATCTGTAAAAT 145 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.88 CpG sites = 18, Kimura (unadjusted) = 39.24 Transitions / transversions = 1.00 (18/18) Gap_init rate = 0.02 (2 / 118), avg. gap size = 1.00 (2 / 2) 17 3.66 3.33 3.33 chr4qtel1M 94958 94987 (905013) (CTCC)n#Simple_repeat 1 30 (0) m_b192s252i17 7544 chr4qtel1M 94958 CTCCCTCCCTCCCTTACCTCCC-CCCTCCCT 94987 - v - (CTCC)n#Simpl 1 CTCCCTCCCTCCC-TCCCTCCCTCCCTCCCT 30 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.07 (2 / 29), avg. gap size = 1.00 (2 / 2) 180 33.33 2.74 1.35 chr4qtel1M 95336 95408 (904592) MIR3#SINE/MIR 135 208 (0) m_b192s601i9 7545 chr4qtel1M 95336 TGCAGAACAAGCTAGTTCAATGAGATGATCTCTATGTGTCCTTCCAGTTC 95385 i i ii vvi vi iv v vvi i MIR3#SINE/MIR 135 TGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTC 184 chr4qtel1M 95386 TAGAG--CTGTGATTTTTATAAATC 95408 iivi-- i - i i v MIR3#SINE/MIR 185 TGACATTCTATGA-TTCTATGATTC 208 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.20 CpG sites = 15, Kimura (unadjusted) = 46.20 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.03 (2 / 72), avg. gap size = 1.50 (3 / 2) 31 25.09 6.49 3.14 chr4qtel1M 95467 95620 (904380) (AAG)n#Simple_repeat 1 159 (0) m_b192s252i18 7546 chr4qtel1M 95467 AAAAAGAAGGATGGAGAGGAGGAGGAGGAGAAAGAAG-GGATGAGGAAG- 95514 i - v i i i i i ii -i v i - (AAG)n#Simple 1 AAGAAGAA-GAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA 49 chr4qtel1M 95515 AGAA-ATGAA-AGGAGGAGGAAGAGAAAGAAG-GGAGGAAGAGAGAAGAA 95561 - v - i i i ii -i i - (AAG)n#Simple 50 AGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA-AGAAGAA 98 chr4qtel1M 95562 -AAGAAG-AGATACAAGAAGAGAGATG-GGACTGAGAGAGAAG-AGAAAA 95607 - - - v - v -i vvi - - i (AAG)n#Simple 99 GAAGAAGAAGA-AGAAGAAGA-AGAAGAAGAAGAAGA-AGAAGAAGAAGA 145 chr4qtel1M 95608 AG-GGGAGAAGCAG 95620 -i i v (AAG)n#Simple 146 AGAAGAAGAAGAAG 159 Matrix = Unknown Transitions / transversions = 2.75 (22/8) Gap_init rate = 0.10 (15 / 153), avg. gap size = 1.00 (15 / 15) 16 29.06 5.32 3.12 chr4qtel1M 95473 95566 (904434) (AAGGA)n#Simple_repeat 1 96 (0) m_b192s252i19 7546 chr4qtel1M 95473 AAGG-ATGGAGAGGAGGAGGAGGAGAAA-GAAGGGATGAGGAAGAGAAAT 95520 - v i -i iii - i -i ii v (AAGGA)n#Simp 1 AAGGAAAGGAAAGGA-AAGGAAAGGAAAGGAAAGGA-AAGGAAAGGAAAG 48 chr4qtel1M 95521 GAAAGGAGGAGGAAGAGAAA-G-AAGG-GAGGAAGAGAGAAGAAAAGAA 95566 -i ii - - -i ii i i i (AAGGA)n#Simp 49 GAAAGGA-AAGGAAAGGAAAGGAAAGGAAAGGAAAGGAAAGGAAAGGAA 96 Matrix = Unknown Transitions / transversions = 9.00 (18/2) Gap_init rate = 0.09 (8 / 93), avg. gap size = 1.00 (8 / 8) 295 29.21 3.37 0.00 chr4qtel1M 96042 96130 (903870) MIR3#SINE/MIR 78 169 (39) m_b192s601i10 7547 chr4qtel1M 96042 CCAGCTGTGCAACCTCGAGGCCCTCATTCCCTCTCCTC---CCTCAGCTT 96088 i? ii i i vvvv i i vi iii--- i MIR3#SINE/MIR 78 CTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTT 127 chr4qtel1M 96089 CCTCACCTGCAAAATGAGGGGCTTGGACAAGTCCAGCTCTGA 96130 i i v v viv v i MIR3#SINE/MIR 128 CCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAA 169 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.88 CpG sites = 16, Kimura (unadjusted) = 38.88 Transitions / transversions = 1.60 (16/10) Gap_init rate = 0.01 (1 / 88), avg. gap size = 3.00 (3 / 1) 289 26.98 0.00 0.00 chr4qtel1M 96765 96827 (903173) MIRb#SINE/MIR 192 254 (14) m_b192s601i11 7548 chr4qtel1M 96765 ATGAAGCAGTATCTGAACAGCACTTGGCAGAGTGCCTGACATATAATAAG 96814 iii i iiv v v i i v i i i MIRb#SINE/MIR 192 ATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAG 241 chr4qtel1M 96815 TGCTTAATAAATG 96827 i i MIRb#SINE/MIR 242 CGCTCAATAAATG 254 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.55 CpG sites = 13, Kimura (unadjusted) = 35.73 Transitions / transversions = 3.25 (13/4) Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0) 295 35.81 8.11 0.00 chr4qtel1M 97156 97303 (902697) L3#LINE/CR1 3828 3987 (112) m_b192s601i12 7549 chr4qtel1M 97156 CCCTAGAGGGAAGAAGCAAGAACAATGGGTGGGGCTTGTAAAGAGA-ATC 97204 i i v vi i v iiv ii ii i- vv L3#LINE/CR1 3828 CTCCAGAGGGCAGAACTAGGACCAATGGGTGGAAGTTACAGGGAGGCAGA 3877 chr4qtel1M 97205 TATGGGTTTTATGTACAAGAAAACTTCCTCCTGATAGGAGATGTCC-GAC 97253 v v i iv i viii i i vvii vi v -i v L3#LINE/CR1 3878 TTTCGGCTCAATATAAGGAAGAACTTTCTAACAATCAGAGCTGTCCAAAA 3927 chr4qtel1M 97254 GCAGAAT-GGCCGCTCC------TGGCGGCCTCCC--TCATT-GAGGCTT 97293 iii - i ii ------ i i iv -- i - iv L3#LINE/CR1 3928 ATGGAATGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGTCACTGGAGGTGT 3977 chr4qtel1M 97294 TCAGACAGAG 97303 ii L3#LINE/CR1 3978 TCAAGCAGAG 3987 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 52.51 CpG sites = 36, Kimura (unadjusted) = 52.51 Transitions / transversions = 2.12 (36/17) Gap_init rate = 0.04 (6 / 147), avg. gap size = 2.00 (12 / 6) 511 32.36 3.30 2.34 chr4qtel1M 97592 97803 (902197) C MIR1_Amn#SINE/MIR (11) 219 6 m_b192s601i13 7550 chr4qtel1M 97592 TGGCTCCCATTTCTAGCATGTTTAA--GGCAAAT---AATGCACTGTGAG 97636 i ii v -- iv v --i i i --- v v i-- C MIR1_Amn#SINE 219 TAGCTCTTATGT--AGCACTTTTCATCAGTAGATCTCAAAGCACTTTA-- 174 chr4qtel1M 97637 GTGATGGGTATAAGTGTTCTTATTCCCATTTAACAGGTAAGGAAACTGAA 97686 -ii v ivi v i iv i v i i i C MIR1_Amn#SINE 173 -CAAAGGAGGTCAGTATCATTATCCCCATTTTACAGATGAGGAAACTGAG 125 chr4qtel1M 97687 GCTCATTGAGATGAAATGATTCACCCACAGGCACGCAGCT-ACAAGTGTC 97735 ? vv i ? i i ii vi v ? ?-i ? v C MIR1_Amn#SINE 124 GCNCAGAGAGGTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNAGTGGC 75 chr4qtel1M 97736 AGAGTTGGGA-TTGCACACAGACCTTCTGACTCTGCATTCAGGGCCTTTT 97784 ii - ? v v ii i i v ivvi i v ii v C MIR1_Amn#SINE 74 AGAGCCGGGANTNGAACCCAGGTCTCCCGAGTCCCAGTCCAGTGCTCTAT 25 chr4qtel1M 97785 CAGATAAACTGCCCCGACT 97803 viv i ii v i v C MIR1_Amn#SINE 24 CCACTAGACCACACTGCCT 6 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.12 CpG sites = 41, Kimura (unadjusted) = 46.02 Transitions / transversions = 1.58 (41/26) Gap_init rate = 0.04 (9 / 211), avg. gap size = 1.33 (12 / 9) 605 28.85 1.92 0.00 chr4qtel1M 97630 97785 (902215) C MIRc#SINE/MIR (89) 179 21 m_b192s601i14 7550 chr4qtel1M 97630 CTGTGAGGTGATGGGTATAAGTGTTCTTATTCCCATTTAACAGGTAAGGA 97679 iivvi vii i i v i v i i C MIRc#SINE/MIR 179 CTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGA 130 chr4qtel1M 97680 AACTGAAGCTCATTGAGATGAAATGATTCACCCACAGGCACGCAGCTA-C 97728 i vv i v i i ii vi v i -i C MIRc#SINE/MIR 129 AACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGT 80 chr4qtel1M 97729 AAGTGTCAGAGTTGGGA-TTGCACACAGACCTT-CTGACTCTGCATTCAG 97776 v ii - i v v ii - iivi i C MIRc#SINE/MIR 79 AAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAG 30 chr4qtel1M 97777 GGCCTTTTC 97785 v ii C MIRc#SINE/MIR 29 TGCTCTTTC 21 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.94 CpG sites = 30, Kimura (unadjusted) = 38.11 Transitions / transversions = 2.00 (30/15) Gap_init rate = 0.02 (3 / 155), avg. gap size = 1.00 (3 / 3) 14 15.75 5.41 0.00 chr4qtel1M 98615 98651 (901349) (GAGGGG)n#Simple_repeat 1 39 (0) m_b192s252i20 7551 chr4qtel1M 98615 GAGGGGGA-GAGG-GGGAGAGGGAGAGAGGGAGAGGGAG 98651 - i - i i i i (GAGGGG)n#Sim 1 GAGGGGGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGGAG 39 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 299 27.56 6.72 2.42 chr4qtel1M 99003 99121 (900879) MIRb#SINE/MIR 81 204 (64) m_b192s601i15 7552 chr4qtel1M 99003 TTCCTGGC-ATGAGTCCTCAAGCAATTTATTTGAACTGTCTGAGCCTCGG 99051 v i -i v v iii v i i v v i MIRb#SINE/MIR 81 TTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAG 130 chr4qtel1M 99052 TTTCCTCATCCTTAAAATGGCATCTCTCATAACTACCT-----GGT--CT 99094 iv vivivv v v ----- --i MIRb#SINE/MIR 131 TTTCCTCATCTGTAAAATGGGGATAATAATACCTACCTCGCAGGGTTGTT 180 chr4qtel1M 99095 GTAAGACTTTGCAAACCACATACTGCA 99121 i iv --- iv v v MIRb#SINE/MIR 181 GTGAGGATT---AAATGAGATAATGCA 204 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.65 CpG sites = 15, Kimura (unadjusted) = 34.65 Transitions / transversions = 0.88 (15/17) Gap_init rate = 0.05 (6 / 118), avg. gap size = 1.83 (11 / 6) 17 0.00 4.17 0.00 chr4qtel1M 99188 99211 (900789) (TAAA)n#Simple_repeat 1 25 (0) m_b192s252i21 7553 chr4qtel1M 99188 TAAA-AAATAAATAAATAAATAAAT 99211 - (TAAA)n#Simpl 1 TAAATAAATAAATAAATAAATAAAT 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 403 23.59 0.72 8.53 chr4qtel1M 99226 99364 (900636) MIR1_Amn#SINE/MIR 3 131 (99) m_b192s601i16 7554 chr4qtel1M 99226 GGGGGGCAGTGCAGCTAGATGGTTCAGTGCATAGAATACTGGCCCTGAAG 99275 i -------- ii v ii v iv i v MIR1_Amn#SINE 3 GGGAGGCAGTG--------TGGTCTAGTGGATAGAGCACTGGACTGGGAC 44 chr4qtel1M 99276 TCAGGAGGACCCGAGTTCAAATCTGGTCTCAAACACTTAACACTTCTCTG 99325 i - i i ? ? iv v viv ?iv ?v-- v? MIR1_Amn#SINE 45 TCGGGAG-ACCTGGGTTCNANTCCCGGCTCTGCCACTNGCCNG--CTGNG 91 chr4qtel1M 99326 TGACCCTGGACAAGTCACTTAACCCCAAT-TGCCTCAATT 99364 i i ? i vv -? i MIR1_Amn#SINE 92 TGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTT 131 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.43 CpG sites = 17, Kimura (unadjusted) = 30.63 Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.09 (12 / 138), avg. gap size = 1.00 (12 / 12) 467 25.43 0.83 1.68 chr4qtel1M 99245 99364 (900636) MIRc#SINE/MIR 11 129 (139) m_b192s601i17 7554 chr4qtel1M 99245 TGGTTCAGTGCATAGAATACTGGCCCTGAAGTCAGGAGGACCCGAGTTCA 99294 v v v ii v i i i i i i MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr4qtel1M 99295 AATCTGGTCTCAAACACTTAACACTTCTCTGTGACCCTGGACAAGTCACT 99344 i iv v viv vi --v v i i MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTACTA--GCTGTGTGACCTTGGGCAAGTCACT 108 chr4qtel1M 99345 TAACCCCAAT-TGCCTCAATT 99364 i vv -v i MIRc#SINE/MIR 109 TAACCTCTCTGAGCCTCAGTT 129 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.24 CpG sites = 16, Kimura (unadjusted) = 31.47 Transitions / transversions = 1.14 (16/14) Gap_init rate = 0.03 (3 / 119), avg. gap size = 1.00 (3 / 3) 442 36.10 1.54 5.18 chr4qtel1M 99735 99994 (900006) C MIRb#SINE/MIR (5) 263 13 m_b192s601i18 7555 chr4qtel1M 99735 TAGAGCAATGACTTATTGACCACTTG--GCGGGCTGCACCCAACTTCTAG 99782 v iv i v i i--ii v iivi v vi- v i C MIRb#SINE/MIR 263 TAGAGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTG-TGCTAA 215 chr4qtel1M 99783 TGCACATTTCTGTTATTCTTTCACTACTTTCTTCACCTCTGCCCTGTCAG 99832 - i v v vvvi v i i -ivv i vv vi iv C MIRb#SINE/MIR 214 -GCGCTTTACATGCATTATCTCATT-TAATCCTCACAACAACCCTGCGAG 167 chr4qtel1M 99833 GTAGGCAGGGAAAGTATTATTAAACCCACTTTGCAGATGAGGAAACTGAT 99882 --------- vv i i v C MIRb#SINE/MIR 166 GTAGG---------TATTATTATCCCCATTTTACAGATGAGGAAACTGAG 126 chr4qtel1M 99883 GTTCATGGTGGCTGAGCGATTCTCCCTACATCATATCACTAGCAAAAAGT 99932 i vi v i i ii i iv v vi i ivi i ivi i C MIRb#SINE/MIR 125 GCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGC 76 chr4qtel1M 99933 CTAACATGGTATTTGAAGCC-GGTGT-CCTGACTCCAAGGGCAAAGCTTT 99980 vv i -i v i v - v -i i v viv i C MIRb#SINE/MIR 75 AGAGC-CGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCT 27 chr4qtel1M 99981 TCATAATACACTGC 99994 ivi v i ii C MIRb#SINE/MIR 26 TTCCACTGCACCAC 13 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.96 CpG sites = 49, Kimura (unadjusted) = 50.69 Transitions / transversions = 1.23 (49/40) Gap_init rate = 0.06 (16 / 259), avg. gap size = 1.06 (17 / 16) 591 33.93 1.35 0.89 chr4qtel1M 99773 99995 (900005) C MIRc#SINE/MIR (36) 232 9 m_b192s601i19 7555 chr4qtel1M 99773 CAACTTCTAGTGCACATTTCTGT-TATTCTTTCACTACTTTCTTCACCTC 99821 ii vi iv i v ivii -i v i i -ivv i vv C MIRc#SINE/MIR 232 CAGTTTACAAAGCGCTTTCACATACATTATCTCATT-TGATCCTCACAAC 184 chr4qtel1M 99822 TGCCCTGTCAGGTAGGCAGGGAAAGTATTATTAAACCCACTTTGCAGATG 99871 vi v v i vv i i C MIRc#SINE/MIR 183 AACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATG 134 chr4qtel1M 99872 AGGAAACTGATGTTCATGGTGGCTGAGCGATTCTCCCTACATCATATCAC 99921 v i vi v i i i i iv v vi i ivi C MIRc#SINE/MIR 133 AGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGC 84 chr4qtel1M 99922 TAGCAAAAAGTCTAACATGGTATTTGAAGCC-GGT-GTCCTGACTCCAAG 99969 i ivi ivv i -i v i i v - -v C MIRc#SINE/MIR 83 TAGTAAGTGGCAGAGC-CGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr4qtel1M 99970 GGCAAAGCTTTTCATAATACACTGCA 99995 vv iv i ivi v i ii C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTGCACCACA 9 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.16 CpG sites = 43, Kimura (unadjusted) = 46.72 Transitions / transversions = 1.34 (43/32) Gap_init rate = 0.02 (5 / 222), avg. gap size = 1.00 (5 / 5) 282 35.86 0.92 2.80 chr4qtel1M 100253 100361 (899639) MIR3#SINE/MIR 82 188 (20) m_b192s601i20 7556 chr4qtel1M 100253 CCATGTGATCTCAG-CAAGTGACCTGGCTTCTCTGTGCTGCTTCCACTTT 100301 ii i ii - v i vi i v i--- vii i MIR3#SINE/MIR 82 CTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCC---TCAGTTTC 128 chr4qtel1M 100302 GTCCTTTGTAAAACAGGAGCCCTGGCCTATATGACTTCTGAGGCCCCTCC 100351 v v i iii i vvi v v ii i i i MIR3#SINE/MIR 129 CTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTC 178 chr4qtel1M 100352 AAAGTCTAGC 100361 v iv ii MIR3#SINE/MIR 179 CAGCTCTGAC 188 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 52.71 CpG sites = 26, Kimura (unadjusted) = 52.71 Transitions / transversions = 2.17 (26/12) Gap_init rate = 0.04 (4 / 108), avg. gap size = 1.00 (4 / 4) 220 38.55 0.00 0.00 chr4qtel1M 100395 100477 (899523) MIR3#SINE/MIR 120 202 (6) m_b192s601i21 7557 chr4qtel1M 100395 CTCAATTTCCCTTCTTATGAAAAAAGGTCACTGGACCAGTTAACTTCTAC 100444 i iivii i i vi vvii i v i ii v MIR3#SINE/MIR 120 CTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAA 169 chr4qtel1M 100445 AATTGCTTTGTGCCCTGACAGTCTAGAATTTTA 100477 ii iv ivv i v vi i MIR3#SINE/MIR 170 GGTCCCTTCCAGCTCTGACATTCTATGATTCTA 202 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 58.58 CpG sites = 21, Kimura (unadjusted) = 58.58 Transitions / transversions = 1.91 (21/11) Gap_init rate = 0.00 (0 / 82), avg. gap size = 0.0 (0 / 0) 370 23.62 2.03 5.59 chr4qtel1M 101036 101183 (898817) CR1_Mam#LINE/CR1 511 653 (1551) m_b192s551i0 7558 chr4qtel1M 101036 GAGGAGGTTTGGGAATCCTG--AATTATGGCAGGTCAGGAATGGAGCTA- 101082 iviv v i -- v v iii - - CR1_Mam#LINE/ 511 GAGGAGAACAGGGAAGCCCGCAAAGTATGGCAGGTCAGGTACAAA-CTAG 559 chr4qtel1M 101083 AAATTAGGTGAGACCAAAAAAAGATATGAGGAATGATTTGCAAAGGTTTC 101132 i i - ii v iiivi i vi CR1_Mam#LINE/ 560 AAATTAGGCGGG-CCAAAAAAGAATTTGAGGAGCACCTTGCAAGGGACTC 608 chr4qtel1M 101133 CAACACCACTAATAAAAAGTGCTTCGTAATGCTGCACATCCAAGGAAAGA 101182 vi v i v -- ----ii v ? i CR1_Mam#LINE/ 609 CAAAGCCAATAATAAAAGGTTCTT--TAA----ATACATCAAAGGNAGGA 652 chr4qtel1M 101183 A 101183 CR1_Mam#LINE/ 653 A 653 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 27.26 CpG sites = 21, Kimura (unadjusted) = 29.33 Transitions / transversions = 1.75 (21/12) Gap_init rate = 0.07 (10 / 147), avg. gap size = 1.10 (11 / 10) 23 22.07 0.00 0.00 chr4qtel1M 102295 102342 (897658) (G)n#Simple_repeat 1 48 (0) m_b192s252i22 7559 chr4qtel1M 102295 GGGGCTGGGGGAAGGGAAGGAGGCAGGGGGGGGGGGGGGGGGGGGGGG 102342 vv ii ii i vi (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 48 Matrix = Unknown Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 261 20.38 0.00 1.85 chr4qtel1M 102965 103019 (896981) MIRc#SINE/MIR 104 157 (111) m_b192s601i22 7560 chr4qtel1M 102965 TCAATTAATTTTCTCTAAACCTCAGGGGTCTCATCTGTAAGATGGGGATA 103014 v ii - i i vvvi i MIRc#SINE/MIR 104 TCACTTAACCT-CTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATA 152 chr4qtel1M 103015 ATAGT 103019 i MIRc#SINE/MIR 153 ATAAT 157 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 24.28 CpG sites = 7, Kimura (unadjusted) = 24.28 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1) 469 24.18 5.52 3.61 chr4qtel1M 103014 103176 (896824) C MIRc#SINE/MIR (0) 268 103 m_b192s601i23 7561 chr4qtel1M 103014 AATAGTCACAATAGCTTAGCTCGAATTTATGTTGCCCTTTGGCATCTTTC 103063 i v i i?v v----- i i v v i- vi v C MIRc#SINE/MIR 268 AATAATAATAACNCCTTAC-----ATTTGTATAGCACTTTA-CAGTTTAC 225 chr4qtel1M 103064 AAATTCTTTGCAAATAC--TATCTCTTTGGGGATTTACAATAAGCCTGTG 103111 vivi v v -- v v ivvi i i v C MIRc#SINE/MIR 224 AAAGCGCTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTG 175 chr4qtel1M 103112 AGGTAG--ATGGC---CACT-CTA-CCCCATCTTACAGATGGGGAAACTG 103154 -- v ---i i -i - i i C MIRc#SINE/MIR 174 AGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTG 125 chr4qtel1M 103155 AGGTTGAGAGAGGTTAAATGAC 103176 i v i C MIRc#SINE/MIR 124 AGGCTCAGAGAGGTTAAGTGAC 103 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.89 CpG sites = 20, Kimura (unadjusted) = 29.80 Transitions / transversions = 1.11 (20/18) Gap_init rate = 0.07 (11 / 162), avg. gap size = 1.36 (15 / 11) 20 0.00 0.00 0.00 chr4qtel1M 103395 103416 (896584) (GT)n#Simple_repeat 1 22 (0) m_b192s252i23 7562 chr4qtel1M 103395 GTGTGTGTGTGTGTGTGTGTGT 103416 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGT 22 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 25 24.34 1.59 0.00 chr4qtel1M 103434 103496 (896504) (GA)n#Simple_repeat 1 64 (0) m_b192s252i24 7563 chr4qtel1M 103434 GAGACAGAGATTGACAGAGACA-AGACAGAGGGACAGAGAGAAACACAGA 103482 v vv v v - v i v i v v (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr4qtel1M 103483 GAGAGAGTCAGAGA 103496 vv (GA)n#Simple_ 51 GAGAGAGAGAGAGA 64 Matrix = Unknown Transitions / transversions = 0.18 (2/11) Gap_init rate = 0.02 (1 / 62), avg. gap size = 1.00 (1 / 1) 341 23.53 6.72 0.00 chr4qtel1M 103614 103732 (896268) MIR1_Amn#SINE/MIR 33 159 (71) m_b192s601i24 7564 chr4qtel1M 103614 CTGGATTAGGAGTTCTGAGTCCTGGAGCCCAATCCAGGCTCTGTTCCTC- 103662 i i v ivv v ivi ? ? v iiv ?- MIR1_Amn#SINE 33 CTGGACTGGGACTCGGGAGACCTGGGTTCNANTCCCGGCTCTGCCACTNG 82 chr4qtel1M 103663 CCAGCTTTGTAGCCTTAGGCAGGTCG--TAACCTCTCAAATTCTGGG--T 103708 ? v? ii i i i-- ? vi?vi vi -- MIR1_Amn#SINE 83 CCNGCTGNGTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTT 132 chr4qtel1M 103709 CCTCCTCT-TAAAA-GGGGA-AGTGAT 103732 v - - - i MIR1_Amn#SINE 133 CCTCATCTGTAAAATGGGGATAATGAT 159 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.67 CpG sites = 16, Kimura (unadjusted) = 30.98 Transitions / transversions = 1.33 (16/12) Gap_init rate = 0.05 (6 / 118), avg. gap size = 1.33 (8 / 6) 254 32.39 1.41 0.00 chr4qtel1M 105030 105100 (894900) MamTip2#DNA/hAT-Tip100 3 74 (231) m_b192s601i25 7565 chr4qtel1M 105030 GGGGTGACCTTACAC-CAGGCCACAGAGACTGCTGCCTACATAGTGTAAT 105078 vi i i -i viviv i v i i i i MamTip2#DNA/h 3 GGGCCGGCCTTACGCGTAGGCAGAGTAGGCGGCCGCCTACGTGGTGTGAT 52 chr4qtel1M 105079 TTCAGAGGAGCCAGAAAGGTCC 105100 v i v i i ii MamTip2#DNA/h 53 TTGAGGGGCGCCGGGAAGGCTC 74 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.95 CpG sites = 16, Kimura (unadjusted) = 45.34 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.01 (1 / 70), avg. gap size = 1.00 (1 / 1) 357 28.81 5.93 0.00 chr4qtel1M 105150 105267 (894733) MIR3#SINE/MIR 78 202 (6) m_b192s601i26 7566 chr4qtel1M 105150 CTGCCTTTGTAACCCTGGGCAAGTTAC---ACTTCCCTGGGCCTACATTC 105196 ?v v i i i --- i i vvi i MIR3#SINE/MIR 78 CTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTT 127 chr4qtel1M 105197 ACCCATCTGTTATCTGAGGGAATTGGACTGCCTGGCCTCCGA-GTCCCTC 105245 v i v vv ii ivv ii ii - i MIR3#SINE/MIR 128 CCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTT 177 chr4qtel1M 105246 CTA---CATAGAATTTGTGATCCTA 105267 i --- vv v v i i i MIR3#SINE/MIR 178 CCAGCTCTGACATTCTATGATTCTA 202 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.79 CpG sites = 20, Kimura (unadjusted) = 37.79 Transitions / transversions = 1.43 (20/14) Gap_init rate = 0.03 (3 / 117), avg. gap size = 2.33 (7 / 3) 187 29.35 23.91 0.00 chr4qtel1M 105909 106000 (894000) MIRb#SINE/MIR 38 151 (117) m_b192s601i27 7567 chr4qtel1M 105909 TTTGCAGGCAGA-GGACTCCATTTCAAATTCTAACTC-GCTATTTG---- 105952 v v -i iiviv i i iii - i i i---- MIRb#SINE/MIR 38 TTTGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAG 87 chr4qtel1M 105953 ----GGGGCCTATGGCAAGT------------CTGGGCCCTAATTTCCTC 105986 ---- v i vv ------------ i ii i MIRb#SINE/MIR 88 CTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTC 137 chr4qtel1M 105987 AACTGTAAAGTGAG 106000 v i i MIRb#SINE/MIR 138 ATCTGTAAAATGGG 151 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.47 CpG sites = 19, Kimura (unadjusted) = 39.43 Transitions / transversions = 2.38 (19/8) Gap_init rate = 0.05 (5 / 91), avg. gap size = 4.40 (22 / 5) 194 25.00 18.75 0.00 chr4qtel1M 105921 106000 (894000) MIR1_Amn#SINE/MIR 56 150 (80) m_b192s601i28 7567 chr4qtel1M 105921 GGACTCCATTTCAAATTCTA--ACTCGCTATTTGGG-GGCCTATGGCAAG 105967 ii ? ? i viii i-- ? i?vi ? - i vv MIR1_Amn#SINE 56 GGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAG 105 chr4qtel1M 105968 TC------------TGGGCCCTAATTTCCTCAACTGTAAAGTGAG 106000 ------------ ? ii i v i i MIR1_Amn#SINE 106 TCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGG 150 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.40 CpG sites = 15, Kimura (unadjusted) = 35.65 Transitions / transversions = 3.00 (15/5) Gap_init rate = 0.04 (3 / 79), avg. gap size = 5.00 (15 / 3) 375 17.29 13.73 3.57 chr4qtel1M 105938 106039 (893961) MIR3#SINE/MIR 74 185 (23) m_b192s601i29 7567 chr4qtel1M 105938 CTAACTCGCTATTTGGGGGCCTATGGCAAGTC------------TGGGCC 105975 ? i --- v i vv ------------ MIR3#SINE/MIR 74 CTAACTNGCTGT---GTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCC 120 chr4qtel1M 105976 CTAATTTCCTCAACTGTAAAGTGAGAGGGGTTAGATTAAGTAGTCT-TAA 106024 ii i v i - i i ii ii - MIR3#SINE/MIR 121 TCAGTTTCCTCATCTGTAAAATGAG-GGGGTTGGACTAGATGATCTCTAA 169 chr4qtel1M 106025 GGTCTCTT-CAGCTCT 106039 i - MIR3#SINE/MIR 170 GGTCCCTTCCAGCTCT 185 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 20.65 CpG sites = 13, Kimura (unadjusted) = 20.65 Transitions / transversions = 3.25 (13/4) Gap_init rate = 0.07 (7 / 101), avg. gap size = 2.57 (18 / 7) 231 31.27 0.73 15.97 chr4qtel1M 106034 106170 (893830) MIRc#SINE/MIR 26 144 (124) m_b192s601i30 7568 chr4qtel1M 106034 AGCTCTAGATCTG-TGTCCAGAGAACCTGGCTTAGCATTCTGGTTCTGCC 106082 v i ii -v vi ii v v vi i i i MIRc#SINE/MIR 26 AGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCC 75 chr4qtel1M 106083 ACAAAAGAGCAGCGTGGCCTTTCATTGGGCTTCTCTCTAGGCTCCTTCTG 106132 vv vv v i i ----- -------- i iiv ---- MIRc#SINE/MIR 76 ACTTACTAGCTGTGTGACC-----TTGGGC--------AAGTCACT---- 108 chr4qtel1M 106133 TGTCCCCTATATGGGCTTTAGTTTCCTCTTCTGTCAAA 106170 -- vv v v i i i v v MIRc#SINE/MIR 109 --TAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAA 144 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.30 CpG sites = 18, Kimura (unadjusted) = 39.69 Transitions / transversions = 1.00 (18/18) Gap_init rate = 0.15 (20 / 136), avg. gap size = 1.00 (20 / 20) 217 30.35 0.56 23.13 chr4qtel1M 106051 106230 (893770) MIRb#SINE/MIR 46 192 (76) m_b192s601i31 7568 chr4qtel1M 106051 CAGAGA-ACCTGGCTTAGCATTCTGGTTCTGCCACAAAAGAGCAGCGTGG 106099 v - v v v i i i vv vv v i i MIRb#SINE/MIR 46 CAGACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGA 95 chr4qtel1M 106100 CCTTTCATTGGGCTTCTCTCTAGGCTCCTTCTGTGTCCCCTATATGGGCT 106149 ----- -------- i i v ------ vv v v i i MIRb#SINE/MIR 96 CC-----TTGGGC--------AAGTTACT------TAACCTCTCTGAGCC 126 chr4qtel1M 106150 TTAGTTTCCTCTTCTGTCAAAAAGACCACATTGGATTAAATGATCCCCAA 106199 i v v vi -------- -- i v i - MIRb#SINE/MIR 127 TCAGTTTCCTCATCTGTAAAATGG--------GGAT--AATAATACCTA- 165 chr4qtel1M 106200 GGTCTTTTGCAGGATTCTAGTTAGATCCAAA 106230 ----ii i i v v v ivii MIRb#SINE/MIR 166 ----CCTCGCAGGGTTGTTGTGAGGATTAAA 192 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.51 CpG sites = 20, Kimura (unadjusted) = 36.61 Transitions / transversions = 0.91 (20/22) Gap_init rate = 0.20 (35 / 179), avg. gap size = 1.00 (35 / 35) 375 28.94 0.00 14.18 chr4qtel1M 106051 106211 (893789) MIR3#SINE/MIR 41 181 (27) m_b192s601i32 7568 chr4qtel1M 106051 CAGAGAACCTGGCTTAGCATTCTGGTTCTGCCACAAAAGAGCAGCGTGGC 106100 iii v vvvi i i i v vv? v i i MIR3#SINE/MIR 41 CAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGAC 90 chr4qtel1M 106101 CTTTCATTGGGCTTCTCTCTAGGCTCCTTCTGTGTCCCCTATATGGGCTT 106150 ----- -------- i iiv ------v v v i MIR3#SINE/MIR 91 CTT-----GGGC--------AAGTCACTTC------ACCTCTCTGGGCCT 121 chr4qtel1M 106151 TAGTTTCCTCTTCTGTCAAAAAGACCACATTGGATTAAATGATCCCCAAG 106200 i v - v vvivi i i i i MIR3#SINE/MIR 122 CAGTTTCCTCATCTGT-AAAATGAGGGGGTTGGACTAGATGATCTCTAAG 170 chr4qtel1M 106201 GTCTTTTGCAG 106211 ii v MIR3#SINE/MIR 171 GTCCCTTCCAG 181 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.54 CpG sites = 22, Kimura (unadjusted) = 36.68 Transitions / transversions = 1.22 (22/18) Gap_init rate = 0.12 (20 / 160), avg. gap size = 1.00 (20 / 20) 216 30.56 9.30 1.08 chr4qtel1M 106507 106592 (893408) L2d2_3end#LINE/L2 441 533 (22) m_b192s601i33 7569 chr4qtel1M 106507 GTAAGCCTCCTGCAGATAG-----AAGCCTT-TCCATCCTTGTCATCCCC 106550 ii i vi ii ----- v i - v v i - L2d2_3end#LIN 441 GTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACTTCTTTGT-ATCCCC 489 chr4qtel1M 106551 CA--GCACTTAGCATGCTGTTTTGCACAAAGGAGCCATTTAGTA 106592 -- i i iiv ii v v v ii i i L2d2_3end#LIN 490 CACAGCGCCTAGCACAGTGCCTTGCACACAGTAGGCGCTCAATA 533 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.46 CpG sites = 18, Kimura (unadjusted) = 41.67 Transitions / transversions = 2.25 (18/8) Gap_init rate = 0.05 (4 / 85), avg. gap size = 2.25 (9 / 4) 13 14.97 5.13 2.50 chr4qtel1M 106804 106842 (893158) (AGGAGTG)n#Simple_repeat 1 40 (0) m_b192s252i25 7570 chr4qtel1M 106804 AGGAGTGAGAAGTGAGGTGCGAGCAG-G-GGATGTGAGAAG 106842 i v i v - - - i (AGGAGTG)n#Si 1 AGGAGTGAGGAGTGAGGAGTGAGGAGTGAGGA-GTGAGGAG 40 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.08 (3 / 38), avg. gap size = 1.00 (3 / 3) 431 27.63 7.98 2.33 chr4qtel1M 106899 107061 (892939) C MIR1_Amn#SINE/MIR (4) 226 55 m_b192s601i34 7571 chr4qtel1M 106899 TAACAACTAACACTTAGGGAATGCTTTACCATTTGTA-------AAGCAC 106941 i v i v v v iii -i iv ------- C MIR1_Amn#SINE 226 TAATACCTAGCTCTTATGTAGCACTTT-TCATCAGTAGATCTCAAAGCAC 178 chr4qtel1M 106942 TTTATGATCTTGCTTGATCTTTATGTTATCCTTATGTTACAAATGAGGAA 106991 ii vvvv v iii v i---i ii v i C MIR1_Amn#SINE 177 TTTACAAAGGAGGTCAGTATC---ATTATCCCCATTTTACAGATGAGGAA 131 chr4qtel1M 106992 ACTGAGG--CAGAGAGGT----TGGCTTGCTCAGGGTCACTCAGCTGGTA 107035 -- ---- i i i ? ? i? C MIR1_Amn#SINE 130 ACTGAGGCNCAGAGAGGTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCN 81 chr4qtel1M 107036 AGTATCACACGCAAGATCCTGACTCA 107061 iv v vv ii ?i?vi i C MIR1_Amn#SINE 80 AGTGGCAGAGCCGGGANTNGAACCCA 55 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.07 CpG sites = 27, Kimura (unadjusted) = 37.14 Transitions / transversions = 1.59 (27/17) Gap_init rate = 0.04 (7 / 162), avg. gap size = 2.43 (17 / 7) 490 23.73 5.93 0.00 chr4qtel1M 106965 107082 (892918) C MIRc#SINE/MIR (113) 155 31 m_b192s601i35 7571 chr4qtel1M 106965 TGTTATCCTTATGTTACAAATGAGGAAACTGAGG--CAGAGAGGT----T 107008 i ii v i -- ---- C MIRc#SINE/MIR 155 TATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGT 106 chr4qtel1M 107009 GGCTTGCTCAGGGTCACTCAGCTGGTAAGTATCACACGCAAGATCCTGAC 107058 i i i v i iv v vv ii ii vi C MIRc#SINE/MIR 105 GACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAAC 56 chr4qtel1M 107059 TCA-CTCTTTTTACCTCCATGTCCA 107082 i -v ii iv v C MIRc#SINE/MIR 55 CCAGGTCTTCCTGACTCCAAGTCCA 31 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.11 CpG sites = 18, Kimura (unadjusted) = 29.34 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.03 (3 / 117), avg. gap size = 2.33 (7 / 3) 394 34.75 3.61 1.18 chr4qtel1M 108276 108441 (891559) MIRc#SINE/MIR 14 183 (85) m_b192s601i36 7572 chr4qtel1M 108276 TGCTGTGACTTGGGCA--GAGTTTAGCGTCAGGAGACATCTGGGCTTGAA 108323 v ivvv i -- iii i v - v i i i i MIRc#SINE/MIR 14 TGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGA-AGACCTGGGTTCGAG 62 chr4qtel1M 108324 TGCCAGCTCTGACAATTGTACACTGCACCACTGTGGACAAAGTTCTTAA- 108372 v i v v iivvi iiiv iv i iviv - MIRc#SINE/MIR 63 TCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAAC 112 chr4qtel1M 108373 ---ATTGAGCCTCAGTTTCCTCATTTGTAAGTTTGGGAGCATACTATTTA 108419 ---vi i iv v vv v ii i MIRc#SINE/MIR 113 CTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTG 162 chr4qtel1M 108420 CAGGACTTCCCCTCAAAAAGTT 108441 vvvi i -v v ii MIRc#SINE/MIR 163 CCCTGCCT-ACCTCACAGGGTT 183 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.68 CpG sites = 31, Kimura (unadjusted) = 47.99 Transitions / transversions = 1.19 (31/26) Gap_init rate = 0.03 (5 / 165), avg. gap size = 1.60 (8 / 5) 410 29.60 3.17 0.78 chr4qtel1M 108295 108420 (891580) MIRb#SINE/MIR 38 166 (102) m_b192s601i37 7572 chr4qtel1M 108295 TTTAGCGTCAGGAGACATCTGGGCTTGAATGCCAGCTCTGACAATTGTAC 108344 i v - v v i i i v i v v iivv MIRb#SINE/MIR 38 TTTGGAGTCAG-ACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTA 86 chr4qtel1M 108345 ACTGCACCACTGTGGACAAAGTTCTTAA----ATTGAGCCTCAGTTTCCT 108390 i iiiv iv i iv v ----vi MIRb#SINE/MIR 87 GCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCT 136 chr4qtel1M 108391 CATTTGTAAGTTTGGGAGCATACTATTTAC 108420 i iv v vv v ii MIRb#SINE/MIR 137 CATCTGTAAAATGGGGATAATAATACCTAC 166 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.66 CpG sites = 19, Kimura (unadjusted) = 38.20 Transitions / transversions = 1.06 (19/18) Gap_init rate = 0.02 (2 / 125), avg. gap size = 2.50 (5 / 2) 190 30.22 0.50 18.93 chr4qtel1M 108463 108662 (891338) C L2c_3end#LINE/L2 (45) 433 265 m_b192s601i38 7573 chr4qtel1M 108463 GGTGCTGGTGATCCAAAGACAAGAGAAGTACAGGAGCTGCCCTCAAAGAT 108512 i v v ii ivi iii i vvv i v C L2c_3end#LINE 433 GGCGCTGGGGATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAG 384 chr4qtel1M 108513 TTGATATTCTGCTTTGTGGAGATCACTTGGACCCAGATACGT-AACAGAC 108561 i v i v i---- -------- vv i ? - C L2c_3end#LINE 383 CTCACAGTCTA----GTGGA--------GGAGACAGACANGTAAACAGAC 346 chr4qtel1M 108562 AATGAGTTCAGGATGAGCTTCAGCTGAGCTGGGCCAGGAGCCAGAGATGA 108611 v --- iv ii - v -- -------i i v i v - - C L2c_3end#LINE 345 AATTA---CAATACAAG-TTAA--TGA-------TAAGTGCTATA-ATG- 311 chr4qtel1M 108612 AGAGTGTGGGGACAGAGTGGATATTTGGGAGGATCCAGGAATGCACCCAG 108661 i i --i i ---v v v ivv iv i C L2c_3end#LINE 310 GGAGTAT--AGACAGGGTG---CTATGGGAGCACAGAGGAGGGCACCTAG 266 chr4qtel1M 108662 A 108662 C L2c_3end#LINE 265 A 265 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.06 CpG sites = 27, Kimura (unadjusted) = 38.00 Transitions / transversions = 1.23 (27/22) Gap_init rate = 0.17 (33 / 199), avg. gap size = 1.00 (33 / 33) 290 25.27 7.95 1.06 chr4qtel1M 108637 108724 (891276) C MIR3#SINE/MIR (28) 180 87 m_b192s601i39 7574 chr4qtel1M 108637 TGGGAGGATCC--AGGAATGCACCCAG---AACCTGCTTATTTTACAGAG 108681 i iv -- ii - i i --- iv i v C MIR3#SINE/MIR 180 TGGAAGGGACCTTAGAGAT-CATCTAGTCCAACCCCCTCATTTTACAGAT 132 chr4qtel1M 108682 GAAGAAA--GAGGCCCCAGGAAGTGAGCTGACTGGTCCAGGATCA 108724 i -- vii i iv v i i i C MIR3#SINE/MIR 131 GAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCA 87 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.41 CpG sites = 16, Kimura (unadjusted) = 32.41 Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.05 (4 / 87), avg. gap size = 2.00 (8 / 4) 325 33.84 7.06 3.80 chr4qtel1M 108740 108994 (891006) C L3b_3end#LINE/CR1 (454) 752 490 m_b192s601i40 7575 chr4qtel1M 108740 CTGTCCCCGAATGCTCTCTGGC--TTCCAGTGTCTGACACTCAGAACTGA 108787 v i i ? v ivi v -- ii iv? v i?i i C L3b_3end#LINE 752 CTCTCTCCAANTTCTCCACGTCCCTTTTAAANTGTGGNGCCCAGAACTGA 703 chr4qtel1M 108788 ACACAATCCTTGAATTATCTGGGCCTG------GAAGA-TTGAG---GAC 108827 i i v iv i? i?--- ------ v - v --- ? C L3b_3end#LINE 702 ACGCAGTACTCCAGNTGN---GGCCTGACCAGCGCAGAGTAGAGCGGGAN 656 chr4qtel1M 108828 CA-CAATTCCCT--GTCTGCCCCCTAGTCT-CTG--GAGGAGGGCCAGGG 108871 ? - vi --? i vv v v? - --i v vi v i i C L3b_3end#LINE 655 NATCACCTCCCTTGNTCTGTCGGCGATNCTTCTGTTAATGCAGCCCAAGA 606 chr4qtel1M 108872 TTACATCTGAGAGATTTCTTGACTGCAAAGCCTGGCTGCCGACTTGTGCT 108921 ii i---- v i i v viv i vvi i ii ii C L3b_3end#LINE 605 TCGCATT----AGCTTTTTTGGCAGCCGCGTCGCACTGCTGACTCATATT 560 chr4qtel1M 108922 GAACCTGAAGCCCACTGAGACCCTTGGGGTGTTTTCTCATGCGAGATGCC 108971 i i vi i v i i iii viv v -- ? v i C L3b_3end#LINE 559 GAGCTTGCGGTCAACTAAAACCCCCAGGTCTTTTTCACAT--GNGCTGCT 512 chr4qtel1M 108972 ATCCAGCTGCTTCCCTCCACATC 108994 iiiv i v i i - C L3b_3end#LINE 511 GCTAAGCCGCGTCTCCCC-CATC 490 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.00 CpG sites = 51, Kimura (unadjusted) = 50.17 Transitions / transversions = 1.59 (51/32) Gap_init rate = 0.07 (18 / 254), avg. gap size = 1.56 (28 / 18) 339 37.51 12.28 1.13 chr4qtel1M 109145 109543 (890457) C L3#LINE/CR1 (1911) 2188 1746 m_b192s601i41 7576 chr4qtel1M 109145 TCCCACCTTCTGTT------CCTCTTTAAAACTCAATTTGGTGAAAACAG 109188 i i v ------ i v v v vv ii v v? vv C L3#LINE/CR1 2188 TTCCATCTTCTGATACATGTCCTTTTAAAATCTGACATCAGAGAATNCTC 2139 chr4qtel1M 109189 TGTGTGTCCAAACCAGCCTCTTCAAATGAC-TCCCG----TCCTCCTTTT 109233 i ?iv viiii ii - v - v---- i iv C L3#LINE/CR1 2138 TATGNAGCCACGTTGGTTTCTT-AAATGCCCTCCCTCTTTTCTTCCTCAT 2090 chr4qtel1M 109234 TGGATCCTTCCTCTTGATATTGTCTGAATTCCAGCCTTGAAAGTTTCTC- 109282 v iv vv vi -- v i vii i i i i - C L3#LINE/CR1 2089 TGGATCATTTGTAATTGTA--GTCAGAATTTCATTTTTAAGAGCTTCCCA 2042 chr4qtel1M 109283 -CCCTCCTGAACTGACCTACTCTGTAGAACCCTGGGCTGCCAAATGCT-C 109330 - i i iiv i v i v - ii ii? iiivi vv - C L3#LINE/CR1 2041 NCCCTCTTGAGCCATCTTTCTTTTT-GAGTCTCNGGCCATGGAATCATAC 1993 chr4qtel1M 109331 CTTCTTCCTCAGAACTCCCTGAGATC------ATCTC-TAAAACACAGAA 109373 ii i v i iii i ------vi - iivii C L3#LINE/CR1 1992 CTCTTTTCTCTGAATTTTTTGAAATCTGCTTTTCCTCGTAAAGTCTGGAA 1943 chr4qtel1M 109374 CAGACA-ATACTCT--GCTTTCCTCTTCTGTAGC-ATCTGATACGTTGGG 109419 v ii-iv i --i i ii - i - ivviv vi ii C L3#LINE/CR1 1942 CATATGTGGACTTTTAACTTTTCCTTTCT-TGGCTATTACGAACTCTAAG 1894 chr4qtel1M 109420 GTTAAACCATCCCTTTCCCCAAGGACTCCATC-ATTGCC---------AT 109459 i v v iviiv i ii vii i - i v --------- i C L3#LINE/CR1 1893 ATGACATGGCACTTTCTCCCAAGGTTCCTATCGACTTCCACTTCACCAAC 1844 chr4qtel1M 109460 CAGTTCTTTCTTCCA----AGGACCCAATTCAGA--AGT--TTCCCCTCA 109501 i viv---- i iiv i i -- i-- i C L3#LINE/CR1 1843 CAGTTCTTCCTTGTTGGTCAGAATTAAGTCCAGAGTAGCAGTTCCCCTCG 1794 chr4qtel1M 109502 CTG------GTACTTCCAAAAGGATGGAATCATCACTAAGGTAAACCA 109543 i ------v i i vi ii i ii vi i ii C L3#LINE/CR1 1793 TTGCTTCCTCTACCTTCTGAGAGATGAAATTGTCAGCAAGGCAAGTCA 1746 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 55.32 CpG sites = 99, Kimura (unadjusted) = 57.16 Transitions / transversions = 2.02 (99/49) Gap_init rate = 0.06 (22 / 398), avg. gap size = 2.45 (54 / 22) 206 37.98 3.92 1.92 chr4qtel1M 109671 109823 (890177) L2d_3end#LINE/L2 131 286 (230) m_b192s601i42 7577 chr4qtel1M 109671 CCTTTGCTGATTTCACACACAGTTCCTGGAATGGTTGTTGTCCTCCTCAG 109720 v ivi iiv v vviv viiv ivi i -- L2d_3end#LINE 131 CCTTTGCTCACGCCGTTCCCCCCGCCTGGAATGCCCTTCCCCTTCCTC-- 178 chr4qtel1M 109721 CTCTGTCTCTTGGCTTCCTGGCT-TCCTTCAAATCTCAGCTAAAACCTCA 109769 - v v ivivv iv i- iv i v ii i L2d_3end#LINE 179 -TCTCTCTATCCAAATCCTACCCATCCTTCAAGGCCCAGCTCAAGTCCCA 227 chr4qtel1M 109770 GCTTCTGCAAGAAGCTTTTTCTCATCGTTTGAG-----ATTCAAGTCTTC 109814 v i v v i ii v i ii iv ----- i v vv i L2d_3end#LINE 228 CCTCCTCCACGAAGCCTTCCCTGACCACTCCAGCCCACACTGATCTCTCC 277 chr4qtel1M 109815 CTTCTGCGA 109823 vi L2d_3end#LINE 278 CTTCTCTGA 286 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 50.42 CpG sites = 30, Kimura (unadjusted) = 54.53 Transitions / transversions = 1.11 (30/27) Gap_init rate = 0.03 (5 / 152), avg. gap size = 1.80 (9 / 5) 236 35.67 18.11 0.67 chr4qtel1M 109712 109965 (890035) L2b_3end#LINE/L2 163 460 (6) m_b192s601i43 7577 chr4qtel1M 109712 CCTCCTCAGCTCTGTCTCTTGGCT---TCCTG-GCTTCCTTCAAATCTCA 109757 i i v - v i i--- i-v v ii L2b_3end#LINE 163 CTTCCCCACCTCT-TCGCCTGGCCAACTCCTACTCATCCTTCAGGTCTCA 211 chr4qtel1M 109758 GCTAAAACCTCAGCTTCTGCAAGAAGCTTTTTCTCATCGTTTGA---GAT 109804 v iv v i v ii ii ii v i viiiii--- iv L2b_3end#LINE 212 GCTCAAATGTCACCTCCTCCGGGAAGCCCTCCCTGACCCCCCAGGCCGGG 261 chr4qtel1M 109805 TCAAGTCTTCCTTCTGCGATTGTCTCCAGTTTGA-CCTGC--CTCCA--- 109848 i - vi i vi ivivi i iiv - -- ii--- L2b_3end#LINE 262 TCAGG-CGCCCTCCTCTGGGCCCCCCCAGTCCTACCCTGCCACTCTGGGT 310 chr4qtel1M 109849 ------TGTTTGCATAGAT---TGTTGCCCCCATTATATCATGGGCTCTT 109889 ------ i ?v v --- iv i v iii i iv L2b_3end#LINE 311 TATNATTGTCTGNTTACATGTCTGTCTCCCCCACTAGACTGTGAGCTCCG 360 chr4qtel1M 109890 TGGGATCAGACATC---TCTGG-------ACCACT--------------C 109915 i iv iv i --- v------- i --------------i L2b_3end#LINE 361 TGAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTGTATCCCCAGCGCCT 410 chr4qtel1M 109916 AGTATAGTTCCCAGTATATTATACATGCTTAATAAATGCTTGTTGATTGA 109965 i i ?v ii i i ivi vii i i ii v L2b_3end#LINE 411 AGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTTGTTGAATGA 460 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 49.62 CpG sites = 62, Kimura (unadjusted) = 53.16 Transitions / transversions = 2.21 (62/28) Gap_init rate = 0.05 (13 / 253), avg. gap size = 3.69 (48 / 13) 253 33.60 6.84 0.81 chr4qtel1M 109849 109965 (890035) L2c_3end#LINE/L2 349 472 (6) m_b192s601i44 7577 chr4qtel1M 109849 TGTTTGCATAGATTGTTGCCCCCATTATATCATGGGCTCTTTGGGATCAG 109898 i ? - vi iv i i v iii i i i iv L2c_3end#LINE 349 TGTTTACNT-GTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAG 397 chr4qtel1M 109899 ACATC---TCTGGACCA-CTCAGTAT----AGTTCCCAGTATATTATACA 109940 iv i --- vivi - iv ---- iv ii i i vi vi L2c_3end#LINE 398 GGACCGTGTCTTATTCATCTTTGTATCCCCAGCGCCTGGCACATAGTAGG 447 chr4qtel1M 109941 TGCTTAATAAATGCTTGTTGATTGA 109965 i i i v L2c_3end#LINE 448 CGCTCAATAAATGTTTGTTGAATGA 472 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.96 CpG sites = 27, Kimura (unadjusted) = 48.51 Transitions / transversions = 2.25 (27/12) Gap_init rate = 0.03 (4 / 116), avg. gap size = 2.25 (9 / 4) 240 22.22 0.00 0.00 chr4qtel1M 110564 110617 (889383) C L3#LINE/CR1 (1) 4098 4045 m_b192s601i45 7578 chr4qtel1M 110564 ACAGCCTCACAGAATGGGAGAGTTGGAAGGGACCTCAGCTGCCACCGAGT 110613 i vv vvv i vv i i v C L3#LINE/CR1 4098 ATAGAATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGT 4049 chr4qtel1M 110614 CCAA 110617 C L3#LINE/CR1 4048 CCAA 4045 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.35 CpG sites = 4, Kimura (unadjusted) = 26.35 Transitions / transversions = 0.50 (4/8) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 185 18.42 5.26 0.00 chr4qtel1M 111425 111462 (888538) C MIRc#SINE/MIR (162) 106 67 m_b192s601i46 7579 chr4qtel1M 111425 TGGCTTTCTCAAGGTCACT--GCTAAGAAGTGACAGAGCC 111462 i v i v-- iv i C MIRc#SINE/MIR 106 TGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCC 67 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 21.38 CpG sites = 4, Kimura (unadjusted) = 21.38 Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.03 (1 / 37), avg. gap size = 2.00 (2 / 1) 464 31.33 3.86 2.87 chr4qtel1M 111515 111721 (888279) C L3#LINE/CR1 (213) 3886 3678 m_b192s601i47 7578 chr4qtel1M 111515 GAGTTTAAATCTGCTTCTATATGATTAGGGCCCATTGTTCCCAATTCTAC 111564 iiv i iv i i i vvvi v i i i C L3#LINE/CR1 3886 GAGCCGAAATCTGCCTCCCTGTAACTTCCACCCATTGGTCCTAGTTCTGC 3837 chr4qtel1M 111565 CCTCCAGAATAATCCAGAAGTAGG---AAT-TCTCTTCCATATGAGAATC 111610 ii iiv iv - i --- -i i v ii C L3#LINE/CR1 3836 CCTCTGGAGCCACACAGAA-TAAGTCTAATCCCTCTTCCACATGACAGCC 3788 chr4qtel1M 111611 --TC--ATGTGGAAAGAATAATCTCACCACCTCCACCCTAAGGCTTCTCT 111656 -- -- i vvi --v v - i iv iv i v C L3#LINE/CR1 3787 CTTCAAATATTTGAAGA--CAGCT-ATCATGTCTCCTCTAAGTCTTCTCT 3741 chr4qtel1M 111657 TTTCCCAGACTACAGATCCCTGATTCTTTCAATCATTTCTCATGAGATTT 111706 i - i v v iii i i i i iv iv C L3#LINE/CR1 3740 TCT-CCAGGCTAAACATCCCCAGTTCCTTCAACCGTTCCTCATATGACAT 3692 chr4qtel1M 111707 GCCTCCCTAGATGCT 111721 vi i - iv C L3#LINE/CR1 3691 GGTTTCC-AGACCCT 3678 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.78 CpG sites = 41, Kimura (unadjusted) = 42.61 Transitions / transversions = 1.86 (41/22) Gap_init rate = 0.05 (10 / 206), avg. gap size = 1.40 (14 / 10) 423 27.88 2.05 4.20 chr4qtel1M 112630 112775 (887225) MIRc#SINE/MIR 2 144 (124) m_b193s601i1 7580 chr4qtel1M 112630 GAGGGAGC-TGGTGCATTGAAAAGTGTTTTCACACTAGCCCTGGAGCCAG 112678 v i- v i v ------ i v i i MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAG------CACTGGACTTGGAGTCAG 45 chr4qtel1M 112679 -AAGCCCTGGATTCAAGTTCATAC-CTCATACTTACTCCTCAGGCGACCT 112726 - v i i i vvi - vvi vviiiv i MIRc#SINE/MIR 46 GAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCT 95 chr4qtel1M 112727 TGGAAAAGGAACCTCACCATTCTGGGCCTCAGTTTCCTTCTTTGAAAAA 112775 iv vv i v vi i iv i v MIRc#SINE/MIR 96 TGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAA 144 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 34.18 CpG sites = 20, Kimura (unadjusted) = 35.28 Transitions / transversions = 1.05 (20/19) Gap_init rate = 0.06 (9 / 145), avg. gap size = 1.00 (9 / 9) 504 27.58 2.29 4.68 chr4qtel1M 112671 112845 (887155) MIR3#SINE/MIR 36 206 (2) m_b193s601i2 7580 chr4qtel1M 112671 GGAGCCAGAAGCCCTGGATTCAAGTTCATAC-CTCATACTTACTCCTCAG 112719 i i v i v i vvi - vvi v ?viiiv MIR3#SINE/MIR 36 GGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGT 85 chr4qtel1M 112720 GCGACCTTGGAAAAGGAACCTCACCATTCTGGGCCTCAGTTTCCTTCTTT 112769 i iv vv i vi iv i MIR3#SINE/MIR 86 GTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCT 135 chr4qtel1M 112770 GAAAAAAAAAAAAGTATTGGACTAGATGATCT-TAGATTCCCCTCCACCC 112818 v vi iiii -- - iiv i ------ MIR3#SINE/MIR 136 GTAAAATGAGGGGG--TTGGACTAGATGATCTCTAAGGTCCCTT------ 177 chr4qtel1M 112819 CCAGCTCTG--ATCCCATCATGCTCTGGT 112845 -- i i v v v i MIR3#SINE/MIR 178 CCAGCTCTGACATTCTATGATTCTATGAT 206 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 35.33 CpG sites = 26, Kimura (unadjusted) = 35.33 Transitions / transversions = 1.30 (26/20) Gap_init rate = 0.06 (11 / 174), avg. gap size = 1.09 (12 / 11) 20 19.03 0.00 0.00 chr4qtel1M 113654 113690 (886310) (A)n#Simple_repeat 1 37 (0) m_b193s252i0 7581 chr4qtel1M 113654 AAAAAAAAAAAAAAAGAAAAAAAGAAGGAAAGAATAA 113690 i i ii i v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 37 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 352 36.36 7.58 0.99 chr4qtel1M 114000 114474 (885526) L1ME4c_3end#LINE/L1 164 669 (161) m_b193s551i0 7582 chr4qtel1M 114000 AAATATCAATTAAAATACCTCTTAGGTTTTACTTCACATCTAGCAAGTTG 114049 iiv ii v vv v i vii i i ii vi i i L1ME4c_3end#L 164 AAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCTATTAAATTA 213 chr4qtel1M 114050 ACAAAGAAGATAAGAGAAAATAATCATAGCTGATCATAAAGGAAGTGTGG 114099 i - vv i -- v i v v ii vv iiv iii? i L1ME4c_3end#L 214 GCAAA-AATTTAAAA--AATTGATAATACCCAATGCTGGCGAGGNTGCGG 260 chr4qtel1M 114100 GAAAGTGGGTATACTTGTGCATTGTTGATGGAGCTGTGAATCAGCCTAAC 114149 vi iiv i? ii i i i vi? i ii ivi L1ME4c_3end#L 261 TGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACAAC 310 chr4qtel1M 114150 TATCCTGTGAAGCAATTTAGAATTATGTGAAGAAAGTGACTAAAATGT-- 114197 iv ii vi i v v i ivvi i iv iv -- L1ME4c_3end#L 311 CCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAAAATGTTC 360 chr4qtel1M 114198 ----------ATGCAGAGATTTCCTTGCTAGACATTTAGCCCAAGGAGGT 114237 ---------- iv vi i vi v i iv v i ii L1ME4c_3end#L 361 ATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAAT 410 chr4qtel1M 114238 CAAGGACAAAAAAGAAAA--TTTTATTC-CTAAG-TATTCCTAGCCACAC 114283 v vvv v i i --i v v - v - i v v vi ii L1ME4c_3end#L 411 AATTCAAAAGAAGGAAAAAGCTATATGCACGAAGATGTTCATTGCAGCGT 460 chr4qtel1M 114284 TG------ACGGCAATGCATTGTAAACAAAGCAAATGCCCAACCATTGGG 114327 i------ ii i viv v vvi i v v L1ME4c_3end#L 461 TATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGG 510 chr4qtel1M 114328 GAATGGGCAAATAATCTGTGGTA---GGACT-AATGAGATATTA-GTATG 114372 vi i vi i ---v? -i ii - i - L1ME4c_3end#L 511 GAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATATTATGCA-G 559 chr4qtel1M 114373 TC-----AAATAACAAATGTGGGGA--ATAGAGAAACCTGGAAAG-AACT 114414 i ----- i i v i ii -- iv v v i-ivi L1ME4c_3end#L 560 CCATTAAAAATGATAATTATGAAGACTATGTAGCAACATGGAAAATGTTT 609 chr4qtel1M 114415 ATGAACTGATCCAAAATGAAGTAGGCAGACCCCAAAGATTA-ATATACAT 114463 vv i viv i iv i viv - i- ? ii L1ME4c_3end#L 610 ATGATATAATGTTAAGTGAAAAAAGCAGAATACAAA-ATTGTATNTACGC 658 chr4qtel1M 114464 GACAATTCCAA 114474 v ii v L1ME4c_3end#L 659 TATGATTACAA 669 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 49.94 CpG sites = 103, Kimura (unadjusted) = 53.14 Transitions / transversions = 1.51 (103/68) Gap_init rate = 0.04 (18 / 474), avg. gap size = 2.28 (41 / 18) 513 30.92 9.06 3.58 chr4qtel1M 116499 116763 (883237) C L3#LINE/CR1 (103) 3996 3718 m_b193s601i3 7583 chr4qtel1M 116499 TCATCTAGTTCTTGCTCAAAGACTTC-AACAACAGGGAGCTCGCCACCTT 116547 i iiii ii v i - iii i i i i C L3#LINE/CR1 3996 TCATCCAGCCTCTGCTTGAACACCTCCAGTGACGGGGAGCTCACTACCTC 3947 chr4qtel1M 116548 CCAAGCCAGCCCACTC------TGGAAAGA-CTAATTATTCAGAGGATTT 116590 ? i v i ------ v v- i i - iii i C L3#LINE/CR1 3946 NCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGATTGTT-AGAAAGTTC 3898 chr4qtel1M 116591 TTCCCTGACATTGAACCCGAATCGGCCTCTTGGCACTTCCCACCTACTAT 116640 i - i i vi v iiv i vi i i i iv C L3#LINE/CR1 3897 TTCCTT-ATATTGAGCCGAAATCTGCCTCCCTGTAACTTCCACCCATTGG 3849 chr4qtel1M 116641 TCCTGGTTTTGCCTTTGAGGCCCAAGCCAAAGAA-TCTGGATGACCCTTC 116689 i i i ivi iv vi vi v - -i vv i C L3#LINE/CR1 3848 TCCTAGTTCTGCCCTCTGGAGCCACACAGAATAAGTCT-AATCCCTCTTC 3800 chr4qtel1M 116690 AACACAGACACCCCAACCCTTCCTG-AGTTGAGTGCAGCACACCACG--- 116735 v i- ----- i vvi- v ivi -i i i --- C L3#LINE/CR1 3799 CACAT-GA-----CAGCCCTTCAAATATTTGAAGACAGC-TATCATGTCT 3757 chr4qtel1M 116736 ----------TTCTCTTCTCT-GGCTAAAGATCTTTAGT 116763 ---------- i- v iii C L3#LINE/CR1 3756 CCTCTAAGTCTTCTCTTCTCCAGGCTAAACATCCCCAGT 3718 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 41.59 CpG sites = 57, Kimura (unadjusted) = 43.09 Transitions / transversions = 2.59 (57/22) Gap_init rate = 0.07 (18 / 264), avg. gap size = 1.89 (34 / 18) 554 33.51 5.08 1.27 chr4qtel1M 116848 117379 (882621) L1M5_orf2#LINE/L1 2159 2710 (584) m_b193s551i1 7584 chr4qtel1M 116848 AATTAACAACT---TTTTGTAAAGTTGTAGAATATAAAATAAATTCACAC 116894 i i v --- v i i i i? i i ii v vi v L1M5_orf2#LIN 2159 AACTAATAAGTGAATTTAGCAAGGTCGCNGGATACAAGGTCAATATACAA 2208 chr4qtel1M 116895 AAATCATCAGCATTTCTACATATTACTGAGAAAGCCCAGCAGCAA--GAG 116942 viv i i i vii v -- v vii v -- i L1M5_orf2#LIN 2209 AAATCAATTGTATTTCTATATACTAGCAACAAA--CAATTGGAAAATGAA 2256 chr4qtel1M 116943 ATAGAAAGAGGTATTACATTTAAAATAACT-----AAACA--AAATGTCT 116985 vv? i ivv vv v i v----- -- iii L1M5_orf2#LIN 2257 ATTTNAAAAACAATACCATTTACAATAGCATCAAAAAACATNAAATACTT 2306 chr4qtel1M 116986 GGGTCTCTACCTGCCAAGACAAACCCAGGAACCATA---TGAACCAACTA 117032 i vv vv i iv i ? viiv i v i? --- -- L1M5_orf2#LIN 2307 AGGAATAAATCTAACAAAANATGTGCAAGACCTNTACACTGAA--AACTA 2354 chr4qtel1M 117033 TAAAACACTTCTCAGACAAACAAAATCAGACCTAAACAATTGGAAAGATA 117082 i i v v v iv vv i v i L1M5_orf2#LIN 2355 CAAAACATTGCTGAGAGAAATTAAAGAAGACCTAAATAAATGGAGAGATA 2404 chr4qtel1M 117083 TCCATTGCTCATGGGTAGGTTGAGATAATATAAAAGAAATGTCAGTTCTA 117132 v vv i i v vv vvi viv?i i i v L1M5_orf2#LIN 2405 TACCATGTTCATGGATTGGAAGACTCAATATTGTNAAGATGTCAATTCTC 2454 chr4qtel1M 117133 TCTAAATTGGTCTACTTGCTCAGTGTCCTAACAATCAGACTTCCAA-AAA 117181 i i i ivvii i ivv vv i v i i- ii L1M5_orf2#LIN 2455 CCCAAATTGATCTATAGATTCAATGCAATCCCAATCAAAATCCCAGCAGG 2504 chr4qtel1M 117182 TCACTTTATAGAGGTAGGGGGGAAAAATCATAAAATTCACGTGGAGAAAC 117231 ivi i ii v ivii vvi v - i ii i vi L1M5_orf2#LIN 2505 TTTTTTTGTAGAAATTGACAAGCTGATTC-TAAAATTTATATGGAAATGC 2553 chr4qtel1M 117232 AAAAAGTCAAGAATA-TCAAGGGAATTAATGAAAAA-AACCACAATGGAT 117279 iiii ? -i iiv i-v - vv -i v L1M5_orf2#LIN 2554 AAAGGACCNAGAATAGCCAAAACAATC-TTGAAAAAGAAGAACAA-AGTT 2601 chr4qtel1M 117280 GGTGGCCTAATGATACCAGATCTAAA-----ATTATAAAGCAGCAGTCAT 117324 v v v iiv ? ? v ----- vi v L1M5_orf2#LIN 2602 GGAGGACTTACACTACCNGATNTCAAGACTTATTATAAAGCTACAGTAAT 2651 chr4qtel1M 117325 CAAAATCACTTGGTATCAGC-TAAG---AGAGAAGTGGACCAGTGGGATG 117370 i iviiv ii - --- v i i i i i ii L1M5_orf2#LIN 2652 CAAGACAGTGTGGTATTGGCGTAAGGATAGACAAATAGATCAATGGAACA 2701 chr4qtel1M 117371 AGTTAGAGA 117379 iiv L1M5_orf2#LIN 2702 GAATAGAGA 2710 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 46.49 CpG sites = 100, Kimura (unadjusted) = 46.87 Transitions / transversions = 1.32 (100/76) Gap_init rate = 0.03 (18 / 531), avg. gap size = 1.89 (34 / 18) 285 35.85 6.32 3.29 chr4qtel1M 116849 117497 (882503) L1P3_orf2#LINE/L1 2164 2831 (463) m_b193s551i2 7584 chr4qtel1M 116849 ATTAACAACTTTTTGTAAAGTTGTAGAATATAAAATAAATTCACACAAAT 116898 v i iv- i ivi i i v vii v L1P3_orf2#LIN 2164 ATAAGCAACTTCA-GCAAAGTCTCAGGATACAAAATCAATGTGCAAAAAT 2212 chr4qtel1M 116899 CATCAGCATTTCTACATATTACTGAGAAAGCCCAGCAGCAAGAGATAGA- 116947 iv i i i ii v i v i -- v i -- vi i - L1P3_orf2#LIN 2213 CACAAGCATTCCTATACACCAATAATAGA--CAAACAG--AGAGCCAAAT 2258 chr4qtel1M 116948 -AAGAGGTA--TTACATTTAAAATAACTA-------AACAAAATGTCTGG 116987 - v vv -- iv i v vi ------- i ii i L1P3_orf2#LIN 2259 CATGAGTGAACTCCCATTCACAATTGCTACAAAGAGAATAAAATACCTAG 2308 chr4qtel1M 116988 GTCTCTACCTGCCAAGACAAACCCAGGAACCAT---ATGAACCAACTATA 117034 vv vi v vv iv viivv v iv --- v i-- i L1P3_orf2#LIN 2309 GAATACAACTTACAAGGGATGTGAAGGACCTCTTCAAGGAG--AACTACA 2356 chr4qtel1M 117035 AAACACTTCTCAGACAAACAAAATCAGACCTAAACAATTGGAAAGATATC 117084 v v iiv i i vvi vi v i i i L1P3_orf2#LIN 2357 AACCACTGCTCAAGGAAATAAGAGAGGACACAAACAAATGGAAAAACATT 2406 chr4qtel1M 117085 CATTGCTCATGGGTAGGTTGAGATAATATAAAAGAAATGTCAGTTCTATC 117134 vv i vv ivi vivii v vi v ii L1P3_orf2#LIN 2407 CCATGCTCATGGATAGGAAGAATCAATATCGTGAAAATGGCCATACTGCC 2456 chr4qtel1M 117135 TAAATTGGTCTACTTGCTCAGTGTCCTAACAATCAGACTTCCA-AAAATC 117183 i v ii i ivvii i iiv vv v ii v -vi v i L1P3_orf2#LIN 2457 CAAAGTAATTTATAGATTCAATGCTATCCCCATCAAGCTACCATTGACTT 2506 chr4qtel1M 117184 ACTTTATAGAGGTAGGGGGGAAAAATCA---TAAAATTCACGTGGAG-AA 117229 v i i iv ---- i ii --- v ii i-v L1P3_orf2#LIN 2507 TCTTCACAGAATTA----GAAAAAACTACTTTAAATTTCATATGGAACCA 2552 chr4qtel1M 117230 ACAAAAAGTCAAGAATA-TCAAGGGAAT--TAATGAAAAAAACCACAATG 117276 v i i -v v -i iv -- vv i -- -i L1P3_orf2#LIN 2553 AAAAAGAGCC-CGTATAGCCAAGACAATCCTAAGCAAAAAGA--ACAA-A 2598 chr4qtel1M 117277 GATGGTGGCCTAATGATACCAGATCTAAAATTAT-----AAAGCAGCAGT 117321 v v v v i v v ii v i ----- i vi L1P3_orf2#LIN 2599 GCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTACAGT 2648 chr4qtel1M 117322 CATCAAAATCACTTGGTATCAG--CTAAG--AGAGAAGTGGACCAGTGGG 117367 v i ivi v iii -- i i-- v vi i i i L1P3_orf2#LIN 2649 AACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACCAATGGA 2698 chr4qtel1M 117368 ATGAGTTAGAGAC-----ACATGACACAATA-ATCAGTGATGATAGTGGT 117411 iiiivi i ----- v i i v i - ------v i iivi L1P3_orf2#LIN 2699 ACAGAACAGAGGCCTCAGAAATAACGCCACACATC------TACAACCAT 2742 chr4qtel1M 117412 CTGGTGTTTGATAAACCC-CCAGACTCCGGCTTTGAG---AGAACTCACT 117457 i v i i-v i vv vi vv i --- i i v L1P3_orf2#LIN 2743 CTGATCTTTGACAAACCTGACAAAAACAAGCAATGGGGAAAGGATTCCCT 2792 chr4qtel1M 117458 ATTTCACAAAAAATTTCTGGGAAAATTGGAAAATAATATG 117497 v i vii v - i vv iiv L1P3_orf2#LIN 2793 ATTTAATAAATGGTGT-TGGGAAAACTGGCTAGCCATATG 2831 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 49.55 CpG sites = 126, Kimura (unadjusted) = 50.51 Transitions / transversions = 1.27 (126/99) Gap_init rate = 0.06 (39 / 648), avg. gap size = 1.62 (63 / 39) 305 17.04 5.56 2.15 chr4qtel1M 117660 117749 (882251) Charlie4#DNA/hAT-Charlie 3221 3313 (65) m_b193s502i0 7585 chr4qtel1M 117660 TTAATATATATTCATAACCATGTTTCAATAAAATGTGCTTCTTTTGTGAT 117709 - v v i i v vv i i i Charlie4#DNA/ 3221 TTAA-ATATTTTGATAACTATATTTCAATATAATTGGTTTCCTTTGTAAT 3269 chr4qtel1M 117710 GCTATG-----TGTTTTATGCATTTAGAAACCTTATTCTCAAGAA 117749 v ----- i i v -i Charlie4#DNA/ 3270 CCTATGTATTTTATTTTATGCATTTAAAAACATTATTCT-GAGAA 3313 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 19.48 CpG sites = 8, Kimura (unadjusted) = 19.48 Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.03 (3 / 89), avg. gap size = 2.33 (7 / 3) 16 0.00 0.00 0.00 chr4qtel1M 117922 117938 (882062) (A)n#Simple_repeat 1 17 (0) m_b193s252i1 7586 chr4qtel1M 117922 AAAAAAAAAAAAAAAAA 117938 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 15 4.34 0.00 4.00 chr4qtel1M 120457 120482 (879518) (GAGG)n#Simple_repeat 1 25 (0) m_b193s252i2 7587 chr4qtel1M 120457 GAGGGAGGGGGTGGAGGGAGGGAGGG 120482 i - (GAGG)n#Simpl 1 GAGGGAGGGAG-GGAGGGAGGGAGGG 25 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 25), avg. gap size = 1.00 (1 / 1) 114 24.93 2.34 0.00 chr4qtel1M 120702 121000 (879000) (TC)n#Simple_repeat 1 306 (0) m_b193s252i3 7588 chr4qtel1M 120702 TCTC-CTGTCTCTCTGCCTCCTTCCCTCTCTCTTTCTCTATCTCTC-CTC 120749 - v vi ii i i v - (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr4qtel1M 120750 TCTCCCCCTCAGTCTCTATTTTTCT-TCTGTGTCTGTTTCTCT-TCTCTA 120797 i i vv v i i - v v v i - v (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chr4qtel1M 120798 TCTCCCTTTTTCTCTCTGTCTCTCTCTGCCTCCCTCCATCCTTCTGTCTC 120847 i i i v vi i iv ii v (TC)n#Simple_ 101 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 150 chr4qtel1M 120848 TCTCTCTCTCCCCCTCTGTCTCCCTTTTTCTCTCTGTCCCTCTCCTTCCC 120897 i i v i i i v i ii i (TC)n#Simple_ 151 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 200 chr4qtel1M 120898 TCCTTCTGTCTCTGTCTCTGTCTCTGTCTCTCT-TCTCTGGCTCTATGTC 120946 ii v v v v - vv v v (TC)n#Simple_ 201 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 250 chr4qtel1M 120947 TATGTCTC-CCCTCTGTCTCTGTGTCTCTGTCTCCCCCTCTGTCTCTCTC 120995 v v - i v v v v i i v (TC)n#Simple_ 251 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 300 chr4qtel1M 120996 -CTCTC 121000 - (TC)n#Simple_ 301 TCTCTC 306 Matrix = Unknown Transitions / transversions = 1.03 (32/31) Gap_init rate = 0.02 (7 / 298), avg. gap size = 1.00 (7 / 7) 12 14.94 8.11 0.00 chr4qtel1M 121182 121218 (878782) (GGCCGG)n#Simple_repeat 1 40 (0) m_b193s252i4 7589 chr4qtel1M 121182 GGCCCGGGCAGGAGCAGGGGCAGGGGCC---GCCGGGGCC 121218 v v i v v --- (GGCCGG)n#Sim 1 GGCCGGGGCCGGGGCCGGGGCCGGGGCCGGGGCCGGGGCC 40 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.03 (1 / 36), avg. gap size = 3.00 (3 / 1) 612 34.25 11.21 0.58 chr4qtel1M 121661 122124 (877876) C L3#LINE/CR1 (94) 4005 3493 m_b193s601i4 7590 chr4qtel1M 121661 GACAATGTGACC-TTGAGCCT-TGTCTGGAGACCTGTAGTAA-GGGAAAC 121707 - ii - iv - ii i v vi i - i i C L3#LINE/CR1 4005 GACAA-GTGGTCATCCAGCCTCTGCTTGAACACCTCCAGTGACGGGGAGC 3957 chr4qtel1M 121708 CCCCTCTGTCCCCAGGTAGCCCACGAGACTTTCAG-CAGCTCTGGTTATT 121756 i v viv ? v i ivvv i ii - i i C L3#LINE/CR1 3956 TCACTACCTCNCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGATTGTT 3907 chr4qtel1M 121757 AGGAAGCTTTCCCCTGTTCCGAGCCAAGAGCTGCTTCCCTG-------CA 121799 i i i i i i vii i i v i ------- C L3#LINE/CR1 3906 AGAAAGTTCTTCCTTATATTGAGCCGAAATCTGCCTCCCTGTAACTTCCA 3857 chr4qtel1M 121800 GCCA--------AGTTT---CCTTGGGGATCAACTTGGGTGA-TCGACCC 121837 v -------- i--- iv iii vviv ii i - v vi C L3#LINE/CR1 3856 CCCATTGGTCCTAGTTCTGCCCTCTGGAGCCACACAGAATAAGTCTAATC 3807 chr4qtel1M 121838 CCTTTTCCA-GCAA-AACTCTTCAAATATCTGAAGAT-GCCCTC------ 121878 i -iii - i i i i- iv ------ C L3#LINE/CR1 3806 CCTCTTCCACATGACAGCCCTTCAAATATTTGAAGACAGCTATCATGTCT 3757 chr4qtel1M 121879 CCCCCGAATCATCTCTTTGCTGGGTGACCAGCATGACCATGTCCTTGGA- 121927 i ii i v iv ii iv -- i vv vv vi - C L3#LINE/CR1 3756 CCTCTAAGTCTTCTCTTCTCCAGGCTA--AACATCCCCAGTTCCTTCAAC 3709 chr4qtel1M 121928 TGCTCCCCCTTTGATATGGACTCC-GTTCTTCTTCCCTCCCGACCTCCCT 121976 i i i v v i vi - vi i iiv v i ii v i C L3#LINE/CR1 3708 CGTTCCTCATATGACATGGTTTCCAGACCCTTCACCATCCTGGTCGCTCT 3659 chr4qtel1M 121977 CTTC-AGACACTTGCCAGTTTG-------CCCT----AAGTGTGGC-CTG 122013 i -i i viv ------- ---- i - iv C L3#LINE/CR1 3658 CCTCTGGACGCGCTCCAGTTTGTCAATGTCCCTCTTAAAATGTGGCGCCC 3609 chr4qtel1M 122014 AGACTCGAGTACCATCCTTCTGATGAGGTCTGACCAG-GCACAAGACCGT 122062 vii iii v v i v v - v iv v i C L3#LINE/CR1 3608 AGAACTGAACGCAATACTCCAGATGTGGTCTGACCAGCGCAGAGTACAGC 3559 chr4qtel1M 122063 GGGGTCATCGCCATCTGGGAGCTGTTCCCTCTGCCT---TTGGTCCAGCC 122109 iii ii vi ivv ?v vv v v i i --- ii v C L3#LINE/CR1 3558 GGGACTATTACCTCCCTTGNTCTGGACACTATACTTCTATTAATGCAGCC 3509 chr4qtel1M 122110 CAAAGTAGC-TCAGTT 122124 i ii v - i i C L3#LINE/CR1 3508 TAAGATTGCATTAGCT 3493 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 46.52 CpG sites = 102, Kimura (unadjusted) = 48.78 Transitions / transversions = 1.82 (102/56) Gap_init rate = 0.05 (24 / 463), avg. gap size = 2.29 (55 / 24) 294 35.63 7.37 0.43 chr4qtel1M 122245 122461 (877539) C L3#LINE/CR1 (662) 3437 3206 m_b193s601i5 7590 chr4qtel1M 122245 CCCCCAGGTGTGGGTCAGTCGTACGGCTGCCTGCTCAGGTCACCCTCATT 122294 i v vvv vvi v v ivivi i vi ii i C L3#LINE/CR1 3437 CCCCTAGGTCTTTTTCACGTGAACTGCTGCTAAGCCAGATCCTCTCCATC 3388 chr4qtel1M 122295 TGGGACTTGGGCTGTTGACTTACGAGAACCT-----------TTTACATT 122333 iv v v v i viv- ----------- C L3#LINE/CR1 3387 CTGTACTTGTGCAGTTGATTTTTT-GAACCTAAATGCAGGACTTTACATT 3339 chr4qtel1M 122334 GATCT-TACTGAAACCCATCATCGCAGACTTGTTCCAACAGGCTGGCCTG 122382 v i- ii i vii v vvii vi i vi v ivv ii C L3#LINE/CR1 3338 TATCCCTGTTAAATTTCATCTTGTTGGTTTCGGCCCATCGTTCCAGCCTG 3289 chr4qtel1M 122383 T-GGGGTGACTTTGGATCC-AA--CTGTTACCCAAGGCTTTAGCTCGCGC 122428 - i i v?i i i-i -- i i ?v iv vv v C L3#LINE/CR1 3288 TCGAGATCNTTTTGAATCTTGATTCTGTCATCCANCGTATTAGCTATCCC 3239 chr4qtel1M 122429 CGCTAGCTTTGTGTCACCTGCAGATGTGTTGAG 122461 iv i i i v v i C L3#LINE/CR1 3238 TCCCAGCTTTGTGTCATCTGCAAATTTGATAAG 3206 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 48.49 CpG sites = 41, Kimura (unadjusted) = 50.34 Transitions / transversions = 1.14 (41/36) Gap_init rate = 0.03 (6 / 216), avg. gap size = 2.83 (17 / 6) 399 33.74 13.24 1.22 chr4qtel1M 122707 122925 (877075) C L3#LINE/CR1 (891) 3208 2964 m_b193s601i6 7590 chr4qtel1M 122707 AAGCA--CTTTTTGATGCTTTAATCCAAGTCCTTAATGAAAAGATGTTCA 122754 -- i i - ii v v i i -- v C L3#LINE/CR1 3208 AAGCATGCCTTCT-ATGTCTTCATCCAAGTCATTGATAAAAA--TGTTGA 3162 chr4qtel1M 122755 A--GGACAGGGCCAAG--------------------CACT-----CCTCC 122777 -- -------------------- ----- C L3#LINE/CR1 3161 ACAGGACAGGGCCAAGGACAGAGCCCTGTGGCACGCCACTAGAGACCTCC 3112 chr4qtel1M 122778 TGTCATGCTGCCATTGAACCATTAATGGCTGCTTTCTGAAGTTGAATATT 122827 ivi v i v i v vivii i i iivv iivii C L3#LINE/CR1 3111 CTCCAGGTTGACATCGATCCATTAATCAACACCTTTTGGGTATAGTCGTT 3062 chr4qtel1M 122828 CAATTCGTTCCAAATTAAAACATTTATGTTATTGTCTCGCTCATAACTTT 122877 iiv i v i iv vvi vi i ii ii iv i vi i C L3#LINE/CR1 3061 CAACCAGCTACGAATCCACCTAACTGTACTATCATCCAGCCCATATTTCT 3012 chr4qtel1M 122878 CCATCTTGTCTGCAAGAATAACCCAATGAAATCTATCAAGAGCTTTGC 122925 ii i v vii vii v i i iv i C L3#LINE/CR1 3011 CCATCTTGTCCACAAGGATATCATGAGAGACTTTGTCAAATGCCTTGC 2964 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 44.79 CpG sites = 48, Kimura (unadjusted) = 47.65 Transitions / transversions = 1.92 (48/25) Gap_init rate = 0.03 (7 / 218), avg. gap size = 4.57 (32 / 7) 594 30.32 10.17 0.78 chr4qtel1M 122952 123187 (876813) MIRc#SINE/MIR 6 263 (5) m_b193s601i7 7591 chr4qtel1M 122952 CAGTG-AGTGCAGCCTAAAGTAGTTTTGGATCTGGAAACAGAAATAC--- 122997 -i ivv - ivi ii iv i v --- MIRc#SINE/MIR 6 CAGTGTGGTGCAGTGGAAAG-AGCACTGGACTTGGAGTCAGGAAGACCTG 54 chr4qtel1M 122998 ------AGCCTCAGACGTG-----TGTAAGTTGTGTGA--GTAGCCAAAT 123034 ------ i i i viv ----- iiv i --v i v i MIRc#SINE/MIR 55 GGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGT 104 chr4qtel1M 123035 CATTTGATATTTCTAAGCCTTGGTTTCCAAATTTGTCAAATGGGGATAAT 123084 i i iv i i ii vv i v MIRc#SINE/MIR 105 CACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAAT 154 chr4qtel1M 123085 GAT------CATATCTACCTTGCAGAGTTGCTGTGAGAACCAAATGAGGA 123128 i ------ v ii ii i i i i - MIRc#SINE/MIR 155 AATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGA-GA 203 chr4qtel1M 123129 CATTATATAT-AAAATGCTTTACTGATCTTGAAGTGTTGTATAAATGCTG 123177 i v i i - ii iivi iiv i i i i ivi MIRc#SINE/MIR 204 TAATGTATGTGAAAGCGCTTTGTAAACTGTAAAGTGCTATACAAATGTAA 253 chr4qtel1M 123178 GATATTATTA 123187 i?i MIRc#SINE/MIR 254 GGNGTTATTA 263 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 40.37 CpG sites = 52, Kimura (unadjusted) = 41.98 Transitions / transversions = 2.74 (52/19) Gap_init rate = 0.04 (9 / 235), avg. gap size = 2.89 (26 / 9) 180 23.58 12.33 1.23 chr4qtel1M 123185 123257 (876743) C L3#LINE/CR1 (1132) 2967 2887 m_b193s601i8 7590 chr4qtel1M 123185 TTACCAAAATTGAGCTTAAACTGTGTC------ATTCCC-TGATCTATTG 123227 i ii iv v - v ? ------ - iii C L3#LINE/CR1 2967 TTGCTGAAATCCAGAT-ACACTNTGTCTACGGCATTCCCCTGATCTACCA 2919 chr4qtel1M 123228 GTCAAGGAACCCTA--AGAAAATGAAAGAAAG 123257 v v -- i v vi i C L3#LINE/CR1 2918 GTCTAGTAACCCTATCAAAAAAGGAAATGAGG 2887 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 29.42 CpG sites = 10, Kimura (unadjusted) = 29.42 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.06 (4 / 72), avg. gap size = 2.50 (10 / 4) 40 24.50 1.71 2.59 chr4qtel1M 123259 123375 (876625) (AAGG)n#Simple_repeat 1 116 (0) m_b193s252i5 7592 chr4qtel1M 123259 AAGAAAGAGAGAGAGAGGAA-GAAGAGATGGAAGG-AGGGAGAAAAAAGG 123306 i - - ii - - v - i i ii i (AAGG)n#Simpl 1 AAGGAAG-GA-AGGAAGGAAGGAAG-GAAGGAAGGAAGGAAGGAAGGAAG 47 chr4qtel1M 123307 GAAGGAAGGAGAAAAGGAAGAAAGAGAGGGAGGGAGGAAAGAAGAAAGGC 123356 iii i ii i i i i v (AAGG)n#Simpl 48 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 97 chr4qtel1M 123357 AGGAAGGAAGGAAAGGAGG 123375 i i (AAGG)n#Simpl 98 AGGAAGGAAGGAAGGAAGG 116 Matrix = Unknown Transitions / transversions = 10.00 (20/2) Gap_init rate = 0.04 (5 / 116), avg. gap size = 1.00 (5 / 5) 302 30.40 7.80 2.01 chr4qtel1M 123376 123516 (876484) C L3#LINE/CR1 (1201) 2898 2750 m_b193s601i9 7590 chr4qtel1M 123376 AAGGAATGATGAGGGAAA----ACATGAGTTTGTTTTTGGTGCCACCATA 123421 -- vv i----i -i i i vvv i C L3#LINE/CR1 2898 AAGGAA--ATGAGGTTAGTTTGGCATGA-CTTGTTCTTAGTGAACCCATG 2852 chr4qtel1M 123422 ATGGCT----GT--TTACCACTGCCTTTACTACTTGTTCATTACCAACTC 123465 v ---- -- i i v v vv i iv v v iii C L3#LINE/CR1 2851 CTGGCTCCTAGTGATCACCGCTTCCTTTTCTAAGTGCTCACAAACCATCT 2802 chr4qtel1M 123466 TTTTAATAATCTGTTGGAGGA-TTTGTCAGAAATTACGATCAAGCTCACT 123514 v i vv i - i i ii iivvi i i C L3#LINE/CR1 2801 GTTTAATAATCCGTTCTAGAATTTTGCCGGGGATCGACGTCAAGCTTACC 2752 chr4qtel1M 123515 GG 123516 C L3#LINE/CR1 2751 GG 2750 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 32.98 CpG sites = 24, Kimura (unadjusted) = 40.09 Transitions / transversions = 1.33 (24/18) Gap_init rate = 0.05 (7 / 140), avg. gap size = 2.00 (14 / 7) 279 40.34 0.00 0.84 chr4qtel1M 125983 126102 (873898) C L2b_3end#LINE/L2 (12) 454 336 m_b193s601i10 7593 chr4qtel1M 125983 AACAAGCGGCTGTTAAGTCCCTACTATGTGCTAGTTGCCATGATAAGCAA 126032 iiivi ii i iv i i vi? ii v i iv C L2b_3end#LINE 454 AACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGC 405 chr4qtel1M 126033 TGGATACATAAAAAGAAGCAAACACAAAGCTAGTCCCTGATCTCAAAAAG 126082 iv i i iviivi i i- i v?ii vi vii C L2b_3end#LINE 404 TGGGGATACAGCGGTGAACAAG-ACAGACNCGGTCCCTGCCCTCACGGAG 356 chr4qtel1M 126083 CCCCCGGTCTGACAGGGGAG 126102 i v i iiii C L2b_3end#LINE 355 CTCACAGTCTAGTGGGGGAG 336 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 56.73 CpG sites = 36, Kimura (unadjusted) = 69.02 Transitions / transversions = 3.00 (36/12) Gap_init rate = 0.01 (1 / 119), avg. gap size = 1.00 (1 / 1) 21 4.00 0.00 0.00 chr4qtel1M 126671 126696 (873304) (AC)n#Simple_repeat 1 26 (0) m_b193s252i6 7594 chr4qtel1M 126671 ACACACACACACACACGCACACACAC 126696 i (AC)n#Simple_ 1 ACACACACACACACACACACACACAC 26 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 410 26.66 5.66 0.90 chr4qtel1M 128348 128453 (871547) C L2b_3end#LINE/L2 (6) 460 350 m_b193s601i11 7595 chr4qtel1M 128348 TCAATCACCAATCATTTGCCAAGTGGCTGCTATGTGCCAGGTACTGTGCT 128397 v v vi i ii i v i i i? C L2b_3end#LINE 460 TCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCT 411 chr4qtel1M 128398 AAGTGCTGAGAATACAG------ACACAAATAGAGACAGTTCTTGTCCTT 128441 i i i i ------ - i i v? i i i i i C L2b_3end#LINE 410 AGGCGCTGGGGATACAGCGGTGAACA-AGACAGACNCGGTCCCTGCCCTC 362 chr4qtel1M 128442 GAGAAGTTCACA 128453 iv i i C L2b_3end#LINE 361 ACGGAGCTCACA 350 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 31.47 CpG sites = 22, Kimura (unadjusted) = 36.32 Transitions / transversions = 3.67 (22/6) Gap_init rate = 0.02 (2 / 105), avg. gap size = 3.50 (7 / 2) 242 25.88 5.88 0.00 chr4qtel1M 129123 129207 (870793) MIR1_Amn#SINE/MIR 59 148 (82) m_b193s601i12 7596 chr4qtel1M 129123 TTCAGCTCTCACTTCTGAAACTGCCTATCTGGATAAT-----GAAGGTCA 129167 ?i? i ivi vv ?v i?v ?i i i----- v i MIR1_Amn#SINE 59 TTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGTCA 108 chr4qtel1M 129168 CATCATTTCCCAGGGCCTCAGTTTCCTCTTCTGTAACATG 129207 v ? ii i v ? v v MIR1_Amn#SINE 109 CTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATG 148 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 34.03 CpG sites = 12, Kimura (unadjusted) = 36.03 Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.01 (1 / 84), avg. gap size = 5.00 (5 / 1) 257 17.02 0.00 0.00 chr4qtel1M 129162 129208 (870792) MIR3#SINE/MIR 98 144 (64) m_b193s601i13 7596 chr4qtel1M 129162 AGGTCACATCATTTCCCAGGGCCTCAGTTTCCTCTTCTGTAACATGA 129208 i v ii i v v v MIR3#SINE/MIR 98 AAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGA 144 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 19.40 CpG sites = 4, Kimura (unadjusted) = 19.40 Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 247 37.04 1.85 0.00 chr4qtel1M 129544 129651 (870349) MIRc#SINE/MIR 4 113 (155) m_b193s601i14 7597 chr4qtel1M 129544 GGCTGCCTGGCTTAGTGAAAGAGACA-TGGTCATGGGGTCAAGAAGTTCT 129592 v iv ivi i iiii - v v i i vi MIRc#SINE/MIR 4 GGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCT 53 chr4qtel1M 129593 GAGCT-ATGTTCTCCCTCAGATGCTCACAAGCTGTATGACCCAGGATAGC 129641 i i -iv i ivv v vii i v i iv ii iv MIRc#SINE/MIR 54 GGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAG 103 chr4qtel1M 129642 TCACTTCATC 129651 v i MIRc#SINE/MIR 104 TCACTTAACC 113 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 50.16 CpG sites = 25, Kimura (unadjusted) = 54.18 Transitions / transversions = 1.67 (25/15) Gap_init rate = 0.02 (2 / 107), avg. gap size = 1.00 (2 / 2) 241 27.97 20.36 1.52 chr4qtel1M 129551 129717 (870283) MIR3#SINE/MIR 10 207 (1) m_b193s601i15 7597 chr4qtel1M 129551 TGGCTTAGTGAAAGAGA-CATGGTCATGGGGTCAAGAAGTTCTGAGCTAT 129599 v i- i - i v vv i i - vi i i v MIR3#SINE/MIR 10 TGGCTGAGC-AGAGAGAGCACGGACTGGGAGTCAGGA-GACCTGGGTTCT 57 chr4qtel1M 129600 -GTTCTCCCTCAGATGCTCACAAGCTGTATGACCCAGGATAGCTCACTTC 129648 - i ivv v vii v v? i iv ii iv MIR3#SINE/MIR 58 AGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTC 107 chr4qtel1M 129649 A------------TCCATGTCC-CGCCTATACAATGAGGGGG-------- 129677 ------------ vi v - ii i v -------- MIR3#SINE/MIR 108 ACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTA 157 chr4qtel1M 129678 -----TCTCTATATTCTCTTCCA------ATAGGTCGATGATCCTATGAT 129716 ----- viv i ------ i -v v i MIR3#SINE/MIR 158 GATGATCTCTAAGGTCCCTTCCAGCTCTGACA-TTCTATGATTCTATGAT 206 chr4qtel1M 129717 T 129717 MIR3#SINE/MIR 207 T 207 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 34.13 CpG sites = 25, Kimura (unadjusted) = 36.05 Transitions / transversions = 1.19 (25/21) Gap_init rate = 0.06 (10 / 166), avg. gap size = 3.70 (37 / 10) 475 26.20 18.18 0.00 chr4qtel1M 130204 130390 (869610) MIRb#SINE/MIR 40 260 (8) m_b193s601i16 7598 chr4qtel1M 130204 TGAAGTCA---AGGTCTGAGCTCAAAAGTGATGTCGGACA-TTACTAGCT 130249 i --- ii i i i vvivivv v v - MIRb#SINE/MIR 40 TGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCT 89 chr4qtel1M 130250 ATGTGGCCCTGGGCTAGTCTCTTAAGTATTATTTGCCTCAGTTTCCTCAT 130299 i i i v iv vivi v vv MIRb#SINE/MIR 90 GTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCAT 139 chr4qtel1M 130300 CTGTAAATTGGAGATAATAA------------------------AGGACC 130325 v i ------------------------ ii MIRb#SINE/MIR 140 CTGTAAAATGGGGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATT 189 chr4qtel1M 130326 AAATGAAATAA------GAAAGTCTTTAGTACAGTTCCTGGCTCATAGAA 130369 i ------v ivi i v v v MIRb#SINE/MIR 190 AAATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTA 239 chr4qtel1M 130370 CGTGCTATAAAAATGTCAGTT 130390 v i vv v vi i MIRb#SINE/MIR 240 AGCGCTCAATAAATGGTAGCT 260 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 29.46 CpG sites = 24, Kimura (unadjusted) = 32.52 Transitions / transversions = 0.96 (24/25) Gap_init rate = 0.02 (4 / 186), avg. gap size = 8.50 (34 / 4) 22 7.28 0.00 0.00 chr4qtel1M 130540 130568 (869432) (A)n#Simple_repeat 1 29 (0) m_b193s252i7 7599 chr4qtel1M 130540 AAAAAAAAAAAACAAAAAAAAACAAAAAA 130568 v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA 29 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 263 28.14 7.08 2.54 chr4qtel1M 130720 130832 (869168) X17_LINE#LINE/CR1 120 237 (59) m_b193s601i17 7600 chr4qtel1M 130720 ACTGAGCTGTGGA--CAGGCTCTTAAGGGATGAAG-GGAAGGCTCATTGC 130766 i iii --i i? ii v vi - v i X17_LINE#LINE 120 ATTAGACTGTGGAATTAANCTCCCAAGGGAAGTGGTGGAAGCCCCATTGC 169 chr4qtel1M 130767 TCAGAGCCACTTAGAAATAAATAGGCACAAACTCACTTGTGACAGACCTT 130816 i- i i i v i iv - -v vi vvi i i X17_LINE#LINE 170 TT-GAGTCATTTAAAACTAGACTGG-ACAAA-GCACTTGAAAATAATCCT 216 chr4qtel1M 130817 CA-----GAGGACAATCCTGC 130832 ----- i i X17_LINE#LINE 217 CATGGCAGGGAACAATCCTGC 237 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 37.81 CpG sites = 22, Kimura (unadjusted) = 37.81 Transitions / transversions = 2.44 (22/9) Gap_init rate = 0.05 (6 / 112), avg. gap size = 1.83 (11 / 6) 587 19.06 5.81 1.86 chr4qtel1M 131844 131998 (868002) Charlie4#DNA/hAT-Charlie 3218 3378 (0) m_b193s502i1 7601 chr4qtel1M 131844 TTTTTAAAAAATATTTT------TATATTTCAGTATAATTGATTTCATTT 131887 --- ------ i i v Charlie4#DNA/ 3218 TTTTTAAA---TATTTTGATAACTATATTTCAATATAATTGGTTTCCTTT 3264 chr4qtel1M 131888 GTAATATTATTTATTCCATTTTATGCATTT-AAAATAAGATTTTGAAAAG 131936 vi v ii - i vv i i Charlie4#DNA/ 3265 GTAATCCTATGTATTTTATTTTATGCATTTAAAAACATTATTCTGAGAAG 3314 chr4qtel1M 131937 GTATTCATGAGCTCCACCACATTGACAACGGGGTC--TGACCCCAACATG 131984 vi i ii i v i v v -- i v v v v Charlie4#DNA/ 3315 GGGTCCATAGGCTTCACCAGACTGCCAAAGGGGTCCATGGCACAAAAAAG 3364 chr4qtel1M 131985 GTCAAGAACCCCTG 131998 i Charlie4#DNA/ 3365 GTTAAGAACCCCTG 3378 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 22.24 CpG sites = 16, Kimura (unadjusted) = 22.24 Transitions / transversions = 1.23 (16/13) Gap_init rate = 0.04 (6 / 154), avg. gap size = 2.00 (12 / 6) 308 21.88 1.56 0.00 chr4qtel1M 132080 132143 (867857) C MIR3#SINE/MIR (62) 146 82 m_b193s601i18 7602 chr4qtel1M 132080 CTTCATCTTACAAAGAAGGCAGCTGAGGCCCAAAGAGA-AAAGTGACTTG 132128 i i i vi v i i i-i C MIR3#SINE/MIR 146 CCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTG 97 chr4qtel1M 132129 GCCAAGATTTCACAG 132143 v i iv C MIR3#SINE/MIR 96 CCCAAGGTCACACAG 82 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 26.84 CpG sites = 10, Kimura (unadjusted) = 26.84 Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.02 (1 / 63), avg. gap size = 1.00 (1 / 1) 288 30.73 7.38 3.90 chr4qtel1M 132628 132776 (867224) L2d_3end#LINE/L2 363 516 (0) m_b193s601i19 7603 chr4qtel1M 132628 TCTCATACCTGTGTGTTGTGTCTTCCAATTCACATAAGGTGAGCAAGCAC 132677 i iiv vv iv i v --- - iiv --i v L2d_3end#LINE 363 TTTCATGTGTGTTAGTCTTGTCTCCCCA---AC-TAGATTG--TAAGCTC 406 chr4qtel1M 132678 CTTAAGGGAGGGGACAGCTTCATTT-TTGTCTTTTCATCCCC---AGCAC 132723 i vi viiv v v -i ? i ? i i --- i L2d_3end#LINE 407 CTTGAGGGCAGGGACCATGTCTTATACTNTTTTNTCGTTCCCCACAGCGC 456 chr4qtel1M 132724 TCAGGACGGG-------ACATAGTAGGTGCTTAATAAGTGTATATTGGTT 132766 ii v i v------- i i i iiv i i L2d_3end#LINE 457 CTAGCACAGTGCTGAGCACATAGTAGGCGCTCAATAAATACTTGTTGATT 506 chr4qtel1M 132767 GGTTGGTTGA 132776 i i L2d_3end#LINE 507 GATTGATTGA 516 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 38.62 CpG sites = 29, Kimura (unadjusted) = 42.44 Transitions / transversions = 1.93 (29/15) Gap_init rate = 0.06 (9 / 148), avg. gap size = 1.89 (17 / 9) 333 27.05 0.00 5.62 chr4qtel1M 132670 132763 (867237) L2c_3end#LINE/L2 379 467 (11) m_b193s601i20 7603 chr4qtel1M 132670 GCAAGCACCTTAAGGGAGGGGACAGCTTCATTTTTGTCTTTTCATCCCCA 132719 ii v i vi v iv v v ii vi L2c_3end#LINE 379 GTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTATCCCCA 428 chr4qtel1M 132720 GCACTCAGGACGGGACATAGTAGGTGCTTAATAAGTGTATATTG 132763 i i-----i v i i i v i L2c_3end#LINE 429 GCGCC-----TGGCACATAGTAGGCGCTCAATAAATGTTTGTTG 467 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 31.00 CpG sites = 15, Kimura (unadjusted) = 34.48 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.05 (5 / 93), avg. gap size = 1.00 (5 / 5) 220 36.68 0.83 6.11 chr4qtel1M 132858 133098 (866902) L2#LINE/L2 2408 2636 (446) m_b193s601i21 7604 chr4qtel1M 132858 CATCTCCAGCCCTATGTCCCATAAACACCATCAACTTGACATACCTAACA 132907 viivv iv ii i viv i ii i v L2#LINE/L2 2408 CATCTCCACTTGGATGTCTAATAGGCATCTCAAACTTAACATGTCCAAAA 2457 chr4qtel1M 132908 CTGAACCCAGAATATGTCCCCCTCCAAAAAAGATGCTCCCTTTTCCCTAG 132957 i vvi v - ---- vv --- i vi L2#LINE/L2 2458 CTGAACTCCTGATCT-TCCCCCTC----AAACCTGCTCC---TCCCGCAG 2499 chr4qtel1M 132958 T-GCCCCTGTTGTTATTAA-GGCTTCTGCAATCCCTCAGGCTACTCAGAT 133005 -vi ii ivivi ? - vv - v i vi i i ii L2#LINE/L2 2500 TCTTCCCCATCTCAGTNAATGGCAACT-CCATCCTTCCAGTTGCTCAGGC 2548 chr4qtel1M 133006 CCACAAATTTAGAATGATTCTCTACTTTCATTTTGCTTCCCACCAGCCCC 133055 v v vi i i v i iv iiiv i v - i --i L2#LINE/L2 2549 CAAAAACCTTGGAGTCATCCTTGACTCCTCTCTTTC-TCTCAC--ACCCC 2595 chr4qtel1M 133056 AGCATCTTATCAGGTGCCAAGTATCATCAATTCCCCCTCTCAA 133098 - iv viviiv i viii iii iv - L2#LINE/L2 2596 A-CATCCAATCCATCAGCAAATCCTGTCGGCTCTACCT-TCAA 2636 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 52.07 CpG sites = 50, Kimura (unadjusted) = 53.03 Transitions / transversions = 1.52 (50/33) Gap_init rate = 0.07 (16 / 240), avg. gap size = 1.00 (16 / 16) 936 28.61 2.70 2.96 chr4qtel1M 134955 135361 (864639) C L1ME5_3end#LINE/L1 (532) 409 4 m_b193s551i3 7605 chr4qtel1M 134955 GGATCTTTTTGGGATACAGACCTAACAGTGGTATTGCTGGATTAAAGTGT 135004 i i i i v i iv i v i i v v C L1ME5_3end#LI 409 GAATTTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGT 360 chr4qtel1M 135005 ATGCACA-GTTTGATAGTCCTTTGGCATTGTTCTAAATTGCTCTCCAGAA 135053 ii -ii i -v vvi vi i i -- i i C L1ME5_3end#LI 359 ATGCGTATACTTAAT-TTGACTAAGTACTG--CCAGATTGCTCTCCAGAA 313 chr4qtel1M 135054 TGGTTGGATTAGTTCACAA-CTCACCAATAATGCTTCAGTGTTATCATTT 135102 i v ii ii v- i ii i v v v vii ? C L1ME5_3end#LI 312 TGGCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATNT 263 chr4qtel1M 135103 TCCCACATCCTCTCCAATAGCCAACATTTTCCTTTTTTTGGTTATATTAG 135152 i v i viiii v vvi i-- v v v C L1ME5_3end#LI 262 CCCCACATCCTCGCCAACACTTGGCATTATCCAGCTTTC--TAATTTTTG 215 chr4qtel1M 135153 CCAATCTGAAAAGTGTGAGGTGATACCTCAGAGTTGTCTTAATTTGCATT 135202 i i v i i i i vv i C L1ME5_3end#LI 214 CCAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATT 165 chr4qtel1M 135203 TCTCTGATCAGTAATAATTTAGAATATTTTTTCATATGACTATAAATAGC 135252 i v i v v ii i i vi i --- C L1ME5_3end#LI 164 TCTCTGATTACTAATGAGTTTGAGCATCTCTTCATATGCTTGT---TAGC 118 chr4qtel1M 135253 TTT---GATTTCTTTGACTGAAAA----CTGATCATATCCTTTGACTATT 135295 i --- i i ivv v ---- v v i C L1ME5_3end#LI 117 CTTTCGGGTTTCCTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCCATT 68 chr4qtel1M 135296 TGTCAGTTGGGG--AATGACTTGTAGTTTTATAAATTTGACTCAGTTCTC 135343 v vi --?vi v v -- i i vi vvvv - C L1ME5_3end#LI 67 TTTCTATTGGGGTTNCCGTCTTTT--TCTTGTTGATTTGCAGGAGTTC-C 21 chr4qtel1M 135344 TCTATATATTTAAGAAAT 135361 - i iv v C L1ME5_3end#LI 20 T-TGTATATTCTAGATAT 4 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 35.98 CpG sites = 66, Kimura (unadjusted) = 37.23 Transitions / transversions = 1.40 (66/47) Gap_init rate = 0.04 (17 / 406), avg. gap size = 1.35 (23 / 17) 226 32.40 4.91 2.17 chr4qtel1M 135838 136061 (863939) C L1M2_orf2#LINE/L1 (616) 2675 2446 m_b193s551i4 7606 chr4qtel1M 135838 TTTCTCAGCCAGTACCATATTGTTTTGATAATTACCACTTTATAATACAT 135887 i vv ii i v i ivi i i i C L1M2_orf2#LIN 2675 TTTTTATGCCAGTACCATGCTGTTTTGGTTACTATAGCTTTGTAGTATAT 2626 chr4qtel1M 135888 TTTGAGTACGGCTAG------ACCTCCTTCTTTTACATATTTTGTTTCAT 135931 ivv i v ------i vv vviv - i ivi- C L1M2_orf2#LIN 2625 TTTGAAGTCAGGTAGTGTGATGCCTCCAGCTTTGTTCT-TTTTGCTCAG- 2578 chr4qtel1M 135932 TGATTCTTTTG--TGTTTTGAGT-TTTTGTTCTTCCGGGTGAATTTTGCT 135978 - vi -- i iv i - vv ivii ivv C L1M2_orf2#LIN 2577 -GATTGCTTTGGCTATTCGGGGTCTTTTGTGGTTCCATACGAATTTTAGG 2529 chr4qtel1M 135979 ATTACTTTGTC--TCACTGTATAAAATAATTTTTTGATATTTTGATTAGT 136026 ?i v -- iv iv i i-- iv i vi v C L1M2_orf2#LIN 2528 ATTNTTTTTTCTATTTCTGTGAAGAATG--TCATTGGTATTTTGATAGGG 2481 chr4qtel1M 136027 ATGACACAGAATAAATAGATTAATTTAGGTAGAAT 136061 vi iv vvi iiv i v C L1M2_orf2#LIN 2480 ATTGCATTGAATCTGTAGATCGCTTTGGGTAGTAT 2446 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 41.28 CpG sites = 39, Kimura (unadjusted) = 43.81 Transitions / transversions = 1.22 (39/32) Gap_init rate = 0.04 (9 / 223), avg. gap size = 1.78 (16 / 9) 570 24.12 1.50 0.50 chr4qtel1M 136080 136279 (863721) C L1M1_orf2#LINE/L1 (1065) 2229 2028 m_b193s551i5 7606 chr4qtel1M 136080 ATATATAAATGCTGATAATTTATGTGAGTTTATTTTGTATCCTGCAACTT 136129 v iv i v iv v C L1M1_orf2#LIN 2229 ATATAGAAATGCTACTGATTTTTGTATGTTGATTTTGTATCCTGCAACTT 2180 chr4qtel1M 136130 TGCTAAAGTTGTCAATAATTTCAAGTAG-TTTTCAGTTGATTCTCTAGGA 136178 i i v iv v v v i - i? v v i v C L1M1_orf2#LIN 2179 TACTGAATTTGTTTATCAGTTCTAATAGTTTTTTNGTGGAGTCTTTAGGT 2130 chr4qtel1M 136179 TTTTCTAAGTATAACATCATATGATCTGAAAACAGTGATAGCTTTATTTC 136228 i i v v v iv ii v i C L1M1_orf2#LIN 2129 TTTTCCAAATATAAGATCATATCATCTGCAAACAAGGATAATTTGACTTC 2080 chr4qtel1M 136229 CTCACTGTCTATTCTAAAAG-CTTCGATTTCTTT-TCTTCTCTTATTGTT 136276 i - v i v i ii v - i iv - v v i C L1M1_orf2#LIN 2079 TTC-CTTTCCAATTTGGATGCCCTTTATTTCTTTCTCTTGTCTGATTGCT 2031 chr4qtel1M 136277 GTA 136279 v C L1M1_orf2#LIN 2030 CTA 2028 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 29.48 CpG sites = 23, Kimura (unadjusted) = 29.48 Transitions / transversions = 0.92 (23/25) Gap_init rate = 0.02 (4 / 199), avg. gap size = 1.00 (4 / 4) 319 32.74 0.00 0.00 chr4qtel1M 136347 136459 (863541) C L1M5_orf2#LINE/L1 (1276) 2018 1906 m_b193s551i6 7605 chr4qtel1M 136347 TCTAGTATAATATCAAATAAAAGAGGTGATAAGGGGCATCTTTGCATCAC 136396 i i i ii i v ? iv i i iv iii C L1M5_orf2#LIN 2018 TCCAGTACAATGTTGAATAGAAGTGGTGANAGCGGACATCCTTGTCTTGT 1969 chr4qtel1M 136397 CCCTGACTGTATTGGGAAGGCTTCTAGTTTATCCACATTGCAGATAATGT 136446 i i iiv vv i ? ii ? v vv iviv i C L1M5_orf2#LIN 1968 TCCCGATCTTAGGGGGAAAGCNTTCAGTNTTTCACCATTAAGTATGATGT 1919 chr4qtel1M 136447 TTGCTGATGATTT 136459 ? vv i C L1M5_orf2#LIN 1918 TNGCTGTAGGTTT 1906 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 45.98 CpG sites = 24, Kimura (unadjusted) = 47.82 Transitions / transversions = 1.85 (24/13) Gap_init rate = 0.00 (0 / 112), avg. gap size = 0.0 (0 / 0) 499 28.62 0.44 4.59 chr4qtel1M 136705 136931 (863069) C L1MD_orf2#LINE/L1 (1463) 1831 1614 m_b193s551i7 7607 chr4qtel1M 136705 GGTGCTTTATTTGATCAAATACTTTTTTCTGCATCTATTGATAGAATTAC 136754 i vv vi i - v vi i i C L1MD_orf2#LIN 1831 GGTGTTGAATTTTGTCAAATGCTTTTT-CTGCATCAATTGATATGATCAT 1783 chr4qtel1M 136755 ATGATTTCTGTTGGTTTTGTC-GTTGATGTGGTCAATTATACAGATAGTT 136803 i i v -v v i - i i vi i iv v v C L1MD_orf2#LIN 1782 GTGATTTTTCTT-CTTTAGCCTGTTAATATGGTGGATTACATTGATTGAT 1734 chr4qtel1M 136804 TTCTTAATACTGAACCAGTCCTGCATTTCTGGTATAGATATAGAATTCCC 136853 iiv i i i ?i v i --------i C L1MD_orf2#LIN 1733 TTTCGAATATTGAACCAGCCTTGCATNCCTGGAATAAA--------CCCC 1692 chr4qtel1M 136854 ACTTGATTATAGCATATCATCCTTGAGCTATGTTATTGTAGTCCTTTTGC 136903 i i i ii v i vvvv i ii v v ?v C L1MD_orf2#LIN 1691 ACTTGGTCATGGTGTATAATTCTTTTTATATATTGCTGAATTCNATTTGC 1642 chr4qtel1M 136904 TTGGATTTTATTTTAAAATTTTGCGTCT 136931 viv i vvii v C L1MD_orf2#LIN 1641 TAATATTTTGTTGAGGATTTTTGCGTCT 1614 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 36.47 CpG sites = 35, Kimura (unadjusted) = 37.23 Transitions / transversions = 1.30 (35/27) Gap_init rate = 0.05 (11 / 226), avg. gap size = 1.00 (11 / 11) 562 32.30 6.81 1.21 chr4qtel1M 136941 137175 (862825) C L3#LINE/CR1 (159) 3940 3693 m_b193s601i22 7608 chr4qtel1M 136941 CAGACCATTCTTCTCTGGGGCAGTTCTATTAATCAAAGATGTATCTCTTG 136990 v ivi i v i i iv vi i i i - vii i v C L3#LINE/CR1 3940 CAGCCCATTCCATTTTTGGACAGCTCTGATTGTTAGAAA-GTTCTTCCTT 3892 chr4qtel1M 136991 ACATCAAGATTTAATTTGCCTTA--GCCATGTTCAACCAGTTCTCCTGGA 137038 i ii vivv i iv-- iv iv i v v vv i v C L3#LINE/CR1 3891 ATATTGAGCCGAAATCTGCCTCCCTGTAACTTCCACCCATTGGTCCTAGT 3842 chr4qtel1M 137039 TCCACTTTCTAGAACCATCAAGGAACCAGTGTAGTTCCTCCTGCACATAA 137088 ii ii i i - vi iv v i i i v i C L3#LINE/CR1 3841 TCTGCCCTCTGGAGCCA-CACAGAATAAGTCTAATCCCTCTTCCACATGA 3793 chr4qtel1M 137089 CAGCCCTTCAAA-ATGTTGAAGACAGTTTTCACATTCCCCTTGAGTCTT- 137136 - - i v ii ii ii i - C L3#LINE/CR1 3792 CAGCCCTTCAAATAT-TTGAAGACAGCTATCATGTCTCCTCTAAGTCTTC 3744 chr4qtel1M 137137 ------------TAAGCAAGTCCAGTTCTTTCAAGTGATTCTCATATGAC 137174 ------------ i vvi i vi v i C L3#LINE/CR1 3743 TCTTCTCCAGGCTAAACATCCCCAGTTCCTTCAACCGTTCCTCATATGAC 3694 chr4qtel1M 137175 A 137175 C L3#LINE/CR1 3693 A 3693 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 42.77 CpG sites = 48, Kimura (unadjusted) = 44.39 Transitions / transversions = 1.78 (48/27) Gap_init rate = 0.03 (7 / 234), avg. gap size = 2.71 (19 / 7) 374 35.89 13.97 0.65 chr4qtel1M 137255 137526 (862474) L3#LINE/CR1 3785 4092 (7) m_b193s601i23 7609 chr4qtel1M 137255 AAGGGCTGTTCTATAGATCTAAGCCTGGTCTTGTCCTATTTAACCTGAGA 137304 iv i i vvvii vi i v i i i v ii iiv L3#LINE/CR1 3785 AAGGGCTGTCATGTGGAAGAGGGATTAGACTTATTCTGTGTGGCTCCAGA 3834 chr4qtel1M 137305 AGGCCAGGCTACAATTAGTGGGAGGAAGCT----GGA-----ATGTTGTG 137345 i viii vi ii i v i ---- ----- v i - L3#LINE/CR1 3835 GGGCAGAACTAGGACCAATGGGTGGAAGTTACAGGGAGGCAGATTTCG-G 3883 chr4qtel1M 137346 TTTCACACTTGGAGAAACTTCCTGAAAGCTAGAACTGTCCCCAAGGTGAA 137395 i iv i ivv ii i i v iii i v- ii i L3#LINE/CR1 3884 CTCAATATAAGGAAGAACTTTCTAACAATCAGAGCTGTCCA-AAAATGGA 3932 chr4qtel1M 137396 ACGGGTAACTTTGGCTGGTGA--AACTTCCCTT-----GAGGTCTTCA-- 137436 i ivi i i ?vv ii-- i i v ----- v -- L3#LINE/CR1 3933 ATGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGTCACTGGAGGTGTTCAAG 3982 chr4qtel1M 137437 -----------------TTTGCCTGGCATATTGTAGA-GGAAATCTTTCT 137468 -----------------i i v v i - i v i v v L3#LINE/CR1 3983 CAGAGGCTGGATGACCACTTGTCAGGGATGTTGTAGAAGGGATTCCTGCA 4032 chr4qtel1M 137469 TTATATCT-AGGTTTAATTAATTG-CTTCCAAGGTCTTTTCCAGCCCTGA 137516 iv vv- vi i iv - i i ii i i L3#LINE/CR1 4033 TTGGATGGGAGGTTGGACTAGATGACCTCTAAGGTCCCTTCCAACTCTGA 4082 chr4qtel1M 137517 AATTCTCTGA 137526 i v L3#LINE/CR1 4083 GATTCTGTGA 4092 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 51.03 CpG sites = 64, Kimura (unadjusted) = 52.67 Transitions / transversions = 1.94 (64/33) Gap_init rate = 0.04 (11 / 271), avg. gap size = 3.64 (40 / 11) 334 26.86 0.00 8.57 chr4qtel1M 137572 137685 (862315) C MIR3#SINE/MIR (67) 141 37 m_b193s601i25 7610 chr4qtel1M 137572 TTTTGAAGATAAGGAAATTCTCCAGGATTAGAGTGATTAAGTGACTGCCC 137621 iv i i v--- vii v i v vv C MIR3#SINE/MIR 141 TTTTACAGATGAGGAAACTG---AGGCCCAGAGAGGTGAAGTGACTTGCC 95 chr4qtel1M 137622 CAGGGTCATATAGCTGGTTGTATAAATGGTGGAGCCAGGACTGGACCCTC 137671 i i i ?i ----- i ii i i v - C MIR3#SINE/MIR 94 CAAGGTCACACAGCNAGTT-----AGTGGCAGAGCCGGGACTAGAACC-C 51 chr4qtel1M 137672 TGAACTCCTCATTC 137685 v iv v i C MIR3#SINE/MIR 50 AGGTCTCCTGACTC 37 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 32.78 CpG sites = 17, Kimura (unadjusted) = 34.28 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.08 (9 / 113), avg. gap size = 1.00 (9 / 9) 342 22.38 1.02 8.79 chr4qtel1M 137572 137669 (862331) C MIRc#SINE/MIR (124) 144 54 m_b193s601i24 7610 chr4qtel1M 137572 TTTTGAAGATAAGGAAATTCTCCAGGATTAGAGTGATTAAGTGACTGCCC 137621 iv i i v--- v i v i vv C MIRc#SINE/MIR 144 TTTTACAGATGAGGAAACTG---AGGCTCAGAGAGGTTAAGTGACTTGCC 98 chr4qtel1M 137622 CAGGGTCATATAGCTGGTTGTATAAATGGTGGAGCCAGGACT-GGACCC 137669 i i i i ----- i ii i - i C MIRc#SINE/MIR 97 CAAGGTCACACAGCTAG-----TAAGTGGCAGAGCCGGGACTCGAACCC 54 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 25.72 CpG sites = 14, Kimura (unadjusted) = 27.30 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.09 (9 / 97), avg. gap size = 1.00 (9 / 9) 250 32.39 1.41 0.00 chr4qtel1M 137754 137824 (862176) C MIR3#SINE/MIR (15) 193 122 m_b193s601i26 7611 chr4qtel1M 137754 AGGAT-TTAGAATGGGAAGGGATCTCAGAAGCCATCTAGTATGCTCCTTA 137802 i - i iiv i i iii viivi iiv C MIR3#SINE/MIR 193 AGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCT 144 chr4qtel1M 137803 TGTTTTCCAGATAAGGACACTG 137824 ii v i v C MIR3#SINE/MIR 143 CATTTTACAGATGAGGAAACTG 122 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 46.06 CpG sites = 17, Kimura (unadjusted) = 46.06 Transitions / transversions = 2.83 (17/6) Gap_init rate = 0.01 (1 / 70), avg. gap size = 1.00 (1 / 1) 285 35.25 1.35 4.17 chr4qtel1M 138483 138630 (861370) C L2c_3end#LINE/L2 (3) 475 332 m_b193s601i27 7612 chr4qtel1M 138483 CATTTCTTCAATGAGCATTCATTTAATGCTGGGCACTTTGCTAGG-GCCA 138531 iv ii i i v ii ivivi - v i - ii C L2c_3end#LINE 475 CATTCATTCAACAAACATTTATTGAGCGCCTACTA-TGTGCCAGGCGCTG 427 chr4qtel1M 138532 GGACTACAAAGG-GAGAAGGAGACAATCTCTGTCTTCCGGGACTCTCACA 138580 iv i- iv i v ii i i i vi -v C L2c_3end#LINE 426 GGGATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGA-GCTCACA 378 chr4qtel1M 138581 TCCTAATGGGAGAGAACACAAGGTAAGTAAATGTGCAAAGGACATACAAG 138630 vi i ii ----v ii ? iivi vvivv C L2c_3end#LINE 377 GTCTAGTGGAGGAGA----CAGACANGTAAACAGACAATTACAATACAAG 332 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 48.30 CpG sites = 33, Kimura (unadjusted) = 51.31 Transitions / transversions = 1.94 (33/17) Gap_init rate = 0.05 (8 / 147), avg. gap size = 1.00 (8 / 8) 31 19.26 0.00 0.00 chr4qtel1M 138830 138894 (861106) (GAGA)n#Simple_repeat 1 65 (0) m_b193s252i8 7613 chr4qtel1M 138830 GAGAGAGAGAAAGACAGAGACAGAGACAGACTGAGACACAGAGTGGGAGA 138879 i v v v vv v v v i (GAGA)n#Simpl 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr4qtel1M 138880 GAGAGACAGAGAGAG 138894 v (GAGA)n#Simpl 51 GAGAGAGAGAGAGAG 65 Matrix = Unknown Transitions / transversions = 0.22 (2/9) Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0) 293 32.16 8.99 4.57 chr4qtel1M 139176 139364 (860636) C L2#LINE/L2 (611) 2471 2275 m_b193s601i28 7612 chr4qtel1M 139176 GATTAGACAGAGTT--GTTCTGAACATGCTGAGCTCAAAATGCCTCTTGA 139223 i --- -- i i i i i ii i v ii C L2#LINE/L2 2471 GATCAG---GAGTTCAGTTTTGGACATGTTAAGTTTGAGATGCCTATTAG 2425 chr4qtel1M 139224 ACATCTAGTCACAAATGTCCAGGGGGCAGTTAATTGGTGACATG-GAGTC 139272 i iviiv i v vi i------ i i- C L2#LINE/L2 2424 ACATCCAAGTGGAGATGTCGAGTAGGCAGTTG------GATATACGAGTC 2381 chr4qtel1M 139273 -AGAATT--GGAAACCGATTC----------TGCACATCTGAGAGTGATC 139309 -i i -- ii vv i i ---------- ii v i i v C L2#LINE/L2 2380 TGGAGTTCAGGGGAGAGGTCCGGGCTGGAGATATAAATTTGGGAGTCATC 2331 chr4qtel1M 139310 TGCCTAGAGATGATAATGGAGCCGATGGGAACAGATGATA-CACGGAGAC 139358 v v v i v vi iv v i vii v - v? iv C L2#LINE/L2 2330 AGCATATAGATGGTATTTAAAGCCATGAGACTGGATGAGATCACCNAGGG 2281 chr4qtel1M 139359 AGAGAG 139364 v C L2#LINE/L2 2280 AGTGAG 2275 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 44.51 CpG sites = 37, Kimura (unadjusted) = 44.51 Transitions / transversions = 1.76 (37/21) Gap_init rate = 0.08 (15 / 188), avg. gap size = 1.73 (26 / 15) 232 32.91 6.33 0.00 chr4qtel1M 139757 139835 (860165) L2c_3end#LINE/L2 382 465 (13) m_b193s601i29 7614 chr4qtel1M 139757 AGCTTCTTGGGGACA-----TTTCCTCTACTTTTCTTTGACTCCCCAGAA 139801 i i i -----iv viii i iv vv vi L2c_3end#LINE 382 AGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTATCCCCAGCG 431 chr4qtel1M 139802 CCCAGCGCATGACAGGAGCTTAATAAAAATTTGT 139835 ii i iii v i vi L2c_3end#LINE 432 CCTGGCACATAGTAGGCGCTCAATAAATGTTTGT 465 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 41.47 CpG sites = 18, Kimura (unadjusted) = 46.36 Transitions / transversions = 2.25 (18/8) Gap_init rate = 0.01 (1 / 78), avg. gap size = 5.00 (5 / 1) 16 9.78 0.00 0.00 chr4qtel1M 143983 144004 (855996) (A)n#Simple_repeat 1 22 (0) m_b193s252i10 7615 chr4qtel1M 143983 AAAAAAAAACAACAAAAAAAAA 144004 v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAA 22 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 13 13.66 2.94 2.94 chr4qtel1M 145080 145113 (854887) (GGGGC)n#Simple_repeat 1 34 (0) m_b193s252i11 7616 chr4qtel1M 145080 GGGGAGGGGC-GGGCGGGCCGGGCGTGGGACGGGG 145113 v - v - i i (GGGGC)n#Simp 1 GGGGCGGGGCGGGGCGGGGCGGG-GCGGGGCGGGG 34 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2) 12 7.26 6.45 3.12 chr4qtel1M 145161 145191 (854809) (GGGGCA)n#Simple_repeat 1 32 (0) m_b193s252i12 7616 chr4qtel1M 145161 GGGGCAGGGCCAGGAGGC-GGGG-ACGGGCAGG 145191 v - - - v (GGGGCA)n#Sim 1 GGGGCAGGGGCAGG-GGCAGGGGCAGGGGCAGG 32 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.10 (3 / 30), avg. gap size = 1.00 (3 / 3) 12 30.36 1.72 1.72 chr4qtel1M 145390 145447 (854553) (CCGGG)n#Simple_repeat 1 58 (0) m_b193s252i13 7617 chr4qtel1M 145390 CCGGGCCGGGCCGATCCGAGGGCAGACCAGACCCGTCCGTGCCGCGGC-G 145438 iv - v i i i i v v v v v - (CCGGG)n#Simp 1 CCGGGCCGGGCCGGGCCG-GGCCGGGCCGGGCCGGGCCGGGCCGGGCCGG 49 chr4qtel1M 145439 GCTGGGACG 145447 i v (CCGGG)n#Simp 50 GCCGGGCCG 58 Matrix = Unknown Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.04 (2 / 57), avg. gap size = 1.00 (2 / 2) 534 27.66 6.56 3.17 chr4qtel1M 147106 147288 (852712) MIRb#SINE/MIR 49 237 (31) m_b193s601i30 7618 chr4qtel1M 147106 ATAAATTTGAGTTCCGGTCTGGTCTCAGACACTTATCATGGACGATGGGA 147155 i i ii i vii iv v v v ii ---i vi v MIRb#SINE/MIR 49 ACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTA---GCTGTGTGA 95 chr4qtel1M 147156 CCCTGAACACATCGCTCCACCTGTCTG--CCTCAGTTTCCT-----GTAA 147198 i ii vi ii iv v -- ----- MIRb#SINE/MIR 96 CCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAA 145 chr4qtel1M 147199 G-TGGGGATGATACCAGCATCCACCTCCCAGAGCAGCCA--AGGCTCAAA 147245 i- i ---ii i i v i iv iii-- v i MIRb#SINE/MIR 146 AATGGGGATAATA---ATACCTACCTCGCAGGGTTGTTGTGAGGATTAAA 192 chr4qtel1M 147246 TGAGATAATATCTGTAAAGTGCTTA--ACAGTGCCTGGCACAGAG 147288 iiv i -- v MIRb#SINE/MIR 193 TGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAG 237 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 35.34 CpG sites = 34, Kimura (unadjusted) = 36.29 Transitions / transversions = 2.27 (34/15) Gap_init rate = 0.06 (11 / 182), avg. gap size = 1.64 (18 / 11) 55 18.60 0.00 0.00 chr4qtel1M 147300 147402 (852598) (CTCC)n#Simple_repeat 1 103 (0) m_b193s252i14 7619 chr4qtel1M 147300 CTTCCTCCCTCCCTCCCTCCCTCCCTTCCTTCCTTCCTCCCTTCCTTCCT 147349 i i i i i i (CTCC)n#Simpl 1 CTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCT 50 chr4qtel1M 147350 TCCTTTCTTCCTTCTTCCCTCCCTCCCTCCTTCCCTCCCTCCTTTCCTTC 147399 i ii i i i i i i i (CTCC)n#Simpl 51 CCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCC 100 chr4qtel1M 147400 CTC 147402 (CTCC)n#Simpl 101 CTC 103 Matrix = Unknown Transitions / transversions = 1.00 (16/0) Gap_init rate = 0.00 (0 / 102), avg. gap size = 0.0 (0 / 0) 220 24.66 8.43 2.27 chr4qtel1M 148058 148140 (851860) C L2d2_3end#LINE/L2 (0) 555 468 m_b193s601i31 7620 chr4qtel1M 148058 TCAGACTCAACTGGACAAACATT----AAGCGCCTAATTTGTGCAAAGAG 148103 i - v vi i ----i v v i vi C L2d2_3end#LIN 555 TCAAA-TCAAATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCA 507 chr4qtel1M 148104 CTGTGCTAGGCCTT---GGGGACAGTGAGGAAAGAGAAGA 148140 vi --- i -ii i iv v C L2d2_3end#LIN 506 CTGTGCTAGGCGCTGTGGGGGATA-CAAAGAAGTATAAGA 468 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 30.63 CpG sites = 12, Kimura (unadjusted) = 30.63 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.05 (4 / 82), avg. gap size = 2.25 (9 / 4) 229 21.21 9.09 0.00 chr4qtel1M 148072 148137 (851863) C L2b_3end#LINE/L2 (13) 453 382 m_b193s601i32 7620 chr4qtel1M 148072 ACAAACATT----AAGCGCCTAATTTGTGCAAAGAGCTGTGCTAGGCCTT 148117 i ----i v v v i v? vi C L2b_3end#LINE 453 ACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCT 404 chr4qtel1M 148118 GGGG--ACAGTGAGGAAAGAGA 148137 -- i iv vi C L2b_3end#LINE 403 GGGGATACAGCGGTGAACAAGA 382 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 23.57 CpG sites = 7, Kimura (unadjusted) = 25.57 Transitions / transversions = 1.00 (7/7) Gap_init rate = 0.03 (2 / 65), avg. gap size = 3.00 (6 / 2) 489 21.54 3.10 6.40 chr4qtel1M 149132 149260 (850740) C MIRc#SINE/MIR (120) 148 24 m_b194s601i2 7621 chr4qtel1M 149132 CTCATTTTACAGATGAGTAAACTGAGGC---AAATGGTTAAGTGACTTGC 149178 i v ---i iv C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr4qtel1M 149179 TTGGGGTCACACAGGTAAAAAGTGTCAGAGTCTGGATTTGAACTCATGAA 149228 iiii v iv v i v i i i ---- C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCA---- 53 chr4qtel1M 149229 AATGGGTCTTGC-GGCTGCTGGTCTGCTGCTCT 149260 ---- v - i v vi iiv C MIRc#SINE/MIR 52 ----GGTCTTCCTGACTCCAAGTCCAGTGCTCT 24 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 24.71 CpG sites = 16, Kimura (unadjusted) = 25.83 Transitions / transversions = 1.60 (16/10) Gap_init rate = 0.08 (10 / 128), avg. gap size = 1.20 (12 / 10) 456 33.85 6.75 2.15 chr4qtel1M 151890 152200 (847800) L2b_3end#LINE/L2 140 464 (2) m_b194s601i3 7622 chr4qtel1M 151890 CTCTTCTCTCTCCCACTGGG-CATTCT-CCTCATCTTTACCTCCTGGCT- 151936 v i v -- i- iii - i i i -i v i- L2b_3end#LINE 140 CTGTTCCCTCTGCC--TGGAACGCCCTTCCCCACCTCT-TCGCCTGGCCA 186 chr4qtel1M 151937 -TTCCTGACT--TCCTTCAAATTTCAACTAAAGTCCTGCCTC-TGAAAGA 151982 -i - -- ii i i v i viii - vvii L2b_3end#LINE 187 ACTCCT-ACTCATCCTTCAGGTCTCAGCTCAAATGTCACCTCCTCCGGGA 235 chr4qtel1M 151983 AGCCTTTCTTGGACCCCTTAAC---ATCAATGCCTTTTCTCTGAGACTCC 152029 i i i iv ivii ---i ivvv ii i i --i L2b_3end#LINE 236 AGCCCTCCCTGACCCCCCAGGCCGGGTCAGGCGCCCTCCTCTGGG--CCC 283 chr4qtel1M 152030 CCCCATTCATCCTGTAGGGATATGGTTCACACATCG-CTGTTTGCATGTT 152078 v v v iv ivviv v v i i?- i - ? i i L2b_3end#LINE 284 CCCCAGTCCTACCCTGCCACTCTGGGTTATN-ATTGTCTGNTTACATGTC 332 chr4qtel1M 152079 T--CTTCCCCATCACACTAGGAGCTCCATGACAG-AACGACTGT---TAA 152122 -- i ii v iv i vi - iv i ?--- iv L2b_3end#LINE 333 TGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGT 382 chr4qtel1M 152123 CAT-TTCTTTGC---ATCCTTAGTTCTTAGCACAGTTTCTGGCACACGGT 152168 v - vii --- ii iv i ?vi i L2b_3end#LINE 383 CTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGT 432 chr4qtel1M 152169 GAGCACTTAATAAGTGCTAGTCAAATGACTAA 152200 ii i i i i ii v ii v i L2b_3end#LINE 433 AGGCGCTCAGTAAATATTTGTTGAATGAATGA 464 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 44.61 CpG sites = 71, Kimura (unadjusted) = 49.37 Transitions / transversions = 2.22 (71/32) Gap_init rate = 0.06 (20 / 310), avg. gap size = 1.40 (28 / 20) 279 34.74 8.48 2.29 chr4qtel1M 152748 152912 (847088) C L3#LINE/CR1 (259) 3840 3666 m_b194s601i4 7623 chr4qtel1M 152748 CTGCTCCTTGAAGTCCTGAAAAATGAA---AAATGCTCTTTCTCAGAGCA 152794 i ii i i viiv i i i--- viv i v vii C L3#LINE/CR1 3840 CTGCCCTCTGGAGCCACACAGAATAAGTCTAATCCCTCTTCCACATGACA 3791 chr4qtel1M 152795 -TTGTCTAAATGGCCAAAGATAGC----ACCTCTGGGCCCCTAA----TC 152835 -iiv ii iviii i ---- iv --- i ---- C L3#LINE/CR1 3790 GCCCTTCAAATATTTGAAGACAGCTATCATGTCT---CCTCTAAGTCTTC 3744 chr4qtel1M 152836 T-TTCTCCAGATTAAGCACCTTGAGCTCCTTCAAACATTCCTTGGACAAG 152884 - ii i i iiv i v i iiv ii v C L3#LINE/CR1 3743 TCTTCTCCAGGCTAAACATCCCCAGTTCCTTCAACCGTTCCTCATATGAC 3694 chr4qtel1M 152885 ATGGTTTGCCAGTTCC-ACACTAGCTTGG 152912 - vi -v i v i C L3#LINE/CR1 3693 ATGGTTT-CCAGACCCTTCACCATCCTGG 3666 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 49.52 CpG sites = 40, Kimura (unadjusted) = 50.89 Transitions / transversions = 2.50 (40/16) Gap_init rate = 0.06 (10 / 164), avg. gap size = 1.80 (18 / 10) 24 29.37 1.02 3.12 chr4qtel1M 153706 153803 (846197) (TAAA)n#Simple_repeat 1 96 (0) m_b194s252i0 7624 chr4qtel1M 153706 TAAATAAATATTTTTATTTATTTAAATAAA-ATATTTTTTATTTAAAAAA 153754 -vv v v v v - - v vvv v v v v (TAAA)n#Simpl 1 TAAATAAATA-AATAAATAAAT-AAATAAATAAATAAATAAATAAATAAA 48 chr4qtel1M 153755 TATAAATATAAATAAATTAATTAAATATAAAAATAGCTAAATAAATAAA 153803 v v v - v v v iv (TAAA)n#Simpl 49 TAAATAAATAAATAAA-TAAATAAATAAATAAATAAATAAATAAATAAA 96 Matrix = Unknown Transitions / transversions = 0.05 (1/21) Gap_init rate = 0.04 (4 / 97), avg. gap size = 1.00 (4 / 4) 317 22.22 1.39 0.00 chr4qtel1M 153807 153878 (846122) C MIR#SINE/MIR (49) 213 141 m_b194s601i5 7625 chr4qtel1M 153807 TAAGCACTTTACATTTATTACCTCATTCGAGCCTGACCCCAACCCT-CAG 153855 i v v ii v v vv -iii C MIR#SINE/MIR 213 TAAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGA 164 chr4qtel1M 153856 GGTAGGAGTTATTACTATCCCCA 153878 vii i C MIR#SINE/MIR 163 GGTAGGTACTATTATTATCCCCA 141 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 24.85 CpG sites = 9, Kimura (unadjusted) = 26.73 Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.01 (1 / 71), avg. gap size = 1.00 (1 / 1) 261 26.74 11.63 0.00 chr4qtel1M 153897 153982 (846018) C L2c_3end#LINE/L2 (15) 463 368 m_b194s601i6 7626 chr4qtel1M 153897 AAATATTTA-------CCTATT-TAGGCCAA-TGTTTGAG-TACAAAGAA 153936 i ------- i - iv i-i i v i - v C L2c_3end#LINE 463 AAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGATACAAAGAT 414 chr4qtel1M 153937 AGGCAAAAGACAATCCCTATTCTCAAGGAGTTCACAGTCTAATGGA 153982 iiii i v ii iii i i C L2c_3end#LINE 413 GAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAGTGGA 368 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 32.02 CpG sites = 19, Kimura (unadjusted) = 35.95 Transitions / transversions = 4.75 (19/4) Gap_init rate = 0.05 (4 / 85), avg. gap size = 2.50 (10 / 4) 217 38.03 0.00 0.00 chr4qtel1M 153925 153995 (846005) C L2d2_3end#LINE/L2 (68) 487 417 m_b194s601i7 7626 chr4qtel1M 153925 GAGTACAAAGAAAGGCAAAAGACAATCCCTATTCTCAAGGAGTTCACAGT 153974 ii ivii i v iii iii i i i C L2d2_3end#LIN 487 GGATACAAAGAAGTATAAGACATGGTCCCTGCCCTCAAGGAGCTTACAAT 438 chr4qtel1M 153975 CTAATGGACAGGATTAGCTAT 153995 i v ivii iv vi C L2d2_3end#LIN 437 CTAGTTGGGGAGACAAGACAT 417 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 60.99 CpG sites = 21, Kimura (unadjusted) = 60.99 Transitions / transversions = 3.50 (21/6) Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0) 18 24.83 3.45 1.69 chr4qtel1M 155422 155440 (844560) (AT)n#Simple_repeat 1 21 (38) m_b194s252i1 7627 chr4qtel1M 155422 ATA-ATATACATACATAT-TA 155440 - i i - (AT)n#Simple_ 1 ATATATATATATATATATATA 21 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.11 (2 / 18), avg. gap size = 1.00 (2 / 2) 33 5.62 0.00 0.00 chr4qtel1M 155441 155477 (844523) (AT)n#Simple_repeat 1 37 (0) c_b194s251i0 7627 chr4qtel1M 155441 ATATATATATATATATATATATATATAAATGTATATA 155477 v i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATA 37 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 18 24.83 3.45 1.69 chr4qtel1M 155478 155515 (844485) (AT)n#Simple_repeat 22 58 (1) m_b194s252i1 7627 chr4qtel1M 155478 AAATACACACATATATGTCATATACATATACACACATA 155515 v i i i i - i i i i (AT)n#Simple_ 22 ATATATATATATATATAT-ATATATATATATATATATA 58 Matrix = Unknown Transitions / transversions = 8.00 (8/1) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 12 18.37 4.26 4.26 chr4qtel1M 162091 162137 (837863) (TCCCTAG)n#Simple_repeat 1 47 (0) m_b194s252i2 7628 chr4qtel1M 162091 TCCCTAGTCCTTAGTCTCTCTAGTCACTGGTTGCT--TCCCTGGTGCCT 162137 i - - v i iv -- i v (TCCCTAG)n#Si 1 TCCCTAGTCCCTAGTC-C-CTAGTCCCTAGTCCCTAGTCCCTAGTCCCT 47 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.07 (3 / 46), avg. gap size = 1.33 (4 / 3) 426 37.33 11.23 1.07 chr4qtel1M 162168 162844 (837156) L2#LINE/L2 1858 2602 (480) m_b194s601i8 7629 chr4qtel1M 162168 CTTTCTTCCCTTTCATAGTCAAACGCCTAGGCCAGGCCATCTACACTCAT 162217 i vi i i i iv v v ivvii iii i ii L2#LINE/L2 1858 CTCTGCTCCCCTTTACAGCAAAACTCCTCGAAAGAGTTGTCTATACTCGC 1907 chr4qtel1M 162218 GGGCTCCCCTTCCTCTTTTTTCACTTCTCTCACTCTTGGTCGTTCTGCAG 162267 v v vv ii ii - ---- iv viv v i L2#LINE/L2 1908 TGTCTCCAATTCCTCTCCTCCCA-TTCTCTC----TTGAACCCACTCCAA 1952 chr4qtel1M 162268 TCTGGCTTTC-TCTACACT-CTGCAC--AAACATCCCTCTCCAACACTAC 162313 v - iv i- v -- vv i ivi viii L2#LINE/L2 1953 TCAGGCTTTCGTCCCCACCACTCCACCGAAACTGCTCTTGTCAAGGTCAC 2002 chr4qtel1M 162314 GAA-GAC--------TGGGAA--CTAACGGCTAACAGAACGGCTCCATCC 162352 v - -------- vv -- i i ii ivvvvv v ii i L2#LINE/L2 2003 CAATGACCTCCACGTTGCTAAATCCAATGGTCAATTCTCAGTCCTCATCT 2052 chr4qtel1M 162353 GTCCTTGGCTTCTTGG-AGCCTCTGTAGAAGCTGATGGCTCCTTC--TCC 162399 - v i i ? ii - v i vviv i vi i -- i L2#LINE/L2 2053 -TACTTGACCTNTCAGCAGCATTTGACACAGTTGATCACTCCCTCCTTCT 2101 chr4qtel1M 162400 TGGAA---TGTCGTCGA--GGTTTCCATGA-AGCTTATTCTCC-AATTCT 162442 i --- v v iv-- i v - v vi i -ii i L2#LINE/L2 2102 TGAAACACTTTCTTCACTTGGCTTCCAGGACACCACACTCTCCTGGTTTT 2151 chr4qtel1M 162443 CCCCCCGCC-CATGGGACTGCTTTTTCTCAGGCTCCTGTACAGGATTATC 162491 i ii - iv - i ii v v i v v iv L2#LINE/L2 2152 CCTCCTACCTCACTGG-CCGCTCCTTCTCAGTCTCCTTTGCTGGTTCCTC 2200 chr4qtel1M 162492 CTG---TGCATG-CCACT-AACG-------ACTCCAGG---CTGTCCT-G 162525 v--- v vi - v - -------i i --- v - L2#LINE/L2 2201 CTCATCTCCCCGACCTCTNAACGTTGGAGTGCCCCAGGGCTCAGTCCTTG 2250 chr4qtel1M 162526 GA--TCTTCTTGTT--------------CTCTCTTGGTGATTCCATCT-G 162558 -- iv i-------------- i ? ii i- L2#LINE/L2 2251 GACCTCTTCTCTTCTCTATCTACACTCACTCCCTNGGTGATCTCATCCAG 2300 chr4qtel1M 162559 CCCCAAGAATTCAAATGTTACTTCCATACACGTGGCTCCTAAGAAGGCAT 162608 i i v iv i iii ii vi i vvi i i ivvvii L2#LINE/L2 2301 TCTCATGGCTTTAAATACCATCTATATGCTGATGACTCCCAAATTTATAT 2350 chr4qtel1M 162609 CTCCTGCCTCGGCTTCCCCC---------AGTCCCACATTTGCAATTGTC 162649 v iv i i i --------- v i ii v v i i L2#LINE/L2 2351 CTCCAGCCCGGACCTCTCCCCTGAACTCCAGACTCGTATATCCAACTGCC 2400 chr4qtel1M 162650 CCCTAAATAGCTCTTCTTGGACGCCCCATTGCTCCCTTGAACTCAGTGCC 162699 iv vi i v iv i i iv v vivi ii i iiiiv L2#LINE/L2 2401 TACTCGACATCTCCACTTGGATGTCTAATAGGCATCTCAAACTTAACATG 2450 chr4qtel1M 162700 TCTATCAGAAAGCATATTCTCTTTTTCCATAAA--TACCTCT-TTGGAG- 162745 i vv vvi i viv vv iii vi -- i ii -ii v - L2#LINE/L2 2451 TCCAAAACTGAACTCCTGATCTTCCCCCTCAAACCTGCTCCTCCCGCAGT 2500 chr4qtel1M 162746 CGTCCCTGTTTCTCTCATGGGCGCCACCATTTTTCCAATCACCAAGGGAA 162795 v ii i vv ? vv iv v ii i ii iv vv L2#LINE/L2 2501 CTTCCCCATCTCAGTNAATGGCAACTCCATCCTTCCAGTTGCTCAGGCCA 2550 chr4qtel1M 162796 ACGATCTC----CCATCACTGATGACTCTCCATTCTCCCTCTCTCCACAT 162841 vi i i----i vi ivv i- i v v i L2#LINE/L2 2551 AAAACCTTGGAGTCATCCTTGACTCCTCTCT-TTCTCTCACACCCCACAT 2599 chr4qtel1M 162842 CCA 162844 L2#LINE/L2 2600 CCA 2602 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 52.36 CpG sites = 148, Kimura (unadjusted) = 54.66 Transitions / transversions = 1.45 (148/102) Gap_init rate = 0.05 (35 / 676), avg. gap size = 2.40 (84 / 35) 187 20.00 0.00 0.00 chr4qtel1M 163729 163763 (836237) C L2d_3end#LINE/L2 (11) 505 471 m_b194s601i9 7630 chr4qtel1M 163729 ACCGAGAAGCATTTATTAAGCACCTACTATTTGCT 163763 i i v i i i v C L2d_3end#LINE 505 ATCAACAAGTATTTATTGAGCGCCTACTATGTGCT 471 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 20.26 CpG sites = 5, Kimura (unadjusted) = 24.03 Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 218 30.19 0.00 0.00 chr4qtel1M 163735 163787 (836213) C L2c_3end#LINE/L2 (15) 463 411 m_b194s601i10 7630 chr4qtel1M 163735 AAGCATTTATTAAGCACCTACTATTTGCTACGTGTTGGAAGTGCATGGAG 163784 i i i v i v i i iii i vi v C L2c_3end#LINE 463 AAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGATACAAAGAT 414 chr4qtel1M 163785 AAA 163787 i C L2c_3end#LINE 413 GAA 411 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 34.93 CpG sites = 12, Kimura (unadjusted) = 41.66 Transitions / transversions = 3.00 (12/4) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 468 37.70 6.62 0.81 chr4qtel1M 166201 166668 (833332) C L1ME4c_3end#LINE/L1 (298) 532 38 m_b194s551i0 7631 chr4qtel1M 166201 ACCACAATTTATGAAGCCATTTCCCAGCTGAGGAGCACTCCCTTGGCTCC 166250 i ivv i i vii vv ii i ivvv v i i C L1ME4c_3end#L 532 ACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAGGTTGTTTC 483 chr4qtel1M 166251 TAGTTTTGCCCCAGACCAAAAAA-GCTGCTATTTAGATCTTCCTACATTT 166299 i i v v i vvvi v - v vv v v i v C L1ME4c_3end#L 482 CAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTCGTGCATAT 433 chr4qtel1M 166300 GGCTCCTCTCCTCCTTTCTTTAATCTCTTTGGGG---GCTACC------- 166339 i ii ii i i vvv v i i i i---ii v ------- C L1ME4c_3end#L 432 AGCTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAATTCCCAGAAGTG 383 chr4qtel1M 166340 ------CTGGGACAAATA-TCTGTACAATTCACTAATTCTTTGACCATGT 166382 ------ v vi- v v v ivv iii vivv i i C L1ME4c_3end#L 382 GAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTCTTGATACGTAT 333 chr4qtel1M 166383 CTCCAGATTGCTTTCTAGAGTGGCTGGACTAATCCAGAGCTTCACCAACA 166432 iv i i i iv i v i ii v ?ivi i C L1ME4c_3end#L 332 TGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACANTGCCACCAGCA 283 chr4qtel1M 166433 GAAGATG----TGCTTGTTTCCCCACAGTCCCTCCAGCATT------TGT 166472 iviv ---- i iv v i ?i i v ------ i C L1ME4c_3end#L 282 ATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGCATTGGGTATTAT 233 chr4qtel1M 166473 CATTTTTTTGTGCCAACTTT-ACTCAACTGATGAGTAGGAGATGGAAGCT 166521 v i---- i -i v vi i ii iivi i v v C L1ME4c_3end#L 232 CAATTTTTTA----AATTTTTGCTAATTTAATAGGCGTAAAATGGTATCT 187 chr4qtel1M 166522 CAA-ATTGCTTTAATTTGCACTTCTCCAATTATTAGTTA-TTTGGATAAT 166569 v-i i iii i iv -v i i v C L1ME4c_3end#L 186 CATTGTTGCTTTAATTTGCATTTCTTTGATTACTAGCGAGGTTGAACATT 137 chr4qtel1M 166570 TTTTCATATGACTAGTGATAGCTCAGGTTTCTATCCTTGAAAACTACCCA 166619 i i vi iv v ivi? iivi iviii? vi i ii ii C L1ME4c_3end#L 136 TTTCCATGTGTTTGTTTACTANTTGTATTTCCTCTTNTGTGAATTGTCTG 87 chr4qtel1M 166620 TTCATATCCTTTGACCATTGGTCAGTTTGAGAACAGCTCTTATTTTTAT 166668 i v vi vi v i vviv v ? v i C L1ME4c_3end#L 86 TTCATGTCCTTTGCCCATTTATCTATTGGGGTCTTGATNTTTTTCTTAT 38 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 53.94 CpG sites = 103, Kimura (unadjusted) = 55.94 Transitions / transversions = 1.43 (103/72) Gap_init rate = 0.03 (14 / 467), avg. gap size = 2.50 (35 / 14) 564 31.62 2.52 10.00 chr4qtel1M 166340 166736 (833264) C L1PA17_3end#LINE/L1 (540) 373 4 m_b194s551i1 7631 chr4qtel1M 166340 CTGGGACAAATATCTGTACAATTCACTAATTCTTTGACCATGTCTCCAGA 166389 v i iviv v v i-i i vv -i i C L1PA17_3end#L 373 CTGGGTCGAATGGTAGTTCTATTT-TTAGTTCTTTGAGAA-ATCTCCAAA 326 chr4qtel1M 166390 TTGCTTTCTAGAGTGGCTGGACTAATCCAGAGCTTCACCAACAG-----A 166434 i i v v i ii v viii ----- C L1PA17_3end#L 325 CTGCTTTCCACAGGGGCTGAACTAATTTACATTCCCACCAACAGTGTATA 276 chr4qtel1M 166435 AGATGTGCTTGTTTCCCCACAGTCCCTCCAGCATTTGTCATTTTTT--TG 166482 -i v iiv i i ?i i v i i i --iv C L1PA17_3end#L 275 AG-CGTTCCCTTTTCTCCGCANCCTCGCCAACATCTGTTATTTTTTGACT 227 chr4qtel1M 166483 TGCCAACTTTACTCA-ACTGATGAGTAGGAGATGGAAGCTCA-AATTGCT 166530 vii ivv vi -v ivi iv v v -vi v i C L1PA17_3end#L 226 TTTTAATAATAGCCATTCTGACTGGTGTGAGATGGTATCTCATTGTGGTT 177 chr4qtel1M 166531 TTAATTTGCACTTCTCCAATTATTAGTTAT-TTGGATAATTTTTCATATG 166579 i i ii v v - iii v C L1PA17_3end#L 176 TTGATTTGCATTTCTCTGATGATTAGTGATGTTGAGCATTTTTTCATATG 127 chr4qtel1M 166580 ACTAGTGATAGCTCAGGTTTCTATCCTTGAAAACTACCCATTCATATCCT 166629 vi iv iiv iivi v viii i v ii ii i C L1PA17_3end#L 126 TTTGTTGGCCGCTTGTATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCT 77 chr4qtel1M 166630 TTGACCATTGGTCAGTTTGAGAACAGCTCTTATTTTTATATTCTTATTTT 166679 v i vv i i-- i i------- ---------- i C L1PA17_3end#L 76 TTGCCCACTTTTTAA--TGGGG-------TTAT----------TTGTTTT 46 chr4qtel1M 166680 CTTATTGTTAATAAATATTCTTATATTTTGATTCAGTTCTGTATATATTT 166729 i v i --------------- v v iv v i C L1PA17_3end#L 45 TTTCTTGTTGA---------------TTTGTTTAAGTTCCTTATAGATTC 11 chr4qtel1M 166730 TGGATAT 166736 C L1PA17_3end#L 10 TGGATAT 4 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 40.89 CpG sites = 69, Kimura (unadjusted) = 42.39 Transitions / transversions = 1.57 (69/44) Gap_init rate = 0.11 (42 / 396), avg. gap size = 1.12 (47 / 42) 659 31.85 3.68 0.71 chr4qtel1M 166367 166638 (833362) C L1PA16_3end#LINE/L1 (566) 347 68 m_b194s551i2 7631 chr4qtel1M 166367 AATTCTTTGACCATGTCTCCAGATTGCTTTCTAGAGTGGCTGGACTAATC 166416 i vv -i i i i v i i C L1PA16_3end#L 347 AGTTCTTTGAGAA-ATCTCCAAACTGCTTTCCACAGTGGCTGAACTAATT 299 chr4qtel1M 166417 CAGAGCTTCACCAACAG-----AAGATGTGCTTGTTTCCCCACAGTCCCT 166461 i v viii ----- -i v iiv i i i i v C L1PA16_3end#L 298 TACATTCCCACCAACAGTGTATAAG-CGTTCCCTTTTCTCCGCAGCCTCG 250 chr4qtel1M 166462 CCAGCATTTGTCATTTTTT--TGTGCCAACTTTACTCA-ACTGATGAGTA 166508 i ii --iv vii ivv vi -v ivi i C L1PA16_3end#L 249 CCAGCATCTGTTGTTTTTTGACTTTTTAATAATAGCCATTCTGACTGGTG 200 chr4qtel1M 166509 GGAGATGGAAGCTCA-AATTGCTTTAATTTGCACTTCTCCAATTATTAGT 166557 v v v -vi v i i i ii v C L1PA16_3end#L 199 TGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGATTAGT 150 chr4qtel1M 166558 TAT-TTGGATAATTTTTCATATGACTAGTGATAGCTCAGGTTTCTATCCT 166606 v - iii v vi iv iiv iivi v viii C L1PA16_3end#L 149 GATGTTGAGCATTTTTTCATATGTTTGTTGGCCGCTTGTATGTCTTCTTT 100 chr4qtel1M 166607 TGAAAACTACCCATTCATATCCTTTGACCATT 166638 i v ii ii i v i C L1PA16_3end#L 99 TGAGAAGTGTCTGTTCATGTCCTTTGCCCACT 68 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 42.08 CpG sites = 55, Kimura (unadjusted) = 43.45 Transitions / transversions = 1.77 (55/31) Gap_init rate = 0.03 (7 / 271), avg. gap size = 1.71 (12 / 7) 807 27.76 2.77 3.17 chr4qtel1M 170796 171048 (828952) MIRb#SINE/MIR 3 254 (14) m_b194s601i11 7632 chr4qtel1M 170796 GAGAGGCAGTTCCAGAGTAAGGGGGAGAGAGC-CAGCTGGTAGGATCAGG 170844 i --- ivi ivi v i - i vivv i ii i MIRb#SINE/MIR 3 GAGGGGCAG---CGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGA 49 chr4qtel1M 170845 AAGCTATGAGTTCAAATCCAGCCTCAGATGCTTAGTAGCTGGGTGAGCCG 170894 v viv i i v v v vii v v v iv MIRb#SINE/MIR 50 CAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTT 99 chr4qtel1M 170895 AGGCAAGTCCCTTCACCTTGTTTTGCTTCAGTTTCCTCATCTGTAAAATG 170944 i iv v ivi vv i MIRb#SINE/MIR 100 GGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATG 149 chr4qtel1M 170945 GAGACAATGACAGCACCTGCCATGTAGG---GTTGTGCAG-TCAAACGAG 170990 i i --- ii i vi i --- vi - i i MIRb#SINE/MIR 150 GGGATAAT---AATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAG 196 chr4qtel1M 170991 AT--CGCATTTACCAAGCACTTAGCCCAGCATCTGGCATAAAGTAAGTGC 171038 --i v -- i v iii i v i MIRb#SINE/MIR 197 ATAATGCATGTA--AAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGC 244 chr4qtel1M 171039 TCCATAAATG 171048 v MIRb#SINE/MIR 245 TCAATAAATG 254 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 31.76 CpG sites = 40, Kimura (unadjusted) = 35.55 Transitions / transversions = 1.43 (40/28) Gap_init rate = 0.05 (12 / 252), avg. gap size = 1.25 (15 / 12) 217 24.24 0.00 0.00 chr4qtel1M 171974 172039 (827961) L2c_3end#LINE/L2 202 267 (211) m_b194s601i12 7633 chr4qtel1M 171974 CCTTCAAGTCCCACCTAAAATCCCCTCTCCTCCAGGAAGCCTTCCCCACC 172023 ? i v v i vi vi i iiv L2c_3end#LINE 202 CCTTCAAGNCTCAGCTCAGATGTCACCTCCTCCGGGAAGCCTTCCCTGAC 251 chr4qtel1M 172024 TCCTCAGCCCTAGTCT 172039 i i iv? L2c_3end#LINE 252 CCCCCAAGNCTAGTCT 267 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 28.94 CpG sites = 10, Kimura (unadjusted) = 31.26 Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0) 12 4.29 0.00 11.11 chr4qtel1M 173641 173670 (826330) (GGAGG)n#Simple_repeat 1 27 (0) m_b194s252i3 7634 chr4qtel1M 173641 GGACGGGTAGGGGATGGGGATGGGGAGGGG 173670 - v - - (GGAGG)n#Simp 1 GGA-GGGGAGGGGA-GGGGA-GGGGAGGGG 27 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.10 (3 / 29), avg. gap size = 1.00 (3 / 3) 14 24.57 6.25 1.49 chr4qtel1M 174181 174244 (825756) (GCC)n#Simple_repeat 1 67 (0) m_b194s252i4 7635 chr4qtel1M 174181 GCCGGCGCCGCCGCCGCCTCCGTTGGCG-AGCTGCC-CGGCCTCC-CCTG 174227 v v ii v -v i - v v - vv (GCC)n#Simple 1 GCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGC 50 chr4qtel1M 174228 CGCTCGGGGCC-CCGCCG 174244 - vv - (GCC)n#Simple 51 CGC-CGCCGCCGCCGCCG 67 Matrix = Unknown Transitions / transversions = 0.30 (3/10) Gap_init rate = 0.08 (5 / 63), avg. gap size = 1.00 (5 / 5) 566 28.00 10.05 0.88 chr4qtel1M 177008 177216 (822784) MIR#SINE/MIR 21 248 (14) m_b194s601i13 7636 chr4qtel1M 177008 AGAGCACCCAGCCTGGAGGCCGAAAAGCCTGAGTACAAATCCACCCTCAG 177057 vvivi - ii vv i v i vvv v MIR#SINE/MIR 21 AGAGCACGGGCTCTGGAG-CCAGACTGCCTGGGTTCGAATCCCGGCTCTG 69 chr4qtel1M 177058 ATATTTAACTGGCTGTGTGATCCTGGGCAAATCACTTAGCTCCTGCTTAA 177107 vi i - i i i i i i ii viv iv MIR#SINE/MIR 70 CCACTTA-CTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGC 118 chr4qtel1M 177108 CTCAGTTTCCCCAACTGT-AAATAGAGATCATAATAGCGTCTGCATCAC- 177155 i v - i i v iii i v i- MIR#SINE/MIR 119 CTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTCATA 168 chr4qtel1M 177156 -----------CGAATTAGATAA--TAAT---TTTAAAGCACCTAGCAAA 177189 -----------v i i i -- --- v i i v v MIR#SINE/MIR 169 GGGTTGTTGTGAGGATTAAATGAGTTAATACATGTAAAGCGCTTAGAACA 218 chr4qtel1M 177190 ATGCCTGACACATAG---GTGCTTTTTAAA 177216 i i --- i ivv MIR#SINE/MIR 219 GTGCCTGGCACATAGTAAGCGCTCAATAAA 248 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 33.79 CpG sites = 35, Kimura (unadjusted) = 36.11 Transitions / transversions = 1.52 (35/23) Gap_init rate = 0.04 (8 / 208), avg. gap size = 2.88 (23 / 8) 80 40.36 1.86 0.61 chr4qtel1M 178886 179370 (820630) (CA)n#Simple_repeat 1 491 (0) m_b194s252i5 7637 chr4qtel1M 178886 CACACACATCTAAACATGCA-ACACACACACA-AAACACATGCTCATATA 178933 - - v ii - - v ii v i i (CA)n#Simple_ 1 CACACACA-C-ACACACACACACACACACACACACACACACACACACACA 48 chr4qtel1M 178934 CAGAAACACATGTGTACACACATGTTCACACATACA-AAATGTATGTGCG 178982 v v iiiii iiiv i - v iii iiii i (CA)n#Simple_ 49 CACACACACACACACACACACACACACACACACACACACACACACACACA 98 chr4qtel1M 178983 CACAAACTCGCACAAGAATATGCATACACTCACA-AGCCACTCACACACA 179031 v v i viv i ii i v - vv v (CA)n#Simple_ 99 CACACACACACACACACACACACACACACACACACACACACACACACACA 148 chr4qtel1M 179032 TACATGTTCCCACACACAAACTCATACATTTACATATACGTATACACACA 179081 i iiiv v v v i ivi i i ii i (CA)n#Simple_ 149 CACACACACACACACACACACACACACACACACACACACACACACACACA 198 chr4qtel1M 179082 TGAC-CTCACACATAGTCATGCATCCACACACATACTCATACACATGCAC 179130 -v - v i vv ii iv i v i ii (CA)n#Simple_ 199 -CACACACACACACACACACACACACACACACACACACACACACACACAC 247 chr4qtel1M 179131 ACAGAGAAACGTGCAGTCAGATATACACACGTACACTCCAACACACGTAC 179180 v v v iii vv v i i ii v vv ii (CA)n#Simple_ 248 ACACACACACACACACACACACACACACACACACACACACACACACACAC 297 chr4qtel1M 179181 ATACACAAGCACACACACATTTACTCCTACACCCACTCACACATATAAAC 179230 i vi ivi v vi v v i i v (CA)n#Simple_ 298 ACACACACACACACACACACACACACACACACACACACACACACACACAC 347 chr4qtel1M 179231 TCACATA-ATACATGCCCTCA-ATTCACATACTTATACACATTCACTCAC 179278 v i - i ii v v - iv i vi i iv v (CA)n#Simple_ 348 ACACACACACACACACACACACACACACACACACACACACACACACACAC 397 chr4qtel1M 179279 A-ATCCACTCACACACATATACATACACA-ATTCAGACACTCATGCAAAC 179326 - iv v i i i - iv v v ii v (CA)n#Simple_ 398 ACACACACACACACACACACACACACACACACACACACACACACACACAC 447 chr4qtel1M 179327 ACACACATTTACTTGCATATATACACACAAACACACACACACAC 179370 ivi vii i i i v (CA)n#Simple_ 448 ACACACACACACACACACACACACACACACACACACACACACAC 491 Matrix = Unknown Transitions / transversions = 1.52 (88/58) Gap_init rate = 0.02 (12 / 484), avg. gap size = 1.00 (12 / 12) 229 19.67 4.92 0.00 chr4qtel1M 180558 180618 (819382) Charlie4a#DNA/hAT-Charlie 383 446 (62) m_b194s502i0 7638 chr4qtel1M 180558 TTGTTTCTCTTTCTAATGCT---CATTTTGTTTTCTGCATTTAAAAACAT 180604 v ii v v ---i i v Charlie4a#DNA 383 TTGGTTTCCTTTGTAATCCTATGTATTTTATTTTATGCATTTAAAAACAT 432 chr4qtel1M 180605 GATGTTGAGGAGGG 180618 v vi i Charlie4a#DNA 433 TATTCTGAGAAGGG 446 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 22.96 CpG sites = 6, Kimura (unadjusted) = 22.96 Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.02 (1 / 60), avg. gap size = 3.00 (3 / 1) 211 25.30 5.00 1.20 chr4qtel1M 185138 185217 (814783) L2c_3end#LINE/L2 332 414 (64) m_b194s601i14 7639 chr4qtel1M 185138 CTTGT-TTGTA--CGTCCCTTTTTGAGCCTAAATTCCCCACTAGATTGTG 185184 - --i iv vi?v i ivv i i i L2c_3end#LINE 332 CTTGTATTGTAATTGTCTGTTTACNTGTCTGTCTCCTCCACTAGACTGTG 381 chr4qtel1M 185185 ATCTCCTTGAGAGAAGGGCTTGT-TCATACTTCA 185217 v i v vii - v - L2c_3end#LINE 382 AGCTCCTTGAGGGCAGGGACCGTGTCTTA-TTCA 414 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 30.01 CpG sites = 11, Kimura (unadjusted) = 31.89 Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.05 (4 / 79), avg. gap size = 1.25 (5 / 4) 218 16.33 6.12 0.00 chr4qtel1M 185168 185216 (814784) L2d2_3end#LINE/L2 427 478 (77) m_b194s601i15 7639 chr4qtel1M 185168 TTCCCCACTAGATTGTGATCTCCTTGAGAGAAGGG--CTTGT-TCATACT 185214 i v i v i v -- v - i L2d2_3end#LIN 427 TCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACT 476 chr4qtel1M 185215 TC 185216 L2d2_3end#LIN 477 TC 478 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 18.50 CpG sites = 4, Kimura (unadjusted) = 18.50 Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.04 (2 / 48), avg. gap size = 1.50 (3 / 2) 184 27.28 19.44 1.57 chr4qtel1M 185336 185443 (814557) L2a_3end#LINE/L2 381 507 (10) m_b194s601i16 7640 chr4qtel1M 185336 CTGTCTCTAC--AATGGAAAATAAAATACCACTAAGAGCAGGGTCTGTTT 185383 iv -- v i vi iv - - i i v v v L2a_3end#LINE 381 CTGTCTCCCCCCACTAGAATGTAAGCT-CCA-TGAGGGCAGGGACTTTTG 428 chr4qtel1M 185384 TTTGCCTTCTT---TGTTGT----CCAGCTCTTAG------------CAC 185414 i ii v --- i ---- v i ------------ L2a_3end#LINE 429 TCTGTTTTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCAC 478 chr4qtel1M 185415 ATGGTGGGTATTTAATCAGTACTTGTTGA 185443 i i iii i v i i L2a_3end#LINE 479 ATAGTAGGCGCTCAATAAATATTTGTTGA 507 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 33.68 CpG sites = 19, Kimura (unadjusted) = 35.38 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.06 (6 / 107), avg. gap size = 3.83 (23 / 6) 237 30.77 2.56 0.00 chr4qtel1M 185366 185443 (814557) L2c_3end#LINE/L2 389 468 (10) m_b194s601i17 7640 chr4qtel1M 185366 TAAGAGCAGGGTCTGTTTTTTGC-CTTCTTTGT-TGTCCAGCTCTTAGCA 185413 i i v i v i ii- v - vi v i i L2c_3end#LINE 389 TGAGGGCAGGGACCGTGTCTTATTCATCTTTGTATCCCCAGCGCCTGGCA 438 chr4qtel1M 185414 CATGGTGGGTATTTAATCAGTACTTGTTGA 185443 i i iii i v i ii L2c_3end#LINE 439 CATAGTAGGCGCTCAATAAATGTTTGTTGA 468 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 37.82 CpG sites = 18, Kimura (unadjusted) = 42.84 Transitions / transversions = 3.00 (18/6) Gap_init rate = 0.03 (2 / 77), avg. gap size = 1.00 (2 / 2) 211 28.85 0.00 0.00 chr4qtel1M 185402 185453 (814547) L2d_3end#LINE/L2 463 514 (2) m_b194s601i18 7640 chr4qtel1M 185402 CAGCTCTTAGCACATGGTGGGTATTTAATCAGTACTTGTTGATGACTTGA 185451 iv v i i iii i v i viv L2d_3end#LINE 463 CAGTGCTGAGCACATAGTAGGCGCTCAATAAATACTTGTTGATTGATTGA 512 chr4qtel1M 185452 CT 185453 i L2d_3end#LINE 513 TT 514 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 34.54 CpG sites = 10, Kimura (unadjusted) = 38.11 Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 73 30.73 1.30 4.71 chr4qtel1M 186484 186790 (813210) (GAGGG)n#Simple_repeat 1 297 (0) m_b195s252i0 7641 chr4qtel1M 186484 GAGGGAGGGGGAGGGGAGAGGAGGGGAAGGGGCAAGGAAAGGAAAAGGGA 186533 ii i - -- ii ii i (GAGGG)n#Simp 1 GAGGGGAGGGGAGGGGAGGGGAGGGG-AGGGG--AGGGGAGGGGAGGGGA 47 chr4qtel1M 186534 GGAGAGGGGAAAGGAAAGGAGAGGGGAGGGGAAGGGAAAAGGAAGGAGAA 186583 i -- ii i - -i i i i i (GAGGG)n#Simp 48 GGGGAGGGG--AGGGGAGGGGAGGGGAGGGG-AGGG-GAGGGGAGGGGAG 93 chr4qtel1M 186584 GACAAGGGAGAGGAGAAAGGGGGAAGGGA-AGGAAAGGAGGGGAGGGGGA 186632 iv i i iiii i -i ii - - (GAGGG)n#Simp 94 GGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGA-GGGG- 141 chr4qtel1M 186633 AGGACAGAGGAGGGGAGGGGAAAGGAAATCA-GAGAGGAGGAGAGG-GGG 186680 iv i ii iivv - i - i - (GAGGG)n#Simp 142 AGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGG-GGAGGGGAGGG 190 chr4qtel1M 186681 AAGGAAAGGAGAGGGGAGGGGAAGGGAAAAGGAAGGAGAAGACAAGGGAG 186730 i ii i - -i i i i i iv i (GAGGG)n#Simp 191 GAGGGGAGGGGAGGGGAGGGG-AGGG-GAGGGGAGGGGAGGGGAGGGGAG 238 chr4qtel1M 186731 AGGAGAAAGGGGGAAGGGA-AGGAAAGGAGAGGAAAGGAGGGGAAGAGAA 186779 i iiii i -i ii i ii - - ii (GAGGG)n#Simp 239 GGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGG-AG-GGG 286 chr4qtel1M 186780 AGGGGAGGGGA 186790 (GAGGG)n#Simp 287 AGGGGAGGGGA 297 Matrix = Unknown Transitions / transversions = 12.20 (61/5) Gap_init rate = 0.06 (18 / 306), avg. gap size = 1.00 (18 / 18) 12 3.65 10.00 3.12 chr4qtel1M 189324 189353 (810647) (AGGG)n#Simple_repeat 1 32 (0) m_b195s252i1 7642 chr4qtel1M 189324 AGGGA-GG-GGGAGGGA-GGAGGGATGGCAGGG 189353 - - - - v (AGGG)n#Simpl 1 AGGGAGGGAGGGAGGGAGGGAGGGA-GGGAGGG 32 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.14 (4 / 29), avg. gap size = 1.00 (4 / 4) 14 12.02 8.16 3.92 chr4qtel1M 191431 191479 (808521) (CCGGAGG)n#Simple_repeat 1 51 (0) m_b195s252i2 7643 chr4qtel1M 191431 CCGGGGAGCGGAGGCCGGATGGCCAGCGG--GGA-G-CGGAGGCCGGATG 191476 i iv - i v -- - - - (CCGGAGG)n#Si 1 CCGGAGGCCGGAGGCCGGA-GGCCGGAGGCCGGAGGCCGGAGGCCGGA-G 48 chr4qtel1M 191477 GCC 191479 (CCGGAGG)n#Si 49 GCC 51 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.10 (5 / 48), avg. gap size = 1.20 (6 / 5) 20 8.62 0.00 5.13 chr4qtel1M 191696 191736 (808264) (CAGAACA)n#Simple_repeat 1 39 (0) m_b195s252i3 7644 chr4qtel1M 191696 CAGAACCCAGAACCACAGAAAACAGAACCACAGAACCCAGA 191736 v - v - v (CAGAACA)n#Si 1 CAGAACACAGAA-CACAGAACACAGAA-CACAGAACACAGA 39 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 18 32.84 0.00 1.75 chr4qtel1M 192622 192679 (807321) (AC)n#Simple_repeat 1 57 (0) m_b195s252i4 7645 chr4qtel1M 192622 ACAGCACACACACGTGCACACACAGACACATGTGCATACACGGACACACG 192671 - iii v iiii i iv i (AC)n#Simple_ 1 ACA-CACACACACACACACACACACACACACACACACACACACACACACA 49 chr4qtel1M 192672 TGCACACA 192679 ii (AC)n#Simple_ 50 CACACACA 57 Matrix = Unknown Transitions / transversions = 6.00 (12/2) Gap_init rate = 0.02 (1 / 57), avg. gap size = 1.00 (1 / 1) 13 8.72 4.00 0.00 chr4qtel1M 192903 192927 (807073) (GGACA)n#Simple_repeat 1 26 (0) m_b195s252i5 7646 chr4qtel1M 192903 GGACAGGA-AGGACAGGGCAGGGCAG 192927 - i i (GGACA)n#Simp 1 GGACAGGACAGGACAGGACAGGACAG 26 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 12 0.00 4.35 4.35 chr4qtel1M 193823 193845 (806155) (GGGT)n#Simple_repeat 1 23 (0) m_b195s252i6 7647 chr4qtel1M 193823 GGGTGGG-GGGTGGGATGGGTGGG 193845 - - (GGGT)n#Simpl 1 GGGTGGGTGGGTGGG-TGGGTGGG 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.09 (2 / 22), avg. gap size = 1.00 (2 / 2) 23 25.08 0.00 0.00 chr4qtel1M 195224 195284 (804716) (CACACA)n#Simple_repeat 1 61 (0) m_b195s252i7 7648 chr4qtel1M 195224 CACACATACAAACTCACCCACACTCACACTTAGACACACACACACACATT 195273 i v v v v vi v iv (CACACA)n#Sim 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 chr4qtel1M 195274 CACCTAAACAC 195284 vi v (CACACA)n#Sim 51 CACACACACAC 61 Matrix = Unknown Transitions / transversions = 0.44 (4/9) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 13 14.00 2.13 9.09 chr4qtel1M 196753 196799 (803201) (CCCCT)n#Simple_repeat 1 44 (0) m_b195s252i9 7649 chr4qtel1M 196753 CCCCTCCCCCCCTCTCACCACTGCACCCT-TCAGCCCCTCCCCTCCCC 196799 i i - - - - -i vv (CCCCT)n#Simp 1 CCCCTCCCCTCCCCTC-CC-CT-C-CCCTCCCCTCCCCTCCCCTCCCC 44 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.11 (5 / 46), avg. gap size = 1.00 (5 / 5) 281 27.40 16.07 6.56 chr4qtel1M 198280 198447 (801553) MIRc#SINE/MIR 37 219 (49) m_b195s601i4 7650 chr4qtel1M 198280 TGGCATCAAGAAGACTCATCTGCCTGAGTTCAAATCTGAACTTTG----- 198324 vi i -------- i i i ivii i ----- MIRc#SINE/MIR 37 TGGAGTCAGGAAGAC--------CTGGGTTCGAGTCCCGGCTCTGCCACT 78 chr4qtel1M 198325 -------TGTGTGTCCCTGGGCAAGTCACTTCACC-----------CTGT 198356 ------- v i v ----------- v MIRc#SINE/MIR 79 TACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGT 128 chr4qtel1M 198357 GTTCTCATCTGTAAAACAAGCTGAGAAAGAAATGACCAACC--CCTC-CA 198403 v i iii vvv iv v vv v vi -- - MIRc#SINE/MIR 129 TTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACA 178 chr4qtel1M 198404 GGATGTTTGCCAAGAAAACCCAAATGGGGTCATGAAT-TGAAAAC 198447 i vv iv i ----i i i v v - i MIRc#SINE/MIR 179 GGGTTGTTGTGAGGA----TCAAATGAGATAATGTATGTGAAAGC 219 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.95 CpG sites = 23, Kimura (unadjusted) = 34.91 Transitions / transversions = 1.15 (23/20) Gap_init rate = 0.11 (18 / 167), avg. gap size = 2.17 (39 / 18) 13 17.50 0.00 3.03 chr4qtel1M 201717 201750 (798250) (GGCACG)n#Simple_repeat 1 33 (0) m_b195s252i10 7651 chr4qtel1M 201717 GGCAAGCGCGGGGGCACGGGGACGGGCACGTGGC 201750 v v iv v - (GGCACG)n#Sim 1 GGCACGGGCACGGGCACGGGCACGGGCACG-GGC 33 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 56 21.07 2.07 2.07 chr4qtel1M 202936 203080 (796920) (AGGAGG)n#Simple_repeat 1 145 (0) m_b195s252i11 7652 chr4qtel1M 202936 AGGGGGAAGAGGAGGAGGAGGAGGAAGAGGAGGAGAAGGAGGAGGAAGAG 202985 i i i i i (AGGAGG)n#Sim 1 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG 50 chr4qtel1M 202986 GAGGAGAAAGAGGAGCAGGAGGAGGAGG-GAAGGGGAAAGGGGAAGAGAA 203034 i i v - i i i i i i -i (AGGAGG)n#Sim 51 GAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG-G 99 chr4qtel1M 203035 AAGAGGGAGAGAGAGGA-GACCATGAGGTAGCTGG-GGAGGGGCAGGA 203080 i ii - - vv v - vv - i v (AGGAGG)n#Sim 100 AGGAGGAGGAG-GAGGAGGAGGAGGAGG-AGGAGGAGGAGGAGGAGGA 145 Matrix = Unknown Transitions / transversions = 2.57 (18/7) Gap_init rate = 0.04 (6 / 144), avg. gap size = 1.00 (6 / 6) 32 24.27 1.19 1.19 chr4qtel1M 203461 203544 (796456) (AC)n#Simple_repeat 1 84 (0) m_b195s252i12 7653 chr4qtel1M 203461 ACACTCCAACACATTCA-ACCTACACACTACACACCTCCTCACACACACA 203509 v vv iv - vi - viv v (AC)n#Simple_ 1 ACACACACACACACACACACACACACAC-ACACACACACACACACACACA 49 chr4qtel1M 203510 CACACACACGCACACACTCTCACTCTCTCACACAC 203544 i v v v v v (AC)n#Simple_ 50 CACACACACACACACACACACACACACACACACAC 84 Matrix = Unknown Transitions / transversions = 0.31 (4/13) Gap_init rate = 0.02 (2 / 83), avg. gap size = 1.00 (2 / 2) 239 28.72 1.05 1.05 chr4qtel1M 203834 203928 (796072) L1MD1_3end#LINE/L1 198 292 (697) m_b195s551i0 7654 chr4qtel1M 203834 CACACCTCTAGGATTGGCTAAGATGACAGGAAAAGATAATGACGGATGTT 203883 v vi v i i v iiv iv i iiv ii i L1MD1_3end#LI 198 CACACCTATCAGAATGGCTAAAATAAAAAATAGTGACAACACCAAATGCT 247 chr4qtel1M 203884 GGAGGGGATGCGGGAAAAACTGGGACACTGATGCATTG-TGGGGGG 203928 v i - i iv v i - v L1MD1_3end#LI 248 GGCGAGGATGC-GGAGAAACTGGATCACTCATACATTGCTGGTGGG 292 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 37.24 CpG sites = 16, Kimura (unadjusted) = 37.24 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.02 (2 / 94), avg. gap size = 1.00 (2 / 2) 849 28.12 5.27 2.19 chr4qtel1M 204865 205395 (794605) L1ME3G_3end#LINE/L1 1 547 (377) m_b195s551i1 7655 chr4qtel1M 204865 TTCATTTCCAAAATATATAAAGAATTAATTCCAATTTATAAAAAATCGCT 204914 v v i i vv v v iv i vv v- L1ME3G_3end#L 1 TTAATATCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAAAAGA- 49 chr4qtel1M 204915 TCATTCCTCCAATTGAAAAATGGTCAAA--ATATGAA-AGACAACCCTT- 204960 - ---vi v v -- - i ii vi- L1ME3G_3end#L 50 -CA---ACCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACA 95 chr4qtel1M 204961 GATGAAGAAATTGGAAATATTTAGT---CATAAGGAAAAGATGCTCCAAG 205007 v i -iv ivii i --- -v v vv L1ME3G_3end#L 96 GAAGAGGAAAT-ACAAATGGCCAATAAACATA-TGAAAAGATGCTCAACC 143 chr4qtel1M 205008 TCATTATTAATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTA 205057 i v i i vv i i v L1ME3G_3end#L 144 TCACTAGTAATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTT 193 chr4qtel1M 205058 CACACCTGTCAGATT--CAAAAA-TGACAGGAAAAATAATGATGATTGTT 205104 iv ii -- - v v i ?vvi ivi? v L1ME3G_3end#L 194 TTCACCCATCAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTT 243 chr4qtel1M 205105 GG---GGGATTGGGAAAACTGGGACATTGATTCATTGTTGGTGGAGTTGT 205151 --- vv i v v vi v v i i iiv L1ME3G_3end#L 244 GGCGAGGGTGTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGT 293 chr4qtel1M 205152 GAACGAATCC--CCATTTTGGAGAGTAGTTTGGAACTATGTCAAAAAGTT 205199 i ivii v -- ? i i i v v v vvv i L1ME3G_3end#L 294 AAATTGGTACAGCCNTTTTGGAGGGCAATTTGGCAGTATCTATTAAAATT 343 chr4qtel1M 205200 ATCAAACTTGCATACCCTTTGATC---CAAGGTTATTACTGGGATTATAT 205246 - v ivi i --- vvii i v ? ?v v L1ME3G_3end#L 344 -TAAAATGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTAT 392 chr4qtel1M 205247 CCCAAAAGATTA--TAAAGAAGGG---AAAGGGACCTGTATTGCAAGAAT 205291 i ? ii v --iiv v v v --- i i?i v --- i L1ME3G_3end#L 393 CCTANAGAAATACTCGCACATGTGCACAAGGANGCATGTA---CAAGGAT 439 chr4qtel1M 205292 GTTTGTGGCAGCCC--TTTGTAGTGGCTAGAAACTGGAAACTGAATGGAT 205339 ii v vi-- i i v i i vivv ii L1ME3G_3end#L 440 GTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAAT 489 chr4qtel1M 205340 GTCCA-CGGTTGGAGAATGGCTGAATAAATTTGGGTATGA--AAATTATG 205386 - ii v i i i vv iv-- v i - L1ME3G_3end#L 490 GTCCATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTAT- 538 chr4qtel1M 205387 GGAATATTA 205395 i L1ME3G_3end#L 539 GGAATACTA 547 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 35.69 CpG sites = 74, Kimura (unadjusted) = 36.33 Transitions / transversions = 1.03 (74/72) Gap_init rate = 0.05 (25 / 530), avg. gap size = 1.60 (40 / 25) 366 29.05 7.99 5.08 chr4qtel1M 204871 205483 (794517) L1MC2_3end#LINE/L1 7 636 (455) m_b195s551i2 7655 chr4qtel1M 204871 TCCAAAATATATAAAGAA---TTAATTCCAATTTATAAAAAATCGCTTCA 204917 i --- vv iv viv i v ivviv L1MC2_3end#LI 7 TCCAAAATATACAAAGAACTCTTAAAACTCAACAATAAGAAAACAAACAA 56 chr4qtel1M 204918 TTCCTCCAATTGAAAAATGGTCAAAATAT--GAA-AGACAACCC-TTGAT 204963 i---- ? v v -- - v i -iii v L1MC2_3end#LI 57 C----CCAATTNAAAAATGGGCAAAAGATCTGAACAGACACCTCACCAAA 102 chr4qtel1M 204964 GAAGAAAT-----TGG-AAATATTTAGTCATAAGGAAAAGATGCTCCAAG 205007 v ----- - --- - -v v vi L1MC2_3end#LI 103 GAAGATATACAGATGGCAAATA---AG-CATA-TGAAAAGATGCTCAACA 147 chr4qtel1M 205008 TCATTATTAATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTA 205057 vvv v i i v i vv i L1MC2_3end#LI 148 TCATATGTCATTAGGGAATTGCAAATTAAAACAACAATGAGATACCACTA 197 chr4qtel1M 205058 CACACCTGTCAGATT--CAAAAATGACAGGAAA--AATAATGATGATTGT 205103 i i v -- v -v ii v --i i iivii v i L1MC2_3end#LI 198 CACACCTATTAGAATGGCTAAAAT-CCAAAACACTGACAACACCAAATGC 246 chr4qtel1M 205104 TG--GGGGAT-TGGGAAAACTGGGACATTGATTCATTGTTGGTGGAGTTG 205150 -- i - iiv v i vi v i iiv L1MC2_3end#LI 247 TGGCGAGGATGTGGAGCAACAGGAACTCTCATTCATTGCTGGTGGGAATG 296 chr4qtel1M 205151 TGAACGAATCC--CCATTTTGGAGAGTAGTTTGGAACTATGTCAAAAAGT 205198 ii vvii v -- i iiii v v v v i v i L1MC2_3end#LI 297 CAAAATGGTACAGCCACTTTGGAAGACAGTTTGGCAGTTTCTTACAAAGC 346 chr4qtel1M 205199 T-ATCAAACTTGCATACCCTTTGATCCAAGGTTATTAC------TGGGAT 205241 - v v ? -- v v vi -- iv ii ------ v L1MC2_3end#LI 347 TAAACATANT--CTTACCATACGATCCA--GCAATCGCGCTCCTTGGTAT 392 chr4qtel1M 205242 TATATCCCAAAAGA-TTATAAAGAAGGG-----AAAGGGACCTGTATTGC 205285 - - v - iv vvviv ----- v iii i --- L1MC2_3end#LI 393 T-TA-CCCAAATGAGTTGAAAACTTATGTCCACACAAAAACCTGCA---C 437 chr4qtel1M 205286 AAGAATGTTTGTGGCAGCCC--TTTGTAGTGGCTAGAAACTGGAAACTGA 205333 v i i ii-- ii i v i i vi i -- L1MC2_3end#LI 438 ACGAATGTTTATAGCAGCTTTATTCATAATTGCCAAAACTTGGAAGC--A 485 chr4qtel1M 205334 AT--GGATGTCC-ACGGTTGGAGAATGGCTGAATAAATTTGGGT--ATGA 205378 i--i -v ii v v v i i i vv -- vv L1MC2_3end#LI 486 ACCAAGATGTCCTTCAATAGGTGAATGGATAAACAAACTGTGGTACATCC 535 chr4qtel1M 205379 AAATTATGGGAATATTACT--GTTCT-TGAAGAAATGACCCAACAGGATG 205425 v iv - i -- ivv -vi v i v i --- L1MC2_3end#LI 536 ATACAAT-GGAATATTATTCAGCGATAAAAAGAAATGAGCTATCAAG--- 581 chr4qtel1M 205426 ATTTCAGAAAGGCCTGGAGA---CTTAAACGAACTGATGCTGGAGGAAAT 205472 -iiv ii i v i--- i v - iv ----- i L1MC2_3end#LI 582 -CCACGAAAAGACATGGAGGAACCTTAAATGCA-TATTGCT-----AAGT 624 chr4qtel1M 205473 GAAAGGA-CCAG 205483 i - L1MC2_3end#LI 625 GAAAGAAGCCAG 636 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 36.47 CpG sites = 90, Kimura (unadjusted) = 37.62 Transitions / transversions = 1.14 (90/79) Gap_init rate = 0.09 (55 / 612), avg. gap size = 1.47 (81 / 55) 19 4.55 0.00 0.00 chr4qtel1M 205911 205933 (794067) (A)n#Simple_repeat 1 23 (0) m_b195s252i13 7656 chr4qtel1M 205911 AAAAAAAAAAAAAAAAAAAAGAA 205933 i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAA 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 435 32.34 8.52 1.60 chr4qtel1M 206518 206693 (793307) C MIRb#SINE/MIR (46) 222 35 m_b195s601i5 7657 chr4qtel1M 206518 TGTGCTGGCCACCTGGCAAA-AGTGTCTCATTCGGTCTCCACAGCAACCC 206566 iiv i i vi vi- v i iii ii i C MIRb#SINE/MIR 222 TGTGCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCC 173 chr4qtel1M 206567 TG-GAGGTGGGTGTGGCCTTTATCCCCCCTTTCCT--TGAGGATGCCCAG 206613 - i i vi--- vi v v-- vi iv C MIRb#SINE/MIR 172 TGCGAGGTAGGTATTA---TTATCCCCATTTTACAGATGAGGAAACTGAG 126 chr4qtel1M 206614 AC----AGAGGTAAAATGACTTGCC-------ACACAACTAGAGTGTATT 206652 i ---- v i i ------- i viv ivi C MIRb#SINE/MIR 125 GCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGC 76 chr4qtel1M 206653 AAAGGCAGGATTTAAACTCCAATCCTCCTGAGACCAGAGTC 206693 i v i ii i vii ivi vv i i C MIRb#SINE/MIR 75 AGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCC 35 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.38 CpG sites = 37, Kimura (unadjusted) = 44.76 Transitions / transversions = 1.95 (37/19) Gap_init rate = 0.05 (8 / 175), avg. gap size = 2.25 (18 / 8) 587 27.16 5.49 4.92 chr4qtel1M 207010 207191 (792809) C MIR#SINE/MIR (46) 216 34 m_b195s601i6 7658 chr4qtel1M 207010 TTCTACAGCACCCACCATGTGTCAGGCCTTGTCTCACTGGCTCTTCACAA 207059 - i iivv i i i------- i viv i C MIR#SINE/MIR 216 TTCTA-AGCGCTTTACATGTATTAA-------CTCATTTAATCCTCACAA 175 chr4qtel1M 207060 CAACCCTGAAAAGTGGGCGCTGCTATTGTTCCCCATTTCACAGATAAGGA 207109 ivi i i ii ii i - i i C MIR#SINE/MIR 174 CAACCCTATGAGGTAGGTACTATTATTAT-CCCCATTTTACAGATGAGGA 126 chr4qtel1M 207110 AACTGAGGCAAGCAGAGGTCCAGTAATGTGCCCAA----------CTAGT 207149 viv iv iv ---------- C MIR#SINE/MIR 125 AACTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGT 76 chr4qtel1M 207150 AGGTGTCTGAGGCTGGATTTGCATTCGGGCCCTCCAGATCCA 207191 i v v v v i v ii i vv ii v C MIR#SINE/MIR 75 AAGTGGCAGAGCCGGGATTCGAACCCAGGCAGTCTGGCTCCA 34 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.08 CpG sites = 30, Kimura (unadjusted) = 34.92 Transitions / transversions = 1.76 (30/17) Gap_init rate = 0.06 (10 / 181), avg. gap size = 1.90 (19 / 10) 377 31.40 7.91 1.06 chr4qtel1M 207037 207213 (792787) C MIR1_Amn#SINE/MIR (27) 203 15 m_b195s601i7 7658 chr4qtel1M 207037 CTTGTC-TCACTGGCTCTTCACAACAACCCTGAAAAGTGGGCGCTGCTAT 207085 v - v i v - v i viiivv i v v iv iii C MIR1_Amn#SINE 203 CTTTTCATCAGTAGATCT-CAAAGCACTTTACAAAGGAGGTCAGTATCAT 155 chr4qtel1M 207086 TGTTCCCCATTTCACAGATAAGGAAACTGAGGCAAGCAGAGGTCCAGTAA 207135 i - i i ?viv ?v i C MIR1_Amn#SINE 154 TAT-CCCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGA 106 chr4qtel1M 207136 TGTGCCCAA----------CTAGTAGGTGTCTGAGGCTGGATTTGCATTC 207175 iv ---------- ?i i?i v v v v ? ? v ii C MIR1_Amn#SINE 105 CTTGCCCAAGGTCACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAACCC 56 chr4qtel1M 207176 GGGCCCTCCAGATCC--ATGCAG-GCCGGCCCCACCAGACC 207213 i i ii iii --i v - ivvvi i C MIR1_Amn#SINE 55 AGGTCTCCCGAGTCCCAGTCCAGTGCTCTATCCACTAGACC 15 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.02 CpG sites = 32, Kimura (unadjusted) = 44.10 Transitions / transversions = 1.39 (32/23) Gap_init rate = 0.03 (6 / 176), avg. gap size = 2.67 (16 / 6) 190 19.53 10.64 1.96 chr4qtel1M 207579 207625 (792375) C OldhAT1#DNA/hAT-Ac (1106) 1736 1686 m_b195s601i8 7659 chr4qtel1M 207579 GCTTAGAAGCCATGGCCTCCACCAGTG-----GCAGCCGGCGCTTCCTTT 207623 i v i ii i ----- - ii C OldhAT1#DNA/h 1736 GCTTAAAAGCCATGTCTTCTGCCAGCGTTACTGCAG-CGGCGTCTCCTTT 1688 chr4qtel1M 207624 AC 207625 i C OldhAT1#DNA/h 1687 GC 1686 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 21.17 CpG sites = 8, Kimura (unadjusted) = 24.18 Transitions / transversions = 8.00 (8/1) Gap_init rate = 0.04 (2 / 46), avg. gap size = 3.00 (6 / 2) 40 29.93 2.11 0.00 chr4qtel1M 208107 208248 (791752) (CTCTCT)n#Simple_repeat 1 145 (0) m_b195s252i14 7660 chr4qtel1M 208107 CTCTAGCTCTCTCTCCTTCTCCATCCCT-TATCCCAC-CACTCTCTGTGC 208154 vv ii iv i - v i v - v v vi (CTCTCT)n#Sim 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chr4qtel1M 208155 CTCTCTCTCTGTATCTGTCTGTGTCTCTGTGTCTCTGTCTGTCTGTCTCG 208204 v v v v v v v v v v v (CTCTCT)n#Sim 51 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 100 chr4qtel1M 208205 TTCTGCCTTTCTCTCCCTTTCTCT-TTTCTCTCACCCTCTCCCTC 208248 i vi i i i - i v i i (CTCTCT)n#Sim 101 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 145 Matrix = Unknown Transitions / transversions = 0.67 (14/21) Gap_init rate = 0.02 (3 / 141), avg. gap size = 1.00 (3 / 3) 261 19.19 2.63 4.00 chr4qtel1M 208249 208476 (791524) C HERVIP10FH#LTR/ERV1 (4096) 1006 782 m_b195s701i0 7661 chr4qtel1M 208249 TTCCTGTTTCTGTCTCTGTCTCTCTCTCTCTCTCTGTCTCTCTGTCTCTA 208298 v ii i v i i i v i v C HERVIP10FH#LT 1006 TTACTACTTCTATCTCTCTCTTTCTTTCTCTCTTTGACTTTCTGTCTCTC 957 chr4qtel1M 208299 TCTCCTTTCTCTG--TCTCTGTATCTCTCTCTGTC-CTT--TCTCTCTGT 208343 - i -- i v v v - -- i C HERVIP10FH#LT 956 TCTC-TCTCTCTGACTCCCTCTTTGTCTCTCTGTCTCTTCCTCTCTCTGC 908 chr4qtel1M 208344 CTCTGTCTCTCTGTGTGTATTTGTCTCTCTGTCTCTGTCTCTGTCTCTCT 208393 v v --- i i-i i v vi C HERVIP10FH#LT 907 CTCTCTCTCTCTTTG---ACTC-CCTCTTTGTCTCTCTCTCTCCCTCTCT 862 chr4qtel1M 208394 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTGTGTCCTTTCTCCC 208443 i ii v v --- i i i C HERVIP10FH#LT 861 CTCTCTTTCTCTCTCTCTCTCTTCCTCTCTCTCTCTCT---CTCTCTTCT 815 chr4qtel1M 208444 CTGTCTCCTCT-TGATGTATCTGTCTCTCTCTCT 208476 v i - v -i v i vi C HERVIP10FH#LT 814 CTCTTTCCTCTCTGCTG-GTCTTTCCCTGCCTCT 782 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 22.48 CpG sites = 25, Kimura (unadjusted) = 22.48 Transitions / transversions = 1.47 (25/17) Gap_init rate = 0.06 (13 / 227), avg. gap size = 1.15 (15 / 13) 114 11.65 9.13 0.36 chr4qtel1M 208477 208728 (791272) (CT)n#Simple_repeat 1 274 (0) m_b195s252i15 7662 chr4qtel1M 208477 CTCT-TCTCT-TGTCTCTCT-TCT-TCTGTCTCTCTCTGTGTGT-TCTCT 208521 - - v - - v v v v - (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chr4qtel1M 208522 C-CTC-CTCCCTCTCTCTCTCTCTCTCTCTGTC-CTGTAT-TATCT-TCT 208566 - - i v - v v - v - (CT)n#Simple_ 51 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 100 chr4qtel1M 208567 TTTTCTCTGCCTCT-TCTCTCTCTCTCTCTCT-TCT-TCTC-CTCTCTCT 208612 i i vi - - - - (CT)n#Simple_ 101 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 150 chr4qtel1M 208613 CTCTCTCTCTCTCTCTCT-TCTGTCTCATAT-TAACT-TCTTTTTCCCTC 208659 - v - v - vv - i i i (CT)n#Simple_ 151 CTCTCTCTCTCTCTCTCTCTCTCTCTC-TCTCTCTCTCTCTCTCTCTCTC 199 chr4qtel1M 208660 -CTCGGTCTCTC-CTCTCTCTCTCTCTCTCTCTCT-TCT-TCTGTCTCT- 208704 - vv - - - v - (CT)n#Simple_ 200 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 249 chr4qtel1M 208705 TGTCTCTGTCTCT-TCTTTCTCTCT 208728 v v - i (CT)n#Simple_ 250 TCTCTCTCTCTCTCTCTCTCTCTCT 274 Matrix = Unknown Transitions / transversions = 0.42 (8/19) Gap_init rate = 0.09 (23 / 251), avg. gap size = 1.04 (24 / 23) 42 0.00 4.65 0.00 chr4qtel1M 209588 209630 (790370) (AG)n#Simple_repeat 1 45 (0) c_b195s251i0 7663 chr4qtel1M 209588 AGAGAGAGAGA-AGAGAGAGAGAGAGAGAGAGAGA-AGAGAGAGA 209630 - - (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 45 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.00 (2 / 2) 12 20.57 2.44 2.44 chr4qtel1M 210504 210544 (789456) (AGCCCG)n#Simple_repeat 1 41 (0) m_b195s252i16 7664 chr4qtel1M 210504 AGCCCGA-ACTGAGCCCGAGCCCAGCGCCACAGCCCTCGCCC 210544 -v i - v vv vv (AGCCCG)n#Sim 1 AGCCCGAGCCCGAGCCCGAGCCC-GAGCCCGAGCCCGAGCCC 41 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 192 27.34 0.81 7.83 chr4qtel1M 210903 211025 (788975) MIR1_Amn#SINE/MIR 13 127 (103) m_b195s601i9 7665 chr4qtel1M 210903 GTGGTCTGAGGGCACCCAGAGCGCCAGGCCCGGGGCCACCAAGACTCAGG 210952 - v v i-- i i- v i i ivvvi iii MIR1_Amn#SINE 13 GTGGTCT-AGTGGAT--AGAGCACT-GGACTGGGACTCGGGAGACCTGGG 58 chr4qtel1M 210953 CCCGAGTCCCAGCCCGGCCACAGACCCTCTTAGCTGAGGGACCCCGGGGC 211002 ii ? ? i i v v?i ?----- ? v ii vv MIR1_Amn#SINE 59 TTCNANTCCCGGCTCTGCCACTNGCCN-----GCTGNGTGACCTTGGGCA 103 chr4qtel1M 211003 AGTCACTTAAGCTCGTT-TGCCTC 211025 ? v vi -? MIR1_Amn#SINE 104 AGTCACTTNACCTCTCTGNGCCTC 127 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.05 CpG sites = 18, Kimura (unadjusted) = 37.58 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.08 (10 / 122), avg. gap size = 1.00 (10 / 10) 254 29.44 0.00 5.43 chr4qtel1M 210920 211016 (788984) MIRc#SINE/MIR 24 115 (153) m_b195s601i10 7665 chr4qtel1M 210920 AGAGCGCCAGGCCCGGGGCCACCAAGACTCAGGCCCGAGTCCCAGCCCGG 210969 i ii i ii i i vv iii ii i i v MIRc#SINE/MIR 24 AGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTG 73 chr4qtel1M 210970 CCACAGACCCTCTTAGCTGAGGGACCCCGGGGCAGTCACTTAAGCTC 211016 vv ----- v v ii vv v MIRc#SINE/MIR 74 CCACTTAC-----TAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.82 CpG sites = 17, Kimura (unadjusted) = 38.66 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.05 (5 / 96), avg. gap size = 1.00 (5 / 5) 389 24.30 0.93 3.85 chr4qtel1M 212638 212744 (787256) C MIR3#SINE/MIR (28) 180 77 m_b195s601i11 7666 chr4qtel1M 212638 TGGCAGAGGTCCTGGAGCTCACTGACCTTTCTTCTCCAGCTCATTTGACA 212687 v i ii i i v iiv v-- i vv i -- v C MIR3#SINE/MIR 180 TGGAAGGGACCTTAGAGATCATCTAG--TCCAACCCC--CTCATTTTACA 135 chr4qtel1M 212688 GATCAGAGAACTGAGGCAGAGAG-GGTGACGTGGCTTGCCCAGGGTCACA 212736 v ii vv - v i i C MIR3#SINE/MIR 134 GATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACA 85 chr4qtel1M 212737 CAGCTGGT 212744 ?i C MIR3#SINE/MIR 84 CAGCNAGT 77 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.17 CpG sites = 14, Kimura (unadjusted) = 30.17 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.05 (5 / 106), avg. gap size = 1.00 (5 / 5) 344 26.98 0.82 8.85 chr4qtel1M 212677 212798 (787202) C MIR#SINE/MIR (118) 144 32 m_b195s601i12 7666 chr4qtel1M 212677 CTCATTTGACAGATCAGAGAACTGAGGCAGAGAG-GGTGACGTGGCTTGC 212725 i v v ii v - v v ii C MIR#SINE/MIR 144 CCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGC 95 chr4qtel1M 212726 CCAGGGTCACACAGCTGGTCTCCACTCAAGAGATGGAGCACAGGGCCTCG 212775 i i -------- v iii -- v vi C MIR#SINE/MIR 94 CCAAGGTCACACAGCTAGT--------AAGTGGCAGAG--CCGGGATTCG 55 chr4qtel1M 212776 AGTCAAGAAGAACTGAATTCAGA 212798 ii v iviiv iv i C MIR#SINE/MIR 54 AACCCAGGCAGTCTGGCTCCAGA 32 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.01 CpG sites = 18, Kimura (unadjusted) = 34.01 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.09 (11 / 121), avg. gap size = 1.00 (11 / 11) 255 31.18 8.60 0.00 chr4qtel1M 212752 212844 (787156) MIRc#SINE/MIR 16 116 (152) m_b195s601i13 7667 chr4qtel1M 212752 CAAGAGATGGAGCACAGGGCCTCGAGTCAAGAAGAACTGAATTC-AGATC 212800 ivi vi v i i v i v ii - vi MIRc#SINE/MIR 16 CAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCC 65 chr4qtel1M 212801 TAGCT---TCAC--ATCA--TGCCTAGCCCTGGACAAGTCATTTTATCTC 212843 ii ---i -- ii -- iv ii i i i v i MIRc#SINE/MIR 66 CGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 chr4qtel1M 212844 T 212844 MIRc#SINE/MIR 116 T 116 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.02 CpG sites = 21, Kimura (unadjusted) = 43.29 Transitions / transversions = 2.62 (21/8) Gap_init rate = 0.04 (4 / 92), avg. gap size = 2.00 (8 / 4) 181 23.81 0.00 0.00 chr4qtel1M 212961 213002 (786998) C MIRc#SINE/MIR (217) 51 10 m_b195s601i14 7668 chr4qtel1M 212961 GTTTTCCTGACGCCAGGCCCAGCCCTCTAGCCACTGTGCCAC 213002 i v i i iv vv ii C MIRc#SINE/MIR 51 GTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.26 CpG sites = 6, Kimura (unadjusted) = 29.26 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 15 29.93 5.80 0.00 chr4qtel1M 213270 213338 (786662) (TA)n#Simple_repeat 1 73 (0) m_b195s252i17 7669 chr4qtel1M 213270 TATATGT-TATATAT-TATATATTAATTTTTA-ATATATGCCTATTAACA 213316 i - - vv v v - iiv vv i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr4qtel1M 213317 ATTACATATACACA-ATATAGAT 213338 vv i i i - v (TA)n#Simple_ 51 TATATATATATATATATATATAT 73 Matrix = Unknown Transitions / transversions = 0.70 (7/10) Gap_init rate = 0.06 (4 / 68), avg. gap size = 1.00 (4 / 4) 635 24.14 0.68 2.05 chr4qtel1M 213878 214025 (785975) MIRc#SINE/MIR 1 146 (122) m_b195s601i15 7670 chr4qtel1M 213878 CAAGGCAGCCTGGTGGCTCAGTGAATGGAGTGCTGGGCCTGAATTTAGGA 213927 i iv --- i vi ii i i i v i MIRc#SINE/MIR 1 CGAGGCAGTGTGGTG---CAGTGGAAAGAGCACTGGACTTGGAGTCAGGA 47 chr4qtel1M 213928 AGACCTGAATTCAAATCCAGTCTCAGAAGTTTACTGTCCGTGTGAGTTTG 213977 ii i i v v v vvii iv i vi MIRc#SINE/MIR 48 AGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTG 97 chr4qtel1M 213978 GGCAAATCACTTCACC-CTGTTTACCTCAGTTTCCTCATCTGTAAAATG 214025 i v - v vvi MIRc#SINE/MIR 98 GGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATG 146 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.79 CpG sites = 21, Kimura (unadjusted) = 29.77 Transitions / transversions = 1.50 (21/14) Gap_init rate = 0.03 (4 / 147), avg. gap size = 1.00 (4 / 4) 453 30.33 1.26 2.55 chr4qtel1M 213891 214049 (785951) MIR#SINE/MIR 7 163 (99) m_b195s601i16 7670 chr4qtel1M 213891 TGGCTCAGTGAATG-GAGTGCTGGGCCTGAATTTAGGAAGACCTGAATTC 213939 i vi iv i- ii v vi i vii - vvi ii MIR#SINE/MIR 7 TAGCATAGTGGTTAAGAGCACGGGCTCTGGAGCCAG-ACTGCCTGGGTTC 55 chr4qtel1M 213940 AAATCCAGTCTCAGAAGTTTACTGTCCGTGTGAGTTTGGGCAAATCACTT 213989 i v v v vvii iv i vi i i MIR#SINE/MIR 56 GAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTT 105 chr4qtel1M 213990 CACC-CTGTTTACCTCAGTTTCCTCATCTGTAAAATGAACTGGAGAAGGA 214038 v - v v i i--- v vi MIR#SINE/MIR 106 AACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGG---GGATAATAA 152 chr4qtel1M 214039 AACAACCAACC 214049 v vv v MIR#SINE/MIR 153 TAGTACCTACC 163 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.37 CpG sites = 24, Kimura (unadjusted) = 39.43 Transitions / transversions = 1.04 (24/23) Gap_init rate = 0.04 (6 / 158), avg. gap size = 1.00 (6 / 6) 323 38.89 4.89 5.34 chr4qtel1M 215751 216220 (783780) L2#LINE/L2 2615 3082 (0) m_b195s601i17 7671 chr4qtel1M 215751 ATCTTGTCA-CTTTCATATCAGAGCATCTCTCTCATGTGTCCCCTTCTC- 215798 i i- i vviv i ii v ivvv vi v v - L2#LINE/L2 2615 ATCCTGTCGGCTCTACCTTCAAAATATATCCAGAATCCGACCACTTCTCA 2664 chr4qtel1M 215799 -----TGCTCTGACCCCTACCTTGGAACAGGCCCTCATCTCCTCACATCT 215843 ----- v v - v i i vv i vi vi v ii L2#LINE/L2 2665 CCACCTCCACTG-CCACCACCCTGGTCCAAGCCACCATCATCTCTCGCCT 2713 chr4qtel1M 215844 GGACCATGGCAACAGC-TGCTAAGCCATCTGCTGCCTTGAATCCCT-CCC 215891 ii iv i - v vivi v ivv vv i i - L2#LINE/L2 2714 GGATTACTGCAATAGCCTCCTAACTGGTCTCCCTGCTTCCACCCTTGCCC 2763 chr4qtel1M 215892 CAGTTCAACCCATCC------CAGCCACCAAAGTGATTTTCCTAAAACAC 215935 vv ? ii i i ------ vi i ii ii ii L2#LINE/L2 2764 CCCTNCAGTCTATTCTCAACACAGCAGCCAGAGTGATCCTTTTAAAACGT 2813 chr4qtel1M 215936 AATTTTAACCATGTCACCCCCACACCACACTCTCCTACCCCACTATTCAA 215985 v ivi i --------------- ------ ii L2#LINE/L2 2814 AAGTCAGATCATGTCA---------------CTCCT------CTGCTCAA 2842 chr4qtel1M 215986 TAAACTCTGGAGAAACCCCATCAAATTCAGAATCAAATACAAAAATAAGC 216035 v vv iiiv ivvi vv i i v vv ivivvvv L2#LINE/L2 2843 AACCCTCCAATGGCTTCCCATCTCACTCAGAGTAAAAGCCAAAGTCCTTA 2892 chr4qtel1M 216036 TGTTTGATTCTAAAGCCCTTCATCACCCAGCCCCTTCTTCTCTTTCTAG- 216084 iiv v vi vi i v v i ii i iiv vi i ii- L2#LINE/L2 2893 CAATGGCCTACAAGGCCCTACATGATCTGGTCCCCCGTTACCTCTCTGAC 2942 chr4qtel1M 216085 --TATTTGACACCTTAGTCCCTGACATCTACTCTTTGAGCCAATAATCCT 216132 --i i vvi vivv ivv iiii --i vv iiv iv L2#LINE/L2 2943 CTCATCTCCTACCACTCTCCCCCTCGCTCACTC--CGCTCCAGCCACACT 2990 chr4qtel1M 216133 GGCCTCCAGCCTCACCCACGAACAAGGCCCTCCAT-CTCTCAGCTCCAGG 216181 vvv vvi v - v vvv i- i iv vi L2#LINE/L2 2991 GGCCTCCTTGCTGTTCCTCGAAC-ACGCCAGGCACGCTCCCGCCTCAGGG 3039 chr4qtel1M 216182 CAT----ATTTTCTGTCTCCTGTGCCTGTAATGCTCTCCCTCC 216220 v ---- i v ii v v i i i L2#LINE/L2 3040 CCTTTGCACTTGCTGTTCCCTCTGCCTGGAACGCTCTTCCCCC 3082 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 51.83 CpG sites = 90, Kimura (unadjusted) = 56.57 Transitions / transversions = 1.08 (90/83) Gap_init rate = 0.07 (35 / 469), avg. gap size = 1.37 (48 / 35) 456 32.26 12.77 3.25 chr4qtel1M 216053 216475 (783525) L2c_3end#LINE/L2 1 462 (16) m_b195s601i18 7671 chr4qtel1M 216053 CTTCATCACCCAGCCCCTTCTTCTCTTTCTAGTATTTGACACCTT-AGTC 216101 ? iv i ii v i vi i i i-i iiv v i- v L2c_3end#LINE 1 CTNCACGATCTGGCCCCTGCCTACCTCTCCAGC-CTCATCTCCTCCACTC 49 chr4qtel1M 216102 CCTGACATCTACTCTTTGAGCCAATAATCCTGGCCTCCA-GCCTCACCCA 216150 ivv viviv v v vv iiv iv iv ? v- v iv L2c_3end#LINE 50 CCCTCCTCGCCCACTATGCTCCAGCCACACTGAACTNCTTGCATTCCCCA 99 chr4qtel1M 216151 CGAACAAGGCCCTCCATCTCTCAGCTCCAGGCAT----ATTTTCTGTCTC 216196 viv ivv vv i - i iiiv i? v ---- iv v ii L2c_3end#LINE 100 AACACGCCGCAGTTC-TTTCCTGCCTCCGNGCCTTTGCACATGCTGTTCC 148 chr4qtel1M 216197 CTGTGCCTGTAATGCTCTCCCTCCTCTGTTCCAACTA-CTGACTTCCCCG 216245 v v i i iiiv v i- i i iv v L2c_3end#LINE 149 CTCTGCCTGGAATGCTCTTCCCCCCTCCTTCCACCTGGCTAACTCCTACT 198 chr4qtel1M 216246 GCTTTCTTTAAGGCTCAACAAAAATCCGACCTCCTACAGGAAGCCTTCCC 216295 - v i i ? i vv i viv v i L2c_3end#LINE 199 -CATCCTTCAAGNCTCAGCTCAGATGTCACCTCCTCCGGGAAGCCTTCCC 247 chr4qtel1M 216296 -AACTTCCC---TCAATTCCATG---CCTTCTTTATGTT---------TC 216329 -i ii ---? v v i v --- i i i i ---------i L2c_3end#LINE 248 TGACCCCCCAAGNCTAGTCTAGGTGCCCTCCTCTGTGCTCCCATAGCACC 297 chr4qtel1M 216330 CTATTTA---TCCCA-TATAA-----------AGCTTGCTTTATATATGT 216364 i i --- - i----------- i iv i vv L2c_3end#LINE 298 CTGTCTATACTCCCATTATAGCACTTATCATTAACTTGTATTGTAATTGT 347 chr4qtel1M 216365 GTGTTTGCTTGTCT------CCCATTGGATTAGGAAGTGCTGGAGGGCA- 216407 v i ? ------i i i i iv iv v v - L2c_3end#LINE 348 CTGTTTACNTGTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAG 397 chr4qtel1M 216408 GAAC--TGACTT-------TTTGTATCCCCAGTATTTAGCAGGGTGACTG 216448 i -- v ------- ------------ i v L2c_3end#LINE 398 GGACCGTGTCTTATTCATCTTTGTATCCCCA------------GCGCCTG 435 chr4qtel1M 216449 GAACATAGTAGGCATTGAATAAATGCT 216475 v ii v i L2c_3end#LINE 436 GCACATAGTAGGCGCTCAATAAATGTT 462 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.31 CpG sites = 74, Kimura (unadjusted) = 44.43 Transitions / transversions = 1.28 (74/58) Gap_init rate = 0.07 (30 / 422), avg. gap size = 2.30 (69 / 30) 473 35.74 8.86 0.77 chr4qtel1M 216115 216475 (783525) L2b_3end#LINE/L2 61 450 (16) m_b195s601i19 7671 chr4qtel1M 216115 CTTTGAGCCAATAATCCTGGCCTCCAGCCTCACCCACGAACAAGGCCCTC 216164 i vv iiv iv vvv vvi v v v v?v L2b_3end#LINE 61 CTCTGCTCCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACACGCCANGC 110 chr4qtel1M 216165 CATCTCTCAGCTCCAGGCAT----ATTTTCTGTCTCCTGTGCCTGTAATG 216210 iv? i iv vi v ---- i? v ii v v i L2b_3end#LINE 111 TCNCTCCCGCCTCAGGGCCTTTGCACNTGCTGTTCCCTCTGCCTGGAACG 160 chr4qtel1M 216211 CTCTCCCTCCTCTGTTCCAACTA-CTGACTTCCCCGGCTTTCTTTAAGGC 216259 i i i vi v -iv i- ii i iv v- v i i i v L2b_3end#LINE 161 CCCTTCCCCACCTCTTC-GCCTGGCCAACTCCTACT-CATCCTTCAGGTC 208 chr4qtel1M 216260 TCAACAAAAATCCGACCTCCTACAGGAAGCCTTCCC-AACTTCCC---TC 216305 i vv viv v i i -i ii ---i L2b_3end#LINE 209 TCAGCTCAAATGTCACCTCCTCCGGGAAGCCCTCCCTGACCCCCCAGGCC 258 chr4qtel1M 216306 AATTCC-ATGCCTTCTTTATG--TTTCCTATTTATCCCATATAAAGCTTG 216352 iiv v-ii i i ivv --iii i v iv v v iiv vv - L2b_3end#LINE 259 GGGTCAGGCGCCCTCCTCTGGGCCCCCCCAGTCCTACCCTGCCACTC-TG 307 chr4qtel1M 216353 CTTTATATATGTGTGTTTGCTTGTCT------CCCATTGGATTAGGAAGT 216396 vv ?vv v ? i v ------ i i i iv iv L2b_3end#LINE 308 GGTTATNATTGTCTGNTTACATGTCTGTCTCCCCCACTAGACTGTGAGCT 357 chr4qtel1M 216397 GCTGGAGGGCAGAA-------CTGACTTTT-------TGTATCCCCAGTA 216432 v vv ii------- v v ------- ii L2b_3end#LINE 358 CCGTGAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTGTATCCCCAGCG 407 chr4qtel1M 216433 TTTAGCAGGGTGACTGGAACATAGTAGGCATTGAATAAATGCT 216475 ii vi ? v v i ii v i ii L2b_3end#LINE 408 CCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATT 450 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.56 CpG sites = 67, Kimura (unadjusted) = 51.01 Transitions / transversions = 1.10 (67/61) Gap_init rate = 0.03 (12 / 360), avg. gap size = 2.92 (35 / 12) 629 27.32 12.20 0.00 chr4qtel1M 218127 218331 (781669) MIRc#SINE/MIR 6 235 (33) m_b195s601i20 7672 chr4qtel1M 218127 CAGCTTGATGAAAGGTCTAGAATGCTGGACTGGGAGTC----AGAGCTGC 218172 iv i v iv vvv iii v ---- v v MIRc#SINE/MIR 6 CAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGG 55 chr4qtel1M 218173 ATCTGAATCTTGCCTTTA-TACTTATTTACTATGTGAC------------ 218209 i ii i ii v i i-i i vi i ------------ MIRc#SINE/MIR 56 GTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTC 105 chr4qtel1M 218210 -ATTAATCTCTCTAAACCTCAGTTTCTTCACCTGTAAAGTGGGATTAATA 218258 -v i i i i i i iv MIRc#SINE/MIR 106 ACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATA 155 chr4qtel1M 218259 AGGGC------ACCAACCTCACAGGCTTGTTGTGAGGCTCAGATGATATA 218302 viv ------i v v v i v MIRc#SINE/MIR 156 ATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATA 205 chr4qtel1M 218303 ATGAACAT-AAAGAGCTTTACAAGCCTTAA 218331 v ii - v ii i iv MIRc#SINE/MIR 206 ATGTATGTGAAAGCGCTTTGTAAACTGTAA 235 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.40 CpG sites = 34, Kimura (unadjusted) = 34.94 Transitions / transversions = 1.55 (34/22) Gap_init rate = 0.03 (6 / 204), avg. gap size = 4.17 (25 / 6) 13 25.71 0.00 5.56 chr4qtel1M 218600 218656 (781344) (GGGGAGA)n#Simple_repeat 1 54 (0) m_b195s252i18 7673 chr4qtel1M 218600 GGGAAGTGGGGAGCAGAGAGTGAGGAAAGGGAGAGAGAAGGAAGCAGGGA 218649 i v vi i v i i - -- i vi (GGGGAGA)n#Si 1 GGGGAGAGGGGAGAGGGGAGAGGGGAGAGGG-GAGAG--GGGAGAGGGGA 47 chr4qtel1M 218650 GAGGGGA 218656 (GGGGAGA)n#Si 48 GAGGGGA 54 Matrix = Unknown Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.05 (3 / 56), avg. gap size = 1.00 (3 / 3) 13 30.81 3.39 0.00 chr4qtel1M 218621 218679 (781321) (GAAGAAA)n#Simple_repeat 1 61 (0) m_b195s252i19 7673 chr4qtel1M 218621 GAGGAAAG-GGAGAG-AGAAGGAAGCAGGGAGAGGGGATGAAGAAGAAAG 218668 i -i i - i v i i ii i vi (GAAGAAA)n#Si 1 GAAGAAAGAAGAAAGAAGAAAGAAGAAAGAAGAAAGAAGAAAGAAGAAAG 50 chr4qtel1M 218669 AGGAAAAAAGA 218679 i i (GAAGAAA)n#Si 51 AAGAAAGAAGA 61 Matrix = Unknown Transitions / transversions = 6.00 (12/2) Gap_init rate = 0.03 (2 / 58), avg. gap size = 1.00 (2 / 2) 371 33.48 16.12 1.04 chr4qtel1M 218709 219043 (780957) C L3#LINE/CR1 (116) 3983 3599 m_b195s601i21 7674 chr4qtel1M 218709 GCTTAACTA--TCAAGAGAAGGAGAGCCCATCATCTCTCAGGGATGACCA 218756 i vi -- v v v i i ii i ? ii vv v C L3#LINE/CR1 3983 GCTTGAACACCTCCAGTGACGGGGAGCTCACTACCTCNCGAGGCAGCCCA 3934 chr4qtel1M 218757 TCCCAGGCTGGGAGATCTTTCCCTGT--GGA-------CCCT-----GGG 218792 i vvi v v v i vvi -- i ------- i ----- i C L3#LINE/CR1 3933 TTCCATTTTTGGACAGCTCTGATTGTTAGAAAGTTCTTCCTTATATTGAG 3884 chr4qtel1M 218793 CCTAAGGCAACTCCCTTGTAATTTCC-CTCATGTCTCCAGGTTCCGCC-- 218839 v iv vi ii i i - i vvv vi i -- C L3#LINE/CR1 3883 CCGAAATCTGCCTCCCTGTAACTTCCACCCATTGGTCCTAGTTCTGCCCT 3834 chr4qtel1M 218840 -TGGAGGC---CAAAA-AGGTC--ATCA---TTCCATGTGATGACCCTTC 218879 - v --- i - i -- v--- ii iii C L3#LINE/CR1 3833 CTGGAGCCACACAGAATAAGTCTAATCCCTCTTCCACATGACAGCCCTTC 3784 chr4qtel1M 218880 AAATACCTAAGGAGAGTGGCCTGGTTCCATCTTCCCCGGCTCCTTCTCCA 218929 ii i i v ivii vv ii v vvvi vv - C L3#LINE/CR1 3783 AAATATTTGAAGACAGCTATCATGTCTCCTCTAAGTCTTCT-CTTCTCCA 3735 chr4qtel1M 218930 GATCAGACAT------TTTTATC------TCCTCCCGTGA----GCCTCC 218963 iii i ------ iiv ------ vii ---- ii C L3#LINE/CR1 3734 GGCTAAACATCCCCAGTTCCTTCAACCGTTCCTCATATGACATGGTTTCC 3685 chr4qtel1M 218964 GGGCCCTTCTCACTAT-GGGGCTGCCCTCCTC----CACCCCCACAGCCT 219008 i i -- i -vv ii i ---- i v i - ii C L3#LINE/CR1 3684 AGACCCT--TCACCATCCTGGTCGCTCTCCTCTGGACGCGCTC-CAGTTT 3638 chr4qtel1M 219009 CTCGCTGCCCTTCCCAAA----GGTGCCCCGGGCTGAAC 219043 v iv i i ii ---- i v ii C L3#LINE/CR1 3637 GTCAATGTCCCTCTTAAAATGTGGCGCCCAGAACTGAAC 3599 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.54 CpG sites = 70, Kimura (unadjusted) = 46.90 Transitions / transversions = 1.71 (70/41) Gap_init rate = 0.06 (21 / 334), avg. gap size = 2.76 (58 / 21) 226 21.82 7.27 0.00 chr4qtel1M 221817 221871 (778129) L2b_3end#LINE/L2 402 460 (6) m_b195s601i22 7675 chr4qtel1M 221817 CCAGCGCCGAGCCCAGGGCCTGGCACACAGCTGGTACCT----AATACTT 221862 v v ? iv ii ii---- i L2b_3end#LINE 402 CCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTT 451 chr4qtel1M 221863 AATGACTGA 221871 iv v L2b_3end#LINE 452 GTTGAATGA 460 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 24.02 CpG sites = 7, Kimura (unadjusted) = 26.80 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.02 (1 / 54), avg. gap size = 4.00 (4 / 1) 191 30.65 6.45 0.00 chr4qtel1M 221818 221879 (778121) L2d_3end#LINE/L2 451 516 (0) m_b195s601i23 7675 chr4qtel1M 221818 CAGCGCCGAGCCCAGGGCCTGGCACACAGCTGGTACCT----AATACTTA 221863 v v v ivi i iv ii ii---- i L2d_3end#LINE 451 CAGCGCCTAGCACAGTGCTGAGCACATAGTAGGCGCTCAATAAATACTTG 500 chr4qtel1M 221864 ATGACTGATGCACTGA 221879 v i vv i L2d_3end#LINE 501 TTGATTGATTGATTGA 516 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.50 CpG sites = 11, Kimura (unadjusted) = 40.53 Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.02 (1 / 61), avg. gap size = 4.00 (4 / 1) 185 30.00 15.00 0.00 chr4qtel1M 222027 222106 (777894) MIRc#SINE/MIR 104 195 (73) m_b195s601i24 7676 chr4qtel1M 222027 TCACGCAATGCCCCCCGGCCTCAGCATCTCCATCATTAAAAT-GGGACAA 222075 vi ivi i ivi iv ii vv - i MIRc#SINE/MIR 104 TCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAA 153 chr4qtel1M 222076 GAGCA----------CTACCTCA-GGGGCTGCTGGGAAGATC 222106 v ii ---------- -i i i v i MIRc#SINE/MIR 154 TAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATC 195 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.24 CpG sites = 16, Kimura (unadjusted) = 40.24 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.04 (3 / 79), avg. gap size = 4.00 (12 / 3) 219 22.58 9.68 0.00 chr4qtel1M 222044 222105 (777895) MIR#SINE/MIR 117 184 (78) m_b195s601i25 7676 chr4qtel1M 222044 GCCTCAGCATCTCCATCATTAAAATGGG----ACAAGAGCA-CTACCTCA 222088 iv ii vv ---- i v i - MIR#SINE/MIR 117 GCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTCA 166 chr4qtel1M 222089 -GGGGCTGCTGGGAAGAT 222105 -i i i v i MIR#SINE/MIR 167 TAGGGTTGTTGTGAGGAT 184 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.58 CpG sites = 9, Kimura (unadjusted) = 27.58 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.05 (3 / 61), avg. gap size = 2.00 (6 / 3) 1029 32.17 2.35 1.08 chr4qtel1M 223925 224562 (775438) L1ME4c_3end#LINE/L1 1 646 (184) m_b196s551i0 7677 chr4qtel1M 223925 TTCATTTCTAAAATATGGAGAGAACTGACTCAAACTTAGAAGAATACAAG 223974 v v ?v ? iv i i v i i v v v v? v L1ME4c_3end#L 1 TTAATATCTNTANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANAT 50 chr4qtel1M 223975 TCATTCCCCAGTTGATAAATGGTCAAAGAACATGAACAATT--TTCAGAT 224022 iv vv i v v i ivi-- v ? L1ME4c_3end#L 51 CAAGACCCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACAN 100 chr4qtel1M 224023 GAAAAAAATTA-AAGTCATCGCTATTCATATA-AAAAATGCTTCAAA-TC 224069 i i ii v - ? vi vivi vv i i- - v- L1ME4c_3end#L 101 AAGAGGAAATACAANTAGTAAACAAACACATGGAAAAATG-TTCAACCTC 149 chr4qtel1M 224070 ACTATCGATTAGAGAAATGAAAATTAAGACAAGTCTGAGGTACCATTTCA 224119 i vii i i v ii vvv i i L1ME4c_3end#L 150 GCTAGTAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTA 199 chr4qtel1M 224120 TGCCTCTCAAGTTGGTTAAGATAACAGGAAAAGATAATGAAAAATATTGG 224169 i v i i i iv i vvv ii vv ivvv ii L1ME4c_3end#L 200 CGCCTATTAAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGCTGG 249 chr4qtel1M 224170 AAAGGATGTGGGAAAACTGGAACACTGGTGCATTGTTGGTGGAGTTGTGA 224219 vi ? i vi v ? vi i i vi? i L1ME4c_3end#L 250 CGAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAA 299 chr4qtel1M 224220 ATGGATCCAACCATTGTGAATAGTAAATTGGAACTATGCCAAAAGAA-TA 224268 v i v v v i v i v v v i ivvv i-i L1ME4c_3end#L 300 ATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCA 349 chr4qtel1M 224269 TCAAACTGTGCATACTCTTTGATCCAGTAGTCTCACTACTAGGTCTATAT 224318 v v v i i i ii v i vv v L1ME4c_3end#L 350 TAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTAT 399 chr4qtel1M 224319 CCCAAAGAGATCAG--AAAACTAGGCAAAGGACCCACATGTGCAAAAATG 224366 i i i v v-- vv v i -- i i ii i i L1ME4c_3end#L 400 CCTAAGGAAATAATTCAAAAGAAGGAAAAAG--CTATATGCACGAAGATG 447 chr4qtel1M 224367 TATGTAGCAGCCTT-TTTGTGGTGGCAAGGAAGTGCAAACAGAGCGGATG 224415 vii v v - i ii i i ii v v ivviii L1ME4c_3end#L 448 TTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATG 497 chr4qtel1M 224416 CCCATCAGTTGGACAATGGCTGAAGAAGTTATGGTATATATATGTTTTGG 224465 i v i v iv i i iv i i v? ivivv L1ME4c_3end#L 498 TCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGG 547 chr4qtel1M 224466 AATATTAT---TCTATTAAAAA-AAT-ATTGAGCAGCTGATTTCAGAAAA 224510 ---v i -i - iv v viv v - v - L1ME4c_3end#L 548 AATATTATGCAGCCATTAAAAATGATAATTATGAAGACTATGT-AGCAA- 595 chr4qtel1M 224511 GCCAGAAAAGATTTCCATGAATGGATGCTGAGTGAAGTGAGCAGAA-GCA 224559 -- vii i v ii vvvi i i ivi -i L1ME4c_3end#L 596 --CATGGAAAATGTTTATGATATAATGTTAAGTGAAAAAAGCAGAATACA 643 chr4qtel1M 224560 AAA 224562 L1ME4c_3end#L 644 AAA 646 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 41.51 CpG sites = 108, Kimura (unadjusted) = 43.77 Transitions / transversions = 1.14 (108/95) Gap_init rate = 0.03 (18 / 637), avg. gap size = 1.22 (22 / 18) 339 21.74 1.45 0.00 chr4qtel1M 227550 227618 (772382) C MIR3#SINE/MIR (24) 184 115 m_b196s601i4 7678 chr4qtel1M 227550 GAGCAGGAAGGGACCTCAGAGGCCCCTTAGTCCGA-CTCTTCACTCTGCA 227598 v i ii vii i - i i i i i C MIR3#SINE/MIR 184 GAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACA 135 chr4qtel1M 227599 GCTGAGGAAACTGAGGCACA 227618 v v C MIR3#SINE/MIR 134 GATGAGGAAACTGAGGCCCA 115 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.73 CpG sites = 11, Kimura (unadjusted) = 26.73 Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.01 (1 / 68), avg. gap size = 1.00 (1 / 1) 305 20.08 27.21 1.17 chr4qtel1M 228611 228746 (771254) C MIR3#SINE/MIR (2) 206 36 m_b196s601i5 7679 chr4qtel1M 228611 ATCATCGGATCTTAGATT--TGGACCTGGAGGGGACCTTGGAGGTCA--- 228655 v i v v --ii v i i i --- C MIR3#SINE/MIR 206 ATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCT 157 chr4qtel1M 228656 ---CCAA-------AGTCAACAAAGGAGGAAACTGAGG--CAGGCAGGGT 228693 --- ------- v iv i v -- iv - C MIR3#SINE/MIR 156 AGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGA-GGT 108 chr4qtel1M 228694 GAAGCAACTT--CCAAGTGTCTCA-----AGT-------------GGGAT 228723 ii -- - v ----- ------------- i C MIR3#SINE/MIR 107 GAAGTGACTTGCCCAAG-GTCACACAGCNAGTTAGTGGCAGAGCCGGGAC 59 chr4qtel1M 228724 CTGACCCCAGGTTTTCTGGCTCC 228746 iv v i i i C MIR3#SINE/MIR 58 TAGAACCCAGGTCTCCTGACTCC 36 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 23.83 CpG sites = 16, Kimura (unadjusted) = 23.83 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.07 (10 / 135), avg. gap size = 3.90 (39 / 10) 185 34.38 7.29 0.00 chr4qtel1M 229359 229454 (770546) MIR#SINE/MIR 113 215 (47) m_b196s601i6 7680 chr4qtel1M 229359 CTCTGCCTCTGGTACCCACTCTGGGAAATGGGGACAATCCCAGGCCCCAT 229408 v v v v ivv vi i vvi vv i i MIR#SINE/MIR 113 CTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTAC 162 chr4qtel1M 229409 CTC----GGC--TCACGAGGA-CGCAGGAGGCCTTGCCTGTAAAGCACTT 229451 ---- i-- iii -iiv v vivv i v i MIR#SINE/MIR 163 CTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATACATGTAAAGCGCTT 212 chr4qtel1M 229452 GGA 229454 i MIR#SINE/MIR 213 AGA 215 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.76 CpG sites = 16, Kimura (unadjusted) = 46.64 Transitions / transversions = 0.94 (16/17) Gap_init rate = 0.03 (3 / 95), avg. gap size = 2.33 (7 / 3) 14 0.00 0.00 0.00 chr4qtel1M 229675 229692 (770308) (AGG)n#Simple_repeat 1 18 (0) m_b196s252i0 7681 chr4qtel1M 229675 AGGAGGAGGAGGAGGAGG 229692 (AGG)n#Simple 1 AGGAGGAGGAGGAGGAGG 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 22 10.14 4.35 4.35 chr4qtel1M 229860 229905 (770095) (TG)n#Simple_repeat 1 46 (0) m_b196s252i1 7682 chr4qtel1M 229860 TGTGT-TGT-TGTGCTGTGTCTCTGCGTCTGTGTGTGATGTGTGTGTG 229905 - - - v v i v - (TG)n#Simple_ 1 TGTGTGTGTGTGTG-TGTGTGTGTGTGTGTGTGTGTG-TGTGTGTGTG 46 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.09 (4 / 45), avg. gap size = 1.00 (4 / 4) 22 7.42 0.00 0.00 chr4qtel1M 230448 230476 (769524) (G)n#Simple_repeat 1 29 (0) m_b196s252i2 7683 chr4qtel1M 230448 GGGGGGGGGGGGGGGGGGGGGGAGAGGGG 230476 i i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG 29 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 16 15.86 0.00 0.00 chr4qtel1M 231257 231284 (768716) (G)n#Simple_repeat 1 28 (0) m_b196s252i3 7684 chr4qtel1M 231257 GGCGGGGGACTGGGGGGGGGGGGGGGGG 231284 v ivv (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGG 28 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 197 28.24 17.00 0.86 chr4qtel1M 234356 234455 (765545) L2c_3end#LINE/L2 352 467 (11) m_b196s601i7 7685 chr4qtel1M 234356 TTTCTGGACTGTCTCCTCCATGAGTCTGTG----------GGACAGGGGC 234395 v ?v v iv v ---------- i i L2c_3end#LINE 352 TTACNTGTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGAC 401 chr4qtel1M 234396 -GTGTTCCTGCCTTTCTTTG-GT-----GCGACTGGTGCACAATGAACCC 234438 - - i iiiiv -i ----- v ii i i iii v L2c_3end#LINE 402 CGTGT-CTTATTCATCTTTGTATCCCCAGCGCCTGGCACATAGTAGGCGC 450 chr4qtel1M 234439 TTAATAAAAGCTTGATG 234455 i v i v L2c_3end#LINE 451 TCAATAAATGTTTGTTG 467 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.39 CpG sites = 18, Kimura (unadjusted) = 37.39 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.05 (5 / 99), avg. gap size = 3.60 (18 / 5) 319 28.09 0.00 0.00 chr4qtel1M 236918 237006 (762994) C Charlie1b#DNA/hAT-Charlie (434) 89 1 m_b196s502i0 7686 chr4qtel1M 236918 TATTATAAAACCCGTCTTCACTGCCAAGACCCCCCTAAAGGCTCTCGGGG 236967 i viv i v iv vvi iv v C Charlie1b#DNA 89 TATTATGAAAATAGTTTTGACCTCGCGGACCCCCTGAAAGGGTCTCGGGG 40 chr4qtel1M 236968 GCCCCCAGGGGTGCTCAGGCCACACTCAAGAAACCACTG 237006 i v i i i iviii i C Charlie1b#DNA 39 ACCCCCAGGGGTCCCCGGACCACACTTTGAGAACCGCTG 1 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 30.98 CpG sites = 15, Kimura (unadjusted) = 36.20 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.00 (0 / 88), avg. gap size = 0.0 (0 / 0) 224 28.00 7.27 2.61 chr4qtel1M 237740 237849 (762151) C MIR3#SINE/MIR (1) 207 93 m_b196s601i8 7687 chr4qtel1M 237740 AATCTGAGGCGCGCAGACTG--AGGGC-AAAACGGGCCTTGGGGGGCCGC 237786 vv ivv ii v -- i -ii v i i i iv vv C MIR3#SINE/MIR 207 AATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATC 158 chr4qtel1M 237787 T-GTCCCCCAAATGCTTCATGCTACTGATGAGGAAACC-AGGCCCAGGGA 237834 - --- viv i vi v i- i C MIR3#SINE/MIR 157 TAGTCC---AACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGA 111 chr4qtel1M 237835 GG---AGGGGCTTGCCCA 237849 --- v i C MIR3#SINE/MIR 110 GGTGAAGTGACTTGCCCA 93 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.68 CpG sites = 16, Kimura (unadjusted) = 35.68 Transitions / transversions = 1.14 (16/14) Gap_init rate = 0.07 (8 / 109), avg. gap size = 1.38 (11 / 8) 12 23.51 3.33 5.08 chr4qtel1M 238569 238628 (761372) (TCCCCTC)n#Simple_repeat 1 59 (0) m_b196s252i4 7688 chr4qtel1M 238569 TCCCGCCTCCTCTCTCCCCTGCTGCGC-CTGCCCT-TCCCAGTCTGACCC 238616 vi i - v v - v - -v vv i (TCCCCTC)n#Si 1 TCCCCTCTCCCCTCTCCCCT-CTCCCCTCTCCCCTCTCCC-CTCTCCCCT 48 chr4qtel1M 238617 CTCCCTTCCTCC 238628 i - (TCCCCTC)n#Si 49 CTCCCCT-CTCC 59 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.08 (5 / 59), avg. gap size = 1.00 (5 / 5) 30 17.72 10.62 0.81 chr4qtel1M 238994 239106 (760894) (AGAGAG)n#Simple_repeat 1 124 (0) m_b196s252i5 7689 chr4qtel1M 238994 AGGGAGAGACAGAGACAGAGAG-GAGAGGCAGAGA-AGA-AGGGTAG-GG 239039 i v v - iv - - i - - i (AGAGAG)n#Sim 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG-AGAGA 49 chr4qtel1M 239040 GGGAGAGAGAGAG-GAG-GAGAAGGAG-GAGA-AGGAAAAGA-AGA-AAA 239083 i - - ii - - ii i - - i (AGAGAG)n#Sim 50 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 99 chr4qtel1M 239084 GAAAGAG-GAGGGAGGGA-AGAGAG 239106 i - i i - (AGAGAG)n#Sim 100 GAGAGAGAGAGAGAGAGAGAGAGAG 124 Matrix = Unknown Transitions / transversions = 4.67 (14/3) Gap_init rate = 0.12 (13 / 112), avg. gap size = 1.00 (13 / 13) 25 7.78 1.67 5.17 chr4qtel1M 239470 239529 (760471) (GGCAGTTCCT)n#Simple_repeat 1 58 (0) c_b196s251i0 7690 chr4qtel1M 239470 GGCAGTTCCTGGCAGTT-CTGGGGCAGTTCCTGGCCGCTCCGGGGCAGTT 239518 - -- v i -v (GGCAGTTCCT)n 1 GGCAGTTCCTGGCAGTTCCT--GGCAGTTCCTGGCAGTTCC-TGGCAGTT 47 chr4qtel1M 239519 CCCGGCAGTTC 239529 i (GGCAGTTCCT)n 48 CCTGGCAGTTC 58 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.07 (4 / 59), avg. gap size = 1.00 (4 / 4) 13 24.30 4.44 0.00 chr4qtel1M 239873 239917 (760083) (ATAC)n#Simple_repeat 1 47 (0) m_b196s252i6 7691 chr4qtel1M 239873 ATATATACATACA-A-ATACACCCCCACACACATATATGTATACATA 239917 i - - iv vi i i ii (ATAC)n#Simpl 1 ATACATACATACATACATACATACATACATACATACATACATACATA 47 Matrix = Unknown Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.05 (2 / 44), avg. gap size = 1.00 (2 / 2) 12 31.01 0.00 0.00 chr4qtel1M 239875 239919 (760081) (ATACAC)n#Simple_repeat 1 45 (0) m_b196s252i7 7691 chr4qtel1M 239875 ATATACATACAAATACACCCCCACACACATATATGTATACATATA 239919 i v viv i i iii i (ATACAC)n#Sim 1 ATACACATACACATACACATACACATACACATACACATACACATA 45 Matrix = Unknown Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 420 33.16 7.99 1.46 chr4qtel1M 240848 241811 (758189) C L1M3_orf2#LINE/L1 (1198) 2090 1065 m_b196s551i1 7692 chr4qtel1M 240848 AAAAAAAATTCTATTTTCTC--TTC--ACTTG--TGCTTATTCTCAATAA 240891 i i v i i ii -- -- i -- i v ---- vv C L1M3_orf2#LIN 2090 AGAGATAATTTTACTTCTTCCTTTCCGATTTGGATGCCTTTT----ATTT 2045 chr4qtel1M 240892 CTTTAACTTGTCTTATTTCCGTAGCTAGCAACTCTAGAAATATACCACAT 240941 vv i v v iv i v vi i v v iiiiv C L1M3_orf2#LIN 2044 CTTTTTCTTGCCTAATTGCTCTGGCTAGGACTTCCAGTACTATGTTGAAT 1995 chr4qtel1M 240942 CATAATA-CAATAA--GACATCCTTGCCTTACTCTTGATCTTCAAAGAAA 240988 viv i i- i v i-- i ii i vi i C L1M3_orf2#LIN 1994 AGAAGTGGCGAGAGTGGGCATCCTTGCCTTGTTCCTGATCTTAGAGGAAA 1945 chr4qtel1M 240989 GGCCTGTAGCTTTTC-CAATTATATATAATGTTCACTC--GGTTTCAGAA 241035 i i vi i - v ivi i vi v-- i ivv v C L1M3_orf2#LIN 1944 AGCTTTCAGTTTTTCACCATTGAGTATGATGTTAGCTGTGGGCTTTTCAT 1895 chr4qtel1M 241036 AGATATTTTTTACCAGATTAAGGAAAGTTCCATCTATCTCTAGGTTTTCT 241085 v ivii ii vi i v ?? v ?i v v iv C L1M3_orf2#LIN 1894 ATATGGCCTTTATTATGTTGAGGTANNTTCCTTCTATNCCTAGTTTGTTG 1845 chr4qtel1M 241086 AATTTTTTTTTCAGTAAAAATGTGCTGAATTTTGTCAAAAGCTTTGCCAG 241135 ivv v - i ivi i v vi v C L1M3_orf2#LIN 1844 AGAGTTTTTATCA-TGAAAGGATGTTGAATTTTGTCAAATGCTTTTTCTG 1796 chr4qtel1M 241136 AATCTACTGATATAATCACG-GTTTTTTATTCTTCTTTGTTCTTAATATA 241184 v i v i i - v i v -i v i i C L1M3_orf2#LIN 1795 CATCTATTGAGATGATCATGTGATTTTTATCCTTCATT-CTGTTAATGTG 1747 chr4qtel1M 241185 GCCCTTTGTAGT-ATAATTTTCCTTATGCTGAATAAAACCTACATTCCTG 241233 iviv iii v - viv ? v i iv vv i i i v C L1M3_orf2#LIN 1746 GTGTATCACATTNATTGATTTNCGTATGTTGAACCATCCTTGCATCCCAG 1697 chr4qtel1M 241234 ATAGAAAA---ACCTGGTCATGGTGTCTTAG-CTTTTAATGTGTTGTCAG 241279 iv v v--- i v v v- i i- C L1M3_orf2#LIN 1696 GGATAAATCCCACTTGGTCATGGTGTATGATCCTTTTAATGTGCTGTT-G 1648 chr4qtel1M 241280 GA---GACTTTTAGGTAGTGTATTTAATATTTTTGCATCACTGTTCATTA 241326 i --- ii vivi v v i v iv vv i C L1M3_orf2#LIN 1647 AATTCGGTTTGCTAGTATTTTGTTGAGGATTTTTGCATCTATGTTCATCA 1598 chr4qtel1M 241327 GCAACATTAGCCTACA-TTTTCTTTCTTTGC----TCTCTTCTTGGTTTG 241371 vi i i ii - ii i---- i vii i v C L1M3_orf2#LIN 1597 GGGATATTGGCCTGTAGTTTTCTTTTCTTGTAGTGTCTTTGTCTGGCTTT 1548 chr4qtel1M 241372 GGTT----GACCATATTTGTGTGGTA----GAGTTTGGAAGGATCTCTTC 241413 v---- iiv ii v iv vi ---- vi ii i C L1M3_orf2#LIN 1547 GGTATCAGGGTAATGCTGGCCTCATAAAATGAGTTTGGAAGTGTTCCCTC 1498 chr4qtel1M 241414 TTTTTCTATTTCT----GCAGTTTATATTTTATTGG----AATTGTTATG 241455 i i v i ----iv ivivvvv ---- v v v C L1M3_orf2#LIN 1497 CTCTTCAATTTTTTGGAAGAGTTTGAGAAGGATTGGTATTAATTCTTCTT 1448 chr4qtel1M 241456 TGAATGTTTGATAGAATTCACTGGTAAATCCATCTGGTCCT-GATTTTTT 241504 i i ii i v - ii i C L1M3_orf2#LIN 1447 TAAATGTTTGGTAGAATTCACCAGTGAAGCCATCTGGTCCTGGGCTTTTC 1398 chr4qtel1M 241505 TTTAATTTGGGAGTTTATTTATAGTTTGTTTAATTTCTTTATCTAAGATG 241554 i-- v v v vii vi i i i iiiivv v C L1M3_orf2#LIN 1397 TTTG--TTGGGAGGTTTTTGATTACTGATTCAATCTCCTTACTCGTTATT 1350 chr4qtel1M 241555 AGT-TAAACAGCT----AAATTCTTCTTCTGTTAAACTGAATA--TTTTA 241597 i - ivv v ----v v v vvv i iv vii -- v C L1M3_orf2#LIN 1349 GGTCTGTTCAGATTTTCTATTTCTTCATGATTCAGTCTTGGTAGGTTGTA 1300 chr4qtel1M 241598 TAGTTTTGTAAA--TATTCGTTTTATCTAAATTTTCAACATTATTTTCAT 241645 iv i ivi -- i i iv ii v v vv i vv i C L1M3_orf2#LIN 1299 TGTTTCTAGGAATTTATCCATTTCTTCTAGGTTATCCAATTTGTTGGCGT 1250 chr4qtel1M 241646 ATAATTAAACAAAATAAG-TCTGACAATTTCCTTTATCTC---ATCTTCA 241691 ivv v i iv- v ii iiii i ---iv v C L1M3_orf2#LIN 1249 ATAATTGTTCATAGTAGTCTCTTATGATCCTTTTTATTTCTGTGGCATCA 1200 chr4qtel1M 241692 AT--TACTGTGTTTTTTTAAAAAATATTTCTG---TTA-TGAGTTGAGTC 241735 i -- v v ii i -----vi --- - v v C L1M3_orf2#LIN 1199 GTTGTAATGTCTCCTCTT-----TCATTTCTGATTTTATTTATTTGAGTC 1155 chr4qtel1M 241736 TGTTTCATTGTTGCTTC-TCTAAT------TTTGCCAGATTTG-TTATTG 241777 - i v v v v- ii------ i iv - iv C L1M3_orf2#LIN 1154 T-TCTCTTTTTTTCTTAGTCTAGCTAAAGGTTTGTCAATTTTGTTTATCT 1106 chr4qtel1M 241778 T-----ATAACCAACTCACTGGTCTGTT--TTTTCTCTCTT 241811 ----- v viv v ii -- i v C L1M3_orf2#LIN 1105 TTTCAAAAAACCAACTCTTAGTTTCGTTGATTTTTTCTATT 1065 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 44.46 CpG sites = 173, Kimura (unadjusted) = 45.26 Transitions / transversions = 1.22 (173/142) Gap_init rate = 0.05 (48 / 963), avg. gap size = 1.92 (92 / 48) 772 33.03 6.05 0.72 chr4qtel1M 240892 241684 (758316) C L1M4_orf2#LINE/L1 (1244) 2050 1216 m_b196s551i2 7692 chr4qtel1M 240892 CTTTAACTTGTCTTATTTCCGTAGCTAGCAACTCTAGAAATATACCACAT 240941 vv i v v v i v v i v vv iiiiv C L1M4_orf2#LIN 2050 CTTTTTCTTGCCTAATTGCCCTGGCTAGAACCTCCAGTACAATGTTGAAT 2001 chr4qtel1M 240942 CATAATA-CAATAA--GACATCCTTGCCTTACTCTTGATCTTCAAAGAAA 240988 viv i i- i v i-- i ii i viii i C L1M4_orf2#LIN 2000 AGAAGTGGCGAGAGCGGACATCCTTGTCTTGTTCCTGATCTTAGGGGGAA 1951 chr4qtel1M 240989 GGCCTGTAGCTTTTC-CAATTATATATAATGTTCACTC--GGTTTCAGAA 241035 i ? vi ii - v vi i vi v-- ivviv C L1M4_orf2#LIN 1950 AGCNTTCAGTCTTTCACCATTAAGTATGATGTTAGCTGTGGGTTTTTCGT 1901 chr4qtel1M 241036 AGATATTTTTTACCAGATTAAGGAAAGTTCCATCTATCTCTAGGTTTTCT 241085 iiii i i i iv i v ii v v iv C L1M4_orf2#LIN 1900 AGATGCCCTTTATCAGGTTGAGGAAGTTCCCTTCTATTCCTAGTTTGTTG 1851 chr4qtel1M 241086 AATTTTTTTTTCAGTAAAAATGTGCTGAATTTTGTCAAAAGCTTTGCCAG 241135 i v v - i iv i i v vi v C L1M4_orf2#LIN 1850 AGTGTTTTTATCA-TGAAAGGGTGTTGGATTTTGTCAAATGCTTTTTCTG 1802 chr4qtel1M 241136 AATCTACTGATATAATCACG-GTTTTTTATTCTTCTTTGTTCTTAATATA 241184 vi i v i i - v i i iv -i v i C L1M4_orf2#LIN 1801 CGTCTATTGAGATGATCATGTGGTTTTTGTCCTTTATT-CTATTAATATG 1753 chr4qtel1M 241185 GCCCTTTGTAGTA--TAATTTTCCTTATGCTGAATAAAACCTACATTCCT 241232 iviv ii v i-- i v?- i iv v i i C L1M4_orf2#LIN 1752 GTGTATTACATTGATTGATTTTCGN-ATGTTGAACCAACCTTGCATTCCT 1704 chr4qtel1M 241233 GATAGAAAA---ACCTGGTCATGGTGTCTTAGC-TTTTAATGTGTTGTCA 241278 iv v v--- i v v v - v i - v C L1M4_orf2#LIN 1703 GGGATAAATCCCACTTGGTCATGGTGTATAATCCTTTTTATATGTTG-CT 1655 chr4qtel1M 241279 GGA---GACTTTTAGGTAGTGTATTTAATATTTTTGCATCACTGTTCATT 241325 --- ii vivi v v i v iv vv i v C L1M4_orf2#LIN 1654 GGATTCGGTTTGCTAGTATTTTGTTGAGGATTTTTGCATCTATATTCATA 1605 chr4qtel1M 241326 AGCAACATTAGCCTACA-TTTTCTTTCTTTGC----TCTCTTCTTGGTTT 241370 vi i i i ii - ii i---- i vii C L1M4_orf2#LIN 1604 AGGGATATTGGTCTGTAGTTTTCTTTTCTTGTGATGTCTTTGTCTGGTTT 1555 chr4qtel1M 241371 GGGTT----GACCATATTTGTGTGGTAGA----GTTTGGAAGGATCTCTT 241412 v v---- iiv i v iv vi ---- v vi ii i C L1M4_orf2#LIN 1554 TGGTATCAGGGTAATACTGGCCTCATAGAATGAGTTGGGAAGTGTTCCCT 1505 chr4qtel1M 241413 CTTTTTCTATTTCT----GCAGTTTATATTTTATTGG----AATTGTTAT 241454 i i i ----iv i ivvvv ---- v v C L1M4_orf2#LIN 1504 CCTCTTCTATTTTTTGGAAGAGTTTGTGAAGGATTGGTGTTAATTCTTCT 1455 chr4qtel1M 241455 GTGAATGTTTGATAGAATTCACTGGTAAATCCATCTGGTCCTGATTTTTT 241504 v i i ii i v ? ivi C L1M4_orf2#LIN 1454 TTAAATGTTTGGTAGAATTCACCAGTGAAGCCATCTGGNCCTGGGCTTTT 1405 chr4qtel1M 241505 TTTAATTTGGG-AGTTTATTTATAGTTTGTTTAATTTCTTTATCTAAGAT 241553 i -- v - v v vii vi i i ii ivv C L1M4_orf2#LIN 1404 CTT--TGTGGGAAGTTTTTTGATTACTAATTCAATCTCTTTACTTGTTAT 1357 chr4qtel1M 241554 GAGT-TAAACAGCT----AAATTCTTCTTCTGTTAAACTGAATATTTTAT 241598 ii - vv v ----v v vv i ivi vii v i C L1M4_orf2#LIN 1356 AGGTCTATTCAGATTTTCTATTTCTTCTTGAGTCAGTTTCGGTAGTTTGT 1307 chr4qtel1M 241599 AGTTTTGTAAATATT----CGTTTTATCTAAATTTTCAACATTATTTTCA 241644 ivi v iiv ---- i i ii v v vv i vv C L1M4_orf2#LIN 1306 GTCTTTCTAGGAATTTGTCCATTTCATCTAGGTTATCTAATTTGTTGGCA 1257 chr4qtel1M 241645 TATAATTAAACAAAATAAG-TCTGACAATTTCCTTTATCTC 241684 i ivv v i vv-i v i iiii i C L1M4_orf2#LIN 1256 TACAATTGTTCATAGTATTCCCTTATAATCCTTTTTATTTC 1216 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 44.12 CpG sites = 146, Kimura (unadjusted) = 45.07 Transitions / transversions = 1.28 (146/114) Gap_init rate = 0.03 (26 / 792), avg. gap size = 2.08 (54 / 26) 245 24.71 1.16 1.16 chr4qtel1M 241800 241885 (758115) C L1MD_orf2#LINE/L1 (2362) 932 847 m_b196s551i3 7693 chr4qtel1M 241800 TTTTTCTCTCTTACTGATAAGTGCATTTAGAGAGATCA-TTTCCCCTTAA 241848 i i - i ivi? v vv v - ii v C L1MD_orf2#LIN 932 TTTTCCTCTTTT-CTAATGTANGCATTTAGTGCTATAAATTTCCCTCTCA 884 chr4qtel1M 241849 GGACTGCTTTATCAGCATTCCAAAAGTTTTGGTATGT 241885 v v v i i v i i C L1MD_orf2#LIN 883 GCACTGCTTTAGCTGCGTCCCACAAATTTTGATATGT 847 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 29.08 CpG sites = 11, Kimura (unadjusted) = 30.78 Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.02 (2 / 85), avg. gap size = 1.00 (2 / 2) 234 26.32 0.00 0.00 chr4qtel1M 242548 242604 (757396) C MER99#DNA/hAT (0) 831 775 m_b196s502i1 7694 chr4qtel1M 242548 TAATATTTCCATGTGGGAATTATTTCCTGGCACTTCTTAAGAAATGTCTA 242597 i i i vi i i iii v v C MER99#DNA/hAT 831 TAGTGTTTCCATGCGGGAATTCCTTCCCGGCATTTCTCGGGAAATTTATA 782 chr4qtel1M 242598 CATTTCT 242604 ii i C MER99#DNA/hAT 781 TGTTTTT 775 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 26.32 CpG sites = 12, Kimura (unadjusted) = 34.87 Transitions / transversions = 4.00 (12/3) Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0) 1737 23.85 10.40 0.47 chr4qtel1M 242605 243181 (756819) C MER99#DNA/hAT (98) 733 100 m_b196s502i2 7694 chr4qtel1M 242605 AAAACCGGAAAAC-TACTATAATTTG---GCCAGATTTAAATGTTAACAA 242650 v v- i iv--- v v vv C MER99#DNA/hAT 733 AAAACGGGAAAAAGTATTATAATTCTCCTGCGAGAATTAAAGCTTAACAA 684 chr4qtel1M 242651 TTACTATAGAGATATTACAGATTTACAGGAACCCGCCATTGTTAAATTCA 242700 i vi ii v i iiv i i iivi i i iv C MER99#DNA/hAT 683 TCAACATAGAGACGTTACTGGTTCGAAGGAATCCACTGACGTCAAGTCGA 634 chr4qtel1M 242701 AAGCAAGAGCAAGAAAAGC--------AGAGTCAAAAGTTAAGTTTCACA 242742 i v --------i i i v iv C MER99#DNA/hAT 633 AAGCAAGAGCAGGAAACGCTGACACGCGGAGTCGAAGGTTAAGGTCGACA 584 chr4qtel1M 242743 TTTCCAGGAACTAGAAAAGGAACATGGGAGACAGGAGCAGGCAGGAGCTA 242792 i ii i v i i vii v i i v v v C MER99#DNA/hAT 583 TTTCCGGGAACCGGGACAGGAGCACGTAGGAGAGAAGCGGTCACGATCTA 534 chr4qtel1M 242793 ATCAGTCAATCTTG-TAGTAACTGTTAACATGCT-TACG----------- 242829 i - v i iv i - v ----------- C MER99#DNA/hAT 533 ATCAGTCAGTCTTGCTTGTAGCTGTTGCCATGTTATAAGTGTGTGTTCGT 484 chr4qtel1M 242830 ------GTCTGCTGATAAC----AGTCATCTTTGCAAATACAATAAATAT 242869 ------ v ---- ii v C MER99#DNA/hAT 483 GGCCCTGTCTGCTGCTAACGGTGAGTCATTCTTGCAAATAAAATAAATAT 434 chr4qtel1M 242870 CACTAAGTTTACATGCATAGTATA-TTTATACTAGTTCTATGAGAAGCGG 242918 i v i i - v i i vi i v C MER99#DNA/hAT 433 TAATAAGTTTATACGCATAGTATACTTTATACAAATCCTATGAGTGGTGT 384 chr4qtel1M 242919 TCTAAGAAATGACTTGTTTGGGGACCCAAGCTGGGTTTTTAAATGGACAA 242968 i i vv v i -v iv ii ii v i C MER99#DNA/hAT 383 TCCAAGAAATAACAAGTTTTGGAA-GCAAAATAAGTCCTTAAATTGGCAA 335 chr4qtel1M 242969 CTTTGACAGGTGATT-------------TTAATCTTGCAAGG-GACCTGA 243004 i i v ------------- i v - i i C MER99#DNA/hAT 334 TTTCGACACGTGATTCTGTGTAGTGCTGTTAACCTTGCTAGGAGATCCGA 285 chr4qtel1M 243005 CTGGAATGTT----GACTACCGTCCGCTGATGTCCGCTGACATTTTCTAG 243050 v vv i ---- v iii iv i i i i i C MER99#DNA/hAT 284 ATGTTACGTTATTCGAATACTACCCAATAATGTTCGCTGGCGTTTTCCAG 235 chr4qtel1M 243051 TGTTTGAATGTTCACTATAGGCTAC-GTTCTTAGTCAATGCTACCAAGC- 243098 i i - v v i i i - C MER99#DNA/hAT 234 TGTTTGAATATTCGCTATAGGCTACAGTTCTTTGTAAATACTACTAAACT 185 chr4qtel1M 243099 ----GCTTCCTATTTATGAAACAAAAAATTTTAGTTACACATGTGAAGGA 243144 ----ii i v -- v v iv ivv v C MER99#DNA/hAT 184 TAATATTTCTTATTTATTAAAC--AAATTTTTAGATATCCATAATAATGA 137 chr4qtel1M 243145 GCAAAGACTATGAAGGAGCTAGGAAGTATTTTAAGAA 243181 i v i vv v C MER99#DNA/hAT 136 GTAAAGAGTATGAAGAATGTTGGAAGTATTTTAAGAA 100 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 25.11 CpG sites = 81, Kimura (unadjusted) = 29.31 Transitions / transversions = 1.45 (81/56) Gap_init rate = 0.03 (18 / 576), avg. gap size = 3.50 (63 / 18) 200 36.21 4.71 6.59 chr4qtel1M 243495 243834 (756166) C L2#LINE/L2 (172) 2910 2577 m_b196s601i9 7695 chr4qtel1M 243495 GGAACTTCAAGGTCAGTGAGAGGAGGTTA-CATTTATCCTG---GAGACA 243540 iv vv i v vi vv i- v ii --- ii C L2#LINE/L2 2910 GGGCCTTGTAGGCCATTGTAAGGACTTTGGCTTTTACTCTGAGTGAGATG 2861 chr4qtel1M 243541 AAAGGGAGCTGGGGCATTTCTTGGGACAGGACTGATGTGGTCAGA-TTGG 243589 ii i vvii i vi - vi v v v ii i v - iv C L2#LINE/L2 2860 GGAAGCCATTGGAGGGTTT-TGAGCAGAGGAGTGACATGATCTGACTTAC 2812 chr4qtel1M 243590 GCGCTAGGAAGATTATTTTGGCAGCTGTGAGGAAGCTGGATTAGGCGGCC 243639 ivi ii i i i i v vv iiv i i - ?v vv C L2#LINE/L2 2811 GTTTTAAAAGGATCACTCTGGCTGCTGTGTTGAGAATAGACT-GNAGGGG 2763 chr4qtel1M 243640 GGCTGGAAGAGGGGGAGGAGGGAGGGAGCAATGTCCAGGAGGGCTCAGGG 243689 --- i v i v -- v i ---i - ----- C L2#LINE/L2 2762 GGC---AAGGGTGGAAGCAGGGA--GACCAGT---TAGGA-GGCT----- 2727 chr4qtel1M 243690 GTCGCA--AATCTGGAGCCTGGGAGGATGAAGAGCTGGAATCAGGGGGAA 243737 i i -- ii - vv i v iv - v i i v -i C L2#LINE/L2 2726 ATTGCAGTAATCCAG-GCGAGAGATGATGGTG-GCTTGGACCAGGGTG-G 2680 chr4qtel1M 243738 TGATA--AGAGCTGGTCAGAA------GGA-CCAGCATGTTCTCTGCAGG 243778 ii --i v v ------ -i v v i vi i v C L2#LINE/L2 2679 TGGCAGTGGAGGTGGTGAGAAGTGGTCGGATTCTGGATATATTTTGAAGG 2630 chr4qtel1M 243779 GAGATCCGGCCGCAGCATTTCTCTAGCGTCTGCAAATCGGGTACAAGGAG 243828 v v ---i v viiv vv vi v vi v iii iii C L2#LINE/L2 2629 TAGAGCCG---ACAGGATTTGCTGATGGATTGGATGTGGGGTGTGAGAGA 2583 chr4qtel1M 243829 AACAGA 243834 v C L2#LINE/L2 2582 AAGAGA 2577 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 51.16 CpG sites = 63, Kimura (unadjusted) = 51.16 Transitions / transversions = 1.21 (63/52) Gap_init rate = 0.09 (29 / 339), avg. gap size = 1.31 (38 / 29) 15 19.46 0.00 0.00 chr4qtel1M 245433 245467 (754533) (GGGAGG)n#Simple_repeat 1 35 (0) m_b196s252i8 7696 chr4qtel1M 245433 GGGGGTGGTAGGGGGAGGGGGGCCGGGAGGGGGAG 245467 i v v ivv (GGGAGG)n#Sim 1 GGGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGGAG 35 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 13 29.39 0.00 6.15 chr4qtel1M 246260 246328 (753672) (GTTTT)n#Simple_repeat 1 65 (0) m_b196s252i9 7697 chr4qtel1M 246260 GTTTTGGGTTTTATTTGCTTTGTTTTGTTGAAATTTAATTTTGGTTTCCT 246309 - v vv i -vvi vi - iv (GTTTT)n#Simp 1 GTTTT-GTTTTGTTTTGTTTTGTTTTGTT-TTGTTTTGTTTT-GTTTTGT 47 chr4qtel1M 246310 ATGGTTCTTGCTGTGTTTT 246328 v v - i v (GTTTT)n#Simp 48 TTTGTT-TTGTTTTGTTTT 65 Matrix = Unknown Transitions / transversions = 0.50 (5/10) Gap_init rate = 0.06 (4 / 68), avg. gap size = 1.00 (4 / 4) 25 19.28 2.99 1.47 chr4qtel1M 246466 246532 (753468) (GGGA)n#Simple_repeat 1 68 (0) m_b196s252i10 7698 chr4qtel1M 246466 GGGAGGGAGGAATGGATGAAACGAGAGAAGGGGGGGA-GGAGGGAGGGAG 246514 i v v i iv - i i - (GGGA)n#Simpl 1 GGGAGGGAGGGAGGGAGGGAGGGAG-GGAGGGAGGGAGGGAGGGAGGGAG 49 chr4qtel1M 246515 CTAGGGA-GGAGGGGGGGA 246532 vv - i (GGGA)n#Simpl 50 GGAGGGAGGGAGGGAGGGA 68 Matrix = Unknown Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.05 (3 / 66), avg. gap size = 1.00 (3 / 3) 371 30.20 2.67 0.65 chr4qtel1M 248163 248312 (751688) Charlie4#DNA/hAT-Charlie 1 153 (3225) m_b196s502i3 7699 chr4qtel1M 248163 CAGGGGCTCTCAAGCTGGGCTCT--GGACTCCCTTGGGAGGCTACAGGGA 248210 i i v v i-- i vv - v iiii iv Charlie4#DNA/ 1 CAGGGGTTCTTAACCTGGGGTCCACGGACCCCCAAGGG-GTCCGTGGATA 49 chr4qtel1M 248211 GA-TTCAGGGAGTCCGTGCCCTGGGACGGAAATAAAGC-CACCGCCCTTT 248258 - i vv v i i v vi- i viiv Charlie4#DNA/ 50 GAATTCAGGGGGTCCGTGAACTTGGATGGGAAAAAATTACATCTTTATTT 99 chr4qtel1M 248259 TGGGTCACCTCCTGCTGAAATCCAGCGTTTCCTTCCATTGCGGACGTGGG 248308 viv v ivi ii i v ii i i i Charlie4#DNA/ 100 TCACTAACCTCTAACTGAAATTTAGCATTTCCTTCAATTATGAATGTAGG 149 chr4qtel1M 248309 CAAC 248312 Charlie4#DNA/ 150 CAAC 153 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 38.64 CpG sites = 27, Kimura (unadjusted) = 39.92 Transitions / transversions = 1.50 (27/18) Gap_init rate = 0.03 (4 / 149), avg. gap size = 1.25 (5 / 4) 12 18.29 0.00 3.12 chr4qtel1M 249143 249175 (750825) (AACCCT)n#Simple_repeat 1 32 (0) m_b196s252i11 7700 chr4qtel1M 249143 AACCAAAACTCCCGACTCTAACCCTAACCCTAA 249175 vv - ii i (AACCCT)n#Sim 1 AACCCTAAC-CCTAACCCTAACCCTAACCCTAA 32 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 235 28.41 1.30 4.00 chr4qtel1M 249228 249304 (750696) MIRc#SINE/MIR 37 111 (157) m_b196s601i10 7701 chr4qtel1M 249228 TGGAG-CGGGAGCAGCCGGGGTCAGGGTTGGCCGCTGCCACCTGCCACCG 249276 - i iv v i v ii viiv v v i i i --- MIRc#SINE/MIR 37 TGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTA--- 83 chr4qtel1M 249277 ACTGTGTGATCCTGGGCAAGTCACCTAA 249304 i i i i MIRc#SINE/MIR 84 GCTGTGTGACCTTGGGCAAGTCACTTAA 111 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.01 CpG sites = 14, Kimura (unadjusted) = 37.27 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.05 (4 / 76), avg. gap size = 1.00 (4 / 4) 14 23.79 1.89 3.85 chr4qtel1M 249325 249377 (750623) (CGGG)n#Simple_repeat 1 52 (0) m_b196s252i12 7702 chr4qtel1M 249325 CGTGCGGGCAGAGGAGGAGGACGGGGAGAGCATGCGGGCGGGCGGG-GGG 249373 v - i vi v i - v i iv - (CGGG)n#Simpl 1 CGGGCGGGC-GGGCGGGCGGGC-GGGCGGGCGGGCGGGCGGGCGGGCGGG 48 chr4qtel1M 249374 CGGG 249377 (CGGG)n#Simpl 49 CGGG 52 Matrix = Unknown Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.06 (3 / 52), avg. gap size = 1.00 (3 / 3) 236 36.56 1.08 0.00 chr4qtel1M 251294 251386 (748614) C MIRc#SINE/MIR (169) 99 6 m_b196s601i11 7703 chr4qtel1M 251294 CCCAAGGTCACAGGACCTGGAGGGGACAGAGGCAGGATGGGCATCTGGGT 251343 vii iv v i v i v i ivv v i ii C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGT 50 chr4qtel1M 251344 CTTCCTG-CCCCAGATCTGGTGACATCTTCTCGGCCCCCTGCTG 251386 - i ii ii viv i i v v v vii C MIRc#SINE/MIR 49 CTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTG 6 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 50.15 CpG sites = 20, Kimura (unadjusted) = 52.41 Transitions / transversions = 1.43 (20/14) Gap_init rate = 0.01 (1 / 92), avg. gap size = 1.00 (1 / 1) 214 26.53 2.04 0.00 chr4qtel1M 251404 251452 (748548) C L3#LINE/CR1 (8) 4091 4042 m_b196s601i12 7704 chr4qtel1M 251404 CACAGAATCTCAGCTTTAGAAGGGA-CTTGGGAGCTACCTGCTCTAACTT 251452 vv i - i ii ii i iv i i C L3#LINE/CR1 4091 CACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCAACCT 4042 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.95 CpG sites = 10, Kimura (unadjusted) = 34.95 Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.02 (1 / 48), avg. gap size = 1.00 (1 / 1) 218 32.07 10.37 1.12 chr4qtel1M 252249 252412 (747588) C L3#LINE/CR1 (1126) 2973 2795 m_b196s601i13 7704 chr4qtel1M 252249 AATGCCTTTGCTGGAATCTGGCT--GCCAGGTACAC-GCATTCTCAGGAA 252295 - i ii v --i i?v vi - i vv v C L3#LINE/CR1 2973 AATGCCTT-GCTGAAATCCAGATACACTNTGTCTACGGCATTCCCCTGAT 2925 chr4qtel1M 252296 CTGGAACCCTGGGGGTCC-AGCAGCAAAGAGGAGCGAGG------CAGCA 252338 ivv vi i viii - v iv - i ii ------ii C L3#LINE/CR1 2924 CTACCAGTCTAGTAACCCTATCAAAAAAG-GAAATGAGGTTAGTTTGGCA 2876 chr4qtel1M 252339 -GGCTT-CTCATTGAGAAGCCACGATGGCCCTTGG-GACCATAGCATCCT 252385 - i -i v v v v i v i i i - i iv v C L3#LINE/CR1 2875 TGACTTGTTCTTAGTGAACCCATGCTGGCTCCTAGTGATCACCGCTTCCT 2826 chr4qtel1M 252386 CCTC--AGT-TTCAT-AACCAGCTCTTTAAT 252412 ii -- -i i- v v C L3#LINE/CR1 2825 TTTCTAAGTGCTCACAAACCATCTGTTTAAT 2795 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.79 CpG sites = 31, Kimura (unadjusted) = 43.79 Transitions / transversions = 1.48 (31/21) Gap_init rate = 0.07 (12 / 163), avg. gap size = 1.58 (19 / 12) 273 29.98 6.06 1.45 chr4qtel1M 253109 253240 (746760) C L3#LINE/CR1 (2480) 1619 1482 m_b196s601i14 7704 chr4qtel1M 253109 CATCTAGTGCCTTCTTCTGGCCGGGTGGTCTG-AGTAAAGGCTGAGGACG 253157 i v?v i v i - v vv iv vi C L3#LINE/CR1 1619 CATCCATNTCCTCCATCTGGCCGGGCGGTCTGTAGTATACTCCCACAACG 1570 chr4qtel1M 253158 GTATGACTT---TTTCTGCCACCTACATGATTCCCAC---AATGCTCTGG 253201 i v --- vi v --v v i i --- vv C L3#LINE/CR1 1569 ATATCACTTCTGTTTCTCTCTCCT--TTTATCCTCACCCAAATGCTCTCC 1522 chr4qtel1M 253202 AATGGGCCCCCGCCTCCA-GTCCCTGCACCTCCTCCCAGG 253240 ?i v ii ii ii - i v v ii v v C L3#LINE/CR1 1521 ANCGCGCTTCTACCCTCAGGTTCGTGGATTTCCACGCAGG 1482 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.04 CpG sites = 19, Kimura (unadjusted) = 39.54 Transitions / transversions = 0.95 (19/20) Gap_init rate = 0.05 (6 / 131), avg. gap size = 1.67 (10 / 6) 245 29.72 0.00 3.12 chr4qtel1M 253285 253350 (746650) C L3#LINE/CR1 (2691) 1408 1345 m_b196s601i15 7704 chr4qtel1M 253285 CTTTTTCACAGCCATTTTCCAGTCAGGAGTCTCATTTCATCAAGCCTGGG 253334 ii i iv i v v i ii i i v C L3#LINE/CR1 1408 CCCTTCCATCGCCGTATTCCAGTCATGAGTCCCATCCCACCAAGTCTCGG 1359 chr4qtel1M 253335 GACGACACCGAGGGGA 253350 --i i v v i C L3#LINE/CR1 1358 --TGATACCTATGAGA 1345 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.11 CpG sites = 13, Kimura (unadjusted) = 39.85 Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.03 (2 / 65), avg. gap size = 1.00 (2 / 2) 14 29.30 2.48 7.83 chr4qtel1M 253664 253784 (746216) (AGGCCGA)n#Simple_repeat 1 115 (0) m_b196s252i13 7705 chr4qtel1M 253664 AGCCCGAAGGCTGTGGGACGGAAG-CGAGGGGCCGGGGAGCCCGAAGGCC 253712 v i vi v i i - -i -- i v (AGGCCGA)n#Si 1 AGGCCGAAGGCCGAAGGCCGAAGGCCGA-AGGCC--GAAGGCCGAAGGCC 47 chr4qtel1M 253713 GCAGGACGGAAG-TGAGGGGCCGGGGAGCCCGAAGGCCGCAGGACGGAAG 253761 v v i i -i -i -- i v v v i i (AGGCCGA)n#Si 48 GAAGGCCGAAGGCCGA-AGGCC--GAAGGCCGAAGGCCGAAGGCCGAAGG 94 chr4qtel1M 253762 -CGAGGGGCCGGGAAGCCTGAAGG 253784 - -i -- v i (AGGCCGA)n#Si 95 CCGA-AGGCC--GAAGGCCGAAGG 115 Matrix = Unknown Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.10 (12 / 120), avg. gap size = 1.00 (12 / 12) 194 27.19 0.00 5.08 chr4qtel1M 256131 256192 (743808) MIRc#SINE/MIR 121 179 (89) m_b196s601i16 7706 chr4qtel1M 256131 GCCTCAAGCTTCTCATCTGCACAATGGGTTGAGAAAAATCCCGAGCCCTG 256180 ivi i i v -- v v v v- MIRc#SINE/MIR 121 GCCTCAGTTTCCTCATCTGTAAAATGGG--GATAATAATACCT-GCCCTG 167 chr4qtel1M 256181 GGCACTTTGCAG 256192 vvi i ii MIRc#SINE/MIR 168 CCTACCTCACAG 179 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.02 CpG sites = 8, Kimura (unadjusted) = 34.02 Transitions / transversions = 1.00 (8/8) Gap_init rate = 0.05 (3 / 61), avg. gap size = 1.00 (3 / 3) 34 9.10 1.59 3.23 chr4qtel1M 259558 259620 (740380) (GGGGAGG)n#Simple_repeat 1 62 (0) m_b196s252i14 7707 chr4qtel1M 259558 GGGGAGGGGGGAGGGGGGAGGGAGG-GGGAGGAGGGCAGGCAGAGGGGAG 259606 i - i -- v i (GGGGAGG)n#Si 1 GGGGAGGGGGGAGGGGGGAGGGGGGAGGGGGGAGGG--GGGAGGGGGGAG 48 chr4qtel1M 259607 GAGGGAGGGGGGAG 259620 i (GGGGAGG)n#Si 49 GGGGGAGGGGGGAG 62 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.05 (3 / 62), avg. gap size = 1.00 (3 / 3) 33 25.71 0.88 3.60 chr4qtel1M 260334 260447 (739553) (GCCGCC)n#Simple_repeat 1 111 (0) m_b197s252i1 7708 chr4qtel1M 260334 GCTGCCTCCGCCGCCGCCGCCGCCGCCGCCCGACTGGCCCTGGCCGGCCC 260383 i v - - -v viv v v (GCCGCC)n#Sim 1 GCCGCCGCCGCCGCCGCCGCCGCCGCCG-CCG-C-CGCCGCCGCCGCCGC 47 chr4qtel1M 260384 AGCGCCCGCGCCCGCGCCCTCCGCCTGCCCGTGCCCGCGCCGCCGCCCCC 260433 v vv vv vv v - vvi vv v (GCCGCC)n#Sim 48 CGCCGCCGCCGCCGCCGCCGCCGCC-GCCGCCGCCGCCGCCGCCGCCGCC 96 chr4qtel1M 260434 GCCGCC-CCGCCTCC 260447 - v (GCCGCC)n#Sim 97 GCCGCCGCCGCCGCC 111 Matrix = Unknown Transitions / transversions = 0.15 (3/20) Gap_init rate = 0.04 (5 / 113), avg. gap size = 1.00 (5 / 5) 13 24.01 0.00 2.50 chr4qtel1M 262547 262587 (737413) (GCCCT)n#Simple_repeat 1 40 (0) m_b197s252i2 7709 chr4qtel1M 262547 GCCCTGCCCCAGTCAGCCCTGCCCTCCCTTGCCCCTTCCCT 262587 iivi v v i - v (GCCCT)n#Simp 1 GCCCTGCCCTGCCCTGCCCTGCCCTGCCCTG-CCCTGCCCT 40 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 185 26.41 3.70 1.82 chr4qtel1M 262818 262871 (737129) L2a_3end#LINE/L2 447 501 (16) m_b197s601i0 7710 chr4qtel1M 262818 GCATCCCGAGGGCTTC--TCTGTGCTTGGCAATGTAGTAGATGCTCAATA 262865 i v v i v--v v i -ii ii L2a_3end#LINE 447 GTATCCCCAGCGCCTAGAACAGTGCCTGGCA-CATAGTAGGCGCTCAATA 495 chr4qtel1M 262866 AATGCT 262871 ii L2a_3end#LINE 496 AATATT 501 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.77 CpG sites = 9, Kimura (unadjusted) = 33.68 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.04 (2 / 53), avg. gap size = 1.50 (3 / 2) 15 20.87 0.00 4.35 chr4qtel1M 263709 263756 (736244) (CCGCAGC)n#Simple_repeat 1 46 (0) m_b197s252i3 7711 chr4qtel1M 263709 CCGCATCCCTCCGCCCGAACGCCCGCAGCCCGTGGGCCCGCTGGCCGC 263756 v v v v - -vi v v (CCGCAGC)n#Si 1 CCGCAGCCCGCAGCCCGCA-GCCCGCAGCCCG-CAGCCCGCAGCCCGC 46 Matrix = Unknown Transitions / transversions = 0.14 (1/7) Gap_init rate = 0.04 (2 / 47), avg. gap size = 1.00 (2 / 2) 418 28.71 4.38 6.37 chr4qtel1M 265231 265390 (734610) C MIR3#SINE/MIR (32) 176 20 m_b197s601i1 7712 chr4qtel1M 265231 AGGGGCTTCTCGGGGGCCTCTCCTCCAACCCCCTCATTCTGCAGATGAGA 265280 i i - v i iv v vv i i i C MIR3#SINE/MIR 176 AGGGACCT-TAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGG 128 chr4qtel1M 265281 AAGCTGAGGCTCAGAGAGG---AACGACCTGCTGAAGGCAATGC--CTGG 265325 i i --- ii i iv iv ii -- ?i C MIR3#SINE/MIR 127 AAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGCNAG 78 chr4qtel1M 265326 --AGTGGCGGGATTCGAACCCAGTCCCAGCTCAAGAACTGTCCTGACTCC 265373 -- i iiiiv i iviiv v -------- C MIR3#SINE/MIR 77 TTAGTGGCAGAGCCGGGACTAGAACCCAGGTC--------TCCTGACTCC 36 chr4qtel1M 265374 AGGTCTATTGCACTTTC 265390 vi ii- v i C MIR3#SINE/MIR 35 CAGTCCG-TGCTCTCTC 20 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.02 CpG sites = 30, Kimura (unadjusted) = 38.45 Transitions / transversions = 2.31 (30/13) Gap_init rate = 0.08 (13 / 159), avg. gap size = 1.31 (17 / 13) 431 26.02 5.38 5.38 chr4qtel1M 265262 265391 (734609) C MIRc#SINE/MIR (119) 149 20 m_b197s601i2 7712 chr4qtel1M 265262 CCTCATTCTGCAGATGAGAAAGCTGAGGCTCAGAGAGG---AACGACCTG 265308 i i i i i --- ii i C MIRc#SINE/MIR 149 CCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTG 100 chr4qtel1M 265309 CTGAAGGCAATGC--CTGG--AGTGGCGGGATTCGAACCCAGTCCCAGCT 265354 iv iv ii -- i -- i iiiiv i i iiv v C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGT 50 chr4qtel1M 265355 CAAGAACTGTCCTGACTCCAGGTCTATTGCACTTTCC 265391 -------v i i v v C MIRc#SINE/MIR 49 C-------TTCCTGACTCCAAGTCCAGTGCTCTTTCC 20 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.24 CpG sites = 24, Kimura (unadjusted) = 33.86 Transitions / transversions = 3.00 (24/8) Gap_init rate = 0.08 (10 / 129), avg. gap size = 1.40 (14 / 10) 208 26.32 1.75 0.00 chr4qtel1M 266333 266389 (733611) C MIRb#SINE/MIR (167) 101 44 m_b197s601i3 7713 chr4qtel1M 266333 CCGGGGTCACACAGCCAGTAAG-GGCACAGTTGGGGTTCTGGGGCAGGTC 266381 ii i - v ii i viivv C MIRb#SINE/MIR 101 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTC 52 chr4qtel1M 266382 TCTCCCAC 266389 v iv C MIRb#SINE/MIR 51 TGTCTGAC 44 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.58 CpG sites = 9, Kimura (unadjusted) = 33.24 Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.02 (1 / 56), avg. gap size = 1.00 (1 / 1) 14 38.56 0.00 0.00 chr4qtel1M 267628 267700 (732300) (CCC)n#Simple_repeat 1 73 (0) m_b197s252i5 7714 chr4qtel1M 267628 CCTCCTCCCTCGCCACCCCCCCCCCACCGGCAGCCTCCCTGCCGGCTTCT 267677 i i i v v v vv vv i iv vv ii i (CCC)n#Simple 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 50 chr4qtel1M 267678 GGGCCGCCCCCCCCCCCCCCCCC 267700 vvv v (CCC)n#Simple 51 CCCCCCCCCCCCCCCCCCCCCCC 73 Matrix = Unknown Transitions / transversions = 0.57 (8/14) Gap_init rate = 0.00 (0 / 72), avg. gap size = 0.0 (0 / 0) 17 10.09 0.00 3.03 chr4qtel1M 267785 267818 (732182) (CCTGCC)n#Simple_repeat 1 33 (0) m_b197s252i6 7715 chr4qtel1M 267785 CCTCCCCCTGCCCCCCGCCCCTGCCCCCGCCCCT 267818 v - i i (CCTGCC)n#Sim 1 CCTGCCCCTG-CCCCTGCCCCTGCCCCTGCCCCT 33 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 21 37.00 0.00 2.83 chr4qtel1M 268937 269045 (730955) (CA)n#Simple_repeat 1 106 (0) m_b197s252i7 7716 chr4qtel1M 268937 CACACAGCACACTCAGAGGCACCTGTTCACACATACACACGCTTACACAC 268986 - v v vi viiiv i i vi (CA)n#Simple_ 1 CACACA-CACACACACACACACACACACACACACACACACACACACACAC 49 chr4qtel1M 268987 GACAAACGGACTCTTGTACACAGACATTCCCACCCGCACATACAGGCACA 269036 - v iv v viii v iv v v i i vi (CA)n#Simple_ 50 -ACACACACACACACACACACACACACACACACACACACACACACACACA 98 chr4qtel1M 269037 CACAGCACA 269045 - (CA)n#Simple_ 99 CACA-CACA 106 Matrix = Unknown Transitions / transversions = 1.00 (15/15) Gap_init rate = 0.03 (3 / 108), avg. gap size = 1.00 (3 / 3) 211 20.52 13.51 1.20 chr4qtel1M 270131 270204 (729796) MIRb#SINE/MIR 45 127 (141) m_b197s601i4 7717 chr4qtel1M 270131 TCAGA--GACTCTGGGTTCAAATTCTGGCTTTGCCCCTTTCTCCCT---- 270174 -- - i i i i v v vv ---- MIRb#SINE/MIR 45 TCAGACAGAC-CTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGT 93 chr4qtel1M 270175 --CCGTGGGCAAA-GACCTAACTGC-CTGGGCCT 270204 -- v i-v i iv - i MIRb#SINE/MIR 94 GACCTTGGGCAAGTTACTTAACCTCTCTGAGCCT 127 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 20.77 CpG sites = 8, Kimura (unadjusted) = 24.24 Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.08 (6 / 73), avg. gap size = 1.83 (11 / 6) 236 18.61 0.00 2.33 chr4qtel1M 273091 273134 (726866) MIR3#SINE/MIR 112 154 (54) m_b197s601i5 7717 chr4qtel1M 273091 CTCTGAACCTCAGCTTTCTCATCTGTGAAATGGGCGGAGATGGA 273134 ii i i i i - i v MIR3#SINE/MIR 112 CTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAG-GGGGTTGGA 154 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 22.64 CpG sites = 7, Kimura (unadjusted) = 22.64 Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.02 (1 / 43), avg. gap size = 1.00 (1 / 1) 238 11.76 0.00 0.00 chr4qtel1M 273091 273124 (726876) MIRb#SINE/MIR 118 151 (117) m_b197s601i6 7717 chr4qtel1M 273091 CTCTGAACCTCAGCTTTCTCATCTGTGAAATGGG 273124 i i i i MIRb#SINE/MIR 118 CTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 151 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 13.41 CpG sites = 4, Kimura (unadjusted) = 13.41 Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 36 20.73 3.53 0.00 chr4qtel1M 274018 274102 (725898) (CT)n#Simple_repeat 1 88 (0) m_b197s252i8 7718 chr4qtel1M 274018 CTCACTCTCTC-CTCCTTCT-TCCTTCTCTCTCTCTCCCTCTCTTGCTCC 274065 v - ii - ii i iv i (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chr4qtel1M 274066 CTCCCTGTTTCTCT-TTTCTTTCTCTCTGTCTCTCTCT 274102 i v i - i i v (CT)n#Simple_ 51 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 88 Matrix = Unknown Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.04 (3 / 84), avg. gap size = 1.00 (3 / 3) 197 31.34 0.00 0.00 chr4qtel1M 275740 275806 (724194) MIR3#SINE/MIR 90 156 (52) m_b197s601i7 7719 chr4qtel1M 275740 CCCTGGCCCAGCCTTTTTGTCTCAATGGGCCTCAGCTTACTCTTCTGTCC 275789 i v v i vi iii vv i v v vv MIR3#SINE/MIR 90 CCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAA 139 chr4qtel1M 275790 AATGCACGGGTAGCACT 275806 viv v v MIR3#SINE/MIR 140 AATGAGGGGGTTGGACT 156 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.63 CpG sites = 8, Kimura (unadjusted) = 40.63 Transitions / transversions = 0.62 (8/13) Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.0 (0 / 0) 243 31.40 12.09 2.00 chr4qtel1M 276181 276271 (723729) C L2c_3end#LINE/L2 (15) 463 364 m_b197s601i8 7720 chr4qtel1M 276181 AAGCATCTATTAGGCACTGACTGTGTGCCAAGAACTCCGGGAAGACAAAG 276230 i i ii i iv i i vi -- i v C L2c_3end#LINE 463 AAACATTTATTGAGCGCCTACTATGTGCCAGGCGCT--GGGGATACAAAG 416 chr4qtel1M 276231 GCAGAT-----------CCTGCCCTCGCGGAGCGTCGGGTCTAACAGGGG 276269 iiii ----------- iv vivvi iii i C L2c_3end#LINE 415 ATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAGTGGAGG 366 chr4qtel1M 276270 AG 276271 C L2c_3end#LINE 365 AG 364 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.96 CpG sites = 21, Kimura (unadjusted) = 44.27 Transitions / transversions = 3.00 (21/7) Gap_init rate = 0.03 (3 / 90), avg. gap size = 4.33 (13 / 3) 14 16.66 2.94 0.00 chr4qtel1M 276758 276791 (723209) (GCCCCG)n#Simple_repeat 1 35 (0) m_b197s252i9 7721 chr4qtel1M 276758 GCCCCTG-CCCGGCCCCGGGGCCCTCCCCGGCCCC 276791 v - vv vv (GCCCCG)n#Sim 1 GCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCC 35 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 23 7.16 0.00 0.00 chr4qtel1M 276877 276906 (723094) (G)n#Simple_repeat 1 30 (0) m_b197s252i10 7722 chr4qtel1M 276877 GGGGGGGGGGAGGGGAGGGGGGGGGGGGGG 276906 i i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 30 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 15 9.55 0.00 0.00 chr4qtel1M 276909 276923 (723077) (A)n#Simple_repeat 1 15 (9) m_b197s252i11 7723 chr4qtel1M 276909 AAAAAAAAAAAAAAA 276923 (A)n#Simple_r 1 AAAAAAAAAAAAAAA 15 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 14), avg. gap size = 0.0 (0 / 0) 27 0.00 0.00 0.00 chr4qtel1M 276924 276949 (723051) (G)n#Simple_repeat 1 26 (0) c_b197s251i0 7724 chr4qtel1M 276924 GGGGGGGGGGGGGGGGGGGGGGGGGG 276949 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGG 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 18 23.03 0.00 0.00 chr4qtel1M 277027 277063 (722937) (G)n#Simple_repeat 1 37 (0) m_b197s252i12 7725 chr4qtel1M 277027 GGGGGGCAAGGGGGGGGGGGAAAGGGGGGGGGGGAGG 277063 vii iii i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 37 Matrix = Unknown Transitions / transversions = 6.00 (6/1) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 185 32.68 4.76 0.92 chr4qtel1M 279118 279222 (720778) C L2d_3end#LINE/L2 (232) 284 176 m_b197s601i10 7720 chr4qtel1M 279118 AGGGGAGGCAGGAGTCC-TGTGGGACTGGGGTGATCCAGGAAGGCTTCTC 279166 i i v iii v- - i i vi vi C L2d_3end#LINE 284 AGAGAAGGGAGAGATCAGTGTGGG-CTGGAGTGGTCAGGGAAGGCTTCGT 236 chr4qtel1M 279167 AGAAGAGGAGGCTCCAGAACCGGG----GAAGGATTCGGGGGCCTCTGGT 279212 i i v vv iv i i ---- vv vi vi iv i C L2d_3end#LINE 235 GGAGGAGGTGGGACTTGAGCTGGGCCTTGAAGGATGGGTAGGATTTGGAT 186 chr4qtel1M 279213 AGACACAGGG 279222 v v i C L2d_3end#LINE 185 AGAGAGAGAG 176 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.14 CpG sites = 19, Kimura (unadjusted) = 44.14 Transitions / transversions = 1.27 (19/15) Gap_init rate = 0.03 (3 / 104), avg. gap size = 2.00 (6 / 3) 208 25.30 6.25 1.19 chr4qtel1M 279118 279197 (720803) C L2d2_3end#LINE/L2 (271) 284 201 m_b197s601i9 7720 chr4qtel1M 279118 AGGGGAGGCAGGAGTC-CTGTGGGACTGGGGTGATCCAGGAAGGCTTCTC 279166 i v iii - ?i - i i vi v C L2d2_3end#LIN 284 AGAGGAGGGAGAGATCACTNCGGG-CTGGAGTGGTCAGGGAAGGCTTCAC 236 chr4qtel1M 279167 AGAAGAGGAGGCTCCAGAACCGGG----GAAGGAT 279197 i i v ?viiv i i ---- C L2d2_3end#LIN 235 GGAGGAGGTGGNATTTGAGCTGGGCCTTGAAGGAT 201 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.35 CpG sites = 14, Kimura (unadjusted) = 33.37 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.04 (3 / 79), avg. gap size = 2.00 (6 / 3) 272 21.82 0.00 0.00 chr4qtel1M 279785 279839 (720161) C MIR3#SINE/MIR (38) 170 116 m_b197s601i11 7726 chr4qtel1M 279785 CTAGGAGGCCATCTGGGCCAACAGCCTCATTCTACAGACAAGTAAACTGA 279834 vi ii i v vv i ii v C MIR3#SINE/MIR 170 CTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGA 121 chr4qtel1M 279835 GGCCC 279839 C MIR3#SINE/MIR 120 GGCCC 116 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.21 CpG sites = 7, Kimura (unadjusted) = 26.21 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 126 24.21 0.00 0.00 chr4qtel1M 280158 280447 (719553) (TGTG)n#Simple_repeat 1 290 (0) m_b197s252i13 7727 chr4qtel1M 280158 TGTGTGAGTGCGAGTGTCTGTGTGAATGTGTGTGTGAATGTGTAAGCGTG 280207 v i v v vi vi iv i (TGTG)n#Simpl 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr4qtel1M 280208 AGTGTGAATATGATTGTGTGTGTCTGTGTGTGTGAGAGAGTGTCAGTGTG 280257 v vi i vv v v v v vv (TGTG)n#Simpl 51 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 100 chr4qtel1M 280258 AGTGGGTGTGTGAGTGTGAGTGTGGGTGTGTCAATGTGAGTGTGTGTGAT 280307 v v v v v vvi v vv (TGTG)n#Simpl 101 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 150 chr4qtel1M 280308 TGTGTCTGTGTGTAAGTGTATGTGTGAATGTGTGTTTGCGTGTGTGAATG 280357 v iv i vi v i vi (TGTG)n#Simpl 151 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 200 chr4qtel1M 280358 TGGGTGTGTCTGTGTGTGAATGTGAGCGTGTGTGTGTGATTGTATAAGTG 280407 v v vi v i vv i iv (TGTG)n#Simpl 201 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 250 chr4qtel1M 280408 TGTGTGTGTGTGTGTGTGTGGGCGTGTGGGAGTGGGTGTG 280447 v i v v v (TGTG)n#Simpl 251 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 290 Matrix = Unknown Transitions / transversions = 0.43 (18/42) Gap_init rate = 0.00 (0 / 289), avg. gap size = 0.0 (0 / 0) 22 6.68 0.00 0.00 chr4qtel1M 282003 282034 (717966) (CTC)n#Simple_repeat 1 32 (0) m_b197s252i15 7728 chr4qtel1M 282003 CTCCTCCTCCTCCTCCTCTTCCTCCTCCCCCT 282034 i i (CTC)n#Simple 1 CTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT 32 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 489 28.97 3.91 1.64 chr4qtel1M 282410 282588 (717412) MIR3#SINE/MIR 5 187 (21) m_b197s601i12 7729 chr4qtel1M 282410 CAGAG-GGTTTAGCACAGTGGGAGCACCGGTCTGGGAGCCAGCAGACGTG 282458 - i v v --i - v i v v MIR3#SINE/MIR 5 CAGAGTGGCTGAGCAGAG--AGAGCAC-GGACTGGGAGTCAGGAGACCTG 51 chr4qtel1M 282459 GGTTCAGATCCCATCTCAGATATTTCCTGGATAAGTGGCCCTGGTCGGGC 282508 vii iv v vi i vv ? v iv i i v ii i MIR3#SINE/MIR 52 GGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGT 101 chr4qtel1M 282509 AAGGAAAGCTTTCTTTGCCTCGGTTTCCTTCTCGGTAAAAT--AGGCATG 282556 v vvvv v i vv i iv v --i vi v MIR3#SINE/MIR 102 CACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTT 151 chr4qtel1M 282557 GGTCCAG----CCTCTCAGGTCCCTTCCAGTTCTAA 282588 v i ----i v i i MIR3#SINE/MIR 152 GGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGA 187 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.24 CpG sites = 23, Kimura (unadjusted) = 37.12 Transitions / transversions = 0.82 (23/28) Gap_init rate = 0.03 (6 / 178), avg. gap size = 1.67 (10 / 6) 15 14.63 11.32 0.00 chr4qtel1M 283043 283095 (716905) (AGGGGAG)n#Simple_repeat 1 59 (0) m_b197s252i16 7730 chr4qtel1M 283043 AGGGGA-AGAGG-GA-GGG-GATGGAAGA-GGAAAAGTGG-TAGGGGAGA 283086 - i - - - v i - i i v -v (AGGGGAG)n#Si 1 AGGGGAGAGGGGAGAGGGGAGAGGGGAGAGGGGAGAGGGGAGAGGGGAGA 50 chr4qtel1M 283087 GGGGAGAGG 283095 (AGGGGAG)n#Si 51 GGGGAGAGG 59 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.12 (6 / 52), avg. gap size = 1.00 (6 / 6) 129 21.44 2.88 4.90 chr4qtel1M 283416 283831 (716169) (AAGA)n#Simple_repeat 1 408 (0) m_b197s252i17 7731 chr4qtel1M 283416 AAG-AAGAAAGGAGAACAAGAAACAAAGAAAGAAAGAAACAAAG-AAGGA 283463 - - i iv v v - i (AAGA)n#Simpl 1 AAGAAAGAAA-GAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAA 49 chr4qtel1M 283464 AGAACAACAAG-AAGAACAGAACAAGAACAAGAAAGAAAGAAAAACAAG- 283511 - iv - - vi i iv i - - (AAGA)n#Simpl 50 AGAA-AGAAAGAAAGAA-AGAAAGAAAGAAAGAAAGAAAGAAAGA-AAGA 96 chr4qtel1M 283512 AAGAACATAAGAAGAAAAAGAAAAAAAGAAAGAAAGAAAGAAAGAAAGAA 283561 viv - i i (AAGA)n#Simpl 97 AAGAAAGAAAGAA-AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAA 145 chr4qtel1M 283562 AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG 283611 (AAGA)n#Simpl 146 AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG 195 chr4qtel1M 283612 AAAACAGGAGGAGGATGAGAG-GAGGAGGAAAGAGAGGAGAGGAAGAAAT 283660 iv i -i i v i -i i i - i i i v (AAGA)n#Simpl 196 AAAGAAAGA-AAGAAAGAAAGAAAGAAAGAAAGA-AAGAAAGAAAGAAAG 243 chr4qtel1M 283661 GGAGGGAGAGGGGAGAAGAGAGGAAAG-GAGAAA-AGAGAAAGAGGAATA 283708 ii ii -ii - - i -i - i -- v (AAGA)n#Simpl 244 AAAGAAAGA-AAGA-AAGA-AAGAAAGAAAGAAAGAAAGAAAGA--AAGA 288 chr4qtel1M 283709 GAGAAAGGAAAAGAGAGATGAATAG-GAGAGGAGAGGAGAAGAAAAGGAA 283757 i i i i - v - -i -i -i - i i (AAGA)n#Simpl 289 AAGAAAGAAAGAAAGA-AAGAA-AGAAAGA-AAGA-AAGAA-AGAAAGAA 333 chr4qtel1M 283758 GGGAAGGAAAGAGAAGAGA-AAAG-GGGAGAGTGAGAATG-AAGAGGAGA 283804 -i i - i - -ii i vi v - -i (AAGA)n#Simpl 334 -AGAAAGAAAGA-AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA-AAGA 380 chr4qtel1M 283805 GAGACAGAAAGACA-ACAGAGAGACAGA 283831 i v v - v i v (AAGA)n#Simpl 381 AAGAAAGAAAGAAAGAAAGAAAGAAAGA 408 Matrix = Unknown Transitions / transversions = 2.63 (50/19) Gap_init rate = 0.08 (32 / 415), avg. gap size = 1.00 (32 / 32) 268 29.22 5.56 1.79 chr4qtel1M 284127 284234 (715766) MIRc#SINE/MIR 82 193 (75) m_b197s601i13 7732 chr4qtel1M 284127 TAGTAGTGTGATACTGGGTATGTCAC---ACCCCTATCTGCCTCAGTTTC 284173 iv ivi i v --- i v vv MIRc#SINE/MIR 82 TAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTC 131 chr4qtel1M 284174 TCTTCCTGTGTAATGGGTATATTAAT--CTGTTCAGAGAGCAGCTCACAG 284221 iiivi iv v v -- ii --v vvi v MIRc#SINE/MIR 132 CTCATCTGTAAAATGGGGATAATAATACCTGCCC--TGCCTACCTCACAG 179 chr4qtel1M 284222 GG-TGGTATAAGAA 284234 - v i i i MIRc#SINE/MIR 180 GGTTGTTGTGAGGA 193 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.61 CpG sites = 16, Kimura (unadjusted) = 37.61 Transitions / transversions = 1.07 (16/15) Gap_init rate = 0.05 (5 / 107), avg. gap size = 1.60 (8 / 5) 239 30.19 1.89 12.50 chr4qtel1M 284363 284468 (715532) C MIR3#SINE/MIR (23) 185 90 m_b197s601i14 7733 chr4qtel1M 284363 AGAAAGGGGAGGGGCCTAAGGGGTCATTTGATCCAAGAGGGGATCCTCAA 284412 ivv i i v i i i ii -------i i -- C MIR3#SINE/MIR 185 AGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAA-------CCCCC-- 145 chr4qtel1M 284413 GGGTTATCTTATTGAGGCAAAAAC--AGGCCCAGGGAAGAGCAATGACTT 284460 --- i i iv v vii -- i i v v i C MIR3#SINE/MIR 144 ---TCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTT 98 chr4qtel1M 284461 GATCAAGG 284468 vi C MIR3#SINE/MIR 97 GCCCAAGG 90 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.97 CpG sites = 19, Kimura (unadjusted) = 39.97 Transitions / transversions = 2.11 (19/9) Gap_init rate = 0.12 (13 / 105), avg. gap size = 1.08 (14 / 13) 61 14.04 3.05 2.27 chr4qtel1M 285030 285160 (714840) (AGAGAC)n#Simple_repeat 1 132 (0) m_b197s252i18 7734 chr4qtel1M 285030 AGAGACAGAGACAGAGATAGGGACAAAGATAGAGA-GGTGA-AGAGAC-- 285075 i i i i -i v - -- (AGAGAC)n#Sim 1 AGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAG 50 chr4qtel1M 285076 AGATAGAGACAGAGAAACAGACAGACAGACAGACACAGAGAGAGACAGAG 285125 i v v v v v v v (AGAGAC)n#Sim 51 AGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAG 100 chr4qtel1M 285126 ACAGAAACAGAGAAACAGAGACAGAGATAGAAGAC 285160 i -- i - (AGAGAC)n#Sim 101 ACAGAGACAGAG--ACAGAGACAGAGACAG-AGAC 132 Matrix = Unknown Transitions / transversions = 1.00 (8/8) Gap_init rate = 0.05 (6 / 130), avg. gap size = 1.17 (7 / 6) 186 29.83 0.00 1.75 chr4qtel1M 286059 286116 (713884) C MIRc#SINE/MIR (89) 179 123 m_b197s601i15 7735 chr4qtel1M 286059 CTGTGAAGGAAGAACCATAGGAGCTGCTCACCCCATTGTACAGATGAGGA 286108 i v i v vvii vii ii vv v C MIRc#SINE/MIR 179 CTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGA 130 chr4qtel1M 286109 GAATTGAG 286116 - i C MIRc#SINE/MIR 129 -AACTGAG 123 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.69 CpG sites = 9, Kimura (unadjusted) = 38.69 Transitions / transversions = 1.12 (9/8) Gap_init rate = 0.02 (1 / 57), avg. gap size = 1.00 (1 / 1) 303 34.34 7.12 2.95 chr4qtel1M 286306 286923 (713077) L1P3_orf2#LINE/L1 2644 3286 (8) m_b197s551i0 7736 chr4qtel1M 286306 ACAGTCATCAAAACCACTTGGTGCTGGCTGAGAAATAGAGCAATGGATCA 286355 v i vi v i ivvvi i vvv i i L1P3_orf2#LIN 2644 ACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGATATATAGACCA 2693 chr4qtel1M 286356 GTGGAATAGGTTCAG----CTCACAAGACACAATAGTCA-ATGACTATAA 286400 i i iv- ---- --- v i i- i - iiv i L1P3_orf2#LIN 2694 ATGGAACAGAA-CAGAGGCCTCA---GAAATAAC-GCCACACATCTACAA 2738 chr4qtel1M 286401 TAACCCAGTGTTTGGTAAACC---CAAAGACCTCAGCTCTGGGATAAGAA 286447 iv i iii v ii --- i v-- vv iv i L1P3_orf2#LIN 2739 CCATCTGATCTTTGACAAACCTGACAAAAACA--AGCAATGGGGAAAGGA 2786 chr4qtel1M 286448 --CCCTATCTGACAAAAAACTGCTGGGAAAATTGGAAACTAG---TATGG 286492 -- i i i vii- i i --- --- - L1P3_orf2#LIN 2787 TTCCCTATTTAATAAATGG-TGTTGGGAAAACTGG---CTAGCCATAT-G 2831 chr4qtel1M 286493 CAGAAACTAGGCATTGG-CGCACACCTAGCACTTTATACCAAGGTAAGGT 286541 viv iv i - v viv vi i v ii v iv L1P3_orf2#LIN 2832 CAGAAAACTGAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAACT 2881 chr4qtel1M 286542 TGAAATGGGTTCAAGATTTAGTCATAAAAGGTGATGCTATAAGCAAACTA 286591 ii i i v i iv i i vv i vi i iv vv L1P3_orf2#LIN 2882 CAAGATGGATTAAAGACTTAAACGTAAGACCTAAAACCATAAAAACCCTA 2931 chr4qtel1M 286592 GGAGAACA-AGGGGCAGTCCACCTTTCAGATCTTTGGAGAAGGGC--AGA 286638 i v -vvi i -- v iv v v -v v -- L1P3_orf2#LIN 2932 GAAGAAAACCTAGGCAAT--ACCATTCAGGACATAGG-CATGGGCAAAGA 2978 chr4qtel1M 286639 ATTTATGAC------------ATTTAT-GCATGAAATG-CAAAATGGATA 286674 v i ------------ viv - vv v - v i L1P3_orf2#LIN 2979 CTTCATGACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACA 3028 chr4qtel1M 286675 ATTTTGATTACATTCAATTAAAACTGTTTTGTA---CAAACAAAACTAAT 286721 v vv ivv v i ivvv i i --- vi -- L1P3_orf2#LIN 3029 AATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTA-- 3076 chr4qtel1M 286722 GCAGCCAAGATTACAAAGGAGGCAGAAAG-GTGGGGGAAAGATTTTG--- 286767 v v -- v iv v vii vv v -i i iv --- L1P3_orf2#LIN 3077 TCATC--AGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAA 3124 chr4qtel1M 286768 ------TTTCTGCTAAAGACTTTATTTCTAAAATATATAGAGAATAGACT 286811 ------iv vi ivi v v i i v i ii ivv vv L1P3_orf2#LIN 3125 TCTATCCATCTGACAAAGGGCTAATATCCAGAATCTACAAGGAACTTAAA 3174 chr4qtel1M 286812 CAAATTTATAAGAATACAGGCCATTTCCCAAATGATAAATGGTCAAAGAA 286861 i v v ivvv ivv v vii v i v i i L1P3_orf2#LIN 3175 CAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGA 3224 chr4qtel1M 286862 TATGAACAGACAATTTTCAGATGAAGAAATTAAAGTCATTTCTAGTTACT 286911 v i i v v v v iviiivvi ivi iv L1P3_orf2#LIN 3225 TATGAACAGACACTTCTCAAAAGAAGACATTTATGCGGCCAACAAACATA 3274 chr4qtel1M 286912 TGAAAAAAAGCT 286923 L1P3_orf2#LIN 3275 TGAAAAAAAGCT 3286 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 45.54 CpG sites = 102, Kimura (unadjusted) = 46.76 Transitions / transversions = 0.98 (102/104) Gap_init rate = 0.06 (34 / 617), avg. gap size = 1.85 (63 / 34) 1122 34.12 1.83 0.36 chr4qtel1M 286782 287328 (712672) L1ME4c_3end#LINE/L1 1 555 (275) m_b197s551i1 7736 chr4qtel1M 286782 TTTATTTCTAAAATATATAGAGAATAGACTCAAATTTATAAGAATACAGG 286831 v v ?v ? i iivv i v v v?iv L1ME4c_3end#L 1 TTAATATCTNTANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANAT 50 chr4qtel1M 286832 CCATTTCCCAAATGATAAATGGTCAAAGAATATGAACAGACAATTTTCAG 286881 v vvi vv v i i iv ? L1ME4c_3end#L 51 CAAGACCCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACAN 100 chr4qtel1M 286882 ATGAAGAAATTAAAGTCATTTCTAGTTACTTGAAAAAAAGCTTGAAATCA 286931 v i vv ? vi vvvi ivi v i v i ii vv i L1ME4c_3end#L 101 AAGAGGAAATACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCG 150 chr4qtel1M 286932 CTGTTGATTAGATCAATGCAAATTAAGACAACTCTGAAGTACCATTTCAC 286981 iv i i i vv ii vv ii i L1ME4c_3end#L 151 CTAGTAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTAC 200 chr4qtel1M 286982 ACCTCTCAGATC-GCTAAAATGACAGGAAAGGCTAATGATGAATGTTGGA 287030 i v i i i- v vvv ii vv v iviv i v L1ME4c_3end#L 201 GCCTATTAAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGCTGGC 250 chr4qtel1M 287031 GGGGATGTGGGAAAACTGGGACACCGGTGCATTGTTGGTGGAGTTGTGAA 287080 i ? i vi v ? ivi i i vi? i L1ME4c_3end#L 251 GAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAA 300 chr4qtel1M 287081 CGGATCCAGCCATTCTGGAGAGCGATCTGGAACGATGCTCAAAGGGCTTT 287130 iv i v i v i i i i v vv i iviv i iv L1ME4c_3end#L 301 TTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCAT 350 chr4qtel1M 287131 GAAACTGTGCATATTCTTGGGTC--------TCACTACTAGGTCTGTATT 287172 i v v ii v ii --------i v i vv v i L1ME4c_3end#L 351 AAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATC 400 chr4qtel1M 287173 CCAAAAAGATCATA-AAGAGAGGGGAAAGGACCCACATATGCAAAGATGT 287221 i ii i v v- i i i i -- i i iii i L1ME4c_3end#L 401 CTAAGGAAATAATTCAAAAGAAGGAAAAAG--CTATATGCACGAAGATGT 448 chr4qtel1M 287222 TTGTGGCAGCTCTTTTTATGGTGGCAAGAAACTGGAGCCTGAGTGGCTGC 287271 ii v vi v ii i i i i iv vivv iiv i L1ME4c_3end#L 449 TCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGT 498 chr4qtel1M 287272 CCGTCTGCTGGGGAACGGCTGAATAAGCTGTGGTTCATGAATGCGATGGG 287321 iv viiv i i i i ii i v v? iv i L1ME4c_3end#L 499 CCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGA 548 chr4qtel1M 287322 ATATTAT 287328 L1ME4c_3end#L 549 ATATTAT 555 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 46.05 CpG sites = 106, Kimura (unadjusted) = 48.21 Transitions / transversions = 1.32 (106/80) Gap_init rate = 0.01 (5 / 546), avg. gap size = 2.40 (12 / 5) 19 17.49 0.00 0.00 chr4qtel1M 288875 288907 (711093) (G)n#Simple_repeat 1 33 (0) m_b197s252i19 7737 chr4qtel1M 288875 GGGGGGGGGGAGGGGAGGGGGGGGGAATGGGGG 288907 i i iiv (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 33 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 200 33.33 0.00 0.00 chr4qtel1M 289429 289485 (710515) L2c_3end#LINE/L2 421 477 (1) m_b197s601i16 7738 chr4qtel1M 289429 TGTCCCCAGCTCCTGGCACACAGCGGGCATTTATGACGTGCATGTGGAGT 289478 i v i ii ii i vv vi iv v i L2c_3end#LINE 421 TATCCCCAGCGCCTGGCACATAGTAGGCGCTCAATAAATGTTTGTTGAAT 470 chr4qtel1M 289479 GTGCGAA 289485 vii L2c_3end#LINE 471 GAATGAA 477 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.95 CpG sites = 12, Kimura (unadjusted) = 46.29 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0) 12 17.10 2.22 6.98 chr4qtel1M 289666 289710 (710290) (GTGTGGG)n#Simple_repeat 1 43 (0) m_b197s252i20 7739 chr4qtel1M 289666 GTGT-GGGTGTGGGGTGGGAAGGGGCTGGGGGATGGGTGAGTGGGG 289710 - v -- vv vi - v (GTGTGGG)n#Si 1 GTGTGGGGTGTGGGGTGTG--GGGTGTGGGGTGTGGG-GTGTGGGG 43 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4) 19 16.87 8.33 0.00 chr4qtel1M 289686 289745 (710255) (GGGGATG)n#Simple_repeat 1 65 (0) m_b197s252i21 7739 chr4qtel1M 289686 GGGGCTGGGGGATGGGTGAGTGGGGAT---GGCTGGGGGAAGGGGG--GT 289730 v v vv --- v v -- v (GGGGATG)n#Si 1 GGGGATGGGGGATGGGGGATGGGGGATGGGGGATGGGGGATGGGGGATGG 50 chr4qtel1M 289731 AGCATGGGGGATGGG 289745 i v (GGGGATG)n#Si 51 GGGATGGGGGATGGG 65 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.03 (2 / 59), avg. gap size = 2.50 (5 / 2) 215 17.95 0.00 0.00 chr4qtel1M 289992 290030 (709970) C L2c_3end#LINE/L2 (11) 467 429 m_b197s601i17 7740 chr4qtel1M 289992 CAACAAGCATTGTTTTGGCGCCTGCTGTGTGCCAGGCGC 290030 i vv vi i i C L2c_3end#LINE 467 CAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGC 429 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 20.74 CpG sites = 4, Kimura (unadjusted) = 20.74 Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 16 25.18 6.06 0.00 chr4qtel1M 291076 291141 (708859) (AGGGGG)n#Simple_repeat 1 70 (0) m_b197s252i23 7741 chr4qtel1M 291076 AGGGGG-GGGGGAGGGCG-GCGGCAGCGGGACACGGTGGGGGA-GGGGAG 291122 - v - v v v viv v - (AGGGGG)n#Sim 1 AGGGGGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGGAG 50 chr4qtel1M 291123 GCCG-GGGGCGGGGCGCGGG 291141 vv - vi v v (AGGGGG)n#Sim 51 GGGGAGGGGGAGGGGGAGGG 70 Matrix = Unknown Transitions / transversions = 0.17 (2/12) Gap_init rate = 0.06 (4 / 65), avg. gap size = 1.00 (4 / 4) 202 32.51 13.17 2.58 chr4qtel1M 292396 292676 (707324) L2#LINE/L2 2368 2677 (405) m_b197s601i18 7742 chr4qtel1M 292396 CTCTCAGACTGCCAACCTCGCCAGCCCCAACGGCCCTTCAGACGTCTCAA 292445 i iiii - iv i- vvi v iviiv i v L2#LINE/L2 2368 CCCCTGAACT-CCAGACTCGT-ATATCCAACTGCCTACTCGACATCTCCA 2415 chr4qtel1M 292446 -ACGGATGGCCAGTGGCCACCTGAGACCCAATGGGTCCAAACCAGAACTC 292494 -vi v i i i v i v i ii iiv v v L2#LINE/L2 2416 CTTGGATGTCTAATAGGCATCTCAAACTTAACATGTCCAAAACTGAACTC 2465 chr4qtel1M 292495 CCCATC------------CCTG-----------ACCTTCCCTA------- 292514 iv ------------ -----------ii i ------- L2#LINE/L2 2466 CTGATCTTCCCCCTCAAACCTGCTCCTCCCGCAGTCTTCCCCATCTCAGT 2515 chr4qtel1M 292515 CAGGGGCCACCCCCGTCCTCCTGTCCCTCAGGCTCCCAACCTAGGACTCA 292564 ? iv v i vvi i v iv ivvv v v L2#LINE/L2 2516 NAATGGCAACTCCATCCTTCCAGTTGCTCAGGCCAAAAACCTTGGAGTCA 2565 chr4qtel1M 292565 TCATGGCCTC--CTTATTCTCTCACCCCCCAGATCCAATATGACACCACA 292612 v v v -- iv v v viiv v v L2#LINE/L2 2566 TCCTTGACTCCTCTCTTTCTCTCACACCCCACATCCAATCCATCAGCAAA 2615 chr4qtel1M 292613 GCCTGTC--CCCTGACCCTCGGCAGCATCTCTCCTGTATGCAGCCCTCTC 292660 v -- i - i --- iv v v v v v ii vii L2#LINE/L2 2616 TCCTGTCGGCTCT-ACCTT---CAAAATATATCCAGAATCCGACCACTTC 2661 chr4qtel1M 292661 CCCTCTGACCT--ACTGC 292676 i vi -- -- L2#LINE/L2 2662 TCACC--ACCTCCACTGC 2677 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.97 CpG sites = 44, Kimura (unadjusted) = 43.61 Transitions / transversions = 0.98 (44/45) Gap_init rate = 0.05 (15 / 280), avg. gap size = 3.00 (45 / 15) 91 30.77 3.75 2.17 chr4qtel1M 292885 293337 (706663) (GTCTCT)n#Simple_repeat 1 460 (0) m_b197s252i24 7743 chr4qtel1M 292885 GTCCCTGTC-CAGTCTCCAGAC-CTCCCTCTG-CT-TGTCTCTGTCTCCC 292930 i - v - v v - vi - - iv (GTCTCT)n#Sim 1 GTCTCTGTCTCTGTCT-CTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTG 49 chr4qtel1M 292931 TCTCTATCTC-CT-TCTTCCTCTGTTTCCATCTCCCTAAATCTCTCCCTC 292978 i -v - vi i - - v i ivv v i v (GTCTCT)n#Sim 50 TCTCTGTCTCTGTCTCTGTCTCTGTCT-C-TGTCTCTGTCTCTGTCTCTG 97 chr4qtel1M 292979 TTGCTGTGTCTGTCTTTGTCTC--TCTCTGGCTCCATCTCTATCTCTCTT 293026 iv v i -- v ii i v i (GTCTCT)n#Sim 98 TCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTC 147 chr4qtel1M 293027 CCTGTTTCCATCT-T-CCTCTGTGTGTCTCTATGTCTCTCTCTCTTTTTA 293074 i i ii - -i v v v v v v i v (GTCTCT)n#Sim 148 TCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTC 197 chr4qtel1M 293075 TCCCCCCGCCTCTTTCTTTTTTGCTCCATTTCCCTCTGTGTGTCTGTCTC 293124 vi i i i v - i v - ii i iv v v (GTCTCT)n#Sim 198 TGTCTCTGTCTCTGTC-TCTGT-CTCTGTCTCTGTCTCTGTCTCTGTCTC 245 chr4qtel1M 293125 CCTCTGTCTCTCCACCCCTTCCTCTGTCCCTCTGTCTGTCTC--CCCATT 293172 iv v v iii i vi i v v --i iv v (GTCTCT)n#Sim 246 TGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTG 295 chr4qtel1M 293173 TCTCTCCATCTTTCTCTATCTCTGTCTCCATCTCTCTTTCTCTC-CTTTC 293221 viv v i ii v i v - v (GTCTCT)n#Sim 296 TCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTC 345 chr4qtel1M 293222 TCTATCT-TGTTCCATCTCGCTGTTTCTGTCTGCCTCCATCTGTCT-TGT 293269 i - - iv v v i -- viv - (GTCTCT)n#Sim 346 TCTGTCTCTG-TCTCTGTCTCTGTCTCTGTCT--CTGTCTCTGTCTCTGT 392 chr4qtel1M 293270 CTC--CCTCCGTCTTTGTTTCTCCATCTTTTTCTGTCTCTGTCTACGTCT 293317 --i i i i viv v i vi (GTCTCT)n#Sim 393 CTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCT 442 chr4qtel1M 293318 CTGTCTGTTTCCCTCTGTCT 293337 v v -- (GTCTCT)n#Sim 443 CTGTCTCTGT--CTCTGTCT 460 Matrix = Unknown Transitions / transversions = 1.02 (55/54) Gap_init rate = 0.05 (24 / 452), avg. gap size = 1.12 (27 / 24) 97 36.46 0.69 0.69 chr4qtel1M 292906 293337 (706663) (CTCT)n#Simple_repeat 1 432 (0) m_b197s252i25 7743 chr4qtel1M 292906 CTCCCTCTGCT-TGTCTCTGTCTCCCTCTCTATCTCCTTCTTCCTCTGTT 292954 i - - v v i v ii ii v i (CTCT)n#Simpl 1 CTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 49 chr4qtel1M 292955 TCCATCTCCCTAAATCTCTCCCTCTTGCTGTGTCTGTCTTTGTCTCTCTC 293004 iv i vvv i iv v v v i v (CTCT)n#Simpl 50 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 99 chr4qtel1M 293005 TGGCTCCATCTCTATCTCTCTTCCTGTTTCCATCTTCCTCTGTGTGTCTC 293054 vv iv v ii v i iv ii v v v (CTCT)n#Simpl 100 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 149 chr4qtel1M 293055 TATGTCTCTCTCTCTTTTTATCCCCCCGCCTCTTTCTTTTTTGCTCCATT 293104 v v i i v i i ivi i i i iv iv i (CTCT)n#Simpl 150 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 199 chr4qtel1M 293105 TCCCTCTGTGTGTCTGTCTCCCTCTGTCTCTCCACCCCTTCCTCTGTCCC 293154 i v v v v i v ivi i ii v i (CTCT)n#Simpl 200 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 249 chr4qtel1M 293155 TCTGTCTGTCTCCCCATTTCTCTCCATCTTTCTCTATCTCTGTCTCCATC 293204 v v i iv i iv i v v iv (CTCT)n#Simpl 250 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 299 chr4qtel1M 293205 TCTCTTTCTCTC-CTTTCTCTATCTTGTTCCATCTCGCTGTTTCTGTCTG 293253 i - i v ivi iv v v i v v (CTCT)n#Simpl 300 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 349 chr4qtel1M 293254 CCTCCATCTGTCT-TGTCTCCCTCCGTCTTTGTTTCTCCATCTTTTTCTG 293302 i iv v - v i iv i v i iv i i v (CTCT)n#Simpl 350 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 399 chr4qtel1M 293303 TCTCTGTCTACGTCTCTGTCTGTTTCCCTCTGTCT 293337 v - - v v i i v (CTCT)n#Simpl 400 TCTCTCTCT-C-TCTCTCTCTCTCTCTCTCTCTCT 432 Matrix = Unknown Transitions / transversions = 1.03 (62/60) Gap_init rate = 0.01 (6 / 431), avg. gap size = 1.00 (6 / 6) 246 30.34 5.62 0.00 chr4qtel1M 294099 294187 (705813) MIR1_Amn#SINE/MIR 86 179 (51) m_b197s601i20 7744 chr4qtel1M 294099 GCTGTGTATCCCTGGGAAACTTATTTAA--TCTCTGAGCTTCCATTTCTT 294146 ? iv i v v i i ? -- ? i vi i MIR1_Amn#SINE 86 GCTGNGTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCT 135 chr4qtel1M 294147 TGTCTCTAGGATGGGAACCAC--CACC-ACCCCCTTGGAAGAAT 294187 ii v ii i iv i--i i- i v v i i MIR1_Amn#SINE 136 CATCTGTAAAATGGGGATAATGATACTGACCTCCTTTGTAAAGT 179 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.42 CpG sites = 19, Kimura (unadjusted) = 43.42 Transitions / transversions = 2.38 (19/8) Gap_init rate = 0.03 (3 / 88), avg. gap size = 1.67 (5 / 3) 271 24.62 3.08 0.00 chr4qtel1M 294099 294163 (705837) MIRb#SINE/MIR 87 153 (115) m_b197s601i19 7744 chr4qtel1M 294099 GCTGTGTATCCCTGGGAAACTTATTTAA--TCTCTGAGCTTCCATTTCTT 294146 iv i v v i -- i vi i MIRb#SINE/MIR 87 GCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCT 136 chr4qtel1M 294147 TGTCTCTAGGATGGGAA 294163 ii v ii i MIRb#SINE/MIR 137 CATCTGTAAAATGGGGA 153 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.02 CpG sites = 11, Kimura (unadjusted) = 31.02 Transitions / transversions = 2.20 (11/5) Gap_init rate = 0.02 (1 / 64), avg. gap size = 2.00 (2 / 1) 14 27.80 1.92 0.00 chr4qtel1M 294223 294274 (705726) (ACCCCC)n#Simple_repeat 1 53 (0) m_b197s252i26 7745 chr4qtel1M 294223 ACTCCCAACTCCAGCCTGGCCCCC-CTCCCTGCCTCACCCCCACCCCCTC 294271 i v i v ivi - i vv i v (ACCCCC)n#Sim 1 ACCCCCACCCCCACCCCCACCCCCACCCCCACCCCCACCCCCACCCCCAC 50 chr4qtel1M 294272 CCC 294274 (ACCCCC)n#Sim 51 CCC 53 Matrix = Unknown Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.02 (1 / 51), avg. gap size = 1.00 (1 / 1) 17 20.59 0.00 0.00 chr4qtel1M 295201 295234 (704766) (C)n#Simple_repeat 1 34 (0) m_b197s252i27 7746 chr4qtel1M 295201 CCCCCACCCCCCCCCCCAGCCCCCGGGCCCCCCC 295234 v vv vvv (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 34 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 46 0.00 0.00 0.00 chr4qtel1M 295584 295622 (704378) (CA)n#Simple_repeat 1 39 (0) c_b197s251i1 7747 chr4qtel1M 295584 CACACACACACACACACACACACACACACACACACACAC 295622 (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACAC 39 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 237 21.28 0.00 0.00 chr4qtel1M 296209 296255 (703745) C MIRc#SINE/MIR (60) 208 162 m_b197s601i21 7748 chr4qtel1M 296209 CACTTTATTAGCTGTCCCTCACAACATCCCTGTGAGGTAGGCGGGGC 296255 i v v i vi vi v i C MIRc#SINE/MIR 208 CATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGC 162 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 25.20 CpG sites = 5, Kimura (unadjusted) = 25.20 Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 17 18.53 0.00 0.00 chr4qtel1M 297453 297483 (702517) (C)n#Simple_repeat 1 31 (0) m_b198s252i0 7749 chr4qtel1M 297453 CCCCCCCCAGCCCACCCCCGCCCCCCCCACC 297483 vv v v v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 31 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 15 5.48 0.00 0.00 chr4qtel1M 299743 299761 (700239) (A)n#Simple_repeat 1 19 (0) m_b198s252i1 7750 chr4qtel1M 299743 AAAAAAAAAAACAAAAAAA 299761 v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAA 19 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 28 8.34 0.00 0.00 chr4qtel1M 300758 300795 (699205) (C)n#Simple_repeat 1 38 (0) m_b198s252i2 7751 chr4qtel1M 300758 CCCCACCCCCCCCCCCACCCCCCCCCTCCCCCCCCCCC 300795 v v i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 38 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 21 20.39 0.00 0.00 chr4qtel1M 301528 301567 (698433) (C)n#Simple_repeat 1 40 (0) m_b198s252i3 7752 chr4qtel1M 301528 CCCCCCGCCCGGGACCCGCCCCCGCCCCCCCCCCCCCCCC 301567 v vvvv v v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 40 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 226 20.01 0.00 2.00 chr4qtel1M 304075 304125 (695875) C L2#LINE/L2 (603) 2479 2430 m_b198s601i1 7753 chr4qtel1M 304075 AGGGGGAGGGACCACGAGTTCTGCTTTGGACCTGGGGAGTTTAAGATGCC 304124 i - i v v i v vvi i C L2#LINE/L2 2479 AGGGGGAAG-ATCAGGAGTTCAGTTTTGGACATGTTAAGTTTGAGATGCC 2431 chr4qtel1M 304125 T 304125 C L2#LINE/L2 2430 T 2430 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 23.41 CpG sites = 5, Kimura (unadjusted) = 23.41 Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.02 (1 / 50), avg. gap size = 1.00 (1 / 1) 21 4.13 0.00 0.00 chr4qtel1M 305362 305386 (694614) (C)n#Simple_repeat 1 25 (0) m_b198s252i4 7754 chr4qtel1M 305362 CCGCCCCCCCCCCCCCCCCCCCCCC 305386 v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCC 25 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 333 29.07 8.11 0.84 chr4qtel1M 306547 306657 (693343) MIRb#SINE/MIR 35 153 (115) m_b198s601i2 7755 chr4qtel1M 306547 GGCTT---AGCTAGAAGGGTCTGCCTGGAAACCCCAGCTCTGCCTCTGCC 306593 --- ii vi ii vv vvi i i v vv MIRb#SINE/MIR 35 GGCTTTGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTAC 84 chr4qtel1M 306594 TA----CATGACTATAGGCAAGTTGTTT--TTCCTTTGGCCCTCAGTTTC 306637 ----ii iv i ii --iii i iv MIRb#SINE/MIR 85 TAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTC 134 chr4qtel1M 306638 CCTCATTTGTGAAATGAGGA 306657 - i i i MIRb#SINE/MIR 135 C-TCATCTGTAAAATGGGGA 153 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.66 CpG sites = 22, Kimura (unadjusted) = 38.77 Transitions / transversions = 2.20 (22/10) Gap_init rate = 0.04 (4 / 110), avg. gap size = 2.50 (10 / 4) 409 27.04 5.69 0.78 chr4qtel1M 306573 306695 (693305) MIR3#SINE/MIR 58 186 (22) m_b198s601i3 7755 chr4qtel1M 306573 AACCCCAGCTCTGCCTCTGCCTA----CATGACTATAGGCAAGTTGTTTT 306618 ii i v iv ?----ii iv i iii i MIR3#SINE/MIR 58 AGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTC 107 chr4qtel1M 306619 TCCTTT--GGCCCTCAGTTTCCCTCATTTGTGAAATGAGGAAGTTGGACA 306666 v i -- v - i i ii v MIR3#SINE/MIR 108 ACCTCTCTGGGCCTCAGTTTCC-TCATCTGTAAAATGAGGGGGTTGGACT 156 chr4qtel1M 306667 TTATGACCTC-AGTGCTCTTCCCAGGTCTG 306695 vv i - iv ii i i v MIR3#SINE/MIR 157 AGATGATCTCTAAGGTCCCTTCCAGCTCTG 186 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.22 CpG sites = 23, Kimura (unadjusted) = 35.59 Transitions / transversions = 2.30 (23/10) Gap_init rate = 0.03 (4 / 122), avg. gap size = 2.00 (8 / 4) 202 29.87 4.49 2.20 chr4qtel1M 307124 307212 (692788) C L2#LINE/L2 (0) 3082 2992 m_b198s601i4 7756 chr4qtel1M 307124 GGAGAGAGAGTGTTCCAGGTCCAGAGAACAGTCAGAGAGAATGCCCGTGA 307173 i ii i ivv i iv v vi v - C L2#LINE/L2 3082 GGGGGAAGAGCGTTCCAGGCAGAGGGAACAGCAAGTGCAAAGGCCC-TGA 3034 chr4qtel1M 307174 CTGAGAGATGAAGTCT----TGTTCAAGGAGTAGCCAGGAGGC 307212 -v v i vviv i ---- i ii v C L2#LINE/L2 3033 -GGCGGGAGCGTGCCTGGCGTGTTCGAGGAACAGCAAGGAGGC 2992 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.42 CpG sites = 14, Kimura (unadjusted) = 38.86 Transitions / transversions = 1.17 (14/12) Gap_init rate = 0.03 (3 / 88), avg. gap size = 2.00 (6 / 3) 16 18.31 3.77 3.77 chr4qtel1M 307556 307608 (692392) (TGACAT)n#Simple_repeat 1 53 (0) m_b198s252i5 7757 chr4qtel1M 307556 TGACACTGACATTGACATCGACA-AGAGATGTTCCA-AGAGAGTTGACAT 307603 i i -v v - vv -v v - (TGACAT)n#Sim 1 TGACATTGACATTGACATTGACATTGACAT-TGACATTGACA-TTGACAT 48 chr4qtel1M 307604 TGACA 307608 (TGACAT)n#Sim 49 TGACA 53 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.08 (4 / 52), avg. gap size = 1.00 (4 / 4) 306 19.73 9.76 1.12 chr4qtel1M 308497 308578 (691422) L3#LINE/CR1 3907 3995 (104) m_b198s601i5 7758 chr4qtel1M 308497 AACAATC----TTGCTAAGAGGCAGAATCGGCTGCCT--GTAGATAGTGA 308540 ----i iiv i iiii v --?v i L3#LINE/CR1 3907 AACAATCAGAGCTGTCCAAAAATGGAATGGGCTGCCTCGNGAGGTAGTGA 3956 chr4qtel1M 308541 GCTCCCTGTCAGTGGAGGGTATTCAAGCAGT--CTGGATG 308578 i v - i v-- L3#LINE/CR1 3957 GCTCCCCGTCACTGGA-GGTGTTCAAGCAGAGGCTGGATG 3995 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 22.26 CpG sites = 11, Kimura (unadjusted) = 23.93 Transitions / transversions = 2.20 (11/5) Gap_init rate = 0.05 (4 / 81), avg. gap size = 2.25 (9 / 4) 242 31.51 5.48 0.00 chr4qtel1M 309859 309931 (690069) C MIR3#SINE/MIR (16) 192 116 m_b198s601i6 7759 chr4qtel1M 309859 GAAGGCTGATGCAGGAAATGACCTCAGAGACCCTCTGTCCCGGCCC---- 309904 v iiiiv v iv i i v ivi ii ---- C MIR3#SINE/MIR 192 GAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTC 143 chr4qtel1M 309905 ATCTTCCAGATGGGAAAGCTGAGGTCC 309931 i v i i i i C MIR3#SINE/MIR 142 ATTTTACAGATGAGGAAACTGAGGCCC 116 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.53 CpG sites = 16, Kimura (unadjusted) = 43.53 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.01 (1 / 72), avg. gap size = 4.00 (4 / 1) 301 24.09 3.57 1.16 chr4qtel1M 310137 310220 (689780) MIRc#SINE/MIR 40 125 (143) m_b198s601i7 7760 chr4qtel1M 310137 AGTCAGAAAGGCCCGAGTTCGGATCCCGCCTTTGGCAGTTGCTGCCTGGG 310186 i i i i ii v i v v i iv v MIRc#SINE/MIR 40 AGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTG 89 chr4qtel1M 310187 TGAGCCCTGAGCACGGC-CTTGA--GCTCTGAGCCTC 310220 - i i v v - i --v MIRc#SINE/MIR 90 TGA-CCTTGGGCAAGTCACTTAACCTCTCTGAGCCTC 125 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.70 CpG sites = 12, Kimura (unadjusted) = 29.70 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.04 (3 / 83), avg. gap size = 1.33 (4 / 3) 19 4.50 0.00 0.00 chr4qtel1M 310614 310636 (689364) (G)n#Simple_repeat 1 23 (0) m_b198s252i6 7761 chr4qtel1M 310614 GGGGGGCGGGGGGGGGGGGGGGG 310636 v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGG 23 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 26 2.69 2.38 4.88 chr4qtel1M 313330 313371 (686629) (GGGACTG)n#Simple_repeat 1 41 (0) c_b198s251i0 7762 chr4qtel1M 313330 GGGACTGGGGATTGGGGAC-GGGGACTGGGGACCTCGGGGACT 313371 i - - - (GGGACTG)n#Si 1 GGGACTGGGGACTGGGGACTGGGGACTGGGGA-CT-GGGGACT 41 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.07 (3 / 41), avg. gap size = 1.00 (3 / 3) 57 3.20 1.56 0.00 chr4qtel1M 313656 313719 (686281) (GGCGGAG)n#Simple_repeat 1 65 (0) c_b198s251i1 7763 chr4qtel1M 313656 GGCGGAGGGCGGAGGG-GCCGGGCGGAGGGCGGAGGGCGGAGGGCGGAGG 313704 - vv (GGCGGAG)n#Si 1 GGCGGAGGGCGGAGGGCGGAGGGCGGAGGGCGGAGGGCGGAGGGCGGAGG 50 chr4qtel1M 313705 GCGGAGGGCGGAGGG 313719 (GGCGGAG)n#Si 51 GCGGAGGGCGGAGGG 65 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.02 (1 / 63), avg. gap size = 1.00 (1 / 1) 16 13.43 0.00 2.94 chr4qtel1M 313956 313990 (686010) (GGAGGG)n#Simple_repeat 1 34 (0) m_b198s252i7 7764 chr4qtel1M 313956 GGTGGGGAAGGGGGGAGGGGAAGGGGGAGGGAGAG 313990 v i - i i (GGAGGG)n#Sim 1 GGAGGGGGA-GGGGGAGGGGGAGGGGGAGGGGGAG 34 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 21 22.64 0.00 4.69 chr4qtel1M 314432 314498 (685502) (AGGG)n#Simple_repeat 1 64 (0) m_b198s252i8 7765 chr4qtel1M 314432 AGGAGAGGCAGGGAGGGGGTTAGGGGGAGGGGCAGGGACTTAGGGAGGGA 314481 - v i vv i i i v vvv (AGGG)n#Simpl 1 AGG-GAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGA 49 chr4qtel1M 314482 GGGAGGGGCAGGCAGGG 314498 - - v (AGGG)n#Simpl 50 GGGA-GGG-AGGGAGGG 64 Matrix = Unknown Transitions / transversions = 0.50 (4/8) Gap_init rate = 0.05 (3 / 66), avg. gap size = 1.00 (3 / 3) 14 24.95 3.85 0.00 chr4qtel1M 314816 314867 (685133) (GGTAGTG)n#Simple_repeat 1 54 (0) m_b198s252i9 7766 chr4qtel1M 314816 GGGAGGGAGTAGTGAGT-GTGGGGAGGGGGTGGTGGGTA-CGGGGAGGGG 314863 v v i i - v v i -i v v (GGTAGTG)n#Si 1 GGTAGTGGGTAGTGGGTAGTGGGTAGTGGGTAGTGGGTAGTGGGTAGTGG 50 chr4qtel1M 314864 GCAG 314867 i (GGTAGTG)n#Si 51 GTAG 54 Matrix = Unknown Transitions / transversions = 0.83 (5/6) Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.00 (2 / 2) 247 37.41 5.45 3.40 chr4qtel1M 314967 315168 (684832) C MIR3#SINE/MIR (0) 208 3 m_b198s601i8 7767 chr4qtel1M 314967 GGATCATTAGGGTTCCAGAGATCTT-GAGCTAAAAAGGGCTGCCAGAGG- 315014 i - ii ivi - v i- ii i i i-ii i- C MIR3#SINE/MIR 208 GAATCAT-AGAATCATAGA-ATGTCAGAGCTGGAAGGGACC-TTAGAGAT 162 chr4qtel1M 315015 -----GGGCCATTCCCC-CATGTTCTAGATGCGACTCCTGAGGCGCAGGG 315058 -----i v vi - v vi v ivvv v i C MIR3#SINE/MIR 161 CATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAG 112 chr4qtel1M 315059 GGG-GCCAT--CTGGCCCCGAGACACAGAGCTAAGGAGAGGCTGAGGTGG 315105 i - vvi -- v vii v v ? ivv v v vi C MIR3#SINE/MIR 111 AGGTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGG 62 chr4qtel1M 315106 AATTTGAATCCAAGGCCCTTGCAGCCAGCTCAGATCTTGCCCCCCTCTCT 315155 i i v i i v i i --i i-- i vi v i i iiiv C MIR3#SINE/MIR 61 GACTAGAACCCAGGTCTCCTG--ACT--CCCAGTCCGTGCTCTCTCTGCT 16 chr4qtel1M 315156 GAGTGGCTTTGTC 315168 v ivi i i C MIR3#SINE/MIR 15 CAGCCACTCTGCC 3 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 53.93 CpG sites = 44, Kimura (unadjusted) = 55.08 Transitions / transversions = 1.52 (44/29) Gap_init rate = 0.06 (13 / 201), avg. gap size = 1.38 (18 / 13) 250 30.24 5.00 0.80 chr4qtel1M 315019 315138 (684862) C MIR1_Amn#SINE/MIR (73) 157 33 m_b198s601i9 7767 chr4qtel1M 315019 CATT-CCCCCATGTTCTAGATGCGACTCCTGAGGCGCAGGGGGGGCCA-- 315065 -i v vi v ivvv ? i i v?v -- C MIR1_Amn#SINE 157 CATTATCCCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGT 108 chr4qtel1M 315066 -TCTGGCCCCGAGACACAGAGCTAAGGAGAGGCTGAGGTGGAATTTGAAT 315114 -v v vii v ?v ?iiv? v v vi i ? ? i C MIR1_Amn#SINE 107 GACTTGCCCAAGGTCACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAAC 58 chr4qtel1M 315115 CCAAGGCCCTTGCAG--CCAGCTCAG 315138 i v i ii - -- ii C MIR1_Amn#SINE 57 CCAGGTCTCCCG-AGTCCCAGTCCAG 33 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.59 CpG sites = 18, Kimura (unadjusted) = 42.60 Transitions / transversions = 1.00 (18/18) Gap_init rate = 0.04 (5 / 119), avg. gap size = 1.40 (7 / 5) 266 33.33 3.12 0.00 chr4qtel1M 315024 315119 (684881) C MIR#SINE/MIR (117) 145 47 m_b198s601i10 7767 chr4qtel1M 315024 CCCCATGTTCTAGATGCGACTCCTGAGGCGCAGGGGGGGC---CATCTGG 315070 v vi v ivvv i i i vi---i v v C MIR#SINE/MIR 145 CCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTG 96 chr4qtel1M 315071 CCCCGAGACACAGAGCTAAGGAGAGGCTGAGGTGGAATTTGAATCCAAG 315119 vii v v ivi v v vi i i i i C MIR#SINE/MIR 95 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGG 47 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.18 CpG sites = 16, Kimura (unadjusted) = 44.79 Transitions / transversions = 1.00 (16/16) Gap_init rate = 0.01 (1 / 95), avg. gap size = 3.00 (3 / 1) 740 30.28 2.69 3.24 chr4qtel1M 315695 316066 (683934) C L1ME3B_3end#LINE/L1 (343) 646 277 m_b198s551i0 7768 chr4qtel1M 315695 TCTCCTG-GTCCTGCTCATTTCACTCAGCATCA-GTTCGTGTCAGTCTC- 315741 ii - i iv i i i - i -- vi - C L1ME3B_3end#L 646 TCTTTTGTGTCTTGCTTCTTTCGCTCAACATTATGTTTGTG--AGATTCA 599 chr4qtel1M 315742 TCCAGGCCTTTC--TGAAATCATCCTGTTGGTCATTTC--TTACCGAACA 315787 v iiv v-- v iiii vv - i v i-- i i v -- C L1ME3B_3end#L 598 TCCATGTTGTTGCGTGTAGCTGTAGT-TCGTTCATTTTCATTGCTGTA-- 552 chr4qtel1M 315788 GTAATATTCCATAATATTCATATACCACAATTTATTCAGCCATTCTCCAA 315837 - i vi vv i v v vi C L1ME3B_3end#L 551 -TAGTATTCCATTGTATGAATATACCACAATTTATTTATCCATTCTACTG 503 chr4qtel1M 315838 CTGATGGGCATCCATTCAGTTTCCAGTTTCTAACCACTACAAACAAGGCT 315887 i i iiivviv i?ii i i i v C L1ME3B_3end#L 502 TTGATGGACATTTGGGTTGTTTCCAGTTTTNGGCTATTACGAACAATGCT 453 chr4qtel1M 315888 GCCACAAACATTCGTGCACATACAGGTCCCT--TTCCCTTCTTTA-GTAT 315934 i ii v i --- v?i -- v v v v vi - ii C L1ME3B_3end#L 452 GCTATGAACATTCTTGTACAT---GTNTCCTGGTGCACATGTGCACGCGT 406 chr4qtel1M 315935 CTCTTTGGGGTATAAGCCCAGTAGTAACACTGCTGGATCAAAGGGTATGC 315984 i i i vi i v iiv i i v C L1ME3B_3end#L 405 TTCTCTAGGGTATATACCTAGGAGTGGAATTGCTGGGTCATAGGGTATGC 356 chr4qtel1M 315985 GCAGTTTGATAACTTTTTGAACATAGTTCCAAACTACTCTCCAGAATGGT 316034 i vi --i v?v i- i v ii i i i C L1ME3B_3end#L 355 GTATCTT--CAACTTTANTAG-ATAATGCCAAACTGTTTTCCAAAGTGGT 309 chr4qtel1M 316035 TGGATTTGTTCACAACTCCACCAACAATGCAT 316066 v iivi i vii i i i C L1ME3B_3end#L 308 TGTACCAATTTACACTCCCACCAGCAGTGTAT 277 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 39.02 CpG sites = 71, Kimura (unadjusted) = 41.06 Transitions / transversions = 1.87 (71/38) Gap_init rate = 0.05 (19 / 371), avg. gap size = 1.16 (22 / 19) 830 27.11 0.72 1.82 chr4qtel1M 315789 316066 (683934) C L1ME3G_3end#LINE/L1 (377) 547 273 m_b198s551i1 7768 chr4qtel1M 315789 TAATATTCCATAATATTCATATACCACAATTTATTCAGCCATTCTCCAAC 315838 i i vv i i i i v i C L1ME3G_3end#L 547 TAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTAT 498 chr4qtel1M 315839 TGATGGGCATCCATTCAGTTTCCAGTTTCTAACCACTACAAACAAGGCTG 315888 i ii vviv i i vi i i v C L1ME3G_3end#L 497 TGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCTG 448 chr4qtel1M 315889 CCACAAACATTCGTGCACATACAGGTCCCTTT-CCCTTCTTT-AGTATCT 315936 v ii i v i i ?-- i v - v v v vi- i C L1ME3G_3end#L 447 CAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATTT 400 chr4qtel1M 315937 CTTTGGGGTATAAGCCCAGTAGTAACACTGCTGGATCAAAGGGTATGCGC 315986 ? i i v v? ? v iiv i i C L1ME3G_3end#L 399 CTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGC 350 chr4qtel1M 315987 AGTTTGATAACTTTTTGAACATAGTTCCAAACTACTCTCCAGAATGGTTG 316036 v --- v viv v v v i i i i ? i C L1ME3G_3end#L 349 ATTT---TAAATTTTAATAGATACTGCCAAATTGCCCTCCAAAANGGCTG 303 chr4qtel1M 316037 GATTTGTTCACAACTCCACCAACAATGCAT 316066 v iivi i vii i i i C L1ME3G_3end#L 302 TACCAATTTACACTCCCACCAGCAGTGTAT 273 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 34.26 CpG sites = 45, Kimura (unadjusted) = 35.45 Transitions / transversions = 1.55 (45/29) Gap_init rate = 0.03 (7 / 277), avg. gap size = 1.00 (7 / 7) 16 14.07 5.13 0.00 chr4qtel1M 317248 317286 (682714) (CCCCT)n#Simple_repeat 1 41 (0) m_b198s252i10 7769 chr4qtel1M 317248 CCCCCCCCTTCCCCTCCCCT-ACC-CCCCACCCCACCCCTC 317286 i i -v - v v (CCCCT)n#Simp 1 CCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTC 41 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2) 246 42.34 0.00 0.00 chr4qtel1M 317331 317441 (682559) C L2c_3end#LINE/L2 (6) 472 362 m_b198s601i11 7770 chr4qtel1M 317331 TCAGCCAGTAAGCATTTGTTAATCACCAACAGTATGCTAAGCCCTGGGGT 317380 vi ii i i i v i v vi i i i v v C L2c_3end#LINE 472 TCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGA 423 chr4qtel1M 317381 GGCTAAAGGAGGCAAAAAGGTGCCTCCACCCTAGGAGAGCTCATGGAAGA 317430 vi v iiviiii i vivv i i ii viii ii vvv C L2c_3end#LINE 422 TACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTA 373 chr4qtel1M 317431 ATGGGGGAGAC 317441 i i C L2c_3end#LINE 372 GTGGAGGAGAC 362 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 66.50 CpG sites = 31, Kimura (unadjusted) = 69.15 Transitions / transversions = 1.94 (31/16) Gap_init rate = 0.00 (0 / 110), avg. gap size = 0.0 (0 / 0) 67 17.86 7.28 4.48 chr4qtel1M 317741 318001 (681999) (TGTGAT)n#Simple_repeat 1 268 (0) m_b198s252i11 7771 chr4qtel1M 317741 TGTGATTGTGTGGCTGTGAGTGTGTATGTGAGTGTGATGGTGATTGTG-- 317788 - - ii v vv v v -- (TGTGAT)n#Sim 1 TGTGA-T-TGTGATTGTGATTGTGATTGTGATTGTGATTGTGATTGTGAT 48 chr4qtel1M 317789 TGTGTGTGTGATCCTGTGATCGTGTTGTGCGCGGGTACAATGATGATTGT 317838 vv -- i v - i vvv -v v - (TGTGAT)n#Sim 49 TGTGATTGTGAT--TGTGATTGTGAT-TGTGATTGT-GATTG-TGATTGT 93 chr4qtel1M 317839 -ATGTGTGATCATAAGTGTGA-T-T-ATTGTGTGTATGATTCTGTGATTG 317884 - - ii i v - - - vv i - - (TGTGAT)n#Sim 94 GAT-TGTGATTGTGATTGTGATTGTGATTGTGATTGTGA-T-TGTGATTG 140 chr4qtel1M 317885 TG-TTGTG-TGGCTGTTTGCAGA-TGTGATGATGATTGTG--TGTGAGTG 317929 - - v - v -v - vi -- v (TGTGAT)n#Sim 141 TGATTGTGATTG-TGATTG-TGATTGTGATTGTGATTGTGATTGTGATTG 188 chr4qtel1M 317930 TGATAGTGATTGTG--TGAGATTATGATTGTG--TGTGATTGTG--TGCG 317973 v -- v i -- -- i (TGTGAT)n#Sim 189 TGATTGTGATTGTGATTGTGATTGTGATTGTGATTGTGATTGTGATTGTG 238 chr4qtel1M 317974 GGTGTGTTGGTGATTGTG--TGTGATTGTG 318001 iv v v -- (TGTGAT)n#Sim 239 ATTGTGATTGTGATTGTGATTGTGATTGTG 268 Matrix = Unknown Transitions / transversions = 0.46 (12/26) Gap_init rate = 0.10 (25 / 260), avg. gap size = 1.24 (31 / 25) 45 20.92 0.00 1.06 chr4qtel1M 318031 318125 (681875) (CT)n#Simple_repeat 1 94 (0) m_b198s252i12 7772 chr4qtel1M 318031 CTCTCTCTCTCTCCCCATCTCTGTCTGTCTGCTCTCTCTGTCTCCATCTG 318080 i iv v v - v iv v (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTC 49 chr4qtel1M 318081 TCTCTCTCCATCACTCTCTCTGTCTTTGTCTCTCTGTCTCTCCCT 318125 iv v v i v v i (CT)n#Simple_ 50 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 94 Matrix = Unknown Transitions / transversions = 0.55 (6/11) Gap_init rate = 0.01 (1 / 94), avg. gap size = 1.00 (1 / 1) 286 34.48 4.42 3.85 chr4qtel1M 318225 318405 (681595) MIR#SINE/MIR 19 200 (62) m_b198s601i12 7773 chr4qtel1M 318225 TAAGTGCAGGGCCACTGGGGTCCCCAGCCCCCCT---CCCCAACCTCATC 318271 v v v v i --- v iv ---ii v i i iv MIR#SINE/MIR 19 TAAGAGCACGGGCTCTGGAG---CCAGACTGCCTGGGTTCGAATCCCGGC 65 chr4qtel1M 318272 ACTGTC-TTTGTT---TCTATGGCTTTGGCTCAGGAAGGCCCAACCCCGT 318317 v i -i ii --- v i i i viv vv -- ii i vi MIR#SINE/MIR 66 TCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTA--CTTAACCTCTC 113 chr4qtel1M 318318 T-TGCCTCAGTTTCCTCCTCAGTAAACGGGGGTGGTGACCACAACTCCTC 318366 - v v vv -- i i iv i iiv v MIR#SINE/MIR 114 TGTGCCTCAGTTTCCTCATCTGTAAAATGGG--GATAATAATAGTACCTA 161 chr4qtel1M 318367 CCTCCCAAGGCTGTTGGGAGGCTCCTATTAGGTGACACA 318405 vi i i v v ivv v v i i MIR#SINE/MIR 162 CCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATACA 200 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.07 CpG sites = 31, Kimura (unadjusted) = 47.15 Transitions / transversions = 1.07 (31/29) Gap_init rate = 0.06 (11 / 180), avg. gap size = 1.36 (15 / 11) 189 30.82 6.19 3.00 chr4qtel1M 318320 318416 (681584) MIR1_Amn#SINE/MIR 123 222 (8) m_b198s601i13 7773 chr4qtel1M 318320 GCCTCAGTTTCCTCCTCAGT-AAACGGGGGTGGTGACCACAACTCCTCCC 318368 v v - i i ii ivvii -- i MIR1_Amn#SINE 123 GCCTCAGTTTCCTCATCTGTAAAATGGGGATAATGATACTGA--CCTCCT 170 chr4qtel1M 318369 TCCCAAGGCTGTTGGGAGG-CTCCTATT---AGGTGACACA-AAGGACTT 318413 ivi i - i vv i- v iv --- i vi - ii v MIR1_Amn#SINE 171 TTGTAAAG-TGCTTTGAGATCTACTGATGAAAAGTGCTACATAAGAGCTA 219 chr4qtel1M 318414 GGT 318416 MIR1_Amn#SINE 220 GGT 222 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.32 CpG sites = 18, Kimura (unadjusted) = 41.32 Transitions / transversions = 1.64 (18/11) Gap_init rate = 0.07 (7 / 96), avg. gap size = 1.29 (9 / 7) 13 12.69 0.00 0.00 chr4qtel1M 318535 318560 (681440) (GAGGG)n#Simple_repeat 1 26 (0) m_b198s252i13 7774 chr4qtel1M 318535 GAGGGGAGGGGCTGTGAGGGGAGGGG 318560 vv v (GAGGG)n#Simp 1 GAGGGGAGGGGAGGGGAGGGGAGGGG 26 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 203 30.16 4.51 7.75 chr4qtel1M 318842 318974 (681026) C MIRb#SINE/MIR (121) 147 19 m_b198s601i14 7775 chr4qtel1M 318842 TTTTG-GGATGAG-AACTTGGGTCCCACAGAGA--GAGCAGCTGAGCCCC 318887 i-i - vi i v i v i--i i i vi-- C MIRb#SINE/MIR 147 TTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTG--CCC 100 chr4qtel1M 318888 AGAGACCAGCAACAGGGGCTTGTCTCTAGCATGGGGTGGGATTTGAACCC 318937 - ii v-- --- v vvv i - i vi i C MIRb#SINE/MIR 99 A-AGGTCAC--ACAG---CTAGTAAGTGGCA-GAGCCGGGATTCGAACCC 57 chr4qtel1M 318938 CAGGTTT--CTATTTCTAGAGTTGGGGCCCTTTCCACTG 318974 - i -- ivi i i iiv v i C MIRb#SINE/MIR 56 -AGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTG 19 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.37 CpG sites = 24, Kimura (unadjusted) = 40.19 Transitions / transversions = 1.85 (24/13) Gap_init rate = 0.11 (14 / 132), avg. gap size = 1.14 (16 / 14) 12 11.26 6.90 0.00 chr4qtel1M 319857 319885 (680115) (GGGAG)n#Simple_repeat 1 31 (0) m_b198s252i14 7776 chr4qtel1M 319857 GGGAGGGG-CCGGATGGG-GGGGAGGGGAGG 319885 -vv v - (GGGAG)n#Simp 1 GGGAGGGGAGGGGAGGGGAGGGGAGGGGAGG 31 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.07 (2 / 28), avg. gap size = 1.00 (2 / 2) 27 0.00 0.00 0.00 chr4qtel1M 319935 319960 (680040) (C)n#Simple_repeat 1 26 (0) c_b198s251i2 7777 chr4qtel1M 319935 CCCCCCCCCCCCCCCCCCCCCCCCCC 319960 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCC 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 46 13.29 0.00 1.28 chr4qtel1M 321144 321222 (678778) (CTCC)n#Simple_repeat 1 78 (0) m_b198s252i15 7778 chr4qtel1M 321144 CTCCCTCCCTCCCCCCTTTCCTCCTTCCCTCCCTCCCCTTCCTCCTTCCT 321193 i i i i - i i i (CTCC)n#Simpl 1 CTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCT-CCCTCCCTCCCTCCC 49 chr4qtel1M 321194 TTCCTCTCTCCCTCCCTCCCTCCCTCCCT 321222 i i (CTCC)n#Simpl 50 TCCCTCCCTCCCTCCCTCCCTCCCTCCCT 78 Matrix = Unknown Transitions / transversions = 1.00 (9/0) Gap_init rate = 0.01 (1 / 78), avg. gap size = 1.00 (1 / 1) 17 18.36 0.00 0.00 chr4qtel1M 322859 322895 (677105) (GGGGC)n#Simple_repeat 1 37 (0) m_b198s252i16 7779 chr4qtel1M 322859 GGGGGGGGGCGGGCCGGGGCTGGACGTGGCGGGGGGG 322895 v v v i v v (GGGGC)n#Simp 1 GGGGCGGGGCGGGGCGGGGCGGGGCGGGGCGGGGCGG 37 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 734 33.84 3.55 1.75 chr4qtel1M 324710 325103 (674897) L1ME4c_3end#LINE/L1 277 677 (153) m_b198s551i2 7780 chr4qtel1M 324710 ATTCATTGTTGGTGGAGTTGTGAACAAATCCAACCATTCTGGAGAGTAGT 324759 v i vi? i ivii v v i i i i L1ME4c_3end#L 277 ATACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGCAAT 326 chr4qtel1M 324760 TTGGAATTATGCTCAAAAAGTTATCAAACTGTGCATACCCTTTGATCCAG 324809 v v i iviv i ii v v v i L1ME4c_3end#L 327 TTGGCAATACGTATCAAGAGCCATAAAAATGTTCATACCCTTTGACCCAG 376 chr4qtel1M 324810 CAGTGTTACTACTGGGCTTATATCCCAAGGAGATCAT---AAAGAAGGGA 324856 i i vii v vv v i i v --- i L1ME4c_3end#L 377 TAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAAGAAGGAA 426 chr4qtel1M 324857 AAGGGACCTGTATGTGCACGAATGTTTGTGGCAGCCCTGTTTGTAGTGGT 324906 i --- i ii ivii ii v vi i i i i i L1ME4c_3end#L 427 AAAG---CTATATGCACGAAGATGTTCATTGCAGCGTTATTTATAATAGC 473 chr4qtel1M 324907 TAGAAACTGGAAACTGAATGGATGCCCATCAGTTGGAGAATGGCTGAATA 324956 v i i vivv ii i v i v i i i i L1ME4c_3end#L 474 GAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAATGGTTAAGTA 523 chr4qtel1M 324957 AATTGTGGTATAT----------GAATATTATTGTTCTGTAAGAAATGAC 324996 i i ---------- vvvv ii v i i L1ME4c_3end#L 524 AATTATGGTACATCNACTCGATGGAATATTATGCAGCCATTAAAAATGAT 573 chr4qtel1M 324997 CAACAGGATGATTCCAGAAAGGCCTGGAGAGACTTACACGAACTGATGCT 325046 v vi v v i viiv ivii v - i iv vi i vv i i L1ME4c_3end#L 574 AATTATGAAGACTATGTAGCAACATGGA-AAATGTTTATGATATAATGTT 622 chr4qtel1M 325047 GAGTGAAATGAGCAGGACCAGGAGATCAT-TATATACTTCAACAACAATA 325095 i vi i -i vi i ii - ? ii vii iv -- L1ME4c_3end#L 623 AAGTGAAAAAAGCAGAA-TACAAAATTGTATNTACGCTATGATTACA--A 669 chr4qtel1M 325096 CTATATAA 325103 i L1ME4c_3end#L 670 CTATGTAA 677 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 45.63 CpG sites = 83, Kimura (unadjusted) = 47.75 Transitions / transversions = 1.73 (83/48) Gap_init rate = 0.03 (10 / 393), avg. gap size = 2.10 (21 / 10) 17 20.32 2.22 0.00 chr4qtel1M 325508 325552 (674448) (TAAA)n#Simple_repeat 1 46 (0) m_b198s252i17 7781 chr4qtel1M 325508 TAAATAAA-AAGCTATTAAATAAAAAAATAAAGAAAGAAAGAAATA 325552 - iiv v v v v v (TAAA)n#Simpl 1 TAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATA 46 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 464 31.19 2.50 2.82 chr4qtel1M 325765 326084 (673916) C L1ME1_3end#LINE/L1 (271) 655 337 m_b198s551i3 7782 chr4qtel1M 325765 AGTATATAATGATCTCCTG-GCCCTGCTCATTTCACTCAGCATCAGTTCG 325813 i ? --- ii - i iv iv - i v?v C L1ME1_3end#LI 655 AGTATGTANT---CTTTTGTGTCTGGCTTCTTTCACTCAGCAT-AATGNT 610 chr4qtel1M 325814 TGTAAGTCTC-TCCAGGCCTTTCTG-GAATCATCCTGTTGGTCATTTCTT 325861 v i vi - v iiv vi - v viv- v ivi i C L1ME1_3end#LI 609 TTTGAGATTCATCCATGTTGTTGCGTGTATCAGTA-GTTCGTTCCTTTTT 561 chr4qtel1M 325862 ACAGAACAGTAATATTCCATAACAATCATATACCACAGTTTCTTCAGCCA 325911 iv vvv i vii vvv i v i v C L1ME1_3end#LI 560 ATTGCTGAGTAGTATTCCATTGTATGGATATACCACAATTTGTTTATCCA 511 chr4qtel1M 325912 TTCTCCA--TGATGGACATCCACTCAGTTTCCAGTTTCTGGCCACTACAA 325959 v ?-- iiivviv i i i i C L1ME1_3end#LI 510 TTCACCNGTTGATGGACATTTGGGTTGTTTCCAGTTTTTGGCTATTACGA 461 chr4qtel1M 325960 ACAGGGCTGCCACAAACATTCGTGCACA--TACAGGTGTTTTCCCCTCCT 326007 i ii i ii i -- vivv vvv viv vi C L1ME1_3end#LI 460 ATAAAGCTGCTATGAACATTCGTGTACAAGTCTTTGTGTGGACATATGTT 411 chr4qtel1M 326008 TTAAGGCCTCTTTGGGATATAAGCCCAGTAGTAACATTGTTGGGTCAAAG 326057 v vvi v v v -- i v iiv i v v C L1ME1_3end#LI 410 TTCATTTCTCTTGGGTAAATA--CCTAGGAGTGGAATTGCTGGGTCATAT 363 chr4qtel1M 326058 GGTAGCACAGTCTG-GTAACTTTTTGAG 326084 -- vv v -v ? i C L1ME1_3end#LI 362 GGTA--AGTGTATGTTTAACTTTNTAAG 337 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 40.36 CpG sites = 46, Kimura (unadjusted) = 41.45 Transitions / transversions = 0.90 (46/51) Gap_init rate = 0.05 (15 / 319), avg. gap size = 1.13 (17 / 15) 555 31.34 2.92 2.17 chr4qtel1M 325789 326062 (673938) C L1MD1_3end#LINE/L1 (356) 633 358 m_b198s551i4 7782 chr4qtel1M 325789 GCTCATTTCACTCAGCATCAGTTCGTGTAAGTCTCTCCAGGCCTTTCTG- 325837 iv v v iiv v ii iiv iiv vi - C L1MD1_3end#LI 633 GCTTTTTTCACTCAGCATAATTCTCTGGAGATTCATCCAGGTTGTTGCGT 584 chr4qtel1M 325838 GAATCATCCTGTTGGTCATTTCTTACAGAACAGTAATATTCCATAACAAT 325887 v viv- v ivi i iv vvv i iii vv C L1MD1_3end#LI 583 GTATCAATA-GTTCGTTCCTTTTTATTGCTGAGTAGTATTCCATGGTATG 535 chr4qtel1M 325888 CATATACCACAGTTTCTTCAGCCATTCTCC--ATGATGGACATCCACTCA 325935 v i v i i v --v v iivviv C L1MD1_3end#LI 534 GATGTACCACAGTTTGTTTAACCATTCACCCGTTGAAGGACATCTGGGTT 485 chr4qtel1M 325936 GTTTCCAGTTTCTGGCCACTACAAACAGGGCTGCCACAAACATTCGTGCA 325985 i i i i i ii i i -- C L1MD1_3end#LI 484 GTTTCCAGTTTTTGGCTATTACGAATAAAGCTGCTATAAACATTCGTG-- 437 chr4qtel1M 325986 CATACAGGTGTTTTCCCCTCCTTTAAG-----GCCTCTTTGGGATATAAG 326030 -- - vivivvviv -----iii i v v C L1MD1_3end#LI 436 --TACAGGT-TTTTGTGTGAACATAAGTTTTCATTTCTCTGGGATAAATG 390 chr4qtel1M 326031 CCCAGTAGTAACATTGTTGGGTCAAAGGGTAG 326062 v ivv i iv v C L1MD1_3end#LI 389 CCCAGGAGTGCAATTGCTGGGTCGTATGGTAG 358 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 39.44 CpG sites = 44, Kimura (unadjusted) = 41.33 Transitions / transversions = 1.10 (44/40) Gap_init rate = 0.03 (9 / 273), avg. gap size = 1.56 (14 / 9) 17 23.88 0.00 0.00 chr4qtel1M 327297 327340 (672660) (GCT)n#Simple_repeat 1 44 (0) m_b198s252i18 7783 chr4qtel1M 327297 GCTGCTCGGGCCGCTGCTGCTGCTGCTGTGGCCGCTCCTCCTGC 327340 vvv i iv i v v (GCT)n#Simple 1 GCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC 44 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 210 32.27 0.00 1.61 chr4qtel1M 328718 328780 (671220) MIR3#SINE/MIR 109 170 (38) m_b198s601i15 7784 chr4qtel1M 328718 CCTTCCTGAGCCTCAGTTTCCCCCTTTGTAAAGCAGAGGGCCCTGAACCC 328767 ii i i v i ii- vvi i iv MIR3#SINE/MIR 109 CCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAAT-GAGGGGGTTGGACTA 157 chr4qtel1M 328768 AGGATTCTCTGAG 328780 iiviv i MIR3#SINE/MIR 158 GATGATCTCTAAG 170 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.12 CpG sites = 14, Kimura (unadjusted) = 45.12 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.02 (1 / 62), avg. gap size = 1.00 (1 / 1) 11 25.14 1.75 5.45 chr4qtel1M 329696 329752 (670248) (TCCCCG)n#Simple_repeat 1 55 (0) m_b198s252i19 7785 chr4qtel1M 329696 TCCCCTCCCTCCTTCTCCCTTGCCCG-CCCCGTCCCCCATTCCCAGGCAC 329744 vi - v - v v - - i i ivv v (TCCCCG)n#Sim 1 TCCCCGTCC-CCGTC-CCCGTCCCCGTCCCCGT-CCCCGTCCCCGTCCCC 47 chr4qtel1M 329745 GTCCCCGT 329752 (TCCCCG)n#Sim 48 GTCCCCGT 55 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.07 (4 / 56), avg. gap size = 1.00 (4 / 4) 18 0.00 0.00 0.00 chr4qtel1M 330363 330384 (669616) (CTG)n#Simple_repeat 1 22 (0) m_b198s252i20 7786 chr4qtel1M 330363 CTGCTGCTGCTGCTGCTGCTGC 330384 (CTG)n#Simple 1 CTGCTGCTGCTGCTGCTGCTGC 22 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 13 11.07 0.00 6.45 chr4qtel1M 330417 330449 (669551) (GGGCCC)n#Simple_repeat 1 31 (0) m_b198s252i21 7787 chr4qtel1M 330417 GGGCACCTGGGGCAGGGCCCGGGCTCGGGCCCG 330449 - - v v i (GGGCCC)n#Sim 1 GGGC-CC-GGGCCCGGGCCCGGGCCCGGGCCCG 31 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.06 (2 / 32), avg. gap size = 1.00 (2 / 2) 11 20.02 1.89 8.00 chr4qtel1M 331205 331257 (668743) (GCCTGGG)n#Simple_repeat 1 50 (0) m_b198s252i22 7788 chr4qtel1M 331205 GCCCGGGTCCTGAGGCCTGGGGGTTGGTGTGCC-GGCCCGCTGGGGCGAT 331253 i v i vi - - - vv - -v (GCCTGGG)n#Si 1 GCCTGGGGCCTGGGGCCTGGGGCCTGG-G-GCCTGGGGC-CTGGGGC-CT 46 chr4qtel1M 331254 GGGG 331257 (GCCTGGG)n#Si 47 GGGG 50 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.10 (5 / 52), avg. gap size = 1.00 (5 / 5) 56 0.00 0.00 0.00 chr4qtel1M 331415 331464 (668536) (G)n#Simple_repeat 1 50 (0) c_b198s251i3 7789 chr4qtel1M 331415 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 331464 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 50 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 20 19.94 0.00 0.00 chr4qtel1M 331988 332027 (667973) (GT)n#Simple_repeat 1 40 (0) m_b198s252i23 7790 chr4qtel1M 331988 GTGTGTGTGTCCGAGTGTGAGTGAGTGTGCGAGTGTGTGT 332027 vi v v v i v (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 40 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 27 0.00 0.00 0.00 chr4qtel1M 332396 332421 (667579) (C)n#Simple_repeat 1 26 (0) c_b198s251i4 7791 chr4qtel1M 332396 CCCCCCCCCCCCCCCCCCCCCCCCCC 332421 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCC 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 12 19.78 2.27 4.65 chr4qtel1M 333733 333776 (666224) (GCTGGCT)n#Simple_repeat 1 43 (0) m_b199s252i0 7792 chr4qtel1M 333733 GCTGGTCTCACTGTCTGTGGGCTGAGCGCT-CTGGCTGCTGGCTG 333776 - -i v iv vvv - (GCTGGCT)n#Si 1 GCTGG-CT-GCTGGCTGCTGGCTGCTGGCTGCTGGCTGCTGGCTG 43 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.07 (3 / 43), avg. gap size = 1.00 (3 / 3) 236 34.45 3.64 0.84 chr4qtel1M 334905 336058 (663942) (AGAG)n#Simple_repeat 1 1186 (0) m_b199s252i1 7793 chr4qtel1M 334905 AGAGAGAAAGATGGAGCTAGAGATGGAGTTAGAGAAGGAGAGAGGAACAG 334954 i vi vv vi vv ii ii v (AGAG)n#Simpl 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr4qtel1M 334955 AAAGAAAAAGGGAAACAGTGCAGGAAGTAG-GAGGTGGAG-GAGAGAGAC 335002 i i i i i v v - ii - - ivi - v (AGAG)n#Simpl 51 AGAGAGAGAGAGAGAGAGAG-AGAGAG-AGAGAGAGAGAGAGAGAGAGAG 98 chr4qtel1M 335003 A-AGAGACAAAAAG-GCGAGAGGAAGAGAGGCAAAGACAAAAAGGGAAGG 335050 - v i i - v ii iv i v i i i ii (AGAG)n#Simpl 99 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 148 chr4qtel1M 335051 AGGAAGAGAAAGACAAAAAG-GAGTGAGGAAGAGAGACAGAGACCAAAAG 335099 ii i v i i - v ii v vvi i (AGAG)n#Simpl 149 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 198 chr4qtel1M 335100 GGAGGGAGGAAGAGAGGTAAAGAGAAAGGCAGAGACAAAAAG-GAGTGAG 335148 i i ii iv i i iv v i i - v (AGAG)n#Simpl 199 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 248 chr4qtel1M 335149 GAAGAGAAAGACAAAAAG-GAGGGAGGAAGAGAGGCAGAGACAAAAAGGG 335197 ii i v i i - i ii iv v i i i (AGAG)n#Simpl 249 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 298 chr4qtel1M 335198 AGGGGGA-AGAGAGAGTGAAAGACAAAAAG-GAGGAAGAGAGGCAGGGAC 335245 i i - v i v i i - ii iv i v (AGAG)n#Simpl 299 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 348 chr4qtel1M 335246 AAAAAG-GAGGGAG-GATGAGA-AGCAGAGACAAAAAG-GAGAGGAAGAG 335291 i i - i - - - - v i i - ii (AGAG)n#Simpl 349 AGAGAGAGAGAGAGAGA-GAGAGAG-AGAGAGAGAGAGAGAGAGAGAGAG 396 chr4qtel1M 335292 AGACAGACACAGACAGACAAAAAGGGAGGGAGGAATAGAAAGAGAAAAAA 335341 v v v v v i i i i ii v i i i i (AGAG)n#Simpl 397 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 446 chr4qtel1M 335342 AG-GAGGGAGGAAGGGA-AGA-AGAGA-AGCAGAGAAAAAGGGAGGAAGA 335387 - i ii i - - - - i i i ii (AGAG)n#Simpl 447 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAG-AGAGAGAGAGAGAGAGAGA 495 chr4qtel1M 335388 GAGTGACAGAAACA-AAAAAGAGGAAGAGGGACAGAGACAAAAAG-GAGG 335435 v v i v - i i ii i v v i i - i (AGAG)n#Simpl 496 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 545 chr4qtel1M 335436 AAGGAAGAGAGTGACAAAAAGAAAGGGAGGAAGAGAAAGAGAGAGAGACA 335485 i ii v v i i i i ii i v (AGAG)n#Simpl 546 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 595 chr4qtel1M 335486 AAAAG-GAGGAAGAGGGACAGAGACAAAAAG-GATGGAGGAAGGGAGACA 335533 i i - ii i v v i i - vi ii i v (AGAG)n#Simpl 596 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 645 chr4qtel1M 335534 GACAAAAAG-GAGGGAGGAAGAGAAAGAGTGACAGACA-AAAGGGAGGAA 335581 v i i - i ii i v v v - i i ii (AGAG)n#Simpl 646 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 695 chr4qtel1M 335582 GAGATTCAGACATGCAGAGACAGACAAAAAGGGAGGGAGGAAGAGAAAGA 335631 vvv v - - v v i i i i ii i (AGAG)n#Simpl 696 GAGAGAGAGAGA-G-AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 743 chr4qtel1M 335632 GTGACAGACAAAAAGGGAGGGAGGAAGAGAGAAAGAGACAGACAAAAAGG 335681 v v v i i i i ii i v v i i i (AGAG)n#Simpl 744 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 793 chr4qtel1M 335682 GAGGGAGGAAGAGAGAGAGACAAAAAG-GAGGAAGAGACAGACAAAAAG- 335729 i ii v i i - ii v v i i - (AGAG)n#Simpl 794 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 843 chr4qtel1M 335730 GAGGGAGGAAGAGATTCAGACATGCAGAGATAGGCAAAAAGGGAGGGAGG 335779 i ii vvv v - - v iv i i i i i (AGAG)n#Simpl 844 GAGAGAGAGAGAGAGAGAGAGA-G-AGAGAGAGAGAGAGAGAGAGAGAGA 891 chr4qtel1M 335780 AAGAGAGAAAGAGAGAGACAAAAAG-GAGAAAGGAAGAGAGAGAGGCAGA 335828 i i v i i - i ii iv (AGAG)n#Simpl 892 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 941 chr4qtel1M 335829 GAAGGACAGAG-GAGGGACGGATAGAGGAAGAGAAAGAAAGAGA-AAAGA 335876 ii v - i vi v ii i i - i (AGAG)n#Simpl 942 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 991 chr4qtel1M 335877 GAG-GAGAAATAGAGAG-GGGAGAAAGA-AGGAACAGCCAGAG-GAAAAA 335922 - i v - i i - ii v vv - i i (AGAG)n#Simpl 992 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 1041 chr4qtel1M 335923 ATGAGTCGGGA-AGGGGGA-AAAGATGGAG-GAGAGGGAAAAAGAGAGA- 335968 iv -v i - i i - i vi - i i i - (AGAG)n#Simpl 1042 GAGAG-AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 1090 chr4qtel1M 335969 AGAGAGACAGAG-GAGAGAG-GAGGGAGAAAG-GAGAGA-AGGAAGGGAG 336014 v - - i i - - ii i (AGAG)n#Simpl 1091 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 1140 chr4qtel1M 336015 AGAG-GAGCGGGAGAGGGAAAGAAGGGGAG-GGGAGGGAGAGAGAG 336058 - v i i i ii i - i i (AGAG)n#Simpl 1141 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 1186 Matrix = Unknown Transitions / transversions = 2.43 (214/88) Gap_init rate = 0.05 (52 / 1153), avg. gap size = 1.00 (52 / 52) 16 9.32 0.00 0.00 chr4qtel1M 336382 336404 (663596) (C)n#Simple_repeat 1 23 (0) m_b199s252i2 7794 chr4qtel1M 336382 CCCCCCCGCCCCCCCCCCCCGCC 336404 v v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCC 23 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 15 5.56 0.00 0.00 chr4qtel1M 336889 336907 (663093) (C)n#Simple_repeat 1 19 (0) m_b199s252i3 7795 chr4qtel1M 336889 CCCCCTCCCCCCCCCCCCC 336907 i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCC 19 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 37 36.41 0.00 0.00 chr4qtel1M 337389 337504 (662496) (AA)n#Simple_repeat 1 116 (0) m_b199s252i4 7796 chr4qtel1M 337389 AAAAAAGGAAAAAAAAAAAAAAAGGGGGAGGGAAAAGGGGGGAAAAAAAG 337438 ii iiiii iii iiiiii i (AA)n#Simple_ 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr4qtel1M 337439 GGAAAGAAAGGGGAAAAAAAAAGGAAAAAAAAAAAAAAAAAAAAAAAAAA 337488 ii i iiii ii (AA)n#Simple_ 51 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 100 chr4qtel1M 337489 AAAAAGGGGAAAAAAA 337504 iiii (AA)n#Simple_ 101 AAAAAAAAAAAAAAAA 116 Matrix = Unknown Transitions / transversions = 1.00 (30/0) Gap_init rate = 0.00 (0 / 115), avg. gap size = 0.0 (0 / 0) 14 16.58 3.77 5.77 chr4qtel1M 337793 337845 (662155) (CCTCTC)n#Simple_repeat 1 52 (0) m_b199s252i5 7797 chr4qtel1M 337793 CCTCTCCCACCTCAGTTTCCCAACTCCC-CTCCC-CTCCCTTTCCCTGCT 337840 -i vv i -v - - i - (CCTCTC)n#Sim 1 CCTCTCCC-TCTCCCTCTCCC-TCTCCCTCTCCCTCTCCCTCTCCCT-CT 47 chr4qtel1M 337841 CCTTC 337845 i (CCTCTC)n#Sim 48 CCCTC 52 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.10 (5 / 52), avg. gap size = 1.00 (5 / 5) 393 23.04 0.00 7.29 chr4qtel1M 338546 338648 (661352) MIRc#SINE/MIR 20 115 (153) m_b199s601i0 7798 chr4qtel1M 338546 GGAGAGAGTGCTGGCCCTTCAGTCAGGAGGGCCTGGATTCAAACCCAACC 338595 i ii v i vv i i i i ii viv MIRc#SINE/MIR 20 GGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGC 69 chr4qtel1M 338596 TCAGATGCTAGACACTTAGTAGCTGAGTGACCCCGGGCAAGTCACTGAAC 338645 --- ---- v v ii v MIRc#SINE/MIR 70 TC---TGC----CACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAAC 112 chr4qtel1M 338646 CCC 338648 i MIRc#SINE/MIR 113 CTC 115 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 25.14 CpG sites = 14, Kimura (unadjusted) = 28.06 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.07 (7 / 102), avg. gap size = 1.00 (7 / 7) 275 21.88 0.00 0.00 chr4qtel1M 339400 339463 (660537) DNM1r#Unknown 2481 2544 (2118) m_b199s502i0 7799 chr4qtel1M 339400 TATATATACATATATATGTGTGTGTGTGTGTGTGTGTGTACATATATGTA 339449 i i ii i i i i i i DNM1r#Unknown 2481 TATGTGTGTATATATGTGTGTATATGTGTGTATGTGTGTATATATGTGTA 2530 chr4qtel1M 339450 TCTGCACATATATA 339463 v ii i ? DNM1r#Unknown 2531 TATATACGTATNTA 2544 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 26.35 CpG sites = 13, Kimura (unadjusted) = 28.79 Transitions / transversions = 13.00 (13/1) Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0) 503 30.86 12.11 0.00 chr4qtel1M 339944 340199 (659801) L2#LINE/L2 2141 2427 (655) m_b199s601i1 7800 chr4qtel1M 339944 CTTCTGGTTCTTCTCCTCCCTCTCTGGCCACTCATCCTCTGCCTTGTTGG 339993 i i i v v i v i v i iv v L2#LINE/L2 2141 CTCCTGGTTTTCCTCCTACCTCACTGGCCGCTCCTTCTCAGTCTCCTTTG 2190 chr4qtel1M 339994 CTGGATTCTCCTCCAGACCATGCCCTCTGACCACGGGGGT-CCCCAAGG- 340041 v i vvvv vi v ? v iiv i - i - L2#LINE/L2 2191 CTGGTTCCTCCTCATCTCCCCGACCTCTNAACGTTGGAGTGCCCCAGGGC 2240 chr4qtel1M 340042 -----------ACCTCTTCTCTCC-------AGACTGCTTCCCTTGGGGA 340073 ----------- i ------- v vvi ? v L2#LINE/L2 2241 TCAGTCCTTGGACCTCTTCTCTTCTCTATCTACACTCACTCCCTNGGTGA 2290 chr4qtel1M 340074 TCTC--------TCGTGGATTT---CATCATCTCTATTCAGATGATGCTC 340112 -------- i v ---i i v v v iv i L2#LINE/L2 2291 TCTCATCCAGTCTCATGGCTTTAAATACCATCTATATGCTGATGACTCCC 2340 chr4qtel1M 340113 AGATACACCCTCCCTGCCCCAAATCCTCGGCAGATCTCCCATCTCGCATC 340162 i vi iviii v vi vii vv v v viv i v L2#LINE/L2 2341 AAATTTATATCTCCAGCCCGGACCTCTCCCCTGAACTCCAGACTCGTATA 2390 chr4qtel1M 340163 CCCAGTTGCCCGCTAGACATCTCAGACTGGACGTCCA 340199 i ii ii v vivi i i L2#LINE/L2 2391 TCCAACTGCCTACTCGACATCTCCACTTGGATGTCTA 2427 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.81 CpG sites = 40, Kimura (unadjusted) = 40.77 Transitions / transversions = 1.03 (40/39) Gap_init rate = 0.02 (6 / 255), avg. gap size = 5.17 (31 / 6) 184 34.20 9.78 1.23 chr4qtel1M 340225 340449 (659551) L2c_3end#LINE/L2 14 257 (221) m_b199s601i2 7800 chr4qtel1M 340225 CCTCTGGATGCCTCT---GTCTC-TCTCATCCCCTCTGCCCCATGGCCAG 340270 i vv i --- i - v v iv i vi v v L2c_3end#LINE 14 CCCCTGCCTACCTCTCCAGCCTCATCTCCTCCACTCCCCTCCTCGCCCAC 63 chr4qtel1M 340271 GCGGTTCCAAGGCCTCTCAGTT--TTACCTTCTCTGA-----CTG-ACCT 340312 vvv i ivvv v v ii -- i v i ii ----- i - vi L2c_3end#LINE 64 TATGCTCCAGCCACACTGAACTNCTTGCATTCCCCAAACACGCCGCAGTT 113 chr4qtel1M 340313 CTTCCTGGGGGCTGGGTCCAT-CTCTGGCTGTCCC----GGCTGGAACCC 340357 i iv vvv i ? i iv - v vv i ---- v iv L2c_3end#LINE 114 CTTTCCTGCCTCCGNGCCTTTGCACATGCTGTTCCCTCTGCCTGGAATGC 163 chr4qtel1M 340358 TTTCCTCCTCTTCTCCAAACACAGAGC---CTCCTG-GCTTCTCTCAAGT 340403 i i i i i i --- vvi --- i-v v ii ? L2c_3end#LINE 164 TCTTCCCCCCTCCTTC---CACCTGGCTAACTCCTACTCATCCTTCAAGN 210 chr4qtel1M 340404 CCCATCTAAAATCTCACCTTCTTTAGGAAG-CTTCCCTAACCCCTCA 340449 i v v i v i iii - i i L2c_3end#LINE 211 CTCAGCTCAGATGTCACCTCCTCCGGGAAGCCTTCCCTGACCCCCCA 257 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.05 CpG sites = 41, Kimura (unadjusted) = 47.52 Transitions / transversions = 1.17 (41/35) Gap_init rate = 0.06 (13 / 224), avg. gap size = 1.92 (25 / 13) 222 27.70 7.86 2.03 chr4qtel1M 340339 340478 (659522) L2b_3end#LINE/L2 139 286 (180) m_b199s601i3 7800 chr4qtel1M 340339 GCTGTCCC----GGCTGGAAC-CCTTTCCT--CCTCTTCTCCAAACACAG 340381 i ---- v - i i-- v vii - i L2b_3end#LINE 139 GCTGTTCCCTCTGCCTGGAACGCCCTTCCCCACCTCTTCGCCTGGC-CAA 187 chr4qtel1M 340382 AGCCTCCTGGCTTCTCTCAAGTCCCATCTAAAATCTCACCTTCTTTAGGA 340431 vv v -- v ii i i v v v i iii L2b_3end#LINE 188 CTCCTACT--CATCCTTCAGGTCTCAGCTCAAATGTCACCTCCTCCGGGA 235 chr4qtel1M 340432 AG-CTTCCCTAACCCCTCATTTC-TGTCATGAGTTTTCATCT--ACCCCC 340477 - i i i vvi -v v v iii v --i L2b_3end#LINE 236 AGCCCTCCCTGACCCCCCAGGCCGGGTCAGGCGCCCTCCTCTGGGCCCCC 285 chr4qtel1M 340478 C 340478 L2b_3end#LINE 286 C 286 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.18 CpG sites = 22, Kimura (unadjusted) = 35.46 Transitions / transversions = 1.38 (22/16) Gap_init rate = 0.06 (9 / 139), avg. gap size = 1.56 (14 / 9) 250 30.32 3.23 1.59 chr4qtel1M 340344 340467 (659533) L2d2_3end#LINE/L2 151 276 (279) m_b199s601i4 7800 chr4qtel1M 340344 CCCGGCTGGAAC-CCTTTCCTCCTCTTCTCCA--AACACAGAGCCTCCTG 340390 v i- i i i i --v iv i v v i- L2d2_3end#LIN 151 CCCGCCTGGAATGCCCTTCCCCTTCCTCTCCACCTATCCAAATCCTACC- 199 chr4qtel1M 340391 GCTTCTCTCAAGTCCCATCTAAAATCTCACCTTCTTTAGGAAG-CTTCCC 340439 - v ii v v v ?i i iiiv - L2d2_3end#LIN 200 -CATCCTTCAAGGCCCAGCTCAAATNCCACCTCCTCCGTGAAGCCTTCCC 248 chr4qtel1M 340440 TAACCCCTCATTTCTGTCATGAGTTTTC 340467 i v vvvi i ?vi vi i L2d2_3end#LIN 249 TGACCACTCCAGCCCGNAGTGATCTCTC 276 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.80 CpG sites = 21, Kimura (unadjusted) = 40.77 Transitions / transversions = 1.31 (21/16) Gap_init rate = 0.04 (5 / 123), avg. gap size = 1.20 (6 / 5) 454 25.22 2.42 4.10 chr4qtel1M 340679 340802 (659198) L2c_3end#LINE/L2 338 459 (19) m_b199s601i5 7800 chr4qtel1M 340679 TTGTGGATATTTTTGTTCCT---TGTCTTCCCCATTAGATTGTGAGCTCC 340725 iiv i i v v v ? --- i i i i L2c_3end#LINE 338 TTGTAATTGTCTGTTTACNTGTCTGTCTCCTCCACTAGACTGTGAGCTCC 387 chr4qtel1M 340726 TTGAGGGAAGGCAAGAACTATCTTTTTATTACACTCTGCATCCCCAGTAC 340775 ---- i i ii v i - vvv i i ii L2c_3end#LINE 388 TTGAGGG----CAGGGACCGTGTCTT-ATTCATCTTTGTATCCCCAGCGC 432 chr4qtel1M 340776 CTGGCGCACAGCAGGTGCTTAATAAAT 340802 i i i i i L2c_3end#LINE 433 CTGGCACATAGTAGGCGCTCAATAAAT 459 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.48 CpG sites = 22, Kimura (unadjusted) = 32.69 Transitions / transversions = 2.75 (22/8) Gap_init rate = 0.05 (6 / 123), avg. gap size = 1.33 (8 / 6) 209 29.27 0.00 0.00 chr4qtel1M 340770 340810 (659190) MIRb#SINE/MIR 221 261 (7) m_b199s601i6 7801 chr4qtel1M 340770 CAGTACCTGGCGCACAGCAGGTGCTTAATAAATAACGGTTC 340810 i i i i i i i iiii i MIRb#SINE/MIR 221 CAGTGCCTGGCACATAGTAAGCGCTCAATAAATGGTAGCTC 261 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.99 CpG sites = 12, Kimura (unadjusted) = 44.02 Transitions / transversions = 1.00 (12/0) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 209 7.14 0.00 0.00 chr4qtel1M 341683 341710 (658290) MIR3#SINE/MIR 118 145 (63) m_b199s601i7 7802 chr4qtel1M 341683 GCCTCAGTTTCCCCATCTGTAAAACGAG 341710 i i MIR3#SINE/MIR 118 GCCTCAGTTTCCTCATCTGTAAAATGAG 145 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 7.71 CpG sites = 2, Kimura (unadjusted) = 7.71 Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 40 24.10 1.87 0.00 chr4qtel1M 341734 341840 (658160) (GCCCCC)n#Simple_repeat 1 109 (0) m_b199s252i6 7803 chr4qtel1M 341734 GCCCCCACCCCC-AGCACGGCCCCGCCCCTTCCCCCACCCCC-AGCACGG 341781 i -vv v v iv i -vv v v (GCCCCC)n#Sim 1 GCCCCCGCCCCCGCCCCCGCCCCCGCCCCCGCCCCCGCCCCCGCCCCCGC 50 chr4qtel1M 341782 CCCCGCCCCTTCCTCCTCCCCCTCCCCCTCCCCCTCCCCCGGCCCCGGCC 341831 iv i v v v v v v (GCCCCC)n#Sim 51 CCCCGCCCCCGCCCCCGCCCCCGCCCCCGCCCCCGCCCCCGCCCCCGCCC 100 chr4qtel1M 341832 CCGGCCCCG 341840 v (GCCCCC)n#Sim 101 CCGCCCCCG 109 Matrix = Unknown Transitions / transversions = 0.29 (5/17) Gap_init rate = 0.02 (2 / 106), avg. gap size = 1.00 (2 / 2) 17 27.14 7.07 0.95 chr4qtel1M 341872 341970 (658030) (CGCACG)n#Simple_repeat 1 105 (0) m_b199s252i7 7804 chr4qtel1M 341872 CGCACGC-C-CG-GCAGGCGCAGGCGCACACG--CGCTCCCGCCCACACG 341916 - - - v v i -- v v v i (CGCACG)n#Sim 1 CGCACGCGCACGCGCACGCGCACGCGCACGCGCACGCGCACGCGCACGCG 50 chr4qtel1M 341917 TTAC-CTC-CACACAAGAACATACGCAAGGACACGCGCACAGACACGCGC 341964 -i - v - i i v vi ii v vi ivi (CGCACG)n#Sim 51 -CACGCGCACGCGCACGCGCACGCGCACGCGCACGCGCACGCGCACGCGC 99 chr4qtel1M 341965 ACGCGC 341970 (CGCACG)n#Sim 100 ACGCGC 105 Matrix = Unknown Transitions / transversions = 1.00 (11/11) Gap_init rate = 0.07 (7 / 98), avg. gap size = 1.14 (8 / 7) 15 27.16 3.45 0.00 chr4qtel1M 342409 342466 (657534) (CGGCGGG)n#Simple_repeat 1 60 (0) m_b199s252i8 7805 chr4qtel1M 342409 CGGCGCCCGGGGGGGCCCAGGGGGCGGGAGG-GCGAGG-GGGCGGCGGTC 342456 vv v vvv i v v - v v - v (CGGCGGG)n#Si 1 CGGCGGGCGGCGGGCGGCGGGCGGCGGGCGGCGGGCGGCGGGCGGCGGGC 50 chr4qtel1M 342457 GGCTGGCGGC 342466 v (CGGCGGG)n#Si 51 GGCGGGCGGC 60 Matrix = Unknown Transitions / transversions = 0.08 (1/12) Gap_init rate = 0.04 (2 / 57), avg. gap size = 1.00 (2 / 2) 18 23.27 0.00 0.00 chr4qtel1M 342505 342544 (657456) (G)n#Simple_repeat 1 40 (0) m_b199s252i9 7805 chr4qtel1M 342505 GGTGGAGGGGGGTGGGGGCGGGCCAGGGGAGGGGGGGGGG 342544 v i v v vvi i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 40 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 155 7.49 0.00 0.00 chr4qtel1M 342986 343182 (656818) (C)n#Simple_repeat 1 197 (0) c_b199s251i0 7806 chr4qtel1M 342986 CCCCCCCCCCCCTCCCCCACCCCCCCTTTCCCCCCCCCACCCCCCCCCCC 343035 i v iii v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 50 chr4qtel1M 343036 CCCCCCCCCACCCCCCCTCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 343085 v i (C)n#Simple_r 51 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 100 chr4qtel1M 343086 CCCCCCCCCCCCGCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCGCC 343135 v v (C)n#Simple_r 101 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 150 chr4qtel1M 343136 CTCTCCCCCCCCCCCCCCCCCCCCCCATCCCCCCCCCCCCCCCCCCC 343182 i i vi (C)n#Simple_r 151 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 197 Matrix = Unknown Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.00 (0 / 196), avg. gap size = 0.0 (0 / 0) 20 26.21 0.00 0.00 chr4qtel1M 347836 347885 (652115) (CC)n#Simple_repeat 1 50 (0) m_b199s252i10 7807 chr4qtel1M 347836 CCCCCCCTCCCCCCCCCCCGGCAGGAGTCCCCCCGCCCCCCCCCGCCCCC 347885 i vv vvvvvi v v (CC)n#Simple_ 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 50 Matrix = Unknown Transitions / transversions = 0.22 (2/9) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 14 30.42 4.55 2.22 chr4qtel1M 348438 348525 (651475) (GGC)n#Simple_repeat 1 90 (0) m_b199s252i11 7808 chr4qtel1M 348438 GGCGG-GGCCGCGTCGAC-TCGGAAGCGGTCGGCGGCGG-GCCGGCAGGG 348484 - v v i -v vi - - v i v (GGC)n#Simple 1 GGCGGCGGCGGCGGCGGCGGCGGCGGCGG-CGGCGGCGGCGGCGGCGGCG 49 chr4qtel1M 348485 CCGGC-GCAGCAGCAGCAGGAGGAGGTAGAGAGAGCGGCGGC 348525 v - i i i - v v ii v ivi (GGC)n#Simple 50 GCGGCGGCGGCGGCGGC-GGCGGCGGCGGCGGCGGCGGCGGC 90 Matrix = Unknown Transitions / transversions = 0.91 (10/11) Gap_init rate = 0.07 (6 / 87), avg. gap size = 1.00 (6 / 6) 14 14.52 0.00 9.52 chr4qtel1M 349052 349097 (650903) (GGCGG)n#Simple_repeat 1 42 (0) m_b199s252i12 7809 chr4qtel1M 349052 GGGGGGGCGGGCCCGGAGGAAGGGGCGGGGCCCGGGAGGGGCGGGG 349097 v -v - -v - v v (GGCGG)n#Simp 1 GGCGGGGCGGG-GCGG-GG-CGGGGCGGGG-CGGGGCGGGGCGGGG 42 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.09 (4 / 45), avg. gap size = 1.00 (4 / 4) 25 2.61 0.00 9.30 chr4qtel1M 349153 349199 (650801) (CGGGG)n#Simple_repeat 1 43 (0) m_b199s252i13 7810 chr4qtel1M 349153 CGGGGCGGGGCCCGTGGCGGGGCGGGGCCAGGGGCGGGGCGGGGCGG 349199 -- v - - (CGGGG)n#Simp 1 CGGGGCGGGG--CGGGGCGGGGCGGGG-C-GGGGCGGGGCGGGGCGG 43 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.09 (4 / 46), avg. gap size = 1.00 (4 / 4) 13 19.24 2.22 4.55 chr4qtel1M 349350 349394 (650606) (GGGCG)n#Simple_repeat 1 44 (0) m_b199s252i14 7811 chr4qtel1M 349350 GGGCGGGGCCCGG-AGGAAGGGGCGGGGCCTGGGTAGGGGCGGGGC 349394 vv -i iv - - vv (GGGCG)n#Simp 1 GGGCGGGGCGGGGCGGGGCGGGGCGGGG-C-GGGGCGGGGCGGGGC 44 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.07 (3 / 44), avg. gap size = 1.00 (3 / 3) 11 16.41 5.88 0.00 chr4qtel1M 350880 350913 (649087) (GGCCTC)n#Simple_repeat 1 36 (0) m_b199s252i15 7812 chr4qtel1M 350880 GGGCTCGGCCTCGGCCT-GTAC-CTGCCTCGGTCTC 350913 v - vv - v i (GGCCTC)n#Sim 1 GGCCTCGGCCTCGGCCTCGGCCTCGGCCTCGGCCTC 36 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2) 13 16.12 5.71 0.00 chr4qtel1M 353047 353081 (646919) (TTTTC)n#Simple_repeat 1 37 (0) m_b199s252i16 7813 chr4qtel1M 353047 TTTTCTTTTCTTTTGTTTT-TGATCTGAT-TTTTCTT 353081 v - vv vv - (TTTTC)n#Simp 1 TTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTT 37 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 237 29.67 15.38 0.00 chr4qtel1M 353269 353359 (646641) L2c_3end#LINE/L2 374 478 (0) m_b199s601i8 7814 chr4qtel1M 353269 AGAATATAAGTCCCTTGAGAACAGGGAC--TGGCTT-----CCTTAGCA- 353310 v i i ii ii -- v -----i v i - L2c_3end#LINE 374 AGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTAT 423 chr4qtel1M 353311 CTCCA------GGTGTACAGTAGATGCTTAATTAATGCTGGCTGACTGGC 353354 i ------ iii i ii i v i v i v iv L2c_3end#LINE 424 CCCCAGCGCCTGGCACATAGTAGGCGCTCAATAAATGTTTGTTGAATGAA 473 chr4qtel1M 353355 TGAGT 353359 i L2c_3end#LINE 474 TGAAT 478 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.51 CpG sites = 20, Kimura (unadjusted) = 40.51 Transitions / transversions = 2.86 (20/7) Gap_init rate = 0.04 (4 / 90), avg. gap size = 3.50 (14 / 4) 184 35.09 0.00 0.00 chr4qtel1M 353488 353544 (646456) C MIRb#SINE/MIR (1) 267 211 m_b199s601i9 7815 chr4qtel1M 353488 ATAGTGGAGAGAGCTTTCATCAGACACCCTCTGTGTGCCAGGCTGTGCGC 353537 i i vv v v i iiii i iiv i vv i C MIRb#SINE/MIR 267 ATAATAGAGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGC 218 chr4qtel1M 353538 TGAGCGC 353544 i C MIRb#SINE/MIR 217 TAAGCGC 211 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.68 CpG sites = 13, Kimura (unadjusted) = 50.30 Transitions / transversions = 1.86 (13/7) Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0) 36 19.97 2.02 4.12 chr4qtel1M 357055 357153 (642847) (GA)n#Simple_repeat 1 97 (0) m_b199s252i17 7816 chr4qtel1M 357055 GAGACAGAGACAGAGAGATGCAGAGGCAAAGGGAGAGACA-ACAGAGAGC 357103 v v - - iv i i v - v v (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGA-G-AGAGAGAGAGAGAGAGAGAGAGAGAGAGA 48 chr4qtel1M 357104 GAGACATGAGAGAGA-ACAGACAGAGAGTGAGAGAGCCACAGATGAGAGA 357152 v - - v v v vv v - (GA)n#Simple_ 49 GAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA-GAGAGA 96 chr4qtel1M 357153 G 357153 (GA)n#Simple_ 97 G 97 Matrix = Unknown Transitions / transversions = 0.23 (3/13) Gap_init rate = 0.06 (6 / 98), avg. gap size = 1.00 (6 / 6) 199 34.43 0.00 0.00 chr4qtel1M 358836 358896 (641104) L2a_3end#LINE/L2 452 512 (5) m_b199s601i10 7817 chr4qtel1M 358836 CCCAGCGCTTTGTACGGTGCCCAGCACCTCACCAGCACTTGCTTAGTAAG 358885 i v v i ii v viivi i iiv v i vv L2a_3end#LINE 452 CCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGGCGCTCAATAAATATT 501 chr4qtel1M 358886 TGTTGCATGAA 358896 v L2a_3end#LINE 502 TGTTGAATGAA 512 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.10 CpG sites = 11, Kimura (unadjusted) = 47.11 Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 205 31.90 18.33 0.71 chr4qtel1M 361229 361348 (638652) L2c_3end#LINE/L2 115 255 (223) m_b199s601i11 7818 chr4qtel1M 361229 TCTCCCACCGCCGAGCCCTTGTACAGGCCATGCCCCCTGCCTGGGAGACC 361278 i ii v ? i i v ii v i i vi i L2c_3end#LINE 115 TTTCCTGCCTCCGNGCCTTTGCACATGCTGTTCCCTCTGCCTGGAATGCT 164 chr4qtel1M 361279 CTTCTTGTCCTCCGAGCATTCGACT-------------------AGGCTC 361309 ii-i vvv iii i ------------------- ? L2c_3end#LINE 165 CTTCCC-CCCTCCTTCCACCTGGCTAACTCCTACTCATCCTTCAAGNCTC 213 chr4qtel1M 361310 AGCCCAAGTG---CTCCCTCCAACAGGCTTTTGCTGAGCCCC 361348 i ii --- ii iiv i i iv v L2c_3end#LINE 214 AGCTCAGATGTCACCTCCTCCGGGAAGCCTTCCCTGACCCCC 255 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.47 CpG sites = 28, Kimura (unadjusted) = 46.20 Transitions / transversions = 2.80 (28/10) Gap_init rate = 0.03 (3 / 119), avg. gap size = 7.67 (23 / 3) 41 2.42 0.00 0.00 chr4qtel1M 363635 363676 (636324) (C)n#Simple_repeat 1 42 (0) c_b199s251i1 7819 chr4qtel1M 363635 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCGCCCCCC 363676 v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 42 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 219 25.73 12.21 2.08 chr4qtel1M 363827 363957 (636043) C L2b_3end#LINE/L2 (171) 295 152 m_b199s601i12 7820 chr4qtel1M 363827 GCAGGCTTGGGGGGATCT-GAG-AGTATGCCGGGT---GCCTGGGG--TC 363869 i vi ii i- - vii v ii--- -- C L2b_3end#LINE 295 GTAGGACTGGGGGGGCCCAGAGGAGGGCGCCTGACCCGGCCTGGGGGGTC 246 chr4qtel1M 363870 AGGGAGGGCTTCCTGAAGGAGGTG---CTCGAGCC-AGAACTGGAGATTT 363915 i i ---i i i- v i iv v C L2b_3end#LINE 245 AGGGAGGGCTTCCCGGAGGAGGTGACATTTGAGCTGAGACCTGAAGGATG 196 chr4qtel1M 363916 C-----CGTTCCTCAGGCACAGGAGGAGGGGAGAAGGAAGTTCCTGG 363957 v-----v vvi i- i v -- iv v C L2b_3end#LINE 195 AGTAGGAGTTGGCCAGGCG-AAGAGGTGGG--GAAGGGCGTTCCAGG 152 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.93 CpG sites = 20, Kimura (unadjusted) = 32.40 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.08 (10 / 130), avg. gap size = 1.90 (19 / 10) 53 6.35 2.27 3.45 chr4qtel1M 365250 365337 (634663) (GT)n#Simple_repeat 1 87 (0) c_b199s251i2 7821 chr4qtel1M 365250 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGAT-TGACTGTG 365298 - - vv (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG-TGTGTGTGTG 49 chr4qtel1M 365299 TGAT-TGTGAGTGCGATGTGTCTGTGTGTGTGTGTGTGTG 365337 - - v i - v (GT)n#Simple_ 50 TG-TGTGTGTGTGTG-TGTGTGTGTGTGTGTGTGTGTGTG 87 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.06 (5 / 87), avg. gap size = 1.00 (5 / 5) 25 22.26 0.00 1.72 chr4qtel1M 365342 365400 (634600) (TG)n#Simple_repeat 1 58 (0) m_b199s252i18 7822 chr4qtel1M 365342 TGTGTGTGTGACAGAGTGTGTGACCGTGTGAGATGTATGTGTGTATGTGT 365391 vvv v vvi v - i i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG-TGTGTGTGTGTGTGTGT 49 chr4qtel1M 365392 GTCTGTGTG 365400 v (TG)n#Simple_ 50 GTGTGTGTG 58 Matrix = Unknown Transitions / transversions = 0.38 (3/8) Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1) 257 30.42 12.23 2.39 chr4qtel1M 365984 366212 (633788) Charlie1a#DNA/hAT-Charlie 1075 1325 (130) m_b199s502i1 7823 chr4qtel1M 365984 TTTTCTTC-TCTGCTTCAACCAGAAAGTGATACGGCAG-GGATTGAACTC 366031 - v i i vivv iv i-i iv Charlie1a#DNA 1075 TTTTCTTCATATACTTCAACCAAAACAACATATCGCAACAGATTGAATGC 1124 chr4qtel1M 366032 AGACCCCACCACA-----CAAGC-GTCCCCCAT---GCCAGACGCGGAAG 366072 vv vivi ii----- v - ii i --- iivi Charlie1a#DNA 1125 AGAAGCAGATATGAGAATCCAGCTGTCTTCTATTAAGCCAGACATTAAAG 1174 chr4qtel1M 366073 GGC----CAAAACTGGAGAAGAAACATGTGCAGCTTTTCTTGTTCGTTTT 366118 i v---- v v i v ----- vi i iii viv Charlie1a#DNA 1175 AGATTTGCAAAAATGTAAAACAA-----TGCCACTCTTCTCACTAAATTT 1219 chr4qtel1M 366119 TGTTTGTCCTAGAAAATAGCATCAATTGTCACAAAAAC--GGAATTTTTG 366166 - ii i vvi i v v i i-- vv v Charlie1a#DNA 1220 T-TTTGTTTTGGAAAATATAGTTATTTTTCATAAAAATATGTTATTTATG 1268 chr4qtel1M 366167 CCAACACATGATG---CTATCGTTATTTTGAAAT--------AAATATTT 366205 ii ii i ---i ii v -------- Charlie1a#DNA 1269 TTAACATGTAATGGGTTTATTATTATTTTTAAATGAATTAATAAATATTT 1318 chr4qtel1M 366206 TCAAAAT 366212 v Charlie1a#DNA 1319 TAAAAAT 1325 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 40.34 CpG sites = 40, Kimura (unadjusted) = 40.34 Transitions / transversions = 1.43 (40/28) Gap_init rate = 0.07 (15 / 228), avg. gap size = 2.27 (34 / 15) 16 17.92 2.08 4.26 chr4qtel1M 367891 367938 (632062) (CCTCCC)n#Simple_repeat 1 47 (0) m_b199s252i19 7824 chr4qtel1M 367891 CCGCCCCACTCCGCC-CCCTCCCCCGCTTCCCCTCCCCCACCCCCCTCC 367938 v - v - i i v i -i (CCTCCC)n#Sim 1 CCTCCCC-CTCCCCCTCCCCCTCCCCCTCCCCCTCCCCC-TCCCCCTCC 47 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.06 (3 / 47), avg. gap size = 1.00 (3 / 3) 252 26.92 15.38 0.00 chr4qtel1M 369747 369824 (630176) MIRc#SINE/MIR 26 115 (153) m_b199s601i13 7825 chr4qtel1M 369747 AGCGCCAGTCCCGAAATCAGGAGGACC------------CAGACACTTAC 369784 i ii v ii i i i ------------ v i v vv MIRc#SINE/MIR 26 AGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCC 75 chr4qtel1M 369785 ACTTCCTGGCTGTGTGGCTCTGGGCAAGTCACTGAACCCC 369824 v i i ii v i MIRc#SINE/MIR 76 ACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.72 CpG sites = 14, Kimura (unadjusted) = 34.72 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.01 (1 / 77), avg. gap size = 12.00 (12 / 1) 237 28.36 1.49 0.00 chr4qtel1M 369769 369835 (630165) MIR#SINE/MIR 56 123 (139) m_b199s601i14 7825 chr4qtel1M 369769 GGACCCAGACACTTACACTTCCTGGCTGTGTGGCTCTGGGCAAGTCACTG 369818 i i v i v vv v i i ii i v MIR#SINE/MIR 56 GAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTT 105 chr4qtel1M 369819 AACCCCGAC-TGCCTCGG 369835 i vvi- i MIR#SINE/MIR 106 AACCTCTCTGTGCCTCAG 123 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.51 CpG sites = 11, Kimura (unadjusted) = 36.51 Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.02 (1 / 66), avg. gap size = 1.00 (1 / 1) 14 4.54 0.00 4.17 chr4qtel1M 369836 369860 (630140) (GAAA)n#Simple_repeat 1 24 (0) m_b199s252i20 7826 chr4qtel1M 369836 GAAAAAAAGAAAGAAAGAAAAGAAA 369860 i - (GAAA)n#Simpl 1 GAAAGAAAGAAAGAAAG-AAAGAAA 24 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 13 4.17 8.00 0.00 chr4qtel1M 369837 369861 (630139) (AAGAA)n#Simple_repeat 1 27 (0) m_b199s252i21 7826 chr4qtel1M 369837 AAAAAAAG-AAAG-AAAGAAAAGAAAA 369861 i - - (AAGAA)n#Simp 1 AAGAAAAGAAAAGAAAAGAAAAGAAAA 27 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.08 (2 / 24), avg. gap size = 1.00 (2 / 2) 280 28.08 4.44 1.08 chr4qtel1M 370378 370467 (629533) MIR#SINE/MIR 90 182 (80) m_b199s601i15 7827 chr4qtel1M 370378 CCTGGACAAGCCCCTGAACCATGGCT-TGCCTCAGCTTCCCCATCTGTCA 370426 i i iiv v - vv - i i v MIR#SINE/MIR 90 CTTGGGCAAGTTACTTAACC-TCTCTGTGCCTCAGTTTCCTCATCTGTAA 138 chr4qtel1M 370427 AATGGGGATCACTGTCGTGCTT-CTGCATGAAG--GTCGTAAGG 370467 v ivi v i i - iv iii -- i i MIR#SINE/MIR 139 AATGGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGG 182 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.52 CpG sites = 16, Kimura (unadjusted) = 36.52 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.04 (4 / 89), avg. gap size = 1.25 (5 / 4) 13 8.89 0.00 4.00 chr4qtel1M 371090 371115 (628885) (CTCC)n#Simple_repeat 1 25 (0) m_b200s252i2 7828 chr4qtel1M 371090 CTCCCGTGCCTCCCTCCCTGCCTCCC 371115 - v v (CTCC)n#Simpl 1 CTCCC-TCCCTCCCTCCCTCCCTCCC 25 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.04 (1 / 25), avg. gap size = 1.00 (1 / 1) 248 18.21 20.00 5.88 chr4qtel1M 371177 371281 (628719) MIRc#SINE/MIR 30 148 (120) m_b200s601i2 7829 chr4qtel1M 371177 CTGGGCCAGGAGTCAGGAAGACTT---CTCCAGGGCCAGATCTGGCCCCA 371223 i iv i ---i v vv i v --- MIRc#SINE/MIR 30 CTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTG---CCA 76 chr4qtel1M 371224 GGCTCTTCCCAGCCGTGT--------GCA--TCACTG----TTTC----C 371255 ---- v i i -------- -- v---- i ---- MIRc#SINE/MIR 77 ----CTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGC 122 chr4qtel1M 371256 TTCAGTTTCCTCTTCTGTAAAATGAG 371281 i v i MIRc#SINE/MIR 123 CTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 20.01 CpG sites = 10, Kimura (unadjusted) = 21.28 Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.12 (12 / 104), avg. gap size = 2.33 (28 / 12) 205 28.72 4.26 0.00 chr4qtel1M 372351 372444 (627556) MIR1_Amn#SINE/MIR 50 147 (83) m_b200s601i3 7830 chr4qtel1M 372351 AGAACCGGGTGCAGGTCCC---TCTGCTGACCGTCACGCGTGTGACCCCG 372397 v i v ?i? --- iivi? i ?vvi ? ii MIR1_Amn#SINE 50 AGACCTGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTG 99 chr4qtel1M 372398 GGGAGCTGGCTTTTGCTCTCCGCACCTCAGGCTTCTCGTCT-TAAAAT 372444 v iv vi ?vv i ?i vi i i - MIR1_Amn#SINE 100 GGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAAT 147 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 41.37 CpG sites = 16, Kimura (unadjusted) = 41.37 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.02 (2 / 93), avg. gap size = 2.00 (4 / 2) 209 28.12 0.93 6.93 chr4qtel1M 375307 375413 (624587) C L2d2_3end#LINE/L2 (338) 217 117 m_b200s601i4 7831 chr4qtel1M 375307 GCTGAACCTTGATGGATCC-CAGGAGCTGGTGGGGGTGGGGAGGAGAAAG 375355 ii v vv-i vi -ivi i - ii C L2d2_3end#LIN 217 GCTGGGCCTTGAAGGATGGGTAGGATTTGG-ATAGGTGGAGAGGA-AGGG 170 chr4qtel1M 375356 GAGGGGAAACATTTGAGGCTTCAGGGATGGCCTGAGCAAAATAGCACAAA 375405 i --- iv vvvi i i v --i i i C L2d2_3end#LIN 169 GAAGGG---CATTCCAGGCGGGGGGAACGGCGTGAGCAAA--GGCGCAGA 125 chr4qtel1M 375406 GGTGGGAA 375413 i C L2d2_3end#LIN 124 GGCGGGAA 117 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 31.62 CpG sites = 18, Kimura (unadjusted) = 36.39 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.08 (8 / 106), avg. gap size = 1.00 (8 / 8) 384 16.92 1.54 0.00 chr4qtel1M 375785 375849 (624151) MIR#SINE/MIR 92 157 (105) m_b200s601i5 7832 chr4qtel1M 375785 TAGGCAAGTTACTTCACCCCATT-TGTCTCAGTTTTCCCATCTATAAAAT 375833 i v i vi - i i i i MIR#SINE/MIR 92 TGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAAT 141 chr4qtel1M 375834 GGGGACAATAATAATA 375849 i i MIR#SINE/MIR 142 GGGGATAATAATAGTA 157 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 19.97 CpG sites = 9, Kimura (unadjusted) = 19.97 Transitions / transversions = 4.50 (9/2) Gap_init rate = 0.02 (1 / 64), avg. gap size = 1.00 (1 / 1) 352 26.93 9.09 4.35 chr4qtel1M 375855 375986 (624014) MIRc#SINE/MIR 11 148 (120) m_b200s601i6 7833 chr4qtel1M 375855 TGGCACTATGGATAAAACTCTGAGCTTGAAATCAGGATGATTTGGCTTCC 375904 ii vi v i i v ii i i v ii v - MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC- 59 chr4qtel1M 375905 TGAGTTCAAA-GCTGAC-CTCA--AGT--------CCTGAGCAAGTCACT 375942 - i vii-v v - i -- i-------- i i MIRc#SINE/MIR 60 -GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACT 108 chr4qtel1M 375943 TAAACTCATTTGGTTTGCCTTAGTTTCCTCAGCTGTAACAGGAG 375986 v - i i--- i v v v i MIRc#SINE/MIR 109 TAACCTC-TCTGA---GCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 33.40 CpG sites = 22, Kimura (unadjusted) = 34.67 Transitions / transversions = 1.83 (22/12) Gap_init rate = 0.08 (10 / 131), avg. gap size = 1.80 (18 / 10) 310 25.00 10.53 0.00 chr4qtel1M 376099 376174 (623826) C MIRc#SINE/MIR (155) 113 30 m_b200s601i7 7834 chr4qtel1M 376099 GGTTAAATGACTTGCCCAGAGTCACATAGTTACTA----GCTGAGTC--- 376141 i ii i i v ---- v i --- C MIRc#SINE/MIR 113 GGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGG 64 chr4qtel1M 376142 -CTTGAACTTGGGTCTTACTGCTTGCAGGCTCAG 376174 - i iii v vi v i ii C MIRc#SINE/MIR 63 ACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAG 30 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 29.95 CpG sites = 14, Kimura (unadjusted) = 32.00 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.04 (3 / 75), avg. gap size = 2.67 (8 / 3) 203 32.88 1.37 0.00 chr4qtel1M 376438 376510 (623490) C L3#LINE/CR1 (223) 3876 3803 m_b200s601i8 7835 chr4qtel1M 376438 CTAACTCCTTGCAGCTTCC-CCCACTTTTCCTGGCCCCATCCTCACGGGC 376486 iv i i i - i vv i ii iii vv i C L3#LINE/CR1 3876 CTGCCTCCCTGTAACTTCCACCCATTGGTCCTAGTTCTGCCCTCTGGAGC 3827 chr4qtel1M 376487 CACATGAAGCAAATCTAGTCCCTC 376510 iii ii i i C L3#LINE/CR1 3826 CACACAGAATAAGTCTAATCCCTC 3803 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 48.15 CpG sites = 19, Kimura (unadjusted) = 48.15 Transitions / transversions = 3.80 (19/5) Gap_init rate = 0.01 (1 / 72), avg. gap size = 1.00 (1 / 1) 15 0.00 0.00 0.00 chr4qtel1M 376583 376599 (623401) (GT)n#Simple_repeat 1 17 (0) m_b200s252i3 7836 chr4qtel1M 376583 GTGTGTGTGTGTGTGTG 376599 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTG 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 236 32.91 1.27 0.00 chr4qtel1M 377165 377243 (622757) MIR3#SINE/MIR 114 193 (15) m_b200s601i9 7837 chr4qtel1M 377165 CTGGCTCTTCCTTTCCTCTCCTGTAAATGAAAAGGGTTGGCCTGGATGGC 377214 vi ivv vi vvi ii v i ii MIR3#SINE/MIR 114 CTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGAT 163 chr4qtel1M 377215 CT-TGAGGTCCCTCTCAATGCTCAGGTTTT 377243 - i ii iiv v vi i MIR3#SINE/MIR 164 CTCTAAGGTCCCTTCCAGCTCTGACATTCT 193 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 45.22 CpG sites = 16, Kimura (unadjusted) = 45.22 Transitions / transversions = 1.60 (16/10) Gap_init rate = 0.01 (1 / 78), avg. gap size = 1.00 (1 / 1) 72 17.67 2.07 0.00 chr4qtel1M 377668 377812 (622188) (CCTCTT)n#Simple_repeat 1 148 (0) m_b200s252i4 7838 chr4qtel1M 377668 CCTCTTCCAGTTCCTCCTCCTTCTCCTCTTCCTC-T--TCTTCCTCTTCC 377714 vv i ii - -- (CCTCTT)n#Sim 1 CCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCC 50 chr4qtel1M 377715 TCTTCCTCCTTCTCCTTCTCCTTCTCTTCCTCTTCCTCCTTCTCCTTCTC 377764 i i i i i i i i i i (CCTCTT)n#Sim 51 TCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTC 100 chr4qtel1M 377765 CTTCTCTTCCTCTTCCTCCTTCTCCTTCTCTTCCTCTTCCTCATCCTC 377812 i i i i i i v (CCTCTT)n#Sim 101 TTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTC 148 Matrix = Unknown Transitions / transversions = 6.33 (19/3) Gap_init rate = 0.01 (2 / 144), avg. gap size = 1.50 (3 / 2) 262 24.56 4.24 3.36 chr4qtel1M 377934 378051 (621949) C Charlie4a#DNA/hAT-Charlie (34) 474 356 m_b200s502i1 7839 chr4qtel1M 377934 CTTTGAGGGTCTGGAGGAGC--ATGGATCCCTCCTCTGAGTGACATTTT- 377980 ivi v i -- i i v i i ii - C Charlie4a#DNA 474 CTTTGGCAGTCTGGTGAAGCCTATGGACCCCTTCTCAGAATAATGTTTTT 425 chr4qtel1M 377981 ATTTGCATAAAATAAAATAAGTAGAGA--AAAATCCAGGAAACCAACTTT 378028 vv vi - -- v --- i v C Charlie4a#DNA 424 AAATGCATAAAATAAAATACATAG-GATTACAA---AGGAAACCAATTAT 379 chr4qtel1M 378029 TGTGATAAACGGTGAGCCAAGTA 378051 vv v v i v v v i C Charlie4a#DNA 378 ATTGAAATACAGTTATCAAAATA 356 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 29.92 CpG sites = 13, Kimura (unadjusted) = 29.92 Transitions / transversions = 0.87 (13/15) Gap_init rate = 0.06 (7 / 117), avg. gap size = 1.29 (9 / 7) 268 20.21 5.38 4.26 chr4qtel1M 377934 378026 (621974) C Charlie4#DNA/hAT-Charlie (34) 3344 3251 m_b200s502i0 7839 chr4qtel1M 377934 CTTTGAGGGTCTGGAGGAGC--ATGGATCCCTCCTCTGAGTGACATTTT- 377980 ivi v i -- i i v i i ii - C Charlie4#DNA/ 3344 CTTTGGCAGTCTGGTGAAGCCTATGGACCCCTTCTCAGAATAATGTTTTT 3295 chr4qtel1M 377981 ATTTGCATAAAATAAAATAAGTAGAGA--AAAATCCAGGAAACCAACT 378026 vv vi - -- v --- i C Charlie4#DNA/ 3294 AAATGCATAAAATAAAATACATAG-GATTACAA---AGGAAACCAATT 3251 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 23.99 CpG sites = 11, Kimura (unadjusted) = 23.99 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.08 (7 / 92), avg. gap size = 1.29 (9 / 7) 15 0.00 4.55 0.00 chr4qtel1M 378260 378281 (621719) (ACAA)n#Simple_repeat 1 23 (0) m_b200s252i5 7840 chr4qtel1M 378260 ACAAACAAACAAACAAA-AAACA 378281 - (ACAA)n#Simpl 1 ACAAACAAACAAACAAACAAACA 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.05 (1 / 21), avg. gap size = 1.00 (1 / 1) 25 21.79 4.08 4.08 chr4qtel1M 378394 378491 (621509) (CAAAA)n#Simple_repeat 1 98 (0) m_b200s252i6 7841 chr4qtel1M 378394 CAAAAGAAAACACAGACTAAAAC-ACAC-ACACGCAAC-ACACAAAACCC 378440 v - i - - v - v iv - v vv (CAAAA)n#Simp 1 CAAAACAAAACA-AAAC-AAAACAAAACAAAACAAAACAAAACAAAACAA 48 chr4qtel1M 378441 AACAACA-ATAACAAACCCAAACACACCAAAAACAAAACCCAACAAAAAC 378489 v - v v v v v - vv - (CAAAA)n#Simp 49 AACAAAACAAAACAAAACAAAACAAAAC-AAAACAAAACAAAAC-AAAAC 96 chr4qtel1M 378490 AA 378491 (CAAAA)n#Simp 97 AA 98 Matrix = Unknown Transitions / transversions = 0.13 (2/15) Gap_init rate = 0.08 (8 / 97), avg. gap size = 1.00 (8 / 8) 521 22.03 3.97 6.80 chr4qtel1M 378785 378935 (621065) MIRc#SINE/MIR 2 148 (120) m_b200s601i10 7842 chr4qtel1M 378785 GAGGCAGCTAGGTGGCGCACTAGATAGCGTGTCACACCT-ACCTGGAGTC 378833 i--- i v i v v ----- iv- i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAG-----CACTGGACTTGGAGTC 43 chr4qtel1M 378834 AGGAAGAGCCATTTTCCTGAATTCAAA-TCT---ACTTACTAGTTCTATG 378879 v iivv -- i i vii- --- i v i MIRc#SINE/MIR 44 AGGAAGACCTGGGTTC--GAGTCCCGGCTCTGCCACTTACTAGCTGTGTG 91 chr4qtel1M 378880 ATCCTGAGCAAGTCATTTAACC-CTATTTGCCTCAGTTTCCTCACCTGTA 378928 i i i i - v vv i MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTA 141 chr4qtel1M 378929 AAATGAG 378935 i MIRc#SINE/MIR 142 AAATGGG 148 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 25.58 CpG sites = 19, Kimura (unadjusted) = 26.56 Transitions / transversions = 1.58 (19/12) Gap_init rate = 0.09 (14 / 150), avg. gap size = 1.14 (16 / 14) 281 27.69 7.49 1.52 chr4qtel1M 379285 379471 (620529) C L1PB4_3end#LINE/L1 (692) 211 14 m_b200s551i0 7843 chr4qtel1M 379285 TTCTGACAGGTGTCAGA----ATTTAA-----GTTCTTAAATTTGTGTTT 379325 v v ---- i v ----- i -- ii C L1PB4_3end#LI 211 TTCTGACTGGTGTAAGATGGTATCTCATTGTGGTTTT--AATTTGCATTT 164 chr4qtel1M 379326 TTCTAATCAATAGTTATCTAGAGCGTTTTCCCCTGTGACC-TAGGTAGCT 379374 i i v v v v v i ii v i vii- v iv C L1PB4_3end#LI 163 CTCTGATGATTAGTGATGTTGAGCATTTTTTCATATGTTTGTTGGCCGCT 114 chr4qtel1M 379375 TTGATTTCTTTTTCTGAAAG----CTGTTCATATCCTTTGACCATTTATC 379420 vv v i i i---- i v i v i C L1PB4_3end#LI 113 TGTATGTCTTCTTTTGAAAAATGTCTGTTCATGTCCTTTGCCCACTTTTT 64 chr4qtel1M 379421 AATTGGGGAATAACTTGTATTCTTACAGATTTGAGTTAGTCTCCTTGTAG 379470 v vv vvv v v iiv v vv v - C L1PB4_3end#LI 63 AATGGGGTTATTTGTTTTTTTCTTGTTGAGTTGTTTGAGT-TCCTTGTAG 15 chr4qtel1M 379471 A 379471 C L1PB4_3end#LI 14 A 14 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 34.69 CpG sites = 21, Kimura (unadjusted) = 34.69 Transitions / transversions = 0.70 (21/30) Gap_init rate = 0.04 (7 / 186), avg. gap size = 2.43 (17 / 7) 12 5.76 13.16 2.38 chr4qtel1M 379656 379693 (620307) (GGAAATA)n#Simple_repeat 1 42 (0) m_b200s252i7 7844 chr4qtel1M 379656 GGAAACAGG-AA-A-GAAAT-GCAAATCAGG-AATAGGAAATA 379693 i - - - - v - - (GGAAATA)n#Si 1 GGAAATAGGAAATAGGAAATAGGAAAT-AGGAAATAGGAAATA 42 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.16 (6 / 37), avg. gap size = 1.00 (6 / 6) 15 13.87 0.00 0.00 chr4qtel1M 380113 380136 (619864) (T)n#Simple_repeat 1 24 (0) m_b200s252i8 7845 chr4qtel1M 380113 TTTTTTTATTTTTGTTTTTGTTTT 380136 v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTT 24 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 394 25.48 3.45 5.26 chr4qtel1M 380149 380264 (619736) C MIRc#SINE/MIR (153) 115 2 m_b200s601i11 7846 chr4qtel1M 380149 GGGGTTAAGTGACTTGCGGAGGTTCATATAGCTAGGAAGTGTTA-AGTGT 380197 i vv i v i i v vi - i-- C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGC-- 68 chr4qtel1M 380198 TTGAGACTAGGA---AGGCCCTCCTGACTTCAGGGCTGGTGCTCTATCCA 380244 -i i v i --- i i i i v ii v C MIRc#SINE/MIR 67 -CGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCA 19 chr4qtel1M 380245 TTGCGTCACCTAGCTGCCCC 380264 i ii ---i i C MIRc#SINE/MIR 18 CTGCACCAC---ACTGCCTC 2 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 31.17 CpG sites = 20, Kimura (unadjusted) = 32.60 Transitions / transversions = 2.50 (20/8) Gap_init rate = 0.07 (8 / 115), avg. gap size = 1.25 (10 / 8) 196 10.00 0.00 0.00 chr4qtel1M 381455 381484 (618516) C L2d_3end#LINE/L2 (0) 516 487 m_b200s601i12 7847 chr4qtel1M 381455 TCAATCAATCAATCAACAGGCATTTATTAA 381484 i i i C L2d_3end#LINE 516 TCAATCAATCAATCAACAAGTATTTATTGA 487 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 11.16 CpG sites = 3, Kimura (unadjusted) = 11.16 Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 229 29.51 0.00 0.00 chr4qtel1M 381481 381541 (618459) C L2d2_3end#LINE/L2 (494) 61 1 m_b200s601i13 7848 chr4qtel1M 381481 TTAATGAAGAGGAGTAACTAAAAATGAGTCTGGAAAGACAGGTTGGAGCC 381530 vi ? i i iivii i i v i? i C L2d2_3end#LIN 61 TTCGTGNAGGGGAATAGTGGGAGATAAGGCTGGAAAGGNAGGTTGGGGCC 12 chr4qtel1M 381531 AGCTTGTACAG 381541 v i iv C L2d2_3end#LIN 11 AGATCGTGGAG 1 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 35.86 CpG sites = 13, Kimura (unadjusted) = 41.91 Transitions / transversions = 2.60 (13/5) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 225 39.32 1.68 1.68 chr4qtel1M 381486 381604 (618396) C AmnL2-1#LINE/L2 (324) 2289 2171 m_b200s601i14 7848 chr4qtel1M 381486 GAAGAGGAGTAACTAAAAATGAGTCTGGAAAGACAGGTTGGAGCCAGCTT 381535 i i ivv i i ii viiv vi ii i v iii C AmnL2-1#LINE/ 2289 GGAGGGGAGTAGAGAGAGACAAGGTCCGTGAGGTAGGCTGGAGCAAGTCC 2240 chr4qtel1M 381536 GTACAGGGCTTTGAATGCCAAACAAAAACA--TTTGTACTTGATCCTAGC 381583 i iv i i vi -- vi ii -- v v iiv C AmnL2-1#LINE/ 2239 ATGGAGGGTTTTAAAAAC--AAGGAAGGCAATTTTGAACTGGATCCTGAA 2192 chr4qtel1M 381584 AGCAAAAGGGAATTACTGGAG 381604 vv vi iii v C AmnL2-1#LINE/ 2191 ATGAATGGGGAGCCAGTGGAG 2171 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 60.42 CpG sites = 30, Kimura (unadjusted) = 60.42 Transitions / transversions = 1.88 (30/16) Gap_init rate = 0.03 (3 / 118), avg. gap size = 1.33 (4 / 3) 393 26.76 4.65 1.50 chr4qtel1M 382110 382238 (617762) C L2a_3end#LINE/L2 (2) 515 383 m_b200s601i15 7849 chr4qtel1M 382110 TCAGTCAGTCAACAGGTATTTTATTA--TGATTACTGTAGGCCAAGGACT 382157 v v ii - i--i vi i iv i v C L2a_3end#LINE 515 TCATTCATTCAACAAATATTT-ATTGAGCGCCTACTATGTGCCAGGCACT 467 chr4qtel1M 382158 GTGCTAAGTGCTGGAGATCCAAATCCTGA-CAAAA-GGA-AACAGCCCCT 382204 v i i i v i-ivv - -i - v i C L2a_3end#LINE 466 GTTCTAGGCGCTGGGGATACAG-CAGTGAACAAAACAGACAAAAGTCCCT 418 chr4qtel1M 382205 GCC-TCAAGGAGCTCACCTTCTAAAAGTAGAAGAC 382238 - v i v ivi vi i C L2a_3end#LINE 417 GCCCTCATGGAGCTTACATTCTAGTGGGGGGAGAC 383 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 31.51 CpG sites = 20, Kimura (unadjusted) = 33.91 Transitions / transversions = 1.43 (20/14) Gap_init rate = 0.05 (7 / 128), avg. gap size = 1.14 (8 / 7) 284 32.18 1.15 0.00 chr4qtel1M 383073 383159 (616841) L2c_3end#LINE/L2 383 470 (8) m_b200s601i16 7850 chr4qtel1M 383073 GCCCTCCGAGAGTGGGGACCGGTTCAT-TTCTTGTCTCCACCCCCAGTAC 383121 i iii i ii vv v - v v i vi i ii L2c_3end#LINE 383 GCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTATCCCCAGCGC 432 chr4qtel1M 383122 CTGGTACACAGTAGGTGCTTAAAATATGCTCTTTGCAT 383159 i i i i v v i iv v L2c_3end#LINE 433 CTGGCACATAGTAGGCGCTCAATAAATGTTTGTTGAAT 470 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 39.72 CpG sites = 18, Kimura (unadjusted) = 44.15 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.01 (1 / 86), avg. gap size = 1.00 (1 / 1) 180 24.39 0.00 0.00 chr4qtel1M 383797 383837 (616163) MIR3#SINE/MIR 148 188 (20) m_b200s601i17 7851 chr4qtel1M 383797 GGTTGGCCTTCATGGCCATTAGGGCCCCTTCCAGCTCTAAC 383837 v vv ii vi i i i MIR3#SINE/MIR 148 GGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGAC 188 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 30.16 CpG sites = 6, Kimura (unadjusted) = 30.16 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 225 13.75 0.00 11.86 chr4qtel1M 385201 385266 (614734) HSAT5v1#Satellite 5222 5280 (618) m_b200s502i2 7852 chr4qtel1M 385201 TGTGCATGTGCACACGTGTGTGCGTATGTGTGTGGGTGTGTGCACTGTGT 385250 ii i i i ii ---- ? - i HSAT5v1#Satel 5222 TGTGTGTGTGCACGCGCGTGCGCGCGTGTGT----GTGTGTGNAC-GCGT 5266 chr4qtel1M 385251 GTGTGCGTACGTGTGT 385266 -- HSAT5v1#Satel 5267 GTGTGCG--CGTGTGT 5280 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 6.24 CpG sites = 8, Kimura (unadjusted) = 16.14 Transitions / transversions = 1.00 (8/0) Gap_init rate = 0.11 (7 / 65), avg. gap size = 1.00 (7 / 7) 18 21.38 0.00 0.00 chr4qtel1M 385270 385307 (614693) (TG)n#Simple_repeat 1 38 (0) m_b200s252i9 7853 chr4qtel1M 385270 TGTGTGTCCGTGTGTGTCCATGTGTGGATGTGTGTGTG 385307 vi vii vi (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 38 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 229 20.55 8.33 5.41 chr4qtel1M 385309 385380 (614620) HSAT5v1#Satellite 5208 5281 (617) m_b200s502i3 7854 chr4qtel1M 385309 ATGTGTGCAC------TGTGTGTGCATACGTGTGTGCATGTGCATGTGTG 385352 i i------ ii i i ii ii HSAT5v1#Satel 5208 ATGCGTGCATGCAATGTGTGTGTGCACGCGCGTGCGCGCGTGTGTGTGTG 5257 chr4qtel1M 385353 TGTATGTGTGTACACGTGCATGTGTGTC 385380 ? i i ---- ii HSAT5v1#Satel 5258 TGNACGCGTGT----GTGCGCGTGTGTC 5281 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 7.91 CpG sites = 14, Kimura (unadjusted) = 27.06 Transitions / transversions = 1.00 (14/0) Gap_init rate = 0.07 (5 / 71), avg. gap size = 2.00 (10 / 5) 229 29.41 1.47 0.00 chr4qtel1M 385320 385387 (614613) HSAT5v1#Satellite 5212 5280 (618) m_b200s502i4 7854 chr4qtel1M 385320 GTGTGTGCA-TACGTGTGTGCATGTGCATGTGTGTGTATGTGTGTACACG 385368 ii - ii i i i i i i i iii?i HSAT5v1#Satel 5212 GTGCATGCAATGTGTGTGTGCACGCGCGTGCGCGCGTGTGTGTGTGTGNA 5261 chr4qtel1M 385369 TGCATGTGTGTCCATGTGT 385387 i i iv i HSAT5v1#Satel 5262 CGCGTGTGTGCGCGTGTGT 5280 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 19.56 CpG sites = 19, Kimura (unadjusted) = 44.38 Transitions / transversions = 19.00 (19/1) Gap_init rate = 0.01 (1 / 67), avg. gap size = 1.00 (1 / 1) 225 23.52 4.29 2.82 chr4qtel1M 385381 385450 (614550) HSAT5v1#Satellite 5207 5277 (621) m_b200s502i5 7854 chr4qtel1M 385381 CATGTGTGGACATG---TGGGTGTGTGCACATGTGTGTGTACATGTGTGC 385427 i -- --- v ii i i ii i i HSAT5v1#Satel 5207 CATGCGTG--CATGCAATGTGTGTGTGCACGCGCGTGCGCGCGTGTGTGT 5254 chr4qtel1M 385428 GCATGTGCATGTGTGTGTGCGTG 385450 ii ?i ii i HSAT5v1#Satel 5255 GTGTGNACGCGTGTGTGCGCGTG 5277 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 11.36 CpG sites = 15, Kimura (unadjusted) = 31.82 Transitions / transversions = 15.00 (15/1) Gap_init rate = 0.04 (3 / 69), avg. gap size = 1.67 (5 / 3) 212 32.37 1.43 2.90 chr4qtel1M 386045 386114 (613886) C MIRc#SINE/MIR (76) 192 124 m_b200s601i18 7855 chr4qtel1M 386045 CCTTACTTCATCCTTGATCAAGGCAGATGAGGTCAGTGTTGTTG-ACCCA 386093 i vv v i --ii i iiii ivi i i i-v C MIRc#SINE/MIR 192 CCTCACAACAACCCTG--TGAGGTAGGCAGGGCAGGTATTATTATCCCCA 145 chr4qtel1M 386094 CTTAACAGATAAGGAAACTGA 386114 i v i C MIRc#SINE/MIR 144 TTTTACAGATGAGGAAACTGA 124 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 45.77 CpG sites = 16, Kimura (unadjusted) = 45.77 Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.04 (3 / 69), avg. gap size = 1.00 (3 / 3) 217 22.22 3.70 0.00 chr4qtel1M 386068 386121 (613879) C MIR1_Amn#SINE/MIR (57) 173 118 m_b200s601i19 7855 chr4qtel1M 386068 CAGATGAGGTCAGTGTTGTTG-ACCCACTTAACAGATAAGGAAACTGAAA 386116 i v i ii i-v i v i ii C MIR1_Amn#SINE 173 CAAAGGAGGTCAGTATCATTATCCCCATTTTACAGATGAGGAAACTGAGG 124 chr4qtel1M 386117 -ACAGA 386121 -? C MIR1_Amn#SINE 123 CNCAGA 118 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 28.23 CpG sites = 9, Kimura (unadjusted) = 28.23 Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.04 (2 / 53), avg. gap size = 1.00 (2 / 2) 181 24.39 23.53 3.52 chr4qtel1M 386248 386366 (613634) MIRc#SINE/MIR 7 148 (120) m_b200s601i20 7856 chr4qtel1M 386248 AGTGCCTGGGGCACTGGAAAGTGAGCTGGATTTGAAG---GGAGGTCACT 386294 -- v v v vi i i --- i -- i MIRc#SINE/MIR 7 AGTG--TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAG--ACC 52 chr4qtel1M 386295 TGGCTTCAAAAAAATGGCTTTGCAGCTT-------------------GCA 386325 v i ivvv-i i vi ------------------- MIRc#SINE/MIR 53 TGGGTTCGAGTCC-CGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 101 chr4qtel1M 386326 --TCCC----CTTCTCTGGGCCTCAGTTTGCTGGTCTGAAAGATGAG 386366 -- v ---- i i v vi v i i MIRc#SINE/MIR 102 AGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 27.67 CpG sites = 15, Kimura (unadjusted) = 30.15 Transitions / transversions = 1.15 (15/13) Gap_init rate = 0.08 (9 / 118), avg. gap size = 3.67 (33 / 9) 262 19.40 2.90 2.90 chr4qtel1M 386330 386398 (613602) MIR3#SINE/MIR 109 177 (31) m_b200s601i21 7856 chr4qtel1M 386330 CTTCTCTGGGCCTCAGTTTGCTGGTCTGAAAGATGAGAGGCTTGTTCTTG 386379 i v vi v i i v vv v MIR3#SINE/MIR 109 CCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAG 158 chr4qtel1M 386380 A--ATCTCCTAGAAGACCCTT 386398 -- - - i v MIR3#SINE/MIR 159 ATGATCT-CTA-AGGTCCCTT 177 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 22.47 CpG sites = 5, Kimura (unadjusted) = 22.47 Transitions / transversions = 0.62 (5/8) Gap_init rate = 0.04 (3 / 68), avg. gap size = 1.33 (4 / 3) 59 25.01 5.78 0.85 chr4qtel1M 386489 386713 (613287) (AGACAG)n#Simple_repeat 1 236 (0) m_b200s252i10 7857 chr4qtel1M 386489 AGATAGACACAGACAGACAGACAAAGAATTAGGGGAGAGAGCGGGGAGAG 386538 i v v v v i vvv - iv - i i v (AGACAG)n#Sim 1 AGACAGAGACAGAGACAGAGACAGAGACAGA-GACAGAGA-CAGAGACAG 48 chr4qtel1M 386539 AGATAGAGACAGAG--AGAGACAGA-A-AGACACAGACCCACAGAAAGAG 386584 i -- - - v vv v v (AGACAG)n#Sim 49 AGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAG 98 chr4qtel1M 386585 ACAGAGACAAAGACAGAG-C-GAGACAGAGAAACA-TCA-AAATAGAGAC 386630 i - - v v -v - i i (AGACAG)n#Sim 99 ACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGAC 148 chr4qtel1M 386631 AGAGA-A-AGACAGAAACAGAGGCAGAG--GGGGGGGGGGA-AGGGAGAG 386675 - - i i --i i ivi i - i v (AGACAG)n#Sim 149 AGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAG 198 chr4qtel1M 386676 AGAGAGTGGGGGAGAAAGAGAGAGCGAAGGAGAAAGAG 386713 v v ivi v v v vi v (AGACAG)n#Sim 199 AGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAG 236 Matrix = Unknown Transitions / transversions = 0.74 (20/27) Gap_init rate = 0.06 (13 / 224), avg. gap size = 1.15 (15 / 13) 14 25.82 0.00 5.88 chr4qtel1M 386654 386707 (613293) (GAGG)n#Simple_repeat 1 51 (0) m_b200s252i11 7858 chr4qtel1M 386654 GAGGGGGGGGGGGAAGGGAGAGAGAGAGTGGGGGAGAAAGAGAGAGCGAA 386703 i i - i i - i - ii i v i (GAGG)n#Simpl 1 GAGGGAGGGAGGG-AGGGAGGGAGGGAG-GGAGG-GAGGGAGGGAGGGAG 47 chr4qtel1M 386704 GGAG 386707 (GAGG)n#Simpl 48 GGAG 51 Matrix = Unknown Transitions / transversions = 9.00 (9/1) Gap_init rate = 0.06 (3 / 53), avg. gap size = 1.00 (3 / 3) 59 25.01 5.78 0.85 chr4qtel1M 386489 386713 (613287) (AGACAG)n#Simple_repeat 1 236 (0) m_b200s252i10 7857 chr4qtel1M 386489 AGATAGACACAGACAGACAGACAAAGAATTAGGGGAGAGAGCGGGGAGAG 386538 i v v v v i vvv - iv - i i v (AGACAG)n#Sim 1 AGACAGAGACAGAGACAGAGACAGAGACAGA-GACAGAGA-CAGAGACAG 48 chr4qtel1M 386539 AGATAGAGACAGAG--AGAGACAGA-A-AGACACAGACCCACAGAAAGAG 386584 i -- - - v vv v v (AGACAG)n#Sim 49 AGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAG 98 chr4qtel1M 386585 ACAGAGACAAAGACAGAG-C-GAGACAGAGAAACA-TCA-AAATAGAGAC 386630 i - - v v -v - i i (AGACAG)n#Sim 99 ACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGAC 148 chr4qtel1M 386631 AGAGA-A-AGACAGAAACAGAGGCAGAG--GGGGGGGGGGA-AGGGAGAG 386675 - - i i --i i ivi i - i v (AGACAG)n#Sim 149 AGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAG 198 chr4qtel1M 386676 AGAGAGTGGGGGAGAAAGAGAGAGCGAAGGAGAAAGAG 386713 v v ivi v v v vi v (AGACAG)n#Sim 199 AGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAG 236 Matrix = Unknown Transitions / transversions = 0.74 (20/27) Gap_init rate = 0.06 (13 / 224), avg. gap size = 1.15 (15 / 13) 267 36.02 1.84 1.22 chr4qtel1M 387641 387803 (612197) C L1PA16_3end#LINE/L1 (503) 410 247 m_b200s551i1 7859 chr4qtel1M 387641 TTGTTGTTCTTGGGGCATATGCCTAGCAGTAGGATCTCTTGAGTCCAGAG 387690 i v i v i i i i i i - vi i v - v C L1PA16_3end#L 410 TTATTTTCCTTTGGGTATATACCCAGTAATGGGAT-TGCTGGGTCGA-AT 363 chr4qtel1M 387691 GATA--TCT-TAGTAATTTTCTACACATAATTCTAAGTGGTTTTCCAGGA 387737 i -- - vv v ii vv v v vi i iiv i vii C L1PA16_3end#L 362 GGTAGTTCTGTTTTAAGTTCTTTGAGAAATCTCCAAACTGCTTTCCACAG 313 chr4qtel1M 387738 TGGCTGGAAAAATCCATTGTTCCACCAACAATGTACCAGCGTGCCTCTCT 387787 i vv ii ivv i i iv v ii i C L1PA16_3end#L 312 TGGCTGAACTAATTTACATTCCCACCAACAGTGTATAAGCGTTCCCTTTT 263 chr4qtel1M 387788 TTCCACAATTTTCCCA 387803 i i iii iv C L1PA16_3end#L 262 CTCCGCAGCCTCGCCA 247 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 49.20 CpG sites = 36, Kimura (unadjusted) = 51.82 Transitions / transversions = 1.64 (36/22) Gap_init rate = 0.02 (4 / 162), avg. gap size = 1.25 (5 / 4) 257 35.02 2.78 1.65 chr4qtel1M 387647 387826 (612174) C L1MA9_3end#LINE/L1 (655) 404 223 m_b200s551i2 7859 chr4qtel1M 387647 TTCTTGGGGCATATGCCTAGCAGTAGGATCTCTTGAGTCCAGAGGATA-- 387694 i v ii i i v i iv v --i v v i -- C L1MA9_3end#LI 404 TCCTTTGGATATATACCCAGAAGTGGGATTGCTGGA--TCATATGGTAGT 357 chr4qtel1M 387695 --TCTTAGTAATTTTCTACACATAATTCTAAGTGGTTTTCCAGGATGGCT 387742 -- v vv i iviv - vi i viiv vi C L1MA9_3end#LI 356 TCTATTTTTAATTTTTTGAGGA-ACCTCCATACTGTTTTCCATAATGGCT 308 chr4qtel1M 387743 GGAAAAATCCATTGTTCCACCAACAATGTACCAGCGTGCCTCTCTTTCCA 387792 v vv ii ivv i i v v v ii i i C L1MA9_3end#LI 307 GTACCAATTTACATTCCCACCAACAGTGTACAAGGGTTCCCTTTTCTCCA 258 chr4qtel1M 387793 CAATTTT-CCCACTCTTCCCATTTTTGGTCATCTT 387826 vii i- v v vii i v v i C L1MA9_3end#LI 257 CATCCTCGCCAACACTTGTTATCTTTTGTCTTTTT 223 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 47.31 CpG sites = 33, Kimura (unadjusted) = 48.40 Transitions / transversions = 1.14 (33/29) Gap_init rate = 0.03 (6 / 179), avg. gap size = 1.33 (8 / 6) 281 34.50 2.76 2.05 chr4qtel1M 387650 387794 (612206) C L1MA1_3end#LINE/L1 (648) 401 256 m_b200s551i3 7859 chr4qtel1M 387650 TTGGGGCATATGCCTAGCAGTAGGATCTCTTGAGTCCAGAGGATATCTTA 387699 v i i i i iv v --i v v i v i C L1MA1_3end#LI 401 TTTGGGTATATACCCAGCAGTGGGATTGCTGGA--TCATATGGTAGCTCA 354 chr4qtel1M 387700 GT----AATTTTCTACACATAATTCTAAGTGGTTTTCCAGGATGGCTGGA 387745 i ---- i i iviv - vi i iiv i vii i v C L1MA1_3end#LI 353 ATTTTTAGTTTTTTGAGGA-ACCTCCAAACTGTTCTCCATAGTGGTTGTA 305 chr4qtel1M 387746 AAAATCCATTGTTCCACCAACAATGTACCAGCGTGCCTCTCTTTCCACA 387794 vv ii ivv i i v v v ii i i C L1MA1_3end#LI 304 CTAATTTACATTCCCACCAACAGTGTACAAGGGTTCCCTTTTCTCCACA 256 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 48.42 CpG sites = 30, Kimura (unadjusted) = 48.42 Transitions / transversions = 1.58 (30/19) Gap_init rate = 0.03 (4 / 144), avg. gap size = 1.75 (7 / 4) 278 22.97 9.46 0.00 chr4qtel1M 387894 387967 (612033) L2d2_3end#LINE/L2 439 519 (36) m_b200s601i22 7860 chr4qtel1M 387894 TTGTTTGCTCCTTGAGGGCA-------TGTCTTACTCATCTTTGTGTCCT 387936 vv ------- iv v i i L2d2_3end#LIN 439 TTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACTTCTTTGTATCCC 488 chr4qtel1M 387937 CCACACAGTTAGGAATAGTGTCTTGCCCACA 387967 vv iivi v i i v L2d2_3end#LIN 489 CCACAGCGCCTAGCACAGTGCCTTGCACACA 519 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 27.58 CpG sites = 8, Kimura (unadjusted) = 27.58 Transitions / transversions = 0.89 (8/9) Gap_init rate = 0.01 (1 / 73), avg. gap size = 7.00 (7 / 1) 292 30.74 17.02 1.38 chr4qtel1M 388173 388360 (611640) L2b_3end#LINE/L2 238 454 (12) m_b200s601i23 7861 chr4qtel1M 388173 CCCTTCCTGACTTCCTGGGTGCCTGTGCTGGCCACCTTCATC-----CCC 388217 i ii ii --- i v iii v i i v ----- L2b_3end#LINE 238 CCCTCCCTGACCCCCCAGG---CCGGGTCAGGCGCCCTCCTCTGGGCCCC 284 chr4qtel1M 388218 TCC---CCTGCTTTGCAGCTCT-----ATC----TCTGCCT-----TCT- 388249 i --- i ii vi ----- ?---- ?i ----- - L2b_3end#LINE 285 CCCAGTCCTACCCTGCCACTCTGGGTTATNATTGTCTGNTTACATGTCTG 334 chr4qtel1M 388250 -CTTCCCTCTTAGAATCCACATTCCTGGAGGGTG----CCACCTTTTCCT 388294 - i ivi v viivii vv ii---- i?v i vi L2b_3end#LINE 335 TCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCT 384 chr4qtel1M 388295 TGTTT----TTGTATTCTCAGTGACTAGCACAGTGCCAGGTACACAGCAA 388340 i----i i i i v ? v i i i L2b_3end#LINE 385 TGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAG 434 chr4qtel1M 388341 GTGCTTCATAAATGCTTGTT 388360 i ivi ii L2b_3end#LINE 435 GCGCTCAGTAAATATTTGTT 454 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 38.91 CpG sites = 42, Kimura (unadjusted) = 44.12 Transitions / transversions = 2.80 (42/15) Gap_init rate = 0.06 (12 / 187), avg. gap size = 2.92 (35 / 12) 352 30.36 8.93 0.00 chr4qtel1M 388249 388360 (611640) L2a_3end#LINE/L2 384 505 (12) m_b200s601i24 7861 chr4qtel1M 388249 TCTTCCCTC-TTAGAATCCACATTCCTGGAGGGTGCCACCTTTTCCTTGT 388297 i i -i vi vii vv iivviv vii L2a_3end#LINE 384 TCTCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTCTGT 433 chr4qtel1M 388298 TTT---------TGTATTCTCAGTGACTAGCACAGTGCCAGGTACACAGC 388338 --------- i i i v v v i i i L2a_3end#LINE 434 TTTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACATAGT 483 chr4qtel1M 388339 AAGTGCTTCATAAATGCTTGTT 388360 i i iv ii L2a_3end#LINE 484 AGGCGCTCAATAAATATTTGTT 505 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 37.57 CpG sites = 22, Kimura (unadjusted) = 40.69 Transitions / transversions = 1.83 (22/12) Gap_init rate = 0.02 (2 / 111), avg. gap size = 5.00 (10 / 2) 678 32.74 2.35 3.42 chr4qtel1M 389633 390312 (609688) L1M5_orf2#LINE/L1 2352 3024 (270) m_b200s551i4 7862 chr4qtel1M 389633 CTACAAGACACTTTCCACACAAATTAAGTCTGATCTAACCAACTGGAAAA 389682 i i viiv v v ivvv i vi v i i L1M5_orf2#LIN 2352 CTACAAAACATTGCTGAGAGAAATTAAAGAAGACCTAAATAAATGGAGAG 2401 chr4qtel1M 389683 ATATTAAGTGCTCTTGGATTGGGCGAGCAAATATAATAAAGATGACAATA 389732 vvvi i v iv viv vi ? v v L1M5_orf2#LIN 2402 ATATACCATGTTCATGGATTGGAAGACTCAATATTGTNAAGATGTCAATT 2451 chr4qtel1M 389733 CTACCTAAACTAATCTATTTATTTAGCGCTATACCAATCAGACTCCCAA- 389781 v i i i vv i ii v v i v i- L1M5_orf2#LIN 2452 CTCCCCAAATTGATCTATAGATTCAATGCAATCCCAATCAAAATCCCAGC 2501 chr4qtel1M 389782 AAACTATTTTGATGACCTAGAAAAAATAACAACCAAGTTCATATGGAAAA 389831 iii v vv vv v v iv i ivviv i i v L1M5_orf2#LIN 2502 AGGTTTTTTTGTAGAAATTGACAAGCTGATTCTAAAATTTATATGGAAAT 2551 chr4qtel1M 389832 ACAAAAGGTCAAGAAT-TTCAAGGGAATTAATGAAAAAAAAAATCAAATG 389880 i i ii ? -vi iiv iv- i i v - L1M5_orf2#LIN 2552 GCAAAGGACCNAGAATAGCCAAAACAATCT-TGAAAAAGAAGAACAAA-G 2599 chr4qtel1M 389881 AAGGTGGCCTAACTGTATCAGATCT-AAAATTATATTATAAGGCAGCGGT 389929 vv v v v vv i ? ? - i i - i vi i L1M5_orf2#LIN 2600 TTGGAGGACTTACACTACCNGATNTCAAGACT-TATTATAAAGCTACAGT 2648 chr4qtel1M 389930 TACTGAAACCATCTGGTATTGGC-TAAGAAATAGACTAGTTGATCAATGG 389978 v iii i vi v - i - v i v L1M5_orf2#LIN 2649 AATCAAGACAGTGTGGTATTGGCGTAAGGA-TAGACAAATAGATCAATGG 2697 chr4qtel1M 389979 ACTAGGTTAG---GTTCAAAGGACAAAACAGCCA-ATAACTTTAATTATC 390024 vi iv --- i i ---- v v v - i vv v ii?i ?i L1M5_orf2#LIN 2698 AACAGAATAGAGAGTCCAGA----AATAGACCCACACATATATGGNCANT 2743 chr4qtel1M 390025 TGGTGTTTGACAAAC---CCAAAGACCCCAGTTT-TTGGGATAAGAACGC 390070 i v v--- ? ---- i i-v iv i iiv L1M5_orf2#LIN 2744 TGATTTTTGACAAAGGTGCCAANG----CAATTCAGTGGGGAAAGGATAG 2789 chr4qtel1M 390071 ATTATTTGACAAAAATTGCTGGGAAAATTGGAAATTAGCATGGCAGAAAC 390120 vi v ii viv i v v ivii v i v L1M5_orf2#LIN 2790 TCTTTTCAACAAATGGTGCTGGAACAATTGGATATCCATATGGAAAAAAA 2839 chr4qtel1M 390121 TAGGCATTGACCCACACTTAACACCATACACCAAGATAAGGTTAAAATGC 390170 iii?v i vi i v v i v iv i? i - L1M5_orf2#LIN 2840 TGAANCTCGACCCCTACCTCACACCATACACAAAAATTAATTCNAGATG- 2888 chr4qtel1M 390171 GTTCAT-GATCTAGGCATAAAGAATGAGATCATAAATAAATTGGAAG--A 390217 v - i iiii ii? i i ii vvvvi i -- L1M5_orf2#LIN 2889 GATCATAGACCTAAATGTAAAAGNTAAAACTATAAAACTTCTAGAAGAAA 2938 chr4qtel1M 390218 GCATGGGATAGTTTCCCTCTCG-GACCTGTGGAAGAGGAAGGAATTTATG 390266 i i v i v ---i - - i?v v iii v - L1M5_orf2#LIN 2939 ACATAGGAGAATATC---TTCGTGACCT-TGGGNTAGGCAAAGATTTCT- 2983 chr4qtel1M 390267 ACCAAAGAAGAACTAGAGATCACTATTGACTACAAAATAGAAAATT 390312 --i v i vvi i i v ? --- i i v i L1M5_orf2#LIN 2984 --TAAACAGGACACAAAAAGCACNA---ACCATAAAAGAAAAAATT 3024 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 44.97 CpG sites = 118, Kimura (unadjusted) = 45.26 Transitions / transversions = 1.22 (118/97) Gap_init rate = 0.05 (34 / 679), avg. gap size = 1.15 (39 / 34) 808 29.46 5.29 3.72 chr4qtel1M 391664 392192 (607808) L1ME3Cz_3end#LINE/L1 12 548 (449) m_b200s551i5 7862 chr4qtel1M 391664 AATAGATAGGGAAC-CGGACCAAAATTA-TAAAAAATAAGAGCCATTCCT 391711 v ii - vv -- i - i - -- --v i L1ME3Cz_3end# 12 AATATATAAAGAACTCCTAC--AAATCAATAAGAAA-AAGA--CA--ACC 54 chr4qtel1M 391712 CAATTAATGAATGGTCAAAGGTTATGAACAAGCAGTTTTCATAAGAAAAA 391761 vi vi v v i i iv v ii L1ME3Cz_3end# 55 CAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGGAA 104 chr4qtel1M 391762 GTCAAAGTGATCAATAGAC-TAGGAAAAGCT--TTAA-ATCACAAATAAT 391807 ii vi i ii i - v v -- i -v v i L1ME3Cz_3end# 105 ACCCGAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTAAT 154 chr4qtel1M 391808 TTTTTAAAAGCAAATTACAATAAGCCTCAGGTACCATCTCATACCCATCA 391857 ivvvv v v i? vvv v i i i L1ME3Cz_3end# 155 CAGGGAAATGCAAATTAAAACNACAATGAGATACCATTTCACACCCATCA 204 chr4qtel1M 391858 AATTGTTTAGTGACAG---AAAAG---GAAAATGAGAAGTTCCTAAAGGG 391901 i ---- ii v i--- --- v ivv - vi iiv i L1ME3Cz_3end# 205 GATTG----GCAAAAATTTAAAAGTCTGACAATACCAAG-TGTTGGCGAG 249 chr4qtel1M 391902 GATGTGGAAAAGTAGGTACAT---TGCATTATTGGTGAAGCTGTGAATTG 391948 i iii v vi--- i i ii iiiv i L1ME3Cz_3end# 250 GATGTGGAGAAACGGGAACTCTCATACACTGCTGGTGGGAGTGTAAATTG 299 chr4qtel1M 391949 GCCCAACCATTCTGGAGAACAATCTGGAACAGTGCCCAAAAGGGTATGAA 391998 iv i i i i -- i ii i iv ii - L1ME3Cz_3end# 300 GTACAACCACTTTGGAGAGCAATTTGG--CAATATCTAGTAAAGT-TGAA 346 chr4qtel1M 391999 ACTGCGCTTACCCTTTCACTCAGTAATACCACTACTGGG--CCTGCCCAA 392046 iv v viv i i v v i --iv i v L1ME3Cz_3end# 347 GATGCGCATACCCTACGACCCAGCAATTCCACTTCTAGGTATATACCCTA 396 chr4qtel1M 392047 GAGA-----TCAAAGAACA-ATTTA-AAGGACTCGTATATACCAAAAT-- 392087 ----- --- v -i vi - vv -- i v ii -- L1ME3Cz_3end# 397 GAGAAACTCTC---GCACATGTGCACAAGGAGAC--ATGTACAAGGATGT 441 chr4qtel1M 392088 --ATAGCAGCTCTTTTTGTAGTGGCAAAGAATTGGAAAGTGAGGGAATGC 392135 -- v vi v i i i i vvivvvi i L1ME3Cz_3end# 442 TCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGT 491 chr4qtel1M 392136 CTATTAATCAGGGAATGGCTGAACAAATTGTGGTATATAATTATATTGGG 392185 i i vi v i i vvv i v i L1ME3Cz_3end# 492 CCATCAATAGGGGAATGGATAAATAAATTGTGGTATATTCATACAATGGA 541 chr4qtel1M 392186 ATACTAT 392192 L1ME3Cz_3end# 542 ATACTAT 548 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 37.20 CpG sites = 87, Kimura (unadjusted) = 38.54 Transitions / transversions = 1.38 (87/63) Gap_init rate = 0.06 (34 / 528), avg. gap size = 1.41 (48 / 34) 640 32.12 6.00 3.34 chr4qtel1M 391685 392267 (607733) L1ME4c_3end#LINE/L1 32 629 (201) m_b200s551i6 7862 chr4qtel1M 391685 AAATT-ATAAAAAATAAGAGCCATTCCTCAATTAATGAATGGTCAAAGGT 391733 - i - ? v v vv i vi i v v L1ME4c_3end#L 32 AAATTGATAAGAAA-AANATCAAGACCCCAATAGATAAATGGGCAAAGGA 80 chr4qtel1M 391734 TATGAACAAGCAGTTTTCATAAGAAAAAGTCAAAGTGATCAATAGAC--- 391780 i ii i iv ? ii i vv ? ii v i i --- L1ME4c_3end#L 81 CATGAACAGACAATTCACANAAGAGGAAATACAANTAGTAAACAAACACA 130 chr4qtel1M 391781 TAGGAAAAGCTTTAAA-TCACAAATAATTTTTTAAAAGCAAATTACAATA 391829 i i vv i v- i v i ivvvv v v ii L1ME4c_3end#L 131 TGGAAAAATGTTCAACCTCGCTAGTAATCAAAGAAATGCAAATTAAAGCA 180 chr4qtel1M 391830 AGCCTCAGGTACCATCTCATACCCATCAAATTGTTTAGTGACAGAAA--- 391876 vvv v i i i ii i i ---- --- i --- L1ME4c_3end#L 181 ACAATGAGATACCATTTTACGCCTATTAAATT----AG---CAAAAATTT 223 chr4qtel1M 391877 AGGAAAATGAGAAGTTCCTAA------AGGGGATGTGGAAAAGTAGGTAC 391920 ii v v - v i ------v i ? i vi iiv L1ME4c_3end#L 224 AAAAAATTGATAA-TACCCAATGCTGGCGAGGNTGCGGTGAAACTGGTAC 272 chr4qtel1M 391921 ATT---GCATTATTGGTGAAGCTGTGAATTGGCCCAACCATTCTGGAGAA 391967 ?i ---i ii ivi? i iv v i i i L1ME4c_3end#L 273 NCTCATACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAAAG 322 chr4qtel1M 391968 CAATCTGGAACAGTGCCCA--AAAGGGTATGAAACTGCGCTTACCCTTTC 392015 i -- i i vi -- ii vi i v iv v v L1ME4c_3end#L 323 CAATTTGG--CAATACGTATCAAGAGCCATAAAAATGTTCATACCCTTTG 370 chr4qtel1M 392016 ACTCAGTAATACCACTACTGGG--CCTGCCCAAGAGATCAAAGAACAATT 392063 i v v --ii ii v ii ------ i L1ME4c_3end#L 371 ACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGA------AATAATT 414 chr4qtel1M 392064 TAAAGGA---------CTCGTATATACCAAAAT----ATAGCAGCTCTTT 392100 i i --------- -i ii v i ---- v vi v L1ME4c_3end#L 415 CAAAAGAAGGAAAAAGCT-ATATGCACGAAGATGTTCATTGCAGCGTTAT 463 chr4qtel1M 392101 TTGTAGTGGCAAAGAATTGGAAAGTGAGGGAATGCCTATTAATCAGGGAA 392150 i i i i i vvivvvi i i vi vi L1ME4c_3end#L 464 TTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAA 513 chr4qtel1M 392151 TGGCTGAACAAATTGTGGTATAT-AATTATATTGGGATACTATTGTGCTG 392199 i i ii i i -? i vv - i i vvv ii L1ME4c_3end#L 514 TGGTTAAGTAAATTATGGTACATCNACTCGA-TGGAATATTATGCAGCCA 562 chr4qtel1M 392200 TAACAAATGATGAAGGAGAAAGTTTTAGAAAAACCTGTGAAAACTTGTAT 392249 v v i vviv iii v iv iv v - iv v L1ME4c_3end#L 563 TTAAAAATGATAATTATGAAGACTATGTAGCAACATG-GAAAATGTTTAT 611 chr4qtel1M 392250 GAACTGATATAAAATGAA 392267 vv i i v i L1ME4c_3end#L 612 GATATAATGTTAAGTGAA 629 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 42.92 CpG sites = 108, Kimura (unadjusted) = 44.29 Transitions / transversions = 1.48 (108/73) Gap_init rate = 0.05 (31 / 582), avg. gap size = 1.77 (55 / 31) 221 38.27 5.61 4.02 chr4qtel1M 392785 392980 (607020) C MamRTE1#LINE/RTE-BovB (1277) 2535 2337 m_b200s601i25 7863 chr4qtel1M 392785 GAATACTGACAAATTTCCCTGGGTGAGCAGATTTTGACATAAT--TTTCC 392832 i vi iii i i v iiiv i i --i v i --i v C MamRTE1#LINE/ 2535 GGATCTTGGTGAACTTCTCAGGGCAGCCAAACTT--GCTTAGTAGCTGCC 2488 chr4qtel1M 392833 A----CGAGGTCTCATAACTGAAAGCATCAAAGCCCTTT----GATGGAA 392874 ---- v ---- vi i vv i ---- i v v C MamRTE1#LINE/ 2487 AGAGCCCAGGTCT----ACTGATGGCGTCAAATGCTTTTGTAAGGTCGAT 2442 chr4qtel1M 392875 GAACATTGGGTACAAATCTCTGTTCTGCTCTTGACATTTCTCCTGGACTT 392924 i iv v i v ii ivi vi i iivi ii i v ii C MamRTE1#LINE/ 2441 GAATACAGTGCAGAGGTCTTGATGTTGTTCCCTGCGCTTTTCCTGTATCT 2392 chr4qtel1M 392925 GTCGAACAGCAAATATCCTATCC-CTTTCCTCCTCCTCCCTTTCTAAAGC 392973 v ivi ? v vii - ? v-- v viiv vvi C MamRTE1#LINE/ 2391 GACATGCNGCAAAGATCACGTCCGCTNTA--CCGCGCTGCGGCCTAAAGC 2344 chr4qtel1M 392974 CACACTG 392980 i C MamRTE1#LINE/ 2343 CACATTG 2337 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 53.97 CpG sites = 44, Kimura (unadjusted) = 57.82 Transitions / transversions = 1.57 (44/28) Gap_init rate = 0.06 (12 / 195), avg. gap size = 1.58 (19 / 12) 235 41.33 0.50 1.52 chr4qtel1M 392969 393167 (606833) MamRTE1#LINE/RTE-BovB 2988 3184 (628) m_b200s601i26 7864 chr4qtel1M 392969 AAAGCCA-CACTGGCTCTTGTTTACCTTGACATTAGATTTTCCAAGGATG 393017 ii- i iv ii i - v i vi vii v v MamRTE1#LINE/ 2988 AAAGCTGTCACCGAATTCTGCT-ACCTAGGCAGCACGCTGTCCAATGATG 3036 chr4qtel1M 393018 TCCACGTGGATGATGAGGCTGGAGCATACATTGCCACAGCTAGCTGAGCG 393067 iv vvi ? ii v i iv i ivviiv iivv vi i vviv v MamRTE1#LINE/ 3037 CACTGATNGACAAAGAAGTAGAAAACCGAATCAAGAAGGCCAGCATGTCC 3086 chr4qtel1M 393068 TTTGGGAGGCTGCCAAGGAAAGTATGGGAGAGAAGAGGTATGAGTCTGCC 393117 v iiv i i vivvi v v i v iv v v MamRTE1#LINE/ 3087 TTTGGGAGGCTGGCAGACAGAGTGTGGCGCCAACGTGGCATCAAGCTCCA 3136 chr4qtel1M 393118 CACCACGCCGAAGCTCTGCAGAACAGTTTGCCATAGTTTCACTTTCTGTA 393167 v vi ii v i i - v v v? - iiv i ? MamRTE1#LINE/ 3137 GACCAAACTAAAGGTCTACAGAGC-GATAGCGNT-GTCCAACCTTCTNTA 3184 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 58.63 CpG sites = 42, Kimura (unadjusted) = 63.65 Transitions / transversions = 1.08 (42/39) Gap_init rate = 0.02 (4 / 198), avg. gap size = 1.00 (4 / 4) 638 25.34 0.68 0.00 chr4qtel1M 393146 393291 (606709) MIR#SINE/MIR 116 262 (0) m_b200s601i27 7865 chr4qtel1M 393146 TGCCATAGTTTCACTTTCTGTAAAATGGGGGCAACAATAGCACTTATAGC 393195 vi viiv ii i i i ivv MIR#SINE/MIR 116 TGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTC 165 chr4qtel1M 393196 CAAAGGTTGTTGTGAGGATCAAATGAAATAATAATTGTTAAGTGCTTAAT 393245 vv i i iv vv v i iv MIR#SINE/MIR 166 ATAGGGTTGTTGTGAGGATTAAATGAGTTAATACATGTAAAGCGCTTAGA 215 chr4qtel1M 393246 ACAATACCTAGCACATGGTAGATGCT-GAGAAATATTAGTTATTATT 393291 i i i i iii -i v i i MIR#SINE/MIR 216 ACAGTGCCTGGCACATAGTAAGCGCTCAATAAATGTTAGCTATTATT 262 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 29.88 CpG sites = 24, Kimura (unadjusted) = 31.95 Transitions / transversions = 1.85 (24/13) Gap_init rate = 0.01 (1 / 145), avg. gap size = 1.00 (1 / 1) 13 20.22 0.00 2.78 chr4qtel1M 393329 393365 (606635) (ATGTAT)n#Simple_repeat 1 36 (0) m_b200s252i12 7866 chr4qtel1M 393329 ATGATATATGCATACATATACATATATGTATATCTAT 393365 - i ii ii v (ATGTAT)n#Sim 1 ATG-TATATGTATATGTATATGTATATGTATATGTAT 36 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 14 21.06 0.00 0.00 chr4qtel1M 393332 393365 (606635) (ATAT)n#Simple_repeat 1 34 (0) m_b200s252i13 7866 chr4qtel1M 393332 ATATATGCATACATATACATATATGTATATCTAT 393365 ii i i i v (ATAT)n#Simpl 1 ATATATATATATATATATATATATATATATATAT 34 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 400 21.98 7.69 0.00 chr4qtel1M 393387 393477 (606523) C MIRc#SINE/MIR (134) 134 37 m_b200s601i28 7867 chr4qtel1M 393387 GAGGAA---GAGAATCAGAG---TTAAGTGACTTGCTCA-GGTCATGGAG 393429 --- iv --- i - iiv C MIRc#SINE/MIR 134 GAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAG 85 chr4qtel1M 393430 CTGGTAAGTATCTGAAGCTACATTTGAACTCAAGTCCTCCTGACTCCA 393477 i iv v iv viv i i i i i C MIRc#SINE/MIR 84 CTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCA 37 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 25.17 CpG sites = 13, Kimura (unadjusted) = 26.70 Transitions / transversions = 1.86 (13/7) Gap_init rate = 0.03 (3 / 90), avg. gap size = 2.33 (7 / 3) 296 22.03 0.00 0.00 chr4qtel1M 394431 394489 (605511) L2b_3end#LINE/L2 397 455 (11) m_b200s601i29 7868 chr4qtel1M 394431 TGTCCCCATCTCCCAGCACACTACCTGGAATACAGTAGGTGCTCAATAAA 394480 i v v i v?i v i i i L2b_3end#LINE 397 TATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAA 446 chr4qtel1M 394481 TCCTTGCTG 394489 vi i L2b_3end#LINE 447 TATTTGTTG 455 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 24.83 CpG sites = 8, Kimura (unadjusted) = 27.21 Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.0 (0 / 0) 182 25.95 1.61 6.78 chr4qtel1M 394991 395052 (604948) MIRc#SINE/MIR 16 74 (194) m_b200s601i30 7869 chr4qtel1M 394991 CAGTGGATGGAGTGCAGGATGTGGAATTAGG-GGACCTGTGTTCAAATCT 395039 vi ii v iv i i -i v i i - MIRc#SINE/MIR 16 CAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTC- 64 chr4qtel1M 395040 TCTGGGATTCTGC 395052 - i --i MIRc#SINE/MIR 65 -CCGG--CTCTGC 74 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 28.12 CpG sites = 11, Kimura (unadjusted) = 33.45 Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.08 (5 / 61), avg. gap size = 1.00 (5 / 5) 189 17.14 2.86 0.00 chr4qtel1M 395052 395086 (604914) MIRb#SINE/MIR 118 153 (115) m_b200s601i31 7870 chr4qtel1M 395052 CTCAGA-CCTCAGTTTTCCTTTCTGTAAAATGAGGA 395086 v - i iiv i MIRb#SINE/MIR 118 CTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGA 153 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 19.86 CpG sites = 4, Kimura (unadjusted) = 19.86 Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 277 23.21 3.57 0.00 chr4qtel1M 395056 395111 (604889) MIR3#SINE/MIR 117 174 (34) m_b200s601i32 7871 chr4qtel1M 395056 GACCTCAGTTTTCCTTTCTGTAAAATGAGGAG--TGAGCTACATGACCTC 395103 i i iiv i -- ii v i MIR3#SINE/MIR 117 GGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTC 166 chr4qtel1M 395104 AAGGATCC 395111 v i i MIR3#SINE/MIR 167 TAAGGTCC 174 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 29.28 CpG sites = 10, Kimura (unadjusted) = 29.28 Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.02 (1 / 55), avg. gap size = 2.00 (2 / 1) 14 19.31 2.33 2.33 chr4qtel1M 395561 395603 (604397) (CCATCC)n#Simple_repeat 1 43 (0) m_b200s252i14 7872 chr4qtel1M 395561 CCATCCACATCTCATTCTCCAGCCCCCTCCCCA-CCCCAGTCCC 395603 v i vv i v v - - (CCATCC)n#Sim 1 CCATCCCCATCCCCATCCCCATCCCCATCCCCATCCCCA-TCCC 43 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.00 (2 / 2) 194 26.36 11.01 2.54 chr4qtel1M 396126 396234 (603766) MIRc#SINE/MIR 2 119 (149) m_b200s601i33 7873 chr4qtel1M 396126 GAGACAACGGGG-GCCGCGGCA-GAGTTCT---CTGTGGGGTCAGTAAGA 396170 i ii v - v i v - iv --- - i v MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACT-TGGAGTCAGGAAGA 50 chr4qtel1M 396171 CC-AAGTTTGAGCGTTCC--CTTTGTGACATTCTGGCTGGGTGACCCT-G 396216 -ii i -- i -- i iv v v i v i - MIRc#SINE/MIR 51 CCTGGGTTCGAG--TCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 98 chr4qtel1M 396217 TCGAGCCATTT---CTCACTG 396234 v i i i --- v MIRc#SINE/MIR 99 GCAAGTCACTTAACCTCTCTG 119 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 31.99 CpG sites = 17, Kimura (unadjusted) = 33.44 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.09 (10 / 108), avg. gap size = 1.50 (15 / 10) 12 21.09 5.13 0.00 chr4qtel1M 398119 398157 (601843) (CTTC)n#Simple_repeat 1 41 (0) m_b200s252i15 7874 chr4qtel1M 398119 CTTCCATCCTGCCCCTCTCCCTTCCTTCTTTCC--CCTTCC 398157 v v iii i i -- (CTTC)n#Simpl 1 CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 41 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.03 (1 / 38), avg. gap size = 2.00 (2 / 1) 12 14.89 0.00 6.25 chr4qtel1M 398126 398159 (601841) (CCTTCC)n#Simple_repeat 1 32 (0) m_b200s252i16 7874 chr4qtel1M 398126 CCTGCCCCTCTCCCTTCCTTCTTTCCCCTTCCCC 398159 v ii -- i (CCTTCC)n#Sim 1 CCTTCCCCTTCCCCTTCC--CCTTCCCCTTCCCC 32 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2) 37 25.76 3.51 0.00 chr4qtel1M 398540 398653 (601347) (AGCAGT)n#Simple_repeat 1 118 (0) m_b200s252i17 7875 chr4qtel1M 398540 AGCAATAAGAGTAGCAGCAGCAACAGCAGTGACAGTAACAGCAGAAGCAG 398589 i iv i ii ii i i v i (AGCAGT)n#Sim 1 AGCAGTAGCAGTAGCAGTAGCAGTAGCAGTAGCAGTAGCAGTAGCAGTAG 50 chr4qtel1M 398590 CAGCAGGAGTAACAGTAGCAATTACAGT---ATTATCAGTAACAG-AGCA 398635 i v i i vi --- v v i - (AGCAGT)n#Sim 51 CAGTAGCAGTAGCAGTAGCAGTAGCAGTAGCAGTAGCAGTAGCAGTAGCA 100 chr4qtel1M 398636 ACAGCAGTAACAGTAGCA 398653 ii i (AGCAGT)n#Sim 101 GTAGCAGTAGCAGTAGCA 118 Matrix = Unknown Transitions / transversions = 3.00 (18/6) Gap_init rate = 0.02 (2 / 113), avg. gap size = 2.00 (4 / 2) 201 21.08 0.00 3.51 chr4qtel1M 398654 398712 (601288) OldhAT1#DNA/hAT-Ac 1988 2044 (798) m_b200s601i34 7876 chr4qtel1M 398654 GCAACAGAGCAATAGCAGTAGCAGTAGCAGCCACAGTAACAGTAGTAGCA 398703 v - v i- v i i ? i vi i OldhAT1#DNA/h 1988 GCAAAAGAG-ACTAGT-GAAACAGTAACAGCCACANTGACACCAGCAGCA 2035 chr4qtel1M 398704 AAAGCAGCA 398712 v i OldhAT1#DNA/h 2036 ACAGCGGCA 2044 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 23.26 CpG sites = 7, Kimura (unadjusted) = 25.64 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.03 (2 / 58), avg. gap size = 1.00 (2 / 2) 17 25.42 1.92 0.00 chr4qtel1M 398715 398766 (601234) (AACAGT)n#Simple_repeat 1 53 (0) m_b200s252i18 7877 chr4qtel1M 398715 AACAGTAGCAACCA-AGTAACAGTACCAGTAGTAGCCACAGTAAAAGTAG 398763 i iiv - v ii iv v i (AACAGT)n#Sim 1 AACAGTAACAGTAACAGTAACAGTAACAGTAACAGTAACAGTAACAGTAA 50 chr4qtel1M 398764 CAG 398766 (AACAGT)n#Sim 51 CAG 53 Matrix = Unknown Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.02 (1 / 51), avg. gap size = 1.00 (1 / 1) 238 27.12 0.00 0.00 chr4qtel1M 398771 398829 (601171) OldhAT1#DNA/hAT-Ac 1987 2045 (797) m_b200s601i35 7878 chr4qtel1M 398771 TGCAGTAGCAACTACAGTAACAGTAACAACTACAGTAGCAGTAGCAGTAA 398820 iv vi vv v i i ? ii vi i OldhAT1#DNA/h 1987 TGCAAAAGAGACTAGTGAAACAGTAACAGCCACANTGACACCAGCAGCAA 2036 chr4qtel1M 398821 CAGTAGCAA 398829 ii OldhAT1#DNA/h 2037 CAGCGGCAA 2045 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 32.50 CpG sites = 10, Kimura (unadjusted) = 35.53 Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.0 (0 / 0) 210 23.40 0.00 0.00 chr4qtel1M 398819 398865 (601135) OldhAT1#DNA/hAT-Ac 2005 2051 (791) m_b200s601i36 7879 chr4qtel1M 398819 AACAGTAGCAACTACAGTAACAGTAGCAGCAGTAGCAGCCACAGTAA 398865 i i i ? i vi ii i v v ? OldhAT1#DNA/h 2005 AACAGTAACAGCCACANTGACACCAGCAGCAACAGCGGCAAAAGTNA 2051 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 27.66 CpG sites = 8, Kimura (unadjusted) = 31.01 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 194 17.30 0.00 12.77 chr4qtel1M 398846 398898 (601102) OldhAT1#DNA/hAT-Ac 2005 2051 (791) m_b200s601i37 7879 chr4qtel1M 398846 AGCAGTAGCAGCCACAGTAACAGTAGCAGTAGCAATAACAGCAGCAATAG 398895 i i ? i vi ------i i v OldhAT1#DNA/h 2005 AACAGTAACAGCCACANTGACACCAGCAG------CAACAGCGGCAAAAG 2048 chr4qtel1M 398896 TAA 398898 ? OldhAT1#DNA/h 2049 TNA 2051 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 18.14 CpG sites = 6, Kimura (unadjusted) = 20.96 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.12 (6 / 52), avg. gap size = 1.00 (6 / 6) 220 18.18 4.55 0.00 chr4qtel1M 398893 398936 (601064) OldhAT1#DNA/hAT-Ac 1999 2044 (798) m_b200s601i38 7879 chr4qtel1M 398893 TAGT--AATAATAGCAGCCACAGTAACAGTAGCAGCAGCAGCAGCA 398936 -- i i i ? i vi i i OldhAT1#DNA/h 1999 TAGTGAAACAGTAACAGCCACANTGACACCAGCAGCAACAGCGGCA 2044 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 19.53 CpG sites = 7, Kimura (unadjusted) = 22.64 Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.02 (1 / 43), avg. gap size = 2.00 (2 / 1) 12 0.00 5.26 0.00 chr4qtel1M 398937 398955 (601045) (GCA)n#Simple_repeat 1 20 (0) m_b200s252i19 7880 chr4qtel1M 398937 GCAGCAGCAGCAGCAG-AGC 398955 - (GCA)n#Simple 1 GCAGCAGCAGCAGCAGCAGC 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.06 (1 / 18), avg. gap size = 1.00 (1 / 1) 188 20.00 4.41 4.41 chr4qtel1M 398956 399023 (600977) OldhAT1#DNA/hAT-Ac 1975 2042 (800) m_b200s601i39 7881 chr4qtel1M 398956 AATAGCAGTAACAGTAGCAACAGCAGC-AGT--AACAGTAGTAGCCACAG 399002 i v -- v - v vii - -- ii ? OldhAT1#DNA/h 1975 AACATCAG--AGAGT-GCAAAAGAGACTAGTGAAACAGTAACAGCCACAN 2021 chr4qtel1M 399003 TAACAGTAGCAGCAACAGAGG 399023 i vi v OldhAT1#DNA/h 2022 TGACACCAGCAGCAACAGCGG 2042 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 23.93 CpG sites = 7, Kimura (unadjusted) = 23.93 Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.07 (5 / 67), avg. gap size = 1.20 (6 / 5) 204 17.34 0.00 3.85 chr4qtel1M 399014 399067 (600933) OldhAT1#DNA/hAT-Ac 1988 2039 (803) m_b200s601i40 7881 chr4qtel1M 399014 GCAACAGAGGAATAGCAGTAGCAGTAGCAGCCACAGTAACAGTAGCAGCA 399063 v - v i- v i i ? i vi OldhAT1#DNA/h 1988 GCAAAAGAG-ACTAGT-GAAACAGTAACAGCCACANTGACACCAGCAGCA 2035 chr4qtel1M 399064 ACAG 399067 OldhAT1#DNA/h 2036 ACAG 2039 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 20.31 CpG sites = 5, Kimura (unadjusted) = 20.31 Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.04 (2 / 53), avg. gap size = 1.00 (2 / 2) 196 22.83 0.00 3.51 chr4qtel1M 399061 399119 (600881) OldhAT1#DNA/hAT-Ac 1988 2044 (798) m_b200s601i41 7881 chr4qtel1M 399061 GCAACAGAGAAATAGCAGTAGCAGTAGCAGCCACAGTAACAGTAGCAGCC 399110 v v- i- v i i ? i vi v OldhAT1#DNA/h 1988 GCAAAAGAGAC-TAGT-GAAACAGTAACAGCCACANTGACACCAGCAGCA 2035 chr4qtel1M 399111 ACAGTAACA 399119 iii OldhAT1#DNA/h 2036 ACAGCGGCA 2044 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 25.64 CpG sites = 8, Kimura (unadjusted) = 28.42 Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.03 (2 / 58), avg. gap size = 1.00 (2 / 2) 198 21.32 0.00 4.26 chr4qtel1M 399098 399146 (600854) OldhAT1#DNA/hAT-Ac 2005 2051 (791) m_b200s601i42 7882 chr4qtel1M 399098 AACAGTAGCAGCCACAGTAACAGTAGCAGTAGCAGAGCAATAACAGTCA 399146 i ? i vi i i -- iii v ? OldhAT1#DNA/h 2005 AACAGTAACAGCCACANTGACACCAGCAGCAAC--AGCGGCAAAAGTNA 2051 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 24.64 CpG sites = 8, Kimura (unadjusted) = 27.87 Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.04 (2 / 48), avg. gap size = 1.00 (2 / 2) 193 22.67 0.00 3.77 chr4qtel1M 399127 399181 (600819) OldhAT1#DNA/hAT-Ac 1999 2051 (791) m_b200s601i43 7882 chr4qtel1M 399127 TAGCAGAGCAATAACAGTCACAGTAGAGCAGCAGCAGCAGCAGCAGTGAC 399176 iii i i i ? - - v i i ii v OldhAT1#DNA/h 1999 TAGTGAAACAGTAACAGCCACANT-GA-CACCAGCAGCAACAGCGGCAAA 2046 chr4qtel1M 399177 AGTAA 399181 ? OldhAT1#DNA/h 2047 AGTNA 2051 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 27.26 CpG sites = 10, Kimura (unadjusted) = 30.27 Transitions / transversions = 5.00 (10/2) Gap_init rate = 0.04 (2 / 54), avg. gap size = 1.00 (2 / 2) 20 27.06 1.59 1.59 chr4qtel1M 399182 399244 (600756) (CAG)n#Simple_repeat 1 63 (0) m_b200s252i20 7883 chr4qtel1M 399182 CAGCAGCAG-ATCAATAGCAATAACAGCAGCAGCAGTAACTAACAGTAAC 399230 - v ii ii i i i - i i i (CAG)n#Simple 1 CAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGC-AGCAGCAGC 49 chr4qtel1M 399231 AGCAGTAGTAGCAG 399244 i i (CAG)n#Simple 50 AGCAGCAGCAGCAG 63 Matrix = Unknown Transitions / transversions = 12.00 (12/1) Gap_init rate = 0.03 (2 / 62), avg. gap size = 1.00 (2 / 2) 242 33.80 0.00 0.00 chr4qtel1M 399418 399488 (600512) C MIRc#SINE/MIR (99) 169 99 m_b200s601i44 7884 chr4qtel1M 399418 GGAAGAGTGGGTGTCACGCTTCCCTCTCTACAGATGAAGAAACTGAGGCT 399467 v i ii i i ivv i vi i i C MIRc#SINE/MIR 169 GGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCT 120 chr4qtel1M 399468 CCAAGTTGTAAGATCATCTGC 399488 vi vv v ii v ii C MIRc#SINE/MIR 119 CAGAGAGGTTAAGTGACTTGC 99 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 47.16 CpG sites = 15, Kimura (unadjusted) = 47.16 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0) 492 26.67 3.31 0.81 chr4qtel1M 399523 399643 (600357) MIRb#SINE/MIR 28 151 (117) m_b200s601i45 7885 chr4qtel1M 399523 GAAAACAGGCTTTTGAGGTAGA--GACTTTGAGTTCAAATCCTGTTTCTG 399570 iv i v vi -- i - i i i vi MIRb#SINE/MIR 28 GAGCACGGGCTTTGGAGTCAGACAGACCT-GGGTTCGAATCCCGGCTCTG 76 chr4qtel1M 399571 TTACTTATTAGCTATGTGGTGTTGGGCAAGTACCTTCATCTCTTTGGGCC 399620 ii i i iiv vv v i i i MIRb#SINE/MIR 77 CCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCC 126 chr4qtel1M 399621 T--ATTTCCTTCCCTGTCAAATAAG 399643 --i ivi v ii MIRb#SINE/MIR 127 TCAGTTTCCTCATCTGTAAAATGGG 151 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 30.52 CpG sites = 22, Kimura (unadjusted) = 34.45 Transitions / transversions = 2.20 (22/10) Gap_init rate = 0.03 (3 / 120), avg. gap size = 1.67 (5 / 3) 752 27.47 8.15 0.00 chr4qtel1M 399662 399894 (600106) MIR#SINE/MIR 1 252 (10) c_b200s401i0 7886 chr4qtel1M 399662 ACAGGGTAGT-TAGTGGATA-------GAGCTCTGGGCCTGGAAGTCTTG 399703 vi i- v ------- i iv ii vvv i MIR#SINE/MIR 1 ACAGTATAGCATAGTGGTTAAGAGCACGGGCTCTGGAGCCAGACTGCCTG 50 chr4qtel1M 399704 GGTTCAAATCCAGCCTCAGATCCTTCCTAGTTGAGTGACTCTGGACAAAC 399753 i v v v viv v i v ii i ii MIR#SINE/MIR 51 GGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGT 100 chr4qtel1M 399754 CATGTACTCTCCATCTGTCTTGGTTGCCTTATCTATAAAATGGACACAAT 399803 i iv vi iv v i ii v i i iv i MIR#SINE/MIR 101 TACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAAT 150 chr4qtel1M 399804 CACAGTACCTCCCTTCCAGGGTTGTGATGAGGATCAAATGAGATAAGAAT 399853 v i v ivi vi i v v vv MIR#SINE/MIR 151 AATAGTACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATACA 200 chr4qtel1M 399854 TGTCA-----------CAGTGCCTGGCCCACAGTAGGGGCTTAATAAATG 399892 v ----------- v i i v i MIR#SINE/MIR 201 TGTAAAGCGCTTAGAACAGTGCCTGGCACATAGTAAGCGCTCAATAAATG 250 chr4qtel1M 399893 TT 399894 MIR#SINE/MIR 251 TT 252 Matrix = 18p47g.matrix Kimura (with divCpGMod) = 34.07 CpG sites = 34, Kimura (unadjusted) = 34.73 Transitions / transversions = 1.13 (34/30) Gap_init rate = 0.01 (3 / 232), avg. gap size = 6.33 (19 / 3) 237 23.41 2.13 9.09 chr4qtel1M 401726 401819 (598181) C L2c_3end#LINE/L2 (1) 477 390 m_b200s601i46 7887 chr4qtel1M 401726 TTCATTTCAATTCAATGAAATAAGCAAATATTTAGTCCCAACTATGTGCA 401775 i-- ii ----- vv v iv v v C L2c_3end#LINE 477 TTCATTC--ATTCAACAAA-----CATTTATTGAGCGCCTACTATGTGCC 435 chr4qtel1M 401776 AGTTGCTGGGGTTGC-AAGATGAA-GATTCAGTGGTCTCTTCCCTC 401819 vi v i - -i vv -i i v C L2c_3end#LINE 434 AGGCGCTGGGGATACAAAGATGAATAAGACA-CGGTCCCTGCCCTC 390 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 23.43 CpG sites = 9, Kimura (unadjusted) = 27.95 Transitions / transversions = 0.82 (9/11) Gap_init rate = 0.11 (10 / 93), avg. gap size = 1.00 (10 / 10) 237 18.75 0.00 0.00 chr4qtel1M 403180 403227 (596773) C Charlie4a#DNA/hAT-Charlie (110) 398 351 m_b200s502i6 7888 chr4qtel1M 403180 TCACAAAGGAAACCAAGTATGTTGAAATACAATGATCGGCATCTTAAA 403227 i v i i v iiv v C Charlie4a#DNA 398 TTACAAAGGAAACCAATTATATTGAAATACAGTTATCAAAATATTAAA 351 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 21.80 CpG sites = 5, Kimura (unadjusted) = 21.80 Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 307 21.02 0.00 4.84 chr4qtel1M 403266 403330 (596670) MIRc#SINE/MIR 2 63 (205) m_b200s601i47 7889 chr4qtel1M 403266 GAGGCAGCTAAGTGGTGCAGTGGATAGAGCACCAACCCTGAAGTCAGGAG 403315 i--- v iiiv i i i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr4qtel1M 403316 GACCTGAGCTCAAAT 403330 i i i i MIRc#SINE/MIR 49 GACCTGGGTTCGAGT 63 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 23.83 CpG sites = 11, Kimura (unadjusted) = 26.14 Transitions / transversions = 5.50 (11/2) Gap_init rate = 0.05 (3 / 64), avg. gap size = 1.00 (3 / 3) 378 32.90 15.53 1.62 chr4qtel1M 404085 404464 (595536) C L3#LINE/CR1 (407) 3692 3261 m_b200s601i48 7890 chr4qtel1M 404085 TGGTTCCCAGTCCCTTCAA-GTGATGGTTAC------ATGGTGAGGCTCA 404127 i v v-i vv ii ------v vviv v C L3#LINE/CR1 3692 TGGTTTCCAGACCCTTCACCATCCTGGTCGCTCTCCTCTGGACGCGCTCC 3643 chr4qtel1M 404128 AGGGCCTCTCAATATTCATCC-AAAA-GTGACATCATAAATGGAGCCCAC 404175 --ii v i i v i- - i ii vvi iv i v v C L3#LINE/CR1 3642 AG--TTTGTCAATGTCCCTCTTAAAATGTGGCGCCCAGAACTGAACGCAA 3595 chr4qtel1M 404176 TGCTGCCAAAGGGG--CTGACTAGAGTAGAGTAGGGTCCTACTGTCAGTT 404223 i - i v v -- i v i vi ivvv i i vi C L3#LINE/CR1 3594 TACT-CCAGATGTGGTCTGACCAGCGCAGAGTACAGCGGGACTATTACCT 3546 chr4qtel1M 404224 CC-TTATTACTGAAC------CTTCTCCCTATAGAGAAGAATATGGCCTT 404266 - i? - i ------ viiv iv vvv v v v C L3#LINE/CR1 3545 CCCTTGNT-CTGGACACTATACTTCTATTAATGCAGCCTAAGATTGCATT 3497 chr4qtel1M 404267 --CTTTCTT--CA-CTGTAGCATGTTCTTG----AGATTG-GTCTGTGCT 404306 -- i -- - iii v iii v ---- v - ii i v C L3#LINE/CR1 3496 AGCTTTTTTGGCAGCCACATCACACTGTTGGCTCATATTGAGCTTGCGGT 3447 chr4qtel1M 404307 C--CTCAAGACCACT-GATCCTTTCTG-GTAGAACTGCTGCCAAGCCACA 404352 -- - i v - i i iii- - i v C L3#LINE/CR1 3446 CAACT-AAAACCCCTAGGTCTTTTTCACGT-GAACTGCTGCTAAGCCAGA 3399 chr4qtel1M 404353 CTTTCCCCATTTTGTATTTGTG---------------ACTCAAGTGTGAG 404387 iii i ii i --------------- ii i iii C L3#LINE/CR1 3398 TCCTCTCCATCCTGTACTTGTGCAGTTGATTTTTTGAACCTAAATGCAGG 3349 chr4qtel1M 404388 ACTTGCTAGTTATCATTGTTGA--TTCAATTTAT---------CCCAATG 404426 vvi v vi i -- vi i --------- vi C L3#LINE/CR1 3348 ACTTTACATTTATCCCTGTTAAATTTCATCTTGTTGGTTTCGGCCCATCG 3299 chr4qtel1M 404427 TTCT-GTCTCTCAGGAGCATTCTGGAACCTCACTTTTGT 404464 i- i v ii v ? i - i iiv i C L3#LINE/CR1 3298 TTCCAGCCTGTCGAGATCNTTTT-GAATCTTGATTCTGT 3261 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 42.06 CpG sites = 75, Kimura (unadjusted) = 45.63 Transitions / transversions = 1.56 (75/48) Gap_init rate = 0.07 (26 / 379), avg. gap size = 2.54 (66 / 26) 472 34.26 18.45 1.49 chr4qtel1M 404134 404767 (595233) C L3b_3end#LINE/CR1 (466) 740 1 m_b200s601i49 7890 chr4qtel1M 404134 TCTCAATATTCATCCAAAA--GTGACATCATAAATGGAGCCCACTGCTGC 404181 v ii i v iiv -- i?ii vvi iv i v v i - C L3b_3end#LINE 740 TCTCCACGTCCCTTTTAAANTGTGGNGCCCAGAACTGAACGCAGTACT-C 692 chr4qtel1M 404182 CAAAGGGG--CTGACTAGAGTAGAGTAGGGTCCTACTGTCAGTTCCTT-- 404227 i?v ? -- i v i i ivvv ??i vi i -- C L3b_3end#LINE 691 CAGNTGNGGCCTGACCAGCGCAGAGTAGAGCGGGANNATCACCTCCCTTG 642 chr4qtel1M 404228 ----ATTACTGAACCTTCTCCCTATAGAGAAGAATATGGCCTT--CTTTC 404271 ----i iivi v? viiv iv vvv v v v -- i C L3b_3end#LINE 641 NTCTGTCGGCGATNCTTCTGTTAATGCAGCCCAAGATCGCATTAGCTTTT 592 chr4qtel1M 404272 TTCAC-----TGTAGCA-TGTT--CTTGAGATTG-GTCTGTGCTC--CTC 404310 vi -----i v - i -- i- v - ii i v -- - C L3b_3end#LINE 591 TTGGCAGCCGCGTCGCACTGCTGACTC-ATATTGAGCTTGCGGTCAACT- 544 chr4qtel1M 404311 AAGACCACTGATCCTTTCTGGTA-GAACTGCTGCCAAGCCACACTTTCCC 404359 i v iiivi i vii - ?i i i iii i C L3b_3end#LINE 543 AAAACCCCCAGGTCTTTTTCACATGNGCTGCTGCTAAGCCGCGTCTCCCC 494 chr4qtel1M 404360 CATTTTGTATTTGTG---------------ACTCAAGTGTGAGACTTGCT 404394 ii i i i --------------- i iii vvi C L3b_3end#LINE 493 CATCCTGTACTCGCGCGATTGNTTTTTTGAACCCAAGTGCAGGACTTTAC 444 chr4qtel1M 404395 AGTTATCATTGTTGA--TTCAATTTAT---------CCCAATGTTCT-GT 404432 iv vi -- vi i --------- i?i - C L3b_3end#LINE 443 GTTTATCCCTGTTGAATTTCATCTTGTTGGNTTCGGCCCGNCGTTCTAGT 394 chr4qtel1M 404433 CTCTCAGGAGC-------ATTCTGG------------------AACC-TC 404456 v ii v ------- i i------------------ i - C L3b_3end#LINE 393 CTGTCGAGATCGTTTTGGATCCTGATTTTGCATCCAACGTATTAGCCGTC 344 chr4qtel1M 404457 ACTT-----TTGTGTCACCTGCCAAGT-GAAAAGCATGGCTTCTCCACTT 404500 i i----- v i i? v v - v - vi ivi ii C L3b_3end#LINE 343 GCTCCCAGCTTCTGCCACTNGCAAATTTGATAAGC-TGCTTTCCGTATCT 295 chr4qtel1M 404501 TTGTCCCAGTCCCTGATGAAAATGGGGATC---TAAAACCAA-------- 404539 ii v vi iv vvi iv---i ii -------- C L3b_3end#LINE 294 TCATCCAAGTCATTGATACAAATTCAGACAGGACAAGGCCAAGGACAGAG 245 chr4qtel1M 404540 -----TGGCAT-CCCCTGGAGACTTCCTGCCAAGGTGACACTCAATCACT 404583 -----i i- v i i - i v - i ? --i C L3b_3end#LINE 244 CCCTGCGGCACGCCACTAGAGACTCCCT-CCAGGTTGACA-TCGANC--C 199 chr4qtel1M 404584 GCTTATTACTCCCCCTCATTTTCAAAGGTCC--CCAACCATAGTATGT-- 404629 ii ? i vivi i iivv ? iivv i -- i i ?- v -- C L3b_3end#LINE 198 ATTNATCAACGTCCTTTGGGTNCGGTTGTTCAACCAGCTAN-GAATGTCT 150 chr4qtel1M 404630 ----GACCAT---CTGGTTCTCATCCCTCTATTTT--CCACAAGAATAGC 404670 ---- --- ii ii v ii ii i -- i i v C L3b_3end#LINE 149 AACTGACCATTNTCCAGCCCACATTTCTCCGTCTTGTCCACGAGGATATC 100 chr4qtel1M 404671 AAGGGAGA-TCTG--AAACGT-TTGCTGGACTTTTGGTAAACCATGCCCA 404716 v i - i -- i i- i v ivv i v i i i C L3b_3end#LINE 99 ACGAGAGACTTTGTCAAATGCCTTGCTGAAATCAAGATACACTATGTCTA 50 chr4qtel1M 404717 TGGCATTGTCCTGATCCATCAGGGTTTAGTAACACTAATAAAAAATGAAA 404766 ? vi iiii -- ? iii vi vivv ?i v C L3b_3end#LINE 49 TGGNATTCCCCTGATCTGCTA--GTNTAGCGGCTTTATCTTANGAGGAAA 2 chr4qtel1M 404767 T 404767 C L3b_3end#LINE 1 T 1 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 42.75 CpG sites = 141, Kimura (unadjusted) = 50.83 Transitions / transversions = 1.93 (141/73) Gap_init rate = 0.07 (43 / 633), avg. gap size = 2.98 (128 / 43) 738 30.45 12.72 1.87 chr4qtel1M 404454 404791 (595209) C L3#LINE/CR1 (862) 3237 2864 m_b200s601i50 7890 chr4qtel1M 404454 CTCACTTTTGTGTCACCTGCCAAGT-GAAAAGCATGGCTTCTCCACTTTT 404502 i vi i v v - v v viiii i C L3#LINE/CR1 3237 CCCAGCTTTGTGTCATCTGCAAATTTGATAAGCATGCCTTCTATGTCTTC 3188 chr4qtel1M 404503 GTCCCAGTCCCTGATGAAAATGGGGATC----TAAAACCAA--------- 404539 i v vi i vv v ----i iii --------- C L3#LINE/CR1 3187 ATCCAAGTCATTGATAAAAATGTTGAACAGGACAGGGCCAAGGACAGAGC 3138 chr4qtel1M 404540 ----TGGCAT-CCCCTGGAGACTTCCTGCCAAGGTGACAC-------TCA 404577 ---- i- v i i iv i v i------- i C L3#LINE/CR1 3137 CCTGTGGCACGCCACTAGAGACCTCCCTCCAGGTTGACATCGATCCATTA 3088 chr4qtel1M 404578 ATCACTGCTTATT------ACTCCCCC--TCATTTTCAAAGGTCCCCAAC 404619 vii i v ------ v vii --i vi v i vviv i C L3#LINE/CR1 3087 ATCAACACCTTTTGGGTATAGTCGTTCAACCAGCTACGAATCCACCTAAC 3038 chr4qtel1M 404620 CATAGTATGTGACCATCTGGTTCTCATCCCTCTATTTT--CCACAAGAAT 404667 ii v ----- ii ii vi ii i i -- i C L3#LINE/CR1 3037 TGTACTAT-----CATCCAGCCCATATTTCTCCATCTTGTCCACAAGGAT 2993 chr4qtel1M 404668 AGCAAGGGAGA-TCTG--AAACGT-TTGCTGGACTTTTGGTAAACCATGC 404713 v v i - i -- i i- i v iiv i v i? i C L3#LINE/CR1 2992 ATCATGAGAGACTTTGTCAAATGCCTTGCTGAAATCCAGATACACTNTGT 2943 chr4qtel1M 404714 CCATGGCATTGTCCTGATCCATCAGGGTTTAGTAACACTAATAAAAAATG 404763 i i vi i i -- i v vi v C L3#LINE/CR1 2942 CTACGGCATTCCCCTGATCTACCA--GTCTAGTAACCCTATCAAAAAAGG 2895 chr4qtel1M 404764 AAATGGG---AGTCAGGCATGGCCTGTTTTT 404791 i --- iv i i i C L3#LINE/CR1 2894 AAATGAGGTTAGTTTGGCATGACTTGTTCTT 2864 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 39.60 CpG sites = 66, Kimura (unadjusted) = 41.23 Transitions / transversions = 1.89 (66/35) Gap_init rate = 0.06 (20 / 337), avg. gap size = 2.50 (50 / 20) 186 23.95 1.41 5.88 chr4qtel1M 405742 405812 (594188) C L3#LINE/CR1 (1213) 2886 2819 m_b200s601i51 7890 chr4qtel1M 405742 TTACTGTGACATGGCCTGTTCTTGATTGAAACT-TCTTGCCTCTGCTTTG 405790 v v i i i - v v i- vi v i--- v C L3#LINE/CR1 2886 TTAGTTTGGCATGACTTGTTCTT-AGTGAACCCATGCTGGCTCC---TAG 2841 chr4qtel1M 405791 TGATCACAGCTTCCTTTTTTGA 405812 v i i C L3#LINE/CR1 2840 TGATCACCGCTTCCTTTTCTAA 2819 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 29.00 CpG sites = 8, Kimura (unadjusted) = 29.00 Transitions / transversions = 1.00 (8/8) Gap_init rate = 0.07 (5 / 70), avg. gap size = 1.00 (5 / 5) 211 24.12 7.53 6.38 chr4qtel1M 406500 406592 (593408) C L3#LINE/CR1 (1218) 2881 2788 m_b200s601i52 7890 chr4qtel1M 406500 TTGG-ATAATGTCTTCTTTGGTGG-TCTAGGCGGGC-----GTAATCTCC 406542 - i iv v -i i-i i v v ----- i -v C L3#LINE/CR1 2881 TTGGCATGACTTGTTCTT-AGTGAACCCATGCTGGCTCCTAGTGATC-AC 2834 chr4qtel1M 406543 CCCTTCTCCGCTTTTCTAAATGTTCACTAACCATTTATTTAATCATATGT 406592 v ---- i i v i i v vi C L3#LINE/CR1 2833 CGCTTC----CTTTTCTAAGTGCTCACAAACCATCTGTTTAATAATCCGT 2788 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 28.00 CpG sites = 12, Kimura (unadjusted) = 29.64 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.10 (9 / 92), avg. gap size = 1.44 (13 / 9) 14 15.42 0.00 3.23 chr4qtel1M 406970 407001 (592999) (CCCT)n#Simple_repeat 1 31 (0) m_b200s252i22 7891 chr4qtel1M 406970 CCCTCCCTTCCTCTCTCGCTTCCCTCCCCCCC 407001 i i - i i (CCCT)n#Simpl 1 CCCTCCCTCCCTCCCTC-CCTCCCTCCCTCCC 31 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 378 30.22 3.93 3.35 chr4qtel1M 407407 407584 (592416) C L1ME3E_3end#LINE/L1 (455) 534 356 m_b200s551i7 7892 chr4qtel1M 407407 GAACAT-TCATAACTTCTTCAGCCATTCTTCAACTGATGGGCATCCTCTC 407455 i -i i i v i v i viii i iivvvi C L1ME3E_3end#L 534 GAATATACCACAATTTATTTATCCATTCTCCTGTCGATGGACATTTGGGT 485 chr4qtel1M 407456 AGTTTCCAGTTTCTTGTCACTACAAAAAGGGCTGCCATAAACACTTTTGC 407505 v i ii i v iv i i i i i C L1ME3E_3end#L 484 TGTTTCCAGTTTTTTGCTATTACAAACAATGCTGCTATGAACATTCTTGT 435 chr4qtel1M 407506 ACATGTGGGTCCCT--TTCCCTCCTTTAAGA-TTTCTCTGGGATATAAGC 407552 ---ii -- v v v v vi - i i vi C L1ME3E_3end#L 434 ACATGT---CTCCTGGTGCACACGTGCAAGAGTTTCTCTAGGGTATATAC 388 chr4qtel1M 407553 CC---AGTAGAAACGCATCTGGATCAAAGAGTATG 407584 i--- i vi --- i iv i C L1ME3E_3end#L 387 CTAGGAGTGGAATTG---CTGGGTCGTAGGGTATG 356 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 38.67 CpG sites = 35, Kimura (unadjusted) = 40.75 Transitions / transversions = 2.06 (35/17) Gap_init rate = 0.06 (10 / 177), avg. gap size = 1.30 (13 / 10) 436 28.23 2.36 2.36 chr4qtel1M 408009 408135 (591865) MIRc#SINE/MIR 2 128 (140) m_b201s601i0 7893 chr4qtel1M 408009 GAAGCAGTGAAGTGGCTCAGTGGATAAAGGCCTGGGGCAGGAGTCAGAAA 408058 i vi --- v i vv iviv i MIRc#SINE/MIR 2 GAGGCAGTGTGGTG---CAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr4qtel1M 408059 GACCTGAGATTAAATCTCACCTCGGAGACTCACTAGCCATGTGACC-TGG 408107 i v ii i i iv v vv i ii - MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 98 chr4qtel1M 408108 GCGGTTCCCTTCACCTGTTT--GCCTTAAT 408135 iiv v v v i -- i i MIRc#SINE/MIR 99 GCAAGTCACTTAACCTCTCTGAGCCTCAGT 128 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 33.55 CpG sites = 20, Kimura (unadjusted) = 36.23 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.04 (5 / 126), avg. gap size = 1.20 (6 / 5) 218 13.24 2.05 1.27 chr4qtel1M 410527 410916 (589084) (TTCC)n#Simple_repeat 1 393 (0) m_b201s252i2 7894 chr4qtel1M 410527 TTTCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 410576 i (TTCC)n#Simpl 1 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 50 chr4qtel1M 410577 CCTTCCTTCCTTCCTTCCTTCTTTCCTTCCTCCCTTCCTTTCTTCTTTCC 410626 i i i i (TTCC)n#Simpl 51 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 100 chr4qtel1M 410627 TTCC-TCCCTCTCTCCCTCCCTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 410675 - i ii i i (TTCC)n#Simpl 101 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 150 chr4qtel1M 410676 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCTTTCCTTCCTTCCTTCCTTCT 410725 i - (TTCC)n#Simpl 151 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC- 199 chr4qtel1M 410726 TTTCCTTCTTTTCCTTCTTTTCCTTCTTCTCCTT-CTTCC-TCCTCACTT 410773 i -i -i i - - - iv (TTCC)n#Simpl 200 CTTCCTTC-CTTCCTTC-CTTCCTTCCT-TCCTTCCTTCCTTCCTTCCTT 246 chr4qtel1M 410774 TCTTCTTTTCCTT-CTTCCTTCTTCCCTTCTTTCCACCCATCATTGCTTC 410822 i -i - i i i vi v v v (TTCC)n#Simpl 247 CCTTC-CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC 295 chr4qtel1M 410823 CTTTCCTCCTT-CTTCCCTCCCTCCTTCCTTTCCAACTTCCTTCCTTCCT 410871 i i - i i i ivv (TTCC)n#Simpl 296 CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT 345 chr4qtel1M 410872 TCCTTCC-CCCTCCCCT-TTTCTTTCTTTCC-CCCTTTCTTTCTTTCT 410916 -i i i -i i i -i i i i (TTCC)n#Simpl 346 TCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT 393 Matrix = Unknown Transitions / transversions = 5.43 (38/7) Gap_init rate = 0.03 (13 / 389), avg. gap size = 1.00 (13 / 13) 183 26.14 0.00 4.35 chr4qtel1M 411280 411327 (588673) L2c_3end#LINE/L2 433 478 (0) m_b201s601i1 7895 chr4qtel1M 411280 CTAGCATACAACAGGTGTTCAATAAATGCTTGCAGAAGTAAGCTGAAT 411327 i i i ii i i i iv vv -- L2c_3end#LINE 433 CTGGCACATAGTAGGCGCTCAATAAATGTTTGTTGAATGAA--TGAAT 478 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 30.51 CpG sites = 9, Kimura (unadjusted) = 33.98 Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.04 (2 / 47), avg. gap size = 1.00 (2 / 2) 201 31.14 1.85 7.84 chr4qtel1M 411467 411574 (588426) C MIR1_Amn#SINE/MIR (112) 118 17 m_b201s601i3 7896 chr4qtel1M 411467 AGAGGTTA-GAAAATTGCCTGGAATCACAGCCTCAGTTCAG-GTCAGAGT 411514 ? - vi v iiiii ?- vv ? vi? - v i C MIR1_Amn#SINE 118 AGAGGTNAAGTGACTTGCCCAAGGTCACN-CAGCNGGCNAGTGGCAGAGC 70 chr4qtel1M 411515 GAGGATCATGAATCCAGGTTTCTCAGGCTTCAAGCCAGCCCTCTGGCCTC 411564 vi ?i?- i i i ii iii iv iv ------ C MIR1_Amn#SINE 69 CGGGANTN-GAACCCAGGTCTCCCGAGTCCCAGTCCAGTGCTCT------ 27 chr4qtel1M 411565 ATCCCTTAGA 411574 vi C MIR1_Amn#SINE 26 ATCCACTAGA 17 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 42.15 CpG sites = 21, Kimura (unadjusted) = 46.26 Transitions / transversions = 2.10 (21/10) Gap_init rate = 0.09 (10 / 107), avg. gap size = 1.00 (10 / 10) 219 27.57 6.52 5.38 chr4qtel1M 411467 411558 (588442) C MIRb#SINE/MIR (149) 119 27 m_b201s601i2 7896 chr4qtel1M 411467 AGAGGTT-AGAAAATTGCCTGGAATCACAGCCTCAGTT--CAGGT--CAG 411511 - v v iiiii ---- i --i i -- C MIRb#SINE/MIR 119 AGAGGTTAAGTAACTTGCCCAAGGTCACA----CAGCTAGTAAGTGGCAG 74 chr4qtel1M 411512 AGTGAGGATCATGAATCCAGGTTTCTCAGGCTTC-AAGCCAGCCCTCT 411558 ivi i-i i i v v i i - v iv C MIRb#SINE/MIR 73 AGCCGGGATT-CGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCT 27 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 32.48 CpG sites = 17, Kimura (unadjusted) = 36.25 Transitions / transversions = 2.43 (17/7) Gap_init rate = 0.10 (9 / 91), avg. gap size = 1.22 (11 / 9) 287 24.52 14.66 1.53 chr4qtel1M 411767 411882 (588118) C MIR3#SINE/MIR (17) 191 61 m_b201s601i4 7897 chr4qtel1M 411767 AATATCTAGAGCTGGAAGAGATCTCAGAGGCCAT-TGGTTCAA---CCGC 411812 i - i i i ii - i i --- v C MIR3#SINE/MIR 191 AATGTC-AGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTC 143 chr4qtel1M 411813 A-TTGATGGATAAGGAAAC-----CTC-------TGAGGTCCCTCGTTCA 411849 - v ii i ----- i ------- i vv i ii C MIR3#SINE/MIR 142 ATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCA 93 chr4qtel1M 411850 AGGCTACAAAGGGAGTAAGGGGGCAGAGGTGGG 411882 ii v v? v - v vi C MIR3#SINE/MIR 92 AGGTCACACAGCNAGTTA-GTGGCAGAGCCGGG 61 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 29.88 CpG sites = 19, Kimura (unadjusted) = 31.22 Transitions / transversions = 2.11 (19/9) Gap_init rate = 0.06 (7 / 115), avg. gap size = 2.71 (19 / 7) 16 9.32 0.00 0.00 chr4qtel1M 415456 415478 (584522) (C)n#Simple_repeat 1 23 (0) m_b201s252i3 7898 chr4qtel1M 415456 CCCCCCCCCCCGCCCCCGCCCCC 415478 v v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCC 23 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 20 20.57 4.76 1.54 chr4qtel1M 415898 415960 (584040) (GCT)n#Simple_repeat 1 65 (0) m_b201s252i4 7899 chr4qtel1M 415898 GCTGCTTC-GCTG-TCCTTCCGATGGCTGC-GGTCCTGTTACTGCCCCTG 415944 v - - v v i v - - v v i i iv (GCT)n#Simple 1 GCTGCTGCTGCTGCTGCTGCTGCT-GCTGCTGCTGCTGCTGCTGCTGCTG 49 chr4qtel1M 415945 CTGCTGCTGCTGCTGC 415960 (GCT)n#Simple 50 CTGCTGCTGCTGCTGC 65 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.06 (4 / 62), avg. gap size = 1.00 (4 / 4) 15 3.20 12.50 0.00 chr4qtel1M 416486 416517 (583483) (TCC)n#Simple_repeat 1 36 (0) m_b201s252i6 7900 chr4qtel1M 416486 TCCTCCGCCT-CTCC-CCT-CTCCTCCTCCT-CTCC 416517 v - - - - (TCC)n#Simple 1 TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC 36 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.13 (4 / 31), avg. gap size = 1.00 (4 / 4) 13 13.37 2.70 5.56 chr4qtel1M 416487 416523 (583477) (CCTCC)n#Simple_repeat 1 36 (0) m_b201s252i7 7900 chr4qtel1M 416487 CCTCCGCCTCTCC-CCTCTCCTCCTCCTCTCCCCGCCC 416523 - i - i - i v (CCTCC)n#Simp 1 CCTCC-CCTCCCCTCCCCTCC-CCTCCCCTCCCCTCCC 36 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.08 (3 / 36), avg. gap size = 1.00 (3 / 3) 199 26.42 12.50 1.74 chr4qtel1M 417309 417412 (582588) C MIR1_Amn#SINE/MIR (65) 165 51 m_b201s601i5 7901 chr4qtel1M 417309 GTGAGTCCCATC-TTCTTACTTTACAG-TGAGGAGACTGAG-----GAGA 417351 v vi i- i ii i - i ----- C MIR1_Amn#SINE 165 GTCAGTATCATTATCCCCATTTTACAGATGAGGAAACTGAGGCNCAGAGA 116 chr4qtel1M 417352 AATCCAGGGACGCGGCC--GGTTGCACAG-TAGTAAATTGCAATGAGT-- 417396 ii ?v v vi v -- ii ? -?i i? i v -- i-- C MIR1_Amn#SINE 115 GGTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNAGTGGCA--GAGCCG 68 chr4qtel1M 417397 -GCTTTGATTCCAGATC 417412 - v? ? vi i C MIR1_Amn#SINE 67 GGANTNGAACCCAGGTC 51 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 36.82 CpG sites = 18, Kimura (unadjusted) = 36.82 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.09 (9 / 103), avg. gap size = 1.67 (15 / 9) 237 25.32 11.39 0.00 chr4qtel1M 417312 417390 (582610) C MIR3#SINE/MIR (52) 156 69 m_b201s601i6 7901 chr4qtel1M 417312 AGTCCCATCTTCTTACTTTACAG-TGAGGAGACTGAG-----GAGAAATC 417355 v i ii i i - i ----- ii v C MIR3#SINE/MIR 156 AGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTG 107 chr4qtel1M 417356 CAGGGACGCGGCC--GGTTGCACAG-TAGTAAATTGCA 417390 v v vi v -- ii -? v i v C MIR3#SINE/MIR 106 AAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCA 69 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 32.14 CpG sites = 12, Kimura (unadjusted) = 32.14 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.05 (4 / 78), avg. gap size = 2.25 (9 / 4) 259 29.55 10.62 4.17 chr4qtel1M 417321 417433 (582567) C MIRb#SINE/MIR (115) 153 34 m_b201s601i7 7901 chr4qtel1M 417321 TTCTTACTTTACAG-TGAGGAGACTGAG-----GAGAAATCCAGGGACGC 417364 i ii i - i ----- ii iv vi vi C MIRb#SINE/MIR 153 TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTT 104 chr4qtel1M 417365 GGCC--GGTTGCACAG-TAGTAAATTGCAATGAGT---GCTTTGATTCCA 417408 v -- ii - i v -- i--- v i vi C MIRb#SINE/MIR 103 GCCCAAGGTCACACAGCTAGTAAGTGGCA--GAGCCGGGATTCGAACCCA 56 chr4qtel1M 417409 GATCCAGCCTCTGATCTCAGAATCC 417433 i ii--- iii i ii C MIRb#SINE/MIR 55 GGTCTG---TCTGACTCCAAAGCCC 34 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 39.25 CpG sites = 25, Kimura (unadjusted) = 40.99 Transitions / transversions = 3.57 (25/7) Gap_init rate = 0.09 (10 / 112), avg. gap size = 1.70 (17 / 10) 196 7.89 15.79 0.00 chr4qtel1M 417403 417440 (582560) Penelope1_Vert#LINE/Penelope 786 829 (250) m_b201s601i8 7902 chr4qtel1M 417403 ATTCCAGATC-CAGCCT--CTGATCTCAGAA---TCCCAATAGA 417440 i i - -- i --- Penelope1_Ver 786 ACTCCAGACCACAGCCTTGCTGATCTCAGGATTTTCCCAATAGA 829 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 8.59 CpG sites = 3, Kimura (unadjusted) = 8.59 Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.08 (3 / 37), avg. gap size = 2.00 (6 / 3) 16 0.00 0.00 0.00 chr4qtel1M 418177 418194 (581806) (T)n#Simple_repeat 1 18 (0) m_b201s252i8 7903 chr4qtel1M 418177 TTTTTTTTTTTTTTTTTT 418194 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTT 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 549 27.86 0.00 6.57 chr4qtel1M 418615 418760 (581240) MIRc#SINE/MIR 10 146 (122) m_b201s601i9 7904 chr4qtel1M 418615 GTGCTTCAGTGGATAGAGCACCAGGCTTGGAATCAAGAAGATATGCATTA 418664 v v v ii i i i iv vi v MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr4qtel1M 418665 AAATCTAACCTTAAACATCTAAATCTAAATCCAGCTATATAACCCCGGGC 418714 i i iviv iviv ii --------- i i i i ii MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTA---------CTAGCTGTGTGACCTTGGGC 100 chr4qtel1M 418715 AAGCCACTTAACCTCTGTTTGCCTCAGTCTCTTCATTTGTAAAATG 418760 i v vv i i i MIRc#SINE/MIR 101 AAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATG 146 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 33.68 CpG sites = 25, Kimura (unadjusted) = 36.06 Transitions / transversions = 1.92 (25/13) Gap_init rate = 0.06 (9 / 145), avg. gap size = 1.00 (9 / 9) 392 29.27 1.18 11.04 chr4qtel1M 418622 418790 (581210) MIR#SINE/MIR 13 166 (96) m_b201s601i10 7904 chr4qtel1M 418622 AGTGGATA-GAGCACCAGGCT-TGGAATCAAGAAGATATGCATTAAAATC 418669 v - -i - ii - vviiv vi vi MIR#SINE/MIR 13 AGTGGTTAAGAGCAC-GGGCTCTGGAGCCA-GACTGCCTGGGTTCGAATC 60 chr4qtel1M 418670 TAACCTTAAACATCTAAATCTAAATCCAGCTATATAACCCCGGGCAAGCC 418719 iviv iviv ii --------- i i i i ii ii MIR#SINE/MIR 61 CCGGCTCTGCCACTTA---------CTAGCTGTGTGACCTTGGGCAAGTT 101 chr4qtel1M 418720 ACTTAACCTCTGTTTGCCTCAGTCTCTTCATTTGTAAAATGAACTGGAGA 418769 v v i i i ----- i MIR#SINE/MIR 102 ACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAA-----TGGGGA 146 chr4qtel1M 418770 AAGAAATGGTAAACTACTCCA 418790 v iv i - v ii MIR#SINE/MIR 147 TAATAATAGT-ACCTACCTCA 166 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 34.91 CpG sites = 29, Kimura (unadjusted) = 38.22 Transitions / transversions = 1.93 (29/15) Gap_init rate = 0.11 (19 / 168), avg. gap size = 1.00 (19 / 19) 740 24.97 11.87 1.24 chr4qtel1M 419324 419542 (580458) MIRb#SINE/MIR 16 257 (11) m_b201s601i11 7905 chr4qtel1M 419324 GTGCCGTGGATGAACCACTGGGTCTGGAGTTAGAAAGGCCTGAGTTGAAA 419373 v vii v v v i i v i i vi MIRb#SINE/MIR 16 GTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCGAA 65 chr4qtel1M 419374 TCCTGACTC-----------AG-------AC--TGGGCAAGTCATGTAAC 419403 i i ----------- ------- -- i iv MIRb#SINE/MIR 66 TCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAAC 115 chr4qtel1M 419404 CTTTGTTTACCT--GTTTCCTCTTCAATAAAATGAGGATAATAATAGCAC 419451 i v vvi -- v vi i --- MIRb#SINE/MIR 116 CTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATA---C 162 chr4qtel1M 419452 CTACTTCTCAGGGTAGTTGT----ATCAATTGAGATAATATTTGTAAATT 419497 i v v ---- i v iiv vi MIRb#SINE/MIR 163 CTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGC 212 chr4qtel1M 419498 ACCTAGTACAATCCCTGACATATAGTGGATGCTCTCTAGATATTA 419542 i i i i v i i iiii vv i iv MIRb#SINE/MIR 213 GCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAAATGGTA 257 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 28.31 CpG sites = 32, Kimura (unadjusted) = 31.08 Transitions / transversions = 1.45 (32/22) Gap_init rate = 0.04 (8 / 218), avg. gap size = 3.62 (29 / 8) 16 8.48 4.00 0.00 chr4qtel1M 420944 420968 (579032) (TG)n#Simple_repeat 1 26 (0) m_b201s252i9 7906 chr4qtel1M 420944 TGTGTGTGTGTGTGTGTATTTG-GTG 420968 i v - (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTG 26 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 28 0.00 0.00 0.00 chr4qtel1M 421690 421715 (578285) (ACC)n#Simple_repeat 1 26 (0) c_b201s251i0 7907 chr4qtel1M 421690 ACCACCACCACCACCACCACCACCAC 421715 (ACC)n#Simple 1 ACCACCACCACCACCACCACCACCAC 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 578 30.93 2.97 10.96 chr4qtel1M 422585 422820 (577180) L3#LINE/CR1 2429 2647 (1452) m_b201s601i12 7908 chr4qtel1M 422585 TTTGCTT---TTTTCTTTGCCAGGGACAGTGACCTTTGTACTAAAAAAGA 422631 --- i i ii i v i i iiv ii i i L3#LINE/CR1 2429 TTTGCTTCCGTCTTCTCTATCAAGGAGAATGATCTTCAGACTGGAAAGGG 2478 chr4qtel1M 422632 CTGAGCAGAAATGGAAAATGGAAAATTGATATCCAAAATAAGGAAGGAGA 422681 iv i i v v vv vi ii vii i i vi L3#LINE/CR1 2479 TAGAACAAACATCGTTAAGAGGGAATTGAAGCCCAAGATAGGTGAGGAGA 2528 chr4qtel1M 422682 TAGTAAGCGAGTACTTCATTGTC----ATGGATTCAAGGTTCCTAGCCCA 422727 v i i viii ii---- ii vi vi L3#LINE/CR1 2529 TAGTAAGAGAGCACCTAGCCGCTTTAAATGAGTTCAAGTCTCCAGGCCCA 2578 chr4qtel1M 422728 GATGAATGGCATCCTTGGGTATTGGGTCCTGGAAAGCAGTATCAATAGCA 422777 i vi iv i -------- ------- i---- L3#LINE/CR1 2579 GACGAATTACATCCCAGGGTACT--------GAAAG-------AAC---- 2609 chr4qtel1M 422778 ATGGCAGATGTGATTGCTGAGCCACTCAAGATCAATAATTTTT 422820 - v i v i i ----i ii i L3#LINE/CR1 2610 -TTGCAGATGTGATCGCGGAACCGCT----GTCGGTAATCTTT 2647 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 37.91 CpG sites = 47, Kimura (unadjusted) = 42.22 Transitions / transversions = 2.61 (47/18) Gap_init rate = 0.11 (26 / 235), avg. gap size = 1.19 (31 / 26) 18 18.44 5.26 1.69 chr4qtel1M 422825 422881 (577119) (TTATTCT)n#Simple_repeat 1 59 (0) m_b201s252i10 7909 chr4qtel1M 422825 TTATTGTTTGTTATTTGCCCTTTATTCTTTATTC-TTATT-ATTATAGCT 422872 v i v iii - -v -v (TTATTCT)n#Si 1 TTATTCTTTATTCTTTATTCTTTATTCTTTATTCTTTATTCTTTAT-TCT 49 chr4qtel1M 422873 TT-TTATTTA 422881 - v (TTATTCT)n#Si 50 TTATTCTTTA 59 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.07 (4 / 56), avg. gap size = 1.00 (4 / 4) 282 30.04 0.00 3.57 chr4qtel1M 422990 423134 (576866) CR1-12_AMi#LINE/CR1 450 589 (25) m_b201s551i1 7910 chr4qtel1M 422990 CAATAATATTTCAAAGATCATGGAGAACAGGAGAGGTCCCACAAGACTCG 423039 v v v ii v i - v i v CR1-12_AMi#LI 450 CAATTATTTTTGAAAAGTCATGGAGAACTGGGGAGGT-CCAGAGGACTGG 498 chr4qtel1M 423040 AGGAGGACAAGTGTTGTTCTGAGTCTTATAAAATGGAAGACTATAGAATG 423089 i iii i v v i? vii i v v vv v? viv CR1-12_AMi#LI 499 AGAAAAGCAAATGTAGTACCNATCTTCAAAAAAGGGAAGAAGAGNGATCC 548 chr4qtel1M 423090 TGAAACCTACAGGCCAGTGAACTTGACTTCCAATGTCTCTAGAAA 423134 ? iv vi - v iii ? i v --- i i ? CR1-12_AMi#LI 549 NGGCAATTACA-GCCAGTCAGTCTNACCTCAA---TCCCTGGNAA 589 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 40.91 CpG sites = 22, Kimura (unadjusted) = 40.91 Transitions / transversions = 1.10 (22/20) Gap_init rate = 0.03 (5 / 144), avg. gap size = 1.00 (5 / 5) 247 29.92 0.00 3.90 chr4qtel1M 423141 423220 (576780) L3#LINE/CR1 2780 2856 (1243) m_b201s601i13 7908 chr4qtel1M 423141 ATTCTAGGGTGAGTCATTAAACGTGAACATCGGTGAACACCAAGAAAGGG 423190 iii ii i i- vvi iv i iv i L3#LINE/CR1 2780 ATTCTAGAACGGATTATTAAACA-GATGGTTTGTGAGCACTTAGAAAAGG 2828 chr4qtel1M 423191 AAACGCAGTGATCACCAAAAGCCAAGATAG 423220 i -- i ii iv i L3#LINE/CR1 2829 AAGCG--GTGATCACTAGGAGCCAGCATGG 2856 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 39.05 CpG sites = 18, Kimura (unadjusted) = 41.49 Transitions / transversions = 3.60 (18/5) Gap_init rate = 0.04 (3 / 79), avg. gap size = 1.00 (3 / 3) 23 7.16 0.00 0.00 chr4qtel1M 423526 423555 (576445) (T)n#Simple_repeat 1 30 (0) m_b201s252i11 7911 chr4qtel1M 423526 TTTTCCTTTTTTTTTTTTTTTTTTTTTTTT 423555 ii (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 30 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 298 25.79 0.00 5.71 chr4qtel1M 424631 424704 (575296) MIR#SINE/MIR 115 184 (78) m_b201s601i14 7912 chr4qtel1M 424631 GTGCCTTCAGTTTCCTCATCCATACAACAGGAATAACAGAAACAACAATT 424680 - ii v ii i i--- i ii vi MIR#SINE/MIR 115 GTGCCT-CAGTTTCCTCATCTGTAAAATGGGGATAAT---AATAGTACCT 160 chr4qtel1M 424681 GGCTCATGGGGCTGTTGTAAGAAT 424704 iv i i i i MIR#SINE/MIR 161 ACCTCATAGGGTTGTTGTGAGGAT 184 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 34.12 CpG sites = 15, Kimura (unadjusted) = 34.12 Transitions / transversions = 5.00 (15/3) Gap_init rate = 0.05 (4 / 73), avg. gap size = 1.00 (4 / 4) 201 30.00 0.00 0.00 chr4qtel1M 424939 424998 (575002) C MIR1_Amn#SINE/MIR (167) 63 4 m_b201s601i15 7913 chr4qtel1M 424939 TGGAGTTCAGGGCTCCAGATTCCTAGTCTTGTGCTCTCACCACTCTACCA 424988 ? iii v v v i iv vv vv C MIR1_Amn#SINE 63 TNGAACCCAGGTCTCCCGAGTCCCAGTCCAGTGCTCTATCCACTAGACCA 14 chr4qtel1M 424989 TCTTGTTTCC 424998 ivi ii C MIR1_Amn#SINE 13 CACTGCCTCC 4 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 39.69 CpG sites = 9, Kimura (unadjusted) = 39.69 Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0) 921 23.74 3.66 2.41 chr4qtel1M 425078 425323 (574677) C MIRc#SINE/MIR (4) 264 16 m_b201s601i16 7914 chr4qtel1M 425078 ATAATAATATCTGGCATTTACATAGCTCCTTAAAGTTTGCAAAATATTGT 425127 i?i vi ii v i v i iiii v C MIRc#SINE/MIR 264 ATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCGCTTT 215 chr4qtel1M 425128 ACACA-ATGTCAAATCATTGGATCCTCACAACAGTCCTGGGAGG-AGGAA 425175 - - ii i vv v ii v - v C MIRc#SINE/MIR 214 -CACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCA 166 chr4qtel1M 425176 GGTGC---TATTATGATCCTCATTTGTA-AAATGAGGAAACTGAGG--CA 425219 - --- v i - - i -- C MIRc#SINE/MIR 165 GG-GCAGGTATTATTATCCCCATTT-TACAGATGAGGAAACTGAGGCTCA 118 chr4qtel1M 425220 GACTGAAGTCAAATGGTTTGCTTAGAGTCACA-AGCTAGGAAGTAGTAGA 425268 -- i i i ii ii ii - v i i C MIRc#SINE/MIR 117 GA--GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGA 70 chr4qtel1M 425269 GATAGGATTTTAACTCTGGGCTTCTTCACTCCAAGCACGAGGGCATTTTC 425318 vii i iv i v v i v i- v v vi C MIRc#SINE/MIR 69 GCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGT-CCAGTGCTCTTTC 21 chr4qtel1M 425319 CCCTG 425323 v C MIRc#SINE/MIR 20 CACTG 16 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 27.60 CpG sites = 37, Kimura (unadjusted) = 29.57 Transitions / transversions = 1.85 (37/20) Gap_init rate = 0.05 (12 / 245), avg. gap size = 1.25 (15 / 12) 221 29.17 0.00 0.00 chr4qtel1M 425456 425503 (574497) MIR3#SINE/MIR 109 156 (52) m_b201s601i17 7915 chr4qtel1M 425456 CCTCATTGAATTTCAGTTTCTTTAGCTGTAAAATGAGACAGTTGAATT 425503 vi iiii i i v ivi i i MIR3#SINE/MIR 109 CCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACT 156 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 40.12 CpG sites = 11, Kimura (unadjusted) = 40.12 Transitions / transversions = 3.67 (11/3) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 328 33.58 4.55 2.99 chr4qtel1M 425520 425651 (574349) C MIRb#SINE/MIR (133) 135 2 m_b201s601i19 7916 chr4qtel1M 425520 GGAGTCTGGGGCCAGGAGAGGAGAAGTGACTC-CTCAGAGCCACAGAACC 425568 iv i ivi vv i i- i ii i v i i C MIRb#SINE/MIR 135 GGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCT 86 chr4qtel1M 425569 AATTTGTGTCTGAGGCAGGACCTGAATTCAGGTGTTCCTGCCTCCAAAGT 425618 i vv v v v i iii ii v vi v i C MIRb#SINE/MIR 85 AGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGC 36 chr4qtel1M 425619 CAG----CTTTCTATTACTTTGACCAT-TTATCTCTCT 425651 v ---- i i i ---- i-i ii i C MIRb#SINE/MIR 35 CCGTGCTCTTTCCACTGC----ACCACGCTGCCCCTCT 2 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 42.90 CpG sites = 29, Kimura (unadjusted) = 47.51 Transitions / transversions = 2.07 (29/14) Gap_init rate = 0.05 (7 / 131), avg. gap size = 1.43 (10 / 7) 372 30.97 4.42 0.00 chr4qtel1M 425520 425632 (574368) C MIRc#SINE/MIR (136) 132 15 m_b201s601i18 7916 chr4qtel1M 425520 GGAGTCTGGGGCCAGGAGAGGAGAAGTGACTC-CTCAGAGCCACAGAACC 425568 iv i ivi vv i- i ii i v i i C MIRc#SINE/MIR 132 GGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCT 83 chr4qtel1M 425569 AATTTGTGTCTGAGGCAGGACCTGAATTCAGGTGTTCCTGCCTCCAAAGT 425618 i vv v v v i ii ii v v ivi C MIRc#SINE/MIR 82 AGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTC 33 chr4qtel1M 425619 CAG----CTTTCTATTAC 425632 ---- i i i C MIRc#SINE/MIR 32 CAGTGCTCTTTCCACTGC 15 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 38.52 CpG sites = 22, Kimura (unadjusted) = 41.64 Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.02 (2 / 112), avg. gap size = 2.50 (5 / 2) 276 34.34 5.30 0.72 chr4qtel1M 427854 427985 (572015) L2d2_3end#LINE/L2 418 555 (0) m_b201s601i20 7917 chr4qtel1M 427854 TGCTTCATTTCTCTCATTAGAATGGAAGCTCTTTGAGGGC----ACTATC 427899 ii ii i i iv i v v i ---- i v L2d2_3end#LIN 418 TGTCTTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATG 467 chr4qtel1M 427900 TTTCTGACAGCATTTGTA---CTCACAACACATAACAGACTGCCGGGCAA 427946 i ivv vv - --- i i i v i v v vv v L2d2_3end#LIN 468 TCTTATACTTC-TTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCAC 516 chr4qtel1M 427947 AGAGAAACCCATTAGTAAGTACTTCTTTAATTCACTTGA 427985 v v iv vv i i i i v v v v i L2d2_3end#LIN 517 ACAGTAGGCGCTCAATAAATATTTGTTGATTTGATTTGA 555 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 45.24 CpG sites = 22, Kimura (unadjusted) = 46.63 Transitions / transversions = 0.96 (22/23) Gap_init rate = 0.02 (3 / 131), avg. gap size = 2.67 (8 / 3) 341 37.16 7.63 1.02 chr4qtel1M 428460 428826 (571174) L2#LINE/L2 2530 2920 (162) m_b201s601i21 7918 chr4qtel1M 428460 TCCTACAAGTCCCTTAGACTCATCACCTAGGAGTCAACCTGGA----TAT 428505 v v iv i i iv vv v v v ---- v L2#LINE/L2 2530 TCCTTCCAGTTGCTCAGGCCAAAAACCTTGGAGTCATCCTTGACTCCTCT 2579 chr4qtel1M 428506 CTTGCTCTCATCCCACAAATCCAATATGATGCCACAATCTGTCAATTTTT 428555 v iv v v viiviiv v vi iii i v L2#LINE/L2 2580 CTTTCTCTCACACCCCACATCCAATCCATCAGCAAATCCTGTCGGCTCTA 2629 chr4qtel1M 428556 CCTTTGCTATATTTCTCTAATATG-CTACTTTTGTTGATTTCAA------ 428598 iivv v ivv vi - i i vviv ii v ------ L2#LINE/L2 2630 CCTTCAAAATATATCCAGAATCCGACCACTTCTCACCACCTCCACTGCCA 2679 chr4qtel1M 428599 ------TAGTTGAGAGACAT-ATTATCTCATGCCTTGGGTGTTGCACAT- 428640 ------ i iv - v i- i vi v iv ii - - L2#LINE/L2 2680 CCACCCTGGTCCA-AGCCACCATCATCTCTCGCCTGGATTACTGCA-ATA 2727 chr4qtel1M 428641 GCCTGTTGATAGGTCTGCCCAGTGAAAGCCT-ACTCTAAACCAA---ATT 428686 vi i iv v iiv vvv v -i i ivvv? i--- L2#LINE/L2 2728 GCCTCCTAACTGGTCTCCCTGCTTCCACCCTTGCCCCCCTNCAGTCTATT 2777 chr4qtel1M 428687 CT--ATTCAGATCCTAAAGTGAGTGTATTCCAGTGTGGTTCTAATCATGT 428734 -- iv vvv i i viv v vv ii iiv vi L2#LINE/L2 2778 CTCAACACAGCAGCCAGAGTGATCCTTTTAAAACGTAAGTCAGATCATGT 2827 chr4qtel1M 428735 AACT--TATGACTCAATAAGTTTCAGGGGCTTCCTAATGCA-TCAAAGAT 428781 v -- v - v vvi i iv i viv - i - L2#LINE/L2 2828 CACTCCTCTG-CTCAAAACCCTCCAATGGCTTCCCATCTCACTCAGAG-T 2875 chr4qtel1M 428782 AAAATCCAAAATGTTCTCTATGGATTACAAAGTCCTTGATAAACT 428826 v i vi iv v vi i i vv i v L2#LINE/L2 2876 AAAAGCCAAAGTCCTTACAATGGCCTACAAGGCCCTACATGATCT 2920 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 50.06 CpG sites = 62, Kimura (unadjusted) = 52.19 Transitions / transversions = 0.85 (62/73) Gap_init rate = 0.04 (14 / 366), avg. gap size = 2.29 (32 / 14) 11 21.08 2.50 2.50 chr4qtel1M 429870 429909 (570091) (AGGGGCC)n#Simple_repeat 1 40 (0) m_b201s252i12 7919 chr4qtel1M 429870 AGGGACCAGGGGCCA-GAGAAAGGGTGCCTGGGGGCGGGGG 429909 i - i vv - v v i (AGGGGCC)n#Si 1 AGGGGCCAGGGGCCAGGGGCCAGGG-GCCAGGGGCCAGGGG 40 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 26 6.26 0.00 0.00 chr4qtel1M 430817 430850 (569150) (TGTGGG)n#Simple_repeat 1 34 (0) c_b201s251i1 7920 chr4qtel1M 430817 TGTGGGTGTGGGTGTGGGTGTGAGTGTGAGTGTG 430850 i i (TGTGGG)n#Sim 1 TGTGGGTGTGGGTGTGGGTGTGGGTGTGGGTGTG 34 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 15 23.63 3.33 5.08 chr4qtel1M 431046 431105 (568895) (TG)n#Simple_repeat 1 59 (0) m_b201s252i13 7921 chr4qtel1M 431046 TGTGTGAGTGTGACTGTGCTGCTGCTG-GCTTCTGTGTGTGTATGAGTCT 431094 v vv - - - - iv v i v v (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTG-TG-TG-TGTGTGTGTGTGTGTGTGTGTGTGT 47 chr4qtel1M 431095 -TGTCAGTGTGT 431105 - vv (TG)n#Simple_ 48 GTGTGTGTGTGT 59 Matrix = Unknown Transitions / transversions = 0.22 (2/9) Gap_init rate = 0.08 (5 / 59), avg. gap size = 1.00 (5 / 5) 38 2.78 0.00 0.00 chr4qtel1M 431114 431150 (568850) (TG)n#Simple_repeat 1 37 (0) c_b201s251i2 7921 chr4qtel1M 431114 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGTGTGT 431150 i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 37 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 16 10.03 0.00 0.00 chr4qtel1M 432454 432475 (567525) (T)n#Simple_repeat 1 22 (0) m_b201s252i14 7922 chr4qtel1M 432454 TTTTTCTTTTCTTTTTTTTTTT 432475 i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTT 22 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 796 26.65 8.32 2.75 chr4qtel1M 432960 433476 (566524) C L1ME3G_3end#LINE/L1 (376) 548 4 m_b201s551i3 7923 chr4qtel1M 432960 ATAATATTCCATAACATTTATATACTCACAATT-ACCCAACTGTTCTCCA 433008 i ii vv - i - iii ii i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATAC-CATAATTTATTTAACCATTCCCCT 500 chr4qtel1M 433009 AACTGATGGGCATCCATTCATTTTCCAGTTTCTAGCCATCATAAATTG-G 433057 -i i ii vvivv i i v i i i ivi- C L1ME3G_3end#L 499 A-TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATG 451 chr4qtel1M 433058 CCACAAGAAACGTTTCCAGTACATGGGTCCTT-----CCT-TCTTAGTAT 433101 ii vi i i- iv v? ----- v - viv C L1ME3G_3end#L 450 CTGCAATGAACATC-CTTGTACATGCNTCCTTGTGCACATGTGCGAGTAT 402 chr4qtel1M 433102 CTCTTTGGGGTA--TGCTCAGTAGC--AACTGCTGGATCAAAGGGTA--- 433144 i ? i i -- ? i? v i-- i i --- C L1ME3G_3end#L 401 TTCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGC 352 chr4qtel1M 433145 -CAGTTTGATAACTTTTTGGGCATAATTCCAGATTGGTCTCCGTGAATGG 433193 - v --- v viviv v v i vi i-i ? C L1ME3G_3end#L 351 GCATTT---TAAATTTTAATAGATACTGCCAAATTGCCCTCCA-AAANGG 306 chr4qtel1M 433194 CTG-AT--GTCTACAGCTCCACCAACAATGTATCAGTATCCCTGGTTTCC 433240 - i--i i vii i i v vi v i v i C L1ME3G_3end#L 305 CTGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCC 256 chr4qtel1M 433241 TACATTC-CTCCAACATTCCGGTGTTAT----CT------TTCCTGTCAT 433279 i ii - v i -? i i ---- ------ ii i v C L1ME3G_3end#L 255 CACACCCTCGCCAACACT-NGATATTATCAANCTTTTAAATTTTTGCCAA 207 chr4qtel1M 433280 TCTAACCACGTG--TAGTGGTACCTCAGAGTTGTCTTAATTTGCATTTCT 433327 i -iiv --v i i vv i i C L1ME3G_3end#L 206 TCTGA-TGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCC 158 chr4qtel1M 433328 CTGATCAATAGTGA-TTTGA-CA-CCTTTCATATG---AGTGGAAGGTTT 433371 i v -v - - i --- v -vvi C L1ME3G_3end#L 157 CTGATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGG-CCATTT 109 chr4qtel1M 433372 CAATTTCATCATCTGAAAATTGTCTGTTCATATCCTTTGGACCAGCTATC 433421 vv v v vi i - v vi v C L1ME3G_3end#L 108 GTATTTCCTCTTCTGTGAATTGCCTGTTCATATCCTTT-GCCCATTTTTC 60 chr4qtel1M 433422 AATTGTAATGGTCGATTTCTTA-TAACT----GGAGTCAATTTCATATAT 433466 v -ii v vv - i i ---- i--i i - C L1ME3G_3end#L 59 TATTG-GGTTGTCTTTTTCTTATTGATTTGTAGGAGTT--CTTTATATA- 14 chr4qtel1M 433467 TTCTGGAAAT 433476 v C L1ME3G_3end#L 13 TTCTGGATAT 4 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 33.79 CpG sites = 81, Kimura (unadjusted) = 34.42 Transitions / transversions = 1.53 (81/53) Gap_init rate = 0.07 (35 / 516), avg. gap size = 1.66 (58 / 35) 886 25.82 8.43 2.09 chr4qtel1M 432960 433410 (566590) C L1ME5_3end#LINE/L1 (389) 552 74 m_b201s551i2 7923 chr4qtel1M 432960 ATAATATTCCATAACATTTATATACTCACAATT-ACCCAACTGTTCTCCA 433008 i i iiii vi vi - v - i v iii v C L1ME5_3end#LI 552 ATAGTACTCCATGGTGTGCATCCAC-CACATTTTACCTATCCACTCTCCC 504 chr4qtel1M 433009 AACTGATGGGCATCCATTCATTTTCCAGTTTCTAGCCATCATAAATTG-G 433057 i- i i vvivvii ii i iv i i ivi- C L1ME5_3end#LI 503 AG-TGATGGACACCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACG 455 chr4qtel1M 433058 CCACAAGAAACGTTTCCAGTACATGGGTCCTT-----CCT-TCTTAGTAT 433101 ii vi i iii - vvi ----- - v v v C L1ME5_3end#LI 454 CTGCAATGAACATCCTC-GTACATGTCCCCTTATGGACCTGTGTGAGAAT 406 chr4qtel1M 433102 CTCTTTGGGGTATG--CTCAGTAGC--AACTGCTGGATCAAAGGGTACA- 433146 i i i-- i v -- i i v ii- C L1ME5_3end#LI 405 TTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATGC 356 chr4qtel1M 433147 GTTTGATAACTT--TTTGGGCA--TAATTCCAGATTGGTCTCCGTGAATG 433192 --- - -- ivi -- v v v i- C L1ME5_3end#LI 355 GT---ATA-CTTAATTTGACTAAGTACTGCCAGATTGCTCTCCA-GAATG 311 chr4qtel1M 433193 GCTG-AT--GTCTACAGCTCCACCAACAATGTATCAGTATCCCTGGTTTC 433239 - i-- vii i i i v vi i iv? i C L1ME5_3end#LI 310 GCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATNTCC 261 chr4qtel1M 433240 CTACATTC-CTCCAACATTCCGGTGTTATC----TTTCC------TGTCA 433278 i i - v i i- ii ---- i------ i C L1ME5_3end#LI 260 CCACATCCTCGCCAACACTT-GGCATTATCCAGCTTTCTAATTTTTGCCA 212 chr4qtel1M 433279 TTCTAACCACGTGTA--GTGGTACCTCAGAGTTGTCTTAATTTGCATTTC 433326 v i- v -- i i vv i C L1ME5_3end#LI 211 GTCTAAT-AGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATTTC 163 chr4qtel1M 433327 TCTGATCAATAGTGA-TTTGA-CACCT-TTCATATGAGTGGAAG-GTTTC 433372 i v i - - i - vv vv -v C L1ME5_3end#LI 162 TCTGATTACTAATGAGTTTGAGCATCTCTTCATATGCTTGTTAGCCTTTC 113 chr4qtel1M 433373 -AATTTCATCATCTGAAAATTGTCTGTTCATATCCTTTG 433410 -ii v v v i C L1ME5_3end#LI 112 GGGTTTCCTCTTCTGTAAATTGCCTGTTCATATCCTTTG 74 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 32.83 CpG sites = 73, Kimura (unadjusted) = 32.83 Transitions / transversions = 1.78 (73/41) Gap_init rate = 0.07 (30 / 450), avg. gap size = 1.60 (48 / 30) 35 14.55 0.00 2.86 chr4qtel1M 436112 436183 (563817) (TGTGGG)n#Simple_repeat 1 70 (0) m_b201s252i15 7924 chr4qtel1M 436112 TGTGGGTGTGGGTGTGGGTGTGGGGATGTGGGTGTGAGTGTGAGTGTGAG 436161 - - i i i (TGTGGG)n#Sim 1 TGTGGGTGTGGGTGTGGGTGT-GGG-TGTGGGTGTGGGTGTGGGTGTGGG 48 chr4qtel1M 436162 TGAAGCTGTGGGGCTGTGTGTG 436183 vi v vv v (TGTGGG)n#Sim 49 TGTGGGTGTGGGTGTGGGTGTG 70 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.03 (2 / 71), avg. gap size = 1.00 (2 / 2) 26 20.00 2.70 4.11 chr4qtel1M 436355 436428 (563572) (TG)n#Simple_repeat 1 73 (0) m_b201s252i16 7925 chr4qtel1M 436355 TGTGTGAGTGTGAGTGTGCTGCTGCTG-GCTTCTGTGTGTTTATGAGTCT 436403 v v - - - - iv v v i v v (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTG-TG-TG-TGTGTGTGTGTGTGTGTGTGTGTGT 47 chr4qtel1M 436404 -TGTCAGTGCGTGTGTGTGTGTGTGT 436428 - vv i (TG)n#Simple_ 48 GTGTGTGTGTGTGTGTGTGTGTGTGT 73 Matrix = Unknown Transitions / transversions = 0.33 (3/9) Gap_init rate = 0.07 (5 / 73), avg. gap size = 1.00 (5 / 5) 221 29.06 3.79 8.73 chr4qtel1M 439051 439182 (560818) C MIR3#SINE/MIR (35) 173 48 m_b201s601i22 7926 chr4qtel1M 439051 GACTTCTGAGATCAAC-AGTC--ACCTCATCCAGTTATAGCTGCAGGTAA 439097 i iv v - -- i v - v ----- i i i C MIR3#SINE/MIR 173 GACCTTAGAGATCATCTAGTCCAACCCCCTC-ATTT-----TACAGATGA 130 chr4qtel1M 439098 AGAAAAGACTGAGGGCCAG-GAGGTACAAGGACTTCTTGGAGATCCCACA 439146 i --- v - iv iv viivi i v C MIR3#SINE/MIR 129 GGAAA---CTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACA 83 chr4qtel1M 439147 GGCAGTGAA-GAAAGGACAACAGGACCAGAGCCCGAG 439182 v? v i- iv ii -- i i i ii C MIR3#SINE/MIR 82 GCNAGTTAGTGGCAGAGC--CGGGACTAGAACCCAGG 48 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 36.91 CpG sites = 22, Kimura (unadjusted) = 38.32 Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.11 (15 / 131), avg. gap size = 1.07 (16 / 15) 384 16.09 12.61 0.75 chr4qtel1M 439453 439571 (560429) C Charlie1a#DNA/hAT-Charlie (6) 1449 1317 m_b201s502i0 7927 chr4qtel1M 439453 TTCTCAAACTTCT-GGTCTCA--ACATCTTTACATTATTAAAAATTATTG 439499 i - -- vi i v C Charlie1a#DNA 1449 TTCTCAAACTTTTTGGTCTCAGGACCCCTTTACACTCTTAAAAATTATTG 1400 chr4qtel1M 439500 AGTCTGTCCAAAAAGCTTTTTCTTATGTG--------TTATGAATATTTA 439541 vvi-i i vi --------i vi C Charlie1a#DNA 1399 AGGAC-CCCAAAGAGCTTTTGTTTATGTGGGTTATATCTATCGATATTTA 1351 chr4qtel1M 439542 CCATATTAAAAGTAAAAACT----AACTTTTAAA 439571 i i v ---- i C Charlie1a#DNA 1350 CCATATTAGAAATTAAAACTGAGAAATTTTTAAA 1317 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 17.37 CpG sites = 12, Kimura (unadjusted) = 18.40 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.04 (5 / 118), avg. gap size = 3.20 (16 / 5) 199 25.42 10.91 7.02 chr4qtel1M 439660 439769 (560231) C L2c_3end#LINE/L2 (15) 463 350 m_b201s601i23 7928 chr4qtel1M 439660 AAGCATTTATTAAGCACTTACTACA-GCCAGGCA-TGTGCATACAAATGA 439707 i i i i ii- i- v v --- C L2c_3end#LINE 463 AAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGATACAAA--- 417 chr4qtel1M 439708 AAGCAAGAAGCAAAACA-GGGCTCTCCCTTCTAATAG------GTCTA-- 439748 ----i vi ii i - v i v i v iv ------ -- C L2c_3end#LINE 416 ----GATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAGT 371 chr4qtel1M 439749 -AAGGAAACTCACAAGATAAAC 439769 -i i vv ? - C L2c_3end#LINE 370 GGAGGAGACAGACANG-TAAAC 350 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 29.63 CpG sites = 17, Kimura (unadjusted) = 32.64 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.12 (13 / 109), avg. gap size = 1.54 (20 / 13) 18 18.88 6.45 1.54 chr4qtel1M 440141 440202 (559798) (CCTG)n#Simple_repeat 1 65 (0) m_b201s252i17 7929 chr4qtel1M 440141 CCTGCCAGCCTGCCTG-CTTCATGTGTAGCC--CCTGCCAGTCTGCCTG- 440186 v - v v iv - -- v i - (CCTG)n#Simpl 1 CCTGCCTGCCTGCCTGCCTGCCTGCCT-GCCTGCCTGCCTGCCTGCCTGC 49 chr4qtel1M 440187 CTGCCCGCCCACCTGC 440202 i ii (CCTG)n#Simpl 50 CTGCCTGCCTGCCTGC 65 Matrix = Unknown Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.07 (4 / 61), avg. gap size = 1.25 (5 / 4) 15 17.84 0.00 8.33 chr4qtel1M 440603 440654 (559346) (CCGCCCC)n#Simple_repeat 1 48 (0) m_b201s252i18 7930 chr4qtel1M 440603 CCGCCCGCTCGGTCCCCGACTCCCCTCCTTCCCCCCTCCCCGCCCCCCGC 440652 - i vi - i v -- v i (CCGCCCC)n#Si 1 CCGCCC-CCCGCCCCCCG-CCCCCCGCC--CCCCGCCCCCCGCCCCCCGC 46 chr4qtel1M 440653 CC 440654 (CCGCCCC)n#Si 47 CC 48 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.08 (4 / 51), avg. gap size = 1.00 (4 / 4) 266 33.68 6.38 0.50 chr4qtel1M 440968 441155 (558845) C L3b_3end#LINE/CR1 (670) 536 338 m_b201s601i24 7931 chr4qtel1M 440968 CCAGGTCTTTATTAGAATAACGGCTGCCGAGCTTCCGGTCTTCTACGATG 441017 v i v vv?i v ii iv vvv ii i ivv C L3b_3end#LINE 536 CCAGGTCTTTTTCACATGNGCTGCTGCTAAGCCGCGTCTCCCCCATCCTG 487 chr4qtel1M 441018 CCCTTGGGC-ACAG----TTTGAACCCGAGTGTAGAACTTTA-ATTCATC 441061 iv i v - iv ---- i i i -i i C L3b_3end#LINE 486 TACTCGCGCGATTGNTTTTTTGAACCCAAGTGCAGGACTTTACGTTTATC 437 chr4qtel1M 441062 TCC-TAAAATTCCGCCTTAGAAGAATCTTCCCTATGATCTAGAGCTACCG 441110 i i- vi i ii ivvi ?v vv v?i v -v ii C L3b_3end#LINE 436 CCTGTTGAATTTCATCTTGTTGGNTTCGGCCCGNCGTTCTAG-TCTGTCG 388 chr4qtel1M 441111 AGATCTTCGTGGACCCC-CTCTTG--TCCTTC-T-TTAGCCGTTTCCCCC 441155 v iv i i-v i -- vv - - iv i C L3b_3end#LINE 387 AGATCGTTTTGGATCCTGATTTTGCATCCAACGTATTAGCCGTCGCTCCC 338 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 42.00 CpG sites = 34, Kimura (unadjusted) = 46.92 Transitions / transversions = 1.17 (34/29) Gap_init rate = 0.05 (9 / 187), avg. gap size = 1.44 (13 / 9) 52 22.76 3.16 5.38 chr4qtel1M 441156 441345 (558655) (CCTTC)n#Simple_repeat 1 186 (0) m_b201s252i19 7932 chr4qtel1M 441156 CCTCCCCTTCCTTTCTCCCTCTCCCTTCCCTCTCCCCTTCCCTTCTCCCT 441205 i -i - - - - - i (CCTTC)n#Simp 1 CCTTCCCTTCC-CT-TCCCT-TCCCTTCCCT-T-CCCTTCCCTTC-CCTT 44 chr4qtel1M 441206 -CTTCCCCTTCCCTTTCCTTTTTCTCCC-TCCCTCCCCCTTCTTTCCCTT 441253 - i i i iiii - i i i i (CCTTC)n#Simp 45 CCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTT 94 chr4qtel1M 441254 TTCCTCTTTTCCCTTCCCTT-TC-ACCCCCCCCTTCCCGTTCTGTCCTCC 441301 ii i ii -i -v ii - iv i - (CCTTC)n#Simp 95 CCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCC-TTCCCTTC-CC 142 chr4qtel1M 441302 TCCCCCTCCTATCCCTCCCCTCTGCTCTTCCCTTCCC-T-CCTTCC 441345 i i iv i - - i - - (CCTTC)n#Simp 143 TTCCCTTCCCTTCCCTTCCCT-T-CCCTTCCCTTCCCTTCCCTTCC 186 Matrix = Unknown Transitions / transversions = 9.67 (29/3) Gap_init rate = 0.08 (16 / 189), avg. gap size = 1.00 (16 / 16) 79 4.86 0.00 0.00 chr4qtel1M 441352 441436 (558564) (TC)n#Simple_repeat 1 85 (0) c_b201s251i3 7933 chr4qtel1M 441352 TCTCTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 441401 i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr4qtel1M 441402 TCTCTCTCTGTCTCTGTCTCTCTCTGTCTCTCTCT 441436 v v v (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 85 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 84), avg. gap size = 0.0 (0 / 0) 383 33.00 3.81 1.87 chr4qtel1M 441865 442074 (557926) C L1ME5_3end#LINE/L1 (338) 603 390 m_b201s551i4 7934 chr4qtel1M 441865 ATCAGTTCATGTCTCTCTGTAT---TCTTGCTGGTCGTTTCTTACAGAAC 441911 vi i iv v i --- v iiv i i v v vvv C L1ME5_3end#LI 603 ATCCATCCATGTTGCTATGTGTACATCTAGTCCGTTGCTTCTAACTGCTG 554 chr4qtel1M 441912 AATAATATTCTATAACATTCATATGCCACAATTTACTCAACCATTCTTCA 441961 v i i i iiii v vii v ii v i i v C L1ME5_3end#LI 553 CATAGTACTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCC 504 chr4qtel1M 441962 ATTGATGGGCATCCAT-TCATTTTCAGCTTCTGGCCACTACAAACAGGGC 442010 v i i v- iiii i i i iv i iv C L1ME5_3end#LI 503 AGTGATGGACACCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGC 454 chr4qtel1M 442011 TGCCACAAACATTTTGGCACATACTGGTCCCTTTC----CCTTCTTTAGT 442056 v ii ii v i ---- i v---- viv v v C L1ME5_3end#LI 453 TGCAATGAACATCCTCGTACAT----GTCCCCTTATGGACCTGTGTGAGA 408 chr4qtel1M 442057 ATTTCTTTGGGATATACA 442074 i C L1ME5_3end#LI 407 ATTTCTTTGGGATATATA 390 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 45.26 CpG sites = 41, Kimura (unadjusted) = 45.26 Transitions / transversions = 1.52 (41/27) Gap_init rate = 0.03 (7 / 209), avg. gap size = 1.71 (12 / 7) 279 31.16 3.14 5.91 chr4qtel1M 441912 442102 (557898) C L1MB3_3end#LINE/L1 (377) 553 368 m_b201s551i5 7934 chr4qtel1M 441912 AATAATATTCTATAACATTCATATGCCACAATTTACTCAACCATTCTTCA 441961 i vii vi i v ii i v v v C L1MB3_3end#LI 553 AATAATATTCCATTGTATGTATATACCACATTTTGTTTATCCATTCATCC 504 chr4qtel1M 441962 ATTGATGGGCA-TCCATTCATTTTCAGCTTCTGGCCACTACAAACAGGGC 442010 i i i - iviv iii i v i i i iii i iv C L1MB3_3end#LI 503 GTCGATGGACACTTGGGTTGCTTCCACCTTTTGGCTATTGTGAATAATGC 454 chr4qtel1M 442011 TGCCACAAACAT---TTTGGCACATACTGGTCCCTTTCCCTTCTTTAGTA 442057 i ii --- v -i v iiv? i vvv? v --i C L1MB3_3end#LI 453 TGCTATGAACATGGGTGT-ACAAATATCTNTTCGAGNCCCTGCTTT--CA 407 chr4qtel1M 442058 TTTCTTTGGGATATACAGGCCCCTCAGAGGTGGTTTAATT--TGGAT 442102 v v i i ----- i i --- -- C L1MB3_3end#LI 406 ATTCTTTTGGGTATATA-----CCCAGAAGTGG---AATTGCTGGAT 368 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 40.89 CpG sites = 37, Kimura (unadjusted) = 42.96 Transitions / transversions = 1.95 (37/19) Gap_init rate = 0.07 (14 / 190), avg. gap size = 1.21 (17 / 14) 441 28.39 2.53 1.89 chr4qtel1M 441913 442070 (557930) C L1ME4c_3end#LINE/L1 (275) 555 397 m_b201s551i6 7934 chr4qtel1M 441913 ATAATATTCTATAACATTCATATGCCACAATTTACTCAACCATTCTTCAA 441962 i vivi ?v i i i i ii v C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chr4qtel1M 441963 TTGATGGGCATCCA-TTCATTTTCAGCTTCTGGCCACTACAAACAGGGCT 442011 v i ii -v ii i ii i v i i i i iv C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCT 456 chr4qtel1M 442012 GCCACAAACATTTTGGCACATACTGGTCCCTTTCCCTTCTTT---AGTAT 442058 v ii i v ii - i -- i i --- v C L1ME4c_3end#L 455 GCAATGAACATCTTCGTGCATA-TAG--CTTTTTCCTTCTTTTGAATTAT 409 chr4qtel1M 442059 TTCTTTGGGATA 442070 i i C L1ME4c_3end#L 408 TTCCTTAGGATA 397 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 37.36 CpG sites = 33, Kimura (unadjusted) = 38.51 Transitions / transversions = 3.00 (33/11) Gap_init rate = 0.03 (5 / 157), avg. gap size = 1.40 (7 / 5) 364 26.97 4.49 0.00 chr4qtel1M 442811 442899 (557101) MIR#SINE/MIR 52 144 (118) m_b201s601i25 7935 chr4qtel1M 442811 GTTTAAATCTGGTTTCAGACATTTACTAGCCATGTGACTGTGGGCAAGTC 442860 ii iv vi v v i ii iv i MIR#SINE/MIR 52 GTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTT 101 chr4qtel1M 442861 ACTTACCCTTGTT-TGTCTTAGTT---TCACCTACAAAATGAG 442899 v ivi - i i --- i ii i MIR#SINE/MIR 102 ACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGG 144 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 33.11 CpG sites = 17, Kimura (unadjusted) = 35.15 Transitions / transversions = 2.43 (17/7) Gap_init rate = 0.02 (2 / 88), avg. gap size = 2.00 (4 / 2) 21 0.00 0.00 0.00 chr4qtel1M 443628 443650 (556350) (T)n#Simple_repeat 1 23 (0) m_b201s252i21 7936 chr4qtel1M 443628 TTTTTTTTTTTTTTTTTTTTTTT 443650 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTT 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 368 25.78 0.74 8.73 chr4qtel1M 443652 443787 (556213) C MIR1_Amn#SINE/MIR (101) 129 4 m_b201s601i26 7937 chr4qtel1M 443652 CTAAGGCA-ATTGGGGTTAAGGGACTTGTCTAGGGTCACACAGCTAGGAA 443700 i ?- vv i ? v i i i ? ?i v? C MIR1_Amn#SINE 129 CTGAGGCNCAGAGAGGTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNA 80 chr4qtel1M 443701 GTGTTAAGTGTCTGAGGCCAGATTTGAACTCAGGACCTCCTGACTTCAGG 443750 vi ------- v vi ? ? i -i i v i vi C MIR1_Amn#SINE 79 GTGGCA-------GAGCCGGGANTNGAACCCAGG-TCTCCCGAGTCCCAG 38 chr4qtel1M 443751 ACTGGTTCTCTATCTGCTGCACCACCTGGCTGCCCCC 443787 v ii v ii iv ---i i C MIR1_Amn#SINE 37 TCCAGTGCTCTATCCACTAGACCAC---ACTGCCTCC 4 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 33.39 CpG sites = 20, Kimura (unadjusted) = 34.74 Transitions / transversions = 1.67 (20/12) Gap_init rate = 0.09 (12 / 135), avg. gap size = 1.00 (12 / 12) 496 22.40 0.84 6.19 chr4qtel1M 443663 443781 (556219) C MIRc#SINE/MIR (153) 115 3 m_b201s601i27 7937 chr4qtel1M 443663 GGGGTTAAGGGACTTGTCTAGGGTCACACAGCTAGGAAGTGTTAAGTGTC 443712 i v i i i ------- v C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGC 73 chr4qtel1M 443713 TGAGGCCAGATTTGAACTCAGGACCTCCTGACTTCAGGACTGGTTCTCTA 443762 v v vi i i i v i i i v ii v v C MIRc#SINE/MIR 72 AGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTT 23 chr4qtel1M 443763 TCTGCTGCACCAC-CTGGCT 443781 ii - v C MIRc#SINE/MIR 22 TCCACTGCACCACACTGCCT 3 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 25.77 CpG sites = 15, Kimura (unadjusted) = 27.01 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.07 (8 / 118), avg. gap size = 1.00 (8 / 8) 19 0.00 0.00 0.00 chr4qtel1M 444036 444056 (555944) (T)n#Simple_repeat 1 21 (0) m_b201s252i22 7938 chr4qtel1M 444036 TTTTTTTTTTTTTTTTTTTTT 444056 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTT 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 13 28.66 0.00 0.00 chr4qtel1M 444151 444192 (555808) (TTT)n#Simple_repeat 1 42 (0) m_b201s252i23 7939 chr4qtel1M 444151 TTTTTTTTTTTTATTCTTTTGACTTTGTTTTATTATCTTGTT 444192 v i vvi v v v i v (TTT)n#Simple 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 42 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 15 0.00 0.00 0.00 chr4qtel1M 445365 445383 (554617) (TGC)n#Simple_repeat 1 19 (0) m_b202s252i3 7940 chr4qtel1M 445365 TGCTGCTGCTGCTGCTGCT 445383 (TGC)n#Simple 1 TGCTGCTGCTGCTGCTGCT 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 205 29.66 8.68 9.17 chr4qtel1M 445624 445842 (554158) L2a_3end#LINE/L2 298 515 (2) m_b202s601i2 7941 chr4qtel1M 445624 CCCCCTGTCCTGATTTACTTT-------AAAATTTAACTCC-TCCTACTT 445665 i ii v i ------- iv i v v - iv v L2a_3end#LINE 298 CCCCTTACCCTGCTTTATTTTTCTCCATAGCACTTATCACCATCTGACAT 347 chr4qtel1M 445666 ATTAATGCCAGATTTCACCTTGCATTAATTTTGTGTATGTTTACATGTAT 445715 i ----i v i i --- v ------- i- -i L2a_3end#LINE 348 ACTA----TATATTTTACTT---ATTTATTT-------GTTTAT-TGT-C 381 chr4qtel1M 445716 TGTCTTTGTTGA-TAAAATGGAAGTTCCCTAAGG-CAGGGATTATTGAAC 445763 iiviiv - i v i v i - i v v-- L2a_3end#LINE 382 TGTCTCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGT-- 429 chr4qtel1M 445764 CACT-TTTTGTTT-TTGTTTT-------GTGGTTAGCATAGGATCTGGTC 445804 -- - i-i i v ------- i vi v i vii iv L2a_3end#LINE 430 --CTGTTTTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCA 477 chr4qtel1M 445805 CATAAGTGGGGCTCAATAAATGCTTGTATATTGATTGA 445842 ivv v ii vv v v L2a_3end#LINE 478 CATAGTAGGCGCTCAATAAATATTTGTTGAATGAATGA 515 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 37.76 CpG sites = 33, Kimura (unadjusted) = 38.60 Transitions / transversions = 1.27 (33/26) Gap_init rate = 0.12 (27 / 218), avg. gap size = 1.44 (39 / 27) 220 30.27 6.00 5.30 chr4qtel1M 445694 445843 (554157) L2d_3end#LINE/L2 363 513 (3) m_b202s601i3 7941 chr4qtel1M 445694 TTTTGTGTATGTTTACATGTATTGTCTTTGTTGATAAAATGGAAGTTCCC 445743 ii i --- - v iiviviv i v v i i L2d_3end#LINE 363 TTTCATGTGTGTT---A-GTCTTGTCTCCCCAACTAGATTGTAAGCTCCT 408 chr4qtel1M 445744 TAAGG-CAGGGATTAT---TGAACCACTTTTTGTTTTTGTTTT-----GT 445784 i - ii --- v --i ? -- ? i ii----- i L2d_3end#LINE 409 TGAGGGCAGGGACCATGTCTTA--TACTNTTT--TNTCGTTCCCCACAGC 454 chr4qtel1M 445785 GGTTAGCATAGGATCTGGTCCATAAGTGGGGCTCAATAAATGCTTGTATA 445834 vi i viiivi iv ivv v i vv L2d_3end#LINE 455 GCCTAGCACAGTGCTGAGCACATAGTAGGCGCTCAATAAATACTTGTTGA 504 chr4qtel1M 445835 TTGATTGAT 445843 L2d_3end#LINE 505 TTGATTGAT 513 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 38.64 CpG sites = 27, Kimura (unadjusted) = 41.15 Transitions / transversions = 1.69 (27/16) Gap_init rate = 0.07 (11 / 149), avg. gap size = 1.55 (17 / 11) 195 34.25 2.74 0.00 chr4qtel1M 448589 448661 (551339) MIRc#SINE/MIR 74 148 (120) m_b202s601i4 7942 chr4qtel1M 448589 CCATTTGCT--CTATTTCATTTTGTGTAAGACATCTGACCTCATTGGATT 448636 i i -- i v v ii v i v ii i vi iiii MIRc#SINE/MIR 74 CCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCC 123 chr4qtel1M 448637 TTATTTTTCACATGTGTAAAATGAG 448661 i v i v v i MIRc#SINE/MIR 124 TCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 49.01 CpG sites = 17, Kimura (unadjusted) = 49.01 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.01 (1 / 72), avg. gap size = 2.00 (2 / 1) 233 37.70 4.10 0.00 chr4qtel1M 448598 448719 (551281) MIR3#SINE/MIR 82 208 (0) m_b202s601i5 7942 chr4qtel1M 448598 CTATTTCATTTTGTGTAAGACATCTGACCTCATTGGATTTTATTTTTCAC 448647 i v v ii v i v ii v vi iii i v i v MIR3#SINE/MIR 82 CTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTC 131 chr4qtel1M 448648 ATGTGTAAAATGAGCACTCCAGGTTACACTACCTT---GATACCTTCAAA 448694 v vivviii ii v iv i i--- i v v i MIR3#SINE/MIR 132 ATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAG 181 chr4qtel1M 448695 CTCT--TGGTCTATGATCCTGTACTTC 448719 --iiv i i iv MIR3#SINE/MIR 182 CTCTGACATTCTATGATTCTATGATTC 208 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 55.38 CpG sites = 28, Kimura (unadjusted) = 55.38 Transitions / transversions = 1.56 (28/18) Gap_init rate = 0.02 (2 / 121), avg. gap size = 2.50 (5 / 2) 49 0.00 0.00 0.00 chr4qtel1M 449728 449769 (550231) (AT)n#Simple_repeat 1 42 (0) c_b202s251i0 7943 chr4qtel1M 449728 ATATATATATATATATATATATATATATATATATATATATAT 449769 (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATAT 42 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 13 18.91 0.00 0.00 chr4qtel1M 449936 449965 (550035) (AGAA)n#Simple_repeat 1 30 (0) m_b202s252i4 7944 chr4qtel1M 449936 AGAAAGAAAAAAATCATGAAAGAAATAAAG 449965 i vv v v (AGAA)n#Simpl 1 AGAAAGAAAGAAAGAAAGAAAGAAAGAAAG 30 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 233 31.47 1.21 3.73 chr4qtel1M 450196 450360 (549640) C L1MC5a_3end#LINE/L1 (2195) 582 422 m_b202s551i0 7945 chr4qtel1M 450196 GAAATCTTCCT-GTTCAAGATTTCTTAGTGTAAAATACTATTCCAGTACA 450244 i -i ----i i vv iviv v i v iii C L1MC5a_3end#L 582 GAGATCTTCCTCATTC----CTTTTTACAGCTGCATAGTACTCCATTGTG 537 chr4qtel1M 450245 TTCATTTACCATA-CTTGTTCAATCCTTCCCCAATTGATGGGCATCTCCT 450293 vv v -i i i vv v i i vvv C L1MC5a_3end#L 536 TGGATGTACCATAGTTTATTCAACCAGTCCCCTATTGATGGACATTTGGG 487 chr4qtel1M 450294 CAATTTCCAGTATTTTGGTTTGATAGAAAGGGCTACTATAAATATTATTG 450343 ivi v v v v i i v iv i v i viv C L1MC5a_3end#L 486 TTGTTTCCAGTCTTTTGCTATTACAAATAATGCTGCAATGAATAACCTTG 437 chr4qtel1M 450344 TGCATGTAAATCCTTTC 450360 -- vi ? C L1MC5a_3end#L 436 TGCA--TACGTCNTTTC 422 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 40.51 CpG sites = 24, Kimura (unadjusted) = 41.57 Transitions / transversions = 0.92 (24/26) Gap_init rate = 0.05 (8 / 164), avg. gap size = 1.00 (8 / 8) 285 31.34 1.48 0.74 chr4qtel1M 450216 450350 (549650) C L1ME2z_3end#LINE/L1 (626) 565 430 m_b202s551i1 7945 chr4qtel1M 450216 TTCTTAGTGTAAAATACTATTCCAGTACATTCATTTACCATA-CTTGTTC 450264 i v ivi i v v ii vv v i -i i C L1ME2z_3end#L 565 TTTTTATTGCTGAGTAGTATTCCATTGTATGAATATACCACAGTTTGTTT 516 chr4qtel1M 450265 AATCCTTCCCCAATTGATGGGCATCTCCTCAATTTCCAGTATTTTGGTT- 450313 vi v i vi i i vvv vi - i - C L1ME2z_3end#L 515 ATCCATTCTCCTGTTGATGGACACCTGGGCTGTTTCCAGT-TTTTGGCTA 467 chr4qtel1M 450314 TGATAGAAAGGGCTACTATAAATATTATTGTGCATGT 450350 v ii v ii i i i v i v C L1ME2z_3end#L 466 TTATGAATAAAGCTGCTATGAACATTCTTGTACAAGT 430 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 41.74 CpG sites = 24, Kimura (unadjusted) = 41.74 Transitions / transversions = 1.33 (24/18) Gap_init rate = 0.02 (3 / 134), avg. gap size = 1.00 (3 / 3) 250 32.88 0.68 1.36 chr4qtel1M 450229 450376 (549624) C L1ME4b_3end#LINE/L1 (340) 552 406 m_b202s551i2 7945 chr4qtel1M 450229 ATACTATTCCAGTACATTCATTTACCATA-CTTGTTCAATCCTTCCCCAA 450277 v v ii vv v -i i i i vv v C L1ME4b_3end#L 552 ATAGTATTCCATTGTATGGATGTACCATAATTTATTTAACCAGTCCCCTA 503 chr4qtel1M 450278 TTGATGGGCATCTCCTCAATTTCCAGTATTTTGGTTTGATAGAAAGGGCT 450327 i i vvvivi i v v v v i i v iv C L1ME4b_3end#L 502 TTGATGGACATTTAGGTTGTTTCCAATCTTTTGCTATTACAAACAATGCT 453 chr4qtel1M 450328 ACTATAAATATTATTGTGCATGTAAATCCTTTCCCCTATGTGTGTGTGT 450376 i v i viv i -- vi v v vi i v i C L1ME4b_3end#L 452 GCAATGAATAACCTTGTACA--TACGTCATTTCGCACATGTGCGAGTAT 406 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 41.34 CpG sites = 22, Kimura (unadjusted) = 43.65 Transitions / transversions = 0.85 (22/26) Gap_init rate = 0.02 (3 / 147), avg. gap size = 1.00 (3 / 3) 17 22.65 0.00 2.13 chr4qtel1M 452020 452067 (547933) (GGTG)n#Simple_repeat 1 47 (0) m_b202s252i5 7946 chr4qtel1M 452020 GGTGGGTGTGTGGTCGGGTGTGTGAGTGTTGGGGTGGGTGTGTGTGGT 452067 v vi v i vvv v - (GGTG)n#Simpl 1 GGTGGGTGGGTGGGTGGGTGGGTGGGTGGGTGGGTGGGTGGGTG-GGT 47 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.02 (1 / 47), avg. gap size = 1.00 (1 / 1) 182 34.36 3.15 12.93 chr4qtel1M 453422 453548 (546452) L2c_3end#LINE/L2 360 475 (3) m_b202s601i6 7947 chr4qtel1M 453422 CTGCTTCCTCTCCCAGGGTTCTTGCTCCTCATGAGTAAAGTTATTGTGTT 453471 ii iv i iv vivv iiv i i ii -- ii i L2c_3end#LINE 360 CTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGG--ACCGTGTC 407 chr4qtel1M 453472 TTAATTATTTGTCTTCATGTTCCTAATGTCGGACATAT----GGCGACTC 453517 ---- ii ii i i i ii i v i i ---- - L2c_3end#LINE 408 TTA----TTCATCTTTGTATCCCCAGCGCCTGGCACATAGTAGGCG-CTC 452 chr4qtel1M 453518 AGCAAAAGGTTATGGATTCGTTGATTGAATG 453548 ii ------ -- i v L2c_3end#LINE 453 AATAAA------TG--TTTGTTGAATGAATG 475 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 46.64 CpG sites = 30, Kimura (unadjusted) = 50.57 Transitions / transversions = 3.75 (30/8) Gap_init rate = 0.13 (16 / 126), avg. gap size = 1.19 (19 / 16) 281 29.98 13.04 4.28 chr4qtel1M 453848 454192 (545808) L2#LINE/L2 2138 2511 (571) m_b202s601i7 7948 chr4qtel1M 453848 ACTCTCCAG---CCCCCTCTATCTC-CCAATCCCTCCTCCTGGTTCTTCT 453893 v ---ii ii i - iiii v i viv i L2#LINE/L2 2138 ACTCTCCTGGTTTTCCTCCTACCTCACTGGCCGCTCCTTCTCAGTCTCCT 2187 chr4qtel1M 453894 CT-CTGATCCCAGTCTCCTTTTCCAGATTGCCATCCATATTGT--TGCTT 453940 i - i i -vi v i i v iiv -- ?v ii v-- i- L2#LINE/L2 2188 TTGCTGGTTCC-TCCTCATCTCCCCGACCTC--TNAACGTTGGAGTGCC- 2233 chr4qtel1M 453941 CCAAAGCTTTGTCCTGGG--CCCTGC-CTTCTCT---TACTCT-ACTTTC 453983 ii iv v -- i v - --- v - ii L2#LINE/L2 2234 CCAGGGCTCAGTCCTTGGACCTCTTCTCTTCTCTATCTACACTCACTCCC 2283 chr4qtel1M 453984 TGGGTGATTTCATCAGTTTTCATGGGCTCAG---CCA----------GGT 454020 ? i viv i vi i i--- ---------- i L2#LINE/L2 2284 TNGGTGATCTCATCCAGTCTCATGGCTTTAAATACCATCTATATGCTGAT 2333 chr4qtel1M 454021 G-CTCACACATCTG---CTCTGGCCTG----TCTC---TGAGCTACAA-- 454057 - v v i i--- ii i ---- --- i v i-- L2#LINE/L2 2334 GACTCCCAAATTTATATCTCCAGCCCGGACCTCTCCCCTGAACTCCAGAC 2383 chr4qtel1M 454058 TCATACATTGCCAACTGCC-ACCGGCCACCTCAATTTATTTGTCCCATAA 454106 i i -- - iv v i v i ivv iv i L2#LINE/L2 2384 TCGTATAT--CCAACTGCCTACTCGACATCTCCACTTGGATGTCTAATAG 2431 chr4qtel1M 454107 GCATTTCAACCCCA--ATGTCCAAAAAGTAAAAAAGCCATTTAATATCTT 454154 i v ii -- - v i ----- vii i-- L2#LINE/L2 2432 GCATCTCAAACTTAACATGTCC-AAAACTGAA-----CTCCTG--ATCTT 2473 chr4qtel1M 454155 TGACTCAAAACCATTGCTTCTTCC-CAA-CTTTCCTATTT 454192 ivv iiv -- i i - i- i i i L2#LINE/L2 2474 CCCCCTCAAACC--TGCTCCTCCCGCAGTCTTCCCCATCT 2511 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 39.16 CpG sites = 67, Kimura (unadjusted) = 40.87 Transitions / transversions = 2.09 (67/32) Gap_init rate = 0.10 (35 / 344), avg. gap size = 1.74 (61 / 35) 17 10.11 3.12 0.00 chr4qtel1M 454821 454852 (545148) (TAATA)n#Simple_repeat 1 33 (0) m_b202s252i6 7949 chr4qtel1M 454821 TAGTATAATATACTATAA-ATAGTATAATATAA 454852 i v - i (TAATA)n#Simp 1 TAATATAATATAATATAATATAATATAATATAA 33 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 14 13.96 3.12 0.00 chr4qtel1M 455032 455063 (544937) (TAATA)n#Simple_repeat 1 33 (0) m_b202s252i7 7950 chr4qtel1M 455032 TAGTATAATATACTATAA-GTAGTATAATATAA 455063 i v -i i (TAATA)n#Simp 1 TAATATAATATAATATAATATAATATAATATAA 33 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 17 10.11 3.12 0.00 chr4qtel1M 455092 455123 (544877) (TAATA)n#Simple_repeat 1 33 (0) m_b202s252i8 7950 chr4qtel1M 455092 TAGTATAATATACTATAA-ATAGTATAATATAA 455123 i v - i (TAATA)n#Simp 1 TAATATAATATAATATAATATAATATAATATAA 33 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 14 13.96 3.12 0.00 chr4qtel1M 455259 455290 (544710) (TAATA)n#Simple_repeat 1 33 (0) m_b202s252i9 7951 chr4qtel1M 455259 TAGTATAATATACTATAA-GTAGTATAATATAA 455290 i v -i i (TAATA)n#Simp 1 TAATATAATATAATATAATATAATATAATATAA 33 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 17 10.11 3.12 0.00 chr4qtel1M 455319 455350 (544650) (TAATA)n#Simple_repeat 1 33 (0) m_b202s252i10 7951 chr4qtel1M 455319 TAGTATAATATACTATAA-ATAGTATAATATAA 455350 i v - i (TAATA)n#Simp 1 TAATATAATATAATATAATATAATATAATATAA 33 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 14 13.96 3.12 0.00 chr4qtel1M 455489 455520 (544480) (TAATA)n#Simple_repeat 1 33 (0) m_b202s252i11 7952 chr4qtel1M 455489 TAGTATAATATACTATAA-GTAGTATAATATAA 455520 i v -i i (TAATA)n#Simp 1 TAATATAATATAATATAATATAATATAATATAA 33 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 17 10.11 3.12 0.00 chr4qtel1M 455657 455688 (544312) (TAATA)n#Simple_repeat 1 33 (0) m_b202s252i12 7953 chr4qtel1M 455657 TAGTATAATATACTATAA-ATAGTATAATATAA 455688 i v - i (TAATA)n#Simp 1 TAATATAATATAATATAATATAATATAATATAA 33 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 14 13.96 3.12 0.00 chr4qtel1M 455717 455748 (544252) (TAATA)n#Simple_repeat 1 33 (0) m_b202s252i13 7953 chr4qtel1M 455717 TAGTATAATATACTATAA-ATAGCATAATATAA 455748 i v - ii (TAATA)n#Simp 1 TAATATAATATAATATAATATAATATAATATAA 33 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 198 31.37 2.88 1.90 chr4qtel1M 455800 455903 (544097) L2d_3end#LINE/L2 398 502 (14) m_b202s601i8 7948 chr4qtel1M 455800 TATAAGTTCCTTGAAGGCCGGGCCCGCACCTAGTAGTATGATATAAGTTC 455849 i i i v v iiii vi v ? vv ? -v L2d_3end#LINE 398 TGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACTNTTTTNT-CGTTC 446 chr4qtel1M 455850 CTTGAAG-GCCCAGGCCCAG-GCCCGCCAC-TAGTAGTACCTCAGTAGAA 455896 iiiv - i - v - iviv - vvv i i v L2d_3end#LINE 447 CCCACAGCGCCTA-GCACAGTGCTGAGCACATAGTAGGCGCTCAATAAAT 495 chr4qtel1M 455897 GCTTGTT 455903 i L2d_3end#LINE 496 ACTTGTT 502 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 42.58 CpG sites = 17, Kimura (unadjusted) = 42.58 Transitions / transversions = 1.13 (17/15) Gap_init rate = 0.05 (5 / 103), avg. gap size = 1.00 (5 / 5) 13 0.00 0.00 0.00 chr4qtel1M 458551 458567 (541433) (AGG)n#Simple_repeat 1 17 (0) m_b202s252i14 7954 chr4qtel1M 458551 AGGAGGAGGAGGAGGAG 458567 (AGG)n#Simple 1 AGGAGGAGGAGGAGGAG 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 17 15.26 0.00 0.00 chr4qtel1M 458851 458879 (541121) (A)n#Simple_repeat 1 29 (0) m_b202s252i15 7955 chr4qtel1M 458851 AATAAAAAAGAAAAAAATAAAAAAAACAA 458879 v i v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA 29 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 189 20.63 5.97 5.97 chr4qtel1M 458891 458957 (541043) C MIR3#SINE/MIR (139) 69 3 m_b202s601i9 7956 chr4qtel1M 458891 AAAACAAAAACAAAAACTCAGGTCCTCCTGACTTC-AG---GTGCTCTCT 458936 i i viii v i i - i - --- C MIR3#SINE/MIR 69 AGAGCCGGGACTAGAACCCAGGTC-TCCTGACTCCCAGTCCGTGCTCTCT 21 chr4qtel1M 458937 CTACTGCACCAACTAGCTGCC 458957 i - v v -- C MIR3#SINE/MIR 20 CTGCT-CAGCCACT--CTGCC 3 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 22.72 CpG sites = 9, Kimura (unadjusted) = 24.87 Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.09 (6 / 66), avg. gap size = 1.33 (8 / 6) 240 16.00 12.00 0.00 chr4qtel1M 458905 458954 (541046) C MIRc#SINE/MIR (210) 58 3 m_b202s601i10 7956 chr4qtel1M 458905 AACTCAGGTCCTCCTGACTTCA-----GGTGCTCTCTCTACTGCACCA-A 458948 i i i -----i i i - C MIRc#SINE/MIR 58 AACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACA 9 chr4qtel1M 458949 CTAGCT 458954 iv C MIRc#SINE/MIR 8 CTGCCT 3 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 18.85 CpG sites = 7, Kimura (unadjusted) = 18.85 Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.04 (2 / 49), avg. gap size = 3.00 (6 / 2) 22 17.29 0.00 0.00 chr4qtel1M 459157 459195 (540805) (T)n#Simple_repeat 1 39 (0) m_b202s252i16 7957 chr4qtel1M 459157 TTTTTTTTAATCTTTCTTTTTTTTTTTCTTTATTTTTTT 459195 vv i i i v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 39 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 1471 28.53 2.67 3.15 chr4qtel1M 459662 460298 (539702) C L1ME5_3end#LINE/L1 (304) 637 4 m_b202s551i3 7958 chr4qtel1M 459662 TCCTGCTCATTTCACTCAGCATCA-GTTCGTGTAAGGCTC-TCCAGGCCT 459709 i i iv ii - -- v iii - v iiv C L1ME5_3end#LI 637 TCTTACTTTTTTCACTCAGCACTATGTT--TTTAAGATCCATCCATGTTG 590 chr4qtel1M 459710 TTCTGAAATCATCCTGTTGGTCATTTCTTACAGA-ACAGTAATATTCCAT 459758 i v vivv iv iv iii v v v-i - i i C L1ME5_3end#LI 589 CTATGTGTACATCTAGTCCGTTGCTTCTAACTGCTGCA-TAGTACTCCAT 541 chr4qtel1M 459759 AATATTCATATACCACAATTTATTCAGCCATTCTCCAACTGATGGACATC 459808 ii i v vi v iii v i v v i C L1ME5_3end#LI 540 GGTGTGCATCCACCACATTTTACCTATCCACTCTCCCAGTGATGGACACC 491 chr4qtel1M 459809 CATTCAGTTTCCAGTTTCTAGCCACTACAAAAAGGGCTGCCACAAACATT 459858 vviv ii ii i iv i v iv v ii i C L1ME5_3end#LI 490 CAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCTGCAATGAACATC 441 chr4qtel1M 459859 CGTGCACATACAGGTCCCTTTC----CCTTCTTTATAATCTCTTTGGGAT 459904 vi i ---- i v---- viv v v i C L1ME5_3end#LI 440 CTCGTACAT----GTCCCCTTATGGACCTGTGTGAGAATTTCTTTGGGAT 395 chr4qtel1M 459905 ATAATCCCAGTAGTAACACTGCTGGATCAAAGGGTATGCACAGTTTGATA 459954 vv v iiiv i i v ii vvi -- C L1ME5_3end#LI 394 ATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATGCGTATACT--TA 347 chr4qtel1M 459955 ACTTTTTGAGCA--TAGTTCCAAACTACTCTCCAAAATGGTTGGATTCGT 460002 --- vi -- v v i i i i i v iiv C L1ME5_3end#LI 346 A---TTTGACTAAGTACTGCCAGATTGCTCTCCAGAATGGCTGCACCAGT 300 chr4qtel1M 460003 TCACAACTCCACCAACAATGCATCAATGTCCCAGTTTTCCCACATCCCCT 460052 ii vii i i v iv i vi ? i i v C L1ME5_3end#LI 299 CTACACTCCCACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATCCTCG 250 chr4qtel1M 460053 CCAACAATCATCATTATTT---TTTCCTGTCATCTTAGCCAATCTGACAG 460099 v iiv ii--- --- v i v i i i C L1ME5_3end#LI 249 CCAACACTTGGCATTATCCAGCTTTC---TAATTTTTGCCAGTCTAATAG 203 chr4qtel1M 460100 GTGTGTAGTGGTATCTTAGAGTTGTCTTAATTTGCATTTCTCTGATTAAT 460149 iv i i vv i v C L1ME5_3end#LI 202 GTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATTTCTCTGATTACT 153 chr4qtel1M 460150 AATGACTTGGAGCATCTTTTCATATGACTAGAAATAG--TTTCAA-TTTC 460196 v v i - v v-- -- ii- C L1ME5_3end#LI 152 AATGAGTTTGAGCATCTCTTCATATG-CTTGT--TAGCCTTTCGGGTTTC 106 chr4qtel1M 460197 TTCATCTGAGAATTGTCTGTTCATATCCTTTGACCATTTTTCAATTGGAG 460246 i v vi i v v i C L1ME5_3end#LI 105 CTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGGGG 56 chr4qtel1M 460247 --AATGGCTTGATTTTTTATAAATTAGAGTTAATTCTCTATATATTTTGG 460294 --?vi v -- i i vi v vivv i ii i i i C L1ME5_3end#LI 55 TTNCCGTCTT--TTTCTTGTTGATTTGCAGGAGTTCCTTGTATATTCTAG 8 chr4qtel1M 460295 AAAT 460298 v C L1ME5_3end#LI 7 ATAT 4 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 35.65 CpG sites = 103, Kimura (unadjusted) = 37.00 Transitions / transversions = 1.41 (103/73) Gap_init rate = 0.05 (29 / 636), avg. gap size = 1.28 (37 / 29) 1590 27.13 0.36 1.65 chr4qtel1M 459748 460298 (539702) C L1ME3G_3end#LINE/L1 (377) 547 4 m_b202s551i4 7958 chr4qtel1M 459748 TAATATTCCATAATATTCATATACCACAATTTATTCAGCCATTCTCCAAC 459797 i i vv i i i i v i C L1ME3G_3end#L 547 TAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTAT 498 chr4qtel1M 459798 TGATGGACATCCATTCAGTTTCCAGTTTCTAGCCACTACAAAAAGGGCTG 459847 ii vviv i i v i i v iv C L1ME3G_3end#L 497 TGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCTG 448 chr4qtel1M 459848 CCACAAACATTCGTGCACATACAGGTCCCTTT-CCCTTCTTT-ATAATCT 459895 v ii i v i i ?-- i v - v v v vi- vv i C L1ME3G_3end#L 447 CAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATTT 400 chr4qtel1M 459896 CTTTGGGATATAATCCCAGTAGTAACACTGCTGGATCAAAGGGTATGCAC 459945 ? i v v? ? v iiv i i i C L1ME3G_3end#L 399 CTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGC 350 chr4qtel1M 459946 AGTTTGATAACTTTTTGAGCATAGTTCCAAACTACTCTCCAAAATGGTTG 459995 v i -- i vvv - v v i i i ? i C L1ME3G_3end#L 349 ATTTTAA--ATTTTAATAG-ATACTGCCAAATTGCCCTCCAAAANGGCTG 303 chr4qtel1M 459996 GATTCGTTCACAACTCCACCAACAATGCATCAATGTCCCAGTTTTCCCAC 460045 v iivi i vii i i i v iv v v i C L1ME3G_3end#L 302 TACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCAC 253 chr4qtel1M 460046 ATCCCCTCCAACAATCATCATTATTTTTTCCTGTCATCTTAGCCAATCTG 460095 i i v v ?ivi ivv?iii vvv i v C L1ME3G_3end#L 252 ACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATCTG 203 chr4qtel1M 460096 ACAGGTGTGTAGTGGTATCTTAGAGTTGTCTTAATTTGCATTTCTCTGAT 460145 ii viv i i vv i i C L1ME3G_3end#L 202 ATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGAT 153 chr4qtel1M 460146 TAATAATGACTTGGAGCATCTTTTCATATGACTAGAAATAGTTTCAATTT 460195 v i vv v vi vviiivi vv C L1ME3G_3end#L 152 TACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGTATTT 103 chr4qtel1M 460196 CTTCATCTGAGAATTGTCTGTTCATATCCTTTGACCATTTTTCAATTGGA 460245 i v v i v v i C L1ME3G_3end#L 102 CCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGGG 53 chr4qtel1M 460246 GAATGGCTTGATTTTTTATAAATTAGAGTTAATTCTCTATATATTTTGGA 460295 v-- v -- i vi v vivv i i i C L1ME3G_3end#L 52 T--TGTCTT--TTTCTTATTGATTTGTAGGAGTTCTTTATATATTCTGGA 7 chr4qtel1M 460296 AAT 460298 v C L1ME3G_3end#L 6 TAT 4 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 34.13 CpG sites = 77, Kimura (unadjusted) = 34.71 Transitions / transversions = 1.10 (77/70) Gap_init rate = 0.02 (11 / 550), avg. gap size = 1.00 (11 / 11) 2265 30.59 2.36 2.43 chr4qtel1M 460152 461635 (538365) C L1M5_orf2#LINE/L1 (0) 3294 1812 m_b202s551i5 7958 chr4qtel1M 460152 TGACTTGGAGCATCTTTTCATATGACTAGAAATAGTTTCAATTTCTTCAT 460201 ?v v i vi vviiivi v? v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr4qtel1M 460202 CTGAGAATTGTCTGTTCATATCCTTTGACCATTTTTCAATTGGAGAATGG 460251 i v v vi i v ?v ---i v C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGG---GTTG 3198 chr4qtel1M 460252 CTTGATTTTTTATAAATTAGAGTT-----AATTCTCTATATATTTTGGAA 460296 i vi ? -v - ? ----- i i i v C L1M5_orf2#LIN 3197 TTTGTCTTTTTNT-TATT-GANTTGTAGGAGTTCTTTATATATTCTGGAT 3150 chr4qtel1M 460297 ATGAGGCCTTTATCAGA-ACCTTTGACTGTAAAAATATTTTCCCAGTTTA 460345 i v i - iv v -?i i v v i ? i i C L1M5_orf2#LIN 3149 ACGAGTCCTTTGTCAGATATATGT-NTTGCAAATATTTTCTCCCANTCTG 3101 chr4qtel1M 460346 TTGCTTCCCTTCTAATCTTGTCTGCATTAGTTTTGTTTGTACAAAAACTT 460395 v v i v i v ivi iv ivi vvv? vi i ii C L1M5_orf2#LIN 3100 TGGCTTGCCTTTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTT 3051 chr4qtel1M 460396 TTCAGTTTGGTATAATCGA-------AATTTTCTATTTTGTGATCAGTAA 460438 v v i i? i v ------- i v i i i? i- C L1M5_orf2#LIN 3050 TTAATTTTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGGTTNGTG- 3002 chr4qtel1M 460439 TGATCTCTAGTTCTGCTTTGGTCATAAAGACCTTCCCCT-TCCACAGGTC 460487 ---- i -- v iii v i - i i i iv -? vv C L1M5_orf2#LIN 3001 ----CTTT--TTGTGTCCTGTTTA-AGAAATCTTTGCCTANCCCAAGGTC 2959 chr4qtel1M 460488 TGAGAGGTAAACTATCCTATG--TTCCTCTAATTTATTAATAATTTCATT 460535 vvii i -- i v -- i ivvvv v i i ?i C L1M5_orf2#LIN 2958 ACGAAGAT--ATTCTCCTATGTTTTCTTCTAGAAGTTTTATAGTTTTANC 2911 chr4qtel1M 460536 CTTTATGCCTAGGTC-ATGAACCCATTTTGACCTTATCTTGGTGTACGGC 460584 i iiii - - i i ? vi v i v i i C L1M5_orf2#LIN 2910 TTTTACATTTAGGTCTATG-ATCCATCTNGAATTAATTTTTGTGTATGGT 2862 chr4qtel1M 460585 GTTAAGTATGGATCAATGCCTAGTTTCTGCCATATTAGTTTCCAATTTTC 460634 v i v i i v?iii v i v vii v v i C L1M5_orf2#LIN 2861 GTGAGGTAGGGGTCGAGNTTCATTTTTTTCCATATGGATATCCAATTGTT 2812 chr4qtel1M 460635 CCAGCAATTTTTATCAAACAGTAAGTTCTTATCCCAAAAGCTGGGAT-CT 460683 viv i ii v vvvi i vi ---- iiv - ? C L1M5_orf2#LIN 2811 CCAGCACCATTTGTTGAAAAGACTATCCTTTCCCCA----CTGAATTGCN 2766 chr4qtel1M 460684 TTGG---GTTTGTCAAAGACTAGGTTGCTATATTTGT-TGACTGTTTTAT 460729 ---v i ii i? v? i v - --- v i C L1M5_orf2#LIN 2765 TTGGCACCTTTGTCAAAAATCAANTGNCCATATATGTGTG---GGTCTAT 2719 chr4qtel1M 460730 CCCTTGAAC---CTAATCTATTCCACTGATCAACTAATCTATTCCTTA-G 460775 ii - i --- v i i v i vi - - C L1M5_orf2#LIN 2718 TTC-TGGACTCTCTATTCTGTTCCATTGATCTATTTGTCTA-TCCTTACG 2671 chr4qtel1M 460776 CCAATACCAAATAGTTTTGGTAACTGCTGCTCTATAATATAATTTT-AGA 460824 v iv i i v iv i - i i - ? C L1M5_orf2#LIN 2670 CCAATACCACACTGTCTTGATTACTGTAGCTTTATAATA-AGTCTTGANA 2622 chr4qtel1M 460825 TCTGGTACAGCTAAG-CCACCATCATTTGAT-TTTTTTTTCATTAATTCC 460872 ? vv - - v v - v - i -vi vi C L1M5_orf2#LIN 2621 TCNGGTAGTG-TAAGTCCTCCAAC-TTTGTTCTTCTTTTTCA-AGATTGT 2575 chr4qtel1M 460873 CTTGAA-ATTCTTGACCTTTTGTTTTTCCATATGAACTTTGTTGTTATTT 460921 i iv- ? ii i iv i i ivvi i vi C L1M5_orf2#LIN 2574 TTTGGCTATTCTNGGTCCTTTGCATTTCCATATAAATTTTAGAATCAGCT 2525 chr4qtel1M 460922 TTTCTAGGTCATTAAAATAGTTTTTTGGGAGTCTGATTGGTATAGCGCTA 460971 v v vv vvi v iii vi v i v v ii i C L1M5_orf2#LIN 2524 TGTCAATTTCTACAAAAAAACCTGCTGGGATTTTGATTGGGATTGCATTG 2475 chr4qtel1M 460972 AATAAATAGATTAGTTTAGGTAATATTGTCATCTTTATTATATTTGCTCG 461021 vv i i i v iv v ? iv viv v C L1M5_orf2#LIN 2474 AATCTATAGATCAATTTGGGGAGAATTGACATCTTNACAATATTGAGTCT 2425 chr4qtel1M 461022 CCCTATCCAAGAGCATTTAATATTTTTCCAATTGGTTAGATCAGACTTAA 461071 i v v i vvv i i v iv i vvvi C L1M5_orf2#LIN 2424 TCCAATCCATGAACATGGTATATCTCTCCATTTATTTAGGTCTTCTTTAA 2375 chr4qtel1M 461072 TTTGTGTGAAAAGTGGTCTGTAATTTTGCTCATAAAGTTTCTG---ATTT 461118 v v v iv i v i i vvvii ? v ii --- ? C L1M5_orf2#LIN 2374 TTTCTCTCAGCAATGTTTTGTAGTTTTCAGTGTANAGGTCTTGCACATNT 2325 chr4qtel1M 461119 TCCCTTGGCAGATAGATTCCTAAATATTTTATATTATCAGTAGTTACTTT 461168 --- vi vv i ? i v iv vv i i v C L1M5_orf2#LIN 2324 T---TTGTTAGATTTATTCCTAAGTATTTNATGTTTTTTGATGCTATTGT 2278 chr4qtel1M 461169 AAATGGAATTTCTCTTTGTAACTCTGACTGTTGGAT--TTTGTTAGTGAT 461216 v vi i --? v i v i v ivi -- iv ii C L1M5_orf2#LIN 2277 AAATGGTATTGTTTTT--NAAATTTCATTTTCCAATTGTTTGTTGCTAGT 2230 chr4qtel1M 461217 ATATAAGAATGCTGATGACTTATGTGGGTTTATTTTATAACCAGCAACTT 461266 ii i viv i v ivi v ii i v ? i i C L1M5_orf2#LIN 2229 ATATAGAAATACAATTGATTTTTGTATATTGACCTTGTATCCNGCGACCT 2180 chr4qtel1M 461267 TGCTAAAGTTGTGGATTATTTCTAATAACTTTTAAGTAGAATCTCTGGGG 461316 v iiivv v i ii ? vv v i ? i C L1M5_orf2#LIN 2179 TGCTAAATTCACTTATTAGTTCTAGTAGTTTNTTTGTAGATTCTTTNGGA 2130 chr4qtel1M 461317 TTCTCTAAATATACCATCATGTCGTCGGCAAAGAGTGATAATTTGGTTTC 461366 i vi ? v i v i v i? i i vi C L1M5_orf2#LIN 2129 TTTTCTACGTANACAATCATGTCATCTGCGAATAANGACAGTTTTATTTC 2080 chr4qtel1M 461367 CTCATTGCCTATTCTTATTCCTTTAATCTCTTTCTCAGCTCTTATTGCTA 461416 i v v v ii v v i i vvvi vv C L1M5_orf2#LIN 2079 TTCCTTTCCAATCTTTATGCCTTTTATTTCTTTTTCTTGCCTTATTGCAC 2030 chr4qtel1M 461417 AAGCTAGCGTTCCTAATACAATATTAAATAGTAACGGTGATAGTGGGCAA 461466 vi viiii i i i i v ii ? i i v C L1M5_orf2#LIN 2029 TGGCTAGGACCTCCAGTACAATGTTGAATAGAAGTGGTGANAGCGGACAT 1980 chr4qtel1M 461467 CCTTGTTTCACTCCAGATCTTATTGGGAATGGTTGCAGTTTGTCTCCATT 461516 i iii v vv v v? v ? v v C L1M5_orf2#LIN 1979 CCTTGTCTTGTTCCCGATCTTAGGGGGAAAGCNTTCAGTNTTTCACCATT 1930 chr4qtel1M 461517 ACATATGATGTTTACTGATGGTTTTAAATAGATGCTGCTGATTATTTTAA 461566 vi ?i vv vvi ivi v i vv i C L1M5_orf2#LIN 1929 AAGTATGATGTTNGCTGTAGGTTTTTCGTAGATGCCCTTTATCAGGTTGA 1880 chr4qtel1M 461567 GGAAAAGTCCATTTATTCCTATACTCTCAAGTGTTTTTTAATAGGAATGG 461616 ivvi v i vvi viii v - vi v C L1M5_orf2#LIN 1879 GGAAGTTCCCTTCTATTCCTAGTTTGCTGAGAG-TTTTTATCATGAATGG 1831 chr4qtel1M 461617 ATGTTGGATTTTGTCAAAT 461635 i i C L1M5_orf2#LIN 1830 GTGTTGAATTTTGTCAAAT 1812 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 40.32 CpG sites = 238, Kimura (unadjusted) = 41.41 Transitions / transversions = 1.16 (238/205) Gap_init rate = 0.04 (53 / 1483), avg. gap size = 1.34 (71 / 53) 219 31.92 6.93 3.85 chr4qtel1M 461923 462023 (537977) L2c_3end#LINE/L2 371 474 (4) m_b202s601i11 7959 chr4qtel1M 461923 ACCAGAATGGAAGCTGCT-GCAGGCAGGAAT-GAGTC-----CATTTTTG 461965 i v vi v - vi i i- v ----- i L2c_3end#LINE 371 ACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTG 420 chr4qtel1M 461966 GATAGCTGTGCAGCATCTAGCACTTTGCAGGTATTTAATAAATACCTATT 462015 v vv ---- ii i v v i iii i iii i L2c_3end#LINE 421 TATCCC----CAGCGCCTGGCACATAGTAGGCGCTCAATAAATGTTTGTT 466 chr4qtel1M 462016 TGATTAAT 462023 vi v L2c_3end#LINE 467 GAATGAAT 474 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 39.45 CpG sites = 19, Kimura (unadjusted) = 43.33 Transitions / transversions = 1.58 (19/12) Gap_init rate = 0.07 (7 / 100), avg. gap size = 1.57 (11 / 7) 12 26.80 5.56 0.00 chr4qtel1M 463141 463194 (536806) (TCTG)n#Simple_repeat 1 57 (0) m_b202s252i17 7960 chr4qtel1M 463141 TCTGTCTG-CTGTGTGTCCAGC-CCCTGCCAATCTGCCTG-CTGTGTGCC 463187 - v iiv -vi i vi i - v i (TCTG)n#Simpl 1 TCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTC 50 chr4qtel1M 463188 TGTCTGT 463194 (TCTG)n#Simpl 51 TGTCTGT 57 Matrix = Unknown Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.06 (3 / 53), avg. gap size = 1.00 (3 / 3) 631 30.71 6.72 3.73 chr4qtel1M 464079 464558 (535442) C L1ME4c_3end#LINE/L1 (294) 536 42 m_b202s551i6 7961 chr4qtel1M 464079 ATGTGCTACAAAATGCTTAGCTATTTCTCATTTGATGGGTATCTACTTTG 464128 i i i vv i i i i i vv v ii i vv C L1ME4c_3end#L 536 ATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAGGTTG 487 chr4qtel1M 464129 TTTTCGGTTCACAGCTATCACAAAAAGTACCACTATTAATATTCTGGGAT 464178 i ii iviv i i v iii ii v v i ii v vii C L1ME4c_3end#L 486 TTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTCGTGC 437 chr4qtel1M 464179 ATATAAGCATTTTCTTTCCATT-AATGGCTTCCTTGGGGGTATAAG--CC 464225 - v i iv - vii i --- i-- C L1ME4c_3end#L 436 ATATA-GCTTTTTCCTTCTTTTGAATTATTTCCTTAGG---ATAAATTCC 391 chr4qtel1M 464226 CAGGAGGGGAGTCTCTGGTTCAAAG-------ACACTT------CCTTTG 464262 i v i iv v ------- i ------ ii C L1ME4c_3end#L 390 CAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTCTTG 341 chr4qtel1M 464263 ---CATATTTCCAAATGGCTTTCCAAAATGGCTGTAGAGTTTCACAGCTG 464309 --- i v v v i vviv i -? C L1ME4c_3end#L 340 ATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACA-NTG 292 chr4qtel1M 464310 CT-CCAACAATGTATTAGTATACTA-TCCTACCCTCCAATTAGTATTACC 464357 i- i v ?i i - iii --------- i ?i- i C L1ME4c_3end#L 291 CCACCAGCAATGTATGAGNGTACCAGTTTCACC---------GCANC-CT 252 chr4qtel1M 464358 CCCCAATATTGACTGTTGTTA--TTTTTAATCTATTTGCAGA-------- 464397 v ii iv i i i -- vi - vi -------- C L1ME4c_3end#L 251 CGCCAGCATTGGGTATTATCAATTTTTTAAATT-TTTGCTAATTTAATAG 203 chr4qtel1M 464398 GTGTGGAATGAAACCTCTGCGTTGTTTTGATTTGCATTTTTCTTATTATT 464447 i ii iv i vvi i i i i v i C L1ME4c_3end#L 202 GCGTAAAATGGTATCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACT 153 chr4qtel1M 464448 AGTGATCTGGAGCATTCATTCATGTGGTTGTGAATAATTTGTAACCCTTC 464497 i vv v i iv i v vv iv ? vii i C L1ME4c_3end#L 152 AGCGAGGTTGAACATTTTTCCATGTGTTTGTTTACTANTTGTATTTCCTC 103 chr4qtel1M 464498 TTTTGAAAAT--TTTGTTTATATCTTTTGATCATTTATTGGGGAAT--GG 464543 ? vi -- i i i i vi iv---- -- C L1ME4c_3end#L 102 TTNTGTGAATTGTCTGTTCATGTCCTTTGCCCATTTATCT----ATTGGG 57 chr4qtel1M 464544 GTGTTAGTCTTTTAT 464558 v ii ? vi C L1ME4c_3end#L 56 GTCTTGATNTTTTTC 42 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 40.76 CpG sites = 97, Kimura (unadjusted) = 42.27 Transitions / transversions = 1.86 (91/49) Gap_init rate = 0.06 (31 / 479), avg. gap size = 1.77 (55 / 31) 29 0.00 0.00 0.00 chr4qtel1M 464559 464583 (535417) (AC)n#Simple_repeat 1 25 (0) c_b202s251i1 7962 chr4qtel1M 464559 ACACACACACACACACACACACACA 464583 (AC)n#Simple_ 1 ACACACACACACACACACACACACA 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 275 27.31 6.52 3.16 chr4qtel1M 464584 464749 (535251) C L1M5_orf2#LINE/L1 (109) 3185 3011 m_b202s551i7 7961 chr4qtel1M 464584 TATATATATATATTATTTGTTTATATATCTTGGATACCAAACCCTTATCA 464633 vv ?v i vv v v ii v iv i i C L1M5_orf2#LIN 3185 TATTGANTTGTAGGAGTTCTTTATATATTCTGGATACGAGTCCTTTGTCA 3136 chr4qtel1M 464634 GAAAAATCTG------ATATTT--TCCCATTCAACTACTT-CCTTCTTAT 464674 v v v ?------ -- ? viivi - i i C L1M5_orf2#LIN 3135 GATATATGTNTTGCAAATATTTTCTCCCANTCTGTGGCTTGCCTTTTCAT 3086 chr4qtel1M 464675 CCTAGACACATTAATGTTGTCTGT------GCAAAAGCTTCTTAGTTCCA 464718 ii ------v i v v ------ i i i v v iv C L1M5_orf2#LIN 3085 TTT------CTTAACGGTGTCTTTTGANGAGCAGAAGTTTTTAATTTTGA 3042 chr4qtel1M 464719 AGTAATCAAAATGACCAATTTTATCTTTTGT 464749 v ? i v v v i v i C L1M5_orf2#LIN 3041 TGNAGTCCAATTTATCAATTTTTTCTTTTAT 3011 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 35.19 CpG sites = 34, Kimura (unadjusted) = 35.78 Transitions / transversions = 0.84 (21/25) Gap_init rate = 0.06 (10 / 165), avg. gap size = 2.10 (21 / 10) 631 30.71 6.72 3.73 chr4qtel1M 464584 464623 (535377) C L1ME4c_3end#LINE/L1 (789) 41 2 m_b202s551i6 7961 chr4qtel1M 464584 TATATATATATATTATTTGTTTATATATCTTGGATACCAA 464623 vv v iv v vi v ?iv?i ii C L1ME4c_3end#L 41 TATCAATTTGAATGAGCTCTTTATATANTANAGATATTAA 2 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 40.76 CpG sites = 97, Kimura (unadjusted) = 42.27 Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 492 30.05 0.57 9.26 chr4qtel1M 464867 465042 (534958) C MIRc#SINE/MIR (92) 176 15 m_b202s601i12 7963 chr4qtel1M 464867 TGAGGTTTGCTGGGCAAATATCCTTCTTTCTCCAGCTCAATTTGCAGATG 464916 vv v ii iv v ii ------- v i C MIRc#SINE/MIR 176 TGAGGTAGGCAGGGCAGGTATTATTATCCC-------CATTTTACAGATG 134 chr4qtel1M 464917 AGAAAATGGAAGCAAATAG-GGTAAAGTGCCTTGCCCAGGGTCACACATC 464965 i iv i vv v - v v i v C MIRc#SINE/MIR 133 AGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGC 84 chr4qtel1M 464966 CCATGAGTGTCTGAGGTCGGATTTGAACTCAAGGAGAGGAGTCTTCTTGA 465015 ivi i v v viv i i i --------i i C MIRc#SINE/MIR 83 TAGTAAGTGGCAGAGCCGGGACTCGAACCCA--------GGTCTTCCTGA 42 chr4qtel1M 465016 CTCTAGGCCTGGCACTCTGTGCAGTAC 465042 i i i ii ii v v v i C MIRc#SINE/MIR 41 CTCCAAGTCCAGTGCTCTTTCCACTGC 15 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 36.86 CpG sites = 27, Kimura (unadjusted) = 38.91 Transitions / transversions = 1.29 (27/21) Gap_init rate = 0.09 (16 / 175), avg. gap size = 1.00 (16 / 16) 405 29.91 0.63 9.59 chr4qtel1M 464902 465060 (534940) C MIRb#SINE/MIR (117) 151 6 m_b202s601i13 7963 chr4qtel1M 464902 CTCAATTTGCAGATGAGAAAATGGAAGCAAATAG-GGTAAAGTGCCTTGC 464950 i v i i iv i vv v - v iv C MIRb#SINE/MIR 151 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGC 102 chr4qtel1M 464951 CCAGGGTCACACATCCCATGAGTGTCTGAGGTCGGATTTGAACTCAAGGA 465000 i v ivi i v v viv i i ---- C MIRb#SINE/MIR 101 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCA---- 56 chr4qtel1M 465001 GAGGAGTCTTCTTGACTCTAGGCCTGGCACTCTGTGCAGTACGGTGCCAC 465050 ----i vii i iiv iv ii v v --- v ii C MIRb#SINE/MIR 55 ----GGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCC---ACTGCACCAC 13 chr4qtel1M 465051 CTAGCTGCCC 465060 --- C MIRb#SINE/MIR 12 ---GCTGCCC 6 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 36.34 CpG sites = 24, Kimura (unadjusted) = 38.60 Transitions / transversions = 1.26 (24/19) Gap_init rate = 0.09 (15 / 158), avg. gap size = 1.00 (15 / 15) 23 15.51 0.00 3.85 chr4qtel1M 466885 466938 (533062) (GTGTGA)n#Simple_repeat 1 52 (0) m_b202s252i18 7964 chr4qtel1M 466885 GTGTGTGTTTGAGTGTATGTGTGAGTGTGACTGTGTGTGTCTGTGTGTGA 466934 v v iv -- v v v (GTGTGA)n#Sim 1 GTGTGAGTGTGAGTGTGAGTGTGAGTGTGA--GTGTGAGTGTGAGTGTGA 48 chr4qtel1M 466935 GTGT 466938 (GTGTGA)n#Sim 49 GTGT 52 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.04 (2 / 53), avg. gap size = 1.00 (2 / 2) 263 13.09 0.00 5.80 chr4qtel1M 466939 467011 (532989) DNM1r#Unknown 2478 2546 (2116) m_b202s502i0 7965 chr4qtel1M 466939 GTGTATGTGTGTGAGTATGTGTGTATATGTGTGTGTGAGTGTGTGTGTAT 466988 ivi i ---- i DNM1r#Unknown 2478 GTGTATGTGTGTATATATGTGTGTATATGTGTGTATG----TGTGTATAT 2523 chr4qtel1M 466989 ATGTGTGTATATATGCGTGTATA 467011 i i ii ? DNM1r#Unknown 2524 ATGTGTATATATACGTATNTATA 2546 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 13.40 CpG sites = 8, Kimura (unadjusted) = 15.13 Transitions / transversions = 8.00 (8/1) Gap_init rate = 0.06 (4 / 72), avg. gap size = 1.00 (4 / 4) 246 16.43 0.00 2.99 chr4qtel1M 466953 467021 (532979) DNM1r#Unknown 2480 2546 (2116) m_b202s502i1 7965 chr4qtel1M 466953 GTATGTGTGTATATGTGTGTGTGAGTGTGTGTGTATATGTGTGTATATAT 467002 i i-- i i i i DNM1r#Unknown 2480 GTATGTGTGTATATATGTGTGTA--TATGTGTGTATGTGTGTATATATGT 2527 chr4qtel1M 467003 GCGTGTATATGTGTGTATA 467021 ii i i i ? DNM1r#Unknown 2528 GTATATATACGTATNTATA 2546 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 18.27 CpG sites = 11, Kimura (unadjusted) = 20.27 Transitions / transversions = 1.00 (11/0) Gap_init rate = 0.03 (2 / 68), avg. gap size = 1.00 (2 / 2) 252 17.19 0.00 0.00 chr4qtel1M 466977 467040 (532960) DNM1r#Unknown 2480 2543 (2119) m_b202s502i2 7965 chr4qtel1M 466977 GTGTGTGTGTATATGTGTGTATATATGCGTGTATATGTGTGTATATGTGT 467026 i i i i i i DNM1r#Unknown 2480 GTATGTGTGTATATATGTGTGTATATGTGTGTATGTGTGTATATATGTGT 2529 chr4qtel1M 467027 GTGTGTATGTGTGT 467040 i i i i i ? DNM1r#Unknown 2530 ATATATACGTATNT 2543 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 19.33 CpG sites = 11, Kimura (unadjusted) = 21.48 Transitions / transversions = 1.00 (11/0) Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0) 257 9.27 0.00 3.70 chr4qtel1M 466985 467040 (532960) DNM1r#Unknown 2478 2531 (2131) m_b202s502i3 7965 chr4qtel1M 466985 GTATATGTGTGTATATATGCGTGTATATGTGTGTATATGTGTGTGTGTAT 467034 i i -- i i DNM1r#Unknown 2478 GTGTATGTGTGTATATATGTGTGTATATGTGTG--TATGTGTGTATATAT 2525 chr4qtel1M 467035 GTGTGT 467040 i DNM1r#Unknown 2526 GTGTAT 2531 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 10.24 CpG sites = 5, Kimura (unadjusted) = 10.24 Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.04 (2 / 55), avg. gap size = 1.00 (2 / 2) 246 27.18 4.85 0.00 chr4qtel1M 467004 467106 (532894) DNM1r#Unknown 2477 2584 (2078) m_b202s502i4 7965 chr4qtel1M 467004 CGTGTATATGTGTGTATATGTGTGTGTGTATGTGTGTGGGTGTAAGTACC 467053 i i i i i i v vi iv DNM1r#Unknown 2477 CGTGTATGTGTGTATATATGTGTGTATATGTGTGTATGTGTGTATATATG 2526 chr4qtel1M 467054 TGTGTCTCTCTGTATGTAT-GTGTGGGCTATGTACATA----AGAGGGAG 467098 i v v vi ? - viii vi v vi ---- i DNM1r#Unknown 2527 TGTATATATACGTATNTATAGAACAGGGCAGGGGCATACCACAGAGGGGG 2576 chr4qtel1M 467099 CAGAAGCT 467106 v i DNM1r#Unknown 2577 CACAAGTT 2584 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 33.62 CpG sites = 17, Kimura (unadjusted) = 35.17 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.02 (2 / 102), avg. gap size = 2.50 (5 / 2) 195 32.28 3.05 3.05 chr4qtel1M 469126 469256 (530744) C MIRc#SINE/MIR (136) 132 2 m_b202s601i14 7966 chr4qtel1M 469126 GGAAGC--AGACTACAGGGAGCTTCTATGCCTTGCCCAGGGTCAGCCCAG 469173 i -- i - i v vvi v i - v C MIRc#SINE/MIR 132 GGAAACTGAGGCT-CAGAGAGGTTAAGTGACTTGCCCAAGGTCA-CACAG 85 chr4qtel1M 469174 --GGTTATCATCTGAGGCAGCCTTCACATGCCAGCCTTCCTGCCTCCAAG 469221 --i v viiv v v i vvi iv iv vi i v C MIRc#SINE/MIR 84 CTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr4qtel1M 469222 GGCAGCGTGCTATCCCCTGCCCGCCTCAGAGCCTC 469256 vv i iv v v -- i v vv C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTG--CACCACACTGCCTC 2 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 39.83 CpG sites = 17, Kimura (unadjusted) = 42.37 Transitions / transversions = 0.71 (17/24) Gap_init rate = 0.05 (6 / 130), avg. gap size = 1.33 (8 / 6) 11 24.94 2.56 0.00 chr4qtel1M 471303 471341 (528659) (AGGGAA)n#Simple_repeat 1 40 (0) m_b202s252i19 7967 chr4qtel1M 471303 AGGGTGAGGGAAA-GGAAAAGAAATGGGGAGGGAAAAGGG 471341 vi - i i v i i i (AGGGAA)n#Sim 1 AGGGAAAGGGAAAGGGAAAGGGAAAGGGAAAGGGAAAGGG 40 Matrix = Unknown Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.03 (1 / 38), avg. gap size = 1.00 (1 / 1) 18 14.34 0.00 4.88 chr4qtel1M 471749 471791 (528209) (CCTAAC)n#Simple_repeat 1 41 (0) m_b202s252i20 7968 chr4qtel1M 471749 CCTAACCCTGAACCCTAAATTCAACTCTAACCCCTAACCCTAA 471791 - viii i - (CCTAAC)n#Sim 1 CCTAACCCT-AACCCTAACCCTAACCCTAA-CCCTAACCCTAA 41 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.00 (2 / 2) 452 28.78 1.42 1.42 chr4qtel1M 473266 473406 (526594) MIRc#SINE/MIR 3 143 (125) m_b202s601i15 7969 chr4qtel1M 473266 AGGCAGTGAGGGTTCTGGGCCTAGAGCTACAAGGCCTGGAGTCAGGAAAA 473315 -v v v v vvv - vi i i i MIRc#SINE/MIR 3 AGGCAGTG-TGGTGCAGTGGAAAGAGC-ACTGGACTTGGAGTCAGGAAGA 50 chr4qtel1M 473316 CCCAAATTAAAATGTGGCCTCAGACACTCACTAGCCATGAGATGCTGGGT 473365 iiii vi i viv v v v i ii v ivi i MIRc#SINE/MIR 51 CCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGC 100 chr4qtel1M 473366 GAGTCAC-TGACTCCTATTTGCCTCAGTTT-CTCATCTGTAAA 473406 i - i ii v vv - MIRc#SINE/MIR 101 AAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAA 143 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 35.73 CpG sites = 21, Kimura (unadjusted) = 36.87 Transitions / transversions = 1.11 (21/19) Gap_init rate = 0.03 (4 / 140), avg. gap size = 1.00 (4 / 4) 385 30.33 2.17 5.03 chr4qtel1M 473267 473450 (526550) MIR3#SINE/MIR 3 181 (27) m_b202s601i16 7969 chr4qtel1M 473267 GGCAGTGAGGGTTCTGGGCCTAGAGCTACAAGGCCTGG-AGTCAGGAAAA 473315 v v --- i vv v-i v v - i - MIR3#SINE/MIR 3 GGCAGAGTGG---CTGAGCAGAGAGA-GCACGGACTGGGAGTCAGGAGA- 47 chr4qtel1M 473316 CCCAAATTAAAATGTGGCCTCAGACACTCACTAGCCATGAGATGCTGGGT 473365 iiii vv i viv v v v v ? ii v ivi i MIR3#SINE/MIR 48 CCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGC 97 chr4qtel1M 473366 GAGTCACTG-ACTCCTATTTGCCTCAGTTT-CTCATCTGT-AAATGAGCT 473412 i v- ii v vv - - --- MIR3#SINE/MIR 98 AAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGA--- 144 chr4qtel1M 473413 GGAGATGGAAATGGCTAATACTTCCAGGTCTTTGCAAG 473450 i i v i v i v i - iiv ii v v MIR3#SINE/MIR 145 GGGGGTTGGACTAGATGAT-CTCTAAGGTCCCTTCCAG 181 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 39.55 CpG sites = 26, Kimura (unadjusted) = 39.55 Transitions / transversions = 0.96 (26/27) Gap_init rate = 0.07 (13 / 183), avg. gap size = 1.00 (13 / 13) 398 31.25 2.42 4.97 chr4qtel1M 473288 473452 (526548) MIRb#SINE/MIR 27 187 (81) m_b202s601i17 7969 chr4qtel1M 473288 AGAGCTACAAGGCCTGGAGTCAGGAAAACCCAAATTAAAATGTGGCCTCA 473337 - ii vii iv i iiii vi viv v v MIRb#SINE/MIR 27 AGAGC-ACGGGCTTTGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTCT 75 chr4qtel1M 473338 GACACTCACTAGCCATGAGATGCTGGGTGAGTCAC-TGACTCCTATTTGC 473386 v i ii v ivi ii i - i ii v vv MIRb#SINE/MIR 76 GCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGC 125 chr4qtel1M 473387 CTCAGTTT-CTCATCTGTAAATGAGCTGGAGATGGAAATGGCTAATACTT 473435 - ----v i iiv iv --- i MIRb#SINE/MIR 126 CTCAGTTTCCTCATCTGTAAA----ATGGGGATAATAATACC---TACCT 168 chr4qtel1M 473436 C-CA-GGTCTTTGCAAGAA 473452 - - iv ii i MIRb#SINE/MIR 169 CGCAGGGTTGTTGTGAGGA 187 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 40.06 CpG sites = 32, Kimura (unadjusted) = 42.38 Transitions / transversions = 1.88 (32/17) Gap_init rate = 0.07 (12 / 164), avg. gap size = 1.00 (12 / 12) 17 3.57 10.34 0.00 chr4qtel1M 473617 473645 (526355) (AC)n#Simple_repeat 1 32 (0) m_b202s252i21 7970 chr4qtel1M 473617 ACACA-ACA-ACA-ATACACACACACACACAC 473645 - - - i (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACAC 32 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.11 (3 / 28), avg. gap size = 1.00 (3 / 3) 26 9.00 3.92 3.92 chr4qtel1M 473871 473921 (526079) (AT)n#Simple_repeat 1 51 (0) m_b202s252i22 7971 chr4qtel1M 473871 ATATTTATATATAT-TATGTGATTTATATAT-TTTACTATATATATATAT 473918 v - i - v - v - (AT)n#Simple_ 1 ATATATATATATATATATAT-ATATATATATATATA-TATATATATATAT 48 chr4qtel1M 473919 ATA 473921 (AT)n#Simple_ 49 ATA 51 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.08 (4 / 50), avg. gap size = 1.00 (4 / 4) 195 32.28 3.05 3.05 chr4qtel1M 476457 476587 (523413) C MIRc#SINE/MIR (136) 132 2 m_b202s601i18 7972 chr4qtel1M 476457 GGAAGC--AGACTACAGGGAGCTTCTATGCCTTGCCCAGGGTCAGCCCAG 476504 i -- i - i v vvi v i - v C MIRc#SINE/MIR 132 GGAAACTGAGGCT-CAGAGAGGTTAAGTGACTTGCCCAAGGTCA-CACAG 85 chr4qtel1M 476505 --GGTTATCATCTGAGGCAGCCTTCACATGCCAGCCTTCCTGCCTCCAAG 476552 --i v viiv v v i vvi iv iv vi i v C MIRc#SINE/MIR 84 CTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr4qtel1M 476553 GGCAGCGTGCTATCCCCTGCCCGCCTCAGAGCCTC 476587 vv i iv v v -- i v vv C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTG--CACCACACTGCCTC 2 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 39.83 CpG sites = 17, Kimura (unadjusted) = 42.37 Transitions / transversions = 0.71 (17/24) Gap_init rate = 0.05 (6 / 130), avg. gap size = 1.33 (8 / 6) 17 15.26 0.00 0.00 chr4qtel1M 476989 477017 (522983) (C)n#Simple_repeat 1 29 (0) m_b202s252i23 7973 chr4qtel1M 476989 CCCCCTCCCCGCCCCCCCCCCCCGACCCC 477017 i v vv (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC 29 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 283 25.85 10.47 1.06 chr4qtel1M 477176 477261 (522739) MIR3#SINE/MIR 115 208 (0) m_b202s601i19 7974 chr4qtel1M 477176 TGGCTCTC--TTTTCTCATCTGTAAAGTGAAAGAAATAGACTTGCTGGTT 477223 vi -- i i ii iiv i v v i i MIR3#SINE/MIR 115 TGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATC 164 chr4qtel1M 477224 TCTAAGG----TTCTAACTCTAGGCA---TGGGGTCCTATGATCC 477261 ---- i i - i --- iv i i i MIR3#SINE/MIR 165 TCTAAGGTCCCTTCCAGCTCT-GACATTCTATGATTCTATGATTC 208 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 33.83 CpG sites = 17, Kimura (unadjusted) = 33.83 Transitions / transversions = 3.40 (17/5) Gap_init rate = 0.05 (4 / 85), avg. gap size = 2.50 (10 / 4) 43 4.48 0.00 0.00 chr4qtel1M 477335 477380 (522620) (AC)n#Simple_repeat 1 46 (0) c_b202s251i2 7975 chr4qtel1M 477335 ACACACACACACACACACACACACACACACACAAACATACACACAC 477380 v i (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACAC 46 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 285 29.03 14.78 4.95 chr4qtel1M 478146 478348 (521652) MIRc#SINE/MIR 20 241 (27) m_b202s601i20 7976 chr4qtel1M 478146 GGAAATATCTTTTGGCTTGGAGTTCAAGAACTGAGCTGGCTTTGACTGGA 478195 v v vi v i - i -- v v i v v-- MIRc#SINE/MIR 20 GGAAAGAGCACTGGACTTGGAGT-CAGGAA--GACCTGGGTTCGAGTC-- 64 chr4qtel1M 478196 AGAACTGGCTTTG--ACTCTCCCACTGGGTGACCC--GTCAGGTCAC--- 478238 ---- i i -- iv ivi v i-- v i --- MIRc#SINE/MIR 65 ----CCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTA 110 chr4qtel1M 478239 GCCTTT----GCTTCAGTTTTCACATCTCTAAGGTGAAGAGGA------- 478277 i i ---- i i v v ii ii vi ------- MIRc#SINE/MIR 111 ACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACC 160 chr4qtel1M 478278 -----GGCCCAACT----GATTTATAATGAGGACAACATAGGATTCCATA 478318 -----v i v ---- iv i vi iv v ii --v i MIRc#SINE/MIR 161 TGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGAT--AATG 208 chr4qtel1M 478319 GATATGAAA-CGC--TGCAAACCTGAAAGTGCT 478348 v i - -- i ivv MIRc#SINE/MIR 209 TATGTGAAAGCGCTTTGTAAACTGTAAAGTGCT 241 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 36.03 CpG sites = 31, Kimura (unadjusted) = 37.72 Transitions / transversions = 1.24 (31/25) Gap_init rate = 0.09 (19 / 202), avg. gap size = 2.16 (41 / 19) 233 29.76 0.00 4.69 chr4qtel1M 478584 478650 (521350) MIRc#SINE/MIR 2 65 (203) m_b202s601i21 7977 chr4qtel1M 478584 GGGGCAGTCAGATGGCCCAGTGGCTAGAGCACCAGCCCTGAAGTCAGGAG 478633 i ---i iv vv ii v i i i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr4qtel1M 478634 GACTTCAGCTCAAATTC 478650 i vi i i i i MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCC 65 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 37.67 CpG sites = 14, Kimura (unadjusted) = 40.49 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.05 (3 / 66), avg. gap size = 1.00 (3 / 3) 101 18.57 0.00 0.00 chr4qtel1M 479227 479411 (520589) (TGC)n#Simple_repeat 1 185 (0) m_b202s252i24 7978 chr4qtel1M 479227 TGTTGCTGCTGTTACTGTTGCTGCTGCTGCTACTCTTGTTGCTGCTGCTG 479276 i i i i i vi i (TGC)n#Simple 1 TGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG 50 chr4qtel1M 479277 TTGTTATTGTTGCTGCTACTGCTCCTACTATTGTTGCTGTTGCTGCTGTT 479326 i i ii i i v i ii i i i (TGC)n#Simple 51 CTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT 100 chr4qtel1M 479327 ACTGTTGTTGCTGCTGCTGCTGCTGCTGTTACTGTTGCTGCTGCTGCTGC 479376 i i i i i i (TGC)n#Simple 101 GCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC 150 chr4qtel1M 479377 TGCTGCTGCTGCTGCTGCTGCTGCTGCTGTTACTG 479411 i i (TGC)n#Simple 151 TGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG 185 Matrix = Unknown Transitions / transversions = 13.50 (27/2) Gap_init rate = 0.00 (0 / 184), avg. gap size = 0.0 (0 / 0) 187 13.39 0.00 6.67 chr4qtel1M 479414 479461 (520539) C OldhAT1#DNA/hAT-Ac (793) 2049 2005 m_b202s601i22 7979 chr4qtel1M 479414 ACTGTGGCTGCTGTTGCTGCTGCTGTTGCCATTGCTGCTGTTACTGTT 479461 v v i v --- ? iv C OldhAT1#DNA/h 2049 ACTTTTGCCGCTGTTGCTGCTGGTGT---CANTGTGGCTGTTACTGTT 2005 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 12.61 CpG sites = 2, Kimura (unadjusted) = 15.05 Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.06 (3 / 47), avg. gap size = 1.00 (3 / 3) 38 6.25 0.00 1.92 chr4qtel1M 479472 479524 (520476) (CTAACC)n#Simple_repeat 1 52 (0) c_b202s251i3 7980 chr4qtel1M 479472 CTAACCCTAACCCTAACCCTGAACCCTAATTCTAACTCTAACCCTAACCC 479521 - ii i (CTAACC)n#Sim 1 CTAACCCTAACCCTAACCCT-AACCCTAACCCTAACCCTAACCCTAACCC 49 chr4qtel1M 479522 TAA 479524 (CTAACC)n#Sim 50 TAA 52 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.02 (1 / 52), avg. gap size = 1.00 (1 / 1) 485 25.37 1.32 4.05 chr4qtel1M 481087 481238 (518762) MIR3#SINE/MIR 7 154 (54) m_b202s601i23 7981 chr4qtel1M 481087 GAGTGGTTCTGGGCCTAGAGCTACAAGGCCTGG-AGTCAGGAAAACCCAA 481135 -- i vv v-i v v - i - iii MIR3#SINE/MIR 7 GAGTGG--CTGAGCAGAGAGA-GCACGGACTGGGAGTCAGGAGA-CCTGG 52 chr4qtel1M 481136 ATTAAAATGTGGCCTCAGACACTCACTAGCCATGAGATCCTGGGTGAGTC 481185 i vv i viv v v v v ? ii v i i ii MIR3#SINE/MIR 53 GTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTC 102 chr4qtel1M 481186 ACTG-ACTCCTATTTGCCTCAGTTTCCTCATCTGTAAAATGAGCTGGAGA 481234 v- ii v vv -- i v MIR3#SINE/MIR 103 ACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAG--GGGGT 150 chr4qtel1M 481235 TGGA 481238 MIR3#SINE/MIR 151 TGGA 154 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 31.44 CpG sites = 18, Kimura (unadjusted) = 31.44 Transitions / transversions = 0.95 (18/19) Gap_init rate = 0.05 (8 / 151), avg. gap size = 1.00 (8 / 8) 533 26.61 0.80 0.80 chr4qtel1M 481103 481227 (518773) MIRc#SINE/MIR 24 148 (120) m_b202s601i24 7981 chr4qtel1M 481103 AGAGCTACAAGGCCTGGAGTCAGGAAAACCCAAATTAAAATGTGGCCTCA 481152 - vi i i i iiii vi i viv v v MIRc#SINE/MIR 24 AGAGC-ACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCT 72 chr4qtel1M 481153 GACACTCACTAGCCATGAGATCCTGGGTGAGTCAC-TGACTCCTATTTGC 481201 v i ii v i i ii - i ii v vv MIRc#SINE/MIR 73 GCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGC 122 chr4qtel1M 481202 CTCAGTTTCCTCATCTGTAAAATGAG 481227 i MIRc#SINE/MIR 123 CTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 32.90 CpG sites = 22, Kimura (unadjusted) = 34.19 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.02 (2 / 124), avg. gap size = 1.00 (2 / 2) 251 27.91 10.87 1.32 chr4qtel1M 481314 481451 (518549) C L2d_3end#LINE/L2 (25) 491 341 m_b202s601i25 7982 chr4qtel1M 481314 ACTGACCACCAAC-ATTTGCTAGGCACTGTACTAGTC---------AA-A 481352 i v i v - v vi i v --------- -i C L2d_3end#LINE 491 ATTGAGCGCCTACTATGTGCTCAGCACTGTGCTAGGCGCTGTGGGGAACG 442 chr4qtel1M 481353 AAAAAATAG-GCAAAAGCT-GTTCCTCCCTTTGAGGAGCTCACATTGTGA 481400 ? ? -ii i vv - i v i ii i v v ii C L2d_3end#LINE 441 ANAAAANAGTATAAGACATGGTCCCTGCCCTCAAGGAGCTTACAATCTAG 392 chr4qtel1M 481401 AGGGAGAGACAACATGAAAATAACATGGAAATAACTAGATACC--TGCAA 481448 vv i v iv v i- - i i v v -- i C L2d_3end#LINE 391 TTGGGGAGACAAGACTAACAC-ACAT-GAAACAATTAGAGAACAATACAA 344 chr4qtel1M 481449 GAC 481451 C L2d_3end#LINE 343 GAC 341 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 33.99 CpG sites = 21, Kimura (unadjusted) = 36.33 Transitions / transversions = 1.24 (21/17) Gap_init rate = 0.06 (8 / 137), avg. gap size = 2.12 (17 / 8) 63 44.36 0.62 1.46 chr4qtel1M 481452 481934 (518066) (CA)n#Simple_repeat 1 479 (0) m_b202s252i25 7983 chr4qtel1M 481452 CACACACACACACACACACACACTCTCTCTCATACTCTTACA-ATACATA 481500 v v v v i v vi - i i (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 chr4qtel1M 481501 CATATACACATACACAGCTATATATTCTCACATACACTTATACTCTCTCA 481550 i i i - - i i iv v i vi i v v v (CA)n#Simple_ 51 CACACACACACACACA-C-ACACACACACACACACACACACACACACACA 98 chr4qtel1M 481551 CATACAATTACCTATGCACATACACACAGTCATATCCTCACATACATGTA 481600 i vvi vi ii i vv i iv v i iii (CA)n#Simple_ 99 CACACACACACACACACACACACACACACACACACACACACACACACACA 148 chr4qtel1M 481601 TACACACACACTCTCACTATATATTTATAATCTTAGA-ATACATACACAT 481649 i v v - i i ivi i vv vi v - i i i (CA)n#Simple_ 149 CACACACACACACACAC-ACACACACACACACACACACACACACACACAC 197 chr4qtel1M 481650 ATACACATACTCTATTGCACACACTCACACTCTTACATGCATGTATACTC 481699 i i v - -ii v v vi ii iii i v (CA)n#Simple_ 198 ACACACACACAC-A-CACACACACACACACACACACACACACACACACAC 245 chr4qtel1M 481700 ACACTCATATTTATATATATATTATGTATTTATATATTTACATTATATAT 481749 v i ivi i i i i -i iii ivi i i ivi -i i i i (CA)n#Simple_ 246 ACACACACACACACACACACA-CACACACACACACACACACA-CACACAC 293 chr4qtel1M 481750 ATATATATACACACTCTCACA-ACACATACACACACTCACACTTTTACAT 481798 i i i i v v - i v vivi i (CA)n#Simple_ 294 ACACACACACACACACACACACACACACACACACACACACACACACACAC 343 chr4qtel1M 481799 ATACATACACTCATGTACACTCATACTCTTGCACAGACATATACCCACCC 481848 i i v iii v i v vii v i i v v (CA)n#Simple_ 344 ACACACACACACACACACACACACACACACACACACACACACACACACAC 393 chr4qtel1M 481849 ACACTCTTACATACTCACACACACATCCACATAGTCACACTTACACAAAG 481898 v vi i v iv i vv vi v v (CA)n#Simple_ 394 ACACACACACACACACACACACACACACACACACACACACACACACACAC 443 chr4qtel1M 481899 ATACACACACTCATACTCTCACATACATACACACAC 481934 i v i v v i i (CA)n#Simple_ 444 ACACACACACACACACACACACACACACACACACAC 479 Matrix = Unknown Transitions / transversions = 1.59 (94/59) Gap_init rate = 0.02 (10 / 482), avg. gap size = 1.00 (10 / 10) 230 25.89 0.00 3.45 chr4qtel1M 482638 482697 (517303) MIR3#SINE/MIR 119 176 (32) m_b203s601i4 7981 chr4qtel1M 482638 CCTCAGCTTTCCTGTCTGTGAAATGGGAAGGTTGCTGACTCTATGATCTC 482687 i i iii i i ii -- vv MIR3#SINE/MIR 119 CCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTG--GACTAGATGATCTC 166 chr4qtel1M 482688 TACTGTTTCT 482697 vv ii MIR3#SINE/MIR 167 TAAGGTCCCT 176 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 33.45 CpG sites = 11, Kimura (unadjusted) = 33.45 Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.03 (2 / 59), avg. gap size = 1.00 (2 / 2) 25 6.36 0.00 0.00 chr4qtel1M 484122 484154 (515846) (TG)n#Simple_repeat 1 33 (0) m_b203s252i1 7984 chr4qtel1M 484122 TGTGTGTGTGTGTGTCTGTGTGTCTGTGTGTGT 484154 v v (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 33 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 242 36.09 8.24 1.10 chr4qtel1M 484802 485056 (514944) L2d2_3end#LINE/L2 2 274 (281) m_b203s601i5 7985 chr4qtel1M 484802 TCCACTGGCTGAGTCCTTCCCAGCTTTCAAGCTTCTTTCCATATTATCTC 484851 viv ivi vv i?v v i iv ii vi i ii L2d2_3end#LIN 2 TCCACGATCTGGCCCCAACCTNCCTTTCCAGCCTTATCTCCCACTATTCC 51 chr4qtel1M 484852 CTTTATCAAGTTCTCT-CTC-AGCCAGACTACCCTGCCTACTGTGCCTTA 484899 i ?vv i iii i- - i ivi i ii v iii L2d2_3end#LIN 52 CCTNCACGAACCCTCCGCTCCAGCCAAACTGGTCTACTCACTGTCCCCCG 101 chr4qtel1M 484900 TAAACAACATGCTGTTTCCCACCTCCATGCCTTTGCCCAAACTGCCCCCC 484949 v v iv v vv? i iii i vi i ii L2d2_3end#LIN 102 AACACGCCTTGCGCNTTCCCGCCTCTGCGCCTTTGCTCACGCCGTTCCCC 151 chr4qtel1M 484950 ATGCCT-AAGTG-ACTCTCCCTTC----ACACCT---------CTGTT-- 484982 vi -i i -v ii ----v --------- iii-- L2d2_3end#LIN 152 CCGCCTGGAATGCCCTTCCCCTTCCTCTCCACCTATCCAAATCCTACCCA 201 chr4qtel1M 484983 TGCTTTGAGACTAAGCTCAAGCCCCTCCTGATCCCTGAAG--ATTCCAGC 485030 v ii i iv ii? v vv v --v i v v L2d2_3end#LIN 202 TCCTTCAAGGCCCAGCTCAAATNCCACCTCCTCCGTGAAGCCTTCCCTGA 251 chr4qtel1M 485031 CCCCTCTGTCCTTCTGAAATGACCTC 485056 v iiv --- i ? i i L2d2_3end#LIN 252 CCACTCCAGC---CCGNAGTGATCTC 274 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 45.33 CpG sites = 57, Kimura (unadjusted) = 53.76 Transitions / transversions = 1.68 (57/34) Gap_init rate = 0.04 (11 / 254), avg. gap size = 2.18 (24 / 11) 195 26.47 10.29 0.00 chr4qtel1M 485083 485150 (514850) X9_LINE#LINE/L1 780 854 (82) m_b203s601i6 7986 chr4qtel1M 485083 TTTTCCTGGTAGGCTGCAAGTTCCC----GAGACCAGAC---TGTCTCAC 485125 v vi vii v ---- i --- iv X9_LINE#LINE/ 780 TTATCCTGCCAGGCTGAGGGTTCGCTGTGGAGGCCAGACATATGTCTTTC 829 chr4qtel1M 485126 TTTTGTCCTTGGATGCTGCAGTCTT 485150 ivi vi i iv X9_LINE#LINE/ 830 TTTCTCCCACGGATGCTACAGCGTT 854 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 28.93 CpG sites = 10, Kimura (unadjusted) = 33.24 Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.03 (2 / 67), avg. gap size = 3.50 (7 / 2) 202 34.54 4.29 2.82 chr4qtel1M 485278 485417 (514583) C L3b_3end#LINE/CR1 (214) 992 851 m_b203s601i7 7987 chr4qtel1M 485278 TATCAAACGTGAGCCTCTGCAGGTCCCCCATTTTTATCC---TTCTCCTG 485324 v v i ii i - v -- iv v v v --- ii v C L3b_3end#LINE 992 TATCTAACCTAAATCCCT-CATG--CTGCAGTTTAAGCCCATTTCCTCTT 946 chr4qtel1M 485325 GTTGTGCTCTGGGGGAAGAAGGCAAGAAGCC--TCATCTCTCTCT-TGTC 485371 v ii vi v i v vi iv i-- i vii -i v C L3b_3end#LINE 945 GTTCTGTCCTCAGTGGAGATGGAGAACAGCTGGTCACCGTCCTCTACGTA 896 chr4qtel1M 485372 TATATCCCTCCACACCCCTGCAGACAGTTGTCAAATTTTCCCTTAG 485417 - v i i iv i v ? i i i i?i i C L3b_3end#LINE 895 -ATAACCCTTCATATACTTGAAGACNGTTATTAAGTCNCCCCTCAG 851 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 47.85 CpG sites = 28, Kimura (unadjusted) = 49.35 Transitions / transversions = 1.47 (28/19) Gap_init rate = 0.05 (7 / 139), avg. gap size = 1.43 (10 / 7) 30 21.64 0.00 1.41 chr4qtel1M 487017 487088 (512912) (GAG)n#Simple_repeat 1 71 (0) m_b203s252i2 7988 chr4qtel1M 487017 GAGGCAGCAAGAGGAGGAAGAAGAGGAGGAAGAAGATGAGGAAGAAGAGG 487066 - v i i i i i v i i (GAG)n#Simple 1 GAGG-AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGG 49 chr4qtel1M 487067 AAGATGAGGAGGATGAGCAGGA 487088 i v v v (GAG)n#Simple 50 AGGAGGAGGAGGAGGAGGAGGA 71 Matrix = Unknown Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.01 (1 / 71), avg. gap size = 1.00 (1 / 1) 15 18.29 0.00 2.63 chr4qtel1M 487767 487805 (512195) (GGCTGT)n#Simple_repeat 1 38 (0) m_b203s252i3 7989 chr4qtel1M 487767 GGTTGGGGCTGGTGTCTGTGCCTGTGGGTGTGGGTGTGG 487805 i v - v v v v (GGCTGT)n#Sim 1 GGCTGTGGCT-GTGGCTGTGGCTGTGGCTGTGGCTGTGG 38 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.03 (1 / 38), avg. gap size = 1.00 (1 / 1) 24 21.89 0.00 3.08 chr4qtel1M 487783 487849 (512151) (TGTGAG)n#Simple_repeat 1 65 (0) m_b203s252i4 7989 chr4qtel1M 487783 TGTGCCTGTGGGTGTGGGTGTGGGGATGTGAGTGTGAGTGTGAGTGAAAC 487832 vv i i - i - vi v (TGTGAG)n#Sim 1 TGTGAGTGTGAGTGTGAGTGT-GAG-TGTGAGTGTGAGTGTGAGTGTGAG 48 chr4qtel1M 487833 TGTGGGGCTGTGTGTGA 487849 i vv v (TGTGAG)n#Sim 49 TGTGAGTGTGAGTGTGA 65 Matrix = Unknown Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.03 (2 / 66), avg. gap size = 1.00 (2 / 2) 41 0.00 0.00 0.00 chr4qtel1M 488074 488108 (511892) (GT)n#Simple_repeat 1 35 (0) c_b203s251i0 7990 chr4qtel1M 488074 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 488108 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 35 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 13 38.96 0.00 0.00 chr4qtel1M 491342 491411 (508589) (GGG)n#Simple_repeat 1 70 (0) m_b203s252i5 7991 chr4qtel1M 491342 GGGAGGGGGGGCAGCAGGTGGGGGGCTGGACAGGAGGGGTGGCAGGGAGG 491391 i vi vi v vv ivi i v vi i (GGG)n#Simple 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 50 chr4qtel1M 491392 AGGACGTGGGGGGGGAGGGG 491411 i iv v i (GGG)n#Simple 51 GGGGGGGGGGGGGGGGGGGG 70 Matrix = Unknown Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0) 12 16.84 5.77 5.77 chr4qtel1M 492148 492199 (507801) (GTGGA)n#Simple_repeat 1 52 (0) m_b203s252i7 7992 chr4qtel1M 492148 GTGGGGTGTGGGT-GTGGGGATGTGG-G-GGTTTGGAGTGGAGTGTGAGT 492194 i - i - v v - - - vv - (GTGGA)n#Simp 1 GTGGAGTG-GAGTGGAGTGGA-GTGGAGTGGAGTGGAGTGGAGTG-GAGT 47 chr4qtel1M 492195 GAAGT 492199 i (GTGGA)n#Simp 48 GGAGT 52 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.12 (6 / 51), avg. gap size = 1.00 (6 / 6) 22 14.39 6.15 2.99 chr4qtel1M 492147 492211 (507789) (TGTGGGG)n#Simple_repeat 1 67 (0) m_b203s252i6 7993 chr4qtel1M 492147 TGTGGGGTGT-GGGTGTGGGGATGTGGGG-GTTTGGAGTGGAGTGT-GAG 492193 - - - vv v i - i (TGTGGGG)n#Si 1 TGTGGGGTGTGGGGTGTGGGG-TGTGGGGTGTGGGGTGTGGGGTGTGGGG 49 chr4qtel1M 492194 TG-AAGTTGTGGGGCTGTG 492211 -ii v - (TGTGGGG)n#Si 50 TGTGGGGTGTGGGG-TGTG 67 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.09 (6 / 64), avg. gap size = 1.00 (6 / 6) 280 30.03 6.19 4.86 chr4qtel1M 493884 494513 (505487) L1M5_orf2#LINE/L1 2614 3251 (43) m_b203s551i0 7994 chr4qtel1M 493884 CCACCTGATCTAAAAACTT-TTATAAAGCAGCAGTCCCCAAAACCATTTG 493932 i ? ? v i - vi vvi i vi v L1M5_orf2#LIN 2614 CTACCNGATNTCAAGACTTATTATAAAGCTACAGTAATCAAGACAGTGTG 2663 chr4qtel1M 493933 GTACCGGC-TAAGAAATAGATTAGTTGGATCAGTCGAACAGGTTAG---G 493978 ii - i - iv i -i i v iv --- L1M5_orf2#LIN 2664 GTATTGGCGTAAGGA-TAGACAAAT-AGATCAATGGAACAGAATAGAGAG 2711 chr4qtel1M 493979 TTCACAAGCAGA---ATAGTCAACTATAG-CAATCCAGGTATGACAAAAC 494024 i v ii --- i -- vv i - ? iv vv v iv L1M5_orf2#LIN 2712 TCCAGAAATAGACCCACA--CATATATGGNCANTTGATTTTTGACAAAGG 2759 chr4qtel1M 494025 --CCAAAGATCCTAACTTTTTGGGAAAGAATTCATTATTTCA-CAAAAAC 494071 -- ? ----i i ivv i iiiv vi iv - viv L1M5_orf2#LIN 2760 TGCCAANG----CAATTCAGTGGGGAAAGGATAGTCTTTTCAACAAATGG 2805 chr4qtel1M 494072 TGCTGGG-TAATTGGAAATTAGTATGGAGAAA--TTAGGCACGGACCCAA 494118 i-i v ivi i -- v i? v iv v L1M5_orf2#LIN 2806 TGCTGGAACAATTGGATATCCATATGGAAAAAAATGAANCTCGACCCCTA 2855 chr4qtel1M 494119 CCCTAACAACCGATACCAAGATAAGATCAA-ATGGGTCCAAGGATTTAAT 494167 - v v vv i v i v iv ? - i vv ivi v L1M5_orf2#LIN 2856 CC-TCACACCATACACAAAAATTAATTCNAGATGGATCATAGACCTAAAT 2904 chr4qtel1M 494168 -TAAAGAATGAGATTATAAAAAAT-TAGAGGAAA-CATAGGATTTTAAAT 494214 - ii? i i i vv - i - vvv vv L1M5_orf2#LIN 2905 GTAAAAGNTAAAACTATAAAACTTCTAGAAGAAAACATAGGAGAATATCT 2954 chr4qtel1M 494215 CTGTCGACCCGTGGAGGAAGGAAGGAAGAAATTTTGGACCAAAGAGGAAC 494264 ii - i- ----- ?v v i i i---ii v vv L1M5_orf2#LIN 2955 TCGT-GACCT-TGG-----GNTAGGCAAAGATTTC---TTAAACAGGACA 2994 chr4qtel1M 494265 TAGAGATCATTATTGATCACAAAAAAAATT------TTTGATTACATCAA 494308 i i i v i? viv v v i ------ v i ? L1M5_orf2#LIN 2995 CAAAAAGCACNAACCATAAAAGAAAAAATTGATAAATTGGACTNCATCAA 3044 chr4qtel1M 494309 AA---AAAGCTTTTG---TACAAACAAAACCA--AAGCAAACAAAGGGAA 494350 --- i i ---?v vi v i-- v ii --- L1M5_orf2#LIN 3045 AATTAAAAACTTCTGCTCNTCAAAAGACACCGTTAAGAAAATGAA---AA 3091 chr4qtel1M 494351 GGGAAGCAAATAACCGGGGAAAAAGATTTCACAAAGT-TAAAGGTTCTGA 494399 v v vvi ?i ii v -i ?ii- v --- L1M5_orf2#LIN 3092 GGCAAGCCACAGANTGGGAGAAAATATTT-GCAANACATATA---TCTGA 3137 chr4qtel1M 494400 --AAGGCCC--TTTTAAAAATGTATAGAGAATTGACTTTAATTTA-TAAG 494444 -- v i-- v iv i i i i v- vi ? i - ? L1M5_orf2#LIN 3138 CAAAGGACTCGTATCCAGAATATATAAAGAACTC-CTACAANTCAATAAN 3186 chr4qtel1M 494445 AATTCAAAGCCATTTCTCCAATTGGATAAATGGTCAAAGGATATGAACAG 494494 --- v vvivv v v i? v v i iv L1M5_orf2#LIN 3187 AA---AAAGACAAACAACCCAATANAAAAATGGGCAAAAGACTTGAACAG 3233 chr4qtel1M 494495 ACAATTTTAGAGATGAAAA 494513 - i i v i v i L1M5_orf2#LIN 3234 AC-ACTTCACAAAAGAAGA 3251 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 39.90 CpG sites = 94, Kimura (unadjusted) = 40.48 Transitions / transversions = 1.09 (94/86) Gap_init rate = 0.08 (52 / 629), avg. gap size = 1.35 (70 / 52) 693 29.14 6.00 3.92 chr4qtel1M 494414 494963 (505037) L1ME4c_3end#LINE/L1 12 572 (258) m_b203s551i1 7994 chr4qtel1M 494414 AATGTATAGAGAATTGACTTTAATTTATAAGAATTCAAAGCCATTTCTCC 494463 ? i i ii v i iv v --v ?ii vvv i L1ME4c_3end#L 12 ANTATATAAAGAGCTCATTCAAATTGATAAGAA--AAANATCAAGACCCC 59 chr4qtel1M 494464 AATTGGATAAATGGTCAAAGGATATGAACAGACAATTT-TAGAGATGAAA 494512 -i v i i-i ? iiv i L1ME4c_3end#L 60 AAT-AGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAGGAA 108 chr4qtel1M 494513 AGGAAACTATTACTACCAAA-----GGAAAGGTGTGTTCCAAATCACTAT 494557 viv ? v -- v ----- i--i v vv i v L1ME4c_3end#L 109 ATACAANTAGTA--AACAAACACATGGAAAA--ATGTTCAACCTCGCTAG 154 chr4qtel1M 494558 TGATCAGAGAAAATGCAAA--AAAGACAACCCGGAGTTATGA---TACAC 494602 i i - -- - vvv v iv --- i L1ME4c_3end#L 155 TAATCAAAG-AAATGCAAATTAAAG-CAACAATGAGATACCATTTTACGC 202 chr4qtel1M 494603 CTGTCAGATTGGTCAGA--TGAAGGAAAAAATAATATGGAATGTT---GA 494647 i i i i iv i -- v ii vvi ivv i --- L1ME4c_3end#L 203 CTATTAAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGCTGGCGA 252 chr4qtel1M 494648 GGGAG-GGGAAAACCGGGCCACTGATGCATTGTT--TGGAGTTGTGAA-T 494693 ?v - vi i vv ? v i i -- vi? i - L1ME4c_3end#L 253 GGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATT 302 chr4qtel1M 494694 GAACCAACCATTCTTGGAGAG-AAACTGGAATTATGC-CCAAAAGTTATC 494741 ivv v - i - vi v v i i-i i ii v L1ME4c_3end#L 303 GGTACAACCCTT-TTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATA 351 chr4qtel1M 494742 AAACTGTGTAC-CCCTTTGATTCGGCAGTGTCAC-ACTGAG--CTTAT-- 494785 v vi i- ii i i i vi -v i --i -- L1ME4c_3end#L 352 AAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCC 401 chr4qtel1M 494786 AAAGGAGATACT---AAAGAAGGAAAAGGGACCTGTATGTGCCAAAATGT 494832 v i v --- i --- i ii v i L1ME4c_3end#L 402 TAAGGAAATAATTCAAAAGAAGGAAAAAG---CTATATGCACGAAGATGT 448 chr4qtel1M 494833 CTATGGCAGCTCTGTTTGTGGTGGCCAGAAACTGGAAA-AATTTTGATTT 494881 ii v vi i i ii i v i i - ii vi --- L1ME4c_3end#L 449 TCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAA--- 495 chr4qtel1M 494882 TTTTTTTCCACCAATTTGGGAGAATGGTT-TGAAAATTGTTAAATATGAA 494930 ---- v v -- i i -v v i viv i v? L1ME4c_3end#L 496 ----TGTCCAACAA--TAGGGGAATGGTTAAGTAAATTATGGTACATCNA 539 chr4qtel1M 494931 CCTTAAGGAATATTATTGTTCTATAAGAAATGA 494963 iiv v vvvv i v i L1ME4c_3end#L 540 CTCGATGGAATATTATGCAGCCATTAAAAATGA 572 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 37.35 CpG sites = 88, Kimura (unadjusted) = 38.63 Transitions / transversions = 1.33 (88/66) Gap_init rate = 0.07 (40 / 549), avg. gap size = 1.38 (55 / 40) 296 32.35 8.16 5.72 chr4qtel1M 494461 495024 (504976) L1MD1_3end#LINE/L1 57 633 (356) m_b203s551i2 7994 chr4qtel1M 494461 TCCAATTGGATAAATGGTCAAAGGATATGAACAGACAATTTTAGAGATGA 494510 i - v i i v - i v---i L1MD1_3end#LI 57 TCCAATTAGA-AAATGGGCAAAAGACATGAAGAGACA-TTTCAC---CGA 101 chr4qtel1M 494511 AAAGGAAACTATTACTACCAAA---------GGAAAGGTGTGTTCCAAAT 494551 i v - iviv iv --------- i i -- v v L1MD1_3end#LI 102 AGAGGATA-TACAGATGGCAAATAAGCACATGAAAAGATGT--TCAACAT 148 chr4qtel1M 494552 CACTATTGATCAGAGAAAATGCAAAA-AAGACAACCCGGAGTTAT---GA 494597 i viv i i - v- i v vvv v ---v L1MD1_3end#LI 149 CATTAGCCATTAGGGAAA-TGCAAATTAAAACCACAATGAGATATCACTA 197 chr4qtel1M 494598 TACACCTGTCAGATTGGTCAGATGAAGGAAAAA--ATAATATGGAATGTT 494645 i i v ii i vv ii v i-- i i ivi i L1MD1_3end#LI 198 CACACCTATCAGAATGGCTAAAATAAAAAATAGTGACAACACCAAATGCT 247 chr4qtel1M 494646 G---AGGGAGGGGA-AAACCGGGCCACTGATGCATTGTT--TGGAGTTGT 494689 --- iv v - i ii v i i -- iiv L1MD1_3end#LI 248 GGCGAGGATGCGGAGAAACTGGATCACTCATACATTGCTGGTGGGAATGT 297 chr4qtel1M 494690 GAA-TGAACCAACCATTCTTGGAGAGAAACTGGAATTATGCCCAAAAGTT 494738 i - ivv i i v i i v ivi v v - v ii i-- L1MD1_3end#LI 298 AAAATGGTACAGCCACTCTGGAAAACAGTTTGGCAGT-TTCTTAAAAA-- 344 chr4qtel1M 494739 ATCAAACTGTGTACC---CCTTTGATTCGGCAGTGTCACAC-TGAGC--T 494782 ii -i i v --- v vi ii i i vv v - i -- L1MD1_3end#LI 345 ACTAAAC-ATGCAACTACCATACGACCCAGCAATTGCACTCCTGGGCATT 393 chr4qtel1M 494783 TAT-------AAAGGAGATACTAAAG---AAGGAAAAGGGACCTGTATGT 494822 ------- v i - v v --- viv --- iii L1MD1_3end#LI 394 TATCCCAGAGAAATGAAA-ACTTATGTTCACACAAAA---ACCTGTACAC 439 chr4qtel1M 494823 GCCAAAATGTCTATGGCAGCTCTGTTTGTGGTGGCCAGAAACTGGAAA-A 494871 ---- i i i i i ii i i - L1MD1_3end#LI 440 G----AATGTTTATAGCAGCTTTATTCGTAATAGCCAAAAACTGGAAACA 485 chr4qtel1M 494872 ATTTTGATTTTTTTTTTCCACCAATTTGGGAGAATGGTTTGA-AAATTGT 494920 iiiv v ii ------- --i v vi - i L1MD1_3end#LI 486 ACCCAGATGTCCTT-------CAA--CGGGTGAATGGTTAAACAAACTGT 526 chr4qtel1M 494921 TAAATATGAACCTTAAGGAATATTATTGTTCTATAAGAAATGACCAGCAG 494970 viv i vv ivii v i i vvv v i ivi v i -- L1MD1_3end#LI 527 GGTACATCCATACCATGGAATACTACTCAGCAATAAAAAGGAACGAAC-- 574 chr4qtel1M 494971 GGATGGAAATACAGAGGAAAGAGAATAAAGCATCCG------ATGCTGAG 495014 -v v v i iv iv vvv i i v vi v ------ L1MD1_3end#LI 575 -TATTGATACACGCAACAACCTGGATGAATCTCCAGAGAATTATGCTGAG 623 chr4qtel1M 495015 TGAAATGAGC 495024 vi L1MD1_3end#LI 624 TGAAAAAAGC 633 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 41.65 CpG sites = 98, Kimura (unadjusted) = 43.68 Transitions / transversions = 1.32 (98/74) Gap_init rate = 0.09 (49 / 563), avg. gap size = 1.61 (79 / 49) 12 9.78 0.00 0.00 chr4qtel1M 496144 496165 (503835) (CCTC)n#Simple_repeat 1 22 (0) m_b203s252i8 7995 chr4qtel1M 496144 CCTCCCTCCCTCCAACCCTCCC 496165 vv (CCTC)n#Simpl 1 CCTCCCTCCCTCCCTCCCTCCC 22 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 54 0.00 0.00 0.00 chr4qtel1M 497943 497988 (502012) (GT)n#Simple_repeat 1 46 (0) c_b203s251i1 7996 chr4qtel1M 497943 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 497988 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 46 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 21 7.71 0.00 0.00 chr4qtel1M 499282 499309 (500691) (T)n#Simple_repeat 1 28 (0) m_b203s252i9 7997 chr4qtel1M 499282 TTTTTTTTCTTTTTCTTTTTTTTTTTTT 499309 i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 28 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 16 8.00 0.00 3.57 chr4qtel1M 499391 499419 (500581) (TCCC)n#Simple_repeat 1 28 (0) m_b203s252i10 7998 chr4qtel1M 499391 TCCCTCCTTCCCTCCCTCCACCCCCTCCC 499419 i - i (TCCC)n#Simpl 1 TCCCTCCCTCCCTCCCTCC-CTCCCTCCC 28 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1) 1681 30.96 0.47 0.63 chr4qtel1M 499723 500356 (499644) C L1ME4c_3end#LINE/L1 (191) 639 7 m_b203s551i3 7999 chr4qtel1M 499723 TTCTGCTCATTTCACTCAGCATCAGTTCATGTAAGTCTCTCCAAGCCTCT 499772 iv i i i vv iv vi i - v iiv C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATAAACATTT-TCCATGTTGCT 591 chr4qtel1M 499773 CTGTATTCAGCCTGCTGATCATTTCTTACAGAACAATAATATTCCATAAC 499822 vii v vv v iv v i v ii vvvv viv C L1ME4c_3end#L 590 ACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCGA 541 chr4qtel1M 499823 ATTCATATACCACAATTTATCCAACCATTCTCCAATTGATGGGCATCCAC 499872 i ?v i i iii i v v i ii v C L1ME4c_3end#L 540 GTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAG 491 chr4qtel1M 499873 TCAGTTTCCAGTTTCTGGCCACTACACACAGGGCTGCCACAAACATTTTG 499922 viv i i v i i i v i iv v ii i v C L1ME4c_3end#L 490 GTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTC 441 chr4qtel1M 499923 GCACATACAGGTCCCTTTCCCTTCTTT---AGTATCTCTTTGGGGTATAA 499969 ii i --- i i --- v i i i i v v C L1ME4c_3end#L 440 GTGCATATAG---CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAAT 394 chr4qtel1M 499970 GCCCAGTAGAAACACTGCCGGGTCAAAGGGTATGCACAGTTTGATAACTT 500019 v v viiv i i i v v v ii i C L1ME4c_3end#L 393 TCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTC 344 chr4qtel1M 500020 TTTGGGCATAATTCCAGATTGTTCTCCAGAATGGCTGGATCTGTTCACAA 500069 vivi i v v i i i i v i v i vi i ? C L1ME4c_3end#L 343 TTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACAN 294 chr4qtel1M 500070 TTCCACCAACAATGTATCAGTGTCCCTGGTTTCCCACATCCCCTCCAACA 500119 v i v ? v v v iv i ? i v i C L1ME4c_3end#L 293 TGCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGCA 244 chr4qtel1M 500120 TTCTGCATTATCTTTCCCTTTCATTCTAGCCAATCTGACAGGTGTGTCAT 500169 vv i vv iii vv i v i i i i i ivv C L1ME4c_3end#L 243 TTGGGTATTATCAATTTTTTAAATTTTTGCTAATTTAATAGGCGTAAAAT 194 chr4qtel1M 500170 GGTATCTCAGAGTTGTCTTAATTTGCATTTCTTGGATAAATAATGATTTG 500219 vv ii v v v ii vv v C L1ME4c_3end#L 193 GGTATCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACTAGCGAGGTT 144 chr4qtel1M 500220 AAACACTCTTTCATATGAGTAGTAATAGTTTCAATTTCATCATCTGAAAA 500269 i i i i i vv iv v ivi? vv v v ? vi C L1ME4c_3end#L 143 GAACATTTTTCCATGTGTTTGTTTACTANTTGTATTTCCTCTTNTGTGAA 94 chr4qtel1M 500270 TTGTCTGTTCATATCCTTTGACCATTTATCAATTGGAGAATGGCTTGATT 500319 i v v i vv v v ?vv C L1ME4c_3end#L 93 TTGTCTGTTCATGTCCTTTGCCCATTTATCTATTGGGGTCTTGATNTTTT 44 chr4qtel1M 500320 TCTTATAAATTAGAGTCAATTCTCTATATATTTCAGA 500356 v v i v ii i ? v? C L1ME4c_3end#L 43 TCTTATCAATTTGAATGAGCTCTTTATATANTANAGA 7 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 39.99 CpG sites = 100, Kimura (unadjusted) = 41.35 Transitions / transversions = 1.05 (100/95) Gap_init rate = 0.01 (5 / 633), avg. gap size = 1.40 (7 / 5) 31 5.56 0.00 0.00 chr4qtel1M 502912 502949 (497051) (TGTGAG)n#Simple_repeat 1 38 (0) c_b203s251i2 8000 chr4qtel1M 502912 TGTGAGTGTGGGTGTGGGTGTGAGTGTGAGTGTGAGTG 502949 i i (TGTGAG)n#Sim 1 TGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTG 38 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 52 5.36 0.00 0.00 chr4qtel1M 503195 503252 (496748) (GT)n#Simple_repeat 1 58 (0) c_b203s251i3 8001 chr4qtel1M 503195 GTGTGTGTTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTCTGTGTGTGTGT 503244 v v (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50 chr4qtel1M 503245 ATGTGTGT 503252 i (GT)n#Simple_ 51 GTGTGTGT 58 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0) 770 31.73 3.48 3.63 chr4qtel1M 504797 505486 (494514) L1M5_orf2#LINE/L1 2606 3294 (0) m_b203s551i4 8002 chr4qtel1M 504797 GGCTTGCTGTACCTGATCT-AAAACTATATTATAAAGCAGCAGTCCCCAA 504845 i i vv ? ? - i - vi vvi L1M5_orf2#LIN 2606 GACTTACACTACCNGATNTCAAGACT-TATTATAAAGCTACAGTAATCAA 2654 chr4qtel1M 504846 AACCATTTGGTACTGGC-TAAGAAATACATTAGTTGATCAGTGGAACAGG 504894 i vi v i - i - v iv i v i i L1M5_orf2#LIN 2655 GACAGTGTGGTATTGGCGTAAGGA-TAGACAAATAGATCAATGGAACAGA 2703 chr4qtel1M 504895 TTAG---GTTCACAAGACAGA---ATAGTCAACTATAGCAATCTAGTGTT 504938 v --- i v - i --- i -- vv i ?v ?i ii v L1M5_orf2#LIN 2704 ATAGAGAGTCCAGAA-ATAGACCCACA--CATATATGGNCANTTGATTTT 2750 chr4qtel1M 504939 TGACAAAC---CCAAAGATCCTAACTTT-TGGGATAAGAATTCATTATTT 504984 v--- ? ----i i iv- iv i vvvi v i L1M5_orf2#LIN 2751 TGACAAAGGTGCCAANG----CAATTCAGTGGGGAAAGGATAGTCTTTTC 2796 chr4qtel1M 504985 CACAAAAACTGCTGGGATAACTGGAAATTAGTATGGCAGAAATTAGGCAC 505034 v viv i i i v ivi v i v iii?vi L1M5_orf2#LIN 2797 AACAAATGGTGCTGGAACAATTGGATATCCATATGGAAAAAAATGAANCT 2846 chr4qtel1M 505035 AAACCCACACTTAACACCGTATACCAAGATAAGATCAAAATGGGTCCTTG 505084 vi vi i v i i v i v iv ? i i v v L1M5_orf2#LIN 2847 CGACCCCTACCTCACACCATACACAAAAATTAATTCNAGATGGATCATAG 2896 chr4qtel1M 505085 ATTTAGGCATAAAGAACGAGATTATAAATAAATTAGAGGAA--CATAGGA 505132 ii iiii ii?ii i i vvvvi i -- L1M5_orf2#LIN 2897 ACCTAAATGTAAAAGNTAAAACTATAAAACTTCTAGAAGAAAACATAGGA 2946 chr4qtel1M 505133 TAGTTTATCTGTCAGACCTGTGGAGGAGGAAGGAAGAAATTTGTGACCAA 505182 v i v v ii -- - ---- ?v v i i v ---i L1M5_orf2#LIN 2947 GAATATCTTCGT--GACCT-TGG----GNTAGGCAAAGATTTCT---TAA 2986 chr4qtel1M 505183 AGAGGAACTAAAGAGCATTATTGATCACAAAATAGAACATT-------TT 505225 v vvi i i? --- i i v i v ------- v L1M5_orf2#LIN 2987 ACAGGACACAAAAAGCACNA---ACCATAAAAGAAAAAATTGATAAATTG 3033 chr4qtel1M 505226 GATTATATCAAATTAAAAAGCTTTTGTACAAACAAAACTAATGCAAACAA 505275 i ?i v v i i iv ?vvv ivi vi iv v L1M5_orf2#LIN 3034 GACTNCATCAAAATTAAAAACTTCTGCTCNTCAAAAGACACCGTTAAGAA 3083 chr4qtel1M 505276 GATCAGAAGGGAAGCAACAAACTGGGAAAACATCTTCACAATTAAAGGTT 505325 i v i v v i ? i v v ii ?vv vivv L1M5_orf2#LIN 3084 AATGAAAAGGCAAGCCACAGANTGGGAGAAAATATTTGCAANACATATAT 3133 chr4qtel1M 505326 CTGATAAAGGCCTCATTTCCAAAATGTATAGAGAATTGACTCTAATTTA- 505374 i v i v i i i i v- vi ? i - L1M5_orf2#LIN 3134 CTGACAAAGGACTCGTATCCAGAATATATAAAGAACTC-CTACAANTCAA 3182 chr4qtel1M 505375 TAAGAATTCAAGCCATTC--TCCAATTGATAAATGGTCAAAGGATATGAA 505422 ? --v v vv --i v? v v i iv L1M5_orf2#LIN 3183 TAANAA--AAAGACAAACAACCCAATANAAAAATGGGCAAAAGACTTGAA 3230 chr4qtel1M 505423 CAGACAATTTTCAGATGATGAAAATGAAACTATTACTACTCATATGAAAG 505472 v iv i v v v v?v iviii v vv i i L1M5_orf2#LIN 3231 CAGACACTTCACAAAAGAAGATATNCAAATGGCCAATAAGCACATGAAAA 3280 chr4qtel1M 505473 TGTGTTCCAAATCA 505486 vi i v v? L1M5_orf2#LIN 3281 GATGCTCAACNTCA 3294 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 42.63 CpG sites = 110, Kimura (unadjusted) = 43.72 Transitions / transversions = 1.09 (110/101) Gap_init rate = 0.05 (35 / 689), avg. gap size = 1.40 (49 / 35) 1423 32.35 1.54 1.07 chr4qtel1M 505340 505989 (494011) L1ME4c_3end#LINE/L1 4 656 (174) m_b203s551i5 8002 chr4qtel1M 505340 ATTTCCAAAATGTATAGAGAATTGACTCTAATTTATAAGAATTCAAGCCA 505389 v i?v ? i i ii v i v v vvv? v v L1ME4c_3end#L 4 ATATCTNTANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAA 53 chr4qtel1M 505390 TTCTCCAATTGATAAATGGTCAAAGGATATGAACAGACAATTTTCAGATG 505439 vv i v v i iv ? v L1ME4c_3end#L 54 GACCCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAG 103 chr4qtel1M 505440 ATGAAAATGAAACTATTAC-TACTCATATGAAAGTGTGTTCCAAATCACT 505488 - i iv ? v v-i vv i i ivi v vv i L1ME4c_3end#L 104 A-GGAAATACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCT 152 chr4qtel1M 505489 ATTGATCAGAGAAATGCAAATTAAGACAACTCCGAGATACCACTACACAC 505538 v i i ii vvi i vi i L1ME4c_3end#L 153 AGTAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGC 202 chr4qtel1M 505539 CTGTCAGATTGGCTCAGATGACAGGAAAAAATAATGATGATTGTTGGAGG 505588 i i i i vv i vvv ii vvi iviv v i v i L1ME4c_3end#L 203 CTATTAAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGCTGGCGA 252 chr4qtel1M 505589 GGATGTGGGAAAACTGGGACACTGATACATTGTTGGTTGAGTTGTGAACG 505638 ? i vi v ? v i v vi? i iv L1ME4c_3end#L 253 GGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATT 302 chr4qtel1M 505639 AATCCAACCATTCTGGAGAGAAATCTGGAATTATGCCCAAAAAGTTATCA 505688 ii v v i i v i v v i iviv i ii v L1ME4c_3end#L 303 GGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAA 352 chr4qtel1M 505689 AACTG------CCCTTTGACCCAGCAGTGCTACTCATTGGGTTATACCCC 505732 v ------ i i v i iv v iv v i i L1ME4c_3end#L 353 AAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCT 402 chr4qtel1M 505733 AAAGAGATACT---AAAGAAGGGAAAGGGACCCGTATGTGCCAAAATGTT 505779 i i v --- i i --- ii ii v i L1ME4c_3end#L 403 AAGGAAATAATTCAAAAGAAGGAAAAAG---CTATATGCACGAAGATGTT 449 chr4qtel1M 505780 TGTGGCAGCCCTGTTTGTACTGGCTAGAAGCTAGAAAATGAATGGATGCC 505829 ii v vi i i v i v i ii i vvivv ii i L1ME4c_3end#L 450 CATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTC 499 chr4qtel1M 505830 CATCAGTTGGAGAATGGTTGGGTAAATTGTGGTATATGAATGTTATGGAA 505879 v i v i ii i i v? iviv L1ME4c_3end#L 500 CAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAA 549 chr4qtel1M 505880 TATTATTGTTCTGTAAGAAATGACCAGCAGGATGAATACAGAGAGGTTTG 505929 vvvv ii v i iv vi v v v iiv viiiv L1ME4c_3end#L 550 TATTATGCAGCCATTAAAAATGATAATTATGAAGACTATGTAGCAACATG 599 chr4qtel1M 505930 GAGAGAATTACATGAACTGATGCTGAGCGAAATGAGCAGAACCAGGAAAT 505979 i ivi -i vv i i i i vi -i vi L1ME4c_3end#L 600 GAAAATGTT-TATGATATAATGTTAAGTGAAAAAAGCAGAA-TACAAAAT 647 chr4qtel1M 505980 CATTATATAC 505989 ii- ? L1ME4c_3end#L 648 TG-TATNTAC 656 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 42.96 CpG sites = 115, Kimura (unadjusted) = 44.39 Transitions / transversions = 1.24 (115/93) Gap_init rate = 0.02 (10 / 649), avg. gap size = 1.70 (17 / 10) 16 3.96 3.85 0.00 chr4qtel1M 506386 506411 (493589) (AAGA)n#Simple_repeat 1 27 (0) m_b203s252i11 8003 chr4qtel1M 506386 AATAAA-AAAGAAAGAAAGAAAGAAAG 506411 v - (AAGA)n#Simpl 1 AAGAAAGAAAGAAAGAAAGAAAGAAAG 27 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.04 (1 / 25), avg. gap size = 1.00 (1 / 1) 13 4.76 0.00 4.35 chr4qtel1M 507102 507125 (492875) (CCCT)n#Simple_repeat 1 23 (0) m_b203s252i12 8004 chr4qtel1M 507102 CCCTCCCTCCCTCCACCCCCTCCC 507125 - i (CCCT)n#Simpl 1 CCCTCCCTCCCTCC-CTCCCTCCC 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 15 18.80 3.85 3.85 chr4qtel1M 508077 508128 (491872) (GTGGTA)n#Simple_repeat 1 52 (0) m_b203s252i13 8005 chr4qtel1M 508077 GTGGTAGTGGTAGTGGACAGAAGGA-AAATACGTGGTAGTGG-AGGGGTA 508124 -i vi v -vii - - v (GTGGTA)n#Sim 1 GTGGTAGTGGTAGTGG-TAGTGGTAGTGGTA-GTGGTAGTGGTAGTGGTA 48 chr4qtel1M 508125 GTGG 508128 (GTGGTA)n#Sim 49 GTGG 52 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.08 (4 / 51), avg. gap size = 1.00 (4 / 4) 31 5.56 0.00 0.00 chr4qtel1M 508647 508684 (491316) (TGTGAG)n#Simple_repeat 1 38 (0) c_b203s251i4 8006 chr4qtel1M 508647 TGTGAGTGTGGGTGTGGGTGTGAGTGTGAGTGTGAGTG 508684 i i (TGTGAG)n#Sim 1 TGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTGTGAGTG 38 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 47 7.24 0.00 0.00 chr4qtel1M 508930 508987 (491013) (GT)n#Simple_repeat 1 58 (0) c_b203s251i5 8007 chr4qtel1M 508930 GTGTGTGTTTGTGTGTGTGTGTGTGTGTGTCTGTGTGTCTGTGTGTGTGT 508979 v v v (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50 chr4qtel1M 508980 ATGTGTGT 508987 i (GT)n#Simple_ 51 GTGTGTGT 58 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0) 13 21.81 2.70 0.00 chr4qtel1M 516637 516673 (483327) (GCA)n#Simple_repeat 1 38 (0) m_b203s252i14 8008 chr4qtel1M 516637 GCAGCAGGAGGGGC-GCAGCAGCTGGGGCCGCAGCAGC 516673 v vi - v vi v (GCA)n#Simple 1 GCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGC 38 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 30 19.52 0.00 0.00 chr4qtel1M 516961 517024 (482976) (TGTGGG)n#Simple_repeat 1 64 (0) m_b203s252i15 8009 chr4qtel1M 516961 TGTGGGTGTGTGTGGGGATGTGGGTGTGGGTGTGAGTGTGAGTGAAGCTG 517010 v v i i i vi v (TGTGGG)n#Sim 1 TGTGGGTGTGGGTGTGGGTGTGGGTGTGGGTGTGGGTGTGGGTGTGGGTG 50 chr4qtel1M 517011 TGGGGCTGCGTGTG 517024 vv v (TGTGGG)n#Sim 51 TGGGTGTGGGTGTG 64 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0) 96 28.90 5.49 1.63 chr4qtel1M 517895 518368 (481632) (GAGAGA)n#Simple_repeat 1 492 (0) m_b203s252i16 8010 chr4qtel1M 517895 GAG-GAGA-AGGGAATGGGGGAGAGGGACACACACAGAGAAACAGAGATA 517942 - - i iv i i i v v v v i v v (GAGAGA)n#Sim 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr4qtel1M 517943 GAAAGAGACAGAAATAGAGA-AGCTGAGAAAGAGACATACACAAACACAC 517991 i v i v - -v i v v v v i v v v (GAGAGA)n#Sim 51 GAGAGAGAGAGAGAGAGAGAGAG-AGAGAGAGAGAGAGAGAGAGAGAGAG 99 chr4qtel1M 517992 AGAGAAAGAGTGACAAGGAGAGATAGAAATGGAAATGGAGAGGGAGAGAA 518041 i v v ii v i vi i vi i i (GAGAGA)n#Sim 100 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 149 chr4qtel1M 518042 AGGAAGAGACAGAGATAAAGAGATAGAG-GAGA-AAAGATGCAGAAAGAA 518089 ii v v i v - - i - - i i (GAGAGA)n#Sim 150 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA-G-AGAGAGAG 197 chr4qtel1M 518090 AAAGCTAGTAATGAG-GAGAGATATTGGAAGACAGAGAGAAAGACAGACA 518138 i vv - iv - v vv ii v i v v (GAGAGA)n#Sim 198 AGAGAGAG-AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 246 chr4qtel1M 518139 GAGATAGAGGGGGCGCAAGAG-GGGGGAGA-AGAAAAATA-AGA-AGAGG 518184 v i i v vi - i i - i i v - - i (GAGAGA)n#Sim 247 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 296 chr4qtel1M 518185 AAGAGAAAGA-AGAG-GAGGAAGA-AGTAGAG-GAG-GAG-GAGGAAGA- 518227 i i - - ii - - - - - ii - (GAGAGA)n#Sim 297 GAGAGAGAGAGAGAGAGAGAGAGAGAG-AGAGAGAGAGAGAGAGAGAGAG 345 chr4qtel1M 518228 AGA-AGAG-GAG-GAGGAAGAGGAAGAGGAAGAAAGACAGAGACAG-GAG 518273 - - - ii ii ii i v v - (GAGAGA)n#Sim 346 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 395 chr4qtel1M 518274 -GTAACAAAGATGGAGGGAAAGAGATGCAGAGACAAAGAGCTGA-AGAG- 518320 - vi v i vi i i - - v i -v - - (GAGAGA)n#Sim 396 AGAGAGAGAGAGAGAGAGAGAGAGA-G-AGAGAGAGAGAG-AGAGAGAGA 442 chr4qtel1M 518321 GAG-GAGAGATAGAGGGAGAGAGAGAGACAGAGGGGCAGAGACAGA-AGA 518368 - v i v i iv v - (GAGAGA)n#Sim 443 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 492 Matrix = Unknown Transitions / transversions = 1.22 (60/49) Gap_init rate = 0.07 (33 / 473), avg. gap size = 1.03 (34 / 33) 33 0.00 0.00 0.00 chr4qtel1M 519188 519215 (480785) (CA)n#Simple_repeat 1 28 (0) c_b204s251i0 8011 chr4qtel1M 519188 CACACACACACACACACACACACACACA 519215 (CA)n#Simple_ 1 CACACACACACACACACACACACACACA 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 181 28.35 1.61 3.28 chr4qtel1M 520011 520072 (479928) C L2d2_3end#LINE/L2 (18) 537 477 m_b204s601i0 8012 chr4qtel1M 520011 TATCGATTAGGCACCTGCTGTGTCCTAGGCACTAGTACATAGGC-CTCCA 520059 iv ii i i v v - i - - vii C L2d2_3end#LIN 537 TATTTATTGAGCGCCTACTGTGTGCAAGGCACT-GTGC-TAGGCGCTGTG 490 chr4qtel1M 520060 GTGAATGGGAAGA 520072 v i ivi C L2d2_3end#LIN 489 GGGGATACAAAGA 477 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.27 CpG sites = 11, Kimura (unadjusted) = 37.01 Transitions / transversions = 1.83 (11/6) Gap_init rate = 0.05 (3 / 61), avg. gap size = 1.00 (3 / 3) 77 9.51 0.00 0.00 chr4qtel1M 521306 521417 (478583) (GTGTGT)n#Simple_repeat 1 112 (0) m_b204s252i1 8013 chr4qtel1M 521306 GTGTTTGTGTGTGTGTGTATATGTGTGTGTGTGTGTGTGTGTGTGTGTGT 521355 v i i (GTGTGT)n#Sim 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50 chr4qtel1M 521356 GTGTGTGTGTGTTTGTGTTTGTGTGTGTGTGTTTGTGTATGTTTGTGTTT 521405 v v v i v v (GTGTGT)n#Sim 51 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 100 chr4qtel1M 521406 GTGTGTGTGGGT 521417 v (GTGTGT)n#Sim 101 GTGTGTGTGTGT 112 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.00 (0 / 111), avg. gap size = 0.0 (0 / 0) 504 28.57 6.12 0.00 chr4qtel1M 523533 523679 (476321) C MIRb#SINE/MIR (73) 195 40 m_b204s601i1 8014 chr4qtel1M 523533 TTATTTAGCACCCGCTACAACTCTGTGTGGTAGGTATTATTTTT---ACT 523579 i iiv i i v i i v v i--- i C MIRb#SINE/MIR 195 TCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATTATCCCCATT 146 chr4qtel1M 523580 TTACAATTGAGGAAGCTGAGGC------AGATGAAGTGACTCACCCAGGG 523623 iv i ------ i v i ii i C MIRb#SINE/MIR 145 TTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGG 96 chr4qtel1M 523624 TGACACAGATTTTAAGGATCTGAAGCCAGATTCAAACTTGGTTTTTCCTG 523673 v v vv viv v iv vi i iii v i vi C MIRb#SINE/MIR 95 TCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTG 46 chr4qtel1M 523674 ACTCCA 523679 C MIRb#SINE/MIR 45 ACTCCA 40 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.80 CpG sites = 25, Kimura (unadjusted) = 37.00 Transitions / transversions = 1.47 (25/17) Gap_init rate = 0.01 (2 / 146), avg. gap size = 4.50 (9 / 2) 358 29.16 5.79 0.79 chr4qtel1M 523575 523695 (476305) C MIR3#SINE/MIR (64) 144 18 m_b204s601i2 8014 chr4qtel1M 523575 TTACTTTACAATTGAGGAAGCTGAGGC------AGATGAAGTGACTCACC 523618 i i iv i ------ i ii C MIR3#SINE/MIR 144 TCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCC 95 chr4qtel1M 523619 CAGGGTGACACAGATTTTAAGGATCTGAAGCCAGATTCAAACTTGGTTTT 523668 i v v?vv v viv v iv vi i vi iii -v i C MIR3#SINE/MIR 94 CAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAG-GTC 46 chr4qtel1M 523669 TCCTGACTCCATGCCCA-GCTGTCTCTG 523695 vv i i- v C MIR3#SINE/MIR 45 TCCTGACTCCCAGTCCGTGCTCTCTCTG 18 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.70 CpG sites = 19, Kimura (unadjusted) = 38.07 Transitions / transversions = 1.19 (19/16) Gap_init rate = 0.03 (3 / 120), avg. gap size = 2.67 (8 / 3) 182 30.61 0.00 0.00 chr4qtel1M 523690 523738 (476262) MIRc#SINE/MIR 114 162 (106) m_b204s601i3 8015 chr4qtel1M 523690 TCTCTGAGACCAGGGCTCCTCATCTGTCAAGGGGAAATCATCAGGCCTG 523738 v ivi vi v iv ii v v vi MIRc#SINE/MIR 114 TCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTG 162 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.68 CpG sites = 7, Kimura (unadjusted) = 39.68 Transitions / transversions = 0.88 (7/8) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 293 32.24 5.32 1.02 chr4qtel1M 524239 524332 (475668) L2c_3end#LINE/L2 369 466 (12) m_b204s601i4 8016 chr4qtel1M 524239 CCCCCAGCCCAGAAGCTCTTTGAGGGCAGAGATCATTGTCCTCCCTGTGC 524288 v i v iivi i i i i- i viiii vi L2c_3end#LINE 369 CCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCG-TGTCTTATTCATCT 417 chr4qtel1M 524289 TTGTTTTCCCAGC-----ACACATAGTAGGTGCTGGAGAAGCGCTGGTT 524332 v i -----i i vi v ii i v L2c_3end#LINE 418 TTGTATCCCCAGCGCCTGGCACATAGTAGGCGCTCAATAAATGTTTGTT 466 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.01 CpG sites = 21, Kimura (unadjusted) = 45.12 Transitions / transversions = 2.33 (21/9) Gap_init rate = 0.02 (2 / 93), avg. gap size = 3.00 (6 / 2) 201 24.32 22.58 2.70 chr4qtel1M 524251 524343 (475657) L2d_3end#LINE/L2 401 511 (5) m_b204s601i5 8016 chr4qtel1M 524251 AAGCTCTTTGAGGGCAGAGATCATTGTCCT---CCCTGTGCTTGTTTTCC 524297 i i i - i --- i? v v? i ii L2d_3end#LINE 401 AAGCTCCTTGAGGGCAGGGACCA-TGTCTTATACTNTTTTNTCGTTCCCC 449 chr4qtel1M 524298 -CAGC-----------------ACACATAGTAGGTGCTGGAGAAGCGCTG 524329 - -----------------i i vi v iii v L2d_3end#LINE 450 ACAGCGCCTAGCACAGTGCTGAGCACATAGTAGGCGCTCAATAAATACTT 499 chr4qtel1M 524330 GTTAGCACTGGTTG 524343 i-- i i L2d_3end#LINE 500 GTTG--ATTGATTG 511 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.75 CpG sites = 17, Kimura (unadjusted) = 32.29 Transitions / transversions = 3.40 (17/5) Gap_init rate = 0.07 (6 / 92), avg. gap size = 4.00 (24 / 6) 184 33.02 7.69 4.48 chr4qtel1M 524585 524714 (475286) C L3#LINE/CR1 (252) 3847 3714 m_b204s601i6 8017 chr4qtel1M 524585 CCTAGCTCGGGCCTCTGGAGCCAAGCAAATCCAGGCTGGCCCCCCTCCC- 524633 i v v vi i viv v iii i i - C L3#LINE/CR1 3847 CCTAGTTCTGCCCTCTGGAGCCACACAGAATAAGTCTAATCCCTCTTCCA 3798 chr4qtel1M 524634 CAGGCTGGAGACGGCCCC-----TACCTCCAGATAGC--GCGTTTCGCCA 524676 v------ i i----- ii vv i --v i v v v C L3#LINE/CR1 3797 CAT------GACAGCCCTTCAAATATTTGAAGACAGCTATCATGTCTCCT 3754 chr4qtel1M 524677 TCA--TTTTCTTGTCTGCAAGCTGAGCAGCACCAGCCCCT 524714 ii -- i iv v i i i v v ii C L3#LINE/CR1 3753 CTAAGTCTTCTCTTCTCCAGGCTAAACATCCCCAGTTCCT 3714 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.15 CpG sites = 24, Kimura (unadjusted) = 45.15 Transitions / transversions = 1.41 (24/17) Gap_init rate = 0.08 (10 / 129), avg. gap size = 1.60 (16 / 10) 157 20.23 0.31 0.63 chr4qtel1M 524789 525108 (474892) (AC)n#Simple_repeat 1 319 (0) m_b204s252i2 8018 chr4qtel1M 524789 ACACACACACACACACACACACACACACACACACTCTCTCACTCACACAC 524838 v v v v (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50 chr4qtel1M 524839 ACACACACACACTCTCTCACACATACACACACTCACACACACACACACAC 524888 v v v i v (AC)n#Simple_ 51 ACACACACACACACACACACACACACACACACACACACACACACACACAC 100 chr4qtel1M 524889 ACACTCTCACTCACACAATTCCATACACACACTCACA-ATCCCCCCACAC 524937 v v v vviv i v - iv v v (AC)n#Simple_ 101 ACACACACACACACACACACACACACACACACACACACACACACACACAC 150 chr4qtel1M 524938 TCACACACACTCTCACACATACACACATACACTCTTTCACACACACACAT 524987 v v v i i v viv i (AC)n#Simple_ 151 ACACACACACACACACACACACACACACACACACACACACACACACACAC 200 chr4qtel1M 524988 TCTCACTCTCACACACACACACTCACACACACACTTACAATCTCACACAC 525037 v v v v v vi vv v (AC)n#Simple_ 201 ACACACACACACACACACACACACACACACACACACACACACACACACAC 250 chr4qtel1M 525038 TCACACACTATCACATACACTCTTACACACACACATTCACACTCATACAC 525087 v - - i v vi iv v i (AC)n#Simple_ 251 ACACACAC-A-CACACACACACACACACACACACACACACACACACACAC 298 chr4qtel1M 525088 ACACCCTGACACATACAAACA 525108 v vv i v (AC)n#Simple_ 299 ACACACACACACACACACACA 319 Matrix = Unknown Transitions / transversions = 0.33 (14/42) Gap_init rate = 0.01 (3 / 319), avg. gap size = 1.00 (3 / 3) 13 12.12 0.00 3.57 chr4qtel1M 525405 525433 (474567) (TCCT)n#Simple_repeat 1 28 (0) m_b204s252i3 8019 chr4qtel1M 525405 TCTTTTCTGTCCTTCCGTCCTTCCTTCCT 525433 i i - v (TCCT)n#Simpl 1 TCCTTCCT-TCCTTCCTTCCTTCCTTCCT 28 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1) 194 18.18 0.00 0.00 chr4qtel1M 525741 525773 (474227) MIR#SINE/MIR 116 148 (114) m_b204s601i7 8020 chr4qtel1M 525741 TGCCTCAGTGTTCTCATCTGCCAAATGGGGGCA 525773 v i iv ii MIR#SINE/MIR 116 TGCCTCAGTTTCCTCATCTGTAAAATGGGGATA 148 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 21.28 CpG sites = 4, Kimura (unadjusted) = 21.28 Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 2319 27.93 0.00 0.13 chr4qtel1M 526680 527475 (472525) C L1M5_orf2#LINE/L1 (1134) 2160 1366 m_b204s551i0 8021 chr4qtel1M 526680 TTCTAATAACTTTTTAGTAGAATCTTTGGGGTTCTCTAAGTATACCATCA 526729 i ii ? v v ? i i v ? v C L1M5_orf2#LIN 2160 TTCTAGTAGTTTNTTTGTAGATTCTTTNGGATTTTCTACGTANACAATCA 2111 chr4qtel1M 526730 TATCGTCAGCAAAGAGTGATAATTTGGTTTCCTCATTGCCTGTTCTTATT 526779 i i v i v i? i i vi i v v vi ii v C L1M5_orf2#LIN 2110 TGTCATCTGCGAATAANGACAGTTTTATTTCTTCCTTTCCAATCTTTATG 2061 chr4qtel1M 526780 CCATTAATCTCTTTCTCAGCTCTTATTGCCAAAGCTAGCATTTCTAATAC 526829 v v i i vvvi vvvi v ii i i C L1M5_orf2#LIN 2060 CCTTTTATTTCTTTTTCTTGCCTTATTGCACTGGCTAGGACCTCCAGTAC 2011 chr4qtel1M 526830 AATATTAAATAGTAACGGTGATAGTGGGCAACCTTGTTTCATTCCTGATC 526879 i i v ii ? i i v i ii i C L1M5_orf2#LIN 2010 AATGTTGAATAGAAGTGGTGANAGCGGACATCCTTGTCTTGTTCCCGATC 1961 chr4qtel1M 526880 TTAATGGGAATGGTTGAAATTTTTCCCCATTACATATGATGCTTACTGCT 526929 iv v v? vv i ? v vi i ?i iv C L1M5_orf2#LIN 1960 TTAGGGGGAAAGCNTTCAGTNTTTCACCATTAAGTATGATGTTNGCTGTA 1911 chr4qtel1M 526930 GGTTTTAAATAGATGCTACTGATTATTTTAAGGAAAAGTCCATTTATTCC 526979 vvi ivi v i vv i ivvi v i C L1M5_orf2#LIN 1910 GGTTTTTCGTAGATGCCCTTTATCAGGTTGAGGAAGTTCCCTTCTATTCC 1861 chr4qtel1M 526980 TATATTCTCAAGTGTTTTTAATAGGAATGGATGTTGGATTTTATCAAATG 527029 vv viii v vi v i i i C L1M5_orf2#LIN 1860 TAGTTTGCTGAGAGTTTTTATCATGAATGGGTGTTGAATTTTGTCAAATG 1811 chr4qtel1M 527030 CTTTTTCTGCATCTATTGAGGTGATCATATGGTTTTTGTTAATTTGGTTA 527079 i i v ivv vvvi i C L1M5_orf2#LIN 1810 CTTTTTCTGCATCTATTGAGATGATCATATGATTTTTCTCCTTTATTCTG 1761 chr4qtel1M 527080 TTAATATGGCCAATTATACTGATAGTTTTCCTACTATTGAACCAGCCCTG 527129 iv i i v v i v v i i i i C L1M5_orf2#LIN 1760 TTAATATGGTGAATTACATTGATTGATTTTCGAATGTTAAACCAACCTTG 1711 chr4qtel1M 527130 CATTCTTGGTATAAATCCTACTTGATCATAGTGTATTATCCTGGGGATGA 527179 i v i i i ii vvvv iv C L1M5_orf2#LIN 1710 CATTCCTGGGATAAACCCCACTTGGTCATGATGTATTATCCTTTTTATAT 1661 chr4qtel1M 527180 TTTTCTGTAGTCTTTTTGCTAATATCTTATTTAAGATTTTAGCATCAATA 527229 v v v v vv i i ? i v v i C L1M5_orf2#LIN 1660 ATTGCTGGATTCGATTTGCTAATATTTTGTTNAGGATTTTTGCATCTATG 1611 chr4qtel1M 527230 TTCATTAGGGAGATTGGTCTATAATTTTCTTTCTCTGTTTTCAGCCTACC 527279 v v i iii vv vvvii ii C L1M5_orf2#LIN 1610 TTCATGAGGGATATTGGTCTGTAATTTTCTTTTCTTGTAATGTCTTTGTC 1561 chr4qtel1M 527280 TGGTTTAGGTATCAGTACCATGTCTGTGTCATAAAAGGAATTTGGTAGGA 527329 ? v vii? iiv iv v i v v vi C L1M5_orf2#LIN 1560 NGGTTTTGGTATCAGGGTNATGCTGGCCTCATAAAATGAGTTGGGAAGTG 1511 chr4qtel1M 527330 CTCCTTCATTCCCTGTTTTTTCAAATAGTTTATAAAGCATTGGGGCAAAT 527379 i i v ii i i vi v i iv iv viiv v C L1M5_orf2#LIN 1510 TTCCCTCTTTTTCTATTTTCTGGAAGAGTTTGTGTAAGATTGGTATTATT 1461 chr4qtel1M 527380 TGTTCTTTGAATGTTTGGTAGAATTCACATGTAAATCCATCTGGTCCTGG 527429 v i i vv i v v C L1M5_orf2#LIN 1460 TCTTCCTTAAATGTTTGGTAGAATTCACCAGTGAAGCCATCTGGGCCTGG 1411 chr4qtel1M 527430 GGATTTTTTTTTTAGGGAGTTGATTAATAGTTTGTTCTATTTCTTT 527475 i - i v i i v vv viivvi v C L1M5_orf2#LIN 1410 AG-TTTTCTTTGTGGGAAGGTTTTTAATTACAAATTCAATTTCTTT 1366 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 35.29 CpG sites = 116, Kimura (unadjusted) = 36.09 Transitions / transversions = 1.09 (116/106) Gap_init rate = 0.00 (1 / 795), avg. gap size = 1.00 (1 / 1) 120 24.94 5.17 2.72 chr4qtel1M 527602 527728 (472272) (AGACAG)n#Simple_repeat 1 134 (381) m_b204s252i4 8022 chr4qtel1M 527602 AGACAGAGACAGACAGAGTGAGAAAGTAAGAG-CA-AGAGAGAGACAGAG 527649 v v v v i vv - - v (AGACAG)n#Sim 1 AGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAG 50 chr4qtel1M 527650 AC--ACACAGAGAGATAGACAGAAATCCATAG-GA-AAACAGAGA-TG-G 527693 -- v v v i -- v -v - i -v - (AGACAG)n#Sim 51 ACAGAGACAGAGACAGAGACAGAGA--CAGAGACAGAGACAGAGACAGAG 98 chr4qtel1M 527694 AAAGAGAC--AGACAGAGACAGAGTTAGAGATGGAGG 527728 v -- vi ii - (AGACAG)n#Sim 99 ACAGAGACAGAGACAGAGACAGAGACAGAGACAGA-G 134 Matrix = Unknown Transitions / transversions = 0.40 (6/15) Gap_init rate = 0.09 (11 / 126), avg. gap size = 1.18 (13 / 11) 71 4.18 0.00 0.00 chr4qtel1M 527729 527802 (472198) (GA)n#Simple_repeat 1 74 (0) c_b204s251i1 8023 chr4qtel1M 527729 GAGACAGAGAGAGAGAGAGAGACAGAGAGAGAGACAGAGAGAGAGAGAGA 527778 v v v (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr4qtel1M 527779 GAGAGAGAGAGAGAGAGAGAGAGA 527802 (GA)n#Simple_ 51 GAGAGAGAGAGAGAGAGAGAGAGA 74 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 73), avg. gap size = 0.0 (0 / 0) 120 24.94 5.17 2.72 chr4qtel1M 527803 527868 (472132) (AGACAG)n#Simple_repeat 135 196 (319) m_b204s252i4 8024 chr4qtel1M 527803 TCCATAGAACAGAGAGATGGGA-AGAGATAGAGACAGACACACACATGCA 527851 -v v - v - i - i v v v -- (AGACAG)n#Sim 135 -ACAGAG-ACAGAGACA-GAGACAGAGACAGAGACAGAGACAGAGA--CA 179 chr4qtel1M 527852 CACACACACACACACAC 527868 v v v v v v (AGACAG)n#Sim 180 GAGACAGAGACAGAGAC 196 Matrix = Unknown Transitions / transversions = 0.17 (2/12) Gap_init rate = 0.09 (6 / 65), avg. gap size = 1.00 (6 / 6) 53 0.00 0.00 0.00 chr4qtel1M 527869 527913 (472087) (AG)n#Simple_repeat 1 45 (0) c_b204s251i2 8025 chr4qtel1M 527869 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 527913 (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 45 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 120 24.94 5.17 2.72 chr4qtel1M 527914 528221 (471779) (AGACAG)n#Simple_repeat 197 514 (1) m_b204s252i4 8026 chr4qtel1M 527914 CATATAGAGCTCA-ATGGAGACACACAGAGAGAGATAGAGACACATATAG 527962 v v i -v - viv v v v i v v i (AGACAG)n#Sim 197 GAGACAGAG-ACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAG 245 chr4qtel1M 527963 AGACAGAG-CA-ATCCATAGA-A-AAACAG-GAAAGAGACAGAAACAGAC 528007 - - vv v - - i - v i v (AGACAG)n#Sim 246 AGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAG 295 chr4qtel1M 528008 ACAGAGATAGAGAGCA-ATCAAAAGCAATACACCCTGAGACAGACAGA-A 528055 i - - vvv i vv v v vvv v v - (AGACAG)n#Sim 296 ACAGAGACAGAGA-CAGAGACAGAGACAGAGACAGAGACAGAGACAGAGA 344 chr4qtel1M 528056 -AGAGATCTGTAGA-A-AAACAGAGAGATGGAAAGAGACAGAGACAGAGT 528102 - - v - - - i v vi v v (AGACAG)n#Sim 345 CAGAGA-CAG-AGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGA 392 chr4qtel1M 528103 CAGAGATAGAGTGAGAGGAAGAGAGATACACAGAGACAGACACACAGAGA 528152 i vv iv v v v v v v (AGACAG)n#Sim 393 CAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACA 442 chr4qtel1M 528153 GAGACAGACACAGAGATAAAGAGTGAGGGAGAGA-GGA-AAAGGGAAAGG 528200 v i i vv iv -i - v i v - (AGACAG)n#Sim 443 GAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACA-G 491 chr4qtel1M 528201 AGACACAG--AGAGAAAGAGACA 528221 v -- v (AGACAG)n#Sim 492 AGACAGAGACAGAGACAGAGACA 514 Matrix = Unknown Transitions / transversions = 0.35 (17/49) Gap_init rate = 0.06 (19 / 307), avg. gap size = 1.05 (20 / 19) 16 19.47 2.56 2.56 chr4qtel1M 529047 529085 (470915) (TG)n#Simple_repeat 1 39 (0) m_b204s252i5 8027 chr4qtel1M 529047 TGTGTATGTGTGTGTGTGTGCACGTGCATGTGCTG-GTGT 529085 i iii ii - - (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG-TGTGTGT 39 Matrix = Unknown Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2) 370 30.53 1.64 3.33 chr4qtel1M 529982 530103 (469897) MIRc#SINE/MIR 30 149 (119) m_b204s601i8 8028 chr4qtel1M 529982 CTGGACTTGGGGCTGGGAAGCCCTCAGTTCCAATCCT-GCATAGACACTT 530030 i iii v vi v i i- viv v MIRc#SINE/MIR 30 CTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTT 79 chr4qtel1M 530031 CTTAGAATCCTGTGTGACCCTGAGCAAATCCCCTTACTTC-CTGGGCCTT 530079 vi ---- i i i v i v i - i i MIRc#SINE/MIR 80 ACTAG----CTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTC 125 chr4qtel1M 530080 GGTGCCTCCCCTTGTCCAATGGAG 530103 i vi ii vii vv i MIRc#SINE/MIR 126 AGTTTCCTCATCTGTAAAATGGGG 149 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.38 CpG sites = 23, Kimura (unadjusted) = 40.88 Transitions / transversions = 1.77 (23/13) Gap_init rate = 0.05 (6 / 121), avg. gap size = 1.00 (6 / 6) 292 29.84 12.27 3.39 chr4qtel1M 529984 530146 (469854) MIR3#SINE/MIR 30 206 (2) m_b204s601i9 8028 chr4qtel1M 529984 GGACTTGGGGCTGGGAAGCCCTCAGTTCCAATCCTG-CATAGACACTTCT 530032 v i iii - v vi i i i - viv v vvi MIR3#SINE/MIR 30 GGACTGGGAGTCAGGA-GACCTGGGTTCTAGTCCCGGCTCTGCCACTAAC 78 chr4qtel1M 530033 TAGAATCCTGTGTGACCCTGAGCAAATCCCCTTACTTC-CTGGGCCTTGG 530081 ? ---- i i i v i i i - ii MIR3#SINE/MIR 79 TNG----CTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAG 124 chr4qtel1M 530082 TGCCTCCCCTTGTCCAATG--------------GAGGCTCTCTGGGGTCC 530117 vi ii vii vv -------------- v v ii MIR3#SINE/MIR 125 TTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCC 174 chr4qtel1M 530118 CTT-CAGCATCTGG---ACTATGATCTCAGGGT 530146 - - i---v iii v i MIR3#SINE/MIR 175 CTTCCAGC-TCTGACATTCTATGATTCTATGAT 206 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.04 CpG sites = 30, Kimura (unadjusted) = 40.17 Transitions / transversions = 1.76 (30/17) Gap_init rate = 0.07 (11 / 162), avg. gap size = 2.36 (26 / 11) 16 0.00 0.00 0.00 chr4qtel1M 532881 532897 (467103) (T)n#Simple_repeat 1 17 (0) m_b204s252i6 8029 chr4qtel1M 532881 TTTTTTTTTTTTTTTTT 532897 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTT 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 340 20.69 3.45 20.00 chr4qtel1M 532898 533042 (466958) C MIRb#SINE/MIR (139) 129 5 m_b204s601i10 8030 chr4qtel1M 532898 TGAGGCAATTAG---GGTTAAGTGATTTATTTGCCCTGGGTCACA--GCT 532942 -- i --- i i ---- vi -- C MIRb#SINE/MIR 129 TGAGGC--TCAGAGAGGTTAAGTAACTT----GCCCAAGGTCACACAGCT 86 chr4qtel1M 532943 AGGAAGTATTAAGTGTGTGAGGCCTGAGGCCTGAGATTTGAACTCAGGTT 532992 v ------------- --- iv i i i i i C MIRb#SINE/MIR 85 AGTAAGT-------------GGC---AGAGCCGGGATTCGAACCCAGGTC 52 chr4qtel1M 532993 CTTCTTACTTCAGGGCTGGTGCTCTATCCACTGTGCCACCTAGCTGCCCC 533042 iv v i ii iv v ii --- C MIRb#SINE/MIR 51 TGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCACCAC---GCTGCCCC 5 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 21.78 CpG sites = 17, Kimura (unadjusted) = 24.00 Transitions / transversions = 2.43 (17/7) Gap_init rate = 0.19 (27 / 144), avg. gap size = 1.11 (30 / 27) 197 32.76 1.72 0.00 chr4qtel1M 534464 534521 (465479) MIRc#SINE/MIR 90 148 (120) m_b204s601i11 8031 chr4qtel1M 534464 TAAGCCTGGGTGAGCCATTTAGCCATGTT-AGCCTTAATTTCTCCAAATG 534512 i v i ii i i i vivi - i i ii vv MIRc#SINE/MIR 90 TGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTG 139 chr4qtel1M 534513 TAAAATGAG 534521 i MIRc#SINE/MIR 140 TAAAATGGG 148 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.81 CpG sites = 14, Kimura (unadjusted) = 46.81 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.02 (1 / 57), avg. gap size = 1.00 (1 / 1) 556 34.93 15.12 0.81 chr4qtel1M 535142 535571 (464429) C L3#LINE/CR1 (2932) 1167 677 m_b204s601i12 8032 chr4qtel1M 535142 CTGGCACTTTCTATGGCATCTAGTGGTG--GCTGGAGGTGGAAACGTTTC 535189 ?i iii i i i ii vv i-- i vv vv iv iv i C L3#LINE/CR1 1167 CTGNTATCCTCCATAGTATCCGGTTTTACAGTTTTATCTGGGCATTTTTT 1118 chr4qtel1M 535190 TTCCCTGCTTTCCA-TTGTGGTT---AGATCTGTGAGGTACCAAGTCAGC 535235 i v ii v - vii --- vi v vi--- i i i C L3#LINE/CR1 1117 TTCCTTTCCCTCAAATTTCAGTTTAAAGTCCTCTTG---ATCAGGTCGGC 1071 chr4qtel1M 535236 G-----CCAGGCTGCCA-GTCCTTGCT--TGCTCCCGGGGTGTACGCCAT 535277 ----- ? ? viv - i v i-- vi vi i i i v i C L3#LINE/CR1 1070 GAGTCTCCNGNCAAACACGTTCTTCCCGGTCTTCGTGAGATGCACTCCGT 1021 chr4qtel1M 535278 CCCTGGCCAGGAGCCTGAGGTTCAAGT-------GCCA--ATCTCGAGA- 535317 ? iivv vi ------- --i iv i - C L3#LINE/CR1 1020 CCCTNGCCAGGAGCCCATCGTTCTGGTATCNTAAGCCATGGTCCAGAAAA 971 chr4qtel1M 535318 -----TGGTTTTCTTCAACA---------------GCTGCTCCCTTCTCA 535347 ----- vv v i --------------- i v i C L3#LINE/CR1 970 CCAAATCCTGTTCTTCGACACCATCTACGTAGCCAGCTGTTCACTTCCCA 921 chr4qtel1M 535348 CACCTGCCACCCT-------GGCCATTA--GTCAGCC------ACAGATA 535382 i i iv vii -------i i iv --v i i------ v i C L3#LINE/CR1 920 TATCCTCCTTTCTCTTCCAAAGTCACGACCTTCAACTGGAAGAAGAGATG 871 chr4qtel1M 535383 AGAACACCACCTGTGTCCTGGGGTCTTT-AGTTCCTTGCCCAAGACTTAG 535431 i i ivii i - i i i vi C L3#LINE/CR1 870 AAAACACCACCTGTGCCCCCAAGTCCTTCAGTTTCCTGCCCAGGACTTCA 821 chr4qtel1M 535432 TCATCCTTGGCAGGGCTTTCAGGGCTCCCTTGGGCAGCAGCCTTCGTGCC 535481 vvi vi i viiv v vi i i i iv i v iiv v v C L3#LINE/CR1 820 AAGTCACTAGAGATGCATTCCAGGTTTCTTCTGACTGTGTCATTCGTTCC 771 chr4qtel1M 535482 CACATGAGTCACCAGTGAGAAAG-AGCTGTCATCCACCTGGACGAGTCAC 535530 i i v - vii - v iv vivi v i vi C L3#LINE/CR1 770 CACGTGAATCAGCAG-GAGTGGGTAGCGGTCGGCGGGTTTGATGAGTCTT 722 chr4qtel1M 535531 GGAAGGTTCTCTGTCACATCTGGGCTG---GCCTCAGG-AGACAG 535571 v i i i v v i--- ii - C L3#LINE/CR1 721 GGCAGGCTCTCCGTCACGTCTCGGATACACGCTCCAGGAAGACAG 677 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.32 CpG sites = 91, Kimura (unadjusted) = 50.09 Transitions / transversions = 1.57 (91/58) Gap_init rate = 0.05 (22 / 429), avg. gap size = 3.14 (69 / 22) 308 32.65 9.82 2.29 chr4qtel1M 536062 536224 (463776) C MIR#SINE/MIR (25) 237 63 m_b204s601i13 8033 chr4qtel1M 536062 CTGACTACTGACCTGACAGTCTGTGAAGCGCTCTATATCCAGGAACTCAT 536111 v ivvi v i v v viv i i vi vv C MIR#SINE/MIR 237 CTTACTATGTGCCAGGCACTGTTCTAAGCGCTTTACATGTATTAACTCAT 188 chr4qtel1M 536112 GTTGTCCCCACGATACCCTCA--GGGTCACCGCTTGCTAGTAAAATCTCT 536159 v vi i i i v ii --i viv---- i v vv i i C MIR#SINE/MIR 187 TTAATCCTCACAACAACCCTATGAGGTAGG----TACTATTATTATCCCC 142 chr4qtel1M 536160 ATTCGACAGCTGAGGAAACTGAGTC---------TGAAGCACCT--CCTG 536198 iv v v --------- v i v -- ii C MIR#SINE/MIR 141 ATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCCA 92 chr4qtel1M 536199 GGGTCATCCACCTAG--AG-GGCAGGGTC 536224 i iv v -- - i i C MIR#SINE/MIR 91 AGGTCACACAGCTAGTAAGTGGCAGAGCC 63 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.62 CpG sites = 26, Kimura (unadjusted) = 43.62 Transitions / transversions = 1.00 (26/26) Gap_init rate = 0.06 (9 / 162), avg. gap size = 2.22 (20 / 9) 13 0.00 0.00 0.00 chr4qtel1M 536693 536709 (463291) (GCT)n#Simple_repeat 1 17 (0) m_b204s252i7 8034 chr4qtel1M 536693 GCTGCTGCTGCTGCTGC 536709 (GCT)n#Simple 1 GCTGCTGCTGCTGCTGC 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 39 24.79 0.00 0.00 chr4qtel1M 537360 537449 (462551) (TG)n#Simple_repeat 1 90 (0) m_b204s252i8 8035 chr4qtel1M 537360 TGTGTGTGCGTGTGTAAGGGAGGGTGTGTGTGTTAGTGGGTGTGTGTGCA 537409 i iv v v v vv v ii (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr4qtel1M 537410 TGTGTGAATGTGTGTGACAGCGAGTGTGTGTGTGTGAGTG 537449 vi vvv i v v (TG)n#Simple_ 51 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 90 Matrix = Unknown Transitions / transversions = 0.46 (6/13) Gap_init rate = 0.00 (0 / 89), avg. gap size = 0.0 (0 / 0) 233 32.14 0.00 0.00 chr4qtel1M 537979 538062 (461938) C MIRc#SINE/MIR (153) 115 32 m_b204s601i14 8036 chr4qtel1M 537979 GAGGTCATGTGACTTGGCCAGGGTTCTTTGGCTAGGACGGGGTTGAGGCT 538028 i v v i ivivii v v v iv v v C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 66 chr4qtel1M 538029 GGAATCCATAGCAGCTGTTCCTGGCTCCAGGCCC 538062 v v vvv v v i i i C MIRc#SINE/MIR 65 GGACTCGAACCCAGGTCTTCCTGACTCCAAGTCC 32 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.00 CpG sites = 10, Kimura (unadjusted) = 42.00 Transitions / transversions = 0.59 (10/17) Gap_init rate = 0.00 (0 / 83), avg. gap size = 0.0 (0 / 0) 180 27.81 7.41 2.35 chr4qtel1M 538078 538158 (461842) C MIR3#SINE/MIR (63) 145 61 m_b204s601i15 8037 chr4qtel1M 538078 CTCTTTTTGTCAATGAGGAAATGAAGGCCCAGGGATGGCAAAGTGA---G 538124 v iivi ivi i - ii --- C MIR3#SINE/MIR 145 CTCATTTTACAGATGAGGAAACTGAGGCCCAGAGA-GGTGAAGTGACTTG 97 chr4qtel1M 538125 CCTGGAGGACAGAAGGC---TTGGGGGCTGGGCTGGG 538158 i-i v v vi --- i v v i i C MIR3#SINE/MIR 96 CCC-AAGGTCACACAGCNAGTTAGTGGCAGAGCCGGG 61 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.02 CpG sites = 14, Kimura (unadjusted) = 36.07 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.05 (4 / 80), avg. gap size = 2.00 (8 / 4) 333 33.06 0.82 0.82 chr4qtel1M 539489 539610 (460390) L3#LINE/CR1 2675 2796 (1303) m_b204s601i16 8038 chr4qtel1M 539489 CCAGGAGCCCAAAGGGGGGCACTTATCTTCCCAGGCTGCCAAAAGGGAAG 539538 i v iii iv vv i ?v ? vi?i viv i L3#LINE/CR1 2675 CCAGAAGACTGGAGACGGGCAAATGTNGTNCCTANTTTTAAAAAGGGAAA 2724 chr4qtel1M 539539 AAGGTCGG-CTCCAGAAACCACAGACTTGTTAGTTTGGTGTCAATCCCAA 539587 i vi -i ii? i iv v i ii i -v L3#LINE/CR1 2725 AAAGATGGATTCTGNAAACTACAGACCGGTAAGCTTGACGTCGATCCC-C 2773 chr4qtel1M 539588 GGGAAAAAATTAGGCTGGATTAT 539610 v vvi ivi L3#LINE/CR1 2774 GGCAAAATTCTAGAACGGATTAT 2796 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.21 CpG sites = 24, Kimura (unadjusted) = 47.58 Transitions / transversions = 1.50 (24/16) Gap_init rate = 0.02 (2 / 121), avg. gap size = 1.00 (2 / 2) 269 26.98 19.05 0.00 chr4qtel1M 539625 539750 (460250) C L2d_3end#LINE/L2 (0) 516 367 m_b204s601i17 8039 chr4qtel1M 539625 TTGATCAATCAGTCCACAAGTGCAGATTAAACACCTCCTGTGTGC-CAGC 539673 ii i v iivv i i i v i - C L2d_3end#LINE 516 TCAATCAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGC 467 chr4qtel1M 539674 AC---------------AGGGGACAAAGAAAAAGCAGAAAGCACG---CA 539705 ---------------i i i ?i ? i v ii i --- v C L2d_3end#LINE 466 ACTGTGCTAGGCGCTGTGGGGAACGANAAAANAGTATAAGACATGGTCCC 417 chr4qtel1M 539706 GGCCCTCCCGGAGCTGGCACTGTAA-CGGAGAGACA----CAACACACAT 539750 v vv vi v v i-i i ----i C L2d_3end#LINE 416 TGCCCTCAAGGAGCTTACAATCTAGTTGGGGAGACAAGACTAACACACAT 367 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.84 CpG sites = 22, Kimura (unadjusted) = 35.42 Transitions / transversions = 1.83 (22/12) Gap_init rate = 0.04 (5 / 125), avg. gap size = 4.80 (24 / 5) 228 29.07 11.63 0.00 chr4qtel1M 539935 540020 (459980) L3#LINE/CR1 2928 3023 (1076) m_b204s601i18 8038 chr4qtel1M 539935 AGGGGAATATCCAAGCTCTGGGG---CTGGCTGCCAGCAGGGC----GCC 539977 ii vv viv?i v --- v vi i ---- v L3#LINE/CR1 2928 AGGGGAATGCCGTAGACANAGTGTATCTGGATTTCAGCAAGGCATTTGAC 2977 chr4qtel1M 539978 A---TCTCCCAAAACGTCCTTATGAATGAATTGGAGAAATATGGGC 540020 --- i vi ii i i ii iv L3#LINE/CR1 2978 AAAGTCTCTCATGATATCCTTGTGGACAAGATGGAGAAATATGGGC 3023 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.51 CpG sites = 15, Kimura (unadjusted) = 38.51 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.04 (3 / 85), avg. gap size = 3.33 (10 / 3) 265 33.75 10.97 0.58 chr4qtel1M 540030 540184 (459816) MIR3#SINE/MIR 15 185 (23) m_b204s601i19 8040 chr4qtel1M 540030 GAGGAAAGACGGC-TGAACCTGGAGTGGGAGGGGCCAGGTTCAAATCCTG 540078 v i vi -i i iv vi ii iv ii v i i MIR3#SINE/MIR 15 GAGCAGAGAGAGCACGGACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCG 64 chr4qtel1M 540079 ACCCAGC-------------TGTGAGCTTCGAGAAATCTCTCC-CCAGCC 540114 i i v ------------- v v iv i v i - vvi MIR3#SINE/MIR 65 GCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTC 114 chr4qtel1M 540115 AGGACCGCCATTTTCTCATCTGC-AAATCAGCGGCTTGGACTTCG-GAAC 540162 v i v vi i i- v v v vvi- v MIR3#SINE/MIR 115 TGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATC 164 chr4qtel1M 540163 CCTGGGGCCCTTTCCCAGCGCT 540184 i ii i i - v MIR3#SINE/MIR 165 TCTAAGGTCCCTT-CCAGCTCT 185 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.79 CpG sites = 29, Kimura (unadjusted) = 46.20 Transitions / transversions = 1.26 (29/23) Gap_init rate = 0.04 (6 / 154), avg. gap size = 3.00 (18 / 6) 267 29.77 11.66 5.20 chr4qtel1M 540460 540622 (459378) C MIR3#SINE/MIR (27) 181 9 m_b204s601i20 8041 chr4qtel1M 540460 CTGGCAGGGATGTCGGAGGCCATTT-------CTTTCTTTTTTTTCC--T 540500 v iv ii ii i ------- iii iv v v-- C MIR3#SINE/MIR 181 CTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGAT 132 chr4qtel1M 540501 GAGGCAATTG-GGT---------TTAAGTGACTTGCCCAGGCTCACACAG 540540 v i - i--------- v i v C MIR3#SINE/MIR 131 GAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAG 82 chr4qtel1M 540541 CTGGGAAGTGTTAAGTGTCTGAGGTCAGATTTGAACTCAGGTCCTCCTGG 540590 ?i ------- v v v vivi i v i - i C MIR3#SINE/MIR 81 CNAG-------TTAGTGGCAGAGCCGGGACTAGAACCCAGGT-CTCCTGA 40 chr4qtel1M 540591 ATTCAGGGCTGGTGTTCTATCCACTGCACCAC 540622 v i vi v i- i v ii vvi C MIR3#SINE/MIR 39 CTCCCAGTCC-GTGCTCTCTCTGCTCAGCCAC 9 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.20 CpG sites = 26, Kimura (unadjusted) = 39.38 Transitions / transversions = 1.30 (26/20) Gap_init rate = 0.08 (13 / 162), avg. gap size = 2.15 (28 / 13) 484 23.33 0.74 7.94 chr4qtel1M 540499 540633 (459367) C MIRc#SINE/MIR (141) 127 2 m_b204s601i21 8041 chr4qtel1M 540499 CTGAGGCA-ATTGGGTTTAAGTGACTTGCCCAGGCTCACACAGCTGGGAA 540547 v- vv i v i v i --- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG--- 81 chr4qtel1M 540548 GTGTTAAGTGTCTGAGGTCAGATTTGAACTCAGGTCCTCCTGGATTCAGG 540597 ---- v v vivi i i i i iv i i C MIRc#SINE/MIR 80 ----TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr4qtel1M 540598 GCTGGTGTTCTATCCACTGCACCACCTAGCTGCCCC 540633 v ii i v ---i i C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTGCACCAC---ACTGCCTC 2 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.05 CpG sites = 17, Kimura (unadjusted) = 28.27 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.08 (11 / 134), avg. gap size = 1.00 (11 / 11) 219 23.64 0.00 1.82 chr4qtel1M 542016 542071 (457929) C L2d_3end#LINE/L2 (2) 514 460 m_b204s601i22 8042 chr4qtel1M 542016 AATGAATGAATGGAAAAGCCTTTAATGAGCTCCTATTTGTGTGCTCAGTG 542065 v v vi v iv v v i -i ii C L2d_3end#LINE 514 AATCAATCAATCAACAAGTATTTATTGAGCGCCTACT-ATGTGCTCAGCA 466 chr4qtel1M 542066 CTGTGC 542071 C L2d_3end#LINE 465 CTGTGC 460 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.53 CpG sites = 6, Kimura (unadjusted) = 28.53 Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.02 (1 / 55), avg. gap size = 1.00 (1 / 1) 1354 32.53 1.29 0.64 chr4qtel1M 542569 543190 (456810) C L1ME4c_3end#LINE/L1 (193) 637 12 m_b204s551i1 8043 chr4qtel1M 542569 CTGCTCATCTCACTCAGCATCA-GTCCTGT-CAGTCTCTCCATCGCTCTG 542616 iv i i i i -i v iv- v i ivii i vii C L1ME4c_3end#L 637 CTGCTTTTTTCACTTAACATTATATCATAAACATTTTCCATGTTGCTACA 588 chr4qtel1M 542617 AAATCCTCCTGCTGGTCGTTTCTTACAGAGAAATCATATCCCATAGCAGT 542666 v i i v iv vi i i v ii vviv v i v - C L1ME4c_3end#L 587 TAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCG-AGT 539 chr4qtel1M 542667 C-ATAAACCACAGCTTATTCAGCCATTCCCCCATTGATGGGCATCCACTC 542715 ?- iv i ii i i i i v i ii vvi C L1ME4c_3end#L 538 NGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAGGT 489 chr4qtel1M 542716 AGTTTCCAGTTTCTGGCCACTA-AAACAGGGTTGCTACAAACATTTTGGC 542764 v i i v i i - i iv i v ii i v i C L1ME4c_3end#L 488 TGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTCGT 439 chr4qtel1M 542765 ACATGTGGGTCCCTTTCCCTTCGTT---AACATTTCTTTGGGGTATAAGC 542811 i i i --- i i v --- vi i i i v vv C L1ME4c_3end#L 438 GCATATAG---CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAATTC 392 chr4qtel1M 542812 CCAGTAGAAACACTGCTGGATCAAAGGGTAGGCACAGTTTGATAACTTTT 542861 v viiv i i i v v v v ii i C L1ME4c_3end#L 391 CCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTCTT 342 chr4qtel1M 542862 TGAGCATAGTTCTAAATTGCTCTCCAGAATGGCTGGATGGATTCACAATT 542911 vivi i v v i i i v i v ivi i ? v C L1ME4c_3end#L 341 GATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACANTG 292 chr4qtel1M 542912 CCACAAACAATGTATTAGTGTCCCTGTTTTCCCGCATCTCCTCCAACATT 542961 v i v ? v v iv ? ii v i C L1ME4c_3end#L 291 CCACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGCATT 242 chr4qtel1M 542962 CCGCATTATCTTTCCCTGTCATTCTAGCCAATCTGCCAGGTGTATCATGG 543011 vv i vv iii vvv i v i i ivi i vv C L1ME4c_3end#L 241 GGGTATTATCAATTTTTTAAATTTTTGCTAATTTAATAGGCGTAAAATGG 192 chr4qtel1M 543012 TATCTCAGAGTTGTCTTACTTTGCATTTCTCTGATCAATAGTGATTTGGA 543061 vv ii v i i v i vv v C L1ME4c_3end#L 191 TATCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACTAGCGAGGTTGA 142 chr4qtel1M 543062 ACACTCTTTCATATGGGTAGAAATAATTTCCATTTCATCATCTG-AAAGT 543110 i i i i vv ivvv iv ? vi v v ? -i v C L1ME4c_3end#L 141 ACATTTTTCCATGTGTTTGTTTACTANTTGTATTTCCTCTTNTGTGAATT 92 chr4qtel1M 543111 GTCTGTCCATATCCTTTGACTATTTATCAATTGGAGAATGGCTTGATTTC 543160 i i v i v i vv v v ?vv C L1ME4c_3end#L 91 GTCTGTTCATGTCCTTTGCCCATTTATCTATTGGGGTCTTGATNTTTTTC 42 chr4qtel1M 543161 TTATAAATTAGAGTCAATTCTCTCTATATT 543190 v v i v ii i v ? C L1ME4c_3end#L 41 TTATCAATTTGAATGAGCTCTTTATATANT 12 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 43.61 CpG sites = 110, Kimura (unadjusted) = 44.51 Transitions / transversions = 1.21 (110/91) Gap_init rate = 0.02 (10 / 621), avg. gap size = 1.20 (12 / 10) 1379 29.74 0.73 1.66 chr4qtel1M 542649 543195 (456805) C L1ME3G_3end#LINE/L1 (376) 548 7 m_b204s551i2 8043 chr4qtel1M 542649 ATCATATCCCATAGCAGTCATAAACCACAGCTTATTCAGCCATTCCCCCA 542698 vi i i vvv v i ii i i i C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr4qtel1M 542699 TTGATGGGCATCCACTCAGTTTCCAGTTTCTGGCCACTA-AAACAGGGTT 542747 i ii vviv i i v i i - iv i C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr4qtel1M 542748 GCTACAAACATTTTGGCACATGTGGGTCCCTTT--CCCTTCGTTAACATT 542795 v ii ii v i i?-- i v --v v vi iv ii C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATT 401 chr4qtel1M 542796 TCTTTGGGGTATAAGCCCAGTAGAAACACTGCTGGATCAAAGGGTAGGCA 542845 ? i i v v? ? v viiv i i v i C L1ME3G_3end#L 400 TCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCG 351 chr4qtel1M 542846 CAGTTTGATAACTTTTTGAGCATAGTTCTAAATTGCTCTCCAGAATGGCT 542895 v --- v viviv v v i i i ? C L1ME3G_3end#L 350 CATTTT---AAATTTTAATAGATACTGCCAAATTGCCCTCCAAAANGGCT 304 chr4qtel1M 542896 GGATGGATTCACAATTCCACAAACAATGTATTAGTGTCCCTGTTTTCCCG 542945 v ivi i v i v i i v v v i i i C L1ME3G_3end#L 303 GTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCA 254 chr4qtel1M 542946 CATCTCCTCCAACATTCCGCATTATCTTTCCCTGTCATTCTAGCCAATCT 542995 i ii v i ?vii vv? ii vvv i v C L1ME3G_3end#L 253 CACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATCT 204 chr4qtel1M 542996 GCCAGGTGTATCATGGTATCTCAGAGTTGTCTTACTTTGCATTTCTCTGA 543045 vii v vv vv i v i C L1ME3G_3end#L 203 GATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGA 154 chr4qtel1M 543046 TCAATAGTGATTTGGAACACTCTTTCATATGGGTAGAAATAATTTCCATT 543095 i v vv v i iii vv vviiiv vi C L1ME3G_3end#L 153 TTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGTATT 104 chr4qtel1M 543096 TCATCATCTG-AAAGTGTCTGTCCATATCCTTTGACTATTTATCAATTGG 543144 v v -i v i i v i v v C L1ME3G_3end#L 103 TCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGG 54 chr4qtel1M 543145 AGAATGGCTTGATTTCTTATAAATTAGAGTCAATTCTCTCTATATTTTGA 543194 iv-- v -- vi v vivv i i v i i C L1ME3G_3end#L 53 GT--TGTCTT--TTTCTTATTGATTTGTAGGAGTTCTTTATATATTCTGG 8 chr4qtel1M 543195 A 543195 C L1ME3G_3end#L 7 A 7 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 38.26 CpG sites = 84, Kimura (unadjusted) = 39.19 Transitions / transversions = 1.11 (84/76) Gap_init rate = 0.02 (12 / 546), avg. gap size = 1.08 (13 / 12) 239 30.47 4.15 3.08 chr4qtel1M 543053 543245 (456755) C L1MC_orf2#LINE/L1 (0) 3294 3100 m_b204s551i3 8043 chr4qtel1M 543053 TGATTTGGAACACTCTTTCATATGGGTAGAAATAATTTCCATTTCATCAT 543102 v ? i iii vv vvviiv i vi v v v C L1MC_orf2#LIN 3294 TGATGTNGAGCATCTTTTCATATGCTTATTTGCCATCTGTATATCTTCTT 3245 chr4qtel1M 543103 CTG-AAAGTGTCTGTCCATATCCTTTGACTATTTATCAATTGGAGAATGG 543151 iv -i i i vi i v i v ? i i--- v C L1MC_orf2#LIN 3244 TGGTGAGGTGTCTGTTCAGGTCTTTTGCCCATTTTTNAATCGGG---TTG 3198 chr4qtel1M 543152 CTTGATTTCTTATAAATTAGAGTCAA---TTCTCTCTATATTTTGAA-AT 543197 i v viv v vv i --- i v i - v C L1MC_orf2#LIN 3197 TTTGTTTTCTTATTGTTGAGTTTTAAGAGTTCTTTGTATATTTTGGATAA 3148 chr4qtel1M 543198 GAAGCCTTTATCAGA---ACCTTTAACTGTAAAGATGTTTTCCCAGTTTA 543244 v iv ---ii --- i v v i i i C L1MC_orf2#LIN 3147 CAGTCCTTTATCAGATATGTCTTT---TGCAAATATTTTCTCCCAGTCTG 3101 chr4qtel1M 543245 T 543245 C L1MC_orf2#LIN 3100 T 3100 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 39.37 CpG sites = 29, Kimura (unadjusted) = 40.28 Transitions / transversions = 1.04 (29/28) Gap_init rate = 0.05 (10 / 192), avg. gap size = 1.40 (14 / 10) 542 24.50 3.27 3.95 chr4qtel1M 543492 543644 (456356) C MIR#SINE/MIR (78) 184 33 m_b204s601i23 8044 chr4qtel1M 543492 ATTTTCACAGC----CTG-GGGGCAGGTGCTGTAATGAGTCCCACTTTAC 543536 ii i ---- i- i i i i v v vi i C MIR#SINE/MIR 184 ATCCTCACAACAACCCTATGAGGTAGGTACTATTATTATCCCCATTTTAC 135 chr4qtel1M 543537 CTATGAGGAAACTGAGGCAAACAGATGCAATGTGACTTGTCCAGGCTCAC 543586 vv v v v iv v i i i v C MIR#SINE/MIR 134 AGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCAC 85 chr4qtel1M 543587 ATGACTAGTAAGTGTCTGAGGCTGGATTTGAACTCACTGAGACAGTGTGG 543636 iii v v v v i i ---- i v C MIR#SINE/MIR 84 ACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCC----AGGCAGTCTGG 39 chr4qtel1M 543637 CCCTCCAG 543644 -- C MIR#SINE/MIR 38 --CTCCAG 33 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.14 CpG sites = 20, Kimura (unadjusted) = 30.12 Transitions / transversions = 1.25 (20/16) Gap_init rate = 0.05 (8 / 152), avg. gap size = 1.38 (11 / 8) 338 24.56 13.28 1.40 chr4qtel1M 548479 548606 (451394) C MIR3#SINE/MIR (7) 201 59 m_b204s601i24 8045 chr4qtel1M 548479 AGAATCCATAGGATTTCGG-GCGGGAGGGGGACCCCATAACCTGTCTGGT 548527 - i v i - v i - ii v iviii i C MIR3#SINE/MIR 201 AGAATC-ATAGAATGTCAGAGCTGGAAGGG-ACCTTAGAGATCATCTAGT 154 chr4qtel1M 548528 CCAGTCCCCCC--TTTACAGATAAGGAGGTAGAGGCCCAGAG----GGAC 548571 ii i -- i iiiv ---- i v C MIR3#SINE/MIR 153 CCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAG 104 chr4qtel1M 548572 TGA----------ATCACACAGGGGGCAAGTGGCTGAGCGGGGAC 548606 ----------i v?i iv v v C MIR3#SINE/MIR 103 TGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGAC 59 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.25 CpG sites = 21, Kimura (unadjusted) = 31.25 Transitions / transversions = 2.10 (21/10) Gap_init rate = 0.05 (6 / 127), avg. gap size = 3.17 (19 / 6) 244 24.62 14.29 7.14 chr4qtel1M 548532 548636 (451364) C MIR#SINE/MIR (116) 146 35 m_b204s601i25 8045 chr4qtel1M 548532 TCCCCCCTTTACAGATAAGGAGGTAGAGGCCCAGAGGGACTGA------- 548574 vi i iiiv v i ii i ------- C MIR#SINE/MIR 146 TCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTT 97 chr4qtel1M 548575 -------ATCACACAGGGGGCAAGTGGCTGAGCGGGGACGCAAAATGGGG 548617 -------i vvi i v v iv i ------ C MIR#SINE/MIR 96 GCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAA------ 53 chr4qtel1M 548618 GTCCTGGGCAG-CTGGCTCC 548636 -- ii - C MIR#SINE/MIR 52 --CCCAGGCAGTCTGGCTCC 35 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.54 CpG sites = 16, Kimura (unadjusted) = 31.09 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.11 (11 / 104), avg. gap size = 2.09 (23 / 11) 53 24.50 0.75 0.00 chr4qtel1M 551686 551819 (448181) (TCTCTC)n#Simple_repeat 1 135 (0) m_b204s252i9 8046 chr4qtel1M 551686 TCTCTGTCTCTCTAAATCTTTCTCTGTATCTCTCTTTGCCTTTGTCTCTG 551735 v vvv i v v i vi i v v (TCTCTC)n#Sim 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr4qtel1M 551736 TCTCT-TTTTTGTCTCTGTCTCTCTGTCTCTCCCTCTCTGTCCCTCTGTC 551784 - i i v v v i v i v (TCTCTC)n#Sim 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chr4qtel1M 551785 TCTCCCTCTCTGTCTCTGTCCCTCTCTGTCTGTCT 551819 i v v i v v (TCTCTC)n#Sim 101 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 135 Matrix = Unknown Transitions / transversions = 0.56 (10/18) Gap_init rate = 0.01 (1 / 133), avg. gap size = 1.00 (1 / 1) 225 35.17 7.59 0.00 chr4qtel1M 552098 552242 (447758) L2d2_3end#LINE/L2 118 273 (282) m_b204s601i27 8047 chr4qtel1M 552098 TCCAGCCTCCGTGCCTTTGCCCAGGCTGCGGCCTCCCCCCCAAATGTTCC 552147 v i i i v i ivv i v ivi ii i L2d2_3end#LIN 118 TCCCGCCTCTGCGCCTTTGCTCACGCCGTTCCCCCCGCCTGGAATGCCCT 167 chr4qtel1M 552148 TCCCCTTCTCCTC------TCGGAGTCTCTCCTTCCCTGAAAGACTGTGC 552191 ii ------ vi i iiv ivi vv i ivv L2d2_3end#LIN 168 TCCCCTTCCTCTCCACCTATCCAAATCCTACCCATCCTTCAAGGCCCAGC 217 chr4qtel1M 552192 TCAAGTCCTCTCTCTTGCAAGAGGCTGGCCCCG---CCTCC--CCTGAAG 552236 i ? ivi i v iv i ivv i ---v -- i ? L2d2_3end#LIN 218 TCAAATNCCACCTCCTCCGTGAAGCCTTCCCTGACCACTCCAGCCCGNAG 267 chr4qtel1M 552237 TTATTT 552242 v i L2d2_3end#LIN 268 TGATCT 273 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.22 CpG sites = 31, Kimura (unadjusted) = 50.80 Transitions / transversions = 1.55 (31/20) Gap_init rate = 0.02 (3 / 144), avg. gap size = 3.67 (11 / 3) 256 35.43 4.72 0.00 chr4qtel1M 552098 552224 (447776) L2d_3end#LINE/L2 118 250 (266) m_b204s601i26 8047 chr4qtel1M 552098 TCCAGCCTCCGTGCCTTTGCCCAGGCTGCGGCCTCCCCCCCAAATGTTCC 552147 v i i i v i ivv i v ivi ii i L2d_3end#LINE 118 TCCCGCCTCTGCGCCTTTGCTCACGCCGTTCCCCCCGCCTGGAATGCCCT 167 chr4qtel1M 552148 TCCCCTTCTCCTCTCG------GAGTCTCTCCTTCCCTGAAAGACTGTGC 552191 ii v------i i iiv ivi vv i ivv L2d_3end#LINE 168 TCCCCTTCCTCTCTCTCTATCCAAATCCTACCCATCCTTCAAGGCCCAGC 217 chr4qtel1M 552192 TCAAGTCCTCTCTCTTGCAAGAGGCTGGCCCCG 552224 ivi i v v i ivv i L2d_3end#LINE 218 TCAAGTCCCACCTCCTCCACGAAGCCTTCCCTG 250 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 47.01 CpG sites = 27, Kimura (unadjusted) = 50.18 Transitions / transversions = 1.50 (27/18) Gap_init rate = 0.01 (1 / 126), avg. gap size = 6.00 (6 / 1) 209 27.28 12.12 2.78 chr4qtel1M 552234 552365 (447635) L2c_3end#LINE/L2 330 473 (5) m_b204s601i28 8047 chr4qtel1M 552234 AAGTTATTTTGTACTTATGTGATG--CTGATTAATTCCTGAA-TACACAA 552280 v i v v i v v v--? vi ivi vv - v v- L2c_3end#LINE 330 AACTTGTATTGTAATTGTCTGTTTACNTGTCTGTCTCCTCCACTAGACT- 378 chr4qtel1M 552281 AGTGTGCTCCTTGAGGGCAGGGCCCGTTTC-------TCTTTATA-CCCC 552322 - v v v ------- i - L2c_3end#LINE 379 -GTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTATCCCC 427 chr4qtel1M 552323 AGAA---GGCCC--AGGAGGCACTCAGGATAGACAGAGATGGGATGAA 552365 vi--- v -- v i -- i iivvvi v i L2c_3end#LINE 428 AGCGCCTGGCACATAGTAGGCGCTCA--ATAAATGTTTGTTGAATGAA 473 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.14 CpG sites = 13, Kimura (unadjusted) = 34.37 Transitions / transversions = 0.59 (13/22) Gap_init rate = 0.08 (10 / 131), avg. gap size = 2.00 (20 / 10) 186 35.40 0.00 1.54 chr4qtel1M 552447 552512 (447488) C L2d2_3end#LINE/L2 (6) 549 485 m_b204s601i29 8048 chr4qtel1M 552447 CAAAGCCATAAGCATCAATTAAGCACCTACTGGATACTGTGTAACTAGGC 552496 v v i ii iv i i vi i viv i- iv C L2d2_3end#LIN 549 CAAATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGC-ACTGTGC 501 chr4qtel1M 552497 TAAGTGCTGGGGATGA 552512 i i v iv C L2d2_3end#LIN 500 TAGGCGCTGTGGGGGA 485 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.17 CpG sites = 14, Kimura (unadjusted) = 50.22 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.02 (1 / 65), avg. gap size = 1.00 (1 / 1) 196 20.00 2.22 0.00 chr4qtel1M 552514 552558 (447442) C L2c_3end#LINE/L2 (85) 393 348 m_b204s601i30 8049 chr4qtel1M 552514 CCTCTAAGAACTCACAATCAAATGGGGGAGACAG-CCTGCAAACAG 552558 v i i i v i i - v? i C L2c_3end#LINE 393 CCTCAAGGAGCTCACAGTCTAGTGGAGGAGACAGACANGTAAACAG 348 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 24.51 CpG sites = 6, Kimura (unadjusted) = 24.51 Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 363 30.08 8.43 6.63 chr4qtel1M 552875 553052 (446948) C MIR3#SINE/MIR (1) 207 27 m_b204s601i31 8050 chr4qtel1M 552875 AATCGCAGAAAAATGAGATGT-AGAGACTAAAACAGGGAAGGACCTTTGG 552923 ii vv iii - - ------- iv i i C MIR3#SINE/MIR 207 AATCATAGAATCATAGAATGTCAGAG-CT-------GGAAGGGACCTTAG 166 chr4qtel1M 552924 AGGCCGCCCAGCCCAATCCTCTTCTTTTCCAGAGGAAGGGGCTGAGACCC 552973 ii ii i i i i iv v v i iii i C MIR3#SINE/MIR 165 AGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCC 116 chr4qtel1M 552974 AGGAGGGGGAGGTG--------------ACACAGGGAGGAAGGGGCTGAG 553009 iii v i -------------- v? vv v v C MIR3#SINE/MIR 115 AGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAG 66 chr4qtel1M 553010 CCTGAGCTTGAGCCTAGCTCCTCCTAGTAACTCTGGGTCAGTG 553052 v ii v i i v - --- i ivi v C MIR3#SINE/MIR 65 CCGGGACTAGAACCCAGGT-CTCC---TGACTCCCAGTCCGTG 27 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.73 CpG sites = 33, Kimura (unadjusted) = 40.73 Transitions / transversions = 1.94 (33/17) Gap_init rate = 0.08 (14 / 177), avg. gap size = 1.93 (27 / 14) 29 0.00 0.00 0.00 chr4qtel1M 553277 553303 (446697) (GCCTCG)n#Simple_repeat 1 27 (0) c_b204s251i3 8051 chr4qtel1M 553277 GCCTCGGCCTCGGCCTCGGCCTCGGCC 553303 (GCCTCG)n#Sim 1 GCCTCGGCCTCGGCCTCGGCCTCGGCC 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 219 34.81 10.07 4.61 chr4qtel1M 554433 554700 (445300) C L2d2_3end#LINE/L2 (245) 310 29 m_b204s601i32 8049 chr4qtel1M 554433 ACAGACAATGAAATATTAT-----TCTGGGAGAGAGAGTGAGCACTAGCA 554477 - ? ii ----- iii ii i v v ?vvi C L2d2_3end#LIN 310 ACAGACAAT-AANTGCTATAGGAGTTCAGAGGAGGGAGAGATCACTNCGG 262 chr4qtel1M 554478 GCTAGGGGAATCAGGGAAAGATTTGCA--------TGTACCTGTGCAGGA 554519 i i vii i v ii i--------v ? ii v v i C L2d2_3end#LIN 261 GCTGGAGTGGTCAGGGAAGGCTTCACGGAGGAGGTGGNATTTGAGCTGGG 212 chr4qtel1M 554520 TCT-----GCTG---AGGATGCTAAGAAGCAGGGGTGAGGAGGGACGGTG 554561 i ----- v --- vivi v i ii i iv i i i v ii C L2d2_3end#LIN 211 CCTTGAAGGATGGGTAGGATTTGGATAGGTGGAGAGGAAGGGGAAGGGCA 162 chr4qtel1M 554562 -TCCAGGTACAGGGAACAAGCTGTTCAAAGGCTTGGAGAGGGGAGATGGT 554610 - iivi iivv vv -- v v i v? i C L2d2_3end#LIN 161 TTCCAGGCGGGGGGAACGGCGTGAGCAAAGGC--GCAGAGGCGGGAANGC 114 chr4qtel1M 554611 GTCAAGG-----ACAGGAAATTGCTTGTAATCCAGTTTGGCTGGAAAGTA 554655 - -----v i ii iv ivv iv iv v C L2d2_3end#LIN 113 G-CAAGGCGTGTTCGGGGGACAGTGAGTAGACCAGTTTGGCTGGAGCGGA 65 chr4qtel1M 554656 AGATCCCTGAGGAAGTCTGGAAGGGGTAGTAGGATGCAGAGCTGG 554700 i i i v ?i i----- ---- i vii ii C L2d2_3end#LIN 64 GGGTTCGTGNAGG-----GGAA----TAGTGGGAGATAAGGCTGG 29 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 47.01 CpG sites = 57, Kimura (unadjusted) = 51.25 Transitions / transversions = 1.78 (57/32) Gap_init rate = 0.07 (19 / 267), avg. gap size = 2.11 (40 / 19) 485 30.34 4.83 0.00 chr4qtel1M 555045 555189 (444811) MIRc#SINE/MIR 2 153 (115) m_b204s601i33 8052 chr4qtel1M 555045 GAGGCAGTGCGGTGCAATGGAAAGTGC--TGGACTGGGAGTC-GAAGGCC 555091 i i v -- v - i i v MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr4qtel1M 555092 CAAAGTTCGGACCCTGCCTCTGCTCCTTCCTGCCCCTGTGACCTTGGA-G 555140 vii iii i v iv v iv iv i-i MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 101 chr4qtel1M 555141 GGACATTCCATCTTCCTGGTTTTTGGTTTCCTCCTC---AAAGTGAGAGC 555187 i v i iv i ii ivii ii v --- i i iii MIRc#SINE/MIR 102 AGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGAT 151 chr4qtel1M 555188 AA 555189 MIRc#SINE/MIR 152 AA 153 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.08 CpG sites = 31, Kimura (unadjusted) = 41.35 Transitions / transversions = 2.38 (31/13) Gap_init rate = 0.03 (4 / 144), avg. gap size = 1.75 (7 / 4) 215 32.65 6.96 3.05 chr4qtel1M 555995 556152 (443848) C L2c_3end#LINE/L2 (174) 304 141 m_b205s601i3 8053 chr4qtel1M 555995 TAGACAGGATAAATTGGAGATAACCAATGAGGGAACGCTCTGGAGTGAAG 556044 i ivvv - vv vi v v --- i v - i? C L2c_3end#LINE 304 TAGACAGGGTGCTATGG-GAGCACAGAGGAGGGCAC---CTAGACT-AGN 260 chr4qtel1M 556045 CACTATGGGTTGGGAAGGGCTTCCAGTACAAAGTGGGATTTTCACTGGGA 556094 viviv ii i i v v vi i iv i vvi i ? C L2c_3end#LINE 259 CTTGGGGGGTCAGGGAAGGCTTCCCGGAGGAGGTGACATCTGAGCTGAGN 210 chr4qtel1M 556095 CTTCAA--------AGAAGCTGG--GGGTGGAGATAAGGAGCAAGAACAT 556134 v -------- i i i --i iiv i i v i C L2c_3end#LINE 209 CTTGAAGGATGAGTAGGAGTTAGCCAGGTGGAAGGAGGGGGGAAGAGCAT 160 chr4qtel1M 556135 TCC-GGCAGGGGAAATAGC 556152 - i i i C L2c_3end#LINE 159 TCCAGGCAGAGGGAACAGC 141 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 45.18 CpG sites = 29, Kimura (unadjusted) = 45.18 Transitions / transversions = 1.38 (29/21) Gap_init rate = 0.05 (8 / 157), avg. gap size = 2.00 (16 / 8) 229 30.59 8.46 4.44 chr4qtel1M 556023 556152 (443848) C L2d2_3end#LINE/L2 (279) 276 142 m_b205s601i4 8053 chr4qtel1M 556023 GAGGGAACGCTCTGGAGTGAAGCACTATGGGTTGGGAAGGGCTTCCAGTA 556072 i v i ?i iv i i------ ii i i vv v C L2d2_3end#LIN 276 GAGAGATCACTNCGGGCTGGAGT------GGTCAGGGAAGGCTTCACGGA 233 chr4qtel1M 556073 CAAAGTGGGATTTTCACTGGGACTTCAAAGA-AGCTGGG---------GG 556112 vi i ? vvi v v i -i v i --------- C L2d2_3end#LIN 232 GGAGGTGGNATTTGAGCTGGGCCTTGAAGGATGGGTAGGATTTGGATAGG 183 chr4qtel1M 556113 TGGAGATAAGGAGCAAGAACATTCC-GGCAGGGGAAATAGC 556152 vi i i v ii - i i ii C L2d2_3end#LIN 182 TGGAGAGGAAGGGGAAGGGCATTCCAGGCGGGGGGAACGGC 142 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 37.78 CpG sites = 25, Kimura (unadjusted) = 42.32 Transitions / transversions = 1.92 (25/13) Gap_init rate = 0.07 (9 / 129), avg. gap size = 1.89 (17 / 9) 257 25.94 2.38 3.61 chr4qtel1M 556576 556659 (443341) MIR3#SINE/MIR 110 192 (16) m_b205s601i5 8054 chr4qtel1M 556576 CTCTCTGGACCTCATTTTTCT--TTTACACCATGAGGGGTTCGGAATAGA 556623 i v i -- i ii vv v i v MIR3#SINE/MIR 110 CTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGA 159 chr4qtel1M 556624 GGGTCTCCAGGATCCTAAATCTTGCTATGATCATTC 556659 v i i i i i--v iv v - MIR3#SINE/MIR 160 TGATCTCTAAGGTCCC--TTCCAGCTCTGA-CATTC 192 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 32.45 CpG sites = 12, Kimura (unadjusted) = 32.45 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.05 (4 / 83), avg. gap size = 1.25 (5 / 4) 17 4.94 0.00 0.00 chr4qtel1M 557170 557190 (442810) (G)n#Simple_repeat 1 21 (0) m_b205s252i0 8055 chr4qtel1M 557170 GGGGCGGGGGGGGGGGGGGGG 557190 v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGG 21 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 355 27.27 11.11 0.00 chr4qtel1M 557455 557553 (442447) L3#LINE/CR1 3772 3881 (218) m_b205s601i6 8056 chr4qtel1M 557455 CTATAGATGTTTGAAGAGCCA-CATATGGAAGAGAGATTATGTTCATTCT 557503 vi i i i ii- i i vii i L3#LINE/CR1 3772 CTTCAAATATTTGAAGGGCTGTCATGTGGAAGAGGGATTAGACTTATTCT 3821 chr4qtel1M 557504 GTGCTGCTCCAAGAGGTCAAACTGGG----------GGAAGTTCTGGGGA 557543 iv iii ivi i ---------- vii L3#LINE/CR1 3822 GTGTGGCTCCAGAGGGCAGAACTAGGACCAATGGGTGGAAGTTACAGGGA 3871 chr4qtel1M 557544 GACAGATTCC 557553 i i L3#LINE/CR1 3872 GGCAGATTTC 3881 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 36.82 CpG sites = 22, Kimura (unadjusted) = 36.82 Transitions / transversions = 4.40 (22/5) Gap_init rate = 0.02 (2 / 98), avg. gap size = 5.50 (11 / 2) 266 35.92 4.93 0.00 chr4qtel1M 557552 557693 (442307) L3#LINE/CR1 3941 4089 (10) m_b205s601i7 8056 chr4qtel1M 557552 CCCTGTGAGAGAGGGAGCTCCCTGTCACTGGAAGGACACAAACAAAGG-A 557600 ii ? iv v i i viiv i i -v L3#LINE/CR1 3941 CCTCGNGAGGTAGTGAGCTCCCCGTCACTGGAGGTGTTCAAGCAGAGGCT 3990 chr4qtel1M 557601 AGCTGGTCG--TCTCAGGACCATGGAAGCAG----CCTTGCTTTGGGAGC 557644 i v ii i-- v ivii v v v ----i i v iv v L3#LINE/CR1 3991 GGATGACCACTTGTCAGGGATGTTGTAGAAGGGATTCCTGCATTGGATGG 4040 chr4qtel1M 557645 TAGGTTGGCCTCCGTGGTTTCCGATGCCCCTTCCTGCTGGGAGGTTGTG 557693 v v vvi iii ii v i vi vv i v L3#LINE/CR1 4041 GAGGTTGGACTAGATGACCTCTAAGGTCCCTTCCAACTCTGAGATTCTG 4089 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 48.13 CpG sites = 28, Kimura (unadjusted) = 50.95 Transitions / transversions = 1.22 (28/23) Gap_init rate = 0.02 (3 / 141), avg. gap size = 2.33 (7 / 3) 305 32.24 0.81 2.46 chr4qtel1M 558367 558490 (441510) C Charlie4#DNA/hAT-Charlie (46) 3332 3211 m_b205s502i0 8057 chr4qtel1M 558367 GGAGAAGCCTGGGGCCCTCTCTTCAGAATCGTGTTTTTAATAGGCCCCAA 558416 v iv v i ii vi - v viv C Charlie4#DNA/ 3332 GGTGAAGCCTATGGACCCCTTCTCAGAATAATGTTTTTAA-ATGCATAAA 3284 chr4qtel1M 558417 ATAAAATGCGCAGAATTATGGAGAAAGCCAAATGTG-GGAGGCAGAGTTA 558465 i ii i iii i i v i i-v iii v C Charlie4#DNA/ 3283 ATAAAATACATAGGATTACAAAGGAAACCAATTATATTGAAATATAGTTA 3234 chr4qtel1M 558466 GCCAGGTGTTCTTAAAAGTGAAGTT 558490 v v ii i -- iii v C Charlie4#DNA/ 3233 TCAAAATAT--TTAAAAACAAATTT 3211 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 44.57 CpG sites = 26, Kimura (unadjusted) = 44.57 Transitions / transversions = 2.00 (26/13) Gap_init rate = 0.03 (4 / 123), avg. gap size = 1.00 (4 / 4) 314 27.50 0.00 1.25 chr4qtel1M 558367 558447 (441553) C Charlie4a#DNA/hAT-Charlie (46) 462 383 m_b205s502i1 8057 chr4qtel1M 558367 GGAGAAGCCTGGGGCCCTCTCTTCAGAATCGTGTTTTTAATAGGCCCCAA 558416 v iv v i ii vi - v viv C Charlie4a#DNA 462 GGTGAAGCCTATGGACCCCTTCTCAGAATAATGTTTTTAA-ATGCATAAA 414 chr4qtel1M 558417 ATAAAATGCGCAGAATTATGGAGAAAGCCAA 558447 i ii i iii i i C Charlie4a#DNA 413 ATAAAATACATAGGATTACAAAGGAAACCAA 383 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 35.85 CpG sites = 15, Kimura (unadjusted) = 35.85 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.01 (1 / 80), avg. gap size = 1.00 (1 / 1) 206 37.96 4.63 0.00 chr4qtel1M 559613 559720 (440280) C L2c_3end#LINE/L2 (33) 445 333 m_b205s601i8 8058 chr4qtel1M 559613 TACTGTATGTCAGACACTGGA-ATACAATGGGAAAAATGAAAGTGTCCCT 559661 i i i i i i- v ivi v v v vv C L2c_3end#LINE 445 TACTATGTGCCAGGCGCTGGGGATACAAAGATGAATAAGACACGGTCCCT 396 chr4qtel1M 559662 GCCTTTTAGGAGCCTTCC-CCTGATAGGGGGATTAGAT---TAGACCAGT 559707 i iv iiv v-i ii i i iivi i--- i viii C L2c_3end#LINE 395 GCCCTCAAGGAGCTCACAGTCTAGTGGAGGAGACAGACANGTAAACAGAC 346 chr4qtel1M 559708 AGATACAGAACAA 559720 iv iv C L2c_3end#LINE 345 AATTACAATACAA 333 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 54.96 CpG sites = 27, Kimura (unadjusted) = 57.17 Transitions / transversions = 1.93 (27/14) Gap_init rate = 0.03 (3 / 107), avg. gap size = 1.67 (5 / 3) 188 31.69 8.40 3.65 chr4qtel1M 559618 559748 (440252) C L2b_3end#LINE/L2 (50) 416 280 m_b205s601i9 8058 chr4qtel1M 559618 TATGTCAGACACTGGA-ATACAATGGGAAAAATGAAAGT----GTCCCTG 559662 i ii i i i- ii vi v v v v---- C L2b_3end#LINE 416 TGTGCTAGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTG 367 chr4qtel1M 559663 CCTTTTAGGAGCCTTCC-CCTGATAGGGGGATTAGATTAGACCAGTAGAT 559711 i ivv iiv v-i ii i ---- -i vv i?i C L2b_3end#LINE 366 CCCTCACGGAGCTCACAGTCTAGTGGGGG----AGA-CAGACATGTAANC 322 chr4qtel1M 559712 ACAGAACA--AACCCAAAGTGGT---TTAGGGATGAGGGGGC 559748 v v i?-- i i---v iv i C L2b_3end#LINE 321 AGACAATNATAACCCAGAGTGGCAGGGTAGGACTGGGGGGGC 280 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 41.10 CpG sites = 25, Kimura (unadjusted) = 44.06 Transitions / transversions = 1.67 (25/15) Gap_init rate = 0.08 (10 / 130), avg. gap size = 1.60 (16 / 10) 252 29.08 4.39 3.48 chr4qtel1M 560420 560533 (439467) L2b_3end#LINE/L2 349 463 (3) m_b205s601i10 8059 chr4qtel1M 560420 CTGTTAGTCTTTGCTGAGGGCAGGAA--GAGTTGGATTTTTGCATTCCTG 560467 v - ii - i -- ? iv vi v v iiv L2b_3end#LINE 349 CTGTGAG-CTCCG-TGAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTG 396 chr4qtel1M 560468 TTTCC--AGCACCCAGCACAAGTATCCGACACA-AAAAGGTACCCAATAA 560514 v -- i i - ?ii i i - iv ii i i L2b_3end#LINE 397 TATCCCCAGCGCCTAGCAC-AGNGCCTGGCACACAGTAGGCGCTCAGTAA 445 chr4qtel1M 560515 AGACGTCAATAAATGAATG 560533 v i- iiv i L2b_3end#LINE 446 ATAT-TTGTTGAATGAATG 463 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 33.36 CpG sites = 22, Kimura (unadjusted) = 39.78 Transitions / transversions = 2.20 (22/10) Gap_init rate = 0.06 (7 / 113), avg. gap size = 1.29 (9 / 7) 275 30.61 2.97 2.97 chr4qtel1M 561263 561363 (438637) C MIR3#SINE/MIR (20) 188 88 m_b205s601i11 8060 chr4qtel1M 561263 GTCAGTCCTGACCCAAGAAACATCACAGGCCATTTGAACCAACTCTTCCA 561312 vv i--- ii v i v ii i iiv i iii C MIR3#SINE/MIR 188 GTCAGAGCTGG---AAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCA 142 chr4qtel1M 561313 GTA-ACAGATGAGGAAACCAAGACCCAGAGAG--AAAGTGGCTTAGCCAG 561359 v v- ii i --i i iv i C MIR3#SINE/MIR 141 TTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAA 92 chr4qtel1M 561360 AGCC 561363 i i C MIR3#SINE/MIR 91 GGTC 88 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 42.27 CpG sites = 22, Kimura (unadjusted) = 42.27 Transitions / transversions = 2.75 (22/8) Gap_init rate = 0.05 (5 / 100), avg. gap size = 1.20 (6 / 5) 276 26.07 6.67 9.09 chr4qtel1M 561740 561874 (438126) C MIRc#SINE/MIR (31) 237 106 m_b205s601i12 8061 chr4qtel1M 561740 CTTTTTAGTTCACAGTGAGCTTT-ACAGGTAAGATCTC---TGATCCTCC 561785 vi i iv v - vii vv --- v C MIRc#SINE/MIR 237 CTTTACAGTTTACAAAGCGCTTTCACATACATTATCTCATTTGATCCTCA 188 chr4qtel1M 561786 CAGAGAGCATTGTCTCCTACCAGTGTGGGAGACAGGGCACAAGCTATT-- 561833 - v i ----------- v v v i vivii -- C MIRc#SINE/MIR 187 CA-ACAAC-----------CCTGTGAGGTAGGCAGGGCAGGTATTATTAT 150 chr4qtel1M 561834 -CCCACTTTACAGATGGGAACACTGAG--TCACAAGGGGTAGGT 561874 - i i i v -- v ii v i C MIRc#SINE/MIR 149 CCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGT 106 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 32.27 CpG sites = 16, Kimura (unadjusted) = 32.27 Transitions / transversions = 1.00 (16/16) Gap_init rate = 0.13 (17 / 134), avg. gap size = 1.24 (21 / 17) 213 22.64 1.89 0.00 chr4qtel1M 561830 561882 (438118) C MIR1_Amn#SINE/MIR (76) 154 101 m_b205s601i13 8061 chr4qtel1M 561830 TATTCCCACTTTACAGATGGGAACACTGAGTCACA-AGGGGTAGGTTGTC 561878 i i i i v v ? - i ?iiv v C MIR1_Amn#SINE 154 TATCCCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGAC 105 chr4qtel1M 561879 ATGC 561882 v C MIR1_Amn#SINE 104 TTGC 101 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 28.76 CpG sites = 7, Kimura (unadjusted) = 28.76 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.02 (1 / 52), avg. gap size = 1.00 (1 / 1) 285 28.42 1.11 2.25 chr4qtel1M 561891 561980 (438020) C MIR3#SINE/MIR (16) 192 104 m_b205s601i14 8062 chr4qtel1M 561891 GACTGCCTGAGCTAGACACCATGTTAGGG-TTGTTTTGGCCAACAGCCTC 561939 v i v i vivv iv i - ii i v v vv C MIR3#SINE/MIR 192 GAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTC 143 chr4qtel1M 561940 ATTTCACAGCTGAGGAACCTGAGGTTCAGTGAGGGGTGGAG 561980 i v v ii -- i i C MIR3#SINE/MIR 142 ATTTTACAGATGAGGAAACTGAGGCCCA--GAGAGGTGAAG 104 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 36.23 CpG sites = 13, Kimura (unadjusted) = 36.23 Transitions / transversions = 1.08 (13/12) Gap_init rate = 0.03 (3 / 89), avg. gap size = 1.00 (3 / 3) 479 30.54 12.73 0.67 chr4qtel1M 562542 562808 (437192) C L3#LINE/CR1 (14) 4085 3787 m_b205s601i15 8063 chr4qtel1M 562542 ATCCCTGAGTGGGAAGGGGTCCTAGAA-TCTCCTAAGAGACCCTTTGGCC 562590 i v v ii i i- vi ivvv v iivii C L3#LINE/CR1 4085 ATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCAACCTCCCATC 4036 chr4qtel1M 562591 CAAT--AGGAGTCCCCTGGGCAACATCCCTGACAGAGAAGCCTCCAGTCT 562638 -- i i vvi iiviiv v i C L3#LINE/CR1 4035 CAATGCAGGAATCCCTTCTACAACATCCCTGACAAGTGGTCATCCAGCCT 3986 chr4qtel1M 562639 CTGCTAGGAGAGCTCCAGTAA-AGGAAACTCATCATCTCCTG-GACAGGC 562686 v i v v i -i i i ii i ?i - i - C L3#LINE/CR1 3985 CTGCTTGAACACCTCCAGTGACGGGGAGCTCACTACCTCNCGAGGCA-GC 3937 chr4qtel1M 562687 TCACCCC--TTGGGGTCAGCCCTCATTG--GGAAAA-----CCAGACAGC 562727 i ii -- vv v i v --i i----- vv i vi C L3#LINE/CR1 3936 CCATTCCATTTTTGGACAGCTCTGATTGTTAGAAAGTTCTTCCTTATATT 3887 chr4qtel1M 562728 -AACCTAATTCTGTCCTCTTG---CTTC-------TGGTC------CTGC 562760 - i v v i ii i --- ------- ------ C L3#LINE/CR1 3886 GAGCCGAAATCTGCCTCCCTGTAACTTCCACCCATTGGTCCTAGTTCTGC 3837 chr4qtel1M 562761 CCAGTGGCACCA---AGAACAAGGCTAGGCTCTCCTCTGGCAGGACAGGC 562807 vv vi --- i v iv i i i-i v v C L3#LINE/CR1 3836 CCTCTGGAGCCACACAGAATAAGTCTAATCCCTCTTCC-ACATGACAGCC 3788 chr4qtel1M 562808 C 562808 C L3#LINE/CR1 3787 C 3787 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 39.52 CpG sites = 49, Kimura (unadjusted) = 40.85 Transitions / transversions = 1.53 (49/32) Gap_init rate = 0.05 (14 / 266), avg. gap size = 2.57 (36 / 14) 405 35.00 5.84 1.77 chr4qtel1M 562880 563804 (436196) L1PREC2_orf2#LINE/L1 2296 3257 (37) m_b205s551i0 8064 chr4qtel1M 562880 ATAGAATATTTAGGAGTCTCCCTGCCAAGACAAACCCAGGAACTGTATGA 562929 i ii i vivv iv v iv iiivv i v v ii L1PREC2_orf2# 2296 ATAAAATACCTAGGAATACAGCTAACCAGGGAGGTGAAAGATCTCTACAA 2345 chr4qtel1M 562930 AGACAATTATAAAATACTTTTTCACACAAATAAAGTCAGGTCTAAACAAC 562979 v v i i vi - v v v iivvv iivi v L1PREC2_orf2# 2346 TGAGAATTACAAAACACTGCT-CAAAGAAATCAGAGATGACACAAACAAA 2394 chr4qtel1M 562980 TGGAAAA-TATCAATTGCTTATGGGTAGGCCAAATTAATATAATAAAAAT 563028 -i ivvv i i vvi i vi v L1PREC2_orf2# 2395 TGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTTAAAAT 2444 chr4qtel1M 563029 CACAAT-CTACCTAAATTAATTTACTTATTCAATG----TCATACCACAT 563073 vi v - i i vi vv ---- v i v i L1PREC2_orf2# 2445 GGCCATACTGCCCAAAGCAATTTACAGATTCAATGCTATTCCTATCAAAC 2494 chr4qtel1M 563074 TACCAAAAATCATTTT--ATAGAGCTAGAAAAAACAGTAACAAAATTCAT 563121 vi - i -- i i vi vvi L1PREC2_orf2# 2495 TACCAATGA-CATTCTTCACAGAACTAGAAAAAACTATTTTAAAATTCAT 2543 chr4qtel1M 563122 CTGGAAGAAGAAAAGGTCAAAAATA-TCAAGGGAAT--TAATGAAAACAA 563168 v vv i iv vvi -i v -- vv vi L1PREC2_orf2# 2544 ATGGAACCAAAAAAGAGCCCGAATAGCCAAGGCAATCCTAAGCAAAAAGA 2593 chr4qtel1M 563169 ATGTGAAAGAAGGTGGCCTAGCTCTACTAGATCTCAAGTTGTATTATAAA 563218 i--- vv v v vi v iv ii ii i i i ii L1PREC2_orf2# 2594 AC---AAAGCTGGAGGCATCACGCTACCCGACTTCAAACTATACTACAGG 2640 chr4qtel1M 563219 GCAGTAATTAACAAAACATTTTGGTACTGGCTAAAAAGTAGACTGTTGGA 563268 vii i v v viv ivv ii vvv i L1PREC2_orf2# 2641 GCTACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGACACATAGA 2690 chr4qtel1M 563269 GCAGAAGAATAGATCAGGCACACCAGAAATAGTAGTAAATGACCATAGTG 563318 v ivi i vi iv vv iviviiv iiv i i iiv L1PREC2_orf2# 2691 CCAATGGAACAGAATAGAGAGCCCAGAAATAAGGCCGCACACCTACAACC 2740 chr4qtel1M 563319 ACACAGTGTTTGATAAACC---CAAAGACCCCAGATTTGGGGACAAAAAC 563365 iviii v i i v --- i -- v vvv - ii L1PREC2_orf2# 2741 ATCTGATCTTCGACAAAGCTGACAAAAA--CAAGCAATGGGGA-AAGGAC 2787 chr4qtel1M 563366 TTACTATCTAACCAAAAACTGCTGGGAAAACTGGAATACAATA-GCA-AA 563413 iv ii -i viv v vvvi v - - L1PREC2_orf2# 2788 TCCCTATTCAA-TAAATGGTGCTGGGATAACTGGCTAGCCATATGCAGAA 2836 chr4qtel1M 563414 AATTAAGTATAAATCAACATCTTATACAGCATATTAAGATGACATCAAAA 563463 i i ivv ii i vvivi i vii iv i v vv i L1PREC2_orf2# 2837 GATTGAAACTGGACCCCTTCCTTACACCATATACAAAAATCAACTCAAGA 2886 chr4qtel1M 563464 TAAA-TAAATTCTT----------CCTTTCTCCATAGA---TCTGATAGG 563499 ii - vv ---------- ivvvv i i ---i iv i L1PREC2_orf2# 2887 TGGATTAAAGACTTAAATGTAAAACCCAAAACTATAAAAACCCTGGAAGA 2936 chr4qtel1M 563500 TAAACTATTCAATTC---TCTGGAGAAAGGAAGAATTTAAGA--CCA-AA 563543 i v vv v --- v v viiviv --i -i L1PREC2_orf2# 2937 CAACCTAGGCAATACCATTCTGGACATAGGAACGGGCAAAGATTTCATGA 2986 chr4qtel1M 563544 C-AAGAAACCGAGAGC-ATTGCTAGATA---TAAAATGAGCAATTTTGAA 563588 - vi i i - v v v ---v vii v vv v L1PREC2_orf2# 2987 CGAAGACGCCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATGGGAT 3036 chr4qtel1M 563589 TATATTAAATTAAAAAGGGTTTGCACAAACAAAAACCACTGCAATCA--A 563636 ivv i i vv i - i ivv --- -- L1PREC2_orf2# 3037 CTAATTAAACTAAAGAGCTTCTGCAC-AGCAAAAGAAACT---ATCAACA 3082 chr4qtel1M 563637 GATTAGAAGGAAAACAAAAAAACTGGGGAACAATTTTTACAGCAACTTT- 563685 v i vi v vv v i v ii v ? i -- v - L1PREC2_orf2# 3083 GAGTAAACAGACAACCTACAGAATGGGAGAAAATNTTTGCA--AACTATG 3130 chr4qtel1M 563686 -CTCTGATAAAGACCTCATTCTCAAT-TATATAAAGAATTGAACCAAATA 563733 -v i ii v vii ii- v i i v v v L1PREC2_orf2# 3131 CATCTGACAAAGGTCTAATATCCAGCATCTATAAGGAACTTAAACAAATT 3180 chr4qtel1M 563734 TACAAGAAATAAGT---CATTCCCCAATTGATAAATGATCAGTGGATATA 563780 v ii--- vi -- i v i iv iv i i L1PREC2_orf2# 3181 TACAAGAAAAAAACAAACAACCCC--ATTAAAAAGTGGGCAAAGGACATG 3228 chr4qtel1M 563781 AACAG----TGTTCAGATGAAAGC-TACA 563804 ---- v i v ii - L1PREC2_orf2# 3229 AACAGACACTTTTCAAAAGAAGACATACA 3257 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 46.91 CpG sites = 161, Kimura (unadjusted) = 48.17 Transitions / transversions = 1.03 (161/157) Gap_init rate = 0.05 (42 / 924), avg. gap size = 1.69 (71 / 42) 372 32.87 12.43 3.55 chr4qtel1M 563704 564274 (435726) L1MD1_3end#LINE/L1 7 626 (363) m_b205s551i2 8064 chr4qtel1M 563704 TCTCAATTATATAAAGAATT----GAACCAAATATACAAGAAATAAGTCA 563749 vi v i ----i iv i vvv i i iiv L1MD1_3end#LI 7 TCTAGAATATATAAAGAACTCTCAAAACTCAACAGTAAAAAAACAAACAA 56 chr4qtel1M 563750 TTCCCCAATTGATAAATGATCAGTGGATATAAACAG-------------- 563785 --- iiv iv ivi i i v -------------- L1MD1_3end#LI 57 T---CCAATTAGAAAATGGGCAAAAGACATGAAGAGACATTTCACCGAAG 103 chr4qtel1M 563786 ----TGTTCAGATGAAAGCTACAGC-CATATAAAAACCTTTTAAATCACT 563830 ---- i v iv iv - - iv i iv iv v i L1MD1_3end#LI 104 AGGATATACAGATGGCAAATA-AGCACATGAAAAGATGTTCAACATCATT 152 chr4qtel1M 563831 ATTGATCAGAAAAATGCCAAT--------------GATAACATCTCACAC 563866 viv i ii v -------------- v iiv L1MD1_3end#LI 153 AGCCATTAGGGAAATGCAAATTAAAACCACAATGAGATATCACTACACAC 202 chr4qtel1M 563867 CTATCAGATTGGCTAATATGACAGGAAAGGAAAATAATAAATGTTGGAAG 563916 v v i v iiv iv v i vi i vii L1MD1_3end#LI 203 CTATCAGAATGGCTAAAATAAAAAATAGTGACAACACCAAATGCTGGCGA 252 chr4qtel1M 563917 GTTTGTGGGAAAAGTGGGACACTAATGTACTCACTGTCGGTGAGATTGTG 563966 vv i ii v iv v i---- i ii i v i L1MD1_3end#LI 253 GGATGCGGAGAAACTGGATCACTCATA----CATTGCTGGTGGGAATGTA 298 chr4qtel1M 563967 AATTGATGCAACCACTCTGGAGAGCAATTTGGAACTTTGCTTTAATACT- 564015 v i i i i i i v v vi vv v - L1MD1_3end#LI 299 AAATGGTACAGCCACTCTGGAAAACAGTTTGGCAGTTTCTTAAAAAACTA 348 chr4qtel1M 564016 -----GCA--TACCCTTTGACCCAGAAATGAGACTA---------TATTC 564049 ----- -- v vi v viv v--------- i L1MD1_3end#LI 349 AACATGCAACTACCATACGACCCAGCAATTGCACTCCTGGGCATTTATCC 398 chr4qtel1M 564050 CAAAGAAAAGTTTTAAAAATTGG-------AAAAGGACCTAGTTATCCAA 564092 i ----- i i vi------- v ii i-- iv i L1MD1_3end#LI 399 CAGAGAAA-----TGAAAACTTATGTTCACACAAAAACCTG--TACACGA 441 chr4qtel1M 564093 AAACTATTTATAGCAGTT---TTTG---TGGCAAAGAACTAGAAATTAAG 564136 --- i i --- i --- i v i i iv vv L1MD1_3end#LI 442 A---TGTTTATAGCAGCTTTATTCGTAATAGCCAAAAACTGGAAACAACC 488 chr4qtel1M 564137 GTGATGCCCATCAATTGGGGAAATGACCGGACAAGTTGTAGTTTAAGATT 564186 vv i v -i vi iiiii ii i vi vvvv L1MD1_3end#LI 489 CAGATGTCCTTCAA-CGGGTGAATGGTTAAACAAACTGTGGTACATCCAT 537 chr4qtel1M 564187 ACATTGGAATATTACTGTGCTGT---AAGAAATGAGCAGTGTGTTTCA-G 564232 vv i vv vi --- i i i vi - v v - L1MD1_3end#LI 538 ACCATGGAATACTACTCAGCAATAAAAAGGAACGAACTAT-TGATACACG 586 chr4qtel1M 564233 AAAAAACCTGGAAAAATTGAACTAGGATATTGTACAGAGTAA 564274 v v vi iv-- i iiv i i v i L1MD1_3end#LI 587 CAACAACCTGGATGAATCT--CCAGAGAATTATGCTGAGTGA 626 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 42.35 CpG sites = 101, Kimura (unadjusted) = 44.66 Transitions / transversions = 1.26 (101/80) Gap_init rate = 0.06 (36 / 570), avg. gap size = 2.58 (93 / 36) 611 25.08 15.25 2.00 chr4qtel1M 563704 564057 (435943) L1ME5_3end#LINE/L1 7 406 (535) m_b205s551i1 8064 chr4qtel1M 563704 TCTCAATTATATAAAGAATTGAACCAAATATACAAGAAATAAGTCATT-- 563751 vi v i i i vvvv vv - v iv?-- L1ME5_3end#LI 7 TCTAGAATATACAAGGAACTCCTGCAAATCAACAAGAAA-AAGACGGNAA 55 chr4qtel1M 563752 CCCCAATTGATAAATGATCAGTGGATATAAACAG----TGTTCAGATGA- 563796 v v iv iv i ---- v v v - L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chr4qtel1M 563797 ----------AAGCTA-CAGCCATATAAAAACCT-TTTAAA-TCACTATT 563833 ---------- i - iv i i vv -i i - i v L1ME5_3end#LI 106 GAAACCCGAAAGGCTAACAAGCATATGAAGAGATGCTCAAACTCATTAGT 155 chr4qtel1M 563834 GATCAGAAAAATGCCAAT--------------GATAACATCTCACACCTA 563869 i i v -------------- v ii i L1ME5_3end#LI 156 AATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCTA 205 chr4qtel1M 563870 TCAGATTGGCTAATATGACAGGAAA--GGAAAATAATAAATGTTGGAAGG 563917 i i v v --i i i-- v ivi i vii L1ME5_3end#LI 206 TTAGACTGGCAAAAAT--TAGAAAGCTGGATAATGCCAAGTGTTGGCGAG 253 chr4qtel1M 563918 TTTGTGGGAAAAGTGGGACACTAATGTACTCACTGTCGGTGAGATTGTGA 563967 vv i ? vv i v v ---- ii i v ii L1ME5_3end#LI 254 GATGTGGGGANATAGGAACCCTCATG----CACTGCTGGTGGGAGTGTAG 299 chr4qtel1M 563968 ATTGATGCAACCACTCTGGAGAGCAATTTG---GAACTTTGCT---TTA- 564010 i i i i i --- v v ii--- - L1ME5_3end#LI 300 ACTGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTAA 349 chr4qtel1M 564011 --ATACTGCATACCCTTTGACCCAGAAA---------TGAGACTATATTC 564049 -- - v v --------- i vv i L1ME5_3end#LI 350 GTATAC-GCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATATCC 398 chr4qtel1M 564050 CAAAGAAA 564057 L1ME5_3end#LI 399 CAAAGAAA 406 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 30.40 CpG sites = 46, Kimura (unadjusted) = 31.25 Transitions / transversions = 1.12 (46/41) Gap_init rate = 0.06 (22 / 353), avg. gap size = 2.82 (62 / 22) 586 28.29 11.84 2.62 chr4qtel1M 563711 564200 (435800) L1ME3Cz_3end#LINE/L1 14 547 (450) m_b205s551i3 8064 chr4qtel1M 563711 TATATAAAGAATTGAACCAAATATACAAGAAATAAGTCATTCCCCAATTG 563760 i vvvv vv i - v --v v L1ME3Cz_3end# 14 TATATAAAGAACTCCTACAAATCAATAAGAAA-AAGACA--ACCCAATAG 60 chr4qtel1M 563761 ATAAATGATCAGTGGATATAAACAG--TGTTC-----AGATGAAAGCT-- 563801 v iv iv i --vi ----- v v i-- L1ME3Cz_3end# 61 AAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGGAAACCCGA 110 chr4qtel1M 563802 ACAGC-------CATATAAAAACCTTTTAAA--TCACTATTGATCAGAAA 563842 ii ------- i vv vi v -- v i ii L1ME3Cz_3end# 111 ATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTAATCAGGGA 160 chr4qtel1M 563843 AATGCCAAT--------------GATAACATCTCACACCTATCAGATTGG 563878 v -------------- v i i L1ME3Cz_3end# 161 AATGCAAATTAAAACNACAATGAGATACCATTTCACACCCATCAGATTGG 210 chr4qtel1M 563879 CTAATATGACAGGAAAG---GAAAATAATAAATGTTGGAAGGTTTGTGGG 563925 v v v---vi --- v vi i vii vv i L1ME3Cz_3end# 211 CAAAAATT---TAAAAGTCTGACAATACCAAGTGTTGGCGAGGATGTGGA 257 chr4qtel1M 563926 AAAAGTGGGACACTAATGTACTCACTGTCGGTGAGATTGTGAATTGATGC 563975 i vv i v v i---- ii i v i i i L1ME3Cz_3end# 258 GAAACGGGAACTCTCATA----CACTGCTGGTGGGAGTGTAAATTGGTAC 303 chr4qtel1M 563976 AACCACTCTGGAGAGCAATTTGGAACTTTGCTTTAATACT--------GC 564017 i v v v vivv vii -------- L1ME3Cz_3end# 304 AACCACTTTGGAGAGCAATTTGGCAATATCTAGTAAAGTTGAAGATGCGC 353 chr4qtel1M 564018 ATACCCTTTGACCCAGAAATGAGAC-------TATATTCCAAAGA-AAAG 564059 vi v vvv ------- v vv - v L1ME3Cz_3end# 354 ATACCCTACGACCCAGCAATTCCACTTCTAGGTATATACCCTAGAGAAAC 403 chr4qtel1M 564060 TTTTAAAAAT-TGGAAAAGGACCTAGTTATCCAAAAACTATTTAT---AG 564105 i iiv v - v v vvi -- i v ii - i i --- L1ME3Cz_3end# 404 TCTCGCACATGTGCACAAGGAGACA--TGTACAAGGA-TGTTCATTGCAG 450 chr4qtel1M 564106 CAGTTTTTG---TGGCAAAGAACTAGAAATTAAGGTGATGCCCATCAATT 564152 v v --- i i i i i iv vvvvi i v L1ME3Cz_3end# 451 CATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCAATA 500 chr4qtel1M 564153 GGGGAAATGACCGGACAAGTTGTAGTTTAAGATTACATTGGAATATTA 564200 - iviii i i i v vvvv v i L1ME3Cz_3end# 501 GGGG-AATGGATAAATAAATTGTGGTATATTCATACAATGGAATACTA 547 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 34.23 CpG sites = 61, Kimura (unadjusted) = 35.84 Transitions / transversions = 0.82 (61/74) Gap_init rate = 0.06 (27 / 489), avg. gap size = 2.67 (72 / 27) 17 23.90 1.28 6.76 chr4qtel1M 565571 565648 (434352) (CCCCCTC)n#Simple_repeat 1 74 (0) m_b205s252i1 8065 chr4qtel1M 565571 CCCACTCCCCCCTCCCCCCGCCTTTGTGGGATCCTCCCCATCTCCCACCC 565620 v v iiiv -vvvi -i - (CCCCCTC)n#Si 1 CCCCCTCCCCCCTCCCCCCTCCCCCCT-CCCCCCTCCCC-CCTCCC-CCC 47 chr4qtel1M 565621 AGTCCTCCTTCCCCCC-CCCCCCTACCCC 565648 -- i i - v (CCCCCTC)n#Si 48 --TCCCCCCTCCCCCCTCCCCCCTCCCCC 74 Matrix = Unknown Transitions / transversions = 1.00 (7/7) Gap_init rate = 0.08 (6 / 77), avg. gap size = 1.00 (6 / 6) 12 26.34 0.00 0.00 chr4qtel1M 565869 565905 (434095) (AAAACCC)n#Simple_repeat 1 37 (0) m_b205s252i2 8066 chr4qtel1M 565869 AAAACCCCCCCCCCACAAGCATAAACCCAAAACCCAA 565905 vvvv v v vv (AAAACCC)n#Si 1 AAAACCCAAAACCCAAAACCCAAAACCCAAAACCCAA 37 Matrix = Unknown Transitions / transversions = 0.00 (0/8) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 30 6.13 5.77 0.00 chr4qtel1M 566163 566214 (433786) (CTC)n#Simple_repeat 1 55 (0) c_b205s251i0 8067 chr4qtel1M 566163 CTCC-CCTCCTCCTCCCCCTCCTTCTCCTCCTCCTCCTCC-CTTCC-CCT 566209 - i i - i - (CTC)n#Simple 1 CTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT 50 chr4qtel1M 566210 CCTCC 566214 (CTC)n#Simple 51 CCTCC 55 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.00 (3 / 3) 63 22.79 3.96 2.44 chr4qtel1M 566929 567130 (432870) (AAAGA)n#Simple_repeat 1 205 (0) m_b205s252i3 8068 chr4qtel1M 566929 AAAAACAACAAAACACAAAAAAAAAAAAACAAAAGGAAA-AAAACAAAAC 566977 i v v v - i i v i - v v (AAAGA)n#Simp 1 AAAGAAAAGAAAAGA-AAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAG 49 chr4qtel1M 566978 AAAA-AAAAG-GGAGAAAGGAAAAGGGAAAAGAAAAAGGGAAAAAAAAAA 567025 - -ii i -- - ii i i (AAAGA)n#Simp 50 AAAAGAAAAGAAAAGAAAAGAAAA--GAAAAG-AAAAGAAAAGAAAAGAA 96 chr4qtel1M 567026 AAAAAAAAAAAAAAGTAGGAAA-AAAATAAAACACAACAAAAG-GGGGAA 567073 i i i iv i - v v v v -iii (AAAGA)n#Simp 97 AAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAA 146 chr4qtel1M 567074 AAGGAAAGAAAA-AAAA-AAAA-AAAAAAAAAAAAAAGAGGGGAAGGAGA 567120 i - - - i i iii -i (AAAGA)n#Simp 147 AAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAA-AAGA 195 chr4qtel1M 567121 AAAGAAAAGA 567130 (AAAGA)n#Simp 196 AAAGAAAAGA 205 Matrix = Unknown Transitions / transversions = 2.36 (26/11) Gap_init rate = 0.06 (13 / 201), avg. gap size = 1.00 (13 / 13) 74 25.72 0.00 0.00 chr4qtel1M 566929 567107 (432893) (AAAAA)n#Simple_repeat 1 179 (0) m_b205s252i4 8068 chr4qtel1M 566929 AAAAACAACAAAACACAAAAAAAAAAAAACAAAAGGAAAAAAACAAAACA 566978 v v v v v ii v v (AAAAA)n#Simp 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr4qtel1M 566979 AAAAAAAGGGAGAAAGGAAAAGGGAAAAGAAAAAGGGAAAAAAAAAAAAA 567028 iii i ii iii i iii (AAAAA)n#Simp 51 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 100 chr4qtel1M 567029 AAAAAAAAAAAGTAGGAAAAAAATAAAACACAACAAAAGGGGGAAAAGGA 567078 iv ii v v v v iiiii ii (AAAAA)n#Simp 101 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 150 chr4qtel1M 567079 AAGAAAAAAAAAAAAAAAAAAAAAAAAAA 567107 i (AAAAA)n#Simp 151 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA 179 Matrix = Unknown Transitions / transversions = 2.17 (26/12) Gap_init rate = 0.00 (0 / 178), avg. gap size = 0.0 (0 / 0) 32 20.39 4.95 2.91 chr4qtel1M 567117 567217 (432783) (GA)n#Simple_repeat 1 103 (0) m_b205s252i5 8069 chr4qtel1M 567117 GAGA-AAAGA-AAAGAGGCAGGGAGAGAGGGAGCAAAGGGAGAG-GACAG 567163 - i - i iv i i - i i - v (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG-AGAGAGAGAGAGAGAG 49 chr4qtel1M 567164 ACAGAGACAGAGATGCACAGAGAGCTAGAGAGGGA-AGA-AGAGACACAG 567211 v v - - v vv i - - v v (GA)n#Simple_ 50 AGAGAGAGAGAGA-G-AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 97 chr4qtel1M 567212 AGAGAG 567217 (GA)n#Simple_ 98 AGAGAG 103 Matrix = Unknown Transitions / transversions = 0.89 (8/9) Gap_init rate = 0.08 (8 / 100), avg. gap size = 1.00 (8 / 8) 192 10.81 2.63 2.63 chr4qtel1M 567417 567454 (432546) C L2b_3end#LINE/L2 (30) 436 399 m_b205s601i16 8070 chr4qtel1M 567417 GCCTACTGTGTGCCAAGCT-TCTGCTAAGCACTCGGGGA 567454 i ?- v i i - C L2b_3end#LINE 436 GCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCT-GGGGA 399 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 9.23 CpG sites = 3, Kimura (unadjusted) = 12.24 Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 325 28.57 3.08 3.08 chr4qtel1M 567490 567619 (432381) MIRb#SINE/MIR 5 134 (134) m_b205s601i17 8071 chr4qtel1M 567490 GGGCCAGAGCGGGACAGTGGCAAACAGCCACAGGCTT-GGAGTTGG---G 567535 v v i vi - v - i - ii --- MIRb#SINE/MIR 5 GGGGCAGCGTGGTGCAGTGG-AAAGAGC-ACGGGCTTTGGAGTCAGACAG 52 chr4qtel1M 567536 ACCTGTGGCAGCTCCCCAGCTCAACCATATATTGTCGACGTGACCTTGGA 567585 v viv vvi i vi iv i iv vii i MIRb#SINE/MIR 53 ACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGG 102 chr4qtel1M 567586 CAAGTCCTGGGCCCTCTCTGCAAGCCTCATTTTC 567619 ivivviv -- v MIRb#SINE/MIR 103 CAAGTTACTTAACCTCTCTG--AGCCTCAGTTTC 134 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 33.95 CpG sites = 18, Kimura (unadjusted) = 36.39 Transitions / transversions = 1.00 (18/18) Gap_init rate = 0.05 (6 / 129), avg. gap size = 1.33 (8 / 6) 18 48.48 0.00 0.00 chr4qtel1M 568129 568236 (431764) (GG)n#Simple_repeat 1 108 (0) m_b205s252i6 8072 chr4qtel1M 568129 GGGGTGTGTGAGGGGGGGGAGAGGGGAAAGAGAGGGGGGAGAAGGGAGGA 568178 v v v i i i iii i i i ii i i (GG)n#Simple_ 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 50 chr4qtel1M 568179 AGAGAGGGGAGAGACAGAGACAGAGGGGGGGGGGGGGGGGGAAGGGAGAG 568228 i i i i i ivi i ivi i ii i i (GG)n#Simple_ 51 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 100 chr4qtel1M 568229 AGGGAGGG 568236 i i (GG)n#Simple_ 101 GGGGGGGG 108 Matrix = Unknown Transitions / transversions = 6.00 (30/5) Gap_init rate = 0.00 (0 / 107), avg. gap size = 0.0 (0 / 0) 34 28.65 4.27 0.00 chr4qtel1M 568147 568263 (431737) (GA)n#Simple_repeat 1 122 (0) m_b205s252i7 8072 chr4qtel1M 568147 GAGAG-GGGAAAGAGAG-GGGGGAGA-AGGGAGGAAGAGAG-GGGAGAGA 568192 - i i - i i - i ii - i (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr4qtel1M 568193 CAGAGACAGAGGGGGGGGGGGGGGGGGA-AGGGAGAGAGGGAGGGAGAGA 568241 v v i i i i i i i i - i i i (GA)n#Simple_ 51 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 100 chr4qtel1M 568242 CAGACACAGAGACACTGAGAGA 568263 v v v v vv (GA)n#Simple_ 101 GAGAGAGAGAGAGAGAGAGAGA 122 Matrix = Unknown Transitions / transversions = 2.38 (19/8) Gap_init rate = 0.04 (5 / 116), avg. gap size = 1.00 (5 / 5) 16 21.86 7.81 0.00 chr4qtel1M 568458 568521 (431479) (GCTGGA)n#Simple_repeat 1 69 (0) m_b205s252i8 8073 chr4qtel1M 568458 GCCGGAGCTGGAACTGGCCCTGG-GC-GGGGCTGGA-CTTTAGGCGGA-- 568502 i i vv - - i - vv vi -- (GCTGGA)n#Sim 1 GCTGGAGCTGGAGCTGGAGCTGGAGCTGGAGCTGGAGCTGGAGCTGGAGC 50 chr4qtel1M 568503 TGGAGCCGGGGCTGAAGCT 568521 i i i (GCTGGA)n#Sim 51 TGGAGCTGGAGCTGGAGCT 69 Matrix = Unknown Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.06 (4 / 63), avg. gap size = 1.25 (5 / 4) 39 5.29 3.28 1.61 chr4qtel1M 568634 568694 (431306) (CCTC)n#Simple_repeat 1 62 (0) c_b205s251i1 8074 chr4qtel1M 568634 CCTCCCTCCCTCCC-CCCTTCCTTCCCTCCCTCTCTCCCTCCCTCCCTCC 568682 - - i i (CCTC)n#Simpl 1 CCTCCCTCCCTCCCTCCC-TCCCTCCCTCCCTCCCTCCCTCCCTCCCTCC 49 chr4qtel1M 568683 C-CCCTGCCTCCC 568694 - v (CCTC)n#Simpl 50 CTCCCTCCCTCCC 62 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.05 (3 / 60), avg. gap size = 1.00 (3 / 3) 100 32.70 1.97 0.49 chr4qtel1M 569006 569089 (430911) (CT)n#Simple_repeat 1 88 (324) m_b205s252i9 8075 chr4qtel1M 569006 CTCTCCTTCCCTCTCCCTCTC-CTCTCTCTCCATCTCCCTCTTTGCCTC- 569053 ii i i - iv i i vi - (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chr4qtel1M 569054 CTCTCTCTC-CTCTCCCTTTTTGTCTCT-TCTCCCTTT 569089 - i i i v - i i (CT)n#Simple_ 51 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 88 Matrix = Unknown Transitions / transversions = 4.33 (13/3) Gap_init rate = 0.05 (4 / 83), avg. gap size = 1.00 (4 / 4) 63 3.18 0.00 0.00 chr4qtel1M 569090 569154 (430846) (TCC)n#Simple_repeat 1 65 (0) c_b205s251i2 8076 chr4qtel1M 569090 TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTTCTCTTCCTCCTC 569139 i i (TCC)n#Simple 1 TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC 50 chr4qtel1M 569140 CTCCTCCTCCTCCTC 569154 (TCC)n#Simple 51 CTCCTCCTCCTCCTC 65 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0) 100 32.70 1.97 0.49 chr4qtel1M 569155 569336 (430664) (CT)n#Simple_repeat 89 271 (141) m_b205s252i9 8077 chr4qtel1M 569155 TTTCTCCGTCTCTCTTTCTCTGTCTCTGTGTGTGTGTCTATCTC-CTCTC 569203 i iv i v v v v v v v - (CT)n#Simple_ 89 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 138 chr4qtel1M 569204 TCTGTCTCTCTGTCTGGCTCTGAATCTCTCTTTCTTTGTCTCTGTGTCTC 569253 v v vv vvv i i v v v (CT)n#Simple_ 139 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 188 chr4qtel1M 569254 CGTCTTTCTGTCTCTCTGTGTGCCTCTGTATGTCTCTGTGTGTATGTGTG 569303 iv i v v v vi v v v v v v v v v v (CT)n#Simple_ 189 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 238 chr4qtel1M 569304 TGTGTGTATGTCTGTGTCTGTCTC-CTCTCTGTG 569336 v v v v v v v v - v - (CT)n#Simple_ 239 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT- 271 Matrix = Unknown Transitions / transversions = 0.19 (8/42) Gap_init rate = 0.02 (3 / 181), avg. gap size = 1.00 (3 / 3) 30 6.98 2.22 0.00 chr4qtel1M 569337 569381 (430619) (TGTCTC)n#Simple_repeat 1 46 (0) c_b205s251i3 8078 chr4qtel1M 569337 TGTCTCTGTCTGTATCTCTGTCTCTGTC-CTTTCTCTGTCTCTGTC 569381 v i - v (TGTCTC)n#Sim 1 TGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTC 46 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 100 32.70 1.97 0.49 chr4qtel1M 569382 569519 (430481) (CT)n#Simple_repeat 272 410 (2) m_b205s252i9 8079 chr4qtel1M 569382 ACTTTCTGTCTTTGCTGGCCGGCCGACTCTGGCTATGGCTCTCTCTGTCT 569431 v i v i - vv ivv ivv vv v vv v (CT)n#Simple_ 272 TCTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 320 chr4qtel1M 569432 GGCTCTGGTTCTCTGTCAGTGTCTCTTTCTCTATCTCCCTCTGTCTCTGT 569481 vv vvi v vv v i v i v v (CT)n#Simple_ 321 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 370 chr4qtel1M 569482 CTCTCTTTGTGTGTGTCTCT-TGTCTCTGTGTCTCT-TCT 569519 i v v v v - v v v - (CT)n#Simple_ 371 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 410 Matrix = Unknown Transitions / transversions = 0.25 (8/32) Gap_init rate = 0.02 (3 / 137), avg. gap size = 1.00 (3 / 3) 232 23.21 1.79 0.00 chr4qtel1M 570790 570845 (429155) C L2c_3end#LINE/L2 (10) 468 412 m_b205s601i18 8080 chr4qtel1M 570790 TCAATAAACACTTATTAAGCACCTACTAAATGCCAGATTCAGGGGTTA-G 570838 i i i i vi iiv v v -i C L2c_3end#LINE 468 TCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGATACA 419 chr4qtel1M 570839 AACATGA 570845 v C L2c_3end#LINE 418 AAGATGA 412 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 23.52 CpG sites = 8, Kimura (unadjusted) = 28.42 Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.02 (1 / 55), avg. gap size = 1.00 (1 / 1) 965 22.63 5.71 0.78 chr4qtel1M 571574 571818 (428182) MIR#SINE/MIR 6 262 (0) m_b205s601i19 8081 chr4qtel1M 571574 ATGGCACAGTGG---AGAGTGCTGGAGCTGGAGTTAGGAAGACCAGAGTT 571620 i i --- ii v vv ii - vvi v i MIR#SINE/MIR 6 ATAGCATAGTGGTTAAGAGCACGGGCTCTGGAGCCAG-ACTGCCTGGGTT 54 chr4qtel1M 571621 CAAATCCATCCTCTAACCCTT------TGTGTGACCTTTGGCAAACCACT 571664 i vvv iv v ------ v iii MIR#SINE/MIR 55 CGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACT 104 chr4qtel1M 571665 TCATCTCT----GCCTCAGTTTCCTCCTCTGTGAAATGGGGTTAATAATA 571710 v i ---- v i v MIR#SINE/MIR 105 TAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATA 154 chr4qtel1M 571711 GCACCTGCCTCCTGGGGTTCTCATGAGGATGAAATGAAATAATAATTGCA 571760 i i v i v ii v iv vv i MIR#SINE/MIR 155 GTACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATACATGTA 204 chr4qtel1M 571761 AGGCACTTAGCACAATGCCTGACACACAGTAAAAG-TCATTTAAATATAA 571809 i i v i i i iv - -v i v MIR#SINE/MIR 205 AAGCGCTTAGAACAGTGCCTGGCACATAGTAAGCGCTCA-ATAAATGTTA 253 chr4qtel1M 571810 GCTATGATT 571818 v MIR#SINE/MIR 254 GCTATTATT 262 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 26.11 CpG sites = 29, Kimura (unadjusted) = 27.23 Transitions / transversions = 1.12 (29/26) Gap_init rate = 0.02 (6 / 244), avg. gap size = 2.67 (16 / 6) 538 22.48 12.56 5.43 chr4qtel1M 572156 572362 (427638) MIRc#SINE/MIR 10 230 (38) m_b205s601i20 8082 chr4qtel1M 572156 GTAGTGCAGTGGATAGAGCACCAGCCCTGAAGTCAGGAGGATCTGAGTTC 572205 i v ii v i i i i i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr4qtel1M 572206 AAATATGGTCTCAGACATTTAATACTTCCTAGCTGTGTGACCCTGGGCAA 572255 i ----- i i --v i ivi v i MIRc#SINE/MIR 60 GA-----GTCCCGG--CTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 102 chr4qtel1M 572256 GTCACTTAA-CTC---------CAGTTGCCTCAGC----AAATGAGGTTA 572291 - --------- v v ---- i v MIRc#SINE/MIR 103 GTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATA 152 chr4qtel1M 572292 ATACAATCT---CTGCAGACCTTCAATAAAA----TATGAG---CAAACA 572331 vv i --- vv i-- i iii---- i --- ii MIRc#SINE/MIR 153 ATAATACCTGCCCTGCCTACCTC--ACAGGGTTGTTGTGAGGATCAAATG 200 chr4qtel1M 572332 ACAAAAAG--AGTGAAAATGCTATGTTGTGAAC 572362 v v v --v ii --- i MIRc#SINE/MIR 201 AGATAATGTATGTGAAAGCGCT---TTGTAAAC 230 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 25.37 CpG sites = 28, Kimura (unadjusted) = 27.52 Transitions / transversions = 1.75 (28/16) Gap_init rate = 0.09 (19 / 206), avg. gap size = 2.00 (38 / 19) 1216 29.23 3.28 1.98 chr4qtel1M 572459 573006 (426994) C L1ME4c_3end#LINE/L1 (275) 555 1 m_b205s551i4 8083 chr4qtel1M 572459 ATAATATTCCATAACATTCATAGACCATAAT--ATTTAGCCATTCCCAAA 572506 vivi ?v iv -- i i vv C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chr4qtel1M 572507 CTGATGGGAAGCCACTCAGTTTCCAGTTTCTTGCCACTACAAA-AAGGGT 572555 i v iv vii vviv i i i i i i - v v C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCT 456 chr4qtel1M 572556 GC--TG--CATTTTTGCATATGTGGGTCCTTTTCCCTCCTTT--ATGATC 572599 -- -- i i iii i i -- i i i -- v i C L1ME4c_3end#L 455 GCAATGAACATCTTCGTGCATATAG--CTTTTTCCTTCTTTTGAATTATT 408 chr4qtel1M 572600 TCTTTGGAATATGAGCCCAGGAGAGACACTGCTGGATCAAAGGATATG-- 572647 i i i vivv i v iv i i i i -- C L1ME4c_3end#L 407 TCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAA 358 chr4qtel1M 572648 CATAATGATAGCTTTTTGGACATAGTTCCATATTGTTCTCCAGAATGGTT 572697 vv v i i viv i v v v i i i v C L1ME4c_3end#L 357 CATTTTTATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTT 308 chr4qtel1M 572698 GGATCCATTCACAACTCCAC-AACAATGTTTTAGTGTCCCAGTTTTTCCA 572746 v i v i ?iv - i v v ? v iv i C L1ME4c_3end#L 307 GTACCAATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCACCG 258 chr4qtel1M 572747 CAACCACTCCAGCATTTATTATTATC--TTTTCCAATCATCTTAGGCAAT 572794 ? v v viv -- ii -- i v vi C L1ME4c_3end#L 257 CANCCTCGCCAGCATTGGGTATTATCAATTTTTTAA--ATTTTTGCTAAT 210 chr4qtel1M 572795 CTGAGAGCTGTGAAATGTGAAATGGTACCTCAGAATTGTCTTAATTTTCA 572844 i i v -------ii i i vvi ii v C L1ME4c_3end#L 209 TTAATAG-------GCGTAAAATGGTATCTCATTGTTGCTTTAATTTGCA 167 chr4qtel1M 572845 TTTCTCTAATCAATAGTGATGCAGAGCACCTATTTATATGACTAGAAATG 572894 i i i v i v iv i ii v ii i vi ivvv iv C L1ME4c_3end#L 166 TTTCTTTGATTACTAGCGAGGTTGAACATTTTTCCATGTGTTTGTTTACT 117 chr4qtel1M 572895 ACTTTAATTTCATCATATGAAAATTGTTTGTTCATATCCTTTGACCATTT 572944 ? vv v v ? vi i i v C L1ME4c_3end#L 116 ANTTGTATTTCCTCTTNTGTGAATTGTCTGTTCATGTCCTTTGCCCATTT 67 chr4qtel1M 572945 ATC-ATTGCAGAATGGTTTGTATTCCTATAAATTTGAATCAATTCTCTAT 572993 - vi vv v v ?v v i v v ii i C L1ME4c_3end#L 66 ATCTATTGGGGTCTTGATNTTTTTCTTATCAATTTGAATGAGCTCTTTAT 17 chr4qtel1M 572994 A---TATAGATATAAA 573006 --- ? v C L1ME4c_3end#L 16 ATANTANAGATATTAA 1 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 36.41 CpG sites = 86, Kimura (unadjusted) = 38.56 Transitions / transversions = 1.21 (86/71) Gap_init rate = 0.04 (21 / 547), avg. gap size = 1.38 (29 / 21) 283 36.14 4.60 3.27 chr4qtel1M 572861 573555 (426445) C L1P3_orf2#LINE/L1 (0) 3294 2591 m_b205s551i5 8083 chr4qtel1M 572861 TGATGCAGAGCACCTATTTATATGACTAGAAATGACTTTAATTTCATCAT 572910 vv vii v i vi ivviiivi v v v v v C L1P3_orf2#LIN 3294 TGATGATGAGCTTTTTTTCATATGTTTGTTGGCCGCATAAATGTCTTCTT 3245 chr4qtel1M 572911 ATGAAAATTGTTTGTTCATATCCTTTGACCATTTATCATTGCAGAATGGT 572960 v i v i i v i v iiv -- ii v C L1P3_orf2#LIN 3244 TTGAGAAGTGTCTGTTCATATCCTTCGCCCACTTTTTGATG--GGGTTGT 3197 chr4qtel1M 572961 TTGTATT---CCTATAAATTTGAATCAATTCTCTATATAT---AGATATA 573004 v --- i i vv v i ii i v ---i v C L1P3_orf2#LIN 3196 TTGTTTTTTTCTTGTAAATTTGTTTAAGTTCCTTGTAGATTCTGGATATT 3147 chr4qtel1M 573005 AAGCTTTTATCAGAACCCTTGAATGTAAAAAACTTTCCCCAGTTTTCTGC 573054 iv i i vvvv v v i vi ii v i viv v C L1P3_orf2#LIN 3146 AGCCCTTTGTCAGATGGATAGATTGCAAAAATTTTCTCCCATTCTGTAGG 3097 chr4qtel1M 573055 TTCCCTTCTAATCTTGGCTGCA-TTGCTTTTGTT-TGTACAAACTCTTTT 573102 v vi v iii iivii - v i - i v i - C L1P3_orf2#LIN 3096 TTGCCTGTTCACTCTGATGATAGTTTCTTTTGCTGTGCAGAAGCTCTTT- 3048 chr4qtel1M 573103 AAATTTAATATAATCAAAATTAACCGTTTTGCATTCCATAAGGTACTCTA 573152 - i vvi vv v iv vi vv iii ---- i iv v C L1P3_orf2#LIN 3047 -AGTTTAATTAGATCCCATTTGTCAATTTTGGCTTTTGT----TGCCATT 3003 chr4qtel1M 573153 GTTCTT----CTTTGGCCATAAATTTTTTCCTTCTCCACAGATC-TGAGA 573197 i i ----i i i i v i v iiv v vi vi - -- C L1P3_orf2#LIN 3002 GCTTTTGGTGTTTTAGTCATGAAGTCTTTGCCCATGCCTATGTCCTGA-- 2955 chr4qtel1M 573198 CATAACTATCCCT---TGTTCTCCT--GATTTGCTTATAATATTGCTCTT 573242 - iiivv v --- v i -- i -- ii v ivvii C L1P3_orf2#LIN 2954 -ATGGTATTGCCTAGGTTTTCTTCTAGGGTTT--TTATGGTTTTAGGTCT 2908 chr4qtel1M 573243 TATGTTTAAATCATGAACCCATTTTGACCTTATCTTGGTATAGGGTGTTA 573292 i i v v i i vi v i v i v C L1P3_orf2#LIN 2907 TACGTTTAAGTCTTTAATCCATCTTGAGTTAATTTTTGTATAAGGTGTAA 2858 chr4qtel1M 573293 GATTTTGATC-AGTGCCTAGTTTCTGCCATA---CTAGTTTCCAATTTTC 573338 ivvvv i - vi viv - --- --- i C L1P3_orf2#LIN 2857 GGAAGGGGTCCAGTTTCAGTTTTCTGC-ATATGGCTAG---CCAGTTTTC 2812 chr4qtel1M 573339 TCAGGAATTTTTGTCAAATAGTGAGTCTTTATTTGAAAAGCTGGGGTCTT 573388 i iv viv i i v i i - iivv vv v -- i C L1P3_orf2#LIN 2811 CCAACACCATTTATTAAATAGGGAATCCTT-TCCCCATTGCTTG--TTTT 2765 chr4qtel1M 573389 TG---GGTTTATCAAATACTAAATTACTATAGTCAC-TGACTATTGTGTC 573434 --- i v ii i vii i viii- i -i i v C L1P3_orf2#LIN 2764 TGTCAGGTTTGTCAAAGATCAGATGGTTGTAGATGTGTGGC-GTTATTTC 2716 chr4qtel1M 573435 TTATGAACCTCCTCTACTCCACTGATCTAC-TACTTTATTTCTTAGCCAG 573483 v v vvi vi ii i i i- ii vv vv - C L1P3_orf2#LIN 2715 TGAGGCCTCTGTTCTGTTCCATTGGTCTATATATCTGTTTTGGTA-CCAG 2667 chr4qtel1M 573484 TACCAAATGGTTTTGATGACTACTGCTTAATAATACAATTTTAGGTCTGG 573533 viiv i v iiv i vi i i i v i v C L1P3_orf2#LIN 2666 TACCATGCTGTTTTGGTTACTGTAGCCTTGTAGTATAGTTTGAAGTCAGG 2617 chr4qtel1M 573534 TAATTTAGA-----CCACCTTTGTTTT 573555 iiv - ----- v i C L1P3_orf2#LIN 2616 TAGCGT-GATGCCTCCAGCTTTGTTCT 2591 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 49.36 CpG sites = 132, Kimura (unadjusted) = 50.85 Transitions / transversions = 1.19 (132/111) Gap_init rate = 0.05 (37 / 694), avg. gap size = 1.49 (55 / 37) 280 34.96 7.65 2.03 chr4qtel1M 573494 573820 (426180) C L1ME4a_3end#LINE/L1 (303) 568 224 m_b205s551i6 8083 chr4qtel1M 573494 TTTTGATGACTACTGCTTAATAATACAATTT-TAGGTCTG--GTAATTTA 573540 i i --- v v v v ? - i i v i--i C L1ME4a_3end#L 568 TTTTAATGGCT---GCATAATATTCCATTNTATGGATGTACCATAATTTA 522 chr4qtel1M 573541 ---GACCA--CCTTTGTT-TTGGGCATCTACTTTGTTTCTAGTATTCTGT 573584 ---i -- ii i - i i vv i i v ii i C L1ME4a_3end#L 521 TTTAACCANTCCCCTATTGTTGGACATTTAGGTTGTTTCCAATTTTTCGC 472 chr4qtel1M 573585 CACCACAAA-AGTCCTGATAATGAGTGTTTTGCTATATATGGAGCTTTTC 573633 i ii i - i v -ii iii ii vv i --- iii v C L1ME4a_3end#L 471 TATTATAAATAATGCTG-CGATGAACATCCTTGTACATA---AATCTTTG 426 chr4qtel1M 573634 TTTTTGTCTTTGACT---TTCTTGGG-TGTGTGCCCAGCTGTGA------ 573673 ?ivii i i --- i i - ivi v i vv i------ C L1ME4a_3end#L 425 TNCACATCTCTGATTATTTCCTTAGGATAAATTCCTAGAAGTGGAATTAC 376 chr4qtel1M 573674 ----TCAAAGGGTATGAGCATTTTATTCACTTTCTTCATATAATTTCAAA 573719 ---- ?i vvvvi ivvi i v vi C L1ME4a_3end#L 375 TGGGTCAAAGGGTATGNACATTTTTAAGGCTTTTGATACATATTGCCAAA 326 chr4qtel1M 573720 TTGCTTTCCAGAGAATTCAGATCAGTTTACAGTTTCACCAACAGTATGCT 573769 ii i iv iiv i i v ii i i iiv C L1ME4a_3end#L 325 TTGCCCTCCAGAAAGGTTGTACCAATTTACACTCCCACCAGCAGTGTATG 276 chr4qtel1M 573770 AGTGTGCCTGACTTTCTACTGCTCCTCCAATATT-ATTGTTGTTAAGCTT 573818 v i vi i? i vv ii v i i -iv i i i v C L1ME4a_3end#L 275 AGAGTGCCCGTTTCNCCACACCCTCGCCAACACTGGGTATTATCAATCTT 226 chr4qtel1M 573819 TT 573820 C L1ME4a_3end#L 225 TT 224 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 49.51 CpG sites = 76, Kimura (unadjusted) = 51.65 Transitions / transversions = 2.11 (76/36) Gap_init rate = 0.06 (18 / 326), avg. gap size = 1.78 (32 / 18) 337 31.81 0.65 2.63 chr4qtel1M 573667 573821 (426179) C L1ME4b_3end#LINE/L1 (518) 374 223 m_b205s551i7 8083 chr4qtel1M 573667 GCTGTGATCAAAGGGTATGAGCATTTTATTCACTTTCTTCATATAATTTC 573716 - i v v-- v i vv - v v vi C L1ME4b_3end#L 374 GCTG-GGTCAAAGGGTATGTGCATTTG--TAATTTTGAT-AGATATTGCC 329 chr4qtel1M 573717 AAATTGCTTTCCAGAGAATTCAGATCAGTTTACAGTTTCACCAACAGTAT 573766 ii v iv iiv i i v ii i i i C L1ME4b_3end#L 328 AAATTGCCCTCCATAGAGGTTGTACCAATTTACACTCCCACCAGCAATGT 279 chr4qtel1M 573767 GCTAGTGTGCCTGACTTTCTACTGCTCCTCCAATATTAT-TGTTGTTAAG 573815 iiv v vi ii i vv ii v i ivi - i i i C L1ME4b_3end#L 278 ATGAGAGTGCCTGTTTCCCCACACCCTCGCCAACACAGTGTGTTATCAAA 229 chr4qtel1M 573816 CTTTTT 573821 C L1ME4b_3end#L 228 CTTTTT 223 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 42.91 CpG sites = 29, Kimura (unadjusted) = 42.91 Transitions / transversions = 1.53 (29/19) Gap_init rate = 0.03 (5 / 154), avg. gap size = 1.00 (5 / 5) 418 19.78 5.49 0.00 chr4qtel1M 573895 573985 (426015) C MIR#SINE/MIR (117) 145 50 m_b205s601i21 8084 chr4qtel1M 573895 CCTCATTTTACAGATAAGGAAACTGAGGCAAACTG-GGTTAAGTGACTTG 573943 i i v vv - i C MIR#SINE/MIR 145 CCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTG 96 chr4qtel1M 573944 CCCAGAGTCATATAGTTAGTATCT----GAGGCCAGATTGGAACTC 573985 ii i i i vv ---- v vi v i C MIR#SINE/MIR 95 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCC 50 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 23.22 CpG sites = 10, Kimura (unadjusted) = 23.22 Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.02 (2 / 90), avg. gap size = 2.50 (5 / 2) 17 6.12 0.00 7.89 chr4qtel1M 575061 575095 (424905) (TCTCTG)n#Simple_repeat 1 32 (6) m_b205s252i10 8085 chr4qtel1M 575061 TCTCTGTCTCTGTCTCTATGTGTCTGTCATCTGTC 575095 -- v - (TCTCTG)n#Sim 1 TCTCTGTCTCTGTCTC--TGTCTCTGTC-TCTGTC 32 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.09 (3 / 34), avg. gap size = 1.00 (3 / 3) 29 0.00 0.00 0.00 chr4qtel1M 575096 575120 (424880) (TG)n#Simple_repeat 1 25 (0) c_b205s251i4 8086 chr4qtel1M 575096 TGTGTGTGTGTGTGTGTGTGTGTGT 575120 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGT 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 31 11.55 0.00 0.00 chr4qtel1M 575125 575171 (424829) (CA)n#Simple_repeat 1 47 (0) m_b205s252i11 8087 chr4qtel1M 575125 CACACAAACACACACACAAACATACACACACACATGCACACACACAC 575171 v v i ii (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACAC 47 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 276 30.07 4.76 2.33 chr4qtel1M 575347 575472 (424528) C L2d_3end#LINE/L2 (5) 511 383 m_b205s601i22 8088 chr4qtel1M 575347 CAGTCAACCAACAAGCATTTGTTAAGTGCTTGCTATGT--CAAGCTCTAT 575394 i i i i i i i i --iv v i C L2d_3end#LINE 511 CAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTGT 462 chr4qtel1M 575395 TTGAGGACCT---GGGAAAGCAAAGAGAATTGATAAAAAATAATCTCTGC 575441 viv vv --- v v? i ? i -- i v ii i C L2d_3end#LINE 461 GCTAGGCGCTGTGGGGAACGANAAAANAGT--ATAAGACATGGTCCCTGC 414 chr4qtel1M 575442 CTGAAAAAATGTCTACATTC-AAAGGGGGAGA 575472 ivv ii - ii v - ivv C L2d_3end#LINE 413 CCTCAAGGA-GCTTACAATCTAGTTGGGGAGA 383 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 39.37 CpG sites = 23, Kimura (unadjusted) = 40.83 Transitions / transversions = 1.64 (23/14) Gap_init rate = 0.05 (6 / 125), avg. gap size = 1.50 (9 / 6) 291 27.27 1.30 0.00 chr4qtel1M 575523 575599 (424401) C MIR3#SINE/MIR (60) 148 71 m_b205s601i23 8089 chr4qtel1M 575523 CCCCTCATTTTTCCAATGAGGAAGCTAAGGCCCAGAGACGTTGTGAGACT 575572 v vi i i v viv v C MIR3#SINE/MIR 148 CCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACT 99 chr4qtel1M 575573 GACTTGGAGTGACGTAGCTC-TTAGTGG 575599 vi iiiii v ii ?v- C MIR3#SINE/MIR 98 TGCCCAAGGTCACACAGCNAGTTAGTGG 71 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 35.23 CpG sites = 12, Kimura (unadjusted) = 35.23 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.01 (1 / 76), avg. gap size = 1.00 (1 / 1) 288 35.94 0.00 7.27 chr4qtel1M 575951 576127 (423873) L2b_3end#LINE/L2 284 448 (18) m_b205s601i24 8090 chr4qtel1M 575951 CTCAAGTCTTGTCCCTTCCAATTCCAAGGACTTTTGGGTGCCTGTGTATT 576000 i v i i- v -i iii --- v ?iv i ?v iv L2b_3end#LINE 284 CCCCAGTCCTA-CCCTGCCA-CTCTGGG---TTATNATTGTCTGNTTACA 328 chr4qtel1M 576001 GGCCTGCCCTCCACCAGGGGATCATAAACCCCTCAAAGCCAGGAGCCACC 576050 v i i - v vvi iii i i i vii i v ii i?v L2b_3end#LINE 329 TGTCTGTC-TCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNG 377 chr4qtel1M 576051 TTTTCCTTTTCTGGCTTCCCCACCTTATCCCCAGGACCTAGTCCAATACT 576100 i vi v ------ v i iv vi iv i?i i L2b_3end#LINE 378 TCTGTCTTGT------TCACCGCTGTATCCCCAGCGCCTAGCACAGNGCC 421 chr4qtel1M 576101 GGGCATCCAGTGGGTGCTCAATAAATA 576127 v iv i i i L2b_3end#LINE 422 TGGCACACAGTAGGCGCTCAGTAAATA 448 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 48.35 CpG sites = 38, Kimura (unadjusted) = 53.68 Transitions / transversions = 1.81 (38/21) Gap_init rate = 0.07 (12 / 176), avg. gap size = 1.00 (12 / 12) 346 30.26 2.22 6.98 chr4qtel1M 575993 576127 (423873) L2d_3end#LINE/L2 368 496 (20) m_b205s601i25 8090 chr4qtel1M 575993 TGTGTATTGGCCTGCCCTCCACCAGGGGATCATAAACCCCTCAAAGCCAG 576042 i i i vvi v v vvi ii i i ii i v L2d_3end#LINE 368 TGTGTGTTAGTCTTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAG 417 chr4qtel1M 576043 GAGCCAC--CTTTTCCTTTTCTGGC-TTCCCCACCTTATCCCCAGGACCT 576089 ii i-- v v ? i ?v - --------- vi L2d_3end#LINE 418 GGACCATGTCTTATACTNTTTTNTCGTTCCCCAC---------AGCGCCT 458 chr4qtel1M 576090 AGTCCAATACTGGGCATCCAGTGGGTGCTCAATAAATA 576127 iv i i i ivi i i L2d_3end#LINE 459 AGCACAGTGCTGAGCACATAGTAGGCGCTCAATAAATA 496 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 38.49 CpG sites = 25, Kimura (unadjusted) = 41.35 Transitions / transversions = 1.92 (25/13) Gap_init rate = 0.08 (11 / 134), avg. gap size = 1.09 (12 / 11) 233 34.29 0.00 0.00 chr4qtel1M 576319 576388 (423612) C L2b_3end#LINE/L2 (0) 466 397 m_b205s601i26 8091 chr4qtel1M 576319 ATCTAACCAACCAACAAGGACTCATTAAGCCTTCACTTTATTCCAGGCCC 576368 ii vi vi iv i i i i viii v i v ? C L2b_3end#LINE 466 ATTCATTCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNC 417 chr4qtel1M 576369 TAGACTGGGCACTGGGGATA 576388 ivi i i C L2b_3end#LINE 416 TGTGCTAGGCGCTGGGGATA 397 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 47.65 CpG sites = 17, Kimura (unadjusted) = 50.76 Transitions / transversions = 2.43 (17/7) Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0) 208 37.48 3.51 1.72 chr4qtel1M 576327 576440 (423560) C L2d2_3end#LINE/L2 (8) 547 432 m_b205s601i27 8091 chr4qtel1M 576327 AACCAACAAGGACTCATTAAGCCTTCACTTTATTCCAGGCCCTAGACTGG 576376 i iv i i i viii v i v v v ivi i C L2d2_3end#LIN 547 AATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAG 498 chr4qtel1M 576377 GCACT---GGGGATATTAAGTGGGACATCTTGTGGGATGTCT-TCCACAA 576422 i --- iv vi v i vvvii -- vi -i v C L2d2_3end#LIN 497 GCGCTGTGGGGGATACAAAGAAGTATAAGACATGG--TCCCTGCCCTCAA 450 chr4qtel1M 576423 GGGTCTTATAGTACAGCT 576440 iv i i vi i C L2d2_3end#LIN 449 GGAGCTTACAATCTAGTT 432 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 52.68 CpG sites = 25, Kimura (unadjusted) = 54.64 Transitions / transversions = 1.47 (25/17) Gap_init rate = 0.04 (4 / 113), avg. gap size = 1.50 (6 / 4) 199 32.00 0.83 7.02 chr4qtel1M 577076 577196 (422804) C MamTip2b#DNA/hAT-Tip100 (76) 373 260 m_b205s601i28 8092 chr4qtel1M 577076 GGCCCAGAATCCCTTACTG-AGACACCCTGCCCAGCCCTGCCTTCCTGAA 577124 vii v i v- - v v ?i iiv i i--- C MamTip2b#DNA/ 373 GGCCCAGTGCCCCATGCTCCAGAC-CCCTCCCGANTCTCCCCCTCCC--- 328 chr4qtel1M 577125 TCTCCAACCAAACCCACCCATCCTGGGTCTTCCTCCCTCACGGACTTGCA 577174 --- v v ii i v iivi v v i - C MamTip2b#DNA/ 327 ---CCATCAAAACTTACCCGTCCTGTGTCCCATTCCCTCAGGGCCCTGC- 282 chr4qtel1M 577175 GAGGAGATGAAATAATGAATTT 577196 v v i?ii?? iiv i C MamTip2b#DNA/ 281 TAGGTGACNGGNNAGCTAATCT 260 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 43.35 CpG sites = 21, Kimura (unadjusted) = 45.05 Transitions / transversions = 1.40 (21/15) Gap_init rate = 0.07 (9 / 120), avg. gap size = 1.00 (9 / 9) 565 15.49 12.99 3.57 chr4qtel1M 577488 577641 (422359) Charlie4#DNA/hAT-Charlie 3211 3378 (0) m_b205s502i2 8093 chr4qtel1M 577488 AATTTTGTTTTCTACACACTTTTATAACTAT--TTTAAGATACCTGGTTT 577535 v - v i i v -- i v vi Charlie4#DNA/ 3211 AAATTTGTTTT-TAAATATTTTGATAACTATATTTCAATATAATTGGTTT 3259 chr4qtel1M 577536 CCTT-GTAAGCCCGTTTGGGGTATTTTATTTGATGCATTTTAAAACATGA 577584 - v ii ----- v v v Charlie4#DNA/ 3260 CCTTTGTAATCCTAT-----GTATTTTATTTTATGCATTTAAAAACATTA 3304 chr4qtel1M 577585 TTCTGAAAAGGGCTCCATGGGCTTCACCAGA-----------------GG 577617 i v i ----------------- Charlie4#DNA/ 3305 TTCTGAGAAGGGGTCCATAGGCTTCACCAGACTGCCAAAGGGGTCCATGG 3354 chr4qtel1M 577618 AACACAAAGGGTTAAGGAGCCCTG 577641 v v i i v Charlie4#DNA/ 3355 CACAAAAAAGGTTAAGAACCCCTG 3378 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 17.44 CpG sites = 10, Kimura (unadjusted) = 17.44 Transitions / transversions = 0.77 (10/13) Gap_init rate = 0.06 (9 / 153), avg. gap size = 2.89 (26 / 9) 190 38.65 1.67 0.83 chr4qtel1M 580375 580494 (419506) C L3#LINE/CR1 (2021) 2078 1958 m_b205s601i29 8094 chr4qtel1M 580375 TGATCATCACCTGAATTTCTCTCCTCAGAGCTCCCCAGTCCTCCTGAATT 580424 i ii vii v vi ii v i ?i i iii C L3#LINE/CR1 2078 TAATTGTAGTCAGAATTTCATTTTTAAGAGCTTCCCANCCCTCTTGAGCC 2029 chr4qtel1M 580425 ATCTTTCACCATATAATTTTGTCCATGAGATGCTACTTACCTTTGTCCAA 580474 viiv ivivi i? v ii vv i - i v ii C L3#LINE/CR1 2028 ATCTTTCTTTTTGAGTCTCNGGCCATGGAATCATACCT-CTTTTCTCTGA 1980 chr4qtel1M 580475 CCCATTTAGAA--CGCTCTTCC 580494 viiv ii --i i C L3#LINE/CR1 1979 ATTTTTTGAAATCTGCTTTTCC 1958 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 61.77 CpG sites = 32, Kimura (unadjusted) = 61.77 Transitions / transversions = 2.29 (32/14) Gap_init rate = 0.02 (2 / 119), avg. gap size = 1.50 (3 / 2) 214 34.03 7.65 2.07 chr4qtel1M 580508 580690 (419310) L2d_3end#LINE/L2 87 279 (237) m_b205s601i30 8095 chr4qtel1M 580508 CTTCCCTGTCCTTCAGAAATCTCTGAGGGATTTCCTGTCTCCACGACTTT 580557 v ii ii v ivi viv v i - i ii v L2d_3end#LINE 87 CTTCACTGTCCCCCGAACACGCCTTGCGCATTCCC-GCCTCTGCGCCTTT 135 chr4qtel1M 580558 GCA-GTGCCTCTACCCCATACCTGGAAGA-----------TCTCTGCTTT 580595 v-ii vi v -ii vi-----------i - i L2d_3end#LINE 136 GCTCACGCCGTTCCCCC-CGCCTGGAATGCCCTTCCCCTTCCTCT-CTCT 183 chr4qtel1M 580596 CTATCAATATCCCTGGCTTCCTTCAGGATCCAGTTC-AGTATCAGCCTCC 580644 v v ivvv v i ii i - vi - L2d_3end#LINE 184 CTATCCAAATCCTACCCATCCTTCAAGGCCCAGCTCAAGTCCCA-CCTCC 232 chr4qtel1M 580645 TCC-TGAAGCCCTCCCCAGCCATTTGCACCCTTCCTGCCTTCACCTT 580690 -i i iii i ivvi viv vii v i L2d_3end#LINE 233 TCCACGAAGCCTTCCCTGACCACTCCAGCCCACACTGATCTCTCCCT 279 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 42.07 CpG sites = 37, Kimura (unadjusted) = 47.45 Transitions / transversions = 1.54 (37/24) Gap_init rate = 0.04 (8 / 182), avg. gap size = 2.25 (18 / 8) 236 30.29 8.23 1.79 chr4qtel1M 580510 580667 (419333) L2d2_3end#LINE/L2 89 256 (299) m_b205s601i31 8095 chr4qtel1M 580510 TCCCTGTCCTTCAGAAATCTCTGAGGGATTTCCTGTCTCCACGACTTTGC 580559 v ii ii v ivi v- v v? i i ii v L2d2_3end#LIN 89 TCACTGTCCCCCGAACACGCCTT-GCGCNTTCCCGCCTCTGCGCCTTTGC 137 chr4qtel1M 580560 A-GTGCCTCTACCCCATACCTGGAAGATC--TCTGCTTTCTATCAA--TA 580604 v-ii vi v -ii vii -- iv i v v -- L2d2_3end#LIN 138 TCACGCCGTTCCCCC-CGCCTGGAATGCCCTTCCCCTTCCTCTCCACCTA 186 chr4qtel1M 580605 TCC-----CTGGCT-TCCTTCAGGATCCAGTTCAG-TATCAGCCTCCTCC 580647 ----- iv i- i ii i i- ?i - L2d2_3end#LIN 187 TCCAAATCCTACCCATCCTTCAAGGCCCAGCTCAAATNCCA-CCTCCTCC 235 chr4qtel1M 580648 -TGAAGCCCTCCCCAGCCATT 580667 - i iii i L2d2_3end#LIN 236 GTGAAGCCTTCCCTGACCACT 256 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 35.92 CpG sites = 32, Kimura (unadjusted) = 41.77 Transitions / transversions = 2.13 (32/15) Gap_init rate = 0.06 (10 / 157), avg. gap size = 1.60 (16 / 10) 237 31.12 2.15 3.26 chr4qtel1M 580751 580843 (419157) L2d_3end#LINE/L2 424 515 (1) m_b205s601i32 8095 chr4qtel1M 580751 TATCTTGCAGTTCCTAGT-GTTTACCACAGCAC-TAGTGTACTATGGGGC 580798 i ii v ?ii v? - iv i - iii v iiv i L2d_3end#LINE 424 TGTCTTATACTNTTTTNTCGTTCCCCACAGCGCCTAGCACAGTGCTGAGC 473 chr4qtel1M 580799 ACATAATAGTAGCCTTTTAATAAATGTTTACTGATTGATCAATTG 580843 i vv --- i ii ii ii L2d_3end#LINE 474 ACATAGTAGGCGC---TCAATAAATACTTGTTGATTGATTGATTG 515 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 42.76 CpG sites = 21, Kimura (unadjusted) = 45.02 Transitions / transversions = 3.00 (21/7) Gap_init rate = 0.05 (5 / 92), avg. gap size = 1.00 (5 / 5) 194 40.37 1.71 2.59 chr4qtel1M 581283 581399 (418601) C L3#LINE/CR1 (2690) 1409 1294 m_b205s601i33 8094 chr4qtel1M 581283 ATCCCTTCATGATCTCATGCCAGACACAGATCTCATCCCATTAGTACTTG 581332 i i i vii vi v v iiii i ii ivv i C L3#LINE/CR1 1409 ACCCTTCCATCGCCGTATTCCAGTCATGAGTCCCATCCCACCAAGTCTCG 1360 chr4qtel1M 581333 CTGACACC--TGAGGTCAAACTGACTTCTCTCTGCCAAGACAATGCTGTG 581380 v i -- i iv i v i ii v ii --- viiiv C L3#LINE/CR1 1359 GTGATACCTATGAGATCGTATTTACCTCCTTGTGTTAA---AATTTCAAG 1313 chr4qtel1M 581381 TTGGTCTTTCTTGGTGCCC 581399 ?iii ?i iv i C L3#LINE/CR1 1312 TTNACTTTNTTTATTACCC 1294 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 60.13 CpG sites = 33, Kimura (unadjusted) = 67.70 Transitions / transversions = 2.54 (33/13) Gap_init rate = 0.03 (4 / 116), avg. gap size = 1.25 (5 / 4) 350 35.16 3.12 0.00 chr4qtel1M 581472 581599 (418401) MIRb#SINE/MIR 66 197 (71) m_b205s601i34 8096 chr4qtel1M 581472 TCTTAATTCTTCCATTTAGTCCCTAGGAGACCTTGGGCAACTCATCCCAC 581521 iiiii v i v vv iv v v i iiiv MIRb#SINE/MIR 66 TCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAAC 115 chr4qtel1M 581522 TACCCTAAGCCTCAGTTTCCCCACCTGTAGAAGGAGAACAATCATCCTTG 581571 iv i i i i i v i i i v v i i MIRb#SINE/MIR 116 CTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTA 165 chr4qtel1M 581572 TACCACCTGAAGGCTGTGA----TAAAAGAGA 581599 ivi i vv ivv i ---- v MIRb#SINE/MIR 166 CCTCGCAGGGTTGTTGTGAGGATTAAATGAGA 197 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 46.31 CpG sites = 27, Kimura (unadjusted) = 49.59 Transitions / transversions = 1.50 (27/18) Gap_init rate = 0.01 (1 / 127), avg. gap size = 4.00 (4 / 1) 356 33.33 0.00 0.00 chr4qtel1M 581472 581579 (418421) MIRc#SINE/MIR 63 170 (98) m_b205s601i35 8096 chr4qtel1M 581472 TCTTAATTCTTCCATTTAGTCCCTAGGAGACCTTGGGCAACTCATCCCAC 581521 iiiii v i v vv iv v v iiiv MIRc#SINE/MIR 63 TCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAAC 112 chr4qtel1M 581522 TACCCTAAGCCTCAGTTTCCCCACCTGTAGAAGGAGAACAATCATCCTTG 581571 iv i i i i i v i i i v v i MIRc#SINE/MIR 113 CTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTG 162 chr4qtel1M 581572 TACCACCT 581579 iv ii MIRc#SINE/MIR 163 CCCTGCCT 170 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 44.40 CpG sites = 23, Kimura (unadjusted) = 46.40 Transitions / transversions = 1.77 (23/13) Gap_init rate = 0.00 (0 / 107), avg. gap size = 0.0 (0 / 0) 424 27.66 0.00 0.00 chr4qtel1M 582592 582685 (417315) C MIRc#SINE/MIR (117) 151 58 m_b205s601i36 8097 chr4qtel1M 582592 ATTCCCATTTTACAGATGAACAAATCAGGGGTCAAAGAAGTGTAGGGATC 582641 i iv iiii v i i vv v ii C MIRc#SINE/MIR 151 ATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACT 102 chr4qtel1M 582642 TGTCCATGGTCACACAATTGGCAAATGGCAGAGCTAAGACTGGA 582685 i v ii i i i iii v C MIRc#SINE/MIR 101 TGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGA 58 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 34.61 CpG sites = 19, Kimura (unadjusted) = 36.61 Transitions / transversions = 2.71 (19/7) Gap_init rate = 0.00 (0 / 93), avg. gap size = 0.0 (0 / 0) 183 34.31 0.00 2.86 chr4qtel1M 582977 583048 (416952) L2b_3end#LINE/L2 397 466 (0) m_b205s601i37 8098 chr4qtel1M 582977 TATCCCTTACCTTTTGGCACAGGTCCTTGTGCAAAGTGAGTATTTAACAA 583026 i- v vii i ?v v ii v ii iii i ii L2b_3end#LINE 397 TATCCCC-AGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAA 445 chr4qtel1M 583027 ACATCTGAATGAATAAATGGAT 583048 i i -v i i L2b_3end#LINE 446 ATATTTG-TTGAATGAATGAAT 466 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 48.12 CpG sites = 18, Kimura (unadjusted) = 51.69 Transitions / transversions = 3.00 (18/6) Gap_init rate = 0.03 (2 / 71), avg. gap size = 1.00 (2 / 2) 241 27.89 0.15 0.31 chr4qtel1M 584779 585300 (414700) (AC)n#Simple_repeat 1 523 (125) m_b205s252i12 8099 chr4qtel1M 584779 ACACACACACACACACACAATTACACACACACTTACACTCACACTCACAC 584828 vvi vi v v (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50 chr4qtel1M 584829 TCACATACTCAGAATCACACTCACACACACAATCACACTCACTCACTCTC 584878 v i v v vv v vv v v v v (AC)n#Simple_ 51 ACACACACACACACACACACACACACACACACACACACACACACACACAC 100 chr4qtel1M 584879 ACACATGCACTAATACACTCACACACAGCCTCACACA-ACTTACATCCTT 584927 ii vv i v vv v - vi iv vi (AC)n#Simple_ 101 ACACACACACACACACACACACACACACACACACACACACACACACACAC 150 chr4qtel1M 584928 ACACTAACACACACTCACACAGACTCACACACACACTTACTCTCACACAC 584977 vv v v v vi v v (AC)n#Simple_ 151 ACACACACACACACACACACACACACACACACACACACACACACACACAC 200 chr4qtel1M 584978 ACACACTCGCACACACTTATATACTCACACTAACACACACACACTCACAC 585027 v i vi i i v vv v (AC)n#Simple_ 201 ACACACACACACACACACACACACACACACACACACACACACACACACAC 250 chr4qtel1M 585028 ACACTCTCTCGCACTCACACACTCACATACATTAACACACTCACACACAC 585077 v v v i v v i ivv v (AC)n#Simple_ 251 ACACACACACACACACACACACACACACACACACACACACACACACACAC 300 chr4qtel1M 585078 TCACACACTTACATCCTTACACTAACACACTCACACAGACTCACACACAC 585127 v vi iv vi vv v v v (AC)n#Simple_ 301 ACACACACACACACACACACACACACACACACACACACACACACACACAC 350 chr4qtel1M 585128 ACTTACTCTCTCACATACACACTCGCACACACTTATATACTCACACTAAC 585177 vi v v v i v i vi i i v vv (AC)n#Simple_ 351 ACACACACACACACACACACACACACACACACACACACACACACACACAC 400 chr4qtel1M 585178 ACACACTCACACACTCTCTCTCACACACTCACACTCACATACACTAACAC 585227 v v v v v v v i vv (AC)n#Simple_ 401 ACACACACACACACACACACACACACACACACACACACACACACACACAC 450 chr4qtel1M 585228 ACAGACTCACACACACACACTTACTCTCTCACACACACATTCACACACAC 585277 v v vi v v v iv (AC)n#Simple_ 451 ACACACACACACACACACACACACACACACACACACACACACACACACAC 500 chr4qtel1M 585278 TTATATACTCACACTAACACATT 585300 vi i i v vv iv (AC)n#Simple_ 501 ACACACACACACACACACACACA 523 Matrix = Unknown Transitions / transversions = 0.38 (33/87) Gap_init rate = 0.00 (1 / 521), avg. gap size = 1.00 (1 / 1) 28 6.71 4.26 0.00 chr4qtel1M 585301 585347 (414653) (CTCACA)n#Simple_repeat 1 49 (0) c_b205s251i5 8100 chr4qtel1M 585301 CTCACACTCACACACACACTCACA-T-ACACTGACACACACACTCACAC 585347 v - - v v (CTCACA)n#Sim 1 CTCACACTCACACTCACACTCACACTCACACTCACACTCACACTCACAC 49 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.04 (2 / 46), avg. gap size = 1.00 (2 / 2) 241 27.89 0.15 0.31 chr4qtel1M 585348 585473 (414527) (AC)n#Simple_repeat 524 647 (1) m_b205s252i12 8101 chr4qtel1M 585348 ACTTACATACTTATACTAACACACACACTTACTCACACACACTTATAGAC 585397 vi i vi i vv vi v vi i v (AC)n#Simple_ 524 ACACACACACACACACACACACACACACACACACACACACACACACACAC 573 chr4qtel1M 585398 TCACACTAACACACACTCATACTCACACTCACACACATTTACACACTCTC 585447 v vv v i v v ivi v v (AC)n#Simple_ 574 ACACACACACACACACACACACACACACACACACACACACACACACACAC 623 chr4qtel1M 585448 ACACATCTACACCCCCACACATACAC 585473 - - v v i (AC)n#Simple_ 624 ACACA-C-ACACACACACACACACAC 647 Matrix = Unknown Transitions / transversions = 0.58 (11/19) Gap_init rate = 0.02 (2 / 125), avg. gap size = 1.00 (2 / 2) 266 20.99 3.57 3.57 chr4qtel1M 585918 586001 (413999) MIR1_Amn#SINE/MIR 3 86 (144) m_b205s601i38 8102 chr4qtel1M 585918 GGGAGGCAGTGTGGTCCAGGGGACAAAGAGCT-GACTGGGG--CAGGAGA 585964 i v i i vi - i-- i MIR1_Amn#SINE 3 GGGAGGCAGTGTGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGAGA 52 chr4qtel1M 585965 CCCCAATTCAAATCCTGCCCCCAGTGCCAACTGCCAG 586001 ivii ? ? i v i --- vi? ? MIR1_Amn#SINE 53 CCTGGGTTCNANTCCCGGCTC---TGCCACTNGCCNG 86 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 23.49 CpG sites = 12, Kimura (unadjusted) = 27.11 Transitions / transversions = 2.40 (12/5) Gap_init rate = 0.06 (5 / 83), avg. gap size = 1.20 (6 / 5) 206 29.41 9.80 0.00 chr4qtel1M 585920 586021 (413979) MIRc#SINE/MIR 2 113 (155) m_b205s601i39 8102 chr4qtel1M 585920 GAGGCAGTGTGGTCCAGGGGACAAAGAGCT-GACT--GGGGCAGG-AGAC 585965 v v v i vi - -- i v - MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr4qtel1M 585966 CCCAATTCAAATCCTGCCCCCAGTGCCAACTGCCAGTGTGCCC----ACA 586011 ivii i i i v i iivii iv iv v v ----i MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 101 chr4qtel1M 586012 AG--ACTTACCC 586021 -- v MIRc#SINE/MIR 102 AGTCACTTAACC 113 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 35.07 CpG sites = 17, Kimura (unadjusted) = 38.24 Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.05 (5 / 101), avg. gap size = 2.00 (10 / 5) 273 17.67 0.00 3.92 chr4qtel1M 587292 587344 (412656) L2b_3end#LINE/L2 408 458 (8) m_b205s601i40 8103 chr4qtel1M 587292 CCTAGGGCACAGTGCCTGGCACACAGCAGGTGCCTAATATATGTTTACTG 587341 -- ? i i ii i v i ii L2b_3end#LINE 408 CCTAG--CACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTTGTTG 455 chr4qtel1M 587342 AAT 587344 L2b_3end#LINE 456 AAT 458 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 19.14 CpG sites = 8, Kimura (unadjusted) = 21.80 Transitions / transversions = 8.00 (8/1) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.00 (2 / 2) 12 27.41 1.79 3.64 chr4qtel1M 589625 589680 (410320) (CTC)n#Simple_repeat 1 55 (0) m_b205s252i13 8104 chr4qtel1M 589625 CTCCCCCACATCATCCCTCCTCACTCC-CCCCGACCACCCCCTCCTCCAT 589673 i v v v - - - i vv v i vi (CTC)n#Simple 1 CTCCTCCTCCTCCT-CCTCCTC-CTCCTCCTCCTCCTCCTCCTCCTCCTC 48 chr4qtel1M 589674 CTCCCCC 589680 i (CTC)n#Simple 49 CTCCTCC 55 Matrix = Unknown Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.05 (3 / 55), avg. gap size = 1.00 (3 / 3) 15 33.75 0.00 0.00 chr4qtel1M 589747 589805 (410195) (GAG)n#Simple_repeat 1 59 (0) m_b205s252i14 8105 chr4qtel1M 589747 GATGAGGAGGTTGAGGAGCAGGATGTTGGTGAAGAGCAGGTAGAGGCAGA 589796 v vv v v vv iv i v vi vi (GAG)n#Simple 1 GAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA 50 chr4qtel1M 589797 GGAGGATGA 589805 v (GAG)n#Simple 51 GGAGGAGGA 59 Matrix = Unknown Transitions / transversions = 0.33 (4/12) Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.0 (0 / 0) 509 26.52 8.08 2.88 chr4qtel1M 590318 590515 (409485) C MIR#SINE/MIR (34) 228 21 m_b205s601i41 8106 chr4qtel1M 590318 TACTAAGCACC-TACTAAGTGCCAGGCAAATAGCACCTCATCTGCTCC-- 590364 i i i i- v i ivvi vi vi v i iv -- C MIR#SINE/MIR 228 TGCCAGGCACTGTTCTAAGCGCTTTACATGTATTAACTCATTTAATCCTC 179 chr4qtel1M 590365 ------ATCCCAGGAAGTTGGGTCTGTTATTATGCCCATTTTACAGAAGA 590408 ------ i i v i v vv i v v C MIR#SINE/MIR 178 ACAACAACCCTATGAGGTAGGTACTATTATTATCCCCATTTTACAGATGA 129 chr4qtel1M 590409 GCAAACCAAGGCAAACTGAGGAGAGG-TAAGTGCCT--CCCAGGGTCCTA 590455 v ii v ----- - iv -- i vi C MIR#SINE/MIR 128 GGAAACTGAGGCACA-----GAGAGGTTAAGTAACTTGCCCAAGGTCACA 84 chr4qtel1M 590456 CAGCTAGTAAACG--TGAGGCAGAATTTGGACCCTGGTATCGCTGCCTCC 590503 ii --v v i i i i v i vi- v C MIR#SINE/MIR 83 CAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGCAGT-CTGGCTCC 35 chr4qtel1M 590504 AG-GCCCG-GCCCT 590515 - - i C MIR#SINE/MIR 34 AGAGCCCGTGCTCT 21 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 31.10 CpG sites = 29, Kimura (unadjusted) = 33.46 Transitions / transversions = 1.32 (29/22) Gap_init rate = 0.07 (14 / 197), avg. gap size = 1.57 (22 / 14) 12 21.77 9.09 1.41 chr4qtel1M 591682 591747 (408253) (AGAAGG)n#Simple_repeat 1 71 (0) m_b205s252i15 8107 chr4qtel1M 591682 AGAA-GACAAGGAG--GGAGGGGGAGAAGGAGGA-G-GAAGGTGAA-GAT 591725 - v -- ii i - - v - v (AGAAGG)n#Sim 1 AGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAG 50 chr4qtel1M 591726 GAGAAATATGAAAAGGATGAAG 591747 i i iv v i - (AGAAGG)n#Sim 51 AAGGAGAAGGAGAAGGA-GAAG 71 Matrix = Unknown Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.09 (6 / 65), avg. gap size = 1.17 (7 / 6) 206 34.71 6.19 1.98 chr4qtel1M 593427 593523 (406477) MIR3#SINE/MIR 106 206 (2) m_b206s601i0 8108 chr4qtel1M 593427 TCACCCTTCTGGGTCTCA----CTGCATGCGATGAGGTAGAGAGAAGAGG 593472 ii i ---- iv - vi i ii - i iivv MIR3#SINE/MIR 106 TCACCTCTCTGGGCCTCAGTTTCCTCAT-CTGTAAAAT-GAGGGGGTTGG 153 chr4qtel1M 593473 A--AGCTGACTTTGGAAGCTGCTTCTGGCTCTAACAATCTATAACACTGT 593520 -- v ii ivi i iiv ii i v i iv i MIR3#SINE/MIR 154 ACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTAT 203 chr4qtel1M 593521 GAT 593523 MIR3#SINE/MIR 204 GAT 206 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 51.07 CpG sites = 24, Kimura (unadjusted) = 51.07 Transitions / transversions = 2.67 (24/9) Gap_init rate = 0.04 (4 / 96), avg. gap size = 2.00 (8 / 4) 44 0.00 0.00 0.00 chr4qtel1M 597350 597387 (402613) (CA)n#Simple_repeat 1 38 (0) c_b206s251i0 8109 chr4qtel1M 597350 CACACACACACACACACACACACACACACACACACACA 597387 (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACA 38 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 40 8.85 3.41 2.25 chr4qtel1M 599593 599680 (400320) (ATGG)n#Simple_repeat 1 89 (0) c_b206s251i1 8110 chr4qtel1M 599593 ATGGATGGATGGATAGAT-GATGGATGGATGAATAGATCGATGGAT-TAT 599640 i - i i v -v - (ATGG)n#Simpl 1 ATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGA- 49 chr4qtel1M 599641 TGGATAGATGGA-GGAAGGAATGGATGGATGGATGGATGGA 599680 i - v - (ATGG)n#Simpl 50 TGGATGGATGGATGGATGG-ATGGATGGATGGATGGATGGA 89 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.06 (5 / 87), avg. gap size = 1.00 (5 / 5) 27 3.42 0.00 0.00 chr4qtel1M 599706 599735 (400265) (GAGG)n#Simple_repeat 1 30 (0) c_b206s251i2 8111 chr4qtel1M 599706 GAGGGATGGAGGGAGGGAGGGAGGGAGGGA 599735 v (GAGG)n#Simpl 1 GAGGGAGGGAGGGAGGGAGGGAGGGAGGGA 30 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 34 19.77 1.33 0.00 chr4qtel1M 599742 599816 (400184) (GATG)n#Simple_repeat 1 76 (0) m_b206s252i1 8112 chr4qtel1M 599742 GATGGAGGAAAGGATAGAAGGATGGAGGGTTGGAAAAAGGGATGGAT-GA 599790 v i v i v v v vii v - (GATG)n#Simpl 1 GATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGA 50 chr4qtel1M 599791 TGAATGGATGGATGGATAGATGGATG 599816 i i (GATG)n#Simpl 51 TGGATGGATGGATGGATGGATGGATG 76 Matrix = Unknown Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.01 (1 / 74), avg. gap size = 1.00 (1 / 1) 209 20.51 0.00 0.00 chr4qtel1M 599884 599922 (400078) C MIR3#SINE/MIR (2) 206 168 m_b206s601i1 8113 chr4qtel1M 599884 ATTGTAGAATCACAGAGGGTCAGAGTTGGGAGGGACCCT 599922 ii i iv i i i C MIR3#SINE/MIR 206 ATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTT 168 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 25.59 CpG sites = 7, Kimura (unadjusted) = 25.59 Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 197 26.42 1.89 0.00 chr4qtel1M 600553 600605 (399395) C MIR3#SINE/MIR (7) 201 148 m_b206s601i2 8114 chr4qtel1M 600553 AGAACCATAGAAAATCATAATAGGAAGGGATCTTGGGAACCATC-AACCC 600601 i vi v iiv i i ii i - ii C MIR3#SINE/MIR 201 AGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCC 152 chr4qtel1M 600602 AACC 600605 C MIR3#SINE/MIR 151 AACC 148 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 34.91 CpG sites = 11, Kimura (unadjusted) = 34.91 Transitions / transversions = 3.67 (11/3) Gap_init rate = 0.02 (1 / 52), avg. gap size = 1.00 (1 / 1) 14 7.42 6.90 0.00 chr4qtel1M 600648 600676 (399324) (TAGAAA)n#Simple_repeat 1 31 (0) m_b206s252i2 8115 chr4qtel1M 600648 TAGAAAT-G-GATGGAAATAGAAATAGAAAT 600676 - -i i (TAGAAA)n#Sim 1 TAGAAATAGAAATAGAAATAGAAATAGAAAT 31 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.07 (2 / 28), avg. gap size = 1.00 (2 / 2) 218 31.90 2.54 1.68 chr4qtel1M 600690 600807 (399193) L2d_3end#LINE/L2 398 516 (0) m_b206s601i3 8116 chr4qtel1M 600690 TGCAAGAACTTGGATGGGCAGAGATT-TGATTCATTCATTATCCTTGTAT 600738 i vv i v - i ii- vi i v v? v i? i vi L2d_3end#LINE 398 TGTAAGCTCCTTGA-GGGCAGGGACCATGTCTTATACTNTTTTNTCGTTC 446 chr4qtel1M 600739 CCCATGGA--CTACCCACAGGGCTTTGCTGAGAGTTGGAACTTGCTAAAT 600786 ii v-- v - v vv vv v v vi iiv L2d_3end#LINE 447 CCCACAGCGCCTAGC-ACAGTGCTGAGCACATAGTAGGCGCTCAATAAAT 495 chr4qtel1M 600787 GCTTGGTGATTGATTGACTGA 600807 i v i L2d_3end#LINE 496 ACTTGTTGATTGATTGATTGA 516 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 39.98 CpG sites = 17, Kimura (unadjusted) = 42.90 Transitions / transversions = 0.85 (17/20) Gap_init rate = 0.03 (4 / 117), avg. gap size = 1.25 (5 / 4) 389 21.43 2.38 0.00 chr4qtel1M 600853 600936 (399064) C L3#LINE/CR1 (106) 3993 3908 m_b206s601i4 8117 chr4qtel1M 600853 TCCAATCTTT--TTGAAGACCTCCAAGGAAGGGGAATTCACCACATCCTG 600900 ii i -- v iv v ii i v ?i C L3#LINE/CR1 3993 TCCAGCCTCTGCTTGAACACCTCCAGTGACGGGGAGCTCACTACCTCNCG 3944 chr4qtel1M 600901 AGACAGCCCATTCCTTTCTGGGACAGCTCTCATGGT 600936 i v i v v v C L3#LINE/CR1 3943 AGGCAGCCCATTCCATTTTTGGACAGCTCTGATTGT 3908 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 24.32 CpG sites = 10, Kimura (unadjusted) = 25.93 Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.01 (1 / 83), avg. gap size = 2.00 (2 / 1) 455 29.85 7.78 6.13 chr4qtel1M 600954 601210 (398790) C L3b_3end#LINE/CR1 (613) 593 333 m_b206s601i5 8118 chr4qtel1M 600954 TTTTGGCAGCTGCTCCATCCCCAATGATCTATATCAATTTCCCAAATTTG 601003 i vi i- v iiv iii ii --------ii C L3b_3end#LINE 593 TTTTGGCAGCCGCGTCG-CACTGCTGACTCATATTGA--------GCTTG 553 chr4qtel1M 601004 TACTGTATCTACTCCAATCCCCAGATCTTTTCCAGAACCACTGGT-CTA- 601051 ii----i v vv i i i v vv?i v - - C L3b_3end#LINE 552 CG----GTCAACTAAAACCCCCAGGTCTTTTTCACATGNGCTGCTGCTAA 507 chr4qtel1M 601052 GCCAAGCCTTCCC-----------------ATTGAATTTTTTTGTGCCCA 601084 iv i i ----------------- ?-- vi C L3b_3end#LINE 506 GCCGCGTCTCCCCCATCCTGTACTCGCGCGATTGN--TTTTTTGAACCCA 459 chr4qtel1M 601085 AGGGCAAGACTTTCCATTTATTCCTACTGAATTTAATCTCATTCAATTCT 601134 v i v i i ii v ii vi? v C L3b_3end#LINE 458 AGTGCAGGACTTTACGTTTATCCCTGTTGAATTTCATCTTGTTGGNTTCG 409 chr4qtel1M 601135 GCCCATTGCTTCAGCCTATCAA-ATCCTTCTTGATCCTGACTCAGTCATC 601183 i?i i ii i i i - v i v i iv - C L3b_3end#LINE 408 GCCCGNCGTTCTAGTCTGTCGAGATCGTTTTGGATCCTGATTTTG-CATC 360 chr4qtel1M 601184 CAATATGTCAGCTATCCCTCACTGTTT 601210 ii i i ii v v v i C L3b_3end#LINE 359 CAACGTATTAGCCGTCGCTCCCAGCTT 333 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 33.68 CpG sites = 49, Kimura (unadjusted) = 41.12 Transitions / transversions = 2.13 (49/23) Gap_init rate = 0.08 (20 / 256), avg. gap size = 1.80 (36 / 20) 584 24.74 8.30 2.90 chr4qtel1M 601011 601239 (398761) C L3#LINE/CR1 (652) 3447 3207 m_b206s601i6 8118 chr4qtel1M 601011 TCTACTCCAATCCCCAGATCTTTTCCA---GAACCACTGGTCTAGCCA-A 601056 v vv i i i i --- ii v v- - C L3#LINE/CR1 3447 TCAACTAAAACCCCTAGGTCTTTTTCACGTGAACTGCTGCTA-AGCCAGA 3399 chr4qtel1M 601057 GCCTTCCCAT--TG---------AAT---TTTTTTGTGCCCAAGGGCAAG 601092 v ii -- --------- i --- vi i iv i C L3#LINE/CR1 3398 TCCTCTCCATCCTGTACTTGTGCAGTTGATTTTTTGAACCTAAATGCAGG 3349 chr4qtel1M 601093 ACTTTCCATTTATTCCTACTGAATTTAATCTCATTCAATTCTGCCCATTG 601142 v i ii i v ii viv v i C L3#LINE/CR1 3348 ACTTTACATTTATCCCTGTTAAATTTCATCTTGTTGGTTTCGGCCCATCG 3299 chr4qtel1M 601143 CTTCAGCCTATC-AAATCCTTCTTGATCCTGACTCAGTCATCCAATATGT 601191 i i i - i ? i vi i i v ?ii i C L3#LINE/CR1 3298 TTCCAGCCTGTCGAGATCNTTTTGAATCTTGATTCTGTCATCCANCGTAT 3249 chr4qtel1M 601192 CAGCTATCCCTCACTGTTTGGGAGTCATACTGTCCAAGGCATTGATAA 601239 i v v i v v- - -- iv-- C L3#LINE/CR1 3248 TAGCTATCCCTCCCAGCTTTGT-GTCAT-CTG--CAAAT--TTGATAA 3207 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 29.88 CpG sites = 35, Kimura (unadjusted) = 31.32 Transitions / transversions = 1.75 (35/20) Gap_init rate = 0.06 (13 / 228), avg. gap size = 2.00 (26 / 13) 371 31.04 0.00 1.72 chr4qtel1M 602857 602974 (397026) C MIRb#SINE/MIR (150) 118 3 m_b206s601i7 8119 chr4qtel1M 602857 GGGGTGAAGTGACTTGCTCAGAGCCACATAGTAGGTAAGTGTCTGAGGTC 602906 i v i i ii i i ivi v v viv C MIRb#SINE/MIR 118 GAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 69 chr4qtel1M 602907 AGATTTGAACTCAGGAGCTCCCGGTTCTAGGGTCAGTGCTCTCTCCACTG 602956 i i i vvivi i ii i ii i v i C MIRb#SINE/MIR 68 GGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTG 19 chr4qtel1M 602957 TCACCCGGCTCGCCCTTC 602974 - vv - i C MIRb#SINE/MIR 18 -CACCACGCT-GCCCCTC 3 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 39.09 CpG sites = 24, Kimura (unadjusted) = 42.21 Transitions / transversions = 2.00 (24/12) Gap_init rate = 0.02 (2 / 117), avg. gap size = 1.00 (2 / 2) 407 28.85 0.00 0.96 chr4qtel1M 602857 602961 (397039) C MIRc#SINE/MIR (153) 115 12 m_b206s601i8 8119 chr4qtel1M 602857 GGGGTGAAGTGACTTGCTCAGAGCCACATAGTAGGTAAGTGTCTGAGGTC 602906 i v i ii i i ivi v v viv C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 66 chr4qtel1M 602907 AGATTTGAACTCAGGAGCTCCCGGTTCTAGGGTCAGTGCTCTCTCCACTG 602956 i i i i vvi i ii i i vi i C MIRc#SINE/MIR 65 GGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTG 16 chr4qtel1M 602957 TCACC 602961 - C MIRc#SINE/MIR 15 -CACC 12 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 35.17 CpG sites = 21, Kimura (unadjusted) = 38.46 Transitions / transversions = 2.33 (21/9) Gap_init rate = 0.01 (1 / 104), avg. gap size = 1.00 (1 / 1) 20 20.62 2.22 0.00 chr4qtel1M 602998 603042 (396958) (CA)n#Simple_repeat 1 46 (0) m_b206s252i3 8120 chr4qtel1M 602998 CACGCACACACATGAACACACACACACACA-ATACTTACACCCACA 603042 i iiv - i vi v (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACA 46 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 22 25.71 3.80 2.50 chr4qtel1M 603095 603173 (396827) (AC)n#Simple_repeat 1 80 (0) m_b206s252i4 8121 chr4qtel1M 603095 ACACACACGGCACATGTAACCACACATGTGCACACACA-ACACA-ACACA 603142 -i iii vv iiii - - (AC)n#Simple_ 1 ACACACAC-ACACACACACACACACACACACACACACACACACACACACA 49 chr4qtel1M 603143 AGCACACAGTACACA-ATACACACACCCCCAC 603173 vi -i - i v v (AC)n#Simple_ 50 CACACACA-CACACACACACACACACACACAC 80 Matrix = Unknown Transitions / transversions = 2.20 (11/5) Gap_init rate = 0.06 (5 / 78), avg. gap size = 1.00 (5 / 5) 17 15.68 4.65 0.00 chr4qtel1M 603125 603167 (396833) (CACACAA)n#Simple_repeat 1 45 (0) m_b206s252i5 8122 chr4qtel1M 603125 CACACACAACACAACACA-AGCACACAGTACACAATACAC-ACAC 603167 vv - i ii i - (CACACAA)n#Si 1 CACACAACACACAACACACAACACACAACACACAACACACAACAC 45 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.00 (2 / 2) 22 25.71 3.80 2.50 chr4qtel1M 603095 603173 (396827) (AC)n#Simple_repeat 1 80 (0) m_b206s252i4 8121 chr4qtel1M 603095 ACACACACGGCACATGTAACCACACATGTGCACACACA-ACACA-ACACA 603142 -i iii vv iiii - - (AC)n#Simple_ 1 ACACACAC-ACACACACACACACACACACACACACACACACACACACACA 49 chr4qtel1M 603143 AGCACACAGTACACA-ATACACACACCCCCAC 603173 vi -i - i v v (AC)n#Simple_ 50 CACACACA-CACACACACACACACACACACAC 80 Matrix = Unknown Transitions / transversions = 2.20 (11/5) Gap_init rate = 0.06 (5 / 78), avg. gap size = 1.00 (5 / 5) 388 25.51 2.68 5.50 chr4qtel1M 604149 604260 (395740) C MIRc#SINE/MIR (142) 126 18 m_b206s601i9 8123 chr4qtel1M 604149 TAAGGCAATCAG---GGTTAAGTGACTTATCCAGGGTCACACAGCTAGGT 604195 i -- --- ii i -- C MIRc#SINE/MIR 126 TGAGGC--TCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG-- 81 chr4qtel1M 604196 TTCAAGTGTCTGTGGCTGGATTTAAACTCTGGTCCTTTTGACTTCAGGAC 604245 --i v v v v v i ii i v i ii i i v C MIRc#SINE/MIR 80 --TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTC 33 chr4qtel1M 604246 TGGTATTCCATCCAC 604260 ii ii iv C MIRc#SINE/MIR 32 CAGTGCTCTTTCCAC 18 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 30.91 CpG sites = 19, Kimura (unadjusted) = 32.55 Transitions / transversions = 2.38 (19/8) Gap_init rate = 0.06 (7 / 111), avg. gap size = 1.29 (9 / 7) 234 28.89 18.85 0.69 chr4qtel1M 605588 605709 (394291) L2d2_3end#LINE/L2 404 547 (8) m_b206s601i10 8124 chr4qtel1M 605588 TTCTTAGATGTGTATGTGTTAT-TCCCTAGGTAGAACAGAAGTTCCCTGA 605636 i i vi v v i - i iv viiv i i L2d2_3end#LIN 404 TTTTCACGTGTTTATGTCTTGTCTCCCCAACTAGATTGTAAGCTCCTTGA 453 chr4qtel1M 605637 GGGCAGG---------------TTCTGGTAGATCCCT----GGACCCAGA 605667 --------------- -v iv i---- vi i v L2d2_3end#LIN 454 GGGCAGGGACCATGTCTTATACTTCT-TTGTATCCCCCACAGCGCCTAGC 502 chr4qtel1M 605668 GCAGTGGCTGGTACAC---AGGTGCTTACTAAATGATTGCTGACT 605709 i v v i --- i i v iv i i L2d2_3end#LIN 503 ACAGTGCCTTGCACACAGTAGGCGCTCAATAAATATTTGTTGATT 547 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 33.66 CpG sites = 21, Kimura (unadjusted) = 37.65 Transitions / transversions = 1.50 (21/14) Gap_init rate = 0.04 (5 / 121), avg. gap size = 4.80 (24 / 5) 129 16.48 10.37 0.24 chr4qtel1M 605843 606218 (393782) (CT)n#Simple_repeat 1 414 (0) m_b206s252i7 8125 chr4qtel1M 605843 CTCTCCATCTTTCTCTC-CTTTCTCTC-CTCTCCCCTTCTCTCT-TTTGT 605889 iv i - i - i ii - i v (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chr4qtel1M 605890 CTCT-TCTCCCACT-TCT-TCT-TAGCTTCCTCT-TCTCTCTGCTCTCTC 605934 - i v - - - vv ii - - (CT)n#Simple_ 51 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT-CTCTCTC 99 chr4qtel1M 605935 T-TCTCTCTCCTTTTCTCCCCTTCT-TCCCT-TCTCTC-CTTTGTCTC-C 605979 - ii i i ii - i - - i v - (CT)n#Simple_ 100 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 149 chr4qtel1M 605980 TCTCCCCCACTCT-TCTC-CTTTCTCT-TCTCTC-CTTTGTCT-TCTCTC 606024 i i v - - i - - i v - (CT)n#Simple_ 150 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 199 chr4qtel1M 606025 CCT-TCTCTC-CTTTCTC-CTCTCTCTTCCTCTC-CTCTCACT-TCTCTC 606069 i - - i - ii - v - (CT)n#Simple_ 200 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 249 chr4qtel1M 606070 T-TCTCTCTC-CTCTCCCTTTCCCCCT-TTTCTC-CTTTCTCTC-CTCTC 606114 - - i i i i - i - i - (CT)n#Simple_ 250 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 299 chr4qtel1M 606115 CCCCTCTCT-TCT-TCTCTCCCT-TCT-TCCCTTTCTCT-TCTCTCTC-C 606158 i i - - i - - i i - - (CT)n#Simple_ 300 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 349 chr4qtel1M 606159 TCTTTCTCAC-CTCTCTCTC-CTCTC-CTCTC-CTCTCTCTCTCCTTACC 606204 i v - - - - ii vi (CT)n#Simple_ 350 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 399 chr4qtel1M 606205 TTTGTCT-TCTCTCT 606218 i v - (CT)n#Simple_ 400 TCTCTCTCTCTCTCT 414 Matrix = Unknown Transitions / transversions = 3.50 (42/12) Gap_init rate = 0.11 (40 / 375), avg. gap size = 1.00 (40 / 40) 44 34.52 3.50 5.88 chr4qtel1M 605838 606237 (393763) (CCTTC)n#Simple_repeat 1 391 (0) m_b206s252i6 8126 chr4qtel1M 605838 CCTTCCTCTCCATCTTTCTCTCCTTTCTCTCCTCTCCCCTTCTCTCTTTT 605887 - i -i i ii i i i i i i - iii (CCTTC)n#Simp 1 CCTTCC-CTTC-CCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCT-TCCC 47 chr4qtel1M 605888 GTCTCTTCTC-CCACTTCTTCTTAGCTTCCTCTTCTCTCTGCTCTCTCTT 605936 v i i -i v -i vv - i - v ii i (CCTTC)n#Simp 48 TTCCCTTCCCTTCCCTTC-CCTTCCCTTCC-CTTCCCT-TCCCTTCCCTT 94 chr4qtel1M 605937 CTCTCTCCTTTTCTCCCCTT--CTTCCCTTCTC-TCCTTTGTCTCCTCTC 605983 i ii ii i -- i - i vi i i i (CCTTC)n#Simp 95 CCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTT 144 chr4qtel1M 605984 CCCCACTCTTCTCCTTTCTCTTCTC-TCCTTTGTCTTCTC-TCCCTTCTC 606031 iv i - - i i - i vi i - i (CCTTC)n#Simp 145 CCCTTCCCTTC-CC-TTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCC 192 chr4qtel1M 606032 -TCCTTTCTCCTCTCTCTTCCTCTCCTCTCACTTCTCTCTTCTCTCTCCT 606080 - i - - i ii ii v - - i - i (CCTTC)n#Simp 193 TTCCCTTC-CCT-TCCCTTCCCTTCCCTTCCCTTC-C-CTTCCCT-TCCC 237 chr4qtel1M 606081 CTCCCTTTCC--CCCTTTTC-TCCTTTCTCTCCTCTCCCCCTCTCTTCTT 606127 i i -- ii - i i i i i i i -i (CCTTC)n#Simp 238 TTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTC-C 286 chr4qtel1M 606128 CTCTCCCTT--CTTCCCTTTCTCTTCTCTCTCCTCTT-TC-TCACCTCTC 606173 - -- - i i - - -i - v i i (CCTTC)n#Simp 287 CT-TCCCTTCCCTTCCC-TTCCCTTCCCT-TCC-CTTCCCTTCCCTTCCC 332 chr4qtel1M 606174 TCTCCTCTCCTCTCCTCTCTCTCTCCTTACCTTTGTCTTCTCTCTGCGTC 606223 - ii ii ii i - i v i vi - - v -i (CCTTC)n#Simp 333 T-TCCCTTCCCTTCCCTTCCCT-TCCCTTCCCTTCCCTTC-C-CTTC-CC 377 chr4qtel1M 606224 TCCCCTTCCCTCCC 606237 i i (CCTTC)n#Simp 378 TTCCCTTCCCTTCC 391 Matrix = Unknown Transitions / transversions = 6.15 (80/13) Gap_init rate = 0.09 (34 / 399), avg. gap size = 1.09 (37 / 34) 306 30.91 8.18 0.00 chr4qtel1M 607218 607327 (392673) C MIR3#SINE/MIR (72) 136 18 m_b206s601i11 8127 chr4qtel1M 607218 CAGATGCA-AAACGGAAGCCCAGAGAAGGTAAATGACTTA-TCAGGATCA 607265 vi- v i i vv i i-i i i C MIR3#SINE/MIR 136 CAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCA 87 chr4qtel1M 607266 CATGGTCAGTAAATATCCGAGGCAGAATTA-AAC------TTTGTGACTT 607308 ii i? v i iv v v i i i - ------i iv i C MIR3#SINE/MIR 86 CACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGTCTCCTGACTC 37 chr4qtel1M 607309 CCAGTTTGCGTTCTTTGTG 607327 ii i i i v C MIR3#SINE/MIR 36 CCAGTCCGTGCTCTCTCTG 18 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 39.63 CpG sites = 24, Kimura (unadjusted) = 43.04 Transitions / transversions = 2.40 (24/10) Gap_init rate = 0.04 (4 / 109), avg. gap size = 2.25 (9 / 4) 245 33.39 14.81 3.33 chr4qtel1M 608288 608665 (391335) L2b_3end#LINE/L2 44 463 (3) m_b206s601i12 8128 chr4qtel1M 608288 CACTTTCCACTTCCCTCCACTTTATAATCAGCCTAATTGGCTTATCTGAC 608337 i v v i-- i iiv-i vv i i vii vi L2b_3end#LINE 44 CACTCTCCCCTTGCT--CACTCTGCT-CCAGCCACACTGGCCTCCTTGCT 90 chr4qtel1M 608338 ATTTCTCACCCAC---AACCTCCATTTCCTGTCTCTGCGCCTTTGCACTG 608384 i i ivv --- ?v ?--i i i v v ?v L2b_3end#LINE 91 GTTCCTCGAACACGCCANGCTCN--CTCCCGCCTCAGGGCCTTTGCACNT 138 chr4qtel1M 608385 GCTGTTGC----ACCTGGAATGCCGCT-----CCTGCTCA-CTGAC--AC 608422 v ----i i vi ----- vi i- i -- L2b_3end#LINE 139 GCTGTTCCCTCTGCCTGGAACGCCCTTCCCCACCTCTTCGCCTGGCCAAC 188 chr4qtel1M 608423 TTAT-CTGAATCTTGAGATTT--GTTCAAGTGCCACCTTCTCTTGTGAGG 608469 iv - v vi v i i -- i i i i iv vi -- L2b_3end#LINE 189 TCCTACTCATCCTTCAGGTCTCAGCTCAAATGTCACCTCCTCCGGGAA-- 236 chr4qtel1M 608470 GTTTTCCCAGACCCTGTAGCT---GCTAGTGACCTTTTTCC--ACTCTCC 608514 iii v ivi vi--- ii vvi i ii i--i i i L2b_3end#LINE 237 GCCCTCCCTGACCCCCCAGGCCGGGTCAGGCGCCCTCCTCTGGGCCCCCC 286 chr4qtel1M 608515 CA-----AAAATGT--ATCTGGGATTGGATTTGTTCATACCTATAATGT- 608556 ----- vvv i--v - iv?v i-- i?i i- - L2b_3end#LINE 287 CAGTCCTACCCTGCCACTCTGGG-TTATNATTGTC--TGNTTAC-ATGTC 332 chr4qtel1M 608557 --TTTCTCTGGCTAGATTACAATTTTTTTGAGGGCAGGGACTATTTCCCT 608604 -- i i ivi i iii vi iiv ii?v iv L2b_3end#LINE 333 TGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGT 382 chr4qtel1M 608605 TCTGTG------TGTATCC-----------------ACCTAGCTCACAGA 608631 ii v------ -----------------i i v v L2b_3end#LINE 383 CTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGT 432 chr4qtel1M 608632 AGATGCTTAATAAATGCTTGCTCTTGAATTATTG 608665 ii i i ii --- v v L2b_3end#LINE 433 AGGCGCTCAGTAAATATTTG---TTGAATGAATG 463 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 43.11 CpG sites = 79, Kimura (unadjusted) = 48.08 Transitions / transversions = 1.84 (79/43) Gap_init rate = 0.08 (29 / 377), avg. gap size = 2.41 (70 / 29) 297 34.08 8.45 3.59 chr4qtel1M 608300 608512 (391488) L2d2_3end#LINE/L2 62 284 (271) m_b206s601i13 8128 chr4qtel1M 608300 CCCTCCACTTTATAATCAGCCTAATTGGCTTATCTGACATTTCTCACCCA 608349 i i------ v i ii iiiivii ii i ivv L2d2_3end#LIN 62 CCCTCCGCTC------CAGCCAAACTGGTCTACTCACTGTCCCCCGAACA 105 chr4qtel1M 608350 CAACCTCCA-TTTCCTGTCTCTGCGCCTTTGCACTGGCTGTT----GCAC 608394 iv i v i-? i i v vv i ----v i L2d2_3end#LIN 106 CGCCTTGCGCNTTCCCGCCTCTGCGCCTTTGCTCACGCCGTTCCCCCCGC 155 chr4qtel1M 608395 CTGGAATGCCGCTCCTGCTCACTGACACTTATCTGAATC----------- 608433 vi ivi viivv i ii ----------- L2d2_3end#LIN 156 CTGGAATGCCCTTCCCCTTCCTCTCCACCTATCCAAATCCTACCCATCCT 205 chr4qtel1M 608434 TTGAGATTT-GTTCAAGTGCCACCTTCTCTTGTGAGGGTTTTCCCAGACC 608482 ii iiii- i i ? i -i -i ii v L2d2_3end#LIN 206 TCAAGGCCCAGCTCAAATNCCACCTCCTC-CGTGA-AGCCTTCCCTGACC 253 chr4qtel1M 608483 -CTGTAGCTGCTAGTGACCTTTTTCCACTCT 608512 - vi ivv? i i ii iv L2d2_3end#LIN 254 ACTCCAGCCCGNAGTGATCTCTCCCTCCTCT 284 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 42.50 CpG sites = 50, Kimura (unadjusted) = 50.59 Transitions / transversions = 2.50 (50/20) Gap_init rate = 0.06 (13 / 212), avg. gap size = 2.00 (26 / 13) 291 25.97 4.83 7.04 chr4qtel1M 608521 608665 (391335) L2c_3end#LINE/L2 334 475 (3) m_b206s601i14 8128 chr4qtel1M 608521 TGTATCTGGGATTGGATTTGTTCATACCTATAATGTTTTCTCTGGCTAGA 608570 - vi -- i -- ? i v- i i ii- L2c_3end#LINE 334 TGTAT-TGTAATTG--TCTGTT--TACNTGTC-TGTCTCCTCCA-CTAGA 376 chr4qtel1M 608571 TTACAATTTTTTTGAGGGCAGGGACTATTTCCC-TTC-TGTGTGTATCC- 608617 i iii vi ii ii v ii- - v v - L2c_3end#LINE 377 CTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTATCCC 426 chr4qtel1M 608618 ----ACCTAGCTCACAGAAGATGCTTAATAAATGCTTGCTCTTGAATTAT 608663 ----i i v i v ii i i --- v v L2c_3end#LINE 427 CAGCGCCTGGCACATAGTAGGCGCTCAATAAATGTTTG---TTGAATGAA 473 chr4qtel1M 608664 TG 608665 L2c_3end#LINE 474 TG 475 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 30.08 CpG sites = 25, Kimura (unadjusted) = 33.73 Transitions / transversions = 2.50 (25/10) Gap_init rate = 0.10 (14 / 144), avg. gap size = 1.21 (17 / 14) 195 21.43 0.00 0.00 chr4qtel1M 608946 608987 (391013) C L2d2_3end#LINE/L2 (15) 540 499 m_b206s601i15 8129 chr4qtel1M 608946 AAATAGTTATTAATCACCTACTGTAAGCAAGGCCCTGGGATA 608987 v i v i iv v v v C L2d2_3end#LIN 540 AAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTA 499 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 22.32 CpG sites = 3, Kimura (unadjusted) = 25.24 Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 687 20.97 11.27 1.79 chr4qtel1M 609194 609397 (390603) MIRc#SINE/MIR 1 223 (45) m_b206s601i16 8130 chr4qtel1M 609194 CAAGGCAG-ATGGTAGCTGGTGGACAGTATGCT----CTGGAGTCAGGAA 609238 i -i i--ii v viii ----i MIRc#SINE/MIR 1 CGAGGCAGTGTGGTG--CAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr4qtel1M 609239 GACCTGAATTC------TGCCTCAAATACTTGCCAGCTATGTGACCT-GG 609281 ii ------i v vivi i i i - MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 98 chr4qtel1M 609282 ACAAGTCACTTTAACTTCT----GCCTCTATTTCCTTATCTATAAAATGG 609327 i - i ---- vi i i MIRc#SINE/MIR 99 GCAAGTCACTT-AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGG 147 chr4qtel1M 609328 GGCTGATAACAGC--ATCTGCTTAC----CAGGATTGTTGTGGGGAATCC 609371 v i i v --vi i ---- i i - v MIRc#SINE/MIR 148 GGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGG-ATCA 196 chr4qtel1M 609372 AATGTGATAATCATTGTG-AAGCGCTT 609397 v vvv - MIRc#SINE/MIR 197 AATGAGATAATGTATGTGAAAGCGCTT 223 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 23.94 CpG sites = 28, Kimura (unadjusted) = 25.31 Transitions / transversions = 2.00 (28/14) Gap_init rate = 0.06 (12 / 203), avg. gap size = 2.25 (27 / 12) 884 20.76 5.63 2.74 chr4qtel1M 609223 609435 (390565) MIRb#SINE/MIR 36 254 (14) m_b206s601i17 8130 chr4qtel1M 609223 GCTCTGGAGTCAGGAAGACCTG------AATTCTGCCTCAAATACTTGCC 609266 i iv ------ i i v vivi i i MIRb#SINE/MIR 36 GCTTTGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACT 85 chr4qtel1M 609267 AGCTATGTGACCT-GGACAAGTCACTTTAACTTCT----GCCTCTATTTC 609311 i - i i - i ---- vi MIRb#SINE/MIR 86 AGCTGTGTGACCTTGGGCAAGTTACTT-AACCTCTCTGAGCCTCAGTTTC 134 chr4qtel1M 609312 CTTATCTATAAAATGGGGCTGATAACAGCATCTGCTTACCAGGATTGTTG 609361 i i --- i ii i i i vv i MIRb#SINE/MIR 135 CTCATCTGTAAAATGGGG---ATAATAATACCTACCTCGCAGGGTTGTTG 181 chr4qtel1M 609362 TGGGGAATCCAATGTGATAAT-CATTGTGAAGCGCTTAACCCAGTACCTG 609410 i - iv v - - i i v i MIRb#SINE/MIR 182 TGAGGA-TTAAATGAGATAATGCAT-GTAAAGCGCTTAGCACAGTGCCTG 229 chr4qtel1M 609411 GCACACAATAGGTGTTTAATAAATG 609435 i i i i i i MIRb#SINE/MIR 230 GCACATAGTAAGCGCTCAATAAATG 254 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 24.06 CpG sites = 33, Kimura (unadjusted) = 25.42 Transitions / transversions = 3.30 (33/10) Gap_init rate = 0.05 (10 / 212), avg. gap size = 1.80 (18 / 10) 271 25.00 0.00 0.00 chr4qtel1M 609391 609446 (390554) L2d2_3end#LINE/L2 493 548 (7) m_b206s601i18 8128 chr4qtel1M 609391 AGCGCTTAACCCAGTACCTGGCACACAATAGGTGTTTAATAAATGTGTAT 609440 i i v i v i i i i i v i L2d2_3end#LIN 493 AGCGCCTAGCACAGTGCCTTGCACACAGTAGGCGCTCAATAAATATTTGT 542 chr4qtel1M 609441 TCCTTT 609446 vv L2d2_3end#LIN 543 TGATTT 548 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 28.70 CpG sites = 9, Kimura (unadjusted) = 31.36 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0) 395 29.08 4.96 0.00 chr4qtel1M 610009 610149 (389851) C L3#LINE/CR1 (652) 3447 3300 m_b206s601i19 8131 chr4qtel1M 610009 TTAACTGAAACTGCCCCGCCCTTTTTACATGAACCAAGGTTAACCCTGAT 610058 i i iv ivv i i i i iivv i v v C L3#LINE/CR1 3447 TCAACTAAAACCCCTAGGTCTTTTTCACGTGAACTGCTGCTAAGCCAGAT 3398 chr4qtel1M 610059 C---TCCATGGTATGTTTGTTCCATTGATTGTTTGGATCTCAGTGTAGGT 610105 --- vv i ii v vi v i i v i i v C L3#LINE/CR1 3397 CCTCTCCATCCTGTACTTGTGCAGTTGATTTTTTGAACCTAAATGCAGGA 3348 chr4qtel1M 610106 CTTTACATTTGTCTC--TTGAATTTAACCTT-TTCATTT-AGCCCATC 610149 i i -- i v i - vi -i C L3#LINE/CR1 3347 CTTTACATTTATCCCTGTTAAATTTCATCTTGTTGGTTTCGGCCCATC 3300 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 35.65 CpG sites = 25, Kimura (unadjusted) = 38.00 Transitions / transversions = 1.56 (25/16) Gap_init rate = 0.03 (4 / 140), avg. gap size = 1.75 (7 / 4) 195 26.79 0.00 0.00 chr4qtel1M 610421 610476 (389524) C L3#LINE/CR1 (726) 3373 3318 m_b206s601i20 8132 chr4qtel1M 610421 TTGACTTTCTGAGCCGCTATGAAAGACTTTACATTTAGACTAATTAAATG 610470 i i i vvv v i vv ivi v C L3#LINE/CR1 3373 TTGATTTTTTGAACCTAAATGCAGGACTTTACATTTATCCCTGTTAAATT 3324 chr4qtel1M 610471 TAATCT 610476 v C L3#LINE/CR1 3323 TCATCT 3318 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 33.19 CpG sites = 6, Kimura (unadjusted) = 33.19 Transitions / transversions = 0.67 (6/9) Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0) 30 24.05 0.78 8.33 chr4qtel1M 611358 611486 (388514) (AGGGG)n#Simple_repeat 1 120 (0) m_b206s252i8 8133 chr4qtel1M 611358 AGGGGAGGGGGGGAGAAGAGGGAGGAAAAAAGGAGGGGAGGGAAGAGGAA 611407 i - i - -ii ii i - i (AGGGG)n#Simp 1 AGGGGAGGGGAGG-GGAG-GGGAGG-GGAGGGGAGGGGAGGGGAG-GGGA 46 chr4qtel1M 611408 CAAAGAAAGGAGGGAGAGGAGAGGGGAGGAGAGAAGAGAGAGGAGGGGAG 611457 -iii ii - i - - i i i (AGGGG)n#Simp 47 -GGGGAGGGGAGGG-GAGGGGAGGGGAGG-G-GAGGGGAGGGGAGGGGAG 92 chr4qtel1M 611458 TCGAGGAGTCGGGGA-GGGAGTGGGCGGGG 611486 vv - vv - - v (AGGGG)n#Simp 93 GGGAGG-GGAGGGGAGGGGAG-GGGAGGGG 120 Matrix = Unknown Transitions / transversions = 3.40 (17/5) Gap_init rate = 0.09 (11 / 128), avg. gap size = 1.00 (11 / 11) 15 15.30 0.00 0.00 chr4qtel1M 611619 611647 (388353) (TCC)n#Simple_repeat 1 29 (0) m_b206s252i9 8134 chr4qtel1M 611619 TCGTCCTCCTCGTCTCCCTCCTCCTCCTC 611647 v v ii (TCC)n#Simple 1 TCCTCCTCCTCCTCCTCCTCCTCCTCCTC 29 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 259 20.47 12.99 4.82 chr4qtel1M 612401 612477 (387523) MIRb#SINE/MIR 172 254 (14) m_b206s601i21 8135 chr4qtel1M 612401 AGAGGTGTTGTGAAGATCAAATAAGAT----CATATAG------TACCAT 612440 i v i i i ---- i i------ v i MIRb#SINE/MIR 172 AGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGCAC 221 chr4qtel1M 612441 GGTGCCTGATACACAATTTATAAGCGCTTAATAAATG 612477 i ii i ----i i MIRb#SINE/MIR 222 AGTGCCTGGCACATA----GTAAGCGCTCAATAAATG 254 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 25.60 CpG sites = 13, Kimura (unadjusted) = 25.60 Transitions / transversions = 6.50 (13/2) Gap_init rate = 0.08 (6 / 76), avg. gap size = 2.33 (14 / 6) 239 28.42 7.03 3.79 chr4qtel1M 612593 612720 (387280) C MIRb#SINE/MIR (131) 137 6 m_b206s601i22 8136 chr4qtel1M 612593 GAGGAAACTGAAGGTCAGGGGGGGTTTAGTCACTAAACCAGGGATACTCA 612642 i v - i i v v viv i vi v C MIRb#SINE/MIR 137 GAGGAAACTGAGGCTCA-GAGAGGTTAAGTAACTTGCCCAAGGTCACACA 89 chr4qtel1M 612643 TTCT--------GCAGAGATGCTACTCACTCCAAGATCC-TCTGACTCCA 612683 -v -------- vi vv i ivv v i i- C MIRb#SINE/MIR 88 -GCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCA 40 chr4qtel1M 612684 GAAGCTGGACTCTCTCCCTTGCACAGCACCCCTGCCC 612720 i iv i vi i vi -- - v C MIRb#SINE/MIR 39 AAGCCCGTGCTCTTTCCACTGCAC--CA-CGCTGCCC 6 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 32.47 CpG sites = 17, Kimura (unadjusted) = 36.13 Transitions / transversions = 0.94 (17/18) Gap_init rate = 0.06 (7 / 127), avg. gap size = 2.00 (14 / 7) 304 31.28 0.00 3.12 chr4qtel1M 612839 612937 (387063) MIRb#SINE/MIR 4 99 (169) m_b206s601i23 8137 chr4qtel1M 612839 AGGGGCTGCTAAGCTGTTCAGTGGGTAGAGAATCAACCTTACACTCAAGA 612888 v --- iv v iv v ivii i iv v iiv MIRb#SINE/MIR 4 AGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGAC 50 chr4qtel1M 612889 AGATCTGAATTCAAATCCAGCCTTAGACACTCACTAGCTGTGTGATCCT 612937 i ii i v v iv v i i i MIRb#SINE/MIR 51 AGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTT 99 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 37.98 CpG sites = 17, Kimura (unadjusted) = 41.52 Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.03 (3 / 98), avg. gap size = 1.00 (3 / 3) 317 30.95 0.00 0.00 chr4qtel1M 612854 612937 (387063) MIRc#SINE/MIR 13 96 (172) m_b206s601i24 8137 chr4qtel1M 612854 GTTCAGTGGGTAGAGAATCAACCTTACACTCAAGAAGATCTGAATTCAAA 612903 v iv v iiiiv iv v i i ii i i MIRc#SINE/MIR 13 GTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAG 62 chr4qtel1M 612904 TCCAGCCTTAGACACTCACTAGCTGTGTGATCCT 612937 v v iv v i i i MIRc#SINE/MIR 63 TCCCGGCTCTGCCACTTACTAGCTGTGTGACCTT 96 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 39.36 CpG sites = 16, Kimura (unadjusted) = 41.46 Transitions / transversions = 1.60 (16/10) Gap_init rate = 0.00 (0 / 83), avg. gap size = 0.0 (0 / 0) 14 4.49 0.00 4.17 chr4qtel1M 613224 613248 (386752) (AAAG)n#Simple_repeat 1 24 (0) m_b206s252i10 8138 chr4qtel1M 613224 AAAGAAAGAAAGAAAAGAAACAAAG 613248 - v (AAAG)n#Simpl 1 AAAGAAAGAAAG-AAAGAAAGAAAG 24 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 229 32.52 3.88 2.29 chr4qtel1M 613685 613813 (386187) C CR1-3_Croc#LINE/CR1 (1021) 2584 2454 m_b206s551i0 8139 chr4qtel1M 613685 ACAGAATACTCCAAATAGTGCCTGACCAG-GCCAGGAAACACAGGGATGA 613733 v i i iiv i - ii v i- v v iv C CR1-3_Croc#LI 2584 ACACAGTACTCCAGATGAGGCCTAACCAGTGCCGAGTAG-AGAGGCACTA 2536 chr4qtel1M 613734 CCATCCCTCATTTCTTGAAACTCTTGCCCCT--CAGGGCAGCCCAAAATA 613781 i i i i i v v v vv ii --iiiv v iv C CR1-3_Croc#LI 2535 TCACCTCCCGTGTCTTGCACCTAATGCTTCTATTGATGCATCCCAAAACC 2486 chr4qtel1M 613782 GCACTGACTCTTTGGGCCAGGATG--TCACACTG 613813 i vi ii v -- v -- C CR1-3_Croc#LI 2485 GCATTCGCCTTTTGTGC--GGCTGCATCACACTG 2454 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 39.89 CpG sites = 24, Kimura (unadjusted) = 44.13 Transitions / transversions = 1.41 (24/17) Gap_init rate = 0.05 (6 / 128), avg. gap size = 1.33 (8 / 6) 185 32.26 7.53 0.00 chr4qtel1M 613814 613906 (386094) Tigger19b#DNA/TcMar-Tigger 334 433 (117) m_b206s601i25 8140 chr4qtel1M 613814 GCCTCCCAGATCTTCCTCAGATAAGTTTT--CGGTG-AGCCCCACCTTTT 613860 i v i v vi i i -- i -i ii iiv Tigger19b#DNA 334 GCTTCCCAGCTCCTCCTGAGTCAGGTCTTCACAGTGTGGCTTCATTATTT 383 chr4qtel1M 613861 GGTGAAGAGCATCATTAGCT-CCAGA--ATCAGA-AAACCCATATTAGAA 613906 v vvii ii ii v ii - -- - v vi Tigger19b#DNA 384 TGTTTGAAGTGTTGTGAATTCCCAGAACATCAGACACACCCATATTCAAA 433 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 44.62 CpG sites = 20, Kimura (unadjusted) = 44.62 Transitions / transversions = 2.00 (20/10) Gap_init rate = 0.05 (5 / 92), avg. gap size = 1.40 (7 / 5) 270 33.76 3.18 1.89 chr4qtel1M 613858 614014 (385986) MIR1_Amn#SINE/MIR 17 175 (55) m_b206s601i26 8141 chr4qtel1M 613858 TTTGGTGAAGAGCATCATTAGCTCCAGAATCAGAAAACCCATATTAGAAC 613907 i i i v - v i i viivi v i i i iivi v? ?- MIR1_Amn#SINE 17 TCTAGTGGATAG-AGCACTGGACTGGGACTCGGGAGACCTGGGTTCNAN- 64 chr4qtel1M 613908 TCCC--CTCTGCCATTTGCCCA---GGTAACATTGGACTGGTCATTTAAA 613952 -- i ? ?i---? i v i vi i ? v MIR1_Amn#SINE 65 TCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGTCACTTNAC 114 chr4qtel1M 613953 CTCACCGAGTTTTAACATCCTCAGTTCTAAAATGAATTTGATGCCTTCTG 614002 v i ? ii i iiv vi v iivv i -v v MIR1_Amn#SINE 115 CTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATG-ATACTG 163 chr4qtel1M 614003 AGGTCATTTCTA 614014 vv v v MIR1_Amn#SINE 164 ACCTCCTTTGTA 175 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 48.33 CpG sites = 30, Kimura (unadjusted) = 49.69 Transitions / transversions = 1.36 (30/22) Gap_init rate = 0.03 (5 / 156), avg. gap size = 1.60 (8 / 5) 300 32.50 4.80 1.55 chr4qtel1M 613862 613986 (386014) MIRb#SINE/MIR 21 149 (119) m_b206s601i27 8141 chr4qtel1M 613862 GTGAAGAGCATCATTAGCTCCAGAATCAGA-AAACCCATATTAGAACTCC 613910 i i - v ivi iii i - i iivi v - MIRb#SINE/MIR 21 GTGGAAAG-AGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCGAA-TCC 68 chr4qtel1M 613911 C--CTCTGCCATTTGC---CCAGGTAACATTGGACTGGTCATTTAAACTC 613955 -- i i --- iiv i v i vi i i v MIRb#SINE/MIR 69 CGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTC 118 chr4qtel1M 613956 ACCGAGTTTTAACATCCTCAGTTCTAAAATG 613986 v i ii i iiv vi v MIRb#SINE/MIR 119 TCTGAGCCTCAGTTTCCTCATCTGTAAAATG 149 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 44.06 CpG sites = 28, Kimura (unadjusted) = 45.67 Transitions / transversions = 2.33 (28/12) Gap_init rate = 0.04 (5 / 124), avg. gap size = 1.60 (8 / 5) 278 34.02 9.86 0.65 chr4qtel1M 613884 614025 (385975) MIR3#SINE/MIR 37 191 (17) m_b206s601i28 8141 chr4qtel1M 613884 GAATCAGAAAACCCATATTAGAACTCCC--CTCTGCCATT---TGCCCAG 613928 i i i iivi vv i- -- i --- ?v iiv MIR3#SINE/MIR 37 GAGTCAGGAGACCTGGGTTCTAG-TCCCGGCTCTGCCACTAACTNGCTGT 85 chr4qtel1M 613929 GTAACATTGGACTGGTCATTTAAACTCACCGAGTTTTAACATCCTCAGTT 613978 i v i vi i v v v i i ii i iiv vi MIR3#SINE/MIR 86 GTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCT 135 chr4qtel1M 613979 CTAAAATGA---------ATTTGATGCCTTCTGAGGTCATTTCTAGGTCT 614019 v --------- i v vii i vi i v MIR3#SINE/MIR 136 GTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCT 185 chr4qtel1M 614020 AGAATT 614025 iiv MIR3#SINE/MIR 186 GACATT 191 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 48.16 CpG sites = 30, Kimura (unadjusted) = 48.16 Transitions / transversions = 1.67 (30/18) Gap_init rate = 0.03 (4 / 141), avg. gap size = 3.75 (15 / 4) 181 30.00 0.00 0.00 chr4qtel1M 614027 614076 (385924) C L3#LINE/CR1 (722) 3377 3328 m_b206s601i29 8142 chr4qtel1M 614027 GCAGGTGGCTTTTTGAACCCCTTGACAGAACTTTAAGTTTGTTCCTATTA 614076 v ii ivvvvi i vi i i i C L3#LINE/CR1 3377 GCAGTTGATTTTTTGAACCTAAATGCAGGACTTTACATTTATCCCTGTTA 3328 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 39.56 CpG sites = 9, Kimura (unadjusted) = 39.56 Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 273 31.28 2.24 4.58 chr4qtel1M 614087 614220 (385780) L1ME5_3end#LINE/L1 353 483 (458) m_b206s551i1 8143 chr4qtel1M 614087 TATACATAGCCTTTGATCCAGCAATATCACTGAGAAGTCAATATCCCAAG 614136 ii v v i vi i vvvii vv i L1ME5_3end#LI 353 TACGCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATATCCCAAA 402 chr4qtel1M 614137 GAGA---TCATAAAAAGATGAAAGGGCCCAGGTGTACCAGAAAATATTTA 614183 i --- i v iivviiv vv -- -- ii i i L1ME5_3end#LI 403 GAAATTCTCACACAGGTCCATAAGGGGACA--TGTAC--GAGGATGTTCA 448 chr4qtel1M 614184 GAGCAGCTCTTTTTGTGGTGGCAGGAAAAGTTGGAAG 614220 vv vi v i --i i L1ME5_3end#LI 449 TTGCAGCGTTGTTTGTGGTGGCGGG--GAGTTGGAGG 483 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 37.30 CpG sites = 22, Kimura (unadjusted) = 41.37 Transitions / transversions = 1.22 (22/18) Gap_init rate = 0.05 (7 / 133), avg. gap size = 1.29 (9 / 7) 14 0.00 0.00 4.76 chr4qtel1M 614458 614479 (385521) (CTTT)n#Simple_repeat 1 21 (0) m_b206s252i11 8144 chr4qtel1M 614458 CTTTCTTTTCTTTCTTTCTTTC 614479 - (CTTT)n#Simpl 1 CTTTC-TTTCTTTCTTTCTTTC 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.05 (1 / 21), avg. gap size = 1.00 (1 / 1) 12 0.00 9.09 0.00 chr4qtel1M 614595 614616 (385384) (AAAC)n#Simple_repeat 1 24 (0) m_b206s252i12 8145 chr4qtel1M 614595 AAACAAACAAACAAA-AAA-AAAC 614616 - - (AAAC)n#Simpl 1 AAACAAACAAACAAACAAACAAAC 24 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.10 (2 / 21), avg. gap size = 1.00 (2 / 2) 225 33.33 0.00 0.00 chr4qtel1M 614638 614706 (385294) C L3b_3end#LINE/CR1 (761) 445 377 m_b206s601i30 8146 chr4qtel1M 614638 ATATGTGTCCCCATTGGATCCCCACTTATTAGGTTCAGCCCAGTGTTCTA 614687 ii v i ii i ii vv i i ? i i?i C L3b_3end#LINE 445 ACGTTTATCCCTGTTGAATTTCATCTTGTTGGNTTCGGCCCGNCGTTCTA 396 chr4qtel1M 614688 GGCTGGCAAGGACTCTTTG 614706 v v i iv vi C L3b_3end#LINE 395 GTCTGTCGAGATCGTTTTG 377 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 35.28 CpG sites = 16, Kimura (unadjusted) = 49.48 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.00 (0 / 68), avg. gap size = 0.0 (0 / 0) 379 36.11 16.14 1.90 chr4qtel1M 614716 615130 (384870) C L3#LINE/CR1 (889) 3210 2738 m_b206s601i31 8142 chr4qtel1M 614716 ACAAGCCACGCTTCCTATGCCTTTATCCAAGTCACTGATAG------TGG 614759 i - i i i i i i i------ i C L3#LINE/CR1 3210 ATAAGC-ATGCCTTCTATGTCTTCATCCAAGTCATTGATAAAAATGTTGA 3162 chr4qtel1M 614760 ATAGTACAGCTCCCCAGTATAAA----TGGATCAAACATTGGCTTGAGAC 614805 i v vv v- v i i ---- viv vi v---i v C L3#LINE/CR1 3161 ACAGGACAGGGCCA-AGGACAGAGCCCTGTGGCACGCC---ACTAGAGAC 3116 chr4qtel1M 614806 CTTCTTC---ATTGACATCCAACCATTCATGATTATTCCTTGAGTCCAAC 614852 i i ---i v v v v vi iiii i vi ii C L3#LINE/CR1 3115 CTCCCTCCAGGTTGACATCGATCCATTAATCAACACCTTTTGGGTATAGT 3066 chr4qtel1M 614853 CATCAAAACTACTGCAACTCCATATAATTGTGCTATTGTGTAGTCCAGAA 614902 i iv v vi i i v iv i i ii vi i v v C L3#LINE/CR1 3065 CGTTCAACCAGCTACGAATCCACCTAACTGTACTATCATCCAGCCCATAT 3016 chr4qtel1M 614903 AGCACCACCTTTTCTATGGGAAT--------AAACTTTACTAAA------ 614938 vv v i v i iii i -------- i iii ------ C L3#LINE/CR1 3015 TTCTCCATCTTGTCCACAAGGATATCATGAGAGACTTTGTCAAATGCCTT 2966 chr4qtel1M 614939 ACAACAAT---GACA-ACTTTGTAAATTCTATCTCCCTGGCATCTGGACT 614984 i viv --- i - ? vv ivvi ii -- -- i C L3#LINE/CR1 2965 GCTGAAATCCAGATACACTNTGTCTACGGCATTCCCCTG--ATCT--ACC 2920 chr4qtel1M 614985 AGTTTAGAAGTCTCTCCCAAAGAGGA------TCCAGTTTGG-------- 615020 i v ii iivi v i ------vii -------- C L3#LINE/CR1 2919 AGTCTAGTAACCCTATCAAAAAAGGAAATGAGGTTAGTTTGGCATGACTT 2870 chr4qtel1M 615021 -------GGG---CTGTGCTGGCTCTTGGTAATCA-----TCATTTATTA 615055 ------- v --- ii i i i ----- v vi C L3#LINE/CR1 2869 GTTCTTAGTGAACCCATGCTGGCTCCTAGTGATCACCGCTTCCTTTTCTA 2820 chr4qtel1M 615056 -------ACCAGCTGTCTCTGTGACAGTTAACTCTGACACATTCCTAAAA 615098 ------- v i ii v v i i i ivii iiv iv v iiiii C L3#LINE/CR1 2819 AGTGCTCACAAACCATCTGTTTAATAATCCGTTCTAGAATTTTGCCGGGG 2770 chr4qtel1M 615099 ATCAAAATCAAGCTCATTGGCCCATAGTTCTC 615130 i vi i ii i ii i? C L3#LINE/CR1 2769 ATCGACGTCAAGCTTACCGGTCTGTAGTTTNC 2738 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 48.66 CpG sites = 98, Kimura (unadjusted) = 53.57 Transitions / transversions = 2.00 (98/49) Gap_init rate = 0.05 (22 / 414), avg. gap size = 3.45 (76 / 22) 12 0.00 9.09 0.00 chr4qtel1M 615870 615891 (384109) (CCTG)n#Simple_repeat 1 24 (0) m_b206s252i13 8147 chr4qtel1M 615870 CCTG-CTGCCTGCCTGCC-GCCTG 615891 - - (CCTG)n#Simpl 1 CCTGCCTGCCTGCCTGCCTGCCTG 24 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.10 (2 / 21), avg. gap size = 1.00 (2 / 2) 585 26.94 7.77 0.00 chr4qtel1M 616869 617061 (382939) C MIRc#SINE/MIR (0) 268 61 m_b206s601i32 8148 chr4qtel1M 616869 AATAATAATAATACTTAGCATTTAGATAGCATTGTAGGGTTTGCAAAGCA 616918 i? i vi iv i v vi i i C MIRc#SINE/MIR 268 AATAATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCG 219 chr4qtel1M 616919 CTGT-ACAGATATGATCTCCTTTTGTCCTCACCA-----CTATGAA--AG 616960 v - v i v v vi v ----- i i-- C MIRc#SINE/MIR 218 CTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAG 169 chr4qtel1M 616961 GC-TGACA-CTCTTATGATTCCCATTTTATAGATGAGAAAGCTGAGGATT 617008 -v i -v v v i i i i v i C MIRc#SINE/MIR 168 GCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC 119 chr4qtel1M 617009 GAGGAGATT--GTGACTTA---AAAGCTTCACGGCTAATAAACATCTGAG 617053 iii i -- i--- i iiv i i iiiv v C MIRc#SINE/MIR 118 AGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAG 69 chr4qtel1M 617054 GCTGAACT 617061 v v i C MIRc#SINE/MIR 68 CCGGGACT 61 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 33.78 CpG sites = 32, Kimura (unadjusted) = 34.61 Transitions / transversions = 1.60 (32/20) Gap_init rate = 0.04 (7 / 192), avg. gap size = 2.14 (15 / 7) 242 30.33 4.03 2.65 chr4qtel1M 617513 617661 (382339) L1MC_orf2#LINE/L1 3086 3236 (58) m_b206s551i2 8149 chr4qtel1M 617513 TGGAAGGA-AAGCAGAAAATAGCGGGAAAAT-TTTGCAACAAATATCTCT 617560 i i - viv i iv v i - v i i v L1MC_orf2#LIN 3086 TGAAAAGACAAGCCACAGACTGGGAGAAAATATTTGCAAAAGACATATCT 3135 chr4qtel1M 617561 AATAAAGGCCTCATTTCTCAAATATATTGAGAACT----GAGTCTATTAA 617606 i v vv v iv ivi ----i iiii vi L1MC_orf2#LIN 3136 GATAAAGGACTGTTATCCAAAATATACAAAGAACTCTTAAAACTCAACAA 3185 chr4qtel1M 617607 TAGAAAATACAAGTCATTCCTCAATTTACAAATGGTCAAAAGACATAAAT 617656 ii - iiv --- i i ? v v v i i L1MC_orf2#LIN 3186 TAAGAAA-ACAAACAA---CCCGATTNAAAAATGGGCAAAAGACCTGAAC 3231 chr4qtel1M 617657 AGGCA 617661 i L1MC_orf2#LIN 3232 AGACA 3236 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 39.48 CpG sites = 27, Kimura (unadjusted) = 40.70 Transitions / transversions = 1.59 (27/17) Gap_init rate = 0.05 (7 / 148), avg. gap size = 1.43 (10 / 7) 848 32.78 5.20 1.03 chr4qtel1M 617573 618130 (381870) L1ME4c_3end#LINE/L1 4 584 (246) m_b206s551i3 8149 chr4qtel1M 617573 ATTTCTCAAATATATTGAGAACTGAGTCTA-TTAATAGAAAATACAAGTC 617621 v ?v ? vi i v v v - i ii v ? -- L1ME4c_3end#L 4 ATATCTNTANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANA--TC 51 chr4qtel1M 617622 ATT-CCTCAATTTACAAATGGTCAAAAGACATAAATAGGCAGTTTTCAGA 617670 vv- i vv i v i i i i i iv ? L1ME4c_3end#L 52 AAGACCCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANA 101 chr4qtel1M 617671 CAA--AAATCAGATCTAG---------ACTTGAAAAAATGTTCTAAATTG 617709 vi -- - v v? --------- v i v vv i L1ME4c_3end#L 102 AGAGGAAAT-ACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCG 150 chr4qtel1M 617710 CTATTGATCAGAGAAATACAAACTAAAACAATTCTGAGGTATGATCTTTC 617759 v i i i i i ivv i iv i v L1ME4c_3end#L 151 CTAGTAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTAC 200 chr4qtel1M 617760 ACCTAAGAGAGTGGCTAATGTGACAAAAAACTGA-AATGTTGGATTTAGG 617808 i vv i v i v vi v-i i - iiivi viv L1ME4c_3end#L 201 GCCTATTAAATTAGCAAAAATT-TAAAAAATTGATAATACCCAATGCTGG 249 chr4qtel1M 617809 GGAGGATGTGAGAAAACTAAGACACTAAGGCACAGTAGGTAGAATTGTGA 617858 v ? i ivi iiv ? v vi iv iv i v ? i L1ME4c_3end#L 250 CGAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAA 299 chr4qtel1M 617859 -------------TTCTGGAGAACAATGTAACTGTACCCA--AAGGACTA 617893 ------------- i i i v ii vi vi -- ii i L1ME4c_3end#L 300 ATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCA 349 chr4qtel1M 617894 TAAGACTATGCATATCCTTTGATCCAGAAATACCACTGCTAGATCTATAT 617943 i v i v i i v v v i ivv v L1ME4c_3end#L 350 TAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTAT 399 chr4qtel1M 617944 CCCCCCAAAAAATTTTAAAAGGAGGGGAAAGACCTATAAATACAAAAATA 617993 ivvvi v v i i ii -- vii i i i L1ME4c_3end#L 400 CCTAAGGAAATAATTCAAAAGAAGGAAAAAG--CTATATGCACGAAGATG 447 chr4qtel1M 617994 TTTACAGCAGCTCTTTTTATGGTGACTAAGGATTGGAAATCAAAGGGATG 618043 i iv vi v ii ii v ii iv vvvii L1ME4c_3end#L 448 TTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATG 497 chr4qtel1M 618044 CCCATTAATTGGAGAATGGATAAACAAACTATGGTATATGGTTGCAACAG 618093 i vi v i v ii i i v?viv i ii L1ME4c_3end#L 498 TCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGG 547 chr4qtel1M 618094 AATACTATTGGGCTATTAAAAAAAAAAGTGATAAGGA 618130 i vvi i vi v i v i i L1ME4c_3end#L 548 AATATTATGCAGCCATTAAAAATGATAATTATGAAGA 584 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 43.77 CpG sites = 103, Kimura (unadjusted) = 45.48 Transitions / transversions = 1.32 (103/78) Gap_init rate = 0.02 (13 / 557), avg. gap size = 2.69 (35 / 13) 15 7.22 3.23 3.23 chr4qtel1M 618356 618386 (381614) (TTTC)n#Simple_repeat 1 31 (0) m_b206s252i15 8150 chr4qtel1M 618356 TTTCTAT-TTTCTTTCTTTCATTTTTTTCTTT 618386 v - - i (TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTC-TTTCTTTCTTT 31 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2) 15 16.56 6.12 1.96 chr4qtel1M 618352 618400 (381600) (CTATTTT)n#Simple_repeat 1 51 (0) m_b206s252i14 8151 chr4qtel1M 618352 CTATTTTCTATTTTCTTTCTTTC-ATTTT-T-TTCTTTAATTTGAATCTT 618398 v - - - - i i v vv i (CTATTTT)n#Si 1 CTATTTTCTATTTTCTAT-TTTCTATTTTCTATTTTCTATTTTCTATTTT 49 chr4qtel1M 618399 CT 618400 (CTATTTT)n#Si 50 CT 51 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.08 (4 / 48), avg. gap size = 1.00 (4 / 4) 17 10.44 0.00 3.12 chr4qtel1M 618505 618537 (381463) (AAATA)n#Simple_repeat 1 32 (0) m_b206s252i16 8152 chr4qtel1M 618505 AAATAAAAATATTAAAAAATAAAATAAAATAAA 618537 - vv v (AAATA)n#Simp 1 AAAT-AAAATAAAATAAAATAAAATAAAATAAA 32 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 506 36.46 5.46 2.99 chr4qtel1M 618602 619059 (380941) C L2#LINE/L2 (524) 2558 2090 m_b206s601i33 8153 chr4qtel1M 618602 AGGGCTGTGAGTCTGA-TGACTGGGAGGATGGTGATACCCTTAAGAAAAA 618650 i i v vi i -ii i v v i v ? vvi i C L2#LINE/L2 2558 AAGGTTTTTGGCCTGAGCAACTGGAAGGATGGAGTTGCCATTNACTGAGA 2509 chr4qtel1M 618651 TGG--ACATTTGGAAAAGGCCTGGATTTGGACAGGAAGAGAAAAGGATGA 618698 -- vivi viii vvii i iivi vv iii v v C L2#LINE/L2 2508 TGGGGAAGACTGCGGGAGGAGCAGGTTTGAGGGGGAAGATCAGGAGTTCA 2459 chr4qtel1M 618699 GTTCTTGCTCCGGCCATGCTAAGACTGAGCTCTCTCCAGGATGTGTAGCT 618748 i ------ v i vi v vi vivi ii vi iv C L2#LINE/L2 2458 GTTTT------GGACATGTTAAGTTTGAGATGCCTATTAGACATCCAAGT 2415 chr4qtel1M 618749 GGA-ACATCTGATAGGTAGTTGCTGATCTAGTA--CTGGAGATTGGGGGA 618795 - ii vii i -- v vv -- v ii C L2#LINE/L2 2414 GGAGATGTCGAGTAGGCAGTTG--GATATACGAGTCTGGAGTTCAGGGGA 2367 chr4qtel1M 618796 AAGACAAGGGT-----ACCTAGATCTGGCCATCATT--TACATAGATGAT 618838 i iivv i----- iv i i vvi i--i i i C L2#LINE/L2 2366 GAGGTCCGGGCTGGAGATATAAATTTGGGAGTCATCAGCATATAGATGGT 2317 chr4qtel1M 618839 ---TGGATCCATGGGAGCTGATGATATCACTGAATG--TGAG----AACA 618879 --- ii v i viv v i? iv -- ----i i C L2#LINE/L2 2316 ATTTAAAGCCATGAGACTGGATGAGATCACCNAGGGAGTGAGTGTAGATA 2267 chr4qtel1M 618880 CAGGAGAGATGAGAGGGCTCAAGATAGAGCCTTGGGGAATACCCACAGTT 618929 v i -- v iv i iv i v iv v - C L2#LINE/L2 2266 GAGAAGAGA--AGAGGTCCAAGGACTGAGCCCTGGGGCACTCCAAC-GTT 2220 chr4qtel1M 618930 ATAAGGGATGGGACCCTGATGGAGATCTAGCAAAGGGGACTGAGAACAAG 618979 ?- ii vi ivvv v ii v i i vi C L2#LINE/L2 2219 N-AGAGGTCGGGGAGATGAGGAGGAACCAGCAAAGGAGACTGAGAAGGAG 2171 chr4qtel1M 618980 TGGTCAAAAAAACAGGAG---AATCAGAAGGGCTTAGCCACAATATGAGC 619026 i i ivi iii --- i i i iv i ivv -v ivi C L2#LINE/L2 2170 CGGCCAGTGAGGTAGGAGGAAAACCAGGAGAGTGTGGTGTC-CTGGAAGC 2122 chr4qtel1M 619027 CAGGAGAAGGAAGCACTGTCACATACCAGGGAG 619059 i v i iii - viv vv C L2#LINE/L2 2121 CAAGTGAAGAAAGTGTT-TCAAGAAGGAGGGAG 2090 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 51.52 CpG sites = 97, Kimura (unadjusted) = 52.98 Transitions / transversions = 1.49 (97/65) Gap_init rate = 0.05 (24 / 457), avg. gap size = 1.62 (39 / 24) 13 21.96 0.00 2.63 chr4qtel1M 620458 620496 (379504) (ATTG)n#Simple_repeat 1 38 (0) m_b206s252i17 8154 chr4qtel1M 620458 ATTGCTCTGATTAACTGATTGATTAATTGATGGGTTCAT 620496 v - i i i v i v (ATTG)n#Simpl 1 ATTGAT-TGATTGATTGATTGATTGATTGATTGATTGAT 38 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.03 (1 / 38), avg. gap size = 1.00 (1 / 1) 183 30.26 13.16 0.00 chr4qtel1M 622080 622155 (377845) MIR3#SINE/MIR 120 205 (3) m_b206s601i34 8155 chr4qtel1M 622080 CTCAGTTTTCCCAGATGTAAAATGGAAGAG-----CTAGAAG-CCCCCAA 622123 i i vv iii i ----- v -i i i MIR3#SINE/MIR 120 CTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAA 169 chr4qtel1M 622124 CATCCCCGCTGGCTCTAAAAT----GGATTCTGTAA 622155 vi iv ii i v ----v i i MIR3#SINE/MIR 170 GGTCCCTTCCAGCTCTGACATTCTATGATTCTATGA 205 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 41.08 CpG sites = 16, Kimura (unadjusted) = 41.08 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.04 (3 / 75), avg. gap size = 3.33 (10 / 3) 195 25.00 1.92 0.00 chr4qtel1M 622178 622229 (377771) MIRc#SINE/MIR 160 212 (56) m_b206s601i35 8156 chr4qtel1M 622178 CTGCCCCACTTCCCTCTCCTGATTGTTGTGAGGAT-AAGGGAGATGAAGA 622226 ii i v v vv i - iv i v v MIRc#SINE/MIR 160 CTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGT 209 chr4qtel1M 622227 ATG 622229 MIRc#SINE/MIR 210 ATG 212 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 30.58 CpG sites = 6, Kimura (unadjusted) = 30.58 Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.02 (1 / 51), avg. gap size = 1.00 (1 / 1) 188 26.09 0.00 0.00 chr4qtel1M 622532 622577 (377423) C L2c_3end#LINE/L2 (0) 478 433 m_b206s601i36 8157 chr4qtel1M 622532 ATTCATTCACTCGACGACCATTTATTCAGTAGCTGCTCCCTGCCAG 622577 i i i v v iiv i viv C L2c_3end#LINE 478 ATTCATTCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAG 433 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 29.20 CpG sites = 7, Kimura (unadjusted) = 32.77 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 30 13.50 6.41 2.47 chr4qtel1M 623645 623722 (376278) (GAG)n#Simple_repeat 1 81 (0) m_b206s252i18 8158 chr4qtel1M 623645 GAAGAGCAGGGAGAGG-GG-GGAGGGGGCAGG-GG-GGAGAAGGGAGGAG 623690 i v ii - - i - - - i - (GAG)n#Simple 1 GAGGAGGAGGAGGAGGAGGAGGAGGAGG-AGGAGGAGGAGGA-GGAGGAG 48 chr4qtel1M 623691 GAGAGGGAGCAGGAGGAGGAGG-GGAGGAGGAG 623722 ii v - (GAG)n#Simple 49 GAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG 81 Matrix = Unknown Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.09 (7 / 77), avg. gap size = 1.00 (7 / 7) 131 19.05 6.35 1.05 chr4qtel1M 623869 624230 (375770) (CTCTC)n#Simple_repeat 1 381 (0) m_b206s252i19 8159 chr4qtel1M 623869 CTCTTC-CTCC-CTCC-CTCC-CTCCTTTCCTCCTCC-CTTCTCTTCTCC 623913 i - - - - i - - i i i (CTCTC)n#Simp 1 CTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCT-CTCCTCTCCTCTCCTCT 49 chr4qtel1M 623914 CCT-TCCCCTCCTAT-CTCCTTTCTCCTCTTCT-TCC-CTCCTCTTCACT 623959 - i v - iii i - - i v (CTCTC)n#Simp 50 CCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCT 99 chr4qtel1M 623960 TCTCTCCCCTCCTCTCTTCAACTCT-CTC-CCTCTCCTCCCCTTTCCTGC 624007 i i i vv - - i i vi (CTCTC)n#Simp 100 CCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCT 149 chr4qtel1M 624008 ACT-TCC-CTCCTTTCTTCTTCTCTTCTC-CCCCACCTCCTCTTACTCAC 624054 v - - i i i i - i v - i - - (CTCTC)n#Simp 150 CCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCT-CTCCT-CTC-C 196 chr4qtel1M 624055 TC-CCTCTCCTCTCCTCTCCCAACTTTTCCTCTCCTTTCTCCTCC-AT-C 624101 - ivv i i i ii -v - (CTCTC)n#Simp 197 TCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCC 246 chr4qtel1M 624102 TCTTCTTTCCTCTCCCTTCCTCTCCTCTCCTCTCCTCT--TTTCATCTCC 624149 i i ii -- i v (CTCTC)n#Simp 247 TCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCC 296 chr4qtel1M 624150 TCTCCCCTTCTCTCTTCT-CTCTCAACTCCTTTCCTTTTCTCTCCCCTCC 624198 i i i - vv i i i i (CTCTC)n#Simp 297 TCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCC 346 chr4qtel1M 624199 CCTTTTCTCCTCT--TTTCCTCTCCTCTCC-CTCC 624230 i ii -- i - (CTCTC)n#Simp 347 TCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCC 381 Matrix = Unknown Transitions / transversions = 3.46 (45/13) Gap_init rate = 0.07 (25 / 361), avg. gap size = 1.08 (27 / 25) 26 28.35 2.13 2.13 chr4qtel1M 624864 624957 (375043) (GAAGAA)n#Simple_repeat 1 94 (0) m_b206s252i20 8160 chr4qtel1M 624864 GAAGAATGGGAAGAAGAAGAGGAAGAAGAGGAAGAGAAAGAGGATGAAG- 624912 vii i i ii i v - (GAAGAA)n#Sim 1 GAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA 50 chr4qtel1M 624913 AGAAAGAGATGGAGGAGGAGGAAGAGGAGGGGAGGAGAGGAA-AAG 624957 ii -i i i i i -i i i i - (GAAGAA)n#Sim 51 AGAAGAAGA-AGAAGAAGAAGAAGAAGA-AGAAGAAGAAGAAGAAG 94 Matrix = Unknown Transitions / transversions = 9.00 (18/2) Gap_init rate = 0.04 (4 / 93), avg. gap size = 1.00 (4 / 4) 187 33.55 14.05 1.47 chr4qtel1M 624958 625078 (374922) MIRb#SINE/MIR 3 138 (130) m_b206s601i37 8161 chr4qtel1M 624958 GAGGAGGAGGGTAGAGAGCAGTGCAAAGAGGCCTGGACCTGGAGTCAAGA 625007 i v v i v -- v vv v vii iiv MIRb#SINE/MIR 3 GAGGGGCAGCGTGGTG--CAGTGGAAAGAGCACGGGCTTTGGAGTCAGAC 50 chr4qtel1M 625008 AAACC-------GA----TGGCTCCACCATTCGTAGGCTCCATGACTTCT 625046 i ------- ----i ii i iiivi vii i iv MIRb#SINE/MIR 51 AGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTG 100 chr4qtel1M 625047 G------TGCTTCGTGTCTTTGAGCCTCGGCCTCCTCA 625078 ------ i viiv i i ii MIRb#SINE/MIR 101 GGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCA 138 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 45.48 CpG sites = 26, Kimura (unadjusted) = 47.15 Transitions / transversions = 1.86 (26/14) Gap_init rate = 0.04 (5 / 120), avg. gap size = 3.80 (19 / 5) 259 29.81 16.35 0.00 chr4qtel1M 624975 625078 (374922) MIRc#SINE/MIR 15 135 (133) m_b206s601i38 8161 chr4qtel1M 624975 GCAGTGCAAAGAGGCCTGGACCTGGAGTCAAGAAAACC-------GA--- 625014 v vv i i i ------- --- MIRc#SINE/MIR 15 GCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTC 64 chr4qtel1M 625015 -TGGCTCCACCATTCGTAGGCTCCATGACTTCTG------TGCTTCGTGT 625057 -i ii i iiivi vii i iv ------ii viiv MIRc#SINE/MIR 65 CCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCT 114 chr4qtel1M 625058 CTTTGAGCCTCGGCCTCCTCA 625078 i i ii MIRc#SINE/MIR 115 CTCTGAGCCTCAGTTTCCTCA 135 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 39.03 CpG sites = 23, Kimura (unadjusted) = 40.79 Transitions / transversions = 2.88 (23/8) Gap_init rate = 0.04 (4 / 103), avg. gap size = 4.25 (17 / 4) 209 23.43 19.19 0.85 chr4qtel1M 625583 625681 (374319) C MIR3#SINE/MIR (85) 123 7 m_b206s601i40 8162 chr4qtel1M 625583 TGAGGCTCAG------GACATGCCTTGGTCAAGGTCCCAGAGAA----AG 625622 i ------ vi v vi v v v?---- C MIR3#SINE/MIR 123 TGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAG 74 chr4qtel1M 625623 TGGCAGA------ACTGGAATCTGGGTCCTCTGACCCCAGAGCCAGGGCT 625666 ------ i i ii ii i v- i v v C MIR3#SINE/MIR 73 TGGCAGAGCCGGGACTAGAACCCAGGTCTCCTGACTCCC-AGTCCGTGCT 25 chr4qtel1M 625667 CT-TTTGCT--GCCATCC 625681 - i -- ii C MIR3#SINE/MIR 24 CTCTCTGCTCAGCCACTC 7 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 29.15 CpG sites = 14, Kimura (unadjusted) = 29.15 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.06 (6 / 98), avg. gap size = 3.33 (20 / 6) 242 21.59 19.32 0.00 chr4qtel1M 625583 625670 (374330) C MIRc#SINE/MIR (142) 126 22 m_b206s601i39 8162 chr4qtel1M 625583 TGAGGCTCAGG------ACATGCCTTGGTCAAGGTCCCAGAGA----AAG 625622 i------ vi v vi v v v---- C MIRc#SINE/MIR 126 TGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAG 77 chr4qtel1M 625623 TGGCAGA------ACTGGAATCTGGGTCCTC-TGACCCCAGAGCCAGGGC 625665 ------ v i ii i - i iiv v C MIRc#SINE/MIR 76 TGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGC 27 chr4qtel1M 625666 TCTTT 625670 C MIRc#SINE/MIR 26 TCTTT 22 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 25.71 CpG sites = 10, Kimura (unadjusted) = 25.71 Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.05 (4 / 87), avg. gap size = 4.25 (17 / 4) 50 0.00 0.00 0.00 chr4qtel1M 626183 626227 (373773) (C)n#Simple_repeat 1 45 (0) c_b206s251i3 8163 chr4qtel1M 626183 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 626227 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 45 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 321 30.36 8.93 0.00 chr4qtel1M 626497 626608 (373392) L2b_3end#LINE/L2 332 453 (13) m_b206s601i41 8164 chr4qtel1M 626497 CCATCTTCTTCCTTAGAAGGGAAGCTTCCTGAGGGCAGG--CCCCATCTT 626544 ii i ii vi vv vi i v -- v?i v L2b_3end#LINE 332 CTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTG 381 chr4qtel1M 626545 TCT-----ACC--TGTATCCCCAGCACC-AGCATGATATCTGGCATGCAG 626586 ----- -- i - iii?ii ii L2b_3end#LINE 382 TCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAG 431 chr4qtel1M 626587 TAAGAGTTTAATAAGTGCTCAT 626608 i v i i i i ii ii L2b_3end#LINE 432 TAGGCGCTCAGTAAATATTTGT 453 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 41.58 CpG sites = 26, Kimura (unadjusted) = 43.35 Transitions / transversions = 3.25 (26/8) Gap_init rate = 0.04 (4 / 111), avg. gap size = 2.50 (10 / 4) 190 28.57 2.04 0.00 chr4qtel1M 628139 628187 (371813) L2d_3end#LINE/L2 462 511 (5) m_b206s601i42 8164 chr4qtel1M 628139 ATAGTGTTTGGCCCAC-GTAGGCATTTAATAAGTGCTTATTGGCTGATTG 628187 i i vi v i- ii i i i i ii L2d_3end#LINE 462 ACAGTGCTGAGCACATAGTAGGCGCTCAATAAATACTTGTTGATTGATTG 511 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 36.18 CpG sites = 12, Kimura (unadjusted) = 39.95 Transitions / transversions = 6.00 (12/2) Gap_init rate = 0.02 (1 / 48), avg. gap size = 1.00 (1 / 1) 192 24.24 12.12 0.00 chr4qtel1M 628340 628405 (371595) C MIR#SINE/MIR (20) 242 169 m_b206s601i43 8165 chr4qtel1M 628340 GAGTCCCTACTATGTGC-AGGCA---TTC----CACCTCATCGGTGTTAC 628381 iv i - --- ---- i i i ivv i v C MIR#SINE/MIR 242 GAGCGCTTACTATGTGCCAGGCACTGTTCTAAGCGCTTTACATGTATTAA 193 chr4qtel1M 628382 CTCATTTGAGCCTTACAATCACCC 628405 i v i iv C MIR#SINE/MIR 192 CTCATTTAATCCTCACAACAACCC 169 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 25.75 CpG sites = 10, Kimura (unadjusted) = 30.06 Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.05 (3 / 65), avg. gap size = 2.67 (8 / 3) 1123 31.18 2.37 5.41 chr4qtel1M 628444 629033 (370967) L1ME5_3end#LINE/L1 56 628 (313) m_b206s551i5 8166 chr4qtel1M 628444 CTCCAGCTGATAAATGGTCAAAGGATGTGAACAGACAATTTTCAGATGAA 628493 i iiv v v i i v v i L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chr4qtel1M 628494 GAAACTGAAACTATTTCTAGTCAGATGGAAAG-TGTTCCAAATCACTATT 628542 ivi vvii vvi iv v i i - i v v i v L1ME5_3end#LI 106 GAAACCCGAAAGGCTAACAAGCATATGAAGAGATGCTCAAACTCATTAGT 155 chr4qtel1M 628543 GATCAGAGAAATGCAAATTAAGACAACTCTGAGGTACCACTGCACACCTC 628592 i i vv i i vi v L1ME5_3end#LI 156 AATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCTA 205 chr4qtel1M 628593 TCAGATTGGCTAAGATGGCAGGAAA--AGACAAGGACCAATACTGGAGGG 628640 i i v i --i i i--i i v v v i ii v i L1ME5_3end#LI 206 TTAGACTGGCAAAAAT--TAGAAAGCTGGATAATGCCAAGTGTTGGCGAG 253 chr4qtel1M 628641 GATATGGGAAAACTGGGATACAGTTTTAAAAAACGGGAATACATTGTTAG 628690 i i ? - i - vv i------------- i i i i L1ME5_3end#LI 254 GATGTGGGGANA-TAGGA-ACCCTC-------------ATGCACTGCTGG 288 chr4qtel1M 628691 TGAAGCTGTGAATGGATCCAACCATTCTGGAGAGCAATTTGGAACTA--T 628738 iiiv ii iv i v i i v v -- L1ME5_3end#LI 289 TGGGAGTGTAGACTGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTT 338 chr4qtel1M 628739 GCTCAAAAAGTTATCAAACTGTGCATTCCCCTTTGACCCAACAGTGTTTC 628788 iv --- -- ivv ii - v v i i viiv L1ME5_3end#LI 339 AGTCAAA---TTA--AGTATACGCA-TACCCTATGACCCAGCAATTCCGC 382 chr4qtel1M 628789 TACTGGGCCTGTATCCCCAAGACATCTTAAAGGAGG----GAAAGGGACC 628834 v iv i v v ii v viv ----v i v L1ME5_3end#LI 383 TCCTGGGTATATATCCCAAAGAAATTCTCACACAGGTCCATAAGGGGACA 432 chr4qtel1M 628835 TGTACGTGCACGAATGTTTGTGGCAGCCCT-TTTGTAGTGGCCAGAAACT 628883 ----v i ii v vi - i vi i ii L1ME5_3end#LI 433 TGTACG----AGGATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTT 478 chr4qtel1M 628884 GGAAAGTAA-GTGGCTGCCCATCGGTGGGGGAATGGCTGAATAAACTGTG 628932 - i i -v v i iv i i v iii v L1ME5_3end#LI 479 GG-AGGCAACCTGGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTG 527 chr4qtel1M 628933 GTATATGAATGTTATGGAATTTTGTTGTTCTGTAAGAAATGACCGGCAGG 628982 iv v iiii i vi i vvvv v v iii v i vi L1ME5_3end#LI 528 GTGGATGCACACCATGGAGTACTATGCAGCAGTTAGAAGCAACGGACTAG 577 chr4qtel1M 628983 ATGATTCCAGAAAGT--CCTGGAGAGA-CTTACAGGAATTGATGCTGAGT 629029 -- v v v i-- v vi - v iiv v - L1ME5_3end#LI 578 ATG--TACACATAGCAACATGGATGGATCTTAAAAACATAG-TGCTGAGT 624 chr4qtel1M 629030 GAAA 629033 L1ME5_3end#LI 625 GAAA 628 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 40.48 CpG sites = 99, Kimura (unadjusted) = 41.42 Transitions / transversions = 1.32 (99/75) Gap_init rate = 0.07 (39 / 589), avg. gap size = 1.15 (45 / 39) 1213 29.85 1.36 4.20 chr4qtel1M 628444 628957 (371043) L1ME4c_3end#LINE/L1 56 555 (275) m_b206s551i4 8166 chr4qtel1M 628444 CTCCAGCTGATAAATGGTCAAAGGATGTGAACAGACAATTTTCAGATGAA 628493 i iiv v ii iv ? v i L1ME4c_3end#L 56 CCCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAG 105 chr4qtel1M 628494 GAAACTGAAACTATTTC-TAGTCAGATGGAAAG-TGTTCCAAATCACTAT 628541 - iv ? v vv-i iv v i- v vv i v L1ME4c_3end#L 106 GAAA-TACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTAG 154 chr4qtel1M 628542 TGATCAGAGAAATGCAAATTAAGACAACTCTGAGGTACCACTGCACACCT 628591 i i ii vv i i vi i L1ME4c_3end#L 155 TAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCT 204 chr4qtel1M 628592 CTCAGATTGGCTAAGATGGCAGGAAAAGACAAGGACCAATACTGGAGGGG 628641 v i i i v i vvv ii vv i viv i v i L1ME4c_3end#L 205 ATTAAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGCTGGCGAGG 254 chr4qtel1M 628642 ATATGGGAAAACTGGGATACAGTTTTAAAAAACGGGAATACATTGTTAGT 628691 ? ii vi -- ?v i------------- i i L1ME4c_3end#L 255 NTGCGGTGAAACTGG--TACNCTC-------------ATACATTGCTGGT 289 chr4qtel1M 628692 GAAGCTGTGAATGGATCCAACCATTCTGGAGAGCAATTTGGAACTATGCT 628741 ivi? i v i v v i i v v i iv L1ME4c_3end#L 290 GGCANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTA 339 chr4qtel1M 628742 CAAAAAGTTATCAAACTGTGCATTCCCCTTTGACCCAACAGTGTTTCTAC 628791 iv i ii v v v - v ii i viiv v L1ME4c_3end#L 340 TCAAGAGCCATAAAAATGTTCA-TACCCTTTGACCCAGTAATTCCACTTC 388 chr4qtel1M 628792 TGGGCCTGTATCCCCAAGACAT--CTTAAAGGAGGGAAAGGGACCTGTAC 628839 vv v iv i v --i i i i ii -- i - L1ME4c_3end#L 389 TGGGAATTTATCCTAAGGAAATAATTCAAAAGAAGGAAAAAG--CTATA- 435 chr4qtel1M 628840 GTGCACGA--ATGTTTGTGGCAGCCCT-TTTGTAGTGGCCAGAAACTGGA 628886 - -- ii v vi - i i i v i i L1ME4c_3end#L 436 -TGCACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGA 484 chr4qtel1M 628887 AAGTAAGTGGCTGCCCATCGGTGGGGGAATGGCTGAATAAACTGTGGTAT 628936 vv vv iiv i v ii i i i i i i i L1ME4c_3end#L 485 AACAACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTAC 534 chr4qtel1M 628937 ATGAATGTTATGGAATTTTGT 628957 v? iviv v i L1ME4c_3end#L 535 ATCNACTCGATGGAATATTAT 555 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 37.96 CpG sites = 85, Kimura (unadjusted) = 39.70 Transitions / transversions = 1.37 (85/62) Gap_init rate = 0.05 (26 / 513), avg. gap size = 1.08 (28 / 26) 213 7.67 0.67 0.67 chr4qtel1M 629442 629740 (370260) (GAAG)n#Simple_repeat 1 299 (0) m_b207s252i0 8167 chr4qtel1M 629442 GAAGGAAGGAAGGAAGGAAGGAGGGAAGGGAGGAAGGAAGGAAGGAGGGA 629491 i i i (GAAG)n#Simpl 1 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 50 chr4qtel1M 629492 AGGAAGGAAGGAAGAAAGAAAGGAAGGAGGGAAGG-AGGAAGGAAGAGAG 629540 i i i - ii (GAAG)n#Simpl 51 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG 100 chr4qtel1M 629541 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAGGGGAAGGAAGGAAGGAAGG 629590 -i (GAAG)n#Simpl 101 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGA-AGGAAGGAAGGAAGGAAGG 149 chr4qtel1M 629591 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 629640 (GAAG)n#Simpl 150 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 199 chr4qtel1M 629641 GGAAGGAAGGAGGGAAGGAAGAAAAGAAGGAAGGAGGGAAGGAAGG-AGG 629689 i i i i - (GAAG)n#Simpl 200 GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG 249 chr4qtel1M 629690 GAGGGAGGGAGGGAGGAAGGAAGGGAGGGAGGGAGGGAAGAAAGGAAGGA 629739 i i i i - i i i i (GAAG)n#Simpl 250 AAGGAAGGAAGGAAGGAAGGAA-GGAAGGAAGGAAGGAAGGAAGGAAGGA 298 chr4qtel1M 629740 A 629740 (GAAG)n#Simpl 299 A 299 Matrix = Unknown Transitions / transversions = 1.00 (21/0) Gap_init rate = 0.01 (4 / 298), avg. gap size = 1.00 (4 / 4) 310 31.88 3.42 0.83 chr4qtel1M 629817 629933 (370067) MIRc#SINE/MIR 27 146 (122) m_b207s601i0 8168 chr4qtel1M 629817 GCACCAGGTCTGGGGATGGGAAAGTCTGCCTTC-AGTTCCAGCCTCCAAG 629865 ii iii i vii iii vv - i i - iivv MIRc#SINE/MIR 27 GCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGC-TCTGCC 75 chr4qtel1M 629866 ACATCCTAGCTGTGAGATCCT-AACAAGTCACTTCACC-CTGCCTGCCTC 629913 v v v i i -ii v - vivv MIRc#SINE/MIR 76 ACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTC 125 chr4qtel1M 629914 AGTTTCCTT-CCTAGAAAACG 629933 i-i iv i MIRc#SINE/MIR 126 AGTTTCCTCATCTGTAAAATG 146 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.05 CpG sites = 24, Kimura (unadjusted) = 43.66 Transitions / transversions = 1.85 (24/13) Gap_init rate = 0.04 (5 / 116), avg. gap size = 1.00 (5 / 5) 13 19.74 0.00 6.98 chr4qtel1M 631021 631066 (368934) (GGGGGAG)n#Simple_repeat 1 43 (0) m_b207s252i1 8169 chr4qtel1M 631021 GGGGGTGGGGGGAGGGGGAAGGAATGGGACGCGGAGAGTGGGCAGG 631066 v i --v - v i v v (GGGGGAG)n#Si 1 GGGGGAGGGGGGAGGGGGGAGG--GGGGA-GGGGGGAGGGGGGAGG 43 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.07 (3 / 45), avg. gap size = 1.00 (3 / 3) 288 21.11 16.67 0.00 chr4qtel1M 634955 635044 (364956) C MIR3#SINE/MIR (26) 182 78 m_b207s601i1 8170 chr4qtel1M 634955 GCTGGAGGAG---TTGGCCATTCCCTTCTCCAGC----TCATTTTCCAGA 634997 i i --- i vv ivi vv i ---- v C MIR3#SINE/MIR 182 GCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGA 133 chr4qtel1M 634998 TGAGGAAACTGAGGC------AGGC--AGGGACCTGGCCAGAGTCACGCA 635039 ------ i-- v i v ii i C MIR3#SINE/MIR 132 TGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACA 83 chr4qtel1M 635040 GCTAG 635044 ? C MIR3#SINE/MIR 82 GCNAG 78 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 25.51 CpG sites = 11, Kimura (unadjusted) = 25.51 Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.04 (4 / 89), avg. gap size = 3.75 (15 / 4) 292 15.62 12.50 0.00 chr4qtel1M 634985 635048 (364952) C MIRc#SINE/MIR (120) 148 77 m_b207s601i2 8170 chr4qtel1M 634985 CTCATTTTCCAGATGAGGAAACTGAGGC------AGGC--AGGGACCTGG 635026 i v ------ i-- v i v C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr4qtel1M 635027 CCAGAGTCACGCAGCTAGGAAG 635048 ii i v C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAG 77 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 17.72 CpG sites = 6, Kimura (unadjusted) = 17.72 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.03 (2 / 63), avg. gap size = 4.00 (8 / 2) 203 21.28 0.00 0.00 chr4qtel1M 635119 635165 (364835) MIR1_Amn#SINE/MIR 117 163 (67) m_b207s601i4 8171 chr4qtel1M 635119 CTCTCAGCCTGAGTTTGCTCATCTGGAAAATGGGGGTGGGGGTTCTG 635165 v? v v v i iiv i v MIR1_Amn#SINE 117 CTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATGATACTG 163 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 25.70 CpG sites = 4, Kimura (unadjusted) = 25.70 Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 219 13.51 0.00 0.00 chr4qtel1M 635119 635155 (364845) MIRb#SINE/MIR 118 154 (114) m_b207s601i3 8171 chr4qtel1M 635119 CTCTCAGCCTGAGTTTGCTCATCTGGAAAATGGGGGT 635155 v v v v i MIRb#SINE/MIR 118 CTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGAT 154 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 14.94 CpG sites = 1, Kimura (unadjusted) = 14.94 Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 18 8.48 0.00 0.00 chr4qtel1M 635899 635923 (364077) (C)n#Simple_repeat 1 25 (0) m_b207s252i2 8172 chr4qtel1M 635899 CCCCCCTCCCCCCCGCCCCCCCCCC 635923 i v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCC 25 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 1097 23.45 6.31 4.78 chr4qtel1M 637456 637867 (362133) C Charlie1a#DNA/hAT-Charlie (577) 878 461 m_b207s502i0 8173 chr4qtel1M 637456 TTTTTCACTTGGAAAAGATCTTTTACCC---TATAATTCGGTAACTTTGT 637502 i v v vi ---i i iv v ii C Charlie1a#DNA 878 TCTTGCACTTTGAATGGATCTTTTACCCATGCATGATTTTGTAACATCAT 829 chr4qtel1M 637503 GCTTGGGTCGTTTGGAAAATGTAGGTTCACTGAGTTACTAGGATCTTCCA 637552 v v i i v ivvi C Charlie1a#DNA 828 GCATTGGTCATTTGGAAAATATTGGTTCACTGAGTTATGCAGATCTTCCA 779 chr4qtel1M 637553 AATAGGGACACTTTTCATGATCCAGCTGCAAAAAAATTAAAAAAAAAAAG 637602 ivv v v v --------- v i v----- C Charlie1a#DNA 778 AATGTTGACACATTTCATTATACA---------ATATCAAAAAAT----- 743 chr4qtel1M 637603 GAACAAGATCGCATTAATATCAGCAGAGA----ATCAGAAAGATCTTTCA 637648 --- viv -- v vv ---- ii v C Charlie1a#DNA 742 ---CACATTCG--TTAATATCACCACCGATCTCATCAGAAAAGTCTTTAA 698 chr4qtel1M 637649 TGATTGGGA--TTGTGTGGGTTTTAGGGGCAGCAGCA-GTTTTCCAAAAT 637695 vv --i vvi v ivii v i vvi - C Charlie1a#DNA 697 GTATTGGGAAGCTGTCAAGCTCACGGTGGCGGATACAAGTTTTCCAAAAT 648 chr4qtel1M 637696 TCTAACTTTCACTTGAAGGCTCAGATTTTATCAGTGGTAAGAAACACGGT 637745 i i i ii v i v i v C Charlie1a#DNA 647 TCTAATTTTCGCTTGAAAGCTCGAATTTTATCATTGGCAACAAATACTGT 598 chr4qtel1M 637746 CCGTTG---TCCGGGAAGTCACAGA------TGGCTCATTTTTTAGGAGA 637786 v --- vv v i------ v i iv i i C Charlie1a#DNA 597 CAGTTGTTTTCCTTGAAGTGACAGGCTCACTTCGTTCATTTTCGAGAAAA 548 chr4qtel1M 637787 TGTCTACCCAGTGCCCTAGCCTGAAGAACCAGA--TTGTC-----GGCAT 637829 i v i i v i v v -- ----- v i C Charlie1a#DNA 547 TGTCTGCCAAATACCCAAGTCTGAATAACCATAGTTTGTCTGTCAGTCGT 498 chr4qtel1M 637830 GGTTTCAGATAAAAATGGCCTTCCATGAAAAACAGCGG 637867 vv ii iv - C Charlie1a#DNA 497 TCTTTCAAGTAAAAATGGTGTTCCATGAAAAA-AGCGG 461 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 26.21 CpG sites = 43, Kimura (unadjusted) = 28.30 Transitions / transversions = 0.88 (43/49) Gap_init rate = 0.07 (28 / 411), avg. gap size = 1.64 (46 / 28) 295 35.89 9.50 1.68 chr4qtel1M 638214 638434 (361566) L3b_3end#LINE/CR1 358 595 (611) m_b207s601i5 8174 chr4qtel1M 638214 TGGAAGACAAAT-GGGAGCTAAATCATTCCTAGGACATGAATCAAAGGTT 638262 v vv -i v i v iv ii-- - v vi v ?i L3b_3end#LINE 358 TGGATGCAAAATCAGGATCCAAAACGATCTC--GACA-GACTAGAACGNC 404 chr4qtel1M 638263 AAATTGAAGGCAACAAAATG----TCG-TGGGAATAAGTGTGATTTCCTG 638307 iiiii ?v i ---- i-ii i ii i vv L3b_3end#LINE 405 GGGCCGAANCCAACAAGATGAAATTCAACAGGGATAAACGTAAAGTCCTG 454 chr4qtel1M 638308 AACTCAGGG-CAGAAAATCAGTTTCACATGTACAGGACAG---------G 638347 v ii v- i ? i iv i iv ii --------- L3b_3end#LINE 455 CACTTGGGTTCAAAAAANCAATCGCGCGAGTACAGGATGGGGGAGACGCG 504 chr4qtel1M 638348 GCTTGGT-----CCCTGGGGAGGAAGATCTGAGGGGCCTTAATGAGCCAC 638392 i i----- ? vv v ii i - ii i vii i L3b_3end#LINE 505 GCTTAGCAGCAGCNCATGTGAAAAAGACCTG-GGGGTTTTAGTTGACCGC 553 chr4qtel1M 638393 AAGCTCTCTGGGAGTCTAGGGTAGGTTATGGTGGCCAGACAA 638434 vv iv vivi iv viii iv i v L3b_3end#LINE 554 AAGCTCAATATGAGTCAGCAGTGCGACGCGGCTGCCAAAAAA 595 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.75 CpG sites = 49, Kimura (unadjusted) = 53.29 Transitions / transversions = 1.69 (49/29) Gap_init rate = 0.05 (10 / 220), avg. gap size = 2.50 (25 / 10) 333 35.01 11.24 0.51 chr4qtel1M 638257 638434 (361566) L3#LINE/CR1 3297 3493 (606) m_b207s601i6 8174 chr4qtel1M 638257 AAGGTTAAATTGAAGGCAACAAAATG-----TCGTGGGAATAAGTGTGAT 638301 v v iiiii iv i ----- viii i i i v L3#LINE/CR1 3297 AACGATGGGCCGAAACCAACAAGATGAAATTTAACAGGGATAAATGTAAA 3346 chr4qtel1M 638302 TTCCTGAACTCAGGG-CAGAAAATCAGTTTCACATGTACAGGACAG---- 638346 v v i i v- i ii v v ii ---- L3#LINE/CR1 3347 GTCCTGCATTTAGGTTCAAAAAATCAACTGCACAAGTACAGGATGGAGAG 3396 chr4qtel1M 638347 -----GGCTTGGTCCCTG-----GGGAGGAAGATCTGAGGGGCCTTAATG 638386 ----- i ivv v ----- v ii i - ii i v L3#LINE/CR1 3397 GATCTGGCTTAGCAGCAGTTCACGTGAAAAAGACCT-AGGGGTTTTAGTT 3445 chr4qtel1M 638387 AGCCACAAGCTCTCTGGGAGTCTAGGGTAGGTTATGGTGGCCAGACAA 638434 ii i vv iv i v vi iv v i iv i v L3#LINE/CR1 3446 GACCGCAAGCTCAATATGAGCCAACAGTGTGATGTGGCTGCCAAAAAA 3493 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 47.24 CpG sites = 38, Kimura (unadjusted) = 49.53 Transitions / transversions = 1.58 (38/24) Gap_init rate = 0.03 (6 / 177), avg. gap size = 3.50 (21 / 6) 276 27.86 0.78 10.26 chr4qtel1M 639208 639335 (360665) C MIR1_Amn#SINE/MIR (113) 117 1 m_b207s601i8 8175 chr4qtel1M 639208 GGGGTTAAGTGGCTTGCCCAT-GTCACACAGCTAGGAAGTGTTATGTGTC 639256 i ? i v- ? ?i v? vi ------ C MIR1_Amn#SINE 117 GAGGTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNAGTGGCA------ 74 chr4qtel1M 639257 TGAGGTCAAATTTGAACTCAGGTCCTCCTGACTTCAGGAATGGTGCTCCC 639306 - vivii ? ? i - i v i vi vvii ---- C MIR1_Amn#SINE 73 -GAGCCGGGANTNGAACCCAGGT-CTCCCGAGTCCCAGTCCAGTG----C 30 chr4qtel1M 639307 TCTATCCACTGCGCCTCCTAGCTGCCCCA 639335 ivi v viv iv i C MIR1_Amn#SINE 29 TCTATCCACTAGACCACACTGCCTCCCTA 1 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.74 CpG sites = 18, Kimura (unadjusted) = 37.65 Transitions / transversions = 1.29 (18/14) Gap_init rate = 0.10 (13 / 127), avg. gap size = 1.00 (13 / 13) 406 22.57 0.88 10.58 chr4qtel1M 639208 639321 (360679) C MIRc#SINE/MIR (153) 115 12 m_b207s601i7 8175 chr4qtel1M 639208 GGGGTTAAGTGGCTTGCCCATG-TCACACAGCTAGGAAGTGTTATGTGTC 639256 i i v - v vi ------ C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCA------ 72 chr4qtel1M 639257 TGAGGTCAAATTTGAACTCAGGTCCTCCTGACTTCAGGAATGGTGCTCCC 639306 - vivii i i i i i i vvii ---- C MIRc#SINE/MIR 71 -GAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTG----C 27 chr4qtel1M 639307 TCTATCCACTGCGCC 639321 v i C MIRc#SINE/MIR 26 TCTTTCCACTGCACC 12 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 24.54 CpG sites = 15, Kimura (unadjusted) = 27.24 Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.11 (12 / 113), avg. gap size = 1.00 (12 / 12) 371 27.94 4.90 4.90 chr4qtel1M 639973 640115 (359885) C MIRc#SINE/MIR (120) 148 6 m_b207s601i9 8176 chr4qtel1M 639973 CCCATTTTACAAATGAGGAAGCTGAGGCACACAGC--CTCAG-GACTTCC 640019 i i v v v--i v - v C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr4qtel1M 640020 CCAGGGTCGCACAGAT----AGTGTCTGAGGTGGGGTTTGAGCTCAGGGA 640065 i i v ---- v v vi ii i i i vv C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTC 49 chr4qtel1M 640066 CACCCTTTTGCAGGCTGTTTCTGGTGCCCTCCCCATTCCAGCCCACCCTG 640115 iv ivvi v i ----- ii i ii i v -- v C MIRc#SINE/MIR 48 TTCCTGACTCCAAG-----TCCAGTGCTCTTTCCACTGCA--CCACACTG 6 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.35 CpG sites = 21, Kimura (unadjusted) = 35.63 Transitions / transversions = 1.24 (21/17) Gap_init rate = 0.07 (10 / 142), avg. gap size = 1.40 (14 / 10) 374 20.88 7.69 0.00 chr4qtel1M 639973 640063 (359937) C MIR#SINE/MIR (118) 144 47 m_b207s601i10 8176 chr4qtel1M 639973 CCCATTTTACAAATGAGGAAGCTGAGGCACACAGC--CTCAG-GACTTCC 640019 i i v v--i v -i v C MIR#SINE/MIR 144 CCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGC 95 chr4qtel1M 640020 CCAGGGTCGCACAGAT----AGTGTCTGAGGTGGGGTTTGAGCTCAGG 640063 i i v ---- v v vi i i i i C MIR#SINE/MIR 94 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGG 47 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 21.97 CpG sites = 11, Kimura (unadjusted) = 24.83 Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.03 (3 / 90), avg. gap size = 2.33 (7 / 3) 464 26.08 1.47 6.98 chr4qtel1M 641568 641703 (358297) MIRb#SINE/MIR 2 130 (138) m_b207s601i11 8177 chr4qtel1M 641568 AAAGGGACAGCTAGGTACACAGTGGTTAGAGCATTAGCCCTCAAGTCAGG 641617 i i vv i -- vv ivi ii vi i MIRb#SINE/MIR 2 AGAGGGGCAGCGTGGTGCA--GTGGAAAGAGCACGGGCTTTGGAGTCAGA 49 chr4qtel1M 641618 TGGACTTGAGTTCAAATCTGATCTCAGACACTTAGCACTTCCTGGCTGTG 641667 ii i i i iviv v v ------- i MIRb#SINE/MIR 50 CAGACCTGGGTTCGAATCCCGGCTCTGCCACTTA-------CTAGCTGTG 92 chr4qtel1M 641668 TGACCCTGGGCAAGTCACTTAACCCAATT--GCCTCAG 641703 i i ivvi -- MIRb#SINE/MIR 93 TGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAG 130 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.35 CpG sites = 21, Kimura (unadjusted) = 32.92 Transitions / transversions = 1.75 (21/12) Gap_init rate = 0.07 (10 / 135), avg. gap size = 1.10 (11 / 10) 281 22.64 4.49 5.68 chr4qtel1M 642932 643020 (356980) C MIR3#SINE/MIR (21) 187 100 m_b207s601i12 8178 chr4qtel1M 642932 TCAGAGCAACTGGAAGGAGCTCT---GACCACTCCAAGTCCAATCCCTCC 642978 --- ii ii --- i i-- v i ii C MIR3#SINE/MIR 187 TCAGAGC---TGGAAGGGACCTTAGAGATCAT--CTAGTCCAACCCCCTC 143 chr4qtel1M 642979 ATTT-ACACAGAGGGAAACTGAGGCCCCTAGAGAGCAAGTGAC 643020 - v vii vv ivv C MIR3#SINE/MIR 142 ATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGAC 100 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.58 CpG sites = 12, Kimura (unadjusted) = 27.58 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.08 (7 / 88), avg. gap size = 1.29 (9 / 7) 714 30.84 2.60 4.41 chr4qtel1M 643923 644268 (355732) L2#LINE/L2 2260 2599 (483) m_b207s601i13 8179 chr4qtel1M 643923 TTTTCCTTACC--CTCTTCTTCACCTGGTGATCTTAACAGCTCCCATGGA 643970 i ii i -- v ivi v i? i v viv i v L2#LINE/L2 2260 TCTTCTCTATCTACACTCACTCCCTNGGTGATCTCATCCAGTCTCATGGC 2309 chr4qtel1M 643971 TTTAATGACCGTCTCTATTCAGATAATTCTTAAATCTACCTTTCCTGCCC 644020 vv i v v v i i ii i iv i v L2#LINE/L2 2310 TTTAAATACCATCTATATGCTGATGACTCCCAAATTTATATCTCCAGCCC 2359 chr4qtel1M 644021 CAAACTCTCTGATAACCTCCAATATCGCGCCTCCAACTGCCTTTCAGACA 644070 vi v ivv i v ivv iiiv viiv L2#LINE/L2 2360 GGACCTCTCCCCTGAACTCCAGACTCGTATATCCAACTGCCTACTCGACA 2409 chr4qtel1M 644071 TCTTGAATTAGATGTCCAGTGGACATCTTAAA-TCAATATGTCTAAAAAA 644119 iv v i i i i i i - i i i vv L2#LINE/L2 2410 TCTCCACTTGGATGTCTAATAGGCATCTCAAACTTAACATGTCCAAAACT 2459 chr4qtel1M 644120 GAATTC---ATCTTTCTCCCTAAACCTTCCCACATTTTCACTCAG-CTTC 644165 i --- i i ii v ----- ii v v - L2#LINE/L2 2460 GAACTCCTGATCTTCCCCCTCAAACCTGC-----TCCTCCCGCAGTCTTC 2504 chr4qtel1M 644166 TCACTTTATCCTCATGGGGCCATGGCCAC--CTTCCTGCCAGGCCCCTAG 644213 i ----i - --- v?v v -- v v viv ii L2#LINE/L2 2505 CC----CATC-TCA---GTNAATGGCAACTCCATCCTTCCAGTTGCTCAG 2546 chr4qtel1M 644214 GCCCATGACCTAAGAGTCCTCCTGGACTCTTCACTCTTTTACCCACATCA 644263 v vi vi v v i -- iv i i v L2#LINE/L2 2547 GCCAAAAACCTTGGAGTCATCCTTGACTCCTC--TCTTTCTCTCACACCC 2594 chr4qtel1M 644264 AATAT 644268 v i L2#LINE/L2 2595 CACAT 2599 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.92 CpG sites = 56, Kimura (unadjusted) = 40.92 Transitions / transversions = 1.22 (56/46) Gap_init rate = 0.06 (20 / 345), avg. gap size = 1.20 (24 / 20) 206 33.88 5.88 3.28 chr4qtel1M 644499 644617 (355383) L2#LINE/L2 2606 2727 (355) m_b207s601i14 8179 chr4qtel1M 644499 CATCTGCAGCACCTCTCCAGATTTCACCTGGGCACTCTCTCTCCAATATC 644548 v ivv v -- ii ii v-- vvv v v iv L2#LINE/L2 2606 CATCAGCAAATCCTGTC--GGCTCTACCTT--CAAAATATATCCAGAATC 2651 chr4qtel1M 644549 C--CCTCTTCTCTCCTCTGACACTGCTCCCTTCCTGGCGCAGGCCCTTAC 644596 -- v v v ivv iv vi iv i vii i L2#LINE/L2 2652 CGACCACTTCTCACCACCTCCACTGCCACCACCCTGGTCCAAGCCACCAT 2701 chr4qtel1M 644597 TACCTCATCCCTGGA-----GCAATA 644617 i i viv ----- L2#LINE/L2 2702 CATCTCTCGCCTGGATTACTGCAATA 2727 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.92 CpG sites = 17, Kimura (unadjusted) = 45.43 Transitions / transversions = 0.77 (17/22) Gap_init rate = 0.05 (6 / 118), avg. gap size = 1.83 (11 / 6) 257 35.66 8.26 2.47 chr4qtel1M 644662 644891 (355109) L2#LINE/L2 2766 3008 (74) m_b207s601i15 8179 chr4qtel1M 644662 CTCCACCCCATCCTCTGTTCAGCTGCCAAAGTGATTTTTTTCTAAAGCAC 644711 ? vi i i viiv v i ii -- i ii L2#LINE/L2 2766 CTNCAGTCTATTCTCAACACAGCAGCCAGAGTGATCCTTT--TAAAACGT 2813 chr4qtel1M 644712 GGATTTGACCAAGTCATTCCCTTACTCAGTAAACTCCAGGGGCTCCATAT 644761 iii iv i v i ii i iv vv iv i vi L2#LINE/L2 2814 AAGTCAGATCATGTCACTCCTCTGCTCAAAACCCTCCAATGGCTTCCCAT 2863 chr4qtel1M 644762 TGCCTTCAGCAACAAATAGAAAATGTTC-TAC-TTGGCATTGAAAG-TTT 644808 iv vi - ii - vv v i - -v v vv i -ii L2#LINE/L2 2864 CTCACTCAG-AGTAAA-AGCCAAAGTCCTTACAATGGCCTACAAGGCCCT 2911 chr4qtel1M 644809 ACA--ACCCAGCACCCTCCTCACTTTCTAGTCCT----TCCTGACATGTA 644852 -- i ii i- i v i i iiiv v ---- iv iviv L2#LINE/L2 2912 ACATGATCTGGT-CCCCCGTTACCTCTCTGACCTCATCTCCTACCACTCT 2960 chr4qtel1M 644853 C---------CAGTCAG-TTCAGTGACTCTAGCCTTCTGGCTGTGTCCT 644891 --------- v v - i iv v i i v - L2#LINE/L2 2961 CCCCCTCGCTCACTCCGCTCCAGCCACACTGGCCTCCTTGCTGT-TCCT 3008 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 50.39 CpG sites = 49, Kimura (unadjusted) = 51.34 Transitions / transversions = 1.58 (49/31) Gap_init rate = 0.06 (13 / 229), avg. gap size = 1.92 (25 / 13) 211 31.10 16.67 2.72 chr4qtel1M 644945 645106 (354894) L2c_3end#LINE/L2 285 468 (10) m_b207s601i16 8179 chr4qtel1M 644945 CTCCTACAGGAAGCCTTCCCCAATTCCCCATT-TATCCCTTAG----AGT 644989 i i v -- i vi i vvii - v v v---- ii L2c_3end#LINE 285 CTCCCATAGCA--CCCTGTCTATACTCCCATTATAGCACTTATCATTAAC 332 chr4qtel1M 644990 TTGTATTATACGTATTTATTGTCATGT-TGTTT---------------GA 645023 i vv i i i vv ? - i --------------- L2c_3end#LINE 333 TTGTATTGTAATTGTCTGTTTACNTGTCTGTCTCCTCCACTAGACTGTGA 382 chr4qtel1M 645024 GCTCC--AAGGGCAGGAGCCAT--TTGAACC--CTCAGCATTTGGCTCAG 645067 --i ii i --i v vi -- iv i i--- i L2c_3end#LINE 383 GCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTATC---CCCAG 429 chr4qtel1M 645068 TACCCAGCACATAGTAGGTACTTAATATTTGTAGGTTGA 645106 ii ii ii i vv vv L2c_3end#LINE 430 CGCCTGGCACATAGTAGGCGCTCAATAAATGTTTGTTGA 468 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.84 CpG sites = 31, Kimura (unadjusted) = 42.52 Transitions / transversions = 1.72 (31/18) Gap_init rate = 0.07 (12 / 161), avg. gap size = 2.67 (32 / 12) 238 25.86 6.90 0.00 chr4qtel1M 645049 645106 (354894) L2d_3end#LINE/L2 447 508 (8) m_b207s601i17 8179 chr4qtel1M 645049 CCCTCAGCATTTGGCTCAGTACCCAGCACATAGTAGGTACTT----AATA 645094 v iii i v i iv ii i---- L2d_3end#LINE 447 CCCACAGCGCCTAGCACAGTGCTGAGCACATAGTAGGCGCTCAATAAATA 496 chr4qtel1M 645095 TTTGTAGGTTGA 645106 i v i L2d_3end#LINE 497 CTTGTTGATTGA 508 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.84 CpG sites = 11, Kimura (unadjusted) = 33.45 Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.02 (1 / 57), avg. gap size = 4.00 (4 / 1) 32 0.00 0.00 0.00 chr4qtel1M 646755 646784 (353216) (C)n#Simple_repeat 1 30 (0) c_b207s251i0 8180 chr4qtel1M 646755 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 646784 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 30 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 32 25.50 2.52 6.54 chr4qtel1M 647282 647440 (352560) (AGAGGG)n#Simple_repeat 1 153 (0) m_b207s252i3 8181 chr4qtel1M 647282 AGAGGGAGAAGGCCAGATGAGGAGGGGGAGGGGGAGGGGGA-GGAGCAGG 647330 - -v v ii i i i - - (AGAGGG)n#Sim 1 AGAGGGAG-AGG-GAGAGGGAGAGGGAGAGGGAGAGGGAGAGGGAG-AGG 47 chr4qtel1M 647331 GAGA-GAAGGGGGGGAGGAAGAAAGGGAAGGATTGAGAGCAATAAGGGAG 647379 - i i i -- i - - vv vi -i (AGAGGG)n#Sim 48 GAGAGGGAGAGGGAGAGG--GAGAGGG-A-GAGGGAGAGGGA-GAGGGAG 92 chr4qtel1M 647380 AGTGAGA-AGA-AAGAAGTGGGGAAGGGTTAGGGTTGGGGGAGAGGGAAT 647427 v -i - i i v ii vv -v i - v (AGAGGG)n#Sim 93 AGGGAGAGGGAGAGGGAGAGGGAGAGGGAGAGGG-AGAGGGAGAGGG-AG 140 chr4qtel1M 647428 GGGGAGAGGTAGA 647440 i v (AGAGGG)n#Sim 141 AGGGAGAGGGAGA 153 Matrix = Unknown Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.09 (14 / 158), avg. gap size = 1.00 (14 / 14) 23 21.71 1.82 0.00 chr4qtel1M 647297 647351 (352649) (GAG)n#Simple_repeat 1 56 (0) m_b207s252i4 8182 chr4qtel1M 647297 GATGAGGAGGGGGAGGGGGAGGGGGAGGAGCAGGGAGAGAAGG-GGGGGA 647345 v i i i v ii i - i (GAG)n#Simple 1 GAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA 50 chr4qtel1M 647346 GGAAGA 647351 i (GAG)n#Simple 51 GGAGGA 56 Matrix = Unknown Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1) 32 25.50 2.52 6.54 chr4qtel1M 647282 647440 (352560) (AGAGGG)n#Simple_repeat 1 153 (0) m_b207s252i3 8181 chr4qtel1M 647282 AGAGGGAGAAGGCCAGATGAGGAGGGGGAGGGGGAGGGGGA-GGAGCAGG 647330 - -v v ii i i i - - (AGAGGG)n#Sim 1 AGAGGGAG-AGG-GAGAGGGAGAGGGAGAGGGAGAGGGAGAGGGAG-AGG 47 chr4qtel1M 647331 GAGA-GAAGGGGGGGAGGAAGAAAGGGAAGGATTGAGAGCAATAAGGGAG 647379 - i i i -- i - - vv vi -i (AGAGGG)n#Sim 48 GAGAGGGAGAGGGAGAGG--GAGAGGG-A-GAGGGAGAGGGA-GAGGGAG 92 chr4qtel1M 647380 AGTGAGA-AGA-AAGAAGTGGGGAAGGGTTAGGGTTGGGGGAGAGGGAAT 647427 v -i - i i v ii vv -v i - v (AGAGGG)n#Sim 93 AGGGAGAGGGAGAGGGAGAGGGAGAGGGAGAGGG-AGAGGGAGAGGG-AG 140 chr4qtel1M 647428 GGGGAGAGGTAGA 647440 i v (AGAGGG)n#Sim 141 AGGGAGAGGGAGA 153 Matrix = Unknown Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.09 (14 / 158), avg. gap size = 1.00 (14 / 14) 189 21.74 0.00 0.00 chr4qtel1M 648638 648683 (351317) MIR1_Amn#SINE/MIR 100 145 (85) m_b207s601i18 8183 chr4qtel1M 648638 GGCCCGCCCCTGGGCTGCCCTGGGCCTCAGTTTCCACATCTGTAAA 648683 vv i v v?i iv i ? v MIR1_Amn#SINE 100 GGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAA 145 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.11 CpG sites = 4, Kimura (unadjusted) = 27.11 Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 206 6.90 0.00 0.00 chr4qtel1M 648655 648683 (351317) MIR3#SINE/MIR 112 140 (68) m_b207s601i19 8183 chr4qtel1M 648655 CCCTGGGCCTCAGTTTCCACATCTGTAAA 648683 i v MIR3#SINE/MIR 112 CTCTGGGCCTCAGTTTCCTCATCTGTAAA 140 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 7.25 CpG sites = 1, Kimura (unadjusted) = 7.25 Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 389 33.33 1.54 0.76 chr4qtel1M 650868 650997 (349003) L3#LINE/CR1 3870 4000 (99) m_b207s601i20 8184 chr4qtel1M 650868 GGGATAGAGCTCTACTTAATGTGGAAGAAAACCCTTCTGACTCTGAGAGT 650917 i ii vi vi i i i- i i v i i vv v i L3#LINE/CR1 3870 GAGGCAGATTTCGGCTCAATATA-AGGAAGAACTTTCTAACAATCAGAGC 3918 chr4qtel1M 650918 GACCCCAAAGCGGGCTGAGCTGCC--GGCAGGTGGAGAGCTCCCTGTCCC 650965 vii v ii iv i -- ?v i v i v L3#LINE/CR1 3919 TGTCCAAAAATGGAATGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGTCAC 3968 chr4qtel1M 650966 GGGGGGTCTCCACACATGAGCTGGATGACCGC 650997 v i v i vi vii i L3#LINE/CR1 3969 TGGAGGTGTTCAAGCAGAGGCTGGATGACCAC 4000 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.24 CpG sites = 27, Kimura (unadjusted) = 46.77 Transitions / transversions = 1.69 (27/16) Gap_init rate = 0.02 (2 / 129), avg. gap size = 1.50 (3 / 2) 36 2.94 0.00 0.00 chr4qtel1M 654990 655024 (344976) (TG)n#Simple_repeat 1 35 (0) c_b207s251i1 8185 chr4qtel1M 654990 TGTGTGTGTGTGTGTGTGTGTGTATGTGTGTGTGT 655024 i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 35 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 21 3.81 0.00 3.57 chr4qtel1M 655083 655111 (344889) (CA)n#Simple_repeat 1 28 (0) m_b207s252i5 8186 chr4qtel1M 655083 CACACACACACACACAGATCACACACACA 655111 v - (CA)n#Simple_ 1 CACACACACACACACACA-CACACACACA 28 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1) 44 0.00 0.00 0.00 chr4qtel1M 655338 655375 (344625) (GT)n#Simple_repeat 1 38 (0) c_b207s251i2 8187 chr4qtel1M 655338 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 655375 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 38 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 212 22.33 5.68 3.33 chr4qtel1M 655739 655826 (344174) C MIR1_Amn#SINE/MIR (92) 138 49 m_b207s601i22 8188 chr4qtel1M 655739 ATGAG-AAACTAAGCCTTGGAGGGG--AAGGGACTTTTCCAAGGTCACCC 655785 - i v ?ii i -- v vi ? C MIR1_Amn#SINE 138 ATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGCCCAAGGTCACNC 89 chr4qtel1M 655786 AGACCCAGACCTGTGACT-AGTGGGGA-TGGTGGGCAAGTCTC 655826 --- ? i ?v i v- iv - ? vivv i C MIR1_Amn#SINE 88 AG---CNGGCNAGTGGCAGAGCCGGGANTNGAACCCAGGTCTC 49 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.88 CpG sites = 10, Kimura (unadjusted) = 28.88 Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.08 (7 / 87), avg. gap size = 1.14 (8 / 7) 15 4.13 4.00 0.00 chr4qtel1M 657024 657048 (342952) (CCTC)n#Simple_repeat 1 26 (0) m_b207s252i7 8189 chr4qtel1M 657024 CCTCCCTCCCTCCCTCCC-CCCGCCC 657048 - v (CCTC)n#Simpl 1 CCTCCCTCCCTCCCTCCCTCCCTCCC 26 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 14 25.69 0.00 2.13 chr4qtel1M 657023 657070 (342930) (TCCCCCC)n#Simple_repeat 1 47 (0) m_b207s252i6 8190 chr4qtel1M 657023 TCCTCCCTCCCTCCCTCCCCCCGCCCCGAGCCAGGCTCCCCCTTACCC 657070 i - v vvv vvv i v (TCCCCCC)n#Si 1 TCCCCCCTCCC-CCCTCCCCCCTCCCCCCTCCCCCCTCCCCCCTCCCC 47 Matrix = Unknown Transitions / transversions = 0.25 (2/8) Gap_init rate = 0.02 (1 / 47), avg. gap size = 1.00 (1 / 1) 14 16.91 0.00 2.94 chr4qtel1M 659924 659958 (340042) (CCCCAG)n#Simple_repeat 1 34 (0) m_b207s252i8 8191 chr4qtel1M 659924 CCCCAGGCCCAGCCCACCCCTCCAGCCCCAGACCC 659958 v - vv i v (CCCCAG)n#Sim 1 CCCCAGCCCCAGCCC-CAGCCCCAGCCCCAGCCCC 34 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 18 21.28 0.00 9.86 chr4qtel1M 660060 660137 (339863) (GGAGG)n#Simple_repeat 1 71 (0) m_b207s252i9 8192 chr4qtel1M 660060 GGAGGGAAGAGGAGATGGTGAGCTAAGGGGGTGGGGAGGGGAGGGGAGAC 660109 -- i - v vvi - v -- (GGAGG)n#Simp 1 GGAGGG--GAGGGGA-GGGGAGGGGA-GGGGAGGGGAGGGGAGGGGAG-- 44 chr4qtel1M 660110 GCCAAGGTAAGGGGGCGGGAGGGGAGGG 660137 -vi vi iv (GGAGG)n#Simp 45 G-GGAGGGGAGGGGAGGGGAGGGGAGGG 71 Matrix = Unknown Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.09 (7 / 77), avg. gap size = 1.00 (7 / 7) 21 20.48 1.56 4.84 chr4qtel1M 661656 661719 (338281) (GGA)n#Simple_repeat 1 62 (0) m_b207s252i10 8193 chr4qtel1M 661656 GGAGGAGGGAAGAGGAGGAAGATGGGGGAGG-GGAAGAAAAGGAGGGAAG 661704 - i i - i - i ii - i (GGA)n#Simple 1 GGAGGA-GGAGGAGGAGGAGGA-GGAGGAGGAGGAGGAGGAGGA-GGAGG 47 chr4qtel1M 661705 AGGAGGATGGGGGGG 661719 v i i (GGA)n#Simple 48 AGGAGGAGGAGGAGG 62 Matrix = Unknown Transitions / transversions = 9.00 (9/1) Gap_init rate = 0.06 (4 / 63), avg. gap size = 1.00 (4 / 4) 304 27.81 11.20 2.21 chr4qtel1M 661909 662033 (337967) MIR3#SINE/MIR 9 144 (64) m_b207s601i23 8194 chr4qtel1M 661909 GTGGCCTGGCAAGGCGCAGGGCACGCGTCTGGAGCCAGGAGACCCGAGTT 661958 ivi ii --- i viiiv i i i MIR3#SINE/MIR 9 GTGGCTGAGCAGAG---AGAGCACGGACTGGGAGTCAGGAGACCTGGGTT 55 chr4qtel1M 661959 CAAATCCAGCTGCCGACCTTTACCGGCTGTGGGACCCC-GGCAA------ 662001 v i v viv i v vi v i? v ii- ------ MIR3#SINE/MIR 56 CTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACT 105 chr4qtel1M 662002 -CATCT------GCCTCAGTTTCCTCAGCAGTAACACGA 662033 - i ------ v v v i MIR3#SINE/MIR 106 TCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGA 144 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.13 CpG sites = 20, Kimura (unadjusted) = 36.13 Transitions / transversions = 1.43 (20/14) Gap_init rate = 0.06 (7 / 124), avg. gap size = 2.43 (17 / 7) 325 27.97 16.08 0.00 chr4qtel1M 661926 662068 (337932) MIRb#SINE/MIR 27 192 (76) m_b207s601i24 8194 chr4qtel1M 661926 AGGGCACGCG-TCTGGAGCCAGG-AGACCCGAGTTCAAATCCAGCTGCCG 661973 i v - i i i- i i i v viv i MIRb#SINE/MIR 27 AGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTCTG 76 chr4qtel1M 661974 ACCTTTACCGGCTGTGGGACCCCGG----------CAACATCT----GCC 662009 v vi ii v ii ----------i v ---- MIRb#SINE/MIR 77 CCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCC 126 chr4qtel1M 662010 TCAGTTTCCTCAGCAGTAACAC---GACAGCAGGGCCTG----GAAGGGT 662052 v v v i--- i ii ivi i---- v MIRb#SINE/MIR 127 TCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTACCTCGCAGGGT 176 chr4qtel1M 662053 TGTGCTTAGGGGTAAA 662068 vv v iv MIRb#SINE/MIR 177 TGTTGTGAGGATTAAA 192 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.72 CpG sites = 23, Kimura (unadjusted) = 35.83 Transitions / transversions = 1.35 (23/17) Gap_init rate = 0.04 (6 / 142), avg. gap size = 3.83 (23 / 6) 212 5.71 5.71 0.00 chr4qtel1M 662372 662406 (337594) MIR#SINE/MIR 116 152 (110) m_b207s601i25 8195 chr4qtel1M 662372 TGCCTCAGTTTCC-CATCTACAAAATGGGGA-AATAA 662406 - ii - MIR#SINE/MIR 116 TGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAA 152 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 6.07 CpG sites = 2, Kimura (unadjusted) = 6.07 Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 228 6.67 0.00 0.00 chr4qtel1M 662517 662546 (337454) MIR#SINE/MIR 116 145 (117) m_b207s601i26 8196 chr4qtel1M 662517 TGCCTCAGTTTCCCCATCTGTAAAACGGGG 662546 i i MIR#SINE/MIR 116 TGCCTCAGTTTCCTCATCTGTAAAATGGGG 145 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 7.16 CpG sites = 2, Kimura (unadjusted) = 7.16 Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 284 14.89 2.13 0.00 chr4qtel1M 663571 663617 (336383) C MIR3#SINE/MIR (45) 163 116 m_b207s601i27 8197 chr4qtel1M 663571 ATCATTTGGTCCAGCCCTCTC-TTTTACAAAGGGGGAAACTGAGGCCC 663617 i i i i - i v i C MIR3#SINE/MIR 163 ATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCC 116 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 17.28 CpG sites = 6, Kimura (unadjusted) = 17.28 Transitions / transversions = 6.00 (6/1) Gap_init rate = 0.02 (1 / 46), avg. gap size = 1.00 (1 / 1) 48 1.61 6.35 0.00 chr4qtel1M 664129 664191 (335809) (TCTCTCTGTC)n#Simple_repeat 1 67 (0) c_b207s251i3 8198 chr4qtel1M 664129 TCTCTCTTTCTCTCTCTGTCTCTCTCTGT-T-TCTCTGTCTCTCTC--TC 664174 v - - -- (TCTCTCTGTC)n 1 TCTCTCTGTCTCTCTCTGTCTCTCTCTGTCTCTCTCTGTCTCTCTCTGTC 50 chr4qtel1M 664175 TCTCTCTGTCTCTCTCT 664191 (TCTCTCTGTC)n 51 TCTCTCTGTCTCTCTCT 67 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.05 (3 / 62), avg. gap size = 1.33 (4 / 3) 733 32.90 4.22 3.90 chr4qtel1M 664206 665176 (334824) C L1M1_orf2#LINE/L1 (2293) 1001 28 m_b207s551i2 8199 chr4qtel1M 664206 ATTTGAGGTTTTAAAATTTATTC---CTTTTCTAGCTTTTTTAGTTACAT 664252 vi ---ii ii --- i i v v i C L1M1_orf2#LIN 1001 ATTTTGGGTTT---GGTTTGCTCTTGCTTTTCTAGTTCTTTAAGATGCAT 955 chr4qtel1M 664253 GCCCAA-----TTCTTTGATCTCCTCTTTATTTTATTCATGTAACTATTT 664297 vvii i----- v vv ii ii v - v ivi i C L1M1_orf2#LIN 954 CGTTAGGTTGTTTATTTGAAGTTTTTCTTCTTTT-TTGATGTAGGCACTT 906 chr4qtel1M 664298 GAAGATATAAAATTTCTCCTAAGAACTGCTTTGGGTGCATCTCATAGGTT 664347 iv v v i ii v v v v i i C L1M1_orf2#LIN 905 ATAGCTATAAACTTCCCTCTTAGTACTGCTTTTGCTGTATCCCATAGGTT 856 chr4qtel1M 664348 TTGATAAGTTGTCT---CATT-TCTTTGGCT----GAAATTAT-CGATTG 664388 i v v --- - v v i ---- v - i v C L1M1_orf2#LIN 855 TTGGTATGTTGTGTTTCCATTATCATTTGTTTCAAGAAATTTTTCAATTT 806 chr4qtel1M 664389 TTTCTGTGATTTGTTGTTTGACCCACTCATTATTTAGAATTAGATTGTTT 664438 ii iiv i v vv vi i i i vi v C L1M1_orf2#LIN 805 CCTTCTTAATTTCTTCATTGACCCACTGGTCATTCAGGAGCATATTGTTT 756 chr4qtel1M 664439 AATTTCCAATTGGTT-TTTAGTCT---AGTTTTCCCTGGCCCTTTATTGA 664484 vv v - v i --- iv i i v ---- C L1M1_orf2#LIN 755 AATTTCCATGTGTTTGTATAGTTTCCAAAATTCCTCTTG----TTATTGA 710 chr4qtel1M 664485 AAA-TAGTTTTATTGTGTTGTGGTCTAAAAAAAAA---AGTATTATTTCT 664530 vvv- vii vi i i vi---ii v C L1M1_orf2#LIN 709 TTTCTAGTTTTATTCCATTGTGGTCAGAGAAGATGCTTGATATTATTTCA 660 chr4qtel1M 664531 GCCTTTTTGCATTTGATTGTACGGTTTTTATGCTCTAATACATAGTCAAT 664580 iii v v vv viv vvv i vi i i i v C L1M1_orf2#LIN 659 ATTTTTTTGAATGTTTTAAGACTTGTTTTGTGACCTAACATATGGTCTAT 610 chr4qtel1M 664581 TTTTGTGTAGGTATCATGTACTGCTGAGAAAAAGAGTGTATTCCTTTCTG 664630 ii v v v vvi --- i i i viii v v C L1M1_orf2#LIN 609 CCTTGAGAATGATCCATGT---GCTGAGGAAAAGAATGTGTATTCTGCAG 563 chr4qtel1M 664631 TCCC--GATTCAGTTTTCTCCAGTGATCTATCACATCTTAAGTTT--TCT 664676 i vi-- vv i v vi ivv i vi i---i -- C L1M1_orf2#LIN 562 CCGTTGGATGAAATGTTCTGTAAATATCTATTAGGTCC---ATTTGGTCT 516 chr4qtel1M 664677 AAGATTCTACTAACCTCCCTAGTTTCTTTCTTGTTTTTTTATTTTTTATT 664726 vii v viv v vv vvv v v i i i ------ C L1M1_orf2#LIN 515 ATAGTGCAGATTAAGTCCGATGTTTCTTTGTTGATTTTCTGTCT------ 472 chr4qtel1M 664727 TTTTGTAATTAGATTTGTCTAATTCTGAGAGGGGGAGGTTGAGGTTCCCC 664776 ---- v --- i i v i v iv i ii v C L1M1_orf2#LIN 471 ----GGAA---GATCTGTCCAATGCTGAAAGTGGGGTGTTGAAGTCTCCA 429 chr4qtel1M 664777 ACTAATATGGTTTTGCTGTCTATTTCTTCCTGTAACTTATTTAATAACTT 664826 i v v v vv i ii v i ivvv vi v C L1M1_orf2#LIN 428 GCTATTATTGTATTGGGGTCTATCTCTCTCTTTAGCTCTAATAATATTTG 379 chr4qtel1M 664827 CTCTAAGAATCTGAATGCTCTATCACTTGATGCTTATACATTTAGTGTTG 664876 i viv ii i viii v i v i ?vi C L1M1_orf2#LIN 378 CTTTATATATCTGGGTGCTCCAGTGTTGGGTGCATATATATTTANAATTG 329 chr4qtel1M 664877 ATACTATTTCATTGTT-CATGGGACCCTTTAACA------AGTTTCCTTC 664919 v - iiiv i -v v iv v ------ vv C L1M1_orf2#LIN 328 TTA-TATCCTCTTGCTGAATTGACCCCTTTATCATTATATAGTGACCTTC 280 chr4qtel1M 664920 CTTATCTCTTTTAATTTAATCTGTTTTTACTTTTGCTTTGTCTGAGATCA 664969 i i i v vvvv i i v vv i ii v v C L1M1_orf2#LIN 279 TTTGTCTCTTCTTATAGTTTTTGTCTTGAAATCTATTTTGTCTGATATAA 230 chr4qtel1M 664970 G---AACTGCCCCTGCATTTTTTTTTTGCTTCAGCTGATGTATAATACAT 665016 --- i i i -- i v i vii iii iv iv C L1M1_orf2#LIN 229 GTATAGCTACTCCTGC--TCTTTTTTGGTTTCCATTGGCATGGAATATCT 182 chr4qtel1M 665017 TCTGCTCCAACCTTTTGTCTTTATCCTATATGTATCTCTATT--TCAGAT 665064 i -- v i i i i vi i i i v-- v ii C L1M1_orf2#LIN 181 TTT--TCCATCCCTTTATTTTCAGTCTATGTGTGTCTTTATAGGTGAAGT 134 chr4qtel1M 665065 GTGTTTCTTGTAAACAACATATTACAGGATCCTCATTCTGTCTTTAATCC 665114 ii v i ?v i - ii i v v iv i C L1M1_orf2#LIN 133 GTGTTTCTTGTAGGCAACAGATCANTGGGT-CTTGTTTTTTCATCCATTC 85 chr4qtel1M 665115 ACTCTTGCTGTTTGCTTCTGTTTTGTGAGAGATTCCATCCCATTCATATT 665164 vi viv i v - i v ----i v ii vi i i C L1M1_orf2#LIN 84 AGCCACTCTATGT-CTTTTGATT----GGAGAGTTTAGTCCATTTACATT 40 chr4qtel1M 665165 CAAAGTTATGAT 665176 v v C L1M1_orf2#LIN 39 CAATGTTATTAT 28 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 44.37 CpG sites = 162, Kimura (unadjusted) = 44.37 Transitions / transversions = 1.12 (162/145) Gap_init rate = 0.06 (54 / 970), avg. gap size = 1.46 (79 / 54) 477 17.65 3.92 0.00 chr4qtel1M 668788 668889 (331111) MIR#SINE/MIR 39 144 (118) m_b208s601i0 8200 chr4qtel1M 668788 CCAGGCT--CTGAGTTCAAATCCAGCTTCAGACACTTACTAGCTGTGTGA 668835 i -- i i v vi v v MIR#SINE/MIR 39 CCAGACTGCCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGA 88 chr4qtel1M 668836 CC-TAGACAAACCACTTCACC-CTGTTTGCCTCAGTTTCCTCATCTGCAA 668883 - i i iii v - v v i MIR#SINE/MIR 89 CCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAA 138 chr4qtel1M 668884 AATGAG 668889 i MIR#SINE/MIR 139 AATGGG 144 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 19.20 CpG sites = 11, Kimura (unadjusted) = 20.42 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.03 (3 / 101), avg. gap size = 1.33 (4 / 3) 17 0.00 0.00 0.00 chr4qtel1M 669157 669178 (330822) (AATG)n#Simple_repeat 1 22 (0) m_b208s252i0 8201 chr4qtel1M 669157 AATGAATGAATGAATGAATGAA 669178 (AATG)n#Simpl 1 AATGAATGAATGAATGAATGAA 22 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 261 27.84 6.19 0.00 chr4qtel1M 669474 669570 (330430) MER63D#DNA/hAT-Tip100 336 438 (623) m_b208s502i0 8202 chr4qtel1M 669474 GTGTGACCATTCAGGCTTCGGGAATGGGCAAACTGCAC---TCCGGCCCT 669520 v vi i vi iv i v vvi --- v v i MER63D#DNA/hA 336 GTGGGAGTATTTACACCACGGAAATCGGCAAACGCTACAAATCAGGGCTT 385 chr4qtel1M 669521 GATCT---GTTTTGTTCATTGTTTAGACAGGAGAATAAGACAGAGAAAAT 669567 i --- v i vvi viv ii MER63D#DNA/hA 386 GATTTATTGTTTTGTTGATTGTCTAGACTTAAGAAAGTGATGGAGAAAAT 435 chr4qtel1M 669568 GTT 669570 MER63D#DNA/hA 436 GTT 438 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.10 CpG sites = 13, Kimura (unadjusted) = 35.10 Transitions / transversions = 0.93 (13/14) Gap_init rate = 0.02 (2 / 96), avg. gap size = 3.00 (6 / 2) 412 37.44 6.85 4.13 chr4qtel1M 670151 671259 (328741) L2#LINE/L2 1937 3074 (8) m_b208s601i1 8203 chr4qtel1M 670151 CTTGCACCCCTTCCCACTGGGCTTTCCATCCTATTCATCCACC------- 670193 v vi v iii vvi i iivv ------- L2#LINE/L2 1937 CTTGAACCCACTCCAATCAGGCTTTCGTCCCCACCACTCCACCGAAACTG 1986 chr4qtel1M 670194 ------CCA--GTGACCAGTGATCTCTTAGTGGCCAAGTCCAAGAGCC-- 670233 ------i -- v i i ivv v i i vi i -- L2#LINE/L2 1987 CTCTTGTCAAGGTCACCAATGACCTCCACGTTGCTAAATCCAATGGTCAA 2036 chr4qtel1M 670234 TTTTC--TACTTGTTCTGTTC--TCTCTCTGCAGCCTGGGGCACCCTGGG 670279 i -- v ii ii ii i--i ? v v vv i ----i L2#LINE/L2 2037 TTCTCAGTCCTCATCTTACTTGACCTNTCAGCAGCATTTGACAC----AG 2082 chr4qtel1M 670280 GCGATCTCTCCCATTTTCTGCTTG------CTTCTTT-CTAGGTTTTTAG 670322 vi v --- i v ------i i- v i ii L2#LINE/L2 2083 TTGATCACTCCC---TCCTTCTTGAAACACTTTCTTCACTTGGCTTCCAG 2129 chr4qtel1M 670323 TGTACTCCATGTTCCTGGTTGTCTTCCGTTTCCTCTGCTAGCTCTTCCTC 670372 vii iv ivi v i vviii v viv i i L2#LINE/L2 2130 GACACCACACTCTCCTGGTTTTCCTCCTACCTCACTGGCCGCTCCTTCTC 2179 chr4qtel1M 670373 AG---------CTGGATCCTCCCTCAGATCAT-GCTTTCTGACCATGGGA 670412 --------- v - vv vi- vii ? v i v L2#LINE/L2 2180 AGTCTCCTTTGCTGGTTCCTCC-TCATCTCCCCGACCTCTNAACGTTGGA 2228 chr4qtel1M 670413 GTCCCTCAGGGCTCTGTCCCAGACTCTCTCTGGGCTCTTCTCCCTTTAGG 670462 v i v iv ivi i---- iv i vi L2#LINE/L2 2229 GTGCCCCAGGGCTCAGTCCTTGGACCTCTT----CTCTTCTCTATCTACA 2274 chr4qtel1M 670463 CTACTGCTCCTGGCTTTAATGATCACCTTTAGACTAAAGACTATCAGATC 670512 --ii i---- ?ii v v ii v v v i - i i - L2#LINE/L2 2275 CT--CACTCCC----TNGGTGATCTCATCCAGTCTCATGGCT-TTAAAT- 2316 chr4qtel1M 670513 TAGCATTCCTGCCCCAA--ACTCTCTGGTCACGATCAGATCTAGCAGTCC 670560 - v iiv iiv ii -- i vii ----- i v v- i L2#LINE/L2 2317 -ACCATCTATATGCTGATGACTCCCAAAT-----TTATATCTC-CAGCCC 2359 chr4qtel1M 670561 TGACCCAAACTCTCCGGTGACTCCCTCCCCCCCATTTTTAATTGCCTCAC 670610 v ----- vv vii vvv i vi v ii i vvi L2#LINE/L2 2360 GGACC-----TCTCCCCTGAACTCCAGACTCGTATATCCAACTGCCTACT 2404 chr4qtel1M 670611 AGACACCTCAAACTGGATGTCCAGCAGACATTTTGCACTCAATAGGTCCC 670660 v i v vi i ii i i iiv i i v v L2#LINE/L2 2405 CGACATCTCCACTTGGATGTCTAATAGGCATCTCAAACTTAACATGTCCA 2454 chr4qtel1M 670661 AAATGGAACACATTGTCTTTCCCCTTAAGCCCCATTCCCCTTCTACTTTC 670710 iv v v vi i i i ivv i i iv viii L2#LINE/L2 2455 AAACTGAACTCCTGATCTTCCCCCTCAAACCTGCTCCTCCCGCAGTCTTC 2504 chr4qtel1M 670711 TATAATATTGTAGAGGACCACACCCTTTACTGAGTCCCTCAGGTTCC--- 670757 ivi viviv ?i v i v v v iiviiv iv -- --- L2#LINE/L2 2505 CCCATCTCAGTNAATGGCAACTCCATCCTTCCAGTTGCTCAGG--CCAAA 2552 chr4qtel1M 670758 AACCTAGAAATTATTCTGGATACC---CTCACCCTAATACTCC-CCCCCT 670803 v i i i i v iv --- iv i v i i - vi v L2#LINE/L2 2553 AACCTTGGAGTCATCCTTGACTCCTCTCTTTCTCTCACACCCCACATCCA 2602 chr4qtel1M 670804 ATCCAGTATGGTGCCAAGGCTGTCGATTTCACCTC---------TTTGAG 670844 vi ---- v vv ii ii i--------- iiiii L2#LINE/L2 2603 ATCCATCA----GCAAATCCTGTCGGCTCTACCTTCAAAATATATCCAGA 2648 chr4qtel1M 670845 ATCCTCCCCCTTCT-ATC-CTGCCCCTGCCCCTACCCTAGTACAGACCCT 670892 vv v - i - iv v v i i v ii vi L2#LINE/L2 2649 ATCCGACCACTTCTCACCACCTCCACTGCCACCACCCTGGTCCAAGCCAC 2698 chr4qtel1M 670893 TACCACCTCATGCTTGCACTATGGCAATAGCCACTGTGGGGGTGGGGGAC 670942 i i i vi i v i iv v ivvivv vv---- L2#LINE/L2 2699 CATCATCTCTCGCCTGGATTACTGCAATAGCCTCCTAACTGGTCT----C 2744 chr4qtel1M 670943 TCTGCCTTC-CTCAAGTCTTTC-CCAATCTCATC-CATCTGGGCTATCAA 670989 i i i - i vv i iii -? i vv - v vvi vii i L2#LINE/L2 2745 CCTGCTTCCACCCTTGCCCCCCTNCAGTCTATTCTCAACACAGCAGCCAG 2794 chr4qtel1M 670990 AGTGATTTTCCTAAAAT-----TCAGG----GCCAACCTCCTACTCAATA 671030 ii ii i----- i---- i vi ii i v L2#LINE/L2 2795 AGTGATCCTTTTAAAACGTAAGTCAGATCATGTCACTCCTCTGCTCAAAA 2844 chr4qtel1M 671031 AACCCCAGCAGTTTCCTATTGCCTCCAGGAGAAAATCCAAAATGCTCTGC 671080 vv i iii i i iv vii iiv v i v - i L2#LINE/L2 2845 CCCTCCAATGGCTTCCCATCTCACTCAGAGTAAAAGCCAAAGTCCT-TAC 2893 chr4qtel1M 671081 -TTGGCCTTCAAAGCCCTTTAAGACCT-GCCCCCCATC-CCTTTCCAGTC 671127 -v v i vi v i - i i i- i iiii L2#LINE/L2 2894 AATGGCCTACAAGGCCCTACATGATCTGGTCCCCCGTTACCTCTCTGACC 2943 chr4qtel1M 671128 T--TCTTACACCTCACTCTCCAATCCATTCTCTTGGATCCTGTGCCCTCG 671175 -- ivi -- vvii ii v iv v v ivv vii L2#LINE/L2 2944 TCATCTCCTAC--CACTCTCCCCCTCGCTCACTCCGCTCCAGCCACACTG 2991 chr4qtel1M 671176 GCCTCTCAGCTGTTCTATTGAAGCAGACCCTCCAT-TTTTCAGCTCTGGG 671224 iiv i- i - vi vvv i-i ii iv v L2#LINE/L2 2992 GCCTCCTTGCTGTTCC-TCGAA-CACGCCAGGCACGCTCCCGCCTCAGGG 3039 chr4qtel1M 671225 CATTCTCTGTGGCTATCCTCACACCCTGGGATGTT 671259 v iv vv v i i i v vv i i i L2#LINE/L2 3040 CCTTTGCACTTGCTGTTCCCTCTGCCTGGAACGCT 3074 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 52.52 CpG sites = 233, Kimura (unadjusted) = 54.79 Transitions / transversions = 1.41 (233/165) Gap_init rate = 0.07 (73 / 1108), avg. gap size = 1.68 (123 / 73) 300 32.08 7.81 0.98 chr4qtel1M 671766 671957 (328043) L2c_3end#LINE/L2 226 430 (48) m_b208s601i2 8203 chr4qtel1M 671766 ACCTTCCCCAGGAAGTCCCCTCTAACCCCTC---TCCATTCCAGTTCCGT 671812 i i i i ii i i i ---? i v i v v vi L2c_3end#LINE 226 ACCTCCTCCGGGAAGCCTTCCCTGACCCCCCAAGNCTAGTCTAGGTGCCC 275 chr4qtel1M 671813 CCCTCT---CTTC-ATTATTTCCTGTTCAT---CCTGTATATA-TATATA 671854 i --- i - viivi ii --- ii - -i iv L2c_3end#LINE 276 TCCTCTGTGCTCCCATAGCACCCTGTCTATACTCCCAT-TATAGCACTTA 324 chr4qtel1M 671855 T-ATATAGTTTGT-TTATACAGATGTATTTGCATGT-TGTCTCCGTTATT 671901 - - ii - i vvvi v i i ? - vii i L2c_3end#LINE 325 TCAT-TAACTTGTATTGTAATTGTCTGTTTACNTGTCTGTCTCCTCCACT 373 chr4qtel1M 671902 AGATTGTGAACTCCTGGAGGATGGGGACCATCTTTTGCCCTTTTTGGTA- 671950 i i v iii i v i iii v i v - L2c_3end#LINE 374 AGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTAT 423 chr4qtel1M 671951 CCCTAAC 671957 i i L2c_3end#LINE 424 CCCCAGC 430 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 44.00 CpG sites = 45, Kimura (unadjusted) = 46.15 Transitions / transversions = 2.81 (45/16) Gap_init rate = 0.06 (11 / 191), avg. gap size = 1.55 (17 / 11) 240 26.16 1.49 3.03 chr4qtel1M 672296 672362 (327638) L2d2_3end#LINE/L2 484 549 (6) m_b208s601i3 8203 chr4qtel1M 672296 ATCTCATCACTAGTACTTGGTATAGTGCCTGG-ACAGGGTGGGCACTTAA 672344 i -i - ii i i i i v - vi i i i L2d2_3end#LIN 484 ATCCC-CCAC-AGCGCCTAGCACAGTGCCTTGCACACAGTAGGCGCTCAA 531 chr4qtel1M 672345 TAAATGTTTATTGATTCG 672362 i i i L2d2_3end#LIN 532 TAAATATTTGTTGATTTG 549 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 30.03 CpG sites = 15, Kimura (unadjusted) = 35.48 Transitions / transversions = 7.50 (15/2) Gap_init rate = 0.05 (3 / 66), avg. gap size = 1.00 (3 / 3) 244 25.86 1.72 0.00 chr4qtel1M 672301 672358 (327642) L2a_3end#LINE/L2 449 507 (10) m_b208s601i4 8203 chr4qtel1M 672301 ATCACTAGTACTTGGTATAGTGCCTGG-ACAGGGTGGGCACTTAATAAAT 672349 v i ii i i v i - vi i i i L2a_3end#LINE 449 ATCCCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGGCGCTCAATAAAT 498 chr4qtel1M 672350 GTTTATTGA 672358 i i L2a_3end#LINE 499 ATTTGTTGA 507 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 28.27 CpG sites = 12, Kimura (unadjusted) = 34.05 Transitions / transversions = 4.00 (12/3) Gap_init rate = 0.02 (1 / 57), avg. gap size = 1.00 (1 / 1) 502 27.33 2.84 1.40 chr4qtel1M 674031 674171 (325829) MIR#SINE/MIR 48 190 (72) m_b208s601i5 8204 chr4qtel1M 674031 CTAGGTTTGAAGTCAAATCCTCAGACATTTCCTATCTGTGTGAATGTGGA 674080 i i vi vii-- v v i v v viv i MIR#SINE/MIR 48 CTGGGTTCGAATCCCGG--CTCTGCCACTTACTAGCTGTGTGACCTTGGG 95 chr4qtel1M 674081 CAAGTCACTCAATCTTT----GTCTCAGCTTCCTCACCCATAAGATGGGG 674126 i i i i ---- i i i ii i MIR#SINE/MIR 96 CAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGG 145 chr4qtel1M 674127 ATAATAGTAGCATGTACTTCTTAGAGATTTTGTGAGATTCAAATG 674171 i i iv i v i v v iv i MIR#SINE/MIR 146 ATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGGATTAAATG 190 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.05 CpG sites = 25, Kimura (unadjusted) = 35.36 Transitions / transversions = 1.92 (25/13) Gap_init rate = 0.02 (3 / 140), avg. gap size = 2.00 (6 / 3) 23 25.41 1.54 0.00 chr4qtel1M 674184 674248 (325752) (TTA)n#Simple_repeat 1 66 (0) m_b208s252i1 8205 chr4qtel1M 674184 TTCTTATTATTATTGTCCAAATAGTTATTATTATAATTATTATTAAACTT 674233 v i ivvv vi v vvv (TTA)n#Simple 1 TTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATT 50 chr4qtel1M 674234 ATT-CTCTTATTATTA 674248 -i v (TTA)n#Simple 51 ATTATTATTATTATTA 66 Matrix = Unknown Transitions / transversions = 0.40 (4/10) Gap_init rate = 0.02 (1 / 64), avg. gap size = 1.00 (1 / 1) 75 12.13 0.00 0.84 chr4qtel1M 675434 675553 (324447) (CTC)n#Simple_repeat 1 119 (0) m_b208s252i2 8206 chr4qtel1M 675434 CTCCTCCAACTCCTCCTCCTTCTCCTCCTCCTCCTCCTCCTCCTCCTCCT 675483 vv i (CTC)n#Simple 1 CTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT 50 chr4qtel1M 675484 CCTTCTTCTCCTCCTTCTCCTCCTTCTCCTCCTTCTCCTTCTTCCTCCAC 675533 i i i i i - i v (CTC)n#Simple 51 CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC-TCCTCCTCCTC 99 chr4qtel1M 675534 CTTCTCTTCCTCCTCTTCCT 675553 i i i (CTC)n#Simple 100 CTCCTCCTCCTCCTCCTCCT 119 Matrix = Unknown Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.01 (1 / 119), avg. gap size = 1.00 (1 / 1) 221 15.38 0.00 0.00 chr4qtel1M 675603 675641 (324359) C L2a_3end#LINE/L2 (93) 424 386 m_b208s601i6 8207 chr4qtel1M 675603 AGTCCCTGCTCCCAAGGAGCTTCCATTCTAGAAGGGGGA 675641 i i v v vi C L2a_3end#LINE 424 AGTCCCTGCCCTCATGGAGCTTACATTCTAGTGGGGGGA 386 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 17.29 CpG sites = 3, Kimura (unadjusted) = 17.29 Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 193 16.71 0.00 4.76 chr4qtel1M 675604 675647 (324353) C L2d2_3end#LINE/L2 (92) 463 422 m_b208s601i7 8207 chr4qtel1M 675604 GTCCCTGCTCCCAAGGAGCTTCCATTCTAGAAGGGGGAAGATAA 675647 i i v v vv -- i C L2d2_3end#LIN 463 GTCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGG--AGACAA 422 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 18.88 CpG sites = 3, Kimura (unadjusted) = 18.88 Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2) 227 14.63 0.00 0.00 chr4qtel1M 675713 675753 (324247) C L2a_3end#LINE/L2 (93) 424 384 m_b208s601i8 8207 chr4qtel1M 675713 AGTCCCTGCCCCCAAAGAGCTTACATTCTTTGGGGGGGAGA 675753 i vi vvv C L2a_3end#LINE 424 AGTCCCTGCCCTCATGGAGCTTACATTCTAGTGGGGGGAGA 384 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 16.28 CpG sites = 2, Kimura (unadjusted) = 16.28 Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 15 25.63 1.69 3.45 chr4qtel1M 677021 677079 (322921) (AAGA)n#Simple_repeat 1 58 (0) m_b208s252i3 8208 chr4qtel1M 677021 AAGAAAGAAGAAAACTGAGAAAGAAA-ACAAAATGCAAGCAAACAACAGA 677069 ii vvi - v i v v - v - (AAGA)n#Simpl 1 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG-AAAGAA-AGA 48 chr4qtel1M 677070 AAGAGTGAAA 677079 iv (AAGA)n#Simpl 49 AAGAAAGAAA 58 Matrix = Unknown Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.05 (3 / 58), avg. gap size = 1.00 (3 / 3) 337 32.97 2.19 0.54 chr4qtel1M 677240 677422 (322578) C L1ME4c_3end#LINE/L1 (191) 639 454 m_b208s551i0 8209 chr4qtel1M 677240 TTCTGCTCATTTCACTCAGCATCAGTTCATGTAAGTCTCTTCAAGTTTCT 677289 iv i i i vv iv vi i - i v v C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATAAACATTT-TCCATGTTGCT 591 chr4qtel1M 677290 CTGAAATCATCCTGCTGATCATTTCTTATAGA---ATAA-ATTCCATAAC 677335 viiv i v v iv v i v i v--- - viv C L1ME4c_3end#L 590 ACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCGA 541 chr4qtel1M 677336 ATCCATATACCATAACTTATTCAGCCATTCTCCAAGTGATGGGTATCCAC 677385 i ?v i i i i i i v v v ii ii v C L1ME4c_3end#L 540 GTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAG 491 chr4qtel1M 677386 TCAGTTTCCAGTTTCTTGTCACTATAAAAAGGGCTGC 677422 viv i i i ii i v iv C L1ME4c_3end#L 490 GTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGC 454 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 43.07 CpG sites = 34, Kimura (unadjusted) = 45.10 Transitions / transversions = 1.31 (34/26) Gap_init rate = 0.02 (3 / 182), avg. gap size = 1.67 (5 / 3) 274 32.79 0.61 5.73 chr4qtel1M 677311 677475 (322525) C L1MB8_3end#LINE/L1 (362) 563 407 m_b208s551i1 8209 chr4qtel1M 677311 TTTCTTATAGAATAA-ATTCCATAACATCCATATACCATAACTTATTCAG 677359 v iiv - vii vv i vi i v C L1MB8_3end#LI 563 TTTATTGCCGAATAATATTCCATTGTATGGATATACCACATTTTATTTAT 514 chr4qtel1M 677360 CCATTCTCCAAGTGATGGGTATCCACTCAGTTTCCAGTTTCTTGTCACTA 677409 vi iv ii iiivviv v i v ii i C L1MB8_3end#LI 513 CCATTCATCAGTTGATGGACATTTGGGTTGTTTCCACTTTTTGGCTATTA 464 chr4qtel1M 677410 TAAAAAGGGCTGCCACATGTGGGTCCCTTTCATGAGGACAAACTTTTGAG 677459 i v iv ---- i ii--- v i -- v ii v C L1MB8_3end#LI 463 TGAATAATGCTGC----TATGAA---CATTCGT--GTACAAGTTTTTGTG 423 chr4qtel1M 677460 GGAAAAAATGTTTCCA 677475 v i v v i C L1MB8_3end#LI 422 TGGACATATGTTTTCA 407 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 43.07 CpG sites = 29, Kimura (unadjusted) = 44.24 Transitions / transversions = 1.32 (29/22) Gap_init rate = 0.06 (10 / 164), avg. gap size = 1.00 (10 / 10) 356 28.87 0.00 0.00 chr4qtel1M 677326 677422 (322578) C L1ME3G_3end#LINE/L1 (381) 543 447 m_b208s551i2 8209 chr4qtel1M 677326 ATTCCATAACATCCATATACCATAACTTATTCAGCCATTCTCCAAGTGAT 677375 ii vv i i i i v v C L1ME3G_3end#L 543 ATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTATTGAT 494 chr4qtel1M 677376 GGGTATCCACTCAGTTTCCAGTTTCTTGTCACTATAAAAAGGGCTGC 677422 ii ii vviv i i i ii i i v iv C L1ME3G_3end#L 493 GGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCTGC 447 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 36.50 CpG sites = 19, Kimura (unadjusted) = 38.27 Transitions / transversions = 2.11 (19/9) Gap_init rate = 0.00 (0 / 96), avg. gap size = 0.0 (0 / 0) 19 35.69 0.00 0.00 chr4qtel1M 678058 678131 (321869) (TT)n#Simple_repeat 1 74 (0) m_b208s252i4 8210 chr4qtel1M 678058 TTTTTAGATTTTTTTTTTTTTTTAATAGAATGATTGTTTTTTTGCTGATT 678107 vvv vv vvvv vv v vi vv (TT)n#Simple_ 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr4qtel1M 678108 TTTTTCCTTTTTTCTCTTTCTTTT 678131 ii i i i (TT)n#Simple_ 51 TTTTTTTTTTTTTTTTTTTTTTTT 74 Matrix = Unknown Transitions / transversions = 0.40 (6/15) Gap_init rate = 0.00 (0 / 73), avg. gap size = 0.0 (0 / 0) 228 31.56 0.00 8.21 chr4qtel1M 679546 679690 (320310) L2-1_AMi#LINE/L2 289 422 (813) m_b208s551i3 8211 chr4qtel1M 679546 TCCCACAGAGTTCTGACTTGGGTCTTCCTTTCTCCTTCCTCTTTTTTGGG 679595 i i i v i v -- i i ii vi------ L2-1_AMi#LINE 289 TTCCACAGGGCTCTGTCCTTGGTC--CCCTTCTCTTCTCTCTAC------ 330 chr4qtel1M 679596 GTCCTATTTCATTTGGTGACCTCATCAGCTCCTATGAATTCAACTATTAT 679645 ii i i -- v i i v vvvi ii ii L2-1_AMi#LINE 331 ACCTTATCTC--TGGGTAATCTCATCCGCAAACACAAATTCAACTACCAT 378 chr4qtel1M 679646 CTCTATGATTCTCAGATCTACTCATCTAGCCTTAATCTCTCTTCT 679690 v - i v iiv vi ivi i v i L2-1_AMi#LINE 379 CTGT-TGACTCACAGATCTACCTCTCTACTCCAGACCTGTCTCCT 422 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 42.81 CpG sites = 28, Kimura (unadjusted) = 42.81 Transitions / transversions = 2.00 (28/14) Gap_init rate = 0.08 (11 / 144), avg. gap size = 1.00 (11 / 11) 258 27.23 8.11 3.23 chr4qtel1M 681559 681706 (318294) L2d_3end#LINE/L2 357 511 (5) m_b208s601i9 8212 chr4qtel1M 681559 TAATTATTTCATCAAATGTGTT-GTCTTGTC----CTATTATGAT----A 681599 i ---i - ---- v i - ---- L2d_3end#LINE 357 TAATTGTTTCAT---GTGTGTTAGTCTTGTCTCCCCAACTA-GATTGTAA 402 chr4qtel1M 681600 GATCCTTGGGATCAGGAACTATGTTAT-TACT-TCTAATTG-TATCCACA 681646 v i iv i i iv - - i v? i - vi L2d_3end#LINE 403 GCTCCTTGAGGGCAGGGACCATGTCTTATACTNTTTTNTCGTTCCCCACA 452 chr4qtel1M 681647 GAACTTAGGCATAGGATCCAGCACATACTTACGGTTTAACAAATGCTGAT 681696 vi i - i viiiv v vivv i i i i vi L2d_3end#LINE 453 GCGCCTA-GCACAGTGCTGAGCACATAGTAGGCGCTCAATAAATACTTGT 501 chr4qtel1M 681697 TCATTCATTG 681706 v v L2d_3end#LINE 502 TGATTGATTG 511 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 32.87 CpG sites = 23, Kimura (unadjusted) = 35.07 Transitions / transversions = 1.44 (23/16) Gap_init rate = 0.07 (11 / 147), avg. gap size = 1.55 (17 / 11) 24 6.54 0.00 0.00 chr4qtel1M 683071 683102 (316898) (CA)n#Simple_repeat 1 32 (0) m_b208s252i5 8213 chr4qtel1M 683071 CACACACACACACACAAACACACACACACGCA 683102 v i (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACA 32 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 410 22.59 12.93 0.61 chr4qtel1M 686685 686831 (313169) MIR#SINE/MIR 84 248 (14) m_b208s601i10 8214 chr4qtel1M 686685 TGTGACCTTAAGCTAGTCACTTAACCTGTTTGT--CTCAGTTTTCTCAAC 686732 ii v i v i -- i v MIR#SINE/MIR 84 TGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATC 133 chr4qtel1M 686733 TCTGAAATGGGGATCATAAAAGTACCTAAGTTCACAGCTCTGGT-TGA-C 686780 v i v v - vi i vvi v - -v MIR#SINE/MIR 134 TGTAAAATGGGGATAATAATAGTACCT-ACCTCATAGGGTTGTTGTGAGG 182 chr4qtel1M 686781 ATTAAAGGAGC---TCTCTGTAA------------AGTCCTTGACACACA 686815 v i--- viv ------------ v i i i MIR#SINE/MIR 183 ATTAAATGAGTTAATACATGTAAAGCGCTTAGAACAGTGCCTGGCACATA 232 chr4qtel1M 686816 GTACATGCTCCATAAA 686831 vii v MIR#SINE/MIR 233 GTAAGCGCTCAATAAA 248 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 26.15 CpG sites = 16, Kimura (unadjusted) = 27.07 Transitions / transversions = 0.94 (16/17) Gap_init rate = 0.04 (6 / 146), avg. gap size = 3.33 (20 / 6) 187 23.08 0.00 0.00 chr4qtel1M 687945 687983 (312017) MIR3#SINE/MIR 110 148 (60) m_b208s601i11 8215 chr4qtel1M 687945 CTCTCTGAGCCTCCATTTCTTTACCTCTAACATGAGGAG 687983 i vi i i i v v i MIR3#SINE/MIR 110 CTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGG 148 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 28.45 CpG sites = 6, Kimura (unadjusted) = 28.45 Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 203 24.66 6.85 0.00 chr4qtel1M 688553 688625 (311375) L2a_3end#LINE/L2 394 471 (46) m_b208s601i12 8216 chr4qtel1M 688553 CTGAAACCTAAGCTCCTGGAGGGCAGGGAC-TCTGACCCTTTTGTCC--- 688598 ii iv vv - i v iv i --- L2a_3end#LINE 394 CTAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTCTGTTTTGTTCACT 443 chr4qtel1M 688599 -CTGGGTCCTCAGCACCCAGCACAGGGC 688625 - vi i i i v v L2a_3end#LINE 444 GCTGTATCCCCAGCGCCTAGAACAGTGC 471 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 28.41 CpG sites = 10, Kimura (unadjusted) = 30.38 Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.04 (3 / 72), avg. gap size = 1.67 (5 / 3) 216 29.51 0.00 0.00 chr4qtel1M 688561 688621 (311379) L2c_3end#LINE/L2 380 440 (38) m_b208s601i13 8216 chr4qtel1M 688561 TAAGCTCCTGGAGGGCAGGGACTCTGACCCTTTTGTCCCTGGGTCCTCAG 688610 i v iv v iiv ii ii vi i L2c_3end#LINE 380 TGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTATCCCCAG 429 chr4qtel1M 688611 CACCCAGCACA 688621 i ii L2c_3end#LINE 430 CGCCTGGCACA 440 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 34.29 CpG sites = 13, Kimura (unadjusted) = 39.96 Transitions / transversions = 2.60 (13/5) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 15 14.38 0.00 0.00 chr4qtel1M 690723 690746 (309254) (G)n#Simple_repeat 1 24 (0) m_b208s252i6 8217 chr4qtel1M 690723 GGAGGGGGGGGGAAGGGGGGGGGG 690746 i ii (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGG 24 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 35 28.10 2.47 8.26 chr4qtel1M 690780 691022 (308978) (GGAG)n#Simple_repeat 1 230 (0) m_b208s252i7 8218 chr4qtel1M 690780 GGAGGAGAAGGGAAGG-GGGAGGAACCGGAGCCGGAGGGAGGGGTGGGAG 690828 - - i - i -v -- - v (GGAG)n#Simpl 1 GGAGG-G-AGGGAGGGAGGGAGGGA-GGGAG--GGAGGGA-GGGAGGGAG 44 chr4qtel1M 690829 GGAGAGGGGGAGGG-GTAAGAGGA-GGAGGGAGGGAAAAGAGAAAGGGGA 690876 i i - vi - - - ii ii - (GGAG)n#Simpl 45 GGAGGGAGGGAGGGAGGGAG-GGAGGGAGGGAGGG-AGGGAGGGA-GGGA 91 chr4qtel1M 690877 GGGAGGGGAAGG-GGGAGGTTTGAAGAATAGGCGGTGGGGGAGGGGCCGA 690925 - i - vvv i -iv vi v i ivv (GGAG)n#Simpl 92 GGGA-GGGAGGGAGGGAGGGAGGGAG-GGAGGGAGGGAGGGAGGGAGGGA 139 chr4qtel1M 690926 GAAGAGGGGAGGATAAGG-GGAAGGAAGGTAAGAAATAGGAACAAGAGAA 690974 -i - -v i - i i -i ii -i ivi i i (GGAG)n#Simpl 140 G-GGA-GGGAGG-GAGGGAGGGAGGGAGG-GAGGGA-GGGAGGGAGGGAG 184 chr4qtel1M 690975 GGTGGGAGGGACTGGGAGACAGGAAGGAAGCCACTGGAGGG-GGGAGGG 691022 v -- iv i i vv -v - (GGAG)n#Simpl 185 GGAGGGAGGGA--GGGAGGGAGGGAGGGAGGGA-GGGAGGGAGGGAGGG 230 Matrix = Unknown Transitions / transversions = 1.67 (30/18) Gap_init rate = 0.10 (25 / 242), avg. gap size = 1.00 (25 / 25) 22 33.85 5.64 2.49 chr4qtel1M 690782 690976 (309024) (AGGAGA)n#Simple_repeat 1 201 (0) m_b208s252i8 8218 chr4qtel1M 690782 AGGAGAAGG-GAAGGGGGAGGAACCGGAGCCGGAG--GGAGGGGTGGGAG 690828 - i i ivv vv -- ii - i i (AGGAGA)n#Sim 1 AGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAG-GAGAA 49 chr4qtel1M 690829 GGAG-AGGGGGAGGGGTAAGAGGAGGAGGGAGGGAAAAGAGAAAGGGGAG 690877 - i i i v i i - i ii i i i i (AGGAGA)n#Sim 50 GGAGAAGGAGAAGGAGAAGGAGAAGGA-GAAGGAGAAGGAGAAGGAGAAG 98 chr4qtel1M 690878 G-G-AGGGGAAGGGGGAGGTTTGAA-GAATAGGCGGTGGGGGAGG-GGCC 690923 - - i i i --v - iv v iv i i - ivv (AGGAGA)n#Sim 99 GAGAAGGAGAAGGAGAAGG--AGAAGGAGAAGGAGAAGGAGAAGGAGAAG 146 chr4qtel1M 690924 GAGAAGAGGGGAGGATAAGGGGAA-G-GAAGG-TAAGAAATAGGAACAAG 690970 - i i v i - - -v i iv iv i (AGGAGA)n#Sim 147 GAGAAG-GAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGG 195 chr4qtel1M 690971 AGAAGG 690976 (AGGAGA)n#Sim 196 AGAAGG 201 Matrix = Unknown Transitions / transversions = 2.27 (34/15) Gap_init rate = 0.08 (15 / 194), avg. gap size = 1.07 (16 / 15) 257 19.05 3.17 0.00 chr4qtel1M 692901 692963 (307037) DNM1r#Unknown 2479 2543 (2119) m_b208s502i2 8219 chr4qtel1M 692901 TGTGCGTGTGCATATATGTGTGTGCACGTGTGAATGTGTG--TGTGTGTG 692948 ii i ii i v -- i i DNM1r#Unknown 2479 TGTATGTGTGTATATATGTGTGTATATGTGTGTATGTGTGTATATATGTG 2528 chr4qtel1M 692949 TATACAAATGTATGT 692963 i v i ? DNM1r#Unknown 2529 TATATATACGTATNT 2543 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 21.38 CpG sites = 10, Kimura (unadjusted) = 23.58 Transitions / transversions = 5.00 (10/2) Gap_init rate = 0.02 (1 / 62), avg. gap size = 2.00 (2 / 1) 63 0.00 0.00 0.00 chr4qtel1M 693361 693414 (306586) (AG)n#Simple_repeat 1 54 (0) c_b208s251i0 8220 chr4qtel1M 693361 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 693410 (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr4qtel1M 693411 AGAG 693414 (AG)n#Simple_ 51 AGAG 54 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 16 13.08 0.00 0.00 chr4qtel1M 693600 693624 (306376) (T)n#Simple_repeat 1 25 (0) m_b208s252i9 8221 chr4qtel1M 693600 TTTTTTTTTTTTTTTTTATCTTGTT 693624 v i v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 13 23.96 2.27 0.00 chr4qtel1M 693911 693954 (306046) (TCTTTCT)n#Simple_repeat 1 45 (0) m_b208s252i10 8222 chr4qtel1M 693911 TCTTTCTTCCATTTTC-TTCCTCTATTATCTTTGTTCTTTCTGCT 693954 iv i - i v iv v v (TCTTTCT)n#Si 1 TCTTTCTTCTTTCTTCTTTCTTCTTTCTTCTTTCTTCTTTCTTCT 45 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.02 (1 / 43), avg. gap size = 1.00 (1 / 1) 191 29.88 4.55 1.10 chr4qtel1M 695208 695295 (304705) L2c_3end#LINE/L2 361 451 (27) m_b208s601i14 8223 chr4qtel1M 695208 TATCTCCTCTTGTAGACTG--AGTTT-TAGAGGGCAGGGGCTGTTTCTAT 695254 i ivv -- i i- v i i v - L2c_3end#LINE 361 TGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCT-T 409 chr4qtel1M 695255 ATT-ATTTTTGTGATACAAGCATGTAGCATAAGCTAGGAACT 695295 - i iviv v iiv i i viv vi L2c_3end#LINE 410 ATTCATCTTTGTATCCCCAGCGCCTGGCACATAGTAGGCGCT 451 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.60 CpG sites = 15, Kimura (unadjusted) = 39.15 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.05 (4 / 87), avg. gap size = 1.25 (5 / 4) 346 24.73 6.45 0.00 chr4qtel1M 695331 695423 (304577) MIRb#SINE/MIR 136 234 (34) m_b208s601i15 8224 chr4qtel1M 695331 TTATCTGTAAAATGGA---AATAATATCAACTTTCCAGGATTATGATGAA 695377 i i--- i v i iv i i vi i MIRb#SINE/MIR 136 TCATCTGTAAAATGGGGATAATAATACCTACCTCGCAGGGTTGTTGTGAG 185 chr4qtel1M 695378 ---CAAATGTGCTAACAATTGCAAAGCACTTAGCACAGTGCCTGACATA 695423 ---i v v iivv i i i i MIRb#SINE/MIR 186 GATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACA 234 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 28.03 CpG sites = 16, Kimura (unadjusted) = 31.26 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.02 (2 / 92), avg. gap size = 3.00 (6 / 2) 12 19.32 4.65 2.27 chr4qtel1M 695658 695700 (304300) (TTAATA)n#Simple_repeat 1 44 (0) m_b208s252i11 8225 chr4qtel1M 695658 TTAATA-CAAAATAAGTATT-ATATAAATATTAATTGTTATTATT 695700 -i v v i - v - i v (TTAATA)n#Sim 1 TTAATATTAATATTAATATTAATATTAATATTAA-TATTAATATT 44 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.07 (3 / 42), avg. gap size = 1.00 (3 / 3) 11 32.77 0.00 0.00 chr4qtel1M 695824 695872 (304128) (ACAGCA)n#Simple_repeat 1 49 (0) m_b208s252i12 8226 chr4qtel1M 695824 ACAGCAGCAGCAGGATATATAGCAACAGCAAGATACATAGCAGCAGCAA 695872 i iv vvv i v vvv i i (ACAGCA)n#Sim 1 ACAGCAACAGCAACAGCAACAGCAACAGCAACAGCAACAGCAACAGCAA 49 Matrix = Unknown Transitions / transversions = 0.62 (5/8) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 13 24.89 3.70 1.82 chr4qtel1M 696081 696134 (303866) (ATTAAA)n#Simple_repeat 1 55 (0) m_b208s252i13 8227 chr4qtel1M 696081 ATTAAAAATGAATGTACATATAACCTTAACAATT-AAGTT-AAATTAAAA 696128 v i vv v vv vv - - i - (ATTAAA)n#Sim 1 ATTAAAATTAAAATTAAAATTAAAATTAA-AATTAAAATTAAAATTAAAA 49 chr4qtel1M 696129 TAAAAA 696134 v (ATTAAA)n#Sim 50 TTAAAA 55 Matrix = Unknown Transitions / transversions = 0.22 (2/9) Gap_init rate = 0.06 (3 / 53), avg. gap size = 1.00 (3 / 3) 308 31.96 4.31 6.60 chr4qtel1M 696795 697119 (302881) C L1MB5_3end#LINE/L1 (267) 654 337 m_b208s551i4 8228 chr4qtel1M 696795 ATATAATGATCTCCTGGTTCTG-CTCATTTCACTCAGCATCA-GTTCATT 696842 i- ii ii vv - iv i v - -- C L1MB5_3end#LI 654 ATATG-TGGCCTTTTGTGTCTGGCTTCTTTCACTTAGCATAATGTT--TT 608 chr4qtel1M 696843 TAAGTCTC-TCCA-GTCCTCTC-TGTATTCATCCTGCTGATCATTTCTTA 696889 ii vi - - iv vv - ivi v v -- ivi i C L1MB5_3end#LI 607 CGAGGTTCATCCACGTTGTAGCATGTATCAGTACTTC--ATTCCTTTTTA 560 chr4qtel1M 696890 CAGAACAATAATATTCCATAACATTCATATACCATAATTTACCCAACCAT 696939 ii vvv vii vv i v iiii v C L1MB5_3end#LI 559 TGGCTGAATAATATTCCATTGTATGGATATACCACATTTTGTTTATCCAT 510 chr4qtel1M 696940 TCTCCAGTTGATGGGCATCC--ATTCATTTTCCAGCTTCTAACCACTATA 696987 vi v i ii--i --v v i ii i i i i C L1MB5_3end#LI 509 TCATCCGTTGATGGACATTTGGGTT--GTTTCCACCTTTTGGCTATTGTG 462 chr4qtel1M 696988 AAGAGGGCTGGCACAGCCATTTTGGCACATACAGGTCCTTTT-------C 697030 v v vi iiiv ---- iii i ?i v ------- C L1MB5_3end#LI 461 AATAGTGCTGCTATGAACATT----CGTGTACAAGTNTTTGTTTGAATAC 416 chr4qtel1M 697031 CTTTCTTAAGTATCTCTTTGGGGTATAAGCCCAGTAGAAACACTGCTGGA 697080 v i v i --- v vi i v viiv i i C L1MB5_3end#LI 415 CTGTTTTCAAT---TCTTTTGGGTATATACCTAGGAGTGGAATTGCTGGG 369 chr4qtel1M 697081 TCAAAGGGTATGTATTCACAGTTTGATAATTTTTTTGAG 697119 v v --- vvv i ----i C L1MB5_3end#LI 368 TCATATGGTA---ATTCTATGTTTAA----CTTTTTGAG 337 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 41.79 CpG sites = 56, Kimura (unadjusted) = 43.04 Transitions / transversions = 1.37 (56/41) Gap_init rate = 0.09 (28 / 324), avg. gap size = 1.25 (35 / 28) 535 32.36 1.78 2.14 chr4qtel1M 696812 697092 (302908) C L1ME4c_3end#LINE/L1 (191) 639 360 m_b208s551i5 8228 chr4qtel1M 696812 TTCTGCTCATTTCACTCAGCATCAGTTCATTTAAGT-CTCTCCAGTCCTC 696860 iv i i i vv -- ii-i i vviiv C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCAT--AAACATTTTCCATGTTGC 592 chr4qtel1M 696861 TCTGTATTCATCCTGCTGATCATTTCTTACAGAACAATAATATTCCATAA 696910 vii v v v iv v i v ii vvvv vi C L1ME4c_3end#L 591 TACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCG 542 chr4qtel1M 696911 CATTCATATACCATAATTTACCCAACCATTCTCCAGTTGATGGGCATCCA 696960 vi ?v i ii i vi v i ii C L1ME4c_3end#L 541 AGTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTA 492 chr4qtel1M 696961 --TTCATTTTCCAGCTTCTAACCACTATAAAGAGGGCTGGCACAGCCATT 697008 -- v-- ii i vi i i v iv vv iiiv i C L1ME4c_3end#L 491 GGTTG--TTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATC 444 chr4qtel1M 697009 TTGGCACATACAGGTCCTTTTCCTTTCTT--AAGTATCTCTTTGGGGTAT 697056 v ii i -- i ii -- v i i i i v C L1ME4c_3end#L 443 TTCGTGCATATAG--CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAA 396 chr4qtel1M 697057 AAGCCCAGTAGAAACACTGCTGGATCAAAGGGTATG 697092 vv v viiv i i i C L1ME4c_3end#L 395 ATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATG 360 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 42.67 CpG sites = 52, Kimura (unadjusted) = 44.01 Transitions / transversions = 1.41 (52/37) Gap_init rate = 0.03 (9 / 280), avg. gap size = 1.22 (11 / 9) 12 28.79 0.00 2.13 chr4qtel1M 697730 697777 (302223) (AGAATGA)n#Simple_repeat 1 47 (0) m_b208s252i14 8229 chr4qtel1M 697730 AGACTGAAGACTGAGTAAGGGGCAAAGAAAAGTGAAGAATGAAGCAAT 697777 v v iv v iiv v i i - (AGAATGA)n#Si 1 AGAATGAAGAATGAAGAATGAAGAATGAAGAATGAAGAATGAAG-AAT 47 Matrix = Unknown Transitions / transversions = 0.83 (5/6) Gap_init rate = 0.02 (1 / 47), avg. gap size = 1.00 (1 / 1) 63 23.59 4.86 0.52 chr4qtel1M 697994 698178 (301822) (AGAG)n#Simple_repeat 1 193 (0) m_b208s252i15 8230 chr4qtel1M 697994 AGAGAG-GAG-GAGGGA-AGTAAAGAG-GAAAG-GAAGGGGAGAAAGAGG 698038 - - i - - i - i - ii i i i (AGAG)n#Simpl 1 AGAGAGAGAGAGAGAGAGAG-AGAGAGAGAGAGAGAGAGAGAGAGAGAGA 49 chr4qtel1M 698039 GAGAGAGAGAGAGAGACAGAGAGAGAGAGAGAGAGAGAGAGAGAGGAAGT 698088 v ii v (AGAG)n#Simpl 50 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 99 chr4qtel1M 698089 GAAGGAGGGAGGGAGGGAGAGGGAGAGGGAAGGAGGGAGGGA-AGGAAAA 698137 ii i i i i i ii i i - ii i (AGAG)n#Simpl 100 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 149 chr4qtel1M 698138 GAGAGAGA-AAAGGGAAGGGGAGAG-GAAAAAATGAG-GAGAGA 698178 - i i ii i - i i iv - (AGAG)n#Simpl 150 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 193 Matrix = Unknown Transitions / transversions = 10.67 (32/3) Gap_init rate = 0.05 (10 / 184), avg. gap size = 1.00 (10 / 10) 16 9.71 0.00 0.00 chr4qtel1M 699530 699551 (300449) (C)n#Simple_repeat 1 22 (0) m_b208s252i16 8231 chr4qtel1M 699530 CCCCCCGCCCCCCCCTCCCCCC 699551 v i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCC 22 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 17 14.42 0.00 5.00 chr4qtel1M 700144 700185 (299815) (CAAAAC)n#Simple_repeat 1 40 (0) m_b208s252i17 8232 chr4qtel1M 700144 CAAAACAAAGACCAAAAACAAACCCAAATCCAATTAACCAAA 700185 v i v v v -- (CAAAAC)n#Sim 1 CAAAACCAAAACCAAAACCAAAACCAAAACCAA--AACCAAA 40 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.05 (2 / 41), avg. gap size = 1.00 (2 / 2) 33 0.00 0.00 0.00 chr4qtel1M 700788 700815 (299185) (AC)n#Simple_repeat 1 28 (0) c_b208s251i1 8233 chr4qtel1M 700788 ACACACACACACACACACACACACACAC 700815 (AC)n#Simple_ 1 ACACACACACACACACACACACACACAC 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 26 0.00 0.00 0.00 chr4qtel1M 702147 702171 (297829) (T)n#Simple_repeat 1 25 (0) c_b208s251i2 8234 chr4qtel1M 702147 TTTTTTTTTTTTTTTTTTTTTTTTT 702171 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 204 19.59 5.77 1.85 chr4qtel1M 702273 702324 (297676) MIRb#SINE/MIR 40 93 (175) m_b208s601i16 8235 chr4qtel1M 702273 TAGAGTCAGA-AGACCTGAGTTCAAATCCTATCTCTG--ACTTCATTAAA 702319 i - i i iiv -- - i iv MIRb#SINE/MIR 40 TGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTCTGCCACTT-ACTAGC 88 chr4qtel1M 702320 TGGGT 702324 v MIRb#SINE/MIR 89 TGTGT 93 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 18.10 CpG sites = 7, Kimura (unadjusted) = 23.40 Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.33 (4 / 3) 16 16.80 0.00 0.00 chr4qtel1M 703073 703099 (296901) (T)n#Simple_repeat 1 27 (0) m_b208s252i19 8236 chr4qtel1M 703073 TTTTTTTGTTTGTTTTGTTTTGTTTTT 703099 v v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTT 27 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 324 28.18 8.43 4.62 chr4qtel1M 704881 705319 (294681) C HERVK#LTR/ERVK (2236) 5300 4846 m_b209s701i0 8237 chr4qtel1M 704881 TCTGCTGAAGTCAGTGC----ATCTTTATCAAAAATTTAAAAA--TTAAT 704924 v - v---- i i - vi -- - C HERVK#LTR/ERV 5300 TCTGCAGAAGT-AGTGGTCTGATTTCTAT-AAATGTTTAAAAAATTTAA- 5254 chr4qtel1M 704925 GGTATAGAGAAGTAAATTTAAAAGTTC--TCTGGGG----TTAC---CC- 704964 i viv i --- v-- ----? --- - C HERVK#LTR/ERV 5253 AGTATAGAGTGCTAGATT---AAGTTGCATCTGGGGAGTGNTACACTCCT 5207 chr4qtel1M 704965 --ATGGCTCCTCCTTTCTTTTGTTT------TTGGAG----GAGTGTCTT 705002 --v v i ii ------ - ---- ii C HERVK#LTR/ERV 5206 TACTGTCTCCCCCTTCTTTTTGTTTAACCAATTG-AGCTTTGAGTGTTCT 5158 chr4qtel1M 705003 AATGTCTCTGTTTCTTCTACGATTGCCTGACCTTGAGGATTAAAGGGTAT 705052 v i----- ii v v v v i i v i v C HERVK#LTR/ERV 5157 ATTA-----GTTCTTTCAACTATGGCCTGTCCTTGGGAATTATAAGGAAT 5113 chr4qtel1M 705053 GCCAGTGGTGTGTAAAATCTTATACTGTGCACAAAAGTGTTCAAAATGT- 705101 v v v i iv i vi -iivi i i v iii ? i- C HERVK#LTR/ERV 5112 TCCTGTTGTATGTGTAATTTTCCACTG-ATTTAAGAATTTTTGGAANGCT 5064 chr4qtel1M 705102 ---CTAGAAGCATTTGCAGGCCCATTATCTGTTTTTATTTCTTGTGGCAC 705148 --- v - i i-- v i v v i v v C HERVK#LTR/ERV 5063 TTACTACA-GTATC--CTGGCCCATTGTCAGTTTTAATTTTTTCTGGAAC 5017 chr4qtel1M 705149 ACCCATAATTGCAAATGCCTGGATGAGGAAT-TCAGTGACCACTTGGGCT 705197 v i iv --v vi i vi - ivv v v -- vv C HERVK#LTR/ERV 5016 TCCCATGACAGCAAA--ACAAGATAATAAATGTTTTTTAACA--TGGGAA 4971 chr4qtel1M 705198 GTTTCTTTTGCTGT-TGGTA--TTGCAAAAGTGAAGCCTGAAAAGGTGTC 705244 vii i v - i -- vv vi iiv v i i C HERVK#LTR/ERV 4970 GTACTTTCTCCTGTCTGGCAGGTTGCCCATATGAAATGTGAATAAGTATC 4921 chr4qtel1M 705245 TACTATAACGTAGATAAAAGACAGATGACCAAAAGA-TTTATAATGGGTC 705293 v i v i i i ? v ivivv v -vv i - v v C HERVK#LTR/ERV 4920 AACTGTTACATGGACANATGACAATCTTCCAAATGAAGGTACA-TGCGTG 4872 chr4qtel1M 705294 ACATCCATTTGCCAGATTTCATTGGG 705319 v viv i C HERVK#LTR/ERV 4871 ACATCCATTTGCCATAACGCATTAGG 4846 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.75 CpG sites = 58, Kimura (unadjusted) = 36.12 Transitions / transversions = 0.97 (58/60) Gap_init rate = 0.08 (36 / 438), avg. gap size = 1.61 (58 / 36) 471 28.36 2.83 3.90 chr4qtel1M 704949 705337 (294663) C HERVK14C#LTR/ERVK (2321) 5113 4729 m_b209s701i1 8237 chr4qtel1M 704949 TTCTCTGGGGTTACCCATGGCTCCTCCTTTCTTTTGTTTTTGGAG--GAG 704996 -- v ------ i v v i-- C HERVK14C#LTR/ 5113 TTCTCTGG--TTCCCC------CCTTCTGTCTTTTGTTTTTGTAATTGAG 5072 chr4qtel1M 704997 TGTCTTAATGTC---TCTGTTTCTTCTACGATTGCCTGACCTTGAGGATT 705043 ?- i v i--- iv i iv v i v i ? i C HERVK14C#LTR/ 5071 N-TTTTAAGGTTCGATTAGCTCGTTCAACAATGGCTTGNCCTTGAGAATT 5023 chr4qtel1M 705044 AAAGGGTATGCCAGTGGTGTGTAAAATCTTATACTG-TGCACAAAAGTGT 705092 v v ? i? vv v ?vi i - v vi v i? C HERVK14C#LTR/ 5022 ATAGGGGATNCCAGTANTGTGTTTAATGTNCCATTGTTGAAGGAACGCNT 4973 chr4qtel1M 705093 TCAAAATGTCTAGAAGCATTTGCAGGCCCATTATCTGTTTTTATTTCTTG 705142 ?i i-? i vv ??i vvv v v i ? v ? i C HERVK14C#LTR/ 4972 NTAAAG-NTTTACTANNGTAGCCTGGGCCATTGTCNGTTTTAATNTTTTG 4924 chr4qtel1M 705143 TGGCACACCCATAATTGCAAATGCCTGGATGAGGAAT-TCAGTGACCACT 705191 v ii i i? i --v v viivi - vv v v - C HERVK14C#LTR/ 4923 TGGAATGCCCATGACNGCGAA--ACAGGAAAGCAAATGTCTTTTAACAC- 4877 chr4qtel1M 705192 TGGGCTGTTTCTTTTGCTG-TTGGTA--TTGCAAAAGTGAAGCCTGAAAA 705238 - i v i?v i i?v - i -- ? vv ?iii iivv C HERVK14C#LTR/ 4876 -GAGCAGCNGCCTCNCCTGTTTGGCAAGTNGCCCANACAAAATGAGAAAA 4828 chr4qtel1M 705239 GGTGTCTACTATAACGTAGATAAAAGACAGATGACCAAA-AGATTTATAA 705287 i vi ? i i iiv ? ? v vv -i? vv i- C HERVK14C#LTR/ 4827 GGTATCTACAGTNACATGGACGTANGANAGTTTCCCAAATGNAGGTAC-A 4779 chr4qtel1M 705288 TGGGTCACATCCATTTGCCAGATTTCATTGGGTCTCAAAACACAAGGGTT 705337 ? i ? viv? i ?vi vv v i? C HERVK14C#LTR/ 4778 TGGGTNACGTCCATTTGCCANAGCGNATTAGGNGCCAATCCTCGNGGGTT 4729 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.73 CpG sites = 52, Kimura (unadjusted) = 39.55 Transitions / transversions = 0.96 (52/54) Gap_init rate = 0.06 (22 / 388), avg. gap size = 1.18 (26 / 22) 486 30.82 3.63 3.63 chr4qtel1M 705017 705319 (294681) C HERVK11#LTR/ERVK (2673) 5280 4978 m_b209s701i2 8237 chr4qtel1M 705017 TTCTACGATTGCCTGACCTTGAGGATTAAAGGGTATGCCAGTGGTGTGTA 705066 i v iv v i iv i v v i ii i vi C HERVK11#LTR/E 5280 TTCCACCACAGCCTGTCCCTGAGGATTGTAAGGGATTCCGGTAATATGGG 5231 chr4qtel1M 705067 AAATCTTATACTGT-GCACAAA--AGTGTTCAAAATGTCTAGAAGCATTT 705113 iiivi - i -- i --- vvii vv i v C HERVK11#LTR/E 5230 AAATTCCCCACTGTTGCATAAATAAAT---CAAAAGCCTTACTAACATAT 5184 chr4qtel1M 705114 GCAGGCCCATTATCTGTTTTTATTTCTTGTGGCACACCCATAATTGCAAA 705163 v vv i i i vv i v vv i C HERVK11#LTR/E 5183 CCAGGGGCGTTGTCTGTCTTTATTTGATATGGAAGCCCCATAACTGCAAA 5134 chr4qtel1M 705164 TGCCTGGATGAGGAATTCAG-TGACC----ACTTGGGCTGTTTCTTTTGC 705208 - ------- i v - vii---- v i vi iiv C HERVK11#LTR/E 5133 -GC-------AAGAATACAGATGTTTTTTAACATGGGCCGTGCCTTCCCC 5092 chr4qtel1M 705209 TGTT-GGTA--TTGCAAAAGTGAAGCCTGAAAAGGTGTCTACTATAACGT 705255 - i -- v vv ii i i i i viv i C HERVK11#LTR/E 5091 TGTTTGGCAAGTAGCCCAGATAAAACCTGAGAAGGTATCTACAGAAACAT 5042 chr4qtel1M 705256 AGATAAAAGACAGATGACCAAAAGATTTATAATGGGTCACATCCATTTGC 705305 iv i v v ? vivi i vi vv i C HERVK11#LTR/E 5041 GCACATATGANAGTCTGCCAAAGGAGCTAACATGAGTCACATCCATTTGC 4992 chr4qtel1M 705306 CAGATTTCATTGGG 705319 v vv? i C HERVK11#LTR/E 4991 CATAAANCATTAGG 4978 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.10 CpG sites = 48, Kimura (unadjusted) = 40.85 Transitions / transversions = 1.14 (48/42) Gap_init rate = 0.06 (17 / 302), avg. gap size = 1.29 (22 / 17) 376 26.09 8.70 0.00 chr4qtel1M 707238 707372 (292628) C HERVK3#LTR/ERVK (3652) 3550 3404 m_b209s701i3 8238 chr4qtel1M 707238 CTTCTTTTGTAAGCTGGCGTGGTGAATTTAAAGCAGTGTCTCCCTTTAGA 707287 i v ? i v i v ? v vi i vi i C HERVK3#LTR/ER 3550 CCTCTTTAGTNAGTTGCCGCGGGGAATTTAANGAAGAATCTCCTTGCAGG 3501 chr4qtel1M 707288 GGTTGC------------AATTGATTGGTAGTTAAGCCTAGCACTGGACG 707325 v v------------ i v iv vi ii i C HERVK3#LTR/ER 3500 GTTTGGTAAAGATGTGTAAGTTGATAGGTAGCAATACCTAGCATCGGGCG 3451 chr4qtel1M 707326 CATCCATTGGATATCTCCTATCAATTTTTGGAAATCATTTAGGGTAT 707372 v v vi i vi v i ii v C HERVK3#LTR/ER 3450 CAGCCAATTAATATCCCCTAATAATTGTTGAAAATCATTTAAAGTCT 3404 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 31.22 CpG sites = 19, Kimura (unadjusted) = 33.42 Transitions / transversions = 1.12 (19/17) Gap_init rate = 0.01 (1 / 134), avg. gap size = 12.00 (12 / 1) 29 3.23 0.00 0.00 chr4qtel1M 707373 707404 (292596) (TTAGGG)n#Simple_repeat 1 32 (0) c_b209s251i0 8239 chr4qtel1M 707373 TTAGGGTTGGGGTTAGGGTTAGGGTTAGGGTT 707404 i (TTAGGG)n#Sim 1 TTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTT 32 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 21 0.00 0.00 0.00 chr4qtel1M 707719 707741 (292259) (C)n#Simple_repeat 1 23 (0) m_b209s252i2 8240 chr4qtel1M 707719 CCCCCCCCCCCCCCCCCCCCCCC 707741 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCC 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 576 24.59 1.64 0.00 chr4qtel1M 709727 709848 (290152) MIRc#SINE/MIR 25 148 (120) m_b209s601i0 8241 chr4qtel1M 709727 GAGTGCTGGGTCTGGAGTCAGGAAGACCAGAGTTCAAATCTGGACTCAGA 709776 ii iii v i i i iv i v v MIRc#SINE/MIR 25 GAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGC 74 chr4qtel1M 709777 TACATATTAATTGTA-GACCCTGGGCAAGTTACATAACC-CTGTTTGCCT 709824 i v i ii i- i i v - v vv MIRc#SINE/MIR 75 CACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCT 124 chr4qtel1M 709825 CAATTTTCTCATCAGTAAAATGAG 709848 i i v i MIRc#SINE/MIR 125 CAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.61 CpG sites = 20, Kimura (unadjusted) = 30.84 Transitions / transversions = 2.00 (20/10) Gap_init rate = 0.02 (2 / 121), avg. gap size = 1.00 (2 / 2) 202 30.82 8.29 8.80 chr4qtel1M 712667 712883 (287117) L2d2_3end#LINE/L2 337 552 (3) m_b209s601i1 8242 chr4qtel1M 712667 ATTGC--TATAACCTTGTTTCTCCAATTGTCTTGAA------TTTAAGAA 712708 i -- i i v ivi vivi ------ -- L2d2_3end#LIN 337 ACTGCCTTGTGACATCTCTTCTATTGTTGTCTTGAACTGTTATTTAA--A 384 chr4qtel1M 712709 CTTTGTATATATTTTATATTTATTC-TGTACTTATTTATTGTG----CAA 712753 ii - i v v vi v -i ii v v v---- L2d2_3end#LIN 385 TCTTGTAT-TGTTATTTAACTTTTCACGTGTTTATGTCTTGTCTCCCCAA 433 chr4qtel1M 712754 ATATTGATGCAAAAGTATGTCAGATCCT----GGAAAGGATGATGTCAGT 712799 v -- --------- v v ---- v i iv --- L2d2_3end#LIN 434 CTA--GAT---------TGTAAGCTCCTTGAGGGCAGGGACCATGTC--- 469 chr4qtel1M 712800 TTTAGAGTTCAGAGTGTCTCTC-CAGCACTGAGCCCAGAGCCTGGGCACA 712848 - v v vvv i i i - i iv v v v - L2d2_3end#LIN 470 -TTATACTTCTTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTG-CACA 517 chr4qtel1M 712849 TAGCAAGCATTTAATAAGTTACTGCCCGATTGATT 712883 i i i ii i i vvi iiviv L2d2_3end#LIN 518 CAGTAGGCGCTCAATAAATATTTGTTGATTTGATT 552 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.87 CpG sites = 32, Kimura (unadjusted) = 40.38 Transitions / transversions = 1.10 (32/29) Gap_init rate = 0.12 (25 / 216), avg. gap size = 1.48 (37 / 25) 260 27.49 8.11 3.63 chr4qtel1M 712699 712883 (287117) L2d_3end#LINE/L2 318 510 (6) m_b209s601i2 8242 chr4qtel1M 712699 AATTTAAGAACTT---TGTATA-TATTTTATATTTATTCTGTACTTATTT 712744 - v --- i - i i i -i v v i L2d_3end#LINE 318 AATTTA-GCACTTAATTATATACTGTCTTGTATT-GTTCTCTAATTGTTT 365 chr4qtel1M 712745 -AT-TGTGCAAATATTG-ATGCAAAAGTA---TGTCAGATCCT----GGA 712784 - - iv i v -v v vv v --- v v ---- v L2d_3end#LINE 366 CATGTGTGTTAGTCTTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGC 415 chr4qtel1M 712785 AAGGATGATGTCAGTTTTAG-AGTTCAGAGTGTCTCTCCAGCACTGAGCC 712833 i iv -- v v-?v i?vv - i iv i iv v L2d_3end#LINE 416 AGGGACCATGTC--TTATACTNTTTTNTCGT-TCCCCACAGCGCCTAGCA 462 chr4qtel1M 712834 CAGAGCCTGGGCACATAGCAAGCATTTAATAAGTTACTGCCCGATTGATT 712883 v - i i i ii i i- vvii L2d_3end#LINE 463 CAGTGC-TGAGCACATAGTAGGCGCTCAATAAA-TACTTGTTGATTGATT 510 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.43 CpG sites = 24, Kimura (unadjusted) = 35.14 Transitions / transversions = 0.96 (24/25) Gap_init rate = 0.08 (15 / 184), avg. gap size = 1.47 (22 / 15) 289 27.34 3.90 7.38 chr4qtel1M 712714 712867 (287133) L2a_3end#LINE/L2 350 498 (19) m_b209s601i3 8242 chr4qtel1M 712714 TATATATTTTATATTTATTCTGTACTTATTTATTGTGCAAATATTGATGC 712763 i-- --- i i vii-- v ivviv L2a_3end#LINE 350 TATATATTTTAC--TTATT---TATTTGTTTATTGTCTG--TCTCCCCCC 392 chr4qtel1M 712764 AAAAGTATGTCAGATCC----TGGAAAGGA-TGATGTCAGTTTTAGAGTT 712808 vv v v v ----v v i - vv v --- L2a_3end#LINE 393 ACTAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTCTGTTTT---GTT 439 chr4qtel1M 712809 CAGAG-TGTCTCTCCAGCACTGAGCCCAGAGCCTGGGCACATAGCAAGCA 712857 vv - v i i iv vv v - i i i L2a_3end#LINE 440 CACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGG-CACATAGTAGGCG 488 chr4qtel1M 712858 TTTAATAAGT 712867 i i i L2a_3end#LINE 489 CTCAATAAAT 498 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.01 CpG sites = 17, Kimura (unadjusted) = 34.04 Transitions / transversions = 0.77 (17/22) Gap_init rate = 0.09 (14 / 153), avg. gap size = 1.21 (17 / 14) 16 23.97 0.00 3.92 chr4qtel1M 714066 714118 (285882) (TTATT)n#Simple_repeat 1 51 (0) m_b209s252i3 8243 chr4qtel1M 714066 TTAATATATTATATTTCTATGAAATTTTTTATTTATGTGATTTCATTTTA 714115 v v v - vvv v - v v i (TTATT)n#Simp 1 TTATTTTATTTTATTT-TATTTTATTTTAT-TTTATTTTATTTTATTTTA 48 chr4qtel1M 714116 TTT 714118 (TTATT)n#Simp 49 TTT 51 Matrix = Unknown Transitions / transversions = 0.11 (1/9) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.00 (2 / 2) 277 32.52 2.45 5.70 chr4qtel1M 714264 714426 (285574) MIR3#SINE/MIR 13 170 (38) m_b209s601i4 8244 chr4qtel1M 714264 CTGAGGCAG---GACCACTGGGCTTGGGGTCAGTGGCCATGCCAGAAGTT 714310 - --- v - i v i vi v v -----i MIR3#SINE/MIR 13 CTGAG-CAGAGAGAGCAC-GGACTGGGAGTCAGGAGACCTG-----GGTT 55 chr4qtel1M 714311 GCAGTGCTAGTT-TCCCTCTGGTTACCTGGATGATCTTAGTCAAGTCACC 714359 vi v ii i - v v iii ?v vi i i v i MIR3#SINE/MIR 56 CTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACT 105 chr4qtel1M 714360 CCTTGACTCCCTGAGCCTCCACTGCATCACCTTTAACATGAGGGGGTCAG 714409 -- iiv i i vii v v i v v ii MIR3#SINE/MIR 106 --TCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGG 153 chr4qtel1M 714410 AACAGGAGGCCCCTGAG 714426 vi iv ii i i MIR3#SINE/MIR 154 ACTAGATGATCTCTAAG 170 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.22 CpG sites = 30, Kimura (unadjusted) = 44.58 Transitions / transversions = 1.50 (30/20) Gap_init rate = 0.07 (11 / 162), avg. gap size = 1.18 (13 / 11) 18 8.48 0.00 0.00 chr4qtel1M 716433 716457 (283543) (C)n#Simple_repeat 1 25 (0) m_b209s252i4 8245 chr4qtel1M 716433 CCACCCTCCCCCCCCCCCCCCCCCC 716457 v i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCC 25 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 335 13.54 3.80 6.49 chr4qtel1M 717164 717242 (282758) MIRb#SINE/MIR 114 190 (78) m_b209s601i5 8246 chr4qtel1M 717164 ACCTCTCTGAGCCTCAGTTTGCTCACCTAGAAAATGGGTAAAATCAGTCC 717213 v i iv v v v ---- MIRb#SINE/MIR 114 ACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAA---- 159 chr4qtel1M 717214 CACCTACCTCG--GGGCTGTT-TGGGGCATTA 717242 i -- i - i - MIRb#SINE/MIR 160 TACCTACCTCGCAGGGTTGTTGTGAGG-ATTA 190 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 14.96 CpG sites = 5, Kimura (unadjusted) = 14.96 Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.09 (7 / 78), avg. gap size = 1.14 (8 / 7) 28 30.78 1.92 5.30 chr4qtel1M 717523 717678 (282322) (GAG)n#Simple_repeat 1 151 (0) m_b209s252i5 8247 chr4qtel1M 717523 GAAGAGGAGGAGGTCACAGTGGAGTCAGAGAGGAAGA-GAGGCAGAAGGG 717571 i vvivi v -v - i - - i i (GAG)n#Simple 1 GAGGAGGAGGAGGAGGAGGAGGAG-GAG-GAGGAGGAGGAGG-AGGAGGA 47 chr4qtel1M 717572 GAAAGAGAAGAGGGAAGAAGGGGAGGATGGTGAGGCGTAGTGAAGAAGAG 717621 i i i ii i i i v iv v v - i i (GAG)n#Simple 48 GGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG-GAGGAGGAG 96 chr4qtel1M 717622 AAGCCGTGAGAGAGGGAGGATGAGGAAG-GGAGGAGAAAGAGGGAGGAGG 717670 i vv - - - v i - i i - (GAG)n#Simple 97 GAGGAG-GAG-GA-GGAGGAGGAGGAGGAGGAGGAGGAGGA-GGAGGAGG 142 chr4qtel1M 717671 -GCAGGGGG 717678 - v i (GAG)n#Simple 143 AGGAGGAGG 151 Matrix = Unknown Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.07 (11 / 155), avg. gap size = 1.00 (11 / 11) 13 3.96 7.69 0.00 chr4qtel1M 721344 721369 (278631) (TTTAA)n#Simple_repeat 1 28 (0) m_b209s252i6 8248 chr4qtel1M 721344 TTTAATTTAATTTAATTT--TTTACTTT 721369 -- v (TTTAA)n#Simp 1 TTTAATTTAATTTAATTTAATTTAATTT 28 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.04 (1 / 25), avg. gap size = 2.00 (2 / 1) 262 22.22 10.19 0.00 chr4qtel1M 723379 723486 (276514) C L1PB_orf2#LINE/L1 (1759) 1535 1417 m_b209s551i0 8249 chr4qtel1M 723379 GCTTC-TAAAAGGATTTTGGTAGGATTC----TTTCTCAACTTTTAAGAA 723423 - i v v v ---- v ii vvi C L1PB_orf2#LIN 1535 GCTTCATAGAATGATTTAGGGAGGATTCCCTCTTTCTCTATCTTGTGGAA 1486 chr4qtel1M 723424 TAATTTGGATGGTATGGGTAGTA----TTCTTT--ATGTTTGGTAGAATT 723467 i v vi i v v vi ---- -- i C L1PB_orf2#LIN 1485 TAGTGTCAATAGGATTGGTACCAATTCTTCTTTGAATGTCTGGTAGAATT 1436 chr4qtel1M 723468 CTCTTGTGAATCCTTCTAG 723486 ?vi v i C L1PB_orf2#LIN 1435 CNGCTGTGAATCCGTCTGG 1417 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 26.77 CpG sites = 11, Kimura (unadjusted) = 26.77 Transitions / transversions = 0.85 (11/13) Gap_init rate = 0.04 (4 / 107), avg. gap size = 2.75 (11 / 4) 16 18.23 4.35 2.13 chr4qtel1M 723494 723539 (276461) (GTA)n#Simple_repeat 1 47 (0) m_b209s252i7 8250 chr4qtel1M 723494 GTATTAGTAGTA-TA-TAGTAAATAAGAGTAGTGGTAGTAATAATAGT 723539 v - - - i iv i i i (GTA)n#Simple 1 GTAGTAGTAGTAGTAGTAGT-AGTAGTAGTAGTAGTAGTAGTAGTAGT 47 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.07 (3 / 45), avg. gap size = 1.00 (3 / 3) 15 13.66 2.17 6.82 chr4qtel1M 724203 724248 (275752) (TTTAT)n#Simple_repeat 1 44 (0) m_b209s252i8 8251 chr4qtel1M 724203 TTTATTTACTATTTTA-TTAATTTTATTTTATGCTCATTTCCTTTTA 724248 -- - v -i i iv (TTTAT)n#Simp 1 TTTATTT--TATTTTATTTTATTTTATTTTAT-TTTATTTTATTTTA 44 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.09 (4 / 45), avg. gap size = 1.00 (4 / 4) 17 0.00 0.00 0.00 chr4qtel1M 724297 724315 (275685) (T)n#Simple_repeat 1 19 (0) m_b209s252i9 8252 chr4qtel1M 724297 TTTTTTTTTTTTTTTTTTT 724315 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 646 26.98 7.87 2.19 chr4qtel1M 726028 726243 (273757) C MIRb#SINE/MIR (14) 254 27 m_b209s601i6 8253 chr4qtel1M 726028 CATTTATAGGATGCCTACTATGTACCATGCACAGTTTCTATG-GCT---- 726072 v iii i i v v v- v - ---- C MIRb#SINE/MIR 254 CATTTATTGAGCGCTTACTATGTGCCAGGCACTGTG-CTAAGCGCTTTAC 206 chr4qtel1M 726073 ATG----ATTTAATTTAATTCTTACAACCACTATGGGAGGTAAGTGCTAG 726118 ---- i v i i v iv v i ii - C MIRb#SINE/MIR 205 ATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTA- 157 chr4qtel1M 726119 CGTGATCCCCATTTTATAAGCTAGAAAACTGAGG--CAAAGAGGAAAAGT 726166 -- v i iiiv i -- i vv C MIRb#SINE/MIR 156 --TTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGT 109 chr4qtel1M 726167 GACTTGTGCAGGGTT------CCAGCCAGTGTCTGAGACTGGAATTAAAC 726210 i iv i i------ i iv v v v v v ii C MIRb#SINE/MIR 108 AACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAAC 59 chr4qtel1M 726211 TCAGATTTTACCGACTCTTAAGTCCAGCACTCT 726243 i i i vv i iv i - ii C MIRb#SINE/MIR 58 CCAGGTCTGTCTGACTCCAAAGCCC-GTGCTCT 27 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.81 CpG sites = 34, Kimura (unadjusted) = 34.37 Transitions / transversions = 1.48 (34/23) Gap_init rate = 0.05 (10 / 215), avg. gap size = 2.20 (22 / 10) 186 23.68 0.00 0.00 chr4qtel1M 726298 726335 (273665) MIRc#SINE/MIR 119 156 (112) m_b209s601i7 8254 chr4qtel1M 726298 GAATCACCATTCACTCATCTGTGAAATGGGGACAATAA 726335 ii v vi iv i i MIRc#SINE/MIR 119 GAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAA 156 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.40 CpG sites = 6, Kimura (unadjusted) = 29.40 Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 483 22.16 3.40 4.83 chr4qtel1M 726429 726575 (273425) C MIRc#SINE/MIR (122) 146 2 m_b209s601i8 8255 chr4qtel1M 726429 CATTTTATAGATAAG-AAATGGAGGCAAACAGGGAA---AAGTGACTGTC 726474 i i - iv v-- i i--- vv C MIRc#SINE/MIR 146 CATTTTACAGATGAGGAAACTGAGGCT--CAGAGAGGTTAAGTGACTTGC 99 chr4qtel1M 726475 CCAGGCTCACCTAGCTGGCCAGTGTTGAGGACAG-AGTTGAACGCAGGTC 726523 i v vi i iv viiii v i - v i v C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTC 49 chr4qtel1M 726524 TTTCTGACTCCAGGTCCAGTGCTCTGTGCACTATGGCACTCCCAGCTGCC 726573 i i v v --- - v - C MIRc#SINE/MIR 48 TTCCTGACTCCAAGTCCAGTGCTCTTTCCACT---GCAC-CACA-CTGCC 4 chr4qtel1M 726574 TC 726575 C MIRc#SINE/MIR 3 TC 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.65 CpG sites = 17, Kimura (unadjusted) = 26.57 Transitions / transversions = 1.21 (17/14) Gap_init rate = 0.07 (10 / 146), avg. gap size = 1.20 (12 / 10) 210 29.13 0.00 3.64 chr4qtel1M 727293 727349 (272651) L2d2_3end#LINE/L2 500 554 (1) m_b209s601i9 8256 chr4qtel1M 727293 AGTACAGTGTCTAATATATAATAGATACTTAATCAATATTTGTGGACTAC 727342 i i vii i i i iii i v v i -- L2d2_3end#LIN 500 AGCACAGTGCCTTGCACACAGTAGGCGCTCAATAAATATTTGTTGATT-- 547 chr4qtel1M 727343 TGACTTG 727349 i L2d2_3end#LIN 548 TGATTTG 554 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.64 CpG sites = 13, Kimura (unadjusted) = 40.35 Transitions / transversions = 4.33 (13/3) Gap_init rate = 0.04 (2 / 56), avg. gap size = 1.00 (2 / 2) 231 14.29 0.00 0.00 chr4qtel1M 728163 728204 (271796) C DNM1r#Unknown (2116) 2546 2505 m_b209s502i0 8257 chr4qtel1M 728163 TACAGATATGTATGTATATATATATATACACACACACACACA 728204 i ? i i i i i C DNM1r#Unknown 2546 TATANATACGTATATATACACATATATACACACATACACACA 2505 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 14.30 CpG sites = 6, Kimura (unadjusted) = 17.31 Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 12 14.12 3.03 3.03 chr4qtel1M 728483 728515 (271485) (CAGAGG)n#Simple_repeat 1 33 (0) m_b209s252i10 8258 chr4qtel1M 728483 CAGAGGTAGAGCCAAGATGCAGA-GCAGAGGAAG 728515 i v - v - v (CAGAGG)n#Sim 1 CAGAGGCAGAGGC-AGAGGCAGAGGCAGAGGCAG 33 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.06 (2 / 32), avg. gap size = 1.00 (2 / 2) 486 23.53 1.48 8.73 chr4qtel1M 729703 729837 (270163) MIRc#SINE/MIR 2 127 (141) m_b209s601i10 8259 chr4qtel1M 729703 GAGGCAGCTAGGTGGTTAAGTGAATAGAGCACCAACCCTGAAGTCAGGAG 729752 i--- vv i v iiiv i i i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr4qtel1M 729753 GACCTGAGTTCAAATCTGGTCTCAGACACCTAACACTTCTTAGCTGTGTG 729802 i i i iv v ------- iv vi MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCT-------CTGCCACTTACTAGCTGTGTG 91 chr4qtel1M 729803 ACCCCAGGCACGTCATTTAACTTCAACT--GCCTCAG 729837 iii v i i -v -- MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACCTC-TCTGAGCCTCAG 127 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.70 CpG sites = 19, Kimura (unadjusted) = 28.87 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.09 (12 / 134), avg. gap size = 1.08 (13 / 12) 807 30.88 5.65 2.35 chr4qtel1M 730443 731185 (268815) L1M4_orf2#LINE/L1 918 1684 (1610) m_b209s551i1 8260 chr4qtel1M 730443 TAAAAAAGCAAAAGGG---CAGGTCAATAAGTTGATCATACAACTAAAAA 730489 v i i i--- ii vi i i v v v v i L1M4_orf2#LIN 918 TAAAAAAGAAGAAAGATCTCAAATCAATAACCTAACCTTCCACCTTAAGA 967 chr4qtel1M 730490 AATTAGAAAAAGAA---CAAAATAAAAATTCCAAATTAAATGCCAAAATG 730536 i --- v ---i vi iiivv ii v L1M4_orf2#LIN 968 AACTAGAAAAAGAAGAGCAAACTAAA---CCCAAAGCAAGCAGAAGGAAG 1014 chr4qtel1M 730537 AAAATCCTAAAAATCAAAGGAGAGATTAATAAAATTGAAAGTTAGAAAAC 730586 i vv i i i vi i v i v i i - v L1M4_orf2#LIN 1015 GAAATAATAAAGATTAGAGCGGAAATAAATGAAATAGAGAAT-AGAAAAA 1063 chr4qtel1M 730587 CAATA-----AATTAATAAAAACTATGAGTTGGTTTTATGAAAAAGTCAA 730631 ----- i ii - i vi i v ii L1M4_orf2#LIN 1064 CAATAGAGAAAATCAACGAAA-CCAAAAGTTGGTTCTTTGAAAAGATCAA 1112 chr4qtel1M 730632 CAAA-TAGACAAACCATTGCTTAATTTGATTAAAATAA-------GAAAA 730673 - v v ivi ivi ii i v ------- i L1M4_orf2#LIN 1113 CAAAATTGACAAACCTTTAGCTAGACTGACCAAGAAAAAAAGAGAGAAGA 1162 chr4qtel1M 730674 C-CAAATTATTTATATTAAAAGTTAAAAAGGATAAATGTATCATCAA--T 730720 - i v v i ii i v i iv v - ii i i -- L1M4_orf2#LIN 1163 CTCAAATTACTAAAATCAGGAATGAAAGAGGGGACAT-TACTACCGACCT 1211 chr4qtel1M 730721 GACTAAGAAGTTAAAGTAATTATAA---ATTATTTTGCTTAATTATATAT 730767 v -- i v ivi --- v i v vvi i ii L1M4_orf2#LIN 1212 TAC--AGAAATAAAAAGGATTATAAGGGAATACTATGAACAATTGTATGC 1259 chr4qtel1M 730768 AAGCAAAGCTGACAATCTAAATGAAATGGATGGATATTTACAAAAATACA 730817 v i viv i i i iii vii v i i L1M4_orf2#LIN 1260 CAACAAATTAGATAACCTAGATGAAATGGACAAATTCCTAGAAAGACACA 1309 chr4qtel1M 730818 AACTACCTAGATTAATAGAAGAGGAAACAGAATACTTAAATAACCCTATT 730867 v i i i ivv i i v ii i iv v L1M4_orf2#LIN 1310 AACTACCGAAACTGACTCAAGAAGAAATAGAAAATCTGAATAGACCTATA 1359 chr4qtel1M 730868 TTAGAAAAATAAAATGAACAAGCTATAAATGAGCTCCCTA------AGAC 730911 vi iiv v i v iv iv v vi i i i ------ i v L1M4_orf2#LIN 1360 ACAAGTAAAGAGATTGAATTAGTAATCAAAAAACTTCCCACAAAGAAAAG 1409 chr4qtel1M 730912 CCCAACATCAGATGCATTTACAAGTGAATTCTACTAAACATTTAAAGAAT 730961 iv?i vv i vi i v L1M4_orf2#LIN 1410 CCCAGGNCCAGATGGCTTCACTGGTGAATTCTACCAAACATTTAAAGAAG 1459 chr4qtel1M 730962 GATTAATCCCAACACTATATTAACTATTTAAAAAAAAAAAAAAAACATGT 731011 i iv iv vi iv v iv v i i ----- v L1M4_orf2#LIN 1460 AATTAACACCAATCCTTCACAAACTCTTCCAAAAAATAGAAGA-----GG 1504 chr4qtel1M 731012 AAAGAAGAAATCCCATGAAATTTTTTCTATGACACAAATATT--TTTGAC 731059 ii v vv ---- i iv vi v i --ii i L1M4_orf2#LIN 1505 AGGGAACACTTCCC----AACTCATTCTATGAGGCCAGTATTACCCTGAT 1550 chr4qtel1M 731060 A--AAGGGGAGAATAAAA----ACAGAGAAAGAAAACTATAGACCAATTT 731103 -- iivv vv i ---- iii i v L1M4_orf2#LIN 1551 ACCAAAACCAGACAAAGACATCACAAGAAAAGAAAACTACAGACCAATAT 1600 chr4qtel1M 731104 CTTTAATGACTATCGATGCAAAATTTTTCAATAAAATGCCAGCAAG-GAA 731152 ii v v v v ii i i i i-vi L1M4_orf2#LIN 1601 CCCTTATGAATATAGATGCAAAAATCCTCAACAAAATACTAGCAAACCGA 1650 chr4qtel1M 731153 ATCACAGCAATATATCACA--GACCATGCACTATG 731185 - i v v -- ii i i L1M4_orf2#LIN 1651 ATC-CAGCAACATATAAAAAGGATTATACACCATG 1684 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.38 CpG sites = 137, Kimura (unadjusted) = 41.39 Transitions / transversions = 1.57 (137/87) Gap_init rate = 0.04 (32 / 742), avg. gap size = 1.88 (60 / 32) 686 22.37 0.69 0.69 chr4qtel1M 731186 731329 (268671) MIRc#SINE/MIR 2 145 (123) m_b209s601i11 8261 chr4qtel1M 731186 GAAGCTAGGTGGTGCAGTGGATATTGTATCAGGTCTGGAGTCAGGAAGAC 731235 i viv v vv i iii iii MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr4qtel1M 731236 CCACGTTGAAATCCAGTCTCAGACACTTACTAGCTATATGACCCTGGGCA 731285 iiv vi i v v v v i i i MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 101 chr4qtel1M 731286 AGTCACTTAACC-CTGTTTGCCTCAGTTTTTCTCATATGTAAAAT 731329 - v vv - i v MIRc#SINE/MIR 102 AGTCACTTAACCTCTCTGAGCCTCAG-TTTCCTCATCTGTAAAAT 145 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.92 CpG sites = 17, Kimura (unadjusted) = 26.86 Transitions / transversions = 1.13 (17/15) Gap_init rate = 0.01 (2 / 143), avg. gap size = 1.00 (2 / 2) 416 31.31 12.33 0.24 chr4qtel1M 731438 731802 (268198) L1MC_orf2#LINE/L1 1685 2093 (1201) m_b209s551i3 8260 chr4qtel1M 731438 ACCAAGTTGGATTTGTATCAGGAATTCAGGATTTGTTCAATGTTAGGAAA 731487 v i vi v v i ii v ii v i L1MC_orf2#LIN 1685 ACCAAGTGGGATTTATCCCAGGTATGCAAGGCTGGTTCAACATTCGAAAA 1734 chr4qtel1M 731488 ACTATCAGCATGATTAACCATATCAATAATAAAAACAACAAAAA--ATAT 731535 v v i iii i iv i i i ivvv v v -- i L1MC_orf2#LIN 1735 TCAATTAATGTAATCCATCACATCAACAGGCTAAAGAAGAAAAATCACAT 1784 chr4qtel1M 731536 AATTATGTCAATAGTTGCAGAAAAAATCTTTGATAAAAT---ACACCTTT 731582 i i i v iiv i --- iv L1MC_orf2#LIN 1785 GATCATATCAATAGATGCAGAAAAAGCATTTGACAAAATCCAACACCCAT 1834 chr4qtel1M 731583 TACTATTAAAAACACT-AGAAAACATAGTAATCCAGT----CTTTCTTAA 731627 vv iv v - v - v vv v---- i i L1MC_orf2#LIN 1835 TCATGATAAAAACTCTCAGCAAAC-TAGGAATAGAGGGGAACTTCCTCAA 1883 chr4qtel1M 731628 TATGTTAAGAACTATCTATATAAAACCAAGAACAAGCATTATCTATAACA 731677 iv v ii vi i v v v i v i i viv ii L1MC_orf2#LIN 1884 CTTGATAAAGAACATCTACAAAAAACCTACAGCTAACATCATACTTAATG 1933 chr4qtel1M 731678 --GATAAACTTGA---------------------------------ATGT 731692 -- v ? --------------------------------- L1MC_orf2#LIN 1934 GTGAGAAACTNGAAGCTTTCCCGCTAAGATCAGGAACAAGGCAAGGATGT 1983 chr4qtel1M 731693 CCATTATCACCACCATTATTTAATGTTGTATGAGAAATGTCAATTATGGC 731742 vi v ivi v i ii i ivi i vii ii vv L1MC_orf2#LIN 1984 CCCCTCTCACCACTCCTTTTCAACATCGTACTGGAAGTCCTAGCTAATGC 2033 chr4qtel1M 731743 AATAAGACAAGGAAAAGAAATTGAAGAAATAAAAATAGGTCACAAGGAAA 731792 i i vi iv v i v vv vi i L1MC_orf2#LIN 2034 AATAAGACAAGAAAAGGAAATAAAAGGTATACAGATTGGGAAGGAAGAAA 2083 chr4qtel1M 731793 CAAAACTATC 731802 i i L1MC_orf2#LIN 2084 TAAAACTGTC 2093 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.20 CpG sites = 63, Kimura (unadjusted) = 41.68 Transitions / transversions = 1.24 (63/51) Gap_init rate = 0.02 (7 / 364), avg. gap size = 6.57 (46 / 7) 450 29.00 4.31 0.41 chr4qtel1M 731438 731669 (268331) L1M4_orf2#LINE/L1 1685 1925 (1369) m_b209s551i2 8260 chr4qtel1M 731438 ACCAAGTTGGATTTGTATCAGGAATTCAGGATTTGTTCAATGTTAGGAAA 731487 v i vi v i i v ii ?v i L1M4_orf2#LIN 1685 ACCAAGTGGGATTTATCCCAGGAATGCAAGGTTGGTTCAACATNCGAAAA 1734 chr4qtel1M 731488 ACTATCAGCATGATTAACCATATCAATAATAAAAACAACAAAAA--ATAT 731535 v v iii i vv i iv v vi -- i L1M4_orf2#LIN 1735 TCAATCAATGTAATACACCATATTAATAGAATAAAGGACAAAAACCACAT 1784 chr4qtel1M 731536 AATTATGTCAATAGTTGCAGAAAAAATCTTTGATAAAAT---ACACCTTT 731582 i i v vi iiv i --- i L1M4_orf2#LIN 1785 GATCATCTCAATAGACGCAGAAAAAGCATTTGACAAAATCCAACACCCTT 1834 chr4qtel1M 731583 TACTATTAAAAACACT-AGAAAACATAGTAATCCAGT----CTTTCTTAA 731627 vv iv - iv - v vv iv---- i i L1M4_orf2#LIN 1835 TCATGATAAAAACACTCAACAAAC-TAGGAATAGAAGGGAACTTCCTCAA 1883 chr4qtel1M 731628 TATGTTAAGAACTATCTATATAAAACCAAGAACAAGCATTAT 731669 iv v iiivi iiv v v i v i i L1M4_orf2#LIN 1884 CCTGATAAAGGGCATCTACGAAAAACCCACAGCTAACATCAT 1925 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.16 CpG sites = 37, Kimura (unadjusted) = 37.65 Transitions / transversions = 1.23 (37/30) Gap_init rate = 0.02 (5 / 231), avg. gap size = 2.20 (11 / 5) 343 30.98 1.40 0.69 chr4qtel1M 731687 731829 (268171) L1M5_orf2#LINE/L1 1978 2121 (1173) m_b209s551i4 8260 chr4qtel1M 731687 GAATGTCCATTATCACCACCATTATTTAATGTTGTATGAGAAATGTCAAT 731736 i ii ? ivi i ii ivi ii vii ii L1M5_orf2#LIN 1978 GGATGTCCGCTNTCACCACTTCTATTCAACATTGTACTGGAGGTCCTAGC 2027 chr4qtel1M 731737 TATGGCAATAAGACAAGGAAAAGAAATTGAAGAAATAAAAATAGGTCACA 731786 i vv i i vi iv i v vv vi L1M5_orf2#LIN 2028 CAGTGCAATAAGGCAAGAAAAAGAAATAAAAGGCATAAAGATTGGAAAGG 2077 chr4qtel1M 731787 AGGAAACAAAACTATCACTCT--GTGGATGATAACGATGGTATAC 731829 i i i ?i v -- ii i- i v ? L1M5_orf2#LIN 2078 AAGAAATAAAACTGTCNTTATTCGCAGATGAC-ATGATTGTNTAC 2121 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 42.57 CpG sites = 31, Kimura (unadjusted) = 43.96 Transitions / transversions = 2.38 (31/13) Gap_init rate = 0.01 (2 / 142), avg. gap size = 1.50 (3 / 2) 323 29.97 9.05 1.15 chr4qtel1M 732824 733066 (266934) C L1ME3G_3end#LINE/L1 (546) 378 117 m_b209s551i5 8262 chr4qtel1M 732824 GTGGTATTGCTGGGTCAAATGATATGCATAGTTTAGGGAATCTGATGACA 732873 v v i ii v --- i v vv v C L1ME3G_3end#L 378 GTGGAATTGCTGGGTCAAAGGGTATGCGCATTTTA---AATTTTAATAGA 332 chr4qtel1M 732874 TAGTTCTAAATTGCTTTTGAAAATGACTG---CAATTT-------CATCG 732913 v v i ii iv ? i --- ------- i i C L1ME3G_3end#L 331 TACTGCCAAATTGCCCTCCAAAANGGCTGTACCAATTTACACTCCCACCA 282 chr4qtel1M 732914 GGAGC--ATGGATGCAACTATTTTCT-ATATTTCTTCCAACAATGAGAAT 732960 v i-- iiv i v ii i i- i iiiiiv v ?iiv C L1ME3G_3end#L 281 GCAGTGTATGAGAGTACCCGTTTCCCCACACCCTCGCCAACACTNGATAT 232 chr4qtel1M 732961 TTCCCTCCTTTGTCATTTTTGCCAGTGTGAT-GGTGGTGAGCAGAGTCTG 733009 vi vv? vvv i v - ivi iii vi v C L1ME3G_3end#L 231 TATCAANCTTTTAAATTTTTGCCAATCTGATGGGTGAAAAATGGTATCTC 182 chr4qtel1M 733010 A--GTTGCTTTAATGTACATCTCTCTCA----CAGTAATTTAGAGCATCT 733053 -- i v i i i v ----i i vv v C L1ME3G_3end#L 181 ATTGTTGTTTTAATTTGCATTTCCCTGATTACTAGTGAGGTTGAGCATCT 132 chr4qtel1M 733054 TTTC--ATGTTTATT 733066 -- C L1ME3G_3end#L 131 TTTCATATGTTTATT 117 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.76 CpG sites = 41, Kimura (unadjusted) = 39.97 Transitions / transversions = 1.32 (41/31) Gap_init rate = 0.05 (11 / 242), avg. gap size = 2.27 (25 / 11) 15 19.86 0.00 0.00 chr4qtel1M 733402 733436 (266564) (TGGCTC)n#Simple_repeat 1 35 (0) m_b209s252i11 8263 chr4qtel1M 733402 TGGCTTTATCTCTAGCTCTGGTTCTGGCTCAGGCT 733436 i iv i i v (TGGCTC)n#Sim 1 TGGCTCTGGCTCTGGCTCTGGCTCTGGCTCTGGCT 35 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 197 24.45 0.00 2.22 chr4qtel1M 738724 738769 (261231) C L3b_3end#LINE/CR1 (3) 1203 1159 m_b209s601i12 8264 chr4qtel1M 738724 AAAATCACAAGAATTTCACAACTGGAAAGGAACTTGGAAGCCATTT 738769 i i - i v i v ii i i i C L3b_3end#LINE 1203 AAAACCATA-GAATCTCAGAATTGGAAAGGACCTCAGAGGTCATCT 1159 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.72 CpG sites = 9, Kimura (unadjusted) = 31.72 Transitions / transversions = 4.50 (9/2) Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1) 20 11.26 0.00 0.00 chr4qtel1M 738971 738999 (261001) (A)n#Simple_repeat 1 29 (0) m_b209s252i13 8265 chr4qtel1M 738971 AAAAAAAAAAAAAAAAATAAAACAACAAA 738999 v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA 29 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 12 18.36 5.41 0.00 chr4qtel1M 738969 739005 (260995) (ACAA)n#Simple_repeat 1 39 (0) m_b209s252i12 8266 chr4qtel1M 738969 ACAAA-AAA-AAAAAAAAAAATAAAACAACAAACACACA 739005 - - v v i vv v (ACAA)n#Simpl 1 ACAAACAAACAAACAAACAAACAAACAAACAAACAAACA 39 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 245 31.59 2.13 3.00 chr4qtel1M 739600 739834 (260166) L1M1_orf2#LINE/L1 1516 1748 (1546) m_b209s551i6 8267 chr4qtel1M 739600 CCAAACTTGTTTGATGAGGAAAATATAGTTCAACTACCAAAACTAG-CAA 739648 ii iv i vv i viii viv i - L1M1_orf2#LIN 1516 CCAAACTCATTCTACGAGGCCAGTATTACCCTGATACCAAAACCAGACAA 1565 chr4qtel1M 739649 AGGTTAAAGCAAAGAAAGAGAATTATA-GCCAATATTATTAA-GAATTTT 739696 i-i v v i i i i - ivi i - v L1M1_orf2#LIN 1566 AGA-CACATCAAAAAAAGAAAACTACAGGCCAATATCTCTGATGAATATT 1614 chr4qtel1M 739697 TAAAAAGAAAT--TAAATGAAATCTTGGCTAAAGGATAACAGCAATTTAC 739744 v viv i -- v ii vi i v vv vvv i -- L1M1_orf2#LIN 1615 GATGCAAAAATCCTCAACAAAATACTAGCAAACCGAATTCAACAA--TAC 1662 chr4qtel1M 739745 CAATTAAAAAAAAATAATTTTCTATTATCAAATTGGATATATATCTGGAA 739794 -- -- i v ivii v i i v v vi ? i L1M1_orf2#LIN 1663 --ATT--AAAAAGATCATTCATCATGACCAAGTGGGATTTATCCCNGGGA 1708 chr4qtel1M 739795 TGCAAGGATGATTCACCATTAGGAAGACAATTAACATAAT 739834 i v vv v iv i ii i L1M1_orf2#LIN 1709 TGCAAGGATGGTTCAACATACGCAAATCAATCAATGTGAT 1748 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.50 CpG sites = 40, Kimura (unadjusted) = 42.28 Transitions / transversions = 1.25 (40/32) Gap_init rate = 0.05 (11 / 234), avg. gap size = 1.09 (12 / 11) 15 10.38 3.03 0.00 chr4qtel1M 740581 740598 (259402) (TACTAT)n#Simple_repeat 1 18 (16) m_b210s252i0 8268 chr4qtel1M 740581 TACTATTACTATTATTAT 740598 i (TACTAT)n#Sim 1 TACTATTACTATTACTAT 18 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 26 0.00 0.00 0.00 chr4qtel1M 740599 740623 (259377) (TGC)n#Simple_repeat 1 25 (0) c_b210s251i0 8269 chr4qtel1M 740599 TGCTGCTGCTGCTGCTGCTGCTGCT 740623 (TGC)n#Simple 1 TGCTGCTGCTGCTGCTGCTGCTGCT 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 15 10.38 3.03 0.00 chr4qtel1M 740624 740637 (259363) (TACTAT)n#Simple_repeat 19 33 (1) m_b210s252i0 8270 chr4qtel1M 740624 ACTACTA-TACTACT 740637 i - i (TACTAT)n#Sim 19 ACTATTACTATTACT 33 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.08 (1 / 13), avg. gap size = 1.00 (1 / 1) 321 26.08 15.09 1.10 chr4qtel1M 740664 740822 (259178) C MIR1_Amn#SINE/MIR (5) 225 45 m_b210s601i0 8271 chr4qtel1M 740664 AATAGCTAGCTCTTATTTAGGACTTT--AT--GTATATTCTCACTTGATC 740709 v v v -- -- v - vvvv - C MIR1_Amn#SINE 225 AATACCTAGCTCTTATGTAGCACTTTTCATCAGTAGAT-CTCAAAGCA-C 178 chr4qtel1M 740710 TTCACAA-------CAAT---------CCTATTTTACAGATGGGGAAACC 740743 i ------- i --------- i i i C MIR1_Amn#SINE 177 TTTACAAAGGAGGTCAGTATCATTATCCCCATTTTACAGATGAGGAAACT 128 chr4qtel1M 740744 AAGGTTGAGAGAGACTAGGTGACTTGTTCA--GTAGCTGAGATA--AAGG 740789 i i?v ii? i ii -- vi ?v v?i--? v C MIR1_Amn#SINE 127 GAGGCNCAGAGAGGTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNAGT 78 chr4qtel1M 740790 ATCTGAAGCCAGACAGGAACTTAGATTTTCCAA 740822 iv v iv vi ?v? ii i i i i C MIR1_Amn#SINE 77 GGCAGAGCCGGGANTNGAACCCAGGTCTCCCGA 45 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 33.64 CpG sites = 23, Kimura (unadjusted) = 34.68 Transitions / transversions = 1.28 (23/18) Gap_init rate = 0.05 (8 / 158), avg. gap size = 3.25 (26 / 8) 338 22.83 27.17 0.00 chr4qtel1M 740682 740773 (259227) C MIRb#SINE/MIR (53) 215 99 m_b210s601i1 8271 chr4qtel1M 740682 AGGACTTTATGTATATT--CTCACTTGATCTTCACAACAATCCT------ 740723 vi ii ii -- i i i i ------ C MIRb#SINE/MIR 215 AGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGG 166 chr4qtel1M 740724 -----------------ATTTTACAGATGGGGAAACCAAGGTTGAGAGAG 740756 ----------------- i ii i v C MIRb#SINE/MIR 165 TAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAG 116 chr4qtel1M 740757 ACTAGGTGACTTGTTCA 740773 ii i i ii C MIRb#SINE/MIR 115 GTTAAGTAACTTGCCCA 99 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 27.94 CpG sites = 19, Kimura (unadjusted) = 29.64 Transitions / transversions = 9.50 (19/2) Gap_init rate = 0.03 (3 / 91), avg. gap size = 8.33 (25 / 3) 332 30.00 4.00 0.00 chr4qtel1M 740721 740820 (259180) C MIRc#SINE/MIR (120) 148 45 m_b210s601i2 8271 chr4qtel1M 740721 CCTATTTTACAGATGGGGAAACCAAGGTTGAGAGAGACTAGGTGACTTGT 740770 i i ii i v ii i i C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr4qtel1M 740771 TCA--GTAGCTGAGATA--AAGGATCTGAAGCCAGACAGGAACTTAGATT 740816 i -- vi vv v -- viv v iv vi vv ii i i C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTC 49 chr4qtel1M 740817 TTCC 740820 C MIRc#SINE/MIR 48 TTCC 45 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 39.56 CpG sites = 18, Kimura (unadjusted) = 39.56 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.02 (2 / 99), avg. gap size = 2.00 (4 / 2) 22 11.13 0.00 2.50 chr4qtel1M 740861 740901 (259099) (AACA)n#Simple_repeat 1 40 (0) m_b210s252i1 8272 chr4qtel1M 740861 AAAAAACAAACAAACAAACAAAAAACCAAAACAAAAAAACA 740901 v v v - v (AACA)n#Simpl 1 AACAAACAAACAAACAAACAAACAAAC-AAACAAACAAACA 40 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 16 21.70 0.00 0.00 chr4qtel1M 742934 742965 (257035) (C)n#Simple_repeat 1 32 (0) m_b210s252i3 8273 chr4qtel1M 742934 CCCCCCTCCCCTCCCACGGCCCCCCTCCCCCC 742965 i i v vv i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 32 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 222 13.51 0.00 0.00 chr4qtel1M 743331 743367 (256633) MIR1_Amn#SINE/MIR 115 151 (79) m_b210s601i3 8274 chr4qtel1M 743331 CCCCCCACGCCTCAGTTTCCTCCTCTGTAAAATGGGG 743367 i i ii? v MIR1_Amn#SINE 115 CTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGG 151 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 15.81 CpG sites = 4, Kimura (unadjusted) = 15.81 Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 234 3.45 0.00 0.00 chr4qtel1M 743339 743367 (256633) MIRc#SINE/MIR 121 149 (119) m_b210s601i4 8274 chr4qtel1M 743339 GCCTCAGTTTCCTCCTCTGTAAAATGGGG 743367 v MIRc#SINE/MIR 121 GCCTCAGTTTCCTCATCTGTAAAATGGGG 149 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 3.54 CpG sites = 0, Kimura (unadjusted) = 3.54 Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 15 0.00 8.00 0.00 chr4qtel1M 743487 743511 (256489) (GCCC)n#Simple_repeat 1 27 (0) m_b210s252i4 8275 chr4qtel1M 743487 GCCC-CCC-CCCGCCCGCCCGCCCGCC 743511 - - (GCCC)n#Simpl 1 GCCCGCCCGCCCGCCCGCCCGCCCGCC 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.08 (2 / 24), avg. gap size = 1.00 (2 / 2) 181 16.22 2.70 0.00 chr4qtel1M 745302 745338 (254662) C MIR3#SINE/MIR (59) 149 112 m_b210s601i5 8276 chr4qtel1M 745302 CCGCCTTGTATTACAGAAGAG-AAACTGAGGCCCACAG 745338 v ii v v - v C MIR3#SINE/MIR 149 CCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAG 112 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 18.27 CpG sites = 2, Kimura (unadjusted) = 18.27 Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 355 29.12 4.55 1.90 chr4qtel1M 750127 750280 (249720) C L1ME3Cz_3end#LINE/L1 (787) 210 53 m_b210s551i1 8277 chr4qtel1M 750127 CCAATCTCATGAGTGTGAGACG---CGCCACAGTTGTTTGAATTCACATT 750173 v i i i ---ivi iv ? v ii C L1ME3Cz_3end# 210 CCAATCTGATGGGTGTGAAATGGTATCTCATTGTNGTTTTAATTTGCATT 161 chr4qtel1M 750174 TCTGTAATCAGTAGTGGCTTAGAGCAT-GTTTCACAT---TAGTAGAGAA 750219 iv i i v ivv v -v i --- v i vv - C L1ME3Cz_3end# 160 TCCCTGATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCA- 112 chr4qtel1M 750220 AGCTTTGATTTCTCCCTCTGAGAACTACCCGCTTATATCCTTTGACCATT 750269 --i iv i ii i v i i i i i v C L1ME3Cz_3end# 111 --TTCGGGTTTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATT 64 chr4qtel1M 750270 TATTAATTGGG 750280 v iv C L1ME3Cz_3end# 63 TTTCTATTGGG 53 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 37.18 CpG sites = 26, Kimura (unadjusted) = 38.29 Transitions / transversions = 1.44 (26/18) Gap_init rate = 0.04 (6 / 153), avg. gap size = 1.67 (10 / 6) 351 28.22 9.82 0.00 chr4qtel1M 750655 750817 (249183) C L2d2_3end#LINE/L2 (8) 547 369 m_b210s601i6 8278 chr4qtel1M 750655 AATCAACAAGCTTTTAA-AAGTACCGTCTATGTGCCAGGTACTGTGCTAA 750703 iiv v-i ii vv i v i i C L2d2_3end#LIN 547 AATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAG 498 chr4qtel1M 750704 GTGCTGAATGTGA---AAAGAGGCAAAAGACAC--TACCAGCTTTCAAGG 750748 i viv v --- i i v i-- v v ii C L2d2_3end#LIN 497 GCGCTGTGGGGGATACAAAGAAGTATAAGACATGGTCCCTGCCCTCAAGG 448 chr4qtel1M 750749 A-CTCCCAGATTAATAGGGGTG---GGA-ATAACCATGT-ACAAGCAAAG 750792 - iv ivi i v v ---i - v i - v iv i C L2d2_3end#LIN 447 AGCTTACAATCTAGTTGGGGAGACAAGACATAAACACGTGAAAAGTTAAA 398 chr4qtel1M 750793 TA--TATACAAAATT--AATTGGAGTTCA 750817 --v i -- viv C L2d2_3end#LIN 397 TAACAATACAAGATTTAAATAACAGTTCA 369 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 33.09 CpG sites = 25, Kimura (unadjusted) = 36.05 Transitions / transversions = 1.19 (25/21) Gap_init rate = 0.06 (9 / 162), avg. gap size = 1.78 (16 / 9) 329 20.93 3.09 6.38 chr4qtel1M 752963 753059 (246941) MIR#SINE/MIR 107 200 (62) m_b210s601i8 8279 chr4qtel1M 752963 ACCTCTCTGAGCCTCAGTTTGCTCACCTAGAAAATGGGTAAAATCAGTCC 753012 v v i iv v v - i vv MIR#SINE/MIR 107 ACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAAT-AATAG 155 chr4qtel1M 753013 CACCTACCTC--GGGGCTGTT-TGGGGCATTAGGGGCATAAATCAATTCA 753059 i --i i - i - i---- i i i v MIR#SINE/MIR 156 TACCTACCTCATAGGGTTGTTGTGAGG-ATTAA----ATGAGTTAATACA 200 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 24.83 CpG sites = 11, Kimura (unadjusted) = 24.83 Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.08 (8 / 96), avg. gap size = 1.12 (9 / 8) 353 13.54 3.80 6.49 chr4qtel1M 752963 753041 (246959) MIRb#SINE/MIR 114 190 (78) m_b210s601i7 8279 chr4qtel1M 752963 ACCTCTCTGAGCCTCAGTTTGCTCACCTAGAAAATGGGTAAAATCAGTCC 753012 v i iv v v v ---- MIRb#SINE/MIR 114 ACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAA---- 159 chr4qtel1M 753013 CACCTACCTCG--GGGCTGTT-TGGGGCATTA 753041 i -- i - i - MIRb#SINE/MIR 160 TACCTACCTCGCAGGGTTGTTGTGAGG-ATTA 190 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 14.96 CpG sites = 5, Kimura (unadjusted) = 14.96 Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.09 (7 / 78), avg. gap size = 1.14 (8 / 7) 14 19.39 1.89 5.88 chr4qtel1M 755216 755268 (244732) (GGCAGAG)n#Simple_repeat 1 51 (0) m_b210s252i5 8280 chr4qtel1M 755216 GGCA-AAGGTAGAGATAAGAAGGGCAGAGGACAGAGGGTCCAGTGGACAG 755264 - i i ivv - i -- v i (GGCAGAG)n#Si 1 GGCAGAGGGCAGAGGGCAG-AGGGCAGAGGGCAGAGGG--CAGAGGGCAG 47 chr4qtel1M 755265 AGGG 755268 (GGCAGAG)n#Si 48 AGGG 51 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.08 (4 / 52), avg. gap size = 1.00 (4 / 4) 755 31.27 2.59 8.88 chr4qtel1M 758368 758869 (241131) C HERVP71A#LTR/ERV1 (2301) 5289 4817 m_b210s701i0 8281 chr4qtel1M 758368 ACTATGAACTCCAAAGGTGTTATCTGGATCAGTAATCCTTGTTTTCTAAG 758417 iii v i i vvi i ii v i v vvi C HERVP71A#LTR/ 5289 ACCGCGAACTCAAGAGGCGGAGTTTGAGTCAGAAGTCCTTTTAACCTAAG 5240 chr4qtel1M 758418 GGCTAAAATGGGATGACGGTTAATAACTCTAAATGCCAGTATATAGTTTC 758467 v i v -- i iv --- ---- i--- i C HERVP71A#LTR/ 5239 GGATGACA--GGGTGGAGG---ATA----TG---GCCAGTATATAATTTC 5202 chr4qtel1M 758468 TTAAAAACTTATCCTTTGTTTCAAAAG-----AGGTCTTTTCCTTTTTTT 758512 i i vi v v v ----- i v vv ii v--- C HERVP71A#LTR/ 5201 TTAAGAATTGGTCCTTGGTTTCCATAGTAGGAAGATCTGTAGCCCTG--- 5155 chr4qtel1M 758513 TTCCCCAAATAAAAGTAAACCAAGCAGCATCACATCTGGGGAAGATCACT 758562 --- vii ---------- -i i --------i v C HERVP71A#LTR/ 5154 ---CCCAAATATGGG----------AGC-CCATAT--------AATAACT 5127 chr4qtel1M 758563 TCT--GGGAACAGTTCTAATTTTTTTTTT-----TTTTTTTTTTTTAATA 758605 iv -- i i i i v i i ----- v ii vv ii vi C HERVP71A#LTR/ 5126 CGTAGGGGGACAATCCCAAGTCTTTTCTTGGGGCTGTCCTAATCCTAAGG 5077 chr4qtel1M 758606 AA-ACAATGGGCAAGCATTTGGTCCAAGGCAATCTAGTCTCTAACATCAA 758654 i-i v v v ii v i i v i i C HERVP71A#LTR/ 5076 AGTGCTATTGGGAGACATTTGGTCCAAGGCATTTTAGTTTCTAAGATTAG 5027 chr4qtel1M 758655 TTTAGTAATCCATTTCTTAAGAATCTGATTCATTCTTTTTACTTTCTCTG 758704 i i viii i i i i i i ii v C HERVP71A#LTR/ 5026 TTTGGTGATATGCTTTTTGAGAGTTTGATTCATTCTTTCTACCTTTCCAG 4977 chr4qtel1M 758705 ATGAGGGCAGTTGCCTAGGTACGTGGAATTGTCACTCAATTTGCAATCCT 758754 v i vi v v vii iv v vi iii i v C HERVP71A#LTR/ 4976 AGGAAGGGGGATGCCAAGGGGTGTGATAATCCCATCTAATTTGTAAACCT 4927 chr4qtel1M 758755 TCCCTATTATTTCTTTAAAAACCTTAGAAGTAAAACATGTTCCTTTGTCA 758804 v -- i ii v v i v i iiivv i v v C HERVP71A#LTR/ 4926 TCCATA--ATTCCCCTTAACACCCTTGAGGTAAAGTGGCTCCCATTGTCT 4879 chr4qtel1M 758805 GAGTCAATAATCTCTACCAATCCATACATGGGTACAATTTGTTCCAATAT 758854 i v i i iv v iv i i i C HERVP71A#LTR/ 4878 GAATCAATATTTTCCACCAGGCCAAATCTAGGTACAATCTGTTCTAATAT 4829 chr4qtel1M 758855 TATTCCACTAACCAC 758869 ---i i C HERVP71A#LTR/ 4828 TATT---TTGACCAC 4817 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 40.19 CpG sites = 89, Kimura (unadjusted) = 41.78 Transitions / transversions = 1.65 (89/54) Gap_init rate = 0.09 (46 / 501), avg. gap size = 1.20 (55 / 46) 14 18.27 2.70 0.00 chr4qtel1M 759328 759364 (240636) (TTTAAA)n#Simple_repeat 1 38 (0) m_b210s252i6 8282 chr4qtel1M 759328 TTTAAATTTAAA-ATAAAATGAAATACAGATTTAAATT 759364 -v v v vi i (TTTAAA)n#Sim 1 TTTAAATTTAAATTTAAATTTAAATTTAAATTTAAATT 38 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 20 8.02 0.00 0.00 chr4qtel1M 759478 759504 (240496) (AC)n#Simple_repeat 1 27 (0) m_b210s252i7 8283 chr4qtel1M 759478 ACACACACATACATACACACACACACA 759504 i i (AC)n#Simple_ 1 ACACACACACACACACACACACACACA 27 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 20 12.31 9.43 0.00 chr4qtel1M 759795 759847 (240153) (GTTTT)n#Simple_repeat 1 58 (0) m_b210s252i8 8284 chr4qtel1M 759795 GTTTT-TTTT-TTTCCTTCTGCAGT-TTTTGTTTTGTTTTGTTTTG-TTT 759840 - - iv i ivv - - (GTTTT)n#Simp 1 GTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTT 50 chr4qtel1M 759841 G-TTTGTT 759847 - (GTTTT)n#Simp 51 GTTTTGTT 58 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.10 (5 / 52), avg. gap size = 1.00 (5 / 5) 216 33.92 1.59 4.07 chr4qtel1M 762391 762516 (237484) C L2d2_3end#LINE/L2 (281) 274 152 m_b210s601i9 8285 chr4qtel1M 762391 GAGGTCATTTTGGGAGGGAGAA--CACCAAAGGATCTCTGTAGAAGATGG 762438 i i ?i vv vi-- vvi v iivi v i i C L2d2_3end#LIN 274 GAGATCACTNCGGGCTGGAGTGGTCAGGGAAGGCTTCACGGAGGAGGTGG 225 chr4qtel1M 762439 CATCTCAGCTCAGGTGCTACTTTGAGGAGATCCAGAAGTCCAAGAGGCAG 762488 ? i v -- - -- vi vivvi i v ivi v ii C L2d2_3end#LIN 224 NATTTGAGCT--GG-GC--CTTGAAGGATGGGTAGGATTTGGATAGGTGG 180 chr4qtel1M 762489 AGGTGAAGAGGAAGAGCCTTCCAGGTGG 762516 iv i i v i C L2d2_3end#LIN 179 AGAGGAAGGGGAAGGGCATTCCAGGCGG 152 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 42.91 CpG sites = 23, Kimura (unadjusted) = 47.60 Transitions / transversions = 1.28 (23/18) Gap_init rate = 0.05 (6 / 125), avg. gap size = 1.17 (7 / 6) 29 27.14 4.27 2.52 chr4qtel1M 763043 763159 (236841) (TTC)n#Simple_repeat 1 119 (0) m_b210s252i9 8286 chr4qtel1M 763043 TTCCTC-TCTTCGTTTTCCTCCTCCTCTCCTTCCTCTTCCCCTCCCTTTT 763091 i - v i i i i i i ii i i i (TTC)n#Simple 1 TTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTT 50 chr4qtel1M 763092 CTTCCATC-CCTTC-CCATCCTCTTCTTCCCCCTCTTCTGTGCTTCTTTT 763139 - v -i -i v i ii i - - i (TTC)n#Simple 51 CTT-CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCT-T-CTTCTTCT 97 chr4qtel1M 763140 TCTTCTCCCTCTT-TT-TTCTT 763159 i i - - (TTC)n#Simple 98 TCTTCTTCTTCTTCTTCTTCTT 119 Matrix = Unknown Transitions / transversions = 7.00 (21/3) Gap_init rate = 0.07 (8 / 116), avg. gap size = 1.00 (8 / 8) 67 29.84 2.04 2.46 chr4qtel1M 764330 764574 (235426) (CCTC)n#Simple_repeat 1 244 (0) m_b210s252i10 8287 chr4qtel1M 764330 CCTCTCTCCCTTCTTCACTTCCTCCTTCCCTCCCTCCCTTCCTATCTTTC 764379 i i i v i i i vi ii (CCTC)n#Simpl 1 CCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCC 50 chr4qtel1M 764380 TTCCTTCCTCCCTCACTCTATCCCTCTCTCCC-ACTTCCTTTTATCCCTC 764428 i i v iv i -v i i iiv (CCTC)n#Simpl 51 TCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTC 100 chr4qtel1M 764429 CCTCCCTTCCTCCTTCCCTCTCTCCCTCTCTCCCTCTCT-CTTTTTTCTC 764477 i i i i i - i iii - (CCTC)n#Simpl 101 CCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTC-C 149 chr4qtel1M 764478 TTCCTTTCCCTTCCTTTC-CCTTCCTTTCCCTTCCTTTC-CCTTCCTTTC 764525 i -i i ii - i -i i ii - i -i (CCTC)n#Simpl 150 CTCC-CTCCCTCCCTCCCTCCCTCC-CTCCCTCCCTCCCTCCCTCC-CTC 196 chr4qtel1M 764526 CCTTCCTTTC-CCTTCCTTCCCTTCCTTCCTTTCCTTCCCTTCCTTCCTC 764574 i ii - i i - i -i i i i (CCTC)n#Simpl 197 CCTCCCTCCCTCCCTCCCTCCC-TCCCTCC-CTCCCTCCCTCCCTCCCTC 244 Matrix = Unknown Transitions / transversions = 8.00 (48/6) Gap_init rate = 0.05 (11 / 244), avg. gap size = 1.00 (11 / 11) 233 31.30 0.86 0.86 chr4qtel1M 765992 766107 (233893) L1MC4a_3end#LINE/L1 490 605 (2024) m_b210s551i2 8288 chr4qtel1M 765992 ATGCCCATTAATTGGGGAATGGCTGAACAAATGGTGGTATGTGATTGTGA 766041 ?? v i ? i i ivi ii vvviiii L1MC4a_3end#L 490 ATGCCCATNNATAGGAGANTGGTTGAATAAACTATGGTACATCCACACAA 539 chr4qtel1M 766042 TGAAATATTATTGTGTTGTAAGAAATGATGAGCAGGATGCTCTCAGAAA- 766090 i i i vvv i i vi v i - vv v- L1MC4a_3end#L 540 TGGAGTACTATGCAGCTGTAAAAAAGAATGAGGAAGAT-CTCTATGAACT 588 chr4qtel1M 766091 AACCTGGAAAGATTTCC 766107 i iv iv L1MC4a_3end#L 589 GATATGGAGTGATTTCC 605 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 43.35 CpG sites = 21, Kimura (unadjusted) = 43.35 Transitions / transversions = 1.40 (21/15) Gap_init rate = 0.02 (2 / 115), avg. gap size = 1.00 (2 / 2) 15 27.69 0.00 0.00 chr4qtel1M 766288 766326 (233674) (TT)n#Simple_repeat 1 39 (0) m_b210s252i11 8289 chr4qtel1M 766288 TTTTTTGTGTTTTTTTTTTTCCTTGAAGGTTTTTTTTTT 766326 v v ii vvvvv (TT)n#Simple_ 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 39 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 13 14.78 2.33 7.32 chr4qtel1M 769730 769772 (230228) (AACA)n#Simple_repeat 1 41 (0) m_b210s252i12 8290 chr4qtel1M 769730 AACAAAGAAA-AAACAAATAAATAAAACCCAACAACCAAAGCAA 769772 v - i -v - v v - (AACA)n#Simpl 1 AACAAACAAACAAACAAACAAA-CAAA-CAAACAAACAAA-CAA 41 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.10 (4 / 42), avg. gap size = 1.00 (4 / 4) 431 27.05 13.93 0.00 chr4qtel1M 770157 770278 (229722) MIRc#SINE/MIR 10 148 (120) m_b210s601i10 8291 chr4qtel1M 770157 GTGGCATAGTGAACTGAGTGCTGGGCCTGAAATTACGGAGACCTGAGTTT 770206 iii i vv ii i i i i i v i i i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr4qtel1M 770207 AAAT------------AC--AATACCTGTGTGATCCTGGGTAAGTCACAT 770242 i i ------------ -- v v i i i v MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTT 109 chr4qtel1M 770243 AAATGTTT---GTCTCAGTTTACTCATCTGTAAAATGAG 770278 vivi i--- i v i MIRc#SINE/MIR 110 AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 33.96 CpG sites = 24, Kimura (unadjusted) = 35.47 Transitions / transversions = 2.67 (24/9) Gap_init rate = 0.02 (3 / 121), avg. gap size = 5.67 (17 / 3) 251 15.94 7.25 0.00 chr4qtel1M 770528 770596 (229404) C L1MC_orf2#LINE/L1 (878) 2416 2343 m_b210s551i3 8292 chr4qtel1M 770528 ATGAACACTGAAT-TCCATCCAATTATTTAG---TTCTTTAATTTACTTC 770573 iv - iv v --- i vi C L1MC_orf2#LIN 2416 ATGAACATGGAATATCTCTCCATTTATTTAGNTCTTCTTTGATTTCTTTC 2367 chr4qtel1M 770574 -TCAGAATTTTGTAGTTGTCCACA 770596 - i v v C L1MC_orf2#LIN 2366 ATCAGAGTTTTGTAGTTTTCCTCA 2343 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 17.97 CpG sites = 5, Kimura (unadjusted) = 17.97 Transitions / transversions = 0.83 (5/6) Gap_init rate = 0.04 (3 / 68), avg. gap size = 1.67 (5 / 3) 16 22.07 0.00 0.00 chr4qtel1M 773027 773058 (226942) (A)n#Simple_repeat 1 32 (0) m_b210s252i13 8293 chr4qtel1M 773027 AAAAAAAAAAAGAACAAAGGAAATAAAGAAAA 773058 i v ii v i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 32 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 15 21.58 0.00 0.00 chr4qtel1M 773127 773158 (226842) (TG)n#Simple_repeat 1 32 (0) m_b210s252i14 8294 chr4qtel1M 773127 TGTGTCTATGTGTGTGCTTCTGTGTGTCTGTG 773158 v i iv v v (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 32 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 12 25.69 0.00 0.00 chr4qtel1M 773442 773478 (226522) (TTTTA)n#Simple_repeat 1 37 (0) m_b210s252i15 8295 chr4qtel1M 773442 TTATACTTTAATTTATGTGACTTCATTTTATTTCATT 773478 v i v v v i i i (TTTTA)n#Simp 1 TTTTATTTTATTTTATTTTATTTTATTTTATTTTATT 37 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 238 31.07 5.04 5.04 chr4qtel1M 773615 773753 (226247) MIRc#SINE/MIR 11 149 (119) m_b210s601i11 8296 chr4qtel1M 773615 TGGTTCTGAGGCAAGACCACTGG-----GGGTCAGTGGCCATGCCAGAAG 773659 v v v v v ----- i - i-- vi v iiv MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAG-GA--AGACCTGGGT 57 chr4qtel1M 773660 TTGCAGTGCTAGTT-TCCCTCTGGTTACCTGGATGATCTTAGTCAAGTCA 773708 i - v ii i - v v vii v vi i i v MIRc#SINE/MIR 58 TCG-AGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCA 106 chr4qtel1M 773709 CCCCTTGA-CGCCCTGAGCCTCCACTGCATCACCTTTAACATGAGG 773753 --- i - v i vii v v i v v i MIRc#SINE/MIR 107 ---CTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGG 149 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 37.97 CpG sites = 20, Kimura (unadjusted) = 40.58 Transitions / transversions = 0.95 (20/21) Gap_init rate = 0.07 (10 / 138), avg. gap size = 1.40 (14 / 10) 303 34.86 0.69 5.04 chr4qtel1M 773633 773777 (226223) MIR3#SINE/MIR 32 170 (38) m_b210s601i12 8296 chr4qtel1M 773633 ACTGGGGGTCAGTGGCCATGCCAGAAGTTGCAGTGCTAGTT-TCCCTCTG 773681 i vi v v -----i vi v ii i - v v i MIR3#SINE/MIR 32 ACTGGGAGTCAGGAGACCTG-----GGTTCTAGTCCCGGCTCTGCCACTA 76 chr4qtel1M 773682 GTTACCTGGATGATCTTAGTCAAGTCACCCCTTGACGCCCTGAGCCTCCA 773731 ii ?v vi i i v i-- iiv v i i vi MIR3#SINE/MIR 77 ACTNGCTGTGTGACCTTGGGCAAGTCACT--TCACCTCTCTGGGCCTCAG 124 chr4qtel1M 773732 CTGCATCACCTTTAACATGAGGGGGTCAGAACAGGAGGCCCCTGAG 773777 i v v i v v ii vi iv ii i i MIR3#SINE/MIR 125 TTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAG 170 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 47.76 CpG sites = 29, Kimura (unadjusted) = 49.40 Transitions / transversions = 1.53 (29/19) Gap_init rate = 0.06 (8 / 144), avg. gap size = 1.00 (8 / 8) 209 27.81 3.74 19.35 chr4qtel1M 776799 776905 (223095) C L2c_3end#LINE/L2 (24) 454 362 m_b210s601i13 8297 chr4qtel1M 776799 TTCAGCGCC----GTCTGCCAGATGTTGGGGATATGTGGATAAAGAAAGC 776844 v ----i v ii i iivi i v ii C L2c_3end#LINE 454 TTGAGCGCCTACTATGTGCCAGGCGCTGGGGATACAAAGATGAATAAGAC 405 chr4qtel1M 776845 ACCGCTGGTCCCCCAGAACCTTATGTTCCCAGGGAGAGGCTCAAAGTCCA 776894 ---- ----------- ii i i --- v i C L2c_3end#LINE 404 AC----GGTCCC-----------TGCCCTCAAGGA---GCTCACAGTCTA 373 chr4qtel1M 776895 GTCTAAGAAAC 776905 vv i i C L2c_3end#LINE 372 GTGGAGGAGAC 362 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 33.31 CpG sites = 17, Kimura (unadjusted) = 35.15 Transitions / transversions = 2.43 (17/7) Gap_init rate = 0.18 (19 / 106), avg. gap size = 1.16 (22 / 19) 329 20.93 3.09 6.38 chr4qtel1M 776938 777034 (222966) MIR#SINE/MIR 107 200 (62) m_b210s601i15 8298 chr4qtel1M 776938 ACCTCTCTGAGCCTCAGTTTGCTCACCTAGAAAATGGGTAAAATCAGTCC 776987 v v i iv v v - i vv MIR#SINE/MIR 107 ACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAAT-AATAG 155 chr4qtel1M 776988 CACCTACCTC--GGGGCTGTT-TGGGGCATTAGGGGCATAAATCAATTCA 777034 i --i i - i - i---- i i i v MIR#SINE/MIR 156 TACCTACCTCATAGGGTTGTTGTGAGG-ATTAA----ATGAGTTAATACA 200 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 24.83 CpG sites = 11, Kimura (unadjusted) = 24.83 Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.08 (8 / 96), avg. gap size = 1.12 (9 / 8) 353 13.54 3.80 6.49 chr4qtel1M 776938 777016 (222984) MIRb#SINE/MIR 114 190 (78) m_b210s601i14 8298 chr4qtel1M 776938 ACCTCTCTGAGCCTCAGTTTGCTCACCTAGAAAATGGGTAAAATCAGTCC 776987 v i iv v v v ---- MIRb#SINE/MIR 114 ACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAA---- 159 chr4qtel1M 776988 CACCTACCTCG--GGGCTGTT-TGGGGCATTA 777016 i -- i - i - MIRb#SINE/MIR 160 TACCTACCTCGCAGGGTTGTTGTGAGG-ATTA 190 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 14.96 CpG sites = 5, Kimura (unadjusted) = 14.96 Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.09 (7 / 78), avg. gap size = 1.14 (8 / 7) 89 29.97 3.27 4.41 chr4qtel1M 777212 777670 (222330) (GAG)n#Simple_repeat 1 454 (0) m_b211s252i0 8299 chr4qtel1M 777212 GAGGAGGAGAAGGGGGAGCAGACAGGGAAAGGAGAAGGAAGAAAGGGAGG 777261 i i v -v iii i i iii (GAG)n#Simple 1 GAGGAGGAGGAGGAGGAGGAG-GAGGAGGAGGAGGAGGAGGAGGAGGAGG 49 chr4qtel1M 777262 A-GAGGGAGAGAGAGAGAGAAAGAGGAGGGAGGGTTAAGGA-GAAAAGGC 777309 - ii - - i i - - vvi - ii v (GAG)n#Simple 50 AGGAGGAGGAG-GAG-GAGGAGGAGGA-GGA-GGAGGAGGAGGAGGAGGA 95 chr4qtel1M 777310 AGAGGAGGGGAAAGAGGA-AAAAAGGGGGGGGAGGAAGTGGTAACAGGAG 777358 i i i i -i ii i i i v - iv - (GAG)n#Simple 96 GGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGG-AGGAGGA- 143 chr4qtel1M 777359 GGAGGA-GAAGAGAAGGGAGGGGGA-AAGGTGGGTGGGCAGAGAAGAGGG 777406 - i i - i -i v iv i v - i - (GAG)n#Simple 144 GGAGGAGGAGGAGGA-GGAGGAGGAGGAGGAGGAGGAGGAG-GAGGA-GG 190 chr4qtel1M 777407 AGGAAGAGAAAGGGGGGCGAGAGTTAAGGA-GAAAAGGGGGAGGA-GAGG 777454 i -i i iv - vvi - ii i - (GAG)n#Simple 191 AGGAGGAG-GAGGAGGAGGAG-GAGGAGGAGGAGGAGGAGGAGGAGGAGG 238 chr4qtel1M 777455 AAG-GGGGGAAAAGGGGGAGGAAGGGGAACAGGATG-GGGGGA-GAAGAG 777501 i - i ii i i i iv v - i - i (GAG)n#Simple 239 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG 288 chr4qtel1M 777502 GAGGAGGTAGAGGAGACAGAGAAGAACAATGA-TAGAAGG-GGATGGAGG 777549 vi ivi i i vi v -v i - - (GAG)n#Simple 289 GAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA-GGAGG 337 chr4qtel1M 777550 AGGATTAGGAGGGAGAAGAGAGGAGGGGGAAGAAGGGGAGGAGGTAGG-T 777598 vv - i - i i i i - -v (GAG)n#Simple 338 AGGAGGAGGA-GGAGGAG-GAGGAGGAGGAGGAGGAGGAGGAGG-AGGAG 384 chr4qtel1M 777599 GAGGAAAAGTAGTGAGGAAGAGAAGCAGTGAGAGAGGGAGGATGAGGAAG 777648 ii v - i i v - - - v i (GAG)n#Simple 385 GAGGAGGAGGAG-GAGGAGGAGGAGGAG-GAG-GA-GGAGGAGGAGGAGG 430 chr4qtel1M 777649 -GGA-AATGGTGAGGGGGAGGAGG 777670 - -i v iv i (GAG)n#Simple 431 AGGAGGAGGAGGAGGAGGAGGAGG 454 Matrix = Unknown Transitions / transversions = 2.61 (73/28) Gap_init rate = 0.08 (35 / 458), avg. gap size = 1.00 (35 / 35) 28 0.00 0.00 0.00 chr4qtel1M 778014 778040 (221960) (G)n#Simple_repeat 1 27 (0) c_b211s251i0 8300 chr4qtel1M 778014 GGGGGGGGGGGGGGGGGGGGGGGGGGG 778040 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGG 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 645 27.26 7.81 0.84 chr4qtel1M 780817 781149 (218851) C L1M5_orf2#LINE/L1 (1448) 1846 1491 m_b211s551i0 8301 chr4qtel1M 780817 TTTTTAATAGGAATGAGTGTTGTATTTTGTCAAAAGTTTTTTCTTCATTT 780866 vi v i v v i v i C L1M5_orf2#LIN 1846 TTTTTATCATGAATGGGTGTTGAATTTTGTCAAATGCTTTTTCTGCATCT 1797 chr4qtel1M 780867 AATGAGATGATTATA-----TTTCTG--TTAGT-TATTGATATGGTCAAT 780908 v i ----- v-- v - i i v C L1M5_orf2#LIN 1796 ATTGAGATGATCATATGATTTTTCTCCTTTATTCTGTTAATATGGTGAAT 1747 chr4qtel1M 780909 TGTGCTAATTATTTTCCTAATATTGAACCAGTCCTGGATTGCTGTTATTA 780958 iiii i iv i v i i ii i v v vv - C L1M5_orf2#LIN 1746 TACATTGATTGATTTTCGAATGTTAAACCAACCTTGCATTCCTGGGA-TA 1698 chr4qtel1M 780959 AGTCCCACCTGTTTAGAGTATATTATTCTCTTGATAAATTGCTCTATATT 781008 ii i v i vii i i i v v -- iv C L1M5_orf2#LIN 1697 AACCCCACTTGGTCATGATGTATTATCCTTTTTATATATTG--CTGGATT 1650 chr4qtel1M 781009 C--TCTACTAATATTTTATTTAAAGTGTTTACATCAATATTCATCAGGGA 781056 -- i i i ? iii v i v i v C L1M5_orf2#LIN 1649 CGATTTGCTAATATTTTGTTNAGGATTTTTGCATCTATGTTCATGAGGGA 1600 chr4qtel1M 781057 -----------AATTTTCTCTATTT----TGGCTCTTCCTGGATTAGCTA 781091 ----------- i vi ---- v i vi ? v v v C L1M5_orf2#LIN 1599 TATTGGTCTGTAATTTTCTTTTCTTGTAATGTCTTTGTCNGGTTTTGGTA 1550 chr4qtel1M 781092 TCAACATCATTTCTGTGTCATAAAA-GAATTTGGCAGGACTCCTTCTTTG 781140 ivi ? viiv iv - i v v vii i v C L1M5_orf2#LIN 1549 TCAGGGTNATGCTGGCCTCATAAAATGAGTTGGGAAGTGTTCCCTCTTTT 1500 chr4qtel1M 781141 GCTGTTTCC 781149 v i i C L1M5_orf2#LIN 1499 TCTATTTTC 1491 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.09 CpG sites = 52, Kimura (unadjusted) = 35.09 Transitions / transversions = 1.37 (52/38) Gap_init rate = 0.03 (10 / 332), avg. gap size = 2.90 (29 / 10) 285 15.71 4.23 1.37 chr4qtel1M 781466 781536 (218464) C L1MD_orf2#LINE/L1 (1831) 1463 1391 m_b211s551i1 8301 chr4qtel1M 781466 AATTGTTCTTTTCACTGTTTGGTAAAATTCAGTA-TGAATCCATCTGGAC 781514 v vv - i vvi - v i C L1MD_orf2#LIN 1463 AATTCTTCTTTAAAC-GTTTGGTAGAATTCTCCAGTGAAACCATCTGGGC 1415 chr4qtel1M 781515 CTGGAGATT--TTCTTAGGGAGTT 781536 -- i i C L1MD_orf2#LIN 1414 CTGGAGATTTCTTTTTGGGGAGTT 1391 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 17.68 CpG sites = 5, Kimura (unadjusted) = 17.68 Transitions / transversions = 0.83 (5/6) Gap_init rate = 0.04 (3 / 70), avg. gap size = 1.33 (4 / 3) 243 21.24 23.50 1.40 chr4qtel1M 781481 781714 (218286) C L1M5_orf2#LINE/L1 (1845) 1449 1165 m_b211s551i2 8301 chr4qtel1M 781481 TGTTTGGTAAAATTCAGTA-TGAATCCATCTGGACCTGGAGATTTTCTT- 781528 i vi - v i - - C L1M5_orf2#LIN 1449 TGTTTGGTAGAATTCACCAGTGAAGCCATCTGGGCCTGGAG-TTTTCTTT 1401 chr4qtel1M 781529 --AGGGAGTTCATTAAT----------GTTTTTTT--------------- 781551 --i i v iv ----------i i --------------- C L1M5_orf2#LIN 1400 GTGGGAAGGTTTTTAATTACAAATTCAATTTCTTTAATAGATATAGGGCT 1351 chr4qtel1M 781552 --TC---CTTTCTATTT--TATTCTGTTAATCTGGGTAATTTATATTTTT 781594 -- ---i -- v v? i i i v ? i i C L1M5_orf2#LIN 1350 ATTCAGATTTTCTATTTCTTCTTGNGTCAGTTTTGGTAANTTGTGTTTTT 1301 chr4qtel1M 781595 GTAAA-----TATCCATTTCAT-------GTCAGATTAATTGGCATACAA 781632 -i i----- i -------? i v v i C L1M5_orf2#LIN 1300 -CAAGGAATTTGTCCATTTCATCTAAGTTNTCAAATTTATTGGCATAAAG 1252 chr4qtel1M 781633 TTGAGCAAAAGGG-CTCTGAATTATTGCTTTTATTTCCT------CCTTT 781675 vv v viv- v - i- v vi ------i v C L1M5_orf2#LIN 1251 TTGTTCATAATATTCTCTTA-TTATC-CTTTTAATGTCTGTAGGATCTGT 1204 chr4qtel1M 781676 GGTGATTTCACCCTTTTGATTTTTGATACTGGTAATTTG 781714 i v v i v ii i C L1M5_orf2#LIN 1203 AGTGATGTCTCCTTTTTCATTCCTGATATTGGTAATTTG 1165 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 25.83 CpG sites = 28, Kimura (unadjusted) = 25.83 Transitions / transversions = 1.33 (28/21) Gap_init rate = 0.06 (15 / 233), avg. gap size = 3.93 (59 / 15) 15 16.35 3.51 9.26 chr4qtel1M 782419 782475 (217525) (GA)n#Simple_repeat 1 54 (0) m_b211s252i1 8302 chr4qtel1M 782419 GAGAGA-AGA-AGTGAGGCAGAGATGTAGAGAGATTAGGGATGCAGAGAG 782466 - - v iv - - -v i - - (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGA-G-AGAGAGA-GAGAGA-G-AGAGAG 45 chr4qtel1M 782467 ACACAGAGA 782475 v v (GA)n#Simple_ 46 AGAGAGAGA 54 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.12 (7 / 56), avg. gap size = 1.00 (7 / 7) 27 0.00 0.00 0.00 chr4qtel1M 783297 783322 (216678) (T)n#Simple_repeat 1 26 (0) c_b211s251i1 8303 chr4qtel1M 783297 TTTTTTTTTTTTTTTTTTTTTTTTTT 783322 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 295 29.75 2.94 8.53 chr4qtel1M 783324 783459 (216541) C MIR1_Amn#SINE/MIR (101) 129 1 m_b211s601i3 8304 chr4qtel1M 783324 CTGAGGCA-ATTGGGGTTAGATGACTTGTCCAGGATCACACAGCTAGGAA 783372 ?- vv i ? ii i i i ? ?i v? C MIR1_Amn#SINE 129 CTGAGGCNCAGAGAGGTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNA 80 chr4qtel1M 783373 GTGTTATGTGTCTGAGGTCAGATTTGAACTCAA--TTCCTGACT-TCAGT 783419 vi ------- vivi ? ? i i--i i v -i C MIR1_Amn#SINE 79 GTGGCA-------GAGCCGGGANTNGAACCCAGGTCTCCCGAGTCCCAGT 37 chr4qtel1M 783420 GCTGATATGCTACCCACTGTGCCACCTAGTTGTCCCCTTA 783459 - iii iiv i ivi ---ii i i i C MIR1_Amn#SINE 36 -CCAGTGCTCTATCCACTAGACCAC---ACTGCCTCCCTA 1 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.87 CpG sites = 28, Kimura (unadjusted) = 44.16 Transitions / transversions = 3.11 (28/9) Gap_init rate = 0.10 (14 / 135), avg. gap size = 1.07 (15 / 14) 366 29.87 3.31 5.93 chr4qtel1M 783324 783444 (216556) C MIRc#SINE/MIR (141) 127 10 m_b211s601i2 8304 chr4qtel1M 783324 CTGAGGC-AATTGGGGTTAGATGACTTGTCCAGGATCACACAGCTAGGAA 783372 -v vv i ii i i i v C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAA 78 chr4qtel1M 783373 GTGTTATGTGTCTGAGGTCAGATTTGAACTCAA---TTCCTGACTTCAGT 783419 vi ------- vivi i i i i--- i iv C MIRc#SINE/MIR 77 GTGGCA-------GAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr4qtel1M 783420 GCTGATATGCTACCCACTGTGCCAC 783444 v iii iiv vi ii C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.96 CpG sites = 23, Kimura (unadjusted) = 40.02 Transitions / transversions = 2.09 (23/11) Gap_init rate = 0.07 (9 / 120), avg. gap size = 1.22 (11 / 9) 377 24.39 0.00 0.00 chr4qtel1M 784144 784225 (215775) C MIR#SINE/MIR (105) 157 76 m_b211s601i4 8305 chr4qtel1M 784144 TGCTATTAGTATTCCTATTTTGAAGCTGAGGAAACTGAAGCAGTTAAAAG 784193 i v i i iv v i vvv i i C MIR#SINE/MIR 157 TACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGG 108 chr4qtel1M 784194 TGAAGGAACTTGCCCCAAATAACACAGCTGGT 784225 v v v ii v i C MIR#SINE/MIR 107 TTAAGTAACTTGCCCAAGGTCACACAGCTAGT 76 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.76 CpG sites = 10, Kimura (unadjusted) = 29.76 Transitions / transversions = 1.00 (10/10) Gap_init rate = 0.00 (0 / 81), avg. gap size = 0.0 (0 / 0) 180 21.43 12.50 0.00 chr4qtel1M 784797 784852 (215148) C L3#LINE/CR1 (2432) 1667 1605 m_b211s601i5 8306 chr4qtel1M 784797 CTCAATCTTGCTTCTGTA------TGGTGCTCTGTATGAAGGAAGCAT-A 784839 v? i i------ v iv v i i - C L3#LINE/CR1 1667 CTGNATCTTGCCTCTGTGCCAGTTTTGTAATCTGTATCAGGAAAGCATCA 1618 chr4qtel1M 784840 CCCACTTCCTGCA 784852 i i? v C L3#LINE/CR1 1617 TCCATNTCCTCCA 1605 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.80 CpG sites = 7, Kimura (unadjusted) = 26.80 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.04 (2 / 55), avg. gap size = 3.50 (7 / 2) 22 24.76 1.45 1.45 chr4qtel1M 786000 786068 (213932) (ATATAT)n#Simple_repeat 1 69 (0) m_b211s252i2 8307 chr4qtel1M 786000 ATA-ATTTACATTTGATATTTATATATATATGTAAATTTATATGTGCATA 786048 - v i v - v i v v i ii (ATATAT)n#Sim 1 ATATATATATATAT-ATATATATATATATATATATATATATATATATATA 49 chr4qtel1M 786049 TATGTAGATATGTACATATA 786068 i v i i (ATATAT)n#Sim 50 TATATATATATATATATATA 69 Matrix = Unknown Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.03 (2 / 68), avg. gap size = 1.00 (2 / 2) 466 19.46 5.88 5.00 chr4qtel1M 786075 786193 (213807) MIRc#SINE/MIR 27 146 (122) m_b211s601i6 8308 chr4qtel1M 786075 GCACAGGA--TGGAGTCAGGAAGACATTTTCTTGAATTCAAATCT-GG-T 786120 v -- ------i ii i i i- - MIRc#SINE/MIR 27 GCACTGGACTTGGAGTCAGGAAGAC------CTGGGTTCGAGTCCCGGCT 70 chr4qtel1M 786121 CTTAAAC--ACTACCTGTGTGACCCTGGGCAAGTCACTTAACCCTTTTTA 786168 vvv -- v i ii i v MIRc#SINE/MIR 71 CTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGA 120 chr4qtel1M 786169 -TCTCATTTTCCTAATTTATAAAGTG 786193 -i v v i i i MIRc#SINE/MIR 121 GCCTCAGTTTCCTCATCTGTAAAATG 146 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 21.84 CpG sites = 14, Kimura (unadjusted) = 23.00 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.09 (11 / 118), avg. gap size = 1.18 (13 / 11) 15 4.49 0.00 4.17 chr4qtel1M 786290 786314 (213686) (CAC)n#Simple_repeat 1 24 (0) m_b211s252i3 8309 chr4qtel1M 786290 CACCACCTCCACCACCACCACACAC 786314 v - (CAC)n#Simple 1 CACCACCACCACCACCACCAC-CAC 24 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 13 8.18 3.85 0.00 chr4qtel1M 786669 786694 (213306) (ATTTA)n#Simple_repeat 1 27 (0) m_b211s252i4 8310 chr4qtel1M 786669 ATTTAATGTAAATT-ATTTAATTTAAT 786694 v v - (ATTTA)n#Simp 1 ATTTAATTTAATTTAATTTAATTTAAT 27 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.04 (1 / 25), avg. gap size = 1.00 (1 / 1) 484 21.64 0.00 12.30 chr4qtel1M 787267 787403 (212597) C MIRc#SINE/MIR (145) 123 2 m_b211s601i7 8311 chr4qtel1M 787267 GGCTGAGACAATTGGGGTTAAGTGATTTGCCCAGGGTCAAACAGCTAGGA 787316 v ----- i i i v v C MIRc#SINE/MIR 123 GGCTCAGA-----GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTA 79 chr4qtel1M 787317 AGTGTAACCTGTCTGAGGTCATATTTGAACTCAGGTCCTCCTGACTTCAA 787366 vv ------- viviv i i i i i C MIRc#SINE/MIR 78 AGTGGCA-------GAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAA 36 chr4qtel1M 787367 GGCTGGTTCTCTATCCACTGCGCCACCTAGCTGCCCC 787403 v ii v v i ---i i C MIRc#SINE/MIR 35 GTCCAGTGCTCTTTCCACTGCACCAC---ACTGCCTC 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 23.28 CpG sites = 15, Kimura (unadjusted) = 25.45 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.11 (15 / 136), avg. gap size = 1.00 (15 / 15) 32 3.23 0.00 0.00 chr4qtel1M 788085 788116 (211884) (GT)n#Simple_repeat 1 32 (0) c_b211s251i2 8312 chr4qtel1M 788085 GTGTATGTGTGTGTGTGTGTGTGTGTGTGTGT 788116 i (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 32 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 15 5.56 0.00 0.00 chr4qtel1M 788530 788548 (211452) (T)n#Simple_repeat 1 19 (0) m_b211s252i5 8313 chr4qtel1M 788530 TTTTCTTTTTTTTTTTTTT 788548 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 341 15.09 8.99 3.19 chr4qtel1M 788822 788871 (211129) C Tigger1#DNA/TcMar-Tigger (193) 2225 2168 m_b211s502i0 8314 chr4qtel1M 788822 ATTTTATTGCTAAAAA-TTCTAACCATCATCTGAGCCTTCAGAGAGCAGT 788870 i - v v v iv C Tigger1#DNA/T 2225 ACTTTATTGCTAAAAAATGCTAACGATCATCTGAGCCTTCAGCGAGTCGT 2176 chr4qtel1M 788871 A------- 788871 ------- C Tigger1#DNA/T 2175 AATCTTTT 2168 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 15.80 CpG sites = 6, Kimura (unadjusted) = 17.15 Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.04 (2 / 49), avg. gap size = 4.00 (8 / 2) 30 0.00 0.00 0.00 chr4qtel1M 788872 788899 (211101) (T)n#Simple_repeat 1 28 (0) c_b211s251i3 8315 chr4qtel1M 788872 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 788899 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 341 15.09 8.99 3.19 chr4qtel1M 788900 788937 (211063) C Tigger1#DNA/TcMar-Tigger (251) 2167 2133 m_b211s502i0 8314 chr4qtel1M 788900 GCTAGTGGGATGCTCTTACTTTCATGTTGGGATGGCTG 788937 i - v v i i iv -- C Tigger1#DNA/T 2167 GCTGGT-GGAGGGTCTTGCCTCGATGTT--GATGGCTG 2133 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 15.80 CpG sites = 6, Kimura (unadjusted) = 17.15 Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.08 (3 / 37), avg. gap size = 1.00 (3 / 3) 255 12.24 18.37 0.00 chr4qtel1M 788925 788973 (211027) C Tigger1#DNA/TcMar-Tigger (316) 2102 2045 m_b211s502i1 8314 chr4qtel1M 788925 GTTGGGATGGCTGTGGCAGTTTCTTAAACTAA---------GAAATTTGC 788965 i i v --------- i C Tigger1#DNA/T 2102 GTTGGGGTGGCTGTGGCAATTTCTTAAAATAAGACAACAATGAAGTTTGC 2053 chr4qtel1M 788966 TGCATCAA 788973 i i C Tigger1#DNA/T 2052 CGCATCGA 2045 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 9.23 CpG sites = 5, Kimura (unadjusted) = 13.75 Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.02 (1 / 48), avg. gap size = 9.00 (9 / 1) 1471 21.92 1.80 0.29 chr4qtel1M 788972 789305 (210695) C Tigger1#DNA/TcMar-Tigger (2077) 341 3 m_b211s502i2 8314 chr4qtel1M 788972 AACAACTGGTTGGTGGAGGGATCAGAACATACACA-CATTTACTGCTTAA 789020 ii i i vii i - ii v C Tigger1#DNA/T 341 AACGGCCGGTCGGTGGAGCAGTCAGAACACACACAACATTTATCGATTAA 292 chr4qtel1M 789021 GGTCTCCATCTTGCATAGGTGTGGTTCACGGCACCCCAAA-CATCCCAAA 789069 v v i ii i i i ii i - viivv C Tigger1#DNA/T 291 GTTCGCCGTCTTATATGGGCGCGGTTCGTGGCGCCCCAAAACAATTACAA 242 chr4qtel1M 789070 CATCAGCATCAAAGATCAGTGATCACAAATCACTATAACAGATGTGATAT 789119 i vi i v i i i i v C Tigger1#DNA/T 241 TAGTAACATCAAAGATCACTGATCACAGATCACCATAACAGATATAATAA 192 chr4qtel1M 789120 CAATGAGAAAGTTAGAAAT---GTGATAGTTACCAAGCTGTGACACAGAG 789166 i i v --- i v i iv C Tigger1#DNA/T 191 TAATGAAAAAGTTTGAAATATTGCGAGAATTACCAAAATGTGACACAGAG 142 chr4qtel1M 789167 ACATGACATGAGCATATGCTGTTAGAAAAATAGTGCCTAGAGAA-TGGTC 789215 i vi i i i i v v v- v C Tigger1#DNA/T 141 ACACGAAGTGAGCACATGCTGTTGGAAAAATGGCGCCGATAGACTTGCTC 92 chr4qtel1M 789216 GATGCAGAGTTGCCACACACCTTTAATGTGTAAAAAAATGCAACATCTGC 789265 i i v i v - i i C Tigger1#DNA/T 91 GACGCAGGGTTGCCACAAACCTTCAATTTGT-AAAAAACGCAATATCTGC 43 chr4qtel1M 789266 AAAGTACAATAAAGCAAAATGCAAAGAAACAAGGTCTGCC 789305 i ii i ii vi i v C Tigger1#DNA/T 42 GAAGCGCAATAAAGCGAAGCGCAATAAAACGAGGTATGCC 3 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 19.21 CpG sites = 51, Kimura (unadjusted) = 26.83 Transitions / transversions = 2.32 (51/22) Gap_init rate = 0.02 (5 / 333), avg. gap size = 1.40 (7 / 5) 13 14.60 7.89 0.00 chr4qtel1M 792718 792755 (207245) (TTCCCT)n#Simple_repeat 1 41 (0) m_b211s252i6 8316 chr4qtel1M 792718 TTCCCTCTTCC-TT-CCTTCACCTTTCCCTAT-CCTTTCCC 792755 i i - - iv v - (TTCCCT)n#Sim 1 TTCCCTTTCCCTTTCCCTTTCCCTTTCCCTTTCCCTTTCCC 41 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.08 (3 / 37), avg. gap size = 1.00 (3 / 3) 268 26.03 0.00 0.00 chr4qtel1M 794252 794324 (205676) MIR3#SINE/MIR 134 206 (2) m_b211s601i8 8317 chr4qtel1M 794252 CTGTCAAATGTGGGGCATGGAGCACGGGACCACTGAGGCCCCTTCTAGTT 794301 v v vv vi viv i v i i i i MIR3#SINE/MIR 134 CTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCT 183 chr4qtel1M 794302 CTGTCATTCTAGGATTCCAGGAT 794324 v v i v MIR3#SINE/MIR 184 CTGACATTCTATGATTCTATGAT 206 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.06 CpG sites = 8, Kimura (unadjusted) = 32.06 Transitions / transversions = 0.73 (8/11) Gap_init rate = 0.00 (0 / 72), avg. gap size = 0.0 (0 / 0) 497 26.70 4.88 1.78 chr4qtel1M 795087 795250 (204750) C MIR3#SINE/MIR (19) 189 21 m_b211s601i9 8318 chr4qtel1M 795087 TGACAGAGATAACAGAGGCTTTG----CCATTTCTTCT--CCAGCTCATT 795130 v v iiv i i i i----i i vv i-- vv C MIR3#SINE/MIR 189 TGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATT 140 chr4qtel1M 795131 TTATAGATGAGGAAACTGAGGCAAACATA-GTGAAGTGATTTGCCCAGAG 795179 i vv v v - i ii C MIR3#SINE/MIR 139 TTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGG 90 chr4qtel1M 795180 TCACACAGGTTGTTGAGTTCCTGGGGCCAGATTTGGACTCAGGTGATTCC 795229 v?v - vv v i v vi i v i i --i C MIR3#SINE/MIR 89 TCACACAGCNAGTT-AGTGGCAGAGCCGGGACTAGAACCCAGGT--CTCC 43 chr4qtel1M 795230 TAA-TTCCAGGCCCTGCACTCT 795250 i - i v v v C MIR3#SINE/MIR 42 TGACTCCCAGTCCGTGCTCTCT 21 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.58 CpG sites = 21, Kimura (unadjusted) = 33.58 Transitions / transversions = 0.95 (21/22) Gap_init rate = 0.04 (7 / 163), avg. gap size = 1.57 (11 / 7) 573 24.50 1.34 4.14 chr4qtel1M 795125 795273 (204727) C MIRc#SINE/MIR (120) 148 4 m_b211s601i10 8318 chr4qtel1M 795125 CTCATTTTATAGATGAGGAAACTGAGG--CAAACATAGTGAAGTGATTTG 795172 i i -- i v -i v i C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGA-GGTTAAGTGACTTG 100 chr4qtel1M 795173 CCCAGAGTCACACAGGTTGTTGAGTTCCTGGGGCCAGATTTGGACTCAGG 795222 ii v v - i vv v i v vi i i i i C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAG-TAAGTGGCAGAGCCGGGACTCGAACCCAGG 51 chr4qtel1M 795223 TGATTCCTAATTCCAGGCCCTGCACTCTATTCATTGTACCACCAAACTGC 795272 -v i i i i v ii v i i i --- C MIRc#SINE/MIR 50 T-CTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC---ACTGC 5 chr4qtel1M 795273 C 795273 C MIRc#SINE/MIR 4 C 4 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.55 CpG sites = 23, Kimura (unadjusted) = 30.60 Transitions / transversions = 1.92 (23/12) Gap_init rate = 0.05 (7 / 148), avg. gap size = 1.14 (8 / 7) 294 29.41 4.20 0.00 chr4qtel1M 795290 795408 (204592) L2c_3end#LINE/L2 305 428 (50) m_b211s601i11 8319 chr4qtel1M 795290 TATTCCCTCTTTATCCTGTAT--TTAGCTTGCTTTGTCTATATTTGTTAG 795337 i vi v v viv -- i iv vvv i i vi L2c_3end#LINE 305 TACTCCCATTATAGCACTTATCATTAACTTGTATTGTAATTGTCTGTTTA 354 chr4qtel1M 795338 CATGT-TGTCTCCCCCATCAGATTGTAAACTCCTTAAGGGCAAGGACAGA 795386 ? - i ii i i i i i v v L2c_3end#LINE 355 CNTGTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGT 404 chr4qtel1M 795387 CTTTTGTC--TCTTTCTCACCCCA 795408 v i i i-- v vv L2c_3end#LINE 405 GTCTTATTCATCTTTGTATCCCCA 428 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.50 CpG sites = 19, Kimura (unadjusted) = 38.50 Transitions / transversions = 1.19 (19/16) Gap_init rate = 0.03 (3 / 118), avg. gap size = 1.67 (5 / 3) 313 18.95 11.54 3.57 chr4qtel1M 795301 795404 (204596) L2d_3end#LINE/L2 340 451 (65) m_b211s601i12 8319 chr4qtel1M 795301 TATCCTGTATTTAGCTTGCT--TTGTCT-ATATTTGTTAGCATGTTGTCT 795347 i i -- i iv -- i - i v -- v L2d_3end#LINE 340 TGTCTTGTATT--GTTCTCTAATTGTTTCATGTGTGTTAG--TCTTGTCT 385 chr4qtel1M 795348 CCCCCATCAGATTGTAAACTCCTTAAGGGCAAGGAC--------AGACTT 795389 v ii i i i -------- v ? L2d_3end#LINE 386 CCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACTN 435 chr4qtel1M 795390 TTGTCTC-TTTCTCAC 795404 v ? - i i L2d_3end#LINE 436 TTTTNTCGTTCCCCAC 451 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 23.03 CpG sites = 13, Kimura (unadjusted) = 23.03 Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.08 (8 / 103), avg. gap size = 2.00 (16 / 8) 18 22.06 7.25 0.00 chr4qtel1M 795678 795746 (204254) (TTCCCTT)n#Simple_repeat 1 74 (0) m_b211s252i7 8320 chr4qtel1M 795678 TTCCCTTTT--C-TTTCCC-CTT-CTTGTTCCATGTTCCTTTTTGCTTCT 795722 -- - -i - i v v v i v i i (TTCCCTT)n#Si 1 TTCCCTTTTCCCTTTTCCCTTTTCCCTTTTCCCTTTTCCCTTTTCCCTTT 50 chr4qtel1M 795723 TTCTGTTTCTCTTTTCCCTTTTCC 795746 i iv i (TTCCCTT)n#Si 51 TCCCTTTTCCCTTTTCCCTTTTCC 74 Matrix = Unknown Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.06 (4 / 68), avg. gap size = 1.25 (5 / 4) 417 37.45 1.56 1.96 chr4qtel1M 796138 796393 (203607) C L3#LINE/CR1 (137) 3962 3708 m_b211s601i13 8321 chr4qtel1M 796138 GGGAGTCCAAGGCCTTAGAACACAACCCATTC---TGTTGAAGGGCCCTA 796184 ii vvi i?vi vi i --- v i vi i i C L3#LINE/CR1 3962 GGGAGCTCACTACCTCNCGAGGCAGCCCATTCCATTTTTGGACAGCTCTG 3913 chr4qtel1M 796185 ACTTTTAGGAAATTTCTGTTGGAAATGAAAAAAAAAAGGTTTTACTTTTA 796234 i v i i ii vi viv v ivvi vvv ii i- i v C L3#LINE/CR1 3912 ATTGTTAGAAAGTTCTTCCTTATATTGAGCCGAAATCTGCCTC-CCTGTA 3864 chr4qtel1M 796235 ATTTTTACCCACAGGTTCTTGTGACATTCTCTTGGAGCCAGACAAACATA 796284 i ii iv i v vviiii - v i - C L3#LINE/CR1 3863 ACTTCCACCCATTGGTCCTAGTTCTGCCCTCT-GGAGCCACACAGA-ATA 3816 chr4qtel1M 796285 TTCCTTATCCCTCTTCCCCCATGACA-TTTTCCATATGGTTGAAAAGAAC 796333 vvi v - v -iii i v iv i v i C L3#LINE/CR1 3815 AGTCTAATCCCTCTT-CCACATGACAGCCCTTCAAATATTTGAAGACAGC 3767 chr4qtel1M 796334 TGTGGTTTCCCATCACAGTCTTCTTAATCTTCACTCTAGCCAGGCTCCAT 796383 i vi v i v vv i-v i vv iv vv i vi C L3#LINE/CR1 3766 TATCATGTCTCCTCTAAGTCTTCTC-TTCTCCAGGCTAAACATCCCCAGT 3718 chr4qtel1M 796384 TGAGTCAACC 796393 vvv C L3#LINE/CR1 3717 TCCTTCAACC 3708 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 52.08 CpG sites = 50, Kimura (unadjusted) = 53.75 Transitions / transversions = 1.14 (50/44) Gap_init rate = 0.03 (7 / 255), avg. gap size = 1.29 (9 / 7) 23 16.74 0.00 0.00 chr4qtel1M 800484 800523 (199477) (GA)n#Simple_repeat 1 40 (0) m_b211s252i8 8322 chr4qtel1M 800484 GAGAGAGAGAGGCAGAGACAGAGAGACACAGAGAAAGAGA 800523 iv v v v i (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 40 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 330 17.05 4.55 0.00 chr4qtel1M 801059 801146 (198854) C L1MC_orf2#LINE/L1 (2146) 1148 1057 m_b211s551i3 8323 chr4qtel1M 801059 TTTTTAGTCAGATTAGCTA-AGGTTTATCAATTTGATTAATTTTTTCAGA 801107 i i vi i - i v i i i C L1MC_orf2#LIN 1148 TTCTTAGTTAGCCTGGCTAGAGGCTTATCAATTTTATTGATCTTTTCAAA 1099 chr4qtel1M 801108 GAACCAGCTTTT--TTTGTTTGATCTTTTCTA-TGTTTTCCT 801146 -- vv i i - v C L1MC_orf2#LIN 1098 GAACCAGCTTTTGGTTTCGTTGATTTTCTCTATTGATTTCCT 1057 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 19.73 CpG sites = 10, Kimura (unadjusted) = 19.73 Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.03 (3 / 87), avg. gap size = 1.33 (4 / 3) 47 0.00 0.00 0.00 chr4qtel1M 802496 802538 (197462) (T)n#Simple_repeat 1 43 (0) c_b211s251i4 8324 chr4qtel1M 802496 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 802538 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 43 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 755 30.83 2.21 8.17 chr4qtel1M 804099 804370 (195630) MIRb#SINE/MIR 1 257 (11) m_b211s601i14 8325 chr4qtel1M 804099 CAAAGGTGGCCAAATGCCACAGTGGCTAGAACATTGGGTCTGGATTCAAG 804148 i - vivi vii vv i iv v i v ii MIRb#SINE/MIR 1 CAGAGG-GGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGA 49 chr4qtel1M 804149 GAGACCTGAGTTTAAATCTTGCTTCAGATGTTTTCTGGCTGTGTGCCCCT 804198 v i ii ii vi v viii v i v i MIRb#SINE/MIR 50 CAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTT 99 chr4qtel1M 804199 GGACAAGTCACTTAGTTTCTATTTACCTCCATTTACTCAATTGTAAAATG 804248 i i iii v vvi vi v vi MIRb#SINE/MIR 100 GGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATG 149 chr4qtel1M 804249 GAGAAAATAAGAGCAAAATAATTATTTTGGAGATAACCTTGCAAGGCTCT 804298 i v ------------ ii -------- i i i v MIRb#SINE/MIR 150 GGGATAATAA------------TACCT--------ACCTCGCAGGGTTGT 179 chr4qtel1M 804299 TATGAAGATCAATTGAGATAATGTTTATAAAG------GCATAGTGCATG 804342 i i i v iv i ------ i v MIRb#SINE/MIR 180 TGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTG 229 chr4qtel1M 804343 GCATACAGTGGGGACACTGTAAATACTA 804370 i i ii vi v vi iv MIRb#SINE/MIR 230 GCACATAGTAAGCGCTCAATAAATGGTA 257 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.84 CpG sites = 48, Kimura (unadjusted) = 41.03 Transitions / transversions = 1.66 (48/29) Gap_init rate = 0.08 (22 / 271), avg. gap size = 1.23 (27 / 22) 285 25.30 5.00 1.20 chr4qtel1M 805000 805079 (194921) C MIRc#SINE/MIR (175) 93 11 m_b211s601i15 8326 chr4qtel1M 805000 GTCCCCTAGCTAGGAAGCAACAGAGGTTGGATTTGAACTT--GTCTTTCT 805047 v vi v iii viv i i ii-- i C MIRc#SINE/MIR 93 GTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCT 44 chr4qtel1M 805048 GGCTCCAGGGCCA--GCTCTTTCTCCTGGCACCA 805079 i i v -- iv - C MIRc#SINE/MIR 43 GACTCCAAGTCCAGTGCTCTTTCCACT-GCACCA 11 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.15 CpG sites = 13, Kimura (unadjusted) = 31.92 Transitions / transversions = 1.86 (13/7) Gap_init rate = 0.04 (3 / 79), avg. gap size = 1.67 (5 / 3) 16 7.13 3.12 3.12 chr4qtel1M 805496 805527 (194473) (AACCCT)n#Simple_repeat 1 32 (0) m_b211s252i9 8327 chr4qtel1M 805496 AACCC-AACTCCTGACTCTAACCCTAACCCTAA 805527 - - i i (AACCCT)n#Sim 1 AACCCTAAC-CCTAACCCTAACCCTAACCCTAA 32 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.06 (2 / 31), avg. gap size = 1.00 (2 / 2) 395 27.21 7.35 0.00 chr4qtel1M 805632 805767 (194233) MIR1_Amn#SINE/MIR 7 152 (78) m_b211s601i16 8328 chr4qtel1M 805632 GGCATTCAGGTTTGCTGCACAGAGT-CAGGACCTGGACTC-----ATCTA 805675 v vv i iv v i i- v iv ----- i i MIR1_Amn#SINE 7 GGCAGTGTGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGAGACCTG 56 chr4qtel1M 805676 G--TTAAATGTAACTTCAGACACTTACTAGCTGTGTGACCCTGAGCAAGT 805723 -- i? ? vivivi v v ?i i? ? i i MIR1_Amn#SINE 57 GGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGT 106 chr4qtel1M 805724 CACTTTACCCATTTAT--TTCAGTTTACTCCACTGTAAAAAGGAGA 805767 ? iv i i?--i v vv v i MIR1_Amn#SINE 107 CACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGGA 152 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.57 CpG sites = 20, Kimura (unadjusted) = 36.81 Transitions / transversions = 1.18 (20/17) Gap_init rate = 0.03 (4 / 135), avg. gap size = 2.50 (10 / 4) 664 24.95 8.89 3.81 chr4qtel1M 805648 805872 (194128) MIR#SINE/MIR 24 259 (3) m_b211s601i17 8328 chr4qtel1M 805648 GCACAGAGTCAGGACCTGGACTCATCTAG--TTAAATGTAACTTCAGACA 805695 i iv v v ii -ii i -- ii vivivi v v MIR#SINE/MIR 24 GCACGGGCTCTGGAGCCAGACT-GCCTGGGTTCGAATCCCGGCTCTGCCA 72 chr4qtel1M 805696 CTTACTAGCTGTGTGACCCTGAGCAAGTCACTTTACCCATTTAT--TTCA 805743 i i i v iv i i --i MIR#SINE/MIR 73 CTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCA 122 chr4qtel1M 805744 GTTTACTCCACTGTAAAAAGGAGA-AA-------GCCTTCCTCACAAAGC 805785 v vv v i - -------i v i ii i MIR#SINE/MIR 123 GTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTCATAGGGT 172 chr4qtel1M 805786 T-TTGGGAGGACAAAATGTGGTAAGAATTGTAAAGC-C------CAGTGT 805827 - v iv v v v vv - ------ i MIR#SINE/MIR 173 TGTTGTGAGGATTAAATGAGTTAATACATGTAAAGCGCTTAGAACAGTGC 222 chr4qtel1M 805828 CCAAGCTGGTGGCACATAGTAGGTGCTTAATAAATGTTAGTTTTT 805872 -------- i i i i v MIR#SINE/MIR 223 C--------TGGCACATAGTAAGCGCTCAATAAATGTTAGCTATT 259 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.24 CpG sites = 31, Kimura (unadjusted) = 30.99 Transitions / transversions = 1.35 (31/23) Gap_init rate = 0.07 (16 / 224), avg. gap size = 1.81 (29 / 16) 188 15.79 5.26 0.00 chr4qtel1M 805839 805876 (194124) L2d2_3end#LINE/L2 513 552 (3) m_b211s601i18 8329 chr4qtel1M 805839 GCACATAGTAGGTGCTTAATAAATGTTAGTT--TTTCATT 805876 i i i i v -- v L2d2_3end#LIN 513 GCACACAGTAGGCGCTCAATAAATATTTGTTGATTTGATT 552 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 14.93 CpG sites = 4, Kimura (unadjusted) = 18.05 Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.03 (1 / 37), avg. gap size = 2.00 (2 / 1) 20 22.78 0.00 0.00 chr4qtel1M 806381 806422 (193578) (TG)n#Simple_repeat 1 42 (0) m_b211s252i11 8330 chr4qtel1M 806381 TGTGTGTGTGTATGTGTGTGTGTGCATGTAAATGTGCCTGTG 806422 i ii ivi iv (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 42 Matrix = Unknown Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 80 13.15 0.75 0.00 chr4qtel1M 807075 807207 (192793) (ATGG)n#Simple_repeat 1 134 (0) m_b211s252i12 8331 chr4qtel1M 807075 ATGGATGGATGGATAGAAGGATGGATGAATGGAAGGATACATGGATGGAT 807124 i v i v iv (ATGG)n#Simpl 1 ATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGAT 50 chr4qtel1M 807125 GGATGGATTGATGGAT-GATGGATGGATGGATGGAAGGAAGGAAGGAAGG 807173 v - v v v v (ATGG)n#Simpl 51 GGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGG 100 chr4qtel1M 807174 GTGAATGGATGGATAAATGGATGGATGGATGAAT 807207 i i ii i (ATGG)n#Simpl 101 ATGGATGGATGGATGGATGGATGGATGGATGGAT 134 Matrix = Unknown Transitions / transversions = 1.00 (8/8) Gap_init rate = 0.01 (1 / 132), avg. gap size = 1.00 (1 / 1) 17 20.23 0.00 0.00 chr4qtel1M 808095 808128 (191872) (T)n#Simple_repeat 1 34 (0) m_b211s252i13 8332 chr4qtel1M 808095 TTTTTTTTTTTTTTTGATCTGCCTTTTTTTTTTT 808128 vv i vii (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 34 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 442 23.66 5.34 0.00 chr4qtel1M 809417 809547 (190453) C Tigger9b#DNA/TcMar-Tigger (0) 624 487 m_b211s502i3 8333 chr4qtel1M 809417 CAGTCTATTCTACTGTAACAGAACACATG--TTCCTAAACATCCCTG-GC 809463 vi i i ivi i -- v v i - C Tigger9b#DNA/ 624 CAGTCAGTTCTGCTATAACGCGACATATGCGTTCCTAAAAATCACCGCGC 575 chr4qtel1M 809464 TACACAAAATCACACAATAAAAGTCTCAAAGG--AATGGAAAAATGGAGT 809511 ii i i ii v ii v-- vv i i C Tigger9b#DNA/ 574 TATGCAAAATCGCGCAATAAAAACCACAGGGCTTATGGGGAAAATGGGGT 525 chr4qtel1M 809512 CAGGAGCAAAACACTC--AATCTGTGTCAGTGACACAT 809547 i i v -- v vi C Tigger9b#DNA/ 524 TAGGGGCACAACACTCAAAAACTTCGTCAGTGACACAT 487 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 22.92 CpG sites = 20, Kimura (unadjusted) = 29.25 Transitions / transversions = 1.82 (20/11) Gap_init rate = 0.03 (4 / 130), avg. gap size = 1.75 (7 / 4) 15 10.73 3.33 0.00 chr4qtel1M 809548 809577 (190423) (TTATTT)n#Simple_repeat 1 31 (0) m_b211s252i14 8334 chr4qtel1M 809548 TTATTTTTATTTTTACTGTT-TATTTATTTT 809577 i v - v (TTATTT)n#Sim 1 TTATTTTTATTTTTATTTTTATTTTTATTTT 31 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 275 17.71 4.88 3.61 chr4qtel1M 809601 809682 (190318) C Tigger9b#DNA/TcMar-Tigger (145) 479 397 m_b211s502i4 8333 chr4qtel1M 809601 AAAAAAAGGAACCAAATCAAGACTATGGAGGCACAGT----CACATGCTA 809646 i v v v i --- vi ---- i C Tigger9b#DNA/ 479 AAAGATAGGAACCTAATAAAAAC---GGTAGCACAGTTTTACACATGTTA 433 chr4qtel1M 809647 AATGGTTCAGAAATACTCAAATACTGTAGTAAATAT 809682 v vi ii i C Tigger9b#DNA/ 432 AATGGTTAAGAAATACATAAATACTACAATAAATAT 397 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 20.44 CpG sites = 8, Kimura (unadjusted) = 20.44 Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.05 (4 / 81), avg. gap size = 1.75 (7 / 4) 276 24.72 5.21 3.06 chr4qtel1M 809864 809959 (190041) C Tigger9b#DNA/TcMar-Tigger (217) 407 310 m_b211s502i5 8333 chr4qtel1M 809864 ATAATAAATGTGGTACTTCACCCTAACAAAGACCTGAAGT----TTTTGG 809909 i i i i i i v ---- v C Tigger9b#DNA/ 407 ACAATAAATATGGCACTTTACCTTGAAAAAGACCTGAAGTTTGCTTGTGG 358 chr4qtel1M 809910 ACATGGG-ATCAGAACGAGGGTAACAGCTCAGGAGTTCTGAGGAACTAGT 809958 vi -i i --- vi iiv v viv v i C Tigger9b#DNA/ 357 AAGTGGGCGTCGGA---AGGGTTGCAGCTTGTGAGTTATTGTGAAGTGGT 311 chr4qtel1M 809959 G 809959 C Tigger9b#DNA/ 310 G 310 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 27.62 CpG sites = 14, Kimura (unadjusted) = 30.74 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.05 (5 / 95), avg. gap size = 1.60 (8 / 5) 17 20.93 0.00 0.00 chr4qtel1M 810761 810800 (189200) (CTCC)n#Simple_repeat 1 40 (0) m_b211s252i15 8335 chr4qtel1M 810761 CTTCCTCCCTCCATTCCTTTTTCCCTCTCTCCCTCCCTCC 810800 i v i iii i (CTCC)n#Simpl 1 CTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCC 40 Matrix = Unknown Transitions / transversions = 6.00 (6/1) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 216 31.11 11.50 3.28 chr4qtel1M 811102 811214 (188786) C MIRc#SINE/MIR (117) 151 30 m_b211s601i19 8336 chr4qtel1M 811102 ATCTCCATTTTACAGATAGGGAAATTGAGATT--GAG----TAAGCAA-- 811143 i ii i ii -- ---- ii -- C MIRc#SINE/MIR 151 ATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACT 102 chr4qtel1M 811144 --CCCAGGAAGTCATTTATAAGAAATACATGACAAAA--ATAATTCTAAT 811189 -- -- i --i i ivv i vi i i i--ivi i v i C MIRc#SINE/MIR 101 TGCCCA--AGGTCA--CACAGCTAGTAAGTGGCAGAGCCGGGACTCGAAC 56 chr4qtel1M 811190 GCAGTTCTTTCTT-CCCTAACTCTAG 811214 v v i v- i i v i C MIRc#SINE/MIR 55 CCAGGTCTTCCTGACTCCAAGTCCAG 30 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.71 CpG sites = 25, Kimura (unadjusted) = 43.48 Transitions / transversions = 2.78 (25/9) Gap_init rate = 0.09 (10 / 112), avg. gap size = 1.70 (17 / 10) 202 15.54 0.00 10.26 chr4qtel1M 812525 812567 (187433) L3#LINE/CR1 3545 3583 (516) m_b211s601i20 8337 chr4qtel1M 812525 GAGGTGATAATCCTGTTGTACCTTGCCTGACCTGGTCAGACCA 812567 i i i i ii -- -- L3#LINE/CR1 3545 GAGGTAATAGTCCCGCTGTACTCTGC--G--CTGGTCAGACCA 3583 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 15.16 CpG sites = 6, Kimura (unadjusted) = 18.39 Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.10 (4 / 42), avg. gap size = 1.00 (4 / 4) 473 23.55 6.06 4.79 chr4qtel1M 812576 812740 (187260) C L2d_3end#LINE/L2 (5) 511 345 m_b211s601i21 8338 chr4qtel1M 812576 CAGTCAGTCAACAAGAATGTGTTAAGCACCTATTATATTCCAGGCATTGA 812625 i i v v i i i i i v ivi i v C L2d_3end#LINE 511 CAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTGT 462 chr4qtel1M 812626 ACTGAGC-CTCTGACCCAGGGACACCAAAAAATGGCAAAAGACAT--TCC 812672 i ii - v ----- - v ? ?i i v -- C L2d_3end#LINE 461 GCTAGGCGCTGTG-----GGGA-ACGANAAAANAGTATAAGACATGGTCC 418 chr4qtel1M 812673 CTGCTCACAAGGAGCTCACAGTCTAATGGAAGTGACAACACAGAAATATA 812722 i v i i i v ii v v --v i i C L2d_3end#LINE 417 CTGCCCTCAAGGAGCTTACAATCTAGTTGGGGAGACAAGAC--TAACACA 370 chr4qtel1M 812723 CATGA------CAGAGAAC-ATACA 812740 ------i - C L2d_3end#LINE 369 CATGAAACAATTAGAGAACAATACA 345 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.65 CpG sites = 24, Kimura (unadjusted) = 29.60 Transitions / transversions = 1.85 (24/13) Gap_init rate = 0.07 (12 / 164), avg. gap size = 1.50 (18 / 12) 251 31.32 3.95 1.28 chr4qtel1M 812827 812978 (187022) Plat_L3#LINE/CR1 3155 3310 (263) m_b211s551i4 8339 chr4qtel1M 812827 GATGGAGATTTTGCCATATGAAGACTAGCTGAAAGAACTGAGGCTGCTTA 812876 i v vv i v i vvi i i i i i i i Plat_L3#LINE/ 3155 GATGGAAAATAGGTCCTATGAGGAAAGGTTAAAGGAATTGGGGTTGTTTA 3204 chr4qtel1M 812877 ACCTGAAGAAGAGAAAACT--TGGGCAACACAA-AATACTCTTTAA-TAC 812922 i i ii --v ii vi - ivv i - i Plat_L3#LINE/ 3205 GCCTGGAGAAGAGAAGGCTAAGGGGTGACTTAATAACTGTCTTCAAGTAT 3254 chr4qtel1M 812923 CTGAAAGGCTTTAATATCTAGGAAG--AATCACTCTTGTTCTGCTTGGCC 812970 v i i v ivvv v --i i --v v v v Plat_L3#LINE/ 3255 ATGAAGGGTTTTTATGGGGAGGACGCTGACCA--GTTGTTCTCCATGTCC 3302 chr4qtel1M 812971 CCAGAGGA 812978 v ? Plat_L3#LINE/ 3303 ACNGAGGA 3310 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.94 CpG sites = 26, Kimura (unadjusted) = 41.94 Transitions / transversions = 1.24 (26/21) Gap_init rate = 0.04 (6 / 151), avg. gap size = 1.33 (8 / 6) 17 20.23 0.00 0.00 chr4qtel1M 816193 816226 (183774) (A)n#Simple_repeat 1 34 (0) m_b212s252i0 8340 chr4qtel1M 816193 AAAAAAGAAAAAAACAACAACAAAATAAAACAAA 816226 i v v v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 34 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 197 23.06 7.58 1.43 chr4qtel1M 816385 816450 (183550) C MIRc#SINE/MIR (37) 231 162 m_b212s601i0 8341 chr4qtel1M 816385 AATTTACAAATAG-TTTCCCACACAATTA----AATGGATCTTCCCAATA 816429 i vv - v i - ---- v v i v i C MIRc#SINE/MIR 231 AGTTTACAAAGCGCTTTCACATACA-TTATCTCATTTGATCCTCACAACA 183 chr4qtel1M 816430 AACCTGTGATACAGGAAGGGC 816450 v vii v C MIRc#SINE/MIR 182 ACCCTGTGAGGTAGGCAGGGC 162 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.62 CpG sites = 6, Kimura (unadjusted) = 27.62 Transitions / transversions = 0.67 (6/9) Gap_init rate = 0.05 (3 / 65), avg. gap size = 2.00 (6 / 3) 19 22.94 0.00 0.00 chr4qtel1M 817832 817877 (182123) (ATT)n#Simple_repeat 1 46 (0) m_b212s252i1 8342 chr4qtel1M 817832 ATTATTATTAATATAATTATTATAATAACTCTTAGGATTCTTATTA 817877 v v v v i v vv v (ATT)n#Simple 1 ATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTA 46 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 253 34.75 7.63 0.00 chr4qtel1M 818085 818202 (181798) L2d2_3end#LINE/L2 424 550 (5) m_b212s601i1 8343 chr4qtel1M 818085 GTCTGTCCCATCAGTTTGTACCCTCCAAGAGAACAAGAA--ATGTCTCAT 818132 vi v ii v vv vv ii i i -- i L2d2_3end#LIN 424 GTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTAT 473 chr4qtel1M 818133 ATCTCTATGT-TCCT----GGTACTCATCTGAGGGCCTGGCTTGTAGCAG 818177 ii v - i----i ii ii v vv v v viii i L2d2_3end#LIN 474 ACTTCTTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAGTAG 523 chr4qtel1M 818178 ATAATTAA--AATATTTATTGACTTGA 818202 iiiv i -- i i L2d2_3end#LIN 524 GCGCTCAATAAATATTTGTTGATTTGA 550 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.50 CpG sites = 26, Kimura (unadjusted) = 49.28 Transitions / transversions = 1.73 (26/15) Gap_init rate = 0.03 (4 / 117), avg. gap size = 2.25 (9 / 4) 341 19.73 11.36 2.08 chr4qtel1M 818304 818391 (181609) C MIR3#SINE/MIR (27) 181 86 m_b212s601i2 8341 chr4qtel1M 818304 CTGCAAGGGAGCTAAAAGACCATGGAATCCAAACTTCTCATTTTATAGAT 818353 v v v i i vv i v ii i C MIR3#SINE/MIR 181 CTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGAT 132 chr4qtel1M 818354 GAGGAAACTGAGAT---------TGAA-TGACTAGCCCAGGAAGCCAC 818391 ii--------- - v -- i i C MIR3#SINE/MIR 131 GAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCA--AGGTCAC 86 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 23.28 CpG sites = 10, Kimura (unadjusted) = 23.28 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.05 (4 / 87), avg. gap size = 3.00 (12 / 4) 302 25.15 12.30 8.73 chr4qtel1M 818338 818459 (181541) C MIRc#SINE/MIR (118) 150 25 m_b212s601i3 8341 chr4qtel1M 818338 TTCTCATTTTATAGATGAGGAAACT----------GAGATTGAATGACTA 818377 i i i ---------- i i i v C MIRc#SINE/MIR 150 TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTT 101 chr4qtel1M 818378 GCCCAGGAAGCCACTGTTAAAAAAAAAAAAAAAGGTGGAAAA----GAAT 818423 i ivvv v i iv ----------- v i ---- i i C MIRc#SINE/MIR 100 GCCCAAGGTCACACAGCTAGTAA-----------GTGGCAGAGCCGGGAC 62 chr4qtel1M 818424 TCTAAGGCAGGTCTTTCT-ACCCCAACTCTAGTACTC 818459 v vv i - i v i i C MIRc#SINE/MIR 61 TCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTC 25 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.52 CpG sites = 17, Kimura (unadjusted) = 31.52 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.12 (14 / 121), avg. gap size = 1.86 (26 / 14) 544 29.28 8.29 0.00 chr4qtel1M 819036 819216 (180784) MIRc#SINE/MIR 10 205 (63) m_b212s601i4 8344 chr4qtel1M 819036 GTAGTGCAATGGAGACAGACCTGGACATAGAATCAGGAGTGCCTGAGTTT 819085 i i i v vv v i i ivi i i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr4qtel1M 819086 AAATTGAGTCTCAGACAATCACTAGCTGTGTGCCCCTTCTTAACT-ACTT 819134 i i ivv v v v v i v i vvvi v - MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTT 109 chr4qtel1M 819135 AACATCAGTTTGCCTCAGTTTCCTCAACTCTCAA--------AATAATAT 819176 v vv vv v v v -------- i MIRc#SINE/MIR 110 AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAC 159 chr4qtel1M 819177 C------ATCTCATTTGTAAGGTTATTGTGAGGATAAAGTGACATA 819216 ------ii vvi iii i i v i v MIRc#SINE/MIR 160 CTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATA 205 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.48 CpG sites = 25, Kimura (unadjusted) = 37.44 Transitions / transversions = 0.89 (25/28) Gap_init rate = 0.02 (3 / 180), avg. gap size = 5.00 (15 / 3) 255 23.67 4.08 5.15 chr4qtel1M 820219 820316 (179684) C MIR3#SINE/MIR (1) 207 111 m_b212s601i5 8345 chr4qtel1M 820219 AATCACCAAAATCATATGTTGT-AGAGCTGAAAGACACTTGAGA-ATTAA 820266 i- i viv - i iv i v - i v C MIR3#SINE/MIR 207 AATCAT-AGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCAT 159 chr4qtel1M 820267 AGAGTTCACAGACCCTCACCAATTTATAG--GAGGAAACTGAAACACAGA 820314 vv i --- i -i v i -- ii v C MIR3#SINE/MIR 158 CTAGTCCA---ACCCCC-TCATTTTACAGATGAGGAAACTGAGGCCCAGA 113 chr4qtel1M 820315 GA 820316 C MIR3#SINE/MIR 112 GA 111 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.99 CpG sites = 13, Kimura (unadjusted) = 28.99 Transitions / transversions = 1.44 (13/9) Gap_init rate = 0.08 (8 / 97), avg. gap size = 1.12 (9 / 8) 195 15.92 17.31 3.39 chr4qtel1M 820282 820333 (179667) C MIR#SINE/MIR (116) 146 88 m_b212s601i6 8345 chr4qtel1M 820282 TCACCAATTTATAG--GAGGAAACTGAAACACAGAGAACGATT------- 820322 v v i -- ii -- i ------- C MIR#SINE/MIR 146 TCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGA--GGTTAAGTAAC 99 chr4qtel1M 820323 TTGCCTAAAGT 820333 i i C MIR#SINE/MIR 98 TTGCCCAAGGT 88 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 18.51 CpG sites = 6, Kimura (unadjusted) = 18.51 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.08 (4 / 51), avg. gap size = 2.75 (11 / 4) 458 31.76 6.57 3.18 chr4qtel1M 820464 820889 (179111) L1M2_orf2#LINE/L1 1665 2104 (1187) m_b212s551i1 8346 chr4qtel1M 820464 AAGAATAATTCATTCTGATCAAATGGGATTTGTACCAGAGATGCAAGGAT 820513 ii ? ? iiv i i v i L1M2_orf2#LIN 1665 AAAGATNATNCACCATGATCAAGTGGGATTTATCCCAGGGATGCAAGGAT 1714 chr4qtel1M 820514 AGTTCAATGTTAGGACAACAATGAACATAACCAATCACATT--CTAAACC 820561 i ii vv v v v i i i ivv i-- vi iv L1M2_orf2#LIN 1715 GGTTCAACATACGCAAATCAATAAACGTGATACATCACATCAACAGAATG 1764 chr4qtel1M 820562 AA-AACATCCAAGACCACACAGTCATTTCAACAGATAAAGAAAGTGCATT 820610 -i --- i i iii i i iv iv L1M2_orf2#LIN 1765 AAGGACA---AAAACCATATGATCATCTCAATAGATGCAGAAAAAGCATT 1811 chr4qtel1M 820611 GCATAAAGTACACCATTCTTTTATGGCAAAAATTT------AATTAGTAG 820654 vv i v v i i i ii i i------ -- L1M2_orf2#LIN 1812 TGATAAAATTCAACATCCCTTCATGATAAAAACTCTCAACAAATTAG--G 1859 chr4qtel1M 820655 TATAGGCCTAATGGGACCACTTTCAAGAGTATAAAAA-CATCTATCTAAA 820703 ---- - i vvvii v vv ii- v vvv L1M2_orf2#LIN 1860 TATAG----AA-GGAACGTACCTCAACACAATAAAGGCCATATATGACAA 1904 chr4qtel1M 820704 ACCAAAAG----TATCACACAAAATGGGATTTCATTAGAAGTTTTTCCGA 820749 v v ----i i vi ivvvvi ii ii vv L1M2_orf2#LIN 1905 ACCCACAGCTAACATCATACTGAATGGGGAAAAGTTGAAAGCCTTTCCTC 1954 chr4qtel1M 820750 TAAATTCAGGAGGGAAGCAAGGATGGTTACTCTCCCTAGTCTT------- 820792 iv? v ivi ii vii i v i v ii ------- L1M2_orf2#LIN 1955 TAAGANCTGGAACAAGACAAGGATGCCCACTTTCACCACTTCTATTCAAC 2004 chr4qtel1M 820793 ---GTA---GAAATGCTGGCAATTGCAAAAAGACAAGAGAAAGGACTTAG 820836 --- --- i v i v vv vv i i v v i L1M2_orf2#LIN 2005 ATAGTACTGGAAGTCCTAGCCAGAGCAATTAGGCAAGAGAAAGAAATAAA 2054 chr4qtel1M 820837 AGGAACAAAAACAAGTT-AAAAAAAGAGCATCAAAATATACCTGTATGCT 820885 v i----v i -i ii iivi v i v v v L1M2_orf2#LIN 2055 AGGCAT----CCAAATTGGAAAGGAGGAAGTCAAATTGTCCCTGTTTGCA 2100 chr4qtel1M 820886 GATG 820889 L1M2_orf2#LIN 2101 GATG 2104 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 42.51 CpG sites = 74, Kimura (unadjusted) = 42.95 Transitions / transversions = 1.30 (74/57) Gap_init rate = 0.05 (23 / 425), avg. gap size = 1.83 (42 / 23) 533 30.91 5.98 1.56 chr4qtel1M 820464 820831 (179169) L1MC_orf2#LINE/L1 1668 2051 (1243) m_b212s551i0 8346 chr4qtel1M 820464 AAGAATAATTCATTCTGATCAAATGGGATTTGTACCAGAGATGCAAGGAT 820513 v v iivi i i i v iv v L1MC_orf2#LIN 1668 AAGAATTATACACCACGACCAAGTGGGATTTATCCCAGGTATGCAAGGCT 1717 chr4qtel1M 820514 AGTTCAATGTTAGGACAACAATGAACATAACCAATCACATTCTAAACCAA 820563 i ii v i v v v ii i v ivvv iv v L1MC_orf2#LIN 1718 GGTTCAACATTCGAAAATCAATTAATGTAATCCATCACATCAACAGGCTA 1767 chr4qtel1M 820564 AACATCCAAGACCACACAGTCATTTCAACAGATAAAGAAAGTGCATTGCA 820613 v vvv i i iii v i iv iv vv L1MC_orf2#LIN 1768 AAGAAGAAAAATCACATGATCATATCAATAGATGCAGAAAAAGCATTTGA 1817 chr4qtel1M 820614 TAAAGTACACCATTCTTTTATGGCAAAAATTTAATTAGTAGTATAGGCCT 820663 i i v v ii v i ii i i-- i i ivv vv L1MC_orf2#LIN 1818 CAAAATCCAACACCCATTCATGATAAAAACTC--TCAGCAAACTAGGAAT 1865 chr4qtel1M 820664 A-ATGGGACCACTTTCAAGAGTATAAA-AACATCTATCTAAAACCAAAAG 820711 - v v viii vvvv - ivv v v L1MC_orf2#LIN 1866 AGAGGGGAACTTCCTCAACTTGATAAAGAACATCTACAAAAAACCTACAG 1915 chr4qtel1M 820712 ----TATCACACAAAATGG---GATTTCATTAGAAGTTTTTCCGATAAAT 820754 ----i i vv --- ---v i ? i i v iv L1MC_orf2#LIN 1916 CTAACATCATACTTAATGGTGAGA---AACTNGAAGCTTTCCCGCTAAGA 1962 chr4qtel1M 820755 TCAGGAGGGAAGCAAGGATGGTTACTCTCCCTAGTC----------TTGT 820794 ivi i viiv v i v ---------- i L1MC_orf2#LIN 1963 TCAGGAACAAGGCAAGGATGTCCCCTCTCACCACTCCTTTTCAACATCGT 2012 chr4qtel1M 820795 A---GAAATGCTGGCAATTGCAAAAAGACAAGAGAAAGGA 820831 --- i v i v v v - L1MC_orf2#LIN 2013 ACTGGAAGTCCTAGCTAATGCAATAAGACAAGA-AAAGGA 2051 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.62 CpG sites = 55, Kimura (unadjusted) = 40.54 Transitions / transversions = 0.96 (55/57) Gap_init rate = 0.03 (12 / 367), avg. gap size = 2.33 (28 / 12) 11 25.60 0.00 2.56 chr4qtel1M 823265 823304 (176696) (GAGAGGA)n#Simple_repeat 1 39 (0) m_b212s252i2 8347 chr4qtel1M 823265 GAAAGGAGAGAAGGGAGAGGGGAGTTAGAGTGAGGAGGGA 823304 i i i i -vi v i (GAGAGGA)n#Si 1 GAGAGGAGAGAGGAGAGAGGAGAG-AGGAGAGAGGAGAGA 39 Matrix = Unknown Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1) 19 33.01 0.00 0.00 chr4qtel1M 827915 827989 (172011) (AAAAAA)n#Simple_repeat 1 75 (0) m_b212s252i3 8348 chr4qtel1M 827915 AAAAGAGCAAAGAGAAAAAAGAAAAAAAAAGCAAATAAACCCCAACAGTA 827964 i iv i i i iv v vvvv v iv (AAAAAA)n#Sim 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr4qtel1M 827965 ACCAAAAAAAAAAAAAAAATGAAAA 827989 vv vi (AAAAAA)n#Sim 51 AAAAAAAAAAAAAAAAAAAAAAAAA 75 Matrix = Unknown Transitions / transversions = 0.67 (8/12) Gap_init rate = 0.00 (0 / 74), avg. gap size = 0.0 (0 / 0) 16 33.68 0.00 0.00 chr4qtel1M 828993 829045 (170955) (TT)n#Simple_repeat 1 53 (0) m_b212s252i5 8349 chr4qtel1M 828993 TTTTTCTTCTTTTTTTCTCTCTCATGTTTTTTTTCCTTTTGTTCTGATTT 829042 i i i i i iv v ii v i vv (TT)n#Simple_ 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr4qtel1M 829043 TTT 829045 (TT)n#Simple_ 51 TTT 53 Matrix = Unknown Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 13 25.59 2.38 0.00 chr4qtel1M 830160 830201 (169799) (AAT)n#Simple_repeat 1 43 (0) m_b212s252i6 8350 chr4qtel1M 830160 AATAA-AAAAAAATTAATCATAATAATATTATGAACAATTATA 830201 - v v v v v vv i v (AAT)n#Simple 1 AATAATAATAATAATAATAATAATAATAATAATAATAATAATA 43 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.02 (1 / 41), avg. gap size = 1.00 (1 / 1) 50 0.00 0.00 0.00 chr4qtel1M 830584 830626 (169374) (TA)n#Simple_repeat 1 43 (0) c_b212s251i0 8351 chr4qtel1M 830584 TATATATATATATATATATATATATATATATATATATATATAT 830626 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATAT 43 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 18 23.93 0.00 0.00 chr4qtel1M 834015 834063 (165937) (TATTAA)n#Simple_repeat 1 49 (0) m_b212s252i7 8352 chr4qtel1M 834015 TAATACTAATATTATTAATATTAATAATATTAGCAATATTAATGTAAAT 834063 v v v v v v vi i v (TATTAA)n#Sim 1 TATTAATATTAATATTAATATTAATATTAATATTAATATTAATATTAAT 49 Matrix = Unknown Transitions / transversions = 0.25 (2/8) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 233 25.82 0.00 1.61 chr4qtel1M 836261 836323 (163677) C L3b_3end#LINE/CR1 (4) 1202 1141 m_b212s601i7 8353 chr4qtel1M 836261 AAATCACTAAATCTCGGAATTGGAAAGGAACTCACAGGTTGCTTGCTCCA 836310 i ivi i v v iiii iv - C L3b_3end#LINE 1202 AAACCATAGAATCTCAGAATTGGAAAGGACCTCAGAGGTCATCTAGTCC- 1154 chr4qtel1M 836311 AGCCATACCCCCA 836323 v v ? i C L3b_3end#LINE 1153 ATCCCTNCCCCTA 1141 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.25 CpG sites = 10, Kimura (unadjusted) = 33.25 Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.02 (1 / 62), avg. gap size = 1.00 (1 / 1) 382 36.84 11.34 0.00 chr4qtel1M 836687 836933 (163067) C L3#LINE/CR1 (341) 3758 3484 m_b212s601i8 8354 chr4qtel1M 836687 CTCTTCTAGGTCTTCT--------AACTAAAATTCCTTAGTTTTTCCAAA 836728 i i --------ii vv ii ii i v C L3#LINE/CR1 3758 CTCCTCTAAGTCTTCTCTTCTCCAGGCTAAACATCCCCAGTTCCTTCAAC 3709 chr4qtel1M 836729 CGATCCTCATGGCACATACTT--GAGGTGCTTCATCATCCTGGCTTTCTT 836776 v ivv iv --v iiv i iiviii C L3#LINE/CR1 3708 CGTTCCTCATATGACATGGTTTCCAGACCCTTCACCATCCTGGTCGCTCT 3659 chr4qtel1M 836777 ACGCTGAATACTCTATAATTTATCCACATCTTGGTTAAGCTGTGGC-TAT 836825 v v i ii v vi i i v ii iivv iv -ivi C L3#LINE/CR1 3658 CCTCTGGACGCGCTCCAGTTTGTCAATGTCCCTCTTAAAATGTGGCGCCC 3609 chr4qtel1M 836826 AGGGGTGAACACAA------------AGTTT---CAGGGCAGAGTA-AGT 836859 iiv i ------------i i --- v - i C L3#LINE/CR1 3608 AGAACTGAACGCAATACTCCAGATGTGGTCTGACCAGCGCAGAGTACAGC 3559 chr4qtel1M 836860 GATATTACCACGTCCTTGTTTCAAGAAGTGCTGCCTTTTCCCATGCAGCC 836909 iv i ii v i vv? vi viivv i i i viiv C L3#LINE/CR1 3558 GGGACTATTACCTCCCTTGNTCTGGACACTATACTTCTATTAATGCAGCC 3509 chr4qtel1M 836910 CAACACTGT-TTTCCATTTCTGACA 836933 i v i i- vv v i i C L3#LINE/CR1 3508 TAAGATTGCATTAGCTTTTTTGGCA 3484 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 50.28 CpG sites = 56, Kimura (unadjusted) = 53.88 Transitions / transversions = 1.60 (56/35) Gap_init rate = 0.03 (7 / 246), avg. gap size = 4.00 (28 / 7) 311 31.25 4.48 4.48 chr4qtel1M 837054 837187 (162813) C L2a_3end#LINE/L2 (0) 517 384 m_b212s601i9 8355 chr4qtel1M 837054 ATCCATTCATTGATCATCAAGCATTTGTGAAGTA---ATTATGGGCCAGG 837100 i --- v ii i vi ii--- i v C L2a_3end#LINE 517 ATTCATTCATT---CAACAAATATTTATTGAGCGCCTACTATGTGCCAGG 471 chr4qtel1M 837101 CTCCATTCTAGACAACAAGGACAC--TAA-GAAAAAGGTAAAGAGAAATT 837147 v ii i iviii i --i i- v iii i v i --- C L2a_3end#LINE 470 CACTGTTCTAGGCGCTGGGGATACAGCAGTGAACAAAACAGACAAAA--- 424 chr4qtel1M 837148 GTCCCTGGACTCCAGGAGCTTAAATTCTGTTGATGGAAGA 837187 vv vv v iv iv i C L2a_3end#LINE 423 GTCCCTGCCCTCATGGAGCTTACATTCTAGTGGGGGGAGA 384 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.44 CpG sites = 26, Kimura (unadjusted) = 42.42 Transitions / transversions = 1.86 (26/14) Gap_init rate = 0.07 (9 / 133), avg. gap size = 1.33 (12 / 9) 377 36.66 6.75 4.40 chr4qtel1M 837551 837861 (162139) C L3#LINE/CR1 (159) 3940 3623 m_b212s601i10 8356 chr4qtel1M 837551 CAATCTATTCTACTTT-GAATAGCTCTAATTGCTGGGGAGTTTCCTCCTA 837599 ii i i i - i i i i i ii iiii i C L3#LINE/CR1 3940 CAGCCCATTCCATTTTTGGACAGCTCTGATTGTTAGAAAGTTCTTCCTTA 3891 chr4qtel1M 837600 TCTGTCTTTCTAAACCTGTTTTTCTA-AATATCCACTAACTGTTCTTGGT 837648 v - vvvi v i ii ii i- iv iv i v i i C L3#LINE/CR1 3890 TAT-TGAGCCGAAATCTGCCTCCCTGTAACTTCCACCCATTGGTCCTAGT 3842 chr4qtel1M 837649 TTTGCCTTATGGAA-CACAGTGACACACACTTCTAAAGCTTCCTTTATGT 837697 i i v i- vv --- i vv vv i i ii ii C L3#LINE/CR1 3841 TCTGCCCTCTGGAGCCACACAGA---ATAAGTCTAATCCCTCTTCCACAT 3795 chr4qtel1M 837698 GAAGAGGGTCCTTCATGTTCTCAGAGACACATTTTATATCTCCCGTTAAG 837747 --- vi i vi vi iii vv v i i i-i C L3#LINE/CR1 3794 ---GACAGCCCTTCAAATATTTGAAGACAGCTATCATGTCTCCT-CTAAG 3749 chr4qtel1M 837748 TACTGACATTTATTTCTCT--GCTAAACTTTACCAATAAATGCAATC--- 837792 - ---- i -i i-- v iv i vvv v i --- C L3#LINE/CR1 3748 T-CT----TCT-CTTCTCCAGGCTAAACATCCCCAGTTCCTTCAACCGTT 3705 chr4qtel1M 837793 -------------AGTTTTCAGTCTTTTCCCCATCCTGATTGAACTCCTA 837829 -------------i i v ii v i i vv v C L3#LINE/CR1 3704 CCTCATATGACATGGTTTCCAGACCCTTCACCATCCTGGTCGCTCTCCTC 3655 chr4qtel1M 837830 TGGATATACCTAAGCTTCTCTGTGTTTTCCTT 837861 iiii iiv i v vi iiii C L3#LINE/CR1 3654 TGGACGCGCTCCAGTTTGTCAATGTCCCTCTT 3623 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 52.11 CpG sites = 74, Kimura (unadjusted) = 54.60 Transitions / transversions = 2.11 (74/35) Gap_init rate = 0.06 (20 / 310), avg. gap size = 1.75 (35 / 20) 13 19.32 8.77 1.64 chr4qtel1M 837862 837918 (162082) (TCTCCT)n#Simple_repeat 1 61 (0) m_b212s252i8 8357 chr4qtel1M 837862 TCTCCCTTC-CCCTC-CCCT-TCCTTCTCCTTTTTCTT-TCATTTTCCCT 837907 - - i - i - i i - v i i (TCTCCT)n#Sim 1 TCT-CCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTT 49 chr4qtel1M 837908 -TTCTTTTCCTT 837918 - i i (TCTCCT)n#Sim 50 CTCCTTCTCCTT 61 Matrix = Unknown Transitions / transversions = 8.00 (8/1) Gap_init rate = 0.11 (6 / 56), avg. gap size = 1.00 (6 / 6) 20 10.61 4.88 0.00 chr4qtel1M 837879 837919 (162081) (TTCCTT)n#Simple_repeat 1 43 (0) m_b212s252i9 8357 chr4qtel1M 837879 TTCCTTCTCCTTTTTC-TTTCATTTTCCCTTT-CTTTTCCTTT 837919 i i - v i - (TTCCTT)n#Sim 1 TTCCTTTTCCTTTTCCTTTTCCTTTTCCTTTTCCTTTTCCTTT 43 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 201 26.70 16.67 0.85 chr4qtel1M 837920 838021 (161979) C MIR#SINE/MIR (143) 119 2 m_b212s601i11 8358 chr4qtel1M 837920 GGCA-ATAAGGGTTGTGT--CTTGCCCAGGGTCTTTATAGCTATTAAGTG 837966 - v ii iv -- i -vi i v C MIR#SINE/MIR 119 GGCACAGAGAGGTTAAGTAACTTGCCCAAGGTC-ACACAGCTAGTAAGTG 71 chr4qtel1M 837967 TCAA---CGG--TTTGAGACTA---AGTTTGACTTCAAA-----TGCTCT 838003 v i--- -- i iv i --- i i i i ----- C MIR#SINE/MIR 70 GCAGAGCCGGGATTCGAACCCAGGCAGTCTGGCTCCAGAGCCCGTGCTCT 21 chr4qtel1M 838004 TGATTCCAGTGCT-CACTG 838021 i iiv vi -i C MIR#SINE/MIR 20 TAACCACTATGCTATACTG 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.09 CpG sites = 19, Kimura (unadjusted) = 34.70 Transitions / transversions = 2.38 (19/8) Gap_init rate = 0.08 (8 / 101), avg. gap size = 2.25 (18 / 8) 208 25.77 8.49 8.49 chr4qtel1M 837937 838042 (161958) C MIRb#SINE/MIR (162) 106 1 m_b212s601i12 8358 chr4qtel1M 837937 CTTGCCCAGGGTCTTTATAGCTATTAAGTGTCAA---CGG--TTTGAGAC 837981 i -vi i v v i--- -- i iv C MIRb#SINE/MIR 106 CTTGCCCAAGGTC-ACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACC 58 chr4qtel1M 837982 TAA----GTTTGACTTCAAATGCTCTTGATTCCAGTGCTCACTGAGCAAC 838027 i i---- i i - i v -i --- vii vi v C MIRb#SINE/MIR 57 CAGGTCTGTCTGACTCCAAA-GCCCGTG-CTC---TTTCCACTGCACCAC 13 chr4qtel1M 838028 CCAGCTGCCCTTTTG 838042 --- i i C MIRb#SINE/MIR 12 ---GCTGCCCCTCTG 1 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.27 CpG sites = 17, Kimura (unadjusted) = 32.88 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.11 (12 / 105), avg. gap size = 1.50 (18 / 12) 183 26.00 2.00 0.00 chr4qtel1M 838102 838151 (161849) C L2a_3end#LINE/L2 (89) 428 378 m_b212s601i13 8359 chr4qtel1M 838102 CACAAATGCCTTTCCTCAAGGAGCTAACATTCTAA-AGGAGAAAACACAC 838150 v i v vi v v i-i i i i v C L2a_3end#LINE 428 CAAAAGTCCCTGCCCTCATGGAGCTTACATTCTAGTGGGGGGAGACAGAC 379 chr4qtel1M 838151 A 838151 C L2a_3end#LINE 378 A 378 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.40 CpG sites = 7, Kimura (unadjusted) = 32.40 Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.02 (1 / 49), avg. gap size = 1.00 (1 / 1) 207 22.95 8.20 0.00 chr4qtel1M 838110 838170 (161830) C L2c_3end#LINE/L2 (80) 398 333 m_b212s601i14 8359 chr4qtel1M 838110 CCTTTCCTCAAGGAGCTAACATTCTAAAGGAGAAAACACACAC----ACA 838155 vi v v iv i i v ?---- C L2c_3end#LINE 398 CCTGCCCTCAAGGAGCTCACAGTCTAGTGGAGGAGACAGACANGTAAACA 349 chr4qtel1M 838156 CATAATTGT-ATATAA 838170 v i ii- i C L2c_3end#LINE 348 GACAATTACAATACAA 333 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.42 CpG sites = 8, Kimura (unadjusted) = 28.42 Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.03 (2 / 60), avg. gap size = 2.50 (5 / 2) 292 28.87 5.38 3.16 chr4qtel1M 838209 838301 (161699) C L2c_3end#LINE/L2 (20) 458 364 m_b212s601i15 8360 chr4qtel1M 838209 TTTTTTAAGTACCTACTATACACCAGCTGTT----ATACTAAGTGCAGAA 838254 v i ii iii vi i ---- v --- vi C L2c_3end#LINE 458 TTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGATACAAAG---ATGA 412 chr4qtel1M 838255 ACAGAAC-CAGTCCCTGCTCACAAGAAGCTCATCTTCTAATGCAGGGG 838301 i ii - i i v i ivv i v i C L2c_3end#LINE 411 ATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAGTGGAGGAG 364 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.71 CpG sites = 18, Kimura (unadjusted) = 38.45 Transitions / transversions = 2.25 (18/8) Gap_init rate = 0.05 (5 / 92), avg. gap size = 1.60 (8 / 5) 314 29.63 9.54 4.41 chr4qtel1M 838486 838831 (161169) C L2c_3end#LINE/L2 (102) 376 14 m_b212s601i16 8360 chr4qtel1M 838486 TCCAGTGGTTGAGAT-GACATGTACACA-ACTATGTGCAA-ATAAGTTAA 838532 i vv i- ? v - v - i - i C L2c_3end#LINE 376 TCTAGTGGAGGAGACAGACANGTAAACAGACAAT-TACAATACAAGTTAA 328 chr4qtel1M 838533 -AATA--TGCTA-AATTGGAG-ATAATCTGTGAAAGAG----ATGAGAGG 838573 -i -- - v - ------ v i ---- i v C L2c_3end#LINE 327 TGATAAGTGCTATAATGGGAGTATA------GACAGGGTGCTATGGGAGC 284 chr4qtel1M 838574 AATGGTGAGGAAGTCT---CTAGCAACTGGGAAGATAAGGAAAGGCTTCT 838620 vv iv ivii --- ?-- v ii i v i i C L2c_3end#LINE 283 ACAGAGGAGGGCACCTAGACTAGN--CTTGGGGGGTCAGGGAAGGCTTCC 236 chr4qtel1M 838621 ATGAA-AGGAGTTATTTCAGCCGAGTTTTGAAGTA-----AGCCGTTTG- 838663 vv i- v vi i v i ?i v ----- vv v - C L2c_3end#LINE 235 CGGAGGAGGTGACATCTGAGCTGAGNCTTGAAGGATGAGTAGGAGTTAGC 186 chr4qtel1M 838664 AAGATGCCGAGAGATGGCATAAGAAGCTTCCAGGAATGAGTGGCAGTCAG 838713 v i -- ii v viv ivv v vii vii ivv C L2c_3end#LINE 185 CAGGTG--GAAGGAGGGGGGAAGAGCATTCCAGGCAGAGGGAACAGCATG 138 chr4qtel1M 838714 AACAAAGGTGTGGAAATTGGAGAAGGA--GCACCATATGTGGGGAA-G-A 838759 vi i?i iiiv - i -- iv i i v - - C L2c_3end#LINE 137 TGCAAAGGCNCGGAGGCAGGA-AAGAACTGCGGCGTGTTTGGGGAATGCA 89 chr4qtel1M 838760 AGAA---CAGTTTGGCTGGACCACA---AGCTATCTGAAGGGAAGTGATG 838803 ? --- v v i ---i v --- i i iv C L2c_3end#LINE 88 AGNAGTTCAGTGTGGCTGGAGCATAGTGGGCGA---GGAGGGGAGTGGAG 42 chr4qtel1M 838804 CATAAGAAAGCTGAAAAGAT-GGCAAAAG 838831 v -i vi i i i i - iii C L2c_3end#LINE 41 GA-GATGAGGCTGGAGAGGTAGGCAGGGG 14 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.95 CpG sites = 55, Kimura (unadjusted) = 39.50 Transitions / transversions = 1.28 (55/43) Gap_init rate = 0.10 (34 / 345), avg. gap size = 1.44 (49 / 34) 325 35.41 7.96 2.30 chr4qtel1M 838537 838825 (161175) C L2d2_3end#LINE/L2 (230) 325 21 m_b212s601i17 8360 chr4qtel1M 838537 TGCTAAAT---TGG---AGATAAT--CTGTGA-AAGAGATGAGAGGAATG 838577 i --- --- i --? iv - i v v i-- C L2d2_3end#LIN 325 TGCCAAATGAATGGTACAGACAATAANTGCTATAGGAGTTCAGAGGAG-- 278 chr4qtel1M 838578 GTGAGGAAGTCTCTAGCAACTGGGAAGATAAGGAAAGGCTTCTATGAAAG 838627 -- ii ii v ?vvii iiv i v i - i i i C L2d2_3end#LIN 277 --GGAGAGATCACTNCGGGCTGGAGTGGTCAGGGAAGGCTTC-ACGGAGG 231 chr4qtel1M 838628 GAGT--TATTTCAGCCGAGTTTTGAAG--TAAGCCG--TTTGAAGATGCC 838671 ii --? v i i ii -- ii iv -- i v v iv C L2d2_3end#LIN 230 AGGTGGNATTTGAGCTGGGCCTTGAAGGATGGGTAGGATTTGGATAGGTG 181 chr4qtel1M 838672 GAGAGATGGCATAAGAAGCTTCCAGGAATGAGTGGCAGTCAGAACAAAGG 838721 ivi viv iivv viv i vii i ivv i C L2d2_3end#LIN 180 GAGAGGAAGGGGAAGGGCATTCCAGGCGGGGGGAACGGCGTGAGCAAAGG 131 chr4qtel1M 838722 TGTGGAAATTGGAGAAGGAGCACCATATGT---GGGGA-----AGAAGAA 838763 i ii iii-- i ? v vviii --- ----- v v C L2d2_3end#LIN 130 CGCAGAGGC--GGGAANGCGCAAGGCGTGTTCGGGGGACAGTGAGTAGAC 83 chr4qtel1M 838764 CAGTTTGGCTGGACCACAAGCTATCTGAAGGGAAGTGATGCATAAGAAAG 838813 v iv i v viv ? i i ii vivi v i C L2d2_3end#LIN 82 CAGTTTGGCTGGAGCGGAGGGTTCGTGNAGGGGAATAGTGGGAGATAAGG 33 chr4qtel1M 838814 CTGAAAAGATGG 838825 i i?i C L2d2_3end#LIN 32 CTGGAAAGGNAG 21 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.82 CpG sites = 64, Kimura (unadjusted) = 52.65 Transitions / transversions = 1.78 (64/36) Gap_init rate = 0.06 (16 / 288), avg. gap size = 1.88 (30 / 16) 438 37.01 8.67 1.31 chr4qtel1M 838886 839312 (160688) C L2#LINE/L2 (240) 2842 2385 m_b212s601i18 8360 chr4qtel1M 838886 TTGAGTGG-GGAGCGACAT---TTGTTCCTACATGTTAGGAC-ATTATTG 838930 ii - i ---i v- i i v ii v- i i v C L2#LINE/L2 2842 TTGAGCAGAGGAGTGACATGATCTGA-CTTACGTTTTAAAAGGATCACTC 2794 chr4qtel1M 838931 TGGCAGTT-TAATG-GAA-GGATTGGAGAGGAGAGAGATCTGCCTCAAGA 838977 v i - iv - -i i ? i i vi iviv vvv i i C L2#LINE/L2 2793 TGGCTGCTGTGTTGAGAATAGACTGNAGGGGGGCAAGGGTGGAAGCAGGG 2744 chr4qtel1M 838978 AATCCAATTAGA------------TA--CCAAATGAGATGTGTTTAAAAC 839013 iv i i------------ -- iii vi v vivii C L2#LINE/L2 2743 AGACCAGTTAGGAGGCTATTGCAGTAATCCAGGCGAGAGATGATGGTGGC 2694 chr4qtel1M 839014 TTGAATTAGAGCAGTTGCTGTGTGAATG-----AAG-GGT--AATATAAA 839055 i ii i ii v v viii ----- - --i vivii C L2#LINE/L2 2693 TTGGACCAGGGTGGTGGCAGTGGAGGTGGTGAGAAGTGGTCGGATTCTGG 2644 chr4qtel1M 839056 AGATGTGGTGGCCATTGAAATGACCAGATTTGGCAGCTGATTAGATATGG 839105 v i vv ivvi v ivi vi viiiiv i i C L2#LINE/L2 2643 ATATATTTTGAAGGTAGAGCCGACAGGATTTGCTGATGGATTGGATGTGG 2594 chr4qtel1M 839106 GAATTGAGAGATAGTGAGAAGTGAAGAATAAACCTGGGGTTGTGAATTTG 839155 ivv v v i v i i vi iii v viiii C L2#LINE/L2 2593 GGTGTGAGAGAAAGAGAGGAGTCAAGGATGACTCCAAGGTTTTTGGCCTG 2544 chr4qtel1M 839156 AGTAACTGGAGGAATGTGA--TATCCTTAAGAAAAGTAAGGAAC-TTTTG 839202 i i i - -- ii v ? vvi ii ii v-i vi C L2#LINE/L2 2543 AGCAACTGGAAGGATG-GAGTTGCCATTNACTGAGATGGGGAAGACTGCG 2495 chr4qtel1M 839203 GAAGAAGGGTGAGATTTTGGGGAAAAGTATCA-GATTTTA-TATTGGATA 839250 i i ---v i vi ii - - v i - v i C L2#LINE/L2 2494 GGAGGAG---CAGGTTTGAGGGGGAAG-ATCAGGAGTTCAGTTTTGGACA 2449 chr4qtel1M 839251 TG--GAGTTTGAGATGTCCATTGGATATCTAACTCAAAATGTCTGATAAG 839298 --i i i i i i v vi i vii i C L2#LINE/L2 2448 TGTTAAGTTTGAGATGCCTATTAGACATCCAAGTGGAGATGTCGAGTAGG 2399 chr4qtel1M 839299 TATTTGAATGTATG 839312 i v i i i C L2#LINE/L2 2398 CAGTTGGATATACG 2385 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 52.69 CpG sites = 103, Kimura (unadjusted) = 55.43 Transitions / transversions = 1.94 (103/53) Gap_init rate = 0.05 (22 / 426), avg. gap size = 1.95 (43 / 22) 28 31.73 3.43 3.43 chr4qtel1M 839799 839973 (160027) (ATAC)n#Simple_repeat 1 175 (0) m_b212s252i10 8361 chr4qtel1M 839799 ATACATATATAGATATAGATAGAGACACAAATATACATTTATACCCACCC 839848 i v i v i v v i v i vi -- iv (ATAC)n#Simpl 1 ATACATACATACATACATACATACATACATACATACATACATA--CATAC 48 chr4qtel1M 839849 CTAGATACATATAT-C-TATACACATACATACACAGAGCTACATGCATAC 839896 v v i - - i i i v -- i (ATAC)n#Simpl 49 ATACATACATACATACATACATACATACATACATACA--TACATACATAC 96 chr4qtel1M 839897 CTATCTACATATCCTTGGACACACACATATATACACACATGCATTTGTCC 839946 v iv -- v iv i i i i i vii v (ATAC)n#Simpl 97 ATACATACATA--CATACATACATACATACATACATACATACATACATAC 144 chr4qtel1M 839947 ATATGTA-A-ACATAC-TTCTAACATA-ATA 839973 ii - - - v vv - (ATAC)n#Simpl 145 ATACATACATACATACATACATACATACATA 175 Matrix = Unknown Transitions / transversions = 1.21 (23/19) Gap_init rate = 0.07 (12 / 174), avg. gap size = 1.00 (12 / 12) 296 25.36 5.37 1.89 chr4qtel1M 842412 842616 (157384) C L1PREC2_orf2#LINE/L1 (736) 2558 2347 m_b212s551i3 8362 chr4qtel1M 842412 CTTTTGTTCTTCCTAATGAATTTTAGAATTATTTCT-CTATTTCTAT--- 842457 v vv vv i vi i - v i --- C L1PREC2_orf2# 2558 CTTTTTTGGTTCCATATGAATTTTAAAATAGTTTTTTCTAGTTCTGTGAA 2509 chr4qtel1M 842458 -AATTTT-TTGGTAGTTTGATTGTTATGGCATTGATTAAGAAAATTAATT 842505 - v i- v vv i v vv v iv C L1PREC2_orf2# 2508 GAATGTCATTGGTAGTTTGATAGGAATAGCATTGAATCTGTAAATTGCTT 2459 chr4qtel1M 842506 TAGGTAGAATTGTCATTTTAATTGTTTTAGTTCAGTCTACCCATGAGCAA 842555 i i v v i ivi v ii vvi i v C L1PREC2_orf2# 2458 TGGGCAGTATGGCCATTTTAACGATATTGATTCTTCCTATCCATGAGCAT 2409 chr4qtel1M 842556 GTGATCTTTTCCCAATTATTT-----AAATCTGAATTTACTTGTGGTGAA 842600 vi v i v i ----- vv - - - i- v C L1PREC2_orf2# 2408 GGAATGTTTTTCCATTTGTTTGTGTCATCTCTG-ATTT-CTT-TGA-GCA 2363 chr4qtel1M 842601 ATGTTTTGTAATTGTC 842616 i v C L1PREC2_orf2# 2362 GTGTTTTGTAATTCTC 2347 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 30.35 CpG sites = 21, Kimura (unadjusted) = 31.04 Transitions / transversions = 0.70 (21/30) Gap_init rate = 0.04 (9 / 204), avg. gap size = 1.67 (15 / 9) 327 25.45 3.64 0.00 chr4qtel1M 842412 842576 (157424) C L1M2_orf2#LINE/L1 (736) 2555 2385 m_b212s551i2 8362 chr4qtel1M 842412 CTTTTGTTCTTCCTAATGAATTTTAGAATTATTTCT-CTATTTCTAT--- 842457 vv vv i i ? i - i --- C L1M2_orf2#LIN 2555 CTTTTGTGGTTCCATACGAATTTTAGGATTNTTTTTTCTATTTCTGTGAA 2506 chr4qtel1M 842458 -AATTTT-TTGGTAGTTTGATTGTTATGGCATTGATTAAGAAAATTAATT 842505 - v i- v v vv v v vv v i iiv C L1M2_orf2#LIN 2505 GAATGTCATTGGTATTTTGATAGGGATTGCATTGAATCTGTAGATCGCTT 2456 chr4qtel1M 842506 TAGGTAGAATTGTCATTTTAATTGTTTTAGTTCAGTCTACCCATGAGCAA 842555 i v v ? ivi v i vvi v i v C L1M2_orf2#LIN 2455 TGGGTAGTATGGNCATTTTAACAATATTAATTCTTCCAATCCATGAGCAT 2406 chr4qtel1M 842556 GTGATCTTTTCCCAATTATTT 842576 v v i i v ? C L1M2_orf2#LIN 2405 GGGATATCTTTCCATTTNTTT 2385 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 30.04 CpG sites = 16, Kimura (unadjusted) = 31.84 Transitions / transversions = 0.62 (16/26) Gap_init rate = 0.02 (4 / 164), avg. gap size = 1.50 (6 / 4) 21 0.00 0.00 0.00 chr4qtel1M 844475 844497 (155503) (G)n#Simple_repeat 1 23 (0) m_b212s252i12 8363 chr4qtel1M 844475 GGGGGGGGGGGGGGGGGGGGGGG 844497 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGG 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 16 5.27 0.00 0.00 chr4qtel1M 845676 845695 (154305) (AC)n#Simple_repeat 1 20 (0) m_b212s252i13 8364 chr4qtel1M 845676 ACACACATACACACACACAC 845695 i (AC)n#Simple_ 1 ACACACACACACACACACAC 20 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 196 15.54 0.00 10.26 chr4qtel1M 846135 846177 (153823) L3#LINE/CR1 3545 3583 (516) m_b212s601i19 8365 chr4qtel1M 846135 GAGGTGATAGTCCTGTTGTACCTTGCCTGATCTGGTCAGACTA 846177 i i i ii -- -- i L3#LINE/CR1 3545 GAGGTAATAGTCCCGCTGTACTCTGC--G--CTGGTCAGACCA 3583 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 15.16 CpG sites = 6, Kimura (unadjusted) = 18.39 Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.10 (4 / 42), avg. gap size = 1.00 (4 / 4) 423 24.18 5.56 5.56 chr4qtel1M 846186 846347 (153653) C L2d_3end#LINE/L2 (5) 511 350 m_b212s601i20 8366 chr4qtel1M 846186 CAATCAGTCAACAAGAATGTGTTAAGTCCCTATTTATATTCCAGGGACTG 846235 i v v i i iv i - i v ivi v C L2d_3end#LINE 511 CAATCAATCAACAAGTATTTATTGAGCGCCTACT-ATGTGCTCAGCACTG 463 chr4qtel1M 846236 AACTGAGC-CTCTGACCCAGGGACACCAAAAAATGGCAAAAGACAT--TC 846282 vi ii - v ----- - v ? ?i i v -- C L2d_3end#LINE 462 TGCTAGGCGCTGTG-----GGGA-ACGANAAAANAGTATAAGACATGGTC 419 chr4qtel1M 846283 CCTGCTCACAAGGAGCTCACAGTCTAATGGAAGTGACAACACAGAAATAT 846332 i v i i i v ii v v --v i i C L2d_3end#LINE 418 CCTGCCCTCAAGGAGCTTACAATCTAGTTGGGGAGACAAGAC--TAACAC 371 chr4qtel1M 846333 ACATGA------CAGAGAACA 846347 ------i C L2d_3end#LINE 370 ACATGAAACAATTAGAGAACA 350 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.34 CpG sites = 22, Kimura (unadjusted) = 30.31 Transitions / transversions = 1.47 (22/15) Gap_init rate = 0.07 (12 / 161), avg. gap size = 1.50 (18 / 12) 318 29.32 3.70 1.45 chr4qtel1M 846455 846589 (153411) Plat_L3#LINE/CR1 3172 3309 (264) m_b212s551i4 8367 chr4qtel1M 846455 ATGAGGATCAGTTGAAAGAGTTAAGGCTGCTTAACCTGAAGAAGAGAAAA 846504 vvi i i i ii i i i i ii Plat_L3#LINE/ 3172 ATGAGGAAAGGTTAAAGGAATTGGGGTTGTTTAGCCTGGAGAAGAGAAGG 3221 chr4qtel1M 846505 CT--TGGGCAACACGA-AATACTCTTTAAATATCTGAAAGGCTTTTATGT 846551 --v ii vii - ivv i i v i i v Plat_L3#LINE/ 3222 CTAAGGGGTGACTTAATAACTGTCTTCAAGTATATGAAGGGTTTTTATGG 3271 chr4qtel1M 846552 CTAGGATG--AATCACTCTTGTTCTGCTTGGCCCCAGAGG 846589 vv i --i i --v v v v v ? Plat_L3#LINE/ 3272 GGAGGACGCTGACCA--GTTGTTCTCCATGTCCACNGAGG 3309 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.59 CpG sites = 24, Kimura (unadjusted) = 38.88 Transitions / transversions = 1.60 (24/15) Gap_init rate = 0.04 (5 / 134), avg. gap size = 1.40 (7 / 5) 202 30.88 2.94 0.00 chr4qtel1M 846596 846663 (153337) L3#LINE/CR1 3843 3912 (187) m_b212s601i21 8368 chr4qtel1M 846596 CTAGGACTGAAGAGTGTGAGCTCCAAG-AGGCAAATTTCAGCTGGATATA 846644 ii v i vi i v i - i i vi L3#LINE/CR1 3843 CTAGGACCAATGGGTGGAAGTTACAGGGAGGCAGATTTCGGCTCAATATA 3892 chr4qtel1M 846645 TGGCA-AGTGTCTTAATAAT 846663 v v - iiv ii i L3#LINE/CR1 3893 AGGAAGAACTTTCTAACAAT 3912 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.26 CpG sites = 14, Kimura (unadjusted) = 41.91 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.03 (2 / 67), avg. gap size = 1.00 (2 / 2) 281 32.20 7.63 0.00 chr4qtel1M 850139 850256 (149744) L2d2_3end#LINE/L2 424 550 (5) m_b212s601i22 8369 chr4qtel1M 850139 GTCTGTCCCACCAGTTTGTACCCTCCAAGAGAACAAGAA--ATGTCTCAT 850186 vi v i v vv vv ii i i -- i L2d2_3end#LIN 424 GTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTAT 473 chr4qtel1M 850187 ATCTCTATGT-TCCT----GGTACTCATCTGAGGGCCTGGCTTGTAGCAG 850231 ii v - i----i ii ii v vv v v viii i L2d2_3end#LIN 474 ACTTCTTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAGTAG 523 chr4qtel1M 850232 GCAATTAA--AATGTTTGTTGACTTGA 850256 iv i -- i i L2d2_3end#LIN 524 GCGCTCAATAAATATTTGTTGATTTGA 550 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.49 CpG sites = 23, Kimura (unadjusted) = 43.72 Transitions / transversions = 1.53 (23/15) Gap_init rate = 0.03 (4 / 117), avg. gap size = 2.25 (9 / 4) 348 22.05 11.36 2.08 chr4qtel1M 850357 850444 (149556) C MIR3#SINE/MIR (27) 181 86 m_b212s601i23 8370 chr4qtel1M 850357 CTGCAAGGGAGCTGAAAGGCCATGGATTCCAATCTTTTCATTTTACAGAT 850406 v v v i ii vv v i iii C MIR3#SINE/MIR 181 CTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGAT 132 chr4qtel1M 850407 GAGGAAATTGAGATC----------AAGTGACTAGCCCAGGAAGCCAC 850444 i ii ---------- v -- i i C MIR3#SINE/MIR 131 GAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCA--AGGTCAC 86 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.79 CpG sites = 12, Kimura (unadjusted) = 26.79 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.03 (3 / 87), avg. gap size = 4.00 (12 / 3) 295 28.48 11.97 3.97 chr4qtel1M 850391 850507 (149493) C MIRc#SINE/MIR (118) 150 25 m_b212s601i24 8370 chr4qtel1M 850391 TTTTCATTTTACAGATGAGGAAATT----------GAGATCAAGTGACTA 850430 iii i ---------- i i v C MIRc#SINE/MIR 150 TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTT 101 chr4qtel1M 850431 GCCCAGGAAGCCACTTCTAAAAAAAAATGTGGAAAA----GAACTTTAAG 850476 i ivvv vv iv ----- v i ---- i iv v C MIRc#SINE/MIR 100 GCCCAAGGTCACACAGCTAGTAA-----GTGGCAGAGCCGGGACTCGAAC 56 chr4qtel1M 850477 GCAGGTCTTTCTCTCCCCAACTTTAGCACTC 850507 v i vv i v ii ii C MIRc#SINE/MIR 55 CCAGGTCTTCCTGACTCCAAGTCCAGTGCTC 25 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.33 CpG sites = 18, Kimura (unadjusted) = 36.76 Transitions / transversions = 1.29 (18/14) Gap_init rate = 0.06 (7 / 116), avg. gap size = 2.71 (19 / 7) 725 26.04 5.21 0.00 chr4qtel1M 851106 851297 (148703) MIRc#SINE/MIR 4 205 (63) m_b212s601i25 8371 chr4qtel1M 851106 GGTAGTGTG---CAATGGAAAGAGACCTGGACATAGAGTCAGGAGTGCCT 851152 i --- i vv v i ivi MIRc#SINE/MIR 4 GGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCT 53 chr4qtel1M 851153 GAGTTTAAATTGAGCCTCAGACAGTCACTAGCTGTGTGCCTCTTCTTAAG 851202 i ii i ivv v v v v i v ii vvvi MIRc#SINE/MIR 54 GGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAG 103 chr4qtel1M 851203 T-ACTTAACATCTGTTTACCTCAGTTTCTTCAACTCTCAAATGGGGAGAA 851251 - v v vvi i v v v v MIRc#SINE/MIR 104 TCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAA 153 chr4qtel1M 851252 TAATATC------ACCTAATTTGGAAGGTTATTGTGAGGATAAAGTGACA 851295 i ------i vi iiv i i v i v MIRc#SINE/MIR 154 TAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGA 203 chr4qtel1M 851296 TA 851297 MIRc#SINE/MIR 204 TA 205 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.40 CpG sites = 24, Kimura (unadjusted) = 32.24 Transitions / transversions = 0.92 (24/26) Gap_init rate = 0.02 (3 / 191), avg. gap size = 3.33 (10 / 3) 256 28.75 7.97 4.20 chr4qtel1M 852364 852501 (147499) C MIR3#SINE/MIR (2) 206 64 m_b213s601i4 8372 chr4qtel1M 852364 ATCA-AAAGTCAGAAGATGT-AGAGTTGAAAGACCCTTCAGA-ATGAAAG 852410 - i i v ii - i i ivv i i - v vvv C MIR3#SINE/MIR 206 ATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCT 157 chr4qtel1M 852411 AGTTCATGGACCCTCATCAACTTATAG--GAGGAAACTGAAACACAGAGA 852458 i --- i - vi i -- ii v C MIR3#SINE/MIR 156 AGTCCA---ACCCCC-TCATTTTACAGATGAGGAAACTGAGGCCCAGAGA 111 chr4qtel1M 852459 AG------GATTTTGCCCAAAGCTCATCTCTTTTATGAGTGTCAGAGTC 852501 i ------ -i i - ivivvi?vi v v i C MIR3#SINE/MIR 110 GGTGAAGTGA-CTTGCCCAAGG-TCACACAGCNAGTTAGTGGCAGAGCC 64 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.84 CpG sites = 23, Kimura (unadjusted) = 37.84 Transitions / transversions = 1.53 (23/15) Gap_init rate = 0.08 (11 / 137), avg. gap size = 1.55 (17 / 11) 455 29.75 3.61 2.79 chr4qtel1M 852691 852939 (147061) L1P3_orf2#LINE/L1 3037 3287 (7) m_b213s551i0 8373 chr4qtel1M 852691 CTAACCAAACTGAAAAGTTTTTGTACA---AACAAAACTA--ATGCAGAC 852735 ii i i i i i --- vi -- - - L1P3_orf2#LIN 3037 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAT-CAGA- 3084 chr4qtel1M 852736 AAGATTAGAAGGGAAGCAATAAACTGGGAAAATATTTTTACAGTCAAAGG 852785 ---i v iv v v v i i v i v i i v vvv L1P3_orf2#LIN 3085 ---GTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCC 3131 chr4qtel1M 852786 TTCTGATAAAGGCCTCATTTCCAAAATATATAGAGAATTAACTCTAATTT 852835 v i v v v i v i ii i v vv v L1P3_orf2#LIN 3132 ATCTGACAAAGGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTT 3181 chr4qtel1M 852836 ATAA----AAATCAAGCCATTCTCCAATTGAAAATGGTCAAAGGATATGA 852881 i ---- v i v -- i vivi i v i L1P3_orf2#LIN 3182 ACAAGAAAAAAACAAACAA--CCCCATCAAAAAGTGGGCGAAGGATATGA 3229 chr4qtel1M 852882 ACAGACAATTCTCAGATGAAGAAATTGAAACTATTTCTAGTCATATGAAA 852931 v i v v v vi viiivvi iv L1P3_orf2#LIN 3230 ACAGACACTTCTCAAAAGAAGACATTTATGCGGCCAACAAACATATGAAA 3279 chr4qtel1M 852932 AGATGCTC 852939 i v L1P3_orf2#LIN 3280 AAAAGCTC 3287 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.72 CpG sites = 36, Kimura (unadjusted) = 38.38 Transitions / transversions = 1.00 (36/36) Gap_init rate = 0.04 (10 / 248), avg. gap size = 1.60 (16 / 10) 459 25.96 2.37 1.41 chr4qtel1M 852736 852946 (147054) L1M5_orf2#LINE/L1 3082 3294 (0) m_b213s551i1 8373 chr4qtel1M 852736 AAGATTAGAAGGGAAGCAATAAACTGGGAAAATATTTTTACAGTCAAAGG 852785 i v i v v i i ? i v v i i?- v vi L1M5_orf2#LIN 3082 AAAATGAAAAGGCAAGCCACAGANTGGGAGAAAATATTTGCAAN-ACATA 3130 chr4qtel1M 852786 T-TCTGATAAAGGCCTCATTTCCAAAATATATAGAGAATTAACTCTAATT 852834 - i v i v i i i v- vi ? L1M5_orf2#LIN 3131 TATCTGACAAAGGACTCGTATCCAGAATATATAAAGAACTC-CTACAANT 3179 chr4qtel1M 852835 TA-TAAAAATCAAGCCATTC--TCCAAT-TGAAAATGGTCAAAGGATATG 852880 i - ? -v v vv --i -?i v i iv L1M5_orf2#LIN 3180 CAATAANAA-AAAGACAAACAACCCAATANAAAAATGGGCAAAAGACTTG 3228 chr4qtel1M 852881 AACAGACAATTCTCAGATGAAGAAATTGAAACTATTTCTAGTCATATGAA 852930 v v i v v ?v iviiivv iv i L1M5_orf2#LIN 3229 AACAGACACTTCACAAAAGAAGATATNCAAATGGCCAATAAGCACATGAA 3278 chr4qtel1M 852931 AAGATGCTCCAAGTCA 852946 v v? L1M5_orf2#LIN 3279 AAGATGCTCAACNTCA 3294 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.80 CpG sites = 26, Kimura (unadjusted) = 33.54 Transitions / transversions = 0.93 (26/28) Gap_init rate = 0.03 (7 / 210), avg. gap size = 1.14 (8 / 7) 1519 26.78 1.29 1.66 chr4qtel1M 852805 853347 (146653) L1ME3G_3end#LINE/L1 7 547 (377) m_b213s551i2 8373 chr4qtel1M 852805 TCCAAAATATATAGAGAATTAACTCTAATTTATAAAAATCAAGCCATTCT 852854 i i i vviv v iv i -v v --vi L1ME3G_3end#L 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAA-AAAGACA--AC 53 chr4qtel1M 852855 CCAATTGAAAA-TGGTCAAAGGATATGAACAGACAATTCTCAGATGAAGA 852903 v - v i v v i L1ME3G_3end#L 54 CCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGGA 103 chr4qtel1M 852904 AATTGAAACTATTTCTAGTCATATGAAAAGATGCTCCAAGTCATTATTAA 852953 vv iviiivv iv v vv i v L1ME3G_3end#L 104 AATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTAA 153 chr4qtel1M 852954 TCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACACCTGTC 853003 i i vv i i viv ii L1ME3G_3end#L 154 TCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCATC 203 chr4qtel1M 853004 AGATTGGCTAAGA-TGACAGGAAAAATAATGATGATTGTTGGAGGGGATG 853052 v i - v v i ?vvi ivi? v v i i L1ME3G_3end#L 204 AGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGTG 253 chr4qtel1M 853053 C-GGAAAACTGGGACATTGATGCATTGTTGGTGGAGTTGTGAATGAATCC 853101 i- i v v vi v i i i iiv i vii v L1ME3G_3end#L 254 TGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTAC 303 chr4qtel1M 853102 AACCATTTTGGAGAGTAGTTTGGAACTATGC-TCAAAAGTTATCAAACTG 853150 i ? i i i v v vi- i v --- v L1ME3G_3end#L 304 AGCCNTTTTGGAGGGCAATTTGGCAGTATCTATTAAAATTT---AAAATG 350 chr4qtel1M 853151 TGCATACCCTTTGATCCAGCAGTGTTACTACTGGGATTATATCCCAAAGA 853200 i i i vii v ? ?v v i ? L1ME3G_3end#L 351 CGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAGA 400 chr4qtel1M 853201 GATTAT-AAAGAAG-GGAAAGGGACCTGTATGTGCACGAATGTTTGTGGC 853248 i vv -iv v v - v v i --? i i v i ii v L1ME3G_3end#L 401 AATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTCATTGC 448 chr4qtel1M 853249 AGCCCT-TTTGTAGTGGCTAGAAACTGGAAACTGAATGGATGTCCATCAG 853297 vi - i i v i i vivv ii i L1ME3G_3end#L 449 AGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCAA 498 chr4qtel1M 853298 TTGGAGAAATGGCTGAATAAATTGTGGTATATGAAAATTATGGAATATTA 853347 v - i i i i vv v i i L1ME3G_3end#L 499 TAGG-GGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACTA 547 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.58 CpG sites = 75, Kimura (unadjusted) = 34.16 Transitions / transversions = 1.10 (75/68) Gap_init rate = 0.03 (16 / 542), avg. gap size = 1.00 (16 / 16) 1446 27.22 3.44 3.26 chr4qtel1M 852853 853433 (146567) L1ME5_3end#LINE/L1 56 637 (304) m_b213s551i3 8373 chr4qtel1M 852853 CTCCAATTGAAAA-TGGTCAAAGGATATGAACAGACAATTCTCAGATGAA 852901 i v - v i iv v i L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chr4qtel1M 852902 GAAA-TTGAAA--CTATTTCTAGTCATATGAAAAGATGCTCCAAGTCATT 852948 -ii -- --v v - i v v L1ME5_3end#LI 106 GAAACCCGAAAGGCTA--ACAAG-CATATGAAGAGATGCTCAAACTCATT 152 chr4qtel1M 852949 ATTAATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACAC 852998 v i vv i i vi L1ME5_3end#LI 153 AGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACAC 202 chr4qtel1M 852999 CTGTCAGATTGGCTAAGATGACAGGAA---AAATAATGATGATTGTTGGA 853045 i i i v i --i i ---ii vii v v L1ME5_3end#LI 203 CTATTAGACTGGCAAAAAT--TAGAAAGCTGGATAATGCCAAGTGTTGGC 250 chr4qtel1M 853046 GGGGATGCGGAAAACT-GGGACATTGATGCATTGTTGGTGGAGTTGTGAA 853094 i i ii ?v - i vi v i i iiv ii L1ME5_3end#LI 251 GAGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGA 300 chr4qtel1M 853095 TGAATCCAACCATTTTGGAGAGTAGTTTGGAACTA--TGCTCAAAAGTTA 853142 ivii v i i i i i v v -- iv -- L1ME5_3end#LI 301 CTGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAA--TTA 348 chr4qtel1M 853143 TCAAACTGTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGATTATAT 853192 -- ivv ii v i i viii v vv L1ME5_3end#LI 349 --AGTATACGCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATAT 396 chr4qtel1M 853193 CCCAAAGAGATTATAAAGAAGG----GAAAGGGACCTGTATGTGCACGAA 853238 i v v viv ----v i ---- i iv i L1ME5_3end#LI 397 CCCAAAGAAATTCTCACACAGGTCCATAAGGGGAC----ATGTACGAGGA 442 chr4qtel1M 853239 TGTTTGTGGCAGCCCT-TTTGTAGTGGCTAGAAACTGGAAACTGAATGGA 853287 ii v vi - i vi i ii ii vivv i L1ME5_3end#LI 443 TGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGGG 492 chr4qtel1M 853288 TGTCCATCAGTTGGAGAAATGGCTGAATAAATTGTGGTATATGAAAATTA 853337 v v - i v iii v iv v v ii L1ME5_3end#LI 493 TGTCCATCACTGGGAG-AGTGGATAGGTAAAATGTGGTGGATGCACACCA 541 chr4qtel1M 853338 TGGAATATTACTGT-TCTGTAAGAAATGACCAACAGGATGATTTCAGAAA 853386 i i - i-v v v iii vi vi -- v v v L1ME5_3end#LI 542 TGGAGTACTA-TGCAGCAGTTAGAAGCAACGGACTAGATG--TACACATA 588 chr4qtel1M 853387 G--GCCTGGAGAGA-CTTACATGAAC-TGATGCTGAGTGAAATGAGCAGG 853432 --i v vi - v -- - ii vi i i L1ME5_3end#LI 589 GCAACATGGATGGATCTTAAA--AACATAGTGCTGAGTGAAAAAAGTAAG 636 chr4qtel1M 853433 A 853433 L1ME5_3end#LI 637 A 637 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.59 CpG sites = 90, Kimura (unadjusted) = 34.74 Transitions / transversions = 1.43 (90/63) Gap_init rate = 0.05 (31 / 580), avg. gap size = 1.26 (39 / 31) 20 16.66 0.00 0.00 chr4qtel1M 853891 853924 (146076) (A)n#Simple_repeat 1 34 (0) m_b213s252i1 8374 chr4qtel1M 853891 AAATAAAAAATAAATAAATAAAAAAAAAAATAAA 853924 v v v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 34 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 462 22.04 0.78 12.07 chr4qtel1M 854627 854755 (145245) MIRb#SINE/MIR 3 118 (150) m_b213s601i5 8375 chr4qtel1M 854627 GAGGGGCAGCTTGATGTAATAGTAGATAAAGCACTGGTCCTGAAGTCAG- 854675 v i i --- i v i v iii i - MIRb#SINE/MIR 3 GAGGGGCAGCGTGGTGCA---GTGGAAAGAGCACGGGCTTTGGAGTCAGA 49 chr4qtel1M 854676 CAGAATCTGAGTTCAAATCCGGCCTCAGACACGTAACACTTTTTATTGGT 854725 - i i i v v v v ---------- i i i MIRb#SINE/MIR 50 CAG-ACCTGGGTTCGAATCCCGGCTCTGCCAC----------TTACTAGC 88 chr4qtel1M 854726 TGTGTGACCCTGGGCAAATCACTTAACCCC 854755 i i i i MIRb#SINE/MIR 89 TGTGTGACCTTGGGCAAGTTACTTAACCTC 118 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 25.42 CpG sites = 18, Kimura (unadjusted) = 26.66 Transitions / transversions = 2.57 (18/7) Gap_init rate = 0.12 (15 / 128), avg. gap size = 1.00 (15 / 15) 30 22.11 0.00 0.00 chr4qtel1M 855024 855086 (144914) (A)n#Simple_repeat 1 63 (0) m_b213s252i2 8376 chr4qtel1M 855024 AAAAACCAAGAAACAATAAAACAAAACCAAAAAAAAAAAAAAAAATAAAG 855073 vv i v v v vv v i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr4qtel1M 855074 AAACAATAAAAAA 855086 v v (A)n#Simple_r 51 AAAAAAAAAAAAA 63 Matrix = Unknown Transitions / transversions = 0.20 (2/10) Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0) 1017 28.74 2.40 2.16 chr4qtel1M 855771 856186 (143814) L1ME4c_3end#LINE/L1 159 575 (255) m_b213s551i4 8377 chr4qtel1M 855771 CAGAGAAATGCAAATCAAACCAACTCTGAAGTACCACCTCACACCTGTCA 855820 i i v vv ii ii i i i i L1ME4c_3end#L 159 CAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCTATTA 208 chr4qtel1M 855821 GATCAGCTATTACTGGAAAAGATAATAATA---AATGTTGTAGAAGATGT 855867 i i v vv i vi iv i --- i vv i ? i L1ME4c_3end#L 209 AATTAGCAAAAATTTAAAAAATTGATAATACCCAATGCTGGCGAGGNTGC 258 chr4qtel1M 855868 GA-GAAATTGGGACACTAATACATTCTTGGCGGAGTTGTGAACTGATTCA 855916 i- i v ? v vi i vi? i i i v L1ME4c_3end#L 259 GGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACA 308 chr4qtel1M 855917 ACCATTCTGGAGAACAATTTAGAACT--GTACCCAAAGGAATATGAAAAT 855964 v i i i i v v -- i -- iivi i L1ME4c_3end#L 309 ACCCTTTTGGAAAGCAATTTGGCAATACGTATC--AAGAGCCATAAAAAT 356 chr4qtel1M 855965 GTGCACAATCTTTTTACCTAGCAGTGCCATTACTGGGTCTGTATCCCAAG 856014 v i -i i v i i i v i v vv v i L1ME4c_3end#L 357 GTTCATA-CCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAG 405 chr4qtel1M 856015 GAAATCAT---AAAGGAGGAAAAAGGATCCACATGTGCAAAAAACGTTTG 856061 v --- i --- i i ii i i -i ii L1ME4c_3end#L 406 GAAATAATTCAAAAGAAGGAAAAAG---CTATATGCACGAAGA-TGTTCA 451 chr4qtel1M 856062 TAGCAGTTCTTTTTGTGGAAGCAAAGAAGTGGAAAATGAGTAAATATCTA 856111 v ivi v i iiv i i v vvivv i i L1ME4c_3end#L 452 TTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCA 501 chr4qtel1M 856112 TCGATTGGGGAATGGCTAAACAAGTTGTGGTACATGAAGGTAATGGAATA 856161 v i v i ii i i v? vvii L1ME4c_3end#L 502 ACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATA 551 chr4qtel1M 856162 TTACTGT-TCTATAAAAAAATGATAA 856186 - i-v i -v L1ME4c_3end#L 552 TTA-TGCAGCCAT-TAAAAATGATAA 575 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.59 CpG sites = 74, Kimura (unadjusted) = 38.12 Transitions / transversions = 1.72 (74/43) Gap_init rate = 0.03 (14 / 415), avg. gap size = 1.36 (19 / 14) 557 34.33 2.29 2.29 chr4qtel1M 855772 856251 (143749) L1MC4a_3end#LINE/L1 157 636 (1993) m_b213s551i5 8377 chr4qtel1M 855772 AGAGAAATGCAAATCAAACCAACTCTGAAGTACCACCTCACACCTGTCAG 855821 i v v v ii ii v i L1MC4a_3end#L 157 AGAGAAATGCAAATTAAAACTACACTGAGATACCATTTCTCACCTATCAG 206 chr4qtel1M 855822 ATCAGCTATTACTGGAAAAGATAATAATAAA---TGTTGTAGAAGATGT- 855867 ii v vv i vi ivv i i i v --- vv i v - L1MC4a_3end#L 207 ATTGGCAAAAATTCAAAAGTTTGACAACACACTCTGTTGGCGAGGCTGTG 256 chr4qtel1M 855868 GAGAAATTGGGACACTAATACATTCTTGGCGGAGTTGTGAACTGATTCAA 855917 i iv v v v vi i iiv ii ? i v L1MC4a_3end#L 257 GGGAAACAGGCACTCTCATACATTGCTGGTGGGAATGCAAANTGGTACAA 306 chr4qtel1M 855918 CCATTCTGGAGAACAATTTAGAACTGTACCCAA-AGGAATATGAAAATGT 855966 v ? iiv i -- vi i i - ii v i---- i L1MC4a_3end#L 307 CCCTTNTGGAGGGGAATTTGG--CAATATCTAACAAAACTAC----ATAT 350 chr4qtel1M 855967 GCA-CAATCTTTTTACCTAGCAGTGCCATTACTGGGTCTGTATCCCAAGG 856015 -iv i i v i i v i v i vv v i ii i L1MC4a_3end#L 351 GCATTTACCCTTTGACCCAGCAATCCCACTTCTAGGAATTTACCCTGAAG 400 chr4qtel1M 856016 --AAATCATAAAGGAGGAAAAAGGATCCACATGTGCAAAAAA-CGTTTGT 856062 -- v i viv viv v v -- -? i v ii-ii ii L1MC4a_3end#L 401 ATACACCTCCAACATGTACAAA--AT-NACATATGCACAAGGTTATTCAT 447 chr4qtel1M 856063 AGCAGTTCTTTTTGTGGAAGCAAAGAAGTGGAAAATGAGTAAATATCTAT 856112 v ivi v iivv iv v vvivv ii i L1MC4a_3end#L 448 TGCAGCATTGTTTGTAATTGCAAAATATTGGAAACAACCTAAATGCCCAT 497 chr4qtel1M 856113 CGATTGGGGAATGGCTAAACAAGTTGTGGTACATGAAGGTAATGGAATAT 856162 ?? v i ? i i i ii i vv vii i i L1MC4a_3end#L 498 NNATAGGAGANTGGTTGAATAAACTATGGTACATCCACACAATGGAGTAC 547 chr4qtel1M 856163 TACTGT-TCTATAAAAAAATGATAAACAAGATGATTTTAAAAAGAACTGA 856211 - i-v i i-i i iv vvi v i vv vv i L1MC4a_3end#L 548 TA-TGCAGCTGTAAAAAAG-AATGAGGAAGATCTCTATGAACTGATATGG 595 chr4qtel1M 856212 AA-GATTTACAGGAACTGATGCTGACCAAAACAAACAAAGT 856251 i- v vv iv i i vii v i L1MC4a_3end#L 596 AGTGATTTCCAGGATATATTGTTAAGTGAAAAAAGCAAAGT 636 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 48.30 CpG sites = 91, Kimura (unadjusted) = 48.30 Transitions / transversions = 1.30 (91/70) Gap_init rate = 0.04 (19 / 479), avg. gap size = 1.16 (22 / 19) 16 9.32 0.00 0.00 chr4qtel1M 856360 856382 (143618) (AT)n#Simple_repeat 1 23 (0) m_b213s252i4 8378 chr4qtel1M 856360 ATAAATAAATATATATATATATA 856382 v v (AT)n#Simple_ 1 ATATATATATATATATATATATA 23 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 237 26.83 6.83 3.48 chr4qtel1M 857112 857157 (142843) L1M5_orf2#LINE/L1 781 830 (2464) m_b213s551i6 8379 chr4qtel1M 857112 TGAGTCAGAGAACAAATCTCA---GAAATGATAA----CTTTGCAAAAAA 857154 i i v v --- v v ----i --- vv L1M5_orf2#LIN 781 TGGGTCAAAGAAGAAATCACAANGGAAATTAGAAAATATTTTG---AACT 827 chr4qtel1M 857155 AAA 857157 i L1M5_orf2#LIN 828 GAA 830 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.15 CpG sites = 41, Kimura (unadjusted) = 35.15 Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.11 (5 / 45), avg. gap size = 2.00 (10 / 5) 29 0.00 0.00 0.00 chr4qtel1M 857158 857182 (142818) (AG)n#Simple_repeat 1 25 (0) c_b213s251i0 8380 chr4qtel1M 857158 AGAGAGAGAGAGAGAGAGAGAGAGA 857182 (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGA 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 237 26.83 6.83 3.48 chr4qtel1M 857183 857413 (142587) L1M5_orf2#LINE/L1 831 1066 (2228) m_b213s551i6 8379 chr4qtel1M 857183 AGTAATGATTAAGCAATATTCCAAAATTTCTGGGGTTCAACTAAAGCAGT 857232 ii? vv vi i vi v i v i L1M5_orf2#LIN 831 GANAATGAAAATACAACATATCAAAATTTGTGGGATGCAGCTAAAGCAGT 880 chr4qtel1M 857233 CCTCAGGGGAAAA--CACAGATTTACAT-CATACATTAAGAATATAGAAA 857279 v i i i --i i v? v - ? i ii --- i L1M5_orf2#LIN 881 GCTTAGAGGGAAATTTATAGCNTTAAATGCNTATATTAGAAA---AGAAG 927 chr4qtel1M 857280 AAGAGATT--AATAAATTAACTGAATATACATTTTAA-AAATTAGAAAAA 857326 ii v -- v v v i iiv v ii - ii L1M5_orf2#LIN 928 AAAGGCTTAAAATCAATGATCTAAGCTTCCACCTTAAGAAGCTAGAAAAA 977 chr4qtel1M 857327 TAAATGAGGTAAAT----CCTAAAATAAGTAAAAATGACAAAATATTAAA 857372 v -- - i ---- i i? i ivi vi v L1M5_orf2#LIN 978 GAA--GA-GCAAATTAAACCCAAAGNAAGTAGAAGGAAGGAAATAATAAA 1024 chr4qtel1M 857373 ATTAGAAG--GAAACCAGATTAATTGGAAACAAAAAATAAAAT 857413 iv ii -- i - v v i vv ? ? v L1M5_orf2#LIN 1025 GATAAGAGCAGAAATCA-ATGAAATAGAAAACAAANANACAAT 1066 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.15 CpG sites = 41, Kimura (unadjusted) = 35.15 Transitions / transversions = 1.48 (37/25) Gap_init rate = 0.06 (13 / 230), avg. gap size = 1.46 (19 / 13) 375 31.18 4.48 3.77 chr4qtel1M 857731 858020 (141980) L1M1_orf2#LINE/L1 1555 1846 (1448) m_b213s551i7 8381 chr4qtel1M 857731 AAACCAAGGGAAGTCCAATCACAGAAAGTAAACTACAAGCCAATG----- 857775 iivi v vv v i v i i----- L1M1_orf2#LIN 1555 AAACCAGACAAAGACACATCAAAAAAAGAAAACTACAGGCCAATATCTCT 1604 chr4qtel1M 857776 GATGAACGTTATTCCCTCCCCGAAAT--TTATACAAAGTCTTATCAAAAT 857823 ii iv v v-----i -- i - i vi v vi L1M1_orf2#LIN 1605 GATGAATATTGATGCA-----AAAATCCTCA-ACAAAATACTAGCAAACC 1648 chr4qtel1M 857824 GA---CTATAGGGAATTATCCAAGAATCATTCATTCTGATCAAATGGGAT 857870 --- v i iviv --v ii iv i i L1M1_orf2#LIN 1649 GAATTCAACAATACATTA--AAAAGATCATTCATCATGACCAAGTGGGAT 1696 chr4qtel1M 857871 TTGTACCAGAGATGCAAGGATAGTTCAATGTTAGGATAACAATGAACAAA 857920 i v ? i i ii vv v v v v iivi L1M1_orf2#LIN 1697 TTATCCCNGGGATGCAAGGATGGTTCAACATACGCAAATCAATCAATGTG 1746 chr4qtel1M 857921 ACTAATCA---CAATGTAAACTAAAACATCTAAGAACACATAGTCATTTC 857967 ivv --- --i i v i iv - v i v i ii L1M1_orf2#LIN 1747 ATACATCATATCAA--CAGAATGAAGGA-CAAAAACCATATGATCATTTC 1793 chr4qtel1M 857968 AACAGATAAAGAAAGTGCATTGGATAAAGTACACTATTCTTTTATGGCAA 858017 iv ivv iv v i v vi i i i ii L1M1_orf2#LIN 1794 AATTGATGCTGAAAAAGCATTTGATAAAATTCAACATCCCTTCATGATAA 1843 chr4qtel1M 858018 AAA 858020 L1M1_orf2#LIN 1844 AAA 1846 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.94 CpG sites = 49, Kimura (unadjusted) = 41.57 Transitions / transversions = 1.29 (49/38) Gap_init rate = 0.05 (15 / 289), avg. gap size = 1.60 (24 / 15) 530 32.28 4.26 3.00 chr4qtel1M 857842 858170 (141830) L1MC_orf2#LINE/L1 1668 2000 (1294) m_b213s551i8 8381 chr4qtel1M 857842 AAGAATCATTCATTCTGATCAAATGGGATTTGTACCAGAGATGCAAGGAT 857891 i v iivi i i i v iv v L1MC_orf2#LIN 1668 AAGAATTATACACCACGACCAAGTGGGATTTATCCCAGGTATGCAAGGCT 1717 chr4qtel1M 857892 AGTTCAATGTTAGGATAACAATGAACAAAACTAATCACAAT-GTAAACTA 857940 i ii v i v v v iiv iiv vi-ii ii L1MC_orf2#LIN 1718 GGTTCAACATTCGAAAATCAATTAATGTAATCCATCACATCAACAGGCTA 1767 chr4qtel1M 857941 AAACATCTAAGAA----CACATAGTCATTTCAACAGATAAAGAAAGTGCA 857986 i----- ---- ii v i iv iv L1MC_orf2#LIN 1768 AAG-----AAGAAAAATCACATGATCATATCAATAGATGCAGAAAAAGCA 1812 chr4qtel1M 857987 TTGGATAAAGTACACTATTCTTTTATGGCAAAAATTTAATTAGTAGTATA 858036 v i i v vi ii v i ii i i-- i i ivv L1MC_orf2#LIN 1813 TTTGACAAAATCCAACACCCATTCATGATAAAAACTC--TCAGCAAACTA 1860 chr4qtel1M 858037 GGCCTA-ATGGGACCACTTTCAAGAGTATAAA-AACATCTATCTAAAACC 858084 vv - v v viii vvvv - ivv L1MC_orf2#LIN 1861 GGAATAGAGGGGAACTTCCTCAACTTGATAAAGAACATCTACAAAAAACC 1910 chr4qtel1M 858085 AAAAG----TATCACACAAAATGG---GATTTCATTAGAAGTTTTTCCAG 858127 v v ----i i vv --- ---v i ? i i iv L1MC_orf2#LIN 1911 TACAGCTAACATCATACTTAATGGTGAGA---AACTNGAAGCTTTCCCGC 1957 chr4qtel1M 858128 TAAATGCAGGAGGGAAGCAAGGATGGTTACTCTCCCTAGTCTT 858170 ivv ivi i viiv v i v i L1MC_orf2#LIN 1958 TAAGATCAGGAACAAGGCAAGGATGTCCCCTCTCACCACTCCT 2000 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 42.47 CpG sites = 58, Kimura (unadjusted) = 43.61 Transitions / transversions = 1.29 (58/45) Gap_init rate = 0.05 (16 / 328), avg. gap size = 1.50 (24 / 16) 513 31.23 1.24 3.38 chr4qtel1M 858181 858422 (141578) L1ME3F_3end#LINE/L1 316 552 (438) m_b213s551i9 8382 chr4qtel1M 858181 TGGCAATTAATATGGACTTATGCCCAAAAAGTTATCAAAC-TGTGCATAC 858229 v vi v vv - i iv i--- - vi L1ME3F_3end#L 316 TGGAAAACAATTTGGCATTAT-CTCGTAAAGTTG---AACATTCGCATAC 361 chr4qtel1M 858230 CCTTTGATCCAGCAGTGCAACTACTGGGCTTATACCCCAAAGAGATACTA 858279 vi i i v v v i iv v i i iv v L1ME3F_3end#L 362 CCTACGACCCAGCAATTCCACTCCTAGGTATATACCCAAGAGAAACTCTT 411 chr4qtel1M 858280 AAAAGAAGGGA--AAGGGACCTGTATGTGCCCAAATGTTTGTGGCAGCCC 858327 iv viviv v -- i i ---- i vvi ii i v L1ME3F_3end#L 412 GCACATGTGCACCAGGAGAC----ATGTACAAGAATGTTCATAGCAGCAC 457 chr4qtel1M 858328 TCTTTGTAGTGGCCAGAAACTGGAAACTGAGTAGATGCCCATCAATTGGA 858377 v i i i v i vivvi i i i iv L1ME3F_3end#L 458 TGTTCGTAATAGCAAAAAACTGGAAACAACCCAAATGTCCATCGACAGGA 507 chr4qtel1M 858378 GAATGGCTGGGTAAATTGTGGTATATGAATGTTATGGAGTATTAT 858422 v iii vv iiiv i L1ME3F_3end#L 508 GAATGGATAAATAAATTGTGGTATATTCACACAATGGAATATTAT 552 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.67 CpG sites = 40, Kimura (unadjusted) = 41.26 Transitions / transversions = 1.21 (40/33) Gap_init rate = 0.04 (10 / 241), avg. gap size = 1.10 (11 / 10) 647 30.58 2.36 1.68 chr4qtel1M 858207 858502 (141498) L1ME4c_3end#LINE/L1 342 639 (191) m_b213s551i10 8382 chr4qtel1M 858207 AAAAGTTATCAAACTGTGCATACCCTTTGATCCAGCAGTGCAACTACTGG 858256 i ii v v v i i i v v v L1ME4c_3end#L 342 AAGAGCCATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGG 391 chr4qtel1M 858257 GCTTATACCCCAAAGAGAT-ACTAAAAAGAAGGGAAAGGGACCTGTATGT 858305 vv v i i i i - i v i i --- i i L1ME4c_3end#L 392 GAATTTATCCTAAGGAAATAATTCAAAAGAAGGAAAAAG---CTATATGC 438 chr4qtel1M 858306 GCCCAAATGTTTGTGGCAGCCCTCTTTGTAGTGGCCAGAAACTGGAAACT 858355 i vv i ii v vi v i i i v i i v L1ME4c_3end#L 439 ACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACA 488 chr4qtel1M 858356 GAGTAGATGCCCATCAATTGGAGAATGGCTGGGTAAATTGTGGTATATGA 858405 ivv i i v v i i ii i i v? L1ME4c_3end#L 489 ACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCN 538 chr4qtel1M 858406 ATGTTATGGAGTATTAT-----TGTAAGAAATGACAAGCGGGATGAATAC 858450 iviv i -----ii v i i viiv v v i L1ME4c_3end#L 539 ACTCGATGGAATATTATGCAGCCATTAAAAATGATAATTATGAAGACTAT 588 chr4qtel1M 858451 AGAGAGGTTTGGAGAG-GCTTACATGAACTGATGCTAAGTGAAATGAGCA 858499 iv viiiv i i- i -- vv i i vi L1ME4c_3end#L 589 GTAGCAACATGGAAAATGTTT--ATGATATAATGTTAAGTGAAAAAAGCA 636 chr4qtel1M 858500 GAA 858502 L1ME4c_3end#L 637 GAA 639 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.27 CpG sites = 54, Kimura (unadjusted) = 40.88 Transitions / transversions = 1.54 (54/35) Gap_init rate = 0.03 (8 / 295), avg. gap size = 1.50 (12 / 8) 18 13.09 4.55 2.22 chr4qtel1M 858911 858954 (141046) (AAT)n#Simple_repeat 1 45 (0) m_b213s252i5 8383 chr4qtel1M 858911 AATAAAAAGTTATAATTATTA-AAAAATAATAATAATAA-AATAAT 858954 v - v v v - v - (AAT)n#Simple 1 AATAATAA-TAATAATAATAATAATAATAATAATAATAATAATAAT 45 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.07 (3 / 43), avg. gap size = 1.00 (3 / 3) 253 23.89 9.00 7.92 chr4qtel1M 859460 859559 (140441) MIRc#SINE/MIR 45 145 (123) m_b213s601i6 8384 chr4qtel1M 859460 GGGAGACCT-----CAATTCCCAAGAAGCTTTAGACATTTACTAGCTATG 859504 i ----- i v i---- i - v i i MIRc#SINE/MIR 45 GGAAGACCTGGGTTCGAGTCCCG----GCTCT-GCCACTTACTAGCTGTG 89 chr4qtel1M 859505 TGAAGTTGGGCTAATTCCTTAAAATC----GGACTCAGTTTTTTCAACTA 859550 vv v i iv vv ----i v ii v -- MIRc#SINE/MIR 90 TGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATC-- 137 chr4qtel1M 859551 ATATAAAAT 859559 - i MIRc#SINE/MIR 138 -TGTAAAAT 145 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.18 CpG sites = 12, Kimura (unadjusted) = 29.20 Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.10 (10 / 99), avg. gap size = 1.70 (17 / 10) 11 25.60 0.00 2.56 chr4qtel1M 860899 860938 (139062) (GAGAGGA)n#Simple_repeat 1 39 (0) m_b213s252i6 8385 chr4qtel1M 860899 GAAAGGAGAGAAGGGAGAGGGGAGTTAGAGTGAGGAGGGA 860938 i i i i -vi v i (GAGAGGA)n#Si 1 GAGAGGAGAGAGGAGAGAGGAGAG-AGGAGAGAGGAGAGA 39 Matrix = Unknown Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1) 529 33.34 1.52 2.15 chr4qtel1M 861970 862297 (137703) C L1ME4c_3end#LINE/L1 (163) 667 342 m_b213s551i11 8386 chr4qtel1M 861970 GTAATCATCATGCATTTACAATGTATTCCTTGTTCTGCTTGTTTTGCTCA 862019 vii i ?v ---- iiv i v ii i C L1ME4c_3end#L 667 GTAATCATAGCGTANATACAAT----TTTGTATTCTGCTTTTTTCACTTA 622 chr4qtel1M 862020 GCATCAGTTCATGTAAATCTTTCCAGTTTTTTCTAAAATCAGC-TGTTCA 862068 i i vv iv v - vv vi vi v i vv - iv i C L1ME4c_3end#L 621 ACATTATATCATAAACAT-TTTCCATGTTGCTACATAGTCTTCATAATTA 573 chr4qtel1M 862069 GCAATTTTTATAGAACAATAATATTCCATTACTTTCCTATACCAAAACTT 862118 v v v i vvvv iivv ?vv i v i C L1ME4c_3end#L 572 TCATTTTTAATGGCTGCATAATATTCCATCGAGTNGATGTACCATAATTT 523 chr4qtel1M 862119 ATTCAGCCATTCCCCAATCGATGGGTATCTACTCATTTTTCAATTCTTTG 862168 i i i v i v ii i vvivv i i i C L1ME4c_3end#L 522 ACTTAACCATTCCCCTATTGTTGGACATTTAGGTTGTTTCCAATTTTTCG 473 chr4qtel1M 862169 CTACCACAACAAGAGCTACTACAAATGTTTTTGCACATGTGGGTCCTTTT 862218 ii i vv iv i v ii ii i i ii i i -- i C L1ME4c_3end#L 472 CTATTATAAATAACGCTGCAATGAACATCTTCGTGCATATAG--CTTTTT 425 chr4qtel1M 862219 CCCTCCTTT--ATGATTTCCTTGGGATACAGACCCAGTGATGACACTGCT 862266 i i -- v i v vv vii iv i i C L1ME4c_3end#L 424 CCTTCTTTTGAATTATTTCCTTAGGATAAATTCCCAGAAGTGGAATTACT 375 chr4qtel1M 862267 GGGTCAAAAGATATG--TAGTTTGATAGCTCTT 862297 i i --i v v i C L1ME4c_3end#L 374 GGGTCAAAGGGTATGAACATTTTTATGGCTCTT 342 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.51 CpG sites = 61, Kimura (unadjusted) = 45.90 Transitions / transversions = 1.33 (61/46) Gap_init rate = 0.03 (10 / 327), avg. gap size = 1.20 (12 / 10) 21 0.00 0.00 0.00 chr4qtel1M 864657 864679 (135321) (A)n#Simple_repeat 1 23 (0) m_b213s252i7 8387 chr4qtel1M 864657 AAAAAAAAAAAAAAAAAAAAAAA 864679 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAA 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 16 16.24 0.00 0.00 chr4qtel1M 866333 866360 (133640) (G)n#Simple_repeat 1 28 (0) m_b213s252i8 8388 chr4qtel1M 866333 GGGGAGGGAGAGCGGGGGGGGGGGGGGG 866360 i i i v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGG 28 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 289 31.94 7.31 3.52 chr4qtel1M 867239 867676 (132324) C L1M3_orf2#LINE/L1 (2795) 493 40 m_b213s551i12 8389 chr4qtel1M 867239 TTTTCTTGTATATTTTGTGGTTAGATA---TATCTATTTTTAAGAGAGTA 867285 i i vv v vi i i--- i v i i v vi C L1M3_orf2#LIN 493 TTTCCTTATTGATTTTCTGTCTGGATGNTCTATCCATTGTTGAAAGTGGG 444 chr4qtel1M 867286 G-ATTGGAATCCCTTACTAATATGTTTTTGCTATCTATTTCTTCCTCTAA 867334 - i i i i v vv v i i ii i C L1M3_orf2#LIN 443 GTATTGAAGTCTCCTACTATTATTGTATTGCTGTCTATTTCTCCCTTCAG 394 chr4qtel1M 867335 CTCATTTC--TCTCTCCTCTAAAAATCTAAAAGTGCTAT-ACACTTGGTA 867381 i - v -- v i v i v v i i-- vi- iii v i C L1M3_orf2#LIN 393 TTC-TGTCAATATTTGCTTTATATATTTAG--GTGCTCCGATGTTGGGTG 347 chr4qtel1M 867382 CATGTTTAGTATTGATA-TTACTTTACCATCTATGGTA-------TCTTT 867423 i ---i v - ii v i v - ? i-------i C L1M3_orf2#LIN 346 CATAT---ATATTTATAATTGTTATATCTTCT-TGNTGAATTGACCCTTT 301 chr4qtel1M 867424 CAGCAAGATGTAGTTTCCTTCTTTATCTCTTTTAAATAGAT--------- 867464 i v vv i i v? i v i -i v --------- C L1M3_orf2#LIN 300 TATCATTATATAATGNCCTTCTTTGTCTCTTGTGA-CAGTTTTTGACTTA 252 chr4qtel1M 867465 -ATTTTGTTTTGTCTGAGATAAGGATTCCTACCCCTGCCTTTTTTTTTTT 867513 - v i i v v vv i - i i vv C L1M3_orf2#LIN 251 AAGTCTATTTTGTCTGATATAAGTATAGCCACCCCTG-CTCTCTTTTGGT 203 chr4qtel1M 867514 TAACTTCAGCTGAAGCACAGCATATCTTGCTCCAGCCTCTCCCTTTTATT 867563 ---i vi --- ii v vi v ii v i vi C L1M3_orf2#LIN 202 TA---CCATTT---GCATGGAATATCTTTTTCCATCCCTTCACTTTCAGC 159 chr4qtel1M 867564 CTGTGCTCATCTCT--GCTTCAAATGTATTTCTTCTAAAAAATGAATTGT 867611 i ivii ii --i?i v i vi i v iiv iiiv v C L1M3_orf2#LIN 158 CTATGTGTGTCCTTAAANCTAAAGTGAGTCTCTTGTAGGCAGCATATAGT 109 chr4qtel1M 867612 AGGATTTTGGTTTTTAATCCACTCTG-----CTATGCCCTTCTATTTTAT 867656 v i v v i v ----- i i iv vv - C L1M3_orf2#LIN 108 TGGATCTTGTTTTTTTATCCATTCAGCCACTCTATGTCTTTTGATTGGA- 60 chr4qtel1M 867657 GAATTTATCTCTTTTACATT 867676 i vii v C L1M3_orf2#LIN 59 GAGTTTAATCCATTTACATT 40 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.08 CpG sites = 79, Kimura (unadjusted) = 43.52 Transitions / transversions = 1.41 (79/56) Gap_init rate = 0.06 (26 / 437), avg. gap size = 1.85 (48 / 26) 307 30.51 6.85 3.52 chr4qtel1M 867431 867678 (132322) C L1M1_orf2#LINE/L1 (3001) 293 38 m_b213s551i13 8389 chr4qtel1M 867431 ATGTAGTTTCCTTCTTTATCTCTTTTAAATAGAT---ATTTTG------- 867470 i vv i i v - v ---i i ------- C L1M1_orf2#LIN 293 ATATAGTGACCTTCTTTGTCTCTTCTTA-TAGTTTTTGTCTTGAAATCTA 245 chr4qtel1M 867471 TTTTGTCTGAGATAAGGATTCCTACCCCTGCCTTTTTTTTTTTTAACTTC 867520 v v vv i ----- i iii C L1M1_orf2#LIN 244 TTTTGTCTGATATAAGTATAGCTACTCCTGC-----TCTTTTTTGGTTTC 200 chr4qtel1M 867521 AGCTGAAGCACAGCATATCTTGCTCCAGCCTCTCCCTTTTATTCTGTGCT 867570 vii -- ii v vi v ii ivi i v i iv C L1M1_orf2#LIN 199 CATTG--GCATGGAATATCTTTTTCCATCCCTTTATTTTCAGTCTATGTG 152 chr4qtel1M 867571 CATCTCTGC--TTCAAATGTATTTCTTCTAAAAAATGAATTGTAGGATTT 867618 ii i ii--v v i i v iiv iii ii?v i i C L1M1_orf2#LIN 151 TGTCTTTATAGGTGAAGTGTGTTTCTTGTAGGCAACAGATCANTGGGTCT 102 chr4qtel1M 867619 TGGTTTTTAATCCACTCTG-----CTATGCCCTTCTATTTTATGAATTTA 867663 v v i v ----- i i iv vv - i C L1M1_orf2#LIN 101 TGTTTTTTCATCCATTCAGCCACTCTATGTCTTTTGATTGGA-GAGTTTA 53 chr4qtel1M 867664 TCTCTTTTACATTCA 867678 vii v C L1M1_orf2#LIN 52 GTCCATTTACATTCA 38 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.95 CpG sites = 45, Kimura (unadjusted) = 40.95 Transitions / transversions = 1.61 (45/28) Gap_init rate = 0.05 (13 / 247), avg. gap size = 2.00 (26 / 13) 249 25.77 4.65 0.75 chr4qtel1M 868483 868611 (131389) C L1MCa_5end#LINE/L1 (911) 1523 1390 m_b213s551i14 8390 chr4qtel1M 868483 AAGTCCTGGGTAATTCTGATTGTGGCTCCTGAATATCCAAATTGTTCCTT 868532 ?viv v iv v vv vvi iv ii C L1MCa_5end#LI 1523 AAGTCNGATGTAATTCTTATCTTTGCTCCTCTATAGGTAAGGTGTTTTTT 1474 chr4qtel1M 868533 ---TCTGGCTTCTTTCAGGATTTTCTACTTG-ATCTGATAATTCTGGAAT 868578 --- i i vi -v i -v v i C L1MCa_5end#LI 1473 CCCTCTGGCTTCTTTCAAGATTTTTTCTTTGTCTTTGAT-TTTCTGCAGT 1425 chr4qtel1M 868579 TTAGCTATGGTATTCCTTGGAGT--TTTCATTTTG 868611 iiv i v v v --? ? i? C L1MCa_5end#LI 1424 TTGAATATGATATGCCTAGGTGTAGNTNCGNTTTG 1390 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 31.88 CpG sites = 15, Kimura (unadjusted) = 33.05 Transitions / transversions = 0.83 (15/18) Gap_init rate = 0.03 (4 / 128), avg. gap size = 1.75 (7 / 4) 12 3.81 11.11 0.00 chr4qtel1M 869017 869043 (130957) (TTTC)n#Simple_repeat 1 30 (0) m_b213s252i10 8391 chr4qtel1M 869017 TTTC-TT-TTTCTTTCTTTCTTT-TTTATT 869043 - - - v (TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 30 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.12 (3 / 26), avg. gap size = 1.00 (3 / 3) 15 23.86 0.00 2.22 chr4qtel1M 869015 869060 (130940) (TTTTTC)n#Simple_repeat 1 45 (0) m_b213s252i9 8392 chr4qtel1M 869015 TTTTTCTTTTTCTTTCTTTCTTTTTTATTATTATAGCTTTTTATTT 869060 i i i i v v - vv v (TTTTTC)n#Sim 1 TTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTT-TTTCTTTTTCTTT 45 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1) 321 25.64 3.85 0.00 chr4qtel1M 870225 870302 (129698) C MIRc#SINE/MIR (185) 83 3 m_b213s601i7 8393 chr4qtel1M 870225 TAGTA-GTA-TAGAATCACAATTCCAACCCATGTCTTC-TGACTCCAAAT 870271 - i-i ii ivi i v v - i C MIRc#SINE/MIR 83 TAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGT 34 chr4qtel1M 870272 CTAGTGCTTTTTCTATTTCATCATATTACCT 870302 i i i i v i i i i C MIRc#SINE/MIR 33 CCAGTGCTCTTTCCACTGCACCACACTGCCT 3 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.56 CpG sites = 16, Kimura (unadjusted) = 33.66 Transitions / transversions = 4.00 (16/4) Gap_init rate = 0.04 (3 / 77), avg. gap size = 1.00 (3 / 3) 201 19.70 0.00 9.76 chr4qtel1M 870714 870758 (129242) L3#LINE/CR1 3545 3585 (514) m_b213s601i8 8394 chr4qtel1M 870714 GAGGTGATAATCCTGTTGTATCTTGCTTGACTTGGTCAGACCACA 870758 i i i i iii ---i - L3#LINE/CR1 3545 GAGGTAATAGTCCCGCTGTACTCTGC---GCT-GGTCAGACCACA 3585 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 18.01 CpG sites = 8, Kimura (unadjusted) = 24.73 Transitions / transversions = 1.00 (8/0) Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4) 33 0.00 0.00 0.00 chr4qtel1M 872632 872659 (127341) (TA)n#Simple_repeat 1 28 (0) c_b213s251i1 8395 chr4qtel1M 872632 TATATATATATATATATATATATATATA 872659 (TA)n#Simple_ 1 TATATATATATATATATATATATATATA 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 258 32.14 6.85 1.96 chr4qtel1M 872785 872930 (127070) C MIRc#SINE/MIR (33) 235 83 m_b213s601i9 8396 chr4qtel1M 872785 TTACA-TTTCTAATGC---TTCATACACA--ATTTCATTGGATGAGCATA 872828 - vi v --- i i -- i v vvv i C MIRc#SINE/MIR 235 TTACAGTTTACAAAGCGCTTTCACATACATTATCTCATTTGATCCTCACA 186 chr4qtel1M 872829 ATGAACCTTTGACA---ACAGAGGAAGTGCCTTCATTCTCATCATATACA 872875 ii v v vi---i i v i iiiv i i i iv i v C MIRc#SINE/MIR 185 ACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGA 136 chr4qtel1M 872876 TACTCAGACCATGAG-CTCAGAATGGTTTAGTGACTTGATCCAAATCTCA 872924 ivvv i -- - iv v vi v ii v C MIRc#SINE/MIR 135 TGAGGAAAC--TGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACA 88 chr4qtel1M 872925 GCAGCT 872930 - C MIRc#SINE/MIR 87 -CAGCT 83 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.00 CpG sites = 25, Kimura (unadjusted) = 43.00 Transitions / transversions = 1.19 (25/21) Gap_init rate = 0.06 (8 / 145), avg. gap size = 1.62 (13 / 8) 220 30.94 13.58 2.22 chr4qtel1M 872811 872972 (127028) C MIR1_Amn#SINE/MIR (29) 201 22 m_b213s601i10 8396 chr4qtel1M 872811 TTTCATTGGATGAGCATAATGAACCTTTGACAACAGAGG-AAGTGCCTTC 872859 ii vv v vi v v i -- vi -v ii v i C MIR1_Amn#SINE 201 TTTCATCAGTAGATCTCAAAGCACTTT--ACAAAGGAGGTCAGTATCATT 154 chr4qtel1M 872860 ATTCTCATCATATACATACTCAGACCATGAG-CTCAGAATGGTTTAGTGA 872908 i i iv i v ivvv i -- - ? iv ?v C MIR1_Amn#SINE 153 ATCCCCATTTTACAGATGAGGAAAC--TGAGGCNCAGAGAGGTNAAGTGA 106 chr4qtel1M 872909 CTTGATCCAAAT--CTCAGC-------------AGCTGAGACTAGAACTC 872943 vi v ii -- ? ------------- i i ? ? i C MIR1_Amn#SINE 105 CTTGCCCAAGGTCACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAACCC 56 chr4qtel1M 872944 AAATACTGTGAAT---AGGC--ATGCTCTATCCA 872972 ii viivi i --- v --i C MIR1_Amn#SINE 55 AGGTCTCCCGAGTCCCAGTCCAGTGCTCTATCCA 22 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.69 CpG sites = 28, Kimura (unadjusted) = 43.01 Transitions / transversions = 1.33 (28/21) Gap_init rate = 0.06 (10 / 161), avg. gap size = 2.60 (26 / 10) 364 26.96 12.17 0.00 chr4qtel1M 874488 874602 (125398) MIRc#SINE/MIR 28 156 (112) m_b213s601i11 8397 chr4qtel1M 874488 CAGTGGACCCTGAGTCAGGAAGAGCAGAGTTTTTATCCCAGCTGAGAAAC 874537 v iiv v v i ivvi i vv vv MIRc#SINE/MIR 28 CACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCAC 77 chr4qtel1M 874538 TTGCTAGT--------------CAAGTCACAGGATCTCTGTTTGCCTCAG 874573 i i-------------- vvi i v vv MIRc#SINE/MIR 78 TTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAG 127 chr4qtel1M 874574 TTTCTCTATTTGTAAAATGGGCTTAATAA 874602 iii i vv MIRc#SINE/MIR 128 TTTCCTCATCTGTAAAATGGGGATAATAA 156 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.08 CpG sites = 14, Kimura (unadjusted) = 33.58 Transitions / transversions = 0.82 (14/17) Gap_init rate = 0.01 (1 / 114), avg. gap size = 14.00 (14 / 1) 349 31.94 9.44 2.60 chr4qtel1M 874499 874678 (125322) MIRb#SINE/MIR 42 233 (35) m_b213s601i12 8397 chr4qtel1M 874499 GAGTCAGGAAGAGCAGAGTTTTTATCCCAGCTGAGAAACTTGCTAGT--- 874545 iv v v i ivv i vv vv i i--- MIRb#SINE/MIR 42 GAGTCAGACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGT 91 chr4qtel1M 874546 -----------CAAGTCACAGGATCTCTGTTTGCCTCAGTTTCTCTATTT 874584 ----------- i vvi i v vv iii i MIRb#SINE/MIR 92 GTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCT 141 chr4qtel1M 874585 GTAAAATGGGCTTAATAAGAACACTTAATTTCTAGGGGTTCCCTTGA-GA 874633 ---i v i i vi ivi - viiv - MIRb#SINE/MIR 142 GTAAAATGGG---GATAATAATACCTACCTCGCA-GGGTTGTTGTGAGGA 187 chr4qtel1M 874634 TAAATTAAAACAATATTTATACAGTGC--AGGACATATGACAGGTAC 874678 v v i i i iiv i v i -- v -i v v i MIRb#SINE/MIR 188 TTAAATGAGATAATGCATGTAAAGCGCTTAGCACA-GTGCCTGGCAC 233 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.73 CpG sites = 30, Kimura (unadjusted) = 42.62 Transitions / transversions = 1.15 (30/26) Gap_init rate = 0.05 (9 / 179), avg. gap size = 2.44 (22 / 9) 403 32.92 7.39 1.61 chr4qtel1M 874525 874700 (125300) MIR#SINE/MIR 77 262 (0) m_b213s601i13 8397 chr4qtel1M 874525 CCAGCTGAGAAACTTGCTAGTCAAGTCACAGGATCTCTGTTTGCCTCAGT 874574 i v vi i -- i v i vvi i v v MIR#SINE/MIR 77 CTAGCTGTGTGACCT--TGGGCAAGTTACTTAACCTCTCTGTGCCTCAGT 124 chr4qtel1M 874575 TTCTCTATTTGTAAAATGGGCTTAATAAGAACACTTAATTTCTAGGGGTT 874624 iii i vv v ii i vi iv - MIR#SINE/MIR 125 TTCCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTCATA-GGGTT 173 chr4qtel1M 874625 CCCTTGAG------ATAAATTAAAAC------AATATTTAT-ACAGTGCA 874661 viiv ------ i i v ------ iiii v- v MIR#SINE/MIR 174 GTTGTGAGGATTAAATGAGTTAATACATGTAAAGCGCTTAGAACAGTGCC 223 chr4qtel1M 874662 GGACATATGACAGGTACTGTATAAAAGTTGACTGTTACT 874700 v i i iii i ii vv v ii i i MIR#SINE/MIR 224 TGGCACATAGTAAGCGCTCAATAAATGTTAGCTATTATT 262 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.08 CpG sites = 36, Kimura (unadjusted) = 45.52 Transitions / transversions = 1.71 (36/21) Gap_init rate = 0.03 (6 / 175), avg. gap size = 2.67 (16 / 6) 322 29.62 10.88 1.24 chr4qtel1M 874853 874999 (125001) L2b_3end#LINE/L2 306 466 (0) m_b213s601i14 8398 chr4qtel1M 874853 TGGATTTTTATATAACTGTGGATATGT-TGTCTGCCCCACCAATCTATGA 874901 i v ? - iv ?vv i - v i iv i L2b_3end#LINE 306 TGGGTTATNAT-TGTCTGNTTACATGTCTGTCTCCCCCACTAGACTGTGA 354 chr4qtel1M 874902 GCTCTAGGAGAGCAAGAA--ATATC--TCTTAT--A-------AGTCCTG 874938 iiv i i i --i?i -- i -- ------- vi ii L2b_3end#LINE 355 GCTCCGTGAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTGTATCCCCA 404 chr4qtel1M 874939 GTGCTTATCAGAGGGCCTGGCTTATAGTACACACTTG--AGATGTTTGTT 874986 i i v v ? vi i vi i ii-- i i L2b_3end#LINE 405 GCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTTGTT 454 chr4qtel1M 874987 AACTTGAATAAGT 874999 i v- i i L2b_3end#LINE 455 GAA-TGAATGAAT 466 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.39 CpG sites = 30, Kimura (unadjusted) = 41.56 Transitions / transversions = 2.31 (30/13) Gap_init rate = 0.05 (8 / 146), avg. gap size = 2.25 (18 / 8) 334 28.69 3.64 1.79 chr4qtel1M 875084 875193 (124807) C MIR3#SINE/MIR (11) 197 86 m_b213s601i15 8399 chr4qtel1M 875084 TTATAGATGATCA---CTGCAAGGGAATTAAAGGACCATGGAGTCCAATC 875130 i vvi --- v vi v ii i vv i C MIR3#SINE/MIR 197 TCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACC 148 chr4qtel1M 875131 CCCTCATATTAAAATTGGGGAAATTGAGATTGAGTGAATTG-AGTGACTA 875179 v v iv i i iiiv v iv - v C MIR3#SINE/MIR 147 CCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTT 98 chr4qtel1M 875180 GTCCAGGAAGCCAC 875193 i -- i i C MIR3#SINE/MIR 97 GCCCA--AGGTCAC 86 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.89 CpG sites = 17, Kimura (unadjusted) = 36.89 Transitions / transversions = 1.21 (17/14) Gap_init rate = 0.04 (4 / 109), avg. gap size = 1.50 (6 / 4) 287 37.95 2.17 0.71 chr4qtel1M 875132 875269 (124731) C MIRc#SINE/MIR (119) 149 10 m_b213s601i16 8399 chr4qtel1M 875132 CCTCATATTAAAATTGGGGAAATTGAGATTGAGTGAA-TTGAGTGACTAG 875180 i v v iv i i ii v v i- i v C MIRc#SINE/MIR 149 CCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTG 100 chr4qtel1M 875181 TCCAGGAAGCCACTACTAAAAAATATCTGAAAAAGAATTCTAAGGCAGGT 875230 i i ivvv vi iv i iv v ivvi i i v vv C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGT 50 chr4qtel1M 875231 CTTTCT--TTCCTAGCTCTAGCACTTACCTCATGACAACAC 875269 i --i v - i ii iviii ivi v C MIRc#SINE/MIR 49 CTTCCTGACTCCAAG-TCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 53.71 CpG sites = 30, Kimura (unadjusted) = 55.32 Transitions / transversions = 1.36 (30/22) Gap_init rate = 0.02 (3 / 137), avg. gap size = 1.33 (4 / 3) 261 35.49 0.00 1.08 chr4qtel1M 875826 875919 (124081) MIRc#SINE/MIR 10 102 (166) m_b213s601i17 8400 chr4qtel1M 875826 GTAGTGCAATGGAAAGAGACCTGGGTATAGAGCCTGAAGGGCCTGAGTTT 875875 i i vv iiv i i v i i i i i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr4qtel1M 875876 AAACTGAGTCTCAGAATGTCACTAGCTGTATGCCCCTTAAGTAA 875919 i iiivv v v vvvv i i -v ii i MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTG-ACCTTGGGCAA 102 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 47.94 CpG sites = 20, Kimura (unadjusted) = 50.38 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.01 (1 / 93), avg. gap size = 1.00 (1 / 1) 19 21.66 0.00 6.45 chr4qtel1M 876237 876302 (123698) (TTATT)n#Simple_repeat 1 62 (0) m_b213s252i11 8401 chr4qtel1M 876237 TTATTTTTGTGTTGTTTGCTTGCATTTTATTTTCTTTCTCATTTTATTCT 876286 - i v i vv vi v - - - (TTATT)n#Simp 1 TTA-TTTTATTTTATTTTATTTTATTTTATTTTATTT-T-ATTTTATT-T 46 chr4qtel1M 876287 TTTTTGATTTGATTTT 876302 v v v (TTATT)n#Simp 47 TATTTTATTTTATTTT 62 Matrix = Unknown Transitions / transversions = 0.38 (3/8) Gap_init rate = 0.06 (4 / 65), avg. gap size = 1.00 (4 / 4) 15 13.87 0.00 0.00 chr4qtel1M 876482 876505 (123495) (T)n#Simple_repeat 1 24 (0) m_b213s252i12 8402 chr4qtel1M 876482 TTTTTTTTTTTTTGGTTTTTATTT 876505 vv v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTT 24 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 997 29.29 4.15 4.15 chr4qtel1M 876967 877593 (122407) C L1MC1_3end#LINE/L1 (447) 633 7 m_b213s551i15 8403 chr4qtel1M 876967 GCTCATTTCACTCAGCATCAGTTCATGTAAGTCTCT--CAGGCCTTTCTG 877014 iv i i vi - v v i i-- v i --- C L1MC1_3end#LI 633 GCTTCTTTCACTTAGTAATA-TGCATTTAAGTTTCCTCCATGTCTTT--- 588 chr4qtel1M 877015 AAATCAT--CCTGTTGG-TCATTTCTTAC-AGAAC--AGTAATATTCCAT 877058 --- -- i v i - vi- vi -- i C L1MC1_3end#LI 587 ---TCATGGCTTGATAGCTCATTTCTTTTTAGCGCTGAATAATATTCCAT 541 chr4qtel1M 877059 AATATTCATATACCACAATTTATTCAGCCATTCTCCAACTGATGGACATC 877108 vi v vv i i i v v v v C L1MC1_3end#LI 540 TGTCTGGATGTACCACAGTTTATTTATCCATTCACCTACTGAAGGACATC 491 chr4qtel1M 877109 C-ATTCAGTTTCAGTTTTTAGCCACTACAAA-AGGGCTGCCACAAACATT 877156 i-iv iiv i iv i v i ii - ii i i i C L1MC1_3end#LI 490 TTGGTTGCTTCCAAGTTTTGGCAATTATGAATAAAGCTGCTATAAACATC 441 chr4qtel1M 877157 CATGCACATACAGGTCCCTTTCCCTTC-----TTTATAATCTCTTTGGGA 877201 i ---- i iii v vivvv ----- vi iii - C L1MC1_3end#LI 440 CGTG----TGCAGGTTTTTGTGTGGACATAAGTTTTCAACTCCTTTGGG- 396 chr4qtel1M 877202 TATAATCCCA-GTAGTAACACTGCTGGATCAAAGGGTATGCACAGTTTGA 877250 - v - v iivv i iv v v --- v v C L1MC1_3end#LI 395 TA-AATACCAAGGAGCGCGATTGCTGGATCGTATGGTAAG---AGTATGT 350 chr4qtel1M 877251 TAACTTTT-TGAGCATAGT-TCAAACTACTCTCCAAAATGGTTGGATTCG 877298 v v - i v - v -i iiii i i v iivv C L1MC1_3end#LI 349 TTAGTTTTGTAAGAA-ACTGCCAAACTGTCTTCCAAAGTGGCTGTACCAT 301 chr4qtel1M 877299 TTCACAACTCCACCAACAATGCATCAATGTCCCAGTTTTCCCGCATCCCC 877348 ii vii i v v iv i v vii i i C L1MC1_3end#LI 300 TTTGCATTCCCACCAGCAATGAATGAGAGTTCCTGTTGCTCCACATCCTC 251 chr4qtel1M 877349 TCCAACAATCA---TCATTAATTTTTTCCTGTCATCTTAGCCAATCTGAC 877395 v i v ii--- ii i i v --- v- i i v i i C L1MC1_3end#LI 250 GCCAGCATTTGGTGTTGTCAGTGTT---CTGG-ATTTTGGCCATTCTAAT 205 chr4qtel1M 877396 AGGTGTGTAGTGGATATCTTAGAGTTGTCTTAATTTGCATTTCTCTGATT 877445 - i vv i i v C L1MC1_3end#LI 204 AGGTGTGTAGTGG-TATCTCATTGTTGTTTTAATTTGCATTTCCCTGATG 156 chr4qtel1M 877446 A-ATAATGACTTGGAGCATCTTTTCATATGACTAGAAATAGTTTCAATTT 877494 - - iv vi vvviivi i vv v C L1MC1_3end#LI 155 ACATA-TGATGTGGAGCATCTTTTCATATGCTTATTTGCCATCTGTATAT 107 chr4qtel1M 877495 CTTCATCTGAGAATTGTCTGTTCATATCCTTTGACCATTTTTCAATTGGA 877544 v iv v iv ? vi i v v ? i - C L1MC1_3end#LI 106 CTTCTTTGGTGAGGTGTCTGTTNAGGTCTTTGGCCCATTTTTNAATCGG- 58 chr4qtel1M 877545 GAATGGCTTGATTT-TTATAAATTAGAGTTAA---TTCTCTATATATTTT 877590 --i v i i v - viv v vv --- i i C L1MC1_3end#LI 57 --GTTGTTCGTTTTCTTATTGTTGAGTTTTAAGAGTTCTTTGTATATTTT 10 chr4qtel1M 877591 GGA 877593 C L1MC1_3end#LI 9 GGA 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.41 CpG sites = 97, Kimura (unadjusted) = 38.07 Transitions / transversions = 1.23 (97/79) Gap_init rate = 0.07 (41 / 626), avg. gap size = 1.27 (52 / 41) 1556 26.09 1.47 2.40 chr4qtel1M 877048 877593 (122407) C L1ME3G_3end#LINE/L1 (377) 547 7 m_b213s551i16 8403 chr4qtel1M 877048 TAATATTCCATAATATTCATATACCACAATTTATTCAGCCATTCTCCAAC 877097 i i vv i i i i v i C L1ME3G_3end#L 547 TAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTAT 498 chr4qtel1M 877098 TGATGGACATCCATTCAGTTTC-AGTTTTTAGCCACTACAAA-AGGGCTG 877145 ii vviv - i v i i - iv C L1ME3G_3end#L 497 TGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCTG 448 chr4qtel1M 877146 CCACAAACATTCATGCACATACAGGTCCCTTTCC-CTTCTTT-ATAATCT 877193 v ii i v i i ?-- i v v - v v vi- vv i C L1ME3G_3end#L 447 CAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATTT 400 chr4qtel1M 877194 CTTTGGGATATAATCCCAGTAGTAACACTGCTGGATCAAAGGGTATGCAC 877243 ? i v v? ? v iiv i i i C L1ME3G_3end#L 399 CTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGC 350 chr4qtel1M 877244 AGTTTGATAACTTTTTGAGCATAGT-TCAAACTACTCTCCAAAATGGTTG 877292 v i -- i vvv - v -i i i i ? i C L1ME3G_3end#L 349 ATTTTAA--ATTTTAATAG-ATACTGCCAAATTGCCCTCCAAAANGGCTG 303 chr4qtel1M 877293 GATTCGTTCACAACTCCACCAACAATGCATCAATGTCCCAGTTTTCCCGC 877342 v iivi i vii i i i v iv v v i i C L1ME3G_3end#L 302 TACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCAC 253 chr4qtel1M 877343 ATCCCCTCCAACAATC---ATCATTAATTTTTTCCTGTCATCTTAGCCAA 877389 i i v v ?--- i i ?i vv---- i v C L1ME3G_3end#L 252 ACCCTCGCCAACACTNGATATTATCAANCTTTTAA----ATTTTTGCCAA 207 chr4qtel1M 877390 TCTGACAGGTGTGTAGTGGATATCTTAGAGTTGTCTTAATTTGCATTTCT 877439 ii viv i - i vv i i C L1ME3G_3end#L 206 TCTGATGGGTGAAAAATGG-TATCTCATTGTTGTTTTAATTTGCATTTCC 158 chr4qtel1M 877440 CTGATTAATAATGACTTGGAGCATCTTTTCATATGACTAGAAATAGTTTC 877489 v i vv v vi vviiivi v C L1ME3G_3end#L 157 CTGATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTG 108 chr4qtel1M 877490 AATTTCTTCATCTGAGAATTGTCTGTTCATATCCTTTGACCATTTTTCAA 877539 v i v v i v v C L1ME3G_3end#L 107 TATTTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTA 58 chr4qtel1M 877540 TTGGAGAATGGCTTGATTTTTATAAATTAGAGTTAATTCTCTATATATTT 877589 iv-- v v- i vi v vivv i i i C L1ME3G_3end#L 57 TTGGGT--TGTCTTT-TTCTTATTGATTTGTAGGAGTTCTTTATATATTC 11 chr4qtel1M 877590 TGGA 877593 C L1ME3G_3end#L 10 TGGA 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.51 CpG sites = 75, Kimura (unadjusted) = 33.09 Transitions / transversions = 1.17 (75/64) Gap_init rate = 0.03 (19 / 545), avg. gap size = 1.11 (21 / 19) 4761 29.45 3.62 2.86 chr4qtel1M 877451 880683 (119317) C L1M5_orf2#LINE/L1 (0) 3294 38 m_b213s551i17 8403 chr4qtel1M 877451 TGACTTGGAGCATCTTTTCATATGACTAGAAATAGTTTCAATTTCTTCAT 877500 ?v v i vi vviiivi v? v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr4qtel1M 877501 CTGAGAATTGTCTGTTCATATCCTTTGACCATTTTTCAATTGGA--GAAT 877548 i v v vi i v ?v i-- vv C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTT 3195 chr4qtel1M 877549 GGCTTGATTTTTAT-AAATTAGAGTTAATTCTCTATATATTTTGGAAATG 877597 v v- ? -i ? iv v- i i i v i C L1M5_orf2#LIN 3194 GTCTTT-TTNTTATTGANTTGTAGG-AGTTCTTTATATATTCTGGATACG 3147 chr4qtel1M 877598 AGGCCTTTATCAGAACCTTTGACTGTAAAAATATTTT-TCCCAGTTTATT 877646 v i -iv v v? - iv - ? i i v C L1M5_orf2#LIN 3146 AGTCCTTTGTCAGA-TATATGTNT-TGCAAATATTTTCTCCCANTCTGTG 3099 chr4qtel1M 877647 GCTT-CCTTCTAATCTTGTCTGCATTAGTTTTGTTTGTACAAAAACTTTT 877695 - i v i v ivi iv ivi vvv? vi i ii C L1M5_orf2#LIN 3098 GCTTGCCTTTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTTT 3049 chr4qtel1M 877696 CAGTTTGGTATAATCGAA-------ATTTTCTATTTTGTGATCAGTGATG 877738 v v i i? i v ------- i v i i i? --- C L1M5_orf2#LIN 3048 AATTTTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGGTTNGTG--- 3002 chr4qtel1M 877739 ATCTCTAGTTCTGCTTTGGTCATAAAGACCTCCCCT-TCCACAGGTCTGA 877787 -- i -- v iii v i vi iv i iv -? vv vvi C L1M5_orf2#LIN 3001 --CTTT--TTGTGTCCTGTTTAAGAAATCTTTGCCTANCCCAAGGTCACG 2956 chr4qtel1M 877788 GAGGTAAACTATCCTGTGTT--CCTCTAATTTATTAATAATTTCATTCTT 877835 i i --i v i -- i ivvvv v i i ?ii C L1M5_orf2#LIN 2955 AAGATA--TTCTCCTATGTTTTCTTCTAGAAGTTTTATAGTTTTANCTTT 2908 chr4qtel1M 877836 TATGCCTAGGTC-ATGAACCCATTTTGACCTTATCTTGGTGTACG-TGTT 877883 iiii - -i i ? vi v i v i - v C L1M5_orf2#LIN 2907 TACATTTAGGTCTATGA-TCCATCTNGAATTAATTTTTGTGTATGGTGTG 2859 chr4qtel1M 877884 AAGTATGGATCAATGCCTAGTTTCTGGCATATTAGTTTCCAATT-TTCCA 877932 i v i i v?iii v i vv vii v - C L1M5_orf2#LIN 2858 AGGTAGGGGTCGAGNTTCATTTTTTTCCATATGGATATCCAATTGTTCCA 2809 chr4qtel1M 877933 GCAATTTTTATCAAACAGTAAGTTCTTATCCCAAAGCTGGGAT-CTTTGG 877981 viv i ii v vvvi i vi --- iiv - ? C L1M5_orf2#LIN 2808 GCACCATTTGTTGAAAAGACTATCCTTTCCCCA---CTGAATTGCNTTGG 2762 chr4qtel1M 877982 G---TTTGTCAAAGACTAGGTTGCTATATTTGT-TGACTGTTTTATCCCT 878027 v--- i ii i? v? i v - --- v i ii C L1M5_orf2#LIN 2761 CACCTTTGTCAAAAATCAANTGNCCATATATGTGTG---GGTCTATTTCT 2715 chr4qtel1M 878028 TGAAC---CTAATCTATTCCACTGATCAACTAATCTATTCCTTA-GCCAA 878073 - i --- v i i v i vi - - C L1M5_orf2#LIN 2714 -GGACTCTCTATTCTGTTCCATTGATCTATTTGTCTAT-CCTTACGCCAA 2667 chr4qtel1M 878074 TACCAAATAGTTTTGGTAACTGCTGCTCTATAATATAATTTT-AGATCTG 878122 v iv i i v iv i - i i - ? ? C L1M5_orf2#LIN 2666 TACCACACTGTCTTGATTACTGTAGCTTTATAATA-AGTCTTGANATCNG 2618 chr4qtel1M 878123 GTACAGCTAAG----CCACCTTCATTTGATTTTTTTTCATTAATTCCTTG 878168 vv - ---- v ii i-- i vv v vii C L1M5_orf2#LIN 2617 GTAGTG-TAAGTCCTCCAACTTTGTTC--TTCTTTTTCAAGATTGTTTTG 2571 chr4qtel1M 878169 AA-ATTCTTGA-CCTTTGTTTTTCCATATGAACTTTG--------TTGTT 878208 iv- ? i- iv i i i-------- i C L1M5_orf2#LIN 2570 GCTATTCTNGGTCCTTTGCATTTCCATATAAATTTTAGAATCAGCTTGTC 2521 chr4qtel1M 878209 ATTTTTCTAGGTCATTAAAATAGTTTTTGGTAGTCTGATTGGTATAGCGC 878258 v - --- -- v vi vi v v i v v ii C L1M5_orf2#LIN 2520 AATTT-CTA---CA--AAAAAACCTGCTGGGATTTTGATTGGGATTGCAT 2477 chr4qtel1M 878259 TAAATAAATAGATTAGTTTAGGTAATATTGTCATCTTTATTATATTTGCT 878308 i vv i i i v iv v ? iv viv C L1M5_orf2#LIN 2476 TGAATCTATAGATCAATTTGGGGAGAATTGACATCTTNACAATATTGAGT 2427 chr4qtel1M 878309 CGCCCTATCAA-GAGCATTTAATATTT-TCAATTGGTTTAGATCAGACTT 878356 vi v v - i vvv i - v vi i vvvi C L1M5_orf2#LIN 2426 CTTCCAATCCATGAACATGGTATATCTCTCCATTTATTTAGGTCTTCTTT 2377 chr4qtel1M 878357 AATTTGTGTGAAAAGTGGTCTGTAATTTTGCTCATAAAGTTTCTG---AT 878403 v v v iv i v i i vvvii ? v ii --- C L1M5_orf2#LIN 2376 AATTTCTCTCAGCAATGTTTTGTAGTTTTCAGTGTANAGGTCTTGCACAT 2327 chr4qtel1M 878404 TTTCCCTTGGCAGATAGATTCCTAAATATTTTATATTATCAGTAGTTACT 878453 ? --- vi vv i ? i v iv vv i i C L1M5_orf2#LIN 2326 NTT---TTGTTAGATTTATTCCTAAGTATTTNATGTTTTTTGATGCTATT 2280 chr4qtel1M 878454 TTAAATGGAATTTCTCTTTGTAACTCTGACTGTTGGATT--TTGTTAGTG 878501 v v vi i ?-- v i v i v ivi -- iv i C L1M5_orf2#LIN 2279 GTAAATGGTATTGTTTTTN--AAATTTCATTTTCCAATTGTTTGTTGCTA 2232 chr4qtel1M 878502 ATATATAAGAATGCTGATGACTTATGTGGCTTTTATTTTATAACCAACAA 878551 i ii i viv i v i-iv v ii i v ?i i C L1M5_orf2#LIN 2231 GTATATAGAAATACAATTGATTTTTGTA-TATTGACCTTGTATCCNGCGA 2183 chr4qtel1M 878552 CTTTGCTAAA---AGTTGTGGATTATTTCTAATAATTT-TTAGCAGAATC 878597 i --- v ---- v i i - v i v C L1M5_orf2#LIN 2182 CCTTGCTAAATTCACTT----ATTAGTTCTAGTAGTTTNTTTGTAGATTC 2137 chr4qtel1M 878598 TCTGGGGTTCTCTAAGTATACCATCATGTCATCGGCAAAGAGTGACAATT 878647 i ? i i v ? v v i v i? i C L1M5_orf2#LIN 2136 TTTNGGATTTTCTACGTANACAATCATGTCATCTGCGAATAANGACAGTT 2087 chr4qtel1M 878648 TGGCTTCCTCATTGCCTATTCTTATTCCTTTAATCTCTGTCTCAGCTCTT 878697 vii i v v v ii v v i v i vvvi C L1M5_orf2#LIN 2086 TTATTTCTTCCTTTCCAATCTTTATGCCTTTTATTTCTTTTTCTTGCCTT 2037 chr4qtel1M 878698 ATTGCTATAGCTAGCGTTTCTAATACAATATTAAATAGTAACGGTGAT-G 878746 vv i viii i i i i v ii ?- C L1M5_orf2#LIN 2036 ATTGCACTGGCTAGGACCTCCAGTACAATGTTGAATAGAAGTGGTGANAG 1987 chr4qtel1M 878747 TGGGCAACCTTGTTTCACTCCAGATCTTATTGGGAATGGTTGCAGTTTGT 878796 i i v i iii v vv v v? v ? v C L1M5_orf2#LIN 1986 CGGACATCCTTGTCTTGTTCCCGATCTTAGGGGGAAAGCNTTCAGTNTTT 1937 chr4qtel1M 878797 CTCCATTACATATGATGCTTACTGATGATTTTAAATAGATGCTGCTGATT 878846 v vi i ?i vv i vvi ivi v i C L1M5_orf2#LIN 1936 CACCATTAAGTATGATGTTNGCTGTAGGTTTTTCGTAGATGCCCTTTATC 1887 chr4qtel1M 878847 ATTTTAAGGAAAAGTCCATTTATTCCTATACTCTCAAGTGTTTTTAATAG 878896 vv i ivvi v i vvi viii v vi v C L1M5_orf2#LIN 1886 AGGTTGAGGAAGTTCCCTTCTATTCCTAGTTTGCTGAGAGTTTTTATCAT 1837 chr4qtel1M 878897 GAATGGATGTTGGATTTTATCAAATGCTTTTTCTGCATCTATTGAGATGA 878946 i i i C L1M5_orf2#LIN 1836 GAATGGGTGTTGAATTTTGTCAAATGCTTTTTCTGCATCTATTGAGATGA 1787 chr4qtel1M 878947 TCATATGGTTTTTGTTAATTTGGT-TATTAACATGGCCAATTATATTGAT 878995 i -i vv iv - i i iv i C L1M5_orf2#LIN 1786 TCATATGATTTTT-CTCCTTTATTCTGTTAATATGGTGAATTACATTGAT 1738 chr4qtel1M 878996 AGTTTTCCTAATATTGAACCAGCCCTGCATTCCTGGTATAAATCCTACTT 879045 v v i v i i i i v i i C L1M5_orf2#LIN 1737 TGATTTTCGAATGTTAAACCAACCTTGCATTCCTGGGATAAACCCCACTT 1688 chr4qtel1M 879046 GATCATAGTGTATTATCTTGGAGATGATTTTCTGTAGTCTTTTTGCTAAT 879095 i ii i vvvv ivv v v v vv C L1M5_orf2#LIN 1687 GGTCATGATGTATTATCCTTTTTATATATTGCTGGATTCGATTTGCTAAT 1638 chr4qtel1M 879096 ATCTTATTTAAGATTTTTAGCATCAATA-TCATTAGGGAGATTGGTCTAT 879144 i i ? i - v i- v v i C L1M5_orf2#LIN 1637 ATTTTGTTNAGGATTTTT-GCATCTATGTTCATGAGGGATATTGGTCTGT 1589 chr4qtel1M 879145 AATTTTCTTTCTCTGT--TTTCAGCCTACCTGGTTTAGGTATCAGTACCA 879192 iii -- v --ii ii ? v vii? C L1M5_orf2#LIN 1588 AATTTTCTTTTCTTGTAATGTC--TTTGTCNGGTTTTGGTATCAGGGTNA 1541 chr4qtel1M 879193 TGTCTGTGTCATAGAAGGAATTTGGTAGGACTCCTTCATTCCCTATTTTA 879242 iiv iv i v i v v vii i v ii v C L1M5_orf2#LIN 1540 TGCTGGCCTCATAAAATGAGTTGGGAAGTGTTCCCTCTTTTTCTATTTTC 1491 chr4qtel1M 879243 TCAAATAATTTATATAGCATTTGGGGTCAATTGTTCTTTAAATGTTTAGT 879292 vi v i i i iv - vi i v v i i C L1M5_orf2#LIN 1490 TGGAAGAGTTTGTGTAAGA-TTGGTATTATTTCTTCCTTAAATGTTTGGT 1442 chr4qtel1M 879293 AAAATTCACATGTAAATCCATCTGGTCCTGGTGATTTTTTCTTAGGGAGT 879342 i vv i v v v v i iv i i v C L1M5_orf2#LIN 1441 AGAATTCACCAGTGAAGCCATCTGGGCCTGGAGTTTTCTTTGTGGGAAGG 1392 chr4qtel1M 879343 TGTTTAATTGCCTGTTCTATTTCTTTTCT-GAAATGGGACTTATTCAACA 879391 v i vvi v vv - v i i - --i C L1M5_orf2#LIN 1391 TTTTTAATTACAAATTCAATTTCTTTAATAGATATAGGGC-TATTCA--G 1345 chr4qtel1M 879392 ATT---TACTTCCTCCTCTGTTAA-TCTGGAAGTCTATATTTTTGGAGGT 879437 --- i i i v? i i- i v i?i i i vi v C L1M5_orf2#LIN 1344 ATTTTCTATTTCTTCTTGNGTCAGTTTTGGTAANTTGTGTTTTTCAAGGA 1295 chr4qtel1M 879438 AGTCATCCATTTCACTTAGGTTATCAAATTTATTGGCATAAAGTTGAGCA 879487 v ii ii i ? vv C L1M5_orf2#LIN 1294 ATTTGTCCATTTCATCTAAGTTNTCAAATTTATTGGCATAAAGTTGTTCA 1245 chr4qtel1M 879488 AAATAACTCCTTATTATTTCTCTAATTTCCTCTTCATTGGTGGAAAGTTC 879537 v viii iii i v ivivvv iv i vi vv C L1M5_orf2#LIN 1244 TAATATTCTCTTATTATCCTTTTAATGTCTGTAGGATCTGTAGTGATGTC 1195 chr4qtel1M 879538 TCCCTTTTCATTTTTAAAACTACTAATTTCATTTTCCTCCCTCCTTTTTC 879587 i ii i v i iv vvv i i i ii ii C L1M5_orf2#LIN 1194 TCCTTTTTCATTCCTGATATTGGTAATTTGTGTCTTCTCTCTTTTTTTCT 1145 chr4qtel1M 879588 TAATCAGATTTACCAAAGGCTTATCTATTTTATTGGCTTTTTCTATGAAC 879637 i vi ?i i i i v iii v v C L1M5_orf2#LIN 1144 TGATCAGTCTNGCTAGAGGTTTATCAATTTTATTGATCTTTTCAAAGAAC 1095 chr4qtel1M 879638 CAACTCTTAGTTTTATTAATTAGTTCAATAGT-TTTTTACTTTCAATATT 879686 i i i i ii i vvi v v - ? ii v v i C L1M5_orf2#LIN 1094 CAGCTTTTGGCTTCGTTGATTTTCTCTATTGTNTNTTTGTTTTCTATTTC 1045 chr4qtel1M 879687 TTTAATTTCTCCTTTTAATTTTAGAATTTCCAATTTAGTATTTGATTGGG 879736 v i v i vi vv vvii vv i ?v v C L1M5_orf2#LIN 1044 ATTGATTTCTGCTCTTATCTTTATTATTTCCTTCCTTCTACTTNCTTTGG 995 chr4qtel1M 879737 GGTTTTTAATTTGGTC-----TTTTTAGTTTTTTAGTTTGCAAGCCCAAT 879781 --- v ----- i i i ivv v ii i- C L1M5_orf2#LIN 994 G---TTTAATTTGCTCTTCTTTTTCTAGCTTCTTAAGGTGGAAGCTTAG- 949 chr4qtel1M 879782 TTCATTAATCTT--TTCTTTC-TCTGTTTTATTCAAGTAAGCCTTCTAAG 879828 v i i --vi - v i --- vi ? v - ? C L1M5_orf2#LIN 948 ATCATTGATTTTAAGCCTTTCTTCTTTTCTA---ATATANGCATT-TAAN 903 chr4qtel1M 879829 GATATAAAATTCCC-CTTATTA-TCCTTTGGCTGCATCCACTAAATTTTG 879876 v v - v vi - v i vvi C L1M5_orf2#LIN 902 GCTATAAATTTCCCTCTAAGCACTGCTTTAGCTGCATCCCACAAATTTTG 853 chr4qtel1M 879877 GTATGATGTCTCATCATTGTCATTATCTTGAGTGAAATTATTAATTGTAG 879926 i v v iv ? vvv v iviv v vi viv? C L1M5_orf2#LIN 852 ATATGTTGTATTTTCATTNTCATTCAGTTCAAAATATTTTCTAATTTCCN 803 chr4qtel1M 879927 CTATAATTTGCTGCTTTCACCCAATCATTCTTTAAGATGAGAGTTGTTTA 879976 i i i - v v vvvi v - v v v C L1M5_orf2#LIN 802 TTGTGATTT-CTTCTTTGACCCATGGGTTATTT-AGAAGTGTGTTGTTTA 755 chr4qtel1M 879977 GTTT-CAATTACTTTTTGGTCTATTTCCC--CTAATTTTTTGTTGAATGT 880023 i - v --- -vv i i--? vi -- vv C L1M5_orf2#LIN 754 ATTTCCAAATA---TTTGG-GGATTTTCTAGNTATCTTTTTGTT--ATTG 711 chr4qtel1M 880024 AGTT----TTTTATTGCATCATGATCTGAAAAGAAAGCATTTACTATTTC 880069 v ---- v v ii i v i v v viv v iv C L1M5_orf2#LIN 710 ATTTCTAATTTAATTCCATTGTGGTCAGAGAACATACTCTGTATGATTTC 661 chr4qtel1M 880070 TGCTTTCTTGCATTTAATTTTGAG----GTCTTTATGTCCTAATATATGG 880115 viiii i ?iv --- ---- - v i i? C L1M5_orf2#LIN 660 AATCCTTTNAAATTTA---TTGAGACTTGT-TTTATGGCCCAGNATATGG 615 chr4qtel1M 880116 TCAATTTTTGAATAGGTTCCATGAACTGCTGAGAAGAAAGTATATTCCTT 880165 v i v v v v vi vvi i v i ivi C L1M5_orf2#LIN 614 TCTATCTTGGTAAATGTTCCATGTGCACTTGAAAAGAATGTGTATTCTGC 565 chr4qtel1M 880166 TCTATCTCCATTCAATTTTCTCCAAAGATCCAACATACCTAATT--TTTC 880213 ?v vvi vvi v? i v vi vi v vi vii v i -- vv C L1M5_orf2#LIN 564 NGTTGTTGGGTGNAGTGTTCTATAAATGTCAATTAGGTCAAGTTGGTTGA 515 chr4qtel1M 880214 TAATATTCTATTTACTTCTTTAAT-TTCTTTCTTATTTGTTTTGTG-GTT 880261 i i -- i i vv iv - i v v -- v-ii C L1M5_orf2#LIN 514 TAGTGT--TGTTCAAATCTTCTATATCCTTACTGATT--TTTTGTCTACT 469 chr4qtel1M 880262 TGAGTTGTCTAATT-CTGAGATTGCAAGGTTGAGATCTCCTACTATTACA 880310 vvi i - - vv v?iv i i ? --- C L1M5_orf2#LIN 468 TGTTCTATC-AATTACTGAGAGAGGNGTGTTAAAATCTCCNACTAT---A 423 chr4qtel1M 880311 GTTTTG---TTGTCTATTTCTTCTTGCAACTCTCTTAACTTCTCCTTTAG 880357 i v --- i vi ii v i ii i v i v C L1M5_orf2#LIN 422 ATTGTGGATTTGTCTATTTCTCCTTTTAGTTCTGTCAGTTTTTGCTTCAT 373 chr4qtel1M 880358 GAAGTTGGATGCCATACCACTTGGT-CATATAT-TTTAATATTGATATTG 880405 v v v v iv iii i v - i i- iv v vv C L1M5_orf2#LIN 372 GTATTTTGAAGCTCTGTTATTAGGTGCATACACATTTAGGATTGTTATGT 323 chr4qtel1M 880406 CTTCGTTGTTTA--TGCTACCC-TTTAGCGGATT----AGTTTCCTTCCT 880448 - v v -- -- - v -- ---- i v i i C L1M5_orf2#LIN 322 CTTC-TTGATGAATTG--ACCCTTTTATC--ATTATGAAATGTCCCTCTT 278 chr4qtel1M 880449 TATCTCTTTTAATTAGATCAGTTTTTACTTT------TGCTTGATCTGAG 880492 vv ------ v i i i ------ i vi v C L1M5_orf2#LIN 277 TATCTCTGGTAAT------ATTTCTTGCCTTGAAGTCTACTTTGTCTGAT 234 chr4qtel1M 880493 ATAAGGATGGCTTACCCTGTTTTTGACTTCACCTGAA-----GCATAATA 880537 v iv i ivv? v i --- ivv? v i----- ii C L1M5_orf2#LIN 233 ATTAATATAGCCACNCCAGCTTT---CTTTTGNTTAGTGTTTGCATGGTA 187 chr4qtel1M 880538 GATTTTGCTCCAGCCTTTTACCTTTCACTCTATAAGTATCTCC-TGCTTT 880586 v i vi v - vi ? vv i ii- ii v C L1M5_orf2#LIN 186 TATCTTTTTCCATCCTTTTA-CTTTCAACCTNTCTGTGTCTTTATATTTA 138 chr4qtel1M 880587 AAATGTGTTTCTTGTAAACAACATATTGTAGGGTTCTGACTTTTGATCCA 880636 i i i i i v v ii vi v C L1M5_orf2#LIN 137 AAGTGCGTCTCTTGTAGACAGCATATAGTTGGGTCTTGTTTTTTTATCCA 88 chr4qtel1M 880637 GTCTGCTA---TCTGCCTCCTCTTTCGAGAATTCATCCCATTCACATTTA 880683 vi --- ii vv v vi i v? i C L1M5_orf2#LIN 87 GTCTGACAATCTCTGCCTTTTAATTGGAGTGTTTAGNCCATTTACATTTA 38 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.42 CpG sites = 484, Kimura (unadjusted) = 38.96 Transitions / transversions = 1.10 (484/441) Gap_init rate = 0.05 (150 / 3232), avg. gap size = 1.40 (210 / 150) 333 25.22 5.49 8.12 chr4qtel1M 880581 880744 (119256) C L1MEd_5end#LINE/L1 (7) 2217 2058 m_b213s551i19 8403 chr4qtel1M 880581 TGCTTTAAATGTGTTTCTTGTAAACAACATATTGTAGGGTTCTGACTTTT 880630 i ii i i v iv i ivvvi C L1MEd_5end#LI 2217 TGTTTTAGGTGTGTCTCTTGTAAACAGCATATAGCTGGATTTGTTTTTTT 2168 chr4qtel1M 880631 GATCCAGTCTGCTA---TCTGCCTCCTCTTTCGAGAATTCATCCCATTCA 880677 i i vi --- i ii vvi v ? i i vi i C L1MEd_5end#LI 2167 AATCCAATCTGACAATCTCTGTCTTTTAACTGGNGAGTTTAGTCCATTTA 2118 chr4qtel1M 880678 CATTTACGGTTAGAGATTACTAA---ATCTGTAT---TTCCTACCATCCT 880721 iv ---- i --- i v --- i i C L1MEd_5end#LI 2117 CATTTATTGT----GATTACTGATATATTTGGATTTATTTCTACCATCTT 2072 chr4qtel1M 880722 AATAACCCCAGATTGTGCTTTCT 880744 v --------- C L1MEd_5end#LI 2071 ATT---------TTGTGCTTTCT 2058 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.00 CpG sites = 25, Kimura (unadjusted) = 32.00 Transitions / transversions = 1.92 (25/13) Gap_init rate = 0.10 (16 / 163), avg. gap size = 1.38 (22 / 16) 416 22.13 4.93 1.36 chr4qtel1M 880581 880722 (119278) C L1MEj_5end#LINE/L1 (7) 2153 2007 m_b213s551i18 8403 chr4qtel1M 880581 TGCTTTAAATGTGTTTCTTGTAAACAACATATTGTAGGGTTCTGACTTTT 880630 i i i v iv i vi C L1MEj_5end#LI 2153 TGTTTTAAGTGTGTTTCTTGTAAACAGCATATAGCTGGGTTTTGTTTTTT 2104 chr4qtel1M 880631 GATCCAGTCTGCTA---TCTGCCTCCTCTTTCGAGAATTCATCCCATTCA 880677 i i i vi --- i ii vv vv vi C L1MEj_5end#LI 2103 AACCCAATCTGACAGTCTCTGTCTTTTAATGGGAGAATTCAGTCCATTCA 2054 chr4qtel1M 880678 CATTTACGGTTA-GA--GAT-TACTAAATCTGTATTTCCTACCATCCTA 880722 vv v - -- - vi i - - v i C L1MEj_5end#LI 2053 CATTTAGTGTAACGACTGATATACTTGATTT-TA-TTCCTTCCATCTTA 2007 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 26.57 CpG sites = 17, Kimura (unadjusted) = 26.57 Transitions / transversions = 1.21 (17/14) Gap_init rate = 0.04 (6 / 141), avg. gap size = 1.50 (9 / 6) 19 13.91 1.79 7.55 chr4qtel1M 880847 880902 (119098) (TTTTCCC)n#Simple_repeat 1 53 (0) m_b213s252i13 8404 chr4qtel1M 880847 TTTTCCCTTCCTTCCCTTATTACTCTTTT-TCTTTTCCCTTTTCCTCTCT 880895 -- - - i -i ii i (TTTTCCC)n#Si 1 TTTTCCCTT--TTCCCTT-TT-CCCTTTTCCCTTTTCCCTTTTCCCTTTT 46 chr4qtel1M 880896 CCCGTTT 880902 v (TTTTCCC)n#Si 47 CCCTTTT 53 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.09 (5 / 55), avg. gap size = 1.00 (5 / 5) 347 30.37 4.44 0.00 chr4qtel1M 883033 883167 (116833) MIR#SINE/MIR 58 198 (64) m_b213s601i18 8405 chr4qtel1M 883033 ATCTTGGCTCCGCCCCCCAATAAAAGTTT----TTTAAAAAGT-ACTTGA 883077 ii i v ii v ivv v ---- viiv - i MIR#SINE/MIR 58 ATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAA 107 chr4qtel1M 883078 AGTCTGTTTGCCTAAGTTTTTTCAACTCTCAAATGGGGAGCATAGTATCA 883127 vv v v v ii v v v vv i vi MIR#SINE/MIR 108 CCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTA 157 chr4qtel1M 883128 CCTAACTTAGAAGGTTATTGAGA-TATCAAATGACATAATA 883167 v i v i i v -v i vv MIR#SINE/MIR 158 CCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATA 198 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.90 CpG sites = 17, Kimura (unadjusted) = 39.06 Transitions / transversions = 0.71 (17/24) Gap_init rate = 0.02 (3 / 134), avg. gap size = 2.00 (6 / 3) 12 10.00 0.00 13.51 chr4qtel1M 885009 885050 (114950) (AAAACAA)n#Simple_repeat 1 37 (0) m_b213s252i14 8406 chr4qtel1M 885009 AAAACAAAAAACAAAATATACAAGGAATTCAAATACACAAAA 885050 - - -- vv - v (AAAACAA)n#Si 1 AAAACAAAAAACAAAA-A-ACAA--AAAACAAA-AAACAAAA 37 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.12 (5 / 41), avg. gap size = 1.00 (5 / 5) 413 24.04 9.43 0.58 chr4qtel1M 885597 885755 (114245) C L2#LINE/L2 (879) 2203 2031 m_b213s601i19 8407 chr4qtel1M 885597 GAGGAGG--CCAGGAATGAAGATAGAGAAAAAAATAATCAGATAAGTAAG 885644 -- v v i iv ii i-iiii vv i i C L2#LINE/L2 2203 GAGGAGGAACCAGCAAAGGAGACTGAGAAGGAG-CGGCCAGTGAGGTAGG 2155 chr4qtel1M 885645 AGGAAAGCCAGGAGAGAGTCATGTCCT-AAAACTTTGAGAAGAGAGTA-- 885691 i v vi -i i ivv v i i-- C L2#LINE/L2 2154 AGGAAAACCAGGAGAGTGTGGTGTCCTGGAAGCCAAGTGAAGAAAGTGTT 2105 chr4qtel1M 885692 TCATAAA----GGAGTCATCAATAGTGTCAAA----GATGAAAGGTCAAG 885733 vi ---- v iv ---- v ? C L2#LINE/L2 2104 TCAAGAAGGAGGGAGTGATCAACTGTGTCAAATGCTGCTGANAGGTCAAG 2055 chr4qtel1M 885734 GAAAATGAGGATTGAGA--TGATC 885755 v i i -- i C L2#LINE/L2 2054 TAAGATGAGGACTGAGAATTGACC 2031 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.87 CpG sites = 23, Kimura (unadjusted) = 29.90 Transitions / transversions = 1.53 (23/15) Gap_init rate = 0.04 (7 / 158), avg. gap size = 2.29 (16 / 7) 226 26.22 12.27 2.92 chr4qtel1M 887232 887451 (112549) L1M5_orf2#LINE/L1 694 933 (2361) m_b213s551i20 8408 chr4qtel1M 887232 GAAATTGGTTCAGGGATCGCCAACAAAA-GATAC-----AAA--CCCAAA 887273 i iiv i ii ivi - ?----- -- L1M5_orf2#LIN 694 GGAATTAAATTAGAAATCAATAACAAAAAGATANCTAGAAAATCCCCAAA 743 chr4qtel1M 887274 T----GGAGATTTAATAGTGACATAGT---AAATAATGACTGAGTCAGAG 887316 ---- i v i --- i v --- ivvv i i L1M5_orf2#LIN 744 TATTTGGAAATTAAACA---ACACACTTCTAAATAACCCATGGGTCAAAG 790 chr4qtel1M 887317 GGCAAATCTCA---GAAATGATAA----CTTTGCAAAAGAAAATGAGAAT 887359 iiv v --- v v ----i --- vvi ? L1M5_orf2#LIN 791 AAGAAATCACAANGGAAATTAGAAAATATTTTG---AACTGAATGANAAT 837 chr4qtel1M 887360 GATTAAATGATATCCCAAAATTTCTGTGGCTCAGCTAAAGCAGTCCTCAG 887409 vv v ii i vi v v iiv v i L1M5_orf2#LIN 838 GAAAATACAACATATCAAAATTTGTGGGATGCAGCTAAAGCAGTGCTTAG 887 chr4qtel1M 887410 GGAAAAA--TATAACTTTACAAT---CATATTAAGAATATAGAAAGG 887451 i ii -- i ? - ---i ii viv L1M5_orf2#LIN 888 AGGGAAATTTATAGCNTTA-AATGCNTATATTAGAAAAGAAGAAAGG 933 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.75 CpG sites = 33, Kimura (unadjusted) = 33.75 Transitions / transversions = 1.43 (33/23) Gap_init rate = 0.07 (16 / 219), avg. gap size = 2.12 (34 / 16) 259 25.96 8.39 3.07 chr4qtel1M 887296 887450 (112550) L1M4_orf2#LINE/L1 770 932 (2362) m_b213s551i21 8408 chr4qtel1M 887296 TAAATAATGACTGAGTCAGAGGGCAAATCTCA---GAAATGATAA----C 887338 iv v i i iiv v --- v v ---- L1M4_orf2#LIN 770 TAAATAACCAATGGGTCAAAGAAGAAATCACAAGGGAAATTAGAAAATAC 819 chr4qtel1M 887339 TTTGCAAAAGA-AAATGAGAATGATTAAATGATATCCCAAAATTTCTGTG 887387 ---- -i i i vv v ii i v i v v L1M4_orf2#LIN 820 TTTG----AGATGAATGAAAACGAAAACACAACATACCAAAACTTATGGG 865 chr4qtel1M 887388 GCTCAGCTAAAGCAGTCCTCAGGGAAAAA--TATAACTTTACAAT---CA 887432 iiv ? v i i ii -- i v - ---i L1M4_orf2#LIN 866 ATGCAGCNAAAGCAGTGCTTAGAGGGAAATTTATAGCTGTA-AATGCCTA 914 chr4qtel1M 887433 TATTAAGAATATAGAAAG 887450 i viv L1M4_orf2#LIN 915 TATTAAAAAAGAAGAAAG 932 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 31.79 CpG sites = 22, Kimura (unadjusted) = 32.81 Transitions / transversions = 1.29 (22/17) Gap_init rate = 0.06 (10 / 154), avg. gap size = 1.80 (18 / 10) 435 26.75 0.00 2.97 chr4qtel1M 887452 887555 (112445) MIRc#SINE/MIR 4 104 (164) m_b213s601i20 8409 chr4qtel1M 887452 GGCAGCTAAGTGGGACAGTGGATTAAGCACCAGACCTGAAATCATGAGGA 887501 i--- vi vvi ii i i i v i MIRc#SINE/MIR 4 GGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA 50 chr4qtel1M 887502 CCTGAGTTCAAATCTGATCTCAGACACTTTCTAGCTATGTAACCCTAGGC 887551 i i i iviv v v v i i i i MIRc#SINE/MIR 51 CCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGC 100 chr4qtel1M 887552 AAGT 887555 MIRc#SINE/MIR 101 AAGT 104 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.28 CpG sites = 18, Kimura (unadjusted) = 34.40 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.03 (3 / 103), avg. gap size = 1.00 (3 / 3) 324 26.64 7.48 1.77 chr4qtel1M 887466 887572 (112428) MIR#SINE/MIR 11 123 (139) m_b213s601i21 8409 chr4qtel1M 887466 ACAGTGGATTAAG--CACCAGACCTGAAATCATGAGGACCTGAGTTCAAA 887513 i - -- vi vi i ii - vvi i i MIR#SINE/MIR 11 ATAGTGG-TTAAGAGCACGGGCTCTGGAGCCA-GACTGCCTGGGTTCGAA 58 chr4qtel1M 887514 TCTGATCTCAGACACTTTCTAGCTATGTAACCCTAGGCAAG-----TAAT 887558 iviv v v v i i i i ----- i MIR#SINE/MIR 59 TCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAAC 108 chr4qtel1M 887559 CCCCAT-TGCCTCAG 887572 i iv - MIR#SINE/MIR 109 CTCTCTGTGCCTCAG 123 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.14 CpG sites = 18, Kimura (unadjusted) = 34.10 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.05 (5 / 106), avg. gap size = 2.00 (10 / 5) 18 34.96 0.00 0.00 chr4qtel1M 887574 887641 (112359) (AA)n#Simple_repeat 1 68 (0) m_b213s252i15 8410 chr4qtel1M 887574 AAAAAAAAAAAAAGAATATAGAAAAAGAGAACATTAAATATGCATTCTAA 887623 i v v i i i v vv v viv vvvv (AA)n#Simple_ 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr4qtel1M 887624 AAAAAAGAAAAAAATAAA 887641 i v (AA)n#Simple_ 51 AAAAAAAAAAAAAAAAAA 68 Matrix = Unknown Transitions / transversions = 0.46 (6/13) Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0) 342 30.85 6.64 4.81 chr4qtel1M 888000 888285 (111715) L1M2_orf2#LINE/L1 1507 1797 (1494) m_b213s551i23 8411 chr4qtel1M 888000 ATCCTACCAGAATCCTTTTATAAGAAAAACATAGACCTAATGCTGAGTCC 888049 ? v i v v i ii ivv i viv i i ii iv L1M2_orf2#LIN 1507 ATNCTTCCAAACTCATTCTACGAGGCCAGCATTACCCTGATACCAAAACC 1556 chr4qtel1M 888050 AAGGAAAGTCTGAACAGAGTAAGTAAACTGTACAAGCCAATG-----AAT 888094 iiv i v vv i iv v -- i i-----i L1M2_orf2#LIN 1557 AGACAAGGACACAACAAAAAAAGAAAACT--ACAGGCCAATATCCCTGAT 1604 chr4qtel1M 888095 GAACATTGTCTCCTCCCTCCAG---TTTTAAACAAAGTCCTATCAAAATG 888141 v --------v v i--- ii v i v v vi L1M2_orf2#LIN 1605 GAACATAG--------ATGCAAAAATCCTCAACAAAATACTAGCAAACCG 1646 chr4qtel1M 888142 G---CTATAGTTAATTATTCAAGAAATCATCCATTATGATCAAGTAGAAT 888188 i--- v i ivv --- i i ? ? ii i i L1M2_orf2#LIN 1647 AATTCAACAGCACATTA---AAAAGATNATNCACCATGATCAAGTGGGAT 1693 chr4qtel1M 888189 TTTTATCAGGGATGCAAGAGTAGTTGAACATTTGGAAAACAATAAACATA 888238 v vi ii i v vi v v i i L1M2_orf2#LIN 1694 TTATCCCAGGGATGCAAGGATGGTTCAACATACGCAAATCAATAAACGTG 1743 chr4qtel1M 888239 AT-CACTTTCTAAACCAAAAT-----ATCAAAACCACA--GTCATTTCAA 888280 - iiviv v - i ----- iv i --i i L1M2_orf2#LIN 1744 ATACATCACATCAA-CAGAATGAAGGACAAAAACCATATGATCATCTCAA 1792 chr4qtel1M 888281 TAAAT 888285 i L1M2_orf2#LIN 1793 TAGAT 1797 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.09 CpG sites = 50, Kimura (unadjusted) = 41.76 Transitions / transversions = 1.47 (50/34) Gap_init rate = 0.07 (20 / 285), avg. gap size = 1.65 (33 / 20) 20 4.00 0.00 3.70 chr4qtel1M 888706 888733 (111267) (AC)n#Simple_repeat 1 27 (0) m_b214s252i1 8412 chr4qtel1M 888706 ACACACACACACACACACACATATCACA 888733 i - (AC)n#Simple_ 1 ACACACACACACACACACACACA-CACA 27 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 256 26.54 6.99 7.75 chr4qtel1M 892891 893033 (106967) MamRTE1#LINE/RTE-BovB 345 486 (3326) m_b214s601i2 8413 chr4qtel1M 892891 AGGCAAGCAGC--CGTGGGATTCAGCTCCCTGAGTATATGAAACTGCCAT 892938 - -- vv i-- v? i i v i- v v MamRTE1#LINE/ 345 AGGCA-GCAGCACCGTTCGG--CAGCGNCCTGGGTGTCTGAG-CAGCCCT 390 chr4qtel1M 892939 -TTAAGGGCCATAGTGTTTCTGTCCTGGTGTGAGGAAAAGGCTAGAAATG 892987 - v i? iiiv i ivi- -- vi i ii ? v MamRTE1#LINE/ 391 GTTTAGGANCGCGCTGCTCAC-TCC--GAATGGGGAAGGGNCTAGAAAAG 437 chr4qtel1M 892988 GTGCCCT-AATGTTATCTA-TTTGCC-----CAACCCTGGCATGTTCATC 893030 - i ii i-i i ----- v? ---- i MamRTE1#LINE/ 438 GTGCCCTAAACGTTGCCTGCCTCGCCAAANTCAAANCTGGC----TCACC 483 chr4qtel1M 893031 AAA 893033 i MamRTE1#LINE/ 484 AGA 486 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.34 CpG sites = 23, Kimura (unadjusted) = 35.37 Transitions / transversions = 1.92 (23/12) Gap_init rate = 0.11 (16 / 142), avg. gap size = 1.31 (21 / 16) 19 11.13 0.00 0.00 chr4qtel1M 893066 893094 (106906) (AC)n#Simple_repeat 1 29 (0) m_b214s252i2 8414 chr4qtel1M 893066 ACACACACATAGACACAGACACACACACA 893094 i v v (AC)n#Simple_ 1 ACACACACACACACACACACACACACACA 29 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 289 39.56 4.62 2.77 chr4qtel1M 893139 893528 (106472) MamRTE1#LINE/RTE-BovB 568 964 (2848) m_b214s601i3 8413 chr4qtel1M 893139 CGTGGAATGTGTGAATACTCATG-GACAACACAAAATCCAGCAGACCTGA 893187 i ii vv i ii - - ii ivi vvv iv v v MamRTE1#LINE/ 568 CATGGAACATCAGGACGCT-ATGCGATGACGAGAACAGCAGTCGTCCAGA 616 chr4qtel1M 893188 AAGATGAACAGTTCTTATTGTAAGAGAATTCAGCAGTTCTCACATCCAAA 893237 v i iv ii i i v v i vvv v vivivi v v MamRTE1#LINE/ 617 AAGAAGAACGGCACTCGTCGCACGTGAACTGTCCAGATACGGAGTCGACA 666 chr4qtel1M 893238 GAGAAACCCTGAGTGAAATTGAGGCTGGAAAATGAAGGCCAGCTTATTGA 893287 vv vvi v i ii- i vvvvi v i i- i MamRTE1#LINE/ 667 TCGCCGCACTGAGCGAAACC-AGACTTCCTGATGAAGGACAGCTCAC-GG 714 chr4qtel1M 893288 AGTCAGA-GCTGGCTGCACATTTTTCTGGAG-----TTACTGCAGTGAGG 893331 v i- i ? i i v i ----- v iv -v v i MamRTE1#LINE/ 715 AGACAGGTGCCGGNTACGCCTTCTTCTGGAGAGGTCTTCCCTC-TTCAGA 763 chr4qtel1M 893332 GGGAGAACCATGAAGCTGACATATGTTTGGCAATCAAA-ACTCATCTAGT 893380 v vii iv v i - v --- i v i - v - v MamRTE1#LINE/ 764 GCGACGGCTCTCAGGC-GTCA---GCTTTGCAATCAGACAGTCA-CTTGT 808 chr4qtel1M 893381 CAACAAG-CTTGTATGCCTACTAAAAAGAACAAACAGGCCCCTGACAA-- 893427 -v - ivi viii i iv i i v i? iiiiv vi ii -- MamRTE1#LINE/ 809 C-TCAAGNCTCCCAAATTTGCCCAGAGGCATNAGTGACCGTCTGATGACC 857 chr4qtel1M 893428 -TGTGATTGCCTCTTGCAGGGAAAG-GCCACATCACCAACATCAGTGCTT 893475 - ii vi i ? - v ivi - i?iii iv i v MamRTE1#LINE/ 858 CTACGCCTACNTC-TGAAACAAAAGCGCTNTGCCACCGTCATCAGCGCAT 906 chr4qtel1M 893476 ATCCACCGACCA-----AATCCTAATGATATCAAAGGAAAATTTTGTGAC 893520 v v v ----- v ii vivv i i i iii v MamRTE1#LINE/ 907 ATGCCCCCACCATGACGAATACCGATGAGGAGAAAGAAAGATTCTACAAG 956 chr4qtel1M 893521 GACTTAGA 893528 ii i MamRTE1#LINE/ 957 GATCTGGA 964 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 50.29 CpG sites = 84, Kimura (unadjusted) = 59.75 Transitions / transversions = 1.27 (84/66) Gap_init rate = 0.05 (20 / 389), avg. gap size = 1.45 (29 / 20) 270 28.83 0.90 0.00 chr4qtel1M 894566 894676 (105324) C L1MD3_3end#LINE/L1 (2189) 553 442 m_b214s551i3 8415 chr4qtel1M 894566 AATAATATTCCATCATAATCACATACCATAGTTTATTCAGGTATTCCCCA 894615 i ii vvv ii i i i vvi v v C L1MD3_3end#LI 553 AATAGTATTCCATTGTATGGATGTACCACAGTTTGTTTATCCATTCACCT 504 chr4qtel1M 894616 ATTGATGGGCATCTCCTCAATTTTCAATTTTTTGCCCTGA-GAAGAGAAC 894664 i ? i ?vvivi i i? v ?v v - v i i C L1MD3_3end#LI 503 GTTGANGGACATCTNGGTTGTTTCCAGNTTTTGGCNATTATGAATAAAGC 454 chr4qtel1M 894665 TGCTTTAAACAT 894676 v C L1MD3_3end#LI 453 TGCTATAAACAT 442 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.84 CpG sites = 17, Kimura (unadjusted) = 38.84 Transitions / transversions = 1.13 (17/15) Gap_init rate = 0.01 (1 / 110), avg. gap size = 1.00 (1 / 1) 310 36.55 2.03 2.03 chr4qtel1M 895531 895678 (104322) C MIR3#SINE/MIR (32) 176 29 m_b214s601i4 8416 chr4qtel1M 895531 AGGGACCTGTGTACCCATATGATCTAATCCTCTCATTTCACAAATGAGGG 895580 vv vivi v ii i i i i i i C MIR3#SINE/MIR 176 AGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGA 127 chr4qtel1M 895581 AATTAAATTTCAGGGGGCCTTGGAATTTAGGAGCATAGGA--ACGTAGGA 895628 i i ivii i i vi--- v v vvv vi i i-- ii v? C MIR3#SINE/MIR 126 AACTGAGGCCCAGAGAGGT---GAAGTGACTTGCCCAAGGTCACACAGCN 80 chr4qtel1M 895629 AGTAAGTGTCAGAGCCAGTATTTGAGCCTTGGTGT-CTGGCACCAAATTT 895677 v v i v i v i iv v - i v v i ii C MIR3#SINE/MIR 79 AGTTAGTGGCAGAGCCGGGACTAGAACCCAGGTCTCCTGACTCCCAGTCC 30 chr4qtel1M 895678 G 895678 C MIR3#SINE/MIR 29 G 29 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 49.98 CpG sites = 31, Kimura (unadjusted) = 52.89 Transitions / transversions = 1.41 (31/22) Gap_init rate = 0.03 (5 / 147), avg. gap size = 1.20 (6 / 5) 220 27.42 8.06 0.00 chr4qtel1M 895678 895739 (104261) C L3#LINE/CR1 (4) 4095 4029 m_b214s601i5 8417 chr4qtel1M 895678 GGATCACAGA--TTTAGAATGGAGAGGAA--TTAGAGGCCATCTGGCCCA 895723 i --i i i v ii i -- i i i C L3#LINE/CR1 4095 GAATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCA 4046 chr4qtel1M 895724 ATCT-TTATTCAAAACA 895739 i -ii i vi C L3#LINE/CR1 4045 ACCTCCCATCCAATGCA 4029 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.96 CpG sites = 15, Kimura (unadjusted) = 37.96 Transitions / transversions = 7.50 (15/2) Gap_init rate = 0.05 (3 / 61), avg. gap size = 1.67 (5 / 3) 238 33.33 0.00 0.00 chr4qtel1M 895857 895934 (104066) C MIRc#SINE/MIR (138) 130 53 m_b214s601i6 8418 chr4qtel1M 895857 AGACTTGGACTCTGAGGGCTTCAGTAAGTGGTCCAGGGTCACACAGCCAC 895906 i vi i v i v v i v v i i i v C MIRc#SINE/MIR 130 AAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG 81 chr4qtel1M 895907 CATGGGCTAAAGTTGGGACTTCAGCCCA 895934 i v v vi i ii iv i C MIRc#SINE/MIR 80 TAAGTGGCAGAGCCGGGACTCGAACCCA 53 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.93 CpG sites = 15, Kimura (unadjusted) = 45.57 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.00 (0 / 77), avg. gap size = 0.0 (0 / 0) 648 22.74 3.06 8.02 chr4qtel1M 895991 896186 (103814) C MIRb#SINE/MIR (15) 253 67 m_b214s601i7 8419 chr4qtel1M 895991 ATTTGTTAATCTGTTACTACTATGTGCCATAGTACATG-GCTAAGTGTTT 896039 i i v - i -- -i i - - i i C MIRb#SINE/MIR 253 ATTTATTGAGC-GCT--TACTATGTGCCA-GGCAC-TGTGCTAAGCGCTT 209 chr4qtel1M 896040 CGCA---ATTATCTCATTGGCTCTTCATTCACAACAACCCTTTGAGATAG 896086 ii --- viv i ---- vi i C MIRb#SINE/MIR 208 TACATGCATTATCTCATTTAATCCTCA----CAACAACCCTGCGAGGTAG 163 chr4qtel1M 896087 ATGCTATTTAACATCCATCTATTTGATGAGTGAGCAAACTGAGGC--AAA 896134 i ii ---- -- i v iiii v -- i C MIRb#SINE/MIR 162 GTATTATT----ATCC--CCATTTTACAGATGAGGAAACTGAGGCTCAGA 119 chr4qtel1M 896135 GAGATTAAGTGATTTGCTCAGGGTCCCTCAGTCAGTAAGTGTCTGAGACA 896184 i i i i i v v ii v v v i C MIRb#SINE/MIR 118 GAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 69 chr4qtel1M 896185 GG 896186 C MIRb#SINE/MIR 68 GG 67 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.74 CpG sites = 30, Kimura (unadjusted) = 28.14 Transitions / transversions = 2.73 (30/11) Gap_init rate = 0.09 (18 / 195), avg. gap size = 1.17 (21 / 18) 564 21.96 13.59 3.47 chr4qtel1M 896032 896215 (103785) C MIRc#SINE/MIR (45) 223 22 m_b214s601i8 8419 chr4qtel1M 896032 AAGTG-TTTCGCA---ATTATCTCATTGGCTCTTCATTCACAACAACCCT 896077 i - i --- v v i ---- C MIRc#SINE/MIR 223 AAGCGCTTTCACATACATTATCTCATTTGATCCTCA----CAACAACCCT 178 chr4qtel1M 896078 TTGAGATAGAT---GC---TATTTAACATCCATCTATTTGATGAGTGAGC 896121 v i ii--- --- - vi -- i v iiii v C MIRc#SINE/MIR 177 GTGAGGTAGGCAGGGCAGGTATT-ATTATCC--CCATTTTACAGATGAGG 131 chr4qtel1M 896122 AAACTGAGGC--AAAGAGATTAAGTGATTTGCTCAGGGTCCCTCAGTCAG 896169 -- i i i i i v v ii C MIRc#SINE/MIR 130 AAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG 81 chr4qtel1M 896170 TAAGTG-----TCTGAGA--------CAGGTCTTCCAGCCTCTGGGCCCA 896206 -----v i i -------- v v iii i C MIRc#SINE/MIR 80 TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCA 31 chr4qtel1M 896207 TTACTCCTT 896215 v i i C MIRc#SINE/MIR 30 GTGCTCTTT 22 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.38 CpG sites = 27, Kimura (unadjusted) = 26.97 Transitions / transversions = 2.25 (27/12) Gap_init rate = 0.08 (14 / 183), avg. gap size = 2.29 (32 / 14) 199 33.93 0.00 0.00 chr4qtel1M 896271 896326 (103674) C L3#LINE/CR1 (179) 3920 3865 m_b214s601i9 8417 chr4qtel1M 896271 CAGTCCAGATTGTCAGGAAACTTTTACTTATGTTGGAGTGAAAGGTGCCT 896320 ii v i i ii i v i iivi vv C L3#LINE/CR1 3920 CAGCTCTGATTGTTAGAAAGTTCTTCCTTATATTGAGCCGAAATCTGCCT 3871 chr4qtel1M 896321 TTCTAT 896326 ii i C L3#LINE/CR1 3870 CCCTGT 3865 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.64 CpG sites = 14, Kimura (unadjusted) = 49.41 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0) 310 29.87 2.00 6.25 chr4qtel1M 896300 896399 (103601) C MIR3#SINE/MIR (18) 190 95 m_b214s601i10 8420 chr4qtel1M 896300 ATGTTGGAG-TGAAAGGTGCCTTTCTATCAGAGGCCATCTCATCCAACTC 896348 ii - i vi ------ ii vi i C MIR3#SINE/MIR 190 ATGTCAGAGCTGGAAGGGACCTT------AGAGATCATCTAGTCCAACCC 147 chr4qtel1M 896349 CTTTCTTTTACAAATGAGC-ACCCGATGTCTGTGGAAATGAAATGGTTTG 896397 i iv i v- v i v i iivi ii i ii C MIR3#SINE/MIR 146 CCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTG 97 chr4qtel1M 896398 CC 896399 C MIR3#SINE/MIR 96 CC 95 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.86 CpG sites = 21, Kimura (unadjusted) = 40.86 Transitions / transversions = 3.00 (21/7) Gap_init rate = 0.08 (8 / 99), avg. gap size = 1.00 (8 / 8) 185 26.12 2.38 8.86 chr4qtel1M 896471 896554 (103446) C L3#LINE/CR1 (354) 3745 3667 m_b214s601i11 8417 chr4qtel1M 896471 TCTTTTCTTCAGA-TAAGCACATCCTCAGTTCTGTCAGCTGCTCCTAAGG 896519 i i i- -- i iv i i i v -- C L3#LINE/CR1 3745 TCTCTTCTCCAGGCTAA--ACATCCCCAGTTCCTTCAACCGTTCCTCA-- 3700 chr4qtel1M 896520 TACTGTGAC-TTCTTTCTGGGAGCTTCTCCAGCCTG 896554 --- i - vv ii ivv v v C L3#LINE/CR1 3699 ---TATGACATGGTTTCCAGACCCTTCACCATCCTG 3667 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.72 CpG sites = 12, Kimura (unadjusted) = 32.68 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.11 (9 / 83), avg. gap size = 1.00 (9 / 9) 88 24.60 3.81 2.51 chr4qtel1M 896734 897029 (102971) (TCTGTC)n#Simple_repeat 1 301 (18) m_b214s252i3 8421 chr4qtel1M 896734 TCTGCCTCTGTCTCTCTCTGACTCTCTGTCTCTGTCTCTGCCTCTG-CT- 896781 i v vvv i - - (TCTGTC)n#Sim 1 TCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTC 50 chr4qtel1M 896782 TCTATCTGTCTCTATTTCTTTCT-TTTCTTTTTCTTCTGTCTCT-T-TTT 896828 v v i i v - v i v - - - i (TCTGTC)n#Sim 51 TGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTC-TCTGTCTCTGTCTCT 99 chr4qtel1M 896829 TTCT-TCTCTTTGTCTCTCTGTCTTTCTCTTTTCTCTTTCT-TCTCTCT- 896875 v - v i v v v - v v - v - (TCTGTC)n#Sim 100 GTCTCTGTCTCTGTCTCTGTCTCTGTCTC-TGTCTCTGTCTCTGTCTCTG 148 chr4qtel1M 896876 TC-CTCTCTTTCTCTGTCTCTCTGAATCTGTCTGTCTGTCTCTGTCTCTC 896924 - v i v v v vv -- v (TCTGTC)n#Sim 149 TCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTC--TCTGTCTCTGTCTCTG 196 chr4qtel1M 896925 ACTCTCTCTTTATCCATTCCTCCTGCCTCCATTCTCTTTCTCTTTTCTCT 896974 v v i i iv vi - i - vv v - v (TCTGTC)n#Sim 197 TCTCTGTCTCTGTCTCTGTCT-CTGTCT-CTGTCTCTGTCTC-TGTCTCT 243 chr4qtel1M 896975 TTCT-TCTCTCGGCTTCTCTTTCTTTCTCT-TTTCTTTCT-TCTCTCTGT 897021 v - v v ii v i v - i v - v (TCTGTC)n#Sim 244 GTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGT 293 chr4qtel1M 897022 CTCTATTT 897029 i i (TCTGTC)n#Sim 294 CTCTGTCT 301 Matrix = Unknown Transitions / transversions = 0.49 (19/39) Gap_init rate = 0.06 (19 / 295), avg. gap size = 1.00 (19 / 19) 54 4.35 9.38 0.00 chr4qtel1M 897030 897125 (102875) (TC)n#Simple_repeat 1 105 (0) c_b214s251i0 8422 chr4qtel1M 897030 TCTCTTTCT-TCTCTCTCCCTCTCT-TC-CTCTCT-TC-CTCTCTTTCTC 897074 i - i - - - - i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr4qtel1M 897075 TCT-TC-CTTTCTC-CTCTCTC-CTCTCTCTCTCTCTCTCTCTCTCTCTC 897120 - - i - - (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chr4qtel1M 897121 TCTCT 897125 (TC)n#Simple_ 101 TCTCT 105 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.09 (9 / 95), avg. gap size = 1.00 (9 / 9) 88 24.60 3.81 2.51 chr4qtel1M 897126 897143 (102857) (TCTGTC)n#Simple_repeat 302 319 (0) m_b214s252i3 8423 chr4qtel1M 897126 ATGTCTATATGTCTATCT 897143 v v i v i (TCTGTC)n#Sim 302 CTGTCTCTGTCTCTGTCT 319 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 12 24.89 0.00 0.00 chr4qtel1M 897151 897184 (102816) (TCCC)n#Simple_repeat 1 34 (0) m_b214s252i4 8424 chr4qtel1M 897151 TCCCTCACTCCCTTCCTCTTTCCTTCCACCCCTC 897184 v i ii i vi (TCCC)n#Simpl 1 TCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTC 34 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 288 35.29 10.29 0.00 chr4qtel1M 897763 897898 (102102) C MIR3#SINE/MIR (23) 185 36 m_b214s601i12 8425 chr4qtel1M 897763 AGATGTAGAAGATGCTTTAAAGGCCACCTAATCCAATCCCATCCTTTTGT 897812 vv i ivi i i ii i i i v v ii C MIR3#SINE/MIR 185 AGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTAC 136 chr4qtel1M 897813 AGAT----AAACCTAACATCAAAGAGGTTAGATGATTTGCTGAAAATTG- 897857 ---- iv ivvi i v ii i iv ii ii- C MIR3#SINE/MIR 135 AGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCAC 86 chr4qtel1M 897858 -----AAGTGA---GCAGAACTGGAAAAACAATTTA-TTATCCTAACTTC 897898 -----? v --- i i i vv v iii -v v i i C MIR3#SINE/MIR 85 ACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGTCTCCTGACTCC 36 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 50.05 CpG sites = 32, Kimura (unadjusted) = 51.66 Transitions / transversions = 2.00 (32/16) Gap_init rate = 0.04 (5 / 135), avg. gap size = 2.80 (14 / 5) 221 23.08 9.62 0.00 chr4qtel1M 898250 898301 (101699) C MIRb#SINE/MIR (169) 99 43 m_b214s601i13 8426 chr4qtel1M 898250 AAAGTCACA-AG---ATAAATAGCAGAGTCAGGATTTGAATCTGGGTCT- 898294 i - ---i i i i i i i ii - C MIRb#SINE/MIR 99 AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTG 50 chr4qtel1M 898295 TTTGCCT 898301 i v C MIRb#SINE/MIR 49 TCTGACT 43 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.33 CpG sites = 11, Kimura (unadjusted) = 30.18 Transitions / transversions = 11.00 (11/1) Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.67 (5 / 3) 395 34.84 12.50 0.51 chr4qtel1M 898838 899013 (100987) C MIR3#SINE/MIR (7) 201 5 m_b214s601i14 8427 chr4qtel1M 898838 AGGACCATAGA--TTTAGAGCTGAAACAAACCTTTGAAAT---------- 898875 i i --v i i vii v i ---------- C MIR3#SINE/MIR 201 AGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCC 152 chr4qtel1M 898876 -------TCATTTTACTGATGAGGAT-CTACAATTCAGAA--GTGAAGTG 898915 ------- v v- iviiii i-- C MIR3#SINE/MIR 151 AACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTG 102 chr4qtel1M 898916 ATTCATCCAACATCATGTAGATAATAAGAAGCAAATTCAGGATTCAGACT 898965 i iii vi iii v? i v vi i vi i i vii i C MIR3#SINE/MIR 101 ACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACC 52 chr4qtel1M 898966 TAGGACTTCTGATTACAGATTCAGTGCATTTTTCACTATGTCACTTTG 899013 i v i i v vii i - vi i iii vv i i C MIR3#SINE/MIR 51 CAGGTCTCCTGACTCCCAGTCC-GTGCTCTCTCTGCTCAGCCACTCTG 5 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 50.05 CpG sites = 43, Kimura (unadjusted) = 51.32 Transitions / transversions = 2.39 (43/18) Gap_init rate = 0.03 (6 / 175), avg. gap size = 3.83 (23 / 6) 465 34.04 2.84 0.00 chr4qtel1M 898877 899017 (100983) C MIRc#SINE/MIR (122) 146 2 m_b214s601i15 8427 chr4qtel1M 898877 CATTTTACTGATGAGGAT-CTACAATTCAGAA--GTGAAGTGATTCATCC 898923 v v- iviii i-- v i iii C MIRc#SINE/MIR 146 CATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCC 97 chr4qtel1M 898924 AACATCATGTAGATAATAAGAAGCAAATTCAGGATTCAGACTTAGGACTT 898973 vi iii v i vi i vi i i ii ii v C MIRc#SINE/MIR 96 AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTT 47 chr4qtel1M 898974 -CTGATTACAGATTCAGTGCATTTTTCACTATGTCACTTTGTATC 899017 - i v ii i vi i iiii vi iv C MIRc#SINE/MIR 46 CCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTGCCTC 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 46.50 CpG sites = 35, Kimura (unadjusted) = 49.51 Transitions / transversions = 2.69 (35/13) Gap_init rate = 0.02 (3 / 140), avg. gap size = 1.33 (4 / 3) 1426 29.77 2.49 2.33 chr4qtel1M 899633 900275 (99725) C L1ME5_3end#LINE/L1 (291) 650 7 m_b214s551i4 8428 chr4qtel1M 899633 ATCTC---CTGGTTCT-GCTCATTTCACTTAGCATCA-GTTCATATAAG- 899676 --- v -i iv i ii - -- v - C L1ME5_3end#LI 650 ATCTCATTCTGTTTCTTACTTTTTTCACTCAGCACTATGTT--TTTAAGA 603 chr4qtel1M 899677 TCTCTCCAAGCCTCTCTGTATTCATCCTGCTGGTTATTTCTTACAGAATA 899726 iv v iiv v i v iv iiv ii v v vvvv C L1ME5_3end#LI 602 TCCATCCATGTTGCTATGTGTACATCTAGTCCGTTGCTTCTAACTGCTGC 553 chr4qtel1M 899727 ATAATATTCCATAACATTCATATACCACAATTTGCCCAACCATTCTCCAA 899776 i i iiii v vi v i i v i v C L1ME5_3end#LI 552 ATAGTACTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCA 503 chr4qtel1M 899777 TTGATGGGCATCC---TTTCATTTTCCAGTTTCTAGCCATTACAAACAGG 899823 v i i --- v ---i ii i iv ii iv C L1ME5_3end#LI 502 GTGATGGACACCCAGGTTGC---CTCCAACTCCCCGCCACCACAAACAAC 456 chr4qtel1M 899824 GTTGCCACAAACATTTTGGCACATACAGGTCCCTTTC----CCTTCTTTA 899869 i v ii ii ---- i v i v---- viv v C L1ME5_3end#LI 455 GCTGCAATGAACATCCT----CGTACATGTCCCCTTATGGACCTGTGTGA 410 chr4qtel1M 899870 GTATCTTTTTGGGGTATAAGCCCAGTAGAAACACTGTTGGATCAAAGGGT 899919 v i i i vi v viiv i i i v C L1ME5_3end#LI 409 GAATTTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGT 360 chr4qtel1M 899920 ATGCACAGTTTGATAACTTT-TTGAGCATCGTTCCAAAATGCTCTCCAGA 899968 ii vvi -- i v-i i i ii -- i v C L1ME5_3end#LI 359 ATGCGTATACT--TAATTTGACTAAGTACTG--CCAGATTGCTCTCCAGA 314 chr4qtel1M 899969 ATGGCTGGATGCATTCACAATTCCACCAACAATGTATTAGTGTCCCTGTT 900018 v ivvi ii v i i i i v v i i ? C L1ME5_3end#LI 313 ATGGCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATN 264 chr4qtel1M 900019 TTCCCACATCCCCTACAACATTCCGCATTATCTTTCCCTATCATTCTAGC 900068 i i vv i iv ivv ii v v i v C L1ME5_3end#LI 263 TCCCCACATCCTCGCCAACACTTGGCATTATCCAGCTTTCTAATTTTTGC 214 chr4qtel1M 900069 CAATCTAACAGGTATGTAGTGGTATCTCAGAGTTGTCTTAATTTGCATTT 900118 i i i iv i vv i C L1ME5_3end#LI 213 CAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATTT 164 chr4qtel1M 900119 CTCTAATTAATAATGACTTGGAGCATATTTTCATATGGCTAGAAATAGTT 900168 i v v v v i vi ivv iivv C L1ME5_3end#LI 163 CTCTGATTACTAATGAGTTTGAGCATCTCTTCATATGCTTGTTAGCCTTT 114 chr4qtel1M 900169 CCAATTTCTTCATCTGAGAATTGTCTGTTCATATCCTTTGACCATTTATC 900218 vii i v vi i v v C L1ME5_3end#LI 113 CGGGTTTCCTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCCATTTTTC 64 chr4qtel1M 900219 AATTGGAG--AATGGCTTGATTTCTTATAAATTAGAGTCAATTCTCTATG 900266 v i --?vi v -- i vi v vivv i ii i i C L1ME5_3end#LI 63 TATTGGGGTTNCCGTCTT--TTTCTTGTTGATTTGCAGGAGTTCCTTGTA 16 chr4qtel1M 900267 TATTCTGGA 900275 i C L1ME5_3end#LI 15 TATTCTAGA 7 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.02 CpG sites = 107, Kimura (unadjusted) = 39.09 Transitions / transversions = 1.34 (107/80) Gap_init rate = 0.04 (23 / 642), avg. gap size = 1.35 (31 / 23) 1910 30.46 3.37 2.96 chr4qtel1M 900132 901643 (98357) C L1M5_orf2#LINE/L1 (0) 3294 1777 m_b214s551i5 8428 chr4qtel1M 900132 TGACTTGGAGCATATTTTCATATGGCTAGAAATAGTTCCAATTTCTTCAT 900181 ?v v v i vi vviiivi iv? v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr4qtel1M 900182 CTGAGAATTGTCTGTTCATATCCTTTGACCATTTATCAATTGGA--GAAT 900229 i v v vi i v v ?v i-- vv C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTT 3195 chr4qtel1M 900230 GGCTTGATTTCTTAT-AAATTAGAGTCAATTCTCTATGTATTCTGGAAAT 900278 v -- ? -i ? iv v- i i i v i C L1M5_orf2#LIN 3194 GTCTT--TTTNTTATTGANTTGTAGG-AGTTCTTTATATATTCTGGATAC 3148 chr4qtel1M 900279 GAGGCCTTTATGAGACCCTTTGACTCTAAAAATGTTTACCCAGTTTATTG 900328 v i v iviv vv?i vi v v iv ? i i v C L1M5_orf2#LIN 3147 GAGTCCTTTGTCAGATATATGTNTTGCAAATATTTTCTCCCANTCTGTGG 3098 chr4qtel1M 900329 TTTCCCTTCTAATCTTGTCTGCATTAGTTTTGTTTGTACAAAAATTTTTC 900378 i v i v i v ivi iv ivi vvv? vi i i v C L1M5_orf2#LIN 3097 CTTGCCTTTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTTTA 3048 chr4qtel1M 900379 AATTTGATATAATCGAA-------ATTTTCTATTTTGTAATCAATAGTGA 900421 v i? i v ------- i v i ii --- ? v C L1M5_orf2#LIN 3047 ATTTTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGGT---TNGTGC 3001 chr4qtel1M 900422 TCTCTAGTTCTTCTTTGGTCATAAATTCCTTCCTCTTCCACAGGTCTGAG 900471 i i ivv i v i--- v iii v v?i - vvii C L1M5_orf2#LIN 3000 TTTTTGTGTCCTGTTTA---AGAAATCTTTGCCTANCCCA-AGGTCACGA 2955 chr4qtel1M 900472 AGATAAACTATCCTATGCTCTTTCAATTTA-----TTTATAATCTCATTC 900516 --i v i i i --- i ----- i i i ?ii C L1M5_orf2#LIN 2954 AGATA--TTCTCCTATGTTTTCT---TCTAGAAGTTTTATAGTTTTANCT 2910 chr4qtel1M 900517 TTTATGCCTAGGTC-ATGAACCTATTTTGACCTTATCTTGGTGTATGGTG 900565 iiii - v - i ? vi v i v C L1M5_orf2#LIN 2909 TTTACATTTAGGTCTATGATCC-ATCTNGAATTAATTTTTGTGTATGGTG 2861 chr4qtel1M 900566 TTAAGTGTGGGTCAATGCCTAGTTTCTGCCATACTAATTTCCAATTTTCC 900615 v i iv i v?iii v i v ivi v v i C L1M5_orf2#LIN 2860 TGAGGTAGGGGTCGAGNTTCATTTTTTTCCATATGGATATCCAATTGTTC 2811 chr4qtel1M 900616 CAGCAATTTTTGTCAAATAATGAGTTCTTATCCCAG-AAACTGGGGTCTT 900664 viv ii v ivvvi i vi v-i i ---- ? C L1M5_orf2#LIN 2810 CAGCACCATTTGTTGAAAAGACTATCCTTTCCCCACTGAATTG----CNT 2765 chr4qtel1M 900665 TGGG---TTTGTCAAACACTAGATTATTAAAGTTAT-TGGATGTTTTGTC 900710 v--- v ii i? v?ii v vv i - i v v --- C L1M5_orf2#LIN 2764 TGGCACCTTTGTCAAAAATCAANTGNCCATATATGTGTGGGTCTATT--- 2718 chr4qtel1M 900711 CTTTGAAC---CTAACCTATTCTATTGATCAAATAGCCTATTTCTTA-GC 900756 - i i --- vi i i v v v i i- - C L1M5_orf2#LIN 2717 -TCTGGACTCTCTATTCTGTTCCATTGATCTATTTGTCTATC-CTTACGC 2670 chr4qtel1M 900757 CAATACCAGATGGTTTTGGTAATTGCTGCTTTATAATATAATTTT-AGAT 900805 v iv i i v i iv - i i - ? C L1M5_orf2#LIN 2669 CAATACCACACTGTCTTGATTACTGTAGCTTTATAATA-AGTCTTGANAT 2621 chr4qtel1M 900806 CTGATACAGCTAGGCCACCTTCA--TTTGATTTT-TTTTTCATTAATTCC 900852 ? i vv - i i -- i -- v i - v-i vi C L1M5_orf2#LIN 2620 CNGGTAGTG-TAAGTC--CTCCAACTTTGTTCTTCTTTTTCAA-GATTGT 2575 chr4qtel1M 900853 CTTGAA-ATTCTTGACCTTTTGTTTTTCCATATGAACTTTG--------T 900893 i iv- ? ii i iv i i i-------- C L1M5_orf2#LIN 2574 TTTGGCTATTCTNGGTCCTTTGCATTTCCATATAAATTTTAGAATCAGCT 2525 chr4qtel1M 900894 TGTTATTTTTCTAGGTCATCAAAATAGTTTTTTGGGGTCT-GATTGGTAT 900942 i v - ------ v iii vi i i - v C L1M5_orf2#LIN 2524 TGTCAATTT-CTA------CAAAAAAACCTGCTGGGATTTTGATTGGGAT 2482 chr4qtel1M 900943 AGCACTAAATAAATAGATTAGTTTAGGCAGTATTGTCATCTTTATTATAT 900992 v i i vv i i i v v v ? iv C L1M5_orf2#LIN 2481 TGCATTGAATCTATAGATCAATTTGGGGAGAATTGACATCTTNACAATAT 2432 chr4qtel1M 900993 TTGCTCACCCAATCCAAGAGCATTTAATATTTTTCCAGTTGGTTAGATCA 901042 viv vi v i vvv i i v iv i v C L1M5_orf2#LIN 2431 TGAGTCTTCCAATCCATGAACATGGTATATCTCTCCATTTATTTAGGTCT 2382 chr4qtel1M 901043 GATTTAATTTGCGTGGAAAGTGTTTTGTAGTTTTGCTCATAAAGTTTCTG 901092 vv viv viiv i vvvii ? v ii C L1M5_orf2#LIN 2381 TCTTTAATTTCTCTCAGCAATGTTTTGTAGTTTTCAGTGTANAGGTCTTG 2332 chr4qtel1M 901093 ---ATTTTCCCTTGGCAGATAGATTCCTAAATATTGTATACAATCAGTAG 901139 --- ? --- vi vv i v? iivv iv vv C L1M5_orf2#LIN 2331 CACATNTT---TTGTTAGATTTATTCCTAAGTATTTNATGTTTTTTGATG 2285 chr4qtel1M 901140 TTACTTTAAATGGAATTTCTCTTTGTAACTCTAACTGTTGAGT--TTTGT 901187 i i v v vi i --? v i v i v iv i -- C L1M5_orf2#LIN 2284 CTATTGTAAATGGTATTGTTTTT--NAAATTTCATTTTCCAATTGTTTGT 2237 chr4qtel1M 901188 TAGTGATATATAAGAATGCTGATGACTTATGTGGGTTTATTTTGTATCCT 901237 iv ii ii i viv i v ivi v ii ? C L1M5_orf2#LIN 2236 TGCTAGTATATAGAAATACAATTGATTTTTGTATATTGACCTTGTATCCN 2187 chr4qtel1M 901238 GCAACTTTGCTAA---CAGTGTGGATTGTTTCTAATAACTTTTTAGTAGA 901284 i i --- v ---v iv i ii ? v C L1M5_orf2#LIN 2186 GCGACCTTGCTAAATTCACT---TATTAGTTCTAGTAGTTTNTTTGTAGA 2140 chr4qtel1M 901285 CTATCTGGAGTTCTCTAAGAATACCATCATATCATCAGCAAAGAGTGATA 901334 i v i ? ii i v v ? v i v i v i? i C L1M5_orf2#LIN 2139 TTCTTTNGGATTTTCTACGTANACAATCATGTCATCTGCGAATAANGACA 2090 chr4qtel1M 901335 ATTTGGTTTCCTAATTGCCTATTCTTATTCCTTTAATCTCTTTCTCAACT 901384 i vi i vv v v ii v v i i vvvi C L1M5_orf2#LIN 2089 GTTTTATTTCTTCCTTTCCAATCTTTATGCCTTTTATTTCTTTTTCTTGC 2040 chr4qtel1M 901385 CTTATTGCCAAAGCTACCATTTCTAATATAATATTAAATAGTAACGGTGA 901434 vvvi vv ii i i i i i v ii C L1M5_orf2#LIN 2039 CTTATTGCACTGGCTAGGACCTCCAGTACAATGTTGAATAGAAGTGGTGA 1990 chr4qtel1M 901435 GTGTGGGCAACCTTGTTTCACTCCTGATCTTATTGGGAATGGTTGCAGTT 901484 ?v i i v i iii i vv v v? v ? C L1M5_orf2#LIN 1989 NAGCGGACATCCTTGTCTTGTTCCCGATCTTAGGGGGAAAGCNTTCAGTN 1940 chr4qtel1M 901485 TGTCCCCATTACAT---ATGCTTACTGATGGTTTTAAATAGATGCAACTA 901531 v v vi --- i ?i vv vvi vvi v C L1M5_orf2#LIN 1939 TTTCACCATTAAGTATGATGTTNGCTGTAGGTTTTTCGTAGATGCCCTTT 1890 chr4qtel1M 901532 ATTATTTTAAGGAAAAGTCCATTTATTCCTATACTCTCAAGTGTTTTTAA 901581 i vv i ivvi v i vvi viii v v C L1M5_orf2#LIN 1889 ATCAGGTTGAGGAAGTTCCCTTCTATTCCTAGTTTGCTGAGAGTTTTTAT 1840 chr4qtel1M 901582 TAGGAATGGATGTTGGATTTTATC-AGTGCTTTTTCTGCATCTATTGAGA 901630 i v i i i - i C L1M5_orf2#LIN 1839 CATGAATGGGTGTTGAATTTTGTCAAATGCTTTTTCTGCATCTATTGAGA 1790 chr4qtel1M 901631 TGATCATACGGTT 901643 i i C L1M5_orf2#LIN 1789 TGATCATATGATT 1777 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.09 CpG sites = 240, Kimura (unadjusted) = 41.16 Transitions / transversions = 1.16 (240/207) Gap_init rate = 0.04 (66 / 1511), avg. gap size = 1.45 (96 / 66) 222 27.46 8.54 2.30 chr4qtel1M 902336 902417 (97583) C L2b_3end#LINE/L2 (11) 455 369 m_b214s601i16 8429 chr4qtel1M 902336 CAACAAGT-TTTA---AGCACCTATATTGAGTGCTAGATTCTCTGCTGGA 902381 i - --- i i-- v i ii? v i i C L2b_3end#LINE 455 CAACAAATATTTACTGAGCGCCTAC--TGTGTGCCAGGCNCTGTGCTAGG 408 chr4qtel1M 902382 TGCTGGGAATGCA--AATAAA-AAGAATGAGATAATCCC 902417 i i i --ii i - vv v?iii C L2b_3end#LINE 407 CGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCC 369 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.40 CpG sites = 17, Kimura (unadjusted) = 38.09 Transitions / transversions = 3.40 (17/5) Gap_init rate = 0.07 (6 / 81), avg. gap size = 1.50 (9 / 6) 623 32.79 0.65 2.66 chr4qtel1M 903749 904055 (95945) L1ME4c_3end#LINE/L1 230 530 (300) m_b214s551i6 8430 chr4qtel1M 903749 TTGATAATGATGAGTGTTGGAAGGGGTGTGGGAAAACTGGGACACCAATA 903798 iviv i i vii ? i vi v ? iv L1ME4c_3end#L 230 TTGATAATACCCAATGCTGGCGAGGNTGCGGTGAAACTGGTACNCTCATA 279 chr4qtel1M 903799 TAGATACATTGTTGGTGAAACTGTGAATGGATCCAACCATTCTGGAGAAC 903848 ------ i iv ? i v i v v i i i L1ME4c_3end#L 280 ------CATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGC 323 chr4qtel1M 903849 ACTTTGGAACTATGCACAAAACGTTATCAAAATGTGCACACCCTTTGACA 903898 v v v i i iv iv ii v v i v L1ME4c_3end#L 324 AATTTGGCAATACGTATCAAGAGCCATAAAAATGTTCATACCCTTTGACC 373 chr4qtel1M 903899 CAGCAGTGCTTCTACTGGGCTTCTATCCCAAAGAGCT--CTTAAAAGAGG 903946 i i v iv v vv i i i iv --i i i L1ME4c_3end#L 374 CAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAAGAAG 423 chr4qtel1M 903947 GAAAGGGACCTACATGTGCAAAAATGTTTTCAGCAACCCTTTTCATAGTG 903996 ii -- i ii i i iviv i vi v i i i L1ME4c_3end#L 424 GAAAAAG--CTATATGCACGAAGATGTTCATTGCAGCGTTATTTATAATA 471 chr4qtel1M 903997 GCAAGAGACTGGAATCTGAGTGGATGCCCGTCAGCTGGAGAATGGCTGAA 904046 i i i i v vivv ii i iv iiv i i i i L1ME4c_3end#L 472 GCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAATGGTTAAG 521 chr4qtel1M 904047 AAAGTTATG 904055 v i L1ME4c_3end#L 522 TAAATTATG 530 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 42.77 CpG sites = 63, Kimura (unadjusted) = 46.00 Transitions / transversions = 1.80 (63/35) Gap_init rate = 0.03 (9 / 306), avg. gap size = 1.11 (10 / 9) 19 0.00 0.00 0.00 chr4qtel1M 904606 904629 (95371) (TAA)n#Simple_repeat 1 24 (0) m_b214s252i5 8431 chr4qtel1M 904606 TAATAATAATAATAATAATAATAA 904629 (TAA)n#Simple 1 TAATAATAATAATAATAATAATAA 24 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 354 26.82 14.71 1.30 chr4qtel1M 904690 904825 (95175) MIR3#SINE/MIR 22 175 (33) m_b214s601i17 8432 chr4qtel1M 904690 GAGGATACTGGATTGGGAGGCAGAGAA----------AGTACC---TCAT 904726 iii - i v iii ---------- v --- - MIR3#SINE/MIR 22 GAGAGCAC-GGACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTC-T 69 chr4qtel1M 904727 TCTACTTGTTCTCTAGGTGACCTTAGGCAACTGTCTTCATCTCTGTGAAC 904776 v i vii ?v iv i v vv i v ii MIR3#SINE/MIR 70 GCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGC 119 chr4qtel1M 904777 CTTGGTTTCCTCCTCTATAAAATGAG------ACATTGGATGAGCTTT-G 904819 ii v i ------iv i i v i -i MIR3#SINE/MIR 120 CTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAA 169 chr4qtel1M 904820 GGTCCC 904825 MIR3#SINE/MIR 170 GGTCCC 175 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.75 CpG sites = 23, Kimura (unadjusted) = 34.75 Transitions / transversions = 1.77 (23/13) Gap_init rate = 0.04 (6 / 135), avg. gap size = 3.67 (22 / 6) 450 28.00 4.68 13.36 chr4qtel1M 905035 905269 (94731) MIR#SINE/MIR 1 217 (45) m_b214s601i18 8433 chr4qtel1M 905035 ACAGTTTAGCAGGGTGG-----AGCATTGTACATGGAGTCAA-----CTG 905074 v vi ----- iv vviv i i----- MIR#SINE/MIR 1 ACAGTATAGCATAGTGGTTAAGAGCACGGGCTCTGGAGCCAGACTGCCTG 50 chr4qtel1M 905075 GGTTCAGATTCTGCAGCTAACACTTGTTAGCAGTTGTTGTTAGCTAGTTG 905124 ii i i vvv iv ii ----------------- MIR#SINE/MIR 51 GGTTCGAATCCCGGCTCTGCCACTTACTAGC-----------------TG 83 chr4qtel1M 905125 TGTGACAACAGGCAAATCACTTGAC-TAGCTCAGCCTCAGTTTCCCGATC 905173 vvii i i i - vv vv iv MIR#SINE/MIR 84 TGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATC 133 chr4qtel1M 905174 TGCAAAATGGATTAATGATACCTATAGAACTTTGCTCTCACAAGGTTGTT 905223 i i--i i --- v i --vi i i MIR#SINE/MIR 134 TGTAAAATGGG--GATAATA---ATAGTACCT--ACCTCATAGGGTTGTT 176 chr4qtel1M 905224 ATAAGGCTTAAATATGATAATGAAAATGCATACGAAAGCTTAAAAC 905269 i i v iv v -- v i ---i iv i MIR#SINE/MIR 177 GTGAGGATTAAATGAGTTAAT--ACATGTA---AAGCGCTTAGAAC 217 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.07 CpG sites = 33, Kimura (unadjusted) = 35.35 Transitions / transversions = 1.38 (33/24) Gap_init rate = 0.14 (32 / 234), avg. gap size = 1.25 (40 / 32) 565 24.47 5.64 11.96 chr4qtel1M 905051 905245 (94755) MIRc#SINE/MIR 25 208 (60) m_b214s601i19 8433 chr4qtel1M 905051 GAGCATTGTACATGGAGTCAA------CTGGGTTCAGATTCTGCAGCTAA 905094 i v v i------ iii i i vvv iv MIRc#SINE/MIR 25 GAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGC 74 chr4qtel1M 905095 CACTTGTTAGCAGTTGTTGTTAGCTAGTTGTGTGACAACAGGCAAATCAC 905144 ii ----------------- vvii i MIRc#SINE/MIR 75 CACTTACTAGC-----------------TGTGTGACCTTGGGCAAGTCAC 107 chr4qtel1M 905145 TTGA-CTAGCTCAGCCTCAGTTTCCCGATCTGCAAAATGGAT-TAATGAT 905192 i - vv v iv i iv- i MIRc#SINE/MIR 108 TTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAAT 157 chr4qtel1M 905193 ACCTATAGAACTTTGC---TCTCACAAGGTTGTTATAAGGCTTAAATATG 905239 -----i ii ---i i i i v i iv MIRc#SINE/MIR 158 ACCT-----GCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAG 202 chr4qtel1M 905240 ATAATG 905245 MIRc#SINE/MIR 203 ATAATG 208 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.50 CpG sites = 27, Kimura (unadjusted) = 30.21 Transitions / transversions = 1.80 (27/15) Gap_init rate = 0.13 (26 / 194), avg. gap size = 1.27 (33 / 26) 694 24.06 11.84 1.59 chr4qtel1M 905744 905971 (94029) MIRb#SINE/MIR 4 254 (14) m_b214s601i20 8434 chr4qtel1M 905744 AGGGAAAGCTAGGTAGCTGAGTGGGCAGAGCACTGGCCT-GGTTTCAGGA 905792 iv vv - -- iv v i - vv iv MIRb#SINE/MIR 4 AGGGGCAGCGTGGT-GC--AGTGGAAAGAGCACGGGCTTTGGAGTCAGAC 50 chr4qtel1M 905793 AGATCTG--TTCAAATCCAG--TCTGACACTTAGTAACCATGTGATCCTG 905838 i -- i v -- v v i ii i i MIRb#SINE/MIR 51 AGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTG 100 chr4qtel1M 905839 AGTAAGTCACTTGATTTCT----GCCTCAGTCTCTTCAACTGTTAAATGA 905884 i i i i ii ---- i i v v i MIRb#SINE/MIR 101 GGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGG 150 chr4qtel1M 905885 GGATAAAAAT--CCACC--------TTGTTTTTAGGATCACACAAGA-AA 905923 v -- i -------- v v i v ii - MIRb#SINE/MIR 151 GGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAA 200 chr4qtel1M 905924 TATTTATAAAGTGCTCAGCACA-------GCATAATAGTAAATGGCACAT 905966 iiv i i i ------- i- ii vivv MIRb#SINE/MIR 201 TGCATGTAAAGCGCTTAGCACAGTGCCTGGCAC-ATAGTAAGCGCTCAAT 249 chr4qtel1M 905967 AAATG 905971 MIRb#SINE/MIR 250 AAATG 254 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.84 CpG sites = 33, Kimura (unadjusted) = 29.77 Transitions / transversions = 1.57 (33/21) Gap_init rate = 0.05 (12 / 227), avg. gap size = 2.58 (31 / 12) 597 23.91 0.72 0.72 chr4qtel1M 906045 906183 (93817) MIR#SINE/MIR 103 241 (21) m_b214s601i21 8435 chr4qtel1M 906045 CCTAACCTCTGTTTGCCTCAGTTTTTTCATCTGCAAAAATCAAGATAATA 906094 i v v ii i - vii MIR#SINE/MIR 103 CTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAA-TGGGGATAATA 151 chr4qtel1M 906095 ACAGTACCCATTTCCCAGGCTAGTTGTGAGGATCAACTATGACAGTAATC 906144 i i ii vi v v i v iv vi i vvi MIR#SINE/MIR 152 ATAGTACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATACAT 201 chr4qtel1M 906145 GTAAAGAGCTTAGCACAGTGCTGGGCACAGAGT-AGTGCT 906183 v v iv v - i MIR#SINE/MIR 202 GTAAAGCGCTTAGAACAGTGCCTGGCACATAGTAAGCGCT 241 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.17 CpG sites = 18, Kimura (unadjusted) = 29.20 Transitions / transversions = 1.20 (18/15) Gap_init rate = 0.01 (2 / 138), avg. gap size = 1.00 (2 / 2) 24 30.01 2.60 0.00 chr4qtel1M 906965 907041 (92959) (AT)n#Simple_repeat 1 79 (0) m_b214s252i6 8436 chr4qtel1M 906965 ATATACATGCATATGTATGCATACACATAGACACAT-TATATATATATGT 907013 i ii i ii i i v i i - i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr4qtel1M 907014 GTGTGTATATATAGATAGATATGT-TATA 907041 i i i v v i - (AT)n#Simple_ 51 ATATATATATATATATATATATATATATA 79 Matrix = Unknown Transitions / transversions = 5.00 (15/3) Gap_init rate = 0.03 (2 / 76), avg. gap size = 1.00 (2 / 2) 191 34.88 7.69 2.94 chr4qtel1M 907425 907619 (92381) L2#LINE/L2 2660 2863 (219) m_b214s601i22 8437 chr4qtel1M 907425 TCTCCCTACCTTAATGGTCAGGTAACCACT----TCC---CCACCTTGAG 907467 v i iv iv i ----- i---- --- v v v L2#LINE/L2 2660 TCTCACCACCTCCACTGCCA-----CCACCCTGGTCCAAGCCACCATCAT 2704 chr4qtel1M 907468 CCCTCATCCTGGACCATTGCAGTAGTGTGCTGCATGGTCTTCTTGACTCA 907517 i i- ii i i iv v ivv i i vi v L2#LINE/L2 2705 CTCTCG-CCTGGATTACTGCAATAGCCTCCTAACTGGTCTCCCTGCTTCC 2753 chr4qtel1M 907518 AGGTTGTCCCCCCTAT--TCCATTCTCTATAT-GCTG-CAATGAGATCC- 907562 vvi vv ?i-- i v i i- v - iv v - L2#LINE/L2 2754 ACCCTTGCCCCCCTNCAGTCTATTCTCAACACAGCAGCCAGAGTGATCCT 2803 chr4qtel1M 907563 -CCAAAGGGCCAACCTGAC--TGGGACTACTTTCTTCAGGAAATTCCAAT 907609 -ii iv iv ii v i-- vv v i vi ii vvi L2#LINE/L2 2804 TTTAAAACGTAAGTCAGATCATGTCACTCCTCTGCTCAAAACCCTCCAAT 2853 chr4qtel1M 907610 GGCTCCTTAT 907619 i ii L2#LINE/L2 2854 GGCTTCCCAT 2863 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 47.86 CpG sites = 37, Kimura (unadjusted) = 48.91 Transitions / transversions = 1.28 (37/29) Gap_init rate = 0.07 (14 / 194), avg. gap size = 1.50 (21 / 14) 31 0.00 0.00 0.00 chr4qtel1M 907999 908027 (91973) (ACTG)n#Simple_repeat 1 29 (0) c_b214s251i1 8438 chr4qtel1M 907999 ACTGACTGACTGACTGACTGACTGACTGA 908027 (ACTG)n#Simpl 1 ACTGACTGACTGACTGACTGACTGACTGA 29 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 438 25.81 0.76 9.02 chr4qtel1M 908305 908436 (91564) C MIRc#SINE/MIR (145) 123 2 m_b214s601i23 8439 chr4qtel1M 908305 GGCTCATA-ACATTAAGTGACTTTCCCAGCATCACATAGCTAAGGAAATA 908353 v - vi v ivi i i------- C MIRc#SINE/MIR 123 GGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG------- 81 chr4qtel1M 908354 TTAAGTGTCTAAGGCTGGATTTGATGTCAGGTCCTCCTGATTTCAGGGCC 908403 - v vi v v i i vvi i i i i v C MIRc#SINE/MIR 80 -TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCC 32 chr4qtel1M 908404 AGCACTCTATCTACTGCACCATCTAGCTGCCCC 908436 ii v i i---i i C MIRc#SINE/MIR 31 AGTGCTCTTTCCACTGCACCAC---ACTGCCTC 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.93 CpG sites = 19, Kimura (unadjusted) = 32.18 Transitions / transversions = 1.58 (19/12) Gap_init rate = 0.09 (12 / 131), avg. gap size = 1.00 (12 / 12) 15 5.56 0.00 0.00 chr4qtel1M 908447 908465 (91535) (T)n#Simple_repeat 1 19 (0) m_b214s252i7 8440 chr4qtel1M 908447 TTCTTTTTTTTTTTTTTTT 908465 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 31 24.11 0.00 0.00 chr4qtel1M 908952 909018 (90982) (CA)n#Simple_repeat 1 67 (0) m_b214s252i8 8441 chr4qtel1M 908952 CACACACACATACCCACACACACACACACGTGCATGCACACACATATATA 909001 i v iii ii i i i (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 chr4qtel1M 909002 CATGCATACACACACAC 909018 ii i (CA)n#Simple_ 51 CACACACACACACACAC 67 Matrix = Unknown Transitions / transversions = 12.00 (12/1) Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.0 (0 / 0) 285 18.24 12.63 1.90 chr4qtel1M 909019 909113 (90887) Charlie7a#DNA/hAT-Charlie 167 271 (1) m_b214s502i0 8442 chr4qtel1M 909019 ATATATATATAATTTATAAATAA------GTACACATATTAGAGCAGCAT 909062 i i ------i i i i vv Charlie7a#DNA 167 ACATGTATATAATTTATAAATAAATAAATATACATATATTGGGGGTGCAT 216 chr4qtel1M 909063 GCTCAAAAA------ACTCATAGAAGTAAATGTGATCAAAAAAGGGAGGA 909106 ------ v ii iv -- vvv Charlie7a#DNA 217 GCTCAAAAATTTTTTACTGATAGGGGTGCA--TGATCAAAAAAGTTTGGA 264 chr4qtel1M 909107 GACCATT 909113 i Charlie7a#DNA 265 GACCACT 271 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 21.23 CpG sites = 10, Kimura (unadjusted) = 21.23 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.04 (4 / 94), avg. gap size = 3.50 (14 / 4) 18 18.73 0.00 0.00 chr4qtel1M 909284 909315 (90685) (C)n#Simple_repeat 1 32 (0) m_b214s252i9 8443 chr4qtel1M 909284 CCCCTCCTTCCCTCCTCCCCCCCCCCCCCCCC 909315 i ii i i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 32 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 210 24.15 6.82 10.59 chr4qtel1M 909618 909705 (90295) MIRb#SINE/MIR 126 210 (58) m_b214s601i24 8444 chr4qtel1M 909618 CTTGGTTTCCTTGCCTGTAAAATGG-----ATATCAACTACTTTCTAGGG 909662 ii iii ----- vi v i ivi MIRb#SINE/MIR 126 CTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTACCTCGCAGGG 175 chr4qtel1M 909663 -TGTTTGGGGGGGTGGGTAGATAAAATGAAATAAGATATGTGAA 909705 - ------- i -- v i vii i MIRb#SINE/MIR 176 TTGTT-------GTGAG--GATTAAATGAGATAATGCATGTAAA 210 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.50 CpG sites = 14, Kimura (unadjusted) = 30.42 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.13 (11 / 87), avg. gap size = 1.36 (15 / 11) 446 28.40 8.80 2.17 chr4qtel1M 912814 913029 (86971) L3#LINE/CR1 3866 4095 (4) m_b214s601i25 8445 chr4qtel1M 912814 CAGAGAGGTA-ATTTC----CAGTCTA-GGAAAATCTTTCTAACAATTAG 912857 i i - ---- i v - i v i L3#LINE/CR1 3866 CAGGGAGGCAGATTTCGGCTCAATATAAGGAAGAACTTTCTAACAATCAG 3915 chr4qtel1M 912858 AGATATGCTAAGGTGAAAC------CCTGGGGGAATAGTAGAGCCTCCCT 912901 v i v v ii i i------ v ? iii - ii v L3#LINE/CR1 3916 AGCTGTCCAAAAATGGAATGGGCTGCCTCGNGAGGTAGT-GAGCTCCCCG 3964 chr4qtel1M 912902 TT-TTAGAGATCTTTTAATCAGAGCAAAGATGACCATTTGTCAAGTATAT 912950 i-i i i -v i v vvvi i i v i L3#LINE/CR1 3965 TCACTGGAGGT-GTTCAAGCAGAGGCTGGATGACCACTTGTCAGGGATGT 4013 chr4qtel1M 912951 GAAGCTGATGGGATTATT--ATTCTGTCAGTGGTAGGACTAGAACAATGT 912998 v-- iv v vi -- vvi vi v v vv vivi L3#LINE/CR1 4014 T--GTAGAAGGGATTCCTGCATTGGATGGGAGGTTGGACTAGATGACCTC 4061 chr4qtel1M 912999 TGAGGTCA--TCTAACCTCT--GATTCTGAGATTC 913029 i v-- i - -- v L3#LINE/CR1 4062 TAAGGTCCCTTCCAA-CTCTGAGATTCTGTGATTC 4095 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.58 CpG sites = 32, Kimura (unadjusted) = 36.58 Transitions / transversions = 1.14 (32/28) Gap_init rate = 0.06 (13 / 215), avg. gap size = 1.85 (24 / 13) 361 36.64 0.53 6.15 chr4qtel1M 913280 913468 (86532) C MIRc#SINE/MIR (88) 180 2 m_b214s601i26 8446 chr4qtel1M 913280 CCTTTGAGGTAGTTATAACAGGTGTTCTTATTCCCAGTGTATATAGTTAG 913329 v vi vii i v i v v i v - v C MIRc#SINE/MIR 180 CCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGA-TGAG 132 chr4qtel1M 913330 GAAATTGAAGTTGAGAACAATTAA-TGACCACATTGAAGAATTATATGTT 913378 i i i v ivii - i-iiiiv -i i i ---- C MIRc#SINE/MIR 131 GAAACTGAGGCTCAGAGAGGTTAAGTGACT-TGCCCAAG-GTCACA---- 88 chr4qtel1M 913379 TCTACCTGAAGAAATATCAGGGGCAAGATTTGAATCCAATCTTTCCTAAC 913428 --i v - iv i iv i v ii i i i ivii i C MIRc#SINE/MIR 87 --CAGCT-AGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGAC 41 chr4qtel1M 913429 TCTAAGACTACTAGGCTATCTACTACTTCTCCTATGCCTC 913468 i v i v ivv v i i vi v vi- C MIRc#SINE/MIR 40 TCCAAGTCCAGTGCTCTTTCCACTGCACCACAC-TGCCTC 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 50.67 CpG sites = 41, Kimura (unadjusted) = 53.11 Transitions / transversions = 1.71 (41/24) Gap_init rate = 0.06 (12 / 188), avg. gap size = 1.00 (12 / 12) 420 28.82 3.23 5.96 chr4qtel1M 914494 914648 (85352) MIRb#SINE/MIR 1 151 (117) m_b214s601i27 8447 chr4qtel1M 914494 CAGGAGGGCAGCAAGG--CAGTGCCACAGAGTACCGG-TCTGGAATCAGG 914540 ii iv -- vv - i v - i i i MIRb#SINE/MIR 1 CAGAGGGGCAGCGTGGTGCAGTGGAA-AGAGCACGGGCTTTGGAGTCAGA 49 chr4qtel1M 914541 GAAACTCATCTTCCTAAATTCATATCTGGCCCCAGACATTTGCTAACTGT 914590 v i -------- iii iv iv v i v v i i i MIRb#SINE/MIR 50 CAGAC--------CTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGT 91 chr4qtel1M 914591 GTGACTCTGGGCAAGTCACAAAATCTTGTTTATCC-CAGTTTCCTCGCCT 914639 ii i vv i ivi v v - ii MIRb#SINE/MIR 92 GTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCT 141 chr4qtel1M 914640 A-AAAATGAG 914648 i- i MIRb#SINE/MIR 142 GTAAAATGGG 151 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.46 CpG sites = 27, Kimura (unadjusted) = 37.74 Transitions / transversions = 1.80 (27/15) Gap_init rate = 0.08 (13 / 154), avg. gap size = 1.08 (14 / 13) 323 33.77 4.07 5.29 chr4qtel1M 914500 914671 (85329) MIR3#SINE/MIR 3 172 (36) m_b214s601i28 8447 chr4qtel1M 914500 GGCAGCAAGGCAGTGC-CACAGAGTACCGGTCTGGAATCAGGGAAACTCA 914548 viv v v -v v i v iiiv i ii ----- MIR3#SINE/MIR 3 GGCAGAGTGGCTGAGCAGAGAGAGCACGGACTGGGAGTCAGGAGA----- 47 chr4qtel1M 914549 TCTTCCTAAATTCATATCTGGCCCCAGACATTTGCTAACTGTGTGACTCT 914598 ---- iii vvi iv v i v v i vi ?i ii MIR3#SINE/MIR 48 ----CCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTT 93 chr4qtel1M 914599 GGGCAAGTCACAAAATCTTGTTTATCC-CAGTTTCCTCGCCTA-AAAATG 914646 vvv i ivi viv - ii i- MIR3#SINE/MIR 94 GGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATG 143 chr4qtel1M 914647 AGCAGG--AGA--AGGTGATCCCTGAAAT 914671 vi --i -- i i i ii MIR3#SINE/MIR 144 AGGGGGTTGGACTAGATGATCTCTAAGGT 172 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 47.10 CpG sites = 33, Kimura (unadjusted) = 47.10 Transitions / transversions = 1.50 (33/22) Gap_init rate = 0.08 (14 / 171), avg. gap size = 1.14 (16 / 14) 318 35.97 6.74 1.60 chr4qtel1M 914964 915141 (84859) C MIRc#SINE/MIR (75) 193 7 m_b214s601i29 8448 chr4qtel1M 914964 TCCTTATAAGAACTCCATCGTGTAAATTGTA-AAGTATCAT-ATCTCCCA 915011 i i v i ii viv iiiv vi- i i - - C MIRc#SINE/MIR 193 TCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATC-CCCA 145 chr4qtel1M 915012 TTTTG----TGTGAAAGC--AA---CAGAGAAATTAGGAATAAATGACCC 915052 i---- v i i -- i--- ii -- i i v vi C MIRc#SINE/MIR 144 TTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTA--AGTGACTTGCCC 97 chr4qtel1M 915053 AGATTCACACAGCTGTTAAAAGGCAAGGGTGAGAATCAAGCCCA-ATGTG 915101 iiv iv iv ii vi i v i i -i v v C MIRc#SINE/MIR 96 AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTT 47 chr4qtel1M 915102 GTAGATTCCAAGTTCAGGGCTCCCCTAAGTACAATATACT 915141 viv i i v iiiiv v i vi i C MIRc#SINE/MIR 46 CCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACT 7 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 50.17 CpG sites = 42, Kimura (unadjusted) = 52.68 Transitions / transversions = 2.00 (42/21) Gap_init rate = 0.05 (9 / 177), avg. gap size = 1.67 (15 / 9) 215 22.22 1.82 1.82 chr4qtel1M 915258 915312 (84688) C MIR3#SINE/MIR (0) 208 154 m_b214s601i30 8449 chr4qtel1M 915258 GAATCATAAAATCATAGATTG-CATTACTAGAAGTGATCTGAAGAGATTA 915306 i v - vvi i v i v- i C MIR3#SINE/MIR 208 GAATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTT-AGAGATCA 160 chr4qtel1M 915307 CCTGGT 915312 i i C MIR3#SINE/MIR 159 TCTAGT 154 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.80 CpG sites = 7, Kimura (unadjusted) = 26.80 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.04 (2 / 54), avg. gap size = 1.00 (2 / 2) 593 29.58 8.10 1.79 chr4qtel1M 915421 915630 (84370) C MIRb#SINE/MIR (31) 237 15 m_b214s601i31 8450 chr4qtel1M 915421 CTAT-TGCCTGCTA-TGTGCTAAATACTTTACAAATATGATCTCATTTGA 915468 - v vi - iii vii v i C MIRb#SINE/MIR 237 CTATGTGCCAGGCACTGTGCTAAGCGCTTTACATGCATTATCTCATTTAA 188 chr4qtel1M 915469 TAC-----GTGACCCTGGAAGTTCAATACTACTTTTATCCCCATTTTACA 915513 v -----iii vi v vii i --- C MIRb#SINE/MIR 187 TCCTCACAACAACCCTGCGAGGTAGGTATTA---TTATCCCCATTTTACA 141 chr4qtel1M 915514 ATCAAGGAAATGGAGGCAAATGGAGGTTACATGATTTCCCTAAAAATCAC 915563 ivii iv vv vi vi i i v i- ii C MIRb#SINE/MIR 140 GATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCC-AAGGTCAC 92 chr4qtel1M 915564 ACAGCT----AGTGTCTGAGGCAGAATTTGAACTCAAATCTTCTTCACTC 915609 ---- v v v i i i i ii vii v C MIRb#SINE/MIR 91 ACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTC 42 chr4qtel1M 915610 CGGGTCCCAAATTC------CTGCACC 915630 iiiv ivii ------ C MIRb#SINE/MIR 41 CAAAGCCCGTGCTCTTTCCACTGCACC 15 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.07 CpG sites = 39, Kimura (unadjusted) = 39.23 Transitions / transversions = 1.77 (39/22) Gap_init rate = 0.04 (9 / 209), avg. gap size = 2.33 (21 / 9) 386 32.88 8.97 0.59 chr4qtel1M 916215 916370 (83630) MIR3#SINE/MIR 16 184 (24) m_b214s601i32 8451 chr4qtel1M 916215 AGTAGAAAGAAGCTTGGCTCTGGAGTCAGAAAACTTCCTTTCAAATTTCT 916264 i i - vi viiv i i i vvv v i ii v MIR3#SINE/MIR 16 AGCAGAGAGA-GCACGGACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCG 64 chr4qtel1M 916265 CTCCTGCCACT------TCAAGTGA------GCAAGTCACTTCA--TTGA 916300 vii ------iiiv ------ -- ivv MIR3#SINE/MIR 65 GCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTC 114 chr4qtel1M 916301 TGAGCTTCAGATTCCTTAAATGTAAAATGAGAGGGTACAATGTGAGGACT 916350 i i v i vv i vvi ivv v ii MIR3#SINE/MIR 115 TGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATC 164 chr4qtel1M 916351 TCATGAGTCCTTTCCAACTC 916370 vvii i i MIR3#SINE/MIR 165 TCTAAGGTCCCTTCCAGCTC 184 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.46 CpG sites = 29, Kimura (unadjusted) = 44.64 Transitions / transversions = 1.32 (29/22) Gap_init rate = 0.03 (4 / 155), avg. gap size = 3.75 (15 / 4) 274 28.17 6.12 10.64 chr4qtel1M 916356 916502 (83498) L2c_3end#LINE/L2 110 250 (228) m_b214s601i33 8452 chr4qtel1M 916356 AGTCCTTTCCAACTCAATCTCTGAACTT---AACATTCTGTCTTCCATCT 916402 i vi ----- i ?i i ---v v ------ i L2c_3end#LINE 110 AGTTCTTTCCTGC-----CTCCGNGCCTTTGCACATGCTGT------TCC 148 chr4qtel1M 916403 CTATGCCTGGAATGCACTCCTTCCTCAATTCTGCTTTTTAG--AATTTCT 916450 v ---i i vv i v ivii i -- i i L2c_3end#LINE 149 CTCTGCCTGGAATGC---TCTTCCCCCCTCCTTCCACCTGGCTAACTCCT 195 chr4qtel1M 916451 AGCT--TCCTTCAAAGATCAGGTTAGATA--GTCTTCTATAAGAAGCCTT 916496 - -- i?v v i i--ii i viii L2c_3end#LINE 196 A-CTCATCCTTCAAGNCTCAGCTCAGATGTCACCTCCTCCGGGAAGCCTT 244 chr4qtel1M 916497 TTCTGA 916502 ii L2c_3end#LINE 245 CCCTGA 250 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.02 CpG sites = 26, Kimura (unadjusted) = 37.78 Transitions / transversions = 2.36 (26/11) Gap_init rate = 0.13 (19 / 146), avg. gap size = 1.26 (24 / 19) 228 35.80 4.35 2.86 chr4qtel1M 916400 916537 (83463) L2d_3end#LINE/L2 147 286 (230) m_b214s601i34 8452 chr4qtel1M 916400 TCTCTATGCCTGGAATGCACT---CCTTCCTCAATTCTGCTTTTTAGAAT 916446 i ivi v --- --- - i v vv v L2d_3end#LINE 147 TCCCCCCGCCTGGAATGCCCTTCCCCTTCCTC---TCT-CTCTATCCAAA 192 chr4qtel1M 916447 TTCTAGCT-TCCTTCAAAGATCAGGTTAGAT--AGTCTTCTATAAGAAGC 916493 i v i- i vi v i ii --vii i vi v L2d_3end#LINE 193 TCCTACCCATCCTTCAAGGCCCAGCTCAAGTCCCACCTCCTCCACGAAGC 242 chr4qtel1M 916494 CTTTTCTGAAGGTCCTTGTTACTGCTGCTTTCATCCTTCCCTAA 916537 ii vviii iv iivvii v i vi i i L2d_3end#LINE 243 CTTCCCTGACCACTCCAGCCCACACTGATCTCTCCCTTCTCTGA 286 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 49.52 CpG sites = 29, Kimura (unadjusted) = 51.08 Transitions / transversions = 1.53 (29/19) Gap_init rate = 0.05 (7 / 137), avg. gap size = 1.43 (10 / 7) 402 31.77 14.58 0.00 chr4qtel1M 916664 916855 (83145) C MIRc#SINE/MIR (24) 244 25 m_b214s601i35 8453 chr4qtel1M 916664 TACAGC-TTTGAAGGCTTATAAACCACTTT-ACAGAGGC---CTCATTTG 916708 i -i v vi i i v i - v vii--- C MIRc#SINE/MIR 244 TATAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATCTCATTTG 195 chr4qtel1M 916709 ATTCCTACAGCAATTATGTG-------------------CATTATAAGCA 916739 i ii i iiv -------------------i vvv C MIRc#SINE/MIR 194 ATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCA 145 chr4qtel1M 916740 ATTT-CTTATAATGAAACTGAGACTGGCAGAAGATAAATGACTTCCTCAG 916788 v - vv i v i viv i v i v i i C MIRc#SINE/MIR 144 TTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAA 95 chr4qtel1M 916789 GATTACTAAACTAATAAGTATC-GATGTGGAATTGGAACTCACA--TTTC 916835 i i vv i i iv - vvi i i v i vi-- i C MIRc#SINE/MIR 94 GGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCC 45 chr4qtel1M 916836 TGATTCCAAGTCCAGCATTC 916855 i iii C MIRc#SINE/MIR 44 TGACTCCAAGTCCAGTGCTC 25 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.02 CpG sites = 37, Kimura (unadjusted) = 42.90 Transitions / transversions = 1.54 (37/24) Gap_init rate = 0.04 (7 / 191), avg. gap size = 4.00 (28 / 7) 363 31.28 8.05 4.44 chr4qtel1M 916701 916874 (83126) C MIRb#SINE/MIR (72) 196 17 m_b214s601i36 8453 chr4qtel1M 916701 CTCATTTGATTCCTACAGCAATTATGTG----------CATTATAAGCAA 916740 i i ii i iiv i ----------i vvv v C MIRb#SINE/MIR 196 CTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATTATCCCCAT 147 chr4qtel1M 916741 TTT-CTTATAATGAAACTGAGACTGGCAGAAGATAAATGACTTCCTCAGG 916789 - vv i v i viv i v i i v i i C MIRb#SINE/MIR 146 TTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAG 97 chr4qtel1M 916790 ATTACTAAACTAATAAGTATC-GATGTGGAATTGGAACTCACATT--TCT 916836 i i vv i i iv - vvi i v i vi i-- C MIRb#SINE/MIR 96 GTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCT 47 chr4qtel1M 916837 GATTCCAAGTCCAGCATTCCATGTCCTTTGTCACAGCA 916874 i ---- --- i ii -i v C MIRb#SINE/MIR 46 GACTCCAA----AGC---CCGTGCTCTTT-CCACTGCA 17 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.97 CpG sites = 32, Kimura (unadjusted) = 42.16 Transitions / transversions = 1.60 (32/20) Gap_init rate = 0.07 (12 / 173), avg. gap size = 1.83 (22 / 12) 712 32.64 3.70 3.16 chr4qtel1M 917244 917999 (82001) L1PREC2_orf2#LINE/L1 2535 3294 (0) m_b214s551i7 8454 chr4qtel1M 917244 AAAATTCATATGGAATAATAAAAGGTCGAGAAT-CTCAAGGGAAT--TAA 917290 iv v iv vv -vi v -- L1PREC2_orf2# 2535 AAAATTCATATGGAACCAAAAAAGAGCCCGAATAGCCAAGGCAATCCTAA 2584 chr4qtel1M 917291 TGAAAAAAAAATCAAATGAAGGTGGCCTAGCTGTACCTGATCTAAAACTA 917340 vv i -- - vv v v vi vv i ii v L1PREC2_orf2# 2585 GCAAAAAGAA--CAAA-GCTGGAGGCATCACGCTACCCGACTTCAAACTA 2631 chr4qtel1M 917341 TATTATAAAGCAGCAGTTACCAAAACCATTTGGTATTGGCTAAGAAATAG 917390 i i ii vi v viiv i ivv i i L1PREC2_orf2# 2632 TACTACAGGGCTACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAG 2681 chr4qtel1M 917391 ATTAGTTGATCAGTGGAACAGGTTA---AGTTCAAAGGACAGATTAGTCA 917437 ivvi v i i iv --- ii i iivv iiiivv L1PREC2_orf2# 2682 ACACATAGACCAATGGAACAGAATAGAGAGCCCAGAAATAAGGCCGCACA 2731 chr4qtel1M 917438 ACTATAGCAATCTAGTGTTTGACAAACC---CAAAGATCCTAACTTTTGC 917484 v i i v ii v i v --- i -- v i vv v v L1PREC2_orf2# 2732 CCTACAACCATCTGATCTTCGACAAAGCTGACAAAAA--CAAGCAATGGG 2779 chr4qtel1M 917485 GATAAAAATTCATTATTTGACAAAAACTGCTGGGATAACTGGAAATTAG- 917533 - ii i vi ii i viv ---i - L1PREC2_orf2# 2780 GA-AAGGACTCCCTATTCAATAAATGGTGCTGGGATAACTGG---CTAGC 2825 chr4qtel1M 917534 --TATGGCAGAA-ATTAGGCATGGACCCACACTTAACACCGTATACCAAG 917580 -- - - iiivv viv i v i v i L1PREC2_orf2# 2826 CATATG-CAGAAGATTGAAACTGGACCCCTTCCTTACACCATATACAAAA 2874 chr4qtel1M 917581 ATAAGATCAAAATGGGTCCATGATTTAGGCATAAGGAACGAGATTATAAA 917630 v iv i i iv v i iiii iivv i i i L1PREC2_orf2# 2875 ATCAACTCAAGATGGATTAAAGACTTAAATGTAAAACCCAAAACTATAAA 2924 chr4qtel1M 917631 TAAATTAGAGGA--ACGTAGG--ATAGTTTATCTCTCAGACCTGTGGAGG 917676 v vvi i i -- v -- --ii - -i v i- iv L1PREC2_orf2# 2925 AACCCTGGAAGACAACCTAGGCAATA--CCAT-TCT-GGACATA-GGAAC 2969 chr4qtel1M 917677 AGGAAGAAATTTT-TGACCAAAGATGAACTAGAGACCATTAT--TAAACA 917723 i v i i i- -i i -- i i ii v ii--i vi L1PREC2_orf2# 2970 GGGCAAAGATTTCATGAC-GAAGACG--CCAAAAGCAATTGCAACAAAAG 3016 chr4qtel1M 917724 CAAAA-TAAAAAAGTTTGATTACATCAAATTAAAAAGCTTTTGTACA--- 917769 - vi v i vv ivv i i i i i --- L1PREC2_orf2# 3017 CAAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCA 3066 chr4qtel1M 917770 AACAAAACTAATGCAAACAAGATTAGCAGGGAAGCAACAAACTGGGAAAA 917819 vi vi--- iii v i iv v v i v i L1PREC2_orf2# 3067 AAAGAAACTATC---AACAGAGTAAACAGACAACCTACAGAATGGGAGAA 3113 chr4qtel1M 917820 CATCTTCACAG-TTAAGGCTCTGATAAAGGCCTCATTTTCAAAATATATA 917868 v ? ii i-i v vv i i v v i iv v L1PREC2_orf2# 3114 AATNTTTGCAAACTATGCATCTGACAAAGGTCTAATATCCAGCATCTATA 3163 chr4qtel1M 917869 GAGAACTGACTCTAATTTATAAGAAAC---CAAGCCATTCTCCAGTTGAT 917915 ii v vv v i v--- i v -- i - i v L1PREC2_orf2# 3164 AGGAACTTAAACAAATTTACAAGAAAAAAACAAACAA--CCCCA-TTAAA 3210 chr4qtel1M 917916 AAATGGTCAAAGGATATGAACAGACAATTTTCAGAGGATGAAATTGAAAC 917965 i v i v i i v v vv vi L1PREC2_orf2# 3211 AAGTGGGCAAAGGACATGAACAGACACTTTTCAAAAGAAGACATACATGC 3260 chr4qtel1M 917966 TATTACCACTCATATGAAAGAATGTTCCAAATCA 917999 viii v vv i v i v v L1PREC2_orf2# 3261 GGCCAACAAGCATATGAAAAAAAGCTCAACATCA 3294 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 42.61 CpG sites = 133, Kimura (unadjusted) = 44.12 Transitions / transversions = 1.25 (133/106) Gap_init rate = 0.05 (39 / 755), avg. gap size = 1.33 (52 / 39) 1497 28.91 1.44 1.11 chr4qtel1M 917861 918486 (81514) L1ME4c_3end#LINE/L1 12 639 (191) m_b214s551i8 8454 chr4qtel1M 917861 AATATATAGAGAACTGACTCTAATTTATAAGAAACCAAGCCATTCTCCAG 917910 ? i i v i v v vv? v v vv i i L1ME4c_3end#L 12 ANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAAGACCCCAA 61 chr4qtel1M 917911 TTGATAAATGGTCAAAGGATATGAACAGACAATTTTCAGAGGATGAAATT 917960 v v i iv ? i v v L1ME4c_3end#L 62 TAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAGGAAATA 111 chr4qtel1M 917961 GAAACTATTACCACTCATATGAAAGAATGTTCCAAATCACTATTTATCAG 918010 v ?ivi v v vv i i i v vv i v v i L1ME4c_3end#L 112 CAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTAGTAATCAA 161 chr4qtel1M 918011 AGAAATGCAAATTAAGACAAGTCTAAGATACCACTACACACCTGTCAGAT 918060 ii vvv i i vi i i i i L1ME4c_3end#L 162 AGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCTATTAAAT 211 chr4qtel1M 918061 TGGCTAAGATGACAGGAAAAAATAATGAT------TGTTGGAGGGGATGC 918104 i v i v---vi v i i ------ i v i ? L1ME4c_3end#L 212 TAGCAAAAATT---TAAAAAATTGATAATACCCAATGCTGGCGAGGNTGC 258 chr4qtel1M 918105 GGGAAAACTGGGACACTGATGCATTGTTGGTGGAGTTGTGAACGAATCCA 918154 vi v ? v i i vi? i ivii v L1ME4c_3end#L 259 GGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACA 308 chr4qtel1M 918155 ACCATTCTGGAGAGCAATCTGGAATTATGCCCAAAAAGTTATCAAAATGT 918204 v i i i v v i iviv i ii v L1ME4c_3end#L 309 ACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAAAATGT 358 chr4qtel1M 918205 ACATACCCTTTGACCCAGCAGTGCTACTACTGGGCTTATACCCCAAGGAG 918254 v i i v i v vv v i i i L1ME4c_3end#L 359 TCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAA 408 chr4qtel1M 918255 ATA---CTAAAGAAGGGAAAGGGATCTGTATGTGCCAAAATGTTTGTGGA 918301 --- v i i --- i ii v i ii v v L1ME4c_3end#L 409 ATAATTCAAAAGAAGGAAAAAG---CTATATGCACGAAGATGTTCATTGC 455 chr4qtel1M 918302 AGCCCTGTTTGTAGTGGCTAGAAACTGGAAAATGAATAGATGCCCATCAA 918351 vi i i i i v i i vvivv i i v L1ME4c_3end#L 456 AGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAA 505 chr4qtel1M 918352 TTGGAGAATGGTTGGGTAAATTGTGGTATATGAATGTTATGGAATATTAT 918401 v i ii i i v? iviv L1ME4c_3end#L 506 TAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATATTAT 555 chr4qtel1M 918402 TGTTCTGTAAGAAATGACCAGCAGGATGAATACAGAGAGGCTTGGAGAGA 918451 vvvv ii v i iv vi v v v iiv vii v - i L1ME4c_3end#L 556 GCAGCCATTAAAAATGATAATTATGAAGACTATGTAGCAACATGGA-AAA 604 chr4qtel1M 918452 CTTATGTGAACTGATGCTAAGTGAAATGAGCAGAA 918486 iv v i vv i i vi L1ME4c_3end#L 605 TGTTTATGATATAATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.70 CpG sites = 94, Kimura (unadjusted) = 37.75 Transitions / transversions = 1.11 (94/85) Gap_init rate = 0.01 (9 / 625), avg. gap size = 1.78 (16 / 9) 25 5.48 5.26 0.00 chr4qtel1M 918899 918936 (81064) (TA)n#Simple_repeat 1 40 (0) m_b214s252i10 8455 chr4qtel1M 918899 TATA-ATA-ATATATATAATTATATATATATATATATATA 918936 - - vv (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATA 40 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 239 35.82 0.00 2.47 chr4qtel1M 918939 919021 (80979) L2b_3end#LINE/L2 362 442 (24) m_b214s601i37 8452 chr4qtel1M 918939 GAAAGAAGAGATTTTTTTTTCTTTGTTTTGATCTTTTTATCCCCAGACTC 918988 ii v i iiv?v i vii i-- i vi v vvi L2b_3end#LINE 362 GAGGGCAGGGACCGNGTCTGTCTTGTTC--ACCGCTGTATCCCCAGCGCC 409 chr4qtel1M 918989 CAACACTGCACCTGGCATAAAGTAAGTGCTTAG 919021 i i v ?i i v i i i L2b_3end#LINE 410 TAGCACAGNGCCTGGCACACAGTAGGCGCTCAG 442 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 48.58 CpG sites = 19, Kimura (unadjusted) = 54.07 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.02 (2 / 82), avg. gap size = 1.00 (2 / 2) 333 28.71 1.41 4.35 chr4qtel1M 919870 920011 (79989) C MIRc#SINE/MIR (4) 264 127 m_b214s601i38 8456 chr4qtel1M 919870 ATAATAATAGCTAATTTTTCTGTAGCTCTTTAAGATTTGCATAGTACTTT 919919 i?v v iv v i v vii i v ii C MIRc#SINE/MIR 264 ATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCGCTTT 215 chr4qtel1M 919920 -ACAGATGTTAACTCATTTGATCCTCACAAGCAAATCTAGCAGGTAGGTA 919968 - v ii v - vi ivv i C MIRc#SINE/MIR 214 CACATACATTATCTCATTTGATCCTCACAA-CAACCCTGTGAGGTAGGCA 166 chr4qtel1M 919969 TTATTTCAAATGTTTTATTTTTCCC-TCTTACATGTAAAAACAC 920011 vvi--- i-- v v i - i vi i ii v C MIRc#SINE/MIR 165 GGG---CAG--GTATTATTATCCCCATTTTACAGATGAGGAAAC 127 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.83 CpG sites = 21, Kimura (unadjusted) = 37.14 Transitions / transversions = 1.17 (21/18) Gap_init rate = 0.06 (8 / 141), avg. gap size = 1.00 (8 / 8) 16 21.31 0.00 2.27 chr4qtel1M 920163 920207 (79793) (AAAAT)n#Simple_repeat 1 44 (0) m_b214s252i11 8457 chr4qtel1M 920163 AAAATACAAATTAAATAAATGCAAGAAAAATAAAGTAAAACAAAA 920207 - v vvv iv i i (AAAAT)n#Simp 1 AAAATA-AAATAAAATAAAATAAAATAAAATAAAATAAAATAAAA 44 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 17 44.11 0.00 0.94 chr4qtel1M 920480 920586 (79414) (TAG)n#Simple_repeat 1 106 (0) m_b214s252i12 8458 chr4qtel1M 920480 TAGAAGTAGTAGTAGCAGCAGCAGCAACACTGGTAACAGTGATATTAGCA 920529 v i i i i ii v i ii ii v i (TAG)n#Simple 1 TAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTA 50 chr4qtel1M 920530 GCAGCAGTACCACCAGCAGCAACAGTAATGGCAGTAATAGTAATACAACT 920579 i i vi vi i i ii i i i i i vv -v (TAG)n#Simple 51 GTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTA-G 99 chr4qtel1M 920580 TAGTAGT 920586 (TAG)n#Simple 100 TAGTAGT 106 Matrix = Unknown Transitions / transversions = 3.12 (25/8) Gap_init rate = 0.01 (1 / 106), avg. gap size = 1.00 (1 / 1) 33 0.00 0.00 0.00 chr4qtel1M 921372 921402 (78598) (T)n#Simple_repeat 1 31 (0) c_b214s251i2 8459 chr4qtel1M 921372 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 921402 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 13 16.31 0.00 5.56 chr4qtel1M 921839 921876 (78124) (ATTGA)n#Simple_repeat 1 36 (0) m_b214s252i13 8460 chr4qtel1M 921839 ATTGAATTGAATTGATGTGATTTGAGTGTCAATGTGAA 921876 vv v i - v - (ATTGA)n#Simp 1 ATTGAATTGAATTGAATTGAATTGAAT-TGAAT-TGAA 36 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 34 0.00 0.00 0.00 chr4qtel1M 923477 923508 (76492) (T)n#Simple_repeat 1 32 (0) c_b214s251i3 8461 chr4qtel1M 923477 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 923508 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 32 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 469 23.55 0.82 6.03 chr4qtel1M 925455 925576 (74424) MIRc#SINE/MIR 12 127 (141) m_b215s601i0 8462 chr4qtel1M 925455 GGTACACTGGATAGAGCACCAGCCCTGAAGTCAGTAGGACCCGAGTTCAA 925504 i v v ii v i i v i i i i MIRc#SINE/MIR 12 GGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGA 61 chr4qtel1M 925505 ATCTGGTTTCAGACACTTAACACTTCCTAGTTGTGTGACCCTGGGCAAGT 925554 i iv vi v v ------- i i MIRc#SINE/MIR 62 GTCCCGGCTCTGCCACTTA-------CTAGCTGTGTGACCTTGGGCAAGT 104 chr4qtel1M 925555 CACTTGACCCCAATT-GCCTCAG 925576 i i vv v- MIRc#SINE/MIR 105 CACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 27.49 CpG sites = 16, Kimura (unadjusted) = 28.72 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.07 (8 / 121), avg. gap size = 1.00 (8 / 8) 2037 28.40 6.31 1.85 chr4qtel1M 926247 927229 (72771) C L1M5_orf2#LINE/L1 (1053) 2241 1216 m_b215s551i0 8463 chr4qtel1M 926247 TTTTTTGGCAACATATAGAAATA----TTATTTATGTGAATTTATTTTGT 926292 v vi ii ---- v v iv v ii C L1M5_orf2#LIN 2241 TTTGTTGCTAGTATATAGAAATACAATTGATTTTTGTATATTGACCTTGT 2192 chr4qtel1M 926293 GTCTTGAAGCTTTGCTAAAGTTGTGAAATGTTTCTAGTAGTTT-TTAGTT 926341 i i? vii i v iiivv v iv - v v C L1M5_orf2#LIN 2191 ATCCNGCGACCTTGCTAAATTCACTTATTAGTTCTAGTAGTTTNTTTGTA 2142 chr4qtel1M 926342 GACTCT----------CTAAGTATACCATCATATCATCTGC--AGAGTGA 926379 i ---------- v ? v i -- v i? C L1M5_orf2#LIN 2141 GATTCTTTNGGATTTTCTACGTANACAATCATGTCATCTGCGAATAANGA 2092 chr4qtel1M 926380 TAATTTTGTTTCCTCATTACCTACTCTAATTCCTTT-----ATTGTTCTT 926424 i i i i v v v iii v v -----v v C L1M5_orf2#LIN 2091 CAGTTTTATTTCTTCCTTTCCAATCTTTATGCCTTTTATTTCTTTTTCTT 2042 chr4qtel1M 926425 CTCTTATTGCTAAAGCTAATACTTCTAATACAATATTGAATAGTAATGGT 926474 vi vvvi iv i i i i v i C L1M5_orf2#LIN 2041 GCCTTATTGCACTGGCTAGGACCTCCAGTACAATGTTGAATAGAAGTGGT 1992 chr4qtel1M 926475 GATAGTAAGCAACCTTGTTTCACCCCTTGTCTTACTGGGAATGCTTCTAG 926524 ? iiii v i iiii ivi vv v ? ii C L1M5_orf2#LIN 1991 GANAGCGGACATCCTTGTCTTGTTCCCGATCTTAGGGGGAAAGCNTTCAG 1942 chr4qtel1M 926525 TTTATGCCCATTACATATGATGCTTACTTGT-GGTTTTAGATAGATACAA 926573 ? v vv vi i ?i - - vvi i vv C L1M5_orf2#LIN 1941 TNTTTCACCATTAAGTATGATGTTNGCT-GTAGGTTTTTCGTAGATGCCC 1893 chr4qtel1M 926574 TTGATCATTTTAAAGGAAACTACATT-TATTCCTATGCTCTTTAATGTTT 926622 v vv i - ii v v - vvi vi v iv C L1M5_orf2#LIN 1892 TTTATCAGGTTGA-GGAAGTTCCCTTCTATTCCTAGTTTGCTGAGAGTTT 1844 chr4qtel1M 926623 TTAATAGAAATGGGTGTTGAAATTTGTCAGATGCTTTTTCTGTATCTATT 926672 vi vi v i i C L1M5_orf2#LIN 1843 TTATCATGAATGGGTGTTGAATTTTGTCAAATGCTTTTTCTGCATCTATT 1794 chr4qtel1M 926673 GTATCTGTATCTATTGAGATAATCATATGATTTCTGT---------TATT 926713 --------------- i i v --------- i C L1M5_orf2#LIN 1793 G---------------AGATGATCATATGATTTTTCTCCTTTATTCTGTT 1759 chr4qtel1M 926714 GATATAGTCAATTATACTAAT--ACT----AGTATTGAACCAGCTCTGAA 926757 i i v i i i -- i ---- i i i i ii v C L1M5_orf2#LIN 1758 AATATGGTGAATTACATTGATTGATTTTCGAATGTTAAACCAACCTTGCA 1709 chr4qtel1M 926758 TTCCTGGTATAAATTCTACTTGGTCATGGTGTATTATCCCAGTGATAACT 926807 v ii i i ivv v vv C L1M5_orf2#LIN 1708 TTCCTGGGATAAACCCCACTTGGTCATGATGTATTATCCTTTTTATATAT 1659 chr4qtel1M 926808 TGCTGTGATCTCTTTGCTAATATTTTATTTAAGATTTTTGCATCAACATT 926857 viv vv i ? i v ii C L1M5_orf2#LIN 1658 TGCTGGATTCGATTTGCTAATATTTTGTTNAGGATTTTTGCATCTATGTT 1609 chr4qtel1M 926858 CATTAGGGAAATTAGTCTATAATGTTCTTTTTCTGTTTTGACCCTACTTG 926907 v v i i v ii vv v ii iii? C L1M5_orf2#LIN 1608 CATGAGGGATATTGGTCTGTAATTTTCTTTTCTTGTAATGTCTTTGTCNG 1559 chr4qtel1M 926908 GTTCAAGTATCAGCACTATATCTGTATCATTAAA-AAATTCAATAGAACT 926956 ivi vii? iiiv iv v -i i viiv vii C L1M5_orf2#LIN 1558 GTTTTGGTATCAGGGTNATGCTGGCCTCATAAAATGAGTTGGGAAGTGTT 1509 chr4qtel1M 926957 -TTTCTTTCCCTGTTTTTCCAGAGAGTTTGTATAATATTGGCATTA---- 927001 -ii ii i iivii i v i ---- C L1M5_orf2#LIN 1508 CCCTCTTTTTCTATTTTCTGGAAGAGTTTGTGTAAGATTGGTATTATTTC 1459 chr4qtel1M 927002 -----------TTTGGTAGAATTCAC--ATCAATCCATCTGGCAATGGAA 927038 ----------- --i v v vvv i C L1M5_orf2#LIN 1458 TTCCTTAAATGTTTGGTAGAATTCACCAGTGAAGCCATCTGGGCCTGGAG 1409 chr4qtel1M 927039 TTTTTTTTCTATGA--GTTGATTAATAATTTGTTCAATTACTTTTTCTAA 927086 i v iv -- v- v ivvi v vvivi C L1M5_orf2#LIN 1408 TTTTCTTTGTGGGAAGGTTT-TTAATTACAAATTCAATTTCTTTAATAGA 1360 chr4qtel1M 927087 AGTGGGACCATTTAAGTAATTTATTTCCTCCTCTTTTCA--TTGGGCAAT 927134 vi i i i i ii vv i - i iv?v -- v i ? C L1M5_orf2#LIN 1359 TATAGGGCTATTCAGATTTTCTATTT-CTTCTTGNGTCAGTTTTGGTAAN 1311 chr4qtel1M 927135 TTATGTTTTTGTAAGTATTCATCCATTTCACTTAGATTATTAGAGTTATT 927184 i vv i v ii ii ii ? i i v C L1M5_orf2#LIN 1310 TTGTGTTTTTCAAGGAATTTGTCCATTTCATCTAAGTTNTCAAATTTATT 1261 chr4qtel1M 927185 GGCATACAGTTGAGCAAAATAGCTCCTAATTATTGCTCTAATTTC 927229 v vv v viii v ivi i v C L1M5_orf2#LIN 1260 GGCATAAAGTTGTTCATAATATTCTCTTATTATCCTTTTAATGTC 1216 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.49 CpG sites = 155, Kimura (unadjusted) = 37.19 Transitions / transversions = 1.30 (155/119) Gap_init rate = 0.04 (35 / 982), avg. gap size = 2.31 (81 / 35) 293 36.32 0.50 0.00 chr4qtel1M 927266 927466 (72534) L1ME3G_3end#LINE/L1 429 630 (294) m_b215s551i1 8464 chr4qtel1M 927266 TGTGCGAAAACGTTTGTGGTAACTCTTTTTGTAGTGGCAAGAAACTGGAA 927315 i i ii i ii v i i vi v i i i i i L1ME3G_3end#L 429 TGTACAAGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAA 478 chr4qtel1M 927316 AGTGAGTGGATGCCCCTCAGTTGGAGAATGGCTGAATAATTTATGGTATA 927365 vvivv ii i v i v i i i v L1ME3G_3end#L 479 ACAACCTAAATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGTATA 528 chr4qtel1M 927366 CAAATGTTATGGAAAATTATTGTTCTACAAGAAATGATCAGGAAGATGAT 927415 ivv ii v i vvvv ?iiv i vi v v vvv L1ME3G_3end#L 529 TCCATACTATGGAATACTATGCAGCNGTTAAAAAGAATGAGGTAGATCTA 578 chr4qtel1M 927416 TTCAGAGAGGCCTGGAAAGACTTACAGAAC-TGATGCTGAGTGAAATGAG 927464 viiv vv i v ii v ii - iv i vi L1ME3G_3end#L 579 TATGTACTGACATGGAAAGATCTCCAAGACATATTGTTGAGTGAAAAAAG 628 chr4qtel1M 927465 CA 927466 L1ME3G_3end#L 629 CA 630 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 50.80 CpG sites = 41, Kimura (unadjusted) = 51.84 Transitions / transversions = 1.28 (41/32) Gap_init rate = 0.01 (1 / 200), avg. gap size = 1.00 (1 / 1) 291 31.98 4.90 1.90 chr4qtel1M 927933 928238 (71762) C L1MC_orf2#LINE/L1 (2097) 1197 883 m_b215s551i2 8465 chr4qtel1M 927933 GTTCTCCCTATTAATTTTTGAATATTAGCAGTTTG-ATAATCTTTCCTTT 927981 i i i - v i - i i -i vv i i C L1MC_orf2#LIN 1197 GTCCCCTCT-TTCATTTCTGA-TATTAGTAATTTGTGTCTTCTCTCTTTT 1150 chr4qtel1M 927982 TTC--TAATCAAATTAATGAAAGGTTTATCTATTTT-----TTTCCCCAG 928024 i-- i i ivi iiiv i i v ----- i iii i C L1MC_orf2#LIN 1149 TTTCTTAGTTAGCCTGGCTAGAGGCTTATCAATTTTATTGATCTTTTCAA 1100 chr4qtel1M 928025 AAAACTAATTCTTAGTTTTGTTTATTAGTTCAAAAATTTTCTTACTTTCA 928074 i i ii i i i v vvi v vviv i ii C L1MC_orf2#LIN 1099 AGAACCAGCTTTTGGTTTCGTTGATTTTCTCTATTGATTTCCTGTTTTCA 1050 chr4qtel1M 928075 ATTTGATTACTCTCCCCTTTAATTTTCAGAATTTCAAATTTGATATTTAA 928124 v iv i iv i i vv vvv i vv ii v C L1MC_orf2#LIN 1049 ATTTCATTGATTTCTGCTCTAATTTTTATTATTTCTTTTCTTCTGCTTAC 1000 chr4qtel1M 928125 TTGTGGATTTCCAATTTG---TTCTTTTTCTTAACTGTTTTAGTTGGATG 928171 - -- --- - ii vii v v v C L1MC_orf2#LIN 999 TT-TGGATTT--AATTTGCTCTTCTTTTTC-TAGTTTCCTAAGGTGGAAG 954 chr4qtel1M 928172 TCCAATTTATTGATTCT--CTCTTTC-TCTATTTT-ATGCAAGCATCTAG 928217 iii iv i --v - v i - ii v ii i C L1MC_orf2#LIN 953 CTTAGATTATTGATTTTAGATCTTTCTTCTTTTCTAATATATGCATTCAA 904 chr4qtel1M 928218 AGATATAAAACTCCCCCTAAG 928238 v v vi i C L1MC_orf2#LIN 903 TGCTATAAATTTCCCTCTAAG 883 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.06 CpG sites = 61, Kimura (unadjusted) = 43.69 Transitions / transversions = 1.74 (61/35) Gap_init rate = 0.04 (13 / 305), avg. gap size = 1.62 (21 / 13) 299 31.02 1.52 7.20 chr4qtel1M 928239 928370 (71630) MIRb#SINE/MIR 6 130 (138) m_b215s601i1 8466 chr4qtel1M 928239 GGGCAGCTAGGTGGCACAGTGGATGGAAACACCAGCCCTGAAGTCAGGAC 928288 --- ii vi i- vi ii i i-- MIRb#SINE/MIR 6 GGGCAGC---GTGGTGCAGTGGAAAGAG-CACGGGCTTTGGAGTCAGA-- 49 chr4qtel1M 928289 CACAGCTGAAATTTGATCTAAGACACT-TAACACTTCCTAGCTATGTAAC 928337 v v iiv ivi ivi --- - iv v i i MIRb#SINE/MIR 50 CAGACCTGGGTTCGAATCCCGG---CTCTGCCACTTACTAGCTGTGTGAC 96 chr4qtel1M 928338 CCTATGTAAATCACTTAATCCCAATT-GCCTCAG 928370 i iv i i i i i vv v- MIRb#SINE/MIR 97 CTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAG 130 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.92 CpG sites = 25, Kimura (unadjusted) = 41.83 Transitions / transversions = 1.92 (25/13) Gap_init rate = 0.08 (11 / 131), avg. gap size = 1.00 (11 / 11) 421 30.97 6.77 5.73 chr4qtel1M 928393 929101 (70899) C L1PREC2_orf2#LINE/L1 (2422) 872 157 m_b215s551i3 8467 chr4qtel1M 928393 GCTTCATCCTATAAAATTTGGAATGTTGTCTCATTATTGTCATTCTCTTG 928442 vii i v i v i v v v i v vvi v C L1PREC2_orf2# 872 GCTGTGTCCCAGAGATTCTGGTATGTTGTATCTTTGTTCTCATTAGTTTC 823 chr4qtel1M 928443 GATGAAATTATTGATT----CTTTAGTATTCATTCTTTAGC--------- 928479 i v v v ---- i i - v v --------- C L1PREC2_orf2# 822 AAAGAACTTCTTGATTTCTGCCTTAAT-TTCATTATTTACCCAAAAGTCA 774 chr4qtel1M 928480 ------AGTAGATTACTTAGTTTCCAATTAATT-------TTTGGTCTAT 928516 ------ i i ii i vv ------- iv v C L1PREC2_orf2# 773 TTCAGGAGCAGGTTGTTTAATTTCCATGTAATTGTATGGTTTTGAGCGAT 724 chr4qtel1M 928517 TTTCCCCTGGTCTTTTATTGCATGAAATTTTTGTTGCATCATGATCTGAG 928566 i-- i v- v - --- i iiii i i C L1PREC2_orf2# 723 TTTCT--TAGTCTTG-ATTTC-T---ATTTTTATTGCGCTGTGGTCCGAG 681 chr4qtel1M 928567 AAAAATGTATTG--ACTATTTCTGCCTTTCTGCATTTGATTTTGAGG-TT 928613 i?i- - -- iv v iii i ---i - C L1PREC2_orf2# 680 AGNG-TGT-TTGGTATGATTTCGGTTCTTTTGCATTTG---CTGAGGATT 636 chr4qtel1M 928614 ATTCT--GCCCTAATATATGGTCAATTTTTGTATAGATTCCATGTACTGC 928661 i i -- i v v i i v vi vi v ivi v C L1PREC2_orf2# 635 GTTTTATGTCCGATTATGTGGTCGATTTTAGAGTATGTGCCATGTGGCGA 586 chr4qtel1M 928662 TGAGAAAAAAGTAT--TCCTTTCTATCTCCATTCAATTTTCTCCAAAGGT 928709 i v -- iv v v i?vvi vv ivv vi i v C L1PREC2_orf2# 585 TGAGAAGAATGTATATTCTGTTGTTTTNGGGTGGAGAGTTCTGTAGATGT 536 chr4qtel1M 928710 CTATCATCCCTAACTTTTCTAGGATTCTATTTACCTCCT---TATCTTCT 928756 vvi i vi vv i vi vvi i vv --- -- C L1PREC2_orf2# 535 CTATCAGGTCCATTTGGTCCAGTGTTGAGTTCAGGTCCTGAATATCTT-- 488 chr4qtel1M 928757 TTCTTCTTTATTTTGTGTTT---TGATTTATCTAGTTCTGAAAGAGCAAG 928803 ---- v v v ii --- i i i v vv v viiv C L1PREC2_orf2# 487 ----TGTTAATTTTCTGCCTCGATGATCTGTCTAATACTGTCAGTGGGGT 442 chr4qtel1M 928804 GTTGAGTTCCCCAACTAGTATAGTTTTGCTGTCTAATTCTTCTAGGAGCT 928853 iv i v v v v v vv v ii v ? v C L1PREC2_orf2# 441 GTTGAAGTCTCCCACTATTATTGTGTGGGAGTCTAAGTCTCTTTGNAGGT 392 chr4qtel1M 928854 CTTT--TAACTTCTCCTCTAGGAATCTGGTTGCTGTACCACTTGGTGCAT 928901 i --v v-- i v v vivviii v C L1PREC2_orf2# 391 CTCTAAGAACTTG--CTTTATGAATCTGGGTGCTCCTGTGTTGGGTGCAT 344 chr4qtel1M 928902 ATATATTTAGTATTGATAATACTTCATTATCT-ATGGCATCCCTTAGCAA 928950 v v v ivv - i iv- v v i i v v C L1PREC2_orf2# 343 ATATATTTAGGATAGTTAGGTCTTC-TTGTTGAATTGAACCCTTTACCAT 295 chr4qtel1M 928951 GATGTTGTTTCCTTTCTTAGCTGTTTTCATTAGATCTATTTTTGCTTT-- 928998 v vi vi ii iv v ----- - v v -- C L1PREC2_orf2# 294 TATGTAATGCCCTTCTTTGTCTTTTTT-----GATCT-TTGTTGGTTTAA 251 chr4qtel1M 928999 ----TGTTTGATCTGAGATCAGGATAGTTACCCTTGTGTTTTTTTTTTTT 929044 ---- vi i i v iv i iv i v C L1PREC2_orf2# 250 AGTCTGTTTTGTCTGAAATTAGGATTGCAACCCCTGCTTTTTTCTGTTTT 201 chr4qtel1M 929045 TTTTTTAACTTCAGCTGAAGCATAATAGATTCTGTTCCAGCCTTTTACCT 929094 iiv ------- ------ ii i vi v i ii C L1PREC2_orf2# 200 CCATTT-------GCT------TGGTAGATTTTTCTCCATCCCTTTATTT 164 chr4qtel1M 929095 TTACCCT 929101 v v C L1PREC2_orf2# 163 TGAGCCT 157 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.65 CpG sites = 99, Kimura (unadjusted) = 40.64 Transitions / transversions = 0.92 (99/108) Gap_init rate = 0.08 (55 / 708), avg. gap size = 1.62 (89 / 55) 56 1.96 0.00 0.00 chr4qtel1M 929983 930034 (69966) (AC)n#Simple_repeat 1 52 (0) c_b215s251i0 8468 chr4qtel1M 929983 ACACACATACACACACACACACACACACACACACACACACACACACACAC 930032 i (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50 chr4qtel1M 930033 AC 930034 (AC)n#Simple_ 51 AC 52 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 909 29.60 2.88 4.38 chr4qtel1M 930049 930465 (69535) C L1ME5_3end#LINE/L1 (460) 481 71 m_b215s551i4 8469 chr4qtel1M 930049 TCCAATTCCTTGACATTACAAAAAGAGCTGCCATAAATATATTTGTACAT 930098 i ii v ii v iv v i i vi i C L1ME5_3end#LI 481 TCCAACTCCCCGCCACCACAAACAACGCTGCAATGAACATCCTCGTACAT 432 chr4qtel1M 930099 GTGGGCCCTTTTCTCTTTTTTTGTGA---TGTCTTTGGGATACAGACCTA 930145 ---- ii v vvvii v --- v i v i C L1ME5_3end#LI 431 GT----CCCCTTATGGACCTGTGTGAGAATTTCTTTGGGATATATACCCA 386 chr4qtel1M 930146 ATAGTAGTATTGCTAGATCAAAGGGTATGCATA-ATTTTATGGCCCTTTG 930194 iv ii v i i v i - i v ------- v C L1ME5_3end#LI 385 GGAGCGGAATTGCTGGGTCATAGGGTATGCGTATACTTAAT-------TT 343 chr4qtel1M 930195 GACTGACT-TTGTTCTTAATTCCTCTCCACAATGGTTGGCTCAGTTCACA 930243 i v -i -- ivi v v i vvi ii C L1ME5_3end#LI 342 GACTAAGTACTG--CCAGATTGCTCTCCAGAATGGCTGCACCAGTCTACA 295 chr4qtel1M 930244 AATCAATCAACAAAACATTATTTCTCCAATTTTCCAACATCCTCTCCAAC 930293 vvi v i i ivi v vvvi v ? i v v C L1ME5_3end#LI 294 CTCCCACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATCCTCGCCAAC 245 chr4qtel1M 930294 ATATATCATTTTCC--TTTTCTGTCATATTAGCAAATCTGATAGGTATGA 930341 iv iv v --i i-- v v v i i i i C L1ME5_3end#LI 244 ACTTGGCATTATCCAGCTTTCTA--ATTTTTGCCAGTCTAATAGGTGTAA 197 chr4qtel1M 930342 AATGACATATTAGAGTTGTTTTAACTCGCATTTCTATAATCAATAATTAT 930391 i i v i vv i i v i i v v v C L1ME5_3end#LI 196 AGTGATATCTCATTGTTGTTTTAATTTGCATTTCTCTGATTACTAATGAG 147 chr4qtel1M 930392 TTTGAATATTTTTTCACATGATTATTGAAAGCTTT---AATTTCTTCCAT 930438 ii i i i v i --- i ---ii i ivi C L1ME5_3end#LI 146 TTTGAGCATCTCTTCATATGCTTGTT---AGCCTTTCGGGTTTCCTCTTC 100 chr4qtel1M 930439 TGAAAATTGCCTG--AATATCCTTTAACC 930465 v --v iv C L1ME5_3end#LI 99 TGTAAATTGCCTGTTCATATCCTTTGCCC 71 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.90 CpG sites = 66, Kimura (unadjusted) = 38.60 Transitions / transversions = 1.27 (66/52) Gap_init rate = 0.06 (24 / 416), avg. gap size = 1.25 (30 / 24) 352 29.42 3.29 6.08 chr4qtel1M 932211 932362 (67638) MIRb#SINE/MIR 4 151 (117) m_b215s601i2 8470 chr4qtel1M 932211 AGGAGCACCATAGTGCAC---AGAGCGCGCTGTGTTGGGAATCAGCAAGA 932257 i v i i v--- i v i v vv v i vv MIRb#SINE/MIR 4 AGGGGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGA 53 chr4qtel1M 932258 CTCAACTTTATGTGTTTCAATCGTGCCTCACACACTTATCAGACGTGTCA 932307 i-------- v iv vi v vvv ii vi v MIRb#SINE/MIR 54 CC--------TGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGA 95 chr4qtel1M 932308 ACCTGGCCATGTTACTCCAACCTGTTTG--CCTCACTTTCTCCATCTATA 932355 v i v v i- v i -- v ii i MIRb#SINE/MIR 96 CCTTGGGCAAGTTACTT-AACCTCTCTGAGCCTCAGTTTCCTCATCTGTA 144 chr4qtel1M 932356 AAATGAG 932362 i MIRb#SINE/MIR 145 AAATGGG 151 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.32 CpG sites = 19, Kimura (unadjusted) = 37.51 Transitions / transversions = 0.83 (19/23) Gap_init rate = 0.07 (11 / 151), avg. gap size = 1.27 (14 / 11) 323 30.70 10.53 0.00 chr4qtel1M 935046 935159 (64841) C MIRc#SINE/MIR (140) 128 3 m_b215s601i3 8471 chr4qtel1M 935046 ACTGAGACCCAGTTAATTTGAATTACTTTTTTAAAACCACAGAG---GTA 935092 i i vv iv i i v viii iii v --- C MIRc#SINE/MIR 128 ACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTA 79 chr4qtel1M 935093 -----CAGAA---GAATTTCAATTCATGTTCTC-TGACTCTAAATCTAGT 935133 ----- i--- i i iv ii v ii - i i i C MIRc#SINE/MIR 78 AGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGT 29 chr4qtel1M 935134 GATCTTTCCACTTCACCTTATTGCCT 935159 v v vi i C MIRc#SINE/MIR 28 GCTCTTTCCACTGCACCACACTGCCT 3 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.19 CpG sites = 24, Kimura (unadjusted) = 41.80 Transitions / transversions = 2.18 (24/11) Gap_init rate = 0.04 (4 / 113), avg. gap size = 3.00 (12 / 4) 20 0.00 0.00 0.00 chr4qtel1M 935553 935574 (64426) (T)n#Simple_repeat 1 22 (0) m_b215s252i0 8472 chr4qtel1M 935553 TTTTTTTTTTTTTTTTTTTTTT 935574 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTT 22 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 18 17.57 0.00 0.00 chr4qtel1M 937764 937795 (62205) (A)n#Simple_repeat 1 32 (0) m_b215s252i1 8473 chr4qtel1M 937764 AAAAAAAAGAAAAAAACAAACAATAAAACAAA 937795 i v v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 32 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 245 22.22 0.00 0.00 chr4qtel1M 937822 937875 (62125) DNM1r#Unknown 2475 2528 (2134) m_b215s502i0 8474 chr4qtel1M 937822 CACAAGTGTGTGTGTATGTGTGTATATATATATATATATGTATGTATATA 937871 iv i i i i i i i i i DNM1r#Unknown 2475 CACGTGTATGTGTGTATATATGTGTGTATATGTGTGTATGTGTGTATATA 2524 chr4qtel1M 937872 TATG 937875 i DNM1r#Unknown 2525 TGTG 2528 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 25.87 CpG sites = 11, Kimura (unadjusted) = 28.69 Transitions / transversions = 11.00 (11/1) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 228 31.47 5.85 5.23 chr4qtel1M 938001 938171 (61829) C MIRc#SINE/MIR (9) 259 88 m_b215s601i4 8475 chr4qtel1M 938001 AATACCATTA-ATTTATATCACAAAT-ATAATTTAATATCTATGCAGTTT 938048 i? - - i vi vv - i i ---- v v iv C MIRc#SINE/MIR 259 AACNCC-TTACATTTGTATAGCACTTTACAGTTTA----CAAAGCGCTTT 215 chr4qtel1M 938049 CACTCACAGTTA---CATTGGAACCTCCCAATAAACCTGTGACAT---CA 938092 vi - --- v v v i v vi --- C MIRc#SINE/MIR 214 CACATACA-TTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCA 166 chr4qtel1M 938093 CACAAAGTGCCTTTATTCTCATGGGTGTACAACTCAGGTCATCA--GTTC 938140 vivv i iiiv i i --- v iv v vv iii-- i C MIRc#SINE/MIR 165 GGGCAGGTATTATTATCCCCAT---TTTACAGATGAGGAAACTGAGGCTC 119 chr4qtel1M 938141 AGAAAGACTGAGTGACTTGATCCAAATCACA 938171 i ii i vi v ii C MIRc#SINE/MIR 118 AGAGAGGTTAAGTGACTTGCCCAAGGTCACA 88 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.06 CpG sites = 28, Kimura (unadjusted) = 42.15 Transitions / transversions = 1.22 (28/23) Gap_init rate = 0.08 (14 / 170), avg. gap size = 1.36 (19 / 14) 283 28.14 11.45 5.04 chr4qtel1M 939674 939804 (60196) MIR1_Amn#SINE/MIR 22 160 (70) m_b215s601i5 8476 chr4qtel1M 939674 TGGATAGA-CTGTGGATTAGGGCTTTGAATGAGGAAAACCAGAGTTTTAA 939722 - vv i i i i------- i i v i i? ? MIR1_Amn#SINE 22 TGGATAGAGCACTGGACTGGGACTC-------GGGAGACCTGGGTTCNAN 64 chr4qtel1M 939723 TCCTACCTTAGAACCTTGCTAGT--------------CAAGTTATAGGAC 939758 iiv iv vvv ? i? i-------------- i ivv? MIR1_Amn#SINE 65 TCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGTCACTTNAC 114 chr4qtel1M 939759 CTCTGTTTGATTCAGTTCCTTTATCTGTAAAACGGGCTTAATGATA 939804 v v? vi i i i i vv MIR1_Amn#SINE 115 CTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATGATA 160 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.78 CpG sites = 20, Kimura (unadjusted) = 38.71 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.07 (9 / 130), avg. gap size = 2.44 (22 / 9) 385 30.25 11.40 2.38 chr4qtel1M 939692 939884 (60116) MIRc#SINE/MIR 32 241 (27) m_b215s601i6 8476 chr4qtel1M 939692 GGGCTTTGAATGAGGAAAACCAGAGTTTTAATCCTACCTTAGAACCTTGC 939741 i v i v i v i iv i iiv iv vvv i MIRc#SINE/MIR 32 GGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTAC 81 chr4qtel1M 939742 TAGT--------------CAAGTTATAGGACCTCTGTTTGATTCAGTTCC 939777 i-------------- i ivvi v vv vi i MIRc#SINE/MIR 82 TAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTC 131 chr4qtel1M 939778 TTTATCTGTAAAACGGGCTTAATGATATCAGCAAAGT---CCTCA---GG 939821 i i i vv i i v vvv i--- --- MIRc#SINE/MIR 132 CTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGG 181 chr4qtel1M 939822 TTCTCATGAGGATAAAATAAGACAATGCCATGCATGACACACACCTAG-- 939869 v ii v i i -i -- - vi i i v -- MIRc#SINE/MIR 182 TTGTTGTGAGGATCAAATGAGATAATG-TATG--TGA-AAGCGCTTTGTA 227 chr4qtel1M 939870 AGCTGTGTAAGTGCT 939884 i i- MIRc#SINE/MIR 228 AACTGTA-AAGTGCT 241 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.04 CpG sites = 32, Kimura (unadjusted) = 39.80 Transitions / transversions = 1.28 (32/25) Gap_init rate = 0.05 (9 / 192), avg. gap size = 3.00 (27 / 9) 190 30.25 10.92 0.00 chr4qtel1M 940036 940154 (59846) L2b_3end#LINE/L2 334 465 (1) m_b215s601i7 8477 chr4qtel1M 940036 GTCTGCCCCACCACTCTGTGATCTCTGTGAGAGC--TTACC-TGAC-ATC 940081 v i vv v i i --vv -? v -i L2b_3end#LINE 334 GTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTC 383 chr4qtel1M 940082 TCTTTGAC-----TTTTCCTGGTGCTGAGCCCAGGG-CTGCCACATTGCA 940125 iv v ----- v i ii i iv v ? - v iv i L2b_3end#LINE 384 TTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTA 433 chr4qtel1M 940126 GGCCCTTAAT---TGTTTACTGACTAGAAGAA 940154 v i i --- i ii v ii v L2b_3end#LINE 434 GGCGCTCAGTAAATATTTGTTGAATGAATGAA 465 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.51 CpG sites = 19, Kimura (unadjusted) = 40.34 Transitions / transversions = 1.12 (19/17) Gap_init rate = 0.05 (6 / 118), avg. gap size = 2.17 (13 / 6) 237 29.35 5.43 0.00 chr4qtel1M 940214 940305 (59695) C MIR3#SINE/MIR (3) 205 109 m_b215s601i8 8478 chr4qtel1M 940214 TTATAGGATCACAGA-TG--AGCACTGGAAGGGACCTACAGGGCTGTGGA 940260 i i i - -- vi vvii iiii vv C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTA 156 chr4qtel1M 940261 GTGCGACGCACTCATTTTATAGAT--GGAAACAAGGGTTCACTGAGG 940305 v i v v i -- vii ii vv C MIR3#SINE/MIR 155 GTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGG 109 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.33 CpG sites = 16, Kimura (unadjusted) = 38.33 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.03 (3 / 91), avg. gap size = 1.67 (5 / 3) 340 29.56 2.92 3.68 chr4qtel1M 940943 941079 (58921) MIRc#SINE/MIR 10 145 (123) m_b215s601i9 8479 chr4qtel1M 940943 GTAGTACAGTGGA--TAGTCCTTGTCATAGAGTCAGGTGTACCCTGAGTT 940990 i i --v iv v v v i viv - i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC-TGGGTT 58 chr4qtel1M 940991 TGAAGGAAACCTTAAAGAGTTACTAACTGTAC--CTTTGGGCAAGTCAAT 941038 i ivvvviv ivivv v i ii-- i v MIRc#SINE/MIR 59 CGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACT 108 chr4qtel1M 941039 TATACTCTGTTAATTTGCCTCAGTTTCCTCAGCTCTCAAAT 941079 vv v v ---- v v v MIRc#SINE/MIR 109 TAACCTCTCTGA----GCCTCAGTTTCCTCATCTGTAAAAT 145 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.35 CpG sites = 15, Kimura (unadjusted) = 37.60 Transitions / transversions = 0.62 (15/24) Gap_init rate = 0.05 (7 / 136), avg. gap size = 1.29 (9 / 7) 17 13.56 2.08 8.89 chr4qtel1M 941088 941135 (58865) (TA)n#Simple_repeat 1 45 (0) m_b215s252i3 8480 chr4qtel1M 941088 TATATCACATATAACTATATCAT-TATATATATGATATAGTTATCATAT 941135 - i vv - - - vv - (TA)n#Simple_ 1 TATAT-ATATATATATATAT-ATATATATATAT-ATATATATAT-ATAT 45 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.11 (5 / 47), avg. gap size = 1.00 (5 / 5) 17 37.36 1.05 1.05 chr4qtel1M 941345 941439 (58561) (TATA)n#Simple_repeat 1 95 (0) m_b215s252i4 8481 chr4qtel1M 941345 TACATAGAAATATGTAAACATA-AAAAATAACCACATGCATATATGCATA 941393 i v v i v i - v v vvi i ii ii (TATA)n#Simpl 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr4qtel1M 941394 TATATATACACACATACATTCATATGTAAAACTATGCTATATATAT 941439 i i i i vi i v vv -v (TATA)n#Simpl 51 TATATATATATATATATATATATATATATATATAT-ATATATATAT 95 Matrix = Unknown Transitions / transversions = 1.25 (15/12) Gap_init rate = 0.02 (2 / 94), avg. gap size = 1.00 (2 / 2) 19 28.94 0.00 1.79 chr4qtel1M 941383 941439 (58561) (AT)n#Simple_repeat 1 56 (0) m_b215s252i5 8481 chr4qtel1M 941383 ATATATGCATATATATATACACACATACATTCATATGTAAAACTATGCTA 941432 ii i i i i vi i v vv -v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATAT-ATA 49 chr4qtel1M 941433 TATATAT 941439 (AT)n#Simple_ 50 TATATAT 56 Matrix = Unknown Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.02 (1 / 56), avg. gap size = 1.00 (1 / 1) 362 24.98 7.46 1.41 chr4qtel1M 942246 942379 (57621) C MIR3#SINE/MIR (1) 207 66 m_b215s601i10 8482 chr4qtel1M 942246 AATCAGA-AGTCATAAGATGT-GGAGCTGAAAGAGCCTTCAGA-ATTAAA 942292 v - i ii -i i i v i i - i vv C MIR3#SINE/MIR 207 AATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATC 158 chr4qtel1M 942293 GAGTCCAACTCCCTCCAATTTATAG--GAGGAAATGGAAACACAGA---- 942336 v i - v i -- iv ii v ---- C MIR3#SINE/MIR 157 TAGTCCAACCCCCT-CATTTTACAGATGAGGAAACTGAGGCCCAGAGAGG 109 chr4qtel1M 942337 -GAAGGGATTTGCCCAAAGGTCATAGGCTTTCTGAGTGTCAGAG 942379 - v i - i vivi?vv v v C MIR3#SINE/MIR 108 TGAAGTGACTTGCCC-AAGGTCACACAGCNAGTTAGTGGCAGAG 66 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.16 CpG sites = 18, Kimura (unadjusted) = 31.16 Transitions / transversions = 1.20 (18/15) Gap_init rate = 0.06 (8 / 133), avg. gap size = 1.50 (12 / 8) 221 30.56 8.14 1.09 chr4qtel1M 942305 942390 (57610) C MIRc#SINE/MIR (119) 149 58 m_b215s601i11 8482 chr4qtel1M 942305 CTCCAATTTATAG--GAGGAAATGGAAACACAGAG-----AAGGGATTTG 942347 i v i -- iv ii v ----- v i C MIRc#SINE/MIR 149 CCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTG 100 chr4qtel1M 942348 CCCAAAGGTCATAGGCTTTCTGAGTGTCAGAGTTAACCCTTGA 942390 - i vivi vv i v iiiivv i C MIRc#SINE/MIR 99 CCC-AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGA 58 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.27 CpG sites = 15, Kimura (unadjusted) = 40.41 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.04 (3 / 85), avg. gap size = 2.67 (8 / 3) 15 30.65 0.00 6.25 chr4qtel1M 943862 943946 (56054) (AAGAGA)n#Simple_repeat 1 80 (0) m_b215s252i6 8483 chr4qtel1M 943862 AAGAGAAAGAGAATCTACAAGAGAACTAAAAGGAAAATGGGGATAAAGAA 943911 vvviv vv i i i -i i v i (AAGAGA)n#Sim 1 AAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAA-AGAGAAAGAGAA 49 chr4qtel1M 943912 ATGCAGAATGAGAAAAAGTAGAAGAGATAAACAAA 943946 - - v i - - v i v (AAGAGA)n#Sim 50 A-G-AGAAAGAGAAAGAG-A-AAGAGAAAGAGAAA 80 Matrix = Unknown Transitions / transversions = 0.90 (9/10) Gap_init rate = 0.06 (5 / 84), avg. gap size = 1.00 (5 / 5) 302 24.99 4.13 0.80 chr4qtel1M 944585 944705 (55295) L1M4_orf2#LINE/L1 770 894 (2400) m_b215s551i5 8484 chr4qtel1M 944585 TACATAATGACTGAGTCAGAGAAGAGA--ACT-GAGAAAT--GATAATTT 944629 v iv v i i i -- v- i -- v vi L1M4_orf2#LIN 770 TAAATAACCAATGGGTCAAAGAAGAAATCACAAGGGAAATTAGAAAATAC 819 chr4qtel1M 944630 TATAAAATATAATGAAAATTATTAAACAATATCCCAAAATTTCTGGGATT 944679 v i i i- iv vv v i v i v v L1M4_orf2#LIN 820 TTTGAGATG-AATGAAAACGAAAACACAACATACCAAAACTTATGGGATG 868 chr4qtel1M 944680 CAGTTAAAGCTGTCCTCAGAGGGAAA 944705 i? v v i L1M4_orf2#LIN 869 CAGCNAAAGCAGTGCTTAGAGGGAAA 894 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 29.73 CpG sites = 14, Kimura (unadjusted) = 30.91 Transitions / transversions = 0.88 (14/16) Gap_init rate = 0.03 (4 / 120), avg. gap size = 1.50 (6 / 4) 294 25.33 5.41 1.30 chr4qtel1M 944596 944743 (55257) L1MC_orf2#LINE/L1 781 934 (2360) m_b215s551i6 8484 chr4qtel1M 944596 TGAGTCAGAGAAGAGAACT---GAGAAAT--GATAATTTTATAAAATATA 944640 i i i v --- --i v v v i v - L1MC_orf2#LIN 781 TGGGTCAAAGAAGAAATCTCAAGAGAAATTTAAAAATATTTTGAACTA-A 829 chr4qtel1M 944641 ATGAAAATTATTAAACAATATCCCAAAATTTCTGGGATTCAGTTAAAGCT 944690 v vv v iv vi v v iv v L1MC_orf2#LIN 830 ATGAAAATGAAAATACAACTTATCAAAATTTGTGGGATGCAGCGAAAGCA 879 chr4qtel1M 944691 GTCCTCAGAGGGAAA--CATAGTGTTAGCAT-CACACATTAAGAATATAG 944737 v i --i ii - v - i i ii viv L1MC_orf2#LIN 880 GTGCTTAGAGGGAAATTTATAGCATT-GAATGCATATATTAGAAAAGAAG 928 chr4qtel1M 944738 AAAAAT 944743 i L1MC_orf2#LIN 929 AAAGAT 934 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 30.19 CpG sites = 18, Kimura (unadjusted) = 31.17 Transitions / transversions = 0.95 (18/19) Gap_init rate = 0.04 (6 / 147), avg. gap size = 1.67 (10 / 6) 487 21.97 0.00 5.71 chr4qtel1M 944757 944867 (55133) MIRc#SINE/MIR 11 115 (153) m_b215s601i12 8485 chr4qtel1M 944757 TGGTACAATAGAGAGAGCACCAGTCCTGAAGTCAGGAGGACTTGAATTCA 944806 i i i i ii v i i i i ii i MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr4qtel1M 944807 AACTGGCCCCAGACACTTCACACTTCCTAGCTGTGTGACTCTGAGCAAGT 944856 ---- i i - v v - v ii i MIRc#SINE/MIR 61 A----GTCCCGG-CTCTGC-CACTTACTAGCTGTGTGACCTTGGGCAAGT 104 chr4qtel1M 944857 CACTTAACCCC 944867 i MIRc#SINE/MIR 105 CACTTAACCTC 115 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 24.74 CpG sites = 19, Kimura (unadjusted) = 27.52 Transitions / transversions = 4.75 (19/4) Gap_init rate = 0.05 (6 / 110), avg. gap size = 1.00 (6 / 6) 12 23.70 1.82 5.66 chr4qtel1M 944937 944991 (55009) (AACA)n#Simple_repeat 1 53 (0) m_b215s252i7 8486 chr4qtel1M 944937 AAAAAACAAACAAACTAGAATAAATGAACAAAACAAAAATAAGTACAAA- 944985 v - - i ii - v v viv - (AACA)n#Simpl 1 AACAAACAAACAAAC-A-AACAAACAAAC-AAACAAACAAACAAACAAAC 47 chr4qtel1M 944986 AGACAA 944991 i (AACA)n#Simpl 48 AAACAA 53 Matrix = Unknown Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.07 (4 / 54), avg. gap size = 1.00 (4 / 4) 435 26.31 5.05 4.09 chr4qtel1M 945465 945682 (54318) L1M2_orf2#LINE/L1 1620 1839 (1452) m_b215s551i7 8487 chr4qtel1M 945465 AATTTTAAACAAAATCCTATCAAAACAA---CTACAGTAAATTATCTAAG 945511 ii v v v v i --- v i v --- i L1M2_orf2#LIN 1620 AATCCTCAACAAAATACTAGCAAACCGAATTCAACAGCACATTA---AAA 1666 chr4qtel1M 945512 ATACCATTCATTAAGATCAAGTGGGATTTCTACCAGGGTTGGAATGATAG 945561 v i? ? ii v v v v v v i L1M2_orf2#LIN 1667 AGATNATNCACCATGATCAAGTGGGATTTATCCCAGGGATGCAAGGATGG 1716 chr4qtel1M 945562 TTCAACATTAGGAAAACAATGAACATAATTAATCACATTGTAAACCACAA 945611 vv v v i i i vv ------ v i L1M2_orf2#LIN 1717 TTCAACATACGCAAATCAATAAACGTGATACATCACAT------CAACAG 1760 chr4qtel1M 945612 CAT------CCAAAACCACA-GCTAAT-TCAATAGATAAAGAGAATGCTT 945653 v ------ v i - v v - iv i v v L1M2_orf2#LIN 1761 AATGAAGGACAAAAACCATATGATCATCTCAATAGATGCAGAAAAAGCAT 1810 chr4qtel1M 945654 TGGACAAAGTACCGCACTCTTTTGTAATA 945682 v i i v vi ii i ii i L1M2_orf2#LIN 1811 TTGATAAAATTCAACATCCCTTCATGATA 1839 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 31.59 CpG sites = 25, Kimura (unadjusted) = 32.98 Transitions / transversions = 0.83 (25/30) Gap_init rate = 0.06 (13 / 217), avg. gap size = 1.54 (20 / 13) 23 14.48 0.00 0.00 chr4qtel1M 947411 947448 (52552) (GA)n#Simple_repeat 1 38 (0) m_b215s252i8 8488 chr4qtel1M 947411 GAGAGAAAGAGAAAGAGAGAGAGAGAGAGTGTGTGAGA 947448 i i v v v (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 38 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 14 15.30 0.00 0.00 chr4qtel1M 947755 947783 (52217) (TGTG)n#Simple_repeat 1 29 (0) m_b215s252i10 8489 chr4qtel1M 947755 TGTGTATGTGTGTGTGTGTATCTGTCTGT 947783 i i v v (TGTG)n#Simpl 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGT 29 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 13 18.71 0.00 5.26 chr4qtel1M 947750 947789 (52211) (GTGTAT)n#Simple_repeat 1 38 (0) m_b215s252i9 8490 chr4qtel1M 947750 GTGCATGTGTATGTGTGTGTGTGTATCTGTCTGTCTAGGT 947789 i -- i v v v v (GTGTAT)n#Sim 1 GTGTATGTGTA--TGTGTATGTGTATGTGTATGTGTATGT 38 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 15 13.32 4.44 4.44 chr4qtel1M 948608 948652 (51348) (TCTCC)n#Simple_repeat 1 45 (0) m_b215s252i11 8491 chr4qtel1M 948608 TCTGCTCTCCTCT-GTCTTTTACTCCTCTTCTCCTCC-CTCCTCTCC 948652 v -v ii - i - - (TCTCC)n#Simp 1 TCTCCTCTCCTCTCCTCTCCT-CTCCTCTCCT-CTCCTCTCCTCTCC 45 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4) 20 21.74 6.58 1.25 chr4qtel1M 950146 950221 (49779) (CTCC)n#Simple_repeat 1 80 (0) m_b215s252i12 8492 chr4qtel1M 950146 CTCCC-CCC-CCC-CCCGCCCCCAAGGCCTCCGTCACTTCCTTCTCTCCT 950192 - - - v i vvvv v - i i i i (CTCC)n#Simpl 1 CTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTC-CCTCCCTCCCTCCC 49 chr4qtel1M 950193 TCCCTCCCACACTCACTCCCT-CCT-CCTCC 950221 v v v - - (CTCC)n#Simpl 50 TCCCTCCCTCCCTCCCTCCCTCCCTCCCTCC 80 Matrix = Unknown Transitions / transversions = 0.56 (5/9) Gap_init rate = 0.08 (6 / 75), avg. gap size = 1.00 (6 / 6) 371 28.20 5.93 0.81 chr4qtel1M 950733 950850 (49150) L2b_3end#LINE/L2 325 448 (18) m_b215s601i13 8493 chr4qtel1M 950733 TACATG---GTCTGCCCCACCAGTCTGTGACCTCCATGAGAGCAG----C 950775 --- v i v v i i ---- L2b_3end#LINE 325 TACATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACC 374 chr4qtel1M 950776 GGTTGTGCTTTGTACTTCCTTTTGCTCCTGGTGCTTAGCCCAGGGCCTGA 950825 ?v v ii v vi vi v iii ii i i v ? i L2b_3end#LINE 375 GNGTCTGTCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGG 424 chr4qtel1M 950826 CATGTAGCAGGCACTTGAAAAAATA 950850 iii i i i- iv L2b_3end#LINE 425 CACACAGTAGGCGCTC-AGTAAATA 448 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.53 CpG sites = 22, Kimura (unadjusted) = 37.84 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.03 (3 / 117), avg. gap size = 2.67 (8 / 3) 357 19.27 4.76 1.15 chr4qtel1M 950928 951011 (48989) C MIR3#SINE/MIR (3) 205 119 m_b215s601i14 8494 chr4qtel1M 950928 TTATAGGATCATA-AATGATCA---CTGGAAGGGACCTAACAGGCCATAG 950973 i i - - --- v v ii vv C MIR3#SINE/MIR 205 TCATAGAATCATAGAATG-TCAGAGCTGGAAGGGACCTTAGAGATCATCT 157 chr4qtel1M 950974 AGTGTAACTCCCTCTTTTTACAGATTGGGAAACTTAAG 951011 vi i v vi v i C MIR3#SINE/MIR 156 AGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGG 119 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 22.42 CpG sites = 8, Kimura (unadjusted) = 22.42 Transitions / transversions = 1.00 (8/8) Gap_init rate = 0.04 (3 / 83), avg. gap size = 1.67 (5 / 3) 513 20.42 0.83 6.14 chr4qtel1M 951431 951550 (48450) MIRc#SINE/MIR 2 115 (153) m_b215s601i15 8495 chr4qtel1M 951431 GAGCTAG-GTGGTGCAGTGGATAGAGTGCTGGCCCTGAAGTCAGGGGGAC 951479 vi - v ii v i i ii MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr4qtel1M 951480 CTGAGTTCAAATTTGGCCTCAAACACTTAAAACTTCCTAGGTGTGTGACC 951529 i i i iiv v viv ------- v MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTGACC 94 chr4qtel1M 951530 CTGGGCAAGTCACTTAACCCC 951550 i i MIRc#SINE/MIR 95 TTGGGCAAGTCACTTAACCTC 115 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 23.13 CpG sites = 15, Kimura (unadjusted) = 24.31 Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.07 (8 / 119), avg. gap size = 1.00 (8 / 8) 22 16.10 0.00 0.00 chr4qtel1M 951573 951614 (48386) (ATAT)n#Simple_repeat 1 42 (0) m_b215s252i14 8496 chr4qtel1M 951573 ATATATATATATATATACATACATACCTATATGTATAGATAT 951614 i i iv i v (ATAT)n#Simpl 1 ATATATATATATATATATATATATATATATATATATATATAT 42 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 428 28.22 1.60 0.79 chr4qtel1M 952285 952409 (47591) MIRc#SINE/MIR 10 135 (133) m_b215s601i16 8497 chr4qtel1M 952285 GTAGTACAATGAACAGAGACCTGGGCATAGAGTT-GGAAGAGTCTAACTT 952333 i i i i v vv i v i i- -i iiv MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA-CCTGGGTT 58 chr4qtel1M 952334 TAAATCAAGTTTCAGACAGTTCCTAGCTCTGTGTCCCTTGACAAGT-ACT 952382 ii i vv vi v v v v v v i v i - MIRc#SINE/MIR 59 CGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACT 108 chr4qtel1M 952383 TAAACTCTGTTTGCCTCAGTTTCCTCA 952409 v v vv MIRc#SINE/MIR 109 TAACCTCTCTGAGCCTCAGTTTCCTCA 135 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.29 CpG sites = 16, Kimura (unadjusted) = 35.64 Transitions / transversions = 0.84 (16/19) Gap_init rate = 0.02 (3 / 124), avg. gap size = 1.00 (3 / 3) 28 39.21 0.00 0.00 chr4qtel1M 953537 953654 (46346) (TC)n#Simple_repeat 1 118 (0) m_b215s252i15 8498 chr4qtel1M 953537 TCTTTCTGTCTCTCTGATTCTTGCTCTCTCTCCCTCTCCAATTCTCTTTA 953586 i v vvi iv i ivvi i v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr4qtel1M 953587 TCTCTCTCTCTCTCTTTTTTTTTTTTTTTTTTTTAAATTCTCTCATTCTC 953636 i i i i i i i i i ivvvi vi (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chr4qtel1M 953637 TGTCTACCTCTTTCTTTC 953654 v vi i i (TC)n#Simple_ 101 TCTCTCTCTCTCTCTCTC 118 Matrix = Unknown Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.00 (0 / 117), avg. gap size = 0.0 (0 / 0) 18 0.00 0.00 0.00 chr4qtel1M 953601 953620 (46380) (T)n#Simple_repeat 1 20 (0) m_b215s252i16 8499 chr4qtel1M 953601 TTTTTTTTTTTTTTTTTTTT 953620 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTT 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 28 39.21 0.00 0.00 chr4qtel1M 953537 953654 (46346) (TC)n#Simple_repeat 1 118 (0) m_b215s252i15 8498 chr4qtel1M 953537 TCTTTCTGTCTCTCTGATTCTTGCTCTCTCTCCCTCTCCAATTCTCTTTA 953586 i v vvi iv i ivvi i v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr4qtel1M 953587 TCTCTCTCTCTCTCTTTTTTTTTTTTTTTTTTTTAAATTCTCTCATTCTC 953636 i i i i i i i i i ivvvi vi (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chr4qtel1M 953637 TGTCTACCTCTTTCTTTC 953654 v vi i i (TC)n#Simple_ 101 TCTCTCTCTCTCTCTCTC 118 Matrix = Unknown Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.00 (0 / 117), avg. gap size = 0.0 (0 / 0) 17 8.13 0.00 0.00 chr4qtel1M 954451 954476 (45524) (TTA)n#Simple_repeat 1 26 (0) m_b215s252i17 8500 chr4qtel1M 954451 TTATTATTATTATTATTATTTTTGTT 954476 v i (TTA)n#Simple 1 TTATTATTATTATTATTATTATTATT 26 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 29 0.00 2.78 2.78 chr4qtel1M 955345 955380 (44620) (AGAGTGAA)n#Simple_repeat 1 36 (0) c_b215s251i1 8501 chr4qtel1M 955345 AGAGTGAAAGAGTG-AAGCAGTGAAAGAGTGAAAGAG 955380 - - (AGAGTGAA)n#S 1 AGAGTGAAAGAGTGAAAG-AGTGAAAGAGTGAAAGAG 36 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 12 35.45 0.00 2.90 chr4qtel1M 956884 956954 (43046) (AAAAT)n#Simple_repeat 1 69 (0) m_b215s252i18 8502 chr4qtel1M 956884 AAAATCAAATCAAAAAGGGAAAAATGAGAAAGAAAATAAAATGCAAGCAA 956933 v v v iiiv - - v iv vv (AAAAT)n#Simp 1 AAAATAAAATAAAATAAAATAAAAT-A-AAATAAAATAAAATAAAATAAA 48 chr4qtel1M 956934 ACAACAACGAATAGAGTAAAA 956954 i v vvi i i (AAAAT)n#Simp 49 ATAAAATAAAATAAAATAAAA 69 Matrix = Unknown Transitions / transversions = 0.73 (8/11) Gap_init rate = 0.03 (2 / 70), avg. gap size = 1.00 (2 / 2) 913 34.54 1.82 2.95 chr4qtel1M 957150 957698 (42302) C L1ME5_3end#LINE/L1 (343) 598 56 m_b215s551i8 8503 chr4qtel1M 957150 TCCAGGTCTCTCTGTATTCATCCTGCTGATTGTTTCTTACAGAACAATAC 957199 v iv v i v iv iivi i v v vvvv v C L1ME5_3end#LI 598 TCCATGTTGCTATGTGTACATCTAGTCCGTTGCTTCTAACTGCTGCATAG 549 chr4qtel1M 957200 TATTTTGTAGCACTCATATACCACATATGCATATCCAGCCATTCTCCAAC 957249 i iii i iiiv vi v --- i i v i v v C L1ME5_3end#LI 548 TACTCCATGGTGTGCATCCACCACATTT---TACCTATCCACTCTCCCAG 502 chr4qtel1M 957250 TGATGGGCATCCACTAAGTTTCCATTTTCTTGCCACTCCAACAAGGGCTG 957299 i i vvvv ii vi i ii iv vv iv C L1ME5_3end#LI 501 TGATGGACACCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCTG 452 chr4qtel1M 957300 CCACAAACCTTTTTGCATATTCGGGTCTCTTTTT---CTCATTTAAGA-T 957345 v ii v ii i i i ---- i i v --- iii v i - C L1ME5_3end#LI 451 CAATGAACATCCTCGTACAT----GTCCCCTTATGGACCTGTGTGAGAAT 406 chr4qtel1M 957346 TACTTTTGAA-ATAAGTCCAATGGAAGCACTGCCAGATAAAAAAGATATT 957394 v v i - vii ivi vi v i ii i v v ii - v C L1ME5_3end#LI 405 TTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGG-TATG 357 chr4qtel1M 957395 CACGT-TTTGATAGCCCTTTGGGCA--TAGTTCCAAATTTCTCTCCACAA 957441 iii -i i ------ ivi -- v v i v v C L1ME5_3end#LI 356 CGTATACTTAAT------TTGACTAAGTACTGCCAGATTGCTCTCCAGAA 313 chr4qtel1M 957442 TGGTTGAATCAGTCCACAACTACACCATCAATGTATTAGTGTCCCAGTTT 957491 i v i i viiv v i i v v i vi ? C L1ME5_3end#LI 312 TGGCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATNT 263 chr4qtel1M 957492 TCCCACATCCATTCCAACTTTCATCATTGTCT--TTTTCTGTCATCTCAG 957539 i viv vi iiv i i--i i-- i iv C L1ME5_3end#LI 262 CCCCACATCCTCGCCAACACTTGGCATTATCCAGCTTTCTA--ATTTTTG 215 chr4qtel1M 957540 ACACTCTGAGAGTTATGTAGTGGTACCTCAGAGTTGTATTAATTTACATT 957589 v v i v v i iv i i vv v i C L1ME5_3end#LI 214 CCAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATT 165 chr4qtel1M 957590 TCTCTGATCAATAGTGACTTAGAGCACCTTTTCATATGAGTGGAAATGGT 957639 i v i v v i i vv vv iivv C L1ME5_3end#LI 164 TCTCTGATTACTAATGAGTTTGAGCATCTCTTCATATGCTTGTTAGCCTT 115 chr4qtel1M 957640 TTTAATTTCTTCATTTGAAAATTGTCTGTTCATATCCTTTGGCCACTTAT 957689 ivii i v i v i v i v C L1ME5_3end#LI 114 TCGGGTTTCCTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCCATTTTT 65 chr4qtel1M 957690 TAATTGGAG 957698 iv i C L1ME5_3end#LI 64 CTATTGGGG 56 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 45.34 CpG sites = 103, Kimura (unadjusted) = 47.85 Transitions / transversions = 1.27 (103/81) Gap_init rate = 0.04 (22 / 548), avg. gap size = 1.18 (26 / 22) 16 19.66 0.00 0.00 chr4qtel1M 958555 958590 (41410) (ACAT)n#Simple_repeat 1 36 (0) m_b215s252i19 8504 chr4qtel1M 958555 ACATGCATATATATATATATACACACATACATTCAT 958590 i i i i i v (ACAT)n#Simpl 1 ACATACATACATACATACATACATACATACATACAT 36 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 18 24.62 0.00 4.00 chr4qtel1M 958561 958612 (41388) (AT)n#Simple_repeat 1 50 (0) m_b215s252i20 8504 chr4qtel1M 958561 ATATATATATATATACACACATACATTCATGTAAAAACTATGCTATATAT 958610 i i i i vi i v v - -v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATA-TAT-ATATATAT 48 chr4qtel1M 958611 AT 958612 (AT)n#Simple_ 49 AT 50 Matrix = Unknown Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.00 (2 / 2) 247 23.28 18.03 1.41 chr4qtel1M 959379 959500 (40500) C MIR3#SINE/MIR (1) 207 66 m_b215s601i17 8505 chr4qtel1M 959379 AATCAGGAAGTCACAAGATGT--GAGCTGAAAGAG-CCTT-CAGACTAAA 959424 vii i i ii -- i i - -v ii vv C MIR3#SINE/MIR 207 AATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATC 158 chr4qtel1M 959425 GAGTCCAACTCCTCCAATTTTAT--ATG----AAATGGAACACAGAGAAG 959468 v i ii - i-- ---- v iii v i C MIR3#SINE/MIR 157 TAGTCCAACCCCCTC-ATTTTACAGATGAGGAAACTGAGGCCCAGAGAGG 109 chr4qtel1M 959469 TGA-------TGCCCAAAGGT--CATAGCCG---AGTGTCAGAG 959500 ------- - -- i ?i--- v C MIR3#SINE/MIR 108 TGAAGTGACTTGCCC-AAGGTCACACAGCNAGTTAGTGGCAGAG 66 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.43 CpG sites = 20, Kimura (unadjusted) = 29.43 Transitions / transversions = 2.50 (20/8) Gap_init rate = 0.08 (10 / 121), avg. gap size = 2.40 (24 / 10) 218 32.34 1.75 10.48 chr4qtel1M 961787 961900 (38100) MIRc#SINE/MIR 11 115 (153) m_b215s601i18 8506 chr4qtel1M 961787 TGGTAATAATAGAGAGAGCAATTCAGTCCCAGAAGTCAGGAGGAATTTGA 961836 i-i i i i v vv v i--- i i -ii i MIRc#SINE/MIR 11 TGGTG-CAGTGGAAAGAGCACTGGACTT---GGAGTCAGGAAGA-CCTGG 55 chr4qtel1M 961837 ATTCAA--CCCGGCCCCAGACATCATTTCCCAGCTGTGTGTGACTCTGAG 961884 i i -- i ii----i i v i -- ii i MIRc#SINE/MIR 56 GTTCGAGTCCCGGCTCTG----CCACTTACTAGCTGTGT--GACCTTGGG 99 chr4qtel1M 961885 CAAACATCATAACCCC 961900 iivv v i MIRc#SINE/MIR 100 CAAGTCACTTAACCTC 115 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.66 CpG sites = 25, Kimura (unadjusted) = 45.62 Transitions / transversions = 3.12 (25/8) Gap_init rate = 0.11 (12 / 113), avg. gap size = 1.08 (13 / 12) 25 28.47 2.56 3.45 chr4qtel1M 961967 962083 (37917) (TAAAA)n#Simple_repeat 1 116 (0) m_b215s252i21 8507 chr4qtel1M 961967 TAAAAACAAACAAACTAGAAT-AAATGAACAAAACAAAAATAAGTACAAA 962015 vv i v i - i vv vv -v i (TAAAA)n#Simp 1 TAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAA-AATAAA 49 chr4qtel1M 962016 AGACAAGATATCAAATTAGAAGGAAAAT-AAATAAATTTGAAATAAAATA 962064 v v v v vi v - iv - -v i - (TAAAA)n#Simp 50 ATAAAATAAAATAAAATA-AAATAAAATAAAATAAA-ATAAAATAAAAT- 96 chr4qtel1M 962065 AAAATGACA-AAACTAAAAT 962083 i v - v (TAAAA)n#Simp 97 AAAATAAAATAAAATAAAAT 116 Matrix = Unknown Transitions / transversions = 0.44 (8/18) Gap_init rate = 0.06 (7 / 116), avg. gap size = 1.00 (7 / 7) 17 27.13 3.09 5.26 chr4qtel1M 961970 962066 (37934) (AAAT)n#Simple_repeat 1 95 (0) m_b215s252i22 8507 chr4qtel1M 961970 AAACAAACAAACTAGAATAAATGAACAAA-ACAAAAATAAGTACA-AAAG 962017 i i - - i i - v v i v - v (AAAT)n#Simpl 1 AAATAAATAAA-TA-AATAAATAAATAAATAAATAAATAAATAAATAAAT 48 chr4qtel1M 962018 ACAAGATATCAAATTAGAAGGAAAATAAATAAAT-TTGAAATAAAATAAA 962066 - v v - v iv iiv -vvv - (AAAT)n#Simpl 49 A-AATAAAT-AAATAAATAAATAAATAAATAAATAAATAAAT-AAATAAA 95 Matrix = Unknown Transitions / transversions = 0.67 (8/12) Gap_init rate = 0.08 (8 / 96), avg. gap size = 1.00 (8 / 8) 21 15.37 0.00 0.00 chr4qtel1M 964326 964361 (35639) (GA)n#Simple_repeat 1 36 (0) m_b216s252i2 8508 chr4qtel1M 964326 GAGAAAGAGAAAGAGAGAGAGAGAGAGTGTGTGAGA 964361 i i v v v (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 36 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 13 19.94 5.00 0.00 chr4qtel1M 966926 966965 (33035) (CCCT)n#Simple_repeat 1 42 (0) m_b216s252i3 8509 chr4qtel1M 966926 CCGTCACTTCCT-TCTCCCTCCCACACTCACTCCCT-CCTCC 966965 v v i -i v v v - (CCCT)n#Simpl 1 CCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCC 42 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 256 18.97 10.00 1.15 chr4qtel1M 967637 967716 (32284) C MIR3#SINE/MIR (3) 205 119 m_b216s601i1 8510 chr4qtel1M 967637 TTATAGA-TCATA-AATGATCA---CTGGAAGG-ACCCAACAGGCCAG-- 967678 i - - - --- - iv v ii v-- C MIR3#SINE/MIR 205 TCATAGAATCATAGAATG-TCAGAGCTGGAAGGGACCTTAGAGATCATCT 157 chr4qtel1M 967679 AGTGTAACTCCCTCTTTTTACAGATTGGGAAACTTAAG 967716 vi i v vi v i C MIR3#SINE/MIR 156 AGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGG 119 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 22.08 CpG sites = 8, Kimura (unadjusted) = 22.08 Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.08 (6 / 79), avg. gap size = 1.50 (9 / 6) 435 18.52 2.70 7.55 chr4qtel1M 968119 968229 (31771) MIRc#SINE/MIR 10 115 (153) m_b216s601i2 8511 chr4qtel1M 968119 GTGGTGCAGTGGATAGAGTGCTGGCCCT--AGTCAGGGGGACCTGAGTTC 968166 v ii v i -- ii i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr4qtel1M 968167 AAATTCTGGGCCTCAAACACTTAAAACCTCCAGGTGTGTGACCCTGGGCA 968216 i i i i -- viv ------ i v i MIRc#SINE/MIR 60 GAGTCCCGG--CTCTGCCACTTA------CTAGCTGTGTGACCTTGGGCA 101 chr4qtel1M 968217 AGTCAC-TAACCCC 968229 - i MIRc#SINE/MIR 102 AGTCACTTAACCTC 115 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 19.36 CpG sites = 14, Kimura (unadjusted) = 21.86 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.09 (10 / 110), avg. gap size = 1.10 (11 / 10) 19 15.81 2.78 0.00 chr4qtel1M 968247 968282 (31718) (AT)n#Simple_repeat 1 37 (0) m_b216s252i4 8512 chr4qtel1M 968247 ATATATATATATATACATACACA-ATCTATATGTATA 968282 i i i - v i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATA 37 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) 242 31.55 6.01 0.33 chr4qtel1M 969909 970191 (29809) L1M4_orf2#LINE/L1 964 1262 (2032) m_b216s551i0 8513 chr4qtel1M 969909 AAAAAAATAGAAAAATAAATG--AAC-AAACCAAAAATAAGTACAAAAGA 969955 i v v iv -- - v ii i v iii L1M4_orf2#LIN 964 AAGAAACTAGAAAAAGAAGAGCAAACTAAACCCAAAGCAAGCAGAAGGAA 1013 chr4qtel1M 969956 CAAGATATTAAA-ATTAGAAGGGAAATAGATAAAATTGA-AATAAAA--- 970000 vi i v - iv i i v - i --- L1M4_orf2#LIN 1014 GGAAATAATAAAGATTAGAGCGGAAATAAATGAAATAGAGAATAGAAAAA 1063 chr4qtel1M 970001 -------GAAAAATGACAAAACTAAAAATGGCTTCTTTGTAATGATTCAT 970043 ------- vii i i i v v v v iv i L1M4_orf2#LIN 1064 CAATAGAGAAAATCAACGAAACCAAAAGTTGGTTCTTTGAAAAGATCAAC 1113 chr4qtel1M 970044 AAAGTGGAGAAAACCCTTAGCTAATCTGATCAAAAGGAAGAGAGCATAAA 970093 i v v - i iv i i ii i viv i L1M4_orf2#LIN 1114 AAAATTGACAAA-CCTTTAGCTAGACTGACCAAGAAAAAAAGAGAGAAGA 1162 chr4qtel1M 970094 ATCCAATCATTGAAATAGCAAATAGAAAAAATGAAATCACAAGAAAACCA 970143 v v i i i vivi ii i iiv v i v vvi v iv L1M4_orf2#LIN 1163 CTCAAATTACTAAAATCAGGAATGAAAGAGGGGACATTACTACCGACCTT 1212 chr4qtel1M 970144 GAAGAAATAAAAGGCATAATTGATACATAATAT--ACAATTTTATGCTAA 970191 iv i v v viiviv v -- v i L1M4_orf2#LIN 1213 ACAGAAATAAAAAGGATTATAAGGGAATACTATGAACAATTGTATGCCAA 1262 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.80 CpG sites = 50, Kimura (unadjusted) = 42.05 Transitions / transversions = 1.28 (50/39) Gap_init rate = 0.03 (8 / 282), avg. gap size = 2.25 (18 / 8) 420 28.40 6.78 5.70 chr4qtel1M 970357 970651 (29349) L1M1_orf2#LINE/L1 1545 1842 (1452) m_b216s551i1 8514 chr4qtel1M 970357 CCCAATACTGAAACCAAGGAAAGTC-CAACCAGAGAGTAAAATTACAAGT 970405 ii ii iiv v - v v i i iv i i i L1M1_orf2#LIN 1545 CCTGATACCAAAACCAGACAAAGACACATCAAAAAAAGAAAACTACAGGC 1594 chr4qtel1M 970406 CAAAG-----AATGAATGTTGTCTCCTCCCTCCAA---TTTTAAACAAAA 970447 vi-----i i --------v v --- ii v L1M1_orf2#LIN 1595 CAATATCTCTGATGAATATTG--------ATGCAAAAATCCTCAACAAAA 1636 chr4qtel1M 970448 TCCTATCAAAACAA---CTACAGTAAATTATCTAAGATACCATTCATTAT 970494 v v v i --- v i v --- i v i i L1M1_orf2#LIN 1637 TACTAGCAAACCGAATTCAACAATACATTA---AAAAGATCATTCATCAT 1683 chr4qtel1M 970495 GATCAAGTGGGATTTCTACCAGGGATGGAAAGATAGTTCAACATTAGGAA 970544 i v v ? v i i vv v L1M1_orf2#LIN 1684 GACCAAGTGGGATTTATCCCNGGGATGCAAGGATGGTTCAACATACGCAA 1733 chr4qtel1M 970545 AACAATGAACATAATTAATCACATTGTAAACCACAACAT------CCAAA 970588 v v ii i vv i ------ v iv ------ v L1M1_orf2#LIN 1734 ATCAATCAATGTGATACATCATAT------CAACAGAATGAAGGACAAAA 1777 chr4qtel1M 970589 ACCACA--GTCAATTCAATAGATAAAGAGAATGCTTTGGACAAAGTACCA 970636 i --i v v ivv i v v v i i v v L1M1_orf2#LIN 1778 ACCATATGATCATTTCAATTGATGCTGAAAAAGCATTTGATAAAATTCAA 1827 chr4qtel1M 970637 CACTCTTTTGTAATA 970651 ii i ii i L1M1_orf2#LIN 1828 CATCCCTTCATGATA 1842 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.90 CpG sites = 42, Kimura (unadjusted) = 36.48 Transitions / transversions = 1.14 (42/37) Gap_init rate = 0.08 (23 / 294), avg. gap size = 1.61 (37 / 23) 524 24.97 7.11 4.49 chr4qtel1M 970434 970672 (29328) L1M2_orf2#LINE/L1 1620 1864 (1427) m_b216s551i2 8514 chr4qtel1M 970434 AATTTTAAACAAAATCCTATCAAAACAA---CTACAGTAAATTATCTAAG 970480 ii v v v v i --- v i v --- i L1M2_orf2#LIN 1620 AATCCTCAACAAAATACTAGCAAACCGAATTCAACAGCACATTA---AAA 1666 chr4qtel1M 970481 ATACCATTCATTATGATCAAGTGGGATTTCTACCAGGGATGGAAAGATAG 970530 v i? ? ii v v v i i L1M2_orf2#LIN 1667 AGATNATNCACCATGATCAAGTGGGATTTATCCCAGGGATGCAAGGATGG 1716 chr4qtel1M 970531 TTCAACATTAGGAAAACAATGAACATAATTAATCACATTGTAAACCACAA 970580 vv v v i i i vv ------ v i L1M2_orf2#LIN 1717 TTCAACATACGCAAATCAATAAACGTGATACATCACAT------CAACAG 1760 chr4qtel1M 970581 CAT------CCAAAACCACA--GTCAATTCAATAGATAAAGAGAATGCTT 970622 v ------ v i --i vi iv i v v L1M2_orf2#LIN 1761 AATGAAGGACAAAAACCATATGATCATCTCAATAGATGCAGAAAAAGCAT 1810 chr4qtel1M 970623 TGGACAAAGTACCACACTCTTTTGTAATAGACATTT------AATTAGAA 970666 v i i v v ii i ii i i v i i------ -- L1M2_orf2#LIN 1811 TTGATAAAATTCAACATCCCTTCATGATAAAAACTCTCAACAAATTAG-- 1858 chr4qtel1M 970667 GTATAG 970672 L1M2_orf2#LIN 1859 GTATAG 1864 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 29.85 CpG sites = 30, Kimura (unadjusted) = 31.13 Transitions / transversions = 1.11 (30/27) Gap_init rate = 0.06 (15 / 238), avg. gap size = 1.87 (28 / 15) 225 22.73 3.03 0.00 chr4qtel1M 975687 975752 (24248) C L1MEj_5end#LINE/L1 (1240) 920 853 m_b216s551i3 8515 chr4qtel1M 975687 TTCAGGAAATCCAATAATTCTAAAATTATCTCTCCTAGATCTATTTTCCA 975736 v v v v vv vi vv i ii C L1MEj_5end#LI 920 TTCTGGAACTCCTATTATTCGCATGTTAGGTCTCCTGGATCTATCCTCCA 871 chr4qtel1M 975737 AGTCTGTTG--TTTTCCC 975752 v i-- C L1MEj_5end#LI 870 AGTCTCTTATCTTTTCCC 853 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 27.08 CpG sites = 5, Kimura (unadjusted) = 27.08 Transitions / transversions = 0.50 (5/10) Gap_init rate = 0.02 (1 / 65), avg. gap size = 2.00 (2 / 1) 16 9.78 0.00 0.00 chr4qtel1M 975770 975791 (24209) (T)n#Simple_repeat 1 22 (0) m_b216s252i5 8516 chr4qtel1M 975770 TTTTTTTTTTTTTTTTGGTTTT 975791 vv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTT 22 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 17 18.17 0.00 0.00 chr4qtel1M 976331 976361 (23639) (A)n#Simple_repeat 1 31 (0) m_b216s252i7 8517 chr4qtel1M 976331 AAAAAAGAAACAAAGAAAACAAACAAAAAAA 976361 i v i v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 31 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 282 28.03 16.43 0.62 chr4qtel1M 977637 977776 (22224) L2a_3end#LINE/L2 356 517 (0) m_b216s601i3 8518 chr4qtel1M 977637 TTCTATTTCATTATTGGTGAGTTGTCTG-----CTTCACCAGTCTATGAC 977681 i i vv v vvi ----- ii i vv i i v L2a_3end#LINE 356 TTTTACTTATTTATTTGTTTATTGTCTGTCTCCCCCCACTAGAATGTAAG 405 chr4qtel1M 977682 CTCCCTGAGAGCAGGGGA---TATCCCTTTTGTTC-CTG----------- 977716 v i iv--- i iv - ----------- L2a_3end#LINE 406 CTCCATGAGGGCAGGGACTTTTGTCTGTTTTGTTCACTGCTGTATCCCCA 455 chr4qtel1M 977717 GTGCTTAGTCCAAAGTCTGGCATGTAGCAGGCACT---TAAATGTTTGCT 977763 i i vv iv i ii i i --- i i L2a_3end#LINE 456 GCGCCTAGAACAGTGCCTGGCACATAGTAGGCGCTCAATAAATATTTGTT 505 chr4qtel1M 977764 GACTTGAAGAAAT 977776 v- vi L2a_3end#LINE 506 GAA-TGAATGAAT 517 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.79 CpG sites = 23, Kimura (unadjusted) = 36.07 Transitions / transversions = 1.44 (23/16) Gap_init rate = 0.04 (6 / 139), avg. gap size = 4.00 (24 / 6) 338 28.95 3.39 3.39 chr4qtel1M 977659 977776 (22224) L2c_3end#LINE/L2 361 478 (0) m_b216s601i4 8518 chr4qtel1M 977659 TGTCTGCTTCACCAGTCTATGACCTCCCTGAGAGCAGGGGATATCCCTT- 977707 v i i v i v i i ivii vi - L2c_3end#LINE 361 TGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTA 410 chr4qtel1M 977708 TTGTTCCTGGTGCTTAGTCCAAAGTCTGGCATGTAGCAGGCACT---TAA 977754 vv i v iii---i iv i ii i i --- L2c_3end#LINE 411 TTCATCTTTGTATC---CCCAGCGCCTGGCACATAGTAGGCGCTCAATAA 457 chr4qtel1M 977755 ATGTTTGCTGACTTGAAGAAAT 977776 i v- vi L2c_3end#LINE 458 ATGTTTGTTGAA-TGAATGAAT 478 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.17 CpG sites = 22, Kimura (unadjusted) = 38.29 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.05 (6 / 117), avg. gap size = 1.33 (8 / 6) 368 33.91 5.25 2.68 chr4qtel1M 978783 979182 (20818) L1ME5_3end#LINE/L1 232 641 (300) m_b216s551i4 8519 chr4qtel1M 978783 GATAATAT-AAATGTTGGAGGGGATGTGGGAAAGCTGGGACACTAATAAA 978831 ii- i v i i ?iiv i v v iv L1ME5_3end#LI 232 GATAATGCCAAGTGTTGGCGAGGATGTGGGGANATAGGAACCCTCATGCA 281 chr4qtel1M 978832 CTCGTGAT-GGAG-------TTGTG-AATCATTTTGGAGAGCTCTTTGGA 978872 vv i - ------- v - ii i vv i v L1ME5_3end#LI 282 CTGCTGGTGGGAGTGTAGACTGGTGCAGCCATTCTGGAGAGCAATCTGGC 331 chr4qtel1M 978873 ACTA--TGCCCACAGGAATTTCAAACTGCATACCCTTTGCACCAACAGGG 978920 v -- ivi v vv v -- v - v vv i ivv L1ME5_3end#LI 332 AGTACTTAGTCAAATTAAGT--ATAC-GCATACCCTATGACCCAGCAATT 378 chr4qtel1M 978921 CCTCTACAGGATCTATATACCAGAGAAATCATAAAAAAGA--GAAAAGGA 978968 v v v i v v i iv v v v i--v v i L1ME5_3end#LI 379 CCGCTCCTGGGTATATATCCCAAAGAAATTCTCACACAGGTCCATAAGGG 428 chr4qtel1M 978969 ACTACATGTATAAACACCTTTTGTGGCAGCCTTCTTTGTGATGGCTAAGA 979018 i-- ii iv -iv ii v v v i vii L1ME5_3end#LI 429 G--ACATGTACGAGGA-TGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGA 475 chr4qtel1M 979019 ACTGAAAACTGAGTGGATGCCCATCAGTTAGGGGATGGCAGAATAAGTTA 979068 ii i ii vivv i i v vi i ii vviii iv i L1ME5_3end#LI 476 GTTGGAGGCAACCTGGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATG 525 chr4qtel1M 979069 TGGTATATGAATCTAATGGAATATTATTATTCTATAAGAAACAATCAACA 979118 iv v iviv i i vvvv vi v i ivi v L1ME5_3end#LI 526 TGGTGGATGCACACCATGGAGTACTATGCAGCAGTTAGAAGCAACGGACT 575 chr4qtel1M 979119 GGATG---ATTTAAAAAATGCTTAGAGAGA-CTTACATGAAC-TGATGCT 979163 i --- iv iv --- v i vi - v -- - ii L1ME5_3end#LI 576 AGATGTACACATAGCAA---CATGGATGGATCTTAAA--AACATAGTGCT 620 chr4qtel1M 979164 GAGT-AAAAGAGT-AGAAACA 979182 - i - L1ME5_3end#LI 621 GAGTGAAAAAAGTAAGAAACA 641 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 45.17 CpG sites = 67, Kimura (unadjusted) = 46.16 Transitions / transversions = 1.03 (67/65) Gap_init rate = 0.06 (22 / 399), avg. gap size = 1.45 (32 / 22) 598 29.53 4.15 1.56 chr4qtel1M 978783 979095 (20905) L1ME3G_3end#LINE/L1 228 548 (376) m_b216s551i5 8519 chr4qtel1M 978783 GATAATAT-AAATGTTGGAGGGGATGTGGGAAAGCTGGGACACTAATAAA 978831 -? i v i i i i v v v v v L1ME3G_3end#L 228 GATAATATCNAGTGTTGGCGAGGGTGTGGGGAAACGGGTACTCTCATACA 277 chr4qtel1M 978832 CTCGTGATGGAGTTGTGAAT---------CATTTTGGAGAGCTCTTTGGA 978872 vv i iiv i --------- ? i vv v L1ME3G_3end#L 278 CTGCTGGTGGGAGTGTAAATTGGTACAGCCNTTTTGGAGGGCAATTTGGC 327 chr4qtel1M 978873 ACTATGCCCACAGGAATTTCAAAC-TGCATACCCTTTGCACCAACAGGGC 978921 v -- i ivii v i-i vv i ivv L1ME3G_3end#L 328 AGTAT--CTATTAAAATTTAAAATGCGCATACCCTTTGACCCAGCAATTC 375 chr4qtel1M 978922 CTCTACAGGATCTATATACCAGAGAAAT-CATAAAAAAGAGAA-AAGGAA 978969 v v v? i?v v v i ? - viiv v v v v - ? L1ME3G_3end#L 376 CACTTCTNGGNATCTATCCTANAGAAATACTCGCACATGTGCACAAGGAN 425 chr4qtel1M 978970 CTACATGTATAAACACCTTTTGTGGCAGCCTTCTTTGTGATGGCTAAGAA 979019 --i i iv iv i-i v v v i i v i L1ME3G_3end#L 426 --GCATGTACAAGGATGTTC-ATTGCAGCATTGTTTGTAATAGCGAAAAA 472 chr4qtel1M 979020 CTGAAAACTGAGTGGATGCCCATCAGTTAGGGGATGGCAGAATAAGTTAT 979069 i i vivv ii i i vi i ivi i L1ME3G_3end#L 473 TTGGAAACAACCTAAATGTCCATCAATAGGGGAATGGTTAAATAAATTAT 522 chr4qtel1M 979070 GGTATATGAATCTAATGGAATATTAT 979095 vv viv i L1ME3G_3end#L 523 GGTATATCCATACTATGGAATACTAT 548 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.87 CpG sites = 45, Kimura (unadjusted) = 39.00 Transitions / transversions = 0.98 (45/46) Gap_init rate = 0.03 (10 / 312), avg. gap size = 1.80 (18 / 10) 23 20.62 0.00 0.00 chr4qtel1M 979362 979406 (20594) (T)n#Simple_repeat 1 45 (0) m_b216s252i8 8520 chr4qtel1M 979362 TTTTTTGTTTGTTTTCTTTTTTTTTCTTTCTTTTTATTCCTTTTT 979406 v v i i i v ii (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 45 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 13 13.26 6.06 0.00 chr4qtel1M 979749 979781 (20219) (TACACA)n#Simple_repeat 1 35 (0) m_b216s252i9 8521 chr4qtel1M 979749 TACATATATACATTAACAT--ACATACACATACAC 979781 i i vv -- (TACACA)n#Sim 1 TACACATACACATACACATACACATACACATACAC 35 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.03 (1 / 32), avg. gap size = 2.00 (2 / 1) 241 30.12 0.00 0.00 chr4qtel1M 980458 980540 (19460) C L1M4a2_5end#LINE/L1 (903) 1753 1671 m_b216s551i6 8522 chr4qtel1M 980458 TGAATTGTTTTTTTCTTGTTTCTTGCAAAAGCTTCTCTTTGATCTGGGAG 980507 i i i i v v i vi vii v vv C L1M4a2_5end#L 1753 TGAGTCGTTTTTCTCTTGCTGCTTTCAAGATTTTCTCTTTGTCTTTGGCT 1704 chr4qtel1M 980508 TTTAAAAATTTGGCAATAATATTCCTATGTGTG 980540 i v i i v i i vi v C L1M4a2_5end#L 1703 TTCAACAGTTTGACTATGATGTGTCTAGGTGTG 1671 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.43 CpG sites = 14, Kimura (unadjusted) = 39.43 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.00 (0 / 82), avg. gap size = 0.0 (0 / 0) 16 21.50 2.00 2.00 chr4qtel1M 980772 980821 (19179) (TATTTCT)n#Simple_repeat 1 50 (0) m_b216s252i11 8523 chr4qtel1M 980772 TATTTTTTCATTCTT-TATCTTTTTTGTTATTTCTTGGTTTCTCATATCT 980820 i vv - v v v -i i v (TATTTCT)n#Si 1 TATTTCTTATTTCTTATTTCTTATTTCTTATTTCTT-ATTTCTTATTTCT 49 chr4qtel1M 980821 T 980821 (TATTTCT)n#Si 50 T 50 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.04 (2 / 49), avg. gap size = 1.00 (2 / 2) 19 23.26 5.71 0.00 chr4qtel1M 980940 981009 (18991) (TTTTATT)n#Simple_repeat 1 74 (0) m_b216s252i12 8524 chr4qtel1M 980940 TTTGATTTTTTA-TTTTTCTTCAATGTCTCTCATTTGAT-TTTTGGATTT 980987 v - v ivv i i i i vv - vv (TTTTATT)n#Si 1 TTTTATTTTTTATTTTTTATTTTTTATTTTTTATTTTTTATTTTTTATTT 50 chr4qtel1M 980988 TTT-TTTTTT-TTTTTTAGTTTTT 981009 - - v (TTTTATT)n#Si 51 TTTATTTTTTATTTTTTATTTTTT 74 Matrix = Unknown Transitions / transversions = 0.56 (5/9) Gap_init rate = 0.06 (4 / 69), avg. gap size = 1.00 (4 / 4) 20 32.18 0.00 0.00 chr4qtel1M 980945 981009 (18991) (TT)n#Simple_repeat 1 65 (0) m_b216s252i13 8524 chr4qtel1M 980945 TTTTTTATTTTTCTTCAATGTCTCTCATTTGATTTTTGGATTTTTTTTTT 980994 v i ivv v i i iv vv vvv (TT)n#Simple_ 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr4qtel1M 980995 TTTTTTTTAGTTTTT 981009 vv (TT)n#Simple_ 51 TTTTTTTTTTTTTTT 65 Matrix = Unknown Transitions / transversions = 0.42 (5/12) Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0) 1249 28.76 2.23 2.85 chr4qtel1M 981195 981688 (18312) L1ME5_3end#LINE/L1 152 642 (299) m_b216s551i7 8525 chr4qtel1M 981195 TATTGATCAGAGAAATGCAAATTAAGACAACTCTGAGATACCACTATATA 981244 v i i vv i v i L1ME5_3end#LI 152 TAGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACA 201 chr4qtel1M 981245 CCTGTCAGATTGGCCAGAATGACAGGGAAAGATAATGCAGAATGTTGGAG 981294 i i i v i v v ii vvi vi i v L1ME5_3end#LI 202 CCTATTAGACTGGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTGGCG 251 chr4qtel1M 981295 GGGATGTGGGAAAACAGGGACACTTGATACATTGTTGGTGGAATTGTGAA 981344 i i ? i i - i v i i i i v ii L1ME5_3end#LI 252 AGGATGTGGGGANATAGGAAC-CCTCATGCACTGCTGGTGGGAGTGTAGA 300 chr4qtel1M 981345 TACATCCAGCCATTCTGGAGAGCAATTTGGAATTA--TGCCCAAA--AAG 981390 ivvi v i v v -- ivi -- L1ME5_3end#LI 301 CTGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTAAG 350 chr4qtel1M 981391 TTATCAAACTGTGCATACCCTTTGATAAAGCAGTGTCTCTACTGGGCTTA 981440 - --- --- v ivv i vi v v iv L1ME5_3end#LI 351 -TAT---AC---GCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATA 393 chr4qtel1M 981441 TACCCCAAAGAGATACTAAAAAAG----AGAAAGGGACCTGTATGTACCA 981486 i i v v v v ---- v i ---- v L1ME5_3end#LI 394 TATCCCAAAGAAATTCTCACACAGGTCCATAAGGGGAC----ATGTACGA 439 chr4qtel1M 981487 AAATGTTTGTGGCAGCCCTGTTTGTAGTGGCCAGAAGCTAGAAAATGAAT 981536 ii ii v vi i vi i i i iivvivv L1ME5_3end#LI 440 GGATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCT 489 chr4qtel1M 981537 GGATGCCCATCAATTGGAGAATGGTTGAGTAAATTGTGGTATATGAATGT 981586 i i v v i v ii v iv v iii L1ME5_3end#LI 490 GGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACAC 539 chr4qtel1M 981587 TATGGAATATTATTGTTCTGTAAGAAGTGACCAGCAGGACGAATACAGAG 981636 i i i vvvv v v ii vii vi i v i v L1ME5_3end#LI 540 CATGGAGTACTATGCAGCAGTTAGAAGCAACGGACTAGATGTACACATAG 589 chr4qtel1M 981637 -AAGATTGGCGAGACTTACATGAAC-TGATGCTGAGCGAAATGAGC-AGA 981683 - v v ii iiv v -- - ii i vi i- L1ME5_3end#LI 590 CAACATGGATGGATCTTAAA--AACATAGTGCTGAGTGAAAAAAGTAAGA 637 chr4qtel1M 981684 ACCAG 981688 v L1ME5_3end#LI 638 AACAG 642 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.14 CpG sites = 77, Kimura (unadjusted) = 37.14 Transitions / transversions = 1.26 (77/61) Gap_init rate = 0.04 (20 / 493), avg. gap size = 1.25 (25 / 20) 42 0.00 4.65 0.00 chr4qtel1M 982268 982310 (17690) (AC)n#Simple_repeat 1 45 (0) c_b216s251i0 8526 chr4qtel1M 982268 ACACACACACACACACACACACACACACACACAC-CACAC-CACA 982310 - - (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACA 45 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.00 (2 / 2) 205 34.29 1.43 0.00 chr4qtel1M 982343 982412 (17588) C L2d_3end#LINE/L2 (0) 516 446 m_b216s601i5 8527 chr4qtel1M 982343 TCAAT-AATAAATCAATGAAGACTGATTGCATGCCTACTATATACCAACT 982391 - v ii iv i v vii i i iv vi C L2d_3end#LINE 516 TCAATCAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGC 467 chr4qtel1M 982392 GCTGTAATAAGTGCAGAGAGG 982412 i iv i i v v i C L2d_3end#LINE 466 ACTGTGCTAGGCGCTGTGGGG 446 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.66 CpG sites = 15, Kimura (unadjusted) = 48.16 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.01 (1 / 69), avg. gap size = 1.00 (1 / 1) 15 22.57 4.17 2.04 chr4qtel1M 982672 982719 (17281) (AT)n#Simple_repeat 1 49 (0) m_b216s252i14 8528 chr4qtel1M 982672 ATATA-ATATATAT-TAAACATATACTATTCTTCTATATATCCATATTTA 982719 - - v i - viv v vi v (AT)n#Simple_ 1 ATATATATATATATATATATATATA-TATATATATATATATATATATATA 49 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.06 (3 / 47), avg. gap size = 1.00 (3 / 3) 13 15.78 6.82 2.17 chr4qtel1M 982906 982949 (17051) (TAGAA)n#Simple_repeat 1 46 (0) m_b216s252i15 8529 chr4qtel1M 982906 TACAATACAA-AGAGATAGAATAGAGGAGAGAAGAA-AGAATA-AAT 982949 v v - - iv iv - - (TAGAA)n#Simp 1 TAGAATAGAATAGA-ATAGAATAGAATAGAATAGAATAGAATAGAAT 46 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.09 (4 / 43), avg. gap size = 1.00 (4 / 4) 17 7.81 0.00 0.00 chr4qtel1M 984477 984503 (15497) (TTTTG)n#Simple_repeat 1 27 (0) m_b216s252i16 8530 chr4qtel1M 984477 TTTTGTTTTGTTTTGTTTTGCTTTTTT 984503 i v (TTTTG)n#Simp 1 TTTTGTTTTGTTTTGTTTTGTTTTGTT 27 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 220 26.79 1.79 0.00 chr4qtel1M 986842 986897 (13103) L3#LINE/CR1 4019 4075 (24) m_b216s601i6 8531 chr4qtel1M 986842 AAGAGATACCTGTGCAGG-TATGAGTTTGGACTAGAGGGCCTCTGAAGCC 986890 i v iiiv - iv v v i i i i L3#LINE/CR1 4019 AAGGGATTCCTGCATTGGATGGGAGGTTGGACTAGATGACCTCTAAGGTC 4068 chr4qtel1M 986891 TCTTCCA 986897 i L3#LINE/CR1 4069 CCTTCCA 4075 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.49 CpG sites = 10, Kimura (unadjusted) = 34.49 Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.02 (1 / 55), avg. gap size = 1.00 (1 / 1) 3091 29.35 2.70 2.08 chr4qtel1M 989638 991119 (8881) C L1M5_orf2#LINE/L1 (976) 2318 828 m_b216s551i8 8532 chr4qtel1M 989638 AGATAGATTCCCAAATATTTTATACTAGCGGCAGTTACTTTAAATGGAAT 989687 vv i i ? ii vviv vv i i v v C L1M5_orf2#LIN 2318 AGATTTATTCCTAAGTATTTNATGTTTTTTGATGCTATTGTAAATGGTAT 2269 chr4qtel1M 989688 TTCTCTTTGTATCTCTAACTGTTGGATT--TTGTCAGTGATATATAAGAA 989735 vi i ?iv i -- i v ivi -- iiv ii ii C L1M5_orf2#LIN 2268 TGTTTTTNAAATTTC--ATTTTCCAATTGTTTGTTGCTAGTATATAGAAA 2221 chr4qtel1M 989736 TGC---TGAGCATTTATGTGGGTTTATTTTGTATCCTGTAACTTTGCTAA 989782 i --- --- v ivi v ii ? ii i C L1M5_orf2#LIN 2220 TACAATTGA---TTTTTGTATATTGACCTTGTATCCNGCGACCTTGCTAA 2174 chr4qtel1M 989783 AGTTGTGAATTATTTCTAATAACTTTTTAGTAGAATCTCTGGAGTTCTCT 989832 v iiivv v i ii ? v v i ? ii i C L1M5_orf2#LIN 2173 ATTCACTTATTAGTTCTAGTAGTTTNTTTGTAGATTCTTTNGGATTTTCT 2124 chr4qtel1M 989833 AAGTATACCATCATATCATCTGCAAAGAGTGATAATTTGATTTCCTCATT 989882 v ? v i i v i? i i v i v C L1M5_orf2#LIN 2123 ACGTANACAATCATGTCATCTGCGAATAANGACAGTTTTATTTCTTCCTT 2074 chr4qtel1M 989883 ACCTACTCTAATTCCTTTAATCTCTTCCTCAACTCTTATGGCAAAAGCTA 989932 v v iii v v v i ii vvvi v vvi C L1M5_orf2#LIN 2073 TCCAATCTTTATGCCTTTTATTTCTTTTTCTTGCCTTATTGCACTGGCTA 2024 chr4qtel1M 989933 GCCATTCTAATACAATATTGAATAGTATTGGTGATAGTGGGCAACCTTGT 989982 vvvi i i i v v ? i i v C L1M5_orf2#LIN 2023 GGACCTCCAGTACAATGTTGAATAGAAGTGGTGANAGCGGACATCCTTGT 1974 chr4qtel1M 989983 TTCACTACTGATCTTACTGGGAATGGTTCCAATTTATCCCCATTACATAT 990032 i iii v i vv v v? i i ? v v vi C L1M5_orf2#LIN 1973 CTTGTTCCCGATCTTAGGGGGAAAGCNTTCAGTNTTTCACCATTAAGTAT 1924 chr4qtel1M 990033 GATGCTCACTGATGGTTTTAAATAGATGCTACTCACTATTTTAAGGAAAA 990082 i ?i vv vvi ivi i ii vv i iv C L1M5_orf2#LIN 1923 GATGTTNGCTGTAGGTTTTTCGTAGATGCCCTTTATCAGGTTGAGGAAGT 1874 chr4qtel1M 990083 GTCCTTTTATTTCTAAAT--------GTCTTTAATAGGAATGGATGTTGA 990124 vi i i iv -------- i vi v i C L1M5_orf2#LIN 1873 TCCCTTCTATTCCTAGTTTGCTGAGAGTTTTTATCATGAATGGGTGTTGA 1824 chr4qtel1M 990125 ATTTTATCAAATACTTTTTCTACATCTATTGAGATGATCATATGGTTTTT 990174 i i i i C L1M5_orf2#LIN 1823 ATTTTGTCAAATGCTTTTTCTGCATCTATTGAGATGATCATATGATTTTT 1774 chr4qtel1M 990175 GTTAACTTGGTT--ATTGATATAGTCAGTTATGCTAATAGTTTTCCTAAT 990222 v i-- vi --i i i v i iii i v v i v C L1M5_orf2#LIN 1773 CTC--CTTTATTCTGTTAATATGGTGAATTACATTGATTGATTTTCGAAT 1726 chr4qtel1M 990223 ATTGAACCAGCCCTGCATTCCTGGTATAAATCCTACTTGGTCATGATATG 990272 i i i i v i i i i C L1M5_orf2#LIN 1725 GTTAAACCAACCTTGCATTCCTGGGATAAACCCCACTTGGTCATGATGTA 1676 chr4qtel1M 990273 TTATGCTAGGGATGATTTTCTGTAATCTTTTTGCTAATATTTTATTTAAG 990322 v vvvv ivv v v v vv i ? i C L1M5_orf2#LIN 1675 TTATCCTTTTTATATATTGCTGGATTCGATTTGCTAATATTTTGTTNAGG 1626 chr4qtel1M 990323 ATTTTAGCATTGATATTCATTAGGGGGATTTGTGCATAATTTTCTTT-CT 990371 v iv i v iv v vii - C L1M5_orf2#LIN 1625 ATTTTTGCATCTATGTTCATGAGGGATATTGGTCTGTAATTTTCTTTTCT 1576 chr4qtel1M 990372 CG----GTTTTCAACCTACCTGGTTTAGTTATGACTACCATGTCTGTGTC 990417 i ---- i ----- ii ? v v v vvii? iiv iv C L1M5_orf2#LIN 1575 TGTAATGTCTT-----TGTCNGGTTTTGGTATCAGGGTNATGCTGGCCTC 1531 chr4qtel1M 990418 ATAAAAGAAATTTAGTAGGAGTCTTTCATTCCCTATTTTTTCAAATAGTT 990467 vi i vi v viv ii v ii i vi v C L1M5_orf2#LIN 1530 ATAAAATGAGTTGGGAAGTGTTCCCTCTTTTTCTATTTTCTGGAAGAGTT 1481 chr4qtel1M 990468 TATATAACATTGGAGTTCATTATTCTTTAAATGTTTGGTAGAATTCACAT 990517 i i v vi vv v i vv C L1M5_orf2#LIN 1480 TGTGTAAGATTGGTATTATTTCTTCCTTAAATGTTTGGTAGAATTCACCA 1431 chr4qtel1M 990518 GTAAATCTACCTGGTCTTGGAGATTTTTTTCTTAGGGAGTTGATTAATAG 990567 i v i i v i - i iv i i v vv vi C L1M5_orf2#LIN 1430 GTGAAGCCATCTGGGCCTGGAG-TTTTCTTTGTGGGAAGGTTTTTAATTA 1382 chr4qtel1M 990568 CTTGTTCTATTTCTTTTTCTGAAATGGGACTATTTAAGCAACTTACTTCC 990617 vvi v vviv v i i i iiivvii i i C L1M5_orf2#LIN 1381 CAAATTCAATTTCTTTAATAGATATAGGGCTATTCAGATTTTCTATTTCT 1332 chr4qtel1M 990618 TCCTCTGTTAATCTGGGAAGCCTATATTTTT-AAGGTAGTCTTTTTTTTC 990666 i v? i i i v v i?i i i - v v iv iiv C L1M5_orf2#LIN 1331 TCTTGNGTCAGTTTTGGTAANTTGTGTTTTTCAAGGAATTTGTCCATTTC 1282 chr4qtel1M 990667 ACTTAGGTTATCAAATTTATTGGCATAAAGTTGGGCAAAGTAACTCCTAA 990716 ii i ? vv v i viii v C L1M5_orf2#LIN 1281 ATCTAAGTTNTCAAATTTATTGGCATAAAGTTGTTCATAATATTCTCTTA 1232 chr4qtel1M 990717 TTATTGCATTAATTTCC------TCTTCACTGGTGGAAAGTTCTCCCTTT 990760 iviv v i------ vi v i ------ i C L1M5_orf2#LIN 1231 TTATCCTTTTAATGTCTGTAGGATCTGTAGTGATG------TCTCCTTTT 1188 chr4qtel1M 990761 TCATTTTTAAGACTAACAATTTGATTTTCCTCTTTCCTTTTTCTAATCAG 990810 ii i v i iii vv i i i ii ii i C L1M5_orf2#LIN 1187 TCATTCCTGATATTGGTAATTTGTGTCTTCTCTCTTTTTTTCTTGATCAG 1138 chr4qtel1M 990811 ATTTACCTAACATTTATCTATTTTGTTGGTCTTTTCATAATACCAACTGT 990860 vi ?i ivi vi v i i v iv i v C L1M5_orf2#LIN 1137 TCTNGCTAGAGGTTTATCAATTTTATTGATCTTTTCAAAGAACCAGCTTT 1088 chr4qtel1M 990861 TAGTTTTATTTATTAATTCAATAAT-TTTTTTTACTTTCAATTTTATCAA 990909 i i ii v -- vv v - ? ? ii v i ii C L1M5_orf2#LIN 1087 TGGCTTCGTTGATT--TTCTCTATTGTNTNTTTGTTTTCTATTTCATTGA 1040 chr4qtel1M 990910 TTTCTCCTTTTAATTTTAGAATTTCAAGTTTAGCATGTTATTAAGCATT- 990958 v i vi vv ---i -- v vi i -v? v - C L1M5_orf2#LIN 1039 TTTCTGCTCTTATCTTTATTATTTC---CTT--CCTTCTACT-TNCTTTG 996 chr4qtel1M 990959 --TTCAATTTGC---TTTTTTTCTATCTTTTTAAGTTGCAAGCC--GATT 991001 -- i --- i v i v v i-- - C L1M5_orf2#LIN 995 GGTTTAATTTGCTCTTCTTTTTCTAGCTTCTTAAGGTGGAAGCTTAGA-T 947 chr4qtel1M 991002 TATTGACTTT---CTCTTTTTCTATTTT-ATTCAAGTAACCTCTAAAAAT 991047 i i --- ii i v i - vi ? i --- i ?iv C L1M5_orf2#LIN 946 CATTGATTTTAAGCCTTTCTTCTTTTCTAATATANGCA---TTTAANGCT 900 chr4qtel1M 991048 ATAAATTTTCCCCTTTTTATAGCTTTGGCTATATCCCACAGATTTGGGTA 991097 i i vvvi iv i ii i v i C L1M5_orf2#LIN 899 ATAAATTTCCCTCTAAGCACTGCTTTAGCTGCATCCCACAAATTTTGATA 850 chr4qtel1M 991098 TGTTGTATCATTGTTGTCATTC 991119 iv ii ? C L1M5_orf2#LIN 849 TGTTGTATTTTCATTNTCATTC 828 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.36 CpG sites = 246, Kimura (unadjusted) = 39.10 Transitions / transversions = 1.37 (246/180) Gap_init rate = 0.03 (46 / 1481), avg. gap size = 1.54 (71 / 46) 256 33.86 5.35 2.07 chr4qtel1M 992115 992301 (7699) MamSINE1#SINE/tRNA-RTE 96 288 (2) m_b216s601i7 8533 chr4qtel1M 992115 TTCCATAAGC-CAGACCACTGTCATTGACCACGGCCAGCATCCTTGTAAA 992163 iiv - ii -ii vi i v i vvi i i MamSINE1#SINE 96 TTCCATGGCCACAGACTGC-ACCCCTAACCCCAGCCAGCCGTCTCGCAAA 144 chr4qtel1M 992164 ATGCAGGAATTTGGTCACCAGGAAGGCCCAGCACCAACTAATGGGTTGAC 992213 - iv vvv v i- v i vvi v i- i v ?i MamSINE1#SINE 145 -TGCGTGCCGTTGGTCACAAGGG-GGACCGGCAGAGAGTG-TGGATGGNT 191 chr4qtel1M 992214 CGCTGCAGGTCTCTCCCCACCATTG---ACACACGTCAAATGGAACGTGG 992260 ivi ii iv ? i i --- v vv vviv i vv MamSINE1#SINE 192 CAGCGCAAATCCATCNCCACTACTGGAAAAACAACTCAAAGCACATGTCC 241 chr4qtel1M 992261 GATTGAT---GTGTCAGGA---TCATCTTCACATAGGAAGGAGAACA 992301 v i --- v v --- ii v v i MamSINE1#SINE 242 TACTGATAGTGGGTCAGTAGCGTCATCTTCGTATACGAAGGACAGCA 288 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.78 CpG sites = 32, Kimura (unadjusted) = 46.70 Transitions / transversions = 1.07 (32/30) Gap_init rate = 0.04 (8 / 186), avg. gap size = 1.75 (14 / 8) 18 6.46 6.06 0.00 chr4qtel1M 992385 992417 (7583) (TCTG)n#Simple_repeat 1 35 (0) m_b216s252i17 8534 chr4qtel1M 992385 TCTG-CT-TTTGTCTGTCTGTCTGTCTGTCTATCT 992417 - - i i (TCTG)n#Simpl 1 TCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCT 35 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.06 (2 / 32), avg. gap size = 1.00 (2 / 2) 17 7.54 0.00 3.45 chr4qtel1M 992735 992764 (7236) (TTG)n#Simple_repeat 1 29 (0) m_b216s252i18 8535 chr4qtel1M 992735 TTGTTTGTTTTTGTTGTTGTTGTTGTTTTT 992764 - v v (TTG)n#Simple 1 TTG-TTGTTGTTGTTGTTGTTGTTGTTGTT 29 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 18 6.36 6.06 0.00 chr4qtel1M 993781 993813 (6187) (TCTG)n#Simple_repeat 1 35 (0) m_b216s252i19 8536 chr4qtel1M 993781 TCTGTCTGTCTGTCTTTCTGTCTGT-T-TCTTTCT 993813 v - - v (TCTG)n#Simpl 1 TCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCT 35 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.06 (2 / 32), avg. gap size = 1.00 (2 / 2) 269 29.46 0.00 0.00 chr4qtel1M 993886 993997 (6003) L1ME4b_3end#LINE/L1 492 603 (289) m_b216s551i10 8537 chr4qtel1M 993886 ATGTCCATCAGTTGGGGAACGGTTAAATAAAGTATGGTTTATTAAAATAA 993935 i v vi v vi iv v i L1ME4b_3end#L 492 ATGTCCATCAATAGGGGACTGGTTAAATAAATTATGGTACATCCATACAA 541 chr4qtel1M 993936 TGGAACATTATTATTCTATATCAAATGATGAACAAGCTGATTGTAGAAAG 993985 i i vvvv ii vv vi iv vv? i iv vv L1ME4b_3end#L 542 TGGAATACTATGCAGCCGTAAAAAAGAATGAGGAAGCTCTNTATGTACTG 591 chr4qtel1M 993986 ATCTGGAAAGAT 993997 v ? L1ME4b_3end#L 592 ATATGGAANGAT 603 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.84 CpG sites = 13, Kimura (unadjusted) = 38.38 Transitions / transversions = 0.65 (13/20) Gap_init rate = 0.00 (0 / 111), avg. gap size = 0.0 (0 / 0) 282 19.67 0.00 0.00 chr4qtel1M 993886 993946 (6054) L1ME3G_3end#LINE/L1 488 548 (376) m_b216s551i9 8537 chr4qtel1M 993886 ATGTCCATCAGTTGGGGAACGGTTAAATAAAGTATGGTTTATTAAAATAA 993935 i v i v v iv v iv L1ME3G_3end#L 488 ATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTA 537 chr4qtel1M 993936 TGGAACATTAT 993946 i i L1ME3G_3end#L 538 TGGAATACTAT 548 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 22.96 CpG sites = 6, Kimura (unadjusted) = 22.96 Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 46 0.00 0.00 0.00 chr4qtel1M 994405 994446 (5554) (T)n#Simple_repeat 1 42 (0) c_b216s251i1 8538 chr4qtel1M 994405 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 994446 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 42 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 134 30.88 2.94 0.38 chr4qtel1M 994687 994776 (5224) (TC)n#Simple_repeat 1 90 (433) m_b216s252i20 8539 chr4qtel1M 994687 TCTCTGTGTCTGTCCTTCTGTCCATGTGTGACTCTCT-TCTGTTTCTCTC 994735 v v v ii v iv v v vv - v i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr4qtel1M 994736 TCTCTGTTTCTCTCTGTGTGTGTCTCCCCCATCTCTCTGTC 994776 v i v v v v i i - v (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TCTCTCTCTC 90 Matrix = Unknown Transitions / transversions = 0.44 (7/16) Gap_init rate = 0.02 (2 / 89), avg. gap size = 1.00 (2 / 2) 27 8.12 0.00 0.00 chr4qtel1M 994777 994815 (5185) (TCTCTG)n#Simple_repeat 1 39 (0) c_b216s251i2 8540 chr4qtel1M 994777 TCTCTGTCTCTGTCTTTCACTCTGTCTCTGTCTCTGTCT 994815 i vv (TCTCTG)n#Sim 1 TCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCT 39 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 134 30.88 2.94 0.38 chr4qtel1M 994816 995234 (4766) (TC)n#Simple_repeat 91 523 (0) m_b216s252i20 8541 chr4qtel1M 994816 TC-CTTGGTTTCTCCCTGACTATCTCTGTCTCTTTGGGTCTATTTCTGTC 994864 - ivv i i vv v v i vvv v i v (TC)n#Simple_ 91 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 140 chr4qtel1M 994865 TC-CTGTCTCTCTCTCTTTCTCTGTCTCTCCCTATTGCCCTCTCTGTATA 994913 - v i v i v iv i v v v (TC)n#Simple_ 141 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 190 chr4qtel1M 994914 TCTAAATGTCTCTGTCTCTCTCTGTCTCTGTCTTTGTCTATGTCTGTATC 994963 vvv v v v v i v v v v v (TC)n#Simple_ 191 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 240 chr4qtel1M 994964 TCTCTCTGTTTGTCTTTCTCTGTGTTTGAATGTCGC-CTGTCTCTCTGGT 995012 v i v i v v i vvv v v - v vvi (TC)n#Simple_ 241 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 290 chr4qtel1M 995013 TTTATGTCTCTGCCTCTTTCTTTGTCTC-CTC-CCCACCCTCTCTCTCTC 995060 i v v vi i i v - - i v i (TC)n#Simple_ 291 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 340 chr4qtel1M 995061 -CCCCCTCTCTCTGTCCATCCCTGTCTC-CTTTGTTTCTTTCTCTGTCTT 995108 - i i v iv i v - i v i i v i (TC)n#Simple_ 341 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 390 chr4qtel1M 995109 TCTCATTCACTTATTATGTCTCTCTCTCTC-CTCTTTCT-TCTCTGCCTC 995156 vi v ivi v v - i - vi (TC)n#Simple_ 391 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 440 chr4qtel1M 995157 TTTTTCTCTCTGTCTC-CTCTC-CTCCCCCTCCCTTGCTCTCTCTCTCCC 995204 i i v - - i i i iv i (TC)n#Simple_ 441 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 490 chr4qtel1M 995205 TCTCTTTCTTCCTC-CTTCCTC-CTCTCT-TCT 995234 i ii - ii - - (TC)n#Simple_ 491 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 523 Matrix = Unknown Transitions / transversions = 0.75 (45/60) Gap_init rate = 0.03 (14 / 418), avg. gap size = 1.00 (14 / 14) 316 36.50 2.81 7.65 chr4qtel1M 995292 995469 (4531) C MIR3#SINE/MIR (9) 199 30 m_b216s601i8 8542 chr4qtel1M 995292 AATCACAGATTTTAAGA--TGAGAGGGATGCTGGAAGTGATCTGATAGCA 995339 i v v v -- ii ivi i ii v ii vvv C MIR3#SINE/MIR 199 AATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAA 150 chr4qtel1M 995340 CCTCCT-ATTTTTTTTTTCAAAATAATAAATGAAGAAATTGAGGTCTAGG 995388 i - ------------- i i i i i i i C MIR3#SINE/MIR 149 CCCCCTCATTTT-------------ACAGATGAGGAAACTGAGGCCCAGA 113 chr4qtel1M 995389 GAAAATAAATGGTGGGCTCAAG-TCACTTGG-TAGTAGATAATAGAGCCA 995436 iivv i iivv i - vii -? vii iii i C MIR3#SINE/MIR 112 GAGGTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCG 63 chr4qtel1M 995437 GGATTCAAATGCATATGTTCTGATTTCTCATCC 995469 i vi iv vi v i i i ivi C MIR3#SINE/MIR 62 GGACTAGAACCCAGGTCTCCTGACTCCCAGTCC 30 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 53.02 CpG sites = 41, Kimura (unadjusted) = 54.43 Transitions / transversions = 2.16 (41/19) Gap_init rate = 0.10 (17 / 177), avg. gap size = 1.06 (18 / 17) 329 30.33 2.61 5.36 chr4qtel1M 995364 995478 (4522) C MIRb#SINE/MIR (125) 143 32 m_b216s601i9 8542 chr4qtel1M 995364 ATAAATGAAGAAATTGAGGTCTAGGGAAAATAAATGGTGGGCTCAAG-TC 995412 i i i i iii i iiv i iiivv i - C MIRb#SINE/MIR 143 ACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTC 94 chr4qtel1M 995413 ACTTGG-TAGTAGATAATAGAGCCAGGATTCAAATGCATATGTTCTGATT 995461 vii - ii iii i i iv --- v --- C MIRb#SINE/MIR 93 ACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCA---GGTCTG--- 50 chr4qtel1M 995462 TCTCA-TCCAAAGCCCAT 995478 v - i C MIRb#SINE/MIR 49 TCTGACTCCAAAGCCCGT 32 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.28 CpG sites = 26, Kimura (unadjusted) = 42.40 Transitions / transversions = 3.71 (26/7) Gap_init rate = 0.08 (9 / 114), avg. gap size = 1.00 (9 / 9) 12 9.30 0.00 4.17 chr4qtel1M 995856 995880 (4120) (TAA)n#Simple_repeat 1 24 (0) m_b216s252i21 8543 chr4qtel1M 995856 TATTAATAATATTAACTAATAATAA 995880 v v - (TAA)n#Simple 1 TAATAATAATAATAA-TAATAATAA 24 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 21 23.55 0.00 0.00 chr4qtel1M 996113 996157 (3843) (T)n#Simple_repeat 1 45 (0) m_b216s252i22 8544 chr4qtel1M 996113 TTTTTATTTATTTTTGTTTATTCATTTTTATTTTTTGTTTATTTT 996157 v v v v iv v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 45 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 303 23.68 6.58 0.00 chr4qtel1M 996379 996454 (3546) MIR3#SINE/MIR 114 194 (14) m_b216s601i10 8545 chr4qtel1M 996379 CTGAATTTTGATTT--TCATTTTTAAAATGAGGGGGTTAGATTGGCT-AT 996425 iiii iii -- i v i i i v - MIR3#SINE/MIR 114 CTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGAT 163 chr4qtel1M 996426 CT-TAAAATCCCTTCTAGCTCTAA-ATTTTA 996454 - ii i i - i MIR3#SINE/MIR 164 CTCTAAGGTCCCTTCCAGCTCTGACATTCTA 194 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.00 CpG sites = 16, Kimura (unadjusted) = 31.00 Transitions / transversions = 8.00 (16/2) Gap_init rate = 0.05 (4 / 75), avg. gap size = 1.25 (5 / 4) 12 7.25 10.34 0.00 chr4qtel1M 997064 997092 (2908) (AGGGG)n#Simple_repeat 1 32 (0) m_b216s252i23 8546 chr4qtel1M 997064 AGGGGA-GGG-GGTGAAGGGA-GGGAGGGGAG 997092 - - v i - (AGGGG)n#Simp 1 AGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAG 32 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.11 (3 / 28), avg. gap size = 1.00 (3 / 3) 463 25.04 0.85 4.42 chr4qtel1M 997277 997393 (2607) MIR#SINE/MIR 29 141 (121) m_b216s601i11 8547 chr4qtel1M 997277 GGTCCTGGATTCAGACTCATATTTGTGAGTTCAAATCTGGTCTCAGACAC 997326 ii vi vvi----- i i iv v v v MIR#SINE/MIR 29 GGCTCTGGAGCCAGACTGCC-----TGGGTTCGAATCCCGGCTCTGCCAC 73 chr4qtel1M 997327 TTACTAAATGTGTGATTCTGGGCAAATCACTTAA-CTCTGTTTGCCTTAG 997375 iv iii i i - v v i MIR#SINE/MIR 74 TTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAG 123 chr4qtel1M 997376 TTTCCTCCCCTATGAAAT 997393 vi i i MIR#SINE/MIR 124 TTTCCTCATCTGTAAAAT 141 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.83 CpG sites = 17, Kimura (unadjusted) = 31.16 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.05 (6 / 116), avg. gap size = 1.00 (6 / 6) 654 31.58 6.14 0.00 chr4qtel1M 997808 998035 (1965) C MIRc#SINE/MIR (3) 265 24 m_b216s601i12 8548 chr4qtel1M 997808 AATAATAATTATTCACATTTATGTTGCACTTGAGAGTT-ACAAAGTGCCT 997856 i?vi i i i v v v - i i C MIRc#SINE/MIR 265 AATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCGCTT 216 chr4qtel1M 997857 TT-TAAGTGTTTTCTCATTTAATTCTCTCTACAATCC-----AGTAGGTA 997900 i-i viii v i i v v i -----i i C MIRc#SINE/MIR 215 TCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCA 166 chr4qtel1M 997901 ATGAGAATATGGTTTTTCATAT---ATAGATTAGGAAAT--AGACTCCTA 997945 iv viii vi v i vi --- i v i-- i vv C MIRc#SINE/MIR 165 GGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGA 116 chr4qtel1M 997946 GAGGTTAATTGACTT-CCCTGGGGGATATAATTAGTAAATAATAAAGCTA 997994 v - vi vv i i ii i iii i ii C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 66 chr4qtel1M 997995 GGACTGAAGTACAAATCTT-CTGGCTTCATGTTTAGTACTCT 998035 vi iiv ii - i i v ii i C MIRc#SINE/MIR 65 GGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCT 24 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.16 CpG sites = 49, Kimura (unadjusted) = 43.74 Transitions / transversions = 2.13 (49/23) Gap_init rate = 0.03 (7 / 227), avg. gap size = 2.00 (14 / 7) 355 34.16 9.32 0.00 chr4qtel1M 999405 999565 (435) L2#LINE/L2 2658 2833 (249) m_b216s601i13 8549 chr4qtel1M 999405 CTTTTCTTTACTTTCATAGATATCACCCT-----AAGT-------AGCTC 999442 i vii i i iv vi i ----- i------- v L2#LINE/L2 2658 CTTCTCACCACCTCCACTGCCACCACCCTGGTCCAAGCCACCATCATCTC 2707 chr4qtel1M 999443 TTGCTTGGATTATTGCAATAGTTTTTTATTTGGTCATCTTGCTTCAAGCC 999492 i i i ii ii vi vi i v v L2#LINE/L2 2708 TCGCCTGGATTACTGCAATAGCCTCCTAACTGGTCTCCCTGCTTCCACCC 2757 chr4qtel1M 999493 T--CTCTTTTTCAGGCCATCTTCTTC-CATCTGCTAAAGTTGTTTACCAA 999539 -- i iii ? v i ii vv - v v i i vi iiviiv L2#LINE/L2 2758 TTGCCCCCCTNCAGTCTATTCTCAACACAGCAGCCAGAGTGATCCTTTTA 2807 chr4qtel1M 999540 AGATGTAGGTCTGACCATGTCACTTC 999565 i i i v i i L2#LINE/L2 2808 AAACGTAAGTCAGATCATGTCACTCC 2833 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 46.88 CpG sites = 38, Kimura (unadjusted) = 49.50 Transitions / transversions = 2.24 (38/17) Gap_init rate = 0.03 (4 / 160), avg. gap size = 3.75 (15 / 4) 376 23.60 2.40 8.47 chr5ptel1M 189 313 (999687) MIRc#SINE/MIR 10 127 (141) m_b217s601i0 8550 chr5ptel1M 189 GTGGCTCAGTAGATAGAGACATCAGTCCTGAATTCAAGAGGACCCCAGTT 238 iv i v - iii v i i v i i ivi MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAG-CACTGGACTTGGAGTCAGGAAGACCTGGGTT 58 chr5ptel1M 239 CAAATCTGGCCTCAGACACTTAACACTTCCTAGCTGTGTGACCCTGGGCA 288 i i iv v v v ------- i MIRc#SINE/MIR 59 CGAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTGACCTTGGGCA 101 chr5ptel1M 289 AGTCACTTCA---CTCCAATTGCCTCAG 313 v --- ii -- MIRc#SINE/MIR 102 AGTCACTTAACCTCTCTGA--GCCTCAG 127 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 27.64 CpG sites = 17, Kimura (unadjusted) = 28.89 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.09 (11 / 124), avg. gap size = 1.18 (13 / 11) 17 8.91 0.00 0.00 chr5ptel1M 765 788 (999212) (CT)n#Simple_repeat 1 24 (0) m_b217s252i0 8551 chr5ptel1M 765 CTCTCTCTCTCTCTCACACTCTCT 788 v v (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCT 24 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 29 0.00 0.00 0.00 chr5ptel1M 789 813 (999187) (CA)n#Simple_repeat 1 25 (0) c_b217s251i0 8552 chr5ptel1M 789 CACACACACACACACACACACACAC 813 (CA)n#Simple_ 1 CACACACACACACACACACACACAC 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 18 18.97 0.00 0.00 chr5ptel1M 9809 9846 (990154) (AGGG)n#Simple_repeat 1 38 (0) m_b217s252i1 8553 chr5ptel1M 9809 AGGGAGGGAGAGAAGGAGAGAGGGAGGAAGGAAGGAAG 9846 i i i i i i (AGGG)n#Simpl 1 AGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAG 38 Matrix = Unknown Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 14 26.16 5.56 0.00 chr5ptel1M 9816 9869 (990131) (GAAA)n#Simple_repeat 1 57 (0) m_b217s252i2 8553 chr5ptel1M 9816 GAGAGAAGGAGAG-AGGGAGGAAGGAAGGAAGAAAAGAAAGAAAGGAA-A 9863 i i i - i i i i i ii i - (GAAA)n#Simpl 1 GAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA 50 chr5ptel1M 9864 AA-AAAG 9869 - (GAAA)n#Simpl 51 AAGAAAG 57 Matrix = Unknown Transitions / transversions = 1.00 (11/0) Gap_init rate = 0.06 (3 / 53), avg. gap size = 1.00 (3 / 3) 14 7.11 2.94 6.06 chr5ptel1M 10260 10293 (989707) (CCCTCT)n#Simple_repeat 1 33 (0) m_b217s252i3 8554 chr5ptel1M 10260 CCCT-TCCCTCCCTCCCCCTCCCTCTCTCTCTCCC 10293 - -- i i (CCCTCT)n#Sim 1 CCCTCTCCCT--CTCCCTCTCCCTCTCCCTCTCCC 33 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.09 (3 / 33), avg. gap size = 1.00 (3 / 3) 16 10.03 6.06 0.00 chr5ptel1M 10261 10293 (989707) (CCCT)n#Simple_repeat 1 35 (0) m_b217s252i4 8554 chr5ptel1M 10261 CCTTCCCTCCCT-CC-CCCTCCCTCTCTCTCTCCC 10293 i - - i i (CCCT)n#Simpl 1 CCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCC 35 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.06 (2 / 32), avg. gap size = 1.00 (2 / 2) 91 19.78 4.13 0.44 chr5ptel1M 11557 11774 (988226) (GA)n#Simple_repeat 1 226 (0) m_b217s252i5 8555 chr5ptel1M 11557 GAGAGAAGGAGATGGAAAAGGAGAGAGAGAG-GAAAG-GCGAG-GGGGGA 11603 ii vi i ii - i - v - i i (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr5ptel1M 11604 GAGAGAG-GAAAGGGAGAGGGA-AAAGAGAG-GTAAGGGGGAGAGAGAGA 11650 - i i i - i - vi i i (GA)n#Simple_ 51 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 100 chr5ptel1M 11651 GACAGAGAGACAGAGACAAAGAGAGAGAGAGAGACAGAGAGAGAAACAGA 11700 v v v i v i v (GA)n#Simple_ 101 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 150 chr5ptel1M 11701 GAGACAGAGAGAGAAAGCAGAGAGAGAGACAGAGAGAGAGAG-GAGGGGG 11749 v i - v - i i (GA)n#Simple_ 151 GAGAGAGAGAGAGAGAG-AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 199 chr5ptel1M 11750 GGAG-GGGAGAGATA-ATATAGAGGGA 11774 i - i v - v v i (GA)n#Simple_ 200 AGAGAGAGAGAGAGAGAGAGAGAGAGA 226 Matrix = Unknown Transitions / transversions = 1.85 (24/13) Gap_init rate = 0.05 (10 / 217), avg. gap size = 1.00 (10 / 10) 244 24.42 11.46 1.90 chr5ptel1M 13658 13753 (986247) C MIRc#SINE/MIR (129) 139 35 m_b217s601i1 8556 chr5ptel1M 13658 CAGATTAGGGAGCTCCGGAGCTCGG-GAGGCTAAGGGATTTGCCTCCCGT 13706 v i i -- ii i - i v i ivvv C MIRc#SINE/MIR 139 CAGATGAGGAAACT--GAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGT 92 chr5ptel1M 13707 CACAAAAT--G-AAGTG-------CAGGATTTGAACCCTGATCTTCCTGA 13746 v ii-- - ------- i i i v i C MIRc#SINE/MIR 91 CACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGA 42 chr5ptel1M 13747 CTGCGAG 13753 v i C MIRc#SINE/MIR 41 CTCCAAG 35 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 27.45 CpG sites = 15, Kimura (unadjusted) = 30.56 Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.06 (6 / 95), avg. gap size = 2.17 (13 / 6) 17 8.15 7.32 2.33 chr5ptel1M 13779 13819 (986181) (TTGTCTC)n#Simple_repeat 1 43 (0) m_b217s252i6 8557 chr5ptel1M 13779 TTGTC-CCTGTCTTTTGTCTCTTTGTC-CTTGTGTC-TGTCTCT 13819 - i i - - v - (TTGTCTC)n#Si 1 TTGTCTCTTGTCTCTTGTCTC-TTGTCTCTTGTCTCTTGTCTCT 43 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.10 (4 / 40), avg. gap size = 1.00 (4 / 4) 21 33.27 2.61 2.61 chr5ptel1M 13839 13953 (986047) (TTCCC)n#Simple_repeat 1 115 (0) m_b217s252i8 8558 chr5ptel1M 13839 TTCCCTCCCCTGCTCTCCCCTTCCC-TCCCCTCTCCTCCATTCTC-TCCT 13886 i v i i - i i i v i - i (TTCCC)n#Simp 1 TTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCC 50 chr5ptel1M 13887 CTCTCTTAACTCCCCTCTGCCCTCTTTTGTCTCCCTCCTCTCCTTTCCTT 13936 i i vv i - v i ii vi i - i - i (TTCCC)n#Simp 51 TTCCCTTCCCTTCCCT-TCCCTTCCCTTCCCTTCC-CTTC-CCTTCCCTT 97 chr5ptel1M 13937 -CTTTCTTCTCCCTTCCC 13953 - i iii (TTCCC)n#Simp 98 CCCTTCCCTTCCCTTCCC 115 Matrix = Unknown Transitions / transversions = 3.67 (22/6) Gap_init rate = 0.05 (6 / 114), avg. gap size = 1.00 (6 / 6) 12 13.67 0.00 0.00 chr5ptel1M 13977 14000 (986000) (ATTT)n#Simple_repeat 1 24 (0) m_b217s252i9 8559 chr5ptel1M 13977 ATTTATTTATTTAACTTTTTATTT 14000 vi v (ATTT)n#Simpl 1 ATTTATTTATTTATTTATTTATTT 24 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 484 23.09 0.75 6.30 chr5ptel1M 14005 14138 (985862) C MIRc#SINE/MIR (141) 127 1 m_b217s601i2 8560 chr5ptel1M 14005 CTGAGGC-AATTGGGGTTAAGTGACTTGCCCAAGATCCTACAGCTAGGAC 14053 -v vv i i vi --- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG--- 81 chr5ptel1M 14054 GTTAAGTGTCTGAAGCAAGATTTGAACTCGGGTCCTCTTGACTTCAGGGC 14103 -- v v iv ii i i i i i i i i v C MIRc#SINE/MIR 80 --TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTC 33 chr5ptel1M 14104 TGGTGCTCTATCCACAGCGCCACCTGGCTGCCCCG 14138 ii v v i ---i i C MIRc#SINE/MIR 32 CAGTGCTCTTTCCACTGCACCAC---ACTGCCTCG 1 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 26.04 CpG sites = 19, Kimura (unadjusted) = 28.30 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.07 (9 / 133), avg. gap size = 1.00 (9 / 9) 203 25.97 9.09 0.00 chr5ptel1M 14157 14233 (985767) C MIR3#SINE/MIR (16) 192 109 m_b217s601i3 8561 chr5ptel1M 14157 GAAT-TTAAAACTGAAAGGCTCCT-AGAAATT-TTT--TCTGATCTAC-- 14199 - i i i i vv - i i- i -- ii i iv -- C MIR3#SINE/MIR 192 GAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTC 143 chr5ptel1M 14200 ATATTACAGATGAGAAAAGTGAGATTCAGAGAGG 14233 v i v iii C MIR3#SINE/MIR 142 ATTTTACAGATGAGGAAACTGAGGCCCAGAGAGG 109 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.78 CpG sites = 15, Kimura (unadjusted) = 33.78 Transitions / transversions = 3.00 (15/5) Gap_init rate = 0.07 (5 / 76), avg. gap size = 1.40 (7 / 5) 205 17.50 0.00 0.00 chr5ptel1M 14194 14233 (985767) C MIRc#SINE/MIR (117) 151 112 m_b217s601i4 8561 chr5ptel1M 14194 ATCTACATATTACAGATGAGAAAAGTGAGATTCAGAGAGG 14233 iv v i v ii C MIRc#SINE/MIR 151 ATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGG 112 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 20.14 CpG sites = 4, Kimura (unadjusted) = 20.14 Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 227 25.49 0.00 0.00 chr5ptel1M 14250 14300 (985700) C L2b_3end#LINE/L2 (12) 454 404 m_b217s601i5 8562 chr5ptel1M 14250 AAGAAGCACTTATTGAGCGCCAATTGTGTACCAAGCTCTGTGATAAGGAC 14299 v ii i i v i i i ? v i vi C L2b_3end#LINE 454 AACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGC 405 chr5ptel1M 14300 T 14300 C L2b_3end#LINE 404 T 404 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 30.23 CpG sites = 9, Kimura (unadjusted) = 33.35 Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 13 21.77 0.00 6.67 chr5ptel1M 14330 14377 (985623) (CCTGC)n#Simple_repeat 1 45 (0) m_b217s252i10 8563 chr5ptel1M 14330 CCAGCCCATGCCCCGTCCCTAGCACTCCCCTGCCCTTCACTTCTCTGC 14377 v - i - - v v v v v i (CCTGC)n#Simp 1 CCTGCCC-TGCCCTG-CCCT-GCCCTGCCCTGCCCTGCCCTGCCCTGC 45 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.06 (3 / 47), avg. gap size = 1.00 (3 / 3) 13 21.15 2.63 0.00 chr5ptel1M 15512 15549 (984451) (ATTATA)n#Simple_repeat 1 39 (0) m_b217s252i11 8564 chr5ptel1M 15512 ATTAATAGTATAATTGTAACTATAATTATTAATA-AATT 15549 vv v i i v v - (ATTATA)n#Sim 1 ATTATAATTATAATTATAATTATAATTATAATTATAATT 39 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 198 33.33 0.00 0.00 chr5ptel1M 16051 16110 (983890) L2d2_3end#LINE/L2 496 555 (0) m_b217s601i6 8565 chr5ptel1M 16051 GTTTAATACAATTCTTGGTACATAGTAGGTACTGAATAAATGTTCATTAG 16100 ii ii i v i v i i ii v i ii ii L2d2_3end#LIN 496 GCCTAGCACAGTGCCTTGCACACAGTAGGCGCTCAATAAATATTTGTTGA 545 chr5ptel1M 16101 TTTGTCTTGA 16110 vi L2d2_3end#LIN 546 TTTGATTTGA 555 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 45.39 CpG sites = 16, Kimura (unadjusted) = 49.39 Transitions / transversions = 4.00 (16/4) Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0) 1325 20.13 9.14 1.65 chr5ptel1M 16501 16894 (983106) Charlie1a#DNA/hAT-Charlie 1032 1454 (1) m_b217s502i0 8566 chr5ptel1M 16501 AATTCTCCTTCCCTTTCTGACTACATAT-----------------TTCTT 16533 v i i ii ----------------- Charlie1a#DNA 1032 AATACTCCTCCCTTTTCCAACTACATATCTGTGTGAGGCCGGATTTTCTT 1081 chr5ptel1M 16534 CAGATATTTCAACCACAGTAACATATCACATCCGATCAAATGCTGAAACA 16583 v i v ii i v v ii v i Charlie1a#DNA 1082 CATATACTTCAACCAAAACAACATATCGCAACAGATTGAATGCAGAAGCA 1131 chr5ptel1M 16584 GACATGAAAATCCAGGTGTCTTCTCTTAAGTCAAACATTAAAGATATTTT 16633 i i v v i i v v Charlie1a#DNA 1132 GATATGAGAATCCAGCTGTCTTCTATTAAGCCAGACATTAAAGAGATTTG 1181 chr5ptel1M 16634 TAAAAATCTATA--AAGGTAACTCTTTCCCAT--ATTTTTTTTGTTTTGG 16679 i v v -- v iv - i i-- v Charlie1a#DNA 1182 CAAAAATGTAAAACAATGCCACTC-TTCTCACTAAATTTTTTTGTTTTGG 1230 chr5ptel1M 16680 AAAACCTACTTATTTTT----AAAATATG-----TATG-TAACTTGTAAC 16719 iv v ---- ----- - v i Charlie1a#DNA 1231 AAAATATAGTTATTTTTCATAAAAATATGTTATTTATGTTAACATGTAAT 1280 chr5ptel1M 16720 AGGTTTAGTGTTATTTTTAAATGAAGCAACATAAATGTTTTAAAAAGTAT 16769 i v i vi -- i v - Charlie1a#DNA 1281 GGGTTTATTATTATTTTTAAATGAATTA--ATAAATATTTTAAAAATT-T 1327 chr5ptel1M 16770 CT---TCCTAATTTAAAGCATAGTAAATATCAATTACTCTACCTCACATA 16816 --- ii vv ii i i viv v v i Charlie1a#DNA 1328 CTCAGTTTTAATTTCTAATATGGTAAATATCGATAGATATAACCCACATA 1377 chr5ptel1M 16817 AACAAAAG--TTTTGGGATTCTTCAACAATTTGTAAAAGTATAAAATTTT 16864 --i i- i i v i i ivvv Charlie1a#DNA 1378 AACAAAAGCTCTTTGGGG-TCCTCAATAATTTTTAAGAGTGTAAAGGGGT 1426 chr5ptel1M 16865 TCTAAGCCCCCAAAAAGTTGTAGAACCATT 16894 i i --v vv ii Charlie1a#DNA 1427 CCTGAG--ACCAAAAAGTTTGAGAACCGCT 1454 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 22.76 CpG sites = 44, Kimura (unadjusted) = 23.77 Transitions / transversions = 1.29 (44/34) Gap_init rate = 0.04 (15 / 393), avg. gap size = 2.87 (43 / 15) 471 25.90 2.16 0.00 chr5ptel1M 17249 17387 (982613) C L1PREC2_orf2#LINE/L1 (1392) 1902 1761 m_b217s551i0 8567 chr5ptel1M 17249 ATAGATGCTAGTGATCATTTTAAGGAAAACTCCATTAATACCTATACTCT 17298 vivv v i i v vii v i vvi v C L1PREC2_orf2# 1902 ATAGATGGCTCTTATTATTTTGAGGTATGTTCCTTCAATACCTAGTTTAT 1853 chr5ptel1M 17299 CTGGTATTTTTCATAGGAAGGGATGTTAGGTTTTATCAAATGCTTTTTCT 17348 ivi vi v i v iii i v i C L1PREC2_orf2# 1852 TGAGAGTTTTTAACATGAAGGGATGTTGAATTTTATCGAAAGCCTTTTCT 1803 chr5ptel1M 17349 GCATCTATTGAGGTAATTATATGCTTTTTG---TTAGTTATG 17387 i i i v --- v C L1PREC2_orf2# 1802 GCATCTATTGAGATAATCATGTGGTTTTTGTCTTTAGTTCTG 1761 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 31.14 CpG sites = 19, Kimura (unadjusted) = 32.20 Transitions / transversions = 1.12 (19/17) Gap_init rate = 0.01 (1 / 138), avg. gap size = 3.00 (3 / 1) 15 5.48 0.00 0.00 chr5ptel1M 17410 17428 (982572) (TA)n#Simple_repeat 1 19 (0) m_b217s252i12 8568 chr5ptel1M 17410 TATATATATATATATTTAT 17428 v (TA)n#Simple_ 1 TATATATATATATATATAT 19 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 14 23.79 3.95 5.33 chr5ptel1M 17612 17687 (982313) (AAGAAA)n#Simple_repeat 1 75 (0) m_b217s252i13 8569 chr5ptel1M 17612 AAGAAAAATCAGATCAAGAAGGAAAAAGAAAAACTGAGAAAG-AAAACAA 17660 vv i vv - i -- i - v (AAGAAA)n#Sim 1 AAGAAAAAGAAAAAGAA-AAAGAAAAAGAAAAA--GAAAAAGAAAAAGAA 47 chr5ptel1M 17661 AATG--CAAGCAAATGACAACAGAAAGAG 17687 v --v v v - v i (AAGAAA)n#Sim 48 AAAGAAAAAGAAAAAGA-AAAAGAAAAAG 75 Matrix = Unknown Transitions / transversions = 0.40 (4/10) Gap_init rate = 0.08 (6 / 75), avg. gap size = 1.17 (7 / 6) 697 26.79 2.44 2.86 chr5ptel1M 17948 18193 (981807) C L1ME3G_3end#LINE/L1 (376) 548 304 m_b217s551i1 8570 chr5ptel1M 17948 ATAGTATTCCGTAGCAT--ATATACCCTAATTTATTCAGCCATTCTCCAA 17995 i i -- v i i i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr5ptel1M 17996 GTGATGGGCATCCACTCAGTTTTCAGTTTCTGGCTACTACAAAGCAGACT 18045 v i ii vviv i i i v i vv vi C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr5ptel1M 18046 GCCACAAACATTCTTGCACATACAGGTCTCTTTTC-CTTCTTTAAG-ATC 18093 v ii i i i ?-- ii v v - v v vii - i C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATT 401 chr5ptel1M 18094 TTTTTGGGATATAAGCCCAGGAAAAACACTGCTAGGTTAAAGGGTATGCA 18143 i ? i v v? ? i iviiv i i i i C L1ME3G_3end#L 400 TCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCG 351 chr5ptel1M 18144 CAGTTTGATAACTTT--TTGAGCGTAGTTCCAAATTGTTCTCCAGAATGG 18191 v i-- i -- v --- v v ii i ? C L1ME3G_3end#L 350 CATTTTA--AATTTTAATAGA---TACTGCCAAATTGCCCTCCAAAANGG 306 chr5ptel1M 18192 TT 18193 i C L1ME3G_3end#L 305 CT 304 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 33.69 CpG sites = 40, Kimura (unadjusted) = 35.13 Transitions / transversions = 1.67 (40/24) Gap_init rate = 0.04 (11 / 245), avg. gap size = 1.18 (13 / 11) 729 26.95 3.11 2.41 chr5ptel1M 18490 18778 (981222) C L1ME2_3end#LINE/L1 (611) 300 10 m_b217s551i2 8570 chr5ptel1M 18490 TTCGCAGTTCCACCAACAATATATCAGTGTCCCAGTTTTCCCACACTCCT 18539 ii v i i i v v i vii - C L1ME2_3end#LI 300 TTTACACTCCCACCAGCAATGTATGAGAGTTCCAGTTGCTCCACA-TCCT 252 chr5ptel1M 18540 T-TCAACATTTGTCATTACC---TTTTTCAGTCATCTCAACCAATCTGAG 18585 i-i vi ii ---i i --- i i i v iiv C L1ME2_3end#LI 251 CGCCAACATTTGGTATTGTCAGTCTTTTTA---ATTTTAGCCATTCTAGT 205 chr5ptel1M 18586 AGGTGTGCAGTGGTTTCTCAGAGTTGTCTTGATTTGCATTTCTCTGATCA 18635 i ? v vv v i i i v C L1ME2_3end#LI 204 GGGTGTGNAGTGGTATCTCATTGTGGTTTTAATTTGCATTTCCCTGATGA 155 chr5ptel1M 18636 ATAGTGATTTGGAGCACCTTTTCATGTGAGTACAAATAGTTCA-ATTTCT 18684 v i v v vv iviiivi i- v C L1ME2_3end#LI 154 CTAATGATGTTGAGCACCTTTTCATGTGCTTATTGGCCATTCGTATATCT 105 chr5ptel1M 18685 TCATCTGAAAACTGTCAGTTCATACC--TTGCACCATTTATCAATTGGA- 18731 v i vi v v vii -- - v i i- C L1ME2_3end#LI 104 TCTTTTGTGAAGTGTCTGTTCAAGTCTTTTGC-CCATTTTTTAATTGGGT 56 chr5ptel1M 18732 -GAATGGCTTGAAGTATTATAAATTTGAATCAATTCTTTATATATTTT 18778 - vv v v--v vi v v vv i i C L1ME2_3end#LI 55 TGTTTGTCTTT--TTATTATTGAGTTGTAGGAGTTCTTTATATATTCT 10 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 32.94 CpG sites = 40, Kimura (unadjusted) = 34.02 Transitions / transversions = 1.11 (40/36) Gap_init rate = 0.05 (13 / 288), avg. gap size = 1.23 (16 / 13) 287 30.29 1.77 3.99 chr5ptel1M 18640 18921 (981079) C L1M5_orf2#LINE/L1 (0) 3294 3019 m_b217s551i3 8570 chr5ptel1M 18640 TGATTTGGAGCACCTTTTCATGTGAGTAC-AAATAGTTCAATTTCTTCAT 18688 ?v v i vv i-iivi v v? v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr5ptel1M 18689 CTGAAAACTGTCAGTTCATACCTT--GCACCATTTATCAATTGGA--GAA 18734 i vi v v vii -- - v ?v i-- vv C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGC-CCATTTTTNTATTGGGTTGTT 3196 chr5ptel1M 18735 TGGCTTGAAGTATTATAAATTTGAATCAATTCTTTATATATTTTTAAAAT 18784 v v--v ? vi ? v vv i i vi v i C L1M5_orf2#LIN 3195 TGTCTTT--TTNTTATTGANTTGTAGGAGTTCTTTATATATTCTGGATAC 3148 chr5ptel1M 18785 GAGATCCTTTATCAGATCCTTTGGATGTAAATAATATTTCCCCAGTTAAT 18834 - i viv vv?v i - v ii ? ivi C L1M5_orf2#LIN 3147 GAG-TCCTTTGTCAGATATATGTNTTGCAAAT-ATTTTCTCCCANTCTGT 3100 chr5ptel1M 18835 TGCTTCTCTTCTAATCTGGTCTGCATTAGGGTTTTTTGGGGGGGTACAAA 18884 v vi i v i -- -i vii v i i? i --- i C L1M5_orf2#LIN 3099 GGCTTGCCTTTTCATTT--TCT-TAACGGTGTCTTTTGANGAG---CAGA 3056 chr5ptel1M 18885 ACCTTTTTAACTTAATATAATAAAAATTATCTATTTT 18921 vi v vi i i? i vv v v C L1M5_orf2#LIN 3055 AGTTTTTAATTTTGATGNAGTCCAATTTATCAATTTT 3019 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 39.48 CpG sites = 37, Kimura (unadjusted) = 40.80 Transitions / transversions = 0.82 (37/45) Gap_init rate = 0.05 (14 / 281), avg. gap size = 1.14 (16 / 14) 15 21.92 0.00 2.33 chr5ptel1M 19030 19073 (980927) (TTTCT)n#Simple_repeat 1 43 (0) m_b217s252i14 8571 chr5ptel1M 19030 TTTCTTTCTTTTTCTTTAAGTTTGTATGACTTTTCTTTTCTTTT 19073 ii vvv v - vv (TTTCT)n#Simp 1 TTTCTTTTCTTTTCTTTTCTTTTCT-TTTCTTTTCTTTTCTTTT 43 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.02 (1 / 43), avg. gap size = 1.00 (1 / 1) 11 19.28 2.13 6.67 chr5ptel1M 19034 19080 (980920) (TTTCTT)n#Simple_repeat 1 45 (0) m_b217s252i15 8571 chr5ptel1M 19034 TTTCTTTTTCTTTAAGTTTGTATGACTTTTC-TTTTCTTTTTATTATT 19080 vvv - - -vi - v v (TTTCTT)n#Sim 1 TTTCTTTTTCTTTTTCTTT-T-T-CTTTTTCTTTTTCTTTTTCTTTTT 45 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.09 (4 / 46), avg. gap size = 1.00 (4 / 4) 279 34.83 2.42 1.60 chr5ptel1M 19330 19577 (980423) C L1P1_orf2#LINE/L1 (418) 2876 2627 m_b217s551i4 8570 chr5ptel1M 19330 ATCTTGGTATACGGTGTTAGGTGTGGAACTA-TGCCTTCTTTCTGCTATA 19378 i v v v viv v i - vi vv i - C L1P1_orf2#LIN 2876 ATTTTTGTATAAGGTGTAAGGAAGGGATCCAGTTTCAGCTTTCTAC-ATA 2828 chr5ptel1M 19379 CTACTTTCCAATTTTCCTAGCAGTTTTTGTCAAATAGTGATTTTTTATCG 19428 ivi vv i i viv i i v v ii - v C L1P1_orf2#LIN 2827 TGGCTAGCCAGTTTTCCCAGCACCATTTATTAAATAGGGAATCCTT-TCC 2779 chr5ptel1M 19429 CCAAAGATAGGGCCTTT-GGGTTTGTAAAATACTAGACTCTTATAGTCAT 19477 vv v v vvii i -i v v ii ivv i vi C L1P1_orf2#LIN 2778 CCATTGCTTGTTTTTCTCAGGTTTGTCAAAGATCAGATAGTTGTAGATAT 2729 chr5ptel1M 19478 -TGGC--TATTTTGTTCATCATTCCAC-CTATTCCACTAATCAACTTCTC 19523 -i -- i-- v vvii iii- i i i v iv C L1P1_orf2#LIN 2728 GCGGCGTTATTTC--TGAGGGCTCTGTTCTGTTCCATTGATCTATATCTC 2681 chr5ptel1M 19524 TATTTCTAAGCCAGTACCAAATGGTTTTGATGACTACTGCTTTATAATAT 19573 i ivivi viiv i v iiv i i i C L1P1_orf2#LIN 2680 TGTTTTGGTACCAGTACCATGCTGTTTTGGTTACTGTAGCCTTGTAGTAT 2631 chr5ptel1M 19574 AGTT 19577 C L1P1_orf2#LIN 2630 AGTT 2627 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 47.33 CpG sites = 46, Kimura (unadjusted) = 48.12 Transitions / transversions = 1.18 (46/39) Gap_init rate = 0.04 (9 / 247), avg. gap size = 1.11 (10 / 9) 307 28.39 3.57 3.57 chr5ptel1M 19502 19669 (980331) C L1M5_orf2#LINE/L1 (592) 2702 2535 m_b217s551i5 8570 chr5ptel1M 19502 CTATTCCACTAATCAACTTCTCTATTTCTAAGCCAGTACCAAATGGTTTT 19551 i i i v i v iii v i v iv i C L1M5_orf2#LIN 2702 CTGTTCCATTGATCTATTTGTCTATCCTTACGCCAATACCACACTGTCTT 2653 chr5ptel1M 19552 GATGACTACTGCTTTATAATATAGTTCT-AGATGTGGTACAGCAGGGCCA 19600 v iiv - ii - ? v? vv i i v - C L1M5_orf2#LIN 2652 GATTACTGTAGCTTTATAATA-AGTCTTGANATCNGGTAGTGTAAGTCC- 2605 chr5ptel1M 19601 CTTTCA--TTTGCTTTTCTCTTCATTA--ATTCCTCTGAA-ATTCTTGCC 19645 -- i -- i i i -- i -- vi i iv- ? vi C L1M5_orf2#LIN 2604 --TCCAACTTTGTTCTTCTTTT--TCAAGATTGTTTTGGCTATTCTNGGT 2559 chr5ptel1M 19646 CTTTTGTTCTTTCAGATGAATTTT 19669 i ivi i v i C L1M5_orf2#LIN 2558 CCTTTGCATTTCCATATAAATTTT 2535 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 38.12 CpG sites = 30, Kimura (unadjusted) = 38.12 Transitions / transversions = 1.88 (30/16) Gap_init rate = 0.06 (10 / 167), avg. gap size = 1.20 (12 / 10) 2589 29.36 3.60 1.23 chr5ptel1M 19681 20873 (979127) L1M4_orf2#LINE/L1 1296 2516 (778) m_b217s551i6 8570 chr5ptel1M 19681 CCTACAACAATAGAGATTGCCCAGATTGACAAGAGAGGAAATAAATTACT 19730 v vi i v i i i v i i vvi i i vv ii L1M4_orf2#LIN 1296 CCTAGAAAGACACAAACTACCGAAACTGACTCAAGAAGAAATAGAAAATC 1345 chr5ptel1M 19731 TAGTCTGATTTACAAAAAG-AAAGAGAACAAACTATTAATCAAG----TT 19775 iiviv ii i v - vii i v i---- L1M4_orf2#LIN 1346 TGAATAGACCTATAACAAGTAAAGAGATTGAATTAGTAATCAAAAAACTT 1395 chr5ptel1M 19776 CCTA-AAAAAAATCCCTAGGACCAGATGGATTTAGATGTGAATTCTACCA 19824 i - i vv i ? v i vvv L1M4_orf2#LIN 1396 CCCACAAAGAAAAGCCCAGGNCCAGATGGCTTCACTGGTGAATTCTACCA 1445 chr5ptel1M 19825 AAAATTTAAAGAACAATTAACTCCAGTGCTATATAAACAATTTGAAAAAA 19874 v v v i v vi i vv iv L1M4_orf2#LIN 1446 AACATTTAAAGAAGAATTAACACCAATCCTTCACAAACTCTTCCAAAAAA 1495 chr5ptel1M 19875 CTGGGAATGAAGGAATTCTACCAAATTTCTTTAATGACACAGACATGGTA 19924 iv iii v i iv v v i iv iv vi viii viiv L1M4_orf2#LIN 1496 TAGAAGAGGAGGGAACACTTCCCAACTCATTCTATGAGGCCAGTATTACC 1545 chr5ptel1M 19925 CTGAATCCTAAAGCAGGTAGGTTGAAAACA----GAGAAAGAAAAATTAT 19970 vv v v ii ----- i ----i ii i i L1M4_orf2#LIN 1546 CTGATACCAAAACCAGACA-----AAGACATCACAAGAAAAGAAAACTAC 1590 chr5ptel1M 19971 GGACCAATCTCCCTAATGAATATTGATGCAAAAATCTTAAATAAAACATT 20020 i v v v i v i i i L1M4_orf2#LIN 1591 AGACCAATATCCCTTATGAATATAGATGCAAAAATCCTCAACAAAATACT 1640 chr5ptel1M 20021 AGCAAAGAGATTACAGAAAATCATCCCCAGGATAATACACTATGACCAAG 20070 vv v v v vvi vvvv v i L1M4_orf2#LIN 1641 AGCAAACCGAATCCAGCAACATATAAAAAGGATTATACACCATGACCAAG 1690 chr5ptel1M 20071 TAGGATTTAT-ACAGGAATGCAGGACTGGTTCAGTATTTGGAAAACTATT 20119 i -v i ii ii ?i i v v i L1M4_orf2#LIN 1691 TGGGATTTATCCCAGGAATGCAAGGTTGGTTCAACATNCGAAAATCAATC 1740 chr5ptel1M 20120 AGCATAATTGACTGTATCAATA-ACCAAATTAACAAAAACTATGTAATCA 20168 iii vv ii i - vi -vi i ii i L1M4_orf2#LIN 1741 AATGTAATACACCATATTAATAGAATAAA-GGACAAAAACCACATGATCA 1789 chr5ptel1M 20169 TCTCAATAGATGCAGAAAAAGCAATTGACAAAATCCAGCATCCATTCCTA 20218 i v i i v v i L1M4_orf2#LIN 1790 TCTCAATAGACGCAGAAAAAGCATTTGACAAAATCCAACACCCTTTCATG 1839 chr5ptel1M 20219 TTAAAAAACACATGAGAGTATAGGAATAAATGGACTTTTCCTCTAAACAG 20268 v - vii v ivv i v ivvi - v v L1M4_orf2#LIN 1840 AT-AAAAACACTCAACAAACTAGGAATAGAAGGGAACTTCCTC-AACCTG 1887 chr5ptel1M 20269 -TTAGTAGCATCTATTTAAAACCATCAGCAAGCATCATATGTAATGGGTA 20317 - v ivi ivv vv v i iv vv L1M4_orf2#LIN 1888 ATAAAGGGCATCTACGAAAAACCCACAGCTAACATCATACTTAATGGTGA 1937 chr5ptel1M 20318 TAAACTAGAACCATTACCAATAAGATCAGGGGTGAAACAAGGTTGCCCAC 20367 v i ii ?v v v vv iiii i v i i L1M4_orf2#LIN 1938 AAGACTGAANGCTTTCCCCCTAAGATCAGGAACAAGACAAGGATGTCCGC 1987 chr5ptel1M 20368 TATCATCATTACTATTCAAGATTGTATTAGAAATGCTAGCTTCAGCAATA 20417 v ii i v v i i ii v ivvi v L1M4_orf2#LIN 1988 TCTCGCCACTTCTATTCAACATTGTACTGGAGGTTCTAGCCAGGGCAATT 2037 chr5ptel1M 20418 AGAAAAGAAAAAGAGATTAAA-GCAATTAGAGTAGGTAATGAGGAAACAA 20466 iv i v - vii v - v v i ii L1M4_orf2#LIN 2038 AGGCAAGAAAAAGAAATAAAAGGCATCCAGATT-GGAAAGGAAGAAGTAA 2086 chr5ptel1M 20467 AATTATCACACTTTGCAGATGATATGA--TGGTACCCTAG--ACCCCCAC 20512 i v vv i i -- v -iv -- vi i v L1M4_orf2#LIN 2087 AACTATCTCTATTCGCAGATGACATGATCTTGTA-TATAGAAAATCCTAA 2135 chr5ptel1M 20513 AGATTCTACTAAAAAGCTATTAGAAATAATGCATAACTTTAGCAAAGTTG 20562 i v i ? i v iv ii v i i L1M4_orf2#LIN 2136 GGAATCCACNAAAAAACTATTAGAACTAATAAACGAGTTCAGCAAGGTTG 2185 chr5ptel1M 20563 CAGGATACAAAATAAATCCACATAAATCA---CCATTTTTATACATCACC 20609 i v vi v ---vi i ii v L1M4_orf2#LIN 2186 CAGGATACAAGATCAATATACAAAAATCAATTGTATTTCTATACACTAGC 2235 chr5ptel1M 20610 AACAA--AATCCAACAGCAAGAGATACGAAGAGA--AATTCCATTTAGAA 20655 ii -- i ---- iv v iv i -- v L1M4_orf2#LIN 2236 AATGAACAATCCGA----AAATGAAATTAAGAAAACAATTCCATTTACAA 2281 chr5ptel1M 20656 TAACTGTTGATAA-CATAAAATATTTGGGAATTTATCTGCCAAGTGAAAG 20704 i -i ii v -v i i vv i iv iv iv L1M4_orf2#LIN 2282 TAGC-ATCAAAAAGAATAAAATACTTAGGAATAAATTTAACAAAAGAAGT 2330 chr5ptel1M 20705 TCAGGAACTATATAAGCAAAACTACAAAACACTTTCCACACAAATAAAGT 20754 v i vi i i vvv i v iv v v v iv L1M4_orf2#LIN 2331 GCAAGACTTGTACACTGAAAACTACAAAACATTGTTGAAAGAAATTAAAG 2380 chr5ptel1M 20755 CAGATCTAAGCAATTGGAAAAATAT--CAAGT-----GACCAGCAAATAT 20797 v i ii v i i -- v ----- iii v i iv L1M4_orf2#LIN 2381 AAGACCTAAATAAATGGAAAGACATCCCATGTTCATGGATTGGAAGACTT 2430 chr5ptel1M 20798 AATA-----AAGATGACAATACTCCC-----TAATCTATTTATTTAGTGC 20837 ----- i ----- i ivv i ii L1M4_orf2#LIN 2431 AATATTGTTAAGATGGCAATACTCCCCAAATTGATCTACAGATTCAACGC 2480 chr5ptel1M 20838 TATGCCAATCAAACTTCCAAGAAACTATTTTACTGA 20873 v v v v i ivvi? v i v L1M4_orf2#LIN 2481 AATCCCTATCAAAATCCCAGCTGNCTTTTTTGCAGA 2516 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 36.90 CpG sites = 185, Kimura (unadjusted) = 38.16 Transitions / transversions = 1.15 (185/161) Gap_init rate = 0.03 (33 / 1192), avg. gap size = 1.76 (58 / 33) 538 25.41 4.78 5.95 chr5ptel1M 20896 21167 (978833) C L1MD_orf2#LINE/L1 (1635) 1659 1391 m_b217s551i7 8572 chr5ptel1M 20896 TTGCTGTAATCTCTTTGCTAATATTTTATTTAAGATTTTTGCATAGATAT 20945 v v ?v i v i i vv i C L1MD_orf2#LIN 1659 TTGCTGAATTCNATTTGCTAATATTTTGTTGAGGATTTTTGCGTCTATGT 1610 chr5ptel1M 20946 TCATTAGGGAAATTCATTGGTCTATAATGTTCTTTTTCTTT-TTCACCCT 20994 v ----i i i v i v -i vv ii C L1MD_orf2#LIN 1609 TCATGAGGGA----TATTGGTCTGTAGTTTTCTTTTTTTGTACTGTCTTT 1564 chr5ptel1M 20995 ACCTGGTGTAGGTAGCAGCCCTATAAAGGTGTCATAAAA-GAATTTGGTA 21043 ii v v v vviv vv iv - i v v C L1MD_orf2#LIN 1563 GTCTGGTTTTGGTATCAGGGTAATACTGGCCTCATAAAATGAGTTGGGAA 1514 chr5ptel1M 21044 GGATTCCTTTTTCCTTTATTTT-TGAAACAATTTGCTATTATTAGAATTA 21092 vi i ii i i - i v i------ i -- --- C L1MD_orf2#LIN 1513 GTGTTCCCTCCTCTTCTATTTTCTGGAAGAG------ATTGT--G---TA 1475 chr5ptel1M 21093 GAATTAGAATTAATTGTT-TTTAAAT--------GAATTCACATGTGAAT 21133 i vi v - i-------- v vv v C L1MD_orf2#LIN 1474 GAATTGGTGTTAATTCTTCTTTAAACGTTTGGTAGAATTCTCCAGTGAAA 1425 chr5ptel1M 21134 TCATCTTGGCCCCTGAGATTTTTTCTT-AGGAGTT 21167 i - v iv i i -i C L1MD_orf2#LIN 1424 CCATC-TGGGCCTGGAGATTTCTTTTTGGGGAGTT 1391 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 30.34 CpG sites = 33, Kimura (unadjusted) = 31.48 Transitions / transversions = 1.03 (33/32) Gap_init rate = 0.08 (22 / 271), avg. gap size = 1.32 (29 / 22) 918 26.25 5.97 3.03 chr5ptel1M 21209 21593 (978407) L1MD1_3end#LINE/L1 151 546 (443) m_b217s551i8 8573 chr5ptel1M 21209 TTAACTATTGCTCAGAGAAATGCAAATTAAGACAACTCTGAGAAA-CACT 21257 i i ---- i i v vv v - L1MD1_3end#LI 151 TTAGCCATT----AGGGAAATGCAAATTAAAACCACAATGAGATATCACT 196 chr5ptel1M 21258 ACACACCTCTCAGATTGGCTGACAGGAAAAGATAATGACAA------ATG 21301 v v i - iv i i ------ L1MD1_3end#LI 197 ACACACCTATCAGAATGGCTAA-AATAAAAAATAGTGACAACACCAAATG 245 chr5ptel1M 21302 TTGA--GGGATG-GGA-AAACTGGGACACTGATACATTGCTGTTGGAGTT 21347 i i--i - - iv v v iiv L1MD1_3end#LI 246 CTGGCGAGGATGCGGAGAAACTGGATCACTCATACATTGCTGGTGGGAAT 295 chr5ptel1M 21348 ATGAACAGATTCAACCATTCTG-AGAGTGATCTGGAACTATGCTCAAAAA 21396 i i vv i v i i - i iiii i v v - v i L1MD1_3end#LI 296 GTAAAATGGTACAGCCACTCTGGAAAACAGTTTGGCAGT-TTCTTAAAAA 344 chr5ptel1M 21397 GTTATAAACTGTGCA--TACTTT-TGATCCAGCAGTATTACTACTGGGCT 21443 ii -- -i -- iv -i i i vvi v v L1MD1_3end#LI 345 ACTA--AAC-ATGCAACTACCATACGACCCAGCAATTGCACTCCTGGGCA 391 chr5ptel1M 21444 TATATCCCAAAGAGATAATAAAGAAGGG----AAAGGGACCTGTATGTCA 21489 v i i i v vvv v v---- v iii --- L1MD1_3end#LI 392 TTTATCCCAGAGAAATGAAAACTTATGTTCACACAAAAACCTGTA---CA 438 chr5ptel1M 21490 AGAATGTTTGTGGCAGCCTC--TTGTAGTGGCCAGAAACTGGAAACTGAG 21537 v i i i i-- i i i i vivv L1MD1_3end#LI 439 CGAATGTTTATAGCAGCTTTATTCGTAATAGCCAAAAACTGGAAACAACC 488 chr5ptel1M 21538 TGGATG-CCTTCAATTGA-GAATAGCTGAATAAATTGTGGTATATGAATA 21585 ii - iv i- i i i i i i vv L1MD1_3end#LI 489 CAGATGTCCTTCAACGGGTGAATGGTTAAACAAACTGTGGTACATCCATA 538 chr5ptel1M 21586 TTATGGAA 21593 ii L1MD1_3end#LI 539 CCATGGAA 546 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 32.06 CpG sites = 61, Kimura (unadjusted) = 33.31 Transitions / transversions = 1.65 (61/37) Gap_init rate = 0.06 (24 / 384), avg. gap size = 1.46 (35 / 24) 267 22.54 11.29 6.98 chr5ptel1M 22711 22834 (977166) MIRc#SINE/MIR 20 148 (120) m_b217s601i7 8574 chr5ptel1M 22711 GGATAGAGCATTGGGTTTG-AGTCAGGAAGATTATCTTCTTGAGTTGAAA 22759 v i ii - ------- i i vi i MIRc#SINE/MIR 20 GGAAAGAGCACTGGACTTGGAGTCAGGAAGA-------CCTGGGTTCGAG 62 chr5ptel1M 22760 ---CGATTCAGA-ACCTACTAGCCG---AATCCTGAGCCAG-CACTTA-C 22800 --- ii v v- i i ---i i i i v - - MIRc#SINE/MIR 63 TCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAAC 112 chr5ptel1M 22801 CCCAGTTT---CCTTGGTTTCTTCATCTG-AAAACGGG 22834 i -- i --- ii i - i MIRc#SINE/MIR 113 CTC--TCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 27.24 CpG sites = 21, Kimura (unadjusted) = 28.55 Transitions / transversions = 4.20 (21/5) Gap_init rate = 0.14 (17 / 123), avg. gap size = 1.35 (23 / 17) 420 29.03 8.21 1.82 chr5ptel1M 23341 23547 (976453) C L3#LINE/CR1 (585) 3514 3295 m_b217s601i8 8575 chr5ptel1M 23341 GTAACCTGAGAC--CATGAGTTTTT----CAATCAAATCTTA-TATTGGT 23383 i i i i-- v i ---- ii v vi - i i C L3#LINE/CR1 3514 GCAGCCTAAGATTGCATTAGCTTTTTTGGCAGCCACATCACACTGTTGGC 3465 chr5ptel1M 23384 TCATATTAATTTTTTAAT--ACCAAGACCA-TAGGTCTTTTTTTTAACCT 23430 i vi viii -- i i v- i--- v C L3#LINE/CR1 3464 TCATATTGAGCTTGCGGTCAACTAAAACCCCTAGGTCTTTTTC---ACGT 3418 chr5ptel1M 23431 GAAATATTGTGGAGGCAAA-CTTCCCCATTCTCTACTTGTTGATGTTGAT 23479 v ii ivi v i - i i i v vv - C L3#LINE/CR1 3417 GAACTGCTGCTAAGCCAGATCCTCTCCATCCTGTACTTGTGCA-GTTGAT 3369 chr5ptel1M 23480 CCTTTAAACC-AAGTGTAGGG-TTGATCTTTAT----ATTAAATTTTATC 23523 ii i - i i i- v iv ----i i C L3#LINE/CR1 3368 TTTTTGAACCTAAATGCAGGACTTTACATTTATCCCTGTTAAATTTCATC 3319 chr5ptel1M 23524 TTATAAAATTCAGTCCATTATTCC 23547 i viiv i i ii C L3#LINE/CR1 3318 TTGTTGGTTTCGGCCCATCGTTCC 3295 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 36.23 CpG sites = 42, Kimura (unadjusted) = 38.99 Transitions / transversions = 2.47 (42/17) Gap_init rate = 0.06 (13 / 206), avg. gap size = 1.62 (21 / 13) 251 22.73 6.06 0.00 chr5ptel1M 23556 23621 (976379) C L3#LINE/CR1 (1053) 3046 2977 m_b217s601i9 8575 chr5ptel1M 23556 CCACCCAA----ATTATTATCTATCCCACATCTGTTCATCTTGCCCACAA 23601 i ---- i i i v i i v i i C L3#LINE/CR1 3046 CCACCTAACTGTACTATCATCCAGCCCATATTTCTCCATCTTGTCCACAA 2997 chr5ptel1M 23602 GGAAAGAATGTAAGACTTTG 23621 v vv vi C L3#LINE/CR1 2996 GGATATCATGAGAGACTTTG 2977 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 27.62 CpG sites = 9, Kimura (unadjusted) = 27.62 Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.02 (1 / 65), avg. gap size = 4.00 (4 / 1) 197 33.00 4.00 0.00 chr5ptel1M 23564 23663 (976337) C L3b_3end#LINE/CR1 (1062) 144 41 m_b217s601i10 8575 chr5ptel1M 23564 ATTATTATCTATCCCACATCTGTTCATCTTGCCCACAAGGAAAGAATGTA 23613 ii ? i v i v i i i i v vv i vi C L3b_3end#LINE 144 ACCATTNTCCAGCCCACATTTCTCCGTCTTGTCCACGAGGATATCACGAG 95 chr5ptel1M 23614 AGACTTTG--AAACTATTTTTTAAAATTGTGA-AAATTATG-CCATAAAA 23659 -- ivvi vi i iiv - v i - i ii? C L3b_3end#LINE 94 AGACTTTGTCAAATGCCTTGCTGAAATCAAGATACACTATGTCTATGGNA 45 chr5ptel1M 23660 TCTC 23663 ii C L3b_3end#LINE 44 TTCC 41 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 41.63 CpG sites = 22, Kimura (unadjusted) = 47.54 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.03 (3 / 99), avg. gap size = 1.33 (4 / 3) 189 28.00 0.00 0.00 chr5ptel1M 23652 23701 (976299) C L3b_3end#LINE/CR1 (7) 1199 1150 m_b217s601i11 8576 chr5ptel1M 23652 CCATAAAATCTCAAATTTGGAATGGACCTTAAGAGACTTTTAATCAACCC 23701 i i v v i iii v v i i v i C L3b_3end#LINE 1199 CCATAGAATCTCAGAATTGGAAAGGACCTCAGAGGTCATCTAGTCCATCC 1150 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 36.39 CpG sites = 9, Kimura (unadjusted) = 36.39 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 189 26.87 4.70 7.59 chr5ptel1M 25353 25501 (974499) C L3#LINE/CR1 (1991) 2108 1964 m_b217s601i12 8577 chr5ptel1M 25353 TCCCACTTTTCTTTCTCAATAAA--ATTAGTACCATTTTGTTTTCAGAAT 25400 v i v ii -- v v---- vv C L3#LINE/CR1 2108 TCCCTCTTTTCTTCCTCATTGGATCATTTGTAA----TTGTAGTCAGAAT 2063 chr5ptel1M 25401 GTCATTTCTAAAACTGCTTTCCCATGGCCCAACCCAGCCAGTCTAATTTT 25450 v i i -- - --? vviiv vii vv C L3#LINE/CR1 2062 TTCATTTTTAAGA--GC-TTCCCA--NCCCTCTTGAGCCATCTTTCTTTT 2018 chr5ptel1M 25451 AGA-CCCCAGGAAATAAAGT----TTTTTTTTCCTTCTGAATCCTTTAAA 25495 v -i i ? vv ii i ----ii i -- ii i C L3#LINE/CR1 2017 TGAGTCTCNGGCCATGGAATCATACCTCTTTTC--TCTGAATTTTTTGAA 1970 chr5ptel1M 25496 ATGTGC 25501 v C L3#LINE/CR1 1969 ATCTGC 1964 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 34.35 CpG sites = 20, Kimura (unadjusted) = 34.35 Transitions / transversions = 1.18 (20/17) Gap_init rate = 0.09 (14 / 148), avg. gap size = 1.29 (18 / 14) 722 29.56 4.74 2.05 chr5ptel1M 26607 26986 (973014) L1M5_orf2#LINE/L1 1578 1967 (1327) m_b217s551i9 8578 chr5ptel1M 26607 AAGAGAATATTACACAGTAGATCAATTTTTCTAGTGAACATCGGTACAAA 26656 i v ----- i v ii vi v i i L1M5_orf2#LIN 1578 AAAAGAAAATTACA-----GACCAATATCCCTCATGAACATAGATGCAAA 1622 chr5ptel1M 26657 AATTTTGGACAAAATACTTGCAAAGC-AAT-GAGAAAAATATAACACAAG 26704 ii ?i i v v - -v v v -- v L1M5_orf2#LIN 1623 AATCCTNAACAAAATATTAGCAAATCGAATCCAGCAATATATA--AAAAG 1670 chr5ptel1M 26705 GTTTATATAGTATGATCAGGTGGAATCTACATCAGAAATGCAGAGCTGGT 26754 v v i vi i i ii i ivi i ii i L1M5_orf2#LIN 1671 GATAATACATCATGACCAAGTGGGGTTTATCCCAGGAATGCAAGGTTGGT 1720 chr5ptel1M 26755 TCTTTATTAGGGGAACTACCAACATAA-TGGCCATAGCAATAACAAAACC 26803 ivvi v iii v v i ii - vi vi i iv v vv L1M5_orf2#LIN 1721 TTAACATTCGAAAATCAATCAATGTAATTCACCATATTAACAGAATAAAG 1770 chr5ptel1M 26804 AACAGAAATCATATGATTTTCTCAACAGATGCAGAAAAAGGTTTTGA-AA 26852 i v i iv i vv - L1M5_orf2#LIN 1771 GAGAAAAATCATATGATCATCTCAATAGATGCAGAAAAAGCATTTGACAA 1820 chr5ptel1M 26853 AATATAGCATCCATTTCTATTA-----CCT-------CTAGGAATA-AAG 26889 vi i i iv iv -----i ------- - L1M5_orf2#LIN 1821 AATTCAACACCCATTCATGATAAAAACTCTCAGCAAACTAGGAATAGAAG 1870 chr5ptel1M 26890 GGATCGTTCCTTTAAATGATAAGCAGCATCTATCTCCAGCCATGAGCAAG 26939 v - iv vv ivi ivvvv i vvv ? i L1M5_orf2#LIN 1871 GGAAC-TTCCTCAACCTGATAAAGGGCATCTACGAAAAACCTACAGCNAA 1919 chr5ptel1M 26940 TATTATCTGTAAAAGGGATAAACTAAAT-CCTTCCCAATAAGATCAGG 26986 i i viv vi v v ? i ?- i vv i L1M5_orf2#LIN 1920 CATCATACTTAATGGTGAAANACTGAANGCTTTCCCCCTAAGATCGGG 1967 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 37.96 CpG sites = 59, Kimura (unadjusted) = 38.85 Transitions / transversions = 1.16 (59/51) Gap_init rate = 0.04 (16 / 379), avg. gap size = 1.62 (26 / 16) 338 32.27 4.84 4.84 chr5ptel1M 28160 28820 (971180) L1M1_orf2#LINE/L1 1992 2652 (642) m_b217s551i10 8579 chr5ptel1M 28160 ATCACTGTTGTTCAATATAGTATATTAGAAAAGTGAGCTATGGCAAT--A 28207 i i i i-- i ivviv vi --i L1M1_orf2#LIN 1992 ACCACTGTTATTCAACATAGTAC--TGGAAGTCCTAGCTAGAGCAATCAG 2039 chr5ptel1M 28208 ACAAGAGCAAAATAAATCAAAGG-ATTGAGA--GGAAGCAATGAGGAAAC 28254 -- v v i - iv i -- --- v i ii L1M1_orf2#LIN 2040 ACAAGAG--AAAGAAATAAAGGGCATCCAAATTGGAA---AGGAAGAAGT 2084 chr5ptel1M 28255 AAAATCATCACTGTTTGAATATGATTCAATATTATAGGGGGAAGACCCTG 28304 v i vi v v vii v vvv i v i L1M1_orf2#LIN 2085 CAAATTATCCTTGTTTGCAGATGATATGATCTTATATTTGGAAAAACCTA 2134 chr5ptel1M 28305 GAG-CATCAATAAAAAATTACTTGAAATAATTAACAATTTTAGCAAAATA 28353 i - vi v? i i v v i v v i i i v L1M1_orf2#LIN 2135 AAGACTCCACNAAAAAACTATTAGAACTGATAAACAAATTCAGTAAAGTT 2184 chr5ptel1M 28354 GCAGGCTATGACATAAAACTATGTAAACCATCAGAATTTCTTTATATTA- 28402 v ii v v vv iiv i vi v v iii - L1M1_orf2#LIN 2185 GCAGGATACAAAATCAACATACAAAAATCAGTAGCATTTCTATATGCCAA 2234 chr5ptel1M 28403 ---TCACCAATCCTAGTATCAAGCAATAGAAAGGGAAATTCCATTTAAAA 28449 --- v v - iiv -- v vi ii v i v L1M1_orf2#LIN 2235 CAGTGAACAATC-TGAAA--AAGAAATCAAAAAAGTAATCCCATTTACAA 2281 chr5ptel1M 28450 TATCTGTAAATAATA--GAATA--TGAGAGGTAGACCCTTGCTAAGACAA 28495 v iii v --i -- ii iv i--- iviv i v L1M1_orf2#LIN 2282 TAGCCACAAATAAAATTAAATACCTAGGAATTAA---CTTAACCAAAGAA 2328 chr5ptel1M 28496 ACTCAGGAACTATG---TGAACACTTATAGAACACACTTTTCAT-ACAGA 28541 iivv i v v i--- v - i ----- v - v L1M1_orf2#LIN 2329 GTGAAAGATCTCTACAATGAAAACT-ATAAAACAC-----TGATGAAAGA 2372 chr5ptel1M 28542 A-TT--AGAT----CTAAACAATTGAAAAGACATCAAATATTAATGGGGA 28584 - -- v---- i v - i i ivv i v ivv L1M1_orf2#LIN 2373 AATTGAAGAGGACACCAAAAAAT-GGAAAGATATTCCATGTTCATGGATT 2421 chr5ptel1M 28585 GACATAGCCAATATAATAATTTTTTAAAAA--CTATGCTGCCTAAACTAA 28632 iv v ii ------- v v-- i i i i vi L1M1_orf2#LIN 2422 GGAAGAATCAATAT-------TGTTAAAATGTCCATACTACCCAAAGCAA 2464 chr5ptel1M 28633 TGTACTTCTTCTGTCCCATCACAATCAGGCTACCAA--AAATTATCTGGT 28680 v vvv vi v v v v iiv -- v v - vii L1M1_orf2#LIN 2465 TCTACAGATTCAATGCAATCCCTATCAAAATACCAATGACATTCT-TCAC 2513 chr5ptel1M 28681 AGAGGTAGAAAAATCAATAATAAAATTTATCTAGAAGAACAAAAAGTTAA 28730 ii v vv v i vv iiiiv L1M1_orf2#LIN 2514 AGAAATAGAAAAAACAATCCTAAAATTTATATGGAACCACAAAAGACCCA 2563 chr5ptel1M 28731 GAATA-TCAAGGGGAT--TAATGGAAAAAAAATAGAAAGGAAGTTGACCT 28777 -i i vv -- i - v i i i vv i -- vii L1M1_orf2#LIN 2564 GAATAGCCAAAGCTATCCTGA-GCAAAAAGAACAAAACTGGAG--GAATC 2610 chr5ptel1M 28778 AGCAATATCAGATTTTAAACCATATCATAATAAAGTAGTAACC 28820 - v i v i i ii ii i ivivvi L1M1_orf2#LIN 2611 A-CATTACCTGACTTCAAATTATACTACAGAGCTATAGTAACC 2652 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 43.10 CpG sites = 106, Kimura (unadjusted) = 43.10 Transitions / transversions = 1.09 (106/97) Gap_init rate = 0.07 (49 / 660), avg. gap size = 1.31 (64 / 49) 467 31.33 1.83 0.90 chr5ptel1M 29013 29231 (970769) L1ME5_3end#LINE/L1 57 277 (664) m_b217s551i12 8578 chr5ptel1M 29013 CCCAAT-GATAAATGGTTAAAGGAGATGAACAAGAAGTTTTCAGAGGAAG 29061 - v vi v i v i v i i L1ME5_3end#LI 57 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAGG 106 chr5ptel1M 29062 AA--TCAAAGTGATCTA-TGATTTTATGAAGAAGTACTCTAAATCACTTT 29108 --i i iv -- -ii viv ii i v v i vv L1ME5_3end#LI 107 AAACCCGAAAGG--CTAACAAGCATATGAAGAGATGCTCAAACTCATTAG 154 chr5ptel1M 29109 TGATTAAAGAATTACAAATTAAAACAACTCTGAGGAACCATCTCACACCT 29158 i i i v i vv iv i ii i L1ME5_3end#LI 155 TAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCT 204 chr5ptel1M 29159 ATCAGATGGGTGAGTATGACAAAAAAGGAAAATGATAAATTGTGAGGTGA 29208 i iv ii iv v v ivv v vi i vv iv v i L1ME5_3end#LI 205 ATTAGACTGGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTGGCGAGG 254 chr5ptel1M 29209 ATGTGGGAAAATAAAAAGCTTTA 29231 i ? ii v i i L1ME5_3end#LI 255 ATGTGGGGANATAGGAACCCTCA 277 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 41.19 CpG sites = 39, Kimura (unadjusted) = 42.01 Transitions / transversions = 1.34 (39/29) Gap_init rate = 0.02 (5 / 218), avg. gap size = 1.20 (6 / 5) 485 28.21 1.28 0.00 chr5ptel1M 29013 29168 (970832) L1ME3Cz_3end#LINE/L1 53 210 (787) m_b217s551i11 8578 chr5ptel1M 29013 CCCAAT-GATAAATGGTTAAAGGAGATGAACAAGAAGTTTTCAGAGGAAG 29061 - v vi v i v i iv i i L1ME3Cz_3end# 53 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chr5ptel1M 29062 AA-TCAAAGTGATCTATGATTTTATGAAGAAGTACTCTAAATCACTTTTG 29110 -i vi i ii v i viv i ii i v vv vv i L1ME3Cz_3end# 103 AAACCCGAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTA 152 chr5ptel1M 29111 ATTAAAGAATTACAAATTAAAACAACTCTGAGGAACCATCTCACACCTAT 29160 i ii v i ? vv iv i i L1ME3Cz_3end# 153 ATCAGGGAAATGCAAATTAAAACNACAATGAGATACCATTTCACACCCAT 202 chr5ptel1M 29161 CAGATGGG 29168 v L1ME3Cz_3end# 203 CAGATTGG 210 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.45 CpG sites = 25, Kimura (unadjusted) = 36.49 Transitions / transversions = 1.32 (25/19) Gap_init rate = 0.01 (2 / 155), avg. gap size = 1.00 (2 / 2) 22 0.00 0.00 0.00 chr5ptel1M 29254 29277 (970723) (AT)n#Simple_repeat 1 24 (0) m_b217s252i16 8580 chr5ptel1M 29254 ATATATATATATATATATATATAT 29277 (AT)n#Simple_ 1 ATATATATATATATATATATATAT 24 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 15 5.76 7.50 4.88 chr5ptel1M 29415 29454 (970546) (ACATATG)n#Simple_repeat 1 41 (0) m_b217s252i17 8581 chr5ptel1M 29415 ACATATG-CATATGCACATATGAACATAT-ACAT-GGACAAAT 29454 - - - - -v v (ACATATG)n#Si 1 ACATATGACATATG-ACATATG-ACATATGACATATGACATAT 41 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.13 (5 / 39), avg. gap size = 1.00 (5 / 5) 656 24.23 0.00 1.86 chr5ptel1M 29642 29805 (970195) MIRc#SINE/MIR 10 170 (98) m_b217s601i13 8582 chr5ptel1M 29642 GTCATATAGTAGATAGAGCACGGGATGTAGAGCCAGGAAGTCCTGAGTTC 29691 vi ii i v v iv i i v i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr5ptel1M 29692 AAATTCATCCTCAGACATTTTATTAGCTACGTGATCCCAGGCAAGTCACT 29741 i i i vvv v v i - i ii i iii MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTT-ACTAGCTGTGTGACCTTGGGCAAGTCACT 108 chr5ptel1M 29742 TACCCCCTATGTGGCTCAGTTTCTTCACCTGTAAAATGGGGAATAATAAT 29791 v i v v v i i - MIRc#SINE/MIR 109 TAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGG-ATAATAAT 157 chr5ptel1M 29792 AAACTGCCATGACT 29805 - v v v MIRc#SINE/MIR 158 -ACCTGCCCTGCCT 170 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 28.85 CpG sites = 22, Kimura (unadjusted) = 29.74 Transitions / transversions = 1.29 (22/17) Gap_init rate = 0.02 (3 / 163), avg. gap size = 1.00 (3 / 3) 207 33.33 2.53 1.25 chr5ptel1M 30535 30613 (969387) L2b_3end#LINE/L2 198 277 (189) m_b217s601i14 8583 chr5ptel1M 30535 TCTTCCAAGTCTCAACAAAAATTCCACTTTCCACAGGAAGACTTTCCTGG 30584 i i i i vv vi i i iv i v i i i L2b_3end#LINE 198 TCCTTCAGGTCTCAGCTCAAATGTCACCTCCTCCGGGAAGCCCTCCCTGA 247 chr5ptel1M 30585 TCCCTCAGTGCTAACT--GGAGCCTTCCCCT 30613 i i - iiiv -- v i i L2b_3end#LINE 248 CCCCCCAG-GCCGGGTCAGGCGCCCTCCTCT 277 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 42.51 CpG sites = 19, Kimura (unadjusted) = 47.96 Transitions / transversions = 2.71 (19/7) Gap_init rate = 0.03 (2 / 78), avg. gap size = 1.50 (3 / 2) 18 0.00 0.00 0.00 chr5ptel1M 30715 30734 (969266) (AC)n#Simple_repeat 1 20 (0) m_b217s252i18 8584 chr5ptel1M 30715 ACACACACACACACACACAC 30734 (AC)n#Simple_ 1 ACACACACACACACACACAC 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 216 28.70 6.59 4.30 chr5ptel1M 30750 30840 (969160) L2d2_3end#LINE/L2 413 505 (50) m_b217s601i15 8583 chr5ptel1M 30750 GCTTGTATGTTACCTTTCCTACTAGATTGTGAGCT-CTTGAGCTTAGGGA 30798 i i i v ii ii v i - vvi L2d2_3end#LIN 413 GTTTATGTCTTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGA 462 chr5ptel1M 30799 CTATTTTTGA-----CTTTGTATCTACAATAACTATAGTTTAGTACA 30840 i v i v ----- iv v i i ---- ii i L2d2_3end#LIN 463 CCATGTCTTATACTTCTTTGTATCCCCCACAGC----GCCTAGCACA 505 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 38.04 CpG sites = 17, Kimura (unadjusted) = 38.04 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.07 (6 / 90), avg. gap size = 1.67 (10 / 6) 200 22.45 7.55 11.76 chr5ptel1M 30751 30856 (969144) L2c_3end#LINE/L2 355 456 (22) m_b217s601i16 8583 chr5ptel1M 30751 CTTGTATGTTACCTTTCCTACTAGATTGTGAGCT-CTTGAGCTTAGGGAC 30799 ? v iv --- i i - vvi L2c_3end#LINE 355 CNTGTCTGTCTCCT---CCACTAGACTGTGAGCTCCTTGAGGGCAGGGAC 401 chr5ptel1M 30800 TATTTTTGA-----CTTTGTATCTACAATAACTATAGTTTAGTACATA-T 30843 ii v i v ----- iv ii------- ii i i - L2c_3end#LINE 402 CGTGTCTTATTCATCTTTGTATCCCCAGC-------GCCTGGCACATAGT 444 chr5ptel1M 30844 AATGGCGC-CAATA 30856 -- - L2c_3end#LINE 445 A--GGCGCTCAATA 456 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 24.51 CpG sites = 14, Kimura (unadjusted) = 27.69 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.15 (16 / 105), avg. gap size = 1.25 (20 / 16) 40 2.63 0.00 0.00 chr5ptel1M 31674 31712 (968288) (GT)n#Simple_repeat 1 39 (0) c_b217s251i1 8585 chr5ptel1M 31674 GTGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 31712 i (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 39 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 363 28.65 2.05 1.53 chr5ptel1M 32715 32909 (967091) PRIMA41-int#LTR/ERV1 4583 4778 (2978) m_b217s701i0 8586 chr5ptel1M 32715 GAATGGTTTACAGATGG--GTTGAGCTTCTTTGAAAATGGGGAA-AGAAA 32761 -- -- - v v v?v i - PRIMA41-int#L 4583 GAATGGTTTACAGATGGAAGT--AGCTT-TGTGCACNAGGGAAACAGAAA 4629 chr5ptel1M 32762 GGCAGGATATTCTGTGGTGACTCTCCATGGCACGCTAGAAACCAAGCCAT 32811 ? i v ? v vi vv ? ivii?v v ii ?? v v PRIMA41-int#L 4630 GGCNGGGTATGCTGTNGTTAGCCAACANGAGGTNATCGAGGCNNAGGCCT 4679 chr5ptel1M 32812 TGCCTCCTGGGACCTCTGCCCAGGAAGGTGAACCCATTGCCATGAACAGA 32861 i vv vv? v i ii i vv iiv ? iv ? vi i PRIMA41-int#L 4680 TACCGGCTTCNACCTCAGCTCAAAAGGCGGAATTAATNGCTCTNATTAGG 4729 chr5ptel1M 32862 GCTTTGGAACTGGGGAAGGGAATGAGAGTAAACATC-CTACTGGCTCCA 32909 ii ?v i i ivv i v ?-?i ii PRIMA41-int#L 4730 GCCCTNCAATTGGGAAAGGACTTAAGAGTCAACATNTNCACTGATTCCA 4778 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 40.01 CpG sites = 27, Kimura (unadjusted) = 40.01 Transitions / transversions = 0.96 (27/28) Gap_init rate = 0.03 (6 / 194), avg. gap size = 1.17 (7 / 6) 274 27.88 2.83 1.87 chr5ptel1M 33107 33212 (966788) LTR39-int#LTR/ERV1 8530 8636 (407) m_b217s701i1 8587 chr5ptel1M 33107 GTCTTAGATAACCGAATGGCCTTAAATTGTCTCCTTGCC--TCAAGCAGA 33154 iv i i i iiv i v --? i v LTR39-int#LTR 8530 GTCTTAGATAATAGGATAGCCTTAGATTACATCTTAGCCGANCAGGGAGA 8579 chr5ptel1M 33155 GGTGTCTGTGCCCTGGCCAATACCTCTTGCT-TATGTACATTAACAAGTC 33203 i v i --v v v ? v v - iv v i i LTR39-int#LTR 8580 AGTGTGTATG--GTTGCAAATNCCACATGCTATACTTACATAAACGAATC 8627 chr5ptel1M 33204 AGGAAAGGT 33212 v vii LTR39-int#LTR 8628 TGCGGAGGT 8636 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 33.24 CpG sites = 15, Kimura (unadjusted) = 36.25 Transitions / transversions = 1.07 (15/14) Gap_init rate = 0.04 (4 / 105), avg. gap size = 1.25 (5 / 4) 29 12.48 0.00 0.00 chr5ptel1M 35409 35452 (964548) (T)n#Simple_repeat 1 44 (0) m_b217s252i19 8588 chr5ptel1M 35409 TTTTATTTGTTTTTTTTTTTTTTTTTTTTTTATTTTATTTTATT 35452 v v v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 44 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 22 7.25 0.00 0.00 chr5ptel1M 35922 35950 (964050) (T)n#Simple_repeat 1 29 (0) m_b217s252i20 8589 chr5ptel1M 35922 TTTCTTTTTTTTTTTTTTTTTTTTTATTT 35950 i v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 15 29.02 1.49 3.03 chr5ptel1M 38245 38311 (961689) (GGAGG)n#Simple_repeat 1 66 (0) m_b218s252i0 8590 chr5ptel1M 38245 GGAGGGCAGGAG-GAGGAGGGGAGGTGGAGGCAGAGGAGAAAGCTGGGGC 38293 v i - i - -i i ii vv v (GGAGG)n#Simp 1 GGAGGGGAGGGGAGGGGAGGGGAGG-GGAGG-GGAGGGGAGGGGAGGGGA 48 chr5ptel1M 38294 GGGAAGAGGGGCTGAGGG 38311 i i i vv (GGAGG)n#Simp 49 GGGGAGGGGAGGGGAGGG 66 Matrix = Unknown Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.05 (3 / 66), avg. gap size = 1.00 (3 / 3) 18 11.35 5.26 0.00 chr5ptel1M 38245 38282 (961718) (GGA)n#Simple_repeat 1 40 (0) m_b218s252i1 8590 chr5ptel1M 38245 GGAGG-GCAGGAGGAGGAGG-GGAGGTGGAGGCAGAGGAG 38282 - v - v vi (GGA)n#Simple 1 GGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG 40 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 412 26.47 18.46 3.12 chr5ptel1M 39745 39939 (960061) MIRb#SINE/MIR 13 236 (32) m_b218s601i0 8591 chr5ptel1M 39745 GTGGCGCGGTGGATTGAATGCAGGGTCTAGAATCATGAAGACCTGAATTC 39794 i i vv iii i v i i i viv ii MIRb#SINE/MIR 13 GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTC 62 chr5ptel1M 39795 AAATTC-AACTCCAGACGCATATTAGCTGTGTGAACGTGGGCGGGTCAC- 39842 i i -ii i- v i v i v v ii i - MIRb#SINE/MIR 63 GAATCCCGGCTCT-GCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACT 111 chr5ptel1M 39843 -AATCT------GCCTCA-------------------GGGGTTTACAGCA 39866 - i ------ ------------------- --- i ii MIRb#SINE/MIR 112 TAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGG---ATAATA 158 chr5ptel1M 39867 GCGCCTATATCCCAGGGTTGCTATTATCAGGATT-----AGATA---CCT 39908 iii iv v --- i v ----- --- v MIRb#SINE/MIR 159 ATACCTACCTCGCAGGGTTG---TTGTGAGGATTAAATGAGATAATGCAT 205 chr5ptel1M 39909 GTAAAGCACTAGCCACAGTGTCGGGCACATA 39939 i viv i v MIRb#SINE/MIR 206 GTAAAGCGCTTAGCACAGTGCCTGGCACATA 236 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.92 CpG sites = 34, Kimura (unadjusted) = 34.27 Transitions / transversions = 2.12 (34/16) Gap_init rate = 0.07 (14 / 194), avg. gap size = 3.07 (43 / 14) 16 23.47 0.00 0.00 chr5ptel1M 40140 40174 (959826) (T)n#Simple_repeat 1 35 (0) m_b218s252i2 8592 chr5ptel1M 40140 TTTTAATTTTTTAAATATTTTTTTTTTTCTTTTTT 40174 vv vvv v i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 35 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 404 25.24 0.00 9.62 chr5ptel1M 40196 40309 (959691) C MIRb#SINE/MIR (161) 107 4 m_b218s601i1 8593 chr5ptel1M 40196 ATTTGCCCAGGCTCATGAAGCTAGGAAGCAGTCAGTGATTGAGACCAGAT 40245 i i v iiv v ii - ------ v vi C MIRb#SINE/MIR 107 ACTTGCCCAAGGTCACACAGCTAGTAAGTGG-CAG------AGCCGGGAT 65 chr5ptel1M 40246 TTGAACTTGGGTCCTTCTGACTCCAGGACCTGTGCTCTGTCCACTGTACC 40295 i iii iv iii i v i C MIRb#SINE/MIR 64 TCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCACC 15 chr5ptel1M 40296 ATCTAGCTGTCCCT 40309 i--- i C MIRb#SINE/MIR 14 AC---GCTGCCCCT 4 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.58 CpG sites = 19, Kimura (unadjusted) = 31.96 Transitions / transversions = 2.71 (19/7) Gap_init rate = 0.09 (10 / 113), avg. gap size = 1.00 (10 / 10) 322 13.04 0.00 20.31 chr5ptel1M 40910 40986 (959014) C Charlie4a#DNA/hAT-Charlie (32) 476 413 m_b218s502i0 8594 chr5ptel1M 40910 CCCTTTGGCAGTCTGGTAAAGCGCAAGAGAATCCCTTTAGGATCCCTTTT 40959 i ------------ v - i i C Charlie4a#DNA 476 CCCTTTGGCAGTCTGGTGAAGC------------CTAT-GGACCCCTTCT 440 chr5ptel1M 40960 CAAAATTATGGTTTTAGATGCATAAAA 40986 i v v i C Charlie4a#DNA 439 CAGAATAATGTTTTTAAATGCATAAAA 413 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 13.81 CpG sites = 5, Kimura (unadjusted) = 13.81 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.17 (13 / 76), avg. gap size = 1.00 (13 / 13) 332 24.54 1.94 5.33 chr5ptel1M 41120 41274 (958726) L1M3_orf2#LINE/L1 2991 3140 (148) m_b218s551i0 8595 chr5ptel1M 41120 AAAACCCCAGAGCATTATAAAATGCAAAA-TCGACAATTTTGATTACATT 41168 v v - -- i - - v v vv i i L1M3_orf2#LIN 2991 AAAAGCACAG-GCA--ACAAAA-GCAAAAATAGACAAGTGGGACTACATC 3036 chr5ptel1M 41169 TAATTAAAACATTTTTGCACAGACAAAAGCAACA-TAAACAAGGTTAAAA 41217 v i vii i - i v - v ii v L1M3_orf2#LIN 3037 AAACTAAAAAGCTTCTGCACAG-CAAAGGAAACAATCAACAGAGTGAAAA 3085 chr5ptel1M 41218 GGGAAG-TACACAAAGCTGGGAAAAAAATTTTACAGACAGTGTTTCTGAT 41266 v v- iv --- i vv i i vi i v L1M3_orf2#LIN 3086 GGCAACCTACGGAA---TGGGAGAAAATATTTGCAAACCATATATCTGAT 3132 chr5ptel1M 41267 AAAGGCTT 41274 i v L1M3_orf2#LIN 3133 AAGGGGTT 3140 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 28.89 CpG sites = 17, Kimura (unadjusted) = 29.83 Transitions / transversions = 0.89 (17/19) Gap_init rate = 0.07 (11 / 154), avg. gap size = 1.00 (11 / 11) 194 38.97 4.91 2.62 chr5ptel1M 42976 43199 (956801) C L2#LINE/L2 (242) 2840 2612 m_b218s601i2 8596 chr5ptel1M 42976 GAGCAG--GATTG-CACGGTCAGAATGATGCTTAAGAAAAATCATTTCAG 43022 -- v - i i v v v i i v i ii i iii C L2#LINE/L2 2840 GAGCAGAGGAGTGACATGATCTGACTTACGTTTTAAAAGGATCACTCTGG 2791 chr5ptel1M 43023 TAAAAGGATAGAAGATGAATTGGAGGATTGGACAGAAATG--AGTGGAGG 43070 ivivv vi v ii ii i ? i-- i iiii -- ii - C L2#LINE/L2 2790 CTGCTGTGTTGAGAATAGACTGNAGGG--GGGCAAGGGTGGAAGCAG-GG 2744 chr5ptel1M 43071 AGACAAAACAGAATGCGGTTGAAATAGTTCAGGTGAAATATGA---TGAC 43117 v ivi i v vi v i i i i i v --- i C L2#LINE/L2 2743 AGACCAGTTAGGAGGCTATTGCAGTAATCCAGGCGAGAGATGATGGTGGC 2694 chr5ptel1M 43118 TTCAATTAAGGTGTTAGCTGTATAAAT-ATAAGAATAGGTCAAATGTGAA 43166 vi ii i v i v iv ii -i i vv ii vivii C L2#LINE/L2 2693 TTGGACCAGGGTGGTGGCAGTGGAGGTGGTGAGAAGTGGTCGGATTCTGG 2644 chr5ptel1M 43167 GGATGTTGGGTTAAA--TACAAATGACAAGATTTG 43199 iv i --- i -- v ivi i C L2#LINE/L2 2643 ATATATT---TTGAAGGTAGAGCCGACAGGATTTG 2612 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 56.30 CpG sites = 58, Kimura (unadjusted) = 60.95 Transitions / transversions = 2.15 (58/27) Gap_init rate = 0.05 (12 / 223), avg. gap size = 1.42 (17 / 12) 424 29.17 5.56 0.00 chr5ptel1M 43197 43340 (956660) L2d2_3end#LINE/L2 392 543 (12) m_b218s601i3 8597 chr5ptel1M 43197 TTGTCATTTC-CTCCTCCCTT-TTTAT-TCTTTTATTTCCA--TAGATTG 43241 i v- ii v v - - v v ii -- L2d2_3end#LIN 392 TTGTTATTTAACTTTTCACGTGTTTATGTCTTGTCTCCCCAACTAGATTG 441 chr5ptel1M 43242 TGAATTCTTTGACAGCAGAGACTGTCCTTTGTCTTTCTTTGTATCCT--- 43288 i ii i vi i ii vii i vi i--- L2d2_3end#LIN 442 TAAGCTCCTTGAGGGCAGGGACCATGTCTTATACTTCTTTGTATCCCCCA 491 chr5ptel1M 43289 CAATGCTTAGTATAGTGCCCAAAATATAGCAGGCACTAAATAAAGATTTA 43338 ii i i i iviv i i i i v v i L2d2_3end#LIN 492 CAGCGCCTAGCACAGTGCCTTGCACACAGTAGGCGCTCAATAAATATTTG 541 chr5ptel1M 43339 TT 43340 L2d2_3end#LIN 542 TT 543 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.78 CpG sites = 30, Kimura (unadjusted) = 39.22 Transitions / transversions = 2.50 (30/12) Gap_init rate = 0.03 (5 / 143), avg. gap size = 1.60 (8 / 5) 277 30.43 0.00 0.00 chr5ptel1M 43983 44051 (955949) L2c_3end#LINE/L2 370 438 (40) m_b218s601i4 8598 chr5ptel1M 43983 CAATAGATGGTGAGCTCCTTGAGACCCAGGGCTATCTTTTATATATATTT 44032 v iv iv vi i ii v i vi v L2c_3end#LINE 370 CACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTT 419 chr5ptel1M 44033 ATATATCCAGCATGTGGCA 44051 i vi iiv L2c_3end#LINE 420 GTATCCCCAGCGCCTGGCA 438 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.07 CpG sites = 12, Kimura (unadjusted) = 40.09 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.00 (0 / 68), avg. gap size = 0.0 (0 / 0) 307 26.21 1.90 1.90 chr5ptel1M 44087 44191 (955809) L1ME4c_3end#LINE/L1 271 375 (455) m_b218s551i1 8599 chr5ptel1M 44087 ACATTAATATATTGCTGCTGGAATTGTAGAAGGGCACAATCATTTGGAAA 44136 ?i v i v v ? i vv i i v v i L1ME4c_3end#L 271 ACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAA 320 chr5ptel1M 44137 AGCAATGTGG-AAT-TGTGCAAACGAAGTAACTAAAATGTCCACATCCTT 44184 v - -i iiv --i iv iv i i i L1ME4c_3end#L 321 AGCAATTTGGCAATACGTATCAA--GAGCCATAAAAATGTTCATACCCTT 368 chr5ptel1M 44185 TGAACCA 44191 v L1ME4c_3end#L 369 TGACCCA 375 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 32.16 CpG sites = 15, Kimura (unadjusted) = 33.66 Transitions / transversions = 1.25 (15/12) Gap_init rate = 0.04 (4 / 104), avg. gap size = 1.00 (4 / 4) 237 17.98 4.11 8.57 chr5ptel1M 44195 44267 (955733) L2a_3end#LINE/L2 448 517 (0) m_b218s601i5 8600 chr5ptel1M 44195 TATCCCCTCTGAAGCTCCTTAGTACTCTGCTTGGCACATAGTAGGCACTT 44244 ----- v - v vv i i i L2a_3end#LINE 448 TATCCCC-----AGCGCCT-AGAACAGTGCCTGGCACATAGTAGGCGCTC 491 chr5ptel1M 44245 A--AAATGCTTTTTGACT-AATAAAT 44267 -- ii v v - i L2a_3end#LINE 492 AATAAATATTTGTTGAATGAATGAAT 517 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 18.77 CpG sites = 6, Kimura (unadjusted) = 20.58 Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.11 (8 / 72), avg. gap size = 1.12 (9 / 8) 471 30.85 2.55 3.43 chr5ptel1M 44413 44647 (955353) L3#LINE/CR1 3027 3259 (840) m_b218s601i6 8601 chr5ptel1M 44413 ATGAGAATTTAATTAGGGGGATTCAGAACTGGTTGAATGACTGAATGGAA 44462 v i vi i v iv i i iv ivv L3#LINE/CR1 3027 ATGATAGTACAGTTAGGTGGATTCGTAGCTGGTTGAACGACTATACCCAA 3076 chr5ptel1M 44463 AAAATTAATCATTACTGAATC--TGTGAACAAGAAAGGAAATCTCCCATG 44510 ii- iv v v i -- v vv i i ii ivi L3#LINE/CR1 3077 AAGG-TGTTGATTAATGGATCGATGTCAACCTGGAGGGAGGTCTCTAGTG 3125 chr5ptel1M 44511 GAGCGCCTCCAGAGATCTAGTCTCTGA-CATAT-ATATTGAACATTTTAA 44558 v i -v i v - ii i- v i -v i v v L3#LINE/CR1 3126 GCGTGCC-ACAGGGCTCT-GTCCTTGGCCCTGTCCTGTTCAACATTTTTA 3173 chr5ptel1M 44559 TCCATTACTTGGTTTGAAACATAAGTGTCAT--TTGTCAAAAATTTGCAG 44606 v v v vi i iiv v -- i -- L3#LINE/CR1 3174 TCAATGACTTGGATGAAGACATAGAAGGCATGCTTATC--AAATTTGCAG 3221 chr5ptel1M 44607 TTGAAATAAATCCAAGATCTCAATAAGCTAAAATAGTGGAT 44647 v v i v iii --vvi - v ii? L3#LINE/CR1 3222 ATGACACAAAGCTGGGA--GGGAT-AGCTAATACGNTGGAT 3259 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.41 CpG sites = 37, Kimura (unadjusted) = 40.70 Transitions / transversions = 1.12 (37/33) Gap_init rate = 0.05 (12 / 234), avg. gap size = 1.17 (14 / 12) 357 29.30 6.00 4.43 chr5ptel1M 45149 45348 (954652) C L1ME3G_3end#LINE/L1 (294) 630 428 m_b218s551i2 8602 chr5ptel1M 45149 TGCTCATTTCATGTAACATCAGTTCATGCAGGTCTCTCCAGGCCACTCTG 45198 iv ivi vi vv v v i i v i v vii C L1ME3G_3end#L 630 TGCTTTTTTCACTCAACAATATGTCTTGGAGATCTTTCCATGTCAGTACA 581 chr5ptel1M 45199 ---AAATC-ACCCGGCTGGTCATTTTTTATAAAA----CACTAATATTCC 45240 --- i - ------- i v v?---- - i C L1ME3G_3end#L 580 TATAGATCTACC-------TCATTCTTTTTAACNGCTGCA-TAGTATTCC 539 chr5ptel1M 45241 ATAAGATTTATATACCATGGTTTATTTAGCCGTTCTCGAACTGGGTACCC 45290 iv vv ii i i i vv i - i ivv C L1ME3G_3end#L 538 ATAGTATGGATATACCATAATTTATTTAACCATTCCCCTATT-GATGGAC 490 chr5ptel1M 45291 ACTCA----GTTTCTAGTTTCTTGCCACTACCAAGAGGGCTGCCATGAAC 45336 i i ---- i i i i i i v v iv v C L1ME3G_3end#L 489 ATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCTGCAATGAAC 440 chr5ptel1M 45337 ATTTTTGCACAT 45348 ii i C L1ME3G_3end#L 439 ATCCTTGTACAT 428 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.64 CpG sites = 33, Kimura (unadjusted) = 38.53 Transitions / transversions = 1.43 (33/23) Gap_init rate = 0.07 (13 / 199), avg. gap size = 1.62 (21 / 13) 390 24.54 5.13 2.50 chr5ptel1M 45232 45348 (954652) C L1ME3F_3end#LINE/L1 (439) 551 432 m_b218s551i3 8602 chr5ptel1M 45232 TAATATTCCATAAGATTTATATACCATGGTTTATTTAGCCGTTCTCGAAC 45281 vivi vv iii v i --- C L1ME3F_3end#L 551 TAATATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTC---C 505 chr5ptel1M 45282 TG--GGTACCCACTCAG----TTTCTAGTTTCTTGCCACTACCAAGAGGG 45325 -- i ivv i ii ---- i i i i v v v C L1ME3F_3end#L 504 TGTCGATGGACATTTGGGTTGTTTCCAGTTTTTTGCTATTACGAACAGTG 455 chr5ptel1M 45326 CTGCCATGAACATTTTTGCACAT 45348 i i i C L1ME3F_3end#L 454 CTGCTATGAACATTCTTGTACAT 432 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 30.66 CpG sites = 18, Kimura (unadjusted) = 30.66 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.04 (5 / 116), avg. gap size = 1.80 (9 / 5) 216 30.01 8.95 5.25 chr5ptel1M 45611 45923 (954077) L2a_3end#LINE/L2 158 481 (36) m_b218s601i7 8603 chr5ptel1M 45611 GGAAC-CTCTTCCCACAAA-ATC-ACATTAGCTCTTGAATTCA--TACCT 45655 - v i - -i -i vivvvi -- v i L2a_3end#LINE 158 GGAACGCTCTTCCCCCAGATATCCGCAT-GGCTCGCTCCCTCACCTCCTT 206 chr5ptel1M 45656 CA--TCATTACCTTC---TGCTACCCTTCTTATTGGAGAACCCCTCCCTA 45700 -- v i -- --- ii - i --- ? iv i i L2a_3end#LINE 207 CAGGTCTTTGC--TCAAATGTCACC-TTCTCA---GNGAGGCCTTCCCTG 250 chr5ptel1M 45701 ATCTTTCC---TGAAAGAGGGTACCCAAGCCACCCATCTCTTCATTTCCT 45747 i vii i--- i v? vii vv? - ? v i v v i L2a_3end#LINE 251 ACCACCCTATTTAAAATNGCACACCCTCNCC-CCCANCACTCCCTATCCC 299 chr5ptel1M 45748 ACACTGTTACACTGCTTTGGACCTCTCCATCATGCTCCTC-TTATA-GCC 45795 v ---- v ivvii viii iv -ii v- v L2a_3end#LINE 300 CC----TTACCCTGCTTTATTTTTCTCCATAGCACTTATCACCATCTGAC 345 chr5ptel1M 45796 ATTCCTCAGTTTTTCAACTTCCTT-TTTGT-----GT-TGTCTTCCCTCA 45838 v ivi vv -- vi - ----- - i i L2a_3end#LINE 346 ATACTATATATTTT--ACTTATTTATTTGTTTATTGTCTGTCTCCCCCCA 393 chr5ptel1M 45839 ACAGATTAT--GTTTCTTGAGAG-AGGAAATGGCATTTCTTTTTTGGT-A 45884 vi v i -- i i v i - i v --iv v v v - L2a_3end#LINE 394 CTAGAATGTAAGCTCCATGAGGGCAGGGACT--TTTGTCTGTTTTGTTCA 441 chr5ptel1M 45885 TT--TGTACCACCTAAGGCTTAGAACAGTGTCTGGTGCATA 45923 i -- i - i iv i i ii L2a_3end#LINE 442 CTGCTGTATC-CCCAGCGCCTAGAACAGTGCCTGGCACATA 481 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.59 CpG sites = 51, Kimura (unadjusted) = 40.18 Transitions / transversions = 1.34 (51/38) Gap_init rate = 0.11 (33 / 312), avg. gap size = 1.36 (45 / 33) 260 28.33 1.67 0.00 chr5ptel1M 45933 45992 (954008) MIR3#SINE/MIR 126 186 (22) m_b218s601i8 8604 chr5ptel1M 45933 TTCTTCATCTGCAAAATGGAGAAATTGGATTATACAAACTCTGAGGT-TT 45981 i i ii iii i v ii v i -ii MIR3#SINE/MIR 126 TTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCC 175 chr5ptel1M 45982 TTCCAAGTCTG 45992 iv MIR3#SINE/MIR 176 TTCCAGCTCTG 186 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.99 CpG sites = 14, Kimura (unadjusted) = 38.99 Transitions / transversions = 4.67 (14/3) Gap_init rate = 0.02 (1 / 59), avg. gap size = 1.00 (1 / 1) 474 24.79 0.84 1.69 chr5ptel1M 46042 46160 (953840) MIRc#SINE/MIR 10 127 (141) m_b218s601i9 8605 chr5ptel1M 46042 GTGGCACAGTGGGATAGTGCACCAGCTCTGCAGTCAGGAGGACCCTAAGT 46091 ii i - v ii vii v i - ii MIRc#SINE/MIR 10 GTGGTGCAGTGGAA-AGAGCACTGGACTTGGAGTCAGGAAGACC-TGGGT 57 chr5ptel1M 46092 TCAAATCTAGCCTCAGACACGTTTTAGCTGTGTGATCCTGGGCAAGTCAC 46141 i i iv v v v v vi i i MIRc#SINE/MIR 58 TCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCAC 107 chr5ptel1M 46142 TTAACCCCAATTA-CCTCAG 46160 i vv v - MIRc#SINE/MIR 108 TTAACCTCTCTGAGCCTCAG 127 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.46 CpG sites = 17, Kimura (unadjusted) = 30.71 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.03 (3 / 118), avg. gap size = 1.00 (3 / 3) 15 17.16 2.44 2.44 chr5ptel1M 46501 46541 (953459) (AAACAA)n#Simple_repeat 1 41 (0) m_b218s252i3 8606 chr5ptel1M 46501 AAACAAAAA-AAAAATACACAAGAACAATAACAACAAAAACA 46541 - i - v v v i v (AAACAA)n#Sim 1 AAACAAAAACAAAAACA-AAAACAAAAACAAAAACAAAAACA 41 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 389 31.87 3.57 4.25 chr5ptel1M 46898 47205 (952795) L1ME4a_3end#LINE/L1 104 409 (462) m_b218s551i4 8607 chr5ptel1M 46898 AAGAAAT--AAGTGGTCAACTCTAACAGATTAAAAAAAAGTGCTTCAA-- 46943 -- i i --iv v v ? --- - -- L1ME4a_3end#L 104 AAGAAATACAAATGGCCAA--TAAACATATGAAAANA---TG-TTCAACC 147 chr5ptel1M 46944 --ATCATTAAGGAGGGAAGTGCACACCAAAAGCACCCCGAGGTTTCATAT 46991 -- ii v vv ii i v ii vv vvi i vi v L1ME4a_3end#L 148 TCACTAGTAATCAAAGAAATGCAAATTAAAACAACAATGAGATACCATTT 197 chr5ptel1M 46992 CACATCCTGCAAATTGGTAAAAATGACAAAACCAAGCGGTAGTTCTCAGG 47041 iv i ivv i i v-i --i vi i i v i v L1ME4a_3end#L 198 TTCACCTATCAAATTGGCAAAGATT-TAAAA--GATTGATAATACCCAGT 244 chr5ptel1M 47042 GTTGGACAGATTATGGAATGATGGGCGCACTAATACTTTGCTGCTGGAGT 47091 vv iv i ?ivi i i v v vi v iiv L1ME4a_3end#L 245 GTTGGCGAGGGTGTGGNGAAACGGGCACTCTCATACACTGCTGGTGGGAG 294 chr5ptel1M 47092 TGTAAAACAACAAGATCATTGTGAAAAGCAATGTGGAATTATGGAACTAT 47141 viiii vi i v v i ii v v v ---- L1ME4a_3end#L 295 TGTAAATTGGTACAACCTTTCTGGAGGGCAATTTGGCAATATG----TAT 340 chr5ptel1M 47142 AATAA--TTT--AAATGTTCATATCCTTTGAACCAGAAACT-TACTTCCT 47186 v v --i -- ? i v v i -i iv L1ME4a_3end#L 341 CAAAAGCCTTAAAAATGTNCATACCCTTTGACCCAGTAATTCCACTTCTA 390 chr5ptel1M 47187 GGACTTAAACCCCAAGAAA 47205 v v v iv i L1ME4a_3end#L 391 GGAATTTATCCTAAGGAAA 409 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 42.25 CpG sites = 49, Kimura (unadjusted) = 42.85 Transitions / transversions = 1.09 (49/45) Gap_init rate = 0.06 (19 / 307), avg. gap size = 1.26 (24 / 19) 260 32.72 8.95 5.64 chr5ptel1M 46903 47349 (952651) L1MB4_3end#LINE/L1 111 571 (356) m_b218s551i5 8607 chr5ptel1M 46903 ATAAGTGGTCAACTCTAA-CAGATTAAAAAAAAGTGCTTCAAATCATTA- 46950 i i i --- - v v i --- iv v i - L1MB4_3end#LI 111 ACAAATGGCCAA---TAAGCACATGAAAAGA---TGCTCAACATCACTAG 154 chr5ptel1M 46951 --AGGAGGGAAGTGCACACCAAAAGCACCCCGAGGTTTCATATCACATCC 46998 -- vv i v i v vvi i vi iv i L1MB4_3end#LI 155 TCATTAGGGAAATGCAAATCAAAACCACAATGAGATACCACTTCACACCC 204 chr5ptel1M 46999 TGCAAATTGGTAAAAATGACAAAACCAAGCGGTAGTTCTCAGG-GTTGGA 47047 vvi iiv iv v? -- -- i v iv vv i - v L1MB4_3end#LI 205 ACTAGGATGGCTATNAT--CAAAA--AAACGGAAAATAACAAGTGTTGGC 250 chr5ptel1M 47048 CAGATTATGGAATGATGGGCGCACTAATACTTTGCTGCTGGAGTTGTAAA 47097 v iv i ivi v vi v vi i v v iiv L1MB4_3end#LI 251 GAGGATGTGGAGAAATTGGAACCCTCGTGCATTGCTGGTGGGAATGTAAA 300 chr5ptel1M 47098 ACAACAAGATCATTGTGAAAAGCAATGTGGAATTATGGAACTATAATAAT 47147 iiiiiviii ii i i i v -----i vv ivi v v L1MB4_3end#LI 301 ATGGTGCAGCCGCTGTGGAAAACAGTTTGG-----CGGTTCCTCAAAAAG 345 chr5ptel1M 47148 TTAAATGTTCA--TATCCTTTGAACCAGAAACTTACTTCCTGGACTTAAA 47195 ii vv -- i v v v v i ivvi i iiv v L1MB4_3end#LI 346 TTAAACATAGAATTACCATATGACCCAGCAATTCCACTCCTAGGTATATA 395 chr5ptel1M 47196 CCCCAAGAAAGCTACTGATGG-AGGGA----AGGAAATCCCCATATACAC 47240 v ii ----i vi - ---- iv i v i-- i L1MB4_3end#LI 396 CCCAAAAGAA----TTGAAAGCAGGGACTCAAACAGATACT--TGTACAC 439 chr5ptel1M 47241 CTAATATTTATGAACAACACTTTGTTT--------------GTGGAAACA 47276 - i i - i i -- i i-------------- L1MB4_3end#LI 440 C-AATGTTCAT-AGCAGCA--TTATTCACAATAGCCAAAAGGTGGAAACA 485 chr5ptel1M 47277 A----AGT---------AGATGCAATGTCTAAACAAATTTTGGTACACAA 47313 ---- --------- - vv v v i i v L1MB4_3end#LI 486 ACCCAAGTGTCCATAACAGATG-AATGGATAAACAAAATGTGGTATATAC 534 chr5ptel1M 47314 ATGTAATAGAGTATTATTATGCTGCAACAA-AAATGA 47349 ii i i vv i?i v -i L1MB4_3end#LI 535 ATACAATGGAATATTATTCAGCCNTAAAAAGGAATGA 571 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 43.28 CpG sites = 77, Kimura (unadjusted) = 44.59 Transitions / transversions = 1.26 (77/61) Gap_init rate = 0.08 (37 / 446), avg. gap size = 1.78 (66 / 37) 366 32.46 9.14 4.62 chr5ptel1M 46957 47350 (952650) L1ME4c_3end#LINE/L1 163 573 (257) m_b218s551i6 8607 chr5ptel1M 46957 GAAGTGCACACCAAAAGCACCCCGAGGTTTCATATCACATCCTGCAAATT 47006 i v ii ivv vvi i vi v i ii ivvi L1ME4c_3end#L 163 GAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCTATTAAATT 212 chr5ptel1M 47007 GGTAAAAATGACAAAACCAAGCGGTAGTTCTCAGGGTTGGACAGATTATG 47056 i i v-i -- vi i i v i iv i vv i? ii L1ME4c_3end#L 213 AGCAAAAATT-TAAAA--AATTGATAATACCCAATGCTGGCGAGGNTGCG 259 chr5ptel1M 47057 GAATGATGGGCGCACTAATACTTTGCTGCTGGAGTTGTAAAACAACAAGA 47106 vivi iv ii ? v v v vi? viiii vi L1ME4c_3end#L 260 GTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACAA 309 chr5ptel1M 47107 TCATTGTGAAAAGCAATGTGGAATTATG------GAACTATAATAATTTA 47150 i v v i v v v i ------ i i ------ L1ME4c_3end#L 310 CCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAA------A 353 chr5ptel1M 47151 AATGTTCATATCCTTTGAACCAGAAACT-TACTTCCTGGACTTAAACCCC 47199 i v v i -i iv v v v iv L1ME4c_3end#L 354 AATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTA 403 chr5ptel1M 47200 AAGAAAGCTACTGATGGAGGGAAGGAAATCCCCATATACACCTA-ATATT 47248 i -- v -- vi ii vvv i i vv - i L1ME4c_3end#L 404 AGGAAA--TAAT--TCAAAAGAAGGAAAAAGCTATATGCACGAAGATGTT 449 chr5ptel1M 47249 TATGAACAACACTTTGTTTG--------------TGGAAACAAAGTAGAT 47284 i v-i i i-- i i-------------- vv i L1ME4c_3end#L 450 CATT-GCAGCG--TTATTTATAATAGCGAAAAATTGGAAACAACCTAAAT 496 chr5ptel1M 47285 GC-------------AATGTCTAAACAAATTTTGGTACACAAATGTAATA 47321 i------------- vi ii v iv? ivii i L1ME4c_3end#L 497 GTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATG 546 chr5ptel1M 47322 GAGTATTATTATGCTGCAA-CAAAAATGAT 47350 i--- v v -i L1ME4c_3end#L 547 GAA---TATTATGCAGCCATTAAAAATGAT 573 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 42.16 CpG sites = 70, Kimura (unadjusted) = 44.66 Transitions / transversions = 1.35 (70/52) Gap_init rate = 0.06 (25 / 393), avg. gap size = 2.20 (55 / 25) 12 15.32 6.38 4.17 chr5ptel1M 52499 52545 (947455) (CAGACA)n#Simple_repeat 1 48 (0) m_b218s252i4 8608 chr5ptel1M 52499 CAGA-ACAAACA-TGACAAAGACATTCTG-CACTGACACAAACACAGACA 52545 - i -v v -- v - v i (CAGACA)n#Sim 1 CAGACACAGACACAGACACAGACA--CAGACACAGACACAGACACAGACA 48 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.11 (5 / 46), avg. gap size = 1.00 (5 / 5) 21 0.00 0.00 0.00 chr5ptel1M 53381 53403 (946597) (A)n#Simple_repeat 1 23 (0) m_b218s252i5 8609 chr5ptel1M 53381 AAAAAAAAAAAAAAAAAAAAAAA 53403 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAA 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 402 32.22 8.29 2.70 chr5ptel1M 53970 54355 (945645) C L1PREC2_orf2#LINE/L1 (982) 2312 1906 m_b218s551i7 8610 chr5ptel1M 53970 ATTCCAAAGTACTTTAAATATTTTATAGTAATTGTAAGCGATATTTC--T 54017 v i i vviv i i i i ii iv v -- C L1PREC2_orf2# 2312 ATTCCTAGGTATTTTATTCTTTTTGTGGCAATTGTGAATGGGATTGCGTT 2263 chr5ptel1M 54018 CTTTAT----CTTCCTACTGAGGT-TTATTGGTGTTAGATCGAAATGACA 54062 i v ---- ii vi vi v - i --- v i vi C L1PREC2_orf2# 2262 CCTGATTTGGCTCTCGGCTTGGCTGTTGTTGGTGT---ATAGGAATGCTA 2216 chr5ptel1M 54063 ATGATTTGTGTGGAT-ATTTTTATCTCCTGAAAATTTGCTAAAGGAATTG 54111 i v iv -iv i v v i --- C L1PREC2_orf2# 2215 GTGATTTTTGTACATTGATTTTGTATCCTGAAACTTTGCTGAAG---TTG 2169 chr5ptel1M 54112 TT--TCAATTAA------TTTTTACTTGAATCTA---AGTTCTTTAGGTA 54150 -- ii ? ------ vivii iv ---i i i i C L1PREC2_orf2# 2168 TTTATCAGCTNAAGGAGCTTTTGGGCCGAGACTATGGGGTTTTCTAGATA 2119 chr5ptel1M 54151 C---ATCA-AT-ATCTGCAAA-AGTGATAACTGTGAATCTTCATGGCTTC 54194 i--- -i -i - v ii - -- v vv C L1PREC2_orf2# 2118 TAGAATCATGTCGTCTGCAAACAGGGATAGTT-TGA--CTTCCTCTCTTC 2072 chr5ptel1M 54195 CCATAGTT--ATTCCATCAATTTTCTTTTCAT-CTTG---GTGTTGGTCA 54238 i -- -- v v iv ii i v - i --- ivi i C L1PREC2_orf2# 2071 CTAT--TTGGATGCCCTTTATTTCTTTCTCTTGCCTGATTGCTCTGGCCA 2024 chr5ptel1M 54239 AAATTTCTCATACTGTATCAAACAGAAGCGGTGACAGTGAACATCACTGT 54288 ii i iv i i ii i i i v v ii vi C L1PREC2_orf2# 2023 GGACTTCCAATACTATGTTGAATAGGAGTGGTGAGAGAGGGCATCCTTGT 1974 chr5ptel1M 54289 TTCACTCTGAATTT-ATGGGAAAAGATTGTAGTTTATCTCCATTAATGAT 54337 i iiiv i iv - v i v v vi i v vi v vv C L1PREC2_orf2# 1973 CTTGTGCCGGTTTTCAAGGGGAATGCTTCCAGCTTTTGCCCATTCAGTAT 1924 chr5ptel1M 54338 AATGTTAGGTCTTGATTT 54355 i i v v v i C L1PREC2_orf2# 1923 GATGTTGGCTGTGGGTTT 1906 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 42.59 CpG sites = 74, Kimura (unadjusted) = 44.08 Transitions / transversions = 1.57 (74/47) Gap_init rate = 0.07 (26 / 385), avg. gap size = 1.65 (43 / 26) 281 30.90 4.25 2.31 chr5ptel1M 54372 54583 (945417) L1M3_orf2#LINE/L1 2457 2672 (616) m_b218s551i8 8611 chr5ptel1M 54372 GATTTACTTATTCAGTGCCATGTCTATCAAACTTCCAAAAAAACTATCTG 54421 i vv i v vi v i viiv i - i v L1M3_orf2#LIN 2457 GATCTACAGATTCAATGCAATCCCTATCAAAATCCCAATGGCATT-TTTT 2505 chr5ptel1M 54422 AGAGAAATTTAAAGAA-AAT-----AACTCATCTGGAAGAAAAAAAAGGT 54465 v vv i - ----- i v v-v v ii L1M3_orf2#LIN 2506 ACAGAAATAGAAAAAACAATCCTAAAATTCATATGGAAC-CACAAAAGAC 2554 chr5ptel1M 54466 TAAGAATATCAAGGGAAATAATGGAGGAAAAATAACAAAA--GAAGGTAT 54513 ivv v v ii v -v v i i v i-- i i L1M3_orf2#LIN 2555 CCCGAATAGCCAAAGCAAT-CTTGAGAAAGAAGAACAAAGCTGGAGGCAT 2603 chr5ptel1M 54514 CTAGCAATATCAGATCTCAAATTGCATTATAAAGCAGTAACCATCAAAAT 54563 --i v vi v i v ii i vii iiv i L1M3_orf2#LIN 2604 C--ACACTTCCTGATTTCAAAATATATTACAAAGCTACAGTAATCAAAAC 2651 chr5ptel1M 54564 CATCTGGTATTGGC-TAAAAA 54583 vi v i - L1M3_orf2#LIN 2652 AGTATGGTACTGGCATAAAAA 2672 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.51 CpG sites = 33, Kimura (unadjusted) = 40.51 Transitions / transversions = 1.06 (33/31) Gap_init rate = 0.04 (9 / 211), avg. gap size = 1.56 (14 / 9) 698 31.30 3.60 5.60 chr5ptel1M 55036 55563 (944437) L1ME3Cz_3end#LINE/L1 31 548 (449) m_b218s551i9 8612 chr5ptel1M 55036 CAAATTTGTAAGAATAAAAATTATTTCCCAAGAGATAAAT---CAAAGGA 55082 ivi - i iv --- v v --- L1ME3Cz_3end# 31 CAAATCAATAAGAA-AAAGACAA---CCCAATAGAAAAATGGGCAAAGGA 76 chr5ptel1M 55083 CATGAGCAGGCAGATTTCAGATGAAATAATCAAATCTTTCTCTGGATATA 55132 i i iv iv v iiv i vi vivvi vv ii i L1ME3Cz_3end# 77 TATGAACAGGCAATTCACAGAAGAGGAAACCCGAATGGCCAATAAACATA 126 chr5ptel1M 55133 TGAAGACATGCTCCAAATCACT--TGATTAGAGAATTGCAAATTAAAACA 55180 i v v vv -- i i i v ? L1ME3Cz_3end# 127 TGAAAAGATGCTCAACCTCACTAGTAATCAGGGAAATGCAAATTAAAACN 176 chr5ptel1M 55181 ACTCTGAGATGCCACTTCACACCTATCAGATTGGCCAACATGGAAAAA-A 55229 vv i i i v v vv i-v L1ME3Cz_3end# 177 ACAATGAGATACCATTTCACACCCATCAGATTGGCAAAAATTTAAAAGTC 226 chr5ptel1M 55230 AGGCAAGTGATAAATGTT---GAAGACA-GGAAAAATTGAAACACCTAAT 55275 v i - ivi i --- i ii- i iv i -i v L1ME3Cz_3end# 227 TGACAA-TACCAAGTGTTGGCGAGGATGTGGAGAAACGGGAAC-TCTCAT 274 chr5ptel1M 55276 ATAGAGT---TGGAATCCTGAACTGATCCAGCTATTCT-CAGAGTTATTT 55321 i vv i--- i viv i i i v i i i i -v iv L1ME3Cz_3end# 275 ACACTGCTGGTGGGAGTGTAAATTGGTACAACCACTTTGGAGAGCAATTT 324 chr5ptel1M 55322 GGAACTATGCCCA--AAGGGCAACCAACAGTGCATACACTTTGACTGGGC 55369 v v -- i -- i vii -- ivv i v vi ivi L1ME3Cz_3end# 325 GGCAATAT--CTAGTAAAGTTGA--AGATGCGCATACCCTACGACCCAGC 370 chr5ptel1M 55370 AATACCAGTACTAGGTCTGTATCCCAAAGAGA-TCACACAAAAGGAAAGG 55418 v v v v i i i i i - v i ----------- L1ME3Cz_3end# 371 AATTCCACTTCTAGGTATATACCCTAGAGAAACTCTCGC----------- 409 chr5ptel1M 55419 ACATGAATACATAAATATATATGCATATGCAAAAATATTTATAGCACTCC 55468 -- i i iv v ---- i i ii i i v v- v L1ME3Cz_3end# 410 ACATG--TGCACAAGGAGA----CATGTACAAGGATGTTCATTGCAG-CA 452 chr5ptel1M 55469 TTG-TTGGGGTGTCAAAATATTGGAAATTGAGGGGAA-GCCCATCAGTTA 55516 - vii iv i v -ii vvvi - i i vi L1ME3Cz_3end# 453 TTGTTTGTAATAGCGAAAAATTGGAAA-CAACCTAAATGTCCATCAATAG 501 chr5ptel1M 55517 GAGAATGGATGAAAACATTTTGGTATAGGAATATAAAAGAATATTAT 55563 i i v v v vvv i vi i L1ME3Cz_3end# 502 GGGAATGGATAAATAAATTGTGGTATATTCATACAATGGAATACTAT 548 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.51 CpG sites = 87, Kimura (unadjusted) = 41.58 Transitions / transversions = 1.26 (87/69) Gap_init rate = 0.08 (40 / 527), avg. gap size = 1.20 (48 / 40) 195 15.79 10.53 0.00 chr5ptel1M 56672 56709 (943291) C L3#LINE/CR1 (19) 4080 4039 m_b218s601i10 8613 chr5ptel1M 56672 AGAGTTAAGAGGGACCTGAGAG----TCTAGACCAACCTTCC 56709 iii v ---- v i C L3#LINE/CR1 4080 AGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCAACCTCCC 4039 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 18.05 CpG sites = 4, Kimura (unadjusted) = 18.05 Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.03 (1 / 37), avg. gap size = 4.00 (4 / 1) 201 22.23 0.00 1.85 chr5ptel1M 56773 56827 (943173) C MIRc#SINE/MIR (211) 57 4 m_b218s601i11 8614 chr5ptel1M 56773 ACCCATGCCTTCCTCACTCCCAAACCCAGCTCTTTTTCCACTAGGCCATA 56822 v i v - ii iv i ivi i C MIRc#SINE/MIR 57 ACCCAGGTCTTCCTGACTCC-AAGTCCAGTGCTCTTTCCACTGCACCACA 9 chr5ptel1M 56823 CTGCC 56827 C MIRc#SINE/MIR 8 CTGCC 4 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.14 CpG sites = 8, Kimura (unadjusted) = 27.14 Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1) 228 31.03 0.85 0.85 chr5ptel1M 60782 60898 (939102) C L1ME3G_3end#LINE/L1 (360) 564 448 m_b218s551i10 8615 chr5ptel1M 60782 TCTTTTTGACAATATAATCATATTCCATCCCATGCTTTGACCATCATTGG 60831 i ?iivvv vi vvi vv vv v vi C L1ME3G_3end#L 564 TCTTTTTAACNGCTGCATAGTATTCCATAGTATGGATATACCATAATTTA 515 chr5ptel1M 60832 TTCTAACGTTTCCCCCA-TGATGGGCACCCACTTTGCTTCCACTTTTTGG 60880 - vv i - i iii vv i v v C L1ME3G_3end#L 514 TT-TAACCATTCCCCTATTGATGGACATTTAGGTTGTTTCCAATTTTTCG 466 chr5ptel1M 60881 CTACCATAAATGCTGCTG 60898 ii i iiv C L1ME3G_3end#L 465 CTATTACAAACAATGCTG 448 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.92 CpG sites = 17, Kimura (unadjusted) = 40.92 Transitions / transversions = 0.89 (17/19) Gap_init rate = 0.02 (2 / 116), avg. gap size = 1.00 (2 / 2) 244 27.88 0.95 0.95 chr5ptel1M 60798 60902 (939098) C L1ME4a_3end#LINE/L1 (316) 555 451 m_b218s551i11 8615 chr5ptel1M 60798 ATCATATTCCATCCCATGCTTTGACCATCATTGGTTCTAACGTTTCCCCC 60847 v i?i vv vv v vi - vv? i C L1ME4a_3end#L 555 ATAATATTCCATTNTATGGATGTACCATAATTTATT-TAACCANTCCCCT 507 chr5ptel1M 60848 A-TGATGGGCACCCACTTTGCTTCCACTTTTTGGCTACCATAAATGCTGC 60896 - v i iii vv i v v ii iv C L1ME4a_3end#L 506 ATTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAATGC 457 chr5ptel1M 60897 TGTGGT 60902 i i C L1ME4a_3end#L 456 TGCGAT 451 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 34.58 CpG sites = 14, Kimura (unadjusted) = 36.08 Transitions / transversions = 0.93 (14/15) Gap_init rate = 0.02 (2 / 104), avg. gap size = 1.00 (2 / 2) 31 0.00 0.00 0.00 chr5ptel1M 62767 62795 (937205) (CCCCTT)n#Simple_repeat 1 29 (0) c_b218s251i0 8616 chr5ptel1M 62767 CCCCTTCCCCTTCCCCTTCCCCTTCCCCT 62795 (CCCCTT)n#Sim 1 CCCCTTCCCCTTCCCCTTCCCCTTCCCCT 29 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 12 17.72 3.12 0.00 chr5ptel1M 62900 62931 (937069) (CCTTCG)n#Simple_repeat 1 33 (0) m_b218s252i6 8617 chr5ptel1M 62900 CCTTCGCCTTTGCCTCCACC-TCCCCTTCTCCT 62931 i i i - v v (CCTTCG)n#Sim 1 CCTTCGCCTTCGCCTTCGCCTTCGCCTTCGCCT 33 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 16 0.00 0.00 0.00 chr5ptel1M 71103 71120 (928880) (A)n#Simple_repeat 1 18 (0) m_b218s252i7 8618 chr5ptel1M 71103 AAAAAAAAAAAAAAAAAA 71120 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAA 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 16 0.00 10.71 0.00 chr5ptel1M 71465 71492 (928508) (AAGT)n#Simple_repeat 1 31 (0) m_b218s252i8 8619 chr5ptel1M 71465 AAGT-AGTAAGTAAGTAAGT-AGT-AGTAAG 71492 - - - (AAGT)n#Simpl 1 AAGTAAGTAAGTAAGTAAGTAAGTAAGTAAG 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.11 (3 / 27), avg. gap size = 1.00 (3 / 3) 13 4.17 8.00 0.00 chr5ptel1M 72506 72530 (927470) (AAAGC)n#Simple_repeat 1 27 (0) m_b218s252i9 8620 chr5ptel1M 72506 AAAGCAAAGCAAAG-AAAACAAA-CAA 72530 - i - (AAAGC)n#Simp 1 AAAGCAAAGCAAAGCAAAGCAAAGCAA 27 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.08 (2 / 24), avg. gap size = 1.00 (2 / 2) 16 0.00 0.00 0.00 chr5ptel1M 75791 75807 (924193) (A)n#Simple_repeat 1 17 (0) m_b219s252i0 8621 chr5ptel1M 75791 AAAAAAAAAAAAAAAAA 75807 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 16 10.03 0.00 0.00 chr5ptel1M 76448 76469 (923531) (T)n#Simple_repeat 1 22 (0) m_b219s252i1 8622 chr5ptel1M 76448 TTTTTTTTTTCTTTTTTTCTTT 76469 i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTT 22 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 27 8.26 0.00 8.93 chr5ptel1M 76988 77048 (922952) (AACAAA)n#Simple_repeat 1 56 (0) m_b219s252i2 8623 chr5ptel1M 76988 AACAAGAATCAATCAAGCAAAAACAAAAAACAAAAACAAAAACAAAAAAA 77037 - v -- i - v (AACAAA)n#Sim 1 AACAA-AAACAA--AAACAAAAAC-AAAAACAAAAACAAAAACAAAAACA 46 chr5ptel1M 77038 ATAGACAAAAA 77048 - i (AACAAA)n#Sim 47 A-AAACAAAAA 56 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.08 (5 / 60), avg. gap size = 1.00 (5 / 5) 340 29.66 4.58 3.85 chr5ptel1M 77349 77632 (922368) L1P1_orf2#LINE/L1 2621 2906 (388) m_b219s551i0 8624 chr5ptel1M 77349 ACCTAAAAGTATATTATAAAGCAGTGGTAATTAAAACCATTTGGTACTGG 77398 i v v i i i viii ii viiv L1P1_orf2#LIN 2621 ACTTCAAACTATACTACAAGGCTACAGTAACCAAAACAGCATGGTACTGG 2670 chr5ptel1M 77399 --CTAAGAAATGGAATAATTGATCAGTGGAATAG-ATTGGGTTCACAGGA 77445 -- i -- ii ivv v i i - iv i ii v i L1P1_orf2#LIN 2671 TACCA--AAACAGAGATATAGATCAATGGAACAGAACAGAGCCCTCAGAA 2718 chr5ptel1M 77446 CTAA------ATACTCAACCGCTATAGTAATCTAGTGTTGACAAACC--A 77487 v ------ - v vi -v i ---- -- L1P1_orf2#LIN 2719 ATAACGCCGCATA-TCTACAACTAT-CTGATCT----TTGACAAACCTGA 2762 chr5ptel1M 77488 AAAGATCTCAGCTTTTGGAATAAGAACTCACTATTTGATAAAAACTGCTG 77537 i i v -v vv v i - i i v i viv L1P1_orf2#LIN 2763 GAAAAAC-AAGCAATGGGGA-AAGGATTCCCTATTTAATAAATGGTGCTG 2810 chr5ptel1M 77538 GAAAAATTGGAAATCAGTATAGCAGAAAGTAGACACT-GATCCACACCAA 77586 i i vv v vi - i iv v - viv vv L1P1_orf2#LIN 2811 GGAAAACTGGCTAGCCATAT-GTAGAAAGCTGAAACTGGATCCCTTCCTT 2859 chr5ptel1M 77587 ACACCTTATAC-CAAGTTAACTCTAAATAAATTCATGATTTAGACAT 77632 -v i i v i ii v v i i i L1P1_orf2#LIN 2860 ACACCTTATACAAAAATTAATTCAAGATGGATTAAAGACTTAAACGT 2906 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.00 CpG sites = 45, Kimura (unadjusted) = 38.61 Transitions / transversions = 1.25 (45/36) Gap_init rate = 0.06 (17 / 283), avg. gap size = 1.41 (24 / 17) 404 23.54 0.73 6.98 chr5ptel1M 77663 77799 (922201) C MIR1_Amn#SINE/MIR (101) 129 1 m_b219s601i0 8625 chr5ptel1M 77663 CTGAAGCA-ATTGGGATTAAGTGACTTGCCCAGGGTCACACAGCTAGGAA 77711 i ?- vv i i ? i ? ?i v? C MIR1_Amn#SINE 129 CTGAGGCNCAGAGAGGTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNA 80 chr5ptel1M 77712 GTGTTAAGTGTATGAGGTCACATTTGAACTCAGGTCCTCCTGCCTTCAGG 77761 ------ i - viviv ? ? i - i vv i vi C MIR1_Amn#SINE 79 GTG------GCA-GAGCCGGGANTNGAACCCAGGTC-TCCCGAGTCCCAG 38 chr5ptel1M 77762 CCTGGTGCTCTATCCACTGTGCCACCTAGCCTGCCCTA 77799 i ii ivi viv - C MIR1_Amn#SINE 37 TCCAGTGCTCTATCCACTAGACCACACTGCCT-CCCTA 1 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.39 CpG sites = 18, Kimura (unadjusted) = 30.79 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.07 (10 / 136), avg. gap size = 1.00 (10 / 10) 492 23.10 0.00 6.19 chr5ptel1M 77674 77793 (922207) C MIRc#SINE/MIR (153) 115 3 m_b219s601i1 8625 chr5ptel1M 77674 GGGATTAAGTGACTTGCCCAGGGTCACACAGCTAGGAAGTGTTAAGTGTA 77723 i i i v ------ i C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTG------GCA 72 chr5ptel1M 77724 TGAGGTCACATTTGAACTCAGGTCCTCCTGCCTTCAGGCCTGGTGCTCTA 77773 - viviv i i i i v i i i ii v C MIRc#SINE/MIR 71 -GAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTT 23 chr5ptel1M 77774 TCCACTGTGCCACCTAGCCT 77793 ii viv C MIRc#SINE/MIR 22 TCCACTGCACCACACTGCCT 3 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.94 CpG sites = 18, Kimura (unadjusted) = 28.48 Transitions / transversions = 2.25 (18/8) Gap_init rate = 0.06 (7 / 119), avg. gap size = 1.00 (7 / 7) 650 26.55 10.94 2.31 chr5ptel1M 78091 78410 (921590) L1ME3G_3end#LINE/L1 54 400 (524) m_b219s551i1 8626 chr5ptel1M 78091 CCAATTGAATAATGATTAAATGATATG----GAAAATTTTCAGATGAAGA 78136 v v ivi v ---- iv iv v i L1ME3G_3end#L 54 CCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGGA 103 chr5ptel1M 78137 AAT-TAAA--GCCATTTCTAGTCATATAAAAAGGTGTTGTAAATCACTAT 78183 -i -- ---v iv i i i vv vv v L1ME3G_3end#L 104 AATACAAATGGCCA---ATAAACATATGAAAAGATGCTCAACCTCACTAG 150 chr5ptel1M 78184 TGATCAGAGAAATGCAAATTAAGACAACTCTGAGGTAC--------ACTT 78225 i i i vv i -------- ii L1ME3G_3end#L 151 TAATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCC 200 chr5ptel1M 78226 CTCAGATTGGC------------------TAATATGACATGTTGGAGGGA 78257 v ------------------ v?vi v i i L1ME3G_3end#L 201 ATCAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGG 250 chr5ptel1M 78258 ATGTGGGAAAATTGGGACACTGATGCATTGTTGGTAGAGTTATGAACTGA 78307 i i iv v v v i i i i iiv i i i i L1ME3G_3end#L 251 GTGTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGG 300 chr5ptel1M 78308 TCCAACCGTTCTAGAAAGCAATTTGG-AGC-TCTGACCAAAGGGCTCTCA 78355 v i ? i i ii - i- - ii i----i i L1ME3G_3end#L 301 TACAGCCNTTTTGGAGGGCAATTTGGCAGTATCT-ATTAAAA----TTTA 345 chr5ptel1M 78356 AACTGAGAATACCCTTTGATCCAGCAGTGCTTTTGTTGGGTTTCTATCTC 78405 v v v i i v ivi vi ? ?v ii L1ME3G_3end#L 346 AAATGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCT 395 chr5ptel1M 78406 AAAGA 78410 ? L1ME3G_3end#L 396 ANAGA 400 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 33.93 CpG sites = 50, Kimura (unadjusted) = 34.44 Transitions / transversions = 1.52 (50/33) Gap_init rate = 0.05 (15 / 319), avg. gap size = 2.87 (43 / 15) 16 26.55 1.67 1.67 chr5ptel1M 78482 78541 (921459) (AAAGAT)n#Simple_repeat 1 60 (0) m_b219s252i4 8627 chr5ptel1M 78482 AAAGATAGAGAGCAAGATAAAAGTAATGTAGAAACATGAA-ATATTGATA 78530 i vv ii v - v v i - vv (AAAGAT)n#Sim 1 AAAGATAAAGATAAAGATAAAGATAAAG-ATAAAGATAAAGATAAAGATA 49 chr5ptel1M 78531 AAGATTGAGAT 78541 vi (AAAGAT)n#Sim 50 AAGATAAAGAT 60 Matrix = Unknown Transitions / transversions = 0.62 (5/8) Gap_init rate = 0.03 (2 / 59), avg. gap size = 1.00 (2 / 2) 316 31.50 2.02 8.60 chr5ptel1M 78667 78864 (921136) C MIR1_Amn#SINE/MIR (39) 191 6 m_b219s601i2 8628 chr5ptel1M 78667 AGATCTCAGATGTAACTTTACATAACACTAATAAACAGCATTCTAGAAAC 78716 i - i - v iv --ii v ii v v v---- C MIR1_Amn#SINE 191 AGATCTCAAA-GCA-CTTTACAAAGGA--GGTCAGTATCATTATC----C 150 chr5ptel1M 78717 TTATTTTAAAAATTGGGGGGA--GAGGAATTTGGAA-TTAAATGATGTGG 78763 ii v i - i ii -- v?ivvi i- ? i iv v C MIR1_Amn#SINE 149 CCATTTTACAGAT-GAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGC 101 chr5ptel1M 78764 TGATGGTTACATAGCTAGGAAATGTCAAGTGTCTGAGGCCAGATTTGAAT 78813 iv v i ?i ?i ------- ? v v v vi ? ? i C MIR1_Amn#SINE 100 CCAAGGTCACNCAGCNGG-------CNAGTGGCAGAGCCGGGANTNGAAC 58 chr5ptel1M 78814 TCAGGTCTTTCTGATTTAAGGCCAATGCTCTATCAACTATCCCAC-CTGG 78862 i ii vii iiv v i v vv - v C MIR1_Amn#SINE 57 CCAGGTCTCCCGAGTCCCAGTCCAGTGCTCTATCCACTAGACCACACTGC 8 chr5ptel1M 78863 CT 78864 C MIR1_Amn#SINE 7 CT 6 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.93 CpG sites = 32, Kimura (unadjusted) = 43.93 Transitions / transversions = 1.28 (32/25) Gap_init rate = 0.10 (19 / 197), avg. gap size = 1.05 (20 / 19) 359 32.66 3.36 5.48 chr5ptel1M 78716 78864 (921136) C MIRc#SINE/MIR (120) 148 3 m_b219s601i3 8628 chr5ptel1M 78716 CTTATTTTAAAAATTGGGGGGAGAGGAATTTGGAA---TTAAATGATGTG 78762 ii v i - i ii vv iiii ii i--- i iv C MIRc#SINE/MIR 148 CCCATTTTACAGAT-GAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTG 100 chr5ptel1M 78763 GTGATGGTTACATAGCTAGGAAATGTCAAGTGTCTGAGGCCAGATTTGAA 78812 viv v i i v i v ------- v vi i i C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGGCA-------GAGCCGGGACTCGAA 57 chr5ptel1M 78813 TTCAGGTCTTTCTGA-TTTAAGGCCAATGCTCTATCAACTATCCCAC-CT 78860 ii i - ii v i v v iiv - C MIRc#SINE/MIR 56 CCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACT 7 chr5ptel1M 78861 GGCT 78864 v C MIRc#SINE/MIR 6 GCCT 3 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.79 CpG sites = 30, Kimura (unadjusted) = 45.15 Transitions / transversions = 1.88 (30/16) Gap_init rate = 0.07 (11 / 148), avg. gap size = 1.18 (13 / 11) 26 6.33 0.00 0.00 chr5ptel1M 78900 78932 (921068) (T)n#Simple_repeat 1 33 (0) m_b219s252i5 8629 chr5ptel1M 78900 TTTTTTTTTTTTTTTTTTTTTTTTACTTTTTTT 78932 vi (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 33 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 298 29.82 7.19 4.68 chr5ptel1M 79381 79672 (920328) C L1MC5_3end#LINE/L1 (2037) 657 359 m_b219s551i2 8630 chr5ptel1M 79381 ACTTTGTACACTGTTCTCCTAGCCTTGCTCCTTTCACTT-----TGTATC 79425 v ii v --i ii ----- i C L1MC5_3end#LI 657 ACTATACACACTTTTCTCC--ACCTTGCTTTTTTCACTTAACAATATATC 610 chr5ptel1M 79426 ----AATTCAC---ATA--AGT-TCTAAAAACTGCCTGCTCATTATTTCT 79465 ---- iv --- -- - v i i i--vi v vi i C L1MC5_3end#LI 609 CTGGAGATCACTCCATAGCAGTATATAGAGAT--ATTCCTCATTCCTTTT 562 chr5ptel1M 79466 TATAGC-ACATTATTATTCCATTACATTCATAATCCAGGACTTGCTCAAT 79514 i -i - v i iii vv ivv viii ii i C L1MC5_3end#LI 561 TACAGCTGCAT-AGTACTCCATTGTGTGGATGTACCATAGTTTATTCAAC 513 chr5ptel1M 79515 CATTCACCAGTTGATGACCATC-AGATCATCCCCTGAGTTTCCAATTTGC 79563 v v vi iv i-i i ii ii -- i ---- C L1MC5_3end#LI 512 CAGTCCCCTATTGATGGACATTTGGGTTGTTTCC--AGTCT----TTTGC 469 chr5ptel1M 79564 CACTATAAAAAGAGCTGCTATAAATATTTTTGTATATATAAATCCTTTTC 79613 i i i v v v i vii ii ii---i C L1MC5_3end#LI 468 TATTACAAATAGTGCTGCAATGAATAGCCTTGTGCATACG---TCTTTTC 422 chr5ptel1M 79614 CT-TTTTTATGA---TCTCTTTGGGATACAGACTTAGTAAAAGTATTGAT 79659 v - iiv --- v v vv i v ivi v v C L1MC5_3end#LI 421 GTATTTTTGCCAGTGTATCTTTGGGATAGATTCCTAGAAGTGGGATTGCT 372 chr5ptel1M 79660 GGGTCAAAGGGTA 79672 C L1MC5_3end#LI 371 GGGTCAAAGGGTA 359 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.85 CpG sites = 52, Kimura (unadjusted) = 39.55 Transitions / transversions = 1.68 (52/31) Gap_init rate = 0.08 (23 / 291), avg. gap size = 1.52 (35 / 23) 355 29.30 3.69 5.63 chr5ptel1M 79457 79673 (920327) C L1ME4c_3end#LINE/L1 (257) 573 361 m_b219s551i3 8630 chr5ptel1M 79457 ATTATTTCTTATAGC-ACATTATTATTCCATTACATTCATAATCCAGGAC 79505 i i v i -i v - iivi ?v ivv vi i C L1ME4c_3end#L 573 ATCATTTTTAATGGCTGCATAAT-ATTCCATCGAGTNGATGTACCATAAT 525 chr5ptel1M 79506 TTGCTCAATCATTCACCAGTTGATGACCATC-AGATCATCCCCTGAGTTT 79554 i i i v vi v iv i- i i--------- C L1ME4c_3end#L 524 TTACTTAACCATTCCCCTATTGTTGGACATTTAGGTT---------GTTT 484 chr5ptel1M 79555 CCAATTT---GCCACTATAAAAAGAGCTGCTATAAATATTTTTGTATATA 79601 --- i i v iv v i i i i ii C L1ME4c_3end#L 483 CCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTCGTGCATA 434 chr5ptel1M 79602 TAAATCCTTTTCCTTTTTT---ATGATCTCTTTGGGATACAGACTTAGTA 79648 i-- i i --- v i i i v vv ii v C L1ME4c_3end#L 433 TAG--CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAATTCCCAGAA 386 chr5ptel1M 79649 AAAGTATTGATGGGTCAAAGGGTAT 79673 ivi v iv C L1ME4c_3end#L 385 GTGGAATTACTGGGTCAAAGGGTAT 361 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.05 CpG sites = 38, Kimura (unadjusted) = 38.81 Transitions / transversions = 1.73 (38/22) Gap_init rate = 0.07 (16 / 216), avg. gap size = 1.25 (20 / 16) 253 25.17 5.71 3.50 chr5ptel1M 79553 79692 (920308) C L1PA8_3end#LINE/L1 (437) 482 340 m_b219s551i4 8630 chr5ptel1M 79553 TTCCAA---TTTGCCACTATAAAAAGAGCTGCTATAAATATTTTTGTATA 79599 --- i i i v v v i viv ii C L1PA8_3end#LI 482 TTCCAAGTCTTTGCTATTGTAAATAGTGCTGCAATAAACATACGTGTGCA 433 chr5ptel1M 79600 TATAAATCCTTTTCCT----TT-TTTATGATCTCTTTGGGATACAGACTT 79644 i i-- i v vv ---- v- i - - i v ii C L1PA8_3end#LI 432 TGTG--TCTTTATAGTAGAATGATTTATAATC-CTTTGGG-TATATACCC 387 chr5ptel1M 79645 AGTAAAAGTATTGATGGGTCAAAGGGTATACATGGTTTGTAGACCCTT 79692 vi v v v viv i- i C L1PA8_3end#LI 386 AGTAATGGGATTGCTGGGTCAAATGGTATTTCTGGTTC-TAGATCCTT 340 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 30.01 CpG sites = 18, Kimura (unadjusted) = 31.09 Transitions / transversions = 1.12 (18/16) Gap_init rate = 0.06 (8 / 139), avg. gap size = 1.62 (13 / 8) 263 32.00 0.00 0.00 chr5ptel1M 79697 79771 (920229) MIR#SINE/MIR 49 123 (139) m_b219s601i4 8631 chr5ptel1M 79697 TAGTTTAAAATTCTGCCTTTCATACATTCTGGCTGTGTGAACTTGGACAA 79746 i v vi i i v i vvi v v i v i MIR#SINE/MIR 49 TGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 98 chr5ptel1M 79747 GTCATTTAACATCTCAATTCCCTAG 79771 i i v vi v ii MIR#SINE/MIR 99 GTTACTTAACCTCTCTGTGCCTCAG 123 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.15 CpG sites = 13, Kimura (unadjusted) = 42.68 Transitions / transversions = 1.18 (13/11) Gap_init rate = 0.00 (0 / 74), avg. gap size = 0.0 (0 / 0) 14 4.30 4.17 0.00 chr5ptel1M 80801 80824 (919176) (CCAT)n#Simple_repeat 1 25 (0) m_b219s252i6 8632 chr5ptel1M 80801 CCATCCATGCATCCATCCAT-CATC 80824 v - (CCAT)n#Simpl 1 CCATCCATCCATCCATCCATCCATC 25 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 13 4.55 4.35 0.00 chr5ptel1M 81400 81422 (918578) (GGGA)n#Simple_repeat 1 24 (0) m_b219s252i7 8633 chr5ptel1M 81400 GGGAGGGA-GGAGGGAGGGAGAGA 81422 - i (GGGA)n#Simpl 1 GGGAGGGAGGGAGGGAGGGAGGGA 24 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.05 (1 / 22), avg. gap size = 1.00 (1 / 1) 220 29.86 9.15 3.33 chr5ptel1M 81846 81987 (918013) C L2#LINE/L2 (368) 2714 2565 m_b219s601i5 8634 chr5ptel1M 81846 CAATCAAGAGATGACAG-GGTCTGAACTAGGGCATTTACTGGCAATGGGA 81894 iv i ii - ii i i ---- iv i ii C L2#LINE/L2 2714 CAGGCGAGAGATGATGGTGGCTTGGACCAGGG----TGGTGGCAGTGGAG 2669 chr5ptel1M 81895 GGGGAGAGAA-----TAGA----AGAAATATGATAGAG--AGAAATGACA 81933 v v -----ii ----i v vv ii -- ivi C L2#LINE/L2 2668 GTGGTGAGAAGTGGTCGGATTCTGGATATATTTTGAAGGTAGAGCCGACA 2619 chr5ptel1M 81934 AGATTTAGCTACTGT-CTGGATATGAGGGGTGAGGGAGAATGGGCAGTCA 81982 i - iv v-i i i v i i iv i v C L2#LINE/L2 2618 GGATTT-GCTGATGGATTGGATGTGGGGTGTGAGAGAAAGAGAGGAGTCA 2570 chr5ptel1M 81983 AGGAT 81987 C L2#LINE/L2 2569 AGGAT 2565 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.33 CpG sites = 28, Kimura (unadjusted) = 40.28 Transitions / transversions = 2.15 (28/13) Gap_init rate = 0.07 (10 / 141), avg. gap size = 1.80 (18 / 10) 201 22.50 0.00 0.00 chr5ptel1M 82280 82319 (917681) C L2b_3end#LINE/L2 (32) 434 395 m_b219s601i6 8635 chr5ptel1M 82280 CTGCTAAGTGCCAGGCATTGTGCTGACTGCTGGTGATACA 82319 i iv ?i iivi v C L2b_3end#LINE 434 CTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGGGATACA 395 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.84 CpG sites = 6, Kimura (unadjusted) = 28.45 Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 410 31.50 13.77 2.38 chr5ptel1M 82341 82870 (917130) C L2#LINE/L2 (570) 2512 1924 m_b219s601i7 8634 chr5ptel1M 82341 GAGAAAGAGGGGATTTGGGGAGGGGGGGAATTTG--GGAGAAAAC--GGA 82386 vi i ii i vv i vi i- -- i i i-- C L2#LINE/L2 2512 GAGATGGGGAAGACTGCGGGAGGAGCAGG-TTTGAGGGGGAAGATCAGGA 2464 chr5ptel1M 82387 ATT-GGTTTGGGACATGTTAATTTGGGGATGCCTACACGACA---AAGTC 82432 i -i v v v i ivv --- - C L2#LINE/L2 2463 GTTCAGTTTTGGACATGTTAAGTTTGAGATGCCTATTAGACATCCAAGT- 2415 chr5ptel1M 82433 CCAGATGTCCAAGAGGTGGTTGGA-----GAGAT--GAGGTCAGGAGAGA 82475 vv v iv ii ----- vi-- v i C L2#LINE/L2 2414 GGAGATGTCGAGTAGGCAGTTGGATATACGAGTCTGGAGTTCAGGGGAGA 2365 chr5ptel1M 82476 ACGCCAGCCTGAATCCAGTGGGATA---CTGAGAATCATCTGTATAGAAA 82522 ivv i v i ------ iv ---i i i v i v i C L2#LINE/L2 2364 GGTCCGGGCTGGA------GATATAAATTTGGGAGTCATCAGCATATAGA 2321 chr5ptel1M 82523 TGG---TTGAACCCATGAAAACATATGTTGGCACCAAATCAGAGCATGC- 82568 --- i v i viiv vviv ? ivv v vi i- C L2#LINE/L2 2320 TGGTATTTAAAGCCATGAGACTGGATGAGATCACCNAGGGAGTGAGTGTA 2271 chr5ptel1M 82569 CCTAGAGA----AAAACATCT-GGGATGGAGCCTTGGAAGACCCCTATAA 82613 vv ---- i vi i-i iv i iiv i v iiv C L2#LINE/L2 2270 GATAGAGAAGAGAAGAGGTCCAAGGACTGAGCCCTGGGGCACTCCAACGT 2221 chr5ptel1M 82614 TGAGTAATAACACTTGAAACTTGAGTGATGAACAAGGAGATAAGACACAG 82663 ? vii vivi--- i -- - v v v i vi vv C L2#LINE/L2 2220 TNAGAGGTCGGG---GAGA--TGAG-GAGGAACCAGCAAAGGAGACTGAG 2177 chr5ptel1M 82664 AAGTAGCAGATGGATAGGTAGTAGGAGAATCAGAAGA------------- 82700 v i vii vv v i i i ------------- C L2#LINE/L2 2176 AAGGAGCGGCCAGTGAGGTAGGAGGAAAACCAGGAGAGTGTGGTGTCCTG 2127 chr5ptel1M 82701 GA--------GGAGAAAGTA-GCCAAG-AGAAAAGGGTGGTCAGCAGTAT 82740 -------- i i-vi - i ii i i i v i C L2#LINE/L2 2126 GAAGCCAAGTGAAGAAAGTGTTTCAAGAAGGAGGGAGTGATCAACTGTGT 2077 chr5ptel1M 82741 CAGACGCTG-TGAGACATCAAG--AG--GAGGATATACAAGAGGCCAATA 82785 i i - ? vi -- -- ivv v vv i v i C L2#LINE/L2 2076 CAAATGCTGCTGANAGGTCAAGTAAGATGAGGACTGAGAATTGACCATTG 2027 chr5ptel1M 82786 GCTCTGGAGTCA-GGAGGTCATCAATGACTTTG----GTGCAGTGTCAGT 82830 v i i viv i- iii i ---- v v i C L2#LINE/L2 2026 GATTTAGCAACGTGGAGGTCATTGGTGACCTTGACAAGAGCAGTTTCGGT 1977 chr5ptel1M 82831 -------TGAAGAAGAAA----GACAAGAATGTGTTTTAGA-AGAA-AGG 82867 ------- ii v ---- ivi i v iv - -i C L2#LINE/L2 1976 GGAGTGGTGGGGACGAAAGCCTGATTGGAGTGGGTTCAAGAGAGAATGGG 1927 chr5ptel1M 82868 AGG 82870 C L2#LINE/L2 1926 AGG 1924 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.43 CpG sites = 93, Kimura (unadjusted) = 42.53 Transitions / transversions = 1.33 (93/70) Gap_init rate = 0.07 (38 / 529), avg. gap size = 2.29 (87 / 38) 13 5.20 0.00 0.00 chr5ptel1M 87145 87164 (912836) (TTG)n#Simple_repeat 1 20 (0) m_b219s252i8 8636 chr5ptel1M 87145 TTTTTGTTGTTGTTGTTGTT 87164 v (TTG)n#Simple 1 TTGTTGTTGTTGTTGTTGTT 20 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 18 0.00 0.00 0.00 chr5ptel1M 88309 88328 (911672) (T)n#Simple_repeat 1 20 (0) m_b219s252i9 8637 chr5ptel1M 88309 TTTTTTTTTTTTTTTTTTTT 88328 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTT 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 259 33.85 3.10 1.53 chr5ptel1M 90232 90360 (909640) C L2d2_3end#LINE/L2 (0) 555 425 m_b219s601i8 8638 chr5ptel1M 90232 TCAAATTAT-TTAGCAAACACTGATTGATAACTT-CTCTGAGCAAGACCC 90279 i v- i i i i v vvi i - v v i v C L2d2_3end#LIN 555 TCAAATCAAATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCAC 506 chr5ptel1M 90280 TGGGCTAGGCATAGTAGGGGGACATAAAAATGGATGAATCCT-ATCTTTG 90328 v iiv - i i i v v i iv v -i ii C L2d2_3end#LIN 505 TGTGCTAGGCGCTGT-GGGGGATACAAAGAAGTATAAGACATGGTCCCTG 457 chr5ptel1M 90329 ACTTATAGGAAACTTAGAGGCTAA-GAGGGAGA 90360 v i -i i i i v iv i-vi C L2d2_3end#LIN 456 CCCT-CAAGGAGCTTACAATCTAGTTGGGGAGA 425 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.97 CpG sites = 26, Kimura (unadjusted) = 46.98 Transitions / transversions = 1.53 (26/17) Gap_init rate = 0.05 (6 / 128), avg. gap size = 1.00 (6 / 6) 12 12.08 0.00 6.90 chr5ptel1M 92489 92519 (907481) (TCTG)n#Simple_repeat 1 29 (0) m_b219s252i10 8639 chr5ptel1M 92489 TCTGGTCTGTCTACCTGTTCTGTCTCTCTGT 92519 - ii - v (TCTG)n#Simpl 1 TCT-GTCTGTCTGTCTG-TCTGTCTGTCTGT 29 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2) 18 12.41 5.71 0.00 chr5ptel1M 93123 93157 (906843) (TA)n#Simple_repeat 1 37 (0) m_b219s252i11 8640 chr5ptel1M 93123 TAT-TAAATA-AAAAATATATATATATATATACATAT 93157 - v - v v i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATAT 37 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 783 29.62 3.68 3.68 chr5ptel1M 93303 93982 (906018) L1M5_orf2#LINE/L1 2615 3294 (0) m_b219s551i5 8641 chr5ptel1M 93303 TACCAGATCT-AAAATTATATTATAGAGCAGCAGTTACCAAAACCATTTG 93351 ? ? - i i - i vi v i i vi v L1M5_orf2#LIN 2615 TACCNGATNTCAAGACT-TATTATAAAGCTACAGTAATCAAGACAGTGTG 2663 chr5ptel1M 93352 GTATTGGC-TAAGGAATAGATTAGTTGATCAGTGGAATAGGTTAG---GT 93397 - - iv i v i i iv --- L1M5_orf2#LIN 2664 GTATTGGCGTAAGG-ATAGACAAATAGATCAATGGAACAGAATAGAGAGT 2712 chr5ptel1M 93398 TCAAGGGATAAAACAGTCA-ACAAATATAGCAACCTAGTCTTTGACAAA- 93445 i - ii i v --- - v i ?v ?i ii i - L1M5_orf2#LIN 2713 CC-AGAAATAGACC---CACACATATATGGNCANTTGATTTTTGACAAAG 2758 chr5ptel1M 93446 --CCCAAAG-ATCCCAGCTTTTGGGATAAGAACTTACTGTTTGATAAAAA 93492 --v ? - vii ---- iv i ivvv v ii i vi L1M5_orf2#LIN 2759 GTGCCAANGCAATTCAG----TGGGGAAAGGATAGTCTTTTCAACAAATG 2804 chr5ptel1M 93493 TTGCTGGGAAAATTGGAAACTAATATGGCAGAAACTAGGCATTGATCCAT 93542 v i v v iiv v i v iii?v i i v L1M5_orf2#LIN 2805 GTGCTGGAACAATTGGATATCCATATGGAAAAAAATGAANCTCGACCCCT 2854 chr5ptel1M 93543 ACTTAACGCCGTACACCAAGATAAGGTCAAAATGGGTTCAT-GACCTAGG 93591 i v i i v i v iv ? i i- - ii L1M5_orf2#LIN 2855 ACCTCACACCATACACAAAAATTAATTCNAGATGGA-TCATAGACCTAAA 2903 chr5ptel1M 93592 CATAAAGAATGAAATTATTAATAAATTAGAGG--AACATAGGATAGTTTA 93639 ii ii? i i v vvvvi i -- v i-- L1M5_orf2#LIN 2904 TGTAAAAGNTAAAACTATAAAACTTCTAGAAGAAAACATAGGAGAA--TA 2951 chr5ptel1M 93640 CCTCTCAGACCTGTGGA-AGGGGAAGGTCTTTATGACCAAAGCAGAACTA 93688 i iivv vv ?- vi i i i - i v iii v -- L1M5_orf2#LIN 2952 TCTTCGTGACCTTGGGNTAGGCAAAGATTTCT-TAAACAGGACACAA--A 2998 chr5ptel1M 93689 GAGATCATTACTGATCACAAAATAGAAAAT-------TTCGATTATACCA 93731 i -----i ?i i i v i ------- v i ?i i L1M5_orf2#LIN 2999 AAG-----CACNAACCATAAAAGAAAAAATTGATAAATTGGACTNCATCA 3043 chr5ptel1M 93732 AACTGAAAAGTTTTTGTACAAACAAAACTAATGCAGACAAGATTAGAAGG 93781 v v ii i iv ?vvv ivi vi ivi v i v i L1M5_orf2#LIN 3044 AAATTAAAAACTTCTGCTCNTCAAAAGACACCGTTAAGAAAATGAAAAGG 3093 chr5ptel1M 93782 GAAGCAATAAACTGGGAAAATATTTTTACAGTCAAAGGT-TCTGATAAAG 93830 v v i i ? i v v i i-? v vi - i L1M5_orf2#LIN 3094 CAAGCCACAGANTGGGAGAAAATATTTGCAA-NACATATATCTGACAAAG 3142 chr5ptel1M 93831 GCCTCATTTCCAAAATATATAGAGAATTAACTCTAATTT-ATAAAAAATC 93879 v i v i i i -v vi ? i- ? -- L1M5_orf2#LIN 3143 GACTCGTATCCAGAATATATAAAGAACT-CCTACAANTCAATAANAAA-- 3189 chr5ptel1M 93880 AAGCCATTC--TCCAATTGAAAAATGGTCAAAGGATATGAACAGACAATT 93927 v vv --i v? v i iv v L1M5_orf2#LIN 3190 AAGACAAACAACCCAATANAAAAATGGGCAAAAGACTTGAACAGACACTT 3239 chr5ptel1M 93928 CTCAGATGAAGAAATTGAAACTATTTCTAGTCATATGAAAAGATGCTCCA 93977 v i v v ?v iviiivv iv i v L1M5_orf2#LIN 3240 CACAAAAGAAGATATNCAAATGGCCAATAAGCACATGAAAAGATGCTCAA 3289 chr5ptel1M 93978 AGTCA 93982 v? L1M5_orf2#LIN 3290 CNTCA 3294 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.14 CpG sites = 111, Kimura (unadjusted) = 40.22 Transitions / transversions = 1.34 (111/83) Gap_init rate = 0.06 (39 / 679), avg. gap size = 1.28 (50 / 39) 1497 27.27 0.36 1.66 chr5ptel1M 93839 94386 (905614) L1ME3G_3end#LINE/L1 7 547 (377) m_b219s551i6 8641 chr5ptel1M 93839 TCCAAAATATATAGAGAATTAACTCTAATTTATAAAAAATCAAGCCATTC 93888 i i i vviv v iv i -- v --v L1ME3G_3end#L 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAA--AAGACA--A 52 chr5ptel1M 93889 TCCAATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGAAG 93938 i v v i v v i L1ME3G_3end#L 53 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chr5ptel1M 93939 AAATTGAAACTATTTCTAGTCATATGAAAAGATGCTCCAAGTCATTATTA 93988 vv iviiivv iv v vv i v L1ME3G_3end#L 103 AAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTA 152 chr5ptel1M 93989 ATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACACCTGT 94038 i i vv i i viv ii L1ME3G_3end#L 153 ATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCAT 202 chr5ptel1M 94039 CAGATTGGCTAAGATGACAGGAAAAAATAATGATGATTGTTGGAGGGGAT 94088 v i vvv iii?vvi ivi? v v i i L1ME3G_3end#L 203 CAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGT 252 chr5ptel1M 94089 GCGGGAAAACTGGGACATTGATGCATTGTTGGTGGAGTTGTGAACGAATC 94138 i i v v vi v i i i iiv i ivii v L1ME3G_3end#L 253 GTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTA 302 chr5ptel1M 94139 CAACCATTTTGGAGAGTAGTTTGGAACTATGCTCAAAAAGTTATCAAACT 94188 i ? i i i v v - vvv i -- i v L1ME3G_3end#L 303 CAGCCNTTTTGGAGGGCAATTTGGCAGTAT-CTATTAAAAT--TTAAAAT 349 chr5ptel1M 94189 GTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGATTATATCCCAAAG 94238 i i i vii v ? ?v v i ? L1ME3G_3end#L 350 GCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAG 399 chr5ptel1M 94239 AGATTAT-AAAGAAG-GGAAAGGGACCTGTATGTGCACGAATGTTTGTGG 94286 i vv -iv v v - v v i --? i i v i ii v L1ME3G_3end#L 400 AAATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTCATTG 447 chr5ptel1M 94287 CAGCCCTTTTTGTAGTGGCTAGAAACTGGAAACTGAATGGATGTCCATCA 94336 vi v i i v i i vivv ii L1ME3G_3end#L 448 CAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCA 497 chr5ptel1M 94337 GTTGGAGAATGGCTGAATAAATTGTGGTATATGAATATTATGGAATATTA 94386 i v i i i i vv i i L1ME3G_3end#L 498 ATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACTA 547 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.41 CpG sites = 78, Kimura (unadjusted) = 35.00 Transitions / transversions = 1.13 (78/69) Gap_init rate = 0.02 (11 / 547), avg. gap size = 1.00 (11 / 11) 1057 27.92 2.93 3.65 chr5ptel1M 93890 94469 (905531) L1MC4a_3end#LINE/L1 57 632 (1997) m_b219s551i7 8641 chr5ptel1M 93890 CCAATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGAAGA 93939 i v v i i v i -- L1MC4a_3end#L 57 CCGATAGAAAAATGGGCAAAAGACATGAACAGACAATTCACAAA--AAGA 104 chr5ptel1M 93940 AATTGAAACTATTTCTAGTCATATGAAAAGATGCTCCAAGTCATTATTAA 93989 ? v? iviiiii iv i v vv i vv L1MC4a_3end#L 105 NATANAAATGGCCCTTAAACATATGAAAAGATGTTCAACCTCACTCATAA 154 chr5ptel1M 93990 TCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACACCTGTC 94039 v i v v i i v v i L1MC4a_3end#L 155 TAAGAGAAATGCAAATTAAAACTACACTGAGATACCATTTCTCACCTATC 204 chr5ptel1M 94040 AGATTGGCTAAGAT--GACAG---GAAAAAATAATGATGATTGTTGGAGG 94084 v i --i v --- v v i v -----i v i L1MC4a_3end#L 205 AGATTGGCAAAAATTCAAAAGTTTGACAACACACT-----CTGTTGGCGA 249 chr5ptel1M 94085 GGATGCGGGAAAACTGGGACATTGATGCATTGTTGGTGGAGTTGTGAACG 94134 v i i v v vi v i i iiv ii ?v L1MC4a_3end#L 250 GGCTGTGGGGAAACAGGCACTCTCATACATTGCTGGTGGGAATGCAAANT 299 chr5ptel1M 94135 AATCCAACCATTTTGGAGAGTAGTTTGGAACTATGCTCAAAAAGTTATCA 94184 ii v v ? i v i v v - v v ii - L1MC4a_3end#L 300 GGTACAACCCTTNTGGAGGGGAATTTGGCAATAT-CTAACAAAACTA-CA 347 chr5ptel1M 94185 AACTGTGCA--TACCCTTTGATCCAGCAGTGTTACTACTGGGATTATATC 94232 --- i -- i i vii v i v v i L1MC4a_3end#L 348 ---TATGCATTTACCCTTTGACCCAGCAATCCCACTTCTAGGAATTTACC 394 chr5ptel1M 94233 CCAAAGAGATTATA-----AAGAAG-GGAAAGGGACCTGTATGTGCACGA 94276 ii --- i ----- v v -iv iv? --i ii v i L1MC4a_3end#L 395 CTGAAGA---TACACCTCCAACATGTACAAAATNAC--ATATGCACAAGG 439 chr5ptel1M 94277 ATGTTTGTGGCAGCCCTTTTTGTAGTGGCTAGAAACTGGAAACTGAATGG 94326 v i ii v vi v i v v i v i vivv ii L1MC4a_3end#L 440 TTATTCATTGCAGCATTGTTTGTAATTGCAAAATATTGGAAACAACCTAA 489 chr5ptel1M 94327 ATGTCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATATGAATATTA 94376 i ??i v ? i i i i vv i iv L1MC4a_3end#L 490 ATGCCCATNNATAGGAGANTGGTTGAATAAACTATGGTACATCCACACAA 539 chr5ptel1M 94377 TGGAATATTACTGT-TCTGTAAGAAATGACCAACAGGATGATTTC-AGAA 94424 i i - i-v i - -- vv v i - vi L1MC4a_3end#L 540 TGGAGTACTA-TGCAGCTGTAAAAAA-GA--ATGAGGAAGATCTCTATGA 585 chr5ptel1M 94425 A--GGCCTGGAGAGACTTACACGAACTGATGCTGAGTGAAATGAGCA 94469 -- iiv v i v v vv iv i i vi L1MC4a_3end#L 586 ACTGATATGGAGTGATTTCCAGGATATATTGTTAAGTGAAAAAAGCA 632 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.88 CpG sites = 84, Kimura (unadjusted) = 36.17 Transitions / transversions = 1.17 (84/72) Gap_init rate = 0.05 (29 / 579), avg. gap size = 1.31 (38 / 29) 19 15.79 5.63 5.63 chr5ptel1M 95062 95132 (904868) (TTGTTAT)n#Simple_repeat 1 71 (0) m_b219s252i12 8642 chr5ptel1M 95062 TTGTATATTT-TAAATGTTTATGTGATTA-TTGTTCTTTGTTCTTTGTGA 95109 - - v v vv v - - v v v (TTGTTAT)n#Si 1 TTGT-TATTTGTTATTTGTTATTTG-TTATTTGTTATTTGTTATTTGTTA 48 chr5ptel1M 95110 CTTGTCTATTTG-T-TTTGTTGATT 95132 i - - - - (TTGTTAT)n#Si 49 TTTGT-TATTTGTTATTTGTT-ATT 71 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.11 (8 / 70), avg. gap size = 1.00 (8 / 8) 25 26.43 4.26 1.03 chr5ptel1M 97959 98052 (901948) (TTTTA)n#Simple_repeat 1 97 (0) m_b219s252i13 8643 chr5ptel1M 97959 TTTTATTTATTTTTATTTTA-ATAATATTTAATTTA-TTTATTTAATATT 98006 vv -v v - v - v v (TTTTA)n#Simp 1 TTTTATTTTATTTTATTTTATTTTAT-TTTATTTTATTTTATTTTATTTT 49 chr5ptel1M 98007 ATTAAATAATAAAATATTATATTATA-ATAATATT-TATTATTTTATT 98052 vv vv vvv v v -v v v - v (TTTTA)n#Simp 50 ATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATT 97 Matrix = Unknown Transitions / transversions = 0.00 (0/20) Gap_init rate = 0.05 (5 / 93), avg. gap size = 1.00 (5 / 5) 12 19.33 0.00 3.12 chr5ptel1M 98535 98567 (901433) (TCTCC)n#Simple_repeat 1 32 (0) m_b219s252i14 8644 chr5ptel1M 98535 TCTCCTTTCCTCTCCTCCTCCCTTCCCCTCTTC 98567 i - ii i i (TCTCC)n#Simp 1 TCTCCTCTCCTCTCCT-CTCCTCTCCTCTCCTC 32 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 19 14.21 0.00 0.00 chr5ptel1M 98645 98675 (901325) (A)n#Simple_repeat 1 31 (0) m_b219s252i15 8645 chr5ptel1M 98645 AAAAAAAAAAAAAAAGATCAAAAGAAAAAAA 98675 i vv i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 31 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 260 33.07 0.78 0.78 chr5ptel1M 98902 99029 (900971) C L1ME2z_3end#LINE/L1 (617) 574 447 m_b219s551i8 8646 chr5ptel1M 98902 GTTCATCATTTCTTCTTGTTCAATAGTATTCCATTACATTCTTATATTGT 98951 i ivi i v i v i ii vvv iiii C L1ME2z_3end#L 574 GTTCGTTCCTTTTTATTGCTGAGTAGTATTCCATTGTATGAATATACCAC 525 chr5ptel1M 98952 AGCTTATTCATTCAGCCATTCAACTGATGTGCACCTCAACAGTTTCCAAT 99001 i i i i vi - i vii vi vii v i C L1ME2z_3end#L 524 AGTTTGTTTATCCATTC-TCCTGTTGATGGACACCTGGGCTGTTTCCAGT 476 chr5ptel1M 99002 ATTTTGTTGCCATGAA-AATGCTGCTATG 99029 v v i iii - v C L1ME2z_3end#L 475 TTTTGGCTATTATGAATAAAGCTGCTATG 447 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 44.73 CpG sites = 28, Kimura (unadjusted) = 46.28 Transitions / transversions = 2.00 (28/14) Gap_init rate = 0.02 (2 / 127), avg. gap size = 1.00 (2 / 2) 19 11.59 0.00 0.00 chr5ptel1M 99812 99840 (900160) (GT)n#Simple_repeat 1 29 (0) m_b219s252i16 8647 chr5ptel1M 99812 GTGTGTGTGTATGTGTGTGTGTGCATGTG 99840 i ii (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTG 29 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 13 8.91 11.11 0.00 chr5ptel1M 99817 99852 (900148) (TGTGCA)n#Simple_repeat 1 40 (0) m_b219s252i17 8647 chr5ptel1M 99817 TGTGTATGTG--TGTG--TGTGCATGTGCACGTGCAAGTG 99852 i -- -- i v (TGTGCA)n#Sim 1 TGTGCATGTGCATGTGCATGTGCATGTGCATGTGCATGTG 40 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.06 (2 / 35), avg. gap size = 2.00 (4 / 2) 37 12.51 5.00 1.20 chr5ptel1M 99960 100039 (899961) (ATTAT)n#Simple_repeat 1 83 (0) m_b219s252i18 8648 chr5ptel1M 99960 ATTATTTTATATTATTTTAT-TAATGTT-CATTATTTTATA-T-TATTAT 100005 v v - v i -i v - - (ATTAT)n#Simp 1 ATTATATTATATTATATTATATTATATTATATTATATTATATTATATTAT 50 chr5ptel1M 100006 ATTATATTTATATTATATATTATCATATTATATT 100039 - vv i (ATTAT)n#Simp 51 ATTATA-TTATATTATATTATATTATATTATATT 83 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.06 (5 / 79), avg. gap size = 1.00 (5 / 5) 245 20.76 4.51 9.45 chr5ptel1M 100040 100172 (899828) UCON33#DNA/TcMar-Tigger 79 205 (115) m_b219s502i0 8649 chr5ptel1M 100040 ATTTTATTAATGTTCATTA--TTTTTGTTTA-TTTT--ATTGAGATTGTT 100084 v v i i i v --i i v - -- v - UCON33#DNA/Tc 79 ATTTGAATGATGCTTATGAGCCTTTTATGTAATTTTNAATTGAGTTTGT- 127 chr5ptel1M 100085 TTGTATCCTAATACATTAA-AAGAGAGAAAAGGAAGATCACTTGTCTGTG 100133 -- v - ii i i vi v iv v UCON33#DNA/Tc 128 --GTATCCTAATTCATTAATAAAGGGGAAAAAGAAGAATACTGGCATGTT 175 chr5ptel1M 100134 TTATCTGTGTGATGCTCAATCAGTATTCAAATGGAATAG 100172 ---------i v v i UCON33#DNA/Tc 176 TTATCT---------CCCATCATTATTCAAATAGAATAG 205 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 24.37 CpG sites = 13, Kimura (unadjusted) = 24.37 Transitions / transversions = 1.08 (13/12) Gap_init rate = 0.12 (16 / 132), avg. gap size = 1.12 (18 / 16) 27 21.55 0.00 1.54 chr5ptel1M 100536 100601 (899399) (ATAT)n#Simple_repeat 1 65 (0) m_b219s252i19 8650 chr5ptel1M 100536 ATATAGATATATGTAAATGTATGTATGCTATATAACTATATATATATAGC 100585 v i v i i -v vv vv (ATAT)n#Simpl 1 ATATATATATATATATATATATATAT-ATATATATATATATATATATATA 49 chr5ptel1M 100586 TATATAATTATATATA 100601 vv (ATAT)n#Simpl 50 TATATATATATATATA 65 Matrix = Unknown Transitions / transversions = 0.33 (3/9) Gap_init rate = 0.02 (1 / 65), avg. gap size = 1.00 (1 / 1) 449 34.49 7.81 1.47 chr5ptel1M 101006 101517 (898483) L1ME4c_3end#LINE/L1 7 550 (280) m_b219s551i9 8651 chr5ptel1M 101006 TCTCAAACATATAGAAAACTAAGTCAAATTTATAAGAATACAAGTTATTC 101055 ?v ?i i i i v v v v v? viv vv L1ME4c_3end#L 7 TCTNTANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAAGAC 56 chr5ptel1M 101056 CCCAACTGATAAATGGTCAAAAGTTATGAACAGGCGATTTTCAGATGAAG 101105 iv v i vi i i iv ? v i L1ME4c_3end#L 57 CCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAGG 106 chr5ptel1M 101106 AAAT--------TAAAGCTATAC------------TCTAAATCACTAATG 101135 -------- vvv i ------------ v vv i i i L1ME4c_3end#L 107 AAATACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTAGTA 156 chr5ptel1M 101136 ATTAGAGAAATGCAAATTAAAATGATTCCTAAGTGCCACCTCAGATTGAT 101185 i i iii ivviv ii i ii i viiiv L1ME4c_3end#L 157 ATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCTAT 206 chr5ptel1M 101186 GAGGCTAGTATGTCACAAA---GGGAAATTGATA------AAT-TTGGAG 101225 v iii ----- v ---iii ------ -i v L1ME4c_3end#L 207 TAAATTAG-----CAAAAATTTAAAAAATTGATAATACCCAATGCTGGCG 251 chr5ptel1M 101226 ATGATTTGGGAAAATTGGAACACTAATGTAT---AAGCAGCAATG--AAC 101270 v ? vi vi i v ? v ii ---vi ii ? -- i L1ME4c_3end#L 252 AGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAAT 301 chr5ptel1M 101271 TGAACCAATCATTCTGGAGAACAATTTGAAAGTGCATA--AAGGGATATA 101318 ivv i v i i i iv i i i -- i vi L1ME4c_3end#L 302 TGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATA 351 chr5ptel1M 101319 AAATTATTAACGCCC-TTGATTCATAAATATTACTACTAGATCTGTATCT 101367 v i v ii - ii vv vii v i ivv v i L1ME4c_3end#L 352 AAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCC 401 chr5ptel1M 101368 CAAAG--ATAATGTAAAAAAAGATAAAAGGACCCACATGTACAAAAATAT 101415 i i -- vi i iv --- i i i i i i L1ME4c_3end#L 402 TAAGGAAATAATTCAAAAGAAGGAAAAAG---CTATATGCACGAAGATGT 448 chr5ptel1M 101416 TTATAGTAGCTCTTTTTGTGATGACAAATGATTAGAAATTGTTAGGATGT 101465 i v i vi v i i ii i vi i iviiivii L1ME4c_3end#L 449 TCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGT 498 chr5ptel1M 101466 CCATCAACTGGAGAACAGCTGAACGAGTTGTGGCATATGAATGTAATGGC 101515 v iv i ii i i iii i i i i v? ivii v L1ME4c_3end#L 499 CCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGA 548 chr5ptel1M 101516 AT 101517 L1ME4c_3end#L 549 AT 550 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 47.21 CpG sites = 112, Kimura (unadjusted) = 50.17 Transitions / transversions = 1.81 (112/62) Gap_init rate = 0.04 (18 / 511), avg. gap size = 2.67 (48 / 18) 505 33.38 8.24 1.32 chr5ptel1M 101055 101479 (898521) L1ME5_3end#LINE/L1 56 509 (432) m_b219s551i10 8651 chr5ptel1M 101055 CCCCAACTGATAAATGGTCAAAAGTTATGAACAGGCGATTTTCAGATGAA 101104 iv v v i v i v v i L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chr5ptel1M 101105 GAAATT---AAAGCTA-----------------TACTCTAAATCACTAAT 101134 ii--- i ----------------- i v v i i L1ME5_3end#LI 106 GAAACCCGAAAGGCTAACAAGCATATGAAGAGATGCTCAAACTCATTAGT 155 chr5ptel1M 101135 GATTAGAGAAATGCAAATTAAAATGATTCCTAAGTGCCACCTCAGATTGA 101184 i i ii ivviv ii ii i i v iiv L1ME5_3end#LI 156 AATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCTA 205 chr5ptel1M 101185 TGAGGCTAGT--ATGTCACAAAG--GGAAATTGATAAAT-TTGGAGATGA 101229 v i i i-- vi i v -- v v vi i - v v L1ME5_3end#LI 206 TTAGACTGGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTGGCGAGGA 255 chr5ptel1M 101230 TTTGGGAAAATTGGAACACTAATGTA-TA--AGCAGCAATG--AACTGAA 101274 v i ? v v v i - i--i ii v i --i iv L1ME5_3end#LI 256 TGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACTGGT 305 chr5ptel1M 101275 CCAATCATTCTGGAGAACAATTTGAAAGTGCATAAAGGGATATAAAAT-T 101323 v ii i i iv i v -- vv v v i - L1ME5_3end#LI 306 GCAGCCATTCTGGAGAGCAATCTGGCAGTACTT--AGTCAAATTAAGTAT 353 chr5ptel1M 101324 ATTAACGCCCT-TGATTCATAAATATTACTACTAGATCTGTATCTCAAAG 101372 ivv ii - ii vv viii v i i v i i L1ME5_3end#LI 354 ACGCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATATCCCAAAG 403 chr5ptel1M 101373 ATAATGTAAAAAAAG---ATAAAAGGACCCACATGTACAAAAATATTTAT 101419 v v v v v v i --- ii ---- i ii i i L1ME5_3end#LI 404 AAATTCTCACACAGGTCCATAAGGGG----ACATGTACGAGGATGTTCAT 449 chr5ptel1M 101420 AGTAGCTCTTTTTGTGATGACAAATGATTAGAAATTGTTAGGATGTCCAT 101469 v i vi v i i iiivii i iiiviiiv i L1ME5_3end#LI 450 TGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGGGTGTCCAT 499 chr5ptel1M 101470 CAACTGGAGA 101479 viv L1ME5_3end#LI 500 CACTGGGAGA 509 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 44.39 CpG sites = 85, Kimura (unadjusted) = 46.27 Transitions / transversions = 1.55 (85/55) Gap_init rate = 0.04 (17 / 424), avg. gap size = 2.41 (41 / 17) 234 34.74 5.45 3.42 chr5ptel1M 101117 101575 (898425) L1PB1_3end#LINE/L1 138 605 (293) m_b219s551i11 8651 chr5ptel1M 101117 ATACTCTAAATCACTAATGATTAGAGAAATGCAAATTAAAATGAT--TCC 101164 i v v i i i iv i-- v L1PB1_3end#LI 138 ATGCTCAACATCACTAATGATCAGGGAAATGCAAATCAAAACCACAATGC 187 chr5ptel1M 101165 TAAGTGCCACCTCAGATTGATGAGGCTAG-TAT-GTCACAAAG--GGAAA 101210 v -- i i vviiviii iv i -i -i v i--ii L1PB1_3end#LI 188 GA--TACCACCTTACTCCTGCAAGAATGGCCATAATCAAAAAATCAAAAA 235 chr5ptel1M 101211 TTGATAAAT-TTGGAGATGATTTGGGAAAATTGGAACACTAATGTATA-- 101257 v i i - v vv vi vi vv -- v i -- L1PB1_3end#LI 236 ATAATAGATGTTGGCGTGGATGCGGTGAAAAGGGAACACT--TCTACACT 283 chr5ptel1M 101258 ---AGCAGCAATG--AACTGAACCAATCATTCTGGAGAACAATTTGAAAG 101302 ---i ii v -- iivv i i v i i v i ii L1PB1_3end#LI 284 GCTGGTGGGAATGTAAACTAGTACAACCACTATGGAAAACAGTGTGGAGA 333 chr5ptel1M 101303 TGCATAAAGGGATATAAAATTATTAACGCCC--TTGATTCATAAATATTA 101350 v v v i i i- v -v vv -- i vv vii L1PB1_3end#LI 334 TTCCTTAAAGAAC-TAAAAGTA-GAACTACCATTTGATCCAGCAATCCCA 381 chr5ptel1M 101351 CTACTAGATCTGTATCTCAAAGATAATGTAAAAAAAG--AT------AAA 101392 i i v v - i i i------ i -- ------ L1PB1_3end#LI 382 CTACTGGGTATCTA-CCCAGAGG------AAAAGAAGTCATTATACGAAA 424 chr5ptel1M 101393 AGGACCCACATGTACAAAAATATTTATAGTAGCTCTTTTTGTGATGACAA 101442 i --i v i viv i i v vv i ii vi L1PB1_3end#LI 425 AAGA--TACTTGCACACGCATGTTTATAGCAGCACAATTCGCAATTGCAA 472 chr5ptel1M 101443 ATGAT-TAGAAATTGTTAGGATGTCCATCAACTGGAGAACAGCTGAACGA 101491 -i - i viv iivii i iiiiv iii v i vi L1PB1_3end#LI 473 A-AATATGGAACCAGCCCAAATGCCCATCAATCAACGAGTGGATAAAGAA 521 chr5ptel1M 101492 GTTGTGGCATATGAATGTAATGGCATTCTATTGGTCTATAAGAAGTGATG 101541 i? i iv iiv v v i viv i i vi L1PB1_3end#LI 522 ANTGTGGTATATATATACCATGGAATACTACTCAGCCATAAAAAGGAATG 571 chr5ptel1M 101542 AGCAGGTGGATTTCAGAAAAACCTGGAAGGAATT 101575 i?vii vv iv ivi v L1PB1_3end#LI 572 AANTAATGGCATTCGCAGCGACCTGGATGGAATT 605 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 46.80 CpG sites = 92, Kimura (unadjusted) = 49.06 Transitions / transversions = 1.48 (92/62) Gap_init rate = 0.06 (28 / 458), avg. gap size = 1.46 (41 / 28) 210 30.00 10.00 0.00 chr5ptel1M 103600 103679 (896321) MamRTE1#LINE/RTE-BovB 3023 3110 (702) m_b219s601i9 8652 chr5ptel1M 103600 GTTATACAATAATACACTTATTCATAAAGAAATAGAGAAAACAATCAAT- 103648 i i v i i v ?v i i i vvv v- MamRTE1#LINE/ 3023 GCTGTCCAATGATGCACTGATNGACAAAGAAGTAGAAAACCGAATCAAGA 3072 chr5ptel1M 103649 ------GCATGTTCACCAAGAGGTT-GTAGGCAGTGTG 103679 ------ i viiii i - i i v MamRTE1#LINE/ 3073 AGGCCAGCATGTCCTTTGGGAGGCTGGCAGACAGAGTG 3110 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.49 CpG sites = 15, Kimura (unadjusted) = 40.49 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.04 (3 / 79), avg. gap size = 2.67 (8 / 3) 257 24.71 4.49 4.49 chr5ptel1M 103699 103787 (896213) C MIR#SINE/MIR (55) 207 119 m_b219s601i10 8653 chr5ptel1M 103699 CTTTA-ATACATTAACATTTATAAAAC---CAACAATCCTGTGATGTAAG 103744 - ii viv v vv --- i i v i C MIR#SINE/MIR 207 CTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGGTAGG 158 chr5ptel1M 103745 TAGAAGATATTATTCTTGCTATTTCACAAATGGGGAAATTGAG 103787 v---- v iv i i i i i C MIR#SINE/MIR 157 TAC----TATTATTATCCCCATTTTACAGATGAGGAAACTGAG 119 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.52 CpG sites = 12, Kimura (unadjusted) = 30.52 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.07 (6 / 88), avg. gap size = 1.33 (8 / 6) 318 22.22 3.17 0.00 chr5ptel1M 103725 103787 (896213) C MIRc#SINE/MIR (81) 187 123 m_b219s601i11 8653 chr5ptel1M 103725 CAACAATCCTGTGATGTAAGTAGA--AGATATTATTCTTGCTATTTCACA 103772 i v i i i-- i v iv i i C MIRc#SINE/MIR 187 CAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACA 138 chr5ptel1M 103773 AATGGGGAAATTGAG 103787 i i i C MIRc#SINE/MIR 137 GATGAGGAAACTGAG 123 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.78 CpG sites = 11, Kimura (unadjusted) = 27.78 Transitions / transversions = 3.67 (11/3) Gap_init rate = 0.02 (1 / 62), avg. gap size = 2.00 (2 / 1) 538 31.27 0.83 7.49 chr5ptel1M 103774 104015 (895985) L3#LINE/CR1 3795 4021 (78) m_b219s601i12 8654 chr5ptel1M 103774 ATGGGGAAATTGAGAATGCACTTATTGTGTTTGATCTCAGATGGCAGATC 103823 v iv- i v iv v v iiii v v L3#LINE/CR1 3795 ATGTGGAAGA-GGGATTAGACTTATTCTGTGTGGCTCCAGAGGGCAGAAC 3843 chr5ptel1M 103824 TAGAAACAATGGCCAAATGTCACAAGAAAGGCAGATTCTGGTTGAATGTA 103873 i v viii v i - ii ii i v i L3#LINE/CR1 3844 TAGGACCAATGGGTGGAAGTTAC-AGGGAGGCAGATTTCGGCTCAATATA 3892 chr5ptel1M 103874 AGAGTTAAGGAAACCTTTCTAAAAGTTACTGATATACGGAAGTGGAATTG 103923 ------ i i v v i i vv v i v ii i v L3#LINE/CR1 3893 AG------GAAGAACTTTCTAACAATCAGAGCTGTCCAAAAATGGAATGG 3936 chr5ptel1M 103924 ACAAAGACAGGTAAGG-AGTGGGCTCCTCCCATACCATCAAGAAAAGTGT 103972 i --v v vv ?i - i ------- i vvii i L3#LINE/CR1 3937 GC--TGCCTCGNGAGGTAGTGAGCTCC-------CCGTCACTGGAGGTGT 3977 chr5ptel1M 103973 TCAAGCAGAGATCATTTGTCCATTTGTT-GGGATATAGTAGGAG 104015 iiiivv v i i- i v i L3#LINE/CR1 3978 TCAAGCAGAGGCTGGATGACCACTTGTCAGGGATGTTGTAGAAG 4021 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.14 CpG sites = 41, Kimura (unadjusted) = 41.70 Transitions / transversions = 1.41 (41/29) Gap_init rate = 0.08 (19 / 241), avg. gap size = 1.00 (19 / 19) 16 31.04 3.49 3.49 chr5ptel1M 104421 104506 (895494) (TC)n#Simple_repeat 1 86 (0) m_b219s252i20 8655 chr5ptel1M 104421 TCACTCTTCCTTTCTCTTTACT-TGTCTCTATCTGTCTTTTTTTCTACT- 104468 v ii i i - - v v v i i i - - (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCT-CTC 48 chr5ptel1M 104469 TTTTTCCCATATCCTTATTTCTCTGTCTCTCTCTC-CTC 104506 i i i - v ii v i v - (TC)n#Simple_ 49 TCTCTCTC-TCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 86 Matrix = Unknown Transitions / transversions = 1.86 (13/7) Gap_init rate = 0.07 (6 / 85), avg. gap size = 1.00 (6 / 6) 752 23.08 7.32 3.12 chr5ptel1M 104561 104806 (895194) MIRc#SINE/MIR 13 268 (0) m_b219s601i13 8656 chr5ptel1M 104561 GTGTAGTGAGAATAGCATTGGA-TTAGAGTTAGAGA-ACCTGAGTTCTAA 104608 i ii v i - i i ii - i v i MIRc#SINE/MIR 13 GTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAG 62 chr5ptel1M 104609 CCCCAGTTCTGCCACTGATTTATTGTGTGACCATGGGTAAATTGCTTAAA 104658 i i i v i vii v i i ii - MIRc#SINE/MIR 63 TCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTT-AA 111 chr5ptel1M 104659 ACTCTCTGTGCCTCAGTTCTCTCATCTGTGAAATGGGGCAAAT-TCACTT 104707 v v ii i vv -vi i MIRc#SINE/MIR 112 CCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCT 161 chr5ptel1M 104708 G---TG-CTATCTCA-AGGG-TGTTGTGACATTCATA-GAGGAACATCAT 104750 --- - i - - viv v - ------- MIRc#SINE/MIR 162 GCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAG-------AT 204 chr5ptel1M 104751 AAGGGATG---AAGGAGTTGGCCGATTGTAATGAACTATAT--AT---AG 104792 v v --- viv v ivi i v vi i-- --- MIRc#SINE/MIR 205 AATGTATGTGAAAGCGCTTTGTAAACTGTAAAGTGCTATACAAATGTAAG 254 chr5ptel1M 104793 CTGTTATTATTATT 104806 v? MIRc#SINE/MIR 255 GNGTTATTATTATT 268 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.15 CpG sites = 33, Kimura (unadjusted) = 28.34 Transitions / transversions = 1.50 (33/22) Gap_init rate = 0.08 (19 / 245), avg. gap size = 1.37 (26 / 19) 20 19.60 0.00 0.00 chr5ptel1M 105817 105853 (894147) (AC)n#Simple_repeat 1 37 (0) m_b219s252i22 8657 chr5ptel1M 105817 ACATACATACACACACACACACACACGTGCATACACA 105853 i i iii i (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACA 37 Matrix = Unknown Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 17 21.41 2.22 0.00 chr5ptel1M 105815 105859 (894141) (ATAC)n#Simple_repeat 1 46 (0) m_b219s252i21 8658 chr5ptel1M 105815 ATACATACATACACACACACACACACACGTGCATACACA-ATAAAT 105859 i i i i i i i - v (ATAC)n#Simpl 1 ATACATACATACATACATACATACATACATACATACATACATACAT 46 Matrix = Unknown Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 506 22.78 0.00 8.70 chr5ptel1M 108926 109050 (890950) MIRc#SINE/MIR 1 115 (153) m_b219s601i14 8659 chr5ptel1M 108926 CAGGGCAGCTAGGTGGCGCAGTGGATAGAGCACCAACCCTGAAGTCAGGA 108975 ii i--- i v iiiv i i MIRc#SINE/MIR 1 CGAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGA 47 chr5ptel1M 108976 GGTCCCGAGTTCAAATTTGAACTCAGATACTGAACACTTCCTAGCTGTGT 109025 i v i i i i iivii --- i ---- v MIRc#SINE/MIR 48 AGACCTGGGTTCGAGTCCCGGCTC---TGC----CACTTACTAGCTGTGT 90 chr5ptel1M 109026 GACCCTGGGTAAGTCACTTAACCTC 109050 i i MIRc#SINE/MIR 91 GACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.72 CpG sites = 21, Kimura (unadjusted) = 28.55 Transitions / transversions = 4.20 (21/5) Gap_init rate = 0.08 (10 / 124), avg. gap size = 1.00 (10 / 10) 220 17.51 0.00 2.50 chr5ptel1M 109688 109728 (890272) C L2c_3end#LINE/L2 (14) 464 425 m_b219s601i15 8660 chr5ptel1M 109688 CAAACATTTATTAAGCACCTAATATTTGCAAGGCAGTTGAG 109728 i i v v v - i i C L2c_3end#LINE 464 CAAACATTTATTGAGCGCCTACTATGTGCCAGGC-GCTGGG 425 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 17.13 CpG sites = 4, Kimura (unadjusted) = 20.14 Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 180 14.29 0.00 0.00 chr5ptel1M 110003 110030 (889970) MIRb#SINE/MIR 212 239 (29) m_b219s601i16 8661 chr5ptel1M 110003 CACATAGCACAGTACCTGGCACATAATA 110030 i v i i MIRb#SINE/MIR 212 CGCTTAGCACAGTGCCTGGCACATAGTA 239 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 12.12 CpG sites = 3, Kimura (unadjusted) = 16.24 Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 665 29.85 6.14 6.67 chr5ptel1M 112242 112844 (887156) L1ME3Cz_3end#LINE/L1 31 630 (367) m_b220s551i0 8662 chr5ptel1M 112242 CAAATTTATAAGAATAAAAATAATTCCCCAAAAGATAAAT---CAAAGAA 112288 iv - i i --- v v --- i L1ME3Cz_3end# 31 CAAATCAATAAGAA-AAAGACAA---CCCAATAGAAAAATGGGCAAAGGA 76 chr5ptel1M 112289 TATGAGCAGGCAGATTTCAGATGAAATAATCAAAGCTTTCTCTGGACATA 112338 i iv iv v iiv i vi iivvi vv ii L1ME3Cz_3end# 77 TATGAACAGGCAATTCACAGAAGAGGAAACCCGAATGGCCAATAAACATA 126 chr5ptel1M 112339 TGAAGAAATGCTCCAAATCACT--TGATTAGAAAAATGCAAATTAAAACA 112386 i i v vv -- i i ii ? L1ME3Cz_3end# 127 TGAAAAGATGCTCAACCTCACTAGTAATCAGGGAAATGCAAATTAAAACN 176 chr5ptel1M 112387 ATTCCAAGATACCACCTAAAATTTATCAGATTGGCCAA----------TG 112426 ivvii ii v v iii v ---------- v L1ME3Cz_3end# 177 ACAATGAGATACCATTTCACACCCATCAGATTGGCAAAAATTTAAAAGTC 226 chr5ptel1M 112427 TGACAA-AAAAAATGAT-----AAATGTTGAAGACAGGGGAAAT-TGATA 112469 - vv i v -----ii - i v v v - v L1ME3Cz_3end# 227 TGACAATACCAAGTGTTGGCGAGGATG-TGGAGAAACGGGAACTCTCATA 275 chr5ptel1M 112470 CACCTAATG-TAGTGTTGGAGTCCTGAACTGATCCAACCATTCT-CAGAG 112517 ---- - i -- -v i i i v i i -v L1ME3Cz_3end# 276 CAC----TGCTGGTG--GGAGT-GTAAATTGGTACAACCACTTTGGAGAG 318 chr5ptel1M 112518 TTATTTGAAACTATGCCCAACAGGCAA--CCAAACTGTGCAAACATT--G 112563 iv iv v -- i ii --- --iv iv i v vi -- L1ME3Cz_3end# 319 CAATTTGGCAATAT--CTAGTA---AAGTTGAAGATGCGCATACCCTACG 363 chr5ptel1M 112564 ACTCGGCAATACCTCTCCTAGGTCTGTTTCCCCAAGAGA---TCATACAA 112610 i i v v i v i vi ivi i --- ii -- L1ME3Cz_3end# 364 ACCCAGCAATTCCACTTCTAGGTATATACCCTAGAGAAACTCTCGCAC-- 411 chr5ptel1M 112611 AAAGAAAATGATATAAATACATAAATATATATGCATATGAAATAATATTT 112660 ------- ------- i i iv v i i i---- vi i i L1ME3Cz_3end# 412 -------ATG-------TGCACAAGGAGACATGTAC----AAGGATGTTC 443 chr5ptel1M 112661 ATAATCATCCTT-TTTGGGGTAGTAAAATATTGAAAATAGAGGGGAAGCC 112709 vi- v v - vii ii v i i ivvvii v i L1ME3Cz_3end# 444 ATTG-CAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTC 492 chr5ptel1M 112710 CATCAATTGAGGAATGGATGAATAAGTTGTGGTATATGAATATAAAGGAA 112759 v i i i vv i v L1ME3Cz_3end# 493 CATCAATAGGGGAATGGATAAATAAATTGTGGTATATTCATACAATGGAA 542 chr5ptel1M 112760 TATTATTGTGCACTAAGAAATGAACAGGC-AGATTT-CAGAAA--AACAT 112805 i vvv v v - iiii - i - viv -- L1ME3Cz_3end# 543 TACTATACAGCAGTTA-AAATGAATGAACTAGATCTACATGTATCAACAT 591 chr5ptel1M 112806 GGAAAGATTTGTACAAAC-TGATACAAAGTGAAATGAGCA 112844 v i i -i v - i iivi vi L1ME3Cz_3end# 592 GGATAAATCT-CAAAAACATAATGTTGAGTGAAAAAAGCA 630 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.98 CpG sites = 98, Kimura (unadjusted) = 39.22 Transitions / transversions = 1.40 (98/70) Gap_init rate = 0.09 (56 / 602), avg. gap size = 1.38 (77 / 56) 15 7.80 0.00 3.57 chr5ptel1M 114721 114749 (885251) (AAACA)n#Simple_repeat 1 28 (0) m_b220s252i0 8663 chr5ptel1M 114721 AAGCAAAATCAAACCAAAACAAAACAAAA 114749 i - v (AAACA)n#Simp 1 AAACAAAA-CAAAACAAAACAAAACAAAA 28 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1) 187 32.13 18.43 2.37 chr5ptel1M 116169 116423 (883577) C L3#LINE/CR1 (261) 3838 3544 m_b220s601i0 8664 chr5ptel1M 116169 GCTCTCTGGGGCCCAGCTGAACAAGGCTCAACCCTCCCCCCAGGGACAGA 116218 i i vvi v i v v v ii vviv v C L3#LINE/CR1 3838 GCCCTCTGGAGCCACACAGAATAAGTCTAATCCCTCTTCCACATGACAGC 3789 chr5ptel1M 116219 ACTTCAGATACTGGAAA-----TCTC-TGAATCCTCTGG-----CTCTTC 116257 v i i v i----- v - vv ii----- C L3#LINE/CR1 3788 CCTTCAAATATTTGAAGACAGCTATCATGTCTCCTCTAAGTCTTCTCTTC 3739 chr5ptel1M 116258 T---GGCTAA----TTCCAAATCCATTA---GT----------GCACG-- 116285 --- ----ii iv v i --- ----------i i -- C L3#LINE/CR1 3738 TCCAGGCTAAACATCCCCAGTTCCTTCAACCGTTCCTCATATGACATGGT 3689 chr5ptel1M 116286 ----AGGCCCTT--CCATTCTGGCTGGCTTCTCCAAGATATTCTCTGATT 116329 ---- i -- i ii vii ii vi iiiv iii C L3#LINE/CR1 3688 TTCCAGACCCTTCACCATCCTGGTCGCTCTCCTCTGGACGCGCTCCAGTT 3639 chr5ptel1M 116330 TACTGGTGCCCTTCTCAGACCATGTG--ACCCAAAAGACCCCGGGC-CAA 116376 iiiii i i i i -- --i i ---- i ii - C L3#LINE/CR1 3638 TGTCAATGTCCCTCTTAAA--ATGTGGCGCCCAGAA----CTGAACGCAA 3595 chr5ptel1M 116377 T--TCCAAAAGT--TCTTAGGAGGCCAGAGAATAGTGCTAACTACT-CCT 116421 -- i v -- v vv vv v i i -vi i - C L3#LINE/CR1 3594 TACTCCAGATGTGGTCTGACCAGCGCAGAGTACAGCG-GGACTATTACCT 3546 chr5ptel1M 116422 CC 116423 C L3#LINE/CR1 3545 CC 3544 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 40.57 CpG sites = 52, Kimura (unadjusted) = 44.39 Transitions / transversions = 1.86 (52/28) Gap_init rate = 0.09 (22 / 254), avg. gap size = 2.45 (54 / 22) 12 22.07 0.00 0.00 chr5ptel1M 116576 116607 (883393) (AGGAG)n#Simple_repeat 1 32 (0) m_b220s252i1 8665 chr5ptel1M 116576 AGGAGGGGGGGGCAGAGAAGAGGCGAGGAGAG 116607 i i i v i v (AGGAG)n#Simp 1 AGGAGAGGAGAGGAGAGGAGAGGAGAGGAGAG 32 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 13 8.48 4.00 0.00 chr5ptel1M 117388 117412 (882588) (CTC)n#Simple_repeat 1 26 (0) m_b220s252i2 8666 chr5ptel1M 117388 CTCCTCCTGCT-CTCTTCCTCCTCCT 117412 v - i (CTC)n#Simple 1 CTCCTCCTCCTCCTCCTCCTCCTCCT 26 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 12 18.34 7.84 1.85 chr5ptel1M 117401 117451 (882549) (CTTCCAC)n#Simple_repeat 1 54 (0) m_b220s252i3 8667 chr5ptel1M 117401 CTTCCTCC-TCCTTTTTCCACCTT-CAAATTCCA--TTCCTCCCTCCATC 117446 v - vii - vv -- v i - (CTTCCAC)n#Si 1 CTTCCACCTTCCACCTTCCACCTTCCACCTTCCACCTTCCACCTTCCA-C 49 chr5ptel1M 117447 CTTCC 117451 (CTTCCAC)n#Si 50 CTTCC 54 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.08 (4 / 50), avg. gap size = 1.25 (5 / 4) 244 24.98 6.71 4.79 chr5ptel1M 118654 118817 (881183) L1MEh_5end#LINE/L1 2069 2235 (0) m_b220s551i1 8668 chr5ptel1M 118654 AAAAAACAAAAAA-AAGAAGGATGAAAGGA-----AATA---CAGTAATC 118694 i v - v vv vi ----- --- i L1MEh_5end#LI 2069 AGAAAACAAATAATAAGATGGCAGAAATAAGTCCNAATATANCAGTAATT 2118 chr5ptel1M 118695 ATAACTGCAAATGTTAAGGGGATAAACTCATCCATGAAACAAATTAGAAG 118744 i i--- v v v i v v vi --i ii L1MEh_5end#LI 2119 ACAAT---AAATGTAAATGGGTTAAACTCACCAATTAAAAGA--CAGAGA 2163 chr5ptel1M 118745 TCTATGGAAGAATAGATTTGAAACCGCAATCCAACGACATGTTTTTTGTA 118794 - ? v-- v i ?i v iv i i i v i ii L1MEh_5end#LI 2164 T-TNTC--AGATTGGATTNAAAAACAAAATCCAACAATATGCTGTCTACA 2210 chr5ptel1M 118795 --GGACACTCTTAAAACAGAAAGGC 118817 --i v ? i i L1MEh_5end#LI 2211 AGAGACACACTTAAAACANAAGGAC 2235 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 31.72 CpG sites = 22, Kimura (unadjusted) = 31.72 Transitions / transversions = 1.29 (22/17) Gap_init rate = 0.07 (12 / 163), avg. gap size = 1.58 (19 / 12) 436 30.59 10.78 2.78 chr5ptel1M 119037 119537 (880463) L1ME4c_3end#LINE/L1 16 555 (275) m_b220s551i2 8669 chr5ptel1M 119037 TATAAAA--CTGAATCAAATTTACAAAAATGAAAGTCATT-CTCCAATTG 119083 i-- v v v i i -i ?i vv- i v L1ME4c_3end#L 16 TATAAAGAGCTCATTCAAATTGATAAGAA-AAANATCAAGACCCCAATAG 64 chr5ptel1M 119084 ATAAATGGCCAAATAATCTGATCAGGCTGTTTTTAGAAGGAGAAACTAAA 119133 v vi iv v i vi ivi ? ii - v L1ME4c_3end#L 65 ATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAGGAAA-TACA 113 chr5ptel1M 119134 GCTACTT--CTAGT-TATATAAAAATGCTCCAAATACCT-GT--TTAGAG 119177 i? v v-- v ii-i iv i v vv vv - -- i i L1ME4c_3end#L 114 ANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTAGTAATCAAAG 163 chr5ptel1M 119178 AAATGAAAGTTAAAACCCCTCTAAGTTGTCACCTTATGCCT--------- 119218 v i i vv vv i v ii ii i --------- L1ME4c_3end#L 164 AAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCTATTAAATTA 213 chr5ptel1M 119219 -------CTCAGAAAA--GACAA------ATGCCAG--AGGA---GACAA 119248 -------i i i -- i ------ ii -- ?--- iii L1ME4c_3end#L 214 GCAAAAATTTAAAAAATTGATAATACCCAATGCTGGCGAGGNTGCGGTGA 263 chr5ptel1M 119249 AACAAGGACACTGATGAATATTCC--ATAGAGTTGTGAACTGGTCCAACC 119296 vi v ? v -- i v --i i vi? i i v L1ME4c_3end#L 264 AACTGGTACNCTCAT--ACATTGCTGGTGGCANTGTAAATTGGTACAACC 311 chr5ptel1M 119297 ATTGTGGAGAGTAATTTGGAACTAGACACAAAGAAGTAGAAAACCATGCC 119346 v v i i v v vii iv ivi v vii v v L1ME4c_3end#L 312 CTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAAAATGTTCA 361 chr5ptel1M 119347 TGTGCTTTGTTCCAGCAATACCAGGTCTG------CATCCCAAAGA--TA 119388 iiv vi i v vv ------i i i -- L1ME4c_3end#L 362 TACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATA 411 chr5ptel1M 119389 --TCAAAGGAAAAGAAAAAGGGCCTATATACGTACAAAACTCTACA--GC 119434 -- i i- --- i -- i iv v v -- L1ME4c_3end#L 412 ATTCAAAAGAAG-GAAAAAG---CTATATGC--ACGAAGATGTTCATTGC 455 chr5ptel1M 119435 AGCTCTTTCTTTCTATCTTGGTAAAGAATTGAACATCAAGGCAGATGGTC 119484 v-- v v v-- i ii i i v - vvi i vi L1ME4c_3end#L 456 AGCG--TTATTTATAA--TAGCGAAAAATTGGAAA-CAACCTAAATGTCC 500 chr5ptel1M 119485 AACAATTGCAGAATGGTTGAACAAGTTCTGG--CATCAATGTAATGGAAT 119532 v vi i ii i v -- ? ivii L1ME4c_3end#L 501 AACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAAT 550 chr5ptel1M 119533 AATAT 119537 v L1ME4c_3end#L 551 ATTAT 555 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.31 CpG sites = 83, Kimura (unadjusted) = 41.18 Transitions / transversions = 1.26 (83/66) Gap_init rate = 0.07 (33 / 500), avg. gap size = 2.09 (69 / 33) 415 32.78 12.01 2.71 chr5ptel1M 120040 120547 (879453) L2#LINE/L2 1959 2512 (570) m_b220s601i1 8670 chr5ptel1M 120040 TTTTGTCTTT-CTGCTTCAACTGACACTGCTC----CAAGGTCACTGATG 120084 i iii- ii i - i v ---- ii L2#LINE/L2 1959 TTTCGTCCCCACCACTCCA-CCGAAACTGCTCTTGTCAAGGTCACCAATG 2007 chr5ptel1M 120085 ACCTCC-TGACTCCAGATCTATCGGCCTCTTGTCCATCCTCCTCT--CTT 120131 -i viv i i i vi i vv v vi v -- L2#LINE/L2 2008 ACCTCCACGTTGCTAAATCCAATGGTCAATTCTCAGTCCTCATCTTACTT 2057 chr5ptel1M 120132 GATGTCTCA-CAGCATCTGATGTTGCTGACCACCCTCTTC-TCTTG-GCT 120178 iv ? - i iiiv i i i i i - -ivi L2#LINE/L2 2058 GACCTNTCAGCAGCATTTGACACAGTTGATCACTCCCTCCTTCTTGAAAC 2107 chr5ptel1M 120179 ACTTTCTCCTCTT---------------------TTCTGATTCTCCTCCT 120207 i v --------------------- i i i L2#LINE/L2 2108 ACTTTCTTCACTTGGCTTCCAGGACACCACACTCTCCTGGTTTTCCTCCT 2157 chr5ptel1M 120208 ACCTATCCATATGTTACTTCTGTGTCTTATCTCCTCTTTC--ACTCAAGT 120255 vv iivvi i v vv iv i v vv --v vv L2#LINE/L2 2158 ACCTCACTGGCCGCTCCTTCTCAGTCTCCTTTGCTGGTTCCTCCTCATCT 2207 chr5ptel1M 120256 TTCCAAATGTTATTACTCATTATCGGTGTCTTCCAAGGCTCCATCC-CAG 120304 ii i------ iiv ? vii i v vii i vi -ii L2#LINE/L2 2208 CCCCG------ACCTCTNAACGTTGGAGTGCCCCAGGGCTCAGTCCTTGG 2251 chr5ptel1M 120305 AGGT----TTTTCTCTA-GGGCATGCTCTGATTTGGTGCCAACATATGTT 120349 vv ---- i -vvi iv v vvi ? vivv viiv L2#LINE/L2 2252 ACCTCTTCTCTTCTCTATCTACACTCACTCCCTNGGTGATCTCATCCAGT 2301 chr5ptel1M 120350 TTCATGGGTTCA---ACCATTTCTATACAGATGATTCTCAG---TATCCC 120393 i v i --- i v i v i i i--- vi L2#LINE/L2 2302 CTCATGGCTTTAAATACCATCTATATGCTGATGACTCCCAAATTTATATC 2351 chr5ptel1M 120394 ACTGGATTCAGGCTGGCGTTCTCTCCTG-AC------CTCATGTCTCCAA 120436 ------ i v i vvi i - ------ i i v L2#LINE/L2 2352 ------TCCAGCCCGGACCTCTCCCCTGAACTCCAGACTCGTATATCCAA 2395 chr5ptel1M 120437 CCACCTCTTGGACATCTGGGACTT---TGTCGCGTAGGCATCCCCAGATT 120483 ii vi v -vv --- vvi i v iv L2#LINE/L2 2396 CTGCCTACTCGACATCT-CCACTTGGATGTCTAATAGGCATCTCAAACTT 2444 chr5ptel1M 120484 AACATGCCCCAAACC-AATTCT--ATTTTCTCC--CAAATTCCCCCCCTC 120528 i v i- i i-- i i -- -i iv i L2#LINE/L2 2445 AACATGTCCAAAACTGAACTCCTGATCTTCCCCCTCAAA-CCTGCTCCTC 2493 chr5ptel1M 120529 CTCAAATCCCCTCTTTCTC 120547 ivv i ii i iv L2#LINE/L2 2494 CCGCAGTCTTCCCCATCTC 2512 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 41.82 CpG sites = 96, Kimura (unadjusted) = 45.23 Transitions / transversions = 1.45 (96/66) Gap_init rate = 0.07 (35 / 507), avg. gap size = 2.17 (76 / 35) 202 22.50 0.00 0.00 chr5ptel1M 120569 120608 (879392) L2b_3end#LINE/L2 395 434 (32) m_b220s601i2 8671 chr5ptel1M 120569 TGTATCACCAGCAGTCAGCACAATGCCTGGCACTTAGCAG 120608 v ivii i? vi i L2b_3end#LINE 395 TGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAG 434 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 24.84 CpG sites = 6, Kimura (unadjusted) = 28.45 Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 223 29.36 9.22 3.36 chr5ptel1M 120905 121045 (878955) L2#LINE/L2 2566 2714 (368) m_b220s601i3 8670 chr5ptel1M 120905 TCCTTGACTGCCCATTCTCCCTCACCCCTCATATCCAG-ACAGTAGCTAA 120953 v i vi i i v i i i-v vi - L2#LINE/L2 2566 TCCTTGACTCCTCTCTTTCTCTCACACCCCACATCCAATCCATCAGC-AA 2614 chr5ptel1M 120954 ATCTTGTCATTTCT--CTTTATCATATTTCT----TCTG-----TTCTCT 120992 i ivi -- i vv v i---- i ----- v L2#LINE/L2 2615 ATCCTGTCGGCTCTACCTTCAAAATATATCCAGAATCCGACCACTTCTCA 2664 chr5ptel1M 120993 CCCCTCCCATAGCCAGTAAATGCCCTAGTTCAGACC-CTGTCATCTCTTG 121041 v ii iv vi ---- i i ii - ii i L2#LINE/L2 2665 CCACCTCCACTGCCACCA----CCCTGGTCCAAGCCACCATCATCTCTCG 2710 chr5ptel1M 121042 ATTG 121045 vi L2#LINE/L2 2711 CCTG 2714 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.26 CpG sites = 26, Kimura (unadjusted) = 38.97 Transitions / transversions = 1.86 (26/14) Gap_init rate = 0.07 (10 / 140), avg. gap size = 1.80 (18 / 10) 14 4.30 4.17 0.00 chr5ptel1M 122084 122107 (877893) (GATG)n#Simple_repeat 1 25 (0) m_b220s252i4 8672 chr5ptel1M 122084 GAT-GATGGATGGATGCATGGATGG 122107 - v (GATG)n#Simpl 1 GATGGATGGATGGATGGATGGATGG 25 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 282 16.72 0.00 5.56 chr5ptel1M 126086 126142 (873858) C MER92C#LTR/ERV1 (454) 136 83 m_b220s502i0 8673 chr5ptel1M 126086 GGGTATTTCTTTGCAGAAAGGCATTTCCCAAAACGACAAAAGGATGTTGG 126135 iv i v v ii - i -- C MER92C#LTR/ER 136 GGGTGGTTCTTTGCGGTAAGCCATTTCCCGGAAC-ACAAAAGGGTG--GG 90 chr5ptel1M 126136 GGAATTT 126142 i C MER92C#LTR/ER 89 GGGATTT 83 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 14.80 CpG sites = 6, Kimura (unadjusted) = 19.22 Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.05 (3 / 56), avg. gap size = 1.00 (3 / 3) 306 30.47 6.08 4.67 chr5ptel1M 127336 127483 (872517) MIR3#SINE/MIR 48 197 (11) m_b220s601i4 8674 chr5ptel1M 127336 CCTGGGTCTTATCTGGTCCCCAAGCTC----ACTGAACTCAACAGATGAT 127381 ---- i --i ---- - ?iviivi i MIR3#SINE/MIR 48 CCTGGGT----TCTAGTCCC--GGCTCTGCCACT-AACTNGCTGTGTGAC 90 chr5ptel1M 127382 CTCTG--AGGCCCCTTC-TGGCCCAGAGCCTCAGTTTCCTCATCTGGAAA 127428 iv -- i i v -ivv i v i v MIR3#SINE/MIR 91 CTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAA 140 chr5ptel1M 127429 ACAATTAGACTGAACTAGACAGCTTGTAGGGTACATCTCAGCCCTAAA-- 127476 ii vvi ii i iiiii v i v v ii i i v-- MIR3#SINE/MIR 141 ATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACAT 190 chr5ptel1M 127477 TCTATGA 127483 MIR3#SINE/MIR 191 TCTATGA 197 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 40.38 CpG sites = 29, Kimura (unadjusted) = 41.69 Transitions / transversions = 2.07 (29/14) Gap_init rate = 0.07 (11 / 147), avg. gap size = 1.45 (16 / 11) 267 32.69 7.88 2.82 chr5ptel1M 128591 128996 (871004) C L1P3_orf2#LINE/L1 (982) 2312 1887 m_b220s551i4 8675 chr5ptel1M 128591 ATTCCAAATTATTTTATATATTTTATAGTAATTGTAAGTGATATTT--CT 128638 v iv vivi i i i i iv v -- C L1P3_orf2#LIN 2312 ATTCCTAGGTATTTTATTCTCTTTGTAGCAATTGTGAATGGGAGTTCACT 2263 chr5ptel1M 128639 C----TTTATCTTCCTA-CTGAGTTTTATTGGTGTTACACTGAAATGACA 128683 ---- iv ii i-i vv v - i -- i viv C L1P3_orf2#LIN 2262 CATGATTTGGCTCTCTGTTTGTCTATTATTGGTG-TATA--GGAATGCTT 2216 chr5ptel1M 128684 GTGATTTGTGTGGAAAT---TTTTATCTCCTGAAAATTTGCTAAAG--G- 128727 v i-- v --- i v i v i -- - C L1P3_orf2#LIN 2215 GTGATTTTTGC--ACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGC 2168 chr5ptel1M 128728 -TATCATTTCAATTAATTTTT-GCCTGAATCTA---AGTTCTTTAGGTAC 128772 - vi i vv i? - v iv v ---i i i ii i C L1P3_orf2#LIN 2167 TTATCAGCTTAAGGAGNTTTTGGGCTGAGACGATGGGGTTTTCTAAATAT 2118 chr5ptel1M 128773 ATCAAT-ATATCATGTACAAG-GGTGATAATTGTGAATCTTCTTGACTTC 128820 - - i v i i-i v i - -- i vv C L1P3_orf2#LIN 2117 A-CAATCATGTCATCTGCAAACAGAGACAATT-TGA--CTTCCTCTCTTC 2072 chr5ptel1M 128821 CTATAGTT--ATTCCCTCAATTTTCTTTTC--ATCTTAGTACC--AGTCA 128864 -- -- v iv ii i --ii v v i --i i C L1P3_orf2#LIN 2071 CTAT--TTGAATACCCTTTATTTCTTTCTCTTGCCTGATTGCCCTGGCCA 2024 chr5ptel1M 128865 ACATTTCTCATACGGTATCAAACAGAAATGATGACAATGAACAACACTGT 128914 iv i iv vi i ii i i i i v iv ii v vi C L1P3_orf2#LIN 2023 GAACTTCCAATACTATGTTGAATAGGAGTGGTGAGAGAGGGCATCCTTGT 1974 chr5ptel1M 128915 TTCACCCTGAATTT-ATGGGAAAAGAGTGTGGTTTATTTCCATTATAG-A 128962 i iiiv i iv - vi i v vv vii i v vi -i - C L1P3_orf2#LIN 1973 CTTGTGCCGGTTTTCAAAGGGAATGCTTCCAGCTTTTGCCCATT-CAGTA 1925 chr5ptel1M 128963 GAATATTAGCTCTTGATTT----TAAATATATTCTATT 128996 vi i v v i ---- vv ii C L1P3_orf2#LIN 1924 TGATATTGGCTGTGGGTTTGTCATAAATAGCTCTTATT 1887 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 44.43 CpG sites = 78, Kimura (unadjusted) = 44.92 Transitions / transversions = 1.53 (78/51) Gap_init rate = 0.07 (29 / 405), avg. gap size = 1.52 (44 / 29) 334 30.83 8.12 3.10 chr5ptel1M 128591 128898 (871102) C L1PREC2_orf2#LINE/L1 (982) 2312 1990 m_b220s551i3 8675 chr5ptel1M 128591 ATTCCAAATTATTTTATATATTTTATAGTAATTGTAAGTGATATTTC--T 128638 v iv viv i i i i i iv v -- C L1PREC2_orf2# 2312 ATTCCTAGGTATTTTATTCTTTTTGTGGCAATTGTGAATGGGATTGCGTT 2263 chr5ptel1M 128639 C----TTTATCTTCCTACTGAGTT-TTATTGGTGTTACACTGAAATGACA 128683 ---- iv ii vi vi i - i - i -- i vi C L1PREC2_orf2# 2262 CCTGATTTGGCTCTCGGCTTGGCTGTTGTTGGTG-TATA--GGAATGCTA 2216 chr5ptel1M 128684 GTGATTTGTGTGGAAAT---TTTTATCTCCTGAAAATTTGCTAAAG--G- 128727 v -- v --- i v v i -- - C L1PREC2_orf2# 2215 GTGATTTTTGT--ACATTGATTTTGTATCCTGAAACTTTGCTGAAGTTGT 2168 chr5ptel1M 128728 -TATCATTTCAATTAATTTTT-GCCTGAATCTA---AGTTCTTTAGGTAC 128772 - vi ? vv ii - v i iv ---i i i i i C L1PREC2_orf2# 2167 TTATCAGCTNAAGGAGCTTTTGGGCCGAGACTATGGGGTTTTCTAGATAT 2118 chr5ptel1M 128773 ATCAATATATCATGTACAAG-GGTGATAATTGTGAATCTTCTTGACTTCC 128821 vv vi i i v i i-i v i - -- i vv C L1PREC2_orf2# 2117 AGAATCATGTCGTCTGCAAACAGGGATAGTT-TGA--CTTCCTCTCTTCC 2071 chr5ptel1M 128822 TATAGTT--ATTCCCTCAATTTTCTTTTC--ATCTTAGTA--CCAGTCAA 128865 -- -- v iv ii i --ii v v i-- ii i i C L1PREC2_orf2# 2070 TAT--TTGGATGCCCTTTATTTCTTTCTCTTGCCTGATTGCTCTGGCCAG 2023 chr5ptel1M 128866 CATTTCTCATACGGTATCAAACAGAAATGATGA 128898 v i iv vi i ii i i i i C L1PREC2_orf2# 2022 GACTTCCAATACTATGTTGAATAGGAGTGGTGA 1990 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.57 CpG sites = 59, Kimura (unadjusted) = 41.79 Transitions / transversions = 1.79 (59/33) Gap_init rate = 0.07 (23 / 307), avg. gap size = 1.52 (35 / 23) 817 28.64 5.51 6.30 chr5ptel1M 129654 130197 (869803) L1ME3A_3end#LINE/L1 31 570 (350) m_b220s551i5 8676 chr5ptel1M 129654 CAAATTTATAAGAATAAAAATCATTCCCCAATAGA--------TAAAAGA 129695 iv v i vvv ivv --------i L1ME3A_3end#L 31 CAAATCAATAAGAAAAAGACAGACAACCCAATAGAAAAATGGGCAAAAGA 80 chr5ptel1M 129696 TATGAGCAGGTAGATTTCA---AATACAATACTCAAAAATATTTATAGGC 129742 iv i i --i --- v vi ii vi-iiiv ii L1ME3A_3end#L 81 CTTGAACAGGCA--CTTCACAAAAGAGGATATCCAAATG-GCCAATAAAC 127 chr5ptel1M 129743 ATATGAAGAAGTGATCTAAACAACTTTACTGG-------AGAAATGCAAA 129785 i i -- --- i i i -------i L1ME3A_3end#L 128 ATATGAAAAGGTG--CT---CAACTTCATTAGTCATCAGGGAAATGCAAA 172 chr5ptel1M 129786 TTAAAACAACTCTGAGATACCACCTCACACCTATCAGATTGGCCAATATG 129835 v vv ? iv i i v i v L1ME3A_3end#L 173 TTAAAACCACAATGNGATACCACTACACACCCACCAGAATGGCTAAAATG 222 chr5ptel1M 129836 ACAAAAAAGGAAAGTGATAAATGTT---GAGGGGGGGGAG-AATTGAAAC 129881 v i vi v i ivi i --- iv v - ii i L1ME3A_3end#L 223 AAAAAGACAGACAATACCAAGTGTTGGCGAGGATGTGGAGCAACCGGAAC 272 chr5ptel1M 129882 ATTTAATATAGTGTT----GGAGTCCTGAACTGATCCAACCATTCT-CAG 129926 - i v i v i ---- -v i i i v i i -v i L1ME3A_3end#L 273 -TCTCATACACTGCTGGTGGGAGT-GTAAATTGGTACAACCACTTTGGAA 320 chr5ptel1M 129927 AATTATTTGGAACTATGCCCAAAGGGTAACCAAACTGTGCATACACTTTG 129976 i i v v viv v i v i v --- i v v L1ME3A_3end#L 321 AACTGTTTGGCAGTATCTACTAAAGCTGAACA---TATGCATACCCTATG 367 chr5ptel1M 129977 ACTCAGAAATACCACTGATAGGTCTGTATCCCAAAGAGATCACACAAAAA 130026 i v v vv v i - ---------- i L1ME3A_3end#L 368 ACCCAGCAATTCCACTCCTAGGTATATA-CCCA----------ACAGAAA 406 chr5ptel1M 130027 GGAAAGAACATAAATACATAACTATATATGCATATGCAAAAATATTTATA 130076 v --v v vi --- v i - v vi i i i i i L1ME3A_3end#L 407 TG--CGTACATATGT---TCACCA-AAAGACATGTACAAGAATGTTCATA 450 chr5ptel1M 130077 GCAGTCCTTGTTGGGGT-GTCAAAATATTGGAAACTGAGGGGAAGCCCAT 130125 iv vv i vii - i ?? - i ?ivvvii v i L1ME3A_3end#L 451 GCAGCACTATTCGTAATAGCCNNAA-ACTGGAAACNACCCAAATGTCCAT 499 chr5ptel1M 130126 CAATTGTGGAATGGCTGAATAAGTTGTAGTATAGGAATATAAAGGAATAT 130175 iv i v i i i vvv i i v i L1ME3A_3end#L 500 CAACAGTAGAATGGATAAATAAATTGTGGTATATTCACACAATGGAATAC 549 chr5ptel1M 130176 TATTGTACACC-ATGA-AATGAAC 130197 --- v - - L1ME3A_3end#L 550 TA---TACAGCAATGAGAATGAAC 570 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.55 CpG sites = 81, Kimura (unadjusted) = 37.19 Transitions / transversions = 1.25 (81/65) Gap_init rate = 0.08 (44 / 543), avg. gap size = 1.45 (64 / 44) 411 30.74 5.94 7.22 chr5ptel1M 129683 130271 (869729) L1MA1_3end#LINE/L1 68 649 (400) m_b220s551i6 8676 chr5ptel1M 129683 AATAGATAAAAGATATGAGCAGGTAGATTTCAAATACAATACTCAAAAAT 129732 i ii v ii ii vv i - v v vi v L1MA1_3end#LI 68 AATGGGCAAAAGATTTGAATAGACATTTCTCAAA-AGAAGACATACAAAT 116 chr5ptel1M 129733 ATTTA-TAGGCATATGAAGAAGTGATCTAAACAACTTT----ACTGGAGA 129777 iviv -i i i v -- v v ---- iii L1MA1_3end#LI 117 GGCAAACAGGCATATGAAAAGGTGCTC--AACATCATTGATCATCAGAGA 164 chr5ptel1M 129778 AATGCAAATTAAAACAACTCTGAGATACCACCTCACACCTATCAGATTGG 129827 i v vv i i v vi i i v L1MA1_3end#LI 165 AATGCAAATCAAAACTACAATGAGATATCATCTCACCCCAGTTAAAATGG 214 chr5ptel1M 129828 CCAATATGACAAAAA--AGGAAAGTGATAAATGTT---GAGGGGGGGGAG 129872 iv v- i-- v - i i i --- iv v L1MA1_3end#LI 215 CTTATATC-CAAAAGACAGGCAA-TAACAAATGCTGGCGAGGATGTGGAG 262 chr5ptel1M 129873 -AATTGAAACATTTAATATAGTGTT----GGAGTCCTGAACTGATCCAAC 129917 - vv i vi -i i v ---- i -v i i ii v L1MA1_3end#LI 263 AAAAGGGAACCCTT-GTACACTGTTGGTGGGAAT-GTAAATTAGTACAAC 310 chr5ptel1M 129918 CATTCT-CAGAATTATTTGGAACTATGCCCAAAGGG-TAACCAAACTGTG 129965 i v -v ivi iv - v i iii- -- i v L1MA1_3end#LI 311 CACTATGGAGAACAGTTTGGAGGT-TCCTCAAAAAACTAA--AAATTGAG 357 chr5ptel1M 129966 CATACACTTTGACTCAGAAATACCACTGATAGGTCTGTATCCCAAAGAGA 130015 - vv v ii v v v i v i - ---- L1MA1_3end#LI 358 C-TACCATATGATCCAGCAATCCCACTGCTGGGTATATA-CCCAAA---- 401 chr5ptel1M 130016 TCACACAAAAAGGAAAGAACATAAATACAT---AACTATATATGCATATG 130062 ------ i ----- v i i --- ivv v i- v L1MA1_3end#LI 402 ------AGAAAGGAA-----ATCAGTATATCGAAGAGATATCTGCAC-TC 439 chr5ptel1M 130063 CAAAAATATTTATAGCAGTCCTTGTTGGGGT-GTCAAAATATTGGAAA-- 130109 ---v i i v iv vv ivii - ii i - i-- L1MA1_3end#LI 440 C---TATGTTTGTTGCAGCACTGTTTACAATAGCTAAGAT-TTGGAAGCA 485 chr5ptel1M 130110 --CTGAGGGGAAGCCCATCAATTGTGGAATGGCTGAATAAGTTGTAGTAT 130157 -- i v---- i iv vv v i v iv i i L1MA1_3end#LI 486 ACCTAAGT----GTCCATCAACAGATGAATGGATAAAGAAAATGTGGTAC 531 chr5ptel1M 130158 AGGAATATAAAGGAATATTATTGTACA-CCATGA-----AATGAA---CA 130198 viv i i v i i --- - i ----- i--- L1MA1_3end#LI 532 ATATACACAATGGAGTACTATT---CAGCCATAAAAAAGAATGAGATCCA 578 chr5ptel1M 130199 GGCAGATTTCAGAAAAACCTGGAAAGACTTGTAGAAACTGATACAAAGTA 130248 v --- iiv v v vi vi v vvv v iiv i L1MA1_3end#LI 579 GTCA---TTTGCAACAACATGGATGGAACTGGAGATCATTATGTTAAGTG 625 chr5ptel1M 130249 AAATGAG-CAGAACCAGGAAAACA 130271 i - ivv i i L1MA1_3end#LI 626 AAATAAGCCAGGCACAGAAAGACA 649 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.34 CpG sites = 91, Kimura (unadjusted) = 40.34 Transitions / transversions = 1.18 (91/77) Gap_init rate = 0.10 (58 / 588), avg. gap size = 1.33 (77 / 58) 17 19.25 5.66 0.00 chr5ptel1M 131067 131119 (868881) (GATGATA)n#Simple_repeat 1 56 (0) m_b220s252i5 8677 chr5ptel1M 131067 GAAGAGAGA-GAGAGATGATAAAT-ATATA-AAAAGATGAGAGATAATAG 131113 v v - v i - v -i v v i (GATGATA)n#Si 1 GATGATAGATGATAGATGATAGATGATAGATGATAGATGATAGATGATAG 50 chr5ptel1M 131114 ATGATA 131119 (GATGATA)n#Si 51 ATGATA 56 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.06 (3 / 52), avg. gap size = 1.00 (3 / 3) 232 25.70 4.40 18.75 chr5ptel1M 131285 131375 (868625) C MIR3#SINE/MIR (17) 191 112 m_b220s601i5 8678 chr5ptel1M 131285 AGTGGTAAAGTTAAGAGGGACCTGAGAG----TCTAGACCAACCCTCTCC 131330 i vi i i iii v ---- v i v C MIR3#SINE/MIR 191 AATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCA 142 chr5ptel1M 131331 TTCTCCTCTCCCACTTCTTACTGGTGAGAAAATTGAAGCCCAAGG 131375 --------------- v i i i i ii C MIR3#SINE/MIR 141 TT---------------TTACAGATGAGGAAACTGAGGCCCAGAG 112 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.00 CpG sites = 14, Kimura (unadjusted) = 32.00 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.18 (16 / 90), avg. gap size = 1.19 (19 / 16) 14 20.40 4.44 0.00 chr5ptel1M 135298 135342 (864658) (TTCCCTC)n#Simple_repeat 1 47 (0) m_b220s252i6 8679 chr5ptel1M 135298 TTCCCTCTTCTCTCTTCCTTCCT-CCTCATCTCAC-ACCCTCTTGCC 135342 i i i - v i v -v v (TTCCCTC)n#Si 1 TTCCCTCTTCCCTCTTCCCTCTTCCCTCTTCCCTCTTCCCTCTTCCC 47 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.05 (2 / 44), avg. gap size = 1.00 (2 / 2) 393 30.88 2.60 7.48 chr5ptel1M 135909 136062 (863938) MIRc#SINE/MIR 2 148 (120) m_b220s601i6 8680 chr5ptel1M 135909 GGAGCAGTGAGGTGGAATGGTTGATAGCGTGCTGG-TGTGGTATCAGGAA 135957 ii v v i --- v v ii -iv vi MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGG---AAAGAGCACTGGACTTGGAGTCAGGAA 48 chr5ptel1M 135958 GACCTGAATTCAAATCTGGCCTCAGACACGTGACACTTCCTAGCTATGTA 136007 ii i i iv v ------- v v i i MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTC-------TGCCACTTACTAGCTGTGTG 91 chr5ptel1M 136008 ACCATCAGCACATCACTTAA---TTCCAAATTCCTCTCTCCCCAATTTTT 136054 v vi vi ---i ii iiii vv i i - i v MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTC-ATCTGT 140 chr5ptel1M 136055 AAAATAAG 136062 ii MIRc#SINE/MIR 141 AAAATGGG 148 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 40.09 CpG sites = 28, Kimura (unadjusted) = 41.34 Transitions / transversions = 1.75 (28/16) Gap_init rate = 0.08 (13 / 153), avg. gap size = 1.15 (15 / 13) 11 14.81 4.88 4.88 chr5ptel1M 136242 136282 (863718) (ATCTTT)n#Simple_repeat 1 41 (0) m_b220s252i7 8681 chr5ptel1M 136242 ATCTTTATCATTAT-TTTGTGTTTCTGCATTA-CTCTTATCTT 136282 v - i v v - v - - (ATCTTT)n#Sim 1 ATCTTTATCTTTATCTTTATCTTTAT-CTTTATCT-TTATCTT 41 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.10 (4 / 40), avg. gap size = 1.00 (4 / 4) 947 30.84 2.87 0.70 chr5ptel1M 136341 136758 (863242) C L1ME4c_3end#LINE/L1 (400) 430 4 m_b220s551i7 8682 chr5ptel1M 136341 CTTTTTCCTCCTCT---ATGATCTCTTTGAGATATAAAT--ACAGTAAAA 136385 i i --- v i i ii -- --v v ivi C L1ME4c_3end#L 430 CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATA--AATTCCCAGAAGTG 383 chr5ptel1M 136386 GCACTGCTGGATCAAAGGGTATTCAGAGTTTGAGAGCCCTTTGGT-CAGA 136434 v i i i vv v v v vi i - i - iv C L1ME4c_3end#L 382 GAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTCTT-GATACGTA 334 chr5ptel1M 136435 GCTCCGAATTGCTTTTCAAAACAGTTGGATCAGTTCACAACTCCACCAAC 136484 viv i i vi v i i i ?iv i C L1ME4c_3end#L 333 TTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACANTGCCACCAGC 284 chr5ptel1M 136485 AATGTATAAAA-TCCCAGTTTTCCCGCATTGCCTCCAACATTCATCATTA 136533 i i?- v iv ?ivi v i vivi C L1ME4c_3end#L 283 AATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGCATTGGGTATTA 234 chr5ptel1M 136534 TCTTTTCCTGTCATCTTAGCCAATCTGAGAAGTGTGTAGTGGTACCTCAG 136583 vv ii vvv i v i i i v i i iv i i v C L1ME4c_3end#L 233 TCAATTTTTTAAATTTTTGCTAATTTAATAGGCGTAAAATGGTATCTCAT 184 chr5ptel1M 136584 AGTTGTCTTAATTTGCATTTCTCTGATCAATAGTGATTTACAGCACCTTC 136633 v ii i i v i vv vv i ii i C L1ME4c_3end#L 183 TGTTGCTTTAATTTGCATTTCTTTGATTACTAGCGAGGTTGAACATTTTT 134 chr5ptel1M 136634 TCATATGACTAGAAATGGCTTCCATTTCTTCATCTGAAAATTGTCTGTCC 136683 i i vi ivvv ivi? vi i v ? vi i C L1ME4c_3end#L 133 CCATGTGTTTGTTTACTANTTGTATTTCCTCTTNTGTGAATTGTCTGTTC 84 chr5ptel1M 136684 ATAT-CTTTGATCATTAACCAATTGGAGAATTGA----GTTATTATAAAT 136728 i - vi v i v i vv ----v v v C L1ME4c_3end#L 83 ATGTCCTTTGCCCATTTATCTATTGGGGTCTTGATNTTTTTCTTATCAAT 34 chr5ptel1M 136729 TTGAGTCAATTCTTTGCATATTTTAGAAAT 136758 i v ii ii ? v? v C L1ME4c_3end#L 33 TTGAATGAGCTCTTTATATANTANAGATAT 4 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.36 CpG sites = 71, Kimura (unadjusted) = 41.64 Transitions / transversions = 1.25 (71/57) Gap_init rate = 0.02 (9 / 417), avg. gap size = 1.67 (15 / 9) 310 31.44 6.51 3.73 chr5ptel1M 136625 136885 (863115) C L1M1_orf2#LINE/L1 (8) 3286 3019 m_b220s551i8 8682 chr5ptel1M 136625 AGCACCTTCTCATATGACTAGAAATGGCTT-CCATT------TCTTCATC 136667 i v ------- i - ------ v i C L1M1_orf2#LIN 3286 AGCACCTTTTCATATGCCT-------GTTTGCCATTTGTATGTCTTCTTT 3244 chr5ptel1M 136668 TGAAAATTGTCTGTCCATATC-TTTGATCATTAACCAATTGGAGAATTGA 136716 i v i i v - vi vvii i vv ii C L1M1_orf2#LIN 3243 TGAGAAATGTCTATTCAGATCTTTTGCCCATTTTTTAATCGGATTATTAG 3194 chr5ptel1M 136717 GTTAT----TATAAATTTGAGTCAATTCTTTGCATATTTTAGAAATGAGG 136762 i v ---- i v vv v ii i ii i i vv v iv C L1M1_orf2#LIN 3193 ATTTTTTCCTATAGAGTTGTTTGAGCTCCTTATATATTCTGGTTATTAAT 3144 chr5ptel1M 136763 CCTTTATCAGAACCCTTGAATGTAAAAATTTTCCCCTAATTTATTGCTTC 136812 i i vvvv v vv i v i i v i i v v v C L1M1_orf2#LIN 3143 CCCTTGTCAGATGGGTAGTTTGCAAATATTTTCTCCCATTCTGTGGGTTG 3094 chr5ptel1M 136813 TCTTCTAATCTTGTTTGCATTGGTTTTGTTTGC---ACAAAAAC--TTTA 136857 ii v ii --v - iv ---i i i -- C L1M1_orf2#LIN 3093 TCTCTTCACTTTGTT--GATT-GTTTCCTTTGCTGTGCAGAAGCTTTTTA 3047 chr5ptel1M 136858 AGTTAATATAGTCAGAATTATCCATTTT 136885 v i i ii vv v i C L1M1_orf2#LIN 3046 ACTTGATGTGATCCCATTTGTCCATTTT 3019 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.94 CpG sites = 42, Kimura (unadjusted) = 41.63 Transitions / transversions = 1.14 (42/37) Gap_init rate = 0.06 (16 / 260), avg. gap size = 1.69 (27 / 16) 480 22.50 0.00 8.93 chr5ptel1M 137000 137121 (862879) MIRc#SINE/MIR 4 115 (153) m_b220s601i7 8683 chr5ptel1M 137000 GGCAGTGAGGTGGCATAGTAGATAGAGTACCAGCCCTGAAGGCAGGAGGA 137049 v ---i i v i ii v i i v i MIRc#SINE/MIR 4 GGCAGTGTGGTG---CAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA 50 chr5ptel1M 137050 CCTGAGTTCAAATCTGACCTCAAATACTCAACCCTTCCTAGTTGTGTGAC 137099 i i i iviv --- i ---- v v i MIRc#SINE/MIR 51 CCTGGGTTCGAGTCCCGGCTC---TGC----CACTTACTAGCTGTGTGAC 93 chr5ptel1M 137100 CCTGGGCAAGTCACTTAACCCC 137121 i i MIRc#SINE/MIR 94 CTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 24.85 CpG sites = 17, Kimura (unadjusted) = 27.35 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.08 (10 / 121), avg. gap size = 1.00 (10 / 10) 395 36.27 8.45 1.26 chr5ptel1M 138895 139190 (860810) C 7SLRNA#SINE/Alu (3) 317 1 c_b220s355i0 8684 chr5ptel1M 138895 TTCTTTTGTTTGTTTTT--GAAACTGGATCTT-CTTTTCTATCCAGCTTG 138941 i v v -- i v i i- v vi ii vi C 7SLRNA#SINE/A 317 TTTTTTTTTTTTTTTTTAAGAGACGGGGTCTCGCTATGTTGCCCAGGCTG 268 chr5ptel1M 138942 GAA-GCAAAAG--GTTCTCA-------TCTAAGTGCTGACTGTCAGGAGA 138981 i- ivi --i v ------- iv v i iiiv v i C 7SLRNA#SINE/A 267 GAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGA 218 chr5ptel1M 138982 CTTTTG-CCTGG-CTGTTTCCAACCTGGGCAACTTTGTTCCTCCCTAAGG 139029 v - v- i i viv iiii i i v C 7SLRNA#SINE/A 217 GTTTTGACCTGCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGC 168 chr5ptel1M 139030 -----GGTG-TTCTCTGTTGTGGGTGAGTGGGGCACAGTATTGGTGCAGG 139073 ----- - i i i i viv - --- v vi i v i C 7SLRNA#SINE/A 167 AACCTGGTGGTCCCCCGCTCCCGG-GAG---GTCACCATATTGATGCCGA 122 chr5ptel1M 139074 ACTTCATGTGGATACTTAAGCACCTTGTCGCTCTGCCACTCAAGGCTCCC 139123 vi i i iii v iv v iv v i vi i iii i C 7SLRNA#SINE/A 121 ACTTAGTGCGGACACCCGATCGGCATAGCGCACTACAGCCCAGAACTCCT 72 chr5ptel1M 139124 AAGCCCTAGAGATCT----ACCTCAGCTTGCCCAGTAGCATGAATTACAA 139169 ii i v v i----i i v v vv i i i C 7SLRNA#SINE/A 71 GGGCTCAAGCGATCCTCCCGCCTCAGCCTCCCGAGTAGCTGGGACTACAG 22 chr5ptel1M 139170 GCACATATTATCACACTTAGC 139190 i iiiii i i i iii C 7SLRNA#SINE/A 21 GCGCGCGCCACCGCGCCCGGC 1 Matrix = 18p41g.matrix Kimura (with divCpGMod) = 42.69 CpG sites = 71, Kimura (unadjusted) = 53.44 Transitions / transversions = 2.03 (71/35) Gap_init rate = 0.05 (14 / 295), avg. gap size = 2.07 (29 / 14) 198 25.01 1.35 2.74 chr5ptel1M 139343 139416 (860584) C MIRc#SINE/MIR (3) 265 193 m_b220s601i8 8685 chr5ptel1M 139343 AATGATAGCACCTCACATTTATTTTATTACTTTGAGGGTCTG-AAAGTAC 139391 i i ? i i v - vi - vi i i- ii C MIRc#SINE/MIR 265 AATAATAACNCCTTACATTTGTAT-AGCACTTT-ACAGTTTACAAAGCGC 218 chr5ptel1M 139392 TTTGAGATCTATTATCTCATTTCAT 139416 v v vi v C MIRc#SINE/MIR 217 TTTCACATACATTATCTCATTTGAT 193 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.42 CpG sites = 11, Kimura (unadjusted) = 31.74 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.04 (3 / 73), avg. gap size = 1.00 (3 / 3) 214 25.56 1.28 9.72 chr5ptel1M 139552 139629 (860371) C MIR3#SINE/MIR (112) 96 25 m_b220s601i9 8686 chr5ptel1M 139552 CTCATGAGCACAAAGCTATTTATGGGCACAGATGGAACCGG-ATTAGAAC 139600 i v iv v ? v vv ------ i - i C MIR3#SINE/MIR 96 CCCAAGGTCACACAGCNAGTTAGTGGCA------GAGCCGGGACTAGAAC 53 chr5ptel1M 139601 TCGGATCTCCTGACTATACAGAACATGCT 139629 i i i -iv vv i C MIR3#SINE/MIR 52 CCAGGTCTCCTGACT-CCCAGTCCGTGCT 25 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.75 CpG sites = 9, Kimura (unadjusted) = 31.80 Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.10 (8 / 77), avg. gap size = 1.00 (8 / 8) 44 2.44 0.00 0.00 chr5ptel1M 139976 140017 (859983) (GT)n#Simple_repeat 1 42 (0) c_b220s251i0 8687 chr5ptel1M 139976 GTGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 140017 i (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 42 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 1938 30.86 7.84 1.66 chr5ptel1M 140394 141299 (858701) HERVP71A#LTR/ERV1 3297 4257 (3333) m_b220s701i0 8688 chr5ptel1M 140394 TATTAGAAGAG---CCAGAACTGTTAAAATGGTTAAAAGAGGAGA---AG 140437 i --- v v iv iv ivvv i --- HERVP71A#LTR/ 3297 TACTAGAAGAGGAACCCGATCCCTTGCAATGGTCCCCAGAGGAAATTCAG 3346 chr5ptel1M 140438 GAAATGTTTCAACAAGTAAAAACAGACTCTGGTTACAACCCCAGTATTAG 140487 v i ---- vi iv i i i vi i i vi i HERVP71A#LTR/ 3347 GCAGTG----AAAGAGCTAAAGCAGGCCCTCATTACAGCCCCGGTCCTGG 3392 chr5ptel1M 140488 CCTGCCTAACCTTA-ACAAGCCTTTCCATCTATTTGTAAC--TAGATAAA 140534 iv i v i - v i v i -- iv i HERVP71A#LTR/ 3393 CCCTCCCATCTTTAGAGAAACCATTCCATCTGTTTGTAACAGTAGACCAG 3442 chr5ptel1M 140535 GGAACTGCCTTGAGGGTTTTAACTCAGTTCTGGGCTAGAGAAAAG-CAAC 140583 viiv i vi vi v ivi v- i i - HERVP71A#LTR/ 3443 GGCGTGGCCCTTGGGGTGCTCACTCAAACCTGGGG-AGGGAAGAGGCAAC 3491 chr5ptel1M 140584 CTGTTGCTTTCTTATACAAAGTACTTGATCTGCTCTCCACCGGATGGCCT 140633 iv v v iv v i ivv ivvv i i HERVP71A#LTR/ 3492 CTGTTGCTTTTGTCTCCAAGCTTCTCGATCCTGTCTCTCGGGGGTGGCCC 3541 chr5ptel1M 140634 GAGTGTACACAAGCAGTAGCTGCAACTGCCTTGTGGGTAGGAGAAAGTCA 140683 i iii v v i iv ii i i HERVP71A#LTR/ 3542 GAATGTGTGCAAGCAGTAGCTGCCACAGCCCTGCTGGTAGAGGAGAGTCG 3591 chr5ptel1M 140684 AAAATTGAC--TTGGGAGAGCATTGATATTAAACACCCCAACATCAACTT 140731 ii i -- vi i vi i v i - i iv i HERVP71A#LTR/ 3592 AAAGCTAACCTTTGGCGGGGCCCTAATAGTAAGCACCCC-ACACCAGGTC 3640 chr5ptel1M 140732 AAGACCACTCTACACCAAAGGGCAGGTTGTTGACTGACTTATTCAAGAAT 140781 i vi ivi v i ii v vv v ii i vv vvii HERVP71A#LTR/ 3641 AGGAATATATTAAATCAAAAAGCCGGGAGATGGTTAACGGATTCTCAGAT 3690 chr5ptel1M 140782 TTTTAAATAGGAATCATTATTGCTGGGAAAAAAATGACTTTGTTTTAAGC 140831 i v v v vv i -i i i v iv vv HERVP71A#LTR/ 3691 TCTAAAATATGAAGCCATATTACT-AGAAAAAGATGATTTGGTCGTAACA 3739 chr5ptel1M 140832 ACTAAGAACTGT---AATCAAGTCAG---CCT------------------ 140857 v v vi i--- v i --- ------------------ HERVP71A#LTR/ 3740 ACAAATACTTGCCTGAATCCAGCCAGTTTCCTATGGAAAGGAGAGGAGAA 3789 chr5ptel1M 140858 -------------GAACATAGTTGTCTGAATGTAA------ACCAA---- 140884 ------------- v ii ii ii i v ------ ---- HERVP71A#LTR/ 3790 CGAAGAGGCATCAGACCATAACTGCTTAGATATCATAGAATACCAAACCA 3839 chr5ptel1M 140885 -AGTTAGATCAGATTTGACTAATATTCCTTTTGA-AACAGAACAACGATT 140932 - i ii v vvi vii vi vv -i ii i i - ii HERVP71A#LTR/ 3840 AAGTTAGACCAGACCTTAGGGAAGCTCCACTACATGATGGGATAA-GGCT 3888 chr5ptel1M 140933 GTTTATAGAAGGGTCTTCACGAGTGGTTGAAGGAAAAAGAAGCAATGGTT 140982 i i v v v i v v v i vii i HERVP71A#LTR/ 3889 GTTTGTGGATGGGTCGTCCCGAGTGATAGATGGCAAGAGACATAATGGCT 3938 chr5ptel1M 140983 ATGCAATCGTAAATGGG---AAAGATTGGTCA-GTGTAAGAGTCTGAATC 141028 vi i vi i--- v ? vv i - vi i viv v v HERVP71A#LTR/ 3939 ATGCTGTCATTGATGGAAATAAACANTCCTTATGTGAGAAAGGTAGATTA 3988 chr5ptel1M 141029 CCTGCCAAAGAACTGGTCAGCACAGACATGCAAACTCTATGCTCTAAATC 141078 ---- vii i v i v ii i v v i HERVP71A#LTR/ 3989 CCT----AATGGCTGGTCGGCCCAAACCTGTGAATTATATGCTCTTAACC 4034 chr5ptel1M 141079 AGGCCCTTAAGAAACCGAGTGAGA---AAGAAGGAACTCTATATA--GGT 141123 v --- ivvv ii--- v v -- i HERVP71A#LTR/ 4035 AGGCCCTAAAG---CTCCTTGAAGGCCAAGAAGGCACTATATATACTGAT 4081 chr5ptel1M 141124 TCCAAATATGCCTATGGGGTAATCCATACTTTTGGGAAAATTTGGGAGCA 141173 ii v i i i iviv HERVP71A#LTR/ 4082 TCCAAATATGCCTATGGGGTGGTACACACTTTTGGAAAAATCTGGACAGA 4131 chr5ptel1M 141174 ATGGGGCCTCAATAAATAGTAAGGGAAAGAATTTGGCTCATGGTGAACTA 141223 ii - i i ii v iv v i HERVP71A#LTR/ 4132 GCGGGGCCT-AATAAATAGCAGGGGAAAAGAATTGGTACATGGGGAACTG 4180 chr5ptel1M 141224 ATCGAACAAGTGTTAGAAAATTTACTATTGCCATCAGAGATAGCGGTGGT 141273 i i i v iii v ii v v i vi i HERVP71A#LTR/ 4181 GTCAAACAGGTTTTAGAAAGCCTCCTGCTTCCAGCAGAGGTAGCCATAGT 4230 chr5ptel1M 141274 ACACATCAAAGGTTATCA-AAAGGGAA 141299 v ii v v ii - HERVP71A#LTR/ 4231 TCATGTAAATGGCCATCAGAAAGGGAA 4257 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.30 CpG sites = 159, Kimura (unadjusted) = 41.05 Transitions / transversions = 1.37 (159/116) Gap_init rate = 0.04 (34 / 905), avg. gap size = 2.56 (87 / 34) 15 13.67 0.00 0.00 chr5ptel1M 141386 141409 (858591) (T)n#Simple_repeat 1 24 (0) m_b220s252i8 8689 chr5ptel1M 141386 TTCTTTTTTTTTTTTATTTTATTT 141409 i v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTT 24 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 14 17.30 5.13 0.00 chr5ptel1M 141386 141424 (858576) (TTATT)n#Simple_repeat 1 41 (0) m_b220s252i9 8690 chr5ptel1M 141386 TTCTTTT-TTTT-TTTTATTTTATTTAATAGCCTTTTATTT 141424 v - - v vviv (TTATT)n#Simp 1 TTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTT 41 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2) 250 28.39 3.73 3.73 chr5ptel1M 141871 142031 (857969) C L1MC5a_3end#LINE/L1 (2141) 636 476 m_b220s551i9 8691 chr5ptel1M 141871 CCTGCTCATTTCACTCAGCATCAGTTCGTGTAAGTCTCTCCAGGCCTTTC 141920 i iv i i vi vv v v ii v vi? vv v C L1MC5a_3end#L 636 CTTGCTTTTTTCACTTAACAATATATCCTGGAGATCACTCCATANCAGTA 587 chr5ptel1M 141921 T---GAAATCATCCTGTTGGTCATTTCTTACAGA-ACAGTAATATTCCAT 141966 --- i v vv -- v - v-i - i i C L1MC5a_3end#L 586 TATAGAGATCTTCCTCAT--TCCTTT-TTACAGCTGCA-TAGTACTCCAT 541 chr5ptel1M 141967 AATTTTCATATACCACAATTTATTCAGCCATTCTCCAACTGATGGACATC 142016 vi v vv i i i i v i v i i C L1MC5a_3end#L 540 TGTGTGGATGTACCATAGTTTATTCAACCAGTCCCCTATTGATGGACATT 491 chr5ptel1M 142017 C--ATTCAGTTTCCAGT 142031 i--i -- C L1MC5a_3end#L 490 TGGGTT--GTTTCCAGT 476 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.39 CpG sites = 22, Kimura (unadjusted) = 36.39 Transitions / transversions = 1.00 (22/22) Gap_init rate = 0.06 (9 / 160), avg. gap size = 1.33 (12 / 9) 323 23.53 4.90 4.90 chr5ptel1M 141874 142016 (857984) C L1MC1_3end#LINE/L1 (447) 633 491 m_b220s551i10 8691 chr5ptel1M 141874 GCTCATTTCACTCAGCATCAGTTCGTGTAAGTCTC-TCCAGGCCTTTCTG 141922 iv i i vi - v i v i - v i --- C L1MC1_3end#LI 633 GCTTCTTTCACTTAGTAATA-TGCATTTAAGTTTCCTCCATGTCTTT--- 588 chr5ptel1M 141923 AAATCAT--CCTGTTGG-TCATTTCTTAC-AGAAC--AGTAATATTCCAT 141966 --- -- i v i - vi- vi -- i C L1MC1_3end#LI 587 ---TCATGGCTTGATAGCTCATTTCTTTTTAGCGCTGAATAATATTCCAT 541 chr5ptel1M 141967 AATTTTCATATACCACAATTTATTCAGCCATTCTCCAACTGATGGACATC 142016 vi i vv i i i v v v v C L1MC1_3end#LI 540 TGTCTGGATGTACCACAGTTTATTTATCCATTCACCTACTGAAGGACATC 491 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 27.54 CpG sites = 17, Kimura (unadjusted) = 28.57 Transitions / transversions = 1.13 (17/15) Gap_init rate = 0.08 (12 / 142), avg. gap size = 1.17 (14 / 12) 252 24.13 3.33 3.33 chr5ptel1M 141942 142031 (857969) C L1MC5_3end#LINE/L1 (2129) 565 476 m_b220s551i11 8691 chr5ptel1M 141942 TTCTTACAGA-ACAGTAATATTCCATAATTTTCATATACCACAATTTATT 141990 i v-i - i i vi v vv i i i C L1MC5_3end#LI 565 TTTTTACAGCTGCA-TAGTACTCCATTGTGTGGATGTACCATAGTTTATT 517 chr5ptel1M 141991 CAGCCATTCTCCAACTGATGGACATCC--ATTCAGTTTCCAGT 142031 i v i v i ii--i -- C L1MC5_3end#LI 516 CAACCAGTCCCCTATTGATGGACATTTGGGTT--GTTTCCAGT 476 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 30.12 CpG sites = 14, Kimura (unadjusted) = 30.12 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.06 (5 / 89), avg. gap size = 1.20 (6 / 5) 325 24.36 0.00 0.00 chr5ptel1M 141954 142031 (857969) C L1ME2z_3end#LINE/L1 (638) 553 476 m_b220s551i12 8691 chr5ptel1M 141954 AGTAATATTCCATAATTTTCATATACCACAATTTATTCAGCCATTCTCCA 142003 i vi v vv i i i v v C L1ME2z_3end#L 553 AGTAGTATTCCATTGTATGAATATACCACAGTTTGTTTATCCATTCTCCT 504 chr5ptel1M 142004 ACTGATGGACATCCATTCAGTTTCCAGT 142031 ii i iivv v C L1ME2z_3end#L 503 GTTGATGGACACCTGGGCTGTTTCCAGT 476 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 29.80 CpG sites = 10, Kimura (unadjusted) = 29.80 Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.00 (0 / 77), avg. gap size = 0.0 (0 / 0) 308 25.29 0.00 0.00 chr5ptel1M 141956 142042 (857958) C L1ME3A_3end#LINE/L1 (369) 551 465 m_b220s551i13 8691 chr5ptel1M 141956 TAATATTCCATAATTTTCATATACCACAATTTATTCAGCCATTCTCCAAC 142005 i vi v vv i v v vii C L1ME3A_3end#L 551 TAGTATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTACTGT 502 chr5ptel1M 142006 TGATGGACATCCATTCAGTTTCCAGTGAAAGGTTACT 142042 iiivvi? vv?? i i C L1ME3A_3end#L 501 TGATGGACATTTGGGTNGTTTCCAGTTTNNGGCTATT 465 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 32.54 CpG sites = 11, Kimura (unadjusted) = 32.54 Transitions / transversions = 1.00 (11/11) Gap_init rate = 0.00 (0 / 86), avg. gap size = 0.0 (0 / 0) 753 31.80 9.07 2.33 chr5ptel1M 144049 144853 (855147) L1M4_orf2#LINE/L1 1560 2417 (877) m_b220s551i14 8692 chr5ptel1M 144049 AAACAAAGAGCTAATATAGAGAAAAAGAATAGTAGGCCAATTTTTCTAGT 144098 i vv v i - i i i v -i i v ii vi L1M4_orf2#LIN 1560 AGACAAAGACATCACA-AGAAAAGAAAACTA-CAGACCAATATCCCTTAT 1607 chr5ptel1M 144099 GAATATTGATGCAAACA--CT-AACAAAGCAATGATAAAA---------- 144135 v v -- - ii v iii v---------- L1M4_orf2#LIN 1608 GAATATAGATGCAAAAATCCTCAACAAAATACTAGCAAACCGAATCCAGC 1657 chr5ptel1M 144136 AAAATATTGCAAAGTTTATATA----------GTGGAATTTATATCAGAA 144175 v viv i v i ---------- i vi i L1M4_orf2#LIN 1658 AACATATAAAAAGGATTATACACCATGACCAAGTGGGATTTATCCCAGGA 1707 chr5ptel1M 144176 ATGCA-GATTGATTCTTTATTAGGGGAACTACCAACATAATGGGCCAGAT 144224 - i i vvi ?v iii v v i ii ivi v L1M4_orf2#LIN 1708 ATGCAAGGTTGGTTCAACATNCGAAAATCAATCAATGTAATACACCATAT 1757 chr5ptel1M 144225 CAATAACAAAATCAACCGAAATCATATGATTTTCTCAAAAAATGCAGAAA 144274 i iv v vvi vi i i iv v i i L1M4_orf2#LIN 1758 TAATAGAATAAAGGACAAAAACCACATGATCATCTCAATAGACGCAGAAA 1807 chr5ptel1M 144275 AAGATTTTGAAAAAATATAGCATCCGTTTCTATTACAAACACTAGAGAGG 144324 vv v vi i i v iv iv v vi v ii L1M4_orf2#LIN 1808 AAGCATTTGACAAAATCCAACACCCTTTCATGATAAAAACACTCAACAAA 1857 chr5ptel1M 144325 CTAGGAATA-AAGGGAACTTTACTTCAAA-TGATAAGCAGTATCTGTCTC 144372 - -- i v- ivi i iivvv L1M4_orf2#LIN 1858 CTAGGAATAGAAGGGAACTT--CCTCAACCTGATAAAGGGCATCTACGAA 1905 chr5ptel1M 144373 AAACCATGAACAAGCATTATCTGTAAAAGGGATAAACTAGCAGTCTTCCC 144422 vvv i v i i viv vi v v i iiv? ii L1M4_orf2#LIN 1906 AAACCCACAGCTAACATCATACTTAATGGTGAAAGACTGAANGCTTTCCC 1955 chr5ptel1M 144423 AATAAGATCAGGGATAA----AGGCTGCCTATTGTCATCACAT-TATTCA 144467 vv i i ---- v i iii v ii v - L1M4_orf2#LIN 1956 CCTAAGATCAGGAACAAGACAAGGATGTCCGCTCTCGCCACTTCTATTCA 2005 chr5ptel1M 144468 GTATAATATATTTAAAAAGTTAGCTATAGCAATAAGAAAAGTAAAAGAAA 144517 ii -- i i vi iivvi i vi v iv v L1M4_orf2#LIN 2006 ACAT--TGTACTGGAGGTTCTAGCCAGGGCAATTAGGCAAGAAAAAGAAA 2053 chr5ptel1M 144518 T----------CAAATGAGAAA---------AAAATCATTACTATTTGAA 144548 ---------- i vi --------- ii iv i v L1M4_orf2#LIN 2054 TAAAAGGCATCCAGATTGGAAAGGAAGAAGTAAAACTATCTCTATTCGCA 2103 chr5ptel1M 144549 TATGATACAATATTATATATGGAGGACCCT--GGAGTAGCACTTTTAAAA 144596 v i ii v i i ii i -- i -v ?v-- L1M4_orf2#LIN 2104 GATGACATGATCTTGTATATAGAAAATCCTAAGGAAT-CCACNA--AAAA 2150 chr5ptel1M 144597 ATTATTTGATATAATTAACAATTTTAGCAAAAATAGTACGATATAAAAC- 144645 i v vv v i v i iiv - i v i i i- L1M4_orf2#LIN 2151 ACTATTAGAACTAATAAACGAGTTCAGCAAGGTT-GCAGGATACAAGATC 2199 chr5ptel1M 144646 ----TACATAAATCATCAGAATTTCTTTGTATGACCGTCAAGTTTAGCA- 144690 ---- v viv v --i i- iiv -- v i - L1M4_orf2#LIN 2200 AATATACAAAAATCAATTGTATTTCT--ATAC-ACTAGCAA--TGAACAA 2244 chr5ptel1M 144691 -TCAAGCAAGAGA--AAGAGAA--GTTCCAGTTAAAATAAC--TGAAAAC 144733 -i i iv v i -- i --i v v i --ii v L1M4_orf2#LIN 2245 TCCGAAAATGAAATTAAGAAAACAATTCCATTTACAATAGCATCAAAAAG 2294 chr5ptel1M 144734 AATATAATGTCTGAGGTAGACACGTGCTAAGACAAACTCAGGAACTGTA- 144782 v i- v v v v iv ivi i v iiv i vi - L1M4_orf2#LIN 2295 AATAAAATA-CTTAGGAATAAATTTAACAAAAGAAGTGCAAGACTTGTAC 2343 chr5ptel1M 144783 --TGAACATAATTACAATATACTTTTCACACAAAGTTA-----GATCTAA 144825 -- --- i v i i v v v v - ----- i L1M4_orf2#LIN 2344 ACTGAA---AACTACAAAACATTGTTGAAAGAAA-TTAAAGAAGACCTAA 2389 chr5ptel1M 144826 ACAATTGAAAAGACATTAATTATTCATG 144853 i v i ivvv i L1M4_orf2#LIN 2390 ATAAATGGAAAGACATCCCATGTTCATG 2417 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.18 CpG sites = 140, Kimura (unadjusted) = 42.79 Transitions / transversions = 1.27 (140/110) Gap_init rate = 0.05 (41 / 804), avg. gap size = 2.27 (93 / 41) 670 30.66 8.26 4.52 chr5ptel1M 144068 145157 (854843) L1M1_orf2#LINE/L1 1575 2703 (591) m_b220s551i15 8692 chr5ptel1M 144068 AGAAAAAGAATAGTA--GGCCAATTTTTCTAGTGAATATTGATGCAAACA 144115 i v v -- v i ii v L1M1_orf2#LIN 1575 AAAAAAAGAAAACTACAGGCCAATATCTCTGATGAATATTGATGCAAAAA 1624 chr5ptel1M 144116 --CT-AACAAA------GCAA--TGA--TAAAAAAAATATTGCAAAG--- 144149 -- - ------ --i -- v v v i iv --- L1M1_orf2#LIN 1625 TCCTCAACAAAATACTAGCAAACCGAATTCAACAATACATTAAAAAGATC 1674 chr5ptel1M 144150 -TTTAT-AT-----AGTGGAATTTATATCAGAAATGCA-GATTGATTCTT 144191 - i - ----- i vi ? ii - iv i vv L1M1_orf2#LIN 1675 ATTCATCATGACCAAGTGGGATTTATCCCNGGGATGCAAGGATGGTTCAA 1724 chr5ptel1M 144192 TATTAGGGGAA-CTACCAACATAATGGGCCAGATCAATAACAAAATCAA- 144239 i - v vi - v i ii i ivii v --- i v - L1M1_orf2#LIN 1725 CAT-ACGCAAATCAATCAATGTGATACATCATATCAA---CAGAATGAAG 1770 chr5ptel1M 144240 --CCGAAATCATATGATTTTCTCAAAAAATGCAGAAAAAGATTTTGAAAA 144287 -- vi i iv i vvi v vv v L1M1_orf2#LIN 1771 GACAAAAACCATATGATCATTTCAATTGATGCTGAAAAAGCATTTGATAA 1820 chr5ptel1M 144288 AATATAGCATCCGTTTCTATTACAAACACTAGAGAGGCTAGGAATAAAGG 144337 vi i v iv iv v v vi i ii i v i i L1M1_orf2#LIN 1821 AATTCAACATCCCTTCATGATAAAAACCCTCAAAAAACTGGGTATAGAAG 1870 chr5ptel1M 144338 GAACTTTACTTCAA-ATGAT--AAGCAGTATCTGTCTCAAACCATGAACA 144384 -v i - i -- vi vi --v i vvv i v L1M1_orf2#LIN 1871 GAAC-ATACCTCAACATAATAAAAGCCATATACG--ACAGACCCACAGCT 1917 chr5ptel1M 144385 AGCATTAT-CTGTAAAAGGGATAAACTAGCAGTCTTCCCAATAAGATCAG 144433 i i - - vi v iiv i i vv v L1M1_orf2#LIN 1918 AGTATCATACTG-AATGGGGAAAAACTGAAAGCCTTTCCTCTAAGATCTG 1966 chr5ptel1M 144434 GGATA----AAGGCTGCCTATTGTCATCAC-ATTATTCAGTATAATATAT 144478 i i ---- v i i v i -i ii --i i L1M1_orf2#LIN 1967 GAACACGACAAGGATGCCCACTTTCACCACTGTTATTCAACATA--GTAC 2014 chr5ptel1M 144479 TTAAAAAGTTAGCTATAGCAATAAGAAAAGTAAAAGAAAT---------- 144518 vi ivvi v v v vi ---------- L1M1_orf2#LIN 2015 TGGAAGTCCTAGCTAGAGCAATCAGACAAGAGAAAGAAATAAAGGGCATC 2064 chr5ptel1M 144519 CAAAT----GAGAAAAAAATC--ATTA---CTATTTGAATATGATACAAT 144559 ----i i i i -- ---i i v v ii L1M1_orf2#LIN 2065 CAAATTGGAAAGGAAGAAGTCAAATTATCCTTGTTTGCAGATGATATGAT 2114 chr5ptel1M 144560 ATTATATATGGAGGACCCTGGAGTAGCACT---TTTAAAAATTATTTGAT 144606 v v ii v ii ---- ---i?v i v v L1M1_orf2#LIN 2115 CTTATATTTGGAAAAACCTAAAG----ACTCCACNAAAAAACTATTAGAA 2160 chr5ptel1M 144607 ATAATTAACAATTTTAGCAAAAATAGTACGATATAAAAC-----TACATA 144651 v i v v i i- i v i v i i----- v L1M1_orf2#LIN 2161 CTGATAAACAAATTCAGT-AAAGTTGCAGGATACAAAATCAACATACAAA 2209 chr5ptel1M 144652 AATCATCAGAATTTCTTTGTATG---ACCGTCA--AGTTTAGCATCAAGC 144696 vi v -- i --- v v -- i i iiv -- v L1M1_orf2#LIN 2210 AATCAGTAGCATTTC--TATATGCCAACAGTGAACAATCTGAAA--AAGA 2255 chr5ptel1M 144697 AAGAGAAAGAGAAGTTCCAGTTAAAATAACTGAAAACAATAT--AATGTC 144744 vvi i v i i v v i iiv i v -- ii L1M1_orf2#LIN 2256 AATCAAAAAAGTAATCCCATTTACAATAGCCACAAATAAAATTAAATACC 2305 chr5ptel1M 144745 TGAGGTAGACACGTGCTAAGACAAACTCAGGAACTGTATGAACATAATTA 144794 - v vvv v iviv i v iivv i v v ii vv v i L1M1_orf2#LIN 2306 T-AGGAATTAACTTAACCAAAGAAGTGAAAGATCTCTACAATGAAAACTA 2354 chr5ptel1M 144795 CAATATACTTTTCACACAAAGTTA----GAT-CTAAACAATTGAAAAGAC 144839 i v i vv v v v v v ---- i- i v - i i L1M1_orf2#LIN 2355 TAAAACACTGATGAAAGAAATTGAAGAGGACACCAAAAAA-TGGAAAGAT 2403 chr5ptel1M 144840 ATTAATTATTCATGA---GGAAACATAGGCAATATAATAAAAAGAAAAAA 144886 vvv i i--- iv --- vi v v------ L1M1_orf2#LIN 2404 ATTCCATGTTCATGGATTGGAAGAAT---CAATATTGTTAAAAT------ 2444 chr5ptel1M 144887 AAAAAACTATGCTGCCTGAACTCATTTACTTCCTCAGTGCCATAACAATC 144936 ----iv i i i ii viv i vvvi i v vv v L1M1_orf2#LIN 2445 ----GTCCATACTACCCAAAGCAATCTACAGATTCAATGCAATCCCTATC 2490 chr5ptel1M 144937 AGGCTACCAA--AAATTATCTGGCAGAGGTAG-AAAAACAATAACAAAAT 144983 iiv -- v v - vi ii - vvi L1M1_orf2#LIN 2491 AAAATACCAATGACATTCT-TCACAGAAATAGAAAAAACAATCCTAAAAT 2539 chr5ptel1M 144984 TTATCTGGAAGAACAAAAAGTCGAGAATA-TCAAAGGAATT---AATAAA 145029 v vv iii v -i vv i--- ii L1M1_orf2#LIN 2540 TTATATGGAACCACAAAAGACCCAGAATAGCCAAAGCTATCCTGAGCAAA 2589 chr5ptel1M 145030 AA-ATTAGAAAGGAAGGTGACCTAGCAATATCAGATTTTAAACTATTTTT 145078 - vi i vv i -i i --i v i v i i i ---- L1M1_orf2#LIN 2590 AAGAACAAAACTGGAGG-AATC--ACATTACCTGACTTCAAATTAT---- 2632 chr5ptel1M 145079 AACTAATGATTGTTA-ATTAAACAGATTTTAAACTACCTAGTAATGGCTA 145127 - vv -- i - v v ------ vi v i v vv L1M1_orf2#LIN 2633 -ACTACAGA--GCTATAGTAACCA------AAACAGCATGGTACTGGCAT 2673 chr5ptel1M 145128 AGAAATAGAATGGTGGATCAATGGAATAGA 145157 i i vvvi i i i L1M1_orf2#LIN 2674 AAAAACAGACACATAGACCAATGGAACAGA 2703 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.92 CpG sites = 165, Kimura (unadjusted) = 40.25 Transitions / transversions = 1.07 (165/154) Gap_init rate = 0.08 (87 / 1089), avg. gap size = 1.62 (141 / 87) 194 22.93 6.45 1.54 chr5ptel1M 145274 145335 (854665) L2c_3end#LINE/L2 334 398 (80) m_b220s601i10 8693 chr5ptel1M 145274 TATATT-TATTTATCTGTTTAGATGCTTTGTCTCC---AGTAGAATATAG 145319 i - v i v? - i --- v v i ii L2c_3end#LINE 334 TGTATTGTAATTGTCTGTTTACNTG-TCTGTCTCCTCCACTAGACTGTGA 382 chr5ptel1M 145320 GCTCCTTGAAAAGAGG 145335 iiiv L2c_3end#LINE 383 GCTCCTTGAGGGCAGG 398 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.73 CpG sites = 9, Kimura (unadjusted) = 28.73 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.05 (3 / 61), avg. gap size = 1.67 (5 / 3) 193 19.74 6.17 6.17 chr5ptel1M 145276 145356 (854644) L2a_3end#LINE/L2 359 439 (78) m_b220s601i11 8693 chr5ptel1M 145276 TATTTATTTATCTGTTTAGATGCTTTGTCTCC----AGTAGAATATAGGC 145321 i i v- - i ---- v i i L2a_3end#LINE 359 TACTTATTTATTTGTTTAT-TG-TCTGTCTCCCCCCACTAGAATGTAAGC 406 chr5ptel1M 145322 TCCTTGAAAAGAGGTGAAGTTTTTGCCT-TTGTGTT 145356 v iiiv - --i i - v L2a_3end#LINE 407 TCCATGAGGGCAGG-GA--CTTTTGTCTGTTTTGTT 439 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 23.47 CpG sites = 10, Kimura (unadjusted) = 23.47 Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.09 (7 / 80), avg. gap size = 1.43 (10 / 7) 504 35.12 7.92 5.30 chr5ptel1M 145557 145998 (854002) C L2b_3end#LINE/L2 (10) 456 4 m_b220s601i12 8694 chr5ptel1M 145557 TCAGTAAGCATTTGTTAAGCACTTATT---TGTCAGGTTTTATACTAAGT 145603 ii ii ii i i i i --- i i?i i i i i C L2b_3end#LINE 456 TCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGC 407 chr5ptel1M 145604 GCTAAGGATAACAAAAA-AAACCAGGCAATAAACAGTCCCAGCTCTCAAG 145652 ii - ivii-i v i i- v? i v i v C L2b_3end#LINE 406 GCTGGGGATA-CAGCGGTGAACAAGACAG-ACNCGGTCCCTGCCCTCACG 359 chr5ptel1M 145653 GGGCTTTCAATCTAATGGGGGAGACA-ACATGCAAACAAATA--TATG-- 145697 i iv i i - i ? i i --? i-- C L2b_3end#LINE 358 GAGCTCACAGTCTAGTGGGGGAGACAGACATGTAANCAGACAATNATAAC 309 chr5ptel1M 145698 -CAAAGTGAGGTACGTATAATATAAATGGAAAATAATTAGAAGGAAAGCA 145746 - i ------ i vii vi v iiii-ivii - ii i C L2b_3end#LINE 308 CCAGAGTG------GCAGGGTAGGACTGGGGGG-GCCCAG-AGGAGGGCG 267 chr5ptel1M 145747 CTGGAATTAA---GAGAAGCTGGAGAAAGCTTCATAAAGAAGGTGGGATT 145793 iv viiii--- i ii iii i ii viii i iv C L2b_3end#LINE 266 CCTGACCCGGCCTGGGGGGTCAGGGAGGGCTTCCCGGAGGAGGTGACATT 217 chr5ptel1M 145794 TTAGTTGGGGATCAAATAAAGCCAAGGAGGCTTGTAATCAGAT-CATAGG 145842 v i i iviii vi v vvv -- --ii ii-v v C L2b_3end#LINE 216 TGAGCTGAGACCTGAAGGATGAGTAGGAG--TTG--GCCAGGCGAAGAGG 171 chr5ptel1M 145843 AGGAGGTCTATATAGCATTCCCCAGGCATGGGGAACAGCCAGAGAAAAGG 145892 v i i----- vi i -- vi v? v v C L2b_3end#LINE 170 TGGGGA-----AGGGCGTT--CCAGGCAGAGGGAACAGCANGTGCAAAGG 128 chr5ptel1M 145893 CCTAAATATGGG-GTACAC------TGT--GAGG--CATCCAGGAGTCC- 145930 ivi vii - ?ivi ------ -- -- v v v - C L2b_3end#LINE 127 CCCTGAGGCGGGAGNGAGCNTGGCGTGTTCGAGGAACAGCAAGGAGGCCA 78 chr5ptel1M 145931 TCGTTACTGGATCAAAGAGTATATATTGGGAGTAAGGGTAAAGGA-GAG- 145978 vi vi v -- ivii vv - iv iii - - C L2b_3end#LINE 77 GTGTGGCTGGAGC--AGAGTGAGCAAGGGGAG-AGTGGTAGGAGATGAGG 31 chr5ptel1M 145979 -CGAAAA------GGGGCCAGGTTATG 145998 - i i ------ i ii C L2b_3end#LINE 30 CCGGAGAGGTAGCGGGGCCAGATCGTG 4 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 46.99 CpG sites = 105, Kimura (unadjusted) = 52.99 Transitions / transversions = 2.50 (105/42) Gap_init rate = 0.09 (41 / 441), avg. gap size = 1.44 (59 / 41) 400 34.73 11.26 1.97 chr5ptel1M 145856 146228 (853772) C L2#LINE/L2 (8) 3074 2668 m_b220s601i13 8694 chr5ptel1M 145856 AGCATTCCCCAGGCATGGGGAACAGCCAGAGAAAAGGCCTAAATATGGG- 145904 i -- vi v v v ivi vii - C L2#LINE/L2 3074 AGCGTTCC--AGGCAGAGGGAACAGCAAGTGCAAAGGCCCTGAGGCGGGA 3027 chr5ptel1M 145905 --GTACACTG-------TGAGG--CATCCAGGAGTCC-TCGTTACTGGAT 145942 -- i - -------i -- v v v -vi vi v C L2#LINE/L2 3026 GCGTGC-CTGGCGTGTTCGAGGAACAGCAAGGAGGCCAGTGTGGCTGGAG 2978 chr5ptel1M 145943 CAAAGAGTATATATTGGGAG-----TAAGGG-TAAAG---GAGAGCGAAA 145983 ii v viii- vv ----- i i - i i --- vv v C L2#LINE/L2 2977 CGGAGTGAGCG-AGGGGGAGAGTGGTAGGAGATGAGGTCAGAGAGGTAAC 2929 chr5ptel1M 145984 AGGGG-CCAGGTTATGAAAGGCTTTGAATGCTAA-ACAAGCATTTTA-TA 146030 i - i i v i i v v i v-ii v i i-iv C L2#LINE/L2 2928 GGGGGACCAGATCATGTAGGGCCTTGTAGGCCATTGTAAGGACTTTGGCT 2879 chr5ptel1M 146031 TTTGCTCTTGG--AGACTAGAGTCTATTGATTTGGGGTTTT--------- 146069 i vi -- ivi iv i i---i --------- C L2#LINE/L2 2878 TTTACTCTGAGTGAGATGGGAAGCCATTGG---AGGGTTTTGAGCAGAGG 2832 chr5ptel1M 146070 ----ATATGAT-TGAATT-TGTTTTAGGAAAACCAGTTTAGGGGATGAAT 146113 ---- i - v -i ii ii i v i i vv v vi C L2#LINE/L2 2831 AGTGACATGATCTGACTTACGTTTTAAAAGGATCACTCTGGCTGCTGTGT 2782 chr5ptel1M 146114 GGAGAATGGATTAGAATGGGAAGAGATTGGAAGCTGGCAAGATTTCCCAG 146163 v i i i? iv ivi iv v -i iivvii C L2#LINE/L2 2781 TGAGAATAGACTGNAGGGGGGCAAGGGTGGAAGCAGG-GAGACCAGTTAG 2733 chr5ptel1M 146164 CAGATTATTATAGTGATCAAGGCATGGGGTGATAAGGGCCTCCACTCAAG 146213 v ii ii i v iv i i iiv i vv ivii C L2#LINE/L2 2732 GAGGCTATTGCAGTAATCCAGGCGAGAGATGATGGTGGCTTGGACCAGGG 2683 chr5ptel1M 146214 TGTCAGCAGTGGGAG 146228 vii ii C L2#LINE/L2 2682 TGGTGGCAGTGGAGG 2668 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 44.86 CpG sites = 78, Kimura (unadjusted) = 49.25 Transitions / transversions = 1.59 (78/49) Gap_init rate = 0.06 (24 / 372), avg. gap size = 2.08 (50 / 24) 75 18.10 0.69 0.69 chr5ptel1M 146284 146428 (853572) (GA)n#Simple_repeat 1 145 (0) m_b220s252i10 8695 chr5ptel1M 146284 GAGAGTCAGTACAGTGACAGAGACTGAGACAGAGACTGAAAATCAGAGAG 146333 vv - v v v vv v vv i ivv (GA)n#Simple_ 1 GAGAGAGAG-AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 49 chr5ptel1M 146334 ATAGAGAGAGAGAGAGA-AAATAGAGAGACAGAGACTGAGAGAGAGAGAG 146382 v - i v v vv (GA)n#Simple_ 50 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 99 chr5ptel1M 146383 AGAGAGAGAGAAAGAGAAAGAGAGAGAGAGAGAGAAAGAGAGAGAG 146428 i i i (GA)n#Simple_ 100 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 145 Matrix = Unknown Transitions / transversions = 0.35 (6/17) Gap_init rate = 0.01 (2 / 144), avg. gap size = 1.00 (2 / 2) 23 5.80 2.78 0.00 chr5ptel1M 147172 147207 (852793) (TTAGTT)n#Simple_repeat 1 37 (0) m_b220s252i11 8696 chr5ptel1M 147172 TTAGTTTT-GTTTTAGTTTAAGTTTTAGTATTAGTTT 147207 - v v (TTAGTT)n#Sim 1 TTAGTTTTAGTTTTAGTTTTAGTTTTAGTTTTAGTTT 37 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) 249 16.23 4.05 8.45 chr5ptel1M 148235 148308 (851692) C MIR3#SINE/MIR (23) 185 115 m_b220s601i14 8697 chr5ptel1M 148235 AGAGCTGGGAGGTGAC---AGAGGCCATCTAGCCTCTCCCCCAAACTCAG 148281 i - --- ii i ivv ---- - C MIR3#SINE/MIR 185 AGAGCTGGAAGG-GACCTTAGAGATCATCTAGTCCAACCCCC----TCA- 142 chr5ptel1M 148282 TCTTACGGATGGGGACACTGAGGCCCA 148308 i i i v C MIR3#SINE/MIR 141 TTTTACAGATGAGGAAACTGAGGCCCA 115 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 18.69 CpG sites = 8, Kimura (unadjusted) = 18.69 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.10 (7 / 73), avg. gap size = 1.29 (9 / 7) 252 30.96 5.77 7.84 chr5ptel1M 150438 150749 (849251) C L1ME4c_3end#LINE/L1 (273) 557 252 m_b221s551i0 8698 chr5ptel1M 150438 GCACAATATTACTCCATTACATTGATG--CCAGAACTTGTTCAACCATTC 150485 i --- iivi ? -- v i ii i C L1ME4c_3end#L 557 GCATAATATT---CCATCGAGTNGATGTACCATAATTTACTTAACCATTC 511 chr5ptel1M 150486 TCCCAAGTGCTGACCATCTGCCATG----AAATTCTTTACCAAGATAGAA 150531 - v v i iv i ivvv ----v i ii i vv i v C L1ME4c_3end#L 510 -CCCTATTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAAT 462 chr5ptel1M 150532 AGAACTGC--TGTAGAGTTTTGTACATATATAGGCCCTTTTTCTTTTCCT 150579 ivi -- v v vi i i -----v -i i C L1ME4c_3end#L 461 AACGCTGCAATGAACATCTTCGTGCATATA-----GCTTTTTC-CTTCTT 418 chr5ptel1M 150580 TTGA--TA--TCTTTGGGATG------CAGACCTGGTATTGCTGGAACAA 150619 -- -- i i i------ vv v i iv C L1ME4c_3end#L 417 TTGAATTATTTCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAA 368 chr5ptel1M 150620 AGCACAGGCATAGTTTAATAGTTCTTTGGATCTAGTAATTTGGAACTACA 150669 vii v v i v v i i -- vi- -- --- i v C L1ME4c_3end#L 367 AGGGTATGAACATTTTTATGGCTCTT--GATAC-GTA--TTG---CCAAA 326 chr5ptel1M 150670 TTCCACCGGAACTCCACAATGGTTGGACCAGTTCACAAGTCTATGGACTA 150719 v ------vi v v v i i ?vv i ivii v C L1ME4c_3end#L 325 TTGC------TTTCCAAAAGGGTTGTACCAATTTACANTGCCACCAGCAA 282 chr5ptel1M 150720 TTCATTAGTGTTCCTGTTTTATCTCCTCCT 150749 vi v ? v v i i v v? C L1ME4c_3end#L 281 TGTATGAGNGTACCAGTTTCACCGCANCCT 252 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.21 CpG sites = 46, Kimura (unadjusted) = 41.27 Transitions / transversions = 1.07 (46/43) Gap_init rate = 0.10 (30 / 311), avg. gap size = 1.40 (42 / 30) 249 28.83 5.41 0.00 chr5ptel1M 150783 150893 (849107) C L1MA5A_3end#LINE/L1 (871) 173 57 m_b221s551i1 8698 chr5ptel1M 150783 ACTTTCATTTCTCTAAT---CAGTGATTTAGAGCATTTTT--ATATAACT 150827 i v i i ---i v v -- vi C L1MA5A_3end#L 173 ATTTGCATTTCCCTGATGATTAGTGATGTTGAGCATTTTTTCATATATTT 124 chr5ptel1M 150828 AGAAGCAGCTT-TAGTTTCTCATTCTAAAACTGCCTGATTAGGTTATTTG 150876 ivvi vii - vv ii v iv i v i v i i i C L1MA5A_3end#L 123 GTTGGCCATTTGTATGTCTTCTTTTGAGAAATGTCTGTTCAGATCATTTG 74 chr5ptel1M 150877 GCCATTTTTCAATTGGA 150893 v ? i C L1MA5A_3end#L 73 CCCATTTTTNAATCGGA 57 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.17 CpG sites = 18, Kimura (unadjusted) = 37.65 Transitions / transversions = 1.29 (18/14) Gap_init rate = 0.03 (3 / 110), avg. gap size = 2.00 (6 / 3) 33 17.39 0.00 0.00 chr5ptel1M 151288 151345 (848655) (T)n#Simple_repeat 1 58 (0) m_b221s252i0 8699 chr5ptel1M 151288 TTTTTTTTTTGTTTTTGTTTTTTTTTGGTTTTTGTTTTTTTGTTTTTTTC 151337 v v vv v v i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr5ptel1M 151338 TCTCTTTT 151345 i i (T)n#Simple_r 51 TTTTTTTT 58 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0) 13 15.72 0.00 7.89 chr5ptel1M 151569 151609 (848391) (AAGAGG)n#Simple_repeat 1 38 (0) m_b221s252i1 8700 chr5ptel1M 151569 AAGAGGGTGTGAGATGAGGAGGAAGGAAGAGAGAAGAGGAA 151609 iv v - v i - - (AAGAGG)n#Sim 1 AAGAGGAAGAG-GAAGAGGAAG-AGGAAGAG-GAAGAGGAA 38 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.07 (3 / 40), avg. gap size = 1.00 (3 / 3) 233 26.21 1.90 1.90 chr5ptel1M 151716 151820 (848180) L1ME4a_3end#LINE/L1 451 555 (316) m_b221s551i2 8701 chr5ptel1M 151716 ACCACAGCAACATTTATGGTAGCCAAAAAGTGGAAGCAAAGTGGGTGCCC 151765 i i vi ii v v i vv iii i L1ME4a_3end#L 451 ATCGCAGCATTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCC 500 chr5ptel1M 151766 ATCA-TGGGGGAAATGTCAGAACCAATGATGGTCACA-GCATGGGATGGA 151813 v - i ?vv i - iv v - -v i?i L1ME4a_3end#L 501 AACAATAGGGGANTGGTTA-AATAAATTATGGT-ACATCCATANAATGGA 548 chr5ptel1M 151814 ATATGAT 151820 v L1ME4a_3end#L 549 ATATTAT 555 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 32.16 CpG sites = 15, Kimura (unadjusted) = 33.66 Transitions / transversions = 1.25 (15/12) Gap_init rate = 0.04 (4 / 104), avg. gap size = 1.00 (4 / 4) 12 24.02 4.84 3.17 chr5ptel1M 152530 152591 (847409) (TGGAGGA)n#Simple_repeat 1 63 (0) m_b221s252i2 8702 chr5ptel1M 152530 TGG-GGAAGGATGGAGGGAGGAATGGAATTTGGAGG-TGGAAAAAGGAGG 152577 - v - v - ivv - ii v (TGGAGGA)n#Si 1 TGGAGGATGGA-GGATGGAGG-ATGGAGGATGGAGGATGGAGGATGGAGG 48 chr5ptel1M 152578 AGAGACCAT-GAGGA 152591 vi vv - (TGGAGGA)n#Si 49 ATGGAGGATGGAGGA 63 Matrix = Unknown Transitions / transversions = 0.50 (4/8) Gap_init rate = 0.08 (5 / 61), avg. gap size = 1.00 (5 / 5) 216 27.05 4.40 18.75 chr5ptel1M 155855 155945 (844055) MIR3#SINE/MIR 112 191 (17) m_b221s601i1 8703 chr5ptel1M 155855 CCTTGAGCTTCAGTTTTCTCACCAGTAAGAAGTGCGGGAGGAGAAGGGGA 155904 ii i i i i v --------------- v i i MIR3#SINE/MIR 112 CTCTGGGCCTCAGTTTCCTCATCTGTAA---------------AATGAGG 146 chr5ptel1M 155905 GGGTTGGTCTAGA----CTCTCAGGTCCCTCTTAACTTTACCACT 155945 v ---- v iii i i iv i MIR3#SINE/MIR 147 GGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATT 191 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.39 CpG sites = 15, Kimura (unadjusted) = 34.39 Transitions / transversions = 3.00 (15/5) Gap_init rate = 0.18 (16 / 90), avg. gap size = 1.19 (19 / 16) 228 29.70 4.23 2.78 chr5ptel1M 156938 157079 (842921) C L1MC2_3end#LINE/L1 (480) 611 468 m_b221s551i3 8704 chr5ptel1M 156938 CATTCTGGGTTTCTT--TGTTTTTTT-TAATTCTGCCAGCTCATTTCTT- 156983 ivi i i-- i i- iii - vi - C L1MC2_3end#LI 611 CATTTAAGGTTCCTCCATGTCTTTTCGTGGCT-TGATAGCTCATTTCTTT 563 chr5ptel1M 156984 --AGCGCACAATAATATTCCTTTATATTCCTATACCAAAATTTATTCAGC 157031 -- v vv v i vvv i v i i i v C L1MC2_3end#LI 562 TTATCGCTGAATAATATTCCATTGTATGGATGTACCACAGTTTGTTTATC 513 chr5ptel1M 157032 CATTCCCCAATTAATGGGCTTTTCCCCTCAATTTCCAAAATTTTGACA 157079 v v i v i v i ivvi --ii - i i C L1MC2_3end#LI 512 CATTCACCTATTGAAGGACATCTTGGTT--GCTTCC-AAGTTTTGGCA 468 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.69 CpG sites = 24, Kimura (unadjusted) = 38.91 Transitions / transversions = 1.41 (24/17) Gap_init rate = 0.06 (8 / 141), avg. gap size = 1.25 (10 / 8) 261 24.05 3.80 0.00 chr5ptel1M 156972 157050 (842950) C L1MC3_3end#LINE/L1 (1957) 575 494 m_b221s551i4 8704 chr5ptel1M 156972 AGCTCATTTCTT---AGCGCACAATAATATTCCTTTATATTCCTATACCA 157018 --- v vv v i vvv i C L1MC3_3end#LI 575 AGCTCATTTCTTTTTATCGCTGAATAATATTCCATTGTATGGATGTACCA 526 chr5ptel1M 157019 AAATTTATTCAGCCATTCCCCAATTAATGGGC 157050 v i i i v v v i v i C L1MC3_3end#LI 525 CAGTTTGTTTATCCATTCACCTATTGAAGGAC 494 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 29.01 CpG sites = 7, Kimura (unadjusted) = 29.01 Transitions / transversions = 0.58 (7/12) Gap_init rate = 0.01 (1 / 78), avg. gap size = 3.00 (3 / 1) 565 32.02 6.01 5.60 chr5ptel1M 156992 157507 (842493) C L1ME3Cz_3end#LINE/L1 (449) 548 31 m_b221s551i5 8704 chr5ptel1M 156992 ATAATATTCCTTTATATTCCTATACCAAAATTTATTCAGCCATTCCCCAA 157041 i v i vvv v i v v C L1ME3Cz_3end# 548 ATAGTATTCCATTGTATGAATATACCACAATTTATTTATCCATTCCCCTA 499 chr5ptel1M 157042 TTAATGGGCTTTTCCCCTCAATTTCCAAAATTTTGACACCCCAA-CAAGG 157090 i i v vvvi --i vv i vi iiv - v C L1ME3Cz_3end# 498 TTGATGGACATTTAGGTT--GTTTCCAATTTTTCGCTATTACAAACAATG 451 chr5ptel1M 157091 ACTCCTATGAATATTTTTGCATATGCATATATATGTATATTTATATCCTT 157140 - v v i ii i i iv viv i i i v iii----- C L1ME3Cz_3end# 450 -CTGCAATGAACATCCTTGTACATGTCTCCTTGTGCACATGTGCG----- 407 chr5ptel1M 157141 TCTTTTTTATGATCTCTTT-GGATACAGACCTATCAGTGGTATTTCTGAG 157189 -------- vii i i - i i v vv v v i C L1ME3Cz_3end# 406 --------AGAGTTTCTCTAGGGTATATACCTAGAAGTGGAATTGCTGGG 365 chr5ptel1M 157190 TCAAAGTGTATGCACTGTTGGTTGCCCTT--TGGGCATATTTCCAAATAA 157237 iv v i vvi -- iiv i -- i -- v vi C L1ME3Cz_3end# 364 TCGTAGGGTATGCGCATCT--TCAACTTTACTAG--ATATTGCCAAATTG 319 chr5ptel1M 157238 CTCTG-AGAATGGTTGGATCAGTTCAGGACTCC----AGAACGACATTAG 157282 v- i i v i i i v- ---- v vvii v C L1ME3Cz_3end# 318 CTCTCCAAAGTGGTTGTACCAATTTAC-ACTCCCACCAGCAGTGTATGAG 270 chr5ptel1M 157283 GCTTTTCAATTTTCC-CGTCTTC--TAACATTTATCACTTTC---CTTTT 157326 iv ii iv i - i i --i i ivi i v --- C L1ME3Cz_3end# 269 AGTTCCCGTTTCTCCACATCCTCGCCAACACTTGGTATTGTCAGACTTTT 220 chr5ptel1M 157327 ---TTGTCAGATGTCAATCTGAAAGGGGTGAGGAGATATCTCAGAGTTGC 157373 --- v ---- i vi v iiv i vv ? i C L1ME3Cz_3end# 219 AAATTTT----TGCCAATCTGATGGGTGTGAAATGGTATCTCATTGTNGT 174 chr5ptel1M 157374 TTTAAT--------CTCTAATCA--AGTGATTTGGAGCACTTCTTCATAT 157413 -------- i i i -- vv v ii i C L1ME3Cz_3end# 173 TTTAATTTGCATTTCCCTGATTACTAGTGAGGTTGAGCATCTTTTCATAT 124 chr5ptel1M 157414 GCCTAGAAATAGTTTTGATTATTTCATTTGAAATCTGCCTGCTCATATCC 157463 ii vviiivi iv i vii v i vi vi i C L1ME3Cz_3end# 123 GTTTATTGGCCATTCGGGTTTCCTCTTCTGTGAATTGCCTGTTCATATCC 74 chr5ptel1M 157464 TTTG---ATTTCTCTCTTCAGGAATCCTTTTTATTCTTATAAATTTG 157507 --- i v --- ii iv i - vi C L1ME3Cz_3end# 73 TTTGCCCATTTTTCTATT---GGGTTGTCTTT-TTCTTATTGATTTG 31 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.96 CpG sites = 90, Kimura (unadjusted) = 43.20 Transitions / transversions = 1.36 (90/66) Gap_init rate = 0.08 (41 / 515), avg. gap size = 1.46 (60 / 41) 377 30.38 7.81 2.11 chr5ptel1M 158190 158458 (841542) L1M4_orf2#LINE/L1 1906 2189 (1105) m_b221s551i6 8705 chr5ptel1M 158190 AAATCAAGAGCTAACATCATCTATAATAGAGATAAACTACAATCTTTTCC 158239 i v v viv i v v i iv ?v i L1M4_orf2#LIN 1906 AAACCCACAGCTAACATCATACTTAATGGTGAAAGACTGAANGCTTTCCC 1955 chr5ptel1M 158240 CATAA-ATTAAGGGTGAAACAGTGATGTTCACTGTCACCACTTCTATTTG 158288 v - i i iiii i iv i i v i ii L1M4_orf2#LIN 1956 CCTAAGATCAGGAACAAGACAAGGATGTCCGCTCTCGCCACTTCTATTCA 2005 chr5ptel1M 158289 ACATGGTATGAAAAATGTTGACT--GGCACTAAG--ATGAAAATAAAATA 158334 v ivii ii vi ii i-- v v -- v vi L1M4_orf2#LIN 2006 ACATTGTACTGGAGGTTCTAGCCAGGGCAATTAGGCAAGAAAAAGAAATA 2055 chr5ptel1M 158335 CAA--CAACTATA--GGAAGCCATGAAGATTCACAGTTATCACT-TTTGC 158379 v -- v i v -- --- v vvi v ii v - i L1M4_orf2#LIN 2056 AAAGGCATCCAGATTGGAA---AGGAAGAAGTAAAACTATCTCTATTCGC 2102 chr5ptel1M 158380 AGATGATAAATTGA---TGTATCTAAAGAA--CTTAG--ATTCAAGTAAA 158422 i --- --- v i i -- v -- i v?v L1M4_orf2#LIN 2103 AGATGACA---TGATCTTGTATATAGAAAATCCTAAGGAATCCACNAAAA 2149 chr5ptel1M 158423 AATTA----AATGAAACAATGCCTTTAGCACATTTGCAGG 158458 i ---- iv vv i vv i viv L1M4_orf2#LIN 2150 AACTATTAGAACTAATAAACGAGTTCAGCAAGGTTGCAGG 2189 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.66 CpG sites = 43, Kimura (unadjusted) = 40.20 Transitions / transversions = 1.16 (43/37) Gap_init rate = 0.06 (16 / 268), avg. gap size = 1.69 (27 / 16) 204 20.59 0.00 0.00 chr5ptel1M 159605 159638 (840362) C MIRb#SINE/MIR (25) 243 210 m_b221s601i2 8706 chr5ptel1M 159605 CACATAATATGTGCCAGATACTGTGCTAAGTACT 159638 i v v ii ii C MIRb#SINE/MIR 243 CGCTTACTATGTGCCAGGCACTGTGCTAAGCGCT 210 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 16.93 CpG sites = 5, Kimura (unadjusted) = 24.89 Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 224 30.37 18.54 1.93 chr5ptel1M 161533 161710 (838290) C MIR3#SINE/MIR (1) 207 1 m_b221s601i3 8707 chr5ptel1M 161533 AAACATAGAACCAGAGA---TCTGACCCTGGAAGGGACTTTGGAGGTCAT 161579 v i v --- v v - i i i C MIR3#SINE/MIR 207 AATCATAGAATCATAGAATGTCAGAGC-TGGAAGGGACCTTAGAGATCAT 159 chr5ptel1M 161580 ---GTT--ATCCC------------ATG--------GCATCCCAGAGCAG 161604 --- i-- i ------------ -------- viv - C MIR3#SINE/MIR 158 CTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAG-AG 110 chr5ptel1M 161605 ATG-AGTGGCTAGTCATAAGGTTATGCAGGTAGTCA--AATAAAG-TGGA 161650 i - i v i -i i ii v? i --iii i -i i C MIR3#SINE/MIR 109 GTGAAGTGACTTGCC-CAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGG 61 chr5ptel1M 161651 ATTTGGACCCAGGCTCTCTGAGTGTAGAATAGATACTTTCCCTGCT-AGA 161699 i v i iiii v -ivv i vvi i i i - v C MIR3#SINE/MIR 60 ACTAGAACCCAGGTCTCCTGACT-CCCAGTCCGTGCTCTCTCTGCTCAGC 12 chr5ptel1M 161700 GACCCCGCTGG 161710 v i i ii C MIR3#SINE/MIR 11 CACTCTGCCAG 1 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.71 CpG sites = 37, Kimura (unadjusted) = 41.84 Transitions / transversions = 2.31 (37/16) Gap_init rate = 0.07 (13 / 177), avg. gap size = 2.85 (37 / 13) 428 26.91 17.49 0.47 chr5ptel1M 162524 162706 (837294) C MIR#SINE/MIR (2) 260 47 m_b221s601i4 8708 chr5ptel1M 162524 TAATAA-TAACATTTATTTGACTACCAGCTATGTGTTGGGCACTGCGCTA 162572 i- - vii ivi iii iv C MIR#SINE/MIR 260 TAATAGCTAACATTTATT-GAGCGCTTACTATGTGCCAGGCACTGTTCTA 212 chr5ptel1M 162573 AATGTTTTATAATTATAATCTCTGTTAATCTTC---ACAATTCTAGAAAG 162619 ii i i vv v v vv i --- ii vi i C MIR#SINE/MIR 211 AGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGG 162 chr5ptel1M 162620 TTGG--------CTATCCTTA-TTTACAGAGGAGGAAA--GAAG-GCAAA 162657 v --------i ii - v -- i -i i C MIR#SINE/MIR 161 TAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGA 112 chr5ptel1M 162658 CTGATTAAGTGACTTACTCAGAG--------------AGTCCCAG-GCC- 162691 vv i i i i ii -------------- vv - - C MIR#SINE/MIR 111 GAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 62 chr5ptel1M 162692 AGATTTGAATCCAGG 162706 i i i C MIR#SINE/MIR 61 GGATTCGAACCCAGG 47 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.05 CpG sites = 33, Kimura (unadjusted) = 34.78 Transitions / transversions = 2.06 (33/16) Gap_init rate = 0.05 (10 / 182), avg. gap size = 3.30 (33 / 10) 389 29.10 11.03 2.72 chr5ptel1M 165347 165618 (834382) L1ME4c_3end#LINE/L1 346 639 (191) m_b221s551i7 8709 chr5ptel1M 165347 GCTATGAAACTGTGCACACCCCTTGATCCAGTAGTGTCATTACTGGGTCT 165396 i i v v i i i i vi i v vv L1ME4c_3end#L 346 GCCATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAAT 395 chr5ptel1M 165397 GTGCCCCCAAAAAATCAT--ACAGGAAGGAAAAGGACCCCCATGTGCA-- 165442 v ii iv ii v -- v i i ---- i i -- L1ME4c_3end#L 396 TTATCCTAAGGAAATAATTCAAAAGAAGGAAAAAG----CTATATGCACG 441 chr5ptel1M 165443 AAAATGT-------------------GATAACAAAGAATTAGACAATAAG 165473 i -------------------i i i i i - i v L1ME4c_3end#L 442 AAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGA-AACAAC 490 chr5ptel1M 165474 -TAGATGCCCATCAATTGGAGGGTGGCTGAACAAGTTTTAGTATGTAAAG 165522 - i i v v i ii i i ii i v i ii v? v L1ME4c_3end#L 491 CTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNAC 540 chr5ptel1M 165523 ACA--GGAATATTATT--GTTCTTAAAAATAATAATAAACAAGATGATTT 165568 v i-- v-- iiv i v vv iv v L1ME4c_3end#L 541 TCGATGGAATATTATGCAGCCATTAAAAATGATAATTATGAAGACTATGT 590 chr5ptel1M 165569 TAGAAAGAACTGCAAA--GATTTTGAATTGATGTTGAGCGAAACAAGCAG 165616 - v v -- v -- v v vv i i i v L1ME4c_3end#L 591 -AGCAACA--TGGAAAATGTTTATGATATAATGTTAAGTGAAAAAAGCAG 637 chr5ptel1M 165617 AA 165618 L1ME4c_3end#L 638 AA 639 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.88 CpG sites = 45, Kimura (unadjusted) = 38.14 Transitions / transversions = 1.41 (45/32) Gap_init rate = 0.06 (15 / 271), avg. gap size = 2.53 (38 / 15) 258 23.64 5.21 3.06 chr5ptel1M 166041 166136 (833864) L1MC5_3end#LINE/L1 81 178 (2516) m_b221s551i8 8710 chr5ptel1M 166041 TATCAAAGGACAGTTCATAGGGGGGGAAATGTCAAA--GCTATCAGTTAT 166088 v vi i iiiii - -- v i i?i L1MC5_3end#LI 81 TATGAACAGACAGTTCACAGAAAAAGAAATG-CAAATGGCTCTTAANCAT 129 chr5ptel1M 166089 GTTAAAAAATGTTCCAAATCTAA---ATAATGAAAGAAATGCAAATTAAA 166135 i v i i -- i vi--- i i L1MC5_3end#LI 130 ATGAAAAGATGCTC--AACCTCGCTCATAATAAGAGAAATGCAAATTAAA 177 chr5ptel1M 166136 A 166136 L1MC5_3end#LI 178 A 178 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 28.78 CpG sites = 17, Kimura (unadjusted) = 30.45 Transitions / transversions = 3.40 (17/5) Gap_init rate = 0.05 (5 / 95), avg. gap size = 1.60 (8 / 5) 16 9.78 0.00 0.00 chr5ptel1M 166184 166205 (833795) (A)n#Simple_repeat 1 22 (0) m_b221s252i3 8711 chr5ptel1M 166184 AAAAAAAACAAAAAACAAAAAA 166205 v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAA 22 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 225 33.33 1.96 0.00 chr5ptel1M 166815 166916 (833084) L1ME3E_3end#LINE/L1 427 530 (459) m_b221s551i9 8712 chr5ptel1M 166815 AAATATATAAAAAAATATCAATAGCAG--TTCTTTGTGTTATTAAAGAAC 166862 i i i v i i iv -- v iv vi i L1ME3E_3end#L 427 AGACATGTACAAGAATGTTCATAGCAGCATTGTTTGTAATAGCAAAAAAC 476 chr5ptel1M 166863 TGGAAATTGAGGGGATGCCCATTATTTGGGGAATGGCTGAATAAGTTATG 166912 ivivvvii i iiviv i v i i i L1ME3E_3end#L 477 TGGAAACAACCCAAATGTCCATCGACAGGAGAATGGATAAATAAATTGTG 526 chr5ptel1M 166913 ATAT 166916 i L1ME3E_3end#L 527 GTAT 530 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 44.40 CpG sites = 22, Kimura (unadjusted) = 46.52 Transitions / transversions = 1.83 (22/12) Gap_init rate = 0.01 (1 / 101), avg. gap size = 2.00 (2 / 1) 12 29.44 0.00 5.00 chr5ptel1M 169019 169081 (830919) (CCCAGC)n#Simple_repeat 1 60 (0) m_b221s252i4 8713 chr5ptel1M 169019 CCCTGCCCCTACACCAGTGCCAGCCCCATCCCTCCCGCCAGGCCTCGCCC 169068 v vi v iv v ivv v v iv (CCCAGC)n#Sim 1 CCCAGCCCCAGCCCCAGCCCCAGCCCCAGCCCCAGCCCCAGCCCCAGCCC 50 chr5ptel1M 169069 CTGGAGCCCCAGC 169081 --- (CCCAGC)n#Sim 51 C---AGCCCCAGC 60 Matrix = Unknown Transitions / transversions = 0.40 (4/10) Gap_init rate = 0.05 (3 / 62), avg. gap size = 1.00 (3 / 3) 197 20.74 6.49 12.33 chr5ptel1M 170051 170127 (829873) C OldhAT1#DNA/hAT-Ac (925) 1917 1845 m_b221s601i5 8714 chr5ptel1M 170051 AAAGAGAGGGAGGAGAGTATGGCCGATCCAGCAGCTTTGCTTGTCCAATG 170100 i ii vi i -- - i i-- i vi C OldhAT1#DNA/h 1917 AAGGAGGAGGAGGACGGCATGGCC--TCCAGCA-CTTTGTTTA--CGAGA 1873 chr5ptel1M 170101 GCATGCTCCTTTCCA--GA---ATGTTTGCAC 170127 i ---- i -- --- i C OldhAT1#DNA/h 1872 ACAT----CCTTCCAGTGATCTATGTCTGCAC 1845 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 21.50 CpG sites = 12, Kimura (unadjusted) = 25.61 Transitions / transversions = 6.00 (12/2) Gap_init rate = 0.14 (11 / 76), avg. gap size = 1.27 (14 / 11) 354 32.07 3.74 0.91 chr5ptel1M 170644 170750 (829250) C MIRc#SINE/MIR (156) 112 3 m_b221s601i6 8715 chr5ptel1M 170644 GTTAACTGAGTTGTCCAGGGTAATACTAATTAACAAGTAT--GTGTCAA- 170690 v v i i v i - ii ii iv-- v i ii- C MIRc#SINE/MIR 112 GTTAAGTGACTTGCCCAAGGTCACAC-AGCTAGTAAGTGGCAGAGCCGGG 64 chr5ptel1M 170691 ACTTGAATTCAGATCCTCCTGACTCCAGAGTTGATGTTTTATTCACTGTA 170740 i ii i i iiviiii i i v i i C MIRc#SINE/MIR 63 ACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCA 14 chr5ptel1M 170741 CCAC-CTACCT 170750 - i C MIRc#SINE/MIR 13 CCACACTGCCT 3 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 42.53 CpG sites = 27, Kimura (unadjusted) = 46.38 Transitions / transversions = 3.86 (27/7) Gap_init rate = 0.04 (4 / 106), avg. gap size = 1.25 (5 / 4) 1733 31.86 5.97 4.40 chr5ptel1M 171063 173255 (826745) C L1MD_orf2#LINE/L1 (720) 2574 349 m_b221s551i10 8716 chr5ptel1M 171063 TTTAA-TATTTTAGATCTTTTATTTTTCTAGTTGAATTTTGTTATAATTT 171111 i- i v i iii i vv i ivv ?i C L1MD_orf2#LIN 2574 TTTAGCTATTCTAGTTCCTTTGCCTTTCCATATAAATTTTAGAATAANCT 2525 chr5ptel1M 171112 TGTTTCAT-TTTGTAGAATATCTCTTTGATAGCTTGATTACCGTAGCACT 171160 i - - i ii i v ivi iv vi vivvi v ii C L1MD_orf2#LIN 2524 TGTCT-ATATCTACAAAAAATCTTGCTGGGATTTTGATAGGAATTGCGTT 2476 chr5ptel1M 171161 AAATTTGTAAATAA---TGTAAATAAT-GGTATTTTTA---TATTGATAG 171203 ii ? v --- vii v - ii i --- i -- C L1MD_orf2#LIN 2475 AAACCTGTANATCAATTTGGGGAGAATTGACATCTTTACTATGTTGA--G 2428 chr5ptel1M 171204 TCTGGCCTAGCCATGAACACTAAAGCAAGCCTTACTTCAGCCATTTACAT 171253 v- v v ---i i v i -- i vii v C L1MD_orf2#LIN 2427 TCTT-CCAATCCATGAACAC---GGTATGTCT--CTCCATTTATTTAGAT 2384 chr5ptel1M 171254 TTTTTAAAAATTTCTTTAAAGAACATTTAGTAATATTTA---TACA---- 171296 i i vvi - v vv i i v i v i --- ---- C L1MD_orf2#LIN 2383 CTTCTTTGA-TTTCTTTCATCAGCGTTTTGTAGTTTTCAGCATACAAGTC 2335 chr5ptel1M 171297 --GTAGATTGACTT-TTAAATATTTTATAC------ATTTC-TTAGTTAT 171336 -- v - vi - i --- ------ - -- v C L1MD_orf2#LIN 2334 CTGTACAT-GTTTTGTTAGAT---TTATACCTAAGTATTTCATT--TTTT 2291 chr5ptel1M 171337 TTTGACTG---GTATATTGTCTTATATTGTCTGCTATTAATTTT----TG 171379 vi --- v v v i - i iv v iii i---- C L1MD_orf2#LIN 2290 TTTGAGCGATTGTAAATGGTATTGTATT-TTTAATTTCGGTTTCCACGTG 2242 chr5ptel1M 171380 TT-ATTTTTA-TATATTAGTGATA---TTGATTTTTGT--GTTTATTTTG 171422 - vi - - vi --- -- ? i C L1MD_orf2#LIN 2241 TTCATTGCTAGTATAT-AGAAATACAATTGATTTTTGTATGTTNATCTTG 2193 chr5ptel1M 171423 CAACCTATTCCATT--TGAAG--AAGTATTATCTCAATTATTTTACTTGT 171468 i v iivv v -- v-- vv vi v vv v vi C L1MD_orf2#LIN 2192 TATCCTGCGACCTTGCTGAACTCACTTATTAGTTCTAGGAGTTTTTTTGT 2143 chr5ptel1M 171469 TGATTGCATGAGACATTCTAAGTAAATTATCATGTCAATAGCAAATAGGA 171518 v v v i iv v i iv viv i C L1MD_orf2#LIN 2142 AGATTCCTTGGGATTTTCTACGTAGACAATCATGTCATCTGCAAATAGGG 2093 chr5ptel1M 171519 ATAGTATTGACTTTCTTTTGTCTAATTTTTATGACTG--ATTTTTTTTTT 171566 i - v i ii ii v i i v v v-- ii i C L1MD_orf2#LIN 2092 ACAGT-TTTATTTCTTCCTTTCCAATCTGTATGCCTTTTATTTCCTTTTC 2044 chr5ptel1M 171567 TTAATCCAAATGCTATCCTCGGC---ATCTCTTAGAATTACGCAAAATAA 171613 i-- vv -- iiv - --- v iii v i i ivi C L1MD_orf2#LIN 2043 TTG--CCTTAT--TGCACT-GGCTAGAACTTCCAGTACTATGTTGAATAA 1999 chr5ptel1M 171614 TATTGGGCAAAGGAGACACCCTTATTCTAGCTCTGTATTCTAT-TTATTC 171662 v v vv i vi i ------ ii vii v - --- C L1MD_orf2#LIN 1998 GAGTGGTGAGAGCGGACATCCTT------GCCTTGTTCCCGATCTTA--- 1958 chr5ptel1M 171663 TGGAGAAAAGAAGGCTCAG------AC--TGAAGGATGATATTTGGACTT 171704 - i i v --i ------ -- v v i ------- C L1MD_orf2#LIN 1957 -GGGGGAAAGCA--TTCAGTCTTTCACCATTAAGTATGATGTT------- 1918 chr5ptel1M 171705 TTAAAAATGTAGCCAGTATTTTCAGATGAAAAAATAGATGCTACTGATCA 171754 ---- iv --- v -----------i vi v C L1MD_orf2#LIN 1917 ----AGCTGTAG---GTTTTTT-----------GTAGATGCTCTTTATCA 1886 chr5ptel1M 171755 TTTTAAGAAAAT----ATTTATTCCAATATTCTCT-AGTGTTTTTAATGG 171799 vv i i i ----v i v -i i? - v viiv C L1MD_orf2#LIN 1885 AGTTGAGGAAGTTCCCCTCTATTCCTA-GTTTNCTGAGAGTTTTTATCAT 1837 chr5ptel1M 171800 GAAAGAGTGTGGGATTTTATCAAATGCTTTTTCTCCATCTATTGAGGTAA 171849 v i v i i v v vi i C L1MD_orf2#LIN 1836 GAATGGGTGTTGAATTTTGTCAAATGCTTTTTCTGCATCAATTGATATGA 1787 chr5ptel1M 171850 TTATATGCTTTTTGTTAGTTA---TGCTAATA--GT-------------- 171880 i i v v vv --- i -- -------------- C L1MD_orf2#LIN 1786 TCATGTGATTTTTCTTCTTTAGCCTGTTAATATGGTGGATTACATTGATT 1737 chr5ptel1M 171881 --TTTCCTGATATTGAACCAGCCCTGCATTCCTGGTATAAATCCTACTTG 171928 -- i vi i ? v i i C L1MD_orf2#LIN 1736 GATTTTCGAATATTGAACCAGCCTTGCATNCCTGGAATAAACCCCACTTG 1687 chr5ptel1M 171929 GTCATGATGTATTATCCTGGAAATAACTTGCTGCAATCTTTTTGCTAAAA 171978 i v i vvvv vv v v ?v v C L1MD_orf2#LIN 1686 GTCATGGTGTATAATTCTTTTTATATATTGCTGAATTCNATTTGCTAATA 1637 chr5ptel1M 171979 TTTTATTTAAGATTTTTGCATAGATATTCATTAGAGAAAGTCACTGGTCT 172028 i v i i vv i v i ----i i C L1MD_orf2#LIN 1636 TTTTGTTGAGGATTTTTGCGTCTATGTTCATGAGGGA----TATTGGTCT 1591 chr5ptel1M 172029 ATAAAGTCCTTTCTCTTTTATCCACCCTATCTGGTTTAGGTATCAGCACC 172078 i ivv i - i v iivv ii i v viiv C L1MD_orf2#LIN 1590 GTAGTTTTCTTT-TTTTGTACTGTCTTTGTCTGGTTTTGGTATCAGGGTA 1542 chr5ptel1M 172079 ATAGATGTGTCATAAAAGGAATTTGGTAGGATTCCTTCTTTCCTTATTTG 172128 vvv iv v i v v vi i i iiii v C L1MD_orf2#LIN 1541 ATACTGGCCTCATAAAATGAGTTGGGAAGTGTTCCCTCCTCTTCTATTTT 1492 chr5ptel1M 172129 TCCAAATAATTTGCATAATATTGAAATTCA-TCTTCCTTAAAT------- 172170 iivi v iv ii iv ivi v - i i------- C L1MD_orf2#LIN 1491 CTGGAAGAGATTGTGTAGAATTGGTGTTAATTCTTCTTTAAACGTTTGGT 1442 chr5ptel1M 172171 -GAAT--TCCAGTGTAAATCCATCTGGCCCTGGAGATTTTTTCTTAGGGA 172217 - -- - - v i i i C L1MD_orf2#LIN 1441 AGAATTCTCCAGTG-AAA-CCATCTGGGCCTGGAGATTTCTTTTTGGGGA 1394 chr5ptel1M 172218 ATTGATTAATAGCTTGCTCTAGTTC-TTTTTCTAAA-----ATGGGACTG 172261 i -- ? v -- i-- v i -v i v ----- i i i C L1MD_orf2#LIN 1393 GTT--TTNAAA--TTA--CGAATTCAATTTCCTTAATAGTTATAGGGCTA 1350 chr5ptel1M 172262 GTTAAGTAATTTATTTTCTCTTTTATCATTCTGGGCCATCTCTATTATTG 172311 v i i v i iv ? vvi v v i?v ivi i v i v v C L1MD_orf2#LIN 1349 TTCAAATTATCTATTTCATNTTGGGTGAGTTNTGGTAGTTTGTGTTTTTC 1300 chr5ptel1M 172312 TAGATATTCCTCTATTTCACTTAGATTATCAAATTTA-GTGACATACAGT 172360 v iv vv i ii ii i - - i v C L1MD_orf2#LIN 1299 GAGGAATTGGTCCATTTCATCTAAGTTGTCAAATTTATGTG-CGTAGAGT 1251 chr5ptel1M 172361 TGGATAAAATGACTGCTAATTATTGTTCTCATTTCTTCTTCATTGGTAGA 172410 vviiv i iviiv v iv i v v v vvvi iv v C L1MD_orf2#LIN 1250 TGTTCGTAGTATTCCCTTATTATCCTTTTGATGTCTGCAGGGTCTGTAGT 1201 chr5ptel1M 172411 AAGTTCTCCCTTTTCATTTTTGATAGTAACAATTTCATTTTCTTCTTTCC 172460 i vv i iv ii v iii v-- v i i C L1MD_orf2#LIN 1200 GATATCCCCTGTTTCATTCCTGATATTGGTAATTTG--TGTCTTCTCTCT 1153 chr5ptel1M 172461 TTTTTTTCTAATCAAATTCAATAAAGGTTTCTCTATTCTGTTAGCTTATT 172510 ii vi ivi iiv i v v i i iiii v C L1MD_orf2#LIN 1152 TTTTTTCTTTGTCAGTCTTGCTAGAGGTTTGTCAATTTTATTGATCTTTT 1103 chr5ptel1M 172511 CATGAAACTAATTCTGAGTTTTATTTATTAATTCAATAGTTTTCTTATTT 172560 vii i ii i vv i v vvi v v ii i C L1MD_orf2#LIN 1102 CAAAGAACCAGCTTTTTGTTTCATTGATTTTCTCTATTGTTTTTCTGTTT 1053 chr5ptel1M 172561 TCAGTTTTATTAATCTCCCCTTTCATTTTCAGAATTTCAAATTTGATATT 172610 i i i i iv i i i i vv vvvii vv ii C L1MD_orf2#LIN 1052 TCAATTTCATTGATTTCTGCTCTTATCTTTATTATTTCCTTCCTTCTGCT 1003 chr5ptel1M 172611 TAATTGGAGGTTATTAATG-TTTTCTTTTCCTACTTTTTT-AGTTGGAAG 172658 iv v i v -v - i i v? i - v i C L1MD_orf2#LIN 1002 TGCTTTGGGTTTATT-TTGCTCTTCTTTTTCTAGNTTCTTGAGGTGGGAG 954 chr5ptel1M 172659 CCCAGTTCATTGATCTT---CTCTTTCTTTATTTTATGCAAGTAAGCATC 172705 ii v i i v--- i i i v i --- v ? i C L1MD_orf2#LIN 953 CTTAGATTATTGATTTGAGACTTTTCCTCTTTTCTA---ATGTANGCATT 907 chr5ptel1M 172706 TAGAGATATAAAATCTCACCTATTA--ATCACTTTGGCAGAATCACACAA 172753 v v - i - v i -- iii i v vi v C L1MD_orf2#LIN 906 TAGTGCTAT-AAATTTC-CCTCTCAGCACTGCTTTAGCTGCGTCCCACAA 859 chr5ptel1M 172754 ATTTTGGTATGTTGTTTCGTTATTGTCATTCTCTTGGATGAAATTATTGA 172803 i v iv i v vv vi v v v i C L1MD_orf2#LIN 858 ATTTTGATATGTTGTATTTTCATTTTCATTCAGTTCAATGTATTTTTTAA 809 chr5ptel1M 172804 TTGTGTCTATGGTTGGTTGCTTCACCCACCCAATTTCTAGGATTAGATTA 172853 vivii iv ii vvi vi v ivv v v i i v ivi i C L1MD_orf2#LIN 808 TTTCCCTTGAGACTTCCTCTTTGACCCATGGATTATTTAGAAGTGTGTTG 759 chr5ptel1M 172854 TTTAGTTTCCAATTAATTTTTGGTCTATTTTCCCCTGACCTCTC-ATCAC 172902 --- i v -vv iv v i i -i i i C L1MD_orf2#LIN 758 TTTAGTTTCCA---AGTGTTTGG-AGATTTTCCTGTTATCTTTCTGTTAT 713 chr5ptel1M 172903 --ATGTC-ATTTTTATTGCATCAGGATCAAAAAATTGCATT---TACCAT 172946 -- v - v v v iiv i i i -ii i --- iv C L1MD_orf2#LIN 712 TGATTTCTAGTTTGATTCCATTGTGGTCAGAGAA-CACACTCTGTATGAT 664 chr5ptel1M 172947 TTTTTTCCTTTCTATATTTGGTTTTTAGGT---TTTAATGACCCA-AATA 172992 ivv i - v --- v --- v i -i C L1MD_orf2#LIN 663 TTCAATTCTTT-TAAATTTG---TTGAGGTTTGTTTTATGGCCCAGGATA 618 chr5ptel1M 172993 ------ATTTTTGTATAGTTTCCAT--ACACTGCTGAGAAAAATTCATAT 173034 ------ i v ? vv i --i -- i i vii C L1MD_orf2#LIN 617 TGGTCTATCTTGGTANATGTTCCGTGGGCACT--TGAAAAGAATGTGTAT 570 chr5ptel1M 173035 TCCTTTCTAT--CTCCATTCATTTTTCTCCAAAGGTTTATCATACCTAAC 173082 -- v i --i vvi vv v v vi v iv i v i ivii C L1MD_orf2#LIN 569 TC--TGCTGTTGTTGGGTGGAGTGTTCTATAAATGTCGATTAGATCCTGT 522 chr5ptel1M 173083 TTTTCCAGCTTTCTATTTACCTCCTTAAT-TTCTTTCTTATTTATTTTGT 173131 vv iv vvv vi i ? vi i iv - i v v vi v v C L1MD_orf2#LIN 521 TGGTTGATGGTGTTGTTNAGTTCTTCTATATCCTTGCTGATTTTCTGTCT 472 chr5ptel1M 173132 GGTTCGATTTATCTAGTTCTGAGAGAGGAAGGTTGAGATCCCCCACTAGT 173181 i - v i v v v iiv ii i v vv C L1MD_orf2#LIN 471 AGTT-GTTCTATCAATTGCTGAGAGAGGGGTGTTGAAGTCTCCAACTATA 423 chr5ptel1M 173182 ATAGTTTTTCTATCTATTTCTTCTTGCAGCTCTCTTTACTTCTGCTCTAG 173231 v vvv i i i v i v ivii i ii v C L1MD_orf2#LIN 422 ATTGTGGATTTGTCTATTTCTCCTTTCAGTTCTATCAGTTTTTGCTTCAC 373 chr5ptel1M 173232 GAATTTAGATGCTATACCATTTGG 173255 v v ?v v iiii C L1MD_orf2#LIN 372 GTATTTTGNAGCTCTGTTGTTTGG 349 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.60 CpG sites = 357, Kimura (unadjusted) = 42.80 Transitions / transversions = 1.15 (357/311) Gap_init rate = 0.07 (149 / 2192), avg. gap size = 1.54 (229 / 149) 1899 31.49 4.68 2.25 chr5ptel1M 171739 173255 (826745) C L1M5_orf2#LINE/L1 (1393) 1901 349 m_b221s551i11 8716 chr5ptel1M 171739 TAGATGCTACTGATCATTTTAAGAAAATA----TTTATTCCAATATTCTC 171784 ivi v vv i i i v---- i v -i iv C L1M5_orf2#LIN 1901 TAGATGCCCTTTATCAGGTTGAGGAAGTTCCCTTCTATTCCTA-GTTTGC 1853 chr5ptel1M 171785 T-AGTGTTTTTAATGGGAAAGAGTGTGGGATTTTATCAAATGCTTTTTCT 171833 - v viiv v i v i i C L1M5_orf2#LIN 1852 TGAGAGTTTTTATCATGAATGGGTGTTGAATTTTGTCAAATGCTTTTTCT 1803 chr5ptel1M 171834 CCATCTATTGAGGTAATTATATGCTTTTTGTTAGTTAT---GCTAATA-- 171878 v i i i v v ivv --- i -- C L1M5_orf2#LIN 1802 GCATCTATTGAGATGATCATATGATTTTTCTCCTTTATTCTGTTAATATG 1753 chr5ptel1M 171879 GT----------------TTTCCTGATATTGAACCAGCCCTGCATTCCTG 171912 ---------------- i vi i i i i C L1M5_orf2#LIN 1752 GTGAATTACATTGATTGATTTTCGAATGTTAAACCAACCTTGCATTCCTG 1703 chr5ptel1M 171913 GTATAAATCCTACTTGGTCATGATGTATTATCCTGGAAATAACTTGCTGC 171962 v i i vvvv vv v C L1M5_orf2#LIN 1702 GGATAAACCCCACTTGGTCATGATGTATTATCCTTTTTATATATTGCTGG 1653 chr5ptel1M 171963 AATCTTTTTGCTAAAATTTTATTTAAGATTTTTGCATAGATATTCATTAG 172012 v vv v i ? i vv i v C L1M5_orf2#LIN 1652 ATTCGATTTGCTAATATTTTGTTNAGGATTTTTGCATCTATGTTCATGAG 1603 chr5ptel1M 172013 AGAAAGTCACTGGTCTATAAAGTCCTTTCTCTTTTATCCACCCTATCTGG 172062 i ----i i i vv i - v vivv ii i ? C L1M5_orf2#LIN 1602 GGA----TATTGGTCTGTAATTTTCTTT-TCTTGTAATGTCTTTGTCNGG 1558 chr5ptel1M 172063 TTTAGGTATCAGCACCATAGATGTGTCATAAAAGGAATTTGGTAGGATTC 172112 v vii? ivvv iv v i v v vi C L1M5_orf2#LIN 1557 TTTTGGTATCAGGGTNATGCTGGCCTCATAAAATGAGTTGGGAAGTGTTC 1508 chr5ptel1M 172113 CTTCTTTCCTTATTTGTCCAAATAATTTGCATAATATTGAAATT-CATCT 172161 i iii viivi v i ii v iv -iv C L1M5_orf2#LIN 1507 CCTCTTTTTCTATTTTCTGGAAGAGTTTGTGTAAGATTGGTATTATTTCT 1458 chr5ptel1M 172162 TCCTTAAAT--------GAATT--CCAGTGTAAATCCATCTGGCCCTGGA 172201 -------- -- -- v v C L1M5_orf2#LIN 1457 TCCTTAAATGTTTGGTAGAATTCACCAGTG--AAGCCATCTGGGCCTGGA 1410 chr5ptel1M 172202 GATTTTTTCTTAGGGAATTGATTAATAGCTTGCTCTAGTTCTTTTTCTAA 172251 v i iv i i iv vv vi vvii - i ii vv i C L1M5_orf2#LIN 1409 GTTTTCTTTGTGGGAAGGTTTTTAATTACAAATTC-AATTTCTTTAATAG 1361 chr5ptel1M 172252 A-ATGGGACTGGTTAAGTAATTTATTTTCTCTTTTATCATTCTGGGCCAT 172300 - i i iv i ii vv i ii v?i v i v iv ? C L1M5_orf2#LIN 1360 ATATAGGGCTATTCAGATTTTCTATTTCTTCTTGNGTCAGTTTTGGTAAN 1311 chr5ptel1M 172301 CTCTATTATTGTAGATATTCCTCTATTTCACTTAGATTATCAAATTTAGT 172350 i v i v vv iv iv i ii ii ? v C L1M5_orf2#LIN 1310 TTGTGTTTTTCAAGGAATTTGTCCATTTCATCTAAGTTNTCAAATTTATT 1261 chr5ptel1M 172351 GACATACAGTTGGATAAAATGACTGCTAATTATTGTTCTCATTTCTTCTT 172400 i v vvi v iviiv v iv i v v vivv C L1M5_orf2#LIN 1260 GGCATAAAGTTGTTCATAATATTCTCTTATTATCCTTTTAATGTCTGTAG 1211 chr5ptel1M 172401 CATTGGTAGAAAGTTCTCCCTTTTCATTTTTGATAGTAACAATTTCATTT 172450 v iv vi vv i ii v iii v-- v C L1M5_orf2#LIN 1210 GATCTGTAGTGATGTCTCCTTTTTCATTCCTGATATTGGTAATTTG--TG 1163 chr5ptel1M 172451 TCTTCTTTCCTTTTTTTCTAATCAAATTCAATAAAGGTTTCTCTATTCTG 172500 i i ii i ivi ?iv i v v i i C L1M5_orf2#LIN 1162 TCTTCTCTCTTTTTTTCTTGATCAGTCTNGCTAGAGGTTTATCAATTTTA 1113 chr5ptel1M 172501 TTAGCTTATTCATGAAACTAATTCTGAGTTTTATTTATTAATTCAATAGT 172550 iiii v vii i ii i vi i ii v vvi v v C L1M5_orf2#LIN 1112 TTGATCTTTTCAAAGAACCAGCTTTTGGCTTCGTTGATTTTCTCTATTGT 1063 chr5ptel1M 172551 TTTCTTATTTTCAGTTTTATTAATCTCCCCTTTCATTTTCAGAATTTCAA 172600 ? ?i i vi i i i iv i i i i vv vv C L1M5_orf2#LIN 1062 NTNTTTGTTTTCTATTTCATTGATTTCTGCTCTTATCTTTATTATTTCCT 1013 chr5ptel1M 172601 ATTTGATATTTAATTGGAGGTT-ATTAATG-TTTTCTTTTCCTA-CTTTT 172647 vii vv i ?v v i v - -- - i i - i C L1M5_orf2#LIN 1012 TCCTTCTACTTNCTTTGGGTTTAATT--TGCTCTTCTTTTTCTAGCTTCT 965 chr5ptel1M 172648 TTAGTTGGAAGCCCAGTTCATTGATCTT--CTCTTTCTTTATTTTATGCA 172695 v v ii v i --vi i- v i- C L1M5_orf2#LIN 964 TAAGGTGGAAGCTTAGATCATTGATTTTAAGCCTTTCTTC-TTTTCTA-A 917 chr5ptel1M 172696 AGTAAGCATCTAGAGATATAAAATCTCACCTATTAATCA---CTTTGGCA 172742 vi ? i i? v - i - -i v --- i v C L1M5_orf2#LIN 916 TATANGCATTTAANGCTAT-AAATTTC-CCT-CTAAGCACTGCTTTAGCT 870 chr5ptel1M 172743 GAATCACACAAATTTTGGTATGTTGTTTCGTTATTGTCATTCTCTTGGAT 172792 v v i v iv i ? vv vi v C L1M5_orf2#LIN 869 GCATCCCACAAATTTTGATATGTTGTATTTTCATTNTCATTCAGTTCAAA 820 chr5ptel1M 172793 GAAATTATTGATTGTGTCTATGGTTGGTTGCTTCACCCACCCAATTTCTA 172842 iv v vi i viv?i i i vv vi v ivviv v i C L1M5_orf2#LIN 819 ATATTTTCTAATTTCCNTTGTGATTTCTTCTTTGACCCATGGGTTATTTA 770 chr5ptel1M 172843 GGATTAGATTATTTAGTTTCCAATTAATTTTTGGTCTATTTTCC-CCTGA 172891 i v ivi i i --- v -vv i-v? iv C L1M5_orf2#LIN 769 GAAGTGTGTTGTTTAATTTCCA---AATATTTGG-GGATTTTCTAGNTAT 724 chr5ptel1M 172892 CCTCTCATCAC--ATGTC-ATTTTTATTGCATCAGGATCAAAAAAT-TGC 172937 i i ii i i-- v - v v v iiv i i i i- i C L1M5_orf2#LIN 723 CTTTTTGTTATTGATTTCTAATTTAATTCCATTGTGGTCAGAGAACATAC 674 chr5ptel1M 172938 ATT-TACCATTTTTTTCCTTTC---TATATTTGGTTTTTAGGTTTTAATG 172983 vi - iv ivv ?--- v vi vi --- - C L1M5_orf2#LIN 673 TCTGTATGATTTCAATCCTTTNAAATTTATTGAGACTT---GTTTT-ATG 628 chr5ptel1M 172984 ACCCA-AATA------ATTTTTGTATAGTTTCCA--TACACTGCTGAGAA 173024 i -? ------ i v v vv -- i -- i C L1M5_orf2#LIN 627 GCCCAGNATATGGTCTATCTTGGTAAATGTTCCATGTGCACT--TGAAAA 580 chr5ptel1M 173025 AAATTCATATTCCTTTCTAT--CTCCATTCATTTTTCTCCAAAGGTTTAT 173072 i vii -- v ?i --i vvi v? v v vi v iv C L1M5_orf2#LIN 579 GAATGTGTATTC--TGCNGTTGTTGGGTGNAGTGTTCTATAAATGTCAAT 532 chr5ptel1M 173073 CATACCTAACT--TTTCCAGCTTTCTATTTACCTCCTTAATTTCTTTCTT 173120 i vii v ii -- vvi -- vi i i vv i iv v --- C L1M5_orf2#LIN 531 TAGGTCAAGTTGGTTGATAG--TGTTGTTCAAATCTTCTATATC---CTT 487 chr5ptel1M 173121 ATTTATTTTGTG---GTTCGATTTATCTAGTTCTGAGAGAGGAAGGTTGA 173167 i v v ---ii i v i v v v ?iv i C L1M5_orf2#LIN 486 ACTGATTTTTTGTCTACTTGTTCTATCAATTACTGAGAGAGGNGTGTTAA 437 chr5ptel1M 173168 GATCCCCCACTAGTATAGTTTTTCTATCTATTTCTTCTTGCAGCTCTCTT 173217 i i ? vv v vvv i i i vi i v i C L1M5_orf2#LIN 436 AATCTCCNACTATAATTGTGGATTTGTCTATTTCTCCTTTTAGTTCTGTC 387 chr5ptel1M 173218 TACTTCTGCTCTAGGAATTTAGATGCTATACCATTTGG 173255 vii i ii v v v v v iii v C L1M5_orf2#LIN 386 AGTTTTTGCTTCATGTATTTTGAAGCTCTGTTATTAGG 349 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 42.37 CpG sites = 247, Kimura (unadjusted) = 42.50 Transitions / transversions = 1.12 (247/220) Gap_init rate = 0.04 (61 / 1516), avg. gap size = 1.74 (106 / 61) 229 20.34 3.39 0.00 chr5ptel1M 173257 173315 (826685) DNM1r#Unknown 2484 2544 (2118) m_b221s502i0 8717 chr5ptel1M 173257 GTGTGTGTGTGTGTGTGTATGTATGTATACATATGTATAAATATGTACAT 173306 i i i i i i ii i v i i DNM1r#Unknown 2484 GTGTGTATATATGTGTGTATATGTGTGTATGTGTGTATATATGTGTATAT 2533 chr5ptel1M 173307 ATA--TATTTA 173315 -- ? DNM1r#Unknown 2534 ATACGTATNTA 2544 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 26.13 CpG sites = 11, Kimura (unadjusted) = 26.13 Transitions / transversions = 11.00 (11/1) Gap_init rate = 0.02 (1 / 58), avg. gap size = 2.00 (2 / 1) 277 15.38 0.00 0.00 chr5ptel1M 173258 173309 (826691) DNM1r#Unknown 2495 2546 (2116) m_b221s502i1 8717 chr5ptel1M 173258 TGTGTGTGTGTGTGTGTATGTATGTATACATATGTATAAATATGTACATA 173307 i i i i i v i i? DNM1r#Unknown 2495 TGTGTGTATATGTGTGTATGTGTGTATATATGTGTATATATACGTATNTA 2544 chr5ptel1M 173308 TA 173309 DNM1r#Unknown 2545 TA 2546 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 15.98 CpG sites = 7, Kimura (unadjusted) = 18.42 Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 413 27.83 9.57 0.00 chr5ptel1M 174234 174348 (825652) C MIRc#SINE/MIR (140) 128 3 m_b221s601i7 8718 chr5ptel1M 174234 ACTGAGACCCAGATAGTTTAAATTACTTTATCAAGCCCACACAGCTA--- 174280 i i v v i v vvi vi --- C MIRc#SINE/MIR 128 ACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTA 79 chr5ptel1M 174281 -----CAGAATCAGAATTTCAACTCACGTC---CCGATTCCAAATCTAGT 174322 ----- ii i i i iv i v --- i i i i C MIRc#SINE/MIR 78 AGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGT 29 chr5ptel1M 174323 GATCTTTCCATTCCACTGTATTGTCT 174348 v i v iii i i C MIRc#SINE/MIR 28 GCTCTTTCCACTGCACCACACTGCCT 3 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.61 CpG sites = 22, Kimura (unadjusted) = 36.48 Transitions / transversions = 2.20 (22/10) Gap_init rate = 0.03 (3 / 114), avg. gap size = 3.67 (11 / 3) 308 21.22 8.84 3.68 chr5ptel1M 174619 174799 (825201) C L1MEi_5end#LINE/L1 (3) 2209 2020 m_b221s551i12 8716 chr5ptel1M 174619 TTTGTGTCTTTTTGTTTTAAGAGTG--TCTTACAAAAAACATGTCGTTGG 174666 i v i v -- ii v i i v i C L1MEi_5end#LI 2209 TCTGTGTCGTTTTGTTTTAGGTGTGTCTCTTGTAAACAGCATATAGCTGG 2160 chr5ptel1M 174667 ATTGTGGTTCCTAATCTATTCTCTATAGACTTCTGACTTATTTTATGGAT 174716 v vv ii i v v- - ii v -- v i i C L1MEi_5end#LI 2159 ATTTTTTTTTTTAATCCAATCTG-ATA-ATCTCTGTCT--TTTAATAGGT 2114 chr5ptel1M 174717 GAGTTCAGCCCCTTAACATTTGTAATTATGATTACTG---TATTT---CT 174760 i ii v v --- i --- --- C L1MEi_5end#LI 2113 GAGTTTAATCCATTTACATTT---ATTGTGATTACTGATATATTTGGACT 2067 chr5ptel1M 174761 T-TT-----CATCCTTTTTTTTGTTTT-TGTTTTTC-TCTCTTTTCT 174799 - ----- i v v - v - ?ii C L1MEi_5end#LI 2066 TATTTCTACCATCTTATTTTGTGTTTTCTGTTTATCATNCTTTTTCT 2020 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 25.53 CpG sites = 21, Kimura (unadjusted) = 25.53 Transitions / transversions = 1.31 (21/16) Gap_init rate = 0.08 (14 / 180), avg. gap size = 1.64 (23 / 14) 244 27.88 0.95 0.95 chr5ptel1M 175167 175271 (824729) L1ME4a_3end#LINE/L1 451 555 (316) m_b221s551i13 8719 chr5ptel1M 175167 ACCACAGCAGCATTTATGGTAGCCAAAAAGTGGAAGCAAAGTGGGTGCCC 175216 i i vi ii v v i vv iii i L1ME4a_3end#L 451 ATCGCAGCATTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCC 500 chr5ptel1M 175217 ATCA-TGGGGGAAACGTTAGAACCAATGATGGTCAAAGCATGGGATGGAA 175265 v - i ?vv - iv v vv vv i?i L1ME4a_3end#L 501 AACAATAGGGGANTGGTTA-AATAAATTATGGTACATCCATANAATGGAA 549 chr5ptel1M 175266 TATGAT 175271 v L1ME4a_3end#L 550 TATTAT 555 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 34.58 CpG sites = 14, Kimura (unadjusted) = 36.08 Transitions / transversions = 0.93 (14/15) Gap_init rate = 0.02 (2 / 104), avg. gap size = 1.00 (2 / 2) 243 30.17 0.85 0.85 chr5ptel1M 175171 175287 (824713) L1ME3G_3end#LINE/L1 448 564 (360) m_b221s551i14 8719 chr5ptel1M 175171 CAGCAGCATTTATGGTAGCCAAAAAGTGGAAGCAAAGTGGGTGCCCATCA 175220 vii i ii v v i vv iii i L1ME3G_3end#L 448 CAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCA 497 chr5ptel1M 175221 -TGGGGGAAACGTTAGAACCAATGATGGTCAAAGCATGGGATGGAATATG 175269 - i vv - iv v vv vv ivv iv L1ME3G_3end#L 498 ATAGGGGAATGGTTA-AATAAATTATGGTATATCCATACTATGGAATACT 546 chr5ptel1M 175270 ATTATACTGTCAAAAAGA 175287 vvvi ? i L1ME3G_3end#L 547 ATGCAGCNGTTAAAAAGA 564 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.33 CpG sites = 16, Kimura (unadjusted) = 39.33 Transitions / transversions = 0.84 (16/19) Gap_init rate = 0.02 (2 / 116), avg. gap size = 1.00 (2 / 2) 232 22.99 4.40 18.75 chr5ptel1M 179404 179494 (820506) MIR3#SINE/MIR 112 191 (17) m_b221s601i8 8720 chr5ptel1M 179404 CCTTGGGCTTCAGTTTTCTCACCAGTAAAAAGTGGGGGAGGAGAAGGGGA 179453 ii i i i v -- i ------------- MIR3#SINE/MIR 112 CTCTGGGCCTCAGTTTCCTCATCTGTAAAA--TGAGG------------- 146 chr5ptel1M 179454 GGGTTGGTCTAGA----CTCTCAGGTCCCTCTTAACTTTACCACT 179494 v ---- v iii i i iv i MIR3#SINE/MIR 147 GGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATT 191 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.89 CpG sites = 13, Kimura (unadjusted) = 27.89 Transitions / transversions = 3.25 (13/4) Gap_init rate = 0.18 (16 / 90), avg. gap size = 1.19 (19 / 16) 639 31.69 4.70 4.49 chr5ptel1M 180168 180314 (819686) C L1ME3Cz_3end#LINE/L1 (432) 565 428 m_b221s551i15 8721 chr5ptel1M 180168 TTCATTTCTTACTGCACAATAATATTCCTTTATATTCCTATACCACAAGT 180217 - v vvv i v i vvv v C L1ME3Cz_3end# 565 TTCATTT-TAACTGCTGTATAGTATTCCATTGTATGAATATACCACAATT 517 chr5ptel1M 180218 TATTCAGCCATTCCCCAATAAATGGGC-TTCCCCTCAATTTCCAATATTT 180266 i v v vi i - ivvv ii- v C L1ME3Cz_3end# 516 TATTTATCCATTCCCCTATTGATGGACATTTAGGTTG-TTTCCAATTTTT 468 chr5ptel1M 180267 TCCCACCCCAAAAAGGATTCCTATAAATATTTTTGCATAAGAATACAT 180314 iv i iiv v ivii v v i i ii -------- C L1ME3Cz_3end# 467 CGCTATTACAAACAATGCTGCAATGAACATCCTTG--------TACAT 428 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.17 CpG sites = 81, Kimura (unadjusted) = 42.41 Transitions / transversions = 0.86 (19/22) Gap_init rate = 0.08 (11 / 146), avg. gap size = 1.00 (11 / 11) 38 0.00 0.00 0.00 chr5ptel1M 180315 180347 (819653) (AC)n#Simple_repeat 1 33 (0) c_b221s251i0 8722 chr5ptel1M 180315 ACACACACACACACACACACACACACACACACA 180347 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACA 33 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 639 31.69 4.70 4.49 chr5ptel1M 180348 180688 (819312) C L1ME3Cz_3end#LINE/L1 (570) 427 77 m_b221s551i15 8721 chr5ptel1M 180348 TCCTTTCTTTTT-----TGTGTGA---TCTCTTTGGGATACAGACCTATC 180389 --- i v ----- i --- i i i i i v vv C L1ME3Cz_3end# 427 TC---TCCTTGTGCACATGTGCGAGAGTTTCTCTAGGGTATATACCTAGA 381 chr5ptel1M 180390 AGTGGTATTTCTGAGTCAAAGTATATGCACTGTTTGGTTGCCCTT--TGG 180437 v v i iv vi i -i i -- iiv i -- i C L1ME3Cz_3end# 380 AGTGGAATTGCTGGGTCGTAGGGTATGCGC-ATCT--TCAACTTTACTAG 334 chr5ptel1M 180438 GCATAGTTCCAAATAATTCTG-AGAATGATTGGATCAGTTCAGGACTCC- 180485 -- v v vii v- i i i v i i i v- - C L1ME3Cz_3end# 333 --ATATTGCCAAATTGCTCTCCAAAGTGGTTGTACCAATTTAC-ACTCCC 287 chr5ptel1M 180486 ---AACACTACATTAGCCGTTTCAGTTT-TCCCTGTCTTCAACAGGGAAT 180531 --- i v ii v v- i v - vii i iv ivivv C L1ME3Cz_3end# 286 ACCAGCAGTGTATGAGA-GTTCCCGTTTCTCCACATCCTCGCCAACACTT 238 chr5ptel1M 180532 GACAATATGACAAAAAAGTAAAGTGAT--CAATCTGATAGGTGTGAGGTG 180579 ii v i -- i vvvv v vv -- i ii C L1ME3Cz_3end# 237 GGTATTGT--CAGACTTTTAAATTTTTGCCAATCTGATGGGTGTGAAATG 190 chr5ptel1M 180580 GTATCTCA--GTTGTTTTAACTTGCAATTCTCTAATCA--AGTGATTTGG 180625 -- ? i v i i i -- vv v C L1ME3Cz_3end# 189 GTATCTCATTGTNGTTTTAATTTGCATTTCCCTGATTACTAGTGAGGTTG 140 chr5ptel1M 180626 AGCACTTCTCCATATGTCCAGAGAAAGCTTTGATTATTTCATCTGAAATC 180675 ii i i ii vv ivvii iv i vii v vi vi C L1ME3Cz_3end# 139 AGCATCTTTTCATATGTTTATTGGCCATTCGGGTTTCCTCTTCTGTGAAT 90 chr5ptel1M 180676 TGCCTGCTCATAT 180688 i C L1ME3Cz_3end# 89 TGCCTGTTCATAT 77 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.17 CpG sites = 81, Kimura (unadjusted) = 42.41 Transitions / transversions = 1.38 (62/45) Gap_init rate = 0.06 (21 / 340), avg. gap size = 1.62 (34 / 21) 348 28.22 7.56 1.09 chr5ptel1M 180559 180730 (819270) C L1PA8A_3end#LINE/L1 (665) 213 31 m_b221s551i16 8721 chr5ptel1M 180559 CAATCTGATAGGTGTGAGGTGGTATCTCA--GTTGTTTTAACTTGCAATT 180606 v iv i i -- v i i v C L1PA8A_3end#L 213 CATTCTGACTGGCGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTT 164 chr5ptel1M 180607 CTCTAATCA--AGTGATTTGGAGCACTTCTCCATATGTCCAGAGAAAGCT 180654 i v -- v v vi i i iiivv ivv v C L1PA8A_3end#L 163 CTCTGATGATCAGTGATGTTGAGCTTTTTTTCATATGTTTGTTGGCCGCG 114 chr5ptel1M 180655 TTGATTATTTCATCTGAAATCTGCCTGCTCATA---TTTG---ATTGATC 180698 vi vvi v i i vv i i --- --- i -- i C L1PA8A_3end#L 113 TAAATGTCTTCTTTTGAGAAGTGTCTGTTCATATCCTTTGCCCACT--TT 66 chr5ptel1M 180699 TCGACGGTGTAAT---TTTTATTCTTATAAAGTTG 180730 i i v vi --- v i v C L1PA8A_3end#L 65 TTGATGGGGTTGTTTGTTTTTTTCTTGTAAATTTG 31 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 35.02 CpG sites = 25, Kimura (unadjusted) = 35.94 Transitions / transversions = 1.09 (25/23) Gap_init rate = 0.04 (7 / 171), avg. gap size = 2.14 (15 / 7) 328 29.73 8.75 3.90 chr5ptel1M 181068 181410 (818590) C L1P1_orf2#LINE/L1 (474) 2820 2462 m_b221s551i17 8723 chr5ptel1M 181068 CCAGTTTTCACAGTT---TTTGTCAAATAGTGAATTCTTATCCCAGAA-- 181112 v iv--- i i v i vi vvi-- C L1P1_orf2#LIN 2820 CCAGTTTTCCCAGCACCATTTATTAAATAGGGAATCCTTTCCCCATTGCT 2771 chr5ptel1M 181113 -GTTTTT---GGGTTTATCAAACAGTAGAGTACTATAGACTTTGGGTATT 181158 - ---i i v vi vvii i iv vv ii C L1P1_orf2#LIN 2770 TGTTTTTCTCAGGTTTGTCAAAGATCAGATAGTTGTAGATATGCGGCGTT 2721 chr5ptel1M 181159 AAATGTTATGTACCTAATTTCTTTCATTAATTTAGTATTTCT----TAG- 181203 vv v v v vvi iv i v i i i - i ---- i - C L1P1_orf2#LIN 2720 ATTTCTGAGGGCTCTGTTCTGTTCCATTGATCTA-TATCTCTGTTTTGGT 2672 chr5ptel1M 181204 -CCAGAACCAGGTGGTTTTGATGGTTACTG---CTTTTTAATGTAGTTTG 181249 - v v iv --- --- i v i i C L1P1_orf2#LIN 2671 ACCAGTACCATGCTGTTTTG---GTTACTGTAGCCTTGTAGTATAGTTTG 2625 chr5ptel1M 181250 AGATCTGATATTGCCAGACTACCTTT--CTTTGTTATTTTGTCCCCATTA 181297 ii v i -- vv - i ii-- v v ---- C L1P1_orf2#LIN 2624 AAGTCAGGTA--GCGTGA-TGCCTCCAGCTTTGTTCTTTTGGC----TTA 2582 chr5ptel1M 181298 T--TTTCCTTGATATTTTGACCTTTTTTTTCCTCCCAGATGAG--TTA-- 181341 v-- vv iiiv vi iv i vv i v i-- -- C L1P1_orf2#LIN 2581 GGATTGACTTGGCGATGCGGGCTCTTTTTTGGTTCCATATGAACTTTAAA 2532 chr5ptel1M 181342 -TTGTTTTCTTTAAACTTCTC---AGATAATTTTTTGGTAGTTTGATGGA 181387 - v i ii -- v--- - v iv i i C L1P1_orf2#LIN 2531 GTAGTTTTTTCCAA--TTCTGTGAAGA-AAGTCATTGGTAGCTTGATGGG 2485 chr5ptel1M 181388 CATGGCACCGAATAAGTAAATCA 181410 v ii vvi i C L1P1_orf2#LIN 2484 GATGGCATTGAATCTATAAATTA 2462 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.98 CpG sites = 51, Kimura (unadjusted) = 38.57 Transitions / transversions = 1.09 (51/47) Gap_init rate = 0.08 (28 / 342), avg. gap size = 1.57 (44 / 28) 316 28.19 8.84 5.24 chr5ptel1M 181425 181922 (818078) L1M5_orf2#LINE/L1 1905 2419 (875) m_b221s551i18 8724 chr5ptel1M 181425 AAAATCAAGAGCTAATATTATGTATAATGGGGATAAACTGCAACCTTTTC 181474 i v v ? i i iiv v v ? v ?v i L1M5_orf2#LIN 1905 AAAACCTACAGCNAACATCATACTTAATGGTGAAANACTGAANGCTTTCC 1954 chr5ptel1M 181475 CCATAAATTCAGGG-TGAAACA--GATGTTCCTTTACACCACTTCTGTTT 181521 v iv i i-ii i -- i vi ?v i i L1M5_orf2#LIN 1955 CCCTAAGATCGGGAACAAGACAAGGATGTCCGCTNTCACCACTTCTATTC 2004 chr5ptel1M 181522 GACACGGTATGAGGAATTTTGACCA--ACACTAAG--ATGAAAAGAAAAT 181567 i iv ivi iii ii ii --i v -- v ii L1M5_orf2#LIN 2005 AACATTGTACTGGAGGTCCTAGCCAGTGCAATAAGGCAAGAAAAAGAAAT 2054 chr5ptel1M 181568 TTAGGGTATAATTCTAGCAATTCATGAAG--ATTCAGTTATCACC-TTTA 181614 vv i i vvv v v --- v -- vv ii i ?ii- ii L1M5_orf2#LIN 2055 AAAAGGCATAAAGATTGGAA---AGGAAGAAATAAAACTGTCNTTATTCG 2101 chr5ptel1M 181615 CAGATGATAT-ATTGATGTACCTATGGAA-CTTAAA-----TTCAAGTAA 181657 i - - ? v vii - i? ----- v -- ? L1M5_orf2#LIN 2102 CAGATGACATGATTG-TNTACGTAGAAAATCCNAAAGAATCTACAA--AN 2148 chr5ptel1M 181658 AAATTAATTGAAACAATA--TC--TTTAGCACATTTGCAGGAGATAAA-- 181701 i v v vi -- v-- viv i ? v i i-- L1M5_orf2#LIN 2149 AAACTACTAGAACTAATAAGTGAATTTAGCAAGGTCGCNGGATACAAGGT 2198 chr5ptel1M 181702 -AATATCCACGCAAGTC-ATTGTCATTTCAATCTAACACCAATAAACTTA 181749 - -- iv i - - v v vi v i --- L1M5_orf2#LIN 2199 CAATAT--ACAAAAATCAATTGT-ATTTCTATATACTAGCAACAAAC--- 2242 chr5ptel1M 181750 AGTAGGCAGATAAA----GAGA---AATATCATTTACAATTACTATTACT 181792 i v v i i ----? i --- i - vi i -- L1M5_orf2#LIN 2243 AATTGGAAAATGAAATTTNAAAAACAATACCATTTACAA-TAGCATCA-- 2289 chr5ptel1M 181793 ATAAAATATATAAAATGCTTTGGAAT---TTCCTATCAAGATATATATGT 181839 -- - i ? i v --- -- v i-- ? i i L1M5_orf2#LIN 2290 --AAAA-ACATNAAATACTTAGGAATAAAT--CTAACAAA--ANATGTGC 2332 chr5ptel1M 181840 AAAAATCATAAAAATACAACTGCAAGA-ACTGCTTAC-----TTACACAA 181883 i vii? v vvv v i i - i v v----- v v L1M5_orf2#LIN 2333 AAGACCTNTACACTGAAAACTACAAAACATTGCTGAGAGAAATTAAAGAA 2382 chr5ptel1M 181884 ---CTAAATAATTGGGAAAAATATATATTAACTGCTCATGAA 181922 --- v --- i v ii -- i i L1M5_orf2#LIN 2383 GACCTAAATAAATGG---AGAGATATACCA--TGTTCATGGA 2419 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.51 CpG sites = 76, Kimura (unadjusted) = 37.63 Transitions / transversions = 1.33 (76/57) Gap_init rate = 0.09 (47 / 497), avg. gap size = 1.51 (71 / 47) 341 30.26 8.12 4.41 chr5ptel1M 181425 181818 (818182) L1M4_orf2#LINE/L1 1905 2312 (982) m_b221s551i19 8724 chr5ptel1M 181425 AAAATCAAGAGCTAATATTATGTATAATGGGGATAAACTGCAACCTTTTC 181474 i v v i i iiv v v i v ?v i L1M4_orf2#LIN 1905 AAAACCCACAGCTAACATCATACTTAATGGTGAAAGACTGAANGCTTTCC 1954 chr5ptel1M 181475 CCATAAATTCAGGG-TGAAACA--GATGTTCCTTTACACCACTTCTGTTT 181521 v iv i-ii i -- i vi iv i i i L1M4_orf2#LIN 1955 CCCTAAGATCAGGAACAAGACAAGGATGTCCGCTCTCGCCACTTCTATTC 2004 chr5ptel1M 181522 GACACGGTATGAGGAATTTTGACCAACAC---TAAG-ATGAAAAGAAAAT 181567 i iv ivi iii i ii ivi --- i - v ii L1M4_orf2#LIN 2005 AACATTGTACTGGAGGTTCTAGCCAGGGCAATTAGGCAAGAAAAAGAAAT 2054 chr5ptel1M 181568 TTAGGGTATAATTCTAGCAATTC---ATGAAGA--TTCAGTTATCACC-T 181611 vv i i ---- i -- v--- v -- vv ii v i- L1M4_orf2#LIN 2055 AAAAGGCA----TCCAG--ATTGGAAAGGAAGAAGTAAAACTATCTCTAT 2098 chr5ptel1M 181612 TTACAGATGATATATTGATGTACCTATGGAA---CTTA---AATTCAAGT 181655 ii i iv vv -- i --- i --- i v?v L1M4_orf2#LIN 2099 TCGCAGATGACATGATCTTGTA--TATAGAAAATCCTAAGGAATCCACNA 2146 chr5ptel1M 181656 AAAAATTAATTGAAACAATA----TCTTTAGCACATTTGCAGGAGATAAA 181701 i v v vi ----vv i viv v i i L1M4_orf2#LIN 2147 AAAAACTATTAGAACTAATAAACGAGTTCAGCAAGGTTGCAGGATACAAG 2196 chr5ptel1M 181702 ---AATATCCACGCAAGTC-ATTGTCATTTCAATCTAACACCAATAAAC- 181746 --- -- iv i - - v vi vi v i - L1M4_orf2#LIN 2197 ATCAATAT--ACAAAAATCAATTGT-ATTTCTATACACTAGCAATGAACA 2243 chr5ptel1M 181747 --TTAAGTAGGCAGATAAAGAGA--AATATCATTTACAATTACTATTACT 181792 --iii iv v - i v i -- vi - vi i -- L1M4_orf2#LIN 2244 ATCCGAAAATG-AAATTAAGAAAACAATTCCATTTACAA-TAGCATCA-- 2289 chr5ptel1M 181793 ATAAAATATATAAAATGCTTTGGAAT 181818 -- v - i v L1M4_orf2#LIN 2290 --AAAAGA-ATAAAATACTTAGGAAT 2312 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.83 CpG sites = 67, Kimura (unadjusted) = 40.31 Transitions / transversions = 1.43 (67/47) Gap_init rate = 0.08 (32 / 393), avg. gap size = 1.56 (50 / 32) 196 26.41 0.00 8.20 chr5ptel1M 182709 182774 (817226) L2d2_3end#LINE/L2 481 541 (14) m_b221s601i9 8725 chr5ptel1M 182709 TGTAACTGACACAGCTCACCCAGGACTCAACTGCTGTGCAAATATTAGGT 182758 v ivv --i i v --- v iv v i v i L2d2_3end#LIN 481 TGTATCCCCCACAGC--GCCTAGCAC---AGTGCCTTGCACACAGTAGGC 525 chr5ptel1M 182759 GCTTAATAAATGTTTG 182774 i i L2d2_3end#LIN 526 GCTCAATAAATATTTG 541 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.96 CpG sites = 8, Kimura (unadjusted) = 32.60 Transitions / transversions = 1.00 (8/8) Gap_init rate = 0.08 (5 / 65), avg. gap size = 1.00 (5 / 5) 205 21.35 0.00 9.62 chr5ptel1M 182718 182774 (817226) L2d_3end#LINE/L2 449 500 (16) m_b221s601i10 8725 chr5ptel1M 182718 CACAGCTCACCCAGGACTCAACTGCTGTGCAAATATTAGGTGCTTAATAA 182767 --i i v --- v v v v i i L2d_3end#LINE 449 CACAGC--GCCTAGCAC---AGTGCTGAGCACATAGTAGGCGCTCAATAA 493 chr5ptel1M 182768 ATGTTTG 182774 ii L2d_3end#LINE 494 ATACTTG 500 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 20.24 CpG sites = 6, Kimura (unadjusted) = 25.13 Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.09 (5 / 56), avg. gap size = 1.00 (5 / 5) 18 4.77 0.00 0.00 chr5ptel1M 183422 183443 (816557) (T)n#Simple_repeat 1 22 (0) m_b221s252i5 8726 chr5ptel1M 183422 TTCTTTTTTTTTTTTTTTTTTT 183443 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTT 22 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 516 21.06 0.88 7.55 chr5ptel1M 183457 183569 (816431) C MIRc#SINE/MIR (153) 115 10 m_b221s601i11 8727 chr5ptel1M 183457 GAGGTTAAGTGACTTGCCCAGGATCACACAACTAGGAAGTGTTA-AGTGT 183505 i i i v vi - --- C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAG--- 69 chr5ptel1M 183506 CTATTCTAAGATTTGAACTCAGGTCCTCCTGACTACAGGACTAGCGCTCT 183555 ----- iii i i i i v i v i i C MIRc#SINE/MIR 68 -----CCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCT 24 chr5ptel1M 183556 ATCCACTAGACTAC 183569 v iv i C MIRc#SINE/MIR 23 TTCCACTGCACCAC 10 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 22.74 CpG sites = 16, Kimura (unadjusted) = 25.50 Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.08 (9 / 112), avg. gap size = 1.00 (9 / 9) 342 32.40 8.20 8.20 chr5ptel1M 184085 184511 (815489) L2#LINE/L2 1735 2161 (921) m_b221s601i12 8728 chr5ptel1M 184085 TCAATCATTCCTTTTCTACTAGTCCACTCCC--CGACATCAAAAAACATA 184132 iv i i i vi i -- ii -- v i L2#LINE/L2 1735 TCAATTTTTCCCTCTCTACTGGATCATTCCCATCAGCAT--ACAAACATG 1782 chr5ptel1M 184133 CATGTCTTTTCT---GTCCCTAAAAATC------TTTCACTTGACCTTA- 184172 - ?v ---i ii v ------ i v ii - L2#LINE/L2 1783 C-TGTNATTTCTCCCATCTTTAAAAAACAAAAATTCTCCCTTGACCCCAC 1831 chr5ptel1M 184173 -TCATTTCCGAGCTATTATCATAACTCTCATATCTCTTTCACAGCCCAAC 184221 - viiii v iiii vi vi vvv i i i vv L2#LINE/L2 1832 NTCCCCCTCCAGCTACCGCCCCATTTCTCTGCTCCCCTTTACAGCAAAAC 1881 chr5ptel1M 184222 TTCAAGGGAGATGGAAGGGAAAGGCTGTTTATGCT-GTTGTGCTCACTTA 184270 i -------- v ---- ii i i i - i vii v v L2#LINE/L2 1882 TCC--------TCGAA----AGAGTTGTCTATACTCGCTGTCTCCAATTC 1919 chr5ptel1M 184271 CTCTTTTTTAACTGAATTCTC---AAACCGTTACGATCTGAGGTCTGATG 184317 ii iiv i ---i --- v ii v i v ivv ii viv L2#LINE/L2 1920 CTCTCCTCCCATT---CTCTCTTGAACCCACTCCAATCAGGCTTTCGTCC 1966 chr5ptel1M 184318 TAAACATTCAATTGAAATCGCT-------AGGT-AGCAATGATGTCTTAA 184359 iv v i v ii ii ------- - v iv ivvi L2#LINE/L2 1967 CCACCACTCCACCGAAACTGCTCTTGTCAAGGTCACCAATGACCTCCACG 2016 chr5ptel1M 184360 TTGC--AATCCAATAGTCACTTCT-AGTTTTCATCCT--TTTACCCTGCT 184404 -- i v - ii i -- v i?v v L2#LINE/L2 2017 TTGCTAAATCCAATGGTCAATTCTCAGTCCTCATCTTACTTGACCTNTCA 2066 chr5ptel1M 184405 TTGGCACTAATGACAC-TTTGACCAACCTTTCCTCCTGG--GTATTCTCT 184451 vii i -- -v i vi ii i v --ii i i L2#LINE/L2 2067 GCAGCATT--TGACACAGTTGATCACTCCCTCCTTCTTGAAACACTTTCT 2114 chr5ptel1M 184452 T--CTAGGCTTTCATAGACTCAAAGGCATCATTCTTCTAGTCGGTTTGAA 184499 -- v i -i v ----- - i i i --- --- L2#LINE/L2 2115 TCACTTGGCTTCCA-GGACAC-----CA-CACTCTCCTGGT---TTT--- 2151 chr5ptel1M 184500 AACTTCCTACTT 184511 -- i i L2#LINE/L2 2152 --CCTCCTACCT 2161 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 43.04 CpG sites = 83, Kimura (unadjusted) = 45.05 Transitions / transversions = 1.89 (83/44) Gap_init rate = 0.12 (50 / 426), avg. gap size = 1.40 (70 / 50) 225 28.57 2.27 12.50 chr5ptel1M 184562 184649 (815351) C L2c_3end#LINE/L2 (32) 446 367 m_b221s601i13 8729 chr5ptel1M 184562 CTACTATGTCTCAGGCACCAAGAATATAAAAA--AACAAAAATGCTAAAA 184609 vi i iii i i i -- i i --- ---- C L2c_3end#LINE 446 CTACTATGTGCCAGGCGCTGGGGATACAAAGATGAATAAGA---C----A 404 chr5ptel1M 184610 TAGCCACTACTCTTGAGAAACTCACAGTCGAATAATGGAG 184649 ii i v i i ii i i --- i C L2c_3end#LINE 403 CGGTCCCTGCCCTCAAGGAGCTCACAGTC---TAGTGGAG 367 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.96 CpG sites = 20, Kimura (unadjusted) = 39.98 Transitions / transversions = 10.00 (20/2) Gap_init rate = 0.13 (11 / 87), avg. gap size = 1.09 (12 / 11) 12 9.71 0.00 0.00 chr5ptel1M 184768 184789 (815211) (TTTC)n#Simple_repeat 1 22 (0) m_b221s252i6 8730 chr5ptel1M 184768 TTTCTTTCTTTCCTTCTTTATT 184789 i v (TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTT 22 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 296 28.32 0.00 9.76 chr5ptel1M 184822 184911 (815089) C L2c_3end#LINE/L2 (33) 445 364 m_b221s601i14 8731 chr5ptel1M 184822 TACTATTGTCTCAGGCACCGAGAATATAAAAACAAACAAAAATGCTAAGA 184871 - vi i i i i i i ii i i --- ---- C L2c_3end#LINE 445 TACTAT-GTGCCAGGCGCTGGGGATACAAAGATGAATAAGA---C----A 404 chr5ptel1M 184872 TAGCCACTACTCTTGAGAAACTCACAGTCTAATGGAGGAG 184911 ii i v i i ii i i i C L2c_3end#LINE 403 CGGTCCCTGCCCTCAAGGAGCTCACAGTCTAGTGGAGGAG 364 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.94 CpG sites = 21, Kimura (unadjusted) = 39.71 Transitions / transversions = 10.50 (21/2) Gap_init rate = 0.09 (8 / 89), avg. gap size = 1.00 (8 / 8) 180 10.83 2.56 5.26 chr5ptel1M 185040 185078 (814922) C L3#LINE/CR1 (892) 3207 3170 m_b221s601i15 8732 chr5ptel1M 185040 AGCATGCTTTCTTTCTCAATTTATCCAAGTCA-TGATAAA 185078 i v v -- i - C L3#LINE/CR1 3207 AGCATGCCTTCTATGTC--TTCATCCAAGTCATTGATAAA 3170 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 11.71 CpG sites = 2, Kimura (unadjusted) = 11.71 Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.08 (3 / 38), avg. gap size = 1.00 (3 / 3) 207 17.85 2.94 9.38 chr5ptel1M 188117 188184 (811816) MIRb#SINE/MIR 49 112 (156) m_b222s601i2 8733 chr5ptel1M 188117 ACAGAACCTGAGTGTTGAATCATGG-TCTGGCAGGTGCTAGTTTTGTGA- 188164 - i - i vi - v vv i i v - MIRb#SINE/MIR 49 ACAGA-CCTGGGT-TCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGAC 96 chr5ptel1M 188165 CTTAGGCAAGGAAATTACTT 188184 i ---- MIRb#SINE/MIR 97 CTTGGGCAAG----TTACTT 112 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 16.57 CpG sites = 6, Kimura (unadjusted) = 20.42 Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.12 (8 / 67), avg. gap size = 1.00 (8 / 8) 18 19.66 3.70 1.82 chr5ptel1M 188247 188300 (811700) (TTTAT)n#Simple_repeat 1 55 (0) m_b222s252i0 8734 chr5ptel1M 188247 TTTA-TTTATTTTATTTTAGTTT-TTTAATTTAATAGCCTTTTATTTACA 188294 - v - v v vviv -i (TTTAT)n#Simp 1 TTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTT-TA 49 chr5ptel1M 188295 GTTTAT 188300 v (TTTAT)n#Simp 50 TTTTAT 55 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.06 (3 / 53), avg. gap size = 1.00 (3 / 3) 365 30.58 1.52 2.55 chr5ptel1M 188716 188913 (811087) C L1ME1_3end#LINE/L1 (271) 655 460 m_b222s551i0 8735 chr5ptel1M 188716 AGTATATAATGATCTCCTG-GTCCTGCTCATTTCACTCAGCATCAGTTCG 188764 i ? --- ii - iv iv - i v?v C L1ME1_3end#LI 655 AGTATGTANT---CTTTTGTGTCTGGCTTCTTTCACTCAGCAT-AATGNT 610 chr5ptel1M 188765 TGTAAGTCTC-TCCAGGCCTTTCTGAA-ATCATCCTGTTGGTCACTTCTT 188812 v i vi - v iiv vi vi- viv- v iv i C L1ME1_3end#LI 609 TTTGAGATTCATCCATGTTGTTGCGTGTATCAGTA-GTTCGTTCCTTTTT 561 chr5ptel1M 188813 ACAGAACAATAATATTCCATAATATTCATATACCACAATTTATTCAGCCA 188862 iv vvv i i vi vv i i v C L1ME1_3end#LI 560 ATTGCTGAGTAGTATTCCATTGTATGGATATACCACAATTTGTTTATCCA 511 chr5ptel1M 188863 TTCTCCAACTGATGGGCATCCACTCAGTTTCCAGTTTCTAGCCACTACAA 188912 v ?ii i iiivviv i i i i i C L1ME1_3end#LI 510 TTCACCNGTTGATGGACATTTGGGTTGTTTCCAGTTTTTGGCTATTACGA 461 chr5ptel1M 188913 A 188913 C L1ME1_3end#LI 460 A 460 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.29 CpG sites = 33, Kimura (unadjusted) = 41.10 Transitions / transversions = 1.27 (33/26) Gap_init rate = 0.04 (8 / 197), avg. gap size = 1.00 (8 / 8) 401 23.66 0.00 0.00 chr5ptel1M 188821 188913 (811087) C L1ME3G_3end#LINE/L1 (376) 548 456 m_b222s551i1 8735 chr5ptel1M 188821 ATAATATTCCATAATATTCATATACCACAATTTATTCAGCCATTCTCCAA 188870 i i vv i i i i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr5ptel1M 188871 CTGATGGGCATCCACTCAGTTTCCAGTTTCTAGCCACTACAAA 188913 i i ii vviv i i v i i C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAA 456 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 29.44 CpG sites = 15, Kimura (unadjusted) = 29.44 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.00 (0 / 92), avg. gap size = 0.0 (0 / 0) 268 21.87 5.32 7.61 chr5ptel1M 188916 189009 (810991) C Charlie1b#DNA/hAT-Charlie (31) 492 401 m_b222s502i0 8736 chr5ptel1M 188916 CCCTTTGTAATCTTAAAAATTATTGAGGACTTC-----TCTTTCTCTGAG 188960 ii v ii -----v --- -- C Charlie1b#DNA 492 CCCTTTACACTCTTAAAAATTATTGAGGACCCCAAAGAGCTTT---TG-- 448 chr5ptel1M 188961 CCTTTGTGTGATTTATGAACACTGATATTTACAGTGGTAGAAATTAGAA 189009 -- i iv ivvi ii v iv i C Charlie1b#DNA 447 --TTTATGTGGGTTATATCTATCGATATTTACCGTATTAGAAATTAAAA 401 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 24.83 CpG sites = 12, Kimura (unadjusted) = 26.41 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.09 (8 / 93), avg. gap size = 1.50 (12 / 8) 319 29.35 5.43 0.00 chr5ptel1M 189132 189223 (810777) MIRc#SINE/MIR 37 133 (135) m_b222s601i3 8737 chr5ptel1M 189132 TGGAATCAAGAAGACCCAAGTTCAAAT-CCAGTT---TCAAATACAAGCT 189177 i i iii i i - i i ---i vv v MIRc#SINE/MIR 37 TGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCT 86 chr5ptel1M 189178 ATATAAGCCTGAACTTGTCACTTAACCTTGCTT-GCTTCAGTTTCTT 189223 i i i v i ii vv iv v- i i MIRc#SINE/MIR 87 GTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCT 133 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.67 CpG sites = 19, Kimura (unadjusted) = 39.43 Transitions / transversions = 2.38 (19/8) Gap_init rate = 0.03 (3 / 91), avg. gap size = 1.67 (5 / 3) 1015 32.71 2.34 1.97 chr5ptel1M 191415 191969 (808031) L1ME4c_3end#LINE/L1 17 573 (257) m_b222s551i2 8738 chr5ptel1M 191415 ATAGAGAATTGAGTCAAATTTATGAGACTACAAATCATT-CTCCAATTGA 191463 i ii v v v i v- v ? vv- i v L1ME4c_3end#L 17 ATAAAGAGCTCATTCAAATTGATAAGAA-AAANATCAAGACCCCAATAGA 65 chr5ptel1M 191464 TAAACGATCAAAGGATACACACAGACAATTTTCAGATAAAAAAATTAAAA 191513 i iv i iiv iv ? vi ii vv ? L1ME4c_3end#L 66 TAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAGGAAATACAAN 115 chr5ptel1M 191514 CCGTTTTCAGTGATATGAAAAAAAAATGCTC--TGTCACTATTGATCAGA 191561 iv vvv ivv i ---i i --iv i v i i L1ME4c_3end#L 116 TAGTAAACAAACACATG---GAAAAATGTTCAACCTCGCTAGTAATCAAA 162 chr5ptel1M 191562 GAAATACAAACTAAGACAATTTTGAGTTATTATTAC-CATCTTTCAGATT 191610 i i ii ivv v ii vi- ii v i i L1ME4c_3end#L 163 GAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCTATTAAATT 212 chr5ptel1M 191611 GGCTAAGATGATAGGAAAA--GATAATGATAAATGTTGGAGGGGATGTGG 191658 i v i -- vii -- iviv i v i ? i L1ME4c_3end#L 213 AGCAAAAAT--TTAAAAAATTGATAATACCCAATGCTGGCGAGGNTGCGG 260 chr5ptel1M 191659 GAAAACGGGGACACTAATACATTGTTGGTGGGGTCGTGAACTGATCTAAC 191708 vi v v ? v i vi?i i i i vi L1ME4c_3end#L 261 TGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACAAC 310 chr5ptel1M 191709 CATTCTGGAGAGTAAT----AAAGACCTATCCCCACAGGGTTATCAAACT 191754 v i i i ----v v v ----v i ii v v L1ME4c_3end#L 311 CCTTTTGGAAAGCAATTTGGCAATACGTATC----AAGAGCCATAAAAAT 356 chr5ptel1M 191755 GTATATACTCTTTGATCCAATGGTGTCCCTACTGGGCCTATATGCTAAAG 191804 vi i i i ii vi v v vv v v i L1ME4c_3end#L 357 GTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGG 406 chr5ptel1M 191805 AGATCATTAAAAAGGGGGAAAGGATCCACATGTGGAAAAATGTTTGTAAA 191854 i v v ii -i v i i iivi i ii viv L1ME4c_3end#L 407 AAATAATTCAAAAGAAGGAAA-AAGCTATATGCACGAAGATGTTCATTGC 455 chr5ptel1M 191855 AACCCTTAGTATAGTGTCAAGAAATTGGAAACAA--TGGAT-CCCATCAG 191901 i vi vvv i iv i i -- ii -i v i L1ME4c_3end#L 456 AGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAA 505 chr5ptel1M 191902 TGGGAGAATGGCTGAATAAGTTATAATATGTGAATGTTATGAAATACTAT 191951 i i i i i i ii ii v? iviv i i L1ME4c_3end#L 506 TAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATATTAT 555 chr5ptel1M 191952 TATTCTATAAGAAATGAT 191969 vvvv i v i L1ME4c_3end#L 556 GCAGCCATTAAAAATGAT 573 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 43.28 CpG sites = 105, Kimura (unadjusted) = 45.37 Transitions / transversions = 1.44 (105/73) Gap_init rate = 0.03 (18 / 554), avg. gap size = 1.33 (24 / 18) 1014 29.74 4.30 3.95 chr5ptel1M 191454 192034 (807966) L1ME4a_3end#LINE/L1 56 638 (233) m_b222s551i3 8738 chr5ptel1M 191454 CTCCAATTGATAAACGATCAAAGGATACACACAGACAATTTTCAGATAAA 191503 i v v i iv i iiv iv i vi L1ME4a_3end#L 56 CCCCAATAGAAAAATGGGCAAAGGACATGAACAGACAATTCACAAAAGAA 105 chr5ptel1M 191504 AAAATTAAAACCGTTTTCAGTG---ATATGAAAAAAAAATGCTC--TGTC 191548 i vv iv ---i i i--- --- ? i --iv L1ME4a_3end#L 106 GAAATACAAATGG---CCAATAAACATATG---AAAANATGTTCAACCTC 149 chr5ptel1M 191549 ACTATTGATCAGAGAAATACAAACTAAGACAATTTTGAGTTATTA-TTAC 191597 v i i i i i ivv v ii - vi L1ME4a_3end#L 150 ACTAGTAATCAAAGAAATGCAAATTAAAACAACAATGAGATACCATTTTT 199 chr5ptel1M 191598 CATCTTTCAGATTGGCTAAGATGATAGGAAAAGA-TAATGATA---AATG 191643 i v i v ----vv - i i --- i L1ME4a_3end#L 200 CACCTATCAAATTGGCAAAGAT----TTAAAAGATTGATAATACCCAGTG 245 chr5ptel1M 191644 TTGGAGGGGATGTGGGAAAACGGGGACACTAATACATTGTTGGTGGGGTC 191693 v i i ?i v v v i i ivi L1ME4a_3end#L 246 TTGGCGAGGGTGTGGNGAAACGGGCACTCTCATACACTGCTGGTGGGAGT 295 chr5ptel1M 191694 GTGAACTGATCTAACCATTCTGGAGAGTAAT----AAAGACCTATCCCCA 191739 i i i vi v i i ----v v iv -- v L1ME4a_3end#L 296 GTAAATTGGTACAACCTTTCTGGAGGGCAATTTGGCAATATGTAT--CAA 343 chr5ptel1M 191740 CAGGGTTATCAAACTGTATATACTCTTTGATCCAATGGTGTCCCTACTGG 191789 v vv -- v ?i i i i ii vi v v i L1ME4a_3end#L 344 AAGCCTTA--AAAATGTNCATACCCTTTGACCCAGTAATTCCACTTCTAG 391 chr5ptel1M 191790 GCCTATATGCTAAAGAGATCATTAAAAAGGGGGA-AAGGATCCACATGTG 191838 vv v v i i v i i i v v ? - i i--i i L1ME4a_3end#L 392 GAATTTATCCTAAGGAAATAATCAGAGATGTGNACAAAGATT--TATGTA 439 chr5ptel1M 191839 GAAAAATGTTTGTAAAAACCCTTAGTATAGTGTCAAGAAATTGGAAACAA 191888 v ii ii viv i vi vvv i iv i i L1ME4a_3end#L 440 CAAGGATGTTCATCGCAGCATTATTTATAATAGCGAAAAATTGGAAACAA 489 chr5ptel1M 191889 --TGGAT-CCCATCAGTGGGAGAATGGCTGAATAAGTTATAATATGTGAA 191935 -- ii -i v i i i ? i i i ii ii vv L1ME4a_3end#L 490 CCTAAATGTCCAACAATAGGGGANTGGTTAAATAAATTATGGTACATCCA 539 chr5ptel1M 191936 TGTTATGAAATACTATTATTCTATAAGAAATGATCAG----CG-GGATTA 191980 i?v i i vvvv i v i ? -- ---- -i v L1ME4a_3end#L 540 TANAATGGAATATTATGCAGCCATTAAAAATNAT--GTTTTCGAAGAATA 587 chr5ptel1M 191981 TTTCAGAAAGGCCTGGGGAG--GCTTACATGAATTGATGCTAAGTGAAGT 192028 --- v i v i i-- -- vv i i iv L1ME4a_3end#L 588 TTT---AATGACATGGGAAAATGCT--CATGATATAATGTTAAGTGAAAA 632 chr5ptel1M 192029 GAGTAG 192034 i i L1ME4a_3end#L 633 AAGCAG 638 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.13 CpG sites = 99, Kimura (unadjusted) = 39.75 Transitions / transversions = 1.48 (99/67) Gap_init rate = 0.06 (35 / 580), avg. gap size = 1.37 (48 / 35) 1024 30.33 3.43 3.64 chr5ptel1M 191456 191951 (808049) L1ME3G_3end#LINE/L1 54 548 (376) m_b222s551i4 8738 chr5ptel1M 191456 CCAATTGATAAACGATCAAAGGATACACACAGACAATTTTCAGATAAAAA 191505 v v i iv iiv i iv vi ii L1ME3G_3end#L 54 CCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGGA 103 chr5ptel1M 191506 AATTAAAACCGTTTTCAGTGA---TATGAAAAAAAAATGCTC--TGTCAC 191550 vv iv i--- i i --- i --- --iv L1ME3G_3end#L 104 AATACAAATGGC---CAATAAACATATGAAAAGA---TGCTCAACCTCAC 147 chr5ptel1M 191551 TATTGATCAGAGAAATACAAACTAAGACAATTTTGAGTTATTATTAC-CA 191599 v i i i i i ivv v ii vi- L1ME3G_3end#L 148 TAGTAATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCA 197 chr5ptel1M 191600 TCTTTCAGATTGGCTAAGATGATAGGAAAA---GATAATGATAAATGTTG 191646 i iv v i v- -- i--- ivi? i L1ME3G_3end#L 198 CCCATCAGATTGGCAAAAATT-TA--AAAGNTTGATAATATCNAGTGTTG 244 chr5ptel1M 191647 GAGGGGATGTGGGAAAACGGGGACACTAATACATTGTTGGTGGGGTCGTG 191696 v i i i v v v i i ivi i L1ME3G_3end#L 245 GCGAGGGTGTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTA 294 chr5ptel1M 191697 AACTGATCTAACCATTCTGGAGAGTAAT---AAAG-ACCTATCCCCACAG 191742 i i vi i ? i i i ---iv - i -----i i L1ME3G_3end#L 295 AATTGGTACAGCCNTTTTGGAGGGCAATTTGGCAGTATCTAT-----TAA 339 chr5ptel1M 191743 GGTTATCAAACTGTATATACTCTTTGATCCAATGGTGTCCCTACTGGGCC 191792 ii -- i v iii i i iiii vi v v ? ?v L1ME3G_3end#L 340 AAT--TTAAAATGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNA 387 chr5ptel1M 191793 TATATGCTAAAGAGATCATTAAAAAGGGGGA-AAGGATCCACATGTGGAA 191841 v v ? i vv iiv v v v v - --?i iv L1ME3G_3end#L 388 TCTATCCTANAGAAATACTCGCACATGTGCACAAGGA--NGCATGTACAA 435 chr5ptel1M 191842 AAATGTTTGTAAAAACCCTTAGTATAGTGTCAAGAAATTGGAAACAA--T 191889 ii ii viv i vi vvv i i iv i i -- L1ME3G_3end#L 436 GGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCT 485 chr5ptel1M 191890 GGAT-CCCATCAGTGGGAGAATGGCTGAATAAGTTATAATATGTGAATGT 191938 ii -i i i i i i i ii i vv ii L1ME3G_3end#L 486 AAATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCATAC 535 chr5ptel1M 191939 TATGAAATACTAT 191951 i L1ME3G_3end#L 536 TATGGAATACTAT 548 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.23 CpG sites = 95, Kimura (unadjusted) = 41.46 Transitions / transversions = 1.90 (95/50) Gap_init rate = 0.05 (27 / 495), avg. gap size = 1.30 (35 / 27) 533 20.22 0.00 0.00 chr5ptel1M 193043 193131 (806869) U6#snRNA 1 89 (18) m_b222s502i1 8739 chr5ptel1M 193043 GTGCTTGCTTTGAAAGTACATATCCTAAAATTGGAATCATACAGAGAGGA 193092 i i iv i v iv i U6#snRNA 1 GTGCTCGCTTCGGCAGCACATATACTAAAATTGGAACGATACAGAGAAGA 50 chr5ptel1M 193093 TTAGTGGGGCCCCTGCACAAGGGTGATATGCAAATCCAT 193131 iiv i i i i i i U6#snRNA 51 TTAGCATGGCCCCTGCGCAAGGATGACACGCAAATTCGT 89 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 15.96 CpG sites = 14, Kimura (unadjusted) = 24.63 Transitions / transversions = 3.50 (14/4) Gap_init rate = 0.00 (0 / 88), avg. gap size = 0.0 (0 / 0) 16 9.78 0.00 0.00 chr5ptel1M 193144 193165 (806835) (T)n#Simple_repeat 1 22 (0) m_b222s252i1 8740 chr5ptel1M 193144 TTTTTTTTTTTGTTTGTTTTTT 193165 v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTT 22 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 21 10.85 0.00 0.00 chr5ptel1M 193889 193918 (806082) (A)n#Simple_repeat 1 30 (0) m_b222s252i2 8741 chr5ptel1M 193889 AAAAAAAAAAAACAAAAAACAAAAAACAAA 193918 v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 30 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 12 29.71 2.90 2.90 chr5ptel1M 195374 195442 (804558) (CTCC)n#Simple_repeat 1 69 (0) m_b222s252i3 8742 chr5ptel1M 195374 CTCCCTCCC-CGGCCCCTTCCTTCCTGCTTCCTTCCCCGTCAGT-TGTCG 195421 - vvi i i v i i - - vv -iv v (CTCC)n#Simpl 1 CTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCT-CCC-TCCCTCCCTCC 48 chr5ptel1M 195422 GTCCCGCTCTCCCTCCCTCCC 195442 v v i (CTCC)n#Simpl 49 CTCCCTCCCTCCCTCCCTCCC 69 Matrix = Unknown Transitions / transversions = 0.78 (7/9) Gap_init rate = 0.06 (4 / 68), avg. gap size = 1.00 (4 / 4) 334 22.89 10.84 0.00 chr5ptel1M 195650 195732 (804268) MIRc#SINE/MIR 24 115 (153) m_b222s601i4 8743 chr5ptel1M 195650 AGAGCACCAATCCCGAAGTCAGGAGGACCCGAGTGCAAATC-------TA 195692 iiiv ii i i i i v i i ------- i MIRc#SINE/MIR 24 AGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTG 73 chr5ptel1M 195693 CCG--TCCTGGCTGTGTGACCCTGGGCAAGTCACTTAACCCC 195732 i-- v i i i MIRc#SINE/MIR 74 CCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.42 CpG sites = 16, Kimura (unadjusted) = 29.26 Transitions / transversions = 5.33 (16/3) Gap_init rate = 0.02 (2 / 82), avg. gap size = 4.50 (9 / 2) 13 25.00 0.00 0.00 chr5ptel1M 196252 196289 (803711) (AAAAT)n#Simple_repeat 1 38 (0) m_b222s252i4 8744 chr5ptel1M 196252 AAAATAAAAAGCTTTAATAAAAAATACAATAAAATAAA 196289 vivvv v v v (AAAAT)n#Simp 1 AAAATAAAATAAAATAAAATAAAATAAAATAAAATAAA 38 Matrix = Unknown Transitions / transversions = 0.14 (1/7) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 506 25.73 20.20 0.56 chr5ptel1M 196329 196625 (803375) C L3#LINE/CR1 (3) 4096 3742 m_b222s601i5 8745 chr5ptel1M 196329 AGGATCACAGAATTTGAGAGCAGCAATGGAGCT--ACAGTC-TCTACGTT 196375 i i v iv v v v --ivi - - i C L3#LINE/CR1 4096 AGAATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTA-GTC 4048 chr5ptel1M 196376 GAGCC----ATACAG-GAAGGAATCCCTTA---AAGATCTCTGATACCAG 196417 v i ---- v i- v v--- v i i vvv C L3#LINE/CR1 4047 CAACCTCCCATCCAATGCAGGAATCCCTTCTACAACATCCCTGACAAGTG 3998 chr5ptel1M 196418 ACCATCCAGCCTTTCTTTGGTGACCTTGATGGATGGGGAACCC----CCG 196463 ii i vi ivv iv vv i i i ---- v C L3#LINE/CR1 3997 GTCATCCAGCCTCTGCTTGAACACCTCCAGTGACGGGGAGCTCACTACCT 3948 chr5ptel1M 196464 CCCAGGCCAACCC-TTCCACTA--GGGCA-----------TAG------- 196492 ? ii v i - i v-- i ----------- ------- C L3#LINE/CR1 3947 CNCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGATTGTTAGAAAGTTC 3898 chr5ptel1M 196493 TTCC----AATGATCT-AAATTTGCCT---TG-AACTTCCCCTTTGTTGT 196533 ---- v v i- i --- - v ii-i v C L3#LINE/CR1 3897 TTCCTTATATTGAGCCGAAATCTGCCTCCCTGTAACTTCCACCC-ATTGG 3849 chr5ptel1M 196534 TCCTGGTTCAGCCCTCTGGAGTCGAACAGAATGGGTCTACTCAATCT--- 196580 i v i iv ii v vv --- C L3#LINE/CR1 3848 TCCTAGTTCTGCCCTCTGGAGCCACACAGAATAAGTCTAATCCCTCTTCC 3799 chr5ptel1M 196581 ----------CCTTCAAATGCTTGAAGACTGCTCTAAGGCCCCCCATA-- 196618 ---------- ii v v v v i i iv -- C L3#LINE/CR1 3798 ACATGACAGCCCTTCAAATATTTGAAGACAGCTATCATGTCTCCTCTAAG 3749 chr5ptel1M 196619 TCTTCTC 196625 C L3#LINE/CR1 3748 TCTTCTC 3742 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.57 CpG sites = 39, Kimura (unadjusted) = 32.06 Transitions / transversions = 1.05 (39/37) Gap_init rate = 0.06 (18 / 296), avg. gap size = 3.44 (62 / 18) 363 31.32 12.14 1.43 chr5ptel1M 197566 197944 (802056) C L1ME4c_3end#LINE/L1 (394) 436 18 m_b222s551i5 8746 chr5ptel1M 197566 ATATAGGCCCTTTTTCTTTTCCTTTGA--TATTT--TTGGGATA------ 197605 --- i - i -- -- i ------ C L1ME4c_3end#L 436 ATATAG---CTTTTTCCTT-CTTTTGAATTATTTCCTTAGGATAAATTCC 391 chr5ptel1M 197606 CAGACCTGGTATTGCTGGAACAAAGCACAGGCATAGTTTTAGAGTTCTTT 197655 vv v i iv vii v v i v vi i v C L1ME4c_3end#L 390 CAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTCTTG 341 chr5ptel1M 197656 GGGTCTAGTTCCAAATTACTCTCCACAATGGTTGGACCAGTTCACAACTC 197705 iviiv v v i i v v v i i ?iv C L1ME4c_3end#L 340 ATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACANTGC 291 chr5ptel1M 197706 TATGGACTATTCATTAGTGTCCCTGTTTTATC---TCCTC--CGGCATT- 197749 i ivii v vi v ? v v i i ---? -- i - C L1ME4c_3end#L 290 CACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGCATTG 241 chr5ptel1M 197750 -----TGTC--TTTTCTGAG----------------AGAAATGAGGTGAC 197776 ----- i -- i i i---------------- ivi i ii ii C L1ME4c_3end#L 240 GGTATTATCAATTTTTTAAATTTTTGCTAATTTAATAGGCGTAAAATGGT 191 chr5ptel1M 197777 AACTTAGAGGGCTTTTAACTTTCATCTCTCTAATCA---GTGACTTAGAG 197823 v i vv vvvi i v i i i i --- i vv v i C L1ME4c_3end#L 190 ATCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACTAGCGAGGTTGAA 141 chr5ptel1M 197824 CATTTTT--ATGTAAGTAGA-AGCAGCTTTAGCTTCTCTTTCTAAAAACT 197870 -- ivv ivv- vi ?i v vi i ?- ivi i C L1ME4c_3end#L 140 CATTTTTCCATGTGTTTGTTTACTANTTGTATTTCCTCTTN-TGTGAATT 92 chr5ptel1M 197871 GCCTGATTAGGTTATTTGGCCATTTATCAATTGGAGAAT-GACTTTCATT 197919 i v i v iv v v i vv - i? i- C L1ME4c_3end#L 91 GTCTGTTCATGTCCTTTGCCCATTTATCTATTGGGGTCTTGATNTTT-TT 43 chr5ptel1M 197920 TTTGTAAATTTGAATCAGTTCTCTA 197944 i i v v i i C L1ME4c_3end#L 42 CTTATCAATTTGAATGAGCTCTTTA 18 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.14 CpG sites = 65, Kimura (unadjusted) = 42.58 Transitions / transversions = 1.25 (65/52) Gap_init rate = 0.05 (19 / 378), avg. gap size = 2.74 (52 / 19) 274 25.31 2.19 7.69 chr5ptel1M 198162 198298 (801702) C L1M4c_5end#LINE/L1 (0) 2500 2371 m_b222s551i6 8747 chr5ptel1M 198162 TTTGTGCCTTTCTGCTTTAAA---AGTGTCTTACAAAAAACATGTCATTG 198208 i i v- v i --- v ii i v i i vi C L1M4c_5end#LI 2500 TTTGTGTCCTTA-GATCTAAAGTGAGTCTCTTGTAGACAGCATATAGTTG 2452 chr5ptel1M 198209 GATTGTGGTTTCTAATCCATTCTTCCATAGACTTCTGATTTGTTTCATGG 198258 i? v i ?v --- ii ? -- iv v v C L1M4c_5end#LI 2451 GATCNTGTTTTTTAATCCATTCNGCCA---ATCTNTG--TCTTTTGATTG 2407 chr5ptel1M 198259 ATGAGTTCATTCCCCTTAACATTTACAGTTATGATTACTG 198298 iv i v vi - v --- i C L1M4c_5end#LI 2406 GAGAGTTTAATCCATTT-ACATTTAAAG---TAATTACTG 2371 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 32.21 CpG sites = 18, Kimura (unadjusted) = 32.21 Transitions / transversions = 1.29 (18/14) Gap_init rate = 0.08 (11 / 136), avg. gap size = 1.18 (13 / 11) 12 17.95 0.00 5.88 chr5ptel1M 199557 199592 (800408) (GGA)n#Simple_repeat 1 34 (0) m_b222s252i5 8748 chr5ptel1M 199557 GGAGGAGGAAAAAGAAGGAGGAGAGAACAGGAGGAG 199592 - ii i - iv (GGA)n#Simple 1 GGAGGAGG-AGGAGGAGGAGGAG-GAGGAGGAGGAG 34 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 196 31.43 0.00 0.00 chr5ptel1M 200761 200830 (799170) L3#LINE/CR1 3773 3842 (257) m_b222s601i6 8749 chr5ptel1M 200761 TTCCAGTATCTGAAGTTCTGTCCCTGGGAGGAGGGTTCAGCCTTGTTCAG 200810 v i i vv vivv i v i v i v L3#LINE/CR1 3773 TTCAAATATTTGAAGGGCTGTCATGTGGAAGAGGGATTAGACTTATTCTG 3822 chr5ptel1M 200811 CTGGGCCCCAGAGAACTGAA 200830 ivv i ii v L3#LINE/CR1 3823 TGTGGCTCCAGAGGGCAGAA 3842 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 41.04 CpG sites = 10, Kimura (unadjusted) = 41.04 Transitions / transversions = 0.83 (10/12) Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0) 197 20.38 0.00 1.85 chr5ptel1M 202811 202865 (797135) MIRc#SINE/MIR 4 57 (211) m_b222s601i7 8750 chr5ptel1M 202811 GGCAGTATGGCCTAGTGGAGAGAGAGCTGGGCTTGGGAGTGAGGAAGGCA 202860 i ivi i vi i - v i v MIRc#SINE/MIR 4 GGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTT-GGAGTCAGGAAGACC 52 chr5ptel1M 202861 TGGGT 202865 MIRc#SINE/MIR 53 TGGGT 57 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 24.28 CpG sites = 7, Kimura (unadjusted) = 24.28 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1) 229 33.06 7.55 5.56 chr5ptel1M 204017 204599 (795401) C L1ME3B_3end#LINE/L1 (339) 650 57 m_b222s551i7 8751 chr5ptel1M 204017 GTGTTCTCTTG-GTTCTGCTCATTTCACTTTGTATCA-GTTTGTACAAGT 204064 i i - ii iv i ivii i - ivi v C L1ME3B_3end#L 650 GTATTCTTTTGTGTCTTGCTTCTTTCGCTCAACATTATGTTTGTGAGATT 601 chr5ptel1M 204065 CTTTCCGGGTTTTCTG-ATATCTGC---CTGTTCATTTCTTAGTACACAA 204110 v i vv v v vi -i v i---ii - i v i vvv C L1ME3B_3end#L 600 CATCCATGTTGTTGCGTGTAGCTGTAGTTCGTTCATTT-TCATTGCTGTA 552 chr5ptel1M 204111 TAATATTCCTTTATATTCCTATACCACAACTTATTCAGTCATTCCCCAAT 204160 i v i vvv i i vi iv vi C L1ME3B_3end#L 551 TAGTATTCCATTGTATGAATATACCACAATTTATTTATCCATTCTACTGT 502 chr5ptel1M 204161 CAATGGGC-TTCCTCTTAATTTCTAATATTTTACCACCCC--ACAAAGGA 204207 ii i - ivvv i- i i v ?vi i iiv -- v -- C L1ME3B_3end#L 501 TGATGGACATTTGGGTTG-TTTCCAGTTTTNGGCTATTACGAACAATG-- 455 chr5ptel1M 204208 CTGCTATAAATATTTTTGCATATGCACATATTTATGTATTTATATCCTTC 204257 i i i i i i?-- vi vi i i-- i v viv C L1ME3B_3end#L 454 CTGCTATGAACATTCTTGTACATGTN--TCCTGGTGCAC--ATGTGCACG 409 chr5ptel1M 204258 CCTTTTTATATGATCTTTTGGGCTTACAGACCTAGTACTGGTATTGCCCA 204307 v i v --------- -- i v v v v ivi C L1ME3B_3end#L 408 CGTTTCTCTA---------GGG--TATATACCTAGGAGTGGAATTGCTGG 370 chr5ptel1M 204308 GTAAAAGTGTATGCACTGTTTGGTTGTCCTTTGGGCATAGTTCCAAATAA 204357 v v v i- i i -- iiv i v?viv i v --- C L1ME3B_3end#L 369 GTCATAGGGTATGCG-TATCT--TCAACTTTANTAGATAATGCCAAA--- 326 chr5ptel1M 204358 CTG------AGAATGGTTGGATCAATTCAGGACTCG----AACACTACAT 204397 ------ i i v i i v- v---- i v ii C L1ME3B_3end#L 325 CTGTTTTCCAAAGTGGTTGTACCAATTTAC-ACTCCCACCAGCAGTGTAT 277 chr5ptel1M 204398 AAGGTGTTTCAATT--TCC---TCCGTTTTCAACATTTA------TCCCT 204436 i i- i vi -- --- - ivi i i------ vvv C L1ME3B_3end#L 276 GAGA-GTTCCCGTTGCTCCACATCC-TCGCCAACACTTGGTATTGTCAGA 229 chr5ptel1M 204437 TTTTTGTGTATCATATTGGCCAATTTGATCAATGTGAAGTG--ATCTCAG 204484 i ?-----v v v ? i i vii v -- v C L1ME3B_3end#L 228 CTTTTN-----AATTTTTGCCANTCTGGTGGGTGTGTAGTGGTATCTCAT 184 chr5ptel1M 204485 AGTTGTTTTAATTTGTATTT----AATTTCTCTTA-----GAGCACTTTT 204525 v v i ----i v vv i----- i C L1ME3B_3end#L 183 TGTGGTTTTAATTTGCATTTCCCTGATTACTAATGAGGTTGAGCACCTTT 134 chr5ptel1M 204526 TCATATGTCTAGAGATTGCTTTGACAGTTTCATTTGATATCTACCTGCTC 204575 i vv iiiii v ivvii v vv vv i i C L1ME3B_3end#L 133 TCATATGTTTATTGGCCATTTGGATTTCCTCTTTTGTGAAGTGCCTGTTC 84 chr5ptel1M 204576 ATATTCTTTG---ATTTATCTTTTGGG 204599 vi ii --- v v C L1ME3B_3end#L 83 AAGTCTTTTGCCCATTTTTCTATTGGG 57 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 43.04 CpG sites = 100, Kimura (unadjusted) = 45.38 Transitions / transversions = 1.22 (100/82) Gap_init rate = 0.08 (48 / 582), avg. gap size = 1.60 (77 / 48) 275 31.89 0.71 1.44 chr5ptel1M 204092 204231 (795769) C L1ME3E_3end#LINE/L1 (421) 568 430 m_b222s551i8 8751 chr5ptel1M 204092 TTCATTTCTTAGTACACAATAATATTCCTTTATATTCCTATACCACAACT 204141 - i v i vvv i v i vvv i C L1ME3E_3end#L 568 TTCATTT-TCACTGCTGTATAGTATTCCATTGTATGAATATACCACAATT 520 chr5ptel1M 204142 TATTCAGTCATTCCCCAATCAATGGGC-TTCCTCTTAATTTCTAATATTT 204190 i vi i vi i i - ivvv -i i i v C L1ME3E_3end#L 519 TATTTATCCATTCTCCTGTCGATGGACATTTGGGTT-GTTTCCAGTTTTT 471 chr5ptel1M 204191 TACCACCCCACAAAGGACTGCTATAAATATTTTTGCATATG 204231 i i iiv v v ivi i i i i i C L1ME3E_3end#L 470 TGCTATTACAAACAATGCTGCTATGAACATTCTTGTACATG 430 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.64 CpG sites = 26, Kimura (unadjusted) = 42.94 Transitions / transversions = 1.44 (26/18) Gap_init rate = 0.02 (3 / 139), avg. gap size = 1.00 (3 / 3) 391 31.93 7.35 6.05 chr5ptel1M 204110 204599 (795401) C L1ME3Cz_3end#LINE/L1 (449) 548 53 m_b222s551i9 8751 chr5ptel1M 204110 ATAATATTCCTTTATATTCCTATACCACAACTTATTCAGTCATTCCCCAA 204159 i v i vvv i i vi v C L1ME3Cz_3end# 548 ATAGTATTCCATTGTATGAATATACCACAATTTATTTATCCATTCCCCTA 499 chr5ptel1M 204160 TCAATGGGC-TTCCTCTTAATTTCTAATATTTTACCACCCCACAAAGGAC 204208 ii i - ivvv i- i v ii i iiv v v ivi C L1ME3Cz_3end# 498 TTGATGGACATTTAGGTTG-TTTCCAATTTTTCGCTATTACAAACAATGC 450 chr5ptel1M 204209 TGCTATAAATATTTTTGCATATGCACATATTTATGTATTTATATCCTTCC 204258 v i i ii i i i- - vi i i i-- i v vvvv C L1ME3Cz_3end# 449 TGCAATGAACATCCTTGTACATGT-C-TCCTTGTGCAC--ATGTGCGAGA 404 chr5ptel1M 204259 CTTTTTATATGATCTTTTGGGCTTACAGACCTAGTACTGGTATTGCCCAG 204308 v i v --------- -- i v v v v ivi C L1ME3Cz_3end# 403 GTTTCTCTA---------GGG--TATATACCTAGAAGTGGAATTGCTGGG 365 chr5ptel1M 204309 TAAAAGTGTATGCAC-TGTTTGGTTGTCCTTTGGGCATAGTTCCAAATAA 204357 viv v i - v iiii v v ----iv v v vi C L1ME3Cz_3end# 364 TCGTAGGGTATGCGCATCTTCAACTTTACT----AGATATTGCCAAATTG 319 chr5ptel1M 204358 CTG---AGAATGGTTGGATCAATTCAGGACTCG----AACACTACATAAG 204400 v--- i i v i i v- v---- i v ii i C L1ME3Cz_3end# 318 CTCTCCAAAGTGGTTGTACCAATTTAC-ACTCCCACCAGCAGTGTATGAG 270 chr5ptel1M 204401 GTGTTTCAATTTCCTC-CGTTTTC---AACATTTA------TCCCTTTTT 204440 i- i vi ii - i ii --- i i------ vvvi C L1ME3Cz_3end# 269 A-GTTCCCGTTTCTCCACATCCTCGCCAACACTTGGTATTGTCAGACTTT 221 chr5ptel1M 204441 TGTGTATCATATTGGCCAATTTGATCAATGTGAAGTG--ATCTCAGAGTT 204488 i-----v v v i vii i -- vv ? C L1ME3Cz_3end# 220 TA-----AATTTTTGCCAATCTGATGGGTGTGAAATGGTATCTCATTGTN 176 chr5ptel1M 204489 GTTTTAATTTGTATT----TAATTTCTCTTA-----GAGCACTTTTTCAT 204529 i ---- i v vv i----- ii C L1ME3Cz_3end# 175 GTTTTAATTTGCATTTCCCTGATTACTAGTGAGGTTGAGCATCTTTTCAT 126 chr5ptel1M 204530 ATGTCTAGAGATTGCTTTGACAGTTTCATTTGATAT---CTACCTGCTCA 204576 i vv iiii- i --i v i vv i ---i i i C L1ME3Cz_3end# 125 ATGTTTATTGGCCA-TTCG--GGTTTCCTCTTCTGTGAATTGCCTGTTCA 79 chr5ptel1M 204577 TATTCTTTG---ATTTATCTTTTGGG 204599 i --- v v C L1ME3Cz_3end# 78 TATCCTTTGCCCATTTTTCTATTGGG 53 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.03 CpG sites = 84, Kimura (unadjusted) = 43.01 Transitions / transversions = 1.33 (84/63) Gap_init rate = 0.09 (42 / 489), avg. gap size = 1.57 (66 / 42) 326 27.68 12.80 3.06 chr5ptel1M 204948 205275 (794725) C L1P1_orf2#LINE/L1 (474) 2820 2462 m_b222s551i10 8752 chr5ptel1M 204948 CCAGTTTTCC---CATTTTTTGTCAAATAGTGAGTTCTTACCCCAGAG-- 204992 --- iiv i i v i i v vv -- C L1P1_orf2#LIN 2820 CCAGTTTTCCCAGCACCATTTATTAAATAGGGAATCCTTTCCCCATTGCT 2771 chr5ptel1M 204993 -GTATTT---GGGTTTATCAAA---CAGATTCACTAT-GGTCTTTGGCTA 205034 - v ---i i --- - vii i - i v vi -i C L1P1_orf2#LIN 2770 TGTTTTTCTCAGGTTTGTCAAAGATCAGA-TAGTTGTAGATATGCGGC-G 2723 chr5ptel1M 205035 TTATATCTTACGGACCTAATTTCTTTCACTGATTCACTATTTC----TTG 205080 v v v vi iv i v i i ii - i ---- C L1P1_orf2#LIN 2722 TTATTTCTGAGGGCTCTGTTCTGTTCCATTGATCTA-TATCTCTGTTTTG 2674 chr5ptel1M 205081 G--CCAGTACCAGA------TGGTTACT---GCTTTATAATGTAGTCTGA 205119 -- vi------ --- i i i i i C L1P1_orf2#LIN 2673 GTACCAGTACCATGCTGTTTTGGTTACTGTAGCCTTGTAGTATAGTTTGA 2624 chr5ptel1M 205120 GATGTGATATTGCTAGACTACCTTC--CTTTGTTATTTTGTCCCCTTTAT 205167 ii vv i -- vv - i i -- v v ---- v C L1P1_orf2#LIN 2623 AGTCAGGTA--GCGTGA-TGCCTCCAGCTTTGTTCTTTTGGC----TTAG 2581 chr5ptel1M 205168 --TTCCCTCGATGTTCTTAACCTTTTTTTTCTTCCAGATGAA--TTA--- 205210 -- vv i ii v vivii ii vv v -- --- C L1P1_orf2#LIN 2580 GATTGACTTGGCGATGCGGGCTCTTTTTTGGTTCCATATGAACTTTAAAG 2531 chr5ptel1M 205211 ---TTTTTTTAAACTTCTCTC-AGATATTT-TTGGTAGTTTGATGGACAT 205255 --- iv - v v- v v i- i iv C L1P1_orf2#LIN 2530 TAGTTTTTTCCAA-TTCTGTGAAGAAAGTCATTGGTAGCTTGATGGGGAT 2482 chr5ptel1M 205256 GACACTGAATAAGTAAATCA 205275 i i vvi i C L1P1_orf2#LIN 2481 GGCATTGAATCTATAAATTA 2462 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.40 CpG sites = 49, Kimura (unadjusted) = 35.36 Transitions / transversions = 1.26 (49/39) Gap_init rate = 0.08 (27 / 327), avg. gap size = 1.96 (53 / 27) 442 29.78 7.23 3.73 chr5ptel1M 205290 205704 (794296) L1M5_orf2#LINE/L1 1905 2333 (961) m_b222s551i11 8753 chr5ptel1M 205290 AAAATCAAGAGTTAACATTATCTATAATGGAGATAAACTACAATCTTTTC 205339 i v v i? i viv v v ? iv ?v i L1M5_orf2#LIN 1905 AAAACCTACAGCNAACATCATACTTAATGGTGAAANACTGAANGCTTTCC 1954 chr5ptel1M 205340 CCATAAATTCAGGGTGCAA--CAGTGATGTTCATTGTCACCACTTCTGTT 205387 v iv - vi -- iv i ii ? i L1M5_orf2#LIN 1955 CCCTAAGATC-GGGAACAAGACAAGGATGTCCGCTNTCACCACTTCTATT 2003 chr5ptel1M 205388 TGACATGGTATGAGAAATGTTGACTGGCAC-------CAAGATGAAAAGA 205430 ii v ivi ii vi ii ii ii ------- -- L1M5_orf2#LIN 2004 CAACATTGTACTGGAGGTCCTAGCCAGTGCAATAAGGCAAGA--AAAAGA 2051 chr5ptel1M 205431 AATAACTAATATGGGAATAATATAGGAAGCCAAGAATATTCAGTTATTAC 205480 vviii iiii viv v -v v v i -- i? - L1M5_orf2#LIN 2052 AATAAAAGGCATAAAGATTGGAAAGGAAG-AAATAAAACT--GTCNTTA- 2097 chr5ptel1M 205481 CTTTGCAGATGATAT-ATTG-ATACCTAAAGAATTT---AGATTCAAGTA 205525 - i i - -? v i i ii--- v v vv L1M5_orf2#LIN 2098 -TTCGCAGATGACATGATTGTNTACGTAGAAAATCCNAAAGAATCTACAA 2146 chr5ptel1M 205526 AAAATTAATTGGAACAAA-----AAATTCAGCAAATTTGCAAGAGATAAA 205570 ? viv i i v -----i i iv i ?i v i i L1M5_orf2#LIN 2147 ANAAACTACTAGAACTAATAAGTGAATTTAGCAAGGTCGCNGGATACAAG 2196 chr5ptel1M 205571 ---AATATCCCCACAAATC-ATAGTCATTTCAATGTAACACAAATAAAAA 205616 --- --v v - v - v i vi vv i -- L1M5_orf2#LIN 2197 GTCAATAT--ACAAAAATCAATTGT-ATTTCTATATACTAGCAACAAA-- 2241 chr5ptel1M 205617 CCTCAGTAGGAAGATAGA----GAAA---AATATCACTTACAATGACTAT 205659 --- i v i ii ----? --- i i ii vvi L1M5_orf2#LIN 2242 ---CAATTGGAAAATGAAATTTNAAAAACAATACCATTTACAATAGCATC 2288 chr5ptel1M 205660 AAAATATATAAAGTACTTTGGAATTTCCCTACCAAGATATATACA 205704 v i ? i v vvvi v i ? i i L1M5_orf2#LIN 2289 AAAAAACATNAAATACTTAGGAATAAATCTAACAAAANATGTGCA 2333 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.32 CpG sites = 70, Kimura (unadjusted) = 40.66 Transitions / transversions = 1.43 (70/49) Gap_init rate = 0.06 (26 / 414), avg. gap size = 1.77 (46 / 26) 1125 30.35 5.34 4.83 chr5ptel1M 208994 209817 (790183) HERVK14#LTR/ERVK 2598 3425 (2671) m_b222s701i0 8754 chr5ptel1M 208994 TTTTTAGGCAGGGCTGCCGTTGAAGGCCTGCCAACATGCTCACCCGTTCC 209043 viv iiii -- - i---- -- i HERVK14#LTR/E 2598 TTTTTAGGAGCGGCCATTGTTGA--GCCT-CCG----GCTC--CCATTCC 2638 chr5ptel1M 209044 TCTCCAATGGAAAACTGATACACCAGTGTGGATAGAACAGTAGCC-CTTA 209092 ivvv vv vi v i v i i i i i - v HERVK14#LTR/E 2639 TCTTGTTTGGCTAACTGCCAAACCGGTTTGGGTGGAGCAATGGCCGCTGA 2688 chr5ptel1M 209093 GGTAGTGATAAACTT----CCTTATTAGATATAGTACAGGAGCAACTTGA 209138 iii - v v---- i vv vv i i i i vv HERVK14#LTR/E 2689 AACAG-GAAAAACTGGAGGCTTTAAAAGAACTGGTGCAGGAACAATTGCA 2737 chr5ptel1M 209139 CCAAGGACACTTACAACCT----TCTCT------AAGTCCCCAGTATTGG 209178 vv i iv v i ---- i------ v i v v HERVK14#LTR/E 2738 AAAGGGACATATAGAGCCTACTTTCTCCCCTTGGAATTCTCCTGTATTTG 2787 chr5ptel1M 209179 TTGT-AAGAAAGAAAGCTGGAAAATGGAGGATATTGACTGATTTAAGAAA 209227 ii - - v v i i i i v iiv HERVK14#LTR/E 2788 TCATTAAGAAA-AAATCAGGGAAATGGAGAATGTTAACAGATTTAAGGGC 2836 chr5ptel1M 209228 GGTGAATGAACAGATGGAAACTATGGGAATTCTTCAGCCTAGACTTCCAT 209277 v v vvvv vv v i viiv v i vi i v v HERVK14#LTR/E 2837 TGTTAATGCTGTGATTCAACCCATGGGTGCACTGCAACCAGGGCTGCCCT 2886 chr5ptel1M 209278 CTCCTACTCAGTTGCCTAGAGAATGGCCTCTTTGGGTTACAGACATTAAG 209327 i v vvv v v v i v v ivvi v i iv v HERVK14#LTR/E 2887 CCCCAACAATGATCCCAAAATACTGGCCTCTCATAGTGATAGATCTAAAG 2936 chr5ptel1M 209328 GATTGTTTCTATTCTATCCCTCTAGATAAGGAGGAT-ATGAAAAGATTTG 209376 i i v v i i i v ivvv i - - HERVK14#LTR/E 2937 GATTGCTTTTTTACCATTCCTTTAGCTGCCCAAGATTATGAAAA-ATTTG 2985 chr5ptel1M 209377 CCTTTTCAGTGCCCAGTGTTAAC--TAAGCTGAACCTTATAAAAGATATG 209424 i v v v ivii v i-- i-- vvvvi v iv HERVK14#LTR/E 2986 CTTTTACTGTTCCCGCCATAAATAATAAA--GAACCAGCGGACAGATACC 3033 chr5ptel1M 209425 AAAGGACAGTTTTGCCACAGTGAATGAAAAACAACCCTACTATGTGTCAA 209474 vv v vi i iv v vv i i v v HERVK14#LTR/E 3034 ATTGGAAAGTACTACCACAAGGCATGCTAAATAGCCCGACTATTTGTCAA 3083 chr5ptel1M 209475 ATGTATGTTGCTGCTGCTCTTACTCCAGTAAGAAAAGCATTTCCAAAA-G 209523 iv i vvivv v vv v i vvi vv - HERVK14#LTR/E 3084 ACTTATGTCGGGAAAGCTATTAAGCCAGTTAGAGAACAGTTTAAAAAATG 3133 chr5ptel1M 209524 TTATGTTATCACATTACATGGATGATATATTGGGATGTGCACCTGAGGAA 209573 i - vi --- v -- HERVK14#LTR/E 3134 TTATATTATC-CATTACATGGATGATATTCTG---TGTGCAGCTGA--AA 3177 chr5ptel1M 209574 CAAATAATAGAAC--ATGT----CTACAAAAGACCATGGAAACACTGAGG 209617 v ivi - i-- ---- viiii - i vi -- v HERVK14#LTR/E 3178 CTAGGGA-AGAATTGATGTTGTGCTACAAACAGTTA-GAAAAGGCT--GT 3223 chr5ptel1M 209618 AAATACA--------AATTGTACATAGCTCCAGAAAAAAAAATCAAAGAC 209659 i i-------- ---- i v -- v vi vvi HERVK14#LTR/E 3224 AAATGCGGCAGGGTTAATT----ATAGCCCCCG--ATAAAATCCAAACTT 3267 chr5ptel1M 209660 ATGCTTCTTTTTAATATTTAGGATATGAA-GTATACCCTAAGGTGCTCAC 209708 v i i i i i - - v v -- i --- HERVK14#LTR/E 3268 CTACTCCCTTTCAATATCTAGGA-ATGAAGGTAGAAC--AAAGTGCT--- 3311 chr5ptel1M 209709 AGTA-----CAAAAACTGTCCTTAA----GAACAGAGAAGCTAAACACCT 209749 v ----- iv ---- i ---- v v vi v HERVK14#LTR/E 3312 ATTAAGCCTCAAAAGGT----TCAAATTCGAAGAGATAATTTAAAAACCT 3357 chr5ptel1M 209750 TGAATGACTTTCAGAAATTGACAGGAGATATCCAATGGATGCATCCAGTG 209799 i i i i ivi i iv v v i iiv HERVK14#LTR/E 3358 TAAATGATTTCCAAAAATTATTAGGAGACATTAATTGGATTCGTCCAACT 3407 chr5ptel1M 209800 TTAGGCTTGATTACCTAT 209817 v vvi HERVK14#LTR/E 3408 TTAGGCATTCCTACCTAT 3425 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.00 CpG sites = 110, Kimura (unadjusted) = 39.22 Transitions / transversions = 0.86 (110/128) Gap_init rate = 0.07 (54 / 823), avg. gap size = 1.56 (84 / 54) 236 29.38 7.69 1.82 chr5ptel1M 212194 212297 (787703) C MIRc#SINE/MIR (143) 125 16 m_b222s601i8 8755 chr5ptel1M 212194 GAGACAGAGAGAGGTAAAGTTTCTGCTCCGAAGCCCAACATAG---GTGA 212240 i vv v vv vvi i i i -- i --- i C MIRc#SINE/MIR 125 GAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTC--ACACAGCTAGTAA 78 chr5ptel1M 212241 GTGTCTGGGGCAGGATCTGAATTCAGGTCT--CTGATTACAAG-CTAA-A 212286 v v i v i iii ii -- i v - i i-i C MIRc#SINE/MIR 77 GTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTG 28 chr5ptel1M 212287 C-CTTTCCTCTG 212297 - v C MIRc#SINE/MIR 27 CTCTTTCCACTG 16 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.28 CpG sites = 18, Kimura (unadjusted) = 38.51 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.07 (7 / 103), avg. gap size = 1.43 (10 / 7) 49 0.00 0.00 0.00 chr5ptel1M 212509 212550 (787450) (AC)n#Simple_repeat 1 42 (0) c_b222s251i0 8756 chr5ptel1M 212509 ACACACACACACACACACACACACACACACACACACACACAC 212550 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACAC 42 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 203 31.48 5.56 0.00 chr5ptel1M 213186 213239 (786761) C L2b_3end#LINE/L2 (15) 451 395 m_b222s601i9 8757 chr5ptel1M 213186 AAGCATTGATTAAAGACTTACTGTGTGCCAGA---TGTATTAAGTGCCTG 213232 ii v i i ivi i i--- ii i i iv C L2b_3end#LINE 451 AAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGG 402 chr5ptel1M 213233 GGACACA 213239 i C L2b_3end#LINE 401 GGATACA 395 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.35 CpG sites = 14, Kimura (unadjusted) = 45.62 Transitions / transversions = 4.67 (14/3) Gap_init rate = 0.02 (1 / 53), avg. gap size = 3.00 (3 / 1) 298 22.51 3.19 10.23 chr5ptel1M 213999 214092 (785908) C MIRc#SINE/MIR (141) 127 40 m_b222s601i10 8758 chr5ptel1M 213999 CTGATGCAATTAGAG---TTAAGTGACTTGCCCAGGGTCACGCAGCTGGG 214045 v -- i --- i i i - C MIRc#SINE/MIR 127 CTGAGGC--TCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG- 81 chr5ptel1M 214046 ACGTGTTAAGTGTCTGATATCAGATTTGAACTCGGGAGCTCCTGACT 214092 ------ v v vvivi i i i i vvi C MIRc#SINE/MIR 80 ------TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACT 40 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 23.81 CpG sites = 11, Kimura (unadjusted) = 26.98 Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.11 (10 / 93), avg. gap size = 1.20 (12 / 10) 15 16.18 2.22 4.55 chr5ptel1M 214253 214297 (785703) (GCTCT)n#Simple_repeat 1 44 (0) m_b222s252i6 8759 chr5ptel1M 214253 GCTCTTCTGCCCTCTGCTCT-CTCTCCTCTGACTCTGACCCTGCTC 214297 v viv - v - - i (GCTCT)n#Simp 1 GCTCTGCTCTGCTCTGCTCTGCTCTGCTCTG-CTCTG-CTCTGCTC 44 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.07 (3 / 44), avg. gap size = 1.00 (3 / 3) 644 24.85 11.06 0.91 chr5ptel1M 214481 214679 (785321) C MIR#SINE/MIR (22) 240 22 m_b222s601i11 8760 chr5ptel1M 214481 GCCCTTACTAAGGGCCAGACACTG--CCGAGTGTCTTATAAACACTGGCT 214528 v v v i -- ii i ii i vii i ii C MIR#SINE/MIR 240 GCGCTTACTATGTGCCAGGCACTGTTCTAAGCGCTTTACATGTATTAACT 191 chr5ptel1M 214529 CTTCTGATCCTCATAACCACCCTAGGAGGTATTTGCTTTTTATTATTCCC 214578 v i i i v v vv i v - i C MIR#SINE/MIR 190 CATTTAATCCTCACAACAACCCTATGAGGTAGGTACTATT-ATTATCCCC 142 chr5ptel1M 214579 ATTTTACACATGAGGAAACTGAGGCAAACAGCAATGAAGTGACTCACTCA 214628 v v v vii v i ii i C MIR#SINE/MIR 141 ATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCCA 92 chr5ptel1M 214629 GGATCACCACAG------------AGGGC--GGATTTGCATTC---TAGT 214661 i i - ------------ i -- i v ii ---i C MIR#SINE/MIR 91 AGGTCA-CACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGCAGT 43 chr5ptel1M 214662 CT--TTCCA-AGTCCGGGCTC 214679 --i - i v C MIR#SINE/MIR 42 CTGGCTCCAGAGCCCGTGCTC 22 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.69 CpG sites = 32, Kimura (unadjusted) = 31.22 Transitions / transversions = 1.88 (32/17) Gap_init rate = 0.04 (8 / 198), avg. gap size = 3.00 (24 / 8) 449 34.87 7.14 4.41 chr5ptel1M 214999 215418 (784582) L2b_3end#LINE/L2 5 435 (31) m_b222s601i12 8761 chr5ptel1M 214999 ATAACCTCGCTCCTCTAACTTTTCAGTCTTATCTCAGCCTCTTCCCCCAA 215048 ii i v i v v i i i i i -------- iv v L2b_3end#LINE 5 ACGATCTGGCCCCGCTACCTCTCCGGCCTCATCTC--------CTACCAC 46 chr5ptel1M 215049 CCTCCTCTGTAATT-CTCTGATGCAGTGAAAACGGCCCCCTTGCTGTTCC 215097 i i - iv i- v v iv v vi i L2b_3end#LINE 47 TCTCCCCT-TGCTCACTCTGCTCCAGCCACACTGGCCTCCTTGCTGTTCC 95 chr5ptel1M 215098 TGGCACATCTCACTCTGCCTCTAGGCTCCTGGCCTTCTGTAGTAGCTGTG 215147 v v ivi ?v v? iv v vv - i v?v v L2b_3end#LINE 96 TCGAACACGCCANGCTCNCTCCCGCCTCAGGGCCTT-TGCACNTGCTGTT 144 chr5ptel1M 215148 CCC-ATGGCTAGAATCTCTCCCTCCTCATATCCCCCTTTGTTT--CTCTG 215194 -v v i - v - i i iv ii vii vii-- iv L2b_3end#LINE 145 CCCTCTGCCTGGAA-CGC-CCTTCCCCACCTCTTCGCCTGGCCAACTCCT 192 chr5ptel1M 215195 GCTC---CTTCAAGTTGTAG---GGAAGCCCGACCTCCTGCAAGAAGCCT 215238 i --- i ivi ---ii v i -- v ii i L2b_3end#LINE 193 ACTCATCCTTCAGGTCTCAGCTCAAATGTC--ACCTCCTCCGGGAAGCCC 240 chr5ptel1M 215239 TTCCTATCCTCCTCAACC---TAAAGT-TTCTCTTCTGAAATCCCAGCTA 215284 i iv i ivii --- v i i-ii i iivi -- i L2b_3end#LINE 241 TCCCTGACCCCCCAGGCCGGGTCAGGCGCCCTCCTCTGGGCCCCC--CCA 288 chr5ptel1M 215285 CTTC-ATCCTGTATTTATTTCTTATACAGAATTGATTGCATG-GTATTTC 215332 v i - i ivvi v vvv ?vvvivi ? i -v i i L2b_3end#LINE 289 GTCCTACCCTGCCACTCTGGGTTATNATTGTCTGNTTACATGTCTGTCTC 338 chr5ptel1M 215333 CCCCATTGGATTGTAGGTTT--------------CTGTTTCTTGCCTTTT 215368 i i i ii i i-------------- i ?v - i v L2b_3end#LINE 339 CCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTC-TGTCTTGT 387 chr5ptel1M 215369 TCAACAAGATGTGTCTTCAGAGCTCAGCACATTTCCTAGCACATAAGAGG 215418 v -- v i ii v ii v?v i i iv L2b_3end#LINE 388 TCACC--GCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGG 435 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 47.16 CpG sites = 83, Kimura (unadjusted) = 50.27 Transitions / transversions = 1.46 (83/57) Gap_init rate = 0.07 (29 / 419), avg. gap size = 1.69 (49 / 29) 236 29.51 3.28 0.00 chr5ptel1M 215440 215500 (784500) C MIRb#SINE/MIR (20) 248 186 m_b222s601i13 8762 chr5ptel1M 215440 TTGAGTACCTACTATATGCCAGTC--TGTACTAAATGCTTTATAGATCTC 215487 ii i i v -- i ii i viiv i C MIRb#SINE/MIR 248 TTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACATGCATT 199 chr5ptel1M 215488 GCTTTATTTAATC 215500 iii i C MIRb#SINE/MIR 198 ATCTCATTTAATC 186 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.16 CpG sites = 15, Kimura (unadjusted) = 41.52 Transitions / transversions = 5.00 (15/3) Gap_init rate = 0.02 (1 / 60), avg. gap size = 2.00 (2 / 1) 247 25.56 21.11 0.00 chr5ptel1M 215567 215656 (784344) C MIRc#SINE/MIR (151) 117 9 m_b222s601i14 8763 chr5ptel1M 215567 GAGAAGTTGAGGGATTTGCCCAGGTTCACAC-------------CAG--- 215600 i i v i i v ------------- --- C MIRc#SINE/MIR 117 GAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGC 68 chr5ptel1M 215601 CAGGACTT-AATCCAAGCCTTTCTACCTCCAAGGCAA--GCTCTAGTCAC 215647 i i- i i i i iv v v -- vvi C MIRc#SINE/MIR 67 CGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCAC 18 chr5ptel1M 215648 GACATTACA 215656 vi ii C MIRc#SINE/MIR 17 TGCACCACA 9 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.97 CpG sites = 15, Kimura (unadjusted) = 32.32 Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.04 (4 / 89), avg. gap size = 4.75 (19 / 4) 288 36.64 5.34 0.00 chr5ptel1M 216815 216945 (783055) MIR3#SINE/MIR 45 182 (26) m_b222s601i15 8764 chr5ptel1M 216815 AGACC---ATCCTGATCTTCACACTG--ACCAAAACACTGTATGATTTGA 216859 ---i i ii iivi v -- i vv?i i ii vi MIR3#SINE/MIR 45 AGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTG 94 chr5ptel1M 216860 ATCAAGTGACCTGTCCTCTCTGGGGCT--ATTTTTTCACCTAGAGAATTA 216907 iv v i vv v --i ii i iv i v MIR3#SINE/MIR 95 GGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGA 144 chr5ptel1M 216908 AGAAGGTGGACATGATGGTCCCCAATAACCTTTCTGGC 216945 i ii v vv i i i viv i ii MIR3#SINE/MIR 145 GGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGC 182 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 52.63 CpG sites = 31, Kimura (unadjusted) = 54.37 Transitions / transversions = 1.82 (31/17) Gap_init rate = 0.02 (3 / 130), avg. gap size = 2.33 (7 / 3) 14 4.94 0.00 0.00 chr5ptel1M 217718 217738 (782262) (CCAT)n#Simple_repeat 1 21 (0) m_b222s252i8 8765 chr5ptel1M 217718 CCATCCATGCATCCATCCATC 217738 v (CCAT)n#Simpl 1 CCATCCATCCATCCATCCATC 21 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 216 21.05 0.00 0.00 chr5ptel1M 221578 221615 (778385) MIR3#SINE/MIR 112 149 (59) m_b222s601i16 8766 chr5ptel1M 221578 CCTTGGGCTTCAGTTTTCTCACCAGTAAAATATGGGGG 221615 ii i i i v iv MIR3#SINE/MIR 112 CTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGG 149 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 25.76 CpG sites = 6, Kimura (unadjusted) = 25.76 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 234 31.84 4.35 2.13 chr5ptel1M 222831 222968 (777032) C L1MC2_3end#LINE/L1 (460) 631 491 m_b223s551i0 8767 chr5ptel1M 222831 TTCATTCACTTTGTATCAGTTTGTAT---AAGTCTTTCTGGGTTTTTCTG 222877 v --- v i v i --- i iii iiv i ii C L1MC2_3end#LI 631 TTCTTTCACTT---AGCAATATGCATTTAAGGTTCCTCCATGTCTTTTCG 585 chr5ptel1M 222878 AAATCTGCCTGTTCATTTCTT---AGTGCACAATAATATTCCTTTATATT 222924 viiii viv i --- vi vv v i v C L1MC2_3end#LI 584 TGGCTTGATAGCTCATTTCTTTTTATCGCTGAATAATATTCCATTGTATG 535 chr5ptel1M 222925 CTTATACCACAGCTTATTCAGCCATTCCCCAATTGATGGGCCTC 222968 vv i i i i v v v v i v C L1MC2_3end#LI 534 GATGTACCACAGTTTGTTTATCCATTCACCTATTGAAGGACATC 491 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 39.97 CpG sites = 24, Kimura (unadjusted) = 42.55 Transitions / transversions = 1.26 (24/19) Gap_init rate = 0.04 (5 / 137), avg. gap size = 1.80 (9 / 5) 247 24.42 3.37 3.37 chr5ptel1M 222877 222965 (777035) C L1MC5a_3end#LINE/L1 (2195) 582 494 m_b223s551i1 8767 chr5ptel1M 222877 GAAATCTGCCT-GTTCATTTCT-TAG-TGCACAATAATATTCCTTTATAT 222923 i v -i v i -i - --- i i v i i C L1MC5a_3end#L 582 GAGATCTTCCTCATTCCTTTTTACAGCTGCA---TAGTACTCCATTGTGT 536 chr5ptel1M 222924 TCTTATACCACAGCTTATTCAGCCATTCCCCAATTGATGGGC 222965 vvv i i i i v v i C L1MC5a_3end#L 535 GGATGTACCATAGTTTATTCAACCAGTCCCCTATTGATGGAC 494 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 30.30 CpG sites = 13, Kimura (unadjusted) = 30.30 Transitions / transversions = 1.62 (13/8) Gap_init rate = 0.07 (6 / 88), avg. gap size = 1.00 (6 / 6) 261 24.69 3.70 0.00 chr5ptel1M 222888 222968 (777032) C L1MC1_3end#LINE/L1 (506) 574 491 m_b223s551i2 8767 chr5ptel1M 222888 GTTCATTTCTT---AGTGCACAATAATATTCCTTTATATTCTTATACCAC 222934 i --- i vv v i v vvv i C L1MC1_3end#LI 574 GCTCATTTCTTTTTAGCGCTGAATAATATTCCATTGTCTGGATGTACCAC 525 chr5ptel1M 222935 AGCTTATTCAGCCATTCCCCAATTGATGGGCCTC 222968 i i v v v i v i v C L1MC1_3end#LI 524 AGTTTATTTATCCATTCACCTACTGAAGGACATC 491 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 28.32 CpG sites = 8, Kimura (unadjusted) = 29.99 Transitions / transversions = 0.67 (8/12) Gap_init rate = 0.01 (1 / 80), avg. gap size = 3.00 (3 / 1) 456 30.09 7.17 5.33 chr5ptel1M 222907 223422 (776578) C L1ME4a_3end#LINE/L1 (316) 555 31 m_b223s551i3 8767 chr5ptel1M 222907 ATAATATTCCTTTATATTCTTATACCACAGCTTATTCAGCCATTCCCCAA 222956 v ? vvv i i ii i i ? v C L1ME4a_3end#L 555 ATAATATTCCATTNTATGGATGTACCATAATTTATTTAACCANTCCCCTA 506 chr5ptel1M 222957 TTGATGGGCCTCCCCTCAATATCTAATATTTTTATACCCCACAAAGGACT 223006 v i v iivvvivi v i v ivv iivi v v ivi C L1ME4a_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAATGCT 456 chr5ptel1M 223007 GCTATAAATATTTTTGCATATTCATATATATATTTTTGTACTTATATCCT 223056 v i i ii -------- i v i ? -- i -- C L1ME4a_3end#L 455 GCGATGAACATCCTTG--------TACATAAATCTTTGTNC--ACATC-- 418 chr5ptel1M 223057 TTCCTTCTCATGATTTCTTTTGGATACAAACTTATCAGTGGTATTTGTGA 223106 ----- v v i v v vv i vv v vv i C L1ME4a_3end#L 417 -----TCTGATTATTTCCTTAGGATAAATTCCTAGAAGTGGAATTACTGG 373 chr5ptel1M 223107 ATCAAAGTGTACGCACTGTTGGTT--GCCCTTTGG-GCATAGTTCCAAAT 223153 i v i ? vv -- -- v i i-i v v C L1ME4a_3end#L 372 GTCAAAGGGTATGNACATTT--TTAAGGCTTTTGATACATATTGCCAAAT 325 chr5ptel1M 223154 AACTG---AGAATGGTTGGATTAGTTCAGGACTCC----AGCACTACATT 223196 vi iv--- v v ii i i v- ---- v ii v C L1ME4a_3end#L 324 TGCCCTCCAGAAAGGTTGTACCAATTTAC-ACTCCCACCAGCAGTGTATG 276 chr5ptel1M 223197 AG-GTGTTTCAATTTTCC---CTGTCTCTAACATT------TATCACTTT 223236 - ii- iv i? --- iv v i i ------ v -- C L1ME4a_3end#L 275 AGAGTGCC-CGTTTCNCCACACCCTCGCCAACACTGGGTATTATCAAT-- 229 chr5ptel1M 223237 CCTTTTTTGTCATTGGCCAATCTGAAAGAGGTGAGGTGGTATCTCATTGG 223286 - vvi - v i v iv vi ii v C L1ME4a_3end#L 228 -CTTTTAAATC-TTTGCCAATTTGATAGGTGAAAAATGGTATCTCATTGT 181 chr5ptel1M 223287 TGCTTTAATCACCA--------ATCA--AGTGATTTGGAGCACTTGTTCA 223326 i ivv -------- i -- vv v i i? v C L1ME4a_3end#L 180 TGTTTTAATTTGCATTTCTTTGATTACTAGTGAGGTTGAACATNTTTTCA 131 chr5ptel1M 223327 TATGCCTAGAGATAGC--TTTG-ATTATTTCATTTGAAATCTGCCTGATC 223373 ii v--- i -- - vi v vi vi i v C L1ME4a_3end#L 130 TATGTTTAT---TGGCCATTTGTATTTCTTCTTTTGTGAATTGTCTGTTC 84 chr5ptel1M 223374 ATATCCTT---CTATTTGTCTCTTCAGGAATCCTTTTTATTCTTA-TAAT 223419 i --- i v v vi vi i v i v - i C L1ME4a_3end#L 83 ATGTCCTTTGCCCATTTTTCTATTGGGGTGTTCGTCTTTTTCTTATTGAT 34 chr5ptel1M 223420 TTG 223422 C L1ME4a_3end#L 33 TTG 31 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 38.97 CpG sites = 73, Kimura (unadjusted) = 39.65 Transitions / transversions = 0.99 (73/74) Gap_init rate = 0.08 (41 / 515), avg. gap size = 1.59 (65 / 41) 253 32.26 1.08 0.00 chr5ptel1M 224101 224193 (775807) L1M4_orf2#LINE/L1 1905 1998 (1296) m_b223s551i4 8768 chr5ptel1M 224101 AAAATCAAGAGCTAACATTATCTATAATGGAGATAAACTACAATCTTTTC 224150 i v v i viv v v i iv ?v i L1M4_orf2#LIN 1905 AAAACCCACAGCTAACATCATACTTAATGGTGAAAGACTGAANGCTTTCC 1954 chr5ptel1M 224151 CTATAAATTCAGG-GTGAAACAGTGATGTTCACTGTCACCGTTT 224193 iv iv -iii i iv i i v i ii L1M4_orf2#LIN 1955 CCCTAAGATCAGGAACAAGACAAGGATGTCCGCTCTCGCCACTT 1998 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 40.50 CpG sites = 18, Kimura (unadjusted) = 44.44 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.01 (1 / 92), avg. gap size = 1.00 (1 / 1) 16 16.75 2.38 2.38 chr5ptel1M 226193 226234 (773766) (TTAAAA)n#Simple_repeat 1 42 (0) m_b223s252i0 8769 chr5ptel1M 226193 TTAAAATT-AAATTAAAACCTATTATTAAAAATAATAATAAAA 226234 - -i vv v v v (TTAAAA)n#Sim 1 TTAAAATTAAAATTAAAA-TTAAAATTAAAATTAAAATTAAAA 42 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.05 (2 / 41), avg. gap size = 1.00 (2 / 2) 490 22.92 0.00 0.00 chr5ptel1M 226778 226873 (773127) U6#snRNA 1 96 (11) m_b223s502i0 8770 chr5ptel1M 226778 GTGCTTGCTTTGAAAGCACATATTCGAAAATTGGAATGATACAGAGAAGA 226827 i i iv v v i U6#snRNA 1 GTGCTCGCTTCGGCAGCACATATACTAAAATTGGAACGATACAGAGAAGA 50 chr5ptel1M 226828 TTAGCAAGGCGTTTGCACCAGGGAGATATACAAATTCATTAAGTAT 226873 v vii i v iv i ii i v ii U6#snRNA 51 TTAGCATGGCCCCTGCGCAAGGATGACACGCAAATTCGTGAAGCGT 96 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 18.25 CpG sites = 14, Kimura (unadjusted) = 28.06 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.00 (0 / 95), avg. gap size = 0.0 (0 / 0) 15 0.00 0.00 0.00 chr5ptel1M 230005 230021 (769979) (AC)n#Simple_repeat 1 17 (0) m_b223s252i1 8771 chr5ptel1M 230005 ACACACACACACACACA 230021 (AC)n#Simple_ 1 ACACACACACACACACA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 16 20.86 5.26 1.69 chr5ptel1M 231052 231108 (768892) (TTGCCC)n#Simple_repeat 1 59 (0) m_b223s252i2 8772 chr5ptel1M 231052 TTGCCGCTGCCCTGGCCCTCCCCCTCTGCCC-T-CTC-TGCCCTTTCCCC 231098 vi v iv - - - i - v i (TTGCCC)n#Sim 1 TTGCCCTTGCCCTTGCCCTTGCCCT-TGCCCTTGCCCTTGCCCTTGCCCT 49 chr5ptel1M 231099 GGCTCTTGCC 231108 v i (TTGCCC)n#Sim 50 TGCCCTTGCC 59 Matrix = Unknown Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.07 (4 / 56), avg. gap size = 1.00 (4 / 4) 204 17.51 0.00 2.50 chr5ptel1M 233429 233469 (766531) MIR3#SINE/MIR 25 64 (144) m_b223s601i0 8773 chr5ptel1M 233429 AGCATGTTCTGGATGGTCAGGAGATCTGAGTTCTAGTCCCG 233469 i vv i-i i i MIR3#SINE/MIR 25 AGCACGGACTGGG-AGTCAGGAGACCTGGGTTCTAGTCCCG 64 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 17.35 CpG sites = 5, Kimura (unadjusted) = 20.47 Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 19 12.88 0.00 8.70 chr5ptel1M 236579 236628 (763372) (TGT)n#Simple_repeat 1 46 (0) m_b223s252i3 8774 chr5ptel1M 236579 TGTTGGGGTTTTTGTTGTTGTTGTTGTTACATTGATTGTGTGTTCTTGTT 236628 vv v --i - - v (TGT)n#Simple 1 TGTTGTTGTTGTTGTTGTTGTTGTTGTT--GTTG-TTGT-TGTTGTTGTT 46 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.08 (4 / 49), avg. gap size = 1.00 (4 / 4) 21 16.01 0.00 0.00 chr5ptel1M 236655 236689 (763311) (T)n#Simple_repeat 1 35 (0) m_b223s252i4 8775 chr5ptel1M 236655 TTTTTTTGTTTTGTTTTTTTCCTTTTCTTTTTTTT 236689 v v ii i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 35 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 232 18.93 4.40 18.75 chr5ptel1M 237415 237505 (762495) MIR3#SINE/MIR 112 191 (17) m_b223s601i1 8773 chr5ptel1M 237415 CCTTGGGCTTCAGTTTTCTCACCAGTAAAAAGTGGGGGAGGAGAAGGGGA 237464 ii i i i v -- i ------------- MIR3#SINE/MIR 112 CTCTGGGCCTCAGTTTCCTCATCTGTAAAA--TGAGG------------- 146 chr5ptel1M 237465 GGGTTGGTCTAGAT--TCTC--AGGTCCCTCTTAACTCTACCATT 237505 v -- -- iii i iv MIR3#SINE/MIR 147 GGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATT 191 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 22.00 CpG sites = 11, Kimura (unadjusted) = 22.00 Transitions / transversions = 3.67 (11/3) Gap_init rate = 0.19 (17 / 90), avg. gap size = 1.12 (19 / 17) 270 32.47 6.95 6.11 chr5ptel1M 239593 240225 (759775) C L1ME3F_3end#LINE/L1 (322) 668 31 m_b223s551i5 8776 chr5ptel1M 239593 AATGTTACTGATGCTGTGCACAGTGTTCCTGGTTCTGCTCATTTTACTTT 239642 v - v i iiii v iv? vii iv i iv C L1ME3F_3end#L 668 AATGGTA-TCATACTGTATGTAGTCTTCTGNGACTTGCTTTTTTCACTCA 620 chr5ptel1M 239643 GTATCACAGTTTGTACAAGTCTTGCCAGGTTTTTCCGAA-ATCTGCTTGT 239691 i i i- v vi v v - v v v vi- v - v C L1ME3F_3end#L 619 ATATTAT-GTTTCTAAGATTCAT-CCATGTTGTTGCGTGTAGCTG-TAGT 573 chr5ptel1M 239692 TCATT---TCTTAGTGCGCAATAATATTCCTTTATATTCCTATACCACAA 239738 --- i i v vvv v i i vvv C L1ME3F_3end#L 572 TCATTCATTTTCACTGCTGTATAATATTCCATTGTGTGAATATACCACAA 523 chr5ptel1M 239739 CTTATTCAGCCATTCCCCAATTAATGGG--TTTCCCCTCAGTTTCCAATA 239786 i i v i vi ii i-- vvvi -- i v C L1ME3F_3end#L 522 TTTATTTATCCATTCTCCTGTCGATGGACATTTGGGTT--GTTTCCAGTT 475 chr5ptel1M 239787 TTTTCCCACCCCAAAAAGGATTCCTATAAATGTTTTTGCATATCCACATA 239836 v i iiv i v vii v i ii i i ------ i C L1ME3F_3end#L 474 TTTTGCTATTACGAACAGTGCTGCTATGAACATTCTTGTA------CATG 431 chr5ptel1M 239837 TTTATTTATATATTTATATCCTTCCCTTTTTGTATGATCTTTGGCTTACA 239886 i vi vi ii i-- i v vvvvv i ------- v -- i C L1ME3F_3end#L 430 TCTCCTGGTGCAC--ATGTGCAAGAGTTTCT-------CTTGGG--TATA 392 chr5ptel1M 239887 GACCTAGTACTGGTATTGCCCAGTCAAAGTGTATGCACAGTTTGGTTGCC 239936 v v v v ivi iv v iv --- v iiv C L1ME3F_3end#L 391 TACCTAGGAGTGGAATTGCTGGGTCGTAGGGTATGCGAA---TGTTCAAC 345 chr5ptel1M 239937 CTTTGGACATAGTTCCAAATAACTG---AGAATGCTTGGTTCAGTTCAGG 239983 i vv v i v vii v--- i i v vvi i i v- C L1ME3F_3end#L 344 TTTACGAGATAATGCCAAATTGTTTTCCAAAGTGGTTGTACCAATTTAC- 296 chr5ptel1M 239984 ACTCC----AACACTACATTAGA-----TGTTGGAATTTTC--CCTGTCT 240022 ---- i v ii v -----i -- iiv -- v i C L1ME3F_3end#L 295 ACTCCCACCAGCAGTGTATAAGAGTTCCCGTTG--ATCCACATCCTCTCC 248 chr5ptel1M 240023 AATATTT----CTTTC---CTTTTTTGTCATATTGGCCAATCTGATAGGG 240065 i i ----i v --- i ---v v v vi i v C L1ME3F_3end#L 247 AACACTTGGTATTGTCAGACTTCTT---AATTTTTGCCAATCGAATGGGT 201 chr5ptel1M 240066 GTGAGGTGGTATATCA--GTTGTTTTAATTTGCATTTCTTTAATCA--AG 240111 i i ii v -- v i ii i i -- i C L1ME3F_3end#L 200 ATAAAATGGTATCTCATTGTGGTCTTAATTTGCATTTCCCTGATTACTAA 151 chr5ptel1M 240112 TGATTTGGAGCA---CTTCGTTTTTCTAAAGAAAGC--TTCAATTATTTC 240156 vv v ---i i v v i vv --- -- i-- i C L1ME3F_3end#L 150 TGAGGTTGAGCATCTTTTCATATGTTTATTG---GCCATTCG--TGTTTC 106 chr5ptel1M 240157 ATT-----TGAAATCTGCCTGCTCATATCCTTTG---ATTTATCTATTGG 240198 v i----- -- i i i --- v C L1ME3F_3end#L 105 CTCTTCTGTGAAA--TGCCTGTTCATGTCTTTTGCCCATTTTTCTATTGG 58 chr5ptel1M 240199 GGAATAAATTTTATTCTTATAAATTTG 240225 vvi vvi i v vi C L1ME3F_3end#L 57 GTTGTTTGTCTTTTTCTTATTGATTTG 31 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 41.72 CpG sites = 101, Kimura (unadjusted) = 43.52 Transitions / transversions = 1.10 (101/92) Gap_init rate = 0.09 (54 / 632), avg. gap size = 1.54 (83 / 54) 482 30.32 6.58 4.95 chr5ptel1M 239709 240225 (759775) C L1ME4a_3end#LINE/L1 (316) 555 31 m_b223s551i6 8776 chr5ptel1M 239709 ATAATATTCCTTTATATTCCTATACCACAACTTATTCAGCCATTCCCCAA 239758 v ? vvv i i i i i ? v C L1ME4a_3end#L 555 ATAATATTCCATTNTATGGATGTACCATAATTTATTTAACCANTCCCCTA 506 chr5ptel1M 239759 TTAATGGG--TTTCCCCTCAGTTTCCAATATTTTCCCACCCCAAAAAGGA 239806 iv i-- vvvi -- v iv i iivi v ivi C L1ME4a_3end#L 505 TTGTTGGACATTTAGGTT--GTTTCCAATTTTTCGCTATTATAAATAATG 458 chr5ptel1M 239807 TTCCTATAAATGTTTTTGCATATCCACATATTTATTTATATATTTATATC 239856 i v v i ii ii i i -- v v i ?i i v i i- i C L1ME4a_3end#L 457 CTGCGATGAACATCCTTGTACAT--AAATCTTTGTNCACATCTCTG-ATT 411 chr5ptel1M 239857 CTTCCCTTTTTGTATGATCTTTGGCTTACAGACCTAGTACTGGTATTGCC 239906 v i ----- v --------- v vv v v v i i C L1ME4a_3end#L 410 ATTTCCTT-----AGGAT---------AAATTCCTAGAAGTGGAATTACT 375 chr5ptel1M 239907 CAGTCAAAGTGTATGCACAGTTT---GGTTGCCCTTTGG-ACATAGTTCC 239952 vi v ? v --- i ---- i- v v C L1ME4a_3end#L 374 GGGTCAAAGGGTATGNACATTTTTAAGGCT----TTTGATACATATTGCC 329 chr5ptel1M 239953 AAATAACTG---AGAATGCTTGGTTCAGTTCAGGACTCC----AACACTA 239995 vi iv--- v v vvi i i v- ---- i v i C L1ME4a_3end#L 328 AAATTGCCCTCCAGAAAGGTTGTACCAATTTAC-ACTCCCACCAGCAGTG 280 chr5ptel1M 239996 CATTAGA-TGTTGGAATTTT------CCCTGTCTAATATT---TCTT-TC 240034 i v - iiv -- i------ vv i i i --- v - C L1ME4a_3end#L 279 TATGAGAGTGCCCG--TTTCNCCACACCCTCGCCAACACTGGGTATTATC 232 chr5ptel1M 240035 CTTTTTTGTCATATTGGCCAATCTGATAGGGGTGAGGTGGTATATCA--G 240082 vv i vvv v v i v vi ii v -- C L1ME4a_3end#L 231 AATCTTTTAAATCTTTGCCAATTTGATAGGTGAAAAATGGTATCTCATTG 182 chr5ptel1M 240083 TTGTTTTAATTTGCATTTCTTTAATCA--AGTGATTTGGAGCA---CTTC 240127 i i -- vv v i ---i C L1ME4a_3end#L 181 TTGTTTTAATTTGCATTTCTTTGATTACTAGTGAGGTTGAACATNTTTTC 132 chr5ptel1M 240128 GTTTTTCTAAAGAAAGCTTCAATTATTTCATTTGAAATCTGCCTGCTCAT 240177 i v v i vv ivvii vv vi v vi vi i i C L1ME4a_3end#L 131 ATATGTTTATTGGCCATTTGTATTTCTTCTTTTGTGAATTGTCTGTTCAT 82 chr5ptel1M 240178 ATCCTTTG---ATTTATCTATTGGGGAATAAATTTTATTCTTATAAATTT 240224 i --- v vi vvi i v vi C L1ME4a_3end#L 81 GTCCTTTGCCCATTTTTCTATTGGGGTGTTCGTCTTTTTCTTATTGATTT 32 chr5ptel1M 240225 G 240225 C L1ME4a_3end#L 31 G 31 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 39.11 CpG sites = 73, Kimura (unadjusted) = 39.78 Transitions / transversions = 0.96 (73/76) Gap_init rate = 0.08 (39 / 516), avg. gap size = 1.54 (60 / 39) 187 16.67 0.00 0.00 chr5ptel1M 240966 240995 (759005) C MIRb#SINE/MIR (29) 239 210 m_b223s601i2 8777 chr5ptel1M 240966 TATTATATGCCAGGTACAGTGCTAAGTGCT 240995 i i i v i C MIRb#SINE/MIR 239 TACTATGTGCCAGGCACTGTGCTAAGCGCT 210 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 15.45 CpG sites = 4, Kimura (unadjusted) = 19.56 Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 15 11.69 0.00 0.00 chr5ptel1M 242546 242573 (757427) (CTCAG)n#Simple_repeat 1 28 (0) m_b223s252i5 8778 chr5ptel1M 242546 CTGAGCCCAGCTCAGCTCAGCTTAGCTC 242573 v i i (CTCAG)n#Simp 1 CTCAGCTCAGCTCAGCTCAGCTCAGCTC 28 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 288 28.61 3.21 8.43 chr5ptel1M 243449 243635 (756365) C L1ME3G_3end#LINE/L1 (545) 379 202 m_b223s551i7 8779 chr5ptel1M 243449 AGTGGATATCTTTGGAAGTCAGAAAGTACTCACAGTTCAGTGACATTTTA 243498 - ivi -- i ii iv i v i i---- C L1ME3G_3end#L 379 AGTGGA-ATTGCTGG--GTCAAAGGGTATGCGCATTTTAA----ATTTTA 337 chr5ptel1M 243499 ---GGTACGTTCCAAATTGCTTTACAGATTGGCTAGACCAATTTATAGCT 243545 --- i - v ii v i v? iv i vii C L1ME3G_3end#L 336 ATAGATAC-TGCCAAATTGCCCTCCAAAANGGCTGTACCAATTTACACTC 288 chr5ptel1M 243546 CCACCAAAAGTATGTGACTGTGTTAGTTTTTCTAGGGCAAGGTT-CCTAC 243594 iv i i vv iiiv ii i --- vvv i- v C L1ME3G_3end#L 287 CCACCAGCAGTGTATGAGAGTACCCGTTTCCCCA---CACCCTCGCCAAC 241 chr5ptel1M 243595 ATTTGCTATTCTC--CCTTTTTGATTTACTTTTGTCAATCTGA 243635 i ? v v --? vi ---- i C L1ME3G_3end#L 240 ACTNGATATTATCAANCTTTTAAAT----TTTTGCCAATCTGA 202 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.91 CpG sites = 30, Kimura (unadjusted) = 37.87 Transitions / transversions = 1.58 (30/19) Gap_init rate = 0.10 (18 / 186), avg. gap size = 1.17 (21 / 18) 196 24.57 1.22 10.67 chr5ptel1M 244338 244419 (755581) C L2c_3end#LINE/L2 (0) 478 404 m_b223s601i3 8780 chr5ptel1M 244338 ATTGATTTTATCAACAAGCATTTTAATAATTGCTTAGTATGTGTCCCCTG 244387 v ivv i - v i vi i v ------- C L2c_3end#LINE 478 ATTCATTCATTCAACAAACA-TTTATTGAGCGCCTACTATG-------TG 437 chr5ptel1M 244388 CCAAGCCCTGAGGATCCAAGGA-GAACAAAACA 244419 i v i v i - i i C L2c_3end#LINE 436 CCAGGCGCTGGGGATACAAAGATGAATAAGACA 404 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 27.94 CpG sites = 10, Kimura (unadjusted) = 29.86 Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.11 (9 / 81), avg. gap size = 1.00 (9 / 9) 13 14.94 0.00 3.23 chr5ptel1M 246194 246225 (753775) (GGCCCA)n#Simple_repeat 1 31 (0) m_b223s252i6 8781 chr5ptel1M 246194 GGCCAAGGGCCCAGGCCTGGACCCAGGCCCAG 246225 v - ii i (GGCCCA)n#Sim 1 GGCCCA-GGCCCAGGCCCAGGCCCAGGCCCAG 31 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 13 20.07 5.00 0.00 chr5ptel1M 246909 246948 (753052) (TAAA)n#Simple_repeat 1 42 (0) m_b223s252i7 8782 chr5ptel1M 246909 TAAATAATTATTTTTA-AAATAAAT-AATAAATAAAAGAATA 246948 v vv vv - - vi (TAAA)n#Simpl 1 TAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATA 42 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 20 13.87 0.00 0.00 chr5ptel1M 252436 252467 (747533) (T)n#Simple_repeat 1 32 (0) m_b223s252i8 8783 chr5ptel1M 252436 TTTTTTTTTTGTTTGTTTGTTTTTTTTTTGTT 252467 v v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 32 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 18 19.86 0.00 0.00 chr5ptel1M 252516 252550 (747450) (T)n#Simple_repeat 1 35 (0) m_b223s252i9 8783 chr5ptel1M 252516 TTTTTTTTTGTTCTTCTTTCATTTTCTTTTTTTTT 252550 v i i iv i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 35 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 191 30.76 1.09 8.14 chr5ptel1M 252552 252643 (747357) C MIRc#SINE/MIR (141) 127 42 m_b223s601i4 8784 chr5ptel1M 252552 CTGAGGC-CATTTGGGTTAAATGACTTGGCCAGGGCCACACTGTGGGGAA 252600 - vvvi i v i i ------- i C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACAC-------AG 85 chr5ptel1M 252601 GTGTTAAGTGTCTGAAGCCATATTTGAATTCTAGTCTTCCAGA 252643 v iv v v iv viv i i ii vi v C MIRc#SINE/MIR 84 CTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGA 42 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 37.91 CpG sites = 13, Kimura (unadjusted) = 39.83 Transitions / transversions = 1.00 (13/13) Gap_init rate = 0.09 (8 / 91), avg. gap size = 1.00 (8 / 8) 16 5.27 0.00 0.00 chr5ptel1M 257229 257248 (742752) (AC)n#Simple_repeat 1 20 (0) m_b223s252i10 8785 chr5ptel1M 257229 ACACACACACACATACACAC 257248 i (AC)n#Simple_ 1 ACACACACACACACACACAC 20 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 301 27.94 0.00 7.78 chr5ptel1M 257885 257981 (742019) C MIRc#SINE/MIR (155) 113 24 m_b223s601i5 8786 chr5ptel1M 257885 GGTTAAGTGACTTAGCCAGTGTCACACAGCTGGGAAGTGTTAAGTGTCTG 257934 iv iv i ------- v v C MIRc#SINE/MIR 113 GGTTAAGTGACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGCAG 71 chr5ptel1M 257935 AAGCCAGATTTGAACTCAGAATCTCCTCACTTCAGTGCTGGTGCTCT 257981 iv vi i i i ivii v i ivv ii C MIRc#SINE/MIR 70 AGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCT 24 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.90 CpG sites = 15, Kimura (unadjusted) = 35.67 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.07 (7 / 96), avg. gap size = 1.00 (7 / 7) 14 11.13 3.45 0.00 chr5ptel1M 260577 260605 (739395) (TAAA)n#Simple_repeat 1 30 (0) m_b224s252i0 8787 chr5ptel1M 260577 TAAAAAAATAAAT-AATAAATAAAAGAATA 260605 v - vi (TAAA)n#Simpl 1 TAAATAAATAAATAAATAAATAAATAAATA 30 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1) 206 32.28 2.93 9.33 chr5ptel1M 260928 261132 (738868) C L2#LINE/L2 (1495) 1587 1395 m_b224s601i0 8788 chr5ptel1M 260928 TGGTCACAAAGGTGGGTAAAAGGTATGGGAGATGTGGAAGAGGAGAGAAG 260977 v i v ii --- i- v vi v ------- C L2#LINE/L2 1587 TGGGCACAGATGCAGGTA---GGTG-GGTAGATGTGGTGGTGG------- 1549 chr5ptel1M 260978 AGGGAGCTCATGGAGGATGCCCTTAACTTTTTTTTTTTTTTTTGCAAAAA 261027 --- ??ii i v vi i iviv vi i v i iivvi C L2#LINE/L2 1548 ---GAGNNTGTGGAAGTTCTCTTCTGATTGCTTCTATTTTCTCAGTGAAA 1502 chr5ptel1M 261028 TGAGGTATAAAGTTCTTAGCTGAGAGAGTTGAGGG-AGGGAAGCAAGG-- 261074 ii ivii i iv i --- i- i -i -- C L2#LINE/L2 1501 TAGGAAGCAAGGTCATCAGCTGAGAG---TGAGGATAGGGGAG-GAGGTG 1456 chr5ptel1M 261075 --AAAGGGTTGAGGAG-GATGAGCAGGTTTGGGAGATCTGTTGCAGAGAG 261121 --ii v - v v v ii v vii ivvi C L2#LINE/L2 1455 TTGGAGGTTTGAGGAGAGAGGAGAAGGTGTGAAATAGTCGTCTAGGAGAG 1406 chr5ptel1M 261122 TGGGAGAGTGA 261132 C L2#LINE/L2 1405 TGGGAGAGTGA 1395 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 43.29 CpG sites = 37, Kimura (unadjusted) = 44.30 Transitions / transversions = 1.61 (37/23) Gap_init rate = 0.11 (22 / 204), avg. gap size = 1.09 (24 / 22) 16 33.28 5.68 0.00 chr5ptel1M 261687 261774 (738226) (AG)n#Simple_repeat 1 93 (0) m_b224s252i1 8789 chr5ptel1M 261687 AGAAAAAGAGAGAGA-AGA-AGTGA-AGGGGGGAAGAGAGTAAGAGGTGG 261733 i i - - v - i i ii vi ivi (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr5ptel1M 261734 GGAAAG-GAGAGAGAAACACCTTGGGAAAGGGAGAGAGA-AGA 261774 i i - i v vvvv i i i - (AG)n#Simple_ 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 93 Matrix = Unknown Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.06 (5 / 87), avg. gap size = 1.00 (5 / 5) 190 33.18 0.00 13.04 chr5ptel1M 263113 263216 (736784) L3#LINE/CR1 3437 3528 (571) m_b224s601i1 8790 chr5ptel1M 263113 GTTCTGGTTACTCACTGAGCCCAGTCTCAGTTAACAGCAATGGGGTGGGT 263162 i i ivi i -i i i v v ii ii- iv v L3#LINE/CR1 3437 GTTTTAGTTGACCGC-AAGCTCAATATGAGCCAACAGTG-TGATGTGGCT 3484 chr5ptel1M 263163 GGCAAGTGGACCCCAAGTCAGTGCCATCTTGGACTGCATCAATGCGGGAG 263212 v i-------v ii i v i i i ---i i L3#LINE/CR1 3485 GCCAAA-------AAAGCTAATGCAATCTTAGGCTGCATTAAT---AGAA 3524 chr5ptel1M 263213 GTAT 263216 L3#LINE/CR1 3525 GTAT 3528 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 44.22 CpG sites = 22, Kimura (unadjusted) = 46.42 Transitions / transversions = 2.75 (22/8) Gap_init rate = 0.12 (12 / 103), avg. gap size = 1.00 (12 / 12) 21 13.26 0.00 0.00 chr5ptel1M 265232 265264 (734736) (T)n#Simple_repeat 1 33 (0) m_b224s252i2 8791 chr5ptel1M 265232 TTTTTTTTGTTTTTCTTTTGTTTTCTTTTTTTT 265264 v i v i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 33 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 361 25.72 1.48 7.87 chr5ptel1M 265266 265400 (734600) C MIRb#SINE/MIR (138) 130 4 m_b224s601i2 8792 chr5ptel1M 265266 CTGAGGC-CATTGGGGTTAAGTGACTTGCCCAGGGCCACACTGTTAGGAT 265314 - vv i i i i v i --- C MIRb#SINE/MIR 130 CTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAG--- 84 chr5ptel1M 265315 GTGTTAAGTGTCTGAAGCCAGATTTGAACTCTAGTCTTGCTGAGTTTGGT 265364 ---- v v iv vi i i vi vv v iiiiv C MIRb#SINE/MIR 83 ----TAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAA 38 chr5ptel1M 265365 GCTGGTGCTGTAACCTCTGC-CCACCTAGCTGCCCCT 265400 iv v vv v - --- C MIRb#SINE/MIR 37 GCCCGTGCTCTTTCCACTGCACCAC---GCTGCCCCT 4 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.38 CpG sites = 15, Kimura (unadjusted) = 31.52 Transitions / transversions = 0.88 (15/17) Gap_init rate = 0.09 (12 / 134), avg. gap size = 1.00 (12 / 12) 221 27.05 4.40 18.75 chr5ptel1M 266009 266099 (733901) MIR3#SINE/MIR 112 191 (17) m_b224s601i3 8793 chr5ptel1M 266009 CCTTGGGCTTTAGTTTTCTCACCAGTAAGAAGTGGGGGAGGAGAAGGGGA 266058 ii i i i i v --------------- v i i MIR3#SINE/MIR 112 CTCTGGGCCTCAGTTTCCTCATCTGTAA---------------AATGAGG 146 chr5ptel1M 266059 GGGTTGGTCTAGA----CTCTCAGGTCCCTCTTAACTTTACCACT 266099 v ---- v iii i i iv i MIR3#SINE/MIR 147 GGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATT 191 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 34.39 CpG sites = 15, Kimura (unadjusted) = 34.39 Transitions / transversions = 3.00 (15/5) Gap_init rate = 0.18 (16 / 90), avg. gap size = 1.19 (19 / 16) 226 26.58 5.06 0.00 chr5ptel1M 267635 267713 (732287) C L1ME3A_3end#LINE/L1 (368) 552 470 m_b224s551i0 8794 chr5ptel1M 267635 ATAATATTCCCTAACATTTATATACCACAATTTACTCAGTCATTCT---- 267680 i v viii vv i i vi ---- C L1ME3A_3end#L 552 ATAGTATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTACTG 503 chr5ptel1M 267681 TTGATGAGCATCCATTCAGTTTCCAGTTTGTAG 267713 ii iiivvi? ??i C L1ME3A_3end#L 502 TTGATGGACATTTGGGTNGTTTCCAGTTTNNGG 470 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 35.95 CpG sites = 14, Kimura (unadjusted) = 35.95 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.01 (1 / 78), avg. gap size = 4.00 (4 / 1) 14 8.13 3.85 0.00 chr5ptel1M 268813 268838 (731162) (TAAA)n#Simple_repeat 1 27 (0) m_b224s252i3 8795 chr5ptel1M 268813 TAAATAAATAAA-AAATAAAAGAATAA 268838 - vi (TAAA)n#Simpl 1 TAAATAAATAAATAAATAAATAAATAA 27 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 25), avg. gap size = 1.00 (1 / 1) 15 12.17 5.88 5.88 chr5ptel1M 268947 268997 (731003) (TTCTC)n#Simple_repeat 1 51 (0) m_b224s252i4 8796 chr5ptel1M 268947 TTC-CTTTTC-TCTCTTGGCTGATTCCCTTCT-TTCTCTTCTCCTCTCTT 268993 - i - -- -v i - i (TTCTC)n#Simp 1 TTCTCTTCTCTTCTCTT--CT-CTTCTCTTCTCTTCTCTTCTCTTCTCTT 47 chr5ptel1M 268994 CCCT 268997 i (TTCTC)n#Simp 48 CTCT 51 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.12 (6 / 50), avg. gap size = 1.00 (6 / 6) 180 32.12 6.83 7.35 chr5ptel1M 269167 269371 (730629) C L2#LINE/L2 (1495) 1587 1384 m_b224s601i4 8797 chr5ptel1M 269167 TGGTCACAAAGGTCGGTAAAAGGTATGGGAGATGTGGAAGAGGAGAGAAG 269216 v i v iv --- i- v vi v ------- C L2#LINE/L2 1587 TGGGCACAGATGCAGGTA---GGTG-GGTAGATGTGGTGGTGG------- 1549 chr5ptel1M 269217 AGGGAGCTCATGGAGGATGCCCT-TAA---CTTTTTTTTTTTCTATAAAA 269262 --- ??ii i v vi i - i --- i v i vi i C L2#LINE/L2 1548 ---GAGNNTGTGGAAGTTCTCTTCTGATTGCTTCTATTTTCTCAGTGAAA 1502 chr5ptel1M 269263 GTGAGGTATAAGGTTCTTAGTTGAG-----GGA---GGGAAGTAATG--A 269302 - ii ivii iv i i ----- --- i vii --i C L2#LINE/L2 1501 -TAGGAAGCAAGGTCATCAGCTGAGAGTGAGGATAGGGGAGGAGGTGTTG 1453 chr5ptel1M 269303 AAGGATTGAGGAGGGGTGAGAAGGTTTGGAAGATCTGCTGTGGAGAATGG 269352 i v i iv v i v vii iivv i C L2#LINE/L2 1452 GAGGTTTGAGGAGAGAGGAGAAGGTGTGAAATAGTCGTCTAGGAGAGTGG 1403 chr5ptel1M 269353 GAGAGTGAGCCAATGAGGG 269371 iivi iv C L2#LINE/L2 1402 GAGAGTGAATGGACTAGGG 1384 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 43.61 CpG sites = 39, Kimura (unadjusted) = 44.62 Transitions / transversions = 1.77 (39/22) Gap_init rate = 0.10 (20 / 204), avg. gap size = 1.45 (29 / 20) 118 10.78 0.00 0.00 chr5ptel1M 270242 270422 (729578) (AC)n#Simple_repeat 1 181 (0) c_b224s251i0 8798 chr5ptel1M 270242 ACACACACAGACACACACAGAGAGACACACACAGACACACACACAGACAC 270291 v v v v v v (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50 chr5ptel1M 270292 ACACAGAGAGACACACACAGACACACACACACACAGACACAGACACACAC 270341 v v v v v v (AC)n#Simple_ 51 ACACACACACACACACACACACACACACACACACACACACACACACACAC 100 chr5ptel1M 270342 ACACACAGAGACACACACAGACACACACACAGAGACACACACACACACAC 270391 v v v v v (AC)n#Simple_ 101 ACACACACACACACACACACACACACACACACACACACACACACACACAC 150 chr5ptel1M 270392 ACACACACAAACACACACACACACACACACA 270422 v (AC)n#Simple_ 151 ACACACACACACACACACACACACACACACA 181 Matrix = Unknown Transitions / transversions = 0.00 (0/18) Gap_init rate = 0.00 (0 / 180), avg. gap size = 0.0 (0 / 0) 12 19.85 0.00 0.00 chr5ptel1M 270482 270510 (729490) (GAGG)n#Simple_repeat 1 29 (0) m_b224s252i5 8799 chr5ptel1M 270482 GAGGGAGGGAGGGGAAGCGGCAGGGAGGG 270510 iii v v (GAGG)n#Simpl 1 GAGGGAGGGAGGGAGGGAGGGAGGGAGGG 29 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 206 28.43 1.75 7.41 chr5ptel1M 271037 271150 (728850) C MIR#SINE/MIR (139) 123 16 m_b224s601i5 8800 chr5ptel1M 271037 CTGAGTCACTTGG-GGTTACGTGACTTGCCCAGGGTCACTCGGCCGGGAC 271085 v vvi - v i i v i ii---- C MIR#SINE/MIR 123 CTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTA---- 78 chr5ptel1M 271086 GTGTAAGTGTCCGAGACCAGATTTGAGCCCGGG-AGCTCCCGACTTCGGT 271134 -- v v v vi i i i - --i i i i i v C MIR#SINE/MIR 77 --GTAAGTGGCAGAGCCGGGATTCGAACCCAGGCAG--TCTGGCTCCAGA 32 chr5ptel1M 271135 GCGGGGGCTCTCACCC 271150 vv v i v C MIR#SINE/MIR 31 GCCCGTGCTCTTAACC 16 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 34.65 CpG sites = 16, Kimura (unadjusted) = 36.12 Transitions / transversions = 1.14 (16/14) Gap_init rate = 0.09 (10 / 113), avg. gap size = 1.00 (10 / 10) 245 27.08 0.00 7.69 chr5ptel1M 271048 271131 (728869) C MIRc#SINE/MIR (153) 115 38 m_b224s601i6 8800 chr5ptel1M 271048 GGGGTTACGTGACTTGCCCAGGGTCACTCGGCCGGGACGTGTAAGTGTCC 271097 i v i v i ii------ v v C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTA------GTAAGTGGCA 72 chr5ptel1M 271098 GAGACCAGATTTGAGCCCGGGAGCTCCCGACTTC 271131 v vi i i i i vvi i i C MIRc#SINE/MIR 71 GAGCCGGGACTCGAACCCAGGTCTTCCTGACTCC 38 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 32.36 CpG sites = 13, Kimura (unadjusted) = 34.37 Transitions / transversions = 1.62 (13/8) Gap_init rate = 0.07 (6 / 83), avg. gap size = 1.00 (6 / 6) 12 15.26 3.45 0.00 chr5ptel1M 271282 271310 (728690) (CCG)n#Simple_repeat 1 30 (0) m_b224s252i6 8801 chr5ptel1M 271282 CCGCTCCCGCCGCCGCCGCCG-GGCAGCCG 271310 iv -v v (CCG)n#Simple 1 CCGCCGCCGCCGCCGCCGCCGCCGCCGCCG 30 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1) 575 27.27 10.55 0.46 chr5ptel1M 271932 272130 (727870) C MIR#SINE/MIR (22) 240 22 m_b224s601i7 8802 chr5ptel1M 271932 GCCCTTCCTAAGGGCCAGACCCTG--CCGAGCGCCTTATAAACACCGGCT 271979 v v v v i v -- ii i i vii iiii C MIR#SINE/MIR 240 GCGCTTACTATGTGCCAGGCACTGTTCTAAGCGCTTTACATGTATTAACT 191 chr5ptel1M 271980 CTCCTGATCCTCACAACCACGCTAGGACGGACTTGCTTTTTATTATTCCC 272029 vii i v v v v v vv i v - i C MIR#SINE/MIR 190 CATTTAATCCTCACAACAACCCTATGAGGTAGGTACTATT-ATTATCCCC 142 chr5ptel1M 272030 ATTTTACACATGAGGAAACTGAGGCAAACAGCAATGAAGTGACTCGCTCA 272079 v v v vii v i i i C MIR#SINE/MIR 141 ATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCCA 92 chr5ptel1M 272080 GGATCAC-CA------------CAGAGCTCGGATTTGCATTC---TAGTC 272113 i i - ------------ iv i v ii ---i C MIR#SINE/MIR 91 AGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGCAGTC 42 chr5ptel1M 272114 T---TCCCAAGTCCGGGCTC 272130 --- vi i v C MIR#SINE/MIR 41 TGGCTCCAGAGCCCGTGCTC 22 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 32.99 CpG sites = 30, Kimura (unadjusted) = 34.54 Transitions / transversions = 1.25 (30/24) Gap_init rate = 0.03 (6 / 198), avg. gap size = 3.67 (22 / 6) 248 32.68 1.55 5.35 chr5ptel1M 272435 272628 (727372) L2#LINE/L2 2896 3082 (0) m_b224s601i8 8803 chr5ptel1M 272435 TGGCTTTTAAAGCTCCTCATAACCTCGCTCCTCTCTAACTTTTCAGTCTT 272484 i vi i i iv i i v ii i vi v i iiiii i L2#LINE/L2 2896 TGGCCTACAAGGCCCTACATGATCTGGTCCCCCGTTACCTCTCTGACCTC 2945 chr5ptel1M 272485 ATCTCAGCCTCTTCCCCCCAACCTCCTCGGTAATTCTCTGATGCAGGGAA 272534 ----- v v i v- i v v -- i v v vv v L2#LINE/L2 2946 ATCTC-----CTACCACTCT-CCCCCTCGCTCA--CTCCGCTCCAGCCAC 2987 chr5ptel1M 272535 AACGGCCTCCTTGCTGTTCCTGGCACATCCCACTC-TGCCCCCAGGCTCC 272583 vi v v iv vv -i i - v v L2#LINE/L2 2988 ACTGGCCTCCTTGCTGTTCCTCGAACACGCCAGGCACGCTCCC-GCCTCA 3036 chr5ptel1M 272584 TGGCCTTCTGTAGTAGCTGTGCCCATGGCC-AGAAT-CTCTCCCTCC 272628 v - i v v v viv -i i- i i L2#LINE/L2 3037 GGGCCTT-TGCACTTGCTGTTCCCTCTGCCTGGAACGCTCTTCCCCC 3082 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 39.85 CpG sites = 31, Kimura (unadjusted) = 43.58 Transitions / transversions = 1.07 (31/29) Gap_init rate = 0.07 (13 / 193), avg. gap size = 1.00 (13 / 13) 264 33.23 4.76 5.84 chr5ptel1M 272464 272757 (727243) L2b_3end#LINE/L2 14 304 (162) m_b224s601i9 8803 chr5ptel1M 272464 CCTCTCTAACTTTTCAGTCTTATCTCAGCCTCTTCCCCCCAACCTCCTCG 272513 i v v i i i i i ----- v v i --i i i L2b_3end#LINE 14 CCCCGCTACCTCTCCGGCCTCATCTC-----CTACCACTC--TCCCCTTG 56 chr5ptel1M 272514 GTAATTCTCTGATGCAGGGAAAACGGCCTCCTTGCTGTTCCTGGCACATC 272563 v v -- v v vv v vi v v iv L2b_3end#LINE 57 CTCA--CTCTGCTCCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACACG 104 chr5ptel1M 272564 CCACTCTGCCCCCAGGCTCCTGGCCTTCTGTAGTAGCTGTGCCCATGGCC 272613 ?v v? i v v vv - i v?v v viv L2b_3end#LINE 105 CCANGCTCNCTCCCGCCTCAGGGCCTT-TGCACNTGCTGTTCCCTCTGCC 153 chr5ptel1M 272614 -AGAA---TCTCTCCCTCCTCAT-ACCCCACC--TTCTTTCTCTGGCTCC 272656 -i ---i ii v v -i ivi --i i v ---v L2b_3end#LINE 154 TGGAACGCCCTTCCCCACCTCTTCGCCTGGCCAACTCCTACTC---ATCC 200 chr5ptel1M 272657 TCCAAGTTGCAG---GAAAGTCCGACTTCCTGCAAGGAGCCTTTCCTATC 272703 i i iv ---i v -- i v ii i i i iv L2b_3end#LINE 201 TTCAGGTCTCAGCTCAAATGTC--ACCTCCTCCGGGAAGCCCTCCCTGAC 248 chr5ptel1M 272704 CTCCTCAACC---TAAAGT-TCCTCTTCTGAAATCCCAGCTAATTCCTCC 272749 i ivii --- v i i-i i iivi -- i i i iv L2b_3end#LINE 249 CCCCCAGGCCGGGTCAGGCGCCCTCCTCTGGGCCCCC--CCAGTCCTACC 296 chr5ptel1M 272750 TTGGCGCT 272757 i v i L2b_3end#LINE 297 CTGCCACT 304 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 42.56 CpG sites = 52, Kimura (unadjusted) = 45.91 Transitions / transversions = 1.30 (52/40) Gap_init rate = 0.08 (24 / 293), avg. gap size = 1.29 (31 / 24) 12 8.85 4.17 0.00 chr5ptel1M 273551 273574 (726426) (AAGA)n#Simple_repeat 1 25 (0) m_b224s252i7 8804 chr5ptel1M 273551 AAGAAACAAAG-AAGAAAGAGAGAA 273574 v - i (AAGA)n#Simpl 1 AAGAAAGAAAGAAAGAAAGAAAGAA 25 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 23 13.49 0.00 0.00 chr5ptel1M 276822 276862 (723138) (ATATAT)n#Simple_repeat 1 41 (0) m_b224s252i8 8805 chr5ptel1M 276822 ATATAGATATAGATATATATCTATATATCTATATCTATATA 276862 v v v v v (ATATAT)n#Sim 1 ATATATATATATATATATATATATATATATATATATATATA 41 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 chr5ptel1M 276862 276879 (723121) (AC)n#Simple_repeat 1 18 (0) m_b224s252i9 8806 chr5ptel1M 276862 ACACACACACACACACAC 276879 (AC)n#Simple_ 1 ACACACACACACACACAC 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 231 28.08 5.56 1.06 chr5ptel1M 277222 277311 (722689) C L2a_3end#LINE/L2 (0) 517 424 m_b224s601i10 8807 chr5ptel1M 277222 ATTGATTTCATCAACAAGCATTTCAATAATTGCTTAGGATGGGT--GACA 277269 v ivv ii - v i vi i vv v i-- i C L2a_3end#LINE 517 ATTCATTCATTCAACAAATATTT-ATTGAGCGCCTACTATGTGCCAGGCA 469 chr5ptel1M 277270 CTG--CCAAGCCCTGAGGATACAA-GGAGAACAAAACAGAAGAAA 277311 -- i i v i i-i v vi C L2a_3end#LINE 468 CTGTTCTAGGCGCTGGGGATACAGCAGTGAACAAAACAGACAAAA 424 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 34.16 CpG sites = 14, Kimura (unadjusted) = 35.93 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.04 (4 / 89), avg. gap size = 1.50 (6 / 4) 42 0.00 0.00 0.00 chr5ptel1M 277484 277519 (722481) (AC)n#Simple_repeat 1 36 (0) c_b224s251i1 8808 chr5ptel1M 277484 ACACACACACACACACACACACACACACACACACAC 277519 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACAC 36 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 186 22.63 3.70 1.82 chr5ptel1M 277715 277768 (722232) C L2d_3end#LINE/L2 (260) 256 202 m_b224s601i11 8807 chr5ptel1M 277715 AGGGATTAGGAAAGATTTC-TGGTAGAAGGTGAGACTT-AGCTGGGATTT 277762 v i i i ii - - i i - vi C L2d_3end#LINE 256 AGTGGTCAGGGAAGGCTTCGTGG-AGGAGGTGGGACTTGAGCTGGGCCTT 208 chr5ptel1M 277763 GAAAAA 277768 ii C L2d_3end#LINE 207 GAAGGA 202 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 28.78 CpG sites = 10, Kimura (unadjusted) = 28.78 Transitions / transversions = 5.00 (10/2) Gap_init rate = 0.06 (3 / 53), avg. gap size = 1.00 (3 / 3) 24 16.35 0.00 0.00 chr5ptel1M 280724 280764 (719236) (T)n#Simple_repeat 1 41 (0) m_b224s252i11 8809 chr5ptel1M 280724 TTGTTTCTTTTTTTTTTATTTTATTTTATTTTTTTTTATTT 280764 v i v v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 41 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 444 31.77 1.54 1.54 chr5ptel1M 281221 281415 (718585) C L1MD1_3end#LINE/L1 (356) 633 439 m_b224s551i1 8810 chr5ptel1M 281221 GCTCATTTCACTCAGCATCAGTTCGTGTAAGTCTCTCCAGGCCTTTCTG- 281269 iv v v iiv v ii iiv iiv vi - C L1MD1_3end#LI 633 GCTTTTTTCACTCAGCATAATTCTCTGGAGATTCATCCAGGTTGTTGCGT 584 chr5ptel1M 281270 AAATCATCCTGTTGGTCATTTCTTACAGAACAGTAATATTCCATAATTTT 281319 iv -viv v ivi i iv vvv i ii v v C L1MD1_3end#LI 583 GTATCA-ATAGTTCGTTCCTTTTTATTGCTGAGTAGTATTCCATGGTATG 535 chr5ptel1M 281320 CATATACCACAATTTATTCAGCCATTCTCCAACTGATGGACATCC--ATT 281367 v i i i i i v vii v i--i C L1MD1_3end#LI 534 GATGTACCACAGTTTGTTTAACCATTCACCCGTTGAAGGACATCTGGGTT 485 chr5ptel1M 281368 CAGTTTCCAGTTTCTAGCCACTACAAAAAGGGCTGCCACAAACATTCG 281415 -- i i i i i v ii i i C L1MD1_3end#LI 484 --GTTTCCAGTTTTTGGCTATTACGAATAAAGCTGCTATAAACATTCG 439 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 40.11 CpG sites = 37, Kimura (unadjusted) = 42.90 Transitions / transversions = 1.54 (37/24) Gap_init rate = 0.03 (5 / 194), avg. gap size = 1.20 (6 / 5) 462 22.22 3.12 1.54 chr5ptel1M 281303 281430 (718570) C L1ME3C_3end#LINE/L1 (322) 548 419 m_b224s551i2 8810 chr5ptel1M 281303 TAATATTCCATAATTTTCATATACCACAATTTATTCAGCCATTCTCCAAC 281352 i vi v vv i v vii C L1ME3C_3end#L 548 TAGTATTCCATTGTATGAATATACCACAATTTATTTATCCATTCTCCTGT 499 chr5ptel1M 281353 TGATGGACATCCA--TTCAGTTTCCAGTTTCTAGCCACTACAAAAAGGGC 281400 ii -- -- i i v i i v iv C L1ME3C_3end#L 498 TGATGGACATTTAGGTT--GTTTCCAATTTTTCGCTATTACAAACAATGC 451 chr5ptel1M 281401 TGCCACAAACATTC--GGAGTTGTCACCTTGT 281430 v ii -- v vv v C L1ME3C_3end#L 450 TGCAATGAACATTCTTGTACATGTCTCCTTGT 419 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 26.56 CpG sites = 14, Kimura (unadjusted) = 26.56 Transitions / transversions = 1.00 (14/14) Gap_init rate = 0.03 (4 / 127), avg. gap size = 1.50 (6 / 4) 196 36.87 12.82 0.65 chr5ptel1M 285716 285988 (714012) L3#LINE/CR1 3638 3943 (156) m_b224s601i12 8811 chr5ptel1M 285716 AAATCAGAGAGTGTTTTGGAGAAGCCAGCCAGAATGG--GAGGGCCTGGA 285763 iii v i iiv ii iiv ii i --i i L3#LINE/CR1 3638 AAACTGGAGCGCGTCCAGAGGAGAGCGACCAGGATGGTGAAGGGTCTGGA 3687 chr5ptel1M 285764 GCCCATGTACTCTAATG---GGTT--------TGGAATTGTTTC------ 285796 iv vv v i v --- -------- iiv v------ L3#LINE/CR1 3688 AACCATGTCATATGAGGAACGGTTGAAGGAACTGGGGATGTTTAGCCTGG 3737 chr5ptel1M 285797 AGAAGAG-----CCAGGGGATTCA-GAGA-----TTTCCAGTATCTGAAG 285835 -----ii i vv - v -----i v i i L3#LINE/CR1 3738 AGAAGAGAAGACTTAGAGGAGACATGATAGCTGTCTTCAAATATTTGAAG 3787 chr5ptel1M 285836 TTCTGTCACTGAGGGGAGGGTTCAGCCTTGTTCAGCCGGGTCCCAGAGAG 285885 vv ivvi ii v i v i v ivv ii i L3#LINE/CR1 3788 GGCTGTCATGTGGAAGAGGGATTAGACTTATTCTGTGTGGCTCCAGAGGG 3837 chr5ptel1M 285886 CTGAA--AGGGGCCGGGAAGAGGATTGGCAAAAAAGCCCACTGAGGCTGG 285933 v -- iv viv iivi i v vi iii i vv i vv vi L3#LINE/CR1 3838 CAGAACTAGGACCAATGGGTGGAAGTTACAGGGAGGCAGATTTCGGCTCA 3887 chr5ptel1M 285934 AAGTCGGAGGAAAGTCTTCCT-CCAG--AGAGGTGACCTCCAGTGAAATG 285980 vi --i iiv i -v i-- v v vvv i i L3#LINE/CR1 3888 ATAT--AAGGAAGAACTTTCTAACAATCAGAGCTGTCCAAAAATGGAATG 3935 chr5ptel1M 285981 GGCTGACT 285988 v L3#LINE/CR1 3936 GGCTGCCT 3943 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 51.13 CpG sites = 56, Kimura (unadjusted) = 52.68 Transitions / transversions = 1.27 (56/44) Gap_init rate = 0.04 (12 / 272), avg. gap size = 3.08 (37 / 12) 216 21.05 0.00 0.00 chr5ptel1M 288003 288040 (711960) MIR3#SINE/MIR 112 149 (59) m_b224s601i13 8812 chr5ptel1M 288003 CCTTGGGCTTCAGTTTTCTCACCAATAAAATGTGGGGG 288040 ii i i i vi v MIR3#SINE/MIR 112 CTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGG 149 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 25.76 CpG sites = 6, Kimura (unadjusted) = 25.76 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 471 27.35 6.50 8.73 chr5ptel1M 289127 289711 (710289) C L1PB1_3end#LINE/L1 (251) 647 75 m_b224s551i3 8813 chr5ptel1M 289127 GTTTTCCTGATTC-TGC-TCATTTCACTTTGTAT--CAGTCTGTACAAGT 289172 -- - v- i i v v --i v-- v C L1PB1_3end#LI 647 GTTTTCC--ATTCCTGAGTTACTTCACTTAGAATAATAGTCTC--CAATT 602 chr5ptel1M 289173 CTTTCCAGGTTTTTCTGAAATTTGCC--T-GTTGATTTC-----ATGG-T 289213 iv ivi vi --- -- -? v i ----- - C L1PB1_3end#LI 601 CCATCCAGGTCGCTGCGAA---TGCCATTANTTCATTCCTTTTTATGGCT 555 chr5ptel1M 289214 GTACAATAATATTCCTTTATATTTCTATACCACAACTTATTCAGTCATTC 289263 --- i i v vi v v ?i v i vi i C L1PB1_3end#LI 554 G---AGTAGTATTCCATGGTATATATATACCACANTTTCTTTATCCACTC 508 chr5ptel1M 289264 CCCAACTGATGGG--TTTCCCCTCAGTTTCCAATATTTTGTCACCCCACA 289311 viii i -- vvv -- v - vv vii-i i C L1PB1_3end#LI 507 GTTGATTGATGGGCATTTGGGCT--GGTTCCA-TATTTTTGCAATT-GCG 462 chr5ptel1M 289312 AAAGG-ACTCCTATAAATATTTTTGCATATTCACATATATGTTTATGTAT 289360 vv -i v i ---- i i v vi v v -i C L1PB1_3end#LI 461 AATTGTGCTGCTATAAACAT----GCGTGTGCAAGTATCTTTTT-CGTAT 417 chr5ptel1M 289361 GAATATCATTTCCTTTTTGCATGATCTCTTTCGGATACAGACTTAGTAGT 289410 - i-- i i i-------- --- i v v ii C L1PB1_3end#LI 416 -AATG--ACTTCTTTTC--------CTCT---GGGTAGATACCCAGTAGT 381 chr5ptel1M 289411 GGTATTGCTGAGTCAAAGTGTA--TGCACTGTCTGGTTGCCCTTTGGGCC 289458 v ii vv -- vi - i i --- ii vv C L1PB1_3end#LI 380 GGGATTGCTGGATCAAATGGTAGTTCTACT-TTTAGTT---CTTTAAGGA 335 chr5ptel1M 289459 TAGTTCCA-ACTATCTCTGAGAATGGTTGGATCAGTTCAGGACT----CC 289503 - vi - i i iiv v i v ii i -v i ---- C L1PB1_3end#LI 334 -ATCTCCACACTGTTTTCCATAGTGGTTGTACTAGTTTA-CATTCCCACC 287 chr5ptel1M 289504 AACAATGCCTTAG--GTGTTTCAGTTTTTC-CTGT-----CTTCAACATT 289545 i i --- -- i --i - i i----- vi i C L1PB1_3end#LI 286 AGCAGTG---TAGAAGTGTTCC--CTTTTCACCGCATCCACGCCAACATC 242 chr5ptel1M 289546 TATCACTTAATTT--TTTTTTTCTTATTGCCCAATCTGATAGGTGTGAGG 289593 i i -- -- vv - v v vii v i C L1PB1_3end#LI 241 TATTATTT--TTTGATTTTTTGATTA-TGGCCATTCTTGCAGGAGTAAGG 195 chr5ptel1M 289594 TGGTATCTCAAAGTTGTTTTAATTTGCATTTCTCTAATCA--AGTGATTT 289641 v vv v i i i -- v C L1PB1_3end#LI 194 TGGTATCGCATTGTGGTTTTGATTTGCATTTCCCTGATCATTAGTGATGT 145 chr5ptel1M 289642 GGAGCACTACTCCATATGTCCAGAGAAAGC--TTTGATTATTTTA-TTTG 289688 v i vi i iiivv --- -- vv i v- C L1PB1_3end#LI 144 TGAGCATTTTTTCATATGTTTGTTG---GCCATTTGTATATCTTCTTTTG 98 chr5ptel1M 289689 AAATCTGCCTGCTCATATCTTTA 289711 i vi i ii i i C L1PB1_3end#LI 97 AGAATTGTCTATTCATGTCCTTA 75 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 33.07 CpG sites = 83, Kimura (unadjusted) = 34.82 Transitions / transversions = 1.32 (83/63) Gap_init rate = 0.12 (69 / 584), avg. gap size = 1.28 (88 / 69) 641 30.27 4.07 7.34 chr5ptel1M 289219 289710 (710290) C L1ME3Cz_3end#LINE/L1 (449) 548 72 m_b224s551i4 8813 chr5ptel1M 289219 ATAATATTCCTTTATATTTCTATACCACAACTTATTCAGTCATTCCCCAA 289268 i v i vvv i i vi v C L1ME3Cz_3end# 548 ATAGTATTCCATTGTATGAATATACCACAATTTATTTATCCATTCCCCTA 499 chr5ptel1M 289269 CTGATGGG--TTTCCCCTCAGTTTCCAATATTTTGTCACCCCACAAAAGG 289316 i i-- vvvi -- v i ii iiv v v v C L1ME3Cz_3end# 498 TTGATGGACATTTAGGTT--GTTTCCAATTTTTCGCTATTACAAACAATG 451 chr5ptel1M 289317 ACTCCTATAAATATTTTTGCATATTCACATATATGTTTATGTATGAATAT 289366 - v v i i ii ---------- i i viv i v i C L1ME3Cz_3end# 450 -CTGCAATGAACATCCTTG----------TACATGTCTCCTTGTGCACAT 412 chr5ptel1M 289367 CATTTCCTTTTTGCATGA-TCTCTTTCGGATACAGACTTAGTAGTGGTAT 289415 v---------- iv - i i v i i v i v v C L1ME3Cz_3end# 411 G----------TGCGAGAGTTTCTCTAGGGTATATACCTAGAAGTGGAAT 372 chr5ptel1M 289416 TGCTGAGTCAAAGTGTATGCACTGTCTGGTTGCCCTT--TGGGCCTAGTT 289463 i iv v i -i -- iiv i -- i i-- v v C L1ME3Cz_3end# 371 TGCTGGGTCGTAGGGTATGCGC-ATCT--TCAACTTTACTAGA--TATTG 327 chr5ptel1M 289464 CCAACTATCTCTG-AGAATGGTTGGATCAGTTCAGGACTCC----AACAA 289508 v vv v- i i v i i i v- ---- i i C L1ME3Cz_3end# 326 CCAAATTGCTCTCCAAAGTGGTTGTACCAATTTAC-ACTCCCACCAGCAG 278 chr5ptel1M 289509 TGCCTTAGGTGTTTCAGTTTTTCC-TGTCTTCAACATTTATCACTTAATT 289557 iv v i- i v i -ii i iv --- - ii v C L1ME3Cz_3end# 277 TGTATGAGA-GTTCCCGTTTCTCCACATCCTCGCCA---A-CACTTGGTA 233 chr5ptel1M 289558 TTTT-----TTTTC--TTATTGCCCAATCTGATAGGTGTGAGGTGGTATC 289600 v ----- v-- v - i ii C L1ME3Cz_3end# 232 TTGTCAGACTTTTAAATTTTTGCC-AATCTGATGGGTGTGAAATGGTATC 184 chr5ptel1M 289601 TCAAAGTTGTTTTAATTTGCATTTCTCTAATCA--AGTGATTTGGAGCAC 289648 vv ? i i i -- vv v i C L1ME3Cz_3end# 183 TCATTGTNGTTTTAATTTGCATTTCCCTGATTACTAGTGAGGTTGAGCAT 134 chr5ptel1M 289649 TACTCCATATGTCCAGAGAAAGCTTTGATTATTTTATTTGAAATCTGCCT 289698 ivi i ii vv ivvii iv i vii iv i vi vi C L1ME3Cz_3end# 133 CTTTTCATATGTTTATTGGCCATTCGGGTTTCCTCTTCTGTGAATTGCCT 84 chr5ptel1M 289699 GCTCATATCTTT 289710 i i C L1ME3Cz_3end# 83 GTTCATATCCTT 72 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 37.58 CpG sites = 79, Kimura (unadjusted) = 39.79 Transitions / transversions = 1.34 (79/59) Gap_init rate = 0.09 (44 / 491), avg. gap size = 1.25 (55 / 44) 511 29.86 6.60 2.80 chr5ptel1M 289387 289765 (710235) C L1PA13_3end#LINE/L1 (506) 404 12 m_b224s551i5 8813 chr5ptel1M 289387 TCTTTCGGATACAGACTTAGTAGTGGTATTGCTGAGTCAAAGTGTATGCA 289436 i i i i v ii i v i i vv vi- C L1PA13_3end#L 404 TCCTTTGGGTATATACCCAGTAATGGGATTGCTGGGTCGAATGGTATTT- 356 chr5ptel1M 289437 CTGTCTGGTT-GCCCTTTG-GGCCTAGTTCCA-ACTATCTCTGAGAATGG 289483 -- - vi - vv v -- - i iiv v C L1PA13_3end#L 355 CTGTCT--TTAGGTCTTTGAGGAATCG--CCACACTGTCTTCCACAATGG 310 chr5ptel1M 289484 TTGGATCAGTTCAGGACTCC----AACAATGCCTTAGGTGTTTCAGTTTT 289529 i ii i i v- ---- i iv - i i i vv i C L1PA13_3end#L 309 TTGAACTAATTTAC-ACTCCCACCAACAGTGTAT-AAGCGTTCCTTTTTC 262 chr5ptel1M 289530 TCC----TGTCTTCAACATTTATCACTTAATTTT--TTTTTTCTTATTGC 289573 ----iv vi i i i i i --- --i vv v iv C L1PA13_3end#L 261 TCCGCAACCTCGCCAGCATCTGTTATTT---TTTGACTTTTTAATAATAG 215 chr5ptel1M 289574 CCAATCTGATAGGTGTGAGGTGGTATCTCAAAGTTGTTTTAATTTGCATT 289623 v iv i vv v i C L1PA13_3end#L 214 CCATTCTGACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATT 165 chr5ptel1M 289624 TCTCTAATCA--AGTGATTTGGAGCACTACTCCATATGTCCAGAGAAAGC 289671 v -- v v vi vi i viiivv ivv C L1PA13_3end#L 164 TCTCTAATGATCAGTGATGTTGAGCTTTTTTTCATATGATTGTTGGCCGC 115 chr5ptel1M 289672 TTTGATTATTTTATTTGAAATCTGCCTGCTCATAT-CTTTATC------- 289713 v vv vvi iv vv i i i - ii ------- C L1PA13_3end#L 114 ATGTATGTCTTCTTTTGAAAAGTGTCTGTTCATGTCCTTTGCCCACTTTT 65 chr5ptel1M 289714 TAGTGGGAAAATAATTTTTATTCTTTTAAATTATGCTTATATTTC--ATA 289761 i ivvi vvv v v - i vi i -- C L1PA13_3end#L 64 TAATGGGGTTGTTTGTTTTTTTCTTGTAAATT-TGTTTAAGTTCCTTATA 16 chr5ptel1M 289762 AATG 289765 i C L1PA13_3end#L 15 GATG 12 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 37.90 CpG sites = 58, Kimura (unadjusted) = 38.79 Transitions / transversions = 1.12 (58/52) Gap_init rate = 0.06 (21 / 378), avg. gap size = 1.71 (36 / 21) 227 28.82 9.90 2.43 chr5ptel1M 290088 290279 (709721) C L1P1_orf2#LINE/L1 (474) 2820 2615 m_b224s551i6 8814 chr5ptel1M 290088 CCCGTTTTCCCAGTT---TTTCTGAAATAGTGAGTTCTTACCCCAGAA-- 290132 v iv--- v v v i i v vvi-- C L1P1_orf2#LIN 2820 CCAGTTTTCCCAGCACCATTTATTAAATAGGGAATCCTTTCCCCATTGCT 2771 chr5ptel1M 290133 -GTCTTT---GGGTTTATCAAACAGTAGATTACTATAGTCTTTTACTATT 290178 - i ---i i v vi vii i viv viivii C L1P1_orf2#LIN 2770 TGTTTTTCTCAGGTTTGTCAAAGATCAGATAGTTGTAGATATGCGGCGTT 2721 chr5ptel1M 290179 ATATCTTATGGATCTAATTTCTTTCACTGATTCACTATTTCT----TGG- 290223 v v v v iv i v i i ii - i ---- - C L1P1_orf2#LIN 2720 ATTTCTGAGGGCTCTGTTCTGTTCCATTGATCTA-TATCTCTGTTTTGGT 2672 chr5ptel1M 290224 -CCAGTACCA-GATGACTTTGATGGTTACT---GCTTTATACTGTAGTTT 290268 - - v -- -- --- i i v i C L1P1_orf2#LIN 2671 ACCAGTACCATGCTG--TTT--TGGTTACTGTAGCCTTGTAGTATAGTTT 2626 chr5ptel1M 290269 TAGATCTGATA 290279 v ii v i C L1P1_orf2#LIN 2625 GAAGTCAGGTA 2615 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 35.23 CpG sites = 29, Kimura (unadjusted) = 37.11 Transitions / transversions = 1.16 (29/25) Gap_init rate = 0.07 (14 / 191), avg. gap size = 1.71 (24 / 14) 13 9.08 0.00 4.00 chr5ptel1M 290458 290483 (709517) (CCCT)n#Simple_repeat 1 25 (0) m_b224s252i12 8815 chr5ptel1M 290458 CCCTCTCTCCCTCCACCCCCTCCCTC 290483 i - i (CCCT)n#Simpl 1 CCCTCCCTCCCTCC-CTCCCTCCCTC 25 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.04 (1 / 25), avg. gap size = 1.00 (1 / 1) 1356 29.33 4.11 2.59 chr5ptel1M 290796 291404 (708596) C L1ME4c_3end#LINE/L1 (191) 639 22 m_b224s551i7 8816 chr5ptel1M 290796 TTCTGCTCATTTCACTCAGCATCAGTTCATGTAAGTCTCTCCAAGTCTCT 290845 iv i i i vv iv vi i - v iv C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATAAACATTT-TCCATGTTGCT 591 chr5ptel1M 290846 CT---GTCTTCATCCTGCTGGTCATTTCTTACAGAACAATAATATTCTAT 290892 vi--- ---iv vi i v ii vvvv i C L1ME4c_3end#L 590 ACATAGTCTTCAT---AATTATCATTTTTAATGGCTGCATAATATTCCAT 544 chr5ptel1M 290893 AACATTCATATGCCACAATTTACCCAACCATTCTCCAATTGATGGGCATC 290942 vivi ?v i i i ii i v v i i C L1ME4c_3end#L 543 CGAGTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATT 494 chr5ptel1M 290943 CA--TTCATTTTCTGGTTTCTAGCCACTACAAACAGGGCTGCCGCAAACA 290990 i -- v-- iii i v i i i i iv viii C L1ME4c_3end#L 493 TAGGTTG--TTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACA 446 chr5ptel1M 290991 TTTTGGCACATACAGGTCCCTTTTCCTTCTTT---AGTATCTCTTTGGGG 291037 i v ii i --- i --- v i i i i C L1ME4c_3end#L 445 TCTTCGTGCATATAG---CTTTTTCCTTCTTTTGAATTATTTCCTTAGGA 399 chr5ptel1M 291038 TATAAGCCCAGTAGTAACACTGCTGGCTCAAAGGGTATGCACGGTTTGAT 291087 v vv v iiv i i v v iv v C L1ME4c_3end#L 398 TAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTAT 349 chr5ptel1M 291088 AATTTTTGGGGCATAATTCCAGATTGCTCTCCAGAATGGTTGGATTTGTT 291137 iii i ivi i v v i i i v v iivi C L1ME4c_3end#L 348 GGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATT 299 chr5ptel1M 291138 CACAACTCCACCAACAATGCATCAGTGTCCCAGTTT-------TCCTT-C 291179 i ?iv i i v ? v -------? i- C L1ME4c_3end#L 298 TACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGC 249 chr5ptel1M 291180 CAATATT---CATCATTATTTTTTCCTGTCATCTTAGTTGATCTGACAGG 291226 ii ---i i i v iv---v i v i i i i i C L1ME4c_3end#L 248 CAGCATTGGGTATTATCAATTTTTTA---AATTTTTGCTAATTTAATAGG 202 chr5ptel1M 291227 GGTGTAGTGGTATCTCAGAGTTGTCTTAATTTGCATTTCTCTGATCAATA 291276 v iv i vv ii i i v C L1ME4c_3end#L 201 CGTAAAATGGTATCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACTA 152 chr5ptel1M 291277 ATGATTTGGAACACTTT--CATACGAGTGGTAATAGTTTCAATTTCATCA 291324 ii vv v i -- ii vv v v ivi? vv v v C L1ME4c_3end#L 151 GCGAGGTTGAACATTTTTCCATGTGTTTGTTTACTANTTGTATTTCCTCT 102 chr5ptel1M 291325 ATTGAAAATTGTCTGTTCATATCCTTTGACCATTTATCAATTGGAGAATG 291374 v? vi i v v i---- C L1ME4c_3end#L 101 TNTGTGAATTGTCTGTTCATGTCCTTTGCCCATTTATCTATTGGG----G 56 chr5ptel1M 291375 GCTTGA----TTTCTTATAAATTAGAGTCAATTC 291404 v ---- v v i v ii C L1ME4c_3end#L 55 TCTTGATNTTTTTCTTATCAATTTGAATGAGCTC 22 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 37.61 CpG sites = 101, Kimura (unadjusted) = 38.75 Transitions / transversions = 1.38 (101/73) Gap_init rate = 0.04 (24 / 608), avg. gap size = 1.71 (41 / 24) 185 17.24 0.00 0.00 chr5ptel1M 292450 292478 (707522) C MIRb#SINE/MIR (29) 239 211 m_b224s601i14 8817 chr5ptel1M 292450 TATTATGTGCCAGGTGCTGTGTTAAGTGC 292478 i ii i i C MIRb#SINE/MIR 239 TACTATGTGCCAGGCACTGTGCTAAGCGC 211 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 16.62 CpG sites = 5, Kimura (unadjusted) = 21.14 Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 12 18.79 5.77 3.77 chr5ptel1M 293300 293351 (706649) (GCCCTCT)n#Simple_repeat 1 53 (0) m_b224s252i13 8818 chr5ptel1M 293300 GCCTTTTG-CCTCTGCCCT-GGTCCTC-CCCCTCTACTCCCTCTGCCCTT 293346 i i - -v i -v --v i (GCCCTCT)n#Si 1 GCCCTCTGCCCTCTGCCCTCTGCCCTCTGCCCTCT--GCCCTCTGCCCTC 48 chr5ptel1M 293347 TCCCC 293351 v (GCCCTCT)n#Si 49 TGCCC 53 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.10 (5 / 51), avg. gap size = 1.00 (5 / 5) 12 19.72 0.00 5.41 chr5ptel1M 293678 293716 (706284) (AATAAAT)n#Simple_repeat 1 37 (0) m_b224s252i14 8819 chr5ptel1M 293678 AATAATTATTTTTTAAGTAAATAATAAATAAAAGAATAA 293716 v v vvv - v - (AATAAAT)n#Si 1 AATAAATAATAAATAA-TAAATAATAAATAATA-AATAA 37 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2) 13 15.51 3.33 0.00 chr5ptel1M 293847 293876 (706124) (TTCCC)n#Simple_repeat 1 31 (0) m_b224s252i15 8820 chr5ptel1M 293847 TTCCCTT-CTTTCTCTTCTCCTCCCTTCCCT 293876 - i i i i (TTCCC)n#Simp 1 TTCCCTTCCCTTCCCTTCCCTTCCCTTCCCT 31 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 208 34.44 5.33 1.28 chr5ptel1M 294089 294238 (705762) C L2#LINE/L2 (1532) 1550 1395 m_b224s601i15 8821 chr5ptel1M 294089 GGGAGCTCCTGGAGGATGCCCT-TAACTGTTTTT--TTTTTCAA--AAAT 294133 ??iv i v vi i - i i i i -- i i-- C L2#LINE/L2 1550 GGGAGNNTGTGGAAGTTCTCTTCTGATTGCTTCTATTTTCTCAGTGAAAT 1501 chr5ptel1M 294134 GAGGTATAAAGTTCTTAGTTGACAG---AGTTGAGGGAGGAAAGCAATGA 294180 ii ivii i iv i i v ---i v ii i- iiv i C L2#LINE/L2 1500 AGGAAGCAAGGTCATCAGCTGAGAGTGAGGATAGGGGAGGAG-GTGTTGG 1452 chr5ptel1M 294181 AAGGATTGAGGAGGGGTGAGCAGGTTTGGGAGATCTGCTGCGGAGAGTGG 294230 - v i iv v v ii v vii iivv C L2#LINE/L2 1451 A-GGTTTGAGGAGAGAGGAGAAGGTGTGAAATAGTCGTCTAGGAGAGTGG 1403 chr5ptel1M 294231 GTGAGTGA 294238 v C L2#LINE/L2 1402 GAGAGTGA 1395 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 48.81 CpG sites = 34, Kimura (unadjusted) = 50.26 Transitions / transversions = 2.00 (34/17) Gap_init rate = 0.04 (6 / 149), avg. gap size = 1.67 (10 / 6) 284 9.76 0.00 0.00 chr5ptel1M 296166 296206 (703794) MIRc#SINE/MIR 75 115 (153) m_b224s601i16 8822 chr5ptel1M 296166 CACTTCCTAGCTGTGTGATCCTGGGCCAGTCACTTAACCTC 296206 v i i v MIRc#SINE/MIR 75 CACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 10.48 CpG sites = 2, Kimura (unadjusted) = 10.48 Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 350 29.89 9.29 2.00 chr5ptel1M 296199 296213 (703787) C MIRc#SINE/MIR (115) 153 142 m_b224s601i17 8823 chr5ptel1M 296199 TTAACCTCAATTGCC 296213 v i v --- C MIRc#SINE/MIR 153 TTATCCCCATTT--- 142 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 39.30 CpG sites = 22, Kimura (unadjusted) = 39.30 Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.21 (3 / 14), avg. gap size = 1.00 (3 / 3) 50 3.73 1.82 0.00 chr5ptel1M 296214 296268 (703732) (AT)n#Simple_repeat 1 56 (0) c_b224s251i2 8824 chr5ptel1M 296214 ATATATATATATATATATATATATATATATATATATATCTA-ATACATAT 296262 v - i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr5ptel1M 296263 ATATAT 296268 (AT)n#Simple_ 51 ATATAT 56 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1) 350 29.89 9.29 2.00 chr5ptel1M 296269 296392 (703608) C MIRc#SINE/MIR (127) 141 5 m_b224s601i17 8823 chr5ptel1M 296269 GCATATGAGGAAGCTGAGGCTGAAAGCAGTTAAGTCATTTGTCCAAAGGA 296318 i v i v i vi v i i i vv C MIRc#SINE/MIR 141 ACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTC 92 chr5ptel1M 296319 A-AT-----GTGAAGGGCAGAACCG-------AACTCTGCTCTTCTAGAC 296355 - i----- i iv i ------- i v v iv C MIRc#SINE/MIR 91 ACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGAC 42 chr5ptel1M 296356 TCCAAATCTGGGCCTCTAACTGTTTTGCCACAATTCC 296392 i ii vv vv iii vii v v C MIRc#SINE/MIR 41 TCCAAGTCCAGTGCTCTTTCCACTGCACCACACTGCC 5 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 39.30 CpG sites = 22, Kimura (unadjusted) = 39.30 Transitions / transversions = 1.24 (21/17) Gap_init rate = 0.02 (3 / 123), avg. gap size = 4.33 (13 / 3) 252 18.91 2.65 5.44 chr5ptel1M 297751 297901 (702099) HERVIP10FH#LTR/ERV1 852 998 (4104) m_b225s701i0 8825 chr5ptel1M 297751 AGAGAGAGTCAGAGAGACAGAGAGAGAAGCAGAGACAGAG--AAACAGAG 297798 i vv iv ii i vi -- v HERVIP10FH#LT 852 AGAAAGAGAGAGAGAGGGAGAGAGAGAGACAAAGAGGGAGTCAAAGAGAG 901 chr5ptel1M 297799 AGAGAGACAGAGAGAGAAAGAAACAGATAGAGGGACATAGAGAGAAACAG 297848 i i ---- i i v i iv HERVIP10FH#LT 902 AGAGAGGCAGAGAGAGGAAG----AGACAGAGAGACAAAGAGGGAGTCAG 947 chr5ptel1M 297849 AGACAAAGAGAGAGTGAAGCAGAAA--CAGAGAAAGAAACAGAGACAGAG 297896 ---- v ii -- i i v i v HERVIP10FH#LT 948 AG----AGAGAGAGAGAGACAGAAAGTCAAAGAGAGAAAGAAAGAGAGAG 993 chr5ptel1M 297897 ATAGA 297901 HERVIP10FH#LT 994 ATAGA 998 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 22.15 CpG sites = 17, Kimura (unadjusted) = 22.15 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.07 (10 / 150), avg. gap size = 1.20 (12 / 10) 224 22.16 1.29 1.29 chr5ptel1M 297902 298442 (701558) (GAGAGA)n#Simple_repeat 1 541 (0) m_b225s252i0 8826 chr5ptel1M 297902 GAAAGAAACAGAGAGAGGGACAGAGAGAGAAAGAAACAGGGACAAAGAGA 297951 i i v i v i i v i v i (GAGAGA)n#Sim 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr5ptel1M 297952 GAGAGAGA-AAAGCAGAAACAGAGACAGAGATAGAGAAAGAAACAGAGAG 298000 - i - i v v v i i v (GAGAGA)n#Sim 51 GAGAGAGAGAGAG-AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 99 chr5ptel1M 298001 AGGGACAGACAGAGAAAGAAACAGACACACAGAGAGA-AGCAGAAACATG 298049 i v v i i v v v v - - i v - (GAGAGA)n#Sim 100 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG-AGAGAGA-G 147 chr5ptel1M 298050 AAACAGAGACAGCGATAGAGAAAGAAACGGACACACAGAGAGA-AGCAGA 298098 i v v v v i i vi v v v - - (GAGAGA)n#Sim 148 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG-AGA 196 chr5ptel1M 298099 GAGAGAAAGAAACAGAGACAGAGATAGAGAAAGAAACAGAGAGAGGGACA 298148 i i v v v i i v i v (GAGAGA)n#Sim 197 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 246 chr5ptel1M 298149 CAGAGAGAGAAAGAAACAGAGACAAAGAGAGAAAGAGATAGACACACAGA 298198 v i i v v i i v v v v (GAGAGA)n#Sim 247 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 296 chr5ptel1M 298199 CAGACAGAGAGAAAGAAACAGAGACAAAGAGAGAGAGA-AGCAGAGGCAG 298247 v v i i v v i - - iv (GAGAGA)n#Sim 297 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG-AGAGAGAG 345 chr5ptel1M 298248 AGAAAGAAACAGAGAGAAGGACACACAGAGAGA-AGCAGAGACAGAGAGA 298296 i i v ii v v v - - v (GAGAGA)n#Sim 346 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG-AGAGAGAGAGAGA 394 chr5ptel1M 298297 -ACAGAAAGAGGGACAGAGAGAGAAAGAAACAGACAAAGAGCGAGTCAGA 298345 - v i i v i i v v i v vv (GAGAGA)n#Sim 395 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 444 chr5ptel1M 298346 GAGACAGAGAAAGAGA-AGCAAAGACAGAAAGAAAGACAGAGAGAGAGAG 298394 v i - - i v i i v (GAGAGA)n#Sim 445 GAGAGAGAGAGAGAGAGAG-AGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 493 chr5ptel1M 298395 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAAG 298442 i (GAGAGA)n#Sim 494 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 541 Matrix = Unknown Transitions / transversions = 0.84 (46/55) Gap_init rate = 0.03 (14 / 540), avg. gap size = 1.00 (14 / 14) 422 29.48 12.21 1.27 chr5ptel1M 298988 299200 (700800) MIRc#SINE/MIR 32 267 (1) m_b225s601i3 8827 chr5ptel1M 298988 GGATTTGGATTCAGAAAGATGTGAATTTG-GTCTC---TCTGTAGAGGTT 299033 i v i iv ii i - i --- iviv-- MIRc#SINE/MIR 32 GGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCAC--TT 79 chr5ptel1M 299034 TTTATTTAGGTAATCCTAGGTAAATGAC--AATCTCTCCT--CCTCATTT 299079 vi vi iv i i i i i i v -- i iv-- v MIRc#SINE/MIR 80 ACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTT 129 chr5ptel1M 299080 TCCTCAGCTATAAAATGAGAGAGAAGAGT---------GGCTATCATATA 299120 v i i - v v i --------- v i vi i MIRc#SINE/MIR 130 TCCTCATCTGTAAAATGGG-GATAATAATACCTGCCCTGCCTACCTCACA 178 chr5ptel1M 299121 GGGTTGTTGTGAGGAT---ATTAGGTGATGTAT---AAACTTATTTACAT 299164 --- v i i --- vivv ii v MIRc#SINE/MIR 179 GGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTTTGTAA 228 chr5ptel1M 299165 ACCCTAAACCCATAGATAAATAT---GATTTATTCTTAT 299200 iv vivv v i i --- ?v v MIRc#SINE/MIR 229 ACTGTAAAGTGCTATACAAATGTAAGGNGTTATTATTAT 267 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.08 CpG sites = 35, Kimura (unadjusted) = 38.66 Transitions / transversions = 1.30 (35/27) Gap_init rate = 0.05 (11 / 212), avg. gap size = 2.64 (29 / 11) 296 27.95 0.85 8.26 chr5ptel1M 299343 299459 (700541) L2c_3end#LINE/L2 351 459 (19) m_b225s601i4 8828 chr5ptel1M 299343 TTTATGTGT-TATCTTGCCTTTATTAGACTGAAAACTCATTGAGGGCAGG 299391 i? - i -- ii i vi i v L2c_3end#LINE 351 TTTACNTGTCTGTCT--CCTCCACTAGACTGTGAGCTCCTTGAGGGCAGG 398 chr5ptel1M 299392 AACCCTCTGGCTTCCTTGCCTGTGTATAGCCAGGGCAGTTTTCAGAGTCT 299441 i v -- v vi iii v vv v --i vv v --- L2c_3end#LINE 399 GACCGT--GTCTTATTCATCTTTGTATCCCCAGCGC--CTGGCACA---T 441 chr5ptel1M 299442 AATAGGCATGTAATAAAT 299459 i iivi L2c_3end#LINE 442 AGTAGGCGCTCAATAAAT 459 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.41 CpG sites = 17, Kimura (unadjusted) = 35.88 Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.09 (10 / 116), avg. gap size = 1.00 (10 / 10) 193 26.70 26.80 2.11 chr5ptel1M 299638 299790 (700210) C MIRc#SINE/MIR (47) 221 32 m_b225s601i5 8829 chr5ptel1M 299638 GTGCTTT-ACGAAGATGATCTTATTTGGTCCTCAGA--AGCCTCAGGAGG 299684 i - iv v v i i v -- i iiiv C MIRc#SINE/MIR 221 GCGCTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGG 172 chr5ptel1M 299685 GAAGCGAGG----------------CATTTTACTGGAGGGAAGGACAAGG 299718 v i ii ---------------- --- ivi v vv C MIRc#SINE/MIR 171 TAGGCAGGGCAGGTATTATTATCCCCATTTTAC---AGATGAGGAAACTG 125 chr5ptel1M 299719 AGGC----AAACGCTGAGTGACCTTACCTGGGGTCACAC----------T 299754 ---- i v i i - i iii ---------- C MIRc#SINE/MIR 124 AGGCTCAGAGAGGTTAAGTGA-CTTGCCCAAGGTCACACAGCTAGTAAGT 76 chr5ptel1M 299755 GGCAGCAC-----TTAGAATTCTGGCCT---TAACTCCAAGTCC 299790 vi -----i v ii v i --- i C MIRc#SINE/MIR 75 GGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCC 32 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.39 CpG sites = 26, Kimura (unadjusted) = 34.46 Transitions / transversions = 1.86 (26/14) Gap_init rate = 0.07 (11 / 152), avg. gap size = 4.09 (45 / 11) 217 28.79 7.69 5.00 chr5ptel1M 300732 300848 (699152) C MIR#SINE/MIR (99) 163 44 m_b225s601i6 8830 chr5ptel1M 300732 GGCAGATACTGGAGTGTATCTCCAGCTTAATTTACAGATGAGGAGCCTGA 300781 i i ivvi - i v----- iv C MIR#SINE/MIR 163 GGTAGGTACTATTAT-TATCCCCAT-----TTTACAGATGAGGAAACTGA 120 chr5ptel1M 300782 AG--CAGA---GCTGGGTGACTGGCTTAGGGACACACTGCCACTGATT-- 300824 i -- --- i ii i v ii i v v i v i v -- C MIR#SINE/MIR 119 GGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGG 70 chr5ptel1M 300825 --GAGCTTAGATTTGACCACAGGAAG 300848 -- ivi i v v v C MIR#SINE/MIR 69 CAGAGCCGGGATTCGAACCCAGGCAG 44 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.52 CpG sites = 19, Kimura (unadjusted) = 37.43 Transitions / transversions = 1.46 (19/13) Gap_init rate = 0.09 (10 / 116), avg. gap size = 1.50 (15 / 10) 222 26.31 9.35 7.04 chr5ptel1M 300757 300895 (699105) C MIR3#SINE/MIR (63) 145 4 m_b225s601i7 8830 chr5ptel1M 300757 CTTAATTTACAGATGAGGAGCCTGAAGC----AGAGCTG-GGTGACTGGC 300801 i v iv i ---- v -i v C MIR3#SINE/MIR 145 CTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGC 96 chr5ptel1M 300802 TTAGGGACACACTGCC----ACTGATTGAGCTTAGATTTGACCACAGGAA 300847 ii i v v ?---- v iiv ivi i v v v --- C MIR3#SINE/MIR 95 CCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAG--- 49 chr5ptel1M 300848 GAAGAGTCTGCCTTACCCTCA-TCC---CTCACTCCATCCTACCCACTGT 300893 ----- - v i i - --- v ii- ii v v C MIR3#SINE/MIR 48 -----GTCT-CCTGACTCCCAGTCCGTGCTCTCTCTG-CTCAGCCACTCT 6 chr5ptel1M 300894 GC 300895 C MIR3#SINE/MIR 5 GC 4 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.09 CpG sites = 18, Kimura (unadjusted) = 33.26 Transitions / transversions = 1.12 (18/16) Gap_init rate = 0.11 (15 / 138), avg. gap size = 1.53 (23 / 15) 201 29.56 6.58 10.96 chr5ptel1M 300762 300913 (699087) C MIRb#SINE/MIR (122) 146 1 m_b225s601i9 8830 chr5ptel1M 300762 TTTACAGATGAGGAGCCTGAAG--CAGA---GCTGGGTGACTGGCTTAGG 300806 iv i -- --- i ii i v ii i C MIRb#SINE/MIR 146 TTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAG 97 chr5ptel1M 300807 GACACACTGCCACTGATT----GAGCTTAGATTTGACCACAGGAAGAAGA 300852 v v i v i v ---- ivi i v v -------- C MIRb#SINE/MIR 96 GTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAG-------- 55 chr5ptel1M 300853 GTCTGCCTTAC-CCTCATCCCTCACTCCATCCTACCCACTGTGCAGTTTA 300901 i v - vv v vii ----- vi ii vii--- C MIRb#SINE/MIR 54 GTCTGTCTGACTCCAAAGCCCGTGCT-----CTTTCCACTGCACCAC--- 13 chr5ptel1M 300902 GCTACCCCTTTG 300913 i i C MIRb#SINE/MIR 12 GCTGCCCCTCTG 1 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.89 CpG sites = 24, Kimura (unadjusted) = 38.51 Transitions / transversions = 1.50 (24/16) Gap_init rate = 0.13 (20 / 151), avg. gap size = 1.30 (26 / 20) 225 27.38 10.71 0.00 chr5ptel1M 300762 300845 (699155) C MIRc#SINE/MIR (125) 143 51 m_b225s601i8 8830 chr5ptel1M 300762 TTTACAGATGAGGAGCCTGAAG--CAGA---GCTGGGTGACTGGCTTAGG 300806 iv i -- --- i ii v ii i C MIRc#SINE/MIR 143 TTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAG 94 chr5ptel1M 300807 GACACACTGCCACTGATT----GAGCTTAGATTTGACCACAGG 300845 v v i v i v ---- ivi i i v v C MIRc#SINE/MIR 93 GTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGG 51 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.37 CpG sites = 14, Kimura (unadjusted) = 35.06 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.04 (3 / 83), avg. gap size = 3.00 (9 / 3) 379 27.36 2.08 1.03 chr5ptel1M 301228 301323 (698677) MIR#SINE/MIR 86 182 (80) m_b225s601i10 8831 chr5ptel1M 301228 TAATCCTGAGCAAGTCCCTTA--CTCCCGTTTCTCTCAGTTTCCTCAAGT 301275 i i i i iv -- i - v vi vv MIR#SINE/MIR 86 TGACCTTGGGCAAGTTACTTAACCTCTC-TGTGCCTCAGTTTCCTCATCT 134 chr5ptel1M 301276 GTAAAATGGAAACAATGACAGAATTTACCTTGCAGGGTTTTTGTAAAG 301323 ii i i i v ii iii v i i MIR#SINE/MIR 135 GTAAAATGGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGG 182 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.08 CpG sites = 19, Kimura (unadjusted) = 36.08 Transitions / transversions = 2.71 (19/7) Gap_init rate = 0.02 (2 / 95), avg. gap size = 1.50 (3 / 2) 467 25.07 13.00 2.26 chr5ptel1M 301750 301949 (698051) C L2a_3end#LINE/L2 (2) 515 295 m_b225s601i12 8832 chr5ptel1M 301750 TCATTCAATCAACCAACATTTATTAAGCATCT-C--TGTATCAGGCACTG 301796 v v i i ii - -- ii C L2a_3end#LINE 515 TCATTCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTG 466 chr5ptel1M 301797 TGACAA--GCTGGGGATACA---------AAAAGAGGCAAAAGCCAGTCT 301835 vvi i-- --------- v i i --i C L2a_3end#LINE 465 TTCTAGGCGCTGGGGATACAGCAGTGAACAAAACAGACAAAAGTC--CCT 418 chr5ptel1M 301836 GTCTTCAAGGAACTTACATTCTCATAAGGG-----AGACAACATGCAAAC 301880 i i v i vi ii ----- i vi i C L2a_3end#LINE 417 GCCCTCATGGAGCTTACATTCTAGTGGGGGGAGACAGACAATAAACAAAT 368 chr5ptel1M 301881 AAATACAGACAAAAATA------ATCAGAGAGGGAAAAACACTAAGGTGA 301924 - vv v ------i vi v v iii v v C L2a_3end#LINE 367 AAATA-AGTAAAATATATAGTATGTCAGATGGTGATAAGTGCTATGGAGA 319 chr5ptel1M 301925 AAATTTGGAAGT-GACTAAAAAGGAT 301949 v --i i- iv iii C L2a_3end#LINE 318 AAAAT--AAAGCAGGGTAAGGGGGAT 295 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 30.73 CpG sites = 31, Kimura (unadjusted) = 31.51 Transitions / transversions = 1.72 (31/18) Gap_init rate = 0.06 (12 / 199), avg. gap size = 2.58 (31 / 12) 473 22.33 8.23 3.64 chr5ptel1M 301750 301907 (698093) C L2b_3end#LINE/L2 (2) 464 300 m_b225s601i11 8832 chr5ptel1M 301750 TCATTCAATCAACCAACATTTATTAAGCATCT-CTGTAT--CAGGCACTG 301796 v v i i i ii - i -- ? C L2b_3end#LINE 464 TCATTCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTG 415 chr5ptel1M 301797 TGACAAGC--TGGGGATACAA----AAAGAGGCAAAAGCCAGTC--TGTC 301838 vi i -- i----i v i vv i v? i -- i C L2b_3end#LINE 414 TGCTAGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCC 365 chr5ptel1M 301839 TTCAAGGAACTTACATTCTCATAAGGGAGACA-ACATGCAAACAAATACA 301887 i v i i v vi ii - i ------? C L2b_3end#LINE 364 CTCACGGAGCTCACAGTCTAGTGGGGGAGACAGACATGTAA------NCA 321 chr5ptel1M 301888 GACAAAAATAA-TCAGAGAGG 301907 v? -i v C L2b_3end#LINE 320 GACAATNATAACCCAGAGTGG 300 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.28 CpG sites = 22, Kimura (unadjusted) = 28.19 Transitions / transversions = 1.83 (22/12) Gap_init rate = 0.08 (13 / 157), avg. gap size = 1.46 (19 / 13) 23 3.01 0.00 5.56 chr5ptel1M 302035 302072 (697928) (GTTTTT)n#Simple_repeat 1 36 (0) m_b225s252i2 8833 chr5ptel1M 302035 GTTTTTTTTTTTGTTTGTTTGTTTTTGTTTTTGTTTTT 302072 v - - (GTTTTT)n#Sim 1 GTTTTTGTTTTTG-TT-TTTGTTTTTGTTTTTGTTTTT 36 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 15 25.52 0.00 0.00 chr5ptel1M 302122 302158 (697842) (TT)n#Simple_repeat 1 37 (0) m_b225s252i5 8834 chr5ptel1M 302122 TTTTTTGCTGCTTTTATAATCTTTTTTTTTTTTTTTT 302158 vi vi v vv i (TT)n#Simple_ 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 37 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 18 7.03 3.33 0.00 chr5ptel1M 302551 302580 (697420) (TGT)n#Simple_repeat 1 31 (0) m_b225s252i6 8835 chr5ptel1M 302551 TGTT-TTGTTGTTGTTGTTGTTTTTGTTTTT 302580 - v v (TGT)n#Simple 1 TGTTGTTGTTGTTGTTGTTGTTGTTGTTGTT 31 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 450 23.33 0.74 7.94 chr5ptel1M 302583 302717 (697283) C MIRc#SINE/MIR (141) 127 2 m_b225s601i13 8836 chr5ptel1M 302583 CTGAGGC-AATTGGGGGTAAGTGACTTGCCTAGGGTCACACAGCTGGGAA 302631 -v vv i v i i i --- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG--- 81 chr5ptel1M 302632 GTGTTAAGTGTCTGAGGTCAAACTTTAACCCAGATCCTCCTGACTTCAGG 302681 ---- v v vivii iv i i i i C MIRc#SINE/MIR 80 ----TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr5ptel1M 302682 GCTGGTGCTCTACCCACCGCACCACCTCGCTGCCCC 302717 v ii vi i --- i i C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTGCACCA---CACTGCCTC 2 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.16 CpG sites = 18, Kimura (unadjusted) = 28.42 Transitions / transversions = 1.64 (18/11) Gap_init rate = 0.08 (11 / 134), avg. gap size = 1.00 (11 / 11) 16 9.71 0.00 0.00 chr5ptel1M 303112 303133 (696867) (G)n#Simple_repeat 1 22 (0) m_b225s252i7 8837 chr5ptel1M 303112 GGGGAGGGGGTGGGGGGGGGGG 303133 i v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGG 22 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 17 4.94 0.00 0.00 chr5ptel1M 303222 303242 (696758) (A)n#Simple_repeat 1 21 (0) m_b225s252i8 8838 chr5ptel1M 303222 AAATAAAAAAAAAAAAAAAAA 303242 v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAA 21 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 13 15.86 0.00 0.00 chr5ptel1M 305568 305595 (694405) (TAAAA)n#Simple_repeat 1 28 (0) m_b225s252i9 8839 chr5ptel1M 305568 TAAAAGTAAATAAGATAAAATAAAAGAA 305595 vv i v (TAAAA)n#Simp 1 TAAAATAAAATAAAATAAAATAAAATAA 28 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 14 8.91 0.00 0.00 chr5ptel1M 306479 306502 (693498) (AGTT)n#Simple_repeat 1 24 (0) m_b225s252i10 8840 chr5ptel1M 306479 AGTTAGTTAGTTAGTTTGTTTGTT 306502 v v (AGTT)n#Simpl 1 AGTTAGTTAGTTAGTTAGTTAGTT 24 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 285 29.84 3.50 9.52 chr5ptel1M 306782 306981 (693019) C MIR1_Amn#SINE/MIR (17) 213 25 m_b225s601i14 8841 chr5ptel1M 306782 TTATTTAGTAGTTTATAGTCAA-ATATCTCTGAAGC----TGCAAAGGAT 306826 v i v vi - i- v -i ---- i v C MIR1_Amn#SINE 213 TTATGTAGCACTTTTCA-TCAGTAGATCTC-AAAGCACTTTACAAAGGAG 166 chr5ptel1M 306827 CTTAGCGATACCTATCTATAATCCAACCTTTTCATTTTGTTGGTTAAGAA 306876 v i ------- - v -------i iiv i v i C MIR1_Amn#SINE 165 GTCAG-------TATC-ATTATCC-------CCATTTTACAGATGAGGAA 131 chr5ptel1M 306877 ACTGAGACCCATAATAGTGTA-TGGCATGCCCTTGGTTAAACA-CCAGTA 306924 i ? v ivi ?v - i v vv i v? - ?i i? C MIR1_Amn#SINE 130 ACTGAGGCNCAGAGAGGTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCN 81 chr5ptel1M 306925 ACTTGTGGAGCAGGTATTTGAGCTCAAGTCCTGTAACTCCCAAGTTTTGT 306974 v v ii v v ? ? i i i iivii v - iiv C MIR1_Amn#SINE 80 AGTGGCAGAGCCGGGANTNGAACCCAGGTCTCCCGAGTCCC-AGTCCAGT 32 chr5ptel1M 306975 TCTCTGT 306981 v i C MIR1_Amn#SINE 31 GCTCTAT 25 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.62 CpG sites = 30, Kimura (unadjusted) = 40.71 Transitions / transversions = 1.25 (30/24) Gap_init rate = 0.11 (22 / 199), avg. gap size = 1.14 (25 / 22) 512 30.45 1.20 3.07 chr5ptel1M 306814 306979 (693021) C MIR3#SINE/MIR (25) 183 21 m_b225s601i15 8841 chr5ptel1M 306814 AGCTGCAAAGGATCTTAGCGATACCTATCTATAATCCAACCTTTTCATTT 306863 v i i v ---i --i iii C MIR3#SINE/MIR 183 AGCTGGAAGGGACCTTAGAGAT---CATCTA--GTCCAACCCCCTCATTT 139 chr5ptel1M 306864 TGTTGGTTAAGAAACTGAGACCCATAATAGTGTA-TGGCATGCCCTTGGT 306912 iiv i v i i v ivi v - i v vv C MIR3#SINE/MIR 138 TACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGT 89 chr5ptel1M 306913 TAAACA-CCAGTAACTTGTGGAGCAGGTATTTGAGCTCAAGTCCTGTAAC 306961 i v - ? v v v ii v v i v i i i iiv i C MIR3#SINE/MIR 88 CACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGTCTCCTGAC 39 chr5ptel1M 306962 TCCCAAGTTTTGTTCTCT 306979 iviiv i C MIR3#SINE/MIR 38 TCCCAGTCCGTGCTCTCT 21 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.53 CpG sites = 29, Kimura (unadjusted) = 40.61 Transitions / transversions = 1.45 (29/20) Gap_init rate = 0.04 (7 / 165), avg. gap size = 1.00 (7 / 7) 298 36.31 1.56 3.17 chr5ptel1M 307015 307142 (692858) MIR3#SINE/MIR 17 142 (66) m_b225s601i16 8842 chr5ptel1M 307015 GCAGAAAGACCTTTGGCTAAGGAGTGAAGA-ACTTAAGTTCTAGTTTGAA 307063 i v viv i i- v i - i ii iivii MIR3#SINE/MIR 17 GCAGAGAGAGCACGGACTG-GGAGTCAGGAGACCTGGGTTCTAGTCCCGG 65 chr5ptel1M 307064 TTCTGTTTTCAGCTCATCTCATAATCGTGAATGCCTAAT-GCTTTGCTTC 307112 i iivii i ?iiivii i i v --- v v i -i ii i MIR3#SINE/MIR 66 CTCTGCCACTAACTNGCTGTGTGACCTTG---GGCAAGTCACTTCACCTC 112 chr5ptel1M 307113 TCTGGACCACATTGCCCTCATCTGTAAAAT 307142 i v v vi MIR3#SINE/MIR 113 TCTGGGCCTCAGTTTCCTCATCTGTAAAAT 142 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 51.35 CpG sites = 32, Kimura (unadjusted) = 55.11 Transitions / transversions = 2.46 (32/13) Gap_init rate = 0.05 (6 / 127), avg. gap size = 1.00 (6 / 6) 378 19.48 0.00 4.17 chr5ptel1M 307210 307284 (692716) C MIR3#SINE/MIR (24) 184 113 m_b225s601i17 8843 chr5ptel1M 307210 GAACTAATAGGGAATTTGTAAAGGTCATCTGGTCTTACTCCCTCATTTTA 307259 i iiv vi -- i i i iv i C MIR3#SINE/MIR 184 GAGCTGGAAGGGACCTT--AGAGATCATCTAGTCCAACCCCCTCATTTTA 137 chr5ptel1M 307260 CAGATGAAGAAGCTGAGGCTCCAGA 307284 i i - C MIR3#SINE/MIR 136 CAGATGAGGAAACTGAGGC-CCAGA 113 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 23.50 CpG sites = 11, Kimura (unadjusted) = 23.50 Transitions / transversions = 3.67 (11/3) Gap_init rate = 0.04 (3 / 74), avg. gap size = 1.00 (3 / 3) 196 30.00 10.00 0.00 chr5ptel1M 307284 307353 (692647) C MIRc#SINE/MIR (189) 79 3 m_b225s601i18 8844 chr5ptel1M 307284 AAGTTGCATAGCAAAGTTTTGAACCCCAGTCCTA-TGCCTCCAAATCCAG 307332 v v vii vi i vi i v- v i C MIRc#SINE/MIR 79 AAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAG 30 chr5ptel1M 307333 TACT------ACCATACCATACTTTCT 307353 i ------ iii i vi C MIRc#SINE/MIR 29 TGCTCTTTCCACTGCACCACACTGCCT 3 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.97 CpG sites = 13, Kimura (unadjusted) = 39.74 Transitions / transversions = 1.62 (13/8) Gap_init rate = 0.03 (2 / 69), avg. gap size = 3.50 (7 / 2) 596 31.80 7.61 2.59 chr5ptel1M 308871 309238 (690762) C L2#LINE/L2 (249) 2833 2448 m_b225s601i19 8845 chr5ptel1M 308871 GAAGTAATATGACTGGACTTCCATTAGTAAAACTGTTATT-TGGCAGATG 308919 i i i iiv v i -v vvi i i - v v C L2#LINE/L2 2833 GGAGTGACATGATCTGACTTACGTT-TTAAAAGGATCACTCTGGCTGCTG 2785 chr5ptel1M 308920 TATGGAGGATAGATTGGAAAGGGGAGAGATTGGAAT-----AAACCAGTT 308964 i v i i ? ii vi iv v----- i C L2#LINE/L2 2784 TGTTGAGAATAGACTGNAGGGGGGCAAGGGTGGAAGCAGGGAGACCAGTT 2735 chr5ptel1M 308965 ACGGAGTTACTGGAATAGTTCAGGCAGTAGGTGATAAGGGCCTAAGGTAA 309014 v ii i i v i i i iiv i iiv i iiivi i C L2#LINE/L2 2734 AGGAGGCTATTGCAGTAATCCAGGCGAGAGATGATGGTGGCTTGGACCAG 2685 chr5ptel1M 309015 GGTGATGCTGCGCAGGTGAATCTGAAAAGAAGGGGATGGATGTGTAGGAG 309064 i ---- - i vv ivi v vi - v - v C L2#LINE/L2 2684 GGTGGTG----GCA-GTGGAGGTGGTGAGAAGTGGTCGGAT-TCT-GGAT 2642 chr5ptel1M 309065 ACATTATGAAAATAGAGTTGAGAAAACTTGACAACAG------TGTGGAA 309108 i v ii ii v ii i vii ii ------ ii C L2#LINE/L2 2641 ATATTTTGAAGGTAGAGCCGACAGGATTTGCTGATGGATTGGATGTGGGG 2592 chr5ptel1M 309109 T-TG-GAGAGGGAAGAGAATCAAGGATGTCTTGA--GTTTGTGCACCTGG 309154 - - ii iii i v iv -- v -i i C L2#LINE/L2 2591 TGTGAGAGAAAGAGAGGAGTCAAGGATGACTCCAAGGTTTTTG-GCCTGA 2543 chr5ptel1M 309155 GTGACTGAAAAGGATGG---TGC--TCAGC--AGAAAGAGATGTTTGGGA 309197 ii -i --- -- i?i -- vi i v vi v i C L2#LINE/L2 2542 GCAACTG-GAAGGATGGAGTTGCCATTNACTGAGATGGGGAAGACTGCGG 2494 chr5ptel1M 309198 AAGGGGCAGATTCAAGAGAAAAGAT---GGGTTC--TTTTGGACAT 309238 i i i ii i ii --- i -- C L2#LINE/L2 2493 GAGGAGCAGGTTTGAGGGGGAAGATCAGGAGTTCAGTTTTGGACAT 2448 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.62 CpG sites = 81, Kimura (unadjusted) = 44.80 Transitions / transversions = 2.45 (81/33) Gap_init rate = 0.06 (21 / 367), avg. gap size = 1.81 (38 / 21) 183 26.64 6.45 3.12 chr5ptel1M 309291 309383 (690617) C L2#LINE/L2 (732) 2350 2255 m_b225s601i20 8845 chr5ptel1M 309291 ATATTGATTTTGTAATTATCTGCATAAAGATAATAACTGAACTCATGGGA 309340 vi v v i i v v ii vi i vi -- C L2#LINE/L2 2350 ATATAAATTTGGGAGTCATCAGCATATAGATGGTATTTAAAGCCATG--A 2303 chr5ptel1M 309341 GATT--ATGAG-TGACTGAGAAAGGTCAA---AGATAGAGAGGAGAAAA 309383 i -- - v i? ii - v i--- i i C L2#LINE/L2 2302 GACTGGATGAGATCACCNAGGGAG-TGAGTGTAGATAGAGAAGAGAAGA 2255 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.48 CpG sites = 15, Kimura (unadjusted) = 34.48 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.07 (6 / 92), avg. gap size = 1.50 (9 / 6) 596 29.60 9.09 1.96 chr5ptel1M 310187 310472 (689528) L3#LINE/CR1 3707 4012 (87) m_b225s601i21 8846 chr5ptel1M 310187 CAGTGGAAATAATGGGATATGTTTAGCCAGGAGAAGCGACCACTCGG--G 310234 i v iv iv iv v v vv ii -- L3#LINE/CR1 3707 CGGTTGAAGGAACTGGGGATGTTTAGCCTGGAGAAGAGAAGACTTAGAGG 3756 chr5ptel1M 310235 AGACATGACAG-TG-------AGATCTAAGCGCACTGTAATATGGAAAGA 310276 i - ------- v i i iv -i v i iii L3#LINE/CR1 3757 AGACATGATAGCTGTCTTCAAATATTTGAAGG-GCTGTCATGTGGAAGAG 3805 chr5ptel1M 310277 GCACT-GACTTGTTTCATTGGACTACACAGGGCAGAACTTAGGGACA--G 310323 v i - i iii vv i v v - iv -- L3#LINE/CR1 3806 GGATTAGACTTATTCTGTGTGGCTCCAGAGGGCAGAACT-AGGACCAATG 3854 chr5ptel1M 310324 GGTGGGAAATTGCAAAGAGGTA--TTTAAGC-----ATTAAGAAAAAGTT 310366 - i i ii i -- vi ----- v i i v L3#LINE/CR1 3855 GGTGG-AAGTTACAGGGAGGCAGATTTCGGCTCAATATAAGGAAGAACTT 3903 chr5ptel1M 310367 TCTAATAGTTGGGCCAGGC------TGGAGTGGGCTGGCTCCAGAGGTGA 310410 i i ii iv v v ------ i v v? ii L3#LINE/CR1 3904 TCTAACAATCAGAGCTGTCCAAAAATGGAATGGGCTGCCTCGNGAGGTAG 3953 chr5ptel1M 310411 CAGACTACCTTTTGGTGGAGGTCTTCAAGCATAGGCTGAATGTGGATTGC 310460 iiii v iv iiv v v i --- iii L3#LINE/CR1 3954 TGAGCTCCCCGTCACTGGAGGTGTTCAAGCAGAGGCTGGAT---GACCAC 4000 chr5ptel1M 310461 TGGTTGGGGGTG 310472 v ii i L3#LINE/CR1 4001 TTGTCAGGGATG 4012 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.51 CpG sites = 52, Kimura (unadjusted) = 39.35 Transitions / transversions = 1.68 (52/31) Gap_init rate = 0.05 (14 / 285), avg. gap size = 2.29 (32 / 14) 18 7.25 0.00 9.38 chr5ptel1M 310676 310694 (689306) (AT)n#Simple_repeat 1 19 (13) m_b225s252i11 8847 chr5ptel1M 310676 ATATATATATATATATATA 310694 (AT)n#Simple_ 1 ATATATATATATATATATA 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 29 0.00 0.00 0.00 chr5ptel1M 310695 310719 (689281) (TG)n#Simple_repeat 1 25 (0) c_b225s251i1 8848 chr5ptel1M 310695 TGTGTGTGTGTGTGTGTGTGTGTGT 310719 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGT 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 18 7.25 0.00 9.38 chr5ptel1M 310720 310734 (689266) (AT)n#Simple_repeat 20 32 (0) m_b225s252i11 8849 chr5ptel1M 310720 TTTAAATCATAGTAT 310734 v v - - (AT)n#Simple_ 20 TATATAT-ATA-TAT 32 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.14 (2 / 14), avg. gap size = 1.00 (2 / 2) 364 15.55 30.05 0.36 chr5ptel1M 314372 314584 (685416) C Charlie7#DNA/hAT-Charlie (41) 2574 2299 m_b225s502i0 8850 chr5ptel1M 314372 AAAAAATT--AAGCATACACCCTCAATAAA-ATATATTGAC--ATAAACT 314416 --i i i v -i v i-- i C Charlie7#DNA/ 2574 AAAAAATTTTGAGCATGCACCCCCAATATATGTATATTTATTTATAAATT 2525 chr5ptel1M 314417 GCTTACATGAACAATTGTACTAATATGTCATT--CATTATAAGA---ACA 314461 iiv v v i i i v-- i --- C Charlie7#DNA/ 2524 ATATACATGTACTACTGTACTAATATATTATGTACATTATAAAACATACA 2475 chr5ptel1M 314462 CAAAAATAGAAGTT---AAAGTATGA---------CAAATAAACAGTA-G 314498 i --- v ---------v i -v C Charlie7#DNA/ 2474 CAAAAATAGAAATTTTAAAAGGATGAGATAAAGATGAAATAAACAATATT 2425 chr5ptel1M 314499 TTA----AATTTTTA--------AAAAATGGTACA--------------- 314521 ---- -------- vv --------------- C Charlie7#DNA/ 2424 TTAAAATAATTTTTATTTTATTTATTAATGGTACAAAACATTTTTGCTCT 2375 chr5ptel1M 314522 ---TAAAA------TAGTAATATTTTTGTTGAAAGCA-----ATTGAATA 314557 --- ------ i v - i ----- C Charlie7#DNA/ 2374 CACTAAAATATTATTAATAATATTTTAG-TGAGAGCAATGTGATTGAATA 2326 chr5ptel1M 314558 TACTGTATTATCTTTGAAAAGCTTGGT 314584 i vi i v C Charlie7#DNA/ 2325 TGCTTCATTATTTTTGAAAATCTTGGT 2299 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 17.61 CpG sites = 19, Kimura (unadjusted) = 17.61 Transitions / transversions = 1.36 (19/14) Gap_init rate = 0.07 (15 / 212), avg. gap size = 4.33 (65 / 15) 315 27.39 7.09 2.26 chr5ptel1M 314771 314897 (685103) C MIR#SINE/MIR (50) 212 80 m_b225s601i22 8851 chr5ptel1M 314771 AAATGTGCTACATATAATA--TCAAGTAACCTTT----CAACCTTGATGA 314814 ii ivi i v -- vv i i i---- i - C MIR#SINE/MIR 212 AAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCT-ATGA 164 chr5ptel1M 314815 GATAGGGTACAATTATATA-CCCCATTTAGTAGAGGAAGAAA--GAGCTT 314861 i - v - - vii v i -- viv C MIR#SINE/MIR 163 GGTAGG-TACTATTAT-TATCCCCATTTTACAGATGAGGAAACTGAGGCA 116 chr5ptel1M 314862 TAAAGACACTAAATAACTGTCCCATGGTCATGCAGC 314897 i i vii i vv v ii C MIR#SINE/MIR 115 CAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGC 80 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.90 CpG sites = 21, Kimura (unadjusted) = 35.19 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.06 (7 / 126), avg. gap size = 1.71 (12 / 7) 12 14.91 8.11 0.00 chr5ptel1M 315338 315374 (684626) (TATTTAA)n#Simple_repeat 1 40 (0) m_b225s252i12 8852 chr5ptel1M 315338 TATATAGTAGTTAATATTT-A-ACTTAAT-TTTAAAATTT 315374 v i v - - i - v (TATTTAA)n#Si 1 TATTTAATATTTAATATTTAATATTTAATATTTAATATTT 40 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.08 (3 / 36), avg. gap size = 1.00 (3 / 3) 373 16.07 15.28 0.61 chr5ptel1M 315738 315881 (684119) C Charlie7a#DNA/hAT-Charlie (41) 231 67 m_b225s502i2 8853 chr5ptel1M 315738 AAAAAATT---AAGCACACACCCTCAATATA---ATAC--ATTGATGTAT 315779 ---i ii i --- i-- v v C Charlie7a#DNA 231 AAAAAATTTTTGAGCATGCACCCCCAATATATGTATATTTATTTATTTAT 182 chr5ptel1M 315780 AAATTGCTTACATGAACTATTGTACTAATATGTTATG--CATTATAAGA- 315826 iiv v i i -- i - C Charlie7a#DNA 181 AAATTATATACATGTACTACTGTACTAATATATTATGTACATTATAAAAC 132 chr5ptel1M 315827 ATAC---AAAAATAGAAG--TTAAAGTATGATAGATAAA---AAGCAAAA 315868 --- i-- v i - i --- ii i C Charlie7a#DNA 131 ATACACAAAAAATAGAAATTTTAAAGGATAA-AAATAAATATAAATAGAA 83 chr5ptel1M 315869 GTT---ACATTTTTTT 315881 --- i i C Charlie7a#DNA 82 GTTCTAATATTTTCTT 67 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 18.71 CpG sites = 18, Kimura (unadjusted) = 18.71 Transitions / transversions = 3.60 (18/5) Gap_init rate = 0.07 (10 / 143), avg. gap size = 2.30 (23 / 10) 441 15.43 8.80 1.49 chr5ptel1M 315738 315862 (684138) C Charlie7#DNA/hAT-Charlie (41) 2574 2441 m_b225s502i1 8853 chr5ptel1M 315738 AAAAAATT--AAGCACACACCCTCAATATA-ATACATTGATGTATAAATT 315784 --i ii i -i i v v C Charlie7#DNA/ 2574 AAAAAATTTTGAGCATGCACCCCCAATATATGTATATTTATTTATAAATT 2525 chr5ptel1M 315785 GCTTACATGAACTATTGTACTAATATGTTATG--CATTATAAGA---ATA 315829 iiv v i i -- i --- i C Charlie7#DNA/ 2524 ATATACATGTACTACTGTACTAATATATTATGTACATTATAAAACATACA 2475 chr5ptel1M 315830 CAAAAATAGAAGTT---AAAGTATGATAGATAAAAA 315862 i --- v -- i C Charlie7#DNA/ 2474 CAAAAATAGAAATTTTAAAAGGATG--AGATAAAGA 2441 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 17.74 CpG sites = 14, Kimura (unadjusted) = 17.74 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.06 (7 / 124), avg. gap size = 1.86 (13 / 7) 300 26.48 4.96 3.25 chr5ptel1M 316126 316246 (683754) C MIR#SINE/MIR (60) 202 80 m_b225s601i23 8854 chr5ptel1M 316126 CATGGATAATATCAATTAA-CCTTTCAACA--CTGGTGAGGTGTAGGGTA 316172 v v vv v - iv -- ivi i--- C MIR#SINE/MIR 202 CATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGGTA---GGTA 156 chr5ptel1M 316173 CAATTATATATCC-CATTCAGTAGAGGAAAAAAC--AGGTTTAAAGAAAC 316219 v - - ivii v ii -- ivi i iii C MIR#SINE/MIR 155 CTATTAT-TATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGT 107 chr5ptel1M 316220 TAACTAACTGTCCCATGGTCATACAGC 316246 v vv v i C MIR#SINE/MIR 106 TAAGTAACTTGCCCAAGGTCACACAGC 80 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.09 CpG sites = 16, Kimura (unadjusted) = 33.09 Transitions / transversions = 1.07 (16/15) Gap_init rate = 0.07 (8 / 120), avg. gap size = 1.25 (10 / 8) 386 13.84 30.81 0.73 chr5ptel1M 317324 317534 (682466) C Charlie7#DNA/hAT-Charlie (41) 2574 2301 m_b225s502i3 8855 chr5ptel1M 317324 AAAAAATT--AAGCACACACCCTCAATATA-ATACACTGATGTATAAATT 317370 --i ii i -i i i v v C Charlie7#DNA/ 2574 AAAAAATTTTGAGCATGCACCCCCAATATATGTATATTTATTTATAAATT 2525 chr5ptel1M 317371 GCTTACATGAATTATTGTACTAATATGTTA--TACATTATAAGA---ACA 317415 iiv v i i i -- i --- C Charlie7#DNA/ 2524 ATATACATGTACTACTGTACTAATATATTATGTACATTATAAAACATACA 2475 chr5ptel1M 317416 CAAAAATAGATGTT---AAAGTATGACA-------GAAA-AAACAATAGT 317454 vi --- v v ------- - v C Charlie7#DNA/ 2474 CAAAAATAGAAATTTTAAAAGGATGAGATAAAGATGAAATAAACAATATT 2425 chr5ptel1M 317455 T--AAAT--TTTTTA----A------AATTGTACA--------------- 317475 -- -- ---- ------ v --------------- C Charlie7#DNA/ 2424 TTAAAATAATTTTTATTTTATTTATTAATGGTACAAAACATTTTTGCTCT 2375 chr5ptel1M 317476 ---TAAAATGGTA--------ATTTTAGTGAAAG---TG---TTGAATAT 317508 --- iv -------- i --- --- -- C Charlie7#DNA/ 2374 CACTAAAATATTATTAATAATATTTTAGTGAGAGCAATGTGATTGA--AT 2327 chr5ptel1M 317509 ATACTTCATTATCTTTGAAAATCCTG 317534 i i i C Charlie7#DNA/ 2326 ATGCTTCATTATTTTTGAAAATCTTG 2301 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 15.56 CpG sites = 19, Kimura (unadjusted) = 15.56 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.09 (18 / 210), avg. gap size = 3.72 (67 / 18) 1265 27.47 9.76 3.05 chr5ptel1M 318938 319429 (680571) C Charlie7#DNA/hAT-Charlie (1974) 641 118 m_b225s502i4 8856 chr5ptel1M 318938 CATCATTAGTAATAATGGGTAGAAATACATATTTTAAAGAATTTT---AG 318984 i iii i i iv v i v i i ---ii C Charlie7#DNA/ 641 CATCGTTAACGATAGTGGATGTAAATCCATATTTCAAATAGTCTTCTTGA 592 chr5ptel1M 318985 TACCTTCAAATTATTTTGGTTGACTTTCTGCTTGATTTAATTACTTCGTT 319034 vi i v ii ii iiv i i vv i C Charlie7#DNA/ 591 TAATTTCGAATTTTTTTGGCCGACTTCTTGTCAGATCTGATTAGATCGTC 542 chr5ptel1M 319035 GTATGGTTATTTTTATCTTCTAATATGACTGATAAATA---C-TGCTAGG 319080 i ----- i i iv i i ii v --- - i C Charlie7#DNA/ 541 AT-----TGTTTTTACCTCGTAATGTGGCTGACGAAGAGCTCGTACTAGG 497 chr5ptel1M 319081 AATAAGAAAAATGACAGCTCTTCCAATTT------GTTCATTTGTTGCCC 319124 i i--- i v v v ------ ii - i- C Charlie7#DNA/ 496 AGTAG---AAGTGTCAGCTCTGCCATTTTCTTGTTGTTCGCTTGT-GCT- 452 chr5ptel1M 319125 ATGCATTATTA---CTATCTT-AATCCATAGTTACTTTCTGGGAATCTTT 319170 - ---i - iii v vii C Charlie7#DNA/ 451 -TGCATTATTAGTATTATCTTCAATCCGCGGTTTCTTTGCAGGAATCTTT 403 chr5ptel1M 319171 TTTAAGCTACTTGTCTATTTTGTGAGGGTTAGTCTAGATAAATCCAGATA 319220 - i i i v v i C Charlie7#DNA/ 402 TT-AAGCCACTTGTCCATTTTGTGAGGGTTAGTTTAGTTAAAACTAGATA 354 chr5ptel1M 319221 ATA----CTGTAAGTCCACTTAACTGG-----------CTACAACATGTT 319255 ---- i i i ----------- i i i i C Charlie7#DNA/ 353 ATATAATCCGTAAATCCACTTAACCGGGCACACGTAAACTGCAATACGTC 304 chr5ptel1M 319256 ATTATATGCTGAAAGCAAATAAAGGAATGAGGGTAGTAGTCTCAGTCTTT 319305 iiv i i ii v i iivi v v ii ii C Charlie7#DNA/ 303 GCAATACGCTGAAAGCGAACGAACGAGTGAGGGCGCCACTGTCAACCCCT 254 chr5ptel1M 319306 TTG---TGTGGAGTCTCTCCCACTATTCCCTTAGAACATCTCACATGTTA 319352 ii --- i--- v i i i i i i iiii C Charlie7#DNA/ 253 CCGCGTTGTGGAA---CTCCCACTCTTCCCTCAGGATACCTCGCGTACCG 207 chr5ptel1M 319353 GTCATGATATGTAATTCATCTTA-----------GGTGAGAATATTGGTA 319391 vvii i i i -i i v -----------i iiiiiii i C Charlie7#DNA/ 206 CATGTGACACGTGA-CCGTCTGACATACGGACCGAGTGAGGGCGCCAGTG 158 chr5ptel1M 319392 TTAAGT--TTTATTAAATCTTAATAAAGCTTAATTTTTTT 319429 i vi-- v v i i C Charlie7#DNA/ 157 TCAATCCGTATATTAAATATTAGTAAAGCTTAATTTCTTT 118 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 28.41 CpG sites = 102, Kimura (unadjusted) = 36.87 Transitions / transversions = 3.52 (102/29) Gap_init rate = 0.05 (27 / 491), avg. gap size = 2.37 (64 / 27) 389 25.91 1.64 5.08 chr5ptel1M 319578 319699 (680301) MIRc#SINE/MIR 10 127 (141) m_b225s601i24 8857 chr5ptel1M 319578 GTGGGACCGTAGATAGAGCACCAGCCATGAAGTCAGGAGGACCTGAGGTC 319627 vi v i v ii v v i i i v MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr5ptel1M 319628 TAATGTAACCTCAGATACTTAGCACTTCCAGCTGTATGACC-TGGGCAAA 319676 v i viviv v vi ------ i i - i MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTA------CTAGCTGTGTGACCTTGGGCAAG 103 chr5ptel1M 319677 TCACTTAACCCCAGTTA-CCTCAG 319699 i vv v - MIRc#SINE/MIR 104 TCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 30.77 CpG sites = 15, Kimura (unadjusted) = 32.03 Transitions / transversions = 1.00 (15/15) Gap_init rate = 0.07 (8 / 121), avg. gap size = 1.00 (8 / 8) 28 15.11 0.00 0.00 chr5ptel1M 319702 319747 (680253) (A)n#Simple_repeat 1 46 (0) m_b225s252i13 8858 chr5ptel1M 319702 AAAAAAAAAAAAAAAGAAAAAAAAAGAAAGAAAGAAAGAAAAGAAA 319747 i i i i i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 46 Matrix = Unknown Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 17 11.81 5.41 0.00 chr5ptel1M 319900 319936 (680064) (ATTTA)n#Simple_repeat 1 39 (0) m_b225s252i14 8859 chr5ptel1M 319900 ATTTAATTTAATTT--TTTAATTAAAAATTATTTAATTT 319936 -- v vv v (ATTTA)n#Simp 1 ATTTAATTTAATTTAATTTAATTTAATTTAATTTAATTT 39 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.03 (1 / 36), avg. gap size = 2.00 (2 / 1) 13 7.83 3.45 3.45 chr5ptel1M 321799 321827 (678173) (ATGAT)n#Simple_repeat 1 29 (0) m_b225s252i15 8860 chr5ptel1M 321799 ATGATATGATATTAT-TGTATATGATAAGA 321827 v - - v (ATGAT)n#Simp 1 ATGATATGATATGATATG-ATATGATATGA 29 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.07 (2 / 28), avg. gap size = 1.00 (2 / 2) 192 20.59 0.00 0.00 chr5ptel1M 321871 321904 (678096) C L2d_3end#LINE/L2 (22) 494 461 m_b225s601i25 8861 chr5ptel1M 321871 TTTATTTGGTACCTACTATGTATTCAGTACTGTG 321904 vi ii ii i C L2d_3end#LINE 494 TTTATTGAGCGCCTACTATGTGCTCAGCACTGTG 461 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 21.06 CpG sites = 6, Kimura (unadjusted) = 25.61 Transitions / transversions = 6.00 (6/1) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 663 35.32 10.47 1.97 chr5ptel1M 322074 322541 (677459) C L3#LINE/CR1 (3) 4096 3590 m_b225s601i26 8862 chr5ptel1M 322074 AGAATTATAGA--TTGAGAGCTAAAAGGTAACTTAGACATCCTCTTGATT 322121 i i --i v i ii v v vi v v vii C L3#LINE/CR1 4096 AGAATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCC 4047 chr5ptel1M 322122 AA--TTCCTTCC----TAG---TTCTTTCATTCCAGGATGTCTAATCATT 322162 -- i v ----i --- i i -- v iv vi i iv v C L3#LINE/CR1 4046 AACCTCCCATCCAATGCAGGAATCCCTTC--TACAACATCCCTGACAAGT 3999 chr5ptel1M 322163 GATCCTTCAGCCTAAG--TGAAGATTTCT-CTGATGGAGAACCCATTAAT 322209 i v i vv -- v ii i-v i i i i i vi C L3#LINE/CR1 3998 GGTCATCCAGCCTCTGCTTGAACACCTCCAGTGACGGGGAGCTCACTACC 3949 chr5ptel1M 322210 TTTTAATGTGGGACATT--------GAATA-CTCTCATTTTTAGGAGATT 322250 i?ii v ii vv -------- i i - v v i ii C L3#LINE/CR1 3948 TCNCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGATTGTTAGAAAGTT 3899 chr5ptel1M 322251 TTTT-TTGT-TTGAGCTAAAATTTAATTTT-TAAAATTTCT-----TTAA 322292 i i- i - ii i ivi ii- iv i i----- ii C L3#LINE/CR1 3898 CTTCCTTATATTGAGCCGAAATCTGCCTCCCTGTAACTTCCACCCATTGG 3849 chr5ptel1M 322293 T-----TTTTATCAATTGAGGGCCAGACAAAACAAGCATGATCTTGCCTC 322337 ----- i ii vvi - i v i i iv i iiv i C L3#LINE/CR1 3848 TCCTAGTTCTGCCCTCTG-GAGCCACACAGAATAAGTCTAATCCCTCTTC 3800 chr5ptel1M 322338 CACATGGCAGTGCTTCATATGTTTAAAGATTACT-----GTATCCTCTAT 322382 i iv v i i ivi ----- v - C L3#LINE/CR1 3799 CACATGACAGCCCTTCAAATATTTGAAGACAGCTATCATGTCTCCTCTA- 3751 chr5ptel1M 322383 TAAAGGTTATTTTTTTTCTAGGCTAAACTTTCCTATTTCCTTTAATGAAA 322432 ----i iv i i i i v i i v i ivivv C L3#LINE/CR1 3750 ----AGTCTTCTCTTCTCCAGGCTAAACATCCCCAGTTCCTTCAACCGTT 3705 chr5ptel1M 322433 CCT-GTA-GTCA---TTTAGAGTATTCCTC-CCATCATAGTCATACTC-- 322474 -i - v --- vv - ii i - v i iiv -- C L3#LINE/CR1 3704 CCTCATATGACATGGTTTCCAG-ACCCTTCACCATCCTGGTCGCTCTCCT 3656 chr5ptel1M 322475 CAGGTTGAATATTAACTTTTCACCATTCCTTCAAACAATGTAGTACCCAG 322524 v vi viivii ii v vii i iiv - i ii C L3#LINE/CR1 3655 CTGGACGCGCTCCAGTTTGTCAATGTCCCTCTTAA-AATGTGGCGCCCAG 3607 chr5ptel1M 322525 AACTGGTTATAATACTC 322541 iviii C L3#LINE/CR1 3606 AACTGAACGCAATACTC 3590 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 47.07 CpG sites = 108, Kimura (unadjusted) = 51.42 Transitions / transversions = 2.00 (108/54) Gap_init rate = 0.06 (29 / 467), avg. gap size = 2.03 (59 / 29) 514 19.55 4.41 5.97 chr5ptel1M 322754 322889 (677111) Charlie4#DNA/hAT-Charlie 6 139 (3239) m_b225s502i5 8863 chr5ptel1M 322754 GTTCTTGACCTGGTATATATGGACCCTC------TCCATGTATAGATTTC 322797 i vi vi i i ------ i v v Charlie4#DNA/ 6 GTTCTTAACCTGGGGTCCACGGACCCCCAAGGGGTCCGTGGATAGAATTC 55 chr5ptel1M 322798 AGGTTGTCCATGATAAGACTTAAAATGGGAAAAAAAATTGCAGCTTTATT 322847 vv i ---- ii - -- i v Charlie4#DNA/ 56 AGGGGGTCCGTGA----ACTTGGA-TGGGAAAAAA--TTACATCTTTATT 98 chr5ptel1M 322848 TTCACCAAATTTCTAAATAAAATTCAACATTTTCTTCAATTA 322889 i -ii v i i i i Charlie4#DNA/ 99 TTCACTAA-CCTCTAACTGAAATTTAGCATTTCCTTCAATTA 139 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 20.18 CpG sites = 17, Kimura (unadjusted) = 23.22 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.07 (9 / 135), avg. gap size = 1.56 (14 / 9) 325 24.45 0.00 4.88 chr5ptel1M 322894 322979 (677021) Charlie4#DNA/hAT-Charlie 3296 3377 (1) m_b225s502i6 8864 chr5ptel1M 322894 AAAATATTCTTCTGAGGAGAGGATCCATGAGTTTCACTAGACTGCTAGGG 322943 i v i i - ii i i i ii Charlie4#DNA/ 3296 AAAACATTATTCTGAGAAGGGG-TCCATAGGCTTCACCAGACTGCCAAAG 3344 chr5ptel1M 322944 TGGGAAGGCACAGTACAAAAAAAGTTAGGAACTTCT 322979 - --vv ii i i i ii Charlie4#DNA/ 3345 -GGG--TCCATGGCACAAAAAAGGTTAAGAACCCCT 3377 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 31.90 CpG sites = 17, Kimura (unadjusted) = 31.90 Transitions / transversions = 5.67 (17/3) Gap_init rate = 0.05 (4 / 85), avg. gap size = 1.00 (4 / 4) 383 29.77 5.56 2.01 chr5ptel1M 323855 323998 (676002) MIRb#SINE/MIR 3 151 (117) m_b225s601i27 8865 chr5ptel1M 323855 GAGCAGCTACATGGTGCAGTGGATAGAGTGCCGGGTCTGGAACTAGGAAG 323904 vi vi i v ii v v i iii iv MIRb#SINE/MIR 3 GAGGGGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAG 52 chr5ptel1M 323905 ACTTATCTTCCTGAATTCAAAC-CTGGC-CTCAGAACGTGTGCTAATTAT 323952 i ivv -- i vii - v - i vv vv - i iiv MIRb#SINE/MIR 53 ACCTGGGTTC--GAATCCCGGCTCTGCCACTTACTAGCTGTG-TGACCTT 99 chr5ptel1M 323953 GTG---GCTATTTAAC---TCTATACCTCAGTTCCCTCATCTGTAAAATG 323996 v --- i i --- ivi i MIRb#SINE/MIR 100 GGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATG 149 chr5ptel1M 323997 AG 323998 i MIRb#SINE/MIR 150 GG 151 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.76 CpG sites = 25, Kimura (unadjusted) = 39.13 Transitions / transversions = 1.47 (25/17) Gap_init rate = 0.05 (7 / 143), avg. gap size = 1.57 (11 / 7) 231 27.25 1.41 4.35 chr5ptel1M 324173 324314 (675686) C L1ME3B_3end#LINE/L1 (424) 565 428 m_b225s551i1 8866 chr5ptel1M 324173 TTTTCAT-GCTATACAAGGATGTTTTATATTCATATTCCACAATTTGTTT 324221 - i i iviv viv i vv v i C L1ME3B_3end#L 565 TTTTCATTGCTGTATAGTATTCCATTGTATGAATATACCACAATTTATTT 516 chr5ptel1M 324222 AACTATTTCTCCCAGCTAATGGACACTTGACTTTGTTTCCAGTTTTT-GT 324270 v i - v i- i i i i-v ?- i C L1ME3B_3end#L 515 ATCCA-TTCTACT-GTTGATGGACATTTGG-GTTGTTTCCAGTTTTNGGC 469 chr5ptel1M 324271 AACTGCATAACTGTGTTGCTATGATTGTTTTTCTGTATTTGTAT 324314 v i i i- vi i vii i -- iv ? C L1ME3B_3end#L 468 TATTACG-AACAATGCTGCTATGAACATTCT--TGTACATGTNT 428 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.35 CpG sites = 23, Kimura (unadjusted) = 35.55 Transitions / transversions = 1.64 (23/14) Gap_init rate = 0.06 (8 / 141), avg. gap size = 1.00 (8 / 8) 296 25.44 1.64 3.33 chr5ptel1M 324173 324294 (675706) C L1ME3F_3end#LINE/L1 (425) 565 446 m_b225s551i0 8866 chr5ptel1M 324173 TTTTCA-TGCTATACAAGGATGTTTTATATTCATATTCCACAATTTGTTT 324221 - i i viv viv i i vv v i C L1ME3F_3end#L 565 TTTTCACTGCTGTATAATATTCCATTGTGTGAATATACCACAATTTATTT 516 chr5ptel1M 324222 AACTATTTCTCCCAGCTAATGGACACTTGACTTTGTTTCCAG-TTTTTGT 324270 v i - i- iii i i-v - i C L1ME3F_3end#L 515 ATCCA-TTCTCCT-GTCGATGGACATTTGG-GTTGTTTCCAGTTTTTTGC 469 chr5ptel1M 324271 AACTGCATAACTGTGTTGCTATGA 324294 v i i i- v i C L1ME3F_3end#L 468 TATTACG-AACAGTGCTGCTATGA 446 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 29.31 CpG sites = 19, Kimura (unadjusted) = 31.99 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.05 (6 / 121), avg. gap size = 1.00 (6 / 6) 269 35.65 15.70 0.51 chr5ptel1M 329058 329229 (670771) C MIR1_Amn#SINE/MIR (30) 200 3 m_b225s601i28 8867 chr5ptel1M 329058 TTTATAAGTAGG----AAGGCACTTTAGAAAT-ATATTAGTA-----GAC 329097 i v i---- i v v- vi i -----iv C MIR1_Amn#SINE 200 TTCATCAGTAGATCTCAAAGCACTTTACAAAGGAGGTCAGTATCATTATC 151 chr5ptel1M 329098 CTCATATTACAGATAGGGAAACTGAAATCT---------------CCTAG 329132 i v ii iii?i--------------- i iv C MIR1_Amn#SINE 150 CCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGC 101 chr5ptel1M 329133 TTAA-GTCATTCAG-ATATTAATGACGGAAGTAAGATTCAGATCCAAATT 329180 ii - i? -?vii? i i i iviii ? ?ii i ii i C MIR1_Amn#SINE 100 CCAAGGTCACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAACCCAGGTC 51 chr5ptel1M 329181 TTTGGAATCCTAAATCCATTGTTCTTTATATCAGACCATGGGACCTTCC 329229 iiv i i- i v i v vi ii iivvi i C MIR1_Amn#SINE 50 TCCCGAGTCCC-AGTCCAGTGCTCTATCCACTAGACCACACTGCCTCCC 3 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 55.60 CpG sites = 46, Kimura (unadjusted) = 57.29 Transitions / transversions = 3.07 (46/15) Gap_init rate = 0.04 (7 / 171), avg. gap size = 4.00 (28 / 7) 253 36.31 9.80 1.60 chr5ptel1M 329613 329959 (670041) C L2d_3end#LINE/L2 (25) 491 117 m_b225s601i30 8868 chr5ptel1M 329613 ATTAAACACCAAGTATGCACAAGGC-TTGTGCTAAGTTTTGTGGGGGAGG 329661 i i i v v ii vvi -i i ivi i -- C L2d_3end#LINE 491 ATTGAGCGCCTACTATGTGCTCAGCACTGTGCTAGGCGCTGTGGGGAA-- 444 chr5ptel1M 329662 GAGGTAAGATAATGT-GGAGATCAGTTACTGTCCTCAAATA---TGTAAT 329707 -v i? i ? i i -i v -i iv i iv --- ii C L2d_3end#LINE 443 -CGANAAAANAGTATAAGACAT-GGTCCCTGCCCTCAAGGAGCTTACAAT 396 chr5ptel1M 329708 CTA-CTGGGAAAATAAGA-TAA-ACCTGTGAAA-----AGTGA-----AT 329744 -i i i i - - vii ----- v ----- i C L2d_3end#LINE 395 CTAGTTGGGGAGACAAGACTAACACACATGAAACAATTAGAGAACAATAC 346 chr5ptel1M 329745 AAGGAAGTAGAATATTGAG-ACCAAA-TGAATAATTCAG---ATGAGT-- 329787 iv v vv i -i i - vi ii v --- i -- C L2d_3end#LINE 345 AAGACAGTATATAATTAAGTGCTAAATTGCGTGGTACAGACTATAAGTGC 296 chr5ptel1M 329788 CACAATCATTCACACAA--CACAGATCATTTTCAAATGT-GTGA-CTGGT 329833 i i ivvi v v --v v v v viiv v- i- v v C L2d_3end#LINE 295 TATAGGAGTTCAGAGAAGGGAGAGATCAGTGTGGGCTGGAGTGGTCAGGG 246 chr5ptel1M 329834 AAAACTTCCCAG-GAACATGCTACTTGAGCTGGTCCTCAAGGACTGGAGA 329882 ii vii - i vi vv v ii i iv iv C L2d_3end#LINE 245 AAGGCTTCGTGGAGGAGGTGGGACTTGAGCTGGGCCTTGAAGGATGGGTA 196 chr5ptel1M 329883 AGTACAGGATGAGATGGGGAGGAGGGAGCAAGGTG----AAACAAGAAGA 329928 i vviv - vi i i i v i ii---- ii ii ii C L2d_3end#LINE 195 GGATTTGGAT-AGAGAGAGAGGAAGGGGAAGGGCATTCCAGGCGGGGGGA 147 chr5ptel1M 329929 AAGATTAAAGCTAAAGCCTGAAGGTCGGGAA 329959 v iivvi v i viii - C L2d_3end#LINE 146 ACGGCGTGAGCAAAGGCGCAGAGG-CGGGAA 117 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 49.90 CpG sites = 77, Kimura (unadjusted) = 53.06 Transitions / transversions = 1.64 (77/47) Gap_init rate = 0.07 (23 / 346), avg. gap size = 1.74 (40 / 23) 328 27.10 6.72 3.62 chr5ptel1M 329613 329746 (670254) C L2d2_3end#LINE/L2 (23) 532 395 m_b225s601i29 8868 chr5ptel1M 329613 ATTAAACACCAAGTATGCACAAGGC-TTGTGCTAAGTTTTGTGGGGGAGG 329661 i i i v v i ii -i i ivi vi C L2d2_3end#LIN 532 ATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGTGGGGGATA 483 chr5ptel1M 329662 GAGGTAAG-ATAATGTGGAGATCAGTTACTGTCCTCAAATA---TGTAAT 329707 v iiv - ---- v -i iv i iv --- ii C L2d2_3end#LIN 482 CAAAGAAGTATAA----GACAT-GGTCCCTGCCCTCAAGGAGCTTACAAT 438 chr5ptel1M 329708 CTA-CTGGGAAAATAAG--ATAAACCTGTGAAAAG-TGAATAA 329746 -i i i i -- vi - i C L2d2_3end#LIN 437 CTAGTTGGGGAGACAAGACATAAACACGTGAAAAGTTAAATAA 395 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.73 CpG sites = 25, Kimura (unadjusted) = 35.50 Transitions / transversions = 2.50 (25/10) Gap_init rate = 0.08 (11 / 133), avg. gap size = 1.27 (14 / 11) 262 27.62 9.24 5.69 chr5ptel1M 330561 330679 (669321) C MIRc#SINE/MIR (86) 182 60 m_b225s601i31 8869 chr5ptel1M 330561 ACCTTGTAACTGAGAAGCAGAAACAAGCATTGTCATTCACATTTTA---- 330606 i i -- iv i ii- i i i i i v ---- C MIRc#SINE/MIR 182 ACCCTGTGA--GGTAGGCAGGG-CAGGTATTATTATCCCCATTTTACAGA 136 chr5ptel1M 330607 TGGGTAAA-----GTTTAAAAAGATGAAATGACTTG-CCATCTCCTCACA 330650 i v ----- i i i i i v i - vvvi v C MIRc#SINE/MIR 135 TGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACA 86 chr5ptel1M 330651 GAT-CCAAGTGGCAGAGCTGGTAGGGACTC 330679 v -vi i---- C MIRc#SINE/MIR 85 GCTAGTAAGTGGCAGAGCC----GGGACTC 60 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.65 CpG sites = 21, Kimura (unadjusted) = 36.13 Transitions / transversions = 2.10 (21/10) Gap_init rate = 0.09 (11 / 118), avg. gap size = 1.64 (18 / 11) 220 26.30 16.96 1.55 chr5ptel1M 330586 330697 (669303) C MIR1_Amn#SINE/MIR (68) 162 34 m_b225s601i32 8869 chr5ptel1M 330586 AGCATTGTCATTCACATTTTA----TGGGTAAA-----GTTTAAAAAGAT 330626 i ii i i v ---- i v ----- i?i i i i C MIR1_Amn#SINE 162 AGTATCATTATCCCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGT 113 chr5ptel1M 330627 GAAATGACTTGCC----ATCTCCTCACAGATCCAAGTGGCAGAGCTGGTA 330672 ? i ----i v ?ivi ? i-- ? i v C MIR1_Amn#SINE 112 NAAGTGACTTGCCCAAGGTCACNCAGCNGG--CNAGTGGCAGAGCCGGGA 65 chr5ptel1M 330673 --GGGACTCTGCTCTGC----TCCCATGCCA 330697 --? i i v v v ---- vv C MIR1_Amn#SINE 64 NTNGAACCCAGGTCTCCCGAGTCCCAGTCCA 34 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.71 CpG sites = 19, Kimura (unadjusted) = 36.29 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.06 (7 / 111), avg. gap size = 3.00 (21 / 7) 218 30.27 12.00 0.90 chr5ptel1M 330611 330710 (669290) C MIR3#SINE/MIR (85) 123 13 m_b225s601i33 8869 chr5ptel1M 330611 TAAAGTTTAAAAAGATGAAATGACTTGCCATCTCCTCACAGATCCA---A 330657 i i iii i i i i -ivvvv v v ? --- C MIR3#SINE/MIR 123 TGAGGCCCAGAGAGGTGAAGTGACTTGCC-CAAGGTCACACAGCNAGTTA 75 chr5ptel1M 330658 GTGGCAGAGCTGGTA--GGGACTCTGCTCT----GCTCCCATGCCATG-- 330699 i v --i i i v v ----i vv i -- C MIR3#SINE/MIR 74 GTGGCAGAGCCGGGACTAGAACCCAGGTCTCCTGACTCCCAGTCCGTGCT 25 chr5ptel1M 330700 -TTTCTGCTTGG 330710 - i ii C MIR3#SINE/MIR 24 CTCTCTGCTCAG 13 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.47 CpG sites = 19, Kimura (unadjusted) = 41.01 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.06 (6 / 99), avg. gap size = 2.17 (13 / 6) 14 14.76 0.00 9.76 chr5ptel1M 332019 332063 (667937) (TATT)n#Simple_repeat 1 41 (0) m_b225s252i16 8870 chr5ptel1M 332019 TATTGACTTAGTTTTTGTTATTTGTTTTATTGCATTTATTTATTT 332063 v i - v - -v -i (TATT)n#Simpl 1 TATTTATTTA-TTTAT-TTATTT-ATTTATT-TATTTATTTATTT 41 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4) 238 30.77 0.00 1.28 chr5ptel1M 332465 332543 (667457) L2d2_3end#LINE/L2 19 96 (459) m_b225s601i34 8871 chr5ptel1M 332465 ACTTGGCTTTTCTACCTGTGTCTCACACTTTTTTCTCTCGGGGACTCACT 332514 i ?v i vi - i v v ii ii? iv i i v i L2d2_3end#LIN 19 ACCTNCCTTTCCAGCCT-TATCTCCCACTATTCCCCTNCACGAACCCTCC 67 chr5ptel1M 332515 GCTCCAGCTAAACTGGATTATTTGCTGTC 332543 i vi i ii L2d2_3end#LIN 68 GCTCCAGCCAAACTGGTCTACTCACTGTC 96 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.35 CpG sites = 17, Kimura (unadjusted) = 43.86 Transitions / transversions = 2.43 (17/7) Gap_init rate = 0.01 (1 / 78), avg. gap size = 1.00 (1 / 1) 692 25.90 4.02 2.99 chr5ptel1M 332603 332801 (667199) MIRc#SINE/MIR 10 210 (58) m_b225s601i35 8872 chr5ptel1M 332603 GTGGTACAGTGTATATGGTGCTAGGCTTGGAGTTTGGGGGATCCGAGTTC 332652 i v v vi ii i i iv ii i i i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr5ptel1M 332653 ACATCCAGCTTCTGACAATCGCTAGTTATGTGACCCTGGGCAAGTCATAT 332702 ivi v vi v v ii i i i iv MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTT 109 chr5ptel1M 332703 A--TTCTCTGAGTGCCCCAGTTTTCCCCACTATAAAATAGGTGCTAATAA 332750 --i -- i i i vv i i - v MIRc#SINE/MIR 110 AACCTCTCTGA--GCCTCAGTTTCCTCATCTGTAAAATGGG-GATAATAA 156 chr5ptel1M 332751 TA---GC---ACCTACCTTGCCAGCGTTATTGTAAGGATCAAGGGAATTG 332794 --- ---i ii- v i i iv iv - MIRc#SINE/MIR 157 TACCTGCCCTGCCTACCTCA-CAGGGTTGTTGTGAGGATCAAATGAGAT- 204 chr5ptel1M 332795 CAATGTA 332801 - MIRc#SINE/MIR 205 -AATGTA 210 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.28 CpG sites = 34, Kimura (unadjusted) = 33.10 Transitions / transversions = 2.12 (34/16) Gap_init rate = 0.05 (9 / 198), avg. gap size = 1.56 (14 / 9) 20 6.66 0.00 3.03 chr5ptel1M 333100 333133 (666867) (TTATAT)n#Simple_repeat 1 33 (0) m_b225s252i17 8873 chr5ptel1M 333100 TTATATTTATGTTTACATTTATTATTTATATTTA 333133 i i - (TTATAT)n#Sim 1 TTATATTTATATTTATATTTA-TATTTATATTTA 33 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 14 8.85 0.00 0.00 chr5ptel1M 333780 333803 (666197) (GAAA)n#Simple_repeat 1 24 (0) m_b226s252i1 8874 chr5ptel1M 333780 GAAAAAAAGAAAGAAAGAAAGCAA 333803 i v (GAAA)n#Simpl 1 GAAAGAAAGAAAGAAAGAAAGAAA 24 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 346 29.43 7.27 1.14 chr5ptel1M 334173 334337 (665663) Tigger16b#DNA/TcMar-Tigger 150 324 (7) m_b226s502i0 8875 chr5ptel1M 334173 TAGTACC--TAGTATTATTAATTAAACTGTATTATAGATAAAGTAGACTT 334220 i-- i - ? v i? ii i i v i i Tigger16b#DNA 150 TAGTACTATTAGTACTAT-ANTTCAGNTACATTATGGGTTAAATAGGCTT 198 chr5ptel1M 334221 CTCTGAATTGGGCCTGCAAACCTAGTTTCCATTTGTAGCATTATTTCTAT 334270 i v iii - vi iiiv i i i Tigger16b#DNA 199 TTGTGGGCTGG-CCTGGGAACCTAACCACCATTTATAACATTGTTTCTAT 247 chr5ptel1M 334271 GAGAAGATTGAATCT---TTTCAAAAAATCGATTTGTAA--CAATT---- 334311 i i vviv i--- i v ii i ii --v i ---- Tigger16b#DNA 248 GGGAAAATGCGTTCCGAGTTCCAAACAACTGACTTACAAACGAACTTTTG 297 chr5ptel1M 334312 -AACACAAACCATTTGCAAGGTGAGAA 334337 - v i i i v i i Tigger16b#DNA 298 GAACACAACCCGTTCGTAAGTTGGGGA 324 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.45 CpG sites = 36, Kimura (unadjusted) = 40.92 Transitions / transversions = 3.00 (36/12) Gap_init rate = 0.04 (7 / 164), avg. gap size = 2.00 (14 / 7) 13 24.30 5.66 0.00 chr5ptel1M 334896 334948 (665052) (AAAATG)n#Simple_repeat 1 56 (0) m_b226s252i2 8876 chr5ptel1M 334896 AAAAT-CAGATCAAAAAGGAAA-GAAAACGAGTCAGAAAA-CAAAATGAA 334942 -v i v v i - i ivvv -v (AAAATG)n#Sim 1 AAAATGAAAATGAAAATGAAAATGAAAATGAAAATGAAAATGAAAATGAA 50 chr5ptel1M 334943 AATGAA 334948 (AAAATG)n#Sim 51 AATGAA 56 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.06 (3 / 52), avg. gap size = 1.00 (3 / 3) 344 29.26 5.65 0.77 chr5ptel1M 335924 336047 (663953) MIR1_Amn#SINE/MIR 1 130 (100) m_b226s601i1 8877 chr5ptel1M 335924 TACAGAGACAGCAGGGTATAGTGGATAGAATACTAGTCTGG-AC-----A 335967 vi i iiv v ii i v - ----- MIR1_Amn#SINE 1 TAGGGAGGCAGTGTGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGA 50 chr5ptel1M 335968 GATCTAGGTTCAGATAACACATTGGACACTTGA-AACTAATTTGACCCAG 336016 i i ?i? vv ivv iv v ? v-?i i?v - iv MIR1_Amn#SINE 51 GACCTGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGT-GACCTTG 99 chr5ptel1M 336017 GATGAATCACTCAACCTCTTCGTGCCTTAGT 336047 iii i i? ii ? i MIR1_Amn#SINE 100 GGCAAGTCACTTNACCTCTCTGNGCCTCAGT 130 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.32 CpG sites = 23, Kimura (unadjusted) = 41.87 Transitions / transversions = 1.77 (23/13) Gap_init rate = 0.03 (4 / 123), avg. gap size = 2.00 (8 / 4) 33 0.00 0.00 0.00 chr5ptel1M 336777 336807 (663193) (C)n#Simple_repeat 1 31 (0) c_b226s251i0 8878 chr5ptel1M 336777 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 336807 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 338 27.73 0.80 7.69 chr5ptel1M 337382 337506 (662494) MIRc#SINE/MIR 11 127 (141) m_b226s601i2 8879 chr5ptel1M 337382 TGGCTCAGTGGATACTGCCCCATCCCTGAAGTCAGGAGGACCCAAGTTCT 337431 iv v vv v iivv i i i iii v MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr5ptel1M 337432 AATCTGGTCTCAAGACACTTAACACTTTCTGGCTGTGTGACCCCCGGGCA 337481 i iv v -------- iv v i - ii MIRc#SINE/MIR 61 AGTCCCGGCTC--------TGCCACTTACTAGCTGTGTGA-CCTTGGGCA 101 chr5ptel1M 337482 AGTCACTTAATCCCAATT-GCCTCAG 337506 i i vv v- MIRc#SINE/MIR 102 AGTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.93 CpG sites = 17, Kimura (unadjusted) = 34.93 Transitions / transversions = 1.13 (17/15) Gap_init rate = 0.08 (10 / 124), avg. gap size = 1.00 (10 / 10) 18 14.91 0.00 0.00 chr5ptel1M 337508 337537 (662463) (A)n#Simple_repeat 1 30 (0) m_b226s252i3 8880 chr5ptel1M 337508 AAAAAACAAAAACAAAATAAAACAAAAAAA 337537 v v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 30 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 242 24.53 0.00 0.00 chr5ptel1M 338700 338752 (661248) MIR3#SINE/MIR 147 199 (9) m_b226s601i3 8881 chr5ptel1M 338700 GGGTTAGACTATAGGATTTCTGGGATGCCTTCCGACTCTGATTTTCTGTG 338749 i v v i ii i v ii iv i MIR3#SINE/MIR 147 GGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATG 196 chr5ptel1M 338750 ATT 338752 MIR3#SINE/MIR 197 ATT 199 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.91 CpG sites = 9, Kimura (unadjusted) = 30.91 Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 263 13.04 4.35 0.00 chr5ptel1M 339173 339218 (660782) C MIRc#SINE/MIR (145) 123 76 m_b226s601i4 8882 chr5ptel1M 339173 GGCTCACAG--GTTCAGTGACTTTCCCAGGATCACACGGCTAGTAAGT 339218 v -- v v i i i C MIRc#SINE/MIR 123 GGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGT 76 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 14.38 CpG sites = 3, Kimura (unadjusted) = 14.38 Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.02 (1 / 45), avg. gap size = 2.00 (2 / 1) 219 24.64 10.14 0.00 chr5ptel1M 339180 339248 (660752) C MIR#SINE/MIR (152) 110 35 m_b226s601i5 8882 chr5ptel1M 339180 AGGTTCAGTGACTTTCCCAGGATCACACGGCTAGTAAGT--C----CCCG 339223 v i v i i i -- ---- v C MIR#SINE/MIR 110 AGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGG 61 chr5ptel1M 339224 AATGTG-CCCTAAGCCACCTAGCTCC 339248 i vi -v i i vii i C MIR#SINE/MIR 60 GATTCGAACCCAGGCAGTCTGGCTCC 35 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.65 CpG sites = 11, Kimura (unadjusted) = 30.80 Transitions / transversions = 1.83 (11/6) Gap_init rate = 0.04 (3 / 68), avg. gap size = 2.33 (7 / 3) 15 15.86 2.86 0.00 chr5ptel1M 340064 340098 (659902) (TTCTTT)n#Simple_repeat 1 36 (0) m_b226s252i4 8883 chr5ptel1M 340064 TTCATTTT-TTTTTCTTTTTCTTGGTTTTTTCCTTT 340098 v - vv i i (TTCTTT)n#Sim 1 TTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTT 36 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 316 29.75 0.00 0.00 chr5ptel1M 342022 342142 (657858) C L1MB1_3end#LINE/L1 (643) 272 152 m_b226s551i0 8884 chr5ptel1M 342022 GTTTCAATTTTTTTACGTTCTGGTCAACATTCATTATTTTTCTTTTCTGT 342071 i i ii i i v i i ii iv i v C L1MB1_3end#LI 272 GTTCCAATTTCTCCACATCCTCGCCAACACTTGTTATTTTTTGTTTTTTT 223 chr5ptel1M 342072 CATATTTGCCAATCTGTTAGGTATGAGGTGATACATCAGAGGTGTTGTAA 342121 v v v vi ivi i iv vv vv v i C L1MB1_3end#LI 222 GATAATAGCCATCCTAACAGGTGTGAGGTGATATCTCATTGTGGTTTTGA 173 chr5ptel1M 342122 TTTGCATTTTTCATATGATTA 342142 ii vv C L1MB1_3end#LI 172 TTTGCATTTCCCTGATGATTA 152 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.75 CpG sites = 20, Kimura (unadjusted) = 38.75 Transitions / transversions = 1.25 (20/16) Gap_init rate = 0.00 (0 / 120), avg. gap size = 0.0 (0 / 0) 32 0.00 0.00 0.00 chr5ptel1M 344516 344545 (655455) (T)n#Simple_repeat 1 30 (0) c_b226s251i1 8885 chr5ptel1M 344516 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 344545 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 30 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 281 28.24 2.26 1.49 chr5ptel1M 346197 346329 (653671) C L1ME4c_3end#LINE/L1 (432) 398 265 m_b226s551i1 8886 chr5ptel1M 346197 TAAAGTCCAGGAAGTG-AGTTTGTGGTTCAAAAGACAGGAACAGTTTCGT 346245 v vi - i vv v i ii v v ii C L1ME4c_3end#L 398 TAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTAT 349 chr5ptel1M 346246 TAGTTCATT--TGCACATTTCCATGTTGCTTTTCAAAATGATCTTGCCGT 346293 -i i - -- i ii v vi i v i iv i iv C L1ME4c_3end#L 348 -GGCTC-TTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAA 301 chr5ptel1M 346294 TCTTCAGTTCCAGCAGCAATGTATCAGTGCACCTGT 346329 i v ? v v v ? i v C L1ME4c_3end#L 300 TTTACANTGCCACCAGCAATGTATGAGNGTACCAGT 265 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.57 CpG sites = 20, Kimura (unadjusted) = 36.81 Transitions / transversions = 1.18 (20/17) Gap_init rate = 0.03 (4 / 132), avg. gap size = 1.25 (5 / 4) 28 17.69 3.45 0.00 chr5ptel1M 346518 346575 (653425) (TA)n#Simple_repeat 1 60 (0) m_b226s252i5 8887 chr5ptel1M 346518 TATACATGCATATGTGTAAAT-TATATATATATATATATATATAT-TACA 346565 i ii i i v - - i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr5ptel1M 346566 TATTTTTATA 346575 v v (TA)n#Simple_ 51 TATATATATA 60 Matrix = Unknown Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.04 (2 / 57), avg. gap size = 1.00 (2 / 2) 21 5.96 2.70 2.70 chr5ptel1M 346900 346936 (653064) (TGT)n#Simple_repeat 1 37 (0) m_b226s252i6 8888 chr5ptel1M 346900 TGTTGTTCTTGTTGTTGTT-TTTTTGCTTGTTGTTGTT 346936 v - v - (TGT)n#Simple 1 TGTTGTTGTTGTTGTTGTTGTTGTTG-TTGTTGTTGTT 37 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 237 28.79 3.12 2.33 chr5ptel1M 347311 347438 (652562) C L1ME4c_3end#LINE/L1 (446) 384 256 m_b226s551i2 8889 chr5ptel1M 347311 TGGAATATTTTGATTCAAGGGATATGAACATTTTAATTA--CTTAATTTG 347358 - vi iv i i v vi-- i -- i C L1ME4c_3end#L 384 TGGAAT-TACTGGGTCAAAGGGTATGAACATTTTTATGGCTCTTGA--TA 338 chr5ptel1M 347359 CATAATTCCATATTTCTTTTTAAAATGATTGTCCCATTCTCTGATTCAAG 347408 i v v v v ii v i v v i vii? v v v C L1ME4c_3end#L 337 CGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACANTGCCAC 288 chr5ptel1M 347409 CAGCAACGCATTAGTGTGCC--TGTCATTGCA 347438 i i v ? i -- v ii C L1ME4c_3end#L 287 CAGCAATGTATGAGNGTACCAGTTTCACCGCA 256 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.14 CpG sites = 19, Kimura (unadjusted) = 37.72 Transitions / transversions = 1.12 (19/17) Gap_init rate = 0.04 (5 / 127), avg. gap size = 1.40 (7 / 5) 246 22.22 7.94 0.00 chr5ptel1M 347461 347523 (652477) C L2c_3end#LINE/L2 (41) 437 370 m_b226s601i6 8890 chr5ptel1M 347461 GCCACGTGTTGAG-ATATAGAGA-GAA-AAGACA--GTCCTGGCTCTTCA 347505 v i i i - i i - - -- iv i iv C L2c_3end#LINE 437 GCCAGGCGCTGGGGATACAAAGATGAATAAGACACGGTCCCTGCCCTCAA 388 chr5ptel1M 347506 GGAACTCACAATCTATTG 347523 i i v C L2c_3end#LINE 387 GGAGCTCACAGTCTAGTG 370 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.12 CpG sites = 10, Kimura (unadjusted) = 27.37 Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.06 (4 / 62), avg. gap size = 1.25 (5 / 4) 198 32.96 0.00 3.80 chr5ptel1M 347851 347932 (652068) MIR#SINE/MIR 41 119 (143) m_b226s601i7 8891 chr5ptel1M 347851 AGGCTGGTTGGATTCAATTGCTGTCTCTGACATGGTACCGCCTGTGTGCT 347900 i vi i i v v i v v iv- iiv vi MIR#SINE/MIR 41 AGACTGCCTGGGTTCGAATCCCGGCTCTGCCACT-TACTAGCTGTGTGAC 89 chr5ptel1M 347901 TCTAGGCAAATCACTAAGTTCCTCACTGTTCC 347932 ii i i i v i-- v v MIR#SINE/MIR 90 CTTGGGCAAGTTACTTAA--CCTCTCTGTGCC 119 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.23 CpG sites = 15, Kimura (unadjusted) = 44.75 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.04 (3 / 81), avg. gap size = 1.00 (3 / 3) 344 28.93 8.70 0.81 chr5ptel1M 348087 348201 (651799) C L2d2_3end#LINE/L2 (12) 543 420 m_b226s601i8 8892 chr5ptel1M 348087 AATAAACCTTTAATTAATGCCATATTCTG-----GGCACTCTACTAAGCA 348131 i iv v v ii - i v ----- v i i i C L2d2_3end#LIN 543 AACAAATATTTATTGAGCGCC-TACTGTGTGCAAGGCACTGTGCTAGGCG 495 chr5ptel1M 348132 TTG---GCGATACAAAGAAAGGCAAAGAACAGTCTCTGCTGTCAAGGAAT 348178 i --- v ivii iiv ii i iv ii C L2d2_3end#LIN 494 CTGTGGGGGATACAAAGAAGTATAAGACATGGTCCCTGCCCTCAAGGAGC 445 chr5ptel1M 348179 TCACAATCTAA--AGGGAGAAAAGA 348201 i i--i v C L2d2_3end#LIN 444 TTACAATCTAGTTGGGGAGACAAGA 420 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.60 CpG sites = 23, Kimura (unadjusted) = 38.61 Transitions / transversions = 2.30 (23/10) Gap_init rate = 0.04 (4 / 114), avg. gap size = 2.75 (11 / 4) 264 29.23 10.40 1.47 chr5ptel1M 348520 348644 (651356) L2d2_3end#LINE/L2 420 555 (0) m_b226s601i9 8893 chr5ptel1M 348520 TCATGTTTCTCCAAATAGAATATAAGTTCCCTGTTGG-AAATTCCA-ATT 348567 v i i v v i i i vv - iivv -i i L2d2_3end#LIN 420 TCTTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTC 469 chr5ptel1M 348568 TCACTTTTGGCTTTGAA---CCCATGGAATCCAGTCCAGTGCCTGGCACA 348614 i ivi -- v --- ii vii i iv v L2d2_3end#LIN 470 TTATACTT--CTTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCACA 517 chr5ptel1M 348615 TA-------CTTAATAATTATTTGTTAAATT-ACTTGA 348644 i ------- i v i v - i L2d2_3end#LIN 518 CAGTAGGCGCTCAATAAATATTTGTTGATTTGATTTGA 555 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.98 CpG sites = 22, Kimura (unadjusted) = 38.35 Transitions / transversions = 1.57 (22/14) Gap_init rate = 0.06 (7 / 124), avg. gap size = 2.14 (15 / 7) 20 10.19 4.55 2.22 chr5ptel1M 349196 349239 (650761) (AGAT)n#Simple_repeat 1 45 (0) m_b226s252i8 8894 chr5ptel1M 349196 AGATAGATAGATAAAGAGATAGAAAGATAGAATGGA-A-ATAGATA 349239 i v v - i - - (AGAT)n#Simpl 1 AGATAGATAGATAGATAGATAGATAGATAG-ATAGATAGATAGATA 45 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.07 (3 / 43), avg. gap size = 1.00 (3 / 3) 18 22.65 0.00 5.08 chr5ptel1M 349192 349253 (650747) (AAATAG)n#Simple_repeat 1 59 (0) m_b226s252i7 8895 chr5ptel1M 349192 AAACAGATAGATAGATAAAGAGATAGAAAGATAGAATGGAAATAGATATA 349241 i - - v v i v v - i v (AAATAG)n#Sim 1 AAATAGA-A-ATAGAAATAGAAATAGAAATAGA-AATAGAAATAGAAATA 47 chr5ptel1M 349242 ATAATGGAAATA 349253 iv i (AAATAG)n#Sim 48 GAAATAGAAATA 59 Matrix = Unknown Transitions / transversions = 0.83 (5/6) Gap_init rate = 0.05 (3 / 61), avg. gap size = 1.00 (3 / 3) 12 35.74 1.49 0.00 chr5ptel1M 349198 349264 (650736) (ATAAAT)n#Simple_repeat 1 68 (0) m_b226s252i9 8895 chr5ptel1M 349198 ATAGATAGATAAAGAGATAGAAAGATAGA-ATGGAAATAGATATAATAAT 349246 i v v v v i v v i - ii v i vv (ATAAAT)n#Sim 1 ATAAATATAAATATAAATATAAATATAAATATAAATATAAATATAAATAT 50 chr5ptel1M 349247 GGAAATAATTATAAATAT 349264 ii v v (ATAAAT)n#Sim 51 AAATATAAATATAAATAT 68 Matrix = Unknown Transitions / transversions = 0.73 (8/11) Gap_init rate = 0.02 (1 / 66), avg. gap size = 1.00 (1 / 1) 224 29.58 1.39 1.39 chr5ptel1M 349310 349381 (650619) MIRc#SINE/MIR 17 88 (180) m_b226s601i10 8896 chr5ptel1M 349310 AGTATAAATAGGAGTGAGTCTTGGAATCAGGAAGACATGAAAGCAAATGC 349359 iv v v v - v i v iivv i i v MIRc#SINE/MIR 17 AGTGGAAAGAGCACTG-GACTTGGAGTCAGGAAGACCTGGGTTCGAGTCC 65 chr5ptel1M 349360 CACCTTT-CCTTTTACTAGTTGT 349381 iv i - vi i MIRc#SINE/MIR 66 CGGCTCTGCCACTTACTAGCTGT 88 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.65 CpG sites = 10, Kimura (unadjusted) = 37.96 Transitions / transversions = 0.91 (10/11) Gap_init rate = 0.03 (2 / 71), avg. gap size = 1.00 (2 / 2) 742 31.54 5.77 1.34 chr5ptel1M 349841 350412 (649588) C L1ME4c_3end#LINE/L1 (191) 639 43 m_b226s551i3 8897 chr5ptel1M 349841 TTCTGCTCATTTCACTTAGCATAAGTTCATGTACATCTTTCCAAGCTTCC 349890 iv i v vv iv - v i v i C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATAAACAT-TTTCCATGTTGCT 591 chr5ptel1M 349891 ------TCTCCTT--TGGTCATTTCTTACAGAAAAATTATATTCCATAGC 349932 ------ i v -- vi i v ii vviv v v v C L1ME4c_3end#L 590 ACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCGA 541 chr5ptel1M 349933 ATTCATAAACCATAATTTATTCAGCCATTCTCTAATTAATGGACATCCAT 349982 i ?v iv i i i i iv iv ii v C L1ME4c_3end#L 540 GTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAG 491 chr5ptel1M 349983 TCAGTTTCCAGTGTCTTGCCACTACAAAAAGGGCTACTACAAAC-TTTTT 350031 viv i v i i i i i v iv i v ii - i i C L1ME4c_3end#L 490 GTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTC 441 chr5ptel1M 350032 GCACATATGGGGCCCTTTTCTTCCTTTAAG--ATCTGTTTGGGATACAAG 350079 ii --i ii i i i i-- i vi i v vv C L1ME4c_3end#L 440 GTGCATAT--AGCTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAATT 393 chr5ptel1M 350080 CCC---AGTAAAAACA------CAA-----ATGCACAGTTTGATAACTTT 350115 --- ii vi ------ ----- v v v ii i C L1ME4c_3end#L 392 CCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTCT 343 chr5ptel1M 350116 TTGAGCATAGTTCCAAACTGCTCTCCAGTATGGTTGGATCCATATACAGT 350165 vivi i v v i i iv v v i v v ? C L1ME4c_3end#L 342 TGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACANT 293 chr5ptel1M 350166 TCTACCAGTAATGTATCAGTGTCTCTGTTTTCCTACATCCCCTCCAGT-- 350213 v i i v ? vi v iv ii ? i v i-- C L1ME4c_3end#L 292 GCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGCAT 243 chr5ptel1M 350214 ----CATTATCTTTTCCTGTCATCTTAGTCGATCTGAGAGGT-TGTAGTG 350258 ----i vv ii vvv i v iii i i v i- iv i C L1ME4c_3end#L 242 TGGGTATTATCAATTTTTTAAATTTTTGCTAATTTAATAGGCGTAAAATG 193 chr5ptel1M 350259 GTATCTCAGAGTTGTCTTGATTTGCATTTCTCTGATCAATAGTGATTTAG 350308 vv ii i i i v i vv v C L1ME4c_3end#L 192 GTATCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACTAGCGAGGTTG 143 chr5ptel1M 350309 AGCACCTTTTCATAGGACTA-GAAATAGTTTCAGTTTCATCATCTGAAAA 350357 i ii i iv vi i-vv v ? vi - v v ? vi C L1ME4c_3end#L 142 AACATTTTTCCATGTGTTTGTTTACTANTTGTA-TTTCCTCTTNTGTGAA 94 chr5ptel1M 350358 TTGTCTTCTCCTATCCTTTGATCATTTACCAATTGGAGAATGGCTTGAGT 350407 vi v i vi i v i---- v v? C L1ME4c_3end#L 93 TTGTCTGTTCATGTCCTTTGCCCATTTATCTATTGGG----GTCTTGATN 48 chr5ptel1M 350408 TTTTT 350412 C L1ME4c_3end#L 47 TTTTT 43 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.80 CpG sites = 99, Kimura (unadjusted) = 42.73 Transitions / transversions = 1.25 (99/79) Gap_init rate = 0.03 (19 / 571), avg. gap size = 2.16 (41 / 19) 837 29.19 6.54 2.43 chr5ptel1M 349922 350395 (649605) C L1ME5_3end#LINE/L1 (393) 548 56 m_b226s551i4 8897 chr5ptel1M 349922 TATTCCATAGCATTCATAAACCATAATTTATTCAGCCATTCTCTAATTAA 349971 i i ii v vv i v iii v i iv v i C L1ME5_3end#LI 548 TACTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCAGTGA 499 chr5ptel1M 349972 TGGACATCCATTCAGTTTCCAGTGTCTTGCCACTACAAAAAGGGCTACTA 350021 i vviv ii iivi ii i v iv i v C L1ME5_3end#LI 498 TGGACACCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCTGCAA 449 chr5ptel1M 350022 CAAAC-TTTTTGCACATATGGGGCCCTTTTCTTCCTTT---AAGATCTGT 350067 ii - ii i i i v--- v vvv v --- ii i v C L1ME5_3end#LI 448 TGAACATCCTCGTACATGTC---CCCTTATGGACCTGTGTGAGAATTTCT 402 chr5ptel1M 350068 TTGGGATACAAGCCCAGTAAAAACACAAATGC--------ACAGTTTG-A 350108 i vi ---i i iv v -------- vi v -i C L1ME5_3end#LI 401 TTGGGATATATACCCAG---GAGCGGAATTGCTGGGTCATAGGGTATGCG 355 chr5ptel1M 350109 TA-ACTT--TTTGAGCA--TAGTTCCAAACTGCTCTCCAGTATGGTTGGA 350153 - -- vi -- v v i i v i v C L1ME5_3end#LI 354 TATACTTAATTTGACTAAGTACTGCCAGATTGCTCTCCAGAATGGCTGCA 305 chr5ptel1M 350154 TCCATATACAGTTCTACCAGTAATGTATCAGTGTCTCTGTTTTCCTACAT 350203 i vi v v i i i i i v v ii i ? i i C L1ME5_3end#LI 304 CCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATNTCCCCACAT 255 chr5ptel1M 350204 CCCCTCCA------GTCATTATCT---TTTCCTGTCATCTTAGTCGATCT 350244 i v ------ v i--- --- v i v i ii C L1ME5_3end#LI 254 CCTCGCCAACACTTGGCATTATCCAGCTTTC---TAATTTTTGCCAGTCT 208 chr5ptel1M 350245 GAGAGGT-TGTAGTGGTATCTCAGAGTTGTCTTGATTTGCATTTCTCTGA 350293 i v - iv i vv i i C L1ME5_3end#LI 207 AATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATTTCTCTGA 158 chr5ptel1M 350294 TCAATAGTGATTTAGAGCACCTTTTCATAGGACTAGAAATAG--TTTC-A 350340 i v i v v i i v - v --v -- -i C L1ME5_3end#LI 157 TTACTAATGAGTTTGAGCATCTCTTCATATG-CTTG--TTAGCCTTTCGG 111 chr5ptel1M 350341 GTTTCATCATCTGAAAATTGTCTTCTCCTATCCTTTGATCATTTACCAAT 350390 v v v i vi v vi vi v C L1ME5_3end#LI 110 GTTTCCTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCCATTTTTCTAT 61 chr5ptel1M 350391 TGGAG 350395 i C L1ME5_3end#LI 60 TGGGG 56 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.62 CpG sites = 77, Kimura (unadjusted) = 38.04 Transitions / transversions = 1.33 (77/58) Gap_init rate = 0.05 (24 / 473), avg. gap size = 1.79 (43 / 24) 16 20.82 0.00 0.00 chr5ptel1M 350724 350756 (649244) (T)n#Simple_repeat 1 33 (0) m_b226s252i10 8898 chr5ptel1M 350724 TTCTTTTTGTTTTTTTTTTTAATTCATTTTTTT 350756 i v vv iv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 33 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 12 10.36 0.00 11.43 chr5ptel1M 350985 351023 (648977) (CTCCAA)n#Simple_repeat 1 35 (0) m_b226s252i11 8899 chr5ptel1M 350985 CTACAACGCCATGACTCCCCACTCCAACTCCTAACTCCA 351023 v v -- - v - (CTCCAA)n#Sim 1 CTCCAACTCCA--ACT-CCAACTCCAACTCC-AACTCCA 35 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.11 (4 / 38), avg. gap size = 1.00 (4 / 4) 19 4.50 0.00 0.00 chr5ptel1M 352381 352403 (647597) (T)n#Simple_repeat 1 23 (0) m_b226s252i12 8900 chr5ptel1M 352381 TTGTTTTTTTTTTTTTTTTTTTT 352403 v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTT 23 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 410 23.69 1.71 2.59 chr5ptel1M 353127 353243 (646757) Charlie1a#DNA/hAT-Charlie 1334 1449 (6) m_b226s502i1 8901 chr5ptel1M 353127 TTTAATTTCTAGGATGGTAAATACTGATTGACA-AAGCTGTGTAAACAAA 353175 iv ii v i - v iiii Charlie1a#DNA 1334 TTTAATTTCTAATATGGTAAATATCGATAGATATAACCCACATAAACAAA 1383 chr5ptel1M 353176 AGCTCTCGGGGTAAATCTTTAACA-TTTTTAAGAATGTAGAGGAATTCCA 353224 iv ---i i i i - i i ii i ii Charlie1a#DNA 1384 AGCTCTTTGGG---GTCCTCAATAATTTTTAAGAGTGTAAAGGGGTCCTG 1430 chr5ptel1M 353225 AGATCAAAAACTTTGTGAA 353243 i v v Charlie1a#DNA 1431 AGACCAAAAAGTTTGAGAA 1449 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 28.76 CpG sites = 21, Kimura (unadjusted) = 30.11 Transitions / transversions = 3.50 (21/6) Gap_init rate = 0.04 (5 / 116), avg. gap size = 1.00 (5 / 5) 323 29.18 1.52 2.56 chr5ptel1M 353491 353687 (646313) L1PREC2_orf2#LINE/L1 3100 3294 (0) m_b226s551i5 8902 chr5ptel1M 353491 ATAAACTGGGAAAACATTTTTACAGTCAAAGGTTCTGATAAAGGACTCAT 353540 i i v i v ? i iv v v vv i v v L1PREC2_orf2# 3100 ACAGAATGGGAGAAAATNTTTGCAAACTATGCATCTGACAAAGGTCTAAT 3149 chr5ptel1M 353541 TTCCAACATATATATAGAGAATTGACTCTAATTTATAAGAAAT---CAAG 353587 v i v - - i v vv v i v--- i L1PREC2_orf2# 3150 ATCCAGCATCTATA-AG-GAACTTAAACAAATTTACAAGAAAAAAACAAA 3197 chr5ptel1M 353588 CCATTCTCCAATTGATAAATGGTCAAAGGATATGAACAGACAATTTTCAG 353637 v i--- v i v i v i v i L1PREC2_orf2# 3198 CAAC---CCCATTAAAAAGTGGGCAAAGGACATGAACAGACACTTTTCAA 3244 chr5ptel1M 353638 ATGATGAAATTAAAACTATTACTACTCATATGAAAGAATGTTCCAAATCA 353687 v v v vv vi viii vi vv i v i v v L1PREC2_orf2# 3245 AAGAAGACATACATGCGGCCAACAAGCATATGAAAAAAAGCTCAACATCA 3294 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.25 CpG sites = 22, Kimura (unadjusted) = 37.25 Transitions / transversions = 0.65 (22/34) Gap_init rate = 0.03 (6 / 196), avg. gap size = 1.33 (8 / 6) 1357 29.77 1.51 3.07 chr5ptel1M 353593 354188 (645812) L1ME5_3end#LINE/L1 56 642 (299) m_b226s551i6 8902 chr5ptel1M 353593 CTCCAATTGATAAATGGTCAAAGGATATGAACAGACAATTTTCAGATGAT 353642 i v v v i v v v L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chr5ptel1M 353643 GAAATTAAAACTATTACTACTCATATGAAAGAATGTTCCAAATCACTATT 353692 iivi vvii vi vv iii i v v i v L1ME5_3end#LI 106 GAAACCCGAAAGGCTAACAAGCATATGAAGAGATGCTCAAACTCATTAGT 155 chr5ptel1M 353693 GATCAGAGAAATGCAAATTAAGACAACTCTGAGATAACACTATACACCTG 353742 i i vv v v i L1ME5_3end#LI 156 AATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCTA 205 chr5ptel1M 353743 TCAGATTGGCCAGAATGACAGGGAAAGATAATGCAGAATGTTGGAGGGGA 353792 i i v i v v ii vvi vi i v i L1ME5_3end#LI 206 TTAGACTGGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTGGCGAGGA 255 chr5ptel1M 353793 TGTGGGAAAACAGGGACACTGCTACATTGTTGGTGGAATTGTGAATACAT 353842 i ? i i v vv i i i i v ii ivvi L1ME5_3end#LI 256 TGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACTGGT 305 chr5ptel1M 353843 CCAACCATTCTGGAGAGCAATTTGGAACTATGCCCAAAAAGTTA-TCAAA 353891 v i i v v i---------- - L1ME5_3end#LI 306 GCAGCCATTCTGGAGAGCAATCTGGCAGTAC----------TTAGTCAAA 345 chr5ptel1M 353892 CTGTG-ATAACTGTGATCCCTTTGATCCAGCAGGGTCTCTACTGGGCTTA 353940 i iv - --i iivv v i ivvi v v iv L1ME5_3end#LI 346 TTAAGTATA--CGCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATA 393 chr5ptel1M 353941 TACCCCAAAGAGATACTAAAAAAGG----GAAAGGGACCTGTATGTGCCA 353986 i i v v v v ----v i v i ---- L1ME5_3end#LI 394 TATCCCAAAGAAATTCTCACACAGGTCCATAAGGGGACATGTACG----A 439 chr5ptel1M 353987 AAATGTTTGTGGCAGCCCTGCTTGTAGTGGCCAGAAGCTGGAAAATGAAT 354036 ii ii v vi i i vi i i iivvivv L1ME5_3end#LI 440 GGATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCT 489 chr5ptel1M 354037 GGATGCCCATCAATTGGAGAATGGTTGAGTAAACTGTGATATATGAATGT 354086 i i v v i v ii v i iv v iii L1ME5_3end#LI 490 GGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACAC 539 chr5ptel1M 354087 CATGGAATATTATTGTTCTGTAAGAAGTGACCAGCAGGATGAATACAGAG 354136 i i vvvv v v ii vii vi v i v L1ME5_3end#LI 540 CATGGAGTACTATGCAGCAGTTAGAAGCAACGGACTAGATGTACACATAG 589 chr5ptel1M 354137 -AGGATTGACGAGACCTACATGAAC-TGATGCTGAGCGAAATGAGC-AGA 354183 - iv v i iiv i v -- - ii i vi i- L1ME5_3end#LI 590 CAACATGGATGGATCTTAAA--AACATAGTGCTGAGTGAAAAAAGTAAGA 637 chr5ptel1M 354184 ACCAG 354188 v L1ME5_3end#LI 638 AACAG 642 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.88 CpG sites = 93, Kimura (unadjusted) = 38.74 Transitions / transversions = 1.18 (93/79) Gap_init rate = 0.04 (24 / 595), avg. gap size = 1.12 (27 / 24) 250 30.49 4.92 3.23 chr5ptel1M 354807 354928 (645072) L2d2_3end#LINE/L2 425 548 (7) m_b226s601i11 8903 chr5ptel1M 354807 TTTCCTCAA-TAGAATATCAACTCTTTATGGATAGTTACTA-GT-TTATT 354853 i i - v i v i i iv ii vv i - - v L2d2_3end#LIN 425 TCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATA 474 chr5ptel1M 354854 TTTGTCTTTGTAACCCAAGAACCCTCTAG---AGTGCCTAGTATACAAGA 354900 i -- v vviv v vi --- v i i iv L2d2_3end#LIN 475 CTT--CTTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAGTA 522 chr5ptel1M 354901 AGTGATTAATAAATGCTTATGTTGAGTT 354928 i i v i ii -- v L2d2_3end#LIN 523 GGCGCTCAATAAATATT--TGTTGATTT 548 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.66 CpG sites = 20, Kimura (unadjusted) = 40.09 Transitions / transversions = 1.25 (20/16) Gap_init rate = 0.07 (8 / 121), avg. gap size = 1.25 (10 / 8) 334 29.96 7.14 6.53 chr5ptel1M 356845 357194 (642806) C HERVK11D#LTR/ERVK (2470) 5282 4931 m_b226s701i1 8904 chr5ptel1M 356845 CTCCCTTTTCTTGTTTGACCAGGAGTGTCTTAAGGGTTCTATTAGCTCTT 356894 i i i i vi ivv ivi v ii i vi C HERVK11D#LTR/ 5282 CCCCCTCTTTTTGTTTAAGTAATTGTAATTTTAAAGTTCTGTTACTTCTT 5233 chr5ptel1M 356895 TCAACTATAGCCTGACCTGTTGGGTTATAAGGAATACCTGTCATATG--- 356941 v v i i vv v v --- C HERVK11D#LTR/ 5232 TCTACAATAGCTTGGCCTTGTGGGTTATAAGGAATACCAGTAATATGTTT 5183 chr5ptel1M 356942 AGTGATGCCAAATTCAGAACAGAAGGACTGC--AAACCTTTTGAGGTGTA 356989 i - ---- v v ii ii i vi-- v ---iv i C HERVK11D#LTR/ 5182 AAT-ATGCCA----CTGATCAAGAAAATTTTTAAAAGCTTT---ACTGCA 5141 chr5ptel1M 356990 AGAAGAT---CCATTATCTGTCTTTATCTGTTGAGGGATACCAATAGAAG 357036 v i v --- i i v v vviv i v v ivv C HERVK11D#LTR/ 5140 ATAGGCTGGACCATTGTCTGTTTTGAGCTCACTAGGAATTCCCATAACCG 5091 chr5ptel1M 357037 CATAACAATGATTTAAGTGAGAA-ATAACATGTTTAA-GTGCTGGTTAAA 357084 v ---------- i - vvv v - v-----i C HERVK11D#LTR/ 5090 CAAAACA----------TGAAAACATATGTTTTTTAACGTGA-----GAA 5056 chr5ptel1M 357085 GC-ACTTAACCAGGTTGAAGAGTAGCTACTATAAAATTAGAATGAGTATC 357133 i-i vv i v vii ivvv i i vii i C HERVK11D#LTR/ 5055 GTGGCTTCTCCGGTTTGACAGGTAGCCCAGATGAAATTGGAAAAGGTGTC 5006 chr5ptel1M 357134 TACAGTTACACGAATACAGTC---TTCTCCA-----------GTGAGTAA 357169 v v v i v i i iv --- i -----------i C HERVK11D#LTR/ 5005 AACTGTGACATGCACATAAGCTAATTTTCCAAAAGAAGGAACATGAGTAA 4956 chr5ptel1M 357170 CATCTATTTGCCAGATATCATTAGG 357194 i i v C HERVK11D#LTR/ 4955 CATCCATTTGCCAAATAGCATTAGG 4931 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.32 CpG sites = 50, Kimura (unadjusted) = 38.82 Transitions / transversions = 1.04 (50/48) Gap_init rate = 0.09 (31 / 349), avg. gap size = 1.55 (48 / 31) 411 20.79 1.94 1.94 chr5ptel1M 356845 356947 (643053) C HERVK#LTR/ERVK (2339) 5197 5095 m_b226s701i0 8904 chr5ptel1M 356845 CTCCCTTTTCTTGTTTGACCAGGAGTGTCTTAAGGGTTCTATTAGCTCTT 356894 i i i i i ivv v ii i v i C HERVK#LTR/ERV 5197 CCCCTTCTTTTTGTTTAACCAATTGAGCTTTGAGTGTTCTATTAGTTCTT 5148 chr5ptel1M 356895 TCAACTATAGCCTGACCTGTTGGG--TTATAAGGAATACCTGTCATATGA 356942 i v -- -- v ii v C HERVK#LTR/ERV 5147 TCAACTATGGCCTGTCCT--TGGGAATTATAAGGAATTCCTGTTGTATGT 5100 chr5ptel1M 356943 GTGAT 356947 i C HERVK#LTR/ERV 5099 GTAAT 5095 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 25.00 CpG sites = 14, Kimura (unadjusted) = 25.00 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.03 (3 / 102), avg. gap size = 1.33 (4 / 3) 207 23.61 0.00 5.88 chr5ptel1M 358100 358153 (641847) C L3b_3end#LINE/CR1 (22) 1184 1134 m_b226s601i12 8905 chr5ptel1M 358100 ATTGTAAAGGACATAAGAAGCCATTTGGGAGCCCATCACTCTCCCTACTT 358149 v v v i i i --- i v ?i vi C L3b_3end#LINE 1184 ATTGGAAAGGACCTCAGAGGTCATCT---AGTCCATCCCTNCCCCTAGCT 1138 chr5ptel1M 358150 TTAG 358153 i C L3b_3end#LINE 1137 CTAG 1134 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.48 CpG sites = 7, Kimura (unadjusted) = 29.48 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.06 (3 / 53), avg. gap size = 1.00 (3 / 3) 212 30.82 5.41 3.54 chr5ptel1M 359536 359646 (640354) C MIRb#SINE/MIR (131) 137 25 m_b226s601i13 8906 chr5ptel1M 359536 GAGGGAACAAGCAAGCCCAGAAAGGCTAA-TACATTCTCCAGAGGTCACA 359584 i vi-- i i i i - vv vi - C MIRb#SINE/MIR 137 GAGGAAACTG--AGGCTCAGAGAGGTTAAGTAACTTGCCCA-AGGTCACA 91 chr5ptel1M 359585 TAGCAGATGAGAAGCAGGATATGGGGTTGAAATTGAGG-CTA-CT--CTC 359630 i vii i vi iii-i i vi iiv - i- -- C MIRb#SINE/MIR 90 CAGCTAGTAAGTGGCAGAGC-CGGGATTCGAACCCAGGTCTGTCTGACTC 42 chr5ptel1M 359631 CTAAGTGTGT-CTCTTT 359646 v ivi - C MIRb#SINE/MIR 41 CAAAGCCCGTGCTCTTT 25 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.19 CpG sites = 23, Kimura (unadjusted) = 42.22 Transitions / transversions = 2.30 (23/10) Gap_init rate = 0.08 (9 / 110), avg. gap size = 1.11 (10 / 9) 337 35.66 3.54 3.95 chr5ptel1M 360108 360361 (639639) C L2#LINE/L2 (238) 2844 2592 m_b226s601i14 8907 chr5ptel1M 360108 TTTTGAGCAGATGAGATAACAGGGT--GGC--ACCTGTTCAGGGGAAATA 360153 v - i v i -- i -- v v v ii ---- C L2#LINE/L2 2844 TTTTGAGCAGAGGAG-TGACATGATCTGACTTACGTTTTAAAAGGA---- 2800 chr5ptel1M 360154 TTAATCTGACAG-TACATGGAGAAGGAATTGGCAACAGGAAAGAATAGAC 360202 i v i v - iii v vii i ?viivi v ii i v C L2#LINE/L2 2799 TCACTCTGGCTGCTGTGTTGAGAATAGACTGNAGGGGGGCAAGGGTGGAA 2750 chr5ptel1M 360203 TCAGAGGAGCCAATTAAGAGCCTGTTTAGCA-TACTTCTGGGGAGAAGTG 360251 v i iii i i v i -- - v i v v ii C L2#LINE/L2 2749 GCAGGGAGACCAGTTAGGAGGCTATT--GCAGTAATCCAGGCGAGAGATG 2702 chr5ptel1M 360252 ATGG-GGCTCTGAAATGAGCCGACAGCCATAGGAGCATCTATGCA--GGA 360298 - - i viii vi iii vi i ii ii-v iv v -- v C L2#LINE/L2 2701 ATGGTGGCT-TGGACCAGGGTGGTGGCAGTGGAGGTG-GTGAGAAGTGGT 2654 chr5ptel1M 360299 CAGTCTCTGACAGATATTTTGGAGGTAGAAATGGCAGGACTTGTTAACTG 360348 i vi i- v i ivi i i i i iv C L2#LINE/L2 2653 CGGATTCTGG-ATATATTTTGAAGGTAGAGCCGACAGGATTTGCTGATGG 2605 chr5ptel1M 360349 AGTGGACGTAGGG 360361 v i i C L2#LINE/L2 2604 ATTGGATGTGGGG 2592 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 50.20 CpG sites = 57, Kimura (unadjusted) = 51.99 Transitions / transversions = 1.90 (57/30) Gap_init rate = 0.06 (16 / 253), avg. gap size = 1.19 (19 / 16) 411 35.34 0.00 0.75 chr5ptel1M 361628 361761 (638239) MIR3#SINE/MIR 58 190 (18) m_b226s601i15 8908 chr5ptel1M 361628 AATCTTACTTCTGACACTTGCTACTTACACAGTCTCAACCAAGTCATTTA 361677 i iiivi v vi ?vi iiiiiii iiiv i v MIR3#SINE/MIR 58 AGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTC 107 chr5ptel1M 361678 ATCTCGGTGGGCTTAAGTTCCCTTATCTGTAAAATGACAGGATGCTATTA 361727 i vv i v i i vi i vvv i MIR3#SINE/MIR 108 ACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTA 157 chr5ptel1M 361728 GTTGGCTTCTTGGGTCCCTCCCAGTTCTAGATAT 361761 v iii vi i i - i MIR3#SINE/MIR 158 GATGATCTCTAAGGTCCCTTCCAGCTCT-GACAT 190 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 50.22 CpG sites = 32, Kimura (unadjusted) = 52.07 Transitions / transversions = 2.13 (32/15) Gap_init rate = 0.01 (1 / 133), avg. gap size = 1.00 (1 / 1) 248 27.27 5.79 0.00 chr5ptel1M 362120 362240 (637760) C L1ME3F_3end#LINE/L1 (422) 568 441 m_b226s551i7 8909 chr5ptel1M 362120 TCATTTTTACAGAACAATAATACTCCATTGTCTTCAAGTACCACAAGTTG 362169 i v vvvv i v vv vi v i C L1ME3F_3end#L 568 TCATTTTCACTGCTGTATAATATTCCATTGTGTGAATATACCACAATTTA 519 chr5ptel1M 362170 TTTGGCTATTCCCCAGTAGACAGACATGTATTTTGTTT-CAGTTCTGTGA 362218 iv i i v v ii v ivv - i v v C L1ME3F_3end#L 518 TTTATCCATTCTCCTGTCGATGGACATTTGGGTTGTTTCCAGTTTTTTGC 469 chr5ptel1M 362219 GAC--CGCACAGAGCTG----GAACATT 362240 v i-- v v ---- C L1ME3F_3end#L 468 TATTACGAACAGTGCTGCTATGAACATT 441 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 33.91 CpG sites = 12, Kimura (unadjusted) = 33.91 Transitions / transversions = 0.57 (12/21) Gap_init rate = 0.03 (3 / 120), avg. gap size = 2.33 (7 / 3) 403 29.96 3.77 3.45 chr5ptel1M 362850 363167 (636833) C L1ME4a_3end#LINE/L1 (316) 555 237 m_b226s551i8 8910 chr5ptel1M 362850 ATAATATTCTACAACATTAATGTGCTATGACTTATTCAG-CATTTCCCAG 362898 i iv?i vi i i i i i i- ? i vi C L1ME4a_3end#L 555 ATAATATTCCATTNTATGGATGTACCATAATTTATTTAACCANTCCCCTA 506 chr5ptel1M 362899 CTGATGGGCATCCACTCAGTTTCCAGTTTCTTGCCACTACAAATGGGGCT 362948 i v i ii vviv i i i i i i iiv C L1ME4a_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAATGCT 456 chr5ptel1M 362949 GC-AGAAACATTTCTGTACATATGGGTCCTTTTCC-C-TCCTTTAGGATC 362995 - vi iii --ii i v ? - - ii v vv i C L1ME4a_3end#L 455 GCGATGAACATCCTTGTACATA--AATCTTTGTNCACATCTCTGATTATT 408 chr5ptel1M 362996 TCTTTGGCAAATAAATCC-----AGTAGAAACATTTCTAGTTCAAAGGCA 363040 i i --i i ----- i --- v i v vv C L1ME4a_3end#L 407 TCCTTAG--GATAAATTCCTAGAAGTGGA---ATTACTGGGTCAAAGGGT 363 chr5ptel1M 363041 ATGCACCTGTTGATAGCCCATTGG-GCATGTT-TCATATTGCTCGGCAGA 363088 ? v v v - v iv i-i i -i v i vv C L1ME4a_3end#L 362 ATGNACATTTTTA-AGGCTTTTGATACATATTGCCAAATTGCCCTCCAGA 314 chr5ptel1M 363089 ATGGTTGGATCTGTTCACAATTCCACCAACAATCCATTAGCGTCCCAGAT 363138 v v i vi i v i i i vi v v v v - C L1ME4a_3end#L 313 AAGGTTGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTGCCCG-T 265 chr5ptel1M 363139 TTCCCCCAAAACCCTTTCC-ACACTGGTTA 363167 ? -- v iv - v C L1ME4a_3end#L 264 TTCNCC--ACACCCTCGCCAACACTGGGTA 237 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.23 CpG sites = 55, Kimura (unadjusted) = 40.38 Transitions / transversions = 1.49 (55/37) Gap_init rate = 0.06 (19 / 317), avg. gap size = 1.21 (23 / 19) 29 6.13 0.00 0.00 chr5ptel1M 364566 364599 (635401) (CA)n#Simple_repeat 1 34 (0) c_b226s251i2 8911 chr5ptel1M 364566 CACACACACACACGCACACACACACACTCACACA 364599 i v (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACA 34 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 2223 29.11 0.86 1.25 chr5ptel1M 365897 366943 (633057) C L1M5_orf2#LINE/L1 (1446) 1848 806 m_b226s551i9 8910 chr5ptel1M 365897 AGTGTTTTTCATAGGAATGGATGATGGATTTTGTTAAATGCTTTTTCTGC 365946 v v -- i v i i C L1M5_orf2#LIN 1848 AGTTTTTATCAT--GAATGGGTGTTGAATTTTGTCAAATGCTTTTTCTGC 1801 chr5ptel1M 365947 ATATATTGAGATGATCATATGGTTTTTGTTAATTTGGT-TATTAATATGA 365995 v i v iv- iv - i i C L1M5_orf2#LIN 1800 ATCTATTGAGATGATCATATGATTTTTCTCC-TTTATTCTGTTAATATGG 1752 chr5ptel1M 365996 CCAATTATATTGATAGTTTTCCTAATATTGAACCAGCCCTGCATTCCTGG 366045 iv i v v i v i i i i C L1M5_orf2#LIN 1751 TGAATTACATTGATTGATTTTCGAATGTTAAACCAACCTTGCATTCCTGG 1702 chr5ptel1M 366046 TATAAATCCTACTCGATCATAGTGTATTATCCTGGGAATGATTTTCTGTA 366095 v i i i i ii vvvv ivv v v C L1M5_orf2#LIN 1701 GATAAACCCCACTTGGTCATGATGTATTATCCTTTTTATATATTGCTGGA 1652 chr5ptel1M 366096 GTCTTTTTGCTAATATCTCATTTAAGATTTTAGCATCAATATTCATTAGG 366145 v vv i ii ? i v v i v C L1M5_orf2#LIN 1651 TTCGATTTGCTAATATTTTGTTNAGGATTTTTGCATCTATGTTCATGAGG 1602 chr5ptel1M 366146 GAGATGGGTCTATAATTTTCTTTCTCTGT--TTTCAACCTACCTGTTTTA 366193 v v i iii -- v --ii ii ? v v C L1M5_orf2#LIN 1601 GATATTGGTCTGTAATTTTCTTTTCTTGTAATGTC--TTTGTCNGGTTTT 1554 chr5ptel1M 366194 GGTATCAGTACCATGTCTGTGTCATAAAAGGAATATAGTAGGACTCCTTC 366243 vii? iiv iv v i vvi v vii i C L1M5_orf2#LIN 1553 GGTATCAGGGTNATGCTGGCCTCATAAAATGAGTTGGGAAGTGTTCCCTC 1504 chr5ptel1M 366244 ATTCCCTGTTTTATCAAATAATTTATATAGCATTGGGGCCAATTGTTCTT 366293 v ii i v vi v i i i iv viii v v i C L1M5_orf2#LIN 1503 TTTTTCTATTTTCTGGAAGAGTTTGTGTAAGATTGGTATTATTTCTTCCT 1454 chr5ptel1M 366294 TAAATGTTTGGTAGAATTCACATGTAAATCCATCCAGTCCTGGGGATTTT 366343 vv i v ii v i v i C L1M5_orf2#LIN 1453 TAAATGTTTGGTAGAATTCACCAGTGAAGCCATCTGGGCCTGGAGTTTTC 1404 chr5ptel1M 366344 TTCTTAAGGAGTTGATTAATCGGTTGTTCTATTTCTTTTTCTGAAATGGG 366393 iv ii i v vv iivvvi v vviv v i C L1M5_orf2#LIN 1403 TTTGTGGGAAGGTTTTTAATTACAAATTCAATTTCTTTAATAGATATAGG 1354 chr5ptel1M 366394 ACCATTCAAGCAATTTACTTACTCCTCTGTTAATCTGGGAAGTCTATATT 366443 i i iiivv i i vi i v? i i i v v i?i i i C L1M5_orf2#LIN 1353 GCTATTCAGATTTTCTATTTCTTCTTGNGTCAGTTTTGGTAANTTGTGTT 1304 chr5ptel1M 366444 TTTGGAGGTAGTCTTCCATTTTACTTAGGTTATCAAATTGATTGGCATAA 366493 vi v v iv i ii i ? v C L1M5_orf2#LIN 1303 TTTCAAGGAATTTGTCCATTTCATCTAAGTTNTCAAATTTATTGGCATAA 1254 chr5ptel1M 366494 AGTTGGGCAAAGTAACTCCTGATTATCTCTCTAATTTCCTCTTCATTGGT 366543 vv v i viii v ii i v ivivvv iv C L1M5_orf2#LIN 1253 AGTTGTTCATAATATTCTCTTATTATCCTTTTAATGTCTGTAGGATCTGT 1204 chr5ptel1M 366544 AGAAAGTTCTCCCTTTT-ATTTTTAAGACTACTAATTTGATTTTCCTCCT 366592 vi vv i - ii i v i iv vv i i ii C L1M5_orf2#LIN 1203 AGTGATGTCTCCTTTTTCATTCCTGATATTGGTAATTTGTGTCTTCTCTC 1154 chr5ptel1M 366593 TCCTTTTTCTAATCAGATTTACCAAAGGCTCATCTATTTTATTGGTTTTT 366642 ii ii i vi ?i i i i i v i i C L1M5_orf2#LIN 1153 TTTTTTTCTTGATCAGTCTNGCTAGAGGTTTATCAATTTTATTGATCTTT 1104 chr5ptel1M 366643 TAAATAGAATCAACTCTTAGTTTTACTAATTAGTTCAATAGTTTTTTTTT 366692 v - i i i i i iii i -- vv - v ? ? C L1M5_orf2#LIN 1103 TCAA-AGAACCAGCTTTTGGCTTCGTTGATT--TTCTCTA-TTGTNTNTT 1058 chr5ptel1M 366693 TACTTTCAATATTATTTATTTCTGCTTTTAATTTTAGAATTTCAAATTTA 366742 ii v v i v i vi vv vvvii v C L1M5_orf2#LIN 1057 TGTTTTCTATTTCATTGATTTCTGCTCTTATCTTTATTATTTCCTTCCTT 1008 chr5ptel1M 366743 GTATTTGATTGGGGGTTTTTAATTTGG---TCTTTTTCTAGTTTTTTTAG 366789 v i ?v v --- v--- i i v C L1M5_orf2#LIN 1007 CTACTTNCTTTGGG---TTTAATTTGCTCTTCTTTTTCTAGCTTCTTAAG 961 chr5ptel1M 366790 TTGCAAGCCCAATTCATTGATCTTCTCCTTCTCTATTTTATTCAAGTAAG 366839 v v ii iv i vvv i i vi vi v vi ? C L1M5_orf2#LIN 960 GTGGAAGCTTAGATCATTGATTTTAAGCCTTTCTTCTTTTCTAATATANG 911 chr5ptel1M 366840 CCTCTAAGGATATCAAATTTCTTCTTATTACTGCTTTGGCTGCATCCCAC 366889 v i ? v v v i i v vi i C L1M5_orf2#LIN 910 CATTTAANGCTATAAATTTCCCTCTAAGCACTGCTTTAGCTGCATCCCAC 861 chr5ptel1M 366890 AAATTTTGGTATGATGTGTCTT--TTTTAATTTTAATTTTAAATTTTTTT 366937 i v i i -- ? v - i i iv v i C L1M5_orf2#LIN 860 AAATTTTGATATGTTGTATTTTCATTNTCA-TTCAGTTCAAAATATTTTC 812 chr5ptel1M 366938 TAATTT 366943 C L1M5_orf2#LIN 811 TAATTT 806 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.09 CpG sites = 167, Kimura (unadjusted) = 38.27 Transitions / transversions = 1.25 (167/134) Gap_init rate = 0.02 (18 / 1046), avg. gap size = 1.22 (22 / 18) 18 17.53 0.00 0.00 chr5ptel1M 367282 367313 (632687) (CA)n#Simple_repeat 1 32 (0) m_b226s252i14 8912 chr5ptel1M 367282 CAGACACACACACATAAACACACACATTCACA 367313 v i v iv (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACA 32 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 201 28.23 8.65 4.63 chr5ptel1M 368500 368603 (631397) C MamRTE1#LINE/RTE-BovB (3491) 321 214 m_b226s601i16 8913 chr5ptel1M 368500 TCCTGGGTTACCTA---GAACACG--TCTTGTCCAGA--CTCTAATCGCC 368542 iii --- v ? v -- i ii i--i iv i i C MamRTE1#LINE/ 321 TCCTGGGCCGCCTACTCGCANAGGACTTTTGTTTAGGTTTTCCCACCGTC 272 chr5ptel1M 368543 AGCAAGATGTG-ACCTGGGTCTGCATTCTTGCAGCAGTGCTGGTAGGTTA 368591 i ii -i i i - -- i v i v i i i C MamRTE1#LINE/ 271 AGCAGGACATGCGCTTGAGT-TG--TTTTTCCAGTAGTGGTGATGGGTTG 225 chr5ptel1M 368592 C-CTGAAGACCAT 368603 - --i C MamRTE1#LINE/ 224 CGCTGA--GCCAT 214 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.54 CpG sites = 23, Kimura (unadjusted) = 39.43 Transitions / transversions = 4.60 (23/5) Gap_init rate = 0.10 (10 / 103), avg. gap size = 1.40 (14 / 10) 356 24.43 11.52 1.43 chr5ptel1M 370940 371130 (628870) L1MEh_5end#LINE/L1 2019 2228 (7) m_b227s551i0 8914 chr5ptel1M 370940 GGGAAGGGGGATAAGGGGGAAAGA-AGGGAGAAAAGCA-------TAAAT 370981 i vi v ii i i - ii i -------i L1MEh_5end#LI 2019 GGAAAGCAGGAAAAAAGGAAAAAANAGAAAGAAAAACAGATGGGACAAAT 2068 chr5ptel1M 370982 AGGGGT----TAACAAGATGGCA--AGTAATACAGAAT----TGGTCATT 371021 iiiv---- i -- i vv v? ----ii v L1MEh_5end#LI 2069 AGAAAACAAATAATAAGATGGCAGAAATAAGTCCNAATATANCAGTAATT 2118 chr5ptel1M 371022 TTAACCACAAATG--AACGGGT-AAACTCCCCA-TAAAGAGGAAGCGATT 371067 --- v i -- i - v - v i iv v L1MEh_5end#LI 2119 ---ACAATAAATGTAAATGGGTTAAACTCACCAATTAAAAGACAGAGATT 2165 chr5ptel1M 371068 ACCAGAATGGATTAAAAGCCAGAATCCTACAATATGTTGTTTACAGGAAA 371117 ?i v ? iv i v i i i i L1MEh_5end#LI 2166 NTCAGATTGGATTNAAAAACAAAATCCAACAATATGCTGTCTACAAGAGA 2215 chr5ptel1M 371118 CACACCTGAAGCA 371130 i i i L1MEh_5end#LI 2216 CACACTTAAAACA 2228 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 31.33 CpG sites = 31, Kimura (unadjusted) = 31.33 Transitions / transversions = 2.07 (31/15) Gap_init rate = 0.06 (11 / 190), avg. gap size = 2.27 (25 / 11) 381 23.51 4.43 5.77 chr5ptel1M 370970 371127 (628873) L1M6_5end#LINE/L1 2350 2505 (10) m_b227s551i1 8914 chr5ptel1M 370970 AAAAGCATAAATAGGGGTTAACAAGATGGCAAG--TAATACAGAATTGGT 371017 ? ---------i? i i-- v vi ivvi L1M6_5end#LIN 2350 AAAAGCANAAA---------GNAAGATGACAAANATAAGACCAAACATAT 2390 chr5ptel1M 371018 CATTT-TAACCACAAATG--AACGGGT-AAACTCCCC-ATAAAGAGGAAG 371062 v - i v i -- i - - v i iv i L1M6_5end#LIN 2391 CAGTTATGACAATAAATGTAAATGGGTTAAACTCCCCTATTAAAAGACAA 2440 chr5ptel1M 371063 CGATTACCAGAATGGATTAAAAGCCAGAATCCTACAATATGTTGTTTACA 371112 v i vi v i iv i v v i L1M6_5end#LIN 2441 AGACTCTCAGATTGGGTTAAAAAACAAAATCCAACTATATGCTGTTTACA 2490 chr5ptel1M 371113 GGAAACACACCTGAA 371127 i i i L1M6_5end#LIN 2491 AGAGACACACCTAAA 2505 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 29.26 CpG sites = 21, Kimura (unadjusted) = 29.26 Transitions / transversions = 1.50 (21/14) Gap_init rate = 0.09 (14 / 157), avg. gap size = 1.14 (16 / 14) 458 26.42 4.40 0.00 chr5ptel1M 371023 371181 (628819) L1MEc_5end#LINE/L1 2313 2478 (49) m_b227s551i2 8914 chr5ptel1M 371023 TAACCACA---AATG--AACGG-GTAAACTCCCCA-TAAAGAGGAAGCGA 371065 i --- -- i -v v - v i v v L1MEc_5end#LI 2313 TAATCACATTAAATGTAAATGGTCTAAACACCCCAATTAAAAGGCAGAGA 2362 chr5ptel1M 371066 TTACCAGAATGGATTAAAAGCCAGAATCCTACAATATGTTGTTTACAGGA 371115 ii v v iv ii i v v i ii i L1MEc_5end#LI 2363 TTGTCAGATTGGATAAAAAAGCAAGACCCAACTATATGCTGCCTACAAGA 2412 chr5ptel1M 371116 AACACACCTGAAGCAGGGAGATACATGCAGAATAAAGGTAAAAGGATGGA 371165 ? i v ii vii i vii iv i L1MEc_5end#LI 2413 AACNCACTTTAAATATAAAGACACAAATAGGTTAAAAGTAAAAGGATGGA 2462 chr5ptel1M 371166 GCAAAATCTACTATGC 371181 iv i v i L1MEc_5end#LI 2463 AAAAGATATACCATGC 2478 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.80 CpG sites = 26, Kimura (unadjusted) = 33.80 Transitions / transversions = 1.62 (26/16) Gap_init rate = 0.03 (4 / 158), avg. gap size = 1.75 (7 / 4) 1121 30.23 5.18 3.96 chr5ptel1M 371048 372070 (627930) L1MD_orf2#LINE/L1 61 1095 (2199) m_b227s551i3 8914 chr5ptel1M 371048 CCCATAAAGAGGAAGCGATTACCAGAATGGATTAAAAGCCAGAATCCTAC 371097 v v i iv v iv i iv vi i v L1MD_orf2#LIN 61 CCAATTAAAAGACAGAGATTGGCAGAGTGGATTAAAAAACATGACCCAAC 110 chr5ptel1M 371098 AATATGTTGTTTACAGGAAACACACCTGAAGCAGGGAGATACATGCAGAA 371147 v i i i v i v ii viiv i v i iv L1MD_orf2#LIN 111 TATATGCTGTCTACAAGAAACTCACTTCAAATATAACGATATAGGTAGGT 160 chr5ptel1M 371148 TAAAGGTAAAAGGATGGAGCAAAATCTACTATGCTTCCGGTGAAGTCAAA 371197 i i iv i v i vvv iv i -- L1MD_orf2#LIN 161 TGAAAGTAAAAGGATGGAAAAAGATATACCATGCAAACATTAA--TCAAA 208 chr5ptel1M 371198 A--AAGCAGGGGTAGCCATGATGATCTCAGATCAAG-------CAAAACA 371238 -- i i i iv i v v ------- i i L1MD_orf2#LIN 209 AGAAAGCAGGAGTGGCTATATTAATATCAGATAAAGTAGACTTCAGAGCA 258 chr5ptel1M 371239 AAAATTGATCTAATTAAAAGAGATAAGGAAGGGCAGTATATCTTGCTAAA 371288 i --- --- vv i ii i i v i vv v L1MD_orf2#LIN 259 AAGA---A---AATTACCAGAGACAGAGAGGGACATTACATAATGATAAA 302 chr5ptel1M 371289 -GGGT-AGCATAATAATGAA-----AGCAATATTAAA-ATATATGCACCA 371330 - - iivi vi - ----- vi -i i L1MD_orf2#LIN 303 AGGGTCAATCCACCAA-GAAGACATAGCAATCCTAAATGTGTATGCACCA 351 chr5ptel1M 371331 A-TGGTGTAGTATCTAAAATTCTTAAAG-AGAAATTAAGAGG-CTGCAAG 371377 -iiiiiv i- ?i v v i - i i i v i- v L1MD_orf2#LIN 352 AACAACAGAGC-TNCAAAATACGTGAAGCAAAAACTGATAGAACTGAAAG 400 chr5ptel1M 371378 AATAAATAGATAG---CAAAACTATAATAGTGGAGATCCTCAAT-CCTTG 371423 i v i i--- v i i -- - i i- iiv L1MD_orf2#LIN 401 GAGAAATAGACAAATCCACAATTATAGT--TGGAGA-CTTCAACACCCCT 447 chr5ptel1M 371424 CACTTCAG-AATTAGATAAATCAAAT---CACAAAATAAATAAGAAAGAA 371469 v - - - i v v --- v v ii --- v L1MD_orf2#LIN 448 CTCT-CAGCAATT-GATAGAACAACTAGACAGAAAATCAGCAAG---GAT 492 chr5ptel1M 371470 GTCAAAGAGGTAAATAGAATACTAGAAA--AGTTAGATATGATAGACCTC 371517 i vi iv ? i -- i i vv -- iivi v i v v i L1MD_orf2#LIN 493 ATAGAAGAACTNAACA--ACACCATCAACCAACAGGATCTAATCGACATT 540 chr5ptel1M 371518 CTGGAGAAAAC-GAAATGGAGAAGAAAGGAGTACA--TTCTTTTCAGCAG 371564 - iv v -vv vivi v v ivi i -- ivv L1MD_orf2#LIN 541 -TATAGAACACTCCACCCAACAACAGCAGAATACACATTCTTTTCAAGTG 589 chr5ptel1M 371565 TTCATGGAACCTATACAAAAATAGACCATATATTAGGACATAA---AAAC 371611 ii i v ? v i vi i v --- L1MD_orf2#LIN 590 CCCACGGAACATNTACCAAGATAGACCATATCCTGGGCCATAAAACAAAC 639 chr5ptel1M 371612 CTCAAACTCAAATGCAGTAAGGCA--GAAATAGT---GAATGCATCCTTT 371656 --- vi -- i v -- vi --- i ii i i L1MD_orf2#LIN 640 CTCAA---CAAATTTA--AAAGAATTGAAATCATACAGAGTGTGTTCTCT 684 chr5ptel1M 371657 TCAGACCATGATGCAATAAAAATTACACTC---AACAAAAAGCCAG-GGG 371702 --- ii v v v viv v --- i vi i-i L1MD_orf2#LIN 685 ---GACCACAATGGAATCAAACTAGAAATCAATAACAGAAAGATAACAGG 731 chr5ptel1M 371703 AAAGTAGACCAAAAAATAATTGGAAACTAAATAATCTCA-TACTAAAGAA 371751 i vv- --- i v i - v - v v L1MD_orf2#LIN 732 AAAATCT-CC---AAACACTTGGAAACTAAACAA-CACACTTCTAAATAA 776 chr5ptel1M 371752 TGATTGGGTGAAACAGCAAATCATAGACATAATTAATAACTTCACCCAAG 371801 vvv v v v i vi iiviv v v v iiv v L1MD_orf2#LIN 777 TCCATGGGTCAAAGAGGAAGTCTCAAGGGAAATTAAAAAATACATTGAAC 826 chr5ptel1M 371802 AAAATGACAATAATGAGACATCATATCAAAATGTGTGGGACACAGCCAAA 371851 vi v i vi v v v i i L1MD_orf2#LIN 827 TGAATGAAAATGAAAATACAACATATCAAAATTTGTGGGACGCAGCTAAA 876 chr5ptel1M 371852 GTGATAATAAG-GGGAAATTGCATATCTCTAGAGACTTACTTGCATAAAG 371900 iii iv i - -i v v i vi ? v --- i i L1MD_orf2#LIN 877 GCAGTGCTGAGAGGGAAATT-TATAGCACTAAATGCNTACAT---TAGAA 922 chr5ptel1M 371901 TAGAGAAAGAG---AAGGTCAACGAATTGGGCTTGCAACTAAAAATGCTA 371947 v i i ---v ii ii vi ii iv v v i v? L1MD_orf2#LIN 923 AAGAGGAAAAGTCTCAAATCAATAATCTAAGCTCCCACCTCAAGAANCTA 972 chr5ptel1M 371948 GAAAAGGAA---CAAATTAAAAACCCCCAGTCAAACACTAAACTTGAAAT 371994 i --- v --- v iv i vv iivvv L1MD_orf2#LIN 973 GAAAAAGAAGAGCAAAATAAA---CCCAAAGCAAGCAGAAGGAAGGAAAT 1019 chr5ptel1M 371995 TCTAAAAATAAAAGGAGAGATCAATAAAATTGAAAGTAAAAAAACTATTG 372044 vv i i v i i ii i v v L1MD_orf2#LIN 1020 AATAAAGATAAGAGCAGAAATCAATGAAATTGAAAACAGAAAAACAATAG 1069 chr5ptel1M 372045 AATTAATTAATACAACTAAGAGTTGG 372070 ivv i iv v i i L1MD_orf2#LIN 1070 AGAAAATCAATGAAACAAAAAGCTGG 1095 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.47 CpG sites = 162, Kimura (unadjusted) = 39.81 Transitions / transversions = 1.20 (162/135) Gap_init rate = 0.06 (66 / 1022), avg. gap size = 1.42 (94 / 66) 376 27.71 4.71 4.01 chr5ptel1M 372070 372366 (627634) C L1M5_orf2#LINE/L1 (7) 3287 2989 m_b227s551i4 8915 chr5ptel1M 372070 GACCATTTTTTCACATGGCTAGATATAG----TTTCAATTTCTTCGTCTG 372115 v i ii - --- v ---- v? v v i C L1M5_orf2#LIN 3287 GAGCATCTTTTCATGTG-CT---TATTGGCCATTTGNATATCTTCTTTTG 3242 chr5ptel1M 372116 GGAATTGTCTGTTCATATCCTTTGAC--TTTTGATCAATTGGA--GAATG 372161 v v vi i v -- v? -- i-- vv C L1M5_orf2#LIN 3241 TGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNT--ATTGGGTTGTTTG 3194 chr5ptel1M 372162 GCTTGATTTTTCA-TAAATTAGAGTCAATTCTCTATATATTTTGGATATG 372210 v -- ? i - i ? iv -v i i i i C L1M5_orf2#LIN 3193 TCTT--TTTNTTATTGANTTGTAG-GAGTTCTTTATATATTCTGGATACG 3147 chr5ptel1M 372211 AGGCCTTTATCAGA-ACATTTGACTGTAAAAATGTTTTCCCAGTTTATTG 372259 v i - i v -?i i v v i ? i i v C L1M5_orf2#LIN 3146 AGTCCTTTGTCAGATATATGT-NTTGCAAATATTTTCTCCCANTCTGTGG 3098 chr5ptel1M 372260 CTTCCCTTCTAATCTTGTCTGCATTAGTTTTGTTTGTACAAAAAGTTTTC 372309 v i v i v ivi iv ivi vvv? vi i iv v C L1M5_orf2#LIN 3097 CTTGCCTTTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTTTA 3048 chr5ptel1M 372310 AGTTTGGTATAATTTTA-TAATCAAAATTTTCTATTTTGTGATCAGCAA- 372357 v i i? i iiv - v -- i v i i i? iiv- C L1M5_orf2#LIN 3047 ATTTTGATGNAGTCCAATTTATC--AATTTTTTCTTTTATGGTTNGTGCT 3000 chr5ptel1M 372358 --TTGTGTCCT 372366 -- C L1M5_orf2#LIN 2999 TTTTGTGTCCT 2989 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 35.50 CpG sites = 42, Kimura (unadjusted) = 36.65 Transitions / transversions = 1.14 (42/37) Gap_init rate = 0.07 (20 / 296), avg. gap size = 1.30 (26 / 20) 396 27.11 6.25 6.25 chr5ptel1M 372075 372314 (627686) C L1P3_orf2#LINE/L1 (12) 3282 3043 m_b227s551i5 8915 chr5ptel1M 372075 TTTTTTCACATG---GCTAGATATAGTTTCAATTTCTTCGTCTGGGAATT 372121 i --- i i viii --- v v v i i v C L1P3_orf2#LIN 3282 TTTTTTCATATGTTTGTTGGCCGCA---TAAATGTCTTCTTTTGAGAAGT 3236 chr5ptel1M 372122 GTCTGTTCATATCCTTTGAC----TTTTGATCAATTGGAGAATGGCTTGA 372167 i v ---- ----- i -- v i v C L1P3_orf2#LIN 3235 GTCTGTTCATATCCTTCGCCCACTTTTTGA-----TGGGG--TTGTTTGT 3193 chr5ptel1M 372168 TTTT---TCATAAATTAGAGTCAATTCTCTATATATTTTGGATATGAGGC 372214 --- ii v vv v i ii i v i v v C L1P3_orf2#LIN 3192 TTTTTTCTTGTAAATTTGTTTAAGTTCCTTGTAGATTCTGGATATTAGCC 3143 chr5ptel1M 372215 CTTTATCAGAACATTTGACTGTAAAAATGTTTTCCCAGTTTATTGCTTCC 372264 i vviv v i i v i v i i v v v C L1P3_orf2#LIN 3142 CTTTGTCAGATGGATAGATTGCAAAAATTTTCTCCCATTCTGTAGGTTGC 3093 chr5ptel1M 372265 CTTCTAATCTTGTCTGCAT--TAGTTTTGTT---TGTACAAAAAGTTTTC 372309 vi v i---- - -- iv --- i i iv i i C L1P3_orf2#LIN 3092 CTGTTCAC----TCTG-ATGATAGTTTCTTTTGCTGTGCAGAAGCTCTTT 3048 chr5ptel1M 372310 AGTTT 372314 C L1P3_orf2#LIN 3047 AGTTT 3043 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 32.77 CpG sites = 33, Kimura (unadjusted) = 34.20 Transitions / transversions = 1.18 (33/28) Gap_init rate = 0.08 (20 / 239), avg. gap size = 1.50 (30 / 20) 350 31.65 2.46 2.88 chr5ptel1M 372972 373215 (626785) C L1P3_orf2#LINE/L1 (303) 2991 2749 m_b227s551i6 8915 chr5ptel1M 372972 TTTGGTCATAAATTCCTTCCTCTTCCACAGGTC-TGAGAGGTAAACTATC 373020 i i v i v i v v vi v - iv --- vv C L1P3_orf2#LIN 2991 TTTAGTCATGAAGTCTTTGCCCATGCCTATGTCCTGAATGGTA---TTGC 2945 chr5ptel1M 373021 CT--GTGTTCCTCTAATTTATTTATAATCTCATGCTTTTATGCCTACGTC 373068 -- v i ivv v ii i i - v i i ii v C L1P3_orf2#LIN 2944 CTAGGTTTTCTTCTAGGGTTTTTATGGTTTTA-GGTCTTACGTTTAAGTC 2896 chr5ptel1M 373069 ATGAACCCATTTTGAACTTATCTTGGTGCATGGTGTTAAGTATGGGTCCA 373118 v v i i ii v i v ii v v i v v C L1P3_orf2#LIN 2895 TTTAATCCATCTTGAGTTAATTTTTGTATAAGGTGTAAGGAAGGGGTCCA 2846 chr5ptel1M 373119 TGCCTAGTTT-CTGCCATACTAGTTA-CCAATTTTCCCAGCAATTTTTGT 373166 vviii - - - i i - i i viv i C L1P3_orf2#LIN 2845 GTTTCAGTTTTCTGC-ATA-TGGCTAGCCAGTTTTCCCAACACCATTTAT 2798 chr5ptel1M 373167 CAAACGGTGAGTTCTTATCCCAAAAGCTGGGTTCT-TTGGTTTTGTCAAA 373215 i ii v i i - v vv v v i - ii v C L1P3_orf2#LIN 2797 TAAATAGGGAATCCTT-TCCCCATTGCTTGTTTTTGTCAGGTTTGTCAAA 2749 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.33 CpG sites = 41, Kimura (unadjusted) = 42.07 Transitions / transversions = 1.21 (41/34) Gap_init rate = 0.05 (12 / 243), avg. gap size = 1.08 (13 / 12) 16 9.55 0.00 0.00 chr5ptel1M 375481 375503 (624497) (A)n#Simple_repeat 1 23 (0) m_b227s252i0 8916 chr5ptel1M 375481 AAAAAAAAAAGAAAAAGAAAAAA 375503 i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAA 23 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 259 29.77 6.11 0.00 chr5ptel1M 375753 375883 (624117) C L1ME3F_3end#LINE/L1 (422) 568 430 m_b227s551i7 8917 chr5ptel1M 375753 TCATTTTTACAGAACAATAATAGTCCACGGTCTTCAAGTACCACAAGTTG 375802 i v vvvv v iv v vv vi v i C L1ME3F_3end#L 568 TCATTTTCACTGCTGTATAATATTCCATTGTGTGAATATACCACAATTTA 519 chr5ptel1M 375803 TTCGGCCATTCCCCAATAGACAGACACATATTTTGTTT-CAGTTCTTTGT 375851 iiv i vi v ii iv ivv - i i C L1ME3F_3end#L 518 TTTATCCATTCTCCTGTCGATGGACATTTGGGTTGTTTCCAGTTTTTTGC 469 chr5ptel1M 375852 GAC--CGCACAGAGCTG----GAACATTGCTG-ATATGT 375883 v i-- v v ---- vi - i C L1ME3F_3end#L 468 TATTACGAACAGTGCTGCTATGAACATTCTTGTACATGT 430 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.12 CpG sites = 17, Kimura (unadjusted) = 38.12 Transitions / transversions = 0.77 (17/22) Gap_init rate = 0.03 (4 / 130), avg. gap size = 2.00 (8 / 4) 310 26.70 10.14 4.11 chr5ptel1M 377017 377223 (622777) C L1ME3G_3end#LINE/L1 (356) 568 350 m_b227s551i8 8918 chr5ptel1M 377017 TCATTCCTTATAGAAGGAGGAATAATATGCTACAACATTAATGTGCTATG 377066 i v - v? vv v i v i i ii vi i i i i C L1ME3G_3end#L 568 TCATTCTTTTTA-ACNGCTGCATAGTATTCCATAGTATGGATATACCATA 520 chr5ptel1M 377067 ACTTATTC------TTCCCAGTTGATGGGCATCCTCAG-----TTTCAGT 377105 i i------ i vi i -- i ----- i i C L1ME3G_3end#L 519 ATTTATTTAACCATTCCCCTATTGATGGACAT--TTAGGTTGTTTCCAAT 472 chr5ptel1M 377106 TTCTTGCCACTACAAACAGGGCTGCAG-AAACATTTCTCTGTACATGTGG 377154 i i i i iv i-i -- ii i?v C L1ME3G_3end#L 471 TTTTCGCTATTACAAACAATGCTGCAATGAACA--TCCTTGTACATGCNT 424 chr5ptel1M 377155 GACCTTTT---CAT-CGCTAGGATCTCT-TGGCATATAAACCCAGTAAAG 377199 -- v --- -i v v i - i v v v? ? -- C L1ME3G_3end#L 423 --CCTTGTGCACATGTGCGAGTATTTCTNTAGGATAGATNCCNAG--AAG 378 chr5ptel1M 377200 T---ATTGGTAGTTC-AAGGCTATGCAC 377223 --- v i v - v i C L1ME3G_3end#L 377 TGGAATTGCTGGGTCAAAGGGTATGCGC 350 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.55 CpG sites = 34, Kimura (unadjusted) = 35.20 Transitions / transversions = 1.79 (34/19) Gap_init rate = 0.08 (17 / 206), avg. gap size = 1.76 (30 / 17) 251 31.61 7.82 6.38 chr5ptel1M 377038 377331 (622669) C L1ME3Cz_3end#LINE/L1 (449) 548 251 m_b227s551i9 8918 chr5ptel1M 377038 ATAATATGCTACAACATTAATGTGCTATGACTTATTC------TTCCCAG 377081 i v i ivii v i i i ii i i------ i vi C L1ME3Cz_3end# 548 ATAGTATTCCATTGTATGAATATACCACAATTTATTTATCCATTCCCCTA 499 chr5ptel1M 377082 TTGATGGGCATCCTCAG-----TTTCAGTTTCTTGCCACTACAAACAGGG 377126 i -- i ----- i i i i i i iv C L1ME3Cz_3end# 498 TTGATGGACAT--TTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATG 451 chr5ptel1M 377127 CTGCAG-AAACATTTCTCTGTACATGTGGGACCTTTT---CAT-CGCTAG 377171 i-i -- ii vv-- v --- -i v C L1ME3Cz_3end# 450 CTGCAATGAACA--TCCTTGTACATGTCT--CCTTGTGCACATGTGCGAG 405 chr5ptel1M 377172 GATCTCT-TGGCATATAAACCCAGTAAAGT---ATTGGTAGTTCA-AGGC 377216 ii i - i vi v i -- --- v i v i- v C L1ME3Cz_3end# 404 AGTTTCTCTAGGGTATATACCTAG--AAGTGGAATTGCTGGGTCGTAGGG 357 chr5ptel1M 377217 TATGCACCAGTTGATAGCCCTGGATT--ATATTCCCATGTTGCTCGGCAG 377264 i vvv --i i ii -- i -- v vi vv i C L1ME3Cz_3end# 356 TATGCGCATCTT--CAACTTT--ACTAGATATTGCCAAATTGCTCTCCAA 311 chr5ptel1M 377265 ATAGTTTGGATCCATTCCTGATTCCACCAACAATAATCCCAGATTTCCCC 377314 vv v v i v iviiv i i i -i viv v - C L1ME3Cz_3end# 310 AGTGGTTGTACCAATTTACACTCCCACCAGCAGT-GTATGAGAGTTCCC- 263 chr5ptel1M 377315 CAAAAGCCTTTCCACAT 377331 ----- ii i C L1ME3Cz_3end# 262 -----GTTTCTCCACAT 251 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.08 CpG sites = 56, Kimura (unadjusted) = 43.09 Transitions / transversions = 1.81 (56/31) Gap_init rate = 0.10 (28 / 293), avg. gap size = 1.50 (42 / 28) 12 21.71 0.00 0.00 chr5ptel1M 378425 378456 (621544) (CACA)n#Simple_repeat 1 32 (0) m_b227s252i1 8919 chr5ptel1M 378425 CACACCCACCCACACACACATTCACTCCCACA 378456 v v iv v v (CACA)n#Simpl 1 CACACACACACACACACACACACACACACACA 32 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 18 13.67 6.00 1.92 chr5ptel1M 379723 379772 (620228) (TAAATT)n#Simple_repeat 1 52 (0) m_b227s252i3 8920 chr5ptel1M 379723 TAAATTTAAATCT--TTTTAAATTTTAATTTTAAATTT-TTTTTAATTTT 379769 i --v - v -vv v (TAAATT)n#Sim 1 TAAATTTAAATTTAAATTTAAA-TTTAAATTTAAATTTAAATTTAAATTT 49 chr5ptel1M 379770 AAA 379772 (TAAATT)n#Sim 50 AAA 52 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.06 (3 / 49), avg. gap size = 1.33 (4 / 3) 275 26.67 16.67 0.00 chr5ptel1M 380332 380451 (619549) MIR1_Amn#SINE/MIR 21 160 (70) m_b227s601i0 8921 chr5ptel1M 380332 GTGGATAGAGCCTTAAATTAGGCATC------CCAGGATTTTATTCCCAC 380375 vi ii i i vv ------ v i i? ? iv MIR1_Amn#SINE 21 GTGGATAGAGCACTGGACTGGGACTCGGGAGACCTGGGTTCNANTCCCGG 70 chr5ptel1M 380376 CTCAG-----AACCT----TGTAA-----GTCAAGTTATAGGACTTCTAT 380411 v -----?i ?----? i ----- v i ivv? i v MIR1_Amn#SINE 71 CTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGTCACTTNACCTCTCT 120 chr5ptel1M 380412 TAGATTCAGTTTCTGTATCTGTAAAATGGGTACAATAATA 380451 v? vi ivi v i i MIR1_Amn#SINE 121 GNGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATGATA 160 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.92 CpG sites = 18, Kimura (unadjusted) = 36.33 Transitions / transversions = 1.29 (18/14) Gap_init rate = 0.03 (4 / 119), avg. gap size = 5.00 (20 / 4) 362 25.64 3.31 3.31 chr5ptel1M 380382 380502 (619498) MIR#SINE/MIR 88 208 (54) m_b227s601i1 8921 chr5ptel1M 380382 ACCTTGTAAGTCAAGTTATAGGACTTCTATTAGATTCAGTTTCTGTATCT 380431 --- v ivvi i v vv vi ivi MIR#SINE/MIR 88 ACCTTG---GGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCT 134 chr5ptel1M 380432 GTAAAATGGGTACAATAATAGCACTTAAATCCTCTGGTTCTCATGAGGAT 380481 v i i i vv v vv v ii MIR#SINE/MIR 135 GTAAAATGGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGGAT 184 chr5ptel1M 380482 GAAA----TTAAGACAATGCAGAGC 380502 v ---- v - i i MIR#SINE/MIR 185 TAAATGAGTTAATAC-ATGTAAAGC 208 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.49 CpG sites = 13, Kimura (unadjusted) = 31.49 Transitions / transversions = 0.76 (13/17) Gap_init rate = 0.04 (5 / 120), avg. gap size = 1.60 (8 / 5) 236 28.51 7.27 8.59 chr5ptel1M 380637 380801 (619199) L2b_3end#LINE/L2 293 455 (11) m_b227s601i2 8922 chr5ptel1M 380637 TATCTTGTGCACACTGGGTCGCTCCAGAATTG-CTGGTGTAT-TGTCTGC 380684 i i i- v i----- v? - ? - i- i L2b_3end#LINE 293 TACCCTGC-CACTCTGGGTT-----ATNATTGTCTGNT-TACATGTCTGT 335 chr5ptel1M 380685 C-CCACCACT---CTGTGGTAGGGGAACTCCATGAGGGCAGGGG--ATGT 380728 - v --- ------- i i i--i? L2b_3end#LINE 336 CTCCCCCACTAGACTGTG-------AGCTCCGTGAGGGCAGGGACCGNGT 378 chr5ptel1M 380729 CCCTCATATCTCTATTTGTGTTCCTGGTGTTTAGCCCAGGG-CTGCCCTG 380777 iv v i iivivvi i i ii i ii v ? - v vii L2b_3end#LINE 379 CTGTCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACA 428 chr5ptel1M 380778 TAGCAGGCCCTTAAT---TGTTTATTG 380801 i i v i i --- i i L2b_3end#LINE 429 CAGTAGGCGCTCAGTAAATATTTGTTG 455 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.89 CpG sites = 31, Kimura (unadjusted) = 39.45 Transitions / transversions = 2.58 (31/12) Gap_init rate = 0.13 (21 / 164), avg. gap size = 1.24 (26 / 21) 269 31.09 10.92 0.00 chr5ptel1M 381493 381611 (618389) MIR#SINE/MIR 53 184 (78) m_b227s601i3 8923 chr5ptel1M 381493 TTCTGATCCCAAACCTG--GGTTACTAACTGTGTACCTCTGGACAAGTCA 381540 vi iivi --iv i iv ii i i MIR#SINE/MIR 53 TTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTA 102 chr5ptel1M 381541 ATTAAATTCTATTTGT-----TTTCCTGTTTTTCTCAATGGGGATAACAA 381585 v vi v v i----- vv i vivv i MIR#SINE/MIR 103 CTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAA 152 chr5ptel1M 381586 TATCACCTGACTTAAAA------TGTGAAGAT 381611 vi iv i v i------ i MIR#SINE/MIR 153 TAGTACCTACCTCATAGGGTTGTTGTGAGGAT 184 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.79 CpG sites = 21, Kimura (unadjusted) = 41.24 Transitions / transversions = 1.31 (21/16) Gap_init rate = 0.03 (3 / 118), avg. gap size = 4.33 (13 / 3) 233 31.06 6.67 1.27 chr5ptel1M 382391 382540 (617460) C MIR3#SINE/MIR (2) 206 49 m_b227s601i4 8924 chr5ptel1M 382391 ATCA-AAAGTCAGAAGATGT-GGGGCTGAAAGATCCTTCAGA-AGGAAAG 382437 - i i v ii -i i i ivv i i - vv vvv C MIR3#SINE/MIR 206 ATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCT 157 chr5ptel1M 382438 AGTTCAACCCCCTCCAATTTATAG--GAAGAAACTGAAAGACAGAGAAGG 382485 i - v i -- i iivv i v C MIR3#SINE/MIR 156 AGTCCAACCCCCTC-ATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGT 108 chr5ptel1M 382486 GATATA---TG-CAAAGGTCGTA-GGCTTTCTGAGAGTCAGAGTCAACTC 382530 vi i--- - v ii -i ?vvi - v v i iivv C MIR3#SINE/MIR 107 GAAGTGACTTGCCCAAGGTCACACAGCNAGTT-AGTGGCAGAGCCGGGAC 59 chr5ptel1M 382531 TTGAACCCAG 382540 v C MIR3#SINE/MIR 58 TAGAACCCAG 49 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 40.23 CpG sites = 25, Kimura (unadjusted) = 41.40 Transitions / transversions = 1.19 (25/21) Gap_init rate = 0.06 (9 / 149), avg. gap size = 1.33 (12 / 9) 13 9.32 0.00 0.00 chr5ptel1M 385521 385543 (614457) (GTCT)n#Simple_repeat 1 23 (0) m_b227s252i4 8925 chr5ptel1M 385521 GTGTGTCAGTCTGTCTGTCTGTC 385543 v v (GTCT)n#Simpl 1 GTCTGTCTGTCTGTCTGTCTGTC 23 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 435 21.21 2.00 0.99 chr5ptel1M 387721 387820 (612180) MIR#SINE/MIR 44 144 (118) m_b227s601i5 8926 chr5ptel1M 387721 CTTCATGAGTTCAAATCCCATCTCATATCA-TTACTAGGTATGGGAACTT 387769 v v i i iv - ii - v i v v MIR#SINE/MIR 44 CTGCCTGGGTTCGAATCCCGGCTC-TGCCACTTACTAGCTGTGTGACCTT 92 chr5ptel1M 387770 GGTCAAGTCACTTTACCACATT-TGCCTCAGTTTCCTCATTTGTAAAGTG 387818 v i v v vi - i i MIR#SINE/MIR 93 GGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATG 142 chr5ptel1M 387819 AG 387820 i MIR#SINE/MIR 143 GG 144 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 22.55 CpG sites = 11, Kimura (unadjusted) = 25.16 Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.03 (3 / 99), avg. gap size = 1.00 (3 / 3) 16 5.20 0.00 0.00 chr5ptel1M 389479 389498 (610502) (A)n#Simple_repeat 1 20 (0) m_b227s252i5 8927 chr5ptel1M 389479 AAATAAAAAAAAAAAAAAAA 389498 v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAA 20 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 17 18.38 0.00 0.00 chr5ptel1M 389630 389660 (610340) (A)n#Simple_repeat 1 31 (0) m_b227s252i6 8928 chr5ptel1M 389630 AAAAAAAAAAAAAACTGAGAAAAGAAAAAAA 389660 vvi i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 31 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 247 29.75 5.79 0.00 chr5ptel1M 392454 392574 (607426) C L1ME3F_3end#LINE/L1 (422) 568 441 m_b227s551i10 8929 chr5ptel1M 392454 TCATTTTTACAGAACAATAATAGTCCACGGTCTTCAAGTACCACAAGTTG 392503 i v vvvv v iv v vv vi v i C L1ME3F_3end#L 568 TCATTTTCACTGCTGTATAATATTCCATTGTGTGAATATACCACAATTTA 519 chr5ptel1M 392504 TTCGGCCATTCCCCAATAGACAGACACATATTTTGTTT-CAGTTCTTTGT 392552 iiv i vi v ii iv ivv - i i C L1ME3F_3end#L 518 TTTATCCATTCTCCTGTCGATGGACATTTGGGTTGTTTCCAGTTTTTTGC 469 chr5ptel1M 392553 GAC--CGCACAGAGCTG----GAACATT 392574 v i-- v v ---- C L1ME3F_3end#L 468 TATTACGAACAGTGCTGCTATGAACATT 441 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.02 CpG sites = 15, Kimura (unadjusted) = 38.02 Transitions / transversions = 0.71 (15/21) Gap_init rate = 0.03 (3 / 120), avg. gap size = 2.33 (7 / 3) 592 32.63 2.76 1.71 chr5ptel1M 393747 394036 (605964) C L1ME4c_3end#LINE/L1 (257) 573 281 m_b227s551i11 8930 chr5ptel1M 393747 ATCATTCCTTATAGAAGAATAATATGCTACAACATTAATGTGCTATGACT 393796 ii v i vv v v i ivivi ?i i i i i C L1ME4c_3end#L 573 ATCATTTTTAATGGCTGCATAATATTCCATCGAGTNGATGTACCATAATT 524 chr5ptel1M 393797 TATTCAGC-ATTTCCCAGTTGATGGGCATCCACTCAGTTTCCAGTTTCTT 393845 i i i - i vi v i ii vviv i i i C L1ME4c_3end#L 523 TACTTAACCATTCCCCTATTGTTGGACATTTAGGTTGTTTCCAATTTTTC 474 chr5ptel1M 393846 GCCACTACAAACGGGGCTGCAG-AAACATTTCTGTACATGTGGGACCTTT 393894 i i i iiiv i-i i ii i i i --- C L1ME4c_3end#L 473 GCTATTATAAATAACGCTGCAATGAACATCTTCGTGCATATAG---CTTT 427 chr5ptel1M 393895 TTCCTCCTTTAGG---ATCTCTTTGGCATATAAACCCAGTAGAAACATTG 393941 i v i--- i i i v v vv v viiv i C L1ME4c_3end#L 426 TTCCTTCTTTTGAATTATTTCCTTAGGATAAATTCCCAGAAGTGGAATTA 377 chr5ptel1M 393942 GTAGTTCAAAGGCTATGCACCAGTTGATAGCCCTTTGGATATG---TTCC 393988 v i v v v vvv v i i -- i --- v C L1ME4c_3end#L 376 CTGGGTCAAAGGGTATGAACATTTTTATGGCTCTT--GATACGTATTGCC 329 chr5ptel1M 393989 ATATTGCTCGGCCGAATGGTTGGATCCATTCACAATTCCACCAACAAT 394036 v ivv vi v v i v i ? v i C L1ME4c_3end#L 328 AAATTGCTTTCCAAAAGGGTTGTACCAATTTACANTGCCACCAGCAAT 281 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 42.23 CpG sites = 55, Kimura (unadjusted) = 44.83 Transitions / transversions = 1.45 (55/38) Gap_init rate = 0.03 (9 / 289), avg. gap size = 1.44 (13 / 9) 470 34.28 1.97 4.36 chr5ptel1M 393765 394069 (605931) C L1ME3Cz_3end#LINE/L1 (449) 548 251 m_b227s551i12 8930 chr5ptel1M 393765 ATAATATGCTACAACATTAATGTGCTATGACTTATTCA-GCATTTCCCAG 393813 i v i ivii v i i i ii i i -v i vi C L1ME3Cz_3end# 548 ATAGTATTCCATTGTATGAATATACCACAATTTATTTATCCATTCCCCTA 499 chr5ptel1M 393814 TTGATGGGCATCCACTCAGTTTCCAGTTTCTTGCCACTACAAACGGGGCT 393863 i ii vviv i i i i i iiv C L1ME3Cz_3end# 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr5ptel1M 393864 GCAG-AAACATTTCTGTACATGTGGGACCTTTTTCCTCCTTT---AGGAT 393909 i-i iii v---i i v v v v v --- ii C L1ME3Cz_3end# 448 GCAATGAACATCCTTGTACATGTC---TCCTTGTGCACATGTGCGAGAGT 402 chr5ptel1M 393910 CTCTTTGGCATATAAACCCAGTAGAAACATTGGTAGTTCAAAGGCTATGC 393959 i i i vi v i v viiv v i v iv v C L1ME3Cz_3end# 401 TTCTCTAGGGTATATACCTAGAAGTGGAATTGCTGGGTCGTAGGGTATGC 352 chr5ptel1M 393960 ACCAGTTGATAGCCCT-TTGGATATGTTCCATATTGCTCGGCCGAATGGT 394008 i vvv --i i ii -i i - v v vv vi i C L1ME3Cz_3end# 351 GCATCTT--CAACTTTACTAGATAT-TGCCAAATTGCTCTCCAAAGTGGT 305 chr5ptel1M 394009 TGGATCCATTCACAATTCCACCAACAATAATCCCAGATTTCCCCCAAAAG 394058 v i v i v i i i -i viv v ------ C L1ME3Cz_3end# 304 TGTACCAATTTACACTCCCACCAGCAGT-GTATGAGAGTTCCC------G 262 chr5ptel1M 394059 CCTTTCCACAT 394069 ii i C L1ME3Cz_3end# 261 TTTCTCCACAT 251 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 45.96 CpG sites = 62, Kimura (unadjusted) = 48.00 Transitions / transversions = 1.63 (62/38) Gap_init rate = 0.06 (17 / 304), avg. gap size = 1.12 (19 / 17) 20 10.73 0.00 0.00 chr5ptel1M 395215 395244 (604756) (CA)n#Simple_repeat 1 30 (0) m_b227s252i7 8931 chr5ptel1M 395215 CACACACACACACACACATTCACTCACACA 395244 iv v (CA)n#Simple_ 1 CACACACACACACACACACACACACACACA 30 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 22 6.82 1.79 9.62 chr5ptel1M 396512 396567 (603433) (TAAATTT)n#Simple_repeat 1 52 (0) m_b227s252i9 8932 chr5ptel1M 396512 TAAATTTAAATCTTTTAAATTTT-AATTTTAAATTTTTTTAATTTTAAAA 396560 v -v - -- v -- (TAAATTT)n#Si 1 TAAATTTTAA-ATTTTAAATTTTAAATTTTAAA--TTTTAAATTTT--AA 45 chr5ptel1M 396561 ATTTTAA 396567 (TAAATTT)n#Si 46 ATTTTAA 52 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.11 (6 / 55), avg. gap size = 1.00 (6 / 6) 317 26.71 4.17 3.31 chr5ptel1M 397134 397253 (602747) MIR#SINE/MIR 88 208 (54) m_b227s601i6 8933 chr5ptel1M 397134 ACCTTGTAAGTCAAGTTATGGGACTTCTATTAGATTCAGTT-CTGTATCT 397182 --- v ivvi i v vv vi - ivi MIR#SINE/MIR 88 ACCTTG---GGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCT 134 chr5ptel1M 397183 ATAAAATGGGTACAATAATAGCACTTAAATCCTCTGGTTCTCATGAGGAT 397232 i v i i i vv v vv v ii MIR#SINE/MIR 135 GTAAAATGGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGGAT 184 chr5ptel1M 397233 GAAA----TTAAGACAATGCAGAGC 397253 v ---- v - i i MIR#SINE/MIR 185 TAAATGAGTTAATAC-ATGTAAAGC 208 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.22 CpG sites = 14, Kimura (unadjusted) = 33.22 Transitions / transversions = 0.82 (14/17) Gap_init rate = 0.05 (6 / 119), avg. gap size = 1.50 (9 / 6) 189 29.80 3.65 11.81 chr5ptel1M 397412 397548 (602452) L2c_3end#LINE/L2 342 468 (10) m_b227s601i7 8934 chr5ptel1M 397412 AATTGCTGGTGTA-TTGTCTGCC-CCGCCACTGTGGTGGGGGACCTCCAT 397459 iiv v -? i - v iviv v i -- v L2c_3end#LINE 342 AATTGTCTGTTTACNTGTCTGTCTCCTCCACTAGACTGTGAG--CTCCTT 389 chr5ptel1M 397460 GAGGGCAGGGGATGTCCCTCATATCTCTATTTGTGTTCCTGGTGTTTAGC 397509 ivi vi -- iiv v i i ii i ii i L2c_3end#LINE 390 GAGGGCAGGGACCGTGTCT--TATTCATCTTTGTATCCCCAGCGCCTGGC 437 chr5ptel1M 397510 CCAGGGCTGCCCTGTAGCAGGCCCTTAAT---TGTTTACTGA 397548 v ----------- i v i --- ii L2c_3end#LINE 438 ACA-----------TAGTAGGCGCTCAATAAATGTTTGTTGA 468 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.66 CpG sites = 23, Kimura (unadjusted) = 39.48 Transitions / transversions = 1.77 (23/13) Gap_init rate = 0.13 (18 / 136), avg. gap size = 1.11 (20 / 18) 190 29.75 4.71 1.14 chr5ptel1M 397454 397538 (602462) L2d_3end#LINE/L2 404 491 (25) m_b227s601i8 8934 chr5ptel1M 397454 CTCCATGAGGGCAGGGGATGTCCCTCATATCTCTATTTGTGTTCC---TG 397500 v ivii vi i - ? v ?vi ---ii L2d_3end#LINE 404 CTCCTTGAGGGCAGGGACCATGTCTTATA-CTNTTTTNTCGTTCCCCACA 452 chr5ptel1M 397501 GTGTTTAGCCCAGGGCTG-CCCTGTAGCAGGCCCTTAAT 397538 i ii v v -v vii i v i L2d_3end#LINE 453 GCGCCTAGCACAGTGCTGAGCACATAGTAGGCGCTCAAT 491 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.33 CpG sites = 15, Kimura (unadjusted) = 40.44 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.04 (3 / 84), avg. gap size = 1.67 (5 / 3) 269 31.09 10.92 0.00 chr5ptel1M 398225 398343 (601657) MIR#SINE/MIR 53 184 (78) m_b227s601i9 8935 chr5ptel1M 398225 TTCTGATCCCAAACCTG--GGTTACTAACTGTGTACCTCTGGACAAGTCA 398272 vi iivi --iv i iv ii i i MIR#SINE/MIR 53 TTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTA 102 chr5ptel1M 398273 ATTAAATTCTATTTGT-----TTTCCTGTTTTTCTCAATGGGGATAACAA 398317 v vi v v i----- vv i vivv i MIR#SINE/MIR 103 CTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAA 152 chr5ptel1M 398318 TATCACCTGACTTAAAA------TGTGAAGAT 398343 vi iv i v i------ i MIR#SINE/MIR 153 TAGTACCTACCTCATAGGGTTGTTGTGAGGAT 184 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.79 CpG sites = 21, Kimura (unadjusted) = 41.24 Transitions / transversions = 1.31 (21/16) Gap_init rate = 0.03 (3 / 118), avg. gap size = 4.33 (13 / 3) 231 27.69 6.80 1.85 chr5ptel1M 399164 399266 (600734) C MIR3#SINE/MIR (52) 156 49 m_b227s601i10 8936 chr5ptel1M 399164 AGTTCAACCCCCTCCAATTTATAG--GAAGAAACTGAAAGACAGAGAAGG 399211 i - v i -- i iivv i v C MIR3#SINE/MIR 156 AGTCCAACCCCCTC-ATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGT 108 chr5ptel1M 399212 GATATA---TG-CAAAGGTCGTA-GGCTTTCTGAGAGTCAGAGTCAACTC 399256 vi i--- - v ii -i ?vvi - v v i iivv C MIR3#SINE/MIR 107 GAAGTGACTTGCCCAAGGTCACACAGCNAGTT-AGTGGCAGAGCCGGGAC 59 chr5ptel1M 399257 TTGAACCCAG 399266 v C MIR3#SINE/MIR 58 TAGAACCCAG 49 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.08 CpG sites = 15, Kimura (unadjusted) = 35.63 Transitions / transversions = 1.15 (15/13) Gap_init rate = 0.06 (6 / 102), avg. gap size = 1.50 (9 / 6) 13 9.32 0.00 0.00 chr5ptel1M 402285 402307 (597693) (GTCT)n#Simple_repeat 1 23 (0) m_b227s252i10 8937 chr5ptel1M 402285 GTGTGTCAGTCTGTCTGTCTGTC 402307 v v (GTCT)n#Simpl 1 GTCTGTCTGTCTGTCTGTCTGTC 23 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 311 27.19 4.76 0.76 chr5ptel1M 404895 405020 (594980) C L1MC1_3end#LINE/L1 (481) 599 469 m_b227s551i13 8938 chr5ptel1M 404895 CTCCAGGTCTTTCTAAATCTTGCTCGTTCATCATTTTTACAGAAC--AAT 404942 v ii viv v v i ivi -i vi -- C L1MC1_3end#LI 599 CTCCATGTCTTTTCATGGCTTGATAGCTCATTTCTTTT-TAGCGCTGAAT 551 chr5ptel1M 404943 AATATTCCATTGCCTTCGTGTACCACAACTTGTTCAGCCATTCCCCAATT 404992 i vvi ii i i v v v i C L1MC1_3end#LI 550 AATATTCCATTGTCTGGATGTACCACAGTTTATTTATCCATTCACCTACT 501 chr5ptel1M 404993 GGTAGACATCT--GTT--TTCCAGTTCTTTGC 405020 ivi -- -- iv i v C L1MC1_3end#LI 500 GAAGGACATCTTGGTTGCTTCCAAGTTTTGGC 469 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.21 CpG sites = 19, Kimura (unadjusted) = 34.44 Transitions / transversions = 1.27 (19/15) Gap_init rate = 0.03 (4 / 125), avg. gap size = 1.75 (7 / 4) 347 25.22 3.51 2.61 chr5ptel1M 404909 405022 (594978) C L1MC5a_3end#LINE/L1 (2196) 581 467 m_b227s551i14 8938 chr5ptel1M 404909 AAATCTTGCTCGTTCATCATTTTTACAGAACAATAATATTCCATTGCCTT 404958 i v i -- - vvvv i i iv v C L1MC5a_3end#L 581 AGATCTTCCTCATTC--C-TTTTTACAGCTGCATAGTACTCCATTGTGTG 535 chr5ptel1M 404959 CGTGTACCACAACTTGTTCAGCCATTCCCCAATTGGTAGACATCTG---- 405004 vi i ii i i v v i i i ---- C L1MC5a_3end#L 534 GATGTACCATAGTTTATTCAACCAGTCCCCTATTGATGGACATTTGGGTT 485 chr5ptel1M 405005 TTTTCCAGTTCTTTGCCA 405022 v ii i C L1MC5a_3end#L 484 GTTTCCAGTCTTTTGCTA 467 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 31.52 CpG sites = 17, Kimura (unadjusted) = 31.52 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.04 (4 / 113), avg. gap size = 1.75 (7 / 4) 337 27.73 4.20 0.00 chr5ptel1M 404920 405038 (594962) C L1ME3F_3end#LINE/L1 (416) 574 451 m_b227s551i15 8938 chr5ptel1M 404920 GTTCAT-CATTTTTACAGAACAATAATATTCCATTGCCTTCGTGTACCAC 404968 - i v vvvv iv vvi i C L1ME3F_3end#L 574 GTTCATTCATTTTCACTGCTGTATAATATTCCATTGTGTGAATATACCAC 525 chr5ptel1M 404969 AACTTGTTCAGCCATTCCCCAATTGGTAGACATCTG----TTTTCCAGTT 405014 i i i v i vi i i i i ----v C L1ME3F_3end#L 524 AATTTATTTATCCATTCTCCTGTCGATGGACATTTGGGTTGTTTCCAGTT 475 chr5ptel1M 405015 CTTTGCCACCGCCCAAAGAGCTGC 405038 i i iii vv v v C L1ME3F_3end#L 474 TTTTGCTATTACGAACAGTGCTGC 451 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.94 CpG sites = 18, Kimura (unadjusted) = 35.24 Transitions / transversions = 1.20 (18/15) Gap_init rate = 0.02 (2 / 118), avg. gap size = 2.50 (5 / 2) 693 30.88 2.48 3.45 chr5ptel1M 405537 405858 (594142) C L1ME4c_3end#LINE/L1 (275) 555 237 m_b227s551i16 8939 chr5ptel1M 405537 ATAATATTTTGCAACATTCATGTACTATGACTTATTCAGCCATTCCCCAG 405586 iiiivivi ?v i i i i i i vi C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chr5ptel1M 405587 CTGATGGGCATCCACTCAGTTTCCAGTTTCTTGCCACTACAAACAAGGCT 405636 i v i ii vviv i i i i i i i v C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCT 456 chr5ptel1M 405637 GCCACAAACATTTTTGTGCATGTGGGTCCCTTTCCTTGCTTTAAGTT--C 405684 v ii i i i i -- ii vi i i --i C L1ME4c_3end#L 455 GCAATGAACATCTTCGTGCATATAG--CTTTTTCCTTCTTTTGAATTATT 408 chr5ptel1M 405685 TCTTTGGCATATAAGCCTGCTAGAAAC---ATCACTAGATCAAGGGGTAT 405731 i i v - vi -- i ii--- i i i i C L1ME4c_3end#L 407 TCCTTAGGATA-AATTC--CCAGAAGTGGAATTACTGGGTCAAAGGGTAT 361 chr5ptel1M 405732 GCAGGTTTTGATAGCCCTT--TGGGCATCGTTCCAAATTGCTCCCCAGAA 405779 v vi v i i -- iv i i -- ii i C L1ME4c_3end#L 360 GAACATTTTTATGGCTCTTGATACGTATTG--CCAAATTGCTTTCCAAAA 313 chr5ptel1M 405780 TGGTTGGATCTTTCTATAGCTCCACCACCGATGCATTAATATTCTAGATT 405829 v v i vv i i ?iv v i i v i?i v i - C L1ME4c_3end#L 312 GGGTTGTACCAATTTACANTGCCACCAGCAATGTATGAGNGTACCAG-TT 264 chr5ptel1M 405830 TCCCCCTAAAAACCTTTCCA-CATTGGTTA 405858 v vi--- ? iv - v C L1ME4c_3end#L 263 TCACCGC---ANCCTCGCCAGCATTGGGTA 237 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.65 CpG sites = 67, Kimura (unadjusted) = 43.09 Transitions / transversions = 2.31 (67/29) Gap_init rate = 0.05 (15 / 321), avg. gap size = 1.27 (19 / 15) 18 8.53 0.00 0.00 chr5ptel1M 405996 406020 (593980) (T)n#Simple_repeat 1 25 (0) m_b227s252i11 8940 chr5ptel1M 405996 TTTTGTTTTTTTTTTTTGTTTTTTT 406020 v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 15 37.18 0.00 0.00 chr5ptel1M 406215 406279 (593721) (AAAA)n#Simple_repeat 1 65 (0) m_b227s252i12 8941 chr5ptel1M 406215 AAAAAAAAAAAAAAAAAAGGAAGGAAGCAAGGAATAAAGGAAGGAAGAGA 406264 ii ii iv ii v ii ii i i (AAAA)n#Simpl 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr5ptel1M 406265 AAAAAGAAACAATAA 406279 i v v (AAAA)n#Simpl 51 AAAAAAAAAAAAAAA 65 Matrix = Unknown Transitions / transversions = 3.50 (14/4) Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0) 17 15.30 0.00 0.00 chr5ptel1M 406298 406326 (593674) (AC)n#Simple_repeat 1 29 (0) m_b227s252i13 8942 chr5ptel1M 406298 ACACACACACATAAACACACACATTCACA 406326 i v iv (AC)n#Simple_ 1 ACACACACACACACACACACACACACACA 29 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 446 29.72 10.99 2.02 chr5ptel1M 408123 408304 (591696) MIRc#SINE/MIR 14 211 (57) m_b228s601i0 8943 chr5ptel1M 408123 TACAGTGGATAGAATGTGGATAGGGCCTTGAATCAGGAAGCCCAGGGTTT 408172 i v ---- v iv i i v i v v i MIRc#SINE/MIR 14 TGCAGTGGAAAGA----GCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr5ptel1M 408173 TAATCCCACCTCAGAATCTTCCAAGT--------------CAAGTTATAG 408208 v i iv v vvv v v i-------------- i ivv MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTT 109 chr5ptel1M 408209 GACCTCTGTGGGATTCAGTTTCTTTATCTGTAAAATGGGTATAATGATAG 408258 i v i vi i i v i v MIRc#SINE/MIR 110 AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAC 159 chr5ptel1M 408259 CAGCTAAGTCCTCTT------GTTCTCATGAGGATGAAATAAGACATTGC 408302 v ivv i iv i ------ v ii v i i v i MIRc#SINE/MIR 160 CTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGT 209 chr5ptel1M 408303 AT 408304 MIRc#SINE/MIR 210 AT 211 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.58 CpG sites = 26, Kimura (unadjusted) = 38.37 Transitions / transversions = 0.96 (26/27) Gap_init rate = 0.03 (6 / 181), avg. gap size = 4.00 (24 / 6) 20 7.81 0.00 0.00 chr5ptel1M 408381 408407 (591593) (T)n#Simple_repeat 1 27 (0) m_b228s252i0 8944 chr5ptel1M 408381 TTCTTTTTTTTTTTTTTTTTTTTATTT 408407 i v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTT 27 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 13 25.00 0.00 0.00 chr5ptel1M 408385 408422 (591578) (TTTTA)n#Simple_repeat 1 38 (0) m_b228s252i1 8944 chr5ptel1M 408385 TTTTTTTTTTTTTTTTTTTATTTAATAGCCTTTTATTT 408422 v v v v vviv (TTTTA)n#Simp 1 TTTTATTTTATTTTATTTTATTTTATTTTATTTTATTT 38 Matrix = Unknown Transitions / transversions = 0.14 (1/7) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 415 27.75 2.55 2.55 chr5ptel1M 408873 409068 (590932) C L1MC4_3end#LINE/L1 (2156) 633 438 m_b228s551i0 8945 chr5ptel1M 408873 GCTCATTTCACTTAGCATCAGTTCGTGTAAGTCTC-TCCAGGCCTTTCTG 408921 iv v? - v i v vi - v ii? vi C L1MC4_3end#LI 633 GCTTCTTTCACTTAGCAANA-TGCATTTAAGATTCATCCATGTTNTTGCG 585 chr5ptel1M 408922 -AAATCATCCTGTTGGTCATTTC---TTACAGAACAGTAATATTCCATAA 408967 -i? ---- v v i --- iv vvv i vi C L1MC4_3end#LI 584 TGNATCA----GTAGTTCATTCCTTTTTATCGCTGAGTAGTATTCCATTG 539 chr5ptel1M 408968 TTTTCATATACCACAATTTATTCAGCCATTCTCCAACTGATGGACATCCA 409017 v vv i i i i v v vii v i? C L1MC4_3end#LI 538 TATGGATGTACCACAGTTTGTTTATCCATTCACCTGTTGAAGGACATCTN 489 chr5ptel1M 409018 TTCAGTTTCCAGTTTCTAGCCACTACAAAAAGGGCTGCCACAAACATTCG 409067 vviv ? i i ? i ii v ii i i C L1MC4_3end#LI 488 GGTTGTTTCCAGNTTTTGGCNATTATGAATAAAGCTGCTATAAACATTCG 439 chr5ptel1M 409068 T 409068 C L1MC4_3end#LI 438 T 438 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.82 CpG sites = 28, Kimura (unadjusted) = 36.68 Transitions / transversions = 1.12 (28/25) Gap_init rate = 0.04 (8 / 195), avg. gap size = 1.25 (10 / 8) 457 25.86 0.00 0.00 chr5ptel1M 408953 409068 (590932) C L1ME1_3end#LINE/L1 (373) 553 438 m_b228s551i1 8945 chr5ptel1M 408953 AGTAATATTCCATAATTTTCATATACCACAATTTATTCAGCCATTCTCCA 409002 i vi v vv i i v v ? C L1ME1_3end#LI 553 AGTAGTATTCCATTGTATGGATATACCACAATTTGTTTATCCATTCACCN 504 chr5ptel1M 409003 ACTGATGGACATCCATTCAGTTTCCAGTTTCTAGCCACTACAAAAAGGGC 409052 ii iiivviv i i i i i v ii C L1ME1_3end#LI 503 GTTGATGGACATTTGGGTTGTTTCCAGTTTTTGGCTATTACGAATAAAGC 454 chr5ptel1M 409053 TGCCACAAACATTCGT 409068 i ii C L1ME1_3end#LI 453 TGCTATGAACATTCGT 438 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 31.94 CpG sites = 20, Kimura (unadjusted) = 33.30 Transitions / transversions = 2.00 (20/10) Gap_init rate = 0.00 (0 / 115), avg. gap size = 0.0 (0 / 0) 199 38.04 3.51 0.85 chr5ptel1M 409181 409294 (590706) L2c_3end#LINE/L2 361 477 (1) m_b228s601i1 8946 chr5ptel1M 409181 TGTGTGCCCCACCACTCTGTGACCTCCATGAGAGCAAGGGGTGTCCCTCA 409230 v v i i vv v v i i ivi vi i L2c_3end#LINE 361 TGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTA 410 chr5ptel1M 409231 CATCTCTTTGCGTTCTTGGTGTTTAGCCCAT----GACTGCCCTGTAGAA 409276 iviv ii i iii i ii i v ---- i - i vi i v L2c_3end#LINE 411 TTCATCTTTGTATCCCCAGCGCCTGGCACATAGTAGGC-GCTCAATAAAT 459 chr5ptel1M 409277 GTTTACTGACTAGAAGAA 409294 ii v ii v L2c_3end#LINE 460 GTTTGTTGAATGAATGAA 477 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 53.09 CpG sites = 28, Kimura (unadjusted) = 57.20 Transitions / transversions = 1.87 (28/15) Gap_init rate = 0.02 (2 / 113), avg. gap size = 2.50 (5 / 2) 269 28.17 1.41 0.00 chr5ptel1M 409365 409435 (590565) C MIR3#SINE/MIR (28) 180 109 m_b228s601i2 8947 chr5ptel1M 409365 TGGAAGGGACCTACAAGGCCATAGAGTGTGACCCACTCATTTTGTAGATG 409414 vvi ii vv vii v ii C MIR3#SINE/MIR 180 TGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATG 131 chr5ptel1M 409415 -GGAAATTGAAGTTCACGGAAG 409435 - i i ii vi i C MIR3#SINE/MIR 130 AGGAAACTGAGGCCCAGAGAGG 109 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.75 CpG sites = 13, Kimura (unadjusted) = 36.75 Transitions / transversions = 1.86 (13/7) Gap_init rate = 0.01 (1 / 70), avg. gap size = 1.00 (1 / 1) 700 23.96 4.09 1.33 chr5ptel1M 410386 410605 (589395) C L1ME5_3end#LINE/L1 (712) 229 4 m_b228s551i2 8945 chr5ptel1M 410386 GCTTTCTA------GCCAATCTGACAGGTGTGTAGTGGTATCTCAGAGTT 410429 ------ i i i iv i vv C L1ME5_3end#LI 229 GCTTTCTAATTTTTGCCAGTCTAATAGGTGTAAAGTGATATCTCATTGTT 180 chr5ptel1M 410430 GTCTGCATTTGCATTTCTCTGATTAATAATGACTTGGAGCATCTTTTCAC 410479 i vv v v v i i C L1ME5_3end#LI 179 GTTTTAATTTGCATTTCTCTGATTACTAATGAGTTTGAGCATCTCTTCAT 130 chr5ptel1M 410480 ATGGCTAGATATAGTTTCAA-TTTCTTCGTCTGAGAATTGTCTGTTCATA 410528 - v v vvv ii- i v vi i C L1ME5_3end#LI 129 ATG-CTTGTTAGCCTTTCGGGTTTCCTCTTCTGTAAATTGCCTGTTCATA 81 chr5ptel1M 410529 TCCTTTGTCTATTGATCAATTGGAG--AATGGCTTGATTTTTCATAAATT 410576 i i vv v i --?vi v -- i ii vi C L1ME5_3end#LI 80 TCCTTTGCCCATTTTTCTATTGGGGTTNCCGTCTT--TTTCTTGTTGATT 33 chr5ptel1M 410577 AGAGTCAATTCTCTATATATTTTAGATAT 410605 v vivv i ii i i C L1ME5_3end#LI 32 TGCAGGAGTTCCTTGTATATTCTAGATAT 4 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 28.05 CpG sites = 27, Kimura (unadjusted) = 29.35 Transitions / transversions = 1.08 (27/25) Gap_init rate = 0.03 (6 / 219), avg. gap size = 2.00 (12 / 6) 383 28.99 2.55 2.17 chr5ptel1M 410459 410733 (589267) C L1M5_orf2#LINE/L1 (0) 3294 3019 m_b228s551i3 8945 chr5ptel1M 410459 TGACTTGGAGCATCTTTTCACATGGCTAGATATAGTTTCAATTTCTTCGT 410508 ?v v ii vi vvviivi v? v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr5ptel1M 410509 CTGAGAATTGTCTGTTCATATCCTTTGTCTATTGATCAATTGGA--GAAT 410556 i v v vi i i i vv ?v i-- vv C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTT 3195 chr5ptel1M 410557 GGCTTGATTTTTCA-TAAATTAGAGTCAATTCTCTATATATTTTAGATAT 410605 v -- ? i - i ? iv -v i i i i i C L1M5_orf2#LIN 3194 GTCTT--TTTNTTATTGANTTGTAG-GAGTTCTTTATATATTCTGGATAC 3148 chr5ptel1M 410606 GAGGCCTTTATCAGAACTTTCGACTGTAAAAATGTTTTCTCAGTTTATTG 410655 v i vv v vv?i i v v i i ? i i v C L1M5_orf2#LIN 3147 GAGTCCTTTGTCAGATATATGTNTTGCAAATATTTTCTCCCANTCTGTGG 3098 chr5ptel1M 410656 CATTCCTTTAATC-TTTTCT--GCATTA-CTTTTGTTTGTACAAAAACTA 410701 v v -- - --i iv i- -v? vi i ii v C L1M5_orf2#LIN 3097 CTTGCCTTT--TCATTTTCTTAACGGTGTCTTTTG-ANGAGCAGAAGTTT 3051 chr5ptel1M 410702 TTCACTTTTATATAATCAAAATTATCTATTTT 410733 v i v i? i v v v C L1M5_orf2#LIN 3050 TTAATTTTGATGNAGTCCAATTTATCAATTTT 3019 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.44 CpG sites = 37, Kimura (unadjusted) = 38.67 Transitions / transversions = 0.90 (37/41) Gap_init rate = 0.04 (11 / 274), avg. gap size = 1.18 (13 / 11) 324 29.53 5.11 4.78 chr5ptel1M 410466 410778 (589222) C L1PB_orf2#LINE/L1 (7) 3287 2974 m_b228s551i4 8945 chr5ptel1M 410466 GAGCATCTTTTCACATG---GCTAGATATAGTTTCAATTTCTTCGTCTGA 410512 i i --- i i vi --- vv v v i C L1PB_orf2#LIN 3287 GAGCATTTTTTCATATGTTTGTTGGCCAT---TTGTATATCTTCTTTTGA 3241 chr5ptel1M 410513 GAATTGTCTGTTCATATCCTTTGTCTATTGATCAATTGGAGAATGGCTTG 410562 i i v i i i vv ii v --- v i C L1PB_orf2#LIN 3240 GAATTGTCTATTCATGTCCTTAGCCCACTTTTTGATGGG---ATTGTTTG 3194 chr5ptel1M 410563 -ATTTTTCATA--AATTAGAGTCAATTCTCTATATATTTTAGATATGAGG 410609 -v v i--i v vv v i ?i i v i i v v C L1PB_orf2#LIN 3193 TTTTTTTCTTGCTGATTTGTTTGAGTTCNTTGTAGATTCTGGATATTAGT 3144 chr5ptel1M 410610 CCTTTATCAGAACTTTCGACTGTAAAAATGTTTTCTCAGTTTATTG--CA 410657 i vv v v i i i v i i v i i v --ii C L1PB_orf2#LIN 3143 CCTTTGTCAGATGTATAGATTGTGAAGATTTTCTCCCACTCTGTGGGTTG 3094 chr5ptel1M 410658 TTCCTTTAATCTTTT--CTGCATTACTTTTGTTTGTACAAAAACTATTCA 410705 iiv v vi -- -- v -ii i i i v i C L1PB_orf2#LIN 3093 TCTGTTTACTCTGCTGACTG--TTCCTTTTG-CCGTGCAGAAGCTCTTTA 3047 chr5ptel1M 410706 CTTTTATATAATCAAAATTATCTAT-TTTG----TGAT-CAGTAATGATT 410749 v v vv i vv ?i i - ---- v - v -- v C L1PB_orf2#LIN 3046 GTTTAATTAAGTCCCANCTATTTATCTTTGTTTTTGTTGCATT--TGCTT 2999 chr5ptel1M 410750 TCTAGTTCTTCTTTGGTCATAAATTCCTT 410778 ivi ---- i v C L1PB_orf2#LIN 2998 TTGGGTTC----TTGGTCATGAAGTCCTT 2974 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.93 CpG sites = 46, Kimura (unadjusted) = 38.48 Transitions / transversions = 1.10 (46/42) Gap_init rate = 0.07 (23 / 312), avg. gap size = 1.35 (31 / 23) 3261 30.81 1.89 1.89 chr5ptel1M 410994 412743 (587257) C L1M5_orf2#LINE/L1 (592) 2702 953 m_b228s551i5 8945 chr5ptel1M 410994 CTATTCCACTGATCAACTAATTTATTTTTTAGCCAATACCAAATGGTTTT 411043 i i v i vi i ii vv v iv i C L1M5_orf2#LIN 2702 CTGTTCCATTGATCTATTTGTCTATCCTTACGCCAATACCACACTGTCTT 2653 chr5ptel1M 411044 GGTGACCGCTGCTTTATAATATAATTTCAGATCTGGTACAGCTAAGCCAC 411093 i v i iv vivi v ? ? vv - i -- C L1M5_orf2#LIN 2652 GATTACTGTAGCTTTATAATAAGTCTTGANATCNGGTAGTG-TAAGTC-- 2606 chr5ptel1M 411094 CTTCA--TTTGATTTTTTTTTTCATTAATTCCCTTGGA-ATTCTTGACCT 411140 i -- v i i v-i vii v- ? ii i C L1M5_orf2#LIN 2605 CTCCAACTTTGTTCTTCTTTTTCAA-GATTGTTTTGGCTATTCTNGGTCC 2557 chr5ptel1M 411141 TTTGTTTTTCCGTATGAACTTTG---TTGTTTTTTCCAGGTCATCAAAAT 411187 iv i i i i--- iivi v v vv vv v C L1M5_orf2#LIN 2556 TTTGCATTTCCATATAAATTTTAGAATCAGCTTGTCAATTTCTACAAAAA 2507 chr5ptel1M 411188 AGTTTTTTGGGAGTCTGATTGGTATAGCGATAAATAAATAGATTAGTTAA 411237 iii vi v i v v iv i vv i i vi C L1M5_orf2#LIN 2506 AACCTGCTGGGATTTTGATTGGGATTGCATTGAATCTATAGATCAATTTG 2457 chr5ptel1M 411238 AGTAGTATTTTCATTTTTATTATATTTGCTAGCCCTATCCAAGAGCATTT 411287 i v v vv i ? iv viv vvi v v i vv C L1M5_orf2#LIN 2456 GGGAGAATTGACATCTTNACAATATTGAGTCTTCCAATCCATGAACATGG 2407 chr5ptel1M 411288 AATATTTTTCCAATTGGCTAGATCAGACTTTATTTGTGTGGAAAGTGTTT 411337 v i i v ivi i vvvi v v v viiv i C L1M5_orf2#LIN 2406 TATATCTCTCCATTTATTTAGGTCTTCTTTAATTTCTCTCAGCAATGTTT 2357 chr5ptel1M 411338 TGTAGTTTTGCTCATAAAGTTTCTGATTTTCTCTTGGCAGGTAGACTGTG 411387 vvvii ? v ii vviv ? i vi i vv i viv C L1M5_orf2#LIN 2356 TGTAGTTTTCAGTGTANAGGTCTTGCACATNTTTTGTTAGATTTATTCCT 2307 chr5ptel1M 411388 AAGTATTTTATACTATCAGTAGTTAATTTAAATGGAATTTCACTTTGTAC 411437 ? ii v iv vv i v v v --ii v? v C L1M5_orf2#LIN 2306 AAGTATTTNATGTTTTTTGATGCTATTGTAAATGGTATT--GTTTTTNAA 2259 chr5ptel1M 411438 CTCTGACTGTTGAATT--TTGTTAGAGATATATAAGAATGCTGATGAGTT 411485 v i v i v iv -- ivvii ii i viv v C L1M5_orf2#LIN 2258 ATTTCATTTTCCAATTGTTTGTTGCTAGTATATAGAAATACAATTGATTT 2209 chr5ptel1M 411486 ATGTGGGTTTATTTTGTATCCTGCAACTTTGGTAAAGGTGTAGATTGTTT 411535 v ivi v ii ? i i v vviiivv iv C L1M5_orf2#LIN 2208 TTGTATATTGACCTTGTATCCNGCGACCTTGCTAAATTCACTTATTAGTT 2159 chr5ptel1M 411536 CTAATAACTTTTAAGTAGAATCTCTCGGGTTCTCTAAGTATACCATCATA 411585 i ii ? vv v i ? i i v ? v i C L1M5_orf2#LIN 2158 CTAGTAGTTTNTTTGTAGATTCTTTNGGATTTTCTACGTANACAATCATG 2109 chr5ptel1M 411586 TCATCAGCAAAGAGTGATAATTTGGTTTCCTCATTGCC--TCCTGTAAAT 411633 v i v i? i i vi i v v -- i - vi- C L1M5_orf2#LIN 2108 TCATCTGCGAATAANGACAGTTTTATTTCTTCCTTTCCAATCTT-TATG- 2061 chr5ptel1M 411634 CCTTTAATCTCGTTCTCAACTCTTATTGCCAAAGCTAGCATTTCTAATAC 411683 v i v i vvvi vvvi v ii i i C L1M5_orf2#LIN 2060 CCTTTTATTTCTTTTTCTTGCCTTATTGCACTGGCTAGGACCTCCAGTAC 2011 chr5ptel1M 411684 AATATTGAATAGTAAAGGTGATAGTAGGCAACCTTGTTTCACTCTTGATG 411733 i v iv ? ii i v i iii ii v C L1M5_orf2#LIN 2010 AATGTTGAATAGAAGTGGTGANAGCGGACATCCTTGTCTTGTTCCCGATC 1961 chr5ptel1M 411734 TTATTGGGAATGGTTGCAGTTTGTTCCCATTACAAATGATGCTTACT-TA 411782 vv v v? v ? v iv viv i ?i - C L1M5_orf2#LIN 1960 TTAGGGGGAAAGCNTTCAGTNTTTCACCATTAAGTATGATGTTNGCTGTA 1911 chr5ptel1M 411783 CTGATGATTTTAAATAGATGCTACTGATTATTTTAAGGAAAAGTCCATTT 411832 ----- i vvi ivi v i vv i ivvi v i C L1M5_orf2#LIN 1910 -----GGTTTTTCGTAGATGCCCTTTATCAGGTTGAGGAAGTTCCCTTCT 1866 chr5ptel1M 411833 ATTCCTATACTCGCAGGGGTTTTTAATCA-GAATGGATGTTGGGTTTTAT 411881 -ii i v i iv v - i ii i C L1M5_orf2#LIN 1865 ATTCCTA-GTTTGCTGAGAGTTTTTATCATGAATGGGTGTTGAATTTTGT 1817 chr5ptel1M 411882 CAAATGTTTTTTTTTCTTCATCTATTGAGATGATCATATGGTTTTGTTAA 411931 i --- v i vi vv C L1M5_orf2#LIN 1816 CAAATGCTTTTT---CTGCATCTATTGAGATGATCATATGATTTTTCTCC 1770 chr5ptel1M 411932 TTTGGT-TATTAATATGGCCAATTATATTGATAGTTTTCC---TATAGAA 411977 iv - i iv i v v i --- i vi C L1M5_orf2#LIN 1769 TTTATTCTGTTAATATGGTGAATTACATTGATTGATTTTCGAATGTTAAA 1720 chr5ptel1M 411978 CCAGCCCTGCATTCCTGGTATAAATCCTACTTGATCATAGTGTATTGTCC 412027 i i v i i i ii i C L1M5_orf2#LIN 1719 CCAACCTTGCATTCCTGGGATAAACCCCACTTGGTCATGATGTATTATCC 1670 chr5ptel1M 412028 TGGGGATGATTTTCTGTAGTCTTTTTGCTAATATCTTATTTAAGATTTTA 412077 vvvv ivv v v v vv i i ? i v C L1M5_orf2#LIN 1669 TTTTTATATATTGCTGGATTCGATTTGCTAATATTTTGTTNAGGATTTTT 1620 chr5ptel1M 412078 GCATCAATATTCATTAAGGAGATTGGTCTATAATTTTCTTT-CTTG---- 412122 v i v i v i - ---- C L1M5_orf2#LIN 1619 GCATCTATGTTCATGAGGGATATTGGTCTGTAATTTTCTTTTCTTGTAAT 1570 chr5ptel1M 412123 GTTTTCAACCTACCTGGTTTAGGTATCAGTACCATGTCTGTGTCATAAAA 412172 i ----- ii ? v vii? iiv iv C L1M5_orf2#LIN 1569 GTCTT-----TGTCNGGTTTTGGTATCAGGGTNATGCTGGCCTCATAAAA 1525 chr5ptel1M 412173 GGAGTTTGGTAGGACTCCTTCATTCCCTATTTTATCAAATAATTTATATA 412222 v v v vii i v ii v vi v i i i C L1M5_orf2#LIN 1524 TGAGTTGGGAAGTGTTCCCTCTTTTTCTATTTTCTGGAAGAGTTTGTGTA 1475 chr5ptel1M 412223 GCATTGGGGCCAATTGTTCTTTAAATGTTTGGTAGAATTCACATGTAAAT 412272 iv viii v v i vv i v C L1M5_orf2#LIN 1474 AGATTGGTATTATTTCTTCCTTAAATGTTTGGTAGAATTCACCAGTGAAG 1425 chr5ptel1M 412273 CCATCTGGTCCTGGGGATTTTTTCTTAGGGAG----TTGATTGATAGGTT 412318 v i v i iv i i ---- i - i i--- C L1M5_orf2#LIN 1424 CCATCTGGGCCTGGAGTTTTCTTTGTGGGAAGGTTTTTAATT-ACAA--- 1379 chr5ptel1M 412319 GTTCTATTTCTTTTTCTGAAATGGGACTATTCAAG----CAATTCCTCCT 412364 i v vviv v i i ii---- v i i C L1M5_orf2#LIN 1378 ATTCAATTTCTTTAATAGATATAGGGCTATTCAGATTTTCTATTTCTTCT 1329 chr5ptel1M 412365 T-TGTTAATCTGGGAAGCCTATCTTTTTGGAGGTAGTCATCCATTTCACT 412413 -? i i i v v i?i i v vi v v ii ii C L1M5_orf2#LIN 1328 TGNGTCAGTTTTGGTAANTTGTGTTTTTCAAGGAATTTGTCCATTTCATC 1279 chr5ptel1M 412414 GAGGTTACCAAACTGATTGGCATAAAGTTGGGCAAAGTAACTCCTTATTA 412463 v i ?i i v vv v i viii C L1M5_orf2#LIN 1278 TAAGTTNTCAAATTTATTGGCATAAAGTTGTTCATAATATTCTCTTATTA 1229 chr5ptel1M 412464 TCACTCTAATTTCCTCTTCATTGGTGGAAAGTTCTCCGTCTTCATTTTTA 412513 vi i v ivivvv iv i vi vv v i ii i C L1M5_orf2#LIN 1228 TCCTTTTAATGTCTGTAGGATCTGTAGTGATGTCTCCTTTTTCATTCCTG 1179 chr5ptel1M 412514 AGGCTACTAATTTGATTTTTTTCCTCTCCTTTTTCTAATCAGATTTACCA 412563 vii iv - v i ii ii ii i vi ?i i C L1M5_orf2#LIN 1178 ATATTGGTAATTTG-TGTCTTCTCTCTTTTTTTCTTGATCAGTCTNGCTA 1130 chr5ptel1M 412564 AAGACTTATCTATTTTATTAGTTTTTTTCAGAAAACCAACTCTTAGTTTT 412613 i ii v - v i i i i i i i i C L1M5_orf2#LIN 1129 GAGGTTTATCAATTTTATT-GATCTTTTCAAAGAACCAGCTTTTGGCTTC 1081 chr5ptel1M 412614 ATTTATTAGTTCAATAGTTTTTTTTTACTTTTAATATTATTAATTTCTCC 412663 i v -- vv v v ? ? ii iv v i i v C L1M5_orf2#LIN 1080 GTTGATT--TTCTCTATTGTNTNTTTGTTTTCTATTTCATTGATTTCTGC 1033 chr5ptel1M 412664 TTTTAATATTAGAATTTCAAATTTAGTATTTGATTGGGGATTTTCAATTT 412713 i viv vv vvvii vv i ?v v --- i C L1M5_orf2#LIN 1032 TCTTATCTTTATTATTTCCTTCCTTCTACTTNCTTTGGG---TTTAATTT 986 chr5ptel1M 412714 GG---ACTTTTTCTAGCTTTTTTAGTTGCAGGC 412743 v---v i v v v i C L1M5_orf2#LIN 985 GCTCTTCTTTTTCTAGCTTCTTAAGGTGGAAGC 953 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.68 CpG sites = 281, Kimura (unadjusted) = 41.31 Transitions / transversions = 1.13 (281/248) Gap_init rate = 0.03 (48 / 1749), avg. gap size = 1.38 (66 / 48) 1596 28.67 2.39 3.22 chr5ptel1M 413237 413863 (586137) C L1ME5_3end#LINE/L1 (313) 628 7 m_b228s551i6 8948 chr5ptel1M 413237 TTTCACTCAGCATCA-GTTCGTTTAAG-TCTCTCCAGGC--CTTTCTGAA 413282 ii - -- - iv v i-- v v v C L1ME5_3end#LI 628 TTTCACTCAGCACTATGTT--TTTAAGATCCATCCATGTTGCTATGTGTA 581 chr5ptel1M 413283 ATCATCCTGTTGGTCATTTCTTAC-ATAACAATAATATTCCATAATATTC 413331 -- iv iv iii v -iivi - i i ii i v C L1ME5_3end#LI 580 --CATCTAGTCCGTTGCTTCTAACTGCTGCA-TAGTACTCCATGGTGTGC 534 chr5ptel1M 413332 ATATACCACAATTTATTCAGCCATTCTCCAATTGATGGGCATCCACTCAG 413381 vi v iii v i v v i i vviv C L1ME5_3end#LI 533 ATCCACCACATTTTACCTATCCACTCTCCCAGTGATGGACACCCAGGTTG 484 chr5ptel1M 413382 TTTCCAGTTTCTGGCCACTACAAAGAGGGCTGCCACAAACATTCATGCAC 413431 ii ii i iv i v iv v ii i vi i C L1ME5_3end#LI 483 CCTCCAACTCCCCGCCACCACAAACAACGCTGCAATGAACATCCTCGTAC 434 chr5ptel1M 413432 ATGTAGGTCCCTTT-----CCTTTCTTTAAGATGTCTTTGGGATATAAGC 413476 ---- i ----- v v v- ii v vi C L1ME5_3end#LI 433 ATGT----CCCCTTATGGACCTGTGTG-AGAATTTCTTTGGGATATATAC 389 chr5ptel1M 413477 TGAGTAGTAACACTGCTGGGTCAAAGGATATATGCACAGTTTGATAACTT 413526 iv v iiiv i v i ii i i v ---- --- C L1ME5_3end#LI 388 CCAGGAGCGGAATTGCTGGGTCATAGGGTATGCGTATACTT----AA--- 346 chr5ptel1M 413527 TTTGAGCA--TAGTTCCAAATTGCTCTCCAGAATGATTGGATGTATTCAC 413574 vi -- v v i ii v ivvi ii C L1ME5_3end#LI 345 TTTGACTAAGTACTGCCAGATTGCTCTCCAGAATGGCTGCACCAGTCTAC 296 chr5ptel1M 413575 AATTCCACCAACAATGTATCAGTGTCCCTGTTTTCCCACATCCCCTCCAA 413624 v i i i i v v i i ? i i v C L1ME5_3end#LI 295 ACTCCCACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATCCTCGCCAA 246 chr5ptel1M 413625 CATTCCGCATTATCTTTCCCTATCATTCTAGTCAGTCTGACAGGTGTGTA 413674 i iv ivv ii v v i v i i i iv C L1ME5_3end#LI 245 CACTTGGCATTATCCAGCTTTCTAATTTTTGCCAGTCTAATAGGTGTAAA 196 chr5ptel1M 413675 GTGGTATCTCAGAGTTGTCTTCATTTGCATTTCTCTGATTAATAATGACT 413724 i vv i v v v C L1ME5_3end#LI 195 GTGATATCTCATTGTTGTTTTAATTTGCATTTCTCTGATTACTAATGAGT 146 chr5ptel1M 413725 TGGAGTATCTTTTCATATGGCTAGATATAATATCAA-TTTTTTCATCTGA 413773 v i i - v v vvv v ii- ii v v C L1ME5_3end#LI 145 TTGAGCATCTCTTCATATG-CTTGTTAGCCTTTCGGGTTTCCTCTTCTGT 97 chr5ptel1M 413774 GAATTGTCTGTTCATATCCTTTGACTATTTATCAATTGGAG--AATGCCT 413821 i i v i v v i --?vi i C L1ME5_3end#LI 96 AAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGGGGTTNCCGTCT 47 chr5ptel1M 413822 TGATTTCTTATAAATTAGAGTCAATTCTCTATATATTTTGGA 413863 -- i vi v vivv i ii i i i C L1ME5_3end#LI 46 T--TTTCTTGTTGATTTGCAGGAGTTCCTTGTATATTCTAGA 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.84 CpG sites = 101, Kimura (unadjusted) = 37.21 Transitions / transversions = 1.38 (101/73) Gap_init rate = 0.04 (28 / 626), avg. gap size = 1.25 (35 / 28) 1635 27.23 0.36 2.03 chr5ptel1M 413313 413863 (586137) C L1ME3G_3end#LINE/L1 (376) 548 7 m_b228s551i7 8948 chr5ptel1M 413313 ATAATATTCCATAATATTCATATACCACAATTTATTCAGCCATTCTCCAA 413362 i i vv i i i i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr5ptel1M 413363 TTGATGGGCATCCACTCAGTTTCCAGTTTCTGGCCACTACAAAGAGGGCT 413412 i ii vviv i i v i i v iv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr5ptel1M 413413 GCCACAAACATTCATGCACATGTAGGTCCCTTTCCTT-TCTTTAAG-ATG 413460 v ii i v i i?-- i v v vi- v vii - v C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATT 401 chr5ptel1M 413461 TCTTTGGGATATAAGCTGAGTAGTAACACTGCTGGGTCAAAGGATATATG 413510 ? i v v? i? v iiv i i ii C L1ME3G_3end#L 400 TCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCG 351 chr5ptel1M 413511 CACAGTTTGATAACTTTTTGAGCATAGTTCCAAATTGCTCTCCAGAATGA 413560 --- -- v viviv v v i i ? i C L1ME3G_3end#L 350 CA---TTT--TAAATTTTAATAGATACTGCCAAATTGCCCTCCAAAANGG 306 chr5ptel1M 413561 TTGGATGTATTCACAATTCCACCAACAATGTATCAGTGTCCCTGTTTTCC 413610 i v ivv i v i i i v v v i i C L1ME3G_3end#L 305 CTGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCC 256 chr5ptel1M 413611 CACATCCCCTCCAACATTCCGCATTATCTTTCCCTATCATTCTAGTCAGT 413660 i i v i ?vii vv? ii vvv i v i i C L1ME3G_3end#L 255 CACACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAAT 206 chr5ptel1M 413661 CTGACAGGTGTGTAGTGGTATCTCAGAGTTGTCTTCATTTGCATTTCTCT 413710 ii viv i vv i v i C L1ME3G_3end#L 205 CTGATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCT 156 chr5ptel1M 413711 GATTAATAATGACTTGGAGTATCTTTTCATATGGCTAGATATAATATCAA 413760 v i vv v i vi vvviiv v vv C L1ME3G_3end#L 155 GATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGTA 106 chr5ptel1M 413761 TTTTTTCATCTGAGAATTGTCTGTTCATATCCTTTGACTATTTATCAATT 413810 ii v v i v i v v C L1ME3G_3end#L 105 TTTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATT 56 chr5ptel1M 413811 GGAGAATGCCTTGATTTCTTATAAATTAGAGTCAATTCTCTATATATTTT 413860 iv-- i -- vi v vivv i i i C L1ME3G_3end#L 55 GGGT--TGTCTT--TTTCTTATTGATTTGTAGGAGTTCTTTATATATTCT 10 chr5ptel1M 413861 GGA 413863 C L1ME3G_3end#L 9 GGA 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.98 CpG sites = 77, Kimura (unadjusted) = 34.88 Transitions / transversions = 1.10 (77/70) Gap_init rate = 0.02 (13 / 550), avg. gap size = 1.00 (13 / 13) 413 30.15 1.45 1.45 chr5ptel1M 413720 413995 (586005) C L1M5_orf2#LINE/L1 (0) 3294 3019 m_b228s551i8 8948 chr5ptel1M 413720 TGACTTGGAGTATCTTTTCATATGGCTAGATATAATATCAATTTTTTCAT 413769 ?v v i i vi vvviiv v v? v i v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr5ptel1M 413770 CTGAGAATTGTCTGTTCATATCCTTTGACTATTTATCAATTGGA--GAAT 413817 i v v vi i v i v ?v i-- vv C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTT 3195 chr5ptel1M 413818 GCCTTGATTTCTTA-TAAATTAGAGTCAATTCTCTATATATTTTGGAAAT 413866 i -- ? - i ? iv -v i i i v i C L1M5_orf2#LIN 3194 GTCTT--TTTNTTATTGANTTGTAG-GAGTTCTTTATATATTCTGGATAC 3148 chr5ptel1M 413867 GAGTGCTTTATCAGA-ACCTTTGACTGTAAAAATATTTTCCCAGTTTATT 413915 v i - iv v -?i i v v i ? i i v C L1M5_orf2#LIN 3147 GAGTCCTTTGTCAGATATATGT-NTTGCAAATATTTTCTCCCANTCTGTG 3099 chr5ptel1M 413916 GCTTCCCTTCTAATCTTGTCTGCATTAGTTTTGTTTGTACAAAAAGTTTT 413965 v i v i v ivi iv ivi vvv? vi i iv C L1M5_orf2#LIN 3098 GCTTGCCTTTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTTT 3049 chr5ptel1M 413966 CAGTTTGGTATAATCAAAATTTTCAATTTT 413995 v v i i? i v v v C L1M5_orf2#LIN 3048 AATTTTGATGNAGTCCAATTTATCAATTTT 3019 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.41 CpG sites = 38, Kimura (unadjusted) = 40.65 Transitions / transversions = 0.86 (38/44) Gap_init rate = 0.03 (7 / 275), avg. gap size = 1.14 (8 / 7) 56 0.00 0.00 1.96 chr5ptel1M 414240 414291 (585709) (TA)n#Simple_repeat 1 51 (0) c_b228s251i0 8949 chr5ptel1M 414240 TATATATATATATATATATATATATATATATATATATATATATATATGAT 414289 - (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATAT-AT 49 chr5ptel1M 414290 AT 414291 (TA)n#Simple_ 50 AT 51 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.02 (1 / 51), avg. gap size = 1.00 (1 / 1) 21 0.00 0.00 0.00 chr5ptel1M 415439 415461 (584539) (T)n#Simple_repeat 1 23 (0) m_b228s252i2 8950 chr5ptel1M 415439 TTTTTTTTTTTTTTTTTTTTTTT 415461 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTT 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 528 18.57 0.00 8.77 chr5ptel1M 415474 415597 (584403) C MIRc#SINE/MIR (153) 115 2 m_b228s601i3 8951 chr5ptel1M 415474 GGGGTTAAGTGACTTGTCCAGGGTCACAGAGCTAGGAAGTATTAAGTGTC 415523 i i i v ------- v C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGC 73 chr5ptel1M 415524 TGAGGCCAGATTTGAACTCAGGTCCTCCTGACTTCAGGGCTGGTGCTCTA 415573 v v vi i i i i i i v ii v C MIRc#SINE/MIR 72 AGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTT 23 chr5ptel1M 415574 TCCACTGCACCACCTAGCTGCCCC 415597 ---i i C MIRc#SINE/MIR 22 TCCACTGCACCAC---ACTGCCTC 2 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 20.49 CpG sites = 14, Kimura (unadjusted) = 21.61 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.08 (10 / 123), avg. gap size = 1.00 (10 / 10) 48 0.00 0.00 0.00 chr5ptel1M 417733 417773 (582227) (TA)n#Simple_repeat 1 41 (0) c_b228s251i1 8952 chr5ptel1M 417733 TATATATATATATATATATATATATATATATATATATATAT 417773 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATAT 41 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 486 31.17 4.24 3.21 chr5ptel1M 418148 418548 (581452) C L1P3_orf2#LINE/L1 (303) 2991 2587 m_b228s551i9 8953 chr5ptel1M 418148 TTTGGTCATAAATTCCTTCCTCTTCCACAGGTC-TGAGAGGTAAACTATC 418196 i i v i v i v v vi v - iv --- vv C L1P3_orf2#LIN 2991 TTTAGTCATGAAGTCTTTGCCCATGCCTATGTCCTGAATGGTA---TTGC 2945 chr5ptel1M 418197 CT--GTGTTCCTCTAATTTATTTATAATCTCATGCTTTATGCCTAGGTCA 418244 -- v i ivv v ii i i v ii i ii i v C L1P3_orf2#LIN 2944 CTAGGTTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTTACGTTTAAGTCT 2895 chr5ptel1M 418245 TGAACCCATTTTGAACTTATCTTGGTGTACGGTGTTAAGTATGGGTCCAT 418294 v i i ii v i v i v v i v v v C L1P3_orf2#LIN 2894 TTAATCCATCTTGAGTTAATTTTTGTATAAGGTGTAAGGAAGGGGTCCAG 2845 chr5ptel1M 418295 GCCTAGTTT-CTGCCATACTAGTTA-CCAATTTTCCCAGCAATTTTTGTC 418342 viii - - - i i - i i viv i i C L1P3_orf2#LIN 2844 TTTCAGTTTTCTGC-ATA-TGGCTAGCCAGTTTTCCCAACACCATTTATT 2797 chr5ptel1M 418343 AAAGAGCGAGTTCTTATCCCAAAAGCTGGGGTCTTTG---GGTTTGTCAA 418389 v v i i - v vv v -- i --- C L1P3_orf2#LIN 2796 AAATAGGGAATCCTT-TCCCCATTGCTTG--TTTTTGTCAGGTTTGTCAA 2750 chr5ptel1M 418390 ACACTAGCAAGGTTATTGAC-TCTTTTGTCCTT--TGAA---CCTAACCT 418433 v ii - v i v i- v vvi iv -- i---i ivi C L1P3_orf2#LIN 2749 AGATCAG-ATGGTTGTAGATGTGTGGCGTTATTTCTGAGGCCTCTGTTCT 2701 chr5ptel1M 418434 ATTCCACTGATCAAGTA-ATCTATTCCTTAG--CCAGTACCAAATGGTTT 418480 i i i v - - i -- i -- viiv C L1P3_orf2#LIN 2700 GTTCCATTGGTCTA-TATATCTGTT--TTGGTACCAGTACCATGCTGTTT 2654 chr5ptel1M 418481 TGGTAATTGCTGCTCTATAATATAATTTCAGATCTGGTACAGCTAAGCCA 418530 v i iv ii i i i v ii v vv iv v v C L1P3_orf2#LIN 2653 TGGTTACTGTAGCCTTGTAGTATAGTTTGAAGTCAGGTAGCGTGATGCCT 2604 chr5ptel1M 418531 CCTTCATTTGATTTTTTT 418548 vv - v i C L1P3_orf2#LIN 2603 CCAGC-TTTGTTCTTTTT 2587 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.33 CpG sites = 66, Kimura (unadjusted) = 41.22 Transitions / transversions = 1.20 (66/55) Gap_init rate = 0.06 (23 / 400), avg. gap size = 1.30 (30 / 23) 3508 30.31 1.80 1.51 chr5ptel1M 420703 422424 (577576) C L1M4_orf2#LINE/L1 (739) 2555 829 m_b228s551i10 8954 chr5ptel1M 420703 TTGTCTTTCCGTATGAACTTTATTGTTATTTTTTCTAGGTCATCAAAATA 420752 iv i i vvi i vi v v vv vv v C L1M4_orf2#LIN 2555 TTGCATTTCCATATGAATTTTAGGATCAGCTTGTCAATTTCTGCAAAAAA 2506 chr5ptel1M 420753 GTTTTTTGGGAGTATGATTGGTATAGTGCTAAACAATTAGATTAGCTTAA 420802 ?ivvi v v v v v i i i ivvv i ii ii C L1M4_orf2#LIN 2505 GNCAGCTGGGATTTTGATAGGGATTGCGTTGAATCTGTAGATCAATTTGG 2456 chr5ptel1M 420803 GTAGTATTGTCATCTTCATTATATTTGCTCACCCTATCCAAGAGCATTTA 420852 v i v iv viv vi v v i vvi C L1M4_orf2#LIN 2455 GGAGTATTGCCATCTTAACAATATTAAGTCTTCCAATCCATGAACATGGG 2406 chr5ptel1M 420853 ATATTTTTTCAATTGATTAGATCAGACTTAATTTGTGTGAAAAGTGTTTT 420902 i i i v iv i vvvi v v v v i C L1M4_orf2#LIN 2405 ATGTCTTTCCATTTATTTAGGTCTTCTTTAATTTCTTTCAACAATGTTTT 2356 chr5ptel1M 420903 GTAATTTTGCTCATA-AAGTTTCTGATTTTCCCTTGGCAGATAGATTCTT 420951 i vvvii - i - vvi ii vi i vv i C L1M4_orf2#LIN 2355 GTAGTTTTCAGTGTACAAGTCT-TGCACTTCTTTTGTTAAATTTATTCCT 2307 chr5ptel1M 420952 AAATATTGTATACTATCAGTAGTTAATTTAAATGGAATTTCTCTTTGTAA 421001 i v v v iv vv i v v vi i i - C L1M4_orf2#LIN 2306 AAGTATTTTATTCTTTTTGATGCTATTGTAAATGGAATTGTTTTCT-TAA 2258 chr5ptel1M 421002 CTCTGATTGTTGGATT-----TTGTTAGTGATATATAAGCATGCTGATGA 421046 i - v v i ----- i - v -- i viv C L1M4_orf2#LIN 2257 TT-TCATTTTCGGATTGTTCATTGCTAGTG-TATAGAA--ATACAATTGA 2212 chr5ptel1M 421047 CTTATGTGTGTTTATTTTGTATCCTGCAACTTTGCTAAAGTTGTGGATTA 421096 i v i i v i i i v i vv C L1M4_orf2#LIN 2211 TTTTTGTATATTGATCTTGTATCCTGCAACCTTGCTGAACTCGTTTATTA 2162 chr5ptel1M 421097 TTTCTAATAGCTTTTTAGT-------CTGGGGTTCTCTAAGTATACCATC 421139 v i ? -------i i i i vi i vv C L1M4_orf2#LIN 2161 GTTCTAATAGTTTTTTNGTGGATTCCTTAGGATTTTCTATATACAAGATC 2112 chr5ptel1M 421140 ATATCATCAGCAAAGAGTCATAATTTGGTTTCCTCATTGCCTCTTATAAA 421189 i v i v vv i vii i v v vv i- ii C L1M4_orf2#LIN 2111 ATGTCATCTGCGAATAGAGATAGTTTTACTTCTTCCTTTCCAATC-TGGA 2063 chr5ptel1M 421190 T-CCTTTAATCTCTTTCTCAACTCTTATTGCCAAAACTTGCTTATCTAAT 421238 - v i i vvvi v vvii v vviv i i C L1M4_orf2#LIN 2062 TGCCTTTTATTTCTTTTTCTTGCCTAATTGCCCTGGCTAGAACCTCCAGT 2013 chr5ptel1M 421239 ACAATATTGAATAGTAAAGGTGATAGTGGGCAACCTTGTTTCACTCCTGA 421288 i v iv i v i i v i iii C L1M4_orf2#LIN 2012 ACAATGTTGAATAGAAGTGGCGAGAGCGGACATCCTTGTCTTGTTCCTGA 1963 chr5ptel1M 421289 TCTTATTGGGAATGGTTGCAGTTTGTCTGTCCATTACATATGATGCTTAC 421338 vv v v? v i v v-- vi i vi C L1M4_orf2#LIN 1962 TCTTAGGGGGAAAGCNTTCAGTCTTTCA--CCATTAAGTATGATGTTAGC 1915 chr5ptel1M 421339 TGATGG--TTTTAATAGATGCTACTGATTATTTTTAGGAAAAGTCCATGT 421386 - -- vi ivi v i vv v ivvi v v C L1M4_orf2#LIN 1914 TG-TGGGTTTTTCGTAGATGCCCTTTATCAGGTTGAGGAAGTTCCCTTCT 1866 chr5ptel1M 421387 ATTCCTATGCTCTCACGTGTTTTTCATAGGAATGGATGTTGGATTTTGTT 421436 vvi v iiv vvi v v i i C L1M4_orf2#LIN 1865 ATTCCTAGTTTGTTGAGTGTTTTTATCATGAAAGGGTGTTGGATTTTGTC 1816 chr5ptel1M 421437 AAATGCTTTTTCTGCATCTATTGAGATGATCATATGTTTTTTGTTAATTT 421486 i i v i-v C L1M4_orf2#LIN 1815 AAATGCTTTTTCTGCGTCTATTGAGATGATCATGTGGTTTTTGTC-CTTT 1767 chr5ptel1M 421487 GGT-TATTAATATGACCAATTATATTGATAGTTTTCCTAATATTGAACCA 421535 iv - iivv i v v i v? i C L1M4_orf2#LIN 1766 ATTCTATTAATATGGTGTATTACATTGATTGATTTTCGNATGTTGAACCA 1717 chr5ptel1M 421536 GCCCTGCATTCCTGGTATAAATCCTACTTGATCATAGTGTATTGTCCTGG 421585 i i v i i i vi vv C L1M4_orf2#LIN 1716 ACCTTGCATTCCTGGGATAAATCCCACTTGGTCATGGTGTATAATCCTTT 1667 chr5ptel1M 421586 GGATGATTTTCTGTAGTCTTTTTGCTAATATCTCATTTAAGATTTTAGCA 421635 vv ivv v v v vv i i ii v i v C L1M4_orf2#LIN 1666 TTATATGTTGCTGGATTCGGTTTGCTAGTATTTTGTTGAGGATTTTTGCA 1617 chr5ptel1M 421636 TCAATATTCATTAGGGAGATGGGTCTATAATTTTCTTTCTCTGT----TT 421681 v v v v i i iii ---- i C L1M4_orf2#LIN 1616 TCTATATTCATAAGGGATATTGGTCTGTAGTTTTCTTTTCTTGTGATGTC 1567 chr5ptel1M 421682 TTAACCTACCTGGTTTAGGTATCAGTATCATGTCTGTGTCATAAAAGGAA 421731 ---- ii v vi v iiiv iv i v i C L1M4_orf2#LIN 1566 TT----TGTCTGGTTTTGGTATCAGGGTAATACTGGCCTCATAGAATGAG 1521 chr5ptel1M 421732 TATAGTAGGACTCCTTCATTCCCTGTTTTATCAAATAATTTATATAGCA- 421780 vvi v vii i v iii i v vi v i i iv v - C L1M4_orf2#LIN 1520 TTGGGAAGTGTTCCCTCCTCTTCTATTTTTTGGAAGAGTTTGTGAAGGAT 1471 chr5ptel1M 421781 TGGGGTCAATTGTTCTTTAAATGTTTGGTAGAATTCACATGTAAATCCAT 421830 v i v vv i v C L1M4_orf2#LIN 1470 TGGTGTTAATTCTTCTTTAAATGTTTGGTAGAATTCACCAGTGAAGCCAT 1421 chr5ptel1M 421831 CTGGTCCTGGGGATTTTTTCTTAGGGAGTTGATTGATAGGTTGTTCTATT 421880 ? vv i iv i i vv viv vi v i C L1M4_orf2#LIN 1420 CTGGNCCTGGGCTTTTCTTTGTGGGAAGTTTTTTGATTACTAATTCAATC 1371 chr5ptel1M 421881 TCTTTTTCTGAAATGGGACTATTCAAGCAATTTACTTCCTCCTCTGTTAA 421930 vii vv i v iiivv i i i i vv i i C L1M4_orf2#LIN 1370 TCTTTACTTGTTATAGGTCTATTCAGATTTTCTATTTCTTCTTGAGTCAG 1321 chr5ptel1M 421931 TCTGGGAAGTCTATATTTTTGGAGGTAGTCATCCATTTTACTTAGGTTAT 421980 i v v i i i i vv v v ii i ii C L1M4_orf2#LIN 1320 TTTCGGTAGTTTGTGTCTTTCTAGGAATTTGTCCATTTCATCTAGGTTAT 1271 chr5ptel1M 421981 CAAACTGATTGGCATAAAGTTGGGCAAAGTAACTCCTGATTATCTCTCTA 422030 v i vi v i vv v vii v v ii i v C L1M4_orf2#LIN 1270 CTAATTTGTTGGCATACAATTGTTCATAGTATTCCCTTATAATCCTTTTT 1221 chr5ptel1M 422031 ATTTCCTCTTCATTGGTGG-AAAGTTCTCCCTTTTATTTTTAAGACTACT 422079 ivivvvi i i - v i i i i ii i vvi v C L1M4_orf2#LIN 1220 ATTTCTGTAAGGTCGGTAGTAATGTCCCCTCTTTCATTCCTGATTTTAGT 1171 chr5ptel1M 422080 AATTTGATTTTCCTCCTTCCTTTTTCTAATCAGATTTACCAAAGGCTCAT 422129 v i i ii ii ii ii vi vi i i ii C L1M4_orf2#LIN 1170 AATTTGAGTCTTCTCTCTTTTTTTCTTGGTCAGTCTAGCTAAAGGTTTGT 1121 chr5ptel1M 422130 CTATTTTGTTGGTTTTTTAAAATAGAATCAACTCTAAGTTTTACTAATTA 422179 v i i v -- i i vi iii i - C L1M4_orf2#LIN 1120 CAATTTTGTTGATCTTTTCAA--AGAACCAACTTTTGGTTTCGTTGATT- 1074 chr5ptel1M 422180 GTTCAATAGTTTTTTTTTTAGTTTCAATATTATTTATTTCTGCTTTTAAT 422229 - vv - v i v i v v i i i v vi C L1M4_orf2#LIN 1073 -TTCTCTA-TTGTTTTTCTATTCTCTATTTCATTTATTTCCGCTCTAATC 1026 chr5ptel1M 422230 TTTAGAATTTCAAATTTAGTGTTTGATTGGGGGTTTTTAATTTGG---TC 422276 vv vvvii vv i v v --- i v--- C L1M4_orf2#LIN 1025 TTTATTATTTCCTTCCTTCTGCTTGCTTTGGG---TTTAGTTTGCTCTTC 979 chr5ptel1M 422277 TTTTTCTAGTTTTTT-AGTTGCAGGCCCAATTCATTGATCT--TCTCCTT 422323 i - v v i vii iv i i --vv i C L1M4_orf2#LIN 978 TTTTTCTAGTTTCTTAAGGTGGAAGGTTAGGTTATTGATTTGAGATCTTT 929 chr5ptel1M 422324 C-TCTATTTTATTCAAGTAAGCCTCTAAGGATATCAAATTTCCTCTTATT 422372 - v --- vi i v i vi v v v i v vi C L1M4_orf2#LIN 928 CTTCTTTTTTA---ATATAGGCATTTACAGCTATAAATTTCCCTCTAAGC 882 chr5ptel1M 422373 ACTGCTTTGGCTGCATCCCACAAATTTGGGTATGATGTCTCATC-TTGTC 422421 ? i i v v v iv - v C L1M4_orf2#LIN 881 ACTGCTTTNGCTGCATCCCATAAGTTTTGGTATGTTGTGTTTTCGTTTTC 832 chr5ptel1M 422422 ATT 422424 C L1M4_orf2#LIN 831 ATT 829 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.47 CpG sites = 259, Kimura (unadjusted) = 39.55 Transitions / transversions = 1.02 (259/255) Gap_init rate = 0.02 (40 / 1721), avg. gap size = 1.43 (57 / 40) 54 3.78 0.00 0.00 chr5ptel1M 422954 423008 (576992) (AT)n#Simple_repeat 1 55 (0) c_b228s251i2 8955 chr5ptel1M 422954 ATATATATATATATATATATATATATATATATATACATACATATATATAT 423003 i i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr5ptel1M 423004 ATATA 423008 (AT)n#Simple_ 51 ATATA 55 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 291 36.54 4.00 4.60 chr5ptel1M 423835 424009 (575991) C MIRc#SINE/MIR (93) 175 2 m_b228s601i4 8956 chr5ptel1M 423835 GAAGTATTTAGTATAAAT-TTATTATGTGAATTTTATAAATGAGGAAAAT 423883 i vvi vii ii - vivv i i v C MIRc#SINE/MIR 175 GAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACT 126 chr5ptel1M 423884 GATTTCCTTAGGTCACAG-GATAAAGTGACT--CCTA--GTCACATAACT 423928 -------i v v - i v -- i -- i i C MIRc#SINE/MIR 125 GA-------GGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCT 83 chr5ptel1M 423929 ACTAAGTATATGAATCAAGTTTCAAGCCCATATTTTTTTTTATTCTACAC 423978 v ivvv ii ii vi i i -iv i ii v i i vii C MIRc#SINE/MIR 82 AGTAAGTGGCAGAGCCGGGACTCGAACCCA-GGTCTTCCTGACTCCAAGT 34 chr5ptel1M 423979 CTTGTATTTTTTCCATTTC-TTATATTGTATC 424009 iv ii i i v -ii i i iv C MIRc#SINE/MIR 33 CCAGTGCTCTTTCCACTGCACCACACTGCCTC 2 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 51.00 CpG sites = 40, Kimura (unadjusted) = 53.66 Transitions / transversions = 1.90 (40/21) Gap_init rate = 0.07 (13 / 174), avg. gap size = 1.15 (15 / 13) 305 32.63 3.50 5.71 chr5ptel1M 423853 423995 (576005) C MIRb#SINE/MIR (109) 159 20 m_b228s601i5 8956 chr5ptel1M 423853 TTATTATGTGAATTTTATAAATGAGGAAAATGATTTCCTTAGGTCACAG- 423901 vivv i i v -------i v v - C MIRb#SINE/MIR 159 TTATTATCCCCATTTTACAGATGAGGAAACTGA-------GGCTCAGAGA 117 chr5ptel1M 423902 GATAAAGTGACT--CCTA--GTCACATAACTACTAAGTATATGAATCAAG 423947 i v i -- i -- i i v ivvv ii ii C MIRb#SINE/MIR 116 GGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGG 67 chr5ptel1M 423948 TTTCAAGCCCATATTTTTTTTTATTCTACACCTTGTATTTTTTCCATT 423995 v i i -iv i v i v i i v v ii ii i i C MIRb#SINE/MIR 66 ATTCGAACCCA-GGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACT 20 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.52 CpG sites = 27, Kimura (unadjusted) = 44.57 Transitions / transversions = 1.59 (27/17) Gap_init rate = 0.08 (11 / 142), avg. gap size = 1.18 (13 / 11) 312 26.33 10.77 0.70 chr5ptel1M 424096 424225 (575775) C L2a_3end#LINE/L2 (9) 508 366 m_b228s601i6 8957 chr5ptel1M 424096 TTTAACAGATATTGTTTAAGTGTTTACTATGT-TCAAACACTGT-----G 424139 i i vv i i ii -i ii ----- C L2a_3end#LINE 508 TTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGG 459 chr5ptel1M 424140 T-CTGAGGATAT--CAAGG--CAAAAATGA-AATATTCTCTGCCCTCAAT 424183 i- i i-- iv -- vv - v v i - C L2a_3end#LINE 458 CGCTGGGGATACAGCAGTGAACAAAACAGACAAAAGTCCCTGCCCTC-AT 410 chr5ptel1M 424184 GGA-CTTAAATTTCAAGGGTCAGGGAAAAAC-ATGAACATATAA 424225 - v ii iv vvi i v i - i v C L2a_3end#LINE 409 GGAGCTTACATTCTAGTGGGGGGAGACAGACAATAAACAAATAA 366 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.04 CpG sites = 21, Kimura (unadjusted) = 33.41 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.07 (9 / 129), avg. gap size = 1.67 (15 / 9) 309 22.50 3.75 0.00 chr5ptel1M 424341 424420 (575580) MIR3#SINE/MIR 124 206 (2) m_b228s601i7 8958 chr5ptel1M 424341 GTTTCC-CATCTACAAAATTAATGGATTATCTTAGATGTTCTTTAAGGTC 424389 - ii v iv i ivvi v i MIR3#SINE/MIR 124 GTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTC 173 chr5ptel1M 424390 TCTTTGACCT-TGAAA-TCTATGATTCTATAAT 424420 i iv v - v - i MIR3#SINE/MIR 174 CCTTCCAGCTCTGACATTCTATGATTCTATGAT 206 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 27.12 CpG sites = 10, Kimura (unadjusted) = 27.12 Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.04 (3 / 79), avg. gap size = 1.00 (3 / 3) 335 38.27 2.45 0.60 chr5ptel1M 424639 424801 (575199) L2b_3end#LINE/L2 130 295 (171) m_b228s601i8 8959 chr5ptel1M 424639 TTTGTATTGGCTGTCCCCAGTGCTTGGAATTCTCTCCCTCCTCTCTTCTG 424688 i i?v i vv i iv i i i vi - L2b_3end#LINE 130 TTTGCACNTGCTGTTCCCTCTGCCTGGAACGCCCTTCCCCACCTCTTC-G 178 chr5ptel1M 424689 TCTCTTAGATTCCCTGGCTTCCTTCAAATCTCACGTCACATTGCACCTTC 424738 i vvivi i ivvv v ii vv v vv i L2b_3end#LINE 179 CCTGGCCAACTCCTACTCATCCTTCAGGTCTCAGCTCAAATGTCACCTCC 228 chr5ptel1M 424739 TTCAAGAAACCTTTCCTAA----ATGAGCAGAACCAGGAGATCCATTATA 424784 i ii i i i i ----viii v iii v vi ivi v i L2b_3end#LINE 229 TCCGGGAAGCCCTCCCTGACCCCCCAGGCCGGGTCAGGCGCCCTCCTCTG 278 chr5ptel1M 424785 GGCCTCAACAATCATAC 424801 i vv i v L2b_3end#LINE 279 GGCCCCCCCAGTCCTAC 295 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 53.89 CpG sites = 36, Kimura (unadjusted) = 56.66 Transitions / transversions = 1.38 (36/26) Gap_init rate = 0.01 (2 / 162), avg. gap size = 2.50 (5 / 2) 23 7.03 0.00 0.00 chr5ptel1M 425187 425216 (574784) (A)n#Simple_repeat 1 30 (0) m_b228s252i3 8960 chr5ptel1M 425187 AAAAAAAAAAAACAAAAAACAAAAAAAAAA 425216 v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 30 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 240 32.89 9.21 0.00 chr5ptel1M 425275 425426 (574574) L2a_3end#LINE/L2 350 515 (2) m_b228s601i9 8959 chr5ptel1M 425275 TGTATCTTGTATGTACCTAATTATTTAT-GTATTTCCTCTCTTATTAGAA 425323 i v v iv ii v i - v v ii i ii i L2a_3end#LINE 350 TATATATTTTACTTATTTATTTGTTTATTGTCTGTCTCCCCCCACTAGAA 399 chr5ptel1M 425324 ATTGATTTCCTTGAGTTT-----CCCTTGTGACTTTT-----CT--TATA 425361 vv i vi v vvi----- ii vvv ----- -- i L2a_3end#LINE 400 TGTAAGCTCCATGAGGGCAGGGACTTTTGTCTGTTTTGTTCACTGCTGTA 449 chr5ptel1M 425362 TTCCCAGTTCTTAGAACTGTGCTGGGTCCATAATAAGTCCTTAATAAATG 425411 i iv i v iv iv i i iv i i L2a_3end#LINE 450 TCCCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGGCGCTCAATAAATA 499 chr5ptel1M 425412 TTT-TTGATTGTGTGA 425426 - v vi L2a_3end#LINE 500 TTTGTTGAATGAATGA 515 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.16 CpG sites = 28, Kimura (unadjusted) = 44.53 Transitions / transversions = 1.27 (28/22) Gap_init rate = 0.03 (5 / 151), avg. gap size = 2.80 (14 / 5) 17 24.13 4.17 2.74 chr5ptel1M 425632 425703 (574297) (TTAATTT)n#Simple_repeat 1 73 (0) m_b228s252i4 8961 chr5ptel1M 425632 TTAGTATTTAAATATTAATAGTTTAA--TTTAAGTGGAAATTTTT-ATTT 425678 i v v v -v -- v vvv - (TTAATTT)n#Si 1 TTAATTTTTAATTTTTAAT-TTTTAATTTTTAATTTTTAATTTTTAATTT 49 chr5ptel1M 425679 TTAATTGTCCATTTATATATTATTA 425703 v iv v - v (TTAATTT)n#Si 50 TTAATTTTTAATTTTTA-ATTTTTA 73 Matrix = Unknown Transitions / transversions = 0.17 (2/12) Gap_init rate = 0.06 (4 / 71), avg. gap size = 1.25 (5 / 4) 201 29.93 9.57 4.04 chr5ptel1M 426407 426500 (573500) C MIRb#SINE/MIR (103) 165 67 m_b228s601i10 8962 chr5ptel1M 426407 TAGAT-TTATAATAGTTCCACTTTACAAACGAAAAATAATCAGGGCTCA- 426454 i - -- vii i i i ii -- iiii - C MIRb#SINE/MIR 165 TAGGTATTAT--TATCCCCATTTTACAGATGAGGA--AACTGAGGCTCAG 120 chr5ptel1M 426455 AAAGTATAAGTAGCTT-------ATCACAAAGCTGAAAAGGAGTAGAGCT 426497 i vv i -------i v iiv vi i i C MIRb#SINE/MIR 119 AGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCC 70 chr5ptel1M 426498 AGG 426500 i C MIRb#SINE/MIR 69 GGG 67 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.36 CpG sites = 21, Kimura (unadjusted) = 41.68 Transitions / transversions = 3.50 (21/6) Gap_init rate = 0.08 (7 / 93), avg. gap size = 1.86 (13 / 7) 361 41.94 3.86 0.94 chr5ptel1M 426585 426791 (573209) C MIRc#SINE/MIR (52) 216 4 m_b228s601i11 8963 chr5ptel1M 426585 TTTATATATATTACTTAGTCTGA----CATGACAACCTTTGGAGGGAAAT 426630 i i i ii vi i ---- ii i vv v iii C MIRc#SINE/MIR 216 TTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGC 167 chr5ptel1M 426631 TAATGCAGAGAGTAAAATTTCCACTTTATTGATGAGAAGCCAAAATCATG 426680 - iv iv v vv ii i iv i iv vi iv vii C MIRc#SINE/MIR 166 -AGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCA 118 chr5ptel1M 426681 GAGAAATAAAGTAGTTAGTTTGGAGTTTCAC---TGGTAAGAAAGGGGGC 426727 ii v iii v iiiiii iv --- i viivi i C MIRc#SINE/MIR 117 GAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGC 68 chr5ptel1M 426728 TTAAGTTTTGTATACAAGCCTTC-TGATCCTACATCCAGTGTTGTTTTTA 426776 i-ii vi i v iv i i - ii i vi i v ii C MIRc#SINE/MIR 67 C-GGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCA 19 chr5ptel1M 426777 CCACGTCACATTGCC 426791 ii ii i C MIRc#SINE/MIR 18 CTGCACCACACTGCC 4 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 67.44 CpG sites = 62, Kimura (unadjusted) = 70.67 Transitions / transversions = 2.58 (62/24) Gap_init rate = 0.02 (5 / 206), avg. gap size = 2.00 (10 / 5) 311 24.25 2.97 6.12 chr5ptel1M 426791 426891 (573109) MIR3#SINE/MIR 97 194 (14) m_b228s601i12 8964 chr5ptel1M 426791 CAAGTCACTTGCCCTATAGTTTCTTCAGTTTTTTTTTTTTCATTTTTCAA 426840 vv v vvvvv i ii ------ i v v MIR3#SINE/MIR 97 CAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCT------CATCTGTAAA 140 chr5ptel1M 426841 ATGAGGGGGTTAGATTGGAT-ATCT-TAAAATCCTTTCTAGCTCTAA-AT 426887 i i i - - ii i i i - MIR3#SINE/MIR 141 ATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACAT 190 chr5ptel1M 426888 TTTA 426891 i MIR3#SINE/MIR 191 TCTA 194 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.73 CpG sites = 13, Kimura (unadjusted) = 29.73 Transitions / transversions = 1.30 (13/10) Gap_init rate = 0.09 (9 / 100), avg. gap size = 1.00 (9 / 9) 238 36.99 8.21 7.11 chr5ptel1M 426991 427185 (572815) C L3#LINE/CR1 (2) 4097 3901 m_b228s601i13 8965 chr5ptel1M 426991 TATAATCACAGAATTTTAGAATTGAAA-----TTCA------ATTTATTC 427029 v i i i i -----i i ------ i v C L3#LINE/CR1 4097 TAGAATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTC 4048 chr5ptel1M 427030 CAACC-CATACCTGA-GAAACAACTCCCTTTGGAAAATATTTATTA--TA 427075 - vi i ii - v iv ii i i iv v vii ivi -- i C L3#LINE/CR1 4047 CAACCTCCCATCCAATGCAGGAATCCCTTCTACAACATCCCTGACAAGTG 3998 chr5ptel1M 427076 GTTATTCAACTTTTCCTTAAAAATCCCTGGGGAAAAAATAAAATACTTTA 427125 i i i i i v i v i i ii v viiii------ vi i C L3#LINE/CR1 3997 GTCATCCAGCCTCTGCTTGAACACCTCCAGTGACGGGG------AGCTCA 3954 chr5ptel1M 427126 TTAAAAATTAACATCAT-AGGCAGGCTATTCTACTTCCGGGTACTTCTTA 427174 i -------- v ?i- v i i i ii ii vi v C L3#LINE/CR1 3953 CTA--------CCTCNCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGA 3912 chr5ptel1M 427175 TTGTTGGAAAG 427185 i C L3#LINE/CR1 3911 TTGTTAGAAAG 3901 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 54.55 CpG sites = 49, Kimura (unadjusted) = 57.28 Transitions / transversions = 2.72 (49/18) Gap_init rate = 0.10 (20 / 194), avg. gap size = 1.50 (30 / 20) 515 23.48 1.35 7.91 chr5ptel1M 427210 427357 (572643) MIR#SINE/MIR 28 166 (96) m_b228s601i14 8966 chr5ptel1M 427210 GGGC-CTGGAGTCAGATTCATATCTGTGAGTTCAAATCTGGCCTCAGACA 427258 - i i ---ii --i i iv v v v MIR#SINE/MIR 28 GGGCTCTGGAGCCAGACT---GCCTG--GGTTCGAATCCCGGCTCTGCCA 72 chr5ptel1M 427259 CTTACTAAATGTGTGATTCTGGGTAAATCACTTAACC-CTGTTTGCCTTA 427307 iv iii i i i - v v i MIR#SINE/MIR 73 CTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCA 122 chr5ptel1M 427308 GTTTCCTCTCCTGTAAAATTATCTGGAGAAGGAAATGGTGAACTACTTCA 427357 vi ----- i viiv i - v i MIR#SINE/MIR 123 GTTTCCTCATCTGTAAAA-----TGGGGATAATAATAGT-ACCTACCTCA 166 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 27.77 CpG sites = 21, Kimura (unadjusted) = 28.83 Transitions / transversions = 1.91 (21/11) Gap_init rate = 0.09 (13 / 147), avg. gap size = 1.00 (13 / 13) 291 35.64 1.72 0.85 chr5ptel1M 427428 427543 (572457) C L3#LINE/CR1 (208) 3891 3775 m_b228s601i15 8965 chr5ptel1M 427428 ATCTTCAATTAAAATTTGCTTTTCTTTATTTGTTATTC-TTGGTTCTCAG 427476 v v iiii i i ii v vi vii ii - i - C L3#LINE/CR1 3891 ATATTGAGCCGAAATCTGCCTCCCTGTAACTTCCACCCATTGGTCCT-AG 3843 chr5ptel1M 427477 TTTGGTTCTCTAGAGGAAAATGGAGTAAATATAATATTT-TCCCATATGA 427525 iv ii i vv v ii i i v vii - i i C L3#LINE/CR1 3842 TTCTGCCCTCTGGAGCCACACAGAATAAGTCTAATCCCTCTTCCACATGA 3793 chr5ptel1M 427526 AGGCCTTTCAAATATCTG 427543 vi i i C L3#LINE/CR1 3792 CAGCCCTTCAAATATTTG 3775 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 50.59 CpG sites = 29, Kimura (unadjusted) = 52.77 Transitions / transversions = 2.42 (29/12) Gap_init rate = 0.03 (3 / 115), avg. gap size = 1.00 (3 / 3) 574 30.67 7.56 0.00 chr5ptel1M 427745 427969 (572031) C MIRc#SINE/MIR (3) 265 24 m_b228s601i16 8967 chr5ptel1M 427745 AATCATAATTATTCACATTTATGTTGTACTTGAGAGTT-GCAAAGTGCCT 427793 v i?vi i i i v i v v -i i i C MIRc#SINE/MIR 265 AATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCGCTT 216 chr5ptel1M 427794 TT-TAAGTGTTTTCTCATTTAATTCTCTCTACAATCCAGT-AGGTAG-CA 427840 i-i viii v i i v v i v - - C MIRc#SINE/MIR 215 TCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCA 166 chr5ptel1M 427841 AGA-AGAT-------TTCTCATAT-AGAGTTTAGGAAAT--ATACTCCTA 427879 i i- i ------- i i v - v v v i-- vi vv C MIRc#SINE/MIR 165 GGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGA 116 chr5ptel1M 427880 GACGTTAATTGACTT-CCGTGGGGGATGCAATTAGTAAATAATAAAGCTA 427928 v v - vvi vv ii ii i iii i ii C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 66 chr5ptel1M 427929 GGACTGAAATCCAGATCTT-CTGGCTTCATGTTTAGTACTCT 427969 vi i i - i i v ii i C MIRc#SINE/MIR 65 GGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCT 24 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.96 CpG sites = 44, Kimura (unadjusted) = 41.42 Transitions / transversions = 1.76 (44/25) Gap_init rate = 0.04 (10 / 224), avg. gap size = 1.70 (17 / 10) 234 34.87 11.11 1.96 chr5ptel1M 429030 429263 (570737) L2#LINE/L2 2239 2493 (589) m_b228s601i17 8968 chr5ptel1M 429030 GCTAGGTCTTGGAACCTTTTCCATTTTCTTTCTACTTTTTTTTTTCAATT 429079 vi i v i i iv i v vi ivi iiii?iv L2#LINE/L2 2239 GCTCAGTCCTTGGACCTCTTCTCTTCTCTATCTACACTCACTCCCTNGGT 2288 chr5ptel1M 429080 GGT---ATCC---CTT-TGGATATAA---TCATCTAACTTCTATGCAAAT 429119 i --- --- i- v v ---i ----- vi L2#LINE/L2 2289 GATCTCATCCAGTCTCATGGCTTTAAATACCATCTA-----TATGCTGAT 2333 chr5ptel1M 429120 GACTTCAA------TATCTCT-GTACTAAACTCTAATTCGT-CCCCAGAT 429161 i v ------ i- iv vi v vviii v- i i L2#LINE/L2 2334 GACTCCCAAATTTATATCTCCAGCCCGGACCTCTCCCCTGAACTCCAGAC 2383 chr5ptel1M 429162 TTATACTTGCACCTCTCCATTTG---CCTCTAAT-GGAAGTATCATGAG- 429206 ii iv v v vi i i i ---i i v - v v v ii - L2#LINE/L2 2384 TCGTATATCCAACTGCCTACTCGACATCTCCACTTGGATGTCTAATAGGC 2433 chr5ptel1M 429207 GTCTCTAATCTAATATGTCCAAAATTAAGTTT---ATAGTCACCCTCAAC 429253 i v ii i i i ii i--- vv v v L2#LINE/L2 2434 ATCTCAAACTTAACATGTCCAAAACTGAACTCCTGATCTTCCCCCTCAAA 2483 chr5ptel1M 429254 CTTAATCCTC 429263 i iv L2#LINE/L2 2484 CCTGCTCCTC 2493 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 47.76 CpG sites = 49, Kimura (unadjusted) = 49.65 Transitions / transversions = 1.58 (49/31) Gap_init rate = 0.07 (16 / 233), avg. gap size = 1.94 (31 / 16) 327 34.78 9.32 0.00 chr5ptel1M 429454 429614 (570386) L2#LINE/L2 2658 2833 (249) m_b228s601i18 8968 chr5ptel1M 429454 CTTTTCTTTACTTTCATAGCTGTCACCCTG-----AGT-------AGCTC 429491 i vii i i iv iii ----- i------- v L2#LINE/L2 2658 CTTCTCACCACCTCCACTGCCACCACCCTGGTCCAAGCCACCATCATCTC 2707 chr5ptel1M 429492 TTGCTTGGATTATTGCAATAGTGTTTTAGTTGGTCATCTTGCTTCAAGCC 429541 i i i iv ii ii vi i v v L2#LINE/L2 2708 TCGCCTGGATTACTGCAATAGCCTCCTAACTGGTCTCCCTGCTTCCACCC 2757 chr5ptel1M 429542 T--CTCTTTTTCAGGCCATCTTCTTC-CATCTGCCAAAGTTGTTTACCAA 429588 -- i iii ? v i ii vv - v v i vi iiviiv L2#LINE/L2 2758 TTGCCCCCCTNCAGTCTATTCTCAACACAGCAGCCAGAGTGATCCTTTTA 2807 chr5ptel1M 429589 AGATGTAGGTCTGCCCGTGTCACTTC 429614 i i i v vi i i L2#LINE/L2 2808 AAACGTAAGTCAGATCATGTCACTCC 2833 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 48.32 CpG sites = 39, Kimura (unadjusted) = 51.01 Transitions / transversions = 2.29 (39/17) Gap_init rate = 0.03 (4 / 160), avg. gap size = 3.75 (15 / 4) 1136 29.87 3.78 3.55 chr5ptel1M 430080 430978 (569022) L1M5_orf2#LINE/L1 2394 3294 (0) m_b228s551i11 8969 chr5ptel1M 430080 ATGGTGAAAAATATTAAATGCTCTTGGATAGGGTGAGCAAATATAATAAA 430129 v i v ii -- i v v iv viv vi ? L1M5_orf2#LIN 2394 ATGGAGAGATATACCA--TGTTCATGGATTGGAAGACTCAATATTGTNAA 2441 chr5ptel1M 430130 GATGACAATATTACTTAAACTAATCTATTTATTTAGTGCTATCCCAATCA 430179 v vi v ii i i vv i i v L1M5_orf2#LIN 2442 GATGTCAATTCTCCCCAAATTGATCTATAGATTCAATGCAATCCCAATCA 2491 chr5ptel1M 430180 GACTCCCAAAAAACTATTTTAATGACTTAGAAAAAATAACAACAAAATTC 430229 i v iv iii v ivv vv v v iv i ivvi i L1M5_orf2#LIN 2492 AAATCCCAGCAGGTTTTTTTGTAGAAATTGACAAGCTGATTCTAAAATTT 2541 chr5ptel1M 430230 ATATGGAAAAATAAAAGGTCAAGAAT-TTCAAGGGAATCAATGAAAAAAA 430278 vii i ii ? -vi iiv v- i L1M5_orf2#LIN 2542 ATATGGAAATGCAAAGGACCNAGAATAGCCAAAACAATCT-TGAAAAAGA 2590 chr5ptel1M 430279 AT--CAAAG--GAAGGTGGCTTAGCTGTACCAGATCT-AAAATTATATTA 430323 v-- -- i --i - vv ? ? - i i - L1M5_orf2#LIN 2591 AGAACAAAGTTGGAGG--ACTTA-CACTACCNGATNTCAAGACT-TATTA 2636 chr5ptel1M 430324 TAGAGCAGCAGTTACCAAAACCATTTGGTATTGGC-TAAGGAATAGATTA 430372 i vi v i i vi v - - iv L1M5_orf2#LIN 2637 TAAAGCTACAGTAATCAAGACAGTGTGGTATTGGCGTAAGG-ATAGACAA 2685 chr5ptel1M 430373 GTTGATCAGTGGAATAGGTTAG---GTTCAAGGGACAAAACAATCAACAA 430419 i v i i iv --- i - ii i i v v i-- v L1M5_orf2#LIN 2686 ATAGATCAATGGAACAGAATAGAGAGTCC-AGAAATAGACCCAC--ACAT 2732 chr5ptel1M 430420 CTATAACAACCTAGTCTTTGACAAA---CCCAAAG-ACCCCAGCTTTTGG 430465 v ii?v ?i ii i ---v ? - vii ---- L1M5_orf2#LIN 2733 ATATGGNCANTTGATTTTTGACAAAGGTGCCAANGCAATTCAG----TGG 2778 chr5ptel1M 430466 GATAAGAACTTACTATTTGATAAAAATTGCTGGGAAAATTGGAAACTAAT 430515 iv i ivvv v ii i viv i v v iiv L1M5_orf2#LIN 2779 GGAAAGGATAGTCTTTTCAACAAATGGTGCTGGAACAATTGGATATCCAT 2828 chr5ptel1M 430516 ATGGCAGAAACTAGGCATTGATCCACACTTAACACTGTACACCAAGATAA 430565 v i v iii?v i i vi i v ii v i v L1M5_orf2#LIN 2829 ATGGAAAAAAATGAANCTCGACCCCTACCTCACACCATACACAAAAATTA 2878 chr5ptel1M 430566 GGTCAAAATGGGTTCAT-GACCTAGGCATAAAGAATGAAATTATTAATAA 430614 iv ? i i- - iiii ii? i i v vvv L1M5_orf2#LIN 2879 ATTCNAGATGGA-TCATAGACCTAAATGTAAAAGNTAAAACTATAAAACT 2927 chr5ptel1M 430615 ATTAGAGG--AACACAGGATAGTTTACCTCTCAGACCTGTGGG--AGGGA 430660 vi i -- i v i-- i iivv - -- v L1M5_orf2#LIN 2928 TCTAGAAGAAAACATAGGAGAA--TATCTTCGTGACCT-TGGGNTAGGCA 2974 chr5ptel1M 430661 AGGACTTTATGACCAAAGAAGAACTAGAGATCATTACTGATCACAAAATA 430710 i i iv ---- v i vvi i i v i? --- i i v L1M5_orf2#LIN 2975 AAGATTTCTT----AAACAGGACACAAAAAGCACNA---ACCATAAAAGA 3017 chr5ptel1M 430711 GAAAAT-------TTCGACTATAGC-AAACTGAAAAGTTTTGTACAAACA 430752 i ------- v ?i v - i i v i iv -?v L1M5_orf2#LIN 3018 AAAAATTGATAAATTGGACTNCATCAAAATTAAAAACTTCTGCTC-NTCA 3066 chr5ptel1M 430753 AAACTAATGCAGATAAG---ATTAGAAGGGAAGCAATAAACTGGGAAAAT 430799 --i ii v v --- v i v v i i ? i v L1M5_orf2#LIN 3067 AAA--GACACCGTTAAGAAAATGAAAAGGCAAGCCACAGANTGGGAGAAA 3114 chr5ptel1M 430800 ATTTTTACAGT-CAAAGATTCTGATAAAGGCCTCATTTCCAAAATATATA 430848 v i i?- v v - i v i v i L1M5_orf2#LIN 3115 ATATTTGCAANACATATA-TCTGACAAAGGACTCGTATCCAGAATATATA 3163 chr5ptel1M 430849 GAGAATTAACTCTAATTT-ATAAAAATCAAGCCAGTC--TCCAATTGAAA 430895 i i -v vi ? i- ? -v v iv --i v? L1M5_orf2#LIN 3164 AAGAACT-CCTACAANTCAATAANAA-AAAGACAAACAACCCAATANAAA 3211 chr5ptel1M 430896 AATGGTCAAAGGATATGAACAGACAATTCTCAGATGAAGAAATTGAAACT 430945 v i iv v v i v v ?v iv L1M5_orf2#LIN 3212 AATGGGCAAAAGACTTGAACAGACACTTCACAAAAGAAGATATNCAAATG 3261 chr5ptel1M 430946 ATTTCTAGTCATATGAAAAGATGCTCCAAGTCA 430978 iiivv iv i v v? L1M5_orf2#LIN 3262 GCCAATAAGCACATGAAAAGATGCTCAACNTCA 3294 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.61 CpG sites = 144, Kimura (unadjusted) = 40.21 Transitions / transversions = 1.25 (144/115) Gap_init rate = 0.05 (49 / 898), avg. gap size = 1.35 (66 / 49) 1530 27.44 3.45 3.45 chr5ptel1M 430836 431473 (568527) L1ME5_3end#LINE/L1 7 644 (297) m_b228s551i13 8969 chr5ptel1M 430836 TCCAAAATATATAGAGAATTAACTCTAATTTATAAAAATCAAGCCAGT-- 430883 i i i ii i vviv v iv i i -v v i ?-- L1ME5_3end#LI 7 TCTAGAATATACAAGGAACTCCTGCAAATCAACAAGAA-AAAGACGGNAA 55 chr5ptel1M 430884 CTCCAATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGAA 430933 i v v i iv v i L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chr5ptel1M 430934 GAAA-TTGAAA--CTATTTCTAGTCATATGAAAAGATGCTCCAAGTCATT 430980 -ii -- --v v - i v v L1ME5_3end#LI 106 GAAACCCGAAAGGCTA--ACAAG-CATATGAAGAGATGCTCAAACTCATT 152 chr5ptel1M 430981 ATTAATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACAC 431030 v i vv i i vi L1ME5_3end#LI 153 AGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACAC 202 chr5ptel1M 431031 CTGTCAGATTGGCTAAGATGACAGGAAA---AAATAAGGATGATTGTTGG 431077 i i i v i v --- ---ii v vii v L1ME5_3end#LI 203 CTATTAGACTGGCAAAAATTA---GAAAGCTGGATAATGCCAAGTGTTGG 249 chr5ptel1M 431078 AG-GGATGTGGGAAAACTGGGACATTGATGCATTGTTGGTGGAGATGTGA 431126 v - i ? iv i vi v i i iii ii L1ME5_3end#LI 250 CGAGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAG 299 chr5ptel1M 431127 ACAGATCCAACCATTCTGGAGAGTAGTTTGGAACTA--TGCTCAAA--AA 431172 v i v i i i i v v -- iv -- L1ME5_3end#LI 300 ACTGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTAA 349 chr5ptel1M 431173 GTTATCAAACTGTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGCTT 431222 - --- --- v i i viii v iv L1ME5_3end#LI 350 G-TAT---AC---GCATACCCTATGACCCAGCAATTCCGCTCCTGGGTAT 392 chr5ptel1M 431223 ATACCCCAAAGAGATATTAAAGAAGG----GAAAGGGACCTATATGTGCC 431268 i i vi v viv ----v i ---- i v L1ME5_3end#LI 393 ATATCCCAAAGAAATTCTCACACAGGTCCATAAGGGGAC----ATGTACG 438 chr5ptel1M 431269 AAAATGTTTATGGCAGCCCTCTTTGTAGTGGCCAGAAAGTGGAAACTGAG 431318 ii i v vi v i vi i iv ii vivv L1ME5_3end#LI 439 AGGATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACC 488 chr5ptel1M 431319 TGGATGCCAATCAGATGGAGAATGGCTGAATAAATTGTGGTATATGAATA 431368 i i v vvv i v iii v iv v i L1ME5_3end#LI 489 TGGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACA 538 chr5ptel1M 431369 TTATGGAATATTATTGTTCTGTAAGAAATGACCAACAGGATGATTTCAGA 431418 ii i i vvvv v v iii vi vi -- v v L1ME5_3end#LI 539 CCATGGAGTACTATGCAGCAGTTAGAAGCAACGGACTAGATG--TACACA 586 chr5ptel1M 431419 AAG--GCCTGGAGAGA-CTTATACTAAC-TGATGCTGAGTGAAATGAGC- 431463 v --i v vi - v -- - ii vi i- L1ME5_3end#LI 587 TAGCAACATGGATGGATCTTAAA--AACATAGTGCTGAGTGAAAAAAGTA 634 chr5ptel1M 431464 AGGACCAGAA 431473 i v L1ME5_3end#LI 635 AGAAACAGAA 644 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.17 CpG sites = 94, Kimura (unadjusted) = 34.96 Transitions / transversions = 1.25 (94/75) Gap_init rate = 0.05 (34 / 637), avg. gap size = 1.29 (44 / 34) 1558 27.27 1.83 2.77 chr5ptel1M 430836 431382 (568618) L1ME3Cz_3end#LINE/L1 7 548 (449) m_b228s551i12 8969 chr5ptel1M 430836 TCCAAAATATATAGAGAATTAACTCTAATTTATAAAAATCAAGCCAGTCT 430885 i i i vviv v iv i -v v ii - L1ME3Cz_3end# 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAA-AAAGACAACC- 54 chr5ptel1M 430886 CCAATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGAAGA 430935 - v v i v v i L1ME3Cz_3end# 55 -CAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGGA 103 chr5ptel1M 430936 AATTGAAACTATTTCTAGTCATATGAAAAGATGCTCCAAGTCATTATTAA 430985 iivi iviiivv iv v vv i v L1ME3Cz_3end# 104 AACCCGAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTAA 153 chr5ptel1M 430986 TCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACACCTGTC 431035 i i ? vv i i v ii L1ME3Cz_3end# 154 TCAGGGAAATGCAAATTAAAACNACAATGAGATACCATTTCACACCCATC 203 chr5ptel1M 431036 AGATTGGCTAAGAT--GACAG---GAAAAAATAAGGATGATTGTTGGAG- 431079 v i --i v --- v v iv i ----- v - L1ME3Cz_3end# 204 AGATTGGCAAAAATTTAAAAGTCTGACAATACCAAG-----TGTTGGCGA 248 chr5ptel1M 431080 GGATGTGGGAAAACTGGGACATTGATGCATTGTTGGTGGAGATGTGAACA 431129 ii v i vi v i i i iii i iv L1ME3Cz_3end# 249 GGATGTGGAGAAACGGGAACTCTCATACACTGCTGGTGGGAGTGTAAATT 298 chr5ptel1M 431130 GATCCAACCATTCTGGAGAGTAGTTTGGAACTATGCTCAAAAAGTTATCA 431179 i v i i i i v v - viv i-- L1ME3Cz_3end# 299 GGTACAACCACTTTGGAGAGCAATTTGGCAATAT-CTAGTAAAGTTG--A 345 chr5ptel1M 431180 AACTGTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGCTTATACCCC 431229 iv i vi i i vii v i iv i L1ME3Cz_3end# 346 AGATGCGCATACCCTACGACCCAGCAATTCCACTTCTAGGTATATACCCT 395 chr5ptel1M 431230 AAAGAGA-TATTAAAGAAGGG---AAAGGGACCTATATGTGCCAAAATGT 431275 i i - v iiv v v v --- i i ---- i v ii L1ME3Cz_3end# 396 AGAGAAACTCTCGCACATGTGCACAAGGAGAC----ATGTACAAGGATGT 441 chr5ptel1M 431276 TTATGGCAGCCCTCTTTGTAGTGGCCAGAAAGTGGAAACTGAGTGGATGC 431325 i v vi v i i v i v vivv ii i L1ME3Cz_3end# 442 TCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGT 491 chr5ptel1M 431326 CAATCAGATGGAGAATGGCTGAATAAATTGTGGTATATGAATATTATGGA 431375 v ivv i v i vv iv L1ME3Cz_3end# 492 CCATCAATAGGGGAATGGATAAATAAATTGTGGTATATTCATACAATGGA 541 chr5ptel1M 431376 ATATTAT 431382 i L1ME3Cz_3end# 542 ATACTAT 548 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.42 CpG sites = 81, Kimura (unadjusted) = 34.62 Transitions / transversions = 1.27 (81/64) Gap_init rate = 0.04 (20 / 546), avg. gap size = 1.25 (25 / 20) 2760 29.30 5.01 2.34 chr5ptel1M 432063 433600 (566400) C L1M5_orf2#LINE/L1 (889) 2405 828 m_b228s551i14 8970 chr5ptel1M 432063 ATATTTTTCCAGTTGGTTAGATCTGACTTTATTTGTGTGGAAAGCGTTTT 432112 i i v iv i vvi v v v viiv ii C L1M5_orf2#LIN 2405 ATATCTCTCCATTTATTTAGGTCTTCTTTAATTTCTCTCAGCAATGTTTT 2356 chr5ptel1M 432113 ATAGTTTT-GCTATATGAGTCCTG-ACTTTTCCTTGGCAGATAGATTCCC 432160 i -iv i ?ii i - v ? i- vi vv i C L1M5_orf2#LIN 2355 GTAGTTTTCAGTGTANAGGTCTTGCACATNTT-TTGTTAGATTTATTCCT 2307 chr5ptel1M 432161 AAATATTTTATACCAGCGGCAGTTACTTTATATGGACTTTCTCTTTGTAT 432210 i ? iiivviv vv i i v v vv vi i ?iv C L1M5_orf2#LIN 2306 AAGTATTTNATGTTTTTTGATGCTATTGTAAATGGTATTGTTTTTNAAAT 2257 chr5ptel1M 432211 CTC------TAACTGTTGGGTTTTGTCAGTGATATATAAGAATGCTGAGC 432254 i ------i i v --- ii --- ii i ----v C L1M5_orf2#LIN 2256 TTCATTTTCCAATTGTTTG---TTGCTAGT---ATATAGAAATAC----A 2217 chr5ptel1M 432255 ATTTATTTTGGTTTATT----TTGTATCCTGTAACTTTGCTAAAGTTGTG 432300 v v v ---- ? ii i v iiiv C L1M5_orf2#LIN 2216 ATTGATTTTTGTATATTGACCTTGTATCCNGCGACCTTGCTAAATTCACT 2167 chr5ptel1M 432301 AATTATTTCTAATAGCTTTTTAGTTGAATTTCTGGCATTCTCTAAGTATA 432350 v v i i ? v v v i i ? v i v ? C L1M5_orf2#LIN 2166 TATTAGTTCTAGTAGTTTNTTTGTAGATTCTTTNGGATTTTCTACGTANA 2117 chr5ptel1M 432351 CCATCCTATCATCTGCAGAGAGCCATAATTTGATTTCCTCATTACCTACT 432400 v v i ii v i?v i i v i v v v ii C L1M5_orf2#LIN 2116 CAATCATGTCATCTGCGAATAANGACAGTTTTATTTCTTCCTTTCCAATC 2067 chr5ptel1M 432401 CTAATTCCTTTCATTTCTTTCTCATCTCTTATTGCCAAAGCTAGCATTTC 432450 i v v i i v vi vvvi v ii C L1M5_orf2#LIN 2066 TTTATGCCTTTTATTTCTTTTTCTTGCCTTATTGCACTGGCTAGGACCTC 2017 chr5ptel1M 432451 TAACACGATATTGAATCGTAATGGTGACAGCAGGCAACCTTGTTTCACTC 432500 i ii i i v v i ? i i v i iii C L1M5_orf2#LIN 2016 CAGTACAATGTTGAATAGAAGTGGTGANAGCGGACATCCTTGTCTTGTTC 1967 chr5ptel1M 432501 CTGAGCTTA--------------------TCCCCATTACATATGATGCTT 432530 i v -------------------- v vi i ? C L1M5_orf2#LIN 1966 CCGATCTTAGGGGGAAAGCNTTCAGTNTTTCACCATTAAGTATGATGTTN 1917 chr5ptel1M 432531 ACTGATGGTGTTAAAGAGATGCTACTGACTATTTTAAGGAAAAGTCCATT 432580 i vv v vviv ivi v ii vv i ivvi v i C L1M5_orf2#LIN 1916 GCTGTAGGTTTTTCGTAGATGCCCTTTATCAGGTTGAGGAAGTTCCCTTC 1867 chr5ptel1M 432581 TATTCCTATATTCTTAAGTGTTTTTTAATAGGAATGGATGTTGAATTTTA 432630 vv vi i v - vi v i i C L1M5_orf2#LIN 1866 TATTCCTAGTTTGCTGAGAGTTTTT-ATCATGAATGGGTGTTGAATTTTG 1818 chr5ptel1M 432631 TCAAATACTTTCTCTTCATCTATTGAGATGATCATATAGTTTTTGT---T 432677 i i v ii v --- C L1M5_orf2#LIN 1817 TCAAATGCTTTTTCTGCATCTATTGAGATGATCATATGATTTTTCTCCTT 1768 chr5ptel1M 432678 AATTTGGTTATTGATATAGTCAATTATGCTAATAGTCTTCCTAATATTAA 432727 v iv --- i v iii i v vi i v i C L1M5_orf2#LIN 1767 TATTCTGTTA---ATATGGTGAATTACATTGATTGATTTTCGAATGTTAA 1721 chr5ptel1M 432728 ACGAGCCCTGCATTCCTGGTATAAATCCCACTTGGTTGTTGTGTATTATC 432777 v i i v i ii vi C L1M5_orf2#LIN 1720 ACCAACCTTGCATTCCTGGGATAAACCCCACTTGGTCATGATGTATTATC 1671 chr5ptel1M 432778 CCAGGGATGACTTTCCGTAATCTTTTTGCTAATATTTCATTCCAAGATTT 432827 ivvvv ivv v i v v vv ii -? i C L1M5_orf2#LIN 1670 CTTTTTATATATTGCTGGATTCGATTTGCTAATATTTTGTT-NAGGATTT 1622 chr5ptel1M 432828 TAGCATCAATATTCATTAGGGAGATTGGTTTATAATTTTC-TTTCTCAC- 432875 v v i v v i i - iii- C L1M5_orf2#LIN 1621 TTGCATCTATGTTCATGAGGGATATTGGTCTGTAATTTTCTTTTCTTGTA 1572 chr5ptel1M 432876 ---TCTTCCACCTACCTGGTTTAGTTATGACTATCATGTTTGTGTCATAA 432922 --- ----- ii ? v v v vvi ? i v iv C L1M5_orf2#LIN 1571 ATGTCTT-----TGTCNGGTTTTGGTATCAGGGTNATGCTGGCCTCATAA 1527 chr5ptel1M 432923 AAGGAATTTGGTAGGAGTCCTTCATTCCCTATTTTTTCAAATAGTTTATA 432972 v i v v viv i v ii i vi v i i C L1M5_orf2#LIN 1526 AATGAGTTGGGAAGTGTTCCCTCTTTTTCTATTTTCTGGAAGAGTTTGTG 1477 chr5ptel1M 432973 TAACATTGGAGTTCATTCTTCTTTAAATGTTTTGTAGAATTCACCTGTAA 433022 v vi vv i v v i C L1M5_orf2#LIN 1476 TAAGATTGGTATTATTTCTTCCTTAAATGTTTGGTAGAATTCACCAGTGA 1427 chr5ptel1M 433023 ATCCATCTGGTCTTGGGGATTTTTTCTTAGGGAGTTGATTAATAGCTTGT 433072 v v i i v i iv i i v vv vi vvi C L1M5_orf2#LIN 1426 AGCCATCTGGGCCTGGAGTTTTCTTTGTGGGAAGGTTTTTAATTACAAAT 1377 chr5ptel1M 433073 TCTATTTCTTTTCCTGAAATGGGACTATTTGAG-----CAACTTACTTCT 433117 v vviv v i i i- ----- v i - C L1M5_orf2#LIN 1376 TCAATTTCTTTAATAGATATAGGGCTATTC-AGATTTTCTATTT-CTTCT 1329 chr5ptel1M 433118 ---GTTAATCTGGGAAGCCTATCTTTTTTTGGAGGTAGTCATCTATTTCA 433164 --- i i i v v i?i i v i--i v v ii i C L1M5_orf2#LIN 1328 TGNGTCAGTTTTGGTAANTTGTGTTTTTC--AAGGAATTTGTCCATTTCA 1281 chr5ptel1M 433165 CTTAGGTTGTCAAAGTGATTGGCATAAAGTAGGACAAAGTAACTCCTAAT 433214 ii i ? v v v vv v i viii v C L1M5_orf2#LIN 1280 TCTAAGTTNTCAAATTTATTGGCATAAAGTTGTTCATAATATTCTCTTAT 1231 chr5ptel1M 433215 TATTACTCTAATTTCCTCTTCATTGGTGGAAAGTTCTCCCTTTTCATTTT 433264 ivi i v ivivvv iv i vi vv i ii C L1M5_orf2#LIN 1230 TATCCTTTTAATGTCTGTAGGATCTGTAGTGATGTCTCCTTTTTCATTCC 1181 chr5ptel1M 433265 CAAGACTA--AATTT---TC----------------TAATCAGATTTACC 433293 ii v i i-- --- ---------------- i vi ?i i C L1M5_orf2#LIN 1180 TGATATTGGTAATTTGTGTCTTCTCTCTTTTTTTCTTGATCAGTCTNGCT 1131 chr5ptel1M 433294 AAAGGTTTATCTATTTTGTTGGTTTTTTCATAATACCAACTGTTAGTTTT 433343 i v i i i v iv i v i i i C L1M5_orf2#LIN 1130 AGAGGTTTATCAATTTTATTGATCTTTTCAAAGAACCAGCTTTTGGCTTC 1081 chr5ptel1M 433344 ATTTATTAATTCAATAGTTTTTTTTTTTACTTTCAATTTTATAAATTTCT 433393 i v -- vv -- v ? ? ii v i vi C L1M5_orf2#LIN 1080 GTTGATT--TTCTCTA--TTGTNTNTTTGTTTTCTATTTCATTGATTTCT 1035 chr5ptel1M 433394 CCTTTTAATTTTAGAATTTCC--AGTTTAGCATGTTATTGGGTATTTTCA 433441 v i vi vv --vv ivi v ?i - ---- i C L1M5_orf2#LIN 1034 GCTCTTATCTTTATTATTTCCTTCCTTCTACTTNCT-TTGGG----TTTA 990 chr5ptel1M 433442 ACTTGA---TCTTTTTCTAGCTTTTTAAGTTGCAAACTCAATTTATGGAG 433488 i v--- i v v i i iv i v v C L1M5_orf2#LIN 989 ATTTGCTCTTCTTTTTCTAGCTTCTTAAGGTGGAAGCTTAGATCATTGAT 940 chr5ptel1M 433489 CTT--CTCTTTC-TCTATTTTATTCAAGTAAGCCTCTAAAAATATAAAAT 433535 i --vi - v i --- vi ? v i ?iv v C L1M5_orf2#LIN 939 TTTAAGCCTTTCTTCTTTTCTA---ATATANGCATTTAANGCTATAAATT 893 chr5ptel1M 433536 CTCCCCTTTTTACAGCTTTGGCTGTATCCCATAAATTTGGGTATGTGGTC 433585 ii i vvvi v i i i v i v v C L1M5_orf2#LIN 892 TCCCTCTAAGCACTGCTTTAGCTGCATCCCACAAATTTTGATATGTTGTA 843 chr5ptel1M 433586 TCATTGTTGTCATTC 433600 iv ii ? C L1M5_orf2#LIN 842 TTTTCATTNTCATTC 828 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.92 CpG sites = 234, Kimura (unadjusted) = 38.61 Transitions / transversions = 1.14 (234/206) Gap_init rate = 0.04 (55 / 1537), avg. gap size = 2.07 (114 / 55) 15 9.08 7.89 2.50 chr5ptel1M 434571 434608 (565392) (TCTC)n#Simple_repeat 1 40 (0) m_b228s252i6 8971 chr5ptel1M 434571 TCTCTCTCTCTCTCTCCCTCATC-CTTTCT-TCT-TCCCTC 434608 i - - i - - i (TCTC)n#Simpl 1 TCTCTCTCTCTCTCTCTCTC-TCTCTCTCTCTCTCTCTCTC 40 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.11 (4 / 37), avg. gap size = 1.00 (4 / 4) 23 21.82 0.00 0.00 chr5ptel1M 434632 434679 (565321) (T)n#Simple_repeat 1 48 (0) m_b228s252i7 8972 chr5ptel1M 434632 TTTGTTTTGTTATTGTTTTTTTTTGTTGTTGTTTTTTTTTTACTTTTT 434679 v v v v v v v vi (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 48 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 36 38.66 0.54 1.09 chr5ptel1M 434679 434862 (565138) (TC)n#Simple_repeat 1 183 (0) m_b228s252i8 8973 chr5ptel1M 434679 TCTCAATCTCCTTTTCACTCTCTGGCTTGCTTTATTTCTCTCTCTCTGCC 434728 vv ii i v vv iv i v i vi (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr5ptel1M 434729 TTTCTTTCTGTCTCTTTCTGACTTTTTTTGCTCTTTCTCAATCTCTTTTT 434778 i i v i vv i i i - i vv i i (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCT 99 chr5ptel1M 434779 TACTGCCTAGCTCTTTCTGGCTTACTTTACAATCAACCTCTC-CCCCCTC 434827 iv vi vv i vv iv i - vv vvi - i i (TC)n#Simple_ 100 CTCTCTCTCTCTCTCTCTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTC 148 chr5ptel1M 434828 CCGTTCTATTTCTATCTCTCTCTCTCTCTCTCTCT 434862 i vi v i v (TC)n#Simple_ 149 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 183 Matrix = Unknown Transitions / transversions = 1.00 (27/27) Gap_init rate = 0.02 (3 / 183), avg. gap size = 1.00 (3 / 3) 13 11.20 3.23 3.23 chr5ptel1M 435007 435037 (564963) (AGCA)n#Simple_repeat 1 31 (0) m_b228s252i9 8974 chr5ptel1M 435007 AGAAAGCAAGCAAGCAAACAAG-AGGACAAGC 435037 v i - i - (AGCA)n#Simpl 1 AGCAAGCAAGCAAGCAAGCAAGCAAG-CAAGC 31 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2) 282 30.14 7.09 0.74 chr5ptel1M 435769 435895 (564105) C MIRc#SINE/MIR (131) 137 3 m_b228s601i19 8975 chr5ptel1M 435769 GATGAAGATACTGAGCCT-ATGGAGAATAAATGAATCACCCATAATCACA 435817 i v v - vi iv i v ii vii C MIRc#SINE/MIR 137 GATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACA 88 chr5ptel1M 435818 GAGATCATAAAATTCAGAG-TAGAAATGGAACCCA-GTCGTTCTCTCTCC 435865 v v vi ivvv -ii i v v - v i vv C MIRc#SINE/MIR 87 CAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCC 38 chr5ptel1M 435866 AGG--CAATCCTCTCTCACCCTGC----CACTGTTT 435895 i -- i v i - v ---- ii C MIRc#SINE/MIR 37 AAGTCCAGTGCTCTTTC-CACTGCACCACACTGCCT 3 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.65 CpG sites = 19, Kimura (unadjusted) = 39.08 Transitions / transversions = 1.00 (19/19) Gap_init rate = 0.05 (6 / 126), avg. gap size = 1.67 (10 / 6) 253 20.69 1.72 0.00 chr5ptel1M 436171 436228 (563772) C tRNA-Thr-ACA#tRNA (10) 65 7 m_b228s502i0 8976 chr5ptel1M 436171 GCCAGATTTGAACTCAGTTTCCCTGATTT-CAAGGCCAGTGCTCTATCTC 436219 v ivvvi i - i v i C tRNA-Thr-ACA# 65 GCGAGATTTGAACTCGCGACCCCTGGTTTACAAGACCAGTGCTCTAACCC 16 chr5ptel1M 436220 CTGTTCTAT 436228 vv C tRNA-Thr-ACA# 15 CTGAGCTAT 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 22.10 CpG sites = 5, Kimura (unadjusted) = 24.25 Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.02 (1 / 57), avg. gap size = 1.00 (1 / 1) 2750 29.11 2.71 2.83 chr5ptel1M 436568 438193 (561807) L1M5_orf2#LINE/L1 1671 3294 (0) m_b228s551i15 8977 chr5ptel1M 436568 GATAATACACTATGATCAAGTAGGATTTATACCAGGAATGCAGGGCTGGT 436617 ii i i i v i i L1M5_orf2#LIN 1671 GATAATACATCATGACCAAGTGGGGTTTATCCCAGGAATGCAAGGTTGGT 1720 chr5ptel1M 436618 TCAATATTAGGAAAACTATCAATATAATTGGCCATGTTAATA-ACCAAAT 436666 i i v i v v i vi i i - vi v L1M5_orf2#LIN 1721 TTAACATTCGAAAATCAATCAATGTAATTCACCATATTAACAGAATAAAG 1770 chr5ptel1M 436667 TAACAAAAACCATATGATCATCTCAATAGATGTAGAAAAAGCATTTGATA 436716 v i- i i i L1M5_orf2#LIN 1771 GAG-AAAAATCATATGATCATCTCAATAGATGCAGAAAAAGCATTTGACA 1819 chr5ptel1M 436717 AAATCCAACATCCATTCCTATTAAAAACACTTGAAAGTATAGGAATAAAT 436766 i i v iv v iiiv ivv i v L1M5_orf2#LIN 1820 AAATTCAACACCCATTCATGATAAAAACTCTCAGCAAACTAGGAATAGAA 1869 chr5ptel1M 436767 GG--ACTTTTTCCTTAAAATAATCAGCAGCATCTATTTAAAACCATCAGT 436814 -- --- i vv i v ivi ivv vv i L1M5_orf2#LIN 1870 GGGAAC---TTCCTCAACCTGATAAAGGGCATCTACGAAAAACCTACAGC 1916 chr5ptel1M 436815 AAGCATCATATGTAATGGAGACAAACTGCAACCATTCCCAATAAGATCTG 436864 ? i iv v v ? v ?v v vv v L1M5_orf2#LIN 1917 NAACATCATACTTAATGGTGAAANACTGAANGCTTTCCCCCTAAGATCGG 1966 chr5ptel1M 436865 GAGTAGAAACAGGGTTTGCCCACTATCACGAGTTACTATTTAATATTGTA 436914 ii - i i -v i i ? v v - i i L1M5_orf2#LIN 1967 GAACA-AGACAAGG-ATGTCCGCTNTCACCACTT-CTATTCAACATTGTA 2013 chr5ptel1M 436915 TTAGAAACACTAGCTATAGCAATAAGAGCTGAGAAAAAG--ATTAAAGGA 436962 i i iiiv i vv - -i -- v v L1M5_orf2#LIN 2014 CTGGAGGTCCTAGCCAGTGCAATAAG-GC-AAGAAAAAGAAATAAAAGGC 2061 chr5ptel1M 436963 ATAAGAATAGGCAATGAGGAAGCCAAATTATCACTCTTTGCCGATTGACA 437012 ii v v v i iiv i i ?i v i v - L1M5_orf2#LIN 2062 ATAAAGATTGGAAAGGAAGAAATAAAACTGTCNTTATTCGCAGA-TGACA 2110 chr5ptel1M 437013 TGATAGTATACTTAGAGAACCCCAGAGATTCTGCTAA-AAGTTATTAGAA 437061 v ? v i i ? i v i v - ii i L1M5_orf2#LIN 2111 TGATTGTNTACGTAGAAAATCCNAAAGAATCTACAAANAAACTACTAGAA 2160 chr5ptel1M 437062 ATAATCCACAACTTTAGCAAAGTTGCTGGTTATAAAATAAACCCACATAA 437111 v vviii v i i ? v i ii v ivi v L1M5_orf2#LIN 2161 CTAATAAGTGAATTTAGCAAGGTCGCNGGATACAAGGTCAATATACAAAA 2210 chr5ptel1M 437112 GTCATCAGCATGCTTATATATCACTAACAG--AATCCAACAGTCAGAGTT 437159 i viv i vii ii vi i-- ivi v i v i v L1M5_orf2#LIN 2211 ATCAATTGTATTTCTATATACTAGCAACAAACAATTGGAAAATGAAATTT 2260 chr5ptel1M 437160 ACAAAGAGAAATTCCATTTAAAGTAACTACTGATAATATAAAATATTTAG 437209 --? i iv v v i i vv vi v i ? i L1M5_orf2#LIN 2261 --NAAAAACAATACCATTTACAATAGCATCAAAAAACATNAAATACTTAG 2308 chr5ptel1M 437210 GAATCTATCTGCCAAGGAAAAT---CAGAAACTTTATGAGCAAAATTACA 437256 vv iv -- ? --- ii v ? iivvv i L1M5_orf2#LIN 2309 GAATAAATCTAACAA--AANATGTGCAAGACCTNTACACTGAAAACTACA 2356 chr5ptel1M 437257 GACCACTTTTCACA-AAATTAAATCTGATCTAACCAATTGGAAAAATATT 437305 i v i vi v v - vvv i vi v i i v L1M5_orf2#LIN 2357 AAACATTGCTGAGAGAAATTAAAGAAGACCTAAATAAATGGAGAGATATA 2406 chr5ptel1M 437306 AAATGCTCTTGGATAGGGCGAGCAAATATAATAAAGATGACAATATTACC 437355 vv i v v iv viv vi ? v vi v L1M5_orf2#LIN 2407 CCATGTTCATGGATTGGAAGACTCAATATTGTNAAGATGTCAATTCTCCC 2456 chr5ptel1M 437356 TAAACTAATCTATTTATTTAGCGCTATACCAATCAGACTCCCAAAAAACT 437405 i i i vv i ii v v i v iv iii L1M5_orf2#LIN 2457 CAAATTGATCTATAGATTCAATGCAATCCCAATCAAAATCCCAGCAGGTT 2506 chr5ptel1M 437406 ATTTTAATGACCTAGGAAAAATAACAACAAAGTTCATATGGAAAAACAAA 437455 v ivv vv v iv iv i ivvi i i vi L1M5_orf2#LIN 2507 TTTTTGTAGAAATTGACAAGCTGATTCTAAAATTTATATGGAAATGCAAA 2556 chr5ptel1M 437456 AGGTCAAGAAT-TTCAAGGGAATTAATGAAAAA-AAAATCAAATGATGGT 437503 i ii ? -vi iiv i-v - i v - v v L1M5_orf2#LIN 2557 GGACCNAGAATAGCCAAAACAATC-TTGAAAAAGAAGAACAAA-GTTGGA 2604 chr5ptel1M 437504 GG-CTTAGCTGTACCAGATCT-AAAATTATATTATAGAGCAGCAGTTACC 437551 - - vv ? ? - i i - i vi v i L1M5_orf2#LIN 2605 GGACTTA-CACTACCNGATNTCAAGACT-TATTATAAAGCTACAGTAATC 2652 chr5ptel1M 437552 AAAACTATTTGAGTATTAGC-TAAGGAATAGATTAGTTGATCAGTGGAAT 437600 i vi v - i - - iv i v i i L1M5_orf2#LIN 2653 AAGACAGTGTG-GTATTGGCGTAAGG-ATAGACAAATAGATCAATGGAAC 2700 chr5ptel1M 437601 AGATTAG---GTTCAAGGGACAAAACAGTCA-ACAAATATAGCAACCTAA 437646 v --- i - ii i i v --- - v i ?v ?i i L1M5_orf2#LIN 2701 AGAATAGAGAGTCC-AGAAATAGACC---CACACATATATGGNCANTTGA 2746 chr5ptel1M 437647 TCTTTGACAAA---CCCAAAGATCCCATCTTTTGGGATAAGAACTTACTG 437693 i ---v ? --- v iivv iv i ivvv v L1M5_orf2#LIN 2747 TTTTTGACAAAGGTGCCAANG---CAATTCAGTGGGGAAAGGATAGTCTT 2793 chr5ptel1M 437694 TTTGATAAAAATTGCTGGGAAAATTGGAAACTAATATGGCAGAAACTAGG 437743 ii i viv i v v iiv v i v iii L1M5_orf2#LIN 2794 TTCAACAAATGGTGCTGGAACAATTGGATATCCATATGGAAAAAAATGAA 2843 chr5ptel1M 437744 CATTGATCCACACTTAACGCCGTACAACAAGATAAGGTCAAAATGGGTTC 437793 ?v i i vi i v i i vv i v iv ? i i- L1M5_orf2#LIN 2844 NCTCGACCCCTACCTCACACCATACACAAAAATTAATTCNAGATGGA-TC 2892 chr5ptel1M 437794 AT-GACCTAGGCATAAAGAATGAAATTATCAATAAATTAGAGG--AACAT 437840 - iiii ii? i i v vvvvi i -- L1M5_orf2#LIN 2893 ATAGACCTAAATGTAAAAGNTAAAACTATAAAACTTCTAGAAGAAAACAT 2942 chr5ptel1M 437841 AGGATAGTTTACCTCTCAGACCTGTGGA-AGGGAAGGTCTTTATGACCAA 437889 v i-- i iivv vv ?- v i vi iv ------ L1M5_orf2#LIN 2943 AGGAGAA--TATCTTCGTGACCTTGGGNTAGGCAAAGATTTCTT------ 2984 chr5ptel1M 437890 AAGCAGAAC-TAGAGATCATTACTGATCACAAAATAGAAAAT-------T 437931 i i -i i i v i? --- i i v i ------- L1M5_orf2#LIN 2985 AAACAGGACACAAAAAGCACNA---ACCATAAAAGAAAAAATTGATAAAT 3031 chr5ptel1M 437932 TCGATTATACCAAAA-TGAAAAGTTTTGTACAAACAAAACTAATGCAGAC 437980 v i ?i i - i v i iv ?vvv ivi vi ivi v L1M5_orf2#LIN 3032 TGGACTNCATCAAAATTAAAAACTTCTGCTCNTCAAAAGACACCGTTAAG 3081 chr5ptel1M 437981 AAGATTAGAAGG-AAGCAATAAACTGG--GAAAATATTTTTTACAGTCAA 438027 i v i - v i i ? -- viv ? -- v L1M5_orf2#LIN 3082 AAAATGAAAAGGCAAGCCACAGANTGGGAGAAAATATTTGCAANA--CAT 3129 chr5ptel1M 438028 AGGTTCTGAT-AAGGCCTCATTTCCAAAAATATATAGAGAATTAACTCTA 438076 vi- i- v i v - i i i -v vi L1M5_orf2#LIN 3130 ATA-TCTGACAAAGGACTCGTATCC-AGAATATATAAAGAACT-CCTACA 3176 chr5ptel1M 438077 ATTT-ATAAAAAATCAAGCCATTC--TCCAATTGAAAAATGGTCAAAGGA 438123 ? i- ? -- v vv --i v? v i L1M5_orf2#LIN 3177 ANTCAATAANAAA--AAGACAAACAACCCAATANAAAAATGGGCAAAAGA 3224 chr5ptel1M 438124 TATGAACAGACAATTCTCAGATGAAGAAATTGAAACTATTTCTAGTCATA 438173 iv v v i v v ?v iviiivv iv i L1M5_orf2#LIN 3225 CTTGAACAGACACTTCACAAAAGAAGATATNCAAATGGCCAATAAGCACA 3274 chr5ptel1M 438174 TGAAAAGATGCTCCAAGTCA 438193 v v? L1M5_orf2#LIN 3275 TGAAAAGATGCTCAACNTCA 3294 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.76 CpG sites = 249, Kimura (unadjusted) = 38.62 Transitions / transversions = 1.18 (249/211) Gap_init rate = 0.04 (72 / 1625), avg. gap size = 1.25 (90 / 72) 1351 25.86 3.55 5.15 chr5ptel1M 438099 438689 (561311) L1ME5_3end#LINE/L1 56 637 (304) m_b228s551i16 8977 chr5ptel1M 438099 CTCCAATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGAA 438148 i v v i iv v i L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chr5ptel1M 438149 GAAA-TTGAAA--CTATTTCTAGTCATATGAAAAGATGCTCCAAGTCATT 438195 -ii -- --v v - i v v L1ME5_3end#LI 106 GAAACCCGAAAGGCTA--ACAAG-CATATGAAGAGATGCTCAAACTCATT 152 chr5ptel1M 438196 ATTAATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACAC 438245 v i vv i i vi L1ME5_3end#LI 153 AGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACAC 202 chr5ptel1M 438246 CTGTCAGATTGAGCTAAGATGACAGGAA---AAATAATGATGATTGTTGG 438292 i i i - v i --i i ---ii vii v L1ME5_3end#LI 203 CTATTAGACTG-GCAAAAAT--TAGAAAGCTGGATAATGCCAAGTGTTGG 249 chr5ptel1M 438293 AG-GGATGCGAGGAAAACTGAGGACAATGATGCATTGTTGGTGGAGTTGT 438341 v - i i ? -- ii i vv v i i iiv L1ME5_3end#LI 250 CGAGGATGTGGGGANA--TAGGAACCCTCATGCACTGCTGGTGGGAGTGT 297 chr5ptel1M 438342 GAACAGAATCCAACCATTCTGGAGAAGTAGTTTGGAACTA--TGCTCAAA 438389 ii v -i v i - i i i v v -- iv L1ME5_3end#LI 298 AGACTG-GTGCAGCCATTCTGGAG-AGCAATCTGGCAGTACTTAGTCAAA 345 chr5ptel1M 438390 --AAGTTATCAAACTGTGCATACCCTTTGATCTAGCAGTGATTACTACTG 438437 -- - --- --- v i i i v-iii v L1ME5_3end#LI 346 TTAAG-TAT---AC---GCATACCCTATGACCCAGCAATT-CCGCTCCTG 387 chr5ptel1M 438438 GGATTATATCCCAAAGAGATTATAAAGACAGG-----AAAGGGACCTGTA 438482 vv i v -v v ----- i v - L1ME5_3end#LI 388 GGTATATATCCCAAAGAAATTCT-CACACAGGTCCATAAGGGGACATGT- 435 chr5ptel1M 438483 TGTGACACGAATGTTTGGGGCAGCCCTTTTTGTGAGTGGCTAGAAACTGG 438532 ---- iv i iivv vi v - vi i ii L1ME5_3end#LI 436 ----ACGAGGATGTTCATTGCAGCGTTGTTTGTG-GTGGCGGGGAGTTGG 480 chr5ptel1M 438533 AAACTGAATGGATGCCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTA 438582 ii vivv i i v v i v iii v i L1ME5_3end#LI 481 AGGCAACCTGGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTG 530 chr5ptel1M 438583 TATGAAAATTATGGAATATTACTGT-TCTGTAAGAAATGACCAACAGGAT 438631 v v v ii i i - i-v v v iii vi vi L1ME5_3end#LI 531 GATGCACACCATGGAGTACTA-TGCAGCAGTTAGAAGCAACGGACTAGAT 579 chr5ptel1M 438632 GATTTCAGAAAG--GCCTGGAGAGA-CTTACACGAAC-TGATGCTAAGTG 438677 -- v v v --i v vi - v -- - ii i L1ME5_3end#LI 580 G--TACACATAGCAACATGGATGGATCTTAAA--AACATAGTGCTGAGTG 625 chr5ptel1M 438678 AAATGAGCAGGA 438689 vi i i L1ME5_3end#LI 626 AAAAAAGTAAGA 637 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 31.56 CpG sites = 83, Kimura (unadjusted) = 32.40 Transitions / transversions = 1.34 (83/62) Gap_init rate = 0.07 (41 / 590), avg. gap size = 1.24 (51 / 41) 15 23.33 2.22 0.00 chr5ptel1M 439121 439165 (560835) (AAATA)n#Simple_repeat 1 46 (0) m_b228s252i10 8978 chr5ptel1M 439121 AAATAAAAGGCTATTAAATAAAA-AAAAAAAAGAAAAAGAAAATAA 439165 vivv v - v iv v (AAATA)n#Simp 1 AAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAA 46 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 18 14.73 0.00 0.00 chr5ptel1M 439136 439165 (560835) (A)n#Simple_repeat 1 30 (0) m_b228s252i11 8978 chr5ptel1M 439136 AAATAAAAAAAAAAAAGAAAAAGAAAATAA 439165 v i i v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 30 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 315 27.55 0.00 10.10 chr5ptel1M 439171 439279 (560721) MIRb#SINE/MIR 3 101 (167) m_b228s601i20 8979 chr5ptel1M 439171 GAGGAGCAGCGAGGTGGTGCAGTGGATAGATCTCCGGCCCTGAAGTCAAG 439220 i --- v v v v ii i ii MIRb#SINE/MIR 3 GAGGGGCAGCG---TGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGA 49 chr5ptel1M 439221 AGGACCCGAGTTCAAATTTGATCTCAGACACTTTATATTTCCTAGCTAAG 439270 vi i i i iiviv v v ------- v iv MIRb#SINE/MIR 50 CAGACCTGGGTTCGAATCCCGGCTCTGCCAC-------TTACTAGCTGTG 92 chr5ptel1M 439271 TGACCTCAG 439279 ii MIRb#SINE/MIR 93 TGACCTTGG 101 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.66 CpG sites = 16, Kimura (unadjusted) = 34.77 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.09 (10 / 108), avg. gap size = 1.00 (10 / 10) 32 18.08 0.00 0.00 chr5ptel1M 441594 441650 (558350) (A)n#Simple_repeat 1 57 (0) m_b228s252i12 8980 chr5ptel1M 441594 AAAAAACAACAAACCAACAACAAAAAAAAAACAAAACAAAACAAAAAAAA 441643 v v vv v v v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr5ptel1M 441644 AAAAAAA 441650 (A)n#Simple_r 51 AAAAAAA 57 Matrix = Unknown Transitions / transversions = 0.00 (0/9) Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 chr5ptel1M 444039 444056 (555944) (A)n#Simple_repeat 1 18 (0) m_b228s252i13 8981 chr5ptel1M 444039 AAAAAAAAAAAAAAAAAA 444056 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAA 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 26 12.87 9.76 2.27 chr5ptel1M 444313 444394 (555606) (ACAACAATG)n#Simple_repeat 1 88 (0) m_b228s252i15 8982 chr5ptel1M 444313 ACAACGATGATGACAATGACGACAA--ACTACGATGACAAACAACAACAA 444360 i ii i -- v i - ii (ACAACAATG)n# 1 ACAACAATGACAACAATGACAACAATGACAACAATGAC-AACAATGACAA 49 chr5ptel1M 444361 CAA--ACAACAA--ACAACAA--ACAACAAATAACAACAA 444394 -- -- -- - i (ACAACAATG)n# 50 CAATGACAACAATGACAACAATGACAAC-AATGACAACAA 88 Matrix = Unknown Transitions / transversions = 8.00 (8/1) Gap_init rate = 0.07 (6 / 81), avg. gap size = 1.67 (10 / 6) 11 21.05 2.50 2.50 chr5ptel1M 446318 446357 (553643) (TTGTTT)n#Simple_repeat 1 40 (0) m_b229s252i4 8983 chr5ptel1M 446318 TTATTTTTG-TGTTGTCTTTGTTATTGATTTTTTGGTTTGT 446357 i - v i v - vvv (TTGTTT)n#Sim 1 TTGTTTTTGTTTTTGTTTTTGTTTTTG-TTTTTGTTTTTGT 40 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 483 31.37 1.93 1.54 chr5ptel1M 448979 449237 (550763) L1M3_orf2#LINE/L1 3029 3288 (0) m_b229s551i0 8984 chr5ptel1M 448979 ATTATATCAAACTGAAAAGTTTTTGTACA---AACAAAACTAATGTAGAC 449025 i i i i i i --- vi - v--i L1M3_orf2#LIN 3029 ACTACATCAAACTAAAAAGCTTCTGCACAGCAAAGGAAAC-AATC--AAC 3075 chr5ptel1M 449026 AAGATTAGAAAGGAAGCAATAAACTGGGAAAACATTTTCACAATTAAAGT 449075 iii v i i v v v iii v i v v ii viv vi L1M3_orf2#LIN 3076 AGAGTGAAAAGGCAACCTACGGAATGGGAGAAAATATTTGCAAACCATAT 3125 chr5ptel1M 449076 TTCTGATAAAGGACTCATTTCCAAAATATATAGAGAATTGACTATAATT- 449124 v i ii v v ii i v?- i i - L1M3_orf2#LIN 3126 ATCTGATAAGGGGTTAATATCCAAAATATATAAGGAACTCN-TACAACTC 3174 chr5ptel1M 449125 -ATAAGAAATCAATCCATTCTCCAATTGATAAATGGTCAAAGGATATGAA 449173 - iv vv ivv vvi i ? v v iv L1M3_orf2#LIN 3175 AATAGCAAAAAAACAAATAACCCGATTNAAAAATGGGCAAAGGACCTGAA 3224 chr5ptel1M 449174 CAGACAATTCTCAGATGAAGAAACTGAAACTGTTTCTAGTTATATAAAAA 449223 i v vi v v ivv iv iivvi v i L1M3_orf2#LIN 3225 TAGACATTTCTCCAAAGAAGACATACAAATGGCCAACAGGTATATGAAAA 3274 chr5ptel1M 449224 GATGCTCCAAATCA 449237 v v L1M3_orf2#LIN 3275 GATGCTCAACATCA 3288 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 40.41 CpG sites = 42, Kimura (unadjusted) = 41.84 Transitions / transversions = 1.11 (42/38) Gap_init rate = 0.03 (7 / 258), avg. gap size = 1.29 (9 / 7) 1538 27.70 0.73 1.85 chr5ptel1M 449095 449642 (550358) L1ME3G_3end#LINE/L1 7 548 (376) m_b229s551i1 8984 chr5ptel1M 449095 TCCAAAATATATAGAGAATTGACTATAATT--ATAAGAAATCAATCCATT 449142 i i i v- i v -- -- vv -- L1ME3G_3end#L 7 TCCAGAATATATAAAGAACTC-CTACAAATCAATAAGAAA--AAGACA-- 51 chr5ptel1M 449143 CTCCAATTGATAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGAA 449192 vi v v v i v v i L1ME3G_3end#L 52 ACCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAG 101 chr5ptel1M 449193 GAAACTGAAACTGTTTCTAGTTATATAAAAAGATGCTCCAAATCATTATT 449242 ivv iv iivv ivi i v vv i v L1ME3G_3end#L 102 GAAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGT 151 chr5ptel1M 449243 AATCAGAGAAATTCAAATTAAGACAACTCTGAGATACCACTACACATCTG 449292 i v i vv i viv i ii L1ME3G_3end#L 152 AATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCA 201 chr5ptel1M 449293 TCAGACTGGCTGGAATGACAGGAAAAGATAACGCGGAATGTTGGAGGGGA 449342 i vii vvv iii?vv iiiv? i v i i L1ME3G_3end#L 202 TCAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGG 251 chr5ptel1M 449343 TGCGGGAAAACAGGGACACTGATACATTGTTGGTGGAATTGTGACTATGT 449392 i i i v v v i i i v i v vv L1ME3G_3end#L 252 TGTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGT 301 chr5ptel1M 449393 CCAGCCATTCTGCAGAGCGATTAGGAACTATACTCAAAAAACCATCAAAC 449442 v ? i v i i v v v - vvv i-- i v L1ME3G_3end#L 302 ACAGCCNTTTTGGAGGGCAATTTGGCAGTAT-CTATTAAAAT--TTAAAA 348 chr5ptel1M 449443 TGTGCATACCCTTTGATCCAGCAGTGCTTCTACTGGGCTTATATCCCAAA 449492 i i i v iv v ? ?v v i ? L1ME3G_3end#L 349 TGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANA 398 chr5ptel1M 449493 GAGATACTAG-AGAAG-GAAAAGGGACCTGCTTGTGCCAAAATGTTTGTG 449540 i v - v v - v v i --? v i v ii ii v L1ME3G_3end#L 399 GAAATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTCATT 446 chr5ptel1M 449541 GGAACCCAGTTTGTAGTGGCCAGAAACTGGAAACTGAATGGATACCCATC 449590 v i viv i i v i i vivv ii ii L1ME3G_3end#L 447 GCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATC 496 chr5ptel1M 449591 AATTGGAGAATGGCTGAATAAATTGTGTTATATGAATATTACGGAATATT 449640 v i i i i v vv i i i L1ME3G_3end#L 497 AATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACT 546 chr5ptel1M 449641 AT 449642 L1ME3G_3end#L 547 AT 548 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 35.01 CpG sites = 76, Kimura (unadjusted) = 35.60 Transitions / transversions = 1.04 (76/73) Gap_init rate = 0.02 (13 / 547), avg. gap size = 1.08 (14 / 13) 1100 31.44 2.83 2.99 chr5ptel1M 449100 449735 (550265) L1MC5a_3end#LINE/L1 12 646 (2131) m_b229s551i2 8984 chr5ptel1M 449100 AATATATAGAGAATTGACTATAATT-ATAAGAAATCAATCCATTCTCCAA 449148 i ii vviv v - v vvi i v ivvi L1MC5a_3end#L 12 AATATATAAAGAGCTTCTAAAAATTGAGAAGAAAAAGACCAACAACCCAA 61 chr5ptel1M 449149 TTGATAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGAAGAAACT 449198 v v v i i v vi iv L1MC5a_3end#L 62 TAGAAAAATGGGCAAAAGATATGAACAGACAGTTCACAGAAAAAGAAATG 111 chr5ptel1M 449199 GAAACTGTTTCTAGTTATATAAAAAGATGCTCCAAATCATTATTAATCAG 449248 v iv iiii ivi i v vv i vv v L1MC5a_3end#L 112 CAAATGGCCCTTAAACATATGAAAAGATGCTCAACCTCACTCATAATAAG 161 chr5ptel1M 449249 AGAAATTCAAATTAAGACAACTCTGAGATACCACTACACATCTGTCAGAC 449298 v i v v i v v i i i L1MC5a_3end#L 162 AGAAATGCAAATTAAAACTACACTGAGATACCATTTCTCACCTATCAGAT 211 chr5ptel1M 449299 TGGCTGGAATGACAGGAAAA---GATAACGCGGAATGTTGGAGGGGATGC 449345 vii v- -- i--- i iiivvv v i v i L1MC5a_3end#L 212 TGGCAAAAATC-CA--AAAGTTTGACAACATACTCTGTTGGCGAGGCTGT 258 chr5ptel1M 449346 GGGAAAACAGGGACACTGATACATTGTTGGTGGAATTGTGACTAT-GTCC 449394 i v v v i i v ii v- - v L1MC5a_3end#L 259 GGGGAAACAGGCACTCTCATACATTGCTGGTGGGAATGCAAA-ATGGTAC 307 chr5ptel1M 449395 AGCCATTCTGCAGAGCGATTAGGAACTATACTCAAAAAACCATCAAACTG 449444 i vi v v i vi v v v - viv ii - --- i L1MC5a_3end#L 308 AACCCCTATGGAGGGGAATTTGGCAATAT-CTAGCAAAATTA-CA---TA 352 chr5ptel1M 449445 TGCA--TACCCTTTGATCCAGCAGTGCTTCTACTGGGCTTATATCCCAAA 449492 -- i i v iv v i vv v i L1MC5a_3end#L 353 TGCATTTACCCTTTGACCCAGCAATCCCACTTCTAGGAATCTATCCCGAA 402 chr5ptel1M 449493 GAGATACTAG--AGAAGGAAAAGGGACCTGCTTGTGCCAAAATGTTTGTG 449540 v i ? -- i vivi i? v i-- ii v iiv i ii v L1MC5a_3end#L 403 GATACACTNGCAAAAATACGAAANGACGTA--TGCACAAGGTTATTCATT 450 chr5ptel1M 449541 GGAACCCAGTTTGTAGTGGCCAGAAACTGGAAACTGAATGGATACCCATC 449590 v i vivi i i v i i vivviii ii L1MC5a_3end#L 451 GCAGCATTATTTGTAATAGCAAAAGACTGGAAACAACCCAAATGTCCATC 500 chr5ptel1M 449591 AATTGGAGAATGGCTGAATAAATTGTGTTATATGAATATTACGGAATATT 449640 v i v i i i v i vv i iv i i i L1MC5a_3end#L 501 AATAGGGGACTGGTTGAATAAACTATGGTACATCCACACAATGGAGTACT 550 chr5ptel1M 449641 AT-----TGTTCAGTAAGAAATGACCAGAGGGAGGATTTC---AGAAAGG 449682 ----- -- iv i ------ i i --- v vv ? L1MC5a_3end#L 551 ATGCAGCTGT--AAAAAGGAATGA------GGAAGATCTCTATATACTGN 592 chr5ptel1M 449683 CCTGGAGAGACTTACACGAAGTGATGCTGAGTGAAATGACTAAGGC-CAG 449731 iv v ii v v vi iv i i vi vi i- L1MC5a_3end#L 593 TATGGAGTGATCTCCAGGATATATTGTTAAGTGAAAAAAGCAAGGTGCAG 642 chr5ptel1M 449732 GAGA 449735 i ? L1MC5a_3end#L 643 AANA 646 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 41.41 CpG sites = 104, Kimura (unadjusted) = 41.98 Transitions / transversions = 1.16 (104/90) Gap_init rate = 0.04 (27 / 635), avg. gap size = 1.37 (37 / 27) 233 34.10 10.55 2.26 chr5ptel1M 450358 450888 (549112) C L1MD_orf2#LINE/L1 (826) 2468 1895 m_b229s551i3 8985 chr5ptel1M 450358 TACATTATTTTAGGGAATATTGTCATTTTTTATATG----GTCATAGGTG 450403 ? i v i iv v i vv ---- v --vii C L1MD_orf2#LIN 2468 TANATCAATTTGGGGAGAATTGACATCTTTACTATGTTGAGTCTT--CCA 2421 chr5ptel1M 450404 AACCATTAGCAACTGATATGTTTC-------ACTTAGATCTGTTGTCGTT 450446 v v i --i i i ------- i vi v vi C L1MD_orf2#LIN 2420 ATCCATGAACA--CGGTATGTCTCTCCATTTATTTAGATCTTCTTTGATT 2373 chr5ptel1M 450447 TTTATAAAGATTGTTCTATAATTGTATGTCTATGATTCCTATGTACATCT 450496 i v v vv vi i i i v vv iv ii v i ii ii i C L1MD_orf2#LIN 2372 TCTTTCATCAGCGTTTTGTAGTTTTCAGCATACAAGTCCTGTACATGTTT 2323 chr5ptel1M 450497 TGGTAAATGGACTCTTACTTATTTTGTGTTCTTTCA--TGACTTTTAATA 450544 v i vv iv i vv ii v i ii--i i v v i C L1MD_orf2#LIN 2322 TGTTAGATTTATACCTAAGTATTTCATTTTTTTTTGAGCGATTGTAAATG 2273 chr5ptel1M 450545 ------TAATTTTACTTTCCAGATCTTTTGGTGATTTGTTGATAATATAA 450588 ------ v v -- i i iivv - ii v i v C L1MD_orf2#LIN 2272 GTATTGTATTTTTAATTTC--GGTTTCCACGTG-TTCATTGCTAGTATAT 2226 chr5ptel1M 450589 AGAAAGGCTGAA--GATTTGTTGTGGGTTTATTTCCTACCCTGTTGCTTT 450636 vi -- -- - iv ? i iv i ivi i C L1MD_orf2#LIN 2225 AGAAATAC--AATTGATTT-TTGTATGTTNATCTTGTATCCTGCGACCTT 2179 chr5ptel1M 450637 GCTGAAACT---TTGTTCGTTTAAAG------TTAGCAG-TTCTCTAG-- 450674 - --- i v iv i ------ v i - ii i -- C L1MD_orf2#LIN 2178 GCTGAA-CTCACTTATTAGTTCTAGGAGTTTTTTTGTAGATTCCTTGGGA 2130 chr5ptel1M 450675 -TTT-----------ATCAT--CAAATGCAAAGAATGATCATATTGTTTC 450710 - ----------- -- vv v iv ivi v i C L1MD_orf2#LIN 2129 TTTTCTACGTAGACAATCATGTCATCTGCAAATAGGGACAGTTTTATTTC 2080 chr5ptel1M 450711 TTCTTT------ATGCACGCATTCCCTTTCCCTTTCTTTATCTTATCGCT 450754 i ------v i i v iiv i -ii i v C L1MD_orf2#LIN 2079 TTCCTTTCCAATCTGTATGCCTTTTATTTCCTTTTCTT-GCCTTATTGCA 2031 chr5ptel1M 450755 ATAGCTAATATTTCTGACATTGTGTTAAATAATAGTGGTGATAATAG--A 450802 v i iv i iiii i i i v v iii -- C L1MD_orf2#LIN 2030 CTGGCTAGAACTTCCAGTACTATGTTGAATAAGAGTGGTGAGAGCGGACA 1981 chr5ptel1M 450803 TCTTTACTTCACTTTTGATCTTA-TGATAATGGATTCTAGTTTTTAGTCT 450851 i i i iii iii -v iv v v - i vii v C L1MD_orf2#LIN 1980 TCCTTGCCTTGTTCCCGATCTTAGGGGGAAAGCATTC-AGTCTTTCACCA 1932 chr5ptel1M 450852 TTACACAAAATGTCAGCTTTTATTTTTACATAGATAC 450888 vii vi i v viv vii i C L1MD_orf2#LIN 1931 TTAAGTATGATGTTAGCTGTAGGTTTTTTGTAGATGC 1895 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 45.57 CpG sites = 107, Kimura (unadjusted) = 47.88 Transitions / transversions = 1.53 (107/70) Gap_init rate = 0.05 (28 / 530), avg. gap size = 2.46 (69 / 28) 293 32.51 11.59 2.67 chr5ptel1M 450495 450908 (549092) C L1M3_orf2#LINE/L1 (969) 2319 1870 m_b229s551i4 8985 chr5ptel1M 450495 CTTGGT-AAATGGACTCTTACTTATTTTGTGTTCTTTCATG--ACTTTTA 450541 - i vv i i vv i vi i v -- i v v C L1M3_orf2#LIN 2319 CTTGGTTAAGTTTATTCCTAAGTATTTTATTCTTTTTGATGCTATTGTAA 2270 chr5ptel1M 450542 ATATAATT------TTACTTTCCAGATCTTTTGGTGATTTGTTGATAATA 450585 ivi ------ v --- i iv i ii i v i i C L1M3_orf2#LIN 2269 ATGGGATTGTTTTCTTAATTTCC---TTTTCGGATAGTTCGTTGTTAGTG 2223 chr5ptel1M 450586 TAAAGAAAGGCTGAAGATTTGTTGTGGGTTTATTTCCTACCCTGTTGCTT 450635 v v vivv - iv v iv i ivi C L1M3_orf2#LIN 2222 TATAGAAACGCAACTGATTT-TTGTATGTTGATTTTGTATCCTGCAACTT 2174 chr5ptel1M 450636 TGCTGAAACTTTGTTCGTTTAA-AGTT--AGCAGTT------------CT 450670 i ------ v- -- i ------------ C L1M3_orf2#LIN 2173 TACTGAA------TTCGTTTATTAGTTCTAACAGTTTTTTGGTGGAGTCT 2130 chr5ptel1M 450671 CTAG---TTT-----------ATCAT--CAAATGCAAAGAATGATCATAT 450704 i --- ----------- -- vv v iv v v C L1M3_orf2#LIN 2129 TTAGGGTTTTCTACATATAAGATCATGTCATCTGCAAACAGAGATAATTT 2080 chr5ptel1M 450705 TGTTTCTTCTTT----AT--GCACGCATTCCCTTTCCCTTTCTTTATCTT 450748 ii i ---- -- v i v iiv ii -ii v C L1M3_orf2#LIN 2079 TACTTCTTCCTTTCCGATTTGGATGCCTTTTATTTCTTTTTCTT-GCCTA 2031 chr5ptel1M 450749 ATCGCTATAGCTAATATTTCTGACATTGTGTTAAATAATAGTGGTGATAA 450798 i v i iv i iiii i i i iv i v i C L1M3_orf2#LIN 2030 ATTGCTCTGGCTAGGACTTCCAGTACTATGTTGAATAGAAGTGGCGAGAG 1981 chr5ptel1M 450799 TAG--ATCTTTACTTCACTTTTGATCTTATGATAATGGATTCTAGTTTTT 450846 i -- i i i iii ii viiv vi v ii C L1M3_orf2#LIN 1980 TGGGCATCCTTGCCTTGTTCCTGATCTTAGAGGAAAAGCTTTCAGTTTTT 1931 chr5ptel1M 450847 AGTCTTTACACAAAATGTCAGCTTTTATTTTTACATAGATACCTGTTTAG 450896 vii v ivii vi i v vivi v v iv i- v C L1M3_orf2#LIN 1930 CACCATTGAGTATGATGTTAGCTGTGGGCTTTTCATATATGGCC-TTTAT 1882 chr5ptel1M 450897 TATATAAAGGCA 450908 i vi i C L1M3_orf2#LIN 1881 TATGTTGAGGTA 1870 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 43.04 CpG sites = 79, Kimura (unadjusted) = 44.43 Transitions / transversions = 1.52 (79/52) Gap_init rate = 0.06 (24 / 413), avg. gap size = 2.50 (60 / 24) 24 16.56 0.00 0.00 chr5ptel1M 451518 451565 (548435) (TGTATG)n#Simple_repeat 1 48 (0) m_b229s252i5 8986 chr5ptel1M 451518 TGTATGTGTGTGTGTCCATGTATGTATATGTCTATGTATATGTGTATG 451565 i vii i v i (TGTATG)n#Sim 1 TGTATGTGTATGTGTATGTGTATGTGTATGTGTATGTGTATGTGTATG 48 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 38 13.44 4.12 4.12 chr5ptel1M 452193 452289 (547711) (TCTGTC)n#Simple_repeat 1 97 (0) m_b229s252i6 8987 chr5ptel1M 452193 TCT-TCTCTGCCTCTGTCTCTATCTCTGTGTCTCTGTCTCTGTCGTTGTC 452241 - i i -- -- v v (TCTGTC)n#Sim 1 TCTGTCTCTGTCTCTGTCTCTGTCTC--TGTCTCTGTCTCTGTC--TCTG 46 chr5ptel1M 452242 TCTCTTTCTCTGTCT-TAACTCTGTCTGTGTCTCT-T-TTTTTCTCTGCC 452288 v - iv v - - i v i (TCTGTC)n#Sim 47 TCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTC 96 chr5ptel1M 452289 T 452289 (TCTGTC)n#Sim 97 T 97 Matrix = Unknown Transitions / transversions = 0.83 (5/6) Gap_init rate = 0.08 (8 / 96), avg. gap size = 1.00 (8 / 8) 31 0.00 0.00 0.00 chr5ptel1M 452291 452317 (547683) (TC)n#Simple_repeat 1 27 (0) c_b229s251i0 8988 chr5ptel1M 452291 TCTCTCTCTCTCTCTCTCTCTCTCTCT 452317 (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCT 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 24 0.00 0.00 0.00 chr5ptel1M 452318 452343 (547657) (AT)n#Simple_repeat 1 26 (0) m_b229s252i7 8989 chr5ptel1M 452318 ATATATATATATATATATATATATAT 452343 (AT)n#Simple_ 1 ATATATATATATATATATATATATAT 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 481 29.78 8.29 2.16 chr5ptel1M 454958 455307 (544693) C HERVK#LTR/ERVK (2339) 5197 4827 m_b229s701i0 8990 chr5ptel1M 454958 CTCCTTTTTCTTGTTTGACTAGGAATGTCTTAAGGGTTCTTTTAGCTCTT 455007 i i i i i ivviv ii i v v i C HERVK#LTR/ERV 5197 CCCCTTCTTTTTGTTTAACCAATTGAGCTTTGAGTGTTCTATTAGTTCTT 5148 chr5ptel1M 455008 TCAACTATGGCCTGACCTGAGGGGTTATAAGGAATCACATAAGTGATGTC 455057 v vi ii iv vvvv - v C HERVK#LTR/ERV 5147 TCAACTATGGCCTGTCCTTGGGAATTATAAGGAATTCCTGTTGT-ATGTG 5099 chr5ptel1M 455058 AAATTCAGAATCGAAGGACTGAAAACATTTTGAGGTG---TA----AGAA 455100 v i---- v vv i v i vv iii? --- ---- v C HERVK#LTR/ERV 5098 TAATTT----TCCACTGATTTAAGAATTTTTGGAANGCTTTACTACAGTA 5053 chr5ptel1M 455101 ----GGTCCATTATCTGTCTTTATCTGTTGAGGCACACCAATGGAGGCAA 455146 ---- i i v i v i v vv v v v ivi C HERVK#LTR/ERV 5052 TCCTGGCCCATTGTCAGTTTTAATTTTTTCTGGAACTCCCATGACAGCAA 5003 chr5ptel1M 455147 AACAATGAT-ATAAGTGAGAAATAACATGTTTTAGTGC-CTCTCCAAGTT 455194 - - i vvvvv -vvv i -i vivi C HERVK#LTR/ERV 5002 AACAA-GATAATAAATGTTTTTTAACATG-GGAAGTACTTTCTCCTGTCT 4955 chr5ptel1M 455195 GAAGAGTAGCTACTATAAAA-GTAGAATGAGTATCTACAGTTACATGAAC 455243 ivii v ivv i - - i v v i C HERVK#LTR/ERV 4954 GGCAGGTTGCCCATATGAAATGT-GAATAAGTATCAACTGTTACATGGAC 4906 chr5ptel1M 455244 ACATT---GTTCTCCA-----------GTGAGTAACATCCATTTGCCAGA 455279 ? v---i ii -----------i v i v C HERVK#LTR/ERV 4905 ANATGACAATCTTCCAAATGAAGGTACATGCGTGACATCCATTTGCCATA 4856 chr5ptel1M 455280 TATCATTAGG-CTTATCTCTTTGGGATTA 455307 vvv - vi vvi i C HERVK#LTR/ERV 4855 ACGCATTAGGACACAGACCTCTGGGATTA 4827 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 38.61 CpG sites = 47, Kimura (unadjusted) = 38.61 Transitions / transversions = 0.85 (47/55) Gap_init rate = 0.05 (17 / 349), avg. gap size = 2.18 (37 / 17) 193 25.57 0.00 5.88 chr5ptel1M 456221 456274 (543726) C L3b_3end#LINE/CR1 (22) 1184 1134 m_b229s601i0 8991 chr5ptel1M 456221 ATTGTAAAGGACATAAGAAGCCATTTGGGAGCCCATCACTCTCCCTGCTT 456270 v v v i i i --- i v ?i ivi C L3b_3end#LINE 1184 ATTGGAAAGGACCTCAGAGGTCATCT---AGTCCATCCCTNCCCCTAGCT 1138 chr5ptel1M 456271 TTAG 456274 i C L3b_3end#LINE 1137 CTAG 1134 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 32.81 CpG sites = 8, Kimura (unadjusted) = 32.81 Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.06 (3 / 53), avg. gap size = 1.00 (3 / 3) 261 27.71 4.82 0.00 chr5ptel1M 457241 457323 (542677) C DNM1r#Unknown (2100) 2562 2476 m_b229s502i0 8992 chr5ptel1M 457241 TGTCTCTGTCTGGCTCT-TGTGTA---ATACACACACACATGCACACATA 457286 i i i iv i - i?i --- i i i ii i C DNM1r#Unknown 2562 TGCCCCTGCCCTGTTCTATANATACGTATATATACACATATATACACACA 2513 chr5ptel1M 457287 TGCACACACACACTCACATGTGTACACACAAGCATGT 457323 i i i v i i vi i C DNM1r#Unknown 2512 TACACACATATACACACATATATACACACATACACGT 2476 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.80 CpG sites = 20, Kimura (unadjusted) = 39.06 Transitions / transversions = 6.67 (20/3) Gap_init rate = 0.02 (2 / 82), avg. gap size = 2.00 (4 / 2) 239 23.77 1.92 2.91 chr5ptel1M 459269 459372 (540628) C L1M5_orf2#LINE/L1 (2363) 931 829 m_b229s551i5 8993 chr5ptel1M 459269 TTTTTTCTCTTTCATTGATATAACCATTTGCATATATCAGTTTCCTTCTA 459318 i - -- i ?v iv?vv v i i C L1M5_orf2#LIN 931 TTTCTTCT-TTTC--TAATATANGCATTTAANGCTATAAATTTCCCTCTA 885 chr5ptel1M 459319 AGTATTATTTTGGCTGAATCTCAAAAATTTTG-T-TGTTGTCTCACTGTT 459366 i i ii i v i v - - v iviii C L1M5_orf2#LIN 884 AGCACTGCTTTAGCTGCATCCCACAAATTTTGATATGTTGTATTTTCATT 835 chr5ptel1M 459367 ATCATT 459372 ? C L1M5_orf2#LIN 834 NTCATT 829 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 30.45 CpG sites = 15, Kimura (unadjusted) = 30.45 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.05 (5 / 103), avg. gap size = 1.00 (5 / 5) 457 26.47 0.76 5.56 chr5ptel1M 459407 459538 (540462) MIRc#SINE/MIR 2 127 (141) m_b229s601i1 8994 chr5ptel1M 459407 GGAGCTGGGTGGTGCATTGAATAGAACATCAGCCCTGAAGTCAAGAGGAG 459456 ii v v v i v i iii v i i i i v MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr5ptel1M 459457 CTGAGTTCAAATCTGGCCTCAGACACTTAACACTTCCTAGATGTGTGACC 459506 i i i iv v v v ------- v MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTGACC 94 chr5ptel1M 459507 CTGGGCAAGTCATTTAACTCCAGTT-GCCTCAG 459538 i i ii vv v- MIRc#SINE/MIR 95 TTGGGCAAGTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 32.01 CpG sites = 19, Kimura (unadjusted) = 33.23 Transitions / transversions = 1.36 (19/14) Gap_init rate = 0.06 (8 / 131), avg. gap size = 1.00 (8 / 8) 16 14.21 0.00 0.00 chr5ptel1M 459541 459571 (540429) (AAAC)n#Simple_repeat 1 31 (0) m_b229s252i9 8995 chr5ptel1M 459541 AAACAAACAAACAAACAAATAAAAAGAAAAA 459571 i v i v (AAAC)n#Simpl 1 AAACAAACAAACAAACAAACAAACAAACAAA 31 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 237 23.30 9.71 4.35 chr5ptel1M 459585 459759 (540241) C L1M1_orf2#LINE/L1 (2533) 761 578 m_b229s551i6 8996 chr5ptel1M 459585 TTATTCATTTTCCAAGTATTTTT----TGTCAAAGA--CCTCTTATTAT- 459627 i i v v i v ---- v v i -- i - C L1M1_orf2#LIN 761 TTGTTTAATTTCCATGTGTTTGTATAGTTTCCAAAATTCCTCTTGTTATT 712 chr5ptel1M 459628 -AT--ATAGTTTTATTGCATTATGATCAGGAAAAAATGTT---TACTATT 459671 - --v v i i - i i i --- i C L1M1_orf2#LIN 711 GATTTCTAGTTTTATTCCATTGTGGTCA-GAGAAGATGCTTGATATTATT 663 chr5ptel1M 459672 TTTACTATAATGCATTTTTGTAAG----GTTCTTGTGCCCTAATTCATGA 459717 iv i v vv v v - ---- - v ivi i C L1M1_orf2#LIN 662 TCAATTTTTTTGAATGTTT-TAAGACTTGTT-TTGTGACCTAACATATGG 615 chr5ptel1M 459718 TCAGTTTTTTTGAGAAAGTTCCACACGTAGCTGAGAAATAGA 459759 -- v ii v v -- i - i v C L1M1_orf2#LIN 614 TC--TATCCTTGAGAATGATC--CATGT-GCTGAGGAAAAGA 578 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 28.25 CpG sites = 20, Kimura (unadjusted) = 28.25 Transitions / transversions = 1.05 (20/19) Gap_init rate = 0.09 (15 / 174), avg. gap size = 1.67 (25 / 15) 271 33.06 4.72 4.72 chr5ptel1M 460205 460331 (539669) C MIR1_Amn#SINE/MIR (100) 130 4 m_b229s601i3 8997 chr5ptel1M 460205 ATTAAGGC----AGAGGTTAGGTCACTTGTCCAGGATCAT--AGTTAGGA 460248 i i ---- ? i v i i i i-- i?i v? C MIR1_Amn#SINE 130 ACTGAGGCNCAGAGAGGTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCN 81 chr5ptel1M 460249 AGGGACTAAGATCTGATTTGAACTCAAGTCTTTTCACCTTAGGCCCAGTG 460298 v i vi vivv ? ? i i iiiv viiivi i C MIR1_Amn#SINE 80 AGTGGCAGAGCCGGGANTNGAACCCAGGTCTCCCGAGTCCCAGTCCAGTG 31 chr5ptel1M 460299 CTCTTCTATTTCCTTAGCCACGGAGCTGCTTCC 460331 --- iiv vii ---i i C MIR1_Amn#SINE 30 C---TCTATCCACTAGACCAC---ACTGCCTCC 4 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 46.30 CpG sites = 28, Kimura (unadjusted) = 49.91 Transitions / transversions = 2.33 (28/12) Gap_init rate = 0.06 (8 / 126), avg. gap size = 1.50 (12 / 8) 345 29.29 7.07 0.00 chr5ptel1M 460205 460303 (539697) C MIRc#SINE/MIR (140) 128 23 m_b229s601i2 8997 chr5ptel1M 460205 ATTAAGGC----AGAGGTTAGGTCACTTGTCCAGGAT--CATAGTTAGGA 460248 i i ---- i v i i i -- i i v C MIRc#SINE/MIR 128 ACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTA 79 chr5ptel1M 460249 AGGGACTAAGATCTGATTTGAACTCAAGTCTT-TTCACCTTAGGCCCAGT 460297 v i vi vivv i i i i -i v iii i i C MIRc#SINE/MIR 78 AGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGT 29 chr5ptel1M 460298 GCTCTT 460303 C MIRc#SINE/MIR 28 GCTCTT 23 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 36.03 CpG sites = 21, Kimura (unadjusted) = 39.57 Transitions / transversions = 2.62 (21/8) Gap_init rate = 0.03 (3 / 98), avg. gap size = 2.33 (7 / 3) 34 23.28 1.16 0.00 chr5ptel1M 460332 460417 (539583) (ATAGT)n#Simple_repeat 1 87 (0) m_b229s252i10 8998 chr5ptel1M 460332 ATTGTATAGTATGGTATAGTATAGTAGAGCATAGTATAGCATATTATAAT 460381 v i v i i v i (ATAGT)n#Simp 1 ATAGTATAGTATAGTATAGTATAGTATAGTATAGTATAGTATAGTATAGT 50 chr5ptel1M 460382 GTAGTGTTGAGTAGTGTAGTAGAATGTAGAATA-TAT 460417 i i v vi i v i i v - (ATAGT)n#Simp 51 ATAGTATAGTATAGTATAGTATAGTATAGTATAGTAT 87 Matrix = Unknown Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.01 (1 / 85), avg. gap size = 1.00 (1 / 1) 16 27.83 5.19 2.53 chr5ptel1M 460412 460488 (539512) (AT)n#Simple_repeat 1 79 (0) m_b229s252i11 8999 chr5ptel1M 460412 ATATATGTCTTTTTAAATAT-TGTCTATA-ACATATTAATA-ACATGTTT 460458 i v v v v - i v - i vv - i i v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr5ptel1M 460459 CATATA-ATATACTTTATATATACACACATA 460488 - - - v i i i (AT)n#Simple_ 51 -ATATATATATA-TATATATATATATATATA 79 Matrix = Unknown Transitions / transversions = 0.89 (8/9) Gap_init rate = 0.08 (6 / 76), avg. gap size = 1.00 (6 / 6) 16 19.09 0.00 0.00 chr5ptel1M 460903 460932 (539068) (T)n#Simple_repeat 1 30 (0) m_b229s252i12 9000 chr5ptel1M 460903 TTTTTTTCTTTTTTCTTTTGTTTTGTCTTT 460932 i i v v i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 30 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 43 0.00 0.00 0.00 chr5ptel1M 461061 461097 (538903) (AT)n#Simple_repeat 1 37 (0) c_b229s251i1 9001 chr5ptel1M 461061 ATATATATATATATATATATATATATATATATATATA 461097 (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATA 37 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 230 33.67 8.16 0.00 chr5ptel1M 462497 462594 (537406) C L2a_3end#LINE/L2 (21) 496 391 m_b229s601i4 9002 chr5ptel1M 462497 TTATCAAGTACATACCATATGCCAGATACTTCACTTAGTGAGGTGGAT-- 462544 ii ii v i i ii viv vi i vv v -- C L2a_3end#LINE 496 TTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGCGCTGGGGATAC 447 chr5ptel1M 462545 AACAATTAA-AAAGCAAACAGG----CCTCTCCTCAAGGAACTTGTATTT 462589 i i v - i i ii---- vi v i ii i C L2a_3end#LINE 446 AGCAGTGAACAAAACAGACAAAAGTCCCTGCCCTCATGGAGCTTACATTC 397 chr5ptel1M 462590 CA-TGG 462594 i - C L2a_3end#LINE 396 TAGTGG 391 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 43.74 CpG sites = 23, Kimura (unadjusted) = 48.07 Transitions / transversions = 2.30 (23/10) Gap_init rate = 0.04 (4 / 97), avg. gap size = 2.00 (8 / 4) 689 23.43 10.88 0.47 chr5ptel1M 463350 463542 (536458) C MIR#SINE/MIR (0) 262 50 m_b229s601i5 9003 chr5ptel1M 463350 AATAATAACTAACATCAAAT-AGTGATTATTGTGTGCAAAGCACT----- 463393 i iv v - i v i i v i ----- C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCT 213 chr5ptel1M 463394 -------TTACAATTATTATCTCATTTGATGCTCACAACTATCCCGGGAG 463436 ------- vv v i v v i iiv C MIR#SINE/MIR 212 AAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAG 163 chr5ptel1M 463437 GTAGATGCTGTCGTTATCCCCATTTTATAACTGAAGAAACTGAAGCA--- 463483 i i i ii i iv i i --- C MIR#SINE/MIR 162 GTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAG 113 chr5ptel1M 463484 AATGGTCGAAGTGACTTGCCCAGGGTCAC---CCTGATAGGTCG-GGGGC 463529 iv i- i i ---v ii i v -i i C MIR#SINE/MIR 112 AGAGGTT-AAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGC 64 chr5ptel1M 463530 TGGG-TTTGAACTC 463542 i - i i C MIR#SINE/MIR 63 CGGGATTCGAACCC 50 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 26.86 CpG sites = 31, Kimura (unadjusted) = 29.14 Transitions / transversions = 2.21 (31/14) Gap_init rate = 0.04 (8 / 192), avg. gap size = 2.75 (22 / 8) 14 27.27 0.00 2.04 chr5ptel1M 466446 466495 (533505) (AAAAT)n#Simple_repeat 1 49 (0) m_b229s252i13 9004 chr5ptel1M 466446 AAAACATAATTACATGCAGATTAAATAAATGAAAGAAAAATAAAATAAAA 466495 i v v v -v i v vv iv (AAAAT)n#Simp 1 AAAATAAAATAAAAT-AAAATAAAATAAAATAAAATAAAATAAAATAAAA 49 Matrix = Unknown Transitions / transversions = 0.38 (3/8) Gap_init rate = 0.02 (1 / 49), avg. gap size = 1.00 (1 / 1) 577 17.08 2.38 2.38 chr5ptel1M 468778 468903 (531097) C Charlie1a#DNA/hAT-Charlie (0) 1455 1330 m_b229s502i1 9005 chr5ptel1M 468778 CAGTGGTTCTCAAACTTTT-GTTTTCAGTATC--TTTATCCTATTAAAAA 468824 i - v i v i -- iv v C Charlie1a#DNA 1455 CAGCGGTTCTCAAACTTTTTGGTCTCAGGACCCCTTTACACTCTTAAAAA 1406 chr5ptel1M 468825 TGATTGAGGATCTCTCCAAAGCATTTTTGTTTATCTGGATTATATTTATA 468874 v i --- vii v i i v C Charlie1a#DNA 1405 TTATTGAGGACC---CCAAAGAGCTTTTGTTTATGTGGGTTATATCTATC 1359 chr5ptel1M 468875 CACATTTACCATATTGGAAATAAAAACTG 468903 v i i v C Charlie1a#DNA 1358 GATATTTACCATATTAGAAATTAAAACTG 1330 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 18.52 CpG sites = 11, Kimura (unadjusted) = 19.50 Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.04 (5 / 125), avg. gap size = 1.20 (6 / 5) 388 29.42 0.00 1.18 chr5ptel1M 468894 468979 (531021) C Charlie1b#DNA/hAT-Charlie (438) 85 1 m_b229s502i2 9005 chr5ptel1M 468894 ATAAAAACTGTTCTTGAATTTGTAGATCCTCTAAAGGGGTTTCAGAGATC 468943 i iv - vi i ii i i i i i i i i C Charlie1b#DNA 85 ATGAAAATAGTT-TTGACCTCGCGGACCCCCTGAAAGGGTCTCGGGGACC 37 chr5ptel1M 468944 CCCAGGATTCTCTACACCATACTTTGAGAACCATTG 468979 iv i iiv i ii C Charlie1b#DNA 36 CCCAGGGGTCCCCGGACCACACTTTGAGAACCGCTG 1 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 30.63 CpG sites = 21, Kimura (unadjusted) = 41.43 Transitions / transversions = 5.25 (21/4) Gap_init rate = 0.01 (1 / 85), avg. gap size = 1.00 (1 / 1) 299 27.39 2.80 15.75 chr5ptel1M 468985 469127 (530873) C L2a_3end#LINE/L2 (2) 515 389 m_b229s601i6 9006 chr5ptel1M 468985 TCAGTCATTCATCA----TTTATTAAGTACCTACAATGTCACAGATATGG 469030 v v ---- i ii v vv ii iv C L2a_3end#LINE 515 TCATTCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTG 466 chr5ptel1M 469031 TGATAAGCCCTGGAGATGCAAAAATTGGCATCCCCCCAAAACAACAACAA 469080 vv i v i i iv i -- v ------ -----i C L2a_3end#LINE 465 TTCTAGGCGCTGGGGATACAGCAGT--GAA------CAAAACA-----GA 429 chr5ptel1M 469081 CAAAAACATCTAGTCCTTTTCTTCAAGGAGTTTACAAGCTGATGGGG 469127 ------- i vi i v i vv ii C L2a_3end#LINE 428 CAAA-------AGTCCCTGCCCTCATGGAGCTTACATTCTAGTGGGG 389 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 32.40 CpG sites = 18, Kimura (unadjusted) = 33.77 Transitions / transversions = 1.20 (18/15) Gap_init rate = 0.15 (21 / 142), avg. gap size = 1.14 (24 / 21) 181 32.30 7.20 9.69 chr5ptel1M 468998 469261 (530739) C L2d2_3end#LINE/L2 (19) 536 279 m_b229s601i7 9006 chr5ptel1M 468998 ATTTATTAAGTACCTACAATGTCACAGATATGGTGATAAGCCCTG---GA 469044 i ii vi vvv ii iv v i v --- i C L2d2_3end#LIN 536 ATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGTGGGG 487 chr5ptel1M 469045 GATGCAAAAATTGGCATCCCCCCAAAACAACAACAACAAAAACATCTAGT 469094 i i --i i --------------------- i --i C L2d2_3end#LIN 486 GATACAAAGA--AGTAT---------------------AAGACAT--GGT 462 chr5ptel1M 469095 CCTTTTCTTCAAGGAGTTTACAAGCTGATGGGGAAGATGATGCA-AGGTA 469143 i vi i i v ii v i ii vi - iii C L2d2_3end#LIN 461 CCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGGAGACAAGACATAAACA 412 chr5ptel1M 469144 TGCACAAGATTAA--AAAAAT----GAATT-AATAGGAGGGCACTGGAAT 469186 i iiv ii -- v ---- v - iv vv vviv i C L2d2_3end#LIN 411 CGTGAAAAGTTAAATAACAATACAAGATTTAAATAACAGTTCAAGACAAC 362 chr5ptel1M 469187 CA-AGAAGAGTTG-AAAAAGGCA--ACAAGACAAATAGGTAATTCA---G 469229 v - v -v v -- v iv v vi v v --- C L2d2_3end#LIN 361 AATAGAAGAGATGTCACAAGGCAGTACATGATTAATTGCCAAATGAATGG 312 chr5ptel1M 469230 TAAATATAAT-GCTGGTATTGGAGTCAAGAAGA 469261 v v i -i? v v iv i C L2d2_3end#LIN 311 TACAGACAATAANTGCTATAGGAGTTCAGAGGA 279 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 41.79 CpG sites = 42, Kimura (unadjusted) = 43.37 Transitions / transversions = 1.20 (42/35) Gap_init rate = 0.13 (35 / 263), avg. gap size = 1.26 (44 / 35) 402 30.02 1.37 6.47 chr5ptel1M 469221 469366 (530634) MIRc#SINE/MIR 10 148 (120) m_b229s601i8 9007 chr5ptel1M 469221 GTAATTCAGTAAATATAATGCTGGTATTGGAGTCAAGAAGACTCATCTTT 469270 ii v ii v v iii vv i ---- -- MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC----CT-- 53 chr5ptel1M 469271 CCAAGTTTCAAAACTGGCCTCAGACATTTACTGTCTGTATAACCCT-GGC 469319 ---i v i iv iv v v v i iv i i i - MIRc#SINE/MIR 54 ---GGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGC 100 chr5ptel1M 469320 AAGTCACATAAGC-CTGTTGGCCTCGTTTTCTTCATCAGTAAAGTAAG 469366 v v - v vi iv i v i ii MIRc#SINE/MIR 101 AAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 37.88 CpG sites = 23, Kimura (unadjusted) = 39.10 Transitions / transversions = 1.28 (23/18) Gap_init rate = 0.08 (11 / 145), avg. gap size = 1.00 (11 / 11) 1074 29.18 3.69 3.69 chr5ptel1M 470066 470823 (529177) L1M5_orf2#LINE/L1 2537 3294 (0) m_b229s551i7 9008 chr5ptel1M 470066 AGTTCATATGGAAAAACAAAAGGTCAAGAAT-TTCAAGGGAATTAATGAA 470114 i i vi i ii ? -vi iiv iv- L1M5_orf2#LIN 2537 AATTTATATGGAAATGCAAAGGACCNAGAATAGCCAAAACAATCT-TGAA 2585 chr5ptel1M 470115 AAAAAA-ATCAAATGATGGTGG-CTTAGCTGTACCAGATCT-AAAATTAT 470161 i - v - v v - - vv ? ? - i i - L1M5_orf2#LIN 2586 AAAGAAGAACAAA-GTTGGAGGACTTA-CACTACCNGATNTCAAGACT-T 2632 chr5ptel1M 470162 ATTATAGAGCAGCAGTTACCAAAACTATTTGGTATTGGC-TAAGGAATAG 470210 i vi v i i vi v - - L1M5_orf2#LIN 2633 ATTATAAAGCTACAGTAATCAAGACAGTGTGGTATTGGCGTAAGGA-TAG 2681 chr5ptel1M 470211 ATTAGTTGATCAGTGGAATAGATTAG---GTTCAAGGGACAAAACAGTCA 470257 iv i v i i v --- i - ii i i v --- L1M5_orf2#LIN 2682 ACAAATAGATCAATGGAACAGAATAGAGAGTCCA-GAAATAGACC---CA 2727 chr5ptel1M 470258 -ACAAATATAGCAACCTAGTCTTTGACAAAC---CCAAAG-ATCCCAGCT 470302 - v i ?v ?i ii i v--- ? - vii -- L1M5_orf2#LIN 2728 CACATATATGGNCANTTGATTTTTGACAAAGGTGCCAANGCAATTCAG-- 2775 chr5ptel1M 470303 TTTGGGATAAGAACTTACTGTTTGATAAAAATTGCTGGGAAAATTGGAAA 470352 -- iv i ivvv v ii i viv i v v L1M5_orf2#LIN 2776 --TGGGGAAAGGATAGTCTTTTCAACAAATGGTGCTGGAACAATTGGATA 2823 chr5ptel1M 470353 CTAATATGGCAGAAACTAGGCATTGATCCATACTTAACGCCATACACCAA 470402 iiv v i v iii?v i i v i v i v L1M5_orf2#LIN 2824 TCCATATGGAAAAAAATGAANCTCGACCCCTACCTCACACCATACACAAA 2873 chr5ptel1M 470403 GATAAGGTCAAAATGGGTTCAT-GACCTAGGCATAAAGAATGAAATTATT 470451 i v iv ? i i - - iiii ii? i i v L1M5_orf2#LIN 2874 AATTAATTCNAGATGGAT-CATAGACCTAAATGTAAAAGNTAAAACTATA 2922 chr5ptel1M 470452 AATAAATTAGAGGAA--CATAGGATAGTTTACCTCTCAGACCTGTGGA-A 470498 vvvvi i -- v i -- i iivv vv ?- L1M5_orf2#LIN 2923 AAACTTCTAGAAGAAAACATAGGAGAAT--ATCTTCGTGACCTTGGGNTA 2970 chr5ptel1M 470499 GGGGAAGGTCTTTATGACCAAAGCAGAACTAGAGATCATTACTGATCACA 470548 vi i i i - i v iii v -- i -----i ?i i i L1M5_orf2#LIN 2971 GGCAAAGATTTCT-TAAACAGGACACAA--AAAG-----CACNAACCATA 3012 chr5ptel1M 470549 AAATAGAAAATT-------TCGATTATACCAAACTGAAAAGTTTTTGTAC 470591 v i ------- v i ?i i v v ii i iv L1M5_orf2#LIN 3013 AAAGAAAAAATTGATAAATTGGACTNCATCAAAATTAAAAACTTCTGCTC 3062 chr5ptel1M 470592 AAACAAAACTAATGCAGACAAGATTAGAAGGGAAGCAATAAACTGGGAAA 470641 ?vvv ivi vi ivi v i v i v v i i ? i L1M5_orf2#LIN 3063 NTCAAAAGACACCGTTAAGAAAATGAAAAGGCAAGCCACAGANTGGGAGA 3112 chr5ptel1M 470642 ATATTTTTACAGTCAAAGGT-TCTGATAAAGGCCTCATTTCCAAAATATA 470690 v v i i?- v vi - i v i v i L1M5_orf2#LIN 3113 AAATATTTGCAAN-ACATATATCTGACAAAGGACTCGTATCCAGAATATA 3161 chr5ptel1M 470691 TAGAGAATTAACTCTAATTTA-TAAAAAATCAAGCCATTC--TCCAATTG 470737 i i v- vi ? i - ? -- v vv --i v? L1M5_orf2#LIN 3162 TAAAGAACTC-CTACAANTCAATAANAAA--AAGACAAACAACCCAATAN 3208 chr5ptel1M 470738 AAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGAAGAAATTGAA 470787 v i iv v v i v v ?v L1M5_orf2#LIN 3209 AAAAATGGGCAAAAGACTTGAACAGACACTTCACAAAAGAAGATATNCAA 3258 chr5ptel1M 470788 ACTATTTCTAGTCATATGAAAAGATGCTCCAAGTCA 470823 iviiivv iv i v v? L1M5_orf2#LIN 3259 ATGGCCAATAAGCACATGAAAAGATGCTCAACNTCA 3294 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 38.33 CpG sites = 121, Kimura (unadjusted) = 39.28 Transitions / transversions = 1.32 (121/92) Gap_init rate = 0.06 (44 / 757), avg. gap size = 1.27 (56 / 44) 1648 27.47 0.36 1.66 chr5ptel1M 470680 471227 (528773) L1ME3G_3end#LINE/L1 7 547 (377) m_b229s551i8 9008 chr5ptel1M 470680 TCCAAAATATATAGAGAATTAACTCTAATTTATAAAAAATCAAGCCATTC 470729 i i i vviv v iv i -- v --v L1ME3G_3end#L 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAA--AAGACA--A 52 chr5ptel1M 470730 TCCAATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGAAG 470779 i v v i v v i L1ME3G_3end#L 53 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chr5ptel1M 470780 AAATTGAAACTATTTCTAGTCATATGAAAAGATGCTCCAAGTCATTATTA 470829 vv iviiivv iv v vv i v L1ME3G_3end#L 103 AAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTA 152 chr5ptel1M 470830 ATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACACCTGT 470879 i i vv i i viv ii L1ME3G_3end#L 153 ATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCAT 202 chr5ptel1M 470880 CAGATTGGCTAAGATGACAGGAAAAAATAATGATGATTGTTGGAGGGGAT 470929 v i vvv iii?vvi ivi? v v i i L1ME3G_3end#L 203 CAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGT 252 chr5ptel1M 470930 GCGGGAAAACTGGGACATTGATGCATTGTTGGTGGAGTTGTGAACGAATC 470979 i i v v vi v i i i iiv i ivii v L1ME3G_3end#L 253 GTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTA 302 chr5ptel1M 470980 CAACCATTTTGGAGAGTAGTTTGGAACTATGCTCAAAAAGTTATCAAACT 471029 i ? i i i v v - vvv i -- i v L1ME3G_3end#L 303 CAGCCNTTTTGGAGGGCAATTTGGCAGTAT-CTATTAAAAT--TTAAAAT 349 chr5ptel1M 471030 GTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGATTATATCCCAAAG 471079 i i i vii v ? ?v v i ? L1ME3G_3end#L 350 GCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAG 399 chr5ptel1M 471080 AGATTAT-AAAGAAG-GGAAAGGGACCTGTATGTGCACGAATGTTTGTGG 471127 i vv -iv v v - v v i --? i i v i ii v L1ME3G_3end#L 400 AAATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTCATTG 447 chr5ptel1M 471128 CAGCCCTTTTTGTAGTGGCTAGAAACTGGAAACTGAATGGATGTCCATCA 471177 vi v i i v i i vivv ii L1ME3G_3end#L 448 CAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCA 497 chr5ptel1M 471178 GTTGGAGAATGGCTGAATAAATTGTGGTATATGAAAATTATGGAATATTA 471227 i v i i i i vv v i i L1ME3G_3end#L 498 ATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACTA 547 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 34.70 CpG sites = 78, Kimura (unadjusted) = 35.29 Transitions / transversions = 1.11 (78/70) Gap_init rate = 0.02 (11 / 547), avg. gap size = 1.00 (11 / 11) 13 15.89 5.71 0.00 chr5ptel1M 471760 471794 (528206) (AAATA)n#Simple_repeat 1 37 (0) m_b229s252i14 9009 chr5ptel1M 471760 AAATAAAAGGCTATTAAATAAAAT-AAAT-AAATAAA 471794 vivv v - - (AAATA)n#Simp 1 AAATAAAATAAAATAAAATAAAATAAAATAAAATAAA 37 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 36 41.00 1.86 2.24 chr5ptel1M 472550 472818 (527182) (TTCT)n#Simple_repeat 1 268 (0) m_b229s252i15 9010 chr5ptel1M 472550 TTATTTCTTTTATTGATTTC-ATCCTTCCCTCTTTCCCTTCCTCCCTTCT 472598 v - v vv -v i ii - i i i i (TTCT)n#Simpl 1 TTCTTTC-TTTCTTTCTTTCTTTCTTTCTTTCTTT-CTTTCTTTCTTTCT 48 chr5ptel1M 472599 TCCTTTTCTCTTTTTCTCCCTTTGTCTC-CTCTTCCCTTGTTCTTTTCTC 472647 i - i i ii v i -i i i v ii i (TTCT)n#Simpl 49 TTC-TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 97 chr5ptel1M 472648 TCCTCCCTCCCTCCCTTCCTGCTTT-TTGCTCTCCTTTC-TT-TTTCTTT 472694 i i i i i i i i v - v - i - - (TTCT)n#Simpl 98 TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT-TTCTTTCTTTCTTTCTTT 146 chr5ptel1M 472695 CTTCTATGCCTTCCTTCCTCCCTCTTTTCCTTTCTTCCTCCCTTCATTTT 472744 - v vi i i ii i i i i ii iv i (TTCT)n#Simpl 147 CTT-TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC 195 chr5ptel1M 472745 TTTCCTTCCTCCCCTCCTGTGCCCCTCCCTTCCTTCCTTTTTCTCTTCCT 472794 - i ii i i v viii ii i i i i i (TTCT)n#Simpl 196 TTT-CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 244 chr5ptel1M 472795 CTCTCTGTCTGTGTCTGTCTTTCT 472818 i i v i v v v (TTCT)n#Simpl 245 TTCTTTCTTTCTTTCTTTCTTTCT 268 Matrix = Unknown Transitions / transversions = 3.28 (59/18) Gap_init rate = 0.04 (11 / 268), avg. gap size = 1.00 (11 / 11) 15 8.85 5.00 5.00 chr5ptel1M 472786 472825 (527175) (TCTCTG)n#Simple_repeat 1 40 (0) m_b229s252i16 9011 chr5ptel1M 472786 TCTCT-TC-CTCTCTCTGTCTGTGTCTGTCTTTCTCTGTCTC 472825 - - v v -- v (TCTCTG)n#Sim 1 TCTCTGTCTCTGTCTCTGTCTCTGTC--TCTGTCTCTGTCTC 40 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.10 (4 / 39), avg. gap size = 1.00 (4 / 4) 40 0.00 0.00 0.00 chr5ptel1M 472830 472863 (527137) (AC)n#Simple_repeat 1 34 (0) c_b229s251i2 9012 chr5ptel1M 472830 ACACACACACACACACACACACACACACACACAC 472863 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACAC 34 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 14 27.73 0.00 2.04 chr5ptel1M 475148 475197 (524803) (TAAAAT)n#Simple_repeat 1 49 (0) m_b229s252i17 9013 chr5ptel1M 475148 TAATATTAAAAGAAAAATTAAAGTTAAATTGATCATTTATTTTTAAAATT 475197 v vv i v v -v v vvv (TAAAAT)n#Sim 1 TAAAATTAAAATTAAAATTAAAATTAAAATTA-AAATTAAAATTAAAATT 49 Matrix = Unknown Transitions / transversions = 0.10 (1/10) Gap_init rate = 0.02 (1 / 49), avg. gap size = 1.00 (1 / 1) 657 32.77 3.29 2.03 chr5ptel1M 475265 475507 (524493) C MIRb#SINE/MIR (10) 258 13 m_b229s601i9 9014 chr5ptel1M 475265 CTATCATTTATATGGCATTTA---TGTGCCCAGCATTGTATTAAGTACCT 475311 i vvi ii --- vi i ii ii i C MIRb#SINE/MIR 258 CTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTT 209 chr5ptel1M 475312 TCTAATTGTTATTTCATTTGTTCTT---AATAATCTTGAGGGGTAGATGC 475358 vi vvii i iv i --- i i i v i i i- C MIRb#SINE/MIR 208 TACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTA- 160 chr5ptel1M 475359 TTTTATTATCTTTTTTTTTTCAGGTGAGGAAA-TGAAGGTAAATGAATGC 475407 -- iiiv v- i - i v v iv i- i C MIRb#SINE/MIR 159 --TTATTATCCCCATTTTA-CAGATGAGGAAACTGAGGCTCAGAGAG-GT 114 chr5ptel1M 475408 TAATTAATTTCTCAAGGGTTACACAGCTAATAAATTTTGAAGGCCAAATT 475457 v i vi v i i i i vviii v vii C MIRb#SINE/MIR 113 TAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATT 64 chr5ptel1M 475458 TGAATCTAGTGCTTTTTGACTCCAGATTCAGCA-TTTATCCACTCCACCA 475506 i i i vv v i i vi v ii- i v v C MIRb#SINE/MIR 63 CGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCACCA 14 chr5ptel1M 475507 C 475507 C MIRb#SINE/MIR 13 C 13 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 42.97 CpG sites = 51, Kimura (unadjusted) = 45.48 Transitions / transversions = 1.89 (51/27) Gap_init rate = 0.04 (9 / 242), avg. gap size = 1.44 (13 / 9) 13 6.99 10.00 0.00 chr5ptel1M 476457 476486 (523514) (TATCC)n#Simple_repeat 1 33 (0) m_b229s252i18 9015 chr5ptel1M 476457 TATCCTAT-CTAACCTA--CTATTCTATCCTAT 476486 - v -- i (TATCC)n#Simp 1 TATCCTATCCTATCCTATCCTATCCTATCCTAT 33 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.07 (2 / 29), avg. gap size = 1.50 (3 / 2) 305 33.12 4.14 3.53 chr5ptel1M 476509 476677 (523323) C MIRc#SINE/MIR (3) 265 96 m_b229s601i10 9016 chr5ptel1M 476509 AATACTAATACATTATATTTTT---GTGTTATATAGTTAGCAAAATATAT 476555 v i? v i v --- iii v i vi iiiiv C MIRc#SINE/MIR 265 AATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCGCTT 216 chr5ptel1M 476556 TCACAAATACTTTCTAATTTTTTTC-CACAA-AACATCTGTGAGGTAAGT 476603 v i i v v vv i - - -i i i C MIRc#SINE/MIR 215 TCACATACATTATCTCATTTGATCCTCACAACAAC-CCTGTGAGGTAGGC 167 chr5ptel1M 476604 AGCACAGGCATTGTTAAGGACTATTATGTTTATCGGTCCTAAAACCGAGA 476653 vi i i ---- iivii - iv i vvvi i i C MIRc#SINE/MIR 166 AGGGCAGGTATTATT----ATCCCCAT-TTTACAGATGAGGAAACTGAGG 122 chr5ptel1M 476654 TTC--ATAGTTTAAATTATTTGTCTA 476677 i -- v v i v i i i C MIRc#SINE/MIR 121 CTCAGAGAGGTTAAGTGACTTGCCCA 96 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 44.93 CpG sites = 34, Kimura (unadjusted) = 46.27 Transitions / transversions = 1.70 (34/20) Gap_init rate = 0.06 (10 / 168), avg. gap size = 1.30 (13 / 10) 16 10.82 0.00 3.23 chr5ptel1M 476776 476807 (523193) (TTTG)n#Simple_repeat 1 31 (0) m_b229s252i19 9017 chr5ptel1M 476776 TTTGGGTTTTTGTTTGTTTGTTTGTTTTGTTT 476807 vv v - (TTTG)n#Simpl 1 TTTGTTTGTTTGTTTGTTTGTTTG-TTTGTTT 31 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 379 27.90 0.00 8.93 chr5ptel1M 477434 477555 (522445) MIRc#SINE/MIR 4 115 (153) m_b229s601i11 9018 chr5ptel1M 477434 GGCAGCTAGGTGGCACAGTGAATAGAGCAGCAACCCTAAAGTCAGGAGGA 477483 i--- ii i v viiiv i ii i MIRc#SINE/MIR 4 GGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA 50 chr5ptel1M 477484 CCTGAGTACAAATTTGGCCTCAGACACTTAACACTTTCTACCTGTGTGAT 477533 i v i i iiv v v v ------- v i MIRc#SINE/MIR 51 CCTGGGTTCGAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTGAC 93 chr5ptel1M 477534 CCTGGACAAGTCACTGAACTCC 477555 i i v ii MIRc#SINE/MIR 94 CTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 34.65 CpG sites = 21, Kimura (unadjusted) = 36.13 Transitions / transversions = 2.10 (21/10) Gap_init rate = 0.08 (10 / 121), avg. gap size = 1.00 (10 / 10) 17 11.26 2.27 7.14 chr5ptel1M 477567 477610 (522390) (TAA)n#Simple_repeat 1 42 (0) m_b229s252i20 9019 chr5ptel1M 477567 TAAAAAAAATTAATGATAATAATAATAATTAATGTATAA-AATAA 477610 v v - i - -v - (TAA)n#Simple 1 TAATAATAA-TAATAATAATAATAATAA-TAAT-AATAATAATAA 42 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.09 (4 / 43), avg. gap size = 1.00 (4 / 4) 298 29.84 1.69 3.45 chr5ptel1M 478989 479106 (520894) C L2b_3end#LINE/L2 (290) 176 61 m_b229s601i12 9020 chr5ptel1M 478989 AAAAGGTAGGGGAAGGACAGCATCCTAGGCAGGCAGAACAGCAAGAAAAA 479038 i - --- i i i ivi ? viv C L2b_3end#LINE 176 AAGAGGT-GGGGAAGG---GCGTTCCAGGCAGAGGGAACAGCANGTGCAA 131 chr5ptel1M 479039 TTATCTGGAGTTGAGA-TGA-TATGTCTTATTTGTGGAACAGCAAAGAGG 479086 vvii iv vi i -? -i? v v i i v i C L2b_3end#LINE 130 AGGCCCTGAGGCGGGAGNGAGCNTGGCGTGTTCGAGGAACAGCAAGGAGG 81 chr5ptel1M 479087 TCAATAACACTGGATCAAAG 479106 i i ivvi v i C L2b_3end#LINE 80 CCAGTGTGGCTGGAGCAGAG 61 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 36.28 CpG sites = 21, Kimura (unadjusted) = 40.88 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.05 (6 / 117), avg. gap size = 1.00 (6 / 6) 286 30.00 1.96 1.96 chr5ptel1M 480549 480650 (519350) C MIRc#SINE/MIR (85) 183 82 m_b229s601i13 9021 chr5ptel1M 480549 AATCCTGGGAAAGTAGTTAGGAGAATAAATTATTA-CTTTATTTCTCAGA 480597 i v i- vi - v viv - iii iv C MIRc#SINE/MIR 183 AACCCTGTGAG-GTAGGCAGG-GCAGGTATTATTATCCCCATTTTACAGA 136 chr5ptel1M 480598 TGAGTAAACTGAGTCACAGAGTAAGCAAGCTACTTATCCTGGATCACAT- 480646 v v v viivi iv ii vi i i- C MIRc#SINE/MIR 135 TGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACA 86 chr5ptel1M 480647 GCTA 480650 C MIRc#SINE/MIR 85 GCTA 82 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 39.27 CpG sites = 17, Kimura (unadjusted) = 39.27 Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.04 (4 / 101), avg. gap size = 1.00 (4 / 4) 405 35.74 11.11 2.96 chr5ptel1M 480678 481271 (518729) L2#LINE/L2 2441 3081 (1) m_b229s601i14 9022 chr5ptel1M 480678 ATTCAAAATATCTCAAAGTGAAATTTT-ATCTTTCTCCCTAAACA----- 480721 i i v i iv v v ii - i i ii v----- L2#LINE/L2 2441 ACTTAACATGTCCAAAACTGAACTCCTGATCTTCCCCCTCAAACCTGCTC 2490 chr5ptel1M 480722 CTCCC-----CTTCCCAATTATCGTCACTGTTACTACCATTCTTCTAGTT 480766 ----- v iviv ? v vi viv i i L2#LINE/L2 2491 CTCCCGCAGTCTTCCCCATCTCAGTNAATGGCAACTCCATCCTTCCAGTT 2540 chr5ptel1M 480767 CCCCGGGCTTGCCACAAA----GGCATCACCCGCACCTTCTCATGATCTC 480812 v i i ---- v ---- vi i viiv i ---- i L2#LINE/L2 2541 GCTCAGGC----CAAAAACCTTGGAGTCATCCTTGACTCCTC----TCTT 2582 chr5ptel1M 480813 TCCCTTTCACTCC---TCTAATGAATCTTTGCCAAGGCCTCTCGATTTCA 480859 i iv i --- i vv ---iv iv v ii ii L2#LINE/L2 2583 TCTCTCACACCCCACATCCAATCCATC---AGCAAATCCTGTCGGCTCTA 2629 chr5ptel1M 480860 C---------GTGTTCAG--------CA--TCTCACAAACTTGACACTTT 480890 ---------i i i -------- -- v v i-- vi L2#LINE/L2 2630 CCTTCAAAATATATCCAGAATCCGACCACTTCTCACCACCTC--CACTGC 2677 chr5ptel1M 480891 CGCCATC-TGATGCACGATTCTATCCCCTCACACCTCTGCCATTACAAGT 480939 i i - i v v viv i vi v i vviii i i vv L2#LINE/L2 2678 CACCACCCTGGTCCAAGCCACCATCATCTCTCGCCTGGATTACTGCAATA 2727 chr5ptel1M 480940 GTCTATTGGTAGATCTACCTTTTTCAAGTCACTTATTATTCTAT--TTTA 480987 i vi iiiv i v vi v -- v iiivii ?i-- i L2#LINE/L2 2728 GCCTCCTAACTGGTCTCCCTGCTTCCA--CCCTTGCCCCCCTNCAGTCTA 2775 chr5ptel1M 480988 TCCTC----CAGATTTTAAAGTGATTGTCTTTAAATGTAAGTCTGAACTC 481033 i ---- vvvii i iv i v i v v vi L2#LINE/L2 2776 TTCTCAACACAGCAGCCAGAGTGATCCTTTTAAAACGTAAGTCAGATCAT 2825 chr5ptel1M 481034 ATCACTCTTCTACTC-AGAC-------TGCCTTCCTGTTACCTCTGGGGC 481075 i i i - i ------- v ii iv viiii i i L2#LINE/L2 2826 GTCACTCCTCTGCTCAAAACCCTCCAATGGCTTCCCATCTCACTCAGAGT 2875 chr5ptel1M 481076 CAAATACAAA-TCCTC----TGGTATTCTGAGCCCTTGATGACCT-ATCC 481119 v vv - i---- iv v vii vv i -i L2#LINE/L2 2876 AAAAGCCAAAGTCCTTACAATGGCCTACAAGGCCCTACATGATCTGGTCC 2925 chr5ptel1M 481120 CCC-TTATCTTCTTACACATTA-CACCTTCCA----CCCCAACATCCTCT 481163 - i iii i- v i - v v ---- vv iii v L2#LINE/L2 2926 CCCGTTACCTCTCTG-ACCTCATCTCCTACCACTCTCCCCCTCGCTCACT 2974 chr5ptel1M 481164 TTGATCCAGTGTTATTGACCTCTTTGCTGTTCCACAAATAAGACA--TAT 481211 ii v ivvi i i i v i i v v --i i L2#LINE/L2 2975 CCGCTCCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACACGCCAGGCAC 3024 chr5ptel1M 481212 CATCTCAACTCCAGATAATTTTTCTTGCTGTTCTGCCTGCCTAGGATGCT 481261 vv i iv vi iivv viv ivi i i i L2#LINE/L2 3025 GCTCCCGCCTCAGGGCCTTTGCACTTGCTGTTCCCTCTGCCTGGAACGCT 3074 chr5ptel1M 481262 GTCCTTCCCC 481271 --- L2#LINE/L2 3075 ---CTTCCCC 3081 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 48.37 CpG sites = 123, Kimura (unadjusted) = 51.24 Transitions / transversions = 1.48 (123/83) Gap_init rate = 0.07 (39 / 593), avg. gap size = 2.18 (85 / 39) 277 34.26 16.67 3.46 chr5ptel1M 481097 481480 (518520) L2c_3end#LINE/L2 9 441 (37) m_b229s601i15 9022 chr5ptel1M 481097 TCTGAGCCCTTGATGACCTATCC-CCCTTATCTTCTTACACATTACACCT 481145 - i viv v -v i i i-------- ii L2c_3end#LINE 9 TCTG-GCCCCTGCCTACCTCTCCAGCCTCATCTCCTC--------CACTC 49 chr5ptel1M 481146 TCCACCCCAACATCCTCTTTGATCCAGTGTTATTGACCTCTTTGCTGTTC 481195 i v i i---i v v v ivvi i v ?i -i L2c_3end#LINE 50 CCCTCCTCG---CCCACTATGCTCCAGCCACACTGAACTNCTTGC-ATTC 95 chr5ptel1M 481196 CACAAATAAGACATA--TCATCTC-AACTCCAGATAATTTTTCTTGCTGT 481242 v i v v ii -- v ii -iv i?iivv viv v L2c_3end#LINE 96 CCCAAACACGCCGCAGTTCTTTCCTGCCTCCGNGCCTTTGCACATGCTGT 145 chr5ptel1M 481243 TCTGCCTGCCTAGGATGCTGT--------CCTTCC------------CCT 481272 ivi i i v -------- ------------ L2c_3end#LINE 146 TCCCTCTGCCTGGAATGCTCTTCCCCCCTCCTTCCACCTGGCTAACTCCT 195 chr5ptel1M 481273 ACC--TTTTTTGAGTACCAACTAAAATCACAGCTTCTATTGGAAGGCTTC 481320 i-- ii ii ?vi i v i vv v i viv v L2c_3end#LINE 196 ACTCATCCTTCAAGNCTCAGCTCAGATGTCACCTCCTCCGGGAAGCCTTC 245 chr5ptel1M 481321 CCCAATATCT----GTTACTCTTAGAAGTTTGCTCCAT----TAATTGTT 481362 ii ivi i----?i v vi vivii v ii ----iv v iv L2c_3end#LINE 246 CCTGACCCCCCAAGNCTAGTCTAGGTGCCCTCCTCTGTGCTCCCATAGCA 295 chr5ptel1M 481363 TCCTATTTATCCTG--AATATAGT--------TTAAAT-GTATT----TT 481397 i i i v v-- v i-------- v - ---- L2c_3end#LINE 296 CCCTGTCTATACTCCCATTATAGCACTTATCATTAACTTGTATTGTAATT 345 chr5ptel1M 481398 GCTTGTT-----ATTTTTCTCCTTGCCATTAGATTGTGGGCTCCTTGAGG 481442 ii -----i i v -- i i i L2c_3end#LINE 346 GTCTGTTTACNTGTCTGTCTCCT--CCACTAGACTGTGAGCTCCTTGAGG 393 chr5ptel1M 481443 G--GAGATTAAATC--------CCTTATATCTCTAGTATTTAGTATAT 481480 -- i iiivi -------- i i i i iiii i i i L2c_3end#LINE 394 GCAGGGACCGTGTCTTATTCATCTTTGTATCCCCAGCGCCTGGCACAT 441 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 46.00 CpG sites = 81, Kimura (unadjusted) = 49.44 Transitions / transversions = 1.76 (81/46) Gap_init rate = 0.08 (30 / 383), avg. gap size = 2.63 (79 / 30) 201 32.11 4.53 9.49 chr5ptel1M 481274 481538 (518462) L2a_3end#LINE/L2 242 494 (23) m_b229s601i16 9022 chr5ptel1M 481274 CCTTTTTTGAGTACC--AACTAAAAT--CACAGCTTCTATTGGAAGGCTT 481319 iii vi -- vi -- v i ?viivv ?vi - L2a_3end#LINE 242 CCTTCCCTGACCACCCTATTTAAAATNGCACACCCTCNCCCCCANCACT- 290 chr5ptel1M 481320 CCCCAATATCTGTTACTCT-TAGAAGTTTGCTCCAT--TAATTGTTTCCT 481366 - v vi iv i -ivvv v v --i v i iv - L2a_3end#LINE 291 -CCCTATCCCCCTTACCCTGCTTTATTTTTCTCCATAGCACTTATCACC- 338 chr5ptel1M 481367 ATTT---ATCCTGAATATAGTTTAAATGTAT-TTTGCTTGTTATTTTTCT 481412 i --- v -- v vv i v - i i i i v L2a_3end#LINE 339 ATCTGACATACT--ATATATTTTACTTATTTATTTGTTTATTGTCTGTCT 386 chr5ptel1M 481413 CCTTGCCATTAGATTGTGGGCTCCTTGAGGGGAGATTAAATCCCTTATAT 481462 ii- i v ii v v i--i ---- v i L2a_3end#LINE 387 CCCC-CCACTAGAATGTAAGCTCCATGAGGGCAGG--GA----CTTTTGT 429 chr5ptel1M 481463 CTCTAGTATTTAGTATATTATTTCTGCTTGTCACTTAAAGCTTA-AGCTT 481511 ----- i v --- i i v -- i - ii iv i - i vv L2a_3end#LINE 430 C-----TGTTTTGT---TCACTGCTG--TATC-CCCAGCGCCTAGAACAG 468 chr5ptel1M 481512 TAGCTTGTCACATAATAGATGCTTAAT 481538 - i v i ii i L2a_3end#LINE 469 T-GCCTGGCACATAGTAGGCGCTCAAT 494 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 42.61 CpG sites = 44, Kimura (unadjusted) = 43.37 Transitions / transversions = 1.33 (44/33) Gap_init rate = 0.12 (31 / 264), avg. gap size = 1.16 (36 / 31) 297 33.31 5.13 1.86 chr5ptel1M 481613 481768 (518232) C L1ME3E_3end#LINE/L1 (586) 403 243 m_b230s551i0 9023 chr5ptel1M 481613 TCTTTCAGACATATACCTAGAAGTGGTATTTTTGAAT--TAAGGAATATG 481660 i vi ii i v vi ii -- i v ii C L1ME3E_3end#L 403 TCTCTAGGGTATATACCTAGGAGTGGAATTGCTGGGTCGTAGGGTATGCG 354 chr5ptel1M 481661 CATCTT----TTT-TTGGCATGACTCCAAATTATTTTACAAATTAATTGA 481705 ---- -i i - i iv i v v ii v C L1ME3E_3end#L 353 CATCTTCAACTTTACTAG-ATAATGCCAAATTGTTTTCCAAAGTGGTTGT 305 chr5ptel1M 481706 ACCGATTTGTGGCTCTAACAG-AGTGCATCAGTGTACTTATCTTTCTACA 481754 i iiivii i v - i i v v v iii ivi i C L1ME3E_3end#L 304 ACCAATTTACACTCCCACCAGCAGCGTATAAGAGTTCCCGTTGCTCCACA 255 chr5ptel1M 481755 GGTCTTCGGTAATA 481768 -- i vi i C L1ME3E_3end#L 254 --TCCTCGCCAACA 243 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 43.42 CpG sites = 36, Kimura (unadjusted) = 47.50 Transitions / transversions = 2.40 (36/15) Gap_init rate = 0.05 (7 / 155), avg. gap size = 1.57 (11 / 7) 13 8.53 4.00 0.00 chr5ptel1M 482847 482871 (517129) (CAAAA)n#Simple_repeat 1 26 (0) m_b230s252i0 9024 chr5ptel1M 482847 CAAAA-AAACCAAACCAAAACAAAAC 482871 - v v (CAAAA)n#Simp 1 CAAAACAAAACAAAACAAAACAAAAC 26 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 15 20.14 0.00 2.70 chr5ptel1M 483779 483816 (516184) (TCA)n#Simple_repeat 1 37 (0) m_b230s252i1 9025 chr5ptel1M 483779 TCATCATCATCATCATTACCACTACCACCAATCATCAT 483816 i i ii i i - (TCA)n#Simple 1 TCATCATCATCATCATCATCATCATCATC-ATCATCAT 37 Matrix = Unknown Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 300 31.79 5.80 4.29 chr5ptel1M 483819 483956 (516044) C L2b_3end#LINE/L2 (2) 464 325 m_b230s601i4 9026 chr5ptel1M 483819 TTATTC--TCAACAAATATTTATTAATCAGTTAATGTTAATTAACCAGGT 483866 i -- i i v ivi v --i --i i C L2b_3end#LINE 464 TCATTCATTCAACAAATATTTACTGAGCGCCTACTGT--GT--GCCAGGC 419 chr5ptel1M 483867 ACTATGTGCTAAGTGAAAAGGGTAAAAAGGAAAGCAAAA---ACTTGGTC 483913 ? -- i i vvii i v iv vi i i --- ?i C L2b_3end#LINE 418 NCT--GTGCTAGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTC 371 chr5ptel1M 483914 CCAAGCCTCCGGGGATTCATTTCCTCATGGAGGAAACA---ATGTA 483956 viv vv iii ivvi vi i i --- C L2b_3end#LINE 370 CCTGCCCTCACGGAGCTCACAGTCTAGTGGGGGAGACAGACATGTA 325 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 40.15 CpG sites = 27, Kimura (unadjusted) = 44.39 Transitions / transversions = 1.80 (27/15) Gap_init rate = 0.07 (9 / 137), avg. gap size = 1.56 (14 / 9) 310 22.00 7.38 3.15 chr5ptel1M 486206 486327 (513673) Charlie7#DNA/hAT-Charlie 2488 2614 (1) m_b230s502i0 9027 chr5ptel1M 486206 ATGCACACA-CACATAAATACA-TACATATATATATATAATTTATAAATA 486253 i i -i i v i - -i i i Charlie7#DNA/ 2488 ATGTACATAATATATTAGTACAGTA-GTACATGTATATAATTTATAAATA 2536 chr5ptel1M 486254 AGCATAC--ACATTAGAGGTTCA-----AAAACAGTTTACTGATATAGGT 486296 ii -- i i i v ----- ivv ivi i Charlie7#DNA/ 2537 AATATACATATATTGGGGGTGCATGCTCAAAATTTTTTACTGATGGGGAT 2586 chr5ptel1M 486297 GAATGTGATCAAAACAAGTTAGGAGACGACT 486327 --i i - v v Charlie7#DNA/ 2587 G--CGCGATCAAAA-AAGTTTGGAGACCACT 2614 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 24.76 CpG sites = 19, Kimura (unadjusted) = 27.17 Transitions / transversions = 2.71 (19/7) Gap_init rate = 0.07 (8 / 121), avg. gap size = 1.62 (13 / 8) 464 29.07 2.60 3.95 chr5ptel1M 486329 486482 (513518) C MIR3#SINE/MIR (37) 171 20 m_b230s601i5 9028 chr5ptel1M 486329 CCTTTGAGATCATCTATTCTATCCTCCTCCTCACTTGACAGATGAGAAAA 486378 v v i v i --- i v i C MIR3#SINE/MIR 171 CCTTAGAGATCATCTAGTCCAACCCCCTC---ATTTTACAGATGAGGAAA 125 chr5ptel1M 486379 CATAAACCCAAGAAGGTTAACTTAATTTACCCAAGAT--AACAGGTAATA 486426 vv ii iii v v- i i i i --v v? i v C MIR3#SINE/MIR 124 CTGAGGCCCAGAGAGGTGAAG-TGACTTGCCCAAGGTCACACAGCNAGTT 76 chr5ptel1M 486427 GGCGGCAGAGTTAGGATCCAGACTCAGGTC-CTCGGCTCCCAAAGCCTGT 486475 i i iii iivii i - ii i -- i i C MIR3#SINE/MIR 75 AGTGGCAGAGCCGGGACTAGAACCCAGGTCTCCTGACTCCC--AGTCCGT 28 chr5ptel1M 486476 A-TCTTTC 486482 i- i C MIR3#SINE/MIR 27 GCTCTCTC 20 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 36.92 CpG sites = 31, Kimura (unadjusted) = 39.45 Transitions / transversions = 2.58 (31/12) Gap_init rate = 0.06 (9 / 153), avg. gap size = 1.11 (10 / 9) 492 31.38 2.17 0.71 chr5ptel1M 486356 486493 (513507) C MIRb#SINE/MIR (115) 153 14 m_b230s601i6 9028 chr5ptel1M 486356 TCCTCACTTGACAGATGAGAAAACATAAACCCAAGAAGGTTAACTTAATT 486405 i i v i vv ii i iii v - i C MIRb#SINE/MIR 153 TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGT-AACT 105 chr5ptel1M 486406 TACCCAAGATAACA--GGTAATAGGCGGCAGAGTTAGGATCCAGACTCAG 486453 i i v -- v i i i iii i ii i C MIRb#SINE/MIR 104 TGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAG 55 chr5ptel1M 486454 GTCC-TCGGCTCCCAAAGCCTGTATCTTTCCCATTATAACA 486493 i- v vii i iiii i i ii v C MIRb#SINE/MIR 54 GTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCACCA 14 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 40.34 CpG sites = 34, Kimura (unadjusted) = 44.80 Transitions / transversions = 3.78 (34/9) Gap_init rate = 0.02 (3 / 137), avg. gap size = 1.33 (4 / 3) 333 22.79 8.89 5.76 chr5ptel1M 486566 486700 (513300) C MIR1_Amn#SINE/MIR (64) 166 28 m_b230s601i7 9029 chr5ptel1M 486566 GGTCATT-TCCTTCTCTGGCTCATTTCACAGAGGAGGAAAC--------- 486605 v - v v --- i i v --------- C MIR1_Amn#SINE 166 GGTCAGTATCATTATC---CCCATTTTACAGATGAGGAAACTGAGGCNCA 120 chr5ptel1M 486606 -AG-GGTTAAGTGACTTTTCCAAAGTAACACAGCTAGTGAGTGTCTGAGG 486653 - - ? vi i v ? ?i i? v v - C MIR1_Amn#SINE 119 GAGAGGTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNAGTGGCAGAG- 71 chr5ptel1M 486654 ATTTGGACTGATGAACATGAGTCTTCTCTGTTCCAAACCTAATGCTC 486700 -iiv ? --? viii i ivv i iv - i C MIR1_Amn#SINE 70 -CCGGGANT--NGAACCCAGGTCTCCCGAGTCCCAGTCC-AGTGCTC 28 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 26.99 CpG sites = 16, Kimura (unadjusted) = 29.30 Transitions / transversions = 1.23 (16/13) Gap_init rate = 0.09 (12 / 134), avg. gap size = 1.67 (20 / 12) 423 23.85 9.40 3.23 chr5ptel1M 486584 486700 (513300) C MIRc#SINE/MIR (120) 148 25 m_b230s601i8 9029 chr5ptel1M 486584 CTCATTTCACAGAGGAGGAAAC----------AG-GGTTAAGTGACTTTT 486622 i i v ---------- - vi C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr5ptel1M 486623 CCAAAGTAACACAGCTAGTGAGTGTCTGAGGATTTGGACTGATGAACATG 486672 i v i v v --iiv --i vii C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAG--CCGGGACT--CGAACCCA 53 chr5ptel1M 486673 AGTCTTCTCTGTTCCAAACCTAATGCTC 486700 i iivii ii i i C MIRc#SINE/MIR 52 GGTCTTCCTGACTCCAAGTCCAGTGCTC 25 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 27.33 CpG sites = 19, Kimura (unadjusted) = 29.95 Transitions / transversions = 2.38 (19/8) Gap_init rate = 0.05 (6 / 116), avg. gap size = 2.50 (15 / 6) 524 23.53 14.97 0.00 chr5ptel1M 486768 486954 (513046) C MIRc#SINE/MIR (0) 268 54 m_b230s601i9 9030 chr5ptel1M 486768 AATAACAATAATGACTAAC-TTCAAATAGTGATTAAT-GTGTGCAAAGCA 486815 i i?v v - iiv iiv v i- v i i C MIRc#SINE/MIR 268 AATAATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCG 219 chr5ptel1M 486816 CTTT-ACAATTATCATTTCATTTGATCCTTACAACTATCCCGGGAGGTA- 486863 - vvi i i i v i i v - C MIRc#SINE/MIR 218 CTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAG 169 chr5ptel1M 486864 -----GCTGCTGTTG-----------TTACAACTGAGGAAACTGAGG--C 486895 ----- v v i i----------- iv -- C MIRc#SINE/MIR 168 GCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC 119 chr5ptel1M 486896 AAATGGGTTAAGTGACTTGCCCAGTGTCAC-C-GC-AATA---GGCAGAG 486939 i vi iv - - - i --- C MIRc#SINE/MIR 118 AGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAG 69 chr5ptel1M 486940 GCTGGGTATGAACTC 486954 v v iivi i C MIRc#SINE/MIR 68 CCGGGACTCGAACCC 54 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 27.46 CpG sites = 26, Kimura (unadjusted) = 28.99 Transitions / transversions = 1.44 (26/18) Gap_init rate = 0.06 (11 / 186), avg. gap size = 2.55 (28 / 11) 550 22.00 10.67 0.00 chr5ptel1M 486805 486954 (513046) C MIRb#SINE/MIR (46) 222 57 m_b230s601i10 9030 chr5ptel1M 486805 TGTGCAAAGCACTTTACAATTATCATTTCATTTGATCCTTACAACTATCC 486854 v i vvi i i i i v i C MIRb#SINE/MIR 222 TGTGCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCC 173 chr5ptel1M 486855 CGGGAGGTAGCTGCTGTTG--------TTACAACTGAGGAAACTGAGG-- 486894 i v v ii i i-------- iv -- C MIRb#SINE/MIR 172 TGCGAGGTAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCT 123 chr5ptel1M 486895 CAAATGGGTTAAGTGACTTGCCCAGTGTCAC-C-GC-AATA---GGCAGA 486938 i vi i iv - - - i --- C MIRb#SINE/MIR 122 CAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGA 73 chr5ptel1M 486939 GGCTGGGTATGAACTC 486954 v v i vi i C MIRb#SINE/MIR 72 GCCGGGATTCGAACCC 57 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 24.83 CpG sites = 21, Kimura (unadjusted) = 26.67 Transitions / transversions = 1.75 (21/12) Gap_init rate = 0.04 (6 / 149), avg. gap size = 2.67 (16 / 6) 266 17.35 13.83 1.90 chr5ptel1M 486874 486967 (513033) C MIR3#SINE/MIR (69) 139 35 m_b230s601i11 9030 chr5ptel1M 486874 TTACAACTGAGGAAACTGAGGC--AAATGGGTTAAGTGACTTGCCCAGTG 486921 iv -- i vi v iv C MIR3#SINE/MIR 139 TTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGG 90 chr5ptel1M 486922 TCAC-C-GCAA--TA--GGCAGAGGCTGGGTATGAAC-----TCTCTTGG 486960 - - ? -- -- v v iivv ----- i i C MIR3#SINE/MIR 89 TCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGTCTCCTGA 40 chr5ptel1M 486961 CCATCCC 486967 -- C MIR3#SINE/MIR 39 C--TCCC 35 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 20.14 CpG sites = 8, Kimura (unadjusted) = 20.14 Transitions / transversions = 1.00 (8/8) Gap_init rate = 0.09 (8 / 93), avg. gap size = 1.88 (15 / 8) 16 0.00 0.00 0.00 chr5ptel1M 488749 488765 (511235) (A)n#Simple_repeat 1 17 (0) m_b230s252i2 9031 chr5ptel1M 488749 AAAAAAAAAAAAAAAAA 488765 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 19 8.35 0.00 0.00 chr5ptel1M 488869 488894 (511106) (AT)n#Simple_repeat 1 26 (0) m_b230s252i3 9032 chr5ptel1M 488869 ATATACATACATATATATATATATAT 488894 i i (AT)n#Simple_ 1 ATATATATATATATATATATATATAT 26 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 15 13.26 5.88 0.00 chr5ptel1M 488894 488909 (511091) (TG)n#Simple_repeat 1 16 (20) m_b230s252i4 9033 chr5ptel1M 488894 TGTGTGTGTGTGTGTG 488909 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTG 16 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 15), avg. gap size = 0.0 (0 / 0) 36 0.00 0.00 0.00 chr5ptel1M 488910 488940 (511060) (TA)n#Simple_repeat 1 31 (0) c_b230s251i0 9034 chr5ptel1M 488910 TATATATATATATATATATATATATATATAT 488940 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATAT 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 15 13.26 5.88 0.00 chr5ptel1M 488941 488957 (511043) (TG)n#Simple_repeat 17 35 (1) m_b230s252i4 9035 chr5ptel1M 488941 G-GTAT-TGTATTTGTTTG 488957 - i - i v v (TG)n#Simple_ 17 GTGTGTGTGTGTGTGTGTG 35 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.12 (2 / 16), avg. gap size = 1.00 (2 / 2) 20 12.58 2.13 4.35 chr5ptel1M 489305 489351 (510649) (TATT)n#Simple_repeat 1 46 (0) m_b230s252i5 9036 chr5ptel1M 489305 TATTTTTTTGTTTATTCATTTATTTATTT-TTAATTGCTTTTTATTTA 489351 v i i - v -- v (TATT)n#Simpl 1 TATTTATTTATTTATTTATTTATTTATTTATTTATT--TATTTATTTA 46 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.07 (3 / 46), avg. gap size = 1.00 (3 / 3) 12 14.30 3.03 3.03 chr5ptel1M 489472 489504 (510496) (ATAAAA)n#Simple_repeat 1 33 (0) m_b230s252i6 9037 chr5ptel1M 489472 ATTAAAATATAAAT-TAAATACAAAATAAATATA 489504 v v -v - v (ATAAAA)n#Sim 1 ATAAAAATAAAAATAAAAATA-AAAATAAAAATA 33 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.06 (2 / 32), avg. gap size = 1.00 (2 / 2) 13 20.82 0.00 0.00 chr5ptel1M 490545 490577 (509423) (AAATA)n#Simple_repeat 1 33 (0) m_b230s252i7 9038 chr5ptel1M 490545 AAATTAAATAGATGAAAGAAAAATAAAATAAAA 490577 v i vv iv (AAATA)n#Simp 1 AAATAAAATAAAATAAAATAAAATAAAATAAAA 33 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 20 0.00 3.57 0.00 chr5ptel1M 490612 490639 (509361) (TGTT)n#Simple_repeat 1 29 (0) m_b230s252i8 9039 chr5ptel1M 490612 TGTTT-TTTGTTTGTTTGTTTGTTTGTTT 490639 - (TGTT)n#Simpl 1 TGTTTGTTTGTTTGTTTGTTTGTTTGTTT 29 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 1361 29.36 2.69 2.52 chr5ptel1M 492335 492928 (507072) C L1ME5_3end#LINE/L1 (291) 650 56 m_b230s551i1 9040 chr5ptel1M 492335 ATCTC---CTGGTTCT-GCTCATTTCCCTCAGCATCA-ATTCATGTAAG- 492378 --- v -i iv v ii -i -- v - C L1ME5_3end#LI 650 ATCTCATTCTGTTTCTTACTTTTTTCACTCAGCACTATGTT--TTTAAGA 603 chr5ptel1M 492379 TCTCTCCAAGCCTCTCTATATTCATCCTGCTGGTCATTTCTTACAGAACA 492428 iv v iiv v i i v iv iiv iii v v vvvv C L1ME5_3end#LI 602 TCCATCCATGTTGCTATGTGTACATCTAGTCCGTTGCTTCTAACTGCTGC 553 chr5ptel1M 492429 ATAATATTCCATAACATTCATATATCACAATTTACCCAACCATTCTCCAA 492478 i i iiii v vi i v i v i v C L1ME5_3end#LI 552 ATAGTACTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCA 503 chr5ptel1M 492479 TTGATGGGCATCCAC-TCACTTTCCAGTTTCTAGCCACGACACACAAGGC 492527 v i i v- ii i - ii i iv v v v C L1ME5_3end#LI 502 GTGATGGACACCCAGGTTGCCT-CCAACTCCCCGCCACCACAAACAACGC 454 chr5ptel1M 492528 TGCCACAAACATTTTGGCACATATAGGTCCCTTTC----CCTTCCTTAGT 492573 v ii ii v i ---- i v---- viv v v C L1ME5_3end#LI 453 TGCAATGAACATCCTCGTACAT----GTCCCCTTATGGACCTGTGTGAGA 408 chr5ptel1M 492574 ATCTCTTTCGGGTATAAGCCCAGTAGTCACACTGCTGGATCAAAGGGTAT 492623 i v i vi v iviv i i v C L1ME5_3end#LI 407 ATTTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTAT 358 chr5ptel1M 492624 GCACAGTTTGATAACTT--TTTGGGCA--TAATTCCAGATTGCTCTCCAG 492669 --- --- - -- ivi -- v v C L1ME5_3end#LI 357 GC---GT---ATA-CTTAATTTGACTAAGTACTGCCAGATTGCTCTCCAG 315 chr5ptel1M 492670 AATGGTTGGATTCGTTCACAACTCCACCAACAATGCATCAGTGTCCCAGT 492719 i v iiv ii vii i i v v i vi C L1ME5_3end#LI 314 AATGGCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTAT 265 chr5ptel1M 492720 TTTCCCACATCCCCTCCAACATTCATCATTATTTTCCCCTGTCATTCTAG 492769 ? i i v i iiv iivv ii v v i v C L1ME5_3end#LI 264 NTCCCCACATCCTCGCCAACACTTGGCATTATCCAGCTTTCTAATTTTTG 215 chr5ptel1M 492770 CCAATCTGACAGGTGTTTAGTGGTATCTCAGAGTTGTCTTAATTTGCATT 492819 i i i vv i vv i C L1ME5_3end#LI 214 CCAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATT 165 chr5ptel1M 492820 TCTCTGATCAATCGTGATTTGGAACA-CTCTTTGATATGAATGGAAATAA 492868 i v vi v v i - i- vv vv iivv C L1ME5_3end#LI 164 TCTCTGATTACTAATGAGTTTGAGCATCTCTTC-ATATGCTTGTTAGCCT 116 chr5ptel1M 492869 TTTCAATTTCATCACCTGAAAATTATCTGTTCATATCCTTTCACCATTTA 492918 ivii v vi v ii vv v C L1ME5_3end#LI 115 TTCGGGTTTCCTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCCATTTT 66 chr5ptel1M 492919 TCATTTGGAG 492928 vv i C L1ME5_3end#LI 65 TCTATTGGGG 56 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 37.42 CpG sites = 90, Kimura (unadjusted) = 37.98 Transitions / transversions = 1.12 (90/80) Gap_init rate = 0.04 (24 / 593), avg. gap size = 1.29 (31 / 24) 292 32.39 3.15 2.75 chr5ptel1M 492834 493087 (506913) C L1PB_orf2#LINE/L1 (0) 3294 3040 m_b230s551i2 9040 chr5ptel1M 492834 TGATTTGGAACACTCTTTGATATGAATGGAAATAATTTCAATTTCATCAC 492883 v v i i i v vv vviiiv vv v v vi C L1PB_orf2#LIN 3294 TGATGTTGAGCATTTTTTCATATGTTTGTTGGCCATTTGTATATCTTCTT 3245 chr5ptel1M 492884 CTGAAAATTATCTGTTCATATCCTTTCACCATTTATCATTTGG-AGAATG 492932 i i i i i vvv i ---- i-i i v C L1PB_orf2#LIN 3244 TTGAGAATTGTCTATTCATGTCCTTAGCCCACTT----TTTGATGGGATT 3199 chr5ptel1M 492933 GTTTGATTT---CTTATAAATTAGAGTCCATTCTCTCTATATTTTGGAAA 492979 v --- iivi v vv vvi ?i v v i v C L1PB_orf2#LIN 3198 GTTTGTTTTTTTCTTGCTGATTTGTTTGAGTTCNTTGTAGATTCTGGATA 3149 chr5ptel1M 492980 TGAGGCCTTTATCAGAACCTTTAACTGTGAAGATGTTTTCCCAGTTTGTT 493029 v v i vviv vi i v i v i v C L1PB_orf2#LIN 3148 TTAGTCCTTTGTCAGATGTATAGATTGTGAAGATTTTCTCCCACTCTGTG 3099 chr5ptel1M 493030 GCTTCCCT-TCTAATCT--TGTTTGCATTAGTTTTGTTTGTACA-AGGCT 493075 v vi - i v -- vi -- vv -ii i - i C L1PB_orf2#LIN 3098 GGTTGTCTGTTTACTCTGCTGACTG--TTCCTTTTG-CCGTGCAGAAGCT 3052 chr5ptel1M 493076 TTTTAATTTGAT 493087 i i i C L1PB_orf2#LIN 3051 CTTTAGTTTAAT 3040 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 42.41 CpG sites = 38, Kimura (unadjusted) = 43.11 Transitions / transversions = 0.90 (38/42) Gap_init rate = 0.05 (12 / 253), avg. gap size = 1.25 (15 / 12) 364 35.26 2.84 1.69 chr5ptel1M 493335 493510 (506490) L3#LINE/CR1 3014 3191 (908) m_b230s601i12 9041 chr5ptel1M 493335 AGATATGACACAGATGAGAATTTAATTAGGGGAATTCAGAACTGGCTGAA 493384 i ivvii v i vi i v i iv i i L3#LINE/CR1 3014 AAATATGGGCTGGATGATAGTACAGTTAGGTGGATTCGTAGCTGGTTGAA 3063 chr5ptel1M 493385 TGACTGGACTGAAAAAATAATCATGGCCGAGTC--TGTCAATAGGAAAGG 493432 i iv iv ii iv v vivi ii -- ivv i i L3#LINE/CR1 3064 CGACTATACCCAAAAGGTGTTGATTAATGGATCGATGTCAACCTGGAGGG 3113 chr5ptel1M 493433 AAATCTCGCATGGAGTGCCTCCAGAGATCTAGTTTCTGAC---ATACTGT 493479 ii vvi v -v i v - iii i ---i v L3#LINE/CR1 3114 AGGTCTCTAGTGGCGTGCC-ACAGGGCTCT-GTCCTTGGCCCTGTCCTGT 3161 chr5ptel1M 493480 TGAACATTTAAATCCATTATTTCGTTTGAAG 493510 v vv v v i v -v L3#LINE/CR1 3162 TCAACATTTTTATCAATGACTTGG-ATGAAG 3191 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 46.93 CpG sites = 34, Kimura (unadjusted) = 49.18 Transitions / transversions = 1.26 (34/27) Gap_init rate = 0.03 (5 / 175), avg. gap size = 1.60 (8 / 5) 22 27.38 1.69 0.00 chr5ptel1M 493578 493636 (506364) (AT)n#Simple_repeat 1 60 (0) m_b230s252i9 9042 chr5ptel1M 493578 ATACACACATATATATGTGTGTAGATAGATATATGTATATGTATACATAC 493627 i i i i i i v v i i i i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr5ptel1M 493628 AGA-ATATAT 493636 v - (AT)n#Simple_ 51 ATATATATAT 60 Matrix = Unknown Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1) 195 34.26 7.63 3.88 chr5ptel1M 493909 494157 (505843) L2a_3end#LINE/L2 236 493 (24) m_b230s601i13 9043 chr5ptel1M 493909 GAGAACCCCTCCTGAATCTCC--ACTTAAAG-AGGGTACCCAAGCCACCC 493955 ? iv i ivi i v -- i i-? vii vv? - L2a_3end#LINE 236 GNGAGGCCTTCCCTGACCACCCTATTTAAAATNGCACACCCTCNCC-CCC 284 chr5ptel1M 493956 AACTCTTCATTTCCTAAAGTGTTACGTTGCTTTGGATT-CTCCATCATGC 494004 ? v i v v i----iv vi ivv - viii L2a_3end#LINE 285 ANCACTCCCTATCCC----CCTTACCCTGCTTTATTTTTCTCCATAGCAC 330 chr5ptel1M 494005 TCCTC-CTAT---ACCC-CTAC---CTCAACTTTTCAACTTCCTTTTTGT 494046 iv - i --- vi- i---i iv v iv i vi v L2a_3end#LINE 331 TTATCACCATCTGACATACTATATATTTTACTTATTTATTTGTTTATTGT 380 chr5ptel1M 494047 GTTATCTTCCCTCAACAGATTATAAATTTCTTGAGATTAGAAATGGCCTT 494096 -i i i i vi v i ii i v ivi ii --- i L2a_3end#LINE 381 -CTGTCTCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGA---CTTT 426 chr5ptel1M 494097 TCT---TTTTGGGTATT--TGTATCACCTAAGGTTTAGCACAGTGTCTGG 494141 v --- vvi i -- - i iv ii v i L2a_3end#LINE 427 TGTCTGTTTTGTTCACTGCTGTATC-CCCAGCGCCTAGAACAGTGCCTGG 475 chr5ptel1M 494142 TACAT--CAGGCATTAAA 494157 i --i ii v L2a_3end#LINE 476 CACATAGTAGGCGCTCAA 493 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 48.51 CpG sites = 51, Kimura (unadjusted) = 49.39 Transitions / transversions = 1.65 (51/31) Gap_init rate = 0.08 (20 / 248), avg. gap size = 1.45 (29 / 20) 298 31.28 3.70 5.26 chr5ptel1M 494023 494157 (505843) L2d2_3end#LINE/L2 399 531 (24) m_b230s601i14 9043 chr5ptel1M 494023 TCAACTTTTCAACTTCCTTTTTGTGTTATCTTCCCTCAAC-AGATTATAA 494071 i ---- v v i iv v ii i - i L2d2_3end#LIN 399 TTAACTTTTCA----CGTGTTTATGTCTTGTCTCCCCAACTAGATTGTAA 444 chr5ptel1M 494072 ATTTCTTGAGATTAGAAATGGCCTTTCTTTTTGGGTATTTGTATCACCTA 494121 ii i ivi ii --- v vii v ivv v v i L2d2_3end#LIN 445 GCTCCTTGAGGGCAGGGA---CCATGTCTTATACTTCTTTGTATCCCCCA 491 chr5ptel1M 494122 -AG-GTTTAGCACAGTGTCTGGTACAT--CAGGCATTAAA 494157 - - ii i v i i--i ii v L2d2_3end#LIN 492 CAGCGCCTAGCACAGTGCCTTGCACACAGTAGGCGCTCAA 531 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 40.99 CpG sites = 26, Kimura (unadjusted) = 42.42 Transitions / transversions = 1.86 (26/14) Gap_init rate = 0.08 (11 / 134), avg. gap size = 1.09 (12 / 11) 232 32.23 8.17 2.21 chr5ptel1M 494169 494425 (505575) L1ME4c_3end#LINE/L1 314 585 (245) m_b230s551i3 9044 chr5ptel1M 494169 TTTGAAAAGCAATGTGGAGTTACACGAATGAAG--TAATTAAAATGTTCA 494216 i v vi-- i v v --iv v L1ME4c_3end#L 314 TTTGGAAAGCAATTTGGCA--ATACGTATCAAGAGCCATAAAAATGTTCA 361 chr5ptel1M 494217 TATCTTTTGAATCAGAAACT-CACTTTTTAGACTTAAAAGCCAAGAAAAC 494265 i i vi v i - i vi v -v vv i i i L1ME4c_3end#L 362 TACCCTTTGACCCAGTAATTCCACTTCTGGGAATT-TATCCTAAGGAAAT 410 chr5ptel1M 494266 TGTTGATAGGAAAAAAATCCCCATATACACCTAAATATTTATGAACAATA 494315 vi v v i ii vvv i i vv i i i v-i iii L1ME4c_3end#L 411 AATTCAAAAGAAGGAAAAAGCTATATGCACGAAGATGTTCATT-GCAGCG 459 chr5ptel1M 494316 CTTTCTGTGTTGGC---AAAGTGG-AACAAAGTAGATGC----------- 494350 i v i i iv i --- v - vv i i----------- L1ME4c_3end#L 460 TTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGG 509 chr5ptel1M 494351 --AATGTCTAAACAAATTTTGGTACACAAATGTAATAGAGTATTATTACG 494398 -- vi ii v iv? ivii i i vvv L1ME4c_3end#L 510 GGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATATTATGCAG 559 chr5ptel1M 494399 TTG-TAAAAACGATACATTGATGAATAC 494425 iii- i - - v L1ME4c_3end#L 560 CCATTAAAAATGATA-ATT-ATGAAGAC 585 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 42.08 CpG sites = 46, Kimura (unadjusted) = 43.68 Transitions / transversions = 1.31 (46/35) Gap_init rate = 0.05 (13 / 256), avg. gap size = 2.08 (27 / 13) 203 24.58 15.00 3.37 chr5ptel1M 497304 497383 (502617) MIRc#SINE/MIR 39 127 (141) m_b230s601i15 9045 chr5ptel1M 497304 GAATTAGGAAAACCTGAGTTCGAGTTGGCCCG---CTGCTACGTGCCAGG 497350 i i i i --- --- i v i i v MIRc#SINE/MIR 39 GAGTCAGGAAGACCTGGGTTCGAGT---CCCGGCTCTGCCACTTACTAGC 85 chr5ptel1M 497351 TATATTAACAT-CATAAATC-----ACCTCTC---GTCTCAG 497383 i i v v v -vii i ----- --- i MIRc#SINE/MIR 86 TGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 31.09 CpG sites = 13, Kimura (unadjusted) = 31.09 Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.09 (7 / 79), avg. gap size = 2.14 (15 / 7) 17 11.13 0.00 0.00 chr5ptel1M 497390 497418 (502582) (TTG)n#Simple_repeat 1 29 (0) m_b230s252i10 9046 chr5ptel1M 497390 TTGTTGTTGTTGATGTTGCTGTTGTTTTT 497418 v i v (TTG)n#Simple 1 TTGTTGTTGTTGTTGTTGTTGTTGTTGTT 29 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 247 31.44 3.39 2.95 chr5ptel1M 497995 498230 (501770) C L1M1_orf2#LINE/L1 (586) 2708 2472 m_b230s551i5 9047 chr5ptel1M 497995 TCTGATCTATTCCAGTGATCAACTTTACTATTCCTCAT-CCAAT-CCAAA 498042 iv i v i v iv vv i ii - - i - vi C L1M1_orf2#LIN 2708 TCTATTCTGTTCCATTGGTCTATGTGTCTGTTTTT-ATGCCAGTACCATG 2660 chr5ptel1M 498043 TTGTTTTGATGATTATAGTTTTGCAGTATAGTTTGATATCTGGTACTGTT 498092 i i v i i i i i vi v v - C L1M1_orf2#LIN 2659 CTGTTTTGGTTACTATAGCTCTGTAGTATAATTTGAAGTCAGGTAATGT- 2611 chr5ptel1M 498093 AGGTCCCCTTTCATTTCTACTCTTTTTTATTAGT---TCTTTTGATATTC 498139 - i i -- i v i ii vv i v---v v v C L1M1_orf2#LIN 2610 -GATTCC--TCCAGTTTTGTTCTTTTTGCTCAGGATAGCTTTGGCTATTC 2564 chr5ptel1M 498140 TTAACATTTTATTTCTCTAGGTGCATTTTACTATT--TTTTTCTATCTTT 498187 viiiv i vvi i vi iv vv -- i i C L1M1_orf2#LIN 2563 TGGGTCTTTTGTGGTTCCATATAAATTTTAGGATTGTTTTTTCTATTTCT 2514 chr5ptel1M 498188 ATAAATTAAT-TCTTTGATAGTTTGAAAAAAGACTGAATTCAAT 498230 i i -v - v i v - v ii i v v C L1M1_orf2#LIN 2513 GTGAA-GAATGTCATTGGTATTTTG-ATAGGGATTGCATTGAAT 2472 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 41.77 CpG sites = 40, Kimura (unadjusted) = 41.77 Transitions / transversions = 1.25 (40/32) Gap_init rate = 0.05 (12 / 235), avg. gap size = 1.25 (15 / 12) 260 30.47 1.89 0.93 chr5ptel1M 497995 498100 (501900) C L1P1_orf2#LINE/L1 (586) 2708 2602 m_b230s551i4 9047 chr5ptel1M 497995 TCTGATCTATTCCAGTGATCAACTTTACTATTCCTCAT-CCAAT-CCAAA 498042 v i v v iv iv i i- vi - i - vi C L1P1_orf2#LIN 2708 TCTGTTCTGTTCCATTGATCTATATCTCTGTTT-TGGTACCAGTACCATG 2660 chr5ptel1M 498043 TTGTTTTGATGATTATAGTTTTGCAGTATAGTTTGATATCTGGTACTGTT 498092 i i v i i ii i vi v vi v C L1P1_orf2#LIN 2659 CTGTTTTGGTTACTGTAGCCTTGTAGTATAGTTTGAAGTCAGGTAGCGTG 2610 chr5ptel1M 498093 AGGTCCCC 498100 v i i C L1P1_orf2#LIN 2609 ATGCCTCC 2602 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 38.72 CpG sites = 19, Kimura (unadjusted) = 40.36 Transitions / transversions = 1.46 (19/13) Gap_init rate = 0.03 (3 / 105), avg. gap size = 1.00 (3 / 3) 21 18.55 2.13 2.13 chr5ptel1M 498310 498356 (501644) (AT)n#Simple_repeat 1 47 (0) m_b230s252i11 9048 chr5ptel1M 498310 ATATACACTA-ATGTGTGTGTATATATATATATGTATATATATATGTA 498356 i - - i i i i i i (AT)n#Simple_ 1 ATATATA-TATATATATATATATATATATATATATATATATATATATA 47 Matrix = Unknown Transitions / transversions = 1.00 (7/0) Gap_init rate = 0.04 (2 / 46), avg. gap size = 1.00 (2 / 2) 337 22.32 10.58 0.88 chr5ptel1M 499468 499571 (500429) C MIR#SINE/MIR (2) 260 147 m_b230s601i16 9049 chr5ptel1M 499468 TAATAGCTAGTATTTCTAAAGCTTTT--TAAGTTTT--GCA-------AA 499506 ii v vi vi -- v vii-- ------- C MIR#SINE/MIR 260 TAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAA 211 chr5ptel1M 499507 GTACTTTACAGATATTAATTCATTTGATCCTCACAAACAAATCTATTAGG 499556 ii vi i i - vi v C MIR#SINE/MIR 210 GCGCTTTACATGTATTAACTCATTTAATCCTCAC-AACAACCCTATGAGG 162 chr5ptel1M 499557 TAGATATTATTTTTA 499571 i i v C MIR#SINE/MIR 161 TAGGTACTATTATTA 147 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 25.56 CpG sites = 14, Kimura (unadjusted) = 27.06 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.04 (4 / 103), avg. gap size = 3.00 (12 / 4) 13 15.86 0.00 0.00 chr5ptel1M 499748 499775 (500225) (AAATA)n#Simple_repeat 1 28 (0) m_b230s252i12 9050 chr5ptel1M 499748 AAATAAATGAAAGAAAAATAAAATAAAA 499775 vv iv (AAATA)n#Simp 1 AAATAAAATAAAATAAAATAAAATAAAA 28 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 273 22.64 5.66 0.00 chr5ptel1M 499794 499846 (500154) C MIRc#SINE/MIR (203) 65 10 m_b230s601i17 9051 chr5ptel1M 499794 GGATTTGAACTTAGGTCTT---AACTTCAGGCCCAGTGCTCTATTTATTG 499840 i i ii ---i i i i v ii i C MIRc#SINE/MIR 65 GGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTG 16 chr5ptel1M 499841 CACCAC 499846 C MIRc#SINE/MIR 15 CACCAC 10 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 26.50 CpG sites = 11, Kimura (unadjusted) = 29.42 Transitions / transversions = 11.00 (11/1) Gap_init rate = 0.02 (1 / 52), avg. gap size = 3.00 (3 / 1) 268 30.98 5.88 1.89 chr5ptel1M 500195 500296 (499704) C MIRc#SINE/MIR (146) 122 17 m_b230s601i18 9052 chr5ptel1M 500195 GTTTATAGAGGTT--GTAACTTTCCCATGCTCGCCTAGCTGGT----GTC 500238 i i v -- i v v v i vi i ---- v C MIRc#SINE/MIR 122 GCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGC 73 chr5ptel1M 500239 AGTAATGGAATACAAAATCAGGTCTCAATGGATTCCAAGTCTAATAGTTA 500288 vivi i iv i vi ivv - i i i - i v C MIRc#SINE/MIR 72 AGAGCCGGGACTCGAACCCAGGTCTTCCT-GACTCCAAGTCCAGT-GCTC 25 chr5ptel1M 500289 TTTCCATT 500296 i C MIRc#SINE/MIR 24 TTTCCACT 17 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 37.78 CpG sites = 18, Kimura (unadjusted) = 41.19 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.04 (4 / 101), avg. gap size = 2.00 (8 / 4) 26 15.53 0.00 8.57 chr5ptel1M 500895 500970 (499030) (ATTTTT)n#Simple_repeat 1 70 (0) m_b230s252i13 9053 chr5ptel1M 500895 ATCTTTATTTATTTTTTTAAAGCTTTTTATTTTTATTTTCTTTTTTAAAT 500944 i - v -v -- - v -v (ATTTTT)n#Sim 1 ATTTTTATTT-TTATTTT-TA--TTTTTATTTTTATTTT-TATTTT-TAT 44 chr5ptel1M 500945 TTTTATATATATATATATTTTTATTT 500970 v v v v (ATTTTT)n#Sim 45 TTTTATTTTTATTTTTATTTTTATTT 70 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.08 (6 / 75), avg. gap size = 1.00 (6 / 6) 26 28.41 3.19 0.00 chr5ptel1M 500898 500991 (499009) (TTTA)n#Simple_repeat 1 97 (0) m_b230s252i14 9053 chr5ptel1M 500898 TTTATTTATTTTTTTAAAGCTTTTTATTTTTATTTTCTTTTTTAAATTTT 500947 v vvvv v v v vi v vv v (TTTA)n#Simpl 1 TTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATT 50 chr5ptel1M 500948 TATATATATATATA-TT-TTTATTTACTTA-ATAGCTTTTTATTTAT 500991 v v v - - i -v vi v (TTTA)n#Simpl 51 TATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTAT 97 Matrix = Unknown Transitions / transversions = 0.16 (3/19) Gap_init rate = 0.03 (3 / 93), avg. gap size = 1.00 (3 / 3) 1555 27.83 3.15 3.65 chr5ptel1M 501435 502068 (497932) C L1ME5_3end#LINE/L1 (304) 637 7 m_b230s551i6 9054 chr5ptel1M 501435 TCCTGCTCATTTCACTCAGCATCA-GTTCGTGTAAG-TCTCTCCAGGC-- 501480 i i iv ii - -- v - iv v i-- C L1ME5_3end#LI 637 TCTTACTTTTTTCACTCAGCACTATGTT--TTTAAGATCCATCCATGTTG 590 chr5ptel1M 501481 CTTTCTGAAATCATCCTGTTGGTCATTTCTTACAGA-ACAGTAATATTCC 501529 v v v -- iv iv iii v v v-i - i i C L1ME5_3end#LI 589 CTATGTGTA--CATCTAGTCCGTTGCTTCTAACTGCTGCA-TAGTACTCC 543 chr5ptel1M 501530 ATAATTTTCATATACCACAATTTATTCAGCCATTCACTAACCGATGGACA 501579 ii v v vi v iii v i v iv vi C L1ME5_3end#LI 542 ATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCAGTGATGGACA 493 chr5ptel1M 501580 TCCATTCAGTTTCCAGTTTTTAGCCACTACAAAAAGGGCTGCCACAAACA 501629 i vviv ii ii iiiv i v iv v ii C L1ME5_3end#LI 492 CCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCTGCAATGAACA 443 chr5ptel1M 501630 TTTGTGCACATACAGGTCCCTTTC----CCTTCTTTATAATCTCTTTGGG 501675 i---- v i v i v---- viv v v i C L1ME5_3end#LI 442 TC----CTCGTACATGTCCCCTTATGGACCTGTGTGAGAATTTCTTTGGG 397 chr5ptel1M 501676 ATATAATCCCAGTAGTAACACTGCTGGATCAAAGGGTATGCACAGTTTGA 501725 vv v iiiv i i v --- --- C L1ME5_3end#LI 396 ATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATGC---GT---A 353 chr5ptel1M 501726 TAACTT--TTTGAGCA--TAGTTCCAAACTACTCTCCAAAATGGTTGGAT 501771 - -- vi -- v v i i i i i v i C L1ME5_3end#LI 352 TA-CTTAATTTGACTAAGTACTGCCAGATTGCTCTCCAGAATGGCTGCAC 304 chr5ptel1M 501772 TCGTTCACAACTCCACCAACAATGCATCAATGTCCCAGTTTTCCCACATC 501821 iv ii vii i i v iv i vi ? i C L1ME5_3end#LI 303 CAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATC 254 chr5ptel1M 501822 CCCTCCAACAATCATCATTATTT--TTTCCTGTCATCTTAGCCAATCTGA 501869 i v v iiv ii--i i i-- i v i i C L1ME5_3end#LI 253 CTCGCCAACACTTGGCATTATCCAGCTTTCTA--ATTTTTGCCAGTCTAA 206 chr5ptel1M 501870 CAGGTGTGTAGTGGTATCTTAGAGTTGTCTTAATTTGCATTTCTCTGATT 501919 i iv i i vv i C L1ME5_3end#LI 205 TAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATTTCTCTGATT 156 chr5ptel1M 501920 AATAATGACTTGGAGCATCTTTTCATATGACTAGAAATAG--TTTCAA-T 501966 v v v i - v v-- -- ii- C L1ME5_3end#LI 155 ACTAATGAGTTTGAGCATCTCTTCATATG-CTTGT--TAGCCTTTCGGGT 109 chr5ptel1M 501967 TTCTTCATCTGAGAATTGTCTGTTCATATCCTTTGACCATTTTTCAATTG 502016 i v vi i v v C L1ME5_3end#LI 108 TTCCTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTG 59 chr5ptel1M 502017 GAG--AATGGCTTGATTTTTTATAAATTAGAGTTAATTCTCTATATATTT 502064 i --?vi v -- i i vi v vivv i ii i i C L1ME5_3end#LI 58 GGGTTNCCGTCTT--TTTCTTGTTGATTTGCAGGAGTTCCTTGTATATTC 11 chr5ptel1M 502065 TGGA 502068 i C L1ME5_3end#LI 10 TAGA 7 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 34.70 CpG sites = 99, Kimura (unadjusted) = 35.78 Transitions / transversions = 1.39 (99/71) Gap_init rate = 0.05 (34 / 633), avg. gap size = 1.26 (43 / 34) 1626 27.65 0.36 1.66 chr5ptel1M 501521 502068 (497932) C L1ME3G_3end#LINE/L1 (377) 547 7 m_b230s551i7 9054 chr5ptel1M 501521 TAATATTCCATAATTTTCATATACCACAATTTATTCAGCCATTCACTAAC 501570 i i v vv i i i v iv i C L1ME3G_3end#L 547 TAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTAT 498 chr5ptel1M 501571 CGATGGACATCCATTCAGTTTCCAGTTTTTAGCCACTACAAAAAGGGCTG 501620 i ii vviv i v i i v iv C L1ME3G_3end#L 497 TGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCTG 448 chr5ptel1M 501621 CCACAAACATTTGTGCACATACAGGTCCCTTTCC-CTTCTTT-ATAATCT 501668 v ii iiv i i ?-- i v v - v v vi- vv i C L1ME3G_3end#L 447 CAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATTT 400 chr5ptel1M 501669 CTTTGGGATATAATCCCAGTAGTAACACTGCTGGATCAAAGGGTATGCAC 501718 ? i v v? ? v iiv i i i C L1ME3G_3end#L 399 CTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGC 350 chr5ptel1M 501719 AGTTTGATAACTTTTTGAGCATAGTTCCAAACTACTCTCCAAAATGGTTG 501768 v i -- i vvv - v v i i i ? i C L1ME3G_3end#L 349 ATTTTAA--ATTTTAATAG-ATACTGCCAAATTGCCCTCCAAAANGGCTG 303 chr5ptel1M 501769 GATTCGTTCACAACTCCACCAACAATGCATCAATGTCCCAGTTTTCCCAC 501818 v iivi i vii i i i v iv v v i C L1ME3G_3end#L 302 TACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCAC 253 chr5ptel1M 501819 ATCCCCTCCAACAATCATCATTATTTTTTCCTGTCATCTTAGCCAATCTG 501868 i i v v ?ivi ivv?iii vvv i v C L1ME3G_3end#L 252 ACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATCTG 203 chr5ptel1M 501869 ACAGGTGTGTAGTGGTATCTTAGAGTTGTCTTAATTTGCATTTCTCTGAT 501918 ii viv i i vv i i C L1ME3G_3end#L 202 ATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGAT 153 chr5ptel1M 501919 TAATAATGACTTGGAGCATCTTTTCATATGACTAGAAATAGTTTCAATTT 501968 v i vv v vi vviiivi vv C L1ME3G_3end#L 152 TACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGTATTT 103 chr5ptel1M 501969 CTTCATCTGAGAATTGTCTGTTCATATCCTTTGACCATTTTTCAATTGGA 502018 i v v i v v i C L1ME3G_3end#L 102 CCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGGG 53 chr5ptel1M 502019 GAATGGCTTGATTTTTTATAAATTAGAGTTAATTCTCTATATATTTTGGA 502068 v-- v -- i vi v vivv i i i C L1ME3G_3end#L 52 T--TGTCTT--TTTCTTATTGATTTGTAGGAGTTCTTTATATATTCTGGA 7 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 34.99 CpG sites = 78, Kimura (unadjusted) = 35.58 Transitions / transversions = 1.10 (78/71) Gap_init rate = 0.02 (11 / 547), avg. gap size = 1.00 (11 / 11) 812 30.52 3.73 3.73 chr5ptel1M 501925 502540 (497460) C L1M5_orf2#LINE/L1 (0) 3294 2679 m_b230s551i8 9054 chr5ptel1M 501925 TGACTTGGAGCATCTTTTCATATGACTAGAAATAGTTTCAATTTCTTCAT 501974 ?v v i vi vviiivi v? v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr5ptel1M 501975 CTGAGAATTGTCTGTTCATATCCTTTGACCATTTTTCAATTGGA--GAAT 502022 i v v vi i v ?v i-- vv C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTT 3195 chr5ptel1M 502023 GGCTTGATTTTTTA-TAAATTAGAGTTAATTCTCTATATATTTTGGAAAT 502071 v -- ? - i ? iv -v i i i v i C L1M5_orf2#LIN 3194 GTCTT--TTTNTTATTGANTTGTAG-GAGTTCTTTATATATTCTGGATAC 3148 chr5ptel1M 502072 GAGGCCTTTATCAGA-ACCTTTGACTGTAAAAATATTTTCCCAGTTTATT 502120 v i - iv v -?i i v v i ? i i v C L1M5_orf2#LIN 3147 GAGTCCTTTGTCAGATATATGT-NTTGCAAATATTTTCTCCCANTCTGTG 3099 chr5ptel1M 502121 GCTTCCCTTCTAATCTTGTCTGCATTAGTTTTGTTTGTACAAAAACTTTT 502170 v i v i v ivi iv ivi vvv? vi i ii C L1M5_orf2#LIN 3098 GCTTGCCTTTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTTT 3049 chr5ptel1M 502171 CAGTTTGGTATAATCGA-------AATTTTCTATTTTGTGATCAGTAATG 502213 v v i i? i v ------- i v i i i? i--- C L1M5_orf2#LIN 3048 AATTTTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGGTTNGTG--- 3002 chr5ptel1M 502214 ATCTCTAGTTCTGTTTTGGTCATAAAGACCTTCCCCT-TCCACAGGTCTG 502262 -- i -- v ii v i - i i i iv -? vv vv C L1M5_orf2#LIN 3001 --CTTT--TTGTGTCCTGTTTA-AGAAATCTTTGCCTANCCCAAGGTCAC 2957 chr5ptel1M 502263 AGAGGTAAACTATCCTATG--TTCCTCTAATTTATTAATAATTTCATTCT 502310 ii i -- i v -- i ivvvv v i i ?ii C L1M5_orf2#LIN 2956 GAAGAT--ATTCTCCTATGTTTTCTTCTAGAAGTTTTATAGTTTTANCTT 2909 chr5ptel1M 502311 TTATGCCTAGGTC-ATGAACCCATTTTGACCTTATCTTGGTGTACGGCGT 502359 iiii - - i i ? vi v i v i i C L1M5_orf2#LIN 2908 TTACATTTAGGTCTATG-ATCCATCTNGAATTAATTTTTGTGTATGGTGT 2860 chr5ptel1M 502360 TAAGTATGGATCAATGCCTAGTTTCTGCCATATTAGTTTCCAATTTTCCC 502409 v i v i i v?iii v i v vii v v i C L1M5_orf2#LIN 2859 GAGGTAGGGGTCGAGNTTCATTTTTTTCCATATGGATATCCAATTGTTCC 2810 chr5ptel1M 502410 AGCAATTTTTATCAAACAGTAAGTTCTTATCCCAAAAGCTGGGAT-CTTT 502458 viv i ii v vvvi i vi ---- iiv - ? C L1M5_orf2#LIN 2809 AGCACCATTTGTTGAAAAGACTATCCTTTCCCCA----CTGAATTGCNTT 2764 chr5ptel1M 502459 GG---GTTTGTCAAAGACTAGGTTGCTATATTTGT-TGACTGTTTTGTCC 502504 ---v i ii i? v? i v - --- v i i ii C L1M5_orf2#LIN 2763 GGCACCTTTGTCAAAAATCAANTGNCCATATATGTGTG---GGTCTATTT 2717 chr5ptel1M 502505 CTTGAAC---CTAATCTATTCCACTGATCAACTTATCTA 502540 - i --- v i i v i i C L1M5_orf2#LIN 2716 C-TGGACTCTCTATTCTGTTCCATTGATCTATTTGTCTA 2679 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 40.65 CpG sites = 103, Kimura (unadjusted) = 41.86 Transitions / transversions = 1.32 (103/78) Gap_init rate = 0.06 (34 / 615), avg. gap size = 1.35 (46 / 34) 13 20.82 0.00 0.00 chr5ptel1M 502785 502817 (497183) (ATTTT)n#Simple_repeat 1 33 (0) m_b230s252i15 9055 chr5ptel1M 502785 ATTTTATATGCCTTCATTTTATTTTATTTTTTT 502817 v vvi i v (ATTTT)n#Simp 1 ATTTTATTTTATTTTATTTTATTTTATTTTATT 33 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 407 27.36 1.55 6.50 chr5ptel1M 502842 502970 (497030) MIRc#SINE/MIR 25 147 (121) m_b230s601i19 9056 chr5ptel1M 502842 GAGCACTGGGCTTTGAATCAAGAAGATACATCTTCACAAAATAAAATCTG 502891 i v i i iviivv i-------- i iv MIRc#SINE/MIR 25 GAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG--------AGTCCC 66 chr5ptel1M 502892 GTCTCAGACACTTATTAGCAGGGTAATCATGGGCAAATCACTTAGCC-CT 502940 v v v i v v i i v i i - MIRc#SINE/MIR 67 GGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCT 116 chr5ptel1M 502941 GTTTGTCTCA-TCTCCTCATACATAAAATGG 502970 v vv i - i vii MIRc#SINE/MIR 117 CTGAGCCTCAGTTTCCTCATCTGTAAAATGG 147 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 33.22 CpG sites = 18, Kimura (unadjusted) = 34.49 Transitions / transversions = 1.20 (18/15) Gap_init rate = 0.08 (10 / 128), avg. gap size = 1.00 (10 / 10) 187 23.53 1.92 1.92 chr5ptel1M 503027 503078 (496922) MIRb#SINE/MIR 15 66 (202) m_b230s601i20 9057 chr5ptel1M 503027 GGTGCAGTTCAGAGAGCACCAACCCAGGAATCAGA-AGACTCTGAGTTCA 503075 vv i vii iiv i - - i i MIRb#SINE/MIR 15 GGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGAC-CTGGGTTCG 63 chr5ptel1M 503076 AAT 503078 MIRb#SINE/MIR 64 AAT 66 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 26.34 CpG sites = 8, Kimura (unadjusted) = 29.16 Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.00 (2 / 2) 540 32.67 2.90 3.90 chr5ptel1M 503169 503375 (496625) MIRc#SINE/MIR 2 206 (62) m_b230s601i21 9058 chr5ptel1M 503169 GGGGGAGTGAGGTGAGAGCAATAGTAGCTGGAGCATTAGATT---AGTAA 503215 i v v -------i i vvi i i i --- v MIRc#SINE/MIR 2 GAGGCAGTGTGGTG-------CAGTGGAAAGAGCACTGGACTTGGAGTCA 44 chr5ptel1M 503216 TTAATACCTGAATTTAGATCCAGCTTCTGACATTTACTAGCTGTGTGACC 503265 vv v ii iiii v vi v i MIRc#SINE/MIR 45 GGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACC 94 chr5ptel1M 503266 ACAAATAAAATTGCTTAGCCTCCCTGAGCC-CA-TTTACTCATCTTTGAG 503313 viiiii- i ii i i - - v v i i MIRc#SINE/MIR 95 TTGGGC-AAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAA 143 chr5ptel1M 503314 ATAGAGATAACAACACCTTTAGTACTTACTAAAAAGAGTTATT-TAATAC 503362 i i i i vivv i i ivv v i i - i viv MIRc#SINE/MIR 144 ATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGA 193 chr5ptel1M 503363 TCAGGTGTGACAA 503375 ii v i MIRc#SINE/MIR 194 TCAAATGAGATAA 206 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 44.07 CpG sites = 42, Kimura (unadjusted) = 45.15 Transitions / transversions = 1.83 (42/23) Gap_init rate = 0.06 (12 / 206), avg. gap size = 1.17 (14 / 12) 1340 30.02 3.10 3.10 chr5ptel1M 503389 504292 (495708) L1M5_orf2#LINE/L1 2391 3294 (0) m_b230s551i9 9059 chr5ptel1M 503389 TAACTGGAAAAATATTAAATGCTCTTGGATTGGGCGAGCAAATATAATAA 503438 v i i vvv i v iv viv vi ? L1M5_orf2#LIN 2391 TAAATGGAGAGATATACCATGTTCATGGATTGGAAGACTCAATATTGTNA 2440 chr5ptel1M 503439 AGATGACAATACTACCTAAACTAATCTATTTATTTAGCGCTATACCAATC 503488 v v v i i i vv i ii v v L1M5_orf2#LIN 2441 AGATGTCAATTCTCCCCAAATTGATCTATAGATTCAATGCAATCCCAATC 2490 chr5ptel1M 503489 AGACTCCCAAAAAACTATTTTAATGACCTAGAAAAAATAACAACAAAGTT 503538 i v iv iii v ivv vv v v iv i ivvi i L1M5_orf2#LIN 2491 AAAATCCCAGCAGGTTTTTTTGTAGAAATTGACAAGCTGATTCTAAAATT 2540 chr5ptel1M 503539 CATATGGAAAAACAAAAGGTCAAGAAT-TTCAAGGGAATTAATGAAAAAA 503587 i vi i ii ? -vi iiv iv- i L1M5_orf2#LIN 2541 TATATGGAAATGCAAAGGACCNAGAATAGCCAAAACAATCT-TGAAAAAG 2589 chr5ptel1M 503588 AA-ATCAAATGATGGTGG-CTTAGCTGTACCAGATCT-AAAATTATATTA 503634 - v - v v - - vv ? ? - i i - L1M5_orf2#LIN 2590 AAGAACAAA-GTTGGAGGACTTA-CACTACCNGATNTCAAGACT-TATTA 2636 chr5ptel1M 503635 TAGAGCAGCAGTTACCAAAACTATTTGGTATTGGC-TAAGGAATAGATTA 503683 i vi v i i vi v - - iv L1M5_orf2#LIN 2637 TAAAGCTACAGTAATCAAGACAGTGTGGTATTGGCGTAAGGA-TAGACAA 2685 chr5ptel1M 503684 GTTGATCAGTGGAATAGATTAG---GTTCAAGGGATAAAACAGTCA-ACA 503729 i v i i v --- i - ii i v --- - L1M5_orf2#LIN 2686 ATAGATCAATGGAACAGAATAGAGAGTCCA-GAAATAGACC---CACACA 2731 chr5ptel1M 503730 AATATAGCAACCTAGTCTTTGACAAAC---CCAAAG-ATCCCAGCTTTTG 503775 v i ?v ?i ii i v--- ? - vii ---- L1M5_orf2#LIN 2732 TATATGGNCANTTGATTTTTGACAAAGGTGCCAANGCAATTCAG----TG 2777 chr5ptel1M 503776 GGATAAGAACTTACTGTTTGATAAAAATTGCTGGGAAAATTGGAAACTAA 503825 iv i ivvv v ii i viv i v v iiv L1M5_orf2#LIN 2778 GGGAAAGGATAGTCTTTTCAACAAATGGTGCTGGAACAATTGGATATCCA 2827 chr5ptel1M 503826 TATGGCAGAAACTAGGCATTGATCCATACTTAACGCCGTACACCAAGATA 503875 v i v iii?v i i v i v i i v i v L1M5_orf2#LIN 2828 TATGGAAAAAAATGAANCTCGACCCCTACCTCACACCATACACAAAAATT 2877 chr5ptel1M 503876 AGGTCAAAATGGGTTCAT-GACCTAGGCATAAAGAATGAAATTATTAATA 503924 iv ? i i - - iiii ii? i i v vv L1M5_orf2#LIN 2878 AATTCNAGATGGAT-CATAGACCTAAATGTAAAAGNTAAAACTATAAAAC 2926 chr5ptel1M 503925 AATTAGAGGAA--CATAGGATAGTTTACCTCTCAGACCTGTGGA-AGGGG 503971 vvi i -- v i -- i iivv vv ?- vi L1M5_orf2#LIN 2927 TTCTAGAAGAAAACATAGGAGAAT--ATCTTCGTGACCTTGGGNTAGGCA 2974 chr5ptel1M 503972 AAGGTCTTTATGACCAAAGCAGAACTAGAGATCATTACTGATCACAAAAT 504021 i i i - i v iii v -- i -----i ?i i i v L1M5_orf2#LIN 2975 AAGATTTCT-TAAACAGGACACAA--AAAG-----CACNAACCATAAAAG 3016 chr5ptel1M 504022 AGAAAATT-------TCGATTATACCAAACTGAAAAGTTTTTGTACAAAC 504064 i ------- v i ?i i v v ii i iv ?vvv L1M5_orf2#LIN 3017 AAAAAATTGATAAATTGGACTNCATCAAAATTAAAAACTTCTGCTCNTCA 3066 chr5ptel1M 504065 AAAACTAATGCAGACAAGATTAGAAGGGAAGCAATAAACTGGGAAAATAT 504114 ivi vi ivi v i v i v v i i ? i v L1M5_orf2#LIN 3067 AAAGACACCGTTAAGAAAATGAAAAGGCAAGCCACAGANTGGGAGAAAAT 3116 chr5ptel1M 504115 TTTTACAGTCAAAGGT-TCTGATAAAGGCCTCATTTCCAAAATATATAGA 504163 v i i?- v vi - i v i v i i L1M5_orf2#LIN 3117 ATTTGCAAN-ACATATATCTGACAAAGGACTCGTATCCAGAATATATAAA 3165 chr5ptel1M 504164 GAATTAACTCTAATTTA-TAAAAAATCAAGCCATTC--TCCAATTGAAAA 504210 i v- vi ? i - ? -- v vv --i v? L1M5_orf2#LIN 3166 GAACTC-CTACAANTCAATAANAAA--AAGACAAACAACCCAATANAAAA 3212 chr5ptel1M 504211 ATGGTCAAAGGATATGAACAGACAATTCTCAGATGAAGAAATTGAAACTA 504260 v i iv v v i v v ?v ivi L1M5_orf2#LIN 3213 ATGGGCAAAAGACTTGAACAGACACTTCACAAAAGAAGATATNCAAATGG 3262 chr5ptel1M 504261 TTTCTAGTCATATGAAAAGATGCTCCAAGTCA 504292 iivv iv i v v? L1M5_orf2#LIN 3263 CCAATAAGCACATGAAAAGATGCTCAACNTCA 3294 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 39.65 CpG sites = 143, Kimura (unadjusted) = 40.44 Transitions / transversions = 1.19 (143/120) Gap_init rate = 0.05 (44 / 903), avg. gap size = 1.27 (56 / 44) 1587 28.55 2.81 3.13 chr5ptel1M 504149 504788 (495212) L1ME5_3end#LINE/L1 7 644 (297) m_b230s551i11 9059 chr5ptel1M 504149 TCCAAAATATATAGAGAATTAACTCTAATTTATAAAAAATCAAGCCATT- 504197 i i i ii i vviv v iv i i -- v iv?- L1ME5_3end#LI 7 TCTAGAATATACAAGGAACTCCTGCAAATCAACAAGAAA--AAGACGGNA 54 chr5ptel1M 504198 -CTCCAATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGA 504246 - i v v i iv v L1ME5_3end#LI 55 ACCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGA 104 chr5ptel1M 504247 AGAAA-TTGAAA--CTATTTCTAGTCATATGAAAAGATGCTCCAAGTCAT 504293 i -ii -- --v v - i v v L1ME5_3end#LI 105 GGAAACCCGAAAGGCTA--ACAAG-CATATGAAGAGATGCTCAAACTCAT 151 chr5ptel1M 504294 TATTAATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACA 504343 v i vv i i vi L1ME5_3end#LI 152 TAGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACA 201 chr5ptel1M 504344 CCTGTCAGATTGGCTAAGATGACAGGAAA--AAATAATGATGATTGTTGG 504391 i i i v i --i i i--ii vii v L1ME5_3end#LI 202 CCTATTAGACTGGCAAAAAT--TAGAAAGCTGGATAATGCCAAGTGTTGG 249 chr5ptel1M 504392 AGGGGATGCGGGAAAACTGGGACATTGATGCATTGTTGGTGGAGTTGTGA 504441 v i i i ? iv i vi v i i iiv ii L1ME5_3end#LI 250 CGAGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAG 299 chr5ptel1M 504442 ACGAATCCAACCATTTTGGAGAGTAGTTTGGAACTA--TGCTCAAA--AA 504487 vii v i i i i i v v -- iv -- L1ME5_3end#LI 300 ACTGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTAA 349 chr5ptel1M 504488 GTTATCAAACTGTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGATT 504537 - --- --- v i i viii v vv L1ME5_3end#LI 350 G-TAT---AC---GCATACCCTATGACCCAGCAATTCCGCTCCTGGGTAT 392 chr5ptel1M 504538 ATATCCCAAAGAGATTATAAAGAAGG----GAAAGGGACCTGTATGTGCC 504583 i v v viv ----v i v i ---- L1ME5_3end#LI 393 ATATCCCAAAGAAATTCTCACACAGGTCCATAAGGGGACATGTACG---- 438 chr5ptel1M 504584 AAAATGTTTGTGGCAGCCCTGTTTGTAGTGGCCAGAAGCTGGAAAATGAA 504633 ii ii v vi i vi i i iivvivv L1ME5_3end#LI 439 AGGATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACC 488 chr5ptel1M 504634 TGGATGCCCATCAATTGGAGAATGGTTGAGTAAATTGTGGTATATGAATG 504683 i i v v i v ii v iv v ii L1ME5_3end#LI 489 TGGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACA 538 chr5ptel1M 504684 TTATGGAATAGTATTGTTCTGTAAGAAATGACCAGCAGGACGAATACAGA 504733 ii i v vvvv v v iii vii vi i v i v L1ME5_3end#LI 539 CCATGGAGTACTATGCAGCAGTTAGAAGCAACGGACTAGATGTACACATA 588 chr5ptel1M 504734 G-AGGATTGGCGAGACTTACATGAAC-TGATGCTGAGCGAAATGAGC-AG 504780 - iv v ii iiv v -- - ii i vi i- L1ME5_3end#LI 589 GCAACATGGATGGATCTTAAA--AACATAGTGCTGAGTGAAAAAAGTAAG 636 chr5ptel1M 504781 AACCAGGA 504788 v i L1ME5_3end#LI 637 AAACAGAA 644 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 35.97 CpG sites = 104, Kimura (unadjusted) = 37.06 Transitions / transversions = 1.42 (104/73) Gap_init rate = 0.05 (31 / 639), avg. gap size = 1.23 (38 / 31) 1622 27.78 0.36 1.66 chr5ptel1M 504149 504697 (495303) L1ME3G_3end#LINE/L1 7 548 (376) m_b230s551i10 9059 chr5ptel1M 504149 TCCAAAATATATAGAGAATTAACTCTAATTTATAAAAAATCAAGCCATTC 504198 i i i vviv v iv i -- v --v L1ME3G_3end#L 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAA--AAGACA--A 52 chr5ptel1M 504199 TCCAATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGAAG 504248 i v v i v v i L1ME3G_3end#L 53 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chr5ptel1M 504249 AAATTGAAACTATTTCTAGTCATATGAAAAGATGCTCCAAGTCATTATTA 504298 vv iviiivv iv v vv i v L1ME3G_3end#L 103 AAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTA 152 chr5ptel1M 504299 ATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACACCTGT 504348 i i vv i i viv ii L1ME3G_3end#L 153 ATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCAT 202 chr5ptel1M 504349 CAGATTGGCTAAGATGACAGGAAAAAATAATGATGATTGTTGGAGGGGAT 504398 v i vvv iii?vvi ivi? v v i i L1ME3G_3end#L 203 CAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGT 252 chr5ptel1M 504399 GCGGGAAAACTGGGACATTGATGCATTGTTGGTGGAGTTGTGAACGAATC 504448 i i v v vi v i i i iiv i ivii v L1ME3G_3end#L 253 GTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTA 302 chr5ptel1M 504449 CAACCATTTTGGAGAGTAGTTTGGAACTATGCTCAAAAAGTTATCAAACT 504498 i ? i i i v v - vvv i -- i v L1ME3G_3end#L 303 CAGCCNTTTTGGAGGGCAATTTGGCAGTAT-CTATTAAAAT--TTAAAAT 349 chr5ptel1M 504499 GTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGATTATATCCCAAAG 504548 i i i vii v ? ?v v i ? L1ME3G_3end#L 350 GCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAG 399 chr5ptel1M 504549 AGATTAT-AAAGAAG-GGAAAGGGACCTGTATGTGCCAAAATGTTTGTGG 504596 i vv -iv v v - v v i --? i i v ii ii v L1ME3G_3end#L 400 AAATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTCATTG 447 chr5ptel1M 504597 CAGCCCTGTTTGTAGTGGCCAGAAGCTGGAAAATGAATGGATGCCCATCA 504646 vi i i v i ii vvivv ii i L1ME3G_3end#L 448 CAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCA 497 chr5ptel1M 504647 ATTGGAGAATGGTTGAGTAAATTGTGGTATATGAATGTTATGGAATAGTA 504696 v i i i i vv ii v L1ME3G_3end#L 498 ATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACTA 547 chr5ptel1M 504697 T 504697 L1ME3G_3end#L 548 T 548 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 35.27 CpG sites = 80, Kimura (unadjusted) = 35.86 Transitions / transversions = 1.14 (80/70) Gap_init rate = 0.02 (11 / 548), avg. gap size = 1.00 (11 / 11) 458 23.21 3.57 0.00 chr5ptel1M 505611 505722 (494278) L1ME3G_3end#LINE/L1 433 548 (376) m_b230s551i12 9060 chr5ptel1M 505611 CAAAGATGTTTGTGGCAGCCCTCTTTGTAGTGGCCAGAAACTGGAAACTG 505660 i ii v vi v i i v i i vi L1ME3G_3end#L 433 CAAGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAA 482 chr5ptel1M 505661 AGTGGATGCCCATCAATTGGAGAATG----AATAAATCATGGTATATGAA 505706 vv ii i v i ---- i vv L1ME3G_3end#L 483 CCTAAATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCA 532 chr5ptel1M 505707 TATTATGGAATATTAT 505722 i i L1ME3G_3end#L 533 TACTATGGAATACTAT 548 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 28.42 CpG sites = 16, Kimura (unadjusted) = 28.42 Transitions / transversions = 1.60 (16/10) Gap_init rate = 0.01 (1 / 111), avg. gap size = 4.00 (4 / 1) 377 31.39 3.30 2.34 chr5ptel1M 505616 505827 (494173) L1ME1_3end#LINE/L1 442 655 (271) m_b230s551i13 9060 chr5ptel1M 505616 ATGTTTGTGGCAGCCCTCTTTGTAGTGGCCAGAAACTGGAAACTGAGTGG 505665 ii i ii v i i i i vivviii L1ME1_3end#LI 442 ATGTTCATAGCAGCTTTATTCGTAATAGCCAAAAACTGGAAACAACCCAA 491 chr5ptel1M 505666 ATGCCCATCAATTGGAGAATG----AATAAATCATGGTATATGAATATTA 505711 i i? v ---- i ii vv iv L1ME1_3end#LI 492 ATGTCCATCAACNGGTGAATGGATAAACAAATTGTGGTATATCCATACAA 541 chr5ptel1M 505712 TGGAATATTATTTTTCTGTAAGAAATGACCAGCAGGATGAT-TTCAGAAA 505760 i i ivv vi i ivi v i -viv -iv iv v L1ME1_3end#LI 542 TGGAATACTACTCAGCAATAAAAAGGAACGAAC-TACTGATACACGCAAC 590 chr5ptel1M 505761 GGCCTGGAGAGACTTACATAAAC-TGATGCTGAGTGAAATGAGCAGGAC- 505808 ii v vii ii - v ? - v vi vi - L1ME1_3end#LI 591 AACATGGATGAATCT-CAAAANCATTATGCTGAGTGAAAGAAGCCAGACA 639 chr5ptel1M 505809 CAGGAGATAATTATATACT 505827 ii --- ? i L1ME1_3end#LI 640 CAAAAG---ANTACATACT 655 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 41.56 CpG sites = 41, Kimura (unadjusted) = 43.36 Transitions / transversions = 1.71 (41/24) Gap_init rate = 0.04 (9 / 211), avg. gap size = 1.33 (12 / 9) 379 34.22 2.66 0.52 chr5ptel1M 505616 505803 (494197) L1MD1_3end#LINE/L1 442 633 (356) m_b230s551i14 9060 chr5ptel1M 505616 ATGTTTGTGGCAGCCCTCTTTGTAGTGGCCAGAAACTGGAAACTGAGTGG 505665 i i ii v i i i i vivvii L1MD1_3end#LI 442 ATGTTTATAGCAGCTTTATTCGTAATAGCCAAAAACTGGAAACAACCCAG 491 chr5ptel1M 505666 ATGCCCATCAATTGGAGAATG----AATAAATCATGGTATATGAATATTA 505711 i v iv v ---- i iii i vv ii L1MD1_3end#LI 492 ATGTCCTTCAACGGGTGAATGGTTAAACAAACTGTGGTACATCCATACCA 541 chr5ptel1M 505712 TGGAATATTATTTTTCTGTAAGAAATGACCAGCAGGATGAT-TTCAGAAA 505760 i i ivv vi i ivi v i -viv -iv iv v L1MD1_3end#LI 542 TGGAATACTACTCAGCAATAAAAAGGAACGAAC-TATTGATACACGCAAC 590 chr5ptel1M 505761 GGCCTGGAGAGACTTACATAAACTGATGCTGAGTGAAATGAGC 505803 ii vii ii v v i v v vi L1MD1_3end#LI 591 AACCTGGATGAATCTCCAGAGAATTATGCTGAGTGAAAAAAGC 633 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 44.68 CpG sites = 39, Kimura (unadjusted) = 47.79 Transitions / transversions = 1.56 (39/25) Gap_init rate = 0.02 (3 / 187), avg. gap size = 2.00 (6 / 3) 510 27.23 11.21 2.15 chr5ptel1M 506343 506556 (493444) MIRc#SINE/MIR 36 268 (0) m_b230s601i22 9061 chr5ptel1M 506343 TTGAATTGAGAGAGATTTGGCTTGAAATCTCTCCTTTGAAACTTA-TAGA 506391 i v v ii ii v vi i i vv i vv - v MIRc#SINE/MIR 36 TTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGC 85 chr5ptel1M 506392 TG----------AGCAATTTAC--AACCTCT--GGGTTTT--TTACCTCA 506425 ----------i v i -- -- i ii i-- v MIRc#SINE/MIR 86 TGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCA 135 chr5ptel1M 506426 TCTGTAAAATAACAGAGAGGTAGTGTTAG---TGTC-ATTGCAAAAGGTT 506471 ii-i v i- i iiiv --- i - iiv v i MIRc#SINE/MIR 136 TCTGTAAAATGG-GGATAA-TAATACCTGCCCTGCCTACCTCACAGGGTT 183 chr5ptel1M 506472 GCGGTGAGGATCAAATGAAATAATGTAT---AAAGTACTTTGTAAAAACC 506518 iv i --- ii --- MIRc#SINE/MIR 184 GTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTTTGTAAA---C 230 chr5ptel1M 506519 TTTAAAGTACAATGTAAATGTCAGCTATTATTTTCATT 506556 v i v ii v v?i v i MIRc#SINE/MIR 231 TGTAAAGTGCTATACAAATGTAAGGNGTTATTATTATT 268 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 33.64 CpG sites = 36, Kimura (unadjusted) = 35.27 Transitions / transversions = 1.71 (36/21) Gap_init rate = 0.06 (13 / 213), avg. gap size = 2.23 (29 / 13) 253 38.14 3.91 3.91 chr5ptel1M 506687 506967 (493033) L2#LINE/L2 2526 2806 (276) m_b230s601i23 9062 chr5ptel1M 506687 TTCATTCCTCCTGTCCCCTTGACTCACAACTTGAGAATCATCCTTGACTC 506736 i i i v iv iiv i iv v i vi i L2#LINE/L2 2526 TCCATCCTTCCAGTTGCTCAGGCCAAAAACCTTGGAGTCATCCTTGACTC 2575 chr5ptel1M 506737 TT-TCCTTATCTCCTTCCTTCCTTCCCATGTGTTATCGGTTCCAAATTTT 506785 i - i v viv iiv v v ---ii i --- ii L2#LINE/L2 2576 CTCTCTTTCTCTCACACCCCACATCCAAT---CCATCAG---CAAATCCT 2619 chr5ptel1M 506786 ACCTACTCTTTCTCCATAACCTCTCTTGAAATCATCTGATTCTTTCCACT 506835 ii vi vi i v iv v iv vi iv iiv iv i L2#LINE/L2 2620 GTCGGCTCTACCTTCAAAATATATCCAGAATCCGACCACTTCTCACCACC 2669 chr5ptel1M 506836 CGTATTATCATCATAGTTTGGATATTCATTTCTTTTTC-TCTTTTGCTTT 506884 ivi i ii i i--ii --- i vvi viiv - i i i v L2#LINE/L2 2670 TCCACTGCCACCAC--CCTGG---TCCAAGCCACCATCATCTCTCGCCTG 2714 chr5ptel1M 506885 GA------CCATAGCTTCCTAATTGGTTGCCCTGTTTCTG-ACTTGCCCC 506927 ------ v i i iv i ii-v L2#LINE/L2 2715 GATTACTGCAATAGCCTCCTAACTGGTCTCCCTGCTTCCACCCTTGCCCC 2764 chr5ptel1M 506928 TCTCTAATTGACTTTC--CAAAGTAGACATAGAAACCTGTTT 506967 i ?i i iv i i -- v i v v vi i iv L2#LINE/L2 2765 CCTNCAGTCTATTCTCAACACAGCAGCCAGAGTGATCCTTTT 2806 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 55.75 CpG sites = 66, Kimura (unadjusted) = 57.52 Transitions / transversions = 1.78 (66/37) Gap_init rate = 0.06 (16 / 280), avg. gap size = 1.38 (22 / 16) 310 24.76 24.60 0.64 chr5ptel1M 508305 508430 (491570) C MIRb#SINE/MIR (110) 158 3 m_b230s601i24 9063 chr5ptel1M 508305 TATTGTCTTTATTTTGAAGATGAGAAAAC--AGGTTAAGAGAG--CACAG 508350 i iii iv i -- i v --i - C MIRb#SINE/MIR 158 TATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTA-AG 110 chr5ptel1M 508351 TTATTTGCCC-AGTTCACACAGCTA--------CAAAG-----------G 508380 v i - v -------- i -----------i C MIRb#SINE/MIR 109 TAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAA 60 chr5ptel1M 508381 CCC-------TTTGACTCCAACTTCTTTGCTATTTTCACTAAGTCATGTT 508423 ------- i vvi iv v i ivii i i C MIRb#SINE/MIR 59 CCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCACCACGCT 10 chr5ptel1M 508424 GCTTCTC 508430 ii C MIRb#SINE/MIR 9 GCCCCTC 3 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 29.03 CpG sites = 22, Kimura (unadjusted) = 31.47 Transitions / transversions = 2.44 (22/9) Gap_init rate = 0.06 (7 / 125), avg. gap size = 4.57 (32 / 7) 12 23.27 6.00 0.00 chr5ptel1M 510441 510490 (489510) (TTTCTTGA)n#Simple_repeat 1 53 (0) m_b230s252i16 9064 chr5ptel1M 510441 TTTCCT-ATTTTTTTA-TTCTTTAGGTTTTGTTTTATTG-TGTCTTGATT 510487 i - i v - v vv i v v - v (TTTCTTGA)n#S 1 TTTCTTGATTTCTTGATTTCTTGATTTCTTGATTTCTTGATTTCTTGATT 50 chr5ptel1M 510488 TCT 510490 (TTTCTTGA)n#S 51 TCT 53 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.06 (3 / 49), avg. gap size = 1.00 (3 / 3) 285 40.37 0.00 0.62 chr5ptel1M 511920 512081 (487919) L2#LINE/L2 2612 2772 (310) m_b230s601i25 9065 chr5ptel1M 511920 CAAGTCTTGTCAATTCTACCTTCATAAAGTTTCTCATATCCATTCTCTTA 511969 i i iii v vi v iviv ivi v v L2#LINE/L2 2612 CAAATCCTGTCGGCTCTACCTTCAAAATATATCCAGAATCCGACCACTTC 2661 chr5ptel1M 511970 TCTCTCTTGACTCTGCCAATAACCTAGTATAAGTCCTAATCATCTTTTTC 512019 v iviivv v vi v i vi i viv i iv L2#LINE/L2 2662 TCACCACCTCCACTGCCACCACCCTGGTCCAAGCCACCATCATCTCTCGC 2711 chr5ptel1M 512020 CTGGAGCTTTGCAAAGATTATCTTAAGCAATCTCTCTACTTTTAGTCTCT 512069 vivi viiii- i viii i i ii vi iv L2#LINE/L2 2712 CTGGATTACTGCAATAGCC-TCCTAACTGGTCTCCCTGCTTCCACCCTTG 2760 chr5ptel1M 512070 CTCCCATATAAT 512081 i v ?i i L2#LINE/L2 2761 CCCCCCTNCAGT 2772 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 57.71 CpG sites = 39, Kimura (unadjusted) = 62.32 Transitions / transversions = 1.50 (39/26) Gap_init rate = 0.01 (1 / 161), avg. gap size = 1.00 (1 / 1) 265 30.38 1.25 1.25 chr5ptel1M 512176 512255 (487745) L2d2_3end#LINE/L2 9 88 (467) m_b230s601i26 9065 chr5ptel1M 512176 TTTGGTCCCAAGTTACTTTTCCAACTTGATTTCACATTACT-TTTTTCAT 512224 i i vi ? i i i v i v i i -iii ? i L2d2_3end#LIN 9 TCTGGCCCCAACCTNCCTTTCCAGCCTTATCTCCCACTATTCCCCTNCAC 58 chr5ptel1M 512225 GCACTCTCATGTTACAGACAAGCTAGTCTAC 512255 v i -i i v v i i L2d2_3end#LIN 59 GAACCCTC-CGCTCCAGCCAAACTGGTCTAC 88 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 38.76 CpG sites = 18, Kimura (unadjusted) = 43.66 Transitions / transversions = 3.00 (18/6) Gap_init rate = 0.03 (2 / 79), avg. gap size = 1.00 (2 / 2) 469 20.63 1.50 8.87 chr5ptel1M 512359 512491 (487509) MIRc#SINE/MIR 4 127 (141) m_b230s601i27 9066 chr5ptel1M 512359 GGCAGCTAGGTGGCACAGTGGATAGAGCACCAGCCCTGAAATCAGGAGGA 512408 i--- ii v ii v i i i i MIRc#SINE/MIR 4 GGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA 50 chr5ptel1M 512409 CCTGAGTTCAAATGTGGCCTCAGACACTTTA-CACTTCCTAGATGTGTGA 512457 i i i ----- i i --- i i- v v MIRc#SINE/MIR 51 CCTGGGTTCGAGT-----CCCGG---CTCTGCCACTTACTAGCTGTGTGA 92 chr5ptel1M 512458 CCCTGGGCAAGTCACTTGACCCCACTC-GCCTCAG 512491 i i i v v- MIRc#SINE/MIR 93 CCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 22.70 CpG sites = 19, Kimura (unadjusted) = 24.95 Transitions / transversions = 3.17 (19/6) Gap_init rate = 0.10 (13 / 132), avg. gap size = 1.00 (13 / 13) 25 21.08 0.00 1.72 chr5ptel1M 512493 512551 (487449) (AAAT)n#Simple_repeat 1 58 (0) m_b230s252i17 9067 chr5ptel1M 512493 AAATAAATAAATGGACAAATAAGTAAATGAATGAATGAATGAATAAGTAA 512542 ii i i i i i i i - (AAAT)n#Simpl 1 AAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAAT-A 49 chr5ptel1M 512543 AATAAAGAA 512551 v (AAAT)n#Simpl 50 AATAAATAA 58 Matrix = Unknown Transitions / transversions = 9.00 (9/1) Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1) 220 25.66 5.26 2.56 chr5ptel1M 513393 513468 (486532) L2d2_3end#LINE/L2 473 550 (5) m_b230s601i28 9065 chr5ptel1M 513393 TGCTTCTTTTGTCATATTTC-CAGCACCTAGTACAGTGATTTGC---TTT 513438 i - - viii - i i vi ---ivv L2d2_3end#LIN 473 TACTTCTTT-GT-ATCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAG 520 chr5ptel1M 513439 TTGATGCTTAATAAATGCTTGTTGAATTGA 513468 v ii i ii v L2d2_3end#LIN 521 TAGGCGCTCAATAAATATTTGTTGATTTGA 550 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 28.63 CpG sites = 13, Kimura (unadjusted) = 32.74 Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.05 (4 / 75), avg. gap size = 1.50 (6 / 4) 236 28.12 4.69 0.00 chr5ptel1M 513402 513465 (486535) L2a_3end#LINE/L2 443 509 (8) m_b230s601i29 9065 chr5ptel1M 513402 TGTCATATTTCCAGCACCTAGTACAGTGATTTGC---TTTTTGATGCTTA 513448 iii ii i v vi v --- vv v ii i L2a_3end#LINE 443 TGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGGCGCTCA 492 chr5ptel1M 513449 ATAAATGCTTGTTGAAT 513465 ii L2a_3end#LINE 493 ATAAATATTTGTTGAAT 509 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 31.78 CpG sites = 12, Kimura (unadjusted) = 36.82 Transitions / transversions = 2.00 (12/6) Gap_init rate = 0.02 (1 / 63), avg. gap size = 3.00 (3 / 1) 325 24.08 6.90 3.33 chr5ptel1M 514468 514583 (485417) C L2c_3end#LINE/L2 (12) 466 347 m_b230s601i30 9068 chr5ptel1M 514468 AAAAAATATATAT---ATGCCTATTGTGCTAATAAGCTCAAGGGATTCAA 514514 v i v ---ii i i - ivi i v vi v C L2c_3end#LINE 466 AACAAACATTTATTGAGCGCCTACTATG-TGCCAGGCGCTGGGGATACAA 418 chr5ptel1M 514515 AGATAGGCATAAGA----GTCCCCTCCTTCAAGTGGCTGGCAGTCTAATG 514560 -- v ---- iv i vi vi i C L2c_3end#LINE 417 AGAT--GAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAGTG 370 chr5ptel1M 514561 GAAGGAGACA-ACCTATAAAAAGA 514583 - - v?i v C L2c_3end#LINE 369 G-AGGAGACAGACANGTAAACAGA 347 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 28.57 CpG sites = 15, Kimura (unadjusted) = 29.86 Transitions / transversions = 1.25 (15/12) Gap_init rate = 0.06 (7 / 115), avg. gap size = 1.71 (12 / 7) 207 27.58 1.18 6.17 chr5ptel1M 514514 514598 (485402) C L2a_3end#LINE/L2 (81) 436 356 m_b230s601i31 9068 chr5ptel1M 514514 AAGATAGGCATAAGAGTCCCCTCCTTCAAGTGGCTGGCAGTCTAATGGAA 514563 i i -- i i iv i v vi vi v i ii C L2a_3end#LINE 436 AAAACAG--ACAAAAGTCCCTGCCCTCATGGAGCTTACATTCTAGTGGGG 389 chr5ptel1M 514564 GGAGACAACCTATAAAAAGAAGCTAAA-AAGTATAA 514598 iv v v i --- - v C L2a_3end#LINE 388 GGAGACAGACAATAAACAAA---TAAATAAGTAAAA 356 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 35.14 CpG sites = 13, Kimura (unadjusted) = 35.14 Transitions / transversions = 1.44 (13/9) Gap_init rate = 0.07 (6 / 84), avg. gap size = 1.00 (6 / 6) 404 31.19 12.53 7.48 chr5ptel1M 515466 515912 (484088) C L2c_3end#LINE/L2 (10) 468 1 m_b230s601i32 9069 chr5ptel1M 515466 TCAGCAAACATTTATTAGGTAGTAGGTGTTATGCTTGTGCTAAGCACTGG 515515 i i--- iivv ii ---- i i i C L2c_3end#LINE 468 TCAACAAACATTTATTG---AGCGCCTACTATG----TGCCAGGCGCTGG 426 chr5ptel1M 515516 GGATAAAAGAAAAGAAAAAAATCAAAATAAAAACCAGTATCCTTGTTCTT 515565 v ---------- i --i i vv i -- i ii i C L2c_3end#LINE 425 GGATACAA----------AGAT--GAATAAGACACGGT--CCCTGCCCTC 390 chr5ptel1M 515566 AAAGAACTCACATTCTAATAAGGAAGGCA-ACATGTAAAC-------TAC 515607 i i v i iii i i - ? ------- C L2c_3end#LINE 389 AAGGAGCTCACAGTCTAGTGGAGGAGACAGACANGTAAACAGACAATTAC 340 chr5ptel1M 515608 AATGTACATTCAAGATAATTGC-------AGAGTAAATGAAAAG------ 515644 ii vi v v v -------i v - v i ------ C L2c_3end#LINE 339 AATACAAGTTAATGATAAGTGCTATAATGGGAGTATA-GACAGGGTGCTA 291 chr5ptel1M 515645 TAGTAGCTGAGGGGAGGCGTTCTCGGGAAAAGCAT----GCCCAGAAATG 515690 i v vv i - iv iii ivv i? v ---- vi ii v C L2c_3end#LINE 290 TGGGAGCACAGAGGAGG-GCACCTAGACTAGNCTTGGGGGGTCAGGGAAG 242 chr5ptel1M 515691 CCTTGTCCAGAC--AGTGAGAGTTGAGTTAAAGATTAAAAGAAGCTAGAG 515738 v -i i v--i v vi i i i?v i i v ------ C L2c_3end#LINE 241 GCTT-CCCGGAGGAGGTGACATCTGAGCTGAGNCTTGAAGGATG------ 199 chr5ptel1M 515739 AAATGAGGAGCTAG--AGATGAAAAGATTGAG---CATCAATGCA--CAT 515781 - i - i -- i i i vv i ---v v v v -- v C L2c_3end#LINE 198 -AGT-AGGAGTTAGCCAGGTGGAAGGAGGGGGGAAGAGCATTCCAGGCAG 151 chr5ptel1M 515782 AAGGAACAACCTGTCCAAAG-----------GAAAAGAAA---------- 515810 i i v v ----------- i v---------- C L2c_3end#LINE 150 AGGGAACAGCATGTGCAAAGGCNCGGAGGCAGGAAAGAACTGCGGCGTGT 101 chr5ptel1M 515811 -TGGGAGATGGAGTAAGGCCATTGTGATTGGATTGTAGAGAACCTGTAGA 515859 - ii v iv? vi v ii vii v ii -- vi C L2c_3end#LINE 100 TTGGGGAATGCAAGNAGTTCAGTGTGGCTGGAGCATAGTGGGC--GAGGA 53 chr5ptel1M 515860 GGGAAGTAAAGGATAAGGAGACTAGAAAAGTAAGGATGGGTCCGATTGTG 515909 i ii -i v i i i i i v v i v i C L2c_3end#LINE 52 GGGGAGTGGAGGA-GATGAGGCTGGAGAGGTAGGCAGGGGCCAGATCGTG 4 chr5ptel1M 515910 AAG 515912 ? C L2c_3end#LINE 3 NAG 1 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 40.72 CpG sites = 81, Kimura (unadjusted) = 43.01 Transitions / transversions = 1.69 (81/48) Gap_init rate = 0.11 (47 / 446), avg. gap size = 1.94 (91 / 47) 17 5.95 8.57 0.00 chr5ptel1M 515949 515983 (484017) (AGTAAA)n#Simple_repeat 1 38 (0) m_b230s252i18 9070 chr5ptel1M 515949 AGTAAAAG--AGAGTAAAA-AAAAAGTAAAAGTAAAAG 515983 -- i -v (AGTAAA)n#Sim 1 AGTAAAAGTAAAAGTAAAAGTAAAAGTAAAAGTAAAAG 38 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.50 (3 / 2) 391 34.02 8.27 5.04 chr5ptel1M 516298 516817 (483183) C L2#LINE/L2 (438) 2644 2109 m_b230s601i33 9069 chr5ptel1M 516298 GATATAATGTAACGTTAGAAATGACAAAATTTTCAG-TGTATT---TATG 516343 v v i v v ivi ii v v - v --- i C L2#LINE/L2 2644 GATATATTTTGAAGGTAGAGCCGACAGGATTTGCTGATGGATTGGATGTG 2595 chr5ptel1M 516344 AGGTGT-ATATAAATAGTTGAGC--AGGATA---CCAAA--------TAT 516379 i - v v v vv i-- i--- i--------iv C L2#LINE/L2 2594 GGGTGTGAGAGAAAGAGAGGAGTCAAGGATGACTCCAAGGTTTTTGGCCT 2545 chr5ptel1M 516380 GAATAATTGAGAGACTGCTGGTGCTCTGGATAGTAATGAAAAA-ATTA-A 516427 ii i ii iv vv v iv v? iv vi iii - i i-i C L2#LINE/L2 2544 GAGCAACTGGAAGGATGGAGTTGCCATTNACTGAGATGGGGAAGACTGCG 2495 chr5ptel1M 516428 AAATAAGCAACGGTTGGGTTAAAGGGATTGTAGAGATAATGTTCTTGTTT 516477 ii vi -- v --- ii vvi vii ---- v- C L2#LINE/L2 2494 GGAGGAGCA--GGTTTG---AGGGGGAAGATCAGGA----GTTCA-GTTT 2455 chr5ptel1M 516478 TGAATATGTTAGGTTTTAGATGCATATAGAAGAGGTAATTTGCAATGTCT 516527 i i i v v vii v vvi v v vi v C L2#LINE/L2 2454 TGGACATGTTAAGTTTGAGATGCCTATTAGACATCCAAGTGGAGATGTCG 2405 chr5ptel1M 516528 AAAAGGCAATTCACTGGTGATGTGAGACTGATGCTCAAGGGAGAAATTAG 516577 iv i ---- vv ii v iv i i ii iv C L2#LINE/L2 2404 AGTAGGCAGTT----GGATATACGAGTCTGGAGTTCAGGGGAGAGGTCCG 2359 chr5ptel1M 516578 GCCTGGA--TATAAACCTCTGATAATCATC--TATATAGACGTAATATTT 516623 v -- -- i iv i --i -- ii C L2#LINE/L2 2358 GGCTGGAGATATAAA--TTTGGGAGTCATCAGCATATAGA--TGGTATTT 2313 chr5ptel1M 516624 TAACTCATGAGATTCAATGAGATCATAAAACAAA-GATACTACACA---A 516669 v vi i vi iv? ivi i- vvv v i --- C L2#LINE/L2 2312 AAAGCCATGAGACTGGATGAGATCACCNAGGGAGTGAGTGTAGATAGAGA 2263 chr5ptel1M 516670 ATAGAA-AGG---AACTACT--GTCTAGGAGAATGTTCA--GTT-AGTGG 516710 v - --- vv -- i iv i v i- i -- - v C L2#LINE/L2 2262 AGAGAAGAGGTCCAAGGACTGAGCCCTGGGGCAC-TCCAACGTTNAGAGG 2214 chr5ptel1M 516711 TTATAAATGACATAGATTAAGATCCAGTAAAGGAAGCTAAGAAGATACTT 516760 i---iiv v - vv i v i ii i ivi vv C L2#LINE/L2 2213 TC---GGGGAGAT-GAGGAGGAACCAGCAAAGGAGACTGAGAAGGAGCGG 2168 chr5ptel1M 516761 TCACACTGGT------AAAACAAGGAAAGAAGAATGTTCACAAAAAAAGC 516804 i vvvv ------ v i vivii i ----vii C L2#LINE/L2 2167 CCAGTGAGGTAGGAGGAAAACCAGGAGAGTGTGGTGTCC----TGGAAGC 2122 chr5ptel1M 516805 CTAGACAAGAAAG 516817 v vv C L2#LINE/L2 2121 CAAGTGAAGAAAG 2109 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 45.15 CpG sites = 88, Kimura (unadjusted) = 46.70 Transitions / transversions = 1.10 (88/80) Gap_init rate = 0.09 (45 / 519), avg. gap size = 1.56 (70 / 45) 597 21.23 1.31 7.64 chr5ptel1M 516827 516979 (483021) MIRc#SINE/MIR 3 146 (122) m_b230s601i34 9071 chr5ptel1M 516827 AAGTAG-GTGGTGCCATACTGCATAGAGTAATGGGCTTGGAATCAGGAAG 516875 i i - --- v v v i v i i MIRc#SINE/MIR 3 AGGCAGTGTGGTGC---AGTGGAAAGAGCACTGGACTTGGAGTCAGGAAG 49 chr5ptel1M 516876 ACTCAACTTCATGAGTTCAAATCCTACATCAGATACTTACTGGGTGTGTG 516925 i-------- i i i iivv v vi i v MIRc#SINE/MIR 50 ACC--------TGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTG 91 chr5ptel1M 516926 AACTTGGCCAACTCACTCAACC-CTATTTGCCTCAATTTCCTCATCTGTA 516974 v v v i - v vv i MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTA 141 chr5ptel1M 516975 AAATG 516979 MIRc#SINE/MIR 142 AAATG 146 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 23.07 CpG sites = 15, Kimura (unadjusted) = 24.99 Transitions / transversions = 1.00 (15/15) Gap_init rate = 0.09 (13 / 152), avg. gap size = 1.00 (13 / 13) 343 31.01 0.00 5.15 chr5ptel1M 518662 518763 (481237) L3#LINE/CR1 3545 3641 (458) m_b231s601i0 9072 chr5ptel1M 518662 GAAGTGATAATTGAGTTGAACCTTGCCTATATTGGTCAGACTGCACCTGA 518711 i i i ivv i v ii ----ii ii i i L3#LINE/CR1 3545 GAGGTAATAGTCCCGCTGTACTCTGC----GCTGGTCAGACCACATCTGG 3590 chr5ptel1M 518712 AATATTGTGTTCATTTCCAGGCACCATAGTTCATGAGGCTCAGTTAACAA 518761 i i v ii i i v i v vv - i L3#LINE/CR1 3591 AGTATTGCGTTCAGTTCTGGGCGCCACATTTTAAGAGGGACA-TTGACAA 3639 chr5ptel1M 518762 GC 518763 i L3#LINE/CR1 3640 AC 3641 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.24 CpG sites = 22, Kimura (unadjusted) = 42.91 Transitions / transversions = 2.75 (22/8) Gap_init rate = 0.05 (5 / 101), avg. gap size = 1.00 (5 / 5) 348 31.58 2.63 8.33 chr5ptel1M 518751 518902 (481098) C L2c_3end#LINE/L2 (6) 472 329 m_b231s601i2 9073 chr5ptel1M 518751 TCAGTTAACAAGCATTTATCAAATGCCTACTATGTGTCAAGCACTGAACT 518800 v i i ii ii i ----------- C L2c_3end#LINE 472 TCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCA----------- 434 chr5ptel1M 518801 CGGCACTGGGAACGCAGAGAATGGCAAAAGAGAGTCTCTGCTTTGATGTG 518850 - i i ii i vviii i v vi i ii v v vi C L2c_3end#LINE 433 -GGCGCTGGGGATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGA 385 chr5ptel1M 518851 ACT--CAGTCTAATGGAAGAAACA-ATAAGGAAATGAATGGGGACAA-AC 518896 i -- i i i - i ? v iii iiivv - C L2c_3end#LINE 384 GCTCACAGTCTAGTGGAGGAGACAGACANGTAAACAGACAATTACAATAC 335 chr5ptel1M 518897 AAGATA 518902 v C L2c_3end#LINE 334 AAGTTA 329 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.19 CpG sites = 32, Kimura (unadjusted) = 44.31 Transitions / transversions = 2.67 (32/12) Gap_init rate = 0.10 (15 / 151), avg. gap size = 1.07 (16 / 15) 443 28.68 8.82 0.00 chr5ptel1M 518751 518886 (481114) C L2a_3end#LINE/L2 (6) 511 364 m_b231s601i1 9073 chr5ptel1M 518751 TCAGTTAACAAGCATTTATCAAATGCCTACTATGTGTCAAGCACTGAACT 518800 v i ii ii ii i i vv C L2a_3end#LINE 511 TCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCT 462 chr5ptel1M 518801 CGGCACTGGGAAC---GCAGAGAAT--GGCAAAAGAGAGTCTCTGCTTTG 518845 v i i i--- v i--ii i vi i i ii v C L2a_3end#LINE 461 AGGCGCTGGGGATACAGCAGTGAACAAAACAGACAAAAGTCCCTGCCCTC 412 chr5ptel1M 518846 ATGTGACT--CAGTCTAATGGAAG-----AAACAATAAGGAAATGAAT 518886 vii -- v i ii ----- i iv i C L2a_3end#LINE 411 ATGGAGCTTACATTCTAGTGGGGGGAGACAGACAATAAACAAATAAAT 364 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.05 CpG sites = 29, Kimura (unadjusted) = 38.63 Transitions / transversions = 2.90 (29/10) Gap_init rate = 0.03 (4 / 135), avg. gap size = 3.00 (12 / 4) 398 33.58 13.39 0.35 chr5ptel1M 518920 519173 (480827) L3#LINE/CR1 3597 3883 (216) m_b231s601i3 9074 chr5ptel1M 518920 GTGATCAGTT--GGAGGTCAT-CCTCAAGAAC--CACTGACAAGTTGGAA 518964 i v -- iv i i-ii i iv-- i ii i L3#LINE/CR1 3597 GCGTTCAGTTCTGGGCGCCACATTTTAAGAGGGACATTGACAAACTGGAG 3646 chr5ptel1M 518965 TAGGTCCCAAGAAGGGCTACAAATATGATGAAGAA---------CATGCC 519005 iiv vi i i v v iv i ii--------- i L3#LINE/CR1 3647 CGCGTCCAGAGGAGAGCGACCAGGATGGTGAAGGGTCTGGAAACCATGTC 3696 chr5ptel1M 519006 GAATGAGAATCACTTGACAGAACTGAGGCTGCTTCTCCTGAAGAAGAGAA 519055 iv i v iv vi i v i vv i L3#LINE/CR1 3697 ATATGAGGAACGGTTGAAGGAACTGGGGATGTTTAGCCTGGAGAAGAGAA 3746 chr5ptel1M 519056 AACTTGGTGGGCA-ACAAGAGATA-CTCTAAAT------AGATCT----- 519092 i i v iv - ii v v i- ii ------ iv ----- L3#LINE/CR1 3747 GACTTAGAGGAGACATGATAGCTGTCTTCAAATATTTGAAGGGCTGTCAT 3796 chr5ptel1M 519093 -----AAATGGATCACCCTTTTTCAGCCTGATACCCAGAAAGAATTCCTA 519137 ----- i v i vv v v iv ii-i ii v vvv L3#LINE/CR1 3797 GTGGAAGAGGGATTAGACTTATTCTGTGTGGC-TCCAGAGGGCAGAACTA 3845 chr5ptel1M 519138 GGAGCAGTGAATGC-ACTCACAAGGA-GCAGATTTCAG 519173 v i ii v- v i i - i L3#LINE/CR1 3846 GGACCAATGGGTGGAAGTTACAGGGAGGCAGATTTCGG 3883 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.45 CpG sites = 52, Kimura (unadjusted) = 46.55 Transitions / transversions = 1.58 (52/33) Gap_init rate = 0.05 (12 / 253), avg. gap size = 2.92 (35 / 12) 243 28.17 2.82 0.00 chr5ptel1M 519245 519315 (480685) L3#LINE/CR1 4021 4093 (6) m_b231s601i4 9074 chr5ptel1M 519245 GAGATTCCTGTGCAGGA-GTGAGTTTGGATGAAACTGTCTCTGAAGCCCC 519293 i iiiv - v v iv i ivii i i i L3#LINE/CR1 4021 GGGATTCCTGCATTGGATGGGAGGTTGGACTAGATGACCTCTAAGGTCCC 4070 chr5ptel1M 519294 TTCCAACTC-GAGTTCCTGCGAT 519315 - v i i L3#LINE/CR1 4071 TTCCAACTCTGAGATTCTGTGAT 4093 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.22 CpG sites = 14, Kimura (unadjusted) = 37.22 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.03 (2 / 70), avg. gap size = 1.00 (2 / 2) 244 23.44 0.00 0.00 chr5ptel1M 519377 519440 (480560) C L1MC_orf2#LINE/L1 (2016) 1278 1215 m_b231s551i0 9075 chr5ptel1M 519377 TAGCTTATCAAATTTTTTGGCATAAAGTTGGGCAACGTAACCCCTTATTA 519426 v v v i vv vv vi i C L1MC_orf2#LIN 1278 TAGGTTATCAAATTTGTGGGCATAGAGTTGTTCATAGTATTCCTTTATTA 1229 chr5ptel1M 519427 TTTCTTTAATTTCC 519440 iii v C L1MC_orf2#LIN 1228 TCCTTTTAATGTCC 1215 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 28.14 CpG sites = 6, Kimura (unadjusted) = 28.14 Transitions / transversions = 0.67 (6/9) Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0) 259 33.88 12.40 0.00 chr5ptel1M 519736 519856 (480144) MIRc#SINE/MIR 11 146 (122) m_b231s601i5 9076 chr5ptel1M 519736 TGGTGCGATAGATAGACTGGTAGGCCTTGAGACATGAAGACCTGAGTTTT 519785 ii i v viiv i i i v v v i iv MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr5ptel1M 519786 AATATCAACTCAGAAACTTG---------------TAGTCAAGTCACAGA 519820 i vi ii v vv i--------------- i v vv MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTA 110 chr5ptel1M 519821 TTCTCTGTTTTTCTCAGTTTCTTTTGCTGTAAAATG 519856 vi v vvvi i ivv MIRc#SINE/MIR 111 ACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATG 146 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.82 CpG sites = 20, Kimura (unadjusted) = 45.73 Transitions / transversions = 0.95 (20/21) Gap_init rate = 0.01 (1 / 120), avg. gap size = 15.00 (15 / 1) 205 31.95 5.92 3.21 chr5ptel1M 519918 520069 (479931) L2d_3end#LINE/L2 353 508 (8) m_b231s601i6 9077 chr5ptel1M 519918 TCCCTAGTTGTTCTGTCTAGTTGTTAGTGTTGTCAGTGCCACCAGTCTGT 519967 i i iii v i-- v vviv v i vi L2d_3end#LINE 353 TCTCTAATTGTTTCATGTG--TGTTAGTCTTGTCTCCCCAACTAGATTGT 400 chr5ptel1M 519968 CATCTTCCTGGGTGCAGAGGAC--TCCCTT-TACAACTCTCTTGGTTTCC 520014 v v i i i v - -- vi - v?i i ? i v ii L2d_3end#LINE 401 AAGCTCCTTGAGGGCAG-GGACCATGTCTTATACTNTTTTNTCGTTCCCC 449 chr5ptel1M 520015 -TGGTGCTTAACCCAAGGCCTGAA-ATGTAGCAGGCACTT----AATGCT 520058 -ii i i i v iv - i- ii i i i---- i L2d_3end#LINE 450 ACAGCGCCTAGCACAGTG-CTGAGCACATAGTAGGCGCTCAATAAATACT 498 chr5ptel1M 520059 TGTTTACTTGA 520069 v - L2d_3end#LINE 499 TGTTGA-TTGA 508 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.96 CpG sites = 31, Kimura (unadjusted) = 44.84 Transitions / transversions = 1.94 (31/16) Gap_init rate = 0.07 (10 / 151), avg. gap size = 1.40 (14 / 10) 287 33.73 1.20 0.00 chr5ptel1M 520077 520159 (479841) C MIRc#SINE/MIR (184) 84 1 m_b231s601i7 9078 chr5ptel1M 520077 CTAAGAAAGAGCAGTACCAGAATATCAGCCCATGTCTTT-TGAGTCCAAA 520125 iv ivi vi i i iviv i v i- v i C MIRc#SINE/MIR 84 CTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr5ptel1M 520126 TGTAGTGATCTTTCCCTTATACCATGCTGCCTTG 520159 vi v vi ii ii i C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTGCACCACACTGCCTCG 1 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.48 CpG sites = 18, Kimura (unadjusted) = 47.29 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.01 (1 / 82), avg. gap size = 1.00 (1 / 1) 239 30.69 3.42 2.54 chr5ptel1M 521132 521248 (478752) C MIRc#SINE/MIR (68) 200 83 m_b231s601i8 9079 chr5ptel1M 521132 CATTGGATCCTTACAGTAATCCTGTGACA-ATACAGAA-AGTGATTCCTT 521179 v i ii i vi- vi ii- vv v- C MIRc#SINE/MIR 200 CATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTA-TT 152 chr5ptel1M 521180 CTCACTATGTGCCCAACTCAGGCCAATAA--CTCAGAAAGGTTGAGTGAC 521227 v v i v -iv iv v vv v i -- i i C MIRc#SINE/MIR 151 ATCCCCATTT-TACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGAC 103 chr5ptel1M 521228 TTGACCCAAATCCCAGCAGTT 521248 v v ii v - i C MIRc#SINE/MIR 102 TTGCCCAAGGTCACA-CAGCT 83 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.94 CpG sites = 17, Kimura (unadjusted) = 39.94 Transitions / transversions = 0.94 (17/18) Gap_init rate = 0.05 (6 / 116), avg. gap size = 1.17 (7 / 6) 16 19.25 0.00 0.00 chr5ptel1M 521417 521446 (478554) (T)n#Simple_repeat 1 30 (0) m_b231s252i0 9080 chr5ptel1M 521417 TTGTTTTTGTGTTTTTTTTTTATTTTATTT 521446 v v v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 30 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 12 12.16 3.70 0.00 chr5ptel1M 523071 523097 (476903) (TCCC)n#Simple_repeat 1 28 (0) m_b231s252i1 9081 chr5ptel1M 523071 TCCCTCCCTCCCT-CCACCCTCTCCCCC 523097 - v i i (TCCC)n#Simpl 1 TCCCTCCCTCCCTCCCTCCCTCCCTCCC 28 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.04 (1 / 26), avg. gap size = 1.00 (1 / 1) 1126 29.01 3.18 3.39 chr5ptel1M 523418 523920 (476080) C L1ME5_3end#LINE/L1 (313) 628 127 m_b231s551i1 9082 chr5ptel1M 523418 TTTCACTTAGCATCA-GTTCATATAAGCCTC-TCCAAGCCTCTCTGTCTT 523465 i ii - -- v vii - v iiv v v v C L1ME5_3end#LI 628 TTTCACTCAGCACTATGTT--TTTAAGATCCATCCATGTTGCTATGTGTA 581 chr5ptel1M 523466 CATCCTGCTGGTCATTTCTTACAGAACAATAATATTCCATAACATTCATA 523515 iv iiv iii v v vvvv i i iiii v v C L1ME5_3end#LI 580 CATCTAGTCCGTTGCTTCTAACTGCTGCATAGTACTCCATGGTGTGCATC 531 chr5ptel1M 523516 TACCAAAATTTACCCAACCATTCTCCAATGGATGGGCATCC--CTTCATT 523563 i v v i v i v vv i i --v vvi C L1ME5_3end#LI 530 CACCACATTTTACCTATCCACTCTCCCAGTGATGGACACCCAGGTTGCCT 481 chr5ptel1M 523564 TCAGTTTCTAGCCGCTATAAACAGGGCTGCCACAAACATTTTGGCACATG 523613 i ii i iv i i i iv v ii ii v i C L1ME5_3end#LI 480 CCAACTCCCCGCCACCACAAACAACGCTGCAATGAACATCCTCGTACATG 431 chr5ptel1M 523614 CAGGTCCCTTTC----CCTTTTTTAGTATCTCTTTGGGATATAAGCCCAG 523659 ---- i v---- v v v v i vi C L1ME5_3end#LI 430 ----TCCCCTTATGGACCTGTGTGAGAATTTCTTTGGGATATATACCCAG 385 chr5ptel1M 523660 TAGTAGCACTGCTGGATCAAAGGGTGTGCACAGTTTGATAACTT--TTTG 523707 v ii v i i v i --- --- - -- C L1ME5_3end#LI 384 GAGCGGAATTGCTGGGTCATAGGGTATGC---GT---ATA-CTTAATTTG 342 chr5ptel1M 523708 GGCA--TAATTCCAGATTGCTCTCCAGAATGGTTGGATTCGTTCACAACT 523755 ivi -- v v i v iiv ii vii C L1ME5_3end#LI 341 ACTAAGTACTGCCAGATTGCTCTCCAGAATGGCTGCACCAGTCTACACTC 292 chr5ptel1M 523756 CCACCAACAATGCTTCAGTGTCTCAGTTTTCCCGCATCCACTCCAACACT 523805 i i v v v ii vi ? i i v v C L1ME5_3end#LI 291 CCACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATCCTCGCCAACACT 242 chr5ptel1M 523806 GATCATTATTT---TTTCCTGTCATCTTATCCAATGTTTCAGGTATGTAG 523852 viv ii--- --- v i vv i v vvi i iv C L1ME5_3end#LI 241 TGGCATTATCCAGCTTTC---TAATTTTTGCCAGTCTAATAGGTGTAAAG 195 chr5ptel1M 523853 TGGTATCTCAGAGTTGTTTTAATTTGCATTTCTCTGATCAATAGTGATTT 523902 i vv i v i v C L1ME5_3end#LI 194 TGATATCTCATTGTTGTTTTAATTTGCATTTCTCTGATTACTAATGAGTT 145 chr5ptel1M 523903 GGAACA-CTCTTTAATATG 523920 v i - i- C L1ME5_3end#LI 144 TGAGCATCTCTTC-ATATG 127 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.09 CpG sites = 76, Kimura (unadjusted) = 37.46 Transitions / transversions = 1.17 (76/65) Gap_init rate = 0.05 (25 / 502), avg. gap size = 1.32 (33 / 25) 574 36.85 4.98 1.55 chr5ptel1M 523955 524577 (475423) C Plat_L3#LINE/CR1 (353) 3220 2577 m_b231s551i2 9083 chr5ptel1M 523955 CTTTTCTTTTCCAGCTTAACCATCCCTAGGTCCTTCAAGGAATCCTCATG 524004 i i vi v v i iv i vvvv i C Plat_L3#LINE/ 3220 CTTCTCTTCTCCAGGCTAAACAACCCCAATTCCTTTAACCTTTCCTCATA 3171 chr5ptel1M 524005 GGACATGAACTCAAGACCTTTGACTATCCTCCTTGG----CACAGTACCA 524050 v ivvi v vv i ii ii iv i v---- v v v v C Plat_L3#LINE/ 3170 GGACCTATTTTCCATCCCTTTAATCATTTTTGTCGCTCTTCTCTGGACCC 3121 chr5ptel1M 524051 TCT--AGTTTATCAAAGTCCTTTCTAAAAGATGGTAGCCCAGAAGGAAAC 524098 -- v v vi i ivii - v i vvii C Plat_L3#LINE/ 3120 TCTCCAGTTTCTCCACATCCTTTTTAAAGTGCGGT-GACCAAAACTGGAC 3072 chr5ptel1M 524099 ACAAGAATCTA----TGTTCTTAACCAGGGTAGAGT---CCCCAGGGATT 524141 iv v ----v v -i v i ---v vv i C Plat_L3#LINE/ 3071 ACAGTACTCTAATAAGGGTCT-GACCAGTGCAGAGTATAGCGGAAGGATT 3023 chr5ptel1M 524142 GTCGCCTTCTTCCTGGCCTTGTCATGCA-----TAATGCATTTTGAGGTT 524186 iiiv ivvi i -- v i v----- i iiiiiviii C Plat_L3#LINE/ 3022 ACTTCCCGACTCTTG--CATGTCATACTCCTGTTAATACATCCCAGTACC 2975 chr5ptel1M 524187 ACATTTGCCTTTTTACCTGCCGTATCATGGTGTTGACTCATATTGAGCTG 524236 i v i vivi v i ii iiv i v v C Plat_L3#LINE/ 2974 ACGTTGGCTTTTTTAATAACGGCACTACATTGCTGACTCATATTCAGCTT 2925 chr5ptel1M 524237 CTGGTCCCCTAAAAACCTCAAATTTTTTTCAAAGGAACTC---TATAGCC 524283 ? vv vi v i ii i vivv v i---iv C Plat_L3#LINE/ 2924 NTGGTCGACTATGACCCCCAGGTCTTTTTCTGCTGTACTTGTGCCTAGCC 2875 chr5ptel1M 524284 A-TGTTCTTTCA------ACTTGTGAAGTTGATTTTTTTGAACCTAAGTC 524326 - v iiii ------ i vi vi- i vv v C Plat_L3#LINE/ 2874 AGTCTTTCCCCATCCTGTATTTGTGCGGTTTG-TTTTTCGTCCCTAAGTG 2826 chr5ptel1M 524327 TAATAATATGCATTTATCTTTATTCAATTTTACCTTATTTGATCAGT-CC 524375 i v viv i i ii v i i i i vvv? v- C Plat_L3#LINE/ 2825 CACTACCTTGCACTTGTCCCTATTGAATTTCATCCTGTTTTTGNAGGACC 2776 chr5ptel1M 524376 ACTCTTTTACCCTG-GAAGAGCAATCTTTTCGAATTCTGGCTCTGTTGTT 524424 i i ii vii -v? iv -- -- i ivii iv i C Plat_L3#LINE/ 2775 ATTTTTCCAATTTGTCNAGGTCA--CTTT--GAATTTTATTCCTGTCTTC 2730 chr5ptel1M 524425 CAGAGAATCAGCTGTCCTTCTCAGCTCTGAGGCATCGGCCAATTGGAAAA 524474 i vi i vii iv i ii iv viv v v v vi C Plat_L3#LINE/ 2729 CAAAGTGTTAGCAACCCCGCCCAATTTAGTATCATCTGCAAATTTGATGA 2680 chr5ptel1M 524475 GCATGTTGTATAGTTTTTTCTCCAAGTCATCAATAAAAATATTAGATA-A 524523 i v vv v ii iv i i i ii - C Plat_L3#LINE/ 2679 GCATGCTCTCGATTCCTTCGTCCAGGTCATCGATAAAGATATTGAATAGA 2630 chr5ptel1M 524524 TCCAAGATCAGGAAAAGATGTCTAGGGCATTCCATTGGAGAAGTCTTTCC 524573 v iivvi - vv vi iv v iv i v v v? ii C Plat_L3#LINE/ 2629 ACCGGTCCCAGG-ACCGATCCCTGTGGGACACCACTCGATATNTCCCTCC 2581 chr5ptel1M 524574 AGGT 524577 C Plat_L3#LINE/ 2580 AGGT 2577 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 49.53 CpG sites = 123, Kimura (unadjusted) = 52.88 Transitions / transversions = 1.19 (123/103) Gap_init rate = 0.03 (21 / 622), avg. gap size = 1.95 (41 / 21) 297 38.67 2.00 0.00 chr5ptel1M 524578 524727 (475273) C L3#LINE/CR1 (1411) 2688 2536 m_b231s601i9 9084 chr5ptel1M 524578 CTCCAGCCTTGTGACGCCTAT-CGGTTAGCCACAGTCTGTCTAAAGTTTC 524626 i v i i v - v vv iiii i v v ii v C L3#LINE/CR1 2688 CTCCAGTCTTCTGGCACCTCTTCCGTTCTCCGTGATTTCTCAAAGATTAC 2639 chr5ptel1M 524627 TGAC--TAGTTCAGTAATCACTGCTGCTATTTCTTCTAGTCTCTTGCCCC 524674 i --ii v ii vv v v ii vi i vvvi C L3#LINE/CR1 2638 CGACAGCGGTTCCGCGATCACATCTGCAAGTTCTTTCAGTACCCTGGGAT 2589 chr5ptel1M 524675 ACAGCTTAGCTGGGTCTAGTGACTTGAACTTTTCAGAGGCAGGTAGATGT 524724 ii ii iiv i i v iv ivi i i v i i C L3#LINE/CR1 2588 GTAATTCGTCTGGGCCTGGAGACTTGAACTCATTTAAAGCGGCTAGGTGC 2539 chr5ptel1M 524725 TTT 524727 i C L3#LINE/CR1 2538 TCT 2536 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 48.68 CpG sites = 36, Kimura (unadjusted) = 57.94 Transitions / transversions = 1.64 (36/22) Gap_init rate = 0.01 (2 / 149), avg. gap size = 1.50 (3 / 2) 250 39.50 5.20 0.77 chr5ptel1M 524768 525017 (474983) C L2c_3end#LINE/L2 (10) 468 208 m_b231s601i10 9085 chr5ptel1M 524768 TCAAAAAGCATCTATGAAGTGCCAAGCATATGCCAGGAGCTGGGGTCATA 524817 v i i vi i v vi i v vi i C L2c_3end#LINE 468 TCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGATACA 419 chr5ptel1M 524818 GGGACGAAAATGAACCAG-----AACTTC-AGAAACTTATGTTTTCATGA 524861 ii i v v vv i -----iv i - i i i iiv i vi i C L2c_3end#LINE 418 AAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAGTGG 369 chr5ptel1M 524862 GAGAGACAAACATGTCTCTACAGAGTTACCTTCTAGTATTGCAAGACACA 524911 ii i ? vvvi v v i vv vi i-i i- v i vi C L2c_3end#LINE 368 AGGAGACAGACANGTAAACAGACAATTACAATACAA-GTTA-ATGATAAG 321 chr5ptel1M 524912 TGC-ATAGTGACCTTG-AGGCTGGG-GTTAAAGG-GAAAGGAGGAAGATG 524957 - i ivvv i- i v - i vi - v vi i iii C L2c_3end#LINE 320 TGCTATAATGGGAGTATAGACAGGGTGCTATGGGAGCACAGAGGAGGGCA 271 chr5ptel1M 524958 -CTAGA--AGCCAAGATAAACTGGGAAATGGCTCCTGCAAAAGATAGCAC 525004 - -- ? vv iviiiiii i v vi i v ii i ii i C L2c_3end#LINE 270 CCTAGACTAGNCTTGGGGGGTCAGGGAAGGCTTCCCGGAGGAGGTGACAT 221 chr5ptel1M 525005 TTGAACTGAGTCT 525017 i i ? C L2c_3end#LINE 220 CTGAGCTGAGNCT 208 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 58.55 CpG sites = 62, Kimura (unadjusted) = 61.63 Transitions / transversions = 1.72 (62/36) Gap_init rate = 0.04 (10 / 249), avg. gap size = 1.50 (15 / 10) 315 32.25 17.06 1.53 chr5ptel1M 525136 525305 (474695) C L2b_3end#LINE/L2 (25) 441 246 m_b231s601i11 9086 chr5ptel1M 525136 TAAGCATTTATTATGTGCTAGGCACTCTGCCAAGTGCTGAGGATACAAAG 525185 i iii i i i ? v i i i i iv C L2b_3end#LINE 441 TGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGGGATACAGCG 392 chr5ptel1M 525186 AAAAGCAAAA-------GGT-----------AGGAGCTCAGAAGTCAAAT 525217 ivi i i ------- -----------v -v v i C L2b_3end#LINE 391 GTGAACAAGACAGACNCGGTCCCTGCCCTCACGGAGCTCA-CAGTCTAGT 343 chr5ptel1M 525218 GGGGAAGACA-ACATG----CAAATAACTATGTCCAAAAACAACATG--A 525260 i - ---- i i i? iv v i iiii v -- C L2b_3end#LINE 342 GGGGGAGACAGACATGTAANCAGACAATNATAACCCAGAGTGGCAGGGTA 293 chr5ptel1M 525261 GAGTT----TGTCCCAGAGAAAAATGGCTCACTCTACTTATGGTGGATC 525305 iii ----v v i iiii v v i vi i-- v i C L2b_3end#LINE 292 GGACTGGGGGGGCCCAGAGGAGGGCGCCTGACCCGGCC--TGGGGGGTC 246 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.86 CpG sites = 39, Kimura (unadjusted) = 46.48 Transitions / transversions = 2.60 (39/15) Gap_init rate = 0.05 (9 / 169), avg. gap size = 3.56 (32 / 9) 295 26.34 0.00 9.78 chr5ptel1M 525380 525480 (474520) MIR3#SINE/MIR 113 204 (4) m_b231s601i12 9087 chr5ptel1M 525380 TCTGAGATTGATTTTCCCCATTTATGAAATTAAATGGGGAATAAAATGGA 525429 i vi v v i i i i v ---- ii ---- MIR3#SINE/MIR 113 TCTGGGCCTCAGTTTCCTCATCTGTAAAATGA----GGGGGT----TGGA 154 chr5ptel1M 525430 CTAGCAGGTTTCTAAGGATCCTTCCTTTCTATAACATCTTATGATTCTAT 525479 vv i i vi vv- v i ii MIR3#SINE/MIR 155 CTAGATGATCTCTAAGGTCCCTTCCAG-CTCTGACATTCTATGATTCTAT 203 chr5ptel1M 525480 G 525480 MIR3#SINE/MIR 204 G 204 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.77 CpG sites = 14, Kimura (unadjusted) = 32.77 Transitions / transversions = 1.40 (14/10) Gap_init rate = 0.09 (9 / 100), avg. gap size = 1.00 (9 / 9) 59 3.47 0.00 0.00 chr5ptel1M 526768 526826 (473174) (AT)n#Simple_repeat 1 59 (0) c_b231s251i0 9088 chr5ptel1M 526768 ATATATATATATATATATATATATATATATATATATATATATATATATAC 526817 i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr5ptel1M 526818 ATATTTATA 526826 v (AT)n#Simple_ 51 ATATATATA 59 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.0 (0 / 0) 15 5.48 0.00 0.00 chr5ptel1M 527379 527397 (472603) (AC)n#Simple_repeat 1 19 (0) m_b231s252i2 9089 chr5ptel1M 527379 ACACACACACACACAGACA 527397 v (AC)n#Simple_ 1 ACACACACACACACACACA 19 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 950 29.30 1.39 1.39 chr5ptel1M 527754 528113 (471887) C HERV1_I#LTR/ERV1 (315) 8486 8127 m_b231s701i0 9090 chr5ptel1M 527754 CTGTGCAGGCACATGAACTA--TTCTGCAAATGCCTTTTGTAATTTCTTT 527801 vi v v ii -- i -- v ivviv i iv C HERV1_I#LTR/E 8486 CTGGACCGGGACATGGGCTAACTTCCGCA--TCCTGGCAGTGATTTCCAT 8439 chr5ptel1M 527802 TACCTCTTGTCCATTATCATCAATTTGCATGCAACAAATGGACAAATTTA 527851 v vv iv i i i v i iv ? v v C HERV1_I#LTR/E 8438 GACAGCTCTTCCATTGTCATCGATTTGTAAGCAGCAGTTNGTCAAATTAA 8389 chr5ptel1M 527852 ATTTTCCACAGACTCCTCCTTCATCTGCTAGCAAATAATCTAAAACTAGT 527901 i ? i vvvv v i i vi i C HERV1_I#LTR/E 8388 GTTTNCCACAAACTCCTCCTTCTGAGGCTAGGAGATAGTCTAATGCTAGC 8339 chr5ptel1M 527902 CGATGTTGTAAAACAGCTTCTTGTGTTTGAGTGGCTTGATCAGCTAGCAA 527951 v v vv v ii v ivii i i ? i vvii C HERV1_I#LTR/E 8338 CTATTTTGATATATGGCATCTCTCATCTGGGTNGCCTGTATGGCTAGCAA 8289 chr5ptel1M 527952 AT-CAAGACCCTGAGCAGTCTGGTTAGTTGTTATCTCCAGAACTGCTTGT 528000 - i i - i v i vi iii i v i i v i C HERV1_I#LTR/E 8288 ATCCAAGGCTC-GGGCTGTTTCATTGACTATGATTTCTAGTACTGCTTGC 8240 chr5ptel1M 528001 AATCTAATTAGCCTATT--ATATGTATATATTGGTGTCCTATACCCCCAG 528048 v v vi vi -- i v -- v v vi ? v C HERV1_I#LTR/E 8239 AATCTTATGATTCGGTTTAACATGTAAATA--GGAGTACGGTANCCCCAT 8192 chr5ptel1M 528049 CTTCCATCCTGAGCCCATGTGGCTAGCCCATACTCTTTGATGATTCTTTC 528098 vvi i ? ? i i v v i C HERV1_I#LTR/E 8191 GACCCATCTTGNGCCCANGTAGCTGGCCCATAGTATTTGATAATTCTTTC 8142 chr5ptel1M 528099 TGGGTGCCATGTATT 528113 v iv vi C HERV1_I#LTR/E 8141 AGGAGGCCATTCATT 8127 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.59 CpG sites = 53, Kimura (unadjusted) = 38.52 Transitions / transversions = 1.04 (53/51) Gap_init rate = 0.02 (8 / 359), avg. gap size = 1.25 (10 / 8) 1351 32.55 3.02 2.92 chr5ptel1M 529390 530348 (469652) C HERVIP10B3#LTR/ERV1 (2005) 5598 4639 m_b231s701i1 9091 chr5ptel1M 529390 TTTGACTCAAAAGTGATGTGTCCAACCTTTCTCTTTGGTGCGTATCACCG 529439 iiiv v v i vvi? v v iii ? C HERVIP10B3#LT 5598 TTTGACTCGGGTGTGATGGGTCCATCCTTTTTCGGCNGTTCGGACTGCNG 5549 chr5ptel1M 529440 TATCTGAACTCAATAGGATCTGGAACAGTCCTTCCCAGCTGAGGGTC-AG 529488 v v v?v i iv v iiv v vi vi - v - C HERVIP10B3#LT 5548 TCTCAGTNGTTAGGAGCACTAGGTAAGGTCCTTCCCAGGCG-GGTTCGAG 5500 chr5ptel1M 529489 CTTGTCCTCCTTCCACATCCGAACCAGGACCCAGTATCCAAGCTAGAACT 529538 vi i vv iivi iv viii v ii i vii C HERVIP10B3#LT 5499 CTTTCCCTCTTTCCAACTTTTGATGAGGACGTGATCTCCGGGCTGGTGTT 5450 chr5ptel1M 529539 TATGCACTGTGAACCCTAAGGGAAGAGTCTGAGC-AATAAGCTTTTAGTT 529587 vi ? v ii v i vi ? v - iv i i ? i C HERVIP10B3#LT 5449 GGTGNACTGGGAATTCGAGGGGTGGNGTCTGTGCTAGGAGGCCTTNAGTC 5400 chr5ptel1M 529588 ATAAAGTTTTCAGATGATGCATGCAGTACAGAC--ATGACATATTTCCTT 529635 v i i ----v iv v -i v iv -- vv i v ii v C HERVIP10B3#LT 5399 CTGAGG----GAGGAGAAG-GTGGAAGACAGACCAAGTATATAGTTTTTG 5355 chr5ptel1M 529636 AAAAACAAATCCTTGGTTCCAAATATTGGATCCAAGGAAGAATTTTGAAT 529685 i vi i v i ii v --- ? vv -- vv i - C HERVIP10B3#LT 5354 AGAAACTGATCTTTTGTTTCAAACGTAGGA---ANGTCAG--TAGTGGA- 5311 chr5ptel1M 529686 CTCTTTTGGATAAGGGTGACCATAAAATA-CTCATAGGGTGATAATCCCA 529734 ---v ? i vviv ? ii -i i v iv v C HERVIP10B3#LT 5310 ---GTNTAGATAAGGCAACCCATANAGCATTTCATAAGGGGATAGGCCGA 5264 chr5ptel1M 529735 CATCCCTCCGGGATTTTGTTC-TATCCTCAAAAAGGCAAGGGGAAGGCAC 529783 ii i ivviv -v i i iv v i C HERVIP10B3#LT 5263 CATCTTTCCGAGGGGCAGTTCGGATTCTTAGCAAGGCAATGGGAAGGCAT 5214 chr5ptel1M 529784 TTGGTCCAGGGCAATTGTGTCTCTAATGCCAATTTAGTCAGTTGCGGTTT 529833 ? v i ii v i viii i i -- i C HERVIP10B3#LT 5213 TTNGTCCATGGTAACCGGGTTTCTAAGATTAATTTGGTTAG--GTGGTTT 5166 chr5ptel1M 529834 AATTT----CCTTATTCATCCTTTCCACTTTACCTGATGGGGGCGGATGC 529879 -- ----i v i i i v i i i C HERVIP10B3#LT 5165 --TTTAGAGTCTGATTCATTCTTTCTACTCTCCCTGATGAGGGTGGGTGC 5118 chr5ptel1M 529880 CATGGGGTATGTAAGTCCCAGGATATTTCTAGAGCTCAGGCCA-CAGATC 529928 v vv v vvv ? v ii i - vvv i C HERVIP10B3#LT 5117 CAGGGGGTATGGTATTCCCATTTTATNTCTAGTGCTTGGGCTAGCCCCTT 5068 chr5ptel1M 529929 AGAGGATTTTAACTGTGAAATGGGTGCCTTGGTTCACTTC--TACCTGCT 529976 - v iv vvi v i v v v iiivv -- iii v C HERVIP10B3#LT 5067 A-ATGACGTGTGCAGTGAAGTGGGTCCCATTGTCTGAATCAATGTTTTCT 5019 chr5ptel1M 529977 ACCTCAATCCATACCCTGGAATTATACGCTCAGGGAGGACTTTTACAAC- 530025 -- i i v iv v v i?i viiv vi v v - C HERVIP10B3#LT 5018 A--TTAGTCCAAACCTGGGTATGATATNTTCCAACAGTGCTTTGACTACA 4971 chr5ptel1M 530026 -TATTGAGGCAGTTGCCCAGGCAAGGGGGAAGGCTTACACCCACGAGGTC 530074 - i -- ? v vv vi i v vi vvi v C HERVIP10B3#LT 4970 TTACT--GGCNGTTGCGCTTGGGAAGGGGATGGCTTCTACCCAGTGGGTG 4923 chr5ptel1M 530075 AGATGGTCCACTA-GACCAACAGGTATTTGAGACACCCCACTAGTGGCAG 530123 i i -v i ii ii i ? i iv i i i v v C HERVIP10B3#LT 4922 AGGTGGTCTACTATTACTAGTAAATACTTNAGGCGGCCTATTGGGGGCAT 4873 chr5ptel1M 530124 TTCGGTAAAGTCCACCTGAATGCTTTGGAAAGGCCTGATACCAGGGGGCC 530173 iv v i i ii v v - vv --- C HERVIP10B3#LT 4872 TTCGGTGTAGTCAACTTGGACACTTTGGAACGGCCTTA-ACCCTGGG--- 4827 chr5ptel1M 530174 TTCCTCCTTTCTGGA-CTTG--TCATT-GGGCCGCCTTATTCG-TCCTCT 530218 i i iii v -v ? -- v - iivv v - ii C HERVIP10B3#LT 4826 TTTCTTCCCCCGGGAGGTNGCTTCTTTAGGGTTTGCTTATTAGTTTTTCT 4777 chr5ptel1M 530219 TCACA--GGACACCCACTGGCCAGTTGCCT-GCTATTGTGTACAAGCCGG 530265 v --i?i v i iiv v v - ? vv i ? vv vi C HERVIP10B3#LT 4776 GCACACTANGCAACTATCCGCAACTTGCCTNGCNAGGGTATANATTCCTA 4727 chr5ptel1M 530266 TGCCACCA---ACTT--AGCACCACATCACACAGGTCTTGGACACCCCAA 530310 i vv --- i-- v ii viv iiv? i C HERVIP10B3#LT 4726 TACACCCATAGACTCTGAGGACTGCATCACACATAGCTTGAGGNCCCCAG 4677 chr5ptel1M 530311 TGACTGCCCTGATGTAAATGTGGGAGTACATGTCTCAT 530348 v v i ? iv ? iv iv vi C HERVIP10B3#LT 4676 TGAGTTCCTTGATGNAGCTGNGACAGTATTTCCCTCAT 4639 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.51 CpG sites = 158, Kimura (unadjusted) = 44.91 Transitions / transversions = 1.09 (158/145) Gap_init rate = 0.05 (47 / 958), avg. gap size = 1.21 (57 / 47) 16 16.82 0.00 0.00 chr5ptel1M 535784 535811 (464189) (A)n#Simple_repeat 1 28 (0) m_b231s252i3 9092 chr5ptel1M 535784 AAAAAAAAAAAAAGAAAAAGGGAAAAAA 535811 i iii (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA 28 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 237 32.63 0.00 0.00 chr5ptel1M 536050 536144 (463856) C L1MD1_3end#LINE/L1 (414) 575 481 m_b231s551i3 9093 chr5ptel1M 536050 AGCCCGTTCCTCATTTTTACAGAATAATAGTCCACGGTCTTCAAGTACCA 536099 ii iv v i v i i v i v vv v C L1MD1_3end#LI 575 AGTTCGTTCCTTTTTATTGCTGAGTAGTATTCCATGGTATGGATGTACCA 526 chr5ptel1M 536100 CAAGTTGTTCGGCCATTCCCCAATAGACAGACACATATTTTGTTT 536144 iv iii v vi v vi iv ivv C L1MD1_3end#LI 525 CAGTTTGTTTAACCATTCACCCGTTGAAGGACATCTGGGTTGTTT 481 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.57 CpG sites = 15, Kimura (unadjusted) = 43.37 Transitions / transversions = 0.94 (15/16) Gap_init rate = 0.00 (0 / 94), avg. gap size = 0.0 (0 / 0) 525 33.15 2.65 2.38 chr5ptel1M 536698 537074 (462926) C L1ME4c_3end#LINE/L1 (191) 639 262 m_b231s551i4 9094 chr5ptel1M 536698 TTCTGCTTACTTCACTTTGCATCAGTTCATGTA-GTTCTCACCAGGCCTC 536746 vi vi i vv iv -i i -- v iiv C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATAAACATTTT--CCATGTTGC 592 chr5ptel1M 536747 TCTGAAATCATCCTGCTGATCATTCCTTATAGAACAATAATATGCCACAA 536796 viiv i v v iv v ii v i vvvv v ivi C L1ME4c_3end#L 591 TACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCG 542 chr5ptel1M 536797 CATTAATGTGCTATGACTTATTCAG-CATTTCCCAGCTGATGGGCATCCA 536845 vi ?i i i i i i i i- i vii v i ii C L1ME4c_3end#L 541 AGTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTA 492 chr5ptel1M 536846 CTCAGTTTCCAGTTTCTTGGCACTACAAACAGGGCTGCAG-AAACATTTC 536894 vviv i i i vi i i i iv i-i i i C L1ME4c_3end#L 491 GGTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTT 442 chr5ptel1M 536895 TGTACATGTGGATCCTTTTCCCTCCTTTAGA---ATCTCTTTGGCAAATA 536941 i i i i --- i i v --- i i i --i C L1ME4c_3end#L 441 CGTGCATATAG---CTTTTTCCTTCTTTTGAATTATTTCCTTAG--GATA 397 chr5ptel1M 536942 AA--CCCAGTAGAAACATTGCTAGTTCAAAGGCTACGCGCCTGTTGATAG 536989 -- v viiv i i v v i vi v v v i C L1ME4c_3end#L 396 AATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGG 347 chr5ptel1M 536990 CCCATTGG-GCATGTT-CCATATTGCTCGGCAGAATGGTTGGATCCATTC 537037 i - i-i i i - v ivv i v v i v i C L1ME4c_3end#L 346 CTC-TTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTT 298 chr5ptel1M 537038 ACAATTCCACGAACAATACATTAGCGTCCCAGGTTTC 537074 ? v v i ii v ? v - C L1ME4c_3end#L 297 ACANTGCCACCAGCAATGTATGAGNGTACCA-GTTTC 262 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 44.04 CpG sites = 74, Kimura (unadjusted) = 46.13 Transitions / transversions = 1.54 (74/48) Gap_init rate = 0.04 (16 / 376), avg. gap size = 1.19 (19 / 16) 40 6.56 0.00 0.00 chr5ptel1M 539584 539631 (460369) (CA)n#Simple_repeat 1 48 (0) c_b231s251i1 9095 chr5ptel1M 539584 CACACACACACACACACACACACACACGCACACGCACACACTCACACA 539631 i i v (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACA 48 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 13 8.48 4.00 0.00 chr5ptel1M 540185 540209 (459791) (GTTT)n#Simple_repeat 1 26 (0) m_b231s252i4 9096 chr5ptel1M 540185 GTTTGTTTGTTTGTTTATAT-TTTGT 540209 i v - (GTTT)n#Simpl 1 GTTTGTTTGTTTGTTTGTTTGTTTGT 26 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 240 31.06 4.86 4.86 chr5ptel1M 540433 540679 (459321) L1P1_orf2#LINE/L1 223 469 (2825) m_b231s551i5 9097 chr5ptel1M 540433 GCCATCCTGATCTCAGATCAAGCAAAAACAAAACTTGATCTAA------T 540476 v ii v ------ i vi i v i ------ L1P1_orf2#LIN 223 GCAATCCTAGTCTCTGAT------AAAACAGACTTTAAACCAACAAAGAT 266 chr5ptel1M 540477 TAAAAGAGATAAGGAAGGGCACTATATCTTGCTAAAGGGTAGCA--TAAA 540524 i i i v i i vv v - v -- v L1P1_orf2#LIN 267 CAAAAGAGACAAAGAAGGCCATTACATAATGGTAAAGGG-ATCAATTCAA 315 chr5ptel1M 540525 TAATGAAGCAATATCAATATTAAACATATATGCACCAAGTAATTGTAGCA 540574 i - viv v v vi i v i - iv v L1P1_orf2#LIN 316 CAA-GAAGAGCTAACTATCCTAAATATATATGCACCCAAT-ACAGGAGCA 363 chr5ptel1M 540575 TCTAAATTCTTAAAAGAAAT--TAAG-AAACTGCAAGAAAAATAAGAATA 540621 i i i v iv i -- i -i v i ii i v v v v L1P1_orf2#LIN 364 CCCAGATTCATAAAGCAAGTCCTGAGTGACCTACAAAGAGACTTAGACTC 413 chr5ptel1M 540622 CATAAAAACTATAATAGTAGAGAATCTCAACCTTGCACTCATAA-ATTAG 540670 ---v v v? i i iii ii i viiv vvi - L1P1_orf2#LIN 414 C---CACACANTAATAATGGGAGACTTTAACACCCCACTGTCAACATTAG 460 chr5ptel1M 540671 ATAAATCAA 540679 i i L1P1_orf2#LIN 461 ACAGATCAA 469 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.38 CpG sites = 41, Kimura (unadjusted) = 41.38 Transitions / transversions = 1.28 (41/32) Gap_init rate = 0.07 (17 / 246), avg. gap size = 1.41 (24 / 17) 321 22.04 0.00 0.85 chr5ptel1M 540475 540593 (459407) L1MC4_5end#LINE/L1 2437 2554 (1) m_b231s551i6 9097 chr5ptel1M 540475 ATTAAAAGAGATAAGGAAGGGCACTATATCTTGCTAAAGGGTAGCATAAA 540524 ? i i ? i v vv ? ???vv vv L1MC4_5end#LI 2437 ATTAAANGAGACAAAGAAGGNCATTTTATAATGNTAAAGGNNNCAATTCA 2486 chr5ptel1M 540525 TAATGAAGCAATATCAATATTAAACATATATGCACCAAGTAATTGTAGCA 540574 i vv v vv i ? i -ii? L1MC4_5end#LI 2487 CAATGAAGATATAACAATTATAAATATNTATGCACCAAATAA-CANAGCA 2535 chr5ptel1M 540575 TCTAAATTCTTAAAAGAAA 540593 ? i v? iv iv L1MC4_5end#LI 2536 NCCACNTTTATAAAGCAAA 2554 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 29.11 CpG sites = 11, Kimura (unadjusted) = 29.11 Transitions / transversions = 0.73 (11/15) Gap_init rate = 0.01 (1 / 118), avg. gap size = 1.00 (1 / 1) 15 10.85 3.33 0.00 chr5ptel1M 542174 542203 (457797) (CAATAC)n#Simple_repeat 1 31 (0) m_b231s252i5 9098 chr5ptel1M 542174 CAA-ACCAATACCAATAGCCATACCAAAACC 542203 - v v v (CAATAC)n#Sim 1 CAATACCAATACCAATACCAATACCAATACC 31 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 12 21.98 2.70 0.00 chr5ptel1M 542661 542697 (457303) (AAAAACA)n#Simple_repeat 1 38 (0) m_b231s252i6 9099 chr5ptel1M 542661 AAAAACTAAAAA-GCAATACAAACTTCAAAAAACAAAA 542697 v -iv v vvv (AAAAACA)n#Si 1 AAAAACAAAAAACAAAAAACAAAAAACAAAAAACAAAA 38 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 33 12.96 1.37 4.23 chr5ptel1M 544079 544151 (455849) (AATAAAA)n#Simple_repeat 1 71 (0) m_b231s252i7 9100 chr5ptel1M 544079 AATAAAAAGT-TACTATAATAAAATAAAAAACAAAAAAACAATAAAAAAC 544127 i -v vv - -v i - v v (AATAAAA)n#Si 1 AATAAAAAATAAAAAATAA-AAAATAAAAAA-TAAAAAATAA-AAAATAA 47 chr5ptel1M 544128 AAAATAAAAAATAAAAAATAAAAA 544151 (AATAAAA)n#Si 48 AAAATAAAAAATAAAAAATAAAAA 71 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.06 (4 / 72), avg. gap size = 1.00 (4 / 4) 352 30.36 12.71 3.55 chr5ptel1M 545213 545393 (454607) MIRc#SINE/MIR 14 210 (58) m_b231s601i13 9101 chr5ptel1M 545213 TACAATGGATAGAATGTGGATAGGGCCTTAAATTAGGAATCCCAGGATTT 545262 i i v ---- v iv i i vi i i vv v i i MIRc#SINE/MIR 14 TGCAGTGGAAAGA----GCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr5ptel1M 545263 TATTCCCACCTC-----------AG------AACCTTGCAAGTCAAGTTA 545295 v v iv ----------- ------i --- v i MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTG---GGCAAGTCA 106 chr5ptel1M 545296 TAGGACTTCTGTTAGATTCAGTATCTTTATCTGCAAAATGGGCATAATAA 545345 ivvi i v v vi v i i i v MIRc#SINE/MIR 107 CTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAA 156 chr5ptel1M 545346 TA---G---TACTTAAATCCTCTGGTTCTCATGAGGATGAAATAAGACAA 545389 --- --- i i vv vivv v ii v i i MIRc#SINE/MIR 157 TACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAA 206 chr5ptel1M 545390 TGCA 545393 i MIRc#SINE/MIR 207 TGTA 210 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.89 CpG sites = 28, Kimura (unadjusted) = 39.79 Transitions / transversions = 1.12 (28/25) Gap_init rate = 0.06 (11 / 180), avg. gap size = 2.73 (30 / 11) 426 31.01 0.00 2.82 chr5ptel1M 545278 545423 (454577) MIR#SINE/MIR 88 229 (33) m_b231s601i14 9101 chr5ptel1M 545278 ACCTTGCAAGTCAAGTTATAGGACTTCTGTTAGATTCAGTATCTTTATCT 545327 --- v ivvi i v vv vi v i i MIR#SINE/MIR 88 ACCTTG---GGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCT 134 chr5ptel1M 545328 GCAAAATGGGCATAATAATAGTACTTAAATCCTCTGGTTCTCATGAGGAT 545377 i v i vv v vv v ii MIR#SINE/MIR 135 GTAAAATGGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGGAT 184 chr5ptel1M 545378 GAAATAAGACAATGCAGAGCATGGCACATAGGGCTGTACTCGATAC 545423 v i vi i v- i vi i v ii v i ii ii MIR#SINE/MIR 185 TAAATGAGTTAATACAT-GTAAAGCGCTTAGAACAGTGCCTGGCAC 229 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.50 CpG sites = 23, Kimura (unadjusted) = 40.68 Transitions / transversions = 1.10 (23/21) Gap_init rate = 0.03 (4 / 145), avg. gap size = 1.00 (4 / 4) 16 13.23 0.00 2.94 chr5ptel1M 546924 546958 (453042) (AAAAGG)n#Simple_repeat 1 34 (0) m_b231s252i9 9102 chr5ptel1M 546924 AAAAGGAAGGGTTATAAGGAAAAGGAAAAGGAAAA 546958 ii -v v (AAAAGG)n#Sim 1 AAAAGGAAAAG-GAAAAGGAAAAGGAAAAGGAAAA 34 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 22 7.42 0.00 0.00 chr5ptel1M 548823 548851 (451149) (TA)n#Simple_repeat 1 29 (0) m_b231s252i10 9103 chr5ptel1M 548823 TATATGTGTATATATATATATATATATAT 548851 i i (TA)n#Simple_ 1 TATATATATATATATATATATATATATAT 29 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 4050 29.18 3.91 2.43 chr5ptel1M 549374 550399 (449601) L1M5_orf2#LINE/L1 829 1881 (1413) m_b231s551i7 9104 chr5ptel1M 549374 AATGACAATGATGAGACATCGTACCAAAATTTGTGGGATGCAGCCAAAGT 549423 ? vi v v i i i i L1M5_orf2#LIN 829 AATGANAATGAAAATACAACATATCAAAATTTGTGGGATGCAGCTAAAGC 878 chr5ptel1M 549424 AGTAATAAGAGGAAATTTTATATCCTTAGAGACTTACTTGAATAAAATAG 549473 iv v i v v ? i vi ? iv v iv iv L1M5_orf2#LIN 879 AGTGCTTAGAGGGAAATTTATAGCNTTAAATGCNTATATTAGAAAAGAAG 928 chr5ptel1M 549474 AGAGGAG-AAGATCAATGAATTGGGCTTA-AC--TAAAAAACTAGAAAAA 549519 i vv- i vi ii v- -- i i L1M5_orf2#LIN 929 AAAGGCTTAAAATCAATGATCTAAGCTTCCACCTTAAGAAGCTAGAAAAA 978 chr5ptel1M 549520 GA---CCAAATTAAAAACCCCCAATCAAATACTAAATTTGAAATT-TAAA 549565 ---v --- v v? i vv iivvv v- L1M5_orf2#LIN 979 GAAGAGCAAATTAAA---CCCAAAGNAAGTAGAAGGAAGGAAATAATAAA 1025 chr5ptel1M 549566 ATTAAAAGGAAAATTTAAT--AATAAAAAA--AAACTTTAATT-----AA 549606 iv i v i v i -- i -- ?v?vi v----- L1M5_orf2#LIN 1026 GATAAGAGCAGAAATCAATGAAATAGAAAACAAANANACAATAGAGAAAA 1075 chr5ptel1M 549607 TTAGTAAAACTAAA-GTTGATTCTATTAAAA-ACCAATAAAATAAATGAG 549654 i iii i i - i i v v - i vi i i L1M5_orf2#LIN 1076 TCAACGAAGCCAAAAGCTGGTTCTTTGAAAAGATCAATAAAATTGATAAA 1125 chr5ptel1M 549655 CCCTTGGTAAATCTGATTAG--AAAAAGGAGGGGAAAATCAAATTA---- 549698 ii i i? iv i i-- i i i i vv ---- L1M5_orf2#LIN 1126 CCTCTAGCNAGACTGATCAAGAAAAAAAGAGAGAAGACACAAATTACCAA 1175 chr5ptel1M 549699 TGTCAAAAA---AAAAGGAGAACTTTCCACCAATGA-ACAGAAATTAGAA 549744 i ii --- vv iv i vi vv- v i L1M5_orf2#LIN 1176 TATCAGGAATGAAAAAGGAGACATCACTACAGATCCTACAGACATTAAAA 1225 chr5ptel1M 549745 G-ATAATAAGGAGTTACTTTGCCC--CTTTAT-CCAATAAATTTGATAAC 549790 - iiiv i v vv -- - ? L1M5_orf2#LIN 1226 GGATAATAAGAGAATATTATGAACAACTTTATGCCAATAAATTTGANAAC 1275 chr5ptel1M 549791 --AAGTGAAATGGATATACCTCC----AAAATATAATTTCCCAGA-TTAA 549833 -- ii i - vi ---- i i ? v i -i i L1M5_orf2#LIN 1276 TTAGATGAAATGGACA-AATTCCTTGAAAAACACAANTTACCAAAACTGA 1324 chr5ptel1M 549834 CAGAGGAGGAAGTA--ATTTCTTGAATAGTCCCATTTCAGAAAAAAGAAA 549881 ?v i i i -- vv - i i v -v vv L1M5_orf2#LIN 1325 CNCAAGAAGAAATAGAAAATCT-GAATAGCCCTATATC-TATTAAAGAAA 1372 chr5ptel1M 549882 TACCCAATAT-TAATCAA---CCTTA--ACAAA--AATCCCCAGGACCAG 549923 --iv v - i --- v-- -- v i v L1M5_orf2#LIN 1373 T--TGAATTTGTAATTAAAAACCTTCCCACAAAGAAAACTCCAGGCCCAG 1420 chr5ptel1M 549924 ATGGATTTACATGTGAATTCTACCAAACATTTAAAGAAAAATTGGCCCCA 549973 v i vv i i v iiiv L1M5_orf2#LIN 1421 ATGGCTTCACTGGTGAATTCTACCAAACATTTAAGGAAGAAATAATACCA 1470 chr5ptel1M 549974 ATGCTATACAAATTATTTTATAAAATAGGGAATGAAGGAGTCCTACTAAA 550023 vi i i v ii v ii v i iiv v iv L1M5_orf2#LIN 1471 ATCTTACACAAACTCTTCCAGAAAATAGAAAAAGAGGGAACACTTCCCAA 1520 chr5ptel1M 550024 TTCCTTTTATGACACAGACATGGTACTGATACCTAAACCAGGTAGGTTTA 550073 i v vi vii ?iiv v ? ii iivvi L1M5_orf2#LIN 1521 CTCATTTTATGAGGCCAGCATNACCCTGATACCAAAACCNGACAAAGACA 1570 chr5ptel1M 550074 AAACAGAGAAAGAAAATTATAGACCCCTCTCCTTAATGAATATTGATGCT 550123 vv iii i vv v i v i v v L1M5_orf2#LIN 1571 TTACAAGAAAAGAAAATTACAGACCAATATCCCTCATGAACATAGATGCA 1620 chr5ptel1M 550124 AAAATCTTAAATAAGATATTAGCGAAAAGACTACAGAAAATCATTCCCAG 550173 i ? i i i vv v v v vvi vvvv L1M5_orf2#LIN 1621 AAAATCCTNAACAAAATATTAGCAAATCGAATCCAGCAATATATAAAAAG 1670 chr5ptel1M 550174 GATAATACACTATGATCGAGTAGGATTTATACCAGGAATGCAGGGCTGGT 550223 ii i i i i v i i L1M5_orf2#LIN 1671 GATAATACATCATGACCAAGTGGGGTTTATCCCAGGAATGCAAGGTTGGT 1720 chr5ptel1M 550224 TCAATATTAGGAAAACTATCAATATAATTGGTCATATTAATA-ACCAAAT 550272 i i v i v v i vii i - vi - L1M5_orf2#LIN 1721 TTAACATTCGAAAATCAATCAATGTAATTCACCATATTAACAGAATAAA- 1769 chr5ptel1M 550273 TAACAAAAACCATATGATCATCTCAATAGATGCAGAAAAAGCATTTGACA 550322 vi v i L1M5_orf2#LIN 1770 GGAGAAAAATCATATGATCATCTCAATAGATGCAGAAAAAGCATTTGACA 1819 chr5ptel1M 550323 AAATCCAACATCTATTCCTATGAAAAACATTTGAGAATATAGGAATAAAT 550372 i i i v ivv vi iiiv vv i v L1M5_orf2#LIN 1820 AAATTCAACACCCATTCATGATAAAAACTCTCAGCAAACTAGGAATAGAA 1869 chr5ptel1M 550373 GGACTTTTCCTAAAAATAATCAGTATT 550399 ivvi --------------- i L1M5_orf2#LIN 1870 GGGAACTTCC---------------TC 1881 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.00 CpG sites = 375, Kimura (unadjusted) = 38.71 Transitions / transversions = 1.25 (148/118) Gap_init rate = 0.05 (50 / 1025), avg. gap size = 1.50 (75 / 50) 26 0.00 0.00 0.00 chr5ptel1M 550400 550424 (449576) (TTTAGA)n#Simple_repeat 1 25 (0) c_b231s251i2 9105 chr5ptel1M 550400 TTTAGATTTAGATTTAGATTTAGAT 550424 (TTTAGA)n#Sim 1 TTTAGATTTAGATTTAGATTTAGAT 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 4050 29.18 3.91 2.43 chr5ptel1M 550425 551828 (448172) L1M5_orf2#LINE/L1 1882 3293 (1) m_b231s551i7 9104 chr5ptel1M 550425 ACTTAATAGATCAGTAGCATCTATTAAAACCAT-CAGTAAGCATCATATG 550473 i i i--- -i iv v v - i? i iv L1M5_orf2#LIN 1882 ACCTGATAA---AG-GGCATCTACGAAAAACCTACAGCNAACATCATACT 1927 chr5ptel1M 550474 TAATAGGGACAAACTGCAATCATTCCCAATAAGATCAGGAGTGAAACAAG 550523 i v v ? v ?v v vv i iii i L1M5_orf2#LIN 1928 TAATGGTGAAANACTGAANGCTTTCCCCCTAAGATCGGGAACAAGACAAG 1977 chr5ptel1M 550524 GTTGCCCACTATCACTGTTGCTATTCAATATTGTATTAGAAATGCGAGCT 550573 v i i ? iii v i i i ii v v i L1M5_orf2#LIN 1978 GATGTCCGCTNTCACCACTTCTATTCAACATTGTACTGGAGGTCCTAGCC 2027 chr5ptel1M 550574 ATGGCAATAAGAGTTGAGAAAGAGATTAAAGGAATTAGAGTAGGAAATGA 550623 vv ivvv i i v v v iii v v L1M5_orf2#LIN 2028 AGTGCAATAAGGCAAGAAAAAGAAATAAAAGGCATAAAGATTGGAAAGGA 2077 chr5ptel1M 550624 GGAAACCAAATTATGACTCTTTGCTGATGATATGATGGTATACTTAGACA 550673 i iv i i v?i v i v i v ? v v L1M5_orf2#LIN 2078 AGAAATAAAACTGTCNTTATTCGCAGATGACATGATTGTNTACGTAGAAA 2127 chr5ptel1M 550674 ACTCCAGA----CT---AAAAAGCTATTAGAAATAATCCACAACTTTAGC 550716 ii ? i ---- --- ? i i v vviii v L1M5_orf2#LIN 2128 ATCCNAAAGAATCTACAAANAAACTACTAGAACTAATAAGTGAATTTAGC 2177 chr5ptel1M 550717 AAAGTTGCAGGATACAAAATAAACCCACATAAGTC-ATCAGCTTCTTATA 550765 i i ? ii v ivi v i - iivv ii L1M5_orf2#LIN 2178 AAGGTCGCNGGATACAAGGTCAATATACAAAAATCAATTGTATTTCTATA 2227 chr5ptel1M 550766 TATCACTAACAA--AATCC--AAGTCAGAGTTACAAAGAGAAATTCCATT 550811 ii vi -- iv-- i v i v --? i iv v L1M5_orf2#LIN 2228 TACTAGCAACAAACAATTGGAAAATGAAATTT--NAAAAACAATACCATT 2275 chr5ptel1M 550812 TAAATTAACTACTGATAGTATAAAATACTTAGGAATCTATCTGCCAAGGG 550861 v v i vv vi v ii ? vv iv ii? L1M5_orf2#LIN 2276 TACAATAGCATCAAAAAACATNAAATACTTAGGAATAAATCTAACAAAAN 2325 chr5ptel1M 550862 AAAGTCAGAAACTTTATGAGCAAAACTATAAACCACTTTTCACACAAATT 550911 vivv ii v ? iivvv i v i vi v v v L1M5_orf2#LIN 2326 ATGTGCAAGACCTNTACACTGAAAACTACAAAACATTGCTGAGAGAAATT 2375 chr5ptel1M 550912 AAGTCTGATCTAACCAATTGAAAAAATATTAAATGCTCTTGGATAGGGTG 550961 ivvv i vi v i i i vvv i v v iv L1M5_orf2#LIN 2376 AAAGAAGACCTAAATAAATGGAGAGATATACCATGTTCATGGATTGGAAG 2425 chr5ptel1M 550962 AGCAAATATAATAAAGATGACAATACTACCTAAACTAATCTATTTGTTTA 551011 viv vi ? v v v i i i vvi i L1M5_orf2#LIN 2426 ACTCAATATTGTNAAGATGTCAATTCTCCCCAAATTGATCTATAGATTCA 2475 chr5ptel1M 551012 GCGCTATACCAATCATACTCCCAAAAAACTATTTTGATGACCTAGAAAAA 551061 ii v v v v iv iii v vv vv v v i L1M5_orf2#LIN 2476 ATGCAATCCCAATCAAAATCCCAGCAGGTTTTTTTGTAGAAATTGACAAG 2525 chr5ptel1M 551062 ATAA---CAAAGTTCATATGGAAACACAAAAGGTCAAGAAT-TTCAAGGG 551107 v i ---i i i ii i ii ? -vi iiv L1M5_orf2#LIN 2526 CTGATTCTAAAATTTATATGGAAATGCAAAGGACCNAGAATAGCCAAAAC 2575 chr5ptel1M 551108 AATTAATGAAAAAAAAAAATCAAA--TGAAGGTGGCTTAGCTGTACCAGA 551155 i-v i i - -- i -- i - vv ? L1M5_orf2#LIN 2576 AATC-TTGAAAAAGAAGAA-CAAAGTTGGAG--GACTTA-CACTACCNGA 2620 chr5ptel1M 551156 TCT-AAAATTATATTATAGAGCAGCAATTACCAAAACCATTTGGTACTGG 551204 ? - i i - i vi i v i i vi v i L1M5_orf2#LIN 2621 TNTCAAGACT-TATTATAAAGCTACAGTAATCAAGACAGTGTGGTATTGG 2669 chr5ptel1M 551205 C-TAAGGAATAGATTAGTTGATCGCTGGAATAGGTTAG---GTTCAAAGG 551250 - - iv i v iv i iv --- i i -i L1M5_orf2#LIN 2670 CGTAAGG-ATAGACAAATAGATCAATGGAACAGAATAGAGAGTCCAGA-A 2717 chr5ptel1M 551251 ACAGA---ACAGTCA-ATAACTTTGATACTCTAATGTTTGACAAA---CC 551293 i --- -- - --- v ?i ? - i v ---v L1M5_orf2#LIN 2718 ATAGACCCACA--CATATA---TGGNCANT-TGATTTTTGACAAAGGTGC 2761 chr5ptel1M 551294 CAAAG-ACCCCAGCTTTTGGGATAAGAACTCACTGTTTGACAAAAATTGC 551342 ? - vii ---- iv i ivvv v ii viv L1M5_orf2#LIN 2762 CAANGCAATTCAG----TGGGGAAAGGATAGTCTTTTCAACAAATGGTGC 2807 chr5ptel1M 551343 TGGGAAAATTAGAAACTAGTATGGCAGAAACTAGGCATTGACCCACACTT 551392 i v i v iivi v i v iii?v i vi i L1M5_orf2#LIN 2808 TGGAACAATTGGATATCCATATGGAAAAAAATGAANCTCGACCCCTACCT 2857 chr5ptel1M 551393 AACCCTGTACACCAAGATAAGGTCAAAATGGGTTGATA-ATCTAGGCATA 551441 v v ii v i v iv ? i i i- - i iiii L1M5_orf2#LIN 2858 CACACCATACACAAAAATTAATTCNAGATGGATC-ATAGACCTAAATGTA 2906 chr5ptel1M 551442 AAGAATGAGATTACAAATAAATTAGAGGAAAACAGGATAGTTTACCTCTC 551491 ii? i i i i vvvvi i viiv vv i iiv L1M5_orf2#LIN 2907 AAAGNTAAAACTATAAAACTTCTAGAAGAAAACATAGGAGAATATCTTCG 2956 chr5ptel1M 551492 AGACCTGTGGAAGAGGAAGGAATTT-------ATGACCAAAGAAGAACTA 551534 v - i?v v iii ------- v vv i v ? L1M5_orf2#LIN 2957 TGACCT-TGGGNTAGGCAAAGATTTCTTAAACAGGACACAAAAAGCACNA 3005 chr5ptel1M 551535 GACATCATTACTGATCACAAAATAGATAATTGGGATTATATCAAATTGAA 551584 --- i v vv --- v v v v i ?i v v L1M5_orf2#LIN 3006 ---ACCATAAAAG---AAAAAATTGATAAATTGGACTNCATCAAAATTAA 3049 chr5ptel1M 551585 AAGTTTTTGTACAAACAAAACTAATGCAGACAAGATTAGAAGGGAAGCAA 551634 ii i iv ?vvv ivi vi ivi v i v i v v L1M5_orf2#LIN 3050 AAACTTCTGCTCNTCAAAAGACACCGTTAAGAAAATGAAAAGGCAAGCCA 3099 chr5ptel1M 551635 TAAACTGGGAAAACATTTTTGCAGT-CAAATGTTCTGATAAAGGCCTCAT 551683 i i ? i v v i?- v i- i v i L1M5_orf2#LIN 3100 CAGANTGGGAGAAAATATTTGCAANACATATA-TCTGACAAAGGACTCGT 3148 chr5ptel1M 551684 ATCCAAAATATATAGAGAATTCACTCTAAGTT-ATGAAAAATCACGCCAT 551732 i i i - vi ? i- i ? -- v v v L1M5_orf2#LIN 3149 ATCCAGAATATATAAAGAACTC-CTACAANTCAATAANAAA--AAGACAA 3195 chr5ptel1M 551733 TC--TCCAAATGATCAATAGTCAAAGGATATGAACAGACAATTCTCAGAC 551780 v --i vv? vv i v i iv v v i v L1M5_orf2#LIN 3196 ACAACCCAATANAAAAATGGGCAAAAGACTTGAACAGACACTTCACAAAA 3245 chr5ptel1M 551781 GAAGAAATTGAAACTATATCTAGCCATGTGAAAAGATGCTCCAAGTCA 551828 v ?v iviivvv iv ii v v? L1M5_orf2#LIN 3246 GAAGATATNCAAATGGCCAATAAGCACATGAAAAGATGCTCAACNTCA 3293 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.00 CpG sites = 375, Kimura (unadjusted) = 38.71 Transitions / transversions = 1.14 (227/199) Gap_init rate = 0.04 (57 / 1403), avg. gap size = 1.40 (80 / 57) 675 22.67 4.55 1.77 chr5ptel1M 551682 551901 (448099) L1ME5_3end#LINE/L1 4 229 (712) m_b231s551i8 9104 chr5ptel1M 551682 ATATCCAAAATATATAGAGAATTCACTCTAAGTTAT---GAAAAATCACG 551728 i i i ii i - vi i i v--- v- L1ME5_3end#LI 4 ATATCTAGAATATACAAGGAACTC-CTGCAAATCAACAAGAAAAAG-ACG 51 chr5ptel1M 551729 CCATTCTCCAAATGATCAATAGTCAAAGGATATGAACAGACAATTCTCAG 551778 v? vi - vv vv i v i iv L1ME5_3end#LI 52 GNAACC-CCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAG 100 chr5ptel1M 551779 ACGAAGAAA-TTGAAACTATATCTAGCCATGTGAAAAGATGCTCCAAGTC 551827 v i -ii vvv v v - i i v v L1ME5_3end#LI 101 AAGAGGAAACCCGAAAGGCTAACAAG-CATATGAAGAGATGCTCAAACTC 149 chr5ptel1M 551828 ATTATTAATCAGAGAAATGCATTTTAAGACAACTCTGAGATACCACTACA 551877 v vv i vv i vi L1ME5_3end#LI 150 ATTAGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTA 199 chr5ptel1M 551878 CACCTGTCAGATTGGC------TAGAAAGC 551901 i i i ------ L1ME5_3end#LI 200 CACCTATTAGACTGGCAAAAATTAGAAAGC 229 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 26.73 CpG sites = 24, Kimura (unadjusted) = 27.36 Transitions / transversions = 0.96 (24/25) Gap_init rate = 0.03 (7 / 219), avg. gap size = 2.00 (14 / 7) 313 23.94 1.41 0.00 chr5ptel1M 552824 552894 (447106) MIR3#SINE/MIR 109 180 (28) m_b231s601i15 9106 chr5ptel1M 552824 CTTCTGTGAACCTCAATTTCC-CATCTACAAAATGAGTGGGTCACACTCT 552872 i v ii i - ii v iiv vv MIR3#SINE/MIR 109 CCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAG 158 chr5ptel1M 552873 ATGGTCTTGTAGGTCCCTTCCA 552894 i ivv MIR3#SINE/MIR 159 ATGATCTCTAAGGTCCCTTCCA 180 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.42 CpG sites = 10, Kimura (unadjusted) = 29.42 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.01 (1 / 70), avg. gap size = 1.00 (1 / 1) 418 26.99 9.94 5.85 chr5ptel1M 553255 553435 (446565) C MIRb#SINE/MIR (64) 204 17 m_b231s601i16 9107 chr5ptel1M 553255 TGCATTGTCTTATTTCATCCTCATGAGAAC---AAGAGGACTTAGCTGCT 553301 i i v ii v ---iv --- -- - C MIRb#SINE/MIR 204 TGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGG---TAG--G-T 161 chr5ptel1M 553302 ATCATTATACCCGTTTTACAGATAAAGAAACTGAATCCAACAGAGGTCCT 553351 i v i i i iv iv v ivv C MIRb#SINE/MIR 160 ATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAA 111 chr5ptel1M 553352 ATAACTTGAC-----TTGCAAGACT---------CTGAGGTGGGATTAAA 553387 i v ----- ii vii --------- v vi vi C MIRb#SINE/MIR 110 GTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGA 61 chr5ptel1M 553388 ACCCTGGGCTTCCTGA-TTCAAGGCCTTATCCACATTCTATTCACTGTA 553435 v v vi - i i ----- iiii v i i C MIRb#SINE/MIR 60 ACCCAGGTCTGTCTGACTCCAAAGC-----CCGTGCTCTTTCCACTGCA 17 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.79 CpG sites = 28, Kimura (unadjusted) = 34.52 Transitions / transversions = 1.56 (28/18) Gap_init rate = 0.08 (15 / 180), avg. gap size = 1.93 (29 / 15) 17 14.21 3.23 0.00 chr5ptel1M 555231 555261 (444739) (TG)n#Simple_repeat 1 32 (0) m_b231s252i11 9108 chr5ptel1M 555231 TGTGAATGTGTGTGTTTAT-TGTGTGTGTGTG 555261 vi v i - (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 32 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.03 (1 / 30), avg. gap size = 1.00 (1 / 1) 45 4.13 0.00 0.00 chr5ptel1M 555304 555353 (444647) (T)n#Simple_repeat 1 50 (0) c_b231s251i3 9109 chr5ptel1M 555304 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTGTTTTTTTTTTT 555353 v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 18 12.17 0.00 0.00 chr5ptel1M 555549 555575 (444425) (A)n#Simple_repeat 1 27 (0) m_b232s252i1 9110 chr5ptel1M 555549 AAAACAAAAACAAAAACAAAAAAAAAA 555575 v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAA 27 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 736 29.84 1.65 2.67 chr5ptel1M 555710 556012 (443988) L1ME4c_3end#LINE/L1 237 536 (294) m_b232s551i0 9111 chr5ptel1M 555710 TATCCAATG-TGGAGAGGTTTTTAGGGGGAAACCTGGGACACTGATGCAT 555758 i - v ? ---- v vi v v ? v i L1ME4c_3end#L 237 TACCCAATGCTGGCGAGGNT----GCGGTGAAACTGGTACNCTCATACAT 282 chr5ptel1M 555759 CGCTGGTGGAGCTATAGAAAAATCCAACCATTCTGGGAAGCAATTTGGAA 555808 i vi? i i vvii v v i i -- L1ME4c_3end#L 283 TGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGG-- 330 chr5ptel1M 555809 CGATGCCCA--AAGGGCTATCAAAACCTGCATACCCCTTGATCTAGTGAT 555856 i i vi -- i i v iv v i i i i L1ME4c_3end#L 331 CAATACGTATCAAGAGCCATAAAAATGTTCATACCCTTTGACCCAGTAAT 380 chr5ptel1M 555857 GTTTCTTGTAGGCTTATATGCCAAAG--ACAACTTAAAGCAAGTAAAGGC 555904 viiv v i vv v v i i -- i i i iv v i-- L1ME4c_3end#L 381 TCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAAGAAGGAAAA-- 428 chr5ptel1M 555905 ACCCACATGCAAAAAGATGTTTGTGGTAGCCTTGTTTGTAGTGGCAAGAA 555954 v i i vi ii v i v i i i i i i L1ME4c_3end#L 429 AGCTATATGCACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAA 478 chr5ptel1M 555955 ACTGGAAACTGAGTGGATGCCCATCAGTTGGGGAATGGCTGAATAAGTCA 556004 i vivv ii i v i v i i i i i L1ME4c_3end#L 479 ATTGGAAACAACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTA 528 chr5ptel1M 556005 TAGTACAT 556012 i L1ME4c_3end#L 529 TGGTACAT 536 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.85 CpG sites = 55, Kimura (unadjusted) = 40.05 Transitions / transversions = 1.67 (55/33) Gap_init rate = 0.04 (11 / 302), avg. gap size = 1.18 (13 / 11) 14 3.28 5.41 8.33 chr5ptel1M 556182 556218 (443782) (ACTCTG)n#Simple_repeat 1 36 (0) m_b232s252i2 9112 chr5ptel1M 556182 ACT-TGACTACATGACTCTG-CTCTGACTTCTGTCTCTG 556218 - - - - - v (ACTCTG)n#Sim 1 ACTCTGACT-C-TGACTCTGACTCTGAC-TCTGACTCTG 36 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.14 (5 / 36), avg. gap size = 1.00 (5 / 5) 291 27.12 5.59 2.03 chr5ptel1M 556529 556671 (443329) L1MC3_3end#LINE/L1 451 598 (1934) m_b232s551i2 9111 chr5ptel1M 556529 GCAGCTCTTTGGGTGGTGGCAAAGAACTGGAA--AAC--AAATGTCTACC 556574 i v vvi ii v v i -- -- i ivi L1MC3_3end#LI 451 GCAGCTTTATTCATAATCGCCAAAAACTGGAAGCAACCAAGATGTCCTTC 500 chr5ptel1M 556575 AATTGGGGAATGGCCGAACAAGTTGTGGTACACGAAGGCAATGGAATATT 556624 v v vii ii ivv vi L1MC3_3end#LI 501 AATAGGTGAATGGATAAACAAACTGTGGTACATCCATACAATGGAATATT 550 chr5ptel1M 556625 ATTATTCTGTAA----AAATGATGCTCAAGCAAGTTTTGGAAAGACCTGG 556670 vvv vi ---- - -- v iivi i v L1MC3_3end#LI 551 ATTCAGCGATAAAAAGAAATGA-GCT--ATCAAGCCACGAAAAGACATGG 597 chr5ptel1M 556671 A 556671 L1MC3_3end#LI 598 A 598 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.98 CpG sites = 19, Kimura (unadjusted) = 34.06 Transitions / transversions = 1.00 (19/19) Gap_init rate = 0.04 (6 / 142), avg. gap size = 1.83 (11 / 6) 336 28.07 3.51 0.00 chr5ptel1M 556529 556642 (443358) L1MC5_3end#LINE/L1 451 568 (2126) m_b232s551i1 9111 chr5ptel1M 556529 GCAGCTCTTTGGGTGGTGGCAAAGAACTGGAAAA----CAAATGTCTACC 556574 v v vv ii i ii v---- i i L1MC5_3end#LI 451 GCAGCACTATTTGTAATAGCAAAAGACTGGAAACAACCCAAATGTCCATC 500 chr5ptel1M 556575 AATTGGGGAATGGCCGAACAAGTTGTGGTACACGAAGGCAATGGAATATT 556624 v v ii i ii i ivv vi i i L1MC5_3end#LI 501 AATAGGGGACTGGTTGAATAAACTATGGTACATCCACACAATGGAGTACT 550 chr5ptel1M 556625 ATTATTCTGTAAAAATGA 556642 vvvv v L1MC5_3end#LI 551 ATGCAGCTGTAAAAAGGA 568 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.73 CpG sites = 17, Kimura (unadjusted) = 35.73 Transitions / transversions = 1.13 (17/15) Gap_init rate = 0.01 (1 / 113), avg. gap size = 4.00 (4 / 1) 356 27.89 5.08 2.76 chr5ptel1M 556547 556723 (443277) L1ME4c_3end#LINE/L1 472 652 (178) m_b232s551i3 9111 chr5ptel1M 556547 GCAAAGAACTGGAAA--AC--AAATGTCTACCAATTGGGGAATGGCCGAA 556592 i i i -- -- i v v iii i L1ME4c_3end#L 472 GCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAATGGTTAAG 521 chr5ptel1M 556593 CAAGTTGTGGTACACGAAGGCAATGGAATATTAT-TATTCTGTAAAAATG 556641 i i i iv? vv i -i vi vv L1ME4c_3end#L 522 TAAATTATGGTACATCNACTCGATGGAATATTATGCAGCCATTAAAAATG 571 chr5ptel1M 556642 ATGCTCAAGCAAGTTTTGGAAAGACCTGGA----GTTACATGACCTGATG 556687 iv i v v iii v v ivi v ---- -i iv i L1ME4c_3end#L 572 ATAATTATGAAGACTATGTAGCAACATGGAAAATGTT-TATGATATAATG 620 chr5ptel1M 556688 TTGAGCCAAACAAGCAGAACCCAGAGTACATTGTAT 556723 i iv v iv i ---- L1ME4c_3end#L 621 TTAAGTGAAAAAAGCAGAATACAAA----ATTGTAT 652 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.32 CpG sites = 29, Kimura (unadjusted) = 36.20 Transitions / transversions = 1.53 (29/19) Gap_init rate = 0.05 (9 / 176), avg. gap size = 1.56 (14 / 9) 1000 28.69 4.96 4.63 chr5ptel1M 557554 558178 (441822) C L1MC2_3end#LINE/L1 (458) 633 7 m_b232s551i4 9113 chr5ptel1M 557554 GCTCATTTCACTAAGCATCAGTTCGTGTAAG-TCTCTCCAGGCCTTTCTG 557602 iv v vi - v i v - ii v i ii C L1MC2_3end#LI 633 GCTTCTTTCACTTAGCAATA-TGCATTTAAGGTTCCTCCATGTCTTTTCG 585 chr5ptel1M 557603 AAATTATCCTGTTGG-TCATTCCTT------ACAGAACAGTAATATTCCA 557645 ---- iv i v i - i ------i v --- C L1MC2_3end#LI 584 ----TGGCTTGATAGCTCATTTCTTTTTATCGCTGAA---TAATATTCCA 542 chr5ptel1M 557646 TAATATTCATATACCATAATTTATTCAGCCATTCTCCAACTGATGGACAT 557695 vi vv i i i i i v v v i v C L1MC2_3end#LI 541 TTGTATGGATGTACCACAGTTTGTTTATCCATTCACCTATTGAAGGACAT 492 chr5ptel1M 557696 CC--ATTCAGTTTCCAGTTTTTAGCCACTACAAA-AGGGCTGCCACAAAC 557742 i--i -- i iv i v i ii - ii i i C L1MC2_3end#LI 491 CTTGGTT--GCTTCCAAGTTTTGGCAATTATGAATAAAGCTGCTATAAAC 444 chr5ptel1M 557743 ATTCGTGCACATACAGGTCCCTTT-----CCTTCTTTATAATCTCTTTGG 557787 ---- i iii v ----- v vvv v v v v v C L1MC2_3end#LI 443 ATTCGTG----TGCAGGTTTTTGTGTGGACATAAGTTTTCAACTCATTTG 398 chr5ptel1M 557788 GATATA-ATCCAGTAGTAACACTGCTGGATCAAAGGGTATACACAATTTG 557836 i v - i v v iivv i iv v --- v ? v C L1MC2_3end#LI 397 GGTAAATACCAAGGAGCGCGATTGCTGGATCGTATGGTA---AGANTATG 351 chr5ptel1M 557837 AT-AACTTTTTGAGCATAGTTCCAAACTACTTCTCAAAATGGTTGGATTC 557885 v - i v i v - v v iii ii i i v iiv C L1MC2_3end#LI 350 TTTAGCTTTGTAAGAA-ACTGCCAAACTGTCTTCCAAAGTGGCTGTACCA 302 chr5ptel1M 557886 GTTCACAACTCCACCAACAATGCATCAATGTCCCAGTTTTCCCGCATCCT 557935 v ii vii i v v iv i v vii i C L1MC2_3end#LI 301 TTTTGCATTCCCACCAGCAATGAATGAGAGTTCCTGTTGCTCCACATCCT 252 chr5ptel1M 557936 C--CAACA------ATCATCATTATTTTTTCCTGTCATCTTAGCCAATCT 557977 -- i ------i ii v i v---- -- i v C L1MC2_3end#LI 251 CGCCAGCATTTGGTGTTGTCAGTGTTTTG----G--ATTTTAGCCATTCT 208 chr5ptel1M 557978 GACAGGTGTGTAGTGGTATTTTAAGAGTTGTCTTAATTTGCATTTCTCTG 558027 i i i i vv- i v i i C L1MC2_3end#LI 207 AATAGGTGTGTAGTGGTATCTCATT-GTTGTTTTAATTTGCAATTCCCTA 159 chr5ptel1M 558028 ATTA-ATAATGACTTGGAGCATCTTTTCATATGACTAGAAATAGTTTCAA 558076 v - - iv v vi vvviivi i vv C L1MC2_3end#LI 158 ATGACATA-TGATGTTGAGCATCTTTTCATATGCTTATTTGCCATCTGTA 110 chr5ptel1M 558077 TTTCTTCATCTGAGAATTGTCTGTTCATATCCTTTGACCATTTTTCAATT 558126 v v iv v iv v i v ? C L1MC2_3end#LI 109 TATCTTCTTTGGTGAGGTGTCTGTTCAGATCTTTTGCCCATTTTTNAATT 60 chr5ptel1M 558127 GGAGAATGGCTTGATTT-TTATAAATTAGAGTTAA---TTCTCTATATAT 558172 ---i v i v - viv v vv --- i i C L1MC2_3end#LI 59 GG---GTTGTTTGTTTTCTTATTGTTGAGTTTTAAGAGTTCTTTGTATAT 13 chr5ptel1M 558173 TTTGGA 558178 C L1MC2_3end#LI 12 TTTGGA 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.80 CpG sites = 90, Kimura (unadjusted) = 36.90 Transitions / transversions = 1.11 (90/81) Gap_init rate = 0.07 (42 / 624), avg. gap size = 1.43 (60 / 42) 1502 27.90 1.29 1.66 chr5ptel1M 557636 558178 (441822) C L1ME3G_3end#LINE/L1 (377) 547 7 m_b232s551i5 9113 chr5ptel1M 557636 TAATATTCCATAATATTCATATACCATAATTTATTCAGCCATTCTCCAAC 557685 i i vv i i i v i C L1ME3G_3end#L 547 TAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTAT 498 chr5ptel1M 557686 TGATGGACATCCATTCAGTTTCCAGTTTTTAGCCACTACAAA-AGGGCTG 557734 ii vviv i v i i - iv C L1ME3G_3end#L 497 TGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCTG 448 chr5ptel1M 557735 CCACAAACATTCGTGCACATACAGGTCCCTTTCCTTCTTTATAA---TCT 557781 v ii i v i i ?-- i v v viv v iii --- i C L1ME3G_3end#L 447 CAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATTT 400 chr5ptel1M 557782 CTTTGGGATATA-ATCCAGTAGTAACACTGCTGGATCAAAGGGTATACAC 557830 ? i v -?i ? v iiv i i i i C L1ME3G_3end#L 399 CTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGC 350 chr5ptel1M 557831 AATTTGATAACTTTTTGAGCATAGTTCCAAACTACTTCTCAAAATGGTTG 557880 - -- v viviv v v i i iiii ? i C L1ME3G_3end#L 349 A-TTT--TAAATTTTAATAGATACTGCCAAATTGCCCTCCAAAANGGCTG 303 chr5ptel1M 557881 GATTCGTTCACAACTCCACCAACAATGCATCAATGTCCCAGTTTTCCCGC 557930 v iivi i vii i i i v iv v v i i C L1ME3G_3end#L 302 TACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCAC 253 chr5ptel1M 557931 ATCCTC--CAACAATCATCATTATTTTTTCCTGTCATCTTAGCCAATCTG 557978 i -- v ?ivi ivv?iii vvv i v C L1ME3G_3end#L 252 ACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATCTG 203 chr5ptel1M 557979 ACAGGTGTGTAGTGGTATTTTAAGAGTTGTCTTAATTTGCATTTCTCTGA 558028 ii viv i i i vv- i i C L1ME3G_3end#L 202 ATGGGTGAAAAATGGTATCTCATT-GTTGTTTTAATTTGCATTTCCCTGA 154 chr5ptel1M 558029 TTAATAATGACTTGGAGCATCTTTTCATATGACTAGAAATAGTTTCAATT 558078 v i vv v vi vviiivi vv C L1ME3G_3end#L 153 TTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGTATT 104 chr5ptel1M 558079 TCTTCATCTGAGAATTGTCTGTTCATATCCTTTGACCATTTTTCAATTGG 558128 i v v i v v C L1ME3G_3end#L 103 TCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGG 54 chr5ptel1M 558129 AGAATGGCTTGATTTTTATAAATTAGAGTTAATTCTCTATATATTTTGGA 558178 iv-- v v- i vi v vivv i i i C L1ME3G_3end#L 53 GT--TGTCTTT-TTCTTATTGATTTGTAGGAGTTCTTTATATATTCTGGA 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.62 CpG sites = 84, Kimura (unadjusted) = 36.26 Transitions / transversions = 1.29 (84/65) Gap_init rate = 0.02 (13 / 542), avg. gap size = 1.23 (16 / 13) 654 28.94 4.49 3.97 chr5ptel1M 558036 558636 (441364) C L1M5_orf2#LINE/L1 (0) 3294 2691 m_b232s551i6 9113 chr5ptel1M 558036 TGACTTGGAGCATCTTTTCATATGACTAGAAATAGTTTCAATTTCTTCAT 558085 ?v v i vi vviiivi v? v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr5ptel1M 558086 CTGAGAATTGTCTGTTCATATCCTTTGACCATTTTTCAATTGGA--GAAT 558133 i v v vi i v ?v i-- vv C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTT 3195 chr5ptel1M 558134 GGCTTGATTTTTA-TAAATTAGAGTTAATTCTCTATATATTTTGGAAATG 558182 v v- ? - i ? iv -v i i i v i C L1M5_orf2#LIN 3194 GTCTTT-TTNTTATTGANTTGTAG-GAGTTCTTTATATATTCTGGATACG 3147 chr5ptel1M 558183 AGGCC-TTATCAGA-ACCTTTGACTGTAAA-ATATTTTCCCAGTTTATTG 558229 v - i - iv v -?i i - v i ? i i v C L1M5_orf2#LIN 3146 AGTCCTTTGTCAGATATATGT-NTTGCAAATATTTTCTCCCANTCTGTGG 3098 chr5ptel1M 558230 CTTCCCTTCTAA---TCTTATCTGCATTAGTTTTGTTTGTACAAAAACTT 558276 v i v --- v v ii i-- -v? vi i ii C L1M5_orf2#LIN 3097 CTTGCCTTTTCATTTTCTTAACGGTGTC--TTTTG-ANGAGCAGAAGTTT 3051 chr5ptel1M 558277 TTCAGTTTGGTATAGTCGAAATTTTCTATTTTGTGATCAGTAATGATCTC 558326 v v i i? v v v v v--- vv v i --- C L1M5_orf2#LIN 3050 TTAATTTTGATGNAGTCCAATTTATCAATTTTT---TCTTTTATGGT--- 3007 chr5ptel1M 558327 TAGTTCTTCTTTGGTCATA---AAGA---CCTTCCCT-TCCACAGGTCTC 558369 ? v i vv v i--- --- i v -? vv v C L1M5_orf2#LIN 3006 TNGTGCTTTTTGTGTCCTGTTTAAGAAATCTTTGCCTANCCCAAGGTCAC 2957 chr5ptel1M 558370 AGAGATAAACTATCCTGTG--TTCCTCTAATTTATTAATAATTTCATTCT 558417 ii -- i v i -- i ivvvv v i i ?ii C L1M5_orf2#LIN 2956 GAAGAT--ATTCTCCTATGTTTTCTTCTAGAAGTTTTATAGTTTTANCTT 2909 chr5ptel1M 558418 TTATGCCTAGGTC-ATGAACCCATTTTTGACCTTATCTTGGTGTACAGTG 558466 iiii - - i - i ? vi v i v ii C L1M5_orf2#LIN 2908 TTACATTTAGGTCTATG-ATCCA-TCTNGAATTAATTTTTGTGTATGGTG 2861 chr5ptel1M 558467 TTAAGTATGGATCAATGCCTAGTTTCTGCCATATTAGTTTCCAATTTTCC 558516 v i v i i v?iii v i v vii v v i C L1M5_orf2#LIN 2860 TGAGGTAGGGGTCGAGNTTCATTTTTTTCCATATGGATATCCAATTGTTC 2811 chr5ptel1M 558517 CAGCAATTTTTATCAAACAGTAAGTTCTTATCCCAAAAGCTGGGAT-CTT 558565 viv i ii v vvvi i vi ---- iiv - ? C L1M5_orf2#LIN 2810 CAGCACCATTTGTTGAAAAGACTATCCTTTCCCCA----CTGAATTGCNT 2765 chr5ptel1M 558566 TGG---GTTTGTCAAAGACTAGGTTGCTATATTTGT-TGACTGTTTTATC 558611 ---v i ii i? v? i v - --- v i i C L1M5_orf2#LIN 2764 TGGCACCTTTGTCAAAAATCAANTGNCCATATATGTGTG---GGTCTATT 2718 chr5ptel1M 558612 CCTTGAAC---CTAATCTATTCCACTGA 558636 i - i --- v i i C L1M5_orf2#LIN 2717 TC-TGGACTCTCTATTCTGTTCCATTGA 2691 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.75 CpG sites = 87, Kimura (unadjusted) = 38.63 Transitions / transversions = 1.09 (87/80) Gap_init rate = 0.07 (39 / 600), avg. gap size = 1.31 (51 / 39) 2244 26.69 0.30 0.15 chr5ptel1M 558650 559317 (440683) L1M5_orf2#LINE/L1 1573 2241 (1053) m_b232s551i7 9114 chr5ptel1M 558650 ACAGAGAAAGAAAATTATAGACCAATCTCTCTAATGAATATTGATGCTAA 558699 iii i v i v i v v L1M5_orf2#LIN 1573 ACAAGAAAAGAAAATTACAGACCAATATCCCTCATGAACATAGATGCAAA 1622 chr5ptel1M 558700 AATCTTAAATAAGATATTAGCAAAAAGACTACAGAAAATCATCTCCAAGA 558749 i ? i i vv v v v vvi vvvv i L1M5_orf2#LIN 1623 AATCCTNAACAAAATATTAGCAAATCGAATCCAGCAATATATAAAAAGGA 1672 chr5ptel1M 558750 TAATACACTATGATCAAGTAGGATTTATACCAGGAATGCAGGGCTGGTTC 558799 ii i i i v i i i L1M5_orf2#LIN 1673 TAATACATCATGACCAAGTGGGGTTTATCCCAGGAATGCAAGGTTGGTTT 1722 chr5ptel1M 558800 AATATTAGGAAAACTATCAATATAATTGGCCATATTAATA-ACCAAATTA 558848 i v i v v i vi i - vi -vi L1M5_orf2#LIN 1723 AACATTCGAAAATCAATCAATGTAATTCACCATATTAACAGAATAAA-GG 1771 chr5ptel1M 558849 ACAAAAACCATATGATCATCTCAATAGATGCAGAAAAAGCATTTGATAAA 558898 v i i L1M5_orf2#LIN 1772 AGAAAAATCATATGATCATCTCAATAGATGCAGAAAAAGCATTTGACAAA 1821 chr5ptel1M 558899 ATCCAACATCCATTCCTATTAAAAACACTTGAGAGTATAGGAATAAATGG 558948 i i v iv v iiiv ivv i v L1M5_orf2#LIN 1822 ATTCAACACCCATTCATGATAAAAACTCTCAGCAAACTAGGAATAGAAGG 1871 chr5ptel1M 558949 ACTTTTCCTTAAAATAATCAGCAGCATCTATTTAAAACCATCAGTAAGCA 558998 ivvi i vv i v ivi ivv vv i? i L1M5_orf2#LIN 1872 GAACTTCCTCAACCTGATAAAGGGCATCTACGAAAAACCTACAGCNAACA 1921 chr5ptel1M 558999 TCATATGTAATGGAGACAAACTGCAACCATTCCCAATAAGATCTGGAGTG 559048 iv v v ? v ?v v vv v iii L1M5_orf2#LIN 1922 TCATACTTAATGGTGAAANACTGAANGCTTTCCCCCTAAGATCGGGAACA 1971 chr5ptel1M 559049 AAACAAGGTTGTCCACTATCACCGTTACTATTTAATATTGTATTAGAAAC 559098 i v i ? ii v i i i i iii L1M5_orf2#LIN 1972 AGACAAGGATGTCCGCTNTCACCACTTCTATTCAACATTGTACTGGAGGT 2021 chr5ptel1M 559099 GCTAGCTTTAGCAATAAGAGCTGAGAAAGAGATTAAAGGAATAAGAATAG 559148 v ivvv ivvv i i v v ii v L1M5_orf2#LIN 2022 CCTAGCCAGTGCAATAAGGCAAGAAAAAGAAATAAAAGGCATAAAGATTG 2071 chr5ptel1M 559149 GCAATGAGGAAACCAAATTATCACTCTTTGCCGATGACATGATCGTATAC 559198 v v i iv i i ?i v i v i ? L1M5_orf2#LIN 2072 GAAAGGAAGAAATAAAACTGTCNTTATTCGCAGATGACATGATTGTNTAC 2121 chr5ptel1M 559199 TTAGAGAACCCCAGAGATTCTACTAA-AAGTTATTAGAAATAATCCACAA 559247 v i i ? i v v - ii i v vviii L1M5_orf2#LIN 2122 GTAGAAAATCCNAAAGAATCTACAAANAAACTACTAGAACTAATAAGTGA 2171 chr5ptel1M 559248 CTTTAGCAAAGTTGCTGGTTATAAAATAAACCCACATAAGTCATCAGCAT 559297 v i i ? v i ii v ivi v i viv i L1M5_orf2#LIN 2172 ATTTAGCAAGGTCGCNGGATACAAGGTCAATATACAAAAATCAATTGTAT 2221 chr5ptel1M 559298 TCTTATATATCACTAAGAAA 559317 ii ii vi v L1M5_orf2#LIN 2222 TTCTATATACTAGCAACAAA 2241 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.19 CpG sites = 97, Kimura (unadjusted) = 34.12 Transitions / transversions = 1.20 (97/81) Gap_init rate = 0.00 (3 / 667), avg. gap size = 1.00 (3 / 3) 230 35.53 9.21 0.00 chr5ptel1M 560254 560405 (439595) L2a_3end#LINE/L2 350 515 (2) m_b232s601i0 9115 chr5ptel1M 560254 TGTATCTTGTATGTACCTAGTTATTTAT-GTATTTCCTCTCTTATTAGAA 560302 i v v iv ii v i - v v ii i ii i L2a_3end#LINE 350 TATATATTTTACTTATTTATTTGTTTATTGTCTGTCTCCCCCCACTAGAA 399 chr5ptel1M 560303 TTTGATTACCTTGA------------TTTTCCGTTATGACTTTTCTTATA 560340 v i viv v ------------ v i v viivi vi i L2a_3end#LINE 400 TGTAAGCTCCATGAGGGCAGGGACTTTTGTCTGTTTTGTTCACTGCTGTA 449 chr5ptel1M 560341 TTCCCAGTTTTTAGAACTGTGCTCGGTCCATAATAAATCCTTAATAAATG 560390 i ivii v ii iv i iiiv i i L2a_3end#LINE 450 TCCCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGGCGCTCAATAAATA 499 chr5ptel1M 560391 TTT-TTGATTGTGTGA 560405 - v vi L2a_3end#LINE 500 TTTGTTGAATGAATGA 515 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 47.86 CpG sites = 33, Kimura (unadjusted) = 50.56 Transitions / transversions = 1.57 (33/21) Gap_init rate = 0.02 (3 / 151), avg. gap size = 4.67 (14 / 3) 347 42.15 3.88 0.94 chr5ptel1M 561598 561803 (438197) C MIRc#SINE/MIR (53) 215 4 m_b232s601i1 9116 chr5ptel1M 561598 TTACATATATTATTTAGCCTGA----CATGACAACCTTTGGAAAGAAATT 561643 i i i viii ---- ii i - vi i v ivi C MIRc#SINE/MIR 215 TCACATACATTATCTCATTTGATCCTCACAACAACCCT-GTGAGGTAGGC 167 chr5ptel1M 561644 AATAAAGAGCGTAATATTTCTACTTTATTGATGAGAAGCCAAAGTCATGG 561693 iviv ivvv v ii i i iv i iv vi v vii C MIRc#SINE/MIR 166 AGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAG 117 chr5ptel1M 561694 AGAAATAAAGTAGTTAGTTTGGAGTTTCAC---TGGTAAGAAAGGGGGCT 561740 ii v iii v iiiiii iv --- i viivi i i C MIRc#SINE/MIR 116 AGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCC 67 chr5ptel1M 561741 TAAGTTTTGTATACAAGCCTTC-TGATCCTACATCCAGTGTTGTTTTCAC 561789 -ii vi i v iv i i - ii i vi i v i C MIRc#SINE/MIR 66 -GGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCAC 18 chr5ptel1M 561790 CACATCACATTGCC 561803 ii i i C MIRc#SINE/MIR 17 TGCACCACACTGCC 4 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 67.56 CpG sites = 61, Kimura (unadjusted) = 70.78 Transitions / transversions = 2.44 (61/25) Gap_init rate = 0.02 (5 / 205), avg. gap size = 2.00 (10 / 5) 318 25.27 3.03 4.08 chr5ptel1M 561803 561901 (438099) MIR3#SINE/MIR 97 194 (14) m_b232s601i2 9117 chr5ptel1M 561803 CAAGTCACTTGCCCTATAGTTTCTTCAGTTTTTTTTTTCATTTTTAAAAT 561852 vv v vvvvv i ii ---- i v MIR3#SINE/MIR 97 CAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCT----CATCTGTAAAAT 142 chr5ptel1M 561853 GAGAGAGTTAGATTGGAT-ATCT-TAAAATCCTTTCTAGCTCTAA-ATTT 561899 i i i i i - - ii i i i - i MIR3#SINE/MIR 143 GAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTC 192 chr5ptel1M 561900 TA 561901 MIR3#SINE/MIR 193 TA 194 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.68 CpG sites = 15, Kimura (unadjusted) = 31.68 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.07 (7 / 98), avg. gap size = 1.00 (7 / 7) 14 15.52 4.08 6.25 chr5ptel1M 562483 562531 (437469) (GAA)n#Simple_repeat 1 48 (0) m_b232s252i3 9118 chr5ptel1M 562483 GAAGAAGAAGAAG-AGTAG-TGAAGAAGAAAGCTGAGAGAAGCTACAAGA 562530 - v -v - vv - -v v (GAA)n#Simple 1 GAAGAAGAAGAAGAAGAAGAAGAAGAAG-AAGAAGA-AGAAG-AAGAAGA 47 chr5ptel1M 562531 A 562531 (GAA)n#Simple 48 A 48 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.10 (5 / 48), avg. gap size = 1.00 (5 / 5) 276 31.98 10.32 0.72 chr5ptel1M 563747 563872 (436128) MIRc#SINE/MIR 17 154 (114) m_b232s601i3 9119 chr5ptel1M 563747 AGTGGAATGATTCCT---CTTGGAATCAAGAAGCCCTGGATTCTTCTCCT 563793 v viv --- i i v i vvv i MIRc#SINE/MIR 17 AGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCC 66 chr5ptel1M 563794 AGCTCCACTAC-CATTAGTTTTTGGGATCCCAGTCTAGTTATTT--CATG 563840 i ii i -i i -i v v i iii v v i i -- v v MIRc#SINE/MIR 67 GGCTCTGCCACTTACTAG-CTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 chr5ptel1M 563841 TCTG-----TAGTTTTACCGTC--TAAAACAAGAATAAT 563872 -----i ivi i -- iii i MIRc#SINE/MIR 116 TCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAAT 154 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.21 CpG sites = 26, Kimura (unadjusted) = 43.88 Transitions / transversions = 1.86 (26/14) Gap_init rate = 0.05 (6 / 125), avg. gap size = 2.33 (14 / 6) 390 32.56 5.97 1.43 chr5ptel1M 563986 564119 (435881) MIRc#SINE/MIR 12 151 (117) m_b232s601i4 9120 chr5ptel1M 563986 GATACAGTAGGAAAGACGTTG-AGTTGA--TCAG--AGACTCTGGGTTCA 564030 i i i i iii ii - v i-- -- - i MIRc#SINE/MIR 12 GGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC-CTGGGTTCG 60 chr5ptel1M 564031 AATTCCACTTCTAATGCTAATTGCCTGTATGATTTTAAACAAATCATTTC 564080 i i ivi ivii v i iv i ii iii i i v MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTA 110 chr5ptel1M 564081 ATCTCCCTAGAGCT---GTTTCCTCATTTAAAAAAATGAGAT 564119 i i - i--- i iv vv i MIRc#SINE/MIR 111 ACCTCTCT-GAGCCTCAGTTTCCTCATCTGTAAAATGGGGAT 151 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 44.27 CpG sites = 34, Kimura (unadjusted) = 47.44 Transitions / transversions = 3.78 (34/9) Gap_init rate = 0.05 (6 / 133), avg. gap size = 1.67 (10 / 6) 456 28.31 3.51 0.85 chr5ptel1M 564016 564129 (435871) MIR3#SINE/MIR 44 160 (48) m_b232s601i5 9120 chr5ptel1M 564016 GAGACTCTGGGTTCAAATTCCACTTCTAATGCTAATTGCCTGTATGATTT 564065 - v i i ivi ivii i ?v i ii MIR3#SINE/MIR 44 GAGAC-CTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCT 92 chr5ptel1M 564066 TAAACAAATCATTTCATCTCCCTAGAGCT--GTTTCCTCATT--TAAAAA 564111 iii i i i i i iv -- i-- v MIR3#SINE/MIR 93 TGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAAT 142 chr5ptel1M 564112 AATGAGATTGAACTAGAT 564129 i v i i i MIR3#SINE/MIR 143 GAGGGGGTTGGACTAGAT 160 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.29 CpG sites = 25, Kimura (unadjusted) = 38.90 Transitions / transversions = 3.57 (25/7) Gap_init rate = 0.03 (3 / 113), avg. gap size = 1.67 (5 / 3) 383 23.42 4.58 2.24 chr5ptel1M 564171 564301 (435699) Charlie4a#DNA/hAT-Charlie 359 492 (16) m_b232s502i0 9121 chr5ptel1M 564171 TTGGATAA--GTATT--AATGTAAC--ATTTGTTTTGTGGTCCTCTGTAT 564214 v -- -- i i--i vi ii v Charlie4a#DNA 359 TTTGATAACTGTATTTCAATATAATTGGTTTCCTTTGTAATCCTATGTAT 408 chr5ptel1M 564215 TTTATATTATGTATTTAAAAGCATCATTTCAGGTATAGTATACTTGGGTT 564264 v i i i iiii - vi vi v v i i Charlie4a#DNA 409 TTTATTTTATGCATTTAAAAACATTATTCTGAG-AAGGGGTCCATAGGCT 457 chr5ptel1M 564265 TCACCAGATTGACAAAGCGGGTCTTATGACATAAAAA 564301 i v - -i i i Charlie4a#DNA 458 TCACCAGACTGCCAAAG-GGGTC-CATGGCACAAAAA 492 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 29.20 CpG sites = 21, Kimura (unadjusted) = 29.20 Transitions / transversions = 2.33 (21/9) Gap_init rate = 0.05 (6 / 130), avg. gap size = 1.50 (9 / 6) 191 26.00 2.00 0.00 chr5ptel1M 564551 564600 (435400) C L3#LINE/CR1 (148) 3951 3901 m_b232s601i6 9122 chr5ptel1M 564551 ACCTCAC-AGGCAGGTTGTTCTACTTTGGGGTACTTCTTATTGTTGGAAA 564599 ? - viii i i v ii vi v i C L3#LINE/CR1 3951 ACCTCNCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGATTGTTAGAAA 3902 chr5ptel1M 564600 G 564600 C L3#LINE/CR1 3901 G 3901 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.26 CpG sites = 9, Kimura (unadjusted) = 34.26 Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.02 (1 / 49), avg. gap size = 1.00 (1 / 1) 537 22.01 1.35 7.91 chr5ptel1M 564625 564772 (435228) MIR#SINE/MIR 28 166 (96) m_b232s601i7 9123 chr5ptel1M 564625 GGGC-CTGGAGTCAGACTCATATCTGTGAGTTCAAATCTGGCCTCAGACA 564673 - i ---ii --i i iv v v v MIR#SINE/MIR 28 GGGCTCTGGAGCCAGACT---GCCTG--GGTTCGAATCCCGGCTCTGCCA 72 chr5ptel1M 564674 CTTACTAAATGTGTGATTCTGGGCAAATCACTTAACC-CTGTTTGCCTTA 564722 iv iii i i - v v i MIR#SINE/MIR 73 CTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCA 122 chr5ptel1M 564723 GTTTCCTCTCCTGTAAAATTATCTGGAGAAGGAAATGGTGAACTACTTCA 564772 vi ----- i viiv i - v i MIR#SINE/MIR 123 GTTTCCTCATCTGTAAAA-----TGGGGATAATAATAGT-ACCTACCTCA 166 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 25.50 CpG sites = 19, Kimura (unadjusted) = 26.51 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.09 (13 / 147), avg. gap size = 1.00 (13 / 13) 256 31.17 1.28 1.28 chr5ptel1M 564877 564954 (435046) C L3#LINE/CR1 (247) 3852 3775 m_b232s601i8 9122 chr5ptel1M 564877 TTAGTTCTCAGTTTGGTTCTCTAGAGGAAAATGGAGTAAATATAATATTT 564926 i i - iv ii i vv v ii i i v vii C L3#LINE/CR1 3852 TTGGTCCT-AGTTCTGCCCTCTGGAGCCACACAGAATAAGTCTAATCCCT 3804 chr5ptel1M 564927 -TCCCATATGAAGGCCTTTCAAATATCTG 564954 - i i vi i i C L3#LINE/CR1 3803 CTTCCACATGACAGCCCTTCAAATATTTG 3775 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.03 CpG sites = 17, Kimura (unadjusted) = 43.03 Transitions / transversions = 2.43 (17/7) Gap_init rate = 0.03 (2 / 77), avg. gap size = 1.00 (2 / 2) 561 30.55 5.44 4.13 chr5ptel1M 565159 565397 (434603) C MIRc#SINE/MIR (3) 265 24 m_b232s601i9 9124 chr5ptel1M 565159 AATCATAATTATTCACATTTATGTTGTACTTGAGAGTT-GCAAAGTGCCT 565207 v i?vi i i i v i v v -i i i C MIRc#SINE/MIR 265 AATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCGCTT 216 chr5ptel1M 565208 TTTAAGGCACTAATGAGTGTTTTCTCATTTAATTCTCTCTACAATCC--- 565254 ------ -- i--ii v i i v v i --- C MIRc#SINE/MIR 215 T------CAC--ATA--CATTATCTCATTTGATCCTCACAACAACCCTGT 176 chr5ptel1M 565255 --AGTAGGTAGCGAGAATATGATT--TCTCATAT-AGAGTTTAGGAAAT- 565298 --i i v viii v --i i v - v v v i- C MIRc#SINE/MIR 175 GAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACT 126 chr5ptel1M 565299 -ACACTCCTAGAGGTTAATTGACTT-CCGTGGGGGATGCAATTAGTAAAT 565346 - vi vv v - vvi vv ii ii i C MIRc#SINE/MIR 125 GAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGT 76 chr5ptel1M 565347 AATAAAGCTAGGACTGAAGTCCAGATCTT-CTGGCTTCATGTTTAGTACT 565395 iii i ii vi ii i - i i v ii i C MIRc#SINE/MIR 75 GGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCT 26 chr5ptel1M 565396 CT 565397 C MIRc#SINE/MIR 25 CT 24 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.87 CpG sites = 45, Kimura (unadjusted) = 41.29 Transitions / transversions = 1.80 (45/25) Gap_init rate = 0.08 (18 / 238), avg. gap size = 1.28 (23 / 18) 283 31.80 11.49 2.34 chr5ptel1M 566456 566690 (433310) L2#LINE/L2 2238 2493 (589) m_b232s601i10 9125 chr5ptel1M 566456 GGCTTAGTC-TTGGATCCTTTTCTATTTTCTTTCTACTTTTTCTTCTCAA 566504 i - - i v i v vi iv i ii?i L2#LINE/L2 2238 GGCTCAGTCCTTGGA-CCTCTTCTCTTCTCTATCTACACTCACTCCCTNG 2286 chr5ptel1M 566505 TTGGT---ATCC---CTT-TGGATATAA---TCATCTAACTTCTATGCAA 566544 v i --- --- i- v v ---i ----- vi L2#LINE/L2 2287 GTGATCTCATCCAGTCTCATGGCTTTAAATACCATCTA-----TATGCTG 2331 chr5ptel1M 566545 ATGACTTCAA------TATCTCT-GTACTAAACTCTAATTCGT-CCCCAG 566586 i v ------ i- iv vi v vviii v- i L2#LINE/L2 2332 ATGACTCCCAAATTTATATCTCCAGCCCGGACCTCTCCCCTGAACTCCAG 2381 chr5ptel1M 566587 ATTTATACTTGCACCTCTCCATTTG---CCTCTAAT-GGAAGTATCATGA 566632 i ii iv v v vi i i i ---i i v - v v v ii L2#LINE/L2 2382 ACTCGTATATCCAACTGCCTACTCGACATCTCCACTTGGATGTCTAATAG 2431 chr5ptel1M 566633 G-GTCTCTAATCTAATATGTCCAAAATTAAGTTT---ATAGTCACCCTCA 566678 -i v ii i i i ii i--- vv v L2#LINE/L2 2432 GCATCTCAAACTTAACATGTCCAAAACTGAACTCCTGATCTTCCCCCTCA 2481 chr5ptel1M 566679 ACCTTAATCCTC 566690 v i iv L2#LINE/L2 2482 AACCTGCTCCTC 2493 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.65 CpG sites = 44, Kimura (unadjusted) = 43.33 Transitions / transversions = 1.52 (44/29) Gap_init rate = 0.08 (18 / 234), avg. gap size = 1.83 (33 / 18) 327 34.78 9.32 0.00 chr5ptel1M 566880 567040 (432960) L2#LINE/L2 2658 2833 (249) m_b232s601i11 9125 chr5ptel1M 566880 CTTTTCTTTACTTTCATAGCTGTCACCCTG-----AGT-------AGCTC 566917 i vii i i iv iii ----- i------- v L2#LINE/L2 2658 CTTCTCACCACCTCCACTGCCACCACCCTGGTCCAAGCCACCATCATCTC 2707 chr5ptel1M 566918 TTGCTTGGATTATTGCAATAGTGTTTTAGTTGGTCATCTTGCTTCAAGCC 566967 i i i iv ii ii vi i v v L2#LINE/L2 2708 TCGCCTGGATTACTGCAATAGCCTCCTAACTGGTCTCCCTGCTTCCACCC 2757 chr5ptel1M 566968 T--CTCTTTTTCAGGCCATCTTCTTC-CATCTGCCAAAGTTGTTTACCAA 567014 -- i iii ? v i ii vv - v v i vi iiviiv L2#LINE/L2 2758 TTGCCCCCCTNCAGTCTATTCTCAACACAGCAGCCAGAGTGATCCTTTTA 2807 chr5ptel1M 567015 AGATGTAGGTCTGCCCGTGTCACTTC 567040 i i i v vi i i L2#LINE/L2 2808 AAACGTAAGTCAGATCATGTCACTCC 2833 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 48.32 CpG sites = 39, Kimura (unadjusted) = 51.01 Transitions / transversions = 2.29 (39/17) Gap_init rate = 0.03 (4 / 160), avg. gap size = 3.75 (15 / 4) 1142 30.10 3.45 3.45 chr5ptel1M 567510 568407 (431593) L1M5_orf2#LINE/L1 2397 3294 (0) m_b232s551i8 9126 chr5ptel1M 567510 GAAAAATATTAAATGCTCTTGGATAGGGTGAGCAAATATAATAAAGATGA 567559 i i vvv i v v iv viv vi ? v L1M5_orf2#LIN 2397 GAGAGATATACCATGTTCATGGATTGGAAGACTCAATATTGTNAAGATGT 2446 chr5ptel1M 567560 CAATATTACTTAAACTAATCTATTTATTTAGTGCTATCCCAATCAGACTC 567609 vi v ii i i vv i i v i v L1M5_orf2#LIN 2447 CAATTCTCCCCAAATTGATCTATAGATTCAATGCAATCCCAATCAAAATC 2496 chr5ptel1M 567610 CCAAAAAACTATTTTAATGACTTAGAAAAAATAACAACAAAATTCATATG 567659 iv iii v ivv vv v v iv i ivvi i L1M5_orf2#LIN 2497 CCAGCAGGTTTTTTTGTAGAAATTGACAAGCTGATTCTAAAATTTATATG 2546 chr5ptel1M 567660 GAAAAATAAAAGGTCAAGAAT-TTCAAGGGAATTAATGAAAAA-AAAATC 567707 vii i ii ? -vi iiv i-v - i v L1M5_orf2#LIN 2547 GAAATGCAAAGGACCNAGAATAGCCAAAACAATC-TTGAAAAAGAAGAAC 2595 chr5ptel1M 567708 AAAG--GAAGGTGGCTTAGCTGTACCAGATCT-AAAATTATATTATAGAG 567754 -- i -- i - vv ? ? - i i - i L1M5_orf2#LIN 2596 AAAGTTGGAG--GACTTA-CACTACCNGATNTCAAGACT-TATTATAAAG 2641 chr5ptel1M 567755 CAGCAGTTACCAAAACCATTTGGTATTGGC-TAAGGAATAGATTAGTTGA 567803 vi v i i vi v - - iv i v L1M5_orf2#LIN 2642 CTACAGTAATCAAGACAGTGTGGTATTGGCGTAAGG-ATAGACAAATAGA 2690 chr5ptel1M 567804 TCAGTGGAATAGGTTAG---GTTCAAGGGACAAAACAATCAACAACTATA 567850 i i iv --- i - ii i i v v i-- vv i L1M5_orf2#LIN 2691 TCAATGGAACAGAATAGAGAGTCC-AGAAATAGACCCAC--ACATATATG 2737 chr5ptel1M 567851 ACAACCTAGTCTTTGACAAA---CCCAAAG-ACCCCAGCTTTTGGGATAA 567896 i?v ?i ii i ---v ? - vii ---- iv L1M5_orf2#LIN 2738 GNCANTTGATTTTTGACAAAGGTGCCAANGCAATTCAG----TGGGGAAA 2783 chr5ptel1M 567897 GAACTTACTATTTGATAAAAATTGCTGGGAAAATTGGAAACTAATATGGC 567946 i ivvv v ii i viv i v v iiv v L1M5_orf2#LIN 2784 GGATAGTCTTTTCAACAAATGGTGCTGGAACAATTGGATATCCATATGGA 2833 chr5ptel1M 567947 AGAAACTAGGCATTGATCCACACTTAACACTGTACACCAAGATAAGGTCA 567996 i v iii?v i i vi i v ii v i v iv ? L1M5_orf2#LIN 2834 AAAAAATGAANCTCGACCCCTACCTCACACCATACACAAAAATTAATTCN 2883 chr5ptel1M 567997 AAATGGGTTCAT-GACCTAGGCATAAAGAATGAAATTATTAATAAATTAG 568045 i i- - iiii ii? i i v vvvvi L1M5_orf2#LIN 2884 AGATGGA-TCATAGACCTAAATGTAAAAGNTAAAACTATAAAACTTCTAG 2932 chr5ptel1M 568046 AGG--AACACAGGATAGTTTACCTCTCAGACCTGTGGGA-GGGGAAGGAC 568092 i -- i v i-- i iivv - ?-i v i i L1M5_orf2#LIN 2933 AAGAAAACATAGGAGAA--TATCTTCGTGACCT-TGGGNTAGGCAAAGAT 2979 chr5ptel1M 568093 TTTATGACCAAAGAAGAACTAGAGATCATTACTGATCACAAAATAGAAAA 568142 iv ---- v i vvi i i v i? --- i i v i L1M5_orf2#LIN 2980 TTCTT----AAACAGGACACAAAAAGCACNA---ACCATAAAAGAAAAAA 3022 chr5ptel1M 568143 T-------TTCGACTATAGCAAACTGAAAAGTTTTTGTACAAACAAAACT 568185 ------- v ?i v v v ii i iv -?v -- L1M5_orf2#LIN 3023 TTGATAAATTGGACTNCATCAAAATTAAAAACTTCTGCTC-NTCAAAA-- 3069 chr5ptel1M 568186 AATGCAGATAAG---ATTAGAAGGGAAGCAATAAACTGGGAAAATATTTT 568232 i ii v v --- v i v v i i ? i v v L1M5_orf2#LIN 3070 GACACCGTTAAGAAAATGAAAAGGCAAGCCACAGANTGGGAGAAAATATT 3119 chr5ptel1M 568233 TACAGT-CAAAGATTCTGATAAAGGCCTCATTTCCAAAATATATAGAGAA 568281 i i?- v v - i v i v i i L1M5_orf2#LIN 3120 TGCAANACATATA-TCTGACAAAGGACTCGTATCCAGAATATATAAAGAA 3168 chr5ptel1M 568282 TTAACTCTAATTT-ATAAAAAATCAAGCCAGTC--TCCAATTGAAAAATG 568328 i -v vi ? i- ? -- v iv --i v? L1M5_orf2#LIN 3169 CT-CCTACAANTCAATAANAAA--AAGACAAACAACCCAATANAAAAATG 3215 chr5ptel1M 568329 GTCAAAGGATATGAACAGACAATTCTCAGATGAAGAAATTGAAACTATTT 568378 v i iv v v i v v ?v iviiiv L1M5_orf2#LIN 3216 GGCAAAAGACTTGAACAGACACTTCACAAAAGAAGATATNCAAATGGCCA 3265 chr5ptel1M 568379 CTAGTCATATGAAAAGATGCTCCAAGTCA 568407 v iv i v v? L1M5_orf2#LIN 3266 ATAAGCACATGAAAAGATGCTCAACNTCA 3294 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.09 CpG sites = 145, Kimura (unadjusted) = 40.70 Transitions / transversions = 1.25 (145/116) Gap_init rate = 0.05 (47 / 897), avg. gap size = 1.32 (62 / 47) 1595 26.95 3.44 3.61 chr5ptel1M 568264 568902 (431098) L1ME5_3end#LINE/L1 7 644 (297) m_b232s551i10 9126 chr5ptel1M 568264 TCCAAAATATATAGAGAATTAACTCTAATTTATAAAAAATCAAGCCAGT- 568312 i i i ii i vviv v iv i i -- v i ?- L1ME5_3end#LI 7 TCTAGAATATACAAGGAACTCCTGCAAATCAACAAGAAA--AAGACGGNA 54 chr5ptel1M 568313 -CTCCAATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGA 568361 - i v v i iv v L1ME5_3end#LI 55 ACCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGA 104 chr5ptel1M 568362 AGAAA-TTGAAA--CTATTTCTAGTCATATGAAAAGATGCTCCAAGTCAT 568408 i -ii -- --v v - i v v L1ME5_3end#LI 105 GGAAACCCGAAAGGCTA--ACAAG-CATATGAAGAGATGCTCAAACTCAT 151 chr5ptel1M 568409 TATTAATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACA 568458 v i vv i i vi L1ME5_3end#LI 152 TAGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACA 201 chr5ptel1M 568459 CCTGTCAGATTGGCTAAGATGACAGGAAA---AAATAAGGATGATTGTTG 568505 i i i v i v --- ---ii v vii v L1ME5_3end#LI 202 CCTATTAGACTGGCAAAAATTA---GAAAGCTGGATAATGCCAAGTGTTG 248 chr5ptel1M 568506 GAG-GGATGTGGGAAAACTGGGACATTGATGCATTGTTGGTGGAGTTGTG 568554 v - i ? iv i vi v i i iiv i L1ME5_3end#LI 249 GCGAGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTA 298 chr5ptel1M 568555 AACAGATCCAACCATTCTGGAGAGTAGTTTGGAACTA--TGCTCAAA--A 568600 i v i v i i i i v v -- iv -- L1ME5_3end#LI 299 GACTGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTA 348 chr5ptel1M 568601 AGTTATCAAACTGTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGCT 568650 - --- --- v i i viii v iv L1ME5_3end#LI 349 AG-TAT---AC---GCATACCCTATGACCCAGCAATTCCGCTCCTGGGTA 391 chr5ptel1M 568651 TATACCCCAAAGAGATACTAAAGAAGG----GAAAGGGACCTGTATGTGC 568696 i i v v viv ----v i v i --- L1ME5_3end#LI 392 TATATCCCAAAGAAATTCTCACACAGGTCCATAAGGGGACATGTACG--- 438 chr5ptel1M 568697 CAAAATGTTTGTGGCAGCCCTCTTTGTAGTGGCCAGAAAGTGGAAACTGA 568746 - ii ii v vi v i vi i iv ii viv L1ME5_3end#LI 439 -AGGATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAAC 487 chr5ptel1M 568747 GTGGATGCCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATATGAAT 568796 v i i v v i v iii v iv v i L1ME5_3end#LI 488 CTGGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCAC 537 chr5ptel1M 568797 ATTATGGAATATTATTGTTCTGTAAGAAATGACCAACAGGATGATTTCAG 568846 ii i i vvvv v v iii vi vi -- v v L1ME5_3end#LI 538 ACCATGGAGTACTATGCAGCAGTTAGAAGCAACGGACTAGATG--TACAC 585 chr5ptel1M 568847 AAAG--GCCTGGAGAGA-CTTATACTAAC-TGATGCTGAGTGAAATGAGC 568892 v --i v vi - v -- - ii vi i L1ME5_3end#LI 586 ATAGCAACATGGATGGATCTTAAA--AACATAGTGCTGAGTGAAAAAAGT 633 chr5ptel1M 568893 -AGGACCAGAA 568902 - i v L1ME5_3end#LI 634 AAGAAACAGAA 644 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.15 CpG sites = 93, Kimura (unadjusted) = 34.18 Transitions / transversions = 1.27 (93/73) Gap_init rate = 0.06 (36 / 638), avg. gap size = 1.25 (45 / 36) 1618 27.47 0.55 1.66 chr5ptel1M 568264 568811 (431189) L1ME3G_3end#LINE/L1 7 548 (376) m_b232s551i9 9126 chr5ptel1M 568264 TCCAAAATATATAGAGAATTAACTCTAATTTATAAAAAATCAAGCCAGTC 568313 i i i vviv v iv i -- v ii L1ME3G_3end#L 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAA--AAGACAACC 54 chr5ptel1M 568314 TCCAATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGAAG 568363 -- v v i v v i L1ME3G_3end#L 55 --CAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chr5ptel1M 568364 AAATTGAAACTATTTCTAGTCATATGAAAAGATGCTCCAAGTCATTATTA 568413 vv iviiivv iv v vv i v L1ME3G_3end#L 103 AAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTA 152 chr5ptel1M 568414 ATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACACCTGT 568463 i i vv i i viv ii L1ME3G_3end#L 153 ATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCAT 202 chr5ptel1M 568464 CAGATTGGCTAAGATGACAGGAAAAAATAAGGATGATTGTTGGAG-GGAT 568512 v i vvv iii?vvi vivi? v v - i L1ME3G_3end#L 203 CAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGT 252 chr5ptel1M 568513 GTGGGAAAACTGGGACATTGATGCATTGTTGGTGGAGTTGTGAACAGATC 568562 i v v vi v i i i iiv i iv i v L1ME3G_3end#L 253 GTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTA 302 chr5ptel1M 568563 CAACCATTCTGGAGAGTAGTTTGGAACTATGCTCAAAAAGTTATCAAACT 568612 i ? i i i i v v viviv v --- v L1ME3G_3end#L 303 CAGCCNTTTTGGAGGGCAATTTGGCAGTATCTATTAAAATTTA---AAAT 349 chr5ptel1M 568613 GTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGCTTATACCCCAAAG 568662 i i i vii v ? ?v v i i ? L1ME3G_3end#L 350 GCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAG 399 chr5ptel1M 568663 AGATACT-AAAGAAG-GGAAAGGGACCTGTATGTGCCAAAATGTTTGTGG 568710 i -iv v v - v v i --? i i v ii ii v L1ME3G_3end#L 400 AAATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTCATTG 447 chr5ptel1M 568711 CAGCCCTCTTTGTAGTGGCCAGAAAGTGGAAACTGAGTGGATGCCCATCA 568760 vi v i i v i v vivv ii i L1ME3G_3end#L 448 CAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCA 497 chr5ptel1M 568761 GTTGGAGAATGGCTGAATAAATTGTGGTATATGAATATTATGGAATATTA 568810 i v i i i i vv i i L1ME3G_3end#L 498 ATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACTA 547 chr5ptel1M 568811 T 568811 L1ME3G_3end#L 548 T 548 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.74 CpG sites = 79, Kimura (unadjusted) = 35.32 Transitions / transversions = 1.14 (79/69) Gap_init rate = 0.02 (12 / 547), avg. gap size = 1.00 (12 / 12) 16 16.80 0.00 0.00 chr5ptel1M 569355 569381 (430619) (A)n#Simple_repeat 1 27 (0) m_b232s252i4 9127 chr5ptel1M 569355 AAATAAAAAAATAATAATAAAAAAAAA 569381 v v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAA 27 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 1819 30.66 3.88 0.58 chr5ptel1M 569471 570474 (429526) C L1M2_orf2#LINE/L1 (865) 2426 1390 m_b232s551i11 9128 chr5ptel1M 569471 ATTCCTCTA-TCCAACAACACTTAATATTTTTCCAGTTGGTTAGATCTGA 569519 i i - vv i ivvi i v ?v ivi ivv C L1M2_orf2#LIN 2426 ATTCTTCCAATCCATGAGCATGGGATATCTTTCCATTTNTTTGTGTCCTC 2377 chr5ptel1M 569520 CTTTATTTGTGTGGAAAGCATTTTATAGTTTT-TTTATATGAGTCCTGAC 569568 i iv v v vivv ii -? i - vi vv C L1M2_orf2#LIN 2376 TTCAATTTCTTTCATCAGTGTTTTATAGTTTTCNTTGTA-GAGATCTTTC 2328 chr5ptel1M 569569 TTTCCCTTGGC-AGATAGATTCCCAAATATTTTATACCAGTGGCAGTTAC 569617 viii i- i vv i ii viivv v i i i C L1M2_orf2#LIN 2327 ACCTCCTTGGTTAAATTTATTCCTAGGTATTTTATTTTTTTTGTAGCTAT 2278 chr5ptel1M 569618 TTTATATGGAATTTCTCTTTGTATCTCTAACTGTTGGGT--TTTGTCAGT 569665 v v i v i i vv i --i v ii i -- i iiv C L1M2_orf2#LIN 2277 TGTAAATGGGATTGCTTTCTTGATTTCT--TTTTCAGATAGTTCGTTGTT 2230 chr5ptel1M 569666 GATATATAAGAATGCTGAGCATTTATTTTGGTTTATTTTGTATCCTGTAA 569715 iii ii ivvv v v vv v i C L1M2_orf2#LIN 2229 GGCGTATAGAAATGCTACTGATTTTTGTATGTTGATTTTGTATCCTGCAA 2180 chr5ptel1M 569716 CTTTGCTAAAGTTGTGAATTATTTCTAATAGCTTTTTAGTTGAATTTCTG 569765 i i v i vv i v ? i i v i i i i C L1M2_orf2#LIN 2179 CTTTACTGAATTCGTTTATCAGTTCTAANAGTTTTTTGGTGGAGTCTTTA 2130 chr5ptel1M 569766 GCATTCTCTAAGTATACCATCCTATCATCTGCAGAGAGCCATAATTTGAT 569815 v? i ?i vv v i i v vv i i C L1M2_orf2#LIN 2129 GGNTTTTCTANATATAAGATCATGTCATCTGCAAACAGGGACAATTTGAC 2080 chr5ptel1M 569816 TTCCTCATTACCTACTCTAATTCCTTTCATTTCTTTCTCAGTTCTTATTG 569865 v v v i ivi v i vvvi v C L1M2_orf2#LIN 2079 TTCCTCCTTTCCAATTTGGATGCCTTTTATTTCTTTCTCTTGCCTAATTG 2030 chr5ptel1M 569866 CCAAAGCTAGCATTTGTAACACGATATTGAATCGTAATGGTGACAGCAGG 569915 ivvi v i vi ii v i v v i v ii C L1M2_orf2#LIN 2029 CTCTGGCTAGGACTTCCAGTACTATGTTGAATAGAAGTGGTGAAAGTGGG 1980 chr5ptel1M 569916 CAACCTTGTTTCACTCCTGAGCTTATCGGGAA----TCTAATTTATCCCC 569961 v i iii v ?v vv i ---- ii i v C L1M2_orf2#LIN 1979 CATCCTTGTCTTGTTCCAGNTCTTAGAGGAAAGGCTTTCAACTTTTCCCC 1930 chr5ptel1M 569962 ATTACATATGATGCTTACTGATGGTGTTAAATAGATGCTACTGACTATTT 570011 vvi i vi vv v vvv v vivi v i i v C L1M2_orf2#LIN 1929 ATTCAGTATGATGTTAGCTGTGGGTTTGTCATATATGGCCTTTATTGTGT 1880 chr5ptel1M 570012 TAAGGAAAAGTCCATTTATTCCTATATTCTTAACTGTTTTTAATAGGAAT 570061 i v viv v i v vv v i vv vi v v C L1M2_orf2#LIN 1879 TGAGGTACGTTCCTTCTATACCTAATTTGTTGAGAGTTTTTATCATGAAG 1830 chr5ptel1M 570062 GGATGTTGAATTTTATCAAATACTTTTTCTTCATATATTGAGATGATCAT 570111 i v v C L1M2_orf2#LIN 1829 GGATGTTGAATTTTATCAAATGCTTTTTCTGCATCTATTGAGATGATCAT 1780 chr5ptel1M 570112 ATAGTTTT--TTGTTAATTTGGTTATTGATATAGTCAATTATGCTAATAG 570159 i -- iv v ---i i i ii vv i i i v v C L1M2_orf2#LIN 1779 ATGGTTTTTGTCCTTCATT---CTGTTGATGTGATGTATCACGTTTATTG 1733 chr5ptel1M 570160 -TTTTCA-ATATTAAAACAGCCCT-CATTCCTGGTATAAATCCC-CTCGG 570205 - v i- i i v v i - i v - i i C L1M2_orf2#LIN 1732 ATTTGCGTATGTTGAACCATCCTTGCATCCCTGGGATAAATCCCACTTGA 1683 chr5ptel1M 570206 TT---GTGTGTTATC---GGAATG-ACTTTT---TTTAATC--CTAATAT 570243 i--- ?i ? ---vv -i v --- iii i-- i C L1M2_orf2#LIN 1682 TCATGGTGNATNATCTTTTTAATGTGCTGTTGAATTCGGTTTGCTAGTAT 1633 chr5ptel1M 570244 TTCATTCAAGATTTTAGCATCAATATTCATTA-GGAGATTGGTTTATAGT 570292 ii v i v v i i - v ii i C L1M2_orf2#LIN 1632 TTTGTTGAGGATTTTTGCATCTATGTTCATCAGGGATATTGGCCTGTAGT 1583 chr5ptel1M 570293 TTTTCTTTCTCCTCTTCCACCTACCTGGTTTTATTATGACTACAATGTTT 570342 ii i iv iv viv i ii iv v vvii i v C L1M2_orf2#LIN 1582 TTTCTTTTTTTGTTGTGTCCTTGTCTGGTTTTGGTATCAGGGTAATGCTG 1533 chr5ptel1M 570343 GTGTCATAAAAGGGATTTGTGGG---TCCTTCATTCCCTATTTTTC-AAA 570388 iv i i v ii vii --- i v iii v i-i C L1M2_orf2#LIN 1532 GCCTCGTAGAATGAGTTTGGAAGNATTCCCTCCTCTTCAATTTTTTGGAA 1483 chr5ptel1M 570389 TAGTTTTATAAC-ATTGAT-TTA-TTCTTCTTTAAATGTTT-TTAGAATT 570434 v v v- i - - -v C L1M2_orf2#LIN 1482 TAGTTTGAGAAGAATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAATT 1433 chr5ptel1M 570435 CACC-TTAAATCCATCTGATCTTGGGGTTTTCTTAG--GGGAG 570474 v -v i v ? i i v v -- C L1M2_orf2#LIN 1432 CAGCAGTGAAGCCATCNGGTCCTGGGCTTTTCTTTGNTGGGAG 1390 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.25 CpG sites = 162, Kimura (unadjusted) = 40.65 Transitions / transversions = 1.12 (162/144) Gap_init rate = 0.03 (30 / 1003), avg. gap size = 1.50 (45 / 30) 1809 28.41 8.30 2.21 chr5ptel1M 569494 570987 (429013) C L1M5_orf2#LINE/L1 (889) 2405 823 m_b232s551i12 9128 chr5ptel1M 569494 ATATTTTTCCAGTTGGTTAGATCTGACTTTATTTGTGTGGAAAGCATTTT 569543 i i v iv i vvi v v v viiv iii C L1M5_orf2#LIN 2405 ATATCTCTCCATTTATTTAGGTCTTCTTTAATTTCTCTCAGCAATGTTTT 2356 chr5ptel1M 569544 ATAGTTTTT-TTATATGAGTCCTGACTTTCCCTTGGCAGATAGATTCCCA 569592 i i-v i ?ii i vviv ?ii vi vv i C L1M5_orf2#LIN 2355 GTAGTTTTCAGTGTANAGGTCTTGCACATNTTTTGTTAGATTTATTCCTA 2306 chr5ptel1M 569593 AATATTTTATACCAGTGGCAGTTACTTTATATGGAATTTCTCTTTGTATC 569642 i ? iiivv v vv i i v v v vi i ?iv i C L1M5_orf2#LIN 2305 AGTATTTNATGTTTTTTGATGCTATTGTAAATGGTATTGTTTTTNAAATT 2256 chr5ptel1M 569643 TC------TAACTGTTGGGTTTTGTCAGTGATATATAAGAATGCTGAGCA 569686 ------i i v --- ii --- ii i ----v C L1M5_orf2#LIN 2255 TCATTTTCCAATTGTTTG---TTGCTAGT---ATATAGAAATAC----AA 2216 chr5ptel1M 569687 TTTATTTTGGTTTATT----TTGTATCCTGTAACTTTGCTAAAGTTGTGA 569732 v v v ---- ? ii i v iiivv C L1M5_orf2#LIN 2215 TTGATTTTTGTATATTGACCTTGTATCCNGCGACCTTGCTAAATTCACTT 2166 chr5ptel1M 569733 ATTATTTCTAATAGCTTTTTAGTTGAATTTCTGGCATTCTCTAAGTATAC 569782 v i i ? v v v i i ? v i v ? C L1M5_orf2#LIN 2165 ATTAGTTCTAGTAGTTTNTTTGTAGATTCTTTNGGATTTTCTACGTANAC 2116 chr5ptel1M 569783 CATCCTATCATCTGCAGAGAGCCATAATTTGATTTCCTCATTACCTACTC 569832 v v i ii v i?v i i v i v v v iii C L1M5_orf2#LIN 2115 AATCATGTCATCTGCGAATAANGACAGTTTTATTTCTTCCTTTCCAATCT 2066 chr5ptel1M 569833 TAATTCCTTTCATTTCTTTCTCAGTTCTTATTGCCAAAGCTAGCATTTGT 569882 v v i i vvvi vvvi v ii vi C L1M5_orf2#LIN 2065 TTATGCCTTTTATTTCTTTTTCTTGCCTTATTGCACTGGCTAGGACCTCC 2016 chr5ptel1M 569883 AACACGATATTGAATCGTAATGGTGACAGCAGGCAACCTTGTTTCACTCC 569932 ii i i v v i ? i i v i iii C L1M5_orf2#LIN 2015 AGTACAATGTTGAATAGAAGTGGTGANAGCGGACATCCTTGTCTTGTTCC 1966 chr5ptel1M 569933 TGAGCTTATCGGGAA----TCTAATTTATCCCCATTACATATGATGCTTA 569978 i v vv ---- ii i ? v v vi i ?i C L1M5_orf2#LIN 1965 CGATCTTAGGGGGAAAGCNTTCAGTNTTTCACCATTAAGTATGATGTTNG 1916 chr5ptel1M 569979 CTGATGGTGTTAAATAGATGCTACTGACTATTTTAAGGAAAAGTCCATTT 570028 vv v vvi ivi v ii vv i ivvi v i C L1M5_orf2#LIN 1915 CTGTAGGTTTTTCGTAGATGCCCTTTATCAGGTTGAGGAAGTTCCCTTCT 1866 chr5ptel1M 570029 ATTCCTATATTCTTAACTGTTTTTAATAGGAATGGATGTTGAATTTTATC 570078 vv vi i vv vi v i i C L1M5_orf2#LIN 1865 ATTCCTAGTTTGCTGAGAGTTTTTATCATGAATGGGTGTTGAATTTTGTC 1816 chr5ptel1M 570079 AAATACTTTTTCTTCATATATTGAGATGATCATATAGTTTT--TTGTTAA 570126 i v v ii -- iv v C L1M5_orf2#LIN 1815 AAATGCTTTTTCTGCATCTATTGAGATGATCATATGATTTTTCTCCTTTA 1766 chr5ptel1M 570127 TTTGGTTATTGATATAGTCAATTATGCTAATAG-TTTTC-AATATTAAAA 570174 iv --- i v iii i v - - i v C L1M5_orf2#LIN 1765 TTCTGTTA---ATATGGTGAATTACATTGATTGATTTTCGAATGTTAAAC 1719 chr5ptel1M 570175 CAGCCCT-CATTCCTGGTATAAATCCC-CTCGGT--TG-TGTGTTATCGG 570219 i i - v i - i -- - i -- C L1M5_orf2#LIN 1718 CAACCTTGCATTCCTGGGATAAACCCCACTTGGTCATGATGTATTATC-- 1671 chr5ptel1M 570220 AATGACTTTT--------------TTTAATC--CTAATATTTCATTCAAG 570253 ----- -------------- ii i-- ii ? i C L1M5_orf2#LIN 1670 -----CTTTTTATATATTGCTGGATTCGATTTGCTAATATTTTGTTNAGG 1626 chr5ptel1M 570254 ATTTTAGCATCAATATTCATTA-GGAGATTGGTTTATAGTTTTTCTTTCT 570302 v v i v - v i i i ii C L1M5_orf2#LIN 1625 ATTTTTGCATCTATGTTCATGAGGGATATTGGTCTGTAATTTTCTTTTCT 1576 chr5ptel1M 570303 CCTCTTCCACCTACCTGGTTTTATTATGACTACAATGTTTGTGTCATAAA 570352 iv vv vivii ii ? iv v vvii? i v iv C L1M5_orf2#LIN 1575 TGTAATGTCTTTGTCNGGTTTTGGTATCAGGGTNATGCTGGCCTCATAAA 1526 chr5ptel1M 570353 AGGGATTTGTGGG---TCCTTCATTCCCTATTTT-TCAAATAGTTT-TAT 570397 v ii v vii --- i v ii - vi v - i C L1M5_orf2#LIN 1525 ATGAGTTGGGAAGTGTTCCCTCTTTTTCTATTTTCTGGAAGAGTTTGTGT 1476 chr5ptel1M 570398 AACATTGAT-TTA-TTCTTCTTTAAATGTTT-TTAGAATTCACC-TTAAA 570443 v i - - i -v -v i C L1M5_orf2#LIN 1475 AAGATTGGTATTATTTCTTCCTTAAATGTTTGGTAGAATTCACCAGTGAA 1426 chr5ptel1M 570444 TCCATCTGATCTTGGGGTTTTCTT--AGGGGAGTTGATTAATAGCTTGTT 570491 v iv i i --v i v vv vi vvi C L1M5_orf2#LIN 1425 GCCATCTGGGCCTGGAGTTTTCTTTGTGGGAAGGTTTTTAATTACAAATT 1376 chr5ptel1M 570492 CTATTTCTTTTCCTGAAAT-GGGCTATTT-GA----CAACTTACTTCTTT 570535 v vviv v - i- ---- v i - v C L1M5_orf2#LIN 1375 CAATTTCTTTAATAGATATAGGGCTATTCAGATTTTCTATTT-CTTCTTG 1327 chr5ptel1M 570536 AATC------GGAAGCCTAT-CTTTTGGAGGTA-TCATCTATTTC--CTT 570575 ?i ------ v i?i i -i vi v - ii i -- v C L1M5_orf2#LIN 1326 NGTCAGTTTTGGTAANTTGTGTTTTTCAAGGAATTTGTCCATTTCATCTA 1277 chr5ptel1M 570576 GGTTGT-AAATTGATTGGCATAAAAGTTGGGCAAAAGTAACTCCAAATTA 570624 i ? - v - vv v - viii vv C L1M5_orf2#LIN 1276 AGTTNTCAAATTTATTGGCAT-AAAGTTGTTCATAA-TATTCTCTTATTA 1229 chr5ptel1M 570625 TTACTCTAATTTCCTCTTCATTGGTGGAAAGTTCTCCTTTTTCATTTTTC 570674 ivi i v ivivvv iv i vi vv ii - C L1M5_orf2#LIN 1228 TCCTTTTAATGTCTGTAGGATCTGTAGTGATGTCTCCTTTTTCATTCCT- 1180 chr5ptel1M 570675 AAGACTA--AATTT---TC----------------TAATCAATTTA---A 570700 i v i i-- --- ---------------- i i i ?--- C L1M5_orf2#LIN 1179 GATATTGGTAATTTGTGTCTTCTCTCTTTTTTTCTTGATCAGTCTNGCTA 1130 chr5ptel1M 570701 AAGGTTTATCTATTTT-TTGG--TTTTCATATTTCC--CTTTTTAGTTTA 570745 i v - i-- v vvv -- viv ii C L1M5_orf2#LIN 1129 GAGGTTTATCAATTTTATTGATCTTTTCAAAGAACCAGCTTTTGGCTTCG 1080 chr5ptel1M 570746 TTTATTAATTCAATAGGTTTTTTACTTTA-ATTTTATAAATTTCTCCTTT 570794 v vvi v v v? ? ii v- i vi v i C L1M5_orf2#LIN 1079 TTGATTTTCTCTATTGTNTNTTTGTTTTCTATTTCATTGATTTCTGCTCT 1030 chr5ptel1M 570795 TAATTTTA-AATTTCAAGTTTAAAGTATGTTATTGGCATT---TTCAACT 570840 vi -v ---i ----iv vi i v? v --- i i C L1M5_orf2#LIN 1029 TATCTTTATTATTTC---CTT----CCTTCTACTTNCTTTGGGTTTAATT 987 chr5ptel1M 570841 TGCTC----TTTTCTAGCTT-TTAAGTTTAAAAC-CAATTTATTGAAACT 570884 ---- - v vi i -i iv i --- C L1M5_orf2#LIN 986 TGCTCTTCTTTTTCTAGCTTCTTAAGGTGGAAGCTTAGATCATTGA---T 940 chr5ptel1M 570885 TTC---TCTTTCTTTTTTATTCAATA---ACCTCTAAAAATATAAAATCT 570928 i---i i - ii ---i v i ?iv v ii C L1M5_orf2#LIN 939 TTTAAGCCTTTCTTCTTT-TCTAATATANGCATTTAANGCTATAAATTTC 891 chr5ptel1M 570929 CCTCT-TTTACAGCTTTGGCTGTATCCCATAAA--TTGGTAT-TTG---T 570971 -vvi v i i i -- i - --- C L1M5_orf2#LIN 890 CCTCTAAGCACTGCTTTAGCTGCATCCCACAAATTTTGATATGTTGTATT 841 chr5ptel1M 570972 CTCATTTT--TTCAATTC 570987 i ? -- i C L1M5_orf2#LIN 840 TTCATTNTCATTCAGTTC 823 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.43 CpG sites = 227, Kimura (unadjusted) = 37.25 Transitions / transversions = 1.21 (227/188) Gap_init rate = 0.06 (85 / 1493), avg. gap size = 1.87 (159 / 85) 242 16.65 8.14 2.20 chr5ptel1M 570919 571004 (428996) C L1M2_orf2#LINE/L1 (2391) 900 810 m_b232s551i13 9128 chr5ptel1M 570919 TATAAAATCTCCTCTT-TTACAGCTTTGGCTGTATCCCATAAA--TTGGT 570965 v ii -v? v v ii-- C L1M2_orf2#LIN 900 TATAAACTTCCCTCTTAGNACTGCTTTTGCTGTATCCCATAGGTTTTGGT 851 chr5ptel1M 570966 AT-TTGTCT---CATTTTTTCAATTCTTTCGGGAAATTATTAA 571004 - v --- -- v v ii v ? C L1M2_orf2#LIN 850 ATGTTGTGTTTCCA--TTTTCATTTGTTTCAAGAAATTTTTNA 810 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 19.41 CpG sites = 6, Kimura (unadjusted) = 19.41 Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.07 (6 / 85), avg. gap size = 1.50 (9 / 6) 20 18.36 0.00 0.00 chr5ptel1M 571955 571991 (428009) (T)n#Simple_repeat 1 37 (0) m_b232s252i5 9129 chr5ptel1M 571955 TTTGTTTTGTTATTGTTTTTTTTTTTTTTTACTTTTT 571991 v v v v vi (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 37 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 46 0.00 0.00 0.00 chr5ptel1M 572150 572188 (427812) (TC)n#Simple_repeat 1 39 (0) c_b232s251i1 9130 chr5ptel1M 572150 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 572188 (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 39 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 13 11.20 3.23 3.23 chr5ptel1M 572330 572360 (427640) (AGCA)n#Simple_repeat 1 31 (0) m_b232s252i6 9131 chr5ptel1M 572330 AGAAAGCAAGCAAGCAAACAAG-AGGACAAGC 572360 v i - i - (AGCA)n#Simpl 1 AGCAAGCAAGCAAGCAAGCAAGCAAG-CAAGC 31 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2) 266 32.00 4.80 0.00 chr5ptel1M 573079 573203 (426797) C MIRc#SINE/MIR (131) 137 7 m_b232s601i12 9132 chr5ptel1M 573079 GATGAAGATACTGAGCCT-ATGGAGAATAAATGAATCACCCATAATCACA 573127 i v v - vi iv i v ii vii C MIRc#SINE/MIR 137 GATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACA 88 chr5ptel1M 573128 GAGATTATAAAATTCAGAG-TAGAAATGGAACCCA-GTCGTTCTCTCTCC 573175 v v vi ivvv -ii i v v - v i vv C MIRc#SINE/MIR 87 CAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCC 38 chr5ptel1M 573176 AGG--CAATCCTC-TCCCACCCTGCCACTCT 573203 i -- i v - i ivii v C MIRc#SINE/MIR 37 AAGTCCAGTGCTCTTTCCACTGCACCACACT 7 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.82 CpG sites = 20, Kimura (unadjusted) = 42.34 Transitions / transversions = 1.00 (20/20) Gap_init rate = 0.04 (5 / 124), avg. gap size = 1.20 (6 / 5) 186 19.51 0.00 0.00 chr5ptel1M 573429 573469 (426531) C MIRc#SINE/MIR (153) 115 75 m_b232s601i13 9133 chr5ptel1M 573429 GGGGTTAAGTGACTTGGTCAGGGTCACAGGGTTAGAAAGTG 573469 i vi i vi i v C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTG 75 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 23.02 CpG sites = 5, Kimura (unadjusted) = 23.02 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 255 17.24 1.69 1.69 chr5ptel1M 573483 573541 (426459) C tRNA-Thr-ACA#tRNA (10) 65 7 m_b232s502i2 9134 chr5ptel1M 573483 GCCAGATTTGAACTCAGTTTCCCCTGATTT-CAAGGCCAGTGCTCTATCT 573531 v - ivv i - i v i C tRNA-Thr-ACA# 65 GCGAGATTTGAACTC-GCGACCCCTGGTTTACAAGACCAGTGCTCTAACC 17 chr5ptel1M 573532 CCTGTTCTAT 573541 vv C tRNA-Thr-ACA# 16 CCTGAGCTAT 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 17.60 CpG sites = 4, Kimura (unadjusted) = 19.61 Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.03 (2 / 58), avg. gap size = 1.00 (2 / 2) 3014 29.14 2.84 2.52 chr5ptel1M 573881 575499 (424501) L1M5_orf2#LINE/L1 1671 3294 (0) m_b232s551i14 9135 chr5ptel1M 573881 GATAATACACTATGATCAAGTAGGATTTATACCAGGAATGCAGGGCTGGT 573930 ii i i i v i i L1M5_orf2#LIN 1671 GATAATACATCATGACCAAGTGGGGTTTATCCCAGGAATGCAAGGTTGGT 1720 chr5ptel1M 573931 TCAATATTAGGAAAACTATCAATATAATTGGCCATGTTAATA-ACCAAAT 573979 i i v i v v i vi i i - vi v L1M5_orf2#LIN 1721 TTAACATTCGAAAATCAATCAATGTAATTCACCATATTAACAGAATAAAG 1770 chr5ptel1M 573980 TAACAAAAACCATATGATCATCTCAATAGATGTAGAAAAAGCATTTGATA 574029 v i- i i i L1M5_orf2#LIN 1771 GAG-AAAAATCATATGATCATCTCAATAGATGCAGAAAAAGCATTTGACA 1819 chr5ptel1M 574030 AAATCCAACATCCATTCCTATTAAAAACACTTGAAAGTATAGGAATAAAT 574079 i i v iv v iiiv ivv i v L1M5_orf2#LIN 1820 AAATTCAACACCCATTCATGATAAAAACTCTCAGCAAACTAGGAATAGAA 1869 chr5ptel1M 574080 GGACTTTTCCTTAAAATAATCAGCAGCATCTATTTAAAACCATCAGTAAG 574129 ivvi i vv i v ivi ivv vv i? i L1M5_orf2#LIN 1870 GGGAACTTCCTCAACCTGATAAAGGGCATCTACGAAAAACCTACAGCNAA 1919 chr5ptel1M 574130 CATCATATGTAATGGAGACAAACTGCAACCATTCCCAATAAGATCTGGAG 574179 iv v v ? v ?v v vv v i L1M5_orf2#LIN 1920 CATCATACTTAATGGTGAAANACTGAANGCTTTCCCCCTAAGATCGGGAA 1969 chr5ptel1M 574180 TGAAACAGGGTTGCCCACTATCACGGTTACTATTTAATATTGTATTAGAA 574229 ii i i v i i ? vii v i i i i i L1M5_orf2#LIN 1970 CAAGACAAGGATGTCCGCTNTCACCACTTCTATTCAACATTGTACTGGAG 2019 chr5ptel1M 574230 ACACTAGCTATAGCAATAAGAGCTGAGAAAAAG--ATTAAAGGAATAAGA 574277 iiv i vv - -i -- v v ii L1M5_orf2#LIN 2020 GTCCTAGCCAGTGCAATAAG-GC-AAGAAAAAGAAATAAAAGGCATAAAG 2067 chr5ptel1M 574278 ATAGGCAATGAGGAAGCCAAATTATCACTCTTTGCCGATGACATGATGGT 574327 v v v i iiv i i ?i v i v v L1M5_orf2#LIN 2068 ATTGGAAAGGAAGAAATAAAACTGTCNTTATTCGCAGATGACATGATTGT 2117 chr5ptel1M 574328 ATACTTAGAGAACCCCAGAGATTCTGCTAA-AAGTTATTAGAAATAATCC 574376 ? v i i ? i v i v - ii i v vv L1M5_orf2#LIN 2118 NTACGTAGAAAATCCNAAAGAATCTACAAANAAACTACTAGAACTAATAA 2167 chr5ptel1M 574377 ACAACTTTAGCAAAGTTGCTGGTTATAAAATAAACCCACATAAGTCATCA 574426 iii v i i ? v i ii v ivi v i viv L1M5_orf2#LIN 2168 GTGAATTTAGCAAGGTCGCNGGATACAAGGTCAATATACAAAAATCAATT 2217 chr5ptel1M 574427 GCATGCTTATATATCACTAACAG--AATCCAACAGTCAGAGTTACAAAGA 574474 i vii ii vi i-- ivi v i v i v --? i L1M5_orf2#LIN 2218 GTATTTCTATATACTAGCAACAAACAATTGGAAAATGAAATTT--NAAAA 2265 chr5ptel1M 574475 GAAATTCCATTTAAAGTAACTACTGATAATATAAAATATTTAGGAATCTA 574524 iv v v i i vv vi v i ? i vv L1M5_orf2#LIN 2266 ACAATACCATTTACAATAGCATCAAAAAACATNAAATACTTAGGAATAAA 2315 chr5ptel1M 574525 TCTGCCAAGGGAAAAT---CAGAAACTTTATGAGCAAAATTACAGACCAC 574571 iv --- ? --- ii v ? iivvv i i v i L1M5_orf2#LIN 2316 TCTAACAA---AANATGTGCAAGACCTNTACACTGAAAACTACAAAACAT 2362 chr5ptel1M 574572 TTTTCACACAAATTAAATCTGATCTAACCAATTGGAAAAATATTAAATGC 574621 vi v v v vvv i vi v i i vvv i L1M5_orf2#LIN 2363 TGCTGAGAGAAATTAAAGAAGACCTAAATAAATGGAGAGATATACCATGT 2412 chr5ptel1M 574622 TCTTGGATAGGGCGAGCAAATATAATAAAGATGACAATATTACCTAAACT 574671 v v iv viv vi ? v vi v i i L1M5_orf2#LIN 2413 TCATGGATTGGAAGACTCAATATTGTNAAGATGTCAATTCTCCCCAAATT 2462 chr5ptel1M 574672 AATCTATTTATTTAGC-CTATACCAATCAGACTCCCAAAAACTATTTTAA 574720 i vv i ii- v v i v iv iv v -- L1M5_orf2#LIN 2463 GATCTATAGATTCAATGCAATCCCAATCAAAATCCCAGCAGGTTTTTT-- 2510 chr5ptel1M 574721 TGACCTAGGAAAAATAACAA--------CAAAGTTCATATGGAAAAACAA 574762 --- -- v i --------i i i vi L1M5_orf2#LIN 2511 TG---TAG--AAATTGACAAGCTGATTCTAAAATTTATATGGAAATGCAA 2555 chr5ptel1M 574763 AAGGTCAAGAAT-TTCAAGGAATTAATGAAAAAAAAT--CAAATGATGGT 574809 i ii ? -vi iiv v vv i v-- - v v L1M5_orf2#LIN 2556 AGGACCNAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAAA-GTTGGA 2604 chr5ptel1M 574810 GG-CTTAGCTGTACCAGATCT-AAAATTATATTATAGAGCAGCAGTTACC 574857 - - vv ? ? - i i - i vi v i L1M5_orf2#LIN 2605 GGACTTA-CACTACCNGATNTCAAGACT-TATTATAAAGCTACAGTAATC 2652 chr5ptel1M 574858 AAAACTATTTGGTATTGGC-TAAGGAATAGATTAGTTGATCAGTGGAATA 574906 i vi v - - iv i v i i L1M5_orf2#LIN 2653 AAGACAGTGTGGTATTGGCGTAAGG-ATAGACAAATAGATCAATGGAACA 2701 chr5ptel1M 574907 GATTAG---GTTCAAGGGACAAAACAGTCA-ACAAATATAGCAACCTAAT 574952 v --- i - ii i i v --- - v i ?v ?i i L1M5_orf2#LIN 2702 GAATAGAGAGTCC-AGAAATAGACC---CACACATATATGGNCANTTGAT 2747 chr5ptel1M 574953 CTTTGACAAA---CCCAAAGATCCCATCTTTTGGGATAAGAACTTACTGT 574999 i ---v ? --- v iivv iv i ivvv v L1M5_orf2#LIN 2748 TTTTGACAAAGGTGCCAANG---CAATTCAGTGGGGAAAGGATAGTCTTT 2794 chr5ptel1M 575000 TTGATAAAAATTGCTGGGAAAATTGGAAACTAATATGGCAGAAACTAGGC 575049 ii i viv i v v iiv v i v iii? L1M5_orf2#LIN 2795 TCAACAAATGGTGCTGGAACAATTGGATATCCATATGGAAAAAAATGAAN 2844 chr5ptel1M 575050 ATTGATCCACACTTAACGCCGTACAACAAGATAAGGTCAAAATGGGTTCA 575099 v i i vi i v i i vv i v iv ? i i- L1M5_orf2#LIN 2845 CTCGACCCCTACCTCACACCATACACAAAAATTAATTCNAGATGGA-TCA 2893 chr5ptel1M 575100 T-GACCTAGGCATAAAGAATGAAATTATCAATAAATTAGAGG--AACATA 575146 - iiii ii? i i v vvvvi i -- L1M5_orf2#LIN 2894 TAGACCTAAATGTAAAAGNTAAAACTATAAAACTTCTAGAAGAAAACATA 2943 chr5ptel1M 575147 GGATAGTTTACCTCTCAGACCTGTGGA-AGGGGAAGGTCTTTATGACCAA 575195 v i-- i iivv vv ?- vi i i i - i v i L1M5_orf2#LIN 2944 GGAGAA--TATCTTCGTGACCTTGGGNTAGGCAAAGATTTCT-TAAACAG 2990 chr5ptel1M 575196 AGCAGAACTAGAGATCATTACTGATCACAAAATAGAAAAT-------TTC 575238 ii v -- i -----i ?i i i v i ------- v L1M5_orf2#LIN 2991 GACACAA--AAAG-----CACNAACCATAAAAGAAAAAATTGATAAATTG 3033 chr5ptel1M 575239 GATTATACCAAAATGAAAAGTTTTTGTACAAACAAAACTAATGCAGACAA 575288 i ?i i v ii i iv ?vvv ivi vi ivi v L1M5_orf2#LIN 3034 GACTNCATCAAAATTAAAAACTTCTGCTCNTCAAAAGACACCGTTAAGAA 3083 chr5ptel1M 575289 GATTAGAAGGGAAGCAATAAACTGGGAAAATATTTTTACAGT-CAAAGGT 575337 i v i v v i i ? i v v i i?- v vi- L1M5_orf2#LIN 3084 AATGAAAAGGCAAGCCACAGANTGGGAGAAAATATTTGCAANACATATA- 3132 chr5ptel1M 575338 TCTGATAAAGGCCTCATTTCCAAAATATATAGAGAATTAACTCTAATTT- 575386 i v i v i i i -v vi ? i- L1M5_orf2#LIN 3133 TCTGACAAAGGACTCGTATCCAGAATATATAAAGAACT-CCTACAANTCA 3181 chr5ptel1M 575387 ATAAAAAATCAAGCCATTC--TCCAATTGAAAAATGGTCAAAGGATATGA 575434 ? -- v vv --i v? v i iv L1M5_orf2#LIN 3182 ATAANAAA--AAGACAAACAACCCAATANAAAAATGGGCAAAAGACTTGA 3229 chr5ptel1M 575435 ACAGACAATTCTCAGATGAAGAAATTGAAACTATTTCTAGTCATATGAAA 575484 v v i v v ?v iviiivv iv i L1M5_orf2#LIN 3230 ACAGACACTTCACAAAAGAAGATATNCAAATGGCCAATAAGCACATGAAA 3279 chr5ptel1M 575485 AGATGCTCCAAGTCA 575499 v v? L1M5_orf2#LIN 3280 AGATGCTCAACNTCA 3294 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.86 CpG sites = 251, Kimura (unadjusted) = 38.71 Transitions / transversions = 1.20 (251/209) Gap_init rate = 0.04 (63 / 1618), avg. gap size = 1.38 (87 / 63) 1028 28.43 4.64 4.31 chr5ptel1M 575356 575980 (424020) L1MC1_3end#LINE/L1 7 633 (447) m_b232s551i16 9135 chr5ptel1M 575356 TCCAAAATATATAGAGAA---TTAACTCTAATTTATAAAAAATCAAGCCA 575402 i i --- vv v viv i v i i v L1MC1_3end#LI 7 TCCAAAATATACAAAGAACTCTTAAAACTCAACAATAAGAAAACGAACAA 56 chr5ptel1M 575403 TTCTCCAATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATG 575452 i--- i ? v v i iv ? vi v vi v L1MC1_3end#LI 57 C---CCGATTNAAAAATGGGCCAAAGACCTNAACAGACACCTCACCAAAG 103 chr5ptel1M 575453 AAGAAATTGAAACTATTTCTAGTCATATGAAAAGATGCTCCAAGTCATTA 575502 v vv i iviivvv iv vi - L1MC1_3end#LI 104 AAGATATACAGATGGCAAATAAGCATATGAAAAGATGCTCCACATCA-TA 152 chr5ptel1M 575503 T-TAATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACAC 575551 - v i i vv i L1MC1_3end#LI 153 TGTCATCAGGGAAATGCAAATTAAAACAACAATGAGATACCACTACACAC 202 chr5ptel1M 575552 CTGTCAGATTGGCTAAGATGACAGGAAA--AATAATGATGATTGTTGGAG 575599 i i v i i -v i v --i i iivii v i v L1MC1_3end#LI 203 CTATTAGAATGGCCAAAAT-CCAGAACACTGACAACACCAAATGCTGGCG 251 chr5ptel1M 575600 -GGATGCGGGAAAACTGGGACAATGATGCATTGTTGGTGGAGTTGTGAAC 575648 - i iiv v i vv v v i iiv ii v L1MC1_3end#LI 252 AGGATGTGGAGCAACAGGAACTCTCATTCATTGCTGGTGGGAATGCAAAA 301 chr5ptel1M 575649 GAATCCAACCATTCTGGAGAAGTAGTTTGGAACTATGCTCA-AAAAGTTA 575697 vii v i i i - iii v v - v i - v v L1MC1_3end#LI 302 TGGTACAGCCACTTTGGA-AGACAGTTTGGCAGT-TTCTTACAAAACTAA 349 chr5ptel1M 575698 TCAAACTGTGCATACCCTTTGATCTAGCAGTGTTACTAC-TGGGATTATA 575746 v v --- v v vi i i vvii v - v - L1MC1_3end#LI 350 ACATACT---CTTACCATACGATCCAGCAATCGCGCTCCTTGGTATT-TA 395 chr5ptel1M 575747 TCCCAAAGAGATTATAAA-----G---ACGGAAAGGGACCTGTATGTGCA 575788 - iii iv ----- --- iv --i i ---- L1MC1_3end#LI 396 -CCCAAAGGAGTTGAAAACTTATGTCCACACAAA--AACCTGCA----CA 438 chr5ptel1M 575789 CGAATGTTTG-GGCAGCCCT-TTTGTAGTGGCTAGAAACTGGAAACTGAA 575836 i i-i ii - ii i v i i vi i -- L1MC1_3end#LI 439 CGGATGTTTATAGCAGCTTTATTCATAATTGCCAAAACTTGGAAGC--AA 486 chr5ptel1M 575837 T--GGATGCCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATATGAA 575884 i--i i v v v v i i i vv L1MC1_3end#LI 487 CCAAGATGTCCTTCAGTAGGTGAATGGATAAATAAACTGTGGTACATCCA 536 chr5ptel1M 575885 AATTATGGAATATTACT--GTTCT-GTAAGAAATGA-CCAACAGG--ATG 575928 i iv i -- iv -iv - i v i -- L1MC1_3end#LI 537 GACAATGGAATATTATTCAGCGCTAAAAAGAAATGAGCTATCAAGCCATG 586 chr5ptel1M 575929 ATTTCAGAAAGGCCTG--AGAGACTTACACGAACTGATGCTAAGTGAAAT 575976 ------ i v --i i v i v - iv i v L1MC1_3end#LI 587 A------AAAGACATGGAGGAAACTTAAATGCA-TATTACTAAGTGAAAG 629 chr5ptel1M 575977 GAGC 575980 i L1MC1_3end#LI 630 AAGC 633 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.28 CpG sites = 95, Kimura (unadjusted) = 36.65 Transitions / transversions = 1.27 (95/75) Gap_init rate = 0.07 (43 / 624), avg. gap size = 1.30 (56 / 43) 1498 27.72 1.29 1.85 chr5ptel1M 575356 575899 (424101) L1ME3G_3end#LINE/L1 7 547 (377) m_b232s551i15 9135 chr5ptel1M 575356 TCCAAAATATATAGAGAATTAACTCTAATTTATAAAAAATCAAGCCATTC 575405 i i i vviv v iv i -- v --v L1ME3G_3end#L 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAA--AAGACA--A 52 chr5ptel1M 575406 TCCAATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGAAG 575455 i v v i v v i L1ME3G_3end#L 53 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chr5ptel1M 575456 AAATTGAAACTATTTCTAGTCATATGAAAAGATGCTCCAAGTCATTATTA 575505 vv iviiivv iv v vv i v L1ME3G_3end#L 103 AAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTA 152 chr5ptel1M 575506 ATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACACCTGT 575555 i i vv i i viv ii L1ME3G_3end#L 153 ATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCAT 202 chr5ptel1M 575556 CAGATTGGCTAAGATG-ACAGGAAAAATAATGATGATTGTTGGAG-GGAT 575603 v i v- v i ?vvi ivi? v v - i L1ME3G_3end#L 203 CAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGT 252 chr5ptel1M 575604 GCGGGAAAACTGGGACAATGATGCATTGTTGGTGGAGTTGTGAACGAATC 575653 i i v v vv v i i i iiv i ivii v L1ME3G_3end#L 253 GTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTA 302 chr5ptel1M 575654 CAACCATTCTGGAGAAGTAGTTTGGAACTATGCTCAAAAAGTTATCAAAC 575703 i ? i i- i i v v viviv v --- v L1ME3G_3end#L 303 CAGCCNTTTTGGAGG-GCAATTTGGCAGTATCTATTAAAATTTA---AAA 348 chr5ptel1M 575704 TGTGCATACCCTTTGATCTAGCAGTGTTACTACTGGGATTATATCCCAAA 575753 i i i i vii v ? ?v v i ? L1ME3G_3end#L 349 TGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANA 398 chr5ptel1M 575754 GAGAT---TATAAAGACGGAAAGGGACCTGTATGTGCACGAATGTTTGG- 575799 i ---iii v vii v v i ?-- i i v i iiv- L1ME3G_3end#L 399 GAAATACTCGCACATGTGCACAAGGAN--GCATGTACAAGGATGTTCATT 446 chr5ptel1M 575800 GCAGCCCT-TTTGTAGTGGCTAGAAACTGGAAACTGAATGGATGCCCATC 575848 vi - i i v i i vivv ii i L1ME3G_3end#L 447 GCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATC 496 chr5ptel1M 575849 AGTTGGAGAATGGCTGAATAAATTGTGGTATATGAAAATTATGGAATATT 575898 i v i i i i vv v i i L1ME3G_3end#L 497 AATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACT 546 chr5ptel1M 575899 A 575899 L1ME3G_3end#L 547 A 547 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.21 CpG sites = 81, Kimura (unadjusted) = 35.84 Transitions / transversions = 1.21 (81/67) Gap_init rate = 0.03 (15 / 543), avg. gap size = 1.13 (17 / 15) 15 23.33 2.22 0.00 chr5ptel1M 576415 576459 (423541) (AAATA)n#Simple_repeat 1 46 (0) m_b232s252i7 9136 chr5ptel1M 576415 AAATAAAAGGCTATTAAATAAAA-AAAAAAAAGAAAAAGAAAATAA 576459 vivv v - v iv v (AAATA)n#Simp 1 AAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAA 46 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 18 14.73 0.00 0.00 chr5ptel1M 576430 576459 (423541) (A)n#Simple_repeat 1 30 (0) m_b232s252i8 9136 chr5ptel1M 576430 AAATAAAAAAAAAAAAGAAAAAGAAAATAA 576459 v i i v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 30 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 322 28.58 0.00 10.10 chr5ptel1M 576465 576573 (423427) MIRb#SINE/MIR 3 101 (167) m_b232s601i14 9137 chr5ptel1M 576465 GAGGAGCAGCGAGGCGGTGCAGTGGATAGATCACCAGCCCTGAAGTCAAG 576514 i ---i v v vi ii i ii MIRb#SINE/MIR 3 GAGGGGCAGCG---TGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGA 49 chr5ptel1M 576515 AGGACCTGAGTTCAAATTTGATCTTAGACACTTTATATTTCCTAGCTAAG 576564 vi i i iiviv iv v ------- v iv MIRb#SINE/MIR 50 CAGACCTGGGTTCGAATCCCGGCTCTGCCAC-------TTACTAGCTGTG 92 chr5ptel1M 576565 TGACCTCAG 576573 ii MIRb#SINE/MIR 93 TGACCTTGG 101 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.60 CpG sites = 18, Kimura (unadjusted) = 36.88 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.09 (10 / 108), avg. gap size = 1.00 (10 / 10) 12 25.94 0.00 2.38 chr5ptel1M 578403 578445 (421555) (GGCAGAG)n#Simple_repeat 1 42 (0) m_b232s252i9 9138 chr5ptel1M 578403 GGCAGAGGGAGGAGGAGAGAGGTCAGACCGGGAGATGTCAGAG 578445 vi iv v -v v v v (GGCAGAG)n#Si 1 GGCAGAGGGCAGAGGGCAGAGGGCAGA-GGGCAGAGGGCAGAG 42 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.02 (1 / 42), avg. gap size = 1.00 (1 / 1) 37 0.00 0.00 0.00 chr5ptel1M 578878 578911 (421089) (G)n#Simple_repeat 1 34 (0) c_b232s251i2 9139 chr5ptel1M 578878 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 578911 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 34 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 32 10.99 8.54 2.30 chr5ptel1M 578912 578993 (421007) (AAC)n#Simple_repeat 1 87 (0) m_b232s252i10 9140 chr5ptel1M 578912 AATAACAGCAA-AAAACCAACAA-ACCAACAACAACAACAACAACAACAA 578959 i i - v v - v (AAC)n#Simple 1 AACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAA 50 chr5ptel1M 578960 -AA-AACAA-AA-AACAAACAAACAA-AAAAAAAAAAAC 578993 - - - - - - - v v v (AAC)n#Simple 51 CAACAACAACAACAAC-AAC-AACAACAACAACAACAAC 87 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.11 (9 / 81), avg. gap size = 1.00 (9 / 9) 22 7.25 0.00 0.00 chr5ptel1M 581309 581337 (418663) (A)n#Simple_repeat 1 29 (0) m_b232s252i11 9141 chr5ptel1M 581309 AAAGATAAAAAAAAAAAAAAAAAAAAAAA 581337 i v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA 29 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 19 0.00 0.00 3.85 chr5ptel1M 581381 581407 (418593) (CCA)n#Simple_repeat 1 26 (0) m_b232s252i12 9142 chr5ptel1M 581381 CCACCACCACCACCCACCACCACCACC 581407 - (CCA)n#Simple 1 CCACCACCACCA-CCACCACCACCACC 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.04 (1 / 26), avg. gap size = 1.00 (1 / 1) 270 32.07 10.82 2.24 chr5ptel1M 582115 582567 (417433) C L1M3_orf2#LINE/L1 (933) 2355 1865 m_b232s551i17 9143 chr5ptel1M 582115 TGTTTTATAATTCTATGTCTATGATTCCTATGTACATCTTGGC-AAATGG 582163 i i vv v ii v i viii- vi i- i vv C L1M3_orf2#LIN 2355 TGTTTTATAGTTTTCAGTGTACAAGTCTTTCAC-CTCCTTGGTTAAGTTT 2307 chr5ptel1M 582164 ACTCTTACTTATTTTATGTTCTCTCATTACTTTTAGTGTAAGT----TTA 582209 i i vv -- i -- iv vi v i ---- i C L1M3_orf2#LIN 2306 ATTCCTAAGTATTTTAT--TCTTT--TTGATGCTATTGTAAATGGGATTG 2261 chr5ptel1M 582210 CTTTCTAGAT---CTTTTCGGG--ATTTGTTGATAATATAAAGAAAGGTT 582254 i vi --- i--i i v i i v v iv C L1M3_orf2#LIN 2260 TTTTCTTAATTTCCTTTTCGGATAGTTCGTTGTTAGTGTATAGAAACGCA 2211 chr5ptel1M 582255 GAAGATTTGTTGTGAGTTTATTTCGTACCCTGTTACTTTGCTGAA----- 582299 ivv - iv v i i iv i ----- C L1M3_orf2#LIN 2210 ACTGATTT-TTGTATGTTGATTTTGTATCCTGCAACTTTACTGAATTCGT 2162 chr5ptel1M 582300 ------------ACATTTTTCCTTTAAAGT---TAGCAATTCTCTA---A 582331 ------------ v iivv ii --- -ii i --- C L1M3_orf2#LIN 2161 TTATTAGTTCTAACAGTTTTTTGGTGGAGTCTTTAG-GGTTTTCTACATA 2113 chr5ptel1M 582332 T----TCATCATCAAATGCAAAGAATAATCATTATGTTTCTTCTTTACGC 582377 ---- -i vv v ivi v v ii i v vv C L1M3_orf2#LIN 2112 TAAGATCAT-GTCATCTGCAAACAGAGATAATTTTACTTCTTCCTTTCCG 2064 chr5ptel1M 582378 AT--GCATTCCCTTTCCATTTCTTTATCTT-----ATTGCTATAGCTAGT 582420 -- v v i -- v ----- v i v C L1M3_orf2#LIN 2063 ATTTGGATGCCTTTT--ATTTCTTTTTCTTGCCTAATTGCTCTGGCTAGG 2016 chr5ptel1M 582421 ATTTCTGACATTGGGTTAAATAG---TGATGATAATA--TATCTTTACTT 582465 i iiii i iv i --- ii v i i--i i i i C L1M3_orf2#LIN 2015 ACTTCCAGTACTATGTTGAATAGAAGTGGCGAGAGTGGGCATCCTTGCCT 1966 chr5ptel1M 582466 CACTCCTGATCTTATGCTAATGGATTCTAGTTTTTTGTCTTTACACAAAA 582515 iii vivv vi v ii iii v ivii vi C L1M3_orf2#LIN 1965 TGTTCCTGATCTTAGAGGAAAAGCTTTCAGTTTTTCACCATTGAGTATGA 1916 chr5ptel1M 582516 TGTCAGCTTTTGTTTTTACATAGATACCTATTTAGTATATTAAGGCATAG 582565 i v v vi v v iv i- v i i i ??v C L1M3_orf2#LIN 1915 TGTTAGCTGTGGGCTTTTCATATATGGCC-TTTATTATGTTGAGGTANNT 1867 chr5ptel1M 582566 TC 582567 C L1M3_orf2#LIN 1866 TC 1865 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 42.86 CpG sites = 84, Kimura (unadjusted) = 43.69 Transitions / transversions = 1.45 (84/58) Gap_init rate = 0.05 (24 / 452), avg. gap size = 2.50 (60 / 24) 16 13.20 0.00 2.94 chr5ptel1M 584682 584716 (415284) (ATTTGT)n#Simple_repeat 1 34 (0) m_b232s252i13 9144 chr5ptel1M 584682 ATATGTATTTGTATTTGTATGTATATTTAGAATTT 584716 v v i - v (ATTTGT)n#Sim 1 ATTTGTATTTGTATTTGTATTTGTATTT-GTATTT 34 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 27 23.87 0.00 0.00 chr5ptel1M 584979 585035 (414965) (AC)n#Simple_repeat 1 57 (0) m_b232s252i14 9145 chr5ptel1M 584979 ACACACAGATACATGCACACACGCACACATGTGCACACACACACACGCAT 585028 v i ii i iiii i i (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50 chr5ptel1M 585029 ACACACA 585035 (AC)n#Simple_ 51 ACACACA 57 Matrix = Unknown Transitions / transversions = 10.00 (10/1) Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0) 18 19.46 0.00 0.00 chr5ptel1M 585185 585219 (414781) (T)n#Simple_repeat 1 35 (0) m_b232s252i15 9146 chr5ptel1M 585185 TTCTTTAGTTTGTTACTTTTTTTTTTTTTTTTTTT 585219 i vv v vi (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 35 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 317 33.75 8.12 0.00 chr5ptel1M 586567 586726 (413274) C MIR3#SINE/MIR (2) 206 34 m_b232s601i15 9147 chr5ptel1M 586567 ATCATGAGATCATATA--TTTAGAGAAGGAAGCAACCTCAAAGATCATTG 586614 iii v --v i vv vi i i iv C MIR3#SINE/MIR 206 ATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCT 157 chr5ptel1M 586615 AGTACATACCCATTGTTTTACTAATGAAAAAACT--GGCCTAGAAAGTAG 586662 v vv v ii vi ii -- i i vv C MIR3#SINE/MIR 156 AGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTG 107 chr5ptel1M 586663 A----ACTCATCTAA--TTA-ATCTTTAATTA--AGTATAGGCAAGATTT 586703 ---- iii i -- i - ivvi? i --i i v v ii i v C MIR3#SINE/MIR 106 AAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTA 57 chr5ptel1M 586704 TAATCAATGTCTTCAGAGTTCCA 586726 v i v v i v v i C MIR3#SINE/MIR 56 GAACCCAGGTCTCCTGACTCCCA 34 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 45.58 CpG sites = 31, Kimura (unadjusted) = 46.78 Transitions / transversions = 1.35 (31/23) Gap_init rate = 0.04 (6 / 159), avg. gap size = 2.17 (13 / 6) 21 14.55 5.45 1.75 chr5ptel1M 586786 586840 (413160) (ATTAT)n#Simple_repeat 1 57 (0) m_b232s252i16 9148 chr5ptel1M 586786 ATTATTTTAT-TTAT-TTATATTATATTATAATATCTT-GCCAATATTAT 586832 v - - v v -vviv (ATTAT)n#Simp 1 ATTATATTATATTATATTATATTATATTATATTATATTATATTATATTAT 50 chr5ptel1M 586833 ATATATAT 586840 - (ATTAT)n#Simp 51 AT-TATAT 57 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.07 (4 / 54), avg. gap size = 1.00 (4 / 4) 251 17.65 1.47 0.00 chr5ptel1M 586993 587060 (412940) DNM1r#Unknown 2478 2546 (2116) m_b232s502i3 9149 chr5ptel1M 586993 GTGTATATATATATATATATATATATATATGTGTGTGTGTGTATATATAT 587042 i i i i i i i i i DNM1r#Unknown 2478 GTGTATGTGTGTATATATGTGTGTATATGTGTGTATGTGTGTATATATGT 2527 chr5ptel1M 587043 ATA-GTATATGTATATATA 587060 i -i i ? DNM1r#Unknown 2528 GTATATATACGTATNTATA 2546 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 20.12 CpG sites = 12, Kimura (unadjusted) = 22.17 Transitions / transversions = 1.00 (12/0) Gap_init rate = 0.01 (1 / 67), avg. gap size = 1.00 (1 / 1) 276 19.11 2.90 1.43 chr5ptel1M 587021 587089 (412911) DNM1r#Unknown 2476 2545 (2117) m_b232s502i4 9149 chr5ptel1M 587021 ATGTGTGTGTGTGTATATATATATAGTATATGTATATATATATGTATATA 587070 i i i i - i i i i DNM1r#Unknown 2476 ACGTGTATGTGTGTATATATGTGT-GTATATGTGTGTATGTGTGTATATA 2524 chr5ptel1M 587071 --CATATACATACATATACAT 587089 --ii i i ?i DNM1r#Unknown 2525 TGTGTATATATACGTATNTAT 2545 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 20.35 CpG sites = 13, Kimura (unadjusted) = 24.56 Transitions / transversions = 1.00 (13/0) Gap_init rate = 0.03 (2 / 68), avg. gap size = 1.50 (3 / 2) 1078 32.07 3.48 4.02 chr5ptel1M 587379 587953 (412047) C L1MD1_3end#LINE/L1 (361) 628 57 m_b232s551i18 9150 chr5ptel1M 587379 TTTTACTCAGCATCAGTTCATGTAAGTCTCTCCAGGC-GTCTCTGGAATT 587427 i v v iiv v ii iiv i- iv vv v i C L1MD1_3end#LI 628 TTTCACTCAGCATAATTCTCTGGAGATTCATCCAGGTTGTTGCGTGTATC 579 chr5ptel1M 587428 ATCCTATTGTTCATTTCTT---ATAGACCAATAATATTCCATAACACTGA 587474 ---- v i i --- v viv i i iii iv C L1MD1_3end#LI 578 A----ATAGTTCGTTCCTTTTTATTGCTGAGTAGTATTCCATGGTATGGA 533 chr5ptel1M 587475 TA---CATAATTTATTCAGCCATTCTCCAAATGATGGGCATCCATTCAGT 587521 i--- i i i i i v viv v i iivviv C L1MD1_3end#LI 532 TGTACCACAGTTTGTTTAACCATTCACCCGTTGAAGGACATCTGGGTTGT 483 chr5ptel1M 587522 TTCCAGTTTCTAGCCACCACAAAGAAGGCTGCCACAAACATTTTGGCACA 587571 i i i ii i v i i i ivv i C L1MD1_3end#LI 482 TTCCAGTTTTTGGCTATTACGAATAAAGCTGCTATAAACATTCGTGTACA 433 chr5ptel1M 587572 ------TGTGGGCTCCTTTCCTTCCTTTAAGATCTCTTTGGGATAGAAGC 587615 ------ v vv v vvvi i ------ i i i v C L1MD1_3end#LI 432 GGTTTTTGTGTGAACATAAGTTTTC------ATTTCTCTGGGATAAATGC 389 chr5ptel1M 587616 CCAGTAGAAACACTGCTGGATGAAAGGATA--TGCACAATTTGATAACTT 587663 v vivv i i viv v i -- ii- ii --- C L1MD1_3end#LI 388 CCAGGAGTGCAATTGCTGGGTCGTATGGTAGTTGCATG-TTTAGT---TT 343 chr5ptel1M 587664 TTTGAGTGTAGAT--CCAAATTGTTCTTCAGAATGGTTGGATCCATTCAC 587711 i --- i i-- i i i i i v i vv i C L1MD1_3end#LI 342 TTTAAG---AAACTGCCAAACTGTTTTCCAGAGTGGCTGTACCATTTTAC 296 chr5ptel1M 587712 AGTTCCACCAAGAATGTATCAATGTCCCAGTTTTCCCACATCTCTCCCAA 587761 v i iv v i vi ii i iiiv i C L1MD1_3end#LI 295 ATTCCCACCAGCAATGTATGAGTGATCCAGTTTCTCCGCATCCTCGCCAG 246 chr5ptel1M 587762 CATTCA---TCATCATCATCTTTTCCTATCATCTTAGCCAATCTGACAGG 587808 ii--- ii ii i ------ i v i C L1MD1_3end#LI 245 CATTTGGTGTTGTCACTATTTTTT------ATTTTAGCCATTCTGATAGG 202 chr5ptel1M 587809 TATGTAGTGGTATTTCAGAGTTGTCTTAATTTGCATTTCTCTGATCAATA 587858 i i i vv v i i i viv C L1MD1_3end#LI 201 TGTGTAGTGATATCTCATTGTGGTTTTAATTTGCATTTCCCTAATGGCTA 152 chr5ptel1M 587859 GTGATTGGGAGCACCTTTTCATATGACTAGAAATAATTTTAATTTCTTCA 587908 i vvv i i i vi vvviiv i vv v i v C L1MD1_3end#LI 151 ATGATGTTGAACATCTTTTCATGTGCTTATTTGCCATCTGTATATCCTCT 102 chr5ptel1M 587909 TCTGAGAATTGTCTGTTCATGTCCTTTGACCGTTTATCAGTTGGA 587953 v v v v i v i vii i C L1MD1_3end#LI 101 TCGGTGAAATGTCTCTTCATGTCTTTTGCCCATTTTCTAATTGGA 57 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.09 CpG sites = 106, Kimura (unadjusted) = 43.38 Transitions / transversions = 1.49 (106/71) Gap_init rate = 0.05 (30 / 574), avg. gap size = 1.43 (43 / 30) 1440 26.50 2.41 3.03 chr5ptel1M 587455 587952 (412048) C L1ME3G_3end#LINE/L1 (376) 548 54 m_b232s551i19 9150 chr5ptel1M 587455 ATAATATTCCATAACACTGATA---CATAATTTATTCAGCCATTCTCCAA 587501 i ii iv --- i i i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr5ptel1M 587502 ATGATGGGCATCCATTCAGTTTCCAGTTTCTAGCCACCACAAAGAAGGCT 587551 v i ii vviv i i v i ii v v C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr5ptel1M 587552 GCCACAAACATTTTGGCACATGTGGGCTCCTTTCCTTCCTTTAAGA---T 587598 v ii ii v i i?--- viviv v v iv --- C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACATGCN---TCCTTGTGCACATGTGCGAGTAT 402 chr5ptel1M 587599 CTCTTTGGGATAGAAGCCCAGTAGAAACACTGCTGGATGAAAGGATATGC 587648 i ? i v? ? v viiv i i v i C L1ME3G_3end#L 401 TTCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGC 352 chr5ptel1M 587649 ACAATTTGATAACTTTTTGAGTGTAGAT----CCAAATTGTTCTTCAGAA 587694 i v i -- -- i --- ---- ii i i C L1ME3G_3end#L 351 GCATTTTAA--A--TTTTAA---TAGATACTGCCAAATTGCCCTCCAAAA 309 chr5ptel1M 587695 TGGTTGGATCCATTCACAGTTCCACCAAGAATGTATCAATGTCCCAGTTT 587744 ? i v i v i v i iv i v iv v v C L1ME3G_3end#L 308 NGGCTGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTT 259 chr5ptel1M 587745 TCCCACATCTCTCCCAACATTCATCATCATCATCTTTTCCTATCATCTTA 587794 i i iiiv i ?ivi i v?i -- -v i v C L1ME3G_3end#L 258 CCCCACACCCTCGCCAACACTNGATATTATCAANCTTT--TA-AATTTTT 212 chr5ptel1M 587795 GCCAATCTGACAGGTATGTAGTGGTATTTCAGAGTTGTCTTAATTTGCAT 587844 ii iviv i i vv i C L1ME3G_3end#L 211 GCCAATCTGATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCAT 162 chr5ptel1M 587845 TTCTCTGATCAATAGTGATTGG--GAGCACCTTTTCATATGACTAGAAAT 587892 i i v -- -- i vi vviii C L1ME3G_3end#L 161 TTCCCTGATTACTAGTGA--GGTTGAGCATCTTTTCATATGTTTATTGGC 114 chr5ptel1M 587893 AATTTTAATTTCTTCATCTGAGAATTGTCTGTTCATGTCCTTTGACCGTT 587942 v vv i v v i i v i C L1ME3G_3end#L 113 CATTTGTATTTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATT 64 chr5ptel1M 587943 TATCAGTTGG 587952 v vi C L1ME3G_3end#L 63 TTTCTATTGG 54 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.49 CpG sites = 76, Kimura (unadjusted) = 34.14 Transitions / transversions = 1.46 (76/52) Gap_init rate = 0.04 (19 / 497), avg. gap size = 1.42 (27 / 19) 250 25.09 0.00 5.77 chr5ptel1M 587867 587976 (412024) C L1M5_orf2#LINE/L1 (7) 3287 3184 m_b232s551i20 9150 chr5ptel1M 587867 GAGCACCTTTTCATATGACTAGAAATAATTTTAATTTCTTCATCTGAGAA 587916 i i vi vviiiv v? v v i v C L1M5_orf2#LIN 3287 GAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTTTTGTGAA 3238 chr5ptel1M 587917 TTGTCTGTTCATGTCCTTTGACCGTTTATCAGTTGGAGAATGGCTTGATT 587966 v v i v i v ?vi ---i v i --- C L1M5_orf2#LIN 3237 GTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGG---GTTGTTTG--- 3194 chr5ptel1M 587967 TCTTTTTTTT 587976 ? C L1M5_orf2#LIN 3193 TCTTTTTNTT 3184 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 31.72 CpG sites = 12, Kimura (unadjusted) = 31.72 Transitions / transversions = 0.86 (12/14) Gap_init rate = 0.06 (6 / 109), avg. gap size = 1.00 (6 / 6) 14 4.54 0.00 4.17 chr5ptel1M 588070 588094 (411906) (CCCT)n#Simple_repeat 1 24 (0) m_b232s252i17 9151 chr5ptel1M 588070 CCCTCCCTCCCTCCACCCCCTCCCT 588094 - i (CCCT)n#Simpl 1 CCCTCCCTCCCTCC-CTCCCTCCCT 24 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 370 32.82 3.00 0.98 chr5ptel1M 588381 588580 (411420) C L1ME5_3end#LINE/L1 (291) 650 447 m_b232s551i21 9152 chr5ptel1M 588381 ATCTC---CTGGTTCT-GCTCATTTCACTCGGCATCA-GTTCATGTAAG- 588424 --- v -i iv i ii - -- v - C L1ME5_3end#LI 650 ATCTCATTCTGTTTCTTACTTTTTTCACTCAGCACTATGTT--TTTAAGA 603 chr5ptel1M 588425 TCTCTCCAAGCCTCTCTGTATTCATCCTGCTGGTCATTTCTTACAGAACA 588474 iv v iiv v i v iv iiv iii v v vvvv C L1ME5_3end#LI 602 TCCATCCATGTTGCTATGTGTACATCTAGTCCGTTGCTTCTAACTGCTGC 553 chr5ptel1M 588475 ATAATATTCCATAACATTCATATACCACAATTTACCCAACCATTCTCCAA 588524 i i iiii v vi v i v i v C L1ME5_3end#LI 552 ATAGTACTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCA 503 chr5ptel1M 588525 CTGATGGGCATCCATTCATTTTTCAATTTCTAGCCACTACAAACAGGACT 588574 v i i vvivvii i i i iv i ivi C L1ME5_3end#LI 502 GTGATGGACACCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCT 453 chr5ptel1M 588575 GGAATG 588580 v C L1ME5_3end#LI 452 GCAATG 447 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.42 CpG sites = 36, Kimura (unadjusted) = 44.34 Transitions / transversions = 1.24 (36/29) Gap_init rate = 0.03 (6 / 199), avg. gap size = 1.33 (8 / 6) 388 24.78 5.08 0.81 chr5ptel1M 588760 588877 (411123) CR1-L3A_Croc#LINE/CR1 3700 3822 (466) m_b232s551i22 9153 chr5ptel1M 588760 GAATAGGGAGGTTATATTCTCTCTTTATT--ATGCTTGTCAGACCAC-AC 588806 i vi v --iii v vv i - CR1-L3A_Croc# 3700 GAGTAGGGAGGTTATATTACCTCTGTATTTGGCACTGGTGCGACCGCTAC 3749 chr5ptel1M 588807 TGAAATATTATGTTGGGTTCTGG---CTATAGTTTTAAGGAGGAAATTGA 588853 i i i ivi --- i i -? i i vi CR1-L3A_Croc# 3750 TGGAATACTGTGTCCAGTTCTGGTGTCCACA-NTTCAAGAAGGATGTTGA 3798 chr5ptel1M 588854 GAAATTGGAGAATGTCTGGAGGAG 588877 ? iv iii i CR1-L3A_Croc# 3799 NAAATTGGAGAGGGTTCAGAGAAG 3822 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 30.91 CpG sites = 21, Kimura (unadjusted) = 32.27 Transitions / transversions = 2.62 (21/8) Gap_init rate = 0.03 (4 / 117), avg. gap size = 1.75 (7 / 4) 189 21.62 0.00 0.00 chr5ptel1M 588915 588951 (411049) L3#LINE/CR1 3707 3743 (356) m_b232s601i16 9154 chr5ptel1M 588915 CAATTGAAGGAGCTGAAAGTGTTTAGGCTGGAGAAGA 588951 ii i iiii v L3#LINE/CR1 3707 CGGTTGAAGGAACTGGGGATGTTTAGCCTGGAGAAGA 3743 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 23.45 CpG sites = 7, Kimura (unadjusted) = 27.38 Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 629 35.24 2.03 0.80 chr5ptel1M 589358 589603 (410397) L3#LINE/CR1 3850 4098 (1) m_b232s601i17 9154 chr5ptel1M 589358 CAATGGGTGCTCTTT-TAAAGAAACAAATTTAGATTTGATGCAAAGAAAG 589406 vvvv -i ii ii i v ii ii ii i ii L3#LINE/CR1 3850 CAATGGGTGGAAGTTACAGGGAGGCAGATTTCGGCTCAATATAAGGAAGA 3899 chr5ptel1M 589407 ACTTTCTGACAAT-AGATTCATTCCATGGTAGAAGAGAATGCATATCACA 589455 i - viii i v vii i vi iv v vv?ivi L3#LINE/CR1 3900 ACTTTCTAACAATCAGAGCTGTCCAAAAATGGAATGGGCTGCCTCGNGAG 3949 chr5ptel1M 589456 CTAGTGGATTCCTCCTTATTGGAAATCTTCTGTCAAAAGCTGGGATGATC 589505 v iii i v i i ii v viv i i - - L3#LINE/CR1 3950 GTAGTGAGCTCCCCGTCACTGGAGGTGTTCAAGCAGAGGCTGG-ATGA-C 3997 chr5ptel1M 589506 CTTTTGCCATGTACGTTATAGTGGGGATTCCTT--TCAGGTAT-ATGTTG 589552 vi i v v i i vi v-- ii i iv- v L3#LINE/CR1 3998 CACTTGTCAGGGATGTTGTAGAAGGGATTCCTGCATTGGATGGGAGGTTG 4047 chr5ptel1M 589553 GACTTGATGGCTACCAAGGTGTCTCCCACCTTTAAGATTTTGTGATTCTG 589602 v i iv i vi i v i i i i L3#LINE/CR1 4048 GACTAGATGACCTCTAAGGTCCCTTCCAACTCTGAGATTCTGTGATTCTA 4097 chr5ptel1M 589603 T 589603 L3#LINE/CR1 4098 T 4098 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 50.99 CpG sites = 56, Kimura (unadjusted) = 50.99 Transitions / transversions = 1.87 (56/30) Gap_init rate = 0.02 (6 / 245), avg. gap size = 1.17 (7 / 6) 13 8.41 13.16 0.00 chr5ptel1M 589614 589651 (410349) (TATATCCA)n#Simple_repeat 1 43 (0) m_b232s252i18 9155 chr5ptel1M 589614 TATAT-C-TATAT-C-TGTATCCATATAACCA-ATATCCGTAT 589651 - - - - i v - i (TATATCCA)n#S 1 TATATCCATATATCCATATATCCATATATCCATATATCCATAT 43 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.14 (5 / 37), avg. gap size = 1.00 (5 / 5) 194 28.61 12.61 3.08 chr5ptel1M 590144 590262 (409738) AmnSINE2#SINE/tRNA-Deu 143 272 (86) m_b232s601i18 9156 chr5ptel1M 590144 GTGGTAGTCCTTCC-ATGGGACTGCTTACAAATCAAAGTGCTGTCTTACC 590192 ?vi i v- i -- v i iv - i i AmnSINE2#SINE 143 GTGNGGGTCTTTCGGATGAGAC--CTTAAAAACCAAAGCCCTGTC-TGCT 189 chr5ptel1M 590193 CTTTATAG---TTATGG--TCCATGTCATTTTT--------TAAGGGTCT 590229 vii i --- vi --i i v ii -------- i i AmnSINE2#SINE 190 CTGCGTGGACATTAAAGATCCCGTGGCGCTTTTCGTAAGAGTAGGGGTTT 239 chr5ptel1M 590230 TCCTCAATGCCCTGGAGACCATCTTCT-GAACCC 590262 v i ii v - v v vi - AmnSINE2#SINE 240 GCCCCGGTGCCCTTG-GCCGAATTTCTGGAACCC 272 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.19 CpG sites = 21, Kimura (unadjusted) = 38.00 Transitions / transversions = 1.75 (21/12) Gap_init rate = 0.08 (9 / 118), avg. gap size = 2.11 (19 / 9) 181 15.48 0.00 13.04 chr5ptel1M 590277 590328 (409672) MIRc#SINE/MIR 184 229 (39) m_b232s601i19 9157 chr5ptel1M 590277 GTTGTGAGGACAAAATGTGATAATATATGAAAAGTTTAAAGCTCTATGTA 590326 iv v i ------ v v v MIRc#SINE/MIR 184 GTTGTGAGGATCAAATGAGATAATGTATG------TGAAAGCGCTTTGTA 227 chr5ptel1M 590327 AA 590328 MIRc#SINE/MIR 228 AA 229 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 17.01 CpG sites = 2, Kimura (unadjusted) = 17.01 Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.12 (6 / 51), avg. gap size = 1.00 (6 / 6) 16 21.89 1.92 3.92 chr5ptel1M 590331 590382 (409618) (ATT)n#Simple_repeat 1 51 (0) m_b232s252i19 9158 chr5ptel1M 590331 ATT-TTATTGGCATTATTATTGGCACCATTATTATTATTATTCATTCCTT 590379 - ivi ivi ii - -v (ATT)n#Simple 1 ATTATTATTATTATTATTATTATTATTATTATTATTATTATT-ATT-ATT 48 chr5ptel1M 590380 ATT 590382 (ATT)n#Simple 49 ATT 51 Matrix = Unknown Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.00 (3 / 3) 11 16.86 2.86 2.86 chr5ptel1M 590357 590391 (409609) (ATTCTT)n#Simple_repeat 1 35 (0) m_b232s252i20 9158 chr5ptel1M 590357 ATTATTATTATTATTCAT-TCCTTATTTCTTGTTCT 590391 v v v - i - i (ATTCTT)n#Sim 1 ATTCTTATTCTTATTCTTATTCTTA-TTCTTATTCT 35 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 395 32.20 15.95 2.28 chr5ptel1M 590450 590681 (409319) MIRc#SINE/MIR 1 263 (5) m_b232s601i20 9159 chr5ptel1M 590450 CAAGATAATGTAAAGTAGTGAATAGAAGTCTAGACTTGGAGTCCAGGAAG 590499 i ii i iiv i i v ivv i - MIRc#SINE/MIR 1 CGAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTC-AGGAAG 49 chr5ptel1M 590500 -------TTCAGATATCATCTCTGACATTTATTAACTGGCTGATGTCAGA 590542 ------- iii vi iv v i i i vv iv ii i MIRc#SINE/MIR 50 ACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGG 99 chr5ptel1M 590543 TT-GTTGCTTA--TTCTTGGACAATACTTCATTTTCCTCATATGTCA--- 590586 iv- ii --i iv ----i i v v v --- MIRc#SINE/MIR 100 CAAGTCACTTAACCTCTCTGA----GCCTCAGTTTCCTCATCTGTAAAAT 145 chr5ptel1M 590587 ----------------------CTTATTTCATGGGGTTGTTATGAAGATC 590614 ---------------------- i ii ii i i MIRc#SINE/MIR 146 GGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATC 195 chr5ptel1M 590615 AAATTGGATAA-ATAGTGTAAAATTGTTTCA-AAACTTTATAACTCTCAG 590662 vi -i - i vi i ii- v v iiv vvi MIRc#SINE/MIR 196 AAATGAGATAATGTA-TGTGAAAGCGCTTTGTAAACTGTAAAGTGCTATA 244 chr5ptel1M 590663 GAAATGACAGATATTATTA 590681 v vv i?i MIRc#SINE/MIR 245 CAAATGTAAGGNGTTATTA 263 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.52 CpG sites = 48, Kimura (unadjusted) = 44.87 Transitions / transversions = 1.92 (48/25) Gap_init rate = 0.06 (13 / 231), avg. gap size = 3.31 (43 / 13) 348 29.79 1.28 7.48 chr5ptel1M 590972 591127 (408873) C MIR1_Amn#SINE/MIR (83) 147 1 m_b232s601i22 9160 chr5ptel1M 590972 ATTTTATACATGAGGAAATTGAGGTATACAG-GGTAAAATGGCCTGCCCA 591020 i v i i?i v - ? i i i C MIR1_Amn#SINE 147 ATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGCCCA 98 chr5ptel1M 591021 GGTTCACAAAATAGG-AAGTGTCTGAGGACATATTTGAATTCAGGAAGAG 591069 i v ?v ii? -? v v vvviv ? ? ii ------ C MIR1_Amn#SINE 97 AGGTCACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAACCCAG------ 54 chr5ptel1M 591070 CAGTCTTCTTGACTCCAGGACTGGCACTCCATGCTTTAAGCCATGCCCTA 591119 -- - ii v vi v ii ii i v vi ii -- v i C MIR1_Amn#SINE 53 --GTC-TCCCGAGTCCCAGTCCAGTGCTCTATCCACTAGACCA--CACTG 9 chr5ptel1M 591120 GCTCCCCA 591127 v i C MIR1_Amn#SINE 8 CCTCCCTA 1 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.44 CpG sites = 26, Kimura (unadjusted) = 41.73 Transitions / transversions = 1.53 (26/17) Gap_init rate = 0.08 (13 / 155), avg. gap size = 1.00 (13 / 13) 379 28.66 1.57 6.61 chr5ptel1M 590972 591098 (408902) C MIRc#SINE/MIR (123) 145 25 m_b232s601i21 9160 chr5ptel1M 590972 ATTTTATACATGAGGAAATTGAGGTATACAG-GGTAAAATGGCCTGCCCA 591020 i v i ivi v - v i i i C MIRc#SINE/MIR 145 ATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCA 96 chr5ptel1M 591021 GGTTCACA-AAATAGGAAGTGTCTGAGGACATATTTGAATTCAGGAAGAG 591069 i v - iv v v v vvviv i i ii ------ C MIRc#SINE/MIR 95 AGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAG------ 52 chr5ptel1M 591070 CAGTCTTCTTGACTCCAGGACTGGCACTC 591098 -- i i v ii ii C MIRc#SINE/MIR 51 --GTCTTCCTGACTCCAAGTCCAGTGCTC 25 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.58 CpG sites = 20, Kimura (unadjusted) = 36.94 Transitions / transversions = 1.43 (20/14) Gap_init rate = 0.08 (10 / 126), avg. gap size = 1.00 (10 / 10) 339 28.58 4.53 4.92 chr5ptel1M 592728 592992 (407008) L1ME3Cz_3end#LINE/L1 13 276 (721) m_b233s551i0 9161 chr5ptel1M 592728 ATATATAGAAAACT-----AAATCAAATTTCTAAGAATACAAGTCATTCT 592772 i i ----- ----- --v v --vi L1ME3Cz_3end# 13 ATATATAAAGAACTCCTACAAATCAA-----TAAGAA--AAAGACA--AC 53 chr5ptel1M 592773 CCAATTGATAAATTGTCAAAGGATATAAATAGACAAGTTGTAGATGAAGA 592822 v v v v i i i v iii v i L1ME3Cz_3end# 54 CCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGGA 103 chr5ptel1M 592823 AATTAAAATGAACTATAATCATATGAAAAAATGTACTAAATCAATATTGA 592872 iivi iv v v i iv v vv v v i L1ME3Cz_3end# 104 AACCCGAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTAA 153 chr5ptel1M 592873 TTAGAGAAATTCAAATTACAAGATCTCTGAGGTACAACCTCAAGCCTCTC 592922 i i v v v?v vv i v ii vi iv L1ME3Cz_3end# 154 TCAGGGAAATGCAAATTAAAACNACAATGAGATACCATTTCACACCCATC 203 chr5ptel1M 592923 AGACAGAGTAAGATTACAGGAAAA----GATAATGATAAATGTAGG---G 592965 iv ivv i ----v ---- i ivi i v --- L1ME3Cz_3end# 204 AGATTGGCAAAAATT----TAAAAGTCTGACAATACCAAGTGTTGGCGAG 249 chr5ptel1M 592966 GATGTGGGAAATCTGGAACACTAATGC 592992 ii v v v v i L1ME3Cz_3end# 250 GATGTGGAGAAACGGGAACTCTCATAC 276 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.84 CpG sites = 34, Kimura (unadjusted) = 36.45 Transitions / transversions = 0.89 (34/38) Gap_init rate = 0.06 (16 / 264), avg. gap size = 1.56 (25 / 16) 421 29.67 2.70 1.33 chr5ptel1M 592771 592992 (407008) L1ME5_3end#LINE/L1 56 280 (661) m_b233s551i1 9161 chr5ptel1M 592771 CTCCAATTGATAAATTGTCAAAGGATATAAATAGACAAGTTGTAGATGAA 592820 i v v v v i i i v ii v i L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chr5ptel1M 592821 GAAATTAAAATGAACTATAATCATATGAAAAAATGTACTAAATCAATATT 592870 iivi v iviv i v i i iv v v v v L1ME5_3end#LI 106 GAAACCCGAAAGGCTAACAAGCATATGAAGAGATGCTCAAACTCATTAGT 155 chr5ptel1M 592871 GATTAGAGAAATTCAAATTACAAGATCTCTGAGGTACAACCTCAAGCCTC 592920 i i v v v v vv i iv i i vi v L1ME5_3end#LI 156 AATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCTA 205 chr5ptel1M 592921 TCAGACAGAGTAAGATTACAGGAAA---AGATAATGATAAATGTAGG--- 592964 i v ivv i --- ---i vi i v --- L1ME5_3end#LI 206 TTAGACTGGCAAAAATTA---GAAAGCTGGATAATGCCAAGTGTTGGCGA 252 chr5ptel1M 592965 GGATGTGGGAAATCTGGAACACTAATGC 592992 i ?viv v v L1ME5_3end#LI 253 GGATGTGGGGANATAGGAACCCTCATGC 280 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.64 CpG sites = 31, Kimura (unadjusted) = 38.37 Transitions / transversions = 0.91 (31/34) Gap_init rate = 0.02 (5 / 221), avg. gap size = 1.80 (9 / 5) 1355 31.30 3.93 3.34 chr5ptel1M 593070 594289 (405711) L1PREC2_orf2#LINE/L1 2023 3249 (45) m_b233s551i2 9162 chr5ptel1M 593070 CTAGCCTCAGCAATAAGAGTCAAGAAAGAGATTCAAGGAATTAGAGTAGG 593119 i vv v ivvvi i vv i v ivi i L1PREC2_orf2# 2023 CTGGCCAGAGCAATCAGGCAAGAGAAAGAAATAAAGGGCATCCAAATAGG 2072 chr5ptel1M 593120 CAATAAGGAAACCAAACTATCACTCTTTGCAGATGATATAATGGTATACT 593169 v ivi ii v v i i i vv ii L1PREC2_orf2# 2073 AAGAGAGGAAGTCAAACTATCCCTGTTTGCAGACGACATGATTCTATATC 2122 chr5ptel1M 593170 TAGAGAACCCCAGAGATTTTA--CTAAAAGCTATTAGAAATAATTCACAA 593217 i v - i ii-- i vi v? iv i vv L1PREC2_orf2# 2123 TAGAAAACCCCATAG-TCTCGGCCCAAAAGCTCCTTNAGCTGATAAACAA 2171 chr5ptel1M 593218 CTTTAGCAAAGTTTTAGGATAAAAAATAAATCCCCATAAATCCTCAGCAT 593267 i i v v viv v vii L1PREC2_orf2# 2172 CTTCAGCAAAGTTTCAGGATACAAAATCAATGTACAAAAATCACTAGCAT 2221 chr5ptel1M 593268 TTTTATACATCACCAACAAAATCCAACAGCAAGAGATACA--AAGA--GA 593313 ii --- v v -iv i vi v -- i -- v L1PREC2_orf2# 2222 TCCTATA---CACCAACAACAGCCAA-GCCGAGAGCCAAATCAGGAACGC 2267 chr5ptel1M 593314 AATTCCATTCAAAATAATTGTCCAC----AGCATGAAATATTTGAGAATC 593359 i --- i - ---- v i ii ii v L1PREC2_orf2# 2268 AATCCCATTC---ACAATTG-CCACAAAAAGAATAAAATACCTAGGAATA 2313 chr5ptel1M 593360 TATCT-ACCAAAGAAAAGTCAGGTAT-TAT-ATGAGCAAAATTACAAAAA 593406 i v - ii iiv vv i v - i- --- v L1PREC2_orf2# 2314 CAGCTAACCAGGGAGGTGAAAGATCTCTACAATGAG---AATTACAAAAC 2360 chr5ptel1M 593407 ACTTTCCACACAAATAAACTCAGACTTAAATAATTGGAAAAATATTAAGT 593456 vii v v v ivvvv vi i v i vvi L1PREC2_orf2# 2361 ACTGCTCAAAGAAATCAGAGATGACACAAACAAATGGAAAAACATTCCAT 2410 chr5ptel1M 593457 G-TCTTGGATAGGCCGAGCGAATATAATAAAGATGACAATACTCCCTAAA 593505 - v vv iiv vi v i i v v i L1PREC2_orf2# 2411 GCTCATGGATAGGAAGAATCAATATCGTTAAAATGGCCATACTGCCCAAA 2460 chr5ptel1M 593506 CTAATCTATTTATTTAGTGCTATACCAATCACACTTCCAAGAAAATATTT 593555 vi i ivv i i v v v v vi v vi L1PREC2_orf2# 2461 GCAATTTACAGATTCAATGCTATTCCTATCAAACTACCAATGACATTCTT 2510 chr5ptel1M 593556 TAATGATCTAGAAAAAATAA---CAAAATTCATATGGAAGAACAAAAGA- 593601 i vv v iv ---i vv v - L1PREC2_orf2# 2511 CACAGAACTAGAAAAAACTATTTTAAAATTCATATGGAACCAAAAAAGAG 2560 chr5ptel1M 593602 -TTGAAAATCTCAAGGGAAT--TAATGAAAAAAAAAATCAAATGAAGGTG 593648 -ii v v - v -- vv i --- - vv v L1PREC2_orf2# 2561 CCCGAATAGC-CAAGGCAATCCTAAGCAAAAAGAA---CAAA-GCTGGAG 2605 chr5ptel1M 593649 GCCTAGCTGTACCTAATCTAAAACTATATTATAAAGCAGCAGTCACCAAA 593698 v vi vv ii ii v i i ii vi v L1PREC2_orf2# 2606 GCATCACGCTACCCGACTTCAAACTATACTACAGGGCTACAGTAACCAAA 2655 chr5ptel1M 593699 ACTATTTGGTATTGGCTAAGAAATAGATTAGTTGATCAGTGGAAGAGGTT 593748 viiv i ivv i i ivvi v i i v iv L1PREC2_orf2# 2656 ACAGCATGGTACTGGTACAAAAACAGACACATAGACCAATGGAACAGAAT 2705 chr5ptel1M 593749 AG---GTTCACAAGACAATATAGT-CAACTATAGCAATCTAGTATTTGAC 593794 --- ii v - i viiv i- v i i v ii v i L1PREC2_orf2# 2706 AGAGAGCCCAGAA-ATAAGGCCGCACACCTACAACCATCTGATCTTCGAC 2754 chr5ptel1M 593795 AAACC---CAAAGATCCTAACTTTGGGGATAAGAATTCATTATTTTACAA 593841 v --- i -- v i vv - i i vi iv i L1PREC2_orf2# 2755 AAAGCTGACAAAAA--CAAGCAATGGGGA-AAGGACTCCCTATTCAATAA 2801 chr5ptel1M 593842 AAACTGCTGGGAAAACTGGAAATTAG---TATGGCAGAA-ATTAGCCATG 593887 viv v ---i --- - - iivvv L1PREC2_orf2# 2802 ATGGTGCTGGGATAACTGG---CTAGCCATAT-GCAGAAGATTGAAACTG 2847 chr5ptel1M 593888 GACCCACACTTAACACCATATACCAAGATAAGATCAAAATGGGTCTATGA 593937 viv i v v i v iv i i iv v L1PREC2_orf2# 2848 GACCCCTTCCTTACACCATATACAAAAATCAACTCAAGATGGATTAAAGA 2897 chr5ptel1M 593938 TTTAGGCATAAAGAACGAGATTATAAATAAGTTAGAGG--AACATAAGAC 593985 i iiii ivv i i i v vvi i i -- v - i L1PREC2_orf2# 2898 CTTAAATGTAAAACCCAAAACTATAAAAACCCTGGAAGACAACCT-AGGC 2946 chr5ptel1M 593986 AGTTTACCTCTC-AGACCTGTGGAGGAGGAAGAAATTTGTGACCAAAGAT 594034 i-- vi -i v iv i v i v ii v ii - i i L1PREC2_orf2# 2947 AA--TACCATTCTGGACATAGGAACGGGCAAAGATTTCATGA-CGAAGAC 2993 chr5ptel1M 594035 GAACTAGAGACCATTATTGATCACAAAATAAAAAAT-------TTTGATT 594077 -- i i ii v ----iiv vv ------- vv i L1PREC2_orf2# 2994 G--CCAAAAGCAATT----GCAACAAAAGCAAAAATTGACAAATGGGATC 3037 chr5ptel1M 594078 ACATCAAATTAAAAAGCCTTTGT---CCAAACAAAACTAATGTAAACAAG 594124 vv i i i i i i---v vi --- v ii L1PREC2_orf2# 3038 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTA---TCAACAGA 3084 chr5ptel1M 594125 ATTAGAAGGGAAGCAATAAACTGGGAAAACATCTTCACAGTTAAAGGTTC 594174 i v iv iv v v i i v i v ? ii iviv v vv L1PREC2_orf2# 3085 GTAAACAGACAACCTACAGAATGGGAGAAAATNTTTGCAAACTATGCATC 3134 chr5ptel1M 594175 TGATAAAGGCCTCATTTCCAAAATATATAGAGAGCTGACTCTAATTTATA 594224 i i v v iv v ii i v vv v i L1PREC2_orf2# 3135 TGACAAAGGTCTAATATCCAGCATCTATAAGGAACTTAAACAAATTTACA 3184 chr5ptel1M 594225 AG---AAACCAAGCCATTCTCCAATTGATAAATGGTCAAAGGATATGAAC 594271 --- v i v ---i v i v i v i L1PREC2_orf2# 3185 AGAAAAAAACAAACAA---CCCCATTAAAAAGTGGGCAAAGGACATGAAC 3231 chr5ptel1M 594272 AGACAATTTTCAGATGAA 594289 v i v L1PREC2_orf2# 3232 AGACACTTTTCAAAAGAA 3249 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.95 CpG sites = 190, Kimura (unadjusted) = 41.28 Transitions / transversions = 1.06 (190/179) Gap_init rate = 0.05 (63 / 1219), avg. gap size = 1.41 (89 / 63) 300 31.95 3.66 2.54 chr5ptel1M 594059 594331 (405669) L1M1_orf2#LINE/L1 3019 3294 (0) m_b233s551i3 9162 chr5ptel1M 594059 AAAATAAAAAATTTTGATTACATCAAATTAAAAAGCCTTTGT---CCAAA 594105 ii v v vv i i i i i---v L1M1_orf2#LIN 3019 AAAATGGACAAATGGGATCACATCAAGTTAAAAAGCTTCTGCACAGCAAA 3068 chr5ptel1M 594106 CAAAACTAATGTAAACAAGATTAGAAGGGAAGCAATAAACTGGGAAAACA 594155 vi - -- v ii v ii iv v v i i v i v L1M1_orf2#LIN 3069 GGAAAC-AA--TCAACAAAGTGAAGAGACAACCCACAGAATGGGAGAAAA 3115 chr5ptel1M 594156 TCTTCACAGTTAAAGGTTCTGATAAAGGCCTCATTTCCAAAATATATAGA 594205 v ii iviv vvvv i i vi v vv i ii L1M1_orf2#LIN 3116 TATTTGCAAACTACCCATCTGACAAGGGATTAATAACCAGAATATATAAG 3165 chr5ptel1M 594206 GAGCTGACTCTAATTTATAAGAAACCAAGCC--ATTCTCCAATTGATAAA 594253 v vv v v i i -- ii -- vv i i v L1M1_orf2#LIN 3166 GAGCTCAAACAACTCTATAGGAAA--AAATCTAATAATCCGATTAAAAAA 3213 chr5ptel1M 594254 TGGTCAAAGGATATGAACAGACAATTTTCAGATGAA-----ACTGAAATT 594298 v i v i v i i v ----- -- v L1M1_orf2#LIN 3214 TGGGCAAAAGATCTGAATAGACATTTCTCAAAAGAAGACATAC--AAATG 3261 chr5ptel1M 594299 ATTTCCATTCATATGAAAGAGTGTTCCATATCA 594331 iivvv vv ii i v i L1M1_orf2#LIN 3262 GCAAACAGGCATATGAAAAGGTGCTCAACATCA 3294 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.57 CpG sites = 42, Kimura (unadjusted) = 42.21 Transitions / transversions = 0.98 (42/43) Gap_init rate = 0.04 (10 / 272), avg. gap size = 1.70 (17 / 10) 1362 29.43 2.72 3.05 chr5ptel1M 594191 594814 (405186) L1ME5_3end#LINE/L1 7 628 (313) m_b233s551i4 9162 chr5ptel1M 594191 TCCAAAATATATAGAGAGCTGACTCTAATTTATAAGAAACCAAGCCATT- 594239 i i i ii i vviv v iv i -- v iv?- L1ME5_3end#LI 7 TCTAGAATATACAAGGAACTCCTGCAAATCAACAAGAAA--AAGACGGNA 54 chr5ptel1M 594240 -CTCCAATTGATAAATGGTCAAAGGATATGAACAGACAATTTTCAGA--- 594285 - i v v v i v --- L1ME5_3end#LI 55 ACCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGA 104 chr5ptel1M 594286 TGAAACTGAAATTATTTCCATTCATATGAAAGAGTGTTCCATATCACTAT 594335 v ivi vvii vv vv iiii i v vv i v L1ME5_3end#LI 105 GGAAACCCGAAAGGCTAACAAGCATATGAAGAGATGCTCAAACTCATTAG 154 chr5ptel1M 594336 TGATCAGAGAAATGCAAATTAAGACAACTCTGAGATACCACTACACACCT 594385 i i vv i vi L1ME5_3end#LI 155 TAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCT 204 chr5ptel1M 594386 GTCAGATTGGCTAAGATGACAGGAAA---AAATAATGATGAATGTTGGAG 594432 i i i v i v --- ---ii vii i v L1ME5_3end#LI 205 ATTAGACTGGCAAAAATTA---GAAAGCTGGATAATGCCAAGTGTTGGCG 251 chr5ptel1M 594433 GGGATGTGGGAAAACTGGGACACTGATGCATTGTTGGTGGAGTTGTGAAC 594482 i i ? iv i v v i i iiv ii L1ME5_3end#LI 252 AGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGAC 301 chr5ptel1M 594483 GAATCCACCCATTCTGGAAAGCAATCTGGAATTAT---GCCAAAAAAGTT 594529 vii v v i v v i--- i vv iv L1ME5_3end#LI 302 TGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTAAGT 351 chr5ptel1M 594530 ATCAAACTGTGCATACCCTTTGATCCAGCAGTGCTACTCCTGGGCTTATA 594579 --- --- v i i v ii iv L1ME5_3end#LI 352 AT---AC---GCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATA 395 chr5ptel1M 594580 CCCCAAGGAGATACTAAAGAAGG----GAAAAGGACCTGTATGTGCCAAA 594625 i i i v v viv ----v ii v i ---- ii L1ME5_3end#LI 396 TCCCAAAGAAATTCTCACACAGGTCCATAAGGGGACATGTACG----AGG 441 chr5ptel1M 594626 ATGTTTGTGGCAGCCCTGTTTGTAGTGACTAGAAACTGGAAAATGAATGT 594675 ii v vi i i vi i ii ii--v iv L1ME5_3end#LI 442 ATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGG--CAACCT 489 chr5ptel1M 594676 GGATGCCCATCAATTTGAGAATGGTTGGGTAAATTGTGGTATATGAATGT 594725 i i v vv i v i v iv v iii L1ME5_3end#LI 490 GGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACAC 539 chr5ptel1M 594726 TATGGAATATTATTGTTCTGTAAGAAATGACCAGCAGGATGAAGACAGAG 594775 i i i vvvv v v iii vii vi v v v L1ME5_3end#LI 540 CATGGAGTACTATGCAGCAGTTAGAAGCAACGGACTAGATGTACACATAG 589 chr5ptel1M 594776 AGGCTTGGAGAGA-CTTACACGAAC-TGATGCCGAGTGAAA 594814 vii v vi - v -- - ii i L1ME5_3end#LI 590 CAACATGGATGGATCTTAAA--AACATAGTGCTGAGTGAAA 628 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.26 CpG sites = 100, Kimura (unadjusted) = 38.39 Transitions / transversions = 1.28 (100/78) Gap_init rate = 0.04 (26 / 623), avg. gap size = 1.38 (36 / 26) 1497 27.69 1.10 0.92 chr5ptel1M 594196 594738 (405262) L1ME4c_3end#LINE/L1 12 555 (275) m_b233s551i5 9162 chr5ptel1M 594196 AATATATAGAGAGCTGACTCTAATTTATAAGAAACCAAGCCATTCTCCAA 594245 ? i v i v v vv? v v vv i L1ME4c_3end#L 12 ANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAAGACCCCAA 61 chr5ptel1M 594246 TTGATAAATGGTCAAAGGATATGAACAGACAATTTTCAGATGA--AACTG 594293 v v i iv ? v -- v i L1ME4c_3end#L 62 TAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAGGAAATA 111 chr5ptel1M 594294 AAATTATTTC-CATTCATATGAAAGAGTGTTCCATATCACTATTGATCAG 594342 v ? v vv- vv i i i i v iv i v i i L1ME4c_3end#L 112 CAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTAGTAATCAA 161 chr5ptel1M 594343 AGAAATGCAAATTAAGACAACTCTGAGATACCACTACACACCTGTCAGAT 594392 ii vv i vi i i i i L1ME4c_3end#L 162 AGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCTATTAAAT 211 chr5ptel1M 594393 TGGCTAAGATGACAGGAAAAAATAATGATGAATGTTGGAGGGGATGTGGG 594442 i v i vvv ii vvi iviv i v i ? i v L1ME4c_3end#L 212 TAGCAAAAATTTAAAAAATTGATAATACCCAATGCTGGCGAGGNTGCGGT 261 chr5ptel1M 594443 AAAACTGGGACACTGATGCATTGTTGGTGGAGTTGTGAACGAATCCACCC 594492 i v ? v i i vi? i ivii v v L1ME4c_3end#L 262 GAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACAACC 311 chr5ptel1M 594493 ATTCTGGAAAGCAATCTGGAATTATGCCAAAAAAGTTATCAAACTGTGCA 594542 v i i v v i ivvv i ii v v v L1ME4c_3end#L 312 CTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAAAATGTTCA 361 chr5ptel1M 594543 TACCCTTTGATCCAGCAGTGCTACTCCTGGGCTTATACCCCAAGGAGATA 594592 i i i v i i vv v i i i L1ME4c_3end#L 362 TACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATA 411 chr5ptel1M 594593 ---CTAAAGAAGGGAAAAGGACCTGTATGTGCCAAAATGTTTGTGGCAGC 594639 --- v i --- i ii v i ii v L1ME4c_3end#L 412 ATTCAAAAGAAGGAAAAAG---CTATATGCACGAAGATGTTCATTGCAGC 458 chr5ptel1M 594640 CCTGTTTGTAGTGACTAGAAACTGGAAAATGAATGTGGATGCCCATCAAT 594689 vi i i i ii v i i --v iv ii i v L1ME4c_3end#L 459 GTTATTTATAATAGCGAAAAATTGGAAA--CAACCTAAATGTCCAACAAT 506 chr5ptel1M 594690 TTGAGAATGGTTGGGTAAATTGTGGTATATGAATGTTATGGAATATTAT 594738 vv i ii i i v? iviv L1ME4c_3end#L 507 AGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATATTAT 555 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.39 CpG sites = 81, Kimura (unadjusted) = 35.87 Transitions / transversions = 1.19 (81/68) Gap_init rate = 0.01 (8 / 542), avg. gap size = 1.38 (11 / 8) 20 16.66 0.00 0.00 chr5ptel1M 596142 596175 (403825) (A)n#Simple_repeat 1 34 (0) m_b233s252i0 9163 chr5ptel1M 596142 AAAAAAAAAAAAAACTAAATAAAACAAACAAAAA 596175 vv v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 34 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 chr5ptel1M 596277 596294 (403706) (A)n#Simple_repeat 1 18 (0) m_b233s252i1 9164 chr5ptel1M 596277 AAAAAAAAAAAAAAAAAA 596294 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAA 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 13 11.69 3.57 0.00 chr5ptel1M 596551 596578 (403422) (ATAAA)n#Simple_repeat 1 29 (0) m_b233s252i2 9165 chr5ptel1M 596551 ATAAAACAAAATCAAA-AGAATAAAATAA 596578 i v - i (ATAAA)n#Simp 1 ATAAAATAAAATAAAATAAAATAAAATAA 29 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 13 27.29 4.76 1.54 chr5ptel1M 596641 596703 (403297) (AAT)n#Simple_repeat 1 65 (0) m_b233s252i3 9166 chr5ptel1M 596641 AATAAT-ATAATAGTCAGAATATCAATAA-AA-AAAAAAAAAAAGAATGT 596687 - i v v vi - - v v v v iv (AAT)n#Simple 1 AATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAA 50 chr5ptel1M 596688 TGATACATAACAAGAA 596703 i - i v (AAT)n#Simple 51 TAATA-ATAATAATAA 65 Matrix = Unknown Transitions / transversions = 0.56 (5/9) Gap_init rate = 0.06 (4 / 62), avg. gap size = 1.00 (4 / 4) 398 24.44 0.00 11.61 chr5ptel1M 596839 596963 (403037) C MIRc#SINE/MIR (155) 113 2 m_b233s601i0 9167 chr5ptel1M 596839 GATTAAGTGGTTTTTTAAGCCCTGGGTCACACAGCTAGGAAGTGTTAAGT 596888 i ii ----- vi v vi --- C MIRc#SINE/MIR 113 GGTTAAGTGACTT-----GCCCAAGGTCACACAGCTAGTAAGTGGCA--- 72 chr5ptel1M 596889 TTGAGGTCGCATTTGAACTCCGATCCTCCTGACTTCAAGGCTGGTGCTCT 596938 -- viv v i i i v i i i v ii C MIRc#SINE/MIR 71 --GAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCT 24 chr5ptel1M 596939 GTCCACTGTGCCACCTAGCTGCCCC 596963 v ii ---i i C MIRc#SINE/MIR 23 TTCCACTGCACCAC---ACTGCCTC 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.45 CpG sites = 18, Kimura (unadjusted) = 30.07 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.10 (13 / 124), avg. gap size = 1.00 (13 / 13) 395 27.67 3.70 10.11 chr5ptel1M 597337 597525 (402475) L2b_3end#LINE/L2 281 458 (8) m_b233s601i1 9168 chr5ptel1M 597337 CCTCTCCAATTTGCCGCCCT----CTCTGCTTTTCAATTTCCT-TTCATA 597381 i i i i-- ii ---- vv vi? vi -? i i L2b_3end#LINE 281 CCCCCCCAGTC--CTACCCTGCCACTCTGGGTTATNATTGTCTGNTTACA 328 chr5ptel1M 597382 TATAGTTTTCTCTCATTAGAATGTAAGCTCAGTGAAGACAGGGACT-TGC 597430 i vvv i i i i v i v i i i-? i L2b_3end#LINE 329 TGTCTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGT 378 chr5ptel1M 597431 CT-TCTTTTTGCCTCTGCTGCCTCTGCTTGAAGGCCCAGCAATTAGCACA 597479 - v -- v i iv ---------- ivi L2b_3end#LINE 379 CTGTCTTGTT--CACCGCTGTATC----------CCCAGCGCCTAGCACA 416 chr5ptel1M 597480 GTGACAGGCATACAGAACACACTTAATAAATGCTCATTTGTTGTAT 597525 ? v v i v vi i i i ---- v L2b_3end#LINE 417 GNGCCTGGCACACAGTAGGCGCTCAGTAAAT----ATTTGTTGAAT 458 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.62 CpG sites = 29, Kimura (unadjusted) = 36.43 Transitions / transversions = 1.61 (29/18) Gap_init rate = 0.12 (22 / 188), avg. gap size = 1.14 (25 / 22) 433 26.49 0.71 11.02 chr5ptel1M 597386 597525 (402475) L2a_3end#LINE/L2 383 509 (8) m_b233s601i2 9168 chr5ptel1M 597386 GTTTTCTCTCATTAGAATGTAAGCTCAGTGAAGACAGGGACTTGCCTTCT 597435 i i i i i vi i i viv iiv L2a_3end#LINE 383 GTCTCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTCTG 432 chr5ptel1M 597436 TTTTG-CCTCTGCTGCCTCTGCTTGAAGGCCCAGCAATTAGCACAGTGAC 597484 -i v iv ---------- ivi v v L2a_3end#LINE 433 TTTTGTTCACTGCTGTATC----------CCCAGCGCCTAGAACAGTGCC 472 chr5ptel1M 597485 AGGCATACAGAACACACTTAATAAATGCTCATTTGTTGTAT 597525 v i i v vi i i ---- v L2a_3end#LINE 473 TGGCACATAGTAGGCGCTCAATAAAT----ATTTGTTGAAT 509 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.66 CpG sites = 20, Kimura (unadjusted) = 33.07 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.11 (15 / 139), avg. gap size = 1.00 (15 / 15) 701 31.54 13.49 2.91 chr5ptel1M 597514 597980 (402020) L3#LINE/CR1 3584 4098 (1) m_b233s601i3 9169 chr5ptel1M 597514 CATTTGTTGTATT-CTTTC-TTTCTGAATGTTATGGTTTAAGAAAAATAT 597561 i vv - v -v iii ii iiv iii i L3#LINE/CR1 3584 CATCTGGAGTATTGCGTTCAGTTCTGGGCGCCACATTTTAAGAGGGACAT 3633 chr5ptel1M 597562 -GACAAATTGCAGAGTGTCTAGAAGAAGGCAGTCAGGATGGTGAAGAACC 597610 - i v v i i i ii iii iii L3#LINE/CR1 3634 TGACAAACTGGAGCGCGTCCAGAGGAGAGCGACCAGGATGGTGAAGGGTC 3683 chr5ptel1M 597611 TTCAA--TATTTC---TGA--------TGCAGGAATTTGG---------- 597637 vv --i v --- -------- v i v ---------- L3#LINE/CR1 3684 TGGAAACCATGTCATATGAGGAACGGTTGAAGGAACTGGGGATGTTTAGC 3733 chr5ptel1M 597638 -------AGAGAAGACTTACAGGAGA---AAGTGCCTTCTTGCCAAAGAT 597677 ------- v ---i vv iv -- v L3#LINE/CR1 3734 CTGGAGAAGAGAAGACTTAGAGGAGACATGATAGCTGTCTT--CAAATAT 3781 chr5ptel1M 597678 GTGAATGTTCAGAGGCTG-CAT-TGGGAGCAAGAATTAGCCTTGTTC-AA 597724 v -------i - - i - i i v i -iv L3#LINE/CR1 3782 TTGAA-------GGGCTGTCATGTGGAAG-AGGGATTAGACTTATTCTGT 3823 chr5ptel1M 597725 GTGTCATGAGAGGCTAGGGCTAGAAGTAATGGATGCAAATGCTAAGGAGG 597774 v viv vi ii i vi i v i vvi i L3#LINE/CR1 3824 GTGGCTCCAGAGGGCAGAACTAGGACCAATGGGTGGAAGTTACAGGGAGG 3873 chr5ptel1M 597775 TAAATTTGAGGTTGTTGTAATGAA------------AAT-----CTGCCC 597807 i i vi v iiv i v ------------ ----- i L3#LINE/CR1 3874 CAGATTTCGGCTCAATATAAGGAAGAACTTTCTAACAATCAGAGCTGTCC 3923 chr5ptel1M 597808 AACCATG--ATGAA-TGTCTCAAAGGAGTTTGGGTTCTTTTTCTACTTGT 597854 vv -- ii- i i?ii ivvv i i iiiv - - v L3#LINE/CR1 3924 AAAAATGGAATGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGTC-AC-TGG 3971 chr5ptel1M 597855 AGGTCTTTAAGCAGAGATCCAAGTGACTGCTTGTCAAAGTATGTTGTAAG 597904 v i i- iiii ii ii - - L3#LINE/CR1 3972 AGGTGTTCAAGCAGAGG-CTGGATGACCACTTGTCAGGG-ATGTTGT-AG 4018 chr5ptel1M 597905 GGGAAACATCTACA-TGTATAGGA---TGGAGTGTATGCTTAGTAAGGCC 597950 ii ii ivi i - v i --- v iv viivv i L3#LINE/CR1 4019 AAGGGATTCCTGCATTGGATGGGAGGTTGGACTAGATGACCTCTAAGGTC 4068 chr5ptel1M 597951 CTTTGCAATGTTCTAATTCTGTGACGTTAT 597980 i v ivi vvi ivi L3#LINE/CR1 4069 CCTTCCAACTCTGAGATTCTGTGATTCTAT 4098 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.70 CpG sites = 91, Kimura (unadjusted) = 43.13 Transitions / transversions = 1.75 (91/52) Gap_init rate = 0.07 (33 / 466), avg. gap size = 2.36 (78 / 33) 27 30.51 2.63 0.86 chr5ptel1M 598009 598122 (401878) (GAGA)n#Simple_repeat 1 116 (0) m_b233s252i4 9170 chr5ptel1M 598009 GAGAGAGACAGACTGCCAGGCAGAGA-AAAAAGACAGCAG-GAGATAGAG 598056 v vv vv iv - i i v - - v (GAGA)n#Simpl 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG-AGAGAGAGAGAG 49 chr5ptel1M 598057 CAACAGAGAGAGAGAGA-AAAAAAAAAGAAAGAAAGAAAGACATAGAAAG 598105 vi v - i i i i i i i v v i (GAGA)n#Simpl 50 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 99 chr5ptel1M 598106 AAACAGAGAGACATAGA 598122 i v v v (GAGA)n#Simpl 100 AGAGAGAGAGAGAGAGA 116 Matrix = Unknown Transitions / transversions = 0.87 (13/15) Gap_init rate = 0.04 (4 / 113), avg. gap size = 1.00 (4 / 4) 19 0.00 0.00 0.00 chr5ptel1M 598255 598275 (401725) (T)n#Simple_repeat 1 21 (0) m_b233s252i5 9171 chr5ptel1M 598255 TTTTTTTTTTTTTTTTTTTTT 598275 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTT 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 368 23.21 3.45 3.45 chr5ptel1M 600156 600271 (399729) MIRb#SINE/MIR 138 253 (15) m_b233s601i4 9172 chr5ptel1M 600156 ACCTG-AAAATGGGGATAATAATTGTGGATAACTCTCAGGACTTGTTGTA 600204 i - vvi--- v v i- i MIRb#SINE/MIR 138 ATCTGTAAAATGGGGATAATAATACC---TACCTCGCAGGG-TTGTTGTG 183 chr5ptel1M 600205 AGAATCAAATAAGATAATATTTGTAAAATGCATAACATGGTATCTTGCA- 600253 i i i iiv ii v i ii ii v - MIRb#SINE/MIR 184 AGGATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCAC 233 chr5ptel1M 600254 ACTGTAAG-ACT-AATAAAT 600271 iv -i - MIRb#SINE/MIR 234 ATAGTAAGCGCTCAATAAAT 253 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.22 CpG sites = 18, Kimura (unadjusted) = 28.80 Transitions / transversions = 2.25 (18/8) Gap_init rate = 0.07 (8 / 115), avg. gap size = 1.00 (8 / 8) 382 34.79 10.16 5.76 chr5ptel1M 600803 601235 (398765) C L2b_3end#LINE/L2 (1) 465 15 m_b233s601i5 9173 chr5ptel1M 600803 TTTAATCAATCAATAAACATTTACTAAGTACTTA---TGTGTCAGGTACA 600849 i v v i i i ii i --- i i? - C L2b_3end#LINE 465 TTCATTCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNC- 417 chr5ptel1M 600850 TAAGACCTTAGAGCTGTGGATACA----CAAAAAGGGAAAATACAGTATT 600895 iv -- vi v v ----ii v i iv i i? i vii C L2b_3end#LINE 416 TGTG--CTAGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCC 369 chr5ptel1M 600896 TGCCCTCAAAGATCTTCAAATCTAATCAGAGAGAC-CATATGCAAACATA 600944 vi v ivv i i vi i -v i i ? -- C L2b_3end#LINE 368 TGCCCTCACGGAGCTCACAGTCTAGTGGGGGAGACAGACATGTAANCA-- 321 chr5ptel1M 600945 TGTACAA-AGTAAGTTCTTGAG----AGGGTA-AATAGGAAAGAATTAAC 600988 - - -?i --i iv ---- -i iv iii ivi--- C L2b_3end#LINE 320 -G-ACAATNATAA--CCCAGAGTGGCAGGGTAGGACTGGGGGGGCC---C 278 chr5ptel1M 600989 AGACAGAAAGCACTTGAATTAA---GAAGGGCTGGAGAAAACTTCCTGTA 601035 -i ii i i viiii--- ii iii i iii i v C L2b_3end#LINE 277 AGA-GGAGGGCGCCTGACCCGGCCTGGGGGGTCAGGGAGGGCTTCCCGGA 229 chr5ptel1M 601036 GATCAGG-GAAATTTTAGTTGGGATTTAAAAAA--AATCAGGGTGATGTG 601082 i-- - v v i i ii i ii -- i vi i -- vv C L2b_3end#LINE 228 GG--AGGTGACATTTGAGCTGAGACCTGAAGGATGAGTAGGAGT--TGGC 183 chr5ptel1M 601083 TACTCAGAAAGGTGGAAAAAAAGTATTCTGGGT------GACAGCCAAAG 601126 i vv ii i -ii ii ii ii i------i v?iv C L2b_3end#LINE 182 CAGGCGAAGAGGTGG-GGAAGGGCGTTCCAGGCAGAGGGAACAGCANGTG 134 chr5ptel1M 601127 AAAATGCCTGTAGCTGAGAGATAGGCT--CGTGTTC------C--TAAAA 601166 v v ivv vi i ?v v? -- ------ --i ii C L2b_3end#LINE 133 CAAAGGCCCTGAGGCGGGAGNGAGCNTGGCGTGTTCGAGGAACAGCAAGG 84 chr5ptel1M 601167 AAGCCTTTGTCTTTAAATTGGAG-AGAATGTGTCAGAAGTGGAGCGT--- 601212 i vv -----iii - i v i--- v v --- C L2b_3end#LINE 83 AGGCCAGTGT-----GGCTGGAGCAGAGTGAGC---AAGGGGAGAGTGGT 42 chr5ptel1M 601213 --GAGA--AGACTGGAAAAGTAGGAGG 601235 -- -- i i i i vi C L2b_3end#LINE 41 AGGAGATGAGGCCGGAGAGGTAGCGGG 15 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 46.26 CpG sites = 100, Kimura (unadjusted) = 52.34 Transitions / transversions = 2.38 (100/42) Gap_init rate = 0.10 (43 / 432), avg. gap size = 1.63 (70 / 43) 321 31.98 5.80 2.63 chr5ptel1M 601297 601813 (398187) L1M2_orf2#LINE/L1 1777 2309 (982) m_b233s551i7 9174 chr5ptel1M 601297 CATATGATTATGTCAGTAGATTCTGGAAAAGTTTTTGTCAAAATCT--TA 601344 i v i v v i iv vi ii--i L1M2_orf2#LIN 1777 CATATGATCATCTCAATAGATGCAGAAAAAGCATTTGATAAAATTCAACA 1826 chr5ptel1M 601345 GGCCTGCATTTCTTAATAACTCTAAAATGCAAA---GGAATGAATGGATC 601391 vv v vv-- v v --- --- v ii v v L1M2_orf2#LIN 1827 TCCCTTCATGA--TAAAAACTCTCAA---CAAATTAGGTATAGAAGGAAC 1871 chr5ptel1M 601392 TTTACTTAATATACTCAATTCTATCTATC-TAAATACAAGAGCAACCATT 601440 v vv i i i v v vv i v v-i iv v- v v i L1M2_orf2#LIN 1872 GTACCTCAACACAATAAAGGCCATATATGACAAACCCAC-AGCTAACATC 1920 chr5ptel1M 601441 ATATGTAATGGAGAAAACTTAGAAGCTATTCAAATGATGTCATGAGTAAG 601490 ivv i v ii iv vvv i vi? vv ii L1M2_orf2#LIN 1921 ATACTGAATGGGGAAAAGTTGAAAGCCTTTCCTCTAAGANCTGGAACAAG 1970 chr5ptel1M 601491 ACCAGAATGGCCATTATCATCTCTGGTATTTAAT---GTTCTAGAAATAC 601537 v i v i v i v vv i i--- v i i v L1M2_orf2#LIN 1971 ACAAGGATGCCCACTTTCACCACTTCTATTCAACATAGTACTGGAAGTCC 2020 chr5ptel1M 601538 TAGCTATAGCAATAAGACAATAAAGAGGAATACA-GGAAGCAAGAATAAG 601586 i v v i v i i i v - v v v - vi L1M2_orf2#LIN 2021 TAGCCAGAGCAATTAGGCAAGAGAAAGAAATAAAAGGCATCCA-AATTGG 2069 chr5ptel1M 601587 CAAAAAGGAATCTGAATTCATACTTTTT-CAGATAATATGAGGACTTAT- 601634 v ii viii vviv v - i i v-- - L1M2_orf2#LIN 2070 AAAGGAGGAAGTCAAATTGTCCCTGTTTGCAGATGACATGAT--CTTATA 2117 chr5ptel1M 601635 --TAGAAT-CCCTTAAGAGTC-------AAATTT----AATTGAAAGAAT 601670 -- v-? v v ------- i ?---- i v - i L1M2_orf2#LIN 2118 TNTAGAAAANCCTAAAGACTCCACCAAAAAACTNTTAGAACTGATA-AAC 2166 chr5ptel1M 601671 AAATGCACTAAAATTATAGAAAGTA-AAAAGCAATATATGTAAATCTTCA 601719 i v v i ii i -- - v i iiv vvi L1M2_orf2#LIN 2167 GAATTCAGTAAAGTTGCAGGA--TACAAAATCAACATACAAAAATCAGTA 2214 chr5ptel1M 601720 TTATTTCTATATATCATTAATGAAATAC---AGTGAGAAAACTAGAAGGA 601766 vi iii vi i v i--- ivi v v i v L1M2_orf2#LIN 2215 GCATTTCTATACGCCAACAACGAACTATCTGAAAAAGAAATCAAGAAAGC 2264 chr5ptel1M 601767 CAAATCCTATTCTGAATGACTACAGAAGTTATAAAATATTTGGGGAT 601813 -- i ivv ii i ivv ii i i L1M2_orf2#LIN 2265 --AATCCCATTTACAATAGCTACAAAAAAAATAAAATACCTAGGAAT 2309 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.53 CpG sites = 79, Kimura (unadjusted) = 42.63 Transitions / transversions = 0.96 (79/82) Gap_init rate = 0.05 (27 / 516), avg. gap size = 1.63 (44 / 27) 412 30.33 3.30 2.17 chr5ptel1M 601297 601569 (398431) L1M5_orf2#LINE/L1 1780 2055 (1239) m_b233s551i6 9174 chr5ptel1M 601297 CATATGATTATGTCAGTAGATTCTGGAAAAGTTTTTGTCAAAATCTTAGG 601346 i v i v v i iv v iiv vi L1M5_orf2#LIN 1780 CATATGATCATCTCAATAGATGCAGAAAAAGCATTTGACAAAATTCAACA 1829 chr5ptel1M 601347 CCTGCATTTCT--TAATAACTCTAAAATGCAA---AGGAAT-GAATGGAT 601390 -- iv -- v v --- --- - v v L1M5_orf2#LIN 1830 CC--CATTCATGATAAAAACTCTCA---GCAAACTAGGAATAGAAGGGAA 1874 chr5ptel1M 601391 CTTTACTTAATATACTCAATTCTATCTATCTAAATACAAGAGCAACCATT 601440 i- i iv iv v vvvi ivv vv v v ? v i L1M5_orf2#LIN 1875 CTTC-CTCAACCTGATAAAGGGCATCTACGAAAAACCTACAGCNAACATC 1923 chr5ptel1M 601441 ATATGTAATGGAGAAAACTTAGAAGCTATTCAAATGATGTCATGAGTAAG 601490 iv v ?vi ii ? v i vvv i vi iv ii L1M5_orf2#LIN 1924 ATACTTAATGGTGAAANACTGAANGCTTTCCCCCTAAGATCGGGAACAAG 1973 chr5ptel1M 601491 ACCAGAATGGCCATTATCATCTCTGGTATTTAA---TGTTCTAGAAATAC 601537 v i v ii ? i v vv i --- v i ii v L1M5_orf2#LIN 1974 ACAAGGATGTCCGCTNTCACCACTTCTATTCAACATTGTACTGGAGGTCC 2023 chr5ptel1M 601538 TAGCTATAGCAATAAGACAATAAAGAGGAATA 601569 i vv i v i i L1M5_orf2#LIN 2024 TAGCCAGTGCAATAAGGCAAGAAAAAGAAATA 2055 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.13 CpG sites = 37, Kimura (unadjusted) = 39.96 Transitions / transversions = 0.84 (37/44) Gap_init rate = 0.04 (10 / 272), avg. gap size = 1.50 (15 / 10) 13 25.72 3.51 1.72 chr5ptel1M 605558 605614 (394386) (AATAAC)n#Simple_repeat 1 58 (0) m_b233s252i6 9175 chr5ptel1M 605558 AAT-ACATATAACAGTTA-TATAAGCATAACAATAATAGAAATATAAATA 605605 - - i v -v vv i iv i vv i (AATAAC)n#Sim 1 AATAACA-ATAACAATAACAATAACAATAACAATAACAATAACAATAACA 49 chr5ptel1M 605606 ATAACAATA 605614 (AATAAC)n#Sim 50 ATAACAATA 58 Matrix = Unknown Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.05 (3 / 56), avg. gap size = 1.00 (3 / 3) 752 30.69 1.30 2.09 chr5ptel1M 608134 608519 (391481) C HERVL66#LTR/ERVL (1943) 2386 2004 m_b233s701i0 9176 chr5ptel1M 608134 GCTTCAAATAAATTTTCTTTCCATTTTCTCAAATCATTATTATCACTTAA 608183 i? i ii vv ? - v i-- iiv vv i C HERVL66#LTR/E 2386 GTNTCAAACAGGTGATCNTTCCATTTT-TCTAAC--TTACCTTGCCCTAA 2340 chr5ptel1M 608184 TTTCTTTACTTTTTCCTTCAATAATCCATTCATTCTTTCTATAAGTCCTG 608233 ivi i vi v i? i i vi v v v C HERVL66#LTR/E 2339 CACCTTCAGCTGTTTNTTCAATAACCCGTTCATTCTTTCGGTTAGGCCAG 2290 chr5ptel1M 608234 CTACTTGAGGATAATAAGGAACATGATAAATCCATTCAATATTATTATAA 608283 i i v i iii ? i ii iv ? iii ?v ii C HERVL66#LTR/E 2289 CTGCCTGCGGGTGGCANGGGATGTGGAAAATCCATTCNATGCCATNTTGG 2240 chr5ptel1M 608284 -TTACAATA--TAGTTCAATTTCTTTTCCTTTAAAATGAGTGCCATTATC 608330 -i i vi-- v v iii v--- i i v i i C HERVL66#LTR/E 2239 GCTGCAAAGGTTTGTACAGCCTCA---CCTTTGAAATGGGAGCCACTGTC 2193 chr5ptel1M 608331 ACTCTGGATTTGCATGGGGGTGCCATAATATAATGAA--ACAATGTCTAA 608378 vv i i i viii ? -- -- vi i ? C HERVL66#LTR/E 2192 CGTTTGAATTTGTATGGGCACACCATNATATA--GAATTAGGATGTTTNA 2145 chr5ptel1M 608379 AGTTTTACAAGTGTTCTTTTGTGTAGCTTTCTTATATGGACAAGCAATAA 608428 ? vv vv vv v vvi v vi i v iv C HERVL66#LTR/E 2144 NGTTTTAATAGTGTTAGTTTGGTTAGCATTAGCATAAGCGCAGGCTACTA 2095 chr5ptel1M 608429 GTATCCCAGAGTAGGTATCCACACAAGTACAGGCATATTGGCACCCTTGA 608478 v v v i i i v? viii v C HERVL66#LTR/E 2094 GGAGCCCTGAGCAGGTGTCTACAGNAGTACATATGTATTGGCACCCTTTA 2045 chr5ptel1M 608479 TTCATAGGCAATGGGCCTATATAATCAATTTGCCAGATTTG 608519 vvv vv v i vvi i v ? i C HERVL66#LTR/E 2044 GAAAGTGGCAAGGGACAAGTATAGTCCATTTGNCAAATTTG 2004 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.02 CpG sites = 63, Kimura (unadjusted) = 41.97 Transitions / transversions = 1.19 (63/53) Gap_init rate = 0.03 (11 / 385), avg. gap size = 1.18 (13 / 11) 322 30.65 3.98 0.97 chr5ptel1M 608792 608992 (391008) C ERVL-B4#LTR/ERVL (1689) 4025 3819 m_b233s701i1 9177 chr5ptel1M 608792 ATTATACTCACCTTCCACAGAATCCATCTTTACATGAGCATCTACATGAA 608841 v v vi i ii v ivi i i vvi ii ii C ERVL-B4#LTR/E 4025 ATTAAAATCCTCCTCTGCTGAGGTCACCCTTTGGTGAGCATTCACATGGG 3976 chr5ptel1M 608842 ACACAGACA-CGCTA-GTATTCTGACACCAATCCCATATTTGTAACCACA 608889 i i - vii - v i v -- v vv v vv v v C ERVL-B4#LTR/E 3975 ACACAAATATCTTCACGTTTTTTGCC--CATTCAGAGAGGTCTATCCACA 3928 chr5ptel1M 608890 ATTTTCTGCCCCAGACTTCCTTATCTCTTATCTTCCAGTCATGTTCCTTC 608939 vvii v i i i v iv i i C ERVL-B4#LTR/E 3927 TACCTCTTCCCCAAATTTCCTTGTCACCAATTTTCCAATCATGTTCCTTC 3878 chr5ptel1M 608940 CACATCCA-GACCA-CTAGT----TCATTGGCCACTGCCCATGAGTCAGT 608983 vi v- - i i----i v i i C ERVL-B4#LTR/E 3877 CAAGTCCCTGACCATCCAGCCAAACCATTGGCCACAGCCCATGAATCGGT 3828 chr5ptel1M 608984 AAACAAACG 608992 v i v C ERVL-B4#LTR/E 3827 ATATAATCG 3819 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.38 CpG sites = 33, Kimura (unadjusted) = 40.23 Transitions / transversions = 1.18 (33/28) Gap_init rate = 0.04 (7 / 200), avg. gap size = 1.43 (10 / 7) 426 31.82 5.66 4.26 chr5ptel1M 608824 609194 (390806) C HERVL66#LTR/ERVL (2631) 1698 1323 m_b233s701i2 9177 chr5ptel1M 608824 CATGAGCATCTACATGAAACACAGACACGCTAGTATTCTGACACCAA--- 608870 v i v vv iiv i v v - i i--- C HERVL66#LTR/E 1698 CATGAGCATCAACATGGAAAACAGTGATAATGGTAGTGTG-CGCCAGGAT 1650 chr5ptel1M 608871 TCCCATATTTGTAACCACAATTTTCTGCCCCAGACTTCCTTATCTCTTAT 608920 vv i vi-- vv v i v i i i ii iv C HERVL66#LTR/E 1649 TCAGATATCTTC--CCAGTATTGTTTTCCCCAAACCTCTTTATTCCCAAT 1602 chr5ptel1M 608921 CTTCCAGTCATGTTCCTT-CCA------CATCCAGACCACTAGTTCATTG 608963 ivv v ii - v - ------ iiviiv vi v C HERVL66#LTR/E 1601 TAACCATTTGT-TTCGTTGCCATTGGGGCATCCAGGTAGTAAGACCATTT 1553 chr5ptel1M 608964 GCCACTGCCCATGAGTCAGTAAACAAACGACACTGATTTCCTTT---TTC 609010 i v v ii v ii --- v i i ---i C HERVL66#LTR/E 1552 GCTACTGACCAAGAGTTGGTATACAAGTGACA---AATCCCTCTGGCCTC 1506 chr5ptel1M 609011 AGTCTGTATTGCTTGATAAGCAGCCATTAGTTAAGCCCACTGACTGTTTT 609060 vvi v v i iviii i i i v vi i i ii C HERVL66#LTR/E 1505 CTCCTGAATAGCTCGGAGGACGGCTACTAGTTCAGCCAGCTGGCTGCTCC 1456 chr5ptel1M 609061 GACCTTCTCCTGTAGCCTCCAGAACAG----TATTTTTAACTGGATTTAT 609106 v iii vi ----i vv ---- i v - C HERVL66#LTR/E 1455 CACCCCTTCCTTCA----TCAGAAATGCTTATGTTTTTAACAGGATT-AT 1411 chr5ptel1M 609107 ATGCTATTGCCTTCCAATATCTTTTGGAGCCTA----TGTACTTGGCTGA 609152 v i iv ii ---- iv i ---- i iv C HERVL66#LTR/E 1410 AAGCCACGGCCTTCCAGCATC----GGGTCCCACCAATGTATTTGGTGGA 1365 chr5ptel1M 609153 ACCGTCAGTAAACCAGGCATGGTCCTTTTGCTCTCTGGTTAG 609194 v i i v i vv v vv v C HERVL66#LTR/E 1364 TCCATCAGTAAACCAAGCATGTTTCTGATCCTCTGGGCTTAG 1323 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.47 CpG sites = 62, Kimura (unadjusted) = 42.43 Transitions / transversions = 1.22 (62/51) Gap_init rate = 0.06 (22 / 370), avg. gap size = 1.68 (37 / 22) 339 25.17 2.72 2.72 chr5ptel1M 609420 609566 (390434) C L1MC_orf2#LINE/L1 (3121) 173 27 m_b233s551i8 9178 chr5ptel1M 609420 CCTTTTACCTTTACTCTGTATATATGTGTCTGTATC----AAATGTGTTT 609465 ? i v ---- v v---- i v C L1MC_orf2#LIN 173 CCNTTTACTTTTAATCT----ATATGTGTCTTTATATTTAAAGTGGGTTT 128 chr5ptel1M 609466 CTTGTAAACAACATATTGTAGGATTCTGTTTTTTAATCTACTTTGTTATT 609515 i v v i ii i i i vi v C L1MC_orf2#LIN 127 CTTGTAGACAACATATAGTTGGGTCTTGTTTTTTGATCCACTCTGACAAT 78 chr5ptel1M 609516 TGCTTCCATTTTATGGGAGAGTTCATCCCATTCACACTCACAGTTATGAT 609565 iv vi v v v v vi i vv ? i i v v v C L1MC_orf2#LIN 77 CTCTGTCTTTTAATTGGTGTATTTAGACCATTNACATTTAAAGTGATTAT 28 chr5ptel1M 609566 T 609566 C L1MC_orf2#LIN 27 T 27 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 31.35 CpG sites = 16, Kimura (unadjusted) = 31.35 Transitions / transversions = 0.80 (16/20) Gap_init rate = 0.03 (5 / 146), avg. gap size = 1.60 (8 / 5) 366 23.74 0.00 2.54 chr5ptel1M 609448 609568 (390432) C L1MEh_5end#LINE/L1 (5) 2230 2113 m_b233s551i9 9178 chr5ptel1M 609448 TCTGTATCAAATGTGTTTCTTGTAAACAACATATTGTAGGATTCTGTTTT 609497 ? v i i i i i v i C L1MEh_5end#LI 2230 TNTGTTTTAAGTGTGTCTCTTGTAGACAGCATATTGTTGGATTTTGTTTT 2181 chr5ptel1M 609498 TTAATCTACTTTGTTATTTGCTTCCATTTTATGGGAGAGTTCATCCCATT 609547 ? i v i v? v iv vi v v v v i v C L1MEh_5end#LI 2180 TNAATCCAATCTGANAATCTCTGTCTTTTAATTGGTGAGTTTAACCCATT 2131 chr5ptel1M 609548 CACACTCACAGTTATGATTAC 609568 i i i --- i i C L1MEh_5end#LI 2130 TACATTTA---TTGTAATTAC 2113 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 29.96 CpG sites = 16, Kimura (unadjusted) = 29.96 Transitions / transversions = 1.33 (16/12) Gap_init rate = 0.03 (3 / 120), avg. gap size = 1.00 (3 / 3) 363 26.70 3.38 1.32 chr5ptel1M 609450 609597 (390403) C L1MEj_5end#LINE/L1 (7) 2153 2003 m_b233s551i10 9178 chr5ptel1M 609450 TGTATCAAATGTGTTTCTTGTAAACAACATATTGTAGGATTCTGTTTTTT 609499 v i i i v iv i i C L1MEj_5end#LI 2153 TGTTTTAAGTGTGTTTCTTGTAAACAGCATATAGCTGGGTTTTGTTTTTT 2104 chr5ptel1M 609500 AATCTACTTTGTTATTTGCTTCCATTTTATGGGAGAGTTCATCCCATTCA 609549 i i v i vi v iv vi v v i vi C L1MEj_5end#LI 2103 AACCCAATCTGACAGTCTCTGTCTTTTAATGGGAGAATTCAGTCCATTCA 2054 chr5ptel1M 609550 CACTCACAGTTATGAT-----TACCAGCTCTGTATTTCCCTCCATCCTAT 609594 i i vv v i i----- iv v i - - i i i C L1MEj_5end#LI 2053 CATTTAGTGTAACGACTGATATACTTGATTT-TA-TTCCTTCCATCTTAC 2006 chr5ptel1M 609595 TTT 609597 C L1MEj_5end#LI 2005 TTT 2003 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 32.76 CpG sites = 23, Kimura (unadjusted) = 33.82 Transitions / transversions = 1.44 (23/16) Gap_init rate = 0.02 (3 / 147), avg. gap size = 2.33 (7 / 3) 363 21.39 1.96 8.33 chr5ptel1M 609728 609829 (390171) C MIR#SINE/MIR (139) 123 28 m_b233s601i6 9179 chr5ptel1M 609728 CCGAGGCA-ATTGGGGTTAAGTGACTTGCCCAAGGTCACATAGCTAGGAA 609776 i - vv i i i ------ C MIR#SINE/MIR 123 CTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGC------ 80 chr5ptel1M 609777 ATAGTAAGTGTCTGAGTACAGATTTGAACTCGGGTCCTCCTGACTTCAG- 609825 - v v ivvi i i i ivv - i i - C MIR#SINE/MIR 79 -TAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGCAGT-CTGGCTCCAGA 32 chr5ptel1M 609826 GCCC 609829 C MIR#SINE/MIR 31 GCCC 28 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.04 CpG sites = 12, Kimura (unadjusted) = 25.47 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.09 (9 / 101), avg. gap size = 1.11 (10 / 9) 455 18.72 0.00 8.14 chr5ptel1M 609739 609831 (390169) C MIRc#SINE/MIR (153) 115 30 m_b233s601i7 9179 chr5ptel1M 609739 GGGGTTAAGTGACTTGCCCAAGGTCACATAGCTAGGAAATAGTAAGTGTC 609788 i i ------- v C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGC-------TAGTAAGTGGC 73 chr5ptel1M 609789 TGAGTACAGATTTGAACTCGGGTCCTCCTGACTTCAGGCCCAG 609831 v ivvi i i i i i i i i C MIRc#SINE/MIR 72 AGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAG 30 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 20.61 CpG sites = 12, Kimura (unadjusted) = 22.14 Transitions / transversions = 3.00 (12/4) Gap_init rate = 0.08 (7 / 92), avg. gap size = 1.00 (7 / 7) 12 24.17 4.55 0.00 chr5ptel1M 609890 609933 (390067) (TTTCC)n#Simple_repeat 1 46 (0) m_b233s252i7 9180 chr5ptel1M 609890 TTTCTTTTTCTTGCCTTT--TATCCAATTCTTCCCTTTTCTTTCCT 609933 i i v -- v vv i i i (TTTCC)n#Simp 1 TTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCT 46 Matrix = Unknown Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.02 (1 / 43), avg. gap size = 2.00 (2 / 1) 15 5.48 0.00 0.00 chr5ptel1M 610330 610348 (389652) (C)n#Simple_repeat 1 19 (0) m_b233s252i8 9181 chr5ptel1M 610330 CCCCCCCCCCCCCCCCGCC 610348 v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCC 19 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 223 22.92 0.00 0.00 chr5ptel1M 610762 610809 (389191) MIRb#SINE/MIR 193 240 (28) m_b233s601i8 9182 chr5ptel1M 610762 TGAGATTCTAGCTGTAAAGCACTTAGCACAGTGCTAGACACCTTGTAA 610809 vv ivv i iv i v v MIRb#SINE/MIR 193 TGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAA 240 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.70 CpG sites = 4, Kimura (unadjusted) = 27.36 Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 417 25.63 10.09 2.45 chr5ptel1M 612349 612576 (387424) C L1MC_orf2#LINE/L1 (1460) 1834 1590 m_b233s551i11 9183 chr5ptel1M 612349 ATGAGCATTAGACTATGTCAACAACTTATAAAGCATCTATTAATATGATA 612398 i ii i i v vvi v vvv i v C L1MC_orf2#LIN 1834 ATGGGTGTTGGATTTTGTCAAATGCTTTTTCTGCATCTATTGATATGATC 1785 chr5ptel1M 612399 ATGTGGCTAGT-------AGCTTTTTAAAA-AATATGATCATTTTCACTG 612440 ii vv ------- i v i vi-i i- i iv v i C L1MC_orf2#LIN 1784 ATGTGATTTTTCTTCTTTAGCCTGTTGATGTGATG-GATTACATTAATTG 1736 chr5ptel1M 612441 CTTTCCTAATGTTGAACCATCCTTACAT--TTGAGGTAATAAATTCAGCT 612488 v i v v i --i i --- i vi C L1MC_orf2#LIN 1735 ATTTTCGAATGTTGAACCAGCCTTGCATACCTGGG---ATAAATCCCACT 1689 chr5ptel1M 612489 TGTTCATGGTGAATAATTG----TACACATTGCTATAGAT----TTTCCT 612530 v i v v---- i i-- i ---- v C L1MC_orf2#LIN 1688 TGGTCGTGGTGTATAATTCTTTTTATACATTGT--TGGATTCGATTTGCT 1641 chr5ptel1M 612531 AATATTTTGTTTAAAATGATTGCAT-----TTCATGAGAAATAGTGATCT 612575 v ii vv ----- i v i C L1MC_orf2#LIN 1640 AATATTTTGTTGAGGATTTTTGCATCTATGTTCATGAGAGATATTGGTCT 1591 chr5ptel1M 612576 G 612576 C L1MC_orf2#LIN 1590 G 1590 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 31.25 CpG sites = 31, Kimura (unadjusted) = 31.91 Transitions / transversions = 1.19 (31/26) Gap_init rate = 0.05 (12 / 227), avg. gap size = 2.42 (29 / 12) 342 26.74 5.84 5.43 chr5ptel1M 612351 612607 (387393) C L1M4_orf2#LINE/L1 (1462) 1832 1575 m_b233s551i12 9183 chr5ptel1M 612351 GAGCATTAGACTATGTCAACAACTTATAAAGCATCTATTAATATGATAAT 612400 i ii i i v vvi v vvv i i v v C L1M4_orf2#LIN 1832 GGGTGTTGGATTTTGTCAAATGCTTTTTCTGCGTCTATTGAGATGATCAT 1783 chr5ptel1M 612401 GTGGCTAGTAGCTTTT---TAAAAAATATGAT-CATT---TTCACTGCTT 612443 i vv iv i ---iv vv i -i --- v i v C L1M4_orf2#LIN 1782 GTGGTTTTTGTCCTTTATTCTATTAATATGGTGTATTACATTGATTGATT 1733 chr5ptel1M 612444 TCCTAATGTTGAACCATCCTTACATTTGAGGTAATAAATTCAGCTTGTTC 612493 i v? v i ivv -i i vi v C L1M4_orf2#LIN 1732 TTCGNATGTTGAACCAACCTTGCATTCCTGG-GATAAATCCCACTTGGTC 1684 chr5ptel1M 612494 ATGGTGAATAA----TTGTACACATTGCTATAGAT----TTTCCTAATAT 612535 v ---- v i ii -- i ---- v i C L1M4_orf2#LIN 1683 ATGGTGTATAATCCTTTTTATATGTTGC--TGGATTCGGTTTGCTAGTAT 1636 chr5ptel1M 612536 TTTGTTTAAAATGATTGCATTTCATGAGAAATAGTGATCTGAGTGATATA 612585 v ii vv i -------- v v -- i v v C L1M4_orf2#LIN 1635 TTTGTTGAGGATTTTTGCATCT--------ATATTCA--TAAGGGATATT 1596 chr5ptel1M 612586 GGTGTGTAGGTTTTTTTTTCTT 612607 v - i C L1M4_orf2#LIN 1595 GGTCTGTA-GTTTTCTTTTCTT 1575 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 32.90 CpG sites = 31, Kimura (unadjusted) = 33.51 Transitions / transversions = 0.91 (31/34) Gap_init rate = 0.07 (19 / 256), avg. gap size = 1.53 (29 / 19) 132 40.51 1.97 1.38 chr5ptel1M 614104 614967 (385033) (AGAC)n#Simple_repeat 1 869 (0) m_b233s252i9 9184 chr5ptel1M 614104 AGA-AGA-AGACAGACATACAGACAGGCAAACAAATGGATAGGAAGACAA 614151 - - v i i i ii i iv i (AGAC)n#Simpl 1 AGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAG 50 chr5ptel1M 614152 ACAGGTAGATATTAAAG-CAAGCAGGGAACCAGACAGATGGAGAGACAGA 614200 ii i -v v - ii iv iv ii v (AGAC)n#Simpl 51 ACAGACAGACA-GACAGACAGACAGACAGACAGACAGACAGACAGACAGA 99 chr5ptel1M 614201 CAGACAGGCAGGCAGGCAAATCA-ATAGAGAGGCAGCCAGCCAGA-AGTT 614248 i i i i - - i v i v v - -v (AGAC)n#Simpl 100 CAGACAGACAGACAGACAGA-CAGACAGACAGACAGACAGACAGACAG-A 147 chr5ptel1M 614249 TAGGCAGGCAGGTAGGCCGGCAAATAGACAGGCAGCCAGACAGGTGGCTA 614298 i i i ii i v i i i i v iii vi (AGAC)n#Simpl 148 CAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACA 197 chr5ptel1M 614299 TGCAAGCAGGTGAATAAACCGACAAGTAGGCAGACAAAGAGAAAGGCAG- 614347 vi ii iiii i i v iii i i v v i - (AGAC)n#Simpl 198 GACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGA 247 chr5ptel1M 614348 CAGACAG-TTGGCAGGCAGGGGGATAGATAATCGGGCAGGCAGGGAGGCA 614396 -iv i i ivi i i iv i i i iv i (AGAC)n#Simpl 248 CAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACA 297 chr5ptel1M 614397 GGAAAATAGTCAGACAGGCAGACTGACGGGTAGACAAGCTGGTAGTTAGA 614446 iv i i v i v i ii ii v ii vi (AGAC)n#Simpl 298 GACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGA 347 chr5ptel1M 614447 TAGGCAGAGAAACAGAAGGGCAG-GAGACAGTTGGCTGGGTAGGAAG-GT 614494 i i v i vi i -v vii vii ii iv -vv (AGAC)n#Simpl 348 CAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACA 397 chr5ptel1M 614495 GAGGAGATAGACAATGAGGCAGGTGGAAAGGCAG--AGACAGACAGACAG 614542 -v i ivv i iii v i -- (AGAC)n#Simpl 398 GA-CAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAG 446 chr5ptel1M 614543 ACTGACTGGCAGATAGGCAGCAGAGGCAAACAGACAGGGAGGCAGACTGA 614592 v v i i i - v i i iv i v (AGAC)n#Simpl 447 ACAGACAGACAGACAGACAG-ACAGACAGACAGACAGACAGACAGACAGA 495 chr5ptel1M 614593 -TGAGTAGGCAAGCAGATAAACAGGTAGACAAACAGGCAGTC-GACAGAT 614640 -v -i i ii i i ii i i v - i (AGAC)n#Simpl 496 CAGA-CAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGAC 544 chr5ptel1M 614641 GGCTTGTTAGGGAGACAGGGAGATAGACAAACAGGCAGGCAGAAAGGCAG 614690 i viv vi iv iv i i i i v i (AGAC)n#Simpl 545 AGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAG 594 chr5ptel1M 614691 --AGACAAACAGACAAGA-AGGCAGGCAGATTGGCAGGTAGGCAGCCTGC 614737 -- i - - i i iv i ii i v v v (AGAC)n#Simpl 595 ACAGACAGACAGAC-AGACAGACAGACAGACAGACAGACAGACAGACAGA 643 chr5ptel1M 614738 CAGAAGGGTAGGCAGACAGGCAGGCAGACCAGGGCTTATGCAGACAAGTA 614787 vi ii i i i - - i -- vi iii (AGAC)n#Simpl 644 CAGACAGACAGACAGACAGACAGACAGA-CA-GAC--AGACAGACAGACA 689 chr5ptel1M 614788 GGTAGACAGACCTGAAAG-CAAACAGATAAGCAGACAGATGGAGAGACAG 614836 ii - v v - i i ii ii v (AGAC)n#Simpl 690 GACAGACAGA-CAGACAGACAGACAGACAGACAGACAGACAGACAGACAG 738 chr5ptel1M 614837 ACAGACAACCAGGCAGGCAGACAAACAGGCAGACAGACATCTAAGCAGTC 614886 iv i i i i vvi ii v (AGAC)n#Simpl 739 ACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGAC 788 chr5ptel1M 614887 AAAAAGCCAGGCAAACAGATAGCTGGGAAGACAAATATTTGGGAAGACAC 614936 i v v i i i vii iv i i vvii iv v (AGAC)n#Simpl 789 AGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAG 838 chr5ptel1M 614937 AAAGGCCGGCAGACACAGAGGCAGCTAGACA 614967 v i v i v v i vi (AGAC)n#Simpl 839 ACAGACAGACAGACAGACAGACAGACAGACA 869 Matrix = Unknown Transitions / transversions = 2.24 (175/78) Gap_init rate = 0.03 (27 / 863), avg. gap size = 1.07 (29 / 27) 18 32.95 0.00 0.00 chr5ptel1M 616140 616191 (383809) (CA)n#Simple_repeat 1 52 (0) m_b233s252i10 9185 chr5ptel1M 616140 CACACACATATGCATATGCACATACACACACGTGCAAACATACCCACACA 616189 i ii i ii i iii v i v (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 chr5ptel1M 616190 CA 616191 (CA)n#Simple_ 51 CA 52 Matrix = Unknown Transitions / transversions = 5.50 (11/2) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 32 19.25 0.00 0.00 chr5ptel1M 616818 616877 (383123) (A)n#Simple_repeat 1 60 (0) m_b233s252i11 9186 chr5ptel1M 616818 AAATAAAAAAATAAAAATTAAAAAAACAAAAAATAAAACAAAACAAACAA 616867 v v vv v v v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr5ptel1M 616868 ACAAAAAAAA 616877 v (A)n#Simple_r 51 AAAAAAAAAA 60 Matrix = Unknown Transitions / transversions = 0.00 (0/10) Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0) 40 22.64 0.00 2.06 chr5ptel1M 617423 617521 (382479) (CTTT)n#Simple_repeat 1 97 (0) m_b233s252i12 9187 chr5ptel1M 617423 CTTTCTTTCTTTTCTTATTTCTATCCTTCTTTCCTTTTATCTTTCCTTCT 617472 ii v v i i i v i (CTTT)n#Simpl 1 CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 50 chr5ptel1M 617473 TTACTTTCTTTCTTCCCTCCCTCCTTCCTTCCTTTTTCTTCTTACTTTC 617521 - i i i i i i i i - v (CTTT)n#Simpl 51 TT-CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT-TTCTTTCTTTC 97 Matrix = Unknown Transitions / transversions = 3.50 (14/4) Gap_init rate = 0.02 (2 / 98), avg. gap size = 1.00 (2 / 2) 181 27.28 11.57 3.05 chr5ptel1M 619955 620075 (379925) L2d2_3end#LINE/L2 416 546 (9) m_b233s601i9 9188 chr5ptel1M 619955 TGTGTCTTCTCTGACTA-TTAGAATGTAAGG-CGGTGAGAGCAGGG---G 619999 i v vv i -i v v- vv i ---i L2d2_3end#LIN 416 TATGTCTTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCA 465 chr5ptel1M 620000 TATCTTACCTTAC-TCTTTGTG----ACACCATGCTGAG-ACTGCGGCTT 620043 i --- - i----v vii iv - v i v L2d2_3end#LIN 466 TGTCTTA---TACTTCTTTGTATCCCCCACAGCGCCTAGCACAGTGCCTT 512 chr5ptel1M 620044 -CACGTA--AAGTGCTGGATAAATGATTCACTGAT 620075 - ii -- i i vi - iii L2d2_3end#LIN 513 GCACACAGTAGGCGCTCAATAAAT-ATTTGTTGAT 546 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.25 CpG sites = 19, Kimura (unadjusted) = 34.91 Transitions / transversions = 1.46 (19/13) Gap_init rate = 0.10 (12 / 120), avg. gap size = 1.50 (18 / 12) 241 36.26 0.00 5.81 chr5ptel1M 620121 620284 (379716) C L3b_3end#LINE/CR1 (807) 399 245 m_b233s601i11 9189 chr5ptel1M 620121 TCTAGTCTTTCCAGATTTGTTTCCATTCTGACTGTCATCATCCACTGTGT 620170 v v ivv vv i i v v-- vi i C L3b_3end#LINE 399 TCTAGTCTGTCGAGATCGTTTTGGATCCTGATTTTG--CATCCAACGTAT 352 chr5ptel1M 620171 TACATATTCCTCCAAGATCTGTGTCTTCTACAAATGAGGTTAGGATGCCA 620220 vvii iv v v - v i vii?i vv i - i v iv C L3b_3end#LINE 351 TAGCCGTCGCTCCCAGCT-TCTGCCACTNGCAAATTTGAT-AAGCTGCTT 304 chr5ptel1M 620221 TTTATGCCTTTATCCAGGCTATTGATGAAAACAAAACAAAACAGCAACAC 620270 iii ii i i ii ---- viv i -i v C L3b_3end#LINE 303 TCCGTATCTTCATCCAAGTCATTGAT----ACAAATTCAGACAG-GACAA 259 chr5ptel1M 620271 CACCAAAACCACAG 620284 vi iiv v C L3b_3end#LINE 258 GGCCAAGGACAGAG 245 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.70 CpG sites = 30, Kimura (unadjusted) = 51.17 Transitions / transversions = 1.15 (30/26) Gap_init rate = 0.06 (9 / 163), avg. gap size = 1.00 (9 / 9) 498 28.67 1.39 0.69 chr5ptel1M 620121 620264 (379736) C L3#LINE/CR1 (802) 3297 3153 m_b233s601i10 9189 chr5ptel1M 620121 TCTAGTCTTTCCAGATTTGTTTCCATTCTGACTGTCATCATCCACTGTGT 620170 i i v v i?v vv ii i v -i ?i i C L3#LINE/CR1 3297 TCCAGCCTGTCGAGATCNTTTTGAATCTTGATTCT-GTCATCCANCGTAT 3249 chr5ptel1M 620171 TACATATTCCTCCAAGATCTGTGTCTTCTACAAATGAGGTTAGGATGCCA 620220 vv i v v i v i vv i v v v C L3#LINE/CR1 3248 TAGCTATCCCTCCCAGCTTTGTGTCATCTGCAAATTTGATAAGCATGCCT 3199 chr5ptel1M 620221 TTTATGCCTTTATCCAGGCTATTGATGAAAACA--AAACAAAACAG 620264 i i i i ii i ii--i ii C L3#LINE/CR1 3198 TCTATGTCTTCATCCAAGTCATTGATAAAAATGTTGAACAGGACAG 3153 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.81 CpG sites = 25, Kimura (unadjusted) = 38.00 Transitions / transversions = 1.56 (25/16) Gap_init rate = 0.01 (2 / 143), avg. gap size = 1.50 (3 / 2) 208 20.93 0.00 0.00 chr5ptel1M 621178 621220 (378780) C L2d2_3end#LINE/L2 (0) 555 513 m_b233s601i12 9190 chr5ptel1M 621178 TCAGGTCAATTCCACAAGCATTTATTGAGTCCCTACTGTCTGC 621220 ii v v ii iv v C L2d2_3end#LIN 555 TCAAATCAAATCAACAAATATTTATTGAGCGCCTACTGTGTGC 513 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 21.83 CpG sites = 5, Kimura (unadjusted) = 24.84 Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 189 33.11 10.62 2.46 chr5ptel1M 621286 621511 (378489) C L2c_3end#LINE/L2 (223) 255 12 m_b233s601i14 9191 chr5ptel1M 621286 GGAAGTCAGAGGAAGGT----CAG-GAAAGTGGCATCTGATCTGTATTTG 621330 ii - i---- i - i i i v vi?i v C L2c_3end#LINE 255 GGGGGTCAG-GGAAGGCTTCCCGGAGGAGGTGACATCTGAGCTGAGNCTT 207 chr5ptel1M 621331 AAAGG--GAG-AGGGATTTTCTGGGAAGTGGAGAGCAGGAGGAGGAGTGC 621377 i -- - ii vv i--- i ii vi i i ii- C L2c_3end#LINE 206 GAAGGATGAGTAGGAGTTAGCC---AGGTGGAAGGAGGGGGGAAGAGCA- 161 chr5ptel1M 621378 TTCAAGGTGGAGG---CAGCAAGTAAAAAAGCATGGAG--ATGAGAGAGC 621422 v ii --- v iv i ?i -- v i i C L2c_3end#LINE 160 TTCCAGGCAGAGGGAACAGCATGTGCAAAGGCNCGGAGGCAGGAAAGAAC 111 chr5ptel1M 621423 CATTAT-TGTGTGAGGAAGAACAAAGGGGTCAGTTTGA--AAAGTAT-GT 621468 iiivii- v i v-i i?i v v i--ii i - C L2c_3end#LINE 110 TGCGGCGTGTTTGGGGAAT-GCAAGNAGTTCAGTGTGGCTGGAGCATAGT 62 chr5ptel1M 621469 ------GGAGGGAATCACTCACAATCATCCTGAAGAGG-AGACTGAGGCC 621511 ------ i viivvvivi v vv i - i v i C L2c_3end#LINE 61 GGGCGAGGAGGGGAGTGGAGGAGATGAGGCTGGAGAGGTAGGCAGGGGCC 12 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.90 CpG sites = 49, Kimura (unadjusted) = 47.55 Transitions / transversions = 2.04 (49/24) Gap_init rate = 0.08 (17 / 225), avg. gap size = 1.76 (30 / 17) 207 31.10 7.51 3.33 chr5ptel1M 621286 621458 (378542) C L2b_3end#LINE/L2 (214) 252 73 m_b233s601i13 9191 chr5ptel1M 621286 GGAAGTCAGAGGAAGGT----CAG-GAAAGTGGCATCTGATCTG-TATTT 621329 ii - i i---- i - i i i i v -v ii C L2b_3end#LINE 252 GGGGGTCAG-GGAGGGCTTCCCGGAGGAGGTGACATTTGAGCTGAGACCT 204 chr5ptel1M 621330 GAAAGG-GAG-AGGGATTTTCTGGGAAGTGGAGAGCAGGAGGAGGAGTGC 621377 i i- - ii vv i--- i i i vv i i - i - C L2b_3end#LINE 203 GAAGGATGAGTAGGAGTTGGCC---AGGCGAAGAGGTGGGGAAGG-GCG- 159 chr5ptel1M 621378 TTCAAGGTGGAGG---CAGCAAGTAAAAAAGCATGGAGATGAGAGAGCCA 621424 v ii --- ? iv i viv ii i ? vvv C L2b_3end#LINE 158 TTCCAGGCAGAGGGAACAGCANGTGCAAAGGCCCTGAGGCGGGAGNGAGC 109 chr5ptel1M 621425 TTATTGTGT--GAGGAAGAACAAAGGGGTCAGTTTG 621458 ? ivi -- v i i i i v C L2b_3end#LINE 108 NTGGCGTGTTCGAGGAACAGCAAGGAGGCCAGTGTG 73 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.29 CpG sites = 36, Kimura (unadjusted) = 43.88 Transitions / transversions = 2.25 (36/16) Gap_init rate = 0.08 (13 / 172), avg. gap size = 1.46 (19 / 13) 251 34.73 8.68 4.31 chr5ptel1M 621365 621698 (378302) C L2#LINE/L2 (0) 3082 2735 m_b233s601i15 9191 chr5ptel1M 621365 GGAGGAGGAGTGCTTCAAGGTGGAGG---CAGCAAGTAAAAAAGCATGGA 621411 i i i - v ii --- iv i viv C L2#LINE/L2 3082 GGGGGAAGAGCG-TTCCAGGCAGAGGGAACAGCAAGTGCAAAGGCCCTGA 3034 chr5ptel1M 621412 GATGAGAGAGCCATTATTGTGT--GAGGAAGAACAAAGGGGTCAGTTTGA 621459 ii i v ivvi ivi -- v i i i i v i C L2#LINE/L2 3033 GGCGGGAGCGTGCCTGGCGTGTTCGAGGAACAGCAAGGAGGCCAGTGTGG 2984 chr5ptel1M 621460 -------AAAGTATGTGGAGGGAATCACTCACA----ATCATCCTGAAGA 621498 -------ii iv i ii i -v v vii ---- v vviiii C L2#LINE/L2 2983 CTGGAGCGGAGTGAGCGAGGGGGA-GAGTGGTAGGAGATGAGGTCAGAGA 2935 chr5ptel1M 621499 GGAGACTGAGGCCC------TGTAGAGAAAGTCTTTAAAGGCCAGAGGAA 621542 vi v i v ------ i ----- i iv vv v C L2#LINE/L2 2934 GGTAACGGGGGACCAGATCATGTAGGG-----CCTTGTAGGCCATTGTAA 2890 chr5ptel1M 621543 GGAGTTTTCATTTTTGTCCCAGAGGCAAGAGGGGAA-TCACTGAAGCCTC 621591 -i vii i- i v - ii v -i i i vv i C L2#LINE/L2 2889 GGA-CTTTGGCTTTTA-CTCTGA-GTGAGATGGGAAGCCATTGGAGGGTT 2843 chr5ptel1M 621592 TGGTGCAGGGGAATGACCCAGTC--ACTGCCATATTTTAGGTATGTGATT 621639 v v i i viii -- --i ii iivivi v i C L2#LINE/L2 2842 TTGAGCAGAGGAGTGACATGATCTGACT--TACGTTTTAAAAGGATCACT 2795 chr5ptel1M 621640 G-GGCACCTG-G--GAGTCAATTCACTGGGGAAGGGGAAAGACTGGAGGA 621685 v- vv - -- -- vv ?i -i v iv i v C L2#LINE/L2 2794 CTGGCTGCTGTGTTGAG--AATAGACTGNAG-GGGGGCAAGGGTGGAAGC 2748 chr5ptel1M 621686 AAAGAGACCAGTT 621698 ii C L2#LINE/L2 2747 AGGGAGACCAGTT 2735 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.45 CpG sites = 68, Kimura (unadjusted) = 49.26 Transitions / transversions = 1.58 (68/43) Gap_init rate = 0.08 (25 / 333), avg. gap size = 1.76 (44 / 25) 442 30.57 10.00 1.85 chr5ptel1M 623171 623370 (376630) MIRc#SINE/MIR 17 232 (36) m_b233s601i16 9192 chr5ptel1M 623171 AATGGATGGAGTATTGGACT------CAGGAAGATGTGAATT-AAATTCT 623213 i vi i i ------ iv ii -i i i i MIRc#SINE/MIR 17 AGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCC 66 chr5ptel1M 623214 ACCTGAGACCCTTATGAACTAAAGGACTCTGG-CAAATTATTTAATTTCT 623262 iv vv v v iv i iviv ii - i i i ii MIRc#SINE/MIR 67 GGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCT 116 chr5ptel1M 623263 GTTTGCCTCAGTTTTCTCATGTGAAGAACAGGGATAATAA------CTCA 623306 v vv i v v i ii ------ i v MIRc#SINE/MIR 117 CTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCT 166 chr5ptel1M 623307 GTCT-CCTCAGATACTAGTTATGTGAGAATAGCAAATGATTTACTCTGTC 623355 i - v viv v -- i -- vv v v i v MIRc#SINE/MIR 167 GCCTACCTCACAGGGTTGT--TGTGAGGAT--CAAATGAGATAATGTATG 212 chr5ptel1M 623356 T-----CATTTTGTAAAATG 623370 ----- ii v MIRc#SINE/MIR 213 TGAAAGCGCTTTGTAAACTG 232 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.69 CpG sites = 34, Kimura (unadjusted) = 40.36 Transitions / transversions = 1.31 (34/26) Gap_init rate = 0.05 (10 / 199), avg. gap size = 2.40 (24 / 10) 285 33.42 12.39 1.54 chr5ptel1M 623473 623706 (376294) C L2#LINE/L2 (486) 2596 2338 m_b233s601i17 9191 chr5ptel1M 623473 TAGGGTATT-GAGAGAGAAAAGAGTCAAACATCAATCTGAAGTTACGGTC 623521 i i v- i i i iv v v ii i viv v C L2#LINE/L2 2596 TGGGGTGTGAGAGAAAGAGAGGAGTCAAGGATGACTCCAAGGTTTTTGGC 2547 chr5ptel1M 623522 CTTTGCAAAAGAGATGTTGGTGGTTTTACCAACAGAAATGGGAAACCTTG 623571 vv vv ii v v v v vii ii? v i i vvi C L2#LINE/L2 2546 CTGAGCAACTGGAAGGATGGAGTTGCCATTNACTGAGATGGGGAAGACTG 2497 chr5ptel1M 623572 GAGAAGAAGCAATGTTTGGTAGAAATGACC---AGTTCAT---------T 623609 vi i i i- ivi ii v i --- v--------- C L2#LINE/L2 2496 CGGGAGGAGCAG-GTTTGAGGGGGAAGATCAGGAGTTCAGTTTTGGACAT 2448 chr5ptel1M 623610 GTTGAGTTTGAA----TTATTGGAAGATATCC------AGATGCAGCATA 623649 i i----i --- i ------ iv vi C L2#LINE/L2 2447 GTTAAGTTTGAGATGCCTATT---AGACATCCAAGTGGAGATGTCGAGTA 2401 chr5ptel1M 623650 G--AATTGAAAATGCAGAACTGTA--TCATGGGTGAAGT-TGGGCTGGGC 623694 -- i i v i iiiv v -- v v i -i iv C L2#LINE/L2 2400 GGCAGTTGGATATACGAGTCTGGAGTTCAGGGGAGAGGTCCGGGCTGGAG 2351 chr5ptel1M 623695 ATA-GAGTTTGAG 623706 -i i i C L2#LINE/L2 2350 ATATAAATTTGGG 2338 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.92 CpG sites = 46, Kimura (unadjusted) = 46.41 Transitions / transversions = 1.48 (46/31) Gap_init rate = 0.06 (13 / 233), avg. gap size = 2.54 (33 / 13) 492 29.77 3.05 0.00 chr5ptel1M 624112 624242 (375758) MIRc#SINE/MIR 16 150 (118) m_b233s601i18 9193 chr5ptel1M 624112 CAGTGGGTGGAGTGCTAGGTCTAGAGTCAGGAAGATCTGTGTTCAAATTT 624161 ivi ii i iii i i v i i ii MIRc#SINE/MIR 16 CAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCC 65 chr5ptel1M 624162 GGCTTCTTACATTTTCTAATTGTGAGACCCTAGGCAAGTCACTTTAGGTC 624211 v vi vv i v ii v i i v vv MIRc#SINE/MIR 66 CGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 chr5ptel1M 624212 T----GTCTCAATTTTCTCCCTGGGAAAATGGGGA 624242 ---- i i i viiv v MIRc#SINE/MIR 116 TCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGA 150 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.21 CpG sites = 25, Kimura (unadjusted) = 39.54 Transitions / transversions = 1.79 (25/14) Gap_init rate = 0.01 (1 / 130), avg. gap size = 4.00 (4 / 1) 509 37.70 6.54 3.03 chr5ptel1M 624619 625321 (374679) C L2#LINE/L2 (247) 2835 2109 m_b233s601i19 9194 chr5ptel1M 624619 GAGGCAATGAGACTTTCAGATCTAAGCCTTAGGAAAGTTCTTTTGGCAGC 624668 - i v ivv v ii v ii ii iii ivi i v C L2#LINE/L2 2835 GAGG-AGTGACATGATCTGACTTACGTTTTAAAAGGATCACTCTGGCTGC 2787 chr5ptel1M 624669 TGTGTTGAGGCTAGATTGGAAAGAGAAGAGACCTGAAGCGGAGTAGA-CA 624717 iv i ? ii i ivi iviv i i - - C L2#LINE/L2 2786 TGTGTTGAGAATAGACTGNAGGGGGGCAAGGGTGGAAGCAGGG-AGACCA 2738 chr5ptel1M 624718 ATTAGCAAGTGATTATAGTAGTCAAAGATCAGAG-TGACCAGGGCCTATG 624766 i v i iv ii i -v iiv - iviv i-- C L2#LINE/L2 2737 GTTAGGAGGCTATTGCAGTAATC-CAGGCGAGAGATGATGGTGGCT--TG 2691 chr5ptel1M 624767 AAGCA--TTGGTGACTATGTGAATGAGGAGAAAGGAGTAGAAGT---AAA 624811 i v --v i vi viii iv - vi v i v ---i v C L2#LINE/L2 2690 GACCAGGGTGGTGGCAGTGGAGGTGGTGAG-AAGTGGTCGGATTCTGGAT 2642 chr5ptel1M 624812 AGACCTT-AAAGCAGAATTCTTAGGAACTTGA-AACTTATTAGAGTTATG 624859 v ii - i i iiivvi - i v-i ivv i vv iv C L2#LINE/L2 2641 ATATTTTGAAGGTAGAGCCGACAGG-ATTTGCTGATGGATTGGATGTGGG 2593 chr5ptel1M 624860 CAGAAAGAGGAAAAGTAGGATTTAGGAGAAATATAAAACTAGGAACCTTG 624909 vv vi i i vi ii iv vi v vi iii vvvii vi C L2#LINE/L2 2592 GTGTGAGAGAAAGAGAGGAGTCAAGGATGACTCCAAGGTTTTTGGCCTGA 2543 chr5ptel1M 624910 AAGGCTAGAAGGATGATGATTCCCTCTACAGAAGTAGGAAAGTTT---GG 624956 ivii i iv v v v i? v ii i i vi --- C L2#LINE/L2 2542 GCAACTGGAAGGATGGAGTTGCCATTNACTGAGATGGGGAAGACTGCGGG 2493 chr5ptel1M 624957 AGG---AGATTTGAGTGAGAAAGGAGCTATGACAAATTTCACTTAGGAAA 625003 --- i - i i ----- v vi i ivii v v C L2#LINE/L2 2492 AGGAGCAGGTTTGAG-GGGGAAG-----ATCAGGAGTTCAGTTTTGGACA 2449 chr5ptel1M 625004 TAGCAAATCTGAGA--CTTAATATGGATATCCAAGTGAAGGAGTCCAGTG 625051 ivi i i -- i v -- i i iv v i C L2#LINE/L2 2448 TGTTAAGTTTGAGATGCCTATTA--GACATCCAAGTGGAGATGTCGAGTA 2401 chr5ptel1M 625052 AACAGTTGTTAAAATGACATTGGAGTTCACAAAAACTAG---CAGACTTT 625098 ii vvv v i vvi viii i-- --- i i vv C L2#LINE/L2 2400 GGCAGTTGGATATACGAGTCTGGAGTTCAGGGGAG--AGGTCCGGGCTGG 2353 chr5ptel1M 625099 ACCTATTGATTTGGTGATCATC--TATATAGGTGAAATAATTGAACTCAT 625146 vv vi vii --i i --i v i vi C L2#LINE/L2 2352 AGATATAAATTTGGGAGTCATCAGCATATAGATG--GTATTTAAAGCCAT 2305 chr5ptel1M 625147 GGGAATA--------TAGCAAGGGAGCAAGTATTGAGAAGAAAGGTAAAC 625188 i v i--------i v ? ii i v v iii iv iv C L2#LINE/L2 2304 GAGACTGGATGAGATCACCNAGGGAGTGAGTGTAGATAGAGAAGAGAAGA 2255 chr5ptel1M 625189 TGTCCCAACATAGAGGACATGGGGAAACCTCC-ACTTAAGGAGAT----- 625232 v v iv iv - v v v -- - v v?i i ----- C L2#LINE/L2 2254 GGTCCAAGGACTGA-GCCCTGGGGCA--CTCCAACGTTNAGAGGTCGGGG 2208 chr5ptel1M 625233 AGATTGTGAG---TCA-CAAAAAGGAATTAGAA--AGCAGAC----AGAT 625272 viv ---i - iii v v -- i v ---- i C L2#LINE/L2 2207 AGATGAGGAGGAACCAGCAAAGGAGACTGAGAAGGAGCGGCCAGTGAGGT 2158 chr5ptel1M 625273 AGAATGAGAAGCAGGGAAGGTTAGCATCATGAAAACCAATAGAAAAAAG 625321 i v i v ii vv i ii v i i vv i C L2#LINE/L2 2157 AGGAGGAAAACCAGGAGAGTGTGGTGTCCTGGAAGCCAAGTGAAGAAAG 2109 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 53.97 CpG sites = 152, Kimura (unadjusted) = 55.62 Transitions / transversions = 1.45 (152/105) Gap_init rate = 0.06 (40 / 702), avg. gap size = 1.70 (68 / 40) 355 37.42 0.64 0.64 chr5ptel1M 625772 625927 (374073) L3#LINE/CR1 1744 1899 (2200) m_b233s601i20 9195 chr5ptel1M 625772 CTTGCCTTGCCTTAATAAGAATTTCATGTTTCTAAATGTGAAATTATCAA 625821 v iv i v v i vi v ii ivv v L3#LINE/CR1 1744 CTTGACTTGCCTTGCTGACAATTTCATCTCTCAGAAGGTAGAGGAAGCAA 1793 chr5ptel1M 625822 CAAAAGGTGATTCTACTGCAGATCTGAGTCCCACTAATATGGGGGAATTG 625871 i ii viv v vii ii i v iv i i v ii i L3#LINE/CR1 1794 CGAGGGGAACTGCTACTCTGGACTTAATTCTGACCAACAAGGAAGAACTG 1843 chr5ptel1M 625872 TTTGCTAGAGTAGAAATTCTTA-GAACAGTGTAAGGAAGTAACCACTTCC 625920 v v ii i i ivv - vv vi i -i iv v L3#LINE/CR1 1844 GTTGGTGAAGTGGAAGTCGATAGGAACCTTGGGAGAAAGT-GCCATGTCA 1892 chr5ptel1M 625921 TCCTAAA 625927 i i L3#LINE/CR1 1893 TCTTAGA 1899 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 51.23 CpG sites = 33, Kimura (unadjusted) = 53.96 Transitions / transversions = 1.32 (33/25) Gap_init rate = 0.01 (2 / 155), avg. gap size = 1.00 (2 / 2) 269 22.73 1.60 15.76 chr5ptel1M 625929 626116 (373884) C Charlie4a#DNA/hAT-Charlie (0) 508 344 m_b233s502i0 9196 chr5ptel1M 625929 CAGATGTTCTTAAATTCTTTT-TGTCATCTAAGCCCTTCGAAAATCTGGA 625977 iv vi i - i v-i v i iv i v C Charlie4a#DNA 508 CAGGGGTTCTTAACCTTTTTTGTGCCATG-GACCCCTTTGGCAGTCTGGT 460 chr5ptel1M 625978 AAAGCCCATCGATCCCTTGCCTGAGCAATATTTTTTTTTTTCCAGAGCAT 626027 i i v i -- v - ------------------ C Charlie4a#DNA 459 GAAGCCTATGGACCCCTT--CTCAG-AATA------------------AT 431 chr5ptel1M 626028 GATTTTTAAATGCACAACACAAATTAGTTTTCAAGATTTCAAAGGAAGTC 626077 - i v i v vv --- i v ii C Charlie4a#DNA 430 G-TTTTTAAATGCATAAAATAAAATACAT---AGGATTACAAAGGAAACC 385 chr5ptel1M 626078 AATTATATTGTAATCCTATAGTC-AAATA-TAAAAATTCAA 626116 v v vi vi - - v? C Charlie4a#DNA 384 AATTATATTGAAATACAGTTATCAAAATATTAAAAAANCAA 344 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 26.76 CpG sites = 18, Kimura (unadjusted) = 26.76 Transitions / transversions = 1.00 (18/18) Gap_init rate = 0.16 (29 / 187), avg. gap size = 1.00 (29 / 29) 196 23.32 0.00 10.26 chr5ptel1M 626254 626339 (373661) L3#LINE/CR1 2023 2100 (1999) m_b233s601i21 9195 chr5ptel1M 626254 AAAGATGGCCACTTAAGGAGAAATGGGAAAATCTCAAAACTGACATTCTG 626303 --- i - ii? iv i v v L3#LINE/CR1 2023 AAAGATGGC---TCAAG-AGGGNTGGGAAGCTCTTAAAAATGAAATTCTG 2068 chr5ptel1M 626304 AAAAACATAAGTACAACTGACTTCATTTATGAAAAA 626339 --- vi i v v - i v v v i L3#LINE/CR1 2069 ---ACTACAATTACAAATGA-TCCAATGAGGAAGAA 2100 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.25 CpG sites = 9, Kimura (unadjusted) = 28.25 Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.09 (8 / 85), avg. gap size = 1.00 (8 / 8) 221 21.43 0.00 0.00 chr5ptel1M 626395 626436 (373564) MIR3#SINE/MIR 166 207 (1) m_b233s601i22 9197 chr5ptel1M 626395 CTGAGGTCCCTTCCTACTCTGACATTTTGTAATTTTGTGACT 626436 i vi i i i i i i MIR3#SINE/MIR 166 CTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTATGATT 207 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.16 CpG sites = 8, Kimura (unadjusted) = 27.16 Transitions / transversions = 8.00 (8/1) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 222 36.14 1.73 5.38 chr5ptel1M 626434 626664 (373336) L3#LINE/CR1 2122 2344 (1755) m_b233s601i23 9195 chr5ptel1M 626434 ACTTATGTGGCTGTCTAGGGAAATCGCCAAATAAATACCTTACATTTTTG 626483 iv i ?iv i ? v v ii ----- i-- i v vi L3#LINE/CR1 2122 ACCAACGTGGCTNCATAGAGNATTCTCTGA-----TG--TCAGATTTTAA 2164 chr5ptel1M 626484 TAAGATAGATGTTAAACAATGGAAGTCATGGCAGGTAACAAAAGTGAGTA 626533 v i i vi i i i vi iv- v i vi v i vv ivi L3#LINE/CR1 2165 AAGGACATGTATCAGAAGATGGAAAG-AGGACATATAACCAAGGACAAAG 2213 chr5ptel1M 626534 TAATAATATGGCACCGTCCTATAATATTAATATCAGGAGTGTTAAAGCCC 626583 vi v i ?-- viv i v v i i iv i L3#LINE/CR1 2214 AGAGAGTAN--CACAAGCCTGTAAGAATAGTGTCAGGAAGGCTAAAGCCC 2261 chr5ptel1M 626584 AGAAGGAACTGAAGCTATTGATTAAA---GTAAAGAACAATAATATAGTT 626630 v i i vvii vv --- iv i i - v ?vv L3#LINE/CR1 2262 AGAATGAGCTGAGGCTTGCAAAAAAAAATGCTAAGGACAACAA-AAANAA 2310 chr5ptel1M 626631 AGCTATTTAAACTCTATATT-GACGAAAGAGGAAA 626664 i v i -v i - iv v ii L3#LINE/CR1 2311 GGCTTTTCAAA-GCTATGTTCGGAGCAGAAGGAAA 2344 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 51.14 CpG sites = 43, Kimura (unadjusted) = 52.10 Transitions / transversions = 1.19 (43/36) Gap_init rate = 0.06 (14 / 230), avg. gap size = 1.14 (16 / 14) 362 32.18 6.11 1.60 chr5ptel1M 626971 627150 (372850) L3#LINE/CR1 3095 3282 (817) m_b233s601i24 9195 chr5ptel1M 626971 TTGGTATTACCTTAAAGGAAGG-ATCCAGAGGCCTGAT-CAGAAATATG- 627017 i i i i v i ii i -v i v v vi- iiv v - L3#LINE/CR1 3095 TCGATGTCAACCTGGAGGGAGGTCTCTAGTGGCGTGCCACAGGGCTCTGT 3144 chr5ptel1M 627018 CCTTGATTTTTTTCCACTATACAT------CAGTGATTTTGATAAACACA 627061 iiii v i iii vv ------ i i v i v L3#LINE/CR1 3145 CCTTGGCCCTGTCCTGTTCAACATTTTTATCAATGACTTGGATGAAGACA 3194 chr5ptel1M 627062 AAAATAACATGAATATTGCATTTTCAAATAACAAAAAAGCTGGAAGGAAT 627111 v i vii vv iiv v i i v - i i L3#LINE/CR1 3195 TAGAAGGCATGCTTATCAAATTTGCAGATGACACAAA-GCTGGGAGGGAT 3243 chr5ptel1M 627112 AGCTAAAGCGCAATGTATGACAG--TCAACATACTAAAAGA 627150 vi --? v -- v v v ? L3#LINE/CR1 3244 AGCTAATACG--NTGGATGACAGAATCAAGATTCAAAANGA 3282 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.07 CpG sites = 33, Kimura (unadjusted) = 44.12 Transitions / transversions = 1.38 (33/24) Gap_init rate = 0.04 (8 / 179), avg. gap size = 1.75 (14 / 8) 345 33.77 6.36 3.08 chr5ptel1M 627394 627613 (372387) L3#LINE/CR1 3324 3550 (549) m_b233s601i25 9195 chr5ptel1M 627394 AATCTAATAAGGATATATATAAAATCATATACACAGATTCTAAAAATAAA 627443 i i i v i i v ii ivi i v v L3#LINE/CR1 3324 AATTTAACAGGGATAAATGTAAAGTCCTGCATTTAGGTTCAAAAAATCAA 3373 chr5ptel1M 627444 TTTCACAAGTTCATGGTAGAAGAGAGGTAGCTAGACTGTAGTATGTTGTT 627493 i v v v i i iii vv i vii v i - vvi v L3#LINE/CR1 3374 CTGCACAAGTACAGGATGGAGAGGATCTGGCTTAGCAGCAGT-TCACGTG 3422 chr5ptel1M 627494 TAAATGCTCTGGCAG---TAA------GTAAGCTC---ATGAATTATTAT 627531 v v vi i vi --- i------ i --- iii vi v L3#LINE/CR1 3423 AAAAAGACCTAGGGGTTTTAGTTGACCGCAAGCTCAATATGAGCCAACAG 3472 chr5ptel1M 627532 TGTATTGTGGTAGCCAAACTAAGCTAATCCAGGCTTGGACTATTTTAAGA 627581 iv iv v- v iv i i iiv v L3#LINE/CR1 3473 TGTGATGTGGCTGCCAAAA-AAGCTAATGCAATCTTAGGCTGCATTAATA 3521 chr5ptel1M 627582 TCATTGGATCATA-TATTCAGAG-AAGGAAGCTA 627613 ----- i vi - i i ?- i v L3#LINE/CR1 3522 -----GAAGTATAGTGTCCAGANCAAGGGAGGTA 3550 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.99 CpG sites = 42, Kimura (unadjusted) = 46.90 Transitions / transversions = 1.40 (42/30) Gap_init rate = 0.05 (12 / 219), avg. gap size = 1.75 (21 / 12) 343 23.66 4.30 0.00 chr5ptel1M 627581 627673 (372327) C MIR3#SINE/MIR (2) 206 110 m_b233s601i26 9198 chr5ptel1M 627581 ATCATTGGATCATATA--TTCAGAGAAGGAAGCTACCTCAAAGATCATTG 627628 v i v --v vv vv i i iv C MIR3#SINE/MIR 206 ATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCT 157 chr5ptel1M 627629 AGTCCATACCCATCATTTTACTAATGAAAAAACT--GGCCAAAAAAG 627673 vv v vi ii -- v i i C MIR3#SINE/MIR 156 AGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAG 110 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.47 CpG sites = 9, Kimura (unadjusted) = 28.47 Transitions / transversions = 0.69 (9/13) Gap_init rate = 0.02 (2 / 92), avg. gap size = 2.00 (4 / 2) 336 34.52 7.14 0.84 chr5ptel1M 627798 628133 (371867) CR1-3_Croc#LINE/CR1 2528 2884 (721) m_b233s551i13 9199 chr5ptel1M 627798 GGAGCTTATATTCTCTCTGTATT--ATGCTAGTCAGACCACAT-TGGAAT 627844 v v v vi v i --iii i i i v - i CR1-3_Croc#LI 2528 GGAGGTGATAGTGCCTCTCTACTCGGCACTGGTTAGGCCTCATCTGGAGT 2577 chr5ptel1M 627845 ATTATGTTGGGTTCTGGACACCATAGGTTAAGGAGGAAATGGAGAAGTTG 627894 i i vvi i v i vv ii vi i CR1-3_Croc#LI 2578 ACTGTGTGCAGTTCTGGGCTCCACATTTTAAAAAGGACGTGGAGAAGTTA 2627 chr5ptel1M 627895 GAGAATGTCTGGAAG-GGAAAACAAGAATAGTGATGGTTTTAAAATCCAT 627943 iv ii i - iv ii ii i v vi ii vv v CR1-3_Croc#LI 2628 GAGAGGGTCCAGAGGCGGGCAACAAAGATGATAAAGGGCTTGGAAGGCAA 2677 chr5ptel1M 627944 GT---------ATCAGTTGAAGGAACTGGAAATGTTTAACT---GGAGAA 627981 --------- vvi i i i iv i i --- i CR1-3_Croc#LI 2678 GTCATACGAGGAGAGGCTGAAGGAGCTAGGCATGTTCAGCTTGCGGAAAA 2727 chr5ptel1M 627982 GAC---TGA-AAGGGATATAATAATCATCTGAAATTATTAGAAGGGTTGA 628027 i --- i - i i i iivi vv v i v i v CR1-3_Croc#LI 2728 GGCGCTTAAGAGGGGACATGATAGCAGTCTTCAAATACTTGAAGGGCTGC 2777 chr5ptel1M 628028 TGTGAGAAAGA--GAAATCTCTGATCCTCTGTTAGGTTAAAGAGGGCAGA 628075 ii i ii -- v v ivv i v -- i iv i v i CR1-3_Croc#LI 2778 CATAAAGAAGAGGGAAAGCACCTTTTCTCTCTT--GCTGCAGAGAGGAGG 2825 chr5ptel1M 628076 A-GCAAAAGCAATGGA-TGGTTTTTTAAAGAAATAAATTTAGATTTGATA 628123 - -ii v v- ivv vi ivi i ii v CR1-3_Croc#LI 2826 ACGC-GGACCAATGGCTTGAAGTTGCAGCAAAGTAGGTTTAGATTGGATA 2874 chr5ptel1M 628124 CTAAGAAAAA 628133 iivi CR1-3_Croc#LI 2875 TCCGGAAAAA 2884 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 46.88 CpG sites = 72, Kimura (unadjusted) = 48.70 Transitions / transversions = 1.67 (72/43) Gap_init rate = 0.04 (13 / 335), avg. gap size = 2.08 (27 / 13) 466 30.05 6.10 0.58 chr5ptel1M 628152 628315 (371685) L3#LINE/CR1 3926 4098 (1) m_b233s601i27 9195 chr5ptel1M 628152 AAGTAGAATAGATTGGCTCTCATAGTAGTGAATTTCTCCTTATTGGAGGC 628201 i i i ii v v?ivi ii i i v i i i L3#LINE/CR1 3926 AAATGGAATGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGTCACTGGAGGT 3975 chr5ptel1M 628202 CTTCAATCAAAAACTGGGATGACCTTTTGTCATGTATGT----GA--GGA 628245 v v i ii - vi v v ---- -- L3#LINE/CR1 3976 GTTCAAGCAGAGGCT-GGATGACCACTTGTCAGGGATGTTGTAGAAGGGA 4024 chr5ptel1M 628246 TTCCTT--TCAGGT-ATATGTTGGACTTGATGGTTACCAA-GTTATATCC 628291 v-- ii i -iv v v iiiv i - iviv L3#LINE/CR1 4025 TTCCTGCATTGGATGGGAGGTTGGACTAGATGACCTCTAAGGTCCCTTCC 4074 chr5ptel1M 628292 AAATTTAAGATTTTGTGATTCTGT 628315 v i i i i L3#LINE/CR1 4075 AACTCTGAGATTCTGTGATTCTAT 4098 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.55 CpG sites = 32, Kimura (unadjusted) = 40.55 Transitions / transversions = 1.88 (32/17) Gap_init rate = 0.04 (6 / 163), avg. gap size = 1.83 (11 / 6) 32 3.23 0.00 0.00 chr5ptel1M 628421 628452 (371548) (AC)n#Simple_repeat 1 32 (0) c_b233s251i0 9200 chr5ptel1M 628421 ACACACACACACACACACACACATACACACAC 628452 i (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACAC 32 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 12 25.38 0.00 6.12 chr5ptel1M 628981 629032 (370968) (TAT)n#Simple_repeat 1 49 (0) m_b233s252i13 9201 chr5ptel1M 628981 TATAAATAATTTTATTGGCATTATTATTATTGACAGATTACTATTATTCA 629030 v v v v ivi - -vv i - (TAT)n#Simple 1 TATTATTATTATTATTATTATTATTATTATT-A-TTATTATTATTATT-A 47 chr5ptel1M 629031 TT 629032 (TAT)n#Simple 48 TT 49 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.00 (3 / 3) 512 33.42 11.93 1.49 chr5ptel1M 629107 629349 (370651) MIRc#SINE/MIR 1 268 (0) m_b233s601i28 9202 chr5ptel1M 629107 CAAGATAATGTAGAGTAGTGACTAGAGGGCTAGACTTGGATTCCAGAAAG 629156 i ii i i v i ivv vi i v vi ii MIRc#SINE/MIR 1 CGAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA 50 chr5ptel1M 629157 TATGAGTTCAGATATCATCTCTGACATTCACTAACTGGCTGACGTCAGAT 629206 iv i iii vi iv v i i i vv v ii ii MIRc#SINE/MIR 51 CCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGC 100 chr5ptel1M 629207 TA-TCTCTTA--TTCTTGGAGAATACTTCATTTTCCTCATATGT------ 629247 v - v --i iv ---- i v v ------ MIRc#SINE/MIR 101 AAGTCACTTAACCTCTCTGAG----CCTCAGTTTCCTCATCTGTAAAATG 146 chr5ptel1M 629248 -------------------TACTTATTTCATGGGGTTGCTATAAAGATCA 629278 ------------------- i i ii ii i i i i MIRc#SINE/MIR 147 GGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCA 196 chr5ptel1M 629279 AATTAGATAAATAATGT-AAAATGTTTTGTAAACTTTATAACTCTCTGGA 629327 v vvv - ii i v v iiv v iv MIRc#SINE/MIR 197 AATGAGATAATGTATGTGAAAGCGCTTTGTAAACTGTAAAGTGCTATACA 246 chr5ptel1M 629328 AATGCTAGATAATGTTAGCATT 629349 iv i?iv i vi MIRc#SINE/MIR 247 AATGTAAGGNGTTATTATTATT 268 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.54 CpG sites = 50, Kimura (unadjusted) = 46.77 Transitions / transversions = 1.67 (50/30) Gap_init rate = 0.04 (9 / 242), avg. gap size = 3.67 (33 / 9) 283 29.10 1.77 2.68 chr5ptel1M 629606 629718 (370282) C MIR1_Amn#SINE/MIR (65) 165 54 m_b234s601i1 9203 chr5ptel1M 629606 GTCA-TATCCTTTTCCAGTTCATTTTATAGACAAGGAAACTGAGGTATTT 629654 - v v ---i i ii i?ivv C MIR1_Amn#SINE 165 GTCAGTATCATTATCC---CCATTTTACAGATGAGGAAACTGAGGCNCAG 119 chr5ptel1M 629655 GGGGG-GGAGTGAGCTGTTCAGTGTCACACAGCTAGGAAGGATTTGAGGC 629703 i i -?i vi ii iv ? ?i v? viviv v C MIR1_Amn#SINE 118 AGAGGTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNAGTGGCAGAGCC 69 chr5ptel1M 629704 CATATTTGAATTCAG 629718 viv ? ? ii C MIR1_Amn#SINE 68 GGGANTNGAACCCAG 54 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 41.45 CpG sites = 19, Kimura (unadjusted) = 41.45 Transitions / transversions = 1.46 (19/13) Gap_init rate = 0.04 (5 / 112), avg. gap size = 1.00 (5 / 5) 299 28.30 3.70 12.75 chr5ptel1M 629625 629786 (370214) C MIRb#SINE/MIR (119) 149 1 m_b234s601i3 9203 chr5ptel1M 629625 CATTTTATAGACAAGGAAACTGAGGTATTTGGGGGGG---AGTGAGCTGT 629671 i ii i-- ii i i --- i vi i C MIRb#SINE/MIR 149 CATTTTACAGATGAGGAAACTGAGGC--TCAGAGAGGTTAAGTAACTTGC 102 chr5ptel1M 629672 TCAGTGTCACACAGCTAGGAAGGATTTGAGGCCATATTTGAATTCAGAAA 629721 i iv v viviv v viv i ii --- C MIRb#SINE/MIR 101 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAG--- 55 chr5ptel1M 629722 GAGCAGTCTTCTTTACTCCAAG---CGTGAAACTCCATGCATTATGGCAT 629768 ----- vii v i--- --- iv v i --- - C MIRb#SINE/MIR 54 -----GTCTGTCTGACTCCAAAGCCCGTG---CTCTTTCCACT---GCA- 17 chr5ptel1M 629769 ACCCAAGCTGCCCATGTG 629786 -- v v v C MIRb#SINE/MIR 16 --CCACGCTGCCCCTCTG 1 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 34.88 CpG sites = 24, Kimura (unadjusted) = 36.00 Transitions / transversions = 1.50 (24/16) Gap_init rate = 0.13 (21 / 161), avg. gap size = 1.19 (25 / 21) 346 27.68 2.52 8.93 chr5ptel1M 629625 629743 (370257) C MIRc#SINE/MIR (122) 146 35 m_b234s601i2 9203 chr5ptel1M 629625 CATTTTATAGACAAGGAAACTGAGGTATTTGGGGGGG---AGTGAGCTGT 629671 i ii i-- ii i i --- vi i C MIRc#SINE/MIR 146 CATTTTACAGATGAGGAAACTGAGGC--TCAGAGAGGTTAAGTGACTTGC 99 chr5ptel1M 629672 TCAGTGTCACACAGCTAGGAAGGATTTGAGGCCATATTTGAATTCAGAAA 629721 i iv v viviv v viv i i ii --- C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAG--- 52 chr5ptel1M 629722 GAGCAGTCTTCTTTACTCCAAG 629743 ----- i v C MIRc#SINE/MIR 51 -----GTCTTCCTGACTCCAAG 35 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 34.26 CpG sites = 20, Kimura (unadjusted) = 35.76 Transitions / transversions = 2.00 (20/10) Gap_init rate = 0.09 (11 / 118), avg. gap size = 1.18 (13 / 11) 16 15.87 8.16 0.00 chr5ptel1M 629964 630012 (369988) (TCTAAATC)n#Simple_repeat 1 53 (0) m_b234s252i1 9204 chr5ptel1M 629964 TCCAAATCTCTAAATCACT-AATCTC-AATTCACT-AGTCTC-AAGTCAC 630009 i v - - v v - i - i v (TCTAAATC)n#S 1 TCTAAATCTCTAAATCTCTAAATCTCTAAATCTCTAAATCTCTAAATCTC 50 chr5ptel1M 630010 TAA 630012 (TCTAAATC)n#S 51 TAA 53 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.08 (4 / 48), avg. gap size = 1.00 (4 / 4) 292 27.14 3.90 1.91 chr5ptel1M 631086 631239 (368761) L1MEj_5end#LINE/L1 2004 2160 (0) m_b234s551i0 9205 chr5ptel1M 631086 AAGTAGTATGGAAGGAAATAAAG---AGT-TAGTAATCATTACTCTGAAT 631131 iv - i--- - vi i i v i L1MEj_5end#LI 2004 AAGTAAGATGGAAGGAA-TAAAATCAAGTATATCAGTCGTTACACTAAAT 2052 chr5ptel1M 631132 GTGAATAGGAC-AAACTCTCCCATAAAACGGAAGCAAATATCAGTATGAA 631180 - -i i v v iv vi v i vv ii L1MEj_5end#LI 2053 GTGAAT-GGACTGAATTCTCCCATTAAAAGACAGAGACTGTCAGATTGGG 2101 chr5ptel1M 631181 TGAAAAGCTAGAATACTACAATATGTTGATTTA-AAGAAACAAATATGAA 631229 v ivi i iv vi v i - - v iv i L1MEj_5end#LI 2102 TTAAAAAACAAAACCCAGCTATATGCTG-TTTACAAGAAACACACTTAAA 2150 chr5ptel1M 631230 GCAGAGAGAT 631239 i i v L1MEj_5end#LI 2151 ACAAAGTGAT 2160 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 33.35 CpG sites = 23, Kimura (unadjusted) = 34.38 Transitions / transversions = 1.28 (23/18) Gap_init rate = 0.05 (7 / 153), avg. gap size = 1.29 (9 / 7) 229 27.20 7.38 1.27 chr5ptel1M 631355 631503 (368497) L1M5_orf2#LINE/L1 3123 3280 (14) m_b234s551i1 9206 chr5ptel1M 631355 AAAACATCTTTCTGACAAAGTCCTCATATACAG---------AGAACTGT 631395 ? v v vv i v --------- vi L1M5_orf2#LIN 3123 AANACATATATCTGACAAAGGACTCGTATCCAGAATATATAAAGAACTCC 3172 chr5ptel1M 631396 ATCAAATTTATAAGAATACAAGTCATTCA--CCAATTGATAAATTGTCAA 631443 vv ? iv ? -- v v vv -- v? v v v L1M5_orf2#LIN 3173 TACAANTCAATAANA--AAAAGACAAACAACCCAATANAAAAATGGGCAA 3220 chr5ptel1M 631444 AGGATTTGAATAGACAATTTATAGATGAAGAAACTAAAACCACCTATAAT 631493 i i i v i i i v v i?v ivi v v L1M5_orf2#LIN 3221 AAGACTTGAACAGACACTTCACAAAAGAAGATATNCAAATGGCCAATAAG 3270 chr5ptel1M 631494 AATGTAAAAA 631503 v ii i L1M5_orf2#LIN 3271 CACATGAAAA 3280 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 34.32 CpG sites = 15, Kimura (unadjusted) = 35.35 Transitions / transversions = 0.60 (15/25) Gap_init rate = 0.03 (4 / 148), avg. gap size = 3.25 (13 / 4) 957 32.13 2.99 0.73 chr5ptel1M 631375 631910 (368090) L1ME4a_3end#LINE/L1 7 554 (317) m_b234s551i2 9206 chr5ptel1M 631375 TCCTCA-TATACAGAGAACTGTATCAAATTTATAAGAATACAAGTCATTC 631423 i - i i i v vv iv v vi vvv iv L1ME4a_3end#L 7 TCCTTAATATATAAAGAGCTCTTACAAATCAATAAGAAAAAGACGAACAC 56 chr5ptel1M 631424 ACCAATTGATAAATTGTCAAAGGATTTGAATAGACAATTTATAGATGAAG 631473 v v v v v iv i i i i v L1ME4a_3end#L 57 CCCAATAGAAAAATGGGCAAAGGACATGAACAGACAATTCACAAAAGAAG 106 chr5ptel1M 631474 AAACTAAAACCACCTATAATAATGT-AAAAAATGTGCTAAATCACTATGG 631522 ivv ivi v vv i - ? v v vv vvi L1ME4a_3end#L 107 AAATACAAATGGCCAATAAACATATGAAAANATGTTCAACCTCACTAGTA 156 chr5ptel1M 631523 ATTAGAGAAACTCACATTACAAGAACTCTGGGGTACAACCTCAACCCTCT 631572 i i iv v v v vv i i v ii ivvv v L1ME4a_3end#L 157 ATCAAAGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCTAT 206 chr5ptel1M 631573 CAGATTGACAAAGATTACAGGAAAATT--TAATGATTAATGGTGTAGGGG 631620 i i vv -- i -- ivii i v vv i L1ME4a_3end#L 207 CAAATTGGCAAAGATTTAA--AAGATTGATAATACCCAGTGTTGGCGAGG 254 chr5ptel1M 631621 ATGGGGGAAATCTGGAACATTAAAGCATCGTTGGTGGAATTGTGAAAGGA 631670 i v ?i v v v vi v vi ii i i v i vv i L1ME4a_3end#L 255 GTGTGGNGAAACGGGCACTCTCATACACTGCTGGTGGGAGTGTAAATTGG 304 chr5ptel1M 631671 TCCAACCATTCTGGAGAGCAATTTGGAGCCATG-GCCAAAGGGCTGTAAA 631719 v v i vivi -ii i v - L1ME4a_3end#L 305 TACAACCTTTCTGGAGGGCAATTTGGCAATATGTATCAAAAGCCT-TAAA 353 chr5ptel1M 631720 ACTTTGTTTACCCTTTGATTCAGCAGTGTCACTACTGGGACTGTAACCTA 631769 v v ?iv ii i i vi v i v v v L1ME4a_3end#L 354 AATGTNCATACCCTTTGACCCAGTAATTCCACTTCTAGGAATTTATCCTA 403 chr5ptel1M 631770 AAGAGATCTTAAAAGAGGAGA--AAGGACCCAT--------ATGTTTGTA 631809 i i vv v i v v ?-- i iii -------- ii v L1ME4a_3end#L 404 AGGAAATAATCAGAGATGTGNACAAAGATTTATGTACAAGGATGTTCATC 453 chr5ptel1M 631810 GCAGCTATT-TTTGTGGTGGCAAGGAATTGGAAATTGAGTGCATGTCAAT 631858 - - i ii i i ii ivivv iv v v L1ME4a_3end#L 454 GCAGC-ATTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAA 502 chr5ptel1M 631859 TAACTGGTGAATGGCTGAGTAAGTTATAGTATGTGAATATAATGAAATAC 631908 i iv v ? i i i i i ii vv ? i i L1ME4a_3end#L 503 CAATAGGGGANTGGTTAAATAAATTATGGTACATCCATANAATGGAATAT 552 chr5ptel1M 631909 TA 631910 L1ME4a_3end#L 553 TA 554 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 42.96 CpG sites = 86, Kimura (unadjusted) = 43.29 Transitions / transversions = 1.01 (86/85) Gap_init rate = 0.02 (11 / 535), avg. gap size = 1.82 (20 / 11) 263 31.13 13.21 0.00 chr5ptel1M 633107 633212 (366788) MIRc#SINE/MIR 31 150 (118) m_b234s601i4 9207 chr5ptel1M 633107 TGACCTTGG---CTAAAAGACCTGTGTTCAAATATGAACTCTGAAATTTT 633153 iv --- vii v i i vivii vv i v MIRc#SINE/MIR 31 TGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTA 80 chr5ptel1M 633154 CTAATTGTGTGGCCTCAGG-----CACTT----TGTCT--GTCTCAATAT 633192 ii i ii ----- ---- v -- i i v MIRc#SINE/MIR 81 CTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTT 130 chr5ptel1M 633193 TCTCAATGGGAAAATGAAGA 633212 i viv v ii MIRc#SINE/MIR 131 CCTCATCTGTAAAATGGGGA 150 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 38.41 CpG sites = 20, Kimura (unadjusted) = 41.69 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.04 (4 / 105), avg. gap size = 3.50 (14 / 4) 264 29.35 11.96 0.00 chr5ptel1M 633121 633212 (366788) MIRb#SINE/MIR 51 153 (115) m_b234s601i5 9207 chr5ptel1M 633121 AGACCTGTGTTCAAATATGAACTCTGAAATTTTCTAATTGTGTGGCCTCA 633170 v i vivii vv i v ii i ii MIRb#SINE/MIR 51 AGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTG 100 chr5ptel1M 633171 GGC-----ACTT----TGTCT--GTCTCAATATTCTCAATGGGAAAATGA 633209 ----- ---- v -- i i v i viv v i MIRb#SINE/MIR 101 GGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGG 150 chr5ptel1M 633210 AGA 633212 i MIRb#SINE/MIR 151 GGA 153 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 34.79 CpG sites = 16, Kimura (unadjusted) = 38.33 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.03 (3 / 91), avg. gap size = 3.67 (11 / 3) 247 28.28 0.00 5.13 chr5ptel1M 633442 633523 (366477) C L2c_3end#LINE/L2 (390) 88 11 m_b234s601i6 9208 chr5ptel1M 633442 AGTAGTCCAGATTGTCTAGAACATAGAGTGGACAAAGGAGAATAATAGAG 633491 ? i vv v i i -- i i - iiv i i C L2c_3end#LINE 88 AGNAGTTCAGTGTGGCTGGAGCATAG--TGGGCGA-GGAGGGGAGTGGAG 42 chr5ptel1M 633492 GAAAATCACACTGAAGAGGTAGATAGGAACCA 633523 i - v vi i ii ii C L2c_3end#LINE 41 GAGA-TGAGGCTGGAGAGGTAGGCAGGGGCCA 11 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 35.99 CpG sites = 16, Kimura (unadjusted) = 38.25 Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.05 (4 / 81), avg. gap size = 1.00 (4 / 4) 385 37.71 7.24 2.43 chr5ptel1M 633719 634229 (365771) C L2#LINE/L2 (446) 2636 2102 m_b234s601i7 9208 chr5ptel1M 633719 TTGAAG-TAGAATTGAGGGGAACTGGAAAAATACTAGAGATAGGTAGGAA 633767 - iii vi vi vvi viv i i vi i vv vi C L2#LINE/L2 2636 TTGAAGGTAGAGCCGACAGGATTTGCTGATGGATTGGATGTGGGGTGTGA 2587 chr5ptel1M 633768 GAGGAAAAGTAGAATTTAGGAAAAACATAAGGCTAGGAACCTTGAAGGCT 633817 i i vi i iv vi vivi i vvvii viivii C L2#LINE/L2 2586 GAGAAAGAGAGGAGTCAAGGATGACTCCAAGGTTTTTGGCCTGAGCAACT 2537 chr5ptel1M 633818 AAAAGGATGATGATTCCCTCTACAGAAATAGGAAAGTTTGGAGGAGATTT 633867 ii iv v v v i? v i i i vi vi ivvi C L2#LINE/L2 2536 GGAAGGATGGAGTTGCCATTNACTGAGATGGGGAAGACTGCGGGAGGAGC 2487 chr5ptel1M 633868 AAGT--GAGAAAGAAACTATGACAAATTTCACTTAGGAAATAGCTAA-TC 633914 i -- iii i-- v vi i ivii v v - i - i C L2#LINE/L2 2486 AGGTTTGAGGGGGAAG--ATCAGGAGTTCAGTTTTGGACAT-GTTAAGTT 2440 chr5ptel1M 633915 TGAGATA--TAGTAAGAATATCCAAGTGGAGGTGTCCAATAGACAGTTGT 633962 i-- v i-- i i v i i v C L2#LINE/L2 2439 TGAGATGCCTATTAG--ACATCCAAGTGGAGATGTCGAGTAGGCAGTTGG 2392 chr5ptel1M 633963 CAGGATGAAATTGGAGTTCACAAAAACTAG---CATACTGTATCCACAGA 634009 vviv i ivi viii i-- --- ivi v vvi i i C L2#LINE/L2 2391 ATATACGAGTCTGGAGTTCAGGGGAG--AGGTCCGGGCTGGAGATATAAA 2344 chr5ptel1M 634010 TTTGGTGATCATC--TATATAGGTGAAATAATTGAACTCATGGTAGTA-- 634055 vii --i i --i v i vi iv v i-- C L2#LINE/L2 2343 TTTGGGAGTCATCAGCATATAGATG--GTATTTAAAGCCATGAGACTGGA 2296 chr5ptel1M 634056 ------TAGCAAGGGAGCAAGTACTGAGAAAAAAGGTAAGTTGATCC-AC 634098 ------i v ? ii iiv v i i iv -v i - v C L2#LINE/L2 2295 TGAGATCACCNAGGGAGTGAGTGTAGATAGAGAAGAGAAG-AGGTCCAAG 2247 chr5ptel1M 634099 AAGTGAGGATATGGGAAACCACTAC-TTAAG----CAGATAGATTGTGAG 634143 i v v-iv iv iv v - ? ---- i iv viv C L2#LINE/L2 2246 GACTGAGC-CCTGGGGCACTCCAACGTTNAGAGGTCGGGGAGATGAGGAG 2198 chr5ptel1M 634144 ---TCACAAAAAGAAATTGACAGAGATC--------AAATAGAATGAGAA 634182 ---i vv i i i v ii v -------- ii i v i C L2#LINE/L2 2197 GAACCAGCAAAGGAGACTGAGAAGGAGCGGCCAGTGAGGTAGGAGGAAAA 2148 chr5ptel1M 634183 CCAAGGAAGGTG-AGCATCATGAAAACCAAGGGAATGAAGAGGCTTCA 634229 - ii -i ii v i i v - iiv i C L2#LINE/L2 2147 CC-AGGAGAGTGTGGTGTCCTGGAAGCCAAGTGAA-GAAAGTGTTTCA 2102 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 53.70 CpG sites = 114, Kimura (unadjusted) = 55.97 Transitions / transversions = 1.54 (114/74) Gap_init rate = 0.05 (27 / 510), avg. gap size = 1.85 (50 / 27) 362 34.48 2.74 0.67 chr5ptel1M 634691 634836 (365164) L3#LINE/CR1 1751 1899 (2200) m_b234s601i8 9209 chr5ptel1M 634691 TGCCTTAATAAGAATTTCAGCT-TCATAAA--AGTGGAATTGTCAAAAGG 634737 iv i v v - v i-- v viiv i ii L3#LINE/CR1 1751 TGCCTTGCTGACAATTTCATCTCTCAGAAGGTAGAGGAAGCAACGAGGGG 1800 chr5ptel1M 634738 TGATTCTCTTCCAGATCTGAATCTGATTAATATGGAGGAACTGGTTGCTA 634787 viv v vi ii ii i v ii i v i v i L3#LINE/CR1 1801 AACTGCTACTCTGGACTTAATTCTGACCAACAAGGAAGAACTGGTTGGTG 1850 chr5ptel1M 634788 GAGTAAAAATT-ATTGAAACATCGCGAGGAAGTAACCACTTCCTCCTAGA 634836 i ii i i- v i v i v i -i iv v i L3#LINE/CR1 1851 AAGTGGAAGTCGATAGGAACCTTGGGAGAAAGT-GCCATGTCATCTTAGA 1899 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 45.75 CpG sites = 31, Kimura (unadjusted) = 48.49 Transitions / transversions = 1.63 (31/19) Gap_init rate = 0.03 (4 / 145), avg. gap size = 1.25 (5 / 4) 528 20.74 0.51 13.87 chr5ptel1M 634838 635033 (364967) C Charlie4a#DNA/hAT-Charlie (0) 508 336 m_b234s502i0 9210 chr5ptel1M 634838 CAGGAGTTCTTAACTTCTTTTTGTTATATAGAGCC-TTTGACAATCTGGT 634886 i i - vvi i v - i i C Charlie4a#DNA 508 CAGGGGTTCTTAACCT-TTTTTGTGCCATGGACCCCTTTGGCAGTCTGGT 460 chr5ptel1M 634887 GAAGCCAATGGGTCCCTTGCCTGGGCATTTTTTTTTTCCAGAGCATGATT 634936 v ii -- ---------------- ii vvi C Charlie4a#DNA 459 GAAGCCTATGGACCCCTT--CT----------------CAGAATAATGTT 428 chr5ptel1M 634937 TTTAAATGCACAACACAAATTAGTTTTCAAGATTTCAAAGGAAACCAGTT 634986 i v i v vv --- i v i C Charlie4a#DNA 427 TTTAAATGCATAAAATAAAATACAT---AGGATTACAAAGGAAACCAATT 381 chr5ptel1M 634987 ATATTTGAATACTATACTCAAAATATAAAATAAATTCAAATTCATGA 635033 vi vi vv v - -? ii C Charlie4a#DNA 380 ATATTGAAATACAGTTATCAAAATATTAAA-AAA-NCAAATTTGTGA 336 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 24.15 CpG sites = 19, Kimura (unadjusted) = 24.15 Transitions / transversions = 1.19 (19/16) Gap_init rate = 0.13 (25 / 195), avg. gap size = 1.00 (25 / 25) 184 20.51 0.00 0.00 chr5ptel1M 635168 635206 (364794) L3#LINE/CR1 2031 2069 (2030) m_b234s601i9 9209 chr5ptel1M 635168 CTAAGGAGAAGTGGGAAACTCTCAAAATTGAAATTATGA 635206 v i ii? i i v v L3#LINE/CR1 2031 CTCAAGAGGGNTGGGAAGCTCTTAAAAATGAAATTCTGA 2069 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 25.23 CpG sites = 5, Kimura (unadjusted) = 25.23 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 237 24.07 0.00 0.00 chr5ptel1M 635289 635342 (364658) L3#LINE/CR1 4045 4098 (1) m_b234s601i10 9211 chr5ptel1M 635289 TTGACCAAGAAGCCTACTAAGGTCCCTTCCCACTCTGACATTTTGTAATT 635338 iv v v v iv v v i i L3#LINE/CR1 4045 TTGGACTAGATGACCTCTAAGGTCCCTTCCAACTCTGAGATTCTGTGATT 4094 chr5ptel1M 635339 TTGT 635342 i i L3#LINE/CR1 4095 CTAT 4098 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 29.18 CpG sites = 6, Kimura (unadjusted) = 29.18 Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 246 32.99 0.00 2.13 chr5ptel1M 635853 635948 (364052) L3#LINE/CR1 2715 2808 (1291) m_b234s601i11 9209 chr5ptel1M 635853 AAAAGGGAGAAGTGACTCAAATCTCCACATTGTAGACCAAAGAGCTTGGT 635902 i iv - vi v v? v i ii iivi ii L3#LINE/CR1 2715 AAAAGGGAAAAAAGA-TGGATTCTGNAAACTACAGACCGGTAAGCTTGAC 2763 chr5ptel1M 635903 TTCCCTTTCTGACAAAATTCTAGAATTTGGCATTAAAGGAGATGGT 635948 v vv ii i i ivvivi -v L3#LINE/CR1 2764 GTCGATCCCCGGCAAAATTCTAGAACGGATTATTAAA-CAGATGGT 2808 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 38.04 CpG sites = 18, Kimura (unadjusted) = 45.62 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.02 (2 / 95), avg. gap size = 1.00 (2 / 2) 247 20.88 6.25 10.19 chr5ptel1M 635990 636101 (363899) CR1-3_Croc#LINE/CR1 1895 2002 (1603) m_b234s551i3 9212 chr5ptel1M 635990 AACTGCTCCTGCATGG-TCAGGGCAATGTGCCTGCAGATA----GTATTT 636034 i -- vi - v i v --- ii ---- i CR1-3_Croc#LI 1895 AACTACT--TGGGTGGATGAAGGGAATG---CTGTGGATATAGTGTATCT 1939 chr5ptel1M 636035 --ACTTCAGTTTTTGCAAGGCATTTCAGAAAGTACCTCATAGCATTCTCA 636082 -- ------ v v v i v v ii v CR1-3_Croc#LI 1940 GGACTTCAG------CAAGGCTTTTGACAAGGTCCCGCATGACCTTCTCA 1983 chr5ptel1M 636083 TAAAAAAAGAGGAGAAATG 636101 v vv CR1-3_Croc#LI 1984 TAAACAAATTGGAGAAATG 2002 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 24.40 CpG sites = 9, Kimura (unadjusted) = 24.40 Transitions / transversions = 0.75 (9/12) Gap_init rate = 0.13 (14 / 111), avg. gap size = 1.29 (18 / 14) 427 27.89 8.05 1.08 chr5ptel1M 636134 636307 (363693) L3#LINE/CR1 3105 3290 (809) m_b234s601i12 9209 chr5ptel1M 636134 CCTTAAAGGAAGAATCCAGAGGTCTGAC-CAGGAATATG-CCTTGGTTTT 636181 vi i i vv i v iv v - iv v - iii L3#LINE/CR1 3105 CCTGGAGGGAGGTCTCTAGTGGCGTGCCACAGGGCTCTGTCCTTGGCCCT 3154 chr5ptel1M 636182 TTCC-------CATATTCATCAGTGACTTGGAGAAATACAAACATGGCCT 636224 v ------- v i i vi v v v v v L3#LINE/CR1 3155 GTCCTGTTCAACATTTTTATCAATGACTTGGATGAAGACATAGAAGGCAT 3204 chr5ptel1M 636225 AAGTAGCA--TTTTCAAATGATAAAAAAGCTGGAAGGAATGGCTAAAGTA 636272 ivv v -- v i i v - i i i viii L3#LINE/CR1 3205 GCTTATCAAATTTGCAGATGACACAAA-GCTGGGAGGGATAGCTAATACG 3253 chr5ptel1M 636273 ATGTATGGCAG--TCAACATATCAAAA-GATCTTGATA 636307 ? v i -- v - - i i L3#LINE/CR1 3254 NTGGATGACAGAATCAAGAT-TCAAAANGATCTCGACA 3290 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 32.81 CpG sites = 24, Kimura (unadjusted) = 35.56 Transitions / transversions = 1.00 (24/24) Gap_init rate = 0.05 (8 / 173), avg. gap size = 2.00 (16 / 8) 276 35.53 6.04 1.05 chr5ptel1M 636559 636740 (363260) L3#LINE/CR1 3329 3519 (580) m_b234s601i13 9209 chr5ptel1M 636559 AATATGCATAAA-GTAAAAT---ACAC--AAATTCTAAAAATAAACTTGA 636602 i v v - i ---i i-- ii v v vv L3#LINE/CR1 3329 AACAGGGATAAATGTAAAGTCCTGCATTTAGGTTCAAAAAATCAACTGCA 3378 chr5ptel1M 636603 CAAGTACTTGGTAGAAGAGAGGTAGCTAGACCATAGT--ATGTTTTACAA 636650 vv i i iii vv i vii vii -- i vvv v i L3#LINE/CR1 3379 CAAGTACAGGATGGAGAGGATCTGGCTTAGCAGCAGTTCACGTGAAAAAG 3428 chr5ptel1M 636651 ACTCTGACAGTTTAAGGAGATAGTAAGC---ACATTAATCATCAGTGTAT 636697 - iivi v vv iv i --- i v ii v iv L3#LINE/CR1 3429 AC-CTAGGGGTTTTAGTTGACCGCAAGCTCAATATGAGCCAACAGTGTGA 3477 chr5ptel1M 636698 TGTGGCAGCCAAACTCAGTTAATATAATTTTGTGCTATCCTAA 636740 v v-v i ii i iv iivi L3#LINE/CR1 3478 TGTGGCTGCCAAAA-AAGCTAATGCAATCTTAGGCTGCATTAA 3519 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 48.55 CpG sites = 35, Kimura (unadjusted) = 49.65 Transitions / transversions = 1.21 (35/29) Gap_init rate = 0.04 (7 / 181), avg. gap size = 1.86 (13 / 7) 271 29.58 4.04 0.98 chr5ptel1M 636742 636840 (363160) C MIR3#SINE/MIR (2) 206 105 m_b234s601i14 9213 chr5ptel1M 636742 ATCATTGGATCATATA--TTCAGGGAAGGAAGCTACCTCAAAAGTCACTG 636789 v i v --v i vv vv i i ii iiv C MIR3#SINE/MIR 206 ATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCT 157 chr5ptel1M 636790 AGTCCATACCCATTATTTTACTAATGGAAAAAACT--AGCCTAGAAAGTG 636837 vv v i vi - ii --i i i vv C MIR3#SINE/MIR 156 AGTCCAACCCCCTCATTTTACAGAT-GAGGAAACTGAGGCCCAGAGAGGT 108 chr5ptel1M 636838 GAA 636840 C MIR3#SINE/MIR 107 GAA 105 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 38.21 CpG sites = 15, Kimura (unadjusted) = 38.21 Transitions / transversions = 1.07 (15/14) Gap_init rate = 0.03 (3 / 98), avg. gap size = 1.67 (5 / 3) 265 31.11 3.33 0.00 chr5ptel1M 636948 637037 (362963) CR1-L3A_Croc#LINE/CR1 3700 3792 (496) m_b234s551i4 9214 chr5ptel1M 636948 GAATAAGGAAGTTATATTCTCTCTGTATT--ATGCTGGTCTGATCACT-T 636994 i i i vi --iii vi i i -i CR1-L3A_Croc# 3700 GAGTAGGGAGGTTATATTACCTCTGTATTTGGCACTGGTGCGACCGCTAC 3749 chr5ptel1M 636995 TGAAATATTATGTTGGCTTCTGGACATCATAGGTTAAGGAGGA 637037 i i i iviv vvvi i ?v i i CR1-L3A_Croc# 3750 TGGAATACTGTGTCCAGTTCTGGTGTCCACANTTCAAGAAGGA 3792 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 39.50 CpG sites = 20, Kimura (unadjusted) = 43.71 Transitions / transversions = 2.50 (20/8) Gap_init rate = 0.02 (2 / 89), avg. gap size = 1.50 (3 / 2) 51 3.88 0.00 0.00 chr5ptel1M 637049 637101 (362899) (CA)n#Simple_repeat 1 53 (0) c_b234s251i1 9215 chr5ptel1M 637049 CACACACATACACACACACACACACACACACACACACACACACACACTCA 637098 i v (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 chr5ptel1M 637099 CAC 637101 (CA)n#Simple_ 51 CAC 53 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 17 16.26 0.00 2.78 chr5ptel1M 637626 637662 (362338) (ATT)n#Simple_repeat 1 36 (0) m_b234s252i2 9216 chr5ptel1M 637626 ATTATTATTATTGGCACCATTATTATTATTATTCATT 637662 ivi ii - (ATT)n#Simple 1 ATTATTATTATTATTATTATTATTATTATTATT-ATT 36 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 479 33.00 11.93 1.49 chr5ptel1M 637733 637975 (362025) MIRc#SINE/MIR 1 268 (0) m_b234s601i15 9217 chr5ptel1M 637733 CAAGATAAGGTAGAGTAGTGAATATAGGGCTAGATTTGGATTCCAGAAAG 637782 i ii iv i v i i v v vi i i v vi ii MIRc#SINE/MIR 1 CGAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA 50 chr5ptel1M 637783 TATGAGTTCAGATATCATCTCTGACATTCACTAGCTGTCTGACATCAGAT 637832 iv i iii vi iv v i i v v ii ii MIRc#SINE/MIR 51 CCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGC 100 chr5ptel1M 637833 TA-TCTCTTA--TTCTTGGAGAATACTTCATTTTCCTCATATGT------ 637873 v - v --i iv ---- i v v ------ MIRc#SINE/MIR 101 AAGTCACTTAACCTCTCTGAG----CCTCAGTTTCCTCATCTGTAAAATG 146 chr5ptel1M 637874 ----------TACTT---CT------TTCATAGGGTTGCTATAAATATCA 637904 ---------- i --- ------i i i i i iv MIRc#SINE/MIR 147 GGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCA 196 chr5ptel1M 637905 AATTAAATAAATAATGT-AAAATTCTTTGTAAACTTTATAACTCTCTGGA 637953 v i vvv - iiv v v iiv v iv MIRc#SINE/MIR 197 AATGAGATAATGTATGTGAAAGCGCTTTGTAAACTGTAAAGTGCTATACA 246 chr5ptel1M 637954 AATGCCAGATAATGTTAGCATT 637975 iv i?iv i vi MIRc#SINE/MIR 247 AATGTAAGGNGTTATTATTATT 268 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 42.40 CpG sites = 47, Kimura (unadjusted) = 45.52 Transitions / transversions = 1.47 (47/32) Gap_init rate = 0.05 (11 / 242), avg. gap size = 3.00 (33 / 11) 255 25.44 6.42 2.65 chr5ptel1M 638244 638352 (361648) C MIR1_Amn#SINE/MIR (65) 165 53 m_b234s601i16 9218 chr5ptel1M 638244 GTCA-TATCTTTTTCCAGTTCATTTTATAGAGGAGGACACTGAGATATAT 638292 - v v ---i i v v ii?i v C MIR1_Amn#SINE 165 GTCAGTATCATTATCC---CCATTTTACAGATGAGGAAACTGAGGCNCAG 119 chr5ptel1M 638293 GGGGG-GAAG-----TGTCCATTGTCACACAGCTAGGAAGGGTCTGAGGT 638336 i i -? ----- i vv ? ?i v? v v v vi C MIR1_Amn#SINE 118 AGAGGTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNAGTGGCAGAGCC 69 chr5ptel1M 638337 CATATTTGAATTCAGG 638352 viv ? ? ii C MIR1_Amn#SINE 68 GGGANTNGAACCCAGG 53 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 32.69 CpG sites = 13, Kimura (unadjusted) = 34.19 Transitions / transversions = 0.93 (13/14) Gap_init rate = 0.06 (6 / 108), avg. gap size = 1.67 (10 / 6) 297 23.19 6.78 8.62 chr5ptel1M 638263 638380 (361620) C MIR#SINE/MIR (120) 142 27 m_b234s601i17 9218 chr5ptel1M 638263 CATTTTATAGAGGAGGACACTGAGATATATGGGGGG--AAGT-----GTC 638305 i v v ii i - i i -- ----- i C MIR#SINE/MIR 142 CATTTTACAGATGAGGAAACTGAGGCACA-GAGAGGTTAAGTAACTTGCC 94 chr5ptel1M 638306 CATTGTCACACAGCTAGGAAGGGTCTGAGGTCATATTTGAATTCAGGAAG 638355 vv v v v v viviv i ii ---- C MIR#SINE/MIR 93 CAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAG---- 48 chr5ptel1M 638356 AGCAGTCTTCTTGACTCCAGA-CCTG 638380 - ---- i - i C MIR#SINE/MIR 47 -GCAGTC----TGGCTCCAGAGCCCG 27 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 24.33 CpG sites = 14, Kimura (unadjusted) = 28.10 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.11 (13 / 117), avg. gap size = 1.38 (18 / 13) 12 9.24 0.00 4.17 chr5ptel1M 638625 638649 (361351) (TCCC)n#Simple_repeat 1 24 (0) m_b234s252i3 9219 chr5ptel1M 638625 TCCCTCCCACCCTCCACCCCCTCCC 638649 v - i (TCCC)n#Simpl 1 TCCCTCCCTCCCTCC-CTCCCTCCC 24 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 1769 28.74 2.08 2.57 chr5ptel1M 638966 639590 (360410) C L1ME5_3end#LINE/L1 (313) 628 7 m_b234s551i5 9220 chr5ptel1M 638966 TTTCACTTAGCATCA-GTTCATGTAAT-TCCCTCCAAGCTTCTCTGTATT 639013 i ii - -- v v- v v i v v i v C L1ME5_3end#LI 628 TTTCACTCAGCACTATGTT--TTTAAGATCCATCCATGTTGCTATGTGTA 581 chr5ptel1M 639014 CATCTTGCTGGTCATTTCTTACAGAACAATAATGTTCCATAACATTCATA 639063 v iiv iii v v vvvv i ii iiii v v C L1ME5_3end#LI 580 CATCTAGTCCGTTGCTTCTAACTGCTGCATAGTACTCCATGGTGTGCATC 531 chr5ptel1M 639064 TACCACAATTTACCCAACCATTCTCCAATTGATGGGCATCCACTCAGTTT 639113 i v i v i v v i i vviv ii C L1ME5_3end#LI 530 CACCACATTTTACCTATCCACTCTCCCAGTGATGGACACCCAGGTTGCCT 481 chr5ptel1M 639114 CCAGCTTCTAGCCACTACAAACAGGGCTGCCACAAACATTTTGGCACATA 639163 i i iv i iv v ii ii v i - C L1ME5_3end#LI 480 CCAACTCCCCGCCACCACAAACAACGCTGCAATGAACATCCTCGTACAT- 432 chr5ptel1M 639164 CTGGTCCCTTTC----CCTTCTTTAGTATCTCCTTGGGATATAAGCCCAG 639209 --- i v---- viv v v i i vi C L1ME5_3end#LI 431 ---GTCCCCTTATGGACCTGTGTGAGAATTTCTTTGGGATATATACCCAG 385 chr5ptel1M 639210 TAGAAACACTGCTGGATCAAAGGGTATGCACAGTTTGAAAACTTTTTTGG 639259 v viiv i i v ii vvi v ------ i C L1ME5_3end#LI 384 GAGCGGAATTGCTGGGTCATAGGGTATGCGTATACTTAA------TTTGA 341 chr5ptel1M 639260 C---ATAATTCCAGATTGCTCTCCAGAATGGTTGGATTTGTTCACAGCTC 639306 ---i v v i v iiv ii vii C L1ME5_3end#LI 340 CTAAGTACTGCCAGATTGCTCTCCAGAATGGCTGCACCAGTCTACACTCC 291 chr5ptel1M 639307 CACCAACAATGTATCAGTGTCCCAGTTTTCCCACATCCCCTCCAACACTC 639356 i i i v v i vi ? i i v i C L1ME5_3end#LI 290 CACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATCCTCGCCAACACTT 241 chr5ptel1M 639357 ATCATTATTT--TTTCCTGTCATCTTAGCCAATCTGACAGGTGTGTAGTG 639404 iv ii--i i i-- i v i i i iv C L1ME5_3end#LI 240 GGCATTATCCAGCTTTCTA--ATTTTTGCCAGTCTAATAGGTGTAAAGTG 193 chr5ptel1M 639405 GTATCTCAGAGTTGTCTTAATTTGCATTTCTCTGATTAATAATGATTTGG 639454 i vv i v v v C L1ME5_3end#LI 192 ATATCTCATTGTTGTTTTAATTTGCATTTCTCTGATTACTAATGAGTTTG 143 chr5ptel1M 639455 AACACTCTTTCATATGAGTGGTAATGATTTCAGTTTCATCATCTGAAAAT 639504 i iiii vv v iivv ivi v v v C L1ME5_3end#LI 142 AGCATCTCTTCATATGCTTGTTAGCCTTTCGGGTTTCCTCTTCTGTAAAT 93 chr5ptel1M 639505 TGTCTGTTCATATCCTTTGACCATTTATCAATTGGAG--AATGGCTTGGT 639552 i v v v i --?vi v -- C L1ME5_3end#LI 92 TGCCTGTTCATATCCTTTGCCCATTTTTCTATTGGGGTTNCCGTCTT--T 45 chr5ptel1M 639553 TTCTTATAAATTAGAGTCAGCTCTCTATATATTTTGGA 639590 i vi v vivv i ii i i i C L1ME5_3end#LI 44 TTCTTGTTGATTTGCAGGAGTTCCTTGTATATTCTAGA 7 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.12 CpG sites = 98, Kimura (unadjusted) = 37.19 Transitions / transversions = 1.27 (98/77) Gap_init rate = 0.04 (22 / 624), avg. gap size = 1.32 (29 / 22) 5474 29.96 2.87 2.24 chr5ptel1M 639447 642683 (357317) C L1M5_orf2#LINE/L1 (0) 3294 38 m_b234s551i6 9220 chr5ptel1M 639447 TGATTTGGAACACTCTTTCATATGAGTGGTAATGATTTCAGTTTCATCAT 639496 ?v v i iii i vv iv iiiv v?i v v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr5ptel1M 639497 CTGAAAATTGTCTGTTCATATCCTTTGACCATTTATCAATTGGA--GAAT 639544 i vi v vi i v v ?v i-- vv C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTT 3195 chr5ptel1M 639545 GGCTTGGTTTCTTAT-AAATTAGAGTCAGCTCTCTATATATTTTGGAAAT 639593 v -- ? -i ? iv -v i i i v i C L1M5_orf2#LIN 3194 GTCTT--TTTNTTATTGANTTGTAG-GAGTTCTTTATATATTCTGGATAC 3148 chr5ptel1M 639594 GAGGCCTTTATCAGA-ACCTTTAACTGTGAAGATGTTTTCCCAGTTTGTG 639642 v i - iv v ?-i ii v v i ? i C L1M5_orf2#LIN 3147 GAGTCCTTTGTCAGATATATGTN-TTGCAAATATTTTCTCCCANTCTGTG 3099 chr5ptel1M 639643 -CTT-CCTTCTAATCTTGTTTACATTAGTTTTGTTTGTACAGAAGCTTTT 639690 - - i v i v v iv ivi vvv? vi i C L1M5_orf2#LIN 3098 GCTTGCCTTTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTTT 3049 chr5ptel1M 639691 TAATTTGATGTAATCAAA-------ATTTTCTATTTTGTGATCAATAATG 639733 v v ? i v ------- i v i i --- ?i C L1M5_orf2#LIN 3048 AATTTTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGGT---TNGTG 3002 chr5ptel1M 639734 GTCTCTAGTTCGTCTTTAGTCACAAATTTCTTCCTCTTCCACAAGTCTGA 639783 v i i ivv v v --- v i i v v?i - i vvi C L1M5_orf2#LIN 3001 CTTTTTGTGTCCTGTTTA---AGAAATCTTTGCCTANCCCA-AGGTCACG 2956 chr5ptel1M 639784 GAGATAAACTATCCTATGTT--CCTCCAATTTGTTTATAATCTCGTTCTT 639831 i --i v -- i i ivvvv i i ii?ii C L1M5_orf2#LIN 2955 AAGATA--TTCTCCTATGTTTTCTTCTAGAAGTTTTATAGTTTTANCTTT 2908 chr5ptel1M 639832 TATGTCTAAATC-ATGGACCCATTTTGATCTTCTCTTGGTATACGGTATT 639880 ii i ii - - i i ? vi vv i v i i i v C L1M5_orf2#LIN 2907 TACATTTAGGTCTATG-ATCCATCTNGAATTAATTTTTGTGTATGGTGTG 2859 chr5ptel1M 639881 AAGTGTGGGTCCATGCCTAATTTCTGCCATACTAATTTCCAGTTATCCCA 639930 i iv v v?iii v i v ivi v i i i C L1M5_orf2#LIN 2858 AGGTAGGGGTCGAGNTTCATTTTTTTCCATATGGATATCCAATTGTTCCA 2809 chr5ptel1M 639931 GCAGTTTTTGTCAAATAATGAATTTTTGTCCCA--AAAGTGAGGATCTTT 639978 viv ii v ivvv ii vi --i v ----- ? C L1M5_orf2#LIN 2808 GCACCATTTGTTGAAAAGACTATCCTTTCCCCACTGAATTG-----CNTT 2764 chr5ptel1M 639979 GGG---TTTGTCAAACACTAAATTGCTATAGTTGACTAT---TCTGTCTT 640022 v--- v ii ? v? i vv -- i --- i - C L1M5_orf2#LIN 2763 GGCACCTTTGTCAAAAATCAANTGNCCATATATG--TGTGGGTCTAT-TT 2717 chr5ptel1M 640023 GTGAAC---CTAACCTGTTCCACTGATCAACTAATCTATTTCTTA-GCCA 640068 v i --- vi i v i vi i- - C L1M5_orf2#LIN 2716 CTGGACTCTCTATTCTGTTCCATTGATCTATTTGTCTATC-CTTACGCCA 2668 chr5ptel1M 640069 ATACCAAATGGTTTTGGTGACTGCTGCTTTATAATATAGTTTT-AGATCA 640117 v iv i i v iv - i - ? ? C L1M5_orf2#LIN 2667 ATACCACACTGTCTTGATTACTGTAGCTTTATAATA-AGTCTTGANATCN 2619 chr5ptel1M 640118 GATACAGCTAGGCCACCTTCA--TTTGATTTT-TTTTTCATTAATTCTTT 640164 i vv - i i -- i -- v i - v-i v C L1M5_orf2#LIN 2618 GGTAGTG-TAAGTC--CTCCAACTTTGTTCTTCTTTTTCAA-GATTGTTT 2573 chr5ptel1M 640165 TGAG-ATTCTTGACCTTTTATTATTCCATATGAATTTTG---TTATTTTT 640210 iv- ? ii i iivv i i--- i vi v C L1M5_orf2#LIN 2572 TGGCTATTCTNGGTCCTTTGCATTTCCATATAAATTTTAGAATCAGCTTG 2523 chr5ptel1M 640211 TCTAGATCATTAAAATATTTTCTTGGAAGTCTGATTGGTATAGCACTAAG 640260 v vv vvi v vii vi i v i v v i i i C L1M5_orf2#LIN 2522 TCAATTTCTACAAAAAAACCTGCTGGGATTTTGATTGGGATTGCATTGAA 2473 chr5ptel1M 640261 TAAATAGATTAGTTTAGGGAGTATTGTCATCTTTATTATATTTGCTTGAC 640310 vv i i i v v ? iv viv ivv C L1M5_orf2#LIN 2472 TCTATAGATCAATTTGGGGAGAATTGACATCTTNACAATATTGAGTCTTC 2423 chr5ptel1M 640311 CTATCCAGGAGCACTTGATATTTTTCCAATTGTTTAAGTCTGTCTTTA-T 640359 v v i ivvv i i v i i - - C L1M5_orf2#LIN 2422 CAATCCATGAACATGGTATATCTCTCCATTTATTTAGGTCT-TCTTTAAT 2374 chr5ptel1M 640360 GTGTGTGGAAAGTTTTTTGTAATTTAGCTCA---TATAATTCCTGACTTT 640406 v v v viiv i v i --- --- ? iv i vviv C L1M5_orf2#LIN 2373 TTCTCTCAGCAATGTTTTGTAGTTT---TCAGTGTANAGGTCTTGCACAT 2327 chr5ptel1M 640407 CCTTTGGTAGATAAGATTCCCAAATATTTTATGCTGTC-GACAGTTATTC 640455 ?i v v-v i i ? i v i- i- i v C L1M5_orf2#LIN 2326 NTTTTGTTAGATT-TATTCCTAAGTATTTNATGTTTTTTGAT-GCTATTG 2279 chr5ptel1M 640456 TGAATGGAATTTCTCTTTGTATCTC---TTGCTGTTGGATTTTGTTGGTA 640502 i v vi i ?iv i --- v vi --- v C L1M5_orf2#LIN 2278 TAAATGGTATTGTTTTTNAAATTTCATTTTCCAATTG---TTTGTTGCTA 2232 chr5ptel1M 640503 ATGTATA-AAATGCTGAGGATTTATGGGGATTTATTTTATAACCTGCAAC 640551 i i - i vivv v viv v ii i v ? i C L1M5_orf2#LIN 2231 GTATATAGAAATACAATTGATTTTTGTATATTGACCTTGTATCCNGCGAC 2182 chr5ptel1M 640552 TTTGCTAAAGTTATGGATTATTTCAAATAGCTTTTTTGTAGAATCTCTAG 640601 i v i ivv v v i i ? v i ? C L1M5_orf2#LIN 2181 CTTGCTAAATTCACTTATTAGTTCTAGTAGTTTNTTTGTAGATTCTTTNG 2132 chr5ptel1M 640602 GGTTCTCTAAGTATACCATCATATCATCTGCAAAGAGTGATAGTTTGGTT 640651 i i v ? v i i v i? i vi C L1M5_orf2#LIN 2131 GATTTTCTACGTANACAATCATGTCATCTGCGAATAANGACAGTTTTATT 2082 chr5ptel1M 640652 TCTCACTGCCTATTCTG-ATTCCTTTAATCTCTTTCTCGACTCTTATTGC 640700 iv vi i v v- v v i i vvvi C L1M5_orf2#LIN 2081 TCTTCCTTTCCAATCTTTATGCCTTTTATTTCTTTTTCTTGCCTTATTGC 2032 chr5ptel1M 640701 CGAGGCTAGTGTTTCTAATACAAT-TTGAATAATAATGGTGACAGTGGGC 640749 vvv viii i i - iv i ? i i C L1M5_orf2#LIN 2031 ACTGGCTAGGACCTCCAGTACAATGTTGAATAGAAGTGGTGANAGCGGAC 1982 chr5ptel1M 640750 AACCTTGCTTCACTCCAGATCTTACTGGGAAAGATTCCAGTTTTTCCCTA 640799 v ii iii v vv v? i ? v i C L1M5_orf2#LIN 1981 ATCCTTGTCTTGTTCCCGATCTTAGGGGGAAAGCNTTCAGTNTTTCACCA 1932 chr5ptel1M 640800 TTGCATATGATGCTTACTGATGGTTTTAAATATATGCTCTTGACTATTTT 640849 ivi i ?i vv vvi v i v ii vv C L1M5_orf2#LIN 1931 TTAAGTATGATGTTNGCTGTAGGTTTTTCGTAGATGCCCTTTATCAGGTT 1882 chr5ptel1M 640850 AAGAAAAAGTCCATTTATTCCTATACTCTCAAGTGTTTTTATTAGGAATG 640899 i i ivvi v i vvi viii v i v C L1M5_orf2#LIN 1881 GAGGAAGTTCCCTTCTATTCCTAGTTTGCTGAGAGTTTTTATCATGAATG 1832 chr5ptel1M 640900 GATGTTGGATTTTATCAAATGCTTTTTCTGCATCTATTGAGATGATCATA 640949 i i i C L1M5_orf2#LIN 1831 GGTGTTGAATTTTGTCAAATGCTTTTTCTGCATCTATTGAGATGATCATA 1782 chr5ptel1M 640950 TGGTTTTTGTTAGTTTGCT-TATTGATATAGTCAATTATGCTAATAGTTT 640998 i v i-v ii - i i i v iii i v v C L1M5_orf2#LIN 1781 TGATTTTTCTC-CTTTATTCTGTTAATATGGTGAATTACATTGATTGATT 1733 chr5ptel1M 640999 TCCTAATATTGAACCAGCCCTGCATTCCTAGTATAAATCCTACGTGATCA 641048 i v i i i i i v i i v i C L1M5_orf2#LIN 1732 TTCGAATGTTAAACCAACCTTGCATTCCTGGGATAAACCCCACTTGGTCA 1683 chr5ptel1M 641049 TAGTATATTATCCTGGGGATGATTTTCTGTAATCTTTTTGGTAATATTTT 641098 ii i vvvv ivv v v v vv v C L1M5_orf2#LIN 1682 TGATGTATTATCCTTTTTATATATTGCTGGATTCGATTTGCTAATATTTT 1633 chr5ptel1M 641099 ATTTAAGATTTTAGCATTGATATTCATTAGAGAGATTGGTCTATAATTTT 641148 i ? i v iv i v i v i C L1M5_orf2#LIN 1632 GTTNAGGATTTTTGCATCTATGTTCATGAGGGATATTGGTCTGTAATTTT 1583 chr5ptel1M 641149 CTTTCTCTGT--TTTCAGCCTACCTGGTTTAGGTATCAGTACCATGTCTG 641196 iii -- v --ii ii ? v vii? iiv C L1M5_orf2#LIN 1582 CTTTTCTTGTAATGTC--TTTGTCNGGTTTTGGTATCAGGGTNATGCTGG 1535 chr5ptel1M 641197 TGTCGTAAAAGGAGTTTGGTAGGACTCCTTCAGTCCCTATTTT-TCAAAT 641245 iv i v v v vii i vv ii - vi v C L1M5_orf2#LIN 1534 CCTCATAAAATGAGTTGGGAAGTGTTCCCTCTTTTTCTATTTTCTGGAAG 1485 chr5ptel1M 641246 AGTTTATATAGCATTGGGGTTAATTGTTCTTTAAATGTTTGGTAGAATTC 641295 i i iv vi v v i C L1M5_orf2#LIN 1484 AGTTTGTGTAAGATTGGTATTATTTCTTCCTTAAATGTTTGGTAGAATTC 1435 chr5ptel1M 641296 ACATGTAAATCCATCTGGTCCTGGGGATTTTTTCTTAGGGAGTTGGTTAA 641345 vv i v v i v i iv i i v vv C L1M5_orf2#LIN 1434 ACCAGTGAAGCCATCTGGGCCTGGAGTTTTCTTTGTGGGAAGGTTTTTAA 1385 chr5ptel1M 641346 TAGCTTGTTCTATTTCTTTTTCTAAGATGGGACTGTTTAGGATATTTACT 641395 vi vvi v vvivi v i i i i iv v i i C L1M5_orf2#LIN 1384 TTACAAATTCAATTTCTTTAATAGATATAGGGCTATTCAGATTTTCTATT 1335 chr5ptel1M 641396 TCTTCCTCTGTTAATCTGGGCAAGCTATATTTTTGAAAGTATTCTTCCAT 641445 i v? i i i v i ?i i i v i v iv C L1M5_orf2#LIN 1334 TCTTCTTGNGTCAGTTTTGGTAANTTGTGTTTTTCAAGGAATTTGTCCAT 1285 chr5ptel1M 641446 TTCATTTAAGTTGTCGAATTTATTGCCATAAAGTTGGGCAAAATAATTCC 641495 i ? i v vv v v ii C L1M5_orf2#LIN 1284 TTCATCTAAGTTNTCAAATTTATTGGCATAAAGTTGTTCATAATATTCTC 1235 chr5ptel1M 641496 TAATTATTGCTCTAATTTCCTCTTCATTAGTGGCGGT-TCTCC-TTTTCA 641543 v ivi i v ivivvv iv i i i - - C L1M5_orf2#LIN 1234 TTATTATCCTTTTAATGTCTGTAGGATCTGTAGTGATGTCTCCTTTTTCA 1185 chr5ptel1M 641544 TT-TTAAGACTAACAATTTGATTTTCCTCT-TTCCTTTTTTAATCAGATT 641591 -i i v i iii vv i i - ii i i vi C L1M5_orf2#LIN 1184 TTCCTGATATTGGTAATTTGTGTCTTCTCTCTTTTTTTCTTGATCAGTCT 1135 chr5ptel1M 641592 TACTAAGGGTTTTGTCTATTTTGTTGG--TTTTCAGAGAACCAACTCTTA 641639 ?i ii - i v i i-- i i i i C L1M5_orf2#LIN 1134 NGCTAGAGG-TTTATCAATTTTATTGATCTTTTCAAAGAACCAGCTTTTG 1086 chr5ptel1M 641640 GTTTTATTAATTAATTCAATAGTTTTTTTACTTTCAATTTTATTGATCTC 641689 i ii i vvi v v ? ? ii v i i C L1M5_orf2#LIN 1085 GCTTCGTTGATTTTCTCTATTGTNTNTTTGTTTTCTATTTCATTGATTTC 1036 chr5ptel1M 641690 TCCTTTTATTTTTAGAATTTCAAGTTTAGTGTTTGACTGGGGGGTTTTAA 641739 v i i vv vvvii vv ii ?vi v --- C L1M5_orf2#LIN 1035 TGCTCTTATCTTTATTATTTCCTTCCTTCTACTTNCTTTGGG---TTTAA 989 chr5ptel1M 641740 TTTG---TTCCTTTTCTAGCATTTTTAGTTGCAAGCCC--TTCGTTGACC 641784 --- i v i v v v ii--v i ii C L1M5_orf2#LIN 988 TTTGCTCTTCTTTTTCTAGCTTCTTAAGGTGGAAGCTTAGATCATTGATT 939 chr5ptel1M 641785 TTCTCTTTCTCTACTTTATGCAA-GTAAGCCTCTAGAGATATAAAATTTC 641833 vvvii i v - vi -i ? v i i? v v i C L1M5_orf2#LIN 938 TTAAGCCTTTCTTCTTT-TCTAATATANGCATTTAANGCTATAAATTTCC 890 chr5ptel1M 641834 CCCTTATTACCGCTTTGGCTGCATCCCACACATTTTGATATGATGTCTCA 641883 i v vi i i v v v iv C L1M5_orf2#LIN 889 CTCTAAGCACTGCTTTAGCTGCATCCCACAAATTTTGATATGTTGTATTT 840 chr5ptel1M 641884 TTATTGTCATTTTCTTGGGTGAAGTTATTAATTATGTCTATGATTTGCTG 641933 i ? ivv viiviv v vi viv?i i vi v C L1M5_orf2#LIN 839 TCATTNTCATTCAGTTCAAAATATTTTCTAATTTCCNTTGTGATTTCTTC 790 chr5ptel1M 641934 TTTCACCCAGTCATTTTCTTTAGTATAGAGATTATTTAGTTT-CAATTAT 641982 v --iivv v v vv v - i i - v C L1M5_orf2#LIN 789 TTTGACCCA--TGGGTTATTTAGAAGTGTG-TTGTTTAATTTCCAAATAT 743 chr5ptel1M 641983 TTTTGGTCTACTTTCC--CTGGCTTTTTG---TTGAGTGTAATTTTTATT 642027 vv --- i i--? iv --- v viv v v C L1M5_orf2#LIN 742 TTGGGG---ATTTTCTAGNTATCTTTTTGTTATTGATTTCTAATTTAATT 696 chr5ptel1M 642028 GCACAATGGTCTCAAAAGGATGCATT---TACTATTTCTGCCTTACTGCA 642074 v ivi --- i i iii i --- iv vii i vi?iv C L1M5_orf2#LIN 695 CCATTGTGGTC---AGAGAACATACTCTGTATGATTTCAATCCTTTNAAA 649 chr5ptel1M 642075 TTTGAGTTTGAG----GTTTTATGTCTTAATATATGGTCTATTTTTGTAT 642120 i--- ---- v ii i? i v v C L1M5_orf2#LIN 648 TTTA---TTGAGACTTGTTTTATGGCCCAGNATATGGTCTATCTTGGTAA 602 chr5ptel1M 642121 AGGTTCCATGAACTGCTGAGAGGAAAGTGTA--CTACTTTCTGTCTCCAT 642168 v vi vvi i i v -- i ?v - - vvi C L1M5_orf2#LIN 601 ATGTTCCATGTGCACTTGAAAAGAATGTGTATTCTGCNGT-TGT-TGGGT 554 chr5ptel1M 642169 TTGGTTTTCTACAGAGATCTAGCATATCTAACT--TTTCTAGTATTCTAT 642216 v?i v i i vi v vi vi v ii -- vv i -- i C L1M5_orf2#LIN 553 GNAGTGTTCTATAAATGTCAATTAGGTCAAGTTGGTTGATAGTGT--TGT 506 chr5ptel1M 642217 TTACCTCTTTGAC-TTCTTGCTTATTCATTTTGTG-GTTTGATTTATCTA 642264 i vv iv i- i i v -- v-ii v i - C L1M5_orf2#LIN 505 TCAAATCTTCTATATCCTTACTGATT--TTTTGTCTACTTGTTCTATC-A 459 chr5ptel1M 642265 ATT-CT--GAGGTGCATGTCGGAGATCTCCCACTATTATAGTTTTGCTGT 642311 - -- iv ?i i-i i ? v v vvvvi C L1M5_orf2#LIN 458 ATTACTGAGAGAGGNGTGTT-AAAATCTCCNACTATAATTGTGGATTTGT 410 chr5ptel1M 642312 CTATTTCTTTTTGCAGCTCTCTTAATTTCTCTTTTAAGAATTTAGATGCT 642361 ii vi i v i i i vi i v v v v C L1M5_orf2#LIN 409 CTATTTCTCCTTTTAGTTCTGTCAGTTTTTGCTTCATGTATTTTGAAGCT 360 chr5ptel1M 642362 AAACCACTTGGTGCATATATTTTTAATATTGATATTGCTTCTTTATCTAT 642411 vviii i v i iv iv v vv v vv C L1M5_orf2#LIN 359 CTGTTATTAGGTGCATACACATTTAGGATTGTTATGTCTTCTTGATGAAT 310 chr5ptel1M 642412 GCTATCC-TTTAGCAAGATATAGTGCCCTTCCTTATCTCTTTTAATTAGA 642460 -iv i - v vv iv i i i i vv --- C L1M5_orf2#LIN 309 -TGACCCTTTTATCATTATGAAATGTCCCTCTTTATCTCTGGTAAT---A 264 chr5ptel1M 642461 TCAATTTTTGTTTT------TGCTTGATCTGAGATCAGGGTGGCTTCCCC 642504 --- i ii ------ i vi v i ivi i iv ? C L1M5_orf2#LIN 263 T---TTCTTGCCTTGAAGTCTACTTTGTCTGATATTAATATAGCCACNCC 217 chr5ptel1M 642505 TGCTTT-TTTGACTTCACCTGAAGCATAGTAGATTTTGCTCCATCCTTTT 642553 v - vi? viiv v-v i v i vi C L1M5_orf2#LIN 216 AGCTTTCTTTTGNTTAGTGTT-TGCATGGTATATCTTTTTCCATCCTTTT 168 chr5ptel1M 642554 ACCTTTATTCTGCATGTATCTCCCTGCTTCAGGTGTGTTTCCTGGAAACA 642603 i i vi ?iv i iiv ii v i i i i v i C L1M5_orf2#LIN 167 ACTTTCAACCTNTCTGTGTCTTTATATTTAAAGTGCGTCTCTTGTAGACA 118 chr5ptel1M 642604 ACATATTGTAGGATTCTGGCTTTTAATCCATTCTGCTAATCGCTTCCTCT 642653 i v v i ii vi v v vi v v i C L1M5_orf2#LIN 117 GCATATAGTTGGGTCTTGTTTTTTTATCCAGTCTGACAATCTCTGCCTTT 68 chr5ptel1M 642654 TTATGGGGGAGTTTACGCCATTCACATTTA 642683 v v i v v? i C L1M5_orf2#LIN 67 TAATTGGAGTGTTTAGNCCATTTACATTTA 38 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 39.49 CpG sites = 510, Kimura (unadjusted) = 39.99 Transitions / transversions = 1.16 (510/438) Gap_init rate = 0.04 (123 / 3236), avg. gap size = 1.35 (166 / 123) 379 27.20 6.52 2.08 chr5ptel1M 642571 642754 (357246) C L1MEj_5end#LINE/L1 (0) 2160 1969 m_b234s551i7 9220 chr5ptel1M 642571 ATCTCCCTGCTTCAGGTGTGTTTCCTGGAAACAACATATTGTAGGATTCT 642620 v ii i i i i v i v iv i i C L1MEj_5end#LI 2160 ATCACTTTGTTTTAAGTGTGTTTCTTGTAAACAGCATATAGCTGGGTTTT 2111 chr5ptel1M 642621 GGCTTTTAATCCATTCTGCTAATCGCTTCCTCTTTATGGGGGAGTTTACG 642670 vi i v vi i v vi i v i i i vv C L1MEj_5end#LI 2110 GTTTTTTAACCCAATCTGACAGTCTCTGTCTTTTAATGGGAGAATTCAGT 2061 chr5ptel1M 642671 CCATTCACATTTATGGTTAAAATGACCAAT---TCTG----TATTACTTG 642713 vv --- i ii ---ii ---- v - C L1MEj_5end#LI 2060 CCATTCACATTTAGTGT---AACGACTGATATACTTGATTTTATTCCTT- 2015 chr5ptel1M 642714 CCATCTTG--TTAACCCCTATTTA---TGCTTTTCTCCCTTCTTTC 642754 i-- vi?ii --- i i ?ii i C L1MEj_5end#LI 2014 CCATCTTACTTTATTNTTTATTTATTTTGTTTTTTTNTTTTTTTTC 1969 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 34.90 CpG sites = 33, Kimura (unadjusted) = 35.83 Transitions / transversions = 2.06 (33/16) Gap_init rate = 0.04 (8 / 183), avg. gap size = 2.00 (16 / 8) 438 26.57 2.10 0.00 chr5ptel1M 642581 642723 (357277) C L1M6_5end#LINE/L1 (10) 2505 2360 m_b234s551i8 9220 chr5ptel1M 642581 TTCAGGTGTGTTTCCTGGAAACAACATATTGTAGGATTCTGGCTTTTAAT 642630 i i i v i v v i vi i C L1M6_5end#LIN 2505 TTTAGGTGTGTCTCTTGTAAACAGCATATAGTTGGATTTTGTTTTTTAAC 2456 chr5ptel1M 642631 CCATTCTGCTAATCGCTTCCTCTTTATGGGGGAGTTTACGCCATTCACAT 642680 v vv i vi vi i v i vv i C L1M6_5end#LIN 2455 CCAATCTGAGAGTCTTTGTCTTTTAATAGGGGAGTTTAACCCATTTACAT 2406 chr5ptel1M 642681 TTATGGTTA-AAATGACCAATTCTGTATTA--CTTGCCATCTTGTT 642723 v i - v ivvi iv v --i i ?i C L1M6_5end#LIN 2405 TTATTGTCATAACTGATATGTTTGGTCTTATNTTTGTCATCTTNCT 2360 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 33.56 CpG sites = 20, Kimura (unadjusted) = 33.56 Transitions / transversions = 1.11 (20/18) Gap_init rate = 0.01 (2 / 142), avg. gap size = 1.50 (3 / 2) 16 26.93 2.86 2.86 chr5ptel1M 645018 645087 (354913) (AAGA)n#Simple_repeat 1 70 (0) m_b234s252i4 9221 chr5ptel1M 645018 AAGAAGGAAGAAAAAGGAA-AAACTGAGAAAGAAA-ACATAATGCAAGCA 645065 i - i i - vvi - v v v v - (AAGA)n#Simpl 1 AAGAAAGAA-AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG-A 48 chr5ptel1M 645066 AAGAACAACAGAAAGAGTGAAA 645087 vi v iv (AAGA)n#Simpl 49 AAGAAAGAAAGAAAGAAAGAAA 70 Matrix = Unknown Transitions / transversions = 0.67 (6/9) Gap_init rate = 0.06 (4 / 69), avg. gap size = 1.00 (4 / 4) 1053 28.42 5.92 3.33 chr5ptel1M 645276 645832 (354168) C L1MC5_3end#LINE/L1 (2066) 628 58 m_b234s551i9 9222 chr5ptel1M 645276 TTTCACTTAGCATCAGTAAAT---GTAGGTCTCTCCA-AGCA-TCTCT-G 645319 i ---i v --- v i v - - v v - C L1MC5_3end#LI 628 TTTCACTTAACA---ATATATCCTGGAGATCACTCCATAGCAGTATATAG 582 chr5ptel1M 645320 AAATCATCCTGCTGATTCCTTCTTAAAGAAAAATAGTATTCCATAGCATT 645369 i - i -- v i v vviv i v ii v C L1MC5_3end#LI 581 AGAT-ATTC--CTCATTCCTTTTTACAGCTGCATAGTACTCCATTGTGTG 535 chr5ptel1M 645370 CATATACTATAATTTATTCAGCTATTCTCTAATTGATGGATATCCACTCA 645419 v i i i i i v i iv i iiivviv C L1MC5_3end#LI 534 GATGTACCATAGTTTATTCAACCAGTCCCCTATTGATGGACATTTGGGTT 485 chr5ptel1M 645420 GTTTCCAGTTTCTTGCCACTACAAAGAGGGCTGCCACAAACATTTTTGCA 645469 i i i i v v v ii i vii ii C L1MC5_3end#LI 484 GTTTCCAGTCTTTTGCTATTACAAATAGTGCTGCAATGAATAGCCTTGTG 435 chr5ptel1M 645470 CATGTGGGTCCTTTTCCCTCCTTT---AAAATCTCTTTGGGATATAAGCT 645516 ii ---i vivii --- ivi v v vv i C L1MC5_3end#LI 434 CATACG---TCTTTTCGTATTTTTGCCAGTGTATCTTTGGGATAGATTCC 388 chr5ptel1M 645517 CAGTAGAAACAATGCTGGATTAAAGGGT--ATGCATAGTTTGATAACTTT 645564 i v viiv v i i -- --- - i C L1MC5_3end#LI 387 TAGAAGTGGGATTGCTGGGTCAAAGGGTAAATGCATA---TG-TAATTTT 342 chr5ptel1M 645565 TTGAGCATAGTTCCAAACTACTCTCCAGAATGTTTGGATCTGTTCATAGT 645614 viv - v v i v i v iv v v i vv iii v C L1MC5_3end#LI 341 GCTAG-ATATTGCCAAATTCCCCTCCATAGGGGTTGTACCATTTTGCATT 293 chr5ptel1M 645615 TCCACCAATAGTGTATCAGTGTCCCAGTTTTCCCGCATCCTCTCCAACAT 645664 i ii i v v v v i i v v - C L1MC5_3end#LI 292 CCCACCAGCAATGTATGAGAGTGCCTGTTTCCCCACAGCCTCGCCAACA- 244 chr5ptel1M 645665 TCATCATTATCTTTTC---CTGTC--ATCTTAGACAATCTGACAGGTGTA 645709 ----v v v v --- v i-- i v v i vi C L1MC5_3end#LI 243 ----GAGTATGTTGTCAAACTTTTGGATTTTTGCCAATCTGATAGGTGAG 198 chr5ptel1M 645710 CAGTGGTATCTCAGAGTTGTTTTAATTTACATTTCTCTAATCAATAGTGA 645759 v i v v i v i vv i C L1MC5_3end#LI 197 AAATGGTATCTCAGTGTAGTTTTAATTTGCATTTCTCTTATTATGAGCGA 148 chr5ptel1M 645760 -TTTGGAC-----TAGAAATG-TTA-----CA-----ATTTCTTCATCTG 645792 -v ii ----- vv v - ----- ----- iv C L1MC5_3end#LI 147 GGTTGAGCATCTTTTCATATGNTTAAGAGCCATTTGCATTTCTTTTTCTG 98 chr5ptel1M 645793 AAAATTGTCTGTTCATATCCTTTGACCATTTATCAACAGG 645832 vi i ii v v v v i C L1MC5_3end#LI 97 TGAACTGTCTGTTCATATCTCTAGCCCATTTTTCTATAGG 58 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 35.64 CpG sites = 78, Kimura (unadjusted) = 36.22 Transitions / transversions = 1.04 (78/75) Gap_init rate = 0.06 (32 / 556), avg. gap size = 1.62 (52 / 32) 1368 28.64 4.30 1.45 chr5ptel1M 645352 645886 (354114) C L1ME4c_3end#LINE/L1 (275) 555 6 m_b234s551i10 9222 chr5ptel1M 645352 ATAGTATTCCATAGCATTCATATACTATAATTTATTCAGCTATTCTCTAA 645401 i v vi ?v i i i i i i i iv C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chr5ptel1M 645402 TTGATGGATATCCACTCAGTTTCCAGTTTCTTGCCACTACAAAGAGGGCT 645451 v i ii vviv i i i i i i v iv C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCT 456 chr5ptel1M 645452 GCCACAAACATTTTTGCACATGTGGGTCCTTTTCCCTCCTTTAAA--ATC 645499 v ii i i ii i i -- i i i i -- i C L1ME4c_3end#L 455 GCAATGAACATCTTCGTGCATATAG--CTTTTTCCTTCTTTTGAATTATT 408 chr5ptel1M 645500 TCTTTGGGATATAAGCTCAGTAGAAACAATGCTGGATTAAAGGGTATGCA 645549 i i v vv i v viiv v i i i v C L1ME4c_3end#L 407 TCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAA 358 chr5ptel1M 645550 TAGTTTGATAACTTTTTGAGCATAGTTCCAAACTACTCTCCAGAATGTTT 645599 i v v ii i vivi i v v i i i i v v C L1ME4c_3end#L 357 CATTTTTATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTT 308 chr5ptel1M 645600 GGATCTGTTCATAGTTCCACCAATAGTGTATCAGTGTCCCAGTTTTCCCG 645649 v i vi i i ? v ii i v ? v iv C L1ME4c_3end#L 307 GTACCAATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCACCG 258 chr5ptel1M 645650 CATCCTCTCCAACATTCATCATTATCTTTTCCTGTCATCTTAGACAATCT 645699 ? v i vivi vv ii vvv i v vi i C L1ME4c_3end#L 257 CANCCTCGCCAGCATTGGGTATTATCAATTTTTTAAATTTTTGCTAATTT 208 chr5ptel1M 645700 GACAGGTGTACAGTGGTATCTCAGAGTTGTTTTAATTTACATTTCTCTAA 645749 i i i v i vv i i i i C L1ME4c_3end#L 207 AATAGGCGTAAAATGGTATCTCATTGTTGCTTTAATTTGCATTTCTTTGA 158 chr5ptel1M 645750 TCAATAGTGA-TTTGGAC-----TAGAAATG-----TTAC-A-----ATT 645782 i v i -v i ----- vv vi ----- - ----- C L1ME4c_3end#L 157 TTACTAGCGAGGTTGAACATTTTTCCATGTGTTTGTTTACTANTTGTATT 108 chr5ptel1M 645783 TCTTCATCTGAAAATTGTCTGTTCATATCCTTTGACCATTTATCAACAGG 645832 i v ? vi i v v iv C L1ME4c_3end#L 107 TCCTCTTNTGTGAATTGTCTGTTCATGTCCTTTGCCCATTTATCTATTGG 58 chr5ptel1M 645833 AGAATAGCTTGAAC----TATTATAAATTTGAGTCAATTCTCTCTATATT 645878 i ----v v?---- v v i v i-- i v C L1ME4c_3end#L 57 GG----TCTTGATNTTTTTCTTATCAATTTGAATGAG--CTCTTTATATA 14 chr5ptel1M 645879 TTAGAGAT 645886 ? ? C L1ME4c_3end#L 13 NTANAGAT 6 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.27 CpG sites = 89, Kimura (unadjusted) = 37.86 Transitions / transversions = 1.44 (89/62) Gap_init rate = 0.03 (15 / 534), avg. gap size = 2.07 (31 / 15) 287 29.75 2.42 2.42 chr5ptel1M 645779 645902 (354098) C L1P3_orf2#LINE/L1 (39) 3255 3132 m_b234s551i11 9222 chr5ptel1M 645779 AATTTCTTCATCTGAAAATTGTCTGTTCATATCCTTTGACCATTTATCAA 645828 v v i i v i v i v ii C L1P3_orf2#LIN 3255 AATGTCTTCTTTTGAGAAGTGTCTGTTCATATCCTTCGCCCACTTTTTGA 3206 chr5ptel1M 645829 CAGGAGAATAGCTTG---AACTATTATAAATTTGAGTCAATTCTCTCTAT 645875 ii ---i v i ---vvi v i vv v i ii v v C L1P3_orf2#LIN 3205 TGGG---GTTGTTTGTTTTTTTCTTGTAAATTTGTTTAAGTTCCTTGTAG 3159 chr5ptel1M 645876 ATTTTAGAGATGAGGACTTTATCAGAT 645902 i i v v vv i C L1P3_orf2#LIN 3158 ATTCTGGATATTAGCCCTTTGTCAGAT 3132 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 37.06 CpG sites = 18, Kimura (unadjusted) = 38.38 Transitions / transversions = 1.00 (18/18) Gap_init rate = 0.03 (4 / 123), avg. gap size = 1.50 (6 / 4) 269 29.99 4.64 0.64 chr5ptel1M 648325 648475 (351525) L1MEj_5end#LINE/L1 2004 2160 (0) m_b234s551i12 9223 chr5ptel1M 648325 AAATAGTATGGAAGGAAATAGAAAAAA-------AATCATTACTATAAAT 648367 i iv - i vv ------- i i vv L1MEj_5end#LI 2004 AAGTAAGATGGAAGGAA-TAAAATCAAGTATATCAGTCGTTACACTAAAT 2052 chr5ptel1M 648368 ATGAAAAGAATGAACTATCCCATAAAATGGAAGCAAATATCAGCATGGAT 648417 i vi v i v v v iv vi v i vv i L1MEj_5end#LI 2053 GTGAATGGACTGAATTCTCCCATTAAAAGACAGAGACTGTCAGATTGGGT 2102 chr5ptel1M 648418 AAAAAGCTAGAATATTACAATATGCTGATTATAAGAAACACATTTGAAGC 648467 v ivi i ivivi v v i i i i L1MEj_5end#LI 2103 TAAAAAACAAAACCCAGCTATATGCTGTTTACAAGAAACACACTTAAAAC 2152 chr5ptel1M 648468 AGAGAGAT 648475 i v L1MEj_5end#LI 2153 AAAGTGAT 2160 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 37.79 CpG sites = 23, Kimura (unadjusted) = 38.88 Transitions / transversions = 1.05 (23/22) Gap_init rate = 0.01 (2 / 150), avg. gap size = 4.00 (8 / 2) 238 32.42 3.85 0.00 chr5ptel1M 648352 648533 (351467) L1M5_orf2#LINE/L1 27 215 (3079) m_b234s551i13 9223 chr5ptel1M 648352 AATCATTACTATAAATATGAAAAGAATGAACTATCCCATAAAATGGAAGC 648401 v vv i i vi ?v i vv v v v v v L1M5_orf2#LIN 27 AATAATTACATTAAATGTAAATGGNCTAAACACTCCAATTAAAAGGCAGA 76 chr5ptel1M 648402 AAATATCAGCATGGATAAAAAGCTAGAATATTACAATATGCTGATTATAA 648451 i v i vv ivi ii iviv v vi i L1M5_orf2#LIN 77 GATTGTCAGACTGGATAAAAAAACAAGACCCAACTATATGCTGTCTACAA 126 chr5ptel1M 648452 GAAACACATTTGAAGCAGAGAGATACACATAGAGT-AAAGAGAAAGGCTA 648500 i i i v ii v i i v ? iv - vi v i L1M5_orf2#LIN 127 GAGACGCACTTTAAATATAAAGACACAGANAGGTTGAAAGTAAAAGGATG 176 chr5ptel1M 648501 GAGCAAAAT---CTATTTA---GCTGAAGAAAAGAAAGC 648533 iv i --- i vi ---i i ?v L1M5_orf2#LIN 177 GAAAAAGATATACCATGCAAACACTAANCAAAAGAAAGC 215 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 43.18 CpG sites = 30, Kimura (unadjusted) = 44.17 Transitions / transversions = 1.03 (30/29) Gap_init rate = 0.02 (3 / 181), avg. gap size = 2.33 (7 / 3) 341 28.16 7.17 1.27 chr5ptel1M 648534 648756 (351244) L1P3_orf2#LINE/L1 3050 3285 (9) m_b234s551i14 9223 chr5ptel1M 648534 AAAGTTTTTGCGAAAACAAAACCAAC-ATAACCA-AGGGAA--GGAAGCA 648579 i i i - v i vv - v i - v -- v i v L1P3_orf2#LIN 3050 AGAGCTTCTGC-ACAGCAAAAGAAACTATCATCAGAGTGAACAGGCAACC 3098 chr5ptel1M 648580 GAAAGA-TGGGAAAACATTTTTACAGGCAATGTTTTTGATAAAGTCCTCA 648628 v v - i v i iv v viv i i vv v L1P3_orf2#LIN 3099 TACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAAAGGGCTAA 3148 chr5ptel1M 648629 TATACAGAA---------AACTGAATCAAATTTATAAGAATACAAGTCAT 648669 v --------- v v i v v -- v L1P3_orf2#LIN 3149 TATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAAAAAA--CAA 3196 chr5ptel1M 648670 TCA--CCAATTGACAAATGGTCAAAGGATATGAATGGACAATTTACAGAT 648717 v -- v ii v i v i ii v iv i v L1P3_orf2#LIN 3197 ACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTTCTCAAAA 3246 chr5ptel1M 648718 GAAGAAATTGAAACCATCTATAATCATATGAAAAAATGC 648756 v v vi vii v i v v L1P3_orf2#LIN 3247 GAAGACATTTATGCGGCCAACAAACATATGAAAAAAAGC 3285 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 34.74 CpG sites = 25, Kimura (unadjusted) = 35.41 Transitions / transversions = 0.68 (25/37) Gap_init rate = 0.04 (9 / 222), avg. gap size = 2.11 (19 / 9) 379 24.97 7.73 2.63 chr5ptel1M 648585 648765 (351235) L1PREC2_orf2#LINE/L1 3105 3294 (0) m_b234s551i15 9223 chr5ptel1M 648585 ATGGGAAAACATTTTTACAGGCAATGTTTTTGATAAAGTCCTCATATACA 648634 i v ? i ii v iv i i vi v v L1PREC2_orf2# 3105 ATGGGAGAAAATNTTTGCAAACTATGCATCTGACAAAGGTCTAATATCCA 3154 chr5ptel1M 648635 GAA---------AACTGAATCAAATTTATAAGAATACAAGTCATTCA--C 648673 v --------- v v i v v -- vv -- L1PREC2_orf2# 3155 GCATCTATAAGGAACTTAAACAAATTTACAAGAAAAAAA--CAAACAACC 3202 chr5ptel1M 648674 CAATTGACAAATGGTCAAAGGATATGAATGGACAATTTACAGATGAAGAA 648723 v i v i v i ii v v i v v L1PREC2_orf2# 3203 CCATTAAAAAGTGGGCAAAGGACATGAACAGACACTTTTCAAAAGAAGAC 3252 chr5ptel1M 648724 AT---TGAAACCATCTATAATCATATGAAAAAATGCACTAAATCA 648765 --- vii --- i v v v v v L1PREC2_orf2# 3253 ATACATGCGGCCA---ACAAGCATATGAAAAAAAGCTCAACATCA 3294 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 29.89 CpG sites = 18, Kimura (unadjusted) = 30.68 Transitions / transversions = 0.69 (18/26) Gap_init rate = 0.04 (8 / 180), avg. gap size = 2.38 (19 / 8) 1043 30.72 3.63 2.51 chr5ptel1M 648628 649178 (350822) L1ME3G_3end#LINE/L1 13 569 (355) m_b234s551i16 9223 chr5ptel1M 648628 ATATACAGAAAACTGAATCAAATTTATAAGAATACAAGTCATTCACCAAT 648677 i i i vvvv iv --v v vi -- L1ME3G_3end#L 13 ATATATAAAGAACTCCTACAAATCAATAAGAA--AAAGACAACC--CAAT 58 chr5ptel1M 648678 TGACAAATGGTCAAAGGATATGAATGGACAATTTACAGATGAAGAAATTG 648727 v v v ii i i v i vv L1ME3G_3end#L 59 AGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGGAAATAC 108 chr5ptel1M 648728 AAACCATCTATAATCATATGAAAAAATGCACTAAATCACTATTAATTAGA 648777 ivii v v i v v vv v i i L1ME3G_3end#L 109 AAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTAATCAGG 158 chr5ptel1M 648778 AAAATTCAAATTACAAGAATTCTGAGGTATAACCTCAAATCTCTCAGATT 648827 i v v v ivv i iv ii ivv i iv L1ME3G_3end#L 159 GAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCATCAGATT 208 chr5ptel1M 648828 GACGAAGATTACAGGAAAAAGATCATGATA---AATGTTGCAGGGGATGT 648874 i i i ----v i?v v i --- i vv i i L1ME3G_3end#L 209 GGCAAAAATT----TAAAAGNTTGATAATATCNAGTGTTGGCGAGGGTGT 254 chr5ptel1M 648875 GGGAAATCTGGGACACTAATGCCTTGCTGGTGAAGTTGTGAAATTATCCA 648924 i v v v v v i vi iiiv i v vi v L1ME3G_3end#L 255 GGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTACA 304 chr5ptel1M 648925 ACCATTCCAGAGAGCAATTTAGAACCATGCCCAATGGACTATAAAACTTT 648974 i ? iii i i v vi -- i v ii v v - vi L1ME3G_3end#L 305 GCCNTTTTGGAGGGCAATTTGGCAGTAT--CTATTAAAATTTAAAA-TGC 351 chr5ptel1M 648975 GCTTACCTTCTGATTCAGCAGTGTTACTCCTGGGACTGTAACCCAAAGAG 649024 v i i ii i vii i ? ?v v v i ? i L1ME3G_3end#L 352 GCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAGAA 401 chr5ptel1M 649025 ACACT---AAAAGAGCAGAAAGGACCCAC--------ATGTTTGTAGCA- 649062 i --- v v v v- ?v i-------- ii v - L1ME3G_3end#L 402 ATACTCGCACATGTGCAC-AAGGANGCATGTACAAGGATGTTCATTGCAG 450 chr5ptel1M 649063 -ATTGTTTTTGTGATGGCAAGGAACTAGAAA----TTGAGTGGATGTCAA 649107 - -- i i i ii i i ----i i i vvii L1ME3G_3end#L 451 CATTG--TTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCAA 498 chr5ptel1M 649108 TTGGTGAATGGCTGATGAAGTTATAGTATGTGAATGTAATGGAATACTAT 649157 v v i i vv i i i vv iiv L1ME3G_3end#L 499 TAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACTAT 548 chr5ptel1M 649158 TCTCCTATAAGAAATGATGAG 649178 v vv ?i v i vi L1ME3G_3end#L 549 GCAGCNGTTAAAAAGAATGAG 569 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 40.38 CpG sites = 88, Kimura (unadjusted) = 41.03 Transitions / transversions = 1.14 (88/77) Gap_init rate = 0.04 (20 / 550), avg. gap size = 1.70 (34 / 20) 241 36.96 4.82 0.58 chr5ptel1M 649388 649553 (350447) C MIR1_Amn#SINE/MIR (55) 175 3 m_b234s601i18 9224 chr5ptel1M 649388 TACAAAAAGGAGCAAAAGCACTATTCTAATTT-GCAAATAGGGAAATTGA 649436 iii iv iv v i i iv -i i ii i C MIR1_Amn#SINE 175 TACAAAGGAGGTCAGTATCATTATCCCCATTTTACAGATGAGGAAACTGA 126 chr5ptel1M 649437 GGTCCAAATTAGTATAGAGGCATGGCAATGGTCACTTGAAATGACCACAT 649486 i? i vvi ?v v i v v v v ?i- iv? i ? vvv C MIR1_Amn#SINE 125 GGCNCAGAGAGGTNAAGTGACTTGCCCAAGGTCACNC-AGCNGGCNAGTG 77 chr5ptel1M 649487 TAAGATCAGGGA----AAATCAGGGATTTTCAGTGGCAGAACAATGCTCA 649532 vv v v ---- vi vv iiiv vv vv i v C MIR1_Amn#SINE 76 GCAGAGCCGGGANTNGAACCCAGGTCTCCCGAGTCCCAGTCCAGTGCTCT 27 chr5ptel1M 649533 TTCCATGAAACT---CTGCTTCTC 649553 v iv i i--- i i C MIR1_Amn#SINE 26 ATCCACTAGACCACACTGCCTCCC 3 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 53.02 CpG sites = 30, Kimura (unadjusted) = 54.31 Transitions / transversions = 0.97 (30/31) Gap_init rate = 0.02 (4 / 165), avg. gap size = 2.25 (9 / 4) 186 29.97 12.61 0.81 chr5ptel1M 650679 650789 (349211) C L2a_3end#LINE/L2 (35) 482 359 m_b234s601i19 9225 chr5ptel1M 650679 CTATGT---AGGTCATTCTGCTTGGCACTGAACATACA--AG-GAGGATA 650722 --- - i v v v i iiv -- - iv v C L2a_3end#LINE 482 CTATGTGCCAGG-CACTGTTCTAGGCGCTGGGGATACAGCAGTGAACAAA 434 chr5ptel1M 650723 ACAGA-----ATTCCTGTGTCCATAAAACCTAAAATGTAGAAAAGGGA-- 650765 -----i i ivii ii i i v v v viii -- C L2a_3end#LINE 433 ACAGACAAAAGTCCCTGCCCTCATGGAGCTTACATTCTAGTGGGGGGAGA 384 chr5ptel1M 650766 -AGAAAGTAAGTAAATAAAAAAGTA 650789 - v i ii v C L2a_3end#LINE 383 CAGACAATAAACAAATAAATAAGTA 359 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 38.06 CpG sites = 20, Kimura (unadjusted) = 39.61 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.06 (7 / 110), avg. gap size = 2.14 (15 / 7) 38 31.39 1.50 0.75 chr5ptel1M 650983 651115 (348885) (AT)n#Simple_repeat 1 134 (0) m_b234s252i5 9226 chr5ptel1M 650983 ATATTCAAATACATATACACATGCTTTTATATATATACACACATTCATAT 651032 vi v i i i iiv v i i i vi (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr5ptel1M 651033 GTATAGATATAGATATAGATATA-ATGTATACATATATGTAGCATGTATT 651081 i v v v - i i i -i i v (AT)n#Simple_ 51 ATATATATATATATATATATATATATATATATATATATATA-TATATATA 99 chr5ptel1M 651082 TATA-AAATATAAATATGCACTTATTTATACATAT 651115 - v v ii iv v i (AT)n#Simple_ 100 TATATATATATATATATATATATATATATATATAT 134 Matrix = Unknown Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.02 (3 / 132), avg. gap size = 1.00 (3 / 3) 184 22.35 8.57 4.11 chr5ptel1M 653640 653709 (346291) C Tigger19b#DNA/TcMar-Tigger (95) 455 383 m_b234s601i20 9227 chr5ptel1M 653640 GGATTGTGTTC----ACATACCTTTCAACATAGGTTTCCTGCTTAATGTT 653685 v i---- v v v i i ---v ii i C Tigger19b#DNA 455 GGAATGTGTTTTTGTACTTACATTTGAATATGGGT---GTGTCTGATGTT 409 chr5ptel1M 653686 CTAGGTCTT-ACAGCACTT-AAACAA 653709 i vv - i - C Tigger19b#DNA 408 CTGGGAATTCACAACACTTCAAACAA 383 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 26.89 CpG sites = 8, Kimura (unadjusted) = 26.89 Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.09 (6 / 69), avg. gap size = 1.50 (9 / 6) 12 27.32 5.26 0.00 chr5ptel1M 654207 654263 (345737) (TCCCT)n#Simple_repeat 1 60 (0) m_b234s252i6 9228 chr5ptel1M 654207 TCCCTTGCACTCACTTCTGTT-CCAACTTTTCCCTTCCCTT-CC-TCTAT 654253 v vi v iv - vv ii - - iv (TCCCT)n#Simp 1 TCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCT 50 chr5ptel1M 654254 TCCCTCCCCT 654263 i (TCCCT)n#Simp 51 TCCCTTCCCT 60 Matrix = Unknown Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.05 (3 / 56), avg. gap size = 1.00 (3 / 3) 1393 29.46 1.57 2.71 chr5ptel1M 654578 655212 (344788) C L1ME4c_3end#LINE/L1 (191) 639 12 m_b234s551i17 9229 chr5ptel1M 654578 TTCTGCTCATTTCACTCAGCATCAGTTCATGTTAGTCTTTCCAAGTCTCT 654627 iv i i i vv iv- vvi v iv C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATAA-ACATTTTCCATGTTGCT 591 chr5ptel1M 654628 CTGTATTCATCCTGCTGGTCATTTCTTACAGAACAATAATATTCCATAAC 654677 vii v v v iv vi i v ii vvvv viv C L1ME4c_3end#L 590 ACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCGA 541 chr5ptel1M 654678 ACTCATATACCATAATTTACCCAACCATTCTCCAATTGATGGGCATCCAT 654727 ii?v i ii i v v i ii v C L1ME4c_3end#L 540 GTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAG 491 chr5ptel1M 654728 TCATTTTCCAGTTTCTAGCCATTCCAAAAAAAGCTGCCACAAACATTTTG 654777 vivv i i v i vi v v v ii i v C L1ME4c_3end#L 490 GTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTC 441 chr5ptel1M 654778 GCACATACAGGTTCCTTTCCCCTCTTTT--AGTATCTCTTTGGGATATAA 654825 ii i --- i i i -- v i i i v v C L1ME4c_3end#L 440 GTGCATATAG---CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAAT 394 chr5ptel1M 654826 GCCCAGTAGTAGCACTGCTGGATCAAAGGGTATACACAGTTTCATAACTT 654875 v v i v i i i iv v i ii i C L1ME4c_3end#L 393 TCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTC 344 chr5ptel1M 654876 TTTAGGCATAATTG-CATATTGCTCTCCAGAATGGTTGGATTCCTTCACA 654924 v vi i - - v i i v v iivv i C L1ME4c_3end#L 343 TTGATACGT-ATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACA 295 chr5ptel1M 654925 ACTCCACCAACAATGCATCAATGTCCCAGTTTTCCCGCATCCCCTCCAAC 654974 ?iv i i v i? v iv ? i v i C L1ME4c_3end#L 294 NTGCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGC 245 chr5ptel1M 654975 A---GTCATCATCATTTTTTTCCTGTCATCTTTCCTGTCAATCTGACAGG 655021 --- vi i v v----v i v --- i i i C L1ME4c_3end#L 244 ATTGGGTATTATCAATTTTTTA----AATTTTTGCT---AATTTAATAGG 202 chr5ptel1M 655022 TGTGTAATGATATCTCAGAGTTGTCTTAATTTGCATTTCTCTGATCAATA 655071 i iv i vv ii i i v C L1ME4c_3end#L 201 CGTAAAATGGTATCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACTA 152 chr5ptel1M 655072 GTGATTTGGAACACCCTTTCATATAGGTAGAAAGAGTTTCAATTTCATCA 655121 i vv v iii i i ivv ivvv vvi? vv v v C L1ME4c_3end#L 151 GCGAGGTTGAACATTTTTCCATGTGTTTGTTTACTANTTGTATTTCCTCT 102 chr5ptel1M 655122 TCTGAAAAATTGTCTTTTCATAAACTTTGACCATATATCAATTGGAGAAT 655171 ? -vi v ivv v v v i---- C L1ME4c_3end#L 101 TNTG-TGAATTGTCTGTTCATGTCCTTTGCCCATTTATCTATTGGG---- 57 chr5ptel1M 655172 GGCTTGA----TTTCTTATAAATTAGAGTCAATTCTCTCTATATT 655212 v ---- v v i v ii i v ? C L1ME4c_3end#L 56 GTCTTGATNTTTTTCTTATCAATTTGAATGAGCTCTTTATATANT 12 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 37.45 CpG sites = 93, Kimura (unadjusted) = 38.51 Transitions / transversions = 1.04 (93/89) Gap_init rate = 0.03 (21 / 634), avg. gap size = 1.29 (27 / 21) 4347 30.64 4.75 2.69 chr5ptel1M 655129 658267 (341733) C L1M5_orf2#LINE/L1 (55) 3239 38 m_b234s551i18 9229 chr5ptel1M 655129 AATTGTCTTTTCATAAACTTTGACCATATATCAATTGGA--GAATGGCTT 655176 v v vivvi v v v ?v i-- vv v C L1M5_orf2#LIN 3239 AAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTTGTCTT 3190 chr5ptel1M 655177 GATTTCTTAT-AAATTAGAGTCAATTCTCTCTATATTTTGGAAATGAAGT 655225 -- ? -i ? iv -v i i v i v i ivi C L1M5_orf2#LIN 3189 --TTTNTTATTGANTTGTAG-GAGTTCTTTATATATTCTGGATACGAGTC 3143 chr5ptel1M 655226 CTTTATCAGAAGCTTTA-ACTTTAAAAATGTTTCCTC--AGTTTGTTGCC 655272 i --- v -ii? iv i i -- ? i v i C L1M5_orf2#LIN 3142 CTTTGTCAGA---TATATGTNTTGCAAATATTTTCTCCCANTCTGTGGCT 3096 chr5ptel1M 655273 TCCCTTCTAATCTCGTTTGCATTCGTTTTGGTTGTACAAAGGCTTTTTAA 655322 v i v i iv vi iv vvi v v? vi i i i v v C L1M5_orf2#LIN 3095 TGCCTTTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTTTAAT 3046 chr5ptel1M 655323 TTTGATATAATCAAAATTTTCTATTTTGT----TATCGATAACGATCTCT 655368 i? i v v v v v ---- v v ?ii v i - C L1M5_orf2#LIN 3045 TTTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGGTTNGTGCTTT-T 2997 chr5ptel1M 655369 TGT-TCTTCTTTGGTCATAAATTCCTTCCTCCTCCACAAGTCTGAGAGAT 655417 - i v i--- v iii v v?i - i vvii C L1M5_orf2#LIN 2996 TGTGTCCTGTTTA---AGAAATCTTTGCCTANCCCA-AGGTCACGAAGAT 2951 chr5ptel1M 655418 AAACTATCCTGTGTT--CCTCTAATTTATTTATGATCTTGATCTTTATGC 655465 --i v i -- i ivvvv ii i i?ii iii C L1M5_orf2#LIN 2950 A--TTCTCCTATGTTTTCTTCTAGAAGTTTTATAGTTTTANCTTTTACAT 2903 chr5ptel1M 655466 CTAAATC-ATGGACCCATTTTGATCTTATCTTGGTGTACAGTT--AAGTG 655512 i ii - - i i ? vi v i v ii v-- i i C L1M5_orf2#LIN 2902 TTAGGTCTATG-ATCCATCTNGAATTAATTTTTGTGTATGGTGTGAGGTA 2854 chr5ptel1M 655513 TGGGTCCATGCCTAATTTCTGCCATACTAAT-TTCAATTTTCCCAGCAGT 655561 v v v?iii v i v ivi - i v i vi C L1M5_orf2#LIN 2853 GGGGTCGAGNTTCATTTTTTTCCATATGGATATCCAATTGTTCCAGCACC 2804 chr5ptel1M 655562 TTTTGTCAAATAATGAATTCTTATCCCA--AAAGTGGGGATTTTTGCTTT 655609 v ii v ivvv i vi --i v v?-- vvii i C L1M5_orf2#LIN 2803 ATTTGTTGAAAAGACTATCCTTTCCCCACTGAATTGCN--TTGGCACCTT 2756 chr5ptel1M 655610 TGTCAAATGCTAGATTGCTATAGTTAT-TGA--CTATTTTGTCCTGTGAA 655656 viii i? v? i vv i - i-- i------ i C L1M5_orf2#LIN 2755 TGTCAAAAATCAANTGNCCATATATGTGTGGGTCTATTTC------TGGA 2712 chr5ptel1M 655657 C---CTAACCTGTTCCACTGATCAACTAATCTATTTCTTA-GCCAATACC 655702 --- vi i v i vi i- - C L1M5_orf2#LIN 2711 CTCTCTATTCTGTTCCATTGATCTATTTGTCTATC-CTTACGCCAATACC 2663 chr5ptel1M 655703 AAATGGTTTTGGTGACTGCTGCTTTATAATACAGTTTT-AGATCAGGTAC 655751 v iv i i v iv - i - ? ? v C L1M5_orf2#LIN 2662 ACACTGTCTTGATTACTGTAGCTTTATAATA-AGTCTTGANATCNGGTAG 2614 chr5ptel1M 655752 AGCTAGAACACCTTCA--TTTGATTTT-TTTTTCATTAATTCCCTTGAA- 655797 --- iv vv i -- v i - v-i vii iv- C L1M5_orf2#LIN 2613 ---TGTAAGTCCTCCAACTTTGTTCTTCTTTTTCAA-GATTGTTTTGGCT 2568 chr5ptel1M 655798 ATTCTTGACCTTTTGTTCTTCCATATGAATTTTGTTGTTATTTTTTCTAG 655847 ? ii i ivi i ivvi i vi v v v C L1M5_orf2#LIN 2567 ATTCTNGGTCCTTTGCATTTCCATATAAATTTTAGAATCAGCTTGTCAAT 2518 chr5ptel1M 655848 GTCATTAAAACAGTTTCTCAGGAGTCTGATTGGTATAGCACTAAATAAAT 655897 v vvi v iii viii v i v v i i vv C L1M5_orf2#LIN 2517 TTCTACAAAAAAACCTGCTGGGATTTTGATTGGGATTGCATTGAATCTAT 2468 chr5ptel1M 655898 AGATTAGTTTAAGGAGTATTGTCATCTTTATTATATTCACTCTGCCTATC 655947 i i ii v v ? iv v v v v C L1M5_orf2#LIN 2467 AGATCAATTTGGGGAGAATTGACATCTTNACAATATTGAGTCTTCCAATC 2418 chr5ptel1M 655948 CAAGAGCTCTTAATAGTTTTCCAGTTATTTAAATCTGACTTTATTTGTGT 655997 v i vivvv vi i v ii vvi v v v C L1M5_orf2#LIN 2417 CATGAACATGGTATATCTCTCCATTTATTTAGGTCTTCTTTAATTTCTCT 2368 chr5ptel1M 655998 GGAAAGTGTTTTATAATTTTGCTCATATAATTCCTGACTTTCCTTTGGTA 656047 viiv i i i vvvii ? iv i vviv ?i v C L1M5_orf2#LIN 2367 CAGCAATGTTTTGTAGTTTTCAGTGTANAGGTCTTGCACATNTTTTGTTA 2318 chr5ptel1M 656048 GATAGATTCCCAAATATTTTATGCTATC-GACAGTTATTTTGAATGGAAT 656096 vv i i ? i v i- i- i v i v C L1M5_orf2#LIN 2317 GATTTATTCCTAAGTATTTNATGTTTTTTGAT-GCTATTGTAAATGGTAT 2269 chr5ptel1M 656097 TTCTCCTTGTATTTC---TTGCTGTTGGATTTTGTTGGTGATGTATAAAA 656143 vi ii ?iv --- v vi --- v ii i i C L1M5_orf2#LIN 2268 TGTTTTTNAAATTTCATTTTCCAATTG---TTTGTTGCTAGTATATAGAA 2222 chr5ptel1M 656144 ATGCTGAGGATTTATGTGGATTTATTTTGTATCCTGCAACTTTGCTAAAG 656193 i vivv v iv v ii ? i i v C L1M5_orf2#LIN 2221 ATACAATTGATTTTTGTATATTGACCTTGTATCCNGCGACCTTGCTAAAT 2172 chr5ptel1M 656194 TTGTGAATTATTTATAATAGCTTTTTTAGTAGAATCTCTGGGGGTTGTCT 656243 iiivv v v i i ? - v i ? iv - C L1M5_orf2#LIN 2171 TCACTTATTAGTTCTAGTAGTTTNTTT-GTAGATTCTTTNGGATTT-TCT 2124 chr5ptel1M 656244 AAGTATAC-----------CTTC--ATAGTGATAATTTGATTTCCTCATT 656280 v ? ----------- v -- i? i i v i v C L1M5_orf2#LIN 2123 ACGTANACAATCATGTCATCTGCGAATAANGACAGTTTTATTTCTTCCTT 2074 chr5ptel1M 656281 ACCTACTCTAATTCCTTTAATCTCTTTCTCAACTCTTATTGCCAAGACTA 656330 v v iii v v v i i vvvi vvv i C L1M5_orf2#LIN 2073 TCCAATCTTTATGCCTTTTATTTCTTTTTCTTGCCTTATTGCACTGGCTA 2024 chr5ptel1M 656331 GCATTTTTAATACAATATTAAATAATAATGGTGATAGTGGGCAACCTTGT 656380 v ii ii i i i iv i ? i i v C L1M5_orf2#LIN 2023 GGACCTCCAGTACAATGTTGAATAGAAGTGGTGANAGCGGACATCCTTGT 1974 chr5ptel1M 656381 TTCATTCCTGATCTTACTGGAAATGGTTCAAGTTTATCCCCAATATATAT 656430 i ii i vv i v v? iv ? v v v vi C L1M5_orf2#LIN 1973 CTTGTTCCCGATCTTAGGGGGAAAGCNTTCAGTNTTTCACCATTAAGTAT 1924 chr5ptel1M 656431 GATGCTTATTGATGATTTTAAATAGATGCTTCTCACTATTTTAGGGGAAA 656480 i ?ii vv i vvi iii i ii vv - i i C L1M5_orf2#LIN 1923 GATGTTNGCTGTAGGTTTTTCGTAGATGCCCTTTATCAGGTT-GAGGAAG 1875 chr5ptel1M 656481 GTCCATT-TATTCCTATACTCTCAAGTGTTTTTATTAGGAATGGATGTTG 656529 v v - vvi viii v i v i C L1M5_orf2#LIN 1874 TTCCCTTCTATTCCTAGTTTGCTGAGAGTTTTTATCATGAATGGGTGTTG 1825 chr5ptel1M 656530 GATTTTATCAAATGCTTTTTCTGCATCTATTGAGATGGTCATATGGTTTT 656579 i i i i C L1M5_orf2#LIN 1824 AATTTTGTCAAATGCTTTTTCTGCATCTATTGAGATGATCATATGATTTT 1775 chr5ptel1M 656580 TGTTCATTTGAT-TATTGATATAGTCAATTATGCTAATAGTTTTCCTAAT 656628 v i - iv - i i i v iii i v v i v C L1M5_orf2#LIN 1774 TCTCC-TTTATTCTGTTAATATGGTGAATTACATTGATTGATTTTCGAAT 1726 chr5ptel1M 656629 ATTGAACCAGCCCTGCATTTCTGGTATGAACCCTACTTAGCAATG----- 656673 i i i i i v i i i iv ----- C L1M5_orf2#LIN 1725 GTTAAACCAACCTTGCATTCCTGGGATAAACCCCACTTGGTCATGATGTA 1676 chr5ptel1M 656674 TT---------------------------TTTGCTAATATTTTATTTAAG 656696 --------------------------- i ? i C L1M5_orf2#LIN 1675 TTATCCTTTTTATATATTGCTGGATTCGATTTGCTAATATTTTGTTNAGG 1626 chr5ptel1M 656697 ATTTTT-CATCAATATTCATTAGGGAGATTGGTCTATAATTTTCTT---- 656741 - v i v v i ---- C L1M5_orf2#LIN 1625 ATTTTTGCATCTATGTTCATGAGGGATATTGGTCTGTAATTTTCTTTTCT 1576 chr5ptel1M 656742 -------TCTCTGT----TTTCAAT-----GAACCTGCTTATCTCTGATG 656775 ------- i ---- iii ----- iv?v vii -- i C L1M5_orf2#LIN 1575 TGTAATGTCTTTGTCNGGTTTTGGTATCAGGGTNATGCTGGCCTC--ATA 1528 chr5ptel1M 656776 AAAGGAATTTGGTAGGACTCCTTTAATCCCTATTTTTCCCAGTAGTTTAA 656825 v i v v vii i ivv ii iivv iv iv C L1M5_orf2#LIN 1527 AAATGAGTTGGGAAGTGTTCCCTCTTTTTCTATTTTCTGGAAGAGTTTGT 1478 chr5ptel1M 656826 ATGGCACTGGAGTTAGTTGTTCTTTAAATGTTT-GTAGAATTCACATGTA 656874 i iiv i vi v v i - vv i C L1M5_orf2#LIN 1477 GTAAGATTGGTATTATTTCTTCCTTAAATGTTTGGTAGAATTCACCAGTG 1428 chr5ptel1M 656875 AATCTATCTGGTCCTGGGAATTTTTCT-TAGGGAGTTGATTGATAGCTTG 656923 v i v iiv i i - i i v vv i vi vvi C L1M5_orf2#LIN 1427 AAGCCATCTGGGCCTGGAGTTTTCTTTGTGGGAAGGTTTTTAATTACAAA 1378 chr5ptel1M 656924 TTCTATTTATTTTTCTAAGATGAGACTGTTTAACCAATTTACTTCTTCCT 656973 v v vvivi v ii i i i ivivv i i i C L1M5_orf2#LIN 1377 TTCAATTTCTTTAATAGATATAGGGCTATTCAGATTTTCTATTTCTTCTT 1328 chr5ptel1M 656974 CTATTCATCTGAGCAAGCTACATTTTTGAAGGTATTCTTCCATTTCATTT 657023 v?i ivi i vi i ?i iii v v iv i C L1M5_orf2#LIN 1327 GNGTCAGTTTTGGTAANTTGTGTTTTTCAAGGAATTTGTCCATTTCATCT 1278 chr5ptel1M 657024 AAGTTATCAAATTTATTGGCATAAAGTTGGGCAAAGTAACTCCTAATTAT 657073 ? vv v i viii v C L1M5_orf2#LIN 1277 AAGTTNTCAAATTTATTGGCATAAAGTTGTTCATAATATTCTCTTATTAT 1228 chr5ptel1M 657074 TGCTCTAATTTCCTCTTCG-TTAATGGTGAGGTCTCCCTTTTCATTTTTA 657122 ivi i v - v vv - ivi i v i ii i C L1M5_orf2#LIN 1227 CCTTTTAATGT-CTGTAGGATCTGTAGTGATGTCTCCTTTTTCATTCCTG 1179 chr5ptel1M 657123 AGACTAACAATTTGATTTTTCTCTTTCCTTTTTTTAATCAGATTTACTAA 657172 v i iii vv i i ii i i vi ?i i C L1M5_orf2#LIN 1178 ATATTGGTAATTTGTGTCTTCTCTCTTTTTTTCTTGATCAGTCTNGCTAG 1129 chr5ptel1M 657173 GGGTTTATCTATTTTGTTGTTGTTTTTCTTTCATAGAACCAACTCTTAGT 657222 i v i v v ----- v i i i i C L1M5_orf2#LIN 1128 AGGTTTATCAATTTTATTGATCT-----TTTCAAAGAACCAGCTTTTGGC 1084 chr5ptel1M 657223 TTTATTCATTAACTCAATATATTTTTTTTACTTTCAATTTTATTAATCTC 657272 ii v vv -- vv ? ? ii v i i i C L1M5_orf2#LIN 1083 TTCGTTGATTTTCTC--TATTGTNTNTTTGTTTTCTATTTCATTGATTTC 1036 chr5ptel1M 657273 TCCTTTTATTTTTAGAATTTCAAGTTCAGTGT-TTGACTGGGGGTTTTTA 657321 v i i vv --v vv v -i v? vv -- C L1M5_orf2#LIN 1035 TGCTCTTATCTTTATTATTTC--CTTCCTTCTACTTNCTTTGGG--TTTA 990 chr5ptel1M 657322 ATTTG---TTCCTTTTCTAGCATTTTTAATTGTAAGCCCAATTCA----- 657363 --- i v i v iv v ii iv ----- C L1M5_orf2#LIN 989 ATTTGCTCTTCTTTTTCTAGCTTCTTAAGGTGGAAGCTTAGATCATTGAT 940 chr5ptel1M 657364 -TTAACCTTCTCTTGCACTATTTTATGCAAGTAGGCCTTTAGAGATATGA 657412 - v i i --- v i --- vi ? v i? v i C L1M5_orf2#LIN 939 TTTAAGCCTTTCTT---CTTTTCTA---ATATANGCATTTAANGCTATAA 896 chr5ptel1M 657413 AATTCCC-CTTACTACCGCTTTGGCTGCATCCCACACATTTTGGTATGAT 657461 v - v vi i i v i v C L1M5_orf2#LIN 895 ATTTCCCTCTAAGCACTGCTTTAGCTGCATCCCACAAATTTTGATATGTT 846 chr5ptel1M 657462 GTCTCATTGTTGTCATTTTCTTGGGTGAAGTTACTAATTATGTCTATGAT 657511 v iv ii ? ivv viiviv v v viv?i i C L1M5_orf2#LIN 845 GTATTTTCATTNTCATTCAGTTCAAAATATTTTCTAATTTCCNTTGTGAT 796 chr5ptel1M 657512 TTGCTGTTTCACCCAATAATTCTTTGGTA-TGAGATTTCTTAGTTTGCAA 657560 vi v v vvii v i v - v - vi i v C L1M5_orf2#LIN 795 TTCTTCTTTGACCCATGGGTTATTTAGAAGTGTG-TTGTTTAATTTCCAA 747 chr5ptel1M 657561 TTATTTTTGGTCTATTTTCC-CCTGGCTTT---TTATCGAATATAATTTT 657606 v vv --- i-v? iv --- i v viv v C L1M5_orf2#LIN 746 ATATTTGGGG---ATTTTCTAGNTATCTTTTTGTTATTGATTTCTAATTT 700 chr5ptel1M 657607 CATTGCATAGTGATCTGAAAACAATGCATT-TACTATTCC--TGCCTT-- 657651 v v v i v i - i vi - iv i -- v i -- C L1M5_orf2#LIN 699 AATTCCATTGTGGTCAGAGAAC-ATACTCTGTATGATTTCAATCCTTTNA 651 chr5ptel1M 657652 ACTGCATTTGAATTTGAATTTTTCTGTCCTAATATATGGTCAATTTTTGT 657701 v vi vii i --- v v i i? v i v C L1M5_orf2#LIN 650 AATTTATTGAGACTTG---TTTTATGGCCCAGNATATGGTCTATCTTGGT 604 chr5ptel1M 657702 ATAGGTTCCATGAACGGCTGAGAAGAAAGTGTACTCCTTTCAGT--CTCC 657749 v v vi ivi i v i -- v ? --i vv C L1M5_orf2#LIN 603 AAATGTTCCATGTGCACTTGAAAAGAATGTGTATTC--TGCNGTTGTTGG 556 chr5ptel1M 657750 ATTTAGTTTTCTCCAAAGATCTATCATATCTAACT--TTTCTAGTATTCT 657797 i v? v vi vi v i vi v ii -- vv i -- C L1M5_orf2#LIN 555 GTGNAGTGTTCTATAAATGTCAATTAGGTCAAGTTGGTTGATAGTGT--T 508 chr5ptel1M 657798 ATTTACCTCTTTGACTTCTTTCTTATTTATTTTGTG---GTTTGATTTAT 657844 i i vv iv iv --- i v v ---ii v i - C L1M5_orf2#LIN 507 GTTCAAATCTTCTATATC---CTTACTGATTTTTTGTCTACTTGTTCTA- 462 chr5ptel1M 657845 TTAATT-CTGAGAGTGCAAGGTTGATATCTCCCACT---ATTATAGTTTT 657890 i - v v?iv i v ? --- i i v C L1M5_orf2#LIN 461 TCAATTACTGAGAGAGGNGTGTTAAAATCTCCNACTATAATTGTGGATTT 412 chr5ptel1M 657891 GCCGTATATTTCTTCTTGCAGCTTTCTTAATTTCTCTTTTAAGAAGTTAA 657940 i --- i vi i i v i i i vi i v v v vi C L1M5_orf2#LIN 411 GTC---TATTTCTCCTTTTAGTTCTGTCAGTTTTTGCTTCATGTATTTTG 365 chr5ptel1M 657941 AAGCTACACCACTTGGTGCATATATGTTTAATATTGATATTACTTCATTA 657990 viiii i v i ii iv v vv v v C L1M5_orf2#LIN 364 AAGCTCTGTTATTAGGTGCATACACATTTAGGATTGTTATGTCTTCTTGA 315 chr5ptel1M 657991 TCTATGCTACCC-TTTAGCAAGACATAATGCCCTTCCTTATCTCCTTTAA 658039 vv -iv - v vv iiv i i i i----- C L1M5_orf2#LIN 314 TGAAT-TGACCCTTTTATCATTATGAAATGTCCCTCTTTATCTCT----- 271 chr5ptel1M 658040 TTAGGTAATTTTTTTTTCTTT------TGCTTGATTGGAGATCAGGATGG 658083 --- v i v i ------ i vi iv v i iv i C L1M5_orf2#LIN 270 ---GGTAATATTTCTTGCCTTGAAGTCTACTTTGTCTGATATTAATATAG 224 chr5ptel1M 658084 CTACCCCTGTTTTTTTTTACTTCACCTGAAGCATAGTAGATTCTGCTCCA 658133 i ? v i i i? viiv v-v i v ii vi C L1M5_orf2#LIN 223 CCACNCCAGCTTTCTTTTGNTTAGTGTT-TGCATGGTATATCTTTTTCCA 175 chr5ptel1M 658134 ACCTTTTCTCTTTACTCTGTATGTGTTGCTCTGCTTCAAGTGTGTTTCCT 658183 v vii i vi ? v ivi v ii v i i i C L1M5_orf2#LIN 174 TCCTTTTACTTTCAACCTNTCTGTGTCTTTATATTTAAAGTGCGTCTCTT 125 chr5ptel1M 658184 GTAAACAACATATTGTAGGATTCTGGCTTTTAATGCAGTTTGTTCAATCC 658233 i i v v i ii vi v v i -v i C L1M5_orf2#LIN 124 GTAGACAGCATATAGTTGGGTCTTGTTTTTTTATCCAGTCTG-ACAATCT 76 chr5ptel1M 658234 CT--CTTT--ATGAGGGAGTTTACCCCATTCACATTTA 658267 -- -- vi i v v? i C L1M5_orf2#LIN 75 CTGCCTTTTAATTGGAGTGTTTAGNCCATTTACATTTA 38 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 40.72 CpG sites = 506, Kimura (unadjusted) = 41.24 Transitions / transversions = 1.18 (506/430) Gap_init rate = 0.04 (140 / 3138), avg. gap size = 1.68 (235 / 140) 422 20.40 6.85 2.63 chr5ptel1M 658163 658308 (341692) C L1MEh_5end#LINE/L1 (5) 2230 2079 m_b234s551i19 9229 chr5ptel1M 658163 TCTGCTTCAAGTGTGTTTCCTGTAAACAACATATTGTAGGATTCTGGCTT 658212 ? i i i i i i v i vi C L1MEh_5end#LI 2230 TNTGTTTTAAGTGTGTCTCTTGTAGACAGCATATTGTTGGATTTTGTTTT 2181 chr5ptel1M 658213 TTAATGCAGTTTGTTCAATCCC--TCTTT--ATGAGGGAGTTTACCCCAT 658258 ? v i i -v? i -- -- vi v v C L1MEh_5end#LI 2180 TNAATCCAATCTG-ANAATCTCTGTCTTTTAATTGGTGAGTTTAACCCAT 2132 chr5ptel1M 658259 TCACATTTATGGTTAAAATGACCA----ATTCTGTATTACT--TGCCATC 658302 i v --- v ii---- ?v vv i -- C L1MEh_5end#LI 2131 TTACATTTATTGT---AATTACTGNTATATTNGGACTTATTTCTGCCATC 2085 chr5ptel1M 658303 TTGTTA 658308 i C L1MEh_5end#LI 2084 TTATTA 2079 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 25.05 CpG sites = 17, Kimura (unadjusted) = 25.05 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.06 (8 / 145), avg. gap size = 1.75 (14 / 8) 21 14.11 1.96 4.00 chr5ptel1M 659946 659996 (340004) (AACA)n#Simple_repeat 1 50 (0) m_b234s252i7 9230 chr5ptel1M 659946 AAGAATCAAAGAAAACAAACTAAC-AACAACAAAAACAAACAAACAAACC 659994 v v -v v - - v v (AACA)n#Simpl 1 AACAAACAAA-CAAACAAACAAACAAACAA-ACAAACAAACAAACAAACA 48 chr5ptel1M 659995 AA 659996 (AACA)n#Simpl 49 AA 50 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.06 (3 / 50), avg. gap size = 1.00 (3 / 3) 12 9.24 0.00 4.17 chr5ptel1M 661649 661673 (338327) (TCCC)n#Simple_repeat 1 24 (0) m_b234s252i8 9231 chr5ptel1M 661649 TCCCTCCCACCCTCCACCCCCTCCC 661673 v - i (TCCC)n#Simpl 1 TCCCTCCCTCCCTCC-CTCCCTCCC 24 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 995 30.52 2.58 3.30 chr5ptel1M 661996 662422 (337578) C L1ME5_3end#LINE/L1 (313) 628 205 m_b234s551i20 9232 chr5ptel1M 661996 TTTCACTTAGCATCA-GTTCATGTAAT-TCTCTCCAAGCTTCTCTGTATT 662043 i ii - -- v v- iv v i v v i v C L1ME5_3end#LI 628 TTTCACTCAGCACTATGTT--TTTAAGATCCATCCATGTTGCTATGTGTA 581 chr5ptel1M 662044 CATCTTGCTGGTCGTTTCTTACAGAACAATAATATTCCATAACATTCATA 662093 v iiv i i v v vvvv i i iiii v v C L1ME5_3end#LI 580 CATCTAGTCCGTTGCTTCTAACTGCTGCATAGTACTCCATGGTGTGCATC 531 chr5ptel1M 662094 TACCACAATTTCCCCAACCATTCTCCAATTGATGGGCATCCACTCAGTTT 662143 i v v i v i v v i i vviv ii C L1ME5_3end#LI 530 CACCACATTTTACCTATCCACTCTCCCAGTGATGGACACCCAGGTTGCCT 481 chr5ptel1M 662144 CCAGCTTCTAGCCACTACAAACAGGGCTGCCACAAACATTTTGGCACATA 662193 i i iv i iv v ii ii v i - C L1ME5_3end#LI 480 CCAACTCCCCGCCACCACAAACAACGCTGCAATGAACATCCTCGTACAT- 432 chr5ptel1M 662194 CTGGTCCCTTTC----CCTTCTTTAGTATCTCCTTGGGATATAAGCCCAG 662239 --- i v---- viv v v i i vi C L1ME5_3end#LI 431 ---GTCCCCTTATGGACCTGTGTGAGAATTTCTTTGGGATATATACCCAG 385 chr5ptel1M 662240 TAGAAACACTGCTGGATCAAAGGGTATGCACA-ATTTGATAACTTTTTGG 662288 v viiv i i v ii - i i ------ i C L1ME5_3end#LI 384 GAGCGGAATTGCTGGGTCATAGGGTATGCGTATACTTAA------TTTGA 341 chr5ptel1M 662289 GCA--TAATTCCAGATTGCTCTCCAGAATGGTTGGATTCGTTCACAGCTC 662336 vi -- v v i v iiv ii vii C L1ME5_3end#LI 340 CTAAGTACTGCCAGATTGCTCTCCAGAATGGCTGCACCAGTCTACACTCC 291 chr5ptel1M 662337 CACCAACAATGTATCAGTGTCCCAGTTTTCCCACATCTCCTCCAACACTC 662386 i i i v v i vi ? i ii v i C L1ME5_3end#LI 290 CACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATCCTCGCCAACACTT 241 chr5ptel1M 662387 ATCATTATTT--TTTCCTGTCATCTTAGCCAACCTGAT 662422 iv ii--i i i-- i v ii i C L1ME5_3end#LI 240 GGCATTATCCAGCTTTCTA--ATTTTTGCCAGTCTAAT 205 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 39.72 CpG sites = 75, Kimura (unadjusted) = 40.57 Transitions / transversions = 1.47 (75/51) Gap_init rate = 0.05 (20 / 426), avg. gap size = 1.25 (25 / 20) 247 32.35 0.00 0.00 chr5ptel1M 662447 662548 (337452) C L1ME3Cz_3end#LINE/L1 (449) 548 447 m_b234s551i21 9233 chr5ptel1M 662447 ATATCATCCCTTTACATTCATATACCATTACTTATTTGGCCATTCCCCAA 662496 vi i v ii vv iv i iv v C L1ME3Cz_3end# 548 ATAGTATTCCATTGTATGAATATACCACAATTTATTTATCCATTCCCCTA 499 chr5ptel1M 662497 ATAATGGACATCCACTAAGTTTCCAGTTTCTTGCCACCGCAAAAAGGACT 662546 v i ii vvvv i i i i iii v ivi C L1ME3Cz_3end# 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr5ptel1M 662547 GC 662548 C L1ME3Cz_3end# 448 GC 447 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 41.90 CpG sites = 19, Kimura (unadjusted) = 43.67 Transitions / transversions = 1.36 (19/14) Gap_init rate = 0.00 (0 / 101), avg. gap size = 0.0 (0 / 0) 273 28.92 0.00 0.00 chr5ptel1M 662466 662548 (337452) C L1ME3G_3end#LINE/L1 (395) 529 447 m_b234s551i22 9233 chr5ptel1M 662466 ATATACCATTACTTATTTGGCCATTCCCCAAATAATGGACATCCACTAAG 662515 v i ii v v i ii vvvv C L1ME3G_3end#L 529 ATATACCATAATTTATTTAACCATTCCCCTATTGATGGACATTTAGGTTG 480 chr5ptel1M 662516 TTTCCAGTTTCTTGCCACCGCAAAAAGGACTGC 662548 i i i i iii v ivi C L1ME3G_3end#L 479 TTTCCAATTTTTCGCTATTACAAACAATGCTGC 447 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 35.84 CpG sites = 15, Kimura (unadjusted) = 37.84 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.00 (0 / 82), avg. gap size = 0.0 (0 / 0) 35 30.11 2.16 2.16 chr5ptel1M 664511 664649 (335351) (GAG)n#Simple_repeat 1 139 (0) m_b234s252i9 9234 chr5ptel1M 664511 GAGGAGAAAGGA-GAGGAGGAAGAGAAGAATAAGGAAGAGTAGAAGGAGT 664559 -i - i i i vi i v i v (GAG)n#Simple 1 GAGGAG-GAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGG 49 chr5ptel1M 664560 AGGAACA-GAAGATGATGGAGGAGGAGAAAAAGAAAGATGA-CAGAAGAA 664607 iv - i v - i ii i i v -v i -i (GAG)n#Simple 50 AGGAGGAGGAGGAGGA-GGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG-G 97 chr5ptel1M 664608 AGGAAGAGAAGGAGTGGGAGGAAGAAGAGGTGAAGAAGGAGG 664649 i i vi i i v i i (GAG)n#Simple 98 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGG 139 Matrix = Unknown Transitions / transversions = 2.56 (23/9) Gap_init rate = 0.04 (6 / 138), avg. gap size = 1.00 (6 / 6) 22 0.00 0.00 0.00 chr5ptel1M 665488 665511 (334489) (T)n#Simple_repeat 1 24 (0) m_b234s252i10 9235 chr5ptel1M 665488 TTTTTTTTTTTTTTTTTTTTTTTT 665511 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTT 24 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 516 28.45 2.29 0.75 chr5ptel1M 665746 665876 (334124) L2b_3end#LINE/L2 328 460 (6) m_b234s601i21 9236 chr5ptel1M 665746 ATGT-TGTCTCTCCCATTAAACGATGAGCTTCTTGAGGACAGGAACTGTT 665794 - i i i vi i v i i i ?v L2b_3end#LINE 328 ATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNG 377 chr5ptel1M 665795 TTTGCCTTTTTTTTTCC--TATCTCCAGCACTTAGCATAGTGATTGATAC 665842 i i v iviiv -- i i i i ? vi ii L2b_3end#LINE 378 TCTGTCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCAC 427 chr5ptel1M 665843 AGAGTAGATACATAATAAAATGCTTGTTGATTGA 665876 v iii vi i - ii v L2b_3end#LINE 428 ACAGTAGGCGCTCAGT-AAATATTTGTTGAATGA 460 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 33.43 CpG sites = 27, Kimura (unadjusted) = 38.90 Transitions / transversions = 2.70 (27/10) Gap_init rate = 0.02 (3 / 130), avg. gap size = 1.33 (4 / 3) 24 8.91 0.00 0.00 chr5ptel1M 666791 666826 (333174) (TCA)n#Simple_repeat 1 36 (0) m_b235s252i1 9237 chr5ptel1M 666791 TCATCATCATCATCTTTGTCATCATCATCATCATCA 666826 v ii (TCA)n#Simple 1 TCATCATCATCATCATCATCATCATCATCATCATCA 36 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 531 32.62 9.70 0.39 chr5ptel1M 666832 667068 (332932) C MIRc#SINE/MIR (0) 268 10 m_b235s601i1 9238 chr5ptel1M 666832 AATATTAACAATAGCTAACCTTTATATAATGCTTTA-AATTTGCAA-GTC 666879 v i i?v v v i iii - i i - iv C MIRc#SINE/MIR 268 AATAATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCG 219 chr5ptel1M 666880 CTTT-----ATTTTGTCACATTTAACCTTCACAACAACCCTGTAATGTAA 666924 ----- iv i v i i i i v i C MIRc#SINE/MIR 218 CTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAG 169 chr5ptel1M 666925 GT------TATGTTATTTTCCCTGTTTTATAGATGATGATACTGGGGTAT 666968 i------vi i v ii i v v i ivi C MIRc#SINE/MIR 168 GCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC 119 chr5ptel1M 666969 ACGAAGAT-------CTTGTCTATACT-GCACAACTAGTAAATGTCTAAA 667010 vii i ------- i i viv -i i i v - i C MIRc#SINE/MIR 118 AGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGC-AGA 70 chr5ptel1M 667011 GCAAAG--CAGAACTCATATATTCTTGCCTCCAAAGTCACGACTCTATTT 667058 vii --iv i vi v i v ivi vvi v ii C MIRc#SINE/MIR 69 GCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCC 20 chr5ptel1M 667059 AATATGTCAC 667068 v iiii C MIRc#SINE/MIR 19 ACTGCACCAC 10 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.76 CpG sites = 50, Kimura (unadjusted) = 45.40 Transitions / transversions = 1.85 (50/27) Gap_init rate = 0.03 (8 / 236), avg. gap size = 3.00 (24 / 8) 266 30.14 0.00 13.91 chr5ptel1M 667555 667685 (332315) C MIR3#SINE/MIR (87) 121 7 m_b235s601i2 9239 chr5ptel1M 667555 AGTCTTAGAGTGATGAGAGATTGTGACTTGTCCATAATCACACAGCCAGG 667604 v ii v i i----- i vii ? - C MIR3#SINE/MIR 121 AGGCCCAGAGAGGTGAA-----GTGACTTGCCCAAGGTCACACAGCNAG- 78 chr5ptel1M 667605 ATTCTGTGTTCAAATCTGAGATCAATCCTGAACCCAAGTGTTCCTGATTC 667654 -- iv -v i v i i ii ----- i -i i C MIR3#SINE/MIR 77 --TTAGTG-GCAGAGCCGGGACTA-----GAACCCAGGT-CTCCTGACTC 37 chr5ptel1M 667655 AGAAGTCAGCTCTCTGTCTATTATGTCATTC 667685 -vv v iv v ii vv i i C MIR3#SINE/MIR 36 -CCAGTCCGTGCTCTCTCTGCTCAGCCACTC 7 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.90 CpG sites = 21, Kimura (unadjusted) = 39.40 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.12 (16 / 130), avg. gap size = 1.00 (16 / 16) 311 32.33 1.61 7.69 chr5ptel1M 667569 667692 (332308) C MIRc#SINE/MIR (151) 117 1 m_b235s601i3 9239 chr5ptel1M 667569 GAGAGATT--GTGACTTGTCCATAATCACACAGCCAGGATTCTGTGTTCA 667616 i -- i vii i v v--- v- C MIRc#SINE/MIR 117 GAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAA---GTGG-CA 72 chr5ptel1M 667617 AATCTGAGATCAATCCTGAACCCAAGTGTTCCTGATTCAGAAGTCAGCTC 667666 i v i i ----- ii i v i vi ivi iv C MIRc#SINE/MIR 71 GAGCCGGGA-----CTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGC 27 chr5ptel1M 667667 TCTGTCTATTATGTCATTCCTCTTCG 667692 v i i iiii iv iv i C MIRc#SINE/MIR 26 TCTTTCCACTGCACCACACTGCCTCG 1 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.30 CpG sites = 25, Kimura (unadjusted) = 44.58 Transitions / transversions = 2.08 (25/12) Gap_init rate = 0.08 (10 / 123), avg. gap size = 1.10 (11 / 10) 15 21.08 2.50 2.50 chr5ptel1M 667752 667791 (332209) (AT)n#Simple_repeat 1 40 (0) m_b235s252i2 9240 chr5ptel1M 667752 ATATATATGTGTATTTGTGAAAGA-AAATATATATATATAT 667791 i i v i - v v - v (AT)n#Simple_ 1 ATATATATATATATATAT-ATATATATATATATATATATAT 40 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 17 12.69 0.00 0.00 chr5ptel1M 670410 670435 (329565) (A)n#Simple_repeat 1 26 (0) m_b235s252i3 9241 chr5ptel1M 670410 AAATAAAAAATAAAAAAAATAAAAAA 670435 v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAA 26 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 348 30.25 5.08 0.98 chr5ptel1M 670436 670632 (329368) L1ME4a_3end#LINE/L1 351 555 (316) m_b235s551i0 9242 chr5ptel1M 670436 AAAGAAGTGCATATCATTTGATCCAGTAATACTACTACTAGTTCTGTATC 670485 i v ? i v i v i v vvv v L1ME4a_3end#L 351 AAAAATGTNCATACCCTTTGACCCAGTAATTCCACTTCTAGGAATTTATC 400 chr5ptel1M 670486 CAAAAAAGATCACAAAAAAGGGGAAAAAACCTTCATCTACAAAAATATTT 670535 v ii i v iv i i v v ? v vv i v ii i i L1ME4a_3end#L 401 CTAAGGAAATAATCAGAGATGTGNACAAAGATTTATGTACAAGGATGTTC 450 chr5ptel1M 670536 AT------AT--TTTGTAGTGGCAAAGAATTGGAAATTCAGG--GAATGT 670575 ------ -- i i i i i -- iv--i L1ME4a_3end#L 451 ATCGCAGCATTATTTATAATAGCGAAAAATTGGAAA--CAACCTAAATGT 498 chr5ptel1M 670576 ACATCAGTTGGAGAAAGACTGAATAAGTTGTGGCATATGAATGTAATGGT 670625 v v i v i ?v ii i i i i i vv i? v L1ME4a_3end#L 499 CCAACAATAGGGGANTGGTTAAATAAATTATGGTACATCCATANAATGGA 548 chr5ptel1M 670626 GTGTTAT 670632 i i L1ME4a_3end#L 549 ATATTAT 555 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.04 CpG sites = 34, Kimura (unadjusted) = 40.95 Transitions / transversions = 1.36 (34/25) Gap_init rate = 0.03 (5 / 196), avg. gap size = 2.40 (12 / 5) 13 7.56 7.14 0.00 chr5ptel1M 672043 672070 (327930) (ATCAC)n#Simple_repeat 1 30 (0) m_b235s252i4 9243 chr5ptel1M 672043 ATCACATCACCT-TCATCACATCACA-CAC 672070 v -v - (ATCAC)n#Simp 1 ATCACATCACATCACATCACATCACATCAC 30 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.07 (2 / 27), avg. gap size = 1.00 (2 / 2) 12 22.67 0.00 0.00 chr5ptel1M 674575 674606 (325394) (GGAA)n#Simple_repeat 1 32 (0) m_b235s252i5 9244 chr5ptel1M 674575 GGGAGCAGGGAAAGAAGGAAGGGAGAAAGGAA 674606 i v i i i i (GGAA)n#Simpl 1 GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 32 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 72 0.00 0.00 0.00 chr5ptel1M 674714 674774 (325226) (AG)n#Simple_repeat 1 61 (0) c_b235s251i0 9245 chr5ptel1M 674714 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 674763 (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr5ptel1M 674764 AGAGAGAGAGA 674774 (AG)n#Simple_ 51 AGAGAGAGAGA 61 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 17 11.62 2.44 5.00 chr5ptel1M 675061 675101 (324899) (AAT)n#Simple_repeat 1 40 (0) m_b235s252i6 9246 chr5ptel1M 675061 AATAATAATAATAATAAATAAATAAAAAGGAGAA-AATAATA 675101 - - v vi v - (AAT)n#Simple 1 AATAATAATAATAAT-AAT-AATAATAATAATAATAATAATA 40 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.07 (3 / 40), avg. gap size = 1.00 (3 / 3) 572 30.26 3.21 3.21 chr5ptel1M 675295 675574 (324426) L1ME5_3end#LINE/L1 358 637 (304) m_b235s551i1 9247 chr5ptel1M 675295 ATACCCTTTGATCCAGCAGTGTTACTACTGGGATTATATCCCAAAGAGAT 675344 v i i viii v vv i L1ME5_3end#LI 358 ATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATATCCCAAAGAAAT 407 chr5ptel1M 675345 TATAAAGAAGG----GAAAGGGACCTGTATGTGCACGAATGTTTGTGGCA 675390 v v viv ----v i ---- i iv i ii v L1ME5_3end#LI 408 TCTCACACAGGTCCATAAGGGGAC----ATGTACGAGGATGTTCATTGCA 453 chr5ptel1M 675391 GCCCTTTTTGTAGTGGCTAGAAACTGGAAACTGAATGGATGTCCATCAGT 675440 vi v i vi i ii ii vivv i v L1ME5_3end#LI 454 GCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGGGTGTCCATCACT 503 chr5ptel1M 675441 TGGAGAATGGCTGAATAAATTGTGGTATATGAAAATTATGGAATATTACT 675490 v i v iii v iv v v ii i i - L1ME5_3end#LI 504 GGGAGAGTGGATAGGTAAAATGTGGTGGATGCACACCATGGAGTACTA-T 552 chr5ptel1M 675491 GT-TCTGTAAGAAATGACCAACAGGATGATTTCAGAAAG--GCCTGGAGA 675537 i-v v v iii vi vi -- v v v --i v vi L1ME5_3end#LI 553 GCAGCAGTTAGAAGCAACGGACTAGATG--TACACATAGCAACATGGATG 600 chr5ptel1M 675538 GA-CTTACACGAAC-TGATGCTGAGTGAAATGAGCAGGA 675574 - v -- - ii vi i i L1ME5_3end#LI 601 GATCTTAAA--AACATAGTGCTGAGTGAAAAAAGTAAGA 637 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.29 CpG sites = 45, Kimura (unadjusted) = 39.59 Transitions / transversions = 1.22 (45/37) Gap_init rate = 0.05 (14 / 279), avg. gap size = 1.29 (18 / 14) 596 25.40 2.58 2.58 chr5ptel1M 675295 675488 (324512) L1ME4c_3end#LINE/L1 361 554 (276) m_b235s551i2 9247 chr5ptel1M 675295 ATACCCTTTGATCCAGCAGTGTTACTACTGGGATTATATCCCAAAGAGAT 675344 i i i vii v v v i i i L1ME4c_3end#L 361 ATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAAT 410 chr5ptel1M 675345 TAT---AAAGAAGGGAAAGGGACCTGTATGTGCACGA--ATGTTTGTGGC 675389 v --- i i -- --- i -- ii v L1ME4c_3end#L 411 AATTCAAAAGAAGGAAAAAG--C---TATATGCACGAAGATGTTCATTGC 455 chr5ptel1M 675390 AGCCCTTTTTGTAGTGGCTAGAAACTGGAAACTGAATGGATGTCCATCAG 675439 vi v i i i v i i vivv ii v i L1ME4c_3end#L 456 AGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAA 505 chr5ptel1M 675440 TTGGAGAATGGCTGAATAAATTGTGGTATATGAAAATTATGGAATATTA 675488 v i i i i i i v? vviv L1ME4c_3end#L 506 TAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATATTA 554 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 31.30 CpG sites = 30, Kimura (unadjusted) = 32.11 Transitions / transversions = 1.67 (30/18) Gap_init rate = 0.04 (7 / 193), avg. gap size = 1.43 (10 / 7) 22 4.00 0.00 0.00 chr5ptel1M 676033 676058 (323942) (A)n#Simple_repeat 1 26 (0) m_b235s252i7 9248 chr5ptel1M 676033 AAAAAAAAAAAAAAAAAAAAAAAGAA 676058 i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAA 26 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 22 18.73 1.52 4.69 chr5ptel1M 676681 676746 (323254) (GAAAGA)n#Simple_repeat 1 64 (0) m_b235s252i8 9249 chr5ptel1M 676681 GAAAG-GAAAGAAATAGACACAGAGAAACAGAGACAGAGAGAGAGAGACA 676729 - i v v v v i v i i v (GAAAGA)n#Sim 1 GAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGA 50 chr5ptel1M 676730 AGGAGAGAATAGAGAAA 676746 -- - (GAAAGA)n#Sim 51 A--AGAGAA-AGAGAAA 64 Matrix = Unknown Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.06 (4 / 65), avg. gap size = 1.00 (4 / 4) 24 23.77 1.69 0.00 chr5ptel1M 676686 676744 (323256) (GA)n#Simple_repeat 1 60 (0) m_b235s252i9 9250 chr5ptel1M 676686 GAAAGAAATAGACACAGAGAAACAGAGACAGAGAGAGAGAGACAAGGAGA 676735 i i v v v i v v v ii (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr5ptel1M 676736 GA-ATAGAGA 676744 - v (GA)n#Simple_ 51 GAGAGAGAGA 60 Matrix = Unknown Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1) 741 28.17 2.66 5.47 chr5ptel1M 676786 677123 (322877) L1ME5_3end#LINE/L1 80 408 (533) m_b235s551i3 9251 chr5ptel1M 676786 ATATGAACAGACAATTTTCAGAAAAAGTTATC---AAAGCTATCTGTAGT 676832 i v i i vv i --- i v v-- i L1ME5_3end#LI 80 ATATGAACAGGCAATTTACAGAAGAGGAAACCCGAAAGGCTAACA--AGC 127 chr5ptel1M 676833 GATATAAAAA-ATGCTCTAAATAACCATTGATTAGAGAAATGCAAATTAA 676881 - i i - v v v ii v i i L1ME5_3end#LI 128 -ATATGAAGAGATGCTCAAACTCATTAGTAATCAGAGAAATGCAAATTAA 176 chr5ptel1M 676882 AACAATTCTGAAGTACCATCCCACATCTATCAGATTAGTTAATATGACAG 676931 ivv ii i iiii i i i i iv v --i L1ME5_3end#LI 177 AACAACAATGAGATATCACTTTACACCTATTAGACTGGCAAAAAT--TAG 224 chr5ptel1M 676932 AAAA--GGAAAATGACAAATACTGAAGGGGATGTGGGATGTGGGAAAATT 676979 i-- v v i ii --- v ---- i ? v L1ME5_3end#LI 225 AAAGCTGGATAATGCCAAGTGTT---GGCGA----GGATGTGGGGANATA 267 chr5ptel1M 676980 GAGACATTAATGCACTGTTGTTGAAGTTGTGTACTGATTCAGTCATTCTG 677029 ii vi v i v iiiv iv i v i L1ME5_3end#LI 268 GGAACCCTCATGCACTGCTGGTGGGAGTGTAGACTGGTGCAGCCATTCTG 317 chr5ptel1M 677030 TAGAGCAATTT---AATACTATGCCCAAAGTGTTATAAAATCATGCATCC 677076 v i --- i - ivi --- - iv - i v L1ME5_3end#LI 318 GAGAGCAATCTGGCAGTACT-TAGTCAAA---TTA-AGTAT-ACGCATAC 361 chr5ptel1M 677077 CTTTTGACCAGACAATATCATTATGAGGTCTGTATCCCAAAAAAATT 677123 i v vii vi ii vivi v i i L1ME5_3end#LI 362 CCTATGACCCAGCAATTCCGCTCCTGGGTATATATCCCAAAGAAATT 408 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.64 CpG sites = 57, Kimura (unadjusted) = 36.68 Transitions / transversions = 1.73 (57/33) Gap_init rate = 0.07 (22 / 337), avg. gap size = 1.23 (27 / 22) 27 5.20 2.50 0.00 chr5ptel1M 677134 677173 (322827) (AGGA)n#Simple_repeat 1 41 (0) m_b235s252i10 9252 chr5ptel1M 677134 AGG-AGGAAGGAATGAAGGAACGAAGGAAGGAAGGAAGGAA 677173 - v v (AGGA)n#Simpl 1 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 41 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1) 449 32.35 2.21 0.00 chr5ptel1M 678197 678332 (321668) MIRc#SINE/MIR 6 144 (124) m_b235s601i4 9253 chr5ptel1M 678197 CAGCATAGTACAAAGGATGGGACCCTGTGCTTGG-GCTAAAAATACCTTG 678245 ii i i iv vi ii v vi - ii ii v v MIRc#SINE/MIR 6 CAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGG 55 chr5ptel1M 678246 ATTCAAATCCCATTTCAAACACCTATCAGCTGTGTTAC--TCGGCAAACC 678293 i i i ivi viv i ii v -- v ii MIRc#SINE/MIR 56 GTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTC 105 chr5ptel1M 678294 ACTTAACCTGTTTGTGACTCAGTGTATTCTTTTGTAAAA 678332 v i v v v vi v i MIRc#SINE/MIR 106 ACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAA 144 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.41 CpG sites = 27, Kimura (unadjusted) = 44.11 Transitions / transversions = 1.59 (27/17) Gap_init rate = 0.01 (2 / 135), avg. gap size = 1.50 (3 / 2) 17 0.00 0.00 0.00 chr5ptel1M 680707 680725 (319275) (A)n#Simple_repeat 1 19 (0) m_b235s252i11 9254 chr5ptel1M 680707 AAAAAAAAAAAAAAAAAAA 680725 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAA 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 346 22.86 2.86 0.00 chr5ptel1M 681181 681250 (318750) MIR3#SINE/MIR 108 179 (29) m_b235s601i5 9255 chr5ptel1M 681181 ACTTTTCTGAGCCTT--TTTCCTCATATGAAAAATGAGAGGGTTGTACTG 681228 i i i i-- v v i v i MIR3#SINE/MIR 108 ACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTA 157 chr5ptel1M 681229 AATGAATTCCAAGATGCTTTCC 681250 i vi i i v i MIR3#SINE/MIR 158 GATGATCTCTAAGGTCCCTTCC 179 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.22 CpG sites = 11, Kimura (unadjusted) = 28.22 Transitions / transversions = 2.20 (11/5) Gap_init rate = 0.01 (1 / 69), avg. gap size = 2.00 (2 / 1) 18 0.00 0.00 0.00 chr5ptel1M 683210 683229 (316771) (TA)n#Simple_repeat 1 20 (0) m_b235s252i12 9256 chr5ptel1M 683210 TATATATATATATATATATA 683229 (TA)n#Simple_ 1 TATATATATATATATATATA 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 258 31.02 9.87 2.45 chr5ptel1M 684330 684481 (315519) L2#LINE/L2 2223 2385 (697) m_b235s601i6 9257 chr5ptel1M 684330 GTAGGTATTCCCCAAGACTCTGATTCCT----CCTCTCTTTATTTCTTTC 684375 v vi v i i -- v ---- ii iv i v L2#LINE/L2 2223 GTTGGAGTGCCCCAGGGCTC--AGTCCTTGGACCTCTTCTCTTCTCTATC 2270 chr5ptel1M 684376 TATATATCTCTCATTTGGTGACCTCAT-CAGCTTACATGAGTTCA----- 684419 i i- v vi ? i - ii - iv i ----- L2#LINE/L2 2271 TACAC-TCACTCCCTNGGTGATCTCATCCAGTCT-CATGGCTTTAAATAC 2318 chr5ptel1M 684420 ----TAAATGCAAATGATTACCAGATCTATCTATATAGACTCAGTCTCTC 684465 ---- v vi i v i i v v vi v iviii L2#LINE/L2 2319 CATCTATATGCTGATGACTCCCAAATTTATATCTCCAGCCCGGACCTCTC 2368 chr5ptel1M 684466 TCCTGGGCTCT-GGCTC 684481 i ii i- i L2#LINE/L2 2369 CCCTGAACTCCAGACTC 2385 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.03 CpG sites = 29, Kimura (unadjusted) = 42.26 Transitions / transversions = 1.71 (29/17) Gap_init rate = 0.06 (9 / 151), avg. gap size = 2.11 (19 / 9) 32 5.20 0.00 0.00 chr5ptel1M 684485 684524 (315476) (CT)n#Simple_repeat 1 40 (0) m_b235s252i13 9258 chr5ptel1M 684485 CTCTGGCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 684524 vv (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 40 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 44 0.00 0.00 0.00 chr5ptel1M 684525 684562 (315438) (CA)n#Simple_repeat 1 38 (0) c_b235s251i1 9259 chr5ptel1M 684525 CACACACACACACACACACACACACACACACACACACA 684562 (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACA 38 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 286 32.02 7.29 4.04 chr5ptel1M 685059 685250 (314750) L2a_3end#LINE/L2 318 515 (2) m_b235s601i7 9257 chr5ptel1M 685059 TTTCCCATA----TGATTGCCATCCAATCTATCAT-TATTTTGTCTTATC 685103 ii ---- v ii ii iv ii - i- i L2a_3end#LINE 318 TTCTCCATAGCACTTATCACCATCTGACATACTATATATTTTA-CTTATT 366 chr5ptel1M 685104 TAATTGATAAGTGCTGTCTCTCTCTCACTGTCATTAGAATGT--CCTTAA 685151 v v --- ii v i v --- i --v iv L2a_3end#LINE 367 TATTTGTT---TATTGTCTGTCTCCCCC---CACTAGAATGTAAGCTCCA 410 chr5ptel1M 685152 GGAGGG--GAAACTATTTTTTATCTTTCTC-----TGTATTGCAAGTTCT 685194 v -- ii v v i i i vi ----- iv v iv i L2a_3end#LINE 411 TGAGGGCAGGGACTTTTGTCTGTTTTGTTCACTGCTGTATCCCCAGCGCC 460 chr5ptel1M 685195 TTAGCACTGTATCTGGCCCGTAGAAAGCTCATAATAAATGCTGTCTGATT 685244 - v v ii v i v i v vi ii vvi v L2a_3end#LINE 461 T-AGAACAGTGCCTGGCACATAGTAGGCGCTCAATAAATATTTGTTGAAT 509 chr5ptel1M 685245 GGGTGA 685250 ii L2a_3end#LINE 510 GAATGA 515 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.32 CpG sites = 35, Kimura (unadjusted) = 43.31 Transitions / transversions = 1.46 (35/24) Gap_init rate = 0.07 (13 / 191), avg. gap size = 1.69 (22 / 13) 18 23.51 0.00 0.00 chr5ptel1M 686118 686157 (313843) (GA)n#Simple_repeat 1 40 (0) m_b235s252i14 9260 chr5ptel1M 686118 GAGATACAGAGAAAGAGAGAGTCAGAGACACACAGAGAGA 686157 v v i vv v v v (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 40 Matrix = Unknown Transitions / transversions = 0.14 (1/7) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 17 15.31 8.06 3.08 chr5ptel1M 686773 686834 (313166) (ATATGT)n#Simple_repeat 1 65 (0) m_b235s252i15 9261 chr5ptel1M 686773 ATA-GTA-ATGTTTATGT-T-TGTATATGTATACACACATGTGTATATGT 686818 - - v - - -- iii i (ATATGT)n#Sim 1 ATATGTATATGTATATGTATATGTATATGTAT--ATGTATATGTATATGT 48 chr5ptel1M 686819 GTTTGTA-CTGTATATG 686834 i v -v (ATATGT)n#Sim 49 ATATGTATATGTATATG 65 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.11 (7 / 61), avg. gap size = 1.00 (7 / 7) 449 26.40 11.27 1.28 chr5ptel1M 687061 687202 (312798) MIR1_Amn#SINE/MIR 5 160 (70) m_b235s601i8 9262 chr5ptel1M 687061 GAGGTAATATGATT-----GATTAACCATTGGGCCTGGAATCAGGAAGAC 687105 i i i i i----- vi v i i iv v i - MIR1_Amn#SINE 5 GAGGCAGTGTGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGA-GAC 53 chr5ptel1M 687106 CTGAGTTCAATTT--GACCTCAGCTACTTAC---------AATCCTGAGC 687144 i ? ? i-- i - v i ?i ---------i i i i MIR1_Amn#SINE 54 CTGGGTTCNANTCCCGGC-TCTGCCACTNGCCNGCTGNGTGACCTTGGGC 102 chr5ptel1M 687145 ATATAACTTGACCTCTATTTGCCTTGGTTTTCTCACCTGTAAAATGGAGC 687194 vi v ? v v? ii i i i v MIR1_Amn#SINE 103 AAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGGA 152 chr5ptel1M 687195 TAATAACA 687202 i i MIR1_Amn#SINE 153 TAATGATA 160 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.89 CpG sites = 27, Kimura (unadjusted) = 36.14 Transitions / transversions = 2.70 (27/10) Gap_init rate = 0.04 (5 / 141), avg. gap size = 3.60 (18 / 5) 648 28.04 4.89 4.89 chr5ptel1M 687086 687310 (312690) MIR#SINE/MIR 28 252 (10) m_b235s601i9 9262 chr5ptel1M 687086 GGGC-CTGGAATCAGGAAGACCTGAGTTC-AATTTGACCTCAGCTACTTA 687133 - ii - vvi i - iiviv v i MIR#SINE/MIR 28 GGGCTCTGGAGCCAG-ACTGCCTGGGTTCGAATCCCGGCTCTGCCACTTA 76 chr5ptel1M 687134 C---------AATCCTGAGCATATAACTTGACCTCTATTTGCCTTGGTTT 687174 ---------i i i i vi v i v v ii MIR#SINE/MIR 77 CTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTT 126 chr5ptel1M 687175 TCTCACCTGTAAAATGGAGCTAATAACAGAACCGAGCTTACAAGGTGGTT 687224 i i i v i v v v i i i v MIR#SINE/MIR 127 CCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTCATAGGGTTGTT 176 chr5ptel1M 687225 ATAAAAATAAAATGAAAAGATAGTTTTAAAAAGAAAAAAAGGGCTTAGCT 687274 i i ii v ------- --- v v viv v vv MIR#SINE/MIR 177 GTGAGGATTAAATG-------AGTT---AATACATGTAAAGCGCTTAGAA 216 chr5ptel1M 687275 TGGTTTCTGACACATAGTAGTTGCTACATAAATGTT 687310 ii vi i ivi vv MIR#SINE/MIR 217 CAGTGCCTGGCACATAGTAAGCGCTCAATAAATGTT 252 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.41 CpG sites = 34, Kimura (unadjusted) = 35.88 Transitions / transversions = 1.31 (34/26) Gap_init rate = 0.06 (14 / 224), avg. gap size = 1.57 (22 / 14) 16 9.98 0.00 5.88 chr5ptel1M 689230 689265 (310735) (AAAAC)n#Simple_repeat 1 34 (0) m_b235s252i16 9263 chr5ptel1M 689230 AAAACAAAACAAAACAACTAAAGAACAATAACAAAA 689265 -v v i - (AAAAC)n#Simp 1 AAAACAAAACAAAACAA-AACAAAACAA-AACAAAA 34 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 685 31.08 7.86 3.54 chr5ptel1M 689426 689832 (310168) L1ME3Cz_3end#LINE/L1 123 546 (451) m_b235s551i4 9264 chr5ptel1M 689426 CATATAAAAA--TGCTCTAAATCACTATTGATTAGATAAATGCAAATTAA 689473 i -- v vv v i i iv L1ME3Cz_3end# 123 CATATGAAAAGATGCTCAACCTCACTAGTAATCAGGGAAATGCAAATTAA 172 chr5ptel1M 689474 TACAACGCTGAGGTACCAACTCATACCTATCAGATTAGCTAAGATGTCCC 689523 v ? iv i vi i i i v i v --- L1ME3Cz_3end# 173 AACNACAATGAGATACCATTTCACACCCATCAGATTGGCAAAAATTT--- 219 chr5ptel1M 689524 CCCCCCAAAA----AAAAGAACCA----TTTGAGGGAATGTGGGAAAACT 689565 ------ ----i v iv ---- v v i i ii v L1ME3Cz_3end# 220 ------AAAAGTCTGACAATACCAAGTGTTGGCGAGGATGTGGAGAAACG 263 chr5ptel1M 689566 GGGACATTATTGTACTGTTGGTAGAATTATGAACTGATCCAAGAATTCTG 689615 i vi vv ii i i i v i i i i v vv i i L1ME3Cz_3end# 264 GGAACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTACAACCACTTTG 313 chr5ptel1M 689616 GGGAGCAATTTGGAACTAT--------GCTCAA-----GTATACCCTTGG 689652 i v v -------- i v ----- i vv L1ME3Cz_3end# 314 GAGAGCAATTTGGCAATATCTAGTAAAGTTGAAGATGCGCATACCCTACG 363 chr5ptel1M 689653 ATCCAGAAATACCACTGCTACTTCTGTATCCCAAAGAGATTTTT------ 689696 i v v v vv v i i i i i i i i------ L1ME3Cz_3end# 364 ACCCAGCAATTCCACTTCTAGGTATATACCCTAGAGAAACTCTCGCACAT 413 chr5ptel1M 689697 -TAAAAAGGAAGACCTATTTGAATGAAAATATTTATAGC--CATTCTTTT 689743 - iv v i i v i ---- ii ii i i v -- -- v L1ME3Cz_3end# 414 GTGCACAAGGAGACATGT----ACAAGGATGTTCATTGCAGCAT--TGTT 457 chr5ptel1M 689744 TGTGGTAATTAAGCACTAGAAATCAAAGGGATGTCTATTAATTAGAGAAA 689793 ii iiv iv i i iv vvvii i i vi i v L1ME3Cz_3end# 458 TGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCAATAGGGGAAT 507 chr5ptel1M 689794 GACTAAACAAGTTGTGGTATATGATTGTAATGGAATATT 689832 iv i i vvv ii i L1ME3Cz_3end# 508 GGATAAATAAATTGTGGTATATTCATACAATGGAATACT 546 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.75 CpG sites = 72, Kimura (unadjusted) = 41.66 Transitions / transversions = 1.44 (72/50) Gap_init rate = 0.06 (23 / 406), avg. gap size = 2.04 (47 / 23) 1104 26.96 1.54 1.54 chr5ptel1M 690532 690855 (309145) C L1ME5_3end#LINE/L1 (611) 330 7 m_b235s551i5 9265 chr5ptel1M 690532 CCAGATTGTTCTCCAGAATAGTTGGATTCGTTCACAACTCCACCAACAAT 690581 i i i v iiv ii vii i i C L1ME5_3end#LI 330 CCAGATTGCTCTCCAGAATGGCTGCACCAGTCTACACTCCCACCAGCAGT 281 chr5ptel1M 690582 GCATCAGTGTCCCAGTTTTCCCACATCCCCTCCAACATTCGTCGTTATTT 690631 v v i vi ? i i v i i v i ii C L1ME5_3end#LI 280 GCATGAGGGTTCCTATNTCCCCACATCCTCGCCAACACTTGGCATTATCC 231 chr5ptel1M 690632 ---TTTCCTGTCATCTTAGCCAATCTGACAGGTGTGTAGTGGTATCTCAG 690678 --- --- v i v i i i iv i v C L1ME5_3end#LI 230 AGCTTTC---TAATTTTTGCCAGTCTAATAGGTGTAAAGTGATATCTCAT 184 chr5ptel1M 690679 AGTTGTCTTAATTTGCATTTCTCTGATTAATCGTGATTTTGAACACTCTT 690728 v i v vi v i iiii C L1ME5_3end#LI 183 TGTTGTTTTAATTTGCATTTCTCTGATTACTAATGAGTTTGAGCATCTCT 134 chr5ptel1M 690729 TCATATGAGTGGTAATAGTTTCAATTTCATCATCTGAAAATTGTCCGTTC 690778 vv v iivv ivii v v v i i C L1ME5_3end#LI 133 TCATATGCTTGTTAGCCTTTCGGGTTTCCTCTTCTGTAAATTGCCTGTTC 84 chr5ptel1M 690779 ATATCCTTTGCCCATTTATCAATTGGAG--AATGGCTTGGTTTCTCATAA 690826 v v i --?vi v -- ii vi C L1ME5_3end#LI 83 ATATCCTTTGCCCATTTTTCTATTGGGGTTNCCGTCTT--TTTCTTGTTG 36 chr5ptel1M 690827 ATTAGAGTAAATTCTCTATATATTTTGGA 690855 v vivi i ii i i i C L1ME5_3end#LI 35 ATTTGCAGGAGTTCCTTGTATATTCTAGA 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.69 CpG sites = 53, Kimura (unadjusted) = 34.69 Transitions / transversions = 1.61 (53/33) Gap_init rate = 0.02 (7 / 323), avg. gap size = 1.43 (10 / 7) 1005 31.41 5.95 3.46 chr5ptel1M 690712 691585 (308415) C L1PREC2_orf2#LINE/L1 (0) 3294 2400 m_b235s551i6 9265 chr5ptel1M 690712 TGATTTTGAACACTCTTTCATATGAGTGGTAATAGTTTCAATTTCATCAT 690761 v i vi i vv v iiiv iv vv v v v C L1PREC2_orf2# 3294 TGATGTTGAGCTTTTTTTCATATGCTTGTTGGCCGCATGTATGTCTTCTT 3245 chr5ptel1M 690762 CTGAAAATTGTCCGTTCATATCCTTTGCCCATTTATCAATTGGAGAATGG 690811 i v i i i v i - i -- v C L1PREC2_orf2# 3244 TTGAAAAGTGTCTGTTCATGTCCTTTGCCCACTTTTTAAT-GGGG--TTG 3198 chr5ptel1M 690812 CTTGGTTT---CTCATAAATTAGAGTAAATTCTCTATATATTTTGGAAAT 690858 i v --- ii v vv i ii v vi v C L1PREC2_orf2# 3197 TTTGTTTTTTTCTTGTAAATTTGTTTAAGTTCCTTATAGATGCTGGATAT 3148 chr5ptel1M 690859 GAGGCCTTTATTAGAACCTTTAACTATGAAGATGTTTTCCCAGTTTGTTG 690908 v i i i vv v vivi iii ? v i v i v C L1PREC2_orf2# 3147 TAGACCTTTGTCAGATGCATAGTTTGCAAANATTTTCTCCCATTCTGTAG 3098 chr5ptel1M 690909 CTTCCCTTCTAATCTTGTTTGCA-TTAGTTTTGTTTGTACAAAAGCTTTT 690957 v vi vi v iii vii - vv i - i i i C L1PREC2_orf2# 3097 GTTGTCTGTTTACTCTGTTGATAGTTTCTTTTGCT-GTGCAGAAGCTCTT 3049 chr5ptel1M 690958 TAATTTGATGTAATCAAAATTTTCTATTTT-G----TGATGAATAATGGT 691002 i i vvi vv v v v - ---- v --i v i C L1PREC2_orf2# 3048 TAGTTTAATTAGATCCCATTTGTCAATTTTTGCTTTTGTTG--CAATTGC 3001 chr5ptel1M 691003 CTCTAGTTCATCTTTGGTCAC--AATTTCTTCC---TCCTCGACAGGTCT 691047 i i i -- i i - i-- i i v --- ---- v i C L1PREC2_orf2# 3000 TTTTGG--CGTCTTCG-TCATGAAATCTTTGCCCGTTCCT----ATGTCC 2958 chr5ptel1M 691048 GAGAGATAAACTAT--CTTATGTT--CCTCTAATTTATTTATAATCTCGT 691093 - - ii-- -- i v -- i i ivv v i i i v C L1PREC2_orf2# 2957 -AGA-ATGG--TATTGCCTAGGTTGTCTTCCAGGGTTTTTATAGTTTTGG 2912 chr5ptel1M 691094 TCTTTATGCCTAAATCATGGACCCATTTTGATCTTATCTTGGTACATGGT 691143 vi iiii i v vi i i vi v i v i C L1PREC2_orf2# 2911 GTTTTACATTTAAGTCTTTAATCCATCTTGAGTTGATTTTTGTATATGGT 2862 chr5ptel1M 691144 GTTAAGTGTGGGTCCATGTCTAAT-TTCTGCCATA---CTAATTTCCAGT 691189 v i viv vv ii - - --- i--- C L1PREC2_orf2# 2861 GTAAGGAAGGGGTCCAGTTTCAATCTTCTGC-ATATGGCTAG---CCAGT 2816 chr5ptel1M 691190 TATCCCAGCAGTTTTTGTCAAATAATGAATTCTTATCCCAAAAGTTAGGA 691239 viv i ii iv i i - v vv i v -- C L1PREC2_orf2# 2815 TATCCCAGCACCATTTATTGAATAGGGAGTCCTT-TCCCCATTGCTTG-- 2769 chr5ptel1M 691240 TCTTTG---GGTTTGTCAAACATTAGA--------------CTGTCTTGT 691272 i --- v i v i -------------- v i i C L1PREC2_orf2# 2768 TTTTTGTCAGCTTTGTCGAAGATCAGATGGTTGTAGGTGTGCGGCCTTAT 2719 chr5ptel1M 691273 ----GAAC---CTAACCTGTTCCACTGATCAACTAATCTATTTCTTAGCC 691315 ---- ii --- vi i i v ivvi i i vvi C L1PREC2_orf2# 2718 TTCTGGGCTCTCTATTCTGTTCCATTGGTCTATGTGTCTGTTTTTGTACC 2669 chr5ptel1M 691316 AATACCAAATGGTTTTGGTTACTGCTGCTTTATAATATAGTTTTAGATCA 691365 i viiv iv ii i i v ii i C L1PREC2_orf2# 2668 AGTACCATGCTGTTTTGGTTACTGTAGCCCTGTAGTATAGTTTGAAGTCG 2619 chr5ptel1M 691366 GATACAGGTAGGCCACCTTCA--TTTGATTTTTTTTTTCATTA--ATTCC 691411 i --- iiv vii i -- -- i v - -- v C L1PREC2_orf2# 2618 GGTA---GCGTGATGCCTCCAGCTTTG--TTCTTTTTGC-TTAGGATTGC 2575 chr5ptel1M 691412 CTTGAGATTTTCAACCTTTTATT--ATTCCATATGAATTCTGTTGTTATT 691459 - v v iiv i v --i i ivvi vi C L1PREC2_orf2# 2574 CTTG-GCTATTCGGGCTCTTTTTTGGTTCCATATGAATTTTAAAATAGTT 2526 chr5ptel1M 691460 TTTTCTAGATCATTAAAATATTTTCTTGGAAGTCTGATTGGTATAGCACT 691509 v vv i iv v iv v i v v i C L1PREC2_orf2# 2525 TTTTCTAGTTCTGTGAAGAATGTCATTGGTAGTTTGATAGGAATAGCATT 2476 chr5ptel1M 691510 AAGTAAATAGATTAGTTTAGGGAGTATAGCCATCTTTATTATATTTGCTC 691559 i i vvi i iv i v i i v iv vii C L1PREC2_orf2# 2475 GAATCTGTAAATTGCTTTGGGCAGTATGGCCATTTTAACGATATTGATTC 2426 chr5ptel1M 691560 AGCCTATCCAAGAGCACTTAATATTT 691585 vv v ivv i C L1PREC2_orf2# 2425 TTCCTATCCATGAGCATGGAATGTTT 2400 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.39 CpG sites = 148, Kimura (unadjusted) = 41.86 Transitions / transversions = 1.26 (148/117) Gap_init rate = 0.05 (48 / 873), avg. gap size = 1.73 (83 / 48) 577 27.42 1.59 1.59 chr5ptel1M 691583 691771 (308229) L1ME4c_3end#LINE/L1 367 555 (275) m_b235s551i7 9266 chr5ptel1M 691583 TTTGACCCAGCAGTGCTACTACTGGGCTTATACCCCAAGGAAATA---CT 691629 i i v i v vv v i i --- v L1ME4c_3end#L 367 TTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCA 416 chr5ptel1M 691630 AAAGAAGGGAAAGGGACCTGTATGTGCCAAAATGTTTGTGGCAGCCCTGT 691679 i i --- i ii v i ii v vi i L1ME4c_3end#L 417 AAAGAAGGAAAAAG---CTATATGCACGAAGATGTTCATTGCAGCGTTAT 463 chr5ptel1M 691680 TTGTAGTGGCCAGAAACTGGAAAATGAATGGATGCCCATCAATTGGAGAA 691729 i i i v i i vvivv ii i v v i L1ME4c_3end#L 464 TTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAA 513 chr5ptel1M 691730 TGCTTGGGTAAATTGTGGTATATGAATGTTATGGAATATTAT 691771 v ii i i v? iviv L1ME4c_3end#L 514 TGGTTAAGTAAATTATGGTACATCNACTCGATGGAATATTAT 555 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.51 CpG sites = 31, Kimura (unadjusted) = 35.37 Transitions / transversions = 1.55 (31/20) Gap_init rate = 0.02 (4 / 188), avg. gap size = 1.50 (6 / 4) 509 32.97 2.54 2.17 chr5ptel1M 691585 691860 (308140) L1ME5_3end#LINE/L1 366 642 (299) m_b235s551i8 9266 chr5ptel1M 691585 TGACCCAGCAGTGCTACTACTGGGCTTATACCCCAAGGAAATACTAAAGA 691634 i v ii v iv i i v v viv L1ME5_3end#LI 366 TGACCCAGCAATTCCGCTCCTGGGTATATATCCCAAAGAAATTCTCACAC 415 chr5ptel1M 691635 AGG----GAAAGGGACCTGTATGTGCCAAAATGTTTGTGGCAGCCCTGTT 691680 ----v i v i ---- ii ii v vi L1ME5_3end#LI 416 AGGTCCATAAGGGGACATGTACG----AGGATGTTCATTGCAGCGTTGTT 461 chr5ptel1M 691681 TGTAGTGGCCAGAAACTGGAAAATGAATGGATGCCCATCAATTGGAGAAT 691730 i vi i ii iivvivv i i v v i L1ME5_3end#LI 462 TGTGGTGGCGGGGAGTTGGAGGCAACCTGGGTGTCCATCACTGGGAGAGT 511 chr5ptel1M 691731 GCTTGGGTAAATTGTGGTATATGAATGTTATGGAATATTATTGTTCTGCG 691780 vv i v iv v iiii i i vvvv v iv L1ME5_3end#LI 512 GGATAGGTAAAATGTGGTGGATGCACACCATGGAGTACTATGCAGCAGTT 561 chr5ptel1M 691781 AGAAAGGACCAGCAGGATGAATACAGAGAGGCTTGGAGAGA-CTTACATG 691829 ivi vii vi v i v vii v vi - v -- L1ME5_3end#LI 562 AGAAGCAACGGACTAGATGTACACATAGCAACATGGATGGATCTTAAA-- 609 chr5ptel1M 691830 AAC-TGATGCTAACTGAAATGAGC-AGAACCAG 691860 - ii i v vi i- v L1ME5_3end#LI 610 AACATAGTGCTGAGTGAAAAAAGTAAGAAACAG 642 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.04 CpG sites = 48, Kimura (unadjusted) = 44.45 Transitions / transversions = 1.17 (48/41) Gap_init rate = 0.04 (10 / 275), avg. gap size = 1.30 (13 / 10) 18 10.71 4.76 2.33 chr5ptel1M 692254 692295 (307705) (AATAAAA)n#Simple_repeat 1 43 (0) m_b235s252i17 9267 chr5ptel1M 692254 AATAAAAAGT-TATAAT-AATAATAAATAAATAAAAAATAAAAA 692295 i -v v - v - (AATAAAA)n#Si 1 AATAAAAAATAAAAAATAAAAAATAAA-AAATAAAAAATAAAAA 43 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.07 (3 / 41), avg. gap size = 1.00 (3 / 3) 184 32.84 0.00 3.12 chr5ptel1M 692963 693028 (306972) C L2d2_3end#LINE/L2 (96) 459 396 m_b235s601i10 9268 chr5ptel1M 692963 CTGCCTTCAAGGAGTTTCTCTTCTACTGAGGGAAACAGAGCAGGTGAACT 693012 i i vivv v vi i iii -- i v C L2d2_3end#LIN 459 CTGCCCTCAAGGAGCTTACAATCTAGTTGGGGAGACAAGACA--TAAACA 412 chr5ptel1M 693013 GACAATAAGTCAAATA 693028 viii v i C L2d2_3end#LIN 411 CGTGAAAAGTTAAATA 396 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.16 CpG sites = 13, Kimura (unadjusted) = 45.08 Transitions / transversions = 1.62 (13/8) Gap_init rate = 0.03 (2 / 65), avg. gap size = 1.00 (2 / 2) 242 23.64 0.00 1.82 chr5ptel1M 692963 693018 (306982) C L2c_3end#LINE/L2 (81) 397 343 m_b235s601i11 9268 chr5ptel1M 692963 CTGCCTTCAAGGAGTTTCTCTTCTACTGAGGGAAACAGAGCAGGTGAACT 693012 i i ivivv v ii i - ? i v C L2c_3end#LINE 397 CTGCCCTCAAGGAGCTCACAGTCTAGTGGAGGAGACAGA-CANGTAAACA 349 chr5ptel1M 693013 GACAAT 693018 C L2c_3end#LINE 348 GACAAT 343 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.74 CpG sites = 8, Kimura (unadjusted) = 29.74 Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.02 (1 / 55), avg. gap size = 1.00 (1 / 1) 242 30.47 3.16 6.54 chr5ptel1M 693028 693185 (306815) C L2c_3end#LINE/L2 (213) 265 113 m_b235s601i12 9268 chr5ptel1M 693028 ACTGAGGTTGGGGTGTCAGAAATTAGGCATCCTGTCCAAGGTAATATGAG 693077 ii?v v ii -- v i vvvi i i vv C L2c_3end#LINE 265 ACTAGNCTTGGGGGGTCAGGGA--AGGCTTCCCGGAGGAGGTGACATCTG 218 chr5ptel1M 693078 AAATTTGCTTTGAAGGA--AGCTAAAAATT-GTAAGAAGTGGAGGTGATG 693124 iv vv ?i -- - ii i - iv -- i viiv C L2c_3end#LINE 217 AGCTGAGNCTTGAAGGATGAG-TAGGAGTTAGCCAG--GTGGAAGGAGGG 171 chr5ptel1M 693125 AGGCAGAACATTCCAGGT--TTGATCCAGCTTGTGAAAAGGCATGGAGAC 693172 i v i i--vv ivv v v ?i i C L2c_3end#LINE 170 GGGAAGAGCATTCCAGGCAGAGGGAACAGCATGTGCAAAGGCNCGGAGGC 121 chr5ptel1M 693173 CAGAGGGGAAAGA 693185 -----i C L2c_3end#LINE 120 -----AGGAAAGA 113 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.54 CpG sites = 24, Kimura (unadjusted) = 40.85 Transitions / transversions = 1.14 (24/21) Gap_init rate = 0.08 (13 / 157), avg. gap size = 1.15 (15 / 13) 211 37.65 1.71 5.78 chr5ptel1M 693167 693400 (306600) C L2#LINE/L2 (120) 2962 2738 m_b235s601i13 9268 chr5ptel1M 693167 GGAGACCAG-AGGGGA-AAGATACAGGAAGGAAAATGAGAAATAG--TAA 693212 vii - i -i i - ii v vv i i vi --i v C L2#LINE/L2 2962 GGAGAGTGGTAGGAGATGAGGT-CAGAGAGGTAACGGGGGACCAGATCAT 2914 chr5ptel1M 693213 GTAGGACTTGGCAGTTCAAGAAAAGAGCTGAGGAGTTTGTCTTTTAATCC 693262 i i v i vi vvi------- i v v v i C L2#LINE/L2 2913 GTAGGGCCTTGTAGGCCATTG-------TAAGGACTTTGGCTTTTACTCT 2871 chr5ptel1M 693263 AATGGCTCCTTTGGGAGCCATTCAGGATTTCTGAGCAGGGAAGTAAAAGA 693312 i -- ivvvv v i vii iv i i i i v vi C L2#LINE/L2 2870 GA--GTGAGATGGGAAGCCATTGGAGGGTTTTGAGCAGAGGAGTGACATG 2823 chr5ptel1M 693313 GTTAGGTCTGTGCCTTAGGAAGATGATTTGGGCAGCTGAGTGTAAGGATG 693362 i iv iii ii ii ii i v i iv v v - i i i C L2#LINE/L2 2822 ATCTGACTTACGTTTTAAAAGGATCACTCTGGCTGCTGTGT-TGAGAATA 2774 chr5ptel1M 693363 TGCTGGAGAGGAGAAAGACAGAAAGCTGCTGGAGACCA 693400 vi ? i i v ivv i v -- C L2#LINE/L2 2773 GACTGNAGGGGGGCAAGGGTGGAAGCAG--GGAGACCA 2738 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 54.52 CpG sites = 51, Kimura (unadjusted) = 55.56 Transitions / transversions = 1.59 (51/32) Gap_init rate = 0.07 (16 / 233), avg. gap size = 1.06 (17 / 16) 33 0.00 0.00 0.00 chr5ptel1M 693746 693773 (306227) (GT)n#Simple_repeat 1 28 (0) c_b235s251i2 9269 chr5ptel1M 693746 GTGTGTGTGTGTGTGTGTGTGTGTGTGT 693773 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGT 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 267 24.95 12.75 1.77 chr5ptel1M 695211 695312 (304688) C MIRc#SINE/MIR (74) 194 82 m_b235s601i14 9270 chr5ptel1M 695211 ATCTTCATGGCAACCCTGTGCAGTATG-AG---ATATATTTTGACTGCCA 695256 i iii vi v - --- vi v v iiv C MIRc#SINE/MIR 194 ATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCA 145 chr5ptel1M 695257 TTTTAC-----AGGAAGGTGAA---TAGAGAGGAATGGAATGACTTTTCT 695298 ----- iv i---i -- vi i vi i C MIRc#SINE/MIR 144 TTTTACAGATGAGGAAACTGAGGCTCAGAGAGG--TTAAGTGACTTGCCC 97 chr5ptel1M 695299 GA-GTCACACAGCTA 695312 i - C MIRc#SINE/MIR 96 AAGGTCACACAGCTA 82 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.34 CpG sites = 16, Kimura (unadjusted) = 31.34 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.07 (7 / 101), avg. gap size = 2.14 (15 / 7) 16 13.24 0.00 0.00 chr5ptel1M 696054 696078 (303922) (T)n#Simple_repeat 1 25 (0) m_b235s252i19 9271 chr5ptel1M 696054 TTCTTTTTTCTGTTTTTTTTTTTTT 696078 i i v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 14 29.93 0.00 5.97 chr5ptel1M 696054 696124 (303876) (TTCTCTT)n#Simple_repeat 1 67 (0) m_b235s252i20 9272 chr5ptel1M 696054 TTCTTTTTTCTGTTTTTTTTTTTTTCCCCCTCTCTCCTGGTTTTTCTCTT 696103 i v i i i - iii ii vvi (TTCTCTT)n#Si 1 TTCTCTTTTCTCTTTTCTCTTTTCT-CTTTTCTCTTTTCTCTTTTCTCTT 49 chr5ptel1M 696104 TTGTTCTGATTTCTCTCTTCT 696124 -i -- i (TTCTCTT)n#Si 50 TT-CTCT--TTTCTCTTTTCT 67 Matrix = Unknown Transitions / transversions = 4.00 (12/3) Gap_init rate = 0.06 (4 / 70), avg. gap size = 1.00 (4 / 4) 44 21.28 2.29 3.88 chr5ptel1M 696158 696288 (303712) (AGAA)n#Simple_repeat 1 129 (0) m_b235s252i21 9273 chr5ptel1M 696158 AGATAGATAGAGAAAGAAAGATAGAAA-AAAGAAAGAAAGAAATGACAG- 696205 v - - v - - v - (AGAA)n#Simpl 1 AGAAAGA-A-AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA-GAAAGA 47 chr5ptel1M 696206 AAGGAAGAAAGGAAGAAAG-AAGAGAGGAAGGGAAGGAAGGGATGGAAGA 696254 i i - - i -i i i i v i (AGAA)n#Simpl 48 AAGAAAGAAAGAAAGAAAGAAAGA-AAGAA-AGAAAGAAAGAAAGAAAGA 95 chr5ptel1M 696255 AGAAAAGAAGGAAGGAAGGAGTGCAGAAAAGAAA 696288 ii i i i iv v ii (AGAA)n#Simpl 96 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 129 Matrix = Unknown Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.06 (8 / 130), avg. gap size = 1.00 (8 / 8) 13 6.51 8.82 2.78 chr5ptel1M 697786 697819 (302181) (TAAAAAG)n#Simple_repeat 1 36 (0) m_b235s252i22 9274 chr5ptel1M 697786 TATAAA-TAAAAA-TAAAAAGT-AAAAGTGAAGAAGT 697819 v - - - - i (TAAAAAG)n#Si 1 TAAAAAGTAAAAAGTAAAAAGTAAAAAGT-AAAAAGT 36 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.12 (4 / 33), avg. gap size = 1.00 (4 / 4) 21 19.59 0.00 3.92 chr5ptel1M 698000 698052 (301948) (TCCC)n#Simple_repeat 1 51 (0) m_b235s252i23 9275 chr5ptel1M 698000 TCCCTCCCTCTCTCTCCCTTCTTCTTTCCCTCCCTCTCTTCCTTCTTCCC 698049 - - i i ii i i i i (TCCC)n#Simpl 1 TCCCTCCCTC-C-CTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCC 48 chr5ptel1M 698050 TCC 698052 (TCCC)n#Simpl 49 TCC 51 Matrix = Unknown Transitions / transversions = 1.00 (8/0) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.00 (2 / 2) 15 16.88 0.00 2.94 chr5ptel1M 699050 699084 (300916) (ATT)n#Simple_repeat 1 34 (0) m_b235s252i24 9276 chr5ptel1M 699050 ATTCTTTTTGTATGTTATTATTATTATTATTTTTA 699084 v v i - i v (ATT)n#Simple 1 ATTATTATTAT-TATTATTATTATTATTATTATTA 34 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 16 0.00 0.00 0.00 chr5ptel1M 699273 699289 (300711) (T)n#Simple_repeat 1 17 (0) m_b235s252i25 9277 chr5ptel1M 699273 TTTTTTTTTTTTTTTTT 699289 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTT 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 chr5ptel1M 699912 699928 (300072) (A)n#Simple_repeat 1 17 (0) m_b235s252i26 9278 chr5ptel1M 699912 AAAAAAAAAAAAAAAAA 699928 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 158 24.92 0.79 0.79 chr5ptel1M 700553 700932 (299068) (CCTT)n#Simple_repeat 1 380 (0) m_b235s252i27 9279 chr5ptel1M 700553 CCTTCTTTCCCTCCTTCCCTTCTTCCCTCTCTGCCTCCCTCCTTTTCTCT 700602 i i i i i - v i i i i ii (CCTT)n#Simpl 1 CCTTCCTTCCTTCCTTCCTTCCTTCCTTC-CTTCCTTCCTTCCTTCCTTC 49 chr5ptel1M 700603 CTACCTCCCTTCC-TCTCTCCTTCCCTCCCTTCCCTCTTTCCTT-CTT-T 700649 v i - ii - i i i - -i (CCTT)n#Simpl 50 CTTCCTTCCTTCCTTCCTTCCTT-CCTTCCTTCCTTCCTTCCTTCCTTCC 98 chr5ptel1M 700650 TTTCTTCCTTCCTTCCCTCCTTCTTTCCTACCTTCCCTCCTCCCTTCTTT 700699 i i i v i i i (CCTT)n#Simpl 99 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 148 chr5ptel1M 700700 CCTTCTATCCTTTCTTCCCTCCTTCTTTGTTTCTTTCCTTCCCTCCCTCC 700749 iv i i i vi i i i (CCTT)n#Simpl 149 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 198 chr5ptel1M 700750 TTCCTCCCTTTCTCCCTCCCTCCCTCTCTCTCTTCCTTCCTTCCTTCCTT 700799 i i i i i ii ii (CCTT)n#Simpl 199 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 248 chr5ptel1M 700800 CTTTTTCACCTTTCTTCCTCCCTCCCCCCTCTCCCTTCCTTCCTTCTTTC 700849 i iiiv i i i ii - i i (CCTT)n#Simpl 249 CCTTCCTTCCTTCCTTCCTTCCTTCCTTC-CTTCCTTCCTTCCTTCCTTC 297 chr5ptel1M 700850 CTCCCTCCCTTCTTTCTTTCCTTTGTCCCTCCCTCCCTTTCTTCATTCCT 700899 i i i i iv i i i i v (CCTT)n#Simpl 298 CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT 347 chr5ptel1M 700900 CCCTCCCTCTCTTCCTTCCTTCTCTCCTTCCTT 700932 i i ii ii (CCTT)n#Simpl 348 TCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 380 Matrix = Unknown Transitions / transversions = 8.38 (67/8) Gap_init rate = 0.02 (6 / 379), avg. gap size = 1.00 (6 / 6) 502 20.62 4.94 1.19 chr5ptel1M 701719 701880 (298120) C Charlie4a#DNA/hAT-Charlie (0) 508 341 m_b235s502i0 9280 chr5ptel1M 701719 CAGAAATTCCTAAGCATCTTTGTGTCATGGACCTCCTGGTCATACTG--A 701766 iii i v v i i i i v v vv --i C Charlie4a#DNA 508 CAGGGGTTCTTAACCTTTTTTGTGCCATGGACCCCTTTGGCAGTCTGGTG 459 chr5ptel1M 701767 AAG--TAACGACATTCTTTTTAGAATTATG-TTTTAAATATATAAAATAA 701813 -- vv -ii i i v - ii C Charlie4a#DNA 458 AAGCCTATGGAC-CCCTTCTCAGAATAATGTTTTTAAATGCATAAAATAA 410 chr5ptel1M 701814 AATA-ATAGCATCATAAAAGAAACCCACTATATTTAAAT--AATTATCAA 701860 - v i i i v i v -- i C Charlie4a#DNA 409 AATACATAGGATTACAAAGGAAACCAATTATATTGAAATACAGTTATCAA 360 chr5ptel1M 701861 AATACTTATAAAACCAAATT 701880 - v ? C Charlie4a#DNA 359 AATA-TTAAAAAANCAAATT 341 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 24.74 CpG sites = 20, Kimura (unadjusted) = 24.74 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.04 (7 / 161), avg. gap size = 1.43 (10 / 7) 21 7.71 0.00 0.00 chr5ptel1M 702059 702086 (297914) (CA)n#Simple_repeat 1 28 (0) m_b235s252i28 9281 chr5ptel1M 702059 CACGCACACACACACACATACACACACA 702086 i i (CA)n#Simple_ 1 CACACACACACACACACACACACACACA 28 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 245 32.64 2.68 1.32 chr5ptel1M 703203 703351 (296649) L1MC5_3end#LINE/L1 428 578 (2116) m_b235s551i9 9282 chr5ptel1M 703203 ACCTATGCATACAAAAATATTTATAGCAACTCT-CTTCTCAGGGCAAAGA 703251 v -- iiv i v i v -i v v vi ii L1MC5_3end#LI 428 ACGTATGCA--CAAGGCTATTCATTGCAGCACTATTTGTAATAGCAAAAG 475 chr5ptel1M 703252 ATTGGAAATTGAGGGTATGCCCATCAATTGGGGAAATGCTGAATAAATTG 703301 i ivivvviv i v vvv i i i L1MC5_3end#LI 476 ACTGGAAACAACCCAAATGTCCATCAATAGGGGACTGGTTGAATAAACTA 525 chr5ptel1M 703302 TGGTATATGATTATGATGGAATATTA--CTGTTTT-ATAGGGAATGATGA 703348 i vvvi ii i i -- v i v - v i v L1MC5_3end#LI 526 TGGTACATCCACACAATGGAGTACTATGCAGCTGTAAAAAGGAATGAGGA 575 chr5ptel1M 703349 ACA 703351 i L1MC5_3end#LI 576 ATA 578 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.70 CpG sites = 25, Kimura (unadjusted) = 43.70 Transitions / transversions = 1.09 (25/23) Gap_init rate = 0.03 (5 / 148), avg. gap size = 1.20 (6 / 5) 346 26.08 3.39 2.52 chr5ptel1M 703212 703329 (296671) L1ME2z_3end#LINE/L1 435 553 (638) m_b235s551i10 9282 chr5ptel1M 703212 TACAAAAATATTTATAGCAACTCTCTTC-TCAGGGCAAAGAATTGGAAAT 703260 i i i i i v - v vi v i i i L1ME2z_3end#L 435 TACAAGAATGTTCATAGCAGCTTTATTCATAATAGCCAAAAACTGGAAAC 484 chr5ptel1M 703261 TG---AGGGTATGCCCATCAATTGGGGAAATGCTGAATAAATTGTGGTAT 703307 v --- --- i iv i vv v i i i L1ME2z_3end#L 485 AGCCCAGG---TGTCCATCAACAGGAGAATGGATAAACAAACTGTGGTAT 531 chr5ptel1M 703308 ATGATTATGATGGAATATTACT 703329 vvv ii i L1ME2z_3end#L 532 ATTCATACAATGGAATACTACT 553 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.86 CpG sites = 18, Kimura (unadjusted) = 32.86 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.04 (5 / 117), avg. gap size = 1.40 (7 / 5) 13 17.57 0.00 7.32 chr5ptel1M 703555 703598 (296402) (TTTTTC)n#Simple_repeat 1 41 (0) m_b236s252i0 9283 chr5ptel1M 703555 TTTTTCACTTTATTTTTCTTGAGGGTTTTTTTCTTTTTCTTTTT 703598 vi v ---vv i (TTTTTC)n#Sim 1 TTTTTCTTTTTCTTTTTCTT---TTTCTTTTTCTTTTTCTTTTT 41 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.07 (3 / 43), avg. gap size = 1.00 (3 / 3) 23 10.68 3.57 5.45 chr5ptel1M 703867 703922 (296078) (ATTA)n#Simple_repeat 1 55 (0) m_b236s252i1 9284 chr5ptel1M 703867 ATTAATTAATTAATTAGTTAA--AATAAATTTAATGAATTTAGTTTAAAT 703914 i -- v - v - -v v (ATTA)n#Simpl 1 ATTAATTAATTAATTAATTAATTAATTAA-TTAATTAA-TTA-ATTAATT 47 chr5ptel1M 703915 AATTAATT 703922 (ATTA)n#Simpl 48 AATTAATT 55 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.07 (4 / 55), avg. gap size = 1.25 (5 / 4) 245 32.08 0.00 0.00 chr5ptel1M 704132 704237 (295763) C L1MC_orf2#LINE/L1 (587) 2707 2602 m_b236s551i1 9285 chr5ptel1M 704132 CTACTCTTTTCCATTGATCCACCACTCTGTTTCTTAGCTAATCCCAGATT 704181 i v i iivv i ii v i v v i C L1MC_orf2#LIN 2707 CTATTCTGTTCCATTGATCTATTTGTCTATTCTTTCGCCAATACCACACT 2658 chr5ptel1M 704182 GTTTTGATGATTACCACTTTATAGTACTGTTTGACATCTGGTATGGTTAG 704231 i v i iivi vvvi vi v vv i C L1MC_orf2#LIN 2657 GTCTTGATTACTGTAGCTTTATAGTAAGTCTTGAAGTCGGGTAGTGTCAG 2608 chr5ptel1M 704232 GCCACC 704237 v v C L1MC_orf2#LIN 2607 TCCTCC 2602 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 42.47 CpG sites = 17, Kimura (unadjusted) = 42.47 Transitions / transversions = 1.00 (17/17) Gap_init rate = 0.00 (0 / 105), avg. gap size = 0.0 (0 / 0) 239 23.54 0.00 1.96 chr5ptel1M 704332 704383 (295617) C L2d_3end#LINE/L2 (8) 508 458 m_b236s601i0 9286 chr5ptel1M 704332 TCTATCAAATAAACATTTATTAAGTATCTACTATGTGTTAGGCATTGTGC 704381 v -i ii i iii i vi i C L2d_3end#LINE 508 TCAATCAA-CAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTGTGC 460 chr5ptel1M 704382 TA 704383 C L2d_3end#LINE 459 TA 458 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.93 CpG sites = 10, Kimura (unadjusted) = 30.27 Transitions / transversions = 5.00 (10/2) Gap_init rate = 0.02 (1 / 51), avg. gap size = 1.00 (1 / 1) 251 22.22 0.00 0.00 chr5ptel1M 704339 704383 (295617) C L2d2_3end#LINE/L2 (12) 543 499 m_b236s601i1 9286 chr5ptel1M 704339 AATAAACATTTATTAAGTATCTACTATGTGTTAGGCATTGTGCTA 704383 i i i iii i iv i C L2d2_3end#LIN 543 AACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTA 499 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.86 CpG sites = 9, Kimura (unadjusted) = 28.56 Transitions / transversions = 9.00 (9/1) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 13 4.76 0.00 4.35 chr5ptel1M 704535 704558 (295442) (TCTT)n#Simple_repeat 1 23 (0) m_b236s252i2 9287 chr5ptel1M 704535 TCTTTTTTTCTTTCTCTTCTTTCT 704558 i - (TCTT)n#Simpl 1 TCTTTCTTTCTTTCT-TTCTTTCT 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 447 31.66 4.48 4.48 chr5ptel1M 704574 705198 (294802) C L1MD_orf2#LINE/L1 (1064) 2230 1606 m_b236s551i2 9288 chr5ptel1M 704574 TATACAGACATGCTGACAATTTATTT----GTGTTTATCTTGGATTCTGT 704619 i v ---- v ----i ? v i i C L1MD_orf2#LIN 2230 TATATAGAAAT----ACAATTGATTTTTGTATGTTNATCTTGTATCCTGC 2185 chr5ptel1M 704620 AACTTTGATAAAGTTGTTCATTGTTTGGATTAGTTTTTTTTTTTTTTATT 704669 i i v i v iii i iv vv vv v ----- -- C L1MD_orf2#LIN 2184 GACCTTGCTGAACTCACTTATTAGTTCTAGGAGTTTTTTTGT-----A-- 2142 chr5ptel1M 704670 TGATTATCTTGGG-TTTTCTAAATGTATCATCATAGCATTGGCAAA-AAG 704717 - -i - vi iv iv iv iv - i C L1MD_orf2#LIN 2141 -GATT-CCTTGGGATTTTCTACGTAGACAATCATGTCATCTGCAAATAGG 2094 chr5ptel1M 704718 GATAGTATTGTTTCCTTATTGCCTAT---TCTAACTAGTTCACTTTATTT 704764 i v i i iv v v --- v iv -- i - vi C L1MD_orf2#LIN 2093 GACAGTTTTATTTCTTCCTTTCCAATCTGTATGCCT--TTTA-TTTCCTT 2047 chr5ptel1M 704765 TTCTTATCTTATTTCTATTGCTGGCATTTCTGGTACAACATCAAATATTG 704814 ii v vv v i v i ii v ii ii vvi C L1MD_orf2#LIN 2046 TTCTTGCCTTATTGCACTGGCTAGAACTTCCAGTACTATGTTGAATAAGA 1997 chr5ptel1M 704815 GACGTCAAAAAGTGGACACCCTTACTTCACCCAGGATAGTCCTGGGAGGA 704864 vv --i i i i i i iiii vv --- i i i C L1MD_orf2#LIN 1996 GTGGT--GAGAGCGGACATCCTTGCCTTGTTCCCGAT---CTTAGGGGGA 1952 chr5ptel1M 704865 ---TTTCTAGTTTATCCCCATTAAAGAAAATATTTGTTTTTGGTTTCAGA 704911 ---iv ii i v v iv vi i v i v v ivvi C L1MD_orf2#LIN 1951 AAGCATTCAGTCTTTCACCATTAAGTATGATGTTAGCTGTAGGTTTTTTG 1902 chr5ptel1M 704912 TAGATAACTATTTATCATTTTTTAAAAGC-ATCATTTATTTCTATGTTTT 704960 i- v vv vvii i-vi v i i - ? C L1MD_orf2#LIN 1901 TAGATG-CTCTTTATCAAGTTGAGGAAGTTCCCCTCTATTCCTA-GTTTN 1854 chr5ptel1M 704961 CTGATAATTTTAATTG-GAATGTTTTTTTTTAATTTTGTCAAAAGCTTTT 705009 v i v ii- vv v v-- v C L1MD_orf2#LIN 1853 CTGAGAGTTTTTATCATGAATGGGTGTTG--AATTTTGTCAAATGCTTTT 1806 chr5ptel1M 705010 TCTGCATAAAACATTATAATCATGTAATTTCTGT---------TATTGAT 705050 v viiv i i i v --------- i i C L1MD_orf2#LIN 1805 TCTGCATCAATTGATATGATCATGTGATTTTTCTTCTTTAGCCTGTTAAT 1756 chr5ptel1M 705051 ATGATCAATTTCTATG--TGAAGTTTTCTTGATATTAAGTCAATCCTACA 705098 i vi v vv -- -- -vi i ii ii i i C L1MD_orf2#LIN 1755 ATGGTGGATTACATTGATTGA--TTTTC-GAATATTGAACCAGCCTTGCA 1709 chr5ptel1M 705099 ATTCTTATATAAATCCTATCTGATCATCTTATATAATCTTTGTGATATAT 705148 v?i viv i i ii i vv i ii v v C L1MD_orf2#LIN 1708 TNCCTGGAATAAACCCCACTTGGTCATGGTGTATAATTCTTTTTATATAT 1659 chr5ptel1M 705149 TTCTATAGTTTTCTTGTTATCATTTTATT---AATTTTTGCACTAATATT 705195 v iv v i?vi i vi i ---i iiiv i C L1MD_orf2#LIN 1658 TGCTGAATTCNATTTGCTAATATTTTGTTGAGGATTTTTGCGTCTATGTT 1609 chr5ptel1M 705196 CAT 705198 C L1MD_orf2#LIN 1608 CAT 1606 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.48 CpG sites = 108, Kimura (unadjusted) = 42.72 Transitions / transversions = 1.33 (108/81) Gap_init rate = 0.06 (38 / 624), avg. gap size = 1.47 (56 / 38) 22 36.67 0.00 2.13 chr5ptel1M 705272 705367 (294633) (TA)n#Simple_repeat 1 94 (0) m_b236s252i3 9289 chr5ptel1M 705272 TATGTATGTATATGCACATACACACACACATATATAAACATAAACATGTA 705321 i i ii i i i i i i v i v i i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr5ptel1M 705322 TATATGTATGTGTGTAGATAAACTAGTTATATAAATCAAATATTTA 705367 i i i i v v - vv v - v v (TA)n#Simple_ 51 TATATATATATATATATATATA-TATATATATATAT-ATATATATA 94 Matrix = Unknown Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.02 (2 / 95), avg. gap size = 1.00 (2 / 2) 1145 32.47 7.40 1.86 chr5ptel1M 705887 706548 (293452) L2#LINE/L2 2192 2889 (193) m_b236s601i2 9290 chr5ptel1M 705887 TGACTACTCCTTAATCTCCTTAGCTACATCTTCTTGTAGGA-TCCCCTAA 705935 ii v i - i--- v v ?vvi v - v i i L2#LINE/L2 2192 TGGTTCCTCCTCA-TCTCCC---CGACCTCTNAACGTTGGAGTGCCCCAG 2237 chr5ptel1M 705936 GGTTCTGTCTTGTGTTCTCTTTTCTTCTTTCTCTATACAATTTCACTTGG 705985 i v i vv vi i i v i vvvi v ? L2#LINE/L2 2238 GGCTCAGTCCTTGGACCTCTTCTCTTCTCTATCTACACTCACTCCCTNGG 2287 chr5ptel1M 705986 TGATCTCAT-TAGT----TGATTTCAGTTATCACCTTTTTTGCAGATAAC 706030 -i ---- ii i iv i i - v v v i L2#LINE/L2 2288 TGATCTCATCCAGTCTCATGGCTTTAAATACCATC-TATATGCTGATGAC 2336 chr5ptel1M 706031 TCTCAGATTTGTGTGTCTAGCCCTAACCACTGCCCTGTGATTTCTAA-TC 706079 i i i i v i vi v v -i i i vi - L2#LINE/L2 2337 TCCCAAATTTATATCTCCAGCCCGGACCTCTCCCCTG-AACTCCAGACTC 2385 chr5ptel1M 706080 ATATATCTATTATAGCCTATTAGACATTTTGAACTACATATCCCATAGGT 706129 i i -- iv i v i iv vi iv i iv i L2#LINE/L2 2386 GTATATCCA--ACTGCCTACTCGACATCTCCACTTGGATGTCTAATAGGC 2433 chr5ptel1M 706130 ATCTTAAACTCAACAGGGTCCATAAATGAACTCATCATC-TCCCCCACAA 706178 i i -v v v v v - v - L2#LINE/L2 2434 ATCTCAAACTTAACA-TGTCCAAAACTGAACTCCTGATCTTCCCCCTCA- 2481 chr5ptel1M 706179 CAATCTTTACCT-CTGTAAT-TTCTGTATTAATGTGGAGGATACCACCAT 706226 - i viv - i i i - ivi ivvv ?i v ii v v L2#LINE/L2 2482 -AACCTGCTCCTCCCGCAGTCTTCCCCATCTCAGTNAATGGCAACTCCAT 2530 chr5ptel1M 706227 CCTTCCA-TCACCCAGGCT-CACACCTTAGATATCAACCTCAACTCTCTT 706274 - ii i i-v v i -i v ii iii L2#LINE/L2 2531 CCTTCCAGTTGCTCAGGCCAAAAACCTTGGA-GTCATCCTTGACTCCTCT 2579 chr5ptel1M 706275 CT----------CCCCATATCCAATTCATTATCAAATTTTGTTTTTCCTA 706314 ---------- i i i v ii ivvii L2#LINE/L2 2580 CTTTCTCTCACACCCCACATCCAATCCATCAGCAAATCCTGTCGGCTCTA 2629 chr5ptel1M 706315 CTTTCATGATATCATTTGTAA-ATGCCCA-TTCT------CTCTTCTGC- 706355 i vi - iiiv -vi v - ------ iv - L2#LINE/L2 2630 CCTTCAAAATAT-ATCCAGAATCCGACCACTTCTCACCACCTCCACTGCC 2678 chr5ptel1M 706356 ----TCCTGGAACTTATTACC-TCATATTTGTTCTG--TTACCG---TAG 706395 ----i vv vviii - v i vvi -- i --- L2#LINE/L2 2679 ACCACCCTGGTCCAAGCCACCATCATCTCTCGCCTGGATTACTGCAATAG 2728 chr5ptel1M 706396 CCTGCTGGTTGATCTTCCTGTATTAA-----GTCTTTCTCCACTCCATCC 706440 v iii i i iv iv ----- i iii ? v i i L2#LINE/L2 2729 CCTCCTAACTGGTCTCCCTGCTTCCACCCTTGCCCCCCTNCAGTCTATTC 2778 chr5ptel1M 706441 TCCACTCAGCTATTAAATTGATCCTCCTAAAGTATATATCTGACTATGCC 706490 v v viii i v ii iii vi v ii i L2#LINE/L2 2779 TCAACACAGCAGCCAGAGTGATCCTTTTAAAACGTAAGTCAGATCATGTC 2828 chr5ptel1M 706491 A--CCTCTATTTAATAAAATCTAGTAGCTTTTCA-CTGATTCCAAGTGAA 706537 -- ii i v vvv i i i ii - v i vi i L2#LINE/L2 2829 ACTCCTCTGCTCAAAACCCTCCAATGGCTTCCCATCTCACTCAGAGTAAA 2878 chr5ptel1M 706538 GATAAAAGCCC 706548 iiiv i L2#LINE/L2 2879 AGCCAAAGTCC 2889 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.06 CpG sites = 130, Kimura (unadjusted) = 44.84 Transitions / transversions = 1.60 (130/81) Gap_init rate = 0.05 (34 / 661), avg. gap size = 1.82 (62 / 34) 23 22.13 0.00 0.00 chr5ptel1M 706824 706871 (293129) (A)n#Simple_repeat 1 48 (0) m_b236s252i4 9291 chr5ptel1M 706824 AAAAACCAAACCAAAATAACAATAACCAAAAAAAAAAAAAAAAAAAAA 706871 vv vv v v v vv (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 48 Matrix = Unknown Transitions / transversions = 0.00 (0/9) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 818 28.03 1.67 3.39 chr5ptel1M 708787 709026 (290974) MIRc#SINE/MIR 13 248 (20) m_b236s601i3 9292 chr5ptel1M 708787 GTCCAGTGGAAAGACCTTTGGACTCTG-GTCAATGAAAAGCTTGAGTCTG 708835 v v vi iv - -- i ii i i ii MIRc#SINE/MIR 13 GTGCAGTGGAAAGAGCACTGGACTTGGAGTCA--GGAAGACCTGGGTTCG 60 chr5ptel1M 708836 AATTCTTCTTCTAGTATTTATCAGTTTTGTGATCCTGGACAAGTCTTTAA 708885 i i ivvi ivi i ii i v i i i vi v MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTA 110 chr5ptel1M 708886 ATAATTTTGAGCCTCAGTTTCCTCTTCTGTAAAATTTGAATTATAATAAT 708935 ivvi i v vv i v vi MIRc#SINE/MIR 111 ACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACC 160 chr5ptel1M 708936 TGCAGGAACTACCTCATAAGGATGCTGTAAAGATCCAATGAGACAATCAA 708985 vvviv i i v i i i v ----i MIRc#SINE/MIR 161 TGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGA----TAA 206 chr5ptel1M 708986 TATATGTGAA---GCCTTGTTGAAACTTTAAAATCCACTACAAA 709026 i --- i -- v i v vv MIRc#SINE/MIR 207 TGTATGTGAAAGCGCTTTGT--AAACTGTAAAGTGCTATACAAA 248 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.59 CpG sites = 38, Kimura (unadjusted) = 35.97 Transitions / transversions = 1.41 (38/27) Gap_init rate = 0.04 (10 / 239), avg. gap size = 1.20 (12 / 10) 354 29.37 1.75 7.41 chr5ptel1M 709864 709977 (290023) C MIRc#SINE/MIR (149) 119 12 m_b236s601i4 9293 chr5ptel1M 709864 CAAACAGGAAAAGTGACTCTCCT--GGTCATACAACTAATGAGTTTCTGA 709911 i v vv iv i-- i i i i vv v C MIRc#SINE/MIR 119 CAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGA 70 chr5ptel1M 709912 GGTCATATTTGAACTCAGGAAGAGAAGTCTTCCCGACTCCAGGTCTAGTA 709961 viviv i i i -------- i i i i C MIRc#SINE/MIR 69 GCCGGGACTCGAACCCAGG--------TCTTCCTGACTCCAAGTCCAGTG 28 chr5ptel1M 709962 TTCTATCCACTTTATC 709977 i v vi i C MIRc#SINE/MIR 27 CTCTTTCCACTGCACC 12 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.21 CpG sites = 19, Kimura (unadjusted) = 38.32 Transitions / transversions = 1.58 (19/12) Gap_init rate = 0.08 (9 / 113), avg. gap size = 1.11 (10 / 9) 397 29.07 4.93 0.68 chr5ptel1M 709992 710133 (289867) MIRc#SINE/MIR 121 268 (0) m_b236s601i5 9294 chr5ptel1M 709992 GTTTCAGTTTCTCCTAATATAAAATGGGAGTCATAATA---GC---ACCC 710035 ii ii vvv i ii v --- ---i i MIRc#SINE/MIR 121 GCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCT 170 chr5ptel1M 710036 ACATCCAATAATTCATGGGAAGAGCAAATGAAATCATACATGT-AAAGTG 710084 v vv vii vv v i v i v ii - i MIRc#SINE/MIR 171 ACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCG 220 chr5ptel1M 710085 CTTTGCAAACCTTAAAGTGCCATATAGATGCCAGATAGTTAATTTTACT 710133 i iv i i i iv i-? v v i MIRc#SINE/MIR 221 CTTTGTAAACTGTAAAGTGCTATACAAATGTAAGG-NGTTATTATTATT 268 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.98 CpG sites = 24, Kimura (unadjusted) = 38.16 Transitions / transversions = 1.41 (24/17) Gap_init rate = 0.03 (4 / 141), avg. gap size = 2.00 (8 / 4) 329 26.77 0.81 9.65 chr5ptel1M 710542 710665 (289335) MIRc#SINE/MIR 2 115 (153) m_b236s601i6 9295 chr5ptel1M 710542 GAGGCAGCTAGATGGCGCAGTGCATATAAGTGCGGGCCCTGAAGTCAGGA 710591 i---i i v v -i ii v v i i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAA-GAGCACTGGACTTGGAGTCAGGA 47 chr5ptel1M 710592 GAACCTGAGTTCAAATCCACCTTCAGACAATTAATACTTCCCAACTCTGG 710641 ii i i i vvvi v v ------- v i i v v MIRc#SINE/MIR 48 AGACCTGGGTTCGAGTCCCGGCTCTGCC-------ACTTACTAGCTGTGT 90 chr5ptel1M 710642 GACC-TGGGCAAGTCATTTAACCCC 710665 - i i MIRc#SINE/MIR 91 GACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.25 CpG sites = 18, Kimura (unadjusted) = 33.62 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.10 (12 / 123), avg. gap size = 1.00 (12 / 12) 296 34.21 1.65 3.36 chr5ptel1M 711099 711219 (288781) MIRc#SINE/MIR 27 145 (123) m_b236s601i7 9296 chr5ptel1M 711099 GCACCAAATGTACAGCCAA-ATGACTTGCATGGAAATTTTGGCCCTGCCA 711147 iii iv iv i i- v i vi vvi i iii i MIRc#SINE/MIR 27 GCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCA 76 chr5ptel1M 711148 TTTACT-GCTAGTTTGCCTTTGGACAACAAGTCACACAACATAACCTAAT 711196 i - - v v i ---i vi v vv iv ii MIRc#SINE/MIR 77 CTTACTAGCT-GTGTGACCTTGG---GCAAGTCACTTAACCTCTCTGAGC 122 chr5ptel1M 711197 CTTAATTTCTTCATATATAAAAT 711219 i i i v i MIRc#SINE/MIR 123 CTCAGTTTCCTCATCTGTAAAAT 145 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.95 CpG sites = 26, Kimura (unadjusted) = 48.36 Transitions / transversions = 1.86 (26/14) Gap_init rate = 0.05 (6 / 120), avg. gap size = 1.00 (6 / 6) 304 36.46 0.75 3.08 chr5ptel1M 711112 711244 (288756) MIR3#SINE/MIR 38 167 (41) m_b236s601i8 9296 chr5ptel1M 711112 AGCCAAATGACTTGCATGGAAATTTTGGCCCTGCCATTTACT-GCTAGTT 711160 i iiv i vi vvv i iii i i v - - v MIR3#SINE/MIR 38 AGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCT-GTG 86 chr5ptel1M 711161 TGCCTTTGGACAACAAGTCACACAACATAACCTAATCTTAATTTCTTCAT 711210 v i i --- viv v vv iviii i i i MIR3#SINE/MIR 87 TGACCTTGGGCAA---GTCACTTCACCTCTCTGGGCCTCAGTTTCCTCAT 133 chr5ptel1M 711211 ATATAAAATTAAAGAGTTACACAGAATGACCTCT 711244 v i v ii i iv vii i MIR3#SINE/MIR 134 CTGTAAAATGAGGGGGTTGGACTAGATGATCTCT 167 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 50.99 CpG sites = 29, Kimura (unadjusted) = 52.66 Transitions / transversions = 1.61 (29/18) Gap_init rate = 0.04 (5 / 132), avg. gap size = 1.00 (5 / 5) 17 13.04 2.94 0.00 chr5ptel1M 711421 711454 (288546) (TAAA)n#Simple_repeat 1 35 (0) m_b236s252i5 9297 chr5ptel1M 711421 TAAA-AAATAAAGGAATGAATGAATAAATAAATAA 711454 - vi i i (TAAA)n#Simpl 1 TAAATAAATAAATAAATAAATAAATAAATAAATAA 35 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 13 17.64 0.00 3.03 chr5ptel1M 712955 712988 (287012) (TTCTAA)n#Simple_repeat 1 33 (0) m_b236s252i6 9298 chr5ptel1M 712955 TTCTGAAAGCTAATTCTAATTCTAGCCCTAATTC 712988 - vv iii (TTCTAA)n#Sim 1 TTCT-AATTCTAATTCTAATTCTAATTCTAATTC 33 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 399 34.15 5.77 4.27 chr5ptel1M 713773 713980 (286020) MIRc#SINE/MIR 2 212 (56) m_b236s601i9 9299 chr5ptel1M 713773 GAGGCAGTGTGGTATATTGAATATTATACTGTACTTTAAATACTTGAAAG 713822 ii v i v vvii v vi i --iv i MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGT--CAGGAAG 49 chr5ptel1M 713823 AATTTAATTATTGAA---AGGCTTTGG-----ACTAGCCATGTGACCAAG 713864 vi vii --i i---v i v----- ii vv MIRc#SINE/MIR 50 ACCTGGGTT--CGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTG 97 chr5ptel1M 713865 AGCAAGTCACCTACCCTTTTTTGAGTATCACTTTTCCCATTTGCAAAAAT 713914 i i v - i i iv v i i i i- MIRc#SINE/MIR 98 GGCAAGTCACTTAACC-TCTCTGAGCCTCAGTTTCCTCATCTGT-AAAAT 145 chr5ptel1M 713915 GAAAGCAGTAACAACTATAGTACACATTTTACAAG--TATTTCCAGGA-- 713960 iiiii i i v iivv i vi ii i i -- i viv -- MIRc#SINE/MIR 146 GGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATC 195 chr5ptel1M 713961 AGATGAAACCATAATATATG 713980 i i--- i MIRc#SINE/MIR 196 AAATGAG---ATAATGTATG 212 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 47.73 CpG sites = 46, Kimura (unadjusted) = 48.78 Transitions / transversions = 2.09 (46/22) Gap_init rate = 0.06 (13 / 207), avg. gap size = 1.62 (21 / 13) 15 29.94 0.00 0.00 chr5ptel1M 715139 715185 (284815) (TATC)n#Simple_repeat 1 47 (0) m_b236s252i7 9300 chr5ptel1M 715139 TATCCATTCATCTATCTTTCTATCAACCTGTCTGCTTATCTGTCTAT 715185 i ii v v i i iii i (TATC)n#Simpl 1 TATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTAT 47 Matrix = Unknown Transitions / transversions = 4.50 (9/2) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 13 0.00 0.00 0.00 chr5ptel1M 715239 715255 (284745) (TTG)n#Simple_repeat 1 17 (0) m_b236s252i8 9301 chr5ptel1M 715239 TTGTTGTTGTTGTTGTT 715255 (TTG)n#Simple 1 TTGTTGTTGTTGTTGTT 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 57 11.01 0.00 0.00 chr5ptel1M 715255 715342 (284658) (TCTCTC)n#Simple_repeat 1 88 (0) m_b236s252i10 9302 chr5ptel1M 715255 TCTCTCTCTGTCTCTCTGTCTGTCTCTCTCTCTCTCTGTCTCTGTCTCTC 715304 v v v v v (TCTCTC)n#Sim 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr5ptel1M 715305 CCTCTCTCTCTCTTTCTCTCTCTCGGTCTCTCTCTCTC 715342 i i vv (TCTCTC)n#Sim 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 88 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.00 (0 / 87), avg. gap size = 0.0 (0 / 0) 252 34.74 2.08 1.03 chr5ptel1M 715759 715854 (284146) C L3#LINE/CR1 (190) 3909 3813 m_b236s601i10 9303 chr5ptel1M 715759 GTCAGACAGTTC--CTATACATCAATTCAAAGGTTTTTCCTTTGTAACTT 715806 i v -- iv i ii vi i ivi viii ii C L3#LINE/CR1 3909 GTTAGAAAGTTCTTCCTTATATTGAGCCGAAATCTGCCTCCCTGTAACTT 3860 chr5ptel1M 715807 ACATCCAGCATTCCTAAGTCTTTCCTCTGGTGCCAAGTAGAATGAAGT 715854 v i viiv iv vi v vii - C L3#LINE/CR1 3859 CCACCCATTGGTCCTAGTTCTGCCCTCTGGAGCCACACAGAAT-AAGT 3813 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 47.15 CpG sites = 21, Kimura (unadjusted) = 49.30 Transitions / transversions = 1.75 (21/12) Gap_init rate = 0.02 (2 / 95), avg. gap size = 1.50 (3 / 2) 334 28.06 11.27 4.64 chr5ptel1M 716070 716211 (283789) MIRb#SINE/MIR 1 151 (117) m_b236s601i11 9304 chr5ptel1M 716070 CAGGGCGGCAGCTTGGGGCCTTGCAGTGAATGAAGTGCTCAAA-----GA 716114 i v v ----- i -- v v iii----- MIRb#SINE/MIR 1 CAGAGGGGCAGCGTGG-----TGCAGTGGA--AAGAGCACGGGCTTTGGA 43 chr5ptel1M 716115 CTCAACTTG--CTGAGTCCAAATCCACCCTCAAATATTTCCTAGCTGTGT 716162 v iviv -- i i i vvv vivi i v MIRb#SINE/MIR 44 GTCAGACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGT 93 chr5ptel1M 716163 GACCCTGACTAAAT-------CCCGTTT--GCCTCAGTTTCTTCACCTAT 716203 i ivi i ------- iv i -- i i i MIRb#SINE/MIR 94 GACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGT 143 chr5ptel1M 716204 AAAATGAG 716211 i MIRb#SINE/MIR 144 AAAATGGG 151 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.97 CpG sites = 23, Kimura (unadjusted) = 36.34 Transitions / transversions = 1.53 (23/15) Gap_init rate = 0.08 (11 / 141), avg. gap size = 2.09 (23 / 11) 271 30.96 10.49 2.29 chr5ptel1M 717574 717735 (282265) L2b_3end#LINE/L2 282 456 (10) m_b236s601i12 9305 chr5ptel1M 717574 CTCCCCAGTTCCAA--TGCT--TTTGGCTTTT--TTTTCTG-----ATCT 717612 i i i v-- i-- i v v -- v ----- v L2b_3end#LINE 282 CCCCCCAGTCCTACCCTGCCACTCTGGGTTATNATTGTCTGNTTACATGT 331 chr5ptel1M 717613 TTGTTCTCCATCAT--GAGTTTAAGCACC-TGGAGGTAGGGGC--TGTCT 717657 i - vi i-- v v i v - ii i i --? L2b_3end#LINE 332 CTGT-CTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCT 380 chr5ptel1M 717658 AACT-GCTTATCTTCCTACCCCCAGGTCTTAACACAGAGTCTGGCATAAA 717706 iv - i i i viiv i vv i i ? i i v L2b_3end#LINE 381 GTCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACA 430 chr5ptel1M 717707 TATGTATATGCTTAAGAAAGATTCTTTAA 717735 --- vii i iv v iv i L2b_3end#LINE 431 ---GTAGGCGCTCAGTAAATATTTGTTGA 456 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.13 CpG sites = 30, Kimura (unadjusted) = 42.28 Transitions / transversions = 1.58 (30/19) Gap_init rate = 0.07 (12 / 161), avg. gap size = 1.75 (21 / 12) 203 31.65 0.00 1.27 chr5ptel1M 718026 718105 (281895) MIR1_Amn#SINE/MIR 87 165 (65) m_b236s601i13 9306 chr5ptel1M 718026 CTGGGTAGCTAAGGACAAAGCAGATTACGTCTCTGAGTTTCTCTTTTCCT 718075 ? ii ivv i iv vv ? v ? ii -vv MIR1_Amn#SINE 87 CTGNGTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTC-AGTTTCCT 135 chr5ptel1M 718076 GGTCTCCAAAGTAGGGATGAGCATAATGAC 718105 vi vi i i i vv v MIR1_Amn#SINE 136 CATCTGTAAAATGGGGATAATGATACTGAC 165 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.83 CpG sites = 12, Kimura (unadjusted) = 43.83 Transitions / transversions = 0.92 (12/13) Gap_init rate = 0.01 (1 / 79), avg. gap size = 1.00 (1 / 1) 16 18.28 6.67 3.23 chr5ptel1M 718689 718748 (281252) (TTCT)n#Simple_repeat 1 62 (0) m_b236s252i11 9307 chr5ptel1M 718689 TTC-TTC-TTCTCATCTGTC-TCCTTTCTTTTTTCCTTCCTTTC-TTCCT 718734 - - -v v - i i i i - i (TTCT)n#Simpl 1 TTCTTTCTTTCT-TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 49 chr5ptel1M 718735 TCTATTCATTCCTT 718748 - v i (TTCT)n#Simpl 50 TCT-TTCTTTCTTT 62 Matrix = Unknown Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.10 (6 / 59), avg. gap size = 1.00 (6 / 6) 257 30.51 6.43 2.25 chr5ptel1M 720607 720777 (279223) L1ME3G_3end#LINE/L1 352 529 (395) m_b236s551i3 9308 chr5ptel1M 720607 GCATAGCCTTTGACTCAGCGGTATCACTACTGAGTCTTTATCCCAAGGAA 720656 v i ii vi v ?i ?v i i ?i L1ME3G_3end#L 352 GCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAGAA 401 chr5ptel1M 720657 A---TCATAAAAGAGGGGAAAGGACAAACATGTGCAAAAAAGGTTTGTAG 720703 --- ii v v v viv i --- ?i i - ii v ii v L1ME3G_3end#L 402 ATACTCGCACATGTGCACAAGG---ANGCATGTAC-AAGGATGTTCATTG 447 chr5ptel1M 720704 CAGCTCTTTTTGTGGTCGCAAAGAATTGGAAAATGAGTAGATGCT----- 720748 vi v ii v i i vvivv i ii----- L1ME3G_3end#L 448 CAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCA 497 chr5ptel1M 720749 ---GGGGAATGGCTGAAGAAGTTGTGGTCTAT 720777 --- i i v i i v L1ME3G_3end#L 498 ATAGGGGAATGGTTAAATAAATTATGGTATAT 529 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.83 CpG sites = 31, Kimura (unadjusted) = 42.00 Transitions / transversions = 1.55 (31/20) Gap_init rate = 0.04 (7 / 170), avg. gap size = 2.14 (15 / 7) 326 27.42 2.34 3.15 chr5ptel1M 720608 720735 (279265) L1ME4c_3end#LINE/L1 360 486 (344) m_b236s551i4 9308 chr5ptel1M 720608 CATAGCCTTTGACTCAGCGGTATCACTACTGAGTCTTTATCCCAAGGAAA 720657 v i iii vi v i vv i L1ME4c_3end#L 360 CATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAA 409 chr5ptel1M 720658 TCAT--AAAAGAGGGGAAAGGACAAACATGTGCA-AAAAAGGTTTGTAGC 720704 v -- i i ---- ivi i -i i v ii v L1ME4c_3end#L 410 TAATTCAAAAGAAGGAAAA----AGCTATATGCACGAAGATGTTCATTGC 455 chr5ptel1M 720705 AGCTCTTTTTGTGGTCGCAAAGAATTGGAAA 720735 vi v i ii v i i L1ME4c_3end#L 456 AGCGTTATTTATAATAGCGAAAAATTGGAAA 486 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 32.84 CpG sites = 22, Kimura (unadjusted) = 35.42 Transitions / transversions = 1.83 (22/12) Gap_init rate = 0.05 (6 / 127), avg. gap size = 1.17 (7 / 6) 15 36.77 0.00 0.00 chr5ptel1M 721074 721135 (278865) (TT)n#Simple_repeat 1 62 (0) m_b236s252i12 9309 chr5ptel1M 721074 TTTTTTGTGTGTGTTTATTTTCCTTCTGTTGTGTTTTTTCTCTTTTGTTC 721123 v v v v v ii i v v v i i v i (TT)n#Simple_ 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr5ptel1M 721124 TGATTTTTCTTT 721135 vv i (TT)n#Simple_ 51 TTTTTTTTTTTT 62 Matrix = Unknown Transitions / transversions = 0.64 (7/11) Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0) 12 25.94 0.00 2.38 chr5ptel1M 721602 721644 (278356) (AATAA)n#Simple_repeat 1 42 (0) m_b236s252i13 9310 chr5ptel1M 721602 AAAAAAATAAAATAAAATATCAAAGCAATTTAACAAAAAAAAA 721644 v -v viv vv i v (AATAA)n#Simp 1 AATAAAATAAAATAAAATA-AAATAAAATAAAATAAAATAAAA 42 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.02 (1 / 42), avg. gap size = 1.00 (1 / 1) 28 0.00 0.00 0.00 chr5ptel1M 721645 721671 (278329) (AAAG)n#Simple_repeat 1 27 (0) c_b236s251i0 9311 chr5ptel1M 721645 AAAGAAAGAAAGAAAGAAAGAAAGAAA 721671 (AAAG)n#Simpl 1 AAAGAAAGAAAGAAAGAAAGAAAGAAA 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 521 27.78 1.00 1.50 chr5ptel1M 722388 722588 (277412) L1ME3G_3end#LINE/L1 349 548 (376) m_b236s551i5 9312 chr5ptel1M 722388 TGTGCATAACCCTTTGATCCAGCAGTGCTACTACTGGGCTTATATCCCAA 722437 i - i i v i v ? ?v v i ? L1ME3G_3end#L 349 TGCGCATA-CCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTAN 397 chr5ptel1M 722438 AGAGAT-TTTAAAGAAGGGAAT-GGGACTTGTATGTGCCAAAATGTTTGT 722485 i -i iiv v v v v i-i --? i i v ii ii L1ME3G_3end#L 398 AGAAATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTCAT 445 chr5ptel1M 722486 GGCAGCCCTGTTTGTAGTGGCTAGAAACTTGAAATTGAGTGGATGCCCAT 722535 v vi i i v i i v ivivv ii i L1ME3G_3end#L 446 TGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCAT 495 chr5ptel1M 722536 CCATTGGAGAATGGTTGGATAAATTGTGGTATATGAATGTTATGGAATAT 722585 v v i ii i vv ii i L1ME3G_3end#L 496 CAATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATAC 545 chr5ptel1M 722586 TAT 722588 L1ME3G_3end#L 546 TAT 548 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.02 CpG sites = 34, Kimura (unadjusted) = 36.79 Transitions / transversions = 1.62 (34/21) Gap_init rate = 0.03 (5 / 200), avg. gap size = 1.00 (5 / 5) 477 30.88 3.53 3.90 chr5ptel1M 722391 722673 (277327) L1ME5_3end#LINE/L1 356 637 (304) m_b236s551i6 9312 chr5ptel1M 722391 GCATAACCCTTTGATCCAGCAGTGCTACTACTGGGCTTATATCCCAAAGA 722440 - v i i v ii v iv L1ME5_3end#LI 356 GCATA-CCCTATGACCCAGCAATTCCGCTCCTGGGTATATATCCCAAAGA 404 chr5ptel1M 722441 GATTTTAAAGAAGG----GAATGGGACTTGTATGTGCCAAAATGTTTGTG 722486 i i v viv ----v v v i ---- ii ii v L1ME5_3end#LI 405 AATTCTCACACAGGTCCATAAGGGGACATGTACG----AGGATGTTCATT 450 chr5ptel1M 722487 GCAGCCCTGTTTGTAGTGGCTAGAAACTTGAAATTGAGTGGATGCCCATC 722536 vi i vi i ii v iiivivv i i L1ME5_3end#LI 451 GCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGGGTGTCCATC 500 chr5ptel1M 722537 CATTGGAGAATGGTTGGATAAATTGTGGTATATGAATGTTATGGAATATT 722586 vv v i v i i v iv v iiii i i L1ME5_3end#LI 501 ACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACACCATGGAGTACT 550 chr5ptel1M 722587 ATTGTTCTGTAAGAAA----GGACCAGCAGAATGAATACAGAGAGGCTTG 722632 vvvv v v i---- i ---- v i v vii v L1ME5_3end#LI 551 ATGCAGCAGTTAGAAGCAACGGACTAG----ATGTACACATAGCAACATG 596 chr5ptel1M 722633 GAGAGA-CTTACATGAAC-TGATGCTAAGTGAAATGAGCAGGA 722673 vi - v -- - ii i vi i i L1ME5_3end#LI 597 GATGGATCTTAAA--AACATAGTGCTGAGTGAAAAAAGTAAGA 637 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.46 CpG sites = 47, Kimura (unadjusted) = 40.79 Transitions / transversions = 1.27 (47/37) Gap_init rate = 0.05 (15 / 282), avg. gap size = 1.40 (21 / 15) 13 4.34 3.85 3.85 chr5ptel1M 722989 723014 (276986) (GGGA)n#Simple_repeat 1 26 (0) m_b236s252i14 9313 chr5ptel1M 722989 GGGAGGGGGTGGAGGGAGGGA-GGAGG 723014 i - - (GGGA)n#Simpl 1 GGGAGGGAG-GGAGGGAGGGAGGGAGG 26 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.08 (2 / 25), avg. gap size = 1.00 (2 / 2) 140 0.00 0.80 0.00 chr5ptel1M 723108 723232 (276768) (AGAAG)n#Simple_repeat 1 126 (0) c_b236s251i1 9314 chr5ptel1M 723108 AGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAG 723157 (AGAAG)n#Simp 1 AGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAG 50 chr5ptel1M 723158 AGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAG 723207 (AGAAG)n#Simp 51 AGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAG 100 chr5ptel1M 723208 AGAAGAGAAGAGAAGAGAAGA-AAGA 723232 - (AGAAG)n#Simp 101 AGAAGAGAAGAGAAGAGAAGAGAAGA 126 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.01 (1 / 124), avg. gap size = 1.00 (1 / 1) 651 17.80 0.00 0.00 chr5ptel1M 725162 725279 (274721) C Tigger1#DNA/TcMar-Tigger (43) 2375 2258 m_b236s502i0 9315 chr5ptel1M 725162 GCAATATAGAGACTATCACAATCAAGTAGGTCACATGAACTTTTTGGTTT 725211 v v v i v iii i i C Tigger1#DNA/T 2375 GCAATAAAGCGAATATCGCAATAAAGCGAGTCACACGAATTTTTTGGTTT 2326 chr5ptel1M 725212 CCCAGCACATATAAAAGTTATGTTTACAGTATATTATAGTCTATTAAGTA 725261 ii v i i i C Tigger1#DNA/T 2325 CCCAGTGCATATAAAAGTTATGTTTACACTATACTGTAGTCTATTAAGTG 2276 chr5ptel1M 725262 CACAAGAGTATTGTGTCT 725279 ii v i i C Tigger1#DNA/T 2275 TGCAATAGCATTATGTCT 2258 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 17.58 CpG sites = 15, Kimura (unadjusted) = 20.88 Transitions / transversions = 2.50 (15/6) Gap_init rate = 0.00 (0 / 117), avg. gap size = 0.0 (0 / 0) 997 18.32 6.90 1.22 chr5ptel1M 725637 725868 (274132) C Tigger1#DNA/TcMar-Tigger (146) 2272 2028 m_b236s502i1 9315 chr5ptel1M 725637 AAGAGTATTGTGTCTTAAAAA-AATGTGCACACCTTAGTTAAAAAATATT 725685 v i i v - i i i v i C Tigger1#DNA/T 2272 AATAGCATTATGTCTAAAAAACAATGTACATACCTTAATTTAAAAATACT 2223 chr5ptel1M 725686 TTATTGTTTAAAAACGCTAACCATCACCTGAGCTTTCAATGAGATGTAAT 725735 i v i v i i ii vi C Tigger1#DNA/T 2222 TTATTGCTAAAAAATGCTAACGATCATCTGAGCCTTCAGCGAGTCGTAAT 2173 chr5ptel1M 725736 CTTTTTGT--GTAGAAAGTCTTGCTTCAATGTTGATGGCTGCTGAGTACT 725783 i-- i ii i i v iv C Tigger1#DNA/T 2172 CTTTTTGCTGGTGGAGGGTCTTGCCTCGATGTTGATGGCTGCTGACTGAT 2123 chr5ptel1M 725784 CAGAGTGGTG------GAAGA-TGGGGTGAC--TGGCA----CTTAAAAT 725820 i ------ i- i -- ---- C Tigger1#DNA/T 2122 CAGGGTGGTGGTTGCTGAAGGTTGGGGTGGCTGTGGCAATTTCTTAAAAT 2073 chr5ptel1M 725821 AAGACTTCAGTGTAGTTTGTCATATCACTTGAGTCTTCTTCCCTTCAC 725868 vv i v i ii iv ---i i C Tigger1#DNA/T 2072 AAGACAACAATGAAGTTTGCCGCATCGATTGA---CTCTTCCTTTCAC 2028 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 18.85 CpG sites = 30, Kimura (unadjusted) = 21.64 Transitions / transversions = 2.50 (30/12) Gap_init rate = 0.04 (9 / 231), avg. gap size = 2.11 (19 / 9) 1971 19.50 2.90 2.90 chr5ptel1M 725870 726318 (273682) C Tigger1#DNA/TcMar-Tigger (1963) 455 7 m_b236s502i2 9316 chr5ptel1M 725870 TTTTTTTTTCATTTGAACACTTAGGTGCTACTGTCGGGTTATTAATTGGT 725919 i ii i iv i i v i C Tigger1#DNA/T 455 TCTTCCTTTCACTTGAACACTTAGAGGCCATTGTAGGGTTATTAATTGGC 406 chr5ptel1M 725920 CTAAATTCAATATCAT-ATGTCTCAGGGAATAAGGAAGCTAGAGG----G 725964 v ii -i i i iv ---- C Tigger1#DNA/T 405 CTAATTTCAATATTGTTGTGTCTCAGGGAATAGGGAGGCCCGAGGAGAGG 356 chr5ptel1M 725965 GAGATTGGGGTGAGG-ACCTGCTAGTCATTGGAATAGTCAGAACACACAC 726013 -- i i i - v v ii iv ii C Tigger1#DNA/T 355 GAGA--GAGATGGGGGAACGGCCGGTCGGTGGAGCAGTCAGAACACACAC 308 chr5ptel1M 726014 A---TTTACTGACTAAGTGTGCCATCTGATATGGATGTGGTTCATGGTTC 726060 --- ii i vi i v ii i i iv C Tigger1#DNA/T 307 AACATTTATCGATTAAGTTCGCCGTCTTATATGGGCGCGGTTCGTGGCGC 258 chr5ptel1M 726061 TCCAAAATAATTATAATAGTAATCTTAAAGGTCACTGCTCATAGATCACC 726110 i i i iv i i v i C Tigger1#DNA/T 257 CCCAAAACAATTACAATAGTAACATCAAAGATCACTGATCACAGATCACC 208 chr5ptel1M 726111 ATAATCGATACAATAATCATGAAAATGTTTGAAATATTAAGAGAATTACC 726160 iv i v v iv C Tigger1#DNA/T 207 ATAACAGATATAATAATAATGAAAAAGTTTGAAATATTGCGAGAATTACC 158 chr5ptel1M 726161 -AAATGTGACACAG-GACATGATGTGAGTACATACTATTGGTGGAAAAAA 726208 - - i v i i i ---- C Tigger1#DNA/T 157 AAAATGTGACACAGAGACACGAAGTGAGCACATGCTGTTGG----AAAAA 112 chr5ptel1M 726209 TTAGATGCAGATAGATTTGCTGGATACAGGACTACCACAAAGCTTCATTT 726258 -- ii v i v ii ii i v v C Tigger1#DNA/T 111 T--GGCGCCGATAGACTTGCTCGACGCAGGGTTGCCACAAACCTTCAATT 64 chr5ptel1M 726259 TTTAAAAAAAAAAATGCAATATCT--GAATTGCAATAAAGTGAAGCACAA 726306 v ----- i -- vi i i C Tigger1#DNA/T 63 TGT-----AAAAAACGCAATATCTGCGAAGCGCAATAAAGCGAAGCGCAA 19 chr5ptel1M 726307 CAAAGCAAAGTA 726318 i i i i C Tigger1#DNA/T 18 TAAAACGAGGTA 7 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 18.25 CpG sites = 62, Kimura (unadjusted) = 23.35 Transitions / transversions = 2.70 (62/23) Gap_init rate = 0.04 (20 / 448), avg. gap size = 1.30 (26 / 20) 33 0.00 0.00 0.00 chr5ptel1M 727897 727924 (272076) (TA)n#Simple_repeat 1 28 (0) c_b236s251i2 9317 chr5ptel1M 727897 TATATATATATATATATATATATATATA 727924 (TA)n#Simple_ 1 TATATATATATATATATATATATATATA 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 525 30.33 1.40 1.40 chr5ptel1M 728427 728640 (271360) C L1ME4c_3end#LINE/L1 (275) 555 342 m_b236s551i7 9318 chr5ptel1M 728427 ATAATATTCCAGAACATTCATATACCACAATTTACCCAAGCATTCTCCAA 728476 vvivi ?v i i ii v i v C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chr5ptel1M 728477 TGGATGGGCATCCATTCATTTTCCAGCTTCTGGCCACTACAAACAGGGCT 728526 v v i ii vvivv ii i v i i i i iv C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCT 456 chr5ptel1M 728527 GCCACAAACATTTTGGCACATACAGGTCCCTTTCCCTTCTTTAG---TAT 728573 v ii i v ii i --- i i v --- C L1ME4c_3end#L 455 GCAATGAACATCTTCGTGCATATAG---CTTTTTCCTTCTTTTGAATTAT 409 chr5ptel1M 728574 CTCTTTGGGGTATAAGCCCAGTAATAGCACTGCTGGGTCAAAGGGTGTGC 728623 i i i i v vv v i i v i i i v C L1ME4c_3end#L 408 TTCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGA 359 chr5ptel1M 728624 ACAGTTTGATAACTTTT 728640 v v ii i C L1ME4c_3end#L 358 ACATTTTTATGGCTCTT 342 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.68 CpG sites = 39, Kimura (unadjusted) = 40.51 Transitions / transversions = 1.56 (39/25) Gap_init rate = 0.02 (4 / 213), avg. gap size = 1.50 (6 / 4) 390 26.53 9.18 0.00 chr5ptel1M 729403 729500 (270500) MIRc#SINE/MIR 5 111 (157) m_b236s601i14 9319 chr5ptel1M 729403 GCTATGTGGTGTAGTGGATAGAGTACTGGCCCTGGA---------ACCTG 729443 vi i v i v i --------- MIRc#SINE/MIR 5 GCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTG 54 chr5ptel1M 729444 AATTAAAATCTGAGCTCAGATACTTTCTAGCTATATGACCCTAGGAAAGC 729493 ii vi i ivi v vi v i i i i v i MIRc#SINE/MIR 55 GGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGT 104 chr5ptel1M 729494 CACTGAA 729500 v MIRc#SINE/MIR 105 CACTTAA 111 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.57 CpG sites = 16, Kimura (unadjusted) = 33.69 Transitions / transversions = 1.60 (16/10) Gap_init rate = 0.01 (1 / 97), avg. gap size = 9.00 (9 / 1) 244 29.39 10.83 0.76 chr5ptel1M 730426 730545 (269455) C L2c_3end#LINE/L2 (6) 472 341 m_b236s601i15 9320 chr5ptel1M 730426 TCAGTCAATAAATATTAATGAAAC----ACTGTGGGCCAAACACCAGGGA 730471 v i i v vi i ---- i v ii i ii C L2c_3end#LINE 472 TCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGA 423 chr5ptel1M 730472 TCCAAAG--GACAGAAGACA-GA---CTGCTTATAAGGAGCTCCCAG--T 730513 v -- - v - i--- iivi v -- C L2c_3end#LINE 422 TACAAAGATGA-ATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCT 374 chr5ptel1M 730514 AATTGACAGGATAGATCTACAGA-AAATAATTA 730545 i v vii i iv?ii i - i i C L2c_3end#LINE 373 AGTGGAGGAGACAGACANGTAAACAGACAATTA 341 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.31 CpG sites = 24, Kimura (unadjusted) = 39.82 Transitions / transversions = 2.18 (24/11) Gap_init rate = 0.06 (7 / 119), avg. gap size = 2.00 (14 / 7) 190 31.78 0.00 3.17 chr5ptel1M 730771 730835 (269165) L2#LINE/L2 2692 2754 (328) m_b236s601i16 9321 chr5ptel1M 730771 AAGCTATTCATCACTTCATTTTTTGTAATATTGTAGTAGCCTCCTAACTC 730820 i i- ii - ivii v v i i i v L2#LINE/L2 2692 AAGCCAC-CATCATCTC-TCGCCTGGATTACTGCAATAGCCTCCTAACTG 2739 chr5ptel1M 730821 ATTTTCCTGCCTTTA 730835 i i i i ii L2#LINE/L2 2740 GTCTCCCTGCTTCCA 2754 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.53 CpG sites = 16, Kimura (unadjusted) = 45.76 Transitions / transversions = 4.00 (16/4) Gap_init rate = 0.03 (2 / 64), avg. gap size = 1.00 (2 / 2) 260 24.01 20.91 1.53 chr5ptel1M 730941 731050 (268950) C L2d2_3end#LINE/L2 (9) 546 416 m_b236s601i17 9322 chr5ptel1M 730941 ATTAACAAACAT----TGAGTGACTACTATGTGCTATG---TGAGCTAAG 730983 i i ---- i v i v v --- v i C L2d2_3end#LIN 546 ATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGG 497 chr5ptel1M 730984 TGTGGGGGGAAGGGTACAAAGAAAGGCAAAA----------------AAG 731017 i iv v -- i ivii i ---------------- C L2d2_3end#LIN 496 CGCTGTGGG--GGATACAAAGAAGTATAAGACATGGTCCCTGCCCTCAAG 449 chr5ptel1M 731018 GAACTCACAATCTAATAGGGAAGACAACCCATA 731050 i i i v i vv C L2d2_3end#LIN 448 GAGCTTACAATCTAGTTGGGGAGACAAGACATA 416 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.09 CpG sites = 16, Kimura (unadjusted) = 29.74 Transitions / transversions = 1.60 (16/10) Gap_init rate = 0.05 (5 / 109), avg. gap size = 5.00 (25 / 5) 459 10.22 5.62 1.08 chr5ptel1M 731550 731638 (268362) C Charlie4a#DNA/hAT-Charlie (57) 451 359 m_b236s502i3 9323 chr5ptel1M 731550 TAGACTCTCTTCTCAGAATCATGTTTTTAAATG-----AATAAAATACAT 731594 i i - v ----- C Charlie4a#DNA 451 TGGACCC-CTTCTCAGAATAATGTTTTTAAATGCATAAAATAAAATACAT 403 chr5ptel1M 731595 AGGATTACAAAGGAAAGCAATTCTATTAAACTACAATGATCAAA 731638 v v i v i v C Charlie4a#DNA 402 AGGATTACAAAGGAAACCAATTATATTGAAATACAGTTATCAAA 359 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 11.01 CpG sites = 4, Kimura (unadjusted) = 11.01 Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.02 (2 / 88), avg. gap size = 3.00 (6 / 2) 19 17.46 2.22 0.00 chr5ptel1M 731694 731738 (268262) (AAAGA)n#Simple_repeat 1 46 (0) m_b236s252i15 9324 chr5ptel1M 731694 AAAGAAAAGAAAAGAAAAATAGAGAAGA-AAAACAAAACAAAATAA 731738 iv i i - v v v (AAAGA)n#Simp 1 AAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAA 46 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 32 0.00 0.00 0.00 chr5ptel1M 731851 731880 (268120) (TTTTG)n#Simple_repeat 1 30 (0) c_b236s251i3 9325 chr5ptel1M 731851 TTTTGTTTTGTTTTGTTTTGTTTTGTTTTG 731880 (TTTTG)n#Simp 1 TTTTGTTTTGTTTTGTTTTGTTTTGTTTTG 30 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 256 28.52 10.43 2.42 chr5ptel1M 732486 732600 (267400) MIRc#SINE/MIR 33 156 (112) m_b236s601i18 9326 chr5ptel1M 732486 GACATGGTATCATTAGTGACCATGGTTTAAATCCAACCTTTGACACTGA- 732534 v vi vv i- vv ii i viv i v v - MIRc#SINE/MIR 33 GACTTGGAGTCAGGAA-GACCTGGGTTCGAGTCCCGGCTCTGCCACTTAC 81 chr5ptel1M 732535 --GCTATG-------AGTCAA-TAACTTAACATTTTTGAATTTCAGTTCT 732574 -- i -------i v - v v i i iii ii MIRc#SINE/MIR 82 TAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTC 131 chr5ptel1M 732575 CTCTTCTG-AAAATGAGGAACTAATGA 732600 v - i -- i MIRc#SINE/MIR 132 CTCATCTGTAAAATGGGGA--TAATAA 156 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.79 CpG sites = 18, Kimura (unadjusted) = 36.76 Transitions / transversions = 1.29 (18/14) Gap_init rate = 0.07 (8 / 114), avg. gap size = 1.88 (15 / 8) 245 29.21 11.72 3.18 chr5ptel1M 732503 732647 (267353) MIRb#SINE/MIR 52 208 (60) m_b236s601i19 9326 chr5ptel1M 732503 GACCATGGTTTAAATCCAACCTTTGACACTGA---GCTATG-------AG 732542 vv ii viv i v v --- i -------i MIRb#SINE/MIR 52 GACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 101 chr5ptel1M 732543 TCAA-TAACTTAACATTTTTGAATTTCAGTTCTCTCTTCTG-AAAATGAG 732590 v - v v i i iii ii v - i MIRb#SINE/MIR 102 GCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 151 chr5ptel1M 732591 GAACTAATGAAAGAAC-ACATTGAAAGA--ACTATGGAAATC--ATAAAA 732635 -- -- v v - v i v i i--ii i iii i-- i i MIRb#SINE/MIR 152 GA--TAAT--AATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGA 197 chr5ptel1M 732636 TAATACACTGTA 732647 i - MIRb#SINE/MIR 198 TAATGCA-TGTA 208 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.08 CpG sites = 27, Kimura (unadjusted) = 38.83 Transitions / transversions = 1.93 (27/14) Gap_init rate = 0.08 (12 / 144), avg. gap size = 1.83 (22 / 12) 476 29.17 5.42 2.94 chr5ptel1M 733327 733492 (266508) MIR3#SINE/MIR 36 205 (3) m_b236s601i20 9327 chr5ptel1M 733327 GGACTCAG-AGTACTGGATTCCAGTTCCAGGTAGGCTGC-ATTCTGCT-T 733373 v - vv i i i i v vv ii - vii? - MIR3#SINE/MIR 36 GGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGT 85 chr5ptel1M 733374 GTG----TGGACAAGTCGCTTCCCAGCTCTGGCCTCCAATCTCCTCTCCT 733419 ---- i i v vv v ii i i ---- MIR3#SINE/MIR 86 GTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTC---- 131 chr5ptel1M 733420 TATGTACAAAATGAAGGGATTGAGTTAAATGATCTCTGAGATTCCTTTTG 733469 - v ii i i iii i i i i iii MIR3#SINE/MIR 132 -ATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCA 180 chr5ptel1M 733470 ACTCT--TAATCCAGGAACCTATGA 733492 i --i v i v vi MIR3#SINE/MIR 181 GCTCTGACATTCTATGATTCTATGA 205 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.13 CpG sites = 32, Kimura (unadjusted) = 39.23 Transitions / transversions = 2.13 (32/15) Gap_init rate = 0.06 (10 / 165), avg. gap size = 1.40 (14 / 10) 234 23.25 14.86 1.19 chr5ptel1M 733803 733876 (266124) MIRc#SINE/MIR 6 89 (179) m_b236s601i21 9328 chr5ptel1M 733803 CAGGGTGGTGGAATTGAAAGAGCGCTG----------CAG-AGGACCAGG 733841 v v i v i ---------- - i v MIRc#SINE/MIR 6 CAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGG 55 chr5ptel1M 733842 ATTTAGTTCTAGGCTCTACCACTTAGTTATCTGTG 733876 i iiiv iv i -i v MIRc#SINE/MIR 56 GTTCGAGTCCCGGCTCTGCCACTTA-CTAGCTGTG 89 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.29 CpG sites = 10, Kimura (unadjusted) = 28.41 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.04 (3 / 73), avg. gap size = 4.00 (12 / 3) 24 12.17 0.00 0.00 chr5ptel1M 734774 734809 (265191) (C)n#Simple_repeat 1 36 (0) m_b236s252i16 9329 chr5ptel1M 734774 CCCCCCCCACCCCCCACACCCCCCCCGCCCCCCCCC 734809 v v v v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 36 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 364 30.42 4.29 1.39 chr5ptel1M 735328 735467 (264533) MIR3#SINE/MIR 62 205 (3) m_b236s601i22 9330 chr5ptel1M 735328 CCAGTCCTGAT-CCAACTGGCAG-G-AACTTTTGGCCAGCATAATCTGCT 735374 i ii vi- i ? v - -i i v v i-i v iii i MIR3#SINE/MIR 62 CCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGT-CACTTCACC 110 chr5ptel1M 735375 CCTTTGGGCCTCAGTTTCCTTTTCCATAAAAATGA-AAAGTTGTACTGGA 735423 i i iv ii - -iii v i MIR3#SINE/MIR 111 TCTCTGGGCCTCAGTTTCCTCATCTGT-AAAATGAGGGGGTTGGACTAGA 159 chr5ptel1M 735424 TGGCCTTTGATGTCCCTTCCAG--ATGAAAGTCTGTCATTTGATAA 735467 ii i i v --v v v i v iv i MIR3#SINE/MIR 160 TGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTATGA 205 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.43 CpG sites = 29, Kimura (unadjusted) = 41.78 Transitions / transversions = 2.23 (29/13) Gap_init rate = 0.05 (7 / 139), avg. gap size = 1.14 (8 / 7) 385 21.35 5.62 0.00 chr5ptel1M 735855 735943 (264057) C MIR#SINE/MIR (120) 142 49 m_b236s601i23 9331 chr5ptel1M 735855 CATTTTATAGAAGAAGAAAATGAGGCAGACAGAGATTAAGTGACTTG--- 735901 i v i v v v i i --- C MIR#SINE/MIR 142 CATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCC 93 chr5ptel1M 735902 --GGTCACACAGCTAGGAAGCTTCTGAGGTTGGATTTTAACTCA 735943 -- v ivv v viv iv i C MIR#SINE/MIR 92 AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCA 49 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 22.35 CpG sites = 8, Kimura (unadjusted) = 25.17 Transitions / transversions = 0.73 (8/11) Gap_init rate = 0.02 (2 / 88), avg. gap size = 2.50 (5 / 2) 560 27.91 12.86 1.87 chr5ptel1M 736182 736422 (263578) MIRb#SINE/MIR 1 267 (1) m_b236s601i24 9332 chr5ptel1M 736182 CAGAGAGG-----TGGCACAGAGTATAGACTACCAAGACTGATGTCAGGA 736226 i ----- ii v v v vi viivvi iv iv MIRb#SINE/MIR 1 CAGAGGGGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGAC 50 chr5ptel1M 736227 AAATCTGAGTTCAAATAGAACCTCAGACACTTAATTGGCTGTAGGACTTT 736276 i i i i vvviv v v -i i iv i MIRb#SINE/MIR 51 AGACCTGGGTTCGAATCCCGGCTCTGCCACTTA-CTAGCTGTGTGACCTT 99 chr5ptel1M 736277 GGGCCAGAAAATTACAT--CTTGTTTG--CCTCAGTTTCCCCAGCTG-AA 736321 ---- i v -- i v i -- i v - MIRb#SINE/MIR 100 GGGC----AAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAA 145 chr5ptel1M 736322 AA--GGGACAATAAT---------------TTATCCTGAGA--TATCCTA 736352 -- i --------------- i iv i-- vviv MIRb#SINE/MIR 146 AATGGGGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGA 195 chr5ptel1M 736353 GATAATAATTGCAAAGCACTTAGCACAGTACTTGGAATATAGTAGGCACT 736402 ivv i i i i v i i i MIRb#SINE/MIR 196 GATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCT 245 chr5ptel1M 736403 ATATAAATGTGAA--CTATTAT 736422 vv vv i-- MIRb#SINE/MIR 246 CAATAAATGGTAGCTCTATTAT 267 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.02 CpG sites = 36, Kimura (unadjusted) = 35.63 Transitions / transversions = 1.20 (36/30) Gap_init rate = 0.05 (13 / 240), avg. gap size = 2.77 (36 / 13) 277 32.51 3.94 3.12 chr5ptel1M 736797 736923 (263077) MIR3#SINE/MIR 3 130 (78) m_b236s601i25 9333 chr5ptel1M 736797 GGTAGAATATCTTAGCATCGAGAGAGC-CAGTCTTATAATCATAAAGATA 736845 i i iv v -- - i v viv i -ii iv MIR3#SINE/MIR 3 GGCAGAGTGGCTGAGCA--GAGAGAGCACGGACTGGGAGTCA-GGAGACC 49 chr5ptel1M 736846 TGAGTTCCAATGCCATCTCTGCCA-TA---GATTGTGCATCTCTGGGTAT 736891 i i i v iv - ---?ii iiv ii i v MIR3#SINE/MIR 50 TGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAA 99 chr5ptel1M 736892 GTTGCTTAAGGTCAAAGGACTCTAAGTTTCCT 736923 ii v vv vvv i - v MIR3#SINE/MIR 100 GTCACTTCACCTCTCTGGGC-CTCAGTTTCCT 130 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.53 CpG sites = 23, Kimura (unadjusted) = 44.49 Transitions / transversions = 1.35 (23/17) Gap_init rate = 0.06 (7 / 126), avg. gap size = 1.29 (9 / 7) 16 13.24 4.08 8.51 chr5ptel1M 737132 737180 (262820) (AT)n#Simple_repeat 1 47 (0) m_b236s252i17 9334 chr5ptel1M 737132 ATATCATATACATAGATATGTAAATGAGTCAT-TATA-ATATGTATATAT 737179 - i v i v - - - - - i (AT)n#Simple_ 1 ATAT-ATATATATATATATATATAT-A-T-ATATATATATATATATATAT 46 chr5ptel1M 737180 A 737180 (AT)n#Simple_ 47 A 47 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.12 (6 / 48), avg. gap size = 1.00 (6 / 6) 250 31.88 5.98 0.81 chr5ptel1M 737536 737652 (262348) MIRc#SINE/MIR 28 150 (118) m_b236s601i26 9335 chr5ptel1M 737536 CACTGTAAGTTCTAGTTGGGGTGTCCTGGCTTTAAACCC--ACTTTTCT- 737582 -i v vv ii iv v v ii ii --i i v i- MIRc#SINE/MIR 28 CACTG-GACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCA 76 chr5ptel1M 737583 CTTATTAGCTGGGTGATCTT-ATCACATCAGGAAATCTCACTGA--CTTA 737629 i v i -iv vi vvv i v -- i MIRc#SINE/MIR 77 CTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCA 126 chr5ptel1M 737630 CTTT-CTCAATTGTGAAATGAAGA 737652 v - vi i ii MIRc#SINE/MIR 127 GTTTCCTCATCTGTAAAATGGGGA 150 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.03 CpG sites = 21, Kimura (unadjusted) = 42.73 Transitions / transversions = 1.31 (21/16) Gap_init rate = 0.05 (6 / 116), avg. gap size = 1.33 (8 / 6) 360 24.96 8.55 2.48 chr5ptel1M 737560 737711 (262289) MIR3#SINE/MIR 48 208 (0) m_b236s601i27 9335 chr5ptel1M 737560 CCTGGCTT-TAAACCCA-CTTTTCT-CTTATTAGCTGGGTGATCTTAT-C 737605 v - iv i- i v i- v i ? v i iv- MIR3#SINE/MIR 48 CCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGC 97 chr5ptel1M 737606 ACATCAGGAAATCTCACTGA--CTTACTTTC-TCAATTGTGAAATGAAGA 737652 vi vvvv i v i-- i v - vi i i i MIR3#SINE/MIR 98 AAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGG 147 chr5ptel1M 737653 GTTTGAACTAGATG-TCT-TAAGGACTCTTCCAG----GACCTTCAAACT 737696 v i - - v i ---- v ---- MIR3#SINE/MIR 148 GGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATT----CT 193 chr5ptel1M 737697 ATGATCCTATAAATC 737711 i i v MIR3#SINE/MIR 194 ATGATTCTATGATTC 208 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.02 CpG sites = 19, Kimura (unadjusted) = 31.00 Transitions / transversions = 1.06 (19/18) Gap_init rate = 0.09 (13 / 151), avg. gap size = 1.31 (17 / 13) 401 20.18 9.65 0.00 chr5ptel1M 737723 737836 (262164) C Charlie4a#DNA/hAT-Charlie (30) 478 354 m_b236s502i4 9336 chr5ptel1M 737723 ATCTTTTTGTCAGGCTGGTGAAGTCCAGGGACA---TCTCAGAAT---GT 737766 i ii v v i i v v--- --- C Charlie4a#DNA 478 ACCCCTTTGGCAGTCTGGTGAAGCCTATGGACCCCTTCTCAGAATAATGT 429 chr5ptel1M 737767 CTTTGGATG-----AATAAAATGCATATGTTTACAAAAGAAATCAATGAT 737811 i ii ----- i v v i i v C Charlie4a#DNA 428 TTTTAAATGCATAAAATAAAATACATAGGATTACAAAGGAAACCAATTAT 379 chr5ptel1M 737812 ATGGCAATGCAGTTTTCAGAATATT 737836 v v i v i C Charlie4a#DNA 378 ATTGAAATACAGTTATCAAAATATT 354 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 23.80 CpG sites = 13, Kimura (unadjusted) = 23.80 Transitions / transversions = 1.30 (13/10) Gap_init rate = 0.03 (3 / 113), avg. gap size = 3.67 (11 / 3) 256 40.72 4.79 0.00 chr5ptel1M 737842 738008 (261992) C L2c_3end#LINE/L2 (234) 244 70 m_b236s601i28 9337 chr5ptel1M 737842 AAGATCTCTCACAGGAAGAGGCATCCGAGTTGAGTTGTAGAGAGCTAA-A 737890 iii i iv i v i i i ?iv ii iiiv i- C L2c_3end#LINE 244 AAGGCTTCCCGGAGGAGGTGACATCTGAGCTGAGNCTTGAAGGATGAGTA 195 chr5ptel1M 737891 GAATCTAAC-AGATGGAAAAAAGGCAAGGATACTTTCCAGACATAAATGA 737939 i vi i - i ii i viiiiivi v i v iivi C L2c_3end#LINE 194 GGAGTTAGCCAGGTGGAAGGAGGGGGGAAGAGCATTCCAGGCAGAGGGAA 145 chr5ptel1M 737940 CAGTATACACAAAAACA-GGAAGTAGAAGATAA-TATATCATGTCTCAGT 737987 i iii ii ?- i i i i v - iiiv i i vi v C L2c_3end#LINE 144 CAGCATGTGCAAAGGCNCGGAGGCAGGAAAGAACTGCGGCGTGTTTGGGG 95 chr5ptel1M 737988 AA---AAGCAATTATAT-TGGTTGG 738008 --- ? i vvi - i C L2c_3end#LINE 94 AATGCAAGNAGTTCAGTGTGGCTGG 70 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 65.22 CpG sites = 52, Kimura (unadjusted) = 71.21 Transitions / transversions = 3.25 (52/16) Gap_init rate = 0.04 (6 / 166), avg. gap size = 1.33 (8 / 6) 216 35.29 2.33 1.15 chr5ptel1M 738312 738397 (261603) L2c_3end#LINE/L2 361 447 (31) m_b236s601i29 9338 chr5ptel1M 738312 TGTATCATCTGATAGAATACAAGCTTTCTGAGGGCAGGGACCTTTCC--A 738359 v v iiv v iii iii v vi -- L2c_3end#LINE 361 TGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTA 410 chr5ptel1M 738360 TCCTTCTCTTGTATCCTTTGTATACAGCATTTGGGAGG 738397 i v - iiv iiivii iv i v L2c_3end#LINE 411 TTCATCT-TTGTATCCCCAGCGCCTGGCACATAGTAGG 447 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 47.74 CpG sites = 19, Kimura (unadjusted) = 50.44 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.02 (2 / 85), avg. gap size = 1.50 (3 / 2) 219 24.70 2.86 7.46 chr5ptel1M 738324 738393 (261607) L2d2_3end#LINE/L2 435 501 (54) m_b236s601i30 9338 chr5ptel1M 738324 TAGAATACAAGCTTTCTGAGGGCAGGGACC-TTTC-CATCCTTCTCTTGT 738371 v ii iii - v -i v - L2d2_3end#LIN 435 TAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACTTCT-TTGT 483 chr5ptel1M 738372 ATCCTTTGTATACAGCATTTGG 738393 ii----i iii i L2d2_3end#LIN 484 ATCCCC----CACAGCGCCTAG 501 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.53 CpG sites = 13, Kimura (unadjusted) = 31.96 Transitions / transversions = 4.33 (13/3) Gap_init rate = 0.10 (7 / 69), avg. gap size = 1.00 (7 / 7) 270 21.28 14.89 0.00 chr5ptel1M 739328 739421 (260579) C L2#LINE/L2 (303) 2779 2672 m_b236s601i31 9337 chr5ptel1M 739328 AGAA-AGATTGGAAGGAGGAGAGCTTTAAAGTTGGA----CAGTTAGGAG 739372 - i ? i i vi vv vi iv i---- C L2#LINE/L2 2779 AGAATAGACTGNAGGGGGGCAAGGGTGGAAGCAGGGAGACCAGTTAGGAG 2730 chr5ptel1M 739373 GCTATTGAAGTTGTCCAGGCAAGAGGTGA--------TGGACCA-GATGA 739413 v vi i i -------- - i i C L2#LINE/L2 2729 GCTATTGCAGTAATCCAGGCGAGAGATGATGGTGGCTTGGACCAGGGTGG 2680 chr5ptel1M 739414 TGGCTGTG 739421 v C L2#LINE/L2 2679 TGGCAGTG 2672 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.35 CpG sites = 12, Kimura (unadjusted) = 25.81 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.04 (4 / 93), avg. gap size = 3.50 (14 / 4) 23 7.03 0.00 0.00 chr5ptel1M 740208 740237 (259763) (T)n#Simple_repeat 1 30 (0) m_b236s252i18 9339 chr5ptel1M 740208 TTTTTTTTTTTTTTTTTTTTTTAATTTTTT 740237 vv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 30 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 13 4.76 0.00 4.35 chr5ptel1M 740322 740345 (259655) (CCCT)n#Simple_repeat 1 23 (0) m_b237s252i1 9340 chr5ptel1M 740322 CCCTCCCTCCCTCCACCCCCTCCC 740345 - i (CCCT)n#Simpl 1 CCCTCCCTCCCTCC-CTCCCTCCC 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 307 27.97 4.76 10.00 chr5ptel1M 740722 740868 (259132) L2c_3end#LINE/L2 334 473 (5) m_b237s601i1 9341 chr5ptel1M 740722 TGTTTCATAAGTGTCTGTTGACTTGATGGTTTGACTTAAGCCATTTGACT 740771 v ii v v ? viv i -- i --- i v L2c_3end#LINE 334 TGTATTGTAATTGTCTGTTTACNTGTCTGTCT--CCT---CCACTAGACT 378 chr5ptel1M 740772 GTGAGTTACTGGAAGGGAGAGACTGTTGAAGCTT-----TCTTTACAT-C 740815 i v v i v i i ---iv ----- ii - L2c_3end#LINE 379 GTGAGCTCCTTGAGGGCAGGGACCGT---GTCTTATTCATCTTTGTATCC 425 chr5ptel1M 740816 CTAACGCTTAGCTACACTGCCTGACACATGCTTAATAAACGTTTACTG-A 740864 i i i i - ----- iii vii i i ii - L2c_3end#LINE 426 CCAGCGCCTGGC-ACA-----TAGTAGGCGCTCAATAAATGTTTGTTGAA 469 chr5ptel1M 740865 TGAA 740868 L2c_3end#LINE 470 TGAA 473 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 34.45 CpG sites = 26, Kimura (unadjusted) = 36.99 Transitions / transversions = 2.36 (26/11) Gap_init rate = 0.12 (17 / 146), avg. gap size = 1.24 (21 / 17) 225 27.55 0.65 0.82 chr5ptel1M 744961 745574 (254426) (GA)n#Simple_repeat 1 613 (0) m_b237s252i2 9342 chr5ptel1M 744961 GAGTGGGAGAG-GGGAGAGACGGAGAGACGGGGAGAGAGACGGAGAGACG 745009 v i - i vi vi i vi vi (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr5ptel1M 745010 GGGAGAGAGACGGAGAGACGGGGAGAGAGACGGAGAGAGGGAGAGAGACG 745059 i vi vi i vi i vi (GA)n#Simple_ 51 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 100 chr5ptel1M 745060 GAGAGACGGGGAGAGACGGAGAGACGGGGAGAGAGACGGGGAGAGAGACG 745109 vi i vi vi i vi i vi (GA)n#Simple_ 101 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 150 chr5ptel1M 745110 GAGAGAGAGACGGGGAGAGAGACGGGAGAGAGACGGGGAGAGAGACGGGG 745159 vi i - i vi i vi i (GA)n#Simple_ 151 GAGAGAGAGAGAGAGAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGAG 199 chr5ptel1M 745160 AGAGAGACGGGGAGAGAGACGGGAGAGAG-GAGAGGGA-AGAGAGACGGA 745207 vi i - i - i - vi (GA)n#Simple_ 200 AGAGAGAGAGAGAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 248 chr5ptel1M 745208 GAGAGAGACGGGGAGAGAGACGGGGAGAGAGACGGGGAGAGAGACGGGGA 745257 vi i vi i vi i vi i (GA)n#Simple_ 249 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 298 chr5ptel1M 745258 GAGAGACGGGGAGAGAGACGGGGAGAGAGACGGGGAGAGAGACGGGGAGA 745307 vi i vi i vi i vi i (GA)n#Simple_ 299 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 348 chr5ptel1M 745308 GAGACGGGGAGAGAGACGGGGAGAGAGACGGGGAGAGACGGGGAGAGAGA 745357 vi i vi i vi i vi i (GA)n#Simple_ 349 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 398 chr5ptel1M 745358 CGGGGAGAGAGACGGGAGAGAGACGGGGAGAGAGTGGGAGAGAGATCG-G 745406 vi i - i vi i v i vv - (GA)n#Simple_ 399 GAGAGAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 447 chr5ptel1M 745407 GGAGAGAGACGGGGAGAGAGACGGGAGAGAGACGGGGAGAGAGAGACGGG 745456 i vi i - i vi i - i (GA)n#Simple_ 448 AGAGAGAGAGAGAGAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGA-GAG 495 chr5ptel1M 745457 AGAGAGACGGAGAGACGGGGAGAGAGACGGAGAGACGGGGAGAGAGACGG 745506 vi vi i vi vi i vi (GA)n#Simple_ 496 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 545 chr5ptel1M 745507 AGAGACGGGGAGAGAGACGGAGAGACGGGGAGAGAGACGGAGAGAGAGAG 745556 vi i vi vi i vi (GA)n#Simple_ 546 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 595 chr5ptel1M 745557 CGCGCGCGAGCGAGTGAG 745574 v v v v v v (GA)n#Simple_ 596 AGAGAGAGAGAGAGAGAG 613 Matrix = Unknown Transitions / transversions = 1.58 (84/53) Gap_init rate = 0.01 (9 / 613), avg. gap size = 1.00 (9 / 9) 196 35.33 5.13 0.82 chr5ptel1M 746149 746265 (253735) C L2d_3end#LINE/L2 (14) 502 381 m_b237s601i2 9343 chr5ptel1M 746149 AACAAGCAATTAGAAAGTAGCTACTCTGTGCCAAGTGCTGTTCAAAATTT 746198 i v vvi iiv v iv ii v v iiivi C L2d_3end#LINE 502 AACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTGTGCTAGGCGC 453 chr5ptel1M 746199 TCCTGG---CTATAAAGTAAGGAGAAAACA--GTTGTTGCCTTCCAAGAA 746243 viv --- v ? i-? v v i -- ivi i v i i C L2d_3end#LINE 452 TGTGGGGAACGANAAAA-NAGTATAAGACATGGTCCCTGCCCTCAAGGAG 404 chr5ptel1M 746244 CTGTCAGTCTAA-CAGGGAGACA 746265 vv i i-ii C L2d_3end#LINE 403 CTTACAATCTAGTTGGGGAGACA 381 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 47.03 CpG sites = 23, Kimura (unadjusted) = 50.70 Transitions / transversions = 1.28 (23/18) Gap_init rate = 0.03 (4 / 116), avg. gap size = 1.75 (7 / 4) 461 29.65 0.72 2.21 chr5ptel1M 746759 746896 (253104) C MIR#SINE/MIR (78) 184 49 m_b237s601i3 9344 chr5ptel1M 746759 ATCTTTACAAAAACCCTTATGAGTTAAGTGTTCATATCTGATCTTCGTTC 746808 i i v - v i ii vv i-- ii i i C MIR#SINE/MIR 184 ATCCTCACAACAACCCT-ATGAGGTAGGTACTATTATT--ATCCCCATTT 138 chr5ptel1M 746809 CCCAATTCTGAAAACTGAGGCAAAGAGAAGTTAAATGACTT-TCTGGGTT 746857 iv iv vv i v i i i -i iii v C MIR#SINE/MIR 137 TACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGT 88 chr5ptel1M 746858 CACATAGCTAGTAAGTTTCTGACATTGGATTTGAACTCA 746896 i vv v vviv i i C MIR#SINE/MIR 87 CACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCA 49 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 36.42 CpG sites = 24, Kimura (unadjusted) = 38.89 Transitions / transversions = 1.50 (24/16) Gap_init rate = 0.03 (4 / 137), avg. gap size = 1.00 (4 / 4) 299 30.96 1.18 1.18 chr5ptel1M 747441 747525 (252475) Charlie1b#DNA/hAT-Charlie 1 85 (438) m_b237s502i0 9345 chr5ptel1M 747441 CAGTGATTCTCAAAGTCTG-TCCAGAGCATCCTCGGAATCTCTGAAATCC 747489 i i v - i i vvi v ii i i i i Charlie1b#DNA 1 CAGCGGTTCTCAAAGTGTGGTCCGGGGACCCCTGGGGGTCCCCGAGACCC 50 chr5ptel1M 747490 TTTCAGAGAGTCTACAATTTCATAATTGGTTTTTAT 747525 i i ii i vv v i -i i Charlie1b#DNA 51 TTTCAGGGGGTCCGCGAGGTCAAAACT-ATTTTCAT 85 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 32.33 CpG sites = 19, Kimura (unadjusted) = 42.92 Transitions / transversions = 2.71 (19/7) Gap_init rate = 0.02 (2 / 84), avg. gap size = 1.00 (2 / 2) 437 17.60 0.00 3.30 chr5ptel1M 747518 747611 (252389) Charlie1a#DNA/hAT-Charlie 1332 1422 (33) m_b237s502i1 9346 chr5ptel1M 747518 GTTTTTATTTTTAATGTGATCAATATCTATAACTATATCCCACATAAACA 747567 v i i i v v iv v Charlie1a#DNA 1332 GTTTTAATTTCTAATATGGTAAATATCGATAGATATAACCCACATAAACA 1381 chr5ptel1M 747568 AAAACTCTTTGGACAGATCCTCAATCGTTTTTAATAGGATAAAG 747611 i --- i vi v vi Charlie1a#DNA 1382 AAAGCTCTTTGG---GGTCCTCAATAATTTTTAAGAGTGTAAAG 1422 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 20.14 CpG sites = 8, Kimura (unadjusted) = 20.14 Transitions / transversions = 1.00 (8/8) Gap_init rate = 0.03 (3 / 93), avg. gap size = 1.00 (3 / 3) 265 28.30 7.89 0.82 chr5ptel1M 750119 750232 (249768) MIR3#SINE/MIR 85 206 (2) m_b237s601i4 9347 chr5ptel1M 750119 TATGATCTTTGGCAAA--AATTC-CTTCTCTGTGCTTAAGTTTCTCC--T 750163 i i v i-- v - i v i v ii --i MIR3#SINE/MIR 85 TGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATC 134 chr5ptel1M 750164 TGT-AAATAATGATGGCTGGACTATTTAATTGGCAA-GTATTTTTTAATT 750211 - i - iv i vv i ivvi - vii ii ii MIR3#SINE/MIR 135 TGTAAAATGA-GGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCT 183 chr5ptel1M 750212 CT-ACATTCTATGACTTT-TGAT 750232 - i i - MIR3#SINE/MIR 184 CTGACATTCTATGATTCTATGAT 206 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 37.36 CpG sites = 22, Kimura (unadjusted) = 37.36 Transitions / transversions = 2.20 (22/10) Gap_init rate = 0.07 (8 / 113), avg. gap size = 1.25 (10 / 8) 381 34.14 4.81 2.83 chr5ptel1M 750740 750947 (249053) C MIRc#SINE/MIR (27) 241 30 m_b237s601i5 9348 chr5ptel1M 750740 AGCA-TTTAC-TTTTACCTACTTTCTTTACA-ATATTATATTACTTTATT 750786 - -v vv vivii i - i v i i v i C MIRc#SINE/MIR 241 AGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATCTCATTTGATC 192 chr5ptel1M 750787 CTCACAATCATCTTCCAAGTTCTGC------GATATTATTATCTCCATGT 750830 iv i i vii v vv ------ i i v C MIRc#SINE/MIR 191 CTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTT 142 chr5ptel1M 750831 AACAATTGAGGAAAATAAAGAAAACAGAGGTTAACCCTGTTAACTTTTCC 750880 v iv v i i vvv v v----- i vi C MIRc#SINE/MIR 141 TACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAG-----TGACTTGCCC 97 chr5ptel1M 750881 AGAGCAACACAGCTGGTCACTGTTTGAGGACAGATGTTAAACATGGGCAA 750930 ii iv i v v viv vvvi i- ii vii ivv C MIRc#SINE/MIR 96 AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGAC-TCGAACCCAGGTCT 48 chr5ptel1M 750931 TGCTGATTCTAGG-CCAG 750947 v i i i - C MIRc#SINE/MIR 47 TCCTGACTCCAAGTCCAG 30 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 44.52 CpG sites = 35, Kimura (unadjusted) = 46.43 Transitions / transversions = 1.03 (35/34) Gap_init rate = 0.05 (11 / 207), avg. gap size = 1.45 (16 / 11) 452 32.24 1.09 3.91 chr5ptel1M 750762 750945 (249055) C MIR#SINE/MIR (55) 207 29 m_b237s601i6 9348 chr5ptel1M 750762 CTTTACA-ATATTATATTACTTTATTCTCACAATCATCTTCCAAGTTCTG 750810 -i vv i i v i iv i i vii v vv C MIR#SINE/MIR 207 CTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGGTAGG 158 chr5ptel1M 750811 CGATATTATTATCTCCATGTAACAATTGAGGAAAATAAAGAAAACAGAGG 750860 iiv i v v iv v i i v v v C MIR#SINE/MIR 157 TACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGG 108 chr5ptel1M 750861 TTAACCCTGTTAACTTTTCCAGAGCAACACAGCTGGTCACTGTTTGAGGA 750910 v----- vi ii iv i v v viv vv C MIR#SINE/MIR 107 TTAAG-----TAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCC 63 chr5ptel1M 750911 CAGATGTTAAACATGGGCAATGCTGATTCTAG-GCC 750945 vi - ii vii i - ii i - C MIR#SINE/MIR 62 GGGAT-TCGAACCCAGGCAGT-CTGGCTCCAGAGCC 29 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 41.82 CpG sites = 30, Kimura (unadjusted) = 42.92 Transitions / transversions = 1.11 (30/27) Gap_init rate = 0.05 (9 / 183), avg. gap size = 1.00 (9 / 9) 17 5.00 0.00 0.00 chr5ptel1M 751233 751253 (248747) (T)n#Simple_repeat 1 21 (0) m_b237s252i3 9349 chr5ptel1M 751233 TTTTCTTTTTTTTTTTTTTTT 751253 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTT 21 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 598 31.99 7.16 3.25 chr5ptel1M 752283 752757 (247243) C L1MC5_3end#LINE/L1 (2115) 579 87 m_b237s551i0 9350 chr5ptel1M 752283 ACATCCCTCACAATTTCTTATAG-TAAATATTATTCTGTAACATTCATAT 752331 i i ivvi i i - iv v i ii viii vv i C L1MC5_3end#LI 579 ATATTCCTCATTCCTTTTTACAGCTGCATAGTACTCCATTGTGTGGATGT 530 chr5ptel1M 752332 GCCATCATTTATTCAGCCATTCTCCAAATGACGAACATCCATTCAGTTTC 752381 i vi i v i v v i i iiivviv C L1MC5_3end#LI 529 ACCATAGTTTATTCAACCAGTCCCCTATTGATGGACATTTGGGTTGTTTC 480 chr5ptel1M 752382 TTGTTCCTTTCCACTACAAAAAGGGCTGCTATAAAC-GTTTTG-GCACAT 752429 iv iii v i i v v v i i- ii - i i C L1MC5_3end#LI 479 CAGTCTTTTGCTATTACAAATAGTGCTGCAATGAATAGCCTTGTGCATAC 430 chr5ptel1M 752430 GTGAGTACTTTTCTCTTTTTTTTTAATGATCTTTTTGGGATACAGACTCG 752479 ----- viv vii i - v i v vv iii C L1MC5_3end#LI 429 GT-----CTTTTCGTATTTTTGCCAGTG-TATCTTTGGGATAGATTCCTA 386 chr5ptel1M 752480 GTAGAGACACTGCTGGAT-GAAGGGTA--TGAATAATTTGATAGCCCTTT 752526 v v iv i i -i -- v - v i ----- C L1MC5_3end#LI 385 GAAGTGGGATTGCTGGGTCAAAGGGTAAATGCATA-TGTAAT-----TTT 342 chr5ptel1M 752527 GA-AGATAGTTCCAAATTATTCTCCAGAATGGTGGAATCAGTTCGCAACT 752575 v- v v vii v iv v v i v i vii C L1MC5_3end#LI 341 GCTAGATATTGCCAAATTCCCCTCCATAGGGGTTGTACCATTTTGCATTC 292 chr5ptel1M 752576 CCACTAACAATTTATTAGCATCCTAGTTTCCCCACA-------------- 752611 i i v v vi v iv -------------- C L1MC5_3end#LI 291 CCACCAGCAATGTATGAGAGTGCCTGTTTCCCCACAGCCTCGCCAACAGA 242 chr5ptel1M 752612 -TATCTT-------TTTCCGTCATCTTAGCTAATTTGAGAGGTAAGTAGT 752653 - v ------- iv -- i v i i v i v i C L1MC5_3end#LI 241 GTATGTTGTCAAACTTTTGG--ATTTTTGCCAATCTGATAGGTGAGAAAT 194 chr5ptel1M 752654 GTTACCTTAGAGTTGTTTGAATTTGCCTTTATTCTATTCAGTAGTGCTTT 752703 v i i v v v v v ii - vv i vvv C L1MC5_3end#LI 193 GGTATCTCAGTGTAGTTTTAATTTGCATTTCTCTTATT-ATGAGCGAGGT 145 chr5ptel1M 752704 AGAGCAT-TTTTCATACTACTTAGAAATGATTTTAATGTC----TCTGAA 752748 v - - i? ii iiv vv v ---- vi C L1MC5_3end#LI 144 TGAGCATCTTTTCATA-TGNTTAAGAGCCATTTGCATTTCTTTTTCTGTG 96 chr5ptel1M 752749 AATTGCCTG 752757 i i C L1MC5_3end#LI 95 AACTGTCTG 87 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 42.04 CpG sites = 79, Kimura (unadjusted) = 42.81 Transitions / transversions = 1.16 (79/68) Gap_init rate = 0.06 (27 / 474), avg. gap size = 1.85 (50 / 27) 639 32.13 6.14 2.13 chr5ptel1M 752309 752715 (247285) C L1ME4c_3end#LINE/L1 (275) 555 133 m_b237s551i1 9350 chr5ptel1M 752309 ATATTATTCTGTAACATTCATATGCCATCATTTATTCAGCCATTCTCCAA 752358 v ii vivi ?v i i v i i i i v C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chr5ptel1M 752359 ATGACGAACATCCATTCAGTTTCTTGTTCCTTTCCACTACAAAAAGGGCT 752408 v vi i ii vviv ivi ii iv i i i v iv C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCT 456 chr5ptel1M 752409 GCTATAAACGTTTTGGCACATGTGAGTACTTTTCTCTTTTTTTTTAATGA 752458 v i i i v ii i - -- - i i v v C L1ME4c_3end#L 455 GCAATGAACATCTTCGTGCATAT-AG--CTTTT-TCCTTCTTTTGAATTA 410 chr5ptel1M 752459 TCTTTTTGGGATACAGACTCGGTAGAGACACTGCTGGAT-GAAGGGTATG 752507 i ii i v vv i i v v iv i i i -i C L1ME4c_3end#L 409 TTTCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATG 360 chr5ptel1M 752508 AATAATTTGATAGCCCTTTGAAGATAGTTCCAAATTATTCTCCAGAATGG 752557 i v v i i viv vi v v ii i i v C L1ME4c_3end#L 359 AACATTTTTATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAGGG 310 chr5ptel1M 752558 TGGAATCAGTTCGCAACTCCACTAACAATTTATTAGCATCCTAGTTTCCC 752607 v v i i ii ?iv i i v v ?i v i v C L1ME4c_3end#L 309 TTGTACCAATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCAC 260 chr5ptel1M 752608 CACA--------------------TATC--TTTTTCCGTCATCTTAGCTA 752635 i -------------------- -- ivi-- i v C L1ME4c_3end#L 259 CGCANCCTCGCCAGCATTGGGTATTATCAATTTTTTAA--ATTTTTGCTA 212 chr5ptel1M 752636 ATTTGAGAG--GTAAGTAGTGTTACCTTAGAGTTGTTTGAATTTGCCTTT 752683 i v -- -- i v i i vv i v v C L1ME4c_3end#L 211 ATTTAATAGGCGTAA--AATGGTATCTCATTGTTGCTTTAATTTGCATTT 164 chr5ptel1M 752684 ATTCTATTCAGTAGTGCTTTAGAGCATTTTTC 752715 v iv - v i vvv v i C L1ME4c_3end#L 163 CTTTGATT-ACTAGCGAGGTTGAACATTTTTC 133 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 41.44 CpG sites = 73, Kimura (unadjusted) = 43.71 Transitions / transversions = 1.33 (73/55) Gap_init rate = 0.03 (13 / 406), avg. gap size = 2.62 (34 / 13) 13 0.00 0.00 0.00 chr5ptel1M 753162 753178 (246822) (TTA)n#Simple_repeat 1 17 (0) m_b237s252i4 9351 chr5ptel1M 753162 TTATTATTATTATTATT 753178 (TTA)n#Simple 1 TTATTATTATTATTATT 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 268 28.40 3.37 1.10 chr5ptel1M 753215 753303 (246697) MIR3#SINE/MIR 115 205 (3) m_b237s601i7 9352 chr5ptel1M 753215 TGACCCTCAGTTTCAACATTTGTAAAATGAGAGCGCTGTATTCCAGGGCC 753264 iv vv i i v i v i vv v ii MIR3#SINE/MIR 115 TGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATC 164 chr5ptel1M 753265 TGTCAGCTCCCTTCCAGG---GATCAATCTATAATCTTGTAA 753303 v v v v--- - v i ii i i MIR3#SINE/MIR 165 TCTAAGGTCCCTTCCAGCTCTGA-CATTCTATGATTCTATGA 205 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 36.03 CpG sites = 12, Kimura (unadjusted) = 36.03 Transitions / transversions = 0.92 (12/13) Gap_init rate = 0.02 (2 / 88), avg. gap size = 2.00 (4 / 2) 279 30.75 12.10 0.57 chr5ptel1M 753390 753546 (246454) C L2a_3end#LINE/L2 (10) 507 333 m_b237s601i9 9353 chr5ptel1M 753390 TCAACAAATATTTA---AAAATCTGCTATGTGTCATATCCTGTGCTAAGC 753436 --- ivii i i viiv v i C L2a_3end#LINE 507 TCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGC 458 chr5ptel1M 753437 ACTAGAGACATAA-AGAG-CTGTAATGGACTTA---CCCTGATCCTGTGG 753481 i i i i i i- v -viiv ii vv --- vi iii C L2a_3end#LINE 457 GCTGGGGATACAGCAGTGAACAAAACAGACAAAAGTCCCTGCCCTCATGG 408 chr5ptel1M 753482 AGTTCACAGTC-AGTAG-----GACAGACAACACAT---CAACTATGCAG 753522 i i v - i ----- i v i---i v v i i C L2a_3end#LINE 407 AGCTTACATTCTAGTGGGGGGAGACAGACAATAAACAAATAAATAAGTAA 358 chr5ptel1M 753523 AA-ATATGCTATTGTGAGA-AGTGAT 753546 - iv - v -i C L2a_3end#LINE 357 AATATATAGTA-TGTCAGATGGTGAT 333 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 39.38 CpG sites = 32, Kimura (unadjusted) = 41.70 Transitions / transversions = 2.00 (32/16) Gap_init rate = 0.06 (10 / 156), avg. gap size = 2.00 (20 / 10) 374 27.70 8.20 2.33 chr5ptel1M 753390 753511 (246489) C L2b_3end#LINE/L2 (10) 456 328 m_b237s601i8 9353 chr5ptel1M 753390 TCAACAAATATTTA---AAAATCTGCTATGTGTCATATCCTGTGCTAAGC 753436 --- ivii i i i vii? i C L2b_3end#LINE 456 TCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGC 407 chr5ptel1M 753437 ACTAGAGACATAAAGAGCTGTA----ATGGACTTA--CCCTGATCCTGTG 753480 i i i -- v v v v ---- ii ?ii-- vi iiii C L2b_3end#LINE 406 GCTGGGG--ATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACG 359 chr5ptel1M 753481 GAGTTCACAGTC-AGTAGGACAGACAACACAT 753511 i - i iv i- C L2b_3end#LINE 358 GAGCTCACAGTCTAGTGGGGGAGACAG-ACAT 328 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 32.00 CpG sites = 25, Kimura (unadjusted) = 37.91 Transitions / transversions = 3.12 (25/8) Gap_init rate = 0.06 (7 / 121), avg. gap size = 1.86 (13 / 7) 249 37.31 9.92 1.09 chr5ptel1M 754301 754552 (245448) C L2#LINE/L2 (218) 2864 2591 m_b237s601i10 9353 chr5ptel1M 754301 GAGGGTAAGTAAT--GAAGTTGTTGA--AGAGG--TGACATGGTCAGATA 754344 v v iv -- i v v -- -- i v iv C L2#LINE/L2 2864 GATGGGAAGCCATTGGAGGGTTTTGAGCAGAGGAGTGACATGATCTGACT 2815 chr5ptel1M 754345 GA-GCTTTATGAAGATGAACTTGGCAGCTA-GTTGGAGGAGTGACTGTAT 754392 v - i vi i v vii v i- - i vv ? v C L2#LINE/L2 2814 TACGTTTTAAAAGGATCACTCTGGCTGCTGTGTTG-AGAATAGACTGNAG 2766 chr5ptel1M 754393 TGGGAAGAGATCTGAAGCATCTGAACCAACCAGCAGGCTCTTCAAATAGC 754442 v ivi iviv vvvii iii v v vv i ii C L2#LINE/L2 2765 GGGGGCAAGGGTGGAAGCAGGGAGACCAGTTAGGAGGCTATTGCAGTAAT 2716 chr5ptel1M 754443 TTAGGTATGAGGTAATTGAAGTCTGACCCAAGAAATTGACAAGGGGGGTA 754492 ii iiv i i v vi ii iv i iviv i iv i i C L2#LINE/L2 2715 CCAGGCGAGAGATGATGGTGGCTTGGACCAGGGTGGTGGCAGTGGAGGTG 2666 chr5ptel1M 754493 TATGAGAACTGCCC-----------------CCAAAGTGGAACCAACAGG 754525 -i v vi -----------------iv i i i i C L2#LINE/L2 2665 -GTGAGAAGTGGTCGGATTCTGGATATATTTTGAAGGTAGAGCCGACAGG 2617 chr5ptel1M 754526 ACTTTTCAACAGATTGAACTTGCGGGT 754552 i viii ii i iv - C L2#LINE/L2 2616 ATTTGCTGATGGATTGGATGTG-GGGT 2591 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 52.70 CpG sites = 55, Kimura (unadjusted) = 54.56 Transitions / transversions = 1.45 (55/38) Gap_init rate = 0.04 (9 / 251), avg. gap size = 3.11 (28 / 9) 440 38.02 5.89 4.50 chr5ptel1M 754699 755224 (244776) C L2#LINE/L2 (922) 2160 1628 m_b237s601i11 9353 chr5ptel1M 754699 GGTAGAAGGAGAACCAAGGGAGAATACTGTCATTAAAACCTAGGGAGAAG 754748 i i i i vi iv v vi i v v ii i C L2#LINE/L2 2160 GGTAGGAGGAAAACCAGGAGAGTGTGGTGTCCTGGAAGCCAAGTGAAGAA 2111 chr5ptel1M 754749 AG-----GAGGAAGAAAAGAGGGTGATTAACACTACGAACACCTGCAGAG 754793 -----v i i ii -- i vv iiv vvv v ? C L2#LINE/L2 2110 AGTGTTTCAAGAAGGAGGGAG--TGATCAACTGTGTCAAATGCTGCTGAN 2063 chr5ptel1M 754794 AAGTCAAGAAGAATGCGGATGAGGAAATGGCCATCAAATTGAGCATTTTC 754843 i v ii v ivii v i iii v viv v C L2#LINE/L2 2062 AGGTCAAGTAAGATGAGGACTGAGAATTGACCATTGGATTTAGCAACGTG 2013 chr5ptel1M 754844 AGGATTATTTGTAATTTTTGTTA-AGC-GTTTCAGTTGATCAAAGAAGTT 754891 ii i i v i ii viiv - - i v viiiv ii vi C L2#LINE/L2 2012 GAGGTCATTGGTGACCTTGACAAGAGCAGTTTCGGTGGAGTGGTGGGGAC 1963 chr5ptel1M 754892 GGAAGTCAGACTGAAGT-GTTTCAGAGAAAGTCTGGGAAAAGATGAAT-- 754938 i i v i i - v - i vv ii v -- C L2#LINE/L2 1962 GAAAGCCTGATTGGAGTGGGTTCA-AGAGAGAATGGGAGGAGAGGAATTG 1914 chr5ptel1M 754939 ---GTATTAATTGTGAATGGCTATTTCTAGCTATTCAGTCTCAAAGAAGG 754985 ---ii vii v i ii iii v v vvi iv iivi -- C L2#LINE/L2 1913 GAGACAGCGAGTATAGACAACTCTTTCGAGGAGTTTTGCTGTAAAG--GG 1866 chr5ptel1M 754986 AAAGATAGATATTGAATACTATCT-CAAGGGGATGCATGGATCAAATGAA 755034 i iv v v v iiiiv v -v i ? ii- i iv i C L2#LINE/L2 1865 GAGCAGAGAAATGGGGCGGTAGCTGGAGGGGGANGTG-GGGTCAAGGGAG 1817 chr5ptel1M 755035 ------TGTGTTTTGAGGATTAGAAAGAAAGGGTCTTATTTG--TGGCAA 755076 ------ v i i vi i i v?iviv v i -- vii C L2#LINE/L2 1816 AATTTTTGTTTTTTAAAGATGGGAGAAATNACAGCATGTTTGTATGCTGA 1767 chr5ptel1M 755077 TAGGAAAGGATTCATTATTATAGGAGAGAGTGAAAATTAGTG-----CGG 755121 - i v i v ------ i -i ii -----v i C L2#LINE/L2 1766 T-GGGAATGATCCAGTA------GAGAGGG-AAAAATTGATGATGCAGGA 1725 chr5ptel1M 755122 GAAAATGGGGACA----CCAGAGGCCACAATATAATTACATAGATAAGGG 755167 i iv v ---- ii ---- i i vv ivi iii i C L2#LINE/L2 1724 GAGAGAGGGGAGAATTGCTGGAG----CGATGTCCTTGAGTAGGCGAGAG 1679 chr5ptel1M 755168 GATGGAATGGGATTATTTGCACAGCCAAAAGGATTTGTTTTAGCAAATAG 755217 --- i ivvv iviii i i v ii --- C L2#LINE/L2 1678 ---GGGATGGGATCTAGTGCACAAGTGGAGGGGTTGGCCTTAG---ATAG 1635 chr5ptel1M 755218 AAGGATG 755224 i v i C L2#LINE/L2 1634 GAGCACG 1628 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 53.34 CpG sites = 120, Kimura (unadjusted) = 57.18 Transitions / transversions = 1.69 (120/71) Gap_init rate = 0.07 (35 / 525), avg. gap size = 1.57 (55 / 35) 501 31.33 9.35 2.67 chr5ptel1M 755675 755920 (244080) C MIR#SINE/MIR (0) 262 1 m_b237s601i12 9354 chr5ptel1M 755675 AATTATAGCTGACATTGACAGAATAC--AGTATGTGCCA--CAC------ 755714 v i v iv iii -- v -- ------ C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCT 213 chr5ptel1M 755715 AA----TTTACATAAAAATCTGATTTCATTTGATCCTTATAAGAACCTCA 755760 ---- i---- v v vi i i i v ii C MIR#SINE/MIR 212 AAGCGCTTTACATG----TATTAACTCATTTAATCCTCACAACAACCCTA 167 chr5ptel1M 755761 GCAGTTAGGTGTGATTATTATTGCCACTTTACAGATGAAGAAACTGAGGC 755810 vv v iiv iv i i C MIR#SINE/MIR 166 TGAGGTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGC 117 chr5ptel1M 755811 AAACAGTGGT------ATTTGCTCCCAAT--CATAGTATACATGTTTCTG 755852 v v v ------ i i vvii -- i ivvii v vv v C MIR#SINE/MIR 116 ACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAG 67 chr5ptel1M 755853 AAGTAGGATTTGAACTCAGATGAATCCAACTTTA-AGCCTAACATTCTAT 755901 ivii i i ii- i iii ii - iivvv ii v C MIR#SINE/MIR 66 AGCCGGGATTCGAACCCAGGC-AGTCTGGCTCCAGAGCCCGTGCTCTTAA 18 chr5ptel1M 755902 CTACTTGTACCATCACTGT 755920 i - i i i - C MIR#SINE/MIR 17 CCAC-TATGCTAT-ACTGT 1 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 39.04 CpG sites = 46, Kimura (unadjusted) = 42.24 Transitions / transversions = 1.59 (46/29) Gap_init rate = 0.06 (14 / 245), avg. gap size = 2.14 (30 / 14) 510 33.50 3.72 4.21 chr5ptel1M 755705 755919 (244081) C MIRb#SINE/MIR (46) 222 9 m_b237s601i13 9354 chr5ptel1M 755705 TGTGCCACACAATTTACATAAAAATCTGATTTCATTTGATCCTTATAAGA 755754 i vi iv iv ---- v i i i i v C MIRb#SINE/MIR 222 TGTGCTAAGCGCTTTACATGCA----TTATCTCATTTAATCCTCACAACA 177 chr5ptel1M 755755 ACCTCAGCAGTTAGGTGTGATTATTATTGCCACTTTACAGATGAAGAAAC 755804 iiivv v --- iv i i C MIRb#SINE/MIR 176 ACCCTGCGAGGTAGGT---ATTATTATCCCCATTTTACAGATGAGGAAAC 130 chr5ptel1M 755805 TGAGGCAAACAGTGGT------ATTTGCTCCCAAT--CATAGTATACATG 755846 vv v v ------ i i vvii -- i ivvii v C MIRb#SINE/MIR 129 TGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAG 80 chr5ptel1M 755847 TTTCTGAAGTAGGATTTGAACTCAGATGAATCCAACTTTAAGCCTAACAT 755896 vv v ivii i i i vvi ii ii iv iviiii C MIRb#SINE/MIR 79 TGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGC 30 chr5ptel1M 755897 TCTATCTACTTGTACCATCACTG 755919 v i - i - i C MIRb#SINE/MIR 29 TCTTTCCAC-TGCACCA-CGCTG 9 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 41.68 CpG sites = 42, Kimura (unadjusted) = 46.30 Transitions / transversions = 1.56 (42/27) Gap_init rate = 0.05 (11 / 214), avg. gap size = 1.55 (17 / 11) 260 26.85 8.06 3.88 chr5ptel1M 757882 758005 (241995) L1M1_orf2#LINE/L1 1586 1714 (1580) m_b237s551i2 9355 chr5ptel1M 757882 ACTATATCCTAATTTCATAAATGAATATTGATGTAAAAATTCTAAATAAA 757931 i vv i v vivi i i v i L1M1_orf2#LIN 1586 ACTACAGGCCAATATCTCTGATGAATATTGATGCAAAAATCCTCAACAAA 1635 chr5ptel1M 757932 ACAGTATCTAGGAAATCG----CAGCAATATAGTACAAAGAATTTTATAT 757977 i ---- v i ---- i i v v - iv vi L1M1_orf2#LIN 1636 ATA----CTAGCAAACCGAATTCAACAATACATTAAAAAG-ATCATTCAT 1680 chr5ptel1M 757978 TGTGACAAAA------TTGTCCTATGGGTGCAAG 758005 ii v i------ i i?v i L1M1_orf2#LIN 1681 CATGACCAAGTGGGATTTATCCCNGGGATGCAAG 1714 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 34.52 CpG sites = 19, Kimura (unadjusted) = 34.52 Transitions / transversions = 1.46 (19/13) Gap_init rate = 0.06 (7 / 123), avg. gap size = 2.14 (15 / 7) 274 23.18 9.62 4.59 chr5ptel1M 757902 758005 (241995) L1M4_orf2#LINE/L1 1606 1714 (1580) m_b237s551i3 9355 chr5ptel1M 757902 ATGAATATTGATGTAAAAATTCTAAATAAAACAGTATCTAGGAAATCG-- 757949 v i i v i i ---- v i -- L1M4_orf2#LIN 1606 ATGAATATAGATGCAAAAATCCTCAACAAAATA----CTAGCAAACCGAA 1651 chr5ptel1M 757950 --CAGCAATATAGTACAAAGAATTTTATATTGTGACAAAA------TTGT 757991 -- i - v i v i iii v i------ i L1M4_orf2#LIN 1652 TCCAGCAACATA-TAAAAAGGATTATACACCATGACCAAGTGGGATTTAT 1700 chr5ptel1M 757992 CCTATGGGTGCAAG 758005 i v ii L1M4_orf2#LIN 1701 CCCAGGAATGCAAG 1714 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 28.85 CpG sites = 16, Kimura (unadjusted) = 28.85 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.08 (8 / 103), avg. gap size = 1.88 (15 / 8) 577 35.12 4.30 0.79 chr5ptel1M 759512 759999 (240001) C L1ME4c_3end#LINE/L1 (192) 638 134 m_b237s551i4 9356 chr5ptel1M 759512 TCTGCTTGTTTCACTCAACATTGATTCATGGAAATCTTTCCAGGTCTTTC 759561 v i ivv ii v - v ivi v C L1ME4c_3end#L 638 TCTGCTTTTTTCACTTAACATTATATCATAAACAT-TTTCCATGTTGCTA 590 chr5ptel1M 759562 TAAAATCAGCTCACTCATCTTTTGTTATAGA-GCGATAATATGCCATGAT 759610 i v i vv vi v i v v v i v- - v viv C L1ME4c_3end#L 589 CATAGTCTTCATAATTATCATTTTTAATGGCTGC-ATAATATTCCATCGA 541 chr5ptel1M 759611 CCTCACAGAATGCAACTTCTTCAGCCATTCCCTAAGTGATGGGCATCCAT 759660 vi?v iiv viii i vi i i iv v v i ii v C L1ME4c_3end#L 540 GTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAG 491 chr5ptel1M 759661 TCATTTTCTAATTCTTGGCTACCATAAAAAGAACTGCTATAAATACTTTG 759710 vivv i i v ii v ivi v i i ii v C L1ME4c_3end#L 490 GTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTC 441 chr5ptel1M 759711 GAACATGTGGGTCTTTTTCTCTCCTTTA-------TCCTTGGGATACAAA 759753 vi i i -- ii i i------- i v vv C L1ME4c_3end#L 440 GTGCATATAG--CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAATT 393 chr5ptel1M 759754 CCCAATAATATCACTGCTGGATCAAAGGGTATG--CACTTTTATAACCTT 759801 iv i ivv i i i -- i ii ii C L1ME4c_3end#L 392 CCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTCT 343 chr5ptel1M 759802 TGGGGCATAGTTTCTCATTGTTTACCAGAATGGTTGAATC--TTTTCCAT 759849 ivi i v vi vv i v i v v i -- v v? C L1ME4c_3end#L 342 TGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACANT 293 chr5ptel1M 759850 ACT-TCAACAATGTATTTGTGTCCCAATTTTCCCACAT-TTCCCCAA-AT 759896 i i-i i vv ? v i iv i ?-i v i- C L1ME4c_3end#L 292 GCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGCAT 243 chr5ptel1M 759897 TTATCATTATTCTTTCCTGTCATCTTAGACAATCTGAGAGGTATGAGGTC 759946 vivi ivv ii vvv i v vi i i v ii i ii v C L1ME4c_3end#L 242 TGGGTATTATCAATTTTTTAAATTTTTGCTAATTTAATAGGCGTAAAATG 193 chr5ptel1M 759947 ATATC------TTGTTTTAATTGGCATATCTATAAACAATAGTGATTTGG 759990 i ------ i v v v i vi v i vv v C L1ME4c_3end#L 192 GTATCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACTAGCGAGGTTG 143 chr5ptel1M 759991 AGCTTTTTT 759999 i v C L1ME4c_3end#L 142 AACATTTTT 134 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 46.83 CpG sites = 92, Kimura (unadjusted) = 49.29 Transitions / transversions = 1.18 (92/78) Gap_init rate = 0.02 (12 / 487), avg. gap size = 2.08 (25 / 12) 12 11.10 9.76 2.27 chr5ptel1M 760206 760246 (239754) (ATATTG)n#Simple_repeat 1 44 (0) m_b237s252i5 9357 chr5ptel1M 760206 ATATTGATATTTAAATTTA-ATT-ATATT--TATTGATTTTTGAT 760246 v v v - - -- - v (ATATTG)n#Sim 1 ATATTGATATTGATATTGATATTGATATTGATATTGA-TATTGAT 44 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.10 (4 / 40), avg. gap size = 1.25 (5 / 4) 12 11.51 3.33 3.33 chr5ptel1M 760574 760603 (239397) (TAATA)n#Simple_repeat 1 30 (0) m_b237s252i6 9358 chr5ptel1M 760574 TAACATTAT-TAATAGGAATATAATATAATA 760603 i v - -v (TAATA)n#Simp 1 TAATATAATATAATA-TAATATAATATAATA 30 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.07 (2 / 29), avg. gap size = 1.00 (2 / 2) 192 26.14 4.48 2.94 chr5ptel1M 761175 761241 (238759) C MIR#SINE/MIR (118) 144 77 m_b237s601i14 9359 chr5ptel1M 761175 CTCATTTTGTCGATAAGGGAACAGAAGGAAATAG-GTTTAAATAACT--C 761221 i iiv i i v i v v v - v i -- C MIR#SINE/MIR 144 CCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGC 95 chr5ptel1M 761222 CTAATGGCTCACGGAGCTAG 761241 i -- v iv C MIR#SINE/MIR 94 CCAA--GGTCACACAGCTAG 77 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 32.61 CpG sites = 9, Kimura (unadjusted) = 32.61 Transitions / transversions = 1.12 (9/8) Gap_init rate = 0.06 (4 / 66), avg. gap size = 1.25 (5 / 4) 14 12.69 0.00 0.00 chr5ptel1M 762343 762368 (237632) (TTAT)n#Simple_repeat 1 26 (0) m_b237s252i7 9360 chr5ptel1M 762343 TTAATGATTTCTTTATTTATTTATTT 762368 v v v (TTAT)n#Simpl 1 TTATTTATTTATTTATTTATTTATTT 26 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 302 29.76 11.41 11.83 chr5ptel1M 762685 762947 (237053) L3#LINE/CR1 3828 4089 (10) m_b237s601i15 9361 chr5ptel1M 762685 CCCCAGAGA--AGAAATAAGGTAAACAGGTGAAAGCTATTGATTGAAAGC 762732 i i-- v i iiv ii i i iv --- i i L3#LINE/CR1 3828 CTCCAGAGGGCAGAACTAGGACCAATGGGTGGAAGTTACAG---GGAGGC 3874 chr5ptel1M 762733 AGATTTTGTGTGTTTAACAGATTTCTCAATTTAAACCTTTTAGAACAGAT 762782 i ----------- ---- v i------- v iv L3#LINE/CR1 3875 AGATTTCG-----------G----CTCAATATAAG-------GAAGAACT 3902 chr5ptel1M 762783 TTCC--CAATTAAAATCCTTGT----AAGTATAATAGACT------AAAG 762820 i-- i i ii--- ---- i iv i i ------?i L3#LINE/CR1 3903 TTCTAACAATCAGAGC---TGTCCAAAAATGGAATGGGCTGCCTCGNGAG 3949 chr5ptel1M 762821 ATGTTAGGTTCCCTATCA----AAGTATTTCAAATAGTGATTGGATGAC- 762865 i iv ii i ii ---- i i - ii v ii - L3#LINE/CR1 3950 GTAGTGAGCTCCCCGTCACTGGAGGTGTT-CAAGCAGAGGCTGGATGACC 3998 chr5ptel1M 762866 ---TGTT-GGGATGAAATAGAGGAGATTTGAGAATTGCTGATG---GATT 762908 --- i- vvi i i ivv v -- --- i L3#LINE/CR1 3999 ACTTGTCAGGGATGTTGTAGAAGGGATTCCTGCATTG--GATGGGAGGTT 4046 chr5ptel1M 762909 GAATCAGATCATTTCTGAAGTA----CCAATGCTGAGATTCTG 762947 i ii v ii i i v---- iv L3#LINE/CR1 4047 GGACTAGATGACCTCTAAGGTCCCTTCCAACTCTGAGATTCTG 4089 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 39.38 CpG sites = 52, Kimura (unadjusted) = 41.08 Transitions / transversions = 3.06 (52/17) Gap_init rate = 0.16 (41 / 262), avg. gap size = 1.49 (61 / 41) 379 28.56 5.31 0.85 chr5ptel1M 763409 763521 (236479) L2b_3end#LINE/L2 343 460 (6) m_b237s601i16 9362 chr5ptel1M 763409 ATTAGACTG--AGTTCCCGGAGAGCAGGGACTGTCTTTTTCCTTT----C 763452 i -- i vv i i ?v i v i v ---- L2b_3end#LINE 343 ACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCTTGTTCACC 392 chr5ptel1M 763453 TTTCTATCCCTAGTGCTTAGCATATTGCCTGGGACACATTAGATGCTTAA 763502 vi v i i i i v? v v ii i- L2b_3end#LINE 393 GCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTC-A 441 chr5ptel1M 763503 ATAAATGCCTACTGACTAA 763521 i iii ii v i L2b_3end#LINE 442 GTAAATATTTGTTGAATGA 460 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 33.92 CpG sites = 21, Kimura (unadjusted) = 38.45 Transitions / transversions = 1.91 (21/11) Gap_init rate = 0.03 (3 / 112), avg. gap size = 2.33 (7 / 3) 224 32.25 12.41 2.67 chr5ptel1M 763679 763815 (236185) C MIR#SINE/MIR (112) 150 1 m_b237s601i17 9363 chr5ptel1M 763679 ATCATACCCATTTTGTGGACTTAGAATCAGATTCAGGGGGAGGTTAA--- 763725 i v iii ivvi v v vv vi i --- C MIR#SINE/MIR 150 ATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTA 101 chr5ptel1M 763726 -----CCT---GTTACCTAGTTAGTTACTAGTAGAGCTAGGA----AATC 763763 ----- i--- i vi i v v i i ii ---- i C MIR#SINE/MIR 100 ACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACC 51 chr5ptel1M 763764 AAACCAGATCTGCCTCCA-AACTAGTATTCTC-TCCACTCTCATGTGATA 763811 v iv - v - i iv ii i-v --- iv C MIR#SINE/MIR 50 CAGGCAG-TCTGGCTCCAGAGCCCGTGCTCTTAACCACT---ATGCTATA 5 chr5ptel1M 763812 TTAT 763815 i i C MIR#SINE/MIR 4 CTGT 1 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 42.42 CpG sites = 26, Kimura (unadjusted) = 43.95 Transitions / transversions = 1.53 (26/17) Gap_init rate = 0.07 (10 / 136), avg. gap size = 2.10 (21 / 10) 269 27.65 15.57 2.17 chr5ptel1M 763679 763800 (236200) C MIRc#SINE/MIR (114) 154 17 m_b237s601i18 9363 chr5ptel1M 763679 ATCATACCCATTTTGTGGACTTAGAA--TCAGATTCAGGGGGAGGTTAA- 763725 i v iii ivvi -- v ii i -- - C MIRc#SINE/MIR 154 ATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAG--AGGTTAAG 107 chr5ptel1M 763726 -------CCT---GTTACCTAGTTAGTTACTAGTAGAGCTAGGAAATCAA 763765 ------- i--- i vi i v v i i i- i v i C MIRc#SINE/MIR 106 TGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCC-GGGACTCGA 58 chr5ptel1M 763766 A-CCAGAT----CTGCCTCCAAA-CTAGTATTCTCTCCACT 763800 - i ---- v i- i ii i C MIRc#SINE/MIR 57 ACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACT 17 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 33.88 CpG sites = 24, Kimura (unadjusted) = 36.70 Transitions / transversions = 2.67 (24/9) Gap_init rate = 0.08 (10 / 121), avg. gap size = 2.20 (22 / 10) 233 32.14 5.62 3.87 chr5ptel1M 764335 764512 (235488) L2#LINE/L2 1633 1813 (1269) m_b237s601i19 9364 chr5ptel1M 764335 TCCTTTCCAAGGT-AATCCCTGCACCTCTATTCTTGATTCCATCCTTTTC 764383 v i i- i v i v iiv v i ii ii L2#LINE/L2 1633 TCCTATCTAAGGCCAACCCCTCCACTTGTGCACTAGATCCCATCCCCTCT 1682 chr5ptel1M 764384 CACCTCCTCAAGGACCAAGTTTC----ATTCATCATTTTCTTAATTACTA 764429 i v vvv i i ---- vi vi i ---i v i L2#LINE/L2 1683 CGCCTACTCAAGGACATCGCTCCAGCAATTCTCCCCTCTCT---CTCCTG 1729 chr5ptel1M 764430 AAT-ATGTACAATCCCTCACTCTTCACTGGATCTTTTCTTTTAACTTATC 764478 v - --- iii v ii v i iv i i v iv L2#LINE/L2 1730 CATCAT---CAATTTTTCCCTCTCTACTGGATCATTCCCATCAGCATACA 1776 chr5ptel1M 764479 AACCAGCTTAGATTTTTC----TTTTAAATGCACAAAA 764512 vv vv? i ----i -iv L2#LINE/L2 1777 AACATGCTGTNATTTCTCCCATCTTTAAA-AAACAAAA 1813 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 42.66 CpG sites = 32, Kimura (unadjusted) = 43.74 Transitions / transversions = 1.39 (32/23) Gap_init rate = 0.06 (11 / 177), avg. gap size = 1.55 (17 / 11) 446 35.75 7.59 0.31 chr5ptel1M 764520 764822 (235178) L3#LINE/CR1 2162 2486 (1613) m_b237s601i20 9365 chr5ptel1M 764520 TAAAAACAAATATAAC-GAA--TTAACAGAGGA----TGACTAAG----A 764558 iv v i v - -- vi v ---- i i ---- L3#LINE/CR1 2162 TAAAAGGACATGTATCAGAAGATGGAAAGAGGACATATAACCAAGGACAA 2211 chr5ptel1M 764559 AAAAAGATTGATATAGACTCATAAGAAT---GTTAGAAATTCTAACATTC 764605 i i v i?i i ii iii --- i i vv viii L3#LINE/CR1 2212 AGAGAGAGTANCACAAGCCTGTAAGAATAGTGTCAGGAAGGCTAAAGCCC 2261 chr5ptel1M 764606 AGAAGAAGCAAAAAATAGTAAGAAAAA--TCTAA--ATAATAAAAAT--T 764649 vi vi iiv v i i --v -- i i ?--v L3#LINE/CR1 2262 AGAATGAGCTGAGGCTTGCAAAAAAAAATGCTAAGGACAACAAAAANAAG 2311 chr5ptel1M 764650 GTTTTT---AACTATATTGTTAAGATTAAGATAAAAAAAAGAAGTAAGAT 764696 i --- i i -ivi vvv iv i ?iii i vi L3#LINE/CR1 2312 GCTTTTCAAAGCTATGTT-CGGAGCAGAAGGAAAAAGAAAGNGACAGGCC 2360 chr5ptel1M 764697 TGTTACTCTTTGTAGATAGAATGATGAGAACTGGTAACAGAGAGAAGCCT 764746 i i i ivvv i i vi i vv v i i iv v L3#LINE/CR1 2361 CGCTGCTTGGGGCAGATGGCGTAATGTTAACAGATGACAGAGAGAAAGCA 2410 chr5ptel1M 764747 GAGGTATTCAATTCCTACTTTATTTCTGTTCTCTCTAAAACTTAAAAGTA 764796 iv i i i ii i ii vv vvv i vv L3#LINE/CR1 2411 GAACTACTCAACTCCTATTTTGCTTCCGTCTTCTCTATCAAGGAGAATGA 2460 chr5ptel1M 764797 TTTTTAGATCTGAAGGTATAGGACAA 764822 i i iiv i vi i L3#LINE/CR1 2461 TCTTCAGACTGGAAAGGGTAGAACAA 2486 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 49.35 CpG sites = 68, Kimura (unadjusted) = 52.20 Transitions / transversions = 1.70 (68/40) Gap_init rate = 0.03 (10 / 302), avg. gap size = 2.40 (24 / 10) 274 38.90 2.86 1.77 chr5ptel1M 764823 765102 (234898) CR1-3_Croc#LINE/CR1 1495 1777 (1828) m_b237s551i5 9366 chr5ptel1M 764823 AAAAGTTAATTAAAGAAA-AGTGAGAGAGTATTTAGAGCTGTTCTCAATC 764871 ?i v iv i -i v iv i?v -- v v v CR1-3_Croc#LI 1495 ANGAGATAACAAAAGAGACGGTCAGAGAGCTTTTGNTG--GGTCTGAATG 1542 chr5ptel1M 764872 AGTTCAAATTACTTGATCCAGATGAACTTCATCCCAGAAAAATAAAATTA 764921 i i i viv iv i iiv v i ivv CR1-3_Croc#LI 1543 AATTCAAGTCAGCAGGGCCGGATGAACTTCATCCCAGGGTACTGAAGGAA 1592 chr5ptel1M 764922 CTGTTAGGTGTAATTGCTAAG-TTTTATTAGACATCTCTGAAAGATTGTG 764970 vi iv vi iv vi -ii ivi ivv iiivi ii i CR1-3_Croc#LI 1593 CTGGCAGAGGAGATCTCGGAGCCCTTGGCAATGATCTTCATGAAGTCGTG 1642 chr5ptel1M 764971 GACTACGTGAAGGGTAGCACAAGATTGGAATAGAACAAA-----TGTCCT 765015 ivv v vvi v v i i v ii v ----- i i CR1-3_Croc#LI 1643 GGAGACGGGCCAGGTACCAGAGGACTGGAAAAGGGCCAACGTAGTGCCCC 1692 chr5ptel1M 765016 TGTGTGGAAAAATGTAAGGCAAGTAGCATCT-AAAAACTATAGGCCAGTA 765064 v - vi v i i-- v v i i-iii i i i v CR1-3_Croc#LI 1693 TCT-TTAAAAAAGGCAAA--AAGGAGGACCCGGGGAACTACAGACCGGTT 1739 chr5ptel1M 765065 AGCTTGACTTAAATTTTTGATAAAATCCTAGAATGTAT 765102 i v i v vii iv iv v i iii CR1-3_Croc#LI 1740 AGCCTCACCTCAATACCTGGGAAGTTACTGGAGCATAT 1777 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 54.10 CpG sites = 62, Kimura (unadjusted) = 58.25 Transitions / transversions = 1.38 (62/45) Gap_init rate = 0.03 (9 / 279), avg. gap size = 1.44 (13 / 9) 21 0.00 3.85 0.00 chr5ptel1M 765885 765910 (234090) (TA)n#Simple_repeat 1 27 (0) m_b237s252i8 9367 chr5ptel1M 765885 TAT-TATATATATATATATATATATAT 765910 - (TA)n#Simple_ 1 TATATATATATATATATATATATATAT 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.04 (1 / 25), avg. gap size = 1.00 (1 / 1) 12 27.69 0.00 0.00 chr5ptel1M 765887 765926 (234074) (TTTTAT)n#Simple_repeat 1 40 (0) m_b237s252i9 9367 chr5ptel1M 765887 TTATATATATATATATATATATATTTTTTTTTTTAATTTT 765926 v v v v v v v v v (TTTTAT)n#Sim 1 TTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTT 40 Matrix = Unknown Transitions / transversions = 0.00 (0/9) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 469 33.79 12.25 1.58 chr5ptel1M 765934 766390 (233610) L2#LINE/L2 2139 2643 (439) m_b237s601i21 9364 chr5ptel1M 765934 CTCTGATGGTTATCCTCCTATTTGCTTAAA---TCCTTCTATGTCTCCTT 765980 vv v ii vvi iiv--- vv L2#LINE/L2 2139 CTCTCCTGGTTTTCCTCCTACCTCACTGGCCGCTCCTTCTCAGTCTCCTT 2188 chr5ptel1M 765981 TTCTAGATTTTCATCCAAGTTGC---ACC-CAAAAGGT-------CCTAA 766019 v i v ii v -- vi v --- - v? v ------- iv L2#LINE/L2 2189 TGCTGGTTCCTCCTC--ATCTCCCCGACCTCTNAACGTTGGAGTGCCCCA 2236 chr5ptel1M 766020 AAGTCTTTATCTCTGGGCCATCTTCTCC-CTCTGTAAAATTTTATT---- 766064 ii - ivi ii i - i- i vv vvi i i ---- L2#LINE/L2 2237 GGG-CTCAGTCCTTGGACC-TCTTCTCTTCTCTATCTACACTCACTCCCT 2284 chr5ptel1M 766065 ---TGATCTCATAAGCTCCTGTGATTTTAATTCCAATCTCTATACAGATA 766111 --- vviv iii ii v v v v i v i L2#LINE/L2 2285 NGGTGATCTCATCCAGTCTCATGGCTTTAAATACCATCTATATGCTGATG 2334 chr5ptel1M 766112 ACTTTCAGATCTA---CTTGAGGTCCTAATCTTTCCAC----GTCTAATC 766154 ii i i --- iv - i vi i i v ----v i iv L2#LINE/L2 2335 ACTCCCAAATTTATATCTCCA-GCCCGGACCTCTCCCCTGAACTCCAGAC 2383 chr5ptel1M 766155 TTTCATCTCTGCCAGTTTAATTGACAT-TTGAGGTAGATATCCCATAGAT 766203 ivi v iiv v ii v i - iv vv i i iv ii L2#LINE/L2 2384 TCGTATATCCAACTGCCTACTCGACATCTCCACTTGGATGTCTAATAGGC 2433 chr5ptel1M 766204 ATCATAAACTTAACA--TCCAAAACTGAACTTAATATATTTTTTCTGTAA 766251 vi -- i-v i- i ii iv v L2#LINE/L2 2434 ATCTCAAACTTAACATGTCCAAAACTGAACTC-CTG-ATCTTCCCCCTCA 2481 chr5ptel1M 766252 AACCTTCATCCTTCCTAACTTTTCTTTTGTTC--TCAAGGCTATCACCA- 766298 v - i vv v i iiivvi -- ? v vi v v - L2#LINE/L2 2482 AACCTGC-TCCTCCCGCAGTCTTCCCCATCTCAGTNAATGGCAACTCCAT 2530 chr5ptel1M 766299 CCTCCCAGTTATCCAGGCACACAATTTTGGTTTTATC-------ACTTTC 766341 i iii vv v ii vv i -------v i L2#LINE/L2 2531 CCTTCCAGTTGCTCAGGCCAAAAACCTTGGAGTCATCCTTGACTCCTCTC 2580 chr5ptel1M 766342 TTT--------------ATCCAATCAGTCTCTAAATCCTGTCATTTCTAT 766377 -------------- vi vvi ivi i L2#LINE/L2 2581 TTTCTCTCACACCCCACATCCAATCCATCAGCAAATCCTGTCGGCTCTAC 2630 chr5ptel1M 766378 CTTTGTAACATAT 766390 iiv i L2#LINE/L2 2631 CTTCAAAATATAT 2643 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 45.34 CpG sites = 84, Kimura (unadjusted) = 46.60 Transitions / transversions = 1.24 (84/68) Gap_init rate = 0.05 (23 / 456), avg. gap size = 2.78 (64 / 23) 392 32.64 4.03 1.98 chr5ptel1M 767438 767784 (232216) C L1ME4c_3end#LINE/L1 (191) 639 286 m_b237s551i6 9368 chr5ptel1M 767438 TTCTGCTCTCTTCACTTTTCATCAGTTTACATAAC-TTTCTCAGGTTTTT 767486 i i vv i vv i i - - ii v vi C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATA-AACATTTTCCATGTTGCT 591 chr5ptel1M 767487 CAAAAACCATC-TGCTTCATTATTTCTTATA-TTACAATAACATTCCTTC 767534 vv v ii v - iv - i i v i-i i - i v C L1ME4c_3end#L 590 ACATAGTCTTCATAATT-ATCATTTTTAATGGCTGCA-TAATATTCCATC 543 chr5ptel1M 767535 ACAATC-ATGTA--ACAATTTGTTCAGTCAATTGCTGCTTGATGGACAAT 767581 i- i ?- -- i ii i ii v iv ivv v v C L1ME4c_3end#L 542 G-AGTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATT 494 chr5ptel1M 767582 C--CTAATTTCCAATTCTTTGCTACCACAAA-AAAATTACTATAAGTATT 767628 i--v vi i i ii i - vii i v i ii i C L1ME4c_3end#L 493 TAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATC 444 chr5ptel1M 767629 TTTGTACATATGAGTCTTTTATTTTTCTTTAAT-ATTT--TTGGGATACA 767675 i i - ii vi i i v - -- i v C L1ME4c_3end#L 443 TTCGTGCATAT-AGCTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAA 395 chr5ptel1M 767676 AATCTACTGGTGGTAGTGCTGGGTAAAAAGATTTGCACCATTTTGTAGTC 767725 vvi i vvi v v i v i i v v vv i i ii C L1ME4c_3end#L 394 TTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCT 345 chr5ptel1M 767726 CTT--TGAGTATAGTTCCAAATTGTTGTCCAAAATGATTGGACCAGTTCA 767773 -- iv v -- i v v i v i i C L1ME4c_3end#L 344 CTTGATACGTATTG--CCAAATTGCTTTCCAAAAGGGTTGTACCAATTTA 297 chr5ptel1M 767774 TACCTTCATCA 767784 i ?ivi i C L1ME4c_3end#L 296 CANTGCCACCA 286 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 42.83 CpG sites = 68, Kimura (unadjusted) = 45.05 Transitions / transversions = 1.58 (68/43) Gap_init rate = 0.05 (17 / 346), avg. gap size = 1.24 (21 / 17) 346 34.18 5.26 3.98 chr5ptel1M 767497 767819 (232181) C L1ME4b_3end#LINE/L1 (315) 577 251 m_b237s551i7 9368 chr5ptel1M 767497 CTGCTTCATTATTTCTTATA-TTACAATAACATTCCTTCACAATCATGTA 767545 v i v i ii-i i - ii v iii vvv C L1ME4b_3end#L 577 CTTCCTCATTCTTTTTTACGGCTGCA-TAGTATTCCATTGTATGGATGTA 529 chr5ptel1M 767546 --ACAATTTGTTCAGTCAATTGCTGCTTGATGGACAATC--CTAATTTCC 767591 -- i i i ii i iv ivv v i--v vi C L1ME4b_3end#L 528 CCATAATTTATTTAACCAGTCCCCTATTGATGGACATTTAGGTTGTTTCC 479 chr5ptel1M 767592 AATTCTTTGCTACCACAAAAAA-ATTACTATAAGTATTTTTGTACATATG 767640 ii ii v -ii i v i i vii i C L1ME4b_3end#L 478 AATCTTTTGCTATTACAAACAATGCTGCAATGAATAACCTTGTACATACG 429 chr5ptel1M 767641 AGTCTTTTATTTTTC---TTTA-----ATATTTTTGGGATACAAATCTAC 767682 ------ i iv --- v i----- i v i v vvi v C L1ME4b_3end#L 428 ------TCATTTCGCACATGTGCGAGTATATCTGTAGGATAAATTCCTAG 385 chr5ptel1M 767683 TGGTGGTAGTGCTGGGTAAAAAG--ATTTGCACCATTTTGTAGTCCTTTG 767730 vi v v v i -- v ---- i -- C L1ME4b_3end#L 384 AAGTGGAATTGCTGGGTCAAAGGGTATGTGCA----TTTGTAAT--TTTG 341 chr5ptel1M 767731 A-GTATAGTTCCAAATTGTTGTCCAAAATGATTGGACCAGTTCATACCTT 767779 -iv v v iiv v iv i v i i i iii C L1ME4b_3end#L 340 ATAGATATTGCCAAATTGCCCTCCATAGAGGTTGTACCAATTTACACTCC 291 chr5ptel1M 767780 CATCAATCATTAACCATTGTATCTATTGTCTCACATTTTC 767819 i iiv vv iv vv ii i vi i iii C L1ME4b_3end#L 290 CACCAGCAATGTATGAGAGTGCCTGTTTCCCCACACCCTC 251 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 45.81 CpG sites = 65, Kimura (unadjusted) = 47.79 Transitions / transversions = 1.59 (65/41) Gap_init rate = 0.07 (21 / 322), avg. gap size = 1.43 (30 / 21) 444 31.28 3.90 1.38 chr5ptel1M 767503 767784 (232216) C L1ME4a_3end#LINE/L1 (297) 574 286 m_b237s551i8 9368 chr5ptel1M 767503 CATTATTTCTTATA-TTACAATAACATTCCTTCACAATCATGTA--ACAA 767549 ? i v i-i i - i v i?i vvv -- i C L1ME4a_3end#L 574 CATNATTTTTAATGGCTGCA-TAATATTCCATTNTATGGATGTACCATAA 526 chr5ptel1M 767550 TTTGTTCAGTCAATTGCTGCTTGATGGACAATC--CTAATTTCCAATTCT 767597 i i ii ? iv ivv v v i--v vi i C L1ME4a_3end#L 525 TTTATTTAACCANTCCCCTATTGTTGGACATTTAGGTTGTTTCCAATTTT 476 chr5ptel1M 767598 TTGCTACCACAAAAAA-ATTACTATAAGTATTTTTGTACATATGAGTCTT 767646 i ii i v -ii i v i ii ii -- i C L1ME4a_3end#L 475 TCGCTATTATAAATAATGCTGCGATGAACATCCTTGTACATA--AATCTT 428 chr5ptel1M 767647 T-TATTTTTCTTTAAT-ATTT--TTGGGATACAAATCTACTGGTGGTAGT 767692 - ?iviv i i - -- i v vvi vvi v v C L1ME4a_3end#L 427 TGTNCACATCTCTGATTATTTCCTTAGGATAAATTCCTAGAAGTGGAATT 378 chr5ptel1M 767693 GCTGGGTAAAAAGATTTGCACCATTTTGTAGTCCTTTGA-GTATAGTTCC 767741 i v i i v ? - vv v i -ii v v C L1ME4a_3end#L 377 ACTGGGTCAAAGGGTATGNAC-ATTTTTAAGGCTTTTGATACATATTGCC 329 chr5ptel1M 767742 AAATTGTTGTCCAAAATGATTGGACCAGTTCATACCTTCATCA 767784 iiv i v i v i i i iii i C L1ME4a_3end#L 328 AAATTGCCCTCCAGAAAGGTTGTACCAATTTACACTCCCACCA 286 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 42.58 CpG sites = 54, Kimura (unadjusted) = 43.25 Transitions / transversions = 1.64 (54/33) Gap_init rate = 0.04 (12 / 281), avg. gap size = 1.25 (15 / 12) 12 14.15 3.03 3.03 chr5ptel1M 768782 768814 (231186) (ATATT)n#Simple_repeat 1 33 (0) m_b237s252i10 9369 chr5ptel1M 768782 ATACTTTATTA-GTTATAATATAATTATATTATA 768814 i v -i v - (ATATT)n#Simp 1 ATATTATATTATATTATATTAT-ATTATATTATA 33 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.06 (2 / 32), avg. gap size = 1.00 (2 / 2) 305 36.51 3.12 4.76 chr5ptel1M 769351 769606 (230394) C L2#LINE/L2 (278) 2804 2553 m_b237s601i22 9370 chr5ptel1M 769351 AAGGAATACTAACTGATAGGTATGTTGAGAATGGATTGCAGAGGTGAGAA 769400 vi -- iiv v i i i ? i v vi i C L2#LINE/L2 2804 AAGGATCACT--CTGGCTGCTGTGTTGAGAATAGACTGNAGGGGGGCAAG 2757 chr5ptel1M 769401 ACTAGAAGCAGGGAAAGAAATTAGAAGTCTATTGGAACACTCCTGGTGAG 769450 iv i i vv i i v v ii v v i C L2#LINE/L2 2756 GGTGGAAGCAGGGAGACCAGTTAGGAGGCTATTGCAGTAATCCAGGCGAG 2707 chr5ptel1M 769451 AGGTAA---AGACTTGAACTAGGAAAGAAGTCATGTGAGTAGAGAAAAGA 769497 i i ---v i i i ivi vi ivi vii i v i v C L2#LINE/L2 2706 AGATGATGGTGGCTTGGACCAGGGTGGTGGCAGTGGAGGTGGTGAGAAGT 2657 chr5ptel1M 769498 AAGC-TATGAAAGAGATACCGTGGACA-AGATGCAATAAGATTTAGTCAC 769545 iiv -v vvvi v iiv i vi- vv i i i ----i C L2#LINE/L2 2656 GGTCGGATTCTGGATATATTTTGAAGGTAGAGCCGACAGGATTT----GC 2611 chr5ptel1M 769546 TGATAGGCTTGACAGAGAG---GAAATAAACAAAGGTCATTTAAAATTGC 769592 i ii v iivi i --- i v v i -- v i ---- v C L2#LINE/L2 2610 TGATGGATTGGATGTGGGGTGTGAGAGAAAGAGAGG--AGTCAA----GG 2567 chr5ptel1M 769593 ATGATTGCAAGGTT 769606 i v C L2#LINE/L2 2566 ATGACTCCAAGGTT 2553 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 50.93 CpG sites = 53, Kimura (unadjusted) = 52.68 Transitions / transversions = 1.47 (53/36) Gap_init rate = 0.06 (16 / 255), avg. gap size = 1.25 (20 / 16) 330 33.01 1.94 0.00 chr5ptel1M 769674 769776 (230224) MIRc#SINE/MIR 2 106 (162) m_b237s601i23 9371 chr5ptel1M 769674 GAGGAAGTATTAGAAATTAGAAAGAAAATTGGCTGTAGAGTCAA-AGGAC 769722 v i viviv v i iv i viv i i- i MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr5ptel1M 769723 TTGGATTCAGATCCCATTTCTGATACTTATTA-TAGTGTGACCTTGGACT 769771 i i iii ivi vi i -iv i v MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 101 chr5ptel1M 769772 TGTCA 769776 v MIRc#SINE/MIR 102 AGTCA 106 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 41.83 CpG sites = 21, Kimura (unadjusted) = 45.45 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.02 (2 / 102), avg. gap size = 1.00 (2 / 2) 343 27.50 2.50 0.00 chr5ptel1M 769691 769770 (230230) MIRb#SINE/MIR 22 103 (165) m_b237s601i24 9371 chr5ptel1M 769691 TAGAAAGAAAATTGGCTGTAGAGTCAAA-GGACTTGGATTCAGATCCCAT 769739 i iv iv v i i -i i i ii iv MIRb#SINE/MIR 22 TGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCGAATCCCGG 71 chr5ptel1M 769740 TTCTGATACTTATTA-TAGTGTGACCTTGGAC 769770 i vi i -iv i MIRb#SINE/MIR 72 CTCTGCCACTTACTAGCTGTGTGACCTTGGGC 103 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 30.23 CpG sites = 16, Kimura (unadjusted) = 36.28 Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.03 (2 / 79), avg. gap size = 1.00 (2 / 2) 24 3.57 0.00 0.00 chr5ptel1M 769921 769949 (230051) (GT)n#Simple_repeat 1 29 (0) m_b237s252i11 9372 chr5ptel1M 769921 GTGTGTGTGTGTATGTGTGTGTGTGTGTG 769949 i (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTG 29 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 56 10.78 0.00 1.09 chr5ptel1M 769950 770042 (229958) (TA)n#Simple_repeat 1 92 (0) c_b237s251i0 9373 chr5ptel1M 769950 TATATATATATATATATATATATATATATATACTGTATGTATATATGTGT 769999 - i i i i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATA-TATATATATATATATAT 49 chr5ptel1M 770000 ATTTGTGTGTATATATATATATATATATATATATAAATATATA 770042 v i i i v (TA)n#Simple_ 50 ATATATATATATATATATATATATATATATATATATATATATA 92 Matrix = Unknown Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.01 (1 / 92), avg. gap size = 1.00 (1 / 1) 1402 31.24 5.23 2.94 chr5ptel1M 770711 771973 (228027) L1M5_orf2#LINE/L1 1418 2708 (586) m_b237s551i9 9374 chr5ptel1M 770711 CAGATGACTT-ATAAGTGAATTCTATCAAACATTTAAAGATTAACTAATT 770759 i - ivi i i vv v v L1M5_orf2#LIN 1418 CAGATGGCTTCACTGGTGAATTCTACCAAACATTTAAGGAAGAAATAATA 1467 chr5ptel1M 770760 CTAATATGAAATAAATTAT----GTGGACAGAAAGGAAAAAAGTCCTATC 770805 i v v v i i v ---- vii i iii iii iiv vi L1M5_orf2#LIN 1468 CCAATCTTACACAAACTCTTCCAGAAAATAGAAAAAGAGGGAACACTTCC 1517 chr5ptel1M 770806 AAACTCTTTTTATGAAACAAATATGATATGAATATCTAAACCAGGAAGAG 770855 v v ii v ii ? ivivi i v ? iv i L1M5_orf2#LIN 1518 CAACTCATTTTATGAGGCCAGCATNACCCTGATACCAAAACCNGACAAAG 1567 chr5ptel1M 770856 ----TAAAAACAGAGAAAATTATAGAGCAATTATGTTAATGGCTATGTAT 770901 ---- v iv i i v vvivi v ivi iv L1M5_orf2#LIN 1568 ACATTACAAGAAAAGAAAATTACAGACCAATATCCCTCATGAACATAGAT 1617 chr5ptel1M 770902 GCAAAAG-CCT-AATAAAATTCTATTTAAAAGATTACAACA-TAT-TAAA 770947 i- - i vi viv vv v v i - - L1M5_orf2#LIN 1618 GCAAAAATCCTNAACAAAATATTAGCAAATCGAATCCAGCAATATATAAA 1667 chr5ptel1M 770948 AAGGTTG-TAAATTGTGATCATGGGAGGTTTATACAAGGATTTCAGGAAT 770996 v i- v ii i v v i v v v v i iv L1M5_orf2#LIN 1668 AAGGATAATACATCATGACCAAGTGGGGTTTATCCCAGGAATGCAAGGTT 1717 chr5ptel1M 770997 GGTTTAATATAAAAGAA-CTATTAATATAATTAGCTATATATACTTATAT 771045 i vvi i - v i i vi i ----- - i L1M5_orf2#LIN 1718 GGTTTAACATTCGAAAATCAATCAATGTAATTCACCATAT-----TA-AC 1761 chr5ptel1M 771046 AGCAATAA-GAAAAATAACAAATCAT--GATTATATCAATAGATGCAGAA 771092 - - i i ---- -- i v L1M5_orf2#LIN 1762 AG-AATAAAGGAGAA----AAATCATATGATCATCTCAATAGATGCAGAA 1806 chr5ptel1M 771093 AAAGCTTTTGATAATGAA--CAGCATTCACTCTTATTAAAAATTATTAGA 771140 v i -- -- i ii i v iv i v i - L1M5_orf2#LIN 1807 AAAGCATTTGACAA--AATTCAACACCCATTCATGATAAAAACTCTCAG- 1853 chr5ptel1M 771141 AAAAATAGGCATACATGGATTTTTCATTAAATTGATAAGAAACATTTAGC 771190 v v v v v ivvi v i vi iiii i vv L1M5_orf2#LIN 1854 CAAACTAGGAATAGAAGGGAACTTCCTCAACCTGATAAAGGGCATCTACG 1903 chr5ptel1M 771191 CAAAACCTTCAATAAGCATTATTTGTAATAG-GAATAA--GGTAG----- 771232 v v ii? i i viv i - v? -- iv? ----- L1M5_orf2#LIN 1904 AAAAACCTACAGCNAACATCATACTTAATGGTGAAANACTGAANGCTTTC 1953 chr5ptel1M 771233 ----TAAGGACAAGAATGAAACAAGGATGTCCCTCCACTGTCACTAATAT 771278 ---- iv ii ii i ---- i ? i v vi L1M5_orf2#LIN 1954 CCCCTAAGATCGGGAACAAGACAAGGATG----TCCGCTNTCACCACTTC 1999 chr5ptel1M 771279 TATTCAGCATTTAATA-TGGAAAT-CTAAACAATAGCAATAAGAGAAGAA 771326 i --i - ii - iv i - iv L1M5_orf2#LIN 2000 TATTCAACATT--GTACTGGAGGTCCTAGCCAGT-GCAATAAGGCAAGAA 2046 chr5ptel1M 771327 AAAGAAATAGAAGAAATCAGAATAGGGAATGGAGTGATAAAGTTATCTTT 771376 i iv v ii v i v i vi ii i ? L1M5_orf2#LIN 2047 AAAGAAATAAAAGGCATAAAGATTGGAAAGGAAGAAATAAAACTGTCNTT 2096 chr5ptel1M 771377 TTTTGCTGGTGATATGA---TATATTGAGAAGTTGCTAAAGATTCAACCA 771423 v i v i i --- ? ivv iv v ? v v v L1M5_orf2#LIN 2097 ATTCGCAGATGACATGATTGTNTACGTAGAAAATCCNAAAGAATCTACAA 2146 chr5ptel1M 771424 A-ATGTTAGTTGAAAGAATTAATAATTTTAGCAAAATAGCAGGATATAAA 771472 - vii v v vv v i i v ii v ? i i L1M5_orf2#LIN 2147 ANAAACTACTAGAACTAATAAGTGAATTTAGCAAGGTCGCNGGATACAAG 2196 chr5ptel1M 771473 GCAAAGCCACATAAATCATTAGTGTTTTTATAT-----CAATAAAACTCT 771517 iv vvi v v v i i ----- i vvvi L1M5_orf2#LIN 2197 GTCAATATACAAAAATCAATTGTATTTCTATATACTAGCAACAAACAATT 2246 chr5ptel1M 771518 GAAAGAAGAGAT------AGAGATACCTCATTTAACATAATTCTGGGAAA 771561 i i v i ------ ivi -- vv iiviiiii L1M5_orf2#LIN 2247 GGAAAATGAAATTTNAAAAACAATAC--CATTTACAATAGCATCAAAAAA 2294 chr5ptel1M 771562 TCTAAAATACTTGGGAATATACTTGCCAGAGTAAACTCAAAGATTATATG 771611 iv ? i v ii iv i i? viiv iivi ? ii L1M5_orf2#LIN 2295 CATNAAATACTTAGGAATAAATCTAACAAAANATGTGCAAGACCTNTACA 2344 chr5ptel1M 771612 AACAAAATTATTTTTAAAGCTTT--TTATACAAA-TAAAATTGATTTAAA 771658 vvv i ----i i v -- v v v - ivv ii L1M5_orf2#LIN 2345 CTGAAAACTA----CAAAACATTGCTGAGAGAAATTAAAGAAGACCTAAA 2390 chr5ptel1M 771659 GAATTGGAGAAATAT-TAATGATTTATGGGTAGGTAGGGCCAATATGATA 771707 v v i -iv - i i v v ivi vi ? L1M5_orf2#LIN 2391 TAAATGGAGAGATATACCATG-TTCATGGATTGGAAGACTCAATATTGTN 2439 chr5ptel1M 771708 AAAATGATAATTTTGCCTAAATTA---CATAG--TCAATGCAATTTCAAT 771752 i vi i v i i---i -- ii L1M5_orf2#LIN 2440 AAGATGTCAATTCTCCCCAAATTGATCTATAGATTCAATGCAATCCCAAT 2489 chr5ptel1M 771753 TAAATTACCAACAAATCATTTTACTGCACTTAGAAAAATAA--CCAAAAA 771800 i v v i ii iv iiv v v iiv iv i -- i - L1M5_orf2#LIN 2490 CAAAATCCCAGCAGGTTTTTTTGTAGAAATTGACAAGCTGATTCTAAAA- 2538 chr5ptel1M 771801 AGTTCATTTAGAATAGGAAAAGGTAAAGAATATCAAAGGAAATAATGAGG 771850 -- i v i vv v i iiv? v v iiv vv ii L1M5_orf2#LIN 2539 --TTTATATGGAAATGCAAAGGACCNAGAATAGCCAAAACAATCTTGAAA 2586 chr5ptel1M 771851 GAGGAAATTAAAA--GAAGGAGCTTTTGCAGTACCAGAGCTTAAA--TTA 771896 i i i vi i-- i ---i i v ? v? i i-- L1M5_orf2#LIN 2587 AAGAAGAACAAAGTTGGAGGA---CTTACACTACCNGATNTCAAGACTTA 2633 chr5ptel1M 771897 TCTTATAGG-ACAGTGTTTATCCAAATTATCTGGTATTGGC-TAAGGAAC 771944 iv v v- i--- v i ivi v - - i L1M5_orf2#LIN 2634 TTATAAAGCTACAGTA---ATCAAGACAGTGTGGTATTGGCGTAAGG-AT 2679 chr5ptel1M 771945 AAAAAGATAGATCAACAAAACAGAATAAA 771973 i v i iii i L1M5_orf2#LIN 2680 AGACAAATAGATCAATGGAACAGAATAGA 2708 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 41.70 CpG sites = 220, Kimura (unadjusted) = 42.44 Transitions / transversions = 1.35 (220/163) Gap_init rate = 0.06 (70 / 1262), avg. gap size = 1.49 (104 / 70) 235 32.00 0.99 0.99 chr5ptel1M 772493 772593 (227407) L1PB4_3end#LINE/L1 231 331 (572) m_b237s551i10 9374 chr5ptel1M 772493 AGAAAGCAACAAAAATTGAAGGCAATATGGGAAAAAATGGTACACTGATT 772542 i i i vi iv ivi ii - i v v i v v L1PB4_3end#LI 231 AAAAAACAACAGATGTTGGCGAGGATGCGG-AGAAAAGGGAACGCTTATA 279 chr5ptel1M 772543 CACCGTTGGTGGCTCTGTGAAGTAATCCAACATTT-TGGAGAGTAATATG 772591 i vvv i v i v v i - i ii i L1PB4_3end#LI 280 CACTGTTGGTGGGAATGTAAATTAGTACAACCTCTATGGAAAACAGTATG 329 chr5ptel1M 772592 GA 772593 L1PB4_3end#LI 330 GA 331 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 39.65 CpG sites = 19, Kimura (unadjusted) = 43.20 Transitions / transversions = 1.46 (19/13) Gap_init rate = 0.02 (2 / 100), avg. gap size = 1.00 (2 / 2) 225 33.90 6.27 3.39 chr5ptel1M 772518 772804 (227196) L1ME3G_3end#LINE/L1 252 546 (378) m_b237s551i11 9374 chr5ptel1M 772518 TATGGGAAAAAATGGTACACTGATTCACCGTTGGTGGCTCTGTGAAGTAA 772567 i i vi- v v v i i vvv i v ii L1ME3G_3end#L 252 TGTGGGGAAACG-GGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGG 300 chr5ptel1M 772568 TCCAAC-ATTTTGGAGAGTAATATGG----ATTT-TCATAGTGTTGTTAA 772611 v i -? i i v ---- i - i v i ---- L1ME3G_3end#L 301 TACAGCCNTTTTGGAGGGCAATTTGGCAGTATCTATTAAAAT----TTAA 346 chr5ptel1M 772612 ATTGCTTATTCCCTGTGGTCCAGCAAGGAAAAATGTAATAGTATC----- 772656 v vi v v ii vvvv vv v --?i ? ----- L1ME3G_3end#L 347 AATGCGCATACCCTTTGACCCAGCAATTCCACTTCT--NGGNATCTATCC 394 chr5ptel1M 772657 -AAAAATATATACATAAATAAATTATACATAGATG--TGTATGTGTTTGT 772703 - ? i v iv ii v i--- ii vi ? -- iiv vv L1ME3G_3end#L 395 TANAGAAATACTCGCACATG---TGCACAAGGANGCATGTACAAGGATGT 441 chr5ptel1M 772704 ACATATCACC--TCTCGGTGGTGGTAAAGAACTAGAAATTGTGGGGATGC 772751 v vv v -- v iv ii i ii i i i iviivvii i L1ME3G_3end#L 442 TCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGT 491 chr5ptel1M 772752 TCATCATTTGGGGAATAGCTAAATAAGTTGTGATATGATTGTA--ATGGA 772799 i v v i i i i i iviii -- L1ME3G_3end#L 492 CCATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGA 541 chr5ptel1M 772800 ATACT 772804 L1ME3G_3end#L 542 ATACT 546 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 45.65 CpG sites = 53, Kimura (unadjusted) = 47.84 Transitions / transversions = 1.29 (53/41) Gap_init rate = 0.06 (18 / 286), avg. gap size = 1.56 (28 / 18) 261 27.82 5.17 0.83 chr5ptel1M 772522 772637 (227363) L1ME4c_3end#LINE/L1 259 379 (451) m_b237s551i12 9374 chr5ptel1M 772522 GGAAAAAATGGTACACTGATTCACCGTTGGTGGCTCTGTGAAGTAATCCA 772571 vi v ? v v ii i v? i v ii v L1ME4c_3end#L 259 GGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACA 308 chr5ptel1M 772572 A-CATTTTGGAGAGTAATATGG--AT---TTTCATAGTGTTGTTAAATTG 772615 - v i i v -- --- v - v iii v v L1ME4c_3end#L 309 ACCCTTTTGGAAAGCAATTTGGCAATACGTATCA-AGAGCCATAAAAATG 357 chr5ptel1M 772616 CTTATTCCCTGTGGTCCAGCAA 772637 i i v v ii i L1ME4c_3end#L 358 TTCATACCCTTTGACCCAGTAA 379 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.14 CpG sites = 17, Kimura (unadjusted) = 36.14 Transitions / transversions = 1.13 (17/15) Gap_init rate = 0.03 (4 / 115), avg. gap size = 1.75 (7 / 4) 270 23.94 1.41 0.00 chr5ptel1M 772522 772592 (227408) L1PA14_3end#LINE/L1 259 330 (578) m_b237s551i13 9374 chr5ptel1M 772522 GGAAAAAATGGTACACTGATTCACCGTTGGTGGCTCTGTGAAGTAATCCA 772571 i v v v v i vvv i v i i L1PA14_3end#L 259 GGAGAAAAGGGAACACTTATACACTGTTGGTGGGAGTGTAAATTAGTTCA 308 chr5ptel1M 772572 A-CATTTTGGAGAGTAATATGG 772592 - v i i i L1PA14_3end#L 309 ACCATTGTGGAAAGCAGTATGG 330 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 29.01 CpG sites = 8, Kimura (unadjusted) = 29.01 Transitions / transversions = 0.89 (8/9) Gap_init rate = 0.01 (1 / 70), avg. gap size = 1.00 (1 / 1) 44 29.05 4.83 1.88 chr5ptel1M 773016 773222 (226778) (AT)n#Simple_repeat 1 213 (0) m_b237s252i12 9375 chr5ptel1M 773016 ATAAATAAATAGAAGTATGCATA-ATATGAT-TTTGCATATATAAGTATA 773063 v v v vi ii - - - v ii vi (AT)n#Simple_ 1 ATATATATATATATATATATATATATAT-ATATATATATATATATATATA 49 chr5ptel1M 773064 TGCACATATA-ATATGTATATATGAATATATAGATATATATGGTATGTAT 773112 ii i - i iv v -i i (AT)n#Simple_ 50 TATATATATATATATATATATATATATATATATATATATAT-ATATATAT 98 chr5ptel1M 773113 ATATTTA-ATTTGTATTTTTCTAGCCA-ATA-ATA-ATTTAGA-ATATTT 773157 v - v i v v v vvi - - - v v - v (AT)n#Simple_ 99 ATATATATATATATATATATATATATATATATATATATATATATATATAT 148 chr5ptel1M 773158 TTATTTGAT-TAAAATTATTTTTAT-TGCATATAATTATACATATATATA 773205 v v - - v vv v v - ii vv i (AT)n#Simple_ 149 ATATAT-ATATATATATATATATATATATATATATATATATATATATATA 197 chr5ptel1M 773206 TACACACTACATATATA 773222 i i - i (AT)n#Simple_ 198 TATATA-TATATATATA 213 Matrix = Unknown Transitions / transversions = 0.78 (21/27) Gap_init rate = 0.07 (14 / 206), avg. gap size = 1.00 (14 / 14) 50 26.12 0.79 0.00 chr5ptel1M 774990 775116 (224884) (GT)n#Simple_repeat 1 128 (0) m_b237s252i13 9376 chr5ptel1M 774990 GTGTATGTGTGTGTGTGTG-GGGGGGGTATGATTATGTGTTTGTGAATGT 775038 i - v v v i vv i v vi (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50 chr5ptel1M 775039 GTGAGTGGGGGTGTATTTGTGAATGTGAGTGGGGGTGCGAGTCGGTGTGT 775088 v v v i v vi v v v i v vv (GT)n#Simple_ 51 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 100 chr5ptel1M 775089 GTGTGTTTGTGAATGTGTGTGTGTGTGT 775116 v vi (GT)n#Simple_ 101 GTGTGTGTGTGTGTGTGTGTGTGTGTGT 128 Matrix = Unknown Transitions / transversions = 0.40 (8/20) Gap_init rate = 0.01 (1 / 126), avg. gap size = 1.00 (1 / 1) 17 18.82 0.00 2.33 chr5ptel1M 775905 775948 (224052) (ATAAAAT)n#Simple_repeat 1 43 (0) m_b237s252i15 9377 chr5ptel1M 775905 ATAAAATATAAAATAAATTATTATAAGATATAATATACAAAGTA 775948 v -v v i v i i (ATAAAAT)n#Si 1 ATAAAATATAAAATATA-AAATATAAAATATAAAATATAAAATA 43 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.02 (1 / 43), avg. gap size = 1.00 (1 / 1) 1531 29.31 0.68 1.03 chr5ptel1M 776846 777431 (222569) C L1ME4a_3end#LINE/L1 (232) 639 56 m_b237s551i14 9378 chr5ptel1M 776846 CCTGCTCATGTCACTCAGCATCAGTTCATGCAAGTCTCTTCAGGCCTTTC 776895 iv v i i i vv vivi i iii v i v - C L1ME4a_3end#L 639 CCTGCTTTTTTCACTTAACATTATATCATGAGCATTTTCCCATGTCATT- 591 chr5ptel1M 776896 TGAAATCATCCTGCTGAAA--TTATTTCTTATAGAACAATAATATTCCAT 776943 -- - i v vi -- ? i v i vvvv C L1ME4a_3end#L 590 --AAAT-ATTCTTCGAAAACATNATTTTTAATGGCTGCATAATATTCCAT 544 chr5ptel1M 776944 AATATTCATATACCACAATTTATTCAGCCATTCTCCAGTTGATGGACATC 776993 v? vv i i i i ? i vi v i C L1ME4a_3end#L 543 TNTATGGATGTACCATAATTTATTTAACCANTCCCCTATTGTTGGACATT 494 chr5ptel1M 776994 CACTCAGTTTCCAGTTTCTGGCCACTACCAAGAGGGCTGCCACAAACATT 777043 i vviv i i v i i iv v iv v ii i C L1ME4a_3end#L 493 TAGGTTGTTTCCAATTTTTCGCTATTATAAATAATGCTGCGATGAACATC 444 chr5ptel1M 777044 TTTGAACATACAGGTCCCTTTCC-CTTCTTTAAG-ATCTCTTTCGGATAT 777091 i v v -- ii v ? - v i i v- i i v v C L1ME4a_3end#L 443 CTTGTACATAAA--TCTTTGTNCACATCTCTGATTATTTCCTTAGGATAA 396 chr5ptel1M 777092 AAGCCCAGTAGTAACACTGTTGGGTCAAAGGGAATGCACAGTTTGATAGC 777141 vv i v iiv i ii v ? v v vi C L1ME4a_3end#L 395 ATTCCTAGAAGTGGAATTACTGGGTCAAAGGGTATGNACATTTTTAAGGC 346 chr5ptel1M 777142 TTTTTGAGCATAGTTCCAAATTGCTCTCCAGAATGGCTGGATGTGTTCAC 777191 vivi v v i v i v ivvi i C L1ME4a_3end#L 345 TTTTGATACATATTGCCAAATTGCCCTCCAGAAAGGTTGTACCAATTTAC 296 chr5ptel1M 777192 CATTCCACCAACAATATATCAGTGTCCTAGTTTTCCCACATCCCCTCCAA 777241 vv i i i i v v v iv i? i i v C L1ME4a_3end#L 295 ACTCCCACCAGCAGTGTATGAGAGTGCCCGTTTCNCCACACCCTCGCCAA 246 chr5ptel1M 777242 CATTCTGTATTCTCTTTCCCTGTCATTCTAGCCAATCTGATAGGTGGGTA 777291 i vv v vv ii vvv ii v i iiv C L1ME4a_3end#L 245 CACTGGGTATTATCAATCTTTTAAATCTTTGCCAATTTGATAGGTGAAAA 196 chr5ptel1M 777292 GTGGTATCTCAGAGTTGTCTTAATTTGCATTTCTCTGATTAAAAATGACT 777341 i vv i i vv i vv C L1ME4a_3end#L 195 ATGGTATCTCATTGTTGTTTTAATTTGCATTTCTTTGATTACTAGTGAGG 146 chr5ptel1M 777342 TAGAGCATCTTTTCATATGGCTAGAAATAGTTTCAATTTCTTCATCTGAA 777391 v i ? vi vviiivi vv v i vi C L1ME4a_3end#L 145 TTGAACATNTTTTCATATGTTTATTGGCCATTTGTATTTCTTCTTTTGTG 96 chr5ptel1M 777392 AATTGTCTGTTCATATCCTTTGACCATTTATCAATTGGAG 777431 i v v v i C L1ME4a_3end#L 95 AATTGTCTGTTCATGTCCTTTGCCCATTTTTCTATTGGGG 56 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 38.21 CpG sites = 84, Kimura (unadjusted) = 38.21 Transitions / transversions = 0.98 (84/86) Gap_init rate = 0.02 (9 / 585), avg. gap size = 1.11 (10 / 9) 1637 26.63 0.91 1.85 chr5ptel1M 776932 777478 (222522) C L1ME3G_3end#LINE/L1 (376) 548 7 m_b237s551i15 9378 chr5ptel1M 776932 ATAATATTCCATAATATTCATATACCACAATTTATTCAGCCATTCTCCAG 776981 i i vv i i i i vi C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr5ptel1M 776982 TTGATGGACATCCACTCAGTTTCCAGTTTCTGGCCACTACCAAGAGGGCT 777031 ii vviv i i v i i v v iv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr5ptel1M 777032 GCCACAAACATTTTTGAACATACAGGTCCCTTTCC-CTTCTTTAAG-ATC 777079 v ii ii v i ?-- i v v - v v vii - i C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATT 401 chr5ptel1M 777080 TCTTTCGGATATAAGCCCAGTAGTAACACTGTTGGGTCAAAGGGAATGCA 777129 ? v v v? ? v iiv i i v i C L1ME3G_3end#L 400 TCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCG 351 chr5ptel1M 777130 CAGTTTGATAGCTTTTTGA-GCATAGTTCCAAATTGCTCTCCAGAATGGC 777178 v i - --- i -iv v v i i ? C L1ME3G_3end#L 350 CATTTTAA-A---TTTTAATAGATACTGCCAAATTGCCCTCCAAAANGGC 305 chr5ptel1M 777179 TGGATGTGTTCACCATTCCACCAACAATATATCAGTGTCCTAGTTTTCCC 777228 v ivvi i vv i i i i v v v iv i C L1ME3G_3end#L 304 TGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCC 255 chr5ptel1M 777229 ACATCCCCTCCAACATTCTGTATTCTCTTTCCCTGTCATTCTAGCCAATC 777278 i i v i ?vi v vv? ii vvv i v C L1ME3G_3end#L 254 ACACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATC 205 chr5ptel1M 777279 TGATAGGTGGGTAGTGGTATCTCAGAGTTGTCTTAATTTGCATTTCTCTG 777328 i iiv i vv i i C L1ME3G_3end#L 204 TGATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTG 155 chr5ptel1M 777329 ATTAAAAATGACTTAGAGCATCTTTTCATATGGCTAGAAATAGTTTCAAT 777378 vv i vv v vi vviiivi vv C L1ME3G_3end#L 154 ATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGTAT 105 chr5ptel1M 777379 TTCTTCATCTGAAAATTGTCTGTTCATATCCTTTGACCATTTATCAATTG 777428 i v vi i v v v C L1ME3G_3end#L 104 TTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTG 55 chr5ptel1M 777429 GAGAATGGCTTGATTTCTTAAAAATTAGAGTCAATTCTC--TATATTTTG 777476 iv-- v -- vvi v vivv i i-- i C L1ME3G_3end#L 54 GGT--TGTCTT--TTTCTTATTGATTTGTAGGAGTTCTTTATATATTCTG 9 chr5ptel1M 777477 GA 777478 C L1ME3G_3end#L 8 GA 7 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 33.19 CpG sites = 71, Kimura (unadjusted) = 33.78 Transitions / transversions = 0.99 (71/72) Gap_init rate = 0.03 (14 / 546), avg. gap size = 1.07 (15 / 14) 436 30.57 4.22 3.44 chr5ptel1M 777337 778000 (222000) C L1M5_orf2#LINE/L1 (0) 3294 2626 m_b238s551i1 9378 chr5ptel1M 777337 TGACTTAGAGCATCTTTTCATATGGCTAGAAATAGTTTCAATTTCTTCAT 777386 ?v v i vi vviiivi v? v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr5ptel1M 777387 CTGAAAATTGTCTGTTCATATCCTTTGACCATTTATCAATTGGA--GAAT 777434 i vi v vi i v v ?v i-- vv C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTT 3195 chr5ptel1M 777435 GGCTTGATTTCTTA-AAAATTAGAGTCAATTCTC--TATATTTTGGAAAT 777481 v -- ? -vi ? iv -v i i-- i v i C L1M5_orf2#LIN 3194 GTCTT--TTTNTTATTGANTTGTAG-GAGTTCTTTATATATTCTGGATAC 3148 chr5ptel1M 777482 GAGGTTTTTATCAGA-ACCTTTGACTGTAAAAATGTTTTCCCAGTTTATT 777530 vii i - iv v -?i i v v i ? i i v C L1M5_orf2#LIN 3147 GAGTCCTTTGTCAGATATATGT-NTTGCAAATATTTTCTCCCANTCTGTG 3099 chr5ptel1M 777531 GCTTCCCTTCTAATCTTGTCTGCATTAGTTTTGTTTGTACAAAAATTTTT 777580 v i v i v ivi iv ivi vvv? vi i i C L1M5_orf2#LIN 3098 GCTTGCCTTTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTTT 3049 chr5ptel1M 777581 CAATTTGATATATTCAAATTTTTCTATTTTGTGATCAGTAATGATCTCTA 777630 v v i? v v v v v--- vv v i --- ? C L1M5_orf2#LIN 3048 AATTTTGATGNAGTCCAATTTATCAATTTTT---TCTTTTATGGT---TN 3005 chr5ptel1M 777631 GTTCTTCTTTGGTC-------ATAAATTACTTCCTCTTCCACACGTCTGA 777673 v i vv ------- v ivi v v?i - v vvi C L1M5_orf2#LIN 3004 GTGCTTTTTGTGTCCTGTTTAAGAAATCTTTGCCTANCCCA-AGGTCACG 2956 chr5ptel1M 777674 GAGGTAAACTGTCCTATG--CTCTTCCAATTTATTTATAATCTCATTCTT 777721 i i -- i v --i i ivvvv i i i ?ii C L1M5_orf2#LIN 2955 AAGAT--ATTCTCCTATGTTTTCTTCTAGAAGTTTTATAGTTTTANCTTT 2908 chr5ptel1M 777722 TTTGCCTAGGTC-ATGAACCCATTTTGACATT-ATCTTGGTGTACGGTGT 777769 viiii - - i i ? - - i v i C L1M5_orf2#LIN 2907 TACATTTAGGTCTATG-ATCCATCTNGA-ATTAATTTTTGTGTATGGTGT 2860 chr5ptel1M 777770 CAAGTGTGGGTCCATGCCTAGTTTCTACCATACTAATTTCTAATTTTCCT 777819 v i iv v v?iii v i v ivi v i v i i C L1M5_orf2#LIN 2859 GAGGTAGGGGTCGAGNTTCATTTTTTTCCATATGGATATCCAATTGTTCC 2810 chr5ptel1M 777820 AGCAATTTTTGTCAAACAGTGAGTTCTTATCCCCA--AAACTGGGGTCTT 777867 viv ii v vvvi i - --i i ---- ? C L1M5_orf2#LIN 2809 AGCACCATTTGTTGAAAAGACTATCCTT-TCCCCACTGAATTG----CNT 2765 chr5ptel1M 777868 TGG---GTTTGTCAAATACTAGATTGT---TAAAGTTATTGA-CTGTTT- 777909 ---v v ii - ? ?--- v vv i v i- i - C L1M5_orf2#LIN 2764 TGGCACCTTTGTCAAAAATCA-ANTGNCCATATATGTGTGGGTCTATTTC 2716 chr5ptel1M 777910 TGTCCTTTGAACCTAATTCCACTGATCAACTAATCTATTCCTTA-GCCAA 777958 vv i vv iiivi i v i vi - - C L1M5_orf2#LIN 2715 TGGACTCTCTATTCTGTTCCATTGATCTATTTGTCTA-TCCTTACGCCAA 2667 chr5ptel1M 777959 TACCAAATGGTTTTGGTGATTGCTGCTTTATAATATAGTTTT 778000 v iv i i v i iv - i C L1M5_orf2#LIN 2666 TACCACACTGTCTTGATTACTGTAGCTTTATAATA-AGTCTT 2626 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.50 CpG sites = 99, Kimura (unadjusted) = 41.31 Transitions / transversions = 1.02 (99/97) Gap_init rate = 0.06 (37 / 663), avg. gap size = 1.38 (51 / 37) 549 26.29 2.51 2.51 chr5ptel1M 778003 778201 (221799) L1ME4c_3end#LINE/L1 356 554 (276) m_b238s551i2 9379 chr5ptel1M 778003 TGTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGATTATATCCCAAA 778052 v i i i vii v v v i i L1ME4c_3end#L 356 TGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAG 405 chr5ptel1M 778053 GAGATTAT---AAAGAAGGGAAAGGGACCTGTATGTGCACGA--ATGTTT 778097 i v --- i i -----v i -- i L1ME4c_3end#L 406 GAAATAATTCAAAAGAAGGAAAAAG-----CTATATGCACGAAGATGTTC 450 chr5ptel1M 778098 GTGGCAGCCCTTTTTGTAGTGACTAGAAACTGGAAACTGAATGGATGTCC 778147 i v vi v i i ii v i i vivv ii L1ME4c_3end#L 451 ATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCC 500 chr5ptel1M 778148 ATCAGTTGGAGAATGGCTGAATAAATTGTGGTATATGAAAATTATGGAAT 778197 v i v i i i i i i v? vviv L1ME4c_3end#L 501 AACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAAT 550 chr5ptel1M 778198 ATTA 778201 L1ME4c_3end#L 551 ATTA 554 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 32.66 CpG sites = 31, Kimura (unadjusted) = 33.46 Transitions / transversions = 1.55 (31/20) Gap_init rate = 0.04 (7 / 198), avg. gap size = 1.43 (10 / 7) 293 31.08 3.62 3.25 chr5ptel1M 778009 778284 (221716) L1MC4a_3end#LINE/L1 356 632 (1997) m_b238s551i3 9379 chr5ptel1M 778009 TACCCTTTGATCCAGCAGTGTTACTACTGGGATTATATCCCAAAGAGATT 778058 i i vii v i v v i ii --- L1MC4a_3end#L 356 TACCCTTTGACCCAGCAATCCCACTTCTAGGAATTTACCCTGAAGA---T 402 chr5ptel1M 778059 ATA-----AAGAAG-GGAAAGGGACCTGTATGTGCACGAATGTTTGTGGC 778102 i ----- v v -iv iv? --i ii v iv i ii v L1MC4a_3end#L 403 ACACCTCCAACATGTACAAAATNAC--ATATGCACAAGGTTATTCATTGC 450 chr5ptel1M 778103 AGCCCTTTTTGTAGTGACTAGAAACTGGAAACTGAATGGATGTCCATCAG 778152 vi v i vi v i v i vivv ii i ??i L1MC4a_3end#L 451 AGCATTGTTTGTAATTGCAAAATATTGGAAACAACCTAAATGCCCATNNA 500 chr5ptel1M 778153 TTGGAGAATGGCTGAATAAATTGTGGTATATGAAAATTATGGAATATTAC 778202 v ? i i i i vv v iv i i - L1MC4a_3end#L 501 TAGGAGANTGGTTGAATAAACTATGGTACATCCACACAATGGAGTACTA- 549 chr5ptel1M 778203 TGT-TCTGTAAGAAATGACCAACAGGATGATTTC-AGAAA--GGCCTGGA 778248 i-v i - -- vv v i - vi -- iiv L1MC4a_3end#L 550 TGCAGCTGTAAAAAA-GA--ATGAGGAAGATCTCTATGAACTGATATGGA 596 chr5ptel1M 778249 GAGACTTACACGAACTGATGCTGAGTGAAATGAGCA 778284 v i v v vv iv i i vi L1MC4a_3end#L 597 GTGATTTCCAGGATATATTGTTAAGTGAAAAAAGCA 632 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.98 CpG sites = 46, Kimura (unadjusted) = 41.98 Transitions / transversions = 1.24 (46/37) Gap_init rate = 0.05 (14 / 275), avg. gap size = 1.36 (19 / 14) 351 27.08 4.48 4.48 chr5ptel1M 778083 778283 (221717) L1MC1_3end#LINE/L1 433 633 (447) m_b238s551i5 9379 chr5ptel1M 778083 TGTGCACGAATGTTTGTGGCAGCCCTTTTTGTAGTGACTAGAAACTGGAA 778132 ii i i i ii v ii i vi i i vi L1MC1_3end#LI 433 TGCACACGGATGTTTATAGCAGCTTTATTCATAATTGCCAAAACTTGGAA 482 chr5ptel1M 778133 ACTGAAT--GGATGTCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTA 778180 i -- i--i v v v v i i L1MC1_3end#LI 483 GC--AACCAAGATGTCCTTCAGTAGGTGAATGGATAAATAAACTGTGGTA 530 chr5ptel1M 778181 TATGAAAATTATGGAATATTACT--GTTCT-GTAAGAAATGA-CCAACAG 778226 i vv i iv i -- iv -iv - i v i L1MC1_3end#LI 531 CATCCAGACAATGGAATATTATTCAGCGCTAAAAAGAAATGAGCTATCAA 580 chr5ptel1M 778227 G--ATGATTTCAGAAAGGCCTGGA-GAGACTTACACGAACTGATGCTGAG 778273 -- ------ i v - i v i v - iv i i L1MC1_3end#LI 581 GCCATGA------AAAGACATGGAGGAAACTTAAATGCA-TATTACTAAG 623 chr5ptel1M 778274 TGAAATGAGC 778283 vi L1MC1_3end#LI 624 TGAAAGAAGC 633 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.05 CpG sites = 34, Kimura (unadjusted) = 34.89 Transitions / transversions = 1.89 (34/18) Gap_init rate = 0.07 (15 / 200), avg. gap size = 1.20 (18 / 15) 360 28.26 0.00 2.29 chr5ptel1M 778083 778216 (221784) L1MB8_3end#LINE/L1 433 563 (362) m_b238s551i4 9379 chr5ptel1M 778083 TGTGCACGAATGTTTGTGGCAGCCCTTTTTGTAGTGACTAGAAACTGGAA 778132 i ii i vi v ii i ii i i v L1MB8_3end#LI 433 TGTACACGAATGTTCATAGCAGCATTATTCATAATAGCCAAAAAGTGGAA 482 chr5ptel1M 778133 ACTGAATGGATGTCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATA 778182 vivviii ii iv v i v L1MB8_3end#LI 483 ACAACCCAAATGTCCATCAACTGATGAATGGATAAATAAAATGTGGTATA 532 chr5ptel1M 778183 TGAAAATTATGGAATATTACTGTTCTGTAAGAAA 778216 vv v iv --- v i v L1MB8_3end#LI 533 TCCATACAATGGAATATTA---TTCGGCAATAAA 563 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.43 CpG sites = 22, Kimura (unadjusted) = 36.43 Transitions / transversions = 1.47 (22/15) Gap_init rate = 0.02 (3 / 133), avg. gap size = 1.00 (3 / 3) 16 16.93 0.00 0.00 chr5ptel1M 778747 778773 (221227) (A)n#Simple_repeat 1 27 (0) m_b238s252i0 9380 chr5ptel1M 778747 AAATAAAAAAAAAAAGAGGAAAAAAAA 778773 v i ii (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAA 27 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 3200 30.56 3.98 2.58 chr5ptel1M 778942 781353 (218647) C L1M4_orf2#LINE/L1 (826) 2468 24 m_b238s551i6 9378 chr5ptel1M 778942 TAGATTAGTTTAGGTAGTATTGTCATCTTTATTATTATATTTGCTCACCC 778991 i i i v i v i- -- viv vi C L1M4_orf2#LIN 2468 TAGATCAATTTGGGGAGTATTGCCATCTTAAC-A--ATATTAAGTCTTCC 2422 chr5ptel1M 778992 AATCCAACAGCATTTAATATTTTTCCAATTGTTTAGATCTGACTTTATTT 779041 vv i vvi i i v i i vvi v C L1M4_orf2#LIN 2421 AATCCATGAACATGGGATGTCTTTCCATTTATTTAGGTCTTCTTTAATTT 2372 chr5ptel1M 779042 GTGT--AGAAAGTTTTGTAGTTTTGCACATATAGTTTCTGATTTTCCCTT 779089 v v -- v v vviii i iv ii vvi ii C L1M4_orf2#LIN 2371 CTTTCAACAATGTTTTGTAGTTTTCAGTGTACAAGTCTTGCACTTCTTTT 2322 chr5ptel1M 779090 GGCAGATTGATTCCTAAATATTTTAT-ATTGTCGGTAGTTACTTTAAATG 779138 vi i v i -v v i i - i i v C L1M4_orf2#LIN 2321 GTTAAATTTATTCCTAAGTATTTTATTCTTTTTGAT-GCTATTGTAAATG 2273 chr5ptel1M 779139 GAATTTCTCTTTGTAACTCTAACTGTTGGATT--TTGTTAATGATATATA 779186 vi i i - i - v i v i -- ii iv ii i C L1M4_orf2#LIN 2272 GAATTGTTTTCT-TAATT-TCATTTTCGGATTGTTCATTGCTAGTGTATA 2225 chr5ptel1M 779187 AGAATGCTGATGACTTAGGTGGGTTTATTTTGTATCCTGCAACTTTGCTA 779236 ii i viv i vv ivi v i i i C L1M4_orf2#LIN 2224 GAAATACAATTGATTTTTGTATATTGATCTTGTATCCTGCAACCTTGCTG 2175 chr5ptel1M 779237 AAGGTGTGGATTATTTCTAATAACTTTTT-----ATTC--TGGGGTTCTC 779279 vvi vv v ii ----- -- i i i C L1M4_orf2#LIN 2174 AACTCGTTTATTAGTTCTAATAGTTTTTTNGTGGATTCCTTAGGATTTTC 2125 chr5ptel1M 779280 CAAGTATACCATCATATCATCAGCAAAGAGTCATAATTTGGTTTCTTCGT 779329 i vi i vv i v i v vv i vii v C L1M4_orf2#LIN 2124 TATATACAAGATCATGTCATCTGCGAATAGAGATAGTTTTACTTCTTCCT 2075 chr5ptel1M 779330 TGCCTACTCTA-ATTTCTTTAATTTCTTTCTCAGCTCTTATTGCCATAGC 779378 v - v i- vi v i vvvi v v i C L1M4_orf2#LIN 2074 TTCC-AATCTGGATGCCTTTTATTTCTTTTTCTTGCCTAATTGCCCTGGC 2026 chr5ptel1M 779379 TAGCATTTCTAATACAATATTGAATAGTAATGGTGATAATGGGCCACCTT 779428 v ii i i i v i i v ii i vv C L1M4_orf2#LIN 2025 TAGAACCTCCAGTACAATGTTGAATAGAAGTGGCGAGAGCGGACATCCTT 1976 chr5ptel1M 779429 GTTGCACTTGTGATTTTATTGGGAATAGTTCCAGTTTATCCCCATTACAT 779478 iviii iv i vv viv? i i v v vi C L1M4_orf2#LIN 1975 GTCTTGTTCCTGATCTTAGGGGGAAAGCNTTCAGTCTTTCACCATTAAGT 1926 chr5ptel1M 779479 ATGATGCTTACTGATGGTTTTAAATAGATGCTACTGATTATTTTAAGGAA 779528 i vi vv vvi ivi v i vv i C L1M4_orf2#LIN 1925 ATGATGTTAGCTGTGGGTTTTTCGTAGATGCCCTTTATCAGGTTGAGGAA 1876 chr5ptel1M 779529 AAGACCATTTATTCCTCTACTCTCAAGTGTTTTTA-------A------T 779565 ivvv v i vvvi v ii ------- ------ C L1M4_orf2#LIN 1875 GTTCCCTTCTATTCCTAGTTTGTTGAGTGTTTTTATCATGAAAGGGTGTT 1826 chr5ptel1M 779566 GGATTTTATCAAATGCTTTTTCTGCATCTATTGAAATGATCATATGGTTT 779615 i i i i C L1M4_orf2#LIN 1825 GGATTTTGTCAAATGCTTTTTCTGCGTCTATTGAGATGATCATGTGGTTT 1776 chr5ptel1M 779616 TTGTTAATTTGGT-TATTAATATGGTCAATTATACTACTAGTTTTCCTAA 779664 iv- iv - vv i i iv v v i v? C L1M4_orf2#LIN 1775 TTGTCC-TTTATTCTATTAATATGGTGTATTACATTGATTGATTTTCGNA 1727 chr5ptel1M 779665 TACTGAACCCAGCCCTGCATTCCTGGTATAAATCCTACCTGATCATGGTG 779714 ii - i i v i i i C L1M4_orf2#LIN 1726 TGTTGAACC-AACCTTGCATTCCTGGGATAAATCCCACTTGGTCATGGTG 1678 chr5ptel1M 779715 TATTATCCTGGGGGTGAT-TGT--CTGTAGTTGTTTTGCTAATAACTTGT 779761 v vv--- v - -- v v i v i vi C L1M4_orf2#LIN 1677 TATAATCCTTT---TTATATGTTGCTGGATTCGGTTTGCTAGTATTTTGT 1631 chr5ptel1M 779762 TTAAGATTTTAGCATCAATATTCATTAGGGAGATTGGTCTATAATTTTCT 779811 v i v v v v i i C L1M4_orf2#LIN 1630 TGAGGATTTTTGCATCTATATTCATAAGGGATATTGGTCTGTAGTTTTCT 1581 chr5ptel1M 779812 TTCTCTGT--TTTCAGGCTACCTAGTTTAGGTATCAGTACCATGTCTGTG 779859 iii -- v --vi ii i v viiv iiiv iv C L1M4_orf2#LIN 1580 TTTCTTGTGATGTC--TTTGTCTGGTTTTGGTATCAGGGTAATACTGGCC 1533 chr5ptel1M 779860 TCACAGAAGGAATTTGGTAGGAGTCTTTCATTCCCTATTTTATTTTCAAA 779909 i v i v v viv ii v iii --- vi C L1M4_orf2#LIN 1532 TCATAGAATGAGTTGGGAAGTGTTCCCTCCTCTTCTATTTT---TTGGAA 1486 chr5ptel1M 779910 TAGTTTATATAGCATTGCAGCTAATTGTTCTTTAAATGTTTGGTAGAATT 779959 v i iv v vv i v C L1M4_orf2#LIN 1485 GAGTTTGTGAAGGATTGGTGTTAATTCTTCTTTAAATGTTTGGTAGAATT 1436 chr5ptel1M 779960 CACATGTAAATCCATCTGGTCCTGGGGATTTTTTCTTAGGGAACTGATTA 780009 vv i v ? vv i iv i i ii vv i C L1M4_orf2#LIN 1435 CACCAGTGAAGCCATCTGGNCCTGGGCTTTTCTTTGTGGGAAGTTTTTTG 1386 chr5ptel1M 780010 ATAGCTTGTTCTGTTTCTTTTTCTGAGATGAGACTATTTGAGTAATTTAC 780059 vi vi vi i vii vv ii v iiii vv i i C L1M4_orf2#LIN 1385 ATTACTAATTCAATCTCTTTACTTGTTATAGGTCTATTCAGATTTTCTAT 1336 chr5ptel1M 780060 TTCCTCCTCTGTTAATCTGGGAAGCCTATATTTTTGGAAGTAGTCATCCA 780109 i i vv i i i v v ii i i i vv i v v ii C L1M4_orf2#LIN 1335 TTCTTCTTGAGTCAGTTTCGGTAGTTTGTGTCTTTCTAGGAATTTGTCCA 1286 chr5ptel1M 780110 TTTCACTTAGGTTATCAAATTTTTTGGCATAAAGTTGGGCAAAGTAACTC 780159 ii v v v i vv v vii C L1M4_orf2#LIN 1285 TTTCATCTAGGTTATCTAATTTGTTGGCATACAATTGTTCATAGTATTCC 1236 chr5ptel1M 780160 CTTATTTTTGCTCTAATTTCCTCTTCATTGGTGGAAAGTTCCCCCTTTTC 780209 vv ivi i v ivivvvi i i v vv ii C L1M4_orf2#LIN 1235 CTTATAATCCTTTTTATTTCTGTAAGGTCGGTAGTAATGTCCCCTCTTTC 1186 chr5ptel1M 780210 ATTTTTAAGACTAACAATTTGATTTTCCTCTTTCCTTTTTCTAATCGGAT 780259 ii i vvi ii v i i i ii ii ii i vi C L1M4_orf2#LIN 1185 ATTCCTGATTTTAGTAATTTGAGTCTTCTCTCTTTTTTTCTTGGTCAGTC 1136 chr5ptel1M 780260 TTACCAAAGGTTTATCTATTTTATTGTTTTTTTTATAAAACCAACTCTTA 780309 vi i i v i v i i v i i i C L1M4_orf2#LIN 1135 TAGCTAAAGGTTTGTCAATTTTGTTGATCTTTTCAAAGAACCAACTTTTG 1086 chr5ptel1M 780310 GTTTTATTTATTAATTCAATATT-TTTTTTTACTTTCAGTATTATTAATT 780358 ii v -- vv - i i i vi v i v C L1M4_orf2#LIN 1085 GTTTCGTTGATT--TTCTCTATTGTTTTTCTATTCTCTATTTCATTTATT 1038 chr5ptel1M 780359 TCTCTTTTTAAT-TTTAGAATTTCAAGTTTAGTATTTGATTGGGGTTTTT 780407 - vi i - vv vvvii vv ii v v -- C L1M4_orf2#LIN 1037 TC-CGCTCTAATCTTTATTATTTCCTTCCTTCTGCTTGCTTTGGGTTT-- 991 chr5ptel1M 780408 AAATTTGG---TCTTTTTCTAGCTTTTTAAGTTGCAAGCCCATTTCATTG 780454 - i v--- i i v v vii vv i C L1M4_orf2#LIN 990 -AGTTTGCTCTTCTTTTTCTAGTTTCTTAAGGTGGAAGGTTAGGTTATTG 942 chr5ptel1M 780455 ATCTTATCTTTCTCTATTTTTTTCAAGTAAGCCTCTAAAGATATTAAATT 780504 i v vv i i vi v vi i v i v v v v C L1M4_orf2#LIN 941 ATTTGAGATCTTTCTTCTTTTTTAATATAGGCATTTACAGCTATAAATTT 892 chr5ptel1M 780505 TCCTCTTATTACTGCTTT--------------AGTTTTGGTATGATATCT 780540 i v vi -------------- v i v C L1M4_orf2#LIN 891 CCCTCTAAGCACTGCTTTNGCTGCATCCCATAAGTTTTGGTATGTTGTGT 842 chr5ptel1M 780541 CAACATTGTCATT-ATCTTGAGTGAAATTATTAATTGTGTCTATAATTTG 780589 ivv i v - ii i- v v vi vivii i i v C L1M4_orf2#LIN 841 TTTCGTTTTCATTCATCTCAAA-GTATTTTCTAATTTCCCTTGTGATTTC 793 chr5ptel1M 780590 CTAATTCACCCAATCATTCTTTAAGA-TGAGATTATTTAGTTTCCAATTA 780638 i vv v v vi v i - v - i i vv C L1M4_orf2#LIN 792 TTCTTTGACCCATTGGTTATTTAGGAGTGTG-TTGTTTAATTTCCACATA 744 chr5ptel1M 780639 CTTTTTTGGTCTATTTACCCCTAACTTT------TTGTTGAATATAGCTT 780682 -- v i--- -- v i i------ i v viviv C L1M4_orf2#LIN 743 --TTTGTGA---ATTT--CCCAAATTTCCTTCTGTTATTGATTTCTAATT 701 chr5ptel1M 780683 TTATTGCATCGTGATCTGAAAAGAATGCATT-TATTAGTTCTGCCTTTCT 780731 i v i i v i -v i v - v v vii i i C L1M4_orf2#LIN 700 TCATTCCATTGTGGTCGGAGAA-CATACTTTGTATGATTTCAATCCTTTT 652 chr5ptel1M 780732 GCATTTAATTTTGAGAT---CTTTATGTCCTAATATATGGTCAATTTTTG 780778 iv --- i---i v i v ii v C L1M4_orf2#LIN 651 AAATTTA---TTGAGACTTGTTTTATGGCCTAACATATGGTCTATCCTGG 605 chr5ptel1M 780779 TATAGGTTTCATGAACTGCTGAGAAGAAAGTGTATTCCTTTCTGTCACC- 780827 viv v i vi vvi v -- v iiii- C L1M4_orf2#LIN 604 AGAATGTTCCATGTGCACTTGAGAAGAATGTGTATTC--TGCTGTTGTTG 557 chr5ptel1M 780828 -ATTCAGTTTTTTCCAAAGATCTATCATATCTAATT--TTTCTAATATTC 780874 -i vv v i vi i vi i i vi i -- v i i -- C L1M4_orf2#LIN 556 GGTGGAGTGTTCTATAGATGTCTGTTAGGTCTAGTTGGTTTATAGTGT-- 509 chr5ptel1M 780875 TATTTACCTCTTTAATTTCTTT-TTTATTTGTTTTGTGGTTTGATTTATC 780923 i i vv iv i - v i vi v v i - v i C L1M4_orf2#LIN 508 TGTTCAAGTCTTCTATTTCCTTGTTGATCTTCTGTCTAG-TTGTTCTATC 460 chr5ptel1M 780924 TAATTCTGAGAGTGCAAGATTGAGATCTCCTACTACTATAGTTTGG-TGT 780972 i v vi i viiv ii v i v vii- C L1M4_orf2#LIN 459 CATTATTGAAAGTGGGGTATTGAAGTCTCCAACTATTATTGTTGAATTGT 410 chr5ptel1M 780973 CTATTTCTTCTTGCTATTCTCTTAACTTCTCCTTTAGGAAGTTAGATGCT 781022 i i v v v i ii i v i v v v v iv C L1M4_orf2#LIN 409 CTATTTCTCCCTTCAATTCTGTCAGTTTTTGCTTCATGTATTTTGGGGCT 360 chr5ptel1M 781023 ATACCACTTGGTGCATATATGTTCAGTATTGATATTGCTTCTTTGTCTAT 781072 v iiiii v i vv v vv i vi vv C L1M4_orf2#LIN 359 CTGTTGTTAGGTGCATATATGTTTATAATTGTTATATCTTCCTGATGGAT 310 chr5ptel1M 781073 GCTACCC-TTTAGCAAGTTATA----GTTACCTTCCTTATCTCTTTTAAT 781117 -iv - v -- ---- -- i i vv - C L1M4_orf2#LIN 309 -TGACCCTTTTATCA--TTATAAAATGT--CCTTCTTTGTCTCTAGTAA- 266 chr5ptel1M 781118 TAGATCAATTTTTG-----------GTTTTGTTTGATCTAAGGATGGCTA 781156 ----- ? -----------i i v v v i i C L1M4_orf2#LIN 265 -----CANTTTTTGTCTTAAAGTCTATTTTGTCTGATATTAGTATAGCCA 221 chr5ptel1M 781157 TCCCTG--CTTTTTTGACTTC-ATCTGAAGCATAATAGATTCTGCTCCAG 781203 ii v -- i ii v -i i --- ii v ii vi v C L1M4_orf2#LIN 220 CTCCAGCTCTCTTTTGGTTACTGTTT---GCATGGTATATCTTTTTCCAT 174 chr5ptel1M 781204 CCTTTTACCTTTACTCTGTACTTATCTCCCTG-CTTTAAA-TATATTTCC 781251 i i vi -- i i v ii -v i - i i i i C L1M4_orf2#LIN 173 CCTTTTACTTTCAACC--TATTTGTGTCTTTGAATCTAAAGTGTGTCTCT 126 chr5ptel1M 781252 TGTAATCAACATAT--TCTGTTC-TGACTTTTGATCCAGTCTGCTA---T 781295 iv i -- iv v - vi v v i --- C L1M4_orf2#LIN 125 TGTAGACAGCATATAGTTGGATCATGTTTTTTTATCCATTCTGCCAATCT 76 chr5ptel1M 781296 CTGCCTCTGCTTTATGGGAGAGTTCATCCCATTTACATTTAAGGTTAAAA 781345 ---i v v v i vi v --- C L1M4_orf2#LIN 75 CTGCCT---TTTGATTGGAGTGTTTAATCCATTTACATTTAATGT---AA 32 chr5ptel1M 781346 TTACTAAT 781353 i C L1M4_orf2#LIN 31 TTACTGAT 24 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.35 CpG sites = 387, Kimura (unadjusted) = 40.15 Transitions / transversions = 1.17 (387/331) Gap_init rate = 0.04 (99 / 2411), avg. gap size = 1.61 (159 / 99) 257 20.97 8.97 4.64 chr5ptel1M 781234 781378 (218622) C L1MEh_5end#LINE/L1 (7) 2228 2078 m_b238s551i7 9378 chr5ptel1M 781234 TGCTTTAAATATATTTCCTGTAATCAACATATTCT---GTTCTGACTTTT 781280 i i i i i i iv i v ---i i vi ? C L1MEh_5end#LI 2228 TGTTTTAAGTGTGTCTCTTGTAGACAGCATATTGTTGGATTTTGTTTTTN 2179 chr5ptel1M 781281 GATCCAGTCTGCTATCTGCCTCTG-CTTT--ATGGGAGAGTTCATCCCAT 781327 i i v? ---ii - -- v v i v C L1MEh_5end#LI 2178 AATCCAATCTGANA---ATCTCTGTCTTTTAATTGGTGAGTTTAACCCAT 2132 chr5ptel1M 781328 TTACATTTAAGGTTAAAATTACTA----ATTCTG---TATTTCTTGCCAT 781370 --- iv i---- ?v --- - C L1MEh_5end#LI 2131 TTACATTTA---TTGTAATTACTGNTATATTNGGACTTATTTC-TGCCAT 2086 chr5ptel1M 781371 CATAATAT 781378 v v C L1MEh_5end#LI 2085 CTTATTAT 2078 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 25.84 CpG sites = 18, Kimura (unadjusted) = 25.84 Transitions / transversions = 1.64 (18/11) Gap_init rate = 0.08 (12 / 144), avg. gap size = 1.67 (20 / 12) 288 25.23 3.70 0.90 chr5ptel1M 781269 781376 (218624) C L1PA10_5end#LINE/L1 (45) 2399 2289 m_b238s551i8 9378 chr5ptel1M 781269 GTTCTGACTTTTGATCCAGTCTGCTA-TCTGCCTCTGCTTTATGGGAGAG 781317 ii i v i i i - iv -i v v i vi C L1PA10_5end#L 2399 GTCTTGACTCTTTATCCAATTTGCCAGTCTGTGTCT-TTTAATTGGGGCA 2351 chr5ptel1M 781318 TTCATCCCATTTACATTTAAGGTTAAAATTACTAATTCTGTATT---TCT 781364 i v v ii vv v v --- i C L1PA10_5end#L 2350 TTTAGCCCATTTACATTTAAGGTTAATATTGTTATGTGTGAATTTGATCC 2301 chr5ptel1M 781365 TGCCATCATAAT 781376 i i C L1PA10_5end#L 2300 TGTCATCATGAT 2289 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 31.45 CpG sites = 16, Kimura (unadjusted) = 31.45 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.03 (3 / 107), avg. gap size = 1.67 (5 / 3) 16 13.99 8.51 0.00 chr5ptel1M 781515 781561 (218439) (TCTTTTAC)n#Simple_repeat 1 51 (0) m_b238s252i1 9381 chr5ptel1M 781515 TCTTGTAC-CCTTCCCT-TTTTACTCTTTTTC-CTTTT-CTCTTTTCCTC 781560 v - i iv - v - - v (TCTTTTAC)n#S 1 TCTTTTACTCTTTTACTCTTTTACTCTTTTACTCTTTTACTCTTTTACTC 50 chr5ptel1M 781561 T 781561 (TCTTTTAC)n#S 51 T 51 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.09 (4 / 46), avg. gap size = 1.00 (4 / 4) 235 21.74 1.45 0.00 chr5ptel1M 782147 782215 (217785) C L1M6_5end#LINE/L1 (925) 1590 1521 m_b238s551i9 9382 chr5ptel1M 782147 TGTTTTTTTT-CCTGGCTGCTTGTAATATTTTTTCCTTAATCTCATAGTT 782195 i - v iv i vi ii? i C L1M6_5end#LIN 1590 TGTTTTTTCTGCCTGGATGCTTGTAGGATTTTTTCTTTATCCTTGNAATT 1541 chr5ptel1M 782196 CTGAAATTTGGCCACAATAT 782215 vi v vi C L1M6_5end#LIN 1540 CAAAAATTTTGCCAGGATAT 1521 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 26.62 CpG sites = 9, Kimura (unadjusted) = 26.62 Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.01 (1 / 68), avg. gap size = 1.00 (1 / 1) 16 19.52 4.08 2.00 chr5ptel1M 784351 784399 (215601) (CTC)n#Simple_repeat 1 50 (0) m_b238s252i2 9383 chr5ptel1M 784351 CTGCTCC-CCTCCTTCTTTTATTCCTCCTCCCTCCT-TTCCTCATCCTCC 784398 v - i ii vi - -i v (CTC)n#Simple 1 CTCCTCCTCCTCCTCCTCCTCCTCCTCCT-CCTCCTCCTCCTCCTCCTCC 49 chr5ptel1M 784399 T 784399 (CTC)n#Simple 50 T 50 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.06 (3 / 48), avg. gap size = 1.00 (3 / 3) 14 12.69 0.00 0.00 chr5ptel1M 784508 784533 (215467) (CCTC)n#Simple_repeat 1 26 (0) m_b238s252i3 9384 chr5ptel1M 784508 CCTGCCTCCCTGCCTCCCTGCCTCCC 784533 v v v (CCTC)n#Simpl 1 CCTCCCTCCCTCCCTCCCTCCCTCCC 26 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 28 5.80 0.00 0.00 chr5ptel1M 786402 786437 (213563) (T)n#Simple_repeat 1 36 (0) c_b238s251i0 9385 chr5ptel1M 786402 TTTTTTTTTGTTTTTTTTTTTTGTTTTTTTTTTTTT 786437 v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 36 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 292 24.99 3.06 2.02 chr5ptel1M 787605 787702 (212298) C MIRc#SINE/MIR (4) 264 166 m_b238s601i0 9386 chr5ptel1M 787605 ATACTAATAC--TACTATTTCTAAAGCTTTTTAAGTTTTGCAAAGTACTT 787652 v i? -- - v v vi viv i ii C MIRc#SINE/MIR 264 ATAATAACNCCTTAC-ATTTGTATAGCACTTTACAGTTTACAAAGCGCTT 216 chr5ptel1M 787653 T-ACAGATGTTAATTCATTTGATCCTCACAAACAAATCTAGAAGGTAGAT 787701 - v ii vi - vi ivi ii C MIRc#SINE/MIR 215 TCACATACATTATCTCATTTGATCCTCAC-AACAACCCTGTGAGGTAGGC 167 chr5ptel1M 787702 A 787702 C MIRc#SINE/MIR 166 A 166 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.73 CpG sites = 14, Kimura (unadjusted) = 31.45 Transitions / transversions = 1.40 (14/10) Gap_init rate = 0.04 (4 / 97), avg. gap size = 1.25 (5 / 4) 313 21.22 0.00 1.52 chr5ptel1M 787645 787711 (212289) C MIR#SINE/MIR (50) 212 147 m_b238s601i1 9386 chr5ptel1M 787645 AAGTACTTTACAGATGTTAATTCATTTGATCCTCACAAACAAATCTAGAA 787694 ii vi i i i - vi vi C MIR#SINE/MIR 212 AAGCGCTTTACATGTATTAACTCATTTAATCCTCAC-AACAACCCTATGA 164 chr5ptel1M 787695 GGTAGATATTATTTTTA 787711 i i v C MIR#SINE/MIR 163 GGTAGGTACTATTATTA 147 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 23.50 CpG sites = 10, Kimura (unadjusted) = 25.83 Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.02 (1 / 66), avg. gap size = 1.00 (1 / 1) 13 18.22 0.00 0.00 chr5ptel1M 787884 787914 (212086) (ATAAA)n#Simple_repeat 1 31 (0) m_b238s252i4 9387 chr5ptel1M 787884 ATTAAATAAATGAAAGAAAAATAAAATAAAA 787914 v vv iv (ATAAA)n#Simp 1 ATAAAATAAAATAAAATAAAATAAAATAAAA 31 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 41 0.00 0.00 0.00 chr5ptel1M 787935 787972 (212028) (T)n#Simple_repeat 1 38 (0) c_b238s251i1 9388 chr5ptel1M 787935 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 787972 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 38 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 33 0.00 0.00 0.00 chr5ptel1M 790148 790175 (209825) (GA)n#Simple_repeat 1 28 (0) c_b238s251i2 9389 chr5ptel1M 790148 GAGAGAGAGAGAGAGAGAGAGAGAGAGA 790175 (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGA 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 14 14.42 5.00 2.44 chr5ptel1M 790464 790503 (209497) (TAGGGG)n#Simple_repeat 1 41 (0) m_b238s252i5 9390 chr5ptel1M 790464 TAGGAGTATTGGGTATGGG-A-GGGTGGGGGTAGGGGAAGGG 790503 i -v v - - i v (TAGGGG)n#Sim 1 TAGGGGTA-GGGGTAGGGGTAGGGGTAGGGGTAGGGGTAGGG 41 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.08 (3 / 39), avg. gap size = 1.00 (3 / 3) 15 4.77 0.00 0.00 chr5ptel1M 791779 791800 (208200) (AGC)n#Simple_repeat 1 22 (0) m_b238s252i6 9391 chr5ptel1M 791779 AGTAGCAGCAGCAGCAGCAGCA 791800 i (AGC)n#Simple 1 AGCAGCAGCAGCAGCAGCAGCA 22 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 16 12.06 0.00 0.00 chr5ptel1M 794792 794819 (205181) (CCTC)n#Simple_repeat 1 28 (0) m_b238s252i7 9392 chr5ptel1M 794792 CCTCTCTCTCTCCCTCCCTCCCTTCCTC 794819 i i i (CCTC)n#Simpl 1 CCTCCCTCCCTCCCTCCCTCCCTCCCTC 28 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 456 22.30 0.00 8.85 chr5ptel1M 794836 794958 (205042) C MIRc#SINE/MIR (154) 114 2 m_b238s601i2 9393 chr5ptel1M 794836 AGGTTAAGTGACTTGCCCAGGGTCACAGAGCTACGAAGTGCTAAGTGTCT 794885 i v vv vi - v i - C MIRc#SINE/MIR 114 AGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCA-GAGCC- 67 chr5ptel1M 794886 AAGGTCACATTTGAACTTAGGTCCTCCTGACTTTAGCACTCATGCTCTGT 794935 -i ---- i i ii i ii ivv ivi v C MIRc#SINE/MIR 66 -GGG----ACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTT 22 chr5ptel1M 794936 CCACTGTACCACCTAACTGCCCC 794958 i --- i C MIRc#SINE/MIR 21 CCACTGCACCAC---ACTGCCTC 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.43 CpG sites = 16, Kimura (unadjusted) = 26.87 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.08 (10 / 122), avg. gap size = 1.00 (10 / 10) 16 19.62 0.00 6.12 chr5ptel1M 795130 795181 (204819) (AAAAG)n#Simple_repeat 1 49 (0) m_b238s252i8 9394 chr5ptel1M 795130 AAAGGAAAAAAAAATGAGAAAGAAAACAAAATGAAAGTAAACAGAATGAA 795179 i i - - v vi v v - v (AAAAG)n#Simp 1 AAAAGAAAAGAAAA-GA-AAAGAAAAGAAAAGAAAAGAAAAGA-AAAGAA 47 chr5ptel1M 795180 AA 795181 (AAAAG)n#Simp 48 AA 49 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.00 (3 / 3) 433 28.33 0.55 1.10 chr5ptel1M 795614 795795 (204205) C L1ME3C_3end#LINE/L1 (683) 187 7 m_b238s551i10 9395 chr5ptel1M 795614 ATCTCAGAGTTGTCTTAATTTGCATTTCTCTAATCA-TAGTGATTTCGAG 795662 vv ? i i i i - vv i C L1ME3C_3end#L 187 ATCTCATTGTNGTTTTAATTTGCATTTCCCTGATTACTAGTGAGGTTGAG 138 chr5ptel1M 795663 CACCTTTTCATATGACTAGAAATGGTTTTAATTTCTTTACTTGAAAGTTG 795712 i vi vviiivi iv?i i ivii vi i C L1ME3C_3end#L 137 CATCTTTTCATATGTTTATTGGCCATTCGNGTTTCCTCTTCTGTGAATTG 88 chr5ptel1M 795713 TTTGTTCATATCTTTTGTCCATTTATCAATTGGAGAATGGATGAATTGTT 795762 ii i v v iv-- vv vv v C L1ME3C_3end#L 87 CCTGTTCATATCTTTTGCCCATTTTTCTATTGGGT--TGTCTGTTTTCTT 40 chr5ptel1M 795763 ATAAATTTGAGTCAGTTCTCTATATATTTTAGA 795795 vi vivv i i i C L1ME3C_3end#L 39 ATTGATTTGTAGGAGTTCTTTATATATTCTGGA 7 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.91 CpG sites = 28, Kimura (unadjusted) = 36.81 Transitions / transversions = 1.22 (28/23) Gap_init rate = 0.02 (3 / 181), avg. gap size = 1.00 (3 / 3) 468 23.48 0.76 0.00 chr5ptel1M 795614 795745 (204255) C L1MC5a_3end#LINE/L1 (2587) 190 58 m_b238s551i11 9395 chr5ptel1M 795614 ATCTCAGAGTTGTCTTAATTTGCATTTCTCTAATCAT-AGTGATTTCGAG 795662 v v i v i - vv i C L1MC5a_3end#L 190 ATCTCAGTGTAGTTTTAATTTGCATTTCTCTTATTATGAGTGAGGTTGAG 141 chr5ptel1M 795663 CACCTTTTCATATGACTAGAAATGGTTTTAATTTCTTTACTTGAAAGTTG 795712 i vi iiiiivi vv vii vi ii C L1MC5a_3end#L 140 CATCTTTTCATATGTTTAAGGGCCATTTGCATTTCTTTTTCTGTGAACTG 91 chr5ptel1M 795713 TTTGTTCATATCTTTTGTCCATTTATCAATTGG 795745 i i v v C L1MC5a_3end#L 90 TCTGTTCATATCTTTTGCCCATTTTTCTATTGG 58 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 28.68 CpG sites = 18, Kimura (unadjusted) = 28.68 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.01 (1 / 131), avg. gap size = 1.00 (1 / 1) 288 32.30 0.62 0.00 chr5ptel1M 795653 795813 (204187) C L1M1_orf2#LINE/L1 (0) 3294 3133 m_b238s551i12 9395 chr5ptel1M 795653 TGATTTCGAGCACCTTTTCATATGACTAGAAATGGTTTTAATTTCTTTAC 795702 v i v ivvviivi vv v ivi C L1M1_orf2#LIN 3294 TGATGTTGAGCACCTTTTCATATGCCTGTTTGCCATTTGTATGTCTTCTT 3245 chr5ptel1M 795703 TTGAAAGTTGTTTGTTCATATCTTTTGTCCATTTATCAATTGGA-GAATG 795751 i iv i i v i v i i -v v i C L1M1_orf2#LIN 3244 TTGAGAAATGTCTATTCAGATCTTTTGCCCATTTTTTAATCGGATTATTA 3195 chr5ptel1M 795752 GATGAATTGTTATAAATTTGAGTCAGTTCTCTATATATTTTAGAAATGAG 795801 vvv vi i v vv v i ii i i vv v i C L1M1_orf2#LIN 3194 GATTTTTTCCTATAGAGTTGTTTGAGCTCCTTATATATTCTGGTTATTAA 3145 chr5ptel1M 795802 GCCTTTATCAGA 795813 v i i C L1M1_orf2#LIN 3144 TCCCTTGTCAGA 3133 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.68 CpG sites = 25, Kimura (unadjusted) = 42.74 Transitions / transversions = 0.93 (25/27) Gap_init rate = 0.01 (1 / 160), avg. gap size = 1.00 (1 / 1) 17 0.00 0.00 0.00 chr5ptel1M 799323 799341 (200659) (T)n#Simple_repeat 1 19 (0) m_b238s252i9 9396 chr5ptel1M 799323 TTTTTTTTTTTTTTTTTTT 799341 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 344 34.20 0.86 0.86 chr5ptel1M 800451 800683 (199317) C HERVS71#LTR/ERV1 (3249) 5729 5497 m_b238s701i0 9397 chr5ptel1M 800451 CGGTGGATAATAGCGACAGAGCGGGGCAACCAGATAGAATCTAGCAAGGA 800500 i v i v vvivi i v i v ii vv v i v C HERVS71#LTR/E 5729 CAGTGGATCACAGCTACCTGCTGAGGGAGCCACACGGCTTCAAGCAGGGC 5680 chr5ptel1M 800501 AAGTATCTCTGCCTTATCCCTAATTTCCTTCCCAGAGGATGTCAATAGGC 800550 v v i v i i iii i vv i v vv v v i v C HERVS71#LTR/E 5679 TAGAATTTCTTCTTTGTTTTTGATAGCCTTTCCTGCTGAGGTGAGTAGCC 5630 chr5ptel1M 800551 CCCTTTCTTTGTAGAGAGAGGCATGGACACGAGCCGTTGCAAAGGCATAA 800600 v ? i v vi vvv v i vi v v i v C HERVS71#LTR/E 5629 CGCNTTCCTGGTAGATGGCTCCATGTACATGCACAGTAGCAAAGGCGTAC 5580 chr5ptel1M 800601 TGACTGTCAGTGTAAATATTAGCTGATTTACCCTT-TGCAATGCGCAGTG 800649 ivi i iivvi i -iv v - v v C HERVS71#LTR/E 5579 CTGCTGTCAGTGTAAATGTTAATACGTTTATCCTTACCCCAT-CGGAGAG 5531 chr5ptel1M 800650 CCTGAGTCAATGCTA-CAATCTCCGCTTTCTGGGC 800683 v iv v - - v i i v C HERVS71#LTR/E 5530 CCTGAGTGAGGGCGATCAAT-TCAGCCTTTTGCGC 5497 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 43.87 CpG sites = 34, Kimura (unadjusted) = 46.21 Transitions / transversions = 0.76 (34/45) Gap_init rate = 0.02 (4 / 232), avg. gap size = 1.00 (4 / 4) 340 31.27 2.54 1.00 chr5ptel1M 801070 801266 (198734) C HERV15#LTR/ERV1 (4422) 4329 4130 m_b238s701i1 9397 chr5ptel1M 801070 CTGGCCCAAGGAAAGTTTGTCAGCTTCCTTTACCAGGAGAGCAGTCGCTG 801119 i i i vv i ii v i i iv vv i v C HERV15#LTR/ER 4329 CTGACCTAGGGCTAGCTTGTTGGCATCTTCTATAAGGATTGCGGTAGCTG 4280 chr5ptel1M 801120 GCTATGGCCCTAAGACAGGGGGGCCATCCAGCTGCTACCGAATCTAAGCG 801169 v v i - i i v v vivv i i i i iv v C HERV15#LTR/ER 4279 CCAACG-CCCTGAGGCAGTGGGGCCAACCTAAGGCCACCAAGTCCAGTCT 4231 chr5ptel1M 801170 CTTGGAGAGATATGCAACAGGCCGATGCCAGGGGCCAAGCATTTGGGTCA 801219 i v ii v v i i v i vi i i C HERV15#LTR/ER 4230 TTTGGATAAGTATGCTACCGGCCGATGCCAAGAGCCCAACAACTGAGTTA 4181 chr5ptel1M 801220 GGACGCC--CTTCGCAATCCCCCTAGCT--TCCGC-CACAAAAGGTAGGG 801264 i v -- v - v ii v i -- i -i i v C HERV15#LTR/ER 4180 AGACTCCGACTGC-CATTCCCTTTCGTTCATCCACATACAAAAAGAAGGG 4132 chr5ptel1M 801265 CT 801266 C HERV15#LTR/ER 4131 CT 4130 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.86 CpG sites = 35, Kimura (unadjusted) = 41.65 Transitions / transversions = 1.35 (35/26) Gap_init rate = 0.03 (5 / 196), avg. gap size = 1.40 (7 / 5) 13 18.17 1.69 9.09 chr5ptel1M 802169 802227 (197773) (ACAGAAC)n#Simple_repeat 1 55 (0) m_b238s252i10 9398 chr5ptel1M 802169 ACAAAACAGACAGACAAATCACACAGAACATAGAACACACAGTTAACACA 802218 i v v - v vv i - - -- (ACAGAAC)n#Si 1 ACAGAACACAGA-ACACAGAACACAGAACACAG-A-ACACAG--AACACA 45 chr5ptel1M 802219 -AACCCAGAA 802227 - v (ACAGAAC)n#Si 46 GAACACAGAA 55 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.10 (6 / 58), avg. gap size = 1.00 (6 / 6) 16 0.00 0.00 0.00 chr5ptel1M 803828 803845 (196155) (C)n#Simple_repeat 1 18 (0) m_b238s252i11 9399 chr5ptel1M 803828 CCCCCCCCCCCCCCCCCC 803845 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCC 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 20 19.57 0.00 3.70 chr5ptel1M 803899 803954 (196046) (AGGGGGG)n#Simple_repeat 1 54 (0) m_b238s252i12 9400 chr5ptel1M 803899 AGGTGGAGAGGGGCAAGGGGGGGAGGGGGCGGGGTGGAGTGGGGAGGGGT 803948 - i vi - vi v v v (AGGGGGG)n#Si 1 AGG-GGGGAGGGGGGA-GGGGGGAGGGGGGAGGGGGGAGGGGGGAGGGGG 48 chr5ptel1M 803949 CAGGGG 803954 v (AGGGGGG)n#Si 49 GAGGGG 54 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.04 (2 / 55), avg. gap size = 1.00 (2 / 2) 16 20.94 0.00 0.00 chr5ptel1M 803915 803947 (196053) (G)n#Simple_repeat 1 33 (0) m_b238s252i13 9400 chr5ptel1M 803915 GGGGGGGAGGGGGCGGGGTGGAGTGGGGAGGGG 803947 i v v i v i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 33 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 15 28.62 1.89 1.89 chr5ptel1M 804977 805029 (194971) (TA)n#Simple_repeat 1 53 (0) m_b238s252i14 9401 chr5ptel1M 804977 TATAAACACAAATACATGCATATGTGTAAACTATAAATATATATAT-TTT 805025 v i i v i ii i i v - v - v (TA)n#Simple_ 1 TATATATATATATATATATATATATATATA-TATATATATATATATATAT 49 chr5ptel1M 805026 ATAT 805029 (TA)n#Simple_ 50 ATAT 53 Matrix = Unknown Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.00 (2 / 2) 13 9.78 0.00 0.00 chr5ptel1M 805362 805383 (194617) (TTG)n#Simple_repeat 1 22 (0) m_b238s252i15 9402 chr5ptel1M 805362 TTGTTTTTGTTGTTGTTTTTGT 805383 v v (TTG)n#Simple 1 TTGTTGTTGTTGTTGTTGTTGT 22 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 240 32.79 0.00 0.00 chr5ptel1M 805764 805824 (194176) C MIR3#SINE/MIR (22) 186 126 m_b238s601i3 9403 chr5ptel1M 805764 CAGACTTGGAAAAAACCTCAGAGTCCAGGTAATTCAATTTCTTCATTTTT 805813 vi iii i vi vv i i iii i v C MIR3#SINE/MIR 186 CAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTA 137 chr5ptel1M 805814 CCAATGAGGGA 805824 vi i C MIR3#SINE/MIR 136 CAGATGAGGAA 126 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 46.23 CpG sites = 14, Kimura (unadjusted) = 46.23 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 216 31.36 12.04 2.54 chr5ptel1M 805826 805933 (194067) C L2c_3end#LINE/L2 (0) 478 361 m_b238s601i4 9404 chr5ptel1M 805826 ACTCACTTCCTCAACAAAC----CTTAAATGCCTGATATGTACCAGAC-- 805869 i i ivi ----v i ii iv i i -- C L2c_3end#LINE 478 ATTCATTCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGC 429 chr5ptel1M 805870 ---AGATGCCCAAAAAAGAA-AGGCCA---TTTCTACTCTCAAAAAACTT 805912 ---i i-- i v - i v --- ii i i ii i i C L2c_3end#LINE 428 TGGGGATA--CAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTC 381 chr5ptel1M 805913 ATAATCTCATGAGGGAAGACA 805933 i i vi - i i C L2c_3end#LINE 380 ACAGTCTAGTG-GAGGAGACA 361 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.44 CpG sites = 27, Kimura (unadjusted) = 45.40 Transitions / transversions = 4.50 (27/6) Gap_init rate = 0.07 (8 / 107), avg. gap size = 2.00 (16 / 8) 18 37.20 0.00 0.00 chr5ptel1M 806335 806396 (193604) (AT)n#Simple_repeat 1 62 (0) m_b238s252i16 9405 chr5ptel1M 806335 ATATATGTGTGTATATTTATACATATACATATATGCACAGAGGCATATAT 806384 i i i v i i ii i v vii (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr5ptel1M 806385 ACATGTGTGTAT 806396 i i i i (AT)n#Simple_ 51 ATATATATATAT 62 Matrix = Unknown Transitions / transversions = 4.67 (14/3) Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0) 288 34.17 13.07 0.00 chr5ptel1M 806445 806643 (193357) C L3#LINE/CR1 (861) 3238 3014 m_b238s601i5 9406 chr5ptel1M 806445 TCTCAGATTTATGTTAACTGCAAATTTTTCACAAATGACACGTA-GT-TC 806492 i v i i v vvi viv v viv - - i C L3#LINE/CR1 3238 TCCCAGCTTTGTGTCATCTGCAAATTTGATAAGCATGCCTTCTATGTCTT 3189 chr5ptel1M 806493 AAACCAAGTAATGGATTAAAATTTTCAACAATTTATGTCAGAGGCTAG-- 806540 v v v v v v v ivvi v v vi vi -- C L3#LINE/CR1 3188 CATCCAAGTCATTGATAAAAATGTTGAACAGGACAGGGCCAAGGACAGAG 3139 chr5ptel1M 806541 CTCTTTGG-----------AGGTGCCCC-----------ATGGATTCAGT 806568 i v ----------- iivi ----------- v i v C L3#LINE/CR1 3138 CCCTGTGGCACGCCACTAGAGACCTCCCTCCAGGTTGACATCGATCCATT 3089 chr5ptel1M 806569 AATGATTATTTTTTCAGTCCAGTCATTCAACCAATTCTGCATCCCCCTAA 806618 v vi ii vi vi i ii vi v v C L3#LINE/CR1 3088 AATCAACACCTTTTGGGTATAGTCGTTCAACCAGCTACGAATCCACCTAA 3039 chr5ptel1M 806619 TTAAATTCTCATCTGTCTCATATCT 806643 i iv i v iiv i i C L3#LINE/CR1 3038 CTGTACTATCATCCAGCCCATATTT 3014 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.35 CpG sites = 32, Kimura (unadjusted) = 46.14 Transitions / transversions = 0.89 (32/36) Gap_init rate = 0.03 (5 / 198), avg. gap size = 5.20 (26 / 5) 193 12.90 6.45 0.00 chr5ptel1M 806802 806832 (193168) C MIR#SINE/MIR (10) 252 220 m_b238s601i6 9407 chr5ptel1M 806802 AACATTT--TAAGTGCTTACTGTGTGCCAAGCA 806832 -- i i i i C MIR#SINE/MIR 252 AACATTTATTGAGCGCTTACTATGTGCCAGGCA 220 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 11.16 CpG sites = 4, Kimura (unadjusted) = 14.92 Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.03 (1 / 30), avg. gap size = 2.00 (2 / 1) 258 28.81 0.00 0.00 chr5ptel1M 807017 807075 (192925) C L2c_3end#LINE/L2 (50) 428 370 m_b238s601i7 9408 chr5ptel1M 807017 TGGAGATATAAAGAGAGAGAAAAGACAGTCCTGGCTCTTCAGGAACTCAC 807066 i i vii v i v i iv i iv i C L2c_3end#LINE 428 TGGGGATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCAC 379 chr5ptel1M 807067 AATCTATTG 807075 i v C L2c_3end#LINE 378 AGTCTAGTG 370 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.04 CpG sites = 11, Kimura (unadjusted) = 37.86 Transitions / transversions = 1.83 (11/6) Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.0 (0 / 0) 341 29.81 8.70 0.81 chr5ptel1M 807642 807756 (192244) C L2d2_3end#LINE/L2 (12) 543 420 m_b238s601i8 9409 chr5ptel1M 807642 AATAAACCTTTAATTAGTGCCATATTCTG-----GGCACTATACTAAGCA 807686 i iv v v i - i v ----- i i i i C L2d2_3end#LIN 543 AACAAATATTTATTGAGCGCC-TACTGTGTGCAAGGCACTGTGCTAGGCG 495 chr5ptel1M 807687 TTG---GCAATACAAAGAAAGGCAAAGGACAGTCTCTGCTGTCAAGGGAT 807733 i --- vi ivii iiv ii i iv iii C L2d2_3end#LIN 494 CTGTGGGGGATACAAAGAAGTATAAGACATGGTCCCTGCCCTCAAGGAGC 445 chr5ptel1M 807734 TCACAATCTAA--AGGGAGAAAAGA 807756 i i--i v C L2d2_3end#LIN 444 TTACAATCTAGTTGGGGAGACAAGA 420 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.57 CpG sites = 25, Kimura (unadjusted) = 40.74 Transitions / transversions = 2.78 (25/9) Gap_init rate = 0.04 (4 / 114), avg. gap size = 2.75 (11 / 4) 453 30.82 4.58 5.09 chr5ptel1M 808709 809320 (190680) C L1ME4c_3end#LINE/L1 (191) 639 31 m_b238s551i13 9410 chr5ptel1M 808709 TTCTGCTCTTTTCACTTTGTATCACAGTTTGTACAAGCCTTTCCAGGTTT 808758 i vii i i -- ii - vvi v v C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATA--TCATA-AACATTTTCCATGTTG 593 chr5ptel1M 808759 TTCTGAAATCTGCCTGTTCAT--TTCTTAGTG-CACAATAATATTCCTTT 808805 i viiv i v v iv i -- i i - vvv v i C L1ME4c_3end#L 592 CTACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATC 543 chr5ptel1M 808806 ATATTCCTATACCACAACTTATTCAGCCATTCCCCAATTAATGGG--TTT 808853 ivi ?vv i i i i i i v iv i-- C L1ME4c_3end#L 542 GAGTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTT 493 chr5ptel1M 808854 CCCCTCAATTTCCAATATTTTCCCACCCCAAAAAGGACTGTTATAAATAT 808903 vvvi --i - --------------i i v C L1ME4c_3end#L 492 AGGTT--GTTTCCAAT-TTTTC--------------GCTATTATAAATAA 460 chr5ptel1M 808904 TTTTGCATATGCATATATAGTTATGTATGTATGTCCTTTCCTTTTTGTG- 808952 ivi - v i v -- ii i i - iii i v - C L1ME4c_3end#L 459 CGCTGCA-ATGAACATCT--TCGTGCATATA-GCTTTTTCCTTCTTTTGA 414 chr5ptel1M 808953 -TGATCTCTTTGAGATACAGATCTAGTAGTGGTATTGTCCAGTCAAAGTG 809001 - v i i ii v vvi i v v iiivi v C L1ME4c_3end#L 413 ATTATTTCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGG 364 chr5ptel1M 809002 GATGCACGGTGTAGTTGCCCTT--TGAGTATAGTTCCAAATAACT---GA 809046 v v iv v vi v i -- iv -- v vi ---v C L1ME4c_3end#L 363 TATGAACATTTTTATGGCTCTTGATACGTAT--TGCCAAATTGCTTTCCA 316 chr5ptel1M 809047 GAATGGTTGGATCAGTTCAGAA---CTCCAATACTACATTAGGTGTTTCA 809093 i v v i i i v ?--- v ii v ii v ?- vi C L1ME4c_3end#L 315 AAAGGGTTGTACCAATTTACANTGCCACCAGCAATGTATGAGN-GTACCA 267 chr5ptel1M 809094 ATTTTCCC----TGTCTTCAACATT---TATCGCTTTACTTTTTTGTCAT 809136 i iv ----iv vi i --- ii-- i v i-v C L1ME4c_3end#L 266 GTTTCACCGCANCCTCGCCAGCATTGGGTATTA--TCAATTTTTTA-AAT 220 chr5ptel1M 809137 ATTGGCCAATCTGATAGGGGTGAAGTGGTATCTCAGAGTTGTTTTAATTT 809186 v v i i i v i i vv i C L1ME4c_3end#L 219 TTTTGCTAATTTAATAGGCGTAAAATGGTATCTCATTGTTGCTTTAATTT 170 chr5ptel1M 809187 GCATTTCTTTAATCA--AGTGATTTGGAGCACTTCTTCATTTGTCTAGAG 809234 i i -- i vv v i i i i v i - vv C L1ME4c_3end#L 169 GCATTTCTTTGATTACTAGCGAGGTTGAACATTTTTCCATGTGTTT-GTT 121 chr5ptel1M 809235 AAAGCCTTG-ATTATTTCATTTGAAATCTGCCTGATCATATCCTTTG--- 809280 v vvv? - vii v ? vi vi i v i --- C L1ME4c_3end#L 120 TACTANTTGTATTTCCTCTTNTGTGAATTGTCTGTTCATGTCCTTTGCCC 71 chr5ptel1M 809281 ATTTATCTATTGGGGAGTAAGTTTTATTCTTATAAATTTG 809320 vv vii ? v v C L1ME4c_3end#L 70 ATTTATCTATTGGGGTCTTGATNTTTTTCTTATCAATTTG 31 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.54 CpG sites = 97, Kimura (unadjusted) = 41.09 Transitions / transversions = 1.18 (97/82) Gap_init rate = 0.07 (44 / 611), avg. gap size = 1.34 (59 / 44) 554 27.54 6.63 7.85 chr5ptel1M 808793 809320 (190680) C L1ME4b_3end#LINE/L1 (340) 552 31 m_b238s551i14 9410 chr5ptel1M 808793 ATAATATTCCTTTATATTCCTATACCACAACTTATTCAGCCATTCCCCAA 808842 i v i vvv i i i i i v v C L1ME4b_3end#L 552 ATAGTATTCCATTGTATGGATGTACCATAATTTATTTAACCAGTCCCCTA 503 chr5ptel1M 808843 TTAATGGG--TTTCCCCTCAATTTCCAATATTTTCCCACCCCAAAAAGGA 808890 i i-- vvvi --i v ---------------i C L1ME4b_3end#L 502 TTGATGGACATTTAGGTT--GTTTCCAATCTTTT---------------G 470 chr5ptel1M 808891 CTGTTATAAATATTTTTGCATATGCATATATAGTTATGTATGTATGTCCT 808940 i i i v vi ----- iv iiiv ii i v C L1ME4b_3end#L 469 CTATTACAAACAATGCTGCA-----ATGAATAACCTTGTACATACGTCAT 425 chr5ptel1M 808941 TTCCTTTTTGTGTGA---TCTCTTTGAGATACAGATCTAGTAGTGGTATT 808987 viviv i --- v v ii v vvi v v C L1ME4b_3end#L 424 TTCGCACATGTGCGAGTATATCTGTAGGATAAATTCCTAGAAGTGGAATT 375 chr5ptel1M 808988 GTCCAGTCAAAGTGGATGCACGGT-GTAGTTGCCCTTTGA-GTATAGTTC 809035 iivi v v ii iv - i ----- -iv v v C L1ME4b_3end#L 374 GCTGGGTCAAAGGGTATGTGCATTTGTAATT-----TTGATAGATATTGC 330 chr5ptel1M 809036 CAAATAACTG---AGAATGGTTGGATCAGTTCAGAACTCC----AATACT 809078 vi iv--- v iv v i i i v - ---- ii v C L1ME4b_3end#L 329 CAAATTGCCCTCCATAGAGGTTGTACCAATTTACA-CTCCCACCAGCAAT 281 chr5ptel1M 809079 ACATTAG-GTGTTTCAATTTTCCC----TGTCTTCAACAT------TTAT 809117 ii v - ii --i i ----iv vi i------ C L1ME4b_3end#L 280 GTATGAGAGTGCCT--GTTTCCCCACACCCTCGCCAACACAGTGTGTTAT 233 chr5ptel1M 809118 CGCTTTACTTTTTTGTCATATTGGCCAATCTGATAGGGGTGAAGTGGTAT 809167 i---- vi -- v v v vi i C L1ME4b_3end#L 232 CA----AACTTTTTG--ATCTTTGCCAATCTGATAGGTGAAAAATGGTAT 189 chr5ptel1M 809168 CTCAGAGTTGTTTTAATTTGCATTTCTTTAATCA--AGTGATTTGGAGCA 809215 v v i v i -- vv v C L1ME4b_3end#L 188 CTCAGTGTAGTTTTAATTTGCATTTCTCTTATTATGAGTGAGGTTGAGCA 139 chr5ptel1M 809216 CTTCTTCATTTGTCTAGAGAAAGCC--TTGATTATTTCATT---TGAAAT 809260 ii i v i --- i -- -- v --- vi v C L1ME4b_3end#L 138 TCTTTTCATATGTTTA---AGAGCCATTTG--TATTTCCTTTTCTGTGAA 94 chr5ptel1M 809261 CTGCCTGATCATATCCTTTG---ATTTATCTATTGGGGAGTAAGTTTTAT 809307 i v --- v vv vi i v C L1ME4b_3end#L 93 CTGTCTGTTCATATCCTTTGCCCATTTTTCTATTGGGTTGTTGGTCTTTT 44 chr5ptel1M 809308 TCTTATAAATTTG 809320 vi C L1ME4b_3end#L 43 TCTTATTGATTTG 31 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.13 CpG sites = 70, Kimura (unadjusted) = 34.76 Transitions / transversions = 1.09 (70/64) Gap_init rate = 0.10 (54 / 527), avg. gap size = 1.41 (76 / 54) 649 27.04 6.45 2.59 chr5ptel1M 808949 809320 (190680) C L1ME5_3end#LINE/L1 (525) 416 31 m_b238s551i15 9410 chr5ptel1M 808949 TGTGTGA---TCTCTTTGAGATACAGATCTAGTAGTGGTATTGTCCAGTC 808995 --- i i i v i i v i v iivi C L1ME5_3end#LI 416 TGTGTGAGAATTTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTC 367 chr5ptel1M 808996 AAAGTGGATGCACGGTGTAGTTGCCCTTTGAGTA--TAGTTCCAAATAAC 809043 v v v --- i v iv-- v -- v v i vi C L1ME5_3end#LI 366 ATAGGGTATGC---GTATACTTAA--TTTGACTAAGTACTGCCAGATTGC 322 chr5ptel1M 809044 TG---AGAATGGTTGGATCAGTTCAGAACTCC----AATACTACATTAGG 809086 v--- i v i ii v - ---- ii v i v C L1ME5_3end#LI 321 TCTCCAGAATGGCTGCACCAGTCTACA-CTCCCACCAGCAGTGCATGAGG 273 chr5ptel1M 809087 TGTTTCAATTTTCCC-TGTCTTC---AACATTTATCGCTTTACTTTTTTG 809132 - i v ? i -ii i --- i iv ii v v vvi v C L1ME5_3end#LI 272 -GTTCCTATNTCCCCACATCCTCGCCAACACTTGGCATTATCCAGCTTTC 224 chr5ptel1M 809133 TCATATTGGCCAATCTGATAGGGGTGAAGTGGTATCTCAGAGTTGTTTTA 809182 v v v i i v i i vv C L1ME5_3end#LI 223 TAATTTTTGCCAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTA 174 chr5ptel1M 809183 ATTTGCATTTCTTTAATCA--AGTGATTTGGAGCACTTCTTCATTTGTCT 809230 i i i -- i v v ii v ii C L1ME5_3end#LI 173 ATTTGCATTTCTCTGATTACTAATGAGTTTGAGCATCTCTTCATATGCTT 124 chr5ptel1M 809231 AGAGAAAGCCTT---GATTATTTCATTTGAAATCTGCCTGATCATATCCT 809277 --- vv --- i vii v i v vi v C L1ME5_3end#LI 123 ---GTTAGCCTTTCGGGTTTCCTCTTCTGTAAATTGCCTGTTCATATCCT 77 chr5ptel1M 809278 TTG---ATTTATCTATTGGGGAGTAAGTTTTATTCTTATAAATTTG 809320 --- v vv?vv i v i vi C L1ME5_3end#LI 76 TTGCCCATTTTTCTATTGGGGTTNCCGTCTTTTTCTTGTTGATTTG 31 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 33.81 CpG sites = 50, Kimura (unadjusted) = 34.23 Transitions / transversions = 1.04 (50/48) Gap_init rate = 0.05 (19 / 371), avg. gap size = 1.79 (34 / 19) 183 17.24 0.00 0.00 chr5ptel1M 810061 810089 (189911) C MIRb#SINE/MIR (29) 239 211 m_b238s601i9 9411 chr5ptel1M 810061 TATTATGTGCCAGGTGCTGTGTTAAGTGC 810089 i ii i i C MIRb#SINE/MIR 239 TACTATGTGCCAGGCACTGTGCTAAGCGC 211 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 16.62 CpG sites = 5, Kimura (unadjusted) = 21.14 Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 202 21.35 0.00 9.62 chr5ptel1M 810387 810443 (189557) L2d_3end#LINE/L2 449 500 (16) m_b238s601i10 9412 chr5ptel1M 810387 CACGGCTTGCCCAGGACTTAACTGCTGTGCAAATATTAGGTGCTTAATAA 810436 i -- i v --- v v v v i i L2d_3end#LINE 449 CACAGC--GCCTAGCAC---AGTGCTGAGCACATAGTAGGCGCTCAATAA 493 chr5ptel1M 810437 ATGTTTG 810443 ii L2d_3end#LINE 494 ATACTTG 500 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 22.63 CpG sites = 6, Kimura (unadjusted) = 25.13 Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.09 (5 / 56), avg. gap size = 1.00 (5 / 5) 240 31.99 4.69 10.44 chr5ptel1M 810836 811027 (188973) C L3#LINE/CR1 (7) 4092 3911 m_b238s601i11 9413 chr5ptel1M 810836 TTACAGGATCTCTCAATTGGAAGTG-CCTTTGTGGCTATGCAGCCCAA-G 810883 i i vv i v - v v ii vi i -v C L3#LINE/CR1 4092 TCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCAACC 4043 chr5ptel1M 810884 TAACACTTGA-ACAAGAATCCCTGTATTTTACAGC-CCTCTGTAAAGGGA 810931 vv iiii -i i ---- i i -i i ------- C L3#LINE/CR1 4042 TCCCATCCAATGCAGGAATCCC----TTCTACAACATCCCT-------GA 4004 chr5ptel1M 810932 AAAGGAGCCCTCCAG-CTTTACTAGGA-ACCTCCCAAGAGACAGAACTCT 810979 v vi i v - i i v i - -- v i iivv C L3#LINE/CR1 4003 CAAGTGGTCATCCAGCCTCTGCTTGAACACCTCC--AGTGACGGGGAGCT 3956 chr5ptel1M 810980 GCCTCTTTCCACTTCCCAAGGCAGTTCAGTC---TTTGAAATGGTTCTCA 811026 vv ------ i ? i ii v --- vii ii i v C L3#LINE/CR1 3955 CACT------ACCTCNCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGA 3912 chr5ptel1M 811027 T 811027 C L3#LINE/CR1 3911 T 3911 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.31 CpG sites = 34, Kimura (unadjusted) = 43.43 Transitions / transversions = 1.62 (34/21) Gap_init rate = 0.14 (26 / 191), avg. gap size = 1.08 (28 / 26) 407 25.71 0.81 5.93 chr5ptel1M 811110 811233 (188767) C MIRc#SINE/MIR (141) 127 10 m_b238s601i12 9414 chr5ptel1M 811110 CTGAGG-TAATTGGGGTTAAGTGACTTGCCCTGGGTCACAGAGCTAAGAA 811158 - v vv i vi v i--- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG--- 81 chr5ptel1M 811159 GTACTAAGTGCCTGAGGCCAGATTTGACCTCAGTACTTCCTGACTTCGGG 811208 ---- v v v vi i i v i vv i ii C MIRc#SINE/MIR 80 ----TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr5ptel1M 811209 GCTGGTGCTGTATCCACTGTGCTAC 811233 v ii v v ii i C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.45 CpG sites = 15, Kimura (unadjusted) = 31.68 Transitions / transversions = 1.00 (15/15) Gap_init rate = 0.07 (8 / 123), avg. gap size = 1.00 (8 / 8) 274 28.71 5.26 1.01 chr5ptel1M 812104 812198 (187802) C MIR3#SINE/MIR (29) 179 81 m_b238s601i13 9415 chr5ptel1M 812104 GGAAATGTTCCTAAAGACCATCTACTTCAACACT-TC-TTTGGGAGGTGA 812151 iv vi i i i v i v i- - viv i C MIR3#SINE/MIR 179 GGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGA 130 chr5ptel1M 812152 GAAATTCTGAGGTCTAGAAAGGAAAAGGAGCTTGCCTAA--TCAT-CAGC 812198 i v- i i i vi vii i -- i- C MIR3#SINE/MIR 129 GGAAA-CTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGC 81 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.89 CpG sites = 18, Kimura (unadjusted) = 37.89 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.05 (5 / 94), avg. gap size = 1.20 (6 / 5) 229 27.57 6.82 1.08 chr5ptel1M 814741 814828 (185172) C L2a_3end#LINE/L2 (0) 517 425 m_b239s601i0 9416 chr5ptel1M 814741 ATTGATTTTATCAACAAGCATTTCAATAATTTCTTAGTATGTGTC---CC 814787 v ivv ii - v i viv i v i --- v C L2a_3end#LINE 517 ATTCATTCATTCAACAAATATTT-ATTGAGCGCCTACTATGTGCCAGGCA 469 chr5ptel1M 814788 CTG--CCAAGCCCTGAGGACACAA-GGAGAACAAAACAAACAAA 814828 -- i i v i i i-i v i C L2a_3end#LINE 468 CTGTTCTAGGCGCTGGGGATACAGCAGTGAACAAAACAGACAAA 425 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 33.43 CpG sites = 14, Kimura (unadjusted) = 35.23 Transitions / transversions = 1.40 (14/10) Gap_init rate = 0.05 (4 / 87), avg. gap size = 1.75 (7 / 4) 46 0.00 0.00 0.00 chr5ptel1M 814994 815032 (184968) (CA)n#Simple_repeat 1 39 (0) c_b239s251i0 9417 chr5ptel1M 814994 CACACACACACACACACACACACACACACACACACACAC 815032 (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACAC 39 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 198 30.41 5.08 2.48 chr5ptel1M 818169 818286 (181714) C L2#LINE/L2 (1567) 1515 1395 m_b239s601i1 9418 chr5ptel1M 818169 TTTTTTCTGTAAAA-ATGAA-TAAGGTTCTTAGTTGAGAGAGTTGAGGG- 818215 i v i - v -i iv i i --- i- C L2#LINE/L2 1515 TTTTCTCAGTGAAATAGGAAGCAAGGTCATCAGCTGAGAG---TGAGGAT 1469 chr5ptel1M 818216 -AGGGAAGCAATG--AAAGGTTTGAGGAGGGGTGAACAGGTTTGGGAGAT 818262 -i i vii --ii i iv iv v ii v v C L2#LINE/L2 1468 AGGGGAGGAGGTGTTGGAGGTTTGAGGAGAGAGGAGAAGGTGTGAAATAG 1419 chr5ptel1M 818263 CTGCTGTGGGAAGTGGGAGAGTGA 818286 ii iivv ii C L2#LINE/L2 1418 TCGTCTAGGAGAGTGGGAGAGTGA 1395 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 39.71 CpG sites = 24, Kimura (unadjusted) = 41.29 Transitions / transversions = 2.18 (24/11) Gap_init rate = 0.07 (8 / 117), avg. gap size = 1.12 (9 / 8) 192 25.61 7.32 4.76 chr5ptel1M 819728 819809 (180191) OldhAT1#DNA/hAT-Ac 2062 2145 (697) m_b239s601i2 9419 chr5ptel1M 819728 GCTCACTATCCTTTGGTGCA--GAAGCAC-TGGCT--CTTGGACCTTC-A 819771 i v iii vi -- i i- v -- i i-v OldhAT1#DNA/h 2062 GCCCTCTATTTCTGAGTGCAACGGAGCATATGGATAGCTTGGGCCTTTTC 2111 chr5ptel1M 819772 TCCTTACCTCAGAATCCCAGGGGCAGAACTACCCTGAC 819809 v i ? i i ---- ? i v i OldhAT1#DNA/h 2112 TCATCANCCCAGAGT----GGGGCAGNACTATCCAGGC 2145 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 33.95 CpG sites = 14, Kimura (unadjusted) = 33.95 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.10 (8 / 81), avg. gap size = 1.25 (10 / 8) 14 19.99 2.38 2.38 chr5ptel1M 822299 822340 (177660) (GTT)n#Simple_repeat 1 42 (0) m_b239s252i0 9420 chr5ptel1M 822299 GTT-TTTTTGTTGTTGTTGTTATTCATGTTGAGTGTATTTGTT 822340 - v i vv -v vv (GTT)n#Simple 1 GTTGTTGTTGTTGTTGTTGTTGTTGTTGTTG-TTGTTGTTGTT 42 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.05 (2 / 41), avg. gap size = 1.00 (2 / 2) 315 28.37 1.49 7.94 chr5ptel1M 822389 822522 (177478) C MIRc#SINE/MIR (141) 127 2 m_b239s601i3 9421 chr5ptel1M 822389 CTGAGGC-AATTGGGGTTCAGTGACTAGCCCAGGGCCACACTGTTAGGAT 822437 -v vv i v v i i v i --- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG--- 81 chr5ptel1M 822438 GTGTTAAGTGTCTGAAGCCAGATTTGAACTCTAGTCTTCCTGAGTTTGGG 822487 ---- v v iv vi i i i vi v iiii C MIRc#SINE/MIR 80 ----TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr5ptel1M 822488 GCTGGTGCTGTAACCTCTGC-CCACCTAGCTGCCCC 822522 v ii v vv v - ---i i C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTGCACCAC---ACTGCCTC 2 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 34.64 CpG sites = 18, Kimura (unadjusted) = 35.89 Transitions / transversions = 1.06 (18/17) Gap_init rate = 0.09 (12 / 133), avg. gap size = 1.00 (12 / 12) 224 24.09 3.26 18.75 chr5ptel1M 823139 823230 (176770) MIR3#SINE/MIR 112 191 (17) m_b239s601i4 9422 chr5ptel1M 823139 CCTTGGGCTTCAGTTTTCTCACCAGTAAAAAGTGGGGGAGGAAAAGGGGA 823188 ii i i i v -- i ------------- MIR3#SINE/MIR 112 CTCTGGGCCTCAGTTTCCTCATCTGTAAAA--TGAGG------------- 146 chr5ptel1M 823189 GGGTTGGTCTAA--GAT-TCTCAGGTCCCTCTTAACTTTACCACT 823230 v i-- - v iii i i iv i MIR3#SINE/MIR 147 GGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATT 191 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.60 CpG sites = 14, Kimura (unadjusted) = 29.60 Transitions / transversions = 3.50 (14/4) Gap_init rate = 0.19 (17 / 91), avg. gap size = 1.06 (18 / 17) 14 19.17 0.00 2.70 chr5ptel1M 824324 824361 (175639) (AATAAAT)n#Simple_repeat 1 37 (0) m_b239s252i1 9423 chr5ptel1M 824324 AATAATTATTTTTTAATAAATAATAAATAAAAGAATAA 824361 v v vvv v - (AATAAAT)n#Si 1 AATAAATAATAAATAATAAATAATAAATAATA-AATAA 37 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 48 5.72 5.48 0.00 chr5ptel1M 825650 825722 (174278) (AC)n#Simple_repeat 1 77 (0) c_b239s251i1 9424 chr5ptel1M 825650 ACACACACACACA-AGACACA-ACACACACA-ACACA-AGACACACACAC 825695 - v - - - v (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50 chr5ptel1M 825696 ACACAGACACAGACACACACACACACA 825722 v v (AC)n#Simple_ 51 ACACACACACACACACACACACACACA 77 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.06 (4 / 72), avg. gap size = 1.00 (4 / 4) 14 13.69 3.12 0.00 chr5ptel1M 825775 825806 (174194) (GGAGG)n#Simple_repeat 1 33 (0) m_b239s252i3 9425 chr5ptel1M 825775 GGAGGGG-GGGAAGGGCAGGGGAGGGGTCGGGA 825806 - i v vv (GGAGG)n#Simp 1 GGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGA 33 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 18 15.80 1.75 7.41 chr5ptel1M 826676 826732 (173268) (CCGC)n#Simple_repeat 1 54 (0) m_b239s252i4 9426 chr5ptel1M 826676 CCGCTCCGTCCGCCCGCCC-CCCTCCTGCGCCTCTCCCCCGCCCTGCCTG 826724 - i - v i - v i v - i (CCGC)n#Simpl 1 CCGC-CCGCCCGCCCGCCCGCCCGCCCGC-CCGCCCGCCCGCCC-GCCCG 47 chr5ptel1M 826725 TCCCGCCC 826732 - (CCGC)n#Simpl 48 -CCCGCCC 54 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.09 (5 / 56), avg. gap size = 1.00 (5 / 5) 12 14.12 3.03 3.03 chr5ptel1M 827597 827629 (172371) (GCCCTG)n#Simple_repeat 1 33 (0) m_b239s252i5 9427 chr5ptel1M 827597 GCCCTGGTCCTGGCCCTGTAGC-GGCCCATGGCC 827629 i vvv - - (GCCCTG)n#Sim 1 GCCCTGGCCCTGGCCCTGGCCCTGGCCC-TGGCC 33 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.06 (2 / 32), avg. gap size = 1.00 (2 / 2) 408 33.12 3.73 0.60 chr5ptel1M 828429 828589 (171411) C MIR3#SINE/MIR (3) 205 40 m_b239s601i5 9428 chr5ptel1M 828429 TCAGAAAATCTTATCAT-TTATACGTGGAATATGTCATAGAAATCAACTA 828477 v i v vv - i v vv vivii v i v C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTA 156 chr5ptel1M 828478 ACACAATTCTTTCATCTTTCCAAAAAAGAAACTGAGACCCAGAAAGGTTA 828527 iiv ii ii i v vi vi i i i v C MIR3#SINE/MIR 155 GTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGA 106 chr5ptel1M 828528 --TGAATTACCCAAAGTCAGATAGGTGGTGAGTGGCAGAATGAGCATTCA 828575 -- v i i v i v?i v iivi v i - C MIR3#SINE/MIR 105 AGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACT-A 57 chr5ptel1M 828576 GA---CAAACTTTCTGA 828589 --- iiii i C MIR3#SINE/MIR 56 GAACCCAGGTCTCCTGA 40 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 44.48 CpG sites = 31, Kimura (unadjusted) = 45.67 Transitions / transversions = 1.41 (31/22) Gap_init rate = 0.03 (4 / 160), avg. gap size = 1.75 (7 / 4) 369 33.07 4.32 2.11 chr5ptel1M 828494 828632 (171368) C MIRc#SINE/MIR (125) 143 2 m_b239s601i6 9428 chr5ptel1M 828494 TTTCCAAA-AAAGAAACTGAGACCCAGAAAGGTTA--TGAATTACCCAAA 828540 v i -i i i i i -- v i i C MIRc#SINE/MIR 143 TTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAG 94 chr5ptel1M 828541 GTCAGATAGGTGGTGAGTGGCAGAATGAGCATTCAGA--CAAA-CTTTCT 828587 v i v i i iivi v i ii -- ii- i C MIRc#SINE/MIR 93 GTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCT 44 chr5ptel1M 828588 GAGATATCATATATGGTTCCCTTCATACTATAGCATATTAGCTTC 828632 -- ivi vi vii v i ivi ii v i i - i C MIRc#SINE/MIR 43 --GACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACT-GCCTC 2 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 44.45 CpG sites = 33, Kimura (unadjusted) = 47.46 Transitions / transversions = 2.75 (33/12) Gap_init rate = 0.05 (7 / 138), avg. gap size = 1.29 (9 / 7) 22 3.81 0.00 0.00 chr5ptel1M 829706 829732 (170268) (A)n#Simple_repeat 1 27 (0) m_b239s252i6 9429 chr5ptel1M 829706 AAATAAAAAAAAAAAAAAAAAAAAAAA 829732 v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAA 27 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 285 31.72 4.15 6.91 chr5ptel1M 829736 829928 (170072) C MIR#SINE/MIR (73) 189 2 m_b239s601i7 9430 chr5ptel1M 829736 ATTT--TCTTGGCAATGATACT-TGAAATGGTTTGCTATTTTCTTCTGAC 829782 -- i vi ii iv - ii i v -i v iv --- C MIR#SINE/MIR 189 ATTTAATCCTCACAACAACCCTATGAGGTAGGT-ACTATTATTATC---C 144 chr5ptel1M 829783 TCATTGAAGAGATGAAGTA-TTGTGGCAAACAGAG-TTAAGTGTCTTGCC 829830 i vv v i v -i v v v - iv C MIR#SINE/MIR 143 CCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCC 94 chr5ptel1M 829831 TAGAGTCACAAACCTAGAAGGGATTGGAGGCCAGATTTGTACTCACAAAA 829880 i ii v v v i vivii v vi i v i ------ C MIR#SINE/MIR 93 CAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCC------ 50 chr5ptel1M 829881 AAGGAGTCTCTGATTCCAG-GCTTGCTACT-TTATCCATTGCACTA-ACT 829927 i v -- ii - ii - i - v i iii - C MIR#SINE/MIR 49 AGGCAG--TCTGGCTCCAGAGCCCG-TGCTCTTAACCACTATGCTATACT 3 chr5ptel1M 829928 G 829928 C MIR#SINE/MIR 2 G 2 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 40.61 CpG sites = 34, Kimura (unadjusted) = 42.59 Transitions / transversions = 1.48 (34/23) Gap_init rate = 0.10 (20 / 192), avg. gap size = 1.05 (21 / 20) 337 33.61 2.00 4.79 chr5ptel1M 829782 829931 (170069) C MIRc#SINE/MIR (120) 148 3 m_b239s601i8 9430 chr5ptel1M 829782 CTCATTGAAGAGATGAAGTA-TTGTGGCAAACAGAG-TTAAGTGTCTTGC 829829 i vv v i v -i v vv v - v C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr5ptel1M 829830 CTAGAGTCACAAACCTAGAAGGGATTGGAGGCCAGATTTGTACTCACAAA 829879 i ii v v v i vivii v vi i i v i ----- C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCC----- 54 chr5ptel1M 829880 AAAGGAGTCTCTGATTCCAGGCTTGCTACTTTATCCATTGCACTA-ACTG 829928 -- vv ii i i iiiiv i i v i i - C MIRc#SINE/MIR 53 --AGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTG 6 chr5ptel1M 829929 CTT 829931 i C MIRc#SINE/MIR 5 CCT 3 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 44.55 CpG sites = 27, Kimura (unadjusted) = 45.86 Transitions / transversions = 1.29 (27/21) Gap_init rate = 0.07 (10 / 149), avg. gap size = 1.00 (10 / 10) 1480 27.66 4.40 2.60 chr5ptel1M 831073 831640 (168360) C L1ME5_3end#LINE/L1 (297) 644 67 m_b239s551i1 9431 chr5ptel1M 831073 TCCTGGTTCT-GCTCATTTCGCTCAGCATCA-GTTCATGTAAGTCTCGCC 831120 i v -i iv i ii - -- v vii ii C L1ME5_3end#LI 644 TTCTGTTTCTTACTTTTTTCACTCAGCACTATGTT--TTTAAGATCCATC 597 chr5ptel1M 831121 AATCCT-CTCTGTATTCGTCCTGCTGGTCATTTCTTACAGAACAATAATA 831169 v vi - v i v i iv iiv iii v v vvvv i C L1ME5_3end#LI 596 CATGTTGCTATGTGTACATCTAGTCCGTTGCTTCTAACTGCTGCATAGTA 547 chr5ptel1M 831170 TTCCATAAT--------ACCACAATTTACTCAACCATTCTCCAATGGATG 831211 i ii -------- v ii v i v vv C L1ME5_3end#LI 546 CTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCAGTGATG 497 chr5ptel1M 831212 GGCATCCATTCATT--TTCCAGCTTCTGGCCACTACAAACAGGGCTGCCA 831259 i i v--i --i i i iv i iv v C L1ME5_3end#LI 496 GACACCCAG--GTTGCCTCCAACTCCCCGCCACCACAAACAACGCTGCAA 449 chr5ptel1M 831260 CAAGCATTTTGGCACATACAGGTCCCTTTC----CCTTTTTTAATATCTC 831305 ii i ii ---- i v i v---- v v v iv i C L1ME5_3end#LI 448 TGAACATCCT----CGTACATGTCCCCTTATGGACCTGTGTGAGAATTTC 403 chr5ptel1M 831306 TTTGGGGTATAAGCCCAGTAGAGACACTGCTGGATCAAAGGGTATGCACA 831355 i vi v v iv i i v --- C L1ME5_3end#LI 402 TTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATGC--- 356 chr5ptel1M 831356 GTTTGATAACTT--TTTGGGCA--TAGTTCCAAATTGCTCTCCAGAATGG 831401 --- - -- ivi -- v v i C L1ME5_3end#LI 355 GT---ATA-CTTAATTTGACTAAGTACTGCCAGATTGCTCTCCAGAATGG 310 chr5ptel1M 831402 CTGGATGTATTCACAATTCCACCAACAATGTATCAGTGTCCCTGTTTTCC 831451 v ivvi ii v i i i i v v i i ? i C L1ME5_3end#LI 309 CTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATNTCCC 260 chr5ptel1M 831452 CACATCCCCTCCAACATTCTGCATTATCTTTCCCTGTCATTCTGGCCAAT 831501 i v i iv ivv ii v v i v i C L1ME5_3end#LI 259 CACATCCTCGCCAACACTTGGCATTATCCAGCTTTCTAATTTTTGCCAGT 210 chr5ptel1M 831502 CTGACAGGTGTATAGTGGTATCTCAGAGTTGTCTTAATTTGCATTTCTCT 831551 i i v i vv i C L1ME5_3end#LI 209 CTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATTTCTCT 160 chr5ptel1M 831552 GATCAATAGTGATTTGGAAC-TC---TCATATGAATAGTAATAGTTTTAA 831597 i v i v v i - --- vv iv iivv ivii C L1ME5_3end#LI 159 GATTACTAATGAGTTTGAGCATCTCTTCATATGCTTGTTAGCCTTTCGGG 110 chr5ptel1M 831598 TTTCATCATCTGAAAATTGTCTGTTCATATCCTTTGACCATTT 831640 v v v i v C L1ME5_3end#LI 109 TTTCCTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCCATTT 67 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 34.71 CpG sites = 85, Kimura (unadjusted) = 35.28 Transitions / transversions = 1.25 (85/68) Gap_init rate = 0.04 (25 / 567), avg. gap size = 1.60 (40 / 25) 1506 25.21 3.77 1.85 chr5ptel1M 831164 831640 (168360) C L1ME3G_3end#LINE/L1 (376) 548 63 m_b239s551i2 9431 chr5ptel1M 831164 ATAATATTCCATA--------ATACCACAATTTACTCAACCATTCTCCAA 831205 i -------- i i i i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr5ptel1M 831206 TGGATGGGCATCCA--TTCATTTTCCAGCTTCTGGCCACTACAAACAGGG 831253 v i ii -- v-- ii i v i i iv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTG--TTTCCAATTTTTCGCTATTACAAACAATG 451 chr5ptel1M 831254 CTGCCACAAGCATTTTGGCACATACAGGTCCCTTT--CCCTTTTTTAATA 831301 v ii i ii v i i ?-- i v --v v v viv i C L1ME3G_3end#L 450 CTGCAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTA 403 chr5ptel1M 831302 TCTCTTTGGGGTATAAGCCCAGTAGAGACACTGCTGGATCAAAGGGTATG 831351 i ? i i v v? ? v v iv i i C L1ME3G_3end#L 402 TTTCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATG 353 chr5ptel1M 831352 CACAGTTTGATAACTTTT--TGGGCATAGTTCCAAATTGCTCTCCAGAAT 831399 i v --- v -- i -- v v i i ? C L1ME3G_3end#L 352 CGCATTTT---AAATTTTAATAG--ATACTGCCAAATTGCCCTCCAAAAN 308 chr5ptel1M 831400 GGCTGGATGTATTCACAATTCCACCAACAATGTATCAGTGTCCCTGTTTT 831449 v ivv i v i i i v v v i i C L1ME3G_3end#L 307 GGCTGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTC 258 chr5ptel1M 831450 CCCACATCCCCTCCAACATTCTGCATTATCTTTCCCTGTCATTCTGGCCA 831499 i i v i ?vii vv? ii vvv i v C L1ME3G_3end#L 257 CCCACACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCA 208 chr5ptel1M 831500 ATCTGACAGGTGTATAGTGGTATCTCAGAGTTGTCTTAATTTGCATTTCT 831549 ii v v i vv i i C L1ME3G_3end#L 207 ATCTGATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCC 158 chr5ptel1M 831550 CTGATCAATAGTGATTTGGAAC----TCTCATATGAATAGTAATAGTTTT 831595 i v vv v i ---- i vv v iiivi v C L1ME3G_3end#L 157 CTGATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTG 108 chr5ptel1M 831596 AATTTCATCATCTGAAAATTGTCTGTTCATATCCTTTGACCATTT 831640 v v v vi i v C L1ME3G_3end#L 107 TATTTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTT 63 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 30.79 CpG sites = 63, Kimura (unadjusted) = 31.75 Transitions / transversions = 1.15 (63/55) Gap_init rate = 0.03 (14 / 476), avg. gap size = 1.93 (27 / 14) 15 8.85 0.00 0.00 chr5ptel1M 832462 832485 (167515) (TGC)n#Simple_repeat 1 24 (0) m_b239s252i7 9432 chr5ptel1M 832462 TGCTGCTGCTGCTGCTACTTCTGC 832485 i v (TGC)n#Simple 1 TGCTGCTGCTGCTGCTGCTGCTGC 24 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 16 24.33 0.00 2.04 chr5ptel1M 832735 832784 (167216) (TTTTA)n#Simple_repeat 1 49 (0) m_b239s252i8 9433 chr5ptel1M 832735 TTTTATTTTATTTTTCTTTCATTTATTTAATTTGCATGTAATTATGTTTT 832784 vi vv v -i v v v i (TTTTA)n#Simp 1 TTTTATTTTATTTTATTTTATTTTATTTTATTT-TATTTTATTTTATTTT 49 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.02 (1 / 49), avg. gap size = 1.00 (1 / 1) 309 24.29 0.00 1.43 chr5ptel1M 832940 833010 (166990) MIR#SINE/MIR 147 216 (46) m_b239s601i9 9434 chr5ptel1M 832940 TAAAAATAATATCTACCTTCTAGATTTGTTTGTGAGGATCAAATGAATCA 832989 v i i iv iv - i i i MIR#SINE/MIR 147 TAATAATAGTACCTACCTCATAGGGTTGTT-GTGAGGATTAAATGAGTTA 195 chr5ptel1M 832990 ACGTCTGTAAAGTACTTTGAA 833010 iiiv ii v MIR#SINE/MIR 196 ATACATGTAAAGCGCTTAGAA 216 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 28.22 CpG sites = 12, Kimura (unadjusted) = 30.60 Transitions / transversions = 2.40 (12/5) Gap_init rate = 0.01 (1 / 70), avg. gap size = 1.00 (1 / 1) 278 30.61 1.01 1.01 chr5ptel1M 832949 833047 (166953) MIRc#SINE/MIR 166 264 (4) m_b239s601i10 9434 chr5ptel1M 832949 TATCTACCTTCTAGATTTGTTTGTGAGGATCAAATGAATCAACGTCTGT- 832997 ii ivi iv - ivi i v - MIRc#SINE/MIR 166 TGCCTACCTCACAGGGTTGTT-GTGAGGATCAAATGAGATAATGTATGTG 214 chr5ptel1M 832998 AAAGTACTTTGAAAAACTTAAAAACCTTCAGAAACATTAGGTACTAGTAT 833047 ii v viv ivv vi v ii v ?ii v MIRc#SINE/MIR 215 AAAGCGCTTTGTAAACTGTAAAGTGCTATACAAATGTAAGGNGTTATTAT 264 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 38.97 CpG sites = 17, Kimura (unadjusted) = 40.94 Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.02 (2 / 98), avg. gap size = 1.00 (2 / 2) 689 21.86 10.82 0.94 chr5ptel1M 835617 835810 (164190) MIR#SINE/MIR 50 262 (0) m_b239s601i11 9435 chr5ptel1M 835617 GAGTTCAAA-CCCAGCCCC-CGACCTA-TGG--GGGTGACCCTGGGCAAG 835661 i i - i i i- v i - i -- v i MIR#SINE/MIR 50 GGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAG 99 chr5ptel1M 835662 TCACTTCAACCATT---TGCTTCAGTTTCCTCAGTTGTAAAATGGGGGTA 835708 i - vi --- i vi i MIR#SINE/MIR 100 TTACTT-AACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATA 148 chr5ptel1M 835709 ACGACAGCATCTACCACCCAGGATAGTTGTGAGGATCAAATGAGATAATA 835758 ii i i i v vi i v i v MIR#SINE/MIR 149 ATAATAGTACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATA 198 chr5ptel1M 835759 ATTGTAAAGTGTTT-------T-----GCACACAATAATCACTATTTGAA 835796 vv i i ------- ----- i i v i vvv i MIR#SINE/MIR 199 CATGTAAAGCGCTTAGAACAGTGCCTGGCACATAGTAAGCGCTCAATAAA 248 chr5ptel1M 835797 -GTTAACTTATTATT 835810 - i - MIR#SINE/MIR 249 TGTTAGC-TATTATT 262 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 23.75 CpG sites = 28, Kimura (unadjusted) = 26.61 Transitions / transversions = 2.00 (28/14) Gap_init rate = 0.05 (10 / 193), avg. gap size = 2.30 (23 / 10) 28 0.00 0.00 0.00 chr5ptel1M 836520 836549 (163451) (A)n#Simple_repeat 1 30 (0) m_b239s252i9 9436 chr5ptel1M 836520 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 836549 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 30 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 244 32.63 7.37 0.00 chr5ptel1M 837110 837204 (162796) L2a_3end#LINE/L2 395 496 (21) m_b239s601i12 9437 chr5ptel1M 837110 TGAAATACAAGTTCCTTGAGG--AGAGGCCT--GTTTGCTTT-TTAATTG 837154 ii ii i v -- i i i -- i i - v i L2a_3end#LINE 395 TAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTCTGTTTTGTTCACTG 444 chr5ptel1M 837155 TT--ATCCACTGCACTAAATGAAGTATCTGGCATATGGTATGCACTTGAT 837202 i -- v v i iv iviv ii i i v i ii L2a_3end#LINE 445 CTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGGCGCTCAAT 494 chr5ptel1M 837203 AA 837204 L2a_3end#LINE 495 AA 496 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 42.42 CpG sites = 23, Kimura (unadjusted) = 46.63 Transitions / transversions = 2.88 (23/8) Gap_init rate = 0.04 (4 / 94), avg. gap size = 1.75 (7 / 4) 22 12.93 2.33 0.00 chr5ptel1M 837700 837742 (162258) (AAAAAGA)n#Simple_repeat 1 44 (0) m_b239s252i10 9438 chr5ptel1M 837700 AAAAAGAAAAAAG-AAAACGGAGAAAGAAAAAAAAAAAAAGGAA 837742 - v i i i i (AAAAAGA)n#Si 1 AAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAA 44 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.02 (1 / 42), avg. gap size = 1.00 (1 / 1) 12 28.53 3.64 0.00 chr5ptel1M 838020 838074 (161926) (AAAATG)n#Simple_repeat 1 57 (0) m_b239s252i12 9439 chr5ptel1M 838020 AAAAT-CAAATGAAACCGGAATGGGAAAAAAAAAGAAAAACGAACAT-AA 838067 -v vi i vv i vi vi i v - (AAAATG)n#Sim 1 AAAATGAAAATGAAAATGAAAATGAAAATGAAAATGAAAATGAAAATGAA 50 chr5ptel1M 838068 AATGAAA 838074 (AAAATG)n#Sim 51 AATGAAA 57 Matrix = Unknown Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.04 (2 / 54), avg. gap size = 1.00 (2 / 2) 53 37.95 0.73 1.47 chr5ptel1M 840134 840407 (159593) (CT)n#Simple_repeat 1 272 (0) m_b239s252i13 9440 chr5ptel1M 840134 CTATCTCTATTTCTTCCTCTCTATTCCAATCTCTATGTTTCTCTATTTTT 840183 v v i ii v ii vv v v i v i i (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chr5ptel1M 840184 TTCTCTTTCTCTATCATGCCTTTTTCTCTCTCTCTTTCTCTATTTCCCTA 840233 i i v - vi i i i v i i v (CT)n#Simple_ 51 CTCTCTCTCTCTCTC-TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 99 chr5ptel1M 840234 TATTTTCCTGTTTCATTCTCTTTTTTGATC-CTTTCTTTCACTCTGTGGC 840282 v i ii v i vi i i ivv - i i v v vv (CT)n#Simple_ 100 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 149 chr5ptel1M 840283 TCTCCTTGGCATGCATTTTCTCTCTGGGTCCATGTCTGTCTGTCTCTCTC 840332 ii vv - - vi i vvv iv v v v (CT)n#Simple_ 150 TCTCTCTCTC-T-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 197 chr5ptel1M 840333 ACTGTGTCTCTCTCACACACTCTCTATCTATCTATGTCTTTTTCTCTTTC 840382 v v v v v v v v v v i i i (CT)n#Simple_ 198 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 247 chr5ptel1M 840383 TTTCTCACTCTGCT-TTTCTCTCCCT 840407 i v - - i i (CT)n#Simple_ 248 TCTCTCTCTCT-CTCTCTCTCTCTCT 272 Matrix = Unknown Transitions / transversions = 0.88 (37/42) Gap_init rate = 0.02 (6 / 273), avg. gap size = 1.00 (6 / 6) 44 0.00 0.00 0.00 chr5ptel1M 840490 840527 (159473) (TC)n#Simple_repeat 1 38 (0) c_b239s251i2 9441 chr5ptel1M 840490 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 840527 (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 38 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 14 14.91 5.41 0.00 chr5ptel1M 840597 840633 (159367) (TTCTCA)n#Simple_repeat 1 39 (0) m_b239s252i14 9442 chr5ptel1M 840597 TTCTCATTCT--TTCTCATTCACATTCACTCTTTCATTC 840633 -- v v vi i (TTCTCA)n#Sim 1 TTCTCATTCTCATTCTCATTCTCATTCTCATTCTCATTC 39 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.03 (1 / 36), avg. gap size = 2.00 (2 / 1) 13 9.10 11.43 0.00 chr5ptel1M 840600 840634 (159366) (TCAT)n#Simple_repeat 1 39 (0) m_b239s252i15 9442 chr5ptel1M 840600 TCATTCTTTC--TCATTCA--CATTCACTCTTTCATTCA 840634 v -- -- i v (TCAT)n#Simpl 1 TCATTCATTCATTCATTCATTCATTCATTCATTCATTCA 39 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.06 (2 / 34), avg. gap size = 2.00 (4 / 2) 63 37.35 1.38 0.00 chr5ptel1M 840997 841285 (158715) (TC)n#Simple_repeat 1 293 (0) m_b239s252i16 9443 chr5ptel1M 840997 TCTCTCACT-TTTTTCTTTTTCTCTCTAATTCTCTGTTTCTTCCTCTTTT 841045 v - i i i i vvi v i ii i i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr5ptel1M 841046 TCAAACTCTCTCTTTGTCTTGTTCTCTCTTTTTCTCTCTCTCTGTATCTG 841095 vvv i v ivi i i v v v (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chr5ptel1M 841096 TTTCTCTGTGTCTGTCTTTTTTTCTGTTTGTCTCTGTTTCTATTTCTCTC 841145 i v v v i i i v i v v i v i (TC)n#Simple_ 101 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 150 chr5ptel1M 841146 TATTTCTATCTCTGTCTCTATTTCTTTGACCCTGTCTTTATTTCTCTGTC 841195 v i v v v i i vv i v i v i v (TC)n#Simple_ 151 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 200 chr5ptel1M 841196 TTTCTCTTGCTTTTATTCTC-CTCTCTCT-TTTTTGTTTATATCTGTTTC 841243 i iv i ivi - - i i v i v v v i (TC)n#Simple_ 201 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 250 chr5ptel1M 841244 TCTGACTCTC-CTATTACTTTCTCTTTTTTATTTTCTCTCACT 841285 vv - v iv i i i ivi i v (TC)n#Simple_ 251 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 293 Matrix = Unknown Transitions / transversions = 1.10 (44/40) Gap_init rate = 0.01 (4 / 288), avg. gap size = 1.00 (4 / 4) 16 30.69 0.00 3.03 chr5ptel1M 841862 841929 (158071) (AGAA)n#Simple_repeat 1 66 (0) m_b239s252i17 9444 chr5ptel1M 841862 AGAGAGCAAGAAAGGCAAAAAGAAACAGAAAAAAAGGAAGGGTCAGAGAC 841911 i v iv i - - i i iivv i v (AGAA)n#Simpl 1 AGAAAGAAAGAAAGAAAGAAAG-AA-AGAAAGAAAGAAAGAAAGAAAGAA 48 chr5ptel1M 841912 AGACAGACAGAAAAAAAG 841929 v v i (AGAA)n#Simpl 49 AGAAAGAAAGAAAGAAAG 66 Matrix = Unknown Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.03 (2 / 67), avg. gap size = 1.00 (2 / 2) 3087 29.07 2.64 2.77 chr5ptel1M 842701 844328 (155672) L1M5_orf2#LINE/L1 1669 3294 (0) m_b239s551i3 9445 chr5ptel1M 842701 AAGATAATACACTATGATCAAGTAGGATTTATACCAGGAATGCAGGGCTG 842750 i ii i i i v i i L1M5_orf2#LIN 1669 AGGATAATACATCATGACCAAGTGGGGTTTATCCCAGGAATGCAAGGTTG 1718 chr5ptel1M 842751 GTTCAATATTAGGAAAACTATCAATATAATTGGCCATGTTAATAACCAAA 842800 i i v i v v i vi i i i--- L1M5_orf2#LIN 1719 GTTTAACATTCGAAAATCAATCAATGTAATTCACCATATTAACAG---AA 1765 chr5ptel1M 842801 TTAA--CAAAAAACCATATGATCATCTCAATAGATGCAGAAAAAGCATTT 842848 v --vi i L1M5_orf2#LIN 1766 TAAAGGAGAAAAATCATATGATCATCTCAATAGATGCAGAAAAAGCATTT 1815 chr5ptel1M 842849 GATAAAATCCAACATCCATTCCTATTAAAAACACTTGAGAGTATAGGAAT 842898 i i i v iv v iiiv ivv L1M5_orf2#LIN 1816 GACAAAATTCAACACCCATTCATGATAAAAACTCTCAGCAAACTAGGAAT 1865 chr5ptel1M 842899 AAATGGACTTTTCCTTAAAATAATCAGCAGCATCTATTTAAAACCATCAG 842948 i v ivvi i vv i v ivi ivv vv L1M5_orf2#LIN 1866 AGAAGGGAACTTCCTCAACCTGATAAAGGGCATCTACGAAAAACCTACAG 1915 chr5ptel1M 842949 TAAGCATCATATATAATGGAGACAAACTGCAACCATTCCCAATAAGATCT 842998 i? i iv v v ? v ?v v vv v L1M5_orf2#LIN 1916 CNAACATCATACTTAATGGTGAAANACTGAANGCTTTCCCCCTAAGATCG 1965 chr5ptel1M 842999 GGAGTGAAACAAGGTTGCCCACTATCACCGTTACTATTTAATATTGTATT 843048 iii i v i i ? ii v i i i L1M5_orf2#LIN 1966 GGAACAAGACAAGGATGTCCGCTNTCACCACTTCTATTCAACATTGTACT 2015 chr5ptel1M 843049 AGAAACGCTAGCTATAGCAATAAGAGCTGAGAAAGAGATTAAAGGAATAA 843098 i iiiv i vv ivvv i i v v L1M5_orf2#LIN 2016 GGAGGTCCTAGCCAGTGCAATAAGGCAAGAAAAAGAAATAAAAGGCATAA 2065 chr5ptel1M 843099 GAATAGGCAATGAGGAAGCCAAATTATCACTCTTTGCCGATGACATGATG 843148 ii v v v i iiv i i ?i v i v v L1M5_orf2#LIN 2066 AGATTGGAAAGGAAGAAATAAAACTGTCNTTATTCGCAGATGACATGATT 2115 chr5ptel1M 843149 GTATACTTAGAGAACCCCAGAGATTCTGCTAAAAAGTTATTAGAAATAAT 843198 ? v i i ? i v i v ? ii i v L1M5_orf2#LIN 2116 GTNTACGTAGAAAATCCNAAAGAATCTACAAANAAACTACTAGAACTAAT 2165 chr5ptel1M 843199 CCACAACTTTAGCAAAGTTGCTGGTTATAAAATAAACCCACATAAGTCAT 843248 vviii v i i ? v i ii v ivi v i v L1M5_orf2#LIN 2166 AAGTGAATTTAGCAAGGTCGCNGGATACAAGGTCAATATACAAAAATCAA 2215 chr5ptel1M 843249 CAGCATTCTTATATATCACTAACAA--AATCCAACAGTCAGAGTTACAAA 843296 iv i ii ii vi -- ivi v i v i v --? L1M5_orf2#LIN 2216 TTGTATTTCTATATACTAGCAACAAACAATTGGAAAATGAAATTT--NAA 2263 chr5ptel1M 843297 GAGAAATTCCATTTAAAGTAACTATT-GATAATATAAAATATTTGGGAAT 843345 i iv v v i i - i-i v i ? i i L1M5_orf2#LIN 2264 AAACAATACCATTTACAATAGC-ATCAAAAAACATNAAATACTTAGGAAT 2312 chr5ptel1M 843346 CTATCTGCCAAGGAAAAT---CAGAAACTTTATGAGCAAAATTACAGACC 843392 vv iv -- ? --- ii v ? iivvv i i v L1M5_orf2#LIN 2313 AAATCTAACAA--AANATGTGCAAGACCTNTACACTGAAAACTACAAAAC 2360 chr5ptel1M 843393 ACTTTTCACACAAATTAAGTCTGATCTAACCAATTGGAAAAATATTAAAT 843442 i vi v v v ivvv i vi v i i vvv L1M5_orf2#LIN 2361 ATTGCTGAGAGAAATTAAAGAAGACCTAAATAAATGGAGAGATATACCAT 2410 chr5ptel1M 843443 GCTCTTGGATAGGGCGAGCAAATATAATAAAGATGACAATATTACCTAAA 843492 i v v iv viv vi ? v vi v i L1M5_orf2#LIN 2411 GTTCATGGATTGGAAGACTCAATATTGTNAAGATGTCAATTCTCCCCAAA 2460 chr5ptel1M 843493 CTAATCTATTTATTTAGCACTATACCAATCAGACTCCCAAAAAACTATTT 843542 i i vv i iii v v i v iv iii v L1M5_orf2#LIN 2461 TTGATCTATAGATTCAATGCAATCCCAATCAAAATCCCAGCAGGTTTTTT 2510 chr5ptel1M 843543 TAATGACCTAGAAAAAATAACAACAAAGTTCATATGGAAA-ACAAAAGGT 843591 ivv vv v v iv i ivvi i i -i i ii L1M5_orf2#LIN 2511 TGTAGAAATTGACAAGCTGATTCTAAAATTTATATGGAAATGCAAAGGAC 2560 chr5ptel1M 843592 CAAGAAT-TTCAAGGGAATTAATGAAAAAAAAAAAATCAAATGATGGTGG 843640 ? -vi iiv i-v i i -- - v v L1M5_orf2#LIN 2561 CNAGAATAGCCAAAACAATC-TTGAAAAAGAAGAA--CAAA-GTTGGAGG 2606 chr5ptel1M 843641 -CTTAGCTGTACCAGATCT-AAAATTATATTATAGAGCAGCAGTTACCAA 843688 - - vv ? ? - i i - i vi v i L1M5_orf2#LIN 2607 ACTTA-CACTACCNGATNTCAAGACT-TATTATAAAGCTACAGTAATCAA 2654 chr5ptel1M 843689 AACTATTTGGTATTGGC-TAAGGAATAGATTAGTTGATCAGTGGAATAGA 843737 i vi v - - iv i v i i L1M5_orf2#LIN 2655 GACAGTGTGGTATTGGCGTAAGG-ATAGACAAATAGATCAATGGAACAGA 2703 chr5ptel1M 843738 TTAG---GTTCAAGGGACAAAACAG--TCA-ACAAATATAGCAACCTAGT 843781 v --- i ------i i --i - v i ?v ?i ii L1M5_orf2#LIN 2704 ATAGAGAGTCCA------GAAATAGACCCACACATATATGGNCANTTGAT 2747 chr5ptel1M 843782 CTTTGACAAA---CCCAAAG-ATCCCAGGTTTTGGGATAAGAACTTA--C 843825 i ---v ? - vii ---- iv i -- -- L1M5_orf2#LIN 2748 TTTTGACAAAGGTGCCAANGCAATTCAG----TGGGGAAAGGA--TAGTC 2791 chr5ptel1M 843826 TGTTTGATAAAAATTGCTGGGAAAATTGGAAACTAATATGGCAGAAACTA 843875 v ii i viv i v v iiv v i v i L1M5_orf2#LIN 2792 TTTTCAACAAATGGTGCTGGAACAATTGGATATCCATATGGAAAAAAATG 2841 chr5ptel1M 843876 GGCATTGATCCATACTTAACGCCGTACACCAAGATAAGGTCAAAATGGGT 843925 ii?v i i v i v i i v i v iv ? i i- L1M5_orf2#LIN 2842 AANCTCGACCCCTACCTCACACCATACACAAAAATTAATTCNAGATGGA- 2890 chr5ptel1M 843926 TCAT-GACCTAGGCATAAAGAATGAAATTATTAATAAAT--TAGAGG--A 843970 - iiii ii? i i - - v -- i -- L1M5_orf2#LIN 2891 TCATAGACCTAAATGTAAAAGNTAAAACTA-TAA-AACTTCTAGAAGAAA 2938 chr5ptel1M 843971 ACACAGGATAGTTTACCTCTCAGACCTGTGGA-AGGGGAAGGTCTTTATG 844019 i v i-- i iivv vv ?- vi i i i - i L1M5_orf2#LIN 2939 ACATAGGAGAA--TATCTTCGTGACCTTGGGNTAGGCAAAGATTTCT-TA 2985 chr5ptel1M 844020 ACCAAAGCAGAACTAGAGATCATTACTGATCACAAAATAGAAAAT----- 844064 v iii v -- i -----i ?i i i v i ----- L1M5_orf2#LIN 2986 AACAGGACACAA--AAAG-----CACNAACCATAAAAGAAAAAATTGATA 3028 chr5ptel1M 844065 --TTCGATTATACCAAACTGAAAAGTTTTTGTACAAACAAAACTAATGCA 844112 -- v i ?i i v v ii i iv ?vvv ivi vi iv L1M5_orf2#LIN 3029 AATTGGACTNCATCAAAATTAAAAACTTCTGCTCNTCAAAAGACACCGTT 3078 chr5ptel1M 844113 GACAAGATTAGAAGGGAAGCAATAAACTGGGAAAATATTTTTACAGTCAA 844162 i v i v i v v i i ? i v v i i-? v L1M5_orf2#LIN 3079 AAGAAAATGAAAAGGCAAGCCACAGANTGGGAGAAAATATTTGCAA-NAC 3127 chr5ptel1M 844163 AGGT-TCTGATAAAGGCCTCATTTCCAAAATATATAGAGAATTAACTCTA 844211 vi - i v i v i i i -v vi L1M5_orf2#LIN 3128 ATATATCTGACAAAGGACTCGTATCCAGAATATATAAAGAACT-CCTACA 3176 chr5ptel1M 844212 ATTT-ATAAAAAATCAAAGCCATTC--TCCAAT-TGAAAATGGTCAAAGG 844257 ? i- ? --- v vv --i -?i v i L1M5_orf2#LIN 3177 ANTCAATAANAA---AAAGACAAACAACCCAATANAAAAATGGGCAAAAG 3223 chr5ptel1M 844258 ATATGAACAGACAATTCTCAGATAAAGAAATTGAAACTATTTCTAGTCAT 844307 iv v v i vi v ?v iviiivv iv i L1M5_orf2#LIN 3224 ACTTGAACAGACACTTCACAAAAGAAGATATNCAAATGGCCAATAAGCAC 3273 chr5ptel1M 844308 ATGAAAAGATGCTCCAAGTCA 844328 v v? L1M5_orf2#LIN 3274 ATGAAAAGATGCTCAACNTCA 3294 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 37.90 CpG sites = 262, Kimura (unadjusted) = 38.76 Transitions / transversions = 1.32 (262/198) Gap_init rate = 0.04 (70 / 1627), avg. gap size = 1.26 (88 / 70) 1442 26.98 4.09 4.26 chr5ptel1M 844182 844816 (155184) L1ME5_3end#LINE/L1 4 637 (304) m_b239s551i4 9445 chr5ptel1M 844182 ATTTCCAAAATATATAGAGAATTAACTCTAATTTATAAAAAATCAAAGCC 844231 v i i i ii i vviv v iv i i --- v L1ME5_3end#LI 4 ATATCTAGAATATACAAGGAACTCCTGCAAATCAACAAGAAA---AAGAC 50 chr5ptel1M 844232 ATT--CTCCAATTGAAAA-TGGTCAAAGGATATGAACAGACAATTCTCAG 844278 iv?-- i v - v i iv L1ME5_3end#LI 51 GGNAACCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAG 100 chr5ptel1M 844279 ATAAAGAAA-TTGAAA--CTATTTCTAGTCATATGAAAAGATGCTCCAAG 844325 vi i -ii -- --v v - i v v L1ME5_3end#LI 101 AAGAGGAAACCCGAAAGGCTA--ACAAG-CATATGAAGAGATGCTCAAAC 147 chr5ptel1M 844326 TCATTATTAATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTA 844375 v i vv i i v L1ME5_3end#LI 148 TCATTAGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTT 197 chr5ptel1M 844376 CACACCTGTCAGATTGGCTAAGATGACAGGAAA---AAATAATGATGATT 844422 i i i i v i v --- ---ii vii v L1ME5_3end#LI 198 TACACCTATTAGACTGGCAAAAATTA---GAAAGCTGGATAATGCCAAGT 244 chr5ptel1M 844423 GTTGGAG-GGATGCGGAAAACT-GGGACATTGATGCATTGTTGGTGGAGT 844470 v - i ii ?v - i vi v i i iiv L1ME5_3end#LI 245 GTTGGCGAGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAG 294 chr5ptel1M 844471 TGTGAACGAATCCAACCATTTTGGAGAGTAGTTTGGAACTA--TGCTCAA 844518 ii vii v i i i i i v v -- iv L1ME5_3end#LI 295 TGTAGACTGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAA 344 chr5ptel1M 844519 A--AAGTTATCAAACTGTGCATACCCTTTGATACAGCAGTGTTACTACTG 844566 -- - --- --- v iv i viii v L1ME5_3end#LI 345 ATTAAG-TAT---AC---GCATACCCTATGACCCAGCAATTCCGCTCCTG 387 chr5ptel1M 844567 GGATTATATCCCAGAGAGATTATAAAGAAGG----GAAAGGGACCTGTAT 844612 vv i i v v viv ----v i ---- L1ME5_3end#LI 388 GGTATATATCCCAAAGAAATTCTCACACAGGTCCATAAGGGGAC----AT 433 chr5ptel1M 844613 GTGCACGAATGTTTGTGGCAGCCCTTTTTGTAGTGGCTAGAAACTGGAAA 844662 i iv i ii v vi v i vi i ii ii L1ME5_3end#LI 434 GTACGAGGATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGG 483 chr5ptel1M 844663 CTGAA--TGGATGTCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTAT 844710 -- -- i v v i v iii v iv L1ME5_3end#LI 484 C--AACCTGGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGG 531 chr5ptel1M 844711 ATGAATATTATGGAATATTACTGT-TCTGTAAGAAATGACCAACAGGATG 844759 v i ii i i - i-v v v iii vi vi L1ME5_3end#LI 532 ATGCACACCATGGAGTACTA-TGCAGCAGTTAGAAGCAACGGACTAGATG 580 chr5ptel1M 844760 ATTTCAGAAAG--GCCTGGAGAGA-CTTACACGAAC-TGATGCTGAGTGA 844805 -- v v v --i v vi - v -- - ii L1ME5_3end#LI 581 --TACACATAGCAACATGGATGGATCTTAAA--AACATAGTGCTGAGTGA 626 chr5ptel1M 844806 AATGAGCAGGA 844816 vi i i L1ME5_3end#LI 627 AAAAAGTAAGA 637 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 33.32 CpG sites = 96, Kimura (unadjusted) = 34.38 Transitions / transversions = 1.41 (96/68) Gap_init rate = 0.07 (42 / 634), avg. gap size = 1.26 (53 / 42) 1554 26.52 2.38 3.33 chr5ptel1M 844185 844730 (155270) L1ME3Cz_3end#LINE/L1 7 547 (450) m_b239s551i5 9445 chr5ptel1M 844185 TCCAAAATATATAGAGAATTAACTCTAATTTATAAAAAATCAAAGCCATT 844234 i i i vviv v iv i --- v -- L1ME3Cz_3end# 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAA---AAGACA-- 51 chr5ptel1M 844235 CTCCAATTGAAAA-TGGTCAAAGGATATGAACAGACAATTCTCAGATAAA 844283 vi v - v i v vi i L1ME3Cz_3end# 52 ACCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAG 101 chr5ptel1M 844284 GAAATTGAAACTATTTCTAGTCATATGAAAAGATGCTCCAAGTCATTATT 844333 iivi iviiivv iv v vv i v L1ME3Cz_3end# 102 GAAACCCGAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGT 151 chr5ptel1M 844334 AATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACACCTG 844383 i i ? vv i i v ii L1ME3Cz_3end# 152 AATCAGGGAAATGCAAATTAAAACNACAATGAGATACCATTTCACACCCA 201 chr5ptel1M 844384 TCAGATTGGCTAAGATGACAGGAAAA----AATAATGATGATTGTTGGAG 844429 v i ----vv ----i i ivii v v L1ME3Cz_3end# 202 TCAGATTGGCAAAAAT----TTAAAAGTCTGACAATACCAAGTGTTGGCG 247 chr5ptel1M 844430 -GGATGCGGA-AAACTGGGACATTGATGCATTGTTGGTGGAGTTGTGAAC 844477 - i - v i vi v i i i iiv i i L1ME3Cz_3end# 248 AGGATGTGGAGAAACGGGAACTCTCATACACTGCTGGTGGGAGTGTAAAT 297 chr5ptel1M 844478 GAATCCAACCATTTTGGAGAGTAGTTTGGAACTATGCTCAAAAAGTTATC 844527 vii v i i i v v - viv i-- L1ME3Cz_3end# 298 TGGTACAACCACTTTGGAGAGCAATTTGGCAATAT-CTAGTAAAGTTG-- 344 chr5ptel1M 844528 AAACTGTGCATACCCTTTGATACAGCAGTGTTACTACTGGGATTATATCC 844577 iv i vi iv i vii v i vv i L1ME3Cz_3end# 345 AAGATGCGCATACCCTACGACCCAGCAATTCCACTTCTAGGTATATACCC 394 chr5ptel1M 844578 CAGAGAGATTAT-AAAGAAGGG---AAAGGGACCTGTATGTGCACGAATG 844623 i i i v -iv v v v --- i i ---- i v i L1ME3Cz_3end# 395 TAGAGAAACTCTCGCACATGTGCACAAGGAGAC----ATGTACAAGGATG 440 chr5ptel1M 844624 TTTGTGGCAGCCCTTTTTGTAGTGGCTAGAAACTGGAAACTGAA--TGGA 844671 ii v vi v i i v i i -- -- ii L1ME3Cz_3end# 441 TTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAAC--AACCTAAA 488 chr5ptel1M 844672 TGTCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATATGAATATTAT 844721 i v i v i vv iv L1ME3Cz_3end# 489 TGTCCATCAATAGGGGAATGGATAAATAAATTGTGGTATATTCATACAAT 538 chr5ptel1M 844722 GGAATATTA 844730 i L1ME3Cz_3end# 539 GGAATACTA 547 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 32.28 CpG sites = 79, Kimura (unadjusted) = 33.44 Transitions / transversions = 1.30 (79/61) Gap_init rate = 0.05 (25 / 545), avg. gap size = 1.24 (31 / 25) 22 10.11 0.00 0.00 chr5ptel1M 845277 845308 (154692) (A)n#Simple_repeat 1 32 (0) m_b239s252i18 9446 chr5ptel1M 845277 AAATAAAAAAAAAAAAAAAGAAAAAGAAAAAA 845308 v i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 32 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 780 24.31 11.40 0.79 chr5ptel1M 845858 846085 (153915) MIRc#SINE/MIR 10 261 (7) m_b239s601i13 9447 chr5ptel1M 845858 GCGATATAGTGGATAGAGCATGGAACTTAGACCCAGAAAGTCCCGAGTTC 845907 i i ii v iv i i vi i v i i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr5ptel1M 845908 AAATTCATCCTCAGACATTTTGTTAGCTATGTGACCCCAGGTAAGTCACT 845957 i i i vvv v v i -ii i iii i MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTT-ACTAGCTGTGTGACCTTGGGCAAGTCACT 108 chr5ptel1M 845958 TTTCCTCTGTGA--CTCAGTTTCTTCATCTGTAAAATGGGAATAATAATA 846005 vv v -- i i - MIRc#SINE/MIR 109 TAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAAT- 157 chr5ptel1M 846006 AACTGTCATGCC-------------TGTTATGAGG-----ATGA---AAT 846034 v i v ------------- i ----- --- MIRc#SINE/MIR 158 ACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAAT 207 chr5ptel1M 846035 GTTTGT-AAAGCTCTTTACCAATTTTAAA--ACAATATAAATACCAGCTA 846081 v - v iiv i v --i v i iiv v?i MIRc#SINE/MIR 208 GTATGTGAAAGCGCTTTGTAAACTGTAAAGTGCTATACAAATGTAAGGNG 257 chr5ptel1M 846082 TTAT 846085 MIRc#SINE/MIR 258 TTAT 261 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.68 CpG sites = 34, Kimura (unadjusted) = 30.34 Transitions / transversions = 1.62 (34/21) Gap_init rate = 0.04 (8 / 227), avg. gap size = 3.50 (28 / 8) 13 5.20 0.00 0.00 chr5ptel1M 846322 846341 (153659) (GCA)n#Simple_repeat 1 20 (0) m_b239s252i19 9448 chr5ptel1M 846322 GCAGCAGCAGCAGCAGCCGC 846341 v (GCA)n#Simple 1 GCAGCAGCAGCAGCAGCAGC 20 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 20 24.05 2.86 1.41 chr5ptel1M 846346 846415 (153585) (CCCCCGG)n#Simple_repeat 1 71 (0) m_b239s252i20 9449 chr5ptel1M 846346 CCGCCGGCAGCCAGCCCCCTCCTCCCGGCCTCC-GCCCCCAGCCCCTGGC 846394 v vv i vv i i - i i (CCCCCGG)n#Si 1 CCCCCGGCCCCCGGCCCCCGGCCCCCGGCCCCCGGCCCCCGGCCCCCGGC 50 chr5ptel1M 846395 CCCC-CTGCGCGGCCCCTCGGC 846415 -viv v - (CCCCCGG)n#Si 51 CCCCGGCCCCCGGCCCC-CGGC 71 Matrix = Unknown Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.04 (3 / 69), avg. gap size = 1.00 (3 / 3) 13 15.84 6.82 2.17 chr5ptel1M 850661 850704 (149296) (GACA)n#Simple_repeat 1 46 (0) m_b239s252i21 9450 chr5ptel1M 850661 GAGAGACAGA-A-ACAG-GAGATAGAAGAGACACACAGAGAGACAGA 850704 v - - -v i - v v v (GACA)n#Simpl 1 GACAGACAGACAGACAGACAGACAG-ACAGACAGACAGACAGACAGA 46 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.09 (4 / 43), avg. gap size = 1.00 (4 / 4) 234 18.75 2.08 0.00 chr5ptel1M 851134 851181 (148819) L2b_3end#LINE/L2 332 380 (86) m_b240s601i0 9451 chr5ptel1M 851134 CTATCTTCCCTGTTAGACTGGGAGCTCCGTGAGGGC-GGGACTGGCTTT 851181 i i iii v - i ?v i L2b_3end#LINE 332 CTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCT 380 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 20.21 CpG sites = 7, Kimura (unadjusted) = 23.03 Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.02 (1 / 47), avg. gap size = 1.00 (1 / 1) 189 26.61 2.94 6.06 chr5ptel1M 853935 854002 (145998) X9_LINE#LINE/L1 785 850 (86) m_b240s601i1 9452 chr5ptel1M 853935 CTGACAAAC--AGCATTCAGTGTGCGAGGTCAGCTGTGTGCTCTCTCCGT 853982 v ii -- vi iv - i vii i - i -- X9_LINE#LINE/ 785 CTGCCAGGCTGAGGGTTCGCTGTG-GAGGCCAGACATATG-TCTTTC--T 830 chr5ptel1M 853983 CTCTCCCGCAGATGCTGCAG 854002 i i i i X9_LINE#LINE/ 831 TTCTCCCACGGATGCTACAG 850 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.93 CpG sites = 13, Kimura (unadjusted) = 34.96 Transitions / transversions = 3.25 (13/4) Gap_init rate = 0.07 (5 / 67), avg. gap size = 1.20 (6 / 5) 14 12.44 5.71 0.00 chr5ptel1M 856797 856831 (143169) (CTGGGCC)n#Simple_repeat 1 37 (0) m_b240s252i1 9453 chr5ptel1M 856797 CTGGGCCCTGGTTCCTGGGTCCT--GCCCTGGGACCT 856831 vi i -- v (CTGGGCC)n#Si 1 CTGGGCCCTGGGCCCTGGGCCCTGGGCCCTGGGCCCT 37 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.03 (1 / 34), avg. gap size = 2.00 (2 / 1) 15 11.76 5.13 2.50 chr5ptel1M 858195 858233 (141767) (GGCCCC)n#Simple_repeat 1 40 (0) m_b240s252i2 9454 chr5ptel1M 858195 GGGCCCGGCGCCCGGCCCCGGCCCCTG--GCTGCCCCGGCC 858233 v - v --v v (GGCCCC)n#Sim 1 GGCCCCGGC-CCCGGCCCCGGCCCCGGCCCCGGCCCCGGCC 40 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.50 (3 / 2) 20 18.83 0.00 4.00 chr5ptel1M 860679 860730 (139270) (GGAG)n#Simple_repeat 1 50 (0) m_b240s252i3 9455 chr5ptel1M 860679 GGAGGGAGGGAGGGAGGAAAGGAAGGGGAGGAATGGAGGTGGGGATGGAT 860728 -i i - i v vi v v (GGAG)n#Simpl 1 GGAGGGAGGGAGGGAGG-GAGGGA-GGGAGGGAGGGAGGGAGGGAGGGAG 48 chr5ptel1M 860729 GG 860730 (GGAG)n#Simpl 49 GG 50 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.00 (2 / 2) 17 24.58 4.59 6.54 chr5ptel1M 860694 860802 (139198) (GGAAT)n#Simple_repeat 1 107 (0) m_b240s252i4 9455 chr5ptel1M 860694 GGAAAGGAAGGGGA-GGAATGGAGGTGGGGATGGATGGGGAAATTAAAAG 860742 v v i - -i - i -iv - vi v (GGAAT)n#Simp 1 GGAATGGAATGGAATGGAATGGA-AT-GGAATGGA-ATGG-AATGGAATG 46 chr5ptel1M 860743 GAAAAGAATAGGGTTGGAA--GATTGGGGGGGAATGGGGTGGAAAATGGA 860790 vi - iv -- v iiv ii -- (GGAAT)n#Simp 47 GAATGGAAT-GGAATGGAATGGAATGGAATGGAATGGAATGG--AATGGA 93 chr5ptel1M 860791 A-GG-ATGGAATGG 860802 - - (GGAAT)n#Simp 94 ATGGAATGGAATGG 107 Matrix = Unknown Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.10 (11 / 108), avg. gap size = 1.09 (12 / 11) 26 23.01 3.61 1.18 chr5ptel1M 860786 860868 (139132) (ATGG)n#Simple_repeat 1 85 (0) m_b240s252i5 9456 chr5ptel1M 860786 ATGGAAGGATGGAATGG-TGGAAGAAGGGGT-GAAAAATGGATGGAT-AA 860832 v - - v i v i - vii -i (ATGG)n#Simpl 1 ATGGATGGATGG-ATGGATGGATGGATGGATGGATGGATGGATGGATGGA 49 chr5ptel1M 860833 AAGATAGAAGGATGGAGAGATGGATGGAGGGATGGA 860868 vi i v vi v (ATGG)n#Simpl 50 TGGATGGATGGATGGATGGATGGATGGATGGATGGA 85 Matrix = Unknown Transitions / transversions = 1.00 (8/8) Gap_init rate = 0.05 (4 / 82), avg. gap size = 1.00 (4 / 4) 316 25.52 4.76 4.05 chr5ptel1M 861395 861541 (138459) MIR1_Amn#SINE/MIR 22 169 (61) m_b240s601i2 9457 chr5ptel1M 861395 TGGCCAGGGC-CTGGCACTGAGGATCAG-AGTCCTGGGGTCTAGCCCAGG 861442 vi i - - i iv i - v v ? ?i v MIR1_Amn#SINE 22 TGGATAGAGCACTGG-ACTGGGACTCGGGAGACCTGGGTTCNANTCCCGG 70 chr5ptel1M 861443 CACC----CGGACCTCCGTGACTGGCTTTGGGAAAGTCA-TAAACCGTTT 861487 v i---- v?i ?v - ?v i i v - v? -- i MIR1_Amn#SINE 71 CTCTGCCACTNGCCNGC-TGNGTGACCTTGGGCAAGTCACTTNACC--TC 117 chr5ptel1M 861488 TCTGTGCCTCAGTTTCCCTCCCTGTAAGGGGTGGCGATGGCGCTCCCAAC 861537 ? iivi --ii v iii v v ii MIR1_Amn#SINE 118 TCTGNGCCTCAGTTTCCTCATCTGTAA--AATGGGGATAATGATACTGAC 165 chr5ptel1M 861538 CTCC 861541 MIR1_Amn#SINE 166 CTCC 169 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.88 CpG sites = 21, Kimura (unadjusted) = 34.04 Transitions / transversions = 1.40 (21/15) Gap_init rate = 0.07 (10 / 146), avg. gap size = 1.30 (13 / 10) 13 20.58 0.00 8.33 chr5ptel1M 861851 861902 (138098) (GGCCCGG)n#Simple_repeat 1 48 (0) m_b240s252i6 9458 chr5ptel1M 861851 GGCCCGCAGGGGCCGGGGCCCGGGGCTGAGGGCACCTGGGGAAGGGGGCG 861900 -- v ivi - - vvv v (GGCCCGG)n#Si 1 GGCCCG--GGGCCCGGGGCCCGGGGCCCGGGGC-CC-GGGGCCCGGGGCC 46 chr5ptel1M 861901 CG 861902 (GGCCCGG)n#Si 47 CG 48 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.08 (4 / 51), avg. gap size = 1.00 (4 / 4) 57 17.98 2.48 0.81 chr5ptel1M 862480 862600 (137400) (GA)n#Simple_repeat 1 123 (0) m_b240s252i7 9459 chr5ptel1M 862480 GAGAGGGAAAGTGTGTGTGAGACAGAGAGAGAGAGAGACAGACACAGAGA 862529 i i v v v v v v v v (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr5ptel1M 862530 CAGAGACAAAGACAGAGAGAGACAGAGAGAGAGAGAGACAGAGAGAGAGC 862579 v v i v v v v (GA)n#Simple_ 51 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 100 chr5ptel1M 862580 GAGCAGA-AGA-AGGGTG-GAGAG 862600 - - - i v - (GA)n#Simple_ 101 GAG-AGAGAGAGAGAGAGAGAGAG 123 Matrix = Unknown Transitions / transversions = 0.27 (4/15) Gap_init rate = 0.03 (4 / 120), avg. gap size = 1.00 (4 / 4) 16 0.00 0.00 0.00 chr5ptel1M 863132 863148 (136852) (G)n#Simple_repeat 1 17 (0) m_b240s252i8 9460 chr5ptel1M 863132 GGGGGGGGGGGGGGGGG 863148 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGG 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 15 26.36 0.00 0.00 chr5ptel1M 864155 864199 (135801) (GCTCCC)n#Simple_repeat 1 45 (0) m_b240s252i9 9461 chr5ptel1M 864155 GCTCCAGCTCCAGGCGCCGCTGCCGCTCCTTCTCCAGCTCCTGCT 864199 v v viv v iv v i (GCTCCC)n#Sim 1 GCTCCCGCTCCCGCTCCCGCTCCCGCTCCCGCTCCCGCTCCCGCT 45 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 283 26.13 13.28 4.32 chr5ptel1M 865244 865371 (134629) C MIRc#SINE/MIR (88) 180 42 m_b240s601i3 9462 chr5ptel1M 865244 CTTATGGGGTGGGGACACAGGACAGAGGGAATTGGCCC-AATTTACAGAG 865292 i i i i ---- i ivivv iv - v v C MIRc#SINE/MIR 180 CCTGTGAGGTAGG----CAGGGCAGGTATTATTATCCCCATTTTACAGAT 135 chr5ptel1M 865293 GAAGAAACTGAGCCT------------GGGACTTCCCTAGGGTTTCATAG 865330 i v ------------ v v i i iv i C MIRc#SINE/MIR 134 GAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAG 85 chr5ptel1M 865331 CTTGTAAGTGG----GCCATGTGACTGGGCCCCAGCCCCACCTGA 865371 v ---- -- v v iv vi iv C MIRc#SINE/MIR 84 CTAGTAAGTGGCAGAGCC--GGGACTCGAACCCAGGTCTTCCTGA 42 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.60 CpG sites = 16, Kimura (unadjusted) = 32.60 Transitions / transversions = 1.00 (16/16) Gap_init rate = 0.07 (9 / 127), avg. gap size = 2.56 (23 / 9) 211 33.06 10.53 2.72 chr5ptel1M 865728 865898 (134102) C L3#LINE/CR1 (81) 4018 3835 m_b240s601i4 9463 chr5ptel1M 865728 CTGCAGAATCCCCTTGGAGGCAAGC--TCATCTGGCCCCTGCTTGAACGT 865775 i iv i----- i i-- ii i ii C L3#LINE/CR1 4018 CTACAACATCCCT-----GACAAGTGGTCATCCAGCCTCTGCTTGAACAC 3974 chr5ptel1M 865776 GCTTTGAGGCAGGGAGCTCACTGCCGCCCTCAGGGGCACCTTCTCCTTCT 865825 viiiv v i i i v ? vvi vi v v ivi i C L3#LINE/CR1 3973 CTCCAGTGACGGGGAGCTCACTACCTCNCGAGGCAGCCCATTCCATTTTT 3924 chr5ptel1M 865826 GGAC--CCGCGGGGGTCAGGGAG--------CACA-AGAGCCGGG--CCG 865862 -- ivi ivv i ii --------i i -v ii-- i C L3#LINE/CR1 3923 GGACAGCTCTGATTGTTAGAAAGTTCTTCCTTATATTGAGCCGAAATCTG 3874 chr5ptel1M 865863 CCCCGCTG--ACTTCCACCCGCT-GTCCCACGTCTGTCC 865898 i v -- ii - i vv i C L3#LINE/CR1 3873 CCTCCCTGTAACTTCCACCCATTGGTCCTAGTTCTGCCC 3835 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.71 CpG sites = 37, Kimura (unadjusted) = 46.93 Transitions / transversions = 2.06 (37/18) Gap_init rate = 0.07 (12 / 170), avg. gap size = 1.92 (23 / 12) 224 23.79 20.49 3.52 chr5ptel1M 870397 870518 (129482) MIR1_Amn#SINE/MIR 15 156 (74) m_b240s601i5 9464 chr5ptel1M 870397 GGTCAGGCGCAGAGGGCA----GCTGGGGCACAGTGAGCAAGGCCCGAGT 870442 vi i v v i ----i i v i -----i i i i MIR1_Amn#SINE 15 GGTCTAGTGGATAGAGCACTGGACTGGGACTCGG-----GAGACCTGGGT 59 chr5ptel1M 870443 TCAACCCTGTCCTCAGGCACTTGCTAGCTGTGCGAC--TGAGAAAGTCAA 870490 ? ?i ivvv v v ? i? ? i -- i v v MIR1_Amn#SINE 60 TCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGTCAC 109 chr5ptel1M 870491 TT-----------GCCTC--------CATCTGTAAAATGGGGACGAT 870518 ----------- -------- ii MIR1_Amn#SINE 110 TTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGGATAAT 156 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.83 CpG sites = 17, Kimura (unadjusted) = 31.16 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.07 (9 / 121), avg. gap size = 3.33 (30 / 9) 365 22.79 19.85 0.00 chr5ptel1M 870425 870560 (129440) MIRc#SINE/MIR 40 202 (66) m_b240s601i6 9464 chr5ptel1M 870425 AGTGAGCAAGGCCCGAGTTCAACCCTGTCCTCAGGCACTTGCTAGCTGTG 870474 v v i i i i vi ivvv v v i MIRc#SINE/MIR 40 AGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTG 89 chr5ptel1M 870475 CGAC--TGAGAAAGTCAATT-----------GCCTC--------CATCTG 870503 i -- i v v ----------- -------- MIRc#SINE/MIR 90 TGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTG 139 chr5ptel1M 870504 TAAAATGGGGACGATCA---CCGCAC-GCC--CCTCCCGGGGTCTTTGTA 870547 ii v --- i v - -- v i iv i MIRc#SINE/MIR 140 TAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTG 189 chr5ptel1M 870548 AGGCTCCAATGAG 870560 v v MIRc#SINE/MIR 190 AGGATCAAATGAG 202 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.36 CpG sites = 15, Kimura (unadjusted) = 27.35 Transitions / transversions = 0.94 (15/16) Gap_init rate = 0.04 (6 / 135), avg. gap size = 4.50 (27 / 6) 430 33.68 3.08 2.55 chr5ptel1M 875881 876075 (123925) L3#LINE/CR1 2844 3039 (1060) m_b240s601i7 9465 chr5ptel1M 875881 GGAGCCTGTCTGGTTGCAGCAAGTACAAGCCAGGCCTCTCTCACCTGG-- 875928 v iv v v vi v i v vvv v vi-- L3#LINE/CR1 2844 GGAGCCAGCATGGGTTCACTAAGAACAAGTCATGCCAAACTAACCTCATT 2893 chr5ptel1M 875929 -CCTTCTTTGCT---GCCAAATGACTGGAAAAGCAGGGGAGGAACTATGC 875974 - i v --- ii vvv v i v iviv --- i L3#LINE/CR1 2894 TCCTTTTTTGATAGGGTTACTAGACTGGTAGATCAGGGGAATGCC---GT 2940 chr5ptel1M 875975 AGATACAGTTTTTCTACATCTCAGCCCAGCTTTTGATGAAGTATCTCCTA 876024 i ? v v iv i vvi v ii v v i L3#LINE/CR1 2941 AGACANAGTGTATCTGGATTTCAGCAAGGCATTTGACAAAGTCTCTCATG 2990 chr5ptel1M 876025 CTTGTGTCTTATGGGAAAGGTGGCAAGAGCTGGACTAGATGAGAATGTAG 876074 v- i -i i iv i vi i vv i i v i ii L3#LINE/CR1 2991 A-TAT-CCTTGTGGACAAGATGGAGAAATATGGGCTGGATGATAGTACAG 3038 chr5ptel1M 876075 T 876075 L3#LINE/CR1 3039 T 3039 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.54 CpG sites = 30, Kimura (unadjusted) = 45.54 Transitions / transversions = 0.88 (30/34) Gap_init rate = 0.04 (8 / 194), avg. gap size = 1.38 (11 / 8) 16 0.00 0.00 0.00 chr5ptel1M 876947 876963 (123037) (T)n#Simple_repeat 1 17 (0) m_b240s252i10 9466 chr5ptel1M 876947 TTTTTTTTTTTTTTTTT 876963 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTT 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 14 24.43 8.33 0.00 chr5ptel1M 877232 877303 (122697) (CTTTTA)n#Simple_repeat 1 78 (0) m_b240s252i11 9467 chr5ptel1M 877232 CTTTTCCATTT-CTTGCTCATTTTC-TTTCCTTTT-CTTTTAGTATTTCC 877278 v v - viv v v - v - v v v i (CTTTTA)n#Sim 1 CTTTTACTTTTACTTTTACTTTTACTTTTACTTTTACTTTTACTTTTACT 50 chr5ptel1M 877279 TTTA-TTTT--TTTCTTTTTTACTTTTA 877303 - -- ivi (CTTTTA)n#Sim 51 TTTACTTTTACTTTTACTTTTACTTTTA 78 Matrix = Unknown Transitions / transversions = 0.36 (4/11) Gap_init rate = 0.07 (5 / 71), avg. gap size = 1.20 (6 / 5) 250 24.64 26.80 1.65 chr5ptel1M 877771 877964 (122036) L3#LINE/CR1 3155 3396 (703) m_b240s601i8 9465 chr5ptel1M 877771 GCTCTGTTTACCACTTTGATCAATGATTTGGGT----------AAGGCCT 877810 ii i v i v i i ---------- v L3#LINE/CR1 3155 GTCCTGTTCAACATTTTTATCAATGACTTGGATGAAGACATAGAAGGCAT 3204 chr5ptel1M 877811 A------AAATTCTACAGATAACACAACACAGGGAGGAAAAACTAA---- 877850 i------ - i i vi v i v i ---- L3#LINE/CR1 3205 GCTTATCAAATT-TGCAGATGACACAAAGCTGGGAGGGATAGCTAATACG 3253 chr5ptel1M 877851 ---------AAAATTAAGATTCAAAACAATCTTCA-----TAAAA----- 877881 --------- i i ?i iv ----- ii ----- L3#LINE/CR1 3254 NTGGATGACAGAATCAAGATTCAAAANGATCTCGACAGGCTGGAACGATG 3303 chr5ptel1M 877882 ----AAAATC-TCAA---GAAATATATTAGGGATTTATG----ATCTTAC 877919 ----i i -v --- v vi vv ----i i i L3#LINE/CR1 3304 GGCCGAAACCAACAAGATGAAATTTAACAGGGATAAATGTAAAGTCCTGC 3353 chr5ptel1M 877920 A-CTGGGTTCAGAAAAATCAACTTCCAGTAGGTGGGGGATAGGGAG 877964 -i i - v --ii i ivi i i L3#LINE/CR1 3354 ATTTAGGTTCA-AAAAATCAACTGC--ACAAGTACAGGATGGAGAG 3396 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.90 CpG sites = 33, Kimura (unadjusted) = 31.53 Transitions / transversions = 2.36 (33/14) Gap_init rate = 0.07 (14 / 193), avg. gap size = 4.00 (56 / 14) 365 29.22 12.99 0.00 chr5ptel1M 878129 878282 (121718) L3#LINE/CR1 3706 3879 (220) m_b240s601i9 9465 chr5ptel1M 878129 ATGGCTCAAGAGGATGGA-CTGTTCATTCTGGAGAAAACAAGGCTCCAGG 878177 i i v iiiv i-v i vi i v i ivii L3#LINE/CR1 3706 ACGGTTGAAGGAACTGGGGATGTTTAGCCTGGAGAAGAGAAGACTTAGAG 3755 chr5ptel1M 878178 GGGACA-------------CATGTATATGAAGGGTTGTC-TCAGAAAGAG 878213 i ------------- vi v i - vv i L3#LINE/CR1 3756 GAGACATGATAGCTGTCTTCAAATATTTGAAGGGCTGTCATGTGGAAGAG 3805 chr5ptel1M 878214 GG-CCAGCCCTGTTCTGTTTGCCTCCAGATGGCAGAACCAAGTGCACTGA 878262 -ii v i i v v v i i vv v i L3#LINE/CR1 3806 GGATTAGACTTATTCTGTGTGGCTCCAGAGGGCAGAACTAGGACCAATGG 3855 chr5ptel1M 878263 G-GGTAGGTACA---AGGCAAACT 878282 - v v --- i i L3#LINE/CR1 3856 GTGGAAGTTACAGGGAGGCAGATT 3879 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.92 CpG sites = 26, Kimura (unadjusted) = 37.99 Transitions / transversions = 1.37 (26/19) Gap_init rate = 0.04 (6 / 153), avg. gap size = 3.33 (20 / 6) 195 38.81 1.49 0.00 chr5ptel1M 878367 878433 (121567) C L2c_3end#LINE/L2 (5) 473 406 m_b240s601i10 9468 chr5ptel1M 878367 TTCAGTCGGTCAGTACTTAG-AAGTGTCTACTATGCGTTGAATGCTGGGG 878415 v iiiv ii i v-i i i i iiiiii C L2c_3end#LINE 473 TTCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGG 424 chr5ptel1M 878416 ACACATGGCTGCACAGGA 878433 i vi v v i i C L2c_3end#LINE 423 ATACAAAGATGAATAAGA 406 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 55.03 CpG sites = 20, Kimura (unadjusted) = 62.94 Transitions / transversions = 3.33 (20/6) Gap_init rate = 0.02 (1 / 66), avg. gap size = 1.00 (1 / 1) 231 21.67 0.00 7.69 chr5ptel1M 878974 879043 (120957) C MIR#SINE/MIR (12) 250 186 m_b240s601i11 9469 chr5ptel1M 878974 CATTTATTAATTGCCTACTGCATGCCAGGCACTCTTCTCGAAGCAGCTGT 879023 i vi i iii v -- - -- C MIR#SINE/MIR 250 CATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCT--AAGC-GC--T 206 chr5ptel1M 879024 GTGCAAGTATTATTCCATTT 879043 v i v vii C MIR#SINE/MIR 205 TTACATGTATTAACTCATTT 186 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 23.91 CpG sites = 9, Kimura (unadjusted) = 26.01 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.07 (5 / 69), avg. gap size = 1.00 (5 / 5) 208 25.40 11.11 0.00 chr5ptel1M 879008 879070 (120930) C MIRb#SINE/MIR (81) 187 118 m_b240s601i12 9469 chr5ptel1M 879008 TTCTCGAAGCAGCTGTGTG---CAAGTATTATT----CCATTTCCCAGAT 879050 i iv i i iv i ---i i ---- iv C MIRb#SINE/MIR 187 TCCTCACAACAACCCTGCGAGGTAGGTATTATTATCCCCATTTTACAGAT 138 chr5ptel1M 879051 GAGGATGCTGATGCTCTGAG 879070 vi v v C MIRb#SINE/MIR 137 GAGGAAACTGAGGCTCAGAG 118 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.52 CpG sites = 10, Kimura (unadjusted) = 31.89 Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.03 (2 / 62), avg. gap size = 3.50 (7 / 2) 219 15.56 8.89 0.00 chr5ptel1M 879026 879070 (120930) C MIRc#SINE/MIR (105) 163 115 m_b240s601i13 9469 chr5ptel1M 879026 GCAAGTATTATT----CCATTTCCCAGATGAGGATGCTGATGCTCTGAG 879070 i ---- iv vi v v C MIRc#SINE/MIR 163 GCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAG 115 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 17.46 CpG sites = 3, Kimura (unadjusted) = 17.46 Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.02 (1 / 44), avg. gap size = 4.00 (4 / 1) 311 32.22 11.70 0.96 chr5ptel1M 879132 879319 (120681) L2d_3end#LINE/L2 64 271 (245) m_b240s601i14 9470 chr5ptel1M 879132 CTCCGATCCAGTCAAACTGGACTCCTCG--GTTCCTC------------- 879166 v ii i v i i-- i i ------------- L2d_3end#LINE 64 CTCCGCTCCAGTCAGGCCGGTCTCTTCACTGTCCCCCGAACACGCCTTGC 113 chr5ptel1M 879167 ----TCCCACCTCCGTGCTTTTGCCCTGCTCATGCCCTCATGCTTAGAAT 879212 ---- i i i i i vvvi i v i -i i i L2d_3end#LINE 114 GCATTCCCGCCTCTGCGCCTTTGCTCACGCCGTTCCCCC-CGCCTGGAAT 162 chr5ptel1M 879213 ACACTTCCTCCTCCCTTTACCTCA--CAGATTCCCCCTTCCCTTCAAGGC 879260 i v i i ii iv iii -- i i iv ivi L2d_3end#LINE 163 GCCCTTCCCCTTCCTCTCTCTCTATCCAAATCCTACCCATCCTTCAAGGC 212 chr5ptel1M 879261 TCTGGTGAGATGCCATCT-TTGCATAAAGCCTTTCCTTACCCCTCCTTAC 879309 i v v v ii v i -i v ii i v v -vi L2d_3end#LINE 213 CCAGCTCAAGTCCCACCTCCTCCACGAAGCCTTCCCTGACCACTCC-AGC 261 chr5ptel1M 879310 CCACACTCAT 879319 v L2d_3end#LINE 262 CCACACTGAT 271 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.78 CpG sites = 41, Kimura (unadjusted) = 44.87 Transitions / transversions = 2.16 (41/19) Gap_init rate = 0.04 (7 / 187), avg. gap size = 3.43 (24 / 7) 363 25.81 2.48 3.77 chr5ptel1M 879144 879304 (120696) L2c_3end#LINE/L2 98 256 (222) m_b240s601i15 9470 chr5ptel1M 879144 CAAACTGGACTCCTCGGTTCCTCTCCCACCTCCGTGCTTTTGC-CCTGCT 879192 --- v v i i - ii ? i - v L2c_3end#LINE 98 CAAAC---ACGCCGCAGTTCTT-TCCTGCCTCCGNGCCTTTGCACATGCT 143 chr5ptel1M 879193 CATGCCCTCATGCTTAGAATACACTT-CCTCCTCCCTTTACCTCACAGAT 879241 -i v - i i i v - i i ii vi vi i L2c_3end#LINE 144 -GTTCCCTC-TGCCTGGAATGCTCTTCCCCCCTCCTTCCACCTGGCTAAC 191 chr5ptel1M 879242 TCCCCCTT-CCCTTCAAGGCTCTGGTGAGATGCCATCT-TTGCATAAAGC 879289 iv i-i ? v v v i i -i v ivi L2c_3end#LINE 192 TCCTACTCATCCTTCAAGNCTCAGCTCAGATGTCACCTCCTCCGGGAAGC 241 chr5ptel1M 879290 CTTTCCTTACCCCTC 879304 i v i L2c_3end#LINE 242 CTTCCCTGACCCCCC 256 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.26 CpG sites = 26, Kimura (unadjusted) = 33.28 Transitions / transversions = 1.86 (26/14) Gap_init rate = 0.06 (10 / 160), avg. gap size = 1.00 (10 / 10) 30 16.70 1.61 1.61 chr5ptel1M 879321 879382 (120618) (AC)n#Simple_repeat 1 62 (0) m_b240s252i12 9471 chr5ptel1M 879321 ACACATACACACACACACACACACACACAGTAGACACACATACACTC-CC 879369 i -i v i v - v (AC)n#Simple_ 1 ACACACACACACACACACACACACACACA-CACACACACACACACACACA 49 chr5ptel1M 879370 CCCCCCCACACAC 879382 v v v (AC)n#Simple_ 50 CACACACACACAC 62 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.03 (2 / 61), avg. gap size = 1.00 (2 / 2) 441 20.02 0.00 2.73 chr5ptel1M 879488 879600 (120400) C Charlie32a#DNA/hAT-Charlie (148) 188 79 m_b240s502i0 9472 chr5ptel1M 879488 GAGCCAACAAGCTGAGGTGACGGCTAGCTTCTACTAAAAATCCTAAGTAA 879537 v v -- i v i i i i v v C Charlie32a#DN 188 GAGACACCAA--TGAGGTGATGTCTGGTTTTTATTAAATATCATAAGTAA 141 chr5ptel1M 879538 ATTATTCATTACAGCCAGAAGCAAAAGTACAGACGCTGCCCTATTATAAA 879587 v vvv i i ii i v - C Charlie32a#DN 140 ATTATTAATTCATGCCAGAAACAAAAGTATAGACATTGTCATATTAT-AA 92 chr5ptel1M 879588 AGATTAATATTAC 879600 v i C Charlie32a#DN 91 ACATTAATACTAC 79 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 23.41 CpG sites = 11, Kimura (unadjusted) = 23.41 Transitions / transversions = 1.00 (11/11) Gap_init rate = 0.03 (3 / 112), avg. gap size = 1.00 (3 / 3) 187 28.79 6.06 0.00 chr5ptel1M 881470 881535 (118465) C MIR3#SINE/MIR (28) 180 111 m_b240s601i16 9473 chr5ptel1M 881470 TGGACGGGACCTCAGGGACCCTC-GGGCCAACCCCTAGG---TATAGCAG 881515 v i i i v -i v ivvi--- i vv C MIR3#SINE/MIR 180 TGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATG 131 chr5ptel1M 881516 AAGAAGCTGAGACCCAGGAA 881535 i i i ii C MIR3#SINE/MIR 130 AGGAAACTGAGGCCCAGAGA 111 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.68 CpG sites = 12, Kimura (unadjusted) = 37.68 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.03 (2 / 65), avg. gap size = 2.00 (4 / 2) 198 31.07 9.71 0.00 chr5ptel1M 882830 882932 (117068) MIRc#SINE/MIR 4 116 (152) m_b240s601i17 9474 chr5ptel1M 882830 GGCTGGGTGGTGCGGTGGGGAGCGTCCTGGACTC----CCTGG----CCT 882871 v v i ii v iv i----i v ---- MIRc#SINE/MIR 4 GGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCT 53 chr5ptel1M 882872 GAGATCTAGGGCAGCCTCAGATGC-TACTAGTTGAACGGTCCTGGG-AAG 882919 i v v vv v v v vii - i vii ii i - MIRc#SINE/MIR 54 GGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAG 103 chr5ptel1M 882920 TCACTGAACTGCT 882932 v iv MIRc#SINE/MIR 104 TCACTTAACCTCT 116 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.67 CpG sites = 16, Kimura (unadjusted) = 40.67 Transitions / transversions = 1.00 (16/16) Gap_init rate = 0.04 (4 / 102), avg. gap size = 2.50 (10 / 4) 53 11.12 0.00 0.00 chr5ptel1M 882953 883040 (116960) (AGAGCG)n#Simple_repeat 1 88 (0) c_b240s251i0 9475 chr5ptel1M 882953 AGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCGAGAGCGAG 883002 v v v v v v (AGAGCG)n#Sim 1 AGAGCGAGAGCGAGAGCGAGAGCGAGAGCGAGAGCGAGAGCGAGAGCGAG 50 chr5ptel1M 883003 AGCGAGAGCGAGAGAGAGAGCGAGAGAGAGAGAGAGAG 883040 v v v (AGAGCG)n#Sim 51 AGCGAGAGCGAGAGCGAGAGCGAGAGCGAGAGCGAGAG 88 Matrix = Unknown Transitions / transversions = 0.00 (0/9) Gap_init rate = 0.00 (0 / 87), avg. gap size = 0.0 (0 / 0) 21 25.26 5.95 0.00 chr5ptel1M 883045 883128 (116872) (AGAC)n#Simple_repeat 1 89 (0) m_b240s252i13 9476 chr5ptel1M 883045 AGATAGGGAGACAGAGACA-AGGCAGAAACAGAGAGAGACAGGGAGACAG 883093 i iv v v - i v v v v iv (AGAC)n#Simpl 1 AGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAG 50 chr5ptel1M 883094 ACAGAGAAACAG--AGACCGGGAGGCAG--AGACAGACA 883128 v i -- v iv i -- (AGAC)n#Simpl 51 ACAGACAGACAGACAGACAGACAGACAGACAGACAGACA 89 Matrix = Unknown Transitions / transversions = 0.64 (7/11) Gap_init rate = 0.04 (3 / 83), avg. gap size = 1.67 (5 / 3) 34 18.64 1.20 2.44 chr5ptel1M 883052 883134 (116866) (GAGACA)n#Simple_repeat 1 82 (0) m_b240s252i14 9476 chr5ptel1M 883052 GAGACAGAGACA-AGGCAGAAACAGAGAGAGACAGGGAGACAGACAGAGA 883100 - i i v v vi v v (GAGACA)n#Sim 1 GAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGA 50 chr5ptel1M 883101 AACAGAGACCGGGAGGCAGAGACAGACACAGGGA 883134 i - -i i v i (GAGACA)n#Sim 51 GACAGAGA-C-AGAGACAGAGACAGAGACAGAGA 82 Matrix = Unknown Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.04 (3 / 82), avg. gap size = 1.00 (3 / 3) 197 23.68 7.77 5.71 chr5ptel1M 883168 883270 (116730) L2c_3end#LINE/L2 347 451 (27) m_b240s601i18 9470 chr5ptel1M 883168 TCTGTTTGT---TCTGTGTC-TGCGCCAGGCTGTGCGCTCCAGGAGAAGG 883213 ii--- v - v i i i v vv ---- L2c_3end#LINE 347 TCTGTTTACNTGTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGAG---- 392 chr5ptel1M 883214 TCGGCGGGGGAATTGCCTT-TTC-TCTTTGCATAC--AGGGGCGGGCACA 883259 -- i ivvv i - - i v -- v v v L2c_3end#LINE 393 --GGCAGGGACCGTGTCTTATTCATCTTTGTATCCCCAGCGCCTGGCACA 440 chr5ptel1M 883260 CAGTAGGTGCT 883270 i i L2c_3end#LINE 441 TAGTAGGCGCT 451 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.28 CpG sites = 11, Kimura (unadjusted) = 28.69 Transitions / transversions = 0.92 (11/12) Gap_init rate = 0.11 (11 / 102), avg. gap size = 1.27 (14 / 11) 38 29.36 3.45 0.67 chr5ptel1M 883925 883944 (116056) (GA)n#Simple_repeat 1 20 (129) m_b240s252i15 9477 chr5ptel1M 883925 GAGAGAGACCGGAAAAGAAA 883944 vv ii i i (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGA 20 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 51 0.00 0.00 0.00 chr5ptel1M 883945 883988 (116012) (GT)n#Simple_repeat 1 44 (0) c_b240s251i1 9478 chr5ptel1M 883945 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 883988 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 44 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 38 29.36 3.45 0.67 chr5ptel1M 883989 884112 (115888) (GA)n#Simple_repeat 21 148 (1) m_b240s252i15 9479 chr5ptel1M 883989 A-ATAGGGAGAGGCAGAGGCAGAGACAAAGAGAGGCAGAGAGAGAGAGAA 884037 - v i iv iv v i iv i (GA)n#Simple_ 21 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 70 chr5ptel1M 884038 ACAGAGAGACAGAGACAGAGAGATA-ATAGGGGCAGAGAAAGAAAACAAG 884086 v v v v - v i iv i i ivi (GA)n#Simple_ 71 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 120 chr5ptel1M 884087 ATGAAGGAAAAAG-GAGAGA-AGAG-GAG 884112 - ii i i - - - (GA)n#Simple_ 121 A-GAGAGAGAGAGAGAGAGAGAGAGAGAG 148 Matrix = Unknown Transitions / transversions = 1.33 (16/12) Gap_init rate = 0.05 (6 / 123), avg. gap size = 1.00 (6 / 6) 211 35.02 14.10 1.14 chr5ptel1M 884413 884568 (115432) MIR3#SINE/MIR 10 185 (23) m_b240s601i19 9480 chr5ptel1M 884413 TGGCTGTAGCGGGCTGGGCGTGGGCTGTGCAGTCAGGAGACCGGTGTTGT 884462 - i ivv i ii i v - v v v MIR3#SINE/MIR 10 TGGCTG-AGCAGAGAGAGCACGGACTGGG-AGTCAGGAGACCTGGGTTCT 57 chr5ptel1M 884463 G--CCCCACTCAGACATCTCCTACTTGTAAGAGCCGGAGTAA-------- 884502 i-- vi v v iivv ?vi iv v iv i i -------- MIR3#SINE/MIR 58 AGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTC 107 chr5ptel1M 884503 ----------GCCTCAGTTTCCCTCCCTGTAAACTAA--GGACCAGCTCC 884540 ---------- iivi v i -- iiii viiv MIR3#SINE/MIR 108 ACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTA 157 chr5ptel1M 884541 CCTGGTCTGTCAGGTCCTCCCTGGCTCT 884568 vv i v v iii ii MIR3#SINE/MIR 158 GATGATCTCTAAGGTCCCTTCCAGCTCT 185 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 48.18 CpG sites = 31, Kimura (unadjusted) = 49.49 Transitions / transversions = 1.35 (31/23) Gap_init rate = 0.04 (6 / 155), avg. gap size = 4.00 (24 / 6) 233 14.89 6.38 0.00 chr5ptel1M 885050 885096 (114904) C MIRc#SINE/MIR (101) 167 118 m_b240s601i20 9481 chr5ptel1M 885050 CAGGGCA--CCTTCTGACTCCCATTT-ACAGATGAGGAAACTGAGGCCCA 885096 --iv v v ii - i C MIRc#SINE/MIR 167 CAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCA 118 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 16.75 CpG sites = 4, Kimura (unadjusted) = 16.75 Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.04 (2 / 46), avg. gap size = 1.50 (3 / 2) 185 20.02 2.13 4.35 chr5ptel1M 885816 885862 (114138) C MIRb#SINE/MIR (13) 255 210 m_b240s601i21 9482 chr5ptel1M 885816 CCATGGTCACCGAGCACTTACTAAGTGCCA-GCTGTGTGCCAAGCACT 885862 -- i ii i v - vv i i C MIRb#SINE/MIR 255 CCAT--TTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCT 210 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 18.18 CpG sites = 6, Kimura (unadjusted) = 23.85 Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.07 (3 / 46), avg. gap size = 1.00 (3 / 3) 220 26.28 10.39 1.19 chr5ptel1M 886632 886708 (113292) C MIR3#SINE/MIR (15) 193 110 m_b240s601i22 9483 chr5ptel1M 886632 AGAATGACTAGAGCCCACAGGGACCTCAGACCTCCTT--------CTCCT 886673 v - iviv i vv v i-------- i i C MIR3#SINE/MIR 193 AGAATGTC-AGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCC 145 chr5ptel1M 886674 TCCTCTTCCCTATGGGGAAACAGAGGCCCAGAGGG 886708 v i v vv i v i C MIR3#SINE/MIR 144 TCATTTTACAGATGAGGAAACTGAGGCCCAGAGAG 110 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.57 CpG sites = 9, Kimura (unadjusted) = 32.57 Transitions / transversions = 0.82 (9/11) Gap_init rate = 0.03 (2 / 76), avg. gap size = 4.50 (9 / 2) 339 29.24 20.75 3.23 chr5ptel1M 886843 887054 (112946) MIRb#SINE/MIR 5 252 (16) m_b240s601i23 9484 chr5ptel1M 886843 GGGGCAGCTAGGTGGTACAGTGGG--------------TGGAGGC---TA 886875 --- i i-------------- v ---i MIRb#SINE/MIR 5 GGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACA 51 chr5ptel1M 886876 GACTTGAAGCCAGATCTGGCCTCTGGCACTTA-TAGCTGCAGGATCCTG- 886923 i iivi ii iv v v - iiv i i - MIRb#SINE/MIR 52 GACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 101 chr5ptel1M 886924 ------TGTTT-----------GCCTCAGCTTCCCCTTCTGTCAAATGCA 886956 ------ ii ----------- i i v v vi MIRb#SINE/MIR 102 GCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 151 chr5ptel1M 886957 GATAAAAGAATGTAT-------GAATGCTGTGAGAATC-AATGAAACAAT 886998 v iv iv i------- iv i i i- i i MIRb#SINE/MIR 152 GATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAAT 201 chr5ptel1M 886999 GACTGTAAGATACAGGGCCCAGGGCCCAGTAGACTCTTAGTAAAGAGTTC 887048 vv iiii vvi v v ii i ---- v - v i MIRb#SINE/MIR 202 GCATGTAAAGCGCTTAGCACAGTGCCTGGCA----CATAGT-AAGCGCTC 246 chr5ptel1M 887049 CATGAA 887054 v i MIRb#SINE/MIR 247 AATAAA 252 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.05 CpG sites = 38, Kimura (unadjusted) = 38.81 Transitions / transversions = 1.73 (38/22) Gap_init rate = 0.08 (16 / 211), avg. gap size = 3.25 (52 / 16) 193 32.48 7.03 3.79 chr5ptel1M 887163 887290 (112710) AmnL2-1#LINE/L2 2141 2272 (341) m_b240s601i24 9485 chr5ptel1M 887163 CATGTCCATGTCACTGACATACTCAAGAAGCTCCTATGGCTCCCTCTT-A 887211 ii v ii ivv v iv i vv iv - AmnL2-1#LINE/ 2141 CGCGACCACATCACCCCCATCCTCAAACAACTCCACTGGCTCCCCATTCA 2190 chr5ptel1M 887212 TCTCTGGAGCCA----ACAATTAACT--CTTGTTTGGCATTCAAAGCCCT 887255 i v v ---- v iv -- ----- i i AmnL2-1#LINE/ 2191 TTTCAGGATCCAGTTCAAAATTGCCTTCCTTGTT-----TTTAAAACCCT 2235 chr5ptel1M 887256 GCCCAATCTGGCTCTG--CAAGCACACGAACATTACC 887290 v viiiv v ii-- v v v i v ii AmnL2-1#LINE/ 2236 CCATGGACTTGCTCCAGCCTACCTCACGGACCTTGTC 2272 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.51 CpG sites = 20, Kimura (unadjusted) = 43.29 Transitions / transversions = 1.00 (20/20) Gap_init rate = 0.07 (9 / 127), avg. gap size = 1.56 (14 / 9) 1422 32.18 7.87 2.79 chr5ptel1M 887372 889011 (110989) L1M5_orf2#LINE/L1 1574 3294 (0) m_b241s551i0 9486 chr5ptel1M 887372 CAAGAGAAAGAAAACTCCAGACCAATTTCCCTAATGAATATTGATGTAAA 887421 - i v v v i v i L1M5_orf2#LIN 1574 CAAGA-AAAGAAAATTACAGACCAATATCCCTCATGAACATAGATGCAAA 1622 chr5ptel1M 887422 AATGTTAAATAAAACACTAGCAAGAAAATTACAGTGATACAGCACAAAGG 887471 vi ? i i i ivvi v v ii i vv v i i L1M5_orf2#LIN 1623 AATCCTNAACAAAATATTAGCAAATCGAATCCAGCAATATATAAAAAGGA 1672 chr5ptel1M 887472 TCATATATCAGGACCAGCTGGGATTTATATCAGGGATGCAGGGCTGGCTC 887521 v i v iv i vi i i i i i L1M5_orf2#LIN 1673 TAATACATCATGACCAAGTGGGGTTTATCCCAGGAATGCAAGGTTGGTTT 1722 chr5ptel1M 887522 AATATTAGGAAA------ACTGTGAGTGACCATAATTGACAAAA---ACA 887562 i v i ------ v i v v - i i --- vi L1M5_orf2#LIN 1723 AACATTCGAAAATCAATCAATGTAATTCACCATA-TTAACAGAATAAAGG 1771 chr5ptel1M 887563 ACAAAAATCATCCAATC---TCAATCGATGCAGAAAAAGCTTTTGATAAA 887609 v vii --- v v i L1M5_orf2#LIN 1772 AGAAAAATCATATGATCATCTCAATAGATGCAGAAAAAGCATTTGACAAA 1821 chr5ptel1M 887610 ATACAACACTCATTCCTATTAAAAAAAAAAAAAAAACACACACACCAGAA 887659 v i v iv --------------- v -i v L1M5_orf2#LIN 1822 ATTCAACACCCATTCATGATAAAAA---------------CTC-TCAGCA 1855 chr5ptel1M 887660 AGCATAGGAATAAATGAAGTTTTCCTTAAAATAATCAA---TATCTATCT 887706 i - i v iiivi i vv i v ---i ivv L1M5_orf2#LIN 1856 AAC-TAGGAATAGAAGGGAACTTCCTCAACCTGATAAAGGGCATCTACGA 1904 chr5ptel1M 887707 AAAACCATCAGCAAGCATTATCTGTAATAGAGATGAGCTAGAAGTCTTGA 887756 vv ? i i viv i v vi?i ii ? ii vv L1M5_orf2#LIN 1905 AAAACCTACAGCNAACATCATACTTAATGGTGAAANACTGAANGCTTTCC 1954 chr5ptel1M 887757 CAGTATGATCAGGAGCGAAGCAAGGAAGCCTATTATTATCACTATCATTC 887806 vv v i i i ii v i iii ? i i vii L1M5_orf2#LIN 1955 CCCTAAGATCGGGAACAAGACAAGGATGTCCGCTNTCACCACTTCTATTC 2004 chr5ptel1M 887807 AATATTGTACTAAAAATGCTAGCTCTAGCAATAAGAGAAGAAAAA-ATAT 887855 i ii ii v ivvv iv - v L1M5_orf2#LIN 2005 AACATTGTACTGGAGGTCCTAGCCAGTGCAATAAGGCAAGAAAAAGAAAT 2054 chr5ptel1M 887856 TGAAGGAATTAGAAAAAGCATTGAATTAGCAAAACT---ATTACGTAGCA 887902 vi v v ii vvi v vv vv ii ---? i- v L1M5_orf2#LIN 2055 AAAAGGCATAAAGATTGGAAAGGAAGAAATAAAACTGTCNTTAT-TCGCA 2103 chr5ptel1M 887903 TACAACATGA---------TGGAAAATCTGAGAGAATTCTCAACTTAAAA 887943 v ii --------- i i? i iiv ---- ? L1M5_orf2#LIN 2104 GATGACATGATTGTNTACGTAGAAAATCCNAAAGAATCTACA----AANA 2149 chr5ptel1M 887944 ATCTAGCTGAAATAATTAACCACTTTGGCAAAATTGCAGGATATAAAATA 887993 v viv v v iiv v i ii i ? i ii v L1M5_orf2#LIN 2150 AACTACTAGAACTAATAAGTGAATTTAGCAAGGTCGCNGGATACAAGGTC 2199 chr5ptel1M 887994 AACCCACATGAATCATCTGCATTTCTACATATTACCAACAAAGTCCAGTA 888043 ivi vi vi i i i v -- v v i L1M5_orf2#LIN 2200 AATATACAAAAATCAATTGTATTTCTATATACTAGCAACAAA--CAATTG 2247 chr5ptel1M 888044 G-----GAAACATAGAAAGAAATTCCATTTAAAATAAGTGTAGACAATAT 888088 ----- iv ?i iv v v ivvvi i v i L1M5_orf2#LIN 2248 GAAAATGAAATTTNAAAAACAATACCATTTACAATAGCATCAAAAAACAT 2297 chr5ptel1M 888089 AAAATATCTGGGAGTCTGCCTGCCGAGGTAAACCTAGGAGCTATACAGTG 888138 ? ii i i vvii iv i ii? viivi i v ? v L1M5_orf2#LIN 2298 NAAATACTTAGGAATAAATCTAACAAAANATGTGCAAGACCTNTACACTG 2347 chr5ptel1M 888139 AG------AAAACACTTTTCATAAAA--------------AAATACA--G 888166 i------ i vi v v i -------------- v -- L1M5_orf2#LIN 2348 AAAACTACAAAACATTGCTGAGAGAAATTAAAGAAGACCTAAATAAATGG 2397 chr5ptel1M 888167 AGAAATGTTCATTGTTCATAGTTAGGCCAAGTCAATACGATAAAAAGGAC 888216 i i v vv i v v vvi v ivi ? i v v L1M5_orf2#LIN 2398 AGAGATATACCATGTTCATGGATTGGAAGACTCAATATTGTNAAGATGTC 2447 chr5ptel1M 888217 AATTCTACCTAAATTAATTTAATTATTCAATGTCATACCAATAAAAATGC 888266 v i i i vvv iv v v -- L1M5_orf2#LIN 2448 AATTCTCCCCAAATTGATCTATAGATTCAATGCAATCCCAATCAAAAT-- 2495 chr5ptel1M 888267 CCCCCCCCCAAG---TTTTATAGAACTAGGGAAAATAGTGACAAAATTCA 888313 --- vv i --- i v v iv iv ii vvi i L1M5_orf2#LIN 2496 ---CCCAGCAGGTTTTTTTGTAGAAATTGACAAGCTGATTCTAAAATTTA 2542 chr5ptel1M 888314 CCTTAAAGAACAAAAGGTCAAGAATA-TCAGAGGAATTAATGGAAAAAAA 888362 iv vi ivi i ii ? -i i iv i-v i i L1M5_orf2#LIN 2543 TATGGAAATGCAAAGGACCNAGAATAGCCAAAACAATC-TTGAAAAAGAA 2591 chr5ptel1M 888363 G--TGAAGGGGGGTGGCTTAACAATGCCAGATTTCCAACTTTATTAC-AA 888409 --ii vv iv i - v i ? ? v ivi i- L1M5_orf2#LIN 2592 GAACAAAGTTGGAGGACTT-ACACTACCNGATNTCAAGACTTATTATAAA 2640 chr5ptel1M 888410 GCTGTACTCATCAAAACAAATTGGTCCTGCCTAAAAAACAAAAAGATTCA 888459 ii v v i ivv vi v vv ii i i v i vv L1M5_orf2#LIN 2641 GCTACAGTAATCAAGACAGTGTGGTATTGGCGTAAGGATAGACAAATAGA 2690 chr5ptel1M 888460 TCTGTGGAATCAATTA---AGTACATAGTACATATTTACTACTAGATAAT 888506 vi ivi v --- v v i- i v iii vvv v ii? L1M5_orf2#LIN 2691 TCAATGGAACAGAATAGAGAGTCCAGAA-ATAGACCCACACATATATGGN 2739 chr5ptel1M 888507 AATCTAGTGTTTGATGAA---CCCAAAG--ATCCAAGATTTTGGAACAAG 888551 v ?i ii v ii ---v ? -- i i---- v i v i L1M5_orf2#LIN 2740 CANTTGATTTTTGACAAAGGTGCCAANGCAATTCAG----TGGGGAAAGG 2785 chr5ptel1M 888552 ACCTCAATATTT--GACAAAAATTGTTGGGAAACCTAGAAATCAGTCTGG 888599 ---i i v --i viv i i v vi i v vi v L1M5_orf2#LIN 2786 A---TAGTCTTTTCAACAAATGGTGCTGGAACAATTGGATATCCATATGG 2832 chr5ptel1M 888600 CAGAAACTAGGTATAGAACAACATTTCATGCCATATAAGAAGATACGGTT 888649 v i v iii?v v v vvi ii ii i vi i vviv i L1M5_orf2#LIN 2833 AAAAAAATGAANCTCGACCCCTACCTCACACCATACACAAAAATTAATTC 2882 chr5ptel1M 888650 AAAATGGGTATGAGATTTAAACATAAAGGGTGATATTATA---------- 888689 ? i i vvv ii ii i ? i v i ---------- L1M5_orf2#LIN 2883 NAGATGGATCATAGACCTAAATGTAAAAGNTAAAACTATAAAACTTCTAG 2932 chr5ptel1M 888690 ---AGCACATGGAAAATTTTACTTGTCAGATCTATAGATAACGAAGGATT 888736 --- iv i i i v v vi i -- i vvi ? ivv i L1M5_orf2#LIN 2933 AAGAAAACATAGGAGAATATCTTCGT--GACCTTGGGNTAGGCAAAGATT 2980 chr5ptel1M 888737 T-ATGACCAA---ATAAAAGATA-AGATCATGGGAATTAAAATGGATAAT 888781 -v i v i--- i iii -?i i iii ivv v v L1M5_orf2#LIN 2981 TCTTAAACAGGACACAAAAAGCACNAACCATAAAAGAAAAAATTGATAAA 3030 chr5ptel1M 888782 TTTGACTACATTAAAAATCAA------TGC--------AGCCA------- 888810 v ? i v v ------ -------- v ------- L1M5_orf2#LIN 3031 TTGGACTNCATCAAAATTAAAAACTTCTGCTCNTCAAAAGACACCGTTAA 3080 chr5ptel1M 888811 -AGAAT-AGAAGGAAAG---CAAGCTTGGAAAGAGTTTTCACAGCAAGCA 888855 - i - i v --- ii? v i i i v ii i? vii L1M5_orf2#LIN 3081 GAAAATGAAAAGGCAAGCCACAGANTGGGAGAAAATATTTGCAANACATA 3130 chr5ptel1M 888856 TCTCTGACAAAG---TC-TGCTCA-AATATAGAGAGAACT-----AAGTC 888895 v --- - iii - v i ----- ? L1M5_orf2#LIN 3131 TATCTGACAAAGGACTCGTATCCAGAATATATAAAGAACTCCTACAANTC 3180 chr5ptel1M 888896 AAATTTATAAAAGTATGAATCATTTCCCAATTAATACATAGTCAAAGGAC 888945 -- v ? iv ii iv --- v? v v i v i L1M5_orf2#LIN 3181 AA--TAANAAAAAGACAAACAA---CCCAATANAAAAATGGGCAAAAGAC 3225 chr5ptel1M 888946 ATGAACAAACAGTTTTCAGAAGAAGAAATC--AGTTATCTATAATCATAT 888993 v i v iv i v ?-- i vii v v i L1M5_orf2#LIN 3226 TTGAACAGACACTTCACAAAAGAAGATATNCAAATGGCCAATAAGCACAT 3275 chr5ptel1M 888994 GAAAA-ATGCTCTAAATCA 889011 - v v? L1M5_orf2#LIN 3276 GAAAAGATGCTCAACNTCA 3294 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 43.79 CpG sites = 285, Kimura (unadjusted) = 44.51 Transitions / transversions = 1.25 (285/228) Gap_init rate = 0.05 (84 / 1639), avg. gap size = 2.11 (177 / 84) 859 30.65 5.21 2.22 chr5ptel1M 888872 889485 (110515) L1ME4c_3end#LINE/L1 8 639 (191) m_b241s551i1 9486 chr5ptel1M 888872 CTCAAATATAGAGAGAACTAAGTCAAATTTATAAAAGTATGAATCATTTC 888921 ?v ? v i i v v v i iv v? viv vvi L1ME4c_3end#L 8 CTNTANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAAGACC 57 chr5ptel1M 888922 CCAATTAATACATAGTCAAAGGACATGAACAAACAGTTTTCAGAAGAAGA 888971 vi v i v i i iv ? i L1ME4c_3end#L 58 CCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAGGA 107 chr5ptel1M 888972 AAT-CAGTTA-TCTATAATCATAT-GAAAAATGCTCTAAATCACTATTGA 889018 - i? - vv i v i - i v vv i v i L1ME4c_3end#L 108 AATACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTAGTAA 157 chr5ptel1M 889019 TTAGAGAAAGTCAAATTAAA-----AGGGAAATACCATCTCACACTTATC 889063 i i vv ----- iv i i i i i i L1ME4c_3end#L 158 TCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCTATT 207 chr5ptel1M 889064 AGATT-GCCTAAATGAGAGAAAAGGGAAATGATAAATGTTGGAGGAGACA 889112 i - vv vvi i vv iv iviv i v ii ?ii L1ME4c_3end#L 208 AAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGCTGGCGAGGNTG 257 chr5ptel1M 889113 TGG-GAAATTGGGACACTGCTCTCCTATT-GTGGGGTTGTGAACTGATTT 889160 i - i v ? vv vivi ii - vi? i i i vi L1ME4c_3end#L 258 CGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGTAC 307 chr5ptel1M 889161 AACCATACTGGAGAACAATTTGGGATGATGCCTA-CAAG-GCTATAAAAC 889208 v vi i i v -- i v - - i v L1ME4c_3end#L 308 AACCCTTTTGGAAAGCAATTTGGCA--ATACGTATCAAGAGCCATAAAAA 355 chr5ptel1M 889209 CATTCACATTCATTGAGCCAACAATATCATTAGGAGGTCTTTATCCCAAA 889258 ii i ii v v ii vi i vvvi vv i i L1ME4c_3end#L 356 TGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAG 405 chr5ptel1M 889259 GAAATCA--AAGAAAAAGGAAAAAGACCCCTATG--------TATTAATA 889298 v --v i i -- iv -------- i v v L1ME4c_3end#L 406 GAAATAATTCAAAAGAAGGAAAAAG--CTATATGCACGAAGATGTTCATT 453 chr5ptel1M 889299 GCAGCTCTTTTTGCTATATTAAATTAGAAAACTGGAACACAA--GGGATG 889346 vi v --- v i--iii i - --vii L1ME4c_3end#L 454 GCAGCGTTATT---TATAATAG--CGAAAAATTGGAA-ACAACCTAAATG 497 chr5ptel1M 889347 CCCATCAAGTGGGG-ATGGCTGGACAAGTTATGGTATAT-AACTGTAATG 889394 i v vv - i iiii i i -? -ii L1ME4c_3end#L 498 TCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACT-CGATG 546 chr5ptel1M 889395 GAATACTATTGTGCTATAAGAAATGATGAGCAGGATGTCTCCAGAAAAAC 889444 i vvv i v i i vi v v v viiv iv L1ME4c_3end#L 547 GAATATTATGCAGCCATTAAAAATGATAATTATGAAGACTATGTAGCAAC 596 chr5ptel1M 889445 CTAGAAAGAACG-----GATTTAAAGGGAAGTGAGCAGAAGCAGGA 889485 v i -- i ----- v v vv i- i i L1ME4c_3end#L 597 ATGGAA--AATGTTTATGATATAATGTTAAGTGAA-AAAAGCAGAA 639 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 39.64 CpG sites = 101, Kimura (unadjusted) = 41.15 Transitions / transversions = 1.22 (101/83) Gap_init rate = 0.05 (29 / 613), avg. gap size = 1.59 (46 / 29) 11 6.48 8.33 5.41 chr5ptel1M 889706 889741 (110259) (TAAATGA)n#Simple_repeat 1 37 (0) m_b241s252i0 9487 chr5ptel1M 889706 TAACTGATATAATTGATAAATG---AATGATAAATAATA 889741 v - - --- i (TAAATGA)n#Si 1 TAAATGATA-AA-TGATAAATGATAAATGATAAATGATA 37 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.09 (3 / 35), avg. gap size = 1.67 (5 / 3) 286 34.14 4.45 0.39 chr5ptel1M 889814 890060 (109940) L1P4_orf2#LINE/L1 3038 3294 (0) m_b241s551i2 9488 chr5ptel1M 889814 TAATTAAATTAAAAAGATTTTGCACAAAGAAAGCCAACAGAAACAAGATT 889863 i i v i ivi vv vi vv iii v L1P4_orf2#LIN 3038 TAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAACAGAGTA 3087 chr5ptel1M 889864 AAAAG-CAAAGTACAAAGCTGGGGAAATTTTTTTGCAGCCAGTGTTTCTG 889912 v - vv i i- ii vv v i iv vi iv i L1P4_orf2#LIN 3088 AACAGACAACCTACAGAA-TGGGAGAAAATATTCGCAAACTATGCATCCG 3136 chr5ptel1M 889913 TTAAAAGCCTCATTTCTAAAATATATGTCAAATTTATACGAAT--GCAAG 889960 vi i i v v i i v ivvi i v i ? --i L1P4_orf2#LIN 3137 ACAAAGGTCTAATATCCAGAATCTATAAGGAACTTAAACAANTCAACAAG 3186 chr5ptel1M 889961 TCA--------TTTCTCAATTGATAAATGGTCAAAGGATATGAGGAGACA 890002 iv -------- vv i v i v i v i iv L1P4_orf2#LIN 3187 CAAAAAACAAATAACCCCATTAAAAAGTGGGCAAAGGACATGAACAGACA 3236 chr5ptel1M 890003 AATTTCAGATGAAGAAATTAAAGCCATTTCTAGTCATATGAAAAAATGCT 890052 vv i i v v vv viiivvi iv L1P4_orf2#LIN 3237 CTTCTCAAAAGAAGACATACAAGCGGCCAACAAACATATGAAAAAATGCT 3286 chr5ptel1M 890053 CTAAATCA 890060 v v L1P4_orf2#LIN 3287 CAACATCA 3294 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 45.02 CpG sites = 41, Kimura (unadjusted) = 46.50 Transitions / transversions = 0.95 (41/43) Gap_init rate = 0.02 (4 / 246), avg. gap size = 3.00 (12 / 4) 1215 30.80 1.11 0.66 chr5ptel1M 889940 890390 (109610) L1ME4c_3end#LINE/L1 30 482 (348) m_b241s551i3 9488 chr5ptel1M 889940 TCAAATTTATACGAATGCAAGTCATTTCTCAATTGATAAATGGTCAAAGG 889989 v v viv? viv vvi i v v L1ME4c_3end#L 30 TCAAATTGATAAGAAAAANATCAAGACCCCAATAGATAAATGGGCAAAGG 79 chr5ptel1M 889990 ATATGAGGAGACAAATTTCAGATGAAGAAATTAAAGCCATTTCTAGTCAT 890039 i iv v iv ? v i vv ?ivi vvvi iv i L1ME4c_3end#L 80 ACATGAACAGACAATTCACANAAGAGGAAATACAANTAGTAAACAAACAC 129 chr5ptel1M 890040 ATGAAAAAATGCTCTAAATCACTATTGATCAGA-AAATGCAAATGAATAC 890088 i i v vv i v i i - v vi L1ME4c_3end#L 130 ATGGAAAAATGTTCAACCTCGCTAGTAATCAAAGAAATGCAAATTAAAGC 179 chr5ptel1M 890089 AACTCTGAGATACTGCCTCACACCTCTCAGATTGGCTAAGATGACAGGAA 890138 vv iiii i i v i i i v i vvv ii L1ME4c_3end#L 180 AACAATGAGATACCATTTTACGCCTATTAAATTAGCAAAAATTTAAAAAA 229 chr5ptel1M 890139 AAGATAATGATCAATATTGGAGTGGATGTGGGAAAACTGGGGCACTAATA 890188 vv ivi ii v v ? i vi vi ? v L1ME4c_3end#L 230 TTGATAATACCCAATGCTGGCGAGGNTGCGGTGAAACTGGTACNCTCATA 279 chr5ptel1M 890189 CATTGTTGGGGGAGCTGTGAAATGATCCAACCATTCTGGAGAGCAATTTG 890238 i v vi? i v i v v i i L1ME4c_3end#L 280 CATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTG 329 chr5ptel1M 890239 GAGGTATGCCCAAAGGGCTAT-AAAATTTGCATACCCTTTGACCCAGCAG 890287 vii i iviv i i - v v i i L1ME4c_3end#L 330 GCAATACGTATCAAGAGCCATAAAAATGTTCATACCCTTTGACCCAGTAA 379 chr5ptel1M 890288 TGTCATTACTGAGTCTGTATCCCAAGGAAATCAT---AAAGGAGGAAAAA 890334 vi i v i vv v i v --- i L1ME4c_3end#L 380 TTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAAGAAGGAAAAA 429 chr5ptel1M 890335 GGACCCACATGTGCACAAATGTTTGTAACAGTTCTTCTTGTGATGGCAAC 890384 --- i i ii iv i ii vi ivi vi i i i i v L1ME4c_3end#L 430 G---CTATATGCACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAA 476 chr5ptel1M 890385 AAGTTG 890390 i L1ME4c_3end#L 477 AAATTG 482 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 38.59 CpG sites = 75, Kimura (unadjusted) = 41.27 Transitions / transversions = 1.19 (75/63) Gap_init rate = 0.01 (6 / 450), avg. gap size = 1.33 (8 / 6) 234 31.47 2.17 3.30 chr5ptel1M 890989 891080 (108920) C MIR3#SINE/MIR (14) 194 104 m_b241s601i0 9489 chr5ptel1M 890989 TAGAGGCCCAAAGCTGGATGAGATCTTTGAAGTACTCTAATCCAAGTCCC 891038 ivvi i v i i v ii vv i vi C MIR3#SINE/MIR 194 TAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCC 145 chr5ptel1M 891039 C--TTTTACAGCTTGAAAAGTAAAGAAGGCCCAGCATGGGGAAG 891080 i-- v ---i i v vvi viv v C MIR3#SINE/MIR 144 TCATTTTACAGAT---GAGGAAACTGAGGCCCAGAGAGGTGAAG 104 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 41.37 CpG sites = 14, Kimura (unadjusted) = 41.37 Transitions / transversions = 1.00 (14/14) Gap_init rate = 0.04 (4 / 91), avg. gap size = 1.25 (5 / 4) 220 31.80 6.47 4.96 chr5ptel1M 891130 891268 (108732) C MIRc#SINE/MIR (121) 147 7 m_b241s601i1 9490 chr5ptel1M 891130 CCATTGTGGGGATAAGGAGA--GAGGCTCAGACAAAACTCAGGTAGGCAA 891177 v ivi i i -- v i------ v i ii C MIRc#SINE/MIR 147 CCATTTTACAGATGAGGAAACTGAGGCTCAGAGAG------GTTAAGTGA 104 chr5ptel1M 891178 CTTACCCAAGATCCCACAGGGAGGATTGTGG-GGAGGAAGAGTTCCTGCC 891226 i i v vv v -v -i vvi iii vvi C MIRc#SINE/MIR 103 CTTGCCCAAGGTCACACAGCTAGTA-AGTGGCAGAGCCGGGACTCGAACC 55 chr5ptel1M 891227 CAAATCAT-CTAACCTCAGCTCCAAGG-TCTT----CTGGACCAGATT 891268 ii v - i ii iv iv - ---- v v i C MIRc#SINE/MIR 54 CAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACT 7 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 41.27 CpG sites = 24, Kimura (unadjusted) = 42.62 Transitions / transversions = 1.33 (24/18) Gap_init rate = 0.09 (12 / 138), avg. gap size = 1.33 (16 / 12) 44 14.31 0.00 0.00 chr5ptel1M 891579 891648 (108352) (A)n#Simple_repeat 1 70 (0) m_b241s252i1 9491 chr5ptel1M 891579 AAAAAAAATTAAAAAAAACAAAAAATAAAATAAAATAAAATAAAAAAATT 891628 vv v v v v v vv (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr5ptel1M 891629 AAAAAAAAAAAAAAAAAAAA 891648 (A)n#Simple_r 51 AAAAAAAAAAAAAAAAAAAA 70 Matrix = Unknown Transitions / transversions = 0.00 (0/9) Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0) 252 17.39 0.00 0.00 chr5ptel1M 892165 892210 (107790) MIRc#SINE/MIR 104 149 (119) m_b241s601i2 9492 chr5ptel1M 892165 TCACCAAAAGTCCCCGAGCCTCAGTTTCCTCTTCTATAAAATGGGG 892210 iv vv i i v i MIRc#SINE/MIR 104 TCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGG 149 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 19.89 CpG sites = 4, Kimura (unadjusted) = 19.89 Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 201 28.22 11.71 4.20 chr5ptel1M 892215 892325 (107675) C L2c_3end#LINE/L2 (0) 478 360 m_b241s601i3 9493 chr5ptel1M 892215 ACTTATTCATTCCACAAAC--TGGTTGCACACCTATCGTGCGTGGGGTCA 892262 i i v -- vi vi i iii i i----- C L2c_3end#LINE 478 ATTCATTCATTCAACAAACATTTATTGAGCGCCTACTATGTGC-----CA 434 chr5ptel1M 892263 TGTGTTAGGGA--CAGAG-TGCA---GGCTGGATCCT--CCCT---GGGG 892301 v i i i -- i - v --- i vv i i-- --- i C L2c_3end#LINE 433 GGCGCTGGGGATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAG 384 chr5ptel1M 892302 ATCACAGTCTCAGGGAGGATACAG 892325 v viv v C L2c_3end#LINE 383 CTCACAGTCTAGTGGAGGAGACAG 360 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 33.77 CpG sites = 19, Kimura (unadjusted) = 36.83 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.10 (11 / 110), avg. gap size = 1.64 (18 / 11) 454 30.02 1.52 5.79 chr5ptel1M 892428 892625 (107375) C MIRb#SINE/MIR (45) 223 34 m_b241s601i4 9494 chr5ptel1M 892428 CTTTGCAAAGGGTTTTATAAATACT--CTAATTTGATCCTCACAACAACT 892475 v v v i i vii i -- v i i C MIRb#SINE/MIR 223 CTGTGCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACC 174 chr5ptel1M 892476 GTGGGAGCTGGAGGCTCCTATTATCCCCATTTCGCCTACGAGAAAATTAA 892525 v v -- v - vi ii vv i i i i C MIRb#SINE/MIR 173 CTGCGAG--GTAGG-TATTATTATCCCCATTTTACAGATGAGGAAACTGA 127 chr5ptel1M 892526 GGTGGGCAGCGG-TAACTCTCATGTCGAGGGTCACACTGCTCGGAGATGT 892574 ivviv v - v vv v i v i v v v ii v C MIRb#SINE/MIR 126 GGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGG 77 chr5ptel1M 892575 CCGAGGGCTAATTGGGACACAGGTCTTGCTCTCTGTCTGACTGATAAGCC 892624 v vvvvi v i v -------- vvv C MIRb#SINE/MIR 76 CAGAGCCGGGATTCGAACCCAGG--------TCTGTCTGACTCCAAAGCC 35 chr5ptel1M 892625 C 892625 C MIRb#SINE/MIR 34 C 34 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 38.29 CpG sites = 22, Kimura (unadjusted) = 38.29 Transitions / transversions = 0.65 (22/34) Gap_init rate = 0.07 (13 / 197), avg. gap size = 1.08 (14 / 13) 459 30.11 5.68 0.00 chr5ptel1M 892429 892604 (107396) C MIRc#SINE/MIR (39) 229 44 m_b241s601i5 9494 chr5ptel1M 892429 TTTGCAAAGGGTTTT---ATAAATACTCTAATTTGATCCTCACAACAACT 892475 i v i --- v vv v i C MIRc#SINE/MIR 229 TTTACAAAGCGCTTTCACATACATTATCTCATTTGATCCTCACAACAACC 180 chr5ptel1M 892476 GTGGGAGCTGG---AGGC---TCCTATTATCCCCATTTCGCCTACGAGAA 892519 v v v i ---i --- vi ii vv i i C MIRc#SINE/MIR 179 CTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGA 130 chr5ptel1M 892520 AATTAAGGTGGGCAGCGG-TAACTCTCATGTCGAGGGTCACACTGCTCGG 892568 i i ivviv v - v vv v i v i v v v C MIRc#SINE/MIR 129 AACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGT 80 chr5ptel1M 892569 AGATGTCCGAGGGCTAATTGGGACACAGGTCTTGCT 892604 ii v v vvvvi i v i v v C MIRc#SINE/MIR 79 AAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCT 44 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 38.58 CpG sites = 21, Kimura (unadjusted) = 38.58 Transitions / transversions = 0.66 (21/32) Gap_init rate = 0.02 (4 / 175), avg. gap size = 2.50 (10 / 4) 209 29.31 0.00 1.72 chr5ptel1M 893040 893098 (106902) L3#LINE/CR1 4027 4084 (15) m_b241s601i6 9495 chr5ptel1M 893040 CCTGATATTGGGTCAGAGAGTTGACTCAATGGCCTCCAAGTTGCCTTCCA 893089 -i i vi iv v vi i i v v L3#LINE/CR1 4027 CCTG-CATTGGATGGGAGGTTGGACTAGATGACCTCTAAGGTCCCTTCCA 4075 chr5ptel1M 893090 GCTCCAGGA 893098 i iii L3#LINE/CR1 4076 ACTCTGAGA 4084 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 38.76 CpG sites = 11, Kimura (unadjusted) = 38.76 Transitions / transversions = 1.83 (11/6) Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1) 36 0.00 0.00 0.00 chr5ptel1M 893820 893850 (106150) (CA)n#Simple_repeat 1 31 (0) c_b241s251i0 9496 chr5ptel1M 893820 CACACACACACACACACACACACACACACAC 893850 (CA)n#Simple_ 1 CACACACACACACACACACACACACACACAC 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 27 31.29 3.97 0.77 chr5ptel1M 893938 894063 (105937) (CTCT)n#Simple_repeat 1 130 (0) m_b241s252i2 9497 chr5ptel1M 893938 CTCTGTTTTTGTCTCTATCTCTGCCTAT-TCTCTCTCTGTCTCTCCCTGT 893986 v i i v v vi v - v i v (CTCT)n#Simpl 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chr5ptel1M 893987 -TCT-TCCTTCCTTCTCTCCCT-TCAC-CTGCCTCCTTCCTTCCTTCTCT 894032 - - ii ii i - v - vi ii ii ii (CTCT)n#Simpl 51 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 100 chr5ptel1M 894033 CCCTGTATCTCCCTCATCCCTCCCTCTCTCT 894063 i v v i - i i (CTCT)n#Simpl 101 CTCTCTCTCTCTCTC-TCTCTCTCTCTCTCT 130 Matrix = Unknown Transitions / transversions = 1.82 (20/11) Gap_init rate = 0.05 (6 / 125), avg. gap size = 1.00 (6 / 6) 231 30.67 1.33 0.00 chr5ptel1M 894365 894439 (105561) C MIRc#SINE/MIR (190) 78 3 m_b241s601i7 9498 chr5ptel1M 894365 AGAAGCATGGCAAGAATTCGAACACAAGTAC-CTTGGCTACCAACCCAAA 894413 vi vi vi i i v i vi- i i v v ii iv C MIRc#SINE/MIR 78 AGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGT 29 chr5ptel1M 894414 GCCCTTTCCACTGCACCATCCTGCCT 894439 i iv C MIRc#SINE/MIR 28 GCTCTTTCCACTGCACCACACTGCCT 3 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 38.54 CpG sites = 14, Kimura (unadjusted) = 40.86 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.01 (1 / 74), avg. gap size = 1.00 (1 / 1) 196 23.53 3.92 0.00 chr5ptel1M 894576 894626 (105374) C MIR1_Amn#SINE/MIR (59) 171 119 m_b241s601i8 9499 chr5ptel1M 894576 AAAGAGGCC-GCATC-CCATCCCTACTTTGCAGAAGAGGAAGCTGAGGTT 894623 i i - i -ii i i i v i i? C MIR1_Amn#SINE 171 AAGGAGGTCAGTATCATTATCCCCATTTTACAGATGAGGAAACTGAGGCN 122 chr5ptel1M 894624 GAG 894626 v C MIR1_Amn#SINE 121 CAG 119 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 31.08 CpG sites = 10, Kimura (unadjusted) = 31.08 Transitions / transversions = 5.00 (10/2) Gap_init rate = 0.04 (2 / 50), avg. gap size = 1.00 (2 / 2) 199 25.93 5.88 12.50 chr5ptel1M 895984 896102 (103898) L2d2_3end#LINE/L2 436 547 (8) m_b241s601i9 9500 chr5ptel1M 895984 AGACCGTAAGCCCCTTG-GGGCAGGGGATAGCTCGTTGTTTTCATTTGTG 896032 ii i - ivi vv - i vi iv i L2d2_3end#LIN 436 AGATTGTAAGCTCCTTGAGGGCAGGGACCATGTC-TTATACTTCTTTGTA 484 chr5ptel1M 896033 TGCCCAGCCCCCACACCAGCAGTAGCCCAGTCTCT------CAGGAGGCA 896076 ------ v iv -- v vi ------ v i L2d2_3end#LIN 485 T------CCCCCACAGCGCC--TAGCACAGTGCCTTGCACACAGTAGGCG 526 chr5ptel1M 896077 TTTGGTAAAGGCATATTTAGTGGATT 896102 i iii ---- - v L2d2_3end#LIN 527 CTCAATAA----ATATTT-GTTGATT 547 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 29.40 CpG sites = 16, Kimura (unadjusted) = 32.22 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.14 (16 / 118), avg. gap size = 1.31 (21 / 16) 16 0.00 0.00 0.00 chr5ptel1M 896302 896319 (103681) (G)n#Simple_repeat 1 18 (0) m_b241s252i4 9501 chr5ptel1M 896302 GGGGGGGGGGGGGGGGGG 896319 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGG 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 240 28.56 3.80 2.50 chr5ptel1M 896379 896457 (103543) C L2b_3end#LINE/L2 (9) 457 378 m_b241s601i10 9502 chr5ptel1M 896379 TCCAACAAGCACTTACTGAGTGCCCATTACATGTTCCAGCCCCCGTGCTG 896428 i ii i i i i --i v v ? i i C L2b_3end#LINE 457 TTCAACAAATATTTACTGAGCGCCTACT--GTGTGCCAGGCNCTGTGCTA 410 chr5ptel1M 896429 GACGCTGAG--CACAAGACTAAA-AGGACAAA 896457 i i --i iviv i - i i C L2b_3end#LINE 409 GGCGCTGGGGATACAGCGGTGAACAAGACAGA 378 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 35.38 CpG sites = 18, Kimura (unadjusted) = 40.14 Transitions / transversions = 4.50 (18/4) Gap_init rate = 0.05 (4 / 78), avg. gap size = 1.25 (5 / 4) 272 36.37 1.67 2.23 chr5ptel1M 896678 896857 (103143) L2c_3end#LINE/L2 298 476 (2) m_b241s601i11 9503 chr5ptel1M 896678 CTATCTA-ATTGCCATTTGGTGGCAAATTTCAGTGAGGT-TACTTTGGTT 896725 i - i v --i i vv v v i vv - i v ii L2c_3end#LINE 298 CTGTCTATACTCCCATT--ATAGCACTTATCATTAACTTGTATTGTAATT 345 chr5ptel1M 896726 TTTTTTTAATCTAAGTATCTGTTTTCTGAGAAAAGGAAACTCTTGGGGGC 896775 v i v v i? ivv i vi iiviv vviv ivii i L2c_3end#LINE 346 GTCTGTTTACNTGTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGC 395 chr5ptel1M 896776 AGGGAAGTTGTTTCAATTTTGCCTTTTTTTCTCCAACCCAAGGCACATAG 896825 vvv i i -- iii v v i i v vv L2c_3end#LINE 396 AGGGACCGTGTCTTA--TTCATCTTTGTATCCCCAGCGCCTGGCACATAG 443 chr5ptel1M 896826 TAGGC-CCCCCCAAATGCCTGTTGATTGACTGA 896857 - i vvi ii v v L2c_3end#LINE 444 TAGGCGCTCAATAAATGTTTGTTGAATGAATGA 476 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 51.15 CpG sites = 32, Kimura (unadjusted) = 51.15 Transitions / transversions = 1.00 (32/32) Gap_init rate = 0.04 (7 / 179), avg. gap size = 1.00 (7 / 7) 348 31.90 5.17 0.00 chr5ptel1M 897556 897671 (102329) MIRc#SINE/MIR 6 127 (141) m_b241s601i12 9504 chr5ptel1M 897556 CAGTCTGATATCAGAGAAAGA--ACGGGATTTGGGGACAGGG---CCCGA 897600 v i iivivi -- v i i v i--- i i MIRc#SINE/MIR 6 CAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGG 55 chr5ptel1M 897601 GTTCCAATCCCAGTTCTACCACTTACTCCCAATATGACTTTCAATAAGTC 897650 v i i i i vv vi i i viii MIRc#SINE/MIR 56 GTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTC 105 chr5ptel1M 897651 TTTTGCCCTCTCCTGG-CTCAG 897671 vi iv ivi - MIRc#SINE/MIR 106 ACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 42.05 CpG sites = 24, Kimura (unadjusted) = 43.66 Transitions / transversions = 1.85 (24/13) Gap_init rate = 0.03 (3 / 115), avg. gap size = 2.00 (6 / 3) 333 30.60 3.37 4.55 chr5ptel1M 897781 897958 (102042) C MIR3#SINE/MIR (1) 207 32 m_b241s601i13 9505 chr5ptel1M 897781 AGTTATAAGATCATAGAGT-TCAGAGACACAGAGGCCTTCTTCAAAGACA 897829 i i ii i - viiv ii v -- - i iv C MIR3#SINE/MIR 207 AATCATAGAATCATAGAATGTCAGAGCTGGAAGGGAC--CTT-AGAGATC 161 chr5ptel1M 897830 ATCTGGTCTAACGACCTCATTTTATAGGTGGTAGAAATAAGGCT--GGGG 897877 i i vv i i ivii v i i-- i i C MIR3#SINE/MIR 160 ATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGA 111 chr5ptel1M 897878 GCTAGAAGAGGCCGGGCAGGAAGCAACACACAGCTAA-TAATAAC--AGC 897924 v - v i iv v --v -iv ? i- i ii -- C MIR3#SINE/MIR 110 GGT-GAAGTGACTTGCC--CAAG-GTCACACAGCNAGTTAGTGGCAGAGC 65 chr5ptel1M 897925 TGTGATCTGAACCCAGGTGCCAGGACTCCACAGT 897958 i v iiv vi vv - C MIR3#SINE/MIR 64 CGGGACTAGAACCCAGGTCTCCTGACTCC-CAGT 32 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 40.26 CpG sites = 33, Kimura (unadjusted) = 41.32 Transitions / transversions = 1.74 (33/19) Gap_init rate = 0.07 (12 / 177), avg. gap size = 1.17 (14 / 12) 199 25.93 5.56 0.00 chr5ptel1M 897967 898020 (101980) C MIRc#SINE/MIR (19) 249 193 m_b241s601i14 9506 chr5ptel1M 897967 ATTTACAGAGTGCCTTGGAGCTTGCAATGC---TTCACATAAATCATCTC 898013 ii v ii i iv i i v --- v i C MIRc#SINE/MIR 249 ATTTGTATAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATCTC 200 chr5ptel1M 898014 ATGTGAT 898020 v C MIRc#SINE/MIR 199 ATTTGAT 193 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 32.87 CpG sites = 9, Kimura (unadjusted) = 32.87 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.02 (1 / 53), avg. gap size = 3.00 (3 / 1) 227 36.42 2.41 2.41 chr5ptel1M 898088 898253 (101747) C L2d2_3end#LINE/L2 (370) 185 20 m_b241s601i15 9502 chr5ptel1M 898088 AGGTAGAAGGGAGCGGGGAGGGCACTGTTGGCAGGGGGGG-AGCTTGGGC 898136 i ii iv i i viv i ii-i v i C L2d2_3end#LIN 185 AGGTGGAGAGGAAGGGGAAGGGCATTCCAGGCGGGGGGAACGGCGTGAGC 136 chr5ptel1M 898137 AAAGACAGGGAAGTAGGAGA---TGAAGCATCATTACAAGGAACAACAAA 898183 i ivi i ii i?---ii i i -i - ii i iii i C L2d2_3end#LIN 135 AAAGGCGCAGAGGCGGGAANGCGCAAGGCGT-GTT-CGGGGGACAGTGAG 88 chr5ptel1M 898184 TAGGGCAGTTTGGTTCCATCACATGATGTGTGAAGGAGGTTAATTAGCAC 898233 iv i vv v iv v i vi ? i iv i vi - v C L2d2_3end#LIN 87 TAGACCAGTTTGGCTGGAGCGGAGGGTTCGTGNAGGGGAATAGTGGG-AG 39 chr5ptel1M 898234 ATTAAGACTGGAAGAGTAAG 898253 - i ii ? i C L2d2_3end#LIN 38 AT-AAGGCTGGAAAGGNAGG 20 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 45.82 CpG sites = 44, Kimura (unadjusted) = 57.40 Transitions / transversions = 2.93 (44/15) Gap_init rate = 0.04 (6 / 165), avg. gap size = 1.33 (8 / 6) 490 26.24 11.80 3.65 chr5ptel1M 898752 898929 (101071) C MIRc#SINE/MIR (65) 203 12 m_b241s601i16 9507 chr5ptel1M 898752 TCTCACCCAATGCTCAGTAC---CCTGAGAGGAAGGCGGGATGGCTGGGC 898798 iiii v vv --- v v i iii v i--- C MIRc#SINE/MIR 203 TCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTA--- 157 chr5ptel1M 898799 ACAGTTATCAGTCTCATTGTATAAAAGGAAAAACCGAGGTTCAGAGAGGG 898848 ---- i vi i v i i v iii i i v C MIRc#SINE/MIR 156 ----TTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGT 111 chr5ptel1M 898849 CA--TGATTGGCCTAAGGTCACTCAGCTGGAA------AGAAACGG---- 898886 i -- i v i v i v ------ iv ---- C MIRc#SINE/MIR 110 TAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACT 61 chr5ptel1M 898887 ----CCAAGATTTT--TGACTCCAAGACCAGTGTTTTTTCCACTACACC 898929 ---- v i i -- v i i i C MIRc#SINE/MIR 60 CGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACC 12 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 33.53 CpG sites = 29, Kimura (unadjusted) = 33.53 Transitions / transversions = 1.81 (29/16) Gap_init rate = 0.07 (13 / 177), avg. gap size = 2.15 (28 / 13) 309 23.54 1.63 13.64 chr5ptel1M 899238 899360 (100640) C MIR#SINE/MIR (140) 122 13 m_b241s601i17 9508 chr5ptel1M 899238 TGAGGCA-ATTGGATTTAAGTAACTTGCTCAGGGTCACACAGCTAGGAAG 899286 - vv iiv i i v C MIR#SINE/MIR 122 TGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAG 73 chr5ptel1M 899287 TGTTGAATGTTGAGTGTCTGAGGCCATATCTGAACTCAGGTCCTCCTGAC 899336 ------ iv --- i i ----- ii i ivv - i C MIR#SINE/MIR 72 TG------GCAGAG---CCGGG-----ATTCGAACCCAGGCAGT-CTGGC 38 chr5ptel1M 899337 TTCAGGGCTGGGGCTC-TATCCACT 899360 i i iv v - v C MIR#SINE/MIR 37 TCCAGAGCCCGTGCTCTTAACCACT 13 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 25.67 CpG sites = 15, Kimura (unadjusted) = 28.25 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.14 (17 / 122), avg. gap size = 1.00 (17 / 17) 413 21.20 0.00 13.86 chr5ptel1M 899252 899366 (100634) C MIRc#SINE/MIR (157) 111 11 m_b241s601i18 9508 chr5ptel1M 899252 TTAAGTAACTTGCTCAGGGTCACACAGCTAGGAAGTGTTGAATGTTGAGT 899301 i i i v ------ iv - C MIRc#SINE/MIR 111 TTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTG------GCAGAG- 69 chr5ptel1M 899302 GTCTGAGGCCATATCTGAACTCAGGTCCTCCTGACTTCAGGGCTGGGGCT 899351 -- i i ----- iii i i i i v ii v C MIRc#SINE/MIR 68 --CCGGG-----ACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCT 26 chr5ptel1M 899352 CTATCCACTGCTCCA 899366 v v C MIRc#SINE/MIR 25 CTTTCCACTGCACCA 11 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 22.50 CpG sites = 15, Kimura (unadjusted) = 25.20 Transitions / transversions = 2.50 (15/6) Gap_init rate = 0.12 (14 / 114), avg. gap size = 1.00 (14 / 14) 247 33.90 10.02 8.47 chr5ptel1M 899375 899793 (100207) C L2b_3end#LINE/L2 (5) 461 37 m_b241s601i20 9509 chr5ptel1M 899375 TTCCTTCAATAAACATTTATTAGACACT--CTGGATGGGCCAGCCACAAT 899422 v i i i iii i i-- -- v v ? vi C L2b_3end#LINE 461 TTCATTCAACAAATATTTACTGAGCGCCTACTG--TGTGCCAGGCNCTGT 414 chr5ptel1M 899423 GTTAGGCATTAGGGATACAAAG--AAACAAAA------------------ 899452 i ii i iv --i i ------------------ C L2b_3end#LINE 413 GCTAGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCC 364 chr5ptel1M 899453 ----GAAGCTCACTATCTAATGGGAAAGATA-ACAAGCAAAAAAAAAAAA 899497 ---- i vi i ii i - v i ?v i v v? C L2b_3end#LINE 363 TCACGGAGCTCACAGTCTAGTGGGGGAGACAGACATGTAANCAGACAATN 314 chr5ptel1M 899498 AAAAAAAAAAAAAAAAGGAATAACA-AATAGGATAAATGGGAAATAATTA 899546 v vvv --------- i ii -ii i--- ii------i C L2b_3end#LINE 313 ATAACCCA---------GAGTGGCAGGGTAGGAC---TGGGGG------G 282 chr5ptel1M 899547 GCAGAGGGATGGACGCTAGAATTAA---GAGGACTTGGGGAAGGCTTCCT 899593 vv i iv i iv viiii--- i iv ii i i C L2b_3end#LINE 281 GCCCAGAGGAGGGCGCCTGACCCGGCCTGGGGGGTCAGGGAGGGCTTCCC 232 chr5ptel1M 899594 GAGGAAGATGGGATTTGAGTTGGGACTTGAAGGA--AGCCAGAG-AAACC 899640 ii i i iv i i i -- ivi -vii C L2b_3end#LINE 231 GGAGGAGGTGACATTTGAGCTGAGACCTGAAGGATGAGTAGGAGTTGGCC 182 chr5ptel1M 899641 AAGAGGTGACGTGAGGAGGGAGAGCACTCCAGCTATGGGGGACTATCAGA 899690 i v iv v i --- i ii vi vi i viiv? v C L2b_3end#LINE 181 AGGCGAAGAGGTGGGGA---AGGGCGTTCCAGGCAGAGGGAACAGCANGT 135 chr5ptel1M 899691 GAAAATGCCCCGATAGATGAAGGGTCTTGGT--------GGAACATCCAG 899732 v v i viviv i? iv ? i-------- v v C L2b_3end#LINE 134 GCAAAGGCCCTGAGGCGGGAGNGAGCNTGGCGTGTTCGAGGAACAGCAAG 85 chr5ptel1M 899733 GAGCTGCGTCATGGGATGTAACAGGATGTGAGGAGTAAGAACAAAGGAAA 899782 ---- i ----i ii v --- vi -- i i i i C L2b_3end#LINE 84 GAG----GCCA----GTGTGGCTGGA---GCAGAGT--GAGCAAGGGGAG 48 chr5ptel1M 899783 GGTGAGAGGGG 899793 i iv i C L2b_3end#LINE 47 AGTGGTAGGAG 37 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 45.60 CpG sites = 88, Kimura (unadjusted) = 49.47 Transitions / transversions = 2.10 (88/42) Gap_init rate = 0.11 (46 / 418), avg. gap size = 1.70 (78 / 46) 298 32.31 11.97 4.85 chr5ptel1M 899375 899683 (100317) C L2c_3end#LINE/L2 (5) 473 144 m_b241s601i19 9509 chr5ptel1M 899375 TTCCTTCAATAAACATTTATTAGACACTCTGGATGGGCCAGCCACAATGT 899424 v i iii ----------- vi i ii- i C L2c_3end#LINE 473 TTCATTCAACAAACATTTATTGAGC-----------GCCTACTATG-TGC 436 chr5ptel1M 899425 TAGGCATTAGGGATACAAAGA--AACAA------------------AAGA 899454 i ii i -- i ------------------ i C L2c_3end#LINE 435 CAGGCGCTGGGGATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGG 386 chr5ptel1M 899455 AGCTCACTATCTAATGGGAAAGATA-ACAAGCAAAAAAAAAA----AAAA 899499 vi i iii i - ? i v i v ---- v C L2c_3end#LINE 385 AGCTCACAGTCTAGTGGAGGAGACAGACANGTAAACAGACAATTACAATA 336 chr5ptel1M 899500 AAAAAAAAAAAAAAGGA--ATAACAAATAGGATAAATGGGAAATAATT-- 899545 v ivv vi v vi-- iiii- v i ii iviiv v-- C L2c_3end#LINE 335 CAAGTTAATGATAAGTGCTATAATGGG-AGTATAGACAGGGTGCTATGGG 287 chr5ptel1M 899546 AGCAGAGGGATGGACGCTAGAATTAA----GAGGACTTGGGGAAGGCTTC 899591 v i iv i i ivii i i---- i iv ii C L2c_3end#LINE 286 AGCACAGAGGAGGGCACCTAGACTAGNCTTGGGGGGTCAGGGAAGGCTTC 237 chr5ptel1M 899592 CTGAGGAAGATGGGATTTGAGTTGGGACTTGAAGGA--AGCCAGAG-AAA 899638 i ii i i iv i i i ? -- ivi -v i C L2c_3end#LINE 236 CCGGAGGAGGTGACATCTGAGCTGAGNCTTGAAGGATGAGTAGGAGTTAG 187 chr5ptel1M 899639 CCAAGAGGTGACGTGAGGAGGG-AGAGCACTCCAGCTATGGGGGAC 899683 --- iviv i - i vi vi i C L2c_3end#LINE 186 CC---AGGTGGAAGGAGGGGGGAAGAGCATTCCAGGCAGAGGGAAC 144 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 44.81 CpG sites = 68, Kimura (unadjusted) = 46.20 Transitions / transversions = 2.52 (68/27) Gap_init rate = 0.08 (26 / 308), avg. gap size = 2.04 (53 / 26) 193 33.94 8.53 2.23 chr5ptel1M 900894 901104 (98896) C AmnL2-1#LINE/L2 (1304) 1309 1086 m_b241s601i21 9510 chr5ptel1M 900894 GGAGAGAATGATTCTGGCGGCATGATAAAGTCAGAAGCCAGACTGCAAGA 900943 ii ii i iiv i vi iiv iiv ii v v ?v C AmnL2-1#LINE/ 1309 GAGGAGAGCGGTTTCCGTGCTATGGCCAGAGCGAAACCCAGACTGAAANC 1260 chr5ptel1M 900944 GATTAAAAA---------GGGA-AGAAGA--GGAGAGG-AAGGGAAGGC- 900979 i i ii --------- v - iv -- i-i i - C AmnL2-1#LINE/ 1259 GGTCAAGGATANTGTTGTGTGAGAGGTGACTGGAGAGATGAGAGAAGGCT 1210 chr5ptel1M 900980 ACTGATT---GCAGTTTAGCT-ACAAAAGGCAGAAAAGAACCAGGACAAT 901025 vvi --- v - - v i v ivv ivi i ii C AmnL2-1#LINE/ 1209 ACTTTCTCAAGCACTTT-GCTGAGAAAGGGAAGGTTAGAGATAGGGCGGT 1161 chr5ptel1M 901026 GTTTAGTGGGGATGGAAGGATCAAGTGAGGGTTTTTTGAAAATGGCCGAG 901075 iv v i ii vvi i v i i v vvvi C AmnL2-1#LINE/ 1160 AGTTAGAGAGAGTGTCGGGGTCAAGGGAGGGTTTTTTAAGAAGGGAACGG 1111 chr5ptel1M 901076 ACACAGGCACATCTTAGGACAGAGTCTGG 901104 vv v i --- - C AmnL2-1#LINE/ 1110 ACAGTGGCAGATTTTAG---AGAG-CTGG 1086 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 42.73 CpG sites = 41, Kimura (unadjusted) = 47.30 Transitions / transversions = 1.41 (41/29) Gap_init rate = 0.06 (12 / 210), avg. gap size = 1.92 (23 / 12) 16 16.47 2.78 2.78 chr5ptel1M 901167 901202 (98798) (AG)n#Simple_repeat 1 36 (0) m_b241s252i5 9511 chr5ptel1M 901167 AGAG-GAGAGAGGGAGAGATGAAAAATAGAGACAGAG 901202 - i - i i v v (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGA-GAGAGAGAGAGAGAGAG 36 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 18 7.56 0.00 0.00 chr5ptel1M 901615 901642 (98358) (AAAC)n#Simple_repeat 1 28 (0) m_b241s252i6 9512 chr5ptel1M 901615 AAACAAACAAACAAACAAAAAAACACAC 901642 v v (AAAC)n#Simpl 1 AAACAAACAAACAAACAAACAAACAAAC 28 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 451 31.01 4.40 0.61 chr5ptel1M 901708 901866 (98134) C MIR3#SINE/MIR (23) 185 21 m_b241s601i22 9513 chr5ptel1M 901708 AGGACAGGATGGGACCTCAGAGACCATTTTTTCCAAGCCCCTCCTTTTCC 901757 ii v v i i i vv v v v C MIR3#SINE/MIR 185 AGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTAC 136 chr5ptel1M 901758 AGGGGAGGCAAATGAAGTC--GGGAAATCAAG----CTGTTTAAGGTTAC 901801 iv v v i i -- i ii v ----i iii i C MIR3#SINE/MIR 135 AGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCAC 86 chr5ptel1M 901802 CCAGATAGGAAATAGCAAAGCCAAGACT-GAACCCACACCCTCTGGATCC 901850 v v? vv i i i ii - vii ii iv C MIR3#SINE/MIR 85 ACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGTCTCCTGACTCC 36 chr5ptel1M 901851 AAACCCAAAGCTCTTT 901866 v ii -iv i C MIR3#SINE/MIR 35 CAGTCC-GTGCTCTCT 21 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 39.65 CpG sites = 30, Kimura (unadjusted) = 41.90 Transitions / transversions = 1.58 (30/19) Gap_init rate = 0.03 (4 / 158), avg. gap size = 2.00 (8 / 4) 395 29.26 5.59 2.03 chr5ptel1M 901747 901889 (98111) C MIRc#SINE/MIR (119) 149 2 m_b241s601i23 9513 chr5ptel1M 901747 CCTCCTTTTCCAGGGGAGGCAAATGAAG-TCGG-GAAATCAAGC----TG 901790 i v v iv v v i - i - ii i i---- C MIRc#SINE/MIR 149 CCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTG 100 chr5ptel1M 901791 TTTAAGGTTACCCAGATAGGAAATAGCAAAGCCAAGACT-GAACCCACAC 901839 iii i v v v i i i ii - vii C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGT 50 chr5ptel1M 901840 CCTCTGGA-TCCAAACCCAAAGCTCTTTGATCGTCTGCCCCATGCTGCTT 901888 i iv - ii iv --- vv v ii i C MIRc#SINE/MIR 49 CTTCCTGACTCCAAGTCCAGTGCTCTT---TCCACTGCACCACACTGCCT 3 chr5ptel1M 901889 C 901889 C MIRc#SINE/MIR 2 C 2 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 37.59 CpG sites = 27, Kimura (unadjusted) = 38.83 Transitions / transversions = 1.93 (27/14) Gap_init rate = 0.06 (8 / 142), avg. gap size = 1.38 (11 / 8) 26 30.73 5.15 1.42 chr5ptel1M 901892 902027 (97973) (CT)n#Simple_repeat 1 141 (0) m_b241s252i7 9514 chr5ptel1M 901892 CTCT-TCACTCTC-CACCCTC-CTCCCTATGTCTCCTTCTGTGGATGTCT 901938 - v - v i - i v v ii v vvv v (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chr5ptel1M 901939 CTCTCTGCCTCTACCCCT-TCTTTGT-TCTCTCTCTCATCCATCTCTCTC 901986 vi vi i - i v - - iv (CT)n#Simple_ 51 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TCTCTCTCTCTC 99 chr5ptel1M 901987 TCTGCTTTC-CTC-CTCCCCACCTCCCATTCCCTCTTTCCCTC 902027 - i - - i ivi i vi i i i (CT)n#Simple_ 100 TCT-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 141 Matrix = Unknown Transitions / transversions = 1.20 (18/15) Gap_init rate = 0.07 (9 / 135), avg. gap size = 1.00 (9 / 9) 250 27.50 3.75 0.00 chr5ptel1M 902073 902152 (97848) C L3#LINE/CR1 (6) 4093 4011 m_b241s601i24 9515 chr5ptel1M 902073 ATCCCCAAATCTCGCAGTTTCGAGGGATCTCAGAGGT-ACTTAGTCCAAC 902121 v vi iv vvi i i - ii C L3#LINE/CR1 4093 ATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCAAC 4044 chr5ptel1M 902122 C-CACATCTGA-GCTGCGATTCTCTCTAAAACA 902152 - v ii - v vi i ii v C L3#LINE/CR1 4043 CTCCCATCCAATGCAGGAATCCCTTCTACAACA 4011 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 35.14 CpG sites = 13, Kimura (unadjusted) = 35.14 Transitions / transversions = 1.44 (13/9) Gap_init rate = 0.04 (3 / 79), avg. gap size = 1.00 (3 / 3) 18 0.00 0.00 0.00 chr5ptel1M 902543 902562 (97438) (A)n#Simple_repeat 1 20 (0) m_b241s252i8 9516 chr5ptel1M 902543 AAAAAAAAAAAAAAAAAAAA 902562 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAA 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 328 31.18 1.08 0.00 chr5ptel1M 902692 902784 (97216) MIR3#SINE/MIR 94 187 (21) m_b241s601i25 9517 chr5ptel1M 902692 GGGCCA-TCACCCAAGCTTCCTGGATCTCGGTTTACTTCTCTGTAACATG 902740 v - iiv v ii ii i v iv v MIR3#SINE/MIR 94 GGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATG 143 chr5ptel1M 902741 AAGGGGTTGTATCAGTAGACCTTCAAAGTCCCCTCCCATTCTAA 902784 i v ii vv i ii i i vii i MIR3#SINE/MIR 144 AGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGA 187 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 42.35 CpG sites = 19, Kimura (unadjusted) = 42.35 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.01 (1 / 92), avg. gap size = 1.00 (1 / 1) 629 31.44 8.71 1.51 chr5ptel1M 903019 903328 (96672) C L3#LINE/CR1 (5) 4094 3763 m_b241s601i26 9518 chr5ptel1M 903019 AGTCCTGGACCCTCAGAGGTGGGCATGACCTCAAAG-CCGCCTTGGG-AA 903066 i vii vi v iviv i i -i ii v vv- C L3#LINE/CR1 4094 AATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCAA 4045 chr5ptel1M 903067 CCCCCCAATCACATGTA------CCATTGACATTATTC-TACTAGATGCT 903109 i vi - i ------ v iv vi i - ivi ii v C L3#LINE/CR1 4044 CCTCCCATCCA-ATGCAGGAATCCCTTCTACAACATCCCTGACAAGTGGT 3996 chr5ptel1M 903110 CAATCAGCTTCTTCTTGAAGGCCTAGAATGACAGGAAGCTCACTACCTCT 903159 vi i v vi vv i i i ? C L3#LINE/CR1 3995 CATCCAGCCTCTGCTTGAACACCTCCAGTGACGGGGAGCTCACTACCTCN 3946 chr5ptel1M 903160 --ATGCTACGCATTTCTAGTTTGGGACTGCTTCTATGTTCAGGAAGCTTT 903207 -- v vi v - i v v v iiv vv i i i i C L3#LINE/CR1 3945 CGAGGCAGCCCA-TTCCATTTTTGGACAGCTCTGATTGTTAGAAAGTTCT 3897 chr5ptel1M 903208 TCCTTCAAGGAAGCCAAAATCTGCCTCTCTG---------CCCGTTCTTC 903248 vv vvi i i --------- i vv C L3#LINE/CR1 3896 TCCTTATATTGAGCCGAAATCTGCCTCCCTGTAACTTCCACCCATTGGTC 3847 chr5ptel1M 903249 TTCCCCCTGCCCTCTAAGAG-----CGGAGGAAATTCAATCCCCGTTC-- 903291 i vvii -i ----- i iv i ii iv -- C L3#LINE/CR1 3846 CTAGTTCTGCCCTCT-GGAGCCACACAGAATAAGTCTAATCCCTCTTCCA 3798 chr5ptel1M 903292 CATAAGAGGCCTTGCAATATTTGGAGCTAACACTATC 903328 i v v vv i vi --i C L3#LINE/CR1 3797 CATGACAGCCCTTCAAATATTTGAAGACA--GCTATC 3763 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 40.85 CpG sites = 53, Kimura (unadjusted) = 41.99 Transitions / transversions = 1.23 (53/43) Gap_init rate = 0.04 (13 / 309), avg. gap size = 2.46 (32 / 13) 250 27.14 1.43 0.00 chr5ptel1M 903728 903797 (96203) C MIRc#SINE/MIR (163) 105 35 m_b241s601i27 9519 chr5ptel1M 903728 GATTAGCCCAAGCTCACA-AGCTAGCAACTCCCAGAGGCAAGCCTTGAAC 903776 i v v - i v vv v ii v i C MIRc#SINE/MIR 105 GACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAAC 56 chr5ptel1M 903777 CTGGGACTTTGGGACTCCAGG 903797 ii v ivv i C MIRc#SINE/MIR 55 CCAGGTCTTCCTGACTCCAAG 35 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 29.84 CpG sites = 9, Kimura (unadjusted) = 33.95 Transitions / transversions = 0.90 (9/10) Gap_init rate = 0.01 (1 / 69), avg. gap size = 1.00 (1 / 1) 272 34.17 3.33 0.00 chr5ptel1M 904673 904792 (95208) C MIR3#SINE/MIR (3) 205 82 m_b241s601i28 9520 chr5ptel1M 904673 TTACAGGAGCAAAGAA-GTCAGGG--GAAGGGGAACTTCTGGAAGGCTGA 904719 i i i v v - i -- i i v vvi vviiiv C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTA 156 chr5ptel1M 904720 ATCCCAGGCCCTCATTTAACAAAGAAAAAACCCAAGGTTCAGAAAGAT-A 904768 i v vv v i vi ii v ii ii i i - C MIR3#SINE/MIR 155 GTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGA 106 chr5ptel1M 904769 AGTCTCTTGGCCAGAGTCACGCAG 904792 vv v ii i C MIR3#SINE/MIR 105 AGTGACTTGCCCAAGGTCACACAG 82 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 47.34 CpG sites = 24, Kimura (unadjusted) = 47.34 Transitions / transversions = 1.41 (24/17) Gap_init rate = 0.03 (3 / 119), avg. gap size = 1.33 (4 / 3) 390 36.64 6.39 1.41 chr5ptel1M 905100 905276 (94724) L1MC5_3end#LINE/L1 124 305 (2389) m_b241s551i4 9521 chr5ptel1M 905100 AACCTTGTGACAGAATGCTCCAAATCA---ACAACAGGAGAAATTCACAG 905146 ? v i v ii v vv i--- i i i v v v L1MC5_3end#LI 124 AANCATATGAAAAGATGCTCAACCTCGCTCATAATAAGAGAAATGCAAAT 173 chr5ptel1M 905147 CAAAACCAGCTTTAGGTTTCACTTCCCACC-AGAAAACTGGCACCAGTGA 905195 i i vvi v i vi i i - vv i i vv i v- L1MC5_3end#LI 174 TAAAACTACACTGAGATACCATTTCTCACCTATCAGATTGGCAAAAATC- 222 chr5ptel1M 905196 CAAAAG----ACAGGAGAGTCCACGTTGATGGGATTGGAGGAAGCTAGAC 905241 ---- iv v v i-- ii i ii vi i ivi i L1MC5_3end#LI 223 CAAAAGTTTGACAACATACTCT--GTTGGCGAGGCTGTGGGGAAACAGGC 270 chr5ptel1M 905242 ATACTACTATATTGATCAAGAAACCCTGGACTGAT 905276 iv vv i v viv ii viviii v i L1MC5_3end#LI 271 ACTCTCATACATTGCTGGTGGGAATGCAAAATGGT 305 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 51.79 CpG sites = 85, Kimura (unadjusted) = 52.85 Transitions / transversions = 1.26 (39/31) Gap_init rate = 0.03 (6 / 176), avg. gap size = 1.83 (11 / 6) 29 0.00 0.00 0.00 chr5ptel1M 905277 905303 (94697) (AAAACA)n#Simple_repeat 1 27 (0) c_b241s251i1 9522 chr5ptel1M 905277 AAAACAAAAACAAAAACAAAAACAAAA 905303 (AAAACA)n#Sim 1 AAAACAAAAACAAAAACAAAAACAAAA 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 390 36.64 6.39 1.41 chr5ptel1M 905304 905532 (94468) L1MC5_3end#LINE/L1 306 549 (2145) m_b241s551i4 9521 chr5ptel1M 905304 CA----CTGTGG--GGAAAT--GGCAGT--CAAGTAA--CTACA-ATTTA 905340 ---- i -- i -- i -- v i --i - vi L1MC5_3end#LI 306 CAACCCCTATGGAGGGGAATTTGGCAATATCTAGCAAAATTACATATGCA 355 chr5ptel1M 905341 CATATCTCATGACTCCAAAATCCCACTGCTAAGCATGCACCACAAGGGGT 905390 iv i iiv i viv v i v vi i v i ivv L1MC5_3end#LI 356 TTTACCCTTTGACCCAGCAATCCCACTTCTAGGAATCTATCCCAAAGATA 405 chr5ptel1M 905391 CACTGACCAAAACA----AAGGTTTCCTAGACATCAAAATATTGACAGCA 905436 i v i ---- i--- v vi iv iiv v iv L1MC5_3end#LI 406 CACTGGCAAAAATACGAAAAGA---CGTATGCACAAGGCTATTCATTGCA 452 chr5ptel1M 905437 CCACTTTTTGCAAAGGCAAAGAACTGGAAACAAAGTAGATGCTCTTTGTT 905486 v v i vi ii vvi i ii v iiv L1MC5_3end#LI 453 GCACTATTTGTAATAGCAAAAGACTGGAAACAACCCAAATGTCCATCAAT 502 chr5ptel1M 905487 TGGAAAATGGCT-AACAAATTGTGGTTCATAAATGTAATGGAATATT 905532 v ii v i - i i i v vv iii i i L1MC5_3end#LI 503 AGGGGACTGGTTGAATAAACTATGGTACATCCACACAATGGAGTACT 549 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 51.79 CpG sites = 85, Kimura (unadjusted) = 52.85 Transitions / transversions = 1.48 (46/31) Gap_init rate = 0.05 (11 / 228), avg. gap size = 1.91 (21 / 11) 270 31.52 6.05 5.56 chr5ptel1M 905341 905555 (94445) L1ME3B_3end#LINE/L1 357 572 (417) m_b241s551i5 9521 chr5ptel1M 905341 CATATCTCATGACTCCAAAATCCCACTGCTAAGCATGCACCACAAGGG-- 905388 i ii i viv i v i i ii vi ii i-- L1ME3B_3end#L 357 CATACCCTATGACCCAGCAATTCCACTCCTAGGTATATACCCTAGAGAAA 406 chr5ptel1M 905389 ---GT-CAC---TG-ACCAAAACAAAGGTTTCCTAGACATCAAAATATTG 905430 --- - --- - ii ? v v ------- -- i i v L1ME3B_3end#L 407 CGCGTGCACATGTGCACCAGGANACATGT-------ACA--AGAATGTTC 447 chr5ptel1M 905431 ACAGCACCACTTTTTGCAAAGGCAAAGAACTGGAAACAAAGTAGATGCTC 905480 i v i v i i vi v? i vvi i ii L1ME3B_3end#L 448 ATAGCAGCATTGTTCGTAATAGCCNAAAACTGGAAACAACCCAAATGTCC 497 chr5ptel1M 905481 TTTGTTTGGAAAATGGCT-AACAAATTGTGGTTCATAAATGTAATGGAAT 905529 v iiviv v i v - i vi vv ii L1ME3B_3end#L 498 ATCAACAGTAGAATGGATAAATAAATTGTGGTATATTCATACAATGGAAT 547 chr5ptel1M 905530 ATTCCCATGGAGTA--GGAAATGATCAA 905555 i --- iv i -- i v i L1ME3B_3end#L 548 ACT---ATACAGCAATGAAAATGAACGA 572 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 41.60 CpG sites = 41, Kimura (unadjusted) = 43.44 Transitions / transversions = 1.78 (41/23) Gap_init rate = 0.09 (19 / 214), avg. gap size = 1.32 (25 / 19) 236 24.24 1.04 5.43 chr5ptel1M 906144 906239 (93761) L1M4c_5end#LINE/L1 2370 2461 (39) m_b241s551i6 9523 chr5ptel1M 906144 TTAGTAATCTTAACTGTGAATGTGAATGGGACGAACTCTCCCAATAAAAT 906193 i i--- v i i ivii - v - L1M4c_5end#LI 2370 TCAGTAATT---ACTTTAAATGTAAATGGATTAAACTCT-CCAATCAAA- 2414 chr5ptel1M 906194 AGAAGCGGA-CAGCAGAGTGAATTAAAAGCCAGAATCCTACAATATG 906239 vi?i -ii ? i i iv ?i v v L1M4c_5end#LI 2415 AGACANAGATTGGCNGAATGGATTAAAAAACANGATCCAACTATATG 2461 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 31.61 CpG sites = 15, Kimura (unadjusted) = 31.61 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.06 (6 / 95), avg. gap size = 1.00 (6 / 6) 16 0.00 0.00 0.00 chr5ptel1M 906324 906341 (93659) (A)n#Simple_repeat 1 18 (0) m_b241s252i9 9524 chr5ptel1M 906324 AAAAAAAAAAAAAAAAAA 906341 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAA 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 12 9.73 8.57 2.70 chr5ptel1M 906610 906644 (93356) (TTCTC)n#Simple_repeat 1 37 (0) m_b241s252i10 9525 chr5ptel1M 906610 TTCTCTTCTCTT-T-TTATTTATCTCTTCT-TCCTCTT 906644 - - v i - - i (TTCTC)n#Simp 1 TTCTCTTCTCTTCTCTTCTCT-TCTCTTCTCTTCTCTT 37 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.12 (4 / 34), avg. gap size = 1.00 (4 / 4) 339 27.18 7.83 0.81 chr5ptel1M 907682 907796 (92204) MIR3#SINE/MIR 66 188 (20) m_b241s601i29 9526 chr5ptel1M 907682 CTCTGCTCCAAA---GCTATGGGCCCAT----AAACCACTTAATCACTCC 907724 iv v --- i v v v ---- ii v i v i MIR3#SINE/MIR 66 CTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCT 115 chr5ptel1M 907725 CTACCTCAGTTTCCTTATCTAGAAAGGGAGGGGGAGTAGACCAGCTAATC 907774 vvi i iv iv -v i i v i MIR3#SINE/MIR 116 GGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGG-TTGGACTAGATGATC 164 chr5ptel1M 907775 TCTAAGGTATTTCCT--CTCTGAC 907796 vii i i-- MIR3#SINE/MIR 165 TCTAAGGTCCCTTCCAGCTCTGAC 188 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 34.37 CpG sites = 17, Kimura (unadjusted) = 34.37 Transitions / transversions = 1.21 (17/14) Gap_init rate = 0.04 (4 / 114), avg. gap size = 2.50 (10 / 4) 391 24.97 7.63 2.17 chr5ptel1M 908697 908827 (91173) C MIRb#SINE/MIR (124) 144 7 m_b241s601i30 9527 chr5ptel1M 908697 TACAGATCTGGGGAGACTGA--CTCCTGAGAG---AGGCGACTTGTGTGG 908741 -- i i -- v- --- i ii iviii C MIRb#SINE/MIR 144 TACAGAT--GAGGAAACTGAGGCTCA-GAGAGGTTAAGTAACTTGCCCAA 98 chr5ptel1M 908742 AGTCACGCAG---GTAAGTGTCAGGGCCGAGATTTGAATCCAGAGCTG-- 908786 i i --- v i i i i iv -- C MIRb#SINE/MIR 97 GGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTC 48 chr5ptel1M 908787 CGACTCCAGACCGGAGGCTCTTGCCCCCGCATCATGCTGCC 908827 i i v vviv v v i i i C MIRb#SINE/MIR 47 TGACTCCAAAGCCCGTGCTCTTTCCACTGCACCACGCTGCC 7 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 28.12 CpG sites = 22, Kimura (unadjusted) = 31.65 Transitions / transversions = 2.20 (22/10) Gap_init rate = 0.05 (7 / 130), avg. gap size = 1.86 (13 / 7) 360 21.55 0.00 3.80 chr5ptel1M 908833 908914 (91086) C L3#LINE/CR1 (87) 4012 3934 m_b241s601i31 9528 chr5ptel1M 908833 CATCCCGTGAAAGGGGAAGCTCTCCAACTTCTGCTCGAAGACCTCTAATG 908882 - v i v -- iiv i i i v i i C L3#LINE/CR1 4012 CATCCC-TGACAAGTG--GTCATCCAGCCTCTGCTTGAACACCTCCAGTG 3966 chr5ptel1M 908883 ATGGGGAGCTTACTACCTCCCAAGACAACCCA 908914 i i ? i i i C L3#LINE/CR1 3965 ACGGGGAGCTCACTACCTCNCGAGGCAGCCCA 3934 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 23.36 CpG sites = 13, Kimura (unadjusted) = 26.98 Transitions / transversions = 3.25 (13/4) Gap_init rate = 0.04 (3 / 81), avg. gap size = 1.00 (3 / 3) 189 31.17 11.82 0.82 chr5ptel1M 909743 909852 (90148) MIR3#SINE/MIR 81 202 (6) m_b241s601i32 9529 chr5ptel1M 909743 GCTGGGCCACCTCAGCCTAATGGTACCGCCTCTCTGGGCCTCAAGTTCTC 909792 v iv ii v v i viivi i iv ii MIR3#SINE/MIR 81 GCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCT 130 chr5ptel1M 909793 C---------ACAGGGGAGTCTGGAC-AGA--GTCCCCGAGGCCCCTCCC 909830 --------- iii i - - --i i ii i i MIR3#SINE/MIR 131 CATCTGTAAAATGAGGGGGT-TGGACTAGATGATCTCTAAGGTCCCTTCC 179 chr5ptel1M 909831 AGGCCTGACACCCCCTG-TTCTA 909852 vi ii iv - MIR3#SINE/MIR 180 AGCTCTGACATTCTATGATTCTA 202 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 43.48 CpG sites = 25, Kimura (unadjusted) = 43.48 Transitions / transversions = 2.78 (25/9) Gap_init rate = 0.05 (5 / 109), avg. gap size = 2.80 (14 / 5) 18 3.33 6.45 0.00 chr5ptel1M 910165 910195 (89805) (TGTCTC)n#Simple_repeat 1 33 (0) m_b241s252i11 9530 chr5ptel1M 910165 TGTCTCCGTCTCTGTCTCTG--TCTGTCTCTGT 910195 i -- (TGTCTC)n#Sim 1 TGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGT 33 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.03 (1 / 30), avg. gap size = 2.00 (2 / 1) 55 0.00 0.00 0.00 chr5ptel1M 910196 910242 (89758) (CA)n#Simple_repeat 1 47 (0) c_b241s251i2 9531 chr5ptel1M 910196 CACACACACACACACACACACACACACACACACACACACACACACAC 910242 (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACAC 47 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 183 17.37 8.51 2.00 chr5ptel1M 910638 910684 (89316) MIRb#SINE/MIR 48 97 (171) m_b241s601i33 9532 chr5ptel1M 910638 GACAGACCCAGGGTCAGCGCCCAGCTCTGCCGACTTA----CTGTGTGAC 910683 ii v iivv i - ---- MIRb#SINE/MIR 48 GACAGACCTGGGTTCGAATCCCGGCTCTGCC-ACTTACTAGCTGTGTGAC 96 chr5ptel1M 910684 C 910684 MIRb#SINE/MIR 97 C 97 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 14.92 CpG sites = 5, Kimura (unadjusted) = 20.10 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.04 (2 / 46), avg. gap size = 2.50 (5 / 2) 382 28.45 3.82 0.74 chr5ptel1M 910785 910915 (89085) MIR3#SINE/MIR 74 208 (0) m_b241s601i34 9533 chr5ptel1M 910785 CTCACTA-CTGTGTGGTCTTGGGTAAGTCGGGTCATGACCCTGGGCCTCA 910833 v ?- ii i ivv ivv i MIR3#SINE/MIR 74 CTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCA 123 chr5ptel1M 910834 GTTTCCCCCAATGTAAAATGAAGAGCTTGGGCACGATGG-CACTGAGGCC 910882 i vvv i i v i vv i- v i i MIR3#SINE/MIR 124 GTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTC 173 chr5ptel1M 910883 CCCTCAGGCCCGTGGC---CCATGAGCTCACGGTTC 910915 i vi i - i --- i viii i i MIR3#SINE/MIR 174 CCTTCCAGCTC-TGACATTCTATGATTCTATGATTC 208 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 37.40 CpG sites = 23, Kimura (unadjusted) = 37.40 Transitions / transversions = 1.64 (23/14) Gap_init rate = 0.03 (4 / 130), avg. gap size = 1.50 (6 / 4) 302 33.50 15.48 0.52 chr5ptel1M 911129 911296 (88704) C MIRc#SINE/MIR (72) 196 4 m_b241s601i35 9534 chr5ptel1M 911129 TGAGCCTCCCAACGACTCCGCAGGAAAGGCATTA-AGGGATTGTCTGCTC 911177 v v i i i iii iv vvi- v i ivv i C MIRc#SINE/MIR 196 TGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCC 147 chr5ptel1M 911178 TGCCTTTCAAAACAAAGAAGCTAA--TTCAGAGTGGGTAAGCAGCTTCCC 911225 iiii v i -ii i i i --i v v iii v C MIRc#SINE/MIR 146 CATTTTACAGA-TGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCC 98 chr5ptel1M 911226 CAGGGCCACACAACCAG---------GGGCTGGCCCCTGAA--------- 911257 i i i i --------- i i vv ii --------- C MIRc#SINE/MIR 97 CAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCT 48 chr5ptel1M 911258 -----GCTCCAGGGTCAGTACCCTGCCCACTGGACCACACTGCC 911296 -----i i vi i i vi v C MIRc#SINE/MIR 47 TCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTGCC 4 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 45.32 CpG sites = 39, Kimura (unadjusted) = 47.76 Transitions / transversions = 2.29 (39/17) Gap_init rate = 0.04 (6 / 167), avg. gap size = 4.50 (27 / 6) 223 30.99 1.41 0.00 chr5ptel1M 911293 911363 (88637) C MIRc#SINE/MIR (72) 196 125 m_b241s601i36 9535 chr5ptel1M 911293 TGCCCTTCACAACAACCCTGAGAAGCAGAGGGAAAAAGCCTTCTT-CCCC 911341 vi i v i i ivi iiv i iv v -i C MIRc#SINE/MIR 196 TGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCC 147 chr5ptel1M 911342 CATTTTCCAAACGAACAAACTG 911363 v i i iv C MIRc#SINE/MIR 146 CATTTTACAGATGAGGAAACTG 125 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 41.75 CpG sites = 14, Kimura (unadjusted) = 41.75 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.01 (1 / 70), avg. gap size = 1.00 (1 / 1) 21 7.56 0.00 0.00 chr5ptel1M 914233 914260 (85740) (G)n#Simple_repeat 1 28 (0) m_b241s252i12 9536 chr5ptel1M 914233 GGGGGGGGGGGGGGGGGGGGCGCGGGGG 914260 v v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGG 28 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 18 18.09 7.14 0.00 chr5ptel1M 914557 914612 (85388) (AGCGGGGG)n#Simple_repeat 1 60 (0) m_b241s252i13 9537 chr5ptel1M 914557 AGGGGTGGAG-GGAGGAGC-AGGAAGCGGGGG-GAGGGGGAGCGTGGG-G 914602 v v - i -i i - v v - (AGCGGGGG)n#S 1 AGCGGGGGAGCGGGGGAGCGGGGGAGCGGGGGAGCGGGGGAGCGGGGGAG 50 chr5ptel1M 914603 GGGGGGACCG 914612 v v (AGCGGGGG)n#S 51 CGGGGGAGCG 60 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.07 (4 / 55), avg. gap size = 1.00 (4 / 4) 13 15.66 11.86 1.54 chr5ptel1M 914769 914827 (85173) (CGTCGCG)n#Simple_repeat 1 65 (0) m_b241s252i14 9538 chr5ptel1M 914769 CGT-GCGCGTGCGCGCGT-GCGCGTC-CCCGCCAC-CGTCACACG-C-CG 914812 - - - - v i i - i i - - (CGTCGCG)n#Si 1 CGTCGCGCGT-CGCGCGTCGCGCGTCGCGCGTCGCGCGTCGCGCGTCGCG 49 chr5ptel1M 914813 C-TCGCCCCTTGCGCG 914827 - v v i (CGTCGCG)n#Si 50 CGTCGCGCGTCGCGCG 65 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.14 (8 / 58), avg. gap size = 1.00 (8 / 8) 16 18.91 0.00 4.55 chr5ptel1M 915217 915262 (84738) (GCCCCCT)n#Simple_repeat 1 44 (0) m_b241s252i15 9539 chr5ptel1M 915217 GCTCCCTGGCCCGCTGCCCCCCTCTCCCTGCCCCCTGTCTCCGTGC 915262 i - v iv i - i v (GCCCCCT)n#Si 1 GCCCCCT-GCCCCCTGCCCCCTGCCCCCTGCCCCCTG-CCCCCTGC 44 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.04 (2 / 45), avg. gap size = 1.00 (2 / 2) 77 35.09 5.70 1.01 chr5ptel1M 917289 917762 (82238) (GAGA)n#Simple_repeat 1 496 (0) m_b241s252i16 9540 chr5ptel1M 917289 GAGAG-GAG-GAAAGGGCCAGGGGGAAAGAGA-AAAGAG-GAG-GAGGGA 917333 - - i i vv i i i - i - - i (GAGA)n#Simpl 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr5ptel1M 917334 AGGGGAGAGAG-GAAGGAAAGAGA-AGGAAGGGAG-GAAAGA-AAAGGGA 917379 ii i - ii i - ii i - i - i i (GAGA)n#Simpl 51 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 100 chr5ptel1M 917380 GAGGGAGGGATAGA-AGA-AAAAAGAAAGAGAGGGAGGGA-AGAAAGGGG 917426 i i v - - i i i i i - i i i (GAGA)n#Simpl 101 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 150 chr5ptel1M 917427 GTAGGAAGGGACGGAAGGAAAAGGAAAGA-AAAGAGAGA-AGA-AGGGA- 917472 - ii i vi ii i ii i - i - - i - (GAGA)n#Simpl 151 G-AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 199 chr5ptel1M 917473 AGGGAAAGGGGAAAAGAGGAAGGGA-AGGGGAAGGGGAAAAGAGGAAGGG 917521 i i i ii i ii i - i ii i ii i ii i (GAGA)n#Simpl 200 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 249 chr5ptel1M 917522 AAGGGGAG-GGGGGAAAGAGGAAGGAAGGGAAGGAGAAAGAGAAAG-GAG 917569 ii i - i i i ii ii i ii i i - (GAGA)n#Simpl 250 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 299 chr5ptel1M 917570 AAAGA-AGGTAGAAACAAGGGGAAAG-GGGAGAGAGAGGAAGGGAG-GAA 917616 i - iv i v ii i i - i ii i - i (GAGA)n#Simpl 300 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 349 chr5ptel1M 917617 AGATAG-GAAAGGGAGAGAGAAAGA-AGAATGGGGGGAAGA-AAAGAGGG 917663 v - i i i - iv i i ii - i i (GAGA)n#Simpl 350 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 399 chr5ptel1M 917664 TAGA-AGGGAGGAAGAGCATGCACACA-AGACAGAGAGAGAGAGAGAGAG 917711 - - i ii - - - v v - v (GAGA)n#Simpl 400 -AGAGAGAGAGAGAGAG-A-G-AGAGAGAGAGAGAGAGAGAGAGAGAGAG 445 chr5ptel1M 917712 AGAGAGAAGGAAAAAGAGAGAGATAGACACAGTGAGAGAGAAAGAAAGAG 917761 ii i i v v v v i i (GAGA)n#Simpl 446 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 495 chr5ptel1M 917762 A 917762 (GAGA)n#Simpl 496 A 496 Matrix = Unknown Transitions / transversions = 7.07 (106/15) Gap_init rate = 0.07 (32 / 473), avg. gap size = 1.00 (32 / 32) 253 16.33 12.24 0.00 chr5ptel1M 917836 917884 (82116) C MER63D#DNA/hAT-Tip100 (0) 1061 1007 m_b241s502i0 9541 chr5ptel1M 917836 CAGCTATGTGCTAACAAGTGTTTAACAACCAGCTCTCTG------AAAAT 917879 ivi iii i i ------ C MER63D#DNA/hA 1061 CAGTGGTGTGCTGGTAAATGTTTAACAACCGGCTCTCTGGGGGAAAAAAT 1012 chr5ptel1M 917880 GTATG 917884 C MER63D#DNA/hA 1011 GTATG 1007 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 16.74 CpG sites = 7, Kimura (unadjusted) = 19.31 Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.02 (1 / 48), avg. gap size = 6.00 (6 / 1) 1521 28.14 2.88 2.07 chr5ptel1M 917910 918533 (81467) L1ME3G_3end#LINE/L1 4 632 (292) m_b241s551i7 9542 chr5ptel1M 917910 ATTTCCAAACTATATAGAGAATTGACTCTAATTTATAAGAAATCAAGCCA 917959 v i v i i vviv v iv -- v L1ME3G_3end#L 4 ATATCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAA--AAGACA 51 chr5ptel1M 917960 TTCTCCAATTGATAAATGGTCAAAGGATATGAACAGACAATTCTCAGAAG 918009 --vi v v v i v L1ME3G_3end#L 52 --ACCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAG 99 chr5ptel1M 918010 A---AATTAAAACTATTTCTAGCCATACGAAAAGATGCTCCGAGTCATTC 918056 --- vv iviiivv iv i vivv i v L1ME3G_3end#L 100 AGGAAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTA 149 chr5ptel1M 918057 TTAATCAGAGAAATGCAAATGAAGACAACTCTGAGATACCACTATACACA 918106 v i v i vv i v v - L1ME3G_3end#L 150 GTAATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCAC- 198 chr5ptel1M 918107 CCTGTCAGATTGGCTAGAGTGACAGAGAAAGATAATGTGGAATGTTGGAG 918156 - ii v i i vvv i ?vv i v? i v L1ME3G_3end#L 199 -CCATCAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCG 247 chr5ptel1M 918157 -GGATGTGGGAAAACAGGGACACTGATACATCGTTGGTGGAATTGTGAAC 918205 - i i i v v v ii i i v i i L1ME3G_3end#L 248 AGGGTGTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAAT 297 chr5ptel1M 918206 ACATCCAGCCGTTCTGGAGAGCAGTTTGGAACTATGCTCAAAAAGTTATC 918255 vvi v ? i i i v v viviv v -- L1ME3G_3end#L 298 TGGTACAGCCNTTTTGGAGGGCAATTTGGCAGTATCTATTAAAATTTA-- 345 chr5ptel1M 918256 AAAC-TGCATACC-TTTGACCCAGCAGTGTTACTACTGGGCTTATATCCC 918303 i-i - i vii v ? ?v v i L1ME3G_3end#L 346 AAATGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCT 395 chr5ptel1M 918304 AAGGAGAT-CTTAAAGA-ACGGAAAGGGACCTGTATGTGCACGAATGTTT 918351 ?i i - iiv v -ii v v i --? i i v i i L1ME3G_3end#L 396 ANAGAAATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTC 443 chr5ptel1M 918352 GTGGCAGCCCTCTTTGTAGTGAC-------TGGAAACTGAGTGGATGCCC 918394 i v vi v i ii ------- vivv ii i L1ME3G_3end#L 444 ATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCC 493 chr5ptel1M 918395 ATCAGTTGAAGAATGGCTGAATAAATTGTGGTATATGAATATTATGGAAT 918444 i v ii i i i vv i L1ME3G_3end#L 494 ATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAAT 543 chr5ptel1M 918445 ATTATCCTTCGGTAAGAAATGACCAACAGGAGGATGT---CAGAAAGACC 918491 i v vv ? v i - -- vv vi v ---iiv vv v L1ME3G_3end#L 544 ACTATGCAGCNGTTAAAAA-GA--ATGAGGTAGATCTATATGTACTGACA 590 chr5ptel1M 918492 TGGAGAGACCGATAGGAACTGATATTGAGTGAAATGAGCAGG 918533 i i vvi i vv iv i vi i L1ME3G_3end#L 591 TGGAAAGATCTCCAAGACATATTGTTGAGTGAAAAAAGCAAG 632 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 35.51 CpG sites = 86, Kimura (unadjusted) = 36.31 Transitions / transversions = 1.00 (86/86) Gap_init rate = 0.03 (21 / 623), avg. gap size = 1.48 (31 / 21) 196 31.77 0.00 1.18 chr5ptel1M 919288 919373 (80627) C MIRc#SINE/MIR (182) 86 2 m_b241s601i37 9543 chr5ptel1M 919288 AGCCAGCAATTGTCAGAGCCAGGCCGAGGACACAGATCTGCCAGCATCCA 919337 i i v v i v vv i v i v v vv C MIRc#SINE/MIR 86 AGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCA 37 chr5ptel1M 919338 ACTGGGGTTCTCTTGCCTTCTCTACCAGGCTGGCTC 919373 v vvi v v -v vi vi v C MIRc#SINE/MIR 36 AGTCCAGTGCTCTTTCC-ACTGCACCACACTGCCTC 2 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 39.58 CpG sites = 8, Kimura (unadjusted) = 41.34 Transitions / transversions = 0.42 (8/19) Gap_init rate = 0.01 (1 / 85), avg. gap size = 1.00 (1 / 1) 591 25.53 15.32 1.19 chr5ptel1M 919617 919838 (80162) MIRb#SINE/MIR 13 265 (3) m_b241s601i38 9544 chr5ptel1M 919617 GTGGTACAGTGGAGAGAGCTCCAGGTCTGCA-TCAGG-ATATTACAGTTC 919664 i i v vi v i v - i- v iivvi MIRb#SINE/MIR 13 GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTC 62 chr5ptel1M 919665 AAATGCTGCCTTGGACACTTACTAGCTG----------GGCAAGTCACTT 919704 i v i v iv v ---------- i MIRb#SINE/MIR 63 GAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTT 112 chr5ptel1M 919705 AAATTCTGTTTGTTTCAGTTTCTCCATCTGTATAATGGGGATCATAACAG 919754 vi v vv ii ii v v i - MIRb#SINE/MIR 113 AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATA- 161 chr5ptel1M 919755 CCCCTGCCTCCCAGG------GTGA----TAAATGAGATCATATTTGTAA 919794 -- i v ------ ---- v iiv MIRb#SINE/MIR 162 --CCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAA 209 chr5ptel1M 919795 GAGTTTCAGCA---------GCACA---TAAGTACTTAATAAATGCTCAT 919832 iivvi i --------- --- ii i v vii MIRb#SINE/MIR 210 AGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAAATGGTAGC 259 chr5ptel1M 919833 TCCCTT 919838 iv MIRb#SINE/MIR 260 TCTATT 265 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 29.72 CpG sites = 31, Kimura (unadjusted) = 31.79 Transitions / transversions = 1.24 (31/25) Gap_init rate = 0.05 (10 / 221), avg. gap size = 3.70 (37 / 10) 659 32.76 3.30 1.90 chr5ptel1M 919915 920278 (79722) L1ME4c_3end#LINE/L1 271 639 (191) m_b241s551i8 9545 chr5ptel1M 919915 ACACTACTGCATTGTTGGTGGAGTTGTGAACTGATCCAACA-TTCTGGAG 919963 ? vv i i vi? i i i v v- i i L1ME4c_3end#L 271 ACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAA 320 chr5ptel1M 919964 AGCAATCTGGAACCATGCCCAAAGGGCTGTCAAACTGGGCACACCCTTTG 920013 i v vi i iviv i ii v v vv i L1ME4c_3end#L 321 AGCAATTTGGCAATACGTATCAAGAGCCATAAAAATGTTCATACCCTTTG 370 chr5ptel1M 920014 ATCTAGTAGTGTCCCAACTGGGTCTGTATCCAAAAGAGATCAT--AAAAA 920061 i i i vi v vv vv v v i i v -- i L1ME4c_3end#L 371 ACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAAG 420 chr5ptel1M 920062 AAGGAGAAAGGAGCCACATGTGCCAAAAAA--CGTAGCAGCTCTTTTTGT 920109 i --- i i ii v i vi-- i v vi v i L1ME4c_3end#L 421 AAGGAAAA---AGCTATATGCACGAAGATGTTCATTGCAGCGTTATTTAT 467 chr5ptel1M 920110 GGTCACAAAGAATTGGAAAATGAGTAGATGCCCAGCAGTTGGGGAATGGT 920159 ii vi i i vvivv i i i i v L1ME4c_3end#L 468 AATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAATGGT 517 chr5ptel1M 920160 TG---AAGTTACGGTTTATGAATGGAATGGACTATTAT-TATTCTATAAA 920205 i--- i i vi v? ivvi v -i vi vv L1ME4c_3end#L 518 TAAGTAAATTATGGTACATCNACTCGATGGAATATTATGCAGCCATTAAA 567 chr5ptel1M 920206 AATGACGA--ACAAACTGACTTCAGAAAGGCCTGGAAAG-ATTTACACAA 920252 ii -- ii -- viiv ivii v i-i ii- v L1ME4c_3end#L 568 AATGATAATTATGAA--GACTATGTAGCAACATGGAAAATGTTTATG-AT 614 chr5ptel1M 920253 ACAGATGCTGAGCAAAATAAGCAGAA 920278 i - i i ii v L1ME4c_3end#L 615 ATA-ATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 43.69 CpG sites = 70, Kimura (unadjusted) = 45.28 Transitions / transversions = 1.49 (70/47) Gap_init rate = 0.04 (14 / 363), avg. gap size = 1.36 (19 / 14) 247 35.53 3.23 2.40 chr5ptel1M 920663 920786 (79214) MIRb#SINE/MIR 4 128 (140) m_b241s601i39 9546 chr5ptel1M 920663 AGTGGCAGCCCGGTGCAG--GACTGT-CACGTTCAGCCT-GAAATCCCAA 920708 v vi -- vv v- ---i i - i i vv v MIRb#SINE/MIR 4 AGGGGCAGCGTGGTGCAGTGGAAAGAGCACG---GGCTTTGGAGTCAGAC 50 chr5ptel1M 920709 AGCCTTGGATTCTGATTTTTCCCGTGGTTCTTACTAGCCGCGTGGTTTTA 920758 v i i vi iiivv iv viv i i iii i MIRb#SINE/MIR 51 AGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTG 100 chr5ptel1M 920759 AGTGGGTCACTCAGTCTCTCTGAGTCTC 920786 i iii i i ii i MIRb#SINE/MIR 101 GGCAAGTTACTTAACCTCTCTGAGCCTC 128 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 49.54 CpG sites = 28, Kimura (unadjusted) = 51.31 Transitions / transversions = 1.87 (28/15) Gap_init rate = 0.05 (6 / 123), avg. gap size = 1.17 (7 / 6) 250 39.56 0.00 0.00 chr5ptel1M 920696 920786 (79214) MIRc#SINE/MIR 35 125 (143) m_b241s601i40 9546 chr5ptel1M 920696 CCTGAAATCCCAAAGCCTTGGATTCTGATTTTTCCCGTGGTTCTTACTAG 920745 i i i vvi v i i vii iiivv iv viv MIRc#SINE/MIR 35 CTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAG 84 chr5ptel1M 920746 CCGCGTGGTTTTAAGTGGGTCACTCAGTCTCTCTGAGTCTC 920786 i i iii ii iii i ii i MIRc#SINE/MIR 85 CTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTC 125 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 61.33 CpG sites = 27, Kimura (unadjusted) = 64.44 Transitions / transversions = 3.00 (27/9) Gap_init rate = 0.00 (0 / 90), avg. gap size = 0.0 (0 / 0) 267 25.30 3.49 3.49 chr5ptel1M 920901 920986 (79014) MIRc#SINE/MIR 40 125 (143) m_b241s601i41 9547 chr5ptel1M 920901 AGTCAGGAAGAGCTGGGTCT---CTTCGGGTCTAACACCCCTCCTTGTCT 920947 v ii---iii v iv i-- v v - MIRc#SINE/MIR 40 AGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACT--TACTAG-CT 86 chr5ptel1M 920948 GAGTGACTCTTGGCAAGTCACTCATCCTCCCAGAACCTC 920986 v ii v i v i v i MIRc#SINE/MIR 87 GTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTC 125 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 29.68 CpG sites = 12, Kimura (unadjusted) = 31.45 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.05 (4 / 85), avg. gap size = 1.50 (6 / 4) 394 27.63 13.16 0.00 chr5ptel1M 921006 921157 (78843) MIRc#SINE/MIR 77 248 (20) m_b241s601i42 9548 chr5ptel1M 921006 CCTACTAGCTGTGTGCC---ACGTAAGTCACTCAGCT-------GCCTCA 921045 i v ---iv i i i i------- MIRc#SINE/MIR 77 CTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCA 126 chr5ptel1M 921046 GTTTCCCCCTATGCAGATTGGGGTTGATGAGAAGAG-------TACCCCA 921088 i v v i i v v i i v vvv ------- i MIRc#SINE/MIR 127 GTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCA 176 chr5ptel1M 921089 --GGGTTGTTGGGAGGATGCAATGAGCCCCTATTTGT-AAAGTGCTTTGC 921135 -- v vv vivv i v - i i MIRc#SINE/MIR 177 CAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTTTGT 226 chr5ptel1M 921136 AGACCTTCAAGCACCGTCCAAA 921157 i iv v ii ii v MIRc#SINE/MIR 227 AAACTGTAAAGTGCTATACAAA 248 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 33.95 CpG sites = 22, Kimura (unadjusted) = 34.96 Transitions / transversions = 1.10 (22/20) Gap_init rate = 0.03 (5 / 151), avg. gap size = 4.00 (20 / 5) 405 25.20 10.24 0.00 chr5ptel1M 921006 921132 (78868) MIR#SINE/MIR 73 212 (50) m_b241s601i43 9548 chr5ptel1M 921006 CCTACTAGCTGTGTGCC---ACGTAAGTCACTCAGC-------TGCCTCA 921045 i v ---iv i i i i ------- MIR#SINE/MIR 73 CTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCA 122 chr5ptel1M 921046 GTTTCCCCCTATGCAGATTGGGGTTGATGAGAAGAG-TACCCCA--GGGT 921092 i v v i i v v i i v iv v- i -- MIR#SINE/MIR 123 GTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTCATAGGGT 172 chr5ptel1M 921093 TGTTGGGAGGATGCAATGAGCCCCTATTTGTAAAGTGCTT 921132 v vv iivv iv i MIR#SINE/MIR 173 TGTTGTGAGGATTAAATGAGTTAATACATGTAAAGCGCTT 212 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 29.97 CpG sites = 17, Kimura (unadjusted) = 31.11 Transitions / transversions = 1.13 (17/15) Gap_init rate = 0.03 (4 / 126), avg. gap size = 3.25 (13 / 4) 15 4.71 0.00 0.00 chr5ptel1M 921283 921304 (78696) (TCAG)n#Simple_repeat 1 22 (0) m_b241s252i17 9549 chr5ptel1M 921283 TCAGTCAGTCAGTCAGTCTGTC 921304 v (TCAG)n#Simpl 1 TCAGTCAGTCAGTCAGTCAGTC 22 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 206 19.19 0.00 4.26 chr5ptel1M 921644 921692 (78308) L2d_3end#LINE/L2 470 516 (0) m_b241s601i44 9550 chr5ptel1M 921644 GAGGACATAGCAAGTGCTTAATAAATACTTATGGCATTTGATTGAATGA 921692 v i i i i i v v-- v L2d_3end#LINE 470 GAGCACATAGTAGGCGCTCAATAAATACTTGTTGA--TTGATTGATTGA 516 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 19.69 CpG sites = 5, Kimura (unadjusted) = 22.35 Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.04 (2 / 48), avg. gap size = 1.00 (2 / 2) 298 25.23 10.00 0.92 chr5ptel1M 922703 922802 (77198) C L3#LINE/CR1 (38) 4061 3953 m_b241s601i45 9551 chr5ptel1M 922703 GAGGCCATTTCATCCCACA---CATTCACTGGCAGAAATCCCTTCCACAA 922749 i i vi v v--- i v - i i C L3#LINE/CR1 4061 GAGGTCATCTAGTCCAACCTCCCATCCAATG-CAGGAATCCCTTCTACAA 4013 chr5ptel1M 922750 CACCCTGGACTAATGGCCATCT-GC-----CTTGACCATCTCTGGCAATG 922793 i iv v i i i- ----- v i ii ii i C L3#LINE/CR1 4012 CATCCCTGACAAGTGGTCATCCAGCCTCTGCTTGAACACCTCCAGTGACG 3963 chr5ptel1M 922794 GGAAG-TCAC 922802 i - C L3#LINE/CR1 3962 GGGAGCTCAC 3953 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 30.72 CpG sites = 18, Kimura (unadjusted) = 32.30 Transitions / transversions = 2.57 (18/7) Gap_init rate = 0.05 (5 / 99), avg. gap size = 2.20 (11 / 5) 238 20.00 7.27 0.00 chr5ptel1M 923156 923210 (76790) C L3#LINE/CR1 (328) 3771 3713 m_b241s601i46 9551 chr5ptel1M 923156 ACAGCCATCAC----CCCCCAAGGCTTCTCCTCTTCAGGGTAAACATTTC 923201 i i---- i i v i i v ii C L3#LINE/CR1 3771 ACAGCTATCATGTCTCCTCTAAGTCTTCTCTTCTCCAGGCTAAACATCCC 3722 chr5ptel1M 923202 CAGTCCCTT 923210 i C L3#LINE/CR1 3721 CAGTTCCTT 3713 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 24.49 CpG sites = 9, Kimura (unadjusted) = 24.49 Transitions / transversions = 4.50 (9/2) Gap_init rate = 0.02 (1 / 54), avg. gap size = 4.00 (4 / 1) 60 8.80 0.00 1.16 chr5ptel1M 924140 924226 (75774) (AG)n#Simple_repeat 1 86 (0) m_b241s252i18 9552 chr5ptel1M 924140 AGAGAGAGTAAAGAGAGAGAGAGAGAAAGGCATGGAGGGAGAGAGAGAGA 924189 - i i iv vi i (AG)n#Simple_ 1 AGAGAGAG-AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 49 chr5ptel1M 924190 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 924226 (AG)n#Simple_ 50 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 86 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.01 (1 / 86), avg. gap size = 1.00 (1 / 1) 90 23.31 0.00 0.00 chr5ptel1M 924943 925138 (74862) (GA)n#Simple_repeat 1 196 (0) m_b241s252i19 9553 chr5ptel1M 924943 GAGAGATTGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGACAGAGACACA 924992 vv v v v (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr5ptel1M 924993 GAGACAGAGACAGGCAGAGACAGAGACAGACAAACACAGAGACACACAGC 925042 v v iv v v v i v v v v v v (GA)n#Simple_ 51 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 100 chr5ptel1M 925043 CAGAGAGACACACATGGAGGGAAAGAGAGAGACAGAGAGAGAAACAGAGA 925092 v v v v vi i i v i v (GA)n#Simple_ 101 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 150 chr5ptel1M 925093 CAGAGAGACACCGAGAGACCCAGACAGAGACAGAGAGAGAGAGAGA 925138 v v vv vvv v v (GA)n#Simple_ 151 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 196 Matrix = Unknown Transitions / transversions = 0.18 (6/33) Gap_init rate = 0.00 (0 / 195), avg. gap size = 0.0 (0 / 0) 288 27.56 13.77 4.40 chr5ptel1M 926752 926918 (73082) C MIRc#SINE/MIR (72) 196 15 m_b242s601i0 9554 chr5ptel1M 926752 TGGTCCTTATG-CGGCCCCGGGAGG-----AGAG-AGCTAGTGGGATTCC 926794 i i ii- ii i v ----- i - v v ivv i C MIRc#SINE/MIR 196 TGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCC 147 chr5ptel1M 926795 TATTTTACAGCTCAAGAAAC-----------GTGG----GAGATTTGCCC 926829 i v v i ----------- v ---- v i C MIRc#SINE/MIR 146 CATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCC 97 chr5ptel1M 926830 AGGGTCACACAGCTCGGAAGTGAT-GAGGCTGATTTGGAGCTCAGGCTGT 926878 i v v ii- v v ivi v i i --- C MIRc#SINE/MIR 96 AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAG---GT 50 chr5ptel1M 926879 CTGGCCTGACTCCCCAGCCAGCGGGCTAGCCCTCCACCGC 926918 -v vviv i-- -- ii i C MIRc#SINE/MIR 49 CT-TCCTGACTCCAAGTCCAGT--GCT--CTTTCCACTGC 15 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.28 CpG sites = 25, Kimura (unadjusted) = 35.28 Transitions / transversions = 1.32 (25/19) Gap_init rate = 0.08 (14 / 166), avg. gap size = 2.21 (31 / 14) 318 29.55 12.88 0.00 chr5ptel1M 926752 926883 (73117) C MIR#SINE/MIR (76) 186 38 m_b242s601i1 9554 chr5ptel1M 926752 TGGTCCTTATG-CGGCCCCGGGAGGAGAGAGCTAGTGGGATTCCTATTTT 926800 ii i ii- ii iiv vii vi v ivv i i C MIR#SINE/MIR 186 TAATCCTCACAACAACCCTATGAGGTAGGTACTATTATTATCCCCATTTT 137 chr5ptel1M 926801 ACAGCTCAAGAAAC-GTGG------GAGATT--------TGCCCAGGGTC 926835 v v i - v ------ i -------- i C MIR#SINE/MIR 136 ACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTC 87 chr5ptel1M 926836 ACACAGCTCGGAAGTGAT-GAGGCTGATTTGGAGCTCAGGCTGTCTGGC 926883 v v ii- v v iv v i i v C MIR#SINE/MIR 86 ACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGCAGTCTGGC 38 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.66 CpG sites = 23, Kimura (unadjusted) = 38.66 Transitions / transversions = 1.44 (23/16) Gap_init rate = 0.04 (5 / 131), avg. gap size = 3.40 (17 / 5) 330 24.04 11.41 5.06 chr5ptel1M 926775 926923 (73077) C MIRb#SINE/MIR (99) 169 12 m_b242s601i2 9554 chr5ptel1M 926775 GAGAGAGCTAGTGGGATTCCTATTTTACAGCTCAAGAAAC-GTGG----- 926818 iv v v ivv i i v v i - v ----- C MIRb#SINE/MIR 169 GAGGTAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAG 120 chr5ptel1M 926819 -GAGATT--------TGCCCAGGGTCACACAGCTCGGAAGTGAT-GAGGC 926858 - i -------- i v v ii- v C MIRb#SINE/MIR 119 AGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCC 70 chr5ptel1M 926859 TGATTTGGAGCTCAGGCTGTCTGGCCTGACTCCCCAGCCAGCGGGCTAGC 926908 v iv v i i --- - i vv -- v -- C MIRb#SINE/MIR 69 GGGATTCGAACCCAG---GTCT-GTCTGACTCCAAAGCC--CGTGCT--C 28 chr5ptel1M 926909 CCTCCACCGC-CTACG 926923 ii i - i C MIRb#SINE/MIR 27 TTTCCACTGCACCACG 12 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.35 CpG sites = 17, Kimura (unadjusted) = 29.35 Transitions / transversions = 1.00 (17/17) Gap_init rate = 0.09 (14 / 148), avg. gap size = 1.79 (25 / 14) 522 31.79 2.29 1.13 chr5ptel1M 928958 929132 (70868) MIRb#SINE/MIR 40 216 (52) m_b242s601i3 9555 chr5ptel1M 928958 TGGGGTCAGGGAGGCCTGGGTCCCGGTCCTGTGTCAGTCACTTGCTCCCT 929007 i iv i i vii i vv v i i vv MIRb#SINE/MIR 40 TGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCT 89 chr5ptel1M 929008 GGGTGACCCTGAACTAGGTACCTAAGCTTTTGGAGCCTCAGCCTCCTCAT 929057 v i ii v v i v i iv ii MIRb#SINE/MIR 90 GTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCAT 139 chr5ptel1M 929058 TTGCAAAGTGGGGCATTGATACTGTCCGTCTGTGGGGGCTCCTCTGGGGG 929107 i i i v-- i v ii iii vvvi i vi v i i MIRb#SINE/MIR 140 CTGTAAAATGGGGA--TAATAATACCTACCTCGCAGGGTTGTTGTGAGGA 187 chr5ptel1M 929108 -CAAATGA-ATGA--CATGTGAAGCACCT 929132 -i - i -- i i i MIRb#SINE/MIR 188 TTAAATGAGATAATGCATGTAAAGCGCTT 216 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.38 CpG sites = 36, Kimura (unadjusted) = 43.53 Transitions / transversions = 1.89 (36/19) Gap_init rate = 0.03 (5 / 174), avg. gap size = 1.20 (6 / 5) 184 21.54 5.80 5.80 chr5ptel1M 929165 929233 (70767) L2d_3end#LINE/L2 387 455 (61) m_b242s601i4 9556 chr5ptel1M 929165 CCCTACTGGGTCAGATGGAAGCTTGCTGAGGGCAGAGCCCA-GCCTTA-A 929212 v i i ---- v ivi i v - i - L2d_3end#LINE 387 CCCAACTAGAT----TGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATA 432 chr5ptel1M 929213 CTAGTTCATC--TCCCTTCAGCG 929233 ?v i? -- iv L2d_3end#LINE 433 CTNTTTTNTCGTTCCCCACAGCG 455 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.76 CpG sites = 8, Kimura (unadjusted) = 26.76 Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.10 (7 / 68), avg. gap size = 1.14 (8 / 7) 311 34.89 4.62 2.47 chr5ptel1M 930771 931008 (68992) L2#LINE/L2 2752 2994 (88) m_b242s601i5 9557 chr5ptel1M 930771 CCACCCTCACCCCCATCCA------CCTCCTTGTGGCCGCCAAAGTGACT 930814 ii v ? ------i vviiii v i ii L2#LINE/L2 2752 CCACCCTTGCCCCCCTNCAGTCTATTCTCAACACAGCAGCCAGAGTGATC 2801 chr5ptel1M 930815 TAACTAAAATGCA-GCCTGACCATGTCTTCTCCCTCCTCCACTCAATAAC 930863 ivvi i i - i v i -----v ii v v L2#LINE/L2 2802 CTTTTAAAACGTAAGTCAGATCATGTC-----ACTCCTCTGCTCAAAACC 2846 chr5ptel1M 930864 CTTCCATAGCTCCCTATCACCTCCAGAACAAAA-CCAAAATCCTCAGTTT 930912 i v i i i v vii ii - i i vvv L2#LINE/L2 2847 CTCCAATGGCTTCCCATCTCACTCAGAGTAAAAGCCAAAGTCCTTACAAT 2896 chr5ptel1M 930913 GGCATTCAGGCCTGCAGATCAACCTG--CCCCTCTCACTTTTCTGGTCTC 930960 v v i v ivi v -i i -- iv i i i ii L2#LINE/L2 2897 GGCCTACAAGGCCCTACAT-GATCTGGTCCCCCGTTACCTCTCTGACCTC 2945 chr5ptel1M 930961 CTTCCTCCTCACTCCCCAACACACTCCCACGACACCATCC-TTCTGGCC 931008 v ii iivi i vv v i v v vi v v -iv L2#LINE/L2 2946 ATCTCCTACCACTCTCCCCCTCGCTCACTCCGCTCCAGCCACACTGGCC 2994 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.87 CpG sites = 48, Kimura (unadjusted) = 49.28 Transitions / transversions = 1.45 (48/33) Gap_init rate = 0.05 (11 / 237), avg. gap size = 1.55 (17 / 11) 182 29.41 1.96 0.00 chr5ptel1M 930997 931047 (68953) C MIR3#SINE/MIR (45) 163 112 m_b242s601i6 9558 chr5ptel1M 930997 ATCCTTCTGGCCAAACTCCCCATCTTTTGG-TGGGTAAACTGAGGCTCAG 931045 v iiv v v i i i vii - i v i C MIR3#SINE/MIR 163 ATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAG 114 chr5ptel1M 931046 AG 931047 C MIR3#SINE/MIR 113 AG 112 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.51 CpG sites = 9, Kimura (unadjusted) = 38.51 Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.02 (1 / 50), avg. gap size = 1.00 (1 / 1) 184 18.60 6.98 0.00 chr5ptel1M 932286 932328 (67672) C MIRc#SINE/MIR (99) 169 124 m_b242s601i7 9559 chr5ptel1M 932286 GGCAGAACAGATAATAAT---CCCATTGTACAGATCGGGAAACTGA 932328 ii i v v --- v vi C MIRc#SINE/MIR 169 GGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGA 124 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 21.51 CpG sites = 4, Kimura (unadjusted) = 21.51 Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.02 (1 / 42), avg. gap size = 3.00 (3 / 1) 250 34.31 0.73 0.00 chr5ptel1M 932880 933016 (66984) L1ME3Cz_3end#LINE/L1 53 190 (807) m_b242s551i0 9560 chr5ptel1M 932880 CCTAATTGACAAGTGGTCAAAGAATAAGAA-AGGCAATTTTGTGAGGAAG 932928 i v v i v i v - ivvv i i L1ME3Cz_3end# 53 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chr5ptel1M 932929 AAGTCAGAGCTGTCAAGTTATGTGGGGAAAAACACTCTAAATTACCAATA 932978 ii v iiv i vvv ii iv i i ii v vv i i i L1ME3Cz_3end# 103 AAACCCGAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTA 152 chr5ptel1M 932979 ATTAGGGAAATTAAAATTCAAGTGATTCTGAGGTACCA 933016 i vv v ii? ivv i L1ME3Cz_3end# 153 ATCAGGGAAATGCAAATTAAAACNACAATGAGATACCA 190 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 47.71 CpG sites = 26, Kimura (unadjusted) = 47.71 Transitions / transversions = 1.24 (26/21) Gap_init rate = 0.01 (1 / 136), avg. gap size = 1.00 (1 / 1) 190 24.47 12.60 6.72 chr5ptel1M 933786 933912 (66088) C L2d2_3end#LINE/L2 (8) 547 414 m_b242s601i8 9561 chr5ptel1M 933786 AATCCA-AAGCATTTATTATGTGTCTGCTGGGTACCGGGTCATTGGCCTA 933834 v - ii iv i i i v i vi - i vv C L2d2_3end#LIN 547 AATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGG-CACTGTGCTA 499 chr5ptel1M 933835 TAATGGTGCTATGGAGG---CAAAAA---ATAAGA------CCCT-CTCT 933871 ---- i i i --- i --- ------ - i C L2d2_3end#LIN 498 ----GGCGCTGTGGGGGATACAAAGAAGTATAAGACATGGTCCCTGCCCT 453 chr5ptel1M 933872 GAAGGAG-AGACAAG-TAGTTCGACGTGGAGACAAGGAACAGA 933912 v -vv v- ---- v iv i i C L2d2_3end#LIN 452 CAAGGAGCTTACAATCTAGTT----GGGGAGACAAGACATAAA 414 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.95 CpG sites = 17, Kimura (unadjusted) = 30.39 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.13 (16 / 126), avg. gap size = 1.56 (25 / 16) 187 36.59 1.19 2.41 chr5ptel1M 934128 934211 (65789) MIRb#SINE/MIR 104 186 (82) m_b242s601i9 9562 chr5ptel1M 934128 AAGTCTTTCAATTCCCCTCAGTCTTCCTTTTCTGATCTGTAAAATGGTTT 934177 ivi i iii i v i ivv i v --v MIRb#SINE/MIR 104 AAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGG--G 151 chr5ptel1M 934178 AATCATGGCACTGATCTCCCA-GACAATAGTGAGG 934211 i v iii iv i v - iivi v MIRb#SINE/MIR 152 GATAATAATACCTACCTCGCAGGGTTGTTGTGAGG 186 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 53.32 CpG sites = 19, Kimura (unadjusted) = 53.32 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.04 (3 / 83), avg. gap size = 1.00 (3 / 3) 197 29.88 0.00 2.99 chr5ptel1M 934128 934196 (65804) MIR1_Amn#SINE/MIR 103 169 (61) m_b242s601i10 9562 chr5ptel1M 934128 AAGTCTTTCAATTCCCCTCAGTCTTCCTTTTCTGATCTGTAAAATGGTTT 934177 vi i? iii i v? i ivv i v --v MIR1_Amn#SINE 103 AAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGG--G 150 chr5ptel1M 934178 AATCATGGCACTGATCTCC 934196 i v ii i MIR1_Amn#SINE 151 GATAATGATACTGACCTCC 169 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.50 CpG sites = 13, Kimura (unadjusted) = 41.50 Transitions / transversions = 1.86 (13/7) Gap_init rate = 0.03 (2 / 68), avg. gap size = 1.00 (2 / 2) 253 31.79 5.56 2.15 chr5ptel1M 934324 934413 (65587) MIRc#SINE/MIR 62 154 (114) m_b242s601i11 9563 chr5ptel1M 934324 GTCCCAGACTCCTGATGTCTATCACCTCTGTGACTGTGAGCA-----CTC 934368 i - - viiii ii v v iv i ----- i MIRc#SINE/MIR 62 GTCCCGG-CTC-TGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTT 109 chr5ptel1M 934369 GGCTTTCCCAAGCCTCAGTTTCTCCAGCTGCAAAATGTGGAAGAT 934413 ii i ii ii ii v i v vi MIRc#SINE/MIR 110 AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAAT 154 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.76 CpG sites = 21, Kimura (unadjusted) = 45.02 Transitions / transversions = 3.00 (21/7) Gap_init rate = 0.03 (3 / 89), avg. gap size = 2.33 (7 / 3) 374 31.09 6.72 0.00 chr5ptel1M 934349 934467 (65533) MIR3#SINE/MIR 82 208 (0) m_b242s601i12 9563 chr5ptel1M 934349 CTCTGTGACTGTGAGCA-----CTCGGCTTTCCCAAGCCTCAGTTTCTCC 934393 v iv i ----- ivi i ii iii ii MIR3#SINE/MIR 82 CTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTC 131 chr5ptel1M 934394 AGCTGCAAAATGTGGAAGATGGACTCAATGAACTCCAA-GTTCCTTCCAA 934442 v i v ii v vi v i - i i MIR3#SINE/MIR 132 ATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAG 181 chr5ptel1M 934443 TTTT--TTATCTGTGATCTGATGATCC 934467 i i --ivv i iiv i MIR3#SINE/MIR 182 CTCTGACATTCTATGATTCTATGATTC 208 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.80 CpG sites = 26, Kimura (unadjusted) = 42.80 Transitions / transversions = 2.36 (26/11) Gap_init rate = 0.03 (3 / 118), avg. gap size = 2.67 (8 / 3) 348 28.07 2.61 0.85 chr5ptel1M 934442 934556 (65444) C MIR1_Amn#SINE/MIR (26) 204 88 m_b242s601i13 9564 chr5ptel1M 934442 ATTTTTTATCTGT-GATCTGATGATCCCTAAGTCAAGTACA--AGGATGA 934488 i i v - v viiiv i v -iv v vi-- v v C MIR1_Amn#SINE 204 ACTTTTCATCAGTAGATCTCAAAGCACTTTA-CAAAGGAGGTCAGTATCA 156 chr5ptel1M 934489 TTGTCCCCATTTCACAGATGAGCAAGTGGAGGTTTACAGAGGGGAAGTAT 934538 i i v iiv i?i v v? iv C MIR1_Amn#SINE 155 TTATCCCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGA 106 chr5ptel1M 934539 TTTGTCCAAGGTCACACA 934556 i i ? C MIR1_Amn#SINE 105 CTTGCCCAAGGTCACNCA 88 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.00 CpG sites = 17, Kimura (unadjusted) = 37.00 Transitions / transversions = 1.13 (17/15) Gap_init rate = 0.03 (3 / 114), avg. gap size = 1.33 (4 / 3) 364 22.74 2.20 3.33 chr5ptel1M 934466 934556 (65444) C MIR#SINE/MIR (91) 171 82 m_b242s601i14 9564 chr5ptel1M 934466 CCCTA--AGTCAAGTACAAGGATGATTGTCCCCATTTCACAGATGAGCAA 934513 -- vi i ---v v i i v C MIR#SINE/MIR 171 CCCTATGAGGTAGGTAC---TATTATTATCCCCATTTTACAGATGAGGAA 125 chr5ptel1M 934514 GTGGAGGTTTACAGAGGGGAAGTATTTTGTCCAAGGTCACACA 934556 iiv ivi v vv vi i C MIR#SINE/MIR 124 ACTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACA 82 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.29 CpG sites = 10, Kimura (unadjusted) = 27.29 Transitions / transversions = 1.00 (10/10) Gap_init rate = 0.04 (4 / 90), avg. gap size = 1.25 (5 / 4) 380 22.37 0.00 0.00 chr5ptel1M 934481 934556 (65444) C MIRb#SINE/MIR (104) 164 89 m_b242s601i15 9564 chr5ptel1M 934481 AAGGATGATTGTCCCCATTTCACAGATGAGCAAGTGGAGGTTTACAGAGG 934530 i v v i i v iiv i i v C MIRb#SINE/MIR 164 AGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGG 115 chr5ptel1M 934531 GGAAGTATTTTGTCCAAGGTCACACA 934556 vv vi i C MIRb#SINE/MIR 114 TTAAGTAACTTGCCCAAGGTCACACA 89 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.85 CpG sites = 9, Kimura (unadjusted) = 26.85 Transitions / transversions = 1.12 (9/8) Gap_init rate = 0.00 (0 / 75), avg. gap size = 0.0 (0 / 0) 192 25.06 1.39 5.80 chr5ptel1M 935311 935382 (64618) MIRc#SINE/MIR 81 149 (119) m_b242s601i16 9565 chr5ptel1M 935311 CTGGTTG-GAGACATCTGGGCTAGAATCCTCTTGACCTTTTGGAGGTTCT 935359 i i - v v - v ---i v i i iv vi v MIRc#SINE/MIR 81 CTAGCTGTGTGACCT-TGGGCAAG---TCACTTAACCTCTCTGAGCCTCA 126 chr5ptel1M 935360 GTTTCCTCATCTGAAATATGGAG 935382 v v i MIRc#SINE/MIR 127 GTTTCCTCATCTGTAAAATGGGG 149 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.60 CpG sites = 8, Kimura (unadjusted) = 30.60 Transitions / transversions = 0.89 (8/9) Gap_init rate = 0.07 (5 / 71), avg. gap size = 1.00 (5 / 5) 255 36.13 4.48 2.94 chr5ptel1M 935381 935514 (64486) C MIR3#SINE/MIR (23) 185 50 m_b242s601i18 9566 chr5ptel1M 935381 AGGGTTCACAGAGACCTGAGGGGTCATGGGGTCCAATCCCCTTACTTGGA 935430 i i viv i v i i vvi i i i vi- C MIR3#SINE/MIR 185 AGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTA- 137 chr5ptel1M 935431 AATTAGTTGAAGCACCTGAGACAAAGAGTGGGGAGGTGATTT----AGGA 935476 ---i v i v v i vv v v i i ---- i i C MIR3#SINE/MIR 136 ---CAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGG 90 chr5ptel1M 935477 TTATCTGG--AGAAAGGAGTGGAGCCAGGAATAATTCCCA 935514 i ivii -- vv vi ii i v ivv C MIR3#SINE/MIR 89 TCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCA 50 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 49.72 CpG sites = 27, Kimura (unadjusted) = 51.30 Transitions / transversions = 1.35 (27/20) Gap_init rate = 0.05 (6 / 133), avg. gap size = 1.67 (10 / 6) 283 32.87 11.33 0.60 chr5ptel1M 935501 935650 (64350) L3#LINE/CR1 3893 4058 (41) m_b242s601i19 9567 chr5ptel1M 935501 AGGAATAA-TTCCCACTAGTTCAGGGTT-TCCA-----GGAGGACATTGT 935543 v - i i vi i - i i - ----- ivivii i L3#LINE/CR1 3893 AGGAAGAACTTTCTAACAAT-CAGAGCTGTCCAAAAATGGAATGGGCTGC 3941 chr5ptel1M 935544 CTCAGGAGGAAGGGAGTTCCTTTTCCCCG-AGATCTTCAAACTGAGGCTG 935592 i? v v i iiv v i - i v i v L3#LINE/CR1 3942 CTCGNGAGGTAGTGAGCTCCCCGTCACTGGAGGTGTTCAAGCAGAGGCTG 3991 chr5ptel1M 935593 ACTGGCTATTCATTAGGGATG-CAAGGCTAGTACTCCTGTTTT------- 935634 iv i i i ii i -iivi vvi v i iv ------- L3#LINE/CR1 3992 GATGACCACTTGTCAGGGATGTTGTAGAAGGGATTCCTGCATTGGATGGG 4041 chr5ptel1M 935635 AGG-TAGATTAGATGAC 935650 - i i L3#LINE/CR1 4042 AGGTTGGACTAGATGAC 4058 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.81 CpG sites = 33, Kimura (unadjusted) = 46.47 Transitions / transversions = 2.06 (33/16) Gap_init rate = 0.05 (8 / 149), avg. gap size = 2.25 (18 / 8) 41 0.00 0.00 0.00 chr5ptel1M 936263 936297 (63703) (TG)n#Simple_repeat 1 35 (0) c_b242s251i0 9568 chr5ptel1M 936263 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 936297 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 35 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 521 19.25 2.26 6.25 chr5ptel1M 936339 936471 (63529) C MIRb#SINE/MIR (137) 131 4 m_b242s601i20 9569 chr5ptel1M 936339 ACTGAAGCA-ATTGGGGTTAAGTGACTTGCCCAGGGTTACACAGCCAGGA 936387 i v- vv i i i i i v C MIRb#SINE/MIR 131 ACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTA 82 chr5ptel1M 936388 AGTGTTGTGTCTGAGACCAGATTTGAACTCAGGTCT-TCTGACTTCAAGG 936436 ----- v v v vi i i - i i C MIRb#SINE/MIR 81 A-----GTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAG 37 chr5ptel1M 936437 CTGGTACTCTAT-GACTGCACCACGGAGCTGCCCCT 936471 iv i v -v --- C MIRb#SINE/MIR 36 CCCGTGCTCTTTCCACTGCACCAC---GCTGCCCCT 4 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 21.38 CpG sites = 13, Kimura (unadjusted) = 22.39 Transitions / transversions = 1.18 (13/11) Gap_init rate = 0.08 (11 / 132), avg. gap size = 1.00 (11 / 11) 13 30.01 0.00 0.00 chr5ptel1M 936472 936516 (63484) (AAA)n#Simple_repeat 1 45 (0) m_b242s252i2 9570 chr5ptel1M 936472 AAAAATGAAATGAAACGAAATGAAACAAAAAGAAAAAAAAAGAAA 936516 vi vi vi vi v i i (AAA)n#Simple 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 45 Matrix = Unknown Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 21 20.12 0.00 1.92 chr5ptel1M 936474 936526 (63474) (AAAAG)n#Simple_repeat 1 52 (0) m_b242s252i3 9570 chr5ptel1M 936474 AAATGAAATGAAACGAAATGAAACAAAAAGAAAAAAAAAGAAACATAATA 936523 v v v v vi i - v v (AAAAG)n#Simp 1 AAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAA-AGAAAA 49 chr5ptel1M 936524 GAA 936526 (AAAAG)n#Simp 50 GAA 52 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.02 (1 / 52), avg. gap size = 1.00 (1 / 1) 227 31.82 0.00 13.39 chr5ptel1M 937140 937266 (62734) C MIR1_Amn#SINE/MIR (2) 228 117 m_b242s601i21 9571 chr5ptel1M 937140 AACAACACCTCGCTTTTGTAGGAGGACGCTGACAAGCCGGTGAATCCTTT 937189 i i v i i - v v vi v- --i i ii -- i C MIR1_Amn#SINE 228 AATAATACCTAGCTCTTAT-GTAGCACTTTT-CA--TCAGTAGATC--TC 185 chr5ptel1M 937190 AACCCTAACACCTCATTGAGGCGGGCGTGGGAGTACTAGTGTGCTCATTC 937239 ---- i i i ivi v v ----- ii v i v i i C MIR1_Amn#SINE 184 AA----AGCACTTTACAAAGGAGGTC-----AGTATCATTATCCCCATTT 144 chr5ptel1M 937240 TACAAAGAAGTAAACTGAGGCTCAAAG 937266 i vi v ? i C MIR1_Amn#SINE 143 TACAGATGAGGAAACTGAGGCNCAGAG 117 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.05 CpG sites = 23, Kimura (unadjusted) = 43.05 Transitions / transversions = 1.92 (23/12) Gap_init rate = 0.12 (15 / 126), avg. gap size = 1.00 (15 / 15) 291 27.71 4.82 0.00 chr5ptel1M 937184 937266 (62734) C MIRc#SINE/MIR (67) 201 115 m_b242s601i22 9571 chr5ptel1M 937184 TCCTTTAACCCT---AACACCTCATTGAGGCGGGCGTGGGAG-TACTAGT 937229 v i i --- v i vv ii iv v - i v C MIRc#SINE/MIR 201 TCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATT 152 chr5ptel1M 937230 GTGCTCATTCTACAAAGAAGTAAACTGAGGCTCAAAG 937266 i v i i i vi v i C MIRc#SINE/MIR 151 ATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAG 115 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.33 CpG sites = 13, Kimura (unadjusted) = 35.33 Transitions / transversions = 1.30 (13/10) Gap_init rate = 0.02 (2 / 82), avg. gap size = 2.00 (4 / 2) 190 37.72 5.26 0.00 chr5ptel1M 937565 937678 (62322) C MIR3#SINE/MIR (3) 205 86 m_b242s601i23 9572 chr5ptel1M 937565 TCCTGAGATTATGCAATG---GGGTCGGGGAGG--CTTTGGG-TCCCCCA 937608 v iii i iv --- i ii iii -- v i - vi i C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTA 156 chr5ptel1M 937609 GCCCAACCGCCTCAAGTTACAGCAGGGCACGCTGAGGCTGGAGAAGGGGA 937658 i v vv vv i v vi iviiii v C MIR3#SINE/MIR 155 GTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGA 106 chr5ptel1M 937659 AGCCACGAGCGCAGGATAAC 937678 iv vv v i i v C MIR3#SINE/MIR 105 AGTGACTTGCCCAAGGTCAC 86 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 54.87 CpG sites = 25, Kimura (unadjusted) = 54.87 Transitions / transversions = 1.39 (25/18) Gap_init rate = 0.03 (3 / 113), avg. gap size = 2.00 (6 / 3) 184 35.14 0.00 0.00 chr5ptel1M 938142 938215 (61785) MIR1_Amn#SINE/MIR 87 160 (70) m_b242s601i24 9573 chr5ptel1M 938142 CCGGGGGACTCTGGGCAGCTCCCGGGCCCCGGGTCCGCCTCAGTCTCCTC 938191 i ? v ii iv v vv?v ivvv v? i MIR1_Amn#SINE 87 CTGNGTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTC 136 chr5ptel1M 938192 ATATACAGAAAGGGAGTAGTAACA 938215 v ii i v ii i i i MIR1_Amn#SINE 137 ATCTGTAAAATGGGGATAATGATA 160 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 51.75 CpG sites = 14, Kimura (unadjusted) = 51.75 Transitions / transversions = 1.17 (14/12) Gap_init rate = 0.00 (0 / 73), avg. gap size = 0.0 (0 / 0) 228 25.35 9.86 0.00 chr5ptel1M 938178 938248 (61752) MIRc#SINE/MIR 121 198 (70) m_b242s601i25 9573 chr5ptel1M 938178 GCCTCAGTCTCCTCATATACAGAAAGGGAGTAGTAACA---GCCC--CCC 938222 i v ii i v ii i i --- -- i MIRc#SINE/MIR 121 GCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCT 170 chr5ptel1M 938223 AGCCCACATGGGTGT--TGAAGATGAGA 938248 v i v v -- i v i MIRc#SINE/MIR 171 ACCTCACAGGGTTGTTGTGAGGATCAAA 198 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.08 CpG sites = 12, Kimura (unadjusted) = 32.08 Transitions / transversions = 2.00 (12/6) Gap_init rate = 0.04 (3 / 70), avg. gap size = 2.33 (7 / 3) 249 16.98 3.17 6.56 chr5ptel1M 938519 938581 (61419) C MIR1_Amn#SINE/MIR (66) 164 104 m_b242s601i26 9574 chr5ptel1M 938519 TCCATGTCCTTCTCCAGCTCATTTTACAGATGGGGAAACTGAGG--CAGA 938566 vi i v v ---i i -- C MIR1_Amn#SINE 164 TCAGTATCATTATCC---CCATTTTACAGATGAGGAAACTGAGGCNCAGA 118 chr5ptel1M 938567 CGAAGTGAAGCGTCT 938581 - i ? i v C MIR1_Amn#SINE 117 -GAGGTNAAGTGACT 104 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 19.85 CpG sites = 6, Kimura (unadjusted) = 19.85 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.08 (5 / 62), avg. gap size = 1.20 (6 / 5) 254 8.89 4.35 2.13 chr5ptel1M 938536 938581 (61419) C MIR3#SINE/MIR (63) 145 99 m_b242s601i27 9574 chr5ptel1M 938536 CTCATTTTACAGATGGGGAAACTGAGG--CAGACGAAGTGAAGCGTCT 938581 i -- - i i v C MIR3#SINE/MIR 145 CTCATTTTACAGATGAGGAAACTGAGGCCCAGA-GAGGTGAAGTGACT 99 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 9.59 CpG sites = 3, Kimura (unadjusted) = 9.59 Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.04 (2 / 45), avg. gap size = 1.50 (3 / 2) 218 31.03 0.00 0.00 chr5ptel1M 939601 939658 (60342) C L2d_3end#LINE/L2 (2) 514 457 m_b242s601i28 9575 chr5ptel1M 939601 AACCCATCTGTCAGCAGGGATTCGTTGAGCACCTACTGGGTGCCAGGCCC 939650 i v vi i i v ii i iv ivi v C L2d_3end#LINE 514 AATCAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCAC 465 chr5ptel1M 939651 TGAGCCAG 939658 v i C L2d_3end#LINE 464 TGTGCTAG 457 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.55 CpG sites = 11, Kimura (unadjusted) = 41.56 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0) 236 22.92 0.00 0.00 chr5ptel1M 939611 939658 (60342) C L2b_3end#LINE/L2 (10) 456 409 m_b242s601i29 9575 chr5ptel1M 939611 TCAGCAGGGATTCGTTGAGCACCTACTGGGTGCCAGGCCCTGAGCCAG 939658 i iiv iii i v ? v i C L2b_3end#LINE 456 TCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAG 409 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.20 CpG sites = 8, Kimura (unadjusted) = 29.31 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 201 35.17 8.28 0.00 chr5ptel1M 940254 940398 (59602) C L3#LINE/CR1 (222) 3877 3721 m_b242s601i30 9576 chr5ptel1M 940254 TCTGCCTCGGTGCAGCTTGC---CATGGCTTCTCCATCCGCCCC--GGGG 940298 vv i i v --- v v i vvv i i-- i C L3#LINE/CR1 3877 TCTGCCTCCCTGTAACTTCCACCCATTGGTCCTAGTTCTGCCCTCTGGAG 3828 chr5ptel1M 940299 TCAGACAAGAGCA----CATTCCTCTCCCAGGTGATAGGGGCTGAGACAA 940344 i v ii vv ----v i i vi i vvvi v i i v C L3#LINE/CR1 3827 CCACACAGAATAAGTCTAATCCCTCTTCCACATGACAGCCCTTCAAATAT 3778 chr5ptel1M 940345 GATGAGACAGCTGGGAAGGCA--GCTGAG-CTTCTGTTCTGGAGGCTAAA 940391 vvvi ivv v v v--v i - v vv C L3#LINE/CR1 3777 TTGAAGACAGCTATCATGTCTCCTCTAAGTCTTCTCTTCTCCAGGCTAAA 3728 chr5ptel1M 940392 CCTTCCC 940398 v i C L3#LINE/CR1 3727 CATCCCC 3721 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 47.58 CpG sites = 20, Kimura (unadjusted) = 47.58 Transitions / transversions = 0.65 (20/31) Gap_init rate = 0.03 (5 / 144), avg. gap size = 2.40 (12 / 5) 375 24.09 5.31 0.85 chr5ptel1M 940886 940998 (59002) MER63D#DNA/hAT-Tip100 348 465 (596) m_b242s502i0 9577 chr5ptel1M 940886 ACACCTCAGAAACGGGCACAAGGCGCCAAGGGGGGCTTGGCTTTCTTGTG 940935 v i iv v v vii v vvi i- v v MER63D#DNA/hA 348 ACACCACGGAAATCGGCAAACGCTACAAATCAGGGCTTGA-TTTATTGTT 396 chr5ptel1M 940936 CTGGGGATTGTCTGGACTTAAGAAAGTGGTGGGGAAAACGCTAATA---- 940981 i vv i i i i i ---- MER63D#DNA/hA 397 TTGTTGATTGTCTAGACTTAAGAAAGTGATGGAGAAAATGTTAATAATGC 446 chr5ptel1M 940982 --ACTAAACTTAGAACTGT 940998 -- i i v MER63D#DNA/hA 447 AGATTAAACTTAAAAGTGT 465 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 28.14 CpG sites = 14, Kimura (unadjusted) = 29.39 Transitions / transversions = 1.08 (14/13) Gap_init rate = 0.03 (3 / 112), avg. gap size = 2.33 (7 / 3) 270 27.27 3.90 0.00 chr5ptel1M 941215 941291 (58709) L2d_3end#LINE/L2 433 512 (4) m_b242s601i31 9578 chr5ptel1M 941215 CCTTTTTTTTACCTCCCG-GGCACTTA-CCCAG-GCCTAGCACGCAGTAG 941261 i? ? iiiii i-i i i - v - iv ii L2d_3end#LINE 433 CTNTTTTNTCGTTCCCCACAGCGCCTAGCACAGTGCTGAGCACATAGTAG 482 chr5ptel1M 941262 GTTCTTAATAAATACCTGTTGACTGACTGA 941291 iv i i i i L2d_3end#LINE 483 GCGCTCAATAAATACTTGTTGATTGATTGA 512 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.55 CpG sites = 18, Kimura (unadjusted) = 38.78 Transitions / transversions = 6.00 (18/3) Gap_init rate = 0.04 (3 / 76), avg. gap size = 1.00 (3 / 3) 278 23.44 3.12 0.00 chr5ptel1M 941228 941291 (58709) L2b_3end#LINE/L2 399 464 (2) m_b242s601i32 9578 chr5ptel1M 941228 TCCCGGGCACTTA-CCCAG-GCCTAGCACGCAGTAGGTTCTTAATAAATA 941275 vi i i - v - i i iv i i L2b_3end#LINE 399 TCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATA 448 chr5ptel1M 941276 CCTGTTGACTGACTGA 941291 ii v v L2b_3end#LINE 449 TTTGTTGAATGAATGA 464 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 24.60 CpG sites = 10, Kimura (unadjusted) = 29.01 Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.03 (2 / 63), avg. gap size = 1.00 (2 / 2) 532 24.60 2.38 0.00 chr5ptel1M 941400 941525 (58475) MIRc#SINE/MIR 18 146 (122) m_b242s601i33 9579 chr5ptel1M 941400 GTACAGGGGGCACTGG-CCCAGAGGCAGGAAAACCTTTCTTCAAATCTGG 941448 iv ii i - iii v i vvv i i iv MIRc#SINE/MIR 18 GTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCG 67 chr5ptel1M 941449 CCTCAGAGACTCACTAGCTGTGGGATCCTGGGCAAGTCACTTTGCCTGCT 941498 v v vv i v i i vi vii MIRc#SINE/MIR 68 GCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTC 117 chr5ptel1M 941499 T--GCCTCAGTTTGCTCATCTGTAAAATG 941525 -- v MIRc#SINE/MIR 118 TGAGCCTCAGTTTCCTCATCTGTAAAATG 146 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.12 CpG sites = 17, Kimura (unadjusted) = 30.26 Transitions / transversions = 1.21 (17/14) Gap_init rate = 0.02 (2 / 125), avg. gap size = 1.50 (3 / 2) 186 33.39 0.00 4.00 chr5ptel1M 942649 942726 (57274) MIR1_Amn#SINE/MIR 114 188 (42) m_b242s601i34 9580 chr5ptel1M 942649 CCCCTCCTCCCCACAGTTCCTTCATCTGTGGAATGAGTATAACTTTCTTA 942698 i iv?v v i i ii i v ivv vi i MIR1_Amn#SINE 114 CCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATGATACTG 163 chr5ptel1M 942699 AACTCTGACTTCATAGAGACCTTGGGGA 942726 v --- ii i vv v i MIR1_Amn#SINE 164 ACCTC---CTTTGTAAAGTGCTTTGAGA 188 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.26 CpG sites = 14, Kimura (unadjusted) = 46.26 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.04 (3 / 77), avg. gap size = 1.00 (3 / 3) 359 30.83 12.78 0.00 chr5ptel1M 943171 943303 (56697) C MIRc#SINE/MIR (109) 159 10 m_b242s601i35 9581 chr5ptel1M 943171 GTATAATGTACTTCATCGTATATTTGAGAAAACTGAGGGAAACCGAAGTT 943220 v vvv ii iv i vv i vvv vv i C MIRc#SINE/MIR 159 GTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTT 110 chr5ptel1M 943221 AAGGTACTTG-------TCACACAGCTAGCA----------TCTGAATTT 943253 vv ------- i ----------i v i i i C MIRc#SINE/MIR 109 AAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTC 60 chr5ptel1M 943254 GAATTCCAGTCTTCCTGGCCCCGGGCTCAGTGCTCTATCCATGGGGCCAC 943303 ii vi i i ii ii v iv vi C MIRc#SINE/MIR 59 GAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.24 CpG sites = 22, Kimura (unadjusted) = 40.50 Transitions / transversions = 1.16 (22/19) Gap_init rate = 0.02 (2 / 132), avg. gap size = 8.50 (17 / 2) 182 30.05 9.52 1.77 chr5ptel1M 943511 943615 (56385) C L3#LINE/CR1 (5) 4094 3982 m_b242s601i36 9582 chr5ptel1M 943511 AATCCCAGAACCCTCAGAG----AAGGGCCTCAAGGAGT--TCTAGTCCA 943554 v i - ---- v iiv ii -- C L3#LINE/CR1 4094 AATCACAGAATC-TCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCA 4046 chr5ptel1M 943555 AGGA---AACAGAAGCAAAAGTCCCCCTAACAACAGGCTCTG-CTAGGGG 943600 vvv--- v vi v ii i iiiv -v i - v v C L3#LINE/CR1 4045 ACCTCCCATCCAATGCAGGAATCCCTTCTACAACA-TCCCTGACAAGTGG 3997 chr5ptel1M 943601 ACACTCAGTCTTTGC 943615 v ii i i C L3#LINE/CR1 3996 TCATCCAGCCTCTGC 3982 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.30 CpG sites = 17, Kimura (unadjusted) = 39.30 Transitions / transversions = 1.21 (17/14) Gap_init rate = 0.06 (6 / 104), avg. gap size = 2.00 (12 / 6) 186 31.44 5.49 2.13 chr5ptel1M 943642 943732 (56268) MIRb#SINE/MIR 5 98 (170) m_b242s601i37 9583 chr5ptel1M 943642 GGGGCAGCATCAT--AGTGAATCTAGAGCTCG--CTTTGGTCCCTGGAAG 943687 i vi -- i v-- v -- vvi v iv MIRb#SINE/MIR 5 GGGGCAGCGTGGTGCAGTGGAA--AGAGCACGGGCTTTGGAGTCAGACAG 52 chr5ptel1M 943688 GGATGAACTCGAACCCCAGCTTAGGCACAT-CCCGCTGTGTCACTT 943732 ivv iii i i iv v v - iv v i MIRb#SINE/MIR 53 ACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCT 98 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.68 CpG sites = 14, Kimura (unadjusted) = 41.37 Transitions / transversions = 1.00 (14/14) Gap_init rate = 0.06 (5 / 90), avg. gap size = 1.40 (7 / 5) 484 33.34 1.19 1.59 chr5ptel1M 944045 944297 (55703) L1ME4c_3end#LINE/L1 388 639 (191) m_b242s551i1 9584 chr5ptel1M 944045 CTGGGCTTATACCCCAAGGAGATACT---AAAGAAGGGAAAGGGACCAGT 944091 vv v i i i v --- i i --- vi L1ME4c_3end#L 388 CTGGGAATTTATCCTAAGGAAATAATTCAAAAGAAGGAAAAAG---CTAT 434 chr5ptel1M 944092 ATGTGCCAAAATGTTTGTGGCAGCTCTGTTTGTAGTGGCTAGAAGCTGGA 944141 ii v i ii v vi i i i i v i ii L1ME4c_3end#L 435 ATGCACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGA 484 chr5ptel1M 944142 AACTGAGTGGATGCCTATCAATTGGAGAATGGTTGGGTAAATTGTGGTAT 944191 vivv ii i i v v i ii i i L1ME4c_3end#L 485 AACAACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTAC 534 chr5ptel1M 944192 ATGAATGTTATGGAATATGATTGTTCTGTCAGAAATGACCAGCAGGATGA 944241 v? iviv v vvvv ii i i iv vi v v L1ME4c_3end#L 535 ATCNACTCGATGGAATATTATGCAGCCATTAAAAATGATAATTATGAAGA 584 chr5ptel1M 944242 ATACAGAGAGGCTTGGAGGGACTTACATGAACTGATGCTAAGTGAAATGA 944291 v iiv vii v -ii iv vi vv i i vi L1ME4c_3end#L 585 CTATGTAGCAACATGGA-AAATGTTTATGATATAATGTTAAGTGAAAAAA 633 chr5ptel1M 944292 GCAGAA 944297 L1ME4c_3end#L 634 GCAGAA 639 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 45.09 CpG sites = 48, Kimura (unadjusted) = 45.85 Transitions / transversions = 1.37 (48/35) Gap_init rate = 0.02 (5 / 252), avg. gap size = 1.40 (7 / 5) 16 4.00 0.00 7.14 chr5ptel1M 944594 944623 (55377) (AGGG)n#Simple_repeat 1 28 (0) m_b242s252i4 9585 chr5ptel1M 944594 AGGGAAGGGGGTGGAGGGAGGGAGGGAGGG 944623 - i - (AGGG)n#Simpl 1 AGGG-AGGGAG-GGAGGGAGGGAGGGAGGG 28 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.07 (2 / 29), avg. gap size = 1.00 (2 / 2) 348 27.05 0.00 2.70 chr5ptel1M 945127 945240 (54760) MIR1_Amn#SINE/MIR 39 149 (81) m_b242s601i38 9586 chr5ptel1M 945127 TGAGAATGGGGACTGTACTGGGCACTAGTCTGAGAACCTGCCACTTCCTA 945176 i v v -- vv iv ? ? ivi v-i ?v i? MIR1_Amn#SINE 39 TGGGACTCGGGA--GACCTGGGTTCNANTCCCGGC-TCTGCCACTNGCCN 85 chr5ptel1M 945177 CCTGTGCCATCTTGGCTAGGTCAGATCACTTTTCTAAGCCTCAGTTTTCC 945226 v ? iv i vi i vv ? i i i? i i MIR1_Amn#SINE 86 GCTGNGTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCT 135 chr5ptel1M 945227 CATCTAGAAAATGG 945240 iv MIR1_Amn#SINE 136 CATCTGTAAAATGG 149 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.51 CpG sites = 16, Kimura (unadjusted) = 37.04 Transitions / transversions = 1.14 (16/14) Gap_init rate = 0.03 (3 / 113), avg. gap size = 1.00 (3 / 3) 379 27.08 0.00 1.04 chr5ptel1M 945144 945240 (54760) MIRc#SINE/MIR 52 147 (121) m_b242s601i39 9586 chr5ptel1M 945144 CTGGGCACTAGTCTGAGAACCTGCCACTTCCTACCTGTGCCATCTTGGCT 945193 iv v ivi v-i v v iv i vi MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGC-TCTGCCACTTACTAGCTGTGTGACCTTGGGC 100 chr5ptel1M 945194 AGGTCAGATCACTTTTCTAAGCCTCAGTTTTCCCATCTAGAAAATGG 945240 i vv v i i i i i iv MIRc#SINE/MIR 101 AAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGG 147 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.56 CpG sites = 14, Kimura (unadjusted) = 34.14 Transitions / transversions = 1.17 (14/12) Gap_init rate = 0.01 (1 / 96), avg. gap size = 1.00 (1 / 1) 281 30.93 1.03 0.00 chr5ptel1M 946218 946314 (53686) Charlie4#DNA/hAT-Charlie 46 143 (3235) m_b242s502i1 9587 chr5ptel1M 946218 GGTAGATTCTGGATGTTCTATAAACTTGGAGAGGAAAACAT-ACATCTCA 946266 i v iii iv v ii i vi v - iv Charlie4#DNA/ 46 GATAGAATTCAGGGGGTCCGTGAACTTGGATGGGAAAAAATTACATCTTT 95 chr5ptel1M 946267 GTTTTTCCTGTCCTCTGGATGAAATCAAGCATTTCTTCCAATTAGAAA 946314 i iv iv iiv iv i i vi Charlie4#DNA/ 96 ATTTTCACTAACCTCTAACTGAAATTTAGCATTTCCTTCAATTATGAA 143 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 39.56 CpG sites = 19, Kimura (unadjusted) = 41.61 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.01 (1 / 96), avg. gap size = 1.00 (1 / 1) 277 28.40 1.23 0.00 chr5ptel1M 946320 946400 (53600) Charlie4#DNA/hAT-Charlie 3297 3378 (0) m_b242s502i2 9588 chr5ptel1M 946320 AAACATGATTCTGGGGTTGGGTCCG-GGATTTCACCAGGTTGATAAAGGA 946368 v i ivv i-i ii ii vi i Charlie4#DNA/ 3297 AAACATTATTCTGAGAAGGGGTCCATAGGCTTCACCAGACTGCCAAAGGG 3346 chr5ptel1M 946369 GTCTCTTTCACAAGAAAGACCAAGAAACCCTG 946400 iv vv i iii v Charlie4#DNA/ 3347 GTCCATGGCACAAAAAAGGTTAAGAACCCCTG 3378 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 37.16 CpG sites = 15, Kimura (unadjusted) = 37.16 Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.01 (1 / 80), avg. gap size = 1.00 (1 / 1) 678 31.29 4.40 1.56 chr5ptel1M 946449 946698 (53302) MIRc#SINE/MIR 12 268 (0) m_b242s601i40 9589 chr5ptel1M 946449 GATGCATGGTGGGTAGCCCACAGGTCCCAAATTCGGGAAGATCTGAATTC 946498 i -- iv vv v v iiii v i i ii MIRc#SINE/MIR 12 GGTGCA--GTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr5ptel1M 946499 AAACTCTATCTCAGACACTTAATAATCGGTGTGACCAAGGATGAGCCACA 946548 i iii iiv v v v i- v vv iii i v MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAG-CTGTGTGACCTTGGGCAAGTCACT 108 chr5ptel1M 946549 CACTCTTTCTCTGCCTCAGTTTCATCAACTGTAAAATAAGGATAACAAT- 946597 i vi i vv v v ii i - MIRc#SINE/MIR 109 TAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATA 158 chr5ptel1M 946598 -----CACGCTTGTCTCCAAGAGCGGGTTGTGAAGATCAAATGAGTTAAC 946642 ----- vi i ii vv i i-v i v i MIRc#SINE/MIR 159 CCTGCCCTGCCTACCTCACAGGGT-TGTTGTGAGGATCAAATGAGATAAT 207 chr5ptel1M 946643 ATTGGT-AAATCGATGCCCAAACCTTAAAGGACTATATGAGTGC----TG 946687 i vv - v v vivi iv vi ii i i----? MIRc#SINE/MIR 208 GTATGTGAAAGCGCTTTGTAAACTGTAAAGTGCTATACAAATGTAAGGNG 257 chr5ptel1M 946688 CTATTATTATT 946698 i MIRc#SINE/MIR 258 TTATTATTATT 268 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.50 CpG sites = 45, Kimura (unadjusted) = 42.02 Transitions / transversions = 1.41 (45/32) Gap_init rate = 0.03 (8 / 249), avg. gap size = 1.88 (15 / 8) 226 26.92 0.00 0.00 chr5ptel1M 946708 946759 (53241) C MIRc#SINE/MIR (110) 158 107 m_b242s601i41 9590 chr5ptel1M 946708 TATTAGCATCTCTGTTTCACTGCTGAGAAAGCTGAGGCTCAGAAATGGAA 946757 vi i ii i v v i i i v vv C MIRc#SINE/MIR 158 TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTA 109 chr5ptel1M 946758 AG 946759 C MIRc#SINE/MIR 108 AG 107 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.06 CpG sites = 8, Kimura (unadjusted) = 34.06 Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 316 28.45 5.65 0.77 chr5ptel1M 946919 947042 (52958) MIR1_Amn#SINE/MIR 21 150 (80) m_b242s601i42 9591 chr5ptel1M 946919 GTAGATGGTATCCTGAA-TAGAGCTCACCTGAGTCTGAGTTCAAATCCAG 946967 i i viiv i - i ii ivvv -i i ? ? v MIR1_Amn#SINE 21 GTGGATAGAGCACTGGACTGGGACTCGGGAGA-CCTGGGTTCNANTCCCG 69 chr5ptel1M 946968 CCTCACACATTTACTAGTTGTGTGACCCTGCATAAGTCACTTCACC-CTA 947016 v vvv i ?i i? i ? i vii ? - v MIR1_Amn#SINE 70 GCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGTCACTTNACCTCTC 119 chr5ptel1M 947017 TAT-----AATTTCCTCATGTGTGAAATGAG 947042 i?----- i v i i MIR1_Amn#SINE 120 TGNGCCTCAGTTTCCTCATCTGTAAAATGGG 150 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.64 CpG sites = 22, Kimura (unadjusted) = 40.15 Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.03 (4 / 123), avg. gap size = 2.00 (8 / 4) 363 23.66 6.45 0.00 chr5ptel1M 946950 947042 (52958) MIR#SINE/MIR 46 144 (118) m_b242s601i43 9591 chr5ptel1M 946950 GTCTGAGTTCAAATCCAGCCTCACACATTTACTAGTTGTGTGACCCTGCA 946999 i i i v v vvv i i i vi MIR#SINE/MIR 46 GCCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGG 95 chr5ptel1M 947000 TAAGTCACTTCACC-CTATAT-----AATTTCCTCATGTGTGAAATGAG 947042 i i v - v i ----- i v i i MIR#SINE/MIR 96 CAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGG 144 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.46 CpG sites = 13, Kimura (unadjusted) = 28.99 Transitions / transversions = 1.44 (13/9) Gap_init rate = 0.02 (2 / 92), avg. gap size = 3.00 (6 / 2) 328 33.56 7.41 0.69 chr5ptel1M 947475 947609 (52391) C MIR3#SINE/MIR (1) 207 64 m_b242s601i44 9592 chr5ptel1M 947475 AGTCAGAAGGTCATAGAGCTTGGGATTTGGAA----TCTTCGAGGTTAGG 947520 i v iii iiv vi vi ----i v i i vv C MIR3#SINE/MIR 207 AATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATC 158 chr5ptel1M 947521 AAGTCCAATAGTCCCATTTTCCAGATGGAGGAATTGAGACCTAGGGAAAG 947570 v ivvi i v ii i i i i i iiv C MIR3#SINE/MIR 157 TAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGT 108 chr5ptel1M 947571 GAAGGCGATC------AGGTTACATCAGTAGTAAGTGGCAGAACC 947609 - i ii------ i iviv? v i C MIR3#SINE/MIR 107 GAA-GTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCC 64 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 47.89 CpG sites = 30, Kimura (unadjusted) = 47.89 Transitions / transversions = 2.00 (30/15) Gap_init rate = 0.02 (3 / 134), avg. gap size = 3.67 (11 / 3) 276 24.73 18.87 0.80 chr5ptel1M 947529 947634 (52366) C MIRc#SINE/MIR (116) 152 28 m_b242s601i45 9592 chr5ptel1M 947529 TAGTCCCATTTTCCAGATGGAGGAATTGAGACCTAGGGA----AAGGAAG 947574 vi v ii i i i ii i ---- vi v C MIRc#SINE/MIR 152 TATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGAC 103 chr5ptel1M 947575 GCGATC-AGGTTACATCAGTAGTAAGTGGCA------------GAACCTA 947611 vi vi - i iviv ------------ i C MIRc#SINE/MIR 102 TTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCA 53 chr5ptel1M 947612 -GTCTTCCTATACTTCAA--CCAGTG 947634 - i- i -- C MIRc#SINE/MIR 52 GGTCTTCCTG-ACTCCAAGTCCAGTG 28 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.29 CpG sites = 18, Kimura (unadjusted) = 31.29 Transitions / transversions = 2.25 (18/8) Gap_init rate = 0.06 (6 / 105), avg. gap size = 3.50 (21 / 6) 48 0.00 0.00 0.00 chr5ptel1M 948377 948417 (51583) (AC)n#Simple_repeat 1 41 (0) c_b242s251i1 9593 chr5ptel1M 948377 ACACACACACACACACACACACACACACACACACACACACA 948417 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACA 41 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 462 29.17 3.47 0.00 chr5ptel1M 951153 951296 (48704) C L2d_3end#LINE/L2 (5) 511 363 m_b242s601i46 9594 chr5ptel1M 951153 CAATGGATCAATAAAAATGTATTAAGCACCTACTATGTGCCGGGTACTGT 951202 vi i iv v i i ivi i C L2d_3end#LINE 511 CAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTGT 462 chr5ptel1M 951203 GCTAACTGCTGAGGAGACAAGTGCGATAGAGGAAGACA--ATCCTTCCTC 951250 ivi v i vvii?ivi ? viv --i i v i C L2d_3end#LINE 461 GCTAGGCGCTGTGGGGAACGANAAAANAGTATAAGACATGGTCCCTGCCC 412 chr5ptel1M 951251 TTAAGGAACTTACAGTCTAA--GGGGAGGGAA-AGTGACCCACAAAAAA 951296 i i i i-- iv - v i v vi C L2d_3end#LINE 411 TCAAGGAGCTTACAATCTAGTTGGGGAGACAAGACTAACACACATGAAA 363 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.45 CpG sites = 26, Kimura (unadjusted) = 38.97 Transitions / transversions = 1.62 (26/16) Gap_init rate = 0.02 (3 / 143), avg. gap size = 1.67 (5 / 3) 410 34.06 1.62 1.62 chr5ptel1M 951160 951344 (48656) C L2b_3end#LINE/L2 (10) 456 272 m_b242s601i47 9594 chr5ptel1M 951160 TCAATAAAAATGTATTAAGCACCTACTATGTGCCGGGTACTGTGCTAACT 951209 i v v i i i i i i? ivi C L2b_3end#LINE 456 TCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGC 407 chr5ptel1M 951210 GCTGAGGAGACAAGTGCGATAGAGGAAGACA--ATCCTTCCTCTTAAGGA 951257 i v ivv i vvi iv ?--i i v i i v C L2b_3end#LINE 406 GCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGGA 357 chr5ptel1M 951258 ACTTACAGTCTAAGGGGAGGGAAAGTGACCCACAAAAAAAGCTGGAAGGG 951307 i i iv i i v -- viii ?v i - viv? vii C L2b_3end#LINE 356 GCTCACAGTCTAGTGGGGGAGACA--GACATGTAANCAGA-CAATNATAA 310 chr5ptel1M 951308 CAGGGAGAGGGAGGGTAGGA-TAAAGCAATCCGAAGGA 951344 vvi v v - iii viii ii C L2b_3end#LINE 309 CCCAGAGTGGCAGGGTAGGACTGGGGGGGCCCAGAGGA 272 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 47.09 CpG sites = 39, Kimura (unadjusted) = 49.37 Transitions / transversions = 1.70 (39/23) Gap_init rate = 0.03 (5 / 184), avg. gap size = 1.20 (6 / 5) 208 31.97 5.47 7.14 chr5ptel1M 952278 952405 (47595) C L2d2_3end#LINE/L2 (7) 548 423 m_b242s601i48 9595 chr5ptel1M 952278 AAATCAGAAAGCATT-ATAAAGCACCTAGTGTATATTAGGCCTCCTGTTT 952326 iv ii - vi i v i iiv v-- -- C L2d2_3end#LIN 548 AAATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCA--CTGT-- 503 chr5ptel1M 952327 TTACTTGGCACTG-----GGCACCCAGAAGCAAAAGAGAGCCTGGGGC-T 952370 --i v i ----- ii vv i v --- v vv - C L2d2_3end#LIN 502 --GCTAGGCGCTGTGGGGGATACAAAGAAGTATAAGA---CATGGTCCCT 458 chr5ptel1M 952371 GCCCTGGAGGAGCCTGCACATTAGTCCAGAGAACA 952405 vi i i vvi ivi iii C L2d2_3end#LIN 457 GCCCTCAAGGAGCTTACAATCTAGTTGGGGAGACA 423 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.95 CpG sites = 22, Kimura (unadjusted) = 42.91 Transitions / transversions = 1.38 (22/16) Gap_init rate = 0.09 (12 / 127), avg. gap size = 1.33 (16 / 12) 210 26.39 4.17 0.00 chr5ptel1M 952440 952511 (47489) L2c_3end#LINE/L2 203 277 (201) m_b242s601i49 9596 chr5ptel1M 952440 CTTTGAGCTCCAGCTGAGATGTCACCTCCTCCATGGGGCCTTTCAGGATC 952489 ii ?ii v iv ii i vv i L2c_3end#LINE 203 CTTCAAGNCTCAGCTCAGATGTCACCTCCTCCGGGAAGCCTTCCCTGACC 252 chr5ptel1M 952490 CTCC---CCTTGCCTTCCTGCCCTC 952511 i ---? v i vvv L2c_3end#LINE 253 CCCCAAGNCTAGTCTAGGTGCCCTC 277 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.27 CpG sites = 11, Kimura (unadjusted) = 34.47 Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.01 (1 / 71), avg. gap size = 3.00 (3 / 1) 318 30.44 0.00 1.09 chr5ptel1M 953489 953581 (46419) MIR3#SINE/MIR 88 179 (29) m_b242s601i50 9597 chr5ptel1M 953489 GAGCATGGGCAGTGTGAACCCATCTCCCTGGGCCTCAGTCTCCTGTTTTG 953538 v v i- v vii i i i vv i MIR3#SINE/MIR 88 GACCTTGGGCAA-GTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTG 136 chr5ptel1M 953539 TAACCCAAGGGGATTGGACCAGCTGGCCCCTGGGCCTCCTTCC 953581 vvii i i v ii i ii vii MIR3#SINE/MIR 137 TAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCC 179 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.79 CpG sites = 18, Kimura (unadjusted) = 40.79 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.01 (1 / 92), avg. gap size = 1.00 (1 / 1) 16 0.00 0.00 0.00 chr5ptel1M 953859 953876 (46124) (CA)n#Simple_repeat 1 18 (0) m_b242s252i5 9598 chr5ptel1M 953859 CACACACACACACACACA 953876 (CA)n#Simple_ 1 CACACACACACACACACA 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 502 24.23 7.91 2.04 chr5ptel1M 954152 954290 (45710) MIRc#SINE/MIR 2 148 (120) m_b242s601i51 9599 chr5ptel1M 954152 GGAGCAGAGAGGTGACTCAGTGGACAGATTACCCAGCCTGGA-------- 954193 ii v v --- v vi ivii i -------- MIRc#SINE/MIR 2 GAGGCAGTGTGGTG---CAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr5ptel1M 954194 --CCTAAGTTCAAATCTAGCCTCAGATACTCACTAGCTGTGTGAGCCTGG 954241 -- ii i i iv v v vi i v i MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 98 chr5ptel1M 954242 GCAAGTCCCTTTA-CTCTGTTTACCTCAGTTTCCTCATCTGTAAGATGAG 954290 v v - v vvi i i MIRc#SINE/MIR 99 GCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.68 CpG sites = 18, Kimura (unadjusted) = 29.73 Transitions / transversions = 1.20 (18/15) Gap_init rate = 0.04 (6 / 138), avg. gap size = 2.33 (14 / 6) 54 5.98 1.39 1.39 chr5ptel1M 954410 954481 (45519) (AT)n#Simple_repeat 1 72 (0) c_b242s251i2 9600 chr5ptel1M 954410 ATATATGTATATATATCTACATGTAGTAT-TATATATATATATATATATA 954458 i v i i - - (AT)n#Simple_ 1 ATATATATATATATATATATATATA-TATATATATATATATATATATATA 49 chr5ptel1M 954459 TATATATATATATATATATATAT 954481 (AT)n#Simple_ 50 TATATATATATATATATATATAT 72 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.03 (2 / 71), avg. gap size = 1.00 (2 / 2) 49 0.00 0.00 0.00 chr5ptel1M 954487 954528 (45472) (GA)n#Simple_repeat 1 42 (0) c_b242s251i3 9601 chr5ptel1M 954487 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 954528 (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 42 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 182 34.72 4.12 2.02 chr5ptel1M 954923 955019 (44981) L2#LINE/L2 2763 2861 (221) m_b242s601i52 9602 chr5ptel1M 954923 CCTCTCCAGCCCCCT-TCTTCATAGCTACAGAAGGGATTTTTCTAAAACA 954971 i ? i ivi - vv i vi vii v ii i i L2#LINE/L2 2763 CCCCTNCAGTCTATTCTCAACACAGCAGCCAGAGTGATCCTTTTAAAACG 2812 chr5ptel1M 954972 CAGATCCGACTACATCACTATCTTGCTCAATAAACT---ATGGCGGTTCC 955018 i ii v ii ii viii v vv --- -- L2#LINE/L2 2813 TAAGTCAGATCATGTCACTCCTCTGCTCAAAACCCTCCAATGGC--TTCC 2860 chr5ptel1M 955019 C 955019 L2#LINE/L2 2861 C 2861 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 48.40 CpG sites = 22, Kimura (unadjusted) = 50.65 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.04 (4 / 96), avg. gap size = 1.50 (6 / 4) 221 41.10 0.00 0.68 chr5ptel1M 955525 955671 (44329) L2c_3end#LINE/L2 294 439 (39) m_b242s601i53 9602 chr5ptel1M 955525 CACTCAGTTTCCAGTCTCTTTCAGGGTCTCATTTCTAAGGTGTTTAAAAT 955574 i v i vi v i v vvi vv i ivi vv v viv v L2c_3end#LINE 294 CACCCTGTCTATACTCCCATTATAGCACTTATCATTAACTTGTATTGTAA 343 chr5ptel1M 955575 TTATCCAACTTGTTCTCAACTTCTCCCAGTCGAACGTAAGCTTCCTGAGG 955624 i iivi vv? v viii ii v v vi i i i L2c_3end#LINE 344 TTGTCTGTTTACNTGTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGG 393 chr5ptel1M 955625 ACAGCAACTCTGTTCTTTCTATATATCTTATCTCCAGGGCCTGGCAC 955671 i vi iv ii v ii v - iv i v L2c_3end#LINE 394 GCAGGGACCGTGTCTTATTCATCT-TTGTATCCCCAGCGCCTGGCAC 439 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 60.52 CpG sites = 31, Kimura (unadjusted) = 62.16 Transitions / transversions = 1.07 (31/29) Gap_init rate = 0.01 (1 / 146), avg. gap size = 1.00 (1 / 1) 232 31.67 4.90 0.94 chr5ptel1M 955573 955674 (44326) L2a_3end#LINE/L2 364 469 (48) m_b242s601i54 9602 chr5ptel1M 955573 ATTTATCCAACTTGTTCTCAA-CTTCTCCCAGTCGAACGTAAGCTTCCTG 955621 iii-i i v vi- i i v v i i v L2a_3end#LINE 364 ATTTATTTG-TTTATTGTCTGTCTCCCCCCACTAGAATGTAAGCTCCATG 412 chr5ptel1M 955622 AGGACAGCAACTCTGTTCT-TTCTATATAT--CT-TATCTCCAGGGCCTG 955667 i vi i vv - i i vi i-- - i v i L2a_3end#LINE 413 AGGGCAGGGACTTTTGTCTGTTTTGTTCACTGCTGTATCCCCAGCGCCTA 462 chr5ptel1M 955668 GCACGAT 955674 v ii L2a_3end#LINE 463 GAACAGT 469 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.34 CpG sites = 21, Kimura (unadjusted) = 43.34 Transitions / transversions = 1.91 (21/11) Gap_init rate = 0.05 (5 / 101), avg. gap size = 1.20 (6 / 5) 163 23.33 2.22 0.24 chr5ptel1M 955856 956261 (43739) (GA)n#Simple_repeat 1 414 (0) m_b242s252i6 9603 chr5ptel1M 955856 GAGAGAGACACAAAGAGATAGA-AGAGACAGAGAGAGATAGA-AGAGACA 955903 v v i v - v v - v (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr5ptel1M 955904 AACAGAAAAATGGAGACAGAGACAGAAAGAG-GACAGAAATAGA-AGAGA 955951 i v i i vi v v i - v i v - (GA)n#Simple_ 51 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 100 chr5ptel1M 955952 GACAGAGGCAGAGAGACAAAGAAAGAGAAAGCTAGAGACAGAGAGAGATA 956001 v iv v i i i vv v v (GA)n#Simple_ 101 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 150 chr5ptel1M 956002 CAGGCACAGAAAGAGACAGAGAGATAGAGACAGGGAGAGAGATAGA-AGA 956050 v iv v i v v v i v - (GA)n#Simple_ 151 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 200 chr5ptel1M 956051 GACCGACAGAAAGAGACAGAGAGAGATACAGACAGAGATAGAAAGAGATA 956100 vv v i v v v v v i v (GA)n#Simple_ 201 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 250 chr5ptel1M 956101 CATATAGAGAGAGAGAAAGTCAGA-AGAGCGAGAGAGAGAGAGAGAGAGA 956149 v v v i vv - v (GA)n#Simple_ 251 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 300 chr5ptel1M 956150 GAGAGAGAGAGAGAGAGAGAGAGAGGCGGAGACAGAGAGAGAGTAAAAAC 956199 ivi v - i i v (GA)n#Simple_ 301 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG-AGAGAG 349 chr5ptel1M 956200 AGAAACAGACAG-GAGACAGA-AGAAAGAGACA-ACCCAGAGAGACAGGC 956246 i v v - v - i v - vvv v iv (GA)n#Simple_ 350 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 399 chr5ptel1M 956247 AGTGACACACAGAGA 956261 v v v v (GA)n#Simple_ 400 AGAGAGAGAGAGAGA 414 Matrix = Unknown Transitions / transversions = 0.42 (24/57) Gap_init rate = 0.02 (10 / 405), avg. gap size = 1.00 (10 / 10) 349 35.25 1.64 0.00 chr5ptel1M 956842 956963 (43037) C MIRc#SINE/MIR (24) 244 121 m_b242s601i55 9604 chr5ptel1M 956842 TAGAGCTTTCTAAGACTGGCAAAGT-TTTTTACCTACATAAACTCCAGTG 956890 v vi i viii vi i-i i v v v vvv C MIRc#SINE/MIR 244 TATAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATCTCATTTG 195 chr5ptel1M 956891 CTCTTAGTAGCGACGCTCTGAGGTGAACCCC-CGGGTACTACCGCCCTCA 956939 v i vii i i v v iii vvv- i i iiii i C MIRc#SINE/MIR 194 ATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCA 145 chr5ptel1M 956940 TTTCACAGATGAGGAAACTGAGAC 956963 i i C MIRc#SINE/MIR 144 TTTTACAGATGAGGAAACTGAGGC 121 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 48.18 CpG sites = 26, Kimura (unadjusted) = 49.85 Transitions / transversions = 1.53 (26/17) Gap_init rate = 0.02 (2 / 121), avg. gap size = 1.00 (2 / 2) 25 11.97 3.45 3.45 chr5ptel1M 957605 957662 (42338) (CTGCCCC)n#Simple_repeat 1 58 (0) m_b242s252i7 9605 chr5ptel1M 957605 CTGCCCTCTGAGCCCCCTCCCCCCAG--GCCTGGCCCCCGCCCCCTGCCC 957652 i -- v v --v v i (CTGCCCC)n#Si 1 CTGCCCCCT--GCCCCCTGCCCCCTGCCCCCTGCCCCCTGCCCCCTGCCC 48 chr5ptel1M 957653 CCTGCCCCCT 957662 (CTGCCCC)n#Si 49 CCTGCCCCCT 58 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.05 (3 / 57), avg. gap size = 1.33 (4 / 3) 46 4.08 0.00 0.00 chr5ptel1M 958065 958115 (41885) (G)n#Simple_repeat 1 51 (0) c_b242s251i4 9606 chr5ptel1M 958065 GGGGGGGGGGGGGGGGGGGGGGAAGGGGGGGGGGGGGGGGGGGGGGGGGG 958114 ii (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 50 chr5ptel1M 958115 G 958115 (G)n#Simple_r 51 G 51 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 19 28.77 1.69 7.14 chr5ptel1M 958117 958234 (41766) (GGAAGG)n#Simple_repeat 1 112 (0) m_b242s252i8 9607 chr5ptel1M 958117 GGAGGGGGCAAAGGGACGGGGAAGGGGAA--GGAGGCGGAGGTGGAAAGC 958164 i - i v -- i v i - i v (GGAAGG)n#Sim 1 GGAAGGGG-AAGGGGAAGGGGAAGGGGAAGGGGAAGGGGAAG-GGGAAGG 48 chr5ptel1M 958165 AGTGACGAAAGTAGTGAAGGAGAGAGAGGAGAAAGTGAAGAGAAAGGTGA 958214 i viiv i -- v - - - i i v i i - i (GGAAGG)n#Sim 49 GGAAGGGGAAG--GGGAAGG-G-GA-AGGGGAAGGGGAAGGGGAAGG-GG 92 chr5ptel1M 958215 AAGGGAAAGGGGGAGGAGAA 958234 i i i (GGAAGG)n#Sim 93 AAGGGGAAGGGGAAGGGGAA 112 Matrix = Unknown Transitions / transversions = 2.43 (17/7) Gap_init rate = 0.08 (9 / 117), avg. gap size = 1.11 (10 / 9) 28 17.21 0.00 0.00 chr5ptel1M 959610 959663 (40337) (CCCGC)n#Simple_repeat 1 54 (0) m_b242s252i9 9608 chr5ptel1M 959610 CCCGCCTGGCCCCGCCCCGCCCCGCCCCGTCCTACCCCGCCCCGCTCCAC 959659 iv i ii i i (CCCGC)n#Simp 1 CCCGCCCCGCCCCGCCCCGCCCCGCCCCGCCCCGCCCCGCCCCGCCCCGC 50 chr5ptel1M 959660 TCCG 959663 i (CCCGC)n#Simp 51 CCCG 54 Matrix = Unknown Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 14 19.75 7.46 2.86 chr5ptel1M 959829 959895 (40105) (GCCGCTC)n#Simple_repeat 1 70 (0) m_b242s252i10 9609 chr5ptel1M 959829 GCCGCTCGCGGCTCTCCCGCTCCCTCCCTCGCTGC-CGCC-CTC-CCTCG 959875 v -v v - v i - - - v v (GCCGCTC)n#Si 1 GCCGCTCGCCGCTC-GCCGCTCGC-CGCTCGCCGCTCGCCGCTCGCCGCT 48 chr5ptel1M 959876 CAGCGCCGGCCGCT-GCC-CTC 959895 iv iv - - (GCCGCTC)n#Si 49 CGCCGCTCGCCGCTCGCCGCTC 70 Matrix = Unknown Transitions / transversions = 0.38 (3/8) Gap_init rate = 0.11 (7 / 66), avg. gap size = 1.00 (7 / 7) 15 21.89 6.67 1.59 chr5ptel1M 960256 960315 (39685) (TGC)n#Simple_repeat 1 63 (0) m_b242s252i11 9610 chr5ptel1M 960256 TGCCGCTGCCTTC-CCTCCTGCTGCT-CCGGGGCAGC-GC-CCTGCTGCT 960301 i - v -v v - i vv v - -v (TGC)n#Simple 1 TGCTGCTG-CTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT 49 chr5ptel1M 960302 CCTGCTCCTGCTGC 960315 v v (TGC)n#Simple 50 GCTGCTGCTGCTGC 63 Matrix = Unknown Transitions / transversions = 0.22 (2/9) Gap_init rate = 0.08 (5 / 59), avg. gap size = 1.00 (5 / 5) 14 21.18 4.55 0.00 chr5ptel1M 960571 960614 (39386) (TGGCCG)n#Simple_repeat 1 46 (0) m_b242s252i12 9611 chr5ptel1M 960571 TGACCGTGGCCCTGGCGGTGGCCG-GACC-CGGCCGGGGCTGCGGC 960614 i v v - i -i v i i (TGGCCG)n#Sim 1 TGGCCGTGGCCGTGGCCGTGGCCGTGGCCGTGGCCGTGGCCGTGGC 46 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2) 18 25.43 1.79 0.00 chr5ptel1M 960945 961000 (39000) (CCCGGG)n#Simple_repeat 1 57 (0) m_b242s252i13 9612 chr5ptel1M 960945 CCCAGG-CCGGGCCCGGGCCCGGGCCCGTGGCGGCGCCTGCTCCGGGGAA 960993 i - v v v v i vv v vv (CCCGGG)n#Sim 1 CCCGGGCCCGGGCCCGGGCCCGGGCCCGGGCCCGGGCCCGGGCCCGGGCC 50 chr5ptel1M 960994 GGGGCCC 961000 v (CCCGGG)n#Sim 51 CGGGCCC 57 Matrix = Unknown Transitions / transversions = 0.20 (2/10) Gap_init rate = 0.02 (1 / 55), avg. gap size = 1.00 (1 / 1) 302 26.50 6.93 2.86 chr5ptel1M 964822 964922 (35078) C L2d2_3end#LINE/L2 (16) 539 435 m_b243s601i0 9613 chr5ptel1M 964822 AGCATTTATGGGTCACCTGCTGTACTTCAGGCACTGTGCTAGCCTCTGGG 964871 ii v iv i i iiviv v v v C L2d2_3end#LIN 539 AATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGTG 490 chr5ptel1M 964872 GTGG---CAAAGGCAAAGT----GCCACGGCTCTGGCCCCCGAGGAGCTT 964914 v --- --- ---- v i ii iv i i C L2d2_3end#LIN 489 GGGGATACAAAG---AAGTATAAGACATGGTCCCTGCCCTCAAGGAGCTT 443 chr5ptel1M 964915 ACTCTCTA 964922 vv C L2d2_3end#LIN 442 ACAATCTA 435 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.72 CpG sites = 14, Kimura (unadjusted) = 33.25 Transitions / transversions = 1.17 (14/12) Gap_init rate = 0.05 (5 / 100), avg. gap size = 2.00 (10 / 5) 206 28.89 0.00 0.00 chr5ptel1M 964940 964984 (35016) MIR3#SINE/MIR 109 153 (55) m_b243s601i2 9614 chr5ptel1M 964940 CTTCTCTAAGCCTCGGTGTTCCCATCTGCAAAGTGGGGATGCTGG 964984 i ii i v i i i i i iv i MIR3#SINE/MIR 109 CCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGG 153 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.43 CpG sites = 11, Kimura (unadjusted) = 40.43 Transitions / transversions = 5.50 (11/2) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 235 20.00 0.00 0.00 chr5ptel1M 964940 964979 (35021) MIRc#SINE/MIR 112 151 (117) m_b243s601i1 9614 chr5ptel1M 964940 CTTCTCTAAGCCTCGGTGTTCCCATCTGCAAAGTGGGGAT 964979 i i i v i i i i MIRc#SINE/MIR 112 CCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGAT 151 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 24.78 CpG sites = 7, Kimura (unadjusted) = 24.78 Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 387 31.19 11.52 0.95 chr5ptel1M 965058 965248 (34752) C MIRc#SINE/MIR (28) 240 30 m_b243s601i3 9615 chr5ptel1M 965058 GCACTTTACA-CTCAGAATGTTGCTCATCCATTCATTATCTCATCTGAT- 965105 -i i v v i- iviv v i - C MIRc#SINE/MIR 240 GCACTTTACAGTTTACAAAGC-GCTTTCACATACATTATCTCATTTGATC 192 chr5ptel1M 965106 --------GA----GTCAG--AGCCAGGAT---TGCCATTATGCCCATTC 965138 --------i ---- v -- v ii--- iii v i C MIRc#SINE/MIR 191 CTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTT 142 chr5ptel1M 965139 TGCAGAGGAGAAAATTGAGGTGTAAAGTAGTCAAATGACTT-TCTATGGC 965187 i v i i ivi i vi i i -i i v - C MIRc#SINE/MIR 141 TACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGG- 93 chr5ptel1M 965188 TCCCCTTGCTAATTAATGATAGGGTAGGG-CCAGGACCCGGCTCCT-CAG 965235 v viv i v i ii i iv - iv i i v i - v C MIRc#SINE/MIR 92 TCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTG 43 chr5ptel1M 965236 GCTCCCAGGGCAG 965248 i v vv C MIRc#SINE/MIR 42 ACTCCAAGTCCAG 30 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.95 CpG sites = 36, Kimura (unadjusted) = 41.90 Transitions / transversions = 1.57 (36/23) Gap_init rate = 0.06 (11 / 190), avg. gap size = 2.18 (24 / 11) 394 32.46 1.92 1.27 chr5ptel1M 965122 965277 (34723) C MIR1_Amn#SINE/MIR (70) 160 4 m_b243s601i4 9615 chr5ptel1M 965122 TGCCATTATGCCCATTCTGCAGAGGAGAAAATTGAGGTGTAAAGTAGTCA 965171 ii v i i v i i i?i i vi ? C MIR1_Amn#SINE 160 TATCATTATCCCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNA 111 chr5ptel1M 965172 AATGACTT-TCTATGGCTCCCCTTGCTAATTAATGATAGGGTAGGG-CCA 965219 i -i i v - v ?iv ?iii? i ii i iv -?i? C MIR1_Amn#SINE 110 AGTGACTTGCCCAAGG-TCACNCAGCNGGCNAGTGGCAGAGCCGGGANTN 62 chr5ptel1M 965220 GGACCCGGCTCCTCAGGCTCCCAGGGCAG-GTTCCACCTTACCTGACCTC 965268 i i v ii v iv vv - i i i -i iv v C MIR1_Amn#SINE 61 GAACCCAGGTCTCCCGAGTCCCAGTCCAGTGCTCTATC-CACTAGACCAC 13 chr5ptel1M 965269 AGGGCATCC 965277 vv v C MIR1_Amn#SINE 12 ACTGCCTCC 4 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 48.15 CpG sites = 33, Kimura (unadjusted) = 48.15 Transitions / transversions = 1.94 (33/17) Gap_init rate = 0.03 (5 / 155), avg. gap size = 1.00 (5 / 5) 184 23.91 2.17 0.00 chr5ptel1M 965826 965871 (34129) C MIR3#SINE/MIR (6) 202 156 m_b243s601i5 9616 chr5ptel1M 965826 TAGAA-CAGGGAATATCAGAGCTGGGAGGGGCCTGAGAACCAATTTA 965871 - vi i i i v iviv i C MIR3#SINE/MIR 202 TAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTA 156 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.60 CpG sites = 7, Kimura (unadjusted) = 29.60 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1) 204 22.71 5.80 4.29 chr5ptel1M 965998 966066 (33934) C MIR1_Amn#SINE/MIR (46) 184 115 m_b243s601i6 9616 chr5ptel1M 965998 AAAGCA---TA-ATAGGATGTTAGCACTTGCTAGACCCTCATTTTACAGC 966043 --- - v v i i - iii --i i v C MIR1_Amn#SINE 184 AAAGCACTTTACAAAGGAGGTCAGTA-TCATTA--TCCCCATTTTACAGA 138 chr5ptel1M 966044 CCAGGAAACTGAGTCCCGGAGGG 966066 iv v ? i i C MIR1_Amn#SINE 137 TGAGGAAACTGAGGCNCAGAGAG 115 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.45 CpG sites = 10, Kimura (unadjusted) = 28.45 Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.07 (5 / 68), avg. gap size = 1.40 (7 / 5) 222 15.79 0.00 0.00 chr5ptel1M 966029 966066 (33934) C MIR3#SINE/MIR (61) 147 110 m_b243s601i7 9616 chr5ptel1M 966029 CCCTCATTTTACAGCCCAGGAAACTGAGTCCCGGAGGG 966066 viv v i i C MIR3#SINE/MIR 147 CCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAG 110 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 17.81 CpG sites = 3, Kimura (unadjusted) = 17.81 Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 307 21.69 7.23 0.00 chr5ptel1M 966425 966507 (33493) C Charlie1a#DNA/hAT-Charlie (22) 1433 1345 m_b243s502i0 9617 chr5ptel1M 966425 TCCCAGGACACCTTTACACTCTTGAAAGTTATTGCAGACTCTCCAGA--- 966471 i v i i vi i ivv --- C Charlie1a#DNA 1433 TCTCAGGACCCCTTTACACTCTTAAAAATTATTGAGGACCCCAAAGAGCT 1384 chr5ptel1M 966472 ---GTTTATGTGGATAATATCTATGATTATTAATTATAT 966507 --- i v viv v ii C Charlie1a#DNA 1383 TTTGTTTATGTGGGTTATATCTATCGATATTTACCATAT 1345 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 24.32 CpG sites = 10, Kimura (unadjusted) = 25.93 Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.02 (2 / 82), avg. gap size = 3.00 (6 / 2) 18 18.47 4.65 0.00 chr5ptel1M 966512 966554 (33446) (TA)n#Simple_repeat 1 45 (0) m_b243s252i1 9618 chr5ptel1M 966512 TATTTAGA-ATATATAT-TATATAAAAATATAGTTACATATATAT 966554 v v - - v v vv i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATAT 45 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.00 (2 / 2) 15 19.79 5.56 1.79 chr5ptel1M 966512 966565 (33435) (TATTATA)n#Simple_repeat 1 56 (0) m_b243s252i0 9619 chr5ptel1M 966512 TATT-TAGAATATATATTATATAAAAATATAGT-TACA-TATATATTAGA 966558 - v v - vv v - i - v (TATTATA)n#Si 1 TATTATATATTATATATTATAT-ATTATATATTATATATTATATATTATA 49 chr5ptel1M 966559 AATGATA 966565 v v (TATTATA)n#Si 50 TATTATA 56 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.08 (4 / 53), avg. gap size = 1.00 (4 / 4) 227 29.63 1.22 1.22 chr5ptel1M 966581 966662 (33338) C Charlie1b#DNA/hAT-Charlie (428) 95 14 m_b243s502i1 9617 chr5ptel1M 966581 TAGCACCATCCTTAAAGTAGTTCGGACTTGGAGGGCCTC-TGACAGGGTC 966629 i ii iv v i iv i v v i i - v C Charlie1b#DNA 95 TAGTATTATTATGAAAATAGTTTTGACCTCGCGGACCCCCTGAAAGGGTC 46 chr5ptel1M 966630 TCAGAGGCTCCCCTGGGGTCCCTGGGTGGCACT 966662 i i i - v i iivi C Charlie1b#DNA 45 TCGGGGAC-CCCCAGGGGTCCCCGGACCACACT 14 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 35.34 CpG sites = 16, Kimura (unadjusted) = 39.55 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.02 (2 / 81), avg. gap size = 1.00 (2 / 2) 453 32.13 4.55 0.98 chr5ptel1M 967054 967251 (32749) C MIRc#SINE/MIR (40) 228 24 m_b243s601i8 9620 chr5ptel1M 967054 TTACCAAGGCCTTTC-TGCACATTCTCTCAGGTG--CCTCCCCACATGCC 967100 v vv -iii v vv -- v v vv C MIRc#SINE/MIR 228 TTACAAAGCGCTTTCACATACATTATCTCATTTGATCCTCACAACAACCC 179 chr5ptel1M 967101 CCCGAGGGAGGGAGGGCAAAGCTTATTATCCATATTTTATAGTGGAGGAA 967150 ivi v v iivv vi i vv C MIRc#SINE/MIR 178 TGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAA 129 chr5ptel1M 967151 GCCCCAGCCGAAAGCAG--AAGTGATTTGCTCTGGTGTC-CCCAGTTAAG 967197 i ivvi iv i vi -- i i vi - - v i iv C MIRc#SINE/MIR 128 ACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAG-GTCACACAGCTAGT 80 chr5ptel1M 967198 AACTGTTGGAGCTTGGACTCTAA--GAGGATCTCCCGATGGCCAGGCCCG 967245 v vii iv v --v vii i i-v i i i C MIRc#SINE/MIR 79 AAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGAC-TCCAAGTCCA 31 chr5ptel1M 967246 GC-CTCT 967251 i- C MIRc#SINE/MIR 30 GTGCTCT 24 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.67 CpG sites = 31, Kimura (unadjusted) = 42.54 Transitions / transversions = 0.97 (31/32) Gap_init rate = 0.04 (8 / 197), avg. gap size = 1.38 (11 / 8) 13 9.98 5.88 2.86 chr5ptel1M 967831 967864 (32136) (CCGGG)n#Simple_repeat 1 35 (0) m_b243s252i2 9621 chr5ptel1M 967831 CCAGGCC-GGCCGAGGCCGGGCCTGG-CGGGCAGGG 967864 i - - v - v (CCGGG)n#Simp 1 CCGGGCCGGGCCG-GGCCGGGCCGGGCCGGGCCGGG 35 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.09 (3 / 33), avg. gap size = 1.00 (3 / 3) 265 32.43 1.35 0.00 chr5ptel1M 968230 968303 (31697) MIRc#SINE/MIR 76 150 (118) m_b243s601i9 9622 chr5ptel1M 968230 ATTTATCGTCTGTGTGGCCTCCGGGAAACCGTGTCTCTTCCCC-AGCCTC 968278 i iiiv i iv v ii iiv vv i i i- MIRc#SINE/MIR 76 ACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTC 125 chr5ptel1M 968279 AGCTTTCCCATCTGTAAAATGAAGA 968303 i i i ii MIRc#SINE/MIR 126 AGTTTCCTCATCTGTAAAATGGGGA 150 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.34 CpG sites = 18, Kimura (unadjusted) = 46.34 Transitions / transversions = 3.00 (18/6) Gap_init rate = 0.01 (1 / 73), avg. gap size = 1.00 (1 / 1) 369 29.35 1.09 0.00 chr5ptel1M 968239 968330 (31670) MIR3#SINE/MIR 82 174 (34) m_b243s601i10 9622 chr5ptel1M 968239 CTGTGTGGCCTCCGGGAAACCGTGTCTCTTCCCCAG-CCTCAGCTTTCCC 968287 i iv v ii iiv v i i ii - i i i MIR3#SINE/MIR 82 CTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTC 131 chr5ptel1M 968288 ATCTGTAAAATGAAGAGATTGGACGTCATGGCCACTAAGGCCC 968330 i i i vvv ii v i MIR3#SINE/MIR 132 ATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCC 174 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.43 CpG sites = 19, Kimura (unadjusted) = 39.43 Transitions / transversions = 2.38 (19/8) Gap_init rate = 0.01 (1 / 91), avg. gap size = 1.00 (1 / 1) 13 17.81 5.26 0.00 chr5ptel1M 968823 968860 (31140) (GGGGA)n#Simple_repeat 1 40 (0) m_b243s252i3 9623 chr5ptel1M 968823 GGGTAGGGCA-GGGAGAAGAGTGAAGGGGA-GGGAGGGGA 968860 v v - ii v i - (GGGGA)n#Simp 1 GGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGA 40 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 258 31.13 10.30 4.60 chr5ptel1M 969292 969456 (30544) C MIRc#SINE/MIR (16) 252 79 m_b243s601i11 9624 chr5ptel1M 969292 TATATGTGTATC-CACTTATTGCTATATAATATCCATA-CGTATGTATGT 969339 i v v- ------- i i v v v - iv vi ii C MIRc#SINE/MIR 252 TACATTTGTATAGCACTT-------TACAGTTTACAAAGCGCTTTCACAT 210 chr5ptel1M 969340 ATATAATAT-ATGTGAGTTTTACAAC---TCAGTGAGAAACAACATTAAT 969385 i v v - v vii i ---i v iv -ii vvivv C MIRc#SINE/MIR 209 ACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTA-GGCAGGGCA 161 chr5ptel1M 969386 GGCATCATTATCTCCATTTCACAGATGGGGAAGC----------AGAGGC 969425 i i i i i i ---------- i C MIRc#SINE/MIR 160 GGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGT 111 chr5ptel1M 969426 TGGATGATTTGCCC-AGGTCATCCAGGCAGCA 969456 iii i - iv vi i C MIRc#SINE/MIR 110 TAAGTGACTTGCCCAAGGTCACACAGCTAGTA 79 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.90 CpG sites = 30, Kimura (unadjusted) = 41.90 Transitions / transversions = 1.58 (30/19) Gap_init rate = 0.09 (14 / 164), avg. gap size = 1.79 (25 / 14) 279 23.94 15.49 0.00 chr5ptel1M 969386 969456 (30544) C MIRb#SINE/MIR (105) 163 82 m_b243s601i12 9624 chr5ptel1M 969386 GGCATCATTATCTCCATTTCACAGATGGGGAAGC----------AGAGGC 969425 i i i i i i ---------- i C MIRb#SINE/MIR 163 GGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGT 114 chr5ptel1M 969426 TGGATGATTTGCCC-AGGTCATCCAGGCAGCA 969456 iii i i - iv vi i C MIRb#SINE/MIR 113 TAAGTAACTTGCCCAAGGTCACACAGCTAGTA 82 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.41 CpG sites = 15, Kimura (unadjusted) = 31.41 Transitions / transversions = 7.50 (15/2) Gap_init rate = 0.03 (2 / 70), avg. gap size = 5.50 (11 / 2) 217 32.01 0.00 1.33 chr5ptel1M 969860 969935 (30065) C L2b_3end#LINE/L2 (5) 461 387 m_b243s601i13 9625 chr5ptel1M 969860 TTAGTTCATTAAACCCTTTTAAATTGCCTCCTGTGTGCCAGATCCTATGC 969909 vi vi ivi vivi vi v ii? i C L2b_3end#LINE 461 TTCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGC 412 chr5ptel1M 969910 TTGGTTCTGGAGGATACAAAACTGAA 969935 v iv - iviv C L2b_3end#LINE 411 TAGGCGCTGG-GGATACAGCGGTGAA 387 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.67 CpG sites = 13, Kimura (unadjusted) = 43.48 Transitions / transversions = 1.18 (13/11) Gap_init rate = 0.01 (1 / 75), avg. gap size = 1.00 (1 / 1) 291 35.15 2.74 4.53 chr5ptel1M 970969 971260 (28740) C L1ME4a_3end#LINE/L1 (233) 638 352 m_b243s551i0 9626 chr5ptel1M 970969 CTTCTCATTTCACTCGGCATCAGTTCATGAAAGTCTTCCCAGGTTTTTTT 971018 v iv iii i vv ivi i v iv -- C L1ME4a_3end#L 638 CTGCTTTTTTCACTTAACATTATATCATGAGCATTTTCCCATGTCATT-- 591 chr5ptel1M 971019 CTGAAAGCATCCTGC----TCATCATTTTTTCTAGCACAATAATATCCCA 971064 ---- ii i v ----v ? vv i vvv i C L1ME4a_3end#L 590 ----AAATATTCTTCGAAAACATNATTTTTAATGGCTGCATAATATTCCA 545 chr5ptel1M 971065 TCACAATCGTACGCCGCATCTTGTTTGGCCATTCCCCAGTTGATGGCCAT 971114 i?i vvvi iii ii vi i ii ? vi v v C L1ME4a_3end#L 544 TTNTATGGATGTACCATAATTTATTTAACCANTCCCCTATTGTTGGACAT 495 chr5ptel1M 971115 TCCCTCAATTTCCAATTCTTTGCCATCACAAAAAGAGCTAT--TTAAGAC 971162 ivvvivi i i i i i v iv ii-- v v i C L1ME4a_3end#L 494 TTAGGTTGTTTCCAATTTTTCGCTATTATAAATAATGCTGCGATGAACAT 445 chr5ptel1M 971163 TTTGGTACATGTGGATCCTTGCCTATAATTTT--TGATCTTTTGGGGATA 971210 ii v -- ii i i?i i vi i -- v i ii vi C L1ME4a_3end#L 444 CCTTGTACA--TAAATCTTTGTNCACATCTCTGATTATTTCCTTAGGATA 397 chr5ptel1M 971211 TAGACCTGGTAGTTGTATTTGCTGTATCCAAGGGTATAAAGCATCATTTT 971260 v vv i v - v v i vi v i? ---- C L1ME4a_3end#L 396 AATTCCTAGAAG-TGGAATTACTGGGTCAAAGGGTATGNA----CATTTT 352 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 49.10 CpG sites = 57, Kimura (unadjusted) = 50.59 Transitions / transversions = 1.39 (57/41) Gap_init rate = 0.05 (16 / 291), avg. gap size = 1.31 (21 / 16) 314 35.59 1.69 0.00 chr5ptel1M 971368 971485 (28515) MIR3#SINE/MIR 81 200 (8) m_b243s601i14 9627 chr5ptel1M 971368 GCCATGTAATTCTGGGCTAGTTACCTACTCTGGCTTTTTCTCAGTTCCCT 971417 ii i iii v i i vvi vv vvvi i MIR3#SINE/MIR 81 GCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCT 130 chr5ptel1M 971418 CCCTTATAAGAT-AAAGGCCTGGAAAAGGTGGTCTCCTGGGTTCCTTCCA 971466 vii i i - ii vi vv i i ivi i MIR3#SINE/MIR 131 CATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCA 180 chr5ptel1M 971467 AGTCTCA-GTTCCATGATCC 971485 iv v -i i i MIR3#SINE/MIR 181 GCTCTGACATTCTATGATTC 200 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 51.28 CpG sites = 27, Kimura (unadjusted) = 51.28 Transitions / transversions = 1.80 (27/15) Gap_init rate = 0.02 (2 / 117), avg. gap size = 1.00 (2 / 2) 533 35.75 9.50 1.39 chr5ptel1M 971575 971974 (28026) C L2#LINE/L2 (393) 2689 2258 m_b243s601i15 9625 chr5ptel1M 971575 ATTAAGGTGGTAGGCCCCGTAAATGAAGAGAACAGGGAAAATGCAAGAGA 971624 ii i - vvi v ii iv vv vvii v vi v C L2#LINE/L2 2689 ACCAGGGTGGT-GGCAGTGGAGGTGGTGAGAAGTGGTCGGATTCTGGATA 2641 chr5ptel1M 971625 TGTTATAAAAGCAGAATGGGCAAGATTTGTC----------ATCTTGGGG 971664 i v i i i iiv i i ii---------- v v v C L2#LINE/L2 2640 TATTTTGAAGGTAGAGCCGACAGGATTTGCTGATGGATTGGATGTGGGGT 2591 chr5ptel1M 971665 ATAGAAGAAGGGGGAAATTTGAATATATCTCTGAGGCTCTGAACCGGAGT 971714 i iii i i iii v ii iv iv ii i i vii v i C L2#LINE/L2 2590 GTGAGAGAAAGAGAGGAGTCAAGGATGACTCCAAGGTTTTTGGCCTGAGC 2541 chr5ptel1M 971715 AACAGGAATGGTGACAATGCCCTCAACAGAAACTGAGATGTTCAGAAAAA 971764 v v i iviv v i? v i iv i v viiiviii i C L2#LINE/L2 2540 AACTGGAAGGATGGAGTTGCCATTNACTGAGATGGGGAAGACTGCGGGAG 2491 chr5ptel1M 971765 GAGTGGGGTTTCGGGGAAAAGAT--GGTGT-CTGTTTGGGGCATGGT--G 971809 ii - vi ii -- v - v v i v -- C L2#LINE/L2 2490 GAGCAGG-TTTGAGGGGGAAGATCAGGAGTTCAGTTTTGGACATGTTAAG 2442 chr5ptel1M 971810 TTTGAGAAACCCAGGTTACAAGGATTTTGAAATCCCTAGTAGAGGGTTGG 971859 vi i vvvv vvv vv v i vi v ivi C L2#LINE/L2 2441 TTTGAGATGCCTATTAGACATCCAAGTGGAGATGTCGAGTAGGCAGTTGG 2392 chr5ptel1M 971860 ACATGTGAGACTAGACCTCAGGGAAGAGG-CTGGTCTGGAG------ATC 971902 i ii v i vi i - i v ------ i C L2#LINE/L2 2391 ATATACGAGTCTGGAGTTCAGGGGAGAGGTCCGGGCTGGAGATATAAATT 2342 chr5ptel1M 971903 TGGGAATCATTTGCATAGAGATG----------------GACTTGGTGAA 971936 i iv v ---------------- v i i C L2#LINE/L2 2341 TGGGAGTCATCAGCATATAGATGGTATTTAAAGCCATGAGACTGGATGAG 2292 chr5ptel1M 971937 GTCACCAAGAGAGAGTTAGTGGAGTTAGTTAGTGGAGA 971974 i --? i v v v -- vi C L2#LINE/L2 2291 ATCACC--NAGGGAGTGAGTGTAGATAG--AGAAGAGA 2258 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 48.84 CpG sites = 81, Kimura (unadjusted) = 50.91 Transitions / transversions = 1.35 (81/60) Gap_init rate = 0.03 (13 / 399), avg. gap size = 3.38 (44 / 13) 325 36.05 9.52 0.00 chr5ptel1M 972617 972763 (27237) MIR3#SINE/MIR 16 176 (32) m_b243s601i16 9628 chr5ptel1M 972617 AACAGGAATGAAACGGGCTGA---TTAAGAATCATCGGTTCAGACTTTTG 972663 i ii viiv i i--- i i iv v v viiiiiiv MIR3#SINE/MIR 16 AGCAGAGAGAGCACGGACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCGG 65 chr5ptel1M 972664 CTCACCCATTA-----CTGCATGACCTTGAATTGATCACA--GTTTCTCT 972706 vv i ----- ii iiivii v--iii MIR3#SINE/MIR 66 CTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCT 115 chr5ptel1M 972707 GGGCCTCAGTTCCCTCACCTGTAAAA----GGAGCTGCCCTGAGTAAGGT 972752 i i ---- i i vv iii i vv MIR3#SINE/MIR 116 GGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCT 165 chr5ptel1M 972753 CTGATGTGCCT 972763 i v v MIR3#SINE/MIR 166 CTAAGGTCCCT 176 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 51.55 CpG sites = 36, Kimura (unadjusted) = 53.08 Transitions / transversions = 2.12 (36/17) Gap_init rate = 0.03 (4 / 146), avg. gap size = 3.50 (14 / 4) 400 29.70 2.78 6.47 chr5ptel1M 972980 973123 (26877) C MIRc#SINE/MIR (76) 192 54 m_b243s601i17 9629 chr5ptel1M 972980 CTTCACACACCACCTT-CGAGGTAGTGAGTTCAAATGCTGCTGCCTCCAC 973028 i - v i -i vv vv ii ii ii ii i i C MIRc#SINE/MIR 192 CCTCACA-ACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCAT 144 chr5ptel1M 973029 TTTCTAGATGAGGGAGCTCAGTTTCAGAGAGGTAAAGGGGCTTGCCTGGA 973078 vi i i v vi v v i iiii C MIRc#SINE/MIR 143 TTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAG 94 chr5ptel1M 973079 GTCTCAGCTCATAAGCTAGTAAGT---AGAACCAAGATTTCAGAATCC 973123 v ------v --- i ii i i-- i C MIRc#SINE/MIR 93 GTCACA------CAGCTAGTAAGTGGCAGAGCCGGGACTC--GAACCC 54 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.31 CpG sites = 28, Kimura (unadjusted) = 39.92 Transitions / transversions = 2.33 (28/12) Gap_init rate = 0.08 (11 / 143), avg. gap size = 1.18 (13 / 11) 226 29.52 8.99 1.04 chr5ptel1M 973399 973487 (26513) C L3#LINE/CR1 (1) 4098 4003 m_b243s601i18 9630 chr5ptel1M 973399 ACAGAATCA--GAATTCCTGGGCCAGAAGGGACCTTGGAGCT------GT 973440 i -- ii v i iii i v ------ C L3#LINE/CR1 4098 ATAGAATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGT 4049 chr5ptel1M 973441 TGAACCATCCATACTTGGTTAAGATTTCCTTCCACAACTTGACTGAC 973487 iv vi v vvv -i i v i i v vv C L3#LINE/CR1 4048 CCAACCTCCCATCCAATG-CAGGAATCCCTTCTACAACATCCCTGAC 4003 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.27 CpG sites = 14, Kimura (unadjusted) = 38.27 Transitions / transversions = 1.17 (14/12) Gap_init rate = 0.03 (3 / 88), avg. gap size = 3.00 (9 / 3) 186 28.16 13.08 7.08 chr5ptel1M 973719 973825 (26175) C MIR3#SINE/MIR (13) 195 83 m_b243s601i19 9631 chr5ptel1M 973719 ATAGAGGGTCATTGAGAGGCAAAAGGAGTCCTGAAGCTC-TTTAGCCCAG 973767 iv ---- viii iii i ii v - i i i C MIR3#SINE/MIR 195 ATAGAATGTCA----GAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAA 150 chr5ptel1M 973768 -------ATT------AGGAGGAAATGGAGTCCTATAAAAGTTAGTTAAG 973804 ------- ------ v iv v i v i i v ---- C MIR3#SINE/MIR 149 CCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGA----AG 104 chr5ptel1M 973805 TGACTTGTCCAACATCACACA 973825 i vi C MIR3#SINE/MIR 103 TGACTTGCCCAAGGTCACACA 83 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.21 CpG sites = 19, Kimura (unadjusted) = 37.21 Transitions / transversions = 2.11 (19/9) Gap_init rate = 0.10 (11 / 106), avg. gap size = 2.00 (22 / 11) 195 20.71 0.00 12.96 chr5ptel1M 973765 973825 (26175) C MIRc#SINE/MIR (129) 139 86 m_b243s601i20 9631 chr5ptel1M 973765 CAGATTAGGAGGAAATGGAGTCCTATAAAAGTTAGTTAAGTGACTTGTCC 973814 --- iv v ii v i i ---- i C MIRc#SINE/MIR 139 CAGAT---GAGGAAACTGAGGCTCAGAGAGGTTA----AGTGACTTGCCC 97 chr5ptel1M 973815 AACATCACACA 973825 vi C MIRc#SINE/MIR 96 AAGGTCACACA 86 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 24.28 CpG sites = 7, Kimura (unadjusted) = 24.28 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.12 (7 / 60), avg. gap size = 1.00 (7 / 7) 38 0.00 0.00 0.00 chr5ptel1M 974504 974536 (25464) (TG)n#Simple_repeat 1 33 (0) c_b243s251i0 9632 chr5ptel1M 974504 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 974536 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 33 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 213 22.16 2.17 6.82 chr5ptel1M 974609 974700 (25300) C L2b_3end#LINE/L2 (41) 425 338 m_b243s601i21 9633 chr5ptel1M 974609 GCCAGACACTGTGCTAAGTG-GGGGGGGAAAGCGGGGACGGCGCAAAGGC 974657 i ? i i -v iv v v ----i - i C L2b_3end#LINE 425 GCCAGGCNCTGTGCTAGGCGCTGGGGATACAGCGGTGA----ACAA-GAC 381 chr5ptel1M 974658 AGAGCCAGTCC-TGCCCTCAGGAGGCTCACAGACAACATGGGAG 974700 v? i - v ii v v -i i C L2b_3end#LINE 380 AGACNCGGTCCCTGCCCTCACGGAGCTCACAGTCTA-GTGGGGG 338 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 24.15 CpG sites = 11, Kimura (unadjusted) = 27.37 Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.09 (8 / 91), avg. gap size = 1.00 (8 / 8) 224 28.59 1.39 2.82 chr5ptel1M 975316 975387 (24613) C MIR3#SINE/MIR (34) 174 104 m_b243s601i22 9634 chr5ptel1M 975316 GGTCCTTGGACTTCAAGTCCAGGATAATTTCC-CTTGTTCCAAATGGGGA 975364 v i vv -- i vvi iii - v v v i i C MIR3#SINE/MIR 174 GGACCTTAGAGATCA--TCTAGTCCAACCCCCTCATTTTACAGATGAGGA 127 chr5ptel1M 975365 AACTGAGGCCCTCAGAGATGAGG 975387 vv i i C MIR3#SINE/MIR 126 AACTGAGGCCCAGAGAGGTGAAG 104 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.39 CpG sites = 10, Kimura (unadjusted) = 36.39 Transitions / transversions = 1.00 (10/10) Gap_init rate = 0.04 (3 / 71), avg. gap size = 1.00 (3 / 3) 38 25.45 2.88 2.88 chr5ptel1M 975708 975846 (24154) (CTCTCC)n#Simple_repeat 1 139 (0) m_b243s252i4 9635 chr5ptel1M 975708 CTCTCCTTCATTCCTCTCCCTC-CCC-CTCCCTCTCTTTCTGCCTC-CCT 975754 i - i - - ii v - i (CTCTCC)n#Sim 1 CTCTCCCTC-TCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCC 49 chr5ptel1M 975755 TGTCCTCCTCTTCCTTTTACTTTCACTCTCTCT-TCTTTCCCCATCTGTC 975803 v - - i i iv i v i - ii i v vi (CTCTCC)n#Sim 50 TCT-C-CCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCC 97 chr5ptel1M 975804 TCTCCATCTCTCTGTCTCTCTGGGTCTCCTCCCTCCCTCTCCC 975846 v i v i vvv - i (CTCTCC)n#Sim 98 TCTCCCTCTCCCTCTCCCTCTCCCTCTCC-CTCTCCCTCTCCC 139 Matrix = Unknown Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.06 (8 / 138), avg. gap size = 1.00 (8 / 8) 17 35.62 2.08 5.00 chr5ptel1M 975710 975853 (24147) (CTCC)n#Simple_repeat 1 140 (0) m_b243s252i5 9635 chr5ptel1M 975710 CTCCTTCATTCCTCTCCCT-CC-CCCTCCCTCTCTTTCTGCCTCCCTTGT 975757 i vi - - - i ii v - -i (CTCC)n#Simpl 1 CTCCCTCCCTCC-CTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCC-T-C 47 chr5ptel1M 975758 CCTCCTCTTCCTTTTACTTTCACTCTCTCTTCTTTCCCCATCTGTCTCTC 975807 - i iiiv ii v i -i ii i v iv i (CTCC)n#Simpl 48 CCTCC-CTCCCTCCCTCCCTCCCTCCCTC-CCTCCCTCCCTCCCTCCCTC 95 chr5ptel1M 975808 CATCTCTCTGTCTCTCTGGGTCT-CCTCCCTCCCTCTCCCCACCTCC 975853 v i iv i ivvvi - - i - (CTCC)n#Simpl 96 CCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTC-CCTC-CCTCC 140 Matrix = Unknown Transitions / transversions = 2.27 (25/11) Gap_init rate = 0.07 (10 / 143), avg. gap size = 1.00 (10 / 10) 194 35.25 10.66 0.00 chr5ptel1M 976615 976736 (23264) C L2b_3end#LINE/L2 (87) 379 245 m_b243s601i25 9636 chr5ptel1M 976615 GACATAGGCTCTGCCCTCAAAGAACTTGTAGTCTAAAGGGAGAGAGTGAG 976664 ?ii v i vi i iii iv i vv v C L2b_3end#LINE 379 GACNCGGTCCCTGCCCTCACGGAGCTCACAGTCTAGTGGGGGAGACAGAC 330 chr5ptel1M 976665 AGATTTCCAGG----AATGACCCGGA----CAG---AGAACCGGGAGAAC 976703 vi vv? i----? i i ---- --- i i i ii C L2b_3end#LINE 329 ATGTAANCAGACAATNATAACCCAGAGTGGCAGGGTAGGACTGGGGGGGC 280 chr5ptel1M 976704 TAAAAGGCTTGTGACAGACTT--TCTGGATAGTCA 976736 iv i vvv i v v ii--i ivi C L2b_3end#LINE 279 CCAGAGGAGGGCGCCTGACCCGGCCTGGGGGGTCA 245 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.16 CpG sites = 27, Kimura (unadjusted) = 52.20 Transitions / transversions = 1.69 (27/16) Gap_init rate = 0.03 (4 / 121), avg. gap size = 3.25 (13 / 4) 207 33.82 0.00 3.90 chr5ptel1M 976615 976694 (23306) C L2d_3end#LINE/L2 (89) 427 351 m_b243s601i24 9636 chr5ptel1M 976615 GACATAGGCTCTGCCCTCAAAGAACTTGTAGTCTAAAGGGAGAGAGTGAG 976664 i v i i i ii i ivv i ---vi C L2d_3end#LINE 427 GACATGGTCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGGAGA---CA 381 chr5ptel1M 976665 AGATTTCCAGGAATGACCCGGACAGAGAAC 976694 i vv viv vv iivi C L2d_3end#LINE 380 AGACTAACACACATGAAACAATTAGAGAAC 351 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.43 CpG sites = 15, Kimura (unadjusted) = 46.43 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.04 (3 / 79), avg. gap size = 1.00 (3 / 3) 216 26.67 0.00 0.00 chr5ptel1M 976615 976659 (23341) C L2d2_3end#LINE/L2 (86) 469 425 m_b243s601i23 9636 chr5ptel1M 976615 GACATAGGCTCTGCCCTCAAAGAACTTGTAGTCTAAAGGGAGAGA 976659 i v i i i ii i ivv i C L2d2_3end#LIN 469 GACATGGTCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGGAGA 425 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.01 CpG sites = 9, Kimura (unadjusted) = 35.01 Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 222 28.30 0.00 0.00 chr5ptel1M 977261 977313 (22687) L2c_3end#LINE/L2 414 466 (12) m_b243s601i26 9637 chr5ptel1M 977261 ATCTTTTTATCCTCAGCACCTGGTGTGAGGTGGATGCTGACTAAATGTTT 977310 v i i iiiivi i ii v v L2c_3end#LINE 414 ATCTTTGTATCCCCAGCGCCTGGCACATAGTAGGCGCTCAATAAATGTTT 463 chr5ptel1M 977311 ATT 977313 i L2c_3end#LINE 464 GTT 466 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.56 CpG sites = 11, Kimura (unadjusted) = 37.81 Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 228 34.63 7.63 5.22 chr5ptel1M 977303 977433 (22567) C L2d2_3end#LINE/L2 (15) 540 407 m_b243s601i27 9638 chr5ptel1M 977303 AAATGTTTATTATTAAGCAGGGACTGTGCACAGGGTCCTATA------AC 977346 i i--- ivvv ii i iv i i------i C L2d2_3end#LIN 540 AAATATTTATTG---AGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGC 494 chr5ptel1M 977347 CTTGACAGATACAAGATAGTGAAAG-CACGAGCTCTCCCCTCAGGGTGAT 977395 iv ivi iiv iv - i iv i v i v v C L2d2_3end#LIN 493 TGTGGGGGATACAAAGAAGTATAAGACATGGTCCCTGCCCTCAAGGAGCT 444 chr5ptel1M 977396 TGCGGCCCAGT---GAGGACAAGAATACCCCAAACCTGTGA 977433 i iii i --- ii ---- vi vi C L2d2_3end#LIN 443 TACAATCTAGTTGGGGAGACAAGA----CATAAACACGTGA 407 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.91 CpG sites = 29, Kimura (unadjusted) = 49.85 Transitions / transversions = 2.07 (29/14) Gap_init rate = 0.08 (10 / 130), avg. gap size = 1.70 (17 / 10) 251 31.88 1.45 0.00 chr5ptel1M 977879 977947 (22053) C MIR3#SINE/MIR (3) 205 136 m_b243s601i28 9639 chr5ptel1M 977879 TCATAGGATCATCGGGT-TTGGGGCTGGAAAGAGTGTTAAAGATCATTCG 977927 i v ii - ii i i iiiv i iii C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTA 156 chr5ptel1M 977928 ATCCTCCGCCCTAATTTTGC 977947 i vv v v i C MIR3#SINE/MIR 155 GTCCAACCCCCTCATTTTAC 136 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.78 CpG sites = 16, Kimura (unadjusted) = 44.78 Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.01 (1 / 68), avg. gap size = 1.00 (1 / 1) 214 34.58 17.68 0.95 chr5ptel1M 978640 978820 (21180) MIRc#SINE/MIR 18 228 (40) m_b243s601i29 9640 chr5ptel1M 978640 GTGAAAAGGAGAAACAGAACCGGGACCAGGAG---CTGGGTTCAAATCCG 978686 i - v vii vii iii i--- i i v MIRc#SINE/MIR 18 GTGGAAAG-AGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCC 66 chr5ptel1M 978687 GACT-----------TGGCT-------CTTGGGCGAACTGCTTGAAGCTT 978718 i ----------- i ------- i iiii i vvii MIRc#SINE/MIR 67 GGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCT 116 chr5ptel1M 978719 CTGAG--TTAGTGTCCTTTTTTTTCTCTCTGGGGACAGTAGGAAAACCCC 978766 -- i v iv i v vvv-v i i iv vvvv MIRc#SINE/MIR 117 CTGAGCCTCAGTTTCCTCATCTGTAAA-ATGGGGATAATAATACCTGCCC 165 chr5ptel1M 978767 TCTTTA-------GGATTCTGGTCAGACTCAAAGGAGATAA--TATATTA 978807 vii ------- i v v v iv v -- i v MIRc#SINE/MIR 166 TGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGA 215 chr5ptel1M 978808 ACACACCTTGTGA 978820 vi i i i MIRc#SINE/MIR 216 AAGCGCTTTGTAA 228 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.05 CpG sites = 36, Kimura (unadjusted) = 48.23 Transitions / transversions = 1.38 (36/26) Gap_init rate = 0.04 (8 / 180), avg. gap size = 4.25 (34 / 8) 226 32.07 14.97 2.42 chr5ptel1M 978669 978815 (21185) MIRb#SINE/MIR 52 216 (52) m_b243s601i30 9640 chr5ptel1M 978669 GAGCTGGGTTCAAATCCGGACT-----------TGGCT-------CTTGG 978700 v i v i ----------- i ------- MIRb#SINE/MIR 52 GACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 101 chr5ptel1M 978701 GCGAACTGCTTGAAGCTTCTGAG--TTAGTGTCCTTTTTTTTCTCTCTGG 978748 i ii i i vvii -- i v iv i v vvv-v MIRb#SINE/MIR 102 GCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAA-ATGG 150 chr5ptel1M 978749 GGACAGTAGGAAAACCCCTCTT-TAGGATTCTGGTCAGACTCAAAGGAGA 978797 i i --- v ivi i-i i v v v iv i v MIRb#SINE/MIR 151 GGATAATA---ATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGA 197 chr5ptel1M 978798 TAATATAT-TAACACACCT 978815 ii - vi i i MIRb#SINE/MIR 198 TAATGCATGTAAAGCGCTT 216 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.72 CpG sites = 27, Kimura (unadjusted) = 43.44 Transitions / transversions = 1.42 (27/19) Gap_init rate = 0.06 (9 / 146), avg. gap size = 2.89 (26 / 9) 53 25.02 1.88 2.52 chr5ptel1M 979807 979966 (20034) (CCTC)n#Simple_repeat 1 159 (0) m_b243s252i6 9641 chr5ptel1M 979807 CCTCCCCCTCT-TCTCTCCTCTTTCCCTCCCT-CC-CCCTCCTTCCCCTC 979853 i i -i - ii - - i - (CCTC)n#Simpl 1 CCTCCCTCCCTCCCTC-CCTCCCTCCCTCCCTCCCTCCCTCCCT-CCCTC 48 chr5ptel1M 979854 TTCTTTCTTCCTCCCTCCCTCCCTCTCTCCCTCCCTTCCTCTCTCACTCT 979903 -i ii i i i i v i (CCTC)n#Simpl 49 -CCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCC 97 chr5ptel1M 979904 TTCTCCTCTGTCTCTGTCTCTCTCTCTCCTTCCACCCCTCCCTCCTTCCC 979953 i - iv i vi i i i vi i (CCTC)n#Simpl 98 CTC-CCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCC 146 chr5ptel1M 979954 TTTCTCTCTCACT 979966 ii i v (CCTC)n#Simpl 147 TCCCTCCCTCCCT 159 Matrix = Unknown Transitions / transversions = 5.20 (26/5) Gap_init rate = 0.04 (7 / 159), avg. gap size = 1.00 (7 / 7) 216 31.45 2.74 4.17 chr5ptel1M 980374 980446 (19554) MIRb#SINE/MIR 99 170 (98) m_b243s601i32 9642 chr5ptel1M 980374 TGGGCAGACCGCTC--CCGCCCAGAACCTCAGTTTTCTTATTTGCTAAAT 980421 iiiii i-- v i v i i i i iv MIRb#SINE/MIR 99 TGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAAT 148 chr5ptel1M 980422 GGGGGCCCTAGCAGTTCCTCTCTCG 980446 i--- ii i v vi MIRb#SINE/MIR 149 GGGGA---TAATAATACCTACCTCG 170 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.58 CpG sites = 17, Kimura (unadjusted) = 44.58 Transitions / transversions = 3.40 (17/5) Gap_init rate = 0.06 (4 / 72), avg. gap size = 1.25 (5 / 4) 219 26.92 3.85 0.00 chr5ptel1M 980374 980425 (19575) MIRc#SINE/MIR 96 149 (119) m_b243s601i31 9642 chr5ptel1M 980374 TGGGCAGACCGCTC--CCGCCCAGAACCTCAGTTTTCTTATTTGCTAAAT 980421 iii i i-- v i v i i i i iv MIRc#SINE/MIR 96 TGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAAT 145 chr5ptel1M 980422 GGGG 980425 MIRc#SINE/MIR 146 GGGG 149 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.84 CpG sites = 11, Kimura (unadjusted) = 35.84 Transitions / transversions = 3.67 (11/3) Gap_init rate = 0.02 (1 / 51), avg. gap size = 2.00 (2 / 1) 189 27.50 0.00 0.00 chr5ptel1M 980844 980883 (19117) MIRc#SINE/MIR 114 153 (115) m_b243s601i33 9643 chr5ptel1M 980844 TCCCTGAGCCTTAATGACTCTGTCTGTAAAATGGGAAGAA 980883 i i i vv iiii i v MIRc#SINE/MIR 114 TCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAA 153 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.28 CpG sites = 8, Kimura (unadjusted) = 36.28 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 185 29.23 1.52 1.52 chr5ptel1M 983524 983589 (16411) C MIRc#SINE/MIR (17) 251 186 m_b243s601i34 9644 chr5ptel1M 983524 ACATTTGTTTACCTGCAGGGCACTGTGCTAAGTGCTTT-ACAGATGTTAT 983572 v v -i vvvi v v i v i - v ii C MIRc#SINE/MIR 251 ACATTTGTATAGC-ACTTTACAGTTTACAAAGCGCTTTCACATACATTAT 203 chr5ptel1M 983573 CTCATTTGAGCCTTGTA 983589 v iii C MIRc#SINE/MIR 202 CTCATTTGATCCTCACA 186 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.99 CpG sites = 9, Kimura (unadjusted) = 37.37 Transitions / transversions = 0.90 (9/10) Gap_init rate = 0.03 (2 / 65), avg. gap size = 1.00 (2 / 2) 280 24.56 0.00 0.00 chr5ptel1M 983533 983589 (16411) C MIRb#SINE/MIR (32) 236 180 m_b243s601i35 9644 chr5ptel1M 983533 TACCTGCAGGGCACTGTGCTAAGTGCTTTACAGATGTTATCTCATTTGAG 983582 iv vi i viii i v C MIRb#SINE/MIR 236 TATGTGCCAGGCACTGTGCTAAGCGCTTTACATGCATTATCTCATTTAAT 187 chr5ptel1M 983583 CCTTGTA 983589 iii C MIRb#SINE/MIR 186 CCTCACA 180 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.45 CpG sites = 10, Kimura (unadjusted) = 31.11 Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0) 275 31.50 14.57 1.17 chr5ptel1M 983705 983855 (16145) MIRc#SINE/MIR 98 268 (0) m_b243s601i36 9645 chr5ptel1M 983705 GACAAGCCA--TGATCTCTCGAGAGCCTCCATTGCCTCATCTCTCCAATG 983752 i i -- i i v- vi v v vv MIRc#SINE/MIR 98 GGCAAGTCACTTAACCTCTCT-GAGCCTCAGTTTCCTCATCTGTAAAATG 146 chr5ptel1M 983753 GGCGTCAT---------TCTG-----------GGCTGGCAGTGAGGATCA 983782 vi v ---------i ----------- v v iv MIRc#SINE/MIR 147 GGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCA 196 chr5ptel1M 983783 GGGGAGAAAATAGGGGTATAAAGTCCTTTGTGAGCCCTGACATCACGTGC 983832 iiv v iviv i- iv i i iv i vi vvii i MIRc#SINE/MIR 197 AATGAGATAATGTATGTG-AAAGCGCTTTGTAAACTGTAAAGTGCTATAC 245 chr5ptel1M 983833 AAAAGTCACCCGTTATTCTTATT 983855 v v vv? v MIRc#SINE/MIR 246 AAATGTAAGGNGTTATTATTATT 268 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.57 CpG sites = 22, Kimura (unadjusted) = 41.69 Transitions / transversions = 0.88 (22/25) Gap_init rate = 0.03 (5 / 150), avg. gap size = 4.80 (24 / 5) 268 16.33 0.00 0.00 chr5ptel1M 983954 984002 (15998) C MIR3#SINE/MIR (41) 167 119 m_b243s601i37 9646 chr5ptel1M 983954 AGCGGCCACCTAGTCCAAGCCCCTCATGATACAGATGAGCAAACTGAGG 984002 v ii i v vv v C MIR3#SINE/MIR 167 AGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGG 119 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 18.42 CpG sites = 3, Kimura (unadjusted) = 18.42 Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 468 32.76 4.35 3.78 chr5ptel1M 984097 984280 (15720) MIRb#SINE/MIR 74 258 (10) m_b243s601i39 9647 chr5ptel1M 984097 CTGCTACCTGCCAGGTGGGTGAC--TGGACAAGTCATTTCCTCTCTTCCA 984144 i i i i v v -- i i i vvi iiv MIRb#SINE/MIR 74 CTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGA 123 chr5ptel1M 984145 GCCTCAGTCTTCTTATCTGTAAAACAGGGGCCTGCAATGCAGACCTCATG 984194 i i i i- vivii i vv iii MIRb#SINE/MIR 124 GCCTCAGTTTCCTCATCTGTAAAAT-GGGGATAATAATACCTACCTCGCA 172 chr5ptel1M 984195 GGATGGTCATGGAGATCAAGTGAGAT--TGAGTG---AGTACTTTTTAAA 984239 i v ii ii i i -- vi --- ii ---- i MIRb#SINE/MIR 173 GGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTT----AG 218 chr5ptel1M 984240 CCTCATGCCGCCGATAGA-AGGAAATGCTTCCTAACTGGTAG 984280 vivi -- i ii v - v ii ivv v MIRb#SINE/MIR 219 CACAGTGC--CTGGCACATAGTAAGCGCTCAATAAATGGTAG 258 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.60 CpG sites = 40, Kimura (unadjusted) = 46.02 Transitions / transversions = 2.22 (40/18) Gap_init rate = 0.06 (11 / 183), avg. gap size = 1.36 (15 / 11) 507 27.08 11.11 0.00 chr5ptel1M 984097 984240 (15760) MIRc#SINE/MIR 71 230 (38) m_b243s601i38 9647 chr5ptel1M 984097 CTGCTACCTGCCAGGTGGGTGAC--TGGACAAGTCATTTCCTCTCTTCCA 984144 i i i i v v -- i i vvi iiv MIRc#SINE/MIR 71 CTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGA 120 chr5ptel1M 984145 GCCTCAGTCTTCTTATCTGTAAAACAGGG--------GCCTGCAATGCAG 984186 i i i ii --------i vv vv MIRc#SINE/MIR 121 GCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCT 170 chr5ptel1M 984187 ACCTCATGGGATGGTCATGGAGATCAAGTGAGAT------TGAGTGAGTA 984230 ii i v ii ii i ------ v vi ii MIRc#SINE/MIR 171 ACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCG 220 chr5ptel1M 984231 CTTTTTAAAC 984240 v MIRc#SINE/MIR 221 CTTTGTAAAC 230 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.75 CpG sites = 26, Kimura (unadjusted) = 35.00 Transitions / transversions = 2.00 (26/13) Gap_init rate = 0.02 (3 / 143), avg. gap size = 5.33 (16 / 3) 233 32.60 7.89 3.14 chr5ptel1M 984748 984899 (15101) C MIR1_Amn#SINE/MIR (44) 186 28 m_b243s601i40 9644 chr5ptel1M 984748 TCAGAGGGCTCTGCCAGGGGGTTCTGCAGC--TACCCCTCAGGTTTCATG 984795 i vi i i v i i v v i v -- i - -- i ii C MIR1_Amn#SINE 186 TCAAAGCACTTTACAAAGGAGGTCAGTATCATTATCCC-CA--TTTTACA 140 chr5ptel1M 984796 GTGCTGGAGACATTTGGGCTCATAGGGG--AAGGTACTTTCCCAAGGTCA 984843 --v ii v i vi ? v i -- vv v C MIR1_Amn#SINE 139 G--ATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGCCCAAGGTCA 92 chr5ptel1M 984844 AATAGT--GTAAGTGTTCCAGCAAGGAATTGAA------TTTTTTGACTT 984885 v?i i-- i? vivv vi ? ? ------ i iii v i C MIR1_Amn#SINE 91 CNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAACCCAGGTCTCCCGAGTC 42 chr5ptel1M 984886 CCAATCCGGAGTTC 984899 i i v i C MIR1_Amn#SINE 41 CCAGTCCAGTGCTC 28 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.16 CpG sites = 29, Kimura (unadjusted) = 46.86 Transitions / transversions = 1.53 (29/19) Gap_init rate = 0.06 (9 / 151), avg. gap size = 1.89 (17 / 9) 234 29.95 8.77 3.33 chr5ptel1M 984780 984893 (15107) C MIR3#SINE/MIR (60) 148 29 m_b243s601i41 9644 chr5ptel1M 984780 CCCCTCAGGTTTCATGGTGCTGGAGACATTTGGGCTCATAGGGG--AAGG 984827 -- i ii --v ii v i vi i v i -- v C MIR3#SINE/MIR 148 CCCCTCA--TTTTACAG--ATGAGGAAACTGAGGCCCAGAGAGGTGAAGT 103 chr5ptel1M 984828 TACTTTCCCAAGGTCAAATAGT--GTAAGTGTTCCAGCAAGGAATTGAA- 984874 v v v i i-- v vivv vi v v - C MIR3#SINE/MIR 102 GACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAAC 53 chr5ptel1M 984875 -----TTTTTTGACTTCCAATCCG 984893 ----- i ii i i C MIR3#SINE/MIR 52 CCAGGTCTCCTGACTCCCAGTCCG 29 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.61 CpG sites = 18, Kimura (unadjusted) = 39.11 Transitions / transversions = 1.20 (18/15) Gap_init rate = 0.07 (8 / 113), avg. gap size = 1.75 (14 / 8) 239 31.37 10.78 0.00 chr5ptel1M 984800 984901 (15099) C MIRc#SINE/MIR (133) 135 23 m_b243s601i42 9644 chr5ptel1M 984800 TGGAGACATTTGGGCTCATAGGGG--AAGGTACTTTCCCAAGGTCAAATA 984847 ii v i vi v i -- vv v v i C MIRc#SINE/MIR 135 TGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACA 86 chr5ptel1M 984848 GT--GTAAGTGTTCCAGCAAGGAATTGAA-------TTTTTTGACTTCCA 984888 i-- vivv vi v i -------i ii i v C MIRc#SINE/MIR 85 GCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAA 36 chr5ptel1M 984889 ATCCGGAGTTCCT 984901 i i v i i C MIRc#SINE/MIR 35 GTCCAGTGCTCTT 23 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.36 CpG sites = 18, Kimura (unadjusted) = 41.71 Transitions / transversions = 1.29 (18/14) Gap_init rate = 0.03 (3 / 101), avg. gap size = 3.67 (11 / 3) 21 14.25 5.17 3.39 chr5ptel1M 985465 985522 (14478) (AGG)n#Simple_repeat 1 59 (0) m_b243s252i7 9648 chr5ptel1M 985465 AGGAGAGAGGCCG-GGAGAAAAAGGCAGGAGG-GGAGGCGGAGGAGAAGG 985512 - vv - i ii - - v i (AGG)n#Simple 1 AGGAG-GAGGAGGAGGAGGAGGAGG-AGGAGGAGGAGGAGGAGGAGGAGG 48 chr5ptel1M 985513 -GGAGGAGGAG 985522 - (AGG)n#Simple 49 AGGAGGAGGAG 59 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.09 (5 / 57), avg. gap size = 1.00 (5 / 5) 413 34.58 6.02 1.08 chr5ptel1M 985527 985792 (14208) L3#LINE/CR1 2156 2434 (1665) m_b243s601i43 9649 chr5ptel1M 985527 AGGTTTTAAACGGACAG--ACTGGAGAGCAGGAATCCAGCCCAGAAGCAA 985574 i v v-- iii iiiii i vvvii vi v v L3#LINE/CR1 2156 AGATTTTAAAAGGACATGTATCAGAAGATGGAAAGAGGACATATAACCAA 2205 chr5ptel1M 985575 GGGCGATGGG-GAGGAGCGTCCACCTGGGAGAACGGGGTCAGGGAGGG-- 985621 i i v i - v ? iivvi vi ii v i v-- L3#LINE/CR1 2206 GGACAAAGAGAGAGTANCACAAGCCTGTAAGAATAGTGTCAGGAAGGCTA 2255 chr5ptel1M 985622 ----CCAGGATGAGATCAG--CTGCTGAGGGA---GCCATGGTCAA-AAC 985661 ---- i v v --i vi iii --- i v v - v L3#LINE/CR1 2256 AAGCCCAGAATGAGCTGAGGCTTGCAAAAAAAAATGCTAAGGACAACAAA 2305 chr5ptel1M 985662 CAGAAGCTTTTTCCTCCCAAGAGTTTAGAGCAAGGATGAGAAGGAGAGCT 985711 v ? vi vvvv v v- ii - i v i i i ?v L3#LINE/CR1 2306 AANAAGGCTTTTCAAAGCTAT-GTTCGGAGCA-GAAGGAAAAAGAAAGNG 2353 chr5ptel1M 985712 CCTG-CCCATGGCTTGGGGGCAGATGGTGTCATGTTAAGGGATGAAAGGG 985760 v v - iiv - i v vi v i L3#LINE/CR1 2354 ACAGGCCCGCTGCTTGGGG-CAGATGGCGTAATGTTAACAGATGACAGAG 2402 chr5ptel1M 985761 GCAGAGGAGAGTGACTCAGCCCCTGTGTTGTT 985792 iv i v iiv i i i v i L3#LINE/CR1 2403 AGAAAGCAGAACTACTCAACTCCTATTTTGCT 2434 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.25 CpG sites = 50, Kimura (unadjusted) = 48.55 Transitions / transversions = 1.22 (50/41) Gap_init rate = 0.04 (11 / 265), avg. gap size = 1.73 (19 / 11) 187 33.58 11.54 2.65 chr5ptel1M 985903 986006 (13994) C MIR#SINE/MIR (122) 140 28 m_b243s601i44 9650 chr5ptel1M 985903 TTCTCTAGA--AGCAGATGGGGATACAGAGGGGGGAAACGGCTTATCCAA 985950 i vi -- v i iv i ii i vv iiii ii C MIR#SINE/MIR 140 TTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCCAA 91 chr5ptel1M 985951 GGTCACACG----------GGCAGCCCCCAAGTGTTCAGATCCAGCTGAG 985990 i---------- vv --i vi ii i vi- C MIR#SINE/MIR 90 GGTCACACAGCTAGTAAGTGGCAGAGCC--GGGATTCGAACCCAGGC-AG 44 chr5ptel1M 985991 CCAGGTGCCAGAGCCC 986006 i v iv C MIR#SINE/MIR 43 TCTGGCTCCAGAGCCC 28 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.76 CpG sites = 23, Kimura (unadjusted) = 47.69 Transitions / transversions = 2.09 (23/11) Gap_init rate = 0.05 (5 / 103), avg. gap size = 3.00 (15 / 5) 200 32.56 11.28 2.36 chr5ptel1M 986020 986214 (13786) L3#LINE/CR1 2581 2792 (1307) m_b243s601i45 9649 chr5ptel1M 986020 CAAGTTCCACGCCAGGGACCCTGACAGACCGTGCAGCTGGCAGTGGGGAA 986069 i i v iv -iv v v v v vv vi v L3#LINE/CR1 2581 CGAATTACATCCCAGGG-TACTGAAAGAACTTGCAGATGTGATCGCGGAA 2629 chr5ptel1M 986070 CCCCAG-CATGAGTCTCGGAGGAATCACACCAAGCACCGGGGATGGGC-- 986116 v v - ivv i iv i i--i v v ii v v -- L3#LINE/CR1 2630 CCGCTGTCGGTAATCTTTGAGAAATCACG--GAGAACGGAAGAGGTGCCA 2677 chr5ptel1M 986117 --AGACAGG-GACGGCCTGATGTC-----------CAAAAAGGG--GAAG 986150 -- v - v vi ?-----------i --i i L3#LINE/CR1 2678 GAAGACTGGAGACGGGCAAATGTNGTNCCTANTTTTAAAAAGGGAAAAAA 2727 chr5ptel1M 986151 GTCAGTTGCTGGTAACGGAAGGGCTCAGCCAGCTTGA-GTCA--CTCTGG 986197 vii v v ?v viv i--i i iv - i-- i i L3#LINE/CR1 2728 GATGGATTCTGNAAACTACAGA--CCGGTAAGCTTGACGTCGATCCCCGG 2775 chr5ptel1M 986198 CCAAATGCTGGGATGGA 986214 v v i i i L3#LINE/CR1 2776 CAAAATTCTAGAACGGA 2792 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.02 CpG sites = 30, Kimura (unadjusted) = 44.01 Transitions / transversions = 0.94 (30/32) Gap_init rate = 0.07 (13 / 194), avg. gap size = 2.08 (27 / 13) 302 30.00 3.33 0.00 chr5ptel1M 987584 987673 (12327) MIR3#SINE/MIR 112 204 (4) m_b243s601i46 9651 chr5ptel1M 987584 CTTTGGGCCTCAATTTCCCCTGCTGTAAATTAAAGTGGCTACACTAAAGT 987633 i i i vv v i i v i iv i vv MIR3#SINE/MIR 112 CTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATG 161 chr5ptel1M 987634 GCCTCTGAGCTGCCTTTCAGCAC---CCGTCTGTGATCCTGTG 987673 ii i v v i v --- vv i i i MIR3#SINE/MIR 162 ATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTATG 204 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.18 CpG sites = 15, Kimura (unadjusted) = 39.18 Transitions / transversions = 1.25 (15/12) Gap_init rate = 0.01 (1 / 89), avg. gap size = 3.00 (3 / 1) 191 12.12 0.00 0.00 chr5ptel1M 987937 987969 (12031) C MIR3#SINE/MIR (72) 136 104 m_b243s601i47 9652 chr5ptel1M 987937 CAGATGAGGAAACCGAGGCTCAGGGAGCTGAAG 987969 i i i v C MIR3#SINE/MIR 136 CAGATGAGGAAACTGAGGCCCAGAGAGGTGAAG 104 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 13.48 CpG sites = 3, Kimura (unadjusted) = 13.48 Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 186 16.28 2.33 0.00 chr5ptel1M 991514 991556 (8444) MIR3#SINE/MIR 165 208 (0) m_b243s601i48 9653 chr5ptel1M 991514 TCTAAGCTCCCTCCCAGCTCTGACATCCCCTG-TTCTATGTTCC 991556 v i i iv - v i MIR3#SINE/MIR 165 TCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTATGATTC 208 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 18.53 CpG sites = 4, Kimura (unadjusted) = 18.53 Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.02 (1 / 42), avg. gap size = 1.00 (1 / 1) 382 27.71 12.50 0.75 chr5ptel1M 992325 992444 (7556) C MIRc#SINE/MIR (120) 148 15 m_b243s601i49 9654 chr5ptel1M 992325 CTCATTTTACAGATGGGGAAACTGAGGC-----------AAGTCACTTTG 992363 i i ----------- v - C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGAC-TTG 100 chr5ptel1M 992364 CCTAGAATCCCACAAGTAGGAAGTATCTGAGACCAG----GAAGATGAGT 992409 i iii v iv v iv v v vi ---- vviii C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGT 50 chr5ptel1M 992410 CCTCTCGATTCTAGACCCAGCGTTCTGTCCACTGC 992444 i ii i i iii i i v C MIRc#SINE/MIR 49 CTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGC 15 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.12 CpG sites = 22, Kimura (unadjusted) = 36.12 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.03 (3 / 119), avg. gap size = 5.33 (16 / 3) 217 13.89 0.00 0.00 chr5ptel1M 992469 992504 (7496) C MIR1_Amn#SINE/MIR (81) 149 114 m_b243s601i50 9655 chr5ptel1M 992469 CCTTCTTACAGTTGGAGAAACTGAGGCCCAGAGAGG 992504 v i v ii ? C MIR1_Amn#SINE 149 CCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGG 114 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 16.01 CpG sites = 3, Kimura (unadjusted) = 16.01 Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 213 10.81 2.70 0.00 chr5ptel1M 992472 992508 (7492) C MIR3#SINE/MIR (67) 141 104 m_b243s601i51 9656 chr5ptel1M 992472 TCTTACAGTTGGAGAAACTGAGGCCCAGAGAGG-GAAG 992508 i v ii - C MIR3#SINE/MIR 141 TTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAG 104 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 11.88 CpG sites = 3, Kimura (unadjusted) = 11.88 Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 198 24.39 0.00 0.00 chr5ptel1M 992593 992633 (7367) C L2#LINE/L2 (222) 2860 2820 m_b243s601i52 9657 chr5ptel1M 992593 GGGAGCCACTGAAGACTTTTGAGCAGGGCAGTGATGTGGTC 992633 i i i iv i v ii i C L2#LINE/L2 2860 GGAAGCCATTGGAGGGTTTTGAGCAGAGGAGTGACATGATC 2820 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.47 CpG sites = 8, Kimura (unadjusted) = 31.47 Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 14 22.04 3.08 6.35 chr5ptel1M 993295 993359 (6641) (AGGG)n#Simple_repeat 1 63 (0) m_b243s252i8 9658 chr5ptel1M 993295 AGGTGAAGGA-GGAGCTGA-GGATGGGGGGCCGGAGTGAGGGCAGGAGGC 993342 - i - -v - v i vv v vi v (AGGG)n#Simpl 1 AGG-GAGGGAGGGAG-GGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGG 48 chr5ptel1M 993343 AGAGGAGTGGAGGCAGG 993359 - - v (AGGG)n#Simpl 49 AG-GGAG-GGAGGGAGG 63 Matrix = Unknown Transitions / transversions = 0.38 (3/8) Gap_init rate = 0.09 (6 / 64), avg. gap size = 1.00 (6 / 6) 436 33.33 5.56 0.00 chr5ptel1M 993429 993554 (6446) L3#LINE/CR1 3893 4025 (74) m_b243s601i53 9659 chr5ptel1M 993429 AAAAGAAACTTCTTGGTGCTTTCAGCTGCCCAGA-------TGAACTCCT 993471 ii ii ii iiiiv ivv i i ------- ii v i L3#LINE/CR1 3893 AGGAAGAACTTTCTAACAATCAGAGCTGTCCAAAAATGGAATGGGCTGCC 3942 chr5ptel1M 993472 TCATGAGGTAGTGAGTTTCTCGTTCCCGAAGGTCTTCAAACAGAGAACAG 993521 i? i i i iv i i v i ivii L3#LINE/CR1 3943 TCGNGAGGTAGTGAGCTCCCCGTCACTGGAGGTGTTCAAGCAGAGGCTGG 3992 chr5ptel1M 993522 GGGACCGCTTATCAAGGCTCTTGTAAAAGGGAT 993554 iv i i i v v i L3#LINE/CR1 3993 ATGACCACTTGTCAGGGATGTTGTAGAAGGGAT 4025 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 47.45 CpG sites = 32, Kimura (unadjusted) = 49.18 Transitions / transversions = 3.20 (32/10) Gap_init rate = 0.01 (1 / 125), avg. gap size = 7.00 (7 / 1) 244 20.69 1.72 0.00 chr5ptel1M 993557 993614 (6386) CR1-3_Croc#LINE/CR1 3547 3605 (0) m_b243s551i1 9660 chr5ptel1M 993557 GGGTTGGTCTAAGTGACCT-TGGAGGTCACTTCCAGCTCCAGCTTTCTCT 993605 v ii - v i i vi i v CR1-3_Croc#LI 3547 GGGTTGGACTAGATGACCTCTGGAGGTCCCTTCCAGCCCTACTTCTCTAT 3596 chr5ptel1M 993606 GAGGCTATG 993614 vv CR1-3_Croc#LI 3597 GATTCTATG 3605 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 24.37 CpG sites = 6, Kimura (unadjusted) = 24.37 Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.02 (1 / 57), avg. gap size = 1.00 (1 / 1) 420 29.53 8.52 3.80 chr5ptel1M 993955 994130 (5870) MIRc#SINE/MIR 11 194 (74) m_b243s601i54 9661 chr5ptel1M 993955 TAATACAGTTGGGAAAGT-TGGGGCTTGGGGTCAG--AGACTTAAGTCCA 994001 ii i v ii i i-iv i i -- i ii i i MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr5ptel1M 994002 AGTCCCATCACCAGCAAGTCCTAGC-ATGCGAGTTTGAGCTAGTCTCT-- 994048 iv v iiv vv v -i i vi i v v -- MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTA 110 chr5ptel1M 994049 -CCTTTCTAGG--------GCCTCCTCTGTAAAATGGGGAGAATAAAACA 994089 - i ii --------v v v ---- MIRc#SINE/MIR 111 ACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAA---- 156 chr5ptel1M 994090 GCTACATACTGAGCCCTCCCCAAAGGGGCTCTTGTGAGGAT 994130 -- v i ivv iv i v - i v MIRc#SINE/MIR 157 --TACCTGCCCTGCCTACCTCACA-GGGTTGTTGTGAGGAT 194 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.83 CpG sites = 30, Kimura (unadjusted) = 38.82 Transitions / transversions = 1.50 (30/20) Gap_init rate = 0.07 (13 / 175), avg. gap size = 1.69 (22 / 13) 15 26.71 4.08 0.00 chr5ptel1M 994286 994334 (5666) (TC)n#Simple_repeat 1 51 (0) m_b243s252i9 9662 chr5ptel1M 994286 TCTCTCCCTGTGTCTAATTGTGTCTCTGTCTCTCTCCCT-TCT-TGTCTC 994333 i v v vvi v v v i - - v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr5ptel1M 994334 T 994334 (TC)n#Simple_ 51 T 51 Matrix = Unknown Transitions / transversions = 0.38 (3/8) Gap_init rate = 0.04 (2 / 48), avg. gap size = 1.00 (2 / 2) 233 26.09 8.70 0.00 chr5ptel1M 995617 995685 (4315) MIRb#SINE/MIR 54 128 (140) m_b243s601i55 9663 chr5ptel1M 995617 CCTTGATTCGAATCCCATTTCCGTCACTTATCA------TGACCCTGGCC 995660 v i ivi i i ii ------ i v MIRb#SINE/MIR 54 CCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGC 103 chr5ptel1M 995661 AAGTGACCTGCCATCTCAGAGCCCC 995685 v i iv v v i MIRb#SINE/MIR 104 AAGTTACTTAACCTCTCTGAGCCTC 128 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.73 CpG sites = 11, Kimura (unadjusted) = 32.93 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.01 (1 / 68), avg. gap size = 6.00 (6 / 1) 374 32.73 11.63 0.52 chr5ptel1M 995716 995887 (4113) MIRb#SINE/MIR 1 191 (77) m_b243s601i56 9664 chr5ptel1M 995716 CAGAGGTG----GTGGCCCAGTGAGTAGAGTGCTAGACTTGGAGTCGGGG 995761 v ---- iv iiv ii vi vi i iv MIRb#SINE/MIR 1 CAGAGGGGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGAC 50 chr5ptel1M 995762 AAATCTGTATTCAAATGTTGCAGCAGCTACTGAATTAGCTGAATGACCCT 995811 i i vi i vii vvv v i v- i vi i MIRb#SINE/MIR 51 AGACCTGGGTTCGAATCCCGGCTCTGCCACTT-ACTAGCTGTGTGACCTT 99 chr5ptel1M 995812 GG---------TCACCC------AGACTCAGTTTCCCCATCTGTAAAATG 995846 --------- i v ------ v i MIRb#SINE/MIR 100 GGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATG 149 chr5ptel1M 995847 GTGATGAGATCACTAGCTTCCCAAAGATA-CAAGGGGATTGA 995887 v i v vi ivi i v ii v i-iiv i i MIRb#SINE/MIR 150 GGGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAA 191 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.43 CpG sites = 33, Kimura (unadjusted) = 44.58 Transitions / transversions = 1.43 (33/23) Gap_init rate = 0.03 (5 / 171), avg. gap size = 4.20 (21 / 5) 436 27.32 10.71 0.65 chr5ptel1M 995724 995863 (4137) MIRc#SINE/MIR 10 163 (105) m_b243s601i57 9664 chr5ptel1M 995724 GTGGCCCAGTGAGTAGAGTGCTAGACTTGGAGTCGGGGAAATCTGTATTC 995773 iv iiv ii i i i i i vi MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr5ptel1M 995774 AAATGTTGCAGCAGCTACTGAATTAGCTGAATGACCCTG-----GTCAC- 995817 i i vii vvv v i v- i vi i ----- - MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTT-ACTAGCTGTGTGACCTTGGGCAAGTCACT 108 chr5ptel1M 995818 ---CC------AGACTCAGTTTCCCCATCTGTAAAATGGTGATGAGATCA 995858 --- ------ v i v i v vi MIRc#SINE/MIR 109 TAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATA 158 chr5ptel1M 995859 CTAGC 995863 iv MIRc#SINE/MIR 159 CCTGC 163 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.71 CpG sites = 23, Kimura (unadjusted) = 34.97 Transitions / transversions = 1.53 (23/15) Gap_init rate = 0.04 (5 / 139), avg. gap size = 3.20 (16 / 5) 184 27.72 0.00 6.90 chr5ptel1M 996897 996958 (3042) C MIR3#SINE/MIR (53) 155 98 m_b243s601i58 9665 chr5ptel1M 996897 GTCCAACTGCCTCATTACTGTGTAGAAGGGGGAAACTGAGACCCTGAAAA 996946 iv ---v ii -v i i v i i C MIR3#SINE/MIR 155 GTCCAACCCCCTCATT---TTACAGA-TGAGGAAACTGAGGCCCAGAGAG 110 chr5ptel1M 996947 AGGGAGAGGCTT 996958 iv i v i C MIR3#SINE/MIR 109 GTGAAGTGACTT 98 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.53 CpG sites = 10, Kimura (unadjusted) = 35.53 Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.07 (4 / 61), avg. gap size = 1.00 (4 / 4) 186 30.94 12.75 1.77 chr5ptel1M 997202 997303 (2697) MIRb#SINE/MIR 23 135 (133) m_b243s601i59 9666 chr5ptel1M 997202 GGGAGAAATACAGCCCTTTACTTCCGAGGCTGCCCTGGGATGGACTCCAG 997251 i ii ii i v i vivv -- i v v v v v v MIRb#SINE/MIR 23 GGAAAGAGCACGGGCTTTGGAGTC--AGACAGACCTGGGTTCGAATCCCG 70 chr5ptel1M 997252 GTT-TGCTGCTAACC-----TGAGATCCTGGACAAGCC------CCTCTC 997289 i - ii v i----- v i i i ii------ MIRb#SINE/MIR 71 GCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTC 120 chr5ptel1M 997290 C-AGCCTCAGTTTCC 997303 i- MIRb#SINE/MIR 121 TGAGCCTCAGTTTCC 135 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.75 CpG sites = 19, Kimura (unadjusted) = 41.52 Transitions / transversions = 1.58 (19/12) Gap_init rate = 0.06 (6 / 101), avg. gap size = 2.50 (15 / 6) 189 33.31 8.06 0.75 chr5ptel1M 997617 997740 (2260) C L3#LINE/CR1 (141) 3958 3826 m_b243s601i60 9667 chr5ptel1M 997617 GCTCACTACTTCTGGAGGCCGTCCTTTCTACTCT----CGGCTCTCATCA 997662 i ?v v i v i i i ---- i v ii C L3#LINE/CR1 3958 GCTCACTACCTCNCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGATTG 3909 chr5ptel1M 997663 GAAGGGCATTCTCCGCCATACCAAGTCCTGGACGGGCTTTGCTG--ACTC 997710 vv iivi i vii iii - vii ivv i iv -- i C L3#LINE/CR1 3908 TTAGAAAGTTCTTCCTTATATTGAG-CCGAAATCTGCCTCCCTGTAACTT 3860 chr5ptel1M 997711 CCTGC--TTTGCTCTGG-TCTG-CCTCTGGAGCC 997740 vv -- v ii i - - C L3#LINE/CR1 3859 CCACCCATTGGTCCTAGTTCTGCCCTCTGGAGCC 3826 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.89 CpG sites = 26, Kimura (unadjusted) = 46.89 Transitions / transversions = 1.73 (26/15) Gap_init rate = 0.05 (6 / 123), avg. gap size = 1.83 (11 / 6) 13 14.43 7.69 0.00 chr5ptel1M 999614 999652 (348) (GGGGGAA)n#Simple_repeat 1 42 (0) m_b243s252i11 9668 chr5ptel1M 999614 GGGGGACGGGGGGGGGGGGAA-GGGG--GGGAAAAGGGGGAA 999652 v ii - -- ii (GGGGGAA)n#Si 1 GGGGGAAGGGGGAAGGGGGAAGGGGGAAGGGGGAAGGGGGAA 42 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.50 (3 / 2) 16 16.24 0.00 0.00 chr5ptel1M 999614 999641 (359) (G)n#Simple_repeat 1 28 (0) m_b243s252i10 9668 chr5ptel1M 999614 GGGGGACGGGGGGGGGGGGAAGGGGGGG 999641 iv ii (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGG 28 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 199 35.79 3.16 0.00 chr5qtel1M 1226 1320 (998680) L3#LINE/CR1 3567 3664 (435) m_b244s601i0 9669 chr5qtel1M 1226 CTGCCCAGGTCTGCCCACTTCTGGAGCATCGCACCCCACTCTGGGGACTC 1275 v v v v v i i iii vii vi iv L3#LINE/CR1 3567 CTGCGCTGGTCAGACCACATCTGGAGTATTGCGTTCAGTTCTGGGCGCCA 3616 chr5qtel1M 1276 CTTGTT--GGGGGCCGCTGACGAATGAGAG-GCTTCTGAGGGACCGCG 1320 v v -- i v ii i ivi - v iiii vv L3#LINE/CR1 3617 CATTTTAAGAGGGACATTGACAAACTGGAGCGCGTCCAGAGGAGAGCG 3664 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.19 CpG sites = 19, Kimura (unadjusted) = 50.30 Transitions / transversions = 1.27 (19/15) Gap_init rate = 0.02 (2 / 94), avg. gap size = 1.50 (3 / 2) 11 24.88 0.00 2.56 chr5qtel1M 5744 5783 (994217) (CCTCTCC)n#Simple_repeat 1 39 (0) m_b244s252i0 9670 chr5qtel1M 5744 CCTTTCCCATCTCGCCTCTCCGCTCAGGCCGCGTCCCCTC 5783 i v v v vvv v - (CCTCTCC)n#Si 1 CCTCTCCCCTCTCCCCTCTCCCCTCTCCCCTC-TCCCCTC 39 Matrix = Unknown Transitions / transversions = 0.14 (1/7) Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1) 12 25.79 2.70 7.04 chr5qtel1M 5891 5964 (994036) (CTC)n#Simple_repeat 1 71 (0) m_b244s252i1 9671 chr5qtel1M 5891 CTCC-CTTCCTCCTCCCTCCTTGTTCCTCCAGCTAATTCTCTCTCC-CCC 5938 - i - - vi vv vv i - - i (CTC)n#Simple 1 CTCCTCCTCCTCCT-CCTCC-TCCTCCTCCTCCTCCTCCTC-CTCCTCCT 47 chr5qtel1M 5939 CCCCATCTTCTTCCCTTCTCCTTCCT 5964 i v i i - i - (CTC)n#Simple 48 CCTCCTCCTCCT-CCTCCTCC-TCCT 71 Matrix = Unknown Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.10 (7 / 73), avg. gap size = 1.00 (7 / 7) 14 24.48 4.55 2.99 chr5qtel1M 8411 8476 (991524) (GGGAGG)n#Simple_repeat 1 67 (0) m_b244s252i2 9672 chr5qtel1M 8411 GGGAGGGGG-CCGGGAGGGGG-CCAGGAGGGGGA-GAGCAGCGGCCGGTA 8457 -vv -vvi - i v v vv -- (GGGAGG)n#Sim 1 GGGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGGAGG-- 48 chr5qtel1M 8458 GGGAGGGGGCGGGAGCGGG 8476 v i v (GGGAGG)n#Sim 49 GGGAGGGGGAGGGGGAGGG 67 Matrix = Unknown Transitions / transversions = 0.30 (3/10) Gap_init rate = 0.08 (5 / 65), avg. gap size = 1.00 (5 / 5) 22 23.34 3.95 2.60 chr5qtel1M 8654 8729 (991271) (CCT)n#Simple_repeat 1 77 (0) m_b244s252i3 9673 chr5qtel1M 8654 CCTCCTCCTGTCTCC-CCCGCTTCTCTTCC-CTTCTTCCTCCTCCTGGCC 8701 -i - iv i i - i i -v i (CCT)n#Simple 1 CCTCCTCCT-CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT-CCT 48 chr5qtel1M 8702 CCTCCTCCTCC-GCTTCTCCCCCCCCCCC 8729 -v i i i i (CCT)n#Simple 49 CCTCCTCCTCCTCCTCCTCCTCCTCCTCC 77 Matrix = Unknown Transitions / transversions = 3.67 (11/3) Gap_init rate = 0.07 (5 / 75), avg. gap size = 1.00 (5 / 5) 28 0.00 0.00 0.00 chr5qtel1M 13528 13554 (986446) (C)n#Simple_repeat 1 27 (0) c_b244s251i0 9674 chr5qtel1M 13528 CCCCCCCCCCCCCCCCCCCCCCCCCCC 13554 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCC 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 chr5qtel1M 13688 13708 (986292) (GGAG)n#Simple_repeat 1 21 (0) m_b244s252i4 9675 chr5qtel1M 13688 GGAGGGAGGGAGGGAGGGAGG 13708 (GGAG)n#Simpl 1 GGAGGGAGGGAGGGAGGGAGG 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 216 26.42 1.89 0.00 chr5qtel1M 13784 13836 (986164) C L2d2_3end#LINE/L2 (10) 545 492 m_b244s601i2 9676 chr5qtel1M 13784 TCGGCAAGCACTTATTAAGCGCCTCCTGTGCGCCGGGCACCGGGCCAAG- 13832 ii ii i i v i vi i v i i - C L2d2_3end#LIN 545 TCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGC 496 chr5qtel1M 13833 GCTG 13836 C L2d2_3end#LIN 495 GCTG 492 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.91 CpG sites = 11, Kimura (unadjusted) = 34.91 Transitions / transversions = 3.67 (11/3) Gap_init rate = 0.02 (1 / 52), avg. gap size = 1.00 (1 / 1) 219 25.00 0.00 0.00 chr5qtel1M 13784 13827 (986173) C L2c_3end#LINE/L2 (10) 468 425 m_b244s601i1 9676 chr5qtel1M 13784 TCGGCAAGCACTTATTAAGCGCCTCCTGTGCGCCGGGCACCGGG 13827 ii i i i v i i i i i C L2c_3end#LINE 468 TCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGG 425 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.83 CpG sites = 10, Kimura (unadjusted) = 33.60 Transitions / transversions = 10.00 (10/1) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 13 20.05 4.00 4.00 chr5qtel1M 14203 14252 (985748) (GGCC)n#Simple_repeat 1 50 (0) m_b244s252i5 9677 chr5qtel1M 14203 GGCCGGCCGGGAGG-GGTCCGGGCCGGCCGGGAGG-GGTCCGGGCCGGCC 14250 vv -v v - vv -v v - (GGCC)n#Simpl 1 GGCCGGCCGGCCGGCCGGCC-GGCCGGCCGGCCGGCCGGCC-GGCCGGCC 48 chr5qtel1M 14251 GG 14252 (GGCC)n#Simpl 49 GG 50 Matrix = Unknown Transitions / transversions = 0.00 (0/8) Gap_init rate = 0.08 (4 / 49), avg. gap size = 1.00 (4 / 4) 16 16.93 0.00 0.00 chr5qtel1M 14601 14627 (985373) (C)n#Simple_repeat 1 27 (0) m_b244s252i6 9678 chr5qtel1M 14601 CCCCCCCTCCCCCCTCCCCCCGCTCCC 14627 i i v i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCC 27 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 13 22.00 1.96 4.00 chr5qtel1M 14657 14707 (985293) (GGGGGGC)n#Simple_repeat 1 50 (0) m_b244s252i7 9679 chr5qtel1M 14657 GGGGGGGGGGGCGCCTGGAGCAGCCAGGGC-GGTGGCGGGGGGCGGGGGC 14705 v v vv i - -vi - v v (GGGGGGC)n#Si 1 GGGGGGCGGGGGGCGGGGGGC-G-GGGGGCGGGGGGCGGGGGGCGGGGGG 48 chr5qtel1M 14706 CG 14707 (GGGGGGC)n#Si 49 CG 50 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.06 (3 / 50), avg. gap size = 1.00 (3 / 3) 23 11.15 0.00 0.00 chr5qtel1M 14794 14832 (985168) (CACACT)n#Simple_repeat 1 39 (0) m_b244s252i8 9680 chr5qtel1M 14794 CACACTCTCTCTCACACTCACACACTCACTCACACTCAC 14832 v v v v (CACACT)n#Sim 1 CACACTCACACTCACACTCACACTCACACTCACACTCAC 39 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 31 9.65 4.05 5.48 chr5qtel1M 16920 16993 (983007) (GCCCCGT)n#Simple_repeat 1 73 (0) m_b244s252i10 9681 chr5qtel1M 16920 GCCCCG-GCCCCGTG-CCCTTGTCCCCGTGCCCCCGGCTCCTGTGCCCTC 16967 - - v - vv - i - (GCCCCGT)n#Si 1 GCCCCGTGCCCCGTGCCCCGTG-CCCCGTGCCCCGTGC-CCCGTGCCC-C 47 chr5qtel1M 16968 G-GCCCCTGTGCCCCCGGCCCCGTGCC 16993 - - vv (GCCCCGT)n#Si 48 GTGCCCC-GTGCCCCGTGCCCCGTGCC 73 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.10 (7 / 73), avg. gap size = 1.00 (7 / 7) 13 23.03 3.28 5.00 chr5qtel1M 19396 19456 (980544) (CCCGG)n#Simple_repeat 1 60 (0) m_b244s252i11 9682 chr5qtel1M 19396 CCCGGCCCGCGCCGCTGACCGG-CCGG-CTGGGGCGGCCCCGCCCCGCTC 19443 - - v v - - i vv v v - (CCCGG)n#Simp 1 CCCGGCCCG-GCC-CGGCCCGGCCCGGCCCGGCCCGGCCCGGCCCGGC-C 47 chr5qtel1M 19444 CGACCAAGCGCGG 19456 i vi v (CCCGG)n#Simp 48 CGGCCCGGCCCGG 60 Matrix = Unknown Transitions / transversions = 0.38 (3/8) Gap_init rate = 0.08 (5 / 60), avg. gap size = 1.00 (5 / 5) 15 24.62 0.00 0.00 chr5qtel1M 20433 20475 (979525) (CGGGGG)n#Simple_repeat 1 43 (0) m_b244s252i12 9683 chr5qtel1M 20433 CGGGAGCGAGCTTGGGCGCGGGGGCGGGGAAGGGGGAGGGGGC 20475 i i vvi v iv v (CGGGGG)n#Sim 1 CGGGGGCGGGGGCGGGGGCGGGGGCGGGGGCGGGGGCGGGGGC 43 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 18 28.18 1.56 3.17 chr5qtel1M 21412 21475 (978525) (GA)n#Simple_repeat 1 63 (0) m_b244s252i13 9684 chr5qtel1M 21412 GAGAGAGACCCAGAGAGACAGAGA-AGAAACAAAGGAAGGGAGAGACAGG 21460 vvv v - i v i ii i v i (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr5qtel1M 21461 GACGGGAAATGAGAG 21475 - i i - (GA)n#Simple_ 51 GA-GAGAGA-GAGAG 63 Matrix = Unknown Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.05 (3 / 63), avg. gap size = 1.00 (3 / 3) 209 20.74 0.00 5.17 chr5qtel1M 23608 23668 (976332) C MIR1_Amn#SINE/MIR (78) 152 95 m_b244s601i3 9685 chr5qtel1M 23608 TCCCCTGGTCACAGATGAGGAAACTGAGGCAGCCAGAAGTCGCTTGACCT 23657 vvv i ?vvv i ?ivv - C MIR1_Amn#SINE 152 TCCCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGA-CT 104 chr5qtel1M 23658 TGTACTCAAGG 23668 -- i C MIR1_Amn#SINE 103 TG--CCCAAGG 95 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 25.24 CpG sites = 4, Kimura (unadjusted) = 25.24 Transitions / transversions = 0.50 (4/8) Gap_init rate = 0.05 (3 / 60), avg. gap size = 1.00 (3 / 3) 12 4.30 8.33 0.00 chr5qtel1M 31044 31067 (968933) (GGGA)n#Simple_repeat 1 26 (0) m_b244s252i14 9686 chr5qtel1M 31044 GGGAGGG-GGG-TGGAGGGAGGGAGG 31067 - -v (GGGA)n#Simpl 1 GGGAGGGAGGGAGGGAGGGAGGGAGG 26 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.09 (2 / 23), avg. gap size = 1.00 (2 / 2) 38 7.69 5.56 1.33 chr5qtel1M 32189 32260 (967740) (GGGAGAA)n#Simple_repeat 1 75 (0) m_b244s252i15 9687 chr5qtel1M 32189 GGGAGAAGGGAG-AGGGGGAAGGG-GAAGGCGGGAAGGGAG-AGGGGGAA 32235 - i - - i - i (GGGAGAA)n#Si 1 GGGAGAAGGGAGAAGGGAGAAGGGAGAAGG-GAGAAGGGAGAAGGGAGAA 49 chr5qtel1M 32236 GGAGGAAGGGAGAAGGGAG-AGGGAG 32260 ii - (GGGAGAA)n#Si 50 GGGAGAAGGGAGAAGGGAGAAGGGAG 75 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.07 (5 / 71), avg. gap size = 1.00 (5 / 5) 25 22.80 2.67 2.67 chr5qtel1M 32372 32446 (967554) (AC)n#Simple_repeat 1 75 (0) m_b244s252i16 9688 chr5qtel1M 32372 ACACA-ACACACACA-ATTCACACAGTCACATATACAAATGAGCACATTC 32419 - - iv vv i i v -v - iv (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACA-CA-CACACAC 48 chr5qtel1M 32420 ATACACACGCACACTCACACTCACACA 32446 i i v v (AC)n#Simple_ 49 ACACACACACACACACACACACACACA 75 Matrix = Unknown Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.05 (4 / 74), avg. gap size = 1.00 (4 / 4) 16 16.57 0.00 0.00 chr5qtel1M 32511 32537 (967463) (C)n#Simple_repeat 1 27 (0) m_b244s252i17 9689 chr5qtel1M 32511 CCCCTCCCCCCCACCTCCCCCCACCCC 32537 i v i v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCC 27 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 19 8.18 0.00 0.00 chr5qtel1M 33861 33886 (966114) (G)n#Simple_repeat 1 26 (0) m_b244s252i18 9690 chr5qtel1M 33861 GGGGGCGCGGGGGGGGGGGGGGGGGG 33886 v v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGG 26 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 34 24.74 5.59 2.03 chr5qtel1M 34863 35005 (964995) (GGGT)n#Simple_repeat 1 148 (0) m_b244s252i19 9691 chr5qtel1M 34863 GGGTGGGGGGGT-GG-GGGTGGGTGAG-GGGTGGGAGGTTTGGGCGGGAG 34909 v - - i - v -v i v (GGGT)n#Simpl 1 GGGTGGGTGGGTGGGTGGGTGGGTGGGTGGGTGGGTGG-GTGGGTGGGTG 49 chr5qtel1M 34910 GG-GGGTGGGAGGGATTG-GGGAGGGAGGG-GAGGGGAAAGGAGGGAGGG 34956 - v vvv - v v - i v ivi v -v (GGGT)n#Simpl 50 GGTGGGTGGGTGGGTGGGTGGGTGGGTGGGTGGGTGGGTGGGTGGG-TGG 98 chr5qtel1M 34957 GAAGTTGGGGGGCTGGG-AGATGGGGGGGTCGGGCGGG-GAGTGGGTGGG 35004 vi v v v -i i v - i - i (GGGT)n#Simpl 99 GTGGGTGGGTGGGTGGGTGGGTGGGTGGGT-GGGTGGGTGGGTGGGTGGG 147 chr5qtel1M 35005 T 35005 (GGGT)n#Simpl 148 T 148 Matrix = Unknown Transitions / transversions = 0.53 (10/19) Gap_init rate = 0.08 (11 / 142), avg. gap size = 1.00 (11 / 11) 19 22.84 0.00 0.00 chr5qtel1M 35214 35254 (964746) (T)n#Simple_repeat 1 41 (0) m_b244s252i20 9692 chr5qtel1M 35214 TTTTATTTTTGTTTTTCTTGTTTTGTTTTGTGTTTTTATTT 35254 v v i v v v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 41 Matrix = Unknown Transitions / transversions = 0.14 (1/7) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 14 18.15 0.00 5.13 chr5qtel1M 35617 35657 (964343) (GGGT)n#Simple_repeat 1 39 (0) m_b244s252i21 9693 chr5qtel1M 35617 GGGCGGGTGGGTGGGAGGTAGTGGTTGTTTGGGTGGGTAGG 35657 i v -- v vv i (GGGT)n#Simpl 1 GGGTGGGTGGGTGGGTGG--GTGGGTGGGTGGGTGGGTGGG 39 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 15 16.87 9.43 0.00 chr5qtel1M 35643 35695 (964305) (GTTTGG)n#Simple_repeat 1 58 (0) m_b244s252i22 9694 chr5qtel1M 35643 GTTTGGG--TGGGTAGGGGTTTTGGATTGGGTTTGGG---AGGTTTGGAA 35687 -- vv v v ---i iv (GTTTGG)n#Sim 1 GTTTGGGTTTGGGTTTGGGTTTGGGTTTGGGTTTGGGTTTGGGTTTGGGT 50 chr5qtel1M 35688 ATGGGTTT 35695 v (GTTTGG)n#Sim 51 TTGGGTTT 58 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.04 (2 / 52), avg. gap size = 2.50 (5 / 2) 12 5.00 0.00 4.55 chr5qtel1M 35841 35863 (964137) (TTTC)n#Simple_repeat 1 22 (0) m_b244s252i23 9695 chr5qtel1M 35841 TTTCTTTGTTTTCTTTCTTTCTT 35863 -i (TTTC)n#Simpl 1 TTTCTTT-CTTTCTTTCTTTCTT 22 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.05 (1 / 22), avg. gap size = 1.00 (1 / 1) 60 23.31 4.68 0.00 chr5qtel1M 36661 36831 (963169) (AG)n#Simple_repeat 1 179 (0) m_b244s252i24 9696 chr5qtel1M 36661 AGAG-GGGGGAAAGACAGAGA-ACAGAAAGAGA-AAAGAGAAAGAGAACA 36707 - i i i v - v i - i i ivi (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr5qtel1M 36708 AGAGAGAGA-AAAGAGAGACA-AGAGAGGGA-ACAGAAAAAGAGACAGAG 36754 - i v - i - v i i v (AG)n#Simple_ 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 100 chr5qtel1M 36755 AGACACAGACACAAAGAGAGAGACAGAGAGATATGGAGAGAGACAAAGAT 36804 v v v v i v v vi v i v (AG)n#Simple_ 101 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 150 chr5qtel1M 36805 GGAGA-AAAGAGACAGAGAG-GAAAGAGA 36831 i - i v - i (AG)n#Simple_ 151 AGAGAGAGAGAGAGAGAGAGAGAGAGAGA 179 Matrix = Unknown Transitions / transversions = 1.12 (18/16) Gap_init rate = 0.05 (8 / 170), avg. gap size = 1.00 (8 / 8) 210 27.08 0.00 0.00 chr5qtel1M 36833 36880 (963120) L2b_3end#LINE/L2 404 451 (15) m_b244s601i4 9697 chr5qtel1M 36833 AGGGCCTCACCCAGAGCCTGGCACACAGGAGATGCTTAATCGATGCTT 36880 v vi v ? v ii i i vi ii L2b_3end#LINE 404 AGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTT 451 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.24 CpG sites = 8, Kimura (unadjusted) = 35.58 Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 11 17.22 7.69 0.00 chr5qtel1M 38468 38506 (961494) (CCAGCC)n#Simple_repeat 1 42 (0) m_b245s252i0 9698 chr5qtel1M 38468 CCATCCACAG-CTGAGCCCCAGCCCC-G-CCAGGCCCCAGCC 38506 v v - iv - - vi (CCAGCC)n#Sim 1 CCAGCCCCAGCCCCAGCCCCAGCCCCAGCCCCAGCCCCAGCC 42 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.08 (3 / 38), avg. gap size = 1.00 (3 / 3) 13 19.91 2.27 4.65 chr5qtel1M 40488 40531 (959469) (GGA)n#Simple_repeat 1 43 (0) m_b245s252i1 9699 chr5qtel1M 40488 GGAGGAGGAGGAAG-GGAGGGATCTGCAGGCGGCGGAGGGAGGAG 40531 i - - vvv v v v - (GGA)n#Simple 1 GGAGGAGGAGGAGGAGGA-GGAGGAGGAGGAGGAGGA-GGAGGAG 43 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.07 (3 / 43), avg. gap size = 1.00 (3 / 3) 15 30.46 1.67 0.00 chr5qtel1M 41317 41376 (958624) (CGATGA)n#Simple_repeat 1 61 (0) m_b245s252i2 9700 chr5qtel1M 41317 CGAAGATGGTGAAGATGATGAGGACGATGACAAAGCAGA-CAAGATGAGG 41365 v i i v i v i v vv -v v v (CGATGA)n#Sim 1 CGATGACGATGACGATGACGATGACGATGACGATGACGATGACGATGACG 50 chr5qtel1M 41366 ATGAGGAAGAC 41376 v v (CGATGA)n#Sim 51 ATGACGATGAC 61 Matrix = Unknown Transitions / transversions = 0.36 (4/11) Gap_init rate = 0.02 (1 / 59), avg. gap size = 1.00 (1 / 1) 198 37.76 2.74 2.04 chr5qtel1M 44175 44320 (955680) L3#LINE/CR1 2003 2149 (1950) m_b245s601i0 9701 chr5qtel1M 44175 ACGGACTAAGATTTTACAGGTGAAGTCATTTCAAGAAGGGTTGGAGATTC 44224 i v ?i i iv v i -i viivi i ? v iii L3#LINE/CR1 2003 ATGGCCNGAGACTCAAAAAG-AAAGATGGCTCAAGAGGGNTGGGAAGCTC 2051 chr5qtel1M 44225 CCAAAAATGAAGTTCCGAAACAAAAGGACACAAT--TTCCGTGAATAAGG 44272 ii i i - vi v vv - -- i vi iv i L3#LINE/CR1 2052 TTAAAAATGAAATTCTG-ACTACAATTACA-AATGATCCAATGAGGAAGA 2099 chr5qtel1M 44273 AACAT--GAACTCTGTGAAGGGACCGATGTGCATGCGCAGGGGGCTCTCT 44320 viv-- ivv vv v ii i i vv ? ii i ?ii L3#LINE/CR1 2100 AAAGAGGGAGGGCATTTAAGAAACCAACGTGGCTNCATAGAGNATTCTCT 2149 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 56.45 CpG sites = 33, Kimura (unadjusted) = 58.16 Transitions / transversions = 1.57 (33/21) Gap_init rate = 0.03 (5 / 145), avg. gap size = 1.40 (7 / 5) 35 0.00 0.00 0.00 chr5qtel1M 44767 44798 (955202) (CGGTCA)n#Simple_repeat 1 32 (0) c_b245s251i0 9702 chr5qtel1M 44767 CGGTCACGGTCACGGTCACGGTCACGGTCACG 44798 (CGGTCA)n#Sim 1 CGGTCACGGTCACGGTCACGGTCACGGTCACG 32 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 197 36.17 7.45 0.00 chr5qtel1M 45916 46009 (953991) C L2c_3end#LINE/L2 (9) 469 369 m_b245s601i1 9703 chr5qtel1M 45916 TCCAATGATCGCTGATC-AGCGCTCACTTTGTGCTCATTTCTGGGGCTAT 45964 i ii v ii v i- ii v iviviv v i C L2c_3end#LINE 469 TTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGATAC 420 chr5qtel1M 45965 AAAGAAGGACGA-AC-----TTCTCCCCTGAAGGCGTTTACAGAGTAATA 46008 v i ii - -----ii v v v i i vv i i C L2c_3end#LINE 419 AAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAGTG 370 chr5qtel1M 46009 G 46009 C L2c_3end#LINE 369 G 369 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 49.83 CpG sites = 21, Kimura (unadjusted) = 52.08 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.03 (3 / 93), avg. gap size = 2.33 (7 / 3) 192 31.88 10.81 2.50 chr5qtel1M 45941 46088 (953912) C L2b_3end#LINE/L2 (47) 419 260 m_b245s601i2 9703 chr5qtel1M 45941 CTTTGTGCTCATTTCTGGGGCTATA---------AAGAAGGACG-AACTT 45980 ?i viviv v i --------- vi ?-iiiii C L2b_3end#LINE 419 CNCTGTGCTAGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCC 370 chr5qtel1M 45981 CTCCCCTGAAGGCGTTTACAGAGTAATAGGAATGGCTGGGCATGCAGGGC 46030 v v v v i i vv i i iiv i -i i i -i? C L2b_3end#LINE 369 CTGCCCTCACGGAGCTCACAGTCTAGTGGGGGAGAC-AGACATGTA-ANC 322 chr5qtel1M 46031 AGCCCCAATGA-AGCCCAGAGGGGTCTGG--GGCCTGAGAGGGGCCA--- 46074 --v ? - i v ivv -- v i i v --- C L2b_3end#LINE 321 AG--ACAATNATAACCCAGAGTGGCAGGGTAGGACTGGGGGGGCCCAGAG 274 chr5qtel1M 46075 GAGAGCCCCCGACC 46088 i v i C L2b_3end#LINE 273 GAGGGCGCCTGACC 260 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.15 CpG sites = 27, Kimura (unadjusted) = 44.76 Transitions / transversions = 1.42 (27/19) Gap_init rate = 0.06 (9 / 147), avg. gap size = 2.22 (20 / 9) 234 23.84 0.00 9.09 chr5qtel1M 46181 46240 (953760) L2c_3end#LINE/L2 412 466 (12) m_b245s601i3 9704 chr5qtel1M 46181 TCATATTTGCAAAGCTTACCCAGTGCCCGGCATACAGTAGGCACTTAACC 46230 v i ----- v i i i i i i iv L2c_3end#LINE 412 TCATCTTTGTA-----TCCCCAGCGCCTGGCACATAGTAGGCGCTCAATA 456 chr5qtel1M 46231 AATGCCTGTT 46240 ii L2c_3end#LINE 457 AATGTTTGTT 466 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 24.64 CpG sites = 10, Kimura (unadjusted) = 29.97 Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.08 (5 / 59), avg. gap size = 1.00 (5 / 5) 189 36.10 4.83 0.66 chr5qtel1M 46437 46581 (953419) L2#LINE/L2 2232 2382 (700) m_b245s601i4 9705 chr5qtel1M 46437 CCCCAGG-CTCAGGGCTGGGCCCTCTCCCCCTCTTCCTTTGGGGTGGTTG 46485 - vv v v i i i iiv i iviv vii v L2#LINE/L2 2232 CCCCAGGGCTCAGTCCTTGGACCTCTTCTCTTCTCTATCTACACTCACTC 2281 chr5qtel1M 46486 CCTAG-----CCTTTTCAGCTGTCATGGATCCAGTTGAGATCTGTTTCCT 46530 ? ----- iiv i - v v ii iv ivv i v v L2#LINE/L2 2282 CCTNGGTGATCTCATCCAG-TCTCATGGCTTTAAATACCATCTATATGCT 2330 chr5qtel1M 46531 GCTG-CTCCTGAGGCCCCTTCTCCAGCCCTCACCTCTCTCTTGGACTTGA 46579 v - ii iviiviv vv i i i iv L2#LINE/L2 2331 GATGACTCCCAAATTTATATCTCCAGCCCGGACCTCTCCCCTGAACTCCA 2380 chr5qtel1M 46580 GA 46581 L2#LINE/L2 2381 GA 2382 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 51.21 CpG sites = 28, Kimura (unadjusted) = 51.21 Transitions / transversions = 1.17 (28/24) Gap_init rate = 0.03 (4 / 144), avg. gap size = 2.00 (8 / 4) 245 31.12 15.28 0.38 chr5qtel1M 46794 47022 (952978) L2#LINE/L2 2745 3007 (75) m_b245s601i5 9705 chr5qtel1M 46794 CCTGCCTCTGTCTCTGCCCACCT-CAGGCCACCCTCCATTC-GCCACCAC 46841 i iii ii v - v i ii v iv - vi v L2#LINE/L2 2745 CCTGCTTCCACCCTTGCCCCCCTNCAGTCTATTCTCAACACAGCAGCCAG 2794 chr5qtel1M 46842 AGTGATTTTCCTGAAACACAGGACTGGT-ACGTCCCTC-TCTGCTCAAAA 46889 ii ii i ii i v v i - i v - L2#LINE/L2 2795 AGTGATCCTTTTAAAACGTAAGTCAGATCATGTCACTCCTCTGCTCAAAA 2844 chr5qtel1M 46890 AGCTTCTATGGCTCCC--TCTCACCACCAGGA-----CCAAGTTC----- 46927 vv i v i -- ivvv v ----- v i ----- L2#LINE/L2 2845 CCCTCCAATGGCTTCCCATCTCACTCAGAGTAAAAGCCAAAGTCCTTACA 2894 chr5qtel1M 46928 -------ACAAAGCCCTTTATGA--------CCCG--ACCCCTCC--CCT 46958 ------- i vi -------- -- i i-- L2#LINE/L2 2895 ATGGCCTACAAGGCCCTACATGATCTGGTCCCCCGTTACCTCTCTGACCT 2944 chr5qtel1M 46959 CCCCTCCCATCTTGCTCCCCACCACGTGCTCTTGCTCCAGGGCCCCCGGC 47008 vi i i viv vi i vii -i vvv v i L2#LINE/L2 2945 CATCTCCTACCACTCTCCCCCTCGCTCACTC-CGCTCCAGCCACACTGGC 2993 chr5qtel1M 47009 CGCCTAGACGTCCC 47022 v v vi i L2#LINE/L2 2994 CTCCTTGCTGTTCC 3007 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.15 CpG sites = 41, Kimura (unadjusted) = 41.42 Transitions / transversions = 1.37 (41/30) Gap_init rate = 0.05 (12 / 228), avg. gap size = 3.00 (36 / 12) 196 29.85 5.97 0.00 chr5qtel1M 47154 47220 (952780) L2d_3end#LINE/L2 427 497 (19) m_b245s601i6 9705 chr5qtel1M 47154 CTTCTGCCTCTCTCTAGCTCC----AGGGCGTAGCTTGGTGCTGGGCACT 47199 v i i?i i ? v i ---- v v vii i v L2d_3end#LINE 427 CTTATACTNTTTTNTCGTTCCCCACAGCGCCTAGCACAGTGCTGAGCACA 476 chr5qtel1M 47200 CAGCAGGGACTTAATAATTAC 47220 i i vi i v L2d_3end#LINE 477 TAGTAGGCGCTCAATAAATAC 497 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.30 CpG sites = 12, Kimura (unadjusted) = 40.96 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.02 (1 / 66), avg. gap size = 4.00 (4 / 1) 41 35.65 1.38 3.76 chr5qtel1M 47717 47934 (952066) (GAGG)n#Simple_repeat 1 213 (0) m_b245s252i3 9706 chr5qtel1M 47717 GAGAGAGGGAGGG-GGCCTGGA-GCATGGAGGGAGGAAGGCAGGGGAAAA 47764 i - vvv - v v i v - iii (GAGG)n#Simpl 1 GAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGA-GGGAGGG 49 chr5qtel1M 47765 AGGAAGGGAGGAAGGAAAAGAGGGAGGAAGAGAAGGAAGGAAAGAGACAG 47814 i i i ii i i i i ii iv (GAGG)n#Simpl 50 AGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAG 99 chr5qtel1M 47815 GAAAAAAGACAGGAAGGAAGAAAGAAAAGAGGAAGGAAGAAGGAAAAGAG 47864 i iii iv i i ii -ii - i i i i ii (GAGG)n#Simpl 100 GGAGGGAGGGAGGGAGGGAGGGAG-GGAG-GGAGGGAGGGAGGGAGGGAG 147 chr5qtel1M 47865 GGAGGGAGGGA-GGAAAAAGGGAGGGAGAGAAGAAAAGGAAGAGACAGGA 47913 - iii - i -ii i i -i (GAGG)n#Simpl 148 GGAGGGAGGGAGGGAGGGAGGGAGGGAG-GGAG-GGAGGGAGGGA-GGGA 194 chr5qtel1M 47914 AGGAGGGCAGCAGAGGGAAGG 47934 i - -i i (GAGG)n#Simpl 195 GGGAGGG-AG-GGAGGGAGGG 213 Matrix = Unknown Transitions / transversions = 5.75 (46/8) Gap_init rate = 0.05 (11 / 217), avg. gap size = 1.00 (11 / 11) 17 14.42 0.00 5.00 chr5qtel1M 48648 48689 (951311) (CCACCCC)n#Simple_repeat 1 40 (0) m_b245s252i4 9707 chr5qtel1M 48648 CCTCCCCCCACCCCCCACCCACCCCCCGGCCCAGCCCTCACC 48689 v - v -v v i (CCACCCC)n#Si 1 CCACCCCCCACCCCCCACCC-CCCACC-CCCCACCCCCCACC 40 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.05 (2 / 41), avg. gap size = 1.00 (2 / 2) 183 38.44 0.00 4.04 chr5qtel1M 51192 51294 (948706) C L2c_3end#LINE/L2 (16) 462 364 m_b245s601i7 9708 chr5qtel1M 51192 AGCCTTTATTGAGCACCTACTGCACACACGGGAGCTGGGGCTCTGGGGAC 51241 i v i iiiii - i v v viiii i C L2c_3end#LINE 462 AACATTTATTGAGCGCCTACTATGTGC-CAGGCGCTGGGGATACAAAGAT 414 chr5qtel1M 51242 AAGGCCGGGGTTGCCCCCGCCCGCAGGGAGCCCCCACTGGCCTGGGAAAG 51291 i ivvv iviiv i i v i i v --- i i vii C L2c_3end#LINE 413 GAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACA---GTCTAGTGGAG 367 chr5qtel1M 51292 GAG 51294 C L2c_3end#LINE 366 GAG 364 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 54.03 CpG sites = 26, Kimura (unadjusted) = 58.93 Transitions / transversions = 2.17 (26/12) Gap_init rate = 0.04 (4 / 102), avg. gap size = 1.00 (4 / 4) 204 16.67 0.00 0.00 chr5qtel1M 51984 52019 (947981) MIR3#SINE/MIR 112 147 (61) m_b245s601i8 9709 chr5qtel1M 51984 CCCAGGCCCTCAGTCTCCTCAGCTGTAAAATGGGGG 52019 i v v i v i MIR3#SINE/MIR 112 CTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGG 147 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 18.94 CpG sites = 3, Kimura (unadjusted) = 18.94 Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 253 22.58 15.29 1.03 chr5qtel1M 51991 52075 (947925) MIRc#SINE/MIR 122 218 (50) m_b245s601i10 9710 chr5qtel1M 51991 CCTCAGTCTCCTCAGCTGTAAAATGGGGGCGAAAGTAGC----------A 52030 i v iii v i v ---------- MIRc#SINE/MIR 122 CCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTA 171 chr5qtel1M 52031 CTTCACAGG---GTTGTGAGGGAGAAACCAGAAAGTGCCGAGTGAAAG 52075 i --- ivv iv v i -iiv MIRc#SINE/MIR 172 CCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATG-TATGTGAAAG 218 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.37 CpG sites = 11, Kimura (unadjusted) = 27.37 Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.04 (3 / 84), avg. gap size = 4.67 (14 / 3) 304 22.67 5.33 0.00 chr5qtel1M 51991 52065 (947935) MIRb#SINE/MIR 125 203 (65) m_b245s601i9 9710 chr5qtel1M 51991 CCTCAGTCTCCTCAGCTGTAAAATGGGGGCGAAAGTAGC-ACTTCACAGG 52039 i v iii v i v - i i MIRb#SINE/MIR 125 CCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTACCTCGCAGG 174 chr5qtel1M 52040 ---GTTGTGAGGGAGAAACCAGAAAGTGC 52065 --- ivv iv v i MIRb#SINE/MIR 175 GTTGTTGTGAGGATTAAATGAGATAATGC 203 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 25.64 CpG sites = 10, Kimura (unadjusted) = 27.48 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.03 (2 / 74), avg. gap size = 2.00 (4 / 2) 217 33.08 1.83 5.71 chr5qtel1M 52090 52198 (947802) C MIRc#SINE/MIR (110) 158 54 m_b245s601i11 9711 chr5qtel1M 52090 TACTATTATTCCTCATTTTGCAAAT-AAGACCCTGA-GCCCAGAAGGCAT 52137 i i - i i - i vv - i ii vv C MIRc#SINE/MIR 158 TATTATTATCCC-CATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTT 110 chr5qtel1M 52138 CAATGAGCTCAGCCTGGGCCAAGTGGGCGGTAATTACCGAGGAAAGACGG 52187 v i - iiv vi i viii vii v ----i v i v C MIRc#SINE/MIR 109 AAGTGA-CTTGCCCAAGGTCACACAGCTAGTAAGT----GGCAGAGCCGG 65 chr5qtel1M 52188 GGCTCGATCCC 52198 i v C MIRc#SINE/MIR 64 GACTCGAACCC 54 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.45 CpG sites = 21, Kimura (unadjusted) = 45.45 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.07 (8 / 108), avg. gap size = 1.00 (8 / 8) 15 20.03 0.00 0.00 chr5qtel1M 52530 52558 (947442) (G)n#Simple_repeat 1 29 (0) m_b245s252i6 9712 chr5qtel1M 52530 GGGGGCCCGGGGGGGGGGGGGGTGCGGGG 52558 vvv v v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG 29 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 12 23.32 2.04 4.17 chr5qtel1M 52974 53022 (946978) (GGGAA)n#Simple_repeat 1 48 (0) m_b245s252i7 9713 chr5qtel1M 52974 GGGAAAGAAAGGAAGGGGGAAGGGAATGGCCTGGGAA-GGAATGGAGGGG 53022 i i i -i - vvv - v i (GGGAA)n#Simp 1 GGGAAGGGAAGGGA-AGGGAAGGGAA-GGGAAGGGAAGGGAAGGGAAGGG 48 Matrix = Unknown Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.06 (3 / 48), avg. gap size = 1.00 (3 / 3) 14 21.60 7.50 3.61 chr5qtel1M 52980 53059 (946941) (GAGAGG)n#Simple_repeat 1 83 (0) m_b245s252i8 9713 chr5qtel1M 52980 GAAAGGAAGGGGGA-AGGGA-ATGGCCTGGGA-A-GGA-ATGGAG-GGGT 53023 i i i - - v vvv - - - v - v (GAGAGG)n#Sim 1 GAGAGGGAGAGGGAGAGGGAGAGGGAGAGGGAGAGGGAGAGGGAGAGGGA 50 chr5qtel1M 53024 GAGGGTGGGGGTTGACGGGGAAAGGGTGAGGGAGAG 53059 v i -v -- i v (GAGAGG)n#Sim 51 GAGGGAGAGGG-AGA--GGGAGAGGGAGAGGGAGAG 83 Matrix = Unknown Transitions / transversions = 0.56 (5/9) Gap_init rate = 0.11 (9 / 79), avg. gap size = 1.00 (9 / 9) 243 34.55 3.64 0.00 chr5qtel1M 55764 55873 (944127) C L3#LINE/CR1 (2797) 1302 1189 m_b245s601i12 9714 chr5qtel1M 55764 TTGTGCCTCAGGCTTTGTAGACTGGCGTGTGGGCACTAGAGGCC-CAAGT 55812 i vv i vi i iv i ii i i i iiv -i C L3#LINE/CR1 1302 TTATTACCCATACTCTGTGCATTGGTATATAGACATCTGAGGCCATAAGT 1253 chr5qtel1M 55813 TTTGCTCCTAGCCCCCTTG--GGCTGTTC-CTCCAGGGAGGTTCTGGGTG 55859 v i i ii i v--? i i i- v ? iv v ii C L3#LINE/CR1 1252 ATTGTTTCTAGCTTCTTTTCCNGTTATTTTCTCCTGNGAATTACTGGGCA 1203 chr5qtel1M 55860 GCTTCCCCACTGTT 55873 v i i C L3#LINE/CR1 1202 CCTCCTCCACTGTT 1189 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 51.74 CpG sites = 27, Kimura (unadjusted) = 51.74 Transitions / transversions = 2.45 (27/11) Gap_init rate = 0.03 (3 / 109), avg. gap size = 1.33 (4 / 3) 204 33.84 1.35 4.17 chr5qtel1M 56248 56321 (943679) L2c_3end#LINE/L2 392 463 (15) m_b245s601i13 9715 chr5qtel1M 56248 GGGCCAGGGTTGCTTCAT-TTTGCCTATGTGCCCCACACGGTGCCTGGCA 56296 vi iii iv v - iii v ii --- i i L2c_3end#LINE 392 GGGCAGGGACCGTGTCTTATTCATCTTTGTATCCC---CAGCGCCTGGCA 438 chr5qtel1M 56297 AACAGTGGGCACCTGATAAATGCTT 56321 v i i i iii i L2c_3end#LINE 439 CATAGTAGGCGCTCAATAAATGTTT 463 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.50 CpG sites = 19, Kimura (unadjusted) = 50.32 Transitions / transversions = 3.80 (19/5) Gap_init rate = 0.05 (4 / 73), avg. gap size = 1.00 (4 / 4) 210 31.07 4.00 1.30 chr5qtel1M 56260 56334 (943666) L2d2_3end#LINE/L2 478 554 (1) m_b245s601i14 9715 chr5qtel1M 56260 CTTCATTTTGCCTAT-GTGCCCCACACGGTGCCTGGCAAACAGTGGGCAC 56308 ii v iv i i- i ivi i v v i i L2d2_3end#LIN 478 CTTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAGTAGGCGC 527 chr5qtel1M 56309 CTGATAAATGCTTCAT--TTTGCATTTG 56334 iii ii vv -- - L2d2_3end#LIN 528 TCAATAAATATTTGTTGATTTG-ATTTG 554 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.78 CpG sites = 16, Kimura (unadjusted) = 42.68 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.04 (3 / 74), avg. gap size = 1.33 (4 / 3) 17 4.17 0.00 0.00 chr5qtel1M 56726 56750 (943250) (GTCA)n#Simple_repeat 1 25 (0) m_b245s252i9 9716 chr5qtel1M 56726 GTCGGTCAGTCAGTCAGTCAGTCAG 56750 i (GTCA)n#Simpl 1 GTCAGTCAGTCAGTCAGTCAGTCAG 25 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 234 24.95 8.33 3.54 chr5qtel1M 57973 58080 (941920) MIR#SINE/MIR 25 137 (125) m_b245s601i15 9717 chr5qtel1M 57973 CACAGTGCCCAGAGCCCGG--GCCTGAGGTCTACAAAGCCAGCCTCAGAC 58020 i vvi ii v i-- i v ---i v v v v v MIR#SINE/MIR 25 CACGGGCTCTGGAGCCAGACTGCCTGGGTTC---GAATCCCGGCTCTGCC 71 chr5qtel1M 58021 ATTTCCT-GCTGGGTGAGCCCTGGG-----TGCTCCACC-CTGTGTGCCT 58063 i v - v - i ----- i iv - v MIR#SINE/MIR 72 ACTTACTAGCTGTGTGA-CCTTGGGCAAGTTACTTAACCTCTCTGTGCCT 120 chr5qtel1M 58064 CAGTGTCCTGATCTGTA 58080 v v MIR#SINE/MIR 121 CAGTTTCCTCATCTGTA 137 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.88 CpG sites = 11, Kimura (unadjusted) = 30.49 Transitions / transversions = 0.73 (11/15) Gap_init rate = 0.07 (8 / 107), avg. gap size = 1.62 (13 / 8) 197 24.00 4.00 0.00 chr5qtel1M 58262 58311 (941689) C MIRc#SINE/MIR (106) 162 111 m_b245s601i16 9718 chr5qtel1M 58262 CAAGTCTTTCTG-CTCCATCCTCCAGATGGGGAAACTGAGGC-CAGGGCG 58309 i v vi i- i ii v i - i v C MIRc#SINE/MIR 162 CAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAG 113 chr5qtel1M 58310 GT 58311 C MIRc#SINE/MIR 112 GT 111 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.90 CpG sites = 8, Kimura (unadjusted) = 29.90 Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.04 (2 / 49), avg. gap size = 1.00 (2 / 2) 256 28.04 3.57 2.35 chr5qtel1M 60148 60231 (939769) L2d2_3end#LINE/L2 468 552 (3) m_b245s601i17 9719 chr5qtel1M 60148 TCTAAGGCTTCTTTGTATTCCC---AGCGTGGAGCTGGGTGCCGGGTACA 60194 v vi i --- ivv vvi vv i L2d2_3end#LIN 468 TCTTATACTTCTTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCACA 517 chr5qtel1M 60195 CAGCAGGTGCATAATGTGTGCTTGTTAATGGTTGATT 60231 i i vi ivi ii i -- L2d2_3end#LIN 518 CAGTAGGCGCTCAATAAATATTTGTTGAT--TTGATT 552 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.97 CpG sites = 13, Kimura (unadjusted) = 35.89 Transitions / transversions = 1.30 (13/10) Gap_init rate = 0.04 (3 / 83), avg. gap size = 1.67 (5 / 3) 196 22.23 4.26 4.26 chr5qtel1M 61198 61291 (938709) C MIR1_Amn#SINE/MIR (134) 96 3 m_b245s601i18 9720 chr5qtel1M 61198 GGTCACTGAGCGAGGCCGTGGT-GAGCTGGGAC-AGAGCCCAG-CCTGAG 61244 ?v ?i v?v i- i ?-? i -i --- C MIR1_Amn#SINE 96 GGTCACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAACCCAGGTCT--- 50 chr5qtel1M 61245 GCCCGACTCTCTGTCCCCTTTGCTAACCACAAGACCACAGC-CCTCCC 61291 - v i v vv viv v v vi- C MIR1_Amn#SINE 49 -CCCGAGTCCCAGTCCAGTGCTCTATCCACTAGACCACACTGCCTCCC 3 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.72 CpG sites = 8, Kimura (unadjusted) = 28.27 Transitions / transversions = 0.67 (8/12) Gap_init rate = 0.09 (8 / 93), avg. gap size = 1.00 (8 / 8) 327 31.60 0.00 6.92 chr5qtel1M 62895 63064 (936936) L1PB1_3end#LINE/L1 395 553 (345) m_b245s551i0 9721 chr5qtel1M 62895 ACTCAAATGAAAAAGAAATCAGTGTTTTAAAAAGTGAGTCCCACCTGTAT 62944 i i - i i v i viv ------vi i i - L1PB1_3end#LI 395 ACCCAGA-GGAAAAGAAGTCATTATACGAAAAAG------ATACTTGCA- 436 chr5qtel1M 62945 GTGCACGAATGTTGGTGGCAGCCCTCTTTGTAGTGGCCAGAAACTGGAAA 62994 --- v vi i v vv i i i v v i vv v L1PB1_3end#LI 437 ---CACGCATGTTTATAGCAGCACAATTCGCAATTGCAAAAATATGGAAC 483 chr5qtel1M 62995 CTGAGTGGATGCCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATAT 63044 v vviii i iiiv i v i v ? L1PB1_3end#LI 484 CAGCCCAAATGCCCATCAATCAACGAGTGGATAAAGAAANTGTGGTATAT 533 chr5qtel1M 63045 GAATATTATGGAATATTATT 63064 iv ii i i L1PB1_3end#LI 534 ATATACCATGGAATACTACT 553 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 40.15 CpG sites = 29, Kimura (unadjusted) = 42.38 Transitions / transversions = 1.38 (29/21) Gap_init rate = 0.07 (11 / 169), avg. gap size = 1.00 (11 / 11) 376 31.39 0.00 0.00 chr5qtel1M 62941 63077 (936923) L1ME4b_3end#LINE/L1 430 566 (326) m_b245s551i1 9721 chr5qtel1M 62941 GTATGTGCACGAATGTTGGTGGCAGCCCTCTTTGTAGTGGCCAGAAACTG 62990 i v iv i vi v vi v i i v i i i L1ME4b_3end#L 430 GTATGTACAAGGTTATTCATTGCAGCATTGTTTGTAATAGCAAAAGATTG 479 chr5qtel1M 62991 GAAACTGAGTGGATGCCCATCAGTTGGAGAATGGCTGAATAAATTGTGGT 63040 vivv ii i i v i v i i i L1ME4b_3end#L 480 GAAACAACCTAAATGTCCATCAATAGGGGACTGGTTAAATAAATTATGGT 529 chr5qtel1M 63041 ATATGAATATTATGGAATATTATTGTTCTGTAAGAAA 63077 i vv iv i vvvv i i L1ME4b_3end#L 530 ACATCCATACAATGGAATACTATGCAGCCGTAAAAAA 566 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 40.43 CpG sites = 24, Kimura (unadjusted) = 41.70 Transitions / transversions = 1.26 (24/19) Gap_init rate = 0.00 (0 / 136), avg. gap size = 0.0 (0 / 0) 348 30.28 0.00 1.97 chr5qtel1M 62942 63096 (936904) L1MC4a_3end#LINE/L1 429 580 (2049) m_b245s551i2 9721 chr5qtel1M 62942 TATGTGCACGAATGTTGGTGGCAGCCCTCTTTGTAGTGGCCAGAAACTGG 62991 ii v iv i vi v vi v i v v i v i L1MC4a_3end#L 429 TATGCACAAGGTTATTCATTGCAGCATTGTTTGTAATTGCAAAATATTGG 478 chr5qtel1M 62992 AAACTGAGTGGATGCCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTA 63041 vivv ii ??i v ? i i i L1MC4a_3end#L 479 AAACAACCTAAATGCCCATNNATAGGAGANTGGTTGAATAAACTATGGTA 528 chr5qtel1M 63042 TATGAATATTATGGAATATTATTGTTCTGTAAGAAATGACCAGCAGGAGG 63091 i vv i iv i i vvvv i - -- vv i L1MC4a_3end#L 529 CATCCACACAATGGAGTACTATGCAGCTGTAAAAAA-GA--ATGAGGAAG 575 chr5qtel1M 63092 ATTTC 63096 i L1MC4a_3end#L 576 ATCTC 580 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 40.47 CpG sites = 24, Kimura (unadjusted) = 40.47 Transitions / transversions = 1.09 (24/22) Gap_init rate = 0.02 (3 / 154), avg. gap size = 1.00 (3 / 3) 481 23.97 0.00 0.00 chr5qtel1M 62943 63063 (936937) L1ME3A_3end#LINE/L1 432 552 (368) m_b245s551i3 9721 chr5qtel1M 62943 ATGTGCACGAATGTTGGTGGCAGCCCTCTTTGTAGTGGCCAGAAACTGGA 62992 i v vi i v v i i i ?? L1ME3A_3end#L 432 ATGTACAAGAATGTTCATAGCAGCACTATTCGTAATAGCCNNAAACTGGA 481 chr5qtel1M 62993 AACTGAGTGGATGCCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTAT 63042 ?ivviii i iiv v v i L1ME3A_3end#L 482 AACNACCCAAATGTCCATCAACAGTAGAATGGATAAATAAATTGTGGTAT 531 chr5qtel1M 63043 ATGAATATTATGGAATATTAT 63063 vv i iv i L1ME3A_3end#L 532 ATTCACACAATGGAATACTAT 552 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 29.15 CpG sites = 17, Kimura (unadjusted) = 30.39 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.00 (0 / 120), avg. gap size = 0.0 (0 / 0) 180 25.95 2.36 15.04 chr5qtel1M 63950 64076 (935924) C MIR1_Amn#SINE/MIR (95) 135 23 m_b245s601i19 9722 chr5qtel1M 63950 AAAAAAGTGAGTCCCA-TGAGGAGAA-TGTCCTGCTTGGGGTCACACAGC 63997 ii v v ? -v v? - v i iiii ? C MIR1_Amn#SINE 135 AGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGCCCAAGGTCACNCAGC 86 chr5qtel1M 63998 TAACGGCTAAGGGGACAGGGCAGGG-CTTGGCTCCGGGTTTCTGCCCTCT 64046 ---? ? -- v i i v -? ? ivi i i ------ i C MIR1_Amn#SINE 85 ---NGGCNA--GTGGCAGAGCCGGGANTNGAACCCAGGTCTC------CC 47 chr5qtel1M 64047 GAGGCGGCATCCCAATCCGCTTCTCCACCC 64076 ------ i iv v i i C MIR1_Amn#SINE 46 GAG------TCCCAGTCCAGTGCTCTATCC 23 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.43 CpG sites = 18, Kimura (unadjusted) = 34.98 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.16 (20 / 126), avg. gap size = 1.00 (20 / 20) 211 27.84 13.40 0.00 chr5qtel1M 63950 64046 (935954) C MIR3#SINE/MIR (78) 130 21 m_b245s601i20 9722 chr5qtel1M 63950 AAAAAAGTGAGTCCCA-TGAGGAGAA-TGTCCTGCTTGGGGTCACACAGC 63997 ii v v -v v - v i iiii C MIR3#SINE/MIR 130 AGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGC 81 chr5qtel1M 63998 ----TAACGGCTAAG--GGGACAGGG---CAGGGCT--TGGCTCCGGGTT 64036 ---- ii vi -- vi i--- v -- i vi i C MIR3#SINE/MIR 80 NAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGTCTCCTGACTCCCAGTC 31 chr5qtel1M 64037 TCTGCCCTCT 64046 iv i C MIR3#SINE/MIR 30 CGTGCTCTCT 21 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.32 CpG sites = 17, Kimura (unadjusted) = 35.99 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.06 (6 / 96), avg. gap size = 2.17 (13 / 6) 21 20.93 6.98 2.22 chr5qtel1M 67198 67283 (932717) (GGCAGG)n#Simple_repeat 1 90 (0) m_b245s252i10 9723 chr5qtel1M 67198 GGCAGGCTCA-GGG-AGGGGCAGGGGAGGGGGCAGGGGGCGTGGC-CTGG 67244 vv - - vi vv v -vv (GGCAGG)n#Sim 1 GGCAGGGGCAGGGGCAGGGGCAGGGGCAGGGGCAGGGGCAGGGGCAGGGG 50 chr5qtel1M 67245 --GGGGCAGGGG-AGCGGCGGTGGGCGCGGCCCGGGGCCAGG 67283 -- - v i - iv v v - (GGCAGG)n#Sim 51 CAGGGGCAGGGGCAGGGGCAG-GGGCAGGGGCAGGGG-CAGG 90 Matrix = Unknown Transitions / transversions = 0.25 (3/12) Gap_init rate = 0.08 (7 / 85), avg. gap size = 1.14 (8 / 7) 14 24.35 3.64 1.79 chr5qtel1M 67208 67262 (932738) (GGGAG)n#Simple_repeat 1 56 (0) m_b245s252i11 9724 chr5qtel1M 67208 GGGAGGGGCAGGGGAGGGG-GCAG-GGGGCGTGGCCTGGGGGGCAGGGGA 67255 - - vi - v v vvv i v (GGGAG)n#Simp 1 GGGAGGGG-AGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGA 49 chr5qtel1M 67256 GCGGCGG 67262 v v (GGGAG)n#Simp 50 GGGGAGG 56 Matrix = Unknown Transitions / transversions = 0.22 (2/9) Gap_init rate = 0.06 (3 / 54), avg. gap size = 1.00 (3 / 3) 21 20.93 6.98 2.22 chr5qtel1M 67198 67283 (932717) (GGCAGG)n#Simple_repeat 1 90 (0) m_b245s252i10 9723 chr5qtel1M 67198 GGCAGGCTCA-GGG-AGGGGCAGGGGAGGGGGCAGGGGGCGTGGC-CTGG 67244 vv - - vi vv v -vv (GGCAGG)n#Sim 1 GGCAGGGGCAGGGGCAGGGGCAGGGGCAGGGGCAGGGGCAGGGGCAGGGG 50 chr5qtel1M 67245 --GGGGCAGGGG-AGCGGCGGTGGGCGCGGCCCGGGGCCAGG 67283 -- - v i - iv v v - (GGCAGG)n#Sim 51 CAGGGGCAGGGGCAGGGGCAG-GGGCAGGGGCAGGGG-CAGG 90 Matrix = Unknown Transitions / transversions = 0.25 (3/12) Gap_init rate = 0.08 (7 / 85), avg. gap size = 1.14 (8 / 7) 156 16.22 1.72 0.34 chr5qtel1M 67701 67990 (932010) (AG)n#Simple_repeat 1 294 (0) m_b245s252i13 9725 chr5qtel1M 67701 AGAGGAATAGGGAAACAGAGACACAGAGACAGAGGGGGAGAGAGACAGAG 67750 ii v i i v v v v i i v (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr5qtel1M 67751 ACAGAGAGAG-GGGAAAGACAGAGACAGAGACAGAGAGA-AGTAGAGACA 67798 v - i i v v v - - v (AG)n#Simple_ 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG-AGAGAGA 99 chr5qtel1M 67799 GAGAGACAGACAGAGAG-GGGAGAGATAGAGAGACAGAGAGAGAGAGA-A 67846 v v - i v v - (AG)n#Simple_ 100 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 149 chr5qtel1M 67847 GAGACAAAGACACACCCACAGAGAAAGACAGAGAGAGAGAGAGAGAGAGA 67896 v i v v vvv v i v (AG)n#Simple_ 150 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 199 chr5qtel1M 67897 GAGAGAGAGAGAGAGAGACAGAGAGAGAGAGAGAGAGACAGAGAGAGAGA 67946 v v (AG)n#Simple_ 200 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 249 chr5qtel1M 67947 GAGAGACAGAGGCAGAGACAGAGACAGAGACAGAGAGAGAG-GAG 67990 v iv v v v - (AG)n#Simple_ 250 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 294 Matrix = Unknown Transitions / transversions = 0.40 (12/30) Gap_init rate = 0.02 (6 / 289), avg. gap size = 1.00 (6 / 6) 256 25.76 1.52 0.00 chr5qtel1M 69545 69610 (930390) C MIR#SINE/MIR (87) 175 109 m_b245s601i21 9726 chr5qtel1M 69545 ACATCCCGCTGAGG-GGACAGGACTCATACTCCCCTTTCACAGATAAGGA 69593 v vv -i ii vv i vv ii v i i C MIR#SINE/MIR 175 ACAACCCTATGAGGTAGGTACTATTATTATCCCCATTTTACAGATGAGGA 126 chr5qtel1M 69594 AACTGAGTCACAGAGAG 69610 v C MIR#SINE/MIR 125 AACTGAGGCACAGAGAG 109 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.77 CpG sites = 8, Kimura (unadjusted) = 31.77 Transitions / transversions = 0.89 (8/9) Gap_init rate = 0.02 (1 / 65), avg. gap size = 1.00 (1 / 1) 239 13.61 1.59 6.67 chr5qtel1M 69557 69619 (930381) C MIR1_Amn#SINE/MIR (62) 168 109 m_b245s601i22 9726 chr5qtel1M 69557 GGGGACAGGACTCATACTCCCC-TTTCACAGATAAGGAAACTGAGTCACA 69605 i v v - vv - i i v ? C MIR1_Amn#SINE 168 GAGGTCAGTA-TCATTATCCCCATTTTACAGATGAGGAAACTGAGGCNCA 120 chr5qtel1M 69606 GAGAGAGGGTGAAG 69619 --- ? C MIR1_Amn#SINE 119 GAGA---GGTNAAG 109 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 15.54 CpG sites = 3, Kimura (unadjusted) = 15.54 Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.08 (5 / 62), avg. gap size = 1.00 (5 / 5) 143 25.92 0.55 1.11 chr5qtel1M 69833 70194 (929806) (CCT)n#Simple_repeat 1 360 (0) m_b245s252i14 9727 chr5qtel1M 69833 CCCCCTCCTCCTCTTCCTCCTTCACTTCCTTTGGCTTTCTCCTCTTCTTC 69882 i i i v i - ivv i i i i (CCT)n#Simple 1 CCTCCTCCTCCTCCTCCTCCTCCTCCTCC-TCCTCCTCCTCCTCCTCCTC 49 chr5qtel1M 69883 CTCCCTGTTTTCCTAATTCTCTTTCTCTTCCTCTTCTTCCTCCTCCTCTT 69932 iiv ii vv i i i i i i i (CCT)n#Simple 50 CTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT 99 chr5qtel1M 69933 CCTTTTCTTCTTCCTCCTCCTCCTCTTCTGCCTCCTTCTTCTCCTCTTCC 69982 ii i i i iv i i i (CCT)n#Simple 100 CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC 149 chr5qtel1M 69983 TCCTCCTTCTCCTCTTCCTTCTATTTCTGCTCTTCCTCCTCCTCTTCCTT 70032 i i i vi i v i i i (CCT)n#Simple 150 TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC 199 chr5qtel1M 70033 TTCTTCTTTCTCCTCCTCCTCTTCCT-CTTCTCCTTCCTCCTCCTGCTTT 70081 i i i i i - i - - i i (CCT)n#Simple 200 CTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC-TCCTCCTCCT-CCTC 247 chr5qtel1M 70082 CTCCTCTTTTTCTTCCTCTTCCTCCT-TTTTTCCTCTTCCTCTTCATCCT 70130 i ii i i -i ii i i v (CCT)n#Simple 248 CTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT 297 chr5qtel1M 70131 CCTCCTCCTCCTCCTCTTCCTTCTCTTCCTTCTCCTCCTCTTTCTACTAC 70180 i i i i i i v v (CCT)n#Simple 298 CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC 347 chr5qtel1M 70181 CCCTCCTCCTGCCT 70194 i - (CCT)n#Simple 348 TCCTCCTCCT-CCT 360 Matrix = Unknown Transitions / transversions = 5.17 (62/12) Gap_init rate = 0.02 (6 / 361), avg. gap size = 1.00 (6 / 6) 504 23.31 6.77 0.00 chr5qtel1M 71787 71919 (928081) MIR#SINE/MIR 100 241 (21) m_b245s601i23 9728 chr5qtel1M 71787 TTCTCTCACCACTGCCTGCCTCAGTTTCCTCAACTGTAAAATGGGGA-AA 71835 vii v v viv v - MIR#SINE/MIR 100 TTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAA 149 chr5qtel1M 71836 TACTAGCCCCT-CCTCCCCG----GTTGTGAGACTCGAATGG--TCATAT 71878 v iv - viv ---- iv ii i-- v i MIR#SINE/MIR 150 TAATAGTACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATAC 199 chr5qtel1M 71879 -TACAAAGCGCTTAGCACAGTGCCCGGCACGTGGCAGGCACT 71919 - ii v i i i i i i MIR#SINE/MIR 200 ATGTAAAGCGCTTAGAACAGTGCCTGGCACATAGTAAGCGCT 241 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.35 CpG sites = 18, Kimura (unadjusted) = 28.41 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.04 (5 / 132), avg. gap size = 1.80 (9 / 5) 83 1.29 0.00 0.00 chr5qtel1M 72945 73022 (926978) (C)n#Simple_repeat 1 78 (0) c_b245s251i1 9729 chr5qtel1M 72945 CCCCCCCCCCCCCCCCCCCCGCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 72994 v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 50 chr5qtel1M 72995 CCCCCCCCCCCCCCCCCCCCCCCCCCCC 73022 (C)n#Simple_r 51 CCCCCCCCCCCCCCCCCCCCCCCCCCCC 78 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 77), avg. gap size = 0.0 (0 / 0) 13 27.29 2.82 4.29 chr5qtel1M 73407 73477 (926523) (GGGGGCC)n#Simple_repeat 1 70 (0) m_b245s252i15 9730 chr5qtel1M 73407 GGGGGATTGGGGCCGGGGGGCGGGGAGGAAGTAACC-GGGGCCGGCCGGG 73455 viv v - vvi vii - -- (GGGGGCC)n#Si 1 GGGGGCCGGGGGCCGGGGGCCGGGG-GCCGGGGGCCGGGGGCCGG--GGG 47 chr5qtel1M 73456 TC-CGGGCCGCGGGGCGCGGGCC 73477 i -v v v v (GGGGGCC)n#Si 48 CCGGGGGCCGGGGGCCGGGGGCC 70 Matrix = Unknown Transitions / transversions = 0.50 (5/10) Gap_init rate = 0.07 (5 / 70), avg. gap size = 1.00 (5 / 5) 12 14.21 0.00 8.82 chr5qtel1M 73584 73620 (926380) (GCCCC)n#Simple_repeat 1 34 (0) m_b245s252i16 9731 chr5qtel1M 73584 GCCCCGCCCCTCCCCAGCCCCAAGGGCCCCCCCGCCC 73620 v - -- vv v (GCCCC)n#Simp 1 GCCCCGCCCCGCCCC-GCCCC--GCCCCGCCCCGCCC 34 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.08 (3 / 36), avg. gap size = 1.00 (3 / 3) 15 12.11 7.89 2.50 chr5qtel1M 73999 74036 (925964) (AC)n#Simple_repeat 1 40 (0) m_b245s252i17 9732 chr5qtel1M 73999 ACACACACTACCCAC-CTCACACACAC-CCCCCACAC-CAC 74036 - v - v - v v - (AC)n#Simple_ 1 ACACACAC-ACACACACACACACACACACACACACACACAC 40 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.11 (4 / 37), avg. gap size = 1.00 (4 / 4) 24 12.03 0.00 0.00 chr5qtel1M 74937 74972 (925028) (G)n#Simple_repeat 1 36 (0) m_b246s252i1 9733 chr5qtel1M 74937 GGGGGGGGGGGGGGGGGGAGCCCGGGGGGGGGGGGG 74972 i vvv (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 36 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 262 22.54 8.45 0.00 chr5qtel1M 75725 75795 (924205) C MIRc#SINE/MIR (155) 113 37 m_b246s601i0 9734 chr5qtel1M 75725 GGTTAAGGGACTTGCCC--GATCACACGGGCAGTGGCTGG---AGTCAC- 75768 v -- i i vi iiv --- i iv- C MIRc#SINE/MIR 113 GGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGG 64 chr5qtel1M 75769 ATTCGAACTCAGATCTTGCTGACTGCA 75795 i i i v v C MIRc#SINE/MIR 63 ACTCGAACCCAGGTCTTCCTGACTCCA 37 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 25.47 CpG sites = 10, Kimura (unadjusted) = 27.43 Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.04 (3 / 70), avg. gap size = 2.00 (6 / 3) 68 20.79 1.90 0.62 chr5qtel1M 76420 76577 (923423) (GAGA)n#Simple_repeat 1 160 (0) m_b246s252i2 9735 chr5qtel1M 76420 GAGAGATAGACAGAGAGAGAGAGAGAGAGAGACAGACAGACAGAGACAGA 76469 v v v v v v (GAGA)n#Simpl 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr5qtel1M 76470 GACAGAGAGAGAGTGAGAGAGATGGGGGGAGAGAGAGTAGTGAG-GAAGG 76518 v v vi i i - v - ii (GAGA)n#Simpl 51 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG-AGAGAGAGAGAG 99 chr5qtel1M 76519 AGGGAGGGAGGGAGGGAGGGAGAG-GAAAGA-AGGGAGGGAGGGAGAAAG 76566 i i i i i - i - i i i i (GAGA)n#Simpl 100 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 149 chr5qtel1M 76567 AGAAACAAAGA 76577 i v i (GAGA)n#Simpl 150 AGAGAGAGAGA 160 Matrix = Unknown Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.03 (4 / 157), avg. gap size = 1.00 (4 / 4) 202 20.83 4.17 0.00 chr5qtel1M 76797 76844 (923156) C MIR3#SINE/MIR (46) 162 113 m_b246s601i1 9736 chr5qtel1M 76797 TCATCCCGGCCAACCTCCTTGGTGCACAGATGAGGAAAC--AGGCCGAGA 76844 iv v i iiv vi -- v C MIR3#SINE/MIR 162 TCATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGA 113 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 24.58 CpG sites = 5, Kimura (unadjusted) = 24.58 Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.02 (1 / 47), avg. gap size = 2.00 (2 / 1) 227 14.82 0.77 0.00 chr5qtel1M 77167 77554 (922446) (CTCTCT)n#Simple_repeat 1 391 (0) m_b246s252i3 9737 chr5qtel1M 77167 CTTTCTCTCTGTCTTTCTGTCTCTCTGTCTCTCTGTCTCTCTGTCTCTCT 77216 i v i v v v v (CTCTCT)n#Sim 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chr5qtel1M 77217 GTCTGTCTCTCTCTTTCTGTCTCTCTCTGTCTCTCTGTCTCTCTCTCTCT 77266 v v i v v v (CTCTCT)n#Sim 51 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 100 chr5qtel1M 77267 CTCTCTCTCTCTCTGTCTCTCTCTCTCTGTCTGTCTGTCTCTGTCCGTCT 77316 v v v v v iv (CTCTCT)n#Sim 101 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 150 chr5qtel1M 77317 CTCTCTTTCTCTCTGTCTGTCTCTGTCTCTTTCTC-CTCTCTCTTTCTGT 77365 i v v v i - i v (CTCTCT)n#Sim 151 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 200 chr5qtel1M 77366 CTCT-TGCCTCTC-CTCTGTCTCTCTGTCTCTGTCTCTCTTTCTCTGTCT 77413 - vi - v v v i v (CTCTCT)n#Sim 201 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 250 chr5qtel1M 77414 GTCTCTGTCTCTCTGTCTCTCTCTGTCTCTGTCTCTGTCTCTCTCTCTCT 77463 v v v v v v (CTCTCT)n#Sim 251 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 300 chr5qtel1M 77464 GTGTCTCTCTCTCTCTCTCTGTCTCTCTCTGTCTGTCTCTGTCTCTGTCT 77513 v v v v v v v (CTCTCT)n#Sim 301 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 350 chr5qtel1M 77514 CTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTCTCTCTCTC 77554 v v v v v (CTCTCT)n#Sim 351 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 391 Matrix = Unknown Transitions / transversions = 0.21 (9/43) Gap_init rate = 0.01 (3 / 387), avg. gap size = 1.00 (3 / 3) 20 0.00 7.41 0.00 chr5qtel1M 77554 77580 (922420) (CA)n#Simple_repeat 1 29 (0) m_b246s252i4 9738 chr5qtel1M 77554 CACACACACACACACACACAC-CAC-CAC 77580 - - (CA)n#Simple_ 1 CACACACACACACACACACACACACACAC 29 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.08 (2 / 26), avg. gap size = 1.00 (2 / 2) 397 26.87 20.40 0.00 chr5qtel1M 79083 79283 (920717) C MIR#SINE/MIR (0) 262 21 m_b246s601i2 9739 chr5qtel1M 79083 AATAATAACTAACGTTTATATAGGGTTTACCAGGTGCCAGGCATGGTGCC 79132 i i vv v i i v iv v i C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCT 213 chr5qtel1M 79133 AATTGTT--------ATTGTCTCCTAAGGTCC----------CCTG-GCA 79163 vi i -------- iv v vvii ---------- i- vi C MIR#SINE/MIR 212 AAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAG 163 chr5qtel1M 79164 GTAGGTTATGTGATTGTGCCCACTTT-CAGGTAAGGAAACTGAGG--CAG 79210 vv i v i v i - i i -- C MIR#SINE/MIR 162 GTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAG 113 chr5qtel1M 79211 ACAGGCGAGATTATTCGCGCAGGGT--CATGGCTTGTCAGTG-------C 79251 v iv ii v i i v i -- ii v v ------- C MIR#SINE/MIR 112 AGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCC 63 chr5qtel1M 79252 GCGCATC---TCC-------CTGGCTCCAGGGCCGGTGCTCT 79283 v vv ---i ------- i v C MIR#SINE/MIR 62 GGGATTCGAACCCAGGCAGTCTGGCTCCAGAGCCCGTGCTCT 21 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 32.94 CpG sites = 28, Kimura (unadjusted) = 33.69 Transitions / transversions = 1.08 (28/26) Gap_init rate = 0.04 (9 / 200), avg. gap size = 4.56 (41 / 9) 14 19.56 0.00 2.70 chr5qtel1M 81206 81243 (918757) (CCCCCT)n#Simple_repeat 1 37 (0) m_b246s252i5 9740 chr5qtel1M 81206 CCCCCTCCCCCCTTCTCCTTCGCCCCCCCCCCCCCCTC 81243 - i i i v i i (CCCCCT)n#Sim 1 CCCCCT-CCCCCTCCCCCTCCCCCTCCCCCTCCCCCTC 37 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 17 0.00 0.00 0.00 chr5qtel1M 82998 83016 (916984) (G)n#Simple_repeat 1 19 (0) m_b246s252i6 9741 chr5qtel1M 82998 GGGGGGGGGGGGGGGGGGG 83016 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGG 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 13 27.51 4.48 1.45 chr5qtel1M 83722 83788 (916212) (GGGCGG)n#Simple_repeat 1 69 (0) m_b246s252i7 9742 chr5qtel1M 83722 GGGCGGGGGC--GGG-GGGGGCTGGGGAAGGAGCGGGGCCGTTTTGGGGG 83768 -- - v vi i v -vvv v (GGGCGG)n#Sim 1 GGGCGGGGGCGGGGGCGGGGGCGGGGGCGGGGGCGGGGGCG-GGGGCGGG 49 chr5qtel1M 83769 AGCCGGGCCCGGGGAAGGGG 83788 i v v v vi (GGGCGG)n#Sim 50 GGCGGGGGCGGGGGCGGGGG 69 Matrix = Unknown Transitions / transversions = 0.36 (4/11) Gap_init rate = 0.05 (3 / 66), avg. gap size = 1.33 (4 / 3) 15 20.17 3.64 3.64 chr5qtel1M 85461 85515 (914485) (ACCCCCC)n#Simple_repeat 1 55 (0) m_b246s252i8 9743 chr5qtel1M 85461 ACCCCCCAACCCCGAGCCTGCCCA-ACCGAACCCCCC-GGCCCTACCCCC 85508 v v - -v -v vv -vv i (ACCCCCC)n#Si 1 ACCCCCCACCCCCCA-CC-CCCCACCCCCCACCCCCCACCCCCCACCCCC 48 chr5qtel1M 85509 CACCCCC 85515 (ACCCCCC)n#Si 49 CACCCCC 55 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.07 (4 / 54), avg. gap size = 1.00 (4 / 4) 1452 44.70 0.00 0.00 chr5qtel1M 85793 89379 (910621) (AA)n#Simple_repeat 28 3614 (0) m_b246s252i9 9744 chr5qtel1M 85793 CAAAAAAAAACAAAAACCACAAAAAATCCAAAAAAAAAAAAAACAAAAAA 85842 v v vv v vvv v (AA)n#Simple_ 28 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 77 chr5qtel1M 85843 CCCAAAAAAACCAAAACCAAAACAAAAAAACCAAAAAAACAAAACAAAAA 85892 vvv vv vv v vv v v (AA)n#Simple_ 78 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 127 chr5qtel1M 85893 AAAACAAGACAAAAACCAAAAAAACCAAAAACACCAAAAAAAAACCAAAA 85942 v i v vv vv v vv vv (AA)n#Simple_ 128 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 177 chr5qtel1M 85943 AAACCAAAAAAAACAAAAAAAAAAAAAAAAAAAAACAAAAAAAAACAAAA 85992 vv v v v (AA)n#Simple_ 178 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 227 chr5qtel1M 85993 AAAAAAAAAACTAAAAAAAAAAAAACAAAACAAAAACGGGAAAATAAAAA 86042 vv v v viii v (AA)n#Simple_ 228 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 277 chr5qtel1M 86043 CAAAAACCAAACAAAAAATTAACAAAACAAACAAAAAAAAACACACAAAA 86092 v vv v vv v v v v v v (AA)n#Simple_ 278 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 327 chr5qtel1M 86093 CAAAAAAAAAAGGGGAAAGGAACCAAAAACAAGGGAAAAAAAAAAACCAA 86142 v iiii ii vv v iii vv (AA)n#Simple_ 328 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 377 chr5qtel1M 86143 AACAAAACAAAACAAAAAAAAAACAATAACAAAAACAAAAAAATAAAAAA 86192 v v v v v v v v (AA)n#Simple_ 378 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 427 chr5qtel1M 86193 AAGGGGAAAAAAAAACAAAACAAAACAAAAAAAAAAAAAAAAGGGGGGGG 86242 iiii v v v iiiiiiii (AA)n#Simple_ 428 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 477 chr5qtel1M 86243 GAAAAACACCCAACAAAACAAACAAACAAAAAACAACAACAACAAAACAA 86292 i v vvv v v v v v v v v v (AA)n#Simple_ 478 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 527 chr5qtel1M 86293 AAACAAAAACCCAAATTACCCACAGGACCAAAAACACAAAAAAAAACAAA 86342 v vvv vv vvv v ii vv v v v (AA)n#Simple_ 528 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 577 chr5qtel1M 86343 CAAACACAACAAAAAACAAAAACAAAAACAAATAAAATAAAACAAACAAC 86392 v v v v v v v v v v v v (AA)n#Simple_ 578 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 627 chr5qtel1M 86393 ACCAAATAAAACAAACAACCAAAAGGAAAAAAAAACACAAAAACAAAAAA 86442 vv v v v vv ii v v v (AA)n#Simple_ 628 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 677 chr5qtel1M 86443 ACAAAACAAAACAAAACAAACAAACAAACAAAAAAACAAGAACAAAAATA 86492 v v v v v v v v i v v (AA)n#Simple_ 678 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 727 chr5qtel1M 86493 AAAGCAAAAGAAACAGAAAAAAAAAAAACAGGCACCCAAATAAAAAACGG 86542 iv i v i v iiv vvv v vii (AA)n#Simple_ 728 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 777 chr5qtel1M 86543 AATAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAACAAAAAAAAACA 86592 v v v v (AA)n#Simple_ 778 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 827 chr5qtel1M 86593 AAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAACAGAAGACAACAGG 86642 i v i i v v ii (AA)n#Simple_ 828 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 877 chr5qtel1M 86643 AGAGGAGAAGAAGCAGAAAACAAAGAGAAACAGAGAAAAACAAGGAGGAA 86692 i ii i i iv i v i i v i i v ii ii (AA)n#Simple_ 878 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 927 chr5qtel1M 86693 GAGAAAAAAAGGAGGAGGGAACAGAGAACAGAAAGAAAGAGGACAGAGAA 86742 i i ii ii iii v i i v i i i ii v i i (AA)n#Simple_ 928 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 977 chr5qtel1M 86743 GAGACAAAGAGAGAGAGAACAGAGAGGGCAGAAAAAAAAGGCCAAACAGA 86792 i i v i i i i i v i i iiiv i iivv v i (AA)n#Simple_ 978 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1027 chr5qtel1M 86793 AGAGAGAAGAGAAGAGGAGGGGAAAAGAAAAAAGAAAGAAGAGAAGAGAG 86842 i i i i i i ii iiii i i i i i i i i (AA)n#Simple_ 1028 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1077 chr5qtel1M 86843 ACAAAAAAAAGAAGAGAGAAGAAAGAGAAAAAAGAAAAGGAGGAGAAAGA 86892 v i i i i i i i i ii ii i i (AA)n#Simple_ 1078 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1127 chr5qtel1M 86893 GAAAGGAGAAGAGAAAAAAGAGAGAAAGAAAGAAAAAGGAGGAGACAGAG 86942 i ii i i i i i i i i ii ii i v i i (AA)n#Simple_ 1128 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1177 chr5qtel1M 86943 AAGGGAAAAATGAAGGAAGAGGGAAACAGAAAAGAGAAAGACAGAGAAAA 86992 iii vi ii i iii v i i i i v i i (AA)n#Simple_ 1178 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1227 chr5qtel1M 86993 GAGAAGAGAAAAGAGAGAGAAAAAAGAAAAAAGAGAGAGAGAAGAACAAA 87042 i i i i i i i i i i i i i i i v (AA)n#Simple_ 1228 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1277 chr5qtel1M 87043 AAAAAAGAGACAGGAGAAGAGGAGAGACAGAGGGAGAGAGGACAGAAAGA 87092 i i v ii i i ii i i v i iii i i ii v i i (AA)n#Simple_ 1278 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1327 chr5qtel1M 87093 GAGAGAGGGAGGAGGGGGGAGAGAGGGAGAGAAGAGAAAAAAAGAAACAG 87142 i i i iii ii iiiiii i i iii i i i i i v i (AA)n#Simple_ 1328 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1377 chr5qtel1M 87143 AGAAGAAAGACAAGAGAAACAGAAAGAGAAGAGGAAGGAGAAAGAGAAAG 87192 i i i v i i v i i i i ii ii i i i i (AA)n#Simple_ 1378 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1427 chr5qtel1M 87193 AAGGGAGAGAGAAAGGGAGAAGAGAAAAAAGAAAAGGAAGACAGGAAAGA 87242 iii i i i iii i i i i ii i v ii i (AA)n#Simple_ 1428 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1477 chr5qtel1M 87243 AGGGACAGAGAAAAGAGAGGGGAACAGAGAAAACAAGGAGAAAACAGAGA 87292 iii v i i i i iiii v i i v ii i v i i (AA)n#Simple_ 1478 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1527 chr5qtel1M 87293 CAAGAAAAGAAAAAAGAGGACAGAGAAGAAGGAAAGAAGAGAGAAAGAGA 87342 v i i i ii v i i i ii i i i i i i (AA)n#Simple_ 1528 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1577 chr5qtel1M 87343 GGAAGAGAAAGAGAGACAAAAGAACAGAAGAACAAGAGGAGAGAGAAGAA 87392 ii i i i i i v i v i i v i ii i i i i (AA)n#Simple_ 1578 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1627 chr5qtel1M 87393 AGAAAAAGAGGGTGGGAGGGAAACAGGAAACAGAAAAAGAAAACAAGAAC 87442 i i iiiviii iii v ii v i i v i v (AA)n#Simple_ 1628 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1677 chr5qtel1M 87443 AGAAAAGACAGAAAAAAAAAAAACAGAAAAAAAAAAAAAAACGAAAAAAC 87492 i i v i v i vi v (AA)n#Simple_ 1678 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1727 chr5qtel1M 87493 AAACAAAGAAAAAAAAAGAAGAAGACAGAAAAGGGAAAGAAAGAAAGAAA 87542 v i i i i v i iii i i i (AA)n#Simple_ 1728 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1777 chr5qtel1M 87543 AACAAACAAAAAAACAAGAAAGAAAAAAAAAACAGAAAAAGACAAAAAAA 87592 v v v i i v i i v (AA)n#Simple_ 1778 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1827 chr5qtel1M 87593 AAAAAGAAAAAAAAGAGAAAAAAACAAAACAAGAGACAAGAAAAAGAGAG 87642 i i i v v i i v i i i i (AA)n#Simple_ 1828 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1877 chr5qtel1M 87643 ACAGGGAAAAAAAAAAAAAAGAAGGGGAAAACAAGAAAGAGAGAAAGAGA 87692 v iii i iiii v i i i i i i (AA)n#Simple_ 1878 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1927 chr5qtel1M 87693 AGGAGGAGGGGACAAAAACACAAACAAAAAACAGAACAAAGGAAAGGAAA 87742 ii ii iiii v v v v v i v ii ii (AA)n#Simple_ 1928 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1977 chr5qtel1M 87743 AACAAACAAAAAAAAAAAGAACAAAACAAAAAGCAAAACAAAAGAAAAAA 87792 v v i v v iv v i (AA)n#Simple_ 1978 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2027 chr5qtel1M 87793 AACAAGAAAAAAAAAAAGAAAAAAAAAGAAAGGGAGGGAGAGAAAGAGAG 87842 v i i i iii iii i i i i i (AA)n#Simple_ 2028 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2077 chr5qtel1M 87843 AGACAAAAGAAAAAGAGAGACAAGACAGAGAAACAGAAAAGAAGAGACAG 87892 i v i i i i v i v i i v i i i i v i (AA)n#Simple_ 2078 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2127 chr5qtel1M 87893 AAGAAGACAAGAGAGACAGAGAAGAGAGAGAAGAAGAGAAAAGAAGAGAG 87942 i i v i i i v i i i i i i i i i i i i i (AA)n#Simple_ 2128 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2177 chr5qtel1M 87943 AGAAGAAGGGAAACAGAAGGGAAAAAGAGAAAAAAAAAAAAAAAAAAAAA 87992 i i iii v i iii i i (AA)n#Simple_ 2178 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2227 chr5qtel1M 87993 AGAGGAAGAAGAGAAGAGAAGAAGAGAAGAGAGAGAGAAGGGAAGGGAAA 88042 i ii i i i i i i i i i i i i i iii iii (AA)n#Simple_ 2228 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2277 chr5qtel1M 88043 AGGAAAAAGAAACAAGAGAGGAGACAGAGAAAAGAAAGAGAGAACAAGAC 88092 ii i v i i ii i v i i i i i i v i v (AA)n#Simple_ 2278 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2327 chr5qtel1M 88093 AGAAGAGAGACAGAGAAACCAAAGAGAAAAGAGAGAGAAAGACAAACAGA 88142 i i i i v i i vv i i i i i i i v v i (AA)n#Simple_ 2328 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2377 chr5qtel1M 88143 AAAAAGAGAGAAGAGAGAAAGAGAAAGAGAACAGAAAGAGAGAGAAAAAG 88192 i i i i i i i i i i v i i i i i i (AA)n#Simple_ 2378 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2427 chr5qtel1M 88193 AGACAGAGAAGAAGAGACAGAGAAAAGAAGAGAGAGAAAGAAAGAGAAAG 88242 i v i i i i i v i i i i i i i i i i i (AA)n#Simple_ 2428 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2477 chr5qtel1M 88243 AGAGAGAAGAGAAAAAAGAAACAGAGAAAGAAAAAGAGAAAAGAAAGAGC 88292 i i i i i i v i i i i i i i iv (AA)n#Simple_ 2478 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2527 chr5qtel1M 88293 AGAGAGAAAGAGAGAGAGAGAAGAGAAAGAGAAAAGAGACAGAGAAAAGA 88342 i i i i i i i i i i i i i i i v i i i (AA)n#Simple_ 2528 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2577 chr5qtel1M 88343 AGAGAGAGGAAGAAAGGAAGGGACAAGAGAGAAAGGAAGGAGAAGAACAG 88392 i i i ii i ii iii v i i i ii ii i i v i (AA)n#Simple_ 2578 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2627 chr5qtel1M 88393 AGACAGAAGAGAGACAGAGAGAAAGGGGGAGGGAGAAGAGAAGGAAAGAA 88442 i v i i i i v i i i iiiii iii i i i ii i (AA)n#Simple_ 2628 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2677 chr5qtel1M 88443 GAGAAAAACAGGAAAAGACAGGAAAGAAAAAGAGAACAGAGAAAAGAAGA 88492 i i v ii i v ii i i i v i i i i (AA)n#Simple_ 2678 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2727 chr5qtel1M 88493 AAAGAAAAAAAAAAAAACAAAAAAGAAAAGAGAACAAAACAAAAGACAAA 88542 i v i i i v v i v (AA)n#Simple_ 2728 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2777 chr5qtel1M 88543 GAAGAAAAACAAAAAGAAGACAAAAAAAAGAAGGGAAAAAAAGAAGAAAG 88592 i i v i i v i iii i i i (AA)n#Simple_ 2778 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2827 chr5qtel1M 88593 AAAGGGAAAAGAAAAGAAGGAAAAGAAAACAAAAGAAAGAAAAAAACAAA 88642 iii i i ii i v i i v (AA)n#Simple_ 2828 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2877 chr5qtel1M 88643 GAAAAACAAAAAAAAGAAAAAAAAGAACAAAAAAAGAACAAAAAAGAAGA 88692 i v i i v i v i i (AA)n#Simple_ 2878 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2927 chr5qtel1M 88693 AGACAGGGAAACAAAGAAAAAGAAAAAAATAGAGAGAAAAAAAAAAGAAA 88742 i v iii v i i v i i i i (AA)n#Simple_ 2928 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2977 chr5qtel1M 88743 AGAGAGAGAAGAAGAAGAGGGGAAAAAAAGAAGAAAAAAGAGAAGAAAAG 88792 i i i i i i i iiii i i i i i i (AA)n#Simple_ 2978 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 3027 chr5qtel1M 88793 AGAAAGAGAAAGAGAAAGAGAGAGAAGGAGAGAAAGAGAGACAGAGAAGG 88842 i i i i i i i i i ii i i i i i v i i ii (AA)n#Simple_ 3028 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 3077 chr5qtel1M 88843 ACAAAAAAGAGAGACAGAGACAGAGAAGGACAAAAAGAGAGAGAGACAGA 88892 v i i i v i i v i i ii v i i i i i v i (AA)n#Simple_ 3078 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 3127 chr5qtel1M 88893 GAAGAGAGAGAACAAAGAGAAGAAGAGAGAAGAAGAACAGAGAAAGAGAG 88942 i i i i i v i i i i i i i i v i i i i i (AA)n#Simple_ 3128 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 3177 chr5qtel1M 88943 AGAGGGAGGGAGGGAGGAAAAGAAAAAAAAGAAAAAGGGGAGAGAAAGAG 88992 i iii iii iii ii i i iiii i i i i (AA)n#Simple_ 3178 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 3227 chr5qtel1M 88993 AGACAAACAACAGAAACAGAGAAAGCAGAGACAGAAAGAAAAACAGAAAA 89042 i v v v i v i i iv i i v i i v i (AA)n#Simple_ 3228 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 3277 chr5qtel1M 89043 AGAAAACAGAAAACAAGAAAAGACAAAGACAAAAACAGAGAGAAAGAAGA 89092 i v i v i i v i v v i i i i i (AA)n#Simple_ 3278 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 3327 chr5qtel1M 89093 AAAAGAAGAAAAGAGAAAGGAAGGACAAGAAAGAAAAAGAAAGAAAAAGA 89142 i i i i ii ii v i i i i i (AA)n#Simple_ 3328 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 3377 chr5qtel1M 89143 AAAAAGAAAAAAAAAAGAAAAAAAACAAGAGAGAAAGAAAACAAGAGAAA 89192 i i v i i i i v i i (AA)n#Simple_ 3378 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 3427 chr5qtel1M 89193 GGGAGAGGAAACAGAAGGAGAGAAAGAAGGAGACAGGAGAAGAGAAACAG 89242 iii i ii v i ii i i i ii i v ii i i i v i (AA)n#Simple_ 3428 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 3477 chr5qtel1M 89243 AAAAGAGAGAGAGAGACAGAAGAGAGAAAGAAAAGAAAAAGAGAGAAAGA 89292 i i i i i i v i i i i i i i i i i (AA)n#Simple_ 3478 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 3527 chr5qtel1M 89293 GAGAGGGAAAGAAGAGAAAACAGAAAGAAAGGGAGAGAGAACAGAGAAAA 89342 i i iii i i i v i i iii i i i v i i (AA)n#Simple_ 3528 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 3577 chr5qtel1M 89343 AAGAGAAGAGAAAAAAAAAGGGGAAAAAAAACAGAAA 89379 i i i i iiii v i (AA)n#Simple_ 3578 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 3614 Matrix = Unknown Transitions / transversions = 2.92 (850/291) Gap_init rate = 0.00 (0 / 3586), avg. gap size = 0.0 (0 / 0) 1703 26.06 5.20 3.15 chr5qtel1M 86551 89506 (910494) (AAAGAG)n#Simple_repeat 150 3147 (0) m_b246s252i12 9744 chr5qtel1M 86551 AAAAAAAAAAAAAAAAAAAAACAAAAAAAACAAAAAAAAACAAAAAAAAA 86600 i i i i i i i vi i i v i i v i i i (AAAGAG)n#Sim 150 GAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGA 199 chr5qtel1M 86601 AAAAAAAAAAAAAAAAAAAAGAAAAAAACAGAAGACAACAG-GAGAG-GA 86648 i i i i i i i i v - v - - i - (AAAGAG)n#Sim 200 AAGAGAAAGAGAAAGAGAAAGAGAAAGAGA-AAGAGAA-AGAGAAAGAGA 247 chr5qtel1M 86649 GA-AGAAGCAGAAA-ACAAAGAGAAACAGAGAAAAACAAGGAGGAAGAGA 86696 i - iv - v - - i v i i (AAAGAG)n#Sim 248 AAGAGAAAGAGAAAGAGAAAGAG-AA-AGAGAAAGAGAAAGAGAAAGAGA 295 chr5qtel1M 86697 AA-AAAAGGAG-GAGGGAACAGAG-AACAGAAAGAAAGAG-GACAGAGAA 86742 - i i -i i - - v i i - v (AAAGAG)n#Sim 296 AAGAGAAAGAGAAAGAGAA-AGAGAAAGAGAAAGAGAAAGAGAAAGAGAA 344 chr5qtel1M 86743 GAGACAAAGAGAGAGAGAACAGAGAGGGCAGAAAAAAAAGGCCAAACAG- 86791 - v i - ii - i i i vv v - (AAAGAG)n#Sim 345 -AGAGAAAGAGAAAGAGAA-AGAGAAAG-AGAAAGAGAAAGAGAAAGAGA 391 chr5qtel1M 86792 AAGAGAGAAGAG-AAGAGGAGGGGAAA-AGAAAAAAGAAAGAAGAGAAGA 86839 - - i i i - - i - - (AAAGAG)n#Sim 392 AAGAGA-AAGAGAAAGAGAAAGAGAAAGAG-AAAGAGAAAG-AGA-AAGA 437 chr5qtel1M 86840 GAGACAAAAAAAAGAAGAGAGA-AGAAAGAGAAAAAAGAAA-AGGAGGAG 86887 i v i i ii i - - i - i i (AAAGAG)n#Sim 438 GAAAGAGAAAGAGAAAGAGAAAGAGAAAGAG-AAAGAGAAAGAGAAAGAG 486 chr5qtel1M 86888 AAAGAGAAAG-GAGAAGAGAAA-AAAGAGAGAAAGAAAGAAAAAGGAGGA 86935 - - - i i -- i i i (AAAGAG)n#Sim 487 AAAGAGAAAGAGA-AAGAGAAAGAGAAAGAGAAAG--AGAAAGAGAAAGA 533 chr5qtel1M 86936 GACAGAG-AAGGGAAAAATGAAGGA-AGAGGGAAACAGAAAAGAGAAAGA 86983 v - i i - i - i i v - (AAAGAG)n#Sim 534 GAAAGAGAAAGAGAAAGA-GAAAGAGAAAGAGAAAGAG-AAAGAGAAAGA 581 chr5qtel1M 86984 CAGAGA-AAAGAG-AAGAGAAA-AGAGAGAGAAA-A-AAGAAAAAAGAGA 87028 v i - - - i - - ii i (AAAGAG)n#Sim 582 GAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGA 631 chr5qtel1M 87029 GAGAGAAGAACAAAAAAAAAGAGACAG-GAGAAGAG-GAGAGACAGAGGG 87076 i ii v i i v - - -i v ii (AAAGAG)n#Sim 632 AAGAGAAAGAGAAAGAGAAAGAGAAAGAGA-AAGAGAAAGAGAAAGAGAA 680 chr5qtel1M 87077 AGAGAGGACAGAAAGAGAGAGAGGGAG-GAGGGGGGAGAGAGGGAGAGAA 87125 -i v i ii - -ii i i ii (AAAGAG)n#Sim 681 AGAGA-AAGAGAAAGAGAAAGAGAAAGAGA-AAGAGAAAGAGAAAGAGAA 728 chr5qtel1M 87126 GAGAAAAAAAGAAACAGAGA-AGAAAGA-CAAGAGAAACAGAAAGAG-AA 87172 - i i v i - -v v - (AAAGAG)n#Sim 729 -AGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAA 777 chr5qtel1M 87173 GAGGAAGGAGAAAGAG-AA-AG-AAGGGAGAGAGAAAGGGAGAAGAGAAA 87219 - i - - - i i i - - (AAAGAG)n#Sim 778 GA-GAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGA-AAGAG-AA 824 chr5qtel1M 87220 AAAGAAA-AGGAAGA-CAGGAAAGAAGGGACAGAGAAA-AGAGAGGGGAA 87266 i - i -v i i - i v - - i i (AAAGAG)n#Sim 825 AGAGAAAGAGAAAGAGAAAGAGA-AAGAGAAAGAGAAAGAGA-AAGAGAA 872 chr5qtel1M 87267 CAGAGAAA-ACAAGGAGAAA-ACAGAGA-CAAGA-AAAGAAAAAAGAGGA 87312 - - v i - v i -v - - i - (AAAGAG)n#Sim 873 -AGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAG-AGAAAGA-GA 919 chr5qtel1M 87313 CAGAGAAGAAGGAAAGA-AGAGAGAAAGAGAGGAAGAGAAAGAGAGACA- 87360 v - ii - i -- i v - (AAAGAG)n#Sim 920 AAGAGAA-AGAGAAAGAGAAAGAGAAAGAGA--AAGAGAAAGAGAAAGAG 966 chr5qtel1M 87361 AAAGA-ACAGAAGAACAAG-AGGAGAGAGAAGAAAGAAAAAGAGGGTGGG 87408 - v - vi - i i - i iiv i (AAAGAG)n#Sim 967 AAAGAGAAAG-AGAAAGAGAAAGAGAAAG-AGAAAGAGAAAGAGAAAGAG 1014 chr5qtel1M 87409 AGGGAAACAG-GAAACAGAAAAAGAAAACAAGAACAGAAA-AGACAGAAA 87456 ii i v - v i - v ii v - v - i (AAAGAG)n#Sim 1015 AAAGAGAAAGAGAAAGAGAAAGAG-AAAGAGAAAGAGAAAGAGAAAG-AG 1062 chr5qtel1M 87457 AAAAAAAAACAGAAAAAAAAAAAAAAACGA-AAAAACAAACAAAGAAAAA 87505 i i v i i i i - - i v v i i i i (AAAGAG)n#Sim 1063 AAAGAGAAAGAGAAAGAGAAAGAGAAA-GAGAAAGAGAAAGAGAAAGAGA 1111 chr5qtel1M 87506 AAAAGAAGAAGACAGA-AAAGGGAAAGAAAGAAAGAAAAACAAACA-AAA 87553 i ii v - i i i i i v v - (AAAGAG)n#Sim 1112 AAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAA 1161 chr5qtel1M 87554 -A-AACAAGAAAGAAAAAAAAAACAGAAAAAGACAAAAAAAAAAAAGAAA 87601 - - vi i i i - i -i i i i (AAAGAG)n#Sim 1162 GAGAAAGAGAAAGAGAAAGAGAA-AGAGAAAGA-GAAAGAGAAAGAGAAA 1209 chr5qtel1M 87602 -AAAAAGAGAAAAAAACAAAACAAGAGACAAGAAAAAGAGAGACAGGGAA 87650 - i i i v i iv - i - - i (AAAGAG)n#Sim 1210 GAGAAAGAGAAAGAGAAAGAGAAAGAGA-AAGAGAAAGAGA-A-AGAGAA 1256 chr5qtel1M 87651 A-A-AAA-AAAAAAAGAAGGGGAAA-A-CAAGAAAGAGAGAAAGAGAAGG 87695 - - - i i i i - -v i i i (AAAGAG)n#Sim 1257 AGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAG 1306 chr5qtel1M 87696 AGGAGGGGACA-A-AAACACAAACA-AAAAACAGA-ACAAAG-GAAAG-G 87739 i i i v - - v v v - i v i - v - - (AAAGAG)n#Sim 1307 AGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAG 1356 chr5qtel1M 87740 AAAAACAAACAAAAAAAAAAAGAACAAAACAAAAAGCAAAACAAA-AGAA 87788 i v v i i i iv i v i v i v - (AAAGAG)n#Sim 1357 AAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAA 1406 chr5qtel1M 87789 AAAAAACAAGAAAAAAAAAAAGAAAAAAAAAGAAAGGGAGGGAGAGAAAG 87838 i i vi i i i i i i ii ii (AAAGAG)n#Sim 1407 AGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAG 1456 chr5qtel1M 87839 AGAGAGACAAAAGAAAAAGAGAGACAAGACAGAGAAACAGAAA-AG-AAG 87886 i -i i - vi v v - - (AAAGAG)n#Sim 1457 AGAAAGA-GAAAGAGAAAGAGA-AAGAGAAAGAGAAAGAGAAAGAGAAAG 1504 chr5qtel1M 87887 AGACAGAAGAAGACAAGAGAGACAGAG-AAGAGAGAGAAGAAGAGAAA-A 87934 v ii v - v - i ii - (AAAGAG)n#Sim 1505 AGAAAGAGAAAGAGAA-AGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGA 1553 chr5qtel1M 87935 G-AAGAGAGAGAAGAAGGGAAACAGAAGGGAAAAAGAGAAAAAAAAAAAA 87983 - i ii i v -i i - i i i (AAAGAG)n#Sim 1554 GAAAGAGAAAGAGAAAGAGAAAGAGAA-AGAGAAAGAG-AAAGAGAAAGA 1601 chr5qtel1M 87984 AAAAAAAAAAGAGGAAGAAGAGAAGAGAAGAAGAGAAGAGAGAGAG-AAG 88032 i i i i - - ii - i - (AAAGAG)n#Sim 1602 GAAAGAGAAAGAGAAAG-AGA-AAGAGAAAGAGA-AAGAGAAAGAGAAAG 1648 chr5qtel1M 88033 -GGAAGGGAAAAGGAAAAAGAAACAAGAGAGGAGACAGAGAAA-AGAAAG 88080 - i i ii i -i - i v - (AAAGAG)n#Sim 1649 AGAAAGAGAAAGAGAAAGAGAAA-GAGA-AAGAGAAAGAGAAAGAGAAAG 1696 chr5qtel1M 88081 AGAGAACAAGACAGA-AGAGAGACAGAGAAA-CCAAAGAGAAA-AGAGAG 88127 - -i v - i v -vv - i (AAAGAG)n#Sim 1697 AGA-AA-GAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAG 1744 chr5qtel1M 88128 AGAAAGACAAACAGAAA-AAAGAGAGAAGAGAGAAAGAGAAAGAG-AACA 88175 v v - i i - - v (AAAGAG)n#Sim 1745 AGAAAGAGAAAGAGAAAGAGAAAGAGAA-AGAGAAAGAGAAAGAGAAAGA 1793 chr5qtel1M 88176 GAAAGAGAGAGAAAAAGAGACAGAGAAGAAGAGACAGAGAAA-AGAAGAG 88224 i i v - - v - - (AAAGAG)n#Sim 1794 GAAAGAGAAAGAGAAAGAGAAAGAG-A-AAGAGAAAGAGAAAGAGAA-AG 1840 chr5qtel1M 88225 AGAGAAAGAAAGAGAAAGAGAGAGA-AGAGAAAAAAGAAACAGAGAAAGA 88273 i i i - i - i i v (AAAGAG)n#Sim 1841 AGAAAGAGAAAGAGAAAGAGAAAGAGAAAG-AGAAAGAGAAAGAGAAAGA 1889 chr5qtel1M 88274 AAAAGAGAAA-AGAAAGAGCAGAGAGAAAGAGAGAGAGAGAAGAGAAAGA 88322 i - - i i - (AAAGAG)n#Sim 1890 GAAAGAGAAAGAGAAAGAG-AAAGAGAAAGAGAAAGAGA-AAGAGAAAGA 1937 chr5qtel1M 88323 GAAAAGAGACAGAGAAA-AGAAGAGAGAGGAAGAAAG-GAAGGGACAAGA 88370 - v - - iii - -i v - (AAAGAG)n#Sim 1938 G-AAAGAGAAAGAGAAAGAGAA-AGAGAAAGAGAAAGAGAA-AGAGAA-A 1983 chr5qtel1M 88371 GAGAAAG-GAAGGAG-AAGA-ACAGAGACAGAAGAGAGACAGAGAGAAAG 88417 - i - - v v - i v i (AAAGAG)n#Sim 1984 GAGAAAGAGAAAGAGAAAGAGAAAGAGAAAG-AGAAAGAGAAAGAGAAAG 2032 chr5qtel1M 88418 GGGGAGGGAGAAGAG-AAG-GAAAGA-AGAGAAAAACAGGAAAAGACAG- 88463 i ii i - - - - i i v i i v - (AAAGAG)n#Sim 2033 AGAAAGAGA-AAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGA 2081 chr5qtel1M 88464 GAAAGAAAAAGAGAACAGAGAAA-AG-AAGA-AAAGAAAAAAAAAAAAAC 88510 i - - - - i i i i - (AAAGAG)n#Sim 2082 GAAAGAGAAAGAGAA-AGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGA- 2129 chr5qtel1M 88511 AAAAAAGAAA-AGAGAACA-AAACA-AAAGACAAAGAAGAAAAACAAAAA 88557 i i - - v - v - v - i v i (AAAGAG)n#Sim 2130 GAAAGAGAAAGAGA-AAGAGAAAGAGAAAGAGAAAG-AGAAAGAGAAAGA 2177 chr5qtel1M 88558 G-AAGACAAA-AAAAAGA-AGGGAAAAAAAGAAGAAAGAAAGGGAAA-AG 88603 - v - i - ii i i - i i - (AAAGAG)n#Sim 2178 GAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAA-AGAGAAAGAGAAAGAG 2226 chr5qtel1M 88604 AAA-AG-AAG-GAAA-AGAAA-ACAAA-AGAAAGAAAAAAACAAAGA-AA 88646 - - - - - v - i i v - (AAAGAG)n#Sim 2227 AAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAA 2276 chr5qtel1M 88647 A-ACAAA-AAAAAGAAAAAAAAGAACAAAAAAAGAACAAAAAAGAAGAAG 88694 - v - i i i ii v i i vi i - - (AAAGAG)n#Sim 2277 AGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAG-AGAA- 2324 chr5qtel1M 88695 ACAGGGAAACAAAGAAAAAGAAAAAAATAGAGAGAAA-AAAAAAAGAAA- 88742 v ii i v i i i v i - i i - (AAAGAG)n#Sim 2325 AGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAG 2374 chr5qtel1M 88743 AGAGAGAG-AAGAAGAAGAG-GGGAAAAAAAGAAGAAAAAAGAG-AAGA- 88788 i - ii -ii i i ii i - - (AAAGAG)n#Sim 2375 AGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAG 2424 chr5qtel1M 88789 AAAGAGAAAGAGAAAGAGAAAGAGAGAGAAGGAGAGAAAGAGAGACAGAG 88838 i iii - - (AAAGAG)n#Sim 2425 AAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGA-A-AGAG 2472 chr5qtel1M 88839 AAGGACAAA-AAAGAGAGACAGAGACAGAGAAGGACAAAAAGAGAGAGAG 88887 i v - i i v v i v i i i (AAAGAG)n#Sim 2473 AAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAA 2522 chr5qtel1M 88888 ACAGAGAAGAGAGAGAACAAAGAG-AAGA-AGAGAGAAGAAGAACAGAGA 88935 v - i - v - - i ii - (AAAGAG)n#Sim 2523 AGAGA-AAGAGAAAG-AGAAAGAGAAAGAGAAAGAGAAAGAGAA-AGAGA 2569 chr5qtel1M 88936 AAGAGAGAGAGGGAGGGAGGGAGGAAAAGAAA-AAAAAGAAAAAG-GGGA 88983 i ii i ii i i - i i - ii (AAAGAG)n#Sim 2570 AAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAA 2619 chr5qtel1M 88984 GAGAAAGAG--AGACAAACA-ACAGAAACAGAGAAAGCAGAGACAGAAAG 89030 -- v v - v i v - i v (AAAGAG)n#Sim 2620 GAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAG-AGAAAGAGAAAG 2668 chr5qtel1M 89031 AAAAACAGAAAAAGAAAACAGAAA-A-CAAGA-AAAGACAAAGACAAAAA 89077 i v i - v - -v - v v i (AAAGAG)n#Sim 2669 AGAAAGAGAAAGAG-AAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGA 2717 chr5qtel1M 89078 CAGAGAGAAAGAAGAAAAAG-AAGA-AAAGAGAAAG-GAAGGACAAGAAA 89124 v i - i - - - i v - i (AAAGAG)n#Sim 2718 GAAAGAGAAAG-AGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAA-AGA 2765 chr5qtel1M 89125 GAAAAAGAAAGAAAAAGA-AAAAAGAAA-AAAAAAAGAAA-AAAAACA-A 89170 i i - i - i i - i v - (AAAGAG)n#Sim 2766 GAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGA 2815 chr5qtel1M 89171 GAGAGAAAGAAAACAAGAGAAAGGGAGAG-GAAACAGAAGGAGAGAAAGA 89219 i - i - i i - v i i i (AAAGAG)n#Sim 2816 AAGAGAAAG-AGA-AAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGA 2863 chr5qtel1M 89220 AGGAGACAG-GAGAAGAGAAACAGAAAAGAGAGAGAGAGACAGAAGAGAG 89268 i v - - v - i i v - (AAAGAG)n#Sim 2864 AAGAGAAAGAGA-AAGAGAAAGAG-AAAGAGAAAGAGAAAGAGAA-AGAG 2910 chr5qtel1M 89269 AAAGA-AAAGAAAAAGAGAGAAAGAGAGAGGGAAAGA-AGAGA-AAACAG 89315 - - i - i i - i - v (AAAGAG)n#Sim 2911 AAAGAGAAAG-AGAA-AGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAG 2958 chr5qtel1M 89316 -AA-AGAAAGGGAGAGAGAACAGAGAAAAAAGAGAAGAGAAAAAAAAAGG 89363 - - i i - - i - i i i (AAAGAG)n#Sim 2959 AAAGAGAAAGAGAAAGAGAA-AGAG-AAAGAGA-AAGAGAAAGAGAAAGA 3005 chr5qtel1M 89364 GGAAAAAAAACAGAAACAGAGACAG-AAGAGACAGAGAGAGA-AGAGAAG 89411 i i i v v i v - v i - i ii (AAAGAG)n#Sim 3006 GAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGA 3055 chr5qtel1M 89412 AAGAG-AAGAGAGAGAGAAGGAAGAGAGAGAGAGACACAGAGAAACAGAG 89460 - i i - i i v v v i (AAAGAG)n#Sim 3056 AAGAGAAAGAGAAAGAGAAAG-AGAAAGAGAAAGAGAAAGAGAAAGAGAA 3104 chr5qtel1M 89461 AGAGAGAAGAGAAGAAGAGAAAGAGGACAG-GAAAGGGAAAAAAAAA 89506 - - - - v - i i i (AAAGAG)n#Sim 3105 AGAGA-AAGAG-A-AAGAGAAAGA-GAAAGAGAAAGAGAAAGAGAAA 3147 Matrix = Unknown Transitions / transversions = 2.83 (377/133) Gap_init rate = 0.08 (238 / 2955), avg. gap size = 1.01 (240 / 238) 1452 44.70 0.00 0.00 chr5qtel1M 89969 92954 (907046) (AA)n#Simple_repeat 4204 7189 (0) m_b246s252i10 9745 chr5qtel1M 89969 CAAAAACAAAACAAAAAATCAAAAAACAAACAAACAAAAAAAATAAAACA 90018 v v v vv v v v v v (AA)n#Simple_ 4204 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 4253 chr5qtel1M 90019 AACAACAAAAAAACACAAAACCAAAAAACAAGCCCAAAAAACAAAAAAAC 90068 v v v v vv v ivvv v v (AA)n#Simple_ 4254 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 4303 chr5qtel1M 90069 AAAAAAACAAACAAAAGGGAACGAAACCCAAAAAACAAAACAAAAACAAA 90118 v v iii vi vvv v v v (AA)n#Simple_ 4304 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 4353 chr5qtel1M 90119 AAAACAAAGAAACAAAAAAACAAAACAAAAACAAAAAAAAAAACAAAACA 90168 v i v v v v v v (AA)n#Simple_ 4354 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 4403 chr5qtel1M 90169 AAACAAAAAACAAAAAAAAAAAAAAACCATAAAAAAAACACAACAATTTA 90218 v v vv v v v v vvv (AA)n#Simple_ 4404 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 4453 chr5qtel1M 90219 ATAACAAAAAAACAAATAAACAACAAACAACAACCACCCAAAAAAAAAAT 90268 v v v v v v v v vv vvv v (AA)n#Simple_ 4454 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 4503 chr5qtel1M 90269 AACAGAAAACAAAACAAAAAACAAAAAAAAAACAAAAAAAAACAAAAACA 90318 v i v v v v v v (AA)n#Simple_ 4504 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 4553 chr5qtel1M 90319 ACCAAAAACAAAAAAAAGGAATAAAAAAAGAAGAAAAACAAGAAACAGAG 90368 vv v ii v i i v i v i i (AA)n#Simple_ 4554 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 4603 chr5qtel1M 90369 AAAAAAAAAAAAAAAAGAGAGAGAAGAGAGAGAGAGAGGAACAGAAAAGA 90418 i i i i i i i i i i ii v i i (AA)n#Simple_ 4604 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 4653 chr5qtel1M 90419 GAAGAGAGAGAACAGAAGAGACAGAGAAAGAGAACAGGAACAGAGAGAAA 90468 i i i i i v i i i v i i i i v ii v i i i (AA)n#Simple_ 4654 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 4703 chr5qtel1M 90469 AGAGAGGAAAAGAGAAGGGAAAGAAGAGAAAAAAAACAGAACAGAGAGGA 90518 i i ii i i iii i i i v i v i i ii (AA)n#Simple_ 4704 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 4753 chr5qtel1M 90519 GAGAAGAGGAGAAAGAAAAAAAAGGAGAAAGAACAAGAAGAGAACAGAAA 90568 i i i ii i i ii i i v i i i v i (AA)n#Simple_ 4754 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 4803 chr5qtel1M 90569 ACAGAAAGGAAGGAAAAAGGGAAAAGAAAAACAAAAAGAGAGAACAGAGG 90618 v i ii ii iii i v i i i v i ii (AA)n#Simple_ 4804 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 4853 chr5qtel1M 90619 ACAGAAAAGAGAACAAGAAAGGAAAAAGAAAAAAAAAAAAAAGAAAACAA 90668 v i i i v i ii i i v (AA)n#Simple_ 4854 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 4903 chr5qtel1M 90669 AAGAAAAAAAAGCAAAAACAAGAGGAAAAAAGAGAAAAACAGAGAAAAGA 90718 i iv v i ii i i v i i i (AA)n#Simple_ 4904 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 4953 chr5qtel1M 90719 AAAAAACAAGAGAGAGGGGGAAAGGGAAAAGGGAGGAAGAAGAGACAAAA 90768 v i i i iiiii iii iii ii i i i v (AA)n#Simple_ 4954 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5003 chr5qtel1M 90769 AAACAAAAGAACAAACAAGAAAACAAAAAAGAAAAGAACAGACAAAGAAG 90818 v i v v i v i i v i v i i (AA)n#Simple_ 5004 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5053 chr5qtel1M 90819 AAGAAAAGAAAAAGAACAAAGAAAAAAAAACAGGACACAAAAAAAAAGAA 90868 i i i v i v ii v v i (AA)n#Simple_ 5054 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5103 chr5qtel1M 90869 AAGACAAAGAAAAACCCAAGAGAACAAAGACAAAAAAAAAAAAAGAAAGA 90918 i v i vvv i i v i v i i (AA)n#Simple_ 5104 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5153 chr5qtel1M 90919 AACAGAAGAAAGGGAGAAAAAAAAGACAGAGAGGAAAACACAGACACAAA 90968 v i i iii i i v i i ii v v i v v (AA)n#Simple_ 5154 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5203 chr5qtel1M 90969 GAAAACAAAAAGACAGAAAAAGAAAAAAAAAGAGAGAAACAGACAAAAAA 91018 i v i v i i i i i v i v (AA)n#Simple_ 5204 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5253 chr5qtel1M 91019 CAAAGAAAAAAGGAAAAAGGAAAAACAAGACAGAAAACAAAAGACAAAAA 91068 v i ii ii v i v i v i v (AA)n#Simple_ 5254 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5303 chr5qtel1M 91069 AGACAAAACGGGAAAAGGAAGACAAAAAAGAAAAAGAGAGAGAAAAAGAA 91118 i v viii ii i v i i i i i i (AA)n#Simple_ 5304 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5353 chr5qtel1M 91119 GAAGAGAGGAAAGAGAACAGAGAGAAGAGAAGGGAAGGGGGAGGGAGAGA 91168 i i i ii i i v i i i i i iii iiiii iii i i (AA)n#Simple_ 5354 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5403 chr5qtel1M 91169 AAGAGAAACAAAGAAAAGGAAAGAGAAAAGAGAGAGACAAGAAGACAGAG 91218 i i v i ii i i i i i i v i i v i i (AA)n#Simple_ 5404 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5453 chr5qtel1M 91219 AAAAGAGAGGAGAGAAGAGAAAAGAAAAAAAAGAGAAACAGAGAAAAGAG 91268 i i ii i i i i i i i v i i i i (AA)n#Simple_ 5454 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5503 chr5qtel1M 91269 AACAGAGAAAGAAGAAGAGACAAAACAGAGAGAAAAAGAAACAGAGAGCG 91318 v i i i i i i v v i i i i v i i ivi (AA)n#Simple_ 5504 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5553 chr5qtel1M 91319 GGGAAAGAGAAAAGAGAGAACAAAGAGAAAAAGAAAGAAGAGAGAAAGAG 91368 iii i i i i i v i i i i i i i i i (AA)n#Simple_ 5554 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5603 chr5qtel1M 91369 AAGAGAAAAGAGAAGAAAACAGAGACAAGAGAAAAGGGAGAACAGAGAAA 91418 i i i i i v i i v i i iii i v i i (AA)n#Simple_ 5604 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5653 chr5qtel1M 91419 CAAGAAAGAAGACAGAGAGAGAAGAGACAGAGAAAGAGAGAAAGAAAGAG 91468 v i i i v i i i i i i v i i i i i i i i (AA)n#Simple_ 5654 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5703 chr5qtel1M 91469 AAGAAAAGAAGAAAAGAGGAACAGGAGACAGAGAAGAAGAGGGACAGAGA 91518 i i i i ii v ii i v i i i i iii v i i (AA)n#Simple_ 5704 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5753 chr5qtel1M 91519 GAGAGAAAAGAGAGAAAGAGACAGAAGAGAGAGACAGAGAAGAAGAAAGA 91568 i i i i i i i i v i i i i i v i i i i i (AA)n#Simple_ 5754 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5803 chr5qtel1M 91569 ACAAGAACAAAAGGGGGAAGAGAGAAAGGACAGAAGAGAAAAAGAGAGAG 91618 v i v iiiii i i i ii v i i i i i i i (AA)n#Simple_ 5804 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5853 chr5qtel1M 91619 AGACAGAGACAGAGAGAGAAAGAGAAGGAAAAGAAAAGAGACAAAAGAGA 91668 i v i i v i i i i i i ii i i i v i i (AA)n#Simple_ 5854 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5903 chr5qtel1M 91669 AGAGAGAAAAGAGAGAAAAGAGAGAAAGAGAAGAGAAAGAGACAGAGAAC 91718 i i i i i i i i i i i i i i i v i i v (AA)n#Simple_ 5904 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5953 chr5qtel1M 91719 AAGAGAAAAAAGAGAGAGACAAGAGACAGAAAAAAGAAGAAGAGAGAAAG 91768 i i i i i i v i i v i i i i i i i (AA)n#Simple_ 5954 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6003 chr5qtel1M 91769 AGAACAGAGAAGAAAAAGAGGGAAAGAGAGAAAGAGAAGAGCCAGAGAGA 91818 i v i i i i iii i i i i i i ivv i i i (AA)n#Simple_ 6004 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6053 chr5qtel1M 91819 ACAGAAAGAAAGAAAGAAAAGAGTCCAAAACGAGAGAAGAAGAGAGAAAA 91868 v i i i i i ivvv vi i i i i i i (AA)n#Simple_ 6054 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6103 chr5qtel1M 91869 GAAGGAGAAGCAGAGACAGAAGAGAAAGAGAAAAGAGACAGAGAAGAAAG 91918 i ii i iv i i v i i i i i i i v i i i i (AA)n#Simple_ 6104 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6153 chr5qtel1M 91919 AAGGAGAGAACGAGAGAAAAGAGAGAAAGAGAGAGAAAGAGAGAAAGAGG 91968 ii i i vi i i i i i i i i i i i i i ii (AA)n#Simple_ 6154 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6203 chr5qtel1M 91969 AAGAGAAGAAAGAGAAGAGAGAAAAGAGACAGAAGAGAAGAGAGAAAGAG 92018 i i i i i i i i i i v i i i i i i i i (AA)n#Simple_ 6204 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6253 chr5qtel1M 92019 AAAAGAGAGGGGAAAGAAAGAAGAGAAGAAAGAGAAGAAAGAAGAGAAAG 92068 i i iiii i i i i i i i i i i i i (AA)n#Simple_ 6254 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6303 chr5qtel1M 92069 AGAAGAGAAAGACAGAGACAAGAGAAGAGAAAAGACAAACGAAGAGAAAG 92118 i i i i v i i v i i i i i v vi i i i (AA)n#Simple_ 6304 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6353 chr5qtel1M 92119 AGAGAAGAGACAAAAACAAACAAAAACAAAAAAAAGAAACAGAAACAGAA 92168 i i i i v v v v i v i v i (AA)n#Simple_ 6354 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6403 chr5qtel1M 92169 AAAGAAAAGGAAGAAGGAAAGGAAAAAGAAAGAGAACAGAAAAAAAAAAA 92218 i ii i ii ii i i i v i (AA)n#Simple_ 6404 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6453 chr5qtel1M 92219 AGGAACAAAAAAAGGAACAGAGAAGAAATGAAAAAAGACAACAAAAAAAG 92268 ii v ii v i i i vi i v v i (AA)n#Simple_ 6454 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6503 chr5qtel1M 92269 AAAGGAACAAAGGAAGAAAAAAGAAAAACAAACAAAAAAAAAAAAGAAAA 92318 ii v ii i i v v i (AA)n#Simple_ 6504 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6553 chr5qtel1M 92319 GGAGAAAGAAACAAGGAACAAAACGGGAAAAAAAACAAGACAAAAGAAAA 92368 ii i i v ii v viii v i v i (AA)n#Simple_ 6554 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6603 chr5qtel1M 92369 AAGAAGGGCAAAGAAAAAGAAAAATAAGAGAAGAAAAAAGAGAAGAAAAA 92418 i iiiv i i v i i i i i i (AA)n#Simple_ 6604 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6653 chr5qtel1M 92419 AAACAACAAAGAGACAAAAAAGCAAACACAAGGAAAAACACAAAAACAAA 92468 v v i i v iv v v ii v v v (AA)n#Simple_ 6654 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6703 chr5qtel1M 92469 GAAGAAAAAACAAAAAAGAAAGAAAAAAAAAAAGAAGAAAAGGGAAGAGA 92518 i i v i i i i iii i i (AA)n#Simple_ 6704 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6753 chr5qtel1M 92519 GAAAAAGGAAAGCAAAAAAAGCAAGGAAAAGAAACAAAAAGAAAGGACAC 92568 i ii iv iv ii i v i ii v v (AA)n#Simple_ 6754 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6803 chr5qtel1M 92569 AAACACAAAGAAACAAACAAAGAGGAAAGAAAACAAAAAGACAGAAAAAA 92618 v v i v v i ii i v i v i (AA)n#Simple_ 6804 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6853 chr5qtel1M 92619 GACAAAAACAAAAGGAAAAAAATAGAACAAGGAAAGAAAAAAAAAGAAAG 92668 i v v ii v i v ii i i i (AA)n#Simple_ 6854 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6903 chr5qtel1M 92669 GAAAAACAAGAAGAAAAAAAACAAGAAAACAAAAGGAAAAGAAGAAAACA 92718 i v i i v i v ii i i v (AA)n#Simple_ 6904 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6953 chr5qtel1M 92719 AAAAAACGGAAGGAAAAGGAAAGAAGAAAAAAGAAAAAAAGAAGAAAAAA 92768 vii ii ii i i i i i (AA)n#Simple_ 6954 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 7003 chr5qtel1M 92769 ACAAAAGGAAACAAAGAAGAAAAGAAAGCACAAAGAAGGAAAAGAAAGAC 92818 v ii v i i i iv v i ii i i v (AA)n#Simple_ 7004 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 7053 chr5qtel1M 92819 AAAGGAAAAACAAAAGAAAAGACAAAAAAGGGAAAAAAAAAAAAAGAACA 92868 ii v i i v iii i v (AA)n#Simple_ 7054 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 7103 chr5qtel1M 92869 AACAAAGAAAAAAAAAGCAGAAAGGAAAAAAAGAAGGGGAAAAAAAAACA 92918 v i iv i ii i iiii v (AA)n#Simple_ 7104 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 7153 chr5qtel1M 92919 GAAGAGAGAAGAAGGAAAAGAGAAAAGAGAAGAGAA 92954 i i i i i ii i i i i i i (AA)n#Simple_ 7154 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 7189 Matrix = Unknown Transitions / transversions = 2.87 (694/242) Gap_init rate = 0.00 (0 / 2985), avg. gap size = 0.0 (0 / 0) 1703 26.06 5.20 3.15 chr5qtel1M 90357 93288 (906712) (AAAGAG)n#Simple_repeat 4003 7011 (0) m_b246s252i13 9745 chr5qtel1M 90357 CAAGAAACAGAGAAA-AAAAAAAAAAAAAGAGAGAG-AAGAGAGAGAGAG 90404 v i v - i i i i i - i i (AAAGAG)n#Sim 4003 AAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAA 4052 chr5qtel1M 90405 AG-GAACAGA-AAAGAGAAGAGAGAGAACAG-AAGAGACAGAGAAAGAG- 90450 - - - - - v - v - (AAAGAG)n#Sim 4053 AGAGAA-AGAGAAAGAGAA-AGAGA-AAGAGAAAGAGAAAGAGAAAGAGA 4099 chr5qtel1M 90451 AACAGGAACAGAGAGA-AAAGAG-AGGA-AAAGAG-AAGGGAAAGAAGAG 90496 v i v i - - i - - i - - (AAAGAG)n#Sim 4100 AAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAG-AGA- 4147 chr5qtel1M 90497 AAAAAAAACAGAACAGAGAGGAGAGAAGAGGAGAAAGA-AAA-AAAAGGA 90544 i i v - -i - - - - i i (AAAGAG)n#Sim 4148 AAGAGAAAGAGAA-AGAGA-AAGAGAA-A-GAGAAAGAGAAAGAGAAAGA 4193 chr5qtel1M 90545 GAAAGA-ACA-AG-AAGAGAACAGA-AAACAGAAAG-GAAGGAAAAAGGG 90589 - v - - - - v - i i i (AAAGAG)n#Sim 4194 GAAAGAGAAAGAGAAAGAGAA-AGAGAAAGAGAAAGAGAAAGAGAAAGAG 4242 chr5qtel1M 90590 AAA-AGAAAAACAAAAAGAGAGA-ACAGAGGACAGA-AAAGAGAACAAGA 90636 - i v i i - v - v - vi (AAAGAG)n#Sim 4243 AAAGAGAAAGAGAAAGAGAAAGAGAAAGA-GAAAGAGAAAGAGAAAGAGA 4291 chr5qtel1M 90637 AAG-GAAAAAGAAA-AAAAAAAAAAAGA-AAACA-AAAGAAAAAAAAGCA 90682 - i - i i i - v - - i i v (AAAGAG)n#Sim 4292 AAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAG-AGAAAGAGAA 4340 chr5qtel1M 90683 AAAACAAGAGGAA-A-AAAGAGAAAAACAGAGA-AAAGAAAAAAACAAGA 90729 i iv i - - i v i - i i v - (AAAGAG)n#Sim 4341 AGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAA-A 4389 chr5qtel1M 90730 GAGAGGGGGAAAGGGAAAAGGGAGGAAGAAGAGACAAAAAAACA-AAAGA 90778 ii i i ii i i ii v i i v - - (AAAGAG)n#Sim 4390 GAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAG- 4438 chr5qtel1M 90779 ACAAACAAGAAAACAAAAAAGAAA-AGAACAGACAAAGAAGAAGA-AAAG 90826 v -i ivi i - - v ii - (AAAGAG)n#Sim 4439 AGAAA-GAGAAAGAGAAAGAGAAAGAGAA-AGAGAAAGAGAAAGAGAAAG 4486 chr5qtel1M 90827 AAAAAGA-ACAAAGAAAAAAAAACAG-GACACAAAAAAAAAGA-AAAGAC 90873 i - v i i i v -i v v i i - v (AAAGAG)n#Sim 4487 AGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAG 4536 chr5qtel1M 90874 AAAGA-AAAACCCAAGAGAACAAAGACA-A-AAAAAAAAAAAGAAAGAAA 90920 - ivvv - i v - - i i i i (AAAGAG)n#Sim 4537 AAAGAGAAAGAGAAAGAGAA-AGAGAAAGAGAAAGAGAAAGAGAAAGAGA 4585 chr5qtel1M 90921 CAGAAGAAAGGGAGAAAAAAAAGACAGAGAGGAAAACACAGACACAAAGA 90970 v - i - i i v i i i v v v v i (AAAGAG)n#Sim 4586 AAG-AGAAAGAGA-AAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGA 4633 chr5qtel1M 90971 AA-ACAAAAAGACAGAAAAAGAAAAAAAAAGAGAGAAACAGACA-A-AAA 91017 - v i v i i i i i v v - - (AAAGAG)n#Sim 4634 AAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAA 4683 chr5qtel1M 91018 -ACAAAGAAAAAAGGAAAAAGGAAAAACAAGACAGAAA-ACAAA-AGACA 91064 - v i ii i - i v - v - v - v (AAAGAG)n#Sim 4684 GAGAAAGAGAAAGAGAAAGA-GAAAGAGAA-AGAGAAAGAGAAAGAGAAA 4731 chr5qtel1M 91065 -AAAAAGACAAAACGGGAAA-AGGAAGACAAAAAAGAAAAAGAGAGAGAA 91112 - i -i - i - i -i i i i (AAAGAG)n#Sim 4732 GAGAAAGA-GAAA-GAGAAAGAGAAAGA-GAAAGAGAAAGAGAAAGAGAA 4778 chr5qtel1M 91113 AAAGAAGAAGAGAG-GAAAGAGAACAGAGAGAAGAGAAGGGAAGGGGGAG 91161 i ii i - - - -i - iii (AAAGAG)n#Sim 4779 AGAGAAAGAGAAAGAGAAAGAGAA-AGAGA-AAGAGAA-AG-AGAAAGAG 4824 chr5qtel1M 91162 GGAGAGAAAGAG-AA-ACAAAGA-AAAG-GAAAGAGAAA-AGAGAGAGAC 91206 ii - - v - - - i - (AAAGAG)n#Sim 4825 AAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGA- 4873 chr5qtel1M 91207 AAGAAGACAGAGAAA-AGAGAGGAGAGAAGAGAAA-AGAAA-AAAAAGAG 91253 - v - - i - - - i (AAAGAG)n#Sim 4874 AAG-AGAAAGAGAAAGAGA-AAGAGA-AAGAGAAAGAGAAAGAGAAAGAG 4920 chr5qtel1M 91254 AAACAG--AGA-AAAGAGAACAGAGAAAGAAGAAGAGACAAAACAGAGAG 91300 v -- - - ii - i v i (AAAGAG)n#Sim 4921 AAAGAGAAAGAGAAAGAGAA-AGAGAAAGAGAAAGAGA-AAGAGAAAGAG 4968 chr5qtel1M 91301 AAAAAGAAACAG--AGAG-CGGGGAAAGAGAAA-AGAGAGAACAAAGAGA 91346 i v -- -vi i - i - v (AAAGAG)n#Sim 4969 AAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAG-AGAAAGAGA 5017 chr5qtel1M 91347 AAAAGAAAGA-AGAGAGAAAGAG-AAGAGAAA-AGAGAAGAAAACAGAGA 91393 i - i - - - i - (AAAGAG)n#Sim 5018 AAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGA-AAGAGAA-AGAGA 5065 chr5qtel1M 91394 CAAGAGAAA-AGGGAGA-ACAGAGAAACAAGAAAGA-AGACAGAGAGAG- 91439 - - ii - v -i - i v i - (AAAGAG)n#Sim 5066 -AAGAGAAAGAGAAAGAGAAAGAGAAA-GAGAAAGAGAAAGAGAAAGAGA 5113 chr5qtel1M 91440 AAGAGACAGAGAAAGAGAGAAAGAAAGAG-AAGA-AAAGAAGAAAAGAGG 91487 v i i - - - - - (AAAGAG)n#Sim 5114 AAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAG-AG-AAAGA-G 5160 chr5qtel1M 91488 AACAGGAGACAGAG-AAGA-AGAGGGACAGAGAGAGAGAAA-AG--AGAG 91532 - - v - - i i v i - -- (AAAGAG)n#Sim 5161 AA-A-GAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAG 5208 chr5qtel1M 91533 AAAGAGACAGAAGAGAGAGACAGAGAAGAAGAAAGAACAAGAACAAAAGG 91582 v - i v ii iv iv i i (AAAGAG)n#Sim 5209 AAAGAGAAAG-AGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGA 5257 chr5qtel1M 91583 GGGA-AGAGAGAAAG-GACAGA-AGAGAAAAAGAGAGAGAGACAGAGACA 91629 ii - i - v - i i i v v (AAAGAG)n#Sim 5258 AAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAA 5307 chr5qtel1M 91630 GAG--AGAGAAAGAGAAGGA-AAAGA-AAAGAGACAAAAGAGAAGAGAGA 91675 -- i - - - i - - (AAAGAG)n#Sim 5308 GAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGA-AAGAGA-AAGAGA-A 5354 chr5qtel1M 91676 AAAGAGAGAAAAGAGAGAAAGAG-AAGAGAAAGAGACAGAGAACAAGAGA 91724 i i i - - v - - - (AAAGAG)n#Sim 5355 AGAGAAAGAGAA-AGAGAAAGAGAAAGAGAAAGAGAAAGAG-A-AAGAG- 5400 chr5qtel1M 91725 AAAAAGAGAGAGACAAGAGACAGA-AAAAAG-AAGA-AGAGAGAAAGAGA 91771 i i - v - i - - i (AAAGAG)n#Sim 5401 AAAGAGAAAGAGA-AAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGA 5449 chr5qtel1M 91772 ACAGAG-AAGA-AAA-AGAGGGAAAGAGAGAAAGAG-AAGAGCCAGAGAG 91817 - - - - ii i i - vv - (AAAGAG)n#Sim 5450 A-AGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGA- 5497 chr5qtel1M 91818 AACAGAAAGAAAGAAAGA-AAAGAG-TCCAAAACGAGAGAAGA-AGAGAG 91864 v -- - -vvv i v - - i (AAAGAG)n#Sim 5498 AAGAGAAAG--AGAAAGAGAAAGAGAAAGAGAAAGAGA-AAGAGAAAGAG 5544 chr5qtel1M 91865 AAA-AGAAGGAGAAGCAGAGACAG-AAGAGAAAGAGAAAAGAGACAGAGA 91912 - i iv i v - - v (AAAGAG)n#Sim 5545 AAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAG-AAAGAGAAAGAGA 5593 chr5qtel1M 91913 AGAAAGAAGGAGAGAACGAGAGAAAAGAGAGAAAGAGAGAGAAAGAGAGA 91962 - i i i iv i i - i i i (AAAGAG)n#Sim 5594 A-AGAGAAAGAGAAAGAGAAAGAGAA-AGAGAAAGAGAAAGAGAAAGAGA 5641 chr5qtel1M 91963 AAGAGGAAGAG--A-AGAAAGAGAAGAGAGAAA-AGAGACAG-AAGAGAA 92007 i -- - - - i v - (AAAGAG)n#Sim 5642 AAGAGAAAGAGAAAGAGAAAGAGAA-AGAGAAAGAGAAAGAGAAAGAGAA 5690 chr5qtel1M 92008 GAGAGAAAGAGAAA-AGAGAGGGGAA-AGAAAGA-AGAGAAGAAAGAG-A 92053 - - i i i - - i - - (AAAGAG)n#Sim 5691 -AGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAG-AGAAAGAGAA 5738 chr5qtel1M 92054 AGAAAGAAGAGAAAGAG-AAGAGAAAGACAGAGA-CAAGAG-AAGAGAAA 92100 i - - v i -v - (AAAGAG)n#Sim 5739 AGAGA-AAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAA 5787 chr5qtel1M 92101 -AGACAAACGAAGAGAAAGAGAGAAGAGACAAAAACAAACAAAAACAAA- 92148 - v i vi - v i i v i v i v - (AAAGAG)n#Sim 5788 GAGAAAGAGAAAGAGAAAGAGA-AAGAGAAAGAGAAAGAGAAAGAGAAAG 5836 chr5qtel1M 92149 A-AAA-AGAAACAGAAACAGAAAAAGAAA-AGGAAGAAGGAAAG-GAAAA 92194 - - v v i - i - - - i (AAAGAG)n#Sim 5837 AGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAG-A-GAAAGAGAAAG 5884 chr5qtel1M 92195 AGAAAGAGAACAGA-AAAAAAAAAAAGGAACAAAAAAAGGAACAGAGAAG 92243 - - i i i i v i i i v - (AAAGAG)n#Sim 5885 AGAAAGAGAA-AGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGA-AAG 5932 chr5qtel1M 92244 A-AATGA-AAAAAGACAACAAAAAAAGAAAG-GAACAAAGGAAGA-AAAA 92289 - v - i - v i i - - i i - i (AAAGAG)n#Sim 5933 AGAAAGAGAAAGAGA-AAGAGAAAGAGAAAGAGAA-AGAGAAAGAGAAAG 5980 chr5qtel1M 92290 AGAAAAACAAACAAAAAAAAAAAAGAAAAGGAGAAAGA-AACAAGGAACA 92338 i v -i i i i i i - vi i v (AAAGAG)n#Sim 5981 AGAAAGAGAAA-GAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGA 6029 chr5qtel1M 92339 AAACGGGAAAAAAAACAAGACAAAAGAAAAAAGAAGGGCAA-AGAAAAAG 92387 i v i i i vi - i i ii i v - i (AAAGAG)n#Sim 6030 GAAAGAGAAAGAGAAAGAGA-AAGAGAAAGAGAAAGAGAAAGAGAAAGAG 6078 chr5qtel1M 92388 AAA-AATAAGAG-AAGA-AAAAAGAGA-AGAAAAAAAACAACAAAGAGAC 92433 - iv - - i i - i i vi v v (AAAGAG)n#Sim 6079 AAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAA 6128 chr5qtel1M 92434 A-AAAAAG-CAAACACAAGGAAAAACACAAAAACAAAGA-AGA-AAAAAC 92479 - i -v v v i i v v i v - i - i v (AAAGAG)n#Sim 6129 AGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAG 6178 chr5qtel1M 92480 A-AAAAAGAAAGAAAAAAAAAAAGAAGAAAAGGGAAGAGAGAAAAAGGAA 92528 - i i i i - - i - i - (AAAGAG)n#Sim 6179 AGAAAGAGAAAGAGAAAGAGAAAG-AG-AAAGAGAA-AGAGAAAGA-GAA 6224 chr5qtel1M 92529 AGCAAAAAAAGCAAG-GAAA-AGAAACAAAAAGAAAGGACACAAACACAA 92576 - i i v - - v i i -i v v v v (AAAGAG)n#Sim 6225 AG-AGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGA-AAGAGAAAGAGAA 6272 chr5qtel1M 92577 AGAAACAAACAAAGAGGAA-AGAAA-ACAAAAAGACAGAAAAAAGACAAA 92624 i v i v i - - v i v - i v (AAAGAG)n#Sim 6273 AGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAG-AGAAAGAGAAA 6321 chr5qtel1M 92625 AACAAA-AGGAA-AAAAATAGAACAAGGAA-AGAAA-A-AAAAAGAAAG- 92668 i v - i - i v vi i - - - i - (AAAGAG)n#Sim 6322 GAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGA 6371 chr5qtel1M 92669 GAAAAACAAGAAGAAAAAAAACAAGAAA-ACAAA-AGGAAAAG-AAGA-A 92714 i v ii i i vi - v - i i - - (AAAGAG)n#Sim 6372 GAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGA 6421 chr5qtel1M 92715 AACAAAAAAACGGAAG-GAAA-AGGAA-AGAAGAAAAAAGAAAAAAAG-A 92760 v i i - i - - i - ii i i i - (AAAGAG)n#Sim 6422 AAGAGAAAGA-GAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAA 6470 chr5qtel1M 92761 AGAAAAAAACAAA-AGGAA-ACAAAGAAGAAA-AGAAAGCACAAAGAAGG 92807 i i v - i - v - - - v - i (AAAGAG)n#Sim 6471 AGAGAAAGAGAAAGAGAAAGAGAAAG-AGAAAGAGAAAG-AGAAAG-AGA 6517 chr5qtel1M 92808 AAAAGAAAGACAAAG-GAAAAACAAA-AGAAA-AGACA-AAAAAGGGAAA 92853 i v - i v - - v - i i (AAAGAG)n#Sim 6518 AAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAA 6567 chr5qtel1M 92854 -A-AAAAAAAAAGA-ACAAACAAAGA-AAA-AAAAAGCAGAAAGGAAAAA 92898 - - i i - v i v - - i - - i (AAAGAG)n#Sim 6568 GAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAG-AGAAA-GAGAAA 6615 chr5qtel1M 92899 AAGAAGGGGAAAAAAAAACAG-AAGAGAGA-AGAAGGA-AAAGAGAAA-A 92944 i i i i i v - i - i - - (AAAGAG)n#Sim 6616 GAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGA 6665 chr5qtel1M 92945 GAGAAGAGAACGAGAGAGACAAACAGAGAGAAAGAAAGACAGAGACAAAG 92994 - v i -i - i i v i v (AAAGAG)n#Sim 6666 GA-AAGAGAAAGAGAAAGA-GAA-AGAGAAAGAGAAAGAGAAAGAGAAAG 6712 chr5qtel1M 92995 AAGAAAGAG-AAGAG-AA-AGAAGGAG-GAGAGACAGAGACAAGAGAGAC 93040 - - - - i -i v - i v (AAAGAG)n#Sim 6713 -AGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGA-AAGAGAAAG 6760 chr5qtel1M 93041 AGAGA-AAAAGGAGAGACAGAAAGAGACAAGAG-GAGAAAAACAGAGAGA 93088 i - i i i v - -i i v i (AAAGAG)n#Sim 6761 AGAAAGAGAAAGAGAAAGAGAAAGAGA-AAGAGAAAGAGAAAGAGAAAGA 6809 chr5qtel1M 93089 AGAAGAGACAGA-AAAGAGAAAGAGAAGAGAGAAAG-GAGAGAAAGAGAG 93136 ii v - - - i i i (AAAGAG)n#Sim 6810 GAAAGAGAAAGAGAAAGAGAAAGAGAA-AGAGAAAGAGAAAGAGAAAGAG 6858 chr5qtel1M 93137 AAAAAGAGAGAGAACGAGAGAGA-ACAGAGAGAGAG-AAGAGAGAGA-AG 93183 i i v i - v i - i - i (AAAGAG)n#Sim 6859 AAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAA 6908 chr5qtel1M 93184 AGAGGAAGAAGACA-AGAAAGAGACAAGAGAAGAAGAGAAGAGAGAAAGA 93232 i - v - - - - - (AAAGAG)n#Sim 6909 AGAGAAAG-AGAAAGAGAAAGAGA-AAGAG-A-AAGAGAA-AGAGAAAGA 6953 chr5qtel1M 93233 GAAAGAGACA-A-AAAGAGAGA-AAAGAGAGAAGGAGACAG-GAGAAGAG 93278 v - - i - i i i v - - (AAAGAG)n#Sim 6954 GAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGA-AAGAG 7002 chr5qtel1M 93279 AACAGGGAAA 93288 - i (AAAGAG)n#Sim 7003 AA-AGAGAAA 7011 Matrix = Unknown Transitions / transversions = 2.13 (321/151) Gap_init rate = 0.09 (272 / 2931), avg. gap size = 1.03 (279 / 272) 1452 44.70 0.00 0.00 chr5qtel1M 93469 93765 (906235) (AA)n#Simple_repeat 7704 8000 (0) m_b246s252i11 9746 chr5qtel1M 93469 CAAAAACAAACAAAAAAAAACCCAAAAGGAAACCAAACAAAAAAAAACAA 93518 v v v vvv ii vv v v (AA)n#Simple_ 7704 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 7753 chr5qtel1M 93519 ACAAAAAAAAAAACAAAAACATGAAAAAAACAAAAAACGAAAAAAAAAAC 93568 v v v vi v vi v (AA)n#Simple_ 7754 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 7803 chr5qtel1M 93569 AAAACAAAAAAAGGGAAAAAACAAAAAAAAAAAAAACAAAAGGGCAAACA 93618 v iii v v iiiv v (AA)n#Simple_ 7804 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 7853 chr5qtel1M 93619 AAAAAACAAACAAAACAAAAAAAAAGGCCAAAAAAAACAAAACAAAAAAA 93668 v v v iivv v v (AA)n#Simple_ 7854 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 7903 chr5qtel1M 93669 ACAAAAGAAAGGGAAAAAGGCAAAAAAAACAAAAAGGGAAAAAACAAACA 93718 v i iii iiv v iii v v (AA)n#Simple_ 7904 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 7953 chr5qtel1M 93719 GAGAGAAAAGAGACAGAGAGAGCAAAAGAGGGAAAAACAAAAAAAAA 93765 i i i i i v i i i iv i iii v (AA)n#Simple_ 7954 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 8000 Matrix = Unknown Transitions / transversions = 0.92 (34/37) Gap_init rate = 0.00 (0 / 296), avg. gap size = 0.0 (0 / 0) 1703 26.06 5.20 3.15 chr5qtel1M 93670 93866 (906134) (AAAGAG)n#Simple_repeat 7405 7603 (0) m_b246s252i14 9747 chr5qtel1M 93670 CAAAAGAAAGGGAAAAAGGCAAAAAAAACAAAAAGGGAAAAAACAAACAG 93719 v i i i - v i i v i i - i v v (AAAGAG)n#Sim 7405 AAAGAGAAAGAGAAAGA-GAAAGAGAAAGAGAAAGAG-AAAGAGAAAGAG 7452 chr5qtel1M 93720 AGAGA-AAAGAGACAGAGAGAGCAAAAGAGGGAAAAACAAA-A-AAAAAC 93766 i - v i - i - i i v - - i v (AAAGAG)n#Sim 7453 AAAGAGAAAGAGAAAGAGAAAG-AGAA-AGAGAAAGAGAAAGAGAAAGAG 7500 chr5qtel1M 93767 CAA-AGACAAACAAACAGGAACA-AAAGA-AAAGGGAAAGGGGAAAGAAG 93813 v - v i v v i v - - i - i - (AAAGAG)n#Sim 7501 AAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAA-GAGAAAG-AG 7548 chr5qtel1M 93814 AGAGGGAAAGAGGAGGAG-AAG-GAAAGAGAGACAGGGGGAACAAGAAAA 93861 i i i i - - i v iii iv i (AAAGAG)n#Sim 7549 AAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAA 7598 chr5qtel1M 93862 GGAGA 93866 i (AAAGAG)n#Sim 7599 AGAGA 7603 Matrix = Unknown Transitions / transversions = 1.93 (29/15) Gap_init rate = 0.07 (14 / 196), avg. gap size = 1.00 (14 / 14) 12 13.24 0.00 10.81 chr5qtel1M 94390 94430 (905570) (CCCCGGG)n#Simple_repeat 1 37 (0) m_b246s252i15 9748 chr5qtel1M 94390 CCCGGGGCCAGGGGCCCACGGTGCCCCGGGTCCGCCTGGCC 94430 v vv - - - - v (CCCCGGG)n#Si 1 CCCCGGGCCCCGGGCCC-CGG-GCCCCGGG-CC-CCGGGCC 37 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.10 (4 / 40), avg. gap size = 1.00 (4 / 4) 12 26.75 0.00 0.00 chr5qtel1M 95665 95704 (904296) (AAAAAAC)n#Simple_repeat 1 40 (0) m_b246s252i16 9749 chr5qtel1M 95665 AAACAACAAAATCCAAAAAATAAATTTTAAAAAATAAAAA 95704 v vv i vvvi i (AAAAAAC)n#Si 1 AAAAAACAAAAAACAAAAAACAAAAAACAAAAAACAAAAA 40 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 16 32.81 0.00 0.00 chr5qtel1M 95980 96029 (903971) (AA)n#Simple_repeat 1 50 (0) m_b246s252i17 9750 chr5qtel1M 95980 AAAAACAAAAAGGGGAAAACCCCAAAAAAAAAAAAAAGGGGAAAAAAAAA 96029 v iiii vvvv iiii (AA)n#Simple_ 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 Matrix = Unknown Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 18 0.00 0.00 0.00 chr5qtel1M 96100 96119 (903881) (A)n#Simple_repeat 1 20 (0) m_b246s252i18 9751 chr5qtel1M 96100 AAAAAAAAAAAAAAAAAAAA 96119 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAA 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 17 18.22 0.00 0.00 chr5qtel1M 96160 96190 (903810) (A)n#Simple_repeat 1 31 (0) m_b246s252i19 9752 chr5qtel1M 96160 AAAACAAAAAAAAGCCCAAAAAAAAAAAAAA 96190 v ivvv (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 31 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 23 26.04 5.45 2.65 chr5qtel1M 96705 96814 (903186) (AGGAAAGG)n#Simple_repeat 1 113 (0) m_b246s252i20 9753 chr5qtel1M 96705 AGGAACAGGAGGAAAAG-GGAAAAG-GGAAAGG-GAAAGGGGAGGAAAGA 96751 - i - i - - i -i i (AGGAAAGG)n#S 1 AGGAA-AGGAGGAAAGGAGGAAAGGAGGAAAGGAGGAA-AGGAGGAAAGG 48 chr5qtel1M 96752 GGGGAGGGAAAAAGGGAGGCGGGGAAAAAGGGAGGGAAAGGCAG-AGGGA 96800 i i i ii i vii ii i - vi - i (AGGAAAGG)n#S 49 AGGAAAGGAGGAAAGGAGGAAAGGAGGAAAGGA-GGAAAGGAGGAAAGGA 97 chr5qtel1M 96801 -GAAAGCCGG-AAGGA 96814 - vv - (AGGAAAGG)n#S 98 GGAAAGGAGGAAAGGA 113 Matrix = Unknown Transitions / transversions = 4.50 (18/4) Gap_init rate = 0.08 (9 / 109), avg. gap size = 1.00 (9 / 9) 363 27.57 2.04 8.70 chr5qtel1M 98893 99039 (900961) MIR3#SINE/MIR 3 140 (68) m_b246s601i3 9754 chr5qtel1M 98893 GGCAGGGAGACTAAGTTCCCAGAGAGCTAGGGA--AGGA-TAATGAGACT 98939 i v i i -- vv - v --i - v v i MIR3#SINE/MIR 3 GGCAGAGTGGCTGAG--CAGAGAGAGC-ACGGACTGGGAGTCAGGAGACC 49 chr5qtel1M 98940 TGGAATTCAAATACCCAAATTCAAATTCTGCCGCCAACAAGCTGGGTGCC 98989 i- v i v --------iii i i v? v v MIR3#SINE/MIR 50 TGGG-TTCTAGTCCC--------GGCTCTGCCACTAACTNGCTGTGTGAC 90 chr5qtel1M 98990 CCTGGGCTGCTCACTTTAATTTTCCCAGTCTCAGTTTTTTCATCTGTAAA 99039 i viv i vi i ivi i ii MIR3#SINE/MIR 91 CTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAA 140 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 34.17 CpG sites = 22, Kimura (unadjusted) = 35.35 Transitions / transversions = 1.47 (22/15) Gap_init rate = 0.10 (14 / 146), avg. gap size = 1.07 (15 / 14) 601 30.09 7.41 0.00 chr5qtel1M 98923 99138 (900862) MIRc#SINE/MIR 20 251 (17) m_b246s601i4 9754 chr5qtel1M 98923 GGAAGGATAATGAGACTTGGAATTCA-AATACCCAAATTCAAAT------ 98965 i vv ivi i ivi- v iiii i i ------ MIRc#SINE/MIR 20 GGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGC 69 chr5qtel1M 98966 TCTGCCGCCAACAAGCTGGGTGCCCCTGGGCTGCTCACTTTAATTTTCCC 99015 i iv v v v i viv v vi i iv MIRc#SINE/MIR 70 TCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTG 119 chr5qtel1M 99016 AGTCTCAGTTTTTTCATCTGT-AAACAGGGATAATAA---CTGGCCT--- 99058 i ii - ii --- v --- MIRc#SINE/MIR 120 AGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCC 169 chr5qtel1M 99059 TCCCTCTCAGGGCTATTGTGA-GATCAATAGGGACAATAGCTGC-AGAAT 99106 v v i i - vv i i ivv i- i ii MIRc#SINE/MIR 170 TACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGC 219 chr5qtel1M 99107 GCCTGGAAACCCTTAAAGTACGATATGAATAT 99138 i v v v iv i v ii i MIRc#SINE/MIR 220 GCTTTGTAAACTGTAAAGTGCTATACAAATGT 251 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 38.14 CpG sites = 39, Kimura (unadjusted) = 39.72 Transitions / transversions = 1.50 (39/26) Gap_init rate = 0.03 (7 / 215), avg. gap size = 2.29 (16 / 7) 341 26.99 3.93 6.32 chr5qtel1M 100319 100496 (899504) C L1PB_orf2#LINE/L1 (1575) 1719 1546 m_b246s551i0 9755 chr5qtel1M 100319 CCATCACCTTCCAATCACTGGTATGAATCCGATCTGGTCACAGTGAATCA 100368 - v -- v v v ii i ii i i C L1PB_orf2#LIN 1719 CCATC-CCTGC--ATCCCTGGTATGAAACCCACTTGATCATGGTGGATTA 1673 chr5qtel1M 100369 CTAGGGTG-CATTTTGCTGCATCTC--TTTGCTAAGATTTTATTTAAATT 100415 iivvvv -i vi i v - -- v iv i ------ C L1PB_orf2#LIN 1672 TCTTTTTGATATGCTGTTGGAT-TCGGTTAGCTAGTATTTTGTT------ 1630 chr5qtel1M 100416 GGAGGA----GGAAGCAGTATTCATTAGTGATAGTGGTCTGTAGTTTTCT 100461 - ----? v v vi i i v v C L1PB_orf2#LIN 1629 -GAGGATTTTNGCATCTATGTTCATCAGGGATATTGGTCTGTAGTTTTCT 1581 chr5qtel1M 100462 TTCTCTTCTATATCTGTCCCTGGTTTTACTGTTAG 100496 i i?vi i iv i iv i C L1PB_orf2#LIN 1580 TTTTTNGTTATGTCCTTTCCTGGTTTTGGTATTAG 1546 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 34.54 CpG sites = 25, Kimura (unadjusted) = 34.54 Transitions / transversions = 1.25 (25/20) Gap_init rate = 0.08 (14 / 177), avg. gap size = 1.29 (18 / 14) 276 29.98 3.49 5.33 chr5qtel1M 100324 100552 (899448) C L1M4_orf2#LINE/L1 (1578) 1716 1492 m_b246s551i1 9755 chr5qtel1M 100324 ACCTTCCAATCACTGGTATGAATCCGATCTGGTCACAGTGAATCA-CTAG 100372 v v - v i v ii ii v v - ivv C L1M4_orf2#LIN 1716 ACCTTGCATTC-CTGGGATAAATCCCACTTGGTCATGGTGTATAATCCTT 1668 chr5qtel1M 100373 GGTGCATTTTGCTGCATCTC--TTTGCTAAGATTTTATTTAAATTGGAGG 100420 vv ii v v - -- iv i ------- C L1M4_orf2#LIN 1667 TTTATATGTTGCTGGAT-TCGGTTTGCTAGTATTTTGTT-------GAGG 1626 chr5qtel1M 100421 AG----GAAGCAGTATTCATTAGTGATAGTGGTCTGTAGTTTTCTTTCTC 100466 v---- v v vi v v v - C L1M4_orf2#LIN 1625 ATTTTTGCATCTATATTCATAAGGGATATTGGTCTGTAGTTTTCTTT-TC 1577 chr5qtel1M 100467 TTCT-ATATCTGTCCCTGGTTTTACTGTTAGTTCTATTTTTATCTCCTAA 100515 v - i v vi iv i i vviv vi vii v i C L1M4_orf2#LIN 1576 TTGTGATGTCTTTGTCTGGTTTTGGTATCAGGGTAATACTGGCCTCATAG 1527 chr5qtel1M 100516 AATCTGTCTGGACCAAAGTTTTGCTCTGTTCCGTTTT 100552 vv iv -- iv iivii v ii C L1M4_orf2#LIN 1526 AATGAGTTGGGA--AGTGTTCCCTCCTCTTCTATTTT 1492 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 38.46 CpG sites = 29, Kimura (unadjusted) = 38.46 Transitions / transversions = 0.81 (29/36) Gap_init rate = 0.07 (16 / 228), avg. gap size = 1.25 (20 / 16) 311 29.70 4.43 5.47 chr5qtel1M 100325 100527 (899473) C L1M1_orf2#LINE/L1 (1579) 1715 1515 m_b246s551i2 9755 chr5qtel1M 100325 CCTTCCAATCACTGGTATGAATCCGATCTGGTCACAGTGAATCAC---TA 100371 v - v ? v i v ii iii v i--- v C L1M1_orf2#LIN 1715 CCTTGCA-TCCCNGGGATAAATCCCACTTGGTCATGATGAATGATCTTTT 1667 chr5qtel1M 100372 GGGTGCATTTTGCTGCATCTC--TTTGCTAAGATTTTATTTAAATTGGAG 100419 vii i -- i v - -- iv i ------- C L1M1_orf2#LIN 1666 TAATGTATT--GTTGAAT-TCGGTTTGCTAGTATTTTGTT-------GAG 1627 chr5qtel1M 100420 GAG----GAAGCAGTATTCATTAGTGATAGTGGTCTGTAGTTTTCTTTCT 100465 v---- v v i i v v i i C L1M1_orf2#LIN 1626 GATTTTTGCATCAATATTCATCAGAGATATTGGCCTGTAGTTTTCTTTTT 1577 chr5qtel1M 100466 CTTCTATATCTGTCCCTGGTTTTACTGTTAGTTCTATTTTTATCTCCTAA 100515 i vv i i v vi iv i i vviv vi vii v i C L1M1_orf2#LIN 1576 TTGATGTGTCTTTGTCTGGTTTTGGTATCAGGGTAATACTGGCCTCGTAG 1527 chr5qtel1M 100516 AATCTGTCTGGA 100527 vv i C L1M1_orf2#LIN 1526 AATGAGTTTGGA 1515 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 38.70 CpG sites = 30, Kimura (unadjusted) = 38.70 Transitions / transversions = 1.11 (30/27) Gap_init rate = 0.07 (14 / 202), avg. gap size = 1.43 (20 / 14) 298 24.36 5.04 6.84 chr5qtel1M 102322 102440 (897560) C L2b_3end#LINE/L2 (24) 442 326 m_b246s601i5 9756 chr5qtel1M 102322 CTGAGTGCCTACTGTGTGTCCAGTCCTCCTGTGCTGGGC-TTGGGGACGC 102370 i - v --? i -i ii C L2b_3end#LINE 442 CTGAGCGCCTACTGTGTG-CCAGGC--NCTGTGCTAGGCGCTGGGGATAC 396 chr5qtel1M 102371 AG-GGACAACAATGCAAA---AGACCCTGTCTCCG-AGAGTTTATGTTCG 102415 - vv vi i ---i v i ii i-i i i iiv v C L2b_3end#LINE 395 AGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGGAGCTCACAGTCT 346 chr5qtel1M 102416 GCTGGGAGAGACAGTGTGCACATGT 102440 iv i ----- C L2b_3end#LINE 345 AGTGGGGGAGACAG-----ACATGT 326 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 26.96 CpG sites = 19, Kimura (unadjusted) = 31.01 Transitions / transversions = 2.38 (19/8) Gap_init rate = 0.10 (12 / 118), avg. gap size = 1.17 (14 / 12) 319 19.73 3.90 1.27 chr5qtel1M 103460 103536 (896464) MIR3#SINE/MIR 104 182 (26) m_b246s601i6 9757 chr5qtel1M 103460 CTTC-CTTCTCCAAGCCTCAGTCTTCTCATCTATAAA--GAGGGCCTTGA 103506 - i iii i i i -- vv i MIR3#SINE/MIR 104 CTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGG 153 chr5qtel1M 103507 ACTGACCTGGGCTCTGAGGTCCCTTCCAGC 103536 - vv iv i MIR3#SINE/MIR 154 ACT-AGATGATCTCTAAGGTCCCTTCCAGC 182 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 23.47 CpG sites = 10, Kimura (unadjusted) = 23.47 Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.04 (3 / 76), avg. gap size = 1.33 (4 / 3) 13 25.37 0.00 8.33 chr5qtel1M 104574 104638 (895362) (TGCCC)n#Simple_repeat 1 60 (0) m_b246s252i21 9758 chr5qtel1M 104574 TGCCCTGCCCTGCCCCCCCCAGGAGCCTGGCACTCTTCAGCCTGTGTCCT 104623 iv -v -v - v vii v -v i (TGCCC)n#Simp 1 TGCCCTGCCCTGCCCTGCCC-TG-CCCT-GCCCTGCCCTGCC-CTGCCCT 46 chr5qtel1M 104624 GCCCTTGGCCTGCCC 104638 - v (TGCCC)n#Simp 47 GCCC-TGCCCTGCCC 60 Matrix = Unknown Transitions / transversions = 0.50 (4/8) Gap_init rate = 0.08 (5 / 64), avg. gap size = 1.00 (5 / 5) 18 17.40 2.13 2.13 chr5qtel1M 105692 105738 (894262) (AGGAAA)n#Simple_repeat 1 47 (0) m_b246s252i22 9759 chr5qtel1M 105692 AGGAGATTGAAATGAGACAAGGAAAAAGGAAA-GAAAAGGAAAAGGAA 105738 i vv v - v i i - (AGGAAA)n#Sim 1 AGGAAAAGGAAAAG-GAAAAGGAAAAGGAAAAGGAAAAGGAAAAGGAA 47 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.04 (2 / 46), avg. gap size = 1.00 (2 / 2) 13 15.94 2.70 2.70 chr5qtel1M 105716 105752 (894248) (AAAGG)n#Simple_repeat 1 37 (0) m_b246s252i23 9759 chr5qtel1M 105716 AAAGGAAAGAAAAGGAAAAGGAA-GAAAGTCAAGTGAA 105752 i i i - vv - (AAAGG)n#Simp 1 AAAGGAAAGGAAAGGAAAGGAAAGGAAAGGAAAG-GAA 37 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 204 33.72 2.33 0.00 chr5qtel1M 106804 106889 (893111) C MIR3#SINE/MIR (7) 201 114 m_b246s601i7 9760 chr5qtel1M 106804 AGAATCGGGGACTACGGGTGCTGGAGGGG-CCTTGGACACCACCCAGTCC 106852 ivi v iivi v i - i v i i i C MIR3#SINE/MIR 201 AGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCC 152 chr5qtel1M 106853 AGCCCTTTCCCGTCATACAAGAGGAGAGAGA-GCTCAG 106889 i ii viv i i v v i vv - i C MIR3#SINE/MIR 151 AACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAG 114 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 46.93 CpG sites = 18, Kimura (unadjusted) = 46.93 Transitions / transversions = 1.64 (18/11) Gap_init rate = 0.02 (2 / 85), avg. gap size = 1.00 (2 / 2) 21 24.43 0.00 0.00 chr5qtel1M 107956 108003 (891997) (GG)n#Simple_repeat 1 48 (0) m_b246s252i24 9761 chr5qtel1M 107956 GGGCGGGGGGGGGGGGGGGTAGAGGGGGCAGCCCGGGGGGGGGGAGGG 108003 v vi i vi vvv i (GG)n#Simple_ 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 48 Matrix = Unknown Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 12 21.70 0.00 0.00 chr5qtel1M 108192 108223 (891777) (GCCCGC)n#Simple_repeat 1 32 (0) m_b246s252i25 9762 chr5qtel1M 108192 GCCCGGGCCAGCGCCCGCGCTCGCACACGTGC 108223 v v i i v i (GCCCGC)n#Sim 1 GCCCGCGCCCGCGCCCGCGCCCGCGCCCGCGC 32 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 36 5.27 0.00 0.00 chr5qtel1M 111018 111057 (888943) (GT)n#Simple_repeat 1 40 (0) c_b246s251i0 9763 chr5qtel1M 111018 GTGTGTGTGCATGTGTGTGTGTGTGTGTGTGTGTGTGTGT 111057 ii (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 40 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 330 24.24 10.10 0.00 chr5qtel1M 111194 111292 (888708) C MER63D#DNA/hAT-Tip100 (598) 463 355 m_b246s502i0 9764 chr5qtel1M 111194 ACTTTTCCGTATAATCTGCATCACTAACATTTTCTCTGAGCCGTCCTTAA 111243 vv v i i iivvv v i C MER63D#DNA/hA 463 ACTTTTAAGTTTAATCTGCATTATTAACATTTTCTCCATCACTTTCTTAA 414 chr5qtel1M 111244 GTCTGGGCAATCAAT-CAACAAGTAATCAGGGCT---------GTGTTGG 111283 i i i-v vv i v i--------- i v C MER63D#DNA/hA 413 GTCTAGACAATCAACAAAACAATAAATCAAGCCCTGATTTGTAGCGTTTG 364 chr5qtel1M 111284 CCGATCTCC 111292 i C MER63D#DNA/hA 363 CCGATTTCC 355 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 28.13 CpG sites = 12, Kimura (unadjusted) = 29.54 Transitions / transversions = 1.00 (12/12) Gap_init rate = 0.02 (2 / 98), avg. gap size = 5.00 (10 / 2) 329 30.77 2.04 7.14 chr5qtel1M 112446 112592 (887408) C MIRc#SINE/MIR (127) 141 2 m_b247s601i0 9765 chr5qtel1M 112446 TACAGATGAAGAAACTGAAG--CAAAATGGGTGAATGCCTTACCC-AGAT 112492 i i -- i iv v i i v i - i C MIRc#SINE/MIR 141 TACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGT 92 chr5qtel1M 112493 CACCCAGCTGGCGAGTGTCTGAGGCTGGATTTGAATTTGGGGAGAGGACT 112542 v i ii v v v v i i iiii -------- C MIRc#SINE/MIR 91 CACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGG--------T 50 chr5qtel1M 112543 CAGCCGGACTCCGGCCCTAGTGCTCCGTGTGTGGTGCTCCCCCCTACCTC 112592 vv v iivi i -- v viiv v v v i C MIRc#SINE/MIR 49 CTTCCTGACTCCAAGTCCAGTGCTC--TTTCCACTGCACCACACTGCCTC 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.23 CpG sites = 24, Kimura (unadjusted) = 40.49 Transitions / transversions = 1.33 (24/18) Gap_init rate = 0.08 (12 / 146), avg. gap size = 1.08 (13 / 12) 388 19.55 2.46 7.76 chr5qtel1M 112446 112567 (887433) C MIR1_Amn#SINE/MIR (87) 143 28 m_b247s601i1 9765 chr5qtel1M 112446 TACAGATGAAGAAACTGAAGCA-AAATGGGTGAA-TGCCTTACCCA-GAT 112492 i i ?- i vi ? - v i - i C MIR1_Amn#SINE 143 TACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGCCCAAGGT 94 chr5qtel1M 112493 CACCCAGCTGGCGAGTGTCTGAGGCTGGATTTGAATTTGGGGAGAGGACT 112542 ? ? ? v v v v ? ? iii------ v C MIR1_Amn#SINE 93 CACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAACCC------AGGTCT 50 chr5qtel1M 112543 CAGCCGGACTCCGGCCCTAGTGCTC 112567 -- iiii i i - C MIR1_Amn#SINE 49 C--CCGAGTCCCAGTCC-AGTGCTC 28 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.01 CpG sites = 15, Kimura (unadjusted) = 25.01 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.10 (12 / 121), avg. gap size = 1.00 (12 / 12) 192 35.98 3.92 1.92 chr5qtel1M 112942 113094 (886906) C L2d2_3end#LINE/L2 (236) 319 164 m_b247s601i2 9766 chr5qtel1M 112942 ATAAAATGTACAAACATTAAATACTA-ACTAAACTGGGGAAGGGAGGG-- 112988 i vv i v ? i - vv iviii i i i -- C L2d2_3end#LIN 319 ATGAATGGTACAGACAATAANTGCTATAGGAGTTCAGAGGAGGGAGAGAT 270 chr5qtel1M 112989 CCCTAGGAAC-GGAGGGATTGAAGATGGGTCTCACAATGGAGAGAAAACC 113037 v ?v ii - v i iiii -i ii iiv ivii? ii C L2d2_3end#LIN 269 CACTNCGGGCTGGAGTGGTCAGGGA-AGGCTTCACGGAGGAGGTGGNATT 221 chr5qtel1M 113038 TATGCTGAGCTTTGAAGGA-AGTTAGGAAGTCTGCGT-GGCAGAAGTGAA 113085 iv i i -i v -- i vi - ii iiv C L2d2_3end#LIN 220 TGAGCTGGGCCTTGAAGGATGGGTAGGA--TTTGGATAGGTGGAGAGGAA 173 chr5qtel1M 113086 GGTGATGGG 113094 v v C L2d2_3end#LIN 172 GGGGAAGGG 164 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 53.25 CpG sites = 37, Kimura (unadjusted) = 54.83 Transitions / transversions = 2.18 (37/17) Gap_init rate = 0.05 (8 / 152), avg. gap size = 1.12 (9 / 8) 516 21.91 1.48 8.73 chr5qtel1M 113454 113588 (886412) C MIRc#SINE/MIR (141) 127 2 m_b247s601i3 9767 chr5qtel1M 113454 CTGAGGC--AGTTGGGGCTAAGTGATTTGCCCAAGGTCACACAACTAGGA 113501 -- v- i i i i -- C MIRc#SINE/MIR 127 CTGAGGCTCAGA-GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG-- 81 chr5qtel1M 113502 AGTGTTAAGTGTCTGAGGTAAGATTTGAACTCAGGTCCTTCTGAATTCAA 113551 ----- v v viii i i i i i v i C MIRc#SINE/MIR 80 -----TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAA 36 chr5qtel1M 113552 GGCTGGAACTCCATCCGCTGCACCACCTAGCTGCCTC 113588 v ii vi iv i ---i C MIRc#SINE/MIR 35 GTCCAGTGCTCTTTCCACTGCACCAC---ACTGCCTC 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.25 CpG sites = 19, Kimura (unadjusted) = 26.63 Transitions / transversions = 2.38 (19/8) Gap_init rate = 0.09 (12 / 134), avg. gap size = 1.08 (13 / 12) 377 29.98 6.83 0.58 chr5qtel1M 113903 114063 (885937) MIR1_Amn#SINE/MIR 3 173 (57) m_b247s601i4 9768 chr5qtel1M 113903 GAAAGACAGAGGTGGCCTAATAGCTAGAGC-CTGAA--GGCA---GGAAG 113946 ii i -v i i i v - i -- v --- i MIR1_Amn#SINE 3 GGGAGGCAG-TGTGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGAG 51 chr5qtel1M 113947 GTTTGAGTTCAAATCCAGCCTGAAATGTTTTATAGCTATGGGGGCT-GGG 113995 iii i ? ? v v vviviii ?vvi? i? v iv - MIR1_Amn#SINE 52 ACCTGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGG 101 chr5qtel1M 113996 CAAGACATTCAACCTTTCTCTGCTTCAATT---TCAAACATAAAATGGGG 114042 v i i? i v? i i --- vvii MIR1_Amn#SINE 102 CAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGG 151 chr5qtel1M 114043 TTAATAATAG-AACCTACCTTG 114063 v i v-i v i MIR1_Amn#SINE 152 ATAATGATACTGACCTCCTTTG 173 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.12 CpG sites = 29, Kimura (unadjusted) = 42.12 Transitions / transversions = 1.53 (29/19) Gap_init rate = 0.04 (7 / 160), avg. gap size = 1.71 (12 / 7) 678 26.91 5.74 0.45 chr5qtel1M 113926 114134 (885866) MIRc#SINE/MIR 30 249 (19) m_b247s601i5 9768 chr5qtel1M 113926 CTAGAGCCTGAAGGCAGGAAGGTTTGAGTTCAAATCCAGCCTGAAATGTT 113975 i - i i v iii i i i v v vviviii MIRc#SINE/MIR 30 CTGGA-CTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACT 78 chr5qtel1M 113976 TTATAGCTATGGGGGCT-GGGCAAGACATTCAACCTTTCTCTGCTTCAAT 114024 vv i v iv - v i i i vv i i MIRc#SINE/MIR 79 TACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGT 128 chr5qtel1M 114025 TTC---AAACATAAAATGGGGTTAATAATA---GA---ACCTACCTTGAG 114065 --- vvii v --- v---i iivi MIRc#SINE/MIR 129 TTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACA 178 chr5qtel1M 114066 TGGTGGTTGTGAGGATCAAAAGAGATAATAT-TGT-AAAACGCTTTGCAA 114113 v v v i - - i i MIRc#SINE/MIR 179 GGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTTTGTAA 228 chr5qtel1M 114114 ATCTCAATGTGCTATAGAAAT 114134 iivi v v MIRc#SINE/MIR 229 ACTGTAAAGTGCTATACAAAT 249 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.32 CpG sites = 32, Kimura (unadjusted) = 34.06 Transitions / transversions = 1.33 (32/24) Gap_init rate = 0.03 (7 / 208), avg. gap size = 1.86 (13 / 7) 28 3.31 0.00 0.00 chr5qtel1M 114142 114172 (885828) (ATC)n#Simple_repeat 1 31 (0) c_b247s251i1 9769 chr5qtel1M 114142 ATCATCATCATCATCTTCATCATCATCATCA 114172 v (ATC)n#Simple 1 ATCATCATCATCATCATCATCATCATCATCA 31 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 267 25.34 10.29 1.35 chr5qtel1M 114181 114316 (885684) C L2#LINE/L2 (893) 2189 2042 m_b247s601i6 9770 chr5qtel1M 114181 AAAGGTGACTTCAAAGGAGCGGCCGGGGAGGTAGAAGGACAACCAGGA-A 114229 v vvi i v i v - C L2#LINE/L2 2189 AAAGGAGACTGAGAAGGAGCGGCCAGTGAGGTAGGAGGAAAACCAGGAGA 2140 chr5qtel1M 114230 GAACAATGTTAGGAAAACC---TGGATAAACTATT----GA-----GAAG 114267 viiii ivv i i --- i v v i ---- ----- i C L2#LINE/L2 2139 GTGTGGTGTCCTGGAAGCCAAGTGAAGAAAGTGTTTCAAGAAGGAGGGAG 2090 chr5qtel1M 114268 TGACTGACAGTGTC-AATGGTGATCGAGAAGTCAAGGAGAAGGAGAGACT 114316 iii v - v v - ? i v ii v - C L2#LINE/L2 2089 TGATCAACTGTGTCAAATGCTGCT-GANAGGTCAAGTAAGATGAG-GACT 2042 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.81 CpG sites = 19, Kimura (unadjusted) = 31.81 Transitions / transversions = 1.27 (19/15) Gap_init rate = 0.05 (7 / 135), avg. gap size = 2.29 (16 / 7) 47 0.00 0.00 0.00 chr5qtel1M 114337 114376 (885624) (AG)n#Simple_repeat 1 40 (0) c_b247s251i2 9771 chr5qtel1M 114337 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 114376 (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 40 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 210 37.93 8.15 3.29 chr5qtel1M 114616 114934 (885066) C L2b_3end#LINE/L2 (12) 454 121 m_b247s601i8 9772 chr5qtel1M 114616 AGCAAGCATTCATTAAGCACTTACTGCATGCCAGGTGTTCAGCT---CAC 114662 i ii i i i i i ii i?i vv --- i C L2b_3end#LINE 454 AACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGC 405 chr5qtel1M 114663 TCTGGACATCACG--GGACAAACCAGTAAGTCATTCCCTGGACTCAGGAA 114710 vv i ivi -- i iv -- v? iv vv v i C L2b_3end#LINE 404 TGGGGATACAGCGGTGAACAAGACAG--ACNCGGTCCCTGCCCTCACGGA 357 chr5qtel1M 114711 GCTTACTTTCTAATGGGAAGAGA---ACAGGAAAGTGG-----GATATAT 114752 i vv i -i --- v v ?ii -----? - i C L2b_3end#LINE 356 GCTCACAGTCTAGTGGG-GGAGACAGACATGTAANCAGACAATNATA-AC 309 chr5qtel1M 114753 TTGGGATAT--ATTTGGAACT--GCTGGCTCAGAAGGAACCGTCTGGGCC 114798 iii ii iv--ivv i i -- vv i i iiiv i iv C L2b_3end#LINE 308 CCAGAGTGGCAGGGTAGGACTGGGGGGGCCCAGAGGAGGGCGCCTGACCC 259 chr5qtel1M 114799 AAGATAAGGAG-AAAGAAGGGCACTGAATCCAGCAAAGGT---ATTGGCA 114844 iivv ii i -v i i -i ---i i vii --- v vi C L2b_3end#LINE 258 GGCCTGGGGGGTCAGGGAGGGC-TT---CCCGGAGGAGGTGACATTTGAG 213 chr5qtel1M 114845 CTGGCAA--AGAGAAAGAATA-AAGTCAG--AGATGGGGGGGTGACATCA 114889 iv v--ii i v i -i ii -- ii ii i ivi-- C L2b_3end#LINE 212 CTGAGACCTGAAGGATGAGTAGGAGTTGGCCAGGCGAAGAGGTGGGG--A 165 chr5qtel1M 114890 AGGGTCTTTGGGAGCAAAGAGAAGAGTAGGGGAAATGGAATTGAG 114934 iv ivi - i i v i ? v v v vvi C L2b_3end#LINE 164 AGGGCGTTCCAG-GCAGAGGGAACAGCANGTGCAAAGGCCCTGAG 121 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 53.31 CpG sites = 77, Kimura (unadjusted) = 58.78 Transitions / transversions = 1.93 (77/40) Gap_init rate = 0.07 (22 / 318), avg. gap size = 1.68 (37 / 22) 340 27.72 4.92 2.40 chr5qtel1M 114616 114737 (885263) C L2a_3end#LINE/L2 (12) 505 381 m_b247s601i7 9772 chr5qtel1M 114616 AGCAAGCATTCATTAAGCACTTACTGCATGCCAGG---TGTTCAGCTCAC 114662 i ii i i i i iii --- vivv i C L2a_3end#LINE 505 AACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGCGC 456 chr5qtel1M 114663 TCTGGA--CATCACGGGACAAACCAG-TAAGTCATTCCCTGGACTCAGGA 114709 vv -- v vv i v -i i-- v vv v i C L2a_3end#LINE 455 TGGGGATACAGCAGTGAACAAAACAGACAAA--AGTCCCTGCCCTCATGG 408 chr5qtel1M 114710 AGCTTACTTTCTAATGGGAAGAGAACAG 114737 v i ii - C L2a_3end#LINE 407 AGCTTACATTCTAGTGGGGGGAG-ACAG 381 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.81 CpG sites = 19, Kimura (unadjusted) = 35.43 Transitions / transversions = 1.36 (19/14) Gap_init rate = 0.05 (6 / 121), avg. gap size = 1.50 (9 / 6) 19 19.25 3.39 3.39 chr5qtel1M 115039 115097 (884903) (AGAGAAG)n#Simple_repeat 1 59 (0) m_b247s252i0 9773 chr5qtel1M 115039 AGGGAAGGGAGAAGAGAGGAAAGAAGAAGGAGGGAAGAGTG-GGA-AGGA 115086 i i i i - - i v -i - i (AGAGAAG)n#Si 1 AGAGAAGAGAGAAGAGAGAAGAG-AGAA-GAGAGAAGAGAGAAGAGAGAA 48 chr5qtel1M 115087 GAGAGAAGGGA 115097 i (AGAGAAG)n#Si 49 GAGAGAAGAGA 59 Matrix = Unknown Transitions / transversions = 8.00 (8/1) Gap_init rate = 0.07 (4 / 58), avg. gap size = 1.00 (4 / 4) 12 28.16 0.00 4.08 chr5qtel1M 116147 116197 (883803) (AGAA)n#Simple_repeat 1 49 (0) m_b247s252i1 9774 chr5qtel1M 116147 AGAGAACAAAGAGGAAAAGAATGAAATAACTGGATAAAAGGAAGAAAGAA 116196 - v iii v v -v i vi i (AGAA)n#Simpl 1 AGA-AAGAAAGAAAGAAAGAAAGAAAGAA-AGAAAGAAAGAAAGAAAGAA 48 chr5qtel1M 116197 A 116197 (AGAA)n#Simpl 49 A 49 Matrix = Unknown Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.04 (2 / 50), avg. gap size = 1.00 (2 / 2) 525 27.14 10.82 3.36 chr5qtel1M 117258 117562 (882438) L1ME3Cz_3end#LINE/L1 12 338 (659) m_b247s551i0 9775 chr5qtel1M 117258 AATCCATAGAGAACTACATCAAATTTATAAGAA---TACAATTTGTTCCC 117304 vi i v vv iv ---v ------- L1ME3Cz_3end# 12 AATATATAAAGAACTCCTACAAATCAATAAGAAAAAGACAA-------CC 54 chr5qtel1M 117305 CAATTGATAAATGGTCAAAGAATATAAATAGGCAGTTTTCAGATGAAGAA 117354 v v v i i i i iv v i L1ME3Cz_3end# 55 CAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGGAA 104 chr5qtel1M 117355 AT------------TAAAGTTCTGTATAGTTGT------------ATGAT 117380 i------------ vv v v v v i------------i i L1ME3Cz_3end# 105 ACCCGAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTAAT 154 chr5qtel1M 117381 CAGAGAAATCCAAATTAAAACAATTCTGAGGTATTACCTCACACCTATCA 117430 i v ? ivv i ii ii i L1ME3Cz_3end# 155 CAGGGAAATGCAAATTAAAACNACAATGAGATACCATTTCACACCCATCA 204 chr5qtel1M 117431 GGTTAGCTAATATACCAGAAAAA---GAAAATCATAAGTATTGGAGAAGA 117477 i i v v vi--- i--- v vvi i v i L1ME3Cz_3end# 205 GATTGGCAAAAATTT---AAAAGTCTGACAATACCAAGTGTTGGCGAGGA 251 chr5qtel1M 117478 TG-GGAGAAAGTTGGAACCCTAGTGCATTGTGGGTGGAGTTATGAATTGA 117526 - -iv i vi i i iv iiv i i i L1ME3Cz_3end# 252 TGTGGAGAAA-CGGGAACTCTCATACACTGCTGGTGGGAGTGTAAATTGG 300 chr5qtel1M 117527 TCCAGCCATTCTAGAAAGCAGTTTG--AACTTCTAATA 117562 v i i i i i i -- iv i L1ME3Cz_3end# 301 TACAACCACTTTGGAGAGCAATTTGGCAATATCTAGTA 338 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.25 CpG sites = 47, Kimura (unadjusted) = 34.79 Transitions / transversions = 1.42 (47/33) Gap_init rate = 0.06 (17 / 304), avg. gap size = 2.59 (44 / 17) 635 27.00 10.40 0.73 chr5qtel1M 117302 117551 (882449) L1ME5_3end#LINE/L1 56 329 (612) m_b247s551i1 9775 chr5qtel1M 117302 CCCCAATTGATAAATGGTCAAAGAATATAAATAGGCAGTTTTCAGATGAA 117351 v v v i i i i v v i L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chr5qtel1M 117352 GAAATT--AAAGT----------TCTGTATAGTTGT------------AT 117377 ii-- v---------- v v v v i------------i L1ME5_3end#LI 106 GAAACCCGAAAGGCTAACAAGCATATGAAGAGATGCTCAAACTCATTAGT 155 chr5qtel1M 117378 GATCAGAGAAATCCAAATTAAAACAATTCTGAGGTATTACCTCACACCTA 117427 i v ivv i i i i L1ME5_3end#LI 156 AATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCTA 205 chr5qtel1M 117428 TCAGGTTAGCTAATATACCAGAAAA--AGAAAATCATAAGTATTGGAGAA 117475 i ii i v v --i i--i v vvi i v i L1ME5_3end#LI 206 TTAGACTGGCAAAAAT--TAGAAAGCTGGATAATGCCAAGTGTTGGCGAG 253 chr5qtel1M 117476 GATGGGAGAAAGTTGGAACCCTAGTGCATTGTGGGTGGAGTTATGAATTG 117525 v i i ?i v vi i iv iiv i ii i L1ME5_3end#LI 254 GATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACTG 303 chr5qtel1M 117526 ATCCAGCCATTCTAGAAAGCAGTTTG 117551 i v i i i i L1ME5_3end#LI 304 GTGCAGCCATTCTGGAGAGCAATCTG 329 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.76 CpG sites = 42, Kimura (unadjusted) = 34.76 Transitions / transversions = 1.68 (42/25) Gap_init rate = 0.02 (6 / 249), avg. gap size = 4.67 (28 / 6) 647 22.54 1.70 1.70 chr5qtel1M 117376 117551 (882449) L1MB2_3end#LINE/L1 154 329 (589) m_b247s551i2 9775 chr5qtel1M 117376 ATGATCAGAGAAATCCAAATTAAAACAATTCTGAGGTATTACCTCACACC 117425 v i i v i v ivv i i L1MB2_3end#LI 154 ATCATTAGGGAAATGCAAATCAAAACCACAATGAGATATCACCTCACACC 203 chr5qtel1M 117426 TATCAGGTTAGCTAATATACCAGAAAA--AGAAAATCATAAGTATTGGAG 117473 i i v i v -- i -- v i i v L1MB2_3end#LI 204 CATTAGGATGGCTACTAT--CAAAAAAACAGAAAATAACAAGTGTTGGCG 251 chr5qtel1M 117474 AAGATG-GGAGAAAGTTGGAACCCTAGTGCATTGTGGGTGGAGTTATGAA 117522 i - - v i v iiv i i L1MB2_3end#LI 252 AGGATGTGGAGAAA-TTGGAACCCTTGTGCACTGTTGGTGGGAATGTAAA 300 chr5qtel1M 117523 TTGATCCAGCCATTCTAGAAAGCAGTTTG 117551 v i v ii v i i v L1MB2_3end#LI 301 ATGGTGCAGCCGCTATGGAAAACAGTATG 329 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 26.50 CpG sites = 23, Kimura (unadjusted) = 27.30 Transitions / transversions = 1.44 (23/16) Gap_init rate = 0.03 (5 / 175), avg. gap size = 1.20 (6 / 5) 231 34.97 0.61 0.61 chr5qtel1M 117548 117711 (882289) L1ME4c_3end#LINE/L1 367 530 (300) m_b247s551i3 9775 chr5qtel1M 117548 TTTGAACTTCTAATACCACAATTAGGTCTGTATTCCAAAGAAATCATTTA 117597 v ivv v vvi i vv v i i i v i L1ME4c_3end#L 367 TTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCA 416 chr5qtel1M 117598 AAAAGGAGAAGCATTCTACATGTACAAAAATATTTATAGCAATTCTTTTT 117647 - i i iv vv i i i i i i v iivi v L1ME4c_3end#L 417 AAA-GAAGGAAAAAGCTATATGCACGAAGATGTTCATTGCAGCGTTATTT 465 chr5qtel1M 117648 -TAGGAACAAAGAATTGGAAATTGAGGAAATGCCCATCATTTGGAAAATG 117696 - iv i i i ivivvv i v v v ii L1ME4c_3end#L 466 ATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAATG 515 chr5qtel1M 117697 TGTGAATAAATTGTG 117711 vv i i i L1ME4c_3end#L 516 GTTAAGTAAATTATG 530 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 44.94 CpG sites = 31, Kimura (unadjusted) = 48.42 Transitions / transversions = 1.19 (31/26) Gap_init rate = 0.01 (2 / 163), avg. gap size = 1.00 (2 / 2) 274 28.87 1.03 0.00 chr5qtel1M 117615 117711 (882289) L1ME3F_3end#LINE/L1 430 527 (463) m_b247s551i4 9775 chr5qtel1M 117615 ACATGTACAAAAATATTTATAGCAATTCTTTTT-TAGGAACAAAGAATTG 117663 i i i iiv v i- iv i i i L1ME3F_3end#L 430 ACATGTACAAGAATGTTCATAGCAGCACTGTTCGTAATAGCAAAAAACTG 479 chr5qtel1M 117664 GAAATTGAGGAAATGCCCATCATTTGGAAAATGTGTGAATAAATTGTG 117711 ivivvv i iviv i vi i L1ME3F_3end#L 480 GAAACAACCCAAATGTCCATCGACAGGAGAATGGATAAATAAATTGTG 527 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.51 CpG sites = 18, Kimura (unadjusted) = 37.92 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.01 (1 / 96), avg. gap size = 1.00 (1 / 1) 234 32.08 1.84 2.47 chr5qtel1M 117616 117778 (882222) L1ME3G_3end#LINE/L1 427 588 (336) m_b247s551i5 9775 chr5qtel1M 117616 CATGTACAAAAATATTTATAGCAAT-TCTTTTTTAGGAACAAAGAATTGG 117664 ii i i v ii- iv v iv i i i L1ME3G_3end#L 427 CATGTACAAGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGG 476 chr5qtel1M 117665 AAATTGAGGAAATGCCCATCATTTGGAAAATGTGTGAATAAATTGTGAAG 117714 ivivvv i v v ii vv i i -- L1ME3G_3end#L 477 AAACAACCTAAATGTCCATCAATAGGGGAATGGTTAAATAAATTATG--G 524 chr5qtel1M 117715 CATACTCTTGTACTATAAGAAATGATG-AGTT-TCAGAAAAACTTGGGAA 117762 i ii --i iii v iv - i?- i i i v vi v L1ME3G_3end#L 525 TATATCC--ATACTATGGAATACTATGCAGCNGTTAAAAAGAATGAGGTA 572 chr5qtel1M 117763 GATTTACATGAACTGA 117778 i i v L1ME3G_3end#L 573 GATCTATATGTACTGA 588 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 43.19 CpG sites = 33, Kimura (unadjusted) = 44.39 Transitions / transversions = 1.83 (33/18) Gap_init rate = 0.04 (7 / 162), avg. gap size = 1.00 (7 / 7) 407 23.33 0.85 9.17 chr5qtel1M 118167 118284 (881716) MIRb#SINE/MIR 4 112 (156) m_b247s601i9 9776 chr5qtel1M 118167 AGGGGCAGCTAGGTGGCACAGTGGACAGAGTGCTGGCCCTGAAGTCAGGA 118216 --- ii v ii v ii i iv MIRb#SINE/MIR 4 AGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGAC 50 chr5qtel1M 118217 GGACCTGAGTTCAAATGTGACCTCAGACACTTAATATGTCCTGGCTGTGT 118266 i i i viviv v v ------- i MIRb#SINE/MIR 51 AGACCTGGGTTCGAATCCCGGCTCTGCCACTTA-------CTAGCTGTGT 93 chr5qtel1M 118267 GACCTTGGGTGAA-TACTT 118284 ii i- MIRb#SINE/MIR 94 GACCTTGGGCAAGTTACTT 112 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.98 CpG sites = 17, Kimura (unadjusted) = 28.63 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.09 (11 / 117), avg. gap size = 1.00 (11 / 11) 253 17.65 1.96 0.00 chr5qtel1M 118281 118331 (881669) MIR#SINE/MIR 72 123 (139) m_b247s601i10 9777 chr5qtel1M 118281 ACTTCCTGGCTGTGTGACCTTGGGCAAGTCACCTAATCCCAAC-TGCCTC 118329 v i i i i i vvi- MIR#SINE/MIR 72 ACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTC 121 chr5qtel1M 118330 AG 118331 MIR#SINE/MIR 122 AG 123 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 20.54 CpG sites = 6, Kimura (unadjusted) = 20.54 Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.02 (1 / 50), avg. gap size = 1.00 (1 / 1) 348 27.48 0.72 10.32 chr5qtel1M 121201 121338 (878662) C MIRc#SINE/MIR (141) 127 2 m_b247s601i11 9778 chr5qtel1M 121201 CTGAGGCAATTGGAGGT-AAGTGACTTGTCACCAAGGGTCACATGGCTAG 121249 vvvvi - i -- - ii C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCC--CAAGG-TCACACAGCTAG 81 chr5qtel1M 121250 GAAGTGTTAAGTGACTACGGCCACACTTGAACTTAGTCCCTTCTGACTCC 121299 ------- i viv v viv i ii vi i i C MIRc#SINE/MIR 80 -------TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCC 38 chr5qtel1M 121300 AGGGCTGGTGCTCTATCCACTTTGACATCTAGCTGCCCC 121338 i v ii v ---i i vvi i C MIRc#SINE/MIR 37 AAGTCCAGTGCTCTTTCCACT---GCACCACACTGCCTC 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.37 CpG sites = 20, Kimura (unadjusted) = 34.62 Transitions / transversions = 1.43 (20/14) Gap_init rate = 0.10 (14 / 137), avg. gap size = 1.00 (14 / 14) 12 14.63 0.00 6.25 chr5qtel1M 121628 121661 (878339) (GGAA)n#Simple_repeat 1 32 (0) m_b247s252i2 9779 chr5qtel1M 121628 GGAGAGCAAGGAAGGATAGGAAGGAATGGGGGAA 121661 - v - v ii (GGAA)n#Simpl 1 GGA-AGGAAGGAAGGA-AGGAAGGAAGGAAGGAA 32 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2) 18 4.17 4.00 0.00 chr5qtel1M 121767 121791 (878209) (AC)n#Simple_repeat 1 26 (0) m_b247s252i3 9780 chr5qtel1M 121767 ACACA-ACACACACATACACACACAC 121791 - i (AC)n#Simple_ 1 ACACACACACACACACACACACACAC 26 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 23 15.50 0.00 0.00 chr5qtel1M 121930 121972 (878028) (ACAG)n#Simple_repeat 1 43 (0) m_b247s252i4 9781 chr5qtel1M 121930 ACAGTGAGAGAGACAGGCAGACAGACAGACAGACACACACACA 121972 vv v i v v (ACAG)n#Simpl 1 ACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACA 43 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 59 1.84 0.00 0.00 chr5qtel1M 121974 122028 (877972) (AG)n#Simple_repeat 1 55 (0) c_b247s251i3 9782 chr5qtel1M 121974 AGAGACAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 122023 v (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr5qtel1M 122024 AGAGA 122028 (AG)n#Simple_ 51 AGAGA 55 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 306 22.43 7.22 3.48 chr5qtel1M 122065 122258 (877742) L1MEi_5end#LINE/L1 2000 2200 (12) m_b247s551i6 9783 chr5qtel1M 122065 GGAAAGAGGGAGGGACAG-AGAGAGAGAGAATAACTAAGAGAAAAGAGAA 122113 - i ii v - i i i ? i iv v v v L1MEi_5end#LI 2000 GGAAAG-GAGAGAAAAAGNAAAGAAAAAGNATGATAAACAGAAAACACAA 2048 chr5qtel1M 122114 AATAAGATGG--AAAA-------AAATACA-CAGTAATCAAAACTGTAAA 122153 --i ------- i - v --- L1MEi_5end#LI 2049 AATAAGATGGTAGAAATAAGTCCAAATATATCAGTAATCACAA---TAAA 2095 chr5qtel1M 122154 TGTGAATGAGATGAACTTACCTACAAAACAGAAGCAGAGAG---CAGAAT 122200 i iiv i i iv - -- v--- v L1MEi_5end#LI 2096 TGTAAATGGATTAAACTCACCTATTAAA-AGA--CAGAGATTATCAGATT 2142 chr5qtel1M 122201 GGATTAGAAACAAGAACTTAACAATGTATTATCTACAAGAGACACACTTG 122250 i v i iii i v i ii i i i i L1MEi_5end#LI 2143 GGATTAAAAAAAAAAATCCAGCTATATGCTGTTTACAAGAGACACACCTA 2192 chr5qtel1M 122251 ATACAAAA 122258 v L1MEi_5end#LI 2193 AAACAAAA 2200 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 27.81 CpG sites = 29, Kimura (unadjusted) = 27.81 Transitions / transversions = 2.23 (29/13) Gap_init rate = 0.06 (12 / 193), avg. gap size = 1.75 (21 / 12) 245 24.48 7.01 6.33 chr5qtel1M 122150 122306 (877694) L1M4_orf2#LINE/L1 38 195 (3099) m_b247s551i7 9783 chr5qtel1M 122150 TAAATGTGAATGAGATGAACTTACCTACAAAACAGAAGCAGAGA---GCA 122196 i iiv i viv v iv --- i --- L1M4_orf2#LIN 38 TAAATGTAAATGGATTAAACACTCCAATCAAA---AGGCAGAGATTGGCA 84 chr5qtel1M 122197 GAATGGATTAGAAACAAGAACTTAACAATGTATTATCTACAAGAGACACA 122246 v i vv vi iii v i ii i L1M4_orf2#LIN 85 GAATGGATAAAAAAACATGATCCAACTATATGCTGTCTACAAGAGACACA 134 chr5qtel1M 122247 CTT--GATACAAAAGAAAGCCACAAA---GTTAAAAT---AAGGACCTGG 122288 -- v ----- v --- i v--- -- L1M4_orf2#LIN 135 CTTTAGATTC-----AAAGACACAAATAGGTTGAAAGTAAAAGGA--TGG 177 chr5qtel1M 122289 AACAGGATCTATTATGTA 122306 v i v ii i L1M4_orf2#LIN 178 AAAAAGATATACCATGCA 195 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 30.24 CpG sites = 21, Kimura (unadjusted) = 30.24 Transitions / transversions = 1.40 (21/15) Gap_init rate = 0.09 (14 / 156), avg. gap size = 1.50 (21 / 14) 17 25.77 3.90 2.56 chr5qtel1M 122611 122687 (877313) (ATAAAT)n#Simple_repeat 1 78 (0) m_b247s252i5 9784 chr5qtel1M 122611 ATAAATAGAAAGTTATAAAGTTAGATAT-GATATAACTCTTGAAAAAAAT 122659 v -- vv i -i v v vi v v (ATAAAT)n#Sim 1 ATAAATATAAA--TATAAATATAAATATAAATATAAATATAAATATAAAT 48 chr5qtel1M 122660 -TGAATGGGAATATAAATA-AAATATATAT 122687 - i ivi - v (ATAAAT)n#Sim 49 ATAAATATAAATATAAATATAAATATAAAT 78 Matrix = Unknown Transitions / transversions = 0.60 (6/10) Gap_init rate = 0.07 (5 / 76), avg. gap size = 1.00 (5 / 5) 541 22.10 0.00 8.77 chr5qtel1M 122933 123056 (876944) MIRc#SINE/MIR 2 115 (153) m_b247s601i12 9785 chr5qtel1M 122933 GGGGCAGCTAGGTGGCACAGTGGATAGAGCATTAACCTTGAAGTCAGGAG 122982 i i--- ii v i iiv i i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr5qtel1M 122983 GACCTGAATTCAAATCTAGCCTCAGTCACTTAATACCTCCTAGCTGTGTG 123032 ii i i iv v v i ------- MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTG 91 chr5qtel1M 123033 ACCCTGGACAAGTCTCTTAACTCC 123056 i i v ii MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.90 CpG sites = 19, Kimura (unadjusted) = 27.17 Transitions / transversions = 3.17 (19/6) Gap_init rate = 0.08 (10 / 123), avg. gap size = 1.00 (10 / 10) 15 30.66 0.00 0.00 chr5qtel1M 123070 123113 (876887) (AA)n#Simple_repeat 1 44 (0) m_b247s252i7 9786 chr5qtel1M 123070 AAAAAAAAAAAAAAGAATTATATCAAAAAATATCAAAGAAATAA 123113 i vv v vv v vv i v (AA)n#Simple_ 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 44 Matrix = Unknown Transitions / transversions = 0.22 (2/9) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 257 22.07 3.11 7.10 chr5qtel1M 123143 123303 (876697) L1MD_orf2#LINE/L1 829 983 (2311) m_b247s551i8 9783 chr5qtel1M 123143 AATGCAAATGACAATCCTAACTAAAACTAAATTTGTAAGATGCAACAAAA 123192 v v v - - v v v ii i i v L1MD_orf2#LIN 829 AATGAAAATGAAAATAC-AAC-ATATCAAAATTTGTGGGACGCAGCTAAA 876 chr5qtel1M 123193 TAAGTACTCAG-GAGAAATTTTTACCTCTAACTGCTTATATTAATAAAAC 123241 vv i v - i v v v v ? i --- i v L1MD_orf2#LIN 877 GCAGTGCTGAGAGGGAAATTTATAGCACTAAATGCNTACAT---TAGAAA 923 chr5qtel1M 123242 AGAGGAAGAG---CAGATCAATGAATTTGA-CACCTAATTAAAAAAGAAA 123287 i --- i - i i - v i vi v i ---- L1MD_orf2#LIN 924 AGAGGAAAAGTCTCAAATCAAT-AATCTAAGCTCCCACCTCAAGAA---- 968 chr5qtel1M 123288 CACTAGAAAAAGAAGA 123303 -? L1MD_orf2#LIN 969 -NCTAGAAAAAGAAGA 983 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 25.68 CpG sites = 15, Kimura (unadjusted) = 26.57 Transitions / transversions = 0.83 (15/18) Gap_init rate = 0.09 (14 / 160), avg. gap size = 1.14 (16 / 14) 16 14.38 8.70 0.00 chr5qtel1M 123567 123612 (876388) (AAAATC)n#Simple_repeat 1 50 (0) m_b247s252i8 9787 chr5qtel1M 123567 AAAATC-AAATCAAAATGAAAAT--AAATGAGAAAGAAAAT-AAAAGCAA 123612 - v -- v i vv - v (AAAATC)n#Sim 1 AAAATCAAAATCAAAATCAAAATCAAAATCAAAATCAAAATCAAAATCAA 50 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.07 (3 / 45), avg. gap size = 1.33 (4 / 3) 930 31.85 6.02 4.51 chr5qtel1M 123707 125018 (874982) L1M4_orf2#LINE/L1 1036 2366 (928) m_b247s551i9 9788 chr5qtel1M 123707 GAAATAAATAAAATTAAAAAGTGGAAAATCCTTTGAACCAAAAATAA--A 123754 i - i i i i v vv v i-- vi -- L1M4_orf2#LIN 1036 GAAATAAATGAAAT-AGAGAATAGAAAAACAATAGAG--AAAATCAACGA 1082 chr5qtel1M 123755 AACAAGGAGTTGGTTTTATAGGAGAAAAAA-CAACAACAATAAAATAAAC 123803 v ii i v ---- i - v v i --i L1M4_orf2#LIN 1083 AACCAAAAGTTGGTTCTTT----GAAAAGATCAACAAAATTGA--CAAAC 1126 chr5qtel1M 123804 CATTAGCTAAACTGATTTTTTTAAAAGAAGAAAA---CCAAATTTTCAGT 123850 v i iivvvvv ii i ---i vii iv L1M4_orf2#LIN 1127 CTTTAGCTAGACTGACCAAGAAAAAAAGAGAGAAGACTCAAATTACTAAA 1176 chr5qtel1M 123851 ATCAATAATGAAAAGGAGTGAATGTACCACCAATGAAAATGAAATGAAGA 123900 iv ii i viv - i i ivvv vv i i L1M4_orf2#LIN 1177 ATCAGGAATGAAAGAGGGGACAT-TACTACCGACCTTACAGAAATAAAAA 1225 chr5qtel1M 123901 CAAT-ATTAGGAGTTATTTTATCAAATTATATGCCAATAAAACTTGTGTA 123949 vi - v iiv i v ivvv i i -- ivi L1M4_orf2#LIN 1226 GGATTATAAGGGAATACTATGAACAATTGTATGCCAACAAA--TTAGATA 1273 chr5qtel1M 123950 A-----ATGAAATGAGTGAATATTCACAAAAAG-TATAAATTGTTCAAAG 123993 ----- iiii -- vi i -i i i iiiv v L1M4_orf2#LIN 1274 ACCTAGATGAAATGGACAAAT--TCCTAGAAAGACACAAACTACCGAAAC 1321 chr5qtel1M 123994 TAAC--AAAAACTTGAAATAGAATATTTAAATAACCCTGTCTTAGAAAAA 124041 i -- i --- v i i iv i vvi iiv L1M4_orf2#LIN 1322 TGACTCAAGAA---GAAATAGAAAATCTGAATAGACCTATAACAAGTAAA 1368 chr5qtel1M 124042 GACATTAAGCAAGACATAAATAAAGTTTTGAAGGGTAAATAAAAACGCAG 124091 v i iiv vv v v v iiv ----i v i v L1M4_orf2#LIN 1369 GAGATTGAATTAGTAATCAAAAAACTTCCCA----CAAAGAAAAGCCCAG 1414 chr5qtel1M 124092 GATCAAACATATCTACAGGTGAATTATACCAAAAATTAAAAAAAATAATT 124141 ?i i iivv ii v v v v i i- L1M4_orf2#LIN 1415 GNCCAGATGGCTTCACTGGTGAATTCTACCAAACATTTAAAGAAG-AATT 1463 chr5qtel1M 124142 AATCATAACACTATGTAAACTATTTGGGAAAAAATA------------AT 124179 ivvi iv viii v iv-- ------------ i L1M4_orf2#LIN 1464 AACACCAATCCTTCACAAACTCTTCC--AAAAAATAGAAGAGGAGGGAAC 1511 chr5qtel1M 124180 CCTACTAAAGTCCTTTCTATGA-----------CTTTGATACCTAAACAG 124218 v v iv v v - ----------- ii v vi L1M4_orf2#LIN 1512 ACTTCCCAACTCATT-CTATGAGGCCAGTATTACCCTGATACCAAAACCA 1560 chr5qtel1M 124219 AATAGTAAAA--ATAGAAAAAGAAAACTATAGATTAATTTCCCTAATGAA 124266 i i ivi v -- i ii i ii v v L1M4_orf2#LIN 1561 GACAAAGACATCACAAGAAAAGAAAACTACAGACCAATATCCCTTATGAA 1610 chr5qtel1M 124267 TATTGATGTAAAT-TTTTAAATAAAATACTCACAAGGAGTGTGCAGCAAT 124315 v i v- ii v i vi ivv vi v i L1M4_orf2#LIN 1611 TATAGATGCAAAAATCCTCAACAAAATACTAGCAAACCGAATCCAGCAAC 1660 chr5qtel1M 124316 ATATGACATAAATCCTGCACTTTTGACCAGGTGGGATTTATACCAGGAAT 124365 i v vii iv i iv - i v L1M4_orf2#LIN 1661 ATATAAAAAGGATTATACACCAT-GACCAAGTGGGATTTATCCCAGGAAT 1709 chr5qtel1M 124366 ACTTGTATTCCTTCACTGCTTCAGCATTAGGAAAGC--------TAAT-- 124405 i vv ---------ii v i ?v i v -------- -- L1M4_orf2#LIN 1710 GCAAG---------GTTGGTTCAACATNCGAAAATCAATCAATGTAATAC 1750 chr5qtel1M 124406 ----TGTCAATA---TCAACAACCAATATTA--TGATTATCTCAATAAAT 124446 ---- i i --- v vi v v ii -- i i i L1M4_orf2#LIN 1751 ACCATATTAATAGAATAAAGGACAAAAACCACATGATCATCTCAATAGAC 1800 chr5qtel1M 124447 GCAGAAAAAGCTTTTGATAAAATCCAACATCCATTCCTATTTAAAACATT 124496 v i i v v iv v i L1M4_orf2#LIN 1801 GCAGAAAAAGCATTTGACAAAATCCAACACCCTTTCATGATAAAAACACT 1850 chr5qtel1M 124497 ATAAAATATAGAAATCAATGAAACTTTTCTTAAAATGATAAGTATTATCT 124546 vv v vv i vi v ii vi i i vv ivivi L1M4_orf2#LIN 1851 CAACAAACTAGGAATAGAAGGGAACTTCCTCAACCTGATAAAGGGCATCT 1900 chr5qtel1M 124547 ATCTAAAACCAAGAGGAGGCATTATCTGTTATGGGGATAAACTTGAAGCC 124596 ivv v v vvii i viv v v v i vi ? i L1M4_orf2#LIN 1901 ACGAAAAACCCACAGCTAACATCATACTTAATGGTGAAAGACTGAANGCT 1950 chr5qtel1M 124597 TTTCACATAACATCAGAGATTAATTAAAAGAGATATGAGATGTCCATTAT 124646 i v v v ---------i vi i v - ii v L1M4_orf2#LIN 1951 TTCCCCCTAAGATCAG---------GAACAAGACAAG-GATGTCCGCTCT 1990 chr5qtel1M 124647 CCCCATTATCATTCAATATTGTACCAGAAATGTGAGTTATAACAATAAGA 124696 v i vii i ii ii viv ii vii v i L1M4_orf2#LIN 1991 CGCCACTTCTATTCAACATTGTACTGGAGGTTCTAGCCAGGGCAATTAGG 2040 chr5qtel1M 124697 CAATAAAAGAAGTTGCCTAAGAAAAGGTATCAAG------------GAAA 124734 v ii ------- v i v ------------ i L1M4_orf2#LIN 2041 CAAGAAAAAGA-------AATAAAAGGCATCCAGATTGGAAAGGAAGAAG 2083 chr5qtel1M 124735 CAAAATGATCACTCTTTGCAGATGATATGATGATGCACTTAGAAAACTCT 124784 i iv v v i i vv i iv ii L1M4_orf2#LIN 2084 TAAAACTATCTCTATTCGCAGATGACATGATCTTGTATATAGAAAATCCT 2133 chr5qtel1M 124785 AGAGATCTAACTGAAAACCTAGCTGAAACAATTCATGACTTTTAAGAAAG 124834 ii viiv ?i v viv vi vv i -v i iv i L1M4_orf2#LIN 2134 AAGGAATCCACNAAAAAACTATTAGAACTAATAAACGA-GTTCAGCAAGG 2182 chr5qtel1M 124835 TTACAAGATATAAAATAAATCCACATAAGTCATCAGCATTTCTATACATG 124884 i i i i v vi v i viv i iv L1M4_orf2#LIN 2183 TTGCAGGATACAAGATCAATATACAAAAATCAATTGTATTTCTATACACT 2232 chr5qtel1M 124885 ACCAATA---AATCCCAGAAGGAAAAGCT-AGAAAGTGAAATTCCATTTA 124930 v i--- v i v --i - ii-- L1M4_orf2#LIN 2233 AGCAATGAACAATCCGAAAATGAAA--TTAAGAAAAC--AATTCCATTTA 2278 chr5qtel1M 124931 AAATAACTGCAGACAATATAAAATACTAGGGAGTTTATCTGCCCAGAGAA 124980 v i vv i v iv vi i vv i iv v i L1M4_orf2#LIN 2279 CAATAGCATCAAAAAGAATAAAATACTTAGGAATAAATTTAACAAAAGAA 2328 chr5qtel1M 124981 AGCTAAGAGCTATA---TGAACACGATTACAAAACATTTTT 125018 ivvi vi i --- v --- v L1M4_orf2#LIN 2329 GTGCAAGACTTGTACACTGAAAAC---TACAAAACATTGTT 2366 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.70 CpG sites = 219, Kimura (unadjusted) = 42.69 Transitions / transversions = 1.22 (219/180) Gap_init rate = 0.06 (80 / 1311), avg. gap size = 1.74 (139 / 80) 771 30.68 7.83 4.49 chr5qtel1M 123791 125387 (874613) L1M5_orf2#LINE/L1 1110 2757 (537) m_b247s551i10 9788 chr5qtel1M 123791 CAATAAAAT----AAACCATTAGCTAAACTGATTTTTTTAAAA-GA-AGA 123834 ---- vi ? i ivvvvv - - L1M5_orf2#LIN 1110 CAATAAAATTGATAAACCTCTAGCNAGACTGATCAAGAAAAAAAGAGAGA 1159 chr5qtel1M 123835 AAAC-CAAATTTTCAGTATCAATAATGAAAA-GGAGTGAATGT-ACCACC 123881 i - vi i iv - --- ii - i v L1M5_orf2#LIN 1160 AGACACAAATTACCAATATCAGGAATGAAAAAGGAG---ACATCACTACA 1206 chr5qtel1M 123882 AATGAAAATGAAATGAAGACAATATTAGGAGTTATTTTATCAA--ATTAT 123929 i vvv vv v v i vi v i v- v v -- i v L1M5_orf2#LIN 1207 GATCCTACAGACATTAAAAGGATAATAAGAGA-ATATTATGAACAACTTT 1255 chr5qtel1M 123930 ATGCCAATAAAACTTGTG----TAAATGAAATGAGTGAATATTCACAAAA 123975 -i v?---- i iiii - i vii L1M5_orf2#LIN 1256 ATGCCAATAAA-TTTGANAACTTAGATGAAATGGACAAAT-TCCTTGAAA 1303 chr5qtel1M 123976 AGTATAAATTGTTCAAAGTAAC--AAAAACTTGAAATAGAATATTTAAAT 124023 ii i ? iiiv v i -- i --- v i i L1M5_orf2#LIN 1304 AACACAANTTACCAAAACTGACNCAAGAA---GAAATAGAAAATCTGAAT 1350 chr5qtel1M 124024 AACCCTGTCTTAGAAAAAGACATTAAGCAAGACATAAATAAAGTTTTGAA 124073 i i v ivivv v i iivv vv v - vi ivv L1M5_orf2#LIN 1351 AGCCCTATATCTATTAAAGAAATTGAATTTGTAATTAA-AAACCTTCCCA 1399 chr5qtel1M 124074 GGGTAAATAAAAACGCAGGATCAAACATATCTACAGGTGAATTATACCAA 124123 ---i v viv vi i iivv ii v v L1M5_orf2#LIN 1400 ---CAAAGAAAACTCCAGGCCCAGATGGCTTCACTGGTGAATTCTACCAA 1446 chr5qtel1M 124124 AAATTAAAAAAAATAATTAATCATAACACTATGTAAACTATT-------- 124165 v v ii iv - vvi ivi iii v -------- L1M5_orf2#LIN 1447 ACATTTAAGGAAGAAAT-AATACCAATCTTACACAAACTCTTCCAGAAAA 1495 chr5qtel1M 124166 TGGGAAAAAAT--AATCCTACTAAAGTCCTTTC----------TATGACT 124203 i i i v-- iv v iv v v i----------i ? i L1M5_orf2#LIN 1496 TAGAAAAAGAGGGAACACTTCCCAACTCATTTTATGAGGCCAGCATNACC 1545 chr5qtel1M 124204 TTGATACCTAAACAGAATAGTAAAA--ATAGAAAAAGAAAACTATAGATT 124251 i v v?i i ivi v -- i ii i i ii L1M5_orf2#LIN 1546 CTGATACCAAAACCNGACAAAGACATTACAAGAAAAGAAAATTACAGACC 1595 chr5qtel1M 124252 AATTTCCCTAATGAATATTGATGTAAAT-TTTTAAATAAAATACTCACAA 124300 v v i v i v- ii ? i i vi L1M5_orf2#LIN 1596 AATATCCCTCATGAACATAGATGCAAAAATCCTNAACAAAATATTAGCAA 1645 chr5qtel1M 124301 GGAGTGTGCAGCAATATATGACATAAATCCTGCACTTTTGACCAGGTGGG 124350 ivv vi v i v vii vv i - iv i L1M5_orf2#LIN 1646 ATCGAATCCAGCAATATATAAAAAGGATAATACA-TCATGACCAAGTGGG 1694 chr5qtel1M 124351 ATTTATACCAGGAATACTTGTATTCCTTCACTGCTTCAGCATTAGGAAAG 124400 i v i vv ---------ii v i i v i v L1M5_orf2#LIN 1695 GTTTATCCCAGGAATGCAAG---------GTTGGTTTAACATTCGAAAAT 1735 chr5qtel1M 124401 C--------TAATTGTCAATATCAACA-----------ACCAATATTATG 124431 -------- vv v i ----------- vv vv L1M5_orf2#LIN 1736 CAATCAATGTAATTCACCATATTAACAGAATAAAGGAGAAAAATCATATG 1785 chr5qtel1M 124432 ATTATCTCAATAAATGCAGAAAAAGCTTTTGATAAAATCCAACATCCATT 124481 i i v i i i L1M5_orf2#LIN 1786 ATCATCTCAATAGATGCAGAAAAAGCATTTGACAAAATTCAACACCCATT 1835 chr5qtel1M 124482 CCTATTTAAAAC-ATTATAAAATATAGAAATCAATGAAACTTTTCTTAAA 124530 v iv v -v i vv i- i vi v ii vi i i v L1M5_orf2#LIN 1836 CATGATAAAAACTCTCAGCAAAC-TAGGAATAGAAGGGAACTTCCTCAAC 1884 chr5qtel1M 124531 ATGATAAGTATTATCTATCTAAAACCAAGAGGAGGCATTATCTGTTATGG 124580 v ivivi ivv v v v?ii i viv v L1M5_orf2#LIN 1885 CTGATAAAGGGCATCTACGAAAAACCTACAGCNAACATCATACTTAATGG 1934 chr5qtel1M 124581 GGATAAACTTGAAGCCTTTCACATAACATCAGAGATTAATTAAAAGAGAT 124630 v v ? vi ? i i v v v i ---------i vi i L1M5_orf2#LIN 1935 TGAAANACTGAANGCTTTCCCCCTAAGATCGG---------GAACAAGAC 1975 chr5qtel1M 124631 ATGAGATGTCCATTATCCCCATTATCATTCAATATTGTACCAGAAATGTG 124680 v - ii ? v i vii i ii ii viv L1M5_orf2#LIN 1976 AAG-GATGTCCGCTNTCACCACTTCTATTCAACATTGTACTGGAGGTCCT 2024 chr5qtel1M 124681 AGTTATAACAATAAGACAATAAAAGAAGTTGCCTAAGAAAAGGTATCAAG 124730 ii vvi i v ii ------- v i v L1M5_orf2#LIN 2025 AGCCAGTGCAATAAGGCAAGAAAAAGA-------AATAAAAGGCATAAAG 2067 chr5qtel1M 124731 ------------GAAACAAAATGATCACTCTTTGCAGATGATATGATGAT 124768 ------------ i ivi ?i v i i vi L1M5_orf2#LIN 2068 ATTGGAAAGGAAGAAATAAAACTGTCNTTATTCGCAGATGACATGATTGT 2117 chr5qtel1M 124769 GCACTTAGAAAACTCTAGAG-ATCTAACTGAAAACCTAGCTGAAAC-AAT 124816 ?i v ii ? i - - vi ? v - ii - L1M5_orf2#LIN 2118 NTACGTAGAAAATCCNAAAGAATCT-ACAAANAAACTA-CTAGAACTAAT 2165 chr5qtel1M 124817 TCATGACTTTTAAGAAAGTTACAAGATATAAAATAAATCCACATAAGTCA 124866 vvi v- iv i ii ?i i ii v vi v i L1M5_orf2#LIN 2166 AAGTGAA-TTTAGCAAGGTCGCNGGATACAAGGTCAATATACAAAAATCA 2214 chr5qtel1M 124867 TCAGCATTTCTATACATGACCAATA---AATCCCAGAAGGAAAAGCTAGA 124913 viv i i iv v i --- ivv i v vvi? i L1M5_orf2#LIN 2215 ATTGTATTTCTATATACTAGCAACAAACAATTGGAAAATGAAATTTNAAA 2264 chr5qtel1M 124914 AAGTGAAATTCCATTTAAAATAACTGCAGACAATATAAAATACTAGGGAG 124963 ---v v v i vv i v i ? vi i L1M5_orf2#LIN 2265 AA---CAATACCATTTACAATAGCATCAAAAAACATNAAATACTTAGGAA 2311 chr5qtel1M 124964 TTTATCTGCCCAGAGAAAGCTAAGAGCTATA---TGAACACGATTACAAA 125010 vv iv v i ? vivvi v ? --- v --- L1M5_orf2#LIN 2312 TAAATCTAACAAAANATGTGCAAGACCTNTACACTGAAAAC---TACAAA 2358 chr5qtel1M 125011 ACATTTTTCACA-----CAAAGACAGATATAAAC-AATGAAGAAATAATA 125054 vi v v -----i - iv i- i i - L1M5_orf2#LIN 2359 ACATTGCTGAGAGAAATTAAAGA-AGACCTAAATAAATGGAGAGAT-ATA 2406 chr5qtel1M 125055 TT-TGCTCATGG-TAGGCCAAGTCAATATAATGCAAATGAAAAGGCTAAC 125102 ii- i - v vvi v vi ?v i vv vv vv L1M5_orf2#LIN 2407 CCATGTTCATGGATTGGAAGACTCAATATTGTNAAGATGTCAATTCTCCC 2456 chr5qtel1M 125103 TAAATT---------ATTTAGTGCCACATCAATCTTACTACCAAGAACTA 125143 i --------- i i v ivi vv v v iv ---i L1M5_orf2#LIN 2457 CAAATTGATCTATAGATTCAATGCAATCCCAATCAAAATCCCAGCA---G 2503 chr5qtel1M 125144 GTTTTTTTA-AGAACTTAAATAAAGAAGTAAA---TAAAATTTATCTGGA 125189 i- v -----i v ivi --- v L1M5_orf2#LIN 2504 GTTTTTTTGTAGAAATT-----GACAAGCTGATTCTAAAATTTATATGGA 2548 chr5qtel1M 125190 AGAACAAAAAGTTAAGAATA-TCACAGGAATTGATGAAAAATGCAAAGGA 125238 ivi iiiii? -i v iv iv- - v i iv L1M5_orf2#LIN 2549 AATGCAAAGGACCNAGAATAGCCAAAACAATCT-TGAAAAA-GAAGAACA 2596 chr5qtel1M 125239 AAGT-----GTCCTAGCAGTACCAGATTTGAAACAATAC-AATTGCAAAG 125282 ----- v i - v ? ? ---- v -v ii L1M5_orf2#LIN 2597 AAGTTGGAGGACTTA-CACTACCNGATNT----CAAGACTTATTATAAAG 2641 chr5qtel1M 125283 CAGTTATGATGAAAACAATCTGATA-TGGTGT---GGTGG-------GAT 125321 viivi i v i i v i - i --- i i ------- L1M5_orf2#LIN 2642 CTACAGTAATCAAGACAGTGTGGTATTGGCGTAAGGATAGACAAATAGAT 2691 chr5qtel1M 125322 CATTGGAATAGATTAGGTACACAAAATGCAAAAGTAAATCC-CA-----A 125365 v i v ------ i i v i i i i - ----- L1M5_orf2#LIN 2692 CAATGGAACAGAATAG------AGAGTCCAGAAATAGACCCACACATATA 2735 chr5qtel1M 125366 TAGTCATCTCGTCTTTGATAAA 125387 i ? ?i vi i i L1M5_orf2#LIN 2736 TGGNCANTTGATTTTTGACAAA 2757 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.59 CpG sites = 254, Kimura (unadjusted) = 41.30 Transitions / transversions = 1.19 (254/214) Gap_init rate = 0.07 (111 / 1596), avg. gap size = 1.79 (199 / 111) 956 31.24 6.38 3.63 chr5qtel1M 124076 125015 (874985) L1M1_orf2#LINE/L1 1399 2363 (931) m_b247s551i11 9788 chr5qtel1M 124076 GTAAATAAAAACGCAGGATCAAACATATCTACAGGTGAATTATACCAAAA 124125 v i v i i vi iivv ii v v v v L1M1_orf2#LIN 1399 GTAAAGAAAAGCCCGGGACCCGATGGCTTCACTGCTGAATTCTACCAAAC 1448 chr5qtel1M 124126 ATTAAAAAAAATAATTAATCATAACACTATGTAAACTATTTGGGAAAA-- 124173 v i i- i vvi iv ivi iv i -- L1M1_orf2#LIN 1449 ATTTAAAGAAG-AACTAATACCAATCCTACTCAAACTATTCCGAAAAATA 1497 chr5qtel1M 124174 --------AATAATCCTACTAAAGTCCTTTC----------TATGACTTT 124205 --------iiv v v i v v ii---------- v ii L1M1_orf2#LIN 1498 GAGGAGGAGGGAATACTTCCAAACTCATTCTACGAGGCCAGTATTACCCT 1547 chr5qtel1M 124206 GATACCTAAAC-AGAATAGTAAAAAT-AGAAAAAGAAAACTATAGATTAA 124253 v - vv iv v v - i i iii L1M1_orf2#LIN 1548 GATACCAAAACCAGACAAAGACACATCAAAAAAAGAAAACTACAGGCCAA 1597 chr5qtel1M 124254 TTTCCCTAATGAATATTGATGTAAAT-TTTTAAATAAAATACTCACAAGG 124302 v i i i v- ii v i vi iv L1M1_orf2#LIN 1598 TATCTCTGATGAATATTGATGCAAAAATCCTCAACAAAATACTAGCAAAC 1647 chr5qtel1M 124303 AGTGTGCAGCAATATATGACATAAATCCTGCACTTTTGACCAGGTGGGAT 124352 v vi v i i v v v i v v - iv i L1M1_orf2#LIN 1648 CGAATTCAACAATACATTAAAAAGATCATTCA-TCATGACCAAGTGGGAT 1696 chr5qtel1M 124353 TTATACCAGGAATACTTGTATTCCTTCACTGCTTCAGCATTAGGAAAGCT 124402 v ? i i vv v --------- v i - v v iii L1M1_orf2#LIN 1697 TTATCCCNGGGATGCAAGGAT---------GGTTCAACAT-ACGCAAATC 1736 chr5qtel1M 124403 AAT---TGTCA------ATATCAACA---------ACCAATAT--TATGA 124432 --- v ------ --------- v v i-- L1M1_orf2#LIN 1737 AATCAATGTGATACATCATATCAACAGAATGAAGGACAAAAACCATATGA 1786 chr5qtel1M 124433 TTATCTCAATAAATGCAGAAAAAGCTTTTGATAAAATCCAACATCCATTC 124482 i i vi v v i v L1M1_orf2#LIN 1787 TCATTTCAATTGATGCTGAAAAAGCATTTGATAAAATTCAACATCCCTTC 1836 chr5qtel1M 124483 CTATTTAAAACATTATAAAATATAGAAATCAATGAAACTTTTCTTAAAAT 124532 v iv v vi vv vv i iv vi v i v vi i v L1M1_orf2#LIN 1837 ATGATAAAAACCCTCAAAAAACTGGGTATAGAAGGAACATACCTCAACAT 1886 chr5qtel1M 124533 GATAAGTATTATCTATCTAAAACCAAGAGGAGGCATTAT-CTGTTATGGG 124581 i iviii v ivvv i v v vvi i i - v- L1M1_orf2#LIN 1887 AATAAAAGCCATATACGACAGACCCACAGCTAGTATCATACTGA-ATGGG 1935 chr5qtel1M 124582 GATAAACTTGAAGCCTTTCACATAACATCAGAGATTAATTAAAAGAGATA 124631 v vi viv v v ii i-- iv v ----- L1M1_orf2#LIN 1936 GAAAAACTGAAAGCCTTTCCTCTAAGATCTGGAAC--ACGACAAG----- 1978 chr5qtel1M 124632 TGAGATGTCCATTATCCCCATTATCATTCAATATTGTACCAGAAATGTGA 124681 --- i i v v i i i i v ii i viv L1M1_orf2#LIN 1979 ---GATGCCCACTTTCACCACTGTTATTCAACATAGTACTGGAAGTCCTA 2025 chr5qtel1M 124682 GTTATAACAATAAGACAATA-AAAGAAGTTGCCTAAGAAAAGGTATC--- 124727 i v i v v - i -------- i i --- L1M1_orf2#LIN 2026 GCTAGAGCAATCAGACAAGAGAAAGAAAT--------AAAGGGCATCCAA 2067 chr5qtel1M 124728 ------AAGGAAACA---AAATGATCACTCTTTGCAGATGATATGATGAT 124768 ------ iv --- v vi v vv L1M1_orf2#LIN 2068 ATTGGAAAGGAAGAAGTCAAATTATCCTTGTTTGCAGATGATATGATCTT 2117 chr5qtel1M 124769 GCACTTAGAAAACTCTAGAGATCTAACTGAAAACCTAGCTGAAACAATTC 124818 ii i i vi i iiiv ?i v viv vii vv L1M1_orf2#LIN 2118 ATATTTGGAAAAACCTAAAGACTCCACNAAAAAACTATTAGAACTGATAA 2167 chr5qtel1M 124819 ATGACTTTTAAGAAAGTTACAAGATATAAAATAAATCCACATAAGTCATC 124868 ii v i- iv i i i v ivi v i vi L1M1_orf2#LIN 2168 ACAAATTC-AGTAAAGTTGCAGGATACAAAATCAACATACAAAAATCAGT 2216 chr5qtel1M 124869 AGCATTTCTATACATGACCAATA---AATCCCAGAAGGAAAAGCTAGAAA 124915 iiiv v i i--- iv i i - v v i L1M1_orf2#LIN 2217 AGCATTTCTATATGCCAACAGTGAACAATCTGAAAAAG-AAATCAAAAAA 2265 chr5qtel1M 124916 GTGAAATTCCATTTAAAATAACTGCAGACAATATAAAATACTAGGGAGTT 124965 -- i v i ii i i v v ivi i L1M1_orf2#LIN 2266 GT--AATCCCATTTACAATAGCCACAAATAAAATTAAATACCTAGGAATT 2313 chr5qtel1M 124966 TATCTGCCCAGAGAAAGCTAAGAGCTATATGAACACGATTACAAAACATT 125015 v ii iv i ivvv v v ii vv vi i i i L1M1_orf2#LIN 2314 AACTTAACCAAAGAAGTGAAAGATCTCTACAATGAAAACTATAAAACACT 2363 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.59 CpG sites = 149, Kimura (unadjusted) = 41.35 Transitions / transversions = 1.11 (149/134) Gap_init rate = 0.05 (51 / 939), avg. gap size = 1.86 (95 / 51) 323 32.87 1.93 4.46 chr5qtel1M 125949 126155 (873845) L1ME3Cz_3end#LINE/L1 194 395 (602) m_b247s551i12 9788 chr5qtel1M 125949 CACATCTATAAGACTGAATAACATGACATAAAAG---GAAAATGACAAAT 125995 i i v i ivv v v--- --- v iv i L1ME3Cz_3end# 194 CACACCCATCAGATTGGCAAAAATT---TAAAAGTCTGACAATACCAAGT 240 chr5qtel1M 125996 GCTAAAGGGAATGTGG-GAAATAGGGATACTAATGCACTGTTGGTAGAGT 126044 i iiv i i - ii i iv v i i i iiv L1ME3Cz_3end# 241 GTTGGCGAGGATGTGGAGAAACGGGAACTCTCATACACTGCTGGTGGGAG 290 chr5qtel1M 126045 TGTGAACGGTTCCAGTCATTCTGGAGAGCAATTTGGAAATTGGGCCAAAA 126094 i iv v v ii i i v --iv i iv L1ME3Cz_3end# 291 TGTAAATTGGTACAACCACTTTGGAGAGCAATTTGGCAAT--ATCTAGTA 338 chr5qtel1M 126095 AATTATAAAACTGTGGATAGTTGCCTTTGACTCAGCAGTATCACTACTAA 126144 v - i iv i v ---v vi i i vi v i L1ME3Cz_3end# 339 AAGT-TGAAGATGCGCATA---CCCTACGACCCAGCAATTCCACTTCTAG 384 chr5qtel1M 126145 GTCTGCATCCT 126155 v ii i L1ME3Cz_3end# 385 GTATATACCCT 395 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 42.14 CpG sites = 40, Kimura (unadjusted) = 45.06 Transitions / transversions = 1.60 (40/25) Gap_init rate = 0.05 (11 / 206), avg. gap size = 1.18 (13 / 11) 389 28.24 0.76 0.00 chr5qtel1M 125950 126080 (873920) L1ME5_3end#LINE/L1 199 330 (611) m_b247s551i13 9788 chr5qtel1M 125950 ACATCTATAAGACTGAATAACATGACATAAAAGGAAAATGACAAATGCTA 125999 i v ivv v v v v ivv v v i i i L1ME5_3end#LI 199 ACACCTATTAGACTGGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTG 248 chr5qtel1M 126000 AAGGGAATGTGGG-AAATAGGGATACTAATGCACTGTTGGTAGAGTTGTG 126048 iv i i - ? i iv v i i iiv i L1ME5_3end#LI 249 GCGAGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTA 298 chr5qtel1M 126049 AACGGTTCCAGTCATTCTGGAGAGCAATTTGG 126080 i v v v i i L1ME5_3end#LI 299 GACTGGTGCAGCCATTCTGGAGAGCAATCTGG 330 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.28 CpG sites = 19, Kimura (unadjusted) = 36.28 Transitions / transversions = 1.06 (19/18) Gap_init rate = 0.01 (1 / 130), avg. gap size = 1.00 (1 / 1) 295 32.89 3.25 3.25 chr5qtel1M 125977 126284 (873716) L1ME3G_3end#LINE/L1 219 526 (398) m_b247s551i14 9788 chr5qtel1M 125977 TAAAAG---GAAAATGACAAATGCTAAAGGGAATGTGGG-AAATAGGGAT 126022 --- v iv ? i i iiv i ii - ii v i L1ME3G_3end#L 219 TAAAAGNTTGATAATATCNAGTGTTGGCGAGGGTGTGGGGAAACGGGTAC 268 chr5qtel1M 126023 ACTAATGCACTGTTGGTAGAGTTGTGAACGGTTCCAGTCATTCTGGAGAG 126072 v v i i i iiv i iv v v i ? i i L1ME3G_3end#L 269 TCTCATACACTGCTGGTGGGAGTGTAAATTGGTACAGCCNTTTTGGAGGG 318 chr5qtel1M 126073 CAATTTGGAAATTGGGCCAA--AAAATTATAAAACTGTGGATAGTTGCCT 126120 v i ---ii v -- - - i v ---v L1ME3G_3end#L 319 CAATTTGGCAGT---ATCTATTAAAATT-TAAAA-TGCGCATA---CCCT 360 chr5qtel1M 126121 TTGACTCAGCAGTATCACTACTAAGTCTGCATCCTCAACTTTTTTTTTTA 126170 i i vi v ?i ?v vi v? vvvv vi ivi L1ME3G_3end#L 361 TTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAGAAATACTCGCA 410 chr5qtel1M 126171 AA---GGAAAAGGACCTAAATGGAAAAAAA-ATTTATAGCAGCTCTTTTT 126216 v --- v v --?iv v v ii -i i v vi v L1ME3G_3end#L 411 CATGTGCACAAGGA--NGCATGTACAAGGATGTTCATTGCAGCATTGTTT 458 chr5qtel1M 126217 GCAGGGGCAAAGAATTGGAAATTGAGGGGATACCCACCAGGTGGGGAAGG 126266 i ivi i i ivivvvii ii i ivv v L1ME3G_3end#L 459 GTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCAATAGGGGAATG 508 chr5qtel1M 126267 ATTCAACAAGTTATGGTA 126284 i v i i L1ME3G_3end#L 509 GTTAAATAAATTATGGTA 526 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 43.24 CpG sites = 55, Kimura (unadjusted) = 45.84 Transitions / transversions = 1.28 (55/43) Gap_init rate = 0.05 (15 / 307), avg. gap size = 1.33 (20 / 15) 350 32.97 1.17 4.22 chr5qtel1M 125984 126154 (873846) L1PA16_3end#LINE/L1 233 398 (515) m_b247s551i15 9788 chr5qtel1M 125984 AAAATGACAAATGCTAAAGGGAATGTGGGAAATAGGGA-TACTAATGCAC 126032 ii i iiv i iv i ii v -ii v i L1PA16_3end#L 233 AAAACAACAGATGCTGGCGAGGCTGCGGAGAAAAGGGAACGCTTATACAC 282 chr5qtel1M 126033 TGTTGGTAGAGTTGTGAACGGTTCCAGTCATTCTGGAGAGCAATTTGGAA 126082 i iiv i iviv i i i v i i i L1PA16_3end#L 283 TGTTGGTGGGAATGTAAATTAGTTCAGCCACTGTGGAAAGCAGTTTGGAG 332 chr5qtel1M 126083 ATTGGGCCAAAAAATTATAAAACTGTGGATAGTTGCC-TTTGACTCAGCA 126131 -vvi i i - ----- v ii i - i i L1PA16_3end#L 333 ATT-TCTCAAAGAACT-TAAAAC-----AGAACTACCATTCGACCCAGCA 375 chr5qtel1M 126132 GTATCACTACTAAGTCTGCATCC 126154 i vi i ii v ii i L1PA16_3end#L 376 ATCCCATTACTGGGTATATACCC 398 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 43.70 CpG sites = 41, Kimura (unadjusted) = 47.60 Transitions / transversions = 3.15 (41/13) Gap_init rate = 0.05 (9 / 170), avg. gap size = 1.00 (9 / 9) 282 36.67 1.51 1.77 chr5qtel1M 125993 126389 (873611) L1ME4c_3end#LINE/L1 242 637 (193) m_b247s551i16 9788 chr5qtel1M 125993 AATGCTAAAGGGAATGTGG-GAAATAGGGATACTAATGCACTGTTGGTAG 126041 iiv i i? i - iv v i? v i i i i L1ME4c_3end#L 242 AATGCTGGCGAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGG 291 chr5qtel1M 126042 AGTTGTGAACGGTTCCAGTCATTCTGGAGAGCAATTTGGAAATTGGGCCA 126091 vi? i iv v v ii v i i v vv vviv L1ME4c_3end#L 292 CANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATC 341 chr5qtel1M 126092 AAAAATTATAAAACTGTGGATAGTTGCCTTTGACTCAGCAGTATCACTAC 126141 i iii v vv v--- i i i vi v L1ME4c_3end#L 342 AAGAGCCATAAAAATGTTCATAC---CCTTTGACCCAGTAATTCCACTTC 388 chr5qtel1M 126142 TAAGTCTGCATCCTCAACTTTTTTTTTTAAAG---GAAAAGGACCTAAAT 126188 ii vv vi v ivvvv vv iv --- i -- v L1ME4c_3end#L 389 TGGGAATTTATCCTAAGGAAATAATTCAAAAGAAGGAAAAAG--CTATAT 436 chr5qtel1M 126189 GGAAAAAAA-ATTTATAGCAGCTCTTTTTGCAGGGGCAAAGAATTGGAAA 126237 v vi i -i i v vi v ii ivi i i L1ME4c_3end#L 437 GCACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAA 486 chr5qtel1M 126238 TTGAGGGGATACCCACCAGGTGGGGAAGGATTCAACAAGTTATGGTAAAT 126287 ivivvvii ii v ivv v i v ii i v L1ME4c_3end#L 487 CAACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACAT 536 chr5qtel1M 126288 TATTGTGACAGCATACCATTTGGTTATAAGAAATGACAAAGGGGATGGTT 126337 i?vivi ii v ii vii ii v i i vviv -i vi L1ME4c_3end#L 537 CNACTCGATGGAATATTATGCAGCCATTAAAAATGATAATTATGA-AGAC 585 chr5qtel1M 126338 TTTGAAAAAACCTGGGAAAAGTTACAT-ATATGATGCAAAATGAAGAGAG 126386 v v iv v i v -i - i iv i i i L1ME4c_3end#L 586 TATGTAGCAACATGGAAAATGTT-TATGATATAATGTTAAGTGAAAAAAG 634 chr5qtel1M 126387 CAG 126389 L1ME4c_3end#L 635 CAG 637 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 50.72 CpG sites = 79, Kimura (unadjusted) = 52.87 Transitions / transversions = 1.23 (79/64) Gap_init rate = 0.03 (11 / 396), avg. gap size = 1.18 (13 / 11) 237 28.37 2.65 1.97 chr5qtel1M 126866 127016 (872984) L1M5_orf2#LINE/L1 780 931 (2363) m_b247s551i17 9789 chr5qtel1M 126866 ATGAGTCAGAAAACAAATCATAG----AATTAATCAATAATTTCGTCAAA 126911 i i i v i i---- ivv v viv vi L1M5_orf2#LIN 780 ATGGGTCAAAGAAGAAATCACAANGGAAATTAGAAAATATTTTGAACTGA 829 chr5qtel1M 126912 GATAATTATGGTAATGACAGGACATGCAATATTTGTGGGATTCAACCAAA 126961 - i ?v iv - iv i - v v i i L1M5_orf2#LIN 830 -ATGANAATGAAAAT-ACAACATAT-CAAAATTTGTGGGATGCAGCTAAA 876 chr5qtel1M 126962 ACAGTACTTTGGGAAAAATTTATATCACTAAATACTTTAATCAAGAAAAA 127011 i i v i ii v ?i i ? vv i ii i L1M5_orf2#LIN 877 GCAGTGCTTAGAGGGAAATTTATAGCNTTAAATGCNTATATTAGAAAAGA 926 chr5qtel1M 127012 TGAAA 127016 v L1M5_orf2#LIN 927 AGAAA 931 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.68 CpG sites = 25, Kimura (unadjusted) = 37.68 Transitions / transversions = 1.47 (25/17) Gap_init rate = 0.03 (4 / 150), avg. gap size = 1.75 (7 / 4) 268 26.25 0.00 0.00 chr5qtel1M 126938 127017 (872983) L1MD_orf2#LINE/L1 853 932 (2362) m_b247s551i18 9789 chr5qtel1M 126938 CAATATTTGTGGGATTCAACCAAAACAGTACTTTGGGAAAAATTTATATC 126987 v iv i i i i vv i ii v L1MD_orf2#LIN 853 CAAAATTTGTGGGACGCAGCTAAAGCAGTGCTGAGAGGGAAATTTATAGC 902 chr5qtel1M 126988 ACTAAATACTTTAATCAAGAAAAATGAAAA 127017 i ? vv i ii i v L1MD_orf2#LIN 903 ACTAAATGCNTACATTAGAAAAGAGGAAAA 932 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 31.84 CpG sites = 13, Kimura (unadjusted) = 33.80 Transitions / transversions = 1.62 (13/8) Gap_init rate = 0.00 (0 / 79), avg. gap size = 0.0 (0 / 0) 420 32.45 10.40 1.34 chr5qtel1M 127478 127958 (872042) L1M4_orf2#LINE/L1 1468 1991 (1303) m_b247s551i19 9789 chr5qtel1M 127478 CCAATACTACATAAACTGTTAGAAAAAATT--AGGTAAAGAAGTCCTACT 127525 v v i v vv v-- ivi i i iiv v i L1M4_orf2#LIN 1468 CCAATCCTTCACAAACTCTTCCAAAAAATAGAAGAGGAGGGAACACTTCC 1517 chr5qtel1M 127526 AAATTCATTCTACAACACAAATATGATCTTAACACCTAAACCAGAGAAAA 127575 v i ii vi v i v i i i i v v i L1M4_orf2#LIN 1518 CAACTCATTCTATGAGGCCAGTATTACCCTGATACCAAAACCAGACAAAG 1567 chr5qtel1M 127576 AAATCAAAACAGAGGAAAACTATAAATCAATCT-CCTAATGACTACTGAT 127624 v v v i i i i i v - v v iv L1M4_orf2#LIN 1568 ACATCACAAGAAAAGAAAACTACAGACCAATATCCCTTATGAATATAGAT 1617 chr5qtel1M 127625 GC-AAATTTTTAAATAAAATATTATTATGAAGACTACAATAATAT----- 127668 - v ii v i i vi vivv v v ii i ----- L1M4_orf2#LIN 1618 GCAAAAATCCTCAACAAAATACTAGCAAACCGAATCCAGCAACATATAAA 1667 chr5qtel1M 127669 -----TT---CACAAAGACCAGACTGGACTTATACCAGAAATGAAAAGCT 127710 ----- --- v v iiiv i v i v i i L1M4_orf2#LIN 1668 AAGGATTATACACCATGACCAAGTGGGATTTATCCCAGGAATGCAAGGTT 1717 chr5qtel1M 127711 GATTCAATATTAGGAAAGCTATAATCATCACTAT---CCATCTTGAT--- 127754 i i ?v i v --- viiiv --- v i --- L1M4_orf2#LIN 1718 GGTTCAACATNCGAAAATC---AATCAATGTAATACACCATATTAATAGA 1764 chr5qtel1M 127755 ------GATAAAAACCATATT----TTTCCATAGATGCAGAAAGGAATTT 127794 ------ i i v---- i v i iiivv L1M4_orf2#LIN 1765 ATAAAGGACAAAAACCACATGATCATCTCAATAGACGCAGAAAAAGCATT 1814 chr5qtel1M 127795 TGAGACACTATAACATACATTTCTGTTAAAAAAATACTTAGGAAGGATAA 127844 v v v vi iv v iv -- v i i iv -iv i L1M4_orf2#LIN 1815 TGACAAAATCCAACACCCTTTCATG--ATAAAAACACTCAACAA-ACTAG 1861 chr5qtel1M 127845 GAATAAATGTCTCCTTCTTCAAAATGGTAAGTAGTATCTATCTAAAACTA 127894 i v vvvv i vv i ivi i ivv iv L1M4_orf2#LIN 1862 GAATAGAAGGGAACTTCCTCAACCTGATAAAGGGCATCTACGAAAAACCC 1911 chr5qtel1M 127895 AAAGCCAGCATTTTATCTTA-----------------GTCTTTTCAGTAA 127927 v i i iv - ----------------- ii ii vv L1M4_orf2#LIN 1912 ACAGCTAACATCATA-CTTAATGGTGAAAGACTGAANGCTTTCCCCCTAA 1960 chr5qtel1M 127928 AATCAGGGCCAAAACAAAGATGTCCATTTTC 127958 i iv i i ii i L1M4_orf2#LIN 1961 GATCAGGAACAAGACAAGGATGTCCGCTCTC 1991 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 42.61 CpG sites = 84, Kimura (unadjusted) = 43.75 Transitions / transversions = 1.20 (84/70) Gap_init rate = 0.04 (18 / 480), avg. gap size = 3.17 (57 / 18) 15 20.36 0.00 0.00 chr5qtel1M 128183 128211 (871789) (A)n#Simple_repeat 1 29 (0) m_b247s252i9 9790 chr5qtel1M 128183 AAAAAGAAAAAAAAAAATGAGAAAGAAAA 128211 i vi i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA 29 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 674 31.56 1.00 1.76 chr5qtel1M 128410 128809 (871191) C L1ME4c_3end#LINE/L1 (192) 638 242 m_b247s551i20 9791 chr5qtel1M 128410 TCTGCTTACTTCACTTAGCATTAGTTCATGT-CAGTCTTTCCAGGCTTTT 128458 vi i vv iv- --i v i vi C L1ME4c_3end#L 638 TCTGCTTTTTTCACTTAACATTATATCATAAACA--TTTTCCATGTTGCT 591 chr5qtel1M 128459 CTGAAATCAACCTGCTTATCATTTTTCATAGACCAATAATATTCCATTAC 128508 viiv i vv v iv v i vivv iiv C L1ME4c_3end#L 590 ACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCGA 541 chr5qtel1M 128509 ATTCATATACCATAATTTATTCAGTCATTCCCCAACATATGGGTATCCAC 128558 i ?v i i i ii v ivvv ii ii v C L1ME4c_3end#L 540 GTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAG 491 chr5qtel1M 128559 TCAATTTCCAGTTCTTTGCCACTACAAA-AACAGCTTCTACAAACATTTT 128607 vivi i i i i i i - - v v ii i C L1ME4c_3end#L 490 GTTGTTTCCAATTTTTCGCTATTATAAATAAC-GCTGCAATGAACATCTT 442 chr5qtel1M 128608 TGCACATTTTTCTATTTTCCCTCTTTT--ATGATCTCTTTGGGATACAGA 128655 i ii v vv - i -- v i i i v vv C L1ME4c_3end#L 441 CGTGCATATAGCT-TTTTCCTTCTTTTGAATTATTTCCTTAGGATAAATT 393 chr5qtel1M 128656 ACCAGTAGTTATACTGTTGGATCAAGGGTAATGGACAGTTTTGTAGCCCT 128705 v v viv i ii i i vv i v i i i C L1ME4c_3end#L 392 CCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTCT 343 chr5qtel1M 128706 TTGGGCACAGTTTAGAACAATTGCTCTCCAGAAAGATTGTATCATTTCAC 128755 -- ii - v v vvv i i i i i v i C L1ME4c_3end#L 342 T--GATAC-GTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTAC 296 chr5qtel1M 128756 AATTCTACAAACAATGAATTAGTGTCTCAGTTTTCCCACATCACTTCCAA 128805 ? v i v i v v ? vi iv i ? viiv i C L1ME4c_3end#L 295 ANTGCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAG 246 chr5qtel1M 128806 CATT 128809 C L1ME4c_3end#L 245 CATT 242 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.29 CpG sites = 69, Kimura (unadjusted) = 42.58 Transitions / transversions = 1.25 (69/55) Gap_init rate = 0.03 (10 / 399), avg. gap size = 1.10 (11 / 10) 23 12.64 0.00 2.27 chr5qtel1M 129188 129232 (870768) (CAAA)n#Simple_repeat 1 44 (0) m_b247s252i10 9792 chr5qtel1M 129188 CAAGCCAACATAACAAACAAACAAACAAACAATCAAAAAAAAAAA 129232 i v - v v v (CAAA)n#Simpl 1 CAAACAAACA-AACAAACAAACAAACAAACAAACAAACAAACAAA 44 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 16 23.93 0.00 0.00 chr5qtel1M 129199 129233 (870767) (A)n#Simple_repeat 1 35 (0) m_b247s252i11 9792 chr5qtel1M 129199 AACAAACAAACAAACAAACAATCAAAAAAAAAAAA 129233 v v v v v vv (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 35 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 438 27.14 3.90 1.91 chr5qtel1M 130062 130215 (869785) L1MEj_5end#LINE/L1 2004 2160 (0) m_b247s551i21 9793 chr5qtel1M 130062 AAATGAGATGGCAGGAAATACAGAATTAGTTATTTTAACTGT------GA 130105 i i v ---i i i iv v i iii ------i L1MEj_5end#LI 2004 AAGTAAGATGGAAGGAA---TAAAATCAAGTATATCAGTCGTTACACTAA 2050 chr5qtel1M 130106 ATGTGAATGGGATGAACTCTCCCATAAAACAAAAGCGGATAGCAGACTGG 130155 iv i v vi v v iv iv i L1MEj_5end#LI 2051 ATGTGAATGGACTGAATTCTCCCATTAAAAGACAGAGACTGTCAGATTGG 2100 chr5qtel1M 130156 ATTAAAAGCCAGAATTTTACAATATGTTGTTTACAAGAAACACATTTAAA 130205 i iv i iiivi v i i L1MEj_5end#LI 2101 GTTAAAAAACAAAACCCAGCTATATGCTGTTTACAAGAAACACACTTAAA 2150 chr5qtel1M 130206 GCAGAGTGAT 130215 i i L1MEj_5end#LI 2151 ACAAAGTGAT 2160 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.17 CpG sites = 28, Kimura (unadjusted) = 35.25 Transitions / transversions = 2.15 (28/13) Gap_init rate = 0.03 (4 / 153), avg. gap size = 2.25 (9 / 4) 3263 30.98 3.83 2.23 chr5qtel1M 130105 132666 (867334) L1M5_orf2#LINE/L1 40 2641 (653) m_b247s551i22 9793 chr5qtel1M 130105 AATGTGAATGGGATGAACTCTCCCATAAAACAAAAGCGGATAGCAGACTG 130154 i ?v i v v v viiv v iv iv L1M5_orf2#LIN 40 AATGTAAATGGNCTAAACACTCCAATTAAAAGGCAGAGATTGTCAGACTG 89 chr5qtel1M 130155 GATTAAAAGCCAGAATTTTACAATATGTTGTTTACAAGAAACACATTTAA 130204 v iv ii iiiv v i i i i i v L1M5_orf2#LIN 90 GATAAAAAAACAAGACCCAACTATATGCTGTCTACAAGAGACGCACTTTA 139 chr5qtel1M 130205 AGCAGAGTGATACATTTAGAATGAAGAATAAAGGGCTAGAGCAGAATCTA 130254 ii v iv i vv? iv - i i v i iv ii v L1M5_orf2#LIN 140 AATATAAAGACACAGANAGGTTGAA-AGTAAAAGGATGGAAAAAGATATA 188 chr5qtel1M 130255 TTATGCTTCAGGTGAAGTAAAAAAAAAGCAGGGATAGCAATCCTGATCAC 130304 ii v-v viiv ?i i - v ?i i v vi i vv L1M5_orf2#LIN 189 CCATGCA-AACACTAANCAAAAGAAA-GCTGGNGTGGCTATATTAATATC 236 chr5qtel1M 130305 AGATCAAGGAAAAT-CAAAGAAAGATCTAATTA--AGAGATAAGGAAGGA 130351 iv v i v - i v vv - -- i i L1M5_orf2#LIN 237 AGACAAAGTAGACTTCAAGGCAAGAAATA-TTACCAGAGATAAAGAGGGA 285 chr5qtel1M 130352 AACTATATCTTACTAAA-GGGTC---CCATAGAGAGTGAAGCAATAGCAA 130397 v i vi vv iv - ---i vi ---- vv i L1M5_orf2#LIN 286 CATTTCATAATGATAAAAGGGTCAATTCATCAAGA----AGACATAACAA 331 chr5qtel1M 130398 TACTAAACATATATGCCCCAAGTGGTATAGTATCCAAATTCCTAGAGGAG 130447 v ii i v v i iii v iv v v v ii v i L1M5_orf2#LIN 332 TCCTAAATGTGTATGCACCTAATAACAGAGCTTCAAAATACATGAAGCAA 381 chr5qtel1M 130448 AAGTTAAGAGAGCTGCAAGAAGAAATAGACG---CCAAAATTATACTAGT 130494 ii i v i iv i i--- v --- L1M5_orf2#LIN 382 AAACTGACAGAACTAAAAGGAGAAATAGACAAATCCACAATTATA---GT 428 chr5qtel1M 130495 GGGAGATCTCAATCTTGATCGCTCAGAACTAGATAAACCACAAAATAAAT 130544 ? i i ivi?vv v v v v i v --- i i i L1M5_orf2#LIN 429 NGGAGATTTTAACACNCCTCTCTCAGTAATTGATAGAACA---AGTAGAC 475 chr5qtel1M 130545 AAGAAAGCCGTTAAGGAGGTAAACAGA--------ATACTAGAAA--AGC 130584 i v v - vi i - -------- i vv -- i L1M5_orf2#LIN 476 AAAAAATCAGT-AAGGATATAGA-AGATTTGAACAACACTATCAACCAAC 523 chr5qtel1M 130585 TAGATATGATAGATCTTTGGAGAAAACTGAATGGAG--ACAGAAAGGAGT 130632 v iv i v iv iv v ?v ivv i-- ? v -- i L1M5_orf2#LIN 524 TTGACCTAATTGACATTTATAGAACACTNCACCCAACAACNGCA--GAAT 571 chr5qtel1M 130633 TTACTTTTTTCTCAGTGGTTCATGGAACCAATACAAAAATTGACCATTTG 130682 vi v i i ivv iv vvv v i v v ? L1M5_orf2#LIN 572 ACACATTCTTTTCAAGTGCACATGGAACATTTACCAAGATAGACCATATN 621 chr5qtel1M 130683 TTAGGGCATAAAA---ACCTCAAAATCAAATGCAAAAAGGCAGAAATAGT 130729 i i v ---ii ---i vi? i iiv vi L1M5_orf2#LIN 622 CTGGGCCATAAAACAAGTCTCAA---TAAATTTNAAAGGATTGAAATCAT 668 chr5qtel1M 130730 A-AATGCATTTTTTCAGATCATGATGCAATAAAAGTCATATGCAATA--- 130775 - iv i v i v i ii v v v viv vv --- L1M5_orf2#LIN 669 ACAGAGTATGTTCTCTGACCACAATGGAATTAAATTAGAAATCAATAACA 718 chr5qtel1M 130776 ------TATCCAGGAAAAATACACCAAAAATTAATTGGAATTTAAATAAT 130819 ------ ? i -- v - v --- v i i L1M5_orf2#LIN 719 AAAAGATANCTAG--AAAATCC-CCAAATATT---TGGAAATTAAACAAC 762 chr5qtel1M 130820 CTAATCCTAAAGAATGAATGAGTGAAAGAACAAATCAAAGACACAATCAA 130869 vi v i v ivv i v v v i?viv i i L1M5_orf2#LIN 763 ACACTTCTAAATAACCCATGGGTCAAAGAAGAAATCACAANGGAAATTAG 812 chr5qtel1M 130870 TAACTTCATCCAAGGGAATGACAATAATAAGACAACATATCAGATTTTGT 130919 v v viv iv vv ? i v v i v L1M5_orf2#LIN 813 AAAATATTTTGAACTGAATGANAATGAAAATACAACATATCAAAATTTGT 862 chr5qtel1M 130920 GGGATGCAGCCAAAGCAGTTATTAGGGGAAATTTTATATCTACAGATACT 130969 i vv i i v v ?vi i i ? L1M5_orf2#LIN 863 GGGATGCAGCTAAAGCAGTGCTTAGAGGGAAATTTATAGCNTTAAATGCN 912 chr5qtel1M 130970 TACTTGCATAAAATAGAGAAAGAG---AATATCAATGAATTGGGCTTACA 131016 iv --- i v ii ii --- v vi ii v L1M5_orf2#LIN 913 TATAT---TAGAAAAGAAGAAAGGCTTAAAATCAATGATCTAAGCTTCCA 959 chr5qtel1M 131017 ACTAAAAAAGCTAGAAAAAGAA---CAAATTAAAAATCCCTCAATTAAAT 131063 v v i --- ---- iv v? i L1M5_orf2#LIN 960 CCTTAAGAAGCTAGAAAAAGAAGAGCAAATTAAA----CCCAAAGNAAGT 1005 chr5qtel1M 131064 ACAAAATCTGAAATTCTGAAAATAAAGGGGGAGATTAATAAAATAGAAAA 131113 v iivvv vv i i ii vi i i i L1M5_orf2#LIN 1006 AGAAGGAAGGAAATAATAAAGATAAGAGCAGAAATCAATGAAATAGAAAA 1055 chr5qtel1M 131114 TAAGAAAACTATTGAATTAATAAATAAAACTAAGAGTTGGTTTTATGGAA 131163 i i? ? v v ivv v ii i i i i i v i L1M5_orf2#LIN 1056 CAAANANACAATAGAGAAAATCAACGAAGCCAAAAGCTGGTTCTTTGAAA 1105 chr5qtel1M 131164 AAAACAACAAAATAGATAAACCTTTAGTTAATTTGATTAG--AAAAAGGA 131211 i v i v i i? ivi i i-- i L1M5_orf2#LIN 1106 AGATCAATAAAATTGATAAACCTCTAGCNAGACTGATCAAGAAAAAAAGA 1155 chr5qtel1M 131212 AAAAAAAATCAAATTTTTAATCTCAAAAATGAAAA--GAACTTTCCACCA 131259 i i i vv vii v ii -- iv---- i L1M5_orf2#LIN 1156 GAGAAGACACAAATTACCAATATCAGGAATGAAAAAGGAGA----CATCA 1201 chr5qtel1M 131260 ATGAAGA------GGAAATTAGAGCAATAATTAGGAGTTATATTGCCCAA 131303 v iv ------i v i ivi v iiiv vv vv L1M5_orf2#LIN 1202 CTACAGATCCTACAGACATTAAAAGGATAATAAGAGAATATTATGAACAA 1251 chr5qtel1M 131304 TTATATGTCAATAAATTTGATAATTTAAGCGAAATGAAGGAATATCTACA 131353 i v i ? i iii i vi vi vv L1M5_orf2#LIN 1252 CTTTATGCCAATAAATTTGANAACTTAGATGAAATGGACAAATTCCTTGA 1301 chr5qtel1M 131354 AAAATCTGAATTGCCCAGGTTAACAGAAGAGGAAATAAATTATTTAAATA 131403 ivii ? i v iii i ?v i i vv i i L1M5_orf2#LIN 1302 AAAACACAANTTACCAAAACTGACNCAAGAAGAAATAGAAAATCTGAATA 1351 chr5qtel1M 131404 GTCCCATTTTAGAAAAAGAAATATAACAGCCTATTAATCAACTCCCTAAG 131453 i i v ivivv vv ivvviv vv v i i vi L1M5_orf2#LIN 1352 GCCCTATATCTATTAAAGAAATTGAATTTGTAATTAAAAACCTTCCCACA 1401 chr5qtel1M 131454 AAAAAATTTCCAAGACCAGATGGATTTACGTGTCAATTCTACGAAACATT 131503 i vi i v v i vv v v L1M5_orf2#LIN 1402 AAGAAAACTCCAGGCCCAGATGGCTTCACTGGTGAATTCTACCAAACATT 1451 chr5qtel1M 131504 TAAGGAACAATTAATTCTAATAATATATAAACTATTTGAAAAAATGGGGA 131553 v v v i vv i i v iv i i ii L1M5_orf2#LIN 1452 TAAGGAAGAAATAATACCAATCTTACACAAACTCTTCCAGAAAATAGAAA 1501 chr5qtel1M 131554 AAGAAGAAGTCCTACCAAATTCCTTTTCTGACACAGATGTGGTGCTGATA 131603 i i iiv v v i v v vi viiii ?iiv L1M5_orf2#LIN 1502 AAGAGGGAACACTTCCCAACTCATTTTATGAGGCCAGCATNACCCTGATA 1551 chr5qtel1M 131604 GCTAAACCAGGTGGGATGAAA--ACAAAGAAAGAAAATTATAGACCAATT 131651 v v ? ii--i v v -- ii i v L1M5_orf2#LIN 1552 CCAAAACCNGAC--AAAGACATTACAAGAAAAGAAAATTACAGACCAATA 1599 chr5qtel1M 131652 TCTCTAATGAATATTGATACAAAAATCTTAAATAAAATATTAGCTATGAG 131701 i v i v i i ? i v vvv L1M5_orf2#LIN 1600 TCCCTCATGAACATAGATGCAAAAATCCTNAACAAAATATTAGCAAATCG 1649 chr5qtel1M 131702 ATTAGAGAAGGCCATTCCCAGGATAATATACCATGTCCAAGTACTATTTA 131751 v vv v ivvi vvvv i i v ivvi L1M5_orf2#LIN 1650 AATCCAGCAATATATAAAAAGGATAATACATCATGACCAAGTGGGGTTTA 1699 chr5qtel1M 131752 TATCATGAATGCAGGGCTGGTTCAATATTAGGAAAATATGCTAAAATTAT 131801 vi v i i i i v i vi ---------- L1M5_orf2#LIN 1700 TCCCAGGAATGCAAGGTTGGTTTAACATTCGAAAATCA----------AT 1739 chr5qtel1M 131802 TAGCATAATTCACTATATCAATA-ACCAAACTAAAAAAATTCATATGATT 131850 i iii i i i - vi vv i - i L1M5_orf2#LIN 1740 CAATGTAATTCACCATATTAACAGAATAAAGGAGAAAAA-TCATATGATC 1788 chr5qtel1M 131851 ATCTCAATAGATGCAGAAAAAGCATTTGATAAA----AACAC-------- 131888 i ---- -------- L1M5_orf2#LIN 1789 ATCTCAATAGATGCAGAAAAAGCATTTGACAAAATTCAACACCCATTCAT 1838 chr5qtel1M 131889 --TAGA-------AGTA---TAGAAATAAATGGACTTTTCCTTAAAATGA 131926 -- i ------- i --- i i v ivvi i vv L1M5_orf2#LIN 1839 GATAAAAACTCTCAGCAAACTAGGAATAGAAGGGAACTTCCTCAACCTGA 1888 chr5qtel1M 131927 TCAGTAGCATCTATTAAAAACCATCAGTAAGCATCATATGTAATGGGGAC 131976 v ivi iv vv i? i iv v v L1M5_orf2#LIN 1889 TAAAGGGCATCTACGAAAAACCTACAGCNAACATCATACTTAATGGTGAA 1938 chr5qtel1M 131977 AAACTAGAACCATTCCCAGTAAGATCAGGTATGAAACAAGATTGCCCGCT 132026 ? ii ?v v vv i v ii i iv i L1M5_orf2#LIN 1939 ANACTGAANGCTTTCCCCCTAAGATCGGGAACAAGACAAGGATGTCCGCT 1988 chr5qtel1M 132027 ATCACCATTACTATTCAATATTGTATTAGAAATGCTAGCTTTGGCAATAA 132076 ? i v i i i ii v ivvv L1M5_orf2#LIN 1989 NTCACCACTTCTATTCAACATTGTACTGGAGGTCCTAGCCAGTGCAATAA 2038 chr5qtel1M 132077 GAGATGAAAAAGAGATTAAAGGAATTAGAGA-AGGTCATGAGGAAACCAA 132125 iv v i v v - i -v vv v i iv L1M5_orf2#LIN 2039 GGCAAGAAAAAGAAATAAAAGGCA-TAAAGATTGGAAAGGAAGAAATAAA 2087 chr5qtel1M 132126 ATTATCACTCTTTGCAGACGATATAATGGTATACTTAGAGAACCCCAGGG 132175 i i ?i v i i i i v ? v i i ? ii L1M5_orf2#LIN 2088 ACTGTCNTTATTCGCAGATGACATGATTGTNTACGTAGAAAATCCNAAAG 2137 chr5qtel1M 132176 ATTCAACTAAAAAGGTATTAGAAATAATCCACAACTTTAGCAAAGTTGCA 132225 v v v ? iv i v vviii v i i ? L1M5_orf2#LIN 2138 AATCTACAAANAAACTACTAGAACTAATAAGTGAATTTAGCAAGGTCGCN 2187 chr5qtel1M 132226 GGATATAAAATAAATCCAAATAAGTCATCAGCATTCTTATACATCACTAA 132275 i ii v vi v v i viv i ii i ii vi L1M5_orf2#LIN 2188 GGATACAAGGTCAATATACAAAAATCAATTGTATTTCTATATACTAGCAA 2237 chr5qtel1M 132276 CAAAATCCAACAGCAAA---AGATACAAAGAAAATTTTCATTTAAAATAA 132322 --- iv v --- i vi? i v v vi v i L1M5_orf2#LIN 2238 CAAA---CAATTGGAAAATGAAATTTNAAAAACAATACCATTTACAATAG 2284 chr5qtel1M 132323 TTGCTGATAGTATAAAATATTTGGGAATCTATCTGCCAA-----GGGAAA 132367 ivv vi v ii ? i i vv iv ----- v v L1M5_orf2#LIN 2285 CATCAAAAAACATNAAATACTTAGGAATAAATCTAACAAAANATGTGCAA 2334 chr5qtel1M 132368 GTC---------AGGAACTACAAAACACTTTCCACACAAATAAAGTCAGA 132408 v ---------iii i viiv v v v ivv L1M5_orf2#LIN 2335 GACCTNTACACTGAAAACTACAAAACATTGCTGAGAGAAATTAAAGAAGA 2384 chr5qtel1M 132409 TCT-AATAAGTTGGAAAAATATCAAGCGCTCATGGGTAGGCTGGACAAAT 132457 i - i- i i vvvii i i v vv iviv L1M5_orf2#LIN 2385 CCTAAATAAA-TGGAGAGATATACCATGTTCATGGATTGGAAGACTCAAT 2433 chr5qtel1M 132458 ATAATAAAAATGATAATACTACCTAAATTAATCTACTTATTTAGTGCAAT 132507 vi ? i vi v v i i ivv i i L1M5_orf2#LIN 2434 ATTGTNAAGATGTCAATTCTCCCCAAATTGATCTATAGATTCAATGCAAT 2483 chr5qtel1M 132508 ACCAATCAAACTCCCAAGAAATTATTTTACCGACCTAGAAAATACAATAA 132557 v v iv ii v iiv vv v v vvii vv L1M5_orf2#LIN 2484 CCCAATCAAAATCCCAGCAGGTTTTTTTGTAGAAATTGACAAGCTGATTC 2533 chr5qtel1M 132558 CAAAGTTTATCTGGAAGAACAAAAAGTCAAT-ATTTTCAAGGGAATTAAT 132606 i i v ivi iiii ? v- vvi iiv i-v L1M5_orf2#LIN 2534 TAAAATTTATATGGAAATGCAAAGGACCNAGAATAGCCAAAACAATC-TT 2582 chr5qtel1M 132607 GAAAAAAAATGCCAATGAAGGTGGCCTTAGTTGTACCTGATCTAAAACCA 132656 i viv v vv v v -ivv ? ? v iv v L1M5_orf2#LIN 2583 GAAAAAGAAGAACAAAGTTGGAGGACTTA-CACTACCNGATNTCAAGACT 2631 chr5qtel1M 132657 TATTATAGAG 132666 i L1M5_orf2#LIN 2632 TATTATAAAG 2641 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.16 CpG sites = 405, Kimura (unadjusted) = 41.59 Transitions / transversions = 1.09 (405/371) Gap_init rate = 0.03 (88 / 2561), avg. gap size = 1.77 (156 / 88) 1020 30.28 3.86 3.48 chr5qtel1M 133391 133934 (866066) L1ME5_3end#LINE/L1 7 552 (389) m_b247s551i23 9793 chr5qtel1M 133391 TCTAAGATATACAGAGAATTGACTCAAATTTATAAGAATTTAATCCATT- 133439 ii ii i vviv iv i v-- vv iv?- L1ME5_3end#LI 7 TCTAGAATATACAAGGAACTCCTGCAAATCAACAAGAAA--AAGACGGNA 54 chr5qtel1M 133440 -CTCCAATTAATAAATGT-CAAAGGATATGAACAGATAATTTTTCAGATG 133487 - i vi v v- ii v- v L1ME5_3end#LI 55 ACCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTA-CAGAAG 103 chr5qtel1M 133488 AAGAAATTAAAACCATTTCTAATCATATGAAATGGTGCTCTAAATCATTA 133537 i iivi vvii vvi v iv i v v L1ME5_3end#LI 104 AGGAAACCCGAAAGGCTAACAAGCATATGAAGAGATGCTCAAACTCATTA 153 chr5qtel1M 133538 ATTGATCAGAGAAATATAAATTAAAACAATTCTGAGGTACCACTACACAC 133587 i -i ii ivv i i vi L1ME5_3end#LI 154 GT-AATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACAC 202 chr5qtel1M 133588 -----AGATTGCCTAAGATGACAGGAAAA---GATAATGACACATGTTGG 133629 ----- i v v i v --- i--- v vi L1ME5_3end#LI 203 CTATTAGACTGGCAAAAATTA---GAAAGCTGGATAATGCCAAGTGTTGG 249 chr5qtel1M 133630 AGGAGATGTGGGAAAATTGGAACACTAATACATTGTTGGTGAAACTGTGA 133679 v ii i ? v v v i i i ii v ii L1ME5_3end#LI 250 CGAGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAG 299 chr5qtel1M 133680 ATGGATCCAGCCATTCTGGAAAAAACTTTGGAATTA--TGCCCAAAGAGT 133727 iv i v i iv v i v v -- ivi --- L1ME5_3end#LI 300 ACTGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAA---T 346 chr5qtel1M 133728 TATCAAACTGTGCATACCCTTTGACTTAGCAGTGTTTCTCTTGGGCCTAC 133777 -- ivv ii v ii i viiv i iv i L1ME5_3end#LI 347 TA--AGTATACGCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATAT 394 chr5qtel1M 133778 ATCCCAAAAAGATCTTAAAGGAGG---GAAAGGGACCCACATGTGCAAAA 133824 i i ii v viv ---iv i--- i i ii L1ME5_3end#LI 395 ATCCCAAAGAAATTCTCACACAGGTCCATAAGGGG---ACATGTACGAGG 441 chr5qtel1M 133825 ATGTTTGTGGCAGCTCTTTTTGTAGTGGCTAGAAACTGGAACTGA-ATGG 133873 ii v vi v i vi i ii ivii -v L1ME5_3end#LI 442 ATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGG 491 chr5qtel1M 133874 ATGCCCATAAGTTGTGGAATGGTTGAATAGGTGA----TGGTGTATGAAT 133919 i i v v v vi i ---- i ---- v v i L1ME5_3end#LI 492 GTGTCCATCACTGGGAGAGTGG----ATAGGTAAAATGTGGTGGATGCAC 537 chr5qtel1M 133920 GTTATGGAATATTAT 133934 iii i i L1ME5_3end#LI 538 ACCATGGAGTACTAT 552 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.62 CpG sites = 95, Kimura (unadjusted) = 40.26 Transitions / transversions = 1.48 (95/64) Gap_init rate = 0.05 (28 / 543), avg. gap size = 1.43 (40 / 28) 20 27.90 3.08 0.00 chr5qtel1M 134257 134321 (865679) (TA)n#Simple_repeat 1 67 (0) m_b247s252i12 9794 chr5qtel1M 134257 TATAAATATGTTTATATATAT-TGGAT-TGAACATATATGAACATGTATA 134304 v i v - iv - iv i iv i i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr5qtel1M 134305 AATATGTTTATATATAT 134321 v i v (TA)n#Simple_ 51 TATATATATATATATAT 67 Matrix = Unknown Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.03 (2 / 64), avg. gap size = 1.00 (2 / 2) 394 31.27 6.98 2.48 chr5qtel1M 134539 134925 (865075) L1ME4a_3end#LINE/L1 130 533 (338) m_b247s551i24 9795 chr5qtel1M 134539 ATAAATAAATGCACTAACTTGCTAATACTCACAGAAATTAAAATTAAAAC 134588 i v ? iv v v ii i v v vv L1ME4a_3end#L 130 ATGAAAANATGTTCAACCTCACTAGTAATCAAAGAAATGCAAATTAAAAC 179 chr5qtel1M 134589 AACTCTGAGGTCCCAATTTAAATCCATCGTATCAGCCAACTTGACAAAAA 134638 vv i v - --- i i - ---- v i i L1ME4a_3end#L 180 AACAATGAGATACC-ATTT---TTCACC-TAT----CAAATTGGCAAAGA 220 chr5qtel1M 134639 --AGGAAAATTAAAAAT-CC------TGGGAAGGATACGGAAAAATACTG 134679 --vii i i v - ------ vi i ii ?i iivvv L1ME4a_3end#L 221 TTTAAAAGATTGATAATACCCAGTGTTGGCGAGGGTGTGGNGAAACGGGC 270 chr5qtel1M 134680 ACATTAAAATACTGCTGATGGAGGAACAAACTGGTCCAACTAATCTCCAA 134729 vi v v i i ii vii i v ivv vv i L1ME4a_3end#L 271 ACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTACAACCTTTCTGGAG 320 chr5qtel1M 134730 AGCAATTTGAAATCATGCCTAAAAAGCTCTTAAACTGTTTATACCCATTG 134779 i iv vi iv v ii v v ?i v L1ME4a_3end#L 321 GGCAATTTGGCAATATGTATCAAAAGCCTTAAAAATGTNCATACCCTTTG 370 chr5qtel1M 134780 ACTCAATAATACCACTACTAG--ATACATC------ACATAA-CGAAGA- 134819 i i v v -- vi ------ v - ii - L1ME4a_3end#L 371 ACCCAGTAATTCCACTTCTAGGAATTTATCCTAAGGAAATAATCAGAGAT 420 chr5qtel1M 134820 ------AAGGACTCATGTACAGAGAAAGTTATAGCA--ATTTTTTGTGAT 134861 ------ i i i ii viv i v -- v i i L1ME4a_3end#L 421 GTGNACAAAGATTTATGTACAAGGATGTTCATCGCAGCATTATTTATAAT 470 chr5qtel1M 134862 AATAATGAAACTAGAAAGAGAAGGGATGCCTAACATTTGTGGAATAGCCA 134911 iii -i i i v ivvvii i i v v v ? i ii L1ME4a_3end#L 471 AGCGA-AAAATTGGAAACAACCTAAATGTCCAACAATAGGGGANTGGTTA 519 chr5qtel1M 134912 AACAAGTTATGATA 134925 i i i L1ME4a_3end#L 520 AATAAATTATGGTA 533 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.88 CpG sites = 69, Kimura (unadjusted) = 42.41 Transitions / transversions = 1.41 (69/49) Gap_init rate = 0.05 (19 / 386), avg. gap size = 1.95 (37 / 19) 57 0.00 0.00 0.00 chr5qtel1M 135171 135221 (864779) (CTTC)n#Simple_repeat 1 51 (0) c_b247s251i4 9796 chr5qtel1M 135171 CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT 135220 (CTTC)n#Simpl 1 CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT 50 chr5qtel1M 135221 T 135221 (CTTC)n#Simpl 51 T 51 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 695 29.44 2.45 2.17 chr5qtel1M 135461 135828 (864172) L1M4_orf2#LINE/L1 1691 2059 (1235) m_b247s551i25 9797 chr5qtel1M 135461 TGAGATTTATACCAGGAATGCCGAGCTAGCTCTATATTAGAAAAACCATC 135510 i v vii i i i v i ?v v v L1M4_orf2#LIN 1691 TGGGATTTATCCCAGGAATGCAAGGTTGGTTCAACATNCGAAAATCAATC 1740 chr5qtel1M 135511 A---TAATTGACTATATTAGTA--ACCAACCCAACATAAATCAAATGAT- 135554 --- vv i i -- iv v--i v i v - L1M4_orf2#LIN 1741 AATGTAATACACCATATTAATAGAATAAAG--GACAAAAACCACATGATC 1788 chr5qtel1M 135555 ATCTCAATAGATACAGAAAAGACTTTTTGACAAAATACAAACCCCATTTA 135604 ii ii v - v vv v i L1M4_orf2#LIN 1789 ATCTCAATAGACGCAGAAAAAGCATTT-GACAAAATCCAACACCCTTTCA 1837 chr5qtel1M 135605 -AATTTTAAAAAACACTAGAGAGCATAGGTATA-AATTGAGCTTTTCTAA 135652 -i ---- vi v ivv v - vv i iiii L1M4_orf2#LIN 1838 TGAT----AAAAACACTCAACAAACTAGGAATAGAAGGGAACTTCCTCAA 1883 chr5qtel1M 135653 AATGATAAGTAGTATCTATCTAAAACCATCAGCAAGCATTATCTGTAATG 135702 vv ivi i ivv vv v i i viv L1M4_orf2#LIN 1884 CCTGATAAAGGGCATCTACGAAAAACCCACAGCTAACATCATACTTAATG 1933 chr5qtel1M 135703 AGCATAAGATAGAA-GCCTTCCCAATAAAATCAGGGGTGAAACAAGGATG 135751 - iiv iv - i vv i iiii i L1M4_orf2#LIN 1934 -GTGAAAGACTGAANGCTTTCCCCCTAAGATCAGGAACAAGACAAGGATG 1982 chr5qtel1M 135752 TCCATTTTAGCTAGTATTATTCAATATTGTGCTACAAATATTAACTTTAG 135801 ii i v i v vi i i iv ii vi i ivvi L1M4_orf2#LIN 1983 TCCGCTCTCGCCACTTCTATTCAACATTGTACTGGAGGTTCTAGCCAGGG 2032 chr5qtel1M 135802 CAATAAGAGAAGAAAAAGAAATTGAAG 135828 v iv vi L1M4_orf2#LIN 2033 CAATTAGGCAAGAAAAAGAAATAAAAG 2059 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.88 CpG sites = 58, Kimura (unadjusted) = 38.30 Transitions / transversions = 1.21 (58/48) Gap_init rate = 0.04 (14 / 367), avg. gap size = 1.21 (17 / 14) 247 23.53 10.00 1.73 chr5qtel1M 135867 136026 (863974) L1M3_orf2#LINE/L1 2140 2312 (976) m_b247s551i26 9797 chr5qtel1M 135867 AAAAAACTACTTGAAACAATAAACAATTTTAGCAAAGTTGCAGGATATAA 135916 ii v vi i v i i i L1M3_orf2#LIN 2140 AAAAAACTGTTAGAACTAATAAACGAATTCAGTAAAGTTGCAGGATACAA 2189 chr5qtel1M 135917 AATAAGCCACACAAATATCA---GCATTTCTACATATGATTAACAAAGTC 135963 v i- i v --- i i i iv vi i -- L1M3_orf2#LIN 2190 AATCAA-CATACAAAAATCAGTTGCGTTTCTATACACTAACAACGAA--C 2236 chr5qtel1M 135964 TAGCAGCAAGAGA----CAGAAAA-AAT-CCATTTAAAATAACAGTAGAA 136007 v v v ii ----v - - v i vi i L1M3_orf2#LIN 2237 TATCCGAAAAGGAAATTAAGAAAACAATCCCATTTACAATAGCATCAAAA 2286 chr5qtel1M 136008 A-AAT------TTTAAAAATAAATTT 136026 - ------i ii i L1M3_orf2#LIN 2287 AGAATAAAATACTTAGGAATAAACTT 2312 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 26.38 CpG sites = 24, Kimura (unadjusted) = 29.12 Transitions / transversions = 1.85 (24/13) Gap_init rate = 0.06 (9 / 159), avg. gap size = 2.11 (19 / 9) 358 19.35 8.21 3.57 chr5qtel1M 135867 136000 (864000) L1M1_orf2#LINE/L1 2146 2285 (1009) m_b247s551i27 9797 chr5qtel1M 135867 AAAAAACTACTTGAAACAATAAACAATTTTAGCAAAGTTGCAGGATATAA 135916 i v vii v i i i L1M1_orf2#LIN 2146 AAAAAACTATTAGAACTGATAAACAAATTCAGTAAAGTTGCAGGATACAA 2195 chr5qtel1M 135917 AATAAGCCACACAAATATC---AGCATTTCTACAT----ATGATTAACAA 135959 v i- i v --- i ---- iii v L1M1_orf2#LIN 2196 AATCAA-CATACAAAAATCAGTAGCATTTCTATATGCCAACAGTGAACAA 2244 chr5qtel1M 135960 AGTCTAGCAGCAAGAGA-CAGAAAA--AAT-CCATTTAAAATAAC 136000 -- i-- iv i - i -- - v i L1M1_orf2#LIN 2245 --TCTG--AAAAAGAAATCAAAAAAGTAATCCCATTTACAATAGC 2285 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 23.01 CpG sites = 17, Kimura (unadjusted) = 23.01 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.08 (10 / 133), avg. gap size = 1.60 (16 / 10) 565 32.61 4.69 2.76 chr5qtel1M 136818 137350 (862650) L1ME4c_3end#LINE/L1 12 554 (276) m_b247s551i28 9798 chr5qtel1M 136818 AATATATAGAGAATTGAATTAAAGTTATAAGAATGCAAGTTATTCTTCAA 136867 ? i ii v v i v v -iv ?i i vvvii v L1ME4c_3end#L 12 ANTATATAAAGAGCTCATTCAAATTGATAAGAA-AAANATCAAGACCCCA 60 chr5qtel1M 136868 ATTGATGAATGATCAAAGAATATGAACAG-TAGTTTTTAAACAAAAAAAT 136916 v i iv i i -i i ivi ? vi ii L1ME4c_3end#L 61 ATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAGGAAAT 110 chr5qtel1M 136917 CAAAGCTATATATAGTCATATTTTTAAAAATGCTCCAAATCACTATTGAT 136966 vv ?ivi v i iv i vv-- i v vv i v i L1ME4c_3end#L 111 ACAANTAGTAAACAAACACATGG--AAAAATGTTCAACCTCGCTAGTAAT 158 chr5qtel1M 136967 CACAGAAATGTAAATTAAAATAACCCTGAAATTCCACTTCCCACTTATTA 137016 v i ii vv i v i iv i i L1ME4c_3end#L 159 CAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCTATTA 208 chr5qtel1M 137017 GAGTGACTAA----TA------TGACAACAACAAAAAATGTTGGAGGGGA 137056 i v ii v ---- ------ i i v ---v i v i ? L1ME4c_3end#L 209 AATTAGCAAAAATTTAAAAAATTGATAATACC---CAATGCTGGCGAGGN 255 chr5qtel1M 137057 TGTGGGAAAACTGAAATACTAATGCATTGCTGACGGAGTTGTAAATGGAT 137106 i vi iv i? v i ii vi? v i L1ME4c_3end#L 256 TGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGT 305 chr5qtel1M 137107 CCAACCATTCTGGAGAGCAATTTGGAACTATGT-TCAAAAGGCTATAAAA 137155 v v i i v v i - i - i L1ME4c_3end#L 306 ACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGA-GCCATAAAA 354 chr5qtel1M 137156 CTGCCTG---CCTTTG--TCAGCAATACTAG--CTAGGTCTATGATCCC- 137197 v iiii--- --i i v i v-- i vv - v i- L1ME4c_3end#L 355 ATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAAT-TTATCCTA 403 chr5qtel1M 137198 ---AAATGCATCCCCAAAAAGGGGAAAGCATTTATTTATATGAAAAACAT 137244 --- i- i vv i ii --- v ii i - i ii L1ME4c_3end#L 404 AGGAAATA-ATTCAAAAGAAGGAAAAAGC---TATATGCACG-AAGATGT 448 chr5qtel1M 137245 TTATAGAAGTTCTTTTTGTGGTGGCTAAGAATTAAAAATCAAAGGGACAC 137294 i v v ivi v i ii i v i ii i-- vvv v i L1ME4c_3end#L 449 TCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAAC--AACCTAAAT 496 chr5qtel1M 137295 ATTT--CAATTGGGGAACGGCTAAACAAGTTGTGCTTTATGAATGTAATG 137342 i ii-- v i i ii i i v vi v? ivii L1ME4c_3end#L 497 GTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATG 546 chr5qtel1M 137343 GAATACTA 137350 i L1ME4c_3end#L 547 GAATATTA 554 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 42.98 CpG sites = 103, Kimura (unadjusted) = 45.59 Transitions / transversions = 1.56 (103/66) Gap_init rate = 0.05 (25 / 532), avg. gap size = 1.60 (40 / 25) 654 30.22 5.04 2.67 chr5qtel1M 136875 137350 (862650) L1ME4a_3end#LINE/L1 68 554 (317) m_b247s551i30 9798 chr5qtel1M 136875 AATGATCAAAGAATATGAACAG-TAGTTTTTAAACAAAAAAAT-CAAA-- 136920 iv i i -i i ivi vi i - -- L1ME4a_3end#L 68 AATGGGCAAAGGACATGAACAGACAATTCACAAAAGAAGAAATACAAATG 117 chr5qtel1M 136921 GCTATATATAGTCATATTTTTAAAAATGCTCCAAATCACTATTGATCACA 136970 i --- iv vv-- ? i v vv v i v L1ME4a_3end#L 118 GCCA---ATAAACATATGA--AAANATGTTCAACCTCACTAGTAATCAAA 162 chr5qtel1M 136971 GAAATGTAAATTAAAATAACCCTGAAATTCCACTTCCCACTTATTAGAGT 137020 i i vv i v i ii i i i v L1ME4a_3end#L 163 GAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCTATCAAATT 212 chr5qtel1M 137021 GACTAATAT------GAC-AACAACAAAAAATGTTGGAGGGGATGTGGGA 137063 i v v ------ i-i i i vvv i v i i ?i L1ME4a_3end#L 213 GGCAAAGATTTAAAAGATTGATAATACCCAGTGTTGGCGAGGGTGTGGNG 262 chr5qtel1M 137064 AAACTGAAATACTAATGCATTGCTGACGGAGTTGTAAATGGATCCAACCA 137113 v iv iv v i i ii iiv v i v v L1ME4a_3end#L 263 AAACGGGCACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTACAACCT 312 chr5qtel1M 137114 TTCTGGAGAGCAATTTGGAACTATGT-TCAAAAGGCTATAAAACTGCCTG 137162 i v v - v - v i?ii L1ME4a_3end#L 313 TTCTGGAGGGCAATTTGGCAATATGTATCAAAAGCCT-TAAAAATGTNCA 361 chr5qtel1M 137163 ---CCTTTG--TCAGCAATACTAG--CTAGGTCTATGATCCCAAATGCAT 137205 --- --i i v i v-- vv - v i iviv L1ME4a_3end#L 362 TACCCTTTGACCCAGTAATTCCACTTCTAGGAAT-TTATCCTAAGGAAAT 410 chr5qtel1M 137206 CCCCAAAAAGGGG---AAAGCATTTATTTATATGAAAAACATTTATAGAA 137252 vvi i i v v --- - v i--- ii ii i v v L1ME4a_3end#L 411 AATCAGAGATGTGNACAAAG-ATTTATGTAC---AAGGATGTTCATCGCA 456 chr5qtel1M 137253 GTTCTTTTTGTGGTGGCTAAGAATTAAAAATCAAAGGGACACATTT--CA 137300 ivi v i ii i v i ii i-- vvv v ii ii-- L1ME4a_3end#L 457 GCATTATTTATAATAGCGAAAAATTGGAAAC--AACCTAAATGTCCAACA 504 chr5qtel1M 137301 ATTGGGGAACGGCTAAACAAGTTGTGCTTTATGAATGTAATGGAATACTA 137350 v ?i i i i i v vi vv i? i L1ME4a_3end#L 505 ATAGGGGANTGGTTAAATAAATTATGGTACATCCATANAATGGAATATTA 554 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.39 CpG sites = 81, Kimura (unadjusted) = 40.39 Transitions / transversions = 1.37 (81/59) Gap_init rate = 0.05 (24 / 475), avg. gap size = 1.54 (37 / 24) 663 28.86 7.06 4.76 chr5qtel1M 136942 137352 (862648) L1ME3_3end#LINE/L1 134 553 (356) m_b247s551i31 9798 chr5qtel1M 136942 AAAAATGCTCCAAATCACTATTGATCACAGAAATGTAAATTAAAATAACC 136991 ii v v i v v vi i iv v L1ME3_3end#LI 134 AAAGGTGCTCAACATCATTAGTCATCAGGGAAATGCAAATTAAAACCACA 183 chr5qtel1M 136992 CTGAAATTCCACTTCCCACTTATTAGAGTGACTAATAT------GAC-AA 137034 v i v v v ii ii i i v ------ -i L1ME3_3end#LI 184 ATGAGATACCACTACACACCCACCAGAATGGCTAAAATTAAAAAGACTGA 233 chr5qtel1M 137035 CAACAAAAAATGTTGGAGGGGATGTGGGAAAACTGAAATACTAATGCATT 137084 i vv i v i iiv i iv v i L1ME3_3end#LI 234 CAATACCAAGTGTTGGCGAGGATGTGGAGCAACTGGAACTCTCATACATT 283 chr5qtel1M 137085 GCTGACGGAGTTGTAAATGGATCCAACCATTCTGGAGAGCAATTTGGAAC 137134 ii iiv v i v i i i i vi v v L1ME3_3end#LI 284 GCTGGTGGGAGTGTAAATTGGTACAACCACTTTGGAAAACTGTTTGGCAG 333 chr5qtel1M 137135 TATGTTCAAAAGGCTATAAAACTGCCTGCCTT-TG--TCAGCAATACTA- 137180 v v v - v v vvi i i - --i v i - L1ME3_3end#LI 334 TATCTACTAAA-GCTAAACATACGCCTACCCTATGACCCAGCAATTCCAC 382 chr5qtel1M 137181 -GCTAGGTCTATGATCCCA---------AATGCA----TCCCCAAAAAGG 137216 -v v i-- --------- i ---- v v - L1ME3_3end#LI 383 TCCTAGGTATATA--CCCAAGAGAAATGAGTGCATATGTCCACCAAAAG- 429 chr5qtel1M 137217 GGAAAGCATTTATTTATATGAAAAACATTTATAGAAGTTCTTTTTGTGGT 137266 -----i v i------- i ii i v i i v ii ii L1ME3_3end#LI 430 -----ACATGTAC-------AAGAATGTTCATAGCAGCTTTATTCATAAT 467 chr5qtel1M 137267 GGCTAAGAATTAAAAA----TCAAAGGGACACATTTCAATTGGGGAACGG 137312 i i? i i ii ----i v vv ---- iv ?i i L1ME3_3end#LI 468 AGCCNAAAACTGGAAACAACCCAAATGTCCA----TCAACAGNAGAATGG 513 chr5qtel1M 137313 CTAAACAAGTTGTGCTTTATGAATGTAATGGAATACTACA 137352 v i i v v vv ii L1ME3_3end#LI 514 ATAAATAAATTGTGGTATATTCATACAATGGAATACTACA 553 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.25 CpG sites = 65, Kimura (unadjusted) = 37.67 Transitions / transversions = 1.35 (65/48) Gap_init rate = 0.07 (29 / 410), avg. gap size = 1.69 (49 / 29) 343 29.47 1.05 0.00 chr5qtel1M 137781 137875 (862125) C MIR3#SINE/MIR (12) 196 101 m_b247s601i13 9799 chr5qtel1M 137781 CACAAATTGCTAGAATGAGGTGGAACCTTAGAGATCACCT-GTGCTATGC 137829 i i v ii iivi iv i i - v v iv C MIR3#SINE/MIR 196 CATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCC 147 chr5qtel1M 137830 CCTCATTAAACAGATGAATAAATTGAAACCCATAGAAGGGATGTGA 137875 vv iv i ii v i v v C MIR3#SINE/MIR 146 CCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGA 101 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.38 CpG sites = 16, Kimura (unadjusted) = 38.38 Transitions / transversions = 1.33 (16/12) Gap_init rate = 0.01 (1 / 94), avg. gap size = 1.00 (1 / 1) 25 2.78 2.63 0.00 chr5qtel1M 138150 138161 (861839) (CTTC)n#Simple_repeat 1 13 (26) m_b247s252i13 9800 chr5qtel1M 138150 CTTCC-TCCTTCT 138161 - i (CTTC)n#Simpl 1 CTTCCTTCCTTCC 13 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.09 (1 / 11), avg. gap size = 1.00 (1 / 1) 119 3.39 0.00 0.00 chr5qtel1M 138162 138283 (861717) (CTCC)n#Simple_repeat 1 122 (0) c_b247s251i5 9801 chr5qtel1M 138162 CTCCCTCCCTCCCTCCCTCCCTCCCTTCCTTCCTTCCTTCCTCCCTCCCT 138211 i i i i (CTCC)n#Simpl 1 CTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCT 50 chr5qtel1M 138212 CCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCC 138261 (CTCC)n#Simpl 51 CCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCC 100 chr5qtel1M 138262 CTCCCTCCCTCCCTCCCTCCCT 138283 (CTCC)n#Simpl 101 CTCCCTCCCTCCCTCCCTCCCT 122 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 121), avg. gap size = 0.0 (0 / 0) 25 2.78 2.63 0.00 chr5qtel1M 138284 138308 (861692) (CTTC)n#Simple_repeat 14 38 (1) m_b247s252i13 9802 chr5qtel1M 138284 TCCTTCCTTCCTTCCTTCCTTCCTT 138308 (CTTC)n#Simpl 14 TCCTTCCTTCCTTCCTTCCTTCCTT 38 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 239 27.32 15.89 0.81 chr5qtel1M 138810 138916 (861084) MIR3#SINE/MIR 66 188 (20) m_b247s601i14 9803 chr5qtel1M 138810 CCCTGCCA---ACTCCCTGGATCACCTTGAATA------------TCTTT 138844 i --- ?v vi v iii ------------ i MIR3#SINE/MIR 66 CTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCT 115 chr5qtel1M 138845 GTGCCTCAGTTTCTTCATCTCTATCATGAGAGTACAG--CCAGAGGGTTT 138892 v i v vv i viiv -- i v i i MIR3#SINE/MIR 116 GGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCT 165 chr5qtel1M 138893 CTAAGGGGTCCTCCAGTCTCTAGC 138916 vvi i - ii MIR3#SINE/MIR 166 CTAAGGTCCCTTCCAG-CTCTGAC 188 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.31 CpG sites = 17, Kimura (unadjusted) = 35.31 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.04 (4 / 106), avg. gap size = 4.50 (18 / 4) 502 30.62 3.41 1.68 chr5qtel1M 139042 139217 (860783) C L3#LINE/CR1 (349) 3750 3572 m_b247s601i15 9804 chr5qtel1M 139042 AATCTTCCTTTCTCCAGGATAAACACCCTCAGTTCCTTTCCCCGATTCTC 139091 i ii v i i ivv v i C L3#LINE/CR1 3750 AGTCTTCTCTTCTCCAGGCTAAACATCCCCAGTTCCTTCAACCGTTCCTC 3701 chr5qtel1M 139092 ATTTATCATGAATCAAATCAAGGTCTTAACCATTCTGTCCTCCCTCCTCT 139141 v iv iv i---i iivi v i vi v i C L3#LINE/CR1 3700 ATATGACATGGTTT---CCAGACCCTTCACCATCCTGGTCGCTCTCCTCT 3654 chr5qtel1M 139142 AGACAATCTCCAGCTGTTCCATGACCTTCCTGAAATGTGGT-----GAAC 139186 i ivv i vv v v i i i i----- C L3#LINE/CR1 3653 GGACGCGCTCCAGTTTGTCAATGTCCCTCTTAAAATGTGGCGCCCAGAAC 3604 chr5qtel1M 139187 TGGAATCAA-AGTCCAGGCCTAATGCGATCAG 139217 i vv - v iiv ii vi i C L3#LINE/CR1 3603 TGAACGCAATACTCCAGATGTGGTCTGACCAG 3572 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.59 CpG sites = 31, Kimura (unadjusted) = 40.57 Transitions / transversions = 1.41 (31/22) Gap_init rate = 0.03 (5 / 175), avg. gap size = 1.80 (9 / 5) 466 31.98 4.71 1.91 chr5qtel1M 139322 139576 (860424) C L3#LINE/CR1 (729) 3370 3109 m_b247s601i16 9804 chr5qtel1M 139322 ATTTCTTGAATCCAAGTGTAAGACTT--CATTTCTCCCTTATTAAAGGAC 139369 i i i i i i -- v -i vvv C L3#LINE/CR1 3370 ATTTTTTGAACCTAAATGCAGGACTTTACATTTATCCCT-GTTAAATTTC 3322 chr5qtel1M 139370 ATCATTTTGCATTCATCCCATTGATCTAGGCTGTTGAACTCCT----AAG 139415 v v vv iv i v i v i iv ? ---- v C L3#LINE/CR1 3321 ATCTTGTTGGTTTCGGCCCATCGTTCCAGCCTGTCGAGATCNTTTTGAAT 3272 chr5qtel1M 139416 G--GAGTCTGCTTATCCAGCCTACTCCGTACCAGACAGTCCAGCTTGGTG 139463 v-- v - i ? v i vvv i --- vvi v C L3#LINE/CR1 3271 CTTGATTCTG-TCATCCANCGTATTAGCTATC---CCTCCCAGCTTTGTG 3226 chr5qtel1M 139464 CTGTCC---AATGCGACA-GCATCCCAAGTCTGGTTATGTCCGAGACATT 139509 iii i--- vi i - v vvv v vi vii i v C L3#LINE/CR1 3225 TCATCTGCAAATTTGATAAGCATGCCTTCTATGTCTTCATCCAAGTCATT 3176 chr5qtel1M 139510 GACAAAACGGCTAAAGGGAGCAGGGGCACTGGTTTATCCCTAAGGAAGGC 139559 i vv i i vi ii v vv iivv v iv v v C L3#LINE/CR1 3175 GATAAAAATGTTGAACAGGACAGGGCCAAGGACAGAGCCCTGTGGCACGC 3126 chr5qtel1M 139560 CACTAGAGCCCTCCTTC 139576 v i C L3#LINE/CR1 3125 CACTAGAGACCTCCCTC 3109 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.48 CpG sites = 36, Kimura (unadjusted) = 42.49 Transitions / transversions = 0.82 (36/44) Gap_init rate = 0.04 (10 / 254), avg. gap size = 1.70 (17 / 10) 22 8.91 0.00 0.00 chr5qtel1M 141046 141081 (858919) (GGGAGGA)n#Simple_repeat 1 36 (0) m_b247s252i14 9805 chr5qtel1M 141046 GGCAGGAGGGAGGATGGAGGAGGCAGGAGGGAGGAG 141081 v v v (GGGAGGA)n#Si 1 GGGAGGAGGGAGGAGGGAGGAGGGAGGAGGGAGGAG 36 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 272 22.73 0.00 0.00 chr5qtel1M 141356 141421 (858579) C MIR1_Amn#SINE/MIR (77) 153 88 m_b247s601i17 9806 chr5qtel1M 141356 ATCCCCATTTCACAGAAGGGGAAACTGAGGCCCGCGCAGCTCAAAGGACT 141405 i v i ? iviv v ? iv C MIR1_Amn#SINE 153 ATCCCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACT 104 chr5qtel1M 141406 TGGCCGGGGTTATACA 141421 v ii i i? C MIR1_Amn#SINE 103 TGCCCAAGGTCACNCA 88 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.26 CpG sites = 9, Kimura (unadjusted) = 29.26 Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0) 14 3.99 3.57 3.57 chr5qtel1M 142623 142650 (857350) (AAAGA)n#Simple_repeat 1 28 (0) m_b247s252i15 9807 chr5qtel1M 142623 AAAGAAAA-AAAGGAAAAGGAAAAGAAAA 142650 - i - (AAAGA)n#Simp 1 AAAGAAAAGAAAAGAAAA-GAAAAGAAAA 28 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.07 (2 / 27), avg. gap size = 1.00 (2 / 2) 18 21.81 0.00 0.00 chr5qtel1M 142692 142728 (857272) (T)n#Simple_repeat 1 37 (0) m_b247s252i16 9808 chr5qtel1M 142692 TTCTTTTTTTTTTTTAACTTTATTTATTTATTTTTTT 142728 i vvi v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 37 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 13 4.76 0.00 4.35 chr5qtel1M 142814 142837 (857163) (CCCT)n#Simple_repeat 1 23 (0) m_b247s252i17 9809 chr5qtel1M 142814 CCCTCCCTCCCTCCACCCCCTCCC 142837 - i (CCCT)n#Simpl 1 CCCTCCCTCCCTCC-CTCCCTCCC 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 353 24.49 0.00 0.00 chr5qtel1M 143063 143160 (856840) C Charlie4a#DNA/hAT-Charlie (54) 454 357 m_b247s502i1 9810 chr5qtel1M 143063 CCATGAGCCCTTCTTTAGAATACCGCTTTTAAATACATAAAATAAAATAC 143112 i ii i ii i vi i i C Charlie4a#DNA 454 CTATGGACCCCTTCTCAGAATAATGTTTTTAAATGCATAAAATAAAATAC 405 chr5qtel1M 143113 ACTGAATTACAAATGAAACTAATTGTACAGAAAGCAATTTACCAAAAT 143160 iv i v i i iv vvv v i C Charlie4a#DNA 404 ATAGGATTACAAAGGAAACCAATTATATTGAAATACAGTTATCAAAAT 357 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 30.68 CpG sites = 16, Kimura (unadjusted) = 30.68 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.00 (0 / 97), avg. gap size = 0.0 (0 / 0) 12 7.42 10.34 0.00 chr5qtel1M 143191 143219 (856781) (GGAGA)n#Simple_repeat 1 32 (0) m_b247s252i18 9811 chr5qtel1M 143191 GGGGAGGA-AGG-GAAGAGAGGA-AGGAGAGG 143219 i - - i - (GGAGA)n#Simp 1 GGAGAGGAGAGGAGAGGAGAGGAGAGGAGAGG 32 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.11 (3 / 28), avg. gap size = 1.00 (3 / 3) 476 29.15 9.31 5.20 chr5qtel1M 145052 145384 (854616) L3#LINE/CR1 3671 4016 (83) m_b247s601i18 9812 chr5qtel1M 145052 ATGGTCAAGGA----GGGACAATGCTCA---GGGAATTGAATGAAAAAAC 145094 v i---- ii v - --- i i vi iv ii L3#LINE/CR1 3671 ATGGTGAAGGGTCTGGAAACCATG-TCATATGAGGAACGGTTGAAGGAAC 3719 chr5qtel1M 145095 TGGGCAGGTTTCAACTG---AACACAAGACTTGGA--AGGCAAGAAGGGA 145139 v v viv --- v v i -- i v vi vv L3#LINE/CR1 3720 TGGGGATGTTTAGCCTGGAGAAGAGAAGACTTAGAGGAGACATGATAGCT 3769 chr5qtel1M 145140 G-----AAGTATTTGAAGGGCAGTCACTGGGAAGATG----AGATTTCTT 145180 ----- i v ivv v ---- i v L3#LINE/CR1 3770 GTCTTCAAATATTTGAAGGGCTGTCATGTGGAAGAGGGATTAGACTTATT 3819 chr5qtel1M 145181 GGGTTTGGATGT-GAAGCCAGAACTAGCAACAGTTC-TCCCAGTTGCAGA 145228 vv v v vi- i v v v i vv- vvv i i L3#LINE/CR1 3820 CTGTGTGGCTCCAGAGGGCAGAACTAGGACCAATGGGTGGAAGTTACAGG 3869 chr5qtel1M 145229 GGGCCAGACT-GGGCTTGAGGGAAGGAAGAACTTCCTAACAATTAG---- 145273 i v i -v ii viv i i ---- L3#LINE/CR1 3870 GAGGCAGATTTCGGCTCAATATAAGGAAGAACTTTCTAACAATCAGAGCT 3919 chr5qtel1M 145274 ---CAGAAGTAGAATGGGCTGCCTGGGAAGAAAGCGAGCGTCTCCCTCTT 145320 --- i i i v ?i iv i - i ----- L3#LINE/CR1 3920 GTCCAAAAATGGAATGGGCTGCCTCGNGAGGTAGTGAGC-TCCCC----- 3963 chr5qtel1M 145321 GTTGGGATCACAGTGAACTGATGGACAAGTGGCAAGTAAGGAAACCATTT 145370 ------i -- i -- i vv ii - i ivi ivi i L3#LINE/CR1 3964 ------GTCAC--TGGA--GGTGTTCAAGCAG-AGGCTGGATGACCACTT 4002 chr5qtel1M 145371 GTTAAGCATGTTAT 145384 i i v i L3#LINE/CR1 4003 GTCAGGGATGTTGT 4016 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.78 CpG sites = 49, Kimura (unadjusted) = 37.81 Transitions / transversions = 1.14 (49/43) Gap_init rate = 0.09 (29 / 332), avg. gap size = 1.69 (49 / 29) 290 22.87 0.00 2.86 chr5qtel1M 146580 146651 (853349) C MIR3#SINE/MIR (24) 184 115 m_b247s601i19 9813 chr5qtel1M 146580 GAGATGGAAAGGAACTAAGAGGCTATCTTGTCTCTCCCTCCCATATATTA 146629 v i v v iii v ivv i i - - C MIR3#SINE/MIR 184 GAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCAT-T-TTA 137 chr5qtel1M 146630 CAGATCAGGAAACTGAGGTACA 146651 v iv C MIR3#SINE/MIR 136 CAGATGAGGAAACTGAGGCCCA 115 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.48 CpG sites = 8, Kimura (unadjusted) = 27.48 Transitions / transversions = 1.00 (8/8) Gap_init rate = 0.03 (2 / 71), avg. gap size = 1.00 (2 / 2) 16 16.94 0.00 0.00 chr5qtel1M 146859 146891 (853109) (ACAA)n#Simple_repeat 1 33 (0) m_b247s252i19 9814 chr5qtel1M 146859 ACAAACAAACAAGCAAACAAAAATAAAAATAAA 146891 i v v v i (ACAA)n#Simpl 1 ACAAACAAACAAACAAACAAACAAACAAACAAA 33 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 12 22.67 0.00 2.70 chr5qtel1M 146873 146910 (853090) (AAATAA)n#Simple_repeat 1 37 (0) m_b247s252i20 9814 chr5qtel1M 146873 AAACAAAAATAAAAATAAAGTATTAAATTGAGAGTAAA 146910 i -v v v i i i (AAATAA)n#Sim 1 AAATAAAAATAAAAATAAA-AATAAAAATAAAAATAAA 37 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 567 24.48 8.39 0.00 chr5qtel1M 147878 148020 (851980) C MIRc#SINE/MIR (79) 189 35 m_b247s601i20 9815 chr5qtel1M 147878 CACAGCAACCCCCCAAGGGAGGC---GC---TATAATCATACCCATTTTA 147921 i ivii v --- --- v i v C MIRc#SINE/MIR 189 CACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTA 140 chr5qtel1M 147922 TAGATGAGAAAACTGAAGCAAACAGGGCTCACATGACTTGCCCACAGTCA 147971 i i i vv v i v i vi vi C MIRc#SINE/MIR 139 CAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCA 90 chr5qtel1M 147972 ------TAGTAAGTAACTGAGTCTGGGTTTGAACTCAGGTTTCCCTAACT 148015 ------ ii v i v ii i i i i i C MIRc#SINE/MIR 89 CACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACT 40 chr5qtel1M 148016 CCAGG 148020 i C MIRc#SINE/MIR 39 CCAAG 35 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.55 CpG sites = 23, Kimura (unadjusted) = 30.60 Transitions / transversions = 1.92 (23/12) Gap_init rate = 0.02 (3 / 142), avg. gap size = 4.00 (12 / 3) 370 19.56 5.11 1.87 chr5qtel1M 148099 149135 (850865) (TCTGTC)n#Simple_repeat 1 1070 (0) m_b247s252i21 9816 chr5qtel1M 148099 TCTCTCTCTG-CT-TCTCTCTATACTCTCTACTTCTCTGTGTGTCTCTCT 148146 v - - v i - v - - v v v v (TCTGTC)n#Sim 1 TCTGTCTCTGTCTCTGTCTCTGT-CTCTGT-C-TCTGTCTCTGTCTCTGT 47 chr5qtel1M 148147 GTATGTCTGTCTCTCCATTTCTCTTTCTGTCACTGTCT-T-TCTCTCTCT 148194 v v v v ii i v i v - - v (TCTGTC)n#Sim 48 CTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCT 97 chr5qtel1M 148195 ATCTCTTTGTCTCTGTCTC--TCTGTGTCTCTGTCTCTGTCTCTCTGTTT 148242 v v i -- v v v i (TCTGTC)n#Sim 98 CTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCT 147 chr5qtel1M 148243 TTCTCTGTTTCTGTCTGTCTGTGTCTCTCTGTCTCTCTGTCTCTCTTTGT 148292 v i v v v v v v v v i (TCTGTC)n#Sim 148 GTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGT 197 chr5qtel1M 148293 CTCTGTCTTTCTCTCTGTGTCTTTCTCTGTCTCTATTTCTGTTTCTATGT 148342 i v v v i i i i v (TCTGTC)n#Sim 198 CTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCT 247 chr5qtel1M 148343 CTGTCTTTGTCTCTATCTCTTTGTCTCTGTTTCTGTCTGTCTGTGTCTCT 148392 i i -- i v v v v v (TCTGTC)n#Sim 248 CTGTCTCTGTCTCTGTCTC--TGTCTCTGTCTCTGTCTCTGTCTCTGTCT 295 chr5qtel1M 148393 CTGTCTCTCTC-CTTTCTCTGTTTCTCTTTGTCTCTCTCTCTCTCTCTCT 148441 v - v i v i v v v v (TCTGTC)n#Sim 296 CTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCT 345 chr5qtel1M 148442 GTCTCTGTCTCTGTGTCTCTCT-TTTCTCT-CCT-TTTCTCTGTGT-TTT 148487 v v - v -i - v v - v (TCTGTC)n#Sim 346 GTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGT 395 chr5qtel1M 148488 CTCT-TCT-T-T-TCTATGTCT-TCTTTGTCTCT-TCTCTTTGT-TCTCT 148530 - - - - i v - i - v v - v (TCTGTC)n#Sim 396 CTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCT 445 chr5qtel1M 148531 ATTTCTTTTATTATGTTCTCTATCTC-CTC-CTTTCTTTCTCTCCCTCTT 148578 v v i vvi v - i -v - v i v iv i (TCTGTC)n#Sim 446 CTGTCTCTGTCTCTG-TCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTC 494 chr5qtel1M 148579 TGTCTCTATCTCTCTCT-TGTGTCCGT-TTTCTCTTCTCTCTTTATCTCT 148626 i v - v i - i v - v i i (TCTGTC)n#Sim 495 TGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTC-TCTGTCTCTGTCTCT 543 chr5qtel1M 148627 -TCTCTTTCTCCTTTCTCTCTCT-TTTCTCT-TCTCT-TCTCT-TTTCT- 148670 - v - v v - v - - - i - (TCTGTC)n#Sim 544 GTCTCTGTCT-CTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTG 592 chr5qtel1M 148671 TCTTCT-TTTCTTTCTCTCT-TCTCTCTTTTTCTCTGTCT-TCTCTTTTG 148717 - - i v v - v i v - v - i (TCTGTC)n#Sim 593 TC-TCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTC-TCTG 640 chr5qtel1M 148718 TCTTCTTTCTCTGTGTCTTTCTCTGTCTCTATTTCTATAT-TATCT-TAT 148765 - v v v i i i v - i - i (TCTGTC)n#Sim 641 TC-TCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGT 689 chr5qtel1M 148766 CTCT-TCTCT-TTTCCTTTTCTATTTCTTGTCTCTCT-TC-CTCTCCTTT 148811 - - i iv i i i - v - -v iv i (TCTGTC)n#Sim 690 CTCTGTCTCTGTCTCTGTCTCTGTCTC-TGTCTCTGTCTCTGTCTCTGTC 738 chr5qtel1M 148812 TCTTTCTCTGT-T-TTTCTTTGTCTCTGTCTCTCTGTCTCTGTCTCTGTG 148859 v - - v i -- v (TCTGTC)n#Sim 739 TCTGTCTCTGTCTCTGTCTCTGTCTCTG--TCTCTGTCTCTGTCTCTGTC 786 chr5qtel1M 148860 TC--TCTCTGTCTC--TCTTTGTCTCTGTCT-T-TCTCTGTGTCTTTCTC 148903 -- -- i - - v v (TCTGTC)n#Sim 787 TCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTC 836 chr5qtel1M 148904 TGTCTCTATTTCTGTTTCTATGTCTGTCTTTGTCTCTGTTTCTTTGTCTC 148953 i i i i v i -- i (TCTGTC)n#Sim 837 TGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTG--TCTCTGTCTC 884 chr5qtel1M 148954 TATTTCTG--TCTGTCTGTGTCTCTCTGTCTCTCTCCTTTTCTTTCTCTG 149001 i i -- v v v v iv i v (TCTGTC)n#Sim 885 TGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTG 934 chr5qtel1M 149002 TCTC--TCTTTGTCTCTGTTTCCATCTC--TCTCTGTCTCTGTCTTTGTC 149047 -- i i ii -- i (TCTGTC)n#Sim 935 TCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTC 984 chr5qtel1M 149048 TCTGTCTCTTTGTCTCTGTTTCTGTCTGTTTCTCTCTGTCTCTCTCTCTC 149097 -- i -- i v v v (TCTGTC)n#Sim 985 TCTGTCTC--TGTCTCTGTCTCTGTC--TCTGTCTCTGTCTCTGTCTCTG 1030 chr5qtel1M 149098 TCTCCATTTCTCTCTCTGTCTCTGACTC--TCTCTGTCTC 149135 ii i v v -- (TCTGTC)n#Sim 1031 TCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTC 1070 Matrix = Unknown Transitions / transversions = 0.70 (71/101) Gap_init rate = 0.06 (65 / 1036), avg. gap size = 1.12 (73 / 65) 12 14.15 3.03 3.03 chr5qtel1M 149291 149323 (850677) (GGAG)n#Simple_repeat 1 33 (0) m_b248s252i1 9817 chr5qtel1M 149291 GGAGGGAGAGAGGGTGGG-CGGAGGAGGGGGAGG 149323 i v -v - i (GGAG)n#Simpl 1 GGAGGGAGGGAGGGAGGGAGGGAGG-GAGGGAGG 33 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.06 (2 / 32), avg. gap size = 1.00 (2 / 2) 36 16.57 4.39 5.31 chr5qtel1M 150003 150116 (849884) (CCTGACC)n#Simple_repeat 1 113 (0) m_b248s252i2 9818 chr5qtel1M 150003 CCCGACCCCTGA-CCCTAACCCTGCTGATTCCTGACCCCCGA-CCCTAAC 150050 i - i -- ii i - i - (CCTGACC)n#Si 1 CCTGACCCCTGACCCCTGACCC--CTGACCCCTGACCCCTGACCCCTGA- 47 chr5qtel1M 150051 CCCCCTGACCCCTCACCCC-CAACCCTAACCCTCCTGATTCCTGACCCCC 150099 - v -v v i - - ii i (CCTGACC)n#Si 48 -CCCCTGACCCCTGACCCCTGACCCCTGA-CC-CCTGACCCCTGACCCCT 94 chr5qtel1M 150100 GA-CCCT-AACCCTAACCC 150116 - - v i (CCTGACC)n#Si 95 GACCCCTGACCCCTGACCC 113 Matrix = Unknown Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.10 (11 / 113), avg. gap size = 1.00 (11 / 11) 29 13.87 8.26 5.36 chr5qtel1M 150009 150117 (849883) (CCCTGA)n#Simple_repeat 1 112 (0) m_b248s252i3 9818 chr5qtel1M 150009 CCCTGACCCTAACCCTG---CTGATTCCTGACCCCCGACCCTAACCC--- 150052 i --- -i - i i --- (CCCTGA)n#Sim 1 CCCTGACCCTGACCCTGACCCTGA-CCCTGA-CCCTGACCCTGACCCTGA 48 chr5qtel1M 150053 CCCTGACCCCTCACCCCCAACCCTAACCCT---CCTGATTCCTGACCCCC 150099 - v - ii i --- -i - i (CCCTGA)n#Sim 49 CCCTGA-CCCTGA-CCCTGACCCTGACCCTGACCCTGA-CCCTGA-CCCT 94 chr5qtel1M 150100 GACCCTAACCCTAACCCT 150117 i i (CCCTGA)n#Sim 95 GACCCTGACCCTGACCCT 112 Matrix = Unknown Transitions / transversions = 11.00 (11/1) Gap_init rate = 0.08 (9 / 108), avg. gap size = 1.67 (15 / 9) 268 34.15 7.32 0.00 chr5qtel1M 150795 150917 (849083) L3#LINE/CR1 2497 2628 (1471) m_b248s601i1 9819 chr5qtel1M 150795 GAGGGAGCTG--GTGCAAGATGAGGAAGGAGACGG--GGAGACCGCTTAG 150840 ii -- iv ii vi ii --i v i i L3#LINE/CR1 2497 GAGGGAATTGAAGCCCAAGATAGGTGAGGAGATAGTAAGAGAGCACCTAG 2546 chr5qtel1M 150841 CTGCCCGGGATGAACTCAAGGCACT-GGTCCTGATGAGCCCCTTCTCAGG 150889 i iivii ii v v i- i v i iiiv v i L3#LINE/CR1 2547 CCGCTTTAAATGAGTTCAAGTCTCCAGGCCCAGACGAATTACATCCCAGG 2596 chr5qtel1M 150890 G----GAAAGGGCTGTCGGATGTGATTAGGGA 150917 ---- ii vv i iiv L3#LINE/CR1 2597 GTACTGAAAGAACTTGCAGATGTGATCGCGGA 2628 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.24 CpG sites = 30, Kimura (unadjusted) = 49.44 Transitions / transversions = 2.50 (30/12) Gap_init rate = 0.03 (4 / 122), avg. gap size = 2.25 (9 / 4) 30 0.00 0.00 0.00 chr5qtel1M 151637 151662 (848338) (CA)n#Simple_repeat 1 26 (0) c_b248s251i0 9820 chr5qtel1M 151637 CACACACACACACACACACACACACA 151662 (CA)n#Simple_ 1 CACACACACACACACACACACACACA 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 821 27.04 1.32 2.67 chr5qtel1M 152328 152555 (847445) MIRb#SINE/MIR 1 225 (43) m_b248s601i2 9821 chr5qtel1M 152328 CACGGGGGCCGCTAGGTGACTCTGTGGAGAGAGGTCCCGGTTTGGAGTCA 152377 vi v vv --- v i vv vv v MIRb#SINE/MIR 1 CAGAGGGGCAGCGTGGTG---CAGTGGAAAGAGCACGGGCTTTGGAGTCA 47 chr5qtel1M 152378 GGAAGACCCAAAGCCAAATTTGGCCACAGACACTCGCTAGCTGAGTGACC 152427 iv iiiivi i iiv v v v v ii v MIRb#SINE/MIR 48 GACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACC 97 chr5qtel1M 152428 CTAGGCAAGTCATTTAACCTGTCT--TCTCCAGTTTCCTCAATTGT-AAA 152474 i i i i v --v ii vi - MIRb#SINE/MIR 98 TTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAA 147 chr5qtel1M 152475 TGGAGATAATGATAGAACCTTCTTCCCAGAGTAATTGTGAGGAGAAAATA 152524 i i --- v i v i vi vv i MIRb#SINE/MIR 148 TGGGGATAATAAT---ACCTACCTCGCAGGGTTGTTGTGAGGATTAAATG 194 chr5qtel1M 152525 GGATAATGTTTATAAAGTACTTGGCGCAGTG 152555 i iv i ii i i MIRb#SINE/MIR 195 AGATAATGCATGTAAAGCGCTTAGCACAGTG 225 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.66 CpG sites = 33, Kimura (unadjusted) = 34.11 Transitions / transversions = 1.22 (33/27) Gap_init rate = 0.04 (8 / 227), avg. gap size = 1.12 (9 / 8) 212 32.53 6.02 0.00 chr5qtel1M 152650 152732 (847268) C L2#LINE/L2 (158) 2924 2837 m_b248s601i3 9822 chr5qtel1M 152650 GGCCAGATTGTGTCAGACCTTGAATGCCAAGCCAAGGAGTTGGGACTTTA 152699 i ii vi i v v vvvi v v vi C L2#LINE/L2 2924 GACCAGATCATGTAGGGCCTTGTAGGCCATTGTAAGGACTTTGGCTTTTA 2875 chr5qtel1M 152700 TCCAGTGGGCAATGGGGAGCT-----CGGGTTTTCAGC 152732 ii v v v vi i i-----v v C L2#LINE/L2 2874 CTCTGAGTGAGATGGGAAGCCATTGGAGGGTTTTGAGC 2837 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.95 CpG sites = 12, Kimura (unadjusted) = 42.95 Transitions / transversions = 0.80 (12/15) Gap_init rate = 0.01 (1 / 82), avg. gap size = 5.00 (5 / 1) 194 32.97 4.21 1.02 chr5qtel1M 153013 153107 (846893) C MIR3#SINE/MIR (41) 167 70 m_b248s601i4 9823 chr5qtel1M 153013 AGGGATCGTTTGATACAAGCTCTCCTGCACTGAGAACGAGAAAA-TG-GG 153060 i i i ii v - i i iiiivi ivii i i - - C MIR3#SINE/MIR 167 AGAGATCATCTAGTCCAA-CCCCCTCATTTTACAGATGAGGAAACTGAGG 119 chr5qtel1M 153061 CACAGAGAGGTGCTCT-CCGTGCCCAGGG-CACACGGAAAGCTAGTGAC 153107 v vvv -v v i - i v? i i C MIR3#SINE/MIR 118 CCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGC 70 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 47.00 CpG sites = 21, Kimura (unadjusted) = 47.00 Transitions / transversions = 2.10 (21/10) Gap_init rate = 0.05 (5 / 94), avg. gap size = 1.00 (5 / 5) 81 18.86 3.02 2.50 chr5qtel1M 153219 153417 (846583) (AAGG)n#Simple_repeat 1 200 (0) m_b248s252i4 9824 chr5qtel1M 153219 AAGGAAGGGGAGATGGAAGGAAGGAAGG-AGGAATGGAAGAAAGGAGGAA 153267 iii v - - i i i (AAGG)n#Simpl 1 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA-GGAAGGAAGGAAGGA 49 chr5qtel1M 153268 AGGAAGAAAAG-AGGAAGGGAAGGAAGGAGGGAGGGAGGGAGGGAGGAAA 153316 i i - - i i i i i i (AAGG)n#Simpl 50 AGGAAGGAAGGAAGGAA-GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 98 chr5qtel1M 153317 GGAAAGAAGGGAGGAAGGGAAGGAGGAAAGGAAGGAAGGGAGGGAGGGAG 153366 i i - i i i i i (AAGG)n#Simpl 99 GGAAGGAAGGAAGGAA-GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG 147 chr5qtel1M 153367 AGAGGAAGGAAGGGAGGGAGGGA-GAA-AAAGAGAGAGGGAGGAA--AAG 153412 ii i i i - -i - - i -- (AAGG)n#Simpl 148 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG-GA-AGGAAGGAAGGAAG 195 chr5qtel1M 153413 GGAGG 153417 i (AAGG)n#Simpl 196 GAAGG 200 Matrix = Unknown Transitions / transversions = 29.00 (29/1) Gap_init rate = 0.05 (10 / 198), avg. gap size = 1.10 (11 / 10) 214 36.96 2.21 4.51 chr5qtel1M 153418 153553 (846447) C MIRb#SINE/MIR (131) 137 5 m_b248s601i5 9825 chr5qtel1M 153418 GAGGAAGAGAAGG---AGAGGGAACTGGAGGCTTGTTTAGGGTTACCCAG 153464 ivvi --- i ivivi vii iii i i v C MIRb#SINE/MIR 137 GAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAG 88 chr5qtel1M 153465 CTTGGAATTGTCTAAGGCAGGTTTTAAGTTCAGCTCTGTCTCCCTCTGTC 153514 v v v v vi v i v ii iii v vv --- C MIRb#SINE/MIR 87 CTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTC---C 41 chr5qtel1M 153515 TGTGGCTGTCCAATCTCCCCAGTGCACAAAAGCTGTCCC 153553 viv v i v -- ii v -v v i C MIRb#SINE/MIR 40 AAAGCCCGTGC--TCTTTCCACTGCAC-CACGCTGCCCC 5 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 47.46 CpG sites = 25, Kimura (unadjusted) = 52.14 Transitions / transversions = 1.09 (25/23) Gap_init rate = 0.05 (7 / 135), avg. gap size = 1.29 (9 / 7) 69 28.89 4.14 2.51 chr5qtel1M 154195 154232 (845768) (TAGA)n#Simple_repeat 1 38 (281) m_b248s252i5 9826 chr5qtel1M 154195 TAGAT-GATGGGTAGATGGATACATACATACATGCATAC 154232 - i i i v v v iv - (TAGA)n#Simpl 1 TAGATAGATAGATAGATAGATAGATAGATAGATAGATA- 38 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 28 8.37 1.89 1.89 chr5qtel1M 154233 154285 (845715) (ATGG)n#Simple_repeat 1 53 (0) c_b248s251i1 9827 chr5qtel1M 154233 ATGGATGGGTGGAT-GATGGACAGATGAGAAGGATGGATGGATGGATGGA 154281 i - ii - v (ATGG)n#Simpl 1 ATGGATGGATGGATGGATGGATGGATG-GATGGATGGATGGATGGATGGA 49 chr5qtel1M 154282 TGGA 154285 (ATGG)n#Simpl 50 TGGA 53 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.00 (2 / 2) 69 28.89 4.14 2.51 chr5qtel1M 154286 154560 (845440) (TAGA)n#Simple_repeat 39 319 (0) m_b248s252i5 9828 chr5qtel1M 154286 GAGAGATAAATAGATACATACAGACAGACAGACAGACATGGGGAAGGATG 154335 v i v -- i i i i vivi vi i (TAGA)n#Simpl 39 GATAGATAGATAGATAGAT--AGATAGATAGATAGATAGATAGATAGATA 86 chr5qtel1M 154336 GAT-GATGGAGGGGTAGAT-GATAGACATAAACAAATGGATGGAT--ATA 154381 - i vi i - -- i i i i i -- (TAGA)n#Simpl 87 GATAGATAGATAGATAGATAGATAG--ATAGATAGATAGATAGATAGATA 134 chr5qtel1M 154382 GATAATTAGATACATAGATGGATGAATAGATGGATA-TTGGATAGATGAG 154430 iv v i ii i -v i - (TAGA)n#Simpl 135 GATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGAT-AG 183 chr5qtel1M 154431 ATGGATGAATAGAT-GATAGATGGTTAGATAGGT-GATTGGGACAAATGA 154478 i ii - i v i - v iv v v - (TAGA)n#Simpl 184 ATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATA-GA 232 chr5qtel1M 154479 TAAACGGAT--ATAAATACACAGCTAGATAGGTAAATGGATA-ACAGAT- 154524 i ii -- i v i v i i i - i - (TAGA)n#Simpl 233 TAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATA 282 chr5qtel1M 154525 GCTAGAGAGGTGGA-AGGGAGATGGATGGATAGATAG 154560 v v i i - iv i i (TAGA)n#Simpl 283 GATAGATAGATAGATAGATAGATAGATAGATAGATAG 319 Matrix = Unknown Transitions / transversions = 2.26 (43/19) Gap_init rate = 0.06 (16 / 274), avg. gap size = 1.12 (18 / 16) 680 30.23 3.72 0.00 chr5qtel1M 154648 154862 (845138) C MIRc#SINE/MIR (0) 268 46 m_b248s601i6 9829 chr5qtel1M 154648 AATAATAACAATAACTGGAATTCATAT-GTACTTTAAGATTCACAAAGCA 154696 i i?v viv ii - i vii i i C MIRc#SINE/MIR 268 AATAATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCG 219 chr5qtel1M 154697 CTTT-ACACATATTAGCTCATTTTGTCTTTATAACAATTTTG----GTAG 154741 - i i v vi i i i iii ---- C MIRc#SINE/MIR 218 CTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAG 169 chr5qtel1M 154742 G--GACCTGCTCTTATAACCCTTATTTTACAGATGAGCAAACTGAGGCAG 154789 -- iv v v v v i ii v vv C MIRc#SINE/MIR 168 GCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC 119 chr5qtel1M 154790 GCAGAGATCAAGGGATTTGCGTAGAATCACCCAGGAAGGAAGCACCTGAA 154839 iv i i v i vi iii v vv v iiv v i C MIRc#SINE/MIR 118 AGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAG 69 chr5qtel1M 154840 CCTGAATTTGAACTCAGCCCTCC 154862 v i i i i vi i C MIRc#SINE/MIR 68 CCGGGACTCGAACCCAGGTCTTC 46 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.76 CpG sites = 40, Kimura (unadjusted) = 40.38 Transitions / transversions = 1.60 (40/25) Gap_init rate = 0.02 (4 / 214), avg. gap size = 2.00 (8 / 4) 403 31.78 1.55 0.00 chr5qtel1M 154758 154886 (845114) C MIR3#SINE/MIR (61) 147 17 m_b248s601i7 9829 chr5qtel1M 154758 CCCTTATTTTACAGATGAGCAAACTGAGGCAGGCAGAGATCAAGGGATTT 154807 i v vviv i v v i C MIR3#SINE/MIR 147 CCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTT 98 chr5qtel1M 154808 GCGTAGAATCACCCAGGAAGGAAGCACCTGAACCTGAATTTGAACTCAGC 154857 vi iii v v? vv iiv v i v i i v i v C MIR3#SINE/MIR 97 GCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGG 48 chr5qtel1M 154858 CCTCCAGGCCAGCAGG--ATTTTCTCTCTAC 154886 i v i ivv v--i vi i C MIR3#SINE/MIR 47 TCTCCTGACTCCCAGTCCGTGCTCTCTCTGC 17 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.98 CpG sites = 20, Kimura (unadjusted) = 42.31 Transitions / transversions = 0.95 (20/21) Gap_init rate = 0.01 (1 / 128), avg. gap size = 2.00 (2 / 1) 12 30.01 0.00 0.00 chr5qtel1M 157011 157055 (842945) (CCCCGCG)n#Simple_repeat 1 45 (0) m_b248s252i6 9830 chr5qtel1M 157011 CCTCGCAGCCCGAGCTCCGCGCCACCCACCCCGGGCCCCACGTCC 157055 i iv v i v v i v i i (CCCCGCG)n#Si 1 CCCCGCGCCCCGCGCCCCGCGCCCCGCGCCCCGCGCCCCGCGCCC 45 Matrix = Unknown Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 221 30.77 3.70 3.70 chr5qtel1M 157860 157967 (842033) MIR3#SINE/MIR 11 118 (90) m_b248s601i8 9831 chr5qtel1M 157860 GGATGAGGAGAGGGGACAAGGTCTGGACCTGAGGA-CCCTGA--TCCAGT 157906 v v i ii v v ivv v -v i-- i MIR3#SINE/MIR 11 GGCTGAGCAGAGAGAGCACGGACTGGGAGTCAGGAGACCTGGGTTCTAGT 60 chr5qtel1M 157907 CTCAGCTCCAG-ACGTACTTATTGTGCCAGGCCTTCTTCCAGCCTCACTT 157955 i i iiv- vv ?ii i-- i vvv v -- MIR3#SINE/MIR 61 CCCGGCTCTGCCACTAACTNGCTGTGT--GACCTTGGGCAAG--TCACTT 106 chr5qtel1M 157956 TACTCCTCTGGG 157967 i ii MIR3#SINE/MIR 107 CACCTCTCTGGG 118 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.25 CpG sites = 17, Kimura (unadjusted) = 40.89 Transitions / transversions = 1.13 (17/15) Gap_init rate = 0.07 (7 / 107), avg. gap size = 1.14 (8 / 7) 208 31.58 17.54 0.00 chr5qtel1M 157866 157979 (842021) MIRc#SINE/MIR 20 153 (115) m_b248s601i9 9831 chr5qtel1M 157866 GGAGAGGGGACAAGGTCTGGA--CCTGAGGACCCTGATCC-AGTCTCAGC 157912 i i v vi iii -- vv i iv i i - i i MIRc#SINE/MIR 20 GGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGC 69 chr5qtel1M 157913 TCCAG-ACGTACTTATTGTGCCA-----GGC-----------CTTCTTCC 157945 iiv- v vii iv ----- ----------- i iiv MIRc#SINE/MIR 70 TCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTG 119 chr5qtel1M 157946 AGCCTCACTTTACTCCTCTGGGAAATGGGGATGA 157979 v v v vi i MIRc#SINE/MIR 120 AGCCTCAGTTTCCTCATCTGTAAAATGGGGATAA 153 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.01 CpG sites = 22, Kimura (unadjusted) = 42.59 Transitions / transversions = 1.57 (22/14) Gap_init rate = 0.04 (5 / 113), avg. gap size = 4.00 (20 / 5) 431 21.49 7.44 0.00 chr5qtel1M 158435 158555 (841445) MIR1_Amn#SINE/MIR 29 158 (72) m_b248s601i10 9832 chr5qtel1M 158435 AGCCTCGGGCTGG--TTCTGAGGCTCTGG----AAATTCTGCCCCTGGCG 158478 vii i --i v ii vi ----? ? i i v i v i MIR1_Amn#SINE 29 AGCACTGGACTGGGACTCGGGAGACCTGGGTTCNANTCCCGGCTCTGCCA 78 chr5qtel1M 158479 CTTCTCAGCTGTGTGACCT-GGGCAAGTGGCTTCACCTGTCTG--CCTCG 158525 ?vi ? ? - vi ? v -- i MIR1_Amn#SINE 79 CTNGCCNGCTGNGTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCA 128 chr5qtel1M 158526 GTTTCCCCAACTGTAAAATGGTGATAATAA 158555 i v v i MIR1_Amn#SINE 129 GTTTCCTCATCTGTAAAATGGGGATAATGA 158 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.28 CpG sites = 16, Kimura (unadjusted) = 27.50 Transitions / transversions = 1.60 (16/10) Gap_init rate = 0.03 (4 / 120), avg. gap size = 2.25 (9 / 4) 748 21.08 4.19 3.11 chr5qtel1M 158463 158653 (841347) MIR#SINE/MIR 57 249 (13) m_b248s601i11 9832 chr5qtel1M 158463 AATTCTGCCCCTGGCGCTTCTCAGCTGTGTGACCT-GGGCAAGTGGCTTC 158511 i i v i v i vii - vi v MIR#SINE/MIR 57 AATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTA 106 chr5qtel1M 158512 ACCTGTCTG--CCTCGGTTTCCCCAACTGTAAAATGGTGATAATAAGAGC 158559 v -- i i v v v -- MIR#SINE/MIR 107 ACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATA-- 154 chr5qtel1M 158560 ATGTACCCACCCC-TAGGGCCATTCATGAGGATCCAAAGGAGCTGTT--- 158605 -- i i - iii -i -i v i iv --- MIR#SINE/MIR 155 --GTACCTACCTCATAGGGTTGTT-GTGAGGAT-TAAATGAGTTAATACA 200 chr5qtel1M 158606 TGGGAAGGGCTTAGGCCAGTGTCTGGCACATAGAAGGTGCTT-ATAAAT 158653 vi v iv i v i i i- MIR#SINE/MIR 201 TGTAAAGCGCTTAGAACAGTGCCTGGCACATAGTAAGCGCTCAATAAAT 249 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 23.79 CpG sites = 24, Kimura (unadjusted) = 25.24 Transitions / transversions = 1.60 (24/15) Gap_init rate = 0.05 (10 / 190), avg. gap size = 1.40 (14 / 10) 181 18.42 2.63 0.00 chr5qtel1M 158621 158658 (841342) L2c_3end#LINE/L2 426 464 (14) m_b248s601i12 9833 chr5qtel1M 158621 CCAGTGTCTGGCACATAGAAGGTGCTT-ATAAATTATTG 158658 i i v i i- vv L2c_3end#LINE 426 CCAGCGCCTGGCACATAGTAGGCGCTCAATAAATGTTTG 464 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 15.13 CpG sites = 4, Kimura (unadjusted) = 21.38 Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 290 32.62 7.80 0.00 chr5qtel1M 158877 159017 (840983) MIRc#SINE/MIR 48 199 (69) m_b248s601i13 9834 chr5qtel1M 158877 AAACCTGGGCTTG--CTCCTGCCGGGCC-CTTGCTAGCAGAGAGTCCCCG 158923 i i i --ii v ivv - i v v v v ii MIRc#SINE/MIR 48 AGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTG 97 chr5qtel1M 158924 GGCGATAACCTTAACAGCTGTTTGCCTCAGTTTCCCTACCTCTAAAA--G 158971 i vvvv vv v vv ii i v -- MIRc#SINE/MIR 98 GGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGG 147 chr5qtel1M 158972 GGGTCGTGACA----CCCTGGCTATTCCTCTGAGTTTTCGTGCAGA--AA 159015 i vi i i ---- v iii v v i v i vi -- MIRc#SINE/MIR 148 GGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAA 197 chr5qtel1M 159016 AT 159017 MIRc#SINE/MIR 198 AT 199 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.24 CpG sites = 23, Kimura (unadjusted) = 43.48 Transitions / transversions = 1.00 (23/23) Gap_init rate = 0.04 (5 / 140), avg. gap size = 2.20 (11 / 5) 18 24.83 0.00 0.00 chr5qtel1M 160079 160126 (839874) (GGGG)n#Simple_repeat 1 48 (0) m_b248s252i7 9835 chr5qtel1M 160079 GGGGGGAGGGGCGGGGAGGAGGGAAGGAGGCGTCGGGGGGGGGGGGGG 160126 i v i i ii i v vv (GGGG)n#Simpl 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 48 Matrix = Unknown Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 12 19.53 1.85 7.84 chr5qtel1M 160548 160601 (839399) (CCCGAG)n#Simple_repeat 1 51 (0) m_b248s252i8 9836 chr5qtel1M 160548 CCCGCAGCCGTGACCCCCAGGCC-AGACTCGGGCCCGTGACCGAGGCCCG 160596 - -i v v v - - i i v v - (CCCGAG)n#Sim 1 CCCG-AGCC-CGAGCCCGAGCCCGAG-CCCGAGCCCGAGCCCGA-GCCCG 46 chr5qtel1M 160597 AGCCC 160601 (CCCGAG)n#Sim 47 AGCCC 51 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.09 (5 / 53), avg. gap size = 1.00 (5 / 5) 15 13.88 3.03 0.00 chr5qtel1M 161962 161994 (838006) (TCCCC)n#Simple_repeat 1 34 (0) m_b248s252i9 9837 chr5qtel1M 161962 TCCCCTCCCCCTTCCTCTCCTCCCC-CCCCTCCC 161994 iii i - (TCCCC)n#Simp 1 TCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCC 34 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 17 34.85 0.00 0.00 chr5qtel1M 163136 163196 (836804) (AA)n#Simple_repeat 1 61 (0) m_b248s252i10 9838 chr5qtel1M 163136 AAAAAAAAAAAAAAAAAATCAGATTAAAAGGGGAAAAAACAAGCAAATAA 163185 vv i vv iiii v iv v (AA)n#Simple_ 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr5qtel1M 163186 TCAACCAAAAA 163196 vv vv (AA)n#Simple_ 51 AAAAAAAAAAA 61 Matrix = Unknown Transitions / transversions = 0.55 (6/11) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 341 29.47 3.43 1.12 chr5qtel1M 163369 163543 (836457) C L1MC4a_3end#LINE/L1 (1985) 644 466 m_b248s551i0 9839 chr5qtel1M 163369 TCTCTTG-GTTCTGCTCATTTCACTCAGCATCAGTTCCTGGAAGTCTCCC 163417 i -ii i iv i i vi vv i v i C L1MC4a_3end#L 644 TCTTTTGCACTTTGCTTTTTTCACTTAACAATATATCCTGGAAATCACTC 595 chr5qtel1M 163418 CAGGCC---TCTCTGAAATCATCCTGCTGTTGTTTTTTACAGAACAATAA 163464 vii --- viv i v --ii v vvvv i C L1MC4a_3end#L 594 CATATCAGTTCATAGAGATCTTCCT--CATTCTTTTTTACAGCTGCATAG 547 chr5qtel1M 163465 TATTCCATAACATTCATATACTATAACTTATTCAGCCATTCTCCAATTGA 163514 i viii vv i i ii i ? v ?? C L1MC4a_3end#L 546 TACTCCATTGTGTGGATGTACCATAGTTTATTCAACCANTCTCCTATNNA 497 chr5qtel1M 163515 TGGGCATGCACTCAGTTTCCA--TTTTTGCA 163543 vi vviv --v C L1MC4a_3end#L 496 TGGGCATTTAGGTTGTTTCCAATATTTTGCA 466 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 39.13 CpG sites = 28, Kimura (unadjusted) = 39.13 Transitions / transversions = 1.22 (28/23) Gap_init rate = 0.03 (5 / 174), avg. gap size = 1.60 (8 / 5) 289 34.65 2.36 0.00 chr5qtel1M 163621 163747 (836253) C L1PA5_3end#LINE/L1 (587) 314 185 m_b248s551i1 9840 chr5qtel1M 163621 AGTGATTGGATTAGTTCACAACTCCACCAACAATGCATTAGTGTTTCAAT 163670 i i i i i iii i i vv i v C L1PA5_3end#LI 314 AATGGTTGAACTAGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTAT 265 chr5qtel1M 163671 TTTTCCATATCCCTTCTAATGTTTATTATCTTTT-ACTTCCACCTCAT-- 163717 i i ii i iiiii i i i ii - iivvv v -- C L1PA5_3end#LI 264 TTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGATCG 215 chr5qtel1M 163718 CCAATATGGAAAGTGTGAAATGGTACCTCA 163747 v v iivvi i i C L1PA5_3end#LI 214 CCATTCTAACTGGTGTGAGATGGTATCTCA 185 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 51.36 CpG sites = 33, Kimura (unadjusted) = 51.36 Transitions / transversions = 3.00 (33/11) Gap_init rate = 0.02 (2 / 126), avg. gap size = 1.50 (3 / 2) 759 32.30 0.91 1.22 chr5qtel1M 164757 165085 (834915) C L1ME4c_3end#LINE/L1 (191) 639 312 m_b248s551i2 9841 chr5qtel1M 164757 TTCTGCTCATTTCGCTCAGCATCAGTTCATGTAAGTCTTGCCAATCCTCT 164806 iv i i i i vv iv vi i - vviiv C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATAAACATTTT-CCATGTTGCT 591 chr5qtel1M 164807 CTGTATTCGTCCTGCTGGTCATTTCTTACGGAACAATCATATTCCATAAC 164856 vii v v v iv vi i v i vvvv v viv C L1ME4c_3end#L 590 ACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCGA 541 chr5qtel1M 164857 ATTCATATACCACAATTTACTCAACCATTCTCCAATTGATGGGCATCCAT 164906 i ?v i i i i v v i ii v C L1ME4c_3end#L 540 GTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAG 491 chr5qtel1M 164907 TCATTTTCCAGCTTCTGGCCACTACAAAGAGGGCTGCCACAAACATTTTG 164956 vivv ii i v i i i v iv v ii i v C L1ME4c_3end#L 490 GTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTC 441 chr5qtel1M 164957 GCACATACAGGTCCCTTTCCCTTCTTT---AGTATCTCCTTGGGGTATAA 165003 ii i --- i i --- v i i i v v C L1ME4c_3end#L 440 GTGCATATAG---CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAAT 394 chr5qtel1M 165004 GCCCAGTAGAGACACTGCTGGATCAAAGGGTATGCACAGTTTGTTAACTT 165053 v v v iv i i i v v vv ii i C L1ME4c_3end#L 393 TCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTC 344 chr5qtel1M 165054 TTTGGGCATAGTTCCAAATTGCTCTCCAGAAG 165085 vivi i v v i i C L1ME4c_3end#L 343 TTGATACGTATTGCCAAATTGCTTTCCAAAAG 312 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 42.26 CpG sites = 56, Kimura (unadjusted) = 43.35 Transitions / transversions = 1.14 (56/49) Gap_init rate = 0.02 (5 / 328), avg. gap size = 1.40 (7 / 5) 464 33.72 1.82 2.94 chr5qtel1M 164842 165116 (834884) C L1MC5_3end#LINE/L1 (2142) 552 281 m_b248s551i3 9841 chr5qtel1M 164842 ATCATATTCCATAACATTCATATACCACAATTTACTCAACCATTCTCCAA 164891 vi i viii vv i i i i v i v C L1MC5_3end#LI 552 ATAGTACTCCATTGTGTGGATGTACCATAGTTTATTCAACCAGTCCCCTA 503 chr5qtel1M 164892 TTGATGGGCATCCATTCATTTTCCAGCTTCTGGCCACTACAAAGAGGGCT 164941 i iiivvivv ii i v i i v v C L1MC5_3end#LI 502 TTGATGGACATTTGGGTTGTTTCCAGTCTTTTGCTATTACAAATAGTGCT 453 chr5qtel1M 164942 GCCACAAACATTTTGGCACATACAGGTCCCTTTCCCTTCTT--TAGTATC 164989 v ii i vii v ii -- ii iviv i --i i v C L1MC5_3end#LI 452 GCAATGAATAGCCTTGTGCATAC--GTCTTTTCGTATTTTTGCCAGTGTA 405 chr5qtel1M 164990 TCCTTGGGGTATAAGCCCAGTAGAGACACTGCTGGATCAAAGGGT--ATG 165037 i i v vv i v v iv i i -- C L1MC5_3end#LI 404 TCTTTGGGATAGATTCCTAGAAGTGGGATTGCTGGGTCAAAGGGTAAATG 355 chr5qtel1M 165038 CACAGTTTGTTAACTTTTTGGGCATAGTTCCAAATTGCTCTCCAGAAGCC 165087 i --- v vi vi i -- v v v i v i vv C L1MC5_3end#LI 354 CATA---TGTAATTTTGCTAG--ATATTGCCAAATTCCCCTCCATAGGGG 310 chr5qtel1M 165088 ATCTGTTATTTTTTCATTCTT-TCAGCAGT 165116 v v iii - v ii-i i C L1MC5_3end#LI 309 TTGTACCA-TTTTGCATTCCCACCAGCAAT 281 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 45.74 CpG sites = 53, Kimura (unadjusted) = 46.46 Transitions / transversions = 1.43 (53/37) Gap_init rate = 0.04 (11 / 274), avg. gap size = 1.18 (13 / 11) 362 21.21 15.86 2.44 chr5qtel1M 165320 165464 (834536) C MIR1_Amn#SINE/MIR (14) 216 53 m_b248s601i14 9842 chr5qtel1M 165320 CCCCTATGTGGGCACTTCTTAGCAG-AGATACTGGAGTGATTTGC----- 165363 i i i - i i v - viiii iiv i ----- C MIR1_Amn#SINE 216 CTCTTATGTAG-CACTTTTCATCAGTAGATCTCAAAGCACTTTACAAAGG 168 chr5qtel1M 165364 ----CAGC-TCCTTCTCTAGCTCATGTTATAGATGAAG-------GG--- 165398 ---- i- v v --- i v i i ------- --- C MIR1_Amn#SINE 167 AGGTCAGTATCATTATC---CCCATTTTACAGATGAGGAAACTGAGGCNC 121 chr5qtel1M 165399 -GAG-GATTAAGTGACTTGCCCAGGGTCACACAGCTGGGAAGTGTCTGAG 165446 - - i ? i ? ? v? v v C MIR1_Amn#SINE 120 AGAGAGGTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNAGTGGCAGAG 71 chr5qtel1M 165447 GCTGGATTTGAACTCAGG 165464 v v ? ? i C MIR1_Amn#SINE 70 CCGGGANTNGAACCCAGG 53 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.99 CpG sites = 19, Kimura (unadjusted) = 26.99 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.08 (11 / 144), avg. gap size = 2.45 (27 / 11) 252 31.95 4.00 2.97 chr5qtel1M 165546 165645 (834355) C MIR3#SINE/MIR (47) 161 61 m_b248s601i15 9843 chr5qtel1M 165546 CATCGAGTACAAGTTCCTCATTCTTCCAATGGGGAA----AGACCCAGAG 165591 v v vii i v vi i ---- i C MIR3#SINE/MIR 161 CATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAG 112 chr5qtel1M 165592 AGATAAAATAAGGTGACATCCAGGGACAAGTAGACAGCAAGTGGTTGAAC 165641 i i i i vv ---i i v vii v? iv iv i C MIR3#SINE/MIR 111 AGGTGAAGTGACTTG---CCCAAGGTCACACAGCNAGTTAGTGGCAGAGC 65 chr5qtel1M 165642 TAGG 165645 ii C MIR3#SINE/MIR 64 CGGG 61 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.85 CpG sites = 19, Kimura (unadjusted) = 43.98 Transitions / transversions = 1.58 (19/12) Gap_init rate = 0.04 (4 / 99), avg. gap size = 1.75 (7 / 4) 230 33.39 3.67 6.60 chr5qtel1M 165560 165668 (834332) C MIRb#SINE/MIR (115) 153 48 m_b248s601i16 9843 chr5qtel1M 165560 TCCTCATTCTTCCAATGGGGAAA----GACCCAGAGAGATAAAATAAGGT 165605 i i v vi i ---- i i i v i vv C MIRb#SINE/MIR 153 TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTT 104 chr5qtel1M 165606 GACATCCAGGGACAAGTAGACAGCAAGTGGTTGAACTAGGTCCCCTGAGC 165655 ---i i v vii vi i iv i ii vii -- i C MIRb#SINE/MIR 103 G---CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTC--GAAC 59 chr5qtel1M 165656 TTCCAGGTTCATC 165668 -- iii C MIRb#SINE/MIR 58 --CCAGGTCTGTC 48 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.27 CpG sites = 24, Kimura (unadjusted) = 47.50 Transitions / transversions = 2.40 (24/10) Gap_init rate = 0.07 (8 / 108), avg. gap size = 1.38 (11 / 8) 282 35.42 6.98 1.43 chr5qtel1M 165851 166380 (833620) L1P3_orf2#LINE/L1 2729 3287 (7) m_b248s551i4 9844 chr5qtel1M 165851 ATAACTTTAATAATCTAGTGTTTAACAAACC---CAAAGACCCCACCTTT 165897 i v vi iv ii v i --- i v-- v vv L1P3_orf2#LIN 2729 ACATCTACAACCATCTGATCTTTGACAAACCTGACAAAAACA--AGCAAT 2776 chr5qtel1M 165898 GGGGATAACAACTCACTGTTTGATAAAAAATTGCTGGGAAAATTGGAAAT 165947 - vi i v i i vii - i i vv v L1P3_orf2#LIN 2777 GGGGA-AAGGATTCCCTATTTAATAAATGGT-GTTGGGAAAACTGGCTAG 2824 chr5qtel1M 165948 TAGTATGGCAGAAACTAGGCATTG-ACCCACACTTAACACCGTACACCAA 165996 ivi - viv iv i - viv i v v i v L1P3_orf2#LIN 2825 CCATATG-CAGAAAACTGAAACTGGACCCCTTCCTTACACCTTATACAAA 2873 chr5qtel1M 165997 GATAAGGTCAAAATGGGTTCGTGACCTAGGCATAAAGAATGAGATTATAA 166046 i v iv i i viv i ii i iivv i i ii L1P3_orf2#LIN 2874 AATTAACTCAAGATGGATTAAAGACTTAAACGTAAGACCTAAAACCATAA 2923 chr5qtel1M 166047 A----TTGGAAGAGCA--TAAG--ATA--GTTTA---------CCTGG-- 166075 ----i i iv -- i -- --i i --------- v -- L1P3_orf2#LIN 2924 AAACCCTAGAAGAAAACCTAGGCAATACCATTCAGGACATAGGCATGGGC 2973 chr5qtel1M 166076 AAGGAATTTGTGACCAAAGAAGAACTAGAGATCACTATTGATCATAAAAT 166125 i v ii i iv vv vv vi vi v ivi vvvi L1P3_orf2#LIN 2974 AAAGACTTCATGACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAAT 3023 chr5qtel1M 166126 AGAAAAATTTGATTATATCAAATTGAAAAGTTTTTGCACA---AACAAAA 166172 v v vv ivv i i i i i i --- vi L1P3_orf2#LIN 3024 TGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAA 3073 chr5qtel1M 166173 CTAATGCAGACAAGATTAGAAGGGAAGCAATAAACTGGGAAAACATTTTT 166222 viii--- iii v iv v v v i i v i v L1P3_orf2#LIN 3074 CTATCAT---CAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTT 3120 chr5qtel1M 166223 ACAATCAAAGGTTCTGATAAAGACCTCATCTCCAAAATATAAAGAGAATT 166272 i v vvvv i iv v v i v v ii i L1P3_orf2#LIN 3121 GCAATCTATCCATCTGACAAAGGGCTAATATCCAGAATCTACAAGGAACT 3170 chr5qtel1M 166273 -----GACTCTATATGAAATCAAGCCATTCTCCAATTGATAAATGGACAA 166317 -----i v i i v vv vvv ivvi v ii v i i i L1P3_orf2#LIN 3171 TAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGA 3220 chr5qtel1M 166318 AGGATATGAACAGACAATTCTCA----AAGAAATTGAAACTATTTCTAGC 166363 v ---- v v vi viiivvi iv L1P3_orf2#LIN 3221 AGGATATGAACAGACACTTCTCAAAAGAAGACATTTATGCGGCCAACAAA 3270 chr5qtel1M 166364 CATATGAAAAGATGCTC 166380 i v L1P3_orf2#LIN 3271 CATATGAAAAAAAGCTC 3287 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 48.33 CpG sites = 96, Kimura (unadjusted) = 49.07 Transitions / transversions = 1.08 (96/89) Gap_init rate = 0.04 (19 / 529), avg. gap size = 2.37 (45 / 19) 478 30.32 8.58 1.61 chr5qtel1M 165922 166387 (833613) L1M5_orf2#LINE/L1 2797 3294 (0) m_b248s551i5 9844 chr5qtel1M 165922 AAAAAAT--TGCTGGGAAAATTGGAAATTAGTATGGCAGAAACTAGGCAT 165969 v -- i v v ivi v i v iii?v L1M5_orf2#LIN 2797 AACAAATGGTGCTGGAACAATTGGATATCCATATGGAAAAAAATGAANCT 2846 chr5qtel1M 165970 TGACCCACACTTAACACCGTACACCAAGATAAGGTCAAAATGGGTTCGTG 166019 i vi i v i v i v iv ? i i ivvv L1M5_orf2#LIN 2847 CGACCCCTACCTCACACCATACACAAAAATTAATTCNAGATGGATCATAG 2896 chr5qtel1M 166020 ACCTAGGCATAAAGAATGAGATTATAAA----TTGGAAGAG--CATAAGA 166063 iiii ii? i i i ----i i i-- i L1M5_orf2#LIN 2897 ACCTAAATGTAAAAGNTAAAACTATAAAACTTCTAGAAGAAAACATAGGA 2946 chr5qtel1M 166064 ---TAGTTT----ACCT-------GGAAGGAATTTGTGACCAAAGAAGAA 166099 --- vi ---- ------- v iii v ---i v i v L1M5_orf2#LIN 2947 GAATATCTTCGTGACCTTGGGNTAGGCAAAGATTTCT---TAAACAGGAC 2993 chr5qtel1M 166100 CTAGAGATCACTATTGATCATAAAATAGAAAA-------ATTTGATTATA 166142 vi i i v ? --- i v i ------- v i ?i L1M5_orf2#LIN 2994 ACAAAAAGCACNA---ACCATAAAAGAAAAAATTGATAAATTGGACTNCA 3040 chr5qtel1M 166143 TCAAATTGAAAAGTTTTTGCACAAACAAAACTAATGCAGACAAGATTAGA 166192 v v ii i v ?vvv ivi vi ivi v i v i L1M5_orf2#LIN 3041 TCAAAATTAAAAACTTCTGCTCNTCAAAAGACACCGTTAAGAAAATGAAA 3090 chr5qtel1M 166193 AGGGAAGCAATAAACTGGGAAAACATTTTTACAATCAAAGGTTCTGATAA 166242 v v i i ? i v v i ?vv vivv i L1M5_orf2#LIN 3091 AGGCAAGCCACAGANTGGGAGAAAATATTTGCAANACATATATCTGACAA 3140 chr5qtel1M 166243 AGACCTCATCTCCAAAATATAAAGAGAATT-----GACTCTATATGAAAT 166287 iv i v i v i i -----i ? v v? - L1M5_orf2#LIN 3141 AGGACTCGTATCCAGAATATATAAAGAACTCCTACAANTCAATAANAAA- 3189 chr5qtel1M 166288 CAAGCCATTC--TCCAATTGATAAATGGACAAAGGATATGAACAGACAAT 166335 - v vv --i v? v i i iv v L1M5_orf2#LIN 3190 -AAGACAAACAACCCAATANAAAAATGGGCAAAAGACTTGAACAGACACT 3238 chr5qtel1M 166336 TCTCA----AAGAAATTGAAACTATTTCTAGCCATATGAAAAGATGCTCC 166381 v ---- v ?v iviiivv iv i v L1M5_orf2#LIN 3239 TCACAAAAGAAGATATNCAAATGGCCAATAAGCACATGAAAAGATGCTCA 3288 chr5qtel1M 166382 AAGTCA 166387 v? L1M5_orf2#LIN 3289 ACNTCA 3294 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 40.05 CpG sites = 74, Kimura (unadjusted) = 41.20 Transitions / transversions = 1.14 (74/65) Gap_init rate = 0.04 (18 / 465), avg. gap size = 2.67 (48 / 18) 1558 28.04 1.91 1.59 chr5qtel1M 166250 166876 (833124) L1ME3G_3end#LINE/L1 4 632 (292) m_b248s551i6 9844 chr5qtel1M 166250 ATCTCCAAAATATAAAGAGAATT-----GACTCTATATGAAATCAAGCCA 166294 v i v i i -----i v v v -- v L1ME3G_3end#L 4 ATATCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAA--AAGACA 51 chr5qtel1M 166295 TTCTCCAATTGATAAATGGACAAAGGATATGAACAGACAATTCTCAAA-- 166342 --vi v v i i v i -- L1ME3G_3end#L 52 --ACCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAG 99 chr5qtel1M 166343 --GAAATTGAAACTATTTCTAGCCATATGAAAAGATGCTCCAAGTCATTA 166390 -- vv iviiivv iv v vv i L1ME3G_3end#L 100 AGGAAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTA 149 chr5qtel1M 166391 TTAATCAGAGAAATGCAAATTAAGACAACTCTGAGATACCACTACACACC 166440 v i i vv i viv L1ME3G_3end#L 150 GTAATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACC 199 chr5qtel1M 166441 TGTCAGACTGGCTAGAATAACAGGGAAAGATAATGTGGAATGTTGGAGGG 166490 ii i v i vvv ii ?vv i v? i v i L1ME3G_3end#L 200 CATCAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAG 249 chr5qtel1M 166491 GATGTGGGAAAACTGGGACACTGATACATTGTTGGTGGAATTGTGAATGC 166540 i i v v v v i i i v i vv L1ME3G_3end#L 250 GGTGTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTG 299 chr5qtel1M 166541 ATCCAACCATTCTGGAGAGCAGTTTGGAATTATGCTCAAAAAGTTATCAA 166590 i v i ? i i i v v viviv v --- L1ME3G_3end#L 300 GTACAGCCNTTTTGGAGGGCAATTTGGCAGTATCTATTAAAATTT---AA 346 chr5qtel1M 166591 ACTGTGCATACCCTTTGACCCAGCAGTGTTTCTACTAGGCTTATATCCCA 166640 v i i viiv v ? ?v v i L1ME3G_3end#L 347 AATGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTA 396 chr5qtel1M 166641 AAGAGAT-TTTAAAGAAGGG-AAAGGGACCTGTATGTGTAAGAATGTTTG 166688 ? i -i iiv v v v - v i --? i ii i ii L1ME3G_3end#L 397 NAGAAATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTCA 444 chr5qtel1M 166689 TGGCAGCTCTCTTTGTAGTGGCCAGAAACTGGAAACTGAGTGGATGCCCA 166738 v vi v i i v i i vivv ii i L1ME3G_3end#L 445 TTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCA 494 chr5qtel1M 166739 TCCATTGGAGAATGACTGAATAAATTGTGGTATATGAATATTATGGAATA 166788 v v i ii i i vv i L1ME3G_3end#L 495 TCAATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATA 544 chr5qtel1M 166789 TTATTGTTCAGTAAGAAATGATCA-GCAGAATGATTTCAGAAAGGCCTGG 166837 i vvvv ? v i vi v - i viv v -iv vv i v L1ME3G_3end#L 545 CTATGCAGCNGTTAAAAAGAATGAGGTAGATCTATAT-GTACTGACATGG 593 chr5qtel1M 166838 AGAGACTTACACGAACTGATGCTGAGTGAAATGAGCAGG 166876 i ii v v vv iv i vi i L1ME3G_3end#L 594 AAAGATCTCCAAGACATATTGTTGAGTGAAAAAAGCAAG 632 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 35.54 CpG sites = 85, Kimura (unadjusted) = 36.08 Transitions / transversions = 0.97 (85/88) Gap_init rate = 0.02 (15 / 626), avg. gap size = 1.47 (22 / 15) 15 14.27 7.69 0.00 chr5qtel1M 167851 167889 (832111) (CTG)n#Simple_repeat 1 42 (0) m_b248s252i11 9845 chr5qtel1M 167851 CTG-TGCT-CTGCTGCTGGACCT-CTGCTGCTGCTTCTGGTG 167889 - - vvv - v v (CTG)n#Simple 1 CTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG 42 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.08 (3 / 38), avg. gap size = 1.00 (3 / 3) 196 32.04 5.88 8.20 chr5qtel1M 169159 169345 (830655) L3b_3end#LINE/CR1 679 861 (345) m_b248s601i17 9846 chr5qtel1M 169159 CAAGCTACAA-AGGAGGATTTGGTCC--TTCTGGTGCCCCCATTGTCAAT 169205 i i? ?-v v i vv i -- vv? v ? v v - L3b_3end#LINE 679 CAGGCCNCANCTGGAGTACTGCGTTCAGTTCTGGGCNCCACANTTTAAA- 727 chr5qtel1M 169206 GAGGAAGACCTTAATAAACTAGAGATTGTCTAGTGGTGAGTGACCA---- 169251 - -- v vi v ?i i vv ii v v ii v ---- L3b_3end#LINE 728 -AGG--GACGTGGAGAANTTGGAGAGAGTTCAGAGGAGAGCAACAAAAAT 774 chr5qtel1M 169252 GGTCCAGAATCTGGAGCCTGGTCCACATCACACAAGGAGGAGTTGAAGAA 169301 i iv iiiv ivv vv vi -----i iii i i L3b_3end#LINE 775 GATTAAAGGGCTGGAAAATGGGACCTAT-----GAGGAAAGGTTAAAGGA 819 chr5qtel1M 169302 ACTGAGGGGAGGGGTATTTACCCTGGAGAAGA----TTTAAGGGGAGA 169345 ------ iv i v ----vi i ? L3b_3end#LINE 820 ACTG------GGATTATTCAGCCTGGAGAAGAGAAGGCTGAGGGGNGA 861 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.49 CpG sites = 28, Kimura (unadjusted) = 44.49 Transitions / transversions = 1.04 (28/27) Gap_init rate = 0.10 (18 / 186), avg. gap size = 1.44 (26 / 18) 402 25.65 3.66 9.68 chr5qtel1M 169170 169333 (830667) L3#LINE/CR1 3589 3743 (356) m_b248s601i18 9846 chr5qtel1M 169170 GGAGGATTTGGTCC--TTCTGGTGCCCCCATTGTCAATGAGGAAGACCTT 169217 v vv i -- vvv v - i - -- v L3#LINE/CR1 3589 GGAGTATTGCGTTCAGTTCTGGGCGCCACATT-TTAA-GAGG--GACATT 3634 chr5qtel1M 169218 AATAAACTAGAGATTGTCTAGTGGTGAGTGACCA----GGTCCAGAATCT 169263 i i i vvi i v v i ---- vv ii L3#LINE/CR1 3635 GACAAACTGGAGCGCGTCCAGAGGAGAGCGACCAGGATGGTGAAGGGTCT 3684 chr5qtel1M 169264 GGAGCCTGGTCCACATCACACAAGGAGGAGTTGAAGAAACTGAGGGGAGG 169313 iv----- ii i ii ivi i ------ L3#LINE/CR1 3685 GGAAA-----CCATGTCATATGAGGAACGGTTGAAGGAACTG------GG 3723 chr5qtel1M 169314 GGTATTTACCCTGGAGAAGA 169333 i i v L3#LINE/CR1 3724 GATGTTTAGCCTGGAGAAGA 3743 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.77 CpG sites = 21, Kimura (unadjusted) = 31.68 Transitions / transversions = 1.24 (21/17) Gap_init rate = 0.10 (17 / 163), avg. gap size = 1.24 (21 / 17) 916 35.83 2.30 0.70 chr5qtel1M 169796 170360 (829640) C L1ME4c_3end#LINE/L1 (191) 639 66 m_b248s551i7 9847 chr5qtel1M 169796 TTCTGTTCATTTCACTCAGCATCAGCTCACCTACGTCTCCCCAGGCTCTC 169845 i iv i i i vv ivv i i i vv viv v C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATAAACATTTTCCATGTTGCTA 590 chr5qtel1M 169846 TGAAATCCTCCTGCTGGTCATTTCTTACCGAACAACAATATTCCATAATA 169895 iiv i i v iv vi i v iv vvvv i vivi C L1ME4c_3end#L 589 CATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCGAG 540 chr5qtel1M 169896 TTCATATCCCACAACTTATTCAGCCATTCTCCAAATGATGGGCAGCCACT 169945 ?v i v i i i i i i v v v i vii vv C L1ME4c_3end#L 539 TNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAGG 490 chr5qtel1M 169946 CAGTCTCCAATTTCTCGCCACTACAAGAAGGGTGGCCACAAACACTGTTG 169995 iv i i i i i iv iv iv v ii iiv i C L1ME4c_3end#L 489 TTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTCG 440 chr5qtel1M 169996 CATATACAGGTCCCTTTCCCTCT-----AAGATCTCTTTGGGATATAAGT 170040 iii i -- ii i ----- vv i i i v vvi C L1ME4c_3end#L 439 TGCATATAG--CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAATTC 392 chr5qtel1M 170041 CCAGTAGAAACATTGCTGGATCAAAGGATATGCACAGTTTGATAACTTTT 170090 v viiv i i i v v v ii i C L1ME4c_3end#L 391 CCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTCTT 342 chr5qtel1M 170091 TGAGCATGGTTCCAAATTGCTCTGCAGAATGTTTGGATTTGTTCACAACT 170140 vivi i iv v i v i v v v iivi i ?iv C L1ME4c_3end#L 341 GATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACANTG 292 chr5qtel1M 170141 CCACCAACAATGTATTAGTGTTCCAGTTTTCCCACATCCCCTCCAACATT 170190 i v ? v iv i ? i v i C L1ME4c_3end#L 291 CCACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGCATT 242 chr5qtel1M 170191 TAGCATTATC--TTTTCCCATCATCTTAGTCAATCTGAGAAAAGTGTAGT 170238 vi i -- iiv -- i v ii i i v iiv iv i C L1ME4c_3end#L 241 GGGTATTATCAATTTTTTAA--ATTTTTGCTAATTTAATAGGCGTAAAAT 194 chr5qtel1M 170239 GATCCCTCAGAGTTGTCTTAATTTGCATTTCTCTGATCCAAAATGA-TTT 170287 i vi vv ii i ivvv ii -v C L1ME4c_3end#L 193 GGTATCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACTAGCGAGGTT 144 chr5qtel1M 170288 AGGGACCTTTTCATATGACTAGAAATGGTTTCAATTTCTTCATCTGAAAA 170337 iiiv ii i i vi ivvv ivi? vv i v ? vi C L1ME4c_3end#L 143 GAACATTTTTCCATGTGTTTGTTTACTANTTGTATTTCCTCTTNTGTGAA 94 chr5qtel1M 170338 T----TGTTCATAT-CTTTGATCATTTA 170360 ---- i - vi C L1ME4c_3end#L 93 TTGTCTGTTCATGTCCTTTGCCCATTTA 66 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 49.62 CpG sites = 116, Kimura (unadjusted) = 51.48 Transitions / transversions = 1.36 (116/85) Gap_init rate = 0.02 (9 / 564), avg. gap size = 1.89 (17 / 9) 1076 30.48 3.54 2.26 chr5qtel1M 169880 170359 (829641) C L1ME5_3end#LINE/L1 (389) 552 67 m_b248s551i8 9847 chr5qtel1M 169880 ACAATATTCCATAATATTCATATCCCACAACTTATTCAGCCATTCTCCAA 169929 i i i ii i v viv vi iii v i v C L1ME5_3end#LI 552 ATAGTACTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCA 503 chr5qtel1M 169930 ATGATGGGCAGCCACTCAGTCTCCAATTTCTCGCCACTACAAGAAGGGTG 169979 i i v vviv i i i i i iv iv iv C L1ME5_3end#LI 502 GTGATGGACACCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCT 453 chr5qtel1M 169980 GCCACAAACACTGTTGCATATACAGGTCCCTTTC----CCTCT---AAGA 170022 v ii iiv i ---- v i v---- v --- ii C L1ME5_3end#LI 452 GCAATGAACATCCTCG----TACATGTCCCCTTATGGACCTGTGTGAGAA 407 chr5qtel1M 170023 TCTCTTTGGGATATAAGTCCAGTAGAAACATTGCTGGATCAAAGGATATG 170072 i vii v viiv i v i C L1ME5_3end#LI 406 TTTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATG 357 chr5qtel1M 170073 CACAGTTTGATAACTT-TTTGAGCATGGTTCCAAATTGCTCTGCAGAATG 170121 ii vvi -- i -vi i i iv -- i v C L1ME5_3end#LI 356 CGTATACT--TAATTTGACTAAGTACTG--CCAGATTGCTCTCCAGAATG 311 chr5qtel1M 170122 TTTGGATTTGTTCACAACTCCACCAACAATGTATTAGTGTTCCAGTTTTC 170171 vi v iiv ii vii i i i v v vi ? i C L1ME5_3end#LI 310 GCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATNTCC 261 chr5qtel1M 170172 CCACATCCCCTCCAACATTTAGCATTATCT---TTTCCCATCATCTTAGT 170218 i v i i i--- --- v i v i C L1ME5_3end#LI 260 CCACATCCTCGCCAACACTTGGCATTATCCAGCTTTC---TAATTTTTGC 214 chr5qtel1M 170219 CAATCTGAGAAAAGTGTAGTGATCCCTCAGAGTTGTCTTAATTTGCATTT 170268 i i v iiv iv vi vv i C L1ME5_3end#LI 213 CAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATTT 164 chr5qtel1M 170269 CTCTGATCCAAAATGA-TTTAGGGACCTTTTCATATGACTAGAAATGGTT 170317 ivvv - ii v i i vi ivv iivv C L1ME5_3end#LI 163 CTCTGATTACTAATGAGTTTGAGCATCTCTTCATATGCTTGTTAGCCTTT 114 chr5qtel1M 170318 TCAATTTCTTCATCTGAAAAT----TGTTCATAT-CTTTGATCATTT 170359 ivii i v v ---- - vi C L1ME5_3end#LI 113 CGGGTTTCCTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCCATTT 67 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 39.10 CpG sites = 86, Kimura (unadjusted) = 40.58 Transitions / transversions = 1.51 (86/57) Gap_init rate = 0.04 (18 / 479), avg. gap size = 1.56 (28 / 18) 326 28.45 8.62 0.00 chr5qtel1M 171446 171561 (828439) C MIRc#SINE/MIR (141) 127 2 m_b248s601i19 9848 chr5qtel1M 171446 CTGAGG-GCAGATAGGTTCACTG-------CAGAGTCACAGGGCTCCTAA 171487 -v v v v ------- ii vi vv C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAA 78 chr5qtel1M 171488 GGGGCAAGCCCAGGACTCACACTTAGATTTTCAGGGCTCCAACAGCATTC 171537 v iiv i iv ii i i vv i vvv v v C MIRc#SINE/MIR 77 GTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTG 28 chr5qtel1M 171538 TTCTTTCCACTCCA--ACCCTGTCTC 171561 i v -- v i C MIRc#SINE/MIR 27 CTCTTTCCACTGCACCACACTGCCTC 2 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.35 CpG sites = 14, Kimura (unadjusted) = 35.90 Transitions / transversions = 0.74 (14/19) Gap_init rate = 0.03 (3 / 115), avg. gap size = 3.33 (10 / 3) 16 7.71 3.57 0.00 chr5qtel1M 174124 174151 (825849) (GGA)n#Simple_repeat 1 29 (0) m_b248s252i12 9849 chr5qtel1M 174124 GGAGGGGGAGGAGGGGGAGGAGG-GGAGG 174151 i i - (GGA)n#Simple 1 GGAGGAGGAGGAGGAGGAGGAGGAGGAGG 29 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 12 14.08 0.00 8.82 chr5qtel1M 174325 174361 (825639) (AGGG)n#Simple_repeat 1 34 (0) m_b248s252i13 9850 chr5qtel1M 174325 AGGGTCGGAGGGGAGGGAGGGGGCCAGAGGGAGGGAG 174361 vv - i --i (AGGG)n#Simpl 1 AGGGAGGGA-GGGAGGGAGGGAG--GGAGGGAGGGAG 34 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.08 (3 / 36), avg. gap size = 1.00 (3 / 3) 16 5.20 0.00 0.00 chr5qtel1M 179948 179967 (820033) (G)n#Simple_repeat 1 20 (0) m_b248s252i14 9851 chr5qtel1M 179948 GGGGGGGGGGGGGGGCGGGG 179967 v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGG 20 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 234 10.04 2.14 0.70 chr5qtel1M 181546 181966 (818034) (CATC)n#Simple_repeat 1 427 (0) c_b248s251i2 9852 chr5qtel1M 181546 CATCCACCCATCCATCCATCCTTCCATCCATCCATCCATCCATCCTTCCA 181595 i v v (CATC)n#Simpl 1 CATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCA 50 chr5qtel1M 181596 TCCATTCAT-CATCCATCCTTCCATCCATCCATCCATCCATCCTTCCATC 181644 i - v v (CATC)n#Simpl 51 TCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATC 100 chr5qtel1M 181645 CATCCATCCATCCATCCATCCTTCCATCCATCCTTTCATCCATCCATGCA 181694 v v i v (CATC)n#Simpl 101 CATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCA 150 chr5qtel1M 181695 -CC-TGTATCCATCCTTCCATCCAT-C-TCCATCCATCCTTCCATCCATC 181740 - - vi v - - v (CATC)n#Simpl 151 TCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATC 200 chr5qtel1M 181741 CATCCATCCATCCATCCTTCCATCCATCCTTTCATCCATCCATGCA-CCT 181789 v v i v - - (CATC)n#Simpl 201 CATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCC- 249 chr5qtel1M 181790 GTACATCCATCCTTCCATCCATCCATCCATCCATCCATCCTTCCATCCAT 181839 i v v v (CATC)n#Simpl 250 ATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCAT 299 chr5qtel1M 181840 TCAT-CATCCATCCTTCCATCCATCCTTTCATCCATCCATGCA-CCTGTA 181887 i - v v i v - -i v (CATC)n#Simpl 300 CCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCC-ATC 348 chr5qtel1M 181888 CATCCATCCTTCCAGCCAGCCAGCCATCCTTCCATCCATCTTTCCATCCA 181937 v v v v v iv (CATC)n#Simpl 349 CATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCA 398 chr5qtel1M 181938 TCCATGCA-CCTGTACATCCATCCATCCAT 181966 v - -i v (CATC)n#Simpl 399 TCCATCCATCC-ATCCATCCATCCATCCAT 427 Matrix = Unknown Transitions / transversions = 0.39 (11/28) Gap_init rate = 0.03 (12 / 420), avg. gap size = 1.00 (12 / 12) 14 18.27 2.70 0.00 chr5qtel1M 184073 184109 (815891) (GGGGGCA)n#Simple_repeat 1 38 (0) m_b248s252i15 9853 chr5qtel1M 184073 GGAGGCCGGGGGCAGGGGG-GGGGTCCTGGGGGCAGGG 184109 i v -i vv v (GGGGGCA)n#Si 1 GGGGGCAGGGGGCAGGGGGCAGGGGGCAGGGGGCAGGG 38 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 13 23.87 0.00 2.50 chr5qtel1M 186132 186172 (813828) (GGGA)n#Simple_repeat 1 40 (0) m_b249s252i0 9854 chr5qtel1M 186132 GGGAGGGAGGGAGAGTGAGAGAGCAGTCCAGGAGGGAGGGA 186172 i v i - v vvvi (GGGA)n#Simpl 1 GGGAGGGAGGGAGGGAGGGAG-GGAGGGAGGGAGGGAGGGA 40 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 20 4.17 0.00 0.00 chr5qtel1M 189006 189030 (810970) (GT)n#Simple_repeat 1 25 (0) m_b249s252i1 9855 chr5qtel1M 189006 GTGTGTGTGTGTGTGTGTGTGTATG 189030 i (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTG 25 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 180 28.38 17.57 0.00 chr5qtel1M 191813 191886 (808114) MIR#SINE/MIR 60 146 (116) m_b249s601i0 9856 chr5qtel1M 191813 CCTGGCCCCGCCACTTGCTGGCAG-GTGACCCTG------------AACC 191849 i i i i i v - i ------------ MIR#SINE/MIR 60 CCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACC 109 chr5qtel1M 191850 CCAGTGAGTCTGTGCCTTCTCTGCTGCAAAATAGGGA 191886 i vv v i vv ii i vv i i MIR#SINE/MIR 110 TCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGA 146 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.65 CpG sites = 13, Kimura (unadjusted) = 36.85 Transitions / transversions = 1.62 (13/8) Gap_init rate = 0.03 (2 / 73), avg. gap size = 6.50 (13 / 2) 15 5.48 0.00 0.00 chr5qtel1M 191919 191937 (808063) (G)n#Simple_repeat 1 19 (0) m_b249s252i2 9857 chr5qtel1M 191919 GGGGGGGGGGGGGGGCGGG 191937 v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGG 19 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 23 29.18 0.00 0.00 chr5qtel1M 193276 193346 (806654) (AAAT)n#Simple_repeat 1 71 (0) m_b249s252i3 9858 chr5qtel1M 193276 AAATACATAAATAAACAAATAAAGCAGTGAGTCAATGAATGGATAAAGAC 193325 v i vv i i i v i ii v v (AAAT)n#Simpl 1 AAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAA 50 chr5qtel1M 193326 ATAAATCAATCAATGAATGAA 193346 v v i i (AAAT)n#Simpl 51 ATAAATAAATAAATAAATAAA 71 Matrix = Unknown Transitions / transversions = 1.12 (9/8) Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0) 340 31.03 0.00 0.00 chr5qtel1M 193520 193606 (806394) MIR#SINE/MIR 88 174 (88) m_b249s601i1 9859 chr5qtel1M 193520 ACCCTGGACAAGCCTTTTAATCACTGCCTACCTCACTTTCCCCATCTGTG 193569 i i iivi i v viv i v i i MIR#SINE/MIR 88 ACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTA 137 chr5qtel1M 193570 AACTGGGGCTAATGACAGCATCTGTATCCCAGGGCTG 193606 v v i i i i iiv vi i MIR#SINE/MIR 138 AAATGGGGATAATAATAGTACCTACCTCATAGGGTTG 174 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.21 CpG sites = 18, Kimura (unadjusted) = 42.21 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.00 (0 / 86), avg. gap size = 0.0 (0 / 0) 20 26.94 0.00 0.00 chr5qtel1M 194073 194130 (805870) (CCCCCC)n#Simple_repeat 1 58 (0) m_b249s252i5 9860 chr5qtel1M 194073 CCTCCCCTCTCCCCCACGCTCCCCAACCCCATCCCCCTTCCCCCCCCCCC 194122 i i i v v i vv vi ii (CCCCCC)n#Sim 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 50 chr5qtel1M 194123 CCCCCGCC 194130 v (CCCCCC)n#Sim 51 CCCCCCCC 58 Matrix = Unknown Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0) 15 13.67 0.00 0.00 chr5qtel1M 195044 195067 (804933) (G)n#Simple_repeat 1 24 (0) m_b249s252i6 9861 chr5qtel1M 195044 GGGGGGAGGGGCGGGGGGGGGCGG 195067 i v v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGG 24 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 290 14.08 4.17 1.35 chr5qtel1M 195098 195169 (804831) C L3#LINE/CR1 (117) 3982 3909 m_b249s601i2 9862 chr5qtel1M 195098 CTTGTAGATCCTCCCAAGACGGG-AGCTC-CTACCTCCCGGGGCAGCCCC 195145 v v - viv - - ? i v C L3#LINE/CR1 3982 CTTGAACA-CCTCCAGTGACGGGGAGCTCACTACCTCNCGAGGCAGCCCA 3934 chr5qtel1M 195146 TTCCA-TTTGGGACAGCTCTCGTTG 195169 - v vi C L3#LINE/CR1 3933 TTCCATTTTTGGACAGCTCTGATTG 3909 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 15.85 CpG sites = 3, Kimura (unadjusted) = 15.85 Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.06 (4 / 71), avg. gap size = 1.00 (4 / 4) 12 23.96 4.55 0.00 chr5qtel1M 195194 195237 (804763) (CTCTC)n#Simple_repeat 1 46 (0) m_b249s252i7 9863 chr5qtel1M 195194 CTCCCCTCTCCTCGCCCCACCTCACCCCT-GGC-CCCCTCCTCTCC 195237 i v i v v i -vv - i (CTCTC)n#Simp 1 CTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCC 46 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2) 22 19.40 3.28 1.61 chr5qtel1M 198698 198758 (801242) (GAGAG)n#Simple_repeat 1 62 (0) m_b249s252i8 9864 chr5qtel1M 198698 GAGAGGAGAGGAG-GATCAGGAGGGGGGAGGAGAGGA-AGATCAGGAAAG 198745 - ivv i i - ivv i (GAGAG)n#Simp 1 GAGAGGAGAGGAGAGGAGAGGAGAGGAGAGGAGAGGAGAGGAGAGGAGAG 50 chr5qtel1M 198746 GGGAGGGAGAGGA 198758 i - (GAGAG)n#Simp 51 GAGA-GGAGAGGA 62 Matrix = Unknown Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.05 (3 / 60), avg. gap size = 1.00 (3 / 3) 390 24.40 2.52 7.02 chr5qtel1M 198817 198935 (801065) MIRc#SINE/MIR 35 148 (120) m_b249s601i3 9865 chr5qtel1M 198817 CCTGCAGGCAGAAAGACTCATCTCCTTGAGTTCTAATCTGACCTCAGACA 198866 i v v i i-------- i v i iviv v v MIRc#SINE/MIR 35 CTTGGAGTCAGGAAGACC--------TGGGTTCGAGTCCCGGCTCTGCCA 76 chr5qtel1M 198867 CCTACCGCCTGTGTGAC--TGGGCAAGTCATTTCAC-TCTGTCTGCCTCA 198913 i iiv -- i v - v vv MIRc#SINE/MIR 77 CTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCA 126 chr5qtel1M 198914 GTTTCTTCACCTGTCAAATGAG 198935 i i v i MIRc#SINE/MIR 127 GTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.45 CpG sites = 14, Kimura (unadjusted) = 29.72 Transitions / transversions = 1.08 (14/13) Gap_init rate = 0.08 (10 / 118), avg. gap size = 1.10 (11 / 10) 402 20.86 4.24 2.50 chr5qtel1M 198841 198958 (801042) MIR1_Amn#SINE/MIR 53 172 (58) m_b249s601i4 9865 chr5qtel1M 198841 CTTGAGTTCTAATCTGACCTCAGACACCTACCGCCTGTGTGAC--TGGGC 198888 i i ? ? iviv v v i?i ?v ? -- MIR1_Amn#SINE 53 CCTGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGC 102 chr5qtel1M 198889 AAGTCATTTCAC-TCTGTCTGCCTCAGTTTCTTCACCTGTCAAATGAGCT 198937 i ? - v v? i i v i--- MIR1_Amn#SINE 103 AAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGG--- 149 chr5qtel1M 198938 GGAGAAGGAG--TGGCCCCCCTT 198958 v v v-- i i i MIR1_Amn#SINE 150 GGATAATGATACTGACCTCCTTT 172 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 25.42 CpG sites = 13, Kimura (unadjusted) = 26.67 Transitions / transversions = 1.18 (13/11) Gap_init rate = 0.05 (6 / 117), avg. gap size = 1.33 (8 / 6) 405 21.05 3.16 0.00 chr5qtel1M 198841 198935 (801065) MIR3#SINE/MIR 48 145 (63) m_b249s601i5 9865 chr5qtel1M 198841 CTTGAGTTCTAATCTGACCTCAGACACCTACCGCCTGTGTGAC--TGGGC 198888 i i i iviv v v iv i?v -- MIR3#SINE/MIR 48 CCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGC 97 chr5qtel1M 198889 AAGTCATTTCAC-TCTGTCTGCCTCAGTTTCTTCACCTGTCAAATGAG 198935 i - v vv i i v MIR3#SINE/MIR 98 AAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAG 145 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 23.81 CpG sites = 10, Kimura (unadjusted) = 25.20 Transitions / transversions = 1.00 (10/10) Gap_init rate = 0.02 (2 / 94), avg. gap size = 1.50 (3 / 2) 290 30.78 10.70 0.98 chr5qtel1M 199463 199649 (800351) L2b_3end#LINE/L2 250 454 (12) m_b249s601i6 9866 chr5qtel1M 199463 CCCCATCCTACGTCAGGGGCTTCTCTCCGAACCCCCCCAG-CGGATCCTG 199511 vv iiv v iiii i ii - vv i L2b_3end#LINE 250 CCCCAGGCCGGGTCAGGCGCCCTCCTCTGGGCCCCCCCAGTCCTACCCTG 299 chr5qtel1M 199512 TCTGTGCCGGGCACGG--GCCTTGCTGGCCG-CGGTCTCCCCGGTTAGAC 199558 i vv viv vi i?i-- i v?i ivvi - v vii L2b_3end#LINE 300 CCACTCTGGGTTATNATTGTCTGNTTACATGTCTGTCTCCCCCACTAGAC 349 chr5qtel1M 199559 CGGGAGCTCC-CGGGGGCAGG---CG---CTGGCTT--TCACCACTTTGT 199599 i v -i i --- --- v -- i -- L2b_3end#LINE 350 TGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCT--GT 397 chr5qtel1M 199600 GTCCCCTGTGCTT-------GGCCCGGCGCACAGTAGGCACATAATAAAT 199642 i v i i -------? i i i vi i L2b_3end#LINE 398 ATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAAT 447 chr5qtel1M 199643 GCTCCTT 199649 ii iv L2b_3end#LINE 448 ATTTGTT 454 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.33 CpG sites = 36, Kimura (unadjusted) = 42.33 Transitions / transversions = 1.71 (36/21) Gap_init rate = 0.05 (10 / 186), avg. gap size = 2.20 (22 / 10) 320 27.48 2.80 4.76 chr5qtel1M 199543 199649 (800351) L2c_3end#LINE/L2 362 466 (12) m_b249s601i7 9866 chr5qtel1M 199543 GTCTCCCCGGTTAGACCGGGAGCTCCC-GGGGGCAGGCGCTGGCTTTCAC 199591 i vii i v i- i vi i vv i i i L2c_3end#LINE 362 GTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTAT 411 chr5qtel1M 199592 -CA-CTTTGTGTCCCCTGTGCTTGGCCCGGCGCACAGTAGGCACATAATA 199639 - - i v i i -----i i i vi L2c_3end#LINE 412 TCATCTTTGTATCCCCAGCGCCTGGC-----ACATAGTAGGCGCTCAATA 456 chr5qtel1M 199640 AATGCTCCTT 199649 i iv L2c_3end#LINE 457 AATGTTTGTT 466 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.30 CpG sites = 20, Kimura (unadjusted) = 36.07 Transitions / transversions = 2.50 (20/8) Gap_init rate = 0.08 (8 / 106), avg. gap size = 1.00 (8 / 8) 19 22.23 1.47 4.55 chr5qtel1M 199796 199863 (800137) (CCGGCC)n#Simple_repeat 1 66 (0) m_b249s252i9 9867 chr5qtel1M 199796 CCGGCCCAGCCTCCGCGGCCCCTGCTCCGGACTCTCCCCCCGGCCCCGGC 199845 v v - - v i - i ivv (CCGGCC)n#Sim 1 CCGGCCCCGGC-CC-CGGCCCCGGCCCCGG-CCCCGGCCCCGGCCCCGGC 47 chr5qtel1M 199846 CGCTG-CCTGGCCCTGGCC 199863 v v - i i (CCGGCC)n#Sim 48 CCCGGCCCCGGCCCCGGCC 66 Matrix = Unknown Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.06 (4 / 67), avg. gap size = 1.00 (4 / 4) 15 25.00 3.39 1.67 chr5qtel1M 199815 199873 (800127) (CCCTGG)n#Simple_repeat 1 60 (0) m_b249s252i10 9867 chr5qtel1M 199815 CCCTGCTCCGGACTCTCCCCCCGGCCCCGGCCGCT-G-CCTGGCCCTGGC 199862 vi v i i vv i i - - - (CCCTGG)n#Sim 1 CCCTGGCCCTGGCCCTGGCCCTGGCCCTGGCC-CTGGCCCTGGCCCTGGC 49 chr5qtel1M 199863 CTTGGTGCTGG 199873 i iv (CCCTGG)n#Sim 50 CCTGGCCCTGG 60 Matrix = Unknown Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.05 (3 / 58), avg. gap size = 1.00 (3 / 3) 336 22.38 4.96 11.40 chr5qtel1M 200587 200707 (799293) MIRc#SINE/MIR 2 115 (153) m_b249s601i8 9868 chr5qtel1M 200587 GGGGCAGCTGATGGCGCAGGGGATGGAAC------CCTGAAACCAGCAGC 200630 i - - i v vi i ------ i i ii v iv MIRc#SINE/MIR 2 GAGGCAG-TG-TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAG 49 chr5qtel1M 200631 ACCTGAGGTCAAGTGTGGCCTCAGGCTTAAATCTAACACTCACTAGCTGT 200680 i v i ------i v ----- iv i MIRc#SINE/MIR 50 ACCTGGGTTCGAGT------CCCGGCT-----CTGCCACTTACTAGCTGT 88 chr5qtel1M 200681 GTGACCTTGGCCAAGTCACTTTACCCC 200707 v v i MIRc#SINE/MIR 89 GTGACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 25.67 CpG sites = 15, Kimura (unadjusted) = 26.96 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.12 (14 / 120), avg. gap size = 1.36 (19 / 14) 226 28.95 7.89 0.00 chr5qtel1M 203037 203112 (796888) L3#LINE/CR1 3783 3864 (235) m_b249s601i9 9869 chr5qtel1M 203037 TGGAGAGCTGTCCCATGGAAGAGGAAATAG-CTTTTTCCATCCTTCCCTT 203085 i i vii i v - v ii vivv i iv L3#LINE/CR1 3783 TGAAGGGCTGTCATGTGGAAGAGGGATTAGACTTATTCTGTGTGGCTCCA 3832 chr5qtel1M 203086 GAGAGCA-----AGGAGCAATGGGGAGAACTT 203112 i ----- v vi v L3#LINE/CR1 3833 GAGGGCAGAACTAGGACCAATGGGTGGAAGTT 3864 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.29 CpG sites = 12, Kimura (unadjusted) = 37.29 Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.03 (2 / 75), avg. gap size = 3.00 (6 / 2) 183 34.72 6.25 0.00 chr5qtel1M 203281 203424 (796576) C L2#LINE/L2 (280) 2802 2650 m_b249s601i10 9870 chr5qtel1M 203281 GGGTCGCTC-GGCAGGGGTGCGGTTGATGGATTGGAGTGAGG--AGGCTG 203327 i i - v vv iv vvi i i ? v i -- v C L2#LINE/L2 2802 GGATCACTCTGGCTGCTGTGTTGAGAATAGACTGNAGGGGGGCAAGGGTG 2753 chr5qtel1M 203328 GAAGT-GGGAGATCAAATAGGAGACTGTAGCCTCAGTCCTGGTGGGGAGT 203376 i- i iv i i v vvi i v i i iii C L2#LINE/L2 2752 GAAGCAGGGAGACCAGTTAGGAGGCTATTGCAGTAATCCAGGCGAGAGAT 2703 chr5qtel1M 203377 GAGGAGGGCTG-----AGGCTAGTGGCCATGTGAATACGGAGAAGAGGGC 203421 v iv v----- v i vi viii ivv v v C L2#LINE/L2 2702 GATGGTGGCTTGGACCAGGGTGGTGGCAGTGGAGGTGGTGAGAAGTGGTC 2653 chr5qtel1M 203422 AGA 203424 i C L2#LINE/L2 2652 GGA 2650 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.71 CpG sites = 27, Kimura (unadjusted) = 48.36 Transitions / transversions = 1.17 (27/23) Gap_init rate = 0.03 (4 / 143), avg. gap size = 2.25 (9 / 4) 248 28.23 1.83 13.61 chr5qtel1M 203465 203628 (796372) C MIR1_Amn#SINE/MIR (31) 199 53 m_b249s601i11 9871 chr5qtel1M 203465 TCTTCAGGAGGTTTTCCTGGCAAAG-ATACCGCAGAGGCTGGCCATTTCC 203513 v v i i ------ - iviii i vv v vi v v C MIR1_Amn#SINE 199 TCATCAGTAGATCT------CAAAGCACTTTACAAAGGAGGTCAGTATCA 156 chr5qtel1M 203514 TTCTCTAGTCCATTTTACAGATTTCTATTTTCTAGAAAAC-GAGGCAAAA 203562 v i--- v---------- i - ?v i C MIR1_Amn#SINE 155 TTATCC---CCATTTTACAGATG----------AGGAAACTGAGGCNCAG 119 chr5qtel1M 203563 GCAGGACTAAGTGACTTGCCCAGGCTCAC-CAACTCCTGAGTGTCTGAGG 203611 iv -i? i v - i ?vvi? v v v C MIR1_Amn#SINE 118 AGAGG-TNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNAGTGGCAGAGC 70 chr5qtel1M 203612 GCAGATTTGAACTCGGG 203628 vvi ? ? i i C MIR1_Amn#SINE 69 CGGGANTNGAACCCAGG 53 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.96 CpG sites = 19, Kimura (unadjusted) = 36.96 Transitions / transversions = 0.90 (19/21) Gap_init rate = 0.14 (23 / 163), avg. gap size = 1.00 (23 / 23) 251 27.77 5.69 9.24 chr5qtel1M 203523 203645 (796355) C MIRc#SINE/MIR (121) 147 29 m_b249s601i13 9871 chr5qtel1M 203523 CCATTTTACAGATTTCTATTTTCTAGAAAAC-GAGGCAAAAGCAGGACTA 203571 v---------- i - vv iiv -i C MIRc#SINE/MIR 147 CCATTTTACAGATG----------AGGAAACTGAGGCTCAGAGAGG-TTA 109 chr5qtel1M 203572 AGTGACTTGCCCAGGCTCAC-CAACTCCTGAGTGTCTGAGGGCAGATTTG 203620 i v - i vv i v v vvvi i i C MIRc#SINE/MIR 108 AGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCG 59 chr5qtel1M 203621 AACTCGGGA-----AGATTCCAAACTCAAT 203645 i i v-----v i iii i C MIRc#SINE/MIR 58 AACCCAGGTCTTCCTGACTCCAAGTCCAGT 29 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.79 CpG sites = 17, Kimura (unadjusted) = 35.17 Transitions / transversions = 1.21 (17/14) Gap_init rate = 0.11 (14 / 122), avg. gap size = 1.29 (18 / 14) 280 24.74 1.83 11.00 chr5qtel1M 203523 203631 (796369) C MIR#SINE/MIR (119) 143 44 m_b249s601i12 9871 chr5qtel1M 203523 CCATTTTACAGATTTCTATTTTCTAGAAAAC-GAGGCAAAAGCAGGACTA 203571 v---------- i - v iiv -i C MIR#SINE/MIR 143 CCATTTTACAGATG----------AGGAAACTGAGGCACAGAGAGG-TTA 105 chr5qtel1M 203572 AGTGACTTGCCCAGGCTCAC-CAACTCCTGAGTGTCTGAGGGCAGATTTG 203620 i i v - i vv i v v vvvi i C MIR#SINE/MIR 104 AGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCG 55 chr5qtel1M 203621 AACTCGGGAAG 203631 i i v C MIR#SINE/MIR 54 AACCCAGGCAG 44 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.48 CpG sites = 12, Kimura (unadjusted) = 29.91 Transitions / transversions = 1.00 (12/12) Gap_init rate = 0.12 (13 / 108), avg. gap size = 1.00 (13 / 13) 382 32.83 15.22 5.46 chr5qtel1M 205041 205375 (794625) L3#LINE/CR1 3489 3854 (245) m_b249s601i14 9872 chr5qtel1M 205041 AAAGATTTTATGTAATTTTAATTCTCATTAAGAGAAGCACAGCTTATGGG 205090 i vi v i i iviiv v i i iv vii i L3#LINE/CR1 3489 AAAAAGCTAATGCAATCTTAGGCTGCATTAATAGAAGTATAGTGTCCAGA 3538 chr5qtel1M 205091 AATTGGGCAGTGATAGTCCTATTGTTTTGTCC-CTACACAAGCC-CTTAT 205138 ?vvv vi i iii vi v v - ivv ii - v v L3#LINE/CR1 3539 NCAAGGGAGGTAATAGTCCCGCTGTACTCTGCGCTGGTCAGACCACATCT 3588 chr5qtel1M 205139 AGGGAATAATGTCCA-TTCAGGGCACCAC----------------TGATC 205171 i i v vii i - v i ---------------- iv L3#LINE/CR1 3589 GGAGTATTGCGTTCAGTTCTGGGCGCCACATTTTAAGAGGGACATTGACA 3638 chr5qtel1M 205172 ATCTGGAG---------ATGAGGATAAACAGGATGATGAAGAGCTCTGAG 205212 v --------- v iiii v i i iiiv i L3#LINE/CR1 3639 AACTGGAGCGCGTCCAGAGGAGAGCGACCAGGATGGTGAAGGGTCTGGAA 3688 chr5qtel1M 205213 TTCATGCCATATGAGGTTTCATTAATGG---------CCTTTGGCATAGA 205253 vi i vvivi i v ---------iv i v i L3#LINE/CR1 3689 ACCATGTCATATGAGGAACGGTTGAAGGAACTGGGGATGTTTAGCCTGGA 3738 chr5qtel1M 205254 GATAAGAAAACTTAGGGTGGGAGTGGAGGTGACATGATAGGTATGTTATC 205303 vi i ----------- v --------- L3#LINE/CR1 3739 GAAGAGAAGACTTAG-----------AGGAGACATGATAG---------C 3768 chr5qtel1M 205304 TGTGTTTAAATAGTCAAAAAACTATCATGTGATGGAAGGACT-------- 205345 v i v ii iii i ivi i i -------- L3#LINE/CR1 3769 TGTCTTCAAATATTTGAAGGGCTGTCATGTGGAAGAGGGATTAGACTTAT 3818 chr5qtel1M 205346 --TGTCTGA----AGAAGGCAGAATTAGGAATAATG 205375 -- v i---- i i vi L3#LINE/CR1 3819 TCTGTGTGGCTCCAGAGGGCAGAACTAGGACCAATG 3854 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.52 CpG sites = 64, Kimura (unadjusted) = 45.64 Transitions / transversions = 1.60 (64/40) Gap_init rate = 0.09 (29 / 334), avg. gap size = 2.45 (71 / 29) 20 26.33 0.00 0.00 chr5qtel1M 205376 205431 (794569) (ATAACA)n#Simple_repeat 1 56 (0) m_b249s252i11 9873 chr5qtel1M 205376 ATAATTATAACAATAACAATGACAGCAACAGCCACCACAATAATAACAAC 205425 iv i ii iiv v i i i (ATAACA)n#Sim 1 ATAACAATAACAATAACAATAACAATAACAATAACAATAACAATAACAAT 50 chr5qtel1M 205426 AACAAT 205431 (ATAACA)n#Sim 51 AACAAT 56 Matrix = Unknown Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0) 20 23.03 0.00 0.00 chr5qtel1M 205384 205430 (794570) (AAC)n#Simple_repeat 1 47 (0) m_b249s252i12 9874 chr5qtel1M 205384 AACAATAACAATGACAGCAACAGCCACCACAATAATAACAACAACAA 205430 i ii i i v v i i (AAC)n#Simple 1 AACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAA 47 Matrix = Unknown Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 484 30.35 1.53 4.19 chr5qtel1M 205432 205627 (794373) C MIRb#SINE/MIR (53) 215 25 m_b249s601i15 9875 chr5qtel1M 205432 AGCATTTTACAAATACTATGTCTTTTTTTTTAATCATCACAACAACACTG 205481 ii vii i v v ----- v v C MIRb#SINE/MIR 215 AGCGCTTTACATGCATTATCTCATTT-----AATCCTCACAACAACCCTG 171 chr5qtel1M 205482 GGACACAGAGGTTGTAATTATCCTTTTTTTTTAGATGAGGAAATAGAGAC 205531 v vii ivi --- iiv vi iv i C MIRb#SINE/MIR 170 CGAGGTAGGTATT---ATTATCCCCATTTTACAGATGAGGAAACTGAGGC 124 chr5qtel1M 205532 ACAAAG--GTGGAGTGACTTCTCCAAGATTAAAGAGCTGGTAAATGTCTG 205579 v i -- vi i vi i i v v i i v v C MIRb#SINE/MIR 123 TCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAG 74 chr5qtel1M 205580 AGGCACTGTTTGATCTGAGATATTTCTCACTCCAAAA-CTGTGATATTT 205627 v ivvi i v iv i v v v i- i v v C MIRb#SINE/MIR 73 AGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTT 25 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.00 CpG sites = 29, Kimura (unadjusted) = 39.41 Transitions / transversions = 1.04 (29/28) Gap_init rate = 0.05 (10 / 195), avg. gap size = 1.10 (11 / 10) 264 27.63 0.00 0.00 chr5qtel1M 205637 205712 (794288) CR1-3_Croc#LINE/CR1 2882 2957 (648) m_b249s551i0 9876 chr5qtel1M 205637 AAACTTCTTAACAATTTGAGCTGTCCCGAAGTGGAACAGGCTGCCTTGGG 205686 v vi v i v vvv v i i v CR1-3_Croc#LI 2882 AAACTTCTTCACTGTTAGAACAGTGAGGCAGTGGAATAGACTGCCTAGGG 2931 chr5qtel1M 205687 AAGTAGTGGATCTCCCCTCCCCGGAG 205712 v iiii v v i CR1-3_Croc#LI 2932 AAGTTGTGGACTCTCCATCACTGGAG 2957 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 34.59 CpG sites = 9, Kimura (unadjusted) = 34.59 Transitions / transversions = 0.75 (9/12) Gap_init rate = 0.00 (0 / 75), avg. gap size = 0.0 (0 / 0) 27 0.00 0.00 0.00 chr5qtel1M 206133 206158 (793842) (AAAG)n#Simple_repeat 1 26 (0) c_b249s251i0 9877 chr5qtel1M 206133 AAAGAAAGAAAGAAAGAAAGAAAGAA 206158 (AAAG)n#Simpl 1 AAAGAAAGAAAGAAAGAAAGAAAGAA 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 464 31.82 2.05 5.96 chr5qtel1M 206387 206630 (793370) C MIR#SINE/MIR (21) 241 7 m_b249s601i16 9878 chr5qtel1M 206387 AGCGTTT-CTAGGTCCCAAGTTATATCATAAATGAATTGTTGTTTAGCTG 206435 i - v v i ivv i iv ii v------- vv C MIR#SINE/MIR 241 AGCGCTTACTATGTGCCAGGCACTGTTCTAAGCGC-------TTTACATG 199 chr5qtel1M 206436 TTTTTAGTCCTATCGGAATCTTCATGATC-CCATTTAGGATTTGTCACT- 206483 v v v v v --- i ii iv- v v ii i vv - - C MIR#SINE/MIR 198 TATTAACTCATTT---AATCCTCACAACAACCCTATGAGGTAGGT-ACTA 153 chr5qtel1M 206484 TTCTTCTCCAGCTCATTTAATAAGTGAGAAAATTGAGGCAAACAG-GATG 206532 v v ---i v i ii i i v v - i v C MIR#SINE/MIR 152 TTATTATCC---CCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTT 106 chr5qtel1M 206533 AAGTGACTTACCCAGGCTCAAACAGCTAAGAAGCATCTGAGGCTGGATTT 206582 i i i v v iv iiv v v v i C MIR#SINE/MIR 105 AAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTC 56 chr5qtel1M 206583 GAACTCAGGCCTCCTGATTCCAGGTGTAGTGCTC-TATCCACTACACTA 206630 i vvi ii ivviv - v ii C MIR#SINE/MIR 55 GAACCCAGGCAGTCTGGCTCCAGAGCCCGTGCTCTTAACCACTATGCTA 7 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.35 CpG sites = 36, Kimura (unadjusted) = 41.82 Transitions / transversions = 0.97 (36/37) Gap_init rate = 0.08 (19 / 243), avg. gap size = 1.00 (19 / 19) 594 25.17 2.10 0.00 chr5qtel1M 206495 206637 (793363) C MIRc#SINE/MIR (120) 148 3 m_b249s601i17 9878 chr5qtel1M 206495 CTCATTTAATAAGTGAGAAAATTGAGGCAAACAG-GATGAAGTGACTTAC 206543 i v i ii i i vv v - i v i C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr5qtel1M 206544 CCAGGCTCAAACAGCTAAGAAGCATCTGAGGCTGGATTTGAACTCAGG-C 206592 i v v iv iiv v v v i i i - C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTC 49 chr5qtel1M 206593 CTCCTGATTCCAGGTGTAGTGCTCTATCCACTACACTAC-CTACCT 206637 i i i vi v i i - i C MIRc#SINE/MIR 48 TTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTGCCT 3 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.41 CpG sites = 22, Kimura (unadjusted) = 31.46 Transitions / transversions = 1.57 (22/14) Gap_init rate = 0.02 (3 / 142), avg. gap size = 1.00 (3 / 3) 237 6.06 0.00 0.00 chr5qtel1M 207907 207939 (792061) L3#LINE/CR1 4066 4098 (1) m_b249s601i18 9879 chr5qtel1M 207907 GTCCCTTCCAACTCTGGGATTCTGGGATTCTAT 207939 i v L3#LINE/CR1 4066 GTCCCTTCCAACTCTGAGATTCTGTGATTCTAT 4098 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 6.33 CpG sites = 1, Kimura (unadjusted) = 6.33 Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 385 30.07 4.84 0.78 chr5qtel1M 208102 208225 (791775) C MIRc#SINE/MIR (117) 151 23 m_b249s601i19 9880 chr5qtel1M 208102 ATCTCTTTTTTACACATGAGGACAGTGAGATGGACAGAGGCAAGGTGATT 208151 i iv v v v iivv v iv i i C MIRc#SINE/MIR 151 ATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACT 102 chr5qtel1M 208152 CATCCAATGTTGCACCCCCTAGGAAGTAGCAGTGGCAGAATTTGAAC--- 208198 iii v ii - vv v i v v i i i i --- C MIRc#SINE/MIR 101 TGCCCAAGGTCACA-CAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCA 53 chr5qtel1M 208199 ---TTTCCTGACTCCCTGTCCATTGATTTT 208225 ---i vv v v i C MIRc#SINE/MIR 52 GGTCTTCCTGACTCCAAGTCCAGTGCTCTT 23 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.41 CpG sites = 19, Kimura (unadjusted) = 39.03 Transitions / transversions = 1.06 (19/18) Gap_init rate = 0.02 (3 / 123), avg. gap size = 2.33 (7 / 3) 358 18.27 8.43 1.12 chr5qtel1M 208699 208781 (791219) MIRb#SINE/MIR 77 165 (103) m_b249s601i20 9881 chr5qtel1M 208699 CCACTTACT----GTCTGACCACTGGGCAGG---CATCCCCTCTCCAAGG 208741 ---- v -i i --- v vv ii v MIRb#SINE/MIR 77 CCACTTACTAGCTGTGTGACC-TTGGGCAAGTTACTTAACCTCTCTGAGC 125 chr5qtel1M 208742 CTCAGTTTCTTTATCTGTAAAGTGGGAATAATAATATGTA 208781 i i i i iv MIRb#SINE/MIR 126 CTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTA 165 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 21.27 CpG sites = 9, Kimura (unadjusted) = 21.27 Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.04 (3 / 82), avg. gap size = 2.67 (8 / 3) 210 36.22 4.90 3.45 chr5qtel1M 208814 208956 (791044) MIRb#SINE/MIR 22 166 (102) m_b249s601i21 9882 chr5qtel1M 208814 TGGAGAGAGGGCTGGCCTCAGGATCATGAAGATCTGTGTTCAAGTGCTCC 208863 i vi v i ii ii viv i v i i v ivv MIRb#SINE/MIR 22 TGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCGAATCCCGG 71 chr5qtel1M 208864 CTCTGACACTTATGGGGGCTG----CCTGGACCACTCTCTCAAGCTCTC- 208908 v ivi vvv ---- i i v v iv i v - MIRb#SINE/MIR 72 CTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCT 121 chr5qtel1M 208909 -AGTTACAACTGATTGCTGAGCTACATATCAGGGGGATGA-AATCTCCAC 208956 - iiv --- v v v v ii v -- v i - vi i MIRb#SINE/MIR 122 GAGCCTCA---GTTTCCTCATCTGTAAA--ATGGGGATAATAATACCTAC 166 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 47.68 CpG sites = 25, Kimura (unadjusted) = 50.45 Transitions / transversions = 1.00 (25/25) Gap_init rate = 0.06 (9 / 142), avg. gap size = 1.33 (12 / 9) 277 31.58 4.21 0.00 chr5qtel1M 208814 208908 (791092) MIRc#SINE/MIR 19 117 (151) m_b249s601i22 9882 chr5qtel1M 208814 TGGAGAGAGGGCTGGCCTCAGGATCATGAAGATCTGTGTTCAAGTGCTCC 208863 i vi v ii ii v i v i v ivv MIRc#SINE/MIR 19 TGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGG 68 chr5qtel1M 208864 CTCTGACACTTATGGGGGCTG----CCTGGACCACTCTCTCAAGCTCTC 208908 v ivi vvv ---- i i v v v i v MIRc#SINE/MIR 69 CTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTC 117 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.96 CpG sites = 14, Kimura (unadjusted) = 41.37 Transitions / transversions = 0.88 (14/16) Gap_init rate = 0.01 (1 / 94), avg. gap size = 4.00 (4 / 1) 41 0.00 0.00 6.25 chr5qtel1M 209460 209510 (790490) (CCCTAA)n#Simple_repeat 1 48 (0) c_b249s251i1 9883 chr5qtel1M 209460 CCCTAACCCTAACCCTAACCCTAACCCTAAATTCCCTAACCCTAACCCTA 209509 - -- (CCCTAA)n#Sim 1 CCCTAACCCTAACCCTAACCCTAACCCT-AA--CCCTAACCCTAACCCTA 47 chr5qtel1M 209510 A 209510 (CCCTAA)n#Sim 48 A 48 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.06 (3 / 50), avg. gap size = 1.00 (3 / 3) 63 16.96 3.77 2.48 chr5qtel1M 211245 211403 (788597) (TGTCTC)n#Simple_repeat 1 161 (0) m_b249s252i13 9884 chr5qtel1M 211245 TGT-TCTGCCTCCCTCTCTCCCCCTTTC-CTCCTCATCTGTCTCAGTCTC 211292 - i iv vi i v - -v - v (TGTCTC)n#Sim 1 TGTCTCTGTCTCTGTCTCTGTCTCTGTCTCT-GTC-TCTGTCTCTGTCTC 48 chr5qtel1M 211293 --TCTGTCTCCCTGTCTCTGTCTCTCCCTTTCTCTCTGTCTTTCTGTCTC 211340 -- v v i vi i v -- (TGTCTC)n#Sim 49 TGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTC--TCTGTCTC 96 chr5qtel1M 211341 TGTCCATCTTTCTGTCTCTGTCTCTG--TCTGTCTCTGTCTCAGTCTCTT 211388 iv v i -- v v (TGTCTC)n#Sim 97 TGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTG 146 chr5qtel1M 211389 TCTCTGTCTCAGTCT 211403 v (TGTCTC)n#Sim 147 TCTCTGTCTCTGTCT 161 Matrix = Unknown Transitions / transversions = 0.64 (9/14) Gap_init rate = 0.05 (8 / 158), avg. gap size = 1.25 (10 / 8) 258 21.84 2.53 3.40 chr5qtel1M 211404 211640 (788360) C HERVIP10FH#LTR/ERV1 (4085) 1017 783 m_b249s701i0 9885 chr5qtel1M 211404 CTGTTTCTGTCTCAGTCTCTCTCTCTGTCTCTGTCTCAGTCTCTCTCTG- 211452 i vii i v vii v v v i-- i - C HERVIP10FH#LT 1017 CTGTTTTTTCTTTACTACTTCTATCTCTCTCTTTCTT--TCTCTCTTTGA 970 chr5qtel1M 211453 -TCTCTGTCTCAGTCTCTCTCTCTGTCTCTGTCTCTGTCTCAGTCTCTCT 211501 - i vv v iv i -- v C HERVIP10FH#LT 969 CTTTCTGTCTCTCTCTCTCTCTCTGACTCCCTCTTTGTCTC--TCTGTCT 922 chr5qtel1M 211502 CTGTCTCTCTCAGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 211551 vi v i i vv i i v C HERVIP10FH#LT 921 CTTCCTCTCTCTGCCTCTCTCTCTCTTTGACTCCCTCTTTGTCTCTCTCT 872 chr5qtel1M 211552 CTCTGTCTCTGTCTCATTCTGTCTCTATCTCAGTCTCTATCTCTATCTCT 211601 iv v v v v vvi v v C HERVIP10FH#LT 871 CTCCCTCTCTCTCTCTTTCTCTCTCTCTCTCTTCCTCTCTCTCTCTCTCT 822 chr5qtel1M 211602 GTCTCAGTCTCTCTGTTTCTGTCT----GTCTCTCTTTGTCTC 211640 v --- - i v ---- i ii i C HERVIP10FH#LT 821 CTCT---TCTCTCT-TTCCTCTCTGCTGGTCTTTCCCTGCCTC 783 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 25.92 CpG sites = 23, Kimura (unadjusted) = 25.92 Transitions / transversions = 0.85 (23/27) Gap_init rate = 0.05 (11 / 236), avg. gap size = 1.27 (14 / 11) 266 21.69 4.59 2.70 chr5qtel1M 211588 211805 (788195) C HERVIP10FH#LTR/ERV1 (4099) 1003 782 m_b249s701i1 9885 chr5qtel1M 211588 CTATCTCTATCTCTGTCTCAGTCTCTCTGTTT--CTGTCTGTCTCTCTTT 211635 ii v ivv i v -- v i C HERVIP10FH#LT 1003 CTACTTCTATCTCTCTCTTTCTTTCTCTCTTTGACTTTCTGTCTCTCTCT 954 chr5qtel1M 211636 GTCTCAGTCTCAGTCTCTCTCTGTCTCTCTCTCTGTGTCTGTCTCAGTCT 211685 v -- v v i i v v vi v v i C HERVIP10FH#LT 953 CTCTC--TCTGACTCCCTCTTTGTCTCTCTGTCTCTTCCTCTCTCTGCCT 906 chr5qtel1M 211686 CTCTCTCTCTCTG------TCTCAGTCTCTCTCTCTCTCTGTGTCCCTCT 211729 i ------ iv i v v i C HERVIP10FH#LT 905 CTCTCTCTCTTTGACTCCCTCTTTGTCTCTCTCTCTCCCTCTCTCTCTCT 856 chr5qtel1M 211730 GTCTCAGTCTCTGTCTCTGTCTCTGTCTCAGTCTCTCTCTCTG-TCTCTG 211778 v -- v vi v -- v- v C HERVIP10FH#LT 855 TTCTC--TCTCTCTCTCTTCCTCTCTCTC--TCTCTCTCTCTTCTCTCTT 810 chr5qtel1M 211779 T-CTCTGTCTCAGTCTCTCTGTATCTCT 211805 - v viii i iv ii C HERVIP10FH#LT 809 TCCTCTCTGCTGGTCTTTCCCTGCCTCT 782 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 25.72 CpG sites = 21, Kimura (unadjusted) = 25.72 Transitions / transversions = 0.84 (21/25) Gap_init rate = 0.05 (10 / 217), avg. gap size = 1.60 (16 / 10) 254 32.39 1.41 0.00 chr5qtel1M 213755 213825 (786175) C L2a_3end#LINE/L2 (10) 507 436 m_b249s601i23 9886 chr5qtel1M 213755 TCAAGAAGTGTGTGTTAACTGCCTGCTATACGTTAAGCACTAGTCTAAGT 213804 v i i v i i vi i ii ii i iv i i C L2a_3end#LINE 507 TCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGC 458 chr5qtel1M 213805 GCTGGGACTACAA-AGGGATCA 213825 iv i- v v C L2a_3end#LINE 457 GCTGGGGATACAGCAGTGAACA 436 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.01 CpG sites = 16, Kimura (unadjusted) = 45.34 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.01 (1 / 70), avg. gap size = 1.00 (1 / 1) 16 9.32 0.00 0.00 chr5qtel1M 214301 214323 (785677) (T)n#Simple_repeat 1 23 (0) m_b249s252i14 9887 chr5qtel1M 214301 TTGTTTTTTTGTTTTTTTTTTTT 214323 v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTT 23 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 188 26.53 10.20 3.85 chr5qtel1M 214455 214552 (785448) MIR1_Amn#SINE/MIR 103 206 (24) m_b249s601i24 9888 chr5qtel1M 214455 AAGTTCCTCTCCCTTCCCTGGGCACCA-CTTACTGAACTGTAAAATGAGG 214503 iv - ?v i i ? vi -i v v v i MIR1_Amn#SINE 103 AAGTCACT-TNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGG 151 chr5qtel1M 214504 -----GAGACCAAGTTCCTTCGTAA----TCCTGAGTCAGCTGACTGATT 214544 ----- v ii vi i ----iii -- v - v MIR1_Amn#SINE 152 ATAATGATACTGACCTCCTTTGTAAAGTGCTTTGAG--ATCT-ACTGATG 198 chr5qtel1M 214545 ACAAGTAC 214552 v i MIR1_Amn#SINE 199 AAAAGTGC 206 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.41 CpG sites = 14, Kimura (unadjusted) = 34.41 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.07 (7 / 97), avg. gap size = 2.00 (14 / 7) 191 23.53 1.92 1.92 chr5qtel1M 214455 214506 (785494) MIR3#SINE/MIR 98 149 (59) m_b249s601i25 9888 chr5qtel1M 214455 AAGTTCCTCTCCCTTCCCTGGGCACCA-CTTACTGAACTGTAAAATGAGG 214503 iv - v i i vi -i v v v MIR3#SINE/MIR 98 AAGTCACT-TCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGG 146 chr5qtel1M 214504 GAG 214506 i MIR3#SINE/MIR 147 GGG 149 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.47 CpG sites = 6, Kimura (unadjusted) = 28.47 Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.00 (2 / 2) 832 27.98 4.94 0.00 chr5qtel1M 216043 216285 (783715) C MIR#SINE/MIR (1) 261 7 m_b249s601i26 9889 chr5qtel1M 216043 ATAATAA-GAGCAGTTATTTAGCCTTTACTTTGTGCCAGGCACTGTGCTA 216091 i-v i v v vi v v C MIR#SINE/MIR 261 ATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTA 212 chr5qtel1M 216092 AATGATTTCCAAATATTCTCTCATTTGTTCCTTACAGCCATCCTGAGAGG 216141 ii v v vi vv iv i i v i iv C MIR#SINE/MIR 211 AGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGG 162 chr5qtel1M 216142 TGGATGCTGTTATCATCCCCATTTTACTGTTAAGCAAACTGAGATAGACA 216191 i i i i i v v i v ii v v C MIR#SINE/MIR 161 TAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGA 112 chr5qtel1M 216192 GAGGCTAA-TGAGTTGCCCAAGTTCA---------TCAGTGTTTGAGGCC 216231 i - i v v --------- v viv v v C MIR#SINE/MIR 111 GAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 62 chr5qtel1M 216232 AAATTTGAACTCAGTCTCCCTGACTCCAG-GCCTGGCTTTCTGTCCACTG 216280 ii i i v vvi i - i vvi ii iv i C MIR#SINE/MIR 61 GGATTCGAACCCAGGCAGTCTGGCTCCAGAGCCCGTGCTCTTAACCACTA 12 chr5qtel1M 216281 TGTCA 216285 ii C MIR#SINE/MIR 11 TGCTA 7 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.67 CpG sites = 36, Kimura (unadjusted) = 35.57 Transitions / transversions = 1.12 (36/32) Gap_init rate = 0.02 (4 / 242), avg. gap size = 3.00 (12 / 4) 214 37.90 0.00 1.05 chr5qtel1M 216840 216935 (783065) L2a_3end#LINE/L2 402 496 (21) m_b249s601i27 9890 chr5qtel1M 216840 TAAGTTCCTTAAAGGTAGAGAATACAGGGGGTTTTGGTTTGTATTTGTAT 216889 i v i i i i v viv vvv - iiivvi L2a_3end#LINE 402 TAAGCTCCATGAGGGCAGGGACTTTTGTCTGTTTTG-TTCACTGCTGTAT 450 chr5qtel1M 216890 CACTGGCACTAATCATAGAGCCTGGTGCACAGTAACTGCTTAATAA 216935 v ii i iv vv i v ii i ivi i L2a_3end#LINE 451 CCCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGGCGCTCAATAA 496 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 50.78 CpG sites = 21, Kimura (unadjusted) = 55.30 Transitions / transversions = 1.40 (21/15) Gap_init rate = 0.01 (1 / 95), avg. gap size = 1.00 (1 / 1) 382 28.73 14.35 3.24 chr5qtel1M 218130 218352 (781648) C L3#LINE/CR1 (514) 3585 3339 m_b249s601i28 9891 chr5qtel1M 218130 TGTGGTCTCACTAGAACA----ACAGCCAGGGAC-ATCATCTCCCT---- 218170 v i vi ---- -- - i i ---- C L3#LINE/CR1 3585 TGTGGTCTGACCAGCGCAGAGTACAGC--GGGACTATTACCTCCCTTGNT 3538 chr5qtel1M 218171 -----CATTGCTCTTCCATCAGTGCAACTTGAATTCCCATTCCCTTTCTT 218215 ----- i iiv i i i i i i iv iv vv i C L3#LINE/CR1 3537 CTGGACACTATACTTCTATTAATGCAGCCTAAGATTGCATTAGCTTTTTT 3488 chr5qtel1M 218216 TGCATCCACATCACATTG------CCTA-----CTTGGGATCCAC-AAAA 218253 v v i ------ v ----- v i v - C L3#LINE/CR1 3487 GGCAGCCACATCACACTGTTGGCTCATATTGAGCTTGCGGTCAACTAAAA 3438 chr5qtel1M 218254 CCACTGGACATCTTCTAGGAGAACTGCT------CAACATCCCTGCCATC 218297 v i iiv i ii v v ------ v v iiv C L3#LINE/CR1 3437 CCCCTAGGTCTTTTTCACGTGAACTGCTGCTAAGCCAGATCCTCTCCATC 3388 chr5qtel1M 218298 CTTAAAGTGTGCTTCCAGAGATGTTTTATTTAGAAGAAATGGAAGACTCT 218347 ------ i viiv v v v v ivvv v i i C L3#LINE/CR1 3387 C------TGTACTTGTGCAGTTGATTTTTTGAACCTAAATGCAGGACTTT 3344 chr5qtel1M 218348 CCATT 218352 v C L3#LINE/CR1 3343 ACATT 3339 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.18 CpG sites = 32, Kimura (unadjusted) = 36.92 Transitions / transversions = 1.07 (32/30) Gap_init rate = 0.07 (16 / 222), avg. gap size = 2.50 (40 / 16) 215 31.25 0.00 0.00 chr5qtel1M 218485 218564 (781436) C L3#LINE/CR1 (807) 3292 3213 m_b249s601i29 9891 chr5qtel1M 218485 CCTCTTTAAGTTGTTTTGCATCCTGGCTCTCACATTCAGTCTCTTATTTC 218534 v iv ii i? v i ii vv i ?iv v vi v C L3#LINE/CR1 3292 CCTGTCGAGATCNTTTTGAATCTTGATTCTGTCATCCANCGTATTAGCTA 3243 chr5qtel1M 218535 TTGCTCTTAGCTTGATGTCATCTGCAAATT 218564 iv ii vi C L3#LINE/CR1 3242 TCCCTCCCAGCTTTGTGTCATCTGCAAATT 3213 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.53 CpG sites = 14, Kimura (unadjusted) = 42.94 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.00 (0 / 79), avg. gap size = 0.0 (0 / 0) 199 25.84 11.39 14.29 chr5qtel1M 218651 218808 (781192) MIRc#SINE/MIR 53 206 (62) m_b249s601i31 9892 chr5qtel1M 218651 TGGGTTCAAATCCAACCTCAAACACTCACTA------TGATTCCAGGCAA 218694 i i viv viv i ------ iiiii MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 102 chr5qtel1M 218695 AT-GCTT-------CTGA----CATTTTCCTCATCTATAAAATGGGTCAG 218732 i -i ------- ---- v i --- MIRc#SINE/MIR 103 GTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG---G 149 chr5qtel1M 218733 GTGAAGTTCATATATTGCATGGGATGTCCCTGACATATTGCATAGGGCGT 218782 i i-------- v i v ------ - v iiv i ---- MIRc#SINE/MIR 150 ATA--------ATAATACCTG------CCCTG-CCTACCTCACAGG---- 180 chr5qtel1M 218783 GTTGTTGTGTAGCTCAAAAGGAAGAA 218808 vi v v ii v MIRc#SINE/MIR 181 GTTGTTGTGAGGATCAAATGAGATAA 206 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.24 CpG sites = 22, Kimura (unadjusted) = 32.46 Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.17 (26 / 157), avg. gap size = 1.54 (40 / 26) 207 21.79 23.08 0.00 chr5qtel1M 218651 218728 (781272) MIRb#SINE/MIR 56 151 (117) m_b249s601i30 9892 chr5qtel1M 218651 TGGGTTCAAATCCAACCTCAAACACTCACTA------TGATTCCAGGCAA 218694 i viv viv i ------ iiiii MIRb#SINE/MIR 56 TGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 105 chr5qtel1M 218695 AT-GCTT-------CTGA----CATTTTCCTCATCTATAAAATGGG 218728 i -i ------- ---- v i MIRb#SINE/MIR 106 GTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 151 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 23.13 CpG sites = 12, Kimura (unadjusted) = 26.67 Transitions / transversions = 2.40 (12/5) Gap_init rate = 0.05 (4 / 77), avg. gap size = 4.50 (18 / 4) 340 31.72 4.49 7.71 chr5qtel1M 219248 219715 (780285) C HERVK3#LTR/ERVK (2028) 5174 4721 m_b249s701i2 9893 chr5qtel1M 219248 GGCACCCATCTGATTCCTTCTCCACCTGTAGAGATACAAGCAAACCCTCT 219297 ivi i iv i vi v i i i v ? C HERVK3#LTR/ER 5174 GGCACCCACACGGTTTGTCCATCTCCTGTAAAAACACAAGCATACCCTCN 5125 chr5qtel1M 219298 CCCCCAAG-CAATTAGTCTGTCTGGTCCTTTCCATTCACCACT--TTCTG 219344 i v - i v i iii - v -ii ? -- i C HERVK3#LTR/ER 5124 TCCCCACGTCAGTAAATCCACC-GGACCTTTCCATT-GTCNCTTCTTCCG 5077 chr5qtel1M 219345 GGTCTTTCCACATCACCTGGCGATTATCTAAAGATAGTGGAGCTGCTCGC 219394 vv i v i vvv v v -------- vvvv vi - C HERVK3#LTR/ER 5076 GGGATTTCCATAACACTTTCGGATAAACT--------TTCCTCTTTTC-C 5036 chr5qtel1M 219395 ACTGGACACTGACCTTCCGGTGGGTTATAAAACCTGTCTGCCGGAGCCAG 219444 v -i vi -------------- vii v i i vv C HERVK3#LTR/ER 5035 TCT-AACACTTGCC--------------AATGTCTTTCTGCTGGAGTCTT 5001 chr5qtel1M 219445 TGCATCTTTGTCAAAAATC-AAGAAGTTAATAGTATAAAGGGTTAGATTT 219493 vv iv ii ii i - i i v v v v i i i v C HERVK3#LTR/ER 5000 ACCATCCGTACCAGGAGTCNAAAAAATTTAAAGTAAATAAGGCTAAATGT 4951 chr5qtel1M 219494 AGAAGTTCTCTAGG-----ATTA----CCTGTGGCTCCCCCTTTTGTTTT 219534 vvv vv iv -----i i---- i -i i? i C HERVK3#LTR/ER 4950 AGTTTTGATTGAGGTGGTAGTTGGCCTCCTAT-ACCNCCCTTTTTGTTTT 4902 chr5qtel1M 219535 TGGAGGA-GCGTCTTAATATTTCTGTTTCTCCTCTCTACTATTGCC-TGT 219582 vv iv - iv i -vi v vi v - v - C HERVK3#LTR/ER 4901 TTCAACATGCGTTGTAATGTTT-GATGTGCCCGCTCTA-TAATGCCTTGT 4854 chr5qtel1M 219583 CCTTGAGGATTAAAAGGTATGTCCGTGGTGTG---TAAAATCTTATACTG 219629 iv v v vi i vv i --- v ii iv vi C HERVK3#LTR/ER 4853 CCTCTAGGATTATAAGGAATTCCTGTTTTATGGGTTATAGCCCAAAGCTG 4804 chr5qtel1M 219630 TGCACAAAAGTGTGCTAA--ATGTTTCGAAGTATAAGCAGGACCATTGTC 219677 -- vi v v vv -- vi --- i v C HERVK3#LTR/ER 4803 T--AAGAAATTTTGAAAAGCATGACT---AGTATAAGCGGGTCCATTGTC 4759 chr5qtel1M 219678 TGTTTTT-ATTGCTTGTGGCACACCCATAATGGCAGATG 219715 v - i i- i iv vvi i C HERVK3#LTR/ER 4758 AGTTTTTAATTGTTTA-GGTATCCCCATATGAGCAAATG 4721 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 40.44 CpG sites = 67, Kimura (unadjusted) = 42.01 Transitions / transversions = 0.96 (67/70) Gap_init rate = 0.10 (45 / 467), avg. gap size = 1.24 (56 / 45) 276 32.18 4.95 2.58 chr5qtel1M 219451 219753 (780247) C HERVK22#LTR/ERVK (2157) 4680 4371 m_b249s701i3 9893 chr5qtel1M 219451 TTTGTCA---AAAATCAAGAAGTTAATAGTATAAAGGGTTAGATTTAGAA 219497 i --- v i i i vi v v i i v vvii iv C HERVK22#LTR/E 4680 TTTATCATCTAAATTTAAAAAATTAAGGGTAAATAAGGCTTGTGCCAATA 4631 chr5qtel1M 219498 GTTCTCTAGGAT---TACCTGTGGCTCCCCCTTTT--GTTTTTGGAGGAG 219542 vi vi i --- iii i-i -- iv v v C HERVK22#LTR/E 4630 GTGTTGCAGGGTCCTTACTCATA-TTCCCCCTTTTTTGTTTTCTGAGCAT 4582 chr5qtel1M 219543 CGTCTTAATATTTCTGTTTCTCCTCTCTACTATTGCCTGTCCTTGAGGAT 219592 vv i viv vvv vvviv vi v i i C HERVK22#LTR/E 4581 ATTTTTAAGGGTGGAGTGGGCACGTTCTACTATGGCCTGTCCTTGGGGGT 4532 chr5qtel1M 219593 TAAAAGGTATGTCCGTGGTGTGTAAAATCTTATAC-TGTGCACAAAAGTG 219641 v v v i i vi vii v vi - - v C HERVK22#LTR/E 4531 TATACGGGATGCCTGTGGAATGTTGGATGTTCCACGTGTG-ACAAAATTG 4483 chr5qtel1M 219642 TGCTAAATGTTTCGA---AGTATAAGCAGGACCATTGTCTGTTTTTATTG 219688 -- i -i vi ---i i v i v v - C HERVK22#LTR/E 4482 T--TGAA-ATTGTGAGCTGGCATAAGCCGGACCATTATCAGTTTTAATT- 4437 chr5qtel1M 219689 CTTGTGG--CACACCCATAATGGCAGATGCTTGTGTGAGGA-ATTCAGTG 219735 i -- i - vv i v - iviv i -i i i C HERVK22#LTR/E 4436 TTTGTGGGCCGC-CCCATAAACGCAAAAG-TTAAAAGAAGATGTTTAATG 4389 chr5qtel1M 219736 ACCACTCGGGCTGTCTCT 219753 vvv iv v C HERVK22#LTR/E 4388 ACATATCGGGTGGACTCT 4371 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 42.08 CpG sites = 47, Kimura (unadjusted) = 42.67 Transitions / transversions = 0.98 (47/48) Gap_init rate = 0.05 (15 / 302), avg. gap size = 1.53 (23 / 15) 301 37.04 1.93 1.93 chr5qtel1M 219519 219829 (780171) C HERVK14#LTR/ERVK (1246) 4850 4540 m_b249s701i4 9893 chr5qtel1M 219519 CTCCCCCTTTTGTTTTTGGAGGAGCGTCTTAATATTTCTGTTTCTCCTCT 219568 i i i v vvv v i v v v v vi vvii i C HERVK14#LTR/E 4850 CCCTCCCTTTTGCTTTTGTATTTGAGTTTTTAAAGTACGATTAGCTCTTT 4801 chr5qtel1M 219569 CTACTATTGCCTGTCCTTGAGGATTAAAAGGTATGTCCGTGGTGTGTAAA 219618 i v ii v v v ii i i viv C HERVK14#LTR/E 4800 CCACTATTGCCTGTCCTTGTGAGTTATATGGAATACCCGTAGTATGGGTA 4751 chr5qtel1M 219619 ATCTTATACTGTGCACAAAAGTGT-GCTA-AATGTTTCGA-AGTATAAGC 219665 v vi i vv - i - i -iiiv v v - --v C HERVK14#LTR/E 4750 ATATTCCATTGTTGA-AAAAATGTAGCCATGGCTTTACTACAGTAT--CC 4704 chr5qtel1M 219666 AGGACCATTGTCTGTTTTTATTGCTTGTGGCACACCCATAATGGCAGATG 219715 v i i i v v vi v v iv iv v i - C HERVK14#LTR/E 4703 TGGGCCGTTATCAGTTTTGATTTTTTCTGGGATTCCCATAACTGAAAA-G 4655 chr5qtel1M 219716 CTTGTGTGAGGAATTCAGTGACCACTCGGGCTGTCTCTTTTGCTGCTGG- 219764 vv vvvi i vv vv v v --i i vv iiv i v - C HERVK14#LTR/E 4654 CAAGATAAAAGATGTCTTTTAACA--TGAGCTGTAGCTTCCCCTGTTTGA 4607 chr5qtel1M 219765 --TATTGCAAAAGTGAATCCCGAAAAGGTGTCTACCACAACGTGGATGAA 219812 -- i v vv ii i vivi v i iiv i i ii C HERVK14#LTR/E 4606 CATGTGGCCCAGATAAAATGTGAATAGGTATCTACTGAAACATGAACAAA 4557 chr5qtel1M 219813 AGACAGACGACCAAAAG 219829 i ivivv C HERVK14#LTR/E 4556 GGACAATTTTCCAAAAG 4540 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 51.15 CpG sites = 53, Kimura (unadjusted) = 51.79 Transitions / transversions = 0.88 (53/60) Gap_init rate = 0.04 (11 / 310), avg. gap size = 1.09 (12 / 11) 15 24.45 0.00 0.00 chr5qtel1M 220456 220494 (779506) (AGC)n#Simple_repeat 1 39 (0) m_b249s252i15 9894 chr5qtel1M 220456 AGCAGCAATAGCGGCAGCAGCGGCGGCAGCCGGAGGAGC 220494 ii i i i v v v (AGC)n#Simple 1 AGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGC 39 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 20 19.24 1.82 1.82 chr5qtel1M 220530 220584 (779416) (CCCCCCG)n#Simple_repeat 1 55 (0) m_b249s252i17 9895 chr5qtel1M 220530 CCCCCCAACCCTC-CCCCCGGCGCCCGGCCCGCCGCCCCCCACCCCCCCG 220578 iv i - v v v v -v (CCCCCCG)n#Si 1 CCCCCCGCCCCCCGCCCCCCGCCCCCCGCCCCCCGCCCCCC-GCCCCCCG 49 chr5qtel1M 220579 CCCGCC 220584 v (CCCCCCG)n#Si 50 CCCCCC 55 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.04 (2 / 54), avg. gap size = 1.00 (2 / 2) 16 14.73 0.00 0.00 chr5qtel1M 220614 220643 (779357) (GCA)n#Simple_repeat 1 30 (0) m_b249s252i18 9896 chr5qtel1M 220614 GCAGCAGCCGCCGCGGCAGCGGCAGCAGCA 220643 v v i i (GCA)n#Simple 1 GCAGCAGCAGCAGCAGCAGCAGCAGCAGCA 30 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 331 29.89 1.15 0.00 chr5qtel1M 220741 220827 (779173) C MIR#SINE/MIR (120) 142 55 m_b249s601i32 9897 chr5qtel1M 220741 CATTTTACAGATAAAGAAACTGAGGCA-AATGGAGTTAGCTGGTTTGTCC 220789 i i - iv ii iv iii i C MIR#SINE/MIR 142 CATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCC 93 chr5qtel1M 220790 AGGGCCACATAACTAGGAAGTATCTGAAGTCAGATTTG 220827 i i i i v iv v ivivi i C MIR#SINE/MIR 92 AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCG 55 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.69 CpG sites = 19, Kimura (unadjusted) = 40.80 Transitions / transversions = 2.71 (19/7) Gap_init rate = 0.01 (1 / 86), avg. gap size = 1.00 (1 / 1) 472 31.30 8.30 8.72 chr5qtel1M 221753 222270 (777730) C L2d_3end#LINE/L2 (0) 516 1 m_b249s601i33 9898 chr5qtel1M 221753 TTAGTCA-TCAATCACTAAACATTTACTGAGAACTTACTACGAGCCAGAC 221801 i i - vi ii i vi i i v ivii C L2d_3end#LINE 516 TCAATCAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGC 467 chr5qtel1M 221802 ACTGGGCTAAACACCAC--AGATCCAAAAAGAGGCAAAAGACA--GTCCC 221847 v ii i iii--i v v ? i?i i v -- C L2d_3end#LINE 466 ACTGTGCTAGGCGCTGTGGGGAACGANAAAANAGTATAAGACATGGTCCC 417 chr5qtel1M 221848 TGACCGCAGGAAGTTTACAATCTAA-TGGGAAGGCAACATGCAAGCAAAT 221896 v v i i i i- i i v -- v i v i C L2d_3end#LINE 416 TGCCCTCAAGGAGCTTACAATCTAGTTGGGGAGACAAGA--CTAACACAC 369 chr5qtel1M 221897 ATATAATATACATAAATGGGGAGGCAATATGCAAGCAAATATATAATATA 221946 i------ v i v i i -i -- vv i - C L2d_3end#LINE 368 ATG------AAACAATTAGAGA-ACAATA--CAAGACAGTATATAAT-TA 329 chr5qtel1M 221947 CATA-TAA--TGCATAATACAAGTT-TAAGTTTAAGTAGGAGGTAATTAT 221992 vi i- -- i ii iii - viv - v -----i C L2d_3end#LINE 328 AGTGCTAAATTGCGTGGTACAGACTATAAGTGCTA-TAGGAGTT-----C 285 chr5qtel1M 221993 AGAGATAATATATATATATATACACACACATAATATATAGGTAATAATTG 222042 viiv v v ------- ----------i i i iviv i -- C L2d_3end#LINE 284 AGAGAAGGGAGAGAT-------CA----------GTGTGGGCTGGAGT-- 254 chr5qtel1M 222043 GGCCTAGGGAAGGTTTCCTGTAGGAGGTGGGAGTTAAAGGAAGCC---AG 222089 i - i v v v i ivvii --- i C L2d_3end#LINE 253 GGTC-AGGGAAGGCTTCGTGGAGGAGGTGGGACTTGAGCTGGGCCTTGAA 205 chr5qtel1M 222090 GGA--GGTCAG-------TAGTCAGAGTGG-AGGGGGAGAGCCGTCCAGG 222129 -- vi ------- vv v - i i vv C L2d_3end#LINE 204 GGATGGGTAGGATTTGGATAGAGAGAGAGGAAGGGGAAGGGCATTCCAGG 155 chr5qtel1M 222130 CATGGGGGACGGCCAGAACAAATAACCCATA--CAGCATT---------T 222168 iv i vv i -ii v v -- i v v ---------v C L2d_3end#LINE 154 CGGGGGGAACGGCGTGAGCAAA-GGCGCAGAGGCGGGAATGCGCAAGGCG 106 chr5qtel1M 222169 TATTTGTGGAACAGCCCGGAGGTGGGGGTCACT---------GGTTCCAG 222209 i i v i ivvi iiv vv v --------- -- C L2d_3end#LINE 105 TGTTCGGGGGACAGTGAAGAGACCGGCCTGACTGGAGCGGAGGGTTC--G 58 chr5qtel1M 222210 AGTTGGAGAGTAAGTGAGGTGTGAGAAGCCTAGAAAGGTATGAAGGGACG 222259 v i i - i i--- v v i ? v iv i v C L2d_3end#LINE 57 TGCTGGGGAGT-AGTGGGA---GATAAGGCTGGANAGGTAGGGTGGGGCC 12 chr5qtel1M 222260 AGGGTATGAAG 222270 ivii i C L2d_3end#LINE 11 AGATCGTGGAG 1 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.58 CpG sites = 88, Kimura (unadjusted) = 42.24 Transitions / transversions = 1.47 (88/60) Gap_init rate = 0.11 (59 / 517), avg. gap size = 1.49 (88 / 59) 500 34.41 7.21 1.87 chr5qtel1M 222112 222416 (777584) C L2#LINE/L2 (1) 3081 2761 m_b249s601i34 9898 chr5qtel1M 222112 GGGGGAGAGCCGTCCAGGCATGGGGGACGGCCAGAACAAATAACCC--AT 222159 i vv vi i i v vi -ii -- v C L2#LINE/L2 3081 GGGGAAGAGCGTTCCAGGCAGAGGGAACAGCAAGTGCAAA-GGCCCTGAG 3033 chr5qtel1M 222160 AC---AGCATTT------TATTTGTGGAACAGCCCGGAGGTGGGGGTCAC 222200 i --- i vi------ i i v vv ivi v vi C L2#LINE/L2 3032 GCGGGAGCGTGCCTGGCGTGTTCGAGGAACAGCAAGGAGGCCAGTGTGGC 2983 chr5qtel1M 222201 TGGTTCCAGAGTTGG--AGAGTAAGTGAGGTGTGAGA--AGCCTAGAAAG 222246 vv -i vi -- i vi v v iv -- vii i C L2#LINE/L2 2982 TGGAGC-GGAGTGAGCGAGGGGGAGAGTGGTAGGAGATGAGGTCAGAGAG 2934 chr5qtel1M 222247 GTATGAAGGGACGAGGGTATGAAGAGCTTTACAGGCCA----GAGGATTT 222292 vvii v ivi v i i ii ----i i C L2#LINE/L2 2933 GTAACGGGGGACCAGATCATGTAGGGCCTTGTAGGCCATTGTAAGGACTT 2884 chr5qtel1M 222293 TGCATTTGCTTCTGGAGGCCATAGGGAACCCC---AGTGTTTATTGAATA 222339 vv vvi iiv vv i i i vi--- v -- ii C L2#LINE/L2 2883 TGGCTTTTACTCTGAGTGAGATGGGAAGCCATTGGAGGGTT--TTGAGCA 2836 chr5qtel1M 222340 GGAGAGTGAGACGTGCTCAGATCTATGATTTAGGAAAAGCTCTTTGGTGG 222389 ii -- i v v ii i v ii ii v v i iv C L2#LINE/L2 2835 GAGGAGT--GACATGATCTGACTTACGTTTTAAAAGGATCACTCTGGCTG 2788 chr5qtel1M 222390 CCGAGTAGAGGATGGACTACAAGGGAG 222416 i v v i i i? i i C L2#LINE/L2 2787 CTGTGTTGAGAATAGACTGNAGGGGGG 2761 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.88 CpG sites = 60, Kimura (unadjusted) = 48.10 Transitions / transversions = 1.40 (60/43) Gap_init rate = 0.04 (13 / 304), avg. gap size = 2.15 (28 / 13) 23 21.08 4.55 0.00 chr5qtel1M 223317 223382 (776618) (TCTC)n#Simple_repeat 1 69 (0) m_b250s252i1 9899 chr5qtel1M 223317 TCCCTGTCTCTCTGTGTCTGTCTCTGTCTCTCCCTTTC-CTCCCTCCCCC 223365 i v v v v v i i - i i i (TCTC)n#Simpl 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr5qtel1M 223366 TTTCTC-CTCTCTCT-TCT 223382 i - - (TCTC)n#Simpl 51 TCTCTCTCTCTCTCTCTCT 69 Matrix = Unknown Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.05 (3 / 65), avg. gap size = 1.00 (3 / 3) 41 16.33 1.33 0.00 chr5qtel1M 223733 223807 (776193) (CA)n#Simple_repeat 1 76 (0) m_b250s252i2 9900 chr5qtel1M 223733 CAC-CACACACACACTCACATTCACACTCACACACACATTCACACACTCA 223781 - v iv v iv v (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 chr5qtel1M 223782 CACACGCACTCTCACACACACACTCA 223807 i v v v (CA)n#Simple_ 51 CACACACACACACACACACACACACA 76 Matrix = Unknown Transitions / transversions = 0.38 (3/8) Gap_init rate = 0.01 (1 / 74), avg. gap size = 1.00 (1 / 1) 349 27.18 7.77 0.00 chr5qtel1M 226449 226551 (773449) C MIRc#SINE/MIR (153) 115 5 m_b250s601i3 9901 chr5qtel1M 226449 GAGGTTAAGTGACTTGC-----GTCACATGACTAGGACATGCTGAGACCG 226493 ----- iii v vi viiiii C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 66 chr5qtel1M 226494 G--TTTGAACTCCGGTCCTCCT-ACTTCAGGGCTGGTGCTCTACCCACTG 226540 --i i i v i - i i v ii vi C MIRc#SINE/MIR 65 GGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTG 16 chr5qtel1M 226541 AGCCACCCAGC 226551 vi v v C MIRc#SINE/MIR 15 CACCACACTGC 5 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 33.69 CpG sites = 19, Kimura (unadjusted) = 35.27 Transitions / transversions = 2.11 (19/9) Gap_init rate = 0.03 (3 / 102), avg. gap size = 2.67 (8 / 3) 362 26.95 2.75 4.67 chr5qtel1M 227062 227170 (772830) C MIR#SINE/MIR (95) 167 61 m_b250s601i4 9902 chr5qtel1M 227062 ATGAAGGAAATTCCATTTCCTTCTCCAGTCCCTTTTACAGATGAGGAAAC 227111 i v ii v i viiv i ----- C MIR#SINE/MIR 167 ATGAGGTAGGTACTATTATTATCCCCA-----TTTTACAGATGAGGAAAC 123 chr5qtel1M 227112 TGAGGCA---AAAGGTGAGGGAACTTGTCCCGGACCACACAACTAGGAAA 227158 --- i v i v i vi ii i v i C MIR#SINE/MIR 122 TGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAG 73 chr5qtel1M 227159 TATCTGAGGCAG 227170 iv v v i C MIR#SINE/MIR 72 TGGCAGAGCCGG 61 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 32.78 CpG sites = 17, Kimura (unadjusted) = 34.28 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.06 (6 / 108), avg. gap size = 1.33 (8 / 6) 754 21.28 6.98 1.66 chr5qtel1M 227179 227350 (772650) MIR#SINE/MIR 72 252 (10) m_b250s601i5 9903 chr5qtel1M 227179 ACCTCTTAGCTGTGTGATCCTGGACAAGCCCCTTTACCTTTGTCTTCCTC 227228 i vi i i i iiv v i v v v MIR#SINE/MIR 72 ACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTC 121 chr5qtel1M 227229 AGTTTTCTCATCTGCAAAATGAGGATAATAATAATAGTATCTTCCTCCCA 227278 i i i --- i v vi MIR#SINE/MIR 122 AGTTTCCTCATCTGTAAAATGGGGATAATAATA---GTACCTACCTCATA 168 chr5qtel1M 227279 GGCTTGTTAAGAGGCTCAAACGAGGTAACATTTGTAAAG----------- 227317 v iv v i i v i iv ----------- MIR#SINE/MIR 169 GGGTTGTTGTGAGGATTAAATGAGTTAATACATGTAAAGCGCTTAGAACA 218 chr5qtel1M 227318 -TGCCTGGCACATAGTAGGCACTTAATAAATACT 227350 - i i i ii MIR#SINE/MIR 219 GTGCCTGGCACATAGTAAGCGCTCAATAAATGTT 252 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 24.84 CpG sites = 23, Kimura (unadjusted) = 25.65 Transitions / transversions = 1.77 (23/13) Gap_init rate = 0.03 (5 / 171), avg. gap size = 3.00 (15 / 5) 59 11.05 0.00 0.00 chr5qtel1M 228073 228120 (771880) (CA)n#Simple_repeat 1 48 (41) m_b250s252i3 9904 chr5qtel1M 228073 CACTCACACACACTCACACTCACACACTCTCTCTCACACACACATACA 228120 v v v v v v v i (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACA 48 Matrix = Unknown Transitions / transversions = 0.14 (1/7) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 164 4.72 0.00 0.00 chr5qtel1M 228121 228295 (771705) (CT)n#Simple_repeat 1 175 (0) c_b250s251i0 9905 chr5qtel1M 228121 CTCTCTGTCTCTCTCTCTGTCTCTCTCTCTGTTTCTCTCTCTCTCTCTCT 228170 v v v i (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chr5qtel1M 228171 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 228220 (CT)n#Simple_ 51 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 100 chr5qtel1M 228221 CTCTCTCTCTGTCTCTCTCTCTGTTTCTCTCTCTCTCTCTCTGTCTCTCT 228270 v v i v (CT)n#Simple_ 101 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 150 chr5qtel1M 228271 CTCTCTCTCTCTCTCTCTCTCTCTC 228295 (CT)n#Simple_ 151 CTCTCTCTCTCTCTCTCTCTCTCTC 175 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.00 (0 / 174), avg. gap size = 0.0 (0 / 0) 59 11.05 0.00 0.00 chr5qtel1M 228296 228335 (771665) (CA)n#Simple_repeat 49 88 (1) m_b250s252i3 9906 chr5qtel1M 228296 ACACACACACACACACACACACACACACACACACTCACAC 228335 v (CA)n#Simple_ 49 ACACACACACACACACACACACACACACACACACACACAC 88 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 12 13.69 6.25 0.00 chr5qtel1M 229236 229267 (770733) (GGGCCC)n#Simple_repeat 1 34 (0) m_b250s252i4 9907 chr5qtel1M 229236 GGGCCCGGGCCCATG-GCTGGCCCGGG-CCGGGC 229267 iv -v v - (GGGCCC)n#Sim 1 GGGCCCGGGCCCGGGCCCGGGCCCGGGCCCGGGC 34 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.06 (2 / 31), avg. gap size = 1.00 (2 / 2) 12 31.29 0.00 0.00 chr5qtel1M 229247 229293 (770707) (CAGGG)n#Simple_repeat 1 47 (0) m_b250s252i5 9907 chr5qtel1M 229247 CATGGCTGGCCCGGGCCGGGCAGAGCCAGGAGGGGCAGGGGAGGCCA 229293 v v v v v i vi vi v v (CAGGG)n#Simp 1 CAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCA 47 Matrix = Unknown Transitions / transversions = 0.33 (3/9) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 200 25.78 11.70 0.96 chr5qtel1M 234497 234590 (765410) C MIR3#SINE/MIR (22) 186 83 m_b250s601i6 9908 chr5qtel1M 234497 CAGAGCTGACGGGGGTCCTAGGGGTCAGCTGGCCCACCTGCCCCATT--- 234543 ivi ii i i i v i i v iv i --- C MIR3#SINE/MIR 186 CAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTA 137 chr5qtel1M 234544 ---GTGGGGGAA-GGGGGCCCA-AGGGGTGAAGTGCCAGTGC---AGGTC 234585 ---i i i -v i - i v -v --- C MIR3#SINE/MIR 136 CAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGAC-TTGCCCAAGGTC 88 chr5qtel1M 234586 ATACA 234590 i C MIR3#SINE/MIR 87 ACACA 83 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 33.15 CpG sites = 17, Kimura (unadjusted) = 33.15 Transitions / transversions = 2.43 (17/7) Gap_init rate = 0.06 (6 / 93), avg. gap size = 2.00 (12 / 6) 24 22.66 1.08 6.82 chr5qtel1M 235939 236031 (763969) (GGCGG)n#Simple_repeat 1 88 (0) m_b250s252i6 9909 chr5qtel1M 235939 GGTGGGCCGGGGCAGGGCCGGGTCGAGGGGCAAGGCCGGGGGCAGGGCGG 235988 i v - v -- v -i v - i (GGCGG)n#Simp 1 GGCGGGGCGGGGC-GGGGCGGG--GCGGGGC-GGGGC-GGGGCGGGGCGG 45 chr5qtel1M 235989 GGGGGGGGGTGGGAGTGG-GGGGCGAGGGGAGGAGGGGCAGGGC 236031 v v - v v - i v i v i (GGCGG)n#Simp 46 GGCGGGGCG-GGGCGGGGCGGGGCGGGGCGGGGCGGGGCGGGGC 88 Matrix = Unknown Transitions / transversions = 0.60 (6/10) Gap_init rate = 0.08 (7 / 92), avg. gap size = 1.00 (7 / 7) 23 23.41 0.00 0.00 chr5qtel1M 235976 236025 (763975) (G)n#Simple_repeat 1 50 (0) m_b250s252i7 9910 chr5qtel1M 235976 GGGGGCAGGGCGGGGGGGGGGGTGGGAGTGGGGGGCGAGGGGAGGAGGGG 236025 vi v v i v v i i i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 50 Matrix = Unknown Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 24 22.66 1.08 6.82 chr5qtel1M 235939 236031 (763969) (GGCGG)n#Simple_repeat 1 88 (0) m_b250s252i6 9909 chr5qtel1M 235939 GGTGGGCCGGGGCAGGGCCGGGTCGAGGGGCAAGGCCGGGGGCAGGGCGG 235988 i v - v -- v -i v - i (GGCGG)n#Simp 1 GGCGGGGCGGGGC-GGGGCGGG--GCGGGGC-GGGGC-GGGGCGGGGCGG 45 chr5qtel1M 235989 GGGGGGGGGTGGGAGTGG-GGGGCGAGGGGAGGAGGGGCAGGGC 236031 v v - v v - i v i v i (GGCGG)n#Simp 46 GGCGGGGCG-GGGCGGGGCGGGGCGGGGCGGGGCGGGGCGGGGC 88 Matrix = Unknown Transitions / transversions = 0.60 (6/10) Gap_init rate = 0.08 (7 / 92), avg. gap size = 1.00 (7 / 7) 207 30.43 2.90 0.00 chr5qtel1M 237820 237888 (762112) C L3#LINE/CR1 (342) 3757 3687 m_b250s601i7 9911 chr5qtel1M 237820 TCCT-TAAATGTCCTTGTTTCCAGACCAAATGTCCC-ATTTCCTTCAAGT 237867 - i v i iv i i i ii - v vi C L3#LINE/CR1 3757 TCCTCTAAGTCTTCTCTTCTCCAGGCTAAACATCCCCAGTTCCTTCAACC 3708 chr5qtel1M 237868 AATCCTGATGTGATAGGATCT 237888 iv v i i v i i C L3#LINE/CR1 3707 GTTCCTCATATGACATGGTTT 3687 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 38.20 CpG sites = 14, Kimura (unadjusted) = 41.06 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.03 (2 / 68), avg. gap size = 1.00 (2 / 2) 399 28.43 2.53 8.72 chr5qtel1M 239595 239752 (760248) L2c_3end#LINE/L2 327 475 (3) m_b250s601i8 9912 chr5qtel1M 239595 ATCAGCATGTCTT-TAGCTAATTGGTTGCTAGT-TGTTTCCCCCATTATA 239642 i i v v - ii ivi v i ?v - i i i v L2c_3end#LINE 327 ATTAACTTGTATTGTAATTGTCTGTTTACNTGTCTGTCTCCTCCACTAGA 376 chr5qtel1M 239643 CGGGGAGTTCCTTGAAGACAGGTACTGGGTTTTGACT--TTCTTGTGTCC 239690 v v i i i v i v i - i -- ii i L2c_3end#LINE 377 CTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTT-ATTCATCTTTGTATCC 425 chr5qtel1M 239691 TCAGCACTTAGTTTAAGGCCTGACACAAAATAGGTGCTTAACCAATGCTT 239740 i ------------ i v i i i iv i L2c_3end#LINE 426 CCAGC------------GCCTGGCACATAGTAGGCGCTCAATAAATGTTT 463 chr5qtel1M 239741 GCTGACTGACTG 239752 i v v L2c_3end#LINE 464 GTTGAATGAATG 475 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 35.05 CpG sites = 27, Kimura (unadjusted) = 37.36 Transitions / transversions = 1.93 (27/14) Gap_init rate = 0.10 (16 / 157), avg. gap size = 1.06 (17 / 16) 433 28.67 5.11 0.70 chr5qtel1M 239616 239752 (760248) L2b_3end#LINE/L2 321 463 (3) m_b250s601i9 9912 chr5qtel1M 239616 TGGTTGC-TAGTTGTTTCCCCCATTATACGGGGAGTTCCTTGAAGACAGG 239664 ? i - ivi i i v v v i v i i L2b_3end#LINE 321 TGNTTACATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGG 370 chr5qtel1M 239665 TACTGGGTTTTGACT--TTC----TTGTGTCCTCAGCACTTAGTTTAAGG 239708 v i ? - i v -- ----i i i i i ivi i? L2b_3end#LINE 371 GACCGNG-TCTGTCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNG 419 chr5qtel1M 239709 CCTGACACAAAATAGGTGCTTAACCAATGCTTGCTGACTGACTG 239752 i v i i i iiv ii i v v L2b_3end#LINE 420 CCTGGCACACAGTAGGCGCTCAGTAAATATTTGTTGAATGAATG 463 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 35.38 CpG sites = 27, Kimura (unadjusted) = 39.26 Transitions / transversions = 2.25 (27/12) Gap_init rate = 0.03 (4 / 136), avg. gap size = 2.00 (8 / 4) 590 28.42 6.79 1.29 chr5qtel1M 240193 240413 (759587) MIR#SINE/MIR 29 261 (1) m_b250s601i10 9913 chr5qtel1M 240193 GGTGCTGGAGAGCACACAGC-TGGGCTTGGAGGAGGGC-CTGATGCTCCC 240240 iv v- v v - i i i vvvv - vii iv MIR#SINE/MIR 29 GGCTCTGGAGC-CAGACTGCCTGGGTTCGAATCCCGGCTCTGCCACTTAC 77 chr5qtel1M 240241 TGGCTTGGTGATTCTAGACAACTAGCCCA-------TGTGCCACAATTTT 240283 i vv iii i i v vi ii ------- v i i MIR#SINE/MIR 78 TAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTC 127 chr5qtel1M 240284 CTCAACTGAAAAATGTGGATATTAACAGCACATATAACTCCCAG---TGT 240330 v v v v i i v i-- vi --- MIR#SINE/MIR 128 CTCATCTGTAAAATGGGGATAATAATAGTACCTAC--CTCATAGGGTTGT 175 chr5qtel1M 240331 TGTGAGGATCGAATGAAATAATATTTGTAAACTACTTAG--CAGTG-CTG 240377 ii iv iv vii -- - MIR#SINE/MIR 176 TGTGAGGATTAAATGAGTTAATACATGTAAAGCGCTTAGAACAGTGCCTG 225 chr5qtel1M 240378 ACACAAACTAAGTACTTAACAAATGGCAGCTATAAT 240413 i v v ii i i vi v MIR#SINE/MIR 226 GCACATAGTAAGCGCTCAATAAATGTTAGCTATTAT 261 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 34.12 CpG sites = 34, Kimura (unadjusted) = 36.45 Transitions / transversions = 1.21 (34/28) Gap_init rate = 0.04 (9 / 220), avg. gap size = 2.00 (18 / 9) 111 28.62 4.35 1.82 chr5qtel1M 240414 240896 (759104) (CTAT)n#Simple_repeat 1 495 (0) m_b250s252i8 9914 chr5qtel1M 240414 CTGTCTGTCTGTTTGTCTATGTGTTTGTGTTTCCATCCATCCATTCATCC 240463 i i i i i v i i i v v i i i ii i (CTAT)n#Simpl 1 CTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCT 50 chr5qtel1M 240464 ATCTATCTATCTATCTAACTAACTGTCTGTCTGTCTACCTATATACCTAT 240513 v v i i i i v i (CTAT)n#Simpl 51 ATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTAT 100 chr5qtel1M 240514 CTATCTATATATGTCTGTTTATTTC-ATCTATCTAACTATCCATGTCTGT 240562 v v v v v v v - v - - i i (CTAT)n#Simpl 101 CTATCTATCTATCTATCTATCTATCTATCTATCTATCTAT-C-TATCTAT 148 chr5qtel1M 240563 CTGTCTATATGTCTGTTTCTCTTTCTTTCTATCTATCTATC-CCCTCTCT 240611 i v i i i v v v -vi v (CTAT)n#Simpl 149 CTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCT 198 chr5qtel1M 240612 GTCTGTC--TCTCTCTAT-TAAC-ATCTATCAATCCCTCTAACATAACCA 240657 i i -- v - v - v iv v - v i (CTAT)n#Simpl 199 ATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATC-TATCTA 247 chr5qtel1M 240658 CACACACACATCTATC-ACCTATCAATCTATCTGCATCTA--TATCTGTC 240704 -v -i ivi - i v -- -- i (CTAT)n#Simpl 248 -TC-TATCTATCTATCTATCTATCTATCTATCT--ATCTATCTATCTATC 293 chr5qtel1M 240705 TATCCAAC-ACCTCTTTATC-ATCCATCTGTCTGTCCATCCA-CACACTC 240751 i v - i v i - i i i i i - vvv - (CTAT)n#Simpl 294 TATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCT- 342 chr5qtel1M 240752 ACCCATCTATCCGTCTATCT-T-TTTGTCTCTGTCCATCTATC-ACCTAT 240798 i i ii - - v v v i i - i (CTAT)n#Simpl 343 ATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTAT 392 chr5qtel1M 240799 CTAAC-ACCAATCTAGTTATTTAAC-ATCTATCAATGTAAC-ATCCATC- 240844 v - i v vi i v - v v v - i - (CTAT)n#Simpl 393 CTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCT 442 chr5qtel1M 240845 ATCCCATCAATCCAAC-ATCTATCTAAC-ATCCACCTAGCAATCAATGCA 240892 - i v i v - v - i i v v v vi (CTAT)n#Simpl 443 AT-CTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTA 491 chr5qtel1M 240893 TCTA 240896 (CTAT)n#Simpl 492 TCTA 495 Matrix = Unknown Transitions / transversions = 1.16 (59/51) Gap_init rate = 0.06 (28 / 482), avg. gap size = 1.07 (30 / 28) 507 22.45 2.26 6.25 chr5qtel1M 240913 241045 (758955) MIRc#SINE/MIR 16 143 (125) m_b250s601i11 9915 chr5qtel1M 240913 CAGTGGATCTAGTACTGGATCTGGAATCAGGAAAATTCATCTTCCTGGGT 240962 vvv i ii i i -------- MIRc#SINE/MIR 16 CAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA--------CCTGGGT 57 chr5qtel1M 240963 TCAAATCTAGCTTCAGACCCTTCCTAGCTGTGTGACC-TGAGCAAGTCAT 241011 i i iv vi v v v v - i i MIRc#SINE/MIR 58 TCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCAC 107 chr5qtel1M 241012 TTGTCCTGCCT--GCTTCGGTTTTCTTATCTGTAAA 241045 iv vi -- i i i i MIRc#SINE/MIR 108 TTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAA 143 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 26.04 CpG sites = 17, Kimura (unadjusted) = 27.15 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.08 (10 / 132), avg. gap size = 1.10 (11 / 10) 227 25.27 5.49 0.00 chr5qtel1M 241768 241858 (758142) L1ME3Cz_3end#LINE/L1 118 213 (784) m_b250s551i0 9916 chr5qtel1M 241768 ACAACCATA-AAAAAAATGTTCTAAATCCCTAAGAATTGGATAAATGCAG 241816 i v -i i i v vv v iv ii iv i L1ME3Cz_3end# 118 ATAAACATATGAAAAGATGCTCAACCTCACTAGTAATCAGGGAAATGCAA 167 chr5qtel1M 241817 ATTAAAGCGCT--TGAGTT-CCACCTC-CAACCATCAGATTGGCAA 241858 i ?vi-- v - ii - v L1ME3Cz_3end# 168 ATTAAAACNACAATGAGATACCATTTCACACCCATCAGATTGGCAA 213 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 31.82 CpG sites = 13, Kimura (unadjusted) = 31.82 Transitions / transversions = 1.30 (13/10) Gap_init rate = 0.04 (4 / 90), avg. gap size = 1.25 (5 / 4) 423 22.11 0.95 0.95 chr5qtel1M 242285 242389 (757611) C hAT-N1a_Mam#DNA/hAT-Tip100 (123) 239 135 m_b250s502i0 9917 chr5qtel1M 242285 GTTAATTTAACATTTATTTAATGATATACACAATTGCTACTGTAGTGCAC 242334 i i iv i i i i i iv i C hAT-N1a_Mam#D 239 GTTAATCTGACACATATTTAATGATATGCATAATCGTTATTGTGCTGCAT 190 chr5qtel1M 242335 AGTAATTAGATATAAACGGCACTGCA-TTTAAATAAATGACAGTAATTAG 242383 i ii i i v- - i vi v C hAT-N1a_Mam#D 189 GGTAATTAGGCATAAATGGTAA-GCAGTTCACGTAAATGACTGTAATTAG 141 chr5qtel1M 242384 TGTTAC 242389 i C hAT-N1a_Mam#D 140 TATTAC 135 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 24.81 CpG sites = 18, Kimura (unadjusted) = 27.59 Transitions / transversions = 3.60 (18/5) Gap_init rate = 0.02 (2 / 104), avg. gap size = 1.00 (2 / 2) 16 9.32 0.00 0.00 chr5qtel1M 244661 244683 (755317) (C)n#Simple_repeat 1 23 (0) m_b250s252i9 9918 chr5qtel1M 244661 CCCCCCCCCCCCCGCCCCCGCCC 244683 v v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCC 23 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 23 11.36 4.62 6.25 chr5qtel1M 244835 244899 (755101) (CTCCG)n#Simple_repeat 1 64 (0) m_b250s252i10 9919 chr5qtel1M 244835 CTGCGCTCCGCTGCGCTCCGCTGCGCTCCCGCT-C-CTCCGC-CGGCTCT 244881 v v v - - - - v - (CTCCG)n#Simp 1 CTCCGCTCCGCTCCGCTCCGCTCCGCT-CCGCTCCGCTCCGCTCCGCTC- 48 chr5qtel1M 244882 CTCTCCGGCCTCCCCTCC 244899 v - - v (CTCCG)n#Simp 49 CGCTCC-G-CTCCGCTCC 64 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.11 (7 / 64), avg. gap size = 1.00 (7 / 7) 19 0.00 0.00 0.00 chr5qtel1M 245367 245387 (754613) (G)n#Simple_repeat 1 21 (0) m_b250s252i11 9920 chr5qtel1M 245367 GGGGGGGGGGGGGGGGGGGGG 245387 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGG 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 270 31.51 0.00 0.00 chr5qtel1M 246185 246257 (753743) C MIR1_Amn#SINE/MIR (62) 168 96 m_b250s601i12 9921 chr5qtel1M 246185 GAAACCAATTCTGTTAGTCCTATTTTACAGATGAGGAAATTGAGGCTGAG 246234 iii i viii vi i i ?v C MIR1_Amn#SINE 168 GAGGTCAGTATCATTATCCCCATTTTACAGATGAGGAAACTGAGGCNCAG 119 chr5qtel1M 246235 TAAAAGAAGATGATTCACCCAAG 246257 vi iiv? ii i ii C MIR1_Amn#SINE 118 AGAGGTNAAGTGACTTGCCCAAG 96 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 46.87 CpG sites = 18, Kimura (unadjusted) = 46.87 Transitions / transversions = 3.60 (18/5) Gap_init rate = 0.00 (0 / 72), avg. gap size = 0.0 (0 / 0) 196 26.74 0.00 5.00 chr5qtel1M 246271 246333 (753667) C L2d_3end#LINE/L2 (2) 514 455 m_b250s601i13 9922 chr5qtel1M 246271 AATCAATTAATCAATTTCTTGATTTTATTAAGCACCTTCTCTGTGCCAGG 246320 i --- vv vv i i v v ivi C L2d_3end#LINE 514 AATCAATCAATCAA---CAAGTATTTATTGAGCGCCTACTATGTGCTCAG 468 chr5qtel1M 246321 CAGTGAGCTGAGC 246333 v v ii C L2d_3end#LINE 467 CACTGTGCTAGGC 455 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 30.71 CpG sites = 7, Kimura (unadjusted) = 33.09 Transitions / transversions = 0.78 (7/9) Gap_init rate = 0.05 (3 / 62), avg. gap size = 1.00 (3 / 3) 197 21.74 4.35 0.00 chr5qtel1M 246294 246339 (753661) C L2a_3end#LINE/L2 (20) 497 450 m_b250s601i14 9922 chr5qtel1M 246294 TTTATTAAGCACCTTCTCTGTGCCAGGCAGTGAGCTGAGCA--GGGGA 246339 i i v v v vv ii i-- C L2a_3end#LINE 497 TTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGCGCTGGGGA 450 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 20.37 CpG sites = 5, Kimura (unadjusted) = 25.86 Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.02 (1 / 45), avg. gap size = 2.00 (2 / 1) 354 31.17 2.52 5.16 chr5qtel1M 246816 246974 (753026) C MIRc#SINE/MIR (77) 191 37 m_b250s601i15 9923 chr5qtel1M 246816 CTGATGACATCTTTGTGAGATCAATTGGAAAGTTGGAGCATCAGGCCCAT 246865 v ii v ii i viiiv iv v -- vi i vv C MIRc#SINE/MIR 191 CTCACAACAACCCTGTGAGGTAGGCAGGGCAGGT--ATTATTATCCCCAT 144 chr5qtel1M 246866 TTCCCAGAC-ATGAAACTGAGACTCAGCAGAGGTTAA-TGGCTTGTCCAT 246913 iv i- v i - - i i v C MIRc#SINE/MIR 143 TTTACAGATGAGGAAACTGAGGCTCAG-AGAGGTTAAGTGACTTGCCCAA 95 chr5qtel1M 246914 GGTCACCCAACTGGTCAGCTG--GACCTGAAATTTGGTCATCTATTTCCA 246961 v i i v iv -- v i ii i i i-- i i vv -- C MIRc#SINE/MIR 94 GGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGA--ACCCAGGTC-- 49 chr5qtel1M 246962 TTTCCTGCCTTCA 246974 - v i C MIRc#SINE/MIR 48 -TTCCTGACTCCA 37 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 39.26 CpG sites = 28, Kimura (unadjusted) = 41.57 Transitions / transversions = 1.47 (28/19) Gap_init rate = 0.07 (11 / 158), avg. gap size = 1.09 (12 / 11) 292 29.39 3.76 5.34 chr5qtel1M 246861 246993 (753007) C MIR3#SINE/MIR (63) 145 15 m_b250s601i16 9923 chr5qtel1M 246861 CCCATTTCCCAGAC-ATGAAACTGAGACTCAGCAGAGGTTAA-TGGCTTG 246908 i iv i- v i i - v - i C MIR3#SINE/MIR 145 CTCATTTTACAGATGAGGAAACTGAGGCCCAG-AGAGGTGAAGTGACTTG 97 chr5qtel1M 246909 TCCATGGTCACCCAACTGGTCAGCTG--GACCTGAAATTTGGTCATCTAT 246956 i v v i ?i i iv -- v i ii i v i-- i i - C MIR3#SINE/MIR 96 CCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGA--ACCCA- 50 chr5qtel1M 246957 TTCCATTTCCTGCCT-TCACTTTGTGCTGCCCCTGCTC 246993 ---vi i v -i v ii vi i C MIR3#SINE/MIR 49 ---GGTCTCCTGACTCCCAGTCCGTGCTCTCTCTGCTC 15 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 36.81 CpG sites = 25, Kimura (unadjusted) = 39.59 Transitions / transversions = 2.08 (25/12) Gap_init rate = 0.08 (11 / 132), avg. gap size = 1.09 (12 / 11) 252 22.86 2.78 2.78 chr5qtel1M 247588 247659 (752341) EuthAT-N1#DNA/hAT-Tip100 141 212 (123) m_b250s502i1 9924 chr5qtel1M 247588 CTCCTTCTACAA-GTGGAAACCATGGAGTTTGGC-CTTGGTTAGCAAGAA 247635 vi i- i v iv i i - i i EuthAT-N1#DNA 141 CTCCTTCAGCAGCGTAGAAACAACTGAGCTTAGCACCTAGTTAGCAAGAA 190 chr5qtel1M 247636 GAAAATTAGCTATAAGAGGAAACT 247659 v-- i v v i EuthAT-N1#DNA 191 T--AATTAGTTAAAATAGGAAGCT 212 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 27.92 CpG sites = 10, Kimura (unadjusted) = 27.92 Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.06 (4 / 71), avg. gap size = 1.00 (4 / 4) 184 22.50 2.50 0.00 chr5qtel1M 248120 248159 (751841) L2d2_3end#LINE/L2 422 462 (93) m_b250s601i17 9925 chr5qtel1M 248120 TTGGCCTTCTAA-TGGATTATAAGCTCCTTGAGAGGAGGGA 248159 v iii i - i i i v L2d2_3end#LIN 422 TTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGA 462 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 28.18 CpG sites = 7, Kimura (unadjusted) = 28.18 Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1) 34 19.18 0.00 0.00 chr5qtel1M 250237 250301 (749699) (T)n#Simple_repeat 1 65 (0) m_b250s252i12 9926 chr5qtel1M 250237 TTTTTTTTTTGTTTGTTTGTTTTGTTTTTTTGTGGTTTCTTTTTCTTTCT 250286 v v v v v vv i i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr5qtel1M 250287 TTCTTTTTTTTTTTT 250301 i (T)n#Simple_r 51 TTTTTTTTTTTTTTT 65 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0) 754 30.45 8.74 3.67 chr5qtel1M 250634 251308 (748692) C L1MA8_3end#LINE/L1 (327) 711 4 m_b250s551i1 9927 chr5qtel1M 250634 CTCTTTG--TCAAAGAAATCCACTTCCATCAGATT--ACATCTTCATAAG 250679 i -- v v iv v ii- i -- v vvi i C L1MA8_3end#LI 711 CTCTCTGCTTCTATGAGTTCGACTTTT-TTAGATTCCACATATAAGTGAG 663 chr5qtel1M 250680 ATCATTGTTGACGATATAATGATCTCTTGGTTCT--GCTCATTTCACTTA 250727 -----i i -- vi i iv v i-- i C L1MA8_3end#LI 662 ATCAT-----GCGGTAT--TTGTCTTTCTGTGCCTGGCTTATTTCACTTA 620 chr5qtel1M 250728 GCATCAGTTCGTAATTTTCCAAGCTTCTCTGTATT----CATCTTGTTGG 250773 i - i -----i ii i i iv ii i ---- vv viiv C L1MA8_3end#LI 619 ACAT-AAT-----GTCCTCCAGGTTCATCCATGTTGTCGCAAATGACAGG 576 chr5qtel1M 250774 -------TCGTTTTTACAGAACAATAAT-TTCCATAACATTCATATACCA 250815 ------- v vi vvv i - viii vi C L1MA8_3end#LI 575 ATTTCCTTCTTTTTTAAGGCTGAATAGTATTCCATTGTGTATATATACCA 526 chr5qtel1M 250816 CAATTTGCCCAAC--TTTCCCCATTGATGGGCAC---GGCCGTTTCCAGC 250860 v viii v -- ivi i i --- ii v vv C L1MA8_3end#LI 525 CATTTTCTTTATCCATTCATCCGTTGATGGACACTTAGGTTGATTCCATA 476 chr5qtel1M 250861 TTCTA-CCACTACAAACAGGGCTGCCACAAACATTT---TGCACATACTG 250906 ii i- i i iii i iv v ii vv--- v --- C L1MA8_3end#LI 475 TCTTGGCTATTGTGAATAATGCTGCAATGAACATGGGAGTGCAGATA--- 429 chr5qtel1M 250907 GTCCCTT-----TCCTTCTTTTAGATCTCCTTGGGGTATAAGCCCAGTAG 250951 - i ----- v vv i -- i v i vi C L1MA8_3end#LI 428 -TCTCTTCGACATACTGATTTCA--TTTCCTTTGGATATATACCCAGTAG 382 chr5qtel1M 250952 AAACACTGCTGGATCAAAGGGTA-TGCAAGCTTGATAACTTTTGGGCATA 251000 viiv i v v - v v vi -- i v iviv C L1MA8_3end#LI 381 TGGGATTGCTGGATCATATGGTAGTTCTATTTT--TAATTTTTTGAGGAA 334 chr5qtel1M 251001 ATTCCAGATTGCTCTCCAGAATGG-TGGATTCGTTCACAGCTCCACCAAC 251049 vi v i i i v - v i vi i vii C L1MA8_3end#LI 333 CCTCCATACTGTTTTCCATAATGGCTGTACTAATTTACATTCCCACCAAC 284 chr5qtel1M 251050 AATGTATCAGGGGT------TTTCCCCATCC-CTCCAA-ACC----ATCT 251087 i iiv v ------ i v - v - i---- C L1MA8_3end#LI 283 AGTGTGCAAGGGTTCCCTTTTCTCCACATCCTCGCCAACACTTGTTATCT 234 chr5qtel1M 251088 TT--TTTTCCTGTATCTTAGCCAATCTGACAGGTGT-ATGTGGTAT-TCA 251133 -- i ii - vv v i - v i - C L1MA8_3end#LI 233 TTCGTCTTTTTG-ATAATAGCCATTCTAACAGGTGTGAGGTGATATCTCA 185 chr5qtel1M 251134 GAGTTGTCTTAATTTGCATTT-CTTGATTAATAATGATTTGGGAACACTC 251182 vv v i - i v v i v -v i i i C L1MA8_3end#LI 184 TTGTGGTTTTAATTTGCATTTCCCTGATGATTAGTGATGT-TGAGCATTT 136 chr5qtel1M 251183 TTTCATATGAGTGGTAATGATTTCAATTTCATCATCTGAAAATTGTCTGT 251232 ivv v iiiv vv v v v i i v i C L1MA8_3end#LI 135 TTTCATATACCTGTTGGCCATTTGTATGTCTTCTTTTGAGAAATGTCTAT 86 chr5qtel1M 251233 TCATACCCTTTGACCATTTATCAATTGAGAATGGCTTGTTTCTAAATTA- 251281 vii v v ? i i -- vii iivvii - C L1MA8_3end#LI 85 TCAGGTCCTTTGCCCATTTTTNAATCGGG--TTATTTGTTTTCTTGCTAT 38 chr5qtel1M 251282 -GAGTC-----AGCTTC-TATATATTTTGGAAAT 251308 - i----- i i - v C L1MA8_3end#LI 37 TGAGTTGTTTGAGTTCCTTATATATTTTGGATAT 4 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 39.68 CpG sites = 111, Kimura (unadjusted) = 40.21 Transitions / transversions = 1.28 (111/87) Gap_init rate = 0.08 (51 / 674), avg. gap size = 1.67 (85 / 51) 1232 27.77 7.68 1.42 chr5qtel1M 250710 251308 (748692) C L1ME4c_3end#LINE/L1 (191) 639 4 m_b250s551i2 9927 chr5qtel1M 250710 TTCTGCTCATTTCACTTAGCATCAGTTCGTAA---TTTTCCAAGCTTCTC 250756 iv i i vv i --- v i v v C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATAAACATTTTCCATGTTGCTA 590 chr5qtel1M 250757 TGTATTCATCTTGTTGGTCGTTTTTA----CAGAACAATAATTTCCATAA 250802 ii v v v iv vi i ---- v v i -- vi C L1ME4c_3end#L 589 CATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATA--TTCCATCG 542 chr5qtel1M 250803 CATTCATATACCACAATTTGCCCAAC--TTTCCCCATTGATGGGCAC--- 250847 vi ?v i i i ii -- i i v i i--- C L1ME4c_3end#L 541 AGTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTA 492 chr5qtel1M 250848 GGCCGTTTCCAGCTTCT-ACCACTACAAACAGGGCTGCCACAAACATTTT 250896 ii ii i -i i i i i iv v ii i C L1ME4c_3end#L 491 GGTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTT 442 chr5qtel1M 250897 -GCACATACTGGTCCCTTTCCTTCTTTTAGATC---TCCTTGGGGTATAA 250942 - ii iv -- ii ii i--- i i v v C L1ME4c_3end#L 441 CGTGCATATAG--CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAAT 394 chr5qtel1M 250943 GCCCAGTAGAAACACTGCTGGATCAAAGGGTATGCA-AGCTTGATAACTT 250991 v v viiv i i i v - vi v ii i C L1ME4c_3end#L 393 TCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTC 344 chr5qtel1M 250992 TTGG-GCATAATTCCAGATTGCTCTCCAGAATGGTGG-ATTCGTTCACAG 251039 i-i i v v i i i v v - iivi i ? C L1ME4c_3end#L 343 TTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACAN 294 chr5qtel1M 251040 CTCCACCAACAATGTATCAGGG-----GTTTTCCC-CATCC-CTCCAA-- 251080 iv i v ? ----- iv - ? - v i-- C L1ME4c_3end#L 293 TGCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGCA 244 chr5qtel1M 251081 ------ACCATCTTTTTTTCCTGTATCTTAGCCAATCTGACAGGTGTATG 251124 ------ ii vv -- iv i v i i i i i vi C L1ME4c_3end#L 243 TTGGGTATTATCAATTTTT--TAAATTTTTGCTAATTTAATAGGCGTAAA 196 chr5qtel1M 251125 -TGGTAT-TCAGAGTTGTCTTAATTTGCATTTC-TTGATTAATAATGA-- 251169 - - vv ii - v ii -- C L1ME4c_3end#L 195 ATGGTATCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACTAGCGAGG 146 chr5qtel1M 251170 TTTGGGAACACTCTTTCATATGAGTGGTAATGATTTCAATTTCATCATCT 251219 --- i i i i vv v v iv ? vv v v ? C L1ME4c_3end#L 145 TT---GAACATTTTTCCATGTGTTTGTTTACTANTTGTATTTCCTCTTNT 99 chr5qtel1M 251220 GAAAATTGTCTGTTCATACCCTTTGACCATTTATCAATTGAG-----AAT 251264 vi ii v v i -----i C L1ME4c_3end#L 98 GTGAATTGTCTGTTCATGTCCTTTGCCCATTTATCTATTGGGGTCTTGAT 49 chr5qtel1M 251265 GGCTTGTTTCTAAATTAGAGTCAGCT-TCTATATATTTTGGAAAT 251308 ?vi vi v v v i v - i ? v?i v C L1ME4c_3end#L 48 NTTTTTCTTATCAATTTGAATGAGCTCTTTATATANTANAGATAT 4 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 35.03 CpG sites = 98, Kimura (unadjusted) = 36.42 Transitions / transversions = 1.48 (98/66) Gap_init rate = 0.05 (29 / 598), avg. gap size = 1.90 (55 / 29) 1478 28.22 8.59 2.41 chr5qtel1M 251175 252583 (747417) C L1M5_orf2#LINE/L1 (7) 3287 1794 m_b250s551i3 9927 chr5qtel1M 251175 GAACACTCTTTCATATGAGTGGTAATGATTTCAATTTCATCATCTGAAAA 251224 i iii i vv iv iiiv v? v v v i vi C L1M5_orf2#LIN 3287 GAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTTTTGTGAA 3238 chr5qtel1M 251225 TTGTCTGTTCATACCCTTTGACCATTTATCAATTGAGAATGGCTTGTTTC 251274 v vii i v v ?v i -- v i i i C L1M5_orf2#LIN 3237 GTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGG--TTGTTTGTCTT 3190 chr5qtel1M 251275 TAAATTA--GAGTC-----AGCT-TCTATATATTTTGGAAATGAGGCCTT 251316 vv? -- ? i----- i - i i v i v C L1M5_orf2#LIN 3189 TTTNTTATTGANTTGTAGGAGTTCTTTATATATTCTGGATACGAGTCCTT 3140 chr5qtel1M 251317 TAT-AGA---ACCTTTAACGGAAGATGTTTTCCCAGTTTGTTGCTTCCCT 251362 i - --- iv ? vi i- v v i ? i v v C L1M5_orf2#LIN 3139 TGTCAGATATATGTNTTGCA-AATATTTTCTCCCANTCTGTGGCTTGCCT 3091 chr5qtel1M 251363 TCTAATCTTGTTTACATTAGTTTTGTTTGTACAGAAGCTTTTAATTT-GA 251411 i v i v v iv ivi vvv? vi i - C L1M5_orf2#LIN 3090 TTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTTTAATTTTGA 3041 chr5qtel1M 251412 TGAA---CAA------AATTTTCTATTTTGTGATTAATAATGGTCTCTA- 251451 ? --- ------ i v i i ?i --- v i i i- C L1M5_orf2#LIN 3040 TGNAGTCCAATTTATCAATTTTTTCTTTTATGGTTNGT---GCTTTTTGT 2994 chr5qtel1M 251452 GTTCTCTTTATCACAACTTTCTTTCCTCTTCCACAAGTCTGAGAGTTAAA 251501 i v -- v v i - v v?i - i vvii v -- C L1M5_orf2#LIN 2993 GTCCTGTTTA--AGAAATCT-TTGCCTANCCCA-AGGTCACGAAGATA-- 2950 chr5qtel1M 251502 CTATCCTATGTTT----CTAA----TTTAT--TTATAACTGTTC--TTTA 251539 i v ---- i---- -- v ? v v-- C L1M5_orf2#LIN 2949 TTCTCCTATGTTTTCTTCTAGAAGTTTTATAGTTTTANCTTTTACATTTA 2900 chr5qtel1M 251540 TGCCTAAACATGGACCCATTTTGATCTTTATCTGGTATACGGTGTTAAGT 251589 v i -----v i i ? vi vvv i v i i v i C L1M5_orf2#LIN 2899 GGTCTA-----TGATCCATCTNGAATTAATTTTTGTGTATGGTGTGAGGT 2855 chr5qtel1M 251590 --GGGTCCATGCCAATTT----CCATACTAATTTCCAGTTATCCCAGCAG 251633 -- v v?iiv ---- ivi v i i i v C L1M5_orf2#LIN 2854 AGGGGTCGAGNTTCATTTTTTTCCATATGGATATCCAATTGTTCCAGCAC 2805 chr5qtel1M 251634 T-TTTGTCAAATAATGAATTCTTATCCCAA-AAAGTGAGACTTTGGG--- 251678 i- ii v ivvv i vi v-i v --- ? v--- C L1M5_orf2#LIN 2804 CATTTGTTGAAAAGACTATCCTTTCCCCACTGAATTG---CNTTGGCACC 2758 chr5qtel1M 251679 TTTGTCAAACACTAAATTGCAAGTTGATAT-----TCTATCTTGTGAACC 251723 v ii ? v? v vv - i ----- - v i i C L1M5_orf2#LIN 2757 TTTGTCAAAAATCAANTGNCCATAT-ATGTGTGGGTCTAT-TTCTGGACT 2710 chr5qtel1M 251724 ----AACCTGTTCCAT-GATCAACTAATCTATTTTTAGCCCAATACCAAA 251768 ---- vi - v i vi ii vv v C L1M5_orf2#LIN 2709 CTCTATTCTGTTCCATTGATCTATTTGTCTATCCTTACGCCAATACCACA 2660 chr5qtel1M 251769 TGGTTTTGGTGACTGCTGCTTTATAATATAGTTTT-AGGTCAGGTAAACC 251817 iv i i v iv - i - ?i ? ivvi C L1M5_orf2#LIN 2659 CTGTCTTGATTACTGTAGCTTTATAATA-AGTCTTGANATCNGGTAGTGT 2611 chr5qtel1M 251818 A---CCTTCA--TTTGATTTTTTTCATTAA---TTTTTTGA-GATTCTTG 251858 --- i -- v i i iv i --- v i-v ? C L1M5_orf2#LIN 2610 AAGTCCTCCAACTTTGTTCTTCTTTTTCAAGATTGTTTTGGCTATTCTNG 2561 chr5qtel1M 251859 A-CCTTTATTATTCCATA-GAATTTTG--------TTGTTATTTTTTTCT 251898 i- iivv -i i-------- i v i v v C L1M5_orf2#LIN 2560 GTCCTTTGCATTTCCATATAAATTTTAGAATCAGCTTGTCAATTTCTACA 2511 chr5qtel1M 251899 AGATCTTAAAATTTTTTAAG--TCTGATTGGTATAGCAT-AAATAAAT-G 251944 i ----- ii vi ii -- i v v -i vv - C L1M5_orf2#LIN 2510 AAA-----AAACCTGCTGGGATTTTGATTGGGATTGCATTGAATCTATAG 2466 chr5qtel1M 251945 ATTAATTTAGG-AGTATTGTCATCTTTATTATATCT-GCCGACCTATCCA 251992 i i - v v ? iv iv- i vv v C L1M5_orf2#LIN 2465 ATCAATTTGGGGAGAATTGACATCTTNACAATATTGAGTCTTCCAATCCA 2416 chr5qtel1M 251993 GGAAT-TG--ATATTTTTCCAATTGTTTAAGT-TGATTTATTTTGT---G 252035 v i- -- i i v i i - vv v v ---i C L1M5_orf2#LIN 2415 TGAACATGGTATATCTCTCCATTTATTTAGGTCTTCTTTAATTTCTCTCA 2366 chr5qtel1M 252036 GAAAGTTTTTGTAATTTAGCTCA---TATAATTCCTGACTTTCCTTTGG- 252081 v vv i --- --- ? iv i vviv ?i v- C L1M5_orf2#LIN 2365 GCAATGTTTTGTAGTTT---TCAGTGTANAGGTCTTGCACATNTTTTGTT 2319 chr5qtel1M 252082 AGATAGATTCCCAAATATTTTATGCTGTCGACAGTTATTCTGAATGGAAT 252131 vv i i ? i v ivivv i v i v C L1M5_orf2#LIN 2318 AGATTTATTCCTAAGTATTTNATGTTTTTTGATGCTATTGTAAATGGTAT 2269 chr5qtel1M 252132 T--TCTTTGTATCTC---TTGCCGTTGGATTTTGTT--TGATGTATAAAA 252174 -- i ?iv i --- v vi --- -- ii i i C L1M5_orf2#LIN 2268 TGTTTTTNAAATTTCATTTTCCAATTG---TTTGTTGCTAGTATATAGAA 2222 chr5qtel1M 252175 ATGCTGAGGATTTATGGGGATTTATTTTAAAACCTGCAACTTTGCTAAAG 252224 i vivv v viv v ii iv v ? i i v C L1M5_orf2#LIN 2221 ATACAATTGATTTTTGTATATTGACCTTGTATCCNGCGACCTTGCTAAAT 2172 chr5qtel1M 252225 TTATGGATTATTTCTAG------CTTTTAAGAAC--TTAGG---TTCTAA 252263 i ivv v ------? vv vi-- ? --- v C L1M5_orf2#LIN 2171 TCACTTATTAGTTCTAGTAGTTTNTTTGTAGATTCTTTNGGATTTTCTAC 2122 chr5qtel1M 252264 --ATACCATCATGTCATCTGCAAA-GAGGA-AGTTTGGTTTCC-CCACGC 252308 -- ? v i -i ? - vi i- viv C L1M5_orf2#LIN 2121 GTANACAATCATGTCATCTGCGAATAANGACAGTTTTATTTCTTCCTTTC 2072 chr5qtel1M 252309 CTATTCTGATTCCTTTAACTT--TTCACT---CTTATTGCCGAGGCTAAT 252353 v ii v v v i -- iv --- vvv iv C L1M5_orf2#LIN 2071 CAATCTTTATGCCTTTTATTTCTTTTTCTTGCCTTATTGCACTGGCTAGG 2022 chr5qtel1M 252354 GTTTCTAATACAATATTGAATAGTAATGGTGATAGTGGGCAACCTTGCTT 252403 iii i i i v i ? i i v ii C L1M5_orf2#LIN 2021 ACCTCCAGTACAATGTTGAATAGAAGTGGTGANAGCGGACATCCTTGTCT 1972 chr5qtel1M 252404 CACTCCAGATCTTACTGGGAAAGATTCCAGTTTTTCCCCATTGCATATGA 252453 iii v vv v? i ? v ivi C L1M5_orf2#LIN 1971 TGTTCCCGATCTTAGGGGGAAAGCNTTCAGTNTTTCACCATTAAGTATGA 1922 chr5qtel1M 252454 TGCTTACTGATGGTTTTAAATATATGCTCCTGACTATTTTAAGAAAAAGT 252503 i ?i vv vvi v i i v ii vv i i ivvi C L1M5_orf2#LIN 1921 TGTTNGCTGTAGGTTTTTCGTAGATGCCCTTTATCAGGTTGAGGAAGTTC 1872 chr5qtel1M 252504 CCATTTATTCCTACACTCTCAAGTGTTTTTATTAGGAATGGATGTTGGAT 252553 v i vvi viii v i v i i C L1M5_orf2#LIN 1871 CCTTCTATTCCTAGTTTGCTGAGAGTTTTTATCATGAATGGGTGTTGAAT 1822 chr5qtel1M 252554 TTTATCAAATGCTTTTTCTGCATGGCTATT 252583 i -- C L1M5_orf2#LIN 1821 TTTGTCAAATGCTTTTTCTGCAT--CTATT 1794 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 36.30 CpG sites = 201, Kimura (unadjusted) = 37.13 Transitions / transversions = 1.07 (201/187) Gap_init rate = 0.06 (88 / 1408), avg. gap size = 1.78 (157 / 88) 17 16.14 3.08 8.06 chr5qtel1M 252614 252678 (747322) (GGAA)n#Simple_repeat 1 62 (0) m_b250s252i13 9928 chr5qtel1M 252614 GGAGGGAATGGAAAGAGAGG-AGAAAGGAATACACTGAGGGAAGG-AGGA 252661 i - i - - i -iv vv i - (GGAA)n#Simpl 1 GGAAGGAA-GGAAGGA-AGGAAGGAAGGAA-GGAAGGAAGGAAGGAAGGA 47 chr5qtel1M 252662 AGGAAGGGAAAGGAAGG 252678 - - (GGAA)n#Simpl 48 AGGAA-GG-AAGGAAGG 62 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.11 (7 / 64), avg. gap size = 1.00 (7 / 7) 12 7.22 6.45 3.12 chr5qtel1M 252799 252829 (747171) (AAGGAA)n#Simple_repeat 1 32 (0) m_b250s252i14 9929 chr5qtel1M 252799 AAGGAAATGG--GAGGAAAAGGGAAAAGGAAAA 252829 v --i - (AAGGAA)n#Sim 1 AAGGAAAAGGAAAAGGAAAA-GGAAAAGGAAAA 32 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.50 (3 / 2) 290 32.60 16.02 0.00 chr5qtel1M 253349 253529 (746471) L3#LINE/CR1 3792 4001 (98) m_b250s601i18 9930 chr5qtel1M 253349 GTCCTTTAGCAGAGGGAATGGGCTTCTTCTG-GTCACTC----------- 253386 v v i v v i i v - vi ----------- L3#LINE/CR1 3792 GTCATGTGGAAGAGGGATTAGACTTATTCTGTGTGGCTCCAGAGGGCAGA 3841 chr5qtel1M 253387 ---AGGAGCAATGGGAGGACATTTCAGAGGGGCCAATTGAGACTAGATGT 253433 --- v v vi v i i vi vv i vi i L3#LINE/CR1 3842 ACTAGGACCAATGGGTGGAAGTTACAGGGAGGCAGATTTCGGCTCAATAT 3891 chr5qtel1M 253434 CAGAAAGAA---GGTAACAGTTTAATCTAGTTAGGTATGAAAGGGGTTAC 253480 v i ---vv i ivi v ivii iiv i v i i L3#LINE/CR1 3892 AAGGAAGAACTTTCTAACAATCAGAGCTGTCCAAAAATGGAATGGGCTGC 3941 chr5qtel1M 253481 TTGGAGATGAGGTAGGTTC-----------ATGCCTACATGCAGAGGCTG 253519 i v ? v vi ii i ----------- v iv v v L3#LINE/CR1 3942 CTCGNGAGGTAGTGAGCTCCCCGTCACTGGAGGTGTTCAAGCAGAGGCTG 3991 chr5qtel1M 253520 GATGGCCACT 253529 i L3#LINE/CR1 3992 GATGACCACT 4001 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 43.83 CpG sites = 30, Kimura (unadjusted) = 43.83 Transitions / transversions = 1.03 (30/29) Gap_init rate = 0.03 (5 / 180), avg. gap size = 5.80 (29 / 5) 14 23.55 2.22 0.00 chr5qtel1M 253753 253797 (746203) (TTTTCTT)n#Simple_repeat 1 46 (0) m_b250s252i15 9931 chr5qtel1M 253753 TTTTCTTTTGT-TTTCTGCTGGGTACTTTTTGCTTTATTCTTTTTT 253797 v - i v vvv v v v (TTTTCTT)n#Si 1 TTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTT 46 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 481 23.66 0.00 8.70 chr5qtel1M 253811 253935 (746065) C MIRb#SINE/MIR (150) 118 4 m_b250s601i19 9932 chr5qtel1M 253811 GGGGTTAAGTAACTTACCCAGGGTCACACAACTAGGAAATGTTAAGTGTC 253860 i i i i ------- v C MIRb#SINE/MIR 118 GAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGC 76 chr5qtel1M 253861 TGGGGCTAAATTTGAACTCAGGTCCTCCGGATTTCAGAGTTGGTGCTCTA 253910 v i v vii i i ivi v i i i iiv v C MIRb#SINE/MIR 75 AGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTT 26 chr5qtel1M 253911 TCCACTACACCAACTAGCTGTCCCT 253935 i ---v i C MIRb#SINE/MIR 25 TCCACTGCACCA---CGCTGCCCCT 4 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 27.81 CpG sites = 18, Kimura (unadjusted) = 29.08 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.08 (10 / 124), avg. gap size = 1.00 (10 / 10) 63 0.00 0.00 0.00 chr5qtel1M 254268 254321 (745679) (AG)n#Simple_repeat 1 54 (0) c_b250s251i1 9933 chr5qtel1M 254268 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 254317 (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr5qtel1M 254318 AGAG 254321 (AG)n#Simple_ 51 AGAG 54 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 16 26.13 1.59 3.23 chr5qtel1M 255076 255138 (744862) (TTTA)n#Simple_repeat 1 62 (0) m_b250s252i16 9934 chr5qtel1M 255076 TTCATTTATTTATTTATTTATTT-TAAATGAAATGGCCTTTATTTCTTTT 255124 i - vv -vv -viv v v (TTTA)n#Simpl 1 TTTATTTATTTATTTATTTATTTATTTAT-TTAT-TTATTTATTTATTTA 48 chr5qtel1M 255125 TTTTTTTTTTTCTT 255138 v v v (TTTA)n#Simpl 49 TTTATTTATTTATT 62 Matrix = Unknown Transitions / transversions = 0.18 (2/11) Gap_init rate = 0.05 (3 / 62), avg. gap size = 1.00 (3 / 3) 17 15.30 0.00 0.00 chr5qtel1M 255113 255141 (744859) (T)n#Simple_repeat 1 29 (0) m_b250s252i17 9935 chr5qtel1M 255113 TTTATTTCTTTTTTTTTTTTTTTCTTGTT 255141 v i i v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 443 25.19 0.00 8.62 chr5qtel1M 255151 255276 (744724) C MIRb#SINE/MIR (150) 118 3 m_b250s601i20 9936 chr5qtel1M 255151 GGGGTTAAGTGACTTGCCCACAGTCACACAGTGAGGAAGTGTTAAGTGTC 255200 i i vi iv ------- v C MIRb#SINE/MIR 118 GAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGC 76 chr5qtel1M 255201 TGAGGCCATATTTGAACTCAGATCCTCCTGACTTCAGGGTTGGTACTCTA 255250 v v viv i i i ivi i ii iiv i v C MIRb#SINE/MIR 75 AGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTT 26 chr5qtel1M 255251 TCCACTGCGCCATCTAGCTGCCCATC 255276 i i--- v C MIRb#SINE/MIR 25 TCCACTGCACCAC---GCTGCCCCTC 3 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 28.69 CpG sites = 18, Kimura (unadjusted) = 31.23 Transitions / transversions = 1.64 (18/11) Gap_init rate = 0.08 (10 / 125), avg. gap size = 1.00 (10 / 10) 461 23.92 0.00 6.67 chr5qtel1M 255151 255262 (744738) C MIRc#SINE/MIR (153) 115 11 m_b250s601i21 9936 chr5qtel1M 255151 GGGGTTAAGTGACTTGCCCACAGTCACACAGTGAGGAAGTGTTAAGTGTC 255200 i vi iv ------- v C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGC 73 chr5qtel1M 255201 TGAGGCCATATTTGAACTCAGATCCTCCTGACTTCAGGGTTGGTACTCTA 255250 v v viv i i i i i i i viii i v C MIRc#SINE/MIR 72 AGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTT 23 chr5qtel1M 255251 TCCACTGCGCCA 255262 i C MIRc#SINE/MIR 22 TCCACTGCACCA 11 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 28.07 CpG sites = 16, Kimura (unadjusted) = 29.46 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.06 (7 / 111), avg. gap size = 1.00 (7 / 7) 270 34.34 8.12 0.95 chr5qtel1M 255565 255761 (744239) C MIRc#SINE/MIR (56) 212 2 m_b250s601i22 9937 chr5qtel1M 255565 CACACATTATCTTACCTACTCTCCTCAGTAATTCTGTGATACATACATGG 255614 i i ii iv ii v ii ii vii vi v C MIRc#SINE/MIR 212 CATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGG 163 chr5qtel1M 255615 T---TATTATTATCTC--TTTTACTAGATGGTGAAAATGATGCCCAAAGA 255659 i--- i -- - iv v v i i C MIRc#SINE/MIR 162 CAGGTATTATTATCCCCATTTTAC-AGATGAGGAAACTGAGGCTCAGAGA 114 chr5qtel1M 255660 --TGAAATATTTTGTCCTTTATTTCACAATTACT--GTCATAGA-CTGGA 255704 -- v i ivi i vvvi iv ii v -- vii - i i C MIRc#SINE/MIR 113 GGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGG 64 chr5qtel1M 255705 AC-CAAATATAGATCATCTTTGCTTAGCATCCAA----CTTTCTACCTAC 255749 - i ivi i v i vi ivivi i---- i - i C MIRc#SINE/MIR 63 ACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCA-CTGC 15 chr5qtel1M 255750 A-CAAACTGTTTC 255761 - v ii C MIRc#SINE/MIR 14 ACCACACTGCCTC 2 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 46.98 CpG sites = 45, Kimura (unadjusted) = 49.10 Transitions / transversions = 2.05 (45/22) Gap_init rate = 0.05 (10 / 196), avg. gap size = 1.80 (18 / 10) 195 18.97 15.52 0.00 chr5qtel1M 255905 255962 (744038) L2c_3end#LINE/L2 410 476 (2) m_b250s601i23 9938 chr5qtel1M 255905 ATTGAACTTT-TATTC--AGTGCCTGGTACATAG------CTTAATAAAT 255945 v v - i -- i i ------ i L2c_3end#LINE 410 ATTCATCTTTGTATCCCCAGCGCCTGGCACATAGTAGGCGCTCAATAAAT 459 chr5qtel1M 255946 GTTTATCGGCTGACTGA 255962 i i iv v L2c_3end#LINE 460 GTTTGTTGAATGAATGA 476 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 20.09 CpG sites = 7, Kimura (unadjusted) = 22.29 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.05 (3 / 57), avg. gap size = 3.00 (9 / 3) 203 18.18 13.64 0.00 chr5qtel1M 255919 255962 (744038) L2a_3end#LINE/L2 466 515 (2) m_b250s601i24 9938 chr5qtel1M 255919 CAGTGCCTGGTACATAG------CTTAATAAATGTTTATCGGCTGACTGA 255962 i ------ i i i i iv v L2a_3end#LINE 466 CAGTGCCTGGCACATAGTAGGCGCTCAATAAATATTTGTTGAATGAATGA 515 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 21.53 CpG sites = 6, Kimura (unadjusted) = 21.53 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.02 (1 / 43), avg. gap size = 6.00 (6 / 1) 23 24.67 0.00 1.72 chr5qtel1M 256840 256898 (743102) (TA)n#Simple_repeat 1 58 (0) m_b250s252i18 9939 chr5qtel1M 256840 TATATTCAAATATATTTATATATATATATTCCTATATATTTGAAGAGTAT 256889 vi v v viv v iv v - (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATA-TAT 49 chr5qtel1M 256890 ATATTTATA 256898 v (TA)n#Simple_ 50 ATATATATA 58 Matrix = Unknown Transitions / transversions = 0.33 (3/9) Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1) 27 8.58 0.00 0.00 chr5qtel1M 258236 258272 (741728) (T)n#Simple_repeat 1 37 (0) m_b250s252i19 9940 chr5qtel1M 258236 TTTTCTTTTTGTTTTTTTTTGTTTTTTTTTTTTTTTT 258272 i v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 37 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 237 21.75 1.41 2.86 chr5qtel1M 258346 258416 (741584) C DNM1r#Unknown (2117) 2545 2476 m_b250s502i2 9941 chr5qtel1M 258346 ATAGATATGTTTATGTTTACACATATATAAACACACATGTCCATGTACAC 258395 ? i v i -- v i iiiv i C DNM1r#Unknown 2545 ATANATACGTATATAT--ACACATATATACACACATACACACATATACAC 2498 chr5qtel1M 258396 ATAT-CATATACATATACATGT 258416 i -i i i i C DNM1r#Unknown 2497 ACATATATACACACATACACGT 2476 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 23.40 CpG sites = 12, Kimura (unadjusted) = 27.61 Transitions / transversions = 4.00 (12/3) Gap_init rate = 0.04 (3 / 70), avg. gap size = 1.00 (3 / 3) 16 29.21 3.45 0.00 chr5qtel1M 258417 258474 (741526) (AT)n#Simple_repeat 1 60 (0) m_b250s252i20 9942 chr5qtel1M 258417 ATATATACTTACAGA-ATATAGAGAGAGACATATATGTATATACATATTT 258465 iv i v - v v v v i i i v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr5qtel1M 258466 ACAGAT-TAT 258474 i v - (AT)n#Simple_ 51 ATATATATAT 60 Matrix = Unknown Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.04 (2 / 57), avg. gap size = 1.00 (2 / 2) 16 26.46 0.00 0.00 chr5qtel1M 258710 258747 (741253) (GT)n#Simple_repeat 1 38 (0) m_b250s252i21 9943 chr5qtel1M 258710 GTGTGTGTGTGTGCATGTATGTATTTGTATATATGTGT 258747 ii i i v i i i (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 38 Matrix = Unknown Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 17 16.14 0.00 0.00 chr5qtel1M 258949 258977 (741023) (T)n#Simple_repeat 1 29 (0) m_b250s252i22 9944 chr5qtel1M 258949 TTTTCTTTTTTTTTTTTTCTTCCTTTTTT 258977 i i ii (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 214 22.00 2.00 0.00 chr5qtel1M 258980 259029 (740971) C MIR#SINE/MIR (140) 122 72 m_b250s601i25 9945 chr5qtel1M 258980 TGAGGCA-GTTGGGGCTAAGTGACTTGCTCAGGGTTTCACAGCTAGAAAG 259028 -ivv i i i i i iv v C MIR#SINE/MIR 122 TGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAG 73 chr5qtel1M 259029 T 259029 C MIR#SINE/MIR 72 T 72 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 26.67 CpG sites = 7, Kimura (unadjusted) = 26.67 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.02 (1 / 49), avg. gap size = 1.00 (1 / 1) 230 17.50 0.00 0.00 chr5qtel1M 258990 259029 (740971) C MIRc#SINE/MIR (153) 115 76 m_b250s601i26 9945 chr5qtel1M 258990 GGGGCTAAGTGACTTGCTCAGGGTTTCACAGCTAGAAAGT 259029 i i i i iv v C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGT 76 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 20.47 CpG sites = 5, Kimura (unadjusted) = 20.47 Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 478 27.07 0.75 0.75 chr5qtel1M 260062 260195 (739805) MIR3#SINE/MIR 7 140 (68) m_b251s601i2 9946 chr5qtel1M 260062 GAGTGCCATAGCACCCAGAACCCTGGGTTTGCAGACAGAAGATCTGAGTT 260111 v vv vvv i v - ii v v v i i i MIR3#SINE/MIR 7 GAGTGGCTGAGCAGAGAGAGCAC-GGACTGGGAGTCAGGAGACCTGGGTT 55 chr5qtel1M 260112 CAAATTCTACCTCAGCCACATTCTAGTTGTGTGACTCTGGGCAAGTCATT 260161 v i i iiv v vvv ? i ii i MIR3#SINE/MIR 56 CTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACT 105 chr5qtel1M 260162 TCACCTCATT-TATCTCAGTTTCCTCAACTGTAAA 260195 vi -vii v MIR3#SINE/MIR 106 TCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAA 140 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 32.91 CpG sites = 17, Kimura (unadjusted) = 34.16 Transitions / transversions = 0.89 (17/19) Gap_init rate = 0.02 (2 / 133), avg. gap size = 1.00 (2 / 2) 586 24.26 2.21 0.00 chr5qtel1M 260078 260213 (739787) MIRc#SINE/MIR 24 162 (106) m_b251s601i3 9946 chr5qtel1M 260078 AGAACCCTGGGTTTGCAGACAG-AAGATCTGAGTTCAAATTCTACCTCAG 260126 i v ii v v - i i i i i iiv v MIRc#SINE/MIR 24 AGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTG 73 chr5qtel1M 260127 CCACATTCTAGTTGTGTGACTCTGGGCAAGTCATTTCACCTCATTTA-TC 260175 v v i ii i v vi v -i MIRc#SINE/MIR 74 CCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCC 123 chr5qtel1M 260176 TCAGTTTCCTCAACTGTAAAGCAGGGACAA-AAGGCCTG 260213 v iii i - vi MIRc#SINE/MIR 124 TCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTG 162 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 27.89 CpG sites = 21, Kimura (unadjusted) = 30.15 Transitions / transversions = 1.75 (21/12) Gap_init rate = 0.02 (3 / 135), avg. gap size = 1.00 (3 / 3) 223 33.00 5.00 0.00 chr5qtel1M 261427 261526 (738474) L2#LINE/L2 2704 2808 (274) m_b251s601i4 9947 chr5qtel1M 261427 TCTCTCACCTGGCCCATTGCCATGAGGTCCTCACTAGTCTCTCAGCCTCA 261476 i vii i v iivv v i i v i v L2#LINE/L2 2704 TCTCTCGCCTGGATTACTGCAATAGCCTCCTAACTGGTCTCCCTGCTTCC 2753 chr5qtel1M 261477 GCTCTTCTCC-----CAATCCATCGTCCCCCCAACTGCCAAAGTGAACCT 261521 i i vi ----- i i iv vv v i v i v L2#LINE/L2 2754 ACCCTTGCCCCCCTNCAGTCTATTCTCAACACAGCAGCCAGAGTGATCCT 2803 chr5qtel1M 261522 GCTAA 261526 vi L2#LINE/L2 2804 TTTAA 2808 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 42.78 CpG sites = 18, Kimura (unadjusted) = 44.58 Transitions / transversions = 1.20 (18/15) Gap_init rate = 0.01 (1 / 99), avg. gap size = 5.00 (5 / 1) 402 32.93 5.39 0.00 chr5qtel1M 262968 263134 (736866) MIR3#SINE/MIR 5 180 (28) m_b251s601i5 9948 chr5qtel1M 262968 CAGAGTGGCCAGGCTGGAAGCAAATGGCCT---CGTCTG----CCCAAGT 263010 iii v ii viv i v ---v v ---- iii MIR3#SINE/MIR 5 CAGAGTGGCTGAGCAGAGAGAGCACGGACTGGGAGTCAGGAGACCTGGGT 54 chr5qtel1M 263011 TCAAATCCAGTCTCAGATACTCACTAGCTGTGAGATCCTGGGCCAGTCCC 263060 v i v v v vi v ? v i i v v MIR3#SINE/MIR 55 TCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCAC 104 chr5qtel1M 263061 TTTACC-CTGTTTGCCTCAGCTTCCTC-TCTATAAAATAAGCAGAAGGAA 263108 i - v vv i - i i vi ivv i MIR3#SINE/MIR 105 TTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGA 154 chr5qtel1M 263109 ATGGCCAACCATCAGTATCTCTTCCA 263134 v i vii i vii ivi i MIR3#SINE/MIR 155 CTAGATGATCTCTAAGGTCCCTTCCA 180 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 43.74 CpG sites = 30, Kimura (unadjusted) = 44.84 Transitions / transversions = 1.20 (30/25) Gap_init rate = 0.02 (4 / 166), avg. gap size = 2.25 (9 / 4) 415 24.04 1.92 0.00 chr5qtel1M 263001 263104 (736896) MIR#SINE/MIR 44 149 (113) m_b251s601i6 9948 chr5qtel1M 263001 CTGCCCAAGTTCAAATCCAGTCTCAGATACTCACTAGCTGTGAGATCCTG 263050 iii i v v v vi i v i i MIR#SINE/MIR 44 CTGCCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTG 93 chr5qtel1M 263051 GGCCAGTCCCTTTACC-CTGTTTGCCTCAGCTTCCTC-TCTATAAAATAA 263098 v iv v - v v i - i ii MIR#SINE/MIR 94 GGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGG 143 chr5qtel1M 263099 GCAGAA 263104 v v MIR#SINE/MIR 144 GGATAA 149 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 27.95 CpG sites = 13, Kimura (unadjusted) = 29.30 Transitions / transversions = 1.08 (13/12) Gap_init rate = 0.02 (2 / 103), avg. gap size = 1.00 (2 / 2) 198 33.03 5.00 4.13 chr5qtel1M 264964 265083 (734917) L2c_3end#LINE/L2 354 474 (4) m_b251s601i7 9947 chr5qtel1M 264964 ACCGGTC-ATCTTGTCCACCTGAATGTCAGCTCCTTGCCCACGGGGACTG 265012 ?v -i iv iv v v vvvi i i L2c_3end#LINE 354 ACNTGTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCG 403 chr5qtel1M 265013 -GTC----CCTGCTTTGTGCCTGGGGGCTGTGCCTAGTACAGGGAAGGTG 265057 - ----i vv ii i----v v i i i vi v i L2c_3end#LINE 404 TGTCTTATTCATCTTTGTATCC----CCAGCGCCTGGCACATAGTAGGCG 449 chr5qtel1M 265058 CCTTAGAAATCCTGTATTGAACAAAT 265083 iiv v vi - i ii L2c_3end#LINE 450 CTCAATAAATGTT-TGTTGAATGAAT 474 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 40.61 CpG sites = 21, Kimura (unadjusted) = 45.30 Transitions / transversions = 1.24 (21/17) Gap_init rate = 0.07 (8 / 119), avg. gap size = 1.38 (11 / 8) 230 23.08 1.52 1.52 chr5qtel1M 265186 265251 (734749) CR1-L3A_Croc#LINE/CR1 3582 3647 (641) m_b251s551i0 9949 chr5qtel1M 265186 CTGACAAAGCACTTAGGGG-CTCAGTGGACCATCAGTTTAACATGAGCCA 265234 - v i - v i iv i v iv CR1-L3A_Croc# 3582 CTGA-AAAGGACTTGGGGGTCACGGTGGATAATCAGCTGAACATGAGCTC 3630 chr5qtel1M 265235 ACGGTGGGAGGCTCTGG 265251 v i v v v CR1-L3A_Croc# 3631 CCAGTGCGACGCTGTGG 3647 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 25.61 CpG sites = 6, Kimura (unadjusted) = 27.62 Transitions / transversions = 0.67 (6/9) Gap_init rate = 0.03 (2 / 65), avg. gap size = 1.00 (2 / 2) 257 34.74 2.52 0.83 chr5qtel1M 265812 265930 (734070) C L2c_3end#LINE/L2 (5) 473 353 m_b251s601i8 9950 chr5qtel1M 265812 TTCAGTCAGTCAACATCTGTTAAGTTCCTCCTGCGGGTCTGGCCCCAAAC 265861 v iiv i i i iv v ii v i v v iiiiv C L2c_3end#LINE 473 TTCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGG 424 chr5qtel1M 265862 CCCCCAAATATAAATACAACA--GGCCCTCCCCGCAAGGAGCTTACACTC 265909 viv - v i vi -- v v v i v C L2c_3end#LINE 423 ATAC-AAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTC 375 chr5qtel1M 265910 TGACAGGGGA-ACCAACACATA 265930 iiii i - vi ?i C L2c_3end#LINE 374 TAGTGGAGGAGACAGACANGTA 353 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 47.43 CpG sites = 24, Kimura (unadjusted) = 49.13 Transitions / transversions = 1.41 (24/17) Gap_init rate = 0.03 (3 / 118), avg. gap size = 1.33 (4 / 3) 16 13.43 0.00 2.94 chr5qtel1M 266341 266375 (733625) (ATGGGG)n#Simple_repeat 1 34 (0) m_b251s252i1 9951 chr5qtel1M 266341 ATGGGAAGGAGGGATGGGGGTGGGGATGGGGGTGG 266375 i v - i i (ATGGGG)n#Sim 1 ATGGGGATG-GGGATGGGGATGGGGATGGGGATGG 34 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 13 30.51 0.00 2.00 chr5qtel1M 267100 267150 (732850) (GAGG)n#Simple_repeat 1 50 (0) m_b251s252i2 9952 chr5qtel1M 267100 GAGAGGAGGGAGGCAGGAAAGGAGGGAGACAGAGACAGAGAATGGGAGAG 267149 - v i i iv i vi iiv i (GAGG)n#Simpl 1 GAG-GGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGG 49 chr5qtel1M 267150 A 267150 (GAGG)n#Simpl 50 A 50 Matrix = Unknown Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.02 (1 / 50), avg. gap size = 1.00 (1 / 1) 241 27.89 16.22 5.52 chr5qtel1M 267388 267535 (732465) L2d2_3end#LINE/L2 386 548 (7) m_b251s601i9 9953 chr5qtel1M 267388 CTTGTCATGTTGCCCCATCCAATCTTTTCCTGGATATCAGTGTGCAGTCT 267437 vv ----- ii - vi -- i ivi viv L2d2_3end#LIN 386 CTTGTATTGTT-----ATTTAA-CTTTTCACG--TGTTTATGTCTTGTCT 427 chr5qtel1M 267438 CCCCGGCCAGA------GCAC---GAGGACAAGCACTGTGTTTTAGCCCT 267478 ii i ------ v --- i i v ii i -iv L2d2_3end#LIN 428 CCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTA-TACT 476 chr5qtel1M 267479 TCTTGGTAACCCC---------------AGTGTTTGGCACACAGTAGGTG 267513 v v --------------- ii v i L2d2_3end#LIN 477 TCTTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAGTAGGCG 526 chr5qtel1M 267514 CTTAGTGAATGCTTGTCCACTT 267535 i i i ii iv i L2d2_3end#LIN 527 CTCAATAAATATTTGTTGATTT 548 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 34.32 CpG sites = 26, Kimura (unadjusted) = 36.70 Transitions / transversions = 2.00 (26/13) Gap_init rate = 0.08 (12 / 147), avg. gap size = 2.75 (33 / 12) 354 25.01 0.00 1.32 chr5qtel1M 267453 267529 (732471) L2c_3end#LINE/L2 390 465 (13) m_b251s601i10 9953 chr5qtel1M 267453 GAGGACAAGCACTGTGTTTTAGCCCTTCTTGGTAACCCCAGTGTTTGGCA 267502 i i v i i -ii v v v i ii L2c_3end#LINE 390 GAGGGCAGGGACCGTGTCTTA-TTCATCTTTGTATCCCCAGCGCCTGGCA 438 chr5qtel1M 267503 CACAGTAGGTGCTTAGTGAATGCTTGT 267529 i i i i i i L2c_3end#LINE 439 CATAGTAGGCGCTCAATAAATGTTTGT 465 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 26.39 CpG sites = 15, Kimura (unadjusted) = 32.43 Transitions / transversions = 3.75 (15/4) Gap_init rate = 0.01 (1 / 76), avg. gap size = 1.00 (1 / 1) 13 13.26 6.06 0.00 chr5qtel1M 268987 269019 (730981) (GGAAA)n#Simple_repeat 1 35 (0) m_b251s252i3 9954 chr5qtel1M 268987 GGAGAGG-CAGGAGAGGCAAGGAAAGG-AAGGAAA 269019 i -v i v - (GGAAA)n#Simp 1 GGAAAGGAAAGGAAAGGAAAGGAAAGGAAAGGAAA 35 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.06 (2 / 32), avg. gap size = 1.00 (2 / 2) 581 30.58 1.34 3.65 chr5qtel1M 269066 269289 (730711) C MIRb#SINE/MIR (45) 223 5 m_b251s601i11 9955 chr5qtel1M 269066 CTGTCGTTTAGTGCTCTAGAAATGCA--GTCTCATTGGATCCTCACACCA 269113 - i v i i v -- --i vi v C MIRb#SINE/MIR 223 CTGT-GCTAAGCGCTTTACA--TGCATTATCTCATTTAATCCTCACAACA 177 chr5qtel1M 269114 GCTTGGGGAGGGAGCTGTT-TTCCCCTCATTTTATAGTTAAAGAAACAGA 269162 i iiv v v v i - vi i i v i i v C MIRb#SINE/MIR 176 ACCCTGCGAGGTAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGA 127 chr5qtel1M 269163 GGCAAGCAACGATGAAGTGACTTGTCTAGGGTCATTCACCTAGCAAGTTC 269212 vviv iv i v i i i i iv v i vv C MIRb#SINE/MIR 126 GGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGG 77 chr5qtel1M 269213 CTGAGGCTGAACTGGAACTCCGGTGTTCCTGACTCCAGGAGTGGTGCTCC 269262 v v v i i v i v v vi iiiviv i C MIRb#SINE/MIR 76 CAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCT 27 chr5qtel1M 269263 ATGCCCTCAGGCACCACCCAGTGCTCC 269289 v v v --- v -- i C MIRb#SINE/MIR 26 TTCCACT---GCACCACGC--TGCCCC 5 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 39.01 CpG sites = 33, Kimura (unadjusted) = 39.77 Transitions / transversions = 1.00 (33/33) Gap_init rate = 0.04 (10 / 223), avg. gap size = 1.10 (11 / 10) 584 27.16 5.35 1.55 chr5qtel1M 269093 269279 (730721) C MIRc#SINE/MIR (65) 203 10 m_b251s601i12 9955 chr5qtel1M 269093 TCTCATTGGATCCTCACACCAGCT--------TGGGGAGGG-AGCTGTT- 269132 v v i i-------- i v - v i - C MIRc#SINE/MIR 203 TCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTA 154 chr5qtel1M 269133 TTCCCCTCATTTTATAGTTAAAGAAACAGAGGCAAGCAACGATGAAGTGA 269182 vi i i v i i v vviv iv i v C MIRc#SINE/MIR 153 TTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGA 104 chr5qtel1M 269183 CTTGTCTAGGGTCATTCACCTAGCAAGTTCCTGAGGCTGAACTGGAACTC 269232 i i i iv v i vv v v v i v i C MIRc#SINE/MIR 103 CTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCC 54 chr5qtel1M 269233 CGGTGTTCCTGACTCCAGGAGTGGTGCTCCATGCCCTCAGGCACCAC 269279 v v i vvii iv v v --- C MIRc#SINE/MIR 53 AGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACT---GCACCAC 10 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 33.96 CpG sites = 23, Kimura (unadjusted) = 33.96 Transitions / transversions = 0.85 (23/27) Gap_init rate = 0.03 (6 / 186), avg. gap size = 2.17 (13 / 6) 564 25.31 6.92 0.59 chr5qtel1M 272175 272333 (727667) C MIRc#SINE/MIR (95) 173 5 m_b251s601i13 9956 chr5qtel1M 272175 GGTGTACAAGGGAATTGATTTTTGTTTTTGTTTTTT-GTTGAGGAAATTG 272223 ivi i v iv - v i iiiii vi- v i C MIRc#SINE/MIR 173 GGTAGGCAGGGCAGGT-ATTATTATCCCCATTTTACAGATGAGGAAACTG 125 chr5qtel1M 272224 GGG----------TTAAGTGACTTGCCCAGGGTCACACAGCTGTTAAGTG 272263 i ---------- i iv C MIRc#SINE/MIR 124 AGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTG 75 chr5qtel1M 272264 TCTGAGGCTGGATTTGTACTCAGGTCCTCCTGACTTCAGGGCTGGTGCTC 272313 v v v v i i v i i i i v ii C MIRc#SINE/MIR 74 GCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTC 25 chr5qtel1M 272314 TGCCCACTGCACCACCCAGC 272333 vi v v C MIRc#SINE/MIR 24 TTTCCACTGCACCACACTGC 5 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 30.67 CpG sites = 24, Kimura (unadjusted) = 31.62 Transitions / transversions = 1.50 (24/16) Gap_init rate = 0.02 (3 / 158), avg. gap size = 4.00 (12 / 3) 436 29.01 1.52 0.75 chr5qtel1M 273864 273995 (726005) C L2b_3end#LINE/L2 (3) 463 331 m_b251s601i14 9957 chr5qtel1M 273864 CAGTCAATCAACAAGCATTTATTGAACAATTACTGTGTGCCAGGCGCCAT 273913 v v ii i i ivi ? ii C L2b_3end#LINE 463 CATTCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGT 414 chr5qtel1M 273914 GTTTGG-GCTGGGGCTACAAGTATCTGGCAAGAGAAAGGCAAT-TCTGCC 273961 i v - v - iivivii v i v? ii -i C L2b_3end#LINE 413 GCTAGGCGCTGGGGATAC-AGCGGTGAACAAGACAGACNCGGTCCCTGCC 365 chr5qtel1M 273962 CTCGAGGAGCTCCCATTCTCAGGGGGAAAGGAGA 273995 iv v v viv i iiv C L2b_3end#LINE 364 CTCACGGAGCTCACAGTCTAGTGGGGGAGACAGA 331 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 34.68 CpG sites = 23, Kimura (unadjusted) = 38.63 Transitions / transversions = 1.53 (23/15) Gap_init rate = 0.02 (3 / 131), avg. gap size = 1.00 (3 / 3) 246 36.40 4.78 0.84 chr5qtel1M 274747 274976 (725024) L1P4_orf2#LINE/L1 1999 2237 (1057) m_b251s551i1 9958 chr5qtel1M 274747 CTATTTGGCATTGTGCTGGAAACACTAACCATAGGATCAAGGCAAGGAGA 274796 iii v i iiv i v v viv iii L1P4_orf2#LIN 1999 CTATTCAACATAGTACTGGAAGTCCTAGCCAGAGCAATCAGGCAAGAGAA 2048 chr5qtel1M 274797 GGAAATTGGGGGCAT----GTAGGCAAAGAAGAAACAAAACAAGC-ATTT 274841 i viii ----i v iiv v v -v i L1P4_orf2#LIN 2049 AGAAATAAAAGGCATCCAAATAGGAAAAGAAGAAGTCAAACTATCTCTCT 2098 chr5qtel1M 274842 TTACTCATGATCTGATGGTCTGACTAGAGAATTTTAATGAATCAGCT--A 274889 ii v i v vv v iv i iii v v v i-- L1P4_orf2#LIN 2099 TCGCTGACGATATGATTCTATACCTAGAAAACCCTAAAGACTCCGCCAAA 2148 chr5qtel1M 274890 TGGTTAATTTAAAGT--ATTAATCAGTCCTACACATTTGCAATATA-AAA 274936 v i --ii i ii-- v iv v i vii v v v iv - L1P4_orf2#LIN 2149 AGGCT--CCTAGAACTGATAAACGACTTCAGTAAAGTTTCAGGATACAAA 2196 chr5qtel1M 274937 GTAAATCCACACAAATTACTAGCA-TCCTGAATGTTAATAA 274976 i v vi v i v - i iv iiii L1P4_orf2#LIN 2197 ATCAATGTACAAAAATCAGTAGCATTTCTATACACCAATAA 2237 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 49.09 CpG sites = 48, Kimura (unadjusted) = 51.90 Transitions / transversions = 1.37 (48/35) Gap_init rate = 0.03 (8 / 229), avg. gap size = 1.62 (13 / 8) 228 20.00 0.00 0.00 chr5qtel1M 275691 275745 (724255) L1M4c_5end#LINE/L1 3 57 (2443) m_b251s551i2 9959 chr5qtel1M 275691 AAAACAAATATAGAGGAGAGGATTCTGGTAAGATGACAGAGTAGAAAATT 275740 v ? vv v i i i iiv L1M4c_5end#LI 3 AAAAAAANTAATGAGGAGAGGATTCTGGGAAGATGGCGGAGTAGGAAGCA 52 chr5qtel1M 275741 CCAAG 275745 i L1M4c_5end#LI 53 CCAGG 57 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 21.65 CpG sites = 6, Kimura (unadjusted) = 24.02 Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 257 33.01 3.88 0.00 chr5qtel1M 276828 276930 (723070) L2c_3end#LINE/L2 357 463 (15) m_b251s601i15 9960 chr5qtel1M 276828 TGTC-GTTTCTCCCGGTAGAATAGAGGCTCCTTGAGGACAGGGACTGTCA 276876 - i ii iv v ivii i i vv L2c_3end#LINE 357 TGTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGT 406 chr5qtel1M 276877 CTTTTGAA--TTTGTAGCCTGTGCACTTACCA-GTGATTAGCACACAATA 276923 v vv -- v ivv i i iv -i ii vi i v L2c_3end#LINE 407 CTTATTCATCTTTGTATCCCCAGCGCCTGGCACATAGTAGGCGCTCAATA 456 chr5qtel1M 276924 AGTCTTT 276930 i v L2c_3end#LINE 457 AATGTTT 463 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 39.61 CpG sites = 19, Kimura (unadjusted) = 44.74 Transitions / transversions = 1.27 (19/15) Gap_init rate = 0.03 (3 / 102), avg. gap size = 1.33 (4 / 3) 284 35.56 11.11 0.00 chr5qtel1M 276958 277092 (722908) C L3#LINE/CR1 (142) 3957 3808 m_b251s601i16 9961 chr5qtel1M 276958 CCCAGCACTTCCTGAGGCAACCCATTCTTCTTCTGGA-----TTAATTGT 277002 i vi i ?i i ivi i -----i i C L3#LINE/CR1 3957 CTCACTACCTCNCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGATTGT 3908 chr5qtel1M 277003 GAGGAAAAATTTCCTGACTAAAAGCCAGAATGTGCAAGTTTGTTGCTTT- 277051 v i ivvi v ivvvi ii v vvvii vi i- C L3#LINE/CR1 3907 TAGAAAGTTCTTCCTTATATTGAGCCGAAATCTGCCTCCCTGTAACTTCC 3858 chr5qtel1M 277052 ---------TCCTCGTCCTGCCCTTTGGAGCTGAATGGAACACGCCCAGT 277092 --------- v i i iiv ii i v i i i C L3#LINE/CR1 3857 ACCCATTGGTCCTAGTTCTGCCCTCTGGAGCCACACAGAATAAGTCTAAT 3808 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 48.67 CpG sites = 31, Kimura (unadjusted) = 51.84 Transitions / transversions = 1.82 (31/17) Gap_init rate = 0.02 (3 / 134), avg. gap size = 5.00 (15 / 3) 236 33.33 2.30 0.00 chr5qtel1M 277523 277609 (722391) L2c_3end#LINE/L2 378 466 (12) m_b251s601i17 9962 chr5qtel1M 277523 TGCGAGCTCCTGGAGGGCAAGGACCACTTGGTA-TCGTCCCCGGATCCCT 277571 i v i iiv vv - i iii v i L2c_3end#LINE 378 TGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTATCCCC 427 chr5qtel1M 277572 AATTCCCAGCCCAGAATGGGCAC-AAAGAAATTCTGGTT 277609 iiv ii v v i i i -v v vi v L2c_3end#LINE 428 AGCGCCTGGCACATAGTAGGCGCTCAATAAATGTTTGTT 466 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 39.50 CpG sites = 17, Kimura (unadjusted) = 45.69 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.02 (2 / 86), avg. gap size = 1.00 (2 / 2) 14 10.68 0.00 6.25 chr5qtel1M 278464 278497 (721503) (AGCCC)n#Simple_repeat 1 32 (0) m_b251s252i4 9963 chr5qtel1M 278464 AGCCCAGCCCAAGCCCAGCCCGGTCAGAGCCCAG 278497 - i - vv (AGCCC)n#Simp 1 AGCCCAGCCC-AGCCCAGCCCAG-CCCAGCCCAG 32 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2) 54 20.55 4.50 5.56 chr5qtel1M 278683 278882 (721118) (TCC)n#Simple_repeat 1 198 (0) m_b251s252i5 9964 chr5qtel1M 278683 TCCTCCCTCTTCTTGC-CCTCCTCCTTCTTCTTCCCCCTACTCCTCTTCT 278731 - i i v - - i i i v i i (TCC)n#Simple 1 TCCT-CCTCCTCCTCCTCCTCCTCC-TCCTCCTCCTCCTCCTCCTCCTCC 48 chr5qtel1M 278732 TCC-CCTCGTCCCTCTTCTTCC-CCTCCTCTCTCTTCCCTCCCTCTTCTT 278779 - v - i i - - i - - i i (TCC)n#Simple 49 TCCTCCTCCT-CCTCCTCCTCCTCCTCCTC-CTCCT-CCT-CCTCCTCCT 94 chr5qtel1M 278780 TCCCCTCCCTCTTCTTCCCCCT-CTCCTCTTCTTTC-CCTCGTCCCTCTT 278827 i i - i i i - i i i - v - i (TCC)n#Simple 95 CCTCCT-CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT-CCTCCT 142 chr5qtel1M 278828 CTTCCT-CTCCT-CTCTTCTTCC-CCTCCTCC-CCTGCGCTCCTCTCCCT 278873 i - - i i - - - - ii (TCC)n#Simple 143 CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT-C-CTCCTCCTCCT 190 chr5qtel1M 278874 CCGCCCTCC 278882 -i (TCC)n#Simple 191 CC-TCCTCC 198 Matrix = Unknown Transitions / transversions = 6.75 (27/4) Gap_init rate = 0.10 (20 / 199), avg. gap size = 1.00 (20 / 20) 294 27.72 6.67 0.79 chr5qtel1M 280742 280861 (719139) C MIR1_Amn#SINE/MIR (84) 146 20 m_b251s601i18 9965 chr5qtel1M 280742 TTCTGTAGATGGGGAA-CTGAGGC--AACGGGGTGAAGTGACTGGCCCAG 280788 i ii i - -- iv i ? v i C MIR1_Amn#SINE 146 TTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGCCCAA 97 chr5qtel1M 280789 GTTCAACCAGCG-----GTGTCTGAGACAGAATTAGAATTGCTGCCTTCC 280833 v v? ?----- v v v i i ? ? iivvv i i C MIR1_Amn#SINE 96 GGTCACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAACCCAGGTCTCCC 47 chr5qtel1M 280834 CAACCCCGAGGCTGCGGCTCTGTGCACT 280861 v ii - v iivv i v C MIR1_Amn#SINE 46 GAGTCCC-AGTCCAGTGCTCTATCCACT 20 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 35.88 CpG sites = 18, Kimura (unadjusted) = 37.29 Transitions / transversions = 1.20 (18/15) Gap_init rate = 0.03 (4 / 119), avg. gap size = 2.25 (9 / 4) 183 23.17 13.41 0.00 chr5qtel1M 281728 281809 (718191) C MIR1_Amn#SINE/MIR (79) 151 59 m_b251s601i20 9966 chr5qtel1M 281728 CCCCATTTTACAGAGGAGG-AACCAAGAACCAGAGAG-------GACTTG 281769 v - ii iv? ------- C MIR1_Amn#SINE 151 CCCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTG 102 chr5qtel1M 281770 ATTAAG--TATATAACTGGGGAGAGG-GGCGCTGGAAATGAAA 281809 vii --i i?i i ? v? v -i v i i ? ?i C MIR1_Amn#SINE 101 CCCAAGGTCACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAA 59 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 29.62 CpG sites = 13, Kimura (unadjusted) = 31.62 Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.05 (4 / 81), avg. gap size = 2.75 (11 / 4) 184 13.85 2.00 13.33 chr5qtel1M 281728 281777 (718223) C MIRb#SINE/MIR (116) 152 108 m_b251s601i19 9966 chr5qtel1M 281728 CCCCATTTTACAGAGGAGG-AACCAAGAACCAGAGAGGACTTGATTAAGT 281776 v - ii ivi ------ C MIRb#SINE/MIR 152 CCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGG------TTAAGT 109 chr5qtel1M 281777 A 281777 C MIRb#SINE/MIR 108 A 108 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 15.27 CpG sites = 4, Kimura (unadjusted) = 15.27 Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.14 (7 / 49), avg. gap size = 1.00 (7 / 7) 190 33.72 11.63 0.00 chr5qtel1M 281956 282041 (717959) C L2b_3end#LINE/L2 (7) 459 364 m_b251s601i21 9967 chr5qtel1M 281956 CATCCAGCAGACATTCATTAATCCTCTGCTGTGTACTACA------GTCA 281999 i i i i i i i v vi i i i vi------ ii C L2b_3end#LINE 459 CATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTA 410 chr5qtel1M 282000 GGTGCTGAAGA-ACAAAGACAA--AAGA-AAACTCAGTTCCTGCTC 282041 i ii - iv iii -- - i ? i i i C L2b_3end#LINE 409 GGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCC 364 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 47.41 CpG sites = 25, Kimura (unadjusted) = 52.90 Transitions / transversions = 6.25 (25/4) Gap_init rate = 0.05 (4 / 85), avg. gap size = 2.50 (10 / 4) 257 12.65 2.72 8.63 chr5qtel1M 282327 282473 (717527) C HERV17#LTR/ERV1 (7781) 845 707 m_b251s701i0 9968 chr5qtel1M 282327 TCTCTCTCTCTGTCTCTATCTGTCTCTGTCTCTAGTCTCTCTGTCTCTGT 282376 ? i v v i v v vvi v C HERV17#LTR/ER 845 TNTCTCTTTCTTTCTCTCTTTGACTCTCTCTCTCTCCTCTCTGTCTCTCT 796 chr5qtel1M 282377 CTCTGTCTCTGTCTCTCTCTCTCTGTCTGTCTCTCTCT-CTCTCTGTCTC 282425 v - i ------- - C HERV17#LTR/ER 795 CTCTCT-TCCGTCTCTCTC-------CTGTCTCTCTCTCCTCTCTGTCTC 754 chr5qtel1M 282426 TTTGTCTCTCTTTCTCTTCTGTCTCTCTCTCTCTCC---GTCTCCCTTTC 282472 ---- i i i --- i i C HERV17#LTR/ER 753 ----TCTCTCTCTCTCCTCCGTCTCTCTCTCTCTCCTCTGTCTCTCTTTT 708 chr5qtel1M 282473 C 282473 C HERV17#LTR/ER 707 C 707 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 12.32 CpG sites = 9, Kimura (unadjusted) = 13.96 Transitions / transversions = 1.12 (9/8) Gap_init rate = 0.10 (14 / 146), avg. gap size = 1.14 (16 / 14) 258 27.47 7.69 0.00 chr5qtel1M 283265 283355 (716645) MIR3#SINE/MIR 69 166 (42) m_b251s601i22 9969 chr5qtel1M 283265 TGCCATTTA-TGGCTG-----CTGTGGCCAAATCCCTTT-CCTTCCAGAG 283307 i v - ? ----- iv v i v i- ii v i MIR3#SINE/MIR 69 TGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGG 118 chr5qtel1M 283308 CCTCCATTTCTTCTCCTATAAAAGGAGTGGGTTGGAAGAGATCGCCTC 283355 vi i vi i v v vv vii MIR3#SINE/MIR 119 CCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTC 166 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 35.18 CpG sites = 13, Kimura (unadjusted) = 35.18 Transitions / transversions = 1.08 (13/12) Gap_init rate = 0.03 (3 / 90), avg. gap size = 2.33 (7 / 3) 17 19.66 2.78 0.00 chr5qtel1M 284540 284575 (715425) (CA)n#Simple_repeat 1 37 (0) m_b251s252i6 9970 chr5qtel1M 284540 CACAGA-ACACACACATGCACACACATGTACACACAC 284575 v - ii iii (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACAC 37 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) 49 26.15 0.74 1.48 chr5qtel1M 284731 284866 (715134) (CA)n#Simple_repeat 1 135 (0) m_b251s252i7 9971 chr5qtel1M 284731 CACACACATGCACACA-AGTAACATGCACACTCACACTCACAGACATACA 284779 ii - vvv ii v v v i (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 chr5qtel1M 284780 CATTCACACACCCACATACACTCACACACACTCACACTTACACATGCACA 284829 iv v i v v vi ii (CA)n#Simple_ 51 CACACACACACACACACACACACACACACACACACACACACACACACACA 100 chr5qtel1M 284830 CACTCACAGGACGTGCACATGCACACTCAGCACACAC 284866 v -v iii ii v - (CA)n#Simple_ 101 CACACACA-CACACACACACACACACACA-CACACAC 135 Matrix = Unknown Transitions / transversions = 1.07 (15/14) Gap_init rate = 0.02 (3 / 135), avg. gap size = 1.00 (3 / 3) 19 28.12 1.79 0.00 chr5qtel1M 284962 285017 (714983) (CA)n#Simple_repeat 1 57 (0) m_b251s252i8 9972 chr5qtel1M 284962 CACACACATGCACACA-AGTAACGTGCACACTCACACAGACATACACATT 285010 ii - vvv iii v v i iv (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 chr5qtel1M 285011 CACACAC 285017 (CA)n#Simple_ 51 CACACAC 57 Matrix = Unknown Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.02 (1 / 55), avg. gap size = 1.00 (1 / 1) 234 24.99 4.05 2.67 chr5qtel1M 285020 285093 (714907) C HSAT5v1#Satellite (618) 5280 5206 m_b251s502i0 9973 chr5qtel1M 285020 ACATACACTCACTCACACTTACACATACACACACTCACA---GGGCGTGC 285066 i i v v i v ? i v i i--- v C HSAT5v1#Satel 5280 ACACACGCGCACACACGCGTNCACACACACACACGCGCGCACGCGCGTGC 5231 chr5qtel1M 285067 ACATGCACACTCAGCGCGCACACGTGT 285093 ii i -- ii i i C HSAT5v1#Satel 5230 ACACACACATT--GCATGCACGCATGT 5206 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 22.34 CpG sites = 13, Kimura (unadjusted) = 32.49 Transitions / transversions = 2.60 (13/5) Gap_init rate = 0.04 (3 / 73), avg. gap size = 1.67 (5 / 3) 240 21.37 0.00 14.93 chr5qtel1M 285042 285118 (714882) C HSAT5v1#Satellite (618) 5280 5214 m_b251s502i1 9973 chr5qtel1M 285042 ACATACACACACTCACAGGGCGTGCACATGCACACTCAGCGCGCACACGT 285091 i i i v --- ? ii v - i i C HSAT5v1#Satel 5280 ACACACGCGCACACAC---GCGTNCACACACACACAC-GCGCGCACGCGC 5235 chr5qtel1M 285092 GTGCATATCTGGGTGTACATGGCATGC 285118 i ------iii v C HSAT5v1#Satel 5234 GTGCACA------CACACATTGCATGC 5214 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 18.10 CpG sites = 11, Kimura (unadjusted) = 26.19 Transitions / transversions = 3.67 (11/3) Gap_init rate = 0.13 (10 / 76), avg. gap size = 1.00 (10 / 10) 45 33.75 3.20 5.45 chr5qtel1M 285195 285569 (714431) (CATACA)n#Simple_repeat 1 367 (0) m_b251s252i9 9974 chr5qtel1M 285195 CACACAAATA-ACGTGCACACTCAC-T-CACATAGACACACACATTCACA 285241 i v - i i iv - - v i v (CATACA)n#Sim 1 CATACACATACACATACACATACACATACACATACACATACACATACACA 50 chr5qtel1M 285242 CACACATACAC-T-CACACACACTCACACTTACACATACATACACTCACA 285289 i - - i vi v i i v i (CATACA)n#Sim 51 TACACATACACATACACATACACATACACATACACATACACATACACATA 100 chr5qtel1M 285290 GGGTATGCACATGCACAATCAGCACATACACGTGTGCATATCTGGGTGTA 285339 -vii i i - - - i iii - -ivi ii (CATACA)n#Sim 101 -CACATACACATACAC-AT-A-CACATACACATACACATA-C-ACATACA 144 chr5qtel1M 285340 CAT-GGCGTGCCCGATGTGTGTGCACACAGGGAGCACGCTGCGTTCACCT 285388 -vi i i v - iiiii -- viv - ii -i i v v (CATACA)n#Sim 145 CATACACATACAC-ATACACAT--ACACATACA-CATAC-ACATACACAT 189 chr5qtel1M 285389 ACAGCCCTGTGCACACAGTGTGCA-ATGCACACATGTGCACACAAATA-A 285436 -- v iii i -ii i - -- iii i v - (CATACA)n#Sim 190 ACA--CATACACATACA-CATACACAT--ACACATACACATACACATACA 234 chr5qtel1M 285437 TGTGCACACTCACACTCACATAGACACACACATTTACGCATACACATACA 285486 ii i iv iv v i -- i (CATACA)n#Sim 235 CATACACATACACATACACATACACATACACA--TACACATACACATACA 282 chr5qtel1M 285487 C-T-CACACACACTCACACTTACACAGACACACACACACAGACACACACT 285534 - - i vi v -- i i v i v (CATACA)n#Sim 283 CATACACATACACATACACATACAC--ATACACATACACATACACATACA 330 chr5qtel1M 285535 CACACACATGCAC-T-CACAGACACACTCACACACAC 285569 i i - - v iv i (CATACA)n#Sim 331 CATACACATACACATACACATACACATACACATACAC 367 Matrix = Unknown Transitions / transversions = 2.42 (63/26) Gap_init rate = 0.09 (32 / 374), avg. gap size = 1.00 (32 / 32) 16 0.00 0.00 0.00 chr5qtel1M 286109 286126 (713874) (C)n#Simple_repeat 1 18 (0) m_b251s252i10 9975 chr5qtel1M 286109 CCCCCCCCCCCCCCCCCC 286126 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCC 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 12 12.71 2.50 7.89 chr5qtel1M 286697 286736 (713264) (AGGGC)n#Simple_repeat 1 38 (0) m_b251s252i11 9976 chr5qtel1M 286697 AGGGCAGGGGCAGGGACAGGGACA-AGCAAGGCTGGGGAGG 286736 - - - -i i v v (AGGGC)n#Simp 1 AGGGCA-GGGCAGGG-CAGGG-CAGGGCAGGGCAGGGCAGG 38 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.10 (4 / 39), avg. gap size = 1.00 (4 / 4) 14 9.29 2.38 10.26 chr5qtel1M 286732 286773 (713227) (GGA)n#Simple_repeat 1 39 (0) m_b251s252i12 9977 chr5qtel1M 286732 GGAGGACCGAGTGGGGAGGACGAGGA-GAGTGAGGAGGGAGGA 286773 -v - i v - - - (GGA)n#Simple 1 GGAGGA-GGAG-GAGGAGGAGGAGGAGGAG-GAGGA-GGAGGA 39 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.12 (5 / 41), avg. gap size = 1.00 (5 / 5) 119 23.98 0.00 0.00 chr5qtel1M 286859 287131 (712869) (GTGTGT)n#Simple_repeat 1 273 (0) m_b251s252i13 9978 chr5qtel1M 286859 GTGTATGTGTGTGTGTGAGTGTGACTGTGTATGTGAGTGTGGGTATGAGT 286908 i v vv i v v i v (GTGTGT)n#Sim 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50 chr5qtel1M 286909 GTGACTGTGTATGTGACTATGTGAGTATGACTGGGAGTGAGTGTGTGTGT 286958 vv i vv i v i vv v v v (GTGTGT)n#Sim 51 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 100 chr5qtel1M 286959 ATGAGTGTGAGCGTGTGTGTGTGAGTGTGATTGCATGTGGGAGTGTGTGT 287008 i v v i v vv ii v v (GTGTGT)n#Sim 101 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 150 chr5qtel1M 287009 GTGTGAGTGTGACTGTGTGTGTATGTGAGTGTGACTGGGAGTGTGAATGT 287058 v vv i v vv v v vi (GTGTGT)n#Sim 151 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 200 chr5qtel1M 287059 GTGTGTATGAGTGTGAGTGTGACTGTATGTGTGTGTATGTGAGTGTGACT 287108 i v v vv i i v vv (GTGTGT)n#Sim 201 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 250 chr5qtel1M 287109 GTGTGTGTGTGTAAGTGTGTGTG 287131 iv (GTGTGT)n#Sim 251 GTGTGTGTGTGTGTGTGTGTGTG 273 Matrix = Unknown Transitions / transversions = 0.40 (16/40) Gap_init rate = 0.00 (0 / 272), avg. gap size = 0.0 (0 / 0) 12 14.30 3.03 3.03 chr5qtel1M 287918 287950 (712050) (AGCCC)n#Simple_repeat 1 33 (0) m_b251s252i14 9979 chr5qtel1M 287918 AGCCCACCCCAGCCCA-CAGAGCGCAGCGCCAGC 287950 v - vv v - (AGCCC)n#Simp 1 AGCCCAGCCCAGCCCAGCCCAGCCCAGC-CCAGC 33 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.06 (2 / 32), avg. gap size = 1.00 (2 / 2) 252 31.34 13.53 0.52 chr5qtel1M 289333 289502 (710498) L3#LINE/CR1 3884 4075 (24) m_b251s601i23 9980 chr5qtel1M 289333 CTGAATGTCAGGAGAAA--TCCTAGCTTTAGGAACTGTCCCA---TGA-- 289375 v i v ii -- i i vv vi i v --- i-- L3#LINE/CR1 3884 CTCAATATAAGGAAGAACTTTCTAACAATCAGAGCTGTCCAAAAATGGAA 3933 chr5qtel1M 289376 -GAGCTATGATAAGAGCTGGTGGGGTCACCCTCCTTGG-GGTCATCAAGA 289423 - i iivvii? v i i v v v vi - vv v L3#LINE/CR1 3934 TGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGTCACTGGAGGTGTTCAAGC 3983 chr5qtel1M 289424 AGAGGCT-GATG---ATTGGTCAGAGCTACTGGAGTGGGGGGTTCATGTA 289469 - --- i v i v ii v -ii i v i L3#LINE/CR1 3984 AGAGGCTGGATGACCACTTGTCAGGGATGTTGTAG-AAGGGATTCCTGCA 4032 chr5qtel1M 289470 TGGGGT---------AACTAGATGGCTGCT-GGGTCCCTCTCA 289502 v i ---------i i iv -i ii L3#LINE/CR1 4033 TTGGATGGGAGGTTGGACTAGATGACCTCTAAGGTCCCTTCCA 4075 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 41.07 CpG sites = 31, Kimura (unadjusted) = 42.25 Transitions / transversions = 1.41 (31/22) Gap_init rate = 0.06 (10 / 169), avg. gap size = 2.40 (24 / 10) 623 29.05 0.00 1.90 chr5qtel1M 290184 290397 (709603) L1M5_orf2#LINE/L1 1951 2160 (1134) m_b251s551i3 9981 chr5qtel1M 290184 TTCCCAATAAGATCAGGAGTGAAACAAGGTTGCCCACTATCACCGTCACT 290233 vv i iii i v i i ? iiiv L1M5_orf2#LIN 1951 TTCCCCCTAAGATCGGGAACAAGACAAGGATGTCCGCTNTCACCACTTCT 2000 chr5qtel1M 290234 ATTTCATATTGTATTAGAAATGCTAGCATTGGCAATAAGAGTCGAGAAAG 290283 iv i i i ii v vvvv ivvv i L1M5_orf2#LIN 2001 ATTCAACATTGTACTGGAGGTCCTAGCCAGTGCAATAAGGCAAGAAAAAG 2050 chr5qtel1M 290284 AGATTAAAGGAATAAGAATAGGCAATGAGGAAAGCAAACTATCACTCTGA 290333 i v v ii v v v i vv i ?i v -- L1M5_orf2#LIN 2051 AAATAAAAGGCATAAAGATTGGAAAGGAAGAAATAAAACTGTCNTTAT-- 2098 chr5qtel1M 290334 TATGATGGCTGATATGATGGTATACTTAGAGAACCCCAGAGATTCTACTA 290383 -- viii v i v ? v i i ? i v v L1M5_orf2#LIN 2099 --TCGCAGATGACATGATTGTNTACGTAGAAAATCCNAAAGAATCTACAA 2146 chr5qtel1M 290384 AAAAGTTATTAGAA 290397 ? ii i L1M5_orf2#LIN 2147 ANAAACTACTAGAA 2160 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 36.37 CpG sites = 34, Kimura (unadjusted) = 38.77 Transitions / transversions = 1.26 (34/27) Gap_init rate = 0.02 (4 / 213), avg. gap size = 1.00 (4 / 4) 33 0.00 10.42 0.00 chr5qtel1M 290445 290492 (709508) (TTG)n#Simple_repeat 1 53 (0) c_b251s251i0 9982 chr5qtel1M 290445 TTGTTGTTGTTGTTGTTGTT-TTGTTGTT-TTGTT-TTGTT-TTGTT-TT 290489 - - - - - (TTG)n#Simple 1 TTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTT 50 chr5qtel1M 290490 GTT 290492 (TTG)n#Simple 51 GTT 53 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.11 (5 / 47), avg. gap size = 1.00 (5 / 5) 203 33.78 6.29 2.70 chr5qtel1M 290901 291043 (708957) C L2b_3end#LINE/L2 (1) 465 318 m_b251s601i24 9983 chr5qtel1M 290901 TTTGTTTTTTTATGAAAAATCATTTACTAATCACTTATTATATTTAAAGT 290950 ii iv i -- v - i v i i i i i viv i i C L2b_3end#LINE 465 TTCATTCATTCA--ACAAAT-ATTTACTGAGCGCCTACTGTGTGCCAGGC 419 chr5qtel1M 290951 ATTATGCTAAGTGCCAGGGATATA--AATAGAAAAGAAAGA------CCT 290992 ?i i i i ii i --ii ii v v ------ i C L2b_3end#LINE 418 NCTGTGCTAGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCC 369 chr5qtel1M 290993 TGTTCTCCAAGAATTCACATTTTAATGGGAGAGATTTCACATATAAG-AG 291041 ii vvi ii v i i i -ivv i ?- C L2b_3end#LINE 368 TGCCCTCACGGAGCTCACAGTCTAGTGGGGGAGA-CAGACATGTAANCAG 320 chr5qtel1M 291042 AC 291043 C L2b_3end#LINE 319 AC 318 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 44.30 CpG sites = 35, Kimura (unadjusted) = 50.45 Transitions / transversions = 2.92 (35/12) Gap_init rate = 0.05 (7 / 142), avg. gap size = 1.86 (13 / 7) 201 32.38 3.50 4.96 chr5qtel1M 290920 291062 (708938) C L2c_3end#LINE/L2 (6) 472 332 m_b251s601i25 9983 chr5qtel1M 290920 TCATTTACTAATCACTTATTATATTTAAAGTATTATGCTAAGTGCCAGGG 290969 i vi v i iviivivv v -i i i i ii C L2c_3end#LINE 472 TCATTCAACAAACATTTATTGAGCGCCTACTAT-GTGCCAGGCGCTGGGG 424 chr5qtel1M 290970 ATATAAATA-GAA-AAGAAA--GACCTTGTTCTCCAAGAATTCACATTTT 291015 i v - - v -- v i ii v i ii v i C L2c_3end#LINE 423 ATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCT 374 chr5qtel1M 291016 AATGGGAGAGATTTCACATATAAG-AGACTCCAGTTGCAAGTCACAAG 291062 i ii -ivv ?i i- --- i i --i C L2c_3end#LINE 373 AGTGGAGGAGA-CAGACANGTAAACAGA---CAATTACAA--TACAAG 332 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 42.66 CpG sites = 30, Kimura (unadjusted) = 45.53 Transitions / transversions = 2.14 (30/14) Gap_init rate = 0.08 (11 / 142), avg. gap size = 1.09 (12 / 11) 246 32.12 8.76 0.00 chr5qtel1M 291553 291689 (708311) C CR1-3_Croc#LINE/CR1 (2990) 615 467 m_b251s551i4 9984 chr5qtel1M 291553 TTGTGATCTGTTTCCTGAGCTCCTCATCTATCTCTTCCTTCTGTCCTGGT 291602 v i i vvv iv i i i i i vii C CR1-3_Croc#LI 615 TTGTCACCTGCTTGAAGAGTGCCTCATCCACCTCCTCTTCCTGATTTGGT 566 chr5qtel1M 291603 GATCTGTGATATATGCTGATGACAATATAGTTTCCCCCTCTCCC-TCTGT 291651 ii i i v v iv iv iv v v v iv v ii -i v C CR1-3_Croc#LI 565 GGCCTATAATAAATCCCCACCATTATATCGGTGCTGCATCTTTCACCTTT 516 chr5qtel1M 291652 GATCTTTACCCAAATGCTTTCTAC-----------CTCCCTCCTGGACC 291689 v i v i ----------- i i C CR1-3_Croc#LI 515 CATCTTCACCCAAATGCATTCTGCTTTGCTGTCTTCTTCCTCCTGAACC 467 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 43.15 CpG sites = 25, Kimura (unadjusted) = 43.15 Transitions / transversions = 1.32 (25/19) Gap_init rate = 0.01 (2 / 136), avg. gap size = 6.00 (12 / 2) 380 35.23 2.27 0.00 chr5qtel1M 291727 291902 (708098) C L1ME4b_3end#LINE/L1 (314) 578 399 m_b251s551i5 9985 chr5qtel1M 291727 GCCTGCTCATCATTTTTTGCAGCACAATAGCATTCTATTACATTCATATA 291776 i v iv i i vvv i i ii vv i C L1ME4b_3end#L 578 GCTTCCTCATTCTTTTTTACGGCTGCATAGTATTCCATTGTATGGATGTA 529 chr5qtel1M 291777 CCATAACTTGTTCAGCCATTTCCCCGCTGATGGGCATCCCCTCAATTTCT 291826 i i i i v i iii i iivvvivi i C L1ME4b_3end#L 528 CCATAATTTATTTAACCAGTCCCCTATTGATGGACATTTAGGTTGTTTCC 479 chr5qtel1M 291827 AGTCCTTTGCCTCCACAAAAAAAG--GCTATAAATATTTTTGTATATATG 291874 i i ivii v v -- v i vii i i C L1ME4b_3end#L 478 AATCTTTTGCTATTACAAACAATGCTGCAATGAATAACCTTGTACATACG 429 chr5qtel1M 291875 T--GTGTGTATGTATGTATGTATAGCTCTA 291902 --v vi i ii i iiv v v C L1ME4b_3end#L 428 TCATTTCGCACATGTGCGAGTATATCTGTA 399 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 45.75 CpG sites = 40, Kimura (unadjusted) = 50.51 Transitions / transversions = 1.82 (40/22) Gap_init rate = 0.01 (2 / 175), avg. gap size = 2.00 (4 / 2) 504 30.06 6.77 9.04 chr5qtel1M 292402 292785 (707215) C L3#LINE/CR1 (2212) 1887 1512 m_b251s601i26 9986 chr5qtel1M 292402 TGGTAGCATCTCCAATGATGTCTATC-ACTTCTTCTTCCAGCAACCAGTT 292450 i viv v v i vi - iv - v C L3#LINE/CR1 1887 TGGCACTTTCTCCCAAGGTTCCTATCGACTTCCACTTC-ACCAACCAGTT 1839 chr5qtel1M 292451 CTTCCTTATTGGTGAGAAT------CAGA-TGGTGGTTCCCCTCAT---- 292489 i v ------ - i ii i ---- C L3#LINE/CR1 1838 CTTCCTTGTTGGTCAGAATTAAGTCCAGAGTAGCAGTTCCCCTCGTTGCT 1789 chr5qtel1M 292490 -----CACCTATTGAACACTGAAATTATCCTTATAGCAAATGAAGAAATT 292534 -----i vi iviv i vvi vi i v v C L3#LINE/CR1 1788 TCCTCTACCTTCTGAGAGATGAAATTGTCAGCAAGGCAAGTCAAGAATTT 1739 chr5qtel1M 292535 AAACACACACACATACACAGCTTCCTGCTTTGGGTAAAGAGAGACGAAAC 292584 -------v v ----- -- vi i?i iv ----- C L3#LINE/CR1 1738 A-------TCAGAT-----GCT--CTGCTTTTAGCNGAATGAGAC----- 1708 chr5qtel1M 292585 AGAGACAGGAGCAGAAAATGTCTGGATCATTGGAGT----TGTCGCC-CT 292629 --------vvv v i i vi i ----ii i i- C L3#LINE/CR1 1707 --------TTCCAGCAGATGTCCGGATAGTTGAAGTCCCCCATCACTACT 1666 chr5qtel1M 292630 GTCTATCTTGCTCTTGCCCTAGATTTATGTATGGCCTGTTTCCTCTACTT 292679 --? iii iv i v i i- --- v vvvv vvi C L3#LINE/CR1 1665 G--NATCTTGCCTCTGTGCCAGTTTTGTA-AT---CTGTATCAGGAAAGC 1622 chr5qtel1M 292680 CTCATCTATTCCTACCTTCTGTTCTGATGGTCTGTGGTGTATG--CATGA 292727 v i ?i iv v vi v ii i i iv-- ii C L3#LINE/CR1 1621 ATCATCCATNTCCTCCATCTGGCCGGGCGGTCTGTAGTATACTCCCACAA 1572 chr5qtel1M 292728 CTAGATGGCTTCTATCTCTCCCT-CTGTGATCTTTACCCAAATGAT-TTT 292775 v v vi i i i - v v i i v - ii C L3#LINE/CR1 1571 CGATATCACTTCTGTTTCTCTCTCCTTTTATCCTCACCCAAATGCTCTCC 1522 chr5qtel1M 292776 ATCTCCCTTC 292785 ? v v C L3#LINE/CR1 1521 ANCGCGCTTC 1512 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 38.25 CpG sites = 57, Kimura (unadjusted) = 39.70 Transitions / transversions = 1.19 (57/48) Gap_init rate = 0.11 (44 / 383), avg. gap size = 1.36 (60 / 44) 233 33.14 4.24 4.88 chr5qtel1M 293332 293496 (706504) C L3b_3end#LINE/CR1 (243) 963 800 m_b251s601i27 9987 chr5qtel1M 293332 TCAAACCATTTTTATTTTGGGGCTTTTTTTCTTAGTTAAGA-GGAAAGCA 293380 i i vv iv i ---- i v i i vi - i i C L3b_3end#LINE 963 TTAAGCCCATTTCCTCTTG----TTCTGTCCTCAGTGGAGATGGAGAACA 918 chr5qtel1M 293381 GCTGATTTCTTCTCCTGTTC-CAGTCACTCTTTACAGA---GAAGCCTAC 293426 i iv iv- v v -i i v i i i v --- --- C L3b_3end#LINE 917 GCTGGTCACCG-TCCTCTACGTAATAACCCTTCATATACTTGAAG---AC 872 chr5qtel1M 293427 AGACATAAACTCACCCTTCAGTCTTCTCAGCTTT--GCCAGATCATCTGA 293474 ? vi v v ? i i vv ii-- iii v iv C L3b_3end#LINE 871 NGTTATTAAGTCNCCCCTCAGCCTTCTCTTCTCCAGGCTGAATAATCCCA 822 chr5qtel1M 293475 GGTCCTCTAACTTCTTATTATA 293496 v i i i iv i C L3b_3end#LINE 821 GTTCCTTTAACCTTTCCTCATA 800 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 45.25 CpG sites = 32, Kimura (unadjusted) = 46.50 Transitions / transversions = 1.60 (32/20) Gap_init rate = 0.07 (12 / 164), avg. gap size = 1.25 (15 / 12) 257 28.65 9.52 3.60 chr5qtel1M 294972 295076 (704924) MIR3#SINE/MIR 31 141 (67) m_b251s601i28 9988 chr5qtel1M 294972 GGTTGGGAGTCAGGGAAGCTGAATTTGAATCCCTGCCCTGATACT----- 295016 ii ii v ii iv i v i vi ----- MIR3#SINE/MIR 31 GACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTN 80 chr5qtel1M 295017 --TGTGTGACTTTGGGCCAATCCATGTCCCCCGTTCTGTAAG---AAGTT 295061 -- i v i - iv v --- v ii ---v MIR3#SINE/MIR 81 GCTGTGTGACCTTGGGCAAGT-CACTTCACC---TCTCTGGGCCTCAGTT 126 chr5qtel1M 295062 TGCCTTTCTATAAAA 295076 v iiv i MIR3#SINE/MIR 127 TCCTCATCTGTAAAA 141 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 37.45 CpG sites = 18, Kimura (unadjusted) = 37.45 Transitions / transversions = 1.64 (18/11) Gap_init rate = 0.07 (7 / 104), avg. gap size = 2.00 (14 / 7) 209 26.63 24.26 0.60 chr5qtel1M 296433 296568 (703432) MIR3#SINE/MIR 3 170 (38) m_b251s601i29 9989 chr5qtel1M 296433 GGCAGTGGGGCTGAACAGAGAAGGTAT---CTGGTGGGGCTGGAGAACC- 296478 v v i ii i i--- - i v v v i- MIR3#SINE/MIR 3 GGCAGAGTGGCTGAGCAGAGAGAGCACGGACTGG-GAGTCAGGAGACCTG 51 chr5qtel1M 296479 --------TCTCTG-TATCCCAGTAGCTCCCTG-GTAACCTTACACCAGC 296518 -------- i v - v v v i ?v - i ivi v i MIR3#SINE/MIR 52 GGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGT 101 chr5qtel1M 296519 CACCT-----------------GTTTTCCCACCTGCCAAATGA-GGGGCT 296550 i ----------------- i i i iv - i MIR3#SINE/MIR 102 CACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTT 151 chr5qtel1M 296551 GGACTAAA-GGTCCCTGAG 296568 i - i i i MIR3#SINE/MIR 152 GGACTAGATGATCTCTAAG 170 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 33.22 CpG sites = 23, Kimura (unadjusted) = 34.41 Transitions / transversions = 1.77 (23/13) Gap_init rate = 0.07 (9 / 135), avg. gap size = 3.78 (34 / 9) 16 0.00 0.00 0.00 chr5qtel1M 298526 298543 (701457) (C)n#Simple_repeat 1 18 (0) m_b252s252i0 9990 chr5qtel1M 298526 CCCCCCCCCCCCCCCCCC 298543 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCC 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 11 24.82 1.96 4.00 chr5qtel1M 298726 298776 (701224) (GGGGAT)n#Simple_repeat 1 50 (0) m_b252s252i1 9991 chr5qtel1M 298726 GGGGAGGAGGAGAGGGGGATGCGGATGGGCA-GCCAGGGGGGATGGGAAT 298774 v - - v v v - vviiv i (GGGGAT)n#Sim 1 GGGGATG-GG-GATGGGGATGGGGATGGGGATGGGGATGGGGATGGGGAT 48 chr5qtel1M 298775 GG 298776 (GGGGAT)n#Sim 49 GG 50 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.06 (3 / 50), avg. gap size = 1.00 (3 / 3) 43 30.73 0.00 0.76 chr5qtel1M 300178 300310 (699690) (TC)n#Simple_repeat 1 132 (0) m_b252s252i2 9992 chr5qtel1M 300178 TCTCTCTGTGTGTATCACTCTCTTACTTTCTCACTGCCTGTCTCTCCCCC 300227 v v v v v iv i v vi v i i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr5qtel1M 300228 CGGCCCCATCTCTCTCTGTGTCTCTCTCTCTGTGTCTGTCTCTGTCTCTC 300277 ivv i iv v v v v v v (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chr5qtel1M 300278 TTTCTCTCCCCCCCTCTCTGTCTCCCCCGTCTC 300310 i i i i v i i - (TC)n#Simple_ 101 TCTCTCTCTCTCTCTCTCTCTCTCTCTC-TCTC 132 Matrix = Unknown Transitions / transversions = 0.74 (14/19) Gap_init rate = 0.01 (1 / 132), avg. gap size = 1.00 (1 / 1) 183 27.88 0.00 1.64 chr5qtel1M 300774 300835 (699165) MIR1_Amn#SINE/MIR 13 73 (157) m_b252s601i1 9993 chr5qtel1M 300774 GTGGGACAGTGAATAGATCGCTGGGTTCGGAGTGAGGGAAACCCGAGTTC 300823 vvi i v i ii v v v- i i i MIR1_Amn#SINE 13 GTGGTCTAGTGGATAGAGCACTGGACTGGGACTC-GGGAGACCTGGGTTC 61 chr5qtel1M 300824 AAATACAGCCTC 300835 ? ? v v v MIR1_Amn#SINE 62 NANTCCCGGCTC 73 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.66 CpG sites = 8, Kimura (unadjusted) = 36.66 Transitions / transversions = 0.89 (8/9) Gap_init rate = 0.02 (1 / 61), avg. gap size = 1.00 (1 / 1) 453 29.59 1.37 2.78 chr5qtel1M 300850 300995 (699005) MIRb#SINE/MIR 125 268 (0) m_b252s601i2 9994 chr5qtel1M 300850 CCTCAGTTTCCTCAAGTGTAAAATAGAGGTAATAACAGCAACTGTCTCCC 300899 vv i i i i v v --- v MIRb#SINE/MIR 125 CCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTAC---CTCGC 171 chr5qtel1M 300900 AGGATTGCCTTGAGGCTCCAAGAAGAGACTGTTTGTAAAGCTGGTT--CC 300947 i iiv v iv vi v v iv - v -- v MIRb#SINE/MIR 172 AGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGC-GCTTAGCA 220 chr5qtel1M 300948 TGGCTCCTGGCATGTAGTAGGTGCCTATTAAATGCACGTTCCCTTTTT 300995 ii iv ii i i ii v vvv i iv v MIRb#SINE/MIR 221 CAGTGCCTGGCACATAGTAAGCGCTCAATAAATGGTAGCTCTATTATT 268 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.96 CpG sites = 21, Kimura (unadjusted) = 38.09 Transitions / transversions = 1.00 (21/21) Gap_init rate = 0.03 (5 / 145), avg. gap size = 1.20 (6 / 5) 385 36.49 4.17 1.52 chr5qtel1M 301001 301192 (698808) C MIRc#SINE/MIR (66) 202 6 m_b252s601i3 9995 chr5qtel1M 301001 CTCACTTGAGCTTTAGAACAAGCCTGGGAAGTTGAT------GCTGTCAT 301044 i v i i v v v i v ii------ v i i C MIRc#SINE/MIR 202 CTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTAT 153 chr5qtel1M 301045 TACCCCACCCCCCACCCCTGTAGCAATGGGGAAGTGATGAAGGTTGGGAA 301094 i - viiii vvv vi v iv i iv- v vii ii vi C MIRc#SINE/MIR 152 TATCCC-CATTTTACAGATGAGGAAACTGAGGC-TCAGAGAGGTTAAGTG 105 chr5qtel1M 301095 CCTTGCTTAGTGTCCCG-AACGAGGAAGTCCCTGGGGTAG-ATTTAAGCA 301142 v ii iv v i- i v v vv v i vii - i ii i v C MIRc#SINE/MIR 104 ACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACC 55 chr5qtel1M 301143 CAGGCCTCTTCTGACTCCAAGTCCAGTGTTCTGCCCGCTGAGCCACACTG 301192 i - i i vi i vi C MIRc#SINE/MIR 54 CAGGTCT-TCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTG 6 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 49.71 CpG sites = 40, Kimura (unadjusted) = 52.15 Transitions / transversions = 1.38 (40/29) Gap_init rate = 0.03 (6 / 191), avg. gap size = 1.83 (11 / 6) 24 59.74 0.00 0.00 chr5qtel1M 301310 301526 (698474) (GG)n#Simple_repeat 1 217 (0) m_b252s252i4 9996 chr5qtel1M 301310 GGGGGGAGGGAGGGGGGGGAGAAGGAGGAGGGGAGGACAGGAAAGAGGGG 301359 i i i ii i i i ivi iii i (GG)n#Simple_ 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 50 chr5qtel1M 301360 AAGGAAGGAGGGAGAGAGGGGAGGGGAGAGAGAGGGAGGGGGGAGAAGGA 301409 ii ii i i i i i i i i i i i ii i (GG)n#Simple_ 51 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 100 chr5qtel1M 301410 GGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGGGGAGAGGGAG 301459 i i i i i i i i i i i i i i i i i i i i i (GG)n#Simple_ 101 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 150 chr5qtel1M 301460 AGGAGAGGGAGGGAGAGGAAGGAGAGAGGGGAAGGGGGGAGAGGGAGGGG 301509 i i i i i i ii i i i ii i i i (GG)n#Simple_ 151 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 200 chr5qtel1M 301510 AGAGAGAGAGGGAGGGG 301526 i i i i i i (GG)n#Simple_ 201 GGGGGGGGGGGGGGGGG 217 Matrix = Unknown Transitions / transversions = 75.00 (75/1) Gap_init rate = 0.00 (0 / 216), avg. gap size = 0.0 (0 / 0) 351 18.91 5.09 0.00 chr5qtel1M 301315 302120 (697880) (GAGA)n#Simple_repeat 1 847 (0) m_b252s252i5 9996 chr5qtel1M 301315 GAGGGAG-GGGGGGGAGAAGGAG-GAG-GGGAG-GACAG-GAAAGAG-GG 301358 i - i i i ii - - i - v - i - i (GAGA)n#Simpl 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr5qtel1M 301359 GAAGGAAGGAGGGAGAGAG-GGGAG-GGGAGAGAGAGGGAG-GGGGGAGA 301405 ii ii i - i - i i - i i (GAGA)n#Simpl 51 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 100 chr5qtel1M 301406 AGGAGGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG-GGGAGA 301454 ii i - i (GAGA)n#Simpl 101 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 150 chr5qtel1M 301455 GGGAGAG-GAGAGGGAGGGAGAG-GAAGGAGAGAG-GGGAAGGGGGGAGA 301501 i - i i - ii - i ii i i (GAGA)n#Simpl 151 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 200 chr5qtel1M 301502 GGGAG-GGGAGAGAGAGAGGGAG-GGGAGAGAGAGAAGGAGGGAGAGAGA 301549 i - i i - i ii i (GAGA)n#Simpl 201 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 250 chr5qtel1M 301550 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGACAGAGAGGGAGAGG 301599 v i i (GAGA)n#Simpl 251 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 300 chr5qtel1M 301600 GAGAGGGAGAGGGAGAGGGAGAGGGAGAGGGAGAGGGAGAG-GAGAAGGA 301648 i i i i i i - ii (GAGA)n#Simpl 301 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 350 chr5qtel1M 301649 GAG-GGGAGGGA-AGGGAAGGAGGGAGAGAGGAAGGGAGAGAGAGGGAG- 301695 - i i - i ii i ii i i - (GAGA)n#Simpl 351 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 400 chr5qtel1M 301696 GGGAGA-AGAAAG-GAG-GAGGAAGAGA-AGAGAGA-AGAGAGA-AGAG- 301738 i - i - - ii - - - - (GAGA)n#Simpl 401 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 450 chr5qtel1M 301739 GAGAGGGAGGGAGAGGGAGAGGGAGGGAGAGGGAGAAGGAGAGGGAGAGG 301788 i i i i i i ii i i (GAGA)n#Simpl 451 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 500 chr5qtel1M 301789 GAGAGGGA-AGGAAGGGAGGGAGAG-GGGAG-GGGAGAGAGAGAGGGAG- 301834 i - ii i i - i - i i - (GAGA)n#Simpl 501 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 550 chr5qtel1M 301835 GGGAGAGAAGGAGGGAGGGAGAGAGAGACAGAGAGAGAGACAGAGGGAGA 301884 i ii i i v v i (GAGA)n#Simpl 551 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 600 chr5qtel1M 301885 GGGAGAGGGAGAGGGAGAGGGA-AGGAAGGGAGGGAGAGAGAGGGAG-GG 301932 i i i i - ii i i i - i (GAGA)n#Simpl 601 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 650 chr5qtel1M 301933 GAGAGAGAGAGGGAG-GGGAGAGAGAGAAGGAGGGAGGGAGAGAGAGAGA 301981 i - i ii i i (GAGA)n#Simpl 651 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 700 chr5qtel1M 301982 GAGACAGAGAGAGAGACAGAGAGAGAGACAGAGAGGGAGAGGGAGAGGGA 302031 v v v i i i (GAGA)n#Simpl 701 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 750 chr5qtel1M 302032 GAGGGAGAGGGAGAGGGAGAGGGAGAGGGA-AGAGGGA-AGAG-GGGAGG 302078 i i i i i - i - - i i (GAGA)n#Simpl 751 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 800 chr5qtel1M 302079 GAGGGAG-GAGAGAAAG-GAG-GAG-GAGAGGGAGGGAAGGAG-GAG 302120 i - i - - - i i ii - (GAGA)n#Simpl 801 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 847 Matrix = Unknown Transitions / transversions = 17.29 (121/7) Gap_init rate = 0.05 (41 / 805), avg. gap size = 1.00 (41 / 41) 191 29.69 4.69 0.00 chr5qtel1M 302520 302583 (697417) C MIR3#SINE/MIR (33) 175 109 m_b252s601i4 9997 chr5qtel1M 302520 GGAGCCCGAGAG-TCATGGGGCC--ACCTACTTGTTTTACACATAGGGAA 302566 ii iv - vvi i -- iv ii v ii C MIR3#SINE/MIR 175 GGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGAA 126 chr5qtel1M 302567 ACTGAGGCACGGGGGGG 302583 v i i i C MIR3#SINE/MIR 125 ACTGAGGCCCAGAGAGG 109 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.85 CpG sites = 13, Kimura (unadjusted) = 39.85 Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.03 (2 / 63), avg. gap size = 1.50 (3 / 2) 189 27.69 17.82 3.48 chr5qtel1M 302551 302651 (697349) C MIR#SINE/MIR (122) 140 26 m_b252s601i5 9997 chr5qtel1M 302551 TTTTACACATAGGGAAACTGAGGCACGGGGGGGC--AGT----------- 302587 v ii i i i i-- ----------- C MIR#SINE/MIR 140 TTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCCAA 91 chr5qtel1M 302588 -----CCCAGATGCTAAGTAGTAGAGCCAGGGCCGGAGGACGGGCCAGTC 302632 ----- v v iv i i i iiiv ivv i - C MIR#SINE/MIR 90 GGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGG-CAGTC 42 chr5qtel1M 302633 TGTGCACACCTGAGCTTGT 302651 ---i v v ii C MIR#SINE/MIR 41 TG---GCTCCAGAGCCCGT 26 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.96 CpG sites = 18, Kimura (unadjusted) = 36.30 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.07 (7 / 100), avg. gap size = 3.14 (22 / 7) 14 9.96 2.78 5.71 chr5qtel1M 303469 303504 (696496) (GGGA)n#Simple_repeat 1 35 (0) m_b252s252i6 9998 chr5qtel1M 303469 GGGATGGAGCGAGGG-GGGAGGGCAGGGACAGGAGGG 303504 v v - - -i (GGGA)n#Simpl 1 GGGAGGGAGGGAGGGAGGGAGGG-AGGGA-GGGAGGG 35 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.09 (3 / 35), avg. gap size = 1.00 (3 / 3) 18 23.30 0.00 0.00 chr5qtel1M 304572 304611 (695389) (TG)n#Simple_repeat 1 40 (0) m_b252s252i7 9999 chr5qtel1M 304572 TGTGTGAGATTGTGTGTGTGTGTGCGACTGTGTGAATGTG 304611 v vv i vv vi (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 40 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 12 34.70 0.00 0.00 chr5qtel1M 306332 306385 (693615) (CCCC)n#Simple_repeat 1 54 (0) m_b252s252i8 10000 chr5qtel1M 306332 CCCGCCCCCCCCCGAGCCCCGTTCCCTCCCGAAATTCCCGCCCCCCCCCC 306381 v vvv vii i vvvvii v (CCCC)n#Simpl 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 50 chr5qtel1M 306382 CCCC 306385 (CCCC)n#Simpl 51 CCCC 54 Matrix = Unknown Transitions / transversions = 0.50 (5/10) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 13 25.67 3.70 1.82 chr5qtel1M 308689 308742 (691258) (CCTCC)n#Simple_repeat 1 55 (0) m_b252s252i9 10001 chr5qtel1M 308689 CCTCCCCTCCACTTTCCTCTGCTCTCCCT-TCCT-CCCACTTCTCCCCTC 308736 v ii iv - -i - v ii (CCTCC)n#Simp 1 CCTCCCCTCCCCTCCCCTCCCCTC-CCCTCCCCTCCCCTCCCCTCCCCTC 49 chr5qtel1M 308737 TTCTCC 308742 ii (CCTCC)n#Simp 50 CCCTCC 55 Matrix = Unknown Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.06 (3 / 53), avg. gap size = 1.00 (3 / 3) 25 21.42 3.17 8.33 chr5qtel1M 308883 309008 (690992) (CCGAGCC)n#Simple_repeat 1 120 (0) m_b252s252i10 10002 chr5qtel1M 308883 CCCAGCCCGGAGTCCCAAGCCCC--GCCCCGGGCCTGGCAAAGCCCCGTC 308930 v v i i -- i --- vi vv (CCGAGCC)n#Si 1 CCGAGCCCCGAGCCCCGAGCCCCGAGCCCCGAGCC---CCGAGCCCCGAG 47 chr5qtel1M 308931 CCATCAGGGCCCTG-GCCCGGAGTCCCGAGCCCCGAGCCCCGGGCCTGGC 308979 -- v i i - v i i --- (CCGAGCC)n#Si 48 CC--CCGAGCCCCGAGCCCCGAGCCCCGAGCCCCGAGCCCCGAGCC---C 92 chr5qtel1M 308980 AAAGGCCCGACCCTTCCG-GGCCCGAGCCC 309008 vi v v -- - v (CCGAGCC)n#Si 93 CGAGCCCCGAGCC--CCGAGCCCCGAGCCC 120 Matrix = Unknown Transitions / transversions = 0.82 (9/11) Gap_init rate = 0.10 (13 / 125), avg. gap size = 1.08 (14 / 13) 18 21.89 4.05 4.05 chr5qtel1M 308937 309010 (690990) (GGGCCC)n#Simple_repeat 1 74 (0) m_b252s252i11 10002 chr5qtel1M 308937 GGGCCCTGGCCCGGAGTCCCGAGCCCCGAGCCCCGGGCCTGGCAAAGGCC 308986 v - - - v i v v v vvi (GGGCCC)n#Sim 1 GGGCCCGGGCCCGG-G-CCCG-GGCCCGGGCCCGGGCCCGGGCCCGGGCC 47 chr5qtel1M 308987 C-GACCC--TTCCGGGCCCGAGCCCGG 309010 - i --vi i (GGGCCC)n#Sim 48 CGGGCCCGGGCCCGGGCCCGGGCCCGG 74 Matrix = Unknown Transitions / transversions = 0.62 (5/8) Gap_init rate = 0.07 (5 / 73), avg. gap size = 1.20 (6 / 5) 41 20.72 4.50 0.00 chr5qtel1M 313151 313261 (686739) (GAGGG)n#Simple_repeat 1 116 (0) m_b252s252i12 10003 chr5qtel1M 313151 GAGGGAGGGGGAGAGGA-AGGAGGAAAGGGGGGCGGCGGGGAGCAGA-GG 313198 ii i -i ii i v v vi - (GAGGG)n#Simp 1 GAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGG 50 chr5qtel1M 313199 GAGGGGA-TGGCGGGGA-GGGAGCGGA-GGGAGAGGACGGCGGGGGAGGG 313245 -v v - v - i v vi (GAGGG)n#Simp 51 GAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGG 100 chr5qtel1M 313246 GTGGGGAGGGGACGGG 313261 v v (GAGGG)n#Simp 101 GAGGGGAGGGGAGGGG 116 Matrix = Unknown Transitions / transversions = 1.00 (10/10) Gap_init rate = 0.05 (5 / 110), avg. gap size = 1.00 (5 / 5) 209 31.38 0.96 5.00 chr5qtel1M 314641 314744 (685256) C MIRb#SINE/MIR (165) 103 4 m_b252s601i6 10004 chr5qtel1M 314641 GTCCAGGGTCCCGCAGCTCACATGCATCTGAGGCTGGATTTGAACTCAGG 314690 i i v i vii v iiv v v v i i C MIRb#SINE/MIR 103 GCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGG 54 chr5qtel1M 314691 TCCTTCTGCCTCCATGACGC-CGCTCCATCCCCGCAGGCGCCCCTGGCTG 314739 iv v vii v -i iv v -----i v vv C MIRb#SINE/MIR 53 TCTGTCTGACTCCAAAGCCCGTGCTCTTTCCAC-----TGCACCACGCTG 9 chr5qtel1M 314740 CCCCT 314744 C MIRb#SINE/MIR 8 CCCCT 4 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.33 CpG sites = 15, Kimura (unadjusted) = 41.00 Transitions / transversions = 0.94 (15/16) Gap_init rate = 0.06 (6 / 103), avg. gap size = 1.00 (6 / 6) 237 31.25 0.00 0.00 chr5qtel1M 314641 314704 (685296) C MIRc#SINE/MIR (168) 100 37 m_b252s601i7 10004 chr5qtel1M 314641 GTCCAGGGTCCCGCAGCTCACATGCATCTGAGGCTGGATTTGAACTCAGG 314690 i i v i vii v iiv v v v i i i C MIRc#SINE/MIR 100 GCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGG 51 chr5qtel1M 314691 TCCTTCTGCCTCCA 314704 i i v C MIRc#SINE/MIR 50 TCTTCCTGACTCCA 37 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.11 CpG sites = 12, Kimura (unadjusted) = 41.85 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0) 200 28.13 5.92 8.78 chr5qtel1M 316437 316588 (683412) MIRc#SINE/MIR 6 153 (115) m_b252s601i8 10005 chr5qtel1M 316437 CAGGGTGGTGACCCAGTAAGAGCGAGCCCTG--CTTGG---CAGGAGGAG 316481 v --- i- iv v -- --- i - MIRc#SINE/MIR 6 CAGTGTGGTG---CAGTG-GAAAGAGCACTGGACTTGGAGTCAGGAAGA- 50 chr5qtel1M 316482 CTTGGAGCCGGCCAGTCAGCGCCGACTT--CCACTTGCCAGGGGACACTC 316529 i ivi --- ---- i i-- i i vv vvvvv MIRc#SINE/MIR 51 CCTGGGTTCG---AGTC----CCGGCTCTGCCACTTACTAGCTGTGTGAC 93 chr5qtel1M 316530 CTTTGGAAAGGGATTTAAGGTCTCTGGAGCCTCCCTTCCCCAA--AGTAG 316577 v v vv i vv - vv i iv --v i MIRc#SINE/MIR 94 CTTGGGCAAGTCACTTAACCTCTCT-GAGCCTCAGTTTCCTCATCTGTAA 142 chr5qtel1M 316578 AGCAGGGATGA 316588 iii i MIRc#SINE/MIR 143 AATGGGGATAA 153 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.38 CpG sites = 18, Kimura (unadjusted) = 35.38 Transitions / transversions = 0.86 (18/21) Gap_init rate = 0.11 (17 / 151), avg. gap size = 1.29 (22 / 17) 358 31.09 11.76 1.95 chr5qtel1M 317118 317304 (682696) C MIR#SINE/MIR (8) 254 50 m_b252s601i9 10006 chr5qtel1M 317118 CTAAGCTTCAT--AGCGTGTACA----GCCAGGCCCTGTGCCAAGCCCTT 317161 vv i -- iv v---- v v i v C MIR#SINE/MIR 254 CTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGCGCTT 205 chr5qtel1M 317162 CTCACAAACATCTTCTCACTTAACCCTCTCAACAAGCTAGCAAGGCCGGT 317211 i-- vii ivv i i v v iviii iv C MIR#SINE/MIR 204 T--ACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGGTAGGT 157 chr5qtel1M 317212 GCTGTTAC---CTCC-----------GAGGAAACCGAGGCAGGGAGAAG- 317246 i i i--- i ----------- i vi i - C MIR#SINE/MIR 156 ACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGT 107 chr5qtel1M 317247 -AGGTGCCCTCTGCCCGAGGAAGCACAGCTGGGAAGGGTCCGAGGCTGGG 317295 - i iv --i i vvi i v v v v v v i C MIR#SINE/MIR 106 TAAGTAAC--TTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGA 59 chr5qtel1M 317296 TCTCAGCTC 317304 iiv i i C MIR#SINE/MIR 58 TTCGAACCC 50 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.34 CpG sites = 32, Kimura (unadjusted) = 41.29 Transitions / transversions = 1.28 (32/25) Gap_init rate = 0.05 (10 / 186), avg. gap size = 2.60 (26 / 10) 431 29.60 7.83 2.29 chr5qtel1M 317139 317304 (682696) C MIRb#SINE/MIR (37) 231 57 m_b252s601i10 10006 chr5qtel1M 317139 GCCAGGCCCTGTGCCAAGCCCTTCTCACAAACATCTTCTCACTTAACCCT 317188 v i v i-- vi iv i i C MIRb#SINE/MIR 231 GCCAGGCACTGTGCTAAGCGCTTT--ACATGCATTATCTCATTTAATCCT 184 chr5qtel1M 317189 CTCAACAAGCTAGCAAGGCCGGTGCTGTTACCTCC-----------GAGG 317227 v v iv i iv ii i i i ----------- C MIRb#SINE/MIR 183 CACAACAACCCTGCGAGGTAGGTATTATTATCCCCATTTTACAGATGAGG 134 chr5qtel1M 317228 AAACCGAGG--CAGGGAGAAGAGGTGCCCTCTGCCCGAGGAAGCACAGCT 317275 i -- i ivv i iv --i i vvi C MIRb#SINE/MIR 133 AAACTGAGGCTCAGAGAGGTTAAGTAAC--TTGCCCAAGGTCACACAGCT 86 chr5qtel1M 317276 GGGAAGGGTCCGAGGCTGGGTCTCAGCTC 317304 i v v v v v v i iiv i i C MIRb#SINE/MIR 85 AGTAAGTGGCAGAGCCGGGATTCGAACCC 57 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.70 CpG sites = 28, Kimura (unadjusted) = 38.75 Transitions / transversions = 1.40 (28/20) Gap_init rate = 0.04 (6 / 165), avg. gap size = 2.83 (17 / 6) 278 32.80 2.46 5.04 chr5qtel1M 317698 317819 (682181) C MIR#SINE/MIR (109) 153 35 m_b252s601i12 10007 chr5qtel1M 317698 ATGAACACCCCCAGTTTACAGATAAGGGAATTAAGGCTTTAATTTAAGAA 317747 v vi i v i i i i -----vivi i C MIR#SINE/MIR 153 ATTATTATCCCCATTTTACAGATGAGGAAACTGAGGC-----ACAGAGAG 109 chr5qtel1M 317748 GTTAAACATCTGTGCCCC--GTTAC-TTGCTAGTGAGGACCAAAAGCAGG 317794 ii v - v-- i -iv i viv i iv i C MIR#SINE/MIR 108 GTTAAGTAACT-TGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGG 60 chr5qtel1M 317795 GTTGGAGCCCAGCTATCAGGGCTCC 317819 i v i vi vivv C MIR#SINE/MIR 59 ATTCGAACCCAGGCAGTCTGGCTCC 35 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.90 CpG sites = 22, Kimura (unadjusted) = 44.48 Transitions / transversions = 1.38 (22/16) Gap_init rate = 0.07 (8 / 121), avg. gap size = 1.12 (9 / 8) 286 30.15 2.75 5.66 chr5qtel1M 317698 317806 (682194) C MIRb#SINE/MIR (108) 160 55 m_b252s601i11 10007 chr5qtel1M 317698 ATGAACACCCCCAGTTTACAGATAAGGGAATTAAGGCTTTAATTTAAGAA 317747 v vi i v i i i i ----- ivi i C MIRb#SINE/MIR 160 ATTATTATCCCCATTTTACAGATGAGGAAACTGAGGC-----TCAGAGAG 116 chr5qtel1M 317748 GTTAAACATCTGTGCCCC--GTTAC-TTGCTAGTGAGGACCAAAAGCAGG 317794 ii v - v-- i -iv i viv i iv i C MIRb#SINE/MIR 115 GTTAAGTAACT-TGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGG 67 chr5qtel1M 317795 GTTGGAGCCCAG 317806 i v i C MIRb#SINE/MIR 66 ATTCGAACCCAG 55 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.48 CpG sites = 20, Kimura (unadjusted) = 40.18 Transitions / transversions = 1.82 (20/11) Gap_init rate = 0.07 (8 / 108), avg. gap size = 1.12 (9 / 8) 183 22.23 0.00 2.22 chr5qtel1M 318020 318065 (681935) C MamRTE1#LINE/RTE-BovB (1689) 2123 2079 m_b252s601i13 10008 chr5qtel1M 318020 CAGAGGCCTGAGGCAGGATCTCCCCTCCCTGCAGGAGAACCTCAGC 318065 v i i - vi i vv i i C MamRTE1#LINE/ 2123 CAGACGTCTAAG-CAGCGTCTCCCCTTCCTGCTTGAAAATCTCAGC 2079 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 23.85 CpG sites = 6, Kimura (unadjusted) = 26.86 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1) 215 21.19 0.00 3.85 chr5qtel1M 319891 319944 (680056) L3#LINE/CR1 3566 3617 (482) m_b252s601i14 10009 chr5qtel1M 319891 TCTGCCCTGGCCAGAGCCACATCTGGAACAGTGTGGTCAGCCCTGAGGTG 319940 v i - ii v i v ii - i L3#LINE/CR1 3566 TCTGCGCTGGTCAGA-CCACATCTGGAGTATTGCGTTCAGTTCTG-GGCG 3613 chr5qtel1M 319941 GCAC 319944 v L3#LINE/CR1 3614 CCAC 3617 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 20.39 CpG sites = 7, Kimura (unadjusted) = 25.42 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.04 (2 / 53), avg. gap size = 1.00 (2 / 2) 13 19.56 0.00 0.00 chr5qtel1M 320655 320684 (679316) (CTC)n#Simple_repeat 1 30 (0) m_b252s252i13 10010 chr5qtel1M 320655 CTCCTCCTCTTCCTCCCCCCCCACTTCCTC 320684 i i i v i (CTC)n#Simple 1 CTCCTCCTCCTCCTCCTCCTCCTCCTCCTC 30 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 15 16.09 3.70 5.66 chr5qtel1M 320819 320872 (679128) (GAGGGCC)n#Simple_repeat 1 53 (0) m_b252s252i14 10011 chr5qtel1M 320819 GAGGGCCGAGGGGGCTGAGGGGGCAGGG--GACGGGCCGAGGGCCGGAGG 320866 -- i vvv -- - ii (GAGGGCC)n#Si 1 GAGGGCCGA--GGGCCGAGGGCCGAGGGCCGA-GGGCCGAGGGCCGAGGG 47 chr5qtel1M 320867 CAGAGG 320872 v (GAGGGCC)n#Si 48 CCGAGG 53 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.08 (4 / 53), avg. gap size = 1.25 (5 / 4) 13 0.00 0.00 0.00 chr5qtel1M 321364 321380 (678620) (TGT)n#Simple_repeat 1 17 (0) m_b252s252i15 10012 chr5qtel1M 321364 TGTTGTTGTTGTTGTTG 321380 (TGT)n#Simple 1 TGTTGTTGTTGTTGTTG 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 16 16.12 0.00 0.00 chr5qtel1M 321473 321500 (678500) (C)n#Simple_repeat 1 28 (0) m_b252s252i16 10013 chr5qtel1M 321473 CCCCCACCCCCCCACCCCACCCCCGCCC 321500 v v v v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCC 28 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 246 33.76 8.86 0.00 chr5qtel1M 324851 325087 (674913) C L1P1_orf2#LINE/L1 (1097) 2197 1940 m_b252s551i0 10014 chr5qtel1M 324851 TTTTCTAGCCTGTGACTTTGCTTAAGCTGCTCCTTATTCCGAGGAGACTT 324900 v v v v i iv i viiii i C L1P1_orf2#LIN 2197 TTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGGAGATTT 2148 chr5qtel1M 324901 T---TTTAGTTGA-----TCCTCTA-AGA-ACCAGCAAGTCGCCAGCAG- 324939 ---i v vi ----- ii - v - v v v i v i- C L1P1_orf2#LIN 2147 TGGGCTGAGACGATGGGGTTTTCTAGATATACAATCATGTCGTCTGCAAA 2098 chr5qtel1M 324940 -AGCGATAGCTTGGTTTC--CTTTCCCTAGTCTTGCACCTCCAATTTCC- 324985 - v i ii ii -- i i ivvii iiiv - C L1P1_orf2#LIN 2097 CAGGGACAATTTGACTTCCTCTTTTCCTAATTGAATACCCTTTATTTCCT 2048 chr5qtel1M 324986 TCT----CCTGGTTGCTACGGCGCCCATTTCTAGCGCCATGCTGCGTGGC 325031 ---- i ivi vvvv i i i i i i vi i v C L1P1_orf2#LIN 2047 TCTCCTGCCTGATTGCCCTGGCCAGAACTTCCAACACTATGTTGAATAGG 1998 chr5qtel1M 325032 AGGGGAGACA-CGGACACCCCTGCCTC-TCCCTGATTTCCCTGAGAAGGC 325079 v v v -v i i i i- v v v vvv i v C L1P1_orf2#LIN 1997 AGTGGTGAGAGAGGGCATCCCTGTCTTGTGCCAGTTTTCAAAGGGAATGC 1948 chr5qtel1M 325080 TTCTAGCT 325087 i i C L1P1_orf2#LIN 1947 TTCCAGTT 1940 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 45.43 CpG sites = 45, Kimura (unadjusted) = 46.23 Transitions / transversions = 1.29 (45/35) Gap_init rate = 0.04 (10 / 236), avg. gap size = 2.10 (21 / 10) 234 32.29 0.00 5.08 chr5qtel1M 326033 326156 (673844) L1PB2_3end#LINE/L1 100 217 (681) m_b252s551i1 10015 chr5qtel1M 326033 AAACAAAGTATACAACCAGATTTTCAGAAGAAACCAATGAAAAACTGTTC 326082 v ii v i vi------ v vv v i L1PB2_3end#LI 100 AAAGAAGATATACAAACGGCC------AACAAACATATGAAAAAATGCTC 143 chr5qtel1M 326083 TAAATCACGACTGATTGGAGAAATGCAAATCAGGACCCCTCTGAGGGACC 326132 v v v v v ii i i ii v vv iv L1PB2_3end#LI 144 AACATCACTAATTATCAGGGAAATGCAAATTAAAACCACAATGAGATACC 193 chr5qtel1M 326133 ACCACACACTTACGGGACCGGCTA 326156 vi v i i ii vi i L1PB2_3end#LI 194 ACCTTACTCCTGCAAGAATGGCCA 217 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 41.25 CpG sites = 19, Kimura (unadjusted) = 42.71 Transitions / transversions = 1.00 (19/19) Gap_init rate = 0.05 (6 / 123), avg. gap size = 1.00 (6 / 6) 249 35.67 1.91 0.00 chr5qtel1M 326060 326216 (673784) L1MB3_3end#LINE/L1 121 280 (650) m_b252s551i3 10015 chr5qtel1M 326060 AAGAAACCAATGAAAAACTGTTCTAAATCACGACTGATTGGAGAAATGCA 326109 v i vv iv i v v v v v i i L1MB3_3end#LI 121 AATAAGCACATGAAAAGATGCTCAACATCACTAATCATTAGGGAAATGCA 170 chr5qtel1M 326110 AATCAGGACCCCTCTGAGGGACCACCACACACTTACGGGACCGGCTAACG 326159 ii v vv iv v ii ivi ivi vii L1MB3_3end#LI 171 AATCAAAACCACAATGAGATACCACCTCACACCCATTAGGATGGCTACTA 220 chr5qtel1M 326160 TGAGGGGAA-AGAAAAGGAGAGCCGTTG--AAGGGAGGACAGAAAATCGG 326206 v iiii - vi v ivi --i iv viv v v i L1MB3_3end#LI 221 TCAAAAAAACAGAAAATAACAAGTGTTGGCGAGGATGTGGAGAAATTGGA 270 chr5qtel1M 326207 GCCCCTGCGC 326216 i i i L1MB3_3end#LI 271 ACCCTTGTGC 280 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 48.48 CpG sites = 30, Kimura (unadjusted) = 49.74 Transitions / transversions = 1.15 (30/26) Gap_init rate = 0.01 (2 / 156), avg. gap size = 1.50 (3 / 2) 283 29.59 0.00 0.00 chr5qtel1M 326060 326157 (673843) L1MD3_3end#LINE/L1 121 218 (2524) m_b252s551i2 10015 chr5qtel1M 326060 AAGAAACCAATGAAAAACTGTTCTAAATCACGACTGATTGGAGAAATGCA 326109 v i vv iv i v v i??v v i i L1MD3_3end#LI 121 AATAAGCACATGAAAAGATGCTCAACATCATNNGTCATTAGGGAAATGCA 170 chr5qtel1M 326110 AATCAGGACCCCTCTGAGGGACCACCACACACTTACGGGACCGGCTAA 326157 i ii v vv iv i i ivi vi L1MD3_3end#LI 171 AATTAAAACCACAATGAGATACCACTACACACCTATTAGAATGGCTAA 218 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 39.28 CpG sites = 15, Kimura (unadjusted) = 39.28 Transitions / transversions = 1.07 (15/14) Gap_init rate = 0.00 (0 / 97), avg. gap size = 0.0 (0 / 0) 11 27.85 0.00 2.27 chr5qtel1M 326884 326928 (673072) (CCCTCCG)n#Simple_repeat 1 44 (0) m_b252s252i17 10016 chr5qtel1M 326884 CCCTCAGCCACCAGCCCAGCTGCCTCCGCCCTTCCCCCTCCTGCC 326928 v vi v vv vv i v - (CCCTCCG)n#Si 1 CCCTCCGCCCTCCGCCCTCCGCCCTCCGCCCTCCGCCCTCC-GCC 44 Matrix = Unknown Transitions / transversions = 0.25 (2/8) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 17 4.94 0.00 0.00 chr5qtel1M 326950 326970 (673030) (C)n#Simple_repeat 1 21 (0) m_b252s252i18 10017 chr5qtel1M 326950 CCCCCCCCCCCCCCCCCCACC 326970 v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCC 21 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 13 9.98 5.88 2.86 chr5qtel1M 327151 327184 (672816) (CCCCGT)n#Simple_repeat 1 35 (0) m_b252s252i19 10018 chr5qtel1M 327151 CCCGGGCCCCG-CCCCGTCCCC-TCACCCGTTCCCG 327184 v v - - - i (CCCCGT)n#Sim 1 CCCCGTCCCCGTCCCCGTCCCCGTC-CCCGTCCCCG 35 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.09 (3 / 33), avg. gap size = 1.00 (3 / 3) 301 27.81 15.98 4.26 chr5qtel1M 329351 329519 (670481) C MIRc#SINE/MIR (61) 207 20 m_b252s601i15 10019 chr5qtel1M 329351 ACCATCTTGTCTGACCCTTGCTACCACTCGGGGGCATGGGGGAGG-AGGG 329399 ii ii i i ii v v i v ----- i v - C MIRc#SINE/MIR 207 ATTATCTCATTTGATCCTCACAACAACCCTG-----TGAGGTAGGCAGGG 163 chr5qtel1M 329400 -AGGTGCTGTCATGATCCCTATTGTACAGCTGGGGAAACAGAGG--CAGG 329446 - ii --- v i v v i v -- i C MIRc#SINE/MIR 162 CAGGTATT---ATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGA 116 chr5qtel1M 329447 CAG---CGGTGA---------------GCAACCA-TGAGCGTCTGA---- 329473 v ---vi ---------------i i i - i i v v ---- C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 66 chr5qtel1M 329474 GGCTTAGAACCCAAGTCTTTCTGACTGCAGACCCAGAGCTCCATCC 329519 vi v i i v iii v iv C MIRc#SINE/MIR 65 GGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCC 20 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.13 CpG sites = 28, Kimura (unadjusted) = 36.13 Transitions / transversions = 1.65 (28/17) Gap_init rate = 0.09 (15 / 168), avg. gap size = 2.33 (35 / 15) 16 13.24 0.00 0.00 chr5qtel1M 330719 330743 (669257) (G)n#Simple_repeat 1 25 (0) m_b252s252i21 10020 chr5qtel1M 330719 GGGGGGGGGGGGGGGAGGGCAGGGG 330743 i vi (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGG 25 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 213 17.07 2.44 0.00 chr5qtel1M 332796 332836 (667164) C L2d_3end#LINE/L2 (4) 512 471 m_b252s601i16 10021 chr5qtel1M 332796 TTAATCAATCAATGA-CATTTATTGAGCTCCCACTGTGTGCT 332836 i ii -i v i i C L2d_3end#LINE 512 TCAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCT 471 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 20.32 CpG sites = 6, Kimura (unadjusted) = 20.32 Transitions / transversions = 6.00 (6/1) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 203 17.78 4.44 0.00 chr5qtel1M 332798 332842 (667158) C L2d2_3end#LINE/L2 (3) 552 506 m_b252s601i17 10021 chr5qtel1M 332798 AATCAA-TCAATGA-CATTTATTGAGCTCCCACTGTGTGCTGGGAAC 332842 - ii -i v i vi v C L2d2_3end#LIN 552 AATCAAATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCAC 506 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 20.62 CpG sites = 5, Kimura (unadjusted) = 20.62 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.05 (2 / 44), avg. gap size = 1.00 (2 / 2) 182 35.73 3.79 4.58 chr5qtel1M 335669 335800 (664200) L3#LINE/CR1 2715 2845 (1254) m_b253s601i2 10022 chr5qtel1M 335669 AAAATTGAACCAAAAGAATGGGACTGTAAATGAGAGCCCAGCAAGCCGGA 335718 vv -- vv ivv ? iv v v i i iv L3#LINE/CR1 2715 AAAAGGGAA--AAAAGATGGATTCTGNAAACTACAGACCGGTAAGCTTGA 2762 chr5qtel1M 335719 CTTTGGTTCTTGGGAGAAGTCCACAAGAGAGCGCACATTTGAGAGATGGC 335768 v i i i ii v i v i v vi v----i vi v i L3#LINE/CR1 2763 CGTCGATCCCCGGCAAAATTCTAGAACGGAT----TATTAAACAGATGGT 2808 chr5qtel1M 335769 CAGTGAGCAT-----GAAGGAAGTAGCCAGCCCTCGG 335800 iv i-----i ii iv v v v L3#LINE/CR1 2809 TTGTGAGCACTTAGAAAAGGAAGCGGTGATCACTAGG 2845 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.50 CpG sites = 22, Kimura (unadjusted) = 49.87 Transitions / transversions = 0.96 (22/23) Gap_init rate = 0.05 (7 / 131), avg. gap size = 1.57 (11 / 7) 432 30.83 0.00 0.00 chr5qtel1M 335940 336072 (663928) CR1-3_Croc#LINE/CR1 2090 2222 (1383) m_b253s551i0 10023 chr5qtel1M 335940 ATGGCAGGAGGTCTCCAGTGAAGTGCTACAGGGATCTGTGCTCGGCCTTA 335989 i v i v i i v v ivi CR1-3_Croc#LI 2090 ATGGCAGGAGGTTTCGAGTGGAGTCCCACAGGGGTCTGTCCTGGGCCCGG 2139 chr5qtel1M 335990 TGCTGTTCAATATGTGGCCCAATGACTTGGGTAGAGGCCCAGAAAATTTG 336039 ii vvvii i i ivv vi ii v CR1-3_Croc#LI 2140 TGCTGTTCAACGTGTTTATTAATGATTTGGATGCTGGCATAGAAAGCTTC 2189 chr5qtel1M 336040 CTCCTCAAGTATACAGCTGAGAAGAAGCTAAGA 336072 i vvv v i vi v v i ii CR1-3_Croc#LI 2190 TTGAGCAAGTTTGCAGACGACACGAAACTGGGA 2222 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 36.66 CpG sites = 22, Kimura (unadjusted) = 40.50 Transitions / transversions = 1.16 (22/19) Gap_init rate = 0.00 (0 / 132), avg. gap size = 0.0 (0 / 0) 212 20.64 3.08 3.08 chr5qtel1M 336082 336146 (663854) C MIR#SINE/MIR (81) 181 117 m_b253s601i3 10024 chr5qtel1M 336082 CTCAATACAGTCTTA-GAGCTAT-TATCATTTTAATATCCCCATTTTTCA 336129 vv ii i - v v- ii v -- v C MIR#SINE/MIR 181 CTCACAACAACCCTATGAGGTAGGTACTATTAT--TATCCCCATTTTACA 134 chr5qtel1M 336130 GATGAAGAAACTGAGAC 336146 i i C MIR#SINE/MIR 133 GATGAGGAAACTGAGGC 117 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 24.38 CpG sites = 7, Kimura (unadjusted) = 24.38 Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.06 (4 / 64), avg. gap size = 1.00 (4 / 4) 232 10.81 0.00 0.00 chr5qtel1M 336111 336147 (663853) C MIRb#SINE/MIR (109) 159 123 m_b253s601i4 10024 chr5qtel1M 336111 TTAATATCCCCATTTTTCAGATGAAGAAACTGAGACT 336147 v v i i C MIRb#SINE/MIR 159 TTATTATCCCCATTTTACAGATGAGGAAACTGAGGCT 123 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 11.71 CpG sites = 2, Kimura (unadjusted) = 11.71 Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 461 31.45 8.00 1.71 chr5qtel1M 336618 336892 (663108) L2#LINE/L2 2346 2637 (445) m_b253s601i5 10025 chr5qtel1M 336618 TATATATC-AGCCCTAATCTCTTT--TGACCTCCAATCTCACACCTCTAA 336664 v - vi i ii-- v iv ii iv i L2#LINE/L2 2346 TATATCTCCAGCCCGGACCTCTCCCCTGAACTCCAGACTCGTATATCCAA 2395 chr5qtel1M 336665 CTGCCTCTTAGTTTTCTCAAACTGGATGTTCCATAGATGCCTTAAACTCA 336714 vi v viv v vi iiv iiii i i L2#LINE/L2 2396 CTGCCTACTCGACATCTCCACTTGGATGTCTAATAGGCATCTCAAACTTA 2445 chr5qtel1M 336715 ACATACCCAAAATAGAACTCGTTATCCTTTCCCCACAAATCT-----TTC 336759 ii iv v v - i v i ----- i L2#LINE/L2 2446 ACATGTCCAAAACTGAACTCCTGATC-TTCCCCCTCAAACCTGCTCCTCC 2494 chr5qtel1M 336760 C----TCTTTTTGAACTCTATAATGTGAGGACACAACCATCCTCCCTGTC 336805 ---- iiiv v vi ? ---- v i vvv i v i L2#LINE/L2 2495 CGCAGTCTTCCCCATCTCAGTNA----ATGGCAACTCCATCCTTCCAGTT 2540 chr5qtel1M 336806 TCTCA--------ACTTAGGAGTGACCCCAGCCTCTCTCCTCTCTCTCAC 336847 v -------- i v v i iv v iiii i L2#LINE/L2 2541 GCTCAGGCCAAAAACCTTGGAGTCATCCTTGACTCCTCTCTTTCTCTCAC 2590 chr5qtel1M 336848 CCCTCAACTCCAAGCCATT-GCCAGCGCTTTCACCTCTG-CTGCAAA 336892 v i vv v i- v iiv v iv i- v L2#LINE/L2 2591 ACCCCACATCCAATCCATCAGCAAATCCTGTCGGCTCTACCTTCAAA 2637 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.74 CpG sites = 47, Kimura (unadjusted) = 42.04 Transitions / transversions = 1.24 (47/38) Gap_init rate = 0.04 (12 / 274), avg. gap size = 2.25 (27 / 12) 238 30.16 1.91 17.65 chr5qtel1M 337608 337764 (662236) L2c_3end#LINE/L2 330 465 (13) m_b253s601i6 10025 chr5qtel1M 337608 AACTTG-ATCATACACCAT-TGTTTGCATG-CTCTCTCCCCCCGGAATGC 337654 - ii - iii - i ? - v i vvv i-i L2c_3end#LINE 330 AACTTGTATTGTA-ATTGTCTGTTTACNTGTCTGTCTCCTCCACTAG-AC 377 chr5qtel1M 337655 TGTGAGCTCCTTACAAGCAAAGACTATCTTCCCCCCCCCCCCCACCTTTG 337704 ivii ii ii v ------- iivii i L2c_3end#LINE 378 TGTGAGCTCCTTGAGGGCAGGGACCGTGT-------CTTATTCATCTTTG 420 chr5qtel1M 337705 TTATATCCTTCACACTCAGCACAGTGCTTCTCACACAGCAGGTGTTTAAT 337754 --- i------------ i i vv i i i i i L2c_3end#LINE 421 ---TATCCC------------CAGCGCCTGGCACATAGTAGGCGCTCAAT 455 chr5qtel1M 337755 AAATGCTTGT 337764 i L2c_3end#LINE 456 AAATGTTTGT 465 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.39 CpG sites = 30, Kimura (unadjusted) = 40.65 Transitions / transversions = 3.33 (30/9) Gap_init rate = 0.17 (27 / 156), avg. gap size = 1.00 (27 / 27) 358 29.97 3.25 11.19 chr5qtel1M 337626 337779 (662221) L2d2_3end#LINE/L2 412 554 (1) m_b253s601i7 10025 chr5qtel1M 337626 TGTTTGCATGCTCTCTCCCC--CCGGAATGCTGTGAGCTCCTTACAAGCA 337673 iii vi v -- ii ---i i ivii L2d2_3end#LIN 412 TGTTTATGTCTTGTCTCCCCAACTAGA---TTGTAAGCTCCTTGAGGGCA 458 chr5qtel1M 337674 AAGACTATCTTCCCCCCCCCCCCCACCTTTGTTATATCCTTCACA---CT 337720 ii i v --------- iivi i i - i ii --- i L2d2_3end#LIN 459 GGGACCATGT---------CTTATACTTCT-TTGTATCCCCCACAGCGCC 498 chr5qtel1M 337721 CAGCACAGTGCTTCTCACACAGCAGGTGTTTAATAAATGCTTGTGGTTGA 337770 i i iv i i i i ii --- L2d2_3end#LIN 499 TAGCACAGTGCCTTGCACACAGTAGGCGCTCAATAAATATTT---GTTGA 545 chr5qtel1M 337771 CCTGACTTG 337779 ii i L2d2_3end#LIN 546 TTTGATTTG 554 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.85 CpG sites = 35, Kimura (unadjusted) = 42.28 Transitions / transversions = 5.83 (35/6) Gap_init rate = 0.12 (18 / 153), avg. gap size = 1.17 (21 / 18) 561 37.13 1.26 0.83 chr5qtel1M 338198 338436 (661564) MIR#SINE/MIR 11 250 (12) m_b253s601i8 10026 chr5qtel1M 338198 ATGGTGACTGGAAGCCCTGGGCCTGGAGTTGGGAAGAGCAGGATTCCGCT 338247 i ii iii v v vi iii - vviv v i viv MIR#SINE/MIR 11 ATAGTGGTTAAGAGCACGGGCTCTGGAGCCAG-ACTGCCTGGGTTCGAAT 59 chr5qtel1M 338248 CTAGCCTTGGACCCCTGCTGCCCATGTGATTCTGAGTAAGTCGCCCGGCC 338297 iv v iv v v i i iv ii iii i i ii iiii MIR#SINE/MIR 60 CCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACC 109 chr5qtel1M 338298 TCTGTTTTGCTGCTGTGATCTCAACTATAAAATAGGATTAATAACAGGAC 338347 -i v iv v vvi v i i iv i v MIR#SINE/MIR 110 TCT-CTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTAC 158 chr5qtel1M 338348 CAACCTGCTGGGCTTGTGGAGAGGACTGAACCAGGT-ATGCA--CAAGGC 338394 v vv i v v v i i iv v - i --i i MIR#SINE/MIR 159 CTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATACATGTAAAGC 208 chr5qtel1M 338395 ACTTTGCACTGAGCCGGGCAGATTATAAGAGCTTACTAAATG 338436 i v v v v v v vi v i v MIR#SINE/MIR 209 GCTTAGAACAGTGCCTGGCACATAGTAAGCGCTCAATAAATG 250 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 52.06 CpG sites = 48, Kimura (unadjusted) = 52.94 Transitions / transversions = 1.20 (48/40) Gap_init rate = 0.02 (4 / 238), avg. gap size = 1.25 (5 / 4) 505 26.56 11.32 2.91 chr5qtel1M 339181 339339 (660661) C MIRb#SINE/MIR (3) 265 94 m_b253s601i9 10027 chr5qtel1M 339181 AAGGGAACGAGTACTTAGTAGGTACCTACTGTGTGCCAAGTTCTATGCTA 339230 vi i v vi i v ii ii i i i iv i C MIRb#SINE/MIR 265 AATAGAGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTA 216 chr5qtel1M 339231 AGCACTTTTCACAAACATGATCTCACTGCATCCTCACAACTACCCTGGGA 339280 i -- vi v i vv v v C MIRb#SINE/MIR 215 AGCGCTTT--ACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGA 168 chr5qtel1M 339281 GGGACAAGCTATGAGGACTCCCATTTAACAG------------------A 339312 v--- v v vv ii v ------------------ C MIRb#SINE/MIR 167 GGT---AGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCA 121 chr5qtel1M 339313 AAGGGGTTAAATGGCTTGCCCAAGGCC 339339 i i i ii i C MIRb#SINE/MIR 120 GAGAGGTTAAGTAACTTGCCCAAGGTC 94 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.56 CpG sites = 24, Kimura (unadjusted) = 33.65 Transitions / transversions = 1.41 (24/17) Gap_init rate = 0.04 (6 / 158), avg. gap size = 3.83 (23 / 6) 202 7.14 0.00 0.00 chr5qtel1M 340060 340087 (659913) MIR3#SINE/MIR 118 145 (63) m_b253s601i10 10028 chr5qtel1M 340060 GCCTCAGTTTCCTCATCTGCCAAATGAG 340087 iv MIR3#SINE/MIR 118 GCCTCAGTTTCCTCATCTGTAAAATGAG 145 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 7.52 CpG sites = 1, Kimura (unadjusted) = 7.52 Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 16 9.26 0.00 0.00 chr5qtel1M 342307 342329 (657671) (CA)n#Simple_repeat 1 23 (0) m_b253s252i0 10029 chr5qtel1M 342307 CACACACACTCACACACACGCAC 342329 v i (CA)n#Simple_ 1 CACACACACACACACACACACAC 23 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 238 18.46 0.00 12.12 chr5qtel1M 342898 342948 (657052) C DNM1r#Unknown (2116) 2546 2502 m_b253s502i0 10030 chr5qtel1M 342898 TATGTATGTGTATACATACATATGTGGATACACATACACATTAATTATAT 342947 i? ii i i i iv i -----i C DNM1r#Unknown 2546 TATANATACGTATATATACACATATATACACACATACACA-----CATAT 2502 chr5qtel1M 342948 C 342948 - C DNM1r#Unknown 2502 - 2503 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 20.52 CpG sites = 11, Kimura (unadjusted) = 22.62 Transitions / transversions = 9.00 (9/1) Gap_init rate = 0.12 (6 / 50), avg. gap size = 1.00 (6 / 6) 27 0.00 0.00 0.00 chr5qtel1M 342949 342974 (657026) (TAGA)n#Simple_repeat 1 26 (0) c_b253s251i0 10031 chr5qtel1M 342949 TAGATAGATAGATAGATAGATAGATA 342974 (TAGA)n#Simpl 1 TAGATAGATAGATAGATAGATAGATA 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 238 18.46 0.00 12.12 chr5qtel1M 342975 342996 (657004) C DNM1r#Unknown (2161) 2501 2481 m_b253s502i0 10030 chr5qtel1M 342975 CACACGCATATACACACACATA 342996 - i i C DNM1r#Unknown 2501 -ACACACATATATACACACATA 2481 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 20.52 CpG sites = 11, Kimura (unadjusted) = 22.62 Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.05 (1 / 21), avg. gap size = 1.00 (1 / 1) 281 36.02 7.83 1.32 chr5qtel1M 343010 343507 (656493) L1ME4a_3end#LINE/L1 56 585 (286) m_b253s551i2 10032 chr5qtel1M 343010 CCCCAACAGGTTAAGGAGTCAAAGAATATTAGCAAACACTTCTCAAAAGA 343059 i ivv v i - i i v i i v v L1ME4a_3end#L 56 CCCCAATAGAAAAATGGG-CAAAGGACATGAACAGACAATTCACAAAAGA 104 chr5qtel1M 343060 AAAACTGCCAAG----AATTCACA-GCACACAAATGCTCCAAGCCACTAA 343104 i v i v v---- vv -iiiv v ? i v vvi i L1ME4a_3end#L 105 AGAAATACAAATGGCCAATAAACATATGAAAANATGTTCAACCTCACTAG 154 chr5qtel1M 343105 CAATAAAAAGAGAGATG-ATTTCGCAACAGCCCT----TTTTACTTCACA 343149 i v --- i - vv iiv i vv ---- vii i iv L1ME4a_3end#L 155 TAATCAAA---GAAATGCAAATTAAAACAACAATGAGATACCATTTTTCA 201 chr5qtel1M 343150 TCCTGCAACCTGGGAAAAATGTCAAAAAATGGCCACAGTCTGTGCTGG-- 343197 i ivv vi v i v v i v iiv i vi v i -- L1ME4a_3end#L 202 CCTATCAAATTGGCAAAGATTTAAAAGATTGATAATACCCAGTGTTGGCG 251 chr5qtel1M 343198 AGGTCTATGGGAAGTTGGGCAAACTGAGAGAGCCTTGATGGAGCTGTGAA 343247 v- i ?i ivi vv v v v vivi i iiv i L1ME4a_3end#L 252 AGGG-TGTGGNGAAACGGGCACTCTCATACACTGCTGGTGGGAGTGTAAA 300 chr5qtel1M 343248 ATGGCACAAACATTTTGGAAAGCAACTTGGAATTACGCAGATAATGTGAC 343297 v i v v i ii i v v i i vvv v ivvi L1ME4a_3end#L 301 TTGGTACAACCTTTCTGGAGGGCAATTTGGCAATATGTATCAAAAGCCTT 350 chr5qtel1M 343298 TAAAATGTCCATATCCTTTGAACCGGAGACTTGGACTTTTATGAAG---- 343343 v ? i v i vi - vv i v v---- L1ME4a_3end#L 351 AAAAATGTNCATACCCTTTGACCCAGTAA-TTCCACTTCTAGGAATTTAT 399 chr5qtel1M 343344 ---AAGAAAGTCCTCACAAAC---TCCAAA---------------ATATT 343372 --- i i vv v i i---?v --------------- i L1ME4a_3end#L 400 CCTAAGGAAATAATCAGAGATGTGNACAAAGATTTATGTACAAGGATGTT 449 chr5qtel1M 343373 TATGGCAGCAATTTCTGTGAGAGCTAAGAATTGGAAATAAAGTCAACGGC 343422 i v v v i i i v v i i vv v i v L1ME4a_3end#L 450 CATCGCAGCATTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTC 499 chr5qtel1M 343423 CATTGATTGGGGGAGAACGAAACATTTTG-GGTATGAGAGTATAACGGAA 343471 vii v i?viiiv i vv i- iivvvi ? i L1ME4a_3end#L 500 CAACAATAGGGGANTGGTTAAATAAATTATGGTACATCCATANAATGGAA 549 chr5qtel1M 343472 TAGCCCTGCC-CTGTGAGAAATGATGCTTGTGATGAA 343507 -iiv v- ii v i ? i vi v L1ME4a_3end#L 550 TA-TTATGCAGCCATTAAAAATNATGTTTTCGAAGAA 585 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 50.30 CpG sites = 88, Kimura (unadjusted) = 51.11 Transitions / transversions = 0.99 (88/89) Gap_init rate = 0.04 (18 / 497), avg. gap size = 2.56 (46 / 18) 344 35.67 8.20 0.87 chr5qtel1M 343010 343436 (656564) L1ME4c_3end#LINE/L1 56 513 (317) m_b253s551i1 10032 chr5qtel1M 343010 CCCCAACAGGTTAAGGAGTCAAAGAATATTAGCAAACACTTCTCAAAAGA 343059 i i v v i - i i v i i v v ? L1ME4c_3end#L 56 CCCCAATAGATAAATGGG-CAAAGGACATGAACAGACAATTCACANAAGA 104 chr5qtel1M 343060 AAAACTGCCAAGAATTCACAG-CACAC----AAATGCTCCAAGCCACTAA 343104 ii v i v ?v i vv i- i---- i v vvi i i L1ME4c_3end#L 105 GGAAATACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTAG 154 chr5qtel1M 343105 CAATAAAAAGAGAGATGATTTC--GCAACAGCCC-TTTTTACTTCACATC 343151 i v - i viii v v-- iivv-v vii i i ii L1ME4c_3end#L 155 TAATCAAA-GAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCC 203 chr5qtel1M 343152 CTGCAACCTGGGAAAAATGTCAAAAAATGGCCACAGTCTGTGCTGG--AG 343199 ivvi vi i v v v v iiv i vi vi -- L1ME4c_3end#L 204 TATTAAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGCTGGCGAG 253 chr5qtel1M 343200 GTCTATGG-GAAGTTGGGCAAACTGAGAGAGCCTTGATGGAGCTGTGAAA 343248 ?- ii - ii -i v? v v v vivi i vi? i v L1ME4c_3end#L 254 GN-TGCGGTGAAACTGG-TACNCTCATACATTGCTGGTGGCANTGTAAAT 301 chr5qtel1M 343249 TGGCACAAACATTTTGGAAAGCAACTTGGAATTACGCAGATAATGTGACT 343298 i v v i v v i vvv iv iv iv L1ME4c_3end#L 302 TGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATA 351 chr5qtel1M 343299 AAAATGTCCATATCCTTTGAACCGGAGACT-------TGGACTTTTAT-- 343339 i i v i vi i ------- ivv -- L1ME4c_3end#L 352 AAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCC 401 chr5qtel1M 343340 ---------------GAAGAAGAAAGTCCTCACAAACTCCAAAATATTTA 343374 ---------------i i ivvvii i vi v v i i i L1ME4c_3end#L 402 TAAGGAAATAATTCAAAAGAAGGAAAAAGCTATATGCACGAAGATGTTCA 451 chr5qtel1M 343375 TGGCAGCAATTTCTGTGAGAGCTAAGAATTGGAAATAAAGTCAACGGCCA 343424 v iv v i i i v v i i vv v i v L1ME4c_3end#L 452 TTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCA 501 chr5qtel1M 343425 TTGATTGGGGGA 343436 vii v i L1ME4c_3end#L 502 ACAATAGGGGAA 513 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 48.78 CpG sites = 81, Kimura (unadjusted) = 50.68 Transitions / transversions = 1.16 (81/70) Gap_init rate = 0.03 (13 / 426), avg. gap size = 3.00 (39 / 13) 984 32.11 5.38 1.78 chr5qtel1M 343831 344480 (655520) L1ME4c_3end#LINE/L1 5 677 (153) m_b253s551i3 10033 chr5qtel1M 343831 TATTTCTAAAATACAGAGAACTGACTCAAATTTATAAGAATAGAAGTCAT 343880 i ? ?v i i i v i v v i? viv v L1ME4c_3end#L 5 TATCTNTANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAAG 54 chr5qtel1M 343881 TCCCCAATTGATAAATGGTTAAAGGAGAAAAACAGACAATTCTCGGACAA 343930 v v vi v vi v i? vi L1ME4c_3end#L 55 ACCCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGA 104 chr5qtel1M 343931 AGAAAT-----TA--AAGCCAATTC-TAGTTTTTTTTTTTTTAAATGTTC 343972 i ----- -- i v iv - i vv----------- L1ME4c_3end#L 105 GGAAATACAANTAGTAAACAAACACATGGAA-----------AAATGTTC 143 chr5qtel1M 343973 TAAATTACTCTTGATTAGAGAAATGCAAATTAAGACAACTCTGAAGTAC- 344021 v vv ii vv i i i ii vv ii - L1ME4c_3end#L 144 AACCTCGCTAGTAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACC 193 chr5qtel1M 344022 ACCTCACACCTCTCAGATTGGCCAAAATAAAGGAAAA-GGTAATAGTAAA 344070 ii i i v i i i v vv ii v- i viv L1ME4c_3end#L 194 ATTTTACGCCTATTAAATTAGCAAAAATTTAAAAAATTGATAATACCCAA 243 chr5qtel1M 344071 TATTGGTGAGGATGCAGAAAAACTGGGACACTAATGTGTTGCTGGTGGAG 344120 ii i ? i vi v ? v iii vi L1ME4c_3end#L 244 TGCTGGCGAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCA 293 chr5qtel1M 344121 TTGTAATATCATCCAACTATTCTGGAGAACAATTTGAAACTCTGCCCAAA 344170 ? vv vi v iv i i i iv v vi iviv L1ME4c_3end#L 294 NTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAA 343 chr5qtel1M 344171 GGGCTATAAAACTGTGCAATCCCTTTGATCCAGCAGTGTCTCTACTGGGC 344220 i i v v vv i i i vi v v v L1ME4c_3end#L 344 GAGCCATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGA 393 chr5qtel1M 344221 TTGTATCCCAAAGAGAT--TTTAAAGGAGGGAAAAGG--------ACCGA 344260 v v i i i -- i i i i -------- vi L1ME4c_3end#L 394 ATTTATCCTAAGGAAATAATTCAAAAGAAGGAAAAAGCTATATGCACGAA 443 chr5qtel1M 344261 CATGTGCA----AAAATTA-TTATAGTGGCAAGGAACTGGAAA----ATG 344301 v v ---- ivi - i i i ii i ----v i L1ME4c_3end#L 444 GATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTA 493 chr5qtel1M 344302 ATAGTCC-----TCGGGGAATGACTGAATAAGTTATGGGAAATGAATGTT 344346 vv ----- v ii i i i v v v? iviv L1ME4c_3end#L 494 AATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCG 543 chr5qtel1M 344347 GTGGAATATTATTGTTCTGTAAGAAACGACTGGCAGGATGATTTCAGAGA 344396 i vvvv ii v i i ivivi v v i viiv v L1ME4c_3end#L 544 ATGGAATATTATGCAGCCATTAAAAATGATAATTATGAAGACTATGTAGC 593 chr5qtel1M 344397 CACCTGGAGAGACTTACATGAACTGATGCTGAGTGAAATGAGCAGAGC-C 344445 v v - i iv vi vv i i i vi ii- L1ME4c_3end#L 594 AACATGGA-AAATGTTTATGATATAATGTTAAGTGAAAAAAGCAGAATAC 642 chr5qtel1M 344446 AGAATACTGTGTGCAGTATCAGCAAGATTATGTGA 344480 i vv i ? i iv v vi vi i i L1ME4c_3end#L 643 AAAATTGTATNTACGCTATGATTACAACTATGTAA 677 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 41.22 CpG sites = 111, Kimura (unadjusted) = 43.77 Transitions / transversions = 1.18 (111/94) Gap_init rate = 0.04 (24 / 649), avg. gap size = 1.96 (47 / 24) 17 3.57 3.23 3.23 chr5qtel1M 344620 344650 (655350) (TTTG)n#Simple_repeat 1 31 (0) m_b253s252i1 10034 chr5qtel1M 344620 TTTG-TTGTTTGTTTCATTTGTTTGTTTGTTT 344650 - -i (TTTG)n#Simpl 1 TTTGTTTGTTTGTTT-GTTTGTTTGTTTGTTT 31 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2) 348 26.53 4.40 9.93 chr5qtel1M 349582 349740 (650260) MIRb#SINE/MIR 1 151 (117) m_b253s601i11 10035 chr5qtel1M 349582 CAGAGAAACATTGT--TGCAAGGGTGGGGGGAGGGGCACCACAGATT--- 349626 iii vi -- --- iii ------ i ii --- MIRb#SINE/MIR 1 CAGAGGGGCAGCGTGGTGCA---GTGGAAAGAG------CACGGGCTTTG 41 chr5qtel1M 349627 GAGGCAGAAAGTTCTCCCTGAGTTTAAATCCGGCCTCATGACACTTCCTG 349676 v v ----v i ii v v - v v i MIRb#SINE/MIR 42 GAGTCAGACAG----ACCTGGGTTCGAATCCCGGCTC-TGCCACTTACTA 86 chr5qtel1M 349677 GCTGTGTGGCCCTTCCCAAGTCCCGTTGCCCCGGCTG--CCTCAGTTTCC 349724 i i vvv iv v vi i v- -- MIRb#SINE/MIR 87 GCTGTGTGACCTTGGGCAAGTTACTTAACCTCT-CTGAGCCTCAGTTTCC 135 chr5qtel1M 349725 TCATCTGCCAAACGAG 349740 iv i i MIRb#SINE/MIR 136 TCATCTGTAAAATGGG 151 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.01 CpG sites = 22, Kimura (unadjusted) = 33.23 Transitions / transversions = 1.38 (22/16) Gap_init rate = 0.11 (18 / 158), avg. gap size = 1.22 (22 / 18) 366 29.46 3.31 6.25 chr5qtel1M 349600 349780 (650220) MIR3#SINE/MIR 6 181 (27) m_b253s601i12 10035 chr5qtel1M 349600 AGGGTGG--GGGGAGGGGCACCACAGATTG--AGGCAGAAAGTTCTCCCT 349645 i -- i v i iv v i i -- v i ii----- MIR3#SINE/MIR 6 AGAGTGGCTGAGCAGAGAGAGCACGGACTGGGAGTCAGGAGA-----CCT 50 chr5qtel1M 349646 GAGTTTAAATCCGGCCTCATGACACTTCCTGGCTGTGTGGCCCTTCCCAA 349695 i iv i v v - v vv ? i i vvv MIR3#SINE/MIR 51 GGGTTCTAGTCCCGGCTC-TGCCACTAACTNGCTGTGTGACCTTGGGCAA 99 chr5qtel1M 349696 GTCCCGTTGCCCCGGCTG--CCTCAGTTTCCTCATCTGCCAAACGAGTCG 349743 v v ii i v- -- iv i -- MIR3#SINE/MIR 100 GTCACTTCACCTCT-CTGGGCCTCAGTTTCCTCATCTGTAAAATGAG--G 146 chr5qtel1M 349744 GGGCAGGAGAAGGCAGACCCTGCAGTTTCCCTACCAG 349780 iv vv iiiiv i ivi -- v MIR3#SINE/MIR 147 GGGTTGGACTAGATGATCTCTAAGG--TCCCTTCCAG 181 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.38 CpG sites = 27, Kimura (unadjusted) = 38.35 Transitions / transversions = 1.17 (27/23) Gap_init rate = 0.08 (14 / 180), avg. gap size = 1.21 (17 / 14) 296 28.04 13.08 0.00 chr5qtel1M 350691 350797 (649203) MIR3#SINE/MIR 24 144 (64) m_b253s601i13 10036 chr5qtel1M 350691 GGGCACAAGCTGGG--CCCGAAGAGCCAAATTCAAATCCAGATTCAG--- 350735 i iii --i v i v iiii v i v ii v --- MIR3#SINE/MIR 24 GAGCACGGACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCA 73 chr5qtel1M 350736 ---ACTAGCCGTGTGACCCAGAGCAAGT----GCGCCTGCCTG--CCTCA 350776 --- ? i iv i ----v i vi -- MIR3#SINE/MIR 74 CTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCA 123 chr5qtel1M 350777 GTCTCCTCCCCTGTGAAATGA 350797 i vi i MIR3#SINE/MIR 124 GTTTCCTCATCTGTAAAATGA 144 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.85 CpG sites = 21, Kimura (unadjusted) = 37.46 Transitions / transversions = 2.33 (21/9) Gap_init rate = 0.05 (5 / 106), avg. gap size = 2.80 (14 / 5) 18 6.91 3.23 0.00 chr5qtel1M 351355 351385 (648615) (TCCT)n#Simple_repeat 1 32 (0) m_b253s252i2 10037 chr5qtel1M 351355 TCCTTCCTCCCTTCCTT-CTTCCTTCCTTTCT 351385 i - i (TCCT)n#Simpl 1 TCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT 32 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.03 (1 / 30), avg. gap size = 1.00 (1 / 1) 17 22.84 0.00 0.00 chr5qtel1M 354165 354205 (645795) (GGC)n#Simple_repeat 1 41 (0) m_b253s252i3 10038 chr5qtel1M 354165 GGCGGCCGAGGAGGCTGCGGCGGCGGCTGCGGAGCTGGCGG 354205 v v v v v v vi (GGC)n#Simple 1 GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGG 41 Matrix = Unknown Transitions / transversions = 0.14 (1/7) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 11 23.00 0.00 8.16 chr5qtel1M 354432 354484 (645516) (CGGCCC)n#Simple_repeat 1 49 (0) m_b253s252i4 10039 chr5qtel1M 354432 CGGCCCCTGCCCCGCGGATGCGGCCCCTGCCCCCCGGATGCGGCCCCTGC 354481 - v - viv - -v viv v (CGGCCC)n#Sim 1 CGGCCCC-GGCCC-CGGCCCCGGCCCC-G-GCCCCGGCCCCGGCCCCGGC 46 chr5qtel1M 354482 CCC 354484 (CGGCCC)n#Sim 47 CCC 49 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.08 (4 / 52), avg. gap size = 1.00 (4 / 4) 25 9.79 4.44 0.00 chr5qtel1M 354637 354681 (645319) (TCC)n#Simple_repeat 1 47 (0) m_b253s252i5 10040 chr5qtel1M 354637 TCCTCC-CC-CCCCCTCCTCCTCCCTCTTCTCCTCCTCCTCCTCCTC 354681 - - i ii i (TCC)n#Simple 1 TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC 47 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.05 (2 / 44), avg. gap size = 1.00 (2 / 2) 20 20.95 4.69 3.08 chr5qtel1M 354701 354764 (645236) (CG)n#Simple_repeat 1 65 (0) m_b253s252i6 10041 chr5qtel1M 354701 CGTGCGCGCGCACAGAGACGC-CGCGCGTGACCCCG-GCCCGCACCCGCG 354748 i i - v - - i vv v - v i v (CG)n#Simple_ 1 CGCGCGCGCGCGC-GCG-CGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCG 48 chr5qtel1M 354749 CGCGCACGCGCG-GCGC 354764 i - (CG)n#Simple_ 49 CGCGCGCGCGCGCGCGC 65 Matrix = Unknown Transitions / transversions = 0.83 (5/6) Gap_init rate = 0.08 (5 / 63), avg. gap size = 1.00 (5 / 5) 60 26.34 3.63 1.01 chr5qtel1M 355535 355727 (644273) (CT)n#Simple_repeat 1 198 (0) m_b253s252i7 10042 chr5qtel1M 355535 CTCTCCCTGCCTCCCTTCCTCCCCCT-TCTCTC-CGGTTTCTCTCGCTGT 355582 i vi i ii i i - - vv i v v (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chr5qtel1M 355583 C-CTTTCTGTCTCTCCCTCCCCCCTTCCCTC-CTCTCTCTGTCTCTCTTC 355630 - i v i i i ii i - v ii (CT)n#Simple_ 51 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 100 chr5qtel1M 355631 CTCTCCCTCCCTACCCT-TCTTTCTCCCTTTCTGTTTCTCTGTCTCTC-C 355678 i i - i - i i i v i v - (CT)n#Simple_ 101 CTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 149 chr5qtel1M 355679 CCTCT-TCTCTCTGTCTCTGCTTTTTCTCTGTGTCTCTGTTTCTCTCTCT 355727 i - v - i i v v v i (CT)n#Simple_ 150 TCTCTCTCTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 198 Matrix = Unknown Transitions / transversions = 2.15 (28/13) Gap_init rate = 0.05 (9 / 192), avg. gap size = 1.00 (9 / 9) 12 24.40 0.00 0.00 chr5qtel1M 355864 355897 (644103) (CCCCC)n#Simple_repeat 1 34 (0) m_b253s252i8 10043 chr5qtel1M 355864 CCCCCCTCCCCCTCCCCCCGCTGCCCCCGCCTCC 355897 i i v iv v i (CCCCC)n#Simp 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 34 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 247 36.98 3.36 1.99 chr5qtel1M 357968 358116 (641884) L3#LINE/CR1 3942 4092 (7) m_b253s601i14 10044 chr5qtel1M 357968 CTGGGGAGGACAGTGGGCTTCCCCTCCCGGGAGAGCTTGGAGAAGAGGCG 358017 v ? -i i i v v v ivv vi v v L3#LINE/CR1 3942 CTCGNGAGG-TAGTGAGCTCCCCGTCACTGGAGGTGTTCAAGCAGAGGCT 3990 chr5qtel1M 358018 AGGGGGCTACTTCT---GGACCTCCCGGAGCAGTGAGTCTT-TGCCACAT 358063 i iv i i v --- iv i-- v v v v i -iiiiiv L3#LINE/CR1 3991 GGATGACCACTTGTCAGGGATGTT--GTAGAAGGGATTCCTGCATTGGAT 4038 chr5qtel1M 358064 CC-AGGCAAGACCCCAAGGCTTCTGGGATCTTTTCCAATTCAGAAATCCT 358112 vv- ivi ivv v i i ii i ii i v i i L3#LINE/CR1 4039 GGGAGGTTGGACTAGATGACCTCTAAGGTCCCTTCCAACTCTGAGATTCT 4088 chr5qtel1M 358113 GTGA 358116 L3#LINE/CR1 4089 GTGA 4092 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 53.34 CpG sites = 30, Kimura (unadjusted) = 53.34 Transitions / transversions = 1.25 (30/24) Gap_init rate = 0.04 (6 / 148), avg. gap size = 1.33 (8 / 6) 96 14.24 0.00 0.00 chr5qtel1M 358764 358918 (641082) (CA)n#Simple_repeat 1 155 (0) m_b253s252i9 10045 chr5qtel1M 358764 CACACACACACACACACACACAGACACACACACAGACACACACACACATA 358813 v v i (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 chr5qtel1M 358814 CACATGCACACATATACATGCACAGAGACACACACACTCACACACACATA 358863 ii i i ii v v v i (CA)n#Simple_ 51 CACACACACACACACACACACACACACACACACACACACACACACACACA 100 chr5qtel1M 358864 CATACACAGAGACACACACACACACATACACACAATCACACACACACATA 358913 i v v i vv i (CA)n#Simple_ 101 CACACACACACACACACACACACACACACACACACACACACACACACACA 150 chr5qtel1M 358914 CACAC 358918 (CA)n#Simple_ 151 CACAC 155 Matrix = Unknown Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.00 (0 / 154), avg. gap size = 0.0 (0 / 0) 463 30.75 10.19 2.15 chr5qtel1M 359886 360101 (639899) MIRb#SINE/MIR 27 259 (9) m_b253s601i15 10046 chr5qtel1M 359886 AGGGCACAGCCCCTGGGCCTGGAGGTGAGACCAGAGTTC-AGTCTGTCCT 359934 i i v ii iviii v--- v i - i ivvv MIRb#SINE/MIR 27 AGAGCACGGGCTTTGGAGTCAGAC---AGACCTGGGTTCGAATCCCGGCT 73 chr5qtel1M 359935 CAGACACTTCCTAGCTGCG-GGCTCTGGGCAACTCACTTAACCAGTCTG- 359982 v v v i - i ii v i vv - MIRb#SINE/MIR 74 CTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGA 123 chr5qtel1M 359983 -CCTCAGTGTTCT-------AAAGTGGAGATGATGGGAGC-ACCTC--AG 360021 - v i ------- i i i iiv v - -- MIRb#SINE/MIR 124 GCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTACCTCGCAG 173 chr5qtel1M 360022 GGCTGT---AAAGAGCCAATGAGGTACT-----TAAGGTGCAGATAGTCT 360063 i ---i i viv i v ----- i i v-- ivi MIRb#SINE/MIR 174 GGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCGCT--TAGCAC 221 chr5qtel1M 360064 GAGCCTTGGCATACAGTGGGTGCTTAATAAATGCTTGC 360101 iivv i i i ii i i v v MIRb#SINE/MIR 222 AGTGCCTGGCACATAGTAAGCGCTCAATAAATGGTAGC 259 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.70 CpG sites = 40, Kimura (unadjusted) = 41.18 Transitions / transversions = 1.60 (40/25) Gap_init rate = 0.07 (14 / 215), avg. gap size = 1.93 (27 / 14) 203 25.00 3.33 0.00 chr5qtel1M 360221 360280 (639720) C L2c_3end#LINE/L2 (31) 447 386 m_b253s601i16 10047 chr5qtel1M 360221 CCTACTATGTGCCA-GCCCCAGGGACACAAAGAAGGACAAAAATCACTTC 360269 - v ii i v i i i vv iv i C L2c_3end#LINE 447 CCTACTATGTGCCAGGCGCTGGGGATACAAAGATGAATAAGACACGGTCC 398 chr5qtel1M 360270 CCA-CCTCAAGG 360280 ii- C L2c_3end#LINE 397 CTGCCCTCAAGG 386 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.00 CpG sites = 10, Kimura (unadjusted) = 31.51 Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.03 (2 / 59), avg. gap size = 1.00 (2 / 2) 281 31.43 0.00 0.00 chr5qtel1M 362407 362511 (637489) C L1MC3_3end#LINE/L1 (1958) 574 470 m_b253s551i4 10048 chr5qtel1M 362407 GCTTGTTATTTCTTACCAAACAATAATATTCCATAACATTCATATACCAC 362456 ii vi i i ivvv vii vv i C L1MC3_3end#LI 574 GCTCATTTCTTTTTATCGCTGAATAATATTCCATTGTATGGATGTACCAC 525 chr5qtel1M 362457 AATTTATTCAGCCATTTTCCCATTGATGGGCATCCCCTCAGTTTCCAGTT 362506 i i i v iv i v i iivviv i C L1MC3_3end#LI 524 AGTTTGTTTATCCATTCACCTATTGAAGGACATCTTGGTTGCTTCCAGTT 475 chr5qtel1M 362507 TCTGG 362511 i C L1MC3_3end#LI 474 TTTGG 470 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 40.55 CpG sites = 20, Kimura (unadjusted) = 42.25 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.00 (0 / 104), avg. gap size = 0.0 (0 / 0) 272 24.92 0.00 8.25 chr5qtel1M 362428 362532 (637468) C L1ME2_3end#LINE/L1 (358) 553 457 m_b253s551i5 10048 chr5qtel1M 362428 AATAATATTCCATAACATTCATATACCACAATTTATTCAGCCATTTTCCC 362477 i i vii vv i i v i? i C L1ME2_3end#LI 553 AGTAGTATTCCATTGTATGAATATACCACAATTTGTTTATCCATTCNCCT 504 chr5qtel1M 362478 ATTGATGGGCATCCCCTCAGTTTCCAGTTTCTGGGAGAAATTCCATTCTA 362527 i i iivvviv - ------- i v i C L1ME2_3end#LI 503 GTTGATGGACATTTGGGTTGTTTCCAGTTT-TGGG-------CTATTATG 462 chr5qtel1M 362528 AATAA 362532 C L1ME2_3end#LI 461 AATAA 457 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 31.26 CpG sites = 15, Kimura (unadjusted) = 31.26 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.08 (8 / 104), avg. gap size = 1.00 (8 / 8) 314 26.19 0.00 0.00 chr5qtel1M 362428 362511 (637489) C L1ME2z_3end#LINE/L1 (638) 553 470 m_b253s551i6 10048 chr5qtel1M 362428 AATAATATTCCATAACATTCATATACCACAATTTATTCAGCCATTTTCCC 362477 i i vii vv i i i v i i C L1ME2z_3end#L 553 AGTAGTATTCCATTGTATGAATATACCACAGTTTGTTTATCCATTCTCCT 504 chr5qtel1M 362478 ATTGATGGGCATCCCCTCAGTTTCCAGTTTCTGG 362511 i i i ivvv v i C L1ME2z_3end#L 503 GTTGATGGACACCTGGGCTGTTTCCAGTTTTTGG 470 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 33.26 CpG sites = 14, Kimura (unadjusted) = 33.26 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.00 (0 / 83), avg. gap size = 0.0 (0 / 0) 263 29.08 1.14 2.30 chr5qtel1M 363719 363806 (636194) MIR3#SINE/MIR 81 167 (41) m_b253s601i17 10049 chr5qtel1M 363719 GCTGCTGGGAGCTGGCACAAAGTACCACAATCCCTCCGGGC-TCAGTTTC 363767 - v v v vi ivi iv -i i i - MIR3#SINE/MIR 81 GCTG-TGTGACCTTGGGCAAGTCACTTCA-CCTCTCTGGGCCTCAGTTTC 128 chr5qtel1M 363768 CTCATCTGTAAAACCACACGATTAAACTCGATCGGCTCT 363806 iv viv i ii v viv MIR3#SINE/MIR 129 CTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCT 167 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.34 CpG sites = 13, Kimura (unadjusted) = 37.34 Transitions / transversions = 1.08 (13/12) Gap_init rate = 0.03 (3 / 87), avg. gap size = 1.00 (3 / 3) 12 12.91 5.56 2.70 chr5qtel1M 364972 365007 (634993) (CCTGCCA)n#Simple_repeat 1 37 (0) m_b253s252i10 10050 chr5qtel1M 364972 CCTGCCACCTGGAACTCTG--ACCTGCCCCCAGCCACC 365007 vv - -- v v (CCTGCCA)n#Si 1 CCTGCCACCTGCCAC-CTGCCACCTGCCACCTGCCACC 37 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.50 (3 / 2) 390 31.79 2.03 5.79 chr5qtel1M 365694 365890 (634110) C MIR1_Amn#SINE/MIR (39) 191 2 m_b253s601i18 10051 chr5qtel1M 365694 AGAATTTAGGGAGTCTTACAAACTAAAGTTAAGTCAATTTTGAAATATAT 365743 vi i ii viii --ii v v -- iv v vvivi C MIR1_Amn#SINE 191 AGATCTCAAAGCACTTTACAAA--GGAGGTCAGT--ATCATTATCCCCAT 146 chr5qtel1M 365744 TTTTTGGGTGAGG---CTGAGGCA-ATTGGGGTTAAGTGACTTGCCCAGG 365789 vii i --- ?- vv i ? i C MIR1_Amn#SINE 145 TTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGCCCAAG 96 chr5qtel1M 365790 GTCACACAGCTAGGAAGTGTTAAGAGTCTGAGGTCAGATTTGACCTCAGG 365839 ? ?i v? vi- i v ------ ? ? v i C MIR1_Amn#SINE 95 GTCACNCAGCNGGCNAGTGGC-AGAGCCGG------GANTNGAACCCAGG 53 chr5qtel1M 365840 TCCTCCTGACTTTAGGGCGGTGTTCTATCCGCTGCACCAGCTAGCTGCCC 365889 ii viiiiii vv i i i iv vviv iv C MIR1_Amn#SINE 52 TCTCCCGAGTCCCAGTCCAGTGCTCTATCCACTAGACCACACTGCCTCCC 3 chr5qtel1M 365890 T 365890 C MIR1_Amn#SINE 2 T 2 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.04 CpG sites = 35, Kimura (unadjusted) = 45.04 Transitions / transversions = 1.46 (35/24) Gap_init rate = 0.07 (13 / 196), avg. gap size = 1.15 (15 / 13) 512 20.79 3.65 5.19 chr5qtel1M 365742 365878 (634122) C MIRc#SINE/MIR (123) 145 11 m_b253s601i19 10051 chr5qtel1M 365742 ATTTTTTGGGTGAGG---CTGAGGCA-ATTGGGGTTAAGTGACTTGCCCA 365787 vii i --- v- vv i C MIRc#SINE/MIR 145 ATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCA 96 chr5qtel1M 365788 GGGTCACACAGCTAGGAAGTGTTAAGAGTCTGAGGTCAGATTTGACCTCA 365837 i v vi- i v ------ i i v i C MIRc#SINE/MIR 95 AGGTCACACAGCTAGTAAGTGGC-AGAGCCGG------GACTCGAACCCA 53 chr5qtel1M 365838 GGTCCTCCTGACTTTAGGG-CGGTGTTCTATCCGCTGCACCA 365878 i ii i v- i i v i C MIRc#SINE/MIR 52 GGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCA 11 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 23.80 CpG sites = 17, Kimura (unadjusted) = 24.84 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.07 (10 / 136), avg. gap size = 1.20 (12 / 10) 628 31.79 4.05 3.21 chr5qtel1M 368149 368395 (631605) L3#LINE/CR1 3620 3868 (231) m_b253s601i20 10052 chr5qtel1M 368149 TTTGAAAAGGATAGGGATACTCTCAA------CCAGAGGAGCAGGAGCAG 368192 i i i i vv i vv vi ------ viv v L3#LINE/CR1 3620 TTTAAGAGGGACATTGACAAACTGGAGCGCGTCCAGAGGAGAGCGACCAG 3669 chr5qtel1M 368193 GAAGGTGAAGAACCCAGAATCCAAATGATAGGAAGTTTGGTTCAGAGAAC 368242 v iii ii v vi v v i vvi v ii L3#LINE/CR1 3670 GATGGTGAAGGGTCTGGAAACCATGTCATATGAGGAACGGTTGAAGGAAC 3719 chr5qtel1M 368243 TCGGAATGCTTAGCCTGGAGATGAGAAGTCTCAGGGCCGAAGGGAACGTG 368292 v i i v v i ------ ii i L3#LINE/CR1 3720 TGGGGATGTTTAGCCTGGAGAAGAGAAGACTTAG------AGGAGACATG 3763 chr5qtel1M 368293 ATGGAGATGGTTTCTAGCACTGGAAGGGCTGTCGCAGAGAAGAGAGTTGA 368342 -- v vi v ii i v iiivi i v v L3#LINE/CR1 3764 AT--AGCTGTCTTCAAATATTTGAAGGGCTGTCATGTGGAAGAGGGATTA 3811 chr5qtel1M 368343 AACTTATTCTGCTTATTCTCAGAGGACAGAATCGG---CAACAAATGTAA 368389 i iv iviii i iii --- iiii v L3#LINE/CR1 3812 GACTTATTCTGTGTGGCTCCAGAGGGCAGAACTAGGACCAATGGGTGGAA 3861 chr5qtel1M 368390 A-TACAG 368395 i- L3#LINE/CR1 3862 GTTACAG 3868 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.32 CpG sites = 47, Kimura (unadjusted) = 43.09 Transitions / transversions = 1.62 (47/29) Gap_init rate = 0.04 (11 / 246), avg. gap size = 1.64 (18 / 11) 237 33.27 13.10 1.60 chr5qtel1M 374601 374768 (625232) L3b_3end#LINE/CR1 435 621 (585) m_b254s601i0 10052 chr5qtel1M 374601 GGGACAAATGTCATGTCTCACACTAGGAT-CAAAA---CTTTC---CAAG 374643 i i v v iii v i - --- vv --- i L3b_3end#LINE 435 GGGATAAACGTAAAGTCCTGCACTTGGGTTCAAAAAANCAATCGCGCGAG 484 chr5qtel1M 374644 CCCAAAGGGAGAAAGGCGTGACG-ACCAGCCGCTTGTTTGCAAAAGGTCG 374692 iv iiiv i ii i i i v- v v ?ii v v ii v L3b_3end#LINE 485 TACAGGATGGGGGAGACGCGGCTTAGCAGCAGCNCATGTGAAAAAGACCT 534 chr5qtel1M 374693 GAGGGTTTCAGTCAGTGATCG---GC----------CCAGCAGGACAACG 374729 i i --- i --- ----------i vi i L3b_3end#LINE 535 GGGGGTTTTAGT---TGACCGCAAGCTCAATATGAGTCAGCAGTGCGACG 581 chr5qtel1M 374730 CGG-GGCTGAGAAATCTGAGGCAAATGTGGGCTGTGTAAA 374768 -v ii i v i v i viv ii v L3b_3end#LINE 582 CGGCTGCCAAAAAAGCTAATGCGATCTTGGGCTGCATTAA 621 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 41.04 CpG sites = 35, Kimura (unadjusted) = 46.78 Transitions / transversions = 1.75 (35/20) Gap_init rate = 0.06 (10 / 167), avg. gap size = 2.50 (25 / 10) 221 31.25 0.00 0.00 chr5qtel1M 375508 375571 (624429) L2d2_3end#LINE/L2 403 466 (89) m_b254s601i1 10053 chr5qtel1M 375508 CCTCTCAGCTATTTGCATGTTCTTTCCCCCTTTAGACTGTGGGCTTCTTG 375557 i i vv i iii v v i vvi i ii i L2d2_3end#LIN 403 CTTTTCACGTGTTTATGTCTTGTCTCCCCAACTAGATTGTAAGCTCCTTG 452 chr5qtel1M 375558 AGGGCAGGGACTGT 375571 ii L2d2_3end#LIN 453 AGGGCAGGGACCAT 466 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 43.08 CpG sites = 14, Kimura (unadjusted) = 43.08 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0) 271 18.57 2.82 1.39 chr5qtel1M 375516 375586 (624414) L2b_3end#LINE/L2 320 391 (75) m_b254s601i3 10053 chr5qtel1M 375516 CTATTTGCATGT-TCTTTCCCCCTTTAGACTGTGGGCTTCTTGAGGGCAG 375564 i? i - v i vi i i v L2b_3end#LINE 320 CTGNTTACATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAG 369 chr5qtel1M 375565 GGACTGTAGTGTGT-GTGTGCAC 375586 i -? v -v v L2b_3end#LINE 370 GGACCG-NGTCTGTCTTGTTCAC 391 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 20.43 CpG sites = 7, Kimura (unadjusted) = 22.27 Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.04 (3 / 70), avg. gap size = 1.00 (3 / 3) 288 17.86 1.79 0.00 chr5qtel1M 375516 375571 (624429) L2c_3end#LINE/L2 348 404 (74) m_b254s601i2 10053 chr5qtel1M 375516 CTATTTGCATGT-TCTTTCCCCCTTTAGACTGTGGGCTTCTTGAGGGCAG 375564 i i ? - v i i vi i i L2c_3end#LINE 348 CTGTTTACNTGTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAG 397 chr5qtel1M 375565 GGACTGT 375571 i L2c_3end#LINE 398 GGACCGT 404 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 19.33 CpG sites = 8, Kimura (unadjusted) = 21.71 Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.02 (1 / 55), avg. gap size = 1.00 (1 / 1) 351 26.68 14.81 0.54 chr5qtel1M 375788 375949 (624051) L2b_3end#LINE/L2 259 443 (23) m_b254s601i4 10054 chr5qtel1M 375788 GGCTCAGGTACC-TCCCCTGG-CCCCTCT--TCCTTCTTTTCAGCTCT-- 375831 v ii - i - i i-- v ii v vi -- L2b_3end#LINE 259 GGGTCAGGCGCCCTCCTCTGGGCCCCCCCAGTCCTACCCTGCCACTCTGG 308 chr5qtel1M 375832 -------CT-TCTGAGTAT-----TGTCTCCTGCACTAGAGAGTGAGCTT 375868 -------i - ?v i----- iv vv i L2b_3end#LINE 309 GTTATNATTGTCTGNTTACATGTCTGTCTCCCCCACTAGACTGTGAGCTC 358 chr5qtel1M 375869 CTTGGAGTCAGGGACTATCTTTTGCCTTTTT----G-TGAATCCCCATGG 375913 v ii v ii?v i - i v ---- - v vv L2b_3end#LINE 359 CGTGAGGGCAGGGACCGNGTCT-GTCTTGTTCACCGCTGTATCCCCAGCG 407 chr5qtel1M 375914 CTCAGCACAGTGCCTGGCACGTGGTAGATACTTAAT 375949 ii ? iii iii i i L2b_3end#LINE 408 CCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGT 443 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 31.76 CpG sites = 28, Kimura (unadjusted) = 35.10 Transitions / transversions = 1.87 (28/15) Gap_init rate = 0.06 (10 / 161), avg. gap size = 2.50 (25 / 10) 422 26.36 3.60 0.88 chr5qtel1M 375839 375949 (624051) L2d2_3end#LINE/L2 419 532 (23) m_b254s601i5 10054 chr5qtel1M 375839 GTATTGTCTCCTGCACTAGAGAGTGAGCTTCTTGGAGTCAGGGAC--TAT 375886 v ivv vv i i ii v -- i L2d2_3end#LIN 419 GTCTTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGT 468 chr5qtel1M 375887 CTTTTGCCTTTTTGTGAATCCCCATGGCTC--AGCACAGTGCCTGGCACG 375934 v i i i - vi ii v -- v i L2d2_3end#LIN 469 CTTATACTTCTTTGT-ATCCCCCACAGCGCCTAGCACAGTGCCTTGCACA 517 chr5qtel1M 375935 TGGTAGATACTTAAT 375949 ii iii i L2d2_3end#LIN 518 CAGTAGGCGCTCAAT 532 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 32.10 CpG sites = 19, Kimura (unadjusted) = 33.68 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.03 (3 / 110), avg. gap size = 1.67 (5 / 3) 297 33.15 1.14 2.30 chr5qtel1M 376181 376356 (623644) L1P3_orf2#LINE/L1 3110 3283 (11) m_b254s551i0 10055 chr5qtel1M 376181 AGAAAACATTTTGCAACAAGTTTCTCTGGTAAAGGCCTCATTTCTAAAAT 376230 i- ivvi iiv ii v v v i i L1P3_orf2#LIN 3110 AGAAAAT-TTTTGCAATCTATCCATCTGACAAAGGGCTAATATCCAGAAT 3158 chr5qtel1M 376231 -TATAGAGAACTGAGTCGAATTTATAA-AAAAATACAAGTCATTTTCCAG 376278 - i ii v iv i i - v iiv ii-- - L1P3_orf2#LIN 3159 CTACAAGGAACTTAAACAAATTTACAAGAAAAAAACAAACAACC--CCA- 3205 chr5qtel1M 376279 TTACTACATGGTCAGAGGATATGAACAGGCAGTTTTCAGACAAAGGAATC 376328 i vv vi v ii i v i i vi iv i L1P3_orf2#LIN 3206 TCAAAAAGTGGGCGAAGGATATGAACAGACACTTCTCAAAAGAAGACATT 3255 chr5qtel1M 376329 AAAGCTATCTCTAGTCATGTGAAAAAAA 376356 v v vii vvi iv i L1P3_orf2#LIN 3256 TATGCGGCCAACAAACATATGAAAAAAA 3283 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 44.33 CpG sites = 34, Kimura (unadjusted) = 45.43 Transitions / transversions = 1.48 (34/23) Gap_init rate = 0.03 (6 / 175), avg. gap size = 1.00 (6 / 6) 675 31.38 2.00 2.59 chr5qtel1M 376217 376566 (623434) L1PA17_3end#LINE/L1 1 348 (565) m_b254s551i1 10055 chr5qtel1M 376217 CTCATTTCTAAAAT-TATAGAGAACTGAGTCGAATTTATAA-AAAAATAC 376264 v v i i - ii v iv i iv i - v L1PA17_3end#L 1 CTAATATCCAGAATCTATAAGGAACTTAAACAAATCAACAAGAAAAAAAC 50 chr5qtel1M 376265 AAGTCATTTTCCAGTTACTACATGGTCAGAGGATATGAACAGGCAGTTTT 376314 i v ii-- - vv vi v i i i v i L1PA17_3end#L 51 AAATAACC--CCA-TTAAAAAGTGGGCAAAGGACATGAACAGACACTTCT 97 chr5qtel1M 376315 CAGACAAAGGAATCAAAGCTATCTCTAGTCATGTGAAAAAAATGTTCTAA 376364 i vi iv vv vii vvi iv i - i v v L1PA17_3end#L 98 CAAAAGAAGACATACAAGCGGCCAACAAACATATGAAAAAA-TGCTCAAC 146 chr5qtel1M 376365 ATCACTATAGATCAGAGAAGTGCGAATCAAAACAACTCTAAGGTACCATT 376414 vvv i i v vv i i i L1PA17_3end#L 147 ATCACTAATCATCAGAGAAATGCAAATCAAAACCACAATGAGATACCATC 196 chr5qtel1M 376415 TCACACCTATCAGAGTGATTAATATGACAAAAAAGGAAAATGTTGGATGC 376464 vi i ii v v v ivvii ivii i L1PA17_3end#L 197 TCACACCAGTCAGAATGGCTATTATTAAAAAGTCAAAAAATAACAGATGT 246 chr5qtel1M 376465 TG--GAGGAT-TGGGGAAACTGGGACAA--ATGTACTATTGGTGGAGTTG 376509 -- ? -i i vv i iv-- ii i iiv L1PA17_3end#L 247 TGGCGAGGNTGCGGAGAAAAGGGAACGCTTATACACTGTTGGTGGGAATG 296 chr5qtel1M 376510 TGAACTTTTCTAACTATTTTGGACAACAATTAATTTGGAGCTTTGACCAA 376559 i i vv ii i ivi v v i ---- i v -vi L1PA17_3end#L 297 TAAATTAGTTCAGCCCCTGTGGAAAGC----AGTTTGGAGATTT-CTCAA 341 chr5qtel1M 376560 AGGACTA 376566 i L1PA17_3end#L 342 AGAACTA 348 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 40.92 CpG sites = 61, Kimura (unadjusted) = 41.96 Transitions / transversions = 1.33 (61/46) Gap_init rate = 0.04 (14 / 349), avg. gap size = 1.14 (16 / 14) 268 28.36 6.97 6.49 chr5qtel1M 376603 377047 (622953) L1M4_orf2#LINE/L1 2848 3294 (0) m_b254s551i2 10056 chr5qtel1M 376603 GACCCACACCTAACACCATATACCAGGATAAGGTCGAAATGGGTTCATGA 376652 vi v v ii v iv i i iv v L1M4_orf2#LIN 2848 GACCCCTACCTCACACCATATACAAAAATTAACTCAAAATGGATCAAAGA 2897 chr5qtel1M 376653 TATAGACATA-GAG-TGACATTCTAAGCAAA---TTAGAAGAA--CATAG 376695 iv i ii - - i v i v --- --- -- L1M4_orf2#LIN 2898 CCTAAATGTAAGAGCTAAAACTATAA---AACTCTTAGAAGAAAACATAG 2944 chr5qtel1M 376696 GA-TAGTTCATCACTCAGATCTGTGGAGAAGGAAG---------AAATCT 376735 ?- iv v ii--- i - vv v i--------- i v L1M4_orf2#LIN 2945 GNGTAAATCTTCGT---GACCT-TGGATTAGGCAATGGTTTCTTAGATAT 2990 chr5qtel1M 376736 GTGACCAAAGAAGAACCGGAATACATTATGGAATGCGAAATGGATAATTT 376785 vv -- v vi v - -- vi ---i i v L1M4_orf2#LIN 2991 GACACCAAA--AGCACAAGCA-ACA--AAAGAA---AAAATAGATAAATT 3032 chr5qtel1M 376786 TGATTATAGTCAG--TTAAAAAGGTTAGGGA--CAAACAAAACTAATGCA 376831 v i vi - i-- vv v v v-- vi v - vv L1M4_orf2#LIN 3033 GGACTTCA-TCAAAATTAAAAACTTTTGTGCTTCAAAGGACACTA-TCAA 3080 chr5qtel1M 376832 GACAAGATTAGAAGGGAAGCTATC-AATGAG-GAAAACATTTTTA---CA 376876 - - v i iv v i iv- i - i vi --- L1M4_orf2#LIN 3081 GA-AAG-TGAAAAGACAACCCACAGAATGGGAGAAAATATTTGCAAATCA 3128 chr5qtel1M 376877 TTTAAGGGTTCTGCTAAAGGCCTTATTTCTAAAATATATAGAGAATT--- 376923 v ----- v i v ?i v i i i i --- L1M4_orf2#LIN 3129 TATA-----TCTGATAAGGGACTNGTATCCAGAATATATAAAGAACTCTT 3173 chr5qtel1M 376924 --GACTCAAATTTATAAGAACTCAAGCCATTCTCCAATTGATAAATGGTC 376971 --i --iv i vv --- vvi ? v v L1M4_orf2#LIN 3174 ACAACTCAA--CAATAAAAAGACAA---ATAACCCAATTNAAAAATGGGC 3218 chr5qtel1M 376972 AAAGGATATGAACAGACAGTTTTCAGGTGAAGAAATTAAAACCATTTCTA 377021 v i v i viiv v vv iviiivv L1M4_orf2#LIN 3219 AAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATA 3268 chr5qtel1M 377022 GTCATATGAAAAGGTGCTCCAAATCA 377047 iv i i v v L1M4_orf2#LIN 3269 AGCACATGAAAAGATGCTCAACATCA 3294 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 35.87 CpG sites = 55, Kimura (unadjusted) = 36.24 Transitions / transversions = 0.87 (55/63) Gap_init rate = 0.09 (42 / 444), avg. gap size = 1.43 (60 / 42) 309 32.47 2.55 2.55 chr5qtel1M 376773 377047 (622953) L1M1_orf2#LINE/L1 3020 3294 (0) m_b254s551i3 10056 chr5qtel1M 376773 AAATGGATAATTTTGATTATAGTCAGTTAAAAAGGTTAGGGACA---AAC 376819 i v vv i i viv v vv v --- v L1M1_orf2#LIN 3020 AAATGGACAAATGGGATCACATCAAGTTAAAAAGCTTCTGCACAGCAAAG 3069 chr5qtel1M 376820 AAAACTAATGCAGACAAGATTAGAAGGGAAGCTATC-AATGAG-GAAAAC 376867 i - - - ii v ii iv v i iv- i - i L1M1_orf2#LIN 3070 GAAAC-AAT-CA-ACAAAGTGAAGAGACAACCCACAGAATGGGAGAAAAT 3116 chr5qtel1M 376868 ATTTTTACATTTAAGGGTTCTGCTAAAGGCCTTATTTCTAAAATATATAG 376917 vi v i -- vvvv vi i vi v vv i i i L1M1_orf2#LIN 3117 ATTTGCAAACT--ACCCATCTGACAAGGGATTAATAACCAGAATATATAA 3164 chr5qtel1M 376918 AGAATTGACTCAAATTTATAAGAACTCAAGCC--ATTCTCCAATTGATAA 376965 i ii v vv v i i v-- ii -- vv i i v L1M1_orf2#LIN 3165 GGAGCTCAAACAACTCTATAGGAAA--AAATCTAATAATCCGATTAAAAA 3212 chr5qtel1M 376966 ATGGTCAAAGGATATGAACAGACAGTTTTCAGGTGAAGAAATTAAAACCA 377015 v i v i v i iiv v vv ivi L1M1_orf2#LIN 3213 ATGGGCAAAAGATCTGAATAGACATTTCTCAAAAGAAGACATACAAATGG 3262 chr5qtel1M 377016 TTTCTAGTCATATGAAAAGGTGCTCCAAATCA 377047 ivvvi v v v L1M1_orf2#LIN 3263 CAAACAGGCATATGAAAAGGTGCTCAACATCA 3294 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 42.28 CpG sites = 40, Kimura (unadjusted) = 42.91 Transitions / transversions = 0.85 (40/47) Gap_init rate = 0.04 (11 / 274), avg. gap size = 1.27 (14 / 11) 335 28.11 3.12 3.66 chr5qtel1M 376856 377047 (622953) L1PREC2_orf2#LINE/L1 3104 3294 (0) m_b254s551i4 10056 chr5qtel1M 376856 AATGAGGAAAACATTTTTACATTTAAGGGTTCTGCTAAAGGCCTTATTTC 376905 - i v ? i vviv v vv vi i v v L1PREC2_orf2# 3104 AATG-GGAGAAAATNTTTGCAAACTATGCATCTGACAAAGGTCTAATATC 3152 chr5qtel1M 376906 TAAAATATATAGAGAATTGACTCAAATTTATAAGAACT---CAAGCCATT 376952 i iv v ii i v vv i vv--- i v -- L1PREC2_orf2# 3153 CAGCATCTATAAGGAACTTAAACAAATTTACAAGAAAAAAACAAACAA-- 3200 chr5qtel1M 376953 CTCCAATTGATAAATGGTCAAAGGATATGAACAGACAGTTTTCAGGTGAA 377002 i - i v i v i v iiv L1PREC2_orf2# 3201 CCCCA-TTAAAAAGTGGGCAAAGGACATGAACAGACACTTTTCAAAAGAA 3249 chr5qtel1M 377003 GAAAT---TAAAACCATTTCTAGTCATATGAAAAGGTGCTCCAAATCA 377047 v --- ivii --v v - iiv v v L1PREC2_orf2# 3250 GACATACATGCGGCCA--ACAAG-CATATGAAAAAAAGCTCAACATCA 3294 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 34.83 CpG sites = 23, Kimura (unadjusted) = 35.65 Transitions / transversions = 0.79 (23/29) Gap_init rate = 0.05 (9 / 191), avg. gap size = 1.44 (13 / 9) 1355 31.22 3.55 1.98 chr5qtel1M 376901 377547 (622453) L1ME5_3end#LINE/L1 4 660 (281) m_b254s551i6 10056 chr5qtel1M 376901 ATTTCTAAAATATATAGAGAATTGACTCAAATTTATAAGAACTCAAGCCA 376950 v i i ii i vviv iv i v-- v i L1ME5_3end#LI 4 ATATCTAGAATATACAAGGAACTCCTGCAAATCAACAAGAAA--AAGACG 51 chr5qtel1M 376951 TT--CTCCAATTGATAAATGGTCAAAGGATATGAACAGACAGTTTTCAGG 376998 v?-- i v v v i i v i L1ME5_3end#LI 52 GNAACCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGA 101 chr5qtel1M 376999 TGAAGAAATTAAAACCATTTCTAGTCATATGAAAAGGTGCTCCAAATCAC 377048 v i iivi vvii vvi iv i i v v i L1ME5_3end#LI 102 AGAGGAAACCCGAAAGGCTAACAAGCATATGAAGAGATGCTCAAACTCAT 151 chr5qtel1M 377049 TATTGATCAGAGAAATGCAAATTTGGACAACTCTGAGGAACCACTACACA 377098 v i vii vv iv i vi L1ME5_3end#LI 152 TAGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACA 201 chr5qtel1M 377099 CCTCTCAGATTGGCCAAGGTGAAGGAAA---AGATAAAGACAAATGTTGG 377145 v i i v ii v -- ---i v v i L1ME5_3end#LI 202 CCTATTAGACTGGCAAAAATTA--GAAAGCTGGATAATGCCAAGTGTTGG 249 chr5qtel1M 377146 AGGGGATATGGGAAAACTGGGAAATTGATACATTGTTGGTGGAATTGTGA 377195 v i i i ? iv i vvi v i i i i v ii L1ME5_3end#LI 250 CGAGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAG 299 chr5qtel1M 377196 ATACATCCAGCCATTCTGAAGAGCAACTTAGAATTA--TGCCCAAAGCAC 377243 ivvi v i ii i v v -- ivi ----- L1ME5_3end#LI 300 ACTGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAA----- 344 chr5qtel1M 377244 TATCAAGC-TGTGCATACCCTTTGATCCATCAGTGTTTCTACTGGGATTA 377292 - i i- ii v i v i viiv v vv L1ME5_3end#LI 345 -ATTAAGTATACGCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATA 393 chr5qtel1M 377293 TATCCCAAAAA---TCTTAAAGGAGG----GAAAGGGATACGTGCAAATA 377335 i --- i v -v ----v i i i i i iv L1ME5_3end#LI 394 TATCCCAAAGAAATTCTCACA-CAGGTCCATAAGGGGACATGTACGAGGA 442 chr5qtel1M 377336 TGTTTGTGGCAGCCCTTTTTCTAGTGGCAAGAAACCGGAAGCTAAGTGGC 377385 ii v vi v v i ii i iii i v vv v L1ME5_3end#LI 443 TGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGGG 492 chr5qtel1M 377386 TGCCCATCAATTGAAGAATGGCTGAATAAACTATGGTACATGAATGTGAT 377435 i v v i i v iii v i iv v iiiv L1ME5_3end#LI 493 TGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACACCAT 542 chr5qtel1M 377436 GGAATATCATTGTTCTGTAAGAAACAACAG-CAGGATGATTTCAGAGAGG 377484 i ii vvvv v v i i - vi vviv v vii L1ME5_3end#LI 543 GGAGTACTATGCAGCAGTTAGAAGCAACGGACTAGATGTACACATAGCAA 592 chr5qtel1M 377485 CCTGGAGAGA-CTGGCAGGAAC-TGATGCTGAGTGAAATAAGC-AGAACC 377531 v vi - --i ii - ii v i- v L1ME5_3end#LI 593 CATGGATGGATCT--TAAAAACATAGTGCTGAGTGAAAAAAGTAAGAAAC 640 chr5qtel1M 377532 AG---GAGATC-ATCATACA 377547 --- ?- v i L1ME5_3end#LI 641 AGAATGAGATNTATAACACA 660 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.78 CpG sites = 111, Kimura (unadjusted) = 41.70 Transitions / transversions = 1.28 (111/87) Gap_init rate = 0.04 (25 / 646), avg. gap size = 1.44 (36 / 25) 1366 30.68 2.02 0.72 chr5qtel1M 376901 377445 (622555) L1ME4c_3end#LINE/L1 4 555 (275) m_b254s551i5 10056 chr5qtel1M 376901 ATTTCTAAAATATATAGAGAATTGACTCAAATTTATAAGAAC----TCAA 376946 v ?v ? i ii v i v v---- L1ME4c_3end#L 4 ATATCTNTANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAA 53 chr5qtel1M 376947 GCCATTCTCCAATTGATAAATGGTCAAAGGATATGAACAGACAGTTTTCA 376996 v ----i v v i i iv L1ME4c_3end#L 54 GAC----CCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACA 99 chr5qtel1M 376997 GGTGAAGAAATTAAAACCATTTCTAGTCATATGAAAAGGTGCTCCAAATC 377046 ?iv i vv ?ivi vvvi iv i i ii i v vv L1ME4c_3end#L 100 NAAGAGGAAATACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTC 149 chr5qtel1M 377047 ACTATTGATCAGAGAAATGCAAATTTGGACAACTCTGAGGAACCACTACA 377096 i v i i viii vv iv i vi L1ME4c_3end#L 150 GCTAGTAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTA 199 chr5qtel1M 377097 CACCTCTCAGATTGGCCAAGG-TGAAGGAAAAGATAAAGACAAATGTTGG 377145 i v i i i v ii- v ii vv viv v i L1ME4c_3end#L 200 CGCCTATTAAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGCTGG 249 chr5qtel1M 377146 AGGGGATATGGGAAAACTGGGAAATTGATACATTGTTGGTGGAATTGTGA 377195 v i ? ii vi v v?i v i v ? i L1ME4c_3end#L 250 CGAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAA 299 chr5qtel1M 377196 ATACATCCAGCCATTCTGAAGAGCAACTTAGAATTATGCCCAAAGCACTA 377245 vvi v i v i i i i i v v i iviv vi i L1ME4c_3end#L 300 ATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCA 349 chr5qtel1M 377246 TCAAGCTGTGCATACCCTTTGATCCATCAGTGTTTCTACTGGGATTATAT 377295 v iv v i vi i viiv v v v L1ME4c_3end#L 350 TAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTAT 399 chr5qtel1M 377296 CCCAA--AAAT--CTTAAAGGAGGGAAAGGGATACGTGCA--AATATGTT 377339 i -- --i i i i ii v ii -- v L1ME4c_3end#L 400 CCTAAGGAAATAATTCAAAAGAAGGAAAAAGCTATATGCACGAAGATGTT 449 chr5qtel1M 377340 TGTGGCAGCCCTTTTTCTAGTGGCAAGAAACCGGAAGCTAAGTGGCTGCC 377389 ii v vi v v i i i i ii i v vv iiv i L1ME4c_3end#L 450 CATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTC 499 chr5qtel1M 377390 CATCAATTGAAGAATGGCTGAATAAACTATGGTACATGAATGTGATGGAA 377439 v v ii i i i i v? ivi L1ME4c_3end#L 500 CAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAA 549 chr5qtel1M 377440 TATCAT 377445 i L1ME4c_3end#L 550 TATTAT 555 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.39 CpG sites = 94, Kimura (unadjusted) = 41.33 Transitions / transversions = 1.31 (94/72) Gap_init rate = 0.02 (9 / 544), avg. gap size = 1.67 (15 / 9) 18 27.29 4.84 0.00 chr5qtel1M 377797 377858 (622142) (TA)n#Simple_repeat 1 65 (0) m_b254s252i0 10057 chr5qtel1M 377797 TATATAAATATATATGTGCATATAT-TGGATTTA-ACATATATATTAACA 377844 v i ii - iv v - i vv i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr5qtel1M 377845 TATTTA-ACATGTAT 377858 v - i i (TA)n#Simple_ 51 TATATATATATATAT 65 Matrix = Unknown Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.05 (3 / 61), avg. gap size = 1.00 (3 / 3) 259 18.63 0.00 10.53 chr5qtel1M 378012 378095 (621905) L1MA1_3end#LINE/L1 336 411 (638) m_b254s551i7 10058 chr5qtel1M 378012 CCCCAAAAAACAACAAAAACTGTGTATACCCTTTGATCCAGCAATATTAC 378061 i --i i v i- v v vii L1MA1_3end#LI 336 CCTCAAAAAAC--TAAAAATTGAGC-TACCATATGATCCAGCAATCCCAC 382 chr5qtel1M 378062 TGCTAGATCTATTTCCCAAAAGGATCAAAGGAAA 378095 i i v - v ---- L1MA1_3end#LI 383 TGCTGGGTATA-TACCCAAAAG----AAAGGAAA 411 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 21.38 CpG sites = 8, Kimura (unadjusted) = 21.38 Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.10 (8 / 83), avg. gap size = 1.00 (8 / 8) 268 28.55 6.79 4.89 chr5qtel1M 378028 378248 (621752) L1ME3G_3end#LINE/L1 345 569 (355) m_b254s551i8 10058 chr5qtel1M 378028 AAACTGTGTATACCCTTTGATCCAGCAATATTACTGCTAG--ATCTATTT 378075 v i i i vii v ? -- -- L1ME3G_3end#L 345 AAAATGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTAT-- 392 chr5qtel1M 378076 CCCAAAAGGAT-----CAAAGG---AAAAGGACCCAAAAGCACCAAAAAA 378117 i ? iii ----- v v --- v ?v v-- i -- ii L1ME3G_3end#L 393 CCTANAGAAATACTCGCACATGTGCACAAGGANGCAT--GTAC--AAGGA 438 chr5qtel1M 378118 TGT--ATAGCGGCTCTTTTTTTGTGTGCTCACTAAGAATAAGAAATTAAA 378165 -- v i vi v ---- iv vi v i vi iv vv L1ME3G_3end#L 439 TGTTCATTGCAGCATTGTTT----GTAATAGCGAAAAATTGGAAACAACC 484 chr5qtel1M 378166 GGGATGCCCATCAGTCAGGGAATGGCTAAACAAGCTGTGACATAT-GATG 378214 vii i i vi i i ii i ii -v i L1ME3G_3end#L 485 TAAATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCATA 534 chr5qtel1M 378215 -TGTGGAATATT-TGAGTGCTGTAAAAATTAATGAG 378248 - i i - vi- ? v vv L1ME3G_3end#L 535 CTATGGAATACTATGCA-GCNGTTAAAAAGAATGAG 569 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 37.06 CpG sites = 35, Kimura (unadjusted) = 37.87 Transitions / transversions = 1.40 (35/25) Gap_init rate = 0.08 (18 / 220), avg. gap size = 1.44 (26 / 18) 12 13.67 0.00 0.00 chr5qtel1M 379396 379419 (620581) (AGGA)n#Simple_repeat 1 24 (0) m_b254s252i1 10059 chr5qtel1M 379396 AGGAAGGAAGGATGGAAAGTAGGA 379419 v i v (AGGA)n#Simpl 1 AGGAAGGAAGGAAGGAAGGAAGGA 24 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 256 28.70 3.28 8.62 chr5qtel1M 380972 381093 (618907) MIR3#SINE/MIR 41 156 (52) m_b254s601i6 10060 chr5qtel1M 380972 CAGGAGATGTTGCGAGTTCAAACCCAGCCTCAGCAGCTTAACTGGCC-CG 381020 iv --- i v ii v v v vi - ? i-i MIR3#SINE/MIR 41 CAGGAGACCT---GGGTTCTAGTCCCGGCTCTGCCACT-AACTNGCTGTG 86 chr5qtel1M 381021 -GACTCTAGGCAAATTATCTTAGCCTGTTTG--TCTCCATTTTCTCATCT 381067 - ii i i i ii i - v i --i vi i MIR3#SINE/MIR 87 TGACCTTGGGCAAGTCACTTCA-CCTCTCTGGGCCTCAGTTTCCTCATCT 135 chr5qtel1M 381068 ACTAAATGAGCAGAAGGGGATGGCCT 381093 iiv ----- v v MIR3#SINE/MIR 136 GTAAAATGAG-----GGGGTTGGACT 156 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 37.98 CpG sites = 21, Kimura (unadjusted) = 37.98 Transitions / transversions = 1.91 (21/11) Gap_init rate = 0.11 (13 / 121), avg. gap size = 1.08 (14 / 13) 283 28.11 4.08 2.00 chr5qtel1M 380985 381082 (618918) MIR#SINE/MIR 50 149 (113) m_b254s601i7 10060 chr5qtel1M 380985 GAGTTCAAACCCAGCCTCAGCAGCTTAACTGGCC-CG-GACTCTAGGCAA 381032 i i i v v v vi - i i-i - ii i MIR#SINE/MIR 50 GGGTTCGAATCCCGGCTCTGCCACTTA-CTAGCTGTGTGACCTTGGGCAA 98 chr5qtel1M 381033 ATTATCTTAGCCTGTTTGT--CTCCATTTTCTCATCTACTAAATGAGCAG 381080 i - i v i -- vi i iiv i v v MIR#SINE/MIR 99 GTTA-CTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGAT 147 chr5qtel1M 381081 AA 381082 MIR#SINE/MIR 148 AA 149 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 35.08 CpG sites = 18, Kimura (unadjusted) = 36.82 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.05 (5 / 97), avg. gap size = 1.20 (6 / 5) 644 27.64 6.67 1.82 chr5qtel1M 381731 381940 (618060) MIRc#SINE/MIR 3 222 (46) m_b254s601i8 10061 chr5qtel1M 381731 AGGCAGATAGGTGAACCAGAGGATAGAATGCTGGATGTGGAGTCCAGAAG 381780 vvv --- v v iii iv vi MIRc#SINE/MIR 3 AGGCAGTGTGGTG---CAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAG 49 chr5qtel1M 381781 TCCCGAGTTCAGATCTTGCCTCAGACATCTGCTGGTTATGGGAACCTGGG 381830 v i i iii ii v v v ii i i i i v v i MIRc#SINE/MIR 50 ACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGG 99 chr5qtel1M 381831 AAAGTCACTTGACCTGTGTCTGCTTTAGTTTTTTCCTTTGTAAAATGGAG 381880 v i v v vv i i ii v i i MIRc#SINE/MIR 100 CAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGG 149 chr5qtel1M 381881 ATGATAATA---GCCCTCACTATATTCA----GTTATTGTGAAGA-CA-- 381920 i --- vv i-i ---- i i - -- MIRc#SINE/MIR 150 ATAATAATACCTGCCCTGCCTAC-CTCACAGGGTTGTTGTGAGGATCAAA 198 chr5qtel1M 381921 --AGATA--GTATTTTAAAATCCT 381940 -- -- v v iiv MIRc#SINE/MIR 199 TGAGATAATGTATGTGAAAGCGCT 222 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 33.07 CpG sites = 33, Kimura (unadjusted) = 35.35 Transitions / transversions = 1.38 (33/24) Gap_init rate = 0.05 (10 / 209), avg. gap size = 1.80 (18 / 10) 38 0.00 0.00 0.00 chr5qtel1M 382733 382767 (617233) (T)n#Simple_repeat 1 35 (0) c_b254s251i0 10062 chr5qtel1M 382733 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 382767 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 35 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 18 21.84 0.00 0.00 chr5qtel1M 383044 383080 (616920) (T)n#Simple_repeat 1 37 (0) m_b254s252i2 10063 chr5qtel1M 383044 TTTTTCTATTTTTTTCTTTTTTTTGTTTTGCTTTATT 383080 i v i v vi v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 37 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 35 34.13 1.31 1.31 chr5qtel1M 384048 384200 (615800) (AAAG)n#Simple_repeat 1 153 (0) m_b254s252i3 10064 chr5qtel1M 384048 AAAGAAAAAAAGGAAGGAA-TAAG-AAGAAAGGAAGGAAGGAAGGAAGAA 384095 i i i -v - i i i i - (AAAG)n#Simpl 1 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG-A 49 chr5qtel1M 384096 AAAAAAGGAAGGAAGAAAAAAAAGGAAGGAGGGAGGGAAGGAAGATAGAT 384145 i i i - i i i i i i i i v v (AAAG)n#Simpl 50 AAGAAAGAAAGAAAG-AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAA 98 chr5qtel1M 384146 AAATAGATGGGTGGATGGATGGATAGATAGATGGATATATAGAAAGAAAG 384195 i v vi ivi vi vi v v vi v v v (AAAG)n#Simpl 99 AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG 148 chr5qtel1M 384196 ACAGA 384200 v (AAAG)n#Simpl 149 AAAGA 153 Matrix = Unknown Transitions / transversions = 1.67 (25/15) Gap_init rate = 0.03 (4 / 152), avg. gap size = 1.00 (4 / 4) 237 28.71 9.90 0.00 chr5qtel1M 385335 385435 (614565) L2a_3end#LINE/L2 387 497 (20) m_b254s601i9 10065 chr5qtel1M 385335 CTCCTCCCTGGAGTGGAAGCTCCTGGTGGGCAGGCCCTGCT-TCC-TTTT 385382 i i v i i v vv v vv vi - i- L2a_3end#LINE 387 CCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTCTGTTTT 436 chr5qtel1M 385383 GTT------TGCATTCCCAGCACACAGCACAATAGCTGGCCCCTA--AAA 385424 ------ i i i vi v i iv v v -- ii L2a_3end#LINE 437 GTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGG 486 chr5qtel1M 385425 CGCACAACAAA 385435 v i L2a_3end#LINE 487 CGCTCAATAAA 497 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 35.17 CpG sites = 15, Kimura (unadjusted) = 36.72 Transitions / transversions = 1.07 (15/14) Gap_init rate = 0.04 (4 / 100), avg. gap size = 2.50 (10 / 4) 328 25.64 14.53 0.00 chr5qtel1M 386265 386381 (613619) MIR#SINE/MIR 63 196 (66) m_b254s601i10 10066 chr5qtel1M 386265 GGCTCGGCC-CCTACCAAGTGTGTGACTGTGGGTAAGCCGTTGAACTCCT 386313 v - i i iv iv i iiii v ii MIR#SINE/MIR 63 GGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCT 112 chr5qtel1M 386314 ACCTGCCTCGATTTCCTCAGCTGTACATTGGGG-----------ACCTCT 386352 viv ii v v v ----------- vi MIR#SINE/MIR 113 CTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTAC 162 chr5qtel1M 386353 CTC--AGGGTTTCAGTCAGGATTCA---AGTTAA 386381 -- viv v v --- MIR#SINE/MIR 163 CTCATAGGGTTGTTGTGAGGATTAAATGAGTTAA 196 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 31.81 CpG sites = 16, Kimura (unadjusted) = 31.81 Transitions / transversions = 1.14 (16/14) Gap_init rate = 0.03 (4 / 116), avg. gap size = 4.25 (17 / 4) 206 28.57 0.00 0.00 chr5qtel1M 386744 386792 (613208) L2d_3end#LINE/L2 450 498 (18) m_b254s601i11 10067 chr5qtel1M 386744 ATAGAGCTTACCACTGTACCCAGCACATAGTAGGTGCTTCTTAAGTGCT 386792 i v i v v i iv i ivv i i L2d_3end#LINE 450 ACAGCGCCTAGCACAGTGCTGAGCACATAGTAGGCGCTCAATAAATACT 498 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 33.59 CpG sites = 8, Kimura (unadjusted) = 36.82 Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 16 14.45 2.50 2.50 chr5qtel1M 389287 389326 (610674) (CCTGCT)n#Simple_repeat 1 40 (0) m_b254s252i4 10068 chr5qtel1M 389287 CCTAGCTCCAGCTCCAGCT-CTGCTTCTGCTCATGGTCCTG 389326 - v v - i v v (CCTGCT)n#Sim 1 CCT-GCTCCTGCTCCTGCTCCTGCTCCTGCTCCTGCTCCTG 40 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 12 18.27 5.41 0.00 chr5qtel1M 389758 389794 (610206) (ATAAGT)n#Simple_repeat 1 39 (0) m_b254s252i5 10069 chr5qtel1M 389758 ATATGTTAAAGTATAAGT-TAAATACAA-TATATGTATA 389794 v vv - i i - v (ATAAGT)n#Sim 1 ATAAGTATAAGTATAAGTATAAGTATAAGTATAAGTATA 39 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 136 28.02 0.50 1.51 chr5qtel1M 390051 390451 (609549) (GT)n#Simple_repeat 1 397 (0) m_b254s252i6 10070 chr5qtel1M 390051 GTGTGTGTGTGTATGTGTGTGAGTGTGAGT-TGTGTGATGTGAATATGTG 390099 i v v - - vi i (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG-TGTGTGTGTGTG 49 chr5qtel1M 390100 TGTGAGTGTATGTGTGATGTGCATGTCATTGTGTGTGATTGTGTGAGTGT 390149 v i - ii vvv vv v (GT)n#Simple_ 50 TGTGTGTGTGTGTGTG-TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 98 chr5qtel1M 390150 GTGTGAGTGTGTGAATAAGTGTATGTGTGATATGTGTGTGATTGCGTTTG 390199 v vi iv i - i vv i v (GT)n#Simple_ 99 GTGTGTGTGTGTGTGTGTGTGTGTGTGTG-TGTGTGTGTGTGTGTGTGTG 147 chr5qtel1M 390200 T-TGTGATTGTGAGTGTGTGAATGTAAGAGTGTGTGATTGTATATGATGT 390248 - vv v vi iv v vv i i - (GT)n#Simple_ 148 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG-TGT 196 chr5qtel1M 390249 GCATGTGATTGTGTGTGAGTGTATATGTGATTGTGTGGGTGTGATATGTG 390298 ii vv v i i vv v - i (GT)n#Simple_ 197 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG-TGTGTG 245 chr5qtel1M 390299 TGAGTGTGAATGTAAGCATGTGTGAGTGTGAATGTAAGCATGTGTGTGTG 390348 v vi iv ii v vi iv ii (GT)n#Simple_ 246 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 295 chr5qtel1M 390349 AATATAAGCATGTGATTGTGGGTGGTTGTGTGAGTGTGATATGTGTGTGT 390398 vi i iv ii vv v vv v - i (GT)n#Simple_ 296 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG-TGTGTGTGTGT 344 chr5qtel1M 390399 GTGATTGTGTGAGTGTGTATGTGTAAATGTAAGTATGTGTGATTGTGAGT 390448 vv v i ivi iv i vv v (GT)n#Simple_ 345 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 394 chr5qtel1M 390449 GTG 390451 (GT)n#Simple_ 395 GTG 397 Matrix = Unknown Transitions / transversions = 0.75 (39/52) Gap_init rate = 0.02 (8 / 400), avg. gap size = 1.00 (8 / 8) 28 3.33 0.00 0.00 chr5qtel1M 392094 392124 (607876) (AGCCCC)n#Simple_repeat 1 31 (0) c_b254s251i1 10071 chr5qtel1M 392094 AGCCCCAGCCCCAGCCCCAGCCCCAGTCCCA 392124 i (AGCCCC)n#Sim 1 AGCCCCAGCCCCAGCCCCAGCCCCAGCCCCA 31 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 20 4.35 0.00 0.00 chr5qtel1M 394267 394290 (605710) (A)n#Simple_repeat 1 24 (0) m_b254s252i7 10072 chr5qtel1M 394267 AAAAAAAAAAAAAAGAAAAAAAAA 394290 i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAA 24 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 chr5qtel1M 397551 397568 (602432) (A)n#Simple_repeat 1 18 (0) m_b254s252i8 10073 chr5qtel1M 397551 AAAAAAAAAAAAAAAAAA 397568 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAA 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 16 13.08 0.00 0.00 chr5qtel1M 397764 397788 (602212) (TC)n#Simple_repeat 1 25 (0) m_b254s252i9 10074 chr5qtel1M 397764 TCTCTATTTCTCTCTCTATCTCTCT 397788 v i v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCT 25 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 22 0.00 0.00 0.00 chr5qtel1M 398782 398805 (601195) (A)n#Simple_repeat 1 24 (0) m_b254s252i10 10075 chr5qtel1M 398782 AAAAAAAAAAAAAAAAAAAAAAAA 398805 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAA 24 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 29 15.87 0.00 0.00 chr5qtel1M 399041 399089 (600911) (A)n#Simple_repeat 1 49 (0) m_b254s252i11 10076 chr5qtel1M 399041 AACAAAAAACAAAAAAAAACAAAAACAAAAAGAAAAAAGAAGAAAAAAA 399089 v v v v i i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 49 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 240 31.94 3.57 3.57 chr5qtel1M 399289 399512 (600488) L1M4_orf2#LINE/L1 686 909 (2385) m_b254s551i9 10077 chr5qtel1M 399289 ACCAAAATTCAATAGAATTCATATTTAATAAGAGACTACAGAAATACAGA 399338 v vv ii viv v i v v---i ----- L1M4_orf2#LIN 686 ACCACAATGGAATGAAATTAGAAATCAATAACAGAA---GGAAAT----- 727 chr5qtel1M 399339 TTGGAAAATC----AAT---TGAAGATTAAATAACTTAATTTTAAAGAAC 399381 i i---- --- i i i vi v ii v L1M4_orf2#LIN 728 TTGGGAAATTCACAAATATGTGGAAATTAAACAACACACTCCTAAATAAC 777 chr5qtel1M 399382 GTGTGGATTAAGAAACCAGTCTTAGGAACAATAAATAATTATATTGAAGA 399431 vvi i i ii vv i vi i iiv v iv v iv iiv L1M4_orf2#LIN 778 CAATGGGTCAAAGAAGAAATCACAAGGGAAATTAGAAAATACTTTGAGAT 827 chr5qtel1M 399432 GAATAATAGTAATGAGACAACATACAAGAACT-ATGGGATGCAGCAAAAA 399480 i v iii vi v v i - ? i L1M4_orf2#LIN 828 GAATGAAAACGAAAACACAACATACCAAAACTTATGGGATGCAGCNAAAG 877 chr5qtel1M 399481 CAGTAATGGGAGGAAAATGTGTATCTTTAAAT 399512 iv vi i v i v v L1M4_orf2#LIN 878 CAGTGCTTAGAGGGAAATTTATAGCTGTAAAT 909 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 42.01 CpG sites = 38, Kimura (unadjusted) = 42.93 Transitions / transversions = 1.23 (38/31) Gap_init rate = 0.05 (11 / 223), avg. gap size = 1.45 (16 / 11) 325 30.64 4.28 0.52 chr5qtel1M 399326 399512 (600488) L1MC_orf2#LINE/L1 716 909 (2385) m_b254s551i10 10077 chr5qtel1M 399326 ACAGAAATACAGATTGGAAAATC-------AATTGAAGATTAAATAACTT 399368 v i -i ------- v i i vi L1MC_orf2#LIN 716 ACAGAAAGATAG-CTGGAAAATCCCAAAATACTTGGAGATTAAACAACAC 764 chr5qtel1M 399369 AATTTTAAAGAACGTGTGGATTAAGAAACCAGTCTTAGGAACAATAAATA 399418 v i v iii i i ii vv i i i iv vv v L1MC_orf2#LIN 765 ACTTCTAAATAACACATGGGTCAAAGAAGAAATCTCAAGAGAAATTTAAA 814 chr5qtel1M 399419 ATTATATTGAAGAGAATAATAGTAATGAGACAACATA-CAAGAACTATGG 399467 v v vvi i v i i vi v v - i vi i L1MC_orf2#LIN 815 AATATTTTGAACTAAATGAAAATGAAAATACAACTTATCAAAATTTGTGG 864 chr5qtel1M 399468 GATGCAGCAAAAACAGTAATGGGAGGAAAATGTGTATCTTTAAAT 399512 i i iv vi i v i v v i L1MC_orf2#LIN 865 GATGCAGCGAAAGCAGTGCTTAGAGGGAAATTTATAGCATTGAAT 909 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.46 CpG sites = 32, Kimura (unadjusted) = 40.38 Transitions / transversions = 1.28 (32/25) Gap_init rate = 0.02 (3 / 186), avg. gap size = 3.00 (9 / 3) 236 33.33 1.95 1.95 chr5qtel1M 399352 399556 (600444) L1M1_orf2#LINE/L1 748 952 (2342) m_b254s551i11 10077 chr5qtel1M 399352 TGAAGATTAAATAACTTAATTTTAAAGAACGTGTGGATTAAGAAACCAGT 399401 i i i iv iv ii i vi vv i i vi vv i L1M1_orf2#LIN 748 TGGAAATTAAACAATATGCTCCTGAATGACCAGTGGGTCAATGAAGAAAT 797 chr5qtel1M 399402 CTTAGGAACAA---TAAATAATTATATTGAAGAGAATAATAGTAATGAGA 399448 -- i vi --- i v - v ivi i i iivi v L1M1_orf2#LIN 798 --TAAGAAGGAAATTGAAAAATT-TCTTGAAACAAATGATAATGGAAACA 844 chr5qtel1M 399449 CAACATACAAGAAC-TATGGGATGCAGCAAAAACAGTAATGGGAGGAAAA 399497 v i - i i v ii i i L1M1_orf2#LIN 845 CAACATACCAAAACCTATGGGATACAGCAAAAGCAGTACTAAGAGGGAAG 894 chr5qtel1M 399498 TGTGTATCTTTAAATTATTCAACCAATAAAATAGAGAAAGCTTCGACAAA 399547 v i v v i vvi vv i v iv - i i vv L1M1_orf2#LIN 895 TTTATAGCTATAAGTGCCTACATCAAAAAAGAAGA-AAAACTTCAAATAA 943 chr5qtel1M 399548 GAGACCTAA 399556 ivi L1M1_orf2#LIN 944 ACAACCTAA 952 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 45.64 CpG sites = 39, Kimura (unadjusted) = 45.64 Transitions / transversions = 1.39 (39/28) Gap_init rate = 0.03 (6 / 204), avg. gap size = 1.33 (8 / 6) 12 9.24 0.00 4.17 chr5qtel1M 399785 399809 (600191) (GGGA)n#Simple_repeat 1 24 (0) m_b254s252i12 10078 chr5qtel1M 399785 GGGAGGGGGTGGAGGGTGGGAGGGA 399809 i - v (GGGA)n#Simpl 1 GGGAGGGAG-GGAGGGAGGGAGGGA 24 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 14 16.05 5.56 5.56 chr5qtel1M 399888 399941 (600059) (ATA)n#Simple_repeat 1 54 (0) m_b254s252i13 10079 chr5qtel1M 399888 ATTATAATAATAATAA-AAAAAGAA-AATGCCATATAAAAATAAATAAAT 399935 v - v v - ivi - v - - (ATA)n#Simple 1 ATAATAATAATAATAATAATAATAATAATAATA-ATAATAAT-AAT-AAT 47 chr5qtel1M 399936 AA-AATA 399941 - (ATA)n#Simple 48 AATAATA 54 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.11 (6 / 53), avg. gap size = 1.00 (6 / 6) 311 30.93 6.48 3.14 chr5qtel1M 399971 400296 (599704) L1M3_orf2#LINE/L1 957 1300 (1988) m_b254s551i12 10077 chr5qtel1M 399971 ACAATTTAAAAATCTAGAAAAAGAATAAATTCAAAATA--CTCAA--TTA 400016 vi i ii v v --- v -- i -- - L1M3_orf2#LIN 957 ACACCTCAAGGAACTAGAAAAAGAAGAA---CAAACTAAGCCCAAAGTT- 1002 chr5qtel1M 400017 AACACCAAATTGGAAATCCTAAAAATCAAAGGTGAGATTAATCATATACA 400066 i vv iivv vv i i i vv i v v v v L1M3_orf2#LIN 1003 AGCAGAAGGAAGGAAATAATAAAGATTAGAGCAGAAATAAATGAAATAGA 1052 chr5qtel1M 400067 ATGTAAAAAAGTCATTGTATTAATAAACAAAACTAGAAATTGGCTTTATG 400116 iv? i iiv v v vv v i ii i i v L1M3_orf2#LIN 1053 GANTAGAAAAACAATAGAAAAAATCAACGAAACTAAGAGTTGGTTTTTTG 1102 chr5qtel1M 400117 AAATAAAT-AATAAAATAAACCAACCATTGGTTAA--TATGATTTTTAAA 400163 - i - i vi v v i i i-- v ----- L1M3_orf2#LIN 1103 AAA-AGATAAACAAAATTGACAAACCTTTAGCTAGACTAAGA-----AAA 1146 chr5qtel1M 400164 A---AGAAGAC-CAAATCAGCAGTTATCAACACTAAAAAGGGTGA-ATAT 400208 --- - v ii i-v iv v i ii v - - L1M3_orf2#LIN 1147 AAAGAGAAGACTCAAATAAATAA-AATCAGAAATGAAAGAGGAGACAT-T 1194 chr5qtel1M 400209 ACTACTAATGAAAATAAAATAAAAAGAATTGTTAGAAGTTATTTTGCCCA 400258 v i vv vvi i ii v iii i v vv L1M3_orf2#LIN 1195 ACAACTGATGCCACAGAAATAAAAAGGATCATAAGAGACTACTATGAACA 1244 chr5qtel1M 400259 AATATGTGCCAATAAATTTAATAATTT------AATGGA---------AG 400293 v ii i vi ii ------ --------- L1M3_orf2#LIN 1245 ATTATACGCCAACAAATTGGATAACCTAGAAGAAATGGATAAATTCCTAG 1294 chr5qtel1M 400294 A---AT 400296 --- L1M3_orf2#LIN 1295 AAACAT 1300 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.95 CpG sites = 81, Kimura (unadjusted) = 41.07 Transitions / transversions = 1.11 (49/44) Gap_init rate = 0.07 (22 / 325), avg. gap size = 1.91 (42 / 22) 42 0.00 0.00 0.00 chr5qtel1M 400297 400332 (599668) (AC)n#Simple_repeat 1 36 (0) c_b254s251i2 10080 chr5qtel1M 400297 ACACACACACACACACACACACACACACACACACAC 400332 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACAC 36 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 311 30.93 6.48 3.14 chr5qtel1M 400333 400499 (599501) L1M3_orf2#LINE/L1 1301 1465 (1823) m_b254s551i12 10077 chr5qtel1M 400333 TAAACTGCCTAGATTAAAAATCTAGAGAAAATAGAATATCTAAATAAACC 400382 i v i v i --i vv ii v i i i L1M3_orf2#LIN 1301 CAACCTACCAAGACT--GAATCATGAAGAAATAGAAAATCTGAACAGACC 1348 chr5qtel1M 400383 TATTTTAGAAAAAGAAATTGAACGGATCATAAATGACCTCCT--TAAGAA 400430 v vviiiiv i i ivii v v vi i--i ii L1M3_orf2#LIN 1349 AATAACGAGTAAGGAGATTGAATCAGTAATCAAAAACCTCCCAACAAAGA 1398 chr5qtel1M 400431 AATACCATCAGTATACAATGGATTTGTAAATGAATTCTACCAAACATTTC 400480 vi -- v ivvi v iiivii v L1M3_orf2#LIN 1399 AAAGCC--CAGGACCAGATGGCTTCACTGGTGAATTCTACCAAACATTTA 1446 chr5qtel1M 400481 AAGATCAACTAATTCCAAT 400499 vv i v L1M3_orf2#LIN 1447 AAGAAGAATTAATACCAAT 1465 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.95 CpG sites = 81, Kimura (unadjusted) = 41.07 Transitions / transversions = 1.39 (32/23) Gap_init rate = 0.03 (5 / 166), avg. gap size = 1.20 (6 / 5) 16 16.12 0.00 0.00 chr5qtel1M 400862 400889 (599111) (G)n#Simple_repeat 1 28 (0) m_b254s252i14 10081 chr5qtel1M 400862 GGGGGGGGGGGGGGGTTGGGGGTTGGGG 400889 vv vv (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGG 28 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 796 29.52 6.80 3.35 chr5qtel1M 401175 401924 (598076) L1M1_orf2#LINE/L1 1543 2317 (977) m_b254s551i13 10082 chr5qtel1M 401175 ATTCTAATACCTAAACACAGAGGAGCAAAAAT-AGGGAAAGAAAAATATA 401223 ii i v - vi iv v v - iii v i L1M1_orf2#LIN 1543 ACCCTGATACCAAAAC-CAGACAAAGACACATCAAAAAAAGAAAACTACA 1591 chr5qtel1M 401224 ACCTAATTTCACTAATGAATATGAATACAAAAA--------AAAA-ATTA 401264 iv i v v i vi i -------- - i L1M1_orf2#LIN 1592 GGCCAATATCTCTGATGAATATTGATGCAAAAATCCTCAACAAAATACTA 1641 chr5qtel1M 401265 GCACTAACCAAGAAACTACAACAATACATCACAAAGATTATATACATGAT 401314 -- -- -- v i v i - - v L1M1_orf2#LIN 1642 GCA--AACC--GAA--TTCAACAATACATTAAAAAGATCAT-T-CATCAT 1683 chr5qtel1M 401315 GACAAAATGGGAATCTATACTAGGAATGCAGATATGATTTAACATAAGGA 401364 v i - i v i? i iiv i i v v L1M1_orf2#LIN 1684 GACCAAGTGGGA-TTTATCCCNGGGATGCAAGGATGGTTCAACATACGCA 1732 chr5qtel1M 401365 AAACAATTAACATAAATTGATTATATCAATAGCAAAAATAATGAAATTCA 401414 v i ii i - vv i i v vi vi ii vi L1M1_orf2#LIN 1733 AATCAATCAATGTGA-TACATCATATCAACAGAATGAAGGACAAAAACCA 1781 chr5qtel1M 401415 T--TATTATATTAATAGATGCAGGAAAA-----------AACCCAACTTT 401451 --v i v i v v i ----------- ii v i L1M1_orf2#LIN 1782 TATGATCATTTCAATTGATGCTGAAAAAGCATTTGATAAAATTCAACATC 1831 chr5qtel1M 401452 TTTTGTTCATTCCATT-TAAAAACACTCAGAATCACAGGTATAC---TGA 401497 ii -------- v- v i vvvii v---vi L1M1_orf2#LIN 1832 CCTT--------CATGATAAAAACCCTCAAAAAACTGGGTATAGAAGGAA 1873 chr5qtel1M 401498 TTTTCCTTAAAATGATAAGAAGTATCTAC-------------CTAAAACC 401534 iv v i v i i ivi v ------------- iv i L1M1_orf2#LIN 1874 CATACCTCAACATAATAAAAGCCATATACGACAGACCCACAGCTAGTATC 1923 chr5qtel1M 401535 ATCATGA--GGATAATAATCTAGAAGCCTTCCCAATAAGATCAAGAGTGA 401582 vv -- iv v - ii i vv vi ii- L1M1_orf2#LIN 1924 ATACTGAATGGGGAAAAA-CTGAAAGCCTTTCCTCTAAGATCTGGAAC-A 1971 chr5qtel1M 401583 AAACAAAGATGTCCAGAATCACCAGTATTATTCAAAATTATA-TAAAAAT 401631 vi i i vvv v i v vi - ii i L1M1_orf2#LIN 1972 CGACAAGGATGCCCACTTTCACCACTGTTATTCAACATAGTACTGGAAGT 2021 chr5qtel1M 401632 GCTATCAATAGCAATAAGAATAGAAAAATAAATGGAAAAAATCAAAATAG 401681 v v v v v vv i v ii iiiv v v L1M1_orf2#LIN 2022 CCTAGCTAGAGCAATCAGACAAGAGAAAGAAATAAAGGGCATCCAAATTG 2071 chr5qtel1M 401682 GCTATGAGATAATAAAAATATCTCTATTTTGCAGATGATATGATGATATG 401731 vv v iiv i v v ii i - vv i L1M1_orf2#LIN 2072 GAAAGGAAGAAGTCAAATTATCCTTGTTT-GCAGATGATATGATCTTATA 2120 chr5qtel1M 401732 CTTGGAAAATTCTAGAAATTT-AGAAAAAATCTTGTTGAAACTG-----C 401775 i vi i i i i- v? v -i ii ----- L1M1_orf2#LIN 2121 TTTGGAAAAACCTAAAGACTCCACNAAAAAACT-ATTAGAACTGATAAAC 2169 chr5qtel1M 401776 AATTTTGGCAAAGTAGTGGGATATAAAATAAACCCACATCAACTATCAGC 401825 v ii i v ii i v vi vv ii vi L1M1_orf2#LIN 2170 AAATTCAGTAAAGTTGCAGGATACAAAATCAACATACAAAAATCAGTAGC 2219 chr5qtel1M 401826 ATTTTTATATAACATCAATAAA--ATCATACAAGGAGAGATAATAAAAGA 401873 i iv v i i -- - i- ii i v v v L1M1_orf2#LIN 2220 ATTTCTATATGCCAACAGTGAACAATC-TG-AAAAAGAAATCAAAAAAGT 2267 chr5qtel1M 401874 GATCCTATTTAAAATAGCCATAGACAGCACAAAATACCTGGGAGTATAAC 401923 i i v i i i iv iv i i - L1M1_orf2#LIN 2268 AATCCCATTTACAATAGCCACAAATAAAATTAAATACCTAGGAAT-TAAC 2316 chr5qtel1M 401924 T 401924 L1M1_orf2#LIN 2317 T 2317 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 38.36 CpG sites = 120, Kimura (unadjusted) = 38.59 Transitions / transversions = 1.28 (120/94) Gap_init rate = 0.05 (39 / 749), avg. gap size = 1.97 (77 / 39) 30 0.00 0.00 0.00 chr5qtel1M 401931 401958 (598042) (T)n#Simple_repeat 1 28 (0) c_b254s251i3 10083 chr5qtel1M 401931 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 401958 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 570 27.34 5.28 7.05 chr5qtel1M 402419 402721 (597279) C L1ME4a_3end#LINE/L1 (232) 639 342 m_b254s551i14 10084 chr5qtel1M 402419 CCTGCTCATTTCACTCAGCATCAGTTCATCATCAGCATCAGTCTCTCCAG 402468 iv i i i ---i v --- i - v C L1ME4a_3end#L 639 CCTGCTTTTTTCACTTAACATTA---TATCATGAGCAT---TTTC-CCAT 597 chr5qtel1M 402469 GCC---------TCTCTGAAATCCGGTTGCTGGTCATTTCTTATGGAACA 402509 i --------- ii v ---------i ? i v vvvv C L1ME4a_3end#L 596 GTCATTAAATATTCTTCGAAAAC---------ATNATTTTTAATGGCTGC 556 chr5qtel1M 402510 ATAATATTCCATAATATTCATATGCCACAATTTACCCAACCATTCTCCAA 402559 v? vv i i i iii ? i v C L1ME4a_3end#L 555 ATAATATTCCATTNTATGGATGTACCATAATTTATTTAACCANTCCCCTA 506 chr5qtel1M 402560 TTAATGGGCATCCACTCAGTTTCCAGTTTCTGGCCACTACAACGAGGGCT 402609 iv i ii vviv i i v i i i vv iv C L1ME4a_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAATGCT 456 chr5qtel1M 402610 GCCACAAACATCCTTGCACATACAGGATCCTT-----TACCTTTAAAAAT 402654 v ii i ---i i -----i i i i vv C L1ME4a_3end#L 455 GCGATGAACATCCTTGTACATA---AATCTTTGTNCACATCTCTGATTAT 409 chr5qtel1M 402655 CTCTTTGGGATATAAGCCCAGTAGTAACATTGCTGGATCAAAGGGTATAC 402704 i i i v vv i v iiv i i i? C L1ME4a_3end#L 408 TTCCTTAGGATAAATTCCTAGAAGTGGAATTACTGGGTCAAAGGGTATGN 359 chr5qtel1M 402705 ACAGTTTGCTAA--CTTTT 402721 v -- -- C L1ME4a_3end#L 358 ACATTTT--TAAGGCTTTT 342 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 35.03 CpG sites = 47, Kimura (unadjusted) = 35.61 Transitions / transversions = 1.57 (47/30) Gap_init rate = 0.08 (24 / 302), avg. gap size = 1.54 (37 / 24) 588 30.53 2.18 1.30 chr5qtel1M 402493 402721 (597279) C L1ME4c_3end#LINE/L1 (258) 572 342 m_b254s551i15 10084 chr5qtel1M 402493 TCATTTCTTATGGAACAATAATATTCCATAATATTCATATGCCACAATTT 402542 i v vvvv vivi ?v i i i C L1ME4c_3end#L 572 TCATTTTTAATGGCTGCATAATATTCCATCGAGTNGATGTACCATAATTT 523 chr5qtel1M 402543 ACCCAACCATTCTCCAATTAATGGGCATCCACTCAGTTTCCAGTTTCTGG 402592 ii i v iv i ii vviv i i v C L1ME4c_3end#L 522 ACTTAACCATTCCCCTATTGTTGGACATTTAGGTTGTTTCCAATTTTTCG 473 chr5qtel1M 402593 CCACTACAACGAGGGCTGCCACAAACATCCTTGCACATACAGGATCCTTT 402642 i i i vv iv v ii i i ii i --- i C L1ME4c_3end#L 472 CTATTATAAATAACGCTGCAATGAACATCTTCGTGCATATAG---CTTTT 426 chr5qtel1M 402643 ACC----TTTAAA-AATCTCTTTGGGATATAAGCCCAGTAGTAACATTGC 402687 v ---- i -v i i i v vv v iiv i C L1ME4c_3end#L 425 TCCTTCTTTTGAATTATTTCCTTAGGATAAATTCCCAGAAGTGGAATTAC 376 chr5qtel1M 402688 TGGATCAAAGGGTATACACAGTTTGCTAACTTTT 402721 i iv v vv ii i C L1ME4c_3end#L 375 TGGGTCAAAGGGTATGAACATTTTTATGGCTCTT 342 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.05 CpG sites = 40, Kimura (unadjusted) = 40.58 Transitions / transversions = 1.38 (40/29) Gap_init rate = 0.02 (5 / 228), avg. gap size = 1.60 (8 / 5) 691 25.63 2.48 1.47 chr5qtel1M 402510 402711 (597289) C L1ME3G_3end#LINE/L1 (376) 548 345 m_b254s551i16 10084 chr5qtel1M 402510 ATAATATTCCATAATATTCATATGCCACAATTTACCCAACCATTCTCCAA 402559 i i vv i i iii i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr5qtel1M 402560 TTAATGGGCATCCACTCAGTTTCCAGTTTCTGGCCACTACAACGAGGGCT 402609 i i ii vviv i i v i i vv iv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr5qtel1M 402610 GCCACAAACATCCTTGCACATACAGGATCCTT---TACCTTTAAAA--AT 402654 v ii i i ---? ---i v v ivi -- C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACATGC---NTCCTTGTGCACATGTGCGAGTAT 402 chr5qtel1M 402655 CTCTTTGGGATATAAGCCCAGTAGTAACATTGCTGGATCAAAGGGTATAC 402704 i ? i v v? ? v iiv i i C L1ME3G_3end#L 401 TTCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGC 352 chr5qtel1M 402705 ACAGTTT 402711 i v C L1ME3G_3end#L 351 GCATTTT 345 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 31.56 CpG sites = 32, Kimura (unadjusted) = 33.14 Transitions / transversions = 1.68 (32/19) Gap_init rate = 0.02 (5 / 201), avg. gap size = 1.60 (8 / 5) 13 16.81 7.50 0.00 chr5qtel1M 402814 402853 (597147) (TAAT)n#Simple_repeat 1 43 (0) m_b254s252i15 10085 chr5qtel1M 402814 TAATTAGAGAAAT-ATTAATT-CTTAAAT-ATTAATTAATTAA 402853 ivv v - -v v - (TAAT)n#Simpl 1 TAATTAATTAATTAATTAATTAATTAATTAATTAATTAATTAA 43 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.08 (3 / 39), avg. gap size = 1.00 (3 / 3) 270 29.36 0.91 0.91 chr5qtel1M 402854 402963 (597037) L1PREC2_orf2#LINE/L1 2418 2527 (767) m_b254s551i17 10086 chr5qtel1M 402854 GATAGGCAGAGCCTATATAATAAAAATGGCAACTCTACCTAAA-CGATTC 402902 v ii v vi v v iv i i - i - L1PREC2_orf2# 2418 GATAGGAAGAATCAATATCGTTAAAATGGCCATACTGCCCAAAGCAATT- 2466 chr5qtel1M 402903 TACTTATTCAATACTGTTCCAGTTAAATGACCAAAAACATATTTTAGTGT 402952 vv i i vi i iv vi vi i vv v L1PREC2_orf2# 2467 TACAGATTCAATGCTATTCCTATCAAACTACCAATGACATTCTTCACAGA 2516 chr5qtel1M 402953 GCTAGGAAAAA 402963 i i L1PREC2_orf2# 2517 ACTAGAAAAAA 2527 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 36.42 CpG sites = 17, Kimura (unadjusted) = 37.90 Transitions / transversions = 1.13 (17/15) Gap_init rate = 0.02 (2 / 109), avg. gap size = 1.00 (2 / 2) 229 21.69 3.49 3.49 chr5qtel1M 404049 404134 (595866) L1ME4b_3end#LINE/L1 58 143 (749) m_b254s551i18 10087 chr5qtel1M 404049 CCAATTGATAAATGGTTAAAGGATATAAACAGGCAGTTTTACAATAAAGA 404098 v v vi i i i- iv i L1ME4b_3end#L 58 CCAATAGAAAAATGGGCAAAGGATATGAACAGACAGTTC-ACAGAAAAGG 106 chr5qtel1M 404099 AATCAAAACCATGTATTTT---CATATGAAAAAATTCTC 404134 vi v -- vv i --- i v L1ME4b_3end#L 107 AAATACAA--ATGGCTCTTAAACATATGAAAAGATGCTC 143 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 25.79 CpG sites = 9, Kimura (unadjusted) = 25.79 Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.05 (4 / 85), avg. gap size = 1.50 (6 / 4) 289 29.58 3.57 6.42 chr5qtel1M 404321 404432 (595568) MIRb#SINE/MIR 7 115 (153) m_b254s601i12 10088 chr5qtel1M 404321 GGTAGCTAGATG--GTAGATAGGGTACTGGACCTGTAGTCAGGAGGATCT 404368 i vv i -- i v i i v vii v ivi i MIRb#SINE/MIR 7 GGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCT 56 chr5qtel1M 404369 GAGTTAAAATCCAGCCTCAAGCACTTATTGCTTACTAGTTGTG-GACC-T 404416 i vi v v ------- iiii i - - MIRb#SINE/MIR 57 GGGTTCGAATCCCGGCTC-------TGCCACTTACTAGCTGTGTGACCTT 99 chr5qtel1M 404417 GGGCAAATCATATAAC 404432 i i iv MIRb#SINE/MIR 100 GGGCAAGTTACTTAAC 115 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 37.49 CpG sites = 20, Kimura (unadjusted) = 39.13 Transitions / transversions = 1.82 (20/11) Gap_init rate = 0.09 (10 / 111), avg. gap size = 1.10 (11 / 10) 387 23.75 2.00 7.37 chr5qtel1M 404333 404432 (595568) MIRc#SINE/MIR 18 112 (156) m_b254s601i13 10088 chr5qtel1M 404333 GTAGATAGGGTACTGGACCTGTAGTCAGGAGGATCTGAGTTAAAATCCAG 404382 i v i i i v i i i vi i v MIRc#SINE/MIR 18 GTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCG 67 chr5qtel1M 404383 CCTCAAGCACTTATTGCTTACTAGTTGTG-GACC-TGGGCAAATCATATA 404430 v ------- iiii i - - i iv MIRc#SINE/MIR 68 GCTC-------TGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTA 110 chr5qtel1M 404431 AC 404432 MIRc#SINE/MIR 111 AC 112 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 28.11 CpG sites = 16, Kimura (unadjusted) = 29.72 Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.09 (9 / 99), avg. gap size = 1.00 (9 / 9) 22 3.81 0.00 0.00 chr5qtel1M 404448 404474 (595526) (A)n#Simple_repeat 1 27 (0) m_b254s252i16 10089 chr5qtel1M 404448 AAAAAAAAAAAAAAAAAAAAAAACAAA 404474 v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAA 27 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 48 0.00 0.00 0.00 chr5qtel1M 404475 404515 (595485) (AT)n#Simple_repeat 1 41 (0) c_b254s251i4 10090 chr5qtel1M 404475 ATATATATATATATATATATATATATATATATATATATATA 404515 (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATA 41 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 300 26.70 3.35 12.12 chr5qtel1M 404527 404705 (595295) L1MD1_3end#LINE/L1 148 312 (677) m_b254s551i19 10091 chr5qtel1M 404527 TCATTATTGATTTAAGAAATGAAAATTAAAACAACTTTTTTTTTTCTTTT 404576 viv vii v v --------------- L1MD1_3end#LI 148 TCATTAGCCATTAGGGAAATGCAAATTAAAACCAC--------------- 182 chr5qtel1M 404577 AATAACATCTCAC-----ACCTATCAGATTGGCTAAAATGATAGAATAG- 404620 i v v ----- v i - i - L1MD1_3end#LI 183 AATGAGATATCACTACACACCTATCAGAATGGCTAAAATAA-AAAATAGT 231 chr5qtel1M 404621 GAAAATGAAAAATGTTGGAGGCAATGTGGAAAAATTGGCGTAGTAATACA 404670 v iivv i v ivi i i i vvi v v L1MD1_3end#LI 232 GACAACACCAAATGCTGGCGAGGATGCGGAGAAACTGGATCACTCATACA 281 chr5qtel1M 404671 TGGTTGACAGAAATGGGAAATAAGTGGGGCAGCCA 404705 v i iii i vi ---- vi L1MD1_3end#LI 282 TTGCTGGTGGGAATGTAAAA----TGGTACAGCCA 312 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 32.06 CpG sites = 22, Kimura (unadjusted) = 33.00 Transitions / transversions = 1.10 (22/20) Gap_init rate = 0.12 (22 / 178), avg. gap size = 1.18 (26 / 22) 522 23.58 0.00 0.00 chr5qtel1M 404707 404812 (595188) MIRc#SINE/MIR 10 115 (153) m_b254s601i14 10092 chr5qtel1M 404707 GTGGTGCAGGGGAGAGAGCACTAGCCCTGATGTCAGGAGGACCTGAGTTC 404756 v i i v i iv i i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr5qtel1M 404757 AAATTTGCCCTCAGACACTTAACACCTGTGTGACCCTGGGCAAGTCATTT 404806 i i iivvv v v vi v i i MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTT 109 chr5qtel1M 404807 GACCCC 404812 i i MIRc#SINE/MIR 110 AACCTC 115 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 27.57 CpG sites = 15, Kimura (unadjusted) = 28.92 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.00 (0 / 105), avg. gap size = 0.0 (0 / 0) 266 27.41 0.00 1.37 chr5qtel1M 404977 405050 (594950) L1ME3F_3end#LINE/L1 439 511 (479) m_b254s551i20 10091 chr5qtel1M 404977 AAAATGTGTATAGCAGCGCTCTTTGTGATGGCAAAGAACTAGAAATAGAG 405026 i vi i v i i i i i i ivv L1ME3F_3end#L 439 AGAATGTTCATAGCAGCACTGTTCGTAATAGCAAAAAACTGGAAACAACC 488 chr5qtel1M 405027 GGAATGCCCATCAGGCAGGCGGAT 405050 vi i - i v i L1ME3F_3end#L 489 CAAATGTCCATC-GACAGGAGAAT 511 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 33.58 CpG sites = 14, Kimura (unadjusted) = 35.83 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.01 (1 / 73), avg. gap size = 1.00 (1 / 1) 209 14.71 0.00 0.00 chr5qtel1M 406285 406318 (593682) MIRb#SINE/MIR 118 151 (117) m_b254s601i15 10088 chr5qtel1M 406285 CCCTGGGCCTCAGTTTCCTCGTGTGTAAAACGGG 406318 i i i v i MIRb#SINE/MIR 118 CTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 151 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 16.89 CpG sites = 4, Kimura (unadjusted) = 16.89 Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 13 25.82 0.00 0.00 chr5qtel1M 406774 406810 (593190) (CCC)n#Simple_repeat 1 37 (0) m_b254s252i17 10093 chr5qtel1M 406774 CCCCCCCCCCCCGGCCTCGGGCCGCCCCCCCCCCGCC 406810 vv i vvv v v (CCC)n#Simple 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 37 Matrix = Unknown Transitions / transversions = 0.14 (1/7) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 12 20.32 6.67 0.00 chr5qtel1M 406776 406820 (593180) (CCCCGG)n#Simple_repeat 1 48 (0) m_b254s252i18 10093 chr5qtel1M 406776 CCCCCCCCCCGGCCTCGG-GCC-GCCCC-CCCCCCGCCGCGGTCCCGG 406820 vv i -v - -v v v i (CCCCGG)n#Sim 1 CCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGG 48 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.07 (3 / 44), avg. gap size = 1.00 (3 / 3) 25 27.32 5.20 5.20 chr5qtel1M 408061 408233 (591767) (CTCCTTT)n#Simple_repeat 1 173 (0) m_b255s252i2 10094 chr5qtel1M 408061 CTCTTTGCTCCCTTTCTCC--TC-CC-TCCCCCCCTGTCCGGTCTCC-TT 408105 i v - -- - - i i ii v vv - (CTCCTTT)n#Si 1 CTCCTTTCT-CCTTTCTCCTTTCTCCTTTCTCCTTTCTCCTTTCTCCTTT 49 chr5qtel1M 408106 CTCTTTCCTTCCTTTCTCC-TTC-CCTTTC-CTTTCCTCTCCCCTCATTT 408152 i i - - - - i i iiii v (CTCCTTT)n#Si 50 CTCCTTTC-TCCTTTCTCCTTTCTCCTTTCTCCTTTCTCCTTTCTCCTTT 98 chr5qtel1M 408153 CTTC-CCCTATTTTCTTTAATCATCTCTTTTTTCTTTCTCCTTTCCCCTA 408201 i -ii vi iivv - - i i i - (CTCCTTT)n#Si 99 CTCCTTTCTCCTTTCTCCTTTC-TC-CTTTCTCCTTTCTCCTTTCTCCT- 145 chr5qtel1M 408202 GGGTCCCCTTTCTCTTGTTTCTCCTTATTCCT 408233 --v i --v vi (CTCCTTT)n#Si 146 --TTCTCCTTTCTC--CTTTCTCCTTTCTCCT 173 Matrix = Unknown Transitions / transversions = 2.18 (24/11) Gap_init rate = 0.10 (17 / 172), avg. gap size = 1.06 (18 / 17) 12 4.53 4.00 4.00 chr5qtel1M 408246 408270 (591730) (TCCC)n#Simple_repeat 1 25 (0) m_b255s252i3 10095 chr5qtel1M 408246 TCCCTCCCT-CCTCCCTTCCCTCTCT 408270 - - i (TCCC)n#Simpl 1 TCCCTCCCTCCCTCCC-TCCCTCCCT 25 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.08 (2 / 24), avg. gap size = 1.00 (2 / 2) 252 29.55 2.73 4.63 chr5qtel1M 408796 408905 (591095) L3#LINE/CR1 2832 2939 (1160) m_b255s601i0 10096 chr5qtel1M 408796 CGGTGGGCACCTCCAGGA-CGAGCAAGAGCCCCCATGAGAACAAGTCA-G 408843 iv i--- - v v i ii v - i - L3#LINE/CR1 2832 CGGTGATCACT---AGGAGCCAGCATGGGTTCAC-TAAGAACAAGTCATG 2877 chr5qtel1M 408844 CCGAG-AGGCCCCGTTTCCTTTCTGGGACGGCGTTATTACATGAGTAGAT 408892 i i-vii i i i v - ii v i v ivi L3#LINE/CR1 2878 CCAAACTAACCTCATTTCCTTTTTTG-ATAGGGTTACTAGACTGGTAGAT 2926 chr5qtel1M 408893 AATGGGAACGCTG 408905 v v i i L3#LINE/CR1 2927 CAGGGGAATGCCG 2939 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.49 CpG sites = 20, Kimura (unadjusted) = 39.13 Transitions / transversions = 1.82 (20/11) Gap_init rate = 0.07 (8 / 109), avg. gap size = 1.00 (8 / 8) 369 12.12 2.99 1.47 chr5qtel1M 408922 408988 (591012) MIR3#SINE/MIR 78 145 (63) m_b255s601i1 10097 chr5qtel1M 408922 CTAGCTGCGTGACCCTGGGGAAATCCCTCTGTCCTCTCTG--CCTCAGTT 408969 ? i i v i v iii- -- MIR3#SINE/MIR 78 CTNGCTGTGTGACCTTGGGCAAGTCACTTCA-CCTCTCTGGGCCTCAGTT 126 chr5qtel1M 408970 TCCTCATCTGTAAAATGAG 408988 MIR3#SINE/MIR 127 TCCTCATCTGTAAAATGAG 145 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 13.72 CpG sites = 6, Kimura (unadjusted) = 13.72 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.03 (2 / 66), avg. gap size = 1.50 (3 / 2) 299 37.54 6.25 1.49 chr5qtel1M 409240 409431 (590569) L3#LINE/CR1 3586 3786 (313) m_b255s601i2 10096 chr5qtel1M 409240 TCTGGAACGAGGTACGCAGATTTAGGGCCCCTGGTTTGAGGAGGGCTTGG 409289 iiivv iiiv v i i vv viiv i ii i v v L3#LINE/CR1 3586 TCTGGAGTATTGCGTTCAGTTCTGGGCGCCACATTTTAAGAGGGACATTG 3635 chr5qtel1M 409290 ATGAGCTGGCGAGCCTCCAGAAGAGGGC--CCAGCACGGAGAGGGGCTTG 409337 ii i v v v i i -- v i v i ii L3#LINE/CR1 3636 ACAAACTGGAGCGCGTCCAGAGGAGAGCGACCAGGATGGTGAAGGGTCTG 3685 chr5qtel1M 409338 GGCCCC--------TGGGGAATCA--GAAGGAAGTGAGTCTGTTTGGATC 409377 ivv -------- i ivi-- v i vv i -i L3#LINE/CR1 3686 GAAACCATGTCATATGAGGAACGGTTGAAGGAACTGGGGATGTTTAG-CC 3734 chr5qtel1M 409378 CAGAAAGGATTCAAGTTTGGGCGGGGCCCTGAGTGCTTCTTTCAGATATC 409427 ii i i --v vi vi v i v v vv vii i i L3#LINE/CR1 3735 TGGAGAAGA--GAAGACTTAGAGGAGACATGATAGCTGTCTTCAAATATT 3782 chr5qtel1M 409428 TGAA 409431 L3#LINE/CR1 3783 TGAA 3786 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 52.04 CpG sites = 41, Kimura (unadjusted) = 54.45 Transitions / transversions = 1.37 (41/30) Gap_init rate = 0.03 (6 / 191), avg. gap size = 2.50 (15 / 6) 182 32.63 9.47 0.00 chr5qtel1M 409523 409617 (590383) L3#LINE/CR1 3926 4029 (70) m_b255s601i3 10096 chr5qtel1M 409523 AGGTGGAAAGGGCTGCCTCAAAAGG-AG---GCTTCCCCTGCTTGGAGGC 409568 ii v i?i - --- i v vvi i L3#LINE/CR1 3926 AAATGGAATGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGTCACTGGAGGT 3975 chr5qtel1M 409569 CTTTC--CA---ACCGGACAAGTGCGTGCCAGGCTTGTTGGGGCAAGCGT 409613 v iv-- ---i i ii vii v i vv vi v i vi L3#LINE/CR1 3976 GTTCAAGCAGAGGCTGGATGACCACTTGTCAGGGATGTTGTAGAAGGGAT 4025 chr5qtel1M 409614 TCCT 409617 L3#LINE/CR1 4026 TCCT 4029 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.97 CpG sites = 18, Kimura (unadjusted) = 44.93 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.04 (4 / 94), avg. gap size = 2.25 (9 / 4) 63 3.13 1.52 0.00 chr5qtel1M 409884 409949 (590051) (CT)n#Simple_repeat 1 67 (0) c_b255s251i0 10098 chr5qtel1M 409884 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 409933 (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chr5qtel1M 409934 CTC-CTCCCTCCCTCTC 409949 - i i (CT)n#Simple_ 51 CTCTCTCTCTCTCTCTC 67 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.02 (1 / 65), avg. gap size = 1.00 (1 / 1) 12 23.84 5.08 3.33 chr5qtel1M 410482 410540 (589460) (TACACA)n#Simple_repeat 1 60 (0) m_b255s252i4 10099 chr5qtel1M 410482 TACACAGTCACACACACGCATCCGTA-ACACAGACACCTATGTATA-A-A 410528 - - i i v ii - v v iii - - (TACACA)n#Sim 1 TACACA-T-ACACATACACATACACATACACATACACATACACATACACA 48 chr5qtel1M 410529 TACACATATACA 410540 i (TACACA)n#Sim 49 TACACATACACA 60 Matrix = Unknown Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.09 (5 / 58), avg. gap size = 1.00 (5 / 5) 14 19.82 0.00 4.76 chr5qtel1M 411678 411721 (588279) (GGAGGGG)n#Simple_repeat 1 42 (0) m_b255s252i5 10100 chr5qtel1M 411678 GGAGGGGGGAGGGGGCTGCAGGGAGCGCGGGGAGAGGTGGGGGG 411721 vv vi - - i v i (GGAGGGG)n#Si 1 GGAGGGGGGAGGGGGGAGGGGGGAG-G-GGGGAGGGGGGAGGGG 42 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2) 31 0.00 0.00 0.00 chr5qtel1M 412429 412455 (587545) (GT)n#Simple_repeat 1 27 (0) c_b255s251i1 10101 chr5qtel1M 412429 GTGTGTGTGTGTGTGTGTGTGTGTGTG 412455 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTG 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 18 0.00 4.55 0.00 chr5qtel1M 412815 412836 (587164) (GT)n#Simple_repeat 1 23 (0) m_b255s252i6 10102 chr5qtel1M 412815 GTGTGTGTGTGTGTGTGTG-GTG 412836 - (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTG 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.05 (1 / 21), avg. gap size = 1.00 (1 / 1) 16 27.12 2.94 1.45 chr5qtel1M 414311 414378 (585622) (TGGAGGT)n#Simple_repeat 1 69 (0) m_b255s252i7 10103 chr5qtel1M 414311 TGG-GGTTGGAGGTTGG-GGCTGCAGGAGCGATGGAGGAGGTGGGTGGTT 414358 - - i v vvv v vv v v (TGGAGGT)n#Si 1 TGGAGGTTGGAGGTTGGAGGTTGGAGGTTGGAGGTTGGAGGTTGGAGGTT 50 chr5qtel1M 414359 GGTGGAGTGGGGGCTGCAGG 414378 v -v i i v (TGGAGGT)n#Si 51 GGAGG-TTGGAGGTTGGAGG 69 Matrix = Unknown Transitions / transversions = 0.25 (3/12) Gap_init rate = 0.04 (3 / 67), avg. gap size = 1.00 (3 / 3) 14 10.52 9.30 2.17 chr5qtel1M 415127 415169 (584831) (CTCCTCC)n#Simple_repeat 1 46 (0) m_b255s252i8 10104 chr5qtel1M 415127 CTCGTCCCTCC-CCCTCCT-CC-CC-ACCTCAGACCCTCCTCCCTCC 415169 v - - - -v -vv (CTCCTCC)n#Si 1 CTCCTCCCTCCTCCCTCCTCCCTCCTCCCTC-CTCCCTCCTCCCTCC 46 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.12 (5 / 42), avg. gap size = 1.00 (5 / 5) 12 17.44 0.00 5.88 chr5qtel1M 415193 415228 (584772) (GGGCC)n#Simple_repeat 1 34 (0) m_b255s252i9 10105 chr5qtel1M 415193 GGACCGTGGCGCGCGCGGGCCGGGGCGGGCCGCGGC 415228 i v v v - v - (GGGCC)n#Simp 1 GGGCCGGGCCGGGC-CGGGCCGGGCCGGGCCG-GGC 34 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 35 0.00 0.00 0.00 chr5qtel1M 417022 417053 (582947) (CTG)n#Simple_repeat 1 32 (0) c_b255s251i2 10106 chr5qtel1M 417022 CTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT 417053 (CTG)n#Simple 1 CTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT 32 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 11 31.98 1.85 0.00 chr5qtel1M 417810 417863 (582137) (GGGGGC)n#Simple_repeat 1 55 (0) m_b255s252i10 10107 chr5qtel1M 417810 GGGGGCTGGGGCTGGGGCTGGCCAGGAGCCGGAGACTGGCCCGGGGG-GC 417858 v v v vvv i v i i v vv - v (GGGGGC)n#Sim 1 GGGGGCGGGGGCGGGGGCGGGGGCGGGGGCGGGGGCGGGGGCGGGGGCGG 50 chr5qtel1M 417859 GGGCG 417863 (GGGGGC)n#Sim 51 GGGCG 55 Matrix = Unknown Transitions / transversions = 0.27 (3/11) Gap_init rate = 0.02 (1 / 53), avg. gap size = 1.00 (1 / 1) 444 36.80 1.28 1.71 chr5qtel1M 417932 418166 (581834) C L3#LINE/CR1 (11) 4088 3855 m_b255s601i4 10108 chr5qtel1M 417932 AGGGTCATAAAGGTGAAAAG-CTCTTGGGGGCCAACCAGTCCAGCCCGCA 417980 ii vi i v i i -vi i i i v i i iv v C L3#LINE/CR1 4088 AGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCAACCTCCC 4039 chr5qtel1M 417981 GTCTCAAAACC--AATCCCACCAAGAGCTGCCCCCACCAGGGTTCATCCA 418028 i - vi v-- vi v v i vv iv v v v C L3#LINE/CR1 4038 ATC-CAATGCAGGAATCCCTTCTACAACATCCCTGACAAGTGGTCATCCA 3990 chr5qtel1M 418029 GCCTCCGCTTGGTTTCCTCCAGGGATAGGCAGCTCACTCCCCAGCAAGGA 418078 i iviv v ii v v iv? i v C L3#LINE/CR1 3989 GCCTCTGCTTGAACACCTCCAGTGACGGGGAGCTCACTACCTCNCGAGGC 3940 chr5qtel1M 418079 AGTGCCCCTTCATCTGCAGAAAGCTCTCCTGGGGAGGAAACGCTTCCCTC 418128 i- vi i i vii v vv v vv i iiv i v C L3#LINE/CR1 3939 AGC-CCATTCCATTTTTGGACAGCTCTGATTGTTAGAAAGTTCTTCCTTA 3891 chr5qtel1M 418129 CCCCACACCGGCAATCAGCTGTCCTAAAATTTTTCACC 418166 iviiivi i- v ivi iv -i i C L3#LINE/CR1 3890 TATTGAGCCGA-AATCTGCCTCCCTGTAA-CTTCCACC 3855 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 50.62 CpG sites = 46, Kimura (unadjusted) = 52.50 Transitions / transversions = 1.18 (46/39) Gap_init rate = 0.03 (6 / 234), avg. gap size = 1.17 (7 / 6) 13 20.91 3.77 3.77 chr5qtel1M 420662 420714 (579286) (AGGCGC)n#Simple_repeat 1 53 (0) m_b255s252i11 10109 chr5qtel1M 420662 AGGCGGAAGGCGCTGGCGTAGTC-CA-GCACGGAGCCCAGGCCCTGGCGC 420709 - v v i v - - i i - v v v (AGGCGC)n#Sim 1 AGGC-GCAGGCGCAGGCGCAGGCGCAGGCGCAG-GCGCAGGCGCAGGCGC 48 chr5qtel1M 420710 AGGCG 420714 (AGGCGC)n#Sim 49 AGGCG 53 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.08 (4 / 52), avg. gap size = 1.00 (4 / 4) 14 0.00 0.00 0.00 chr5qtel1M 432669 432686 (567314) (CCG)n#Simple_repeat 1 18 (0) m_b255s252i12 10110 chr5qtel1M 432669 CCGCCGCCGCCGCCGCCG 432686 (CCG)n#Simple 1 CCGCCGCCGCCGCCGCCG 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 288 25.25 3.70 4.67 chr5qtel1M 432754 432861 (567139) C MIR3#SINE/MIR (23) 185 79 m_b255s601i5 10111 chr5qtel1M 432754 AGGGCTACTTGGAGCCTTGGAGAGC---TAGTCCCCCTCCCCTTAATTTA 432800 i ivvv ii i v --- vv - i v C MIR3#SINE/MIR 185 AGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAAC-CCCCTCATTTTA 137 chr5qtel1M 432801 CAGGAGAGGAAACTGAGGCTCC-AGCGGTGAAGCACTAGCTACCGCAAAG 432849 iv i v- v --- ii vv v i C MIR3#SINE/MIR 136 CAGATGAGGAAACTGAGGCCCAGAGAGGTGAAG---TGACTTGCCCAAGG 90 chr5qtel1M 432850 CCGCACTAGCGA 432861 i i - ? C MIR3#SINE/MIR 89 TCACAC-AGCNA 79 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.45 CpG sites = 13, Kimura (unadjusted) = 31.45 Transitions / transversions = 1.00 (13/13) Gap_init rate = 0.07 (7 / 107), avg. gap size = 1.29 (9 / 7) 17 18.31 4.55 0.00 chr5qtel1M 433891 433934 (566066) (CCTC)n#Simple_repeat 1 46 (0) m_b255s252i13 10112 chr5qtel1M 433891 CCTCTCTCCCCTCCTCCCTCCCT-CCACGCTCTCTCCCT-TCTCCC 433934 i ii - v v i -i (CCTC)n#Simpl 1 CCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCC 46 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2) 15 18.29 0.00 3.12 chr5qtel1M 435648 435680 (564320) (AC)n#Simple_repeat 1 32 (0) m_b255s252i15 10113 chr5qtel1M 435648 ACACACTCACATGCACACACAGCTCATACACAC 435680 v ii - v i (AC)n#Simple_ 1 ACACACACACACACACACACA-CACACACACAC 32 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 12 20.44 2.44 2.44 chr5qtel1M 436660 436700 (563300) (ATATTTA)n#Simple_repeat 1 41 (0) m_b255s252i16 10114 chr5qtel1M 436660 ATCTTTTATCCTTAATATTTAATCCTTAA-ATATTATTATTT 436700 v v vi vi - - v (ATATTTA)n#Si 1 ATATTTAATATTTAATATTTAATATTTAATAT-TTAATATTT 41 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 26 23.89 3.80 0.00 chr5qtel1M 437147 437221 (562779) (CTCT)n#Simple_repeat 1 78 (4) m_b255s252i17 10115 chr5qtel1M 437147 CTCTCTTCCTCTCT-TTTGTTTTTC-CTCTTTCCCTCCTTCTCTCTTTCT 437194 ii - i v i i - i i ii i (CTCT)n#Simpl 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chr5qtel1M 437195 TTCCTTCTCTC-CTCTCTCTCTCTCTTT 437221 i ii - i (CTCT)n#Simpl 51 CTCTCTCTCTCTCTCTCTCTCTCTCTCT 78 Matrix = Unknown Transitions / transversions = 14.00 (14/1) Gap_init rate = 0.04 (3 / 74), avg. gap size = 1.00 (3 / 3) 50 0.00 0.00 0.00 chr5qtel1M 437222 437264 (562736) (AC)n#Simple_repeat 1 43 (0) c_b255s251i3 10116 chr5qtel1M 437222 ACACACACACACACACACACACACACACACACACACACACACA 437264 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACA 43 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 296 35.75 4.18 2.86 chr5qtel1M 437274 437584 (562416) C L1ME3G_3end#LINE/L1 (544) 380 66 m_b255s551i0 10117 chr5qtel1M 437274 AAGTGGAATCTCTGAGTCAAAAGATATAGATATTTTAGTCACTTTATTGT 437323 iv i i i ivii i-- i v iv C L1ME3G_3end#L 380 AAGTGGAATTGCTGGGTCAAAGGGTATGCGCATTTTAA--ATTTTAATAG 333 chr5qtel1M 437324 CTAATTAAAAATTTCTTTCCAAAATGGTTGGACCAATTCAATAAGCTACC 437373 v v vvv v ii ? i v --- vi v C L1ME3G_3end#L 332 ATACTGCCAAATTGCCCTCCAAAANGGCTGTACCAATT---TACACTCCC 286 chr5qtel1M 437374 ATCAACAGAGTAACAAGGCGTTCATCTTTCCACAGCACCCCCAGTATCAA 437423 i i v vv ii iiii i i ii v vi v ii ii?i C L1ME3G_3end#L 285 ACCAGCAGTGTATGAGAGTACCCGTTTCCCCACACCCTCGCCAACACTNG 236 chr5qtel1M 437424 CCAAT-TCTATCTTTTATCATCTTCCCAAATTGCTTAGTGAGTATGAGAT 437472 vi v - v ? vvv i v vi v vi ----i i C L1ME3G_3end#L 235 ATATTATCAANCTTTTAAATTTTTGCCAATCTGATGGGTGA----AAAAT 190 chr5qtel1M 437473 GAAATCATGGGGCTAATTTGATTCAAATTTCTC-----GTTAATGATCTG 437517 iv viivv i iv i iiv i -----ii i vv v C L1ME3G_3end#L 189 GGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGATTACTAGTGAGGTT 140 chr5qtel1M 437518 TAGTATC-CTTCACGTGATTGTTAATAATTTGCAA----TCTTTTGAGGA 437562 v i -i ii v i iiiv i v---- i v i C L1ME3G_3end#L 139 GAGCATCTTTTCATATGTTTATTGGCCATTTGTATTTCCTCTTCTGTGAA 90 chr5qtel1M 437563 CTG--TGTTCATAGTCTTTGGCCA 437584 i -- vi v C L1ME3G_3end#L 89 TTGCCTGTTCATATCCTTTGCCCA 66 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 49.99 CpG sites = 63, Kimura (unadjusted) = 51.37 Transitions / transversions = 1.40 (63/45) Gap_init rate = 0.05 (14 / 310), avg. gap size = 1.57 (22 / 14) 536 29.25 3.02 4.78 chr5qtel1M 438899 439196 (560804) C L1ME5_3end#LINE/L1 (581) 360 68 m_b255s551i1 10118 chr5qtel1M 438899 TATGCGTAAGTCCTTAAACTTGAGCATAGT----TTAAACTGCTTCCCAG 438944 -- v -i vi - ----ii i i ii C L1ME5_3end#LI 360 TATGCGTA--TACTTAA-TTTGACTA-AGTACTGCCAGATTGCTCTCCAG 315 chr5qtel1M 438945 AATGGTTGGATCAGATCACAACTTTACCAACAGTGCATTAATGTCCATAT 438994 i v i vii viiii i v iv i v C L1ME5_3end#LI 314 AATGGCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTAT 265 chr5qtel1M 438995 TTTCTTTCCCACATCCTTCTTCTCAGCATTTGCCATTTTTCT-TTTTGTC 439043 ? i ---- ivi--- i i v v i v-i v v C L1ME5_3end#LI 264 NTCC----CCACATCCTCGC---CAACACTTGGCATTATCCAGCTTTCTA 222 chr5qtel1M 439044 ATGTTGGCCAATATGATGGATATGAAGCGGTACCTTAGAGTTGTTTGAAT 439093 v v i v i i i i i i i i i vv v C L1ME5_3end#LI 221 ATTTTTGCCAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAAT 172 chr5qtel1M 439094 TTATATTTGTCTAATTATTGGTTATTTGGAACATTT-TTCATATAACTAT 439142 ii v i i ii v v v i i - ivi i C L1ME5_3end#LI 171 TTGCATTTCTCTGATTACTAATGAGTTTGAGCATCTCTTCATATGCTTGT 122 chr5qtel1M 439143 AGATAGTTTT---GATTCCTTCTTTTGAAAATTTCGTGTTCAGATCCTTT 439189 --- ii --- i i i i v v v v C L1ME5_3end#LI 121 ---TAGCCTTTCGGGTTTCCTCTTCTGTAAATTGCCTGTTCATATCCTTT 75 chr5qtel1M 439190 GACCATT 439196 v C L1ME5_3end#LI 74 GCCCATT 68 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 38.10 CpG sites = 53, Kimura (unadjusted) = 38.71 Transitions / transversions = 1.77 (53/30) Gap_init rate = 0.06 (18 / 297), avg. gap size = 1.28 (23 / 18) 465 33.86 1.21 2.76 chr5qtel1M 438933 439263 (560737) C L1PA13_3end#LINE/L1 (584) 326 1 m_b255s551i2 10118 chr5qtel1M 438933 ACTGCTTCCCAGAATGGTTGGATCAGATCACAACTTTACCAACAGTGCAT 438982 ii i v i ii iv i viiii i C L1PA13_3end#L 326 ACTGTCTTCCACAATGGTTGAACTAATTTACACTCCCACCAACAGTGTAT 277 chr5qtel1M 438983 TAATGTCCATATTTTCTTTCCCACATCCTTCTTCTCAGCATTTGCCATTT 439032 v ii i v - --- i v ivi--- i ii C L1PA13_3end#L 276 AAGCGTTCCT-TTTTCT---CCGCAACCTCGC---CAGCATCTGTTATTT 234 chr5qtel1M 439033 TT---CTTTTTGTCATGTTGGCCAATATGATGGATATGAAGCGGTACCTT 439079 --- i-- iv i v v iv i i iii i i C L1PA13_3end#L 233 TTTGACTTTTTA--ATAATAGCCATTCTGACTGGTGTGAGATGGTATCTC 186 chr5qtel1M 439080 AGAGTTGTTTGAATTTATATTTGTCTAATTATTGGTTATTTGGAACATTT 439129 vv v vi ii v v ii v v v i v C L1PA13_3end#L 185 ATTGTGGTTTTGATTTGCATTTCTCTAATGATCAGTGATGTTGAGCTTTT 136 chr5qtel1M 439130 TT-CATATAACTATAGATAGTTTTGATTCCTTCTTTTGAAAATTTCGTGT 439178 - i i i v iiv iv vv vi v viv C L1PA13_3end#L 135 TTTCATATGATTGTTGGCCGCATGTATGTCTTCTTTTGAAAAGTGTCTGT 86 chr5qtel1M 439179 TCAGATCCTTTGACCATTAAACAGTTGGGAAATAGCTCTTATTTTTATAA 439228 vi v i vvvi i v vvi vvv i v i i C L1PA13_3end#L 85 TCATGTCCTTTGCCCACTTTTTAATGGGGTTGTTTGTTTTTTTCTTGTAA 36 chr5qtel1M 439229 ATGTCATTCACTTCCCAATAGATTTGAGAAATTAG 439263 v vv v v iv vivi v C L1PA13_3end#L 35 ATTTGTTTAAGTTCCTTATAGATGCTGGATATTAG 1 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 44.37 CpG sites = 58, Kimura (unadjusted) = 46.08 Transitions / transversions = 1.14 (58/51) Gap_init rate = 0.03 (11 / 330), avg. gap size = 1.18 (13 / 11) 13 32.59 0.00 0.00 chr5qtel1M 440357 440409 (559591) (AAAA)n#Simple_repeat 1 53 (0) m_b255s252i18 10119 chr5qtel1M 440357 AAAAAAAAAAAACTTGAGAAAGAAAAACAAACAAACAACACTAAAAAGTA 440406 vvvi i i v v v v vv iv (AAAA)n#Simpl 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr5qtel1M 440407 AAA 440409 (AAAA)n#Simpl 51 AAA 53 Matrix = Unknown Transitions / transversions = 0.40 (4/10) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 341 39.81 1.06 3.25 chr5qtel1M 440465 440747 (559253) L2d2_3end#LINE/L2 9 285 (270) m_b255s601i6 10120 chr5qtel1M 440465 TCTGGTCTCAGCTTGTTTCCCCAGGATGACTAGATTTTACTCCCCCTTTA 440514 i i i i ?ii ii vv --- vv iii vii ii ? L2d2_3end#LIN 9 TCTGGCCCCAACCTNCCTTTCCAGCCT---TATCTCCCACTATTCCCCTN 55 chr5qtel1M 440515 CACGGTGTGTCTGAACCAAACATATCTGCTCACTTGCTGTTTCCCACTGA 440564 ivviv i vv iv v iiv iii ii ii ivvv L2d2_3end#LIN 56 CACGAACCCTCCGCTCCAGCCAAACTGGTCTACTCACTGTCCCCCGAACA 105 chr5qtel1M 440565 TGGCGTTCCATCTCCCAGCACCTCC-TCTTTGCATAGGA-GTTCCTCTCT 440612 i v - v ii? i v vi v -i vi v v- i i - L2d2_3end#LIN 106 CGCC-TTGCGCNTTCCCGCCTCTGCGCCTTTGCTCACGCCGTTCCCCCC- 153 chr5qtel1M 440613 CTGCCTAAAATGCTCTCCATCCTCTTTTTCACCTATTAGGAACTTCAGCA 440662 -- ii i i vi i i i i ivii v i - v v L2d2_3end#LIN 154 --GCCTGGAATGCCCTTCCCCTTCCTCTCCACCTATCCAAATCCT-ACCC 200 chr5qtel1M 440663 GACCATCTGAGATCAGCTCAAGTGCCACCTTCTGCAAGAAGCTTGTCTTG 440712 iv v vii vi i ? i v iv i vi i L2d2_3end#LIN 201 ATCCTTCAAGGCCCAGCTCAAATNCCACCTCCTCCGTGAAGCCTTCCCTG 250 chr5qtel1M 440713 ATCTCAGCGGTGATTTAGTGGTTTATCCCT-CTCTG 440747 i v vv i i-viv? i i v - L2d2_3end#LIN 251 ACCACTCCAGC-CCGNAGTGATCTCTCCCTCCTCTG 285 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 56.97 CpG sites = 67, Kimura (unadjusted) = 62.46 Transitions / transversions = 1.60 (67/42) Gap_init rate = 0.04 (12 / 282), avg. gap size = 1.00 (12 / 12) 21 4.13 0.00 0.00 chr5qtel1M 441781 441805 (558195) (T)n#Simple_repeat 1 25 (0) m_b255s252i19 10121 chr5qtel1M 441781 TTTTTTTTTTTTTGTTTTTTTTTTT 441805 v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 227 32.51 0.00 11.01 chr5qtel1M 442221 442341 (557659) C L2c_3end#LINE/L2 (8) 470 362 m_b255s601i7 10122 chr5qtel1M 442221 ACTCAATATTCCTTTATTTGGCACTTCCTAGGTACAAGAATTGGGGGTGG 442270 i i vv v vi i i v v i v ----- v v C L2c_3end#LINE 470 ATTCAACAAACATTTATTGAGCGCCTACTATGTGCCA-----GGCGCTGG 426 chr5qtel1M 442271 CAGTACAAAGATAAAAATGGTAAACAGTGTTTACCACCCAGGGAGCTTAC 442320 vii i v v -- v i vii i - i i i C L2c_3end#LINE 425 GGATACAAAGATGAATAAG--ACACGGTCCCTGCC-CTCAAGGAGCTCAC 379 chr5qtel1M 442321 ATTCTACAAGATAGAGGAAGC 442341 v ----i i ii C L2c_3end#LINE 378 AGTCTA----GTGGAGGAGAC 362 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.94 CpG sites = 20, Kimura (unadjusted) = 43.17 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.10 (12 / 120), avg. gap size = 1.00 (12 / 12) 1421 29.28 1.73 1.73 chr5qtel1M 443127 443762 (556238) C L1ME4a_3end#LINE/L1 (232) 639 4 m_b255s551i3 10123 chr5qtel1M 443127 CCTGCTCATTTCACTCAGCATCAGTTCGTGTAAGTCTCTCCAGGCCTTTC 443176 iv i i i vv i vivi i ii v i v - C L1ME4a_3end#L 639 CCTGCTTTTTTCACTTAACATTATATCATGAGCATTTTCCCATGTCATT- 591 chr5qtel1M 443177 TGAAATCATCCTGTTGG-----TCATTTCTTACAG-AACAGTAATATTCC 443220 -- - i - i i----- ? i v ii -vi - C L1ME4a_3end#L 590 --AAAT-ATTCT-TCGAAAACATNATTTTTAATGGCTGCA-TAATATTCC 546 chr5qtel1M 443221 ATAATATTCATATACCACAATTTATTAAGCCATTCTCCAACTGATGGACA 443270 v? vv i i v i ? i v i v C L1ME4a_3end#L 545 ATTNTATGGATGTACCATAATTTATTTAACCANTCCCCTATTGTTGGACA 496 chr5qtel1M 443271 TCCATTCAGTTTCCAGTTTTTAGCCACTACAAAAAGGGCTGCCACAAACA 443320 ii vviv i v i i i v iv v ii C L1ME4a_3end#L 495 TTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAATGCTGCGATGAACA 446 chr5qtel1M 443321 TTCAGTGCACATACAGGTCCCT-TTCCCTTCTTT-ATAATCTCTTTGGGA 443368 i -v i v -- ii - ? v v i - v i i i C L1ME4a_3end#L 445 TCC-TTGTACATAAA--TCTTTGTNCACATCTCTGATTATTTCCTTAGGA 399 chr5qtel1M 443369 TATAAGCCCAGTAGTAACACTGCTGGATCAAAGGGTATGCACAGTTTGAT 443418 v vv i v iiv i i i ? v v v C L1ME4a_3end#L 398 TAAATTCCTAGAAGTGGAATTACTGGGTCAAAGGGTATGNACATTTTTAA 349 chr5qtel1M 443419 AACTTTTTGAGCATAGTTCCAAACTACTCTCCAAAATGGTTGGATTCGTT 443468 ii vivi v v i i i i v v iivi C L1ME4a_3end#L 348 GGCTTTTGATACATATTGCCAAATTGCCCTCCAGAAAGGTTGTACCAATT 299 chr5qtel1M 443469 CACAACTCCACTAACAATGCATCAATGTCCCAGTTTTCCCACATCCCTCT 443518 i vii i i i i v iv v v i? i iivi C L1ME4a_3end#L 298 TACACTCCCACCAGCAGTGTATGAGAGTGCCCGTTTCNCCACACCCTCGC 249 chr5qtel1M 443519 CAACAATCATCATTATTTTTCCTGTCA-TCTTAGCCAATCTGACAGGTGT 443567 v vivi ivv i v v - v i i v C L1ME4a_3end#L 248 CAACACTGGGTATTATCAATCTTTTAAATCTTTGCCAATTTGATAGGTGA 199 chr5qtel1M 443568 GTAGTGGTATCTTAGAGTTGTCTTAATTTGCATTTCTCTGATTAATAATG 443617 iv i i vv i i v i C L1ME4a_3end#L 198 AAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCTTTGATTACTAGTG 149 chr5qtel1M 443618 ACTTGGAGCATCTTTTCATATGACTAGAAATAGTTTCCATTTCTTCATCT 443667 vv v i ? vi vviiivi vi v i C L1ME4a_3end#L 148 AGGTTGAACATNTTTTCATATGTTTATTGGCCATTTGTATTTCTTCTTTT 99 chr5qtel1M 443668 GAGAATTGTCTGTTCATATCCTTTGACCATTTTTCAATTGGAGAAT--GG 443715 v i v v i vi -- v C L1ME4a_3end#L 98 GTGAATTGTCTGTTCATGTCCTTTGCCCATTTTTCTATTGGGGTGTTCGT 49 chr5qtel1M 443716 CTTGATTTTTTATAAATTAGAGTTAATTCTCTATATATTTTGGAAAT 443762 -- i vi v vivv ii i vv v C L1ME4a_3end#L 48 CTT--TTTCTTATTGATTTGTAAGAGCTCTTTATATATTAAGGATAT 4 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 37.90 CpG sites = 100, Kimura (unadjusted) = 38.44 Transitions / transversions = 1.20 (100/83) Gap_init rate = 0.03 (17 / 635), avg. gap size = 1.29 (22 / 17) 1498 27.18 0.54 1.84 chr5qtel1M 443212 443762 (556238) C L1ME3G_3end#LINE/L1 (377) 547 4 m_b255s551i4 10123 chr5qtel1M 443212 TAATATTCCATAATATTCATATACCACAATTTATTAAGCCATTCTCCAAC 443261 i i vv i v i i v i C L1ME3G_3end#L 547 TAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTAT 498 chr5qtel1M 443262 TGATGGACATCCATTCAGTTTCCAGTTTTTAGCCACTACAAAAAGGGCTG 443311 ii vviv i v i i v iv C L1ME3G_3end#L 497 TGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCTG 448 chr5qtel1M 443312 CCACAAACATTCAGTGCACATACAGGTCCCTTT-CCCTTCTTT-ATAATC 443359 v ii i -v i i ?-- i v - v v v vi- vv i C L1ME3G_3end#L 447 CAATGAACATCC-TTGTACATGCN--TCCTTGTGCACATGTGCGAGTATT 401 chr5qtel1M 443360 TCTTTGGGATATAAGCCCAGTAGTAACACTGCTGGATCAAAGGGTATGCA 443409 ? i v v? ? v iiv i i i C L1ME3G_3end#L 400 TCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCG 351 chr5qtel1M 443410 CAGTTTGATAACTTTTTGAGCATAGTTCCAAACTACTCTCCAAAATGGTT 443459 v --- v viviv v v i i i ? i C L1ME3G_3end#L 350 CATTTT---AAATTTTAATAGATACTGCCAAATTGCCCTCCAAAANGGCT 304 chr5qtel1M 443460 GGATTCGTTCACAACTCCACTAACAATGCATCAATGTCCCAGTTTTCCCA 443509 v iivi i vii i i i i v iv v v i C L1ME3G_3end#L 303 GTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCA 254 chr5qtel1M 443510 CATCCCTCTCAACAATCATCATTATTTTTCCTGTCA-TCTTAGCCAATCT 443558 i iivi v ?ivi ivv? i v v - i v C L1ME3G_3end#L 253 CACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATCT 204 chr5qtel1M 443559 GACAGGTGTGTAGTGGTATCTTAGAGTTGTCTTAATTTGCATTTCTCTGA 443608 ii viv i i vv i i C L1ME3G_3end#L 203 GATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGA 154 chr5qtel1M 443609 TTAATAATGACTTGGAGCATCTTTTCATATGACTAGAAATAGTTTCCATT 443658 v i vv v vi vviiivi vi C L1ME3G_3end#L 153 TTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGTATT 104 chr5qtel1M 443659 TCTTCATCTGAGAATTGTCTGTTCATATCCTTTGACCATTTTTCAATTGG 443708 i v v i v v C L1ME3G_3end#L 103 TCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGG 54 chr5qtel1M 443709 AGAATGGCTTGATTTTTTATAAATTAGAGTTAATTCTCTATATATTTTGG 443758 iv-- v -- i vi v vivv i i i C L1ME3G_3end#L 53 GT--TGTCTT--TTTCTTATTGATTTGTAGGAGTTCTTTATATATTCTGG 8 chr5qtel1M 443759 AAAT 443762 v C L1ME3G_3end#L 7 ATAT 4 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 33.93 CpG sites = 77, Kimura (unadjusted) = 34.79 Transitions / transversions = 1.10 (77/70) Gap_init rate = 0.02 (13 / 550), avg. gap size = 1.00 (13 / 13) 430 26.59 3.26 3.26 chr5qtel1M 443616 443891 (556109) C L1M4_orf2#LINE/L1 (0) 3294 3019 m_b255s551i5 10123 chr5qtel1M 443616 TGACTTGGAGCATCTTTTCATATGACTAGAAATAGTTTCCATTTCTTCAT 443665 iv v i vi vviiivi vi v v C L1M4_orf2#LIN 3294 TGATGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGTATATCTTCTT 3245 chr5qtel1M 443666 CTGAGAATTGTCTGTTCATATCCTTTGACCATTTTTCAATTGGAGAATGG 443715 iv v i v v ? ivv -- C L1M4_orf2#LIN 3244 TGGAGAAATGTCTATTCAAATCCTTTGCCCATTTTTNAATTGGGTTAT-- 3197 chr5qtel1M 443716 CTTGATTTTTTATAAATTAGAGTT-----AATTCTCTATATATTTTGGAA 443760 - vi vi-- v ----- i i i v C L1M4_orf2#LIN 3196 -TTGTCTTTTTATTG--TTGAGTTGTAAGAGTTCTTTATATATTCTGGAT 3150 chr5qtel1M 443761 ATGAGGCCTTTATCAGAATCTTTGA-CTGTAAAAATATTTTCCCAGTTTA 443809 i? v i - v v -i i v v i v i i C L1M4_orf2#LIN 3149 ACNAGTCCCTTATCAG-ATATATGATTTGCAAATATTTTCTCCCATTCTG 3101 chr5qtel1M 443810 TTGCTTCCCTTCTAATCTTGTCTGCATTAGTTTTGTTT---GTACAAAAA 443856 v v vi i v - - vv - v iv --- i i C L1M4_orf2#LIN 3100 TGGGTTGTCTTTTCA-CTT-TCTTGA-TAGTGTCCTTTGAAGCACAAAAG 3054 chr5qtel1M 443857 CTTTTCAGTTTGGTATAATCGAAATTTTCTATTTT 443891 i v v i iv i v v v C L1M4_orf2#LIN 3053 TTTTTAATTTTGATGAAGTCCAATTTATCTATTTT 3019 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 33.32 CpG sites = 32, Kimura (unadjusted) = 33.32 Transitions / transversions = 0.82 (32/39) Gap_init rate = 0.04 (12 / 275), avg. gap size = 1.50 (18 / 12) 17 0.00 0.00 0.00 chr5qtel1M 444077 444095 (555905) (A)n#Simple_repeat 1 19 (0) m_b255s252i20 10124 chr5qtel1M 444077 AAAAAAAAAAAAAAAAAAA 444095 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAA 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 31 12.88 8.89 2.08 chr5qtel1M 444420 444509 (555491) (ACATAT)n#Simple_repeat 1 96 (0) m_b255s252i21 10125 chr5qtel1M 444420 ACATGTATACATACATATATATAT-C-TATACA-ATACATATACATA-AT 444465 i i i i - - - - i (ACATAT)n#Sim 1 ACATATACATATACATATACATATACATATACATATACATATACATATAC 50 chr5qtel1M 444466 ACACACATGAGTATATATACATAT--TTAGACATATACAT-T-CATAT 444509 i i - - i --v v - - (ACATAT)n#Sim 51 ATATACAT-A-TACATATACATATACATATACATATACATATACATAT 96 Matrix = Unknown Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.10 (9 / 89), avg. gap size = 1.11 (10 / 9) 15 7.86 3.70 0.00 chr5qtel1M 444792 444818 (555182) (GTTT)n#Simple_repeat 1 28 (0) m_b256s252i3 10126 chr5qtel1M 444792 GTTT-TTTGTTTGTTTGTTTTTTAGTTT 444818 - v v (GTTT)n#Simpl 1 GTTTGTTTGTTTGTTTGTTTGTTTGTTT 28 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.04 (1 / 26), avg. gap size = 1.00 (1 / 1) 22 17.29 0.00 0.00 chr5qtel1M 445027 445065 (554935) (A)n#Simple_repeat 1 39 (0) m_b256s252i4 10127 chr5qtel1M 445027 AAAAAGAAAAAAAATAAGAAAAAAAAAAACAAGCAAAAA 445065 i v i v iv (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 39 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 1268 28.42 2.43 2.43 chr5qtel1M 445328 445821 (554179) C L1ME3G_3end#LINE/L1 (376) 548 55 m_b256s551i2 10128 chr5qtel1M 445328 ATAATATTCCATAACATTCATATACCATCACTTATTCAGCCATTCTCCCA 445377 i ii vv v i i i i i C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr5qtel1M 445378 CTGATGGGCATCCACTCAGTTTCTAGTTTCTAGCCACCACAAAAAGAGCT 445427 i i ii vviv i i i v i ii v iv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr5qtel1M 445428 GCCACAAATATTTTAGCACATGTGGGTCCTTT--CCCCTGTTTTATGATG 445475 v ii i ii v i i?-- v-- v v viv vv v C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATT 401 chr5qtel1M 445476 TCTTTGGGATATAAGCCCAGTAGAGACACTGCTGGATCAAAGAGTATGCA 445525 ? i v v? ? v v iv i i i i C L1ME3G_3end#L 400 TCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCG 351 chr5qtel1M 445526 CACTTTGATGGCTATTTGAGCA--TAGTTCCAAATTGCTCTCCAGAATGG 445573 i i ----- v ii -- v v i i ? C L1ME3G_3end#L 350 CATTTTAA-----ATTTTAATAGATACTGCCAAATTGCCCTCCAAAANGG 306 chr5qtel1M 445574 TTGGGTCATTTCACAACTCTACCAACAATACATTAGTGTCCTAGTTTTCC 445623 i vii v i vii i i i ii v v v iv i C L1ME3G_3end#L 305 CTGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCC 256 chr5qtel1M 445624 CACATCCCCTCCAAAATTTATCATTTTTTC---CTGTTA--TTTTAGCCA 445668 i i v v i ?i-- v v --- v -- v C L1ME3G_3end#L 255 CACACCCTCGCCAACACTNG--ATATTATCAANCTTTTAAATTTTTGCCA 208 chr5qtel1M 445669 ATTTGAGGGGTGTGAAGTGGTCCCTCAGAATTGTTTTAATTTGCATTTTT 445718 i v vi i vi vvi ii C L1ME3G_3end#L 207 ATCTGATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCC 158 chr5qtel1M 445719 CTAATCAATTGTGATTTAGAACGTTTTAAAATAGGAGTATAAATGGC--T 445766 i i v v vv v i i i vvv v vv --- -- C L1ME3G_3end#L 157 CTGATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTAT---TGGCCAT 111 chr5qtel1M 445767 TTA-ATTTCTTCATCTGAAAATGGTCTGTTCATATCTTATGACCATTTAT 445815 i- i v vi v i i v v v C L1ME3G_3end#L 110 TTGTATTTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTT 61 chr5qtel1M 445816 CAATTG 445821 v C L1ME3G_3end#L 60 CTATTG 55 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 36.30 CpG sites = 74, Kimura (unadjusted) = 36.97 Transitions / transversions = 1.17 (74/63) Gap_init rate = 0.04 (18 / 493), avg. gap size = 1.33 (24 / 18) 333 33.33 0.00 0.00 chr5qtel1M 448625 448714 (551286) MIRc#SINE/MIR 16 105 (163) m_b256s601i0 10129 chr5qtel1M 448625 CAGTGGACAAAGAGCTGGGCCTGGAGTCAGAAAGAGCAGAGTTTCAATCT 448674 v i vi i i i v v i iv i i MIRc#SINE/MIR 16 CAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCC 65 chr5qtel1M 448675 TGCCCTAGACTCTTCTTGGCCATATGACTCTGGACAAGTC 448714 i v iiv v v vi i ii i ii i MIRc#SINE/MIR 66 CGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTC 105 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 42.52 CpG sites = 20, Kimura (unadjusted) = 46.83 Transitions / transversions = 2.00 (20/10) Gap_init rate = 0.00 (0 / 89), avg. gap size = 0.0 (0 / 0) 415 32.87 5.43 0.87 chr5qtel1M 449807 450027 (549973) C L1ME4c_3end#LINE/L1 (244) 586 356 m_b256s551i3 10130 chr5qtel1M 449807 AATCTTCCTGCTGGTCATTTCTTATAGA-ACAGTAATATTCCATAACATT 449855 i v iv vi i v i v-i - vivi ? C L1ME4c_3end#L 586 AGTCTTCATAATTATCATTTTTAATGGCTGCA-TAATATTCCATCGAGTN 538 chr5qtel1M 449856 CATATACTTCAATATATTCAGCCATTCTCCAACTGATGGGCATCCA---- 449901 v i ivi v i i i i v i v i ii ---- C L1ME4c_3end#L 537 GATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAGGTT 488 chr5qtel1M 449902 ---CTCAGTTTCTCGGCACTATTAATGG-GCCACCACAAACAT-TTTGCA 449946 ---ii i i vi i v ii- ii v ii - i ii C L1ME4c_3end#L 487 GTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTCGTG 438 chr5qtel1M 449947 CATGTGGTCCCTTTCCCTCCTTTGAG--ATCTCTTTGGGATATAAGCCCA 449994 i i - ii i i i-- i i i v vv C L1ME4c_3end#L 437 CATATAG-CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAATTCCCA 389 chr5qtel1M 449995 GTAGTAACACTGCTGGATCAAGGGGTCTGCACA 450027 v iiv i i i i v v C L1ME4c_3end#L 388 GAAGTGGAATTACTGGGTCAAAGGGTATGAACA 356 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 44.80 CpG sites = 50, Kimura (unadjusted) = 46.64 Transitions / transversions = 2.27 (50/22) Gap_init rate = 0.04 (8 / 220), avg. gap size = 1.75 (14 / 8) 358 22.87 19.20 2.05 chr5qtel1M 451144 451268 (548732) MIRb#SINE/MIR 89 234 (34) m_b256s601i1 10131 chr5qtel1M 451144 TGTGTGACCTTTGGCAAGTCACTTCCACCT------GCTTTAGTTTTCTC 451187 v i v- ------ i i i MIRb#SINE/MIR 89 TGTGTGACCTTGGGCAAGTTACTTA-ACCTCTCTGAGCCTCAGTTTCCTC 137 chr5qtel1M 451188 AACTG-------------ACAA-ACCCTTCTCTTAGGGTTGTTG----GA 451219 v ------------- i - ivi vi ---- MIRb#SINE/MIR 138 ATCTGTAAAATGGGGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGA 187 chr5qtel1M 451220 TCAAATGAGATCCTATTTGTAAAATCCTTGACGCAGTGTTTATGGTACA 451268 i vv iiv iiv ii i ii-- i MIRb#SINE/MIR 188 TTAAATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCC--TGGCACA 234 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 27.13 CpG sites = 19, Kimura (unadjusted) = 28.32 Transitions / transversions = 2.11 (19/9) Gap_init rate = 0.06 (7 / 124), avg. gap size = 3.86 (27 / 7) 14 13.59 4.55 4.55 chr5qtel1M 451371 451414 (548586) (ATATTT)n#Simple_repeat 1 44 (0) m_b256s252i5 10132 chr5qtel1M 451371 ATATTTATATTTTGTATTT-GATTTATGGTTTTATATTA-ATTTAT 451414 - i -v iv v - - (ATATTT)n#Sim 1 ATATTTATA-TTTATATTTATATTTATATTTATAT-TTATATTTAT 44 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.09 (4 / 43), avg. gap size = 1.00 (4 / 4) 336 20.69 21.30 1.55 chr5qtel1M 451440 451547 (548453) MIR3#SINE/MIR 24 152 (56) m_b256s601i2 10133 chr5qtel1M 451440 GAGCTCAGACTTTGGAGCCAAGAGATTTGTGTTCCATTCCTAGTTCTTCT 451489 v i v- i i ii v i v ii i v i MIR3#SINE/MIR 24 GAGCACGGACTG-GGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCC 72 chr5qtel1M 451490 TATTAACTC----TATAA------ACA-----------CTCTC--AGCCT 451516 - i ?---- i i ------i ----------- --i MIR3#SINE/MIR 73 -ACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCT 121 chr5qtel1M 451517 CAGTTTCCTCATCTGTAAAATGGTGGGGTTG 451547 iv MIR3#SINE/MIR 122 CAGTTTCCTCATCTGTAAAATGAGGGGGTTG 152 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 22.74 CpG sites = 16, Kimura (unadjusted) = 25.50 Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.06 (6 / 107), avg. gap size = 4.17 (25 / 6) 540 23.93 0.85 0.00 chr5qtel1M 452635 452751 (547249) MIRc#SINE/MIR 10 127 (141) m_b256s601i3 10134 chr5qtel1M 452635 GTAGTGCAGTGGATAGAGCACCAGCCCTGAAATCAGGAGGACCTGAGTTC 452684 i v ii v i i i i i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr5qtel1M 452685 AAATCTGATTTCAGACACTTCCTAGCTGTGGCACCCTGGGCAAGTCACTG 452734 i i ivivi v v v vv i v MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTT 109 chr5qtel1M 452735 AACCCCAATT-GCCTCAG 452751 i vv v- MIRc#SINE/MIR 110 AACCTCTCTGAGCCTCAG 127 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 26.81 CpG sites = 15, Kimura (unadjusted) = 29.19 Transitions / transversions = 1.15 (15/13) Gap_init rate = 0.01 (1 / 116), avg. gap size = 1.00 (1 / 1) 460 19.61 0.81 8.77 chr5qtel1M 452824 452946 (547054) MIRc#SINE/MIR 32 145 (123) m_b256s601i4 10135 chr5qtel1M 452824 GAACTTCTGGAGTCAGGAAGACTTATCTCCTGGAGTCCTTATCAGATGTC 452873 i -- i ivv i -- ---- i v v - MIRc#SINE/MIR 32 GGACTT--GGAGTCAGGAAGACCTGGGTTC--GAGTCC----CGGCTCT- 72 chr5qtel1M 452874 AGACACTTCCTAGATGTGTGAGTCTAGACAAGTCACTTCACC-CTGTTTG 452922 - v v v vii i i v - v vv MIRc#SINE/MIR 73 -GCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAG 121 chr5qtel1M 452923 CCTCAGTTTCCTTATCTGTAAAAT 452946 i MIRc#SINE/MIR 122 CCTCAGTTTCCTCATCTGTAAAAT 145 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 21.52 CpG sites = 10, Kimura (unadjusted) = 22.62 Transitions / transversions = 0.83 (10/12) Gap_init rate = 0.09 (11 / 122), avg. gap size = 1.00 (11 / 11) 38 2.33 0.00 0.00 chr5qtel1M 453261 453304 (546696) (TG)n#Simple_repeat 1 44 (0) m_b256s252i6 10136 chr5qtel1M 453261 TGTGTGTGTGTGTGTGTGTGTGTGTGTATGTGTGTGTGTGTGTG 453304 i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 44 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 86 11.21 5.19 0.00 chr5qtel1M 453304 453457 (546543) (GA)n#Simple_repeat 1 162 (0) m_b256s252i7 10137 chr5qtel1M 453304 GAGAGAGAGAGAGAGACAAAGAGAAAGAGAGAGAGAAAGAAAG-GAGAG- 453351 v i i i i - - (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr5qtel1M 453352 GGGAGAG-GAGAGA-AGAGAGAGAGAGAAAGAGAGAGAGAGCGAG-GAGA 453398 i - - i v - (GA)n#Simple_ 51 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 100 chr5qtel1M 453399 GAGAGAAAG-GAGAGAG-GAGAGA-AGAGAGAGACAGAGACAGACAAAGA 453445 i - - - v v v i (GA)n#Simple_ 101 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 150 chr5qtel1M 453446 CACAGAGACAGA 453457 v v v (GA)n#Simple_ 151 GAGAGAGAGAGA 162 Matrix = Unknown Transitions / transversions = 1.00 (8/8) Gap_init rate = 0.05 (8 / 153), avg. gap size = 1.00 (8 / 8) 221 29.16 2.17 6.82 chr5qtel1M 454172 454263 (545737) C L2c_3end#LINE/L2 (10) 468 381 m_b256s601i5 10138 chr5qtel1M 454172 TCAATAAACACGTATTAAATGGCGACTCTGCGCCAGTCACCATAGGCATG 454221 i iv i ii v v v i v i -- i v i C L2c_3end#LINE 468 TCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGC--TGGGGATA 421 chr5qtel1M 454222 CAGAGACCCCAAAATG-GCCACTG-CCCTTTCCTCTGGGAGCTC 454263 i i----i i- v v - vi vi C L2c_3end#LINE 420 CAAAGAT----GAATAAGACACGGTCCCTGCCCTCAAGGAGCTC 381 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 34.14 CpG sites = 15, Kimura (unadjusted) = 37.90 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.09 (8 / 91), avg. gap size = 1.00 (8 / 8) 194 33.32 6.08 4.67 chr5qtel1M 454378 454525 (545475) L2d_3end#LINE/L2 353 502 (14) m_b256s601i6 10139 chr5qtel1M 454378 TCTCTAGTCATTCTG-GTGCCATTTTAGTCCCTGTGCTCTCTAGCAGGAT 454426 i ii iii- --- v i- - i i i vi L2d_3end#LINE 353 TCTCTAATTGTTTCATGTG---TGTTAGTCT-TGT-CTCCCCAACTAGAT 397 chr5qtel1M 454427 TATCA-----TGGAGATTTGGAAGGTTATGG-TGAAACTTTTTTTTTTTT 454470 i v ----- v iviv i --ii v- v v ? ? iv L2d_3end#LINE 398 TGTAAGCTCCTTGAGGGCAGGGA--CCATGTCTTATACTNTTTTNTCGTT 445 chr5qtel1M 454471 TTTAACAGC--TTAGTCTAGTGCCTGGAACACAGTACATGCTTAGTAAAT 454518 iiiv --i ivi ivi v i vii i i L2d_3end#LINE 446 CCCCACAGCGCCTAGCACAGTGCTGAGCACATAGTAGGCGCTCAATAAAT 495 chr5qtel1M 454519 ACTTATT 454525 i L2d_3end#LINE 496 ACTTGTT 502 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 45.17 CpG sites = 32, Kimura (unadjusted) = 48.08 Transitions / transversions = 2.13 (32/15) Gap_init rate = 0.07 (11 / 147), avg. gap size = 1.45 (16 / 11) 200 30.87 2.90 1.43 chr5qtel1M 454457 454525 (545475) L2d2_3end#LINE/L2 474 543 (12) m_b256s601i7 10139 chr5qtel1M 454457 ACTTTTTTTTTTTTTTTAACAGC--TTAGTCTAGTGCCTGGAACACAGTA 454504 i v v iiiii - --i ivi v v L2d2_3end#LIN 474 ACTTCTTTGTATCCCCCA-CAGCGCCTAGCACAGTGCCTTGCACACAGTA 522 chr5qtel1M 454505 CATGCTTAGTAAATACTTATT 454525 vii i i i i L2d2_3end#LIN 523 GGCGCTCAATAAATATTTGTT 543 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 39.81 CpG sites = 15, Kimura (unadjusted) = 42.54 Transitions / transversions = 2.50 (15/6) Gap_init rate = 0.03 (2 / 68), avg. gap size = 1.50 (3 / 2) 260 22.92 0.00 0.00 chr5qtel1M 454478 454525 (545475) L2b_3end#LINE/L2 407 454 (12) m_b256s601i8 10139 chr5qtel1M 454478 GCTTAGTCTAGTGCCTGGAACACAGTACATGCTTAGTAAATACTTATT 454525 i ivi ? v vii i i i L2b_3end#LINE 407 GCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTTGTT 454 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 26.20 CpG sites = 8, Kimura (unadjusted) = 29.31 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 315 27.59 16.55 0.00 chr5qtel1M 454666 454810 (545190) C L3#LINE/CR1 (1) 4098 3930 m_b256s601i9 10140 chr5qtel1M 454666 ACAGAATCGCAGACTCTCAGAGGTGGAAGGAACCTCAGGGGATCCCTGAT 454715 i i v v i i i vivi ii C L3#LINE/CR1 4098 ATAGAATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGT 4049 chr5qtel1M 454716 CCAACC-CACA-CTGACCCA-CCATCTCTTGTGCAGTGTGCCCAACATGT 454762 - v - ii iv -vv i v i iii v ii v C L3#LINE/CR1 4048 CCAACCTCCCATCCAATGCAGGAATCCCTTCTACAACATCCCTGACAAGT 3999 chr5qtel1M 454763 GA-----CAG-----------GCACTTCAAGTGTCGGGGAGCTCATCACC 454796 i----- -----------i i v v ii C L3#LINE/CR1 3998 GGTCATCCAGCCTCTGCTTGAACACCTCCAGTGACGGGGAGCTCACTACC 3949 chr5qtel1M 454797 G-ACAAGG----TCATTCC 454810 v-? i ----i C L3#LINE/CR1 3948 TCNCGAGGCAGCCCATTCC 3930 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 34.92 CpG sites = 26, Kimura (unadjusted) = 36.06 Transitions / transversions = 1.86 (26/14) Gap_init rate = 0.05 (7 / 144), avg. gap size = 3.43 (24 / 7) 16 0.00 0.00 0.00 chr5qtel1M 455123 455139 (544861) (A)n#Simple_repeat 1 17 (0) m_b256s252i8 10141 chr5qtel1M 455123 AAAAAAAAAAAAAAAAA 455139 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 189 28.79 7.58 0.00 chr5qtel1M 455431 455496 (544504) L2a_3end#LINE/L2 420 490 (27) m_b256s601i10 10142 chr5qtel1M 455431 GGACCCTTTTGTGTTTC--TCATTGATG---CCCCAGGGCCCCATATGGT 455475 ii v v i-- i v --- v iviv ii L2a_3end#LINE 420 GGACTTTTGTCTGTTTTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGT 469 chr5qtel1M 455476 GCCTGGAACACAGTAATCACT 455496 v i iv i L2a_3end#LINE 470 GCCTGGCACATAGTAGGCGCT 490 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 34.81 CpG sites = 11, Kimura (unadjusted) = 37.25 Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.03 (2 / 65), avg. gap size = 2.50 (5 / 2) 279 33.33 0.78 0.00 chr5qtel1M 457894 458022 (541978) C L2-1_AMi#LINE/L2 (583) 652 523 m_b256s551i4 10143 chr5qtel1M 457894 TGGGTATGAAGGGCAAGGGGGCAGGACTAATC-AAGATGACCCCTAGGTT 457942 i i i iv v i i vi vv v i - v i C L2-1_AMi#LINE 652 TGGATGTGAGGACCTAGAGAGAGGTCCGAGTCGAAGATGACGCCCAGGTT 603 chr5qtel1M 457943 GCAAGTCTGGGTAACTGGGAGGATGGCAGTGCCCTCCACAGTTATAGGGA 457992 i ii i i i v v ii iiv v v i C L2-1_AMi#LINE 602 ACGGGCCTGAGTGACAGGCAGGATGGTGGTGTTGTCCACAGTGATCGAGA 553 chr5qtel1M 457993 AGGCGGGAAAGGGACAGGGATTGGGGAAAA 458022 iiv i vi v?i v ii C L2-1_AMi#LINE 552 AAAGGGAATGGGGAGNAGGCTTGGGGGGAA 523 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 45.24 CpG sites = 27, Kimura (unadjusted) = 46.77 Transitions / transversions = 1.69 (27/16) Gap_init rate = 0.01 (1 / 128), avg. gap size = 1.00 (1 / 1) 226 33.05 6.78 0.00 chr5qtel1M 458355 458472 (541528) C L2#LINE/L2 (1010) 2072 1947 m_b256s601i11 10144 chr5qtel1M 458355 TGCTGCAGAGATGTCCAGAACGATCAGGACTGAGAA------A--AGAGT 458396 v ? v v v v v ------ --i v C L2#LINE/L2 2072 TGCTGCTGANAGGTCAAGTAAGATGAGGACTGAGAATTGACCATTGGATT 2023 chr5qtel1M 458397 TAGCGGGGAAGAGCTCATTGGCAGCTCTGGAGAGAGGAGTTTTGGGTGAA 458446 iiv vi v iii ii ivi v i vv i C L2#LINE/L2 2022 TAGCAACGTGGAGGTCATTGGTGACCTTGACAAGAGCAGTTTCGGTGGAG 1973 chr5qtel1M 458447 CGGGAAGGTCAGAAGCCCAGCTGTAG 458472 i vii v ii iiii v C L2#LINE/L2 1972 TGGTGGGGACGAAAGCCTGATTGGAG 1947 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 42.31 CpG sites = 22, Kimura (unadjusted) = 45.42 Transitions / transversions = 1.29 (22/17) Gap_init rate = 0.02 (2 / 117), avg. gap size = 4.00 (8 / 2) 213 28.11 0.00 3.51 chr5qtel1M 458484 458542 (541458) C L2b_3end#LINE/L2 (19) 447 391 m_b256s601i12 10145 chr5qtel1M 458484 ATTTACTAAGCACCTGCTGTGTACTTCTAGCACAGTGGCAAGTGTTGGGA 458533 i i i i -- vi ? v vi i i i i C L2b_3end#LINE 447 ATTTACTGAGCGCCTACTGTGTGC--CAGGCNCTGTGCTAGGCGCTGGGG 400 chr5qtel1M 458534 AGGAAGCGG 458542 viv C L2b_3end#LINE 399 ATACAGCGG 391 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 31.97 CpG sites = 11, Kimura (unadjusted) = 37.82 Transitions / transversions = 2.20 (11/5) Gap_init rate = 0.03 (2 / 58), avg. gap size = 1.00 (2 / 2) 485 18.07 0.00 0.00 chr5qtel1M 459340 459422 (540578) MIR#SINE/MIR 66 148 (114) m_b256s601i13 10146 chr5qtel1M 459340 TCTGCCTACTACTAGCTGTATGATACTGGGCAAGTCACTTAAACCCATTT 459389 vvi i ivi i v i vi v MIR#SINE/MIR 66 TCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTG 115 chr5qtel1M 459390 TGCCTCAGTTTCCTCATCTGTAAAATGAGGGTA 459422 i i MIR#SINE/MIR 116 TGCCTCAGTTTCCTCATCTGTAAAATGGGGATA 148 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 20.97 CpG sites = 9, Kimura (unadjusted) = 20.97 Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.00 (0 / 82), avg. gap size = 0.0 (0 / 0) 376 32.44 5.10 5.64 chr5qtel1M 459427 459622 (540378) C L2b_3end#LINE/L2 (2) 464 270 m_b256s601i15 10147 chr5qtel1M 459427 TCAGTCAGTCAGTAAACATTTATTAATTGACTCCTATATATTAGGC--TG 459474 v v ii i i i vi v v i i iii -- C L2b_3end#LINE 464 TCATTCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTG 415 chr5qtel1M 459475 TGTC-----CTGGGGACAGAAAGGAAAGCA-GAAAGAT--GATCCCGGTT 459516 ii----- i v iv vi i - v i-- i v ii C L2b_3end#LINE 414 TGCTAGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCC 365 chr5qtel1M 459517 CTCGAGGAATTTACAGTCTAATGGGAGAAACAGAGGAAAGGTCCTCAAAT 459566 iv ii i i i i --- v v vv? i i C L2b_3end#LINE 364 CTCACGGAGCTCACAGTCTAGTGGGGGAGACA---GACATGTAANCAGAC 318 chr5qtel1M 459567 AAAGGGAATCAGGAAGATTTGCAGCAGATAGGATTTCAGTTGGGGCTCGA 459616 v?iv i ---v v v -- i i --- vv i ii C L2b_3end#LINE 317 AATNATAACC---CAGAGTGGCAG--GGTAGGACT---GGGGGGGCCCAG 276 chr5qtel1M 459617 AGGAAG 459622 i C L2b_3end#LINE 275 AGGAGG 270 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 44.17 CpG sites = 38, Kimura (unadjusted) = 45.22 Transitions / transversions = 1.73 (38/22) Gap_init rate = 0.08 (15 / 195), avg. gap size = 1.40 (21 / 15) 431 29.74 0.00 5.08 chr5qtel1M 459427 459550 (540450) C L2c_3end#LINE/L2 (2) 476 359 m_b256s601i14 10147 chr5qtel1M 459427 TCAGTCAGTCAGTAAACATTTATTAATTGACTCCTATATATTAGGCTGTG 459476 v v ii i vi v v i iii --- C L2c_3end#LINE 476 TCATTCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGC---G 430 chr5qtel1M 459477 TCCTGGGGACAGAAAGGAAAGCAGAAAGATGATCCCGGTTCTCGAGGAAT 459526 -- i v ivi ii - i v i i v ii i ii C L2c_3end#LINE 429 --CTGGGGATACAAAGATGAATA-AGACACGGTCCCTGCCCTCAAGGAGC 383 chr5qtel1M 459527 TTACAGTCTAATGGGAGAAACAGA 459550 i i ii i C L2c_3end#LINE 382 TCACAGTCTAGTGGAGGAGACAGA 359 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 37.46 CpG sites = 26, Kimura (unadjusted) = 40.52 Transitions / transversions = 2.89 (26/9) Gap_init rate = 0.05 (6 / 123), avg. gap size = 1.00 (6 / 6) 265 25.42 5.71 13.85 chr5qtel1M 460900 461109 (538891) C MIR3#SINE/MIR (11) 197 3 m_b256s601i16 10148 chr5qtel1M 460900 TCAGAGAAGG---GAGCCCAAATGAAG-TTAGAGGTACCATCT--TCCCA 460943 v v --- ivi v i v- i -- -- v C MIR3#SINE/MIR 197 TCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGAT--CATCTAGTCCAA 150 chr5qtel1M 460944 CCTCATGATT--AGAGGTGCTTAAACTAATACTTCTTTTTCCCTGAGGCA 460991 i v v -- v i vvv i vi --------- v -- C MIR3#SINE/MIR 149 CCCCCTCATTTTACAGATGAGGAAACTGAGGC---------CCAGAG--A 111 chr5qtel1M 460992 ATTGGGGTGACTTGCTCAGGGT--CACAGCTATGAAGTGTTAAGTGTCTG 461039 iv ii i i -- ? ------ - v v C MIR3#SINE/MIR 110 GGTGAAGTGACTTGCCCAAGGTCACACAGCNA------GTT-AGTGGCAG 68 chr5qtel1M 461040 AG--GACACTTTTGAACTCAGGTCCTCCTGACTTTAGAGCTGGTGCACTA 461087 -- iv -- v i - ii-v iiv v v C MIR3#SINE/MIR 67 AGCCGGGAC--TAGAACCCAGGT-CTCCTGACTCC-CAGTCCGTGCTCTC 22 chr5qtel1M 461088 TCCACTATGCCACTTAGCTGCC 461109 ii vv --- C MIR3#SINE/MIR 21 TCTGCTCAGCCACT---CTGCC 3 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.98 CpG sites = 21, Kimura (unadjusted) = 30.98 Transitions / transversions = 0.84 (21/25) Gap_init rate = 0.16 (33 / 209), avg. gap size = 1.18 (39 / 33) 353 24.21 1.75 9.43 chr5qtel1M 460998 461111 (538889) C MIRb#SINE/MIR (158) 110 5 m_b256s601i17 10148 chr5qtel1M 460998 GTGACTTGCTCAGGGTCACA--GCTATGAAGTGTTAAGTGTCTGAGGACA 461045 i i i -- vv vi - v i --i -- C MIRb#SINE/MIR 110 GTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCA-GAGCC--GGGA-- 66 chr5qtel1M 461046 CTTTTGAACTCAGGTCCTCCTGACTTTAGAGCTGGTGCACTATCCACTAT 461095 -- i i ivi ii i iv v v ii C MIRb#SINE/MIR 65 --TTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGC 18 chr5qtel1M 461096 GCCACTTAGCTGCCCC 461111 i --- C MIRb#SINE/MIR 17 ACCAC---GCTGCCCC 5 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 27.22 CpG sites = 17, Kimura (unadjusted) = 30.04 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.10 (11 / 113), avg. gap size = 1.09 (12 / 11) 12 31.19 1.82 0.00 chr5qtel1M 462565 462619 (537381) (TATCTA)n#Simple_repeat 1 56 (0) m_b256s252i9 10149 chr5qtel1M 462565 TATCTATGTGTATGTATATATCTACATAAGCATACATAAATATATCT-TA 462613 i v i v i vvii vi vv - (TATCTA)n#Sim 1 TATCTATATCTATATCTATATCTATATCTATATCTATATCTATATCTATA 50 chr5qtel1M 462614 ACTATA 462619 v (TATCTA)n#Sim 51 TCTATA 56 Matrix = Unknown Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1) 14 15.34 2.63 2.63 chr5qtel1M 462908 462945 (537055) (CAGAGT)n#Simple_repeat 1 38 (0) m_b256s252i10 10150 chr5qtel1M 462908 CAGAGTAAG-GTCATAGTCAGAGTCACAGCTAAGAGCCA 462945 v - v v - v i (CAGAGT)n#Sim 1 CAGAGTCAGAGTCAGAGTCAGAGTCAGAG-TCAGAGTCA 38 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 398 27.60 0.00 9.43 chr5qtel1M 465801 465916 (534084) MIRc#SINE/MIR 1 106 (162) m_b256s601i18 10151 chr5qtel1M 465801 CAGGGCAGTTAGGTAGCTCAGTGGGTAGAGCACCAGTCCTGGAGTCAGGA 465850 ii --- i iv iv ii v i MIRc#SINE/MIR 1 CGAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGA 47 chr5qtel1M 465851 GGACCTGAGTGCAAATCTAAATTTTGATACTAGACATTTACTAGTTATAT 465900 i i v i i iviii i --- ---- i i i i MIRc#SINE/MIR 48 AGACCTGGGTTCGAGTCCCGGCTCTG---C----CACTTACTAGCTGTGT 90 chr5qtel1M 465901 GACCCTCGGAAAGTCA 465916 i v v MIRc#SINE/MIR 91 GACCTTGGGCAAGTCA 106 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 31.66 CpG sites = 22, Kimura (unadjusted) = 36.35 Transitions / transversions = 3.14 (22/7) Gap_init rate = 0.09 (10 / 115), avg. gap size = 1.00 (10 / 10) 243 30.61 2.04 0.00 chr5qtel1M 466988 467085 (532915) C MIRc#SINE/MIR (167) 101 2 m_b256s601i19 10152 chr5qtel1M 466988 TGCTCAAGATCACAGAGACAGCAAGCAGCCAAACCCAGCTTTGA-CCCAG 467036 i i v vi i ii vi i vi vi i - C MIRc#SINE/MIR 101 TGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAG 52 chr5qtel1M 467037 GTCC-CCTCCCTCCAGACACCCTGACCTCCCCACTGCACCACACTGTCTC 467085 i- vv iiiv vv vi ii i C MIRc#SINE/MIR 51 GTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTGCCTC 2 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 39.21 CpG sites = 19, Kimura (unadjusted) = 41.01 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.02 (2 / 97), avg. gap size = 1.00 (2 / 2) 355 22.58 3.12 3.12 chr5qtel1M 469495 469590 (530410) MIR3#SINE/MIR 55 150 (58) m_b256s601i20 10153 chr5qtel1M 469495 TTTAATCCTA-CT-TACTGTCAACTACCTGTGTGACTCTGGACAAGTCAG 469542 i i ii- - i iiii ?v ii i v MIR3#SINE/MIR 55 TCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCAC 104 chr5qtel1M 469543 TTCCACTCTCTCTGAGCCTCATTTTGTCTCCT-TGTAAAAGGAGAGGAT 469590 - - i v -i v - v i i MIR3#SINE/MIR 105 TT-CAC-CTCTCTGGGCCTCAGTTT-CCTCATCTGTAAAATGAGGGGGT 150 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 26.81 CpG sites = 16, Kimura (unadjusted) = 28.60 Transitions / transversions = 3.20 (16/5) Gap_init rate = 0.06 (6 / 95), avg. gap size = 1.00 (6 / 6) 312 29.85 5.00 3.70 chr5qtel1M 469498 469657 (530343) MIR#SINE/MIR 57 218 (44) m_b256s601i21 10153 chr5qtel1M 469498 AATCCTACTTACTGTCA---ACTACCTGTGTGACTCTGGACAAGTCAGTT 469544 iivi - i --- v ii i i v MIR#SINE/MIR 57 AATCCCGGCT-CTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTT 105 chr5qtel1M 469545 CCACTCTCTCTGAGCCTCATTTTGTCTCCT-TGTAAAA-GGAGAGGATCA 469592 -- vi v v -i v - - i vi v MIR#SINE/MIR 106 --AACCTCTCTGTGCCTCAGTTT-CCTCATCTGTAAAATGGGGATAATAA 152 chr5qtel1M 469593 CAGGCCCTAAACTACAGAATCCTGAAATGA-GATT-CTTGGGTTAAAAAA 469640 i vv vvii i ii -- vvi - -vv i v v MIR#SINE/MIR 153 TAGTACCTACCTCATAGGGT--TGTTGTGAGGATTAAATGAGTTAATACA 200 chr5qtel1M 469641 CA-AAAACGCCTCAGACA 469657 ii- i i vii MIR#SINE/MIR 201 TGTAAAGCGCTTAGAACA 218 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 37.83 CpG sites = 26, Kimura (unadjusted) = 39.03 Transitions / transversions = 1.30 (26/20) Gap_init rate = 0.08 (12 / 159), avg. gap size = 1.17 (14 / 12) 360 31.26 9.56 3.07 chr5qtel1M 470147 470575 (529425) L1M4_orf2#LINE/L1 748 1203 (2091) m_b256s551i5 10154 chr5qtel1M 470147 TGGAAA--AAATAACCTAGTCTTAAAGAATAAGTAGGTTAAAGAACAAGT 470194 -- i vi v i v iv i i i v i L1M4_orf2#LIN 748 TGGAAATTAAACAACACACTCCTAAATAACCAATGGGTCAAAGAAGAAAT 797 chr5qtel1M 470195 ---------AACTAG------TTTT---ATTAAAGAGAATGATGAGACAA 470226 --------- i ------i --- v v i i vi v L1M4_orf2#LIN 798 CACAAGGGAAATTAGAAAATACTTTGAGATGAATGAAAACGAAAACACAA 847 chr5qtel1M 470227 TATACCAAAGCTTATAGGAGGCAGCAAAAA-GGTCATCAGAGGAAAATTT 470275 i i i v ? i-i vv i i L1M4_orf2#LIN 848 CATACCAAAACTTATGGGATGCAGCNAAAGCAGTGCTTAGAGGGAAATTT 897 chr5qtel1M 470276 TTATCT---------TAGATCAACAAAACAGAGAAAAAGCAGATCAATGA 470316 v v --------- v i v iv i i vvv i i L1M4_orf2#LIN 898 ATAGCTGTAAATGCCTATATTAAAAAAGAAGAAAGATCTCAAATCAATAA 947 chr5qtel1M 470317 ATTGGGTACGCAGTTGAAAGAACTAGAAAAAGAA---CAAATTAAAAATC 470363 vi iiviviv vi v ii --- i --- L1M4_orf2#LIN 948 CCTAACCTTCCACCTTAAGAAACTAGAAAAAGAAGAGCAAACTAAA---C 994 chr5qtel1M 470364 TCCAAATAAGCCCCAGATTGGAAATCCTGAATACTAAAAGTAAGATTAAT 470413 i v ii vvv ivv vv i v i i ivvi i v L1M4_orf2#LIN 995 CCAAAGCAAGCAGAAGGAAGGAAATAATAAAGATTAGAGCGGAAATAAAT 1044 chr5qtel1M 470414 AAAACAAAATATGAGAAAACCATTGAATTAATAAATAAAACTAGGAACTG 470463 i i i iv iii v v ivv v ii i ii ii L1M4_orf2#LIN 1045 GAAATAGAGAATAGAAAAACAATAGAGAAAATCAACGAAACCAAAAGTTG 1094 chr5qtel1M 470464 GTTTTATGAAACAACCAACAAAATAGATAAACCATTGGTTAATATGATT- 470512 i v vi i v i v i i ivv ii- L1M4_orf2#LIN 1095 GTTCTTTGAAAAGATCAACAAAATTGACAAACCTTTAGCTAGACTGACCA 1144 chr5qtel1M 470513 ------TTTTTTTTAAAGAGAGAAAA-TCAAATTGCAAGCATTGGAAATG 470555 -------------- i - i v iv ii i L1M4_orf2#LIN 1145 AGAAAA--------AAAGAGAGAAGACTCAAATTACTAAAATCAGGAATG 1186 chr5qtel1M 470556 TAAAAAGTGAACACATTACT 470575 - i v i-- L1M4_orf2#LIN 1187 -AAAGAGGGG--ACATTACT 1203 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 41.14 CpG sites = 77, Kimura (unadjusted) = 42.05 Transitions / transversions = 1.45 (77/53) Gap_init rate = 0.05 (23 / 428), avg. gap size = 2.39 (55 / 23) 1513 30.16 6.61 2.96 chr5qtel1M 470726 472358 (527642) L1M5_orf2#LINE/L1 1219 2909 (385) m_b256s551i6 10154 chr5qtel1M 470726 ATTAAAGTAATTATTAGGAGTTATTTTGTCCACCTGTATGATAATAAATT 470775 ivi v v iiiv v vv v v vi L1M5_orf2#LIN 1219 ATTAAAAGGATAATAAGAGAATATTATGAACAACTTTATGCCAATAAATT 1268 chr5qtel1M 470776 TCACAATCTAAGTCAAGTAGAA----TACTTGCAAAA-ACAAACTGCCTA 470820 v ? ii ii v i i v---- v v - ?i i v L1M5_orf2#LIN 1269 TGANAACTTAGATGAAATGGACAAATTCCTTGAAAAACACAANTTACCAA 1318 chr5qtel1M 470821 AATTAATAAGAAAGGAAATAGGATATTTAGATAAACCTAT-TTTAGAAAA 470869 i i i?vi i i i v i ii iv - i vv L1M5_orf2#LIN 1319 AACTGACNCAAGAAGAAATAGAAAATCTGAATAGCCCTATATCTATTAAA 1368 chr5qtel1M 470870 AGAAGTTGAATAGACCATCAGTAAGTTTCTAATA---------TCAGGAC 470910 - i vviiv i iv vi iv i ---------i v L1M5_orf2#LIN 1369 -GAAATTGAATTTGTAATTAAAAACCTTCCCACAAAGAAAACTCCAGGCC 1417 chr5qtel1M 470911 CAGATGAATTTGCAAGCAAAGTCTACCAAACATTTAAAAATCAATTAATT 470960 iv ii vi ii v ii vv v v L1M5_orf2#LIN 1418 CAGATGGCTTCACTGGTGAATTCTACCAAACATTTAAGGAAGAAATAATA 1467 chr5qtel1M 470961 CCCATTATAAATTTAAAAAAAATTTTTGTAATAATAATAGGCAAAGAAAG 471010 ------- i v v v i i vi i- - iv ii L1M5_orf2#LIN 1468 CC-------AATCTTACACAAACTCTTCCAG-AA-AATAGAAAAAGAGGG 1508 chr5qtel1M 471011 AATCCGAACAAACTTCTTTTATGAAACAA--ATAA-------ACTAAGAA 471051 iv vvv v iv ii v -- ? ------- i i v L1M5_orf2#LIN 1509 AACACTTCCCAACTCATTTTATGAGGCCAGCATNACCCTGATACCAAAAC 1558 chr5qtel1M 471052 -GAACAAAAACA------GAAAA-ACCATTACACTCCAAT-TTCATTATG 471092 -?i i ------ - vv vv - i v i L1M5_orf2#LIN 1559 CNGACAAAGACATTACAAGAAAAGAAAATTACAGACCAATATCCCTCATG 1608 chr5qtel1M 471093 AATGTTGGTGCAAAAATCTTAAACAAAGTACTAGTAAGGAGATTATGACA 471142 ii v i i ? i i i ivv v viii L1M5_orf2#LIN 1609 AACATAGATGCAAAAATCCTNAACAAAATATTAGCAAATCGAATCCAGCA 1658 chr5qtel1M 471143 ATATATCACAAAGATTATGCATTGTGACCAAGTAGGACTTATGTAAGGAA 471192 v v i v i ii i ii viv L1M5_orf2#LIN 1659 ATATATAAAAAGGATAATACATCATGACCAAGTGGGGTTTATCCCAGGAA 1708 chr5qtel1M 471193 TGCAGGGATAGTTTACCATAAGGAAAACTATTAACTTCATTGATTATGAT 471242 i v i v vv i v v i iv v v ii iv L1M5_orf2#LIN 1709 TGCAAGGTTGGTTTAACATTCGAAAATCAATCAATGTAATTCACCATATT 1758 chr5qtel1M 471243 AGTAACAAAAGTAACAAAAATCATATGAATATCTCAATAGATGCAGAAAA 471292 ii iv v ivi v vi L1M5_orf2#LIN 1759 AACAGAATAAAGGAGAAAAATCATATGATCATCTCAATAGATGCAGAAAA 1808 chr5qtel1M 471293 AGCTTTTAACAAAACACAGCACTGATTCCTATGAAAAATTCTTCAAAGCA 471342 v i iv i iv v ivv i i--- L1M5_orf2#LIN 1809 AGCATTTGACAAAATTCAACACCCATTCATGATAAAAACTCTC---AGCA 1855 chr5qtel1M 471343 ---TAGGTATA-AATGTATTTTCCTTAAATTGATGAGAAGCATATATCTC 471388 --- v - v v vi i vi i iii v ivvv L1M5_orf2#LIN 1856 AACTAGGAATAGAAGGGAACTTCCTCAACCTGATAAAGGGCATCTACGAA 1905 chr5qtel1M 471389 AAGC-TATGAGCAAACAT-ATGAGTATAATAA-GCAAGA---AAAGCCTT 471432 i - i- ? - - v - ii- v ? --- ? i L1M5_orf2#LIN 1906 AAACCTAC-AGCNAACATCAT-ACT-TAATGGTGAAANACTGAANGCTTT 1952 chr5qtel1M 471433 TCCAGTAAGATCAGGAA-----------TGCCC-TGATCACCAATATCAT 471470 i vv i ----------- i -iv? v vii L1M5_orf2#LIN 1953 CCCCCTAAGATCGGGAACAAGACAAGGATGTCCGCTNTCACCACTTCTAT 2002 chr5qtel1M 471471 TCA-----TTACTAGAAATTCTAAT-AATAGAAAAAAAAAAAAAAAACAA 471514 -----v i ii i ii- i iv v iiv i v L1M5_orf2#LIN 2003 TCAACATTGTACTGGAGGTCCTAGCCAGTGCAATAAGGCAAGAAAAAGAA 2052 chr5qtel1M 471515 AGCAAAAGAAATCAAAGGAATTAGAATGTTCAGGGGGTAATAAAACTATC 471564 -i iv - -- i ----- ii v i L1M5_orf2#LIN 2053 A-TAAAAGGCAT-AAAG--ATTGGAA-----AGGAAGAAATAAAACTGTC 2093 chr5qtel1M 471565 TGCTTTTGCAGATGACATAATGATATATTTGGAAAATCCTTGAAATTCAA 471614 ?viv i i vi ? iv i ?vi i v v L1M5_orf2#LIN 2094 NTTATTCGCAGATGACATGATTGTNTACGTAGAAAATCCNAAAGAATCTA 2143 chr5qtel1M 471615 CTAAAAAGTTAATTAAAAC-AATAATT----TTAGCAAAGTAGCAACATA 471659 v ? ii -i i - v ---- i v ?iv L1M5_orf2#LIN 2144 CAAANAAACTA-CTAGAACTAATAAGTGAATTTAGCAAGGTCGCNGGATA 2192 chr5qtel1M 471660 TAAAA-CAAAATCCACTTAAATCATCAGCATTTCTATATATCACCAACAA 471708 i ii- v v v-- viv i ii v L1M5_orf2#LIN 2193 CAAGGTCAATATACAA--AAATCAATTGTATTTCTATATACTAGCAACAA 2240 chr5qtel1M 471709 ATCCTTGCAAGAAGAGATAGTAAGGA-------ATTTATGATAACTGTGG 471751 ivv v i v i vv? ii ------- ii i vviii L1M5_orf2#LIN 2241 ACAATTGGAAAATGAAATTTNAAAAACAATACCATTTACAATAGCATCAA 2290 chr5qtel1M 471752 ACAATACAAAATGCCTGGGAGTCTACCTATGGAAAGACAAACCCAGGAAC 471801 v i i? i i i i vv i vvi ? iivi -- i v L1M5_orf2#LIN 2291 AAAACATNAAATACTTAGGAATAAATCTAACAAAANATGTGC--AAGACC 2338 chr5qtel1M 471802 TATA---TGAACATAATTATAAAATAATAATGAAAAAAACTAAAGTGAGA 471848 ? --- --- i i i v iv i i i -i L1M5_orf2#LIN 2339 TNTACACTGAA---AACTACAAAACATTGCTGAGAGAAATTAAAG-AAGA 2384 chr5qtel1M 471849 TTTAAGTTATTGGAGAAATATTAACTTCTCCATAGATGGGCAGATAAAAT 471898 ii i v v i - v v v i i v v ivv L1M5_orf2#LIN 2385 CCTAAATAAATGGAGAGATAT-ACCATGTTCATGGATTGGAAGACTCAAT 2433 chr5qtel1M 471899 A-----AAAATGATAATACTACCTCAACTGATCTATTTATTCAGTGCCAT 471943 ----- i vi v v iv i vv i v L1M5_orf2#LIN 2434 ATTGTNAAGATGTCAATTCTCCCCAAATTGATCTATAGATTCAATGCAAT 2483 chr5qtel1M 471944 CCCAATTAAACTACCAAAAA--TATTTTGTTGAGCTAGAAAAAATAAT-- 471989 i v v iv i-- v v iv v v iv i -- L1M5_orf2#LIN 2484 CCCAATCAAAATCCCAGCAGGTTTTTTTGTAGAAATTGACAAGCTGATTC 2533 chr5qtel1M 471990 -AAAATTCATCTGGAAGAACAAAAGGCCAAAAATAGTAAAGGAATTCATG 472038 - i v ivi i i ? i iv iiv v v L1M5_orf2#LIN 2534 TAAAATTTATATGGAAATGCAAAGGACCNAGAATAGCCAAAACAATCTTG 2583 chr5qtel1M 472039 AAAAA-------AAAGGTAGAAGGTTTATCAGTAACAG--GTCAA-ACTA 472078 ------- v i i ii - v v ? --? - - L1M5_orf2#LIN 2584 AAAAAGAAGAACAAAGTTGGAGGACTTA-CACTACCNGATNTCAAGACT- 2631 chr5qtel1M 472079 TATTTTAAAGCAATAATTATCAAAACTATTTGGTATTGGT-TAAGAAATA 472127 v v i i v i vi v i- -i L1M5_orf2#LIN 2632 TATTATAAAGCTACAGTAATCAAGACAGTGTGGTATTGGCGTAAG-GATA 2680 chr5qtel1M 472128 GAAAAGTATATCAGTGGGACAGAGTAGA-----CATATAAT--ATTTA-A 472169 v i v i i i ----- v - -- iii - L1M5_orf2#LIN 2681 GACAAATAGATCAATGGAACAGAATAGAGAGTCCAGA-AATAGACCCACA 2729 chr5qtel1M 472170 CAGTAAAGAATTCACTTGATGTTTAATAAACACAAAAACCTAAGCTA-TG 472218 - v vii-? ? v i i viiivv ?vi vii - L1M5_orf2#LIN 2730 CA-TATATGG-NCANTTGATTTTTGACAAAGGTGCCAANGCAATTCAGTG 2777 chr5qtel1M 472219 GGGATAAAAATTCACTATTTGGTAAATAAATGCAGTTCTGGGAAAACTGG 472268 - ii -- v v -- v i -- v i v i L1M5_orf2#LIN 2778 GGGA-AAGGAT--AGTCTTT--TCAACAAATG--GTGCTGGAACAATTGG 2820 chr5qtel1M 472269 AAAGCAGTCTGGCAGAAATTAGATATTGATTAATTTTCTTACATTATTTA 472318 v v vi v v i v ii ?v i ii-vi vi i ii vi L1M5_orf2#LIN 2821 ATATCCATATGGAAAAAAATGAANCTCGACC-CCTACCTCACACCATACA 2869 chr5qtel1M 472319 CCAAGATAAGATGAAAATGGGT-ATATGACTTAGATATAAA 472358 v i v iv v? i i - - i i i L1M5_orf2#LIN 2870 CAAAAATTAATTCNAGATGGATCATA-GACCTAAATGTAAA 2909 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.84 CpG sites = 268, Kimura (unadjusted) = 40.51 Transitions / transversions = 1.28 (268/210) Gap_init rate = 0.05 (88 / 1632), avg. gap size = 1.80 (158 / 88) 421 28.95 12.52 3.67 chr5qtel1M 472759 473285 (526715) L1ME4c_3end#LINE/L1 4 575 (255) m_b256s551i7 10154 chr5qtel1M 472759 ATATCTCAAATATACAGAGAACTGAGCCAGATTTATATATATCGCTGAAT 472808 ?v ? i i i v vi i v viv ------ v L1ME4c_3end#L 4 ATATCTNTANTATATAAAGAGCTCATTCAAATTGATAAGAA------AAA 47 chr5qtel1M 472809 TATT----CCTCAATTGATAAATGGTCAAAGGG---GAAAA---AAATCA 472848 ? i---- i v v i--- v --- v L1ME4c_3end#L 48 NATCAAGACCCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCA 97 chr5qtel1M 472849 ---AAGC-----TACATATAG---------ACATAGGGAAATGT--ACTC 472879 --- v----- v? --------- i ii -- vi L1ME4c_3end#L 98 CANAAGAGGAAATACAANTAGTAAACAAACACATGGAAAAATGTTCAACC 147 chr5qtel1M 472880 TAGATTAATATCGATTAAAGAAAGGCAGATTAAAACAACTTTGAGATACC 472929 v -i i --- i v i i vv L1ME4c_3end#L 148 TCG-CTAGTA---ATCAAAGAAATGCAAATTAAAGCAACAATGAGATACC 193 chr5qtel1M 472930 ATTTCACACCCATCAGATTGGCTAAAACAATTAAAAGG--GAAAATG-AA 472976 i i i i i i v i-- ii-- v i-vv L1ME4c_3end#L 194 ATTTTACGCCTATTAAATTAGCAAAAAT--TTAAAAAATTGATAATACCC 241 chr5qtel1M 472977 AATGTTGGAGGGGATGTGG-AAAAGTGGGATACTAATTCCAT-------- 473017 i v i ? i -i v v i? v - v -------- L1ME4c_3end#L 242 AATGCTGGCGAGGNTGCGGTGAAACTGGTACNCTCA-TACATTGCTGGTG 290 chr5qtel1M 473018 -CAG-GAAAGTT----------CTCTGGAA--TAATTT-----TAC--CC 473046 - ?- v i ----------i i --i ----- --vi L1ME4c_3end#L 291 GCANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTAT 340 chr5qtel1M 473047 CCAAAGTTATAAAAC--TTCCTGAGCTCTTTGACCCAGCACTATTACTAC 473094 v i ii v-- v --i i i v vii v L1ME4c_3end#L 341 CAAGAGCCATAAAAATGTTCAT--ACCCTTTGACCCAGTAATTCCACTTC 388 chr5qtel1M 473095 CAGCTCTATTTCCAAAGATGATCAGGGGAAAAGGAGAAGAATCTACATGT 473144 ii vvv v v v ivi v vvvi iiii i v i i L1ME4c_3end#L 389 TGGGAATTTATCCTAAGGAAATAATTCAAAAGAAGGAAAAAGCTATATGC 438 chr5qtel1M 473145 TCTAAAAGGTTTCTAGCAGCTCTCTTTGTGGTGGCAAAGAACTAGAAATT 473194 v v i v iv v vi v i ii i i i i i -i L1ME4c_3end#L 439 ACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAA-C 487 chr5qtel1M 473195 GAGGTGACTGATGCCCATCAACTGGGGAATGGCTGAGGAAGTTGTGGTAT 473244 i vv i --- i v iv i i v i i i L1ME4c_3end#L 488 AACCTAA---ATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTAC 534 chr5qtel1M 473245 AT-AATTGTGATGGAACACTACTGT-GCTTTAAAAAATGATGA 473285 -? i -i i i - i- iv v i L1ME4c_3end#L 535 ATCNACT-CGATGGAATATTA-TGCAGCCATTAAAAATGATAA 575 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 37.23 CpG sites = 86, Kimura (unadjusted) = 38.57 Transitions / transversions = 1.41 (86/61) Gap_init rate = 0.08 (41 / 526), avg. gap size = 2.12 (87 / 41) 496 24.56 2.84 2.84 chr5qtel1M 472830 473005 (526995) L1ME3Cz_3end#LINE/L1 91 266 (731) m_b256s551i8 10154 chr5qtel1M 472830 TCAAAGGGGAAAAAAATCAAA--GCTACATATAGACATAGGGAAATGTAC 472877 v ii ii vi i -- i --- i v i vi i L1ME3Cz_3end# 91 TCACAGAAGAGGAAACCCGAATGGCCA---ATAAACATATGAAAAGATGC 137 chr5qtel1M 472878 TCTAGATTAATATCGATTAAAGAAAGGCAGATTAAAACAACTTTGAGATA 472927 v vv i v vii i ii v i ? vv L1ME3Cz_3end# 138 TCAACCTCACTAGTAATCAGGGAAATGCAAATTAAAACNACAATGAGATA 187 chr5qtel1M 472928 CCATTTCACACCCATCAGATTGGCTAAAACAATTAAAAG--GGAAAATG- 472974 v i-- --v v i- L1ME3Cz_3end# 188 CCATTTCACACCCATCAGATTGGCAAAAAT--TTAAAAGTCTGACAATAC 235 chr5qtel1M 472975 AAAATGTTGGAGGGGATGTGGAAAAGTGGGA 473005 v i v i i ii L1ME3Cz_3end# 236 CAAGTGTTGGCGAGGATGTGGAGAAACGGGA 266 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 28.91 CpG sites = 25, Kimura (unadjusted) = 30.63 Transitions / transversions = 1.47 (25/17) Gap_init rate = 0.05 (8 / 175), avg. gap size = 1.25 (10 / 8) 572 28.90 9.23 4.19 chr5qtel1M 472858 473312 (526688) L1ME3_3end#LINE/L1 122 598 (311) m_b256s551i9 10154 chr5qtel1M 472858 ATAGACATAGGGAAATGTACTCTAGATTAATATCGATTAAAGAAAGGCAG 472907 ii v i v i v v i v viv i ii v i L1ME3_3end#LI 122 ATAAGCATATGAAAAGGTGCTCAACATCATTAGTCATCAGGGAAATGCAA 171 chr5qtel1M 472908 ATTAAAACAACTTTGAGATACCATTTCACACCCATCAGATTGGCTAAAAC 472957 v vv i v i v --- L1ME3_3end#LI 172 ATTAAAACCACAATGAGATACCACTACACACCCACCAGAATGGCTAA--- 218 chr5qtel1M 472958 AATTAAAAGG---GAAAATG-AAAATGTTGGAGGGGATGTGGAA-AAGTG 473002 i --- v i-v i v i i- v L1ME3_3end#LI 219 AATTAAAAAGACTGACAATACCAAGTGTTGGCGAGGATGTGGAGCAACTG 268 chr5qtel1M 473003 GGATACTAATTCCAT------CAGGA----AAGTT----------CTCTG 473032 i iv v - v ------ii ---- i ---------- i L1ME3_3end#LI 269 GAACTCTCA-TACATTGCTGGTGGGAGTGTAAATTGGTACAACCACTTTG 317 chr5qtel1M 473033 GAATA--ATTT-----TACCC-CCAAAGTTATAAAACTTCCTGAGCTCTT 473074 v --i ----- i i- i i v v vviv --i i v L1ME3_3end#LI 318 GAAAACTGTTTGGCAGTATCTACTAAAGCTAAACATACGCCT--ACCCTA 365 chr5qtel1M 473075 TGACCCAGCACTATTACTACCAGCTCTATTTCCAA-AGATGATCAGGGGA 473123 v vii v i v v vi - -i v v v L1ME3_3end#LI 366 TGACCCAGCAATTCCACTCCTAGGTATATACCCAAGAGA-AATGAGTGCA 414 chr5qtel1M 473124 AA-----AGGAGAAGAATCTACATGTTCTAAAAGGTTTCTAGCAGCTCTC 473168 v ----- vv i ----- v v i v iv i v L1ME3_3end#LI 415 TATGTCCACCAAAAGA-----CATGTACAAGAATGTTCATAGCAGCTTTA 459 chr5qtel1M 473169 TTTGTGGTGGCAAAGAACTAGAAATTGAGGTGACT--GATGCCCATCAAC 473216 ii ii i v? i i ------ii i--i i L1ME3_3end#LI 460 TTCATAATAGCCNAAAACTGGAAA------CAACCCAAATGTCCATCAAC 503 chr5qtel1M 473217 TGGGGAATGGCTGAGGAAGTTGTGGTATATAATTGTGATGGAACACTACT 473266 v ?i v i iv i vvv iii i v L1ME3_3end#LI 504 AGNAGAATGGATAAATAAATTGTGGTATATTCATACAATGGAATACTACA 553 chr5qtel1M 473267 GTGCTTTAAAAAATGATGAGCTCCCATGAT-CTTAGAAAAACATGGA 473312 vv vv vi i i v -- ? - viiv v L1ME3_3end#LI 554 CAGCAATAAAAAAGAACGAACTAC--TGNTACACGCAACAACATGGA 598 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 36.33 CpG sites = 65, Kimura (unadjusted) = 37.48 Transitions / transversions = 1.07 (65/61) Gap_init rate = 0.07 (33 / 454), avg. gap size = 1.88 (62 / 33) 240 22.64 1.89 0.00 chr5qtel1M 474395 474447 (525553) C L2d_3end#LINE/L2 (7) 509 456 m_b256s601i22 10155 chr5qtel1M 474395 ATCAGAAAACAAGCATTTGTTAAGCACCTACGGTGTGC-AGGCCCTGTGC 474443 ivv i i i i vi -vi v C L2d_3end#LINE 509 ATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTGTGC 460 chr5qtel1M 474444 TAGG 474447 C L2d_3end#LINE 459 TAGG 456 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 24.84 CpG sites = 7, Kimura (unadjusted) = 27.42 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.02 (1 / 52), avg. gap size = 1.00 (1 / 1) 274 15.22 2.17 0.00 chr5qtel1M 474402 474447 (525553) C L2d2_3end#LINE/L2 (12) 543 497 m_b256s601i23 10155 chr5qtel1M 474402 AACAAGCATTTGTTAAGCACCTACGGTGTGC-AGGCCCTGTGCTAGG 474447 ii i i i v - v C L2d2_3end#LIN 543 AACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGG 497 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 14.81 CpG sites = 5, Kimura (unadjusted) = 17.39 Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1) 230 32.86 18.30 0.56 chr5qtel1M 476811 476963 (523037) L3#LINE/CR1 2441 2620 (1479) m_b256s601i24 10156 chr5qtel1M 476811 TTTTCTGATGAGATGAATGATTTTTGAACTGGAAAGGGTC---------- 476850 i ivii iv i iii v---------- L3#LINE/CR1 2441 TTCTCTATCAAGGAGAATGATCTTCAGACTGGAAAGGGTAGAACAAACAT 2490 chr5qtel1M 476851 -------------TTGA-TCCCCAGATCAGTCAAGGGCTAGTAA--GAGT 476884 ------------- -v v vi v i i v -- i L3#LINE/CR1 2491 CGTTAAGAGGGAATTGAAGCCCAAGATAGGTGAGGAGATAGTAAGAGAGC 2540 chr5qtel1M 476885 CCTTGGCTGCCGGGGGCAAGATCTA-TCTGTATGACCCAAGTGACCTTCA 476933 v i i i ivviiiii v v - vi - i iii vi v L3#LINE/CR1 2541 ACCTAGCCGCTTTAAATGAGTTCAAGTCTCCA-GGCCCAGACGAATTACA 2589 chr5qtel1M 476934 TCCTAGGGT-CTGAAAGAGCAGGCAGGGGTG 476963 i - i vv iv L3#LINE/CR1 2590 TCCCAGGGTACTGAAAGAACTTGCAGATGTG 2620 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 42.78 CpG sites = 31, Kimura (unadjusted) = 45.25 Transitions / transversions = 1.63 (31/19) Gap_init rate = 0.05 (7 / 152), avg. gap size = 4.14 (29 / 7) 469 35.27 1.56 1.04 chr5qtel1M 476984 477175 (522825) L3#LINE/CR1 2719 2911 (1188) m_b256s601i25 10156 chr5qtel1M 476984 GAGGAAGAAGAGGGAGCCATTCCAGCCTA--GACTAGGGAGGCTGGCTTC 477031 i i i v vi -- v? iv -- ii vi vi i v L3#LINE/CR1 2719 GGGAAAAAAGATGGATTC--TGNAAACTACAGACCGGTAAGCTTGACGTC 2766 chr5qtel1M 477032 CATCCCTGA-AAACTCCTAAAATGGATTATTGACGGGATGGTCGCTGCAC 477080 v i i- v i i i i vvi ivv vi L3#LINE/CR1 2767 GATCCCCGGCAAAATTCTAGAACGGATTATTAAACAGATGGTTTGTGAGC 2816 chr5qtel1M 477081 ATCCAGAAAGGGAAGCAGTCATTACTGTGGGCCATGATGGCTTCAGCAAG 477130 iii i i v i iv i vv v vi L3#LINE/CR1 2817 ACTTAGAAAAGGAAGCGGTGATCACTAGGAGCCAGCATGGGTTCACTAAG 2866 chr5qtel1M 477131 AAGGGGATGTGTTAGTCCAAGCTTATTTCCATTTTTATTGGGACT 477175 vii vii ii iv i v i v iv i ii L3#LINE/CR1 2867 AACAAGTCATGCCAAACTAACCTCATTTCCTTTTTTGATAGGGTT 2911 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 46.04 CpG sites = 41, Kimura (unadjusted) = 50.41 Transitions / transversions = 1.58 (41/26) Gap_init rate = 0.02 (4 / 191), avg. gap size = 1.25 (5 / 4) 331 23.88 5.93 7.76 chr5qtel1M 477258 477375 (522625) C MIR3#SINE/MIR (63) 145 30 m_b256s601i26 10157 chr5qtel1M 477258 CTCATTTTACAGACGAGAGAACTGAGG--CAGACAGGTGAAGTGG----- 477300 i ii -- v i----- C MIR3#SINE/MIR 145 CTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGC 96 chr5qtel1M 477301 CCAGGGTCACACAGATGGGCAGCGTTTGAGGCTGGATCTGACCTCGGGAA 477350 i v?i vi i viv v v iiv v i i --- C MIR3#SINE/MIR 95 CCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAG--- 49 chr5qtel1M 477351 GAGGAGTCTCCCTGGCTCTCAACCC 477375 ----- - i i ii C MIR3#SINE/MIR 48 -----GTCT-CCTGACTCCCAGTCC 30 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.95 CpG sites = 17, Kimura (unadjusted) = 29.95 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.09 (11 / 117), avg. gap size = 1.45 (16 / 11) 457 30.95 14.85 2.96 chr5qtel1M 477425 477567 (522433) L3#LINE/CR1 2970 3134 (965) m_b256s601i27 10156 chr5qtel1M 477425 CGTTTGACAGAGTATTTCATGCTGATCTTATGATTAAGA-GGA-----CT 477468 i i v i v ivi i ivi - -----v L3#LINE/CR1 2970 CATTTGACAAAGTCTCTCATGATATCCTTGTGGACAAGATGGAGAAATAT 3019 chr5qtel1M 477469 GAGTTAGCTGGCCACACAATTAA-T--ATTCAGAACTAGTTGAATGAGTG 477515 i i i v iivii i i- -- iv i i i v i L3#LINE/CR1 3020 GGGCTGGATGATAGTACAGTTAGGTGGATTCGTAGCTGGTTGAACGACTA 3069 chr5qtel1M 477516 GACCCAAAGGGTGGCTGGCCATAATG---TGGTATCTGTTTGGAAGGAG- 477561 v i -i ii-- ---i i i viii i - L3#LINE/CR1 3070 TACCCAAAAGGTG-TTGAT--TAATGGATCGATGTCAACCTGGAGGGAGG 3116 chr5qtel1M 477562 -------T----TGC-AT 477567 ------- ---- - i L3#LINE/CR1 3117 TCTCTAGTGGCGTGCCAC 3134 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 40.51 CpG sites = 62, Kimura (unadjusted) = 43.07 Transitions / transversions = 3.09 (34/11) Gap_init rate = 0.08 (12 / 142), avg. gap size = 2.33 (28 / 12) 53 0.00 0.00 0.00 chr5qtel1M 477568 477612 (522388) (AC)n#Simple_repeat 1 45 (0) c_b256s251i0 10158 chr5qtel1M 477568 ACACACACACACACACACACACACACACACACACACACACACACA 477612 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACA 45 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 457 30.95 14.85 2.96 chr5qtel1M 477613 477771 (522229) L3#LINE/CR1 3135 3306 (793) m_b256s601i27 10156 chr5qtel1M 477613 GG--TCTGGGTGGGGTCCTGTGCTTTTGGGCAGTTTTATC------TTGG 477654 -- vvivv i v v vii v ------ L3#LINE/CR1 3135 GGGCTCTGTCCTTGGCCCTGTCCTGTTCAACATTTTTATCAATGACTTGG 3184 chr5qtel1M 477655 ATG------T------CATGTTCCTCCCATTTGCAGATGACACACACCTG 477692 ------ ------ i iv vv v v L3#LINE/CR1 3185 ATGAAGACATAGAAGGCATGCTTATCAAATTTGCAGATGACACAAAGCTG 3234 chr5qtel1M 477693 GGGAGGGGGGATGCTTAGGACACTGGGTAATGGGGAAAGGGTTCAGAAAA 477742 ---- i ivi iv i? i i ii iivv i i i ?i L3#LINE/CR1 3235 ----GGAGGGATAGCTAATACGNTGGATGACAGAATCAAGATTCAAAANG 3280 chr5qtel1M 477743 ACCCCGATGGACTAGAGCAGTGATCGGCC 477771 i i ii i i i --- v L3#LINE/CR1 3281 ATCTCGACAGGCTGGAAC---GATGGGCC 3306 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 40.51 CpG sites = 62, Kimura (unadjusted) = 43.07 Transitions / transversions = 1.56 (28/18) Gap_init rate = 0.07 (11 / 158), avg. gap size = 2.45 (27 / 11) 241 32.01 0.00 1.33 chr5qtel1M 478567 478642 (521358) C CR1-L3A_Croc#LINE/CR1 (930) 3358 3284 m_b256s551i10 10159 chr5qtel1M 478567 TGTGTCTTTGTCTGAGTTGTTGATAAAAGTGGTAAAGAGCATAAAGCCAA 478616 i i iv iii ii i v v i ii C CR1-L3A_Croc# 3358 TATGTTTTCTTCCAGGTCATTGATAAAAATGTTAAATAGCGTAGGGCCAA 3309 chr5qtel1M 478617 GCCCAGACCCCCTGGGGTGCTCCATT 478642 vv v -i v vi i i C CR1-L3A_Croc# 3308 GAACCGA-TCCCTGCGGGACCCCACT 3284 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 41.60 CpG sites = 16, Kimura (unadjusted) = 44.11 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.01 (1 / 75), avg. gap size = 1.00 (1 / 1) 50 0.00 0.00 0.00 chr5qtel1M 479812 479854 (520146) (AC)n#Simple_repeat 1 43 (0) c_b256s251i1 10160 chr5qtel1M 479812 ACACACACACACACACACACACACACACACACACACACACACA 479854 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACA 43 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 18 4.77 0.00 0.00 chr5qtel1M 480172 480193 (519807) (TC)n#Simple_repeat 1 22 (0) m_b256s252i11 10161 chr5qtel1M 480172 TCTCTCTCTCCCTCTCTCTCTC 480193 i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTC 22 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 181 23.29 28.77 0.00 chr5qtel1M 480519 480591 (519409) L2c_3end#LINE/L2 374 467 (11) m_b256s601i28 10162 chr5qtel1M 480519 AGACTCCAAGTCTCTTGAGAGCAGAGGCTGCCTC--------CTTTGT-- 480558 vii iii i i i i iv -------- -- L2c_3end#LINE 374 AGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTAT 423 chr5qtel1M 480559 -------GCTGGGCACA---TAGGCCCT-AATAAATGCTTCTTG 480591 ------- iv --- v - i v L2c_3end#LINE 424 CCCCAGCGCCTGGCACATAGTAGGCGCTCAATAAATGTTTGTTG 467 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 26.99 CpG sites = 12, Kimura (unadjusted) = 29.00 Transitions / transversions = 2.40 (12/5) Gap_init rate = 0.07 (5 / 72), avg. gap size = 4.20 (21 / 5) 202 13.95 9.30 0.00 chr5qtel1M 480557 480599 (519401) L2d_3end#LINE/L2 465 511 (5) m_b256s601i29 10162 chr5qtel1M 480557 GTGCTGGGCACATAG---GCCCT-AATAAATGCTTCTTGGTTGCTTG 480599 i --- v - i v i v L2d_3end#LINE 465 GTGCTGAGCACATAGTAGGCGCTCAATAAATACTTGTTGATTGATTG 511 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 15.50 CpG sites = 3, Kimura (unadjusted) = 15.50 Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.05 (2 / 42), avg. gap size = 2.00 (4 / 2) 413 26.33 15.67 3.72 chr5qtel1M 480630 480846 (519154) C L2b_3end#LINE/L2 (3) 463 222 m_b256s601i31 10163 chr5qtel1M 480630 CAGTCGGTTAACAAATATT----AGGCACCTACTGCATGCCAGGCACTGT 480675 v iv i ----ii i ii ? C L2b_3end#LINE 463 CATTCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGT 414 chr5qtel1M 480676 GCTAAGCCGTGGAGACACAG----AAAC---ACAGA-AAAGTTCCTGCTT 480717 i vv i i ----i --- -?vi i ii C L2b_3end#LINE 413 GCTAGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCC 364 chr5qtel1M 480718 TCAAGGAACTTCCTGTGAGTTGGGGCAACCAGCCAATCCTCCTGCA--CA 480765 v i iv v vviv v iv v ------- i -- C L2b_3end#LINE 363 TCACGGAGCTCACAGTCTAGTGGGGGAGACAGACA-------TGTAANCA 321 chr5qtel1M 480766 AACAAGAAAAATCC---------GGGTA-AACTAAGCAG---CAGAGGGA 480802 i v? v i --------- -i ii vi --- ii C L2b_3end#LINE 320 GACAATNATAACCCAGAGTGGCAGGGTAGGACTGGGGGGGCCCAGAGGAG 271 chr5qtel1M 480803 GGC-TCTG----GGCTTCGGGGAGAGCAAGGACAG--TCCTGGAGAAGGT 480845 -i ---- i -- i iv i vi -- i i C L2b_3end#LINE 270 GGCGCCTGACCCGGCCT--GGGGGGTCAGGGAGGGCTTCCCGGAGGAGGT 223 chr5qtel1M 480846 G 480846 C L2b_3end#LINE 222 G 222 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 32.15 CpG sites = 36, Kimura (unadjusted) = 34.47 Transitions / transversions = 1.89 (36/19) Gap_init rate = 0.09 (20 / 216), avg. gap size = 2.15 (43 / 20) 435 25.60 11.20 0.00 chr5qtel1M 480630 480754 (519246) C L2a_3end#LINE/L2 (3) 514 376 m_b256s601i30 10163 chr5qtel1M 480630 CAGTCGGTTAACAAATATT----AGGCACCTACTGCATGCCAGGCACTGT 480675 v iv i ----ii i iii C L2a_3end#LINE 514 CATTCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGT 465 chr5qtel1M 480676 GCTAAGCCGTGGAGACACAG---------AAACACAGAAAAGTTCCTGCT 480716 v i vv i i --------- v v i i C L2a_3end#LINE 464 TCTAGGCGCTGGGGATACAGCAGTGAACAAAACAGACAAAAGTCCCTGCC 415 chr5qtel1M 480717 TTCAAGGAACTT-CCTGTGAGTTGGGGCAACCAGCCAAT 480754 i v i - v viv v v iv v C L2a_3end#LINE 414 CTCATGGAGCTTACATTCTAGTGGGGGGAGACAGACAAT 376 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.57 CpG sites = 17, Kimura (unadjusted) = 31.74 Transitions / transversions = 1.13 (17/15) Gap_init rate = 0.02 (3 / 124), avg. gap size = 4.67 (14 / 3) 207 30.13 4.60 4.60 chr5qtel1M 481293 481379 (518621) C L2a_3end#LINE/L2 (1) 516 430 m_b256s601i32 10164 chr5qtel1M 481293 TTCAGTCATCCCACATCCCCACATTTCTCCAGTGTCTGCTGAGTGCCCAG 481342 v i v ----v i v iv i i i iv vi C L2a_3end#LINE 516 TTCATTCATTCAACA----AATATTTATTGAGCGCCTACTATGTGCCAGG 471 chr5qtel1M 481343 CACTGTGCCAGGTAGTGGAGCTAC--CA--AGACAAAAGAG 481379 v i iiv i v -- --ii v C L2a_3end#LINE 470 CACTGTTCTAGGCGCTGGGGATACAGCAGTGAACAAAACAG 430 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 35.29 CpG sites = 14, Kimura (unadjusted) = 39.43 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.07 (6 / 86), avg. gap size = 1.33 (8 / 6) 213 30.10 0.00 5.71 chr5qtel1M 481293 481366 (518634) C L2b_3end#LINE/L2 (1) 465 396 m_b256s601i33 10164 chr5qtel1M 481293 TTCAGTCATCCCACATCCCCACATTTCTCCAGTGTCTGCTGAGTGCCCAG 481342 v i v ----v i viiv i i i v vi C L2b_3end#LINE 465 TTCATTCATTCAACA----AATATTTACTGAGCGCCTACTGTGTGCCAGG 420 chr5qtel1M 481343 CACTGTGCCAGGTAGTGGAGCTAC 481366 ? i iiv i v C L2b_3end#LINE 419 CNCTGTGCTAGGCGCTGGGGATAC 396 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 35.07 CpG sites = 12, Kimura (unadjusted) = 40.09 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.05 (4 / 73), avg. gap size = 1.00 (4 / 4) 247 33.03 3.67 0.00 chr5qtel1M 484898 485006 (514994) C X26_DNA#DNA/TcMar-Tigger (4) 887 775 m_b257s502i0 10165 chr5qtel1M 484898 CATTTCTCACTTTTCTGTACA-TG-ATTTCCAGAAACTGT-CCACAAGG- 484943 v i i i vvi - -i i ii i i-i i i - C X26_DNA#DNA/T 887 CAGTCCCCGCTTTTCGCCACAATGCGTTCCTGGAAACCGCATCATAAAGC 838 chr5qtel1M 484944 AAATCGCATTTTCCCATTGAGACACTGTGGCAGGTTAGGGTCCGGTTCTT 484993 ii i v ii v vii iv vi ivv i C X26_DNA#DNA/T 837 GGATCGTATTTTCCCATAGGAACAATGTTATAATTGGGGGTTGCGTTCCT 788 chr5qtel1M 484994 GACCAAGAACTTG 485006 i i C X26_DNA#DNA/T 787 GACCAAGGACTCG 775 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 38.37 CpG sites = 26, Kimura (unadjusted) = 47.13 Transitions / transversions = 2.60 (26/10) Gap_init rate = 0.04 (4 / 108), avg. gap size = 1.00 (4 / 4) 241 34.38 9.68 2.41 chr5qtel1M 485117 485271 (514729) C MIR3#SINE/MIR (24) 184 19 m_b257s601i5 10166 chr5qtel1M 485117 GAGCTGGGGAGGATTTCAGAGG----CTCGTTTCATTTCCTCATTTT-TA 485161 iii ii i i---- v iiv iii -i C MIR3#SINE/MIR 184 GAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACA 135 chr5qtel1M 485162 TGTTGGCAAAC-------CA-AGAGTTG--GTTAGTCGCCCCGGGTCATC 485201 vi vi v ------- - v -- v v i vi iv C MIR3#SINE/MIR 134 GATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACA 85 chr5qtel1M 485202 AGACTGGCCAGTGGCAGGGCAGGGGTTGGCACTCCCATCGCCTACGGCTT 485251 vii ?i ii i v ii i v i vvi v --- vi C MIR3#SINE/MIR 84 CAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGTCTCCT---GACT 38 chr5qtel1M 485252 CTCAGTCCCGCGCCATCCCT 485271 i - i iv i C MIR3#SINE/MIR 37 CCCAGT-CCGTGCTCTCTCT 19 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 49.45 CpG sites = 34, Kimura (unadjusted) = 49.45 Transitions / transversions = 1.89 (34/18) Gap_init rate = 0.06 (9 / 154), avg. gap size = 2.11 (19 / 9) 303 27.03 11.38 0.74 chr5qtel1M 486471 486593 (513407) C Charlie4a#DNA/hAT-Charlie (3) 505 370 m_b257s502i1 10167 chr5qtel1M 486471 GAGTTCTTGATCACTTTTGTGTCATGGA-----TTGTCCGTCTAGCAAAT 486515 i i i vi i ----- v v i ii v C Charlie4a#DNA 505 GGGTTCTTAACCTTTTTTGTGCCATGGACCCCTTTGGCAGTCTGGTGAAG 456 chr5qtel1M 486516 TCCCCAGACTC--TCTCAGAATCCTGTTCTTAAACACTTACCCT------ 486557 i ivii i -- vv i ii v vvv ------ C Charlie4a#DNA 455 CCTATGGACCCCTTCTCAGAATAATGTTTTTAAATGCATAAAATAAAATA 406 chr5qtel1M 486558 -ATCGGATCACAAAGGAAAACCAACTGCATTGAGATA 486593 - v i - i ii i C Charlie4a#DNA 405 CATAGGATTACAAAGG-AAACCAATTATATTGAAATA 370 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 34.70 CpG sites = 21, Kimura (unadjusted) = 34.70 Transitions / transversions = 1.75 (21/12) Gap_init rate = 0.04 (5 / 122), avg. gap size = 3.00 (15 / 5) 188 29.03 13.92 8.43 chr5qtel1M 486994 487151 (512849) C MIR3#SINE/MIR (28) 180 15 m_b257s601i6 10168 chr5qtel1M 486994 TGGCAAAGATACTGGAGACCTTGGCCACTCCCTTCTCCGGCTCATGTTAT 487043 v ii ivi i i v -- i v vvi i --- v i C MIR3#SINE/MIR 180 TGGAAGGGACCTTAGAGATCAT--CTAGTCCAACCCCC---TCATTTTAC 136 chr5qtel1M 487044 CGATGGGCAAACAG-----------GGTGAGGTGACTTGTGCAGGTTTA- 487081 v i v v ----------- i iv i v i - C MIR3#SINE/MIR 135 AGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCAC 86 chr5qtel1M 487082 -----GGACTTGT----GAGATGAGATTTGAACCCGGGAAGAAGCGTCTC 487122 -----?iii v ---- vi i i v i -------- - C MIR3#SINE/MIR 85 ACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAG--------GTCT- 45 chr5qtel1M 487123 CCTGGCT-CCAGTCCCTGCACTCTGTGCCC 487151 i - v v v i C MIR3#SINE/MIR 44 CCTGACTCCCAGTCCGTGCTCTCTCTGCTC 15 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.05 CpG sites = 24, Kimura (unadjusted) = 38.20 Transitions / transversions = 1.33 (24/18) Gap_init rate = 0.12 (19 / 157), avg. gap size = 1.89 (36 / 19) 51 20.47 4.55 3.95 chr5qtel1M 487332 487507 (512493) (CCTCCT)n#Simple_repeat 1 177 (0) m_b257s252i0 10169 chr5qtel1M 487332 CCTCC-CC-CCACATTCT-CTCTTCCTCCTCCCTCCTACAAGCT-CTCCT 487377 - - v v i - i - - vvv - (CCTCCT)n#Sim 1 CCTCCTCCTCCTCCTCCTCCTCCTCCTCCT-CCTCCT-CCTCCTCCTCCT 48 chr5qtel1M 487378 CCTCCTCCTCCCCCTCTCACATACT-CTCCTCCTCCCCCTCC-CCTACCC 487425 i - v v v - i - - i (CCTCCT)n#Sim 49 CCTCCTCCTCCTCCTC-CTCCTCCTCCTCCTCCTCCTCCTCCTCCT-CCT 96 chr5qtel1M 487426 CACAGGTTCTCCCCCTCCCCCTCCCCTTCCCCCATGCT-CTCCTCCCCCT 487474 - vvv i i i i i i - v - i (CCTCCT)n#Sim 97 C-CTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC-TCCTCCTCCTCCTCCT 144 chr5qtel1M 487475 CCCCCTCCCCCATGCT-CTCCTCCCCCTCCCCCT 487507 i i - v - i i (CCTCCT)n#Sim 145 CCTCCTCCTCC-TCCTCCTCCTCCTCCTCCTCCT 177 Matrix = Unknown Transitions / transversions = 1.23 (16/13) Gap_init rate = 0.09 (15 / 175), avg. gap size = 1.00 (15 / 15) 13 8.48 4.00 0.00 chr5qtel1M 488429 488453 (511547) (CTCCC)n#Simple_repeat 1 26 (0) m_b257s252i1 10170 chr5qtel1M 488429 CTCCCCTCCCCTTCCC-CCCCGCCCC 488453 i - v (CTCCC)n#Simp 1 CTCCCCTCCCCTCCCCTCCCCTCCCC 26 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 13 10.80 3.12 3.12 chr5qtel1M 488619 488650 (511350) (CTCCC)n#Simple_repeat 1 32 (0) m_b257s252i2 10171 chr5qtel1M 488619 CTCCCCTCCCCTTCCC-CCCCGCCCCGTTCCCT 488650 i - v - i (CTCCC)n#Simp 1 CTCCCCTCCCCTCCCCTCCCCTCCCC-TCCCCT 32 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.06 (2 / 31), avg. gap size = 1.00 (2 / 2) 199 26.41 1.64 6.90 chr5qtel1M 488835 488895 (511105) C L3#LINE/CR1 (297) 3802 3745 m_b257s601i7 10172 chr5qtel1M 488835 TTCCGTATGACAACTTTTCAAAGATTTG-AGGCAAGTATCATGAAATCCT 488883 ii i ii v - i iv ----i C L3#LINE/CR1 3802 TTCCACATGACAGCCCTTCAAATATTTGAAGACAGCTATCATG----TCT 3757 chr5qtel1M 488884 TGTCCAGGTTTT 488895 iv i i i C L3#LINE/CR1 3756 CCTCTAAGTCTT 3745 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.87 CpG sites = 12, Kimura (unadjusted) = 34.87 Transitions / transversions = 4.00 (12/3) Gap_init rate = 0.08 (5 / 60), avg. gap size = 1.00 (5 / 5) 298 24.41 4.60 1.11 chr5qtel1M 489131 489217 (510783) C MIRc#SINE/MIR (87) 181 92 m_b257s601i8 10173 chr5qtel1M 489131 CCCTGCGAGGGAGG--GGGAGGGCG--GTCGTCCCCATTTCACAGATGAG 489176 i v -- vi ii--i ii i C MIRc#SINE/MIR 181 CCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAG 132 chr5qtel1M 489177 GAAACTGAGTCTTGGAACTCTTAATGCGAGGTCCCCAAGGT 489217 v ii ivvv - i vv v C MIRc#SINE/MIR 131 GAAACTGAGGCTCAGAGAGGTTAA-GTGACTTGCCCAAGGT 92 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.07 CpG sites = 12, Kimura (unadjusted) = 30.07 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.03 (3 / 86), avg. gap size = 1.67 (5 / 3) 261 23.01 0.00 4.05 chr5qtel1M 489155 489231 (510769) C MIR1_Amn#SINE/MIR (75) 155 82 m_b257s601i9 10173 chr5qtel1M 489155 TCGTCCCCATTTCACAGATGAGGAAACTGAGTCTTGGAACTCTTAATGCG 489204 ii i v ?ii ivvv ? - i C MIR1_Amn#SINE 155 TTATCCCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAA-GTG 107 chr5qtel1M 489205 AGGTCCCCAAGGTTGGGCCCAGCCCGC 489231 vv v i--i ? ?v C MIR1_Amn#SINE 106 ACTTGCCCAAGGTC--ACNCAGCNGGC 82 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.70 CpG sites = 9, Kimura (unadjusted) = 29.70 Transitions / transversions = 1.12 (9/8) Gap_init rate = 0.04 (3 / 76), avg. gap size = 1.00 (3 / 3) 39 14.24 0.00 0.00 chr5qtel1M 489307 489368 (510632) (G)n#Simple_repeat 1 62 (0) m_b257s252i3 10174 chr5qtel1M 489307 GGGGGGGGGGGGGGGGGGCGCGCGGGGGGGGGAGGGGGCGGGGGGGGGGG 489356 v v v i v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 50 chr5qtel1M 489357 GCCTGGGGGGGG 489368 vvv (G)n#Simple_r 51 GGGGGGGGGGGG 62 Matrix = Unknown Transitions / transversions = 0.14 (1/7) Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0) 28 0.00 0.00 0.00 chr5qtel1M 489811 489837 (510163) (C)n#Simple_repeat 1 27 (0) c_b257s251i0 10175 chr5qtel1M 489811 CCCCCCCCCCCCCCCCCCCCCCCCCCC 489837 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCC 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 12 13.59 2.78 5.71 chr5qtel1M 492661 492696 (507304) (TTAAT)n#Simple_repeat 1 35 (0) m_b257s252i4 10176 chr5qtel1M 492661 TTAATTT-CTTTATGTTTAATTTAATGTTCATTTCAT 492696 -v -i - v v (TTAAT)n#Simp 1 TTAATTTAATTTA-ATTTAATTTAAT-TTAATTTAAT 35 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.09 (3 / 35), avg. gap size = 1.00 (3 / 3) 13 17.73 5.26 0.00 chr5qtel1M 492977 493014 (506986) (CTTAGT)n#Simple_repeat 1 40 (0) m_b257s252i5 10177 chr5qtel1M 492977 CTTAG-ATTAGTCTTAATTTTAGTCTT-TACTTATTCTTA 493014 -v i i -vv v (CTTAGT)n#Sim 1 CTTAGTCTTAGTCTTAGTCTTAGTCTTAGTCTTAGTCTTA 40 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 84 19.98 1.17 0.00 chr5qtel1M 493578 493748 (506252) (GA)n#Simple_repeat 1 173 (0) m_b257s252i6 10178 chr5qtel1M 493578 GAGAGAGAGACAGAGATAGAGACAGAGAGAGAGACACACACACACACAGA 493627 v v v v v v v v v v (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr5qtel1M 493628 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGGAAGAGAGG 493677 ii i (GA)n#Simple_ 51 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 100 chr5qtel1M 493678 GAGAAGGAGAG-GAGACAGGCACAGACACAGACAGAGACAGAGAGGGAG- 493725 ii - v iv v v v v v i - (GA)n#Simple_ 101 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 150 chr5qtel1M 493726 GAGAGGAAGAGACATATAGAAAG 493748 ii v v v i (GA)n#Simple_ 151 GAGAGAGAGAGAGAGAGAGAGAG 173 Matrix = Unknown Transitions / transversions = 0.50 (10/20) Gap_init rate = 0.01 (2 / 170), avg. gap size = 1.00 (2 / 2) 194 23.21 5.36 0.00 chr5qtel1M 502494 502549 (497451) C MIR1_Amn#SINE/MIR (135) 95 37 m_b257s601i10 10179 chr5qtel1M 502494 GTCATCCCGCTAACAAATGTCTGAGACGGGATTTGAACTCGGCTTTTCC- 502542 i? v ?ii ? i v v v ? ? i i v i i - C MIR1_Amn#SINE 95 GTCACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAACCCAGGTCTCCCG 46 chr5qtel1M 502543 --TCCCAGT 502549 -- C MIR1_Amn#SINE 45 AGTCCCAGT 37 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.99 CpG sites = 8, Kimura (unadjusted) = 31.99 Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.04 (2 / 55), avg. gap size = 1.50 (3 / 2) 13 21.53 4.55 0.00 chr5qtel1M 502723 502766 (497234) (TCCCTCC)n#Simple_repeat 1 46 (0) m_b257s252i7 10180 chr5qtel1M 502723 TCTCTCCT-CTTTCTTGCTCTCCCCTGCTCCCTCCTCCC-CCTCCC 502766 i - i i iv ii v - (TCCCTCC)n#Si 1 TCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCC 46 Matrix = Unknown Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2) 12 8.44 0.00 7.41 chr5qtel1M 506261 506289 (493711) (CCGCC)n#Simple_repeat 1 27 (0) m_b257s252i8 10181 chr5qtel1M 506261 CCGCCCCTGCCCCCTCCTCGCCCCGCCCC 506289 - - v i (CCGCC)n#Simp 1 CCGCCCC-G-CCCCGCCCCGCCCCGCCCC 27 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.07 (2 / 28), avg. gap size = 1.00 (2 / 2) 27 3.42 0.00 0.00 chr5qtel1M 507740 507769 (492231) (C)n#Simple_repeat 1 30 (0) c_b257s251i1 10182 chr5qtel1M 507740 CCCCCCCCCCCCCCCCCCCCCCCCGCCCCC 507769 v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 30 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 11 17.11 5.77 5.77 chr5qtel1M 508877 508928 (491072) (GGGCCAG)n#Simple_repeat 1 52 (0) m_b257s252i9 10183 chr5qtel1M 508877 GGGCCACGCGCATGCGGCC-GGGG-GAGGGGCCA-GGGCAAGCTGGGCCG 508923 v v vv v - -v - v -- - (GGGCCAG)n#Si 1 GGGCCAGGGGCCAGGGGCCAGGGGCCAGGGGCCAGGGGCCAG--GGGCC- 47 chr5qtel1M 508924 AGGGG 508928 (GGGCCAG)n#Si 48 AGGGG 52 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.12 (6 / 51), avg. gap size = 1.00 (6 / 6) 17 26.35 0.00 6.94 chr5qtel1M 509198 509274 (490726) (AGGGGG)n#Simple_repeat 1 72 (0) m_b257s252i10 10184 chr5qtel1M 509198 AGGGAGGAGGGGGCGGGGTCAGGGGAGACTTGGGGCGGGGCCGGGAGCTG 509247 - v -v - --v v vv i vv (AGGGGG)n#Sim 1 AGGG-GGAGGGGGAGGGG-GAGGGG-GA--GGGGGAGGGGGAGGGGGAGG 45 chr5qtel1M 509248 GGGGGCGGGGCCGGGAGCGGGAGGGGG 509274 i v ivv v (AGGGGG)n#Sim 46 GGGAGGGGGAGGGGGAGGGGGAGGGGG 72 Matrix = Unknown Transitions / transversions = 0.25 (3/12) Gap_init rate = 0.07 (5 / 76), avg. gap size = 1.00 (5 / 5) 23 11.76 0.00 6.12 chr5qtel1M 509787 509838 (490162) (GCCC)n#Simple_repeat 1 49 (0) m_b257s252i11 10185 chr5qtel1M 509787 GCCCGCCCGCCCTCTCCGGCCCGCCCGCTCGCCCGCCGGCCCCGCTCACC 509836 v - - i v - i i (GCCC)n#Simpl 1 GCCCGCCCGCCCGC-CC-GCCCGCCCGCCCGCCCGCCCG-CCCGCCCGCC 47 chr5qtel1M 509837 CG 509838 (GCCC)n#Simpl 48 CG 49 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.00 (3 / 3) 14 14.64 0.00 3.23 chr5qtel1M 509990 510021 (489979) (GCG)n#Simple_repeat 1 31 (0) m_b257s252i12 10186 chr5qtel1M 509990 GCGCGCGGCGGCGGCGGCGGGAGCGCGGGCGG 510021 - vi vv (GCG)n#Simple 1 GCG-GCGGCGGCGGCGGCGGCGGCGGCGGCGG 31 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 21 26.20 0.00 0.00 chr5qtel1M 509994 510052 (489948) (GCGGGA)n#Simple_repeat 1 59 (0) m_b257s252i13 10186 chr5qtel1M 509994 GCGGCGGCGGCGGCGGGAGCGCGGGCGGGAGCGCGAGCCGGACCCGGGGC 510043 vi vi v i v v v v i (GCGGGA)n#Sim 1 GCGGGAGCGGGAGCGGGAGCGGGAGCGGGAGCGGGAGCGGGAGCGGGAGC 50 chr5qtel1M 510044 AGGAGCAGG 510052 i i (GCGGGA)n#Sim 51 GGGAGCGGG 59 Matrix = Unknown Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.0 (0 / 0) 23 24.64 5.38 4.58 chr5qtel1M 510148 510277 (489723) (CGCCCG)n#Simple_repeat 1 131 (0) m_b257s252i14 10187 chr5qtel1M 510148 CGCCTCCGCCGCGCGCCACCGCGGCCCCG-CCGTGCCCGCGCGCTCTTCC 510196 iv - - - v v - i v v vi (CGCCCG)n#Sim 1 CGCCCGCGCC-CGCG-C-CCGCGCCCGCGCCCGCGCCCGCGCCCGCGCCC 47 chr5qtel1M 510197 GCGCCTGCGCTCTCCCGCTCGC-CCCGCTCGCCG-GTCTGCGCCTGCG-T 510243 i - - v i - v - - i i i -i (CGCCCG)n#Sim 48 GCGCCCGCGC-C-CGCGCCCGCGCCCGCGC-CCGCGCCCGCGCCCGCGCC 94 chr5qtel1M 510244 AGAAGCGGAGCCCGCGCCC-CG-CCGC-CCCTCGGCC 510277 v viv v v - - - v v (CGCCCG)n#Sim 95 CGCGCCCGCGCCCGCGCCCGCGCCCGCGCCCGCGCCC 131 Matrix = Unknown Transitions / transversions = 0.67 (10/15) Gap_init rate = 0.10 (13 / 129), avg. gap size = 1.00 (13 / 13) 12 24.54 1.92 3.92 chr5qtel1M 510336 510387 (489613) (CGGGGG)n#Simple_repeat 1 51 (0) m_b257s252i15 10188 chr5qtel1M 510336 CGTGGGC-GGGGCCGGGGCGGGGCCTTGGGCTGGCGGAGGCTTACGGGGG 510384 v - v v vv - v v -vvi (CGGGGG)n#Sim 1 CGGGGGCGGGGGCGGGGGCGGGGGCGGGGGC-GGGGGCGG-GGGCGGGGG 48 chr5qtel1M 510385 CGG 510387 (CGGGGG)n#Sim 49 CGG 51 Matrix = Unknown Transitions / transversions = 0.11 (1/9) Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.00 (3 / 3) 44 0.00 0.00 0.00 chr5qtel1M 512053 512090 (487910) (TA)n#Simple_repeat 1 38 (0) c_b257s251i2 10189 chr5qtel1M 512053 TATATATATATATATATATATATATATATATATATATA 512090 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATA 38 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 13 10.02 0.00 11.11 chr5qtel1M 514062 514101 (485899) (AAGGG)n#Simple_repeat 1 36 (0) m_b257s252i16 10190 chr5qtel1M 514062 AAGGCAATGGGAAGCTGAAGGGATAGGGACGGGCAAGGGA 514101 v - -v - v - (AAGGG)n#Simp 1 AAGGGAA-GGGAAG-GGAAGGGA-AGGGAAGGG-AAGGGA 36 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.10 (4 / 39), avg. gap size = 1.00 (4 / 4) 15 21.98 2.38 0.00 chr5qtel1M 514579 514620 (485380) (TTTA)n#Simple_repeat 1 43 (0) m_b257s252i17 10191 chr5qtel1M 514579 TTTCTTT-TTTTTTAATCTATTTATGTGTATATTTATTTGTTT 514620 v - v v i v i v i (TTTA)n#Simpl 1 TTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTT 43 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.02 (1 / 41), avg. gap size = 1.00 (1 / 1) 744 33.01 8.58 0.84 chr5qtel1M 516296 516738 (483262) C L1ME5_3end#LINE/L1 (409) 532 56 m_b257s551i0 10192 chr5qtel1M 516296 TCTATTACACT--ATTCAGCCATTTTCCAACTGATAGGCATCCACTCAAT 516343 i ii i -- iii v i i v v i i i vvivii C L1ME5_3end#LI 532 TCCACCACATTTTACCTATCCACTCTCCCAGTGATGGACACCCAGGTTGC 483 chr5qtel1M 516344 TTCCAGTTTCTTGTCTCTACAAAAGGGGCTTCCACAAACATTTTTG--CA 516391 i ii i ii i v i viiv v v ii ii i -- C L1ME5_3end#LI 482 CTCCAACTCCCCGCCACCACAAACAACGCTGCAATGAACATCCTCGTACA 433 chr5qtel1M 516392 T------TTAAG-------------ATCTCTTTGGGATATAAACCCAGTA 516422 ------ v ------------- i v v C L1ME5_3end#LI 432 TGTCCCCTTATGGACCTGTGTGAGAATTTCTTTGGGATATATACCCAGGA 383 chr5qtel1M 516423 AAAACACTGCTGGATCAAAGGGTATGC----AC--AGTTTGA-----TAC 516461 iviiv i i v ---- -- i ----- C L1ME5_3end#LI 382 GCGGAATTGCTGGGTCATAGGGTATGCGTATACTTAATTTGACTAAGTAC 333 chr5qtel1M 516462 CCCTTTGGATATAGTTCC----GATGGTTGAATTAGTTCACAACTCCACC 516507 iv i---- v v i i----i i v ii ii vii C L1ME5_3end#LI 332 TGCC----AGATTGCTCTCCAGAATGGCTGCACCAGTCTACACTCCCACC 287 chr5qtel1M 516508 AACAATATATTAATGTCCGAGTTTTCCCACATCCCCTCCAATGTTCGTCA 516557 i i ii v iv i vvi ? i i v iii i v C L1ME5_3end#LI 286 AGCAGTGCATGAGGGTTCCTATNTCCCCACATCCTCGCCAACACTTGGCA 237 chr5qtel1M 516558 TTTTCTTTTCCTGTCATCTTAATCAATCTGAGAGGTGTGTAGTGATACCT 516607 v ivviii v v i vii i i v iv i C L1ME5_3end#LI 236 TTATCCAGCTTTCTAATTTTTGCCAGTCTAATAGGTGTAAAGTGATATCT 187 chr5qtel1M 516608 CAGAGTTGTCTTAATTTTCATTTCTTTGATCAATAGTGATTTAGAGCACC 516657 vv i v i i v i v v i C L1ME5_3end#LI 186 CATTGTTGTTTTAATTTGCATTTCTCTGATTACTAATGAGTTTGAGCATC 137 chr5qtel1M 516658 TTTTCATATGACTAGAAATGGTTTCAACTTCTTTATCTGAAAATTGTCTG 516707 i vi ivv iivv iviii i iv v i C L1ME5_3end#LI 136 TCTTCATATGCTTGTTAGCCTTTCGGGTTTCCTCTTCTGTAAATTGCCTG 87 chr5qtel1M 516708 TTCATATGCTTTGACCATTTATCAGTTGGGG 516738 v v v vi C L1ME5_3end#LI 86 TTCATATCCTTTGCCCATTTTTCTATTGGGG 56 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 44.02 CpG sites = 91, Kimura (unadjusted) = 45.78 Transitions / transversions = 1.69 (91/54) Gap_init rate = 0.03 (12 / 442), avg. gap size = 3.50 (42 / 12) 713 32.68 8.23 1.15 chr5qtel1M 516306 516791 (483209) C L1ME3A_3end#LINE/L1 (400) 520 1 m_b257s551i1 10192 chr5qtel1M 516306 TATTCAGCCATTTTCCAACTGATAGGCATCCACTCAATTTCCAGTTTCTT 516355 i v i v vii i i iiivvi?i ??v C L1ME3A_3end#L 520 TATTTATCCATTCTACTGTTGATGGACATTTGGGTNGTTTCCAGTTTNNG 471 chr5qtel1M 516356 GTCTCTACAAAAGGGGCTTCCACAAACATTTTTGCA------TTTAAG-- 516397 iivi i vi v v i ii i i ------ vi -- C L1ME3A_3end#L 470 GCTATTACGAATAGTGCTGCTATGAACATTCTTGTACATGTCTTTTGGTG 421 chr5qtel1M 516398 -------------ATCTCTTTGGGATATAAACCCAGTAAAAACACTGCTG 516434 ------------- i v v i v i v iviiv i C L1ME3A_3end#L 420 AACATATGTACGCATTTCTGTTGGGTATATACCTAGGAGTGGAATTGCTG 371 chr5qtel1M 516435 GATCAAAGGGTATGCA------CAGTTT-----GATACCCCTTTGGATAT 516473 i v ------ i ----- iv i---- v i C L1ME3A_3end#L 370 GGTCATAGGGTATGCATATGTTCAGCTTTAGTAGATACTGCC----AAAC 325 chr5qtel1M 516474 AGTT--CCGA--TGGTTGAATTAGTTCACAACTCCACCAACAATATATTA 516519 -- i -- v ii i i vii i i i v C L1ME3A_3end#L 324 AGTTTTCCAAAGTGGTTGTACCAATTTACACTCCCACCAGCAGTGTATGA 275 chr5qtel1M 516520 ATGTCCGAGTTTTCCCACATCCCCTCCAATGTTCGTCATTTTCTTTTCCT 516569 iv i vi vii i v iii i vi v v iii C L1ME3A_3end#L 274 GAGTTCCGGTTGCTCCACATCCTCGCCAACACTTGGTATTGTCTGTCTTT 225 chr5qtel1M 516570 GTCATCTTAATCAATCTGAGAGGTGTGTAGTGATACCTCAGAGTTGTCTT 516619 v i ii v ivi i i ? vv v i C L1ME3A_3end#L 224 TTCATTTTAGCCATTCTGGTGGGTGTGTAGTGGTATCNCATTGTGGTTTT 175 chr5qtel1M 516620 AATTTTCATTTCTTTGATCAATAGTGATTTAGAGCACCTTTTCATATGAC 516669 v ii v v i vv v vi C L1ME3A_3end#L 174 AATTTGCATTTCCCTGATGACTAATGAAGTTGAGCACCTTTTCATATGTT 125 chr5qtel1M 516670 TAGAAATGGTTTCAACTTCTTTATCTGAAAATTGTCTGTTCATATGCTTT 516719 vviiivi vi iv i iv i vi v i vi vi C L1ME3A_3end#L 124 TATTGGCCATTTGGATATCCTCTTTTGTGAAGTGCCTGTTCAAGTCTTTT 75 chr5qtel1M 516720 GACCATTTATCAGTTGGG--GAATGGCTTGAACTCTAATACATTTGAGTC 516767 v v vi -- vv v v--i v vv vivv C L1ME3A_3end#L 74 GCCCATTTTTCTATTGGGTTGTCTGTCTTT--TTCTTATTGATTTGTAGG 27 chr5qtel1M 516768 AATTCTC--TATATTTTAGAAATGAG 516791 i i-- i i v C L1ME3A_3end#L 26 AGTTCTTTATATATTCTGGATATGAG 1 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 44.07 CpG sites = 90, Kimura (unadjusted) = 44.85 Transitions / transversions = 1.34 (90/67) Gap_init rate = 0.03 (15 / 485), avg. gap size = 3.07 (46 / 15) 234 34.14 2.37 1.57 chr5qtel1M 516644 516896 (483104) C L1PREC2_orf2#LINE/L1 (0) 3294 3040 m_b257s551i2 10192 chr5qtel1M 516644 TGATTTAGAGCACCTTTTCATATGACTAGAAATGGTTTCA---ACTTCTT 516690 v v vii - v v-- iiv --- iv C L1PREC2_orf2# 3294 TGATGTTGAGCTTTTTTTCATATG-CTTGT--TGGCCGCATGTATGTCTT 3248 chr5qtel1M 516691 TATCTGAAAATTGTCTGTTCATATGCTTTGACCATTTATCAGTTGGGGAA 516740 iv i v i v v i v i i v vvi C L1PREC2_orf2# 3247 CTTTTGAAAAGTGTCTGTTCATGTCCTTTGCCCACTTTTTAATGGGGTTG 3198 chr5qtel1M 516741 TGGCTTGAACTCTAATACATTTGAGTCAATTCTCTAT--ATTTTAGAAAT 516788 vvv vvvi vi v vv v i ii -- vi i v C L1PREC2_orf2# 3197 TTTGTTTTTTTCTTGTAAATTTGTTTAAGTTCCTTATAGATGCTGGATAT 3148 chr5qtel1M 516789 GAGGCCTTTATCAGAACCCTTGAATGCAAAGATGTTTTCTTAATTTATAG 516838 v i i vv v v vv ? v i ii v i i C L1PREC2_orf2# 3147 TAGACCTTTGTCAGATGCATAGTTTGCAAANATTTTCTCCCATTCTGTAG 3098 chr5qtel1M 516839 CTTCCCTTCTAATCTTGTCTGCA-TTAGTTTTGCTTGTATAAAATCTTTT 516887 v vi vi v iii ivii - vv - ii i v i C L1PREC2_orf2# 3097 GTTGTCTGTTTACTCTGTTGATAGTTTCTTTTGC-TGTGCAGAAGCTCTT 3049 chr5qtel1M 516888 TAAATTAAT 516896 iv C L1PREC2_orf2# 3048 TAGTTTAAT 3040 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 45.53 CpG sites = 39, Kimura (unadjusted) = 46.25 Transitions / transversions = 0.85 (39/46) Gap_init rate = 0.03 (7 / 252), avg. gap size = 1.43 (10 / 7) 226 29.90 2.22 3.37 chr5qtel1M 517110 517199 (482801) C L1ME3E_3end#LINE/L1 (469) 520 432 m_b257s551i3 10193 chr5qtel1M 517110 TTGTTCAGCTATTGCCCAGTGGGTGGGCATTCCTTCAG--GTTTCCAGCT 517157 i i v i vi v v i i --- vi -- i C L1ME3E_3end#L 520 TTATTTATCCATTCTCCTGTCGATGGACATT---TGGGTTGTTTCCAGTT 474 chr5qtel1M 517158 TTTTGCCACCACAAGGATGGTTGCTATAAATATTTTGATACA 517199 i ii iv vv i i i i vi C L1ME3E_3end#L 473 TTTTGCTATTACAAACAATGCTGCTATGAACATTCTTGTACA 432 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 39.88 CpG sites = 17, Kimura (unadjusted) = 39.88 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.04 (4 / 89), avg. gap size = 1.25 (5 / 4) 346 35.56 7.78 2.11 chr5qtel1M 517965 518234 (481766) L3#LINE/CR1 3269 3553 (546) m_b257s601i11 10194 chr5qtel1M 517965 AAGAATTGTAATGGCCTTTGCAGGATTTAGCACTGCCCGGGATGAAACAA 518014 v iiv ? ii ivi v vv i iv vv v i vvv L3#LINE/CR1 3269 AAGATTCAAAANGATCTCGACAGGCTGGAACGATGGGCCGAAACCAACAA 3318 chr5qtel1M 518015 AA---AAGTCAATAGAGATAAAAATA-----TTACGTTTGGAGCTAAAAA 518056 i --- v i i i vi -----i i i i ivii L3#LINE/CR1 3319 GATGAAATTTAACAGGGATAAATGTAAAGTCCTGCATTTAGGTTCAAAAA 3368 chr5qtel1M 518057 AAAAAATCAACTTCACAA-TACAAGATCAGGAAAGTACA--TTAACAAAA 518103 ----- v - i vii iii vii-- i iv L3#LINE/CR1 3369 A-----TCAACTGCACAAGTACAGGATGGAGAGGATCTGGCTTAGCAGCA 3413 chr5qtel1M 518104 GTTTGTCTGAAAAATATCTGGGGGCTTTATTGGATTGCAAGCCCAGTAGG 518153 iiiv v i i i v v ii i i v L3#LINE/CR1 3414 GTTCACGTGAAAAAGACCTAGGGGTTTTAGTTGACCGCAAGCTCAATATG 3463 chr5qtel1M 518154 AATCATCAGTATGACCACAGAGTCAAGAGAACTGATTGC---CTTAGGTT 518200 ii v i ivvvivv i i i i i - --- i L3#LINE/CR1 3464 AGCCAACAGTGTGATGTGGCTGCCAAAAAAGCTAA-TGCAATCTTAGGCT 3512 chr5qtel1M 518201 ACAT--GGAAAAATATA---TTTAAA--AAGGAAGGAAACA 518234 i --iv i i --- ii i -- i v i L3#LINE/CR1 3513 GCATTAATAGAAGTATAGTGTCCAGANCAAGGGAGGTAATA 3553 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 48.50 CpG sites = 61, Kimura (unadjusted) = 51.72 Transitions / transversions = 1.85 (61/33) Gap_init rate = 0.05 (14 / 269), avg. gap size = 1.93 (27 / 14) 532 29.95 10.60 0.00 chr5qtel1M 518238 518454 (481546) C MIRb#SINE/MIR (15) 253 14 m_b257s601i13 10195 chr5qtel1M 518238 ATTTTTAAAAAACCAACTATATGCCAGGCATGTTGCTAAGCATTTGCC-- 518285 v vi ivi iv i ivv ii vv -- C MIRb#SINE/MIR 253 ATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACAT 204 chr5qtel1M 518286 -CATAAT-TCATTTCATCCTCATAAAAGCCCTGGGAAGTA-CTATTATCA 518332 - v - v i v i v i -v i C MIRb#SINE/MIR 203 GCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATTA 154 chr5qtel1M 518333 TCCCCAGTTTAC--ACGGGGAAACTGAGG--CAAACAGGTTAAATGACTT 518378 v -- i i -- i v i i C MIRb#SINE/MIR 153 TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTT 104 chr5qtel1M 518379 GCTC--------------AGTAAATATCTATGACTGTATTTGATTTTGAA 518414 i -------------- i iv viv v v v i viiiiii C MIRb#SINE/MIR 103 GCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGG 54 chr5qtel1M 518415 GCTTTCTGACCTCAGACCTAATGCTGCATTCATTGCAACA 518454 v v ii i v ivi viv i i v C MIRb#SINE/MIR 53 TCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCACCA 14 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.08 CpG sites = 36, Kimura (unadjusted) = 39.09 Transitions / transversions = 1.24 (36/29) Gap_init rate = 0.03 (7 / 216), avg. gap size = 3.29 (23 / 7) 537 20.68 8.90 0.63 chr5qtel1M 518238 518383 (481617) C MIR#SINE/MIR (13) 249 92 m_b257s601i12 10195 chr5qtel1M 518238 ATTTTTAAAAAACCAACTATATGCCAGGCA-TGTTGCTAAGCA-TTTGCC 518285 v vi ivi iv i - - i- i v C MIR#SINE/MIR 249 ATTTATTGAGCGCTTACTATGTGCCAGGCACTGTT-CTAAGCGCTTTACA 201 chr5qtel1M 518286 CATA---ATTCATTTCATCCTCATAAAAGCCCT----GGGAAGTACTATT 518328 ii --- i v i v i ---- v i C MIR#SINE/MIR 200 TGTATTAACTCATTTAATCCTCACAACAACCCTATGAGGTAGGTACTATT 151 chr5qtel1M 518329 ATCATCCCCAGTTTAC--ACGGGGAAACTGAGG--CAAACAGGTTAAATG 518374 i v -- i i -- i v i i C MIR#SINE/MIR 150 ATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTA 101 chr5qtel1M 518375 ACTTGCTCA 518383 i C MIR#SINE/MIR 100 ACTTGCCCA 92 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 22.99 CpG sites = 20, Kimura (unadjusted) = 24.85 Transitions / transversions = 2.00 (20/10) Gap_init rate = 0.05 (7 / 145), avg. gap size = 2.00 (14 / 7) 190 34.79 1.08 1.08 chr5qtel1M 519291 519383 (480617) L2#LINE/L2 1346 1438 (1644) m_b258s601i3 10196 chr5qtel1M 519291 GTGTGCCCTCACTGCAGCAAGGCAATCTTTTTATGTCTCCTTAATTGACT 519340 v i v v vv ? vi ii i i i iv i L2#LINE/L2 1346 GTGGGCCCTTAATGCTGCCCGGCAATCNTACTACATTTCCCTAGTCCATT 1395 chr5qtel1M 519341 CACTGCTCCATTCAACACAGCTAGCTTTTCCA-ATCTTTTCATC 519383 vii i -v vi viii v i - i i v L2#LINE/L2 1396 CACTCTCCCACTC-TCCTAGACGACTATTTCACACCTTCTCCTC 1438 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 47.07 CpG sites = 19, Kimura (unadjusted) = 49.51 Transitions / transversions = 1.46 (19/13) Gap_init rate = 0.02 (2 / 92), avg. gap size = 1.00 (2 / 2) 738 28.62 4.31 2.11 chr5qtel1M 519385 519616 (480384) MIRb#SINE/MIR 29 265 (3) m_b258s601i4 10197 chr5qtel1M 519385 AGCATGATGGTCCTGGAATCGGGGAGACCTGAGTTCAAATCTAGCATCAG 519434 i -- iii i i iv i i iv vv v MIRb#SINE/MIR 29 AGCACG--GGCTTTGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTCTG 76 chr5qtel1M 519435 ATGCTTACTAGCTATGTTTCCCTGATCAAGTCAC--AACCTGTC-----C 519477 vii i vv i iv i -- v ----- MIRb#SINE/MIR 77 CCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCC 126 chr5qtel1M 519478 T---TTATCTTAATTGTAAAATGAGGGTAGTAAAAGCACCTCTTTGGCAG 519524 --- vi i vi i i i ---i vii v MIRb#SINE/MIR 127 TCAGTTTCCTCATCTGTAAAATGGGGATAATAA---TACCTACCTCGCAG 173 chr5qtel1M 519525 GGTTGTCTTGAGAGTTGAATGAATTAATATTTGTAAAGTGCTTAGCACAA 519574 iv ii i iv iiv i i MIRb#SINE/MIR 174 GGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAG 223 chr5qtel1M 519575 TGGCTAGCATATAATATGTGCTTTATAAATGCTTATTCCCTT 519616 v i i i v i iv v vii iv MIRb#SINE/MIR 224 TGCCTGGCACATAGTAAGCGCTCAATAAATGGTAGCTCTATT 265 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.62 CpG sites = 42, Kimura (unadjusted) = 37.53 Transitions / transversions = 1.83 (42/23) Gap_init rate = 0.03 (8 / 231), avg. gap size = 1.88 (15 / 8) 206 34.52 3.28 5.00 chr5qtel1M 519600 519721 (480279) L2#LINE/L2 1412 1531 (1551) m_b258s601i5 10196 chr5qtel1M 519600 TAAATGCTTATTCC----CTTCCCCTTCCTTCACCCTTCTGCAAAACTTT 519645 i i vi i ---- i ii i v vvvi v v i i L2#LINE/L2 1412 TAGACGACTATTTCACACCTTCTCCTCTCTCCTCAAACCTCCAACACCTC 1461 chr5qtel1M 519646 GGTTGCTTTTCCCCCACTCTCTGCAAAGAACCTTGCCTCATATTGCCCTG 519695 --i v ii vi i v vi vi i v v v L2#LINE/L2 1462 --CTCCCCTATCCTCACTCTCAGCTGATGACCTTGCTTCCTATTTCACTG 1509 chr5qtel1M 519696 AAAAAAAATTGGAGGCTATTTGGAAG 519721 i --- i i - v ii L2#LINE/L2 1510 AGAAAA---TAGAAGC-AATCAGAAG 1531 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.49 CpG sites = 24, Kimura (unadjusted) = 48.19 Transitions / transversions = 1.50 (24/16) Gap_init rate = 0.06 (7 / 121), avg. gap size = 1.43 (10 / 7) 53 24.53 1.46 0.00 chr5qtel1M 520736 520872 (479128) (ACCCTA)n#Simple_repeat 1 139 (0) m_b258s252i0 10198 chr5qtel1M 520736 ACCCAGACTCTAACCCTAACCCCAACCCCTACTCTAATCCTAAACCCCTC 520785 vi i i iv i i v ivv (ACCCTA)n#Sim 1 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC 50 chr5qtel1M 520786 TCTAACCCTAACCCCGACTCTAACCCTAAGCC--CCTCTAACCCTAACCC 520833 i ii i v --v i (ACCCTA)n#Sim 51 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC 100 chr5qtel1M 520834 CGACTCTAACTCTAAACCCACCTCTAACCCTAATCCTAA 520872 ii i i v i v i i (ACCCTA)n#Sim 101 TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA 139 Matrix = Unknown Transitions / transversions = 2.11 (19/9) Gap_init rate = 0.01 (1 / 136), avg. gap size = 2.00 (2 / 1) 42 0.00 0.00 0.00 chr5qtel1M 522426 522461 (477539) (AC)n#Simple_repeat 1 36 (0) c_b258s251i0 10199 chr5qtel1M 522426 ACACACACACACACACACACACACACACACACACAC 522461 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACAC 36 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 15 22.78 7.94 0.00 chr5qtel1M 522824 522886 (477114) (CGAGGG)n#Simple_repeat 1 68 (0) m_b258s252i1 10200 chr5qtel1M 522824 CGAGGACGAGAGCGA-GGTG-GGGAGAGGACGAGAGCGAAGG-G-GGAC- 522868 i i - i - v i i i - - i - (CGAGGG)n#Sim 1 CGAGGGCGAGGGCGAGGGCGAGGGCGAGGGCGAGGGCGAGGGCGAGGGCG 50 chr5qtel1M 522869 AGGACGAGTGCTGGGGCG 522886 i v vi (CGAGGG)n#Sim 51 AGGGCGAGGGCGAGGGCG 68 Matrix = Unknown Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.08 (5 / 62), avg. gap size = 1.00 (5 / 5) 33 0.00 0.00 0.00 chr5qtel1M 524233 524263 (475737) (T)n#Simple_repeat 1 31 (0) c_b258s251i1 10201 chr5qtel1M 524233 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 524263 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 107 24.45 3.26 0.96 chr5qtel1M 526698 527004 (472996) (CTC)n#Simple_repeat 1 314 (0) m_b258s252i2 10202 chr5qtel1M 526698 CTCCACCTCCTCCTCTTCCTCCTTCT-CTTATCCATTTCCTCC-CTTCCT 526745 v i i - iv vii - i (CTC)n#Simple 1 CTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT 50 chr5qtel1M 526746 CCTCCTCCTTTTTCTCTTCCTCCTCCTCCTCCT-GTCCATCTCCTCTTCC 526794 ii i i -v vi i (CTC)n#Simple 51 CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC 100 chr5qtel1M 526795 TCAAGCT-GTCCATTTCCTCCTCTTCCTCCT-CTCCTCTTCTTTCTCCTC 526842 vvv -v vii i - i i i (CTC)n#Simple 101 TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC 150 chr5qtel1M 526843 CTTTTTCTCCTCCTCTTCCT-TTCCTTGTCCTCCTCCTCCTTCCTTTCTC 526891 ii i i -i iv - - i (CTC)n#Simple 151 CTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC-TCC-TCCTC 198 chr5qtel1M 526892 CTTTTTCTCTTCCTCCTCCTCTTCCTCCCTCTCTTCCT-GTCCATCTCCT 526940 ii i i i ii i -v vi (CTC)n#Simple 199 CTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT 248 chr5qtel1M 526941 CTTTATTC-CCTTCTCCCTTCTGCCCCTCCTCCTTCTCCTCTTCC-CCAT 526988 i iv i - i - i v i i i - vi (CTC)n#Simple 249 CCTCCTCCTCCTCCT-CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC 297 chr5qtel1M 526989 CTCC-CCCCTTCCTCCT 527004 - i i (CTC)n#Simple 298 CTCCTCCTCCTCCTCCT 314 Matrix = Unknown Transitions / transversions = 2.81 (45/16) Gap_init rate = 0.04 (13 / 306), avg. gap size = 1.00 (13 / 13) 15 0.00 6.25 6.25 chr5qtel1M 531409 531440 (468560) (GGCCA)n#Simple_repeat 1 32 (0) m_b258s252i3 10203 chr5qtel1M 531409 GGCCAGCGCCAGG-CAGTGCCAGGCCA-GCCAGG 531440 - - - - (GGCCA)n#Simp 1 GGCCAG-GCCAGGCCAG-GCCAGGCCAGGCCAGG 32 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.13 (4 / 31), avg. gap size = 1.00 (4 / 4) 15 23.03 0.00 0.00 chr5qtel1M 532335 532371 (467629) (CTC)n#Simple_repeat 1 37 (0) m_b258s252i5 10204 chr5qtel1M 532335 CTCCTGCTTCTCCCCCTCTTCCTCCCTTTCCTCCTCC 532371 v i i i iii (CTC)n#Simple 1 CTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC 37 Matrix = Unknown Transitions / transversions = 6.00 (6/1) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 12 11.05 10.91 5.17 chr5qtel1M 532333 532387 (467613) (CTCTTC)n#Simple_repeat 1 58 (0) m_b258s252i4 10205 chr5qtel1M 532333 CTC-TCCTGCTT-CTCCCCCTCTTCCTC--CCT-TTCCTCCTCCCATCTT 532377 - - - ii -- - - i - (CTCTTC)n#Sim 1 CTCTTCCT-CTTCCTCTTCCTCTTCCTCTTCCTCTTCCT-CTTCC-TCTT 47 chr5qtel1M 532378 -CTCTGTCTCT 532387 - vi (CTCTTC)n#Sim 48 CCTCTTCCTCT 58 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.15 (8 / 54), avg. gap size = 1.12 (9 / 8) 528 18.49 1.64 6.90 chr5qtel1M 532599 532720 (467280) MIRc#SINE/MIR 12 127 (141) m_b258s601i6 10206 chr5qtel1M 532599 GGCGCAGTGGACAGAGCATCAGCCCTGGAGTCAGGAGGACCTGAGTTCAG 532648 i v iii v i i i ii MIRc#SINE/MIR 12 GGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGA 61 chr5qtel1M 532649 ATTCCGCCTCAGACACTTAACACTTCCTGGCTGTGTGACCCTGGGCAAGG 532698 i i v v v ------- i i v MIRc#SINE/MIR 62 GTCCCGGCTCTGCCACTTA-------CTAGCTGTGTGACCTTGGGCAAGT 104 chr5qtel1M 532699 CACTTAACCCCAACT--GCCTCAG 532720 i -v -- MIRc#SINE/MIR 105 CACTTAACCTC-TCTGAGCCTCAG 127 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 20.49 CpG sites = 14, Kimura (unadjusted) = 21.61 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.07 (9 / 121), avg. gap size = 1.11 (10 / 9) 427 25.77 1.03 0.00 chr5qtel1M 534087 534183 (465817) MIR#SINE/MIR 47 144 (118) m_b258s601i7 10207 chr5qtel1M 534087 CTTGGGTGTAAACCCAAGCCCAGATGCTTCCTAGCTGGGGGGCCCTGGGC 534136 i vii i vi i v vii v v v i i MIR#SINE/MIR 47 CCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGC 96 chr5qtel1M 534137 AAATCACATAAGCCC-CTTTGTCTCAGTTTCCTCATCTGTAAAATGAG 534183 i i v v i - v i i MIR#SINE/MIR 97 AAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGG 144 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.13 CpG sites = 15, Kimura (unadjusted) = 32.36 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.01 (1 / 96), avg. gap size = 1.00 (1 / 1) 12 19.56 2.86 0.00 chr5qtel1M 537251 537285 (462715) (TCCCCCG)n#Simple_repeat 1 36 (0) m_b258s252i6 10208 chr5qtel1M 537251 TCCCCC-TGCTCCGACCCCCGTCCCTGGTCCCCTGT 537285 - v i v iv i (TCCCCCG)n#Si 1 TCCCCCGTCCCCCGTCCCCCGTCCCCCGTCCCCCGT 36 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 16 27.53 0.00 1.89 chr5qtel1M 540373 540426 (459574) (CACA)n#Simple_repeat 1 53 (0) m_b258s252i7 10209 chr5qtel1M 540373 CACTACATGCACCCACTCACCCAGACACTGACACACAGACGCCCAGACAC 540422 - ii v v v v vv v i v v (CACA)n#Simpl 1 CAC-ACACACACACACACACACACACACACACACACACACACACACACAC 49 chr5qtel1M 540423 ACAC 540426 (CACA)n#Simpl 50 ACAC 53 Matrix = Unknown Transitions / transversions = 0.33 (3/9) Gap_init rate = 0.02 (1 / 53), avg. gap size = 1.00 (1 / 1) 16 37.97 1.37 0.00 chr5qtel1M 541964 542036 (457964) (TG)n#Simple_repeat 1 74 (0) m_b258s252i8 10210 chr5qtel1M 541964 TGTGGGGGTGTGCCTGCATGTTTGTGTGAG-GTGTGCATGTGTGCATGGG 542012 v v iv ii v v - ii ii v (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr5qtel1M 542013 CATACGTGTACGTGTGGGTGTATG 542036 ii ii ii v i (TG)n#Simple_ 51 TGTGTGTGTGTGTGTGTGTGTGTG 74 Matrix = Unknown Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.01 (1 / 72), avg. gap size = 1.00 (1 / 1) 18 36.19 0.00 0.00 chr5qtel1M 542218 542285 (457715) (TG)n#Simple_repeat 1 68 (0) m_b258s252i9 10211 chr5qtel1M 542218 TGTGTGTGCGTGTGTGTGCACACGTATACGTGGGGGTTTGTGCGTGGTTG 542267 i iiiii i ii v v v i vv (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr5qtel1M 542268 CATGTGTGGGTGTTTGTG 542285 ii v v (TG)n#Simple_ 51 TGTGTGTGTGTGTGTGTG 68 Matrix = Unknown Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0) 16 24.95 3.61 4.88 chr5qtel1M 550864 550946 (449054) (CGGGG)n#Simple_repeat 1 82 (0) m_b258s252i10 10212 chr5qtel1M 550864 CGGAGGCGGCTGGC-GGG-GGCCCGGGGACGGGAGGGG-GGAGCTGGGCG 550910 - -- - - vv vv v - i v (CGGGG)n#Simp 1 CGG-GGCGG--GGCGGGGCGGGGCGGGGCGGGGCGGGGCGGGGCGGGGCG 47 chr5qtel1M 550911 GAGACTCGAGGGGGGGCTTCGGGGCGGGGCGGGGCG 550946 - i vv iv v vvv (CGGGG)n#Simp 48 G-GGCGGGGCGGGGCGGGGCGGGGCGGGGCGGGGCG 82 Matrix = Unknown Transitions / transversions = 0.23 (3/13) Gap_init rate = 0.09 (7 / 82), avg. gap size = 1.00 (7 / 7) 371 20.00 10.91 0.00 chr5qtel1M 552257 552366 (447634) C MER63D#DNA/hAT-Tip100 (600) 461 340 m_b258s502i0 10213 chr5qtel1M 552257 TTTTCCATTTCATCTGCACCA---GCATTTTCTCCATCACTTTCTTATGT 552303 vvi v ii ---i v C MER63D#DNA/hA 461 TTTTAAGTTTAATCTGCATTATTAACATTTTCTCCATCACTTTCTTAAGT 412 chr5qtel1M 552304 CCAGA-AATCAACAAA--------TCAAGCCCTGACTTTTAGTTTCTGCT 552344 i - -------- i v iv i i C MER63D#DNA/hA 411 CTAGACAATCAACAAAACAATAAATCAAGCCCTGATTTGTAGCGTTTGCC 362 chr5qtel1M 552345 AATTTCTGAGATATAAATGTTC 552366 i i v i i ii C MER63D#DNA/hA 361 GATTTCCGTGGTGTAAATACTC 340 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 20.21 CpG sites = 15, Kimura (unadjusted) = 23.90 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.03 (3 / 109), avg. gap size = 4.00 (12 / 3) 225 27.12 0.00 0.00 chr5qtel1M 552370 552428 (447572) C MER63D#DNA/hAT-Tip100 (1002) 59 1 m_b258s502i1 10213 chr5qtel1M 552370 CTGAAAATTTAACAATCAGCTCCCTGGAACCTGTTGGAGCTGATTCCATA 552419 i i vv i v vv i ii vv C MER63D#DNA/hA 59 CTGAAAATTTAACAATCGGCTCTCGCGAGCCGGTACGAGCCGGCTCCAGC 10 chr5qtel1M 552420 ATGCTACTG 552428 ii i C MER63D#DNA/hA 9 ACACCACTG 1 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 29.30 CpG sites = 9, Kimura (unadjusted) = 34.33 Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.0 (0 / 0) 232 36.39 12.87 0.99 chr5qtel1M 552462 552733 (447267) L2#LINE/L2 700 1003 (2079) m_b258s601i8 10214 chr5qtel1M 552462 CTCCAGGACTCTCTCCTTCCTTCCTGAATGAGTTCAGTGTTTG-TTTACA 552510 i v v i i v vi v v i ivii -i i v L2#LINE/L2 700 CTCCGGGTCACTCCCCCTCATTCCTTGAAGATTTTAGCTCCTGGCTCACT 749 chr5qtel1M 552511 ATT-TTCTCTCTTGCTCAACCCTTGCCTCTGTACCTGGC-ACTTCAGCA- 552557 i i-i ivi v v i i i vivi v i i- i ii - L2#LINE/L2 750 GTCACTCTCTCCAACACTACTCCTGTCATAATTCTTGGTGATTTCAATAT 799 chr5qtel1M 552558 --------------CTTGAGATATTATGACTGCTTCACTTTCTTAATCTG 552593 -------------- vvi iiv i iv - v i i i v L2#LINE/L2 800 CCACGTAGATGATCCTTCCAATACCCTGGCCTCT-CAGTTCCTTGACCTC 848 chr5qtel1M 552594 CTCATTTCCCACGA------CCTCCACTCTACCTCAGCTA--------TG 552629 vii v i ------ i i --------ii L2#LINE/L2 849 CTCTCCTCCAATGATCTTGTCCTCCACCCTACCTCAGCCACTCACTCCCA 898 chr5qtel1M 552630 TGGTCATG-CCTCCACCTTGCCAATACCCACAAGTGGGCTACCTCTGTGG 552678 i- vv i v v i v viviv ii ii L2#LINE/L2 899 TGGTCATACCCTAGACCTTGTCATTACCAATAACTGCAACCCCTCCATAA 948 chr5qtel1M 552679 GCAGCAACTCCGAAGAACCCATTGGCTTCCCACCTCTCCCTTTGCCCTCC 552728 v -v i i i iv v i vv vv v ii v - ii L2#LINE/L2 949 TC-TCAATTTCAAGCATCCCACTCTCTGACCACCACCTCCTAT-CTTTCC 996 chr5qtel1M 552729 --CTCAC 552733 -- L2#LINE/L2 997 AGCTCAC 1003 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 51.40 CpG sites = 58, Kimura (unadjusted) = 52.19 Transitions / transversions = 1.45 (58/40) Gap_init rate = 0.04 (12 / 271), avg. gap size = 3.17 (38 / 12) 590 33.51 5.17 2.23 chr5qtel1M 552781 553128 (446872) C L2#LINE/L2 (1557) 1525 1168 m_b258s601i9 10215 chr5qtel1M 552781 ATAGCCTCCATTTTTTTCTGTAAACTCTGAAACAAAGTTATCAGCTGA-A 552829 v i i i - v i v vv i i i - C L2#LINE/L2 1525 ATTGCTTCTATTTTCT-CAGTGAAATAGGAAGCAAGGTCATCAGCTGAGA 1477 chr5qtel1M 552830 GT-AGGA---GGAAGACCCCACGGAAGGTTTTAGGAGGGATGAGAAAGTT 552875 - --- i ivvviiiv i v i v i v C L2#LINE/L2 1476 GTGAGGATAGGGGAGGAGGTGTTGGAGGTTTGAGGAGAGAGGAGAAGGTG 1427 chr5qtel1M 552876 GGGAAGGGATGCTGTGAAGAGCGGGACAATGAGCGGAGAAGGGAAGGGAG 552925 v i vi vi iivv i i v i ii vv ----- C L2#LINE/L2 1426 TGAAATAGTCGTCTAGGAGAGTGGGAGAGTGAATGGACTAGGGAA----- 1382 chr5qtel1M 552926 GTACAGCAGGATTGCCTGGTGGCAGTGAGGGCCCAATTGAGAATAA-GAT 552974 i ii i ? v ii v i v iv ?i- i C L2#LINE/L2 1381 ATGTAGTANGATTGCCGGGCAGCATTAAGGGCCCACTTGAGGTTNGTGGT 1332 chr5qtel1M 552975 C---AGTTTGTAGTGGACCCGGTCAGAACAGTTAGGTGGATTTTCTCCAC 553021 --- i iv iiv i v ii iv v- v C L2#LINE/L2 1331 CATGAATTTAAAGTGAGACCAGTCAGCATGGTTGTGTGT-TTTTCTCCAG 1283 chr5qtel1M 553022 CTTCGTGCATTAGCATGTGAGAAGGAATAGAGTG---GGAGTGCTAGGAG 553068 iv v viv ?i v v v viii i--- v i - v C L2#LINE/L2 1282 CCACGTTCAGCTGCNCGGGTGCAGGCGCGGAGTAGGCGGAGAGTT-GGAT 1234 chr5qtel1M 553069 TGATCCAAGGCTGAAAATGGGCAGAGC-AGTTAGA-----CATGATAAAG 553112 v v i i ?iiv vv vii - vv ----- iv v ii C L2#LINE/L2 1233 TTAACCAGGGTTGNGGTTTTGCCAGGCGAGTACGACGAAGCGAGAGAGGG 1184 chr5qtel1M 553113 GCCAGGGACTCGAGAG 553128 v v i i C L2#LINE/L2 1183 GCAAGGGAGTTGAGGG 1168 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.56 CpG sites = 62, Kimura (unadjusted) = 46.36 Transitions / transversions = 1.19 (62/52) Gap_init rate = 0.05 (16 / 347), avg. gap size = 1.62 (26 / 16) 14 17.53 0.00 0.00 chr5qtel1M 553133 553164 (446836) (GAAAA)n#Simple_repeat 1 32 (0) m_b258s252i11 10216 chr5qtel1M 553133 GAACAGTGAAGAAAAGAGAAGAAAAGAACAGA 553164 v vi i v (GAAAA)n#Simp 1 GAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGA 32 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 577 31.97 11.54 1.75 chr5qtel1M 553258 553725 (446275) L2#LINE/L2 1691 2203 (879) m_b258s601i10 10214 chr5qtel1M 553258 CAAGGACAACGCCTCCACCTGTTCAAATGCGCCCTTTGATCCTGC-TC-T 553305 v - v vi --- v v i i v- - - L2#LINE/L2 1691 CAAGGACATCGC-TCCAGCAATTC---TCCCCTCTCTC-TCCTGCATCAT 1735 chr5qtel1M 553306 CG--CTCCCCTTGCCTACTGCTTCTTCTCTACTGACG-GCAAACAT-CT- 553350 i--i ii i vi vv v ii i iiii i-i - - L2#LINE/L2 1736 CAATTTTTCCCTCTCTACTGGATCATTCCCATCAGCATACAAACATGCTG 1785 chr5qtel1M 553351 TCATC---CTCAACA--ACAAAACAAACCCCGATCCTCACTTCATCCTTC 553395 ? i--- i v v-- v ----i i v v i iv L2#LINE/L2 1786 TNATTTCTCCCATCTTTAAAAAACAAA----AATTCTCCCTTGACCCCAC 1831 chr5qtel1M 553396 CTCACC-TCTAACT---GCCCTATTTTTCTTCTGCC-TTTGTGACCGAGC 553440 ? v - i i --- i i v v - iiii vi i L2#LINE/L2 1832 NTCCCCCTCCAGCTACCGCCCCATTTCTCTGCTCCCCTTTACAGCAAAAC 1881 chr5qtel1M 553441 CCACTGAAAAAGC-GACTGCAATCA-GAACTCCACTTTCCTTCTTCCCA- 553487 i vii i i- v ii v i-viv v i ii i - L2#LINE/L2 1882 TCCTCGAAAGAGTTGTCTATACTCGCTGTCTCCAATTCCTCTCCTCCCAT 1931 chr5qtel1M 553488 ---CTCTGGAGC-------AAAGTGGCTTCCAGCCTCTTCATCCCACAGA 553527 --- v i ------- vvv i iv i vi ii v L2#LINE/L2 1932 TCTCTCTTGAACCCACTCCAATCAGGCTTTCGTCCCCACCACTCCACCGA 1981 chr5qtel1M 553528 AACTGCCCTCTCCCAAGTTAACAATGATCTCTTAGGGGC-AGATCCAGCG 553576 i ivi v i i v i ivv vv - i ii L2#LINE/L2 1982 AACTGCTCTTGTCAAGGTCACCAATGACCTCCACGTTGCTAAATCCAATG 2031 chr5qtel1M 553577 GGC-ATTCTC-------------CCTGCTCTCCCTGCAGCCTTTGATGCT 553612 v - ------------- i vi ?i v v ii v L2#LINE/L2 2032 GTCAATTCTCAGTCCTCATCTTACTTGACCTNTCAGCAGCATTTGACACA 2081 chr5qtel1M 553613 GTTGGCCCCTCTCCCCTTCT--AGACACTCTTTTCTCCAGGTAGGGGGGA 553660 ii v i i -- i i i v iv ivvvvi L2#LINE/L2 2082 GTTGATCACTCCCTCCTTCTTGAAACACTTTCTTCACTTGGCTTCCAGGA 2131 chr5qtel1M 553661 CACAGCTCTCTC----TTTTCTTCTTAACTGCTTAACC---CCTTCTCAG 553703 vi v ---- i i v vvi ii --- L2#LINE/L2 2132 CACCACACTCTCCTGGTTTTCCTCCTACCTCACTGGCCGCTCCTTCTCAG 2181 chr5qtel1M 553704 TTTCCTTTGCGGGATCTTCATC 553725 i v v i v L2#LINE/L2 2182 TCTCCTTTGCTGGTTCCTCCTC 2203 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.42 CpG sites = 87, Kimura (unadjusted) = 43.63 Transitions / transversions = 1.45 (87/60) Gap_init rate = 0.07 (31 / 467), avg. gap size = 2.03 (63 / 31) 225 25.93 0.00 0.00 chr5qtel1M 553755 553808 (446192) MIR#SINE/MIR 72 125 (137) m_b258s601i11 10217 chr5qtel1M 553755 ACTTCCTAACTGTGTGACCCAGAGCTAGTCACATGCCTTCTGTTTGTCTC 553804 v i iv i v i v iv i v v i MIR#SINE/MIR 72 ACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTC 121 chr5qtel1M 553805 AGTT 553808 MIR#SINE/MIR 122 AGTT 125 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.13 CpG sites = 7, Kimura (unadjusted) = 32.13 Transitions / transversions = 1.00 (7/7) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 224 25.71 8.57 0.00 chr5qtel1M 554029 554098 (445902) MIR#SINE/MIR 65 140 (122) m_b258s601i12 10218 chr5qtel1M 554029 CTCAGACCCTTCCCAGTTTTTGAACCCGGGGCAAGTC------CCTCTGT 554072 v v v v i i v vvi iv i------ v MIR#SINE/MIR 65 CTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCT 114 chr5qtel1M 554073 TTGCCTTAGTTTCCTCATTTGTGAAA 554098 v i i i MIR#SINE/MIR 115 GTGCCTCAGTTTCCTCATCTGTAAAA 140 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.63 CpG sites = 8, Kimura (unadjusted) = 31.63 Transitions / transversions = 0.80 (8/10) Gap_init rate = 0.01 (1 / 69), avg. gap size = 6.00 (6 / 1) 54 0.00 0.00 0.00 chr5qtel1M 554156 554201 (445799) (GT)n#Simple_repeat 1 46 (0) c_b258s251i2 10219 chr5qtel1M 554156 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 554201 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 46 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 332 26.65 8.49 0.88 chr5qtel1M 554237 554342 (445658) C MIRc#SINE/MIR (120) 148 35 m_b258s601i13 10220 chr5qtel1M 554237 CTCATTTTACAGATGGGGAAACTGAGGCAAGGTGGAGG--AAGTGATTTG 554284 i i vvi -i -- i C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAG-AGAGGTTAAGTGACTTG 100 chr5qtel1M 554285 -CTAGGATCACACAG------AACGTCTGAAGCCCTATTTGAACTCAGAG 554327 - i i i ------ ii v v iv vvv i i i iv C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGT 50 chr5qtel1M 554328 GTCCCTGACTTCAGG 554342 v i i i C MIRc#SINE/MIR 49 CTTCCTGACTCCAAG 35 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.60 CpG sites = 18, Kimura (unadjusted) = 34.10 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.04 (4 / 105), avg. gap size = 2.50 (10 / 4) 198 36.26 5.56 1.53 chr5qtel1M 554354 554479 (445521) MIRb#SINE/MIR 124 254 (14) m_b258s601i14 10221 chr5qtel1M 554354 GCCTCCTTGTCCTCTCTTCGAAAATGGGGGTAAGAGATAAGCCGCCTCCC 554403 vv v vii vv i v - - v ii v MIRb#SINE/MIR 124 GCCTCAGTTTCCTCATCTGTAAAATGGGGATAATA-AT-ACCTACCTCGC 171 chr5qtel1M 554404 AGAGGCGCTGTGAGCCCCAGAGGAGTCGATTTGTGCGGGGAGCCCAGC-- 554451 i vi i vvii i v vii vii iiii v ii -- MIRb#SINE/MIR 172 AGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGCAC 221 chr5qtel1M 554452 ----CCGGGCCCACAGTCGGCGC-CGACAGATG 554479 ---- v v i vi - i i i MIRb#SINE/MIR 222 AGTGCCTGGCACATAGTAAGCGCTCAATAAATG 254 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 51.65 CpG sites = 26, Kimura (unadjusted) = 51.65 Transitions / transversions = 1.37 (26/19) Gap_init rate = 0.04 (5 / 125), avg. gap size = 1.80 (9 / 5) 218 16.36 18.18 0.00 chr5qtel1M 554925 554979 (445021) C MIRc#SINE/MIR (201) 67 3 m_b258s601i15 10222 chr5qtel1M 554925 CGGGATTGAAACCCAGCTCCTC----------GGCCAGGGCCCTTTCCGC 554964 i vi v i ---------- v v i i C MIRc#SINE/MIR 67 CGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCAC 18 chr5qtel1M 554965 TGCACCACACTGCCT 554979 C MIRc#SINE/MIR 17 TGCACCACACTGCCT 3 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 16.47 CpG sites = 5, Kimura (unadjusted) = 18.62 Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.02 (1 / 54), avg. gap size = 10.00 (10 / 1) 220 28.02 0.00 2.67 chr5qtel1M 555653 555729 (444271) L2d2_3end#LINE/L2 475 549 (6) m_b259s601i1 10223 chr5qtel1M 555653 CTTCTGTCTAAGCCCCACCAGCACCAAGCATGGCGCCCGTCCTACAGTTG 555702 v v vv - i v ii i ivv vi v L2d2_3end#LIN 475 CTTCTTTGTATCCCCCAC-AGCGCCTAGCACAGTGCCTTGCACACAGTAG 523 chr5qtel1M 555703 GTACTAAATAAAATTCTGTTGCATTTG 555729 ii v vv i - L2d2_3end#LIN 524 GCGCTCAATAAATATTTGTTG-ATTTG 549 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.13 CpG sites = 9, Kimura (unadjusted) = 35.18 Transitions / transversions = 0.75 (9/12) Gap_init rate = 0.03 (2 / 76), avg. gap size = 1.00 (2 / 2) 18 15.51 0.00 0.00 chr5qtel1M 555845 555874 (444126) (T)n#Simple_repeat 1 30 (0) m_b259s252i1 10224 chr5qtel1M 555845 TTCTTTTTTTCTTTTCTTTTCTTTTTTTTT 555874 i i i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 30 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 12 30.56 0.00 2.04 chr5qtel1M 555844 555893 (444107) (ATTTT)n#Simple_repeat 1 49 (0) m_b259s252i0 10225 chr5qtel1M 555844 ATTCTTTTTTTCTTTTCTTTTCTTTTTTTTTAAATTAAACCTTTTTATTT 555893 - v v v v v vv vviiv (ATTTT)n#Simp 1 ATT-TTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTT 49 Matrix = Unknown Transitions / transversions = 0.20 (2/10) Gap_init rate = 0.02 (1 / 49), avg. gap size = 1.00 (1 / 1) 232 28.56 4.39 1.71 chr5qtel1M 556152 556265 (443735) L2#LINE/L2 2364 2480 (602) m_b259s601i2 10214 chr5qtel1M 556152 CTCTTGCTTGAGCTCCAGTCTTGT-CACCCG-CTGCCTGTTGGTCAATTC 556199 iv i i v i -i i i- ii v v vi L2#LINE/L2 2364 CTCTCCCCTGAACTCCAGACTCGTATATCCAACTGCCTACTCGACATCTC 2413 chr5qtel1M 556200 C-CT--GATGAGCCATCCGCAATCTCAAACTCAACATGCCTAAAATGGAA 556246 - -- vviv vv - i i i iv L2#LINE/L2 2414 CACTTGGATGTCTAATAGGCA-TCTCAAACTTAACATGTCCAAAACTGAA 2462 chr5qtel1M 556247 CTCTCTCCTTTTCTCTGTC 556265 - vv i i iv L2#LINE/L2 2463 CTC-CTGATCTTCCCCCTC 2480 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.33 CpG sites = 18, Kimura (unadjusted) = 36.76 Transitions / transversions = 1.29 (18/14) Gap_init rate = 0.05 (6 / 113), avg. gap size = 1.17 (7 / 6) 21 34.00 0.97 1.96 chr5qtel1M 556266 556368 (443632) (TCTC)n#Simple_repeat 1 102 (0) m_b259s252i3 10226 chr5qtel1M 556266 TCTCTATCTTTGTGTTCCTTTGTCTCTCCCTCATTCTGGGTCT-TAGTTC 556314 v i v v ii i v i vi vvv - vvi (TCTC)n#Simpl 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr5qtel1M 556315 TTTCTCTCTGCTCTCCCTGTCTCTCTCCATCCCTCTGTCTTTGTCTCCCT 556364 i - i v iv i v i v i (TCTC)n#Simpl 51 TCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 99 chr5qtel1M 556365 GCTC 556368 - (TCTC)n#Simpl 100 -CTC 102 Matrix = Unknown Transitions / transversions = 0.93 (13/14) Gap_init rate = 0.03 (3 / 102), avg. gap size = 1.00 (3 / 3) 194 26.21 28.16 0.00 chr5qtel1M 557562 557664 (442336) C MIR#SINE/MIR (111) 151 20 m_b259s601i4 10227 chr5qtel1M 557562 TATCATCCCCATTTCACAAGTGAAGAA---GAG-------GAGGCTCAG- 557600 i i ii i --- ------- i v - C MIR#SINE/MIR 151 TATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGT 102 chr5qtel1M 557601 AAGTTGCCC----TC-C------------TGTCAAAGTT-AGACCCAAAC 557632 v ---- - ------------ v i ii-i ii i C MIR#SINE/MIR 101 AACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAAC 52 chr5qtel1M 557633 TCAAGCAGTCTATCTCCCAGTCCTGTGTCCTT 557664 i i iv viiv i ii C MIR#SINE/MIR 51 CCAGGCAGTCTGGCTCCAGAGCCCGTGCTCTT 20 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.78 CpG sites = 21, Kimura (unadjusted) = 34.47 Transitions / transversions = 3.50 (21/6) Gap_init rate = 0.07 (7 / 102), avg. gap size = 4.14 (29 / 7) 221 20.00 0.00 0.00 chr5qtel1M 557562 557601 (442399) C MIRb#SINE/MIR (110) 158 119 m_b259s601i3 10227 chr5qtel1M 557562 TATCATCCCCATTTCACAAGTGAAGAAGAGGAGGCTCAGA 557601 i i ii i ivv C MIRb#SINE/MIR 158 TATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGA 119 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 24.17 CpG sites = 6, Kimura (unadjusted) = 24.17 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 chr5qtel1M 557883 557899 (442101) (C)n#Simple_repeat 1 17 (0) m_b259s252i4 10228 chr5qtel1M 557883 CCCCCCCCCCCCCCCCC 557899 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCC 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 299 35.02 4.32 1.40 chr5qtel1M 559053 559191 (440809) C L2a_3end#LINE/L2 (11) 506 364 m_b259s601i6 10229 chr5qtel1M 559053 CAATAAGCATTTATTAAGCACCTACTACATACCAGGCAAGGGGTTAAATG 559102 i ii i i ii i vv vvi iii C L2a_3end#LINE 506 CAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGCG 457 chr5qtel1M 559103 CTAGGGGTATA--AAT---CCAGAAGGAC-ATACTCCCTGACTTTGCTGA 559146 i i i -- i --- v i vi - v v v i iiiv C L2a_3end#LINE 456 CTGGGGATACAGCAGTGAACAAAACAGACAAAAGTCCCTGCCCTCATGGA 407 chr5qtel1M 559147 ATTTACATTTTTATCACGAGGGATATTTATAATATATAGATATAT 559191 ii i vi --v i v ivv i v i i v C L2a_3end#LINE 406 GCTTACATTCTAGT--GGGGGGAGACAGACAATAAACAAATAAAT 364 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 47.10 CpG sites = 31, Kimura (unadjusted) = 50.11 Transitions / transversions = 1.82 (31/17) Gap_init rate = 0.04 (5 / 138), avg. gap size = 1.60 (8 / 5) 312 36.19 4.76 0.00 chr5qtel1M 559053 559157 (440843) C L2b_3end#LINE/L2 (11) 455 346 m_b259s601i5 10229 chr5qtel1M 559053 CAATAAGCATTTATTAAGCACCTACTACATACCAGGCAAGGGGTTAAATG 559102 i ii i i i iii i ?vv v i iii C L2b_3end#LINE 455 CAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCG 406 chr5qtel1M 559103 CTAGGGGTATA-----AATCCAGAAGGACATACTCCCTGACTTTGCTGAA 559147 i i i -----i v v vi ?iiv v i ii v i C L2b_3end#LINE 405 CTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGGAG 356 chr5qtel1M 559148 TTTACATTTT 559157 i i v i C L2b_3end#LINE 355 CTCACAGTCT 346 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 49.54 CpG sites = 28, Kimura (unadjusted) = 56.59 Transitions / transversions = 2.80 (28/10) Gap_init rate = 0.01 (1 / 104), avg. gap size = 5.00 (5 / 1) 25 26.92 1.09 4.49 chr5qtel1M 559196 559287 (440713) (AT)n#Simple_repeat 1 89 (0) m_b259s252i5 10230 chr5qtel1M 559196 ATATACTCATATATGACATATATACATATGAATGAAGCACATATATATAA 559245 - - - i i iv - vii i v (AT)n#Simple_ 1 ATATA-T-ATATAT-ATATATATATATATATAT-ATATATATATATATAT 46 chr5qtel1M 559246 AT-TCAACAATTACATATATATGTATAAATATATATGTAAATA 559287 - vv i vv i i v i v (AT)n#Simple_ 47 ATATATATATATATATATATATATATATATATATATATATATA 89 Matrix = Unknown Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.05 (5 / 91), avg. gap size = 1.00 (5 / 5) 33 25.34 1.15 0.00 chr5qtel1M 560289 560375 (439625) (GATG)n#Simple_repeat 1 88 (0) m_b259s252i6 10231 chr5qtel1M 560289 GATGGGTGGATGAATAAATGGATAGAT-GAGTGATGGGTGGATGAGTAGA 560337 i i ii i - vv i ii i (GATG)n#Simpl 1 GATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGA 50 chr5qtel1M 560338 TGGGTAGATAGATGAAAGGATAGATTGATGGATGGATG 560375 i i i i v i v (GATG)n#Simpl 51 TGGATGGATGGATGGATGGATGGATGGATGGATGGATG 88 Matrix = Unknown Transitions / transversions = 3.50 (14/4) Gap_init rate = 0.01 (1 / 86), avg. gap size = 1.00 (1 / 1) 636 20.97 0.00 0.00 chr5qtel1M 560446 560569 (439431) MIR#SINE/MIR 74 197 (65) m_b259s601i7 10232 chr5qtel1M 560446 TTACCAGCTGAGTGACCCTGGGCAAGATGCTAAATTTCTCTCTGTTTTAG 560495 i v i v i v ii v ii i MIR#SINE/MIR 74 TTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAG 123 chr5qtel1M 560496 TTTCTGCATCTGGAAAATGGGGATAATAATAGCATCTATTTCCTATAGTT 560545 iv v i i ii v vi MIR#SINE/MIR 124 TTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTCATAGGGTT 173 chr5qtel1M 560546 GTTGTGAGGATATAATGAGATAGT 560569 vv v i MIR#SINE/MIR 174 GTTGTGAGGATTAAATGAGTTAAT 197 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 24.95 CpG sites = 15, Kimura (unadjusted) = 24.95 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.00 (0 / 123), avg. gap size = 0.0 (0 / 0) 237 29.80 5.93 3.31 chr5qtel1M 561263 561380 (438620) L1ME2z_3end#LINE/L1 433 553 (638) m_b259s551i0 10233 chr5qtel1M 561263 TGTGCAAAACTATTTCTACC--CTTTGTTGA-AGTGGCCAAAAATCGGAA 561309 i i v i iv v -- i v - i i ii L1ME2z_3end#L 433 TGTACAAGAATGTTCATAGCAGCTTTATTCATAATAGCCAAAAACTGGAA 482 chr5qtel1M 561310 TCGAAG----GGTGTGCTCATAAATTGAAGACTGCATGAACAAGTTATGG 561355 v -- ---- --i v iv i v v i ii i L1ME2z_3end#L 483 AC--AGCCCAGGTGT--CCATCAACAGGAGAATGGATAAACAAACTGTGG 528 chr5qtel1M 561356 CATATAAGTGTGATGGGATACTATT 561380 i vvi iii i i L1ME2z_3end#L 529 TATATTCATACAATGGAATACTACT 553 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.02 CpG sites = 23, Kimura (unadjusted) = 40.02 Transitions / transversions = 2.09 (23/11) Gap_init rate = 0.06 (7 / 117), avg. gap size = 1.57 (11 / 7) 18 22.00 3.77 0.00 chr5qtel1M 561807 561859 (438141) (TATTT)n#Simple_repeat 1 55 (0) m_b259s252i7 10234 chr5qtel1M 561807 TATTTTATTTTATTTTA-GTTA-ATTAATTAATTTTCTATTATAGCTTTT 561854 -v -v v v v v vviv (TATTT)n#Simp 1 TATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTT 50 chr5qtel1M 561855 TATTT 561859 (TATTT)n#Simp 51 TATTT 55 Matrix = Unknown Transitions / transversions = 0.11 (1/9) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.00 (2 / 2) 14 22.50 0.00 6.12 chr5qtel1M 561810 561861 (438139) (TTTA)n#Simple_repeat 1 49 (0) m_b259s252i8 10234 chr5qtel1M 561810 TTTATTTTATTTTAGTTAATTAATTAATTTTCTATTATAGCTTTTTATTT 561859 - - v v v v v i - vi v (TTTA)n#Simpl 1 TTTA-TTTA-TTTATTTATTTATTTATTTATTTATT-TATTTATTTATTT 47 chr5qtel1M 561860 AT 561861 (TTTA)n#Simpl 48 AT 49 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.00 (3 / 3) 14 7.28 6.90 0.00 chr5qtel1M 561988 562016 (437984) (AAGTAT)n#Simple_repeat 1 31 (0) m_b259s252i9 10235 chr5qtel1M 561988 AAGTTTAAGT-TAAGTATAA-AATAAGTATA 562016 v - -v (AAGTAT)n#Sim 1 AAGTATAAGTATAAGTATAAGTATAAGTATA 31 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.07 (2 / 28), avg. gap size = 1.00 (2 / 2) 1558 26.48 3.85 3.03 chr5qtel1M 562292 562914 (437086) C L1ME4a_3end#LINE/L1 (232) 639 12 m_b259s551i1 10236 chr5qtel1M 562292 CCTGCTCATTTCACTCAGCATCAGTTCATGTAAATCTCTTCAGGCCATTC 562341 iv i i i vv viv i iii v i - C L1ME4a_3end#L 639 CCTGCTTTTTTCACTTAACATTATATCATGAGCATTTTCCCATGTCATT- 591 chr5qtel1M 562342 TGAAATCATCCTGTTGG-----TCATTTCTTACAGAACAATAATATTCCA 562386 -- - i - i i----- ? i v ii vvvv C L1ME4a_3end#L 590 --AAAT-ATTCT-TCGAAAACATNATTTTTAATGGCTGCATAATATTCCA 545 chr5qtel1M 562387 TAATATTCATATACCATAATTTATTCAGCCATTCTCCAACTGATGGGCAT 562436 v? vv i i i ? i v i v i C L1ME4a_3end#L 544 TTNTATGGATGTACCATAATTTATTTAACCANTCCCCTATTGTTGGACAT 495 chr5qtel1M 562437 CTACTACTCAGTTTTCAGTTTCTGTCCAGTACTAAGAGGGTTGCCACAAA 562486 i v-ii -- i i i vv i v iv v iv i v ii C L1ME4a_3end#L 494 TTAG-GTT--GTTTCCAATTTTTCGCTATTATAAATAATGCTGCGATGAA 448 chr5qtel1M 562487 CATTCTTGCATATAGAGGTCTCTTTCC-CTTCTTTAAG-ATTTCTTTGGG 562534 i i i i -- i v ? - v i i v- i i C L1ME4a_3end#L 447 CATCCTTGTACATAAA--TCTTTGTNCACATCTCTGATTATTTCCTTAGG 400 chr5qtel1M 562535 ATATAAGTCC----AGTAGATCTGCTAGATCAAAGGGTATGCACAGTTTG 562580 - v ---- i vi i i i ? v v C L1ME4a_3end#L 399 ATA-AATTCCTAGAAGTGGAATTACTGGGTCAAAGGGTATGNACATTTTT 351 chr5qtel1M 562581 ATAACTTTTTGA-GCATCACT-CCAAATTGCTCTCCAGAATGGTTGGATG 562628 - ivi -i - i - i v v iv C L1ME4a_3end#L 350 A-AGGCTTTTGATACAT-ATTGCCAAATTGCCCTCCAGAAAGGTTGTACC 303 chr5qtel1M 562629 TATTCACAATTCCACCAACAATATATTAGTGTCCCCATTTTCCCGCATCC 562678 v i v i i i i v v v i i? i i C L1ME4a_3end#L 302 AATTTACACTCCCACCAGCAGTGTATGAGAGTGCCCGTTTCNCCACACCC 253 chr5qtel1M 562679 CCTCCAACATTCCGCATTGTCTTTCCCTGTCATCTTAGCCAATCTGACAG 562728 i v i vv i i vv ii vvv v i i C L1ME4a_3end#L 252 TCGCCAACACTGGGTATTATCAATCTTTTAAATCTTTGCCAATTTGATAG 203 chr5qtel1M 562729 GTGTGTAGTGGTATCTCAGAGTTGTCTTAATTTGCATTTCTCTGATTAAT 562778 viv i vv i i v C L1ME4a_3end#L 202 GTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCTTTGATTACT 153 chr5qtel1M 562779 AATGATTTGGAGCTTCTTTTCATATGGCTAGAAATAGTTTCAATTTC--- 562825 i vv v i v ? vi vviiivi vv --- C L1ME4a_3end#L 152 AGTGAGGTTGAACATNTTTTCATATGTTTATTGGCCATTTGTATTTCTTC 103 chr5qtel1M 562826 -TTTGAGAATTGTCTGTTCATATCCTTTGATCATTTATCAATTGGAGAAT 562874 - v i vi v v i vi C L1ME4a_3end#L 102 TTTTGTGAATTGTCTGTTCATGTCCTTTGCCCATTTTTCTATTGGGGTGT 53 chr5qtel1M 562875 --GGCTTGATTTCTTATAAAT-----AGAGTCAATTCTCTATATATT 562914 -- v -- vi ----- ----i i C L1ME4a_3end#L 52 TCGTCTT--TTTCTTATTGATTTGTAAGAG----CTCTTTATATATT 12 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.26 CpG sites = 89, Kimura (unadjusted) = 33.78 Transitions / transversions = 1.25 (89/71) Gap_init rate = 0.05 (29 / 622), avg. gap size = 1.48 (43 / 29) 1558 25.71 2.93 3.30 chr5qtel1M 562376 562922 (437078) C L1ME3G_3end#LINE/L1 (376) 548 4 m_b259s551i2 10236 chr5qtel1M 562376 ATAATATTCCATAATATTCATATACCATAATTTATTCAGCCATTCTCCAA 562425 i i vv i i i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr5qtel1M 562426 CTGATGGGCATCTACTACTCAGTTTTCAGTTTCTGTCCAGTACTAAGAGG 562475 i i i v-ii -- i i i vv i v v v iv C L1ME3G_3end#L 498 TTGATGGACATTTAG-GTT--GTTTCCAATTTTTCGCTATTACAAACAAT 452 chr5qtel1M 562476 GTTGCCACAAACATTCTTGCATATAGAGGTCTCTTT---CCCTTCTTTAA 562522 i v ii i i i ---- i? i --- v v v vii C L1ME3G_3end#L 451 GCTGCAATGAACATCCTTGTACAT----GCNTCCTTGTGCACATGTGCGA 406 chr5qtel1M 562523 G-ATTTCTTTGGGATATAAGTCCAG---TAGATCTGCTAGATCAAAGGGT 562568 - ? i v v?i ? --- i vi i i C L1ME3G_3end#L 405 GTATTTCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGT 356 chr5qtel1M 562569 ATGCACAGTTTGATAACTTTTTGAGCATCACT-CCAAATTGCTCTCCAGA 562617 i v i -- i vvv - - - i i C L1ME3G_3end#L 355 ATGCGCATTTTAA--ATTTTAATAG-AT-ACTGCCAAATTGCCCTCCAAA 310 chr5qtel1M 562618 ATGGTTGGATGTATTCACAATTCCACCAACAATATATTAGTGTCCCCATT 562667 ? i v ivv i v i i i i v v v i C L1ME3G_3end#L 309 ANGGCTGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTT 260 chr5qtel1M 562668 TTCCCGCATCCCCTCCAACATTCCGCATTGTCTTTCCCTGTCATCTTAGC 562717 i i i i v i ?vii i vv? ii vvv i v C L1ME3G_3end#L 259 TCCCCACACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGC 210 chr5qtel1M 562718 CAATCTGACAGGTGTGTAGTGGTATCTCAGAGTTGTCTTAATTTGCATTT 562767 ii viv i vv i C L1ME3G_3end#L 209 CAATCTGATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTT 160 chr5qtel1M 562768 CTCTGATTAATAATGATTTGGAGCTTCTTTTCATATGGCTAGAAATAGTT 562817 i v i vv v v vi vviiivi C L1ME3G_3end#L 159 CCCTGATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATT 110 chr5qtel1M 562818 TCAATTTC----TTTGAGAATTGTCTGTTCATATCCTTTGATCATTTATC 562863 vv ---- i v i vi v C L1ME3G_3end#L 109 TGTATTTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTC 60 chr5qtel1M 562864 AATTGGAGAATGGCTTGATTTCTTATAAA----TAGAGTCAATTCTCTAT 562909 v iv-- v -- vi ---- i--- i i C L1ME3G_3end#L 59 TATTGGGT--TGTCTT--TTTCTTATTGATTTGTAGG---AGTTCTTTAT 17 chr5qtel1M 562910 ATATTTTGGAAAT 562922 i v C L1ME3G_3end#L 16 ATATTCTGGATAT 4 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 31.69 CpG sites = 76, Kimura (unadjusted) = 32.59 Transitions / transversions = 1.27 (76/60) Gap_init rate = 0.04 (24 / 546), avg. gap size = 1.42 (34 / 24) 501 32.00 5.09 4.52 chr5qtel1M 562778 563327 (436673) C L1P3_orf2#LINE/L1 (0) 3294 2742 m_b259s551i3 10236 chr5qtel1M 562778 TAATGATTTGGAGCTTCTTTTCATATG---GCTAG------AAATAGTTT 562818 i --- i --- i i ------ ivi C L1P3_orf2#LIN 3294 TGATGAT---GAGCTTTTTTTCATATGTTTGTTGGCCGCATAAATGTCTT 3248 chr5qtel1M 562819 CAATTTCTTTGAGAATTGTCTGTTCATATCCTTTGATCATTTATCAATTG 562868 -----i v i vi i v ii - C L1P3_orf2#LIN 3247 C-----TTTTGAGAAGTGTCTGTTCATATCCTTCGCCCACTTTTTGA-TG 3204 chr5qtel1M 562869 GAGAATGGCTTG---ATTTCTTATAAATAGAGTCAA-TTCTCTATATATT 562914 i -- v i ---v i vviv i - ii i v C L1P3_orf2#LIN 3203 GGG--TTGTTTGTTTTTTTCTTGTAAATTTGTTTAAGTTCCTTGTAGATT 3156 chr5qtel1M 562915 TTGGAAATGAGGCCTTTATCAGAACCTTTGATTGTAAAAATGTTTTCCCC 562964 i v v v i vvvv v i v i v C L1P3_orf2#LIN 3155 CTGGATATTAGCCCTTTGTCAGATGGATAGATTGCAAAAATTTTCTCCCA 3106 chr5qtel1M 562965 GTTTATTGCTTCCCTTCTAATCGTGTCTGCAT--TAGTTTTGTT---TGT 563009 v i i v v v vi v i---- - -- iv --- C L1P3_orf2#LIN 3105 TTCTGTAGGTTGCCTGTTCAC----TCTG-ATGATAGTTTCTTTTGCTGT 3061 chr5qtel1M 563010 ATAAAAACTTTTCAATTTGATATAATCAAAATTTTCTATTTTGTGATCAG 563059 ii i i i i i i vvi vv v v v vvv iv C L1P3_orf2#LIN 3060 GCAGAAGCTCTTTAGTTTAATTAGATCCCATTTGTCAATTTTGGCTTTTG 3011 chr5qtel1M 563060 TAATGATCTCTAGTTCTTCTTTGGTCATAAATTGCTTCCTCTTCCACAGG 563109 viiv iv vv vv vi i i v vi v i v v vi v C L1P3_orf2#LIN 3010 TTGCCATTGCTTTTGGTGTTTTAGTCATGAAGTCTTTGCCCATGCCTATG 2961 chr5qtel1M 563110 T-CTGAGAAGTAAACTATCCT--GTGTTCCTCTAATTTATTTATAATCTC 563156 - ivi --- vv -- v i ivv v ii i i C L1P3_orf2#LIN 2960 TCCTGAATGGTA---TTGCCTAGGTTTTCTTCTAGGGTTTTTATGGTTTT 2914 chr5qtel1M 563157 ATTCTTTATGCCTACGTCATGAACCCATTTTGATCTTATCTTGGAATATG 563206 vvii i ii v v v i i vi v i v v v C L1P3_orf2#LIN 2913 AGGTCTTACGTTTAAGTCTTTAATCCATCTTGAGTTAATTTTTGTATAAG 2864 chr5qtel1M 563207 GTGTTAAGTGTGAGT-CAATGCCTAGTTTCTGCCATA---CTATTTCCAT 563252 v i viv i - i vi viv - --- --v v C L1P3_orf2#LIN 2863 GTGTAAGGAAGGGGTCCAGTTTCAGTTTTCTG-CATATGGCTA--GCCAG 2817 chr5qtel1M 563253 TTTTCCCAGCAATTTTTGTCAAACAGTGAGTTCTTATCCCAAAAGCTGGG 563302 i viv i i i v i i - v vv --v C L1P3_orf2#LIN 2816 TTTTCCCAACACCATTTATTAAATAGGGAATCCTT-TCCCCATTGCT--T 2770 chr5qtel1M 563303 GTCTTTG---GATTTGTCAAACACTAGA 563327 i --- i v ii C L1P3_orf2#LIN 2769 GTTTTTGTCAGGTTTGTCAAAGATCAGA 2742 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.60 CpG sites = 82, Kimura (unadjusted) = 42.25 Transitions / transversions = 0.95 (82/86) Gap_init rate = 0.07 (36 / 549), avg. gap size = 1.47 (53 / 36) 482 29.16 5.83 4.98 chr5qtel1M 562781 563397 (436603) C L1M5_orf2#LINE/L1 (0) 3294 2673 m_b259s551i4 10236 chr5qtel1M 562781 TGATTTGGAGCTTCTTTTCATATGGCTAGAAATAGTTTCAAT---TTCTT 562827 ?v v v i vi vviiivi v? --- C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr5qtel1M 562828 T-GAGAATTGTCTGTTCATATCCTTTGATCATTTATCAATTGGA--GAAT 562874 - v v vi i vi v ?v i-- vv C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTT 3195 chr5qtel1M 562875 GGCTTGATTTCTTATAAA----TAGAGTCAATTCTCTATATATTTTGGAA 562920 v -- ? vi ---- i--- i i i v C L1M5_orf2#LIN 3194 GTCTT--TTTNTTATTGANTTGTAGG---AGTTCTTTATATATTCTGGAT 3150 chr5qtel1M 562921 ATGAGGCCTTTATCAGA-ACCTTTGATTGTAAAAATGTTTTCCCCGTTTA 562969 i v i - iv v ?- i v v i v? i i C L1M5_orf2#LIN 3149 ACGAGTCCTTTGTCAGATATATGTN-TTGCAAATATTTTCTCCCANTCTG 3101 chr5qtel1M 562970 TTGCTTCCCTTCTAATCGTGTCTGCATTAGTTTTGTTTGTATA--AAAAC 563017 v v i v -- v -i vii v iv v?v -- i v C L1M5_orf2#LIN 3100 TGGCTTGCCTTTTCAT--TTTCT-TAACGGTGTCTTTTGANGAGCAGAAG 3054 chr5qtel1M 563018 TTTTCAATTT-GATATAATCAAA-------ATTTTCTATTTTGTGATCAG 563059 i - i? i v ------- i v i i --- C L1M5_orf2#LIN 3053 TTTTTAATTTTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGGT--- 3007 chr5qtel1M 563060 TAATGATCTCTAGTTCTTCTTTGGTCATAAATTGCTTCCTCTTCCACAGG 563109 ?i v i i ivv i v i--- v ivi v v?i - C L1M5_orf2#LIN 3006 TNGTGCTTTTTGTGTCCTGTTTA---AGAAATCTTTGCCTANCCCA-AGG 2961 chr5qtel1M 563110 TCTGAGAAGTAAACTATCCTGTGTT--CCTCTA--ATTTATTTATAATCT 563155 -iv - v i v i -- i -- v -- i i C L1M5_orf2#LIN 2960 TC-ACGAAG-ATATTCTCCTATGTTTTCTTCTAGAAGTT--TTATAGTTT 2915 chr5qtel1M 563156 CATTCTTTATGCCTACGTC-ATGAACCCATTTTGATCTTATCTTGGAATA 563204 i ?ii iiii v - -i i ? vi v i v vi C L1M5_orf2#LIN 2914 TANCTTTTACATTTAGGTCTATGA-TCCATCTNGAATTAATTTTTGTGTA 2866 chr5qtel1M 563205 TGGTGTTAAGTGTGAGTCAATGCCTAGTTTCTGCCATAC-TATTTCCATT 563253 v i iv i i v?iii v i v i-v v v C L1M5_orf2#LIN 2865 TGGTGTGAGGTAGGGGTCGAGNTTCATTTTTTTCCATATGGATATCCAAT 2816 chr5qtel1M 563254 TTTCCCAGCAATTTTTGTCAAACAGTGAGTTCTTATCCCAAAAGCTGGGG 563303 v i viv ii v vvvi i vi ---- iiv C L1M5_orf2#LIN 2815 TGTTCCAGCACCATTTGTTGAAAAGACTATCCTTTCCCCA----CTGAAT 2770 chr5qtel1M 563304 T-CTTTGG---ATTTGTCAAACACTA---GAACATTAAAGTTATTGA-CT 563345 - ? ---v v ii --- ?v - v vv i v i- C L1M5_orf2#LIN 2769 TGCNTTGGCACCTTTGTCAAAAATCAANTGNCCA-TATATGTGTGGGTCT 2721 chr5qtel1M 563346 ATTT-TGTCCTTTGAACCTAACCTGTTCCACTGATCAAGTAGTCTATTTC 563394 - vv i ---- vi i v v v - i C L1M5_orf2#LIN 2720 ATTTCTGGACTCT----CTATTCTGTTCCATTGATCTATTTGTCTA-TCC 2676 chr5qtel1M 563395 TTA 563397 C L1M5_orf2#LIN 2675 TTA 2673 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.88 CpG sites = 87, Kimura (unadjusted) = 38.77 Transitions / transversions = 1.04 (87/84) Gap_init rate = 0.08 (48 / 616), avg. gap size = 1.40 (67 / 48) 185 32.50 15.82 2.08 chr5qtel1M 563428 563977 (436023) C L2#LINE/L2 (202) 2880 2257 m_b259s601i8 10237 chr5qtel1M 563428 CTTTGACCCAGAG-GACAAGAGAGAGCCGCTGGAGCTTCTTGAG--GAAG 563474 v i v - v v i - ii vv i -- i C L2#LINE/L2 2880 CTTTTACTCTGAGTGAGATGGGA-AGCCATTGGAGGGTTTTGAGCAGAGG 2832 chr5qtel1M 563475 ATGGTGATATAGT-------------TAGGAAAATC--CCTAGCAGCAAT 563509 -- i ii ------------- ii ii --i i v vi C L2#LINE/L2 2831 A--GTGACATGATCTGACTTACGTTTTAAAAGGATCACTCTGGCTGCTGT 2784 chr5qtel1M 563510 GTGAAAGCTGGGTTGGAGGAAGGGAGACTGGATGGA-GCAGGGAG-CTGG 563557 vi iiv i ii ? ii v i--- i - - ii C L2#LINE/L2 2783 GTTGAGAATAGACTGNAGGGGGGCAA---GGGTGGAAGCAGGGAGACCAG 2737 chr5qtel1M 563558 ATAATGGGGACAGAATAATGGTCCATGGAGGAGATGG-GGAGAAATGAGC 563606 v i- i vi vvii i ii v vii i- v ivv ii C L2#LINE/L2 2736 TTAG-GAGGCTATTGCAGTAATCCAGGCGAGAGATGATGGTGGCTTGGAC 2688 chr5qtel1M 563607 TGGGGTTATGCTTGTGA--GTGGAGAGGAGATGGATGA------GAAGTA 563648 ii vi viv i-- v i - vi i------ vi C L2#LINE/L2 2687 CAGGGTGGTGGCAGTGGAGGTGGTGAGAAG-TGGTCGGATTCTGGATATA 2639 chr5qtel1M 563649 TTAGGGAGGAAGAAATGAGAAGAGTTGGCCACTGG-TTGGACACCATGGG 563697 vv i v ivi v i v - iiv - ii--- C L2#LINE/L2 2638 TTTTGAAGGTAGAGCCGACAGGATTTG-CTGATGGATTGGATG---TGGG 2593 chr5qtel1M 563698 GTG--AGAGAAAGGGAAAAGTCAAGGATGAAATTGAACTT------CTGA 563739 -- i ii vviii iv ------ C L2#LINE/L2 2592 GTGTGAGAGAAAGAGAGGAGTCAAGGATGACTCCAAGGTTTTTGGCCTGA 2543 chr5qtel1M 563740 GT--CTGGGAGATTGGGG-------TAACAGAATTTAGGAAGA----GGG 563776 i-- i iv i ------- ? v iv vi ---- C L2#LINE/L2 2542 GCAACTGGAAGGATGGAGTTGCCATTNACTGAGATGGGGAAGACTGCGGG 2493 chr5qtel1M 563777 A-GAGT--GT---AGGGGAAAGATGATGAATGC--TATTGGATA------ 563812 - i-- --- i v v i v -- v i ------ C L2#LINE/L2 2492 AGGAGCAGGTTTGAGGGGGAAGATCAGGAGTTCAGTTTTGGACATGTTAA 2443 chr5qtel1M 563813 ----GCGATGTCTA-CAGGAATTTAGGT-GAAATGTCCCAAAGGCAGTTG 563856 ---- v i -i iv ii i - i vviv C L2#LINE/L2 2442 GTTTGAGATGCCTATTAGACATCCAAGTGGAGATGTCGAGTAGGCAGTTG 2393 chr5qtel1M 563857 GAAATGTAGGACTAGAACCTAGGAGAG-GATTGGGATTGAGTTTTTAAAT 563905 v iiii v i iiii i - i iv ii iivv v C L2#LINE/L2 2392 GATATACGAGTCTGGAGTTCAGGGGAGAGGTCCGGGCTGGAGATATAAAT 2343 chr5qtel1M 563906 ---------AT--GCATGGAGATAACAATTAAGTCCATGGGAGTTAATGA 563944 --------- -- iv iii v iv i v vi C L2#LINE/L2 2342 TTGGGAGTCATCAGCATATAGATGGTATTTAAAGCCATGAGACTGGATGA 2293 chr5qtel1M 563945 GTTTCCCATGAGAG---ATGT-TATAGAGAATGAAAA 563977 v iv ?v i ---i -v - i C L2#LINE/L2 2292 GATCACCNAGGGAGTGAGTGTAGATAGAGAA-GAGAA 2257 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 43.73 CpG sites = 111, Kimura (unadjusted) = 45.20 Transitions / transversions = 1.73 (111/64) Gap_init rate = 0.07 (41 / 549), avg. gap size = 2.44 (100 / 41) 238 30.93 12.37 0.00 chr5qtel1M 563999 564095 (435905) MIR#SINE/MIR 49 157 (105) m_b259s601i9 10238 chr5qtel1M 563999 TGAGTTCAAATGCTGCCCCAGATCCTTATTAGCTGTGTGACCCTAG---- 564044 i i v i v i v viv i i i ---- MIR#SINE/MIR 49 TGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 98 chr5qtel1M 564045 --------ACCTCTGCTTATCTCCATTTGCTCAACTGGATGATGAGGATC 564086 -------- viv ii vi v v v vi i v MIR#SINE/MIR 99 GTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATA 148 chr5qtel1M 564087 GTACTACTA 564095 i v v MIR#SINE/MIR 149 ATAATAGTA 157 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.08 CpG sites = 15, Kimura (unadjusted) = 40.42 Transitions / transversions = 1.00 (15/15) Gap_init rate = 0.02 (2 / 96), avg. gap size = 6.00 (12 / 2) 34 5.46 0.00 0.00 chr5qtel1M 567869 567906 (432094) (AC)n#Simple_repeat 1 38 (0) c_b259s251i0 10239 chr5qtel1M 567869 ACACACACACACACATACACACACACTCACACACACAC 567906 i v (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACAC 38 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 313 26.24 7.26 4.72 chr5qtel1M 568528 568651 (431349) MIRc#SINE/MIR 20 146 (122) m_b259s601i10 10240 chr5qtel1M 568528 GGAAAGAGCCTAACTTAAAACTGGGAGTCTGGCA--CCTGGGCTTTAGTT 568575 --- --ii v v v -- i iv i MIRc#SINE/MIR 20 GGAAAGAGC---ACT--GGACTTGGAGTCAGGAAGACCTGGGTTCGAGTC 64 chr5qtel1M 568576 CCAGACTTGCCAC--AAT--TTGGGTGATCTTGGGCACATCACTTGGCCT 568621 i vii -- v --i v i vi ii MIRc#SINE/MIR 65 CCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCT 114 chr5qtel1M 568622 CTCT---CCTTGATTGCCCGTACGTGTGAGATG 568651 --- iii -i vi iv i i MIRc#SINE/MIR 115 CTCTGAGCCTCAGTT-TCCTCATCTGTAAAATG 146 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.04 CpG sites = 21, Kimura (unadjusted) = 33.69 Transitions / transversions = 2.10 (21/10) Gap_init rate = 0.08 (10 / 123), avg. gap size = 1.50 (15 / 10) 352 26.72 6.84 0.81 chr5qtel1M 568547 568663 (431337) MIR3#SINE/MIR 32 155 (53) m_b259s601i11 10240 chr5qtel1M 568547 ACTGGGAGTCTGGC-ACCTGGGCTTTAGTTCCAGACTTGCCAC-AATT-- 568592 v v- i i i i vii - i -- MIR3#SINE/MIR 32 ACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNG 81 chr5qtel1M 568593 -TGGGTGATCTTGGGCACATCACTTGGCCTCTCT---CCTTGATTGCCCG 568638 - v i vi vi --- iii -i v MIR3#SINE/MIR 82 CTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTT-TCCT 130 chr5qtel1M 568639 TACGTGTGAGATGTTGAATTTGGAC 568663 i iv i i vv iiv MIR3#SINE/MIR 131 CATCTGTAAAATGAGGGGGTTGGAC 155 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.85 CpG sites = 20, Kimura (unadjusted) = 34.22 Transitions / transversions = 1.82 (20/11) Gap_init rate = 0.05 (6 / 116), avg. gap size = 1.50 (9 / 6) 548 30.96 3.75 5.36 chr5qtel1M 570627 571213 (428787) C L1PB4_3end#LINE/L1 (259) 644 67 m_b259s551i5 10241 chr5qtel1M 570627 TCCTGGTTCTG-CTCATTTCACTATGCATCAATT-CATGTAATTCTTTCG 570674 i v -v i vv v - v- v vi i iv v C L1PB4_3end#LI 644 TTCTGTTTCTGAGTTATTTCACTTAGGAT-AATGGCCTCCAGTTCCATCC 596 chr5qtel1M 570675 AGGTTTTTCTAAAAG-CATCCTGCCAGTTCACTTCTTATAGCACAATAGT 570723 v vi vi - vv vi - -i i i vv i C L1PB4_3end#LI 595 ATGTTGCTGCAAAAGACATGATTTCA-TTC-TTTTTTATGGCTGAGTAGT 548 chr5qtel1M 570724 ATT--ATGTTACAATTATATGCCGACACAACTTGTTCAGCCATTCCCCAA 570771 -- v ii -- i --- vi v i v v vi vi C L1PB4_3end#LI 547 ATTCCATGGTGTA--TATATACC---ACATTTTCTTTATCCAGTCATCCG 503 chr5qtel1M 570772 TCTCTGGACACCCCCCTTGACTTCCCAATCTTTGCCATGACAAAAAGAGC 570821 ivv iivvv - vv i viii v v C L1PB4_3end#LI 502 TTGATGGACACTTAGGTTGA-TTCCATATCTTTGCTATTGTGAATAGTGC 454 chr5qtel1M 570822 TGCTATAAATACCTTTTCTAT-AG-ACAAGT-TCTTTTCCTTTTCAAAAC 570868 v i ------- i- -i i - ivv v v vi i C L1PB4_3end#LI 453 TGCGATAAACA-------TACGAGTGCAGGTATCTTTTTGATATAATGAT 411 chr5qtel1M 570869 TCATTTTGTCTGTCTGTACTACATTTTGTAGTAATGGTATTGCTGGGCCA 570918 iv -i v vv v- i iii--- i v ii i C L1PB4_3end#LI 410 TTCTTTT-CCTTTGGGTAG-ATACCC---AGTAGTGGGATTGCTGGATCG 366 chr5qtel1M 570919 AAGAGTATGCACAGTTTATGCCCCTTTGAACCTAGTTCCTA-ATTGTTCT 570967 vi - iv vi v ivii iv-- i ii i - i i C L1PB4_3end#LI 365 AATGGTA-GTTCTATTTTTAGTTCTTTGAGA--AATCTCCATACTGTTTT 319 chr5qtel1M 570968 CCAGAATGGTTGGAATAGTCCACAACTCCTCCAAAAGTGTATTATTGC-C 571016 v iv v v i ii vii v v v vi i- C L1PB4_3end#LI 318 CCATAGAGGTTGTACTAATTTACATTCCCACCAACAGTGTATAAGCGTTC 269 chr5qtel1M 571017 CCAATTTTCCAT-TTCTCTCCCATATCAAAAATTTTC---CTTTTCTGTC 571062 vv i ii- i v v i vivvi i--- --- v C L1PB4_3end#LI 268 CCTTTTCTCCGCATCCTCGCCAACATCTGTTGTTTTTTGACTTTT---TA 222 chr5qtel1M 571063 ATATTAGCCAATCTGATAGGTGTGAGGTGGTACCTCGAAGTTGT--TTTT 571110 v v iv i i i i--- -- C L1PB4_3end#LI 221 ATAATAGCCATTCTGACTGGTGTAAGATGGTATCTCA---TTGTGGTTTT 175 chr5qtel1M 571111 AATTTGAATTTCTCTGATCAATAGTTAT-TTAAGACACTTTTTCATAAG- 571158 v v v v - i - i v - C L1PB4_3end#LI 174 AATTTGCATTTCTCTGATGATTAGTGATGTTGAG-CATTTTTTCATATGT 126 chr5qtel1M 571159 -AGTAAGT--TTTGT-TTTCTTCACCTGAAAACTCCCTGTTCATATCCTT 571204 -v vi i--i - v vii v vi i C L1PB4_3end#LI 125 TTGTTGGCCGCTTGTATGTCTTCTTTTGAAAAATGTCTGTTCATGTCCTT 76 chr5qtel1M 571205 TGACCATTT 571213 v i C L1PB4_3end#LI 75 TGCCCACTT 67 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.98 CpG sites = 87, Kimura (unadjusted) = 40.48 Transitions / transversions = 1.02 (87/85) Gap_init rate = 0.08 (48 / 586), avg. gap size = 1.10 (53 / 48) 751 30.07 3.14 3.80 chr5qtel1M 570747 571223 (428777) C L1ME4a_3end#LINE/L1 (341) 530 57 m_b259s551i6 10241 chr5qtel1M 570747 CACAACTTGTTCAGCCATTCCCCAATCTCTGGACACCCCCCTTGACTTCC 570796 i i i i i ? v ivi iiivvv -- i C L1ME4a_3end#L 530 CATAATTTATTTAACCANTCCCCTATTGTTGGACATTTAGGTTG--TTTC 483 chr5qtel1M 570797 CAATCTTT-GCCATGACAAAAAGAGCTGCTATAAATA-CCTTTTCTATAG 570844 i - i v i v iv v i i - v vi i C L1ME4a_3end#L 482 CAATTTTTCGCTATTATAAATAATGCTGCGATGAACATCCTTGTACATAA 433 chr5qtel1M 570845 ACAAGTTCTTTTCCTTTTCAAAACTCATTTTGTCTGTCTGTACTACATTT 570894 ----- v---- ? v v vvv i i vii iviv v i C L1ME4a_3end#L 432 A-----TCTTTG----TNCACATCTCTGATTATTTCCTTAGGATAAATTC 392 chr5qtel1M 570895 TGTAGTAATGGTATTGCTGGGCCAAAGAGTATGCACAGTTT--ATGCCCC 570942 i- v i v i i i ? v -- v i-- C L1ME4a_3end#L 391 C-TAGAAGTGGAATTACTGGGTCAAAGGGTATGNACATTTTTAAGGCT-- 345 chr5qtel1M 570943 TTTGA-ACCTAGTTCCTAATTGTTCTCCAGAATGGTTGGAATAGTCCACA 570991 - v v v v ii v v vi i ii C L1ME4a_3end#L 344 TTTGATACATATTGCCAAATTGCCCTCCAGAAAGGTTGTACCAATTTACA 295 chr5qtel1M 570992 ACTCCTCCAAAAGTGTATTATTGC-CCCAATTTTCCAT-TTCTCTCCCAT 571039 vii v iv v vv i- iv i? i-ii v v i C L1ME4a_3end#L 294 CTCCCACCAGCAGTGTATGAGAGTGCCCGTTTCNCCACACCCTCGCCAAC 245 chr5qtel1M 571040 ATCAAAAATTTTC---CTTTTCTGTCATATTAGCCAATCTGATAGGTGTG 571086 iiiiiv v --- vvi --- v i vi C L1ME4a_3end#L 244 ACTGGGTATTATCAATCTTTTAAATC---TTTGCCAATTTGATAGGTGAA 198 chr5qtel1M 571087 AGGTGGTACCTCGAAGTTGTTTTTAATTTGAATTTCTCTGATCAATAGTT 571136 ii i ivv - v i i v v C L1ME4a_3end#L 197 AAATGGTATCTCATTGTTGTTTT-AATTTGCATTTCTTTGATTACTAGTG 149 chr5qtel1M 571137 ATTTAAGACACTTTTTCATAAGAGTA--AGT--TTTGT-TTTCTTCACCT 571181 vv vii i? v vv --i i-- - vii C L1ME4a_3end#L 148 AGGTTGAACATNTTTTCATATGTTTATTGGCCATTTGTATTTCTTCTTTT 99 chr5qtel1M 571182 GAAAACTCCCTGTTCATATCCTTTGACCATTTATCATTTGGG 571223 vi i vi i v v vv C L1ME4a_3end#L 98 GTGAATTGTCTGTTCATGTCCTTTGCCCATTTTTCTATTGGG 57 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.32 CpG sites = 73, Kimura (unadjusted) = 39.69 Transitions / transversions = 1.12 (73/65) Gap_init rate = 0.06 (28 / 476), avg. gap size = 1.18 (33 / 28) 543 32.40 3.05 1.67 chr5qtel1M 571628 571922 (428078) C L1ME4c_3end#LINE/L1 (190) 640 342 m_b259s551i7 10242 chr5qtel1M 571628 ATTCTGCTCACTTCACTTA-CATCAGTTTATGT---CTTTCCACGTTTTT 571673 ivi - i vv i iv---i i vi C L1ME4c_3end#L 640 ATTCTGCTTTTTTCACTTAACATTATATCATAAACATTTTCCATGTTGCT 591 chr5qtel1M 571674 CTGAAATCAGACCAT--TCATCATTTCTTATAGAACAATAATATTCCATA 571721 viiv i v--i -- i i v i vvvv v C L1ME4c_3end#L 590 ACATAGTCT--TCATAATTATCATTTTTAATGGCTGCATAATATTCCATC 543 chr5qtel1M 571722 ACATACATATACCATAACTTATTTAGTCATTCCCCAGCTGATGGGCATCC 571771 ivi ?v i i i ii vii v i ii C L1ME4c_3end#L 542 GAGTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTT 493 chr5qtel1M 571772 ACTCAGTTTCCAGTTTCTTACCACTATATAAAGGACCGCCACAAACATTT 571821 vviv i i ii i i v v ivi i v ii i C L1ME4c_3end#L 492 AGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCT 443 chr5qtel1M 571822 TTGCACATGTGGGTCCCTTTCCCTCTTTT---TTGATCTCTTTGGGATAT 571868 i ii i i -- ii i --- - i i i v C L1ME4c_3end#L 442 TCGTGCATATAG--CTTTTTCCTTCTTTTGAATT-ATTTCCTTAGGATAA 396 chr5qtel1M 571869 AAGCCCAGTAAAGACATTTCTGGATCACAAGGTATACACAGTTTTATAAC 571918 vv v iv iv v i v i iv v ii C L1ME4c_3end#L 395 ATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGC 346 chr5qtel1M 571919 CCTT 571922 i C L1ME4c_3end#L 345 TCTT 342 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.97 CpG sites = 59, Kimura (unadjusted) = 44.62 Transitions / transversions = 1.69 (59/35) Gap_init rate = 0.03 (9 / 294), avg. gap size = 1.56 (14 / 9) 26 3.51 7.35 7.35 chr5qtel1M 572697 572764 (427236) (AATTAGA)n#Simple_repeat 1 68 (0) m_b259s252i10 10243 chr5qtel1M 572697 AATTAGAAATTAGAATTTTAGAATTTAGAAAATTAGAAATTTAG-AATT- 572744 -v v - - - - (AATTAGA)n#Si 1 AATTAGAAATTAGAA-ATTAGAAATTAG-AAATTAGAAA-TTAGAAATTA 47 chr5qtel1M 572745 --AATTAGAAAAATTAG-AATTA 572764 -- -- - (AATTAGA)n#Si 48 GAAATTAG--AAATTAGAAATTA 68 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.13 (9 / 67), avg. gap size = 1.11 (10 / 9) 244 34.62 3.76 3.39 chr5qtel1M 572802 573360 (426640) C L1P3_orf2#LINE/L1 (2589) 705 145 m_b259s551i8 10241 chr5qtel1M 572802 TAATTTTATTGCATTATGATCTCAGAAGTATGCATTTAATAATTT--GAT 572849 v i i i v iii- iv v v i -- v C L1P3_orf2#LIN 705 TAATTTGATTGCACTGTGGTCTGAGAGAC-TGTTTGTTATGATTTCCGTT 657 chr5qtel1M 572850 TTTCTGCATTGTTTGTGAGATTTTTAAAGTCCTAATACATAATCAGTTTT 572899 i i vvi v iii v v vv v v ii ii i C L1P3_orf2#LIN 656 CTTTTGCATTTGCTGAGGAGTGTTTTACTTCCAATTATGTGGTCAATTTT 607 chr5qtel1M 572900 TGTGGAGGTGTCATGTGCCATTGAGAAAATGGTATATTCCTTTTCATTCC 572949 v viv i iv v ii i vv - v v iv C L1P3_orf2#LIN 606 AGAATAAGTGCGATGTGGCGCTGAGAAGAATGTATATTC-TGTTGATTTG 558 chr5qtel1M 572950 CCTTC-AGTTTTCTCTAGGAATCTATCATATCATATTTTTCTAAAACTAT 572998 vvv v- vv v ivi i vi vvv vv i i i iv C L1P3_orf2#LIN 557 GGGTGGAGAGTTCTGTAGATGTCTATTAGGTCCGCTTGGTCCAGAGCTGA 508 chr5qtel1M 572999 ATTCATCTCTTTAAC-TTTTTGTTTATGTTATG----GTTAGATTTATCT 573043 i vv i v i- ii v v v ---- - i i C L1P3_orf2#LIN 507 GTTCAAGTCCTGAATATCCTTGTTAATTTTCTGTCTCGTT-GATCTGTCT 459 chr5qtel1M 573044 AGTTCTGAAAGGGGAAAGTAGAGGTCTTCCATTAATATACTTTTACTGTC 573093 i vi v v iiv vi i i i v vv v vivv C L1P3_orf2#LIN 458 AATATTGACAGTGGGGTGTTAAAGTCTCCCACTATTATTGTGTGGGAGTC 409 chr5qtel1M 573094 TA-TTTTCTCATGTAATTTATTTGGTTTTTCCTTTAAAAATTTGGATGC- 573141 -v i i- iv ivi vi vvi v vi i i - C L1P3_orf2#LIN 408 TAAGTCTCTT-TGTAGGTCTCTAAGAACTTGCTTTATGAATCTGGGTGCT 360 chr5qtel1M 573142 CATACAATTTAGTGCATACATGTTTAGTTTTGATA-TTA------CTTGA 573184 v ii - vi i i ---- - ------ - C L1P3_orf2#LIN 359 CCTGTA-TTGGGTGCATATATATTTAG----GATAGTTAGCTCTTCTTG- 316 chr5qtel1M 573185 TTGTATGTAGTTCCTTTTAGGAAAATGTAGTTTCCTTGCTTGTCTTTAAT 573234 i vv -- i vv vv i vi vi --- C L1P3_orf2#LIN 315 TTGCATTGA--TCCCTTTACCATTATGTAATGCCCTTCTTTGTCTTT--- 271 chr5qtel1M 573235 ATTAGGTTTATTTTGGCTT----TTATTTTTGTCTGGAAGCATGATTGCT 573280 - v i i v v i ---- ivv i v ii vi v v C L1P3_orf2#LIN 270 -TTTGATCTTTGTTGGTTTAAAGTCTGTTTTATCAGAGACTAGGATTGCA 222 chr5qtel1M 573281 ACTCTTGCTTTTTAAAAAAATTCAGTTGGTGCATAACTGATTCTGCTCTA 573330 i i vvvivvv i v v vvi --- ?i v i C L1P3_orf2#LIN 221 ACCCCTGCTTTTTTTTGCTTTCCATTTGCTTGGTAA---ATNTTCCTCCA 175 chr5qtel1M 573331 GCCCTTTATCTTTAGTCTCTGTGTCTCTTT 573360 v i v i v v C L1P3_orf2#LIN 174 TCCCTTTATTTTGAGCCTATGTGTGTCTTT 145 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 46.42 CpG sites = 87, Kimura (unadjusted) = 47.09 Transitions / transversions = 0.87 (87/100) Gap_init rate = 0.05 (28 / 558), avg. gap size = 1.43 (40 / 28) 357 26.63 7.29 3.66 chr5qtel1M 573119 573461 (426539) C L1MC4_5end#LINE/L1 (0) 2555 2201 m_b259s551i9 10241 chr5qtel1M 573119 TTTTCCTTTAAAAATTTGGATGCCATACAATTTAGTGCATACATGTTTAG 573168 v v ?v ? i? iiv i ? i v C L1MC4_5end#LI 2555 TTTTGCTTTATAAANGTGGNTGCTNTGTTATTTGGTGCATANATATTTAT 2506 chr5qtel1M 573169 TTTTGATATTACTTGATTGTATGTAGTTCCTTTTAGGAAAATGTAGTTTC 573218 vv v vv v ivi v ??? i ?v vv iv i v? C L1MC4_5end#LI 2505 AATTGTTATATCTTCATTGTGAATTGNNNCCTTTANCATTATAAAATGNC 2456 chr5qtel1M 573219 CTTGCTTGTCT---TTAATATTAGGTTTATTTTGGCTTTTATTTTTGTCT 573265 vi --- ii --v i?i iv? i i - C L1MC4_5end#LI 2455 CTTCTTTGTCTCNTTTAATGCT--TTTTGNCTTGAANTCTACTTT-GTCT 2409 chr5qtel1M 573266 GGAAGCATGATTGCTACTCTTGCTTTTTAAAAAAATTCAGTTGGTGCATA 573315 iv v? v? v i vi -----iv vi -- v i C L1MC4_5end#LI 2408 GATATNAANATTGCAACCCTTCTTTTTT-----GTTTCCATT--TGCCTG 2366 chr5qtel1M 573316 ACTGATTCTGCTCTAGCCCTTTATCTTTAGTCTCTGTG--TCTCTTTTTC 573363 iivv ii v? i v i i i i v -- v i C L1MC4_5end#LI 2365 GTATATCTTTNTCCATCCCTTTATTTTCAGCCTTTCTGAATCACTTTTTT 2316 chr5qtel1M 573364 ---ACATGTTTCTTGTAAACA--ATATA--TTGGTTTTG-TCTGTTAAC- 573404 ---iii i ? -- -- v i - i ? ? ? - C L1MC4_5end#LI 2315 TAGGTGTGTCTCTTGTANACAGCATATAGTTGGGTCTTGCTTTNTNANCC 2266 chr5qtel1M 573405 ----------TGCTTCTGTTTT-ATACATGAATTAAGCCCATTCACACTG 573443 ---------- vi ? v - ?vi i ? i i - C L1MC4_5end#LI 2265 AANTTGAAAATCTTTNTCTTTTAATNGGTGAGTTNAGCCCATTTACATT- 2217 chr5qtel1M 573444 ACCATTATGATTACTAAT 573461 --i i?v ? i C L1MC4_5end#LI 2216 --TATTGNTATNACTGAT 2201 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.81 CpG sites = 48, Kimura (unadjusted) = 36.81 Transitions / transversions = 1.20 (48/40) Gap_init rate = 0.06 (21 / 342), avg. gap size = 1.81 (38 / 21) 251 21.43 15.32 2.14 chr5qtel1M 573367 573490 (426510) C L1MEj_5end#LINE/L1 (18) 2142 2003 m_b259s551i10 10241 chr5qtel1M 573367 TGTTTCTTGTAAACA--ATATA--TTGGTTTTGTCTGTTAACT------- 573405 -- -- v i v i------- C L1MEj_5end#LI 2142 TGTTTCTTGTAAACAGCATATAGCTGGGTTTTGTTTTTTAACCCAATCTG 2093 chr5qtel1M 573406 ---GCTTCTGTTTTATACAT----GAATTAAGCCCATTCACACTGACCAT 573448 --- ii i v - ---- v i i v vii C L1MEj_5end#LI 2092 ACAGTCTCTGTCTTTTA-ATGGGAGAATTCAGTCCATTCACATTTAGTGT 2044 chr5qtel1M 573449 TATGATTACTA-ATTGTGTATTTCCTTCCCTCCATCCTGCTTT 573490 v i i iv - i - - iv i i i C L1MEj_5end#LI 2043 AACGACTGATATACT-TG-ATTTTATTCCTTCCATCTTACTTT 2003 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 24.84 CpG sites = 17, Kimura (unadjusted) = 25.98 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.07 (9 / 123), avg. gap size = 2.44 (22 / 9) 14 16.54 2.94 0.00 chr5qtel1M 573613 573646 (426354) (CTCTT)n#Simple_repeat 1 35 (0) m_b259s252i12 10244 chr5qtel1M 573613 CTCTTCTCTTCTC-CCACTTCTCTTTTGTTTTCTT 573646 -i v i v i (CTCTT)n#Simp 1 CTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTT 35 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 235 25.35 8.05 7.33 chr5qtel1M 574516 574664 (425336) C L1M3_orf2#LINE/L1 (135) 3153 3004 m_b259s551i11 10245 chr5qtel1M 574516 TATCTTGGATACCAAGCTCTTAACAGAGAAAT---TTGCTATGAAACTTT 574562 i ii v i v v v --- ---- iv C L1M3_orf2#LIN 3153 TATTTTGGATATTAACCCCTTATCAGATATATGGTTTGC----AAATATT 3108 chr5qtel1M 574563 TTTTCCC-TCTCAAAGACTTCCCTTCTTATCCTAAAGGTATTGAT-GTTG 574610 i - ii iv i- v i i ii i------ - v C L1M3_orf2#LIN 3107 TTCTCCCATTCCGTAGG-TTGCCTTTTCACTCTG------TTGATTGTTT 3065 chr5qtel1M 574611 TCTCTGC-----AGAAGCTTTTCAGTTTCAAGTAAT--CAGTTATTTATT 574653 i i ----- i v v i -- v i i C L1M3_orf2#LIN 3064 CCTTTGCTGTGCAGAAGCTTTTTAGTTTGATGTAGTCCCACTTGTCTATT 3015 chr5qtel1M 574654 TTATTTTTTGT 574664 vvi C L1M3_orf2#LIN 3014 TTTGCTTTTGT 3004 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 30.76 CpG sites = 22, Kimura (unadjusted) = 31.86 Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.11 (16 / 148), avg. gap size = 1.44 (23 / 16) 295 29.54 17.44 1.23 chr5qtel1M 574692 574972 (425028) L3#LINE/CR1 3769 4094 (5) m_b259s601i12 10246 chr5qtel1M 574692 TGTCTCCAAGAATTGAAAGGTCCAGCTGATGGAGTAGGAAAGAGA--TGT 574739 i iv vi v iiv vvi iv i vv -- i L3#LINE/CR1 3769 TGTCTTCAAATATTTGAAGGGCTGTCATGTGGAAGAGGGATTAGACTTAT 3818 chr5qtel1M 574740 GCTGATTAGCCCCAAAAGGGGCAGAATTATGG-----GAGGGGACAGT-- 574782 v vv i i i -- i v i----- i v - -- L3#LINE/CR1 3819 TCTGTGTGGCTCCAGA--GGGCAGAACTAGGACCAATGGGTGGA-AGTTA 3865 chr5qtel1M 574783 CTAAGAGCCATATTTAGGTTC----TGGG--------TCCT--------- 574811 vii v v v i ---- ii -------- i --------- L3#LINE/CR1 3866 CAGGGAGGCAGATTTCGGCTCAATATAAGGAAGAACTTTCTAACAATCAG 3915 chr5qtel1M 574812 -GCTATCCCAGAGTGGGAGAGGCTGC-TGGAGTGG-GGTGGCCTTCCTCC 574858 - i v i i i vi - v ? v -i iv i - v L3#LINE/CR1 3916 AGCTGTCCAAAAATGGAATGGGCTGCCTCGNGAGGTAGTGAGCTCCC-CG 3964 chr5qtel1M 574859 TCTTTGGAAGTCTTCAGGCAGAGGCTGGATGACAGCTTG---GGG--GCT 574903 vi i v i vi --- -- i L3#LINE/CR1 3965 TCACTGGAGGTGTTCAAGCAGAGGCTGGATGACCACTTGTCAGGGATGTT 4014 chr5qtel1M 574904 GTG-------TTCCCTTGGTGTCCGGGA---TGGGCTAGAC-ACCCCTGA 574942 i------- iviiv vvi --- i i- i i L3#LINE/CR1 4015 GTAGAAGGGATTCCTGCATTGGATGGGAGGTTGGACTAGATGACCTCTAA 4064 chr5qtel1M 574943 AGTCCCTTCCATGTCTCAGCTGCTGAGACT 574972 i vv v v v v i L3#LINE/CR1 4065 GGTCCCTTCCAACTCTGAGATTCTGTGATT 4094 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.63 CpG sites = 45, Kimura (unadjusted) = 38.63 Transitions / transversions = 1.22 (45/37) Gap_init rate = 0.06 (18 / 280), avg. gap size = 2.94 (53 / 18) 23 32.67 3.01 4.91 chr5qtel1M 575563 575662 (424338) (CTT)n#Simple_repeat 1 97 (66) m_b259s252i13 10247 chr5qtel1M 575563 CTTCTTC-CCTCCTTCTGCTTGCTTCCCTCCTCTCCCTTGATATGTTCTT 575611 -i i v - - i i -i -v - v (CTT)n#Simple 1 CTTCTTCTTCTTCTTCTTCTT-CTT-CTTCTTCT-TCTT-CT-TCTTCTT 45 chr5qtel1M 575612 CCTCACCTTTCCCTTTCTCTCCCTC-TCTTCTTCTGTC-CCTCCATCTTT 575659 i vi iii ii i i - - -i i v i (CTT)n#Simple 46 CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCT-TCTTCTTCTTCTTC 94 chr5qtel1M 575660 CTA 575662 i v (CTT)n#Simple 95 TTC 97 Matrix = Unknown Transitions / transversions = 3.00 (18/6) Gap_init rate = 0.09 (9 / 99), avg. gap size = 1.00 (9 / 9) 89 3.31 7.20 0.00 chr5qtel1M 575663 575787 (424213) (TC)n#Simple_repeat 1 134 (0) c_b259s251i1 10248 chr5qtel1M 575663 TCTCTCTCTC-CTCT-TCTCTCT-TCTCTCTCTCTCTCTCTCTCTCTCTC 575709 - - - (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr5qtel1M 575710 TCTCTCTCTCTCTCTCTCTTTCTCTTTCTCTCTCTCTCTCTCTCTC-CT- 575757 i i - - (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chr5qtel1M 575758 TCCCT-TCTCTC-CTCTCCCT-TCTCTC-CTCTC 575787 i - - i - - (TC)n#Simple_ 101 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 134 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.07 (9 / 124), avg. gap size = 1.00 (9 / 9) 23 32.67 3.01 4.91 chr5qtel1M 575788 575852 (424148) (CTT)n#Simple_repeat 98 162 (1) m_b259s252i13 10249 chr5qtel1M 575788 CCTTCCTCTTTTTC-TCTCTGTTCTGTTTCTTCCTC-CCCTCTCCCTTTT 575835 i i i - - v vi i -i i i i i (CTT)n#Simple 98 TCTTCTTCTTCTTCTTCT-TCTTCTTCTTCTTCTTCTTCTTCTTCTTCTT 146 chr5qtel1M 575836 TTTCTTCTTCCTCCTTC 575852 i - i (CTT)n#Simple 147 CTTCTTCTT-CTTCTTC 162 Matrix = Unknown Transitions / transversions = 6.00 (12/2) Gap_init rate = 0.06 (4 / 64), avg. gap size = 1.00 (4 / 4) 21 23.14 4.55 4.55 chr5qtel1M 575815 575902 (424098) (TCTCCC)n#Simple_repeat 1 88 (0) m_b259s252i14 10249 chr5qtel1M 575815 TCTTCCTC-CCCTCTCCCTTTTTTTCTTCTTCCTCCT-TCCC-CCCCCTC 575861 i - i iii i i ii - - i (TCTCCC)n#Sim 1 TCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTC 50 chr5qtel1M 575862 TCTTTC-CCTTCCCCCTCTTGCCCTTTCCTTCTCTCCCTCTC 575902 ii - i i - - i -- (TCTCCC)n#Sim 51 TCCCTCTCCCTCTCCCTC-T-CCCTCTCC--CTCTCCCTCTC 88 Matrix = Unknown Transitions / transversions = 1.00 (15/0) Gap_init rate = 0.09 (8 / 87), avg. gap size = 1.00 (8 / 8) 241 24.15 0.00 5.56 chr5qtel1M 577396 577452 (422548) C MIRb#SINE/MIR (16) 252 199 m_b259s601i13 10250 chr5qtel1M 577396 TTTATTAAGTACCTACTATGTGCCAGATACTGTCTTAAACTGTGTTCCAC 577445 i ii i ii vi --- i i ii C MIRb#SINE/MIR 252 TTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAA---GCGCTTTAC 206 chr5qtel1M 577446 ATTCATT 577452 v C MIRb#SINE/MIR 205 ATGCATT 199 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 25.35 CpG sites = 11, Kimura (unadjusted) = 31.31 Transitions / transversions = 5.50 (11/2) Gap_init rate = 0.05 (3 / 56), avg. gap size = 1.00 (3 / 3) 284 25.22 10.58 0.88 chr5qtel1M 577639 577742 (422258) C MIRc#SINE/MIR (53) 215 102 m_b259s601i14 10250 chr5qtel1M 577639 TCACATTCTGGATCTCATTTGATCTTCTC--CAGTCCTG--------GCA 577678 v vvv i v -- ii -------- C MIRc#SINE/MIR 215 TCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCA 166 chr5qtel1M 577679 GGTGTGTGCCTCATCATCCCCATTTTACAGATAAGGAAAGTG-GACTTGT 577727 - iiv iv i i i v - i iiv C MIRc#SINE/MIR 165 GG-GCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAG 117 chr5qtel1M 577728 AGCTATTTAGTGTCT 577742 vvi v v C MIRc#SINE/MIR 116 AGAGGTTAAGTGACT 102 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.07 CpG sites = 13, Kimura (unadjusted) = 31.07 Transitions / transversions = 1.00 (13/13) Gap_init rate = 0.04 (4 / 103), avg. gap size = 3.00 (12 / 4) 301 20.29 2.82 2.82 chr5qtel1M 577650 577720 (422280) C MIRb#SINE/MIR (70) 198 128 m_b259s601i15 10250 chr5qtel1M 577650 ATCTCATTTGATCTTCTC--CAGTCCTGGCAGGTGTGTGCCTCATCATCC 577697 i i v -- ii vv iv i-- i i C MIRb#SINE/MIR 198 ATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTA--TTATTATCC 151 chr5qtel1M 577698 CCATTTTACAGATAAGGAAAGTG 577720 i v C MIRb#SINE/MIR 150 CCATTTTACAGATGAGGAAACTG 128 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 24.19 CpG sites = 9, Kimura (unadjusted) = 24.19 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.04 (3 / 70), avg. gap size = 1.33 (4 / 3) 187 25.00 0.00 0.00 chr5qtel1M 579663 579698 (420302) L2c_3end#LINE/L2 373 408 (70) m_b259s601i17 10251 chr5qtel1M 579663 TAGATTGTAAGCTCCTTAAGGGCAGACCCTGGGTTT 579698 i i i ivv i v i L2c_3end#LINE 373 TAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCT 408 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.40 CpG sites = 6, Kimura (unadjusted) = 31.51 Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 209 4.00 0.00 0.00 chr5qtel1M 579663 579687 (420313) L2d2_3end#LINE/L2 435 459 (96) m_b259s601i16 10251 chr5qtel1M 579663 TAGATTGTAAGCTCCTTAAGGGCAG 579687 i L2d2_3end#LIN 435 TAGATTGTAAGCTCCTTGAGGGCAG 459 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 4.17 CpG sites = 1, Kimura (unadjusted) = 4.17 Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 320 32.72 4.32 0.00 chr5qtel1M 580196 580357 (419643) L3#LINE/CR1 3738 3906 (193) m_b259s601i18 10252 chr5qtel1M 580196 AGAAGATCAGAGATGGAGGGGATCTGGTCATGATGTTCA----CTGGAAG 580241 vv vv i i iv i viivi v ----i v L3#LINE/CR1 3738 AGAAGAGAAGACTTAGAGGAGACATGATAGCTGTCTTCAAATATTTGAAG 3787 chr5qtel1M 580242 GGCTGTCACCAGGAAGAGGGACTAGGCTTGTGCTGGTTGGGCCCAGGGAG 580291 ivv i i i v vv vi i i L3#LINE/CR1 3788 GGCTGTCATGTGGAAGAGGGATTAGACTTATTCTGTGTGGCTCCAGAGGG 3837 chr5qtel1M 580292 CAGAACCAGGATTGATGG--GAAACTTGGA-AGAGATGTTTTTAGGCTGG 580338 i iii -- i v iv -i iiivv v vi L3#LINE/CR1 3838 CAGAACTAGGACCAATGGGTGGAAGTTACAGGGAGGCAGATTTCGGCTCA 3887 chr5qtel1M 580339 ACATCTGGAAGATCGTCCT 580357 i vv v v i L3#LINE/CR1 3888 ATATAAGGAAGAACTTTCT 3906 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 43.88 CpG sites = 28, Kimura (unadjusted) = 43.88 Transitions / transversions = 1.12 (28/25) Gap_init rate = 0.02 (3 / 161), avg. gap size = 2.33 (7 / 3) 287 28.72 9.49 7.45 chr5qtel1M 580816 580973 (419027) C L2d2_3end#LINE/L2 (0) 555 395 m_b259s601i19 10253 chr5qtel1M 580816 TCAAATGAAGTCAAC-------TAGCAAGTGCCTACTAGGAAGCAGACAT 580858 v i ------- vii i iv vivv i i C L2d2_3end#LIN 555 TCAAATCAAATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCAC 506 chr5qtel1M 580859 TGTTTTAAGTACTA---GGTATACAAAGAAAAGTTGTTTTATTTTAAAGG 580905 vi i ii i--- v i-------- ---- i C L2d2_3end#LIN 505 TGTGCTAGGCGCTGTGGGGGATACAAAGAAG--------TAT----AAGA 468 chr5qtel1M 580906 GA-AGTTTCTGCCCTCAAGGAATGTACAATCTAATGGGAAAGACTATATG 580954 v -i ii iiv i v ii v v ii C L2d2_3end#LIN 467 CATGGTCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGGAGACAAGACA 418 chr5qtel1M 580955 TACACA-ACGAAA---TAAACAA 580973 v -ii --- i C L2d2_3end#LIN 417 TAAACACGTGAAAAGTTAAATAA 395 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.41 CpG sites = 28, Kimura (unadjusted) = 37.97 Transitions / transversions = 2.00 (28/14) Gap_init rate = 0.11 (17 / 157), avg. gap size = 1.59 (27 / 17) 265 37.87 3.82 8.33 chr5qtel1M 580836 580978 (419022) C L2b_3end#LINE/L2 (27) 439 300 m_b259s601i20 10253 chr5qtel1M 580836 AGTGCCTACTAGGAAGCAGACATTGTTTTAAGTACTAGGTATACAAAGAA 580885 i iv viv i ?i vi i ii i v iv iv C L2b_3end#LINE 439 AGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGGGATACAGCGGT 390 chr5qtel1M 580886 AAGTTGTTTTATTTTAAAGGGA---AGTTTCTGCCCTCAAGGAATGTACA 580932 i ii------ ---- i vi ---i ii v iivi C L2b_3end#LINE 389 GAAC------A----AGACAGACNCGGTCCCTGCCCTCACGGAGCTCACA 350 chr5qtel1M 580933 ATCTAATGGGAAAGAC-TATATGTACACA-ACGA-AATAAACAAGC-TAG 580978 i i ii -v i v? - i -? v v v- i C L2b_3end#LINE 349 GTCTAGTGGGGGAGACAGACATGTAANCAGACAATNATAACCCAGAGTGG 300 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 52.72 CpG sites = 67, Kimura (unadjusted) = 58.35 Transitions / transversions = 2.00 (30/15) Gap_init rate = 0.11 (15 / 142), avg. gap size = 1.13 (17 / 15) 42 0.00 0.00 0.00 chr5qtel1M 580979 581014 (418986) (GT)n#Simple_repeat 1 36 (0) c_b259s251i2 10254 chr5qtel1M 580979 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 581014 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 36 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 265 37.87 3.82 8.33 chr5qtel1M 581015 581158 (418842) C L2b_3end#LINE/L2 (167) 299 165 m_b259s601i20 10253 chr5qtel1M 581015 ATGGATTAATTGGGAATATTATCCCCAAAGGGAAAGCAATAAAATTAA-- 581062 v vvvi i iivi----- i - ii ivivi viiii-- C L2b_3end#LINE 299 AGGGTAGGACTGGGGGGG-----CCCAGAGG-AGGGCGCCTGACCCGGCC 256 chr5qtel1M 581063 -GGGGGACTGAAAAAGACTCCCTGTAGGATATGGTATTTTAGCTGATATT 581111 - iiiiiii i i i i v vi ii v ------ C L2b_3end#LINE 255 TGGGGGGTCAGGGAGGGCTTCCCGGAGGAGGTGACATTTGAGCT------ 212 chr5qtel1M 581112 GGAGACTCTAGGGAAGAAAAGGAGTTGAAAATACGTGGA-GTAGGGAA 581158 - iiv i v iv ivv vi vi - i C L2b_3end#LINE 211 -GAGACCTGAAGGATGAGTAGGAGTTGGCCAGGCGAAGAGGTGGGGAA 165 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 52.72 CpG sites = 67, Kimura (unadjusted) = 58.35 Transitions / transversions = 2.06 (37/18) Gap_init rate = 0.11 (16 / 143), avg. gap size = 1.06 (17 / 16) 434 35.58 10.47 3.90 chr5qtel1M 581170 581675 (418325) C L2#LINE/L2 (68) 3014 2477 m_b259s601i21 10253 chr5qtel1M 581170 TATTCCAGAAAAGGCAAGGAGACCCCT----CTGAATTGAAGAATATGAG 581215 i v i vi i vv ---- i vi i vivii C L2#LINE/L2 3014 TGTTCGAGGAACAGCAAGGAGGCCAGTGTGGCTGGAGCGGAGTGAGCGAG 2965 chr5qtel1M 581216 GAAAGGAGTAAGATGGAG--GAAGCCTGGAAAG-------GGACTAGGTG 581256 iiii iiv - -- i i v ii i ------- i i v C L2#LINE/L2 2964 GGGGAGAGTGGTA-GGAGATGAGGTCAGAGAGGTAACGGGGGACCAGATC 2916 chr5qtel1M 581257 ATGAAGAGCTTTAAAAACCA----AACAGTTGTTGTTCTATTTGATTTTG 581302 v i i iv ii ---- viii v v i ---- v i i C L2#LINE/L2 2915 ATGTAGGGCCTTGTAGGCCATTGTAAGGACTTTGGCT----TTTACTCTG 2870 chr5qtel1M 581303 AAGGCATTGAGAAAC-ATTGGAG---TTT---------ATTGACATGGCC 581339 iv viv i i - --- --------- v ii C L2#LINE/L2 2869 AGTGAGATGGGAAGCCATTGGAGGGTTTTGAGCAGAGGAGTGACATGATC 2820 chr5qtel1M 581340 AAACTTGTACTTTAA---GATAAATTTGGCAGTTGAGC-GGGAAGAGACT 581385 vi iiii --- v v i v i v i- i v C L2#LINE/L2 2819 TGACTTACGTTTTAAAAGGATCACTCTGGCTGCTGTGTTGAGAATAGACT 2770 chr5qtel1M 581386 T------GGCA----------CAGGCAGACCCCTCAGCACGGTATTGTAA 581419 v------ ---------- v vv i v v v i i C L2#LINE/L2 2769 GNAGGGGGGCAAGGGTGGAAGCAGGGAGACCAGTTAGGAGGCTATTGCAG 2720 chr5qtel1M 581420 TAA-CCAGACCTGAGGTGATAAGGGTTTATACCAGAGTGAAGACTGTATC 581468 - i vv i iiv i iv i iv i v iv- C L2#LINE/L2 2719 TAATCCAGGCGAGAGATGATGGTGGCTTGGACCAGGGTGGTGGCAGTGG- 2671 chr5qtel1M 581469 AGAGGGAGAAAAGGGGCTTTATTGAAGAGACATTATAAAGGTAAAACCTA 581518 iv v i v iivv vvi v i v i i i v C L2#LINE/L2 2670 AGGTGGTGAGAAGTGGTCGGATTCTGGATATATTTTGAAGGTAGAGCCGA 2621 chr5qtel1M 581519 CAGAATATGACCACAAATTGGATGTTAGGAGTGAGAAAGAACAATGAGCT 581568 i v viv iii vi v i i ivi v ii C L2#LINE/L2 2620 CAGGATTTGCTGATGGATTGGATGTGGGGTGTGAGAGAAAGAGAGGAGTC 2571 chr5qtel1M 581569 GATAAAAAGAATAATGAGTTAAACTTGGGTTGAAAGTCTAGGTAACTGGA 581618 ------ ---i v iv ---- vvvi i ii i C L2#LINE/L2 2570 ------AAG---GATGACTCCAA----GGTTTTTGGCCTGAGCAACTGGA 2534 chr5qtel1M 581619 AGGATTCTAGTGTCCTTGACAGTAAC--AGAAGAATTAGAAAGGAGAGAA 581666 vvviv i v ? v vi i--i v vv ii -- v C L2#LINE/L2 2533 AGGATGGAGTTGCCATTNACTGAGATGGGGAAGACTGCGGGAG--GAGCA 2486 chr5qtel1M 581667 AGTTTAAAG 581675 i i i C L2#LINE/L2 2485 GGTTTGAGG 2477 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 48.76 CpG sites = 100, Kimura (unadjusted) = 50.49 Transitions / transversions = 1.37 (100/73) Gap_init rate = 0.07 (34 / 505), avg. gap size = 2.18 (74 / 34) 50 2.16 0.00 0.00 chr5qtel1M 581679 581725 (418275) (GT)n#Simple_repeat 1 47 (0) c_b259s251i3 10255 chr5qtel1M 581679 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTTGTG 581725 v (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 47 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 390 36.06 5.08 1.93 chr5qtel1M 581760 582664 (417336) L1PREC2_orf2#LINE/L1 2350 3282 (12) m_b259s551i12 10256 chr5qtel1M 581760 AATTACAAAATACTTCTCACACAAATAAAACCAGACGTAAACAAAAGGAA 581809 i v v v v i vvv ii v L1PREC2_orf2# 2350 AATTACAAAACACTGCTCAAAGAAATCAGAGATGACACAAACAAATGGAA 2399 chr5qtel1M 581810 AAATATGAATTGCTTATGGCTAACCTGAGCCAATGTAATAAACATGACAA 581859 i vvvv i v ivvv ii i vi v v i v L1PREC2_orf2# 2400 AAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTTAAAATGGCCA 2449 chr5qtel1M 581860 TTCGATC-----TAATTT---TATTCAATGACATACCCATCAAACTACCT 581901 v vii -----i ---v vi v i - L1PREC2_orf2# 2450 TACTGCCCAAAGCAATTTACAGATTCAATGCTATTCCTATCAAACTACC- 2498 chr5qtel1M 581902 AAAAGTAT--TTTATAATGCCAGAAAAAATAATAACAAAATTTATCCCAA 581949 viii -- i i ivi i iv vvi i vivi L1PREC2_orf2# 2499 AATGACATTCTTCACAGAACTAGAAAAAACTATTTTAAAATTCATATGGA 2548 chr5qtel1M 581950 AGAACAAAAGCGCAAGAATAG-CAAGGGAATTTT--TTAAAAAGTGTAAA 581996 vv v v vv - v ii --vi vii- L1PREC2_orf2# 2549 ACCAAAAAAGAGCCCGAATAGCCAAGGCAATCCTAAGCAAAAAGAAC-AA 2597 chr5qtel1M 581997 AGAAGGAAGTCTAGCCATACTAGATCTCAAACTATATTATAAAGTGGTAA 582046 vv i iv vi vv iv ii i i ii ivii i L1PREC2_orf2# 2598 AGCTGGAGGCATCACGCTACCCGACTTCAAACTATACTACAGGGCTACAG 2647 chr5qtel1M 582047 TCATCAGAACAATCTAGTACTGGCTGAGAAATAGAATGGTGGATTAGTAG 582096 v i i iiv i ivv i i vvvi i ii i i L1PREC2_orf2# 2648 TAACCAAAACAGCATGGTACTGGTACAAAAACAGACACATAGACCAATGG 2697 chr5qtel1M 582097 AATACATTAG---GCACATAATATATTGCAGCAAATGGTCATGGTAATCT 582143 i v v --- v v - vv v v i--ii iiiiv L1PREC2_orf2# 2698 AACAGAATAGAGAGCCCAGAA-ATAAGGCCGCACAC--CTACAACCATCT 2744 chr5qtel1M 582144 AGGGTTTCATAAATCTAA-AGATCTAAGCTTTTGGGACAAAACCTCATTA 582192 iivv iv i v i - i vvi vv v - iiv vi L1PREC2_orf2# 2745 GATCTTCGACAAAGCTGACAAAAACAAGCAATGGGGA-AAGGACTCCCTA 2793 chr5qtel1M 582193 TCTGAGAAAAGCTGCTGAGAAAGCTGGAAAACAGTATGGCAGAAACTAGG 582242 iii v v v i v i vv i vi - iv v i L1PREC2_orf2# 2794 TTCAATAAATGGTGCTGGGATAACTGGCTAGCCATAT-GCAGAAGATTGA 2842 chr5qtel1M 582243 TA-TAGACCACCATTTCACATCATATATCAAGATGAA--TAAAAAGTATT 582289 v - i v ivii i i iv i v --i i v v L1PREC2_orf2# 2843 AACTGGACCCCTTCCTTACACCATATACAAAAATCAACTCAAGATGGATT 2892 chr5qtel1M 582290 TTATATTTATATAT----TTTATAGTATTATAAGCAAATTAGAAG--AGC 582333 vv v i v i ----iii v -- i iv vvi i -- i L1PREC2_orf2# 2893 AAAGACTTAAATGTAAAACCCAAA--ACTATAAAAACCCTGGAAGACAAC 2940 chr5qtel1M 582334 ATGAACAATTTTACCCATCAGGTCTATGGATAAGGG-AATAATTTTAGGA 582382 v iii --- vv v v - i iv v - vi i v L1PREC2_orf2# 2941 CTAGGCAA---TACCATTCTGGAC-ATAGGAACGGGCAAAGATTTCATGA 2986 chr5qtel1M 582383 CCAAATAATTTAGAGC--TTTAAAGAATAT--AAAATAGATAATTTTTAT 582428 v ivviiiv i -- vv v v v-- v i v vvv L1PREC2_orf2# 2987 CGAAGACGCCAAAAGCAATTGCAACAAAAGCAAAAATTGACAAATGGGAT 3036 chr5qtel1M 582429 TATATAAAATTAAAAAG-TTTTGCACAATGA---AAACAATGCAACCAAA 582474 ivv v i i - i iii --- v - -- i L1PREC2_orf2# 3037 CTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTAT-CAAC--AG 3083 chr5qtel1M 582475 ACTAAAAGGAAAGC--AGGAAACTGGAG-GAATTTTTATAACAATTATC- 582520 v vi v i -- vii iv -i ? ii -- i v- L1PREC2_orf2# 3084 AGTAAACAGACAACCTACAGAATGGGAGAAAATNTTTGCA--AACTATGC 3131 chr5qtel1M 582521 -TCTGATACAGGCCTCATTTCTCAAATATATAGAGAACTGAATCAAATTT 582569 - i v i v v iviv v ii v v L1PREC2_orf2# 3132 ATCTGACAAAGGTCTAATATCCAGCATCTATAAGGAACTTAAACAAATTT 3181 chr5qtel1M 582570 ATAAG---AAGACCAGTCATTCC-TCAAAA--TGGTCAAAAGATATGAAT 582613 i --- i v iiv ii - i -- v i i i L1PREC2_orf2# 3182 ACAAGAAAAAAACAAACAACCCCATTAAAAAGTGGGCAAAGGACATGAAC 3231 chr5qtel1M 582614 AAACAGCTTTCAGACAAAGAAATCTAAGCTATCTATAGTTATAAGAAAGA 582663 i vi i vi v vi v vii v i ivi v i L1PREC2_orf2# 3232 AGACACTTTTCAAAAGAAGACATACATGCGGCCAACAAGCATATGAAAAA 3281 chr5qtel1M 582664 A 582664 L1PREC2_orf2# 3282 A 3282 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 49.81 CpG sites = 167, Kimura (unadjusted) = 50.48 Transitions / transversions = 1.09 (167/153) Gap_init rate = 0.05 (41 / 904), avg. gap size = 1.56 (64 / 41) 865 30.44 3.58 2.53 chr5qtel1M 582544 582934 (417066) L1ME3Cz_3end#LINE/L1 12 406 (591) m_b259s551i13 10256 chr5qtel1M 582544 AATATATAGAGAACTGAATCAAATTTATAAGAAGACCAGTCATTCC---- 582589 i vvvv iv i -- v vi ---- L1ME3Cz_3end# 12 AATATATAAAGAACTCCTACAAATCAATAAGAAAA--AGACAACCCAATA 59 chr5qtel1M 582590 TCAAAATGGTCAAAAGATATGAATAAACAGCTTTCAGACAAAGAAATCTA 582639 vv v i i ii ii iv vi i i ii L1ME3Cz_3end# 60 GAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGGAAACCCG 109 chr5qtel1M 582640 AGCTATCTATAGTTATAAGAAAGAATGTCTTTAA--TTACT-TTGATTAG 582686 iivii v ivi v ii i-- i -- i -v i i L1ME3Cz_3end# 110 AATGGCCAATAAACATATGAAAAGATGC--TCAACCTCACTAGTAATCAG 157 chr5qtel1M 582687 AGAAATAAAAATTAAAATAAC--TGAAGTACCACCTCACACCCATCAGAT 582734 i iv i? -- ii ii L1ME3Cz_3end# 158 GGAAATGCAAATTAAAACNACAATGAGATACCATTTCACACCCATCAGAT 207 chr5qtel1M 582735 TGGCTAATATGATAGAAAAT--GAAAATGATTA---GTTGGAAGGAATAT 582779 v v -- vi i -- v - ii --- vii i i L1ME3Cz_3end# 208 TGGCAAAAAT--TTAAAAGTCTGACAAT-ACCAAGTGTTGGCGAGGATGT 254 chr5qtel1M 582780 GAGAAAAGTGAAACACTAATGCCTTGTGGGTGGAGTTATGAATTGATCCA 582829 iii vv i v v i vi iv iiv i i i v L1ME3Cz_3end# 255 GGAGAAACGGGAACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTACA 304 chr5qtel1M 582830 ACCATTCTGGAGAGCAATTTGGAACTATACTCAAAGAGTTATCAAACTGT 582879 i i v v - viv i i-- iv i L1ME3Cz_3end# 305 ACCACTTTGGAGAGCAATTTGGCAATAT-CTAGTAAAGTTG--AAGATGC 351 chr5qtel1M 582880 GAATACCCTTTGATCCATCAATACCATTGCTAGGTCTGTCTCCCAAAGAG 582929 v vi i v v i v v i vi i i i L1ME3Cz_3end# 352 GCATACCCTACGACCCAGCAATTCCACTTCTAGGTATATACCCTAGAGAA 401 chr5qtel1M 582930 ATTTT 582934 i i L1ME3Cz_3end# 402 ACTCT 406 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.91 CpG sites = 73, Kimura (unadjusted) = 40.81 Transitions / transversions = 1.70 (73/43) Gap_init rate = 0.04 (16 / 390), avg. gap size = 1.50 (24 / 16) 347 32.84 0.00 6.73 chr5qtel1M 582959 583069 (416931) MIRc#SINE/MIR 10 113 (155) m_b259s601i22 10257 chr5qtel1M 582959 GTCATACAGTAAATAATGCATTGGCCCTGGAGAGGAGAGAACCTGAATTC 583008 vi i ii v iv i v i vvii ii ii MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr5qtel1M 583009 AACTCTTGTCTCAGACACATGAGACTTACTGAGTGTGTGACCCTGAACAA 583058 i v ii v v v ------- iiv i ii MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCAC-------TTACTAGCTGTGTGACCTTGGGCAA 102 chr5qtel1M 583059 GTTATTTAACC 583069 i i MIRc#SINE/MIR 103 GTCACTTAACC 113 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 41.96 CpG sites = 23, Kimura (unadjusted) = 45.65 Transitions / transversions = 2.09 (23/11) Gap_init rate = 0.06 (7 / 110), avg. gap size = 1.00 (7 / 7) 285 33.87 3.06 3.59 chr5qtel1M 583118 583313 (416687) L1MC2_3end#LINE/L1 442 636 (455) m_b259s551i15 10258 chr5qtel1M 583118 ATATTTACAGCAGCTCTTTTTGTGGTGGCCAAGGATTAGAACTCAAAGGG 583167 i i i v ii ii v iiv i viv vvii L1MC2_3end#LI 442 ATGTTTATAGCAGCTTTATTCATAATTGCCAAAACTTGGAAGCAACCAAG 491 chr5qtel1M 583168 ATGCCTATCAGTTAGGGAATGACCGAACACATTGTGGTATATGATTATAA 583217 i iv i vi v ivii v i i vvv i L1MC2_3end#LI 492 ATGTCCTTCAATAGGTGAATGGATAAACAAACTGTGGTACATCCATACAA 541 chr5qtel1M 583218 TGGAATACTATT--ATGTTATAAAG-AATGA-CAAGCAGGATAATTTCAG 583263 i --ii v v - - v v i vi ---- ii L1MC2_3end#LI 542 TGGAATATTATTCAGCGATAAAAAGAAATGAGCTATCAAGCCA----CGA 587 chr5qtel1M 583264 AAAAACCTGGAAAGACTTAAACTGATGCAAGTTG--AAGTGAGCAGAACC 583311 i v iii i v --- vi -- ivii i L1MC2_3end#LI 588 AAAGACATGGAGGAACCTTAA---ATGCATATTGCTAAGTGAAAGAAGCC 634 chr5qtel1M 583312 AG 583313 L1MC2_3end#LI 635 AG 636 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 45.21 CpG sites = 40, Kimura (unadjusted) = 47.28 Transitions / transversions = 1.67 (40/24) Gap_init rate = 0.06 (11 / 195), avg. gap size = 1.18 (13 / 11) 362 29.17 3.23 3.23 chr5qtel1M 583118 583241 (416759) L1ME1_3end#LINE/L1 442 565 (361) m_b259s551i14 10258 chr5qtel1M 583118 ATATTTACAGCAGCTCTTTTTGTGGTGGCCAAGGATTAGAA----CTCAA 583163 i i i i v i ii i ii i i ---- i L1ME1_3end#LI 442 ATGTTCATAGCAGCTTTATTCGTAATAGCCAAAAACTGGAAACAACCCAA 491 chr5qtel1M 583164 AGGGATGCCTATCAGTTAGGGAATGACCGAACACATTGTGGTATATGATT 583213 ---- i i ii?i v ivii v vvv L1ME1_3end#LI 492 A----TGTCCATCAACNGGTGAATGGATAAACAAATTGTGGTATATCCAT 537 chr5qtel1M 583214 ATAATGGAATACTATTATGTTATAAAGA 583241 i i vv iv i L1ME1_3end#LI 538 ACAATGGAATACTACTCAGCAATAAAAA 565 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.18 CpG sites = 25, Kimura (unadjusted) = 39.68 Transitions / transversions = 2.50 (25/10) Gap_init rate = 0.04 (5 / 123), avg. gap size = 1.60 (8 / 5) 13 7.39 6.45 3.12 chr5qtel1M 583938 583968 (416032) (AGAAA)n#Simple_repeat 1 32 (0) m_b259s252i15 10259 chr5qtel1M 583938 AGAAAAG--AAGGAAAGAAAGGGAAAAGAAAAG 583968 -- i -i (AGAAA)n#Simp 1 AGAAAAGAAAAGAAAAGAAA-AGAAAAGAAAAG 32 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.50 (3 / 2) 254 21.65 4.92 1.59 chr5qtel1M 583970 584030 (415970) C MIRb#SINE/MIR (14) 254 192 m_b259s601i23 10260 chr5qtel1M 583970 CATCCATTAAGCACCCACTATGTGCTTGGTGCTATGCTAAGCTCTTT--- 584016 ii i i ii iv ii i v --- C MIRb#SINE/MIR 254 CATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACA 205 chr5qtel1M 584017 TGCAAATATCTCAT 584030 - v C MIRb#SINE/MIR 204 TGC-ATTATCTCAT 192 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 24.43 CpG sites = 10, Kimura (unadjusted) = 26.81 Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.03 (2 / 60), avg. gap size = 2.00 (4 / 2) 92 31.91 2.15 1.06 chr5qtel1M 584949 585320 (414680) (TCTC)n#Simple_repeat 1 376 (0) m_b259s252i17 10261 chr5qtel1M 584949 TCTGCTGTCTGCT-TCTCTCATTTTCTTTGTCTGTCTCTGTCTCTGCTCT 584997 - v - - vi i i v v v - (TCTC)n#Simpl 1 TCT-CTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT-CTCT 47 chr5qtel1M 584998 TTCTCCCTCCCTCTGTCTCTTTGTCTCTAT-TCCCTTTCCTTTTCTCTCT 585046 i i i v i v v - i i ii i (TCTC)n#Simpl 48 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 97 chr5qtel1M 585047 CTCTTCCTCCCTCCCTC-CTCCCTC-CTCCCGACTCTAACCCTAACCCT- 585093 ii i i - i - i -v vv i vv i - (TCTC)n#Simpl 98 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TCTCTCTCTCTCTCTCTC 146 chr5qtel1M 585094 TCCCCCT-TCCCTCTCT-TCT-TCCCTCTCTCCCCCTCTCTCTAATTCTA 585140 i i - i - - i i i vvi v (TCTC)n#Simpl 147 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 196 chr5qtel1M 585141 ATTCTTTTTTTGTCTCCATGTGTGTGTGTGTGTGTCTCTCACTTCCTCTC 585190 vi i i i v iv v v v v v v v v v ii (TCTC)n#Simpl 197 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 246 chr5qtel1M 585191 TCCTTCCTTCTTTCCCTCTTTCTAATTCTAATTCTCTAATTCTCTCCCTA 585240 ii ii i i i vvi vvi vvi i v (TCTC)n#Simpl 247 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 296 chr5qtel1M 585241 TCTCTGTCTGTCTCTCTGTCTCTATCCCTGTCTCTCTGTCTCTGTCCCTA 585290 v v v v i v v v i v (TCTC)n#Simpl 297 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 346 chr5qtel1M 585291 TCTCTCTTTGTCTCTGTCTCTGTCTCTCTC 585320 i v v v (TCTC)n#Simpl 347 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 376 Matrix = Unknown Transitions / transversions = 1.04 (48/46) Gap_init rate = 0.03 (12 / 371), avg. gap size = 1.00 (12 / 12) 24 25.06 3.33 2.20 chr5qtel1M 585043 585132 (414868) (CTCCCTC)n#Simple_repeat 1 91 (0) m_b259s252i18 10262 chr5qtel1M 585043 CTCTCTCTTCCTCCCTCCCTCCTCCCTCCTCCCGACTCTAACCCTAACCC 585092 i i ii vv -vvi vv i (CTCCCTC)n#Si 1 CTCCCTCCTCCCTCCTCCCTCCTCCCTCCTCCCTCCTC-CCTCCTCCCTC 49 chr5qtel1M 585093 TTCCCCCTTCCCT-CT-CTTCTTCCCTCTCTCCC-CCTCTCTC 585132 i i i - - i i - - i (CTCCCTC)n#Si 50 CTCCCTCCTCCCTCCTCCCTCCTCCCTC-CTCCCTCCTCCCTC 91 Matrix = Unknown Transitions / transversions = 2.00 (12/6) Gap_init rate = 0.06 (5 / 89), avg. gap size = 1.00 (5 / 5) 92 31.91 2.15 1.06 chr5qtel1M 584949 585320 (414680) (TCTC)n#Simple_repeat 1 376 (0) m_b259s252i17 10261 chr5qtel1M 584949 TCTGCTGTCTGCT-TCTCTCATTTTCTTTGTCTGTCTCTGTCTCTGCTCT 584997 - v - - vi i i v v v - (TCTC)n#Simpl 1 TCT-CTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT-CTCT 47 chr5qtel1M 584998 TTCTCCCTCCCTCTGTCTCTTTGTCTCTAT-TCCCTTTCCTTTTCTCTCT 585046 i i i v i v v - i i ii i (TCTC)n#Simpl 48 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 97 chr5qtel1M 585047 CTCTTCCTCCCTCCCTC-CTCCCTC-CTCCCGACTCTAACCCTAACCCT- 585093 ii i i - i - i -v vv i vv i - (TCTC)n#Simpl 98 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TCTCTCTCTCTCTCTCTC 146 chr5qtel1M 585094 TCCCCCT-TCCCTCTCT-TCT-TCCCTCTCTCCCCCTCTCTCTAATTCTA 585140 i i - i - - i i i vvi v (TCTC)n#Simpl 147 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 196 chr5qtel1M 585141 ATTCTTTTTTTGTCTCCATGTGTGTGTGTGTGTGTCTCTCACTTCCTCTC 585190 vi i i i v iv v v v v v v v v v ii (TCTC)n#Simpl 197 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 246 chr5qtel1M 585191 TCCTTCCTTCTTTCCCTCTTTCTAATTCTAATTCTCTAATTCTCTCCCTA 585240 ii ii i i i vvi vvi vvi i v (TCTC)n#Simpl 247 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 296 chr5qtel1M 585241 TCTCTGTCTGTCTCTCTGTCTCTATCCCTGTCTCTCTGTCTCTGTCCCTA 585290 v v v v i v v v i v (TCTC)n#Simpl 297 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 346 chr5qtel1M 585291 TCTCTCTTTGTCTCTGTCTCTGTCTCTCTC 585320 i v v v (TCTC)n#Simpl 347 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 376 Matrix = Unknown Transitions / transversions = 1.04 (48/46) Gap_init rate = 0.03 (12 / 371), avg. gap size = 1.00 (12 / 12) 1077 22.37 0.90 1.36 chr5qtel1M 585529 585750 (414250) MIRb#SINE/MIR 40 260 (8) m_b259s601i24 10263 chr5qtel1M 585529 TAAAGTCAGGAAGATCTGAGTTCAAATTTGTCCTCAGACACTTATTAGCT 585578 ii iv i i i iivvv v v i MIRb#SINE/MIR 40 TGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCT 89 chr5qtel1M 585579 GTGAG--CATGGGCAAGTCACTTAACTTTTTTTGGCCTCAGTTTCCTCAA 585626 v -- v i i i i vi v MIRb#SINE/MIR 90 GTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCAT 139 chr5qtel1M 585627 CTATAAAATGGGGATGATTGTAACACCTGCCTCCCAGAGTTGTTGTAAAG 585676 i i --- i i v i i i MIRb#SINE/MIR 140 CTGTAAAATGGGGATAAT---AATACCTACCTCGCAGGGTTGTTGTGAGG 186 chr5qtel1M 585677 ATCAAATGATGTAATATTTGTAAAGGACTTAGCCCAATGCCTGGCACATA 585726 i vi iiv vi v i MIRb#SINE/MIR 187 ATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATA 236 chr5qtel1M 585727 GCAGGTGCTATGTAAATGTTAGCT 585750 i i i vvi v MIRb#SINE/MIR 237 GTAAGCGCTCAATAAATGGTAGCT 260 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 25.31 CpG sites = 31, Kimura (unadjusted) = 27.22 Transitions / transversions = 1.72 (31/18) Gap_init rate = 0.02 (4 / 221), avg. gap size = 1.25 (5 / 4) 21 24.85 1.61 0.00 chr5qtel1M 587718 587779 (412221) (TTTTG)n#Simple_repeat 1 63 (0) m_b259s252i19 10264 chr5qtel1M 587718 TTTTGTTTTATTTCATTTTGTTTTGTATTGCTTT-TTTGTTTTTCTTTTT 587766 i ii v i - vv v v (TTTTG)n#Simp 1 TTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTG 50 chr5qtel1M 587767 GCTTATTCTGTTT 587779 vi i i (TTTTG)n#Simp 51 TTTTGTTTTGTTT 63 Matrix = Unknown Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.02 (1 / 61), avg. gap size = 1.00 (1 / 1) 26 8.17 1.16 14.47 chr5qtel1M 590268 590353 (409647) (TGTTAA)n#Simple_repeat 1 76 (0) m_b259s252i20 10265 chr5qtel1M 590268 TGTTAAATGTGAATGTTAAATGTGATAATGTGTTAATGTTATATGTGAAA 590317 - v - -- -- - -v (TGTTAA)n#Sim 1 TGTT-AATGTTAATGTT-AATGT--TAA--TGTTAATGTTA-ATGT-TAA 42 chr5qtel1M 590318 TG-TGATGATAATGTGTTAATGTTAAATGTAAATGTT 590353 - i v -- - v (TGTTAA)n#Sim 43 TGTTAATGTTAA--TGTTAATGTT-AATGTTAATGTT 76 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.14 (12 / 85), avg. gap size = 1.00 (12 / 12) 352 31.01 6.04 2.60 chr5qtel1M 590375 590523 (409477) C MamRTE1#LINE/RTE-BovB (3357) 455 302 m_b259s601i25 10266 chr5qtel1M 590375 AGACAATTTTTAACACTCCTTTTTTAGACCCTTCCTCATGCCAAAGGTAA 590424 i iv ivi v i ? i v vi -- i C MamRTE1#LINE/ 455 AGGCAACGTTTAGGGCACCTTTTCTAGNCCCTTCCCCATTCGGA--GTGA 408 chr5qtel1M 590425 G-ATC----TTTTAAAAATGGCTGCTTAGATACCCAGAGAGCTGCCAAAT 590469 - v ---- ii v v i i i?v i i C MamRTE1#LINE/ 407 GCAGCGCGNTCCTAAACAGGGCTGCTCAGACACCCAGGNCGCTGCCGAAC 358 chr5qtel1M 590470 TCCACTG-TGTTTCAATCCAGTGAGAAGACAACC-CTAT--GGGGTTGGC 590515 vvii - ii --?i i vv ii i -v --v ii v C MamRTE1#LINE/ 357 GGTGCTGCTGCCTC--NTCAGCGACTAAGCGACCAATATCCTGGGCCGCC 310 chr5qtel1M 590516 CACTTGTA 590523 i i i C MamRTE1#LINE/ 309 TACTCGCA 302 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.70 CpG sites = 29, Kimura (unadjusted) = 43.20 Transitions / transversions = 1.81 (29/16) Gap_init rate = 0.06 (9 / 148), avg. gap size = 1.44 (13 / 9) 613 33.55 5.25 5.00 chr5qtel1M 591547 592823 (407177) L1P4_orf2#LINE/L1 580 1859 (1435) m_b259s551i16 10267 chr5qtel1M 591547 TTCCTAACTGTACATGGAACTAACAGAAATATTGGCCATGTATATTTAAA 591596 ii v i i vv vvv v i i i-- ii iiiv L1P4_orf2#LIN 580 TTCTCATCTGCACACGGAACATACTCTAAGATCGACCAC--ATGCTCGGC 627 chr5qtel1M 591597 TATAAA---AATCTCACAAAGCAATCTAAAAAAGCAGAA--ATATTAAAT 591641 i --- i vv -- v v v ii -- ii -- L1P4_orf2#LIN 628 CATAAAGCAAGTCTCAATAA--ATTCAAAAAAATCGAAATCATACCAA-- 673 chr5qtel1M 591642 GCTTCTTTTTTTCTGAGCATAGTGAAATAACCAT-TACATT--TGCTAAA 591688 ---i v vi i v v i ? vv -v v i-- i i i L1P4_orf2#LIN 674 ---CCATACTCTCGGACCACAGTGNAATAAAAATAGAAATCAATACCAAG 720 chr5qtel1M 591689 GAGACTTTTCAAAAATAGATTAAAAATTAATTGGAAATTAAATAACCTTA 591738 i ii i vi v i---- vv i i vv L1P4_orf2#LIN 721 AAGATCTCTCAAAACCACAC----AATTACATGGAAATTAAACAACTTGC 766 chr5qtel1M 591739 TCCTAAAGAATGGCCTATT---CCAAGAAC-AAATTATAAAAACAACCCA 591784 --- i i - ---iv v - viiv iv i v L1P4_orf2#LIN 767 TCCT---GAATGACTT-TTGGGTAAACAACGAAATTAAGGCAGAAATCAA 812 chr5qtel1M 591785 TAGCTTCATTAAGGTTAATGAGAACAATAAGACAGCATGCCAAAATTTGT 591834 v iv v i ii ? i ivi v i i i v L1P4_orf2#LIN 813 AAAATTCTTTGAAATNAATGAAAACAGAGACACAACATACCAAAATCTCT 862 chr5qtel1M 591835 GAAAGTCAGCCAAAGTAATCTGTAGGGGGAAATTTACATCTTTAAATGCT 591884 ii vv ? i i v vv i i i i v vi i i L1P4_orf2#LIN 863 GGGATGCAGCNAAAGCAGTGTTAAGAGGAAAGTTTATAGCGCTAAACGCC 912 chr5qtel1M 591885 TAAATCAGTGAAG---GAAAGAGT--AGATCAATGATCTGGATAT-GCAA 591928 v i-i --- vi-- i i ii i- i - v L1P4_orf2#LIN 913 TACATCAA-AAAGTTAGAAAGATCTCAAATTAACAATCTA-ACATCGCAC 960 chr5qtel1M 591929 CTGAACAAATTATAAAATTAATGAATTAAGACACTCCTCCAATTAAATAC 591978 ii vi i v vi - i- iv vi -- -- iv v L1P4_orf2#LIN 961 CTAGAGGAACTAGAAAAACAA-GAAC-AAACCAACCC--CAA--AGCTAG 1004 chr5qtel1M 591979 CCACACAAAAATTCTAA---AAATTTAAGGAGAGAGTAATAAAATTGACA 592025 viv v ivvv --- ivi v ivvv ii v L1P4_orf2#LIN 1005 CAGAAGAAAAGAAATAACTAAAATCAGAGCAGAACTGAACGAAATTGAGA 1054 chr5qtel1M 592026 GGTTAAAAAAATCCCATAGAGCTGAAAAAATCA-TG---CTAAAAGTTGG 592071 v?i--- - v ----- ii -i --- i L1P4_orf2#LIN 1055 CNC---AAAAATCC-ATACA-----AAGGATCAACGAAACCAAAAGTTGG 1095 chr5qtel1M 592072 TTTCTTGAAGAAAAACAAACAAA--CAACAT-TGGTTAATTTGATTTTTT 592118 ii -- ii i i-- i i v-iv i ii v vviv L1P4_orf2#LIN 1096 TTCTTTGAA--AGGATAAACAAGATCGATAGACCGCTAGCTAGATTAACA 1143 chr5qtel1M 592119 AAAAAGAAAATAGAAAA---CCAAATTATTGGTATCATGAATTAAAAAAG 592165 i i v i --- v viivv vi v v i L1P4_orf2#LIN 1144 AAGAAAAAAAGAGAGAAGATCCAAATAAGCACAATCAGAAATGACAAAGG 1193 chr5qtel1M 592166 TAAATTCACAACTAAT--------------GAAGATCACATAAAAGCAAT 592201 i vv i ii --------------i - vi i ii v L1P4_orf2#LIN 1194 TGACATTACAACCGATCCCACAGAAATACAAAAGATC-CTCAGAGACTAT 1242 chr5qtel1M 592202 TATTAAGTACCATTTTGCCAATATAACT-GACAATCTTAATGAAATGGAT 592250 v -i vi v vv i - - v vi v L1P4_orf2#LIN 1243 TATGAA-CACCTCTATGCACACA-AACTAGAAAATCTAGAGGAAATGGAT 1290 chr5qtel1M 592251 GAATATTTACTAAAATATAAATTGCCCACATCAA--CAGAACAGGAAATA 592298 i vii ivv v i i vi v v v ii -- i - i v i L1P4_orf2#LIN 1291 AAATTCCTGGAAACACACAACCTCCCAAGATTGAACCAGGA-AGAAATTG 1339 chr5qtel1M 592299 AGATATTAAAAAAA--AAACTTGATCTTAGAAAAAAAATTGAACAAGTCA 592346 i ivi i v i -- vv?i vi iv ----- iv v L1P4_orf2#LIN 1340 AAACCCTGAACAGACCAATANCGAGTTCCGAAA-----TTGAATCAGTAA 1384 chr5qtel1M 592347 TCAATTAAGGCTAA-----GAAAAAATCTCCAGGACCAGATGAATTTACA 592391 v -- iv v-----i v i - i i L1P4_orf2#LIN 1385 TAAA--AAACCTACCAACCAAAAAAAGCCCC-GGACCAGATGGATTCACA 1431 chr5qtel1M 592392 AT-GCATTCTACTAAACATTTAAAGAACAATTAATTCCAAAACTTCATAA 592440 ii- v i i i vi v ii ii v vv v vv L1P4_orf2#LIN 1432 GCCGAATTCTACCAGACGTACAAAGAAGAGCTGGTACCAATCCTACTGAA 1481 chr5qtel1M 592441 ACTTTTGGGAAAAAT--AGGTAAAGGAGGAATTAT---ATAAAGAAGAAG 592485 v vvi -- --- i i vi---v -------- L1P4_orf2#LIN 1482 ACTATTCCAAAAAATCGAGG---AGGAGGGACTCCTCCCTAA-------- 1520 chr5qtel1M 592486 ACTATCTTCTATAGTACAAAAATGGTCTTGATACCTAAACCAGTGAGAAT 592535 - -iv iiivi v iv vii i v v vv i iv L1P4_orf2#LIN 1521 -CT-CATTCTACGAAGCCAGCATCACCCTGATACCAAAACCTGGCAAAGA 1568 chr5qtel1M 592536 CAAAACAGGAAAACAAAAGTATTAAC-AATTTCCCTAATGAATATTGATG 592584 v iii v v ?ivii - v i i v i L1P4_orf2#LIN 1569 CACAACGAAAAAAGAAAACTNCAGGCCAATATCCCTGATGAACATAGACG 1618 chr5qtel1M 592585 CAAAAAAATTTAAATAAAATACTAGCAAGTAGATTGTAGCAATATATCAT 592634 vvi i -i iiv v vi ii i v L1P4_orf2#LIN 1619 CAAAAATCCTCAA-CAAAATACTAGCAAACCGAATCCAGCAGCACATCAA 1667 chr5qtel1M 592635 AAAGACAATACACTATGCCCATCTGGGATTTATACCAGGAATTCAAGGGC 592684 vi v i i vi vv i v v v i v - i L1P4_orf2#LIN 1668 AAAGTTAATTCACCACGATCAAGTAGGCTTTATTCCTGGGATGCAA-GGT 1716 chr5qtel1M 592685 TGGTTCAATATTAGGAAGCCTTTCAGTATAATTGATGTCAATAACAAAAG 592734 i vv v ii vv v i i i v ivv vv i v L1P4_orf2#LIN 1717 TGGTTCAACATACGCAAATCAATAAATGTGATTCACCACATAAACAGAAT 1766 chr5qtel1M 592735 CAACAACAATTGCT---TGATTATTTCAGTAGATGCAGAAAAATCTATTG 592781 i v vvi i--- i i i i v v i L1P4_orf2#LIN 1767 TAAAAACAAAAACCATATGATCATCTCAATAGACGCAGAAAAAGCTTTCG 1816 chr5qtel1M 592782 ACCAAATACAACTGTCATTTC-TATTAAAAACACT-AGAAAACT 592823 iv v -i vi - iv v - iv L1P4_orf2#LIN 1817 ATAAAATCCAAC-ATCCCTTCATGATAAAAACCCTCAACAAACT 1859 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 43.32 CpG sites = 222, Kimura (unadjusted) = 45.97 Transitions / transversions = 1.20 (222/185) Gap_init rate = 0.07 (91 / 1276), avg. gap size = 1.44 (131 / 91) 1514 31.21 5.20 4.48 chr5qtel1M 591720 592893 (407107) L1M4_orf2#LINE/L1 748 1929 (1365) m_b259s551i17 10267 chr5qtel1M 591720 TGGAAATTAAATAACCTTATCCTAAAGAATGGCCTAT---TCCAAGAACA 591766 i vivv v --- v --- v v L1M4_orf2#LIN 748 TGGAAATTAAACAACACACTCCTAAATAA---CCAATGGGTCAAAGAAGA 794 chr5qtel1M 591767 AATTATAAAAACAACCCATAGCTTCATTAAGGTTAATGAGAACAATAAGA 591816 i i iiiv iiviv iv v v i i v i i v v L1M4_orf2#LIN 795 AATCACAAGGGAAATTAGAAAATACTTTGAGATGAATGAAAACGAAAACA 844 chr5qtel1M 591817 CAGCATGCCAAAATTTGTGAAAGTCAGCCAAAGTAATCTGTAGGGGGAAA 591866 i i i i ii vv ? i i viv i L1M4_orf2#LIN 845 CAACATACCAAAACTTATGGGATGCAGCNAAAGCAGTGCTTAGAGGGAAA 894 chr5qtel1M 591867 TTTACATCTTTAAATGCTTAAATCAGTGAAGGAAAGAG----TAGATCAA 591912 i v v i v i ivi i i i ----i i L1M4_orf2#LIN 895 TTTATAGCTGTAAATGCCTATATTAAAAAAGAAGAAAGATCTCAAATCAA 944 chr5qtel1M 591913 TGATCTGGATATGCAACTGAACAAATTATAAAATTAA---TGAATTAAGA 591959 i i iiviv v v v v i v vv ---ii i i- L1M4_orf2#LIN 945 TAACCTAACCTTCCACCTTAAGAAACTAGAAAAAGAAGAGCAAACTAAA- 993 chr5qtel1M 591960 CACTCCTCCAATTAAATACCCACACAAAAATTCTAAAAATTTAAGGAGAG 592009 ----- i v vi ii vvviv vii vv i vi vi i L1M4_orf2#LIN 994 -----CCCAAAGCAAGCAGAAGGAAGGAAATAATAAAGATTAGAGCGGAA 1038 chr5qtel1M 592010 AGTAATAAAATTGACAGGTTAAAAAAATCCCATAGAGCTGAAAAAATCA- 592058 vv i v v i-- i -- v ----- - L1M4_orf2#LIN 1039 ATAAATGAAATAGAGAA--TAGAAAAA--CAATAGAG-----AAAATCAA 1079 chr5qtel1M 592059 TG---CTAAAAGTTGGTTTCTTGAAGAAA--AACAAA-----CAAACAAC 592098 i --- i ii i i -- ----- -- L1M4_orf2#LIN 1080 CGAAACCAAAAGTTGGTTCTTTGAAAAGATCAACAAAATTGACAAAC--C 1127 chr5qtel1M 592099 ATTGGTTAATTTGATTTTTTAAAAAGAAAATAGAAAA---CCAAATTATT 592145 v i i ivi ii---- i i v i ---i i L1M4_orf2#LIN 1128 TTTAGCTAGACTGACC----AAGAAAAAAAGAGAGAAGACTCAAATTACT 1173 chr5qtel1M 592146 GGTATCATGAATTAAAAAAGTAAATTCACAACTAA---TGAAGATCACAT 592192 iiv v v i i vi vv i v ii --- iv ---v L1M4_orf2#LIN 1174 AAAATCAGGAATGAAAGAGGGGACATTACTACCGACCTTACAGA---AAT 1220 chr5qtel1M 592193 AAAAGCAATTATTAAG---TACCAT------TT---TGCCAATATAACT- 592229 ivi v i --- i ------ --- i - i - L1M4_orf2#LIN 1221 AAAAAGGATTATAAGGGAATACTATGAACAATTGTATGCCAACA-AATTA 1269 chr5qtel1M 592230 GACAATCTTAATGAAATGGATGAATATTTACTAAAATATAAATTGCCCAC 592279 i i vi ii vii vv i i i i i v v L1M4_orf2#LIN 1270 GATAACCTAGATGAAATGGACAAATTCCTAGAAAGACACAAACTACCGAA 1319 chr5qtel1M 592280 ATCAACAGAACAGGAAATAAGATATTAAAAAAAAAACTTGATCTTAGAAA 592329 iii vv v i ii v ivi v i -- i ivvviv v L1M4_orf2#LIN 1320 ACTGACTCAAGAAGAAATAGAAAATCTGAATAGA--CCTATAACAAGTAA 1367 chr5qtel1M 592330 AAAAATTGAACAAGTCATCAATTAAGGCT-------AAGAAAAAATCTCC 592372 i i iv v -- ii ------- i---i L1M4_orf2#LIN 1368 AGAGATTGAATTAGTAATCAA--AAAACTTCCCACAAAGAAAAG---CCC 1412 chr5qtel1M 592373 AGGACCAGATGAATTTAC-AATGCATTCTACTAAACATTTAAAGAACAAT 592421 ? iv i -ii v i v L1M4_orf2#LIN 1413 AGGNCCAGATGGCTTCACTGGTGAATTCTACCAAACATTTAAAGAAGAAT 1462 chr5qtel1M 592422 TAATTCCAAAACTTCATAAACTTTTGGGAAAAATAGGTAAAGGAGGAATT 592471 iv vv i i vvi i- i ---- L1M4_orf2#LIN 1463 TAACACCAATCCTTCACAAACTCTTCCAAAAAATAGA-AGAGGAGG---- 1507 chr5qtel1M 592472 ATATAAAGAAGAAGACTATC-------TTCTATAGTACAAAAATGGTCTT 592514 ---------- v vi ------- iivi v iv vii i L1M4_orf2#LIN 1508 ----------GAACACTTCCCAACTCATTCTATGAGGCCAGTATTACCCT 1547 chr5qtel1M 592515 GATACCTAAACCAGTGAGAATCAAAACAGGAAAACAAAAGTATTAAC-AA 592563 v vv i iv vv i v v ivi - L1M4_orf2#LIN 1548 GATACCAAAACCAGACAAAGACATCACAAGAAAAGAAAACTACAGACCAA 1597 chr5qtel1M 592564 TTTCCCTAATGAATATTGATGCAAAAAAATTTAAATAAAATACTAGCAAG 592613 v v v vvi i -i i L1M4_orf2#LIN 1598 TATCCCTTATGAATATAGATGCAAAAATCCTCAA-CAAAATACTAGCAAA 1646 chr5qtel1M 592614 TAGATTGTAGCAATATATCATAAAGACAATACACTATGCCCATCTGGGAT 592663 iv v vi i v v i iv i v vv L1M4_orf2#LIN 1647 CCGAATCCAGCAACATATAAAAAGGATTATACACCATGACCAAGTGGGAT 1696 chr5qtel1M 592664 TTATACCAGGAATTCAAGGGCTGGTTCAATATTAGGAAGCCTTTCAGTAT 592713 v v - i i ?v i ii vv i i L1M4_orf2#LIN 1697 TTATCCCAGGAATGCAA-GGTTGGTTCAACATNCGAAAATCAATCAATGT 1745 chr5qtel1M 592714 AAT---TGATGTCAATAACAAAAGCAACAACAATTGCTTGATTATTTCAG 592760 ---iv i i iv v ivi v iii v i i i L1M4_orf2#LIN 1746 AATACACCATATTAATAGAATAAAGGACAAAAACCACATGATCATCTCAA 1795 chr5qtel1M 592761 TAGATGCAGAAAAATCTATTGACCAAATACAACTGTCATTTC-TATTAAA 592809 i v vv v v -ii v - iv L1M4_orf2#LIN 1796 TAGACGCAGAAAAAGCATTTGACAAAATCCAAC-ACCCTTTCATGATAAA 1844 chr5qtel1M 592810 AACACTAGAAAACTTTGGAATAAATAGAGATTTTCTTAATACAATAAGTA 592859 vi v vi v i vi ii i i i ivii ivi L1M4_orf2#LIN 1845 AACACTCAACAAACTAGGAATAGAAGGGAACTTCCTCAACCTGATAAAGG 1894 chr5qtel1M 592860 ATACTTGTCTAAAACCATGAGCAAGCATCA-ACTT 592893 ii ii iivv vvv v i - L1M4_orf2#LIN 1895 GCATCTACGAAAAACCCACAGCTAACATCATACTT 1929 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.71 CpG sites = 200, Kimura (unadjusted) = 41.67 Transitions / transversions = 1.33 (200/150) Gap_init rate = 0.06 (73 / 1173), avg. gap size = 1.56 (114 / 73) 21 0.00 0.00 0.00 chr5qtel1M 593868 593890 (406110) (T)n#Simple_repeat 1 23 (0) m_b260s252i0 10268 chr5qtel1M 593868 TTTTTTTTTTTTTTTTTTTTTTT 593890 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTT 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 508 24.64 0.00 6.60 chr5qtel1M 593903 594015 (405985) C MIRc#SINE/MIR (153) 115 10 m_b260s601i0 10269 chr5qtel1M 593903 GGGGTTAAGTGACTTGCCCAGGGTCACACAATTAGGAAGTATTAAGTATC 593952 i i ii v ivi i-- v C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAG--AGC 68 chr5qtel1M 593953 TGAGGTCACATTTGAACTCAGGTCCTCCTGACTTCAAGGTTGGTGCTCTA 594002 i i ----- i i i i i viii v C MIRc#SINE/MIR 67 CGGG-----ACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTT 23 chr5qtel1M 594003 TCCATTATGCCAC 594015 i iii C MIRc#SINE/MIR 22 TCCACTGCACCAC 10 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 28.81 CpG sites = 21, Kimura (unadjusted) = 31.77 Transitions / transversions = 4.20 (21/5) Gap_init rate = 0.06 (7 / 112), avg. gap size = 1.00 (7 / 7) 24 28.79 3.45 0.00 chr5qtel1M 594713 594799 (405201) (AGAC)n#Simple_repeat 1 90 (0) m_b260s252i1 10270 chr5qtel1M 594713 AGA-AGGCAGACAGATCTATGGACAGAGAGACAGACAGACAGGCAGGCAG 594761 - i ivv ii v i i (AGAC)n#Simpl 1 AGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAG 50 chr5qtel1M 594762 GTGGGCA-A-AGGCAGACAGATGGGCAGATAGAAAGCCAG 594799 iii i - - i ii i i v v (AGAC)n#Simpl 51 ACAGACAGACAGACAGACAGACAGACAGACAGACAGACAG 90 Matrix = Unknown Transitions / transversions = 3.00 (15/5) Gap_init rate = 0.03 (3 / 86), avg. gap size = 1.00 (3 / 3) 185 23.47 16.22 4.03 chr5qtel1M 594854 594964 (405036) LFSINE_Vert#SINE/tRNA 168 291 (168) m_b260s601i1 10271 chr5qtel1M 594854 AGAGGTCAGGTCATCAATA-CACAAAAGTCCTATCACCA---GCTGTAAT 594899 v v -i v i - viv i v --- vv LFSINE_Vert#S 168 AGTGGACAGGT-GTCCACATCACAAAACCACCATCACAATTGGCACTAAT 216 chr5qtel1M 594900 T--CACCCTCATTG--------AG--GAGAGG--AAGCACTGAATGGGAA 594935 -- ii -------- -- -- v v LFSINE_Vert#S 217 TGGCACCCTTGTTGGCAGTCTCAGCAGAGAGGCCAAGGACTGAATGGGCA 266 chr5qtel1M 594936 TTGGGGGCCAATCTTATAATCTCTTTCCT 594964 - i i ii v --- vi iv LFSINE_Vert#S 267 -TGGAGACTGAAC---TACCCTCTCACCT 291 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 28.50 CpG sites = 12, Kimura (unadjusted) = 28.50 Transitions / transversions = 0.92 (12/13) Gap_init rate = 0.10 (11 / 110), avg. gap size = 2.09 (23 / 11) 48 32.69 2.23 5.25 chr5qtel1M 595184 595497 (404503) (AGG)n#Simple_repeat 1 305 (0) m_b260s252i2 10272 chr5qtel1M 595184 AGGAAGAAGCAGGAGAGAAGAGGAGAAGAAGGA-GAAGAGGAAGAAGGGG 595232 - i v - i i i - i - i i (AGG)n#Simple 1 AGG-AGGAGGAGGAG-GAGGAGGAGGAGGAGGAGGAGGAGG-AGGAGGAG 47 chr5qtel1M 595233 AAAGAGGCAGCAGGAGAATCAAATACAGAGAGGAGTGGGGAGAAGAGAAG 595282 i i - v i vv iiviv - - i i - i (AGG)n#Simple 48 GAGGAGG-AGGAGGAGGAGGAGGAGGAG-GAGGAG-GAGGAGGAG-GAGG 93 chr5qtel1M 595283 AGAAGCAGGAACAAGCTAGAGGAAAGGGAGAAGGAAG-GGAGGAGAAGCA 595331 i v - vi vvi iii i i - i v (AGG)n#Simple 94 AGGAGGAGG-AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA 142 chr5qtel1M 595332 GTA-CAAGATGCAGAGGAGAAAGGGGAGGAGGA-GATGAGGGACCAAGGG 595379 v -v i v vi i i i - v - -vi i (AGG)n#Simple 143 GGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA-GGA-GGAGGA 190 chr5qtel1M 595380 GGAGCTGGA-GAGGAGGAGGAGGAGTGAGTCAGAGGAGGGAAAGGAGAAG 595428 vv - - vvi iii i (AGG)n#Simple 191 GGAGGAGGAGGAGGAGGAGGAGGAG-GAGGAGGAGGAGGAGGAGGAGGAG 239 chr5qtel1M 595429 AAAGTGAGGAAG-GGAGGAGGGGCAACTCAGGAATGAGGAGCTGAAGCAA 595477 -i - i - i -i -vv - v vv i v i (AGG)n#Simple 240 -GAG-GAGGAGGAGGAGGAGGAG-GA-GGAGG-AGGAGGAGGAGGAGGAG 284 chr5qtel1M 595478 GAAGAAAAGCA-GAGGAGGAG 595497 i ii v - (AGG)n#Simple 285 GAGGAGGAGGAGGAGGAGGAG 305 Matrix = Unknown Transitions / transversions = 1.64 (46/28) Gap_init rate = 0.07 (23 / 313), avg. gap size = 1.00 (23 / 23) 139 20.55 1.06 0.00 chr5qtel1M 595599 595880 (404120) (TCTC)n#Simple_repeat 1 285 (0) m_b260s252i3 10273 chr5qtel1M 595599 TCTCTCTCTCTCTCTCTCTCTCTCTCTTTCTCTCTCTCTCTCTCTCTCTC 595648 i (TCTC)n#Simpl 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr5qtel1M 595649 TCTCTCTCCCTCTCTCTCCCTCTCCCTCCCCTTCCCTCCCTCTCCCTCTC 595698 i i i i ii i i i (TCTC)n#Simpl 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chr5qtel1M 595699 TCTCCCCGTCCCCTTCCCTCCCCCTCCCTCCCTCCCTCTCTCTCCCCCTC 595748 i iv i ii i i i i i i i i (TCTC)n#Simpl 101 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 150 chr5qtel1M 595749 CCGCCCTCCCTCTCTGTCCCCCTCCCTCCCTCCCTCTCTCTCCCCCTCCC 595798 i v i i v i i i i i i i i (TCTC)n#Simpl 151 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 200 chr5qtel1M 595799 TCCCTCCCTCTCTCTCCCCCTCCCTCCCTCTCTCTCTCTCTCCCTC-CTC 595847 i i i i i i i - (TCTC)n#Simpl 201 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 250 chr5qtel1M 595848 -CTCTCTCTCTTCCTCCCTTTCTCTC-CTCTCTCT 595880 - ii i i - (TCTC)n#Simpl 251 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 285 Matrix = Unknown Transitions / transversions = 15.00 (45/3) Gap_init rate = 0.01 (3 / 281), avg. gap size = 1.00 (3 / 3) 81 8.04 0.00 0.00 chr5qtel1M 597435 597539 (402461) (AC)n#Simple_repeat 1 105 (0) c_b260s251i0 10274 chr5qtel1M 597435 ACACACACACACTCACACACACACACACACACACACTCACACACACACAC 597484 v v (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50 chr5qtel1M 597485 ACTCATATACACACACACACTCACATACACTCACACACACACACACACAC 597534 v i i v i v (AC)n#Simple_ 51 ACACACACACACACACACACACACACACACACACACACACACACACACAC 100 chr5qtel1M 597535 ACACA 597539 (AC)n#Simple_ 101 ACACA 105 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.00 (0 / 104), avg. gap size = 0.0 (0 / 0) 17 24.45 0.00 0.00 chr5qtel1M 597542 597580 (402420) (CA)n#Simple_repeat 1 39 (0) m_b260s252i4 10275 chr5qtel1M 597542 CACATATATACTCACACACATCCACAGATACACACACAC 597580 i i i v iv v i (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACAC 39 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 924 24.31 4.57 0.44 chr5qtel1M 597652 597870 (402130) MIRb#SINE/MIR 27 254 (14) m_b260s601i2 10276 chr5qtel1M 597652 AGAGTGCTGGATCTGGTGTCAGGAAGACCTGGGTCCCGATGGAGACTCAG 597701 ii v v i v iv i vi vvv i v MIRb#SINE/MIR 27 AGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTCTG 76 chr5qtel1M 597702 ACACTTACAAGCAATGTGACCCTGAGCAAGTCACTTCAACCTGTTTG--C 597749 v v vi i i i - v i -- MIRb#SINE/MIR 77 CCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTT-AACCTCTCTGAGC 125 chr5qtel1M 597750 CTCAGTTTCCTCATCTGTAAAATGAAG-------TGCCT-TCTCCCAGGG 597791 ii ------- i -i v MIRb#SINE/MIR 126 CTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTACCTCGCAGGG 175 chr5qtel1M 597792 CTATCATAAGAGTTAAATAAGATCCTATTTGTGAAGCCCTTAGCAAAGTG 597841 i i ii i ii i vv iiv i v v MIRb#SINE/MIR 176 TTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAGTG 225 chr5qtel1M 597842 CGTGGCACGTAGTAGGAGCTTCATAAGTG 597870 v i i v iv i MIRb#SINE/MIR 226 CCTGGCACATAGTAAGCGCTCAATAAATG 254 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 29.97 CpG sites = 31, Kimura (unadjusted) = 29.97 Transitions / transversions = 1.41 (31/22) Gap_init rate = 0.02 (4 / 218), avg. gap size = 2.75 (11 / 4) 197 21.05 0.00 0.00 chr5qtel1M 597838 597875 (402125) L2c_3end#LINE/L2 428 465 (13) m_b260s601i3 10277 chr5qtel1M 597838 AGTGCGTGGCACGTAGTAGGAGCTTCATAAGTGCTTGT 597875 i v i v iv i i L2c_3end#LINE 428 AGCGCCTGGCACATAGTAGGCGCTCAATAAATGTTTGT 465 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 21.76 CpG sites = 5, Kimura (unadjusted) = 25.23 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 62 28.97 2.23 2.69 chr5qtel1M 597895 598118 (401882) (TTCC)n#Simple_repeat 1 223 (0) m_b260s252i5 10278 chr5qtel1M 597895 TTTCTTCCTTCCTAAATCTGCCTTCCTTCTTTTCTCCCTCTCTTCCTT-C 597943 i --vi v i i i ii - (TTCC)n#Simpl 1 TTCCTTCCTTCCT--TCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 48 chr5qtel1M 597944 TTCCTTCACTTCCTCTTTTCCTCTCTCCCTCCCTCCCTCTGTCCCTTCCT 597993 - iii ii i i i iiv i (TTCC)n#Simpl 49 TTCCTTC-CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT 97 chr5qtel1M 597994 TCCTT-CTCCTTTTCTCTCTT-TTTCTCTCTCTTCTTTCTTCCCTTCCTC 598041 - i i i ii -i - ii i i i i (TTCC)n#Simpl 98 TCCTTCCTTCCTTCCTTCCTTCCTTC-CTTCCTTCCTTCCTTCCTTCCTT 146 chr5qtel1M 598042 CCTTTCTCTTTTATTTCCTTCTTTCC-TCCCTCTTTCCCTTTCTTTCCCT 598090 i iii vi i - i i - - i i (TTCC)n#Simpl 147 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT-CC-TTCCTTCCTT 194 chr5qtel1M 598091 -TTTCCTTCCTCCCACCCTTCCTTCCTTC 598118 -i i vi (TTCC)n#Simpl 195 CCTTCCTTCCTTCCTTCCTTCCTTCCTTC 223 Matrix = Unknown Transitions / transversions = 8.60 (43/5) Gap_init rate = 0.05 (11 / 223), avg. gap size = 1.00 (11 / 11) 146 8.41 4.38 1.55 chr5qtel1M 598923 599173 (400827) (TTTC)n#Simple_repeat 1 258 (0) m_b260s252i6 10279 chr5qtel1M 598923 TTTCTTTTCCTTCCTTTCTTT-TTT-TTTCTTTCTCTCTTT-TTTCTTTC 598969 - - i - - i - (TTTC)n#Simpl 1 TTTC-TTT-CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC 48 chr5qtel1M 598970 TTTC--TCTTTCTTTCTTTCTTTCTTTCTTTCTCTTTTTTCTTTCTTTCC 599017 -- - i - (TTTC)n#Simpl 49 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT-TTCTTTCTTTCTTT-C 96 chr5qtel1M 599018 CCTGTTTCTTT-TCCCTCCCTTCCTTCCTCTC-TTCCTCCCTTCTTTCTT 599065 ii v - ii ii i i i - i i i (TTTC)n#Simpl 97 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 146 chr5qtel1M 599066 TCTTT-TTTC-TT-TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC 599112 - - - (TTTC)n#Simpl 147 TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC 196 chr5qtel1M 599113 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC-T 599161 - (TTTC)n#Simpl 197 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 246 chr5qtel1M 599162 TCATCCTTCCTT 599173 v i i (TTTC)n#Simpl 247 TCTTTCTTTCTT 258 Matrix = Unknown Transitions / transversions = 8.50 (17/2) Gap_init rate = 0.06 (14 / 250), avg. gap size = 1.07 (15 / 14) 212 30.48 2.41 1.19 chr5qtel1M 599175 599186 (400814) L2d_3end#LINE/L2 433 444 (72) m_b260s601i4 10280 chr5qtel1M 599175 CTCTGTGTTCGT 599186 ? v v? L2d_3end#LINE 433 CTNTTTTNTCGT 444 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 39.99 CpG sites = 14, Kimura (unadjusted) = 42.19 Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 11), avg. gap size = 0.0 (0 / 0) 77 1.45 0.00 0.00 chr5qtel1M 599187 599256 (400744) (TC)n#Simple_repeat 1 70 (0) c_b260s251i1 10281 chr5qtel1M 599187 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 599236 (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr5qtel1M 599237 CCTCTCTCTCTCTCTCTCTC 599256 i (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTC 70 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0) 212 30.48 2.41 1.19 chr5qtel1M 599257 599326 (400674) L2d_3end#LINE/L2 445 515 (1) m_b260s601i4 10280 chr5qtel1M 599257 CTCCAT--CCCTTACGACAATGTCTACTACACAGTAAGCACTTTAAAAAA 599304 i i-- v i vv i iiv vi i i i i- v L2d_3end#LINE 445 CCCCACAGCGCCTAGCACAGTGCTGAGCACATAGTAGGCGCTC-AATAAA 493 chr5qtel1M 599305 TACATTTTGATCAAGTAATTGA 599326 v v ii v i L2d_3end#LINE 494 TACTTGTTGATTGATTGATTGA 515 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 39.99 CpG sites = 14, Kimura (unadjusted) = 42.19 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.03 (2 / 69), avg. gap size = 1.50 (3 / 2) 266 29.48 0.66 3.40 chr5qtel1M 599598 599748 (400252) L1PREC2_orf2#LINE/L1 3107 3253 (41) m_b260s551i1 10282 chr5qtel1M 599598 GGGAAAATTTTTTTTCAACCAATCTCTGTGATAAAGGTCTCATTTCTCAA 599647 i vv ? v v v viv v i v v iviv L1PREC2_orf2# 3107 GGGAGAAAATNTTTGCAAACTATGCATCTGACAAAGGTCTAATATCCAGC 3156 chr5qtel1M 599648 ATCCATGGAGAACTGAGTCAAATTTATAAAAAATGGAAATAATTTA-CCA 599696 i iii v iv i i --i i viv - v L1PREC2_orf2# 3157 ATCTATAAGGAACTTAAACAAATTTACAAGAAA--AAAACAAACAACCCC 3204 chr5qtel1M 599697 ATTGATAAATGATTAAAGGAAATGAATAGGCAATTTTCAGACAAAGAAGT 599746 i v i ivi v i i v --- v L1PREC2_orf2# 3205 ATTAAAAAGTGGGCAAAGGACATGAACAGACACTTTTCA---AAAGAAGA 3251 chr5qtel1M 599747 CA 599748 L1PREC2_orf2# 3252 CA 3253 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 38.15 CpG sites = 21, Kimura (unadjusted) = 38.15 Transitions / transversions = 0.95 (21/22) Gap_init rate = 0.04 (6 / 150), avg. gap size = 1.00 (6 / 6) 564 28.65 12.01 1.52 chr5qtel1M 600159 600516 (399484) L1ME2z_3end#LINE/L1 139 533 (658) m_b260s551i2 10283 chr5qtel1M 600159 TGCTCTAAATAGCTATTGATTAGAGAAATGCAAATTAAAACAACTCCAAG 600208 v v vii v v i i v vvii L1ME2z_3end#L 139 TGCTCAACATCATTAGTCATCAGGGAAATGCAAATTAAAACCACAATGAG 188 chr5qtel1M 600209 GTACCAC--CTCACCTATTAGATTGACAAATATGATAGAAACAGAAAACA 600256 i -- v i ii v i v v v v i i v v L1ME2z_3end#L 189 ATACCACTACACACCCACCAGAATGGCTAAAATTAAAAAGACTGACAACA 238 chr5qtel1M 600257 TCGGATGTTG--GAGGATATGGGAAAACTGGAACATAGATGGATTGTTGG 600304 i ii -- i iiv i vivv iv L1ME2z_3end#L 239 CCAAATGTTGGCGAGGATGTGGAGCAACCGGAACTCTCATACATTGTTGG 288 chr5qtel1M 600305 T-AGAGTGGTGGACTGATCCAACTA---TGCCCAAAGGAC---------- 600340 -i - ii v i v i --- vvv v ---------- L1ME2z_3end#L 289 TGGGAGT-GTAAAATGGTACAACCACTTTGGAAAAAGGTCTGGCAGTTTC 337 chr5qtel1M 600341 -TATCAAA-----------------CTCTGATCCAGCAATACCACTGTTA 600372 - v ----------------- v i v vi L1ME2z_3end#L 338 TTATAAAACTAAACATACACCTACCCTATGACCCAGCAATTCCACTCCTA 387 chr5qtel1M 600373 GGTCTAGATCCCAAAGACATTCAGAAAATGGGG----AAAATGACTTATA 600418 v vv i v i v - v i v iv v---- v i L1ME2z_3end#L 388 GGTATTTACCCAAGAGAAA-TGAAAACATATGTCCACAAAAAGACTTGTA 436 chr5qtel1M 600419 CAAAAAATATTTATAGCAGCTCTTTTTATGGTGGCTAAGAATAGGAAATC 600468 - i i i i v i ii i i i iv - L1ME2z_3end#L 437 C-AAGAATGTTCATAGCAGCTTTATTCATAATAGCCAAAAACTGGAAA-C 484 chr5qtel1M 600469 AA---AGGGATGCCCTTTAGTTATGGAATAGTTAAACAAGCTGTGGTATA 600515 i--- -- i v i iivivi i v i L1ME2z_3end#L 485 AGCCCAGG--TGTCCATCAACAGGAGAATGGATAAACAAACTGTGGTATA 532 chr5qtel1M 600516 T 600516 L1ME2z_3end#L 533 T 533 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 36.33 CpG sites = 54, Kimura (unadjusted) = 36.79 Transitions / transversions = 1.15 (54/47) Gap_init rate = 0.04 (15 / 357), avg. gap size = 3.27 (49 / 15) 430 31.35 10.36 1.67 chr5qtel1M 600175 600560 (399440) L1ME4b_3end#LINE/L1 155 573 (319) m_b260s551i3 10283 chr5qtel1M 600175 TGATTAGAGAAATGCAAATTAAAACAACTCCAAGGTACCA--CCTCACCT 600222 i v v v ii i --ii L1ME4b_3end#L 155 TAATAAGAGAAATGCAAATTAAAACTACACTGAGATACCATTTTTCACCT 204 chr5qtel1M 600223 ATTAGATTGACAAATATGATAGAAACAGAAAACATCGGATGTTG--GAGG 600270 i i v v v i iviv v ivvvi -- L1ME4b_3end#L 205 ATCAGATTGGCAAAGATCAAAAAGTTTGATAACACACTGTGTTGGCGAGG 254 chr5qtel1M 600271 ATATGGGAAAACTGGAACATAGATGGATTGTTGGT-AGAGTGGTGGACTG 600319 i i i v v vivv iv i -i - ii i L1ME4b_3end#L 255 GTGTGGGGAAACAGGCACTCTCATACATTGCTGGTGGGAGT-GTAAATTG 303 chr5qtel1M 600320 ATCCAA---CTATGCC---CAA---AGGA----CTATCAAA--------- 600347 i v --- vv--- ---i v ---- --------- L1ME4b_3end#L 304 GTACAACCTCTATGGAGGGCAATTTGGCAATATCTATCAAAATTACAAAT 353 chr5qtel1M 600348 ---------CTCTGATCCAGCAATACCACTGTTAGGTCTAGATCCCAAAG 600388 --------- i i v vi vv vv i v L1ME4b_3end#L 354 GCACATACCCTTTGACCCAGCAATTCCACTTCTAGGAATTTATCCTACAG 403 chr5qtel1M 600389 ACAT--TCAGAAAATGGGGAAAATGACTTATACAAAAAA-TATTTATAGC 600435 i -- - v v v vi v ii v ii- i v L1ME4b_3end#L 404 ATATACTC-GCACATGTGCGAAATGACGTATGTACAAGGTTATTCATTGC 452 chr5qtel1M 600436 AGCTCTTTTTATGGTGGCTAAGAATAGGAAATCAAAGGGATGCCCTTTAG 600485 vi v i ii i v ii v iv vvvii i v i i L1ME4b_3end#L 453 AGCATTGTTTGTAATAGCAAAAGATTGGAAACAACCTAAATGTCCATCAA 502 chr5qtel1M 600486 TTATGGAATAGTTAAACAAGCTGTGGTATATGATTGTATTGTATTGTAAC 600535 viv v i i ii i i --iii ---i v v i L1ME4b_3end#L 503 TAGGGGACTGGTTAAATAAATTATGGTACAT--CCATA---CAATGGAAT 547 chr5qtel1M 600536 ATTATGT-GTTGTAAGAAATGATAAG 600560 i i- ii i vi i L1ME4b_3end#L 548 ACTATGCAGCCGTAAAAAAGAATGAG 573 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 40.91 CpG sites = 68, Kimura (unadjusted) = 41.84 Transitions / transversions = 1.33 (68/51) Gap_init rate = 0.05 (19 / 385), avg. gap size = 2.47 (47 / 19) 31 31.27 1.82 0.00 chr5qtel1M 600797 600882 (399118) (CTCC)n#Simple_repeat 1 87 (25) m_b260s252i7 10284 chr5qtel1M 600797 CTCCCTCCATCCCTCTTTTACTCCCTTCTTTCCTTCTTCTCTTCCTCCCT 600846 v ii iv i i i i i i i (CTCC)n#Simpl 1 CTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCT 50 chr5qtel1M 600847 -CCTCCCTCCCTTCCTCTTTTACTCTCTCCCTCTCTT 600882 - i ii iv i i i (CTCC)n#Simpl 51 CCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTC 87 Matrix = Unknown Transitions / transversions = 5.67 (17/3) Gap_init rate = 0.01 (1 / 85), avg. gap size = 1.00 (1 / 1) 118 3.97 0.75 0.75 chr5qtel1M 600883 601015 (398985) (TTTC)n#Simple_repeat 1 133 (0) c_b260s251i2 10285 chr5qtel1M 600883 TTTCTTTCTTT-TTTCCTTCCTTCCTTCCTTTCTTTCTTTCTTTCTTTCT 600931 - - i i i (TTTC)n#Simpl 1 TTTCTTTCTTTCTTT-CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 49 chr5qtel1M 600932 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT 600981 (TTTC)n#Simpl 50 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT 99 chr5qtel1M 600982 CTTTCTTTCTTTCTTCCTTTCTTTCTTCCTTTCT 601015 i i (TTTC)n#Simpl 100 CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 133 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.02 (2 / 132), avg. gap size = 1.00 (2 / 2) 31 31.27 1.82 0.00 chr5qtel1M 601016 601038 (398962) (CTCC)n#Simple_repeat 88 111 (1) m_b260s252i7 10286 chr5qtel1M 601016 C-CCTTCCTTCCTTTCTTCTCTCC 601038 - i i i i i i (CTCC)n#Simpl 88 CTCCCTCCCTCCCTCCCTCCCTCC 111 Matrix = Unknown Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.05 (1 / 22), avg. gap size = 1.00 (1 / 1) 215 24.03 0.00 12.73 chr5qtel1M 601086 601147 (398853) MIRb#SINE/MIR 197 251 (17) m_b260s601i5 10287 chr5qtel1M 601086 ATAATGATCCACATATAGAATAGACTTAGCCCAATGCCTGGCACATAGTA 601135 ----- i i iii-- v i MIRb#SINE/MIR 197 ATAATG-----CATGTAAAGCG--CTTAGCACAGTGCCTGGCACATAGTA 239 chr5qtel1M 601136 GATACTTATTAA 601147 iiii i v MIRb#SINE/MIR 240 AGCGCTCAATAA 251 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 24.49 CpG sites = 11, Kimura (unadjusted) = 30.55 Transitions / transversions = 5.50 (11/2) Gap_init rate = 0.11 (7 / 61), avg. gap size = 1.00 (7 / 7) 262 34.55 1.82 0.00 chr5qtel1M 601397 601506 (398494) L2d_3end#LINE/L2 384 495 (21) m_b260s601i6 10288 chr5qtel1M 601397 CCCCCCAAGGAGAATAGAAGTTCGTCAAGGGCAGGGCCTGT-TCTTTTGT 601445 i vv v iv i v ii v ii - v ii L2d_3end#LINE 384 CTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATAC 433 chr5qtel1M 601446 TCTGTTTTTCCCTCCCA-AGAGTCTTGCCCAGTGCTTGCTACGGGGAAGA 601494 ? v ? iviii - v i v v vivi ivi v i L2d_3end#LINE 434 TNTTTTNTCGTTCCCCACAGCGCCTAGCACAGTGCTGAGCACATAGTAGG 483 chr5qtel1M 601495 CGCTTGTTAAAT 601506 iiv L2d_3end#LINE 484 CGCTCAATAAAT 495 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 47.16 CpG sites = 21, Kimura (unadjusted) = 48.97 Transitions / transversions = 1.24 (21/17) Gap_init rate = 0.02 (2 / 109), avg. gap size = 1.00 (2 / 2) 194 21.54 10.77 0.00 chr5qtel1M 601961 602025 (397975) L2c_3end#LINE/L2 352 423 (55) m_b260s601i8 10289 chr5qtel1M 601961 TTACTTCTGTGTCTC----AGCAGCATGTAAACTCTCTGAGGGCAGGGCC 602006 ? v v ---- vi vv i i ii v L2c_3end#LINE 352 TTACNTGTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGAC 401 chr5qtel1M 602007 --TTTCTT-TTCATGCTTGTAT 602025 -- v - vi L2c_3end#LINE 402 CGTGTCTTATTCATCTTTGTAT 423 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 25.93 CpG sites = 6, Kimura (unadjusted) = 25.93 Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.05 (3 / 64), avg. gap size = 2.33 (7 / 3) 197 20.41 8.16 0.00 chr5qtel1M 601961 602009 (397991) L2a_3end#LINE/L2 374 426 (91) m_b260s601i7 10289 chr5qtel1M 601961 TTACT-TCTGTGTCTC---AGCAGCATGTAAACTCTCTGAGGGCAGGGCC 602006 i - v i --- vi v i iv v L2a_3end#LINE 374 TTATTGTCTGTCTCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGAC 423 chr5qtel1M 602007 TTT 602009 L2a_3end#LINE 424 TTT 426 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 23.98 CpG sites = 5, Kimura (unadjusted) = 23.98 Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.04 (2 / 48), avg. gap size = 2.00 (4 / 2) 324 29.98 4.42 2.61 chr5qtel1M 602389 602501 (397499) L2d2_3end#LINE/L2 435 549 (6) m_b260s601i9 10290 chr5qtel1M 602389 TAGTTTGCAAGTTCCTTGACAGGAGAGGC--TGTCTTTTTCTCATATTTG 602436 v i i vi v i i -- v v -- v L2d2_3end#LIN 435 TAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACT--TCTTTG 482 chr5qtel1M 602437 TATTTTC---AGCATTTAGCACAGCATCTGGCACATAGTAGGGGTATGAA 602483 iii --- iii iii v i v i- v L2d2_3end#LIN 483 TATCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAGTAGGCGC-TCAA 531 chr5qtel1M 602484 CCGATGTTTATTAACTCG 602501 ivi i i i i i L2d2_3end#LIN 532 TAAATATTTGTTGATTTG 549 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 38.95 CpG sites = 23, Kimura (unadjusted) = 40.59 Transitions / transversions = 2.30 (23/10) Gap_init rate = 0.04 (5 / 112), avg. gap size = 1.60 (8 / 5) 36 34.39 1.28 0.64 chr5qtel1M 602902 603010 (396990) (TC)n#Simple_repeat 1 110 (47) m_b260s252i8 10291 chr5qtel1M 602902 TCTCCCTCTCTCTCTATCTGACACACTCTCTCCCTCTTTGTCTCTTTCCC 602951 i v vv v v i i v i i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr5qtel1M 602952 TTTCTCTGTCTCTGTCAGATTCTCCCCCTCTCCCTCCCCCCATGTACTC- 603000 i v v vvvi i i i i i iv v - - (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT-CTCT 99 chr5qtel1M 603001 CTAAC-CTTCC 603010 vv - ii (TC)n#Simple_ 100 CTCTCTCTCTC 110 Matrix = Unknown Transitions / transversions = 1.00 (15/15) Gap_init rate = 0.03 (3 / 108), avg. gap size = 1.00 (3 / 3) 27 0.00 0.00 0.00 chr5qtel1M 603011 603036 (396964) (CTCTGT)n#Simple_repeat 1 26 (0) c_b260s251i3 10292 chr5qtel1M 603011 CTCTGTCTCTGTCTCTGTCTCTGTCT 603036 (CTCTGT)n#Sim 1 CTCTGTCTCTGTCTCTGTCTCTGTCT 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 36 34.39 1.28 0.64 chr5qtel1M 603037 603082 (396918) (TC)n#Simple_repeat 111 156 (1) m_b260s252i8 10293 chr5qtel1M 603037 GGCTCTCTTTTTCTCTCTCTCTGTCTGGATTTCTCTGTTTTTCTCT 603082 vv i i v vvv i v i i (TC)n#Simple_ 111 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 156 Matrix = Unknown Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 64 1.72 0.00 0.00 chr5qtel1M 604887 604945 (395055) (GT)n#Simple_repeat 1 59 (0) c_b260s251i4 10294 chr5qtel1M 604887 GTGTTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 604936 v (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50 chr5qtel1M 604937 GTGTGTGTG 604945 (GT)n#Simple_ 51 GTGTGTGTG 59 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.0 (0 / 0) 234 27.76 6.19 4.35 chr5qtel1M 606714 606826 (393174) C Charlie4a#DNA/hAT-Charlie (392) 116 2 m_b260s502i0 10295 chr5qtel1M 606714 AAGGGAAGG--AAATTTTGGGGAGAGATGGGTGGAAATCAAG--GTA--T 606757 i v -- ii vv i vi i v -- -- C Charlie4a#DNA 116 AAGGAAATGCTAAATTTCAGTTAGAGGTTAGTGAAAATAAAGATGTAATT 67 chr5qtel1M 606758 TCATTCCCTGTCCAAGTTCTCAGAAACCCCAAA-TCTATCCAATGTGGGG 606806 iv ii v i vv ii - -----v C Charlie4a#DNA 66 TTTTTCCCCATCCAAGTTCACGGACCCCCTGAATTCTATCCA-----CGG 22 chr5qtel1M 606807 ATCCCAAACTAGAAAGCCTT 606826 i iii ii v i C Charlie4a#DNA 21 ACCCCAGGTTAAGAACCCCT 2 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 34.42 CpG sites = 19, Kimura (unadjusted) = 35.92 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.08 (9 / 112), avg. gap size = 1.33 (12 / 9) 550 32.45 7.73 0.80 chr5qtel1M 607058 607290 (392710) C MIRb#SINE/MIR (14) 254 6 m_b260s601i10 10296 chr5qtel1M 607058 CATTTATCTAACACCTA-TGTATGCCAGG-ACCACGCCAAGCTCTTTACA 607105 iv i i i - i i - iii i v C MIRb#SINE/MIR 254 CATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACA 205 chr5qtel1M 607106 AACATCGTTTTATTGGATCTTCACACCAACTTCACCATGCAGACATGTGT 607155 vi ii i i vi i v iiii v v i ii - i C MIRb#SINE/MIR 204 TGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTAT-TAT 156 chr5qtel1M 607156 CA--------TTATAACTGGGGAAACTGAGG--CAGTTAGATTAAGTGTT 607195 i -------- i iv i -- vv i ivi C MIRb#SINE/MIR 155 TATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAAC 106 chr5qtel1M 607196 TTGCTTGGGATTGCCCAGTTAG--AGT--CTGAAGCTGGATTCGAAATTT 607241 iiii i ii v i -- -- v iv v viiv C MIRb#SINE/MIR 105 TTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCA 56 chr5qtel1M 607242 GGTCTTTCCCTCTCC--AGGCTGTGCCCTGTGCTCTGGTGCCCCCTTGCC 607289 v ivv -- v i i v v v - ii v vi C MIRb#SINE/MIR 55 GGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACT-GCACCACGCTGCC 7 chr5qtel1M 607290 C 607290 C MIRb#SINE/MIR 6 C 6 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 43.20 CpG sites = 49, Kimura (unadjusted) = 44.86 Transitions / transversions = 1.88 (49/26) Gap_init rate = 0.04 (9 / 232), avg. gap size = 2.22 (20 / 9) 33 31.04 3.53 3.53 chr5qtel1M 609449 609618 (390382) (AGA)n#Simple_repeat 1 170 (0) m_b260s252i9 10297 chr5qtel1M 609449 AGAAGAGGAA-AAGGAAAAGAGGAATGGGGAGGGGAAGGAAGAGAGACAG 609497 i - i i i vii i ii - - - (AGA)n#Simple 1 AGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAA-GAAGA-AGA-AG 47 chr5qtel1M 609498 AAGTGGGGGGAAGAGGAAGAGTTTGGAGAA-AAGGAGGA-AAAAAGGAGA 609545 -ii ii i ivvv i - i i - i i - (AGA)n#Simple 48 AAG-AAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAG- 95 chr5qtel1M 609546 AAGAAGGAAGAAG-AGAAGAGGAGGAAGAGGAAGGA-AAGAGGAGGAGGA 609593 - - i i i i - i i i (AGA)n#Simple 96 AAGAA-GAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA 144 chr5qtel1M 609594 TGGA-AAGAGGAGGAGGAGGAGGAAG 609618 v i - i i i i i (AGA)n#Simple 145 AGAAGAAGAAGAAGAAGAAGAAGAAG 170 Matrix = Unknown Transitions / transversions = 6.60 (33/5) Gap_init rate = 0.07 (12 / 169), avg. gap size = 1.00 (12 / 12) 311 33.91 2.61 0.00 chr5qtel1M 611890 612004 (387996) C MIRc#SINE/MIR (137) 131 14 m_b260s601i11 10298 chr5qtel1M 611890 GAAA--GAGGTCCCAGCAGGATATGTGACATGACCAGGGACACACAAAGA 611937 -- ii viiv v v v v i v ivv C MIRc#SINE/MIR 131 GAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTA 82 chr5qtel1M 611938 CCATGCGCCTAAGGCAGGATTTGAATTCAGGACCTCTTG-CTCCAGATAT 611986 vi v i v vi v i i i ii v i i - ii vi C MIRc#SINE/MIR 81 GTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCC 32 chr5qtel1M 611987 CATGTTCTTTCCACTTCA 612004 vi i v C MIRc#SINE/MIR 31 AGTGCTCTTTCCACTGCA 14 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 43.10 CpG sites = 21, Kimura (unadjusted) = 46.27 Transitions / transversions = 1.17 (21/18) Gap_init rate = 0.02 (2 / 114), avg. gap size = 1.50 (3 / 2) 555 27.08 0.68 1.38 chr5qtel1M 613478 613623 (386377) C MIRb#SINE/MIR (11) 257 113 m_b260s601i12 10299 chr5qtel1M 613478 TACCATCCACTAATTACTTACTATGTGCCCCATTCTGTGCTAAGCACTTT 613527 ii i i vii vviiv i C MIRb#SINE/MIR 257 TACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTT 208 chr5qtel1M 613528 ACAAATATTATCTCCTTTGGTCTTCACAATTTCCCTGGGAGGTATTT-TT 613576 vii v ii i ivv v vv - C MIRb#SINE/MIR 207 ACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATT 158 chr5qtel1M 613577 ATTATCCATTTTTTGAGGAGCTGAGAAAACTGAGGTGAAAAAAAGTT 613623 viv ivi -- i ivv i i i C MIRb#SINE/MIR 157 ATTATCCCCATTTTACAGA--TGAGGAAACTGAGGCTCAGAGAGGTT 113 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 32.17 CpG sites = 23, Kimura (unadjusted) = 34.44 Transitions / transversions = 1.44 (23/16) Gap_init rate = 0.02 (3 / 145), avg. gap size = 1.00 (3 / 3) 284 40.15 12.16 0.37 chr5qtel1M 614208 614692 (385308) C L3#LINE/CR1 (3087) 1012 471 m_b260s601i13 10300 chr5qtel1M 614208 AAGAGCCT-TCTTTTCTGTATTTTAA--CACTTATCTAGAAATACAAAGC 614254 i i- v iiv i? -- - vi i vv v C L3#LINE/CR1 1012 AGGAGCCCATCGTTCTGGTATCNTAAGCCA-TGGTCCAGAAAACCAAATC 964 chr5qtel1M 614255 CTGTTCTCTTACACCACCTTCATA-------ATTCTTTGCCCATATTTAC 614297 iiv i v i -------i vi v iiv C L3#LINE/CR1 963 CTGTTCTTCGACACCATCTACGTAGCCAGCTGTTCACTTCCCATATCCTC 914 chr5qtel1M 614298 TTTTCTCTTTTGATGCCTTTTACTTGCAGCAGGCAGTAT-GCTGAGAACA 614346 i iii v i -viv i v i v v v v- v i C L3#LINE/CR1 913 CTTTCTCTTCCAAAGTC-ACGACCTTCAACTGGAAGAAGAGATGAAAACA 865 chr5qtel1M 614347 CTAGTGATAGCCCTAATGTGTCCAAGTTTTTCCAGAAGACACCCCAATTC 614396 i vivi iv i vviv i iv ii v vv i vi vv i iv C L3#LINE/CR1 864 CCACCTGTGCCCCCAAGTCCTTCAGTTTCCTGCCCAGGACTTCAAAGTCA 815 chr5qtel1M 614397 CTACTGGTGAGGATCAG---------GAC--AATCATTTCTGCCCTCATG 614435 vv i vivvi --------- --vi iv v v i C L3#LINE/CR1 814 CTAGAGATGCATTCCAGGTTTCTTCTGACTGTGTCATTCGTTCCCACGTG 765 chr5qtel1M 614436 ATATAGTGGCTATGAGTCACAGTGGACAACTTTGATAAGTTTTTG--AAC 614483 vvi ii vvi i vi i v i iiv i i v --ii C L3#LINE/CR1 764 AATCAGCAGGAGTGGGTAGCGGTCGGCGGGTTTGATGAGTCTTGGCAGGC 715 chr5qtel1M 614484 TC----TCATTTCCTAAA-ACCTGTGCTGGAAAGAGAGCTGCTCTTTCTC 614528 ---- iv iiii - vi iv ii i v vvvi ii vv C L3#LINE/CR1 714 TCTCCGTCACGTCTCGGATACACGCTCCAGGAAGACAGCACACCTCCCGA 665 chr5qtel1M 614529 TTTTCAACGTCAGGAAGACAAAGTGCTGCCTC---A--CCTC-------- 614565 vv v vvvi v vv i --- -- -------- C L3#LINE/CR1 664 TTAGCCACGTCAGGTCTGCATACGGCCGCCTCCGTATCCCTCAGCGGGGA 615 chr5qtel1M 614566 -----------CCACTACTCAT-TTTTACTTATTTTGACATTTACTGGAT 614603 ----------- v v i - i v iv vvv ? v v v C L3#LINE/CR1 614 GTCACCAACCACCACGACGCGTCTCTTCCTCCTGGGGNCAGTAACAGGAT 565 chr5qtel1M 614604 GGATAACTTCTATCAGTAGCTGTGGGTATCTATGACCATTCCTTGGA--- 614650 vvv vi vi iii iv i ii viiiv v iii v --- C L3#LINE/CR1 564 TCCTCGCACCTGCTAGTGCCTGCGAATCCTCCTTATTGTTCCGTGGAGCA 515 chr5qtel1M 614651 --GGATGCTGCTTCCTCTCCCCAGGATCCAATGCTACCCTCCAT 614692 -- i i i vv i i iivvii i C L3#LINE/CR1 514 TGGAATGCTGCTTCTTCTTCAGAAGGTCCGGATTCACCCTCCGT 471 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 52.48 CpG sites = 101, Kimura (unadjusted) = 59.73 Transitions / transversions = 1.09 (101/93) Gap_init rate = 0.04 (18 / 484), avg. gap size = 3.39 (61 / 18) 820 31.13 7.94 2.51 chr5qtel1M 615255 615745 (384255) C L2#LINE/L2 (602) 2480 1964 m_b260s601i14 10301 chr5qtel1M 615255 GGAGGGAAAGAAAATGAATTCAGCTTTGGACATGTTGAATTGAAGATCTC 615304 ii i vv v i i i i vi vi C L2#LINE/L2 2480 GAGGGGGAAGATCAGGAGTTCAGTTTTGGACATGTTAAGTTTGAGATGCC 2431 chr5qtel1M 615305 AATTGGA--------TGAACA-GTTCAATA------T---TATCCAAAG- 615335 v i -------- i v - iv i ------ --- v i iv- C L2#LINE/L2 2430 TATTAGACATCCAAGTGGAGATGTCGAGTAGGCAGTTGGATATACGAGTC 2381 chr5qtel1M 615336 -GGAG---AAGAGAGAAAGATGAGGAATGGAGGAATAAATCTG--AGTCA 615379 - --- i i -- i vv iv iv i -- C L2#LINE/L2 2380 TGGAGTTCAGGGGAGA--GGTCCGGGCTGGAGATATAAATTTGGGAGTCA 2333 chr5qtel1M 615380 TCTGCACAGGGACAATAATTGAAACTACGGAGCTG-ACGAGATCACCAAG 615428 v i vi iii v i i i i iii - i ? C L2#LINE/L2 2332 TCAGCATATAGATGGTATTTAAAGCCATGAGACTGGATGAGATCACCNAG 2283 chr5qtel1M 615429 GAAAT-AGTCTCGAAAGAACAGAAAACGGGGTC--AGGACAAAGCCATGG 615475 i i - v v v iv i - i -- vi v C L2#LINE/L2 2282 GGAGTGAGTGTAGATAGAGAAGAGAA-GAGGTCCAAGGACTGAGCCCTGG 2234 chr5qtel1M 615476 TGCACTCCCTCTGTTAACAA-TCAGGAAGTAGGTGAAAATCTGGCAAAGG 615524 v vv - ? v i- i i vv iv ii v ii C L2#LINE/L2 2233 GGCACTCCAAC-GTTNAGAGGTCGGGGAGATGAGGAGGAACCAGCAAAGG 2185 chr5qtel1M 615525 AGACAAAGAAGGAATAGTCAGAGTGGTGAGAGAGGAACCATAAGACATTG 615574 vi iii i v v ii iii vi vvv C L2#LINE/L2 2184 AGACTGAGAAGGAGCGGCCAGTGAGGTAGGAGGAAAACCAGGAGAGTGTG 2135 chr5qtel1M 615575 GGGTCACAGAAA-CATGCAGAGAATCAAGTGTCCCAGAGAAAAAG---GC 615620 v vii i- v iii --- ii - ii --- i C L2#LINE/L2 2134 GTGTCCTGGAAGCCAAGTGAAGA---AAGTGTTTCA-AGAAGGAGGGAGT 2089 chr5qtel1M 615621 GATCGACAAGTATCAAAGGCTGTAGAGGGGTCAAGAAGAATAAGGGTT-- 615668 i -v i v iv ?i v ii i ii -- C L2#LINE/L2 2088 GATCAAC-TGTGTCAAATGCTGCTGANAGGTCAAGTAAGATGAGGACTGA 2040 chr5qtel1M 615669 -AATCAAAGGCTTGATTTGGTGA--TTGAGATTATCAGTGAGATTGGAAA 615715 - ii vvii v i ii -- v i i ii vv iv C L2#LINE/L2 2039 GAATTGACCATTGGATTTAGCAACGTGGAGGTCATTGGTGACCTTGACAA 1990 chr5qtel1M 615716 GAGGAGTTTTGTTTGAATGAACTGCGGGGA 615745 v i v v i ---- i C L2#LINE/L2 1989 GAGCAGTTTCGGTGGAGTG----GTGGGGA 1964 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 40.47 CpG sites = 94, Kimura (unadjusted) = 42.41 Transitions / transversions = 1.71 (94/55) Gap_init rate = 0.06 (30 / 490), avg. gap size = 1.73 (52 / 30) 250 38.49 6.17 0.58 chr5qtel1M 615730 616053 (383947) C L2#LINE/L2 (1149) 1933 1592 m_b260s601i15 10301 chr5qtel1M 615730 GAATGAACTGCGGGGAATTAAAAAGAGGAAGCAGAGAGCACTGTATGGAG 615779 iivv v i ii i v vi i v vv v v v C L2#LINE/L2 1933 GAATGGGAGGAGAGGAATTGGAGACAGCGAGTATAGACAACTCTTTCGAG 1884 chr5qtel1M 615780 ATGATTT-TTATCAAGCTGGAGACCTAGAA--GATGCAGTG--TGGATGG 615824 iv v -i i v -- iii vv -- iv i i-- v C L2#LINE/L2 1883 GAGTTTTGCTGTAAAG--GGGAGCAGAGAAATGGGGCGGTAGCTGGAGGG 1836 chr5qtel1M 615825 ATA-----GATCAAAGAAGG------GATTTCCAAGGATGGGGAAGACTT 615863 iv ----- i i i i------ v ii i ii i i?v C L2#LINE/L2 1835 GGANGTGGGGTCAAGGGAGAATTTTTGTTTTTTAAAGATGGGAGAAATNA 1786 chr5qtel1M 615864 GGGCATGTCTGTAGG-TAGTAGAGATGAGCCAATGGGCAGGGAGAGATTC 615912 vi i v - ii i ii v i i iv i i v C L2#LINE/L2 1785 CAGCATGTTTGTATGCTGATGGGAATGATCCAGTAGAGAGGGAAAAATTG 1736 chr5qtel1M 615913 AAGATTCATGAGAGAGTTGGGGTGATGGGAAGGGCAATCTGTTGGGGAAG 615962 v v v vv ivi v vvi i i v vi v i v C L2#LINE/L2 1735 ATGATGCAGGAGAGAGAGGGGAGAATTGCTGGAGCGATGTCCTTGAGTAG 1686 chr5qtel1M 615963 ACAGGATAAAATGGGATCCCTTGTGCATACGGAGGAGCTTGCCTTGGTAA 616012 i ii viii ivv ii vii i i v i vv C L2#LINE/L2 1685 GCGAGAGGGGATGGGATCTAGTGCACAAGTGGAGGGGTTGGCCTTAGATA 1636 chr5qtel1M 616013 AAAGGA-GGAC--TGCATCTTCTGAGAGAGAAATGAAGGAGGAG 616053 ii v - -- v iviv vi v i iv vi C L2#LINE/L2 1635 GGAGCACGGACAGTTCATCCGTAGTAACAGGAGGGAAGGCAGAG 1592 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 53.19 CpG sites = 70, Kimura (unadjusted) = 56.62 Transitions / transversions = 1.30 (70/54) Gap_init rate = 0.03 (10 / 323), avg. gap size = 2.20 (22 / 10) 216 31.97 18.89 0.94 chr5qtel1M 616134 616313 (383687) C L2#LINE/L2 (1605) 1477 1266 m_b260s601i16 10301 chr5qtel1M 616134 AGTGAG---AGGAAAGGGAAGTATGGGAGGTTTGAGAAGGGATGAAAAGA 616180 --- ii - i i v i i v i i C L2#LINE/L2 1477 AGTGAGGATAGGGGAGG-AGGTGTTGGAGGTTTGAGGAGAGAGGAGAAGG 1429 chr5qtel1M 616181 TTTGGAAAAGC----------AATGGGATAAGTCAAC--ACT-------- 616210 v i v i---------- i -i v i-- -------- C L2#LINE/L2 1428 TGTGAAATAGTCGTCTAGGAGAGTGGGA-GAGTGAATGGACTAGGGAAAT 1380 chr5qtel1M 616211 -------GATTGCCTTGCTGCAGGGGGAACCCAATTGACATCAGGTAACA 616253 ------- vv v vvii ii v vi i? vviv C L2#LINE/L2 1379 GTAGTANGATTGCCGGGCAGCATTAAGGGCCCACTTGAGGTTNGTGGTCA 1330 chr5qtel1M 616254 TAAATCCATCATGG----AGTCAGCAGAATTTCCTGATTTTCTCGAGCTT 616299 i ii vvi i---- vii viv v v iv C L2#LINE/L2 1329 TGAATTTAAAGTGAGACCAGTCAGCATGGTTGTGTGTTTTTCTCCAGCCA 1280 chr5qtel1M 616300 TCTTGAGCAGCATG 616313 iv v v ?i C L2#LINE/L2 1279 CGTTCAGCTGCNCG 1266 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 41.41 CpG sites = 31, Kimura (unadjusted) = 43.41 Transitions / transversions = 1.19 (31/26) Gap_init rate = 0.04 (8 / 179), avg. gap size = 4.50 (36 / 8) 186 17.02 5.32 12.50 chr5qtel1M 616234 616327 (383673) L2#LINE/L2 2002 2089 (993) m_b260s601i17 10302 chr5qtel1M 616234 CCAATTGACATC-AGGTAACATAAATCCATCATGG--AGTCAGCAGAATT 616280 - v - v vi - -- -- i ivv ---- L2#LINE/L2 2002 CCAAT-GACCTCCACGTTGC-TAAATCCA--ATGGTCAATTCTCAG---- 2043 chr5qtel1M 616281 TCCTGATTTT-CTCGAGCTTTCTTGAGCAGCATGTGAGACAG-TGATCA 616327 v i - i v ? --- v v - L2#LINE/L2 2044 TCCTCATCTTACTTGACCTNTC---AGCAGCATTTGACACAGTTGATCA 2089 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 19.38 CpG sites = 5, Kimura (unadjusted) = 19.38 Transitions / transversions = 0.56 (5/9) Gap_init rate = 0.16 (15 / 93), avg. gap size = 1.07 (16 / 15) 213 26.74 4.67 5.66 chr5qtel1M 617014 617120 (382880) C MIR3#SINE/MIR (86) 122 17 m_b260s601i18 10303 chr5qtel1M 617014 GAGTCACAGAGAGTTGCTCTGAATCCTGTCCAGGGTCACACAGCCAACCC 617063 v v v vvv -- i i i ? iiiv C MIR3#SINE/MIR 122 GAGGCCCAGAGAGGTGAAGTGA--CTTGCCCAAGGTCACACAGCNAGTTA 75 chr5qtel1M 617064 TGTGTCAAA--CATG-CTACGACCTCAGA--TCCTGGCTTCTATGGTCCT 617108 - v i -- iv - - v i i-- i i i -- v C MIR3#SINE/MIR 74 -GTGGCAGAGCCGGGACTA-GAACCCAGGTCTCCTGACTCCCA--GTCCG 29 chr5qtel1M 617109 AGCTCTCTATAC 617120 v v i C MIR3#SINE/MIR 28 TGCTCTCTCTGC 17 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 32.41 CpG sites = 14, Kimura (unadjusted) = 33.91 Transitions / transversions = 1.08 (14/13) Gap_init rate = 0.08 (9 / 106), avg. gap size = 1.22 (11 / 9) 363 21.92 3.33 8.77 chr5qtel1M 617150 617269 (382731) C MIRb#SINE/MIR (150) 118 5 m_b260s601i19 10299 chr5qtel1M 617150 GGGGTTAAGTGAC--GGCTAGGGCCACA--GCTTGTAAGCGTGAAGCGTC 617195 i i -- v i i i -- v i - v v i C MIRb#SINE/MIR 118 GAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTG-GCAGAGCC 70 chr5qtel1M 617196 TGGGGTTGGATTTGAACTCTGGTACACCTGACTCCAGGACTGGTGCTCTA 617245 ---- -- i i v viii iii iv v C MIRb#SINE/MIR 69 ----G--GGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTT 26 chr5qtel1M 617246 TCCACTGCACCACCCAGCTGCCCC 617269 --- C MIRb#SINE/MIR 25 TCCACTGCACCAC---GCTGCCCC 5 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 25.26 CpG sites = 16, Kimura (unadjusted) = 26.53 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.10 (12 / 119), avg. gap size = 1.17 (14 / 12) 219 29.87 5.19 0.00 chr5qtel1M 617514 617590 (382410) C L2#LINE/L2 (328) 2754 2674 m_b260s601i20 10304 chr5qtel1M 617514 TGGAGGCAGGGAACCTGGCTACCAGTCTCCTGCCGTGGTCCAGGCCAGAG 617563 i iv ii i vv v vi v ii v C L2#LINE/L2 2754 TGGAAGCAGGGAGACCAGTTAGGAGGCTATTGCAGTAATCCAGGCGAGAG 2705 chr5qtel1M 617564 GCAATGATGGTCTCAACCA---TGG-GGCAG 617590 iii i ii vi --- - C L2#LINE/L2 2704 ATGATGGTGGCTTGGACCAGGGTGGTGGCAG 2674 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 39.84 CpG sites = 15, Kimura (unadjusted) = 39.84 Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.03 (2 / 76), avg. gap size = 2.00 (4 / 2) 197 27.27 1.82 0.00 chr5qtel1M 617671 617725 (382275) C MIR#SINE/MIR (9) 253 198 m_b260s601i21 10305 chr5qtel1M 617671 TAACTCTCATTG-GCTCTTGTTATGCACTAGGCAGTGTGCTAAGCACTCT 617719 vi i - v ii ii i v v i i C MIR#SINE/MIR 253 TAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGCGCTTT 204 chr5qtel1M 617720 TCTTGT 617725 v v C MIR#SINE/MIR 203 ACATGT 198 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 32.00 CpG sites = 9, Kimura (unadjusted) = 34.82 Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1) 203 23.26 2.33 0.00 chr5qtel1M 617677 617719 (382281) C MIRb#SINE/MIR (17) 251 208 m_b260s601i22 10305 chr5qtel1M 617677 TCATTG-GCTCTTGTTATGCACTAGGCAGTGTGCTAAGCACTCT 617719 i - v ii ii i v i i C MIRb#SINE/MIR 251 TTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTT 208 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 26.08 CpG sites = 8, Kimura (unadjusted) = 29.56 Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.02 (1 / 42), avg. gap size = 1.00 (1 / 1) 182 35.73 3.79 4.58 chr5qtel1M 617784 617915 (382085) MIR3#SINE/MIR 75 205 (3) m_b260s601i23 10306 chr5qtel1M 617784 TACCTGGCCTGTGCTACTTGGGGCAAAAAGCTTCCCTTCCCTGAATCTCG 617833 v ? - iv i v ivvi v i i iii - MIR3#SINE/MIR 75 TAACTNGC-TGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTC- 122 chr5qtel1M 617834 GGGAGAT---TCGCCTG-GAAACAAAGGGCCGAGAATGGTTCCGGCCCAG 617879 --- v --- ii -i ii i vivi v i v vvvvi i i MIR3#SINE/MIR 123 ---AGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAA 169 chr5qtel1M 617880 GATTTTTTCCTGCTCTG-CATCCTGTGAAGTCCATGA 617915 i iii v - i i - v i MIR3#SINE/MIR 170 GGTCCCTTCCAGCTCTGACATTCTATG-ATTCTATGA 205 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 51.79 CpG sites = 28, Kimura (unadjusted) = 51.79 Transitions / transversions = 1.65 (28/17) Gap_init rate = 0.07 (9 / 131), avg. gap size = 1.22 (11 / 9) 183 36.63 2.99 2.22 chr5qtel1M 618821 618954 (381046) C MIR3#SINE/MIR (24) 184 50 m_b260s601i24 10307 chr5qtel1M 618821 GGGTTGGTAAGGATCATAGAGATCA-CTGAAATTCAAGAGAATTGTTTTA 618869 i i v i i v - -- i i vvvvv ii C MIR3#SINE/MIR 184 GAGCTGGAAGGGACCTTAGAGATCATCT--AGTCCAACCCCCTCATTTTA 137 chr5qtel1M 618870 AAGATGGCTCAGCTAAGGTCCAGGAAAGAGCAAAGAGCTGACTGAGGACA 618919 v ivvv i i i ii i v v iv vi v ii v C MIR3#SINE/MIR 136 CAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCA 87 chr5qtel1M 618920 CAAGGATCAG-AAATGGT--GGTCAGGATTTGAACCTA 618954 vi -i? -v i i--i i i i v i C MIR3#SINE/MIR 86 CACAG-CNAGTTAGTGGCAGAGCCGGGACTAGAACCCA 50 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 51.48 CpG sites = 28, Kimura (unadjusted) = 53.12 Transitions / transversions = 1.40 (28/20) Gap_init rate = 0.05 (6 / 133), avg. gap size = 1.17 (7 / 6) 12 12.63 0.00 3.70 chr5qtel1M 619287 619314 (380686) (GAGG)n#Simple_repeat 1 27 (0) m_b260s252i10 10308 chr5qtel1M 619287 GAGGGAGGGAGGGAGAAAGGGTTGGGAG 619314 ii -v (GAGG)n#Simpl 1 GAGGGAGGGAGGGAGGGAGGG-AGGGAG 27 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 668 35.28 6.71 1.71 chr5qtel1M 620038 620484 (379516) L2#LINE/L2 2151 2619 (463) m_b260s601i25 10309 chr5qtel1M 620038 TCCTTCTTTCATCTCTGCCTACTTTTTCTCAGTCTTATTTGCCAGACCAT 620087 i vi - v v ii ii iv ii vi v L2#LINE/L2 2151 TCCTCCTACC-TCACTGGCCGCTCCTTCTCAGTCTCCTTTGCTGGTTCCT 2199 chr5qtel1M 620088 CATCGGCAACATGACCA--AAATGG-GGTGTGCCCCAAGGCTCTCTCCGG 620134 v iv vv vi v--? i v- v i vv vv L2#LINE/L2 2200 CCTCATCTCCCCGACCTCTNAACGTTGGAGTGCCCCAGGGCTCAGTCCTT 2249 chr5qtel1M 620135 GGTCCTCTTTCCTTC----------------CTCTCAGTGCTCTC-TTTA 620167 v ii ---------------- i ?i v - ii L2#LINE/L2 2250 GGACCTCTTCTCTTCTCTATCTACACTCACTCCCTNGGTGATCTCATCCA 2299 chr5qtel1M 620168 CTCCCATAGGTTCGATCATTATCTCTGTGAAGATGACTCTCGGATCTATT 620217 v i i v ii vi ii v i vv i ii i v L2#LINE/L2 2300 GTCTCATGGCTTTAAATACCATCTATATGCTGATGACTCCCAAATTTATA 2349 chr5qtel1M 620218 TCTCTATCAGTGAATTGCTCCCCTGAGCTCCAGGTCTGCACTGCCAGTTG 620267 i v v-i i iiv i iiii i ivv ii L2#LINE/L2 2350 TCTCCAGCC-CGGACCTCTCCCCTGAACTCCAGACTCGTATATCCAACTG 2398 chr5qtel1M 620268 CCTTTGGAAAATCTCAAACTGGGTGTCCCATAGGCATCGCAAATTCAATT 620317 vivvi v v vi i iv v i i iv L2#LINE/L2 2399 CCTACTCGACATCTCCACTTGGATGTCTAATAGGCATCTCAAACTTAACA 2448 chr5qtel1M 620318 TGCTCAAAGCC-AACT-TTAACCTCTTTCTGCCAAATGCACCCCATCTTC 620365 ii i i- -i i -- i iv iv --- ivv i L2#LINE/L2 2449 TGTCCAAAACTGAACTCCTGA--TCTTCCCCCTCAA---ACCTGCTCCTC 2493 chr5qtel1M 620366 TCTGAA-CTTGCCTCTTTCTG-GGATGGCCCTGACATCCTTTCAAACAGT 620413 i vv i- v iv i v -?i vvivv i iviiv L2#LINE/L2 2494 CCGCAGTCTTCCCCATCTCAGTNAATGGCAACTCCATCCTTCCAGTTGCT 2543 chr5qtel1M 620414 TTGGC----AGTTTTGGAGTCCTATGAGACTCTTTCC--CCTCTCCCAGC 620457 iv ---- iii v vivv i ii --i v v L2#LINE/L2 2544 CAGGCCAAAAACCTTGGAGTCATCCTTGACTCCTCTCTTTCTCTCACACC 2593 chr5qtel1M 620458 CCTCTTCTAGGCCATCATACAAGTCTT 620484 v v i iv -i i i L2#LINE/L2 2594 CCACATCCAATCCATCA-GCAAATCCT 2619 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 47.24 CpG sites = 89, Kimura (unadjusted) = 50.02 Transitions / transversions = 1.35 (89/66) Gap_init rate = 0.04 (18 / 446), avg. gap size = 2.11 (38 / 18) 290 26.98 1.59 0.00 chr5qtel1M 620492 620554 (379446) MIRc#SINE/MIR 3 66 (202) m_b260s601i26 10310 chr5qtel1M 620492 AGACAGTGTGGTATAGTTGGAAGGGCACTGGCTCTAGATTCAGG-TGACT 620540 i ii v i i vii i v -v i MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chr5qtel1M 620541 TAAGTTCAAATCCC 620554 ii i i MIRc#SINE/MIR 53 TGGGTTCGAGTCCC 66 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 33.07 CpG sites = 13, Kimura (unadjusted) = 35.73 Transitions / transversions = 3.25 (13/4) Gap_init rate = 0.02 (1 / 62), avg. gap size = 1.00 (1 / 1) 300 29.44 10.11 10.51 chr5qtel1M 620710 620986 (379014) L2#LINE/L2 2616 2891 (191) m_b260s601i27 10309 chr5qtel1M 620710 TCCTCTAGATTCTATCCCTCAAAACCACTGTGGAATATTTGGAACTCT-C 620758 v v ii - i i--------- iii ii v- L2#LINE/L2 2616 TCCTGTCGGCTCTA-CCTTCAAAAT---------ATATCCAGAATCCGAC 2655 chr5qtel1M 620759 CGCATCACATCACCTTCCCTTCCCCCCATCCAAGCCCATACCCAATCTTA 620808 i v v i i v v v - i vi i - v viv i L2#LINE/L2 2656 CACTTCTCACCACCTCCACTGCCACC-ACCCTGGTCCA-AGCCACCATCA 2703 chr5qtel1M 620809 TTTTTGGTCTTCACTAGTTGTTGCTGGCATTGTTTCAATGGCTTCCTAAC 620858 i i ------ i --------- - ii v i i L2#LINE/L2 2704 TCTCT------CGC---------CTGG-ATTACTGCAATAGCCTCCTAAC 2737 chr5qtel1M 620859 TGCTCTTTCTG-----ACTCTT-CCCCTCTCCAGCCTA-----AA-AT-- 620894 v ii ----- i - i ? i ----- - i-- L2#LINE/L2 2738 TGGTCTCCCTGCTTCCACCCTTGCCCCCCTNCAGTCTATTCTCAACACAG 2787 chr5qtel1M 620895 --GTCAGTGTGATTTTCCTAAAGCACAAGTGTAATCA-GTCATTCCCTTG 620941 -- i v ii ii i ii vvi - i ii L2#LINE/L2 2788 CAGCCAGAGTGATCCTTTTAAAACGTAAGTCAGATCATGTCACTCCTCTG 2837 chr5qtel1M 620942 TTC---------TAAGAGCTTCCTATTGTCTCTGGGAACAAACAC-AGAG 620981 i ---------i vi i i- v vi ii vi - i L2#LINE/L2 2838 CTCAAAACCCTCCAATGGCTTCCCATC-TCACTCAGAGTAAAAGCCAAAG 2886 chr5qtel1M 620982 TCCTT 620986 L2#LINE/L2 2887 TCCTT 2891 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 38.47 CpG sites = 52, Kimura (unadjusted) = 39.93 Transitions / transversions = 2.48 (52/21) Gap_init rate = 0.14 (39 / 276), avg. gap size = 1.46 (57 / 39) 324 31.20 16.99 4.68 chr5qtel1M 620977 621282 (378718) L2b_3end#LINE/L2 123 464 (2) m_b260s601i28 10309 chr5qtel1M 620977 CAGAGTCCTTG-GCTAGCCCTTCCCAATCTGGCTCAA--GCCCTTCCCCA 621023 i i i -i ?v iv -- v vi -- L2b_3end#LINE 123 CAGGGCCTTTGCACNTGCTGTTCCC--TCTGCCTGGAACGCCCTTCCCCA 170 chr5qtel1M 621024 CC---------------CTCCT--TAGTTTTTCTGGT-TCAGCTCAAATC 621055 --------------- -- vi ii v - v L2b_3end#LINE 171 CCTCTTCGCCTGGCCAACTCCTACTCATCCTTCAGGTCTCAGCTCAAATG 220 chr5qtel1M 621056 ACACTTATTCCATGAGAGCCCTGCTGATTGCATCTCTCAA-------CAG 621098 v i vi iv - v i--- - i i i i------- L2b_3end#LINE 221 TCACCTCCTCCGGGA-AGCCCTCCC---TG-ACCCCCCAGGCCGGGTCAG 265 chr5qtel1M 621099 TCATTCTCTTATG------------TTTACTTTAT-A--------TATTT 621127 v iii i v ------------ii ii ii- -------- ?v L2b_3end#LINE 266 GCGCCCTCCTCTGGGCCCCCCCAGTCCTACCCTGCCACTCTGGGTTATNA 315 chr5qtel1M 621128 TTGATCTGCTTACAGTTGTTCTTGTTGTTTCACCAAATAGAATATAAAGT 621177 - ? -- i----- i v v v v i i - i L2b_3end#LINE 316 TTG-TCTGNTTACA--TGTC-----TGTCTCCCCCACTAGACTGTGA-GC 356 chr5qtel1M 621178 GTTATAGAGATAGAAA--GAACC-ATTTTATTTGTCTCTGTATCCCCATA 621224 viii iii ii ii -- ?ii -i i i iii v vv L2b_3end#LINE 357 TCCGTGAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTGTATCCCCAGC 406 chr5qtel1M 621225 ACGTAGCACAGAACCTGGCAAGTGGGAAGTACTTAATAAATACATATTAA 621274 i v ?i viii v i ii i i iv i i L2b_3end#LINE 407 GCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTTGTTGA 456 chr5qtel1M 621275 TTGATTGA 621282 v v L2b_3end#LINE 457 ATGAATGA 464 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 40.87 CpG sites = 63, Kimura (unadjusted) = 44.33 Transitions / transversions = 2.25 (63/28) Gap_init rate = 0.09 (27 / 305), avg. gap size = 2.52 (68 / 27) 275 29.30 19.23 3.72 chr5qtel1M 621280 621513 (378487) L3#LINE/CR1 3825 4093 (6) m_b260s601i29 10311 chr5qtel1M 621280 TGACCCCAAAGAGCAG--CTAGAAATTTAGGAGTAGAGTGAGCTACCACA 621327 i i i i -- i -iiv v i i --- i - vi L3#LINE/CR1 3825 TGGCTCCAGAGGGCAGAACTAGGA-CCAATGGGTGGA---AGTTAC-AGG 3869 chr5qtel1M 621328 TGGGAAAGTTTAGGCTTGGATGCAAGGACAAAGTTTCTTAATTTTGAGAA 621377 vi v ii v ii- ii vi v - ivv v i L3#LINE/CR1 3870 GAGGCAGATTTCGGCTCA-ATATAAGGAAGAACTTTCT-AACAATCAGAG 3917 chr5qtel1M 621378 CTGTCCAACA--------GGCTGCCT---------------------TCA 621398 v -------- --------------------- L3#LINE/CR1 3918 CTGTCCAAAAATGGAATGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGTCA 3967 chr5qtel1M 621399 CAGGAGA--------CAGTGGATGGATGACCTGTTGTCAGGG----TGTC 621436 v i-------- v v vv ---- v L3#LINE/CR1 3968 CTGGAGGTGTTCAAGCAGAGGCTGGATGACCACTTGTCAGGGATGTTGTA 4017 chr5qtel1M 621437 GAAGTGGCTTCCCCCACCTCCAACTG--GGTTTGATGAGGTGCTTAATAA 621484 - v iv -- ivi iv -- v iv i viivv L3#LINE/CR1 4018 GAAG-GGATTCCTGCA--TTGGATGGGAGGTTGGACTAGATGACCTCTAA 4064 chr5qtel1M 621485 GGCCTTTTCCAATTGGGGGTTTATGTGAT 621513 i ii i vv i v v L3#LINE/CR1 4065 GGTCCCTTCCAACTCTGAGATTCTGTGAT 4093 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 38.07 CpG sites = 35, Kimura (unadjusted) = 38.07 Transitions / transversions = 1.13 (35/31) Gap_init rate = 0.07 (16 / 233), avg. gap size = 3.44 (55 / 16) 185 26.92 1.92 0.00 chr5qtel1M 622262 622313 (377687) MIR3#SINE/MIR 149 201 (7) m_b260s601i30 10312 chr5qtel1M 622262 GTTTAATTAGATGATTTCTAAAGGTCCTTCCTGCT-TGAACCCCTCTGAA 622310 vi i i i vi v - vvii v v MIR3#SINE/MIR 149 GTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGAT 198 chr5qtel1M 622311 TCT 622313 MIR3#SINE/MIR 199 TCT 201 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 33.70 CpG sites = 7, Kimura (unadjusted) = 33.70 Transitions / transversions = 1.00 (7/7) Gap_init rate = 0.02 (1 / 51), avg. gap size = 1.00 (1 / 1) 244 25.01 5.32 6.45 chr5qtel1M 622336 622429 (377571) L3#LINE/CR1 3256 3348 (751) m_b260s601i31 10313 chr5qtel1M 622336 GAATACCAG--TCGAGATTCTAAGTGATCTTGACAGGCTGGAACCCGGGG 622383 i iv -- i v i? i vvv L3#LINE/CR1 3256 GGATGACAGAATCAAGATTCAAAANGATCTCGACAGGCTGGAACGATGGG 3305 chr5qtel1M 622384 CTGTAGCTGATTTGGAGATG---TTTACTCGTAGATAAGAATGTAAGGT 622429 i v i ii i---i --- viv -i -- i L3#LINE/CR1 3306 CCGAAACCAAC---AAGATGAAATTTAACAG-GGATA--AATGTAAAGT 3348 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 28.37 CpG sites = 14, Kimura (unadjusted) = 31.78 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.09 (8 / 93), avg. gap size = 1.38 (11 / 8) 326 29.03 5.83 2.42 chr5qtel1M 622501 622620 (377380) L2b_3end#LINE/L2 342 465 (1) m_b260s601i32 10314 chr5qtel1M 622501 CATTATATTGTAAGCTCC-TGCAGACCAAGGACTGGG---ATTTTGTCCT 622546 i v i i - - iv i i ? ---i i i v L2b_3end#LINE 342 CACTAGACTGTGAGCTCCGTG-AGGGCAGGGACCGNGTCTGTCTTGTTCA 390 chr5qtel1M 622547 TTTCTGGATCCCTAGCAATTTGAGTACATAGTCTGACACATAGTTTG--- 622593 iiv v i ivi -- i v? i i i vv --- L2b_3end#LINE 391 CCGCTGTATCCCCAGCGCCT--AGCACAGNGCCTGGCACACAGTAGGCGC 438 chr5qtel1M 622594 TTAATAAGTACTTGTTGCCTGATTGAA 622620 i i i i vv v L2b_3end#LINE 439 TCAGTAAATATTTGTTGAATGAATGAA 465 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 34.84 CpG sites = 22, Kimura (unadjusted) = 39.22 Transitions / transversions = 1.83 (22/12) Gap_init rate = 0.05 (6 / 119), avg. gap size = 1.67 (10 / 6) 14 13.29 1.96 10.64 chr5qtel1M 622986 623036 (376964) (AAC)n#Simple_repeat 1 47 (0) m_b260s252i12 10315 chr5qtel1M 622986 AACAACAACAACAACAA-ACCAAACCCCCCCAAACAAGCAAACAACAAAC 623034 - v - vv vv - - - - (AAC)n#Simple 1 AACAACAACAACAACAACAAC-AACAACAAC-AACAA-C-AACAAC-AAC 45 chr5qtel1M 623035 AA 623036 (AAC)n#Simple 46 AA 47 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.12 (6 / 50), avg. gap size = 1.00 (6 / 6) 483 27.70 5.13 5.13 chr5qtel1M 623684 623839 (376161) C MIRb#SINE/MIR (109) 159 4 m_b260s601i33 10316 chr5qtel1M 623684 TTGTCAGCTCATTTTTACAGATGAGGAAAGTGAAGCAAAAAAGGGTTAAG 623733 i i v i vv v i vv i ii C MIRb#SINE/MIR 159 TTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAG 110 chr5qtel1M 623734 TGATTTGCTCAGGGCTATTCAGCTAGTAAATG-----TCTGAGATTTGAA 623778 i i i i ii iv i -----v i i i C MIRb#SINE/MIR 109 TAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAA 60 chr5qtel1M 623779 CTCAGAAAGATGAGTCTTGCT---GGGCCTGGTATTCTATGCGCTGTACC 623825 i ---- i vv vi ---ii i- ii v v i i C MIRb#SINE/MIR 59 CCC----AGGTCTGTCTGACTCCAAAGCCC-GTGCTCTTTCCACTGCACC 15 chr5qtel1M 623826 ACTTAGCTGCCCCT 623839 --- C MIRb#SINE/MIR 14 AC---GCTGCCCCT 4 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 32.91 CpG sites = 28, Kimura (unadjusted) = 36.22 Transitions / transversions = 2.15 (28/13) Gap_init rate = 0.06 (10 / 155), avg. gap size = 1.60 (16 / 10) 238 32.18 3.33 3.33 chr5qtel1M 624153 624242 (375758) MIR3#SINE/MIR 92 181 (27) m_b260s601i34 10317 chr5qtel1M 624153 TTGGATGAGTT-TTTGATGTTTCTGGTCCTCAGTGTCCACATCTATTAAA 624201 iii i-i v iv i v v v i --- MIR3#SINE/MIR 92 TTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGT---A 138 chr5qtel1M 624202 AAAGGAAGAGGCTGGATCTGTGGAGCCCCAAGA--CTCTCCAG 624242 v i i i iiv vv v i i i-- ii MIR3#SINE/MIR 139 AAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAG 181 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 44.15 CpG sites = 18, Kimura (unadjusted) = 44.15 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.06 (5 / 89), avg. gap size = 1.20 (6 / 5) 11 24.17 4.55 0.00 chr5qtel1M 625337 625380 (374620) (TTCTTCC)n#Simple_repeat 1 46 (0) m_b260s252i13 10318 chr5qtel1M 625337 TTCTTCCTTCTTCCGGGCT-CTTCTCCCTT-TTCCCTCCACCCTCT 625380 vvvi - i - i iv i (TTCTTCC)n#Si 1 TTCTTCCTTCTTCCTTCTTCCTTCTTCCTTCTTCCTTCTTCCTTCT 46 Matrix = Unknown Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2) 16 22.40 3.45 3.45 chr5qtel1M 625926 625983 (374017) (TCTCCT)n#Simple_repeat 1 58 (0) m_b260s252i14 10319 chr5qtel1M 625926 TCTCCCTGTCACCTTTTCC-TCTCCTCCTCCCTTTCCTCTTTCTTCCCCT 625974 - - v i - i i i ii i i (TCTCCT)n#Sim 1 TCT-CCT-TCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCCT 48 chr5qtel1M 625975 TCT-TTTCTC 625983 -i (TCTCCT)n#Sim 49 TCTCCTTCTC 58 Matrix = Unknown Transitions / transversions = 9.00 (9/1) Gap_init rate = 0.07 (4 / 57), avg. gap size = 1.00 (4 / 4) 185 33.13 1.60 5.83 chr5qtel1M 626236 626360 (373640) MIR1_Amn#SINE/MIR 6 125 (105) m_b260s601i35 10320 chr5qtel1M 626236 AGGCAACACATCTTAGTGGGTAGAGAGCTGGCCTCTGGGTCATTGAGACC 626285 iiiiivii i vi v vv iv iv- MIR1_Amn#SINE 6 AGGCAGTGTGGTCTAGTGGATAGAGCACTGGACTGGGACTCGG-GAGACC 54 chr5qtel1M 626286 TCAGGCCAGGTTCCAGCTCAGCCACATTCTGGCTTCAT-ATC-TGGACAG 626333 vi vi ?i? i i v v?v i? v?i - i - i i MIR1_Amn#SINE 55 TGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAA 104 chr5qtel1M 626334 TTCCATGGCTTTGCAGCTCCCTGAGTC 626360 v ----i ?i -- i ? i MIR1_Amn#SINE 105 GTC----ACTTNAC--CTCTCTGNGCC 125 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 46.55 CpG sites = 25, Kimura (unadjusted) = 50.24 Transitions / transversions = 1.79 (25/14) Gap_init rate = 0.07 (9 / 124), avg. gap size = 1.00 (9 / 9) 205 32.86 0.00 0.00 chr5qtel1M 626250 626319 (373681) MIRc#SINE/MIR 17 86 (182) m_b260s601i36 10320 chr5qtel1M 626250 AGTGGGTAGAGAGCTGGCCTCTGGGTCATTGAGACCTCAGGCCAGGTTCC 626299 iv vi v iv i vvi vi vi ii i MIRc#SINE/MIR 17 AGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCC 66 chr5qtel1M 626300 AGCTCAGCCACATTCTGGCT 626319 i v v v i MIRc#SINE/MIR 67 GGCTCTGCCACTTACTAGCT 86 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 39.19 CpG sites = 12, Kimura (unadjusted) = 44.09 Transitions / transversions = 1.09 (12/11) Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0) 230 28.40 0.00 2.70 chr5qtel1M 627875 627950 (372050) L3#LINE/CR1 3401 3474 (625) m_b260s601i37 10321 chr5qtel1M 627875 TGGCTGGACCAGCAGTTTGTTTGAGAGAGATCTAGGGGGCTTACTGGACT 627924 v- v iiiv i i i vi v v i L3#LINE/CR1 3401 TGGCTT-AGCAGCAGTTCACGTGAAAAAGACCTAGGGGTTTTAGTTGACC 3449 chr5qtel1M 627925 GCAGTCCAAAGATCAGTCCAACTGTG 627950 iv iv v v - v L3#LINE/CR1 3450 GCAAGCTCAATATGAG-CCAACAGTG 3474 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 31.94 CpG sites = 10, Kimura (unadjusted) = 35.96 Transitions / transversions = 0.91 (10/11) Gap_init rate = 0.03 (2 / 75), avg. gap size = 1.00 (2 / 2) 286 28.33 8.61 6.49 chr5qtel1M 628523 628673 (371327) C MIR3#SINE/MIR (10) 198 45 m_b260s601i38 10322 chr5qtel1M 628523 ATCTTA-AACATCAGACCTAGTGCTTAAAGTACTGCAGAAGCCCTCTAGT 628571 v - ii v i ----- i v ivi iii v C MIR3#SINE/MIR 198 ATCATAGAATGTCAGAGCTGG-----AAGGGACCTTAGAGATCATCTAGT 154 chr5qtel1M 628572 CCA---------TCGTACAGAGAAAGAAACTGAGCTCTTAAAGAG---AA 628609 --------- iv vi i vi i- i --- C MIR3#SINE/MIR 153 CCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCC-AGAGAGGTGAA 105 chr5qtel1M 628610 GGAATTGGCCAAAGGTCCCACAAGCAGCAAGTAGCACAGCCAGGATTCTG 628659 vi i v v v iv? iv i v i i --- C MIR3#SINE/MIR 104 GTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACT--- 58 chr5qtel1M 628660 AGAGCCCCAGACCT 628673 i- ii C MIR3#SINE/MIR 57 AGAA-CCCAGGTCT 45 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 36.05 CpG sites = 25, Kimura (unadjusted) = 37.24 Transitions / transversions = 1.67 (25/15) Gap_init rate = 0.09 (13 / 150), avg. gap size = 1.77 (23 / 13) 366 24.28 6.71 6.00 chr5qtel1M 628572 628720 (371280) C MIRb#SINE/MIR (118) 150 1 m_b260s601i39 10322 chr5qtel1M 628572 CCATCGTACAGAGAAAGAAACTGAGCTCTTAAAGAG---AAGGAATTGGC 628618 iv vi i v- i i --- v i v C MIRb#SINE/MIR 150 CCATTTTACAGATGAGGAAACTGAGG-CTCAGAGAGGTTAAGTAACTTGC 102 chr5qtel1M 628619 CAAAGGTCCCACAAGCAGCAAGTAGCACAGCCAGGATTCTGAGAGCCCCA 628668 v v ivi i i v i - i--- C MIRb#SINE/MIR 101 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTC-GAA---CCCA 56 chr5qtel1M 628669 GACCTG---GGGTGCAAGG--TGTGA-CTTTCCATTAATCA-CACACTGA 628711 ii --- iv v i --i v- i i-- - i - C MIRb#SINE/MIR 55 GGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTG--CACCACGCTG- 9 chr5qtel1M 628712 ATCACTCTG 628720 -i v C MIRb#SINE/MIR 8 -CCCCTCTG 1 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 27.01 CpG sites = 21, Kimura (unadjusted) = 30.09 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.09 (14 / 148), avg. gap size = 1.36 (19 / 14) 183 34.04 6.38 0.00 chr5qtel1M 629033 629126 (370874) C MIR3#SINE/MIR (3) 205 106 m_b260s601i40 10323 chr5qtel1M 629033 TCATCAGGTCCTAGACT--TAAAA-TGGGAAGGACCTTTGACACTGTCTA 629079 viii v v --i i i- i i v v iii C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTA 156 chr5qtel1M 629080 GCCGGATCCCTTCATCTTGCCT-TGGGGCAG-TG-GGACTGGAGGGGTGA 629126 i vi i i i i vv- i v i- - v ii i C MIR3#SINE/MIR 155 GTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGA 106 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 48.70 CpG sites = 22, Kimura (unadjusted) = 48.70 Transitions / transversions = 2.20 (22/10) Gap_init rate = 0.05 (5 / 93), avg. gap size = 1.20 (6 / 5) 184 14.29 17.14 0.00 chr5qtel1M 629337 629371 (370629) C L3#LINE/CR1 (2438) 1661 1621 m_b260s601i41 10324 chr5qtel1M 629337 CTGGCCTCTGTGCTAGTTCT------CATATCAGGAAAGCA 629371 v i i ------ii C L3#LINE/CR1 1661 CTTGCCTCTGTGCCAGTTTTGTAATCTGTATCAGGAAAGCA 1621 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 16.33 CpG sites = 4, Kimura (unadjusted) = 16.33 Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.03 (1 / 34), avg. gap size = 6.00 (6 / 1) 18 4.77 0.00 0.00 chr5qtel1M 629501 629522 (370478) (TG)n#Simple_repeat 1 22 (0) m_b261s252i0 10325 chr5qtel1M 629501 TGTATGTGTGTGTGTGTGTGTG 629522 i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTG 22 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 329 32.44 4.55 1.90 chr5qtel1M 629880 630033 (369967) MIR3#SINE/MIR 3 160 (48) m_b261s601i2 10326 chr5qtel1M 629880 GGAAGAGGAG--GAGTAGCAAGAGG--GGGCTCTGGAGCCAGAGAACCTG 629925 v vi -- i vi v-- i v- i iii MIR3#SINE/MIR 3 GGCAGAGTGGCTGAGCAGAGAGAGCACGGACTG-GGAGTCAGGAGACCTG 51 chr5qtel1M 629926 GTTTCAAATACTAGCTCTACT-CTCACTACATATTTGGTCTTGGGCACAT 629974 v v i v ii i i- v ?vv i v ii vi MIR3#SINE/MIR 52 GGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGT 101 chr5qtel1M 629975 CTCTGCCATCTCTAAGGGCTTTGGGTTCTTCAGCTGT--GATGGGGCAAA 630022 v -i i vv i ii v i v --i i -iii MIR3#SINE/MIR 102 CACT-TCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGG-GGG 149 chr5qtel1M 630023 TTCGAGTAAAT 630033 v v i MIR3#SINE/MIR 150 TTGGACTAGAT 160 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 43.08 CpG sites = 29, Kimura (unadjusted) = 44.45 Transitions / transversions = 1.45 (29/20) Gap_init rate = 0.05 (7 / 153), avg. gap size = 1.43 (10 / 7) 358 29.53 4.51 0.72 chr5qtel1M 629886 630018 (369982) MIRb#SINE/MIR 15 152 (116) m_b261s601i3 10326 chr5qtel1M 629886 GGAGGAGTAGCAAGAGG--GGGCTCTGGAGCCAGAGA-ACCTGGTTTCAA 629932 v v i v v-- i i v - v i MIRb#SINE/MIR 15 GGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCGA 64 chr5qtel1M 629933 ATACTAGCTCTACT-CTCACTACATATTTGGTCTTGGGCACATCTCTGCC 629981 v ii i i- i vv i v ii vi iv -iv MIRb#SINE/MIR 65 ATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACT-TA 113 chr5qtel1M 629982 ATCTCTAAGGGCTTTGGGTTCTTCAGCTGT--GATGGGG 630018 i vv i i ii v i v --i MIRb#SINE/MIR 114 ACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGG 152 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.85 CpG sites = 22, Kimura (unadjusted) = 38.45 Transitions / transversions = 1.29 (22/17) Gap_init rate = 0.04 (5 / 132), avg. gap size = 1.40 (7 / 5) 359 29.56 2.59 0.85 chr5qtel1M 629903 630018 (369982) MIR#SINE/MIR 28 145 (117) m_b261s601i4 10326 chr5qtel1M 629903 GGGCTCTGGAGCCAGAGAACCTGGTTTCAAATACTAGCTCTACT-CTCAC 629951 vvi v i v ii i i- i MIR#SINE/MIR 28 GGGCTCTGGAGCCAGACTGCCTGGGTTCGAATCCCGGCTCTGCCACTTAC 77 chr5qtel1M 629952 TACATATTTGGTCTTGGGCACATCTCTGCCATCTCTAAGGGCTTTGGGTT 630001 vv i v ii vi iv -iv i vv v i ii v MIR#SINE/MIR 78 TAGCTGTGTGACCTTGGGCAAGTTACT-TAACCTCTCTGTGCCTCAGTTT 126 chr5qtel1M 630002 CTTCAGCTGT--GATGGGG 630018 i v --i MIR#SINE/MIR 127 CCTCATCTGTAAAATGGGG 145 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.47 CpG sites = 19, Kimura (unadjusted) = 38.45 Transitions / transversions = 1.27 (19/15) Gap_init rate = 0.03 (3 / 115), avg. gap size = 1.33 (4 / 3) 14 19.22 7.27 1.72 chr5qtel1M 630050 630104 (369896) (TTATAAA)n#Simple_repeat 1 58 (0) m_b261s252i1 10327 chr5qtel1M 630050 TTATAAATAACATTGTTATGAATT-CAAAAT-TAAATTAT-AATT-TATA 630095 v i -vi i -i v - - - v (TTATAAA)n#Si 1 TTATAAATTATA-AATTATAAATTATAAATTATAAATTATAAATTATAAA 49 chr5qtel1M 630096 TTATATATT 630104 v (TTATAAA)n#Si 50 TTATAAATT 58 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.09 (5 / 54), avg. gap size = 1.00 (5 / 5) 365 35.95 6.21 6.02 chr5qtel1M 635206 635785 (364215) L2#LINE/L2 2501 3081 (1) m_b261s601i5 10328 chr5qtel1M 635206 CTTCCCTATTTCTGTCAAGAACAATACCATGCTCCCAG--GTTCA---CA 635250 i i v ? vii iv v i -- i --- L2#LINE/L2 2501 CTTCCCCATCTCAGTNAATGGCAACTCCATCCTTCCAGTTGCTCAGGCCA 2550 chr5qtel1M 635251 A---CCTAGATGTCATCATCAACTCCTATTTCTCGATTTCTCCCTCCCCA 635297 --- v iv v ii ---- -- -------- L2#LINE/L2 2551 AAAACCTTGGAGTCATCCTTGACTCCT----CTC--TTTCTC-------- 2586 chr5qtel1M 635298 ACCCTCCCACCCCGCCCTTAATCCAATCAGTTGTCAAGGCCTATGCATTT 635347 ---- v i viii - ---- iv i vvii i L2#LINE/L2 2587 ----TCACACCCCACATCCAATCCA-TCAG----CAAATCCTGTCGGCTC 2627 chr5qtel1M 635348 CACCTGGGCAACATCTCCCAAATACACTCCTTTCTC------TCCGTT-- 635389 i vviv i v vi v ivi vi ------ ii -- L2#LINE/L2 2628 TACCTTCAAAATATATCCAGAATCCGACCACTTCTCACCACCTCCACTGC 2677 chr5qtel1M 635390 ----ATTCTA---CAGACCCTCATCACCTCACCTTTGTGTTATTGCAATC 635432 ---- ii i--- ii vi i v vii vi i v L2#LINE/L2 2678 CACCACCCTGGTCCAAGCCACCATCATCTCTCGCCTGGATTACTGCAATA 2727 chr5qtel1M 635433 ACCTCCTGGTGGGTTACTCCATGTCAAAATTCTCCCCCCTCTGCTGCAAT 635482 i iiiv iv i iiiv v vvi iv ----- ? i L2#LINE/L2 2728 GCCTCCTAACTGGTCTCCCTGCTTCCACCCTTGCCCCC-----CTNCAGT 2772 chr5qtel1M 635483 GCATCCTCCATTTGGCCAACAAAGTGATTTCCCTAAGGTGCTTGTCTGCC 635532 vi i v ivii viv i iiiii iii ivv v vi L2#LINE/L2 2773 CTATTCTCAACACAGCAGCCAGAGTGATCCTTTTAAAACGTAAGTCAGAT 2822 chr5qtel1M 635533 CATGTCTCTTCTCTCCCCGATAAGTTCAAGT--CTTCTCTATCATCTCCA 635580 v i v i i v vvi v i -- - i vivii L2#LINE/L2 2823 CATGTCACTCCTCTGCTCAAAACCCTCCAATGGCTTC-CCATCTCACTCA 2871 chr5qtel1M 635581 GGATCAAATACAAAATCCC--CCTT--CTTTCCAAACTCTTCATGACTTA 635626 ii v vv i i-- vv -- i v v ii i v ii i L2#LINE/L2 2872 GAGTAAAAGCCAAAGTCCTTACAATGGCCTACAAGGCCCTACATGATCTG 2921 chr5qtel1M 635627 GACATCACCTACATTTCCAGTCT--TCTCATGTCTT-CCTTTCTGCCCTC 635673 --- v -- i v vv --i v i - vi - i L2#LINE/L2 2922 G---TCCCC--CGTTACCTCTCTGACCTCATCTCCTACCACTCT-CCCCC 2965 chr5qtel1M 635674 TC-CCCATT--GATCCCATGACACTGACCCCCTTGCTCATTGTGGAAGAA 635720 - i i -- v viiv i i vv iv v v v L2#LINE/L2 2966 TCGCTCACTCCGCTCCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACAC 3015 chr5qtel1M 635721 GACAGTTAT-CTCTCAGTTCAGGGCGTCTTCTCTGGCTGTCTTCCATGGC 635769 v vi i- i ivi v i v v v iii iv v L2#LINE/L2 3016 GCCAGGCACGCTCCCGCCTCAGGGCCTTTGCACTTGCTGTTCCCTCTGCC 3065 chr5qtel1M 635770 AGGAATCCTCTCCCTC 635785 v iv i i L2#LINE/L2 3066 TGGAACGCTCTTCCCC 3081 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 48.95 CpG sites = 113, Kimura (unadjusted) = 51.21 Transitions / transversions = 1.36 (113/83) Gap_init rate = 0.09 (50 / 579), avg. gap size = 1.42 (71 / 50) 236 33.54 2.89 3.49 chr5qtel1M 635635 635807 (364193) L2b_3end#LINE/L2 19 190 (276) m_b261s601i6 10328 chr5qtel1M 635635 CTACATTTCCAGTCTTCTCATGTCTT-CCTTTCTGCCCTCTCCC-CATTG 635682 v i i i --- v i - vi v iv i - vi L2b_3end#LINE 19 CTACCTCTCCGGCCT---CATCTCCTACCACTCTCCCCTTGCTCACTCTG 65 chr5qtel1M 635683 ATCCCATGACACTGACCCCCTTGCTCATTGTGGAAGAAGACA-GTTATCT 635731 v viiv i i vv iv v v v v - i v? L2b_3end#LINE 66 CTCCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACACGCCANGCTCNCT 115 chr5qtel1M 635732 CTCAGTTCAGGGCGTCTTCTCTGGCTGTCTTCCATGGCAGGAA--TCCTC 635779 i ivi v i v v ?v iii iv v v --i i L2b_3end#LINE 116 CCCGCCTCAGGGCCTTTGCACNTGCTGTTCCCTCTGCCTGGAACGCCCTT 165 chr5qtel1M 635780 TCCCTCTTCTTCACTGTCTGTTGAACTC 635807 i v i --- i viv L2b_3end#LINE 166 CCCCACCTCTTC---GCCTGGCCAACTC 190 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 43.77 CpG sites = 28, Kimura (unadjusted) = 45.94 Transitions / transversions = 1.00 (28/28) Gap_init rate = 0.06 (10 / 172), avg. gap size = 1.10 (11 / 10) 332 31.34 7.46 6.58 chr5qtel1M 635752 636113 (363887) L2#LINE/L2 1903 2267 (815) m_b261s601i7 10328 chr5qtel1M 635752 CTGGCTGTCTTCCATGGCAGGAATCCTCTCCCTCTTCTTCACTGTCTGTT 635801 v i v -------- ii ----- i v v L2#LINE/L2 1903 CTCGCTGTCTCCAAT--------TCCTCTCCTCC-----CATTCTCTCTT 1939 chr5qtel1M 635802 GAACTCGGGTCCTTCTGATTCTGGGCC--AGTGCTCTATC-----CGCTC 635844 i ivvi vv v ii i v v -- vii i i -----i L2#LINE/L2 1940 GAACCCACTCCAATCAGGCTTTCGTCCCCACCACTCCACCGAAACTGCTC 1989 chr5qtel1M 635845 T-ATCACCTAGATGCTCCATTAAGGAACTCCTAATTGCTAAATCTGATTG 635893 -i --- i ---- ii v v vvi ii v L2#LINE/L2 1990 TTGTCA---AGGT----CACCAATGACCTCCACGTTGCTAAATCCAATGG 2032 chr5qtel1M 635894 TGTTTTCTCAGGGCTACTTCTTACTGAACCAGCTA-CTCCATTTGACAGT 635942 vvv vv - v vi v?ii - vv -i L2#LINE/L2 2033 TCAATTCTCAGTCCT-CATCTTACTTGACCTNTCAGCAGCATTTGACA-C 2080 chr5qtel1M 635943 AGT-GATC--TCCCT--TTCTGGAAGC------CTCAC---ACCTCTAGG 635978 - -- -- v i ------i ---i i i L2#LINE/L2 2081 AGTTGATCACTCCCTCCTTCTTGAAACACTTTCTTCACTTGGCTTCCAGG 2130 chr5qtel1M 635979 ATTTT---CTTTCCTGCTTTATCCCCCACCTGTCTGACCACACTTTTGCA 636025 ivii--- i v vi i i vv i i v i iv L2#LINE/L2 2131 ACACCACACTCTCCTGGTTTTCCTCCTACCTCACTGGCCGCTCCTTCTCA 2180 chr5qtel1M 636026 GTCTTCTTTGATGGGTCATCAACTACATCCCAA-CTCCAAATTATGGATG 636074 i v v v vv vv vi i - i? ivv - L2#LINE/L2 2181 GTCTCCTTTGCTGGTTCCTCCTCATCTCCCCGACCTCTNAACGTTGGA-G 2229 chr5qtel1M 636075 TTGCTCAAGGTACTGTGCTGAGTTTTCTGCTCTTTCTCT 636113 vv i i iv v v vi vii v - L2#LINE/L2 2230 TGCCCCAGGGCTCAGTCCTTGGACCTCTTCTC-TTCTCT 2267 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.53 CpG sites = 53, Kimura (unadjusted) = 41.52 Transitions / transversions = 1.00 (53/53) Gap_init rate = 0.10 (35 / 361), avg. gap size = 1.46 (51 / 35) 30 5.64 0.00 0.00 chr5qtel1M 636273 636309 (363691) (T)n#Simple_repeat 1 37 (0) c_b261s251i0 10329 chr5qtel1M 636273 TTTTTTGTTTTTTGTTTTTTTTTTTTTTTTTTTTTTT 636309 v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 37 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 15 20.17 2.04 4.17 chr5qtel1M 637891 637939 (362061) (TTA)n#Simple_repeat 1 48 (0) m_b261s252i2 10330 chr5qtel1M 637891 TTATTATTATTAATTCTTATTACTCTCACTTTTTAATTTTATT-TTTTTA 637939 - v i v i - v v v - v (TTA)n#Simple 1 TTATTATTATT-ATTATTATTATTATTA-TTATTATTATTATTATTATTA 48 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.06 (3 / 48), avg. gap size = 1.00 (3 / 3) 1613 30.39 1.11 1.27 chr5qtel1M 639136 639765 (360235) C L1ME4c_3end#LINE/L1 (190) 640 12 m_b261s551i0 10331 chr5qtel1M 639136 ATTCTGCTCATTTCACTCAGCATCAGTTCATGTAGTTCTCTCCAAGCCTC 639185 iv i i i vv i- iivi i v iiv C L1ME4c_3end#L 640 ATTCTGCTTTTTTCACTTAACATTATATCATA-AACATTTTCCATGTTGC 592 chr5qtel1M 639186 TCTGTATTCATCCTGCTGGTCATTTCTTACAGAACAATAATATTCCATAA 639235 vii v v v iv vi i v ii vvvv vi C L1ME4c_3end#L 591 TACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCG 542 chr5qtel1M 639236 CATTCATATACCACAGTTTATCCAACCATTCTCCATTTGATGGGCATCCA 639285 vi ?v i i i iii i vv v i ii C L1ME4c_3end#L 541 AGTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTA 492 chr5qtel1M 639286 CTCAGTTTCCAGTTTCTGGCCACTACAAACAGGGCTGCCACAAACATTTC 639335 vviv i i v i i i i iv v ii i i C L1ME4c_3end#L 491 GGTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTT 442 chr5qtel1M 639336 GGCACATACCGGTCCCTTTCCCTTCTTT---AGTATTTCTTTGGGATATA 639382 v ii iv --- i i --- v i i v C L1ME4c_3end#L 441 CGTGCATATAG---CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAA 395 chr5qtel1M 639383 AGCCCAGTAGTAGCACTGCTGGATCAAAGGGTATGCACAGTTTGATAACT 639432 vv v i v i i i v v v ii C L1ME4c_3end#L 394 TTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCT 345 chr5qtel1M 639433 TTTTGGGCATAATTCCAGATTGCTCTCCAGAATGGTTGGATTCGTTCACA 639482 i vivi i v v i i i v v iivi i C L1ME4c_3end#L 344 CTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACA 295 chr5qtel1M 639483 ACTCCATCAACAATGCATCAGTGTCCCTGTTTTCCCGCATCCTCTCCAAC 639532 ?iv i i i v ? v v iv ? v i C L1ME4c_3end#L 294 NTGCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGC 245 chr5qtel1M 639533 ATT---CATCATTATTTTTTCATGTCATCTTAGCCAATTTGACAGGTGTG 639579 ---i i i v i ---v i v i i i i i C L1ME4c_3end#L 244 ATTGGGTATTATCAATTTTTTA---AATTTTTGCTAATTTAATAGGCGTA 198 chr5qtel1M 639580 TAGTGGTATCTCGGAGTTGTCTTAATTTGCATTTCTCTGATCAATAGTGA 639629 v i ivv ii i i v i C L1ME4c_3end#L 197 AAATGGTATCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACTAGCGA 148 chr5qtel1M 639630 TTTGAAATACTCTTTCATATGAGTG-GAAATAATTTCATTTTCATCACCT 639678 vv vi i i i i i vv -vv v ? vi i - vi? C L1ME4c_3end#L 147 GGTTGAACATTTTTCCATGTGTTTGTTTACTANTTGTATTTCC-TCTTNT 99 chr5qtel1M 639679 GAAAAGTGTCTGTTCATATCCTTTGACCATTTATCAATTAGAGAATAGCT 639728 vi v i v v i i vv v v C L1ME4c_3end#L 98 GTGAATTGTCTGTTCATGTCCTTTGCCCATTTATCTATTGGGGTCTTGAT 49 chr5qtel1M 639729 TGGTTTCTTATAAATTAGAGTCAATTCTCTATATATT 639765 ?vv v v i v ii i ? C L1ME4c_3end#L 48 NTTTTTCTTATCAATTTGAATGAGCTCTTTATATANT 12 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.50 CpG sites = 106, Kimura (unadjusted) = 40.62 Transitions / transversions = 1.28 (106/83) Gap_init rate = 0.02 (11 / 629), avg. gap size = 1.36 (15 / 11) 273 33.86 3.08 3.08 chr5qtel1M 639627 639821 (360179) C L1PB_orf2#LINE/L1 (0) 3294 3100 m_b261s551i1 10331 chr5qtel1M 639627 TGATTTGAAATACTCTTTCATATGAGTGGAAATAATTT---CATTTTCAT 639673 v vi ii i i vv vviiiv ---i i v C L1PB_orf2#LIN 3294 TGATGTTGAGCATTTTTTCATATGTTTGTTGGCCATTTGTATATCTTCTT 3245 chr5qtel1M 639674 CACCTGAAAAGTGTCTGTTCATATCCTTTGACCATTTATCAATTAGAGAA 639723 ---i i v i i v v i v ii ---i i C L1PB_orf2#LIN 3244 ---TTGAGAATTGTCTATTCATGTCCTTAGCCCACTTTTTGAT---GGGA 3201 chr5qtel1M 639724 TAGCTTG---GTTTCTTATAAATTAGAGTCAATTCTCTATATATTTTGGA 639770 v i ---v iivi v vv v i ?i i v i C L1PB_orf2#LIN 3200 TTGTTTGTTTTTTTCTTGCTGATTTGTTTGAGTTCNTTGTAGATTCTGGA 3151 chr5qtel1M 639771 AATGAGGCCTTTATCAGAACCTTTAACTGTGAAAATGTTTTCCTAGTTTG 639820 v v v i vviv vi i i v i i v i C L1PB_orf2#LIN 3150 TATTAGTCCTTTGTCAGATGTATAGATTGTGAAGATTTTCTCCCACTCTG 3101 chr5qtel1M 639821 T 639821 C L1PB_orf2#LIN 3100 T 3100 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 46.61 CpG sites = 35, Kimura (unadjusted) = 46.61 Transitions / transversions = 1.21 (35/29) Gap_init rate = 0.04 (8 / 194), avg. gap size = 1.50 (12 / 8) 395 30.00 1.96 1.96 chr5qtel1M 639678 639830 (360170) C L1P3_orf2#LINE/L1 (51) 3243 3091 m_b261s551i2 10331 chr5qtel1M 639678 TGAAAAGTGTCTGTTCATATCCTTTGACCATTTATCAATTAGAGAATAGC 639727 i i v i v ii ---i ii v i C L1P3_orf2#LIN 3243 TGAGAAGTGTCTGTTCATATCCTTCGCCCACTTTTTGAT---GGGGTTGT 3197 chr5qtel1M 639728 TTG---GTTTCTTATAAATTAGAGTCAATTCTCTATATATTTTGGAAATG 639774 ---v i v vv v i ii i v i v v C L1P3_orf2#LIN 3196 TTGTTTTTTTCTTGTAAATTTGTTTAAGTTCCTTGTAGATTCTGGATATT 3147 chr5qtel1M 639775 AGGCCTTTATCAGAACCTTTAACTGTGAAAATGTTTTCCTAGTTTGTTGC 639824 v i vvvv vi i ii v i i v i v v C L1P3_orf2#LIN 3146 AGCCCTTTGTCAGATGGATAGATTGCAAAAATTTTCTCCCATTCTGTAGG 3097 chr5qtel1M 639825 TTCCCT 639830 v C L1P3_orf2#LIN 3096 TTGCCT 3091 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.79 CpG sites = 23, Kimura (unadjusted) = 38.88 Transitions / transversions = 1.05 (23/22) Gap_init rate = 0.03 (4 / 152), avg. gap size = 1.50 (6 / 4) 1183 30.59 9.06 3.19 chr5qtel1M 640503 641451 (358549) C L1PREC2_orf2#LINE/L1 (225) 3069 2067 m_b261s551i3 10332 chr5qtel1M 640503 TTTTGTTTGTACAAAGGCTCTTTAATTTGATATAATCAAAATTTTCTATT 640552 i - i i i i i vvi vv v v v C L1PREC2_orf2# 3069 TTTTGCT-GTGCAGAAGCTCTTTAGTTTAATTAGATCCCATTTGTCAATT 3021 chr5qtel1M 640553 TTGTGAT-------CAATAATGATCTGTAGTTCATCTTTGGTCAC-AAAT 640594 - v ------- -- v i - i -- i i - i- C L1PREC2_orf2# 3020 TT-TGCTTTTGTTGCAAT--TGCTTT-TGG--CGTCTTCG-TCATGAAAT 2978 chr5qtel1M 640595 TTCTTCCTTCTCCACAAGTCTGAGAGTTAAACTATCCTATGTT--CCTCT 640642 i i v ivi -i v i- i viv i i- v -- i i C L1PREC2_orf2# 2977 CTTTGCCCGTTCC-TATGTCC-AGAATGGTATTG-CCTAGGTTGTCTTCC 2931 chr5qtel1M 640643 AATTTATTTATAATCTCGTTCTTTATGCCTAAATCATGGACCCATTTTGA 640692 ivv v i i i vvi iiii i v vi i i C L1PREC2_orf2# 2930 AGGGTTTTTATAGTTTTGGGTTTTACATTTAAGTCTTTAATCCATCTTGA 2881 chr5qtel1M 640693 TCTTATCTTGGTATACGGTGTTAAGTGTGGGTCCATGCCTAAT-TTCTGC 640741 vi v i v i v i viv vviii - C L1PREC2_orf2# 2880 GTTGATTTTTGTATATGGTGTAAGGAAGGGGTCCAGTTTCAATCTTCTGC 2831 chr5qtel1M 640742 CATA---CTAATTTCCAGTTTTCCCAGCAGTTTTTGTCAAATAATGAATT 640788 - --- i--- v viv i ii iv i i C L1PREC2_orf2# 2830 -ATATGGCTAG---CCAGTTATCCCAGCACCATTTATTGAATAGGGAGTC 2785 chr5qtel1M 640789 CTTATCCCCAAAATTAGGATCTTTG---GGTTTGTCAAACACTAAATTGC 640835 - vvii v -- i --- v i v ii i v i C L1PREC2_orf2# 2784 CTT-TCCCCATTGCTTG--TTTTTGTCAGCTTTGTCGAAGATCAGATGGT 2738 chr5qtel1M 640836 TATAGTTGAGTA-TTTTGTCTTGTGAAC---CTAACCTATTCCACTGATC 640881 i v v ii-ii i - v ii --- vi i i i C L1PREC2_orf2# 2737 TGTAGGTGTGCGGCCTTAT-TTCTGGGCTCTCTATTCTGTTCCATTGGTC 2689 chr5qtel1M 640882 AACTAATCTATTTCTTAGCCAATACCAATGCTGCTTTA------------ 640919 v ivvi i i vvi i - i i------------ C L1PREC2_orf2# 2688 TATGTGTCTGTTTTTGTACCAGTACCA-TGCTGTTTTGGTTACTGTAGCC 2640 chr5qtel1M 640920 ---TAATATAGTTTTAGATCAGGTACAGCTAGGCCACCTTCA-TTTAATT 640965 --- i v ii i vv iv v --- i -i vi C L1PREC2_orf2# 2639 CTGTAGTATAGTTTGAAGTCGGGTAGCGTGATGCC---TCCAGCTTTGTT 2593 chr5qtel1M 640966 TTTTTTCATTA--ATTCCCTTGAG-ATTCTGGACCTTTTGTTCTTCCATA 641012 i vv -- v iv- v vi v vv C L1PREC2_orf2# 2592 CTTTTTGCTTAGGATTGCCTTGGCTATTCGGGCTCTTTTTTGGTTCCATA 2543 chr5qtel1M 641013 TGAATTTTG---TGATTTTTTCTAGATCATTAAAATATTTTCTTGGGAGT 641059 i--- ii v vv i iv v iv v C L1PREC2_orf2# 2542 TGAATTTTAAAATAGTTTTTTCTAGTTCTGTGAAGAATGTCATTGGTAGT 2493 chr5qtel1M 641060 CTGATTGGTATAGCACTAAATAAATAGATTAGTTTAGGGAATATTGTCAT 641109 i v v i i vvi i iv i v i v i C L1PREC2_orf2# 2492 TTGATAGGAATAGCATTGAATCTGTAAATTGCTTTGGGCAGTATGGCCAT 2443 chr5qtel1M 641110 CTTTATTATATTTGCTCGGCCTATCCAAGAGCACTTAATAATTTTCCAAT 641159 i v iv vii vv v ivv iv v C L1PREC2_orf2# 2442 TTTAACGATATTGATTCTTCCTATCCATGAGCATGGAATGTTTTTCCATT 2393 chr5qtel1M 641160 TATTTAAATCTGACTTC--ATTTATGTGGAAAGTTTTTTGTAATTTTGCT 641207 i ivi -- ii -- v v iiv v i vv C L1PREC2_orf2# 2392 TGTTTGTGTC--ATCTCTGATTTCTTTGAGCAGTGTTTTGTAATTCTCAT 2345 chr5qtel1M 641208 CATATA-ATTCCTGACTTTCCTTTGGT-AGATAGATTCCCATATATTTTA 641255 ii v - iii v i i -- - v iv i vi C L1PREC2_orf2# 2344 TGTAGAGATCTTTCACCTCCCT--GGTTAGCTGTATTCCTAGGTATTTTA 2297 chr5qtel1M 641256 TGCTATTGACAGTTATTTTGAATGGAATT---TTTCT--TTGTATCTCTT 641300 v v viii iv v i --- i -- - iv i C L1PREC2_orf2# 2296 TTCTTTTTGTGGCAATTGTGAATGGGATTGCGTTCCTGATT-TGGCTCTC 2248 chr5qtel1M 641301 GCTGTGGGATTTTGTTGGTGATGTATAAAAATGCTGAGGATTTACATGGA 641350 viv ----i v i ii iiv vii iv C L1PREC2_orf2# 2247 GGCTTGG----CTGTTGTTGGTGTATAGGAATGCTAGTGATTTTTGTACA 2202 chr5qtel1M 641351 TTTATTTTGTATCCTGCAACTTTGCTAAAGTTA----------------- 641383 v v i i----------------- C L1PREC2_orf2# 2201 TTGATTTTGTATCCTGAAACTTTGCTGAAGTTGTTTATCAGCTNAAGGAG 2152 chr5qtel1M 641384 ----TGGG-------------GTTCTCTAAGTATACCATCATATCATCTG 641416 ---- ------------- i ii vv i i C L1PREC2_orf2# 2151 CTTTTGGGCCGAGACTATGGGGTTTTCTAGATATAGAATCATGTCGTCTG 2102 chr5qtel1M 641417 CAAAGAGTGATAATTTGGTTTCCTCATTACCTACT 641451 v v i ii vi v i C L1PREC2_orf2# 2101 CAAACAGGGATAGTTTGACTTCCTCTCTTCCTATT 2067 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.78 CpG sites = 161, Kimura (unadjusted) = 40.48 Transitions / transversions = 1.34 (161/120) Gap_init rate = 0.06 (54 / 948), avg. gap size = 2.19 (118 / 54) 537 28.69 1.35 3.45 chr5qtel1M 642834 642981 (357019) C MIRc#SINE/MIR (120) 148 4 m_b261s601i8 10333 chr5qtel1M 642834 CTCATTTTACAGATGGGGAAACTGAGACAAATAGAGGG-AAATGATTTGC 642882 i i i vv v v- i i C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr5qtel1M 642883 CTGGAG-CACTCAGCTAGTAAGTGCCTGAGGCCTGATTTAAATTCAAGGC 642931 iiii - v v v v vv i ii ii i v C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTC 49 chr5qtel1M 642932 TTCCTAACTCTAGACCTGATGTTTTATTCACTGTCTGTCACCTAGCTGCC 642981 i i iii iii i i v i ----- vvi C MIRc#SINE/MIR 48 TTCCTGACTCCAAGTCCAGTGCTCTTTCCACTG-----CACCACACTGCC 4 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.40 CpG sites = 27, Kimura (unadjusted) = 37.72 Transitions / transversions = 1.93 (27/14) Gap_init rate = 0.05 (7 / 147), avg. gap size = 1.00 (7 / 7) 13 4.76 0.00 4.35 chr5qtel1M 646329 646352 (353648) (CCCT)n#Simple_repeat 1 23 (0) m_b261s252i3 10334 chr5qtel1M 646329 CCCTCCCTCCCTCCACCCCCTCCC 646352 - i (CCCT)n#Simpl 1 CCCTCCCTCCCTCC-CTCCCTCCC 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 236 30.20 4.04 3.00 chr5qtel1M 648488 648586 (351414) L2a_3end#LINE/L2 408 507 (10) m_b261s601i9 10335 chr5qtel1M 648488 CCTTGAGGCTAGGGAC---TGTCTATGTTTATTCA-TATTTTAATCTTCA 648533 v vi --- i - i - ii v - ii L2a_3end#LINE 408 CCATGAGGGCAGGGACTTTTGTCTGT-TTTGTTCACTGCTGT-ATCCCCA 455 chr5qtel1M 648534 GTTCTTTAGTGAAGTCCACGGTTCATAGAAAGCACTTAACAAATGTTTAC 648583 iv -i viv v vi iv v i i i i i ii L2a_3end#LINE 456 GCGC-CTAGAACAGTGCCTGGCACATAGTAGGCGCTCAATAAATATTTGT 504 chr5qtel1M 648584 TGA 648586 L2a_3end#LINE 505 TGA 507 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.88 CpG sites = 19, Kimura (unadjusted) = 40.50 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.05 (5 / 98), avg. gap size = 1.40 (7 / 5) 203 29.85 2.34 11.02 chr5qtel1M 649411 649538 (350462) L2c_3end#LINE/L2 321 438 (40) m_b261s601i10 10336 chr5qtel1M 649411 CCTATCTATAGCTTGT-TTGCAAATAT-TGTTTACTTGT-TGTTTTCCCC 649457 i vv i - i v i - ? - i i i L2c_3end#LINE 321 CTTATCATTAACTTGTATTGTAATTGTCTGTTTACNTGTCTGTCTCCTCC 370 chr5qtel1M 649458 ATTATTTTGTCAGTTTTTTAAGGGCAGAGATTATTGGGGTTTTTTGCTGT 649507 i vvi v i ii i i iii ---- i v v --- L2c_3end#LINE 371 ACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGT----GTCTTATTC--- 413 chr5qtel1M 649508 TGTTGTTTTTTTTTATCCCCAGCATTAAGCA 649538 ------v i v iiivi L2c_3end#LINE 414 ------ATCTTTGTATCCCCAGCGCCTGGCA 438 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.79 CpG sites = 23, Kimura (unadjusted) = 40.02 Transitions / transversions = 2.09 (23/11) Gap_init rate = 0.13 (16 / 127), avg. gap size = 1.00 (16 / 16) 187 29.73 2.26 23.97 chr5qtel1M 649437 649613 (350387) L2b_3end#LINE/L2 321 466 (0) m_b261s601i11 10336 chr5qtel1M 649437 TGTTTACTTGT-TGTTTTCCCCATTATTTTGTCAGTTTTTTAAGGGCAGA 649485 ? v - i i i vvi v i iiv i i L2b_3end#LINE 321 TGNTTACATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGG 370 chr5qtel1M 649486 GATTATTGGGGTTTTTTGCTGTTGTTGTTT--TTTTTTATCCCCAGCATT 649533 ii---- ? ------ i- i--ivi v iii L2b_3end#LINE 371 GACC----GNGT------CTGTC-TTGTTCACCGCTGTATCCCCAGCGCC 409 chr5qtel1M 649534 AAGCATCTGAGATTAGGTTTAGAGTTGGATAGTTATTGGCATACGGCAGG 649583 v i-------------- ? ii---------- i i i L2b_3end#LINE 410 TAGCAC--------------AGNGCC----------TGGCACACAGTAGG 435 chr5qtel1M 649584 CACTTAA-AAATATTTTTTGTATGACTAAGT 649613 i i i- v v v i i L2b_3end#LINE 436 CGCTCAGTAAATATTTGTTGAATGAATGAAT 466 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.56 CpG sites = 29, Kimura (unadjusted) = 38.61 Transitions / transversions = 2.64 (29/11) Gap_init rate = 0.22 (38 / 176), avg. gap size = 1.03 (39 / 38) 288 32.10 8.30 2.06 chr5qtel1M 650333 650561 (349439) C L1ME4c_3end#LINE/L1 (191) 639 397 m_b261s551i4 10337 chr5qtel1M 650333 TTCTGCTCATTTCACTCAGCATCAGTTCCTGTAAGTCTCGCCAATCCT-C 650381 iv i i i vv --i iiv ivi v vi - C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATC--ATAAACATTTTCCATGTTGC 592 chr5qtel1M 650382 TCTGTAGTCATCCTGCTGGTCATTTCTTACAGAACAATAATATTCCATAA 650431 vii v v iv vi i v ii vvvv vi C L1ME4c_3end#L 591 TACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCG 542 chr5qtel1M 650432 CATTCTTATATCACAATTTATCCAACCATTCTCCAATTGATGGGCATCCA 650481 vi ?vv i i i iii i v v i ii C L1ME4c_3end#L 541 AGTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTA 492 chr5qtel1M 650482 CTCATTTTCCAGTTTCTGGCT------------GCTACA---AACATTTT 650516 vvivv i i v ------------ i --- i C L1ME4c_3end#L 491 GGTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTT 442 chr5qtel1M 650517 GGCACATACAGGTCCCTTTCCCTTCTTT---ACTATCTCTTTGGGATA 650561 v ii i --- i i --- i i i i C L1ME4c_3end#L 441 CGTGCATATAG---CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATA 397 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 42.96 CpG sites = 43, Kimura (unadjusted) = 43.78 Transitions / transversions = 1.48 (43/29) Gap_init rate = 0.04 (9 / 228), avg. gap size = 2.67 (24 / 9) 353 26.32 0.00 0.00 chr5qtel1M 650418 650512 (349488) C L1ME3G_3end#LINE/L1 (376) 548 454 m_b261s551i5 10337 chr5qtel1M 650418 ATAATATTCCATAACATTCTTATATCACAATTTATCCAACCATTCTCCAA 650467 i ii vvv i i ii i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr5qtel1M 650468 TTGATGGGCATCCACTCATTTTCCAGTTTCTGGCTGCTACAAACA 650512 i ii vvivv i i v ii C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACA 454 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.50 CpG sites = 16, Kimura (unadjusted) = 33.50 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.00 (0 / 94), avg. gap size = 0.0 (0 / 0) 16 13.25 0.00 0.00 chr5qtel1M 650625 650649 (349351) (T)n#Simple_repeat 1 25 (0) m_b261s252i4 10338 chr5qtel1M 650625 TTTTTTTTTTTTGGTTTGTTTTTTT 650649 vv v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 16 16.52 0.00 0.00 chr5qtel1M 653376 653402 (346598) (T)n#Simple_repeat 1 27 (0) m_b261s252i5 10339 chr5qtel1M 653376 TTATTTCTTTTTTTTTTTTTTATATTT 653402 v i v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTT 27 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 1313 29.13 3.15 1.46 chr5qtel1M 653891 654430 (345570) L1ME4c_3end#LINE/L1 5 553 (277) m_b261s551i6 10340 chr5qtel1M 653891 TATTTCTAAGATATATAGAGAACTGACTAGAATTTTTAAGAATACAAGTC 653940 i ? ?-- i i v i vi vv - v ?i L1ME4c_3end#L 5 TATCTNTAN--TATATAAAGAGCTCATTCAAATTGATAAGAA-AAANATC 51 chr5qtel1M 653941 ATT-CCCCAATTGACAAATGGAAAAGGGATATGAACAGACAATTTTCA-- 653987 vv- v i iv i i iv -- L1ME4c_3end#L 52 AAGACCCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANA 101 chr5qtel1M 653988 -GATGAATTA-AAGCCATATATAGTCATATT-AAAAATGTTCCAA--TCA 654032 - v v - ?ivi v i iv i v- - -- i L1ME4c_3end#L 102 AGAGGAAATACAANTAGTAAACAAACACATGGAAAAATGTTC-AACCTCG 150 chr5qtel1M 654033 CTATTGATTAGAGAAATGCAAATTAAAACAACTCTGAGGTACCACCTCAC 654082 v i i i i vv i ii i L1ME4c_3end#L 151 CTAGTAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTAC 200 chr5qtel1M 654083 ATCTATCAAATTGGCCAAGATGATGGGAAAA--GATCATGATAAATGTTG 654130 ii i i v i -- vii -- v iviv i L1ME4c_3end#L 201 GCCTATTAAATTAGCAAAAAT--TTAAAAAATTGATAATACCCAATGCTG 248 chr5qtel1M 654131 GAGGGGATGTGGGAAAACTGGAACACTGATGCATTGTTGGTGAAGTTGTG 654180 v i ? i vi v ? v i i ivi? i L1ME4c_3end#L 249 GCGAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTA 298 chr5qtel1M 654181 AACCAATCCTACCATTCTGGAGAGCAATCTGGAACTATGCTCTAAGGGCT 654230 iiii v v v i i i v v i ivii i i L1ME4c_3end#L 299 AATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCC 348 chr5qtel1M 654231 ATAAACCTACTCATACCCTTTGATCCAACAATGTCACTATTGGGTTTGTA 654280 vv ii i ii vi vi vv v L1ME4c_3end#L 349 ATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTA 398 chr5qtel1M 654281 TCCCAAAGAGATCAT--AAAAG-AGGGGGAAGTT---TGCTACAAAAA-G 654323 i i i v -- - iii i --- - i i - L1ME4c_3end#L 399 TCCTAAGGAAATAATTCAAAAGAAGGAAAAAGCTATATGC-ACGAAGATG 447 chr5qtel1M 654324 TTTGTAACAGTTCTTTTTAGAGTGGCAAGGAACTGGCAACTGAGTGGATG 654373 ii vi ivi v v i i i ii i v vivv ii L1ME4c_3end#L 448 TTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATG 497 chr5qtel1M 654374 ACCATCAGTTGGGACAATGGCTTAATAAACTCCAGTATATGAATGTCATG 654423 v v i v i- i v i i vii i v? iviv L1ME4c_3end#L 498 TCCAACAATAGGGG-AATGGTTAAGTAAATTATGGTACATCNACTCGATG 546 chr5qtel1M 654424 GAATATT 654430 L1ME4c_3end#L 547 GAATATT 553 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.41 CpG sites = 96, Kimura (unadjusted) = 38.98 Transitions / transversions = 1.63 (96/59) Gap_init rate = 0.04 (19 / 539), avg. gap size = 1.32 (25 / 19) 141 0.00 0.74 1.49 chr5qtel1M 654931 655065 (344935) (GGAA)n#Simple_repeat 1 134 (0) c_b261s251i1 10341 chr5qtel1M 654931 GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG 654980 (GGAA)n#Simpl 1 GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG 50 chr5qtel1M 654981 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGGAAGGAAGGAAGGAAGGA 655030 - (GGAA)n#Simpl 51 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAA-GGAAGGAAGGAAGGAAGGA 99 chr5qtel1M 655031 AGGAAGGAAGGAAGGAAGGAA-GAAGGAAGGGAAGG 655065 - - (GGAA)n#Simpl 100 AGGAAGGAAGGAAGGAAGGAAGGAAGGAA-GGAAGG 134 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.02 (3 / 134), avg. gap size = 1.00 (3 / 3) 79 5.35 4.17 0.81 chr5qtel1M 655068 655187 (344813) (GAGG)n#Simple_repeat 1 124 (0) m_b261s252i6 10342 chr5qtel1M 655068 GAGGGAGGGA-GG-GGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGA-GGA 655114 - - - (GAGG)n#Simpl 1 GAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGA 50 chr5qtel1M 655115 GGGA-GGAGGGAGGGAGGG-GGGAGGGAGGGGGAGGAAGAAGGAAGGAAG 655162 - - i - i i i i (GAGG)n#Simpl 51 GGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAG-GGAGGGAGGGAGGGAG 99 chr5qtel1M 655163 GAAGGGAGGGAGGGAGGGAGGGAGG 655187 i (GAGG)n#Simpl 100 GGAGGGAGGGAGGGAGGGAGGGAGG 124 Matrix = Unknown Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.05 (6 / 119), avg. gap size = 1.00 (6 / 6) 450 20.56 7.64 5.44 chr5qtel1M 655832 655975 (344025) C MIRc#SINE/MIR (120) 148 2 m_b261s601i12 10343 chr5qtel1M 655832 CTCATTTTTCAGATGAGGAAAC--AGGC----AGAG-TAAAGAGACTT-T 655873 i v -- ---- - v v -i C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr5qtel1M 655874 CCAGGGTCACACAGCTAGGAAGTGTCCGAAGTCAGATTCGAACTCAGGTA 655923 i v v v ivivi i i -- C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGG-- 51 chr5qtel1M 655924 GATGAATCTTCCTGACTGCAGGCCAGGTGCTTGTTGCGC--CCCCA-GCT 655970 ------ v i i vi iv v i -- v -i C MIRc#SINE/MIR 50 ------TCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACT 7 chr5qtel1M 655971 GCCCC 655975 i C MIRc#SINE/MIR 6 GCCTC 2 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 23.35 CpG sites = 15, Kimura (unadjusted) = 24.31 Transitions / transversions = 1.15 (15/13) Gap_init rate = 0.10 (14 / 143), avg. gap size = 1.36 (19 / 14) 233 35.24 11.72 5.66 chr5qtel1M 656219 656636 (343364) L2b_3end#LINE/L2 18 459 (7) m_b261s601i13 10344 chr5qtel1M 656219 GCTACTTGACCAGCCT--TCTCCTCCCTTCCTTCCTGCCCCCCACCCATG 656266 i vv i -- v vii i i-iiv i i --v L2b_3end#LINE 18 GCTACCTCTCCGGCCTCATCTCCTACCACTCTCCCC-TTGCTCACTC--T 64 chr5qtel1M 656267 GATTTGATGACTCT---CACCTTGCTCTTCTGGGATGTAGGC--AGTCAC 656311 v iiiiiv v --- v v ivv -ii v --? iiv? L2b_3end#LINE 65 GCTCCAGCCACACTGGCCTCCTTGCTGTTCCTCGA-ACACGCCANGCTCN 113 chr5qtel1M 656312 CTCTCAGCTCAGATCATTCCCTCTGGCTGTCCCCTGGGACTGGAAT--CC 656359 i iv iv v iv v ?v i vv v i-- L2b_3end#LINE 114 CTCCCGCCTCAGGGCCTTTGCACNTGCTGTTCCCTCTGCCTGGAACGCCC 163 chr5qtel1M 656360 T-------CTCTTC--TTGGTC-----------------CAAGTCCCAGT 656383 ------- --i i ----------------- i i i L2b_3end#LINE 164 TTCCCCACCTCTTCGCCTGGCCAACTCCTACTCATCCTTCAGGTCTCAGC 213 chr5qtel1M 656384 TAAAAACCTCATCTGTCACAGGAAGCCTTTCCCAATCCT--GGGTAATTG 656431 v -iv i viiv i i i ii i i--i i---i L2b_3end#LINE 214 TCAAA-TGTCACCTCCTCCGGGAAGCCCTCCCTGACCCCCCAGGC---CG 259 chr5qtel1M 656432 GGGGGAACTCCCCACCTTTTACCATCTTAGT--TATCCCACAGAGCTGGT 656479 vviii v iv ii vvi vi ii -- i ii vivv v L2b_3end#LINE 260 GGTCAGGCGCCCTCCTCTGGGCCCCCCCAGTCCTACCCTGCCACTCTGGG 309 chr5qtel1M 656480 TTGTACACATTTGTTTGCTTGTTGTGTGGCTCTCCCCCCTCCCTCACCCC 656529 i ?vvii i ? i v i- ----------- i --- L2b_3end#LINE 310 TTATNATTGTCTGNTTACATGTC-TGT-----------CTCCCCCAC--- 344 chr5qtel1M 656530 TTTAGGCCGGGAGCTTCTTGAGGGCAGGGA------TTGTCCTCTGCCCC 656573 -- i i v i v ------i i v v v L2b_3end#LINE 345 --TAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCTTGTTCACC 392 chr5qtel1M 656574 TTTCTA---CCAGC-CTCAGTCCAATACCTAATAGATAGTAGGCACTGAA 656619 vi v --- - ii iv i?i iii v i i v i L2b_3end#LINE 393 GCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAG 442 chr5qtel1M 656620 TAAAACTTTATTGACTG 656636 vv i v L2b_3end#LINE 443 TAAATATTTGTTGAATG 459 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 48.10 CpG sites = 84, Kimura (unadjusted) = 51.29 Transitions / transversions = 1.53 (84/55) Gap_init rate = 0.09 (37 / 417), avg. gap size = 2.00 (74 / 37) 327 26.42 7.01 8.39 chr5qtel1M 656480 656636 (343364) L2a_3end#LINE/L2 356 510 (7) m_b261s601i14 10344 chr5qtel1M 656480 TTGTACACATTTGTTTGCTTGTTGTGTGGCTCTCCCCCCTCCCTCACCCC 656529 v vi i i i v -- ------ --- L2a_3end#LINE 356 TTTTACTTATTTATTTGTTTATTGTCTG--TCTCCCCC------CAC--- 394 chr5qtel1M 656530 TTTAGGCCGGGAGCTTCTTGAGGGCAGGGA---TTGTC--CTCTGCCCCT 656574 -- ivi vi i v --- --i i ii vi L2a_3end#LINE 395 --TAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTCTGTTTTGTTCAC 442 chr5qtel1M 656575 TTCTA-----CCAGC-CTCAGTCCAATACCTAATAGATAGTAGGCACTGA 656618 v i----- - ii vv i i iii v i v L2a_3end#LINE 443 TGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGGCGCTCA 492 chr5qtel1M 656619 ATAAAACTTTATTGACTG 656636 vv i v L2a_3end#LINE 493 ATAAATATTTGTTGAATG 510 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.32 CpG sites = 23, Kimura (unadjusted) = 33.39 Transitions / transversions = 1.53 (23/15) Gap_init rate = 0.11 (17 / 156), avg. gap size = 1.41 (24 / 17) 13 12.13 0.00 3.57 chr5qtel1M 661930 661958 (338042) (AAACC)n#Simple_repeat 1 28 (0) m_b261s252i7 10345 chr5qtel1M 661930 AAACCAAACCGAACCCCAAACAAACCAAA 661958 - v v v (AAACC)n#Simp 1 AAACCAAACC-AAACCAAACCAAACCAAA 28 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1) 18 0.00 0.00 0.00 chr5qtel1M 662496 662515 (337485) (T)n#Simple_repeat 1 20 (0) m_b261s252i8 10346 chr5qtel1M 662496 TTTTTTTTTTTTTTTTTTTT 662515 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTT 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 398 21.04 10.43 0.79 chr5qtel1M 662518 662632 (337368) C MIRc#SINE/MIR (141) 127 2 m_b261s601i15 10347 chr5qtel1M 662518 CTGAGGC-AATTGGGGTTAAGTGACTTGCCCAGGGTCACAAAGCCAGGAA 662566 -v vv i i v i v C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAA 78 chr5qtel1M 662567 GTATTTAGTGTC----TTAGATCTCAGGTCCTCCTGACTTCA-----GGT 662607 i-vi v i ----i v v i i i -----i C MIRc#SINE/MIR 77 GTG-GCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGT 29 chr5qtel1M 662608 GCTGTATCCACTGCGCCACCC--CCTC 662632 v v i v -- C MIRc#SINE/MIR 28 GCTCTTTCCACTGCACCACACTGCCTC 2 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 24.88 CpG sites = 12, Kimura (unadjusted) = 24.88 Transitions / transversions = 1.00 (12/12) Gap_init rate = 0.04 (5 / 114), avg. gap size = 2.60 (13 / 5) 298 36.20 6.57 4.41 chr5qtel1M 663047 663335 (336665) L2b_3end#LINE/L2 162 456 (10) m_b261s601i16 10348 chr5qtel1M 663047 CTCTCCCCATCCCAGTTGCCCAAGAAGCTCCCTCTAACTTCCCTGAAGCC 663096 ii i i -v i iiivv i iv v -- i v i i L2b_3end#LINE 162 CCTTCCCCACCTC-TTCGCCTGGCCAACTCCTACTCA--TCCTTCAGGTC 208 chr5qtel1M 663097 CCAGCTGGAGT-CCATCTTGCACAAGGAGGCTTTC--TGAGTTCTCCTTA 663143 i vi i -i i i- v vi i ii -- --- i ii L2b_3end#LINE 209 TCAGCTCAAATGTCACCTC-CTCCGGGAAGCCCTCCCTGA---CCCCCCA 254 chr5qtel1M 663144 ACTC----TAGGACCTTCCCTCTCTGGACTTGGTGCAATT-TATCCTGTC 663188 ivi ----i -- vi ii i iivvi- i i- i - L2b_3end#LINE 255 GGCCGGGTCAGG--CGCCCTCCTCTGGGCCCCCC-CAGTCCTACCCTG-C 300 chr5qtel1M 663189 CATAAAGGGTTTCTACATGGTTGTTGGCAAGT-TGCCTGCCCCATCCCA- 663236 ivvv vi? i- vi ? vi v - i v iivv - L2b_3end#LINE 301 CACTCTGGGTTATNAT-TGTCTGNTTACATGTCTGTCTCCCCCACTAGAC 349 chr5qtel1M 663237 -GCGAGCTCCATGAGAACAAGGGAC---ATC--CCTTGCATATCATTATG 663280 - i i ii - ---i --i ivi i ii i i L2b_3end#LINE 350 TGTGAGCTCCGTGAGGGC-AGGGACCGNGTCTGTCTTGTTCACCGCTGTA 398 chr5qtel1M 663281 TTCCTAGTACTTAGAAGAGGGCCAAACA---AGTAGCAGTTCCTTAAATG 663327 i i ii i v v ? vii --- vv i vv i L2b_3end#LINE 399 TCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATA 448 chr5qtel1M 663328 TTTGTTGA 663335 L2b_3end#LINE 449 TTTGTTGA 456 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 50.46 CpG sites = 69, Kimura (unadjusted) = 54.69 Transitions / transversions = 2.23 (69/31) Gap_init rate = 0.08 (23 / 288), avg. gap size = 1.39 (32 / 23) 292 27.60 6.91 3.61 chr5qtel1M 663449 663636 (336364) C MIR3#SINE/MIR (5) 203 10 m_b261s601i17 10349 chr5qtel1M 663449 ATAGGATCATAGACTGATCC---CTAGAAGGGAGCTGAAAGGCCATGGAG 663495 i v - v--- i v v i ii vv C MIR3#SINE/MIR 203 ATAGAATCATAGAATG-TCAGAGCTGGAAGGGACCTTAGAGATCATCTAG 155 chr5qtel1M 663496 TCCAACTACCTCGTTTTTACAGATGGAGGAAATGGGGCTCCATGGTTCAG 663545 iv i- ii i v i - vi --- C MIR3#SINE/MIR 154 TCCAACCCCCTCA-TTTTACAGATGAGGAAACTGAGGC-CCAGAG---AG 110 chr5qtel1M 663546 GC--AGTGGCTCA-GCAAG--C-CACTGTTAA-AAATGCCTGAAAAGGGA 663588 i-- i ii-v -- - v i? i-v i v v ivv C MIR3#SINE/MIR 109 GTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGA 60 chr5qtel1M 663589 TTCCAAGGCAGCTCTTCCTGCCCCCAAATCCG-GCACTTGCT--TCATCC 663635 i vv vv v - v i v i - v iv -- v C MIR3#SINE/MIR 59 CTAGAACCCAGGTC-TCCTGACTCCCAGTCCGTGCTCTCTCTGCTCAGCC 11 chr5qtel1M 663636 A 663636 C MIR3#SINE/MIR 10 A 10 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.00 CpG sites = 24, Kimura (unadjusted) = 35.00 Transitions / transversions = 0.92 (24/26) Gap_init rate = 0.08 (15 / 187), avg. gap size = 1.33 (20 / 15) 256 26.39 5.56 0.00 chr5qtel1M 666889 666960 (333040) L1P1_orf2#LINE/L1 2624 2699 (595) m_b262s551i0 10350 chr5qtel1M 666889 TCAAACTATGTTATCATGCTCCAGTTACCTAAACCATTTGGTATTGGT-- 666936 ii iv v v v v viiv i -- L1P1_orf2#LIN 2624 TCAAACTATACTACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTAC 2673 chr5qtel1M 666937 --AAATAGGGAGATAAATCAGTGGGA 666960 -- i i v i i i L1P1_orf2#LIN 2674 CAAAACAGAGATATAGATCAATGGAA 2699 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.23 CpG sites = 11, Kimura (unadjusted) = 33.23 Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.03 (2 / 71), avg. gap size = 2.00 (4 / 2) 30 0.00 0.00 0.00 chr5qtel1M 667333 667358 (332642) (AC)n#Simple_repeat 1 26 (0) c_b262s251i0 10351 chr5qtel1M 667333 ACACACACACACACACACACACACAC 667358 (AC)n#Simple_ 1 ACACACACACACACACACACACACAC 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 12 8.85 4.17 0.00 chr5qtel1M 667527 667550 (332450) (CAG)n#Simple_repeat 1 25 (0) m_b262s252i0 10352 chr5qtel1M 667527 CAGAAGTA-CAGCAGCAGCAGCAGC 667550 v i - (CAG)n#Simple 1 CAGCAGCAGCAGCAGCAGCAGCAGC 25 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 15 20.03 3.64 3.64 chr5qtel1M 668605 668659 (331341) (TTTTCT)n#Simple_repeat 1 55 (0) m_b262s252i1 10353 chr5qtel1M 668605 TTTTTGTTTTCTTTCTCAGTTTTTCTTTGTC--TTTCTTCTTCATCTGAT 668652 iv i -- v -- i v i vv (TTTTCT)n#Sim 1 TTTTCTTTTTCTTTTTC--TTTTTCTTTTTCTTTTTCTTTTTCTTTTTCT 48 chr5qtel1M 668653 TTTTCTT 668659 (TTTTCT)n#Sim 49 TTTTCTT 55 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.06 (3 / 54), avg. gap size = 1.33 (4 / 3) 13 26.14 4.00 0.00 chr5qtel1M 668677 668726 (331274) (TATA)n#Simple_repeat 1 52 (0) m_b262s252i2 10354 chr5qtel1M 668677 TATAAATATATATACATATAT-TGGATCTA-ACATGTATTTCTACATATT 668724 v i - iv v - i i v v i v (TATA)n#Simpl 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr5qtel1M 668725 TA 668726 (TATA)n#Simpl 51 TA 52 Matrix = Unknown Transitions / transversions = 0.83 (5/6) Gap_init rate = 0.04 (2 / 49), avg. gap size = 1.00 (2 / 2) 20 23.63 4.55 1.47 chr5qtel1M 669201 669266 (330734) (AT)n#Simple_repeat 1 68 (0) m_b262s252i3 10355 chr5qtel1M 669201 ATATTTGCATAAATATGTATATATATAT-TGGATTTA-ATATATATTTTT 669248 v ii v i - iv v - v v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr5qtel1M 669249 ATCAAGTTTA-ATATATAT 669266 - vi v - (AT)n#Simple_ 51 AT-ATATATATATATATAT 68 Matrix = Unknown Transitions / transversions = 0.62 (5/8) Gap_init rate = 0.06 (4 / 65), avg. gap size = 1.00 (4 / 4) 364 20.98 8.64 2.92 chr5qtel1M 670350 670511 (329489) L1MEj_5end#LINE/L1 1990 2160 (0) m_b262s551i1 10356 chr5qtel1M 670350 ATAAATAAATGA--AAATAGCATAGA-GGAGGAAAATATAGT-TATCA-- 670393 ?i -- i iv i - iv vv - -- L1MEj_5end#LI 1990 ATAAATAAANAATAAAGTAAGATGGAAGGAATAAAATCAAGTATATCAGT 2039 chr5qtel1M 670394 ---TA-ACTATGAATGTGAATGGAATGAATTGATCCAT-AAATCCAGACG 670438 --- - -- v vvi - --- i L1MEj_5end#LI 2040 CGTTACACTA--AATGTGAATGGACTGAATTCTCCCATTAAA---AGACA 2084 chr5qtel1M 670439 CAGA-TAGCAAATTGGATCAAAC--CAAAATCCTGCAATATATCATTTAC 670485 v - iv i i i v-- i v v iiii L1MEj_5end#LI 2085 GAGACTGTCAGATTGGGTTAAAAAACAAAACCCAGCTATATGCTGTTTAC 2134 chr5qtel1M 670486 AAGAAACACATTTGAAGCAGAGAGAT 670511 i i i i v L1MEj_5end#LI 2135 AAGAAACACACTTAAAACAAAGTGAT 2160 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 25.31 CpG sites = 20, Kimura (unadjusted) = 25.31 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.09 (14 / 161), avg. gap size = 1.36 (19 / 14) 420 32.13 5.52 2.00 chr5qtel1M 670380 670814 (329186) L1MC_orf2#LINE/L1 18 467 (2827) m_b262s551i2 10356 chr5qtel1M 670380 AAATATAGTTATCATAACTATGAATGTGAATGGAATGAATTGATCCAT-A 670428 v viv v v v i ? vv i vv i v - L1MC_orf2#LIN 18 AACTATATCAATAATCACTTTAAATGTNAATGGTCTAAATACACCAATTA 67 chr5qtel1M 670429 AATCCAGACGCAGATAG-CAAATTGGATCAAAC--CAAAATCCTGCAATA 670475 --- iv v - i v v-- i i vi v L1MC_orf2#LIN 68 AA---AGACAGAGATTGTCAGAGTGGATCAAAAAACAAGACCCAACTATA 114 chr5qtel1M 670476 TATCATTTACAAGAAACACATTTGAAGCAGAGAGATACACACAG--TAAA 670523 i ii i v i v ii v i i i i -- L1MC_orf2#LIN 115 TGTTGTCTACAAGAAACCCACTTTAAATATAAAGACACATATAGATTAAA 164 chr5qtel1M 670524 GATAAGAGGCTAGAGAAGAACCCATTATGCTTCAGCTGAAGTAAAGAAAG 670573 ii i? v i ii ivi ii vvvi i vvv L1MC_orf2#LIN 165 AGTAAANGGATGGAGAAAGATATACCATGCTAACACTAATCAAAAGAAAG 214 chr5qtel1M 670574 CAGGGGTAGCCATCATGCCCTCAGACAAAGGAAA----GGCAAAAGCCGA 670619 ? i i vv ivii i v i ----i viv vvi L1MC_orf2#LIN 215 CNGGAGTAGCTATATTAATTTCAGACAGAGCAGACTTCAGAGCAAGGAAA 264 chr5qtel1M 670620 TTTAATTGAGAATTAAGGAAGGACACTA-AT--TG--AAAGGTATCAA-- 670662 v -- v iiv i i i i - -- -- vi -- L1MC_orf2#LIN 265 GTTA--TCAGGGATAAAGAGGGGCATTACATAATGATAAAGGGGTCAATT 312 chr5qtel1M 670663 AGACAATGAAATCACATCAACACTAGATATAGGTGCACCAAATGATATGG 670712 vvv - iv i v iv vi ii ivi i v ii i vi L1MC_orf2#LIN 313 CTCCAA-GAAGACATAACAATCCTTAACGTGTATGCGCCTAACAACAGAG 361 chr5qtel1M 670713 CATCTAAA-GTTTGAAG---AAGTTGAATGAATTACAAGAGGAAAT-GAA 670757 i v -iiv i --- ii vv i i ii - v L1MC_orf2#LIN 362 CGTCAAAATACGTGAGGCAAAAACTGATAGAACTGCAAGGAGAAATAGAC 411 chr5qtel1M 670758 AAATCAAACTATATTAGTGGGGGACCTCCAATAGCCCCTC--TCAGAAAA 670805 i -v vv v i - i i - -- ? v L1MC_orf2#LIN 412 GAATC-CACTATTATAGTTGGAGA-CTTCAACA-CCCCTCTATCAGNAAT 458 chr5qtel1M 670806 AGACAAATC 670814 ? i L1MC_orf2#LIN 459 NGACAGATC 467 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.71 CpG sites = 77, Kimura (unadjusted) = 43.88 Transitions / transversions = 1.28 (77/60) Gap_init rate = 0.05 (22 / 434), avg. gap size = 1.50 (33 / 22) 14 22.74 2.44 0.00 chr5qtel1M 671607 671647 (328353) (AGG)n#Simple_repeat 1 42 (0) m_b262s252i4 10357 chr5qtel1M 671607 AGGAGGA-AAGGGGAAGCCTGGGCAGGAGGAGGAGGAGGAGG 671647 -i i i vvv i v (AGG)n#Simple 1 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGG 42 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 341 21.98 15.38 0.00 chr5qtel1M 673538 673628 (326372) C L2b_3end#LINE/L2 (6) 460 356 m_b262s601i0 10358 chr5qtel1M 673538 TCAGTCAGTAAACCTTTATTGAGCACCTACTATGTGTCAGTCAGTAGGCT 673587 v ii iv i i i i v ?v iv C L2b_3end#LINE 460 TCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCT 411 chr5qtel1M 673588 AAGCCCTGAGGATAC---------CAGGAAAGA-----TCCCTCCCCTCA 673623 i v i --------- i v ----- v C L2b_3end#LINE 410 AGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCA 361 chr5qtel1M 673624 AGGAG 673628 v C L2b_3end#LINE 360 CGGAG 356 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 25.19 CpG sites = 11, Kimura (unadjusted) = 26.69 Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.02 (2 / 90), avg. gap size = 7.00 (14 / 2) 243 29.51 5.41 6.12 chr5qtel1M 673628 673775 (326225) MIRc#SINE/MIR 2 148 (120) m_b262s601i1 10359 chr5qtel1M 673628 GGGGCGGTCTGGCCCTGCAGAGAGCGCCCCGGGCTTGGCACCTGGAAGAT 673677 i i v iv v ii i v v i i vii v i MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr5qtel1M 673678 CCGTGGTGATGAGTTCCAATCTGCTCTCAGATGTTTACCAGCTG-G-GGC 673725 i - v-i i i---- -- viii i - - i MIRc#SINE/MIR 52 CTG-GGTT-CGAGTCCCG----GCTCT--GCCACTTACTAGCTGTGTGAC 93 chr5qtel1M 673726 TCTGGACAAGTCACTTAAG---TC---ACTTCAGTTTTCCTCACTTGGCA 673769 ii i v--- ---i i - ii vv MIRc#SINE/MIR 94 CTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGT-TTCCTCATCTGTAA 142 chr5qtel1M 673770 CATGAG 673775 v i MIRc#SINE/MIR 143 AATGGG 148 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.97 CpG sites = 28, Kimura (unadjusted) = 39.48 Transitions / transversions = 2.15 (28/13) Gap_init rate = 0.09 (13 / 147), avg. gap size = 1.31 (17 / 13) 12 14.12 3.03 3.03 chr5qtel1M 674267 674299 (325701) (GCTTTG)n#Simple_repeat 1 33 (0) m_b262s252i5 10360 chr5qtel1M 674267 GCTTTGGCTTTGGCTGCTGG-ATTGTCTTGGGCT 674299 -i -v v v (GCTTTG)n#Sim 1 GCTTTGGCTTTGGCT-TTGGCTTTGGCTTTGGCT 33 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.06 (2 / 32), avg. gap size = 1.00 (2 / 2) 13 15.33 5.26 2.56 chr5qtel1M 674322 674359 (325641) (CTG)n#Simple_repeat 1 39 (0) m_b262s252i6 10361 chr5qtel1M 674322 CTGCTG-TGAGCCTGGCTGCTGCTGCTGCTG-TACTTCTG 674359 - vvv - - i v (CTG)n#Simple 1 CTGCTGCTGCTGCT-GCTGCTGCTGCTGCTGCTGCTGCTG 39 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.08 (3 / 37), avg. gap size = 1.00 (3 / 3) 16 11.53 3.23 3.23 chr5qtel1M 674525 674555 (325445) (GT)n#Simple_repeat 1 31 (0) m_b262s252i7 10362 chr5qtel1M 674525 GTGTGTGTGTGTGTATGTATATGT-TGTAGTG 674555 i i i - - (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGT-GTG 31 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2) 1279 30.48 3.22 4.47 chr5qtel1M 675353 676190 (323810) HERVK14C#LTR/ERVK 2845 3672 (3762) m_b262s701i0 10363 chr5qtel1M 675353 TTTTTAGGCAGGGCTTCTGTTGAAGGCCTGCCAACACTTTCACCTGTTCC 675402 viv iv -- v vi ?------- i HERVK14C#LTR/ 2845 TTTTTAGGGGCGGCCACTGTTGA--GCCTCCAGAN-------CCTATTCC 2885 chr5qtel1M 675403 TATCCAATGGAAAATTGATACACCAGTGTGGATAGAACAGTGGCCCTTAG 675452 iv vv ?i iiv v v? ? v i ? ? vi ?? HERVK14C#LTR/ 2886 CTTAAAATGGANGACCCAAAANCCNGTTTGGGTNGANCAGTGGCCGCTNN 2935 chr5qtel1M 675453 CTAGTGATAAAATTCAGGCCTTATCAGATATAGTACAGGAGCAACTTGAC 675502 viv v v vvi ivi vv vv i i i v ? HERVK14C#LTR/ 2936 CTCAGGAAAAACTGGGGGCCTTACAGGAATTAGTCAAAGAACAATTAGAN 2985 chr5qtel1M 675503 CAAGGACACTTACAACC----TTCTCTAAGTCCTTGCAATTCCCCTGTAT 675548 v v ?v i ---- i ---- ? v ? v i HERVK14C#LTR/ 2986 AAAGGACACATNGAGCCCACATTTTC----TCCNTGGAATTCNCCAGTGT 3031 chr5qtel1M 675549 TTGTTGTAAGAAAGAAATCTGGAAACTGGAGGATGTTGACTGATTTAAGA 675598 vi ? ii i i v iv v ? i i i i v HERVK14C#LTR/ 3032 TTGTAATNAAGAAAAAATCCGGCAGATGGCGNATGCTAACCGACTTACGA 3081 chr5qtel1M 675599 AAGGTAAATGAACAG--ATGGAAACTATGGGAACTCTTCAGCCTGGACTT 675646 ivv v -- -- ?v v ? ii ? v v i v HERVK14C#LTR/ 3082 GCCGTCAATG--CAGTCATNCAACCNATGGGGGCNCTGCAGCCAGGGCTG 3129 chr5qtel1M 675647 CCATCTCCTACT-CAATTGCCTAGAGAATGGCCTCTTTGGGTCATAGACA 675695 ? i ii i-ii - v ?i vvvi i iv HERVK14C#LTR/ 3130 CCNTCCCCCGCCATGATT-CCTAGAGACTGGCCNTTAATAGTTATAGATT 3178 chr5qtel1M 675696 ATAAGGATTGTTTCTATTGTATCCCTCTAGCTAAGGAGGATACGAAAAGA 675745 vv i i v vv i vi vv? vivi i HERVK14C#LTR/ 3179 TGAAGGACTGCTTCTTTACTATTCCTCTAGCAGAGCCNGATTTTGAAAAA 3228 chr5qtel1M 675746 TTTGCCTTTTCAGTGCCCAGCATTAAC--TTAGCTGAGCCTTATAAAAAG 675793 i v vi v iivi v --iv -- i -?ii ivv HERVK14C#LTR/ 3229 TTTGCTTTTACTATTCCTGCTATGAACAACAAG--GAACC-NGCAGCCAG 3275 chr5qtel1M 675794 C-ATTAATGGACAGTTTCACCACAGGGAATGAAAAACAGTCCTATTATGT 675842 ?- i v v ? ii i v vvi i ? i? v HERVK14C#LTR/ 3276 NTATCATTGGAAAGTNTTGCCGCAGGGCATGTTGAATAGTCCNACNATTT 3325 chr5qtel1M 675843 GCTAAATGTGTGTTGCTGCTGCTCTTACTCCAGTAAGAAAAACATTTCCA 675892 ii iv ? v vv?vv v vvv v ? i vvvi HERVK14C#LTR/ 3326 GTCAAACTTNTGTGGGGNAGGCTATTCAACCTGTNAGAGATCAGTTTCCA 3375 chr5qtel1M 675893 AAAGTA-ATGTTATTACATTACATGGATGATATATTGGGATGTGTATCTG 675941 i vvi?- i i - i i ---? iiv i HERVK14C#LTR/ 3376 GATTCNTATATCATT-CATTATATGGATGACATATT---NTGTGCGGCCG 3421 chr5qtel1M 675942 A------AGAACA--------AATGTTAGAAGCATGTCTAACAGAAGACC 675977 ------ v -------- i vvvi v --- i v HERVK14C#LTR/ 3422 AAACTCGAGACCAACTTATCCAGTGTTATTCACATTT---ACAGAAGGCG 3468 chr5qtel1M 675978 ATAG-AAACACTAAGGAACTACAAATTGCACATAGCTCCAGAAAAAATTC 676026 i ? -vi i -- -------- ?v ? ? v HERVK14C#LTR/ 3469 GTNGCCGACGCT--GG--------ATTGNTCATAGCNCCNGATAAAATTC 3508 chr5qtel1M 676027 AAAGACATGCTCCTTTTCAGTATTTAGGATATG-AAGTATACCCTAAGGT 676075 vi?v i i i i - - i vi vvvv i i HERVK14C#LTR/ 3509 AAACGNCTACTCCTTTCCAATATTTGGGA-ATGCAGGTTCAGGAAAGGGC 3557 chr5qtel1M 676076 GCTTACAGTACAAAAACTTTCCTTAAGAACAGAGAAGCTAAACATCTTAA 676125 iv vivi? iv ivvv vv v vvvv i v ii HERVK14C#LTR/ 3558 AATTAAGCCNCAAAAGGTTCAAATTCGAAAAGACTCTCTGAAAACTTTAA 3607 chr5qtel1M 676126 ATGACTTTCAGAAACTGATAGGAGATATCCAATGAATGCGTCCAGTGTTA 676175 i i i iv i iv v i v v viiv HERVK14C#LTR/ 3608 ATGATTTTCAAAAATTATTAGGGGATATTAATTGGATTCGACCTACTTTA 3657 chr5qtel1M 676176 GGCTTGACTACCTAT 676190 v vv HERVK14C#LTR/ 3658 GGCATTCCTACCTAT 3672 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.94 CpG sites = 114, Kimura (unadjusted) = 41.94 Transitions / transversions = 0.88 (114/130) Gap_init rate = 0.06 (47 / 837), avg. gap size = 1.36 (64 / 47) 468 26.37 7.49 4.08 chr5qtel1M 677202 677628 (322372) HERVK14C#LTR/ERVK 4671 5111 (2323) m_b262s701i1 10363 chr5qtel1M 677202 TATACAGC-TTGCCTTCCATTCCACACTTCTACA-TTGCC---TCCAGGG 677246 i ? i - i ??i v vi- v -i --- v HERVK14C#LTR/ 4671 TGTNCAACATTGCCCTNNGTGCCAGG-TGCTACAACTGCCACATCAAGGG 4719 chr5qtel1M 677247 A----AG--AACCCTCGTGGTTTGAGACCCAATGAAAT-TGGTAAAATGT 677289 ----? -- ? v v iv? i ?viv - i - - HERVK14C#LTR/ 4720 ACTGGNGTTAACCCNCGAGGATTGGCNCCTAATNCGCTNTGGCAAA-TG- 4767 chr5qtel1M 677290 GATGTGACCCATTATAAATCT-TTTGGTTGTCTGTCTTTTATCCATGTTG 677338 i ? -i vv ?i- vviv ? ? vii ?i HERVK14C#LTR/ 4768 GACGTNACCCAT-GTACCTNCATTTGGGAAACTNTCNTACGTCCATGTNA 4816 chr5qtel1M 677339 TGGTAGAC-CCTTTTCAGGATTCAGTTTTG-CAA--TACCAGCAGCAAAA 677384 iv i- -vv iv ? v - ? -- i -- i ii? HERVK14C#LTR/ 4817 CTGTAGATACCTTTTC-TCATTTTGTNTGGGCNACTTGCCA--AACAGGN 4863 chr5qtel1M 677385 GAGACAGCC---CGAGT----GGTCACTGAATTCCTTATACAAGCATTTG 677427 i ? i--- v ----i v i viv i i i ------- i HERVK14C#LTR/ 4864 GAGGCNGCTGCTCGTGTTAAAAGACATTTGCTTTCCTGT-------TTCG 4906 chr5qtel1M 677428 CAATTATGGGTATGCCACAAGCAATAAAAACAGATAATGGACCTGCATAT 677477 ?i i i v iv? v ? i v v vv i HERVK14C#LTR/ 4907 CNGTCATGGGCATTCCACAAAANATTAAAACNGACAATGGCCCAGGCTAC 4956 chr5qtel1M 677478 ACTTCTAAACATTTTGCATATTTTTGTGCA-CAGTATAAGATTTTATAGA 677526 ?? vv ?-i i? ?iiv iv v - i iv? v vv i v HERVK14C#LTR/ 4957 NNTAGTAAAN-CTTTANANGCGTTCCTTCAACAATGGNACATTAAACACA 5005 chr5qtel1M 677527 CCACTGGCATACCCTTTAATCCTCAAGGACAGGCAATAGTAGAGAGGAGA 677576 ?i ? v v i ? i v v v - v v HERVK14C#LTR/ 5006 NTACTGGNATCCCCTATAATTCTCAAGGNCAAGCCATTGTTGA-ACGAGC 5054 chr5qtel1M 677577 -AACAGAGATATTAAGACGCTC--CTCCAAAAACAAA----AGAAAGGGG 677619 - iv - iv i ?- --i v ---- i HERVK14C#LTR/ 5055 TAATCGA-ACCTTAAAAN-CTCAATTACAAAAACAAAAGACAGAAGGGGG 5102 chr5qtel1M 677620 GAGCCACAG 677628 i v HERVK14C#LTR/ 5103 GAACCAGAG 5111 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 34.15 CpG sites = 56, Kimura (unadjusted) = 36.24 Transitions / transversions = 1.08 (56/52) Gap_init rate = 0.08 (34 / 426), avg. gap size = 1.47 (50 / 34) 421 26.52 8.27 4.96 chr5qtel1M 677424 677677 (322323) HERVK#LTR/ERVK 5002 5263 (2273) m_b262s701i2 10363 chr5qtel1M 677424 TTTGCAATTATGGGTATGCCACAAGCAATAAAAACAGATAATGGACCTGC 677473 vi i vi v v iv v v i i v v HERVK#LTR/ERV 5002 TTTGCTGTCATGGGAGTTCCAGAAAAAATTAAAACTGACAATGGGCCAGG 5051 chr5qtel1M 677474 ATATACTTCTAAA-CATTTTGCATATTTTTGTGCACAGTATAAGATTTTA 677522 ivv vv - ? iiiv v i ivii- iv i vi HERVK#LTR/ERV 5052 ATACTGTAGTAAAGCNTTCCAAAAATTCTTAAAT-CAGTGGAAAATTACA 5100 chr5qtel1M 677523 TAGACCACTGGCATACCCTTTAATCCTCAAGGACAGGCAATAGTAGAGAG 677572 i v v v v v i v i i v v i HERVK#LTR/ERV 5101 CATACAACAGGAATTCCTTATAATTCCCAAGGACAGGCCATAGTTGAAAG 5150 chr5qtel1M 677573 GAGAAACAGAGATATTAAGACGCTCCTCCAA------AAACAAAAGAAAG 677616 i vv i - i i v i - ---- ------ ii HERVK#LTR/ERV 5151 AACTAATAGA-ACACTCAAA-GCT----CAATTGGTTAAACAAAAAGAAG 5194 chr5qtel1M 677617 GGGGAGCCACAG--------GTAA----CCCTAGA--GAACTTCTAAATC 677652 -- -------- ?---- i --v --- HERVK#LTR/ERV 5195 GGGGAG--ACAGTAAGGAGTGTANCACTCCCCAGATGCAACTT---AATC 5239 chr5qtel1M 677653 TAGCTCTTTATACTATTAACTTCTT 677677 v i - v i HERVK#LTR/ERV 5240 TAGCACTCTATACT-TTAAATTTTT 5263 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.47 CpG sites = 32, Kimura (unadjusted) = 33.47 Transitions / transversions = 1.00 (32/32) Gap_init rate = 0.07 (18 / 253), avg. gap size = 1.89 (34 / 18) 285 12.00 1.96 1.96 chr5qtel1M 678220 678270 (321730) HERV15#LTR/ERV1 8281 8331 (420) m_b262s701i3 10364 chr5qtel1M 678220 AAAATAGATTGGTTTTGGACTATCTCTT-GCCTGCTGAAGGAGGCGTATG 678268 i i i i - - v v HERV15#LTR/ER 8281 AAAATAGATTGGCTTTAGATTACCTCTTAGCCT-CAGAAGGAGGAGTATG 8329 chr5qtel1M 678269 TG 678270 HERV15#LTR/ER 8330 TG 8331 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 13.24 CpG sites = 4, Kimura (unadjusted) = 13.24 Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.04 (2 / 50), avg. gap size = 1.00 (2 / 2) 251 25.58 13.75 2.25 chr5qtel1M 679200 679359 (320641) L1P4_orf2#LINE/L1 2463 2640 (654) m_b262s551i3 10365 chr5qtel1M 679200 AATCTATATATTCAATGCCATTT-----AAACTTTAAAAA--ATTGGTTT 679242 i v i i i----- viv vi-- v- i L1P4_orf2#LIN 2463 AATCTACAGATTCAACGCTATTCCTATCAAACTACCAACGTCATTT-TTC 2511 chr5qtel1M 679243 ACTGAGTTAGAAAAAATAATGATAAGAGTCATTGGGAAGGTCAA------ 679286 v i iv vv i v vv --i ------ L1P4_orf2#LIN 2512 ACAGAATTAGAAAAAACTATTCTAAAATTCATATGGAA--CCAAAAAAGA 2559 chr5qtel1M 679287 ----GAAT-GTCAAAGCAG--CTAAGGAAAAAGATGTAAAG--GAAGATG 679327 ---- - i i-- v -ii -- i iii L1P4_orf2#LIN 2560 GCCCGAATAGCCAAAGCAATCCTAAGCAAAAAGA-ACAAAGCCGGAGGCA 2608 chr5qtel1M 679328 TAACAATACCTGACCTTAAACTATATCATAAG 679359 v v i i i ii i L1P4_orf2#LIN 2609 TCACATTACCCGACTTCAAACTATACTACAAG 2640 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 29.41 CpG sites = 25, Kimura (unadjusted) = 32.29 Transitions / transversions = 1.67 (25/15) Gap_init rate = 0.07 (11 / 159), avg. gap size = 2.36 (26 / 11) 12 13.61 0.00 8.57 chr5qtel1M 680071 680108 (319892) (AAAAAG)n#Simple_repeat 1 35 (0) m_b262s252i8 10366 chr5qtel1M 680071 AAAAAAAAAAAGAAAACTGAAAAGGAAGCACAGAAAAA 680108 i -v i -- v (AAAAAG)n#Sim 1 AAAAAGAAAAAGAAAA-AGAAAAAGAA--AAAGAAAAA 35 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.08 (3 / 37), avg. gap size = 1.00 (3 / 3) 521 21.89 1.49 7.94 chr5qtel1M 680198 680331 (319669) C MIRc#SINE/MIR (141) 127 2 m_b262s601i2 10367 chr5qtel1M 680198 CTGAGGC--AATTGGGTTAAGTGACTTGCCCAGGGTCACACAGCCAAGAA 680245 -- ivvi i i i--- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG--- 81 chr5qtel1M 680246 GTGTTAAGTGTCTGAGGCCAGATTTGAATTCAGGTCTTCCTGACTTCAGG 680295 ---- v v v vi i i ii i i C MIRc#SINE/MIR 80 ----TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr5qtel1M 680296 GCTGGTGCTCTATCCATTGGGTCACCTAGCTGCCCC 680331 v ii v i --- vvi i C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTG---CACCACACTGCCTC 2 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 25.20 CpG sites = 17, Kimura (unadjusted) = 26.31 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.08 (11 / 133), avg. gap size = 1.09 (12 / 11) 452 28.95 4.19 4.48 chr5qtel1M 680747 681104 (318896) L1M5_orf2#LINE/L1 2938 3294 (0) m_b262s551i4 10368 chr5qtel1M 680747 AACATAGGGTAGTTTATCTCTCAGACTTGTGGAGGAGGAAGAAATTTGTG 680796 -- vv iivv i - i?v v i i v - L1M5_orf2#LIN 2938 AACATAGG--AGAATATCTTCGTGACCT-TGGGNTAGGCAAAGATTTCT- 2983 chr5qtel1M 680797 ACTAAAGAGGAACTAGAGACTATTATTGATCACAAAATAGAAAATT---- 680842 -- v vvi i i vi i? --- i i v i ---- L1M5_orf2#LIN 2984 --TAAACAGGACACAAAAAGCACNA---ACCATAAAAGAAAAAATTGATA 3028 chr5qtel1M 680843 ---TTGATTATATCAAA-TTAAAAAGCTTCTGTACAAACAAAACTAATGC 680888 --- v i ?i - - iv ?vvv ivi vi i L1M5_orf2#LIN 3029 AATTGGACTNCATCAAAATTAAAAA-CTTCTGCTCNTCAAAAGACACCGT 3077 chr5qtel1M 680889 AAACAAGATTAGAAGGGAAGCAACAAACTGGGAAAACATCTTCACAGTTA 680938 v v i v i v v i ? i v v ii --- L1M5_orf2#LIN 3078 TAAGAAAATGAAAAGGCAAGCCACAGANTGGGAGAAAATATTTGCA---A 3124 chr5qtel1M 680939 AAGGT---TCTGATAAAGG-CTCATTTCCAAAATATATAGAGAACTGACT 680984 ? vi --- i - i v i i v- L1M5_orf2#LIN 3125 NACATATATCTGACAAAGGACTCGTATCCAGAATATATAAAGAACTC-CT 3173 chr5qtel1M 680985 CTAATTT-ATAAGAAACCAAGCCATTC--TCCAATTGACAAATGATCAAA 681031 vi ? i- ? -- v vv --i v? v iv L1M5_orf2#LIN 3174 ACAANTCAATAANAAA--AAGACAAACAACCCAATANAAAAATGGGCAAA 3221 chr5qtel1M 681032 GGATATGAATAGACAATTTTCAGATGATGAAATTGAAATTATTACCACTC 681081 i iv i v iv i v v v ?v viii vi vv L1M5_orf2#LIN 3222 AGACTTGAACAGACACTTCACAAAAGAAGATATNCAAATGGCCAATAAGC 3271 chr5qtel1M 681082 ATATGAAAGAGTGTTCCAAATCA 681104 i iii i v v? L1M5_orf2#LIN 3272 ACATGAAAAGATGCTCAACNTCA 3294 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.22 CpG sites = 50, Kimura (unadjusted) = 38.68 Transitions / transversions = 1.02 (50/49) Gap_init rate = 0.06 (22 / 357), avg. gap size = 1.41 (31 / 22) 500 29.48 2.91 2.54 chr5qtel1M 680830 681104 (318896) L1M2_orf2#LINE/L1 3016 3291 (0) m_b262s551i5 10368 chr5qtel1M 680830 AAAATAGAAAATTTTGATTATATCAAATTAAAAAGCTTCTGTACA---AA 680876 v v vv i i i --- L1M2_orf2#LIN 3016 AAAATAGACAAATGGGATTACATCAAACTAAAAAGCTTCTGCACAGCAAA 3065 chr5qtel1M 680877 CAAAACTAATGCAAACAAGATTAGAAGGGAAGCAACAAACTGGGAAAACA 680926 vi - v-- iii v ii iv v v i v i v L1M2_orf2#LIN 3066 GGAAAC-AATC--AACAGAGTGAAGAGACAACCTACAGAATGGGAGAAAA 3112 chr5qtel1M 680927 TCTTCACAGTTAAAGGTTCTGATAAAGGCTCATT-TCCAAAATATATAGA 680975 v ii iviv v?vv i i v i v - i ii L1M2_orf2#LIN 3113 TATTTGCAAACTATNCATCTGACAAGGGATTAATATCCAGAATATATAAG 3162 chr5qtel1M 680976 GAACTGACTCTAATTTA----TAAGAAACCAAGCCATTCTCCAATTGACA 681021 v vv - i i ----i i v --- vv i ? v L1M2_orf2#LIN 3163 GAACTCAAAC-AACTCAACAGCAAAAAAACAA---ATAATCCGATTNAAA 3208 chr5qtel1M 681022 AATGATCAAAGGATATGAATAGACAATTTTCAGATGATGAAATTGAAATT 681071 iv iv v i i v v v vv v L1M2_orf2#LIN 3209 AATGGGCAAAGGACCTGAATAGACATTTCTCAAAAGAAGACATACAAATG 3258 chr5qtel1M 681072 ATTACCACTCATATGAAAGAGTGTTCCAAATCA 681104 iii v vvi i i i v v L1M2_orf2#LIN 3259 GCCAACAGGTATATGAAAAAATGCTCAACATCA 3291 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.59 CpG sites = 38, Kimura (unadjusted) = 38.19 Transitions / transversions = 0.93 (38/41) Gap_init rate = 0.04 (10 / 274), avg. gap size = 1.50 (15 / 10) 1709 29.40 1.43 1.59 chr5qtel1M 680966 681594 (318406) L1ME4c_3end#LINE/L1 12 639 (191) m_b262s551i6 10368 chr5qtel1M 680966 AATATATAGAGAACTGACTCTAATTTATAAGAAACCAAGCCATTCTCCAA 681015 ? i i v i v v vv? v v vv i L1ME4c_3end#L 12 ANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAAGACCCCAA 61 chr5qtel1M 681016 TTGACAAATGATCAAAGGATATGAATAGACAATTTTCAGATGATGAAATT 681065 v i iv i i iv ? v v v L1ME4c_3end#L 62 TAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAGGAAATA 111 chr5qtel1M 681066 GAAATTATTACCACTCATATGAAAGAGTGTTCCAAATCATTATTAATCAG 681115 v ? vi v v vv i i i i v vv ii v i L1ME4c_3end#L 112 CAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTAGTAATCAA 161 chr5qtel1M 681116 AGAAATGCAAATTAAGACAACTCTGAAATACCACTATACACCTGTCAGAT 681165 ii vv i i v i i i i L1ME4c_3end#L 162 AGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCTATTAAAT 211 chr5qtel1M 681166 TGGTTAAGATGACAGGAAAAAATAATGATGAT------TGTTGGAGGGGA 681209 i iv i ----vv -- i ------ i v i ? L1ME4c_3end#L 212 TAGCAAAAAT----TTAAAAAAT--TGATAATACCCAATGCTGGCGAGGN 255 chr5qtel1M 681210 TGTGGGAAAACTGGGACACTGATACATTGTTGGTGGAGTTGTGAATGAAT 681259 i vi v ? v i vi? i vii L1ME4c_3end#L 256 TGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGT 305 chr5qtel1M 681260 CCAACCATTCTGGAGAGCAATCTGGAATTATGCCCAAAAAGTTATCAAAC 681309 v v i i i v v i iviv i ii v v L1ME4c_3end#L 306 ACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAAAA 355 chr5qtel1M 681310 TGTGCATACCCTTTGATCCAGCAGTGTTTCTACTGGGCTTATACCCCAAG 681359 v i i i viiv v vv v i i L1ME4c_3end#L 356 TGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAG 405 chr5qtel1M 681360 GAGATACT---AAAGAAGGGAAAGGGACCTGTATGTGCCAAAATATTTGT 681406 i v --- i i --- i ii v i i ii L1ME4c_3end#L 406 GAAATAATTCAAAAGAAGGAAAAAG---CTATATGCACGAAGATGTTCAT 452 chr5qtel1M 681407 GGCAGCCCTGTTTGTAGTGGCTAGAAGCTGGAAACTGAGTGGCTGCCCAT 681456 v vi i i i i v i ii vivv iiv i v L1ME4c_3end#L 453 TGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAA 502 chr5qtel1M 681457 CAATTGGAGAATGGTTGGGTAAATTGTGGTATATGAATGTTATGGAATAT 681506 v i ii i i v? iviv L1ME4c_3end#L 503 CAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATAT 552 chr5qtel1M 681507 TATTGTTCTGTAAGAAATGACCAGCAAGATGAATACAGAGAAGCTTGGAG 681556 vvvv ii v i iv vi v v v iiv v i v i L1ME4c_3end#L 553 TATGCAGCCATTAAAAATGATAATTATGAAGACTATGTAGCAACATGGAA 602 chr5qtel1M 681557 AGAATTACATGAACTGATGCTGAGTGAAATGAGCAGAA 681594 ivi -i vv i i i vi L1ME4c_3end#L 603 AATGTT-TATGATATAATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.38 CpG sites = 99, Kimura (unadjusted) = 38.73 Transitions / transversions = 1.19 (99/83) Gap_init rate = 0.02 (12 / 628), avg. gap size = 1.58 (19 / 12) 12 9.24 0.00 4.17 chr5qtel1M 681913 681937 (318063) (GGGA)n#Simple_repeat 1 24 (0) m_b262s252i9 10369 chr5qtel1M 681913 GGGAGGGGGTGGAGGGTGGGAGGGA 681937 i - v (GGGA)n#Simpl 1 GGGAGGGAG-GGAGGGAGGGAGGGA 24 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 21 21.00 4.23 2.78 chr5qtel1M 682079 682149 (317851) (AAGG)n#Simple_repeat 1 72 (0) m_b262s252i10 10370 chr5qtel1M 682079 AATGAAGGAAGGAAGG-AGGGAGGAAGGGAGGGAGAGAGGGTGGGAGCAA 682127 v - i i i ii iv i v (AAGG)n#Simpl 1 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 50 chr5qtel1M 682128 GGGAAGAGAA--AAAAAAGGAAGG 682149 - - -- ii (AAGG)n#Simpl 51 -GGAAG-GAAGGAAGGAAGGAAGG 72 Matrix = Unknown Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.06 (4 / 70), avg. gap size = 1.25 (5 / 4) 194 29.69 0.00 0.00 chr5qtel1M 683780 683843 (316157) MIRc#SINE/MIR 149 212 (56) m_b262s601i3 10371 chr5qtel1M 683780 GATGAGAGTGCTGGCCCTGCCTTTGTCTCGGGTTTGTTGTGAGGATCCAA 683829 i v i i iv viv v i v v MIRc#SINE/MIR 149 GATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAA 198 chr5qtel1M 683830 CATGATGGTGAATG 683843 iiv ii v MIRc#SINE/MIR 199 TGAGATAATGTATG 212 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.43 CpG sites = 10, Kimura (unadjusted) = 38.43 Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0) 18 8.53 0.00 0.00 chr5qtel1M 683848 683872 (316128) (T)n#Simple_repeat 1 25 (0) m_b262s252i11 10372 chr5qtel1M 683848 TTTTTTTTTATTTTTTTTATTTTTT 683872 v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 419 20.39 3.94 7.32 chr5qtel1M 685018 685144 (314856) C MIRc#SINE/MIR (120) 148 26 m_b262s601i5 10373 chr5qtel1M 685018 CTCATTTTTCAGATGAGGAAACTGAGG--CAGACAGGGTGAAGAGACTT- 685064 i v -- v - v v - C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGA-GGTTAAGTGACTTG 100 chr5qtel1M 685065 TCCAGGGTCATA-AGCTAGGAAGTGTCCGAAGCCAGATTCGAACTCGGGT 685113 i i i - v v v iv vi i i i - C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGG- 51 chr5qtel1M 685114 AGATGAATCTTCCCGATTGCAGG-CAGGTGCT 685144 ------- i i v i - vi C MIRc#SINE/MIR 50 -------TCTTCCTGACTCCAAGTCCAGTGCT 26 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 23.97 CpG sites = 13, Kimura (unadjusted) = 23.97 Transitions / transversions = 1.18 (13/11) Gap_init rate = 0.10 (13 / 126), avg. gap size = 1.08 (14 / 13) 426 20.41 3.06 0.00 chr5qtel1M 685018 685115 (314885) C MIR#SINE/MIR (118) 144 44 m_b262s601i4 10373 chr5qtel1M 685018 CTCATTTTTCAGATGAGGAAACTGAGGCAGACAG-GGTGAAGAGACTT-T 685065 i v v v - v vi -i C MIR#SINE/MIR 144 CCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGC 95 chr5qtel1M 685066 CCAGGGTCATA-AGCTAGGAAGTGTCCGAAGCCAGATTCGAACTCGGGTA 685114 i i - v v v iv vi i i i C MIR#SINE/MIR 94 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGCA 45 chr5qtel1M 685115 G 685115 C MIR#SINE/MIR 44 G 44 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 23.98 CpG sites = 10, Kimura (unadjusted) = 23.98 Transitions / transversions = 1.00 (10/10) Gap_init rate = 0.03 (3 / 97), avg. gap size = 1.00 (3 / 3) 375 23.47 7.26 7.26 chr5qtel1M 685619 685742 (314258) C MIRb#SINE/MIR (117) 151 28 m_b262s601i6 10374 chr5qtel1M 685619 CTCATTTCACAGAGGAGGAAAC--AGGT-----GAC-TTAAGTAACTTAC 685660 i i v -- i----- v- i C MIRb#SINE/MIR 151 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGC 102 chr5qtel1M 685661 CCAAAGTAATACAGCTAGTGAGTGTCTGAGGTCAGATTTGGACTGATGAA 685710 i v i i v v vivi i i ------- C MIRb#SINE/MIR 101 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAAC------- 59 chr5qtel1M 685711 TACGAGGCTTCTCTG-TTCCAAACCTAATGCTC 685742 -- v ii v -i v ivi C MIRb#SINE/MIR 58 --CCAGGTCTGTCTGACTCCAAAGCCCGTGCTC 28 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 25.11 CpG sites = 16, Kimura (unadjusted) = 28.72 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.11 (13 / 123), avg. gap size = 1.38 (18 / 13) 698 23.62 8.04 0.00 chr5qtel1M 685797 685995 (314005) C MIRc#SINE/MIR (0) 268 54 m_b262s601i7 10375 chr5qtel1M 685797 AATAACAATAATAACTAAC-TTCAAATAGTGAGTAAT-GTATGCAAAGCG 685844 i i?v v - iiv iivv v i- v i C MIRc#SINE/MIR 268 AATAATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCG 219 chr5qtel1M 685845 TTTT-ACAAGTATTATCTCATTTGATCCTCACAACTATCCTGGCAGGTAG 685893 i - vii v i vv C MIRc#SINE/MIR 218 CTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAG 169 chr5qtel1M 685894 AT---GC---TGTTGTTTCCCTCATTTTACAATGGAGGAAACTGAGG--C 685935 ii--- --- i i vi i ivv -- C MIRc#SINE/MIR 168 GCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC 119 chr5qtel1M 685936 AAATGGGTTAAGTGACTTGCCCAGGGTCACCTCG---GTAGGT--CAGAG 685980 i vi i viv --- i -- C MIRc#SINE/MIR 118 AGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAG 69 chr5qtel1M 685981 GCTGGGTTTGAACTC 685995 v v ii i i C MIRc#SINE/MIR 68 CCGGGACTCGAACCC 54 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.41 CpG sites = 28, Kimura (unadjusted) = 29.13 Transitions / transversions = 1.47 (28/19) Gap_init rate = 0.04 (8 / 198), avg. gap size = 2.00 (16 / 8) 720 20.75 4.32 1.81 chr5qtel1M 685834 685995 (314005) C MIRb#SINE/MIR (46) 222 57 m_b262s601i8 10375 chr5qtel1M 685834 TATGCAAAGCGTTTTACAAGTATTATCTCATTTGATCCTCACAACTATCC 685883 i v i v i i v i C MIRb#SINE/MIR 222 TGTGCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCC 173 chr5qtel1M 685884 TGGCAGGTAGATGCTGTTGTTTCCCTCATTTTACAATGGAGGAAACTGAG 685933 vv i ii i i --- i ivv C MIRb#SINE/MIR 172 TGCGAGGTAGGTATTATTAT---CCCCATTTTACAGATGAGGAAACTGAG 126 chr5qtel1M 685934 G--CAAATGGGTTAAGTGACTTGCCCAGGGTCACCTCG---GTAGGT--C 685976 -- i vi i i viv --- i -- C MIRb#SINE/MIR 125 GCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGC 76 chr5qtel1M 685977 AGAGGCTGGGTTTGAACTC 685995 v v i i i C MIRb#SINE/MIR 75 AGAGCCGGGATTCGAACCC 57 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 23.99 CpG sites = 21, Kimura (unadjusted) = 24.84 Transitions / transversions = 1.75 (21/12) Gap_init rate = 0.04 (6 / 161), avg. gap size = 1.67 (10 / 6) 476 21.58 8.66 1.47 chr5qtel1M 687132 687258 (312742) C MIR3#SINE/MIR (2) 206 71 m_b262s601i9 10376 chr5qtel1M 687132 ATCATAAGATCATGGAAT--CATAG------AGAATTATAGAGGTGATCT 687173 ii i -- v ------i i iiv i v C MIR3#SINE/MIR 206 ATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCT 157 chr5qtel1M 687174 GCTTCAGCCCC-TCATTTTACAGATGAGAAAAATGAGTCCTGTAGAGA-G 687221 iv i i - i v v iiv i- C MIR3#SINE/MIR 156 AGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTG 107 chr5qtel1M 687222 AAGTGACTTGTCCAAGGTCACATGTAACAAA-TAGTAG 687258 i --i i ? i- i C MIR3#SINE/MIR 106 AAGTGACTTGCCCAAGGTCACA--CAGCNAGTTAGTGG 71 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 26.82 CpG sites = 20, Kimura (unadjusted) = 26.82 Transitions / transversions = 2.86 (20/7) Gap_init rate = 0.06 (7 / 126), avg. gap size = 1.86 (13 / 7) 376 26.60 3.97 1.55 chr5qtel1M 687159 687284 (312716) C MIR1_Amn#SINE/MIR (54) 176 48 m_b262s601i10 10376 chr5qtel1M 687159 TTATAGAGGTGATCTGCTTCAGC-CCCTCATTTTACAGATGAGAAAAATG 687207 i i v i v iv vi-i i i v C MIR1_Amn#SINE 176 TTACAAAGGAGGTCAGTATCATTATCCCCATTTTACAGATGAGGAAACTG 127 chr5qtel1M 687208 AGTCCTGTAGAGA-GAAGTGACTTGTCCAAGGTCACATG--TAACAAATA 687254 v ?iiv i-? i ?ii--?ii ? i i C MIR1_Amn#SINE 126 AGGCNCAGAGAGGTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNAGTG 77 chr5qtel1M 687255 GTAG-TCCCCGATTTGAAATTCCAATTCCCC 687284 i -v vv ? ? --i iv i C MIR1_Amn#SINE 76 GCAGAGCCGGGANTNGAA--CCCAGGTCTCC 48 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.96 CpG sites = 22, Kimura (unadjusted) = 36.96 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.05 (6 / 125), avg. gap size = 1.17 (7 / 6) 378 24.17 11.45 2.10 chr5qtel1M 687183 687313 (312687) C MIRc#SINE/MIR (119) 149 7 m_b262s601i11 10376 chr5qtel1M 687183 CCTCATTTTACAGATGAGAAAAATGAGTCCTGTAGAGAG---AAGTGACT 687229 i i v v i--i --- C MIRc#SINE/MIR 149 CCCCATTTTACAGATGAGGAAACTGAGGCT--CAGAGAGGTTAAGTGACT 102 chr5qtel1M 687230 TGTCCAAGGTCACATG--TAACAAATAGTAG-TCCCCGATTTGAA----- 687271 i ii-- ii i i i -v vv i i ----- C MIRc#SINE/MIR 101 TGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAG 52 chr5qtel1M 687272 --ATTCC-AATTCCCCATCTA-CATTCTTTCACACAGCACCACCCT 687313 --v -i i vvi i -iii - v v C MIRc#SINE/MIR 51 GTCTTCCTGACTCCAAGTCCAGTGCTCTTTC-CACTGCACCACACT 7 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.14 CpG sites = 21, Kimura (unadjusted) = 30.31 Transitions / transversions = 2.10 (21/10) Gap_init rate = 0.08 (10 / 130), avg. gap size = 1.80 (18 / 10) 269 27.31 6.82 8.46 chr5qtel1M 687436 687567 (312433) MIR#SINE/MIR 88 217 (45) m_b262s601i12 10377 chr5qtel1M 687436 ACCTCGGG-AACTTATTTTTGGAATGTACTCAATTCCTCAACTAATTTGG 687484 i - v i ---- iv - vi v i---- -- MIR#SINE/MIR 88 ACCTTGGGCAAGTTACTT----AACCT-CTCTGTGCCTCAG----TTT-- 126 chr5qtel1M 687485 CTTCATCTGTAAAATGGGTGT--------CAACTACCTCATTGGGTGGTT 687526 i vi --------i v v v MIR#SINE/MIR 127 CCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTCATAGGGTTGTT 176 chr5qtel1M 687527 GTAGAGATCAGATGAAATAGCATATGGGAAACTTTGCGAAC 687567 iii i i iv ii i vi i vi vv MIR#SINE/MIR 177 GTGAGGATTAAATGAGTTAATACATGTAAAGCGCTTAGAAC 217 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.86 CpG sites = 20, Kimura (unadjusted) = 34.86 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.10 (13 / 131), avg. gap size = 1.54 (20 / 13) 277 30.16 9.18 1.90 chr5qtel1M 687461 687558 (312442) MIRb#SINE/MIR 108 212 (56) m_b262s601i13 10377 chr5qtel1M 687461 TACTCAATTCCTC--AACT--AATTTGGCTTCATCTGTAAAATGGGTGT- 687505 i iii -- i i-- i -- i vi - MIRb#SINE/MIR 108 TACTTAACCTCTCTGAGCCTCAGTTT--CCTCATCTGTAAAATGGGGATA 155 chr5qtel1M 687506 ----CAACTACCTCATTGGGTGGTTGTAGAGATCAGATGAAATAGCATAT 687551 ----i v iiv v iii i i i iiii MIRb#SINE/MIR 156 ATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCAT 205 chr5qtel1M 687552 GGGAAAC 687558 vi i MIRb#SINE/MIR 206 GTAAAGC 212 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 40.86 CpG sites = 24, Kimura (unadjusted) = 42.91 Transitions / transversions = 4.80 (24/5) Gap_init rate = 0.06 (6 / 97), avg. gap size = 1.83 (11 / 6) 300 24.47 18.09 0.00 chr5qtel1M 687485 687578 (312422) MIRc#SINE/MIR 131 241 (27) m_b262s601i14 10377 chr5qtel1M 687485 CTTCATCTGTAAAATGGG------------TGTC--AACTACCTCATTGG 687520 i ------------ i --iv iv MIRc#SINE/MIR 131 CCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAGG 180 chr5qtel1M 687521 GTGGTTGTAGAGATCAGATGAAATAGCATATGGGAAA---CTTTGCGAAC 687567 v iii i i iii v --- ii MIRc#SINE/MIR 181 GTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTTTGTAAAC 230 chr5qtel1M 687568 CTTTCAATGCT 687578 iv vv i MIRc#SINE/MIR 231 TGTAAAGTGCT 241 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.83 CpG sites = 16, Kimura (unadjusted) = 30.83 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.03 (3 / 93), avg. gap size = 5.67 (17 / 3) 16 21.70 0.00 0.00 chr5qtel1M 691544 691575 (308425) (T)n#Simple_repeat 1 32 (0) m_b262s252i12 10378 chr5qtel1M 691544 TTTCTTATTCTTTAGTTTTTTTTTTTTTCTTT 691575 i v i vv i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 32 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 504 22.60 0.72 7.69 chr5qtel1M 691577 691715 (308285) C MIRb#SINE/MIR (138) 130 1 m_b262s601i15 10379 chr5qtel1M 691577 CTGAGGC-AATTGAGGTTAAGTGACTTGCCCAGGGTCACACAGCTAGGAA 691625 -v vv i i --- C MIRb#SINE/MIR 130 CTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAG--- 84 chr5qtel1M 691626 GTGTTAAGTGTCTGAGGCCAGATTGGAACTCAGGTCCTCCTGACCTCAGG 691675 ---- v v v vi v i ivi ii ii C MIRb#SINE/MIR 83 ----TAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAA 38 chr5qtel1M 691676 GCTGATGCTCTATCCACTGAGCCACCTAACTTCCCCCTTG 691715 ivi v vi ---i v ii C MIRb#SINE/MIR 37 GCCCGTGCTCTTTCCACTGCACCAC---GCTGCCCCTCTG 1 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 24.98 CpG sites = 16, Kimura (unadjusted) = 27.08 Transitions / transversions = 1.23 (16/13) Gap_init rate = 0.08 (11 / 138), avg. gap size = 1.00 (11 / 11) 540 19.72 0.81 5.93 chr5qtel1M 691577 691700 (308300) C MIRc#SINE/MIR (141) 127 10 m_b262s601i16 10379 chr5qtel1M 691577 CTGAGGC-AATTGAGGTTAAGTGACTTGCCCAGGGTCACACAGCTAGGAA 691625 -v vv i --- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG--- 81 chr5qtel1M 691626 GTGTTAAGTGTCTGAGGCCAGATTGGAACTCAGGTCCTCCTGACCTCAGG 691675 ---- v v v vi i v i i ii i C MIRc#SINE/MIR 80 ----TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr5qtel1M 691676 GCTGATGCTCTATCCACTGAGCCAC 691700 v iii v vi C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 22.98 CpG sites = 12, Kimura (unadjusted) = 22.98 Transitions / transversions = 1.09 (12/11) Gap_init rate = 0.07 (8 / 123), avg. gap size = 1.00 (8 / 8) 312 35.58 1.09 6.32 chr5qtel1M 691777 691959 (308041) C MIRc#SINE/MIR (87) 181 8 m_b262s601i17 10380 chr5qtel1M 691777 CTCTGTGTGGTAGTTATAACAGGTGTTCTTATACCCAGTTTATAG-TTAG 691825 i v vi vii i v v v i - v C MIRc#SINE/MIR 181 CCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAG 132 chr5qtel1M 691826 CAAACTGAGGTTGAGAGTCATCAACTGCCACATTGAGGAATTAAATGCCA 691875 v i v vvi i v v --- -----iiv v i C MIRc#SINE/MIR 131 GAAACTGAGGCTCAGAGAGGTTAAGTGAC---TTG-----CCCAAGGTCA 90 chr5qtel1M 691876 C-TATTCAAGAAATATTAGGGGCAGGATTTGAATCCAGGCTGTTCTGTTT 691924 -i vii iv i ivi i v i i i i iiv i vi C MIRc#SINE/MIR 89 CACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACT 40 chr5qtel1M 691925 ACTAGGCTATCTGCTACTTTTCTATGGCTCTGCAC 691959 v v v i -v --i i iv v ii C MIRc#SINE/MIR 39 CCAAGTCCA-GTGCT--CTTTCCACTGCACCACAC 8 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 47.32 CpG sites = 34, Kimura (unadjusted) = 49.60 Transitions / transversions = 1.26 (34/27) Gap_init rate = 0.07 (13 / 182), avg. gap size = 1.00 (13 / 13) 314 21.35 5.32 5.32 chr5qtel1M 692237 692330 (307670) MER63B#DNA/hAT-Tip100 343 436 (0) m_b262s502i0 10381 chr5qtel1M 692237 TAGTTGCACCTTGGAAATTGGCAAAC--CACAACATACATACCTTTTTTT 692284 v i vi i --i - - viv MER63B#DNA/hA 343 TATTTACACCACGGAAATCGGCAAACGCTACAA-AT-CAGGGCTTTTTTT 390 chr5qtel1M 692285 TTTTTTCATTTGAAGAGCCA---TTTAAACATTTACCGGCATACCACTG 692330 iii ---iii i---v i i MER63B#DNA/hA 391 TTTCCCC---CAGAGAGCCGGTTGTTAAACATTTACCAGCACACCACTG 436 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 21.54 CpG sites = 14, Kimura (unadjusted) = 26.14 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.08 (7 / 93), avg. gap size = 1.43 (10 / 7) 16 16.52 0.00 0.00 chr5qtel1M 692467 692493 (307507) (T)n#Simple_repeat 1 27 (0) m_b262s252i13 10382 chr5qtel1M 692467 TTTATTTTTTACGTTTTTTTTTTTTTT 692493 v viv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTT 27 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 215 37.65 1.18 0.00 chr5qtel1M 692578 692662 (307338) L2c_3end#LINE/L2 368 453 (25) m_b262s601i18 10383 chr5qtel1M 692578 TCCACAGGACTGGAAATTCTCCGAAGG-AGGGACTTTTTGGTTTTGGTCT 692626 vi vi ii iii i - iv v vv v vi L2c_3end#LINE 368 TCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCT 417 chr5qtel1M 692627 TTTTATTCCTAGTCTCTAGCACCAAGTGAATGCTTA 692662 v i i ivi i vv iiii i L2c_3end#LINE 418 TTGTATCCCCAGCGCCTGGCACATAGTAGGCGCTCA 453 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 48.02 CpG sites = 20, Kimura (unadjusted) = 55.60 Transitions / transversions = 1.67 (20/12) Gap_init rate = 0.01 (1 / 84), avg. gap size = 1.00 (1 / 1) 326 22.89 1.19 1.19 chr5qtel1M 693617 693700 (306300) C MIRc#SINE/MIR (19) 249 166 m_b262s601i19 10384 chr5qtel1M 693617 ATTTCTAAAGCAATTTAAGTTTTGCAAAGTACTTT-ACAGATGTTAATTC 693665 v v v viv i ii - v ii vi C MIRc#SINE/MIR 249 ATTTGTATAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATCTC 200 chr5qtel1M 693666 ATTTGATCCTCACAAACAAATCTGGAAGGTAGGTA 693700 - vi vi i C MIRc#SINE/MIR 199 ATTTGATCCTCAC-AACAACCCTGTGAGGTAGGCA 166 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 25.79 CpG sites = 10, Kimura (unadjusted) = 27.60 Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.02 (2 / 83), avg. gap size = 1.00 (2 / 2) 18 7.81 0.00 0.00 chr5qtel1M 694162 694188 (305812) (GCA)n#Simple_repeat 1 27 (0) m_b262s252i14 10385 chr5qtel1M 694162 GCAGAAGTAGCAGCAGCAGCAGCAGCA 694188 v i (GCA)n#Simple 1 GCAGCAGCAGCAGCAGCAGCAGCAGCA 27 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 13 19.09 0.00 0.00 chr5qtel1M 696912 696941 (303059) (AGAGA)n#Simple_repeat 1 30 (0) m_b262s252i15 10386 chr5qtel1M 696912 AGAGAAGAAAACAGAATGGAAAAGAAGAGA 696941 i v vi i (AGAGA)n#Simp 1 AGAGAAGAGAAGAGAAGAGAAGAGAAGAGA 30 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 20 29.26 0.00 3.90 chr5qtel1M 697630 697709 (302291) (TTA)n#Simple_repeat 1 77 (0) m_b262s252i16 10387 chr5qtel1M 697630 TTATTAATGTTAATAATTACTGGTTATTACTGGTAGTATTTTTCTTTTTC 697679 v i - v - vi i iv v v v v v (TTA)n#Simple 1 TTATTATTATT-ATTATTA-TTATTATTATTATTATTATTATTATTATTA 48 chr5qtel1M 697680 TTTTTTTTTTTATTATTATAACTTTTTATT 697709 v v v v - v (TTA)n#Simple 49 TTATTATTATTATTATTATTA-TTATTATT 77 Matrix = Unknown Transitions / transversions = 0.29 (4/14) Gap_init rate = 0.04 (3 / 79), avg. gap size = 1.00 (3 / 3) 394 24.91 0.00 7.62 chr5qtel1M 698521 698633 (301367) MIRc#SINE/MIR 11 115 (153) m_b262s601i20 10388 chr5qtel1M 698521 TGGTACAGTGGATAGAGCAGCAGTCCTGGAGTCAGGAGGACCCAATTTCA 698570 i v vii v i i iiiv i MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr5qtel1M 698571 AATCCAGCCTAAGACAGTTTACACATATTAGCTTGTCTGACCCTAGACAT 698620 i v v ---- v i--- v i - v i i i v MIRc#SINE/MIR 61 AGTCCCGGCT----CTGC---CACTTACTAGC-TGTGTGACCTTGGGCAA 102 chr5qtel1M 698621 GTCACTTAACCCC 698633 i MIRc#SINE/MIR 103 GTCACTTAACCTC 115 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.42 CpG sites = 16, Kimura (unadjusted) = 30.82 Transitions / transversions = 1.60 (16/10) Gap_init rate = 0.07 (8 / 112), avg. gap size = 1.00 (8 / 8) 15 13.87 0.00 0.00 chr5qtel1M 698944 698967 (301033) (A)n#Simple_repeat 1 24 (0) m_b262s252i17 10389 chr5qtel1M 698944 AAAAAAACAAAAATATAAAAAAAA 698967 v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAA 24 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 756 26.21 3.11 3.52 chr5qtel1M 699134 699390 (300610) L1ME3G_3end#LINE/L1 273 528 (396) m_b262s551i7 10390 chr5qtel1M 699134 ATACATTGTTGGTGGAACTGTGAACAGATCCAGCCATTCTGGAGAGCAAT 699183 i i i v i iv i v ? i i L1ME3G_3end#L 273 ATACACTGCTGGTGGGAGTGTAAATTGGTACAGCCNTTTTGGAGGGCAAT 322 chr5qtel1M 699184 TTGGAACTATCC-TCAAAAAGTTTTCAAACCTTGCATACCCTTTAATCCA 699232 v v i- i ---- i vivi i i L1ME3G_3end#L 323 TTGGCAGTATCTATTAAAA----TTTAAAATGCGCATACCCTTTGACCCA 368 chr5qtel1M 699233 TCAATGTTTCTACTGGGATTATATCCCATATA-----TCTTAAATGAGGG 699277 v viiv v ? ?v v i ? v ----- vi v v vi L1ME3G_3end#L 369 GCAATTCCACTTCTNGGNATCTATCCTANAGAAATACTCGCACATGTGCA 418 chr5qtel1M 699278 AAAGGGACCGGCATGTGCCAAAATGTTTGTGGCAGCTCTTTTTATAGTGT 699327 v i?--- i v ii ii v vi v i i iv L1ME3G_3end#L 419 CAAGGAN---GCATGTACAAGGATGTTCATTGCAGCATTGTTTGTAATAG 465 chr5qtel1M 699328 CAAAAAAGTGGGAACTGAA--TGGATCCCCATCAATTGGAGAATAGCTAA 699375 i v i -- -- ii vi v i i i L1ME3G_3end#L 466 CGAAAAATTGGAAAC--AACCTAAATGTCCATCAATAGGGGAATGGTTAA 513 chr5qtel1M 699376 ATAAATTATGGTATA 699390 L1ME3G_3end#L 514 ATAAATTATGGTATA 528 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 32.58 CpG sites = 38, Kimura (unadjusted) = 33.85 Transitions / transversions = 1.41 (38/27) Gap_init rate = 0.05 (12 / 256), avg. gap size = 1.42 (17 / 12) 405 33.32 3.08 2.38 chr5qtel1M 699135 699426 (300574) L1MB4_3end#LINE/L1 278 571 (356) m_b262s551i8 10390 chr5qtel1M 699135 TACATTGTTGGTGGAACTGTGAACAGATCCAGCCATTCTGGAGAGCAATT 699184 i i i v i vv i v ii v i i i L1MB4_3end#LI 278 TGCATTGCTGGTGGGAATGTAAAATGGTGCAGCCGCTGTGGAAAACAGTT 327 chr5qtel1M 699185 TGGAACTATCCTCAAAAAGTTTTCAAACCTTGCA-TACCCTTTAATCCAT 699233 viv - --- v v v - v v i i v L1MB4_3end#LI 328 TGGCGGT-TCCTCAAAAAGTT---AAACATAGAATTACCATATGACCCAG 373 chr5qtel1M 699234 CAATGTTTCTACTGGGATTATATCCCATATATCTTAAATGAGGGAAAGGG 699283 viiv v i vv i v v v vi v vv vvvii L1MB4_3end#LI 374 CAATTCCACTCCTAGGTATATACCCAAAAGAATTGAAAGCAGGGACTCAA 423 chr5qtel1M 699284 ACCGGCA--TGTGCCAAAATGTTTGTGGCAGCTCTTTTTATAGTGTCAAA 699331 v ii -- i vvv ii i vi v i i i iv v L1MB4_3end#LI 424 ACAGATACTTGTACACCAATGTTCATAGCAGCATTATTCACAATAGCCAA 473 chr5qtel1M 699332 AAAGTGGGAACTGAATGGA--TCCCCATCAATTGGAGAATAGCTAAATAA 699379 i i -- ivv -- vi - iv iv i v i L1MB4_3end#LI 474 AAGGTGGAAAC--AACCCAAGTGTCCAT-AACAGATGAATGGATAAACAA 520 chr5qtel1M 699380 ATTATGGTATAAATGTTT--TGGGATATTCTTGTTCTGTAAGAA--AATG 699425 v i v ii vi-- i v vvv i? i -- L1MB4_3end#LI 521 AATGTGGTATATACATACAATGGAATATTATTCAGCCNTAAAAAGGAATG 570 chr5qtel1M 699426 A 699426 L1MB4_3end#LI 571 A 571 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 43.64 CpG sites = 46, Kimura (unadjusted) = 44.89 Transitions / transversions = 0.94 (46/49) Gap_init rate = 0.04 (12 / 291), avg. gap size = 1.33 (16 / 12) 201 36.22 7.19 0.68 chr5qtel1M 700332 700470 (299530) L2d2_3end#LINE/L2 403 550 (5) m_b262s601i21 10391 chr5qtel1M 700332 CTTTCCACCTAGCGGTTTGTTGTCAATCCCACCAGTCTGTGATCTCCATA 700381 i v ivivi v v vvi v i vi i v v i L2d2_3end#LIN 403 CTTTTCACGTGTTTATGTCTTGTCTCCCCAACTAGATTGTAAGCTCCTTG 452 chr5qtel1M 700382 GGAGCAGGAGACACCTTTTGCAACTCTCTTTTGGTTCCTACA-TGCCAAG 700430 i i iiv iv i ii vi - v ivii i -i v L2d2_3end#LIN 453 AGGGCAGGGACCATGTCTTATACTTCT-TTGTATCCCCCACAGCGCCTAG 501 chr5qtel1M 700431 ------GCCTGGCATATATCAGGCTC---ATAAATGCTTGTTTACTTGA 700470 ------ v i i vi v --- ii v i L2d2_3end#LIN 502 CACAGTGCCTTGCACACAGTAGGCGCTCAATAAATATTTGTTGATTTGA 550 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 50.06 CpG sites = 29, Kimura (unadjusted) = 51.56 Transitions / transversions = 1.38 (29/21) Gap_init rate = 0.03 (4 / 138), avg. gap size = 2.75 (11 / 4) 216 29.63 9.17 1.55 chr5qtel1M 700351 700470 (299530) L2d_3end#LINE/L2 380 508 (8) m_b262s601i22 10391 chr5qtel1M 700351 TTGTCAATCCCACCAGTCTGTGATCTCCATAGGAGCAGGAGACACCTTTT 700400 vvi v i vi i v v ii i iiv iv i L2d_3end#LINE 380 TTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTT 429 chr5qtel1M 700401 GCAACTCTCTTTTGGTTCCT-ACA-TGCCAAG------GCCTGGCATATA 700442 ii - ? i ? v i- -i v ------ ivi i L2d_3end#LINE 430 ATA-CTNTTTTNTCGTTCCCCACAGCGCCTAGCACAGTGCTGAGCACATA 478 chr5qtel1M 700443 TCAGGCTC---ATAAATGCTTGTTTACTTGA 700470 vi v --- i v - L2d_3end#LINE 479 GTAGGCGCTCAATAAATACTTGTTGA-TTGA 508 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.39 CpG sites = 21, Kimura (unadjusted) = 39.87 Transitions / transversions = 1.50 (21/14) Gap_init rate = 0.05 (6 / 119), avg. gap size = 2.17 (13 / 6) 246 28.58 2.88 9.18 chr5qtel1M 700360 700463 (299537) L2c_3end#LINE/L2 369 466 (12) m_b262s601i23 10391 chr5qtel1M 700360 CCACCAGTCTGTGATCTCCATAGGAGCAGGAGACACCTTTTGCAACTCTC 700409 i v v v ii i iiv iiv i --- i vi L2c_3end#LINE 369 CCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTT---ATTCAT 415 chr5qtel1M 700410 TTTTGGTTCCTACATGCCAAGGCCTGGCATATATCAGGCTC---ATAAAT 700456 i vv ------ iv i vi v --- L2c_3end#LINE 416 CTTTGTATCC------CCAGCGCCTGGCACATAGTAGGCGCTCAATAAAT 459 chr5qtel1M 700457 GCTTGTT 700463 i L2c_3end#LINE 460 GTTTGTT 466 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.02 CpG sites = 16, Kimura (unadjusted) = 36.72 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.10 (10 / 103), avg. gap size = 1.20 (12 / 10) 264 32.50 2.50 0.00 chr5qtel1M 700481 700560 (299440) C MIRc#SINE/MIR (186) 82 1 m_b262s601i24 10392 chr5qtel1M 700481 AGGAAG-AGCGGTGCTAGGATATCAACCCAAGTCTTC-TGAGTCCAAATG 700528 v -i i v ii iviv i - v i v C MIRc#SINE/MIR 82 AGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTC 33 chr5qtel1M 700529 TAGGGATCACTTCATTATACCATGCTGCCTTG 700560 i v v vi i i ii ii i C MIRc#SINE/MIR 32 CAGTGCTCTTTCCACTGCACCACACTGCCTCG 1 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.88 CpG sites = 17, Kimura (unadjusted) = 44.93 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.03 (2 / 79), avg. gap size = 1.00 (2 / 2) 12 7.81 7.41 0.00 chr5qtel1M 702830 702856 (297144) (AACAA)n#Simple_repeat 1 29 (0) m_b262s252i18 10393 chr5qtel1M 702830 AAAAAAACAAAAC-AAA-AAAACGAAACA 702856 v - - i (AACAA)n#Simp 1 AACAAAACAAAACAAAACAAAACAAAACA 29 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.08 (2 / 26), avg. gap size = 1.00 (2 / 2) 14 23.16 0.00 4.26 chr5qtel1M 703940 703988 (296012) (ACATAA)n#Simple_repeat 1 47 (0) m_b263s252i1 10394 chr5qtel1M 703940 ACATAAATCCATATACACACAAATACATATAAGCATATATATAAACATA 703988 -- v i v v v i i v i (ACATAA)n#Sim 1 ACATAAA--CATAAACATAAACATAAACATAAACATAAACATAAACATA 47 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.04 (2 / 48), avg. gap size = 1.00 (2 / 2) 237 33.93 3.57 0.00 chr5qtel1M 704214 704325 (295675) L3#LINE/CR1 3973 4088 (11) m_b263s601i0 10395 chr5qtel1M 704214 GGTTTGTAAGGAAAACCTGATTGAGCAATTTTCAGAGCT-TTGGA-AATA 704261 v vi v i iv iv v v v i v - v - vi L3#LINE/CR1 3973 GGTGTTCAAGCAGAGGCTGGATGACCACTTGTCAGGGATGTTGTAGAAGG 4022 chr5qtel1M 704262 AATT--TGTGTCCAAGTAGAGGTTAGACAACATAACCTCTGAGATTAGTT 704309 i -- ii ivi vvi i v v i i i ivv L3#LINE/CR1 4023 GATTCCTGCATTGGATGGGAGGTTGGACTAGATGACCTCTAAGGTCCCTT 4072 chr5qtel1M 704310 CCATGTCTGAGATGCT 704325 vv v L3#LINE/CR1 4073 CCAACTCTGAGATTCT 4088 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.52 CpG sites = 17, Kimura (unadjusted) = 45.52 Transitions / transversions = 0.81 (17/21) Gap_init rate = 0.03 (3 / 111), avg. gap size = 1.33 (4 / 3) 326 18.78 9.35 5.41 chr5qtel1M 704753 704859 (295141) C MIR3#SINE/MIR (52) 156 46 m_b263s601i1 10396 chr5qtel1M 704753 AATCCAAACCTCTTCAATTTCCAGA--AGGAAACTGAAGCACAGAGA-AT 704799 i - i i v v -- i v -i C MIR3#SINE/MIR 156 AGTCCAA-CCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGT 108 chr5qtel1M 704800 G----GATTTGCTCAAAGGTCATA---CCATTTTGGAGTGTCAGAGTCAG 704842 ---- i i - i --- ? v --- v i i C MIR3#SINE/MIR 107 GAAGTGACTTGCCC-AAGGTCACACAGCNAGTT---AGTGGCAGAGCCGG 62 chr5qtel1M 704843 GTTCTGGAACCATGGTC 704859 -v i vv C MIR3#SINE/MIR 61 G-ACTAGAACCCAGGTC 46 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 20.92 CpG sites = 11, Kimura (unadjusted) = 22.19 Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.09 (10 / 106), avg. gap size = 1.60 (16 / 10) 51 0.00 2.13 0.00 chr5qtel1M 705156 705202 (294798) (AT)n#Simple_repeat 1 48 (0) c_b263s251i0 10397 chr5qtel1M 705156 ATATATATATATATATATATATATATATATATATATATATATA-ATAT 705202 - (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATAT 48 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.02 (1 / 46), avg. gap size = 1.00 (1 / 1) 429 20.93 4.55 9.52 chr5qtel1M 708010 708141 (291859) C MIRb#SINE/MIR (138) 130 5 m_b263s601i2 10398 chr5qtel1M 708010 CTGAGGCAATTAG---GGTTAAATGATTTGCTCAGGGTCACACAGCTAGG 708056 -- i --- i i i i i - C MIRb#SINE/MIR 130 CTGAGGC--TCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAG- 84 chr5qtel1M 708057 AAGTGTTAAGTGTCTGAGGCCAAATTTG--TTCAGTTCT-CCTTACTTCA 708103 ------ v v v vii i --ii v -i v i C MIRb#SINE/MIR 83 ------TAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCA 40 chr5qtel1M 708104 GGGCTGGTCCTCTCTCCACTGCACCACCTAGCTGCCCC 708141 ii iv v i --- C MIRb#SINE/MIR 39 AAGCCCGTGCTCTTTCCACTGCACCAC---GCTGCCCC 5 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 23.98 CpG sites = 17, Kimura (unadjusted) = 25.12 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.11 (15 / 131), avg. gap size = 1.20 (18 / 15) 299 24.11 7.69 4.26 chr5qtel1M 708217 708307 (291693) MIRc#SINE/MIR 45 138 (130) m_b263s601i3 10399 chr5qtel1M 708217 GGAAGACCTTAGTTTCCAAG---GAGCTTCAAGACACTTAATGGCTGTGT 708263 vi -- i ---vi ii-- v v i MIRc#SINE/MIR 45 GGAAGACCTGGGTT--CGAGTCCCGGCTCT--GCCACTTACTAGCTGTGT 90 chr5qtel1M 708264 GACCCTGGGCAAACTACTGAACACCT----GTCTCAGTTTTTGCATCT 708307 i iii v vi ---- i iiv MIRc#SINE/MIR 91 GACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCT 138 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.77 CpG sites = 14, Kimura (unadjusted) = 30.12 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.07 (6 / 90), avg. gap size = 1.83 (11 / 6) 269 33.17 0.00 6.80 chr5qtel1M 709623 709732 (290268) C MIRb#SINE/MIR (152) 116 14 m_b263s601i4 10400 chr5qtel1M 709623 GGTGAGGCAGCTGGGTCTAAGTGTCACAGCTAGCAAGGGTTAAGTGTCTG 709672 v i i i v vi v i vv ------- v v C MIRb#SINE/MIR 116 GGTTAAGTAACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGCAG 74 chr5qtel1M 709673 AGACCAGATTTGAACTCAGGTCTTCCCGATTTCAGGGCTGGTGTTCAGTT 709722 v vi i i vi i i i ii iv i vv i C MIRb#SINE/MIR 73 AGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTC 24 chr5qtel1M 709723 CACCTTACCA 709732 ivi C MIRb#SINE/MIR 23 CACTGCACCA 14 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.97 CpG sites = 19, Kimura (unadjusted) = 44.74 Transitions / transversions = 1.27 (19/15) Gap_init rate = 0.06 (7 / 109), avg. gap size = 1.00 (7 / 7) 304 29.02 0.00 6.67 chr5qtel1M 709637 709732 (290268) C MIRc#SINE/MIR (168) 100 11 m_b263s601i5 10400 chr5qtel1M 709637 GTCTAAGTGTCACAGCTAGCAAGGGTTAAGTGTCTGAGACCAGATTTGAA 709686 i i - --i v --- v v v vi i i C MIRc#SINE/MIR 100 GCCCAAG-GTCACA--CAGCTAG---TAAGTGGCAGAGCCGGGACTCGAA 57 chr5qtel1M 709687 CTCAGGTCTTCCCGATTTCAGGGCTGGTGTTCAGTTCACCTTACCA 709732 i i i i i v ii i vv i ivi C MIRc#SINE/MIR 56 CCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCA 11 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.18 CpG sites = 17, Kimura (unadjusted) = 38.06 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.06 (6 / 95), avg. gap size = 1.00 (6 / 6) 18 12.57 0.00 0.00 chr5qtel1M 711318 711344 (288656) (TG)n#Simple_repeat 1 27 (0) m_b263s252i2 10401 chr5qtel1M 711318 TGTGTATGTATGTATGTGTGTGTGTGT 711344 i i i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGT 27 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 194 26.47 4.04 8.42 chr5qtel1M 711782 711880 (288120) X24_LINE#LINE/L2 192 286 (28) m_b263s601i6 10402 chr5qtel1M 711782 TCTGGTCCCTGGCCTTTACCTCAGAGACCACTGCCCCCACCCTTTATAGC 711831 i v --- i i i -- i i v ? ii v X24_LINE#LINE 192 TTTGGGCCCTGG---TTACCTTAGAGATCGC--CTCTCTCCCTNTGCACC 236 chr5qtel1M 711832 GCTACA--AATGAAGCAACAACT--GAAGCTCTTACTAACCATGGTCACA 711877 ii i-- vi - v i -- v i i vi -- v X24_LINE#LINE 237 GTCACGGCAATTGAG-ATCAGCTAGGATGCTCCTGCTAACGGT--TCCCA 283 chr5qtel1M 711878 GAT 711880 X24_LINE#LINE 284 GAT 286 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.81 CpG sites = 16, Kimura (unadjusted) = 34.28 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.10 (10 / 98), avg. gap size = 1.20 (12 / 10) 16 10.66 2.08 8.89 chr5qtel1M 712328 712375 (287625) (CCTCT)n#Simple_repeat 1 45 (0) m_b263s252i3 10403 chr5qtel1M 712328 CCTCTCCCTCTCTTTCTCCTCTTCTTGTCCT-TCCTCTCCCTGTCCTCT 712375 - -i - i v - - v (CCTCT)n#Simp 1 CCTCT-CCTCTC-CTCTCCTC-TCCTCTCCTCTCCTCT-CCTCTCCTCT 45 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.11 (5 / 47), avg. gap size = 1.00 (5 / 5) 55 12.88 0.00 0.00 chr5qtel1M 713073 713157 (286843) (G)n#Simple_repeat 1 85 (0) m_b263s252i4 10404 chr5qtel1M 713073 GGTGGGGGCGGGGAGGGCGGGGGGGGGGGGGGGGGGGGGCGGGGGGGGGG 713122 v v i v v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 50 chr5qtel1M 713123 GGGGGGGGGGGGGGGGGGGGGGCCGGGCGCCGGGG 713157 vv v vv (G)n#Simple_r 51 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 85 Matrix = Unknown Transitions / transversions = 0.11 (1/9) Gap_init rate = 0.00 (0 / 84), avg. gap size = 0.0 (0 / 0) 24 6.96 8.51 2.00 chr5qtel1M 713921 713967 (286033) (AT)n#Simple_repeat 1 50 (0) m_b263s252i5 10405 chr5qtel1M 713921 ATATATA-ATA-ATATGTA-ATATATATATATATATAT-TATCTGATAGA 713966 - - i - - v - v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATAT-ATATA 49 chr5qtel1M 713967 T 713967 (AT)n#Simple_ 50 T 50 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.11 (5 / 46), avg. gap size = 1.00 (5 / 5) 495 19.89 3.08 7.20 chr5qtel1M 714306 714435 (285565) MIRc#SINE/MIR 24 148 (120) m_b263s601i7 10406 chr5qtel1M 714306 AGAGCCCTGGCTTTGGAATCAGGAATACTCAACTTCAGAGGTTTAAATCC 714355 v vi i v ---- ----i ii i MIRc#SINE/MIR 24 AGAGCACTGGACTTGGAGTCAGGAAGAC----CT----GGGTTCGAGTCC 65 chr5qtel1M 714356 TGCCTCAGTCACTTAACAGATGTGTCAGCCTGGCCAAGTCACTCAAGCCT 714405 i v v i vi v v v i v i - MIRc#SINE/MIR 66 CGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAA-CCT 114 chr5qtel1M 714406 GTTT--GCCT--GTTTCCTCATCTGTAAAATGAG 714435 v i -- -- i MIRc#SINE/MIR 115 CTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 21.05 CpG sites = 13, Kimura (unadjusted) = 23.27 Transitions / transversions = 1.18 (13/11) Gap_init rate = 0.09 (11 / 129), avg. gap size = 1.18 (13 / 11) 223 25.75 2.99 1.47 chr5qtel1M 715626 715692 (284308) C MIRc#SINE/MIR (195) 73 6 m_b263s601i8 10407 chr5qtel1M 715626 CAGAGCCAGGATTCT-ACCCATGTCCT-CTGATTCAAAATCCTAGTCACC 715673 i i v- v i - i v i - vvi C MIRc#SINE/MIR 73 CAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCC-AGTGCTC 25 chr5qtel1M 715674 TTTCTATGCCACTATACTG 715692 i ivv i i C MIRc#SINE/MIR 24 TTTCCACTGCACCACACTG 6 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.01 CpG sites = 10, Kimura (unadjusted) = 32.26 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.05 (3 / 66), avg. gap size = 1.00 (3 / 3) 12 26.62 0.00 7.02 chr5qtel1M 716436 716496 (283504) (TTTATT)n#Simple_repeat 1 57 (0) m_b263s252i6 10408 chr5qtel1M 716436 TTCATTTTCCTTCTCATTTTAATGATTTTAACTTTTCTTTTTATTAAAGC 716485 i iv i i -- - v i v -vvvv (TTTATT)n#Sim 1 TTTATTTTTATTTTTATTTT--T-ATTTTTATTTTTATTTTTATT-TTTA 46 chr5qtel1M 716486 TTTTTATTTTT 716496 (TTTATT)n#Sim 47 TTTTTATTTTT 57 Matrix = Unknown Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.07 (4 / 60), avg. gap size = 1.00 (4 / 4) 13 18.28 2.56 2.56 chr5qtel1M 716870 716908 (283092) (GAGCACA)n#Simple_repeat 1 39 (0) m_b263s252i7 10409 chr5qtel1M 716870 GAGCCCAGACCACAG-GCTAAGGAGCCCAGAGCAAAGAGC 716908 v v - - vi v v (GAGCACA)n#Si 1 GAGCACAGAGCACAGAGC-ACAGAGCACAGAGCACAGAGC 39 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2) 231 30.10 0.00 0.00 chr5qtel1M 717049 717151 (282849) L1P3_orf2#LINE/L1 568 670 (2624) m_b263s551i0 10410 chr5qtel1M 717049 GAATATACTTTTTCCTCAGCAGTACATGGAACTAATACAAAAATTGACCA 717098 v i i ivi v v v v v L1P3_orf2#LIN 568 GAATATACATTCTTCTCAGCGCCACATCGCACTTATTCTAAAATTGACCA 617 chr5qtel1M 717099 TACATTAGGGCATAAAACCCTCAAAATCAAATGCACAAATGTAGAAATAG 717148 i i v v ivi v vvv v v iviii vi L1P3_orf2#LIN 618 CATAATTGGAAGTAAAACACTCCTCAGCAAATGCAAAAGAACGGAAATCA 667 chr5qtel1M 717149 TAA 717151 L1P3_orf2#LIN 668 TAA 670 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.49 CpG sites = 13, Kimura (unadjusted) = 38.61 Transitions / transversions = 0.72 (13/18) Gap_init rate = 0.00 (0 / 102), avg. gap size = 0.0 (0 / 0) 12 31.65 3.51 0.00 chr5qtel1M 717160 717216 (282784) (ATACAT)n#Simple_repeat 1 59 (0) m_b263s252i8 10411 chr5qtel1M 717160 ATAGATATGTGTATACATAT--TTGTATGTTTATGTATATATGTGCATAT 717207 v iii --v i ii v ii i i i (ATACAT)n#Sim 1 ATACATATACATATACATATACATATACATATACATATACATATACATAT 50 chr5qtel1M 717208 ACATATACA 717216 (ATACAT)n#Sim 51 ACATATACA 59 Matrix = Unknown Transitions / transversions = 3.67 (11/3) Gap_init rate = 0.02 (1 / 56), avg. gap size = 2.00 (2 / 1) 245 28.40 7.22 1.96 chr5qtel1M 717219 717315 (282685) C MIR#SINE/MIR (156) 106 5 m_b263s601i10 10412 chr5qtel1M 717219 TAAGTGAATTGCCCAGCATCACAAAGCTAGTCAATATCTGAAGCACAGTT 717268 i v ivi v v i iv v iv ivii C MIR#SINE/MIR 106 TAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATT 57 chr5qtel1M 717269 TGAACC----CAGTCT--TTCCTGATTCTTTGTTCTATAATTAGCTAT-C 717311 i ---- --i v vi iv i - ii - - C MIR#SINE/MIR 56 CGAACCCAGGCAGTCTGGCTCCAGAGCCCGTGCTCT-TAACCA-CTATGC 9 chr5qtel1M 717312 TATA 717315 C MIR#SINE/MIR 8 TATA 5 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.78 CpG sites = 16, Kimura (unadjusted) = 36.72 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.05 (5 / 96), avg. gap size = 1.80 (9 / 5) 290 30.56 0.00 0.00 chr5qtel1M 717219 717290 (282710) C MIRc#SINE/MIR (158) 110 39 m_b263s601i9 10412 chr5qtel1M 717219 TAAGTGAATTGCCCAGCATCACAAAGCTAGTCAATATCTGAAGCACAGTT 717268 v ivi v v i iv v iv iviii C MIRc#SINE/MIR 110 TAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACT 61 chr5qtel1M 717269 TGAACCCAGTCTTTCCTGATTC 717290 i vii i C MIRc#SINE/MIR 60 CGAACCCAGGTCTTCCTGACTC 39 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.84 CpG sites = 13, Kimura (unadjusted) = 40.48 Transitions / transversions = 1.44 (13/9) Gap_init rate = 0.00 (0 / 71), avg. gap size = 0.0 (0 / 0) 15 14.38 0.00 0.00 chr5qtel1M 717359 717382 (282618) (T)n#Simple_repeat 1 24 (0) m_b263s252i9 10413 chr5qtel1M 717359 TTTTTTCTTTTTCTTTTTCTTTTT 717382 i i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTT 24 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 17 20.23 0.00 0.00 chr5qtel1M 717908 717941 (282059) (T)n#Simple_repeat 1 34 (0) m_b263s252i10 10414 chr5qtel1M 717908 TTTTTTTTTTGTTTTTTTTTTACTTTCTCTGTTT 717941 v vi i i v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 34 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 18 5.78 8.33 0.00 chr5qtel1M 718488 718523 (281477) (AACA)n#Simple_repeat 1 39 (0) m_b263s252i11 10415 chr5qtel1M 718488 AAAAAAC-AA-AAACAAACAAATAAACAAACAAA-AAAC 718523 v - - i - (AACA)n#Simpl 1 AACAAACAAACAAACAAACAAACAAACAAACAAACAAAC 39 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.09 (3 / 35), avg. gap size = 1.00 (3 / 3) 221 24.50 0.00 2.04 chr5qtel1M 718845 718894 (281106) C MIRc#SINE/MIR (155) 113 65 m_b263s601i11 10416 chr5qtel1M 718845 GGTTAAGTGACTTGCCTAGGATCACATATCTGATTAGTATCTGAAGCTGG 718894 i i i i v ii v iv v - i C MIRc#SINE/MIR 113 GGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAG-AGCCGG 65 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.67 CpG sites = 8, Kimura (unadjusted) = 30.68 Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.02 (1 / 49), avg. gap size = 1.00 (1 / 1) 582 32.76 1.12 0.56 chr5qtel1M 719667 719844 (280156) C MIR3#SINE/MIR (5) 203 25 m_b263s601i12 10417 chr5qtel1M 719667 ATCAAATCAAAGATTG--AGAGCTGGCAGGGGTCTTAGGAAATCACCTTG 719714 vi v v -- v ii - i i v C MIR3#SINE/MIR 203 ATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAG-AGATCATCTAG 155 chr5qtel1M 719715 TCCACTCCACTCATTTTAAAGCTGTAAGATCTGAGACCCAATGAGATTAA 719764 vi v v v viii v i iv i v C MIR3#SINE/MIR 154 TCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAA 105 chr5qtel1M 719765 ATGACTTACTGAACATCCCATAAATACCAGGTGACAGAGCTAAGATTAAA 719814 i i iv vi v i iv? vivi i iii i i C MIR3#SINE/MIR 104 GTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGA 55 chr5qtel1M 719815 ACTCGGGTTCTCTGCCTTCAGATCAGCACT 719844 i i iii v i vii v ii C MIR3#SINE/MIR 54 ACCCAGGTCTCCTGACTCCCAGTCCGTGCT 25 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.18 CpG sites = 36, Kimura (unadjusted) = 45.38 Transitions / transversions = 1.64 (36/22) Gap_init rate = 0.01 (2 / 177), avg. gap size = 1.50 (3 / 2) 446 36.11 1.39 0.00 chr5qtel1M 719724 719867 (280133) C MIRc#SINE/MIR (120) 148 3 m_b263s601i13 10417 chr5qtel1M 719724 CTCATTTTAAAGCTGTAAGATCTGAGACCCAATGAGATTAAATGACTTAC 719773 i v v viii v i i iv i i i C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr5qtel1M 719774 TGAACATCCCATAAATACCAGGTGACAGAGCTAAGATTAAAACTCGGGT- 719822 iv vi v i iv vi i i iii i vi i i - C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTC 49 chr5qtel1M 719823 TCTCTGCCTTCAGAT-CAGCACTGATTCCATTGTTCCATATCACCT 719867 ii v i ii - ii vv i iv i iii C MIRc#SINE/MIR 48 TTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTGCCT 3 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 50.62 CpG sites = 37, Kimura (unadjusted) = 53.96 Transitions / transversions = 2.47 (37/15) Gap_init rate = 0.01 (2 / 143), avg. gap size = 1.00 (2 / 2) 231 32.17 4.49 2.20 chr5qtel1M 719937 720025 (279975) L2a_3end#LINE/L2 414 504 (13) m_b263s601i14 10418 chr5qtel1M 719937 GGGCAGG----TTTCTCCCTCTGGAACTCAGTGCAGCCCCTCTAGTGCTT 719982 ---- v iv i v --i v v ivi i i i i L2a_3end#LINE 414 GGGCAGGGACTTTTGTCTGTTTTG--TTCACTGCTGTATCCCCAGCGCCT 461 chr5qtel1M 719983 AATAGAGTGCCTGGAACAAAACAGGCACTTAATAAGTGCTTAT 720025 iv v v v ii i i i ii i L2a_3end#LINE 462 AGAACAGTGCCTGGCACATAGTAGGCGCTCAATAAATATTTGT 504 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.94 CpG sites = 18, Kimura (unadjusted) = 44.15 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.03 (3 / 88), avg. gap size = 2.00 (6 / 3) 236 33.87 0.00 0.00 chr5qtel1M 719964 720025 (279975) L2d2_3end#LINE/L2 481 542 (13) m_b263s601i15 10418 chr5qtel1M 719964 TGCAGCCCCTCTAGTGCTTAATAGAGTGCCTGGAACAAAACAGGCACTTA 720013 i v ivi i i ii v v v v ii i i L2d2_3end#LIN 481 TGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAGTAGGCGCTCA 530 chr5qtel1M 720014 ATAAGTGCTTAT 720025 i ii i L2d2_3end#LIN 531 ATAAATATTTGT 542 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.35 CpG sites = 15, Kimura (unadjusted) = 48.83 Transitions / transversions = 2.50 (15/6) Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0) 719 30.36 3.05 0.60 chr5qtel1M 720158 720485 (279515) C L1ME3_3end#LINE/L1 (573) 336 1 m_b263s551i1 10419 chr5qtel1M 720158 ATAGTTCCAAACTGCTCTCCAGAATAGTTGGATCCATTCACAGTTCTACT 720207 v v v i i i i i v i v i v i i i C L1ME3_3end#LI 336 ATACTGCCAAACAGTTTTCCAAAGTGGTTGTACCAATTTACACTCCCACC 287 chr5qtel1M 720208 AAGAATGTAT--------CACTTTTCCCACATCCCCTCCAACCTTTGTCA 720249 iv -------- v vii i v vi vi C L1ME3_3end#LI 286 AGCAATGTATGAGAGTTCCAGTTGCTCCACATCCTCGCCAACACTTGGTA 237 chr5qtel1M 720250 TTATCTTTTCTTGTCATCTTATCCAATCTGACAAGTGTGTAGTGGTATCT 720299 i vv ii v v i v v iiii C L1ME3_3end#LI 236 TTGTCAGTCTTTTTAATTTTAGCCATTCTGGTGGGTGTGTAGTGGTATCT 187 chr5qtel1M 720300 CAGATTGGTCTTAATTTTCATTTCTCTCATTAATAGTGATTTTGAGCACC 720349 vvv i v i v v v i v C L1ME3_3end#LI 186 CATTGTGGTTTTAATTTGCATTTCCCTGATGACTAATGATGTTGAGCACC 137 chr5qtel1M 720350 TTTTCATGTGGCTACAAATAGTTTCAATTTCTTCATCTGAAAATTGTCTG 720399 i vi iviiivi vi v i v i vi v i C L1ME3_3end#LI 136 TTTTCATATGCTTATTGGCCATTTGGATATCCTCTTTTGTGAAGTGCCTG 87 chr5qtel1M 720400 TTCATGTCCTTTGACCCTTTATCAATTGGA--AAATGGCTTCAACTATTA 720447 v i v v v i i--ivv v i--i v C L1ME3_3end#LI 86 TTCAAGTCTTTTGCCCATTTTTTAATTGGGTTGTTTGTCTTT--TTCTTA 39 chr5qtel1M 720448 TAAATTTGAGCCAATTCTTTATTTATTTTAGAAATGAG 720485 vi vivv i v i i v i C L1ME3_3end#LI 38 TTGATTTGTAGGAGTTCTTTATATATTCTGGATACGAG 1 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.03 CpG sites = 51, Kimura (unadjusted) = 39.54 Transitions / transversions = 1.06 (51/48) Gap_init rate = 0.01 (4 / 327), avg. gap size = 3.00 (12 / 4) 16 15.81 0.00 2.78 chr5qtel1M 720827 720863 (279137) (GAGG)n#Simple_repeat 1 36 (0) m_b263s252i13 10420 chr5qtel1M 720827 GAGGGTGTGGAAGGAGTCAGGGAGGGAGGGAGGAAGG 720863 v - i vv i (GAGG)n#Simpl 1 GAGGGAG-GGAGGGAGGGAGGGAGGGAGGGAGGGAGG 36 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 16 14.95 0.00 5.13 chr5qtel1M 720863 720903 (279097) (GAAATA)n#Simple_repeat 1 39 (0) m_b263s252i14 10421 chr5qtel1M 720863 GAAATGGAGATAGAGATAGAAATAGACAGAGACAACTAGAA 720903 i i i v v - - (GAAATA)n#Sim 1 GAAATAGAAATAGAAATAGAAATAGAAATAGA-AA-TAGAA 39 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 337 21.54 20.00 3.45 chr5qtel1M 721469 721593 (278407) MIRc#SINE/MIR 4 148 (120) m_b263s601i16 10422 chr5qtel1M 721469 GGCAGTTAGGTGGCACAGTAGAGAGA--------CTTTGAG-CAGGAAGA 721509 --- ii i i -------- v - MIRc#SINE/MIR 4 GGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA 50 chr5qtel1M 721510 CTCCTATTTCTGAGCTCAAATCCGGCC-----CTAG-------ACCTTGG 721547 -- ivv ii ii viiii v ----- ------- MIRc#SINE/MIR 51 C--CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 98 chr5qtel1M 721548 GCAAGTCATTTTGCCTGT----GCCTCAGCTTCCTCAATTGTAAAATGAG 721593 i vi v ---- i vi i MIRc#SINE/MIR 99 GCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.10 CpG sites = 18, Kimura (unadjusted) = 26.42 Transitions / transversions = 2.25 (18/8) Gap_init rate = 0.08 (10 / 124), avg. gap size = 3.00 (30 / 10) 323 25.26 8.42 0.00 chr5qtel1M 721540 721634 (278366) MIR3#SINE/MIR 88 190 (18) m_b263s601i17 10422 chr5qtel1M 721540 GACCTTGGGCAAGTCATTTTGCCT----GTGCCTCAGCTTCCTCAATTGT 721585 i ii ---- v i vi MIR3#SINE/MIR 88 GACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGT 137 chr5qtel1M 721586 AAAATGAGCTGG-AGGAAGAAATGG---CCAAGCACTCCACTATCTTTGG 721631 vv -v vv i i--- i vv i iv i v i i MIR3#SINE/MIR 138 AAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGA 187 chr5qtel1M 721632 CAT 721634 MIR3#SINE/MIR 188 CAT 190 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.26 CpG sites = 13, Kimura (unadjusted) = 31.26 Transitions / transversions = 1.18 (13/11) Gap_init rate = 0.03 (3 / 94), avg. gap size = 2.67 (8 / 3) 448 25.35 0.75 8.06 chr5qtel1M 722216 722348 (277652) C MIRb#SINE/MIR (138) 130 7 m_b263s601i18 10423 chr5qtel1M 722216 CTGAGGC-AATTGGGATTAAGTGACTTGCCCAGGGTCACACAGCTAGGAC 722264 -v vv i i i i --- C MIRb#SINE/MIR 130 CTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAG--- 84 chr5qtel1M 722265 ATGTTAAATATCTGAGGCTAGATTTGAACTCAGGTCCTTCTGACTTCAGG 722314 ---- i iv v v vi i i iv i ii C MIRb#SINE/MIR 83 ----TAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAA 38 chr5qtel1M 722315 GATGCTGCTCTGTCCATCGAGCCATCTAGCTGCC 722348 vivv v ii vi i--- C MIRb#SINE/MIR 37 GCCCGTGCTCTTTCCACTGCACCAC---GCTGCC 7 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.97 CpG sites = 18, Kimura (unadjusted) = 31.34 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.08 (11 / 132), avg. gap size = 1.00 (11 / 11) 84 0.00 1.33 0.00 chr5qtel1M 722360 722434 (277566) (AT)n#Simple_repeat 1 76 (0) c_b263s251i1 10424 chr5qtel1M 722360 ATATATATATATATATATATATATATATATATATATATATATATATATAT 722409 (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr5qtel1M 722410 ATATATATATATATATATATA-ATAT 722434 - (AT)n#Simple_ 51 ATATATATATATATATATATATATAT 76 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.01 (1 / 74), avg. gap size = 1.00 (1 / 1) 16 15.91 0.00 0.00 chr5qtel1M 722749 722776 (277224) (GT)n#Simple_repeat 1 28 (0) m_b263s252i15 10425 chr5qtel1M 722749 GTGTGTGTGTGTGTGTATGTATTGGTGT 722776 i i vv (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGT 28 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 348 26.18 4.98 4.98 chr5qtel1M 725587 725787 (274213) C L1MC3_3end#LINE/L1 (1899) 633 433 m_b263s551i2 10426 chr5qtel1M 725587 GCTCATTTCACTCAGCATCAGTTCATGTAAGTCTC-TCCAGGCCTTTCTG 725635 iv i vi - v v vi - v i --- C L1MC3_3end#LI 633 GCTTCTTTCACTTAGCAATA-TGCATTTAAGATTCATCCATGTCTTT--- 588 chr5qtel1M 725636 AAATCAT--CTTGCTGG-TCATTTCTT---ACAGAACAATAATATTCCAT 725679 --- i -- v i - --- iv vvv C L1MC3_3end#LI 587 ---TCGTGGCTTGATAGCTCATTTCTTTTTATCGCTGAATAATATTCCAT 541 chr5qtel1M 725680 AATATTCATATACCACAATTTATTCAGCCGTTGTCCAATTGATGTGTATC 725729 vi vv i i i i v i vv v v vii C L1MC3_3end#LI 540 TGTATGGATGTACCACAGTTTGTTTATCCATTCACCTATTGAAGGACATC 491 chr5qtel1M 725730 CACTCAGTT---TCCAGTTTTTGGCCACTACAAAGAGGGCTGCCACAAAC 725776 --- ii --- v i ii v ii i i C L1MC3_3end#LI 490 ---TTGGTTGCTTCCAGTTTTTGGCGATTATGAATAAAGCTGCTATAAAC 444 chr5qtel1M 725777 ATTCTTGAGCA 725787 vi v C L1MC3_3end#LI 443 ATTCGCGTGCA 433 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 31.06 CpG sites = 26, Kimura (unadjusted) = 32.60 Transitions / transversions = 1.08 (26/24) Gap_init rate = 0.07 (15 / 200), avg. gap size = 1.33 (20 / 15) 420 28.80 0.00 0.00 chr5qtel1M 725667 725791 (274209) C L1ME2z_3end#LINE/L1 (638) 553 429 m_b263s551i3 10426 chr5qtel1M 725667 AATAATATTCCATAATATTCATATACCACAATTTATTCAGCCGTTGTCCA 725716 i i vi vv i i i v i v v C L1ME2z_3end#L 553 AGTAGTATTCCATTGTATGAATATACCACAGTTTGTTTATCCATTCTCCT 504 chr5qtel1M 725717 ATTGATGTGTATCCACTCAGTTTCCAGTTTTTGGCCACTACAAAGAGGGC 725766 i vii i iivv v i i ii v ii C L1ME2z_3end#L 503 GTTGATGGACACCTGGGCTGTTTCCAGTTTTTGGCTATTATGAATAAAGC 454 chr5qtel1M 725767 TGCCACAAACATTCTTGAGCAATTC 725791 i ii vi v C L1ME2z_3end#L 453 TGCTATGAACATTCTTGTACAAGTC 429 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.76 CpG sites = 23, Kimura (unadjusted) = 37.76 Transitions / transversions = 1.77 (23/13) Gap_init rate = 0.00 (0 / 124), avg. gap size = 0.0 (0 / 0) 12 18.86 2.63 2.63 chr5qtel1M 727618 727655 (272345) (AAAACTA)n#Simple_repeat 1 38 (0) m_b263s252i16 10427 chr5qtel1M 727618 AAAACTCAAACCTAAAAACCAAGCAAAGAAAAA-TAAAA 727655 v v i -v vv - (AAAACTA)n#Si 1 AAAACTAAAAACTAAAAACTAA-AAACTAAAAACTAAAA 38 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 17 16.74 2.50 0.00 chr5qtel1M 727711 727750 (272250) (AAAC)n#Simple_repeat 1 41 (0) m_b263s252i17 10427 chr5qtel1M 727711 AAACAAACAAACAAACACATAAAAAAACCCA-AAACAGACA 727750 v i v vv - i (AAAC)n#Simpl 1 AAACAAACAAACAAACAAACAAACAAACAAACAAACAAACA 41 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1) 29 30.36 3.17 0.78 chr5qtel1M 727850 727975 (272025) (TCTC)n#Simple_repeat 1 129 (0) m_b263s252i18 10428 chr5qtel1M 727850 TCTGTCTCTGTC-CTGCTACCTCTCTCTGTTTCTTTCTTACACTATGT-T 727897 v v - - vi v i i iv v v v - (TCTC)n#Simpl 1 TCTCTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 49 chr5qtel1M 727898 CACTCTCTGGCTCTGTCTGTCTCTCTGTTTCTCTTGATCTGTCTTTCTCA 727947 v vv v v v i ivv v i v (TCTC)n#Simpl 50 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 99 chr5qtel1M 727948 CT-TCT-TGTTTCCCTCTCTTGCTCTTTCT 727975 - - v i i iv i (TCTC)n#Simpl 100 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 129 Matrix = Unknown Transitions / transversions = 0.55 (11/20) Gap_init rate = 0.04 (5 / 125), avg. gap size = 1.00 (5 / 5) 12 13.67 0.00 0.00 chr5qtel1M 728648 728671 (271329) (GCA)n#Simple_repeat 1 24 (0) m_b263s252i19 10429 chr5qtel1M 728648 GCAGAAGTAGCATCAGCAGCAGCA 728671 v i v (GCA)n#Simple 1 GCAGCAGCAGCAGCAGCAGCAGCA 24 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 15 20.06 0.00 2.44 chr5qtel1M 730100 730141 (269859) (TCTCCCT)n#Simple_repeat 1 41 (0) m_b263s252i20 10430 chr5qtel1M 730100 TCTCTCTTTCTCCCTCATCCCTTGTCCCTTTTATCTTCTCCC 730141 - i iv v i vi (TCTCCCT)n#Si 1 TCTC-CCTTCTCCCTTCTCCCTTCTCCCTTCTCCCTTCTCCC 41 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.02 (1 / 41), avg. gap size = 1.00 (1 / 1) 13 5.27 0.00 0.00 chr5qtel1M 732229 732248 (267752) (CTC)n#Simple_repeat 1 20 (0) m_b263s252i21 10431 chr5qtel1M 732229 CTCCTCCTTCTCCTCCTCCT 732248 i (CTC)n#Simple 1 CTCCTCCTCCTCCTCCTCCT 20 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 230 21.15 1.92 0.00 chr5qtel1M 733269 733320 (266680) MIR#SINE/MIR 71 123 (139) m_b263s601i20 10432 chr5qtel1M 733269 CATTTCCTAGTTGTGTGGCCCTGGGCATGTCACTTAACCCCAAT-TGCCT 733317 i v i i i v i i vv - MIR#SINE/MIR 71 CACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCT 120 chr5qtel1M 733318 AAG 733320 v MIR#SINE/MIR 121 CAG 123 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.13 CpG sites = 6, Kimura (unadjusted) = 25.13 Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.02 (1 / 51), avg. gap size = 1.00 (1 / 1) 28 0.00 0.00 0.00 chr5qtel1M 733335 733361 (266639) (AAAG)n#Simple_repeat 1 27 (0) c_b263s251i2 10433 chr5qtel1M 733335 AAAGAAAGAAAGAAAGAAAGAAAGAAA 733361 (AAAG)n#Simpl 1 AAAGAAAGAAAGAAAGAAAGAAAGAAA 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 782 29.82 6.81 4.06 chr5qtel1M 733573 734292 (265708) HERVK14#LTR/ERVK 2659 3397 (2699) m_b263s701i0 10434 chr5qtel1M 733573 AACCTGCATGGATAGAACAATGGCCTCTCCCCTCAGGAAAGTTACAGGCA 733622 v iv i i i v vvvv- i-- v vi HERVK14#LTR/E 2659 AACCGGTTTGGGTGGAGCAATGGCCGCTGAAA-CAGGAAAA--ACTGGAG 2705 chr5qtel1M 733623 GCT------GAATTATTACTTAAGGAACAATTACAATTGGGACATATTGA 733666 ------ i iv i --- i vv v HERVK14#LTR/E 2706 GCTTTAAAAGAACTGGTGC---AGGAACAATTGCAAAAGGGACATATAGA 2752 chr5qtel1M 733667 ACCTTCCTCTAGTCCTTATAATGTGCCCATTTTTGTTATTAAGAAGAAAA 733716 i v i iivvi iv viv ii v i i v HERVK14#LTR/E 2753 GCCTACTTTCTCCCCTTGGAATTCTCCTGTATTTGTCATTAAGAAAAAAT 2802 chr5qtel1M 733717 GTGGAAAATGGAGACTTCTCCAAGATTTGAGAGCAGTTAATAAAATTATG 733766 vv i v vi vvv i i v ivvi v v HERVK14#LTR/E 2803 CAGGGAAATGGAGAATGTTAACAGATTTAAGGGCTGTTAATGCTGTGATT 2852 chr5qtel1M 733767 GAGCCTATGGGAACTTTGCAACCAGGTTTGCCATCACCAGTTGCTATACC 733816 v i i vi vi vi v v iiviiv v HERVK14#LTR/E 2853 CAACCCATGGGTGCACTGCAACCAGGGCTGCCCTCCCCAACAATGATCCC 2902 chr5qtel1M 733817 AAAAAA--AATTTCAATTATAGTCATAGATTTAGAGGATTGTTTCTATAC 733864 v --iiii -- i v i i i i v HERVK14#LTR/E 2903 AAAATACTGGCCTC--TCATAGTGATAGATCTAAAGGATTGCTTTTTTAC 2950 chr5qtel1M 733865 TATCCCTTTAGCTAAACAAGA-GAGGAAATACTTTGCCCTTAA----CCT 733909 i i ivv -v v - v ii v---- i HERVK14#LTR/E 2951 CATTCCTTTAGCTGCCCAAGATTATGAAA-AATTTGCTTTTACTGTTCCC 2999 chr5qtel1M 733910 ACCAGTAACTAATTTTCACAGACCTTACAGA-AGATTTCAATGGAAAGTT 733958 i - v ---- v v ivi i - vi v v HERVK14#LTR/E 3000 GCCA-TAAATAAT----AAAGAACCAGCGGACAGATACCATTGGAAAGTA 3044 chr5qtel1M 733959 TTACCTCAGGGCATGAAAAACAGCCCTACGTTGTACCAAAAATTTGTAGA 734008 i v i vv i v vv v ii vv v v i HERVK14#LTR/E 3045 CTACCACAAGGCATGCTAAATAGCCCGACTATTTGTCAAACTTATGTCGG 3094 chr5qtel1M 734009 CATTGC-ATTAAAGGATATTAGA-ACTAGTATAAAGAG-----------C 734045 v vv - ivv -i - vi v i i----------- HERVK14#LTR/E 3095 GAAAGCTATTAAGCCA-GTTAGAGAACAGTTTAAAAAATGTTATATTATC 3143 chr5qtel1M 734046 CATTACATGGGTGATATACT-TATG--GC--ACACCCGGATAGAATGCAG 734090 i v - i -- -- v iv iv ----- HERVK14#LTR/E 3144 CATTACATGGATGATATTCTGTGTGCAGCTGAAACTAGGGAAGAA----- 3188 chr5qtel1M 734091 CTTAATAATATCCTGCAAGATGTCACTATAGCTTTAAATAAATATGGC-- 734138 - i iv i v i ivv i vv v vi ---i ii -- HERVK14#LTR/E 3189 -TTGATGTTGTGCTACAAACAGTTAGAAAAGGCT---GTAAATGCGGCAG 3234 chr5qtel1M 734139 --CTCATCATAGTTCCTGATAAAATCCATCATTTTCCTTCCTAGGGAGAA 734186 --i v i ii i vvv i v i vvvi v - HERVK14#LTR/E 3235 GGTTAATTATAGCCCCCGATAAAATCCAAACTTCTACTCCCTTTCAATA- 3283 chr5qtel1M 734187 TTTTACCAA--AAGAT--AACATAGTCTCTTTTCAGTC-----ATTTTCA 734227 - i vv -- i -- v -v v v i ----- vv HERVK14#LTR/E 3284 -TCTAGGAATGAAGGTAGAACAAAGT-GCTATTAAGCCTCAAAAGGTTCA 3331 chr5qtel1M 734228 ---TTGAGGACTGACAAGTTGAAAACACTTAAA-GATTTCCAAAAGTTCT 734273 --- i i -- i v i - - i v HERVK14#LTR/E 3332 AATTCGAAGA--GATAATTTAAAAAC-CTTAAATGATTTCCAAAAATTAT 3378 chr5qtel1M 734274 TAGGAGATATTAACTGGAT 734292 i i HERVK14#LTR/E 3379 TAGGAGACATTAATTGGAT 3397 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.27 CpG sites = 99, Kimura (unadjusted) = 38.45 Transitions / transversions = 0.93 (99/107) Gap_init rate = 0.07 (47 / 719), avg. gap size = 1.68 (79 / 47) 795 27.02 4.68 4.68 chr5qtel1M 733581 734007 (265993) HERVK9#LTR/ERVK 2428 2854 (3167) m_b263s701i1 10434 chr5qtel1M 733581 TGGATAGAACAATGGCCTCTCCCCTCAGGAAAGTTACAGGC---AGCTGA 733627 v vvvivv ii ii iv --- vv HERVK9#LTR/ER 2428 TGGATAGAACAATGGCCGCTAAGTAAAGAGAAACTGGAGGCTTTAGAGGA 2477 chr5qtel1M 733628 ATTA-TTACTTAAGGAACAATTAC--AATTGGGACATA--TTGAACCTTC 733672 - ---- v-- v v -- iv v i HERVK9#LTR/ER 2478 ATTAGTTACT----GAACAATTAGAAAATGGGCACATAGCTCCAACATTT 2523 chr5qtel1M 733673 CTCTAGTCCTTATAATGTGCCCATTTTTGTTATTAAGAAGAAAAGTGGAA 733722 ii ---- iv viv vi i v i vvv v HERVK9#LTR/ER 2524 TCC----CCTTGGAATTCTCCAGTTTTCGTAATTAAGAAAAAATCAGGTA 2569 chr5qtel1M 733723 AATGGAGACTTCTCCAA--GATTTGAGAGCAGTTAATAAAATTATGGAGC 733770 v vi -- -- i i vi i vv i iv i HERVK9#LTR/ER 2570 AATGGAGAATGTT--AACTGACTTAAGAGCCATCAATTCAGTTATACAAC 2617 chr5qtel1M 733771 CTATGGGAACTTTGCAACCAGGTTTGCCATCACCAGTTGCTATA---CCA 733817 i v i i v v v --- --- HERVK9#LTR/ER 2618 CTATGGGAGCATTACAGCCAGGATTGCCTTCTCC---TGCTATAATTCCA 2664 chr5qtel1M 733818 AAAAA---AATTTCAATTATAGTCATAGATTTAGAGGATTGTTTCTATAC 733864 ---ivi i --- i i i v HERVK9#LTR/ER 2665 AAAAATTGGCCTTTA---ATAGTCATAGATTTAAAAGACTGTTTCTTTAC 2711 chr5qtel1M 733865 TATCCCTTTAGCTAAACAAGAGAGGAAATACTTTGCCCTTAA----CCTA 733910 i i i vv vi iiv vi v---- i HERVK9#LTR/ER 2712 TATCCCCTTAGCTGAGCAAGACTGTGAACGGTTTGCATTTACAATTCCTG 2761 chr5qtel1M 733911 CCAGTAACTAATTTTCACAGACCTTACAGAAGATTTCAATGGAAAGTTTT 733960 - vi ii v ---i vvi iiv v v v HERVK9#LTR/ER 2762 -CAGTAAACAACCTGCA---GCCTGCTAAGCGTTTTCATTGGAAAGTGTT 2807 chr5qtel1M 733961 ACCTCAGGGCATGAAAAACAGCCCTACGTTGTACCAAAAATTTGTAG 734007 i v i vv i v iv v i i v? v HERVK9#LTR/ER 2808 GCCACAAGGCATGTTAAACAGTCCAACAATTTGCCAGACNTATGTAG 2854 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 33.13 CpG sites = 53, Kimura (unadjusted) = 33.90 Transitions / transversions = 0.93 (53/57) Gap_init rate = 0.07 (28 / 426), avg. gap size = 1.43 (40 / 28) 278 20.55 1.35 1.35 chr5qtel1M 734243 734316 (265684) HERVKC4#LTR/ERVK 1409 1482 (3780) m_b263s701i2 10434 chr5qtel1M 734243 TTGAAAACACTTAAA-GATTTCCAAAAGTTCTTAGGAGATATTAACTGGA 734291 i - - i i v i HERVKC4#LTR/E 1409 TTAAAAAC-CTTAAATGATTTTCAAAAATTGTTAGGAGATATTAATTGGA 1457 chr5qtel1M 734292 TCAGGCCTTACTTAAAACTACCCAC 734316 iv ivv ii v v i HERVKC4#LTR/E 1458 TTCGGCCCACCTTAGGAATTCCTAC 1482 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 24.42 CpG sites = 9, Kimura (unadjusted) = 24.42 Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.03 (2 / 73), avg. gap size = 1.00 (2 / 2) 520 29.93 3.36 4.17 chr5qtel1M 735353 735739 (264261) HERVK#LTR/ERVK 4792 5175 (2361) m_b263s701i3 10435 chr5qtel1M 735353 CATGTCCTACATCTTTGCCCACCCTCCCATTTGGAGTAAATTCCAGAGGT 735402 v i -- i vvvviviv v i HERVK#LTR/ERV 4792 CAAGTCCTACACCT--GCCCACTCAAGAGGCAGGAGTTAATCCCAGAGGT 4839 chr5qtel1M 735403 CTAAAGAGCCAATGATGTCTGGCAAATGGACGTTACACATGTCTCGTCCT 735452 iv- vv i vvv v i i i vi v v HERVK#LTR/ERV 4840 CTGT-GTCCTAATGCGTTATGGCAAATGGATGTCACGCATGTACCTTCAT 4888 chr5qtel1M 735453 TTGGAAAGATT-TCTTATTTACATGTTATTGTGGACACATTCTCCCACT- 735500 - - v ? v v v iv v i v vi v i - HERVK#LTR/ERV 4889 TTGG-AAGATTGTCATNTGTCCATGTAACAGTTGATACTTATTCACATTT 4937 chr5qtel1M 735501 -ATATTGTCGTCTCCCCAAGGACCAGTGAAGC--CTTTAAAGATGTATCA 735547 - v v iv iiv -- vi v iv-- i--vv - v HERVK#LTR/ERV 4938 CATATGGGCAACCTGCCA--GACAGGAGAAAGTACTTC--CCATGT-TAA 4982 chr5qtel1M 735548 CAAA-ATTTATTTCTTTGCTTTTCTATTATGGGAATGCCAAAAGGTATCA 735596 v - vii i v i i i v i iiv i HERVK#LTR/ERV 4983 AAAACATTTATTATCTTGTTTTGCTGTCATGGGAGTTCCAGAAAAAATTA 5032 chr5qtel1M 735597 AAACAGATAATGGGCCTGCATATACTTCTAAAGCCTT-------TTCTGA 735639 v i v v ivv vv ? ------- v HERVK#LTR/ERV 5033 AAACTGACAATGGGCCAGGATACTGTAGTAAAGCNTTCCAAAAATTCTTA 5082 chr5qtel1M 735640 TTTTTGCTCTAAATTCCATATATCACATATTATTGGCATTCTCTATAACC 735689 vv iv ivvv v i iv ------- v ii ii HERVK#LTR/ERV 5083 AATCAGTGGAAAATTACACATACAACA-------GGAATTCCTTATAATT 5125 chr5qtel1M 735690 CTCAAGGACAAGCCATAGTAGAAAGATCGAATCAAATCCTTAAGGCTCAA 735739 i i v v v vi iv i i HERVK#LTR/ERV 5126 CCCAAGGACAGGCCATAGTTGAAAGAACTAATAGAACACTCAAAGCTCAA 5175 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.17 CpG sites = 47, Kimura (unadjusted) = 38.60 Transitions / transversions = 0.73 (47/64) Gap_init rate = 0.06 (22 / 386), avg. gap size = 1.32 (29 / 22) 611 26.90 4.23 4.55 chr5qtel1M 735385 735715 (264285) HERVK11D#LTR/ERVK 4907 5236 (2516) m_b263s701i4 10435 chr5qtel1M 735385 GGAGTAAATTCCAGAGG----TCTAAAGAGCCAATGATGTCTGGCAAATG 735430 v i v ---- v----- i v i i HERVK11D#LTR/ 4907 GGAGTTAATCCCCGAGGCCTTTCTC-----CTAATGCTATTTGGCAAATG 4951 chr5qtel1M 735431 GACGTTACACATGTCTCGTCCTTTGGAAAGATTTCTTATTTACATGTTAT 735480 i v ii v i iv vv v i i i HERVK11D#LTR/ 4952 GATGTTACTCATGTTCCTTCTTTTGGAAAATTAGCTTATGTGCATGTCAC 5001 chr5qtel1M 735481 TGTGGACACATTCTCCCACTATATTGTCGTCTCCC---CAAGGACCAGTG 735527 v v v i v i vi i- v v v --- -- i v HERVK11D#LTR/ 5002 AGTTGACACCTTTTCCAATTTCATC-TGGGCTACCTGTCAA--ACCGGAG 5048 chr5qtel1M 735528 AAGCC---TTTAAAGATGTATCACAAAATTTATTTCTT--TGCTTTTCTA 735572 --- i v v ----- i v iv v i -- i v vi HERVK11D#LTR/ 5049 AAGCCACTTCTCACG-----TTAAAAAACATATGTTTTCATGTTTTGCGG 5093 chr5qtel1M 735573 TTATGGGAATGCCAAAAGGTATCAAAACAGATAATGGGCCTGCATATACT 735622 v v iv ivv i v v v vvi HERVK11D#LTR/ 5094 TTATGGGAATTCCTAGTGAGCTCAAAACAGACAATGGTCCAGCCTATTGC 5143 chr5qtel1M 735623 TCTAAAGCCTTTTCTGATTT--TTGCTCTAAATTCCATATATCACATATT 735670 vv i vvvi -- v -- i vv vvv HERVK11D#LTR/ 5144 AGTAAAGCTTTTAAAAATTTTCTTGATC--AGTGGCATATTAAACATATT 5191 chr5qtel1M 735671 ATTGGCATTCTCTATAACCCTCAAGGACAAGCCATAGTAGAAAGA 735715 i i ii v v i v HERVK11D#LTR/ 5192 ACTGGTATTCCTTATAACCCACAAGGCCAAGCTATTGTAGAAAGA 5236 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 32.94 CpG sites = 35, Kimura (unadjusted) = 33.39 Transitions / transversions = 0.70 (35/50) Gap_init rate = 0.06 (20 / 330), avg. gap size = 1.45 (29 / 20) 22 28.46 4.55 1.77 chr5qtel1M 738139 738248 (261752) (TATATG)n#Simple_repeat 1 113 (0) m_b263s252i22 10436 chr5qtel1M 738139 TAGATGTATATG-A-ATGTACATGTGTATGTTCGTTGT-TATAGTTAATC 738185 v - - i i - vvv - - vv v (TATATG)n#Sim 1 TATATGTATATGTATATGTATATGTATATG-TATATGTATAT-GTATATG 48 chr5qtel1M 738186 TGTATCTATATGTATA--TATGTGTGTGTGTTTATGGGCATATGTGTGTC 738233 i v -- i i i v vii i i i v (TATATG)n#Sim 49 TATATGTATATGTATATGTATATGTATATGTATATGTATATGTATATGTA 98 chr5qtel1M 738234 TGTGTATAAGTACAT 738248 i v i (TATATG)n#Sim 99 TATGTATATGTATAT 113 Matrix = Unknown Transitions / transversions = 1.08 (13/12) Gap_init rate = 0.06 (6 / 109), avg. gap size = 1.17 (7 / 6) 16 28.91 0.00 0.00 chr5qtel1M 738196 738238 (261762) (TG)n#Simple_repeat 1 43 (0) m_b263s252i23 10437 chr5qtel1M 738196 TGTATATATGTGTGTGTGTTTATGGGCATATGTGTGTCTGTGT 738238 i i i v i v ii i v (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 43 Matrix = Unknown Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 22 28.46 4.55 1.77 chr5qtel1M 738139 738248 (261752) (TATATG)n#Simple_repeat 1 113 (0) m_b263s252i22 10436 chr5qtel1M 738139 TAGATGTATATG-A-ATGTACATGTGTATGTTCGTTGT-TATAGTTAATC 738185 v - - i i - vvv - - vv v (TATATG)n#Sim 1 TATATGTATATGTATATGTATATGTATATG-TATATGTATAT-GTATATG 48 chr5qtel1M 738186 TGTATCTATATGTATA--TATGTGTGTGTGTTTATGGGCATATGTGTGTC 738233 i v -- i i i v vii i i i v (TATATG)n#Sim 49 TATATGTATATGTATATGTATATGTATATGTATATGTATATGTATATGTA 98 chr5qtel1M 738234 TGTGTATAAGTACAT 738248 i v i (TATATG)n#Sim 99 TATGTATATGTATAT 113 Matrix = Unknown Transitions / transversions = 1.08 (13/12) Gap_init rate = 0.06 (6 / 109), avg. gap size = 1.17 (7 / 6) 12 29.71 3.17 1.56 chr5qtel1M 738311 738373 (261627) (AAAAAAG)n#Simple_repeat 1 64 (0) m_b263s252i24 10438 chr5qtel1M 738311 AAAAAAGAATAAAGTAAAAAGTGCACAGCAGCCA-ACAAAAG-AAAAGCT 738358 v v viv v v ivv - v - ivv (AAAAAAG)n#Si 1 AAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGA 50 chr5qtel1M 738359 AAAAGGAAGAAAAGA 738373 i - (AAAAAAG)n#Si 51 AAAAAGAA-AAAAGA 64 Matrix = Unknown Transitions / transversions = 0.36 (4/11) Gap_init rate = 0.05 (3 / 62), avg. gap size = 1.00 (3 / 3) 202 25.31 6.38 7.53 chr5qtel1M 739931 740024 (259976) MIRc#SINE/MIR 162 254 (14) m_b263s601i21 10439 chr5qtel1M 739931 GCCCTCCTGACTTCATGGCCTGAGGTTTGTTGTGAGGATCCAACATGATT 739980 v iv i i------ v v iiv v MIRc#SINE/MIR 162 GCCCTGCCTACCTCAC------AGGGTTGTTGTGAGGATCAAATGAGATA 205 chr5qtel1M 739981 GTGAATGC---AGCTTTTTATAAA-TG-AAAGCATCCAT-CAGATGTGAG 740024 i v i--- vi i - - ii- i - i i MIRc#SINE/MIR 206 ATGTATGTGAAAGCGCTTTGTAAACTGTAAAGTG-CTATACAAATGTAAG 254 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.78 CpG sites = 14, Kimura (unadjusted) = 31.78 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.12 (11 / 93), avg. gap size = 1.18 (13 / 11) 13 18.86 0.00 0.00 chr5qtel1M 740139 740168 (259832) (ATGT)n#Simple_repeat 1 30 (0) m_b263s252i25 10440 chr5qtel1M 740139 ATATATGTATGTATGTGACTTTGTATGTAT 740168 i ivv v (ATGT)n#Simpl 1 ATGTATGTATGTATGTATGTATGTATGTAT 30 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 21 7.71 0.00 0.00 chr5qtel1M 740613 740640 (259360) (T)n#Simple_repeat 1 28 (0) m_b264s252i1 10441 chr5qtel1M 740613 TTTCTTTTTTTTTCTTTTTTTTTTTTTT 740640 i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 28 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 416 30.54 2.42 3.04 chr5qtel1M 741108 741438 (258562) C L1MC4a_3end#LINE/L1 (1997) 632 304 m_b264s551i0 10442 chr5qtel1M 741108 TGCTCATTTCACTCAGCATCAGTTCGTGTAAGTCTCTCCAGGCC--TTTC 741155 iv i i vi vv v v i v vii -- iv C L1MC4a_3end#L 632 TGCTTTTTTCACTTAACAATATATCCTGGAAATCACTCCATATCAGTTCA 583 chr5qtel1M 741156 T-GAAATCATCCTGTTGGTCATTTCTTACAGAACAATAATATTCCATAAT 741204 - i v vv -- - i vvvv i i vi C L1MC4a_3end#L 582 TAGAGATCTTCCTCAT--TC-TTTTTTACAGCTGCATAGTACTCCATTGT 536 chr5qtel1M 741205 TTTCATATACCACAATTTATTCAGCCATTCTCCAACTGATGGGCATCCAT 741254 v vv i i i i ? v i?? ii v C L1MC4a_3end#L 535 GTGGATGTACCATAGTTTATTCAACCANTCTCCTATNNATGGGCATTTAG 486 chr5qtel1M 741255 TCAGTTTCCAGTTTCTAGCCACTACAAACAGGGCTGCCACAAACATTCGT 741304 viv i v i v v i iv v ii i vi v C L1MC4a_3end#L 485 GTTGTTTCCAATATTTTGCAATTACAAACAATGCTGCAATGAATAACCTT 436 chr5qtel1M 741305 GCACATACAGGTCCCTTTCC-CTTCTTT--AGTATCTCTTTGGGATATAA 741351 ii i-- ?vi vi- v v v--i i v ii i v v C L1MC4a_3end#L 435 GTGCATAT--GTNATTTTGTACATGTTGGAGGTGTATCTTCAGGGTAAAT 388 chr5qtel1M 741352 GCCCAGTAGTAACACTGCTGGATCAAAGGGT--ATGAACAGTTTGATAAC 741399 v i v iiv i i -- v i --- - ii C L1MC4a_3end#L 387 TCCTAGAAGTGGGATTGCTGGGTCAAAGGGTAAATGCATA---TG-TAGT 342 chr5qtel1M 741400 TTTTTGAGCATAGTTCCAAACTACTCTCCAGAATGGTTG 741438 v v - v v i v i ? v C L1MC4a_3end#L 341 TTTGTTAG-ATATTGCCAAATTCCCCTCCANAAGGGTTG 304 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.57 CpG sites = 49, Kimura (unadjusted) = 40.57 Transitions / transversions = 1.00 (49/49) Gap_init rate = 0.05 (15 / 330), avg. gap size = 1.20 (18 / 15) 688 27.87 2.01 2.01 chr5qtel1M 741190 741438 (258562) C L1ME4c_3end#LINE/L1 (275) 555 307 m_b264s551i1 10442 chr5qtel1M 741190 ATAATATTCCATAATTTTCATATACCACAATTTATTCAGCCATTCTCCAA 741239 vivv ?v i i i i i i v C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chr5qtel1M 741240 CTGATGGGCATCCATTCAGTTTCCAGTTTCTAGCCACTACAAACAGGGCT 741289 i v i ii vviv i i v i i i i iv C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCT 456 chr5qtel1M 741290 GCCACAAACAT--TCGTGCACATACAGGTCCCTTTCCCTTCTTTAG---T 741334 v ii -- i v----- i i v --- C L1ME4c_3end#L 455 GCAATGAACATCTTCGTGCATATAG-----CTTTTTCCTTCTTTTGAATT 411 chr5qtel1M 741335 ATCTCTTTGGGATATAAGCCCAGTAGTAACACTGCTGGATCAAAGGGTAT 741384 i i i v vv v iiv i i i C L1ME4c_3end#L 410 ATTTCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTAT 361 chr5qtel1M 741385 GAACAGTTTGATAACTTTTTGAGCATAGTTCCAAACTACTCTCCAGAATG 741434 v v ii i vivi i v v i i i i v C L1ME4c_3end#L 360 GAACATTTTTATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAGG 311 chr5qtel1M 741435 GTTG 741438 C L1ME4c_3end#L 310 GTTG 307 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.82 CpG sites = 42, Kimura (unadjusted) = 36.16 Transitions / transversions = 1.62 (42/26) Gap_init rate = 0.03 (7 / 248), avg. gap size = 1.43 (10 / 7) 1451 29.01 1.43 0.95 chr5qtel1M 742501 743130 (256870) C L1ME4c_3end#LINE/L1 (191) 639 7 m_b264s551i2 10443 chr5qtel1M 742501 TTCTGCTCATTTCACTTAGCATCAGTTCATGTAATTCTCTCCAAGCTTCT 742550 iv i i vv i- ivi i v i v C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATA-AACATTTTCCATGTTGCT 591 chr5qtel1M 742551 CTGTATTCATCTTGCTGGTCATTTCTTACAGA-GCAATAATATTCCAAAA 742599 vii v v v iv vi i v ii v- - vvi C L1ME4c_3end#L 590 ACATAGTCTTCATAATTATCATTTTTAATGGCTGCA-TAATATTCCATCG 542 chr5qtel1M 742600 CATTCATATACCACAATTTACCCAACCATTCTCCAATTGATGGGCATCCA 742649 vi ?v i i ii i v v i ii C L1ME4c_3end#L 541 AGTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTA 492 chr5qtel1M 742650 TTCGGTTTCCAGCTTCTAGCCACTACAAACAGGGCTGCCACAAACATTTT 742699 vviv ii i v i i i i iv v ii i C L1ME4c_3end#L 491 GGTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTT 442 chr5qtel1M 742700 GGCACATACAGGTCCCTTTCCCTTCTTTAG---TATCTCCTTGGGGTATA 742746 v ii i --- i i v --- i i i v C L1ME4c_3end#L 441 CGTGCATATAG---CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAA 395 chr5qtel1M 742747 AGCCCGGTAGAAACACTGCTGGATCAAAGGGTATGCA-AGTTTGATAACT 742795 vv i v viiv i i i v - v v ii C L1ME4c_3end#L 394 TTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCT 345 chr5qtel1M 742796 TTTGGGCTATAATTCCAGATTGTCTTCCAGAATGGTTGGATTCATTCACA 742845 i ivvii v v i ii i v v iiv i C L1ME4c_3end#L 344 CTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACA 295 chr5qtel1M 742846 GCTCCACCAACAATGTATCAGTGTCCCAGTTTTCCCTGCATCCCCTTCAA 742895 ?iv i v ? v - v i ? i vi i C L1ME4c_3end#L 294 NTGCCACCAGCAATGTATGAGNGTACCAG-TTTCACCGCANCCTCGCCAG 246 chr5qtel1M 742896 CATTCGTCATTATTTTTTCCTGTCATCTTAGCCAATCTGACAGGTGTGTA 742945 v vi ivv ii vvv i v i i i i i iv C L1ME4c_3end#L 245 CATTGGGTATTATCAATTTTTTAAATTTTTGCTAATTTAATAGGCGTAAA 196 chr5qtel1M 742946 GTGGTATCTCAGAGTTGTCTTAATTTGCATTTCTCTGATTAATAATGATT 742995 i vv ii i v ii vv C L1ME4c_3end#L 195 ATGGTATCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACTAGCGAGG 146 chr5qtel1M 742996 TGGAACACT----CATATGAATGGTAATGATTTCAATTTCATCATCTGAA 743041 v i ---- i vv v v iv ? vv v v ? vi C L1ME4c_3end#L 145 TTGAACATTTTTCCATGTGTTTGTTTACTANTTGTATTTCCTCTTNTGTG 96 chr5qtel1M 743042 AATTGTCTGTTCATATCCTTTGACCATTTATCAATTGGAGAATGGCTTGG 743091 i v v i vv v v ?vv C L1ME4c_3end#L 95 AATTGTCTGTTCATGTCCTTTGCCCATTTATCTATTGGGGTCTTGATNTT 46 chr5qtel1M 743092 TTTCTTATAAATTAGAGTCAGCTCTCTATATATTTTAGA 743130 v v i v i ? v? C L1ME4c_3end#L 45 TTTCTTATCAATTTGAATGAGCTCTTTATATANTANAGA 7 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.64 CpG sites = 95, Kimura (unadjusted) = 37.98 Transitions / transversions = 1.10 (95/86) Gap_init rate = 0.02 (10 / 629), avg. gap size = 1.50 (15 / 10) 337 25.29 2.20 2.20 chr5qtel1M 743021 743202 (256798) C L1M5_orf2#LINE/L1 (34) 3260 3079 m_b264s551i3 10443 chr5qtel1M 743021 ATTTCAATTTCATCATCTGAAAATTGTCTGTTCATATCCTTTGACCATTT 743070 v? v v v i vi v vi i v C L1M5_orf2#LIN 3260 ATTTGNATATCTTCTTTTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTT 3211 chr5qtel1M 743071 ATCAATTGGA--GAATGGCTTGGTTTCTTA-TAAATTAGAGTCAGCTCTC 743117 v ?v i-- vv v -- ? - i ? iv -v i i C L1M5_orf2#LIN 3210 TTNTATTGGGTTGTTTGTCTT--TTTNTTATTGANTTGTAG-GAGTTCTT 3164 chr5qtel1M 743118 TATATATTTTAGAAATGAGGCCTTTATCAGA-ACCTTTAACTGTGAAGAT 743166 i i v i v i - iv v -?i ii v C L1M5_orf2#LIN 3163 TATATATTCTGGATACGAGTCCTTTGTCAGATATATGT-NTTGCAAATAT 3115 chr5qtel1M 743167 TTTTTCCCAGTTTGTTGCTTCCCTTCTTTTTTTTTT 743202 i ? i v v i iv i C L1M5_orf2#LIN 3114 TTTCTCCCANTCTGTGGCTTGCCTTTTCATTTTCTT 3079 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 31.61 CpG sites = 22, Kimura (unadjusted) = 32.46 Transitions / transversions = 0.96 (22/23) Gap_init rate = 0.04 (7 / 181), avg. gap size = 1.14 (8 / 7) 338 28.29 1.94 1.94 chr5qtel1M 743027 743181 (256819) C L1PREC2_orf2#LINE/L1 (40) 3254 3100 m_b264s551i4 10443 chr5qtel1M 743027 ATTTCATCATCTGAAAATTGTCTGTTCATATCCTTTGACCATTTATCAAT 743076 v v v i v i v i v i C L1PREC2_orf2# 3254 ATGTCTTCTTTTGAAAAGTGTCTGTTCATGTCCTTTGCCCACTTTTTAAT 3205 chr5qtel1M 743077 TGGAGAATGGCTTG---GTTTCTTATAAATTAGAGTCAGCTCTCTATATA 743123 v ---i v i ---v i v vv v i ii v C L1PREC2_orf2# 3204 GGG---GTTGTTTGTTTTTTTCTTGTAAATTTGTTTAAGTTCCTTATAGA 3158 chr5qtel1M 743124 TTTTAGAAATGAGGCCTTTATCAGAACCTTTAACTGTGAAGATTTTTTCC 743173 vi i v v i i vv v vivi ii ? i C L1PREC2_orf2# 3157 TGCTGGATATTAGACCTTTGTCAGATGCATAGTTTGCAAANATTTTCTCC 3108 chr5qtel1M 743174 CAGTTTGT 743181 v i C L1PREC2_orf2# 3107 CATTCTGT 3100 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.08 CpG sites = 20, Kimura (unadjusted) = 36.08 Transitions / transversions = 0.87 (20/23) Gap_init rate = 0.03 (4 / 154), avg. gap size = 1.50 (6 / 4) 322 31.45 5.12 4.00 chr5qtel1M 743715 744085 (255915) L1P3_orf2#LINE/L1 2617 2991 (303) m_b264s551i5 10444 chr5qtel1M 743715 CCAGATCTAAAATTATATTATAGAGCAGCAGTTACCAAAACTATTTGGTA 743764 v ii v i i i ii vi v viiv L1P3_orf2#LIN 2617 CCTGACTTCAAACTATACTACAAGGCTACAGTAACCAAAACAGCATGGTA 2666 chr5qtel1M 743765 TTGG--CTAAGGAATAGATTAGTTGATCAGTGGAATAGATT--AGGTCTC 743810 i -- i -- i vvi v i i i vi-- i L1P3_orf2#LIN 2667 CTGGTACCAA--AACAGATATATAGACCAATGGAACAGAACAGAGGCCTC 2714 chr5qtel1M 743811 AAGGATAAAACAGTCGAATCAAATATAGCAATCTAGTC-TTGATAAACC- 743858 iii vi vi- iv --- i i v ii - i - L1P3_orf2#LIN 2715 AGAAATAACGCCA-CACATC---TACAACCATCTGATCTTTGACAAACCT 2760 chr5qtel1M 743859 --CAAAGATCTAGCTTTTGGGATAAGAACTTACTGTTTGATAAA----AT 743902 -- i - v vv v - i i iv i i ----i L1P3_orf2#LIN 2761 GACAAAAA-CAAGCAATGGGGA-AAGGATTCCCTATTTAATAAATGGTGT 2808 chr5qtel1M 743903 TGTGGAAAATTGGAACTA---ATATGGCAG-AAACTAGGCATTGATCCAT 743948 - i -- --- - - iiivv v i v L1P3_orf2#LIN 2809 TG-GGAAAACTGG--CTAGCCATAT-GCAGAAAACTGAAACTGGACCCCT 2854 chr5qtel1M 743949 ACTTAACGCCTGACACCAAGATAAGGTCAAAATGGGTTCATGACCTAGGC 743998 v i v i v i v i v iv i i v v i ii L1P3_orf2#LIN 2855 TCCTTACACCTTATACAAAAATTAACTCAAGATGGATTAAAGACTTAAAC 2904 chr5qtel1M 743999 ATAAAGAATGAAATTATTAATAAATTAGAGGAACAC--AGGATAGTTTAC 744046 i iivv i ii v v vvi i v -- vv --- L1P3_orf2#LIN 2905 GTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCAA---TAC 2951 chr5qtel1M 744047 CTCTCA-GACCTGTGGAAGGGGAAGGTCTTTATGACCAAA 744085 vi - v iv v v v i v i i L1P3_orf2#LIN 2952 CATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAA 2991 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.05 CpG sites = 65, Kimura (unadjusted) = 42.04 Transitions / transversions = 1.38 (65/47) Gap_init rate = 0.07 (25 / 370), avg. gap size = 1.36 (34 / 25) 3744 29.91 2.00 1.62 chr5qtel1M 744103 746256 (253744) C L1M5_orf2#LINE/L1 (192) 3102 941 m_b264s551i6 10443 chr5qtel1M 744103 TGTTGCTTCCCTTCTAATCTTGTTTACATTAGTTTTGTTTGTACAGAAGC 744152 v v i v i v v iv ivi vvv? vi i C L1M5_orf2#LIN 3102 TGTGGCTTGCCTTTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGT 3053 chr5qtel1M 744153 TTTTTAATTTGATGTAATCAAA-------ATTTTCTATTTTGTGATCAAT 744195 v v ? i v ------- i v i i --- C L1M5_orf2#LIN 3052 TTTTAATTTTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGGT---T 3006 chr5qtel1M 744196 AATGGTCTCTAGTTCGTCTTTAATCACAAATTTCTTCTCTTCCACAAGTG 744245 ?i v i i ivv v v v--- i - vi v? v - C L1M5_orf2#LIN 3005 NGTGCTTTTTGTGTCCTGTTTAAG---AAATCT-TTGCCTANCCCAAG-G 2961 chr5qtel1M 744246 TGAGAGATAAACTATCCTATGTT--CCTCCAATTTGTTTATAATCTCGTT 744293 v vii v v i v -- i i ivvvv i i ii?i C L1M5_orf2#LIN 2960 TCACGAAGATATTCTCCTATGTTTTCTTCTAGAAGTTTTATAGTTTTANC 2911 chr5qtel1M 744294 CTTTATGTCTAAATC-ATGGACCCATTTTAATCTTATCTTGGTATATGTT 744342 i ii i ii - - i i ?i vi v i v i v C L1M5_orf2#LIN 2910 TTTTACATTTAGGTCTATG-ATCCATCTNGAATTAATTTTTGTGTATGGT 2862 chr5qtel1M 744343 ---AAGTGTGGGTCCATGCCTAATTTCTGCCATACTAATTTCCAGTTATC 744389 --- i iv v v?iii v i v ivi v i i i C L1M5_orf2#LIN 2861 GTGAGGTAGGGGTCGAGNTTCATTTTTTTCCATATGGATATCCAATTGTT 2812 chr5qtel1M 744390 CCAGCAGTTTTTGTCAAATAATGAATTCTTATCCCA--AAAGTGAGGATC 744437 viv ii v ivvv i vi --i v ----- C L1M5_orf2#LIN 2811 CCAGCACCATTTGTTGAAAAGACTATCCTTTCCCCACTGAATTG-----C 2767 chr5qtel1M 744438 TTTGGG---TTTGTCAAACACTAAATTGCTATATATTTACTATTCTGTCT 744484 ? v--- v ii ? v? i v iiviv i - C L1M5_orf2#LIN 2766 NTTGGCACCTTTGTCAAAAATCAANTGNCCATATATGTGTGGGTCTAT-T 2718 chr5qtel1M 744485 TGTGAAC---CTAACCTGTTCCACTGACCTAACTAATCTATTTCTTAGCC 744531 v i --- vi i i vi i- i- vv C L1M5_orf2#LIN 2717 TCTGGACTCTCTATTCTGTTCCATTGATCTATTTG-TCTATC-CTTACGC 2670 chr5qtel1M 744532 TAATACTCAAATGGTTTTG-TGACTGCTGCTT-ATAATATAGTTTT-AGA 744578 i - v iv i - v iv - - i - ? C L1M5_orf2#LIN 2669 CAATAC-CACACTGTCTTGATTACTGTAGCTTTATAATA-AGTCTTGANA 2622 chr5qtel1M 744579 TCAGGTACAGCTAGGCCACCTTCA--TTTGATTTTTTTTTTCATTAATTC 744626 ? vv - i i -- i -- v i i v-i v C L1M5_orf2#LIN 2621 TCNGGTAGTG-TAAGTC--CTCCAACTTTGTTCTTCTTTTTCAA-GATTG 2576 chr5qtel1M 744627 TTTTGAG-ATTCTTGACCTTTTATTTTTCTATATGAATTTTGTTGTTATT 744675 iv- ? ii i iiv i i ivvi i vi C L1M5_orf2#LIN 2575 TTTTGGCTATTCTNGGTCCTTTGCATTTCCATATAAATTTTAGAATCAGC 2526 chr5qtel1M 744676 TTTTCTAGATCATTAAAATATTTTCTTGGAAGTCTGATTGGTATAGCACT 744725 v v vv vvi v vii vi i v i v v i C L1M5_orf2#LIN 2525 TTGTCAATTTCTACAAAAAAACCTGCTGGGATTTTGATTGGGATTGCATT 2476 chr5qtel1M 744726 AAATAAATAGATTAGTTTAGGGAGTATTGTCATCTTTATTATATTCGCTC 744775 i vv i i i v v ? iv viv C L1M5_orf2#LIN 2475 GAATCTATAGATCAATTTGGGGAGAATTGACATCTTNACAATATTGAGTC 2426 chr5qtel1M 744776 GACCTATCCAGGAGCACTTGATATTTTTCCAATTGTTTAAGTCTGACTTT 744825 vv v v i ivvv i i v i i vvi v C L1M5_orf2#LIN 2425 TTCCAATCCATGAACATGGTATATCTCTCCATTTATTTAGGTCTTCTTTA 2376 chr5qtel1M 744826 ATTTGTGTGGAAAGTTTTTTGTAATTTAGCTCA-TGTAA--TTCCTGACT 744872 v v viiv i v i --- - ?--v i vvi C L1M5_orf2#LIN 2375 ATTTCTCTCAGCAATGTTTTGTAGTTT---TCAGTGTANAGGTCTTGCAC 2329 chr5qtel1M 744873 TTCCTTTGGTAGATAGATTCCCAAATATTTTATGCTGTCAACAGTTATTC 744922 v ?i v vv i i ? i v ivivv i v C L1M5_orf2#LIN 2328 ATNTTTTGTTAGATTTATTCCTAAGTATTTNATGTTTTTTGATGCTATTG 2279 chr5qtel1M 744923 TGAATGGAATTTCTCTTTGTATCTC---TTGCTGTTGGATTTTGTTGGTG 744969 i v vi i ?iv i --- v vi --- v i C L1M5_orf2#LIN 2278 TAAATGGTATTGTTTTTNAAATTTCATTTTCCAATTG---TTTGTTGCTA 2232 chr5qtel1M 744970 ATGTATAAAAATGCTGAGGATTTATGGGGATTTATTTTATAACCTGCAAC 745019 i i i i vivv v viv v ii i v ? i C L1M5_orf2#LIN 2231 GTATATAGAAATACAATTGATTTTTGTATATTGACCTTGTATCCNGCGAC 2182 chr5qtel1M 745020 TTTGCTAAAGTTATGGATTATTTCTAAAAGCTTTTTCATAGAATCTCTAG 745069 i v i ivv v iv i ? ii v i ? C L1M5_orf2#LIN 2181 CTTGCTAAATTCACTTATTAGTTCTAGTAGTTTNTTTGTAGATTCTTTNG 2132 chr5qtel1M 745070 GATTCTCTAAGTATACCATCATATCATCTGCAAAGAGTGATAGTTTGGTT 745119 i v ? v i i v i? i vi C L1M5_orf2#LIN 2131 GATTTTCTACGTANACAATCATGTCATCTGCGAATAANGACAGTTTTATT 2082 chr5qtel1M 745120 TCCTCACTGCCTATTCTGATTCCTTTAATCTCTTTCTCGACTCTTATTGC 745169 i vi v v ii v v v i i vvvi C L1M5_orf2#LIN 2081 TCTTCCTTTCCAATCTTTATGCCTTTTATTTCTTTTTCTTGCCTTATTGC 2032 chr5qtel1M 745170 CGAGGCTAGTGTTTCTAATACAATATTGAATAATAATGGTGACAG--GGC 745217 vvv viii i i i iv i ? -- i C L1M5_orf2#LIN 2031 ACTGGCTAGGACCTCCAGTACAATGTTGAATAGAAGTGGTGANAGCGGAC 1982 chr5qtel1M 745218 AACCTTGT-TTACTCCAGATCTTACTGGGAAAGATTCCAGTTTTTC-CCA 745265 v - ii v vv v? i ? - C L1M5_orf2#LIN 1981 ATCCTTGTCTTGTTCCCGATCTTAGGGGGAAAGCNTTCAGTNTTTCACCA 1932 chr5qtel1M 745266 TTGCATATGATGCTTACTGATGGTTTTAAATATATGCTCCTGACTATTTT 745315 ivi i ?i vv vvi v i i v ii vv C L1M5_orf2#LIN 1931 TTAAGTATGATGTTNGCTGTAGGTTTTTCGTAGATGCCCTTTATCAGGTT 1882 chr5qtel1M 745316 AAGAAAAAGTCCATTTATTTCTATACTCTCAAGTGTTTTTATTAGGAATG 745365 i i ivvi v i i vvi viii v i v C L1M5_orf2#LIN 1881 GAGGAAGTTCCCTTCTATTCCTAGTTTGCTGAGAGTTTTTATCATGAATG 1832 chr5qtel1M 745366 GATGTTGGATTTTATCAAATGCTTTTTCTGCATCTATTGAGATGATCATA 745415 i i i C L1M5_orf2#LIN 1831 GGTGTTGAATTTTGTCAAATGCTTTTTCTGCATCTATTGAGATGATCATA 1782 chr5qtel1M 745416 TGGTTTTTCTTAGTTTGCCTATTGATATAGTCAATTATGCTAATAGTTTT 745465 i ivv vvi i i i v iii i v v C L1M5_orf2#LIN 1781 TGATTTTTCTCCTTTATTCTGTTAATATGGTGAATTACATTGATTGATTT 1732 chr5qtel1M 745466 CCTAATATTGAACCAGCCCTGCATTCCTGTTATAAATCCTACTTGATCAT 745515 i v i i i i vv i i i C L1M5_orf2#LIN 1731 TCGAATGTTAAACCAACCTTGCATTCCTGGGATAAACCCCACTTGGTCAT 1682 chr5qtel1M 745516 AGTGTATTATCCTGGGGATGATTTTCTGTAATCTTTTTGCTAATATTTTA 745565 ii vvvv ivv v v v vv i C L1M5_orf2#LIN 1681 GATGTATTATCCTTTTTATATATTGCTGGATTCGATTTGCTAATATTTTG 1632 chr5qtel1M 745566 TTTAAGATTTTAGTATCGATATTCATTACAGAGATTGGTCTATAATTTTC 745615 ? i v i v i v vi v i C L1M5_orf2#LIN 1631 TTNAGGATTTTTGCATCTATGTTCATGAGGGATATTGGTCTGTAATTTTC 1582 chr5qtel1M 745616 TTTCTCTGT--TTTCAGCCTACCTGGTTTAGGTATCAGTACCATGTCTGT 745663 iii -- v --ii ii ? v vii? iiv i C L1M5_orf2#LIN 1581 TTTTCTTGTAATGTC--TTTGTCNGGTTTTGGTATCAGGGTNATGCTGGC 1534 chr5qtel1M 745664 GTCGTAAAAGGAGTTTGGTAGGACTCCTTCAGTCCCTATTTTTTCAAATA 745713 v i v v v vii i vv ii i vi v C L1M5_orf2#LIN 1533 CTCATAAAATGAGTTGGGAAGTGTTCCCTCTTTTTCTATTTTCTGGAAGA 1484 chr5qtel1M 745714 GTTTATATAGCATTGGGGTTAATTGTTCTTGAAACGTTTGGTAGAATTCA 745763 i i iv vi v v i v i C L1M5_orf2#LIN 1483 GTTTGTGTAAGATTGGTATTATTTCTTCCTTAAATGTTTGGTAGAATTCA 1434 chr5qtel1M 745764 CATGTACATCCATCTGGTCCTGGGGATTTTTTCTTAGGGAGTTGGCTAAT 745813 vv iv v v i v i iv i i v vvi C L1M5_orf2#LIN 1433 CCAGTGAAGCCATCTGGGCCTGGAGTTTTCTTTGTGGGAAGGTTTTTAAT 1384 chr5qtel1M 745814 AGCTTGTTCTATTTCTTTTTCTAAGATGGGACTGTTGAGGATATTGACTT 745863 vi vvi v vvivi v i i i v iv v iv i C L1M5_orf2#LIN 1383 TACAAATTCAATTTCTTTAATAGATATAGGGCTATTCAGATTTTCTATTT 1334 chr5qtel1M 745864 CTTCCTCTGTTAATCTGGGCAAATTATATTGTTGAAGGTATTCTTCCATT 745913 i v? i i i v i ? i i v v v iv C L1M5_orf2#LIN 1333 CTTCTTGNGTCAGTTTTGGTAANTTGTGTTTTTCAAGGAATTTGTCCATT 1284 chr5qtel1M 745914 TCATTTAAGTTGTCAAATTTATTGCCATAAAGTTGGGCAAAATAATCCCT 745963 i ? v vv v v i C L1M5_orf2#LIN 1283 TCATCTAAGTTNTCAAATTTATTGGCATAAAGTTGTTCATAATATTCTCT 1234 chr5qtel1M 745964 AATTATTGCTCTAATTTCCTCTTCATTAGTGGCGAGTTCTCCCTTTTCAT 746013 v ivi i v ivivvv iv i i vv i C L1M5_orf2#LIN 1233 TATTATCCTTTTAATGTCTGTAGGATCTGTAGTGATGTCTCCTTTTTCAT 1184 chr5qtel1M 746014 TTTTAAGACTAACAATTTGATTTTCCTCTTTCCTTTTTTTAATCAGATTT 746063 ii i v i iii vv i i i ii i i vi ? C L1M5_orf2#LIN 1183 TCCTGATATTGGTAATTTGTGTCTTCTCTCTTTTTTTCTTGATCAGTCTN 1134 chr5qtel1M 746064 ACTAAGGGTTTGTCTATTTTGTTGGTTTTTTCATAGAACTAACTCTTAGT 746113 i ii i v i i i v i i i i i C L1M5_orf2#LIN 1133 GCTAGAGGTTTATCAATTTTATTGATCTTTTCAAAGAACCAGCTTTTGGC 1084 chr5qtel1M 746114 TTTATTAATTAATTCAATAGT-TTTTTACTTTCAATTTTATTGATCTCTC 746162 ii i vvi v v - ? ii v i i v C L1M5_orf2#LIN 1083 TTCGTTGATTTTCTCTATTGTNTNTTTGTTTTCTATTTCATTGATTTCTG 1034 chr5qtel1M 746163 CTTTTATTTTTAGAATTTCAAGGTTTAGTGTTTGACTGGGGGTTTTTAAT 746212 i i vv vvvvi -v ii ?vi v --- C L1M5_orf2#LIN 1033 CTCTTATCTTTATTATTTCCTTCCTT-CTACTTNCTTTGGG---TTTAAT 988 chr5qtel1M 746213 TTA---TTCCTTTTCTAGCATTTTTAGTTGCAAGCCCAATTCATTGA 746256 i--- i v i v v v ii iv C L1M5_orf2#LIN 987 TTGCTCTTCTTTTTCTAGCTTCTTAAGGTGGAAGCTTAGATCATTGA 941 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.28 CpG sites = 337, Kimura (unadjusted) = 39.78 Transitions / transversions = 1.13 (337/297) Gap_init rate = 0.03 (56 / 2153), avg. gap size = 1.39 (78 / 56) 248 33.23 5.52 6.21 chr5qtel1M 746848 747155 (252845) C L2c_3end#LINE/L2 (7) 471 166 m_b264s601i2 10445 chr5qtel1M 746848 CAGTCAATAAAGTTTTATTCAGTGCCTACTATCTATTAGGTATTGGAATT 746897 v i vv v i v iii iii i--- C L2c_3end#LINE 471 CATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGG--- 425 chr5qtel1M 746898 AGGTTGGTAGAAAGGGGCAGAGGACA--ATCCCTGCCCTCAAGAAGCTCC 746945 ----- i v iv v v i --i i v C L2c_3end#LINE 424 -----GATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCA 380 chr5qtel1M 746946 CGGCCTAAAGGGGTAAGGGAGGGGGGAGAGCCACACAACAAGCAA-ACAA 746994 i i iv i -i iv ivi? vi i- v iv - - C L2c_3end#LINE 379 CAGTCTAGTGGAG-GAGACAGACANGTAAA-CAGACAATTA-CAATACAA 333 chr5qtel1M 746995 ATGTGTGCAAACCAGCTCT-GTGGG---ATAACTAAGATGGTAAAAG-GT 747039 i vvi vv vi- v -i --- ivi i i v vii - i C L2c_3end#LINE 332 GTTAATGATAAGT-GCTATAATGGGAGTATAGACAGGGTGCTATGGGAGC 284 chr5qtel1M 747040 ---GGGGAGTTCCCCCA-ATTACCC----AGGATTGGGAAAGGCTTCCTG 747081 --- i vv v i - i v? ----i i ii i i C L2c_3end#LINE 283 ACAGAGGAGGGCACCTAGACTAGNCTTGGGGGGTCAGGGAAGGCTTCCCG 234 chr5qtel1M 747082 TGGCAAATGAGGTTTTTAACTGGGACTTGGACCAAGAAGAG-AGGATTCC 747130 vi v ii vi- i v i i ? i--- i v - v -i C L2c_3end#LINE 233 GAGGAGGTGACA-TCTGAGCTGAGNCTTGA---AGGATGAGTAGGAGT-T 189 chr5qtel1M 747131 AGTCCCGGGGGACAGCCAGAGGGAA 747155 - v v - vvi i C L2c_3end#LINE 188 AG-CCAGGTGGA-AGGAGGGGGGAA 166 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.18 CpG sites = 57, Kimura (unadjusted) = 46.24 Transitions / transversions = 1.46 (57/39) Gap_init rate = 0.09 (28 / 307), avg. gap size = 1.29 (36 / 28) 285 25.96 8.05 9.52 chr5qtel1M 746848 746996 (253004) C L2a_3end#LINE/L2 (7) 510 364 m_b264s601i1 10445 chr5qtel1M 746848 CAGTCAATAAAGTTTTATTCAGTGCCTACTATCTATTAGGTATTGGAATT 746897 v i vv v i v iii i i vv-i C L2a_3end#LINE 510 CATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTT-CT 462 chr5qtel1M 746898 AGGT--TGG-----TAGAAAGGGGCAGAG--GACAA---TCCCTGCCCTC 746935 i-- -----i v iv ii i i-- --- C L2a_3end#LINE 461 AGGCGCTGGGGATACAGCAGTGAACAAAACAGACAAAAGTCCCTGCCCTC 412 chr5qtel1M 746936 AAGAAGCTCCCGGCCTAAAGGGGTAAGGGAGGGGGGAGAGCCACACAACA 746985 v i iv ivi ----- ------ -- v i C L2a_3end#LINE 411 ATGGAGCTTACATTCTA-----GT------GGGGGGAGA--CAGACAATA 375 chr5qtel1M 746986 AGCAAACAAAT 746996 i i C L2a_3end#LINE 374 AACAAATAAAT 364 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.52 CpG sites = 22, Kimura (unadjusted) = 32.78 Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.12 (18 / 148), avg. gap size = 1.44 (26 / 18) 293 26.58 10.53 0.96 chr5qtel1M 746849 746943 (253057) C L2d2_3end#LINE/L2 (8) 547 444 m_b264s601i3 10445 chr5qtel1M 746849 AGTCAATAAAGTTTTATTCAGTGCCTACTATCTATTAGGTATTGGAATTA 746898 i i vv v i i v iiv i i v-ii C L2d2_3end#LIN 547 AATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGT-GCTA 499 chr5qtel1M 746899 GGT----TGG----TAGAAAGGGGCAGAGGACA--ATCCCTGCCCTCAAG 746938 i---- ---- v ii i v i --i C L2d2_3end#LIN 498 GGCGCTGTGGGGGATACAAAGAAGTATAAGACATGGTCCCTGCCCTCAAG 449 chr5qtel1M 746939 AAGCT 746943 i C L2d2_3end#LIN 448 GAGCT 444 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.92 CpG sites = 17, Kimura (unadjusted) = 34.27 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.04 (4 / 94), avg. gap size = 2.75 (11 / 4) 16 8.48 0.00 0.00 chr5qtel1M 747836 747860 (252140) (GTG)n#Simple_repeat 1 25 (0) m_b264s252i2 10446 chr5qtel1M 747836 GTGGTATTGGTGGTGGTGGTGGTGG 747860 iv (GTG)n#Simple 1 GTGGTGGTGGTGGTGGTGGTGGTGG 25 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 36 2.63 2.56 0.00 chr5qtel1M 749325 749363 (250637) (TC)n#Simple_repeat 1 40 (0) c_b264s251i0 10447 chr5qtel1M 749325 TCTCTCTC-CTCTCTCTTTCTCTCTCTCTCTCTCTCTCTC 749363 - i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 40 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.03 (1 / 38), avg. gap size = 1.00 (1 / 1) 49 27.03 0.00 0.00 chr5qtel1M 749364 749484 (250516) (AC)n#Simple_repeat 1 121 (0) m_b264s252i3 10448 chr5qtel1M 749364 ACACACACACACAATCTCTCTCTCTCACACACACACACACACAATCTCTC 749413 vv v v v v v vv v v (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50 chr5qtel1M 749414 TCTCTCTCACACACACACACATACACAATCTCTCTCTCTCTCTCACACAC 749463 v v v v i vv v v v v v v v (AC)n#Simple_ 51 ACACACACACACACACACACACACACACACACACACACACACACACACAC 100 chr5qtel1M 749464 ACACACACACACGCACAAACA 749484 i v (AC)n#Simple_ 101 ACACACACACACACACACACA 121 Matrix = Unknown Transitions / transversions = 0.08 (2/25) Gap_init rate = 0.00 (0 / 120), avg. gap size = 0.0 (0 / 0) 274 33.69 4.98 5.50 chr5qtel1M 750220 750420 (249580) L3#LINE/CR1 3894 4093 (6) m_b264s601i4 10449 chr5qtel1M 750220 GGAAAATCTTTCTAACAATTTGGAGATATGCTAAGGTGGAAT---TTG-- 750264 i v - ii v i v v ii ---i -- L3#LINE/CR1 3894 GGAAGAACTTTCTAACAA-TCAGAGCTGTCCAAAAATGGAATGGGCTGCC 3942 chr5qtel1M 750265 --GAGAAGTCGTAGGATCCCCCTGCCTAGAGATTTTTTAATCAGAGCAAA 750312 -- ? i v ii v v vv i i- v i v vvvi L3#LINE/CR1 3943 TCGNGAGGTAGTGAGCTCCCCGTCACTGGAGG-TGTTCAAGCAGAGGCTG 3991 chr5qtel1M 750313 GATGGCAGTTTGTTAAGTATATAATGCTGATAGGATTATTATTCTGTCAC 750362 i vii i i v i -- iv vi vi iivi --iv L3#LINE/CR1 3992 GATGACCACTTGTCAGGGATGT--TGTAGAAGGGATTCCTGCATTG--GA 4037 chr5qtel1M 750363 TGTTATCTTGGATTAGATAG---TTGAGGTCATCTAACCTCTGATTCTGA 750409 vv vv i ii---i i -i ---- ii i L3#LINE/CR1 4038 TGGGAGGTTGGACTAGATGACCTCTAAGGTC-CCT----TCCAACTCTGA 4082 chr5qtel1M 750410 GAGGTTGTGAT 750420 vvi L3#LINE/CR1 4083 GATTCTGTGAT 4093 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 46.63 CpG sites = 37, Kimura (unadjusted) = 46.63 Transitions / transversions = 1.37 (37/27) Gap_init rate = 0.07 (15 / 200), avg. gap size = 1.40 (21 / 15) 535 19.72 0.81 5.93 chr5qtel1M 750643 750766 (249234) C MIRc#SINE/MIR (141) 127 10 m_b264s601i5 10450 chr5qtel1M 750643 CTGAGGC-AATTGAGGTTAAATGACTTGCCCAGGGTCACACAGCTAGGAA 750691 -v vv i i --- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG--- 81 chr5qtel1M 750692 GTGTTAAGTGTCTGAGGCCAGATTGGAACTCAGGTCCTCCTGACCTCAGG 750741 ---- v v v vi i v i i ii i C MIRc#SINE/MIR 80 ----TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr5qtel1M 750742 GCTGGTGCTCTATCCACTGAGCCAC 750766 v ii v vi C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 22.98 CpG sites = 12, Kimura (unadjusted) = 22.98 Transitions / transversions = 1.09 (12/11) Gap_init rate = 0.07 (8 / 123), avg. gap size = 1.00 (8 / 8) 395 33.28 0.53 6.70 chr5qtel1M 750843 751032 (248968) C MIRc#SINE/MIR (87) 181 3 m_b264s601i6 10451 chr5qtel1M 750843 CCCTGTGTGGTGGTTGTAACAGGTGTTCTTATTCCCAGTTTATAG-TTAG 750891 v i viivii i v i v i - v C MIRc#SINE/MIR 181 CCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAG 132 chr5qtel1M 750892 CAAACTGAGGTTGAGAGTCATTAACTGCTACATTGAGGAAATAAACACCA 750941 v i v vvi v -- - vvv ivvv vi C MIRc#SINE/MIR 131 GAAACTGAGGCTCAGAGAGGTTAAGTG--AC-TTGCCCAAGGTCACACAG 85 chr5qtel1M 750942 CTACTGACTTAATATCAGGGGCAGGATTTGAATCCAGGTTGCTCTGACTC 750991 v i---- i iv i v i i i i ivii C MIRc#SINE/MIR 84 CTAGTA----AGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTC 39 chr5qtel1M 750992 TAGGACTACTAGGCTATCTGCTACTCTTACACAGTATGCCT 751032 i i v i v ivv v ii i v -i ---- C MIRc#SINE/MIR 38 CAAGTCCAGTGCTCTTTCCACTGCAC-CACAC----TGCCT 3 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.66 CpG sites = 31, Kimura (unadjusted) = 44.67 Transitions / transversions = 1.11 (31/28) Gap_init rate = 0.07 (13 / 189), avg. gap size = 1.00 (13 / 13) 340 18.45 8.33 4.00 chr5qtel1M 751321 751416 (248584) MER63B#DNA/hAT-Tip100 337 436 (0) m_b264s502i0 10452 chr5qtel1M 751321 TGGGAGTTACTAGTTACACCTTGGAAATTGGCAAAC--TACA---CACAT 751365 ---- v vi i -- --- viv MER63B#DNA/hA 337 TGGGAGT----ATTTACACCACGGAAATCGGCAAACGCTACAAATCAGGG 382 chr5qtel1M 751366 ATTTTTTTTTCCCATTGGAGAGCCATTT---AAACATTTACCAGTATACC 751412 v i viii iv --- i i MER63B#DNA/hA 383 CTTTTTTTTTTCCCCCAGAGAGCCGGTTGTTAAACATTTACCAGCACACC 432 chr5qtel1M 751413 ACTG 751416 MER63B#DNA/hA 433 ACTG 436 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 17.51 CpG sites = 10, Kimura (unadjusted) = 21.50 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.07 (7 / 95), avg. gap size = 1.71 (12 / 7) 261 27.85 1.25 1.25 chr5qtel1M 751842 751921 (248079) C MIRc#SINE/MIR (19) 249 170 m_b264s601i7 10453 chr5qtel1M 751842 ATTTCTGAGGCAATTTAAGTTTTGCAAAGTACTTT-ACAGATGTTAATTC 751890 v ivi v viv i ii - v ii vi C MIRc#SINE/MIR 249 ATTTGTATAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATCTC 200 chr5qtel1M 751891 ACTTGATCCTCACAAACAAATCTGGAAAGTA 751921 i - vi vi i C MIRc#SINE/MIR 199 ATTTGATCCTCAC-AACAACCCTGTGAGGTA 170 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.50 CpG sites = 13, Kimura (unadjusted) = 35.73 Transitions / transversions = 1.44 (13/9) Gap_init rate = 0.03 (2 / 79), avg. gap size = 1.00 (2 / 2) 13 20.03 0.00 2.86 chr5qtel1M 752365 752400 (247600) (CAG)n#Simple_repeat 1 35 (0) m_b264s252i4 10454 chr5qtel1M 752365 CAACACCATGCAGAAGTAGCAGCAGCAGCCCCAGCA 752400 i v - v i vv (CAG)n#Simple 1 CAGCAGCA-GCAGCAGCAGCAGCAGCAGCAGCAGCA 35 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) 13 10.46 6.45 0.00 chr5qtel1M 754937 754967 (245033) (AAAGA)n#Simple_repeat 1 33 (0) m_b264s252i5 10455 chr5qtel1M 754937 AAAGGAAA-AAAAGAAGAG-CAAGAAAAGAAAA 754967 i - i -v (AAAGA)n#Simp 1 AAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAA 33 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2) 12 0.00 8.00 3.85 chr5qtel1M 754999 755023 (244977) (AGGAA)n#Simple_repeat 1 26 (0) m_b264s252i6 10456 chr5qtel1M 754999 AGGAAA-G-AAGGAAAGGGAAAGGAAA 755023 - - - (AGGAA)n#Simp 1 AGGAAAGGAAAGGAAA-GGAAAGGAAA 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.12 (3 / 24), avg. gap size = 1.00 (3 / 3) 393 26.95 0.87 6.42 chr5qtel1M 756147 756261 (243739) MIRc#SINE/MIR 3 111 (157) m_b264s601i8 10457 chr5qtel1M 756147 AGATAG-ATGGTACAGTGGATAGAACAGCAGCCCTGGAATCAGGAGGACC 756195 ii -i i v i vii v i i i MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chr5qtel1M 756196 CAACTTCAAATCCAGCCCAAGACACTTAACACATACTAGCTGTGTGACGC 756245 iiiv i i v v ivv v ------- vi MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCACT-------TACTAGCTGTGTGACCT 95 chr5qtel1M 756246 TGGACATGTCACTTAA 756261 i v MIRc#SINE/MIR 96 TGGGCAAGTCACTTAA 111 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.80 CpG sites = 18, Kimura (unadjusted) = 34.26 Transitions / transversions = 1.64 (18/11) Gap_init rate = 0.07 (8 / 114), avg. gap size = 1.00 (8 / 8) 435 30.03 5.94 5.27 chr5qtel1M 756556 757026 (242974) L1MC5_3end#LINE/L1 79 552 (2142) m_b264s551i7 10458 chr5qtel1M 756556 GAAATGAATGGGCAGTTTTTGAAGGAAAAAAATCAAAAGAAT-TTAGTCA 756604 v ii i iviii ii i vv v iv - i? L1MC5_3end#LI 79 GATATGAACAGACAGTTCACAGAAAAAGAAATGCAAATGGCTCTTAANCA 128 chr5qtel1M 756605 TATGTAAAAAAAG---GATCTAGATCATCATTGATTAAATGTAGACTAAA 756651 - i v ---i i v v v viivv i i i L1MC5_3end#LI 129 TATG-AAAAGATGCTCAACCTCGCTCATAATAAGAGAAATGCAAATTAAA 177 chr5qtel1M 756652 ATTACTTTAAAATGCCATTTTACACCTATCAGATTGGTCAAAATGATCTA 756701 i vi i i i iv - -- i L1MC5_3end#LI 178 ACTACACTGAGATACCATTTCTCACCTATCAGATTGG-CAAAA--ATCCA 224 chr5qtel1M 756702 AAGGTAGAGGAGACATGCTAAACTCTTCCTTAGTTTATGAATATTACTAA 756751 i vviiv - i --- v vviv vi i iiv ----- L1MC5_3end#LI 225 AAAGTTTGACA-ACATACT---CTGTTGGCGAGGCTGTGGGGA-----AA 265 chr5qtel1M 756752 CAGGGGC--------A--GTTAG-GGGACTG---AATGGATCCAACCATT 756787 vi -------- -- i i - v --- - v vi L1MC5_3end#LI 266 CAGGCACTCTCATACATTGCTGGTGGGAATGCAAAATGG-TACAACCCCT 314 chr5qtel1M 756788 CTGGAGAGCAATTTGAAACTATCCTGAAAAAGTTTTCAAATCGTGCAT-- 756835 v i v iv v iv v -- v v --- -- L1MC5_3end#LI 315 ATGGAGGGGAATTTGGCAATATCTAGCAAAA--TTACATAT---GCATTT 359 chr5qtel1M 756836 ACCCTTTGATCCCATCAGTGTTTCTACTGGGATAATATCCCACAGAT--- 756882 - v i viiv v i vvv v --- L1MC5_3end#LI 360 ACCCTTTGA-CCCAGCAATCCCACTTCTAGGAATCTATCCCAAAGATACA 408 chr5qtel1M 756883 CT--TAAATAAGGGAAAAGGACCCACATGTGC-CAAGA-TGTTTGTGGCA 756928 --i v viv ----- i i - i- i ii v L1MC5_3end#LI 409 CTGGCAAAAATACGAAAAG-----ACGTATGCACAAGGCTATTCATTGCA 453 chr5qtel1M 756929 GCTCTTTTTGTAGT-GCAAGAAAGTGGAAACTGAGTGGATGCCCATCAAT 756977 v v i - i i v vivviii i L1MC5_3end#LI 454 GCACTATTTGTAATAGCAAAAGACTGGAAACAACCCAAATGTCCATCAAT 503 chr5qtel1M 756978 TGGAGAATGGCAGAATAAGTTGTGGTATATGAATATTATGGGGCATTAT 757026 v i v iv ii i i vv i iv i i i L1MC5_3end#LI 504 AGGGGACTGGTTGAATAAACTATGGTACATCCACACAATGGAGTACTAT 552 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.60 CpG sites = 74, Kimura (unadjusted) = 39.36 Transitions / transversions = 1.23 (74/60) Gap_init rate = 0.08 (37 / 470), avg. gap size = 1.43 (53 / 37) 561 26.27 3.05 2.66 chr5qtel1M 756765 757026 (242974) L1ME3G_3end#LINE/L1 286 548 (376) m_b264s551i8 10458 chr5qtel1M 756765 GGGACTG--AATGGATCCAACCATTCTGGAGAGCAATTTGAAACTATCC- 756811 v -- v i v i ? i i iv v i- L1ME3G_3end#L 286 GGGAGTGTAAATTGGTACAGCCNTTTTGGAGGGCAATTTGGCAGTATCTA 335 chr5qtel1M 756812 TGAAAAAGTTTTCAAATCGTGCATACCCTTTGATCCCATCAGTGTTTCTA 756861 v --- v - i - v i viiv v L1ME3G_3end#L 336 TTAAAA---TTTAAAAT-GCGCATACCCTTTGA-CCCAGCAATTCCACTT 380 chr5qtel1M 756862 CTGGGATAATATCCCACAGA--T-CTTAAATAAG-GGAAAAGGACCCACA 756907 ? ?vvv i ? -- - iiv i v - v v ?--i L1ME3G_3end#L 381 CTNGGNATCTATCCTANAGAAATACTCGCACATGTGCACAAGGAN--GCA 428 chr5qtel1M 756908 TGTGCCAAGATGTTTGTGGCAGCTCTTTTTGTAGT-GCAAGAAAGTGGAA 756956 i v i ii v vi v i - i i v L1ME3G_3end#L 429 TGTACAAGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAA 478 chr5qtel1M 756957 ACTGAGTGGATGCCCATCAATTGGAGAATGGCAGAATAAGTTGTGGTATA 757006 vivv ii i v i ivi i i L1ME3G_3end#L 479 ACAACCTAAATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGTATA 528 chr5qtel1M 757007 TGAATATTATGGGGCATTAT 757026 vv i iii i L1ME3G_3end#L 529 TCCATACTATGGAATACTAT 548 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 31.87 CpG sites = 37, Kimura (unadjusted) = 33.75 Transitions / transversions = 1.23 (37/30) Gap_init rate = 0.05 (13 / 261), avg. gap size = 1.15 (15 / 13) 263 28.94 0.81 2.46 chr5qtel1M 756917 757040 (242960) L1ME1_3end#LINE/L1 442 563 (363) m_b264s551i9 10458 chr5qtel1M 756917 ATGTTTGTGGCAGCTCTTTTTGTAGT-GCAAGAAAGTGGAAACTGAGTGG 756965 ii i i v i i - v i v vivviii L1ME1_3end#LI 442 ATGTTCATAGCAGCTTTATTCGTAATAGCCAAAAACTGGAAACAACCCAA 491 chr5qtel1M 756966 ATGCCCATCAATTGGAGAATGGCAGAATAAGTTGTGGTATATGAATATTA 757015 i i? v vvi i i vv iv L1ME1_3end#LI 492 ATGTCCATCAACNGGTGAATGGATAAACAAATTGTGGTATATCCATACAA 541 chr5qtel1M 757016 TGGGGCATTATTGTTCTGCAAGAAA 757040 --- v i ii v v L1ME1_3end#LI 542 TGG---AATACTACTCAGCAATAAA 563 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.48 CpG sites = 20, Kimura (unadjusted) = 37.85 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.03 (4 / 123), avg. gap size = 1.00 (4 / 4) 48 0.00 0.00 0.00 chr5qtel1M 757467 757507 (242493) (TA)n#Simple_repeat 1 41 (0) c_b264s251i1 10459 chr5qtel1M 757467 TATATATATATATATATATATATATATATATATATATATAT 757507 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATAT 41 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 13 23.58 6.00 0.00 chr5qtel1M 757636 757685 (242315) (TAAA)n#Simple_repeat 1 53 (0) m_b264s252i7 10460 chr5qtel1M 757636 TAAATAAA-AAAGATTTATTTAAA-AAA-AAATAAAGAAAACAATGAAAA 757682 - v vv vv - - v vv i v (TAAA)n#Simpl 1 TAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATA 50 chr5qtel1M 757683 AAT 757685 (TAAA)n#Simpl 51 AAT 53 Matrix = Unknown Transitions / transversions = 0.11 (1/9) Gap_init rate = 0.06 (3 / 49), avg. gap size = 1.00 (3 / 3) 15 19.61 0.00 0.00 chr5qtel1M 757656 757684 (242316) (A)n#Simple_repeat 1 29 (0) m_b264s252i8 10460 chr5qtel1M 757656 AAAAAAAAATAAAGAAAACAATGAAAAAA 757684 v i v vi (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA 29 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 182 28.19 17.09 5.71 chr5qtel1M 758104 758261 (241739) L2a_3end#LINE/L2 335 509 (8) m_b264s601i9 10461 chr5qtel1M 758104 CACTATCTGGTCCATAGTGAAT-TTCCATCTAGTGGTTTGT--GTTGTTA 758150 i i-- v iv - ii ii v vi --i iv L2a_3end#LINE 335 CACCATCTGA--CATACTATATATTTTACTTATTTATTTGTTTATTGTCT 382 chr5qtel1M 758151 GTC-----CCACCAGTTTGTGATCTCCATAGGAGCAGGGGACACCCTTTA 758195 ----- i vv i v ii i i---- i i L2a_3end#LINE 383 GTCTCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGA----CTTTTG 428 chr5qtel1M 758196 CAACTCTCTTTTGGTTCCTAC----------ATGC------CAGGGCCTG 758229 ---- v v iv i ----------ii ------ v L2a_3end#LINE 429 ----TCTGTTTTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTG 474 chr5qtel1M 758230 GCATATATCAGGCTC---ATAAATGCTTCTTAAAT 758261 i vi v --- ii v i L2a_3end#LINE 475 GCACATAGTAGGCGCTCAATAAATATTTGTTGAAT 509 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.92 CpG sites = 27, Kimura (unadjusted) = 37.05 Transitions / transversions = 1.80 (27/15) Gap_init rate = 0.10 (16 / 157), avg. gap size = 2.31 (37 / 16) 233 28.87 9.23 1.43 chr5qtel1M 758135 758264 (241736) L2d_3end#LINE/L2 369 508 (8) m_b264s601i10 10461 chr5qtel1M 758135 GTG-GTTTGTGTTGTTAGTCCCACCAGTTTGTGATCTCCATAGGAGCAGG 758183 - v v ivvi v i v i v v ii i L2d_3end#LINE 369 GTGTGTTAGTCTTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGG 418 chr5qtel1M 758184 GGACACCCTTTACAACTCTCTTTTGGTT-CCTACA-TGC------CAGGG 758225 iv ivii i- ? i ? v - i -i ------ v L2d_3end#LINE 419 GACCATGTCTTAT-ACTNTTTTNTCGTTCCCCACAGCGCCTAGCACAGTG 467 chr5qtel1M 758226 CCTGGCATATATCAGGCTC---ATAAATGCTTCTTAAATTGA 758264 ivi i vi v --- i v -i L2d_3end#LINE 468 CTGAGCACATAGTAGGCGCTCAATAAATACTTGTT-GATTGA 508 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.86 CpG sites = 21, Kimura (unadjusted) = 38.16 Transitions / transversions = 1.31 (21/16) Gap_init rate = 0.05 (7 / 129), avg. gap size = 2.00 (14 / 7) 255 27.42 2.78 8.82 chr5qtel1M 758154 758261 (241739) L2c_3end#LINE/L2 369 470 (8) m_b264s601i11 10461 chr5qtel1M 758154 CCACCAGTTTGTGATCTCCATAGGAGCAGGGGACACCCTTTACAACTCTC 758203 i vi v v ii i --- v v viv i vi L2c_3end#LINE 369 CCACTAGACTGTGAGCTCCTTGAGGGCAGGG---ACCGTGTCTTATTCAT 415 chr5qtel1M 758204 TTTTGGTTCCTACATGCCAGGGCCTGGCATATATCAGGCTC---ATAAAT 758250 i vv ------ v i vi v --- L2c_3end#LINE 416 CTTTGTATCC------CCAGCGCCTGGCACATAGTAGGCGCTCAATAAAT 459 chr5qtel1M 758251 GCTTCTTAAAT 758261 i v i L2c_3end#LINE 460 GTTTGTTGAAT 470 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.19 CpG sites = 13, Kimura (unadjusted) = 34.19 Transitions / transversions = 0.93 (13/14) Gap_init rate = 0.09 (10 / 107), avg. gap size = 1.20 (12 / 10) 262 31.17 2.60 0.00 chr5qtel1M 758272 758348 (241652) C MIRb#SINE/MIR (183) 85 7 m_b264s601i12 10462 chr5qtel1M 758272 AGGAAG-AGCGGTGTTAGAATATCAACCCAAGTCT-TCTGAGTCCAAATG 758319 v -i i v iii i viv i - v vv C MIRb#SINE/MIR 85 AGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGC 36 chr5qtel1M 758320 TAGGGATCTTTCCATTATATCATGCTGCC 758348 iv v v i ii i i C MIRb#SINE/MIR 35 CCGTGCTCTTTCCACTGCACCACGCTGCC 7 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.82 CpG sites = 14, Kimura (unadjusted) = 41.53 Transitions / transversions = 1.40 (14/10) Gap_init rate = 0.03 (2 / 76), avg. gap size = 1.00 (2 / 2) 278 24.56 1.75 0.00 chr5qtel1M 758295 758351 (241649) C MIRc#SINE/MIR (210) 58 1 m_b264s601i13 10462 chr5qtel1M 758295 AACCCAAGTCTTC-TGAGTCCAAATGTAGGGATCTTTCCATTATATCATG 758343 i - v i vi v v i ii i ii C MIRc#SINE/MIR 58 AACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACA 9 chr5qtel1M 758344 CTGCCTTG 758351 i C MIRc#SINE/MIR 8 CTGCCTCG 1 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.45 CpG sites = 10, Kimura (unadjusted) = 31.11 Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.02 (1 / 56), avg. gap size = 1.00 (1 / 1) 44 0.00 0.00 0.00 chr5qtel1M 758979 759026 (240974) (A)n#Simple_repeat 1 48 (0) m_b264s252i9 10463 chr5qtel1M 758979 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 759026 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 48 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 15 5.56 0.00 0.00 chr5qtel1M 760792 760810 (239190) (T)n#Simple_repeat 1 19 (0) m_b264s252i10 10464 chr5qtel1M 760792 TTTTTTTTTTTTTCTTTTT 760810 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 351 30.67 8.72 3.31 chr5qtel1M 761509 761680 (238320) MIRb#SINE/MIR 4 184 (84) m_b264s601i14 10465 chr5qtel1M 761509 AAGGGGAGCCAGTAGTGCAGTGGAGATAG-ATA-----TAATGT------ 761546 i v -- i i v - ii----- iiv ------ MIRb#SINE/MIR 4 AGGGGCAGC--GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACA 51 chr5qtel1M 761547 -ATCTTAGTTTAAATTAAGCCTCAGGCTGTTACTAACTGTATACCCCTTT 761595 - i vi ii ivv v v v vv i i iv i vv MIRb#SINE/MIR 52 GACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 101 chr5qtel1M 761596 GTAAGTCAATTAAATCTGTTTG--CCTTAGTTTCCTCAGCTCTTCAATGG 761643 i i v -i v i -- i v v vv MIRb#SINE/MIR 102 GCAAGTTACTTAA-CCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGG 150 chr5qtel1M 761644 GGATAACAGTATCATCTAACTGGGAAGGTTAATATGA 761680 i i --- i v v v i iv i MIRb#SINE/MIR 151 GGATAATAAT---ACCTACCTCGCAGGGTTGTTGTGA 184 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.04 CpG sites = 27, Kimura (unadjusted) = 40.27 Transitions / transversions = 1.12 (27/24) Gap_init rate = 0.06 (11 / 171), avg. gap size = 1.91 (21 / 11) 379 33.33 0.74 0.00 chr5qtel1M 761546 761680 (238320) MIR#SINE/MIR 45 180 (82) m_b264s601i15 10465 chr5qtel1M 761546 TATCTTAGTTTAAATTAAGCCTCAGGCTGTTACTAACTGTATACCCCTTT 761595 ii vi ii ivv v v v vv i i iv i vv MIR#SINE/MIR 45 TGCCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 94 chr5qtel1M 761596 GTAAGTCAATTAAA-TCTGTTTGCCTTAGTTTCCTCAGCTCTTCAATGGG 761644 i i v v- v v i v v vv MIR#SINE/MIR 95 GCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGG 144 chr5qtel1M 761645 GATAACAGTATCATCTAACTGGGAAGGTTAATATGA 761680 i i vi i v viv i iv i MIR#SINE/MIR 145 GATAATAATAGTACCTACCTCATAGGGTTGTTGTGA 180 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.11 CpG sites = 21, Kimura (unadjusted) = 44.54 Transitions / transversions = 0.88 (21/24) Gap_init rate = 0.01 (1 / 134), avg. gap size = 1.00 (1 / 1) 33 23.37 0.00 0.00 chr5qtel1M 761858 761928 (238072) (TA)n#Simple_repeat 1 71 (0) m_b264s252i11 10466 chr5qtel1M 761858 TATATAAATATACACACAAATACATACATACATACATATATATATATATA 761907 v i i i v i i i i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr5qtel1M 761908 TATATAAAAACACATATAAAT 761928 v v i i v (TA)n#Simple_ 51 TATATATATATATATATATAT 71 Matrix = Unknown Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0) 29 0.00 0.00 0.00 chr5qtel1M 762747 762771 (237229) (AC)n#Simple_repeat 1 25 (0) c_b264s251i2 10467 chr5qtel1M 762747 ACACACACACACACACACACACACA 762771 (AC)n#Simple_ 1 ACACACACACACACACACACACACA 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 342 26.59 7.75 2.00 chr5qtel1M 765232 765373 (234627) MIR3#SINE/MIR 52 201 (7) m_b264s601i16 10468 chr5qtel1M 765232 GGTTCTGGAAGCTGACTCTGATACTCAAAAATGGTATGACCTTTGAGCAA 765281 i vv- i i vi v vv?iiv i - i MIR3#SINE/MIR 52 GGTTCTAGTC-CCGGCTCTGCCACTAACTNGCTGTGTGACCTT-GGGCAA 99 chr5qtel1M 765282 CTC------CCT-TCTGTGCTTCAGTTTCCT--TCTGGAAATTGAAGGGA 765322 v ------ - v i -- v v - i MIR3#SINE/MIR 100 GTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATG-AGGGG 148 chr5qtel1M 765323 GTTGGATTCT-TGAATTCTGAAGGGACTTCCAGCTCC-ACATCTCATTAT 765370 i vv- vi i i vvv i- iii v MIR3#SINE/MIR 149 GTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGAT 198 chr5qtel1M 765371 TTT 765373 i MIR3#SINE/MIR 199 TCT 201 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.50 CpG sites = 19, Kimura (unadjusted) = 33.58 Transitions / transversions = 1.06 (19/18) Gap_init rate = 0.06 (8 / 141), avg. gap size = 1.75 (14 / 8) 16 21.13 1.89 3.85 chr5qtel1M 765881 765933 (234067) (AAAT)n#Simple_repeat 1 52 (0) m_b264s252i12 10469 chr5qtel1M 765881 AAATAAAAAAACTTTATTAAAAAATAAATAAATAAAAGAAAACAATGAA- 765929 v - vv v v - v vv i - (AAAT)n#Simpl 1 AAATAAATAAA-TAAATAAATAAATAAATAAAT-AAATAAATAAATAAAT 48 chr5qtel1M 765930 AAAT 765933 (AAAT)n#Simpl 49 AAAT 52 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.06 (3 / 52), avg. gap size = 1.00 (3 / 3) 289 31.11 13.01 0.72 chr5qtel1M 766190 766312 (233688) MIRc#SINE/MIR 11 148 (120) m_b264s601i17 10470 chr5qtel1M 766190 TGGTGCAGTAGATAGACTGGTAGGCCTTAAGACATGAAGA-CTGAGTTTT 766238 i v viiv i i i vi v v - i iv MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr5qtel1M 766239 AATCTCAACTCAGAAACTTGATAGT--------------CAAGCCACAGG 766274 i i ii v vv iv i-------------- i vvi MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTA 110 chr5qtel1M 766275 GTCTCTGTTTAG-TTCAGTTTCTTTCTCTGTAAAATGGG 766312 ii -i v -i i iv MIRc#SINE/MIR 111 ACCTCT-CTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.85 CpG sites = 23, Kimura (unadjusted) = 41.71 Transitions / transversions = 1.53 (23/15) Gap_init rate = 0.03 (4 / 122), avg. gap size = 4.25 (17 / 4) 230 30.99 8.46 0.71 chr5qtel1M 766393 766522 (233478) L2d_3end#LINE/L2 369 508 (8) m_b264s601i18 10471 chr5qtel1M 766393 GTG-GTTTGTGTTGTCAGTCCCACCAGTCTGTGATCTTCATAGGAGCAGG 766441 - v v vvi v i vi i v i v ii i L2d_3end#LINE 369 GTGTGTTAGTCTTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGG 418 chr5qtel1M 766442 GGACACCCTTTACAGCTCTCTTTTGCTTCCTACA-TGCCAAG----GT-C 766485 iv ivii i vi?i i ? i i i i -i v ---- - L2d_3end#LINE 419 GACCATGTCTTATACTNTTTTNTCGTTCCCCACAGCGCCTAGCACAGTGC 468 chr5qtel1M 766486 TG-GCATGTATCAGGCTC---ATAAATGCTTGTTAACTTGA 766522 - ii vi v --- i i - L2d_3end#LINE 469 TGAGCACATAGTAGGCGCTCAATAAATACTTGTTGA-TTGA 508 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.03 CpG sites = 26, Kimura (unadjusted) = 42.89 Transitions / transversions = 1.86 (26/14) Gap_init rate = 0.05 (7 / 129), avg. gap size = 1.71 (12 / 7) 238 32.43 9.01 0.00 chr5qtel1M 766497 766607 (233393) C MIRb#SINE/MIR (141) 127 7 m_b264s601i19 10472 chr5qtel1M 766497 AGGCTCATAAATGCTTGTTAACTTGAAGAAGTTC---TA---AGAAAGTG 766540 v i v i viv vvv v ---i --- v C MIRb#SINE/MIR 127 AGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTG 78 chr5qtel1M 766541 AT---CCTAGAATATCAACCCAAGTCT-TCTGAGTACAAATGTAGAGATC 766586 ii---v ii i viv i - v v vviv v v C MIRb#SINE/MIR 77 GCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTC 28 chr5qtel1M 766587 TTTCCATTATACCATGTTGCC 766607 i ii i i C MIRb#SINE/MIR 27 TTTCCACTGCACCACGCTGCC 7 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.32 CpG sites = 17, Kimura (unadjusted) = 42.93 Transitions / transversions = 0.89 (17/19) Gap_init rate = 0.04 (4 / 110), avg. gap size = 2.50 (10 / 4) 247 25.45 1.82 0.00 chr5qtel1M 766554 766608 (233392) C MIRc#SINE/MIR (210) 58 3 m_b264s601i20 10472 chr5qtel1M 766554 AACCCAAGTCTTC-TGAGTACAAATGTAGAGATCTTTCCATTATACCATG 766602 i - v v i vi v v i ii ii C MIRc#SINE/MIR 58 AACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACA 9 chr5qtel1M 766603 TTGCCT 766608 i C MIRc#SINE/MIR 8 CTGCCT 3 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.10 CpG sites = 9, Kimura (unadjusted) = 32.10 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1) 21 13.26 0.00 0.00 chr5qtel1M 768641 768673 (231327) (A)n#Simple_repeat 1 33 (0) m_b264s252i13 10473 chr5qtel1M 768641 AAAAAAAAAAAAAAAAGAAAACAAGAAAATAAA 768673 i v i v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 33 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 12 9.24 0.00 4.17 chr5qtel1M 768934 768958 (231042) (TCCC)n#Simple_repeat 1 24 (0) m_b264s252i14 10474 chr5qtel1M 768934 TCCCTCCCACCCTCCACCCCCTCCC 768958 v - i (TCCC)n#Simpl 1 TCCCTCCCTCCCTCC-CTCCCTCCC 24 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 887 28.73 2.47 2.47 chr5qtel1M 769354 769717 (230283) C L1ME4c_3end#LINE/L1 (277) 553 190 m_b264s551i10 10475 chr5qtel1M 769354 AATATTCCATAACATTCATATACCACAATTTACCCAACCATTCTCCAATT 769403 vivi ?v i i ii i v C L1ME4c_3end#L 553 AATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTATT 504 chr5qtel1M 769404 GATGGGCATCCATTCATTTTCCAGTTTCTAGCCATTACAAACAGGGCTGC 769453 v i ii vvivv i i v i i i iv C L1ME4c_3end#L 503 GTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGC 454 chr5qtel1M 769454 CACAAACATTTTGGCACATACAGGTCCCTTTCCCTTCTTTAG---TATCT 769500 v ii i v ii i --- i i v --- i C L1ME4c_3end#L 453 AATGAACATCTTCGTGCATATAG---CTTTTTCCTTCTTTTGAATTATTT 407 chr5qtel1M 769501 CTTTGGGGTATAAGCCCAGTAGAAACACTGCTGGATCAAAGGGTATGCAC 769550 i i i v vv v viiv i i i v C L1ME4c_3end#L 406 CCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAAC 357 chr5qtel1M 769551 AGTTTGATAACTTTTTGAGCATAGTTCTAAACTACTCTCCAGAATGGTTG 769600 v v ii i vivi i v v i i i i i v C L1ME4c_3end#L 356 ATTTTTATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTG 307 chr5qtel1M 769601 GATTCATTCACAACTCCACCAACAATGTATCAGTGTCCCAGTTTTCCTGC 769650 v iiv i ?iv i v ? v iv i C L1ME4c_3end#L 306 TACCAATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCACCGC 257 chr5qtel1M 769651 ATCCCCTCCAACA------ATCATCATTATTTTTTCCTGTCATCTTAGCC 769694 ? i v i ------ i -- v----v i v i C L1ME4c_3end#L 256 ANCCTCGCCAGCATTGGGTATTATCA--ATTTTTTA----AATTTTTGCT 213 chr5qtel1M 769695 AATCTGACAGGTGTGTAGTGGTA 769717 i i i i iv i C L1ME4c_3end#L 212 AATTTAATAGGCGTAAAATGGTA 190 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.14 CpG sites = 63, Kimura (unadjusted) = 38.03 Transitions / transversions = 1.62 (63/39) Gap_init rate = 0.03 (11 / 363), avg. gap size = 1.64 (18 / 11) 234 30.77 0.00 6.45 chr5qtel1M 770580 770645 (229355) MIRc#SINE/MIR 10 71 (197) m_b264s601i21 10476 chr5qtel1M 770580 GCGGTACAGTGGAGATAATGTAGATAGGGCCTTGAATCAGGAAGACCTGA 770629 i i i v ii---- iv i i v i i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGC----ACTGGACTTGGAGTCAGGAAGACCTGG 55 chr5qtel1M 770630 ATTTTAATCCCATCTC 770645 i iv i iv MIRc#SINE/MIR 56 GTTCGAGTCCCGGCTC 71 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.54 CpG sites = 14, Kimura (unadjusted) = 42.39 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.06 (4 / 65), avg. gap size = 1.00 (4 / 4) 351 34.44 1.95 1.95 chr5qtel1M 771329 771482 (228518) MIRb#SINE/MIR 40 193 (75) m_b264s601i22 10477 chr5qtel1M 771329 TGAAGATAAACAGTGTACCTGAGCTTAAATTAAGCCTTGGACAGTTACTA 771378 i vi i --- i i ii ivv v iv v v MIRb#SINE/MIR 40 TGGAGTCAGACAG---ACCTGGGTTCGAATCCCGGCTCTGCCACTTACTA 86 chr5qtel1M 771379 ATTGAAGACCCCTTCTTAAGTCAATTGACC-CTGTTTGCCTTAGTTTTCT 771427 ii viviv i vvvi i v i - v vv i i MIRb#SINE/MIR 87 GCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCT 136 chr5qtel1M 771428 CAGCTCTTAAATGGGGATAACAGTATCGCCTTTG-AAGGTTGACATGA-C 771475 v v v i i i vv i i - i vii -v MIRb#SINE/MIR 137 CATCTGTAAAATGGGGATAATAATACCTACCTCGCAGGGTTGTTGTGAGG 186 chr5qtel1M 771476 ATCAAAT 771482 i MIRb#SINE/MIR 187 ATTAAAT 193 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.69 CpG sites = 28, Kimura (unadjusted) = 47.29 Transitions / transversions = 1.17 (28/24) Gap_init rate = 0.04 (6 / 153), avg. gap size = 1.00 (6 / 6) 18 22.92 0.00 0.00 chr5qtel1M 771604 771649 (228351) (TACA)n#Simple_repeat 1 46 (0) m_b264s252i15 10478 chr5qtel1M 771604 TACATAGAAACATGCATACATATACACATAAATATATATATAGATA 771649 v v i i i v i i v (TACA)n#Simpl 1 TACATACATACATACATACATACATACATACATACATACATACATA 46 Matrix = Unknown Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 17 13.72 0.00 0.00 chr5qtel1M 771619 771650 (228350) (ATACAT)n#Simple_repeat 1 32 (0) m_b264s252i16 10478 chr5qtel1M 771619 ATACATATACACATAAATATATATATAGATAT 771650 i v i v (ATACAT)n#Sim 1 ATACATATACATATACATATACATATACATAT 32 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 12 17.10 2.22 6.98 chr5qtel1M 771906 771950 (228050) (GCAAT)n#Simple_repeat 1 43 (0) m_b264s252i17 10479 chr5qtel1M 771906 GCAATGGGAAGGCAGAT-CAAGGACAATGCAATGCAAAACACTGCA 771950 - v v - - v - vi v (GCAAT)n#Simp 1 GCAAT-GCAATGCA-ATGCAATG-CAATGCAATGCAATGCAATGCA 43 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4) 297 25.33 8.63 3.42 chr5qtel1M 772227 772365 (227635) C MIR3#SINE/MIR (1) 207 62 m_b264s601i23 10480 chr5qtel1M 772227 AACCA-AAAATCATGAGATAT-GGAGCTGAAATTCCACTCAGAATTCA-A 772273 i - i iii i -i i vvvvv i iv -v C MIR3#SINE/MIR 207 AATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATC 158 chr5qtel1M 772274 GAATCCAACACCCTTCAATTTCCAGA--AGGAAACTAAAGCACAGA---- 772317 v i - i v v -- i i v ---- C MIR3#SINE/MIR 157 TAGTCCAAC-CCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGG 109 chr5qtel1M 772318 -GAAGTGATTTGTTCAAAG-GACACA-CTATTTTGAAGTGTCAAGAGTCA 772364 - i ii i -v - ? v --- v - i i C MIR3#SINE/MIR 108 TGAAGTGACTTGCCCAAGGTCACACAGCNAGTT---AGTGGC-AGAGCCG 63 chr5qtel1M 772365 G 772365 C MIR3#SINE/MIR 62 G 62 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.83 CpG sites = 20, Kimura (unadjusted) = 31.95 Transitions / transversions = 1.43 (20/14) Gap_init rate = 0.09 (13 / 138), avg. gap size = 1.31 (17 / 13) 210 17.52 0.00 8.70 chr5qtel1M 774724 774773 (225227) L2a_3end#LINE/L2 384 429 (88) m_b264s601i24 10481 chr5qtel1M 774724 TCTTCCCCCAAGAGAAGGTAAGCTCCTTAGCGGCAGGGCCTGACTTTTGT 774773 i vv v v iiv ---- L2a_3end#LINE 384 TCTCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGG----GACTTTTGT 429 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 19.79 CpG sites = 3, Kimura (unadjusted) = 19.79 Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.08 (4 / 49), avg. gap size = 1.00 (4 / 4) 364 24.01 6.60 1.80 chr5qtel1M 775557 775662 (224338) C MIRc#SINE/MIR (155) 113 3 m_b264s601i25 10482 chr5qtel1M 775557 GGTTAAGTGACTTGCCCAGGATCACATAGCTGGGAAGTGTTAA----GTG 775602 i i i i v vi i---- v C MIRc#SINE/MIR 113 GGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGG 64 chr5qtel1M 775603 TCTATGG--CCAGATTTCTCCTGACTTCAGGGCTGGCCCTCTAGTCACTG 775650 v -i i-- i i - i i v ii iv vvi C MIRc#SINE/MIR 63 ACT-CGAACCCAGGTCT-TCCTGACTCCAAGTCCAGTGCTCTTTCCACTG 16 chr5qtel1M 775651 CACCAC-CTACCT 775662 - i C MIRc#SINE/MIR 15 CACCACACTGCCT 3 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.61 CpG sites = 17, Kimura (unadjusted) = 30.04 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.05 (5 / 105), avg. gap size = 1.80 (9 / 5) 291 25.16 11.82 6.03 chr5qtel1M 775731 775840 (224160) MIRc#SINE/MIR 23 138 (130) m_b264s601i26 10483 chr5qtel1M 775731 AAAAGCAGGGTGATCTTGG-----GGAAGACCTTAGTTTCCAAGGAGCCC 775775 i v-- iv ----- vi i----- i MIRc#SINE/MIR 23 AAGAGCAC--TGGACTTGGAGTCAGGAAGACCTGGGTTC-----GAGTCC 65 chr5qtel1M 775776 CAA----GACACTTAATGGCTGTGTGACCGTGGGCAAACTCCTGGACACC 775821 ii---- v v i v iiiv vi vi MIRc#SINE/MIR 66 CGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 chr5qtel1M 775822 T----ATCTCAGTTTTTTCATCT 775840 ----ii ii MIRc#SINE/MIR 116 TCTGAGCCTCAGTTTCCTCATCT 138 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.91 CpG sites = 17, Kimura (unadjusted) = 31.82 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.09 (10 / 109), avg. gap size = 2.00 (20 / 10) 231 29.15 7.14 8.11 chr5qtel1M 775751 775862 (224138) MIR3#SINE/MIR 43 153 (55) m_b264s601i27 10483 chr5qtel1M 775751 GAAGACCTTAGTTTCCAAGGAGCCCCAA----GACACTTAATGGCTGTGT 775796 i vi ii----- i ii---- v v v ? MIR3#SINE/MIR 43 GGAGACCTGGGTTCT-----AGTCCCGGCTCTGCCACTAACTNGCTGTGT 87 chr5qtel1M 775797 GACCGTGGGCAAACTCCTGGACACCT----ATCTCAGTTTTTTCATCTTT 775842 v iiiv vv vi ----ii ii --- MIR3#SINE/MIR 88 GACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATC--- 134 chr5qtel1M 775843 TGTCAACCGAGGAACATTGG 775862 v vi ii-i MIR3#SINE/MIR 135 TGTAAAATGAGGGG-GTTGG 153 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.14 CpG sites = 19, Kimura (unadjusted) = 38.81 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.10 (11 / 111), avg. gap size = 1.55 (17 / 11) 286 26.58 0.00 8.79 chr5qtel1M 777149 777247 (222753) C MIRc#SINE/MIR (175) 93 3 m_b265s601i0 10484 chr5qtel1M 777149 GTCACAGCCAACAAGTGTTAAGTGTCTGAGGCCCGATTTGAACTCAGGTC 777198 -- i v --- v v v vv i i i C MIRc#SINE/MIR 93 GTCACA--CAGCTAGT---AAGTGGCAGAGCCGGGACTCGAACCCAGGTC 49 chr5qtel1M 777199 CTCCTGACTTCAGGGCTGGTGCTCTGTTCTCCTTACCATCTAGCTGCCT 777247 i i i v ii v i v ivi i---i C MIRc#SINE/MIR 48 TTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC---ACTGCCT 3 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.56 CpG sites = 14, Kimura (unadjusted) = 33.23 Transitions / transversions = 1.40 (14/10) Gap_init rate = 0.08 (8 / 98), avg. gap size = 1.00 (8 / 8) 12 29.07 3.64 0.00 chr5qtel1M 779790 779844 (220156) (CCCTCT)n#Simple_repeat 1 57 (0) m_b265s252i0 10485 chr5qtel1M 779790 CCCCCTCCCTCTCTTTCT-GTTCTTATTCT-CCTCTCCCTGTCCTGTTCC 779837 i ii -vi ivi - v ivi (CCCTCT)n#Sim 1 CCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCC 50 chr5qtel1M 779838 CTGTCCC 779844 v (CCCTCT)n#Sim 51 CTCTCCC 57 Matrix = Unknown Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.04 (2 / 54), avg. gap size = 1.00 (2 / 2) 14 15.04 5.41 0.00 chr5qtel1M 781053 781089 (218911) (TCCCC)n#Simple_repeat 1 39 (0) m_b265s252i1 10486 chr5qtel1M 781053 TCCCTTCCCC-CCCACCCCCTTCACTCCCCT-CCCTCCC 781089 i - vi i v - (TCCCC)n#Simp 1 TCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCC 39 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 13 13.96 7.14 2.27 chr5qtel1M 781091 781132 (218868) (CCAAACT)n#Simple_repeat 1 44 (0) m_b265s252i2 10487 chr5qtel1M 781091 CCAAGCTCACAAACTCCAAACTCC--GCCCCAGACT-CACACTCC 781132 i - --i i i - v (CCAAACT)n#Si 1 CCAAACTC-CAAACTCCAAACTCCAAACTCCAAACTCCAAACTCC 44 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.07 (3 / 41), avg. gap size = 1.33 (4 / 3) 16 0.00 0.00 0.00 chr5qtel1M 781485 781502 (218498) (AC)n#Simple_repeat 1 18 (0) m_b265s252i3 10488 chr5qtel1M 781485 ACACACACACACACACAC 781502 (AC)n#Simple_ 1 ACACACACACACACACAC 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 41 0.00 0.00 0.00 chr5qtel1M 781503 781537 (218463) (AG)n#Simple_repeat 1 35 (0) c_b265s251i0 10489 chr5qtel1M 781503 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 781537 (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 35 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 59 41.13 1.11 0.55 chr5qtel1M 781980 782340 (217660) (TC)n#Simple_repeat 1 363 (0) m_b265s252i4 10490 chr5qtel1M 781980 TCTGTGTCGCTAACTGTTTCTTTCTCTTTCTCACTGTTTTTCATTCTCTG 782029 v v v vv v i i i v v i i vi v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr5qtel1M 782030 GCTTGCTCTGTGTCAGTCTCTGGCTCTTTC-CTGTCTCTTTCTCCATTTC 782078 v iv v v vv vv i - v i iv i (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chr5qtel1M 782079 TATTTCTTTCTCTTTTTTTTCCAGTTTCGTTCATTCTCAGACTCTTTTTT 782128 v i i i i i ii vv i vi vi vvv i i i (TC)n#Simple_ 101 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 150 chr5qtel1M 782129 TTTTTTTTTTTTTTTGCTTACTGTCT-TTTGTGTCTGGCTTTCACTC-CT 782176 i i i i i i i - iv v - i v v vv i v - (TC)n#Simple_ 151 TCTCTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 199 chr5qtel1M 782177 CTCTCAGTTTTTTTTTTTCTCACTGTTTTTTTGCTTGCTCTCTCTTTTTC 782226 vv i i i i i v v i i i - iv i i (TC)n#Simple_ 200 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT-CTCTCTCTCTCTCTCTC 248 chr5qtel1M 782227 TGTCTCTCACTTTTTCTCTCTGACTCTGTTTCTCTCTCT-TCTCTTTCAC 782275 v v i i vv v i - i v (TC)n#Simple_ 249 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 298 chr5qtel1M 782276 TCACTCTCACTGTTTCTTTCTCTCTTTTTTACTCTCTCAATGTCTTTCTG 782325 v v v i i i i iv vv v i v (TC)n#Simple_ 299 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 348 chr5qtel1M 782326 ACCCACTCTCTCTCT 782340 v i v (TC)n#Simple_ 349 TCTCTCTCTCTCTCT 363 Matrix = Unknown Transitions / transversions = 1.00 (56/56) Gap_init rate = 0.02 (6 / 360), avg. gap size = 1.00 (6 / 6) 19 0.00 0.00 0.00 chr5qtel1M 782123 782143 (217857) (T)n#Simple_repeat 1 21 (0) m_b265s252i5 10491 chr5qtel1M 782123 TTTTTTTTTTTTTTTTTTTTT 782143 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTT 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 59 41.13 1.11 0.55 chr5qtel1M 781980 782340 (217660) (TC)n#Simple_repeat 1 363 (0) m_b265s252i4 10490 chr5qtel1M 781980 TCTGTGTCGCTAACTGTTTCTTTCTCTTTCTCACTGTTTTTCATTCTCTG 782029 v v v vv v i i i v v i i vi v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr5qtel1M 782030 GCTTGCTCTGTGTCAGTCTCTGGCTCTTTC-CTGTCTCTTTCTCCATTTC 782078 v iv v v vv vv i - v i iv i (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chr5qtel1M 782079 TATTTCTTTCTCTTTTTTTTCCAGTTTCGTTCATTCTCAGACTCTTTTTT 782128 v i i i i i ii vv i vi vi vvv i i i (TC)n#Simple_ 101 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 150 chr5qtel1M 782129 TTTTTTTTTTTTTTTGCTTACTGTCT-TTTGTGTCTGGCTTTCACTC-CT 782176 i i i i i i i - iv v - i v v vv i v - (TC)n#Simple_ 151 TCTCTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 199 chr5qtel1M 782177 CTCTCAGTTTTTTTTTTTCTCACTGTTTTTTTGCTTGCTCTCTCTTTTTC 782226 vv i i i i i v v i i i - iv i i (TC)n#Simple_ 200 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT-CTCTCTCTCTCTCTCTC 248 chr5qtel1M 782227 TGTCTCTCACTTTTTCTCTCTGACTCTGTTTCTCTCTCT-TCTCTTTCAC 782275 v v i i vv v i - i v (TC)n#Simple_ 249 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 298 chr5qtel1M 782276 TCACTCTCACTGTTTCTTTCTCTCTTTTTTACTCTCTCAATGTCTTTCTG 782325 v v v i i i i iv vv v i v (TC)n#Simple_ 299 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 348 chr5qtel1M 782326 ACCCACTCTCTCTCT 782340 v i v (TC)n#Simple_ 349 TCTCTCTCTCTCTCT 363 Matrix = Unknown Transitions / transversions = 1.00 (56/56) Gap_init rate = 0.02 (6 / 360), avg. gap size = 1.00 (6 / 6) 250 32.91 2.00 4.79 chr5qtel1M 784317 784466 (215534) L1PB3_3end#LINE/L1 408 553 (348) m_b265s551i0 10492 chr5qtel1M 784317 GAAGTC-TTAAACCCTAAAAGGGACCTGTATGTGCCAAAATGTTTGTGGC 784365 - v i v- iv i i i i---- i v L1PB3_3end#LI 408 GAAGTCATTATATCA-AAAAGACACCTGCACGCGT----ATGTTTATCGC 452 chr5qtel1M 784366 AGCCCTGTTTGTAGTGGCCAGAAGCTGGAAAATGAA--TGGATGCCCATC 784413 v vi iii i v v ii vv --iv -- iii L1PB3_3end#LI 453 AGCACAATTCACAATTGCAAAGATATGGAA--CCAACCTAAGTGCCCATC 500 chr5qtel1M 784414 AATTGGAGAATGGTTGAGTAAATTGTGGTATATGAATGTTATGGAATATT 784463 ii iv i v i iv v iv iiii i L1PB3_3end#LI 501 AACCGATGAGTGGATAAAGAAAATGTGGTATATATACACCATGGAATACT 550 chr5qtel1M 784464 ATT 784466 i L1PB3_3end#LI 551 ACT 553 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.77 CpG sites = 31, Kimura (unadjusted) = 45.76 Transitions / transversions = 1.94 (31/16) Gap_init rate = 0.06 (9 / 149), avg. gap size = 1.11 (10 / 9) 307 31.92 1.38 2.80 chr5qtel1M 784334 784478 (215522) L1MC5a_3end#LINE/L1 423 565 (2212) m_b265s551i1 10492 chr5qtel1M 784334 AAGGGACCTGTATGTGCCAAAATGTTTGTGGCAGCCCTGTTTGTAGTGGC 784383 i? -- ii v iiv i ii v vi i i i L1MC5a_3end#L 423 AAANGAC--GTATGCACAAGGTTATTCATTGCAGCATTATTTGTAATAGC 470 chr5qtel1M 784384 CAGAAGCTGGAAAATGAAT--GGATGCCCATCAATTGGAGAATGGTTGAG 784431 v i ii --v i--ii i v i v i L1MC5a_3end#L 471 AAAAGACTGGAAA--CAACCCAAATGTCCATCAATAGGGGACTGGTTGAA 518 chr5qtel1M 784432 TAAATTGTGGTATATGAATGTTATGGAATATTATTGTTCTGTAAGAA 784478 i i i vv iiiv i i vvvv i L1MC5a_3end#L 519 TAAACTATGGTACATCCACACAATGGAGTACTATGCAGCTGTAAAAA 565 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 44.39 CpG sites = 30, Kimura (unadjusted) = 44.39 Transitions / transversions = 2.00 (30/15) Gap_init rate = 0.03 (5 / 144), avg. gap size = 1.20 (6 / 5) 464 24.79 1.63 1.63 chr5qtel1M 784343 784465 (215535) L1ME3G_3end#LINE/L1 426 548 (376) m_b265s551i2 10492 chr5qtel1M 784343 GTATGTGCCAAAATGTTTGTGGCAGCCCTGTTTGTAGTGGCCAGAAGCTG 784392 i i v ii ii v vi i i v i ii L1ME3G_3end#L 426 GCATGTACAAGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTG 475 chr5qtel1M 784393 GAAAATGAA--TGGATGCCCATCAATTGGAGAATGGTTGAGTAAATTGTG 784440 --v -- ii i v i i i i L1ME3G_3end#L 476 GAAA--CAACCTAAATGTCCATCAATAGGGGAATGGTTAAATAAATTATG 523 chr5qtel1M 784441 GTATATGAATGTTATGGAATATTAT 784465 vv ii i L1ME3G_3end#L 524 GTATATCCATACTATGGAATACTAT 548 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 31.63 CpG sites = 22, Kimura (unadjusted) = 31.63 Transitions / transversions = 2.75 (22/8) Gap_init rate = 0.02 (3 / 122), avg. gap size = 1.33 (4 / 3) 324 26.97 3.91 1.53 chr5qtel1M 784355 784482 (215518) L1MC1_3end#LINE/L1 442 572 (508) m_b265s551i3 10492 chr5qtel1M 784355 ATGTTTGTGGCAGCCCTGTTTGTAGTGGCCAGAAGCTGGAA--AATGAAT 784402 i i ii i ii i v i vi -- iv - L1MC1_3end#LI 442 ATGTTTATAGCAGCTTTATTCATAATTGCCAAAACTTGGAAGCAACCAA- 490 chr5qtel1M 784403 GGATGCCCATCAATTGGAGAATGGTTGAGTAAATTGTGGTATATGAATGT 784452 - i v i v v v i i i i vv vii L1MC1_3end#LI 491 -GATGTCCTTCAGTAGGTGAATGGATAAATAAACTGTGGTACATCCAGAC 539 chr5qtel1M 784453 TATGGAATATTATT--GTTCT-GTAAGAAATGA 784482 v -- iv -iv L1MC1_3end#LI 540 AATGGAATATTATTCAGCGCTAAAAAGAAATGA 572 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.21 CpG sites = 21, Kimura (unadjusted) = 34.46 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.04 (5 / 127), avg. gap size = 1.40 (7 / 5) 15 5.56 0.00 0.00 chr5qtel1M 784973 784991 (215009) (A)n#Simple_repeat 1 19 (0) m_b265s252i6 10493 chr5qtel1M 784973 AAAAAAAAAAAAAAAAGAA 784991 i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAA 19 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 1299 28.48 2.78 2.99 chr5qtel1M 786647 787149 (212851) C L1ME5_3end#LINE/L1 (297) 644 143 m_b265s551i4 10494 chr5qtel1M 786647 TCCTGGTTCT-GCTCATTTCGCTCAGCATCA-GTTCATTTAAG-TCTCTG 786693 i v -i iv i ii - -- - iv v C L1ME5_3end#LI 644 TTCTGTTTCTTACTTTTTTCACTCAGCACTATGTT--TTTAAGATCCATC 597 chr5qtel1M 786694 CAATCCTCTCTGTATTCGTCCTGCTGGTCATTTCTTACAGAACAATAATA 786743 vviiv v i v i iv iiv iii v v vvvv i C L1ME5_3end#LI 596 CATGTTGCTATGTGTACATCTAGTCCGTTGCTTCTAACTGCTGCATAGTA 547 chr5qtel1M 786744 TTCCATAACATTCATATACCACAATTTACTCAACCATTCTCCAATTGATG 786793 i iiii v vi v ii v i v v C L1ME5_3end#LI 546 CTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCAGTGATG 497 chr5qtel1M 786794 GGCATCCATTCATT--TTCCAGCTTCTGGCCACTACAAACAGGGTTGCCA 786841 i i --vi --i i i iv i iv i v C L1ME5_3end#LI 496 GACACCCA--GGTTGCCTCCAACTCCCCGCCACCACAAACAACGCTGCAA 449 chr5qtel1M 786842 CAAACATTTTGGCACATACAGGTCCCTTTC----CCTTTTTTAGTATCTC 786887 ii ii ---- i v i v---- v v v v i C L1ME5_3end#LI 448 TGAACATCCT----CGTACATGTCCCCTTATGGACCTGTGTGAGAATTTC 403 chr5qtel1M 786888 TTTGGGGTATAAGCCCAGTAGAGACACTGCTGGATCAAAGGGTAGACACA 786937 i vi v v iv i i v vi --- C L1ME5_3end#LI 402 TTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATGC--- 356 chr5qtel1M 786938 GTTTGATAACTT--TTTGGGCA--TAGTTCCAAATTGCTCTCCAGAATGG 786983 --- - -- ivi -- v v i C L1ME5_3end#LI 355 GT---ATA-CTTAATTTGACTAAGTACTGCCAGATTGCTCTCCAGAATGG 310 chr5qtel1M 786984 CTGGATGTATTCACAATTCCACCAGCAATGTATCAGTGTCCCTGTTTTCC 787033 v ivvi ii v i i i v v i i ? i C L1ME5_3end#LI 309 CTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATNTCCC 260 chr5qtel1M 787034 CACATCCCCTCCAACATTCTGCATTATCTTTCCCTGTCATTCTGACCAAT 787083 i v i iv ivv ii v v i vi i C L1ME5_3end#LI 259 CACATCCTCGCCAACACTTGGCATTATCCAGCTTTCTAATTTTTGCCAGT 210 chr5qtel1M 787084 CTGACAGGTGTATAGTGGTATGTCAGAGTTATCTTAATTTGCATTTCTCT 787133 i i v i v vv i i C L1ME5_3end#LI 209 CTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATTTCTCT 160 chr5qtel1M 787134 GATCAATAGTGA-TTTG 787149 i v i - C L1ME5_3end#LI 159 GATTACTAATGAGTTTG 143 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.42 CpG sites = 79, Kimura (unadjusted) = 36.75 Transitions / transversions = 1.32 (79/60) Gap_init rate = 0.05 (23 / 502), avg. gap size = 1.26 (29 / 23) 1336 25.57 1.47 2.22 chr5qtel1M 786738 787145 (212855) C L1ME3G_3end#LINE/L1 (376) 548 144 m_b265s551i5 10494 chr5qtel1M 786738 ATAATATTCCATAACATTCATATACCACAATTTACTCAACCATTCTCCAA 786787 i ii vv i i i i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr5qtel1M 786788 TTGATGGGCATCCA--TTCATTTTCCAGCTTCTGGCCACTACAAACAGGG 786835 i ii -- v-- ii i v i i iv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTG--TTTCCAATTTTTCGCTATTACAAACAATG 451 chr5qtel1M 786836 TTGCCACAAACATTTTGGCACATACAGGTCCCTTTCC-C-TTTTTTAGTA 786883 i v ii ii v i i ?-- i v v - - v viv C L1ME3G_3end#L 450 CTGCAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTA 403 chr5qtel1M 786884 TCTCTTTGGGGTATAAGCCCAGTAGAGACACTGCTGGATCAAAGGGTAGA 786933 i ? i i v v? ? v v iv i i vi C L1ME3G_3end#L 402 TTTCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATG 353 chr5qtel1M 786934 CACAGTTTGATAACTTTT--TGGGCATAGTTCCAAATTGCTCTCCAGAAT 786981 i v --- v -- i -- v v i i ? C L1ME3G_3end#L 352 CGCATTTT---AAATTTTAATAG--ATACTGCCAAATTGCCCTCCAAAAN 308 chr5qtel1M 786982 GGCTGGATGTATTCACAATTCCACCAGCAATGTATCAGTGTCCCTGTTTT 787031 v ivv i v i i v v v i i C L1ME3G_3end#L 307 GGCTGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTC 258 chr5qtel1M 787032 CCCACATCCCCTCCAACATTCTGCATTATCTTTCCCTGTCATTCTGACCA 787081 i i v i ?vii vv? ii vvv i vi C L1ME3G_3end#L 257 CCCACACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCA 208 chr5qtel1M 787082 ATCTGACAGGTGTATAGTGGTATGTCAGAGTTATCTTAATTTGCATTTCT 787131 ii v v i v vv i i i C L1ME3G_3end#L 207 ATCTGATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCC 158 chr5qtel1M 787132 CTGATCAATAGTGA 787145 i v C L1ME3G_3end#L 157 CTGATTACTAGTGA 144 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 31.43 CpG sites = 58, Kimura (unadjusted) = 32.58 Transitions / transversions = 1.32 (58/44) Gap_init rate = 0.03 (13 / 407), avg. gap size = 1.15 (15 / 13) 537 26.74 6.82 3.98 chr5qtel1M 787690 788129 (211871) HERVK14C#LTR/ERVK 4660 5111 (2323) m_b265s701i0 10495 chr5qtel1M 787690 GTAAAAGCC--TGTACAGC-TTGCCTTCCTTTTCATCTCCTACA-CTGCC 787735 i? i ? -- ? i - i ??v vi vv v - HERVK14C#LTR/ 4660 GCNAAGGNCATTGTNCAACATTGCCCTNNGTGCCAGGTGCTACAACTGCC 4709 chr5qtel1M 787736 ---TCAAGGAA----AG--AACCCTCATGGTTTGAGACCCAATGAAATTT 787776 --- i ----? -- ? iv v iv? i ?viv ? HERVK14C#LTR/ 4710 ACATCAAGGGACTGGNGTTAACCCNCGAGGATTGGCNCCTAATNCGCTNT 4759 chr5qtel1M 787777 GGCAAATGGATGTGACCCATTATAAATCT-TTTGGTCGTCTGTCTTTTAA 787825 i ? -i vv ?i- vviv ? ? viiv HERVK14C#LTR/ 4760 GGCAAATGGACGTNACCCAT-GTACCTNCATTTGGGAAACTNTCNTACGT 4808 chr5qtel1M 787826 CCATGTTGTGGTAGACACCTTTTCAGGATCCATTTTTT-----CAA--TA 787868 ?iiv i -----i v ----- ? -- i HERVK14C#LTR/ 4809 CCATGTNACTGTAGATACCTTTTC-----TCATTTTGTNTGGGCNACTTG 4853 chr5qtel1M 787869 CCAGCAGCAAAAGAGACAGC--CTGAGTGGTCACTGA-ATTCCTTATACA 787915 -- i ii? i ? -- v- v v vv - ivi v v v HERVK14C#LTR/ 4854 CCA--AACAGGNGAGGCNGCTGCTC-GTGTTAAAAGACATTTGCTTTCCT 4900 chr5qtel1M 787916 GGCATTTGCAATTATGGGTGTGCTGCAAGCAATAAAAACAGACAATGGAC 787965 v-- i ?i i ii v ii iv? v ? v HERVK14C#LTR/ 4901 GT--TTCGCNGTCATGGGCATTCCACAAAANATTAAAACNGACAATGGCC 4948 chr5qtel1M 787966 CTGCATATCCTTCTAAACATTTTGCACACTTTTGTGTGTGTGTGTGTATA 788015 v vv i?? vv ?-i i? ?i v iv viivvvi - ? i HERVK14C#LTR/ 4949 CAGGCTACNNTAGTAAAN-CTTTANANGCGTTCCTTCAACAATG-GNACA 4996 chr5qtel1M 788016 AGATTTTACACACCACTGGCATACCCTTTAATCTTCAAGGACAGGCAATA 788065 --- vv ?i ? v v ii ? i v v HERVK14C#LTR/ 4997 ---TTAAACACANTACTGGNATCCCCTATAATTCTCAAGGNCAAGCCATT 5043 chr5qtel1M 788066 GTAGAAAGGAGAAACAGAGACATTAAGACACTC--CTCCAAAAACAAA-- 788111 v v iivv iv - v i ?- --i v -- HERVK14C#LTR/ 5044 GTTGAACGAGCTAATCGA-ACCTTAAAAN-CTCAATTACAAAAACAAAAG 5091 chr5qtel1M 788112 --AGAAAGGGGGAGCCATAG 788129 -- i i v HERVK14C#LTR/ 5092 ACAGAAGGGGGGAACCAGAG 5111 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 34.85 CpG sites = 55, Kimura (unadjusted) = 36.88 Transitions / transversions = 0.95 (55/58) Gap_init rate = 0.07 (32 / 439), avg. gap size = 1.50 (48 / 32) 308 32.58 3.31 4.07 chr5qtel1M 787920 788191 (211809) HERVK22#LTR/ERVK 4411 4680 (2157) m_b265s701i1 10495 chr5qtel1M 787920 TTTGCAATTATGGGTGTG--CTGCAAGCAATAAAAACAGACAATGGACCT 787967 iv - i -- ii i- v v i v v HERVK22#LTR/E 4411 TTTGCGTTTATGGG-GCGGCCCACAAA-AATTAAAACTGATAATGGTCCG 4458 chr5qtel1M 787968 GCATAT-CCTTCTAAACATTTTGCACACTTTTGTGTGTGTGTGTGTATAA 788016 v - vv v - v vv v -----iiiii iv HERVK22#LTR/E 4459 GCTTATGCCAGCTCA-CAATTTCAACAATTTTGT-----CACACGTGGAA 4502 chr5qtel1M 788017 GATTTTACACACCACTGGCATACCCTTTAATCTTCAAGGACAGGCAATAG 788066 v iiv iv v v v v i ii v HERVK22#LTR/E 4503 CATCCAACATTCCACAGGCATCCCGTATAACCCCCAAGGACAGGCCATAG 4552 chr5qtel1M 788067 TAGAAAGGAGAAACAGAGACATTAAGACACTCCTCCAAAAACAAAAGAAA 788116 v vivvv vvviv v i vvv v vi -- HERVK22#LTR/E 4553 TAGAACGTGCCCACTCCACCCTTAAAAATATGCTCAGAAAACAAA--AAA 4600 chr5qtel1M 788117 GGGGGAGCCATAGGTA---ACCCTAGAGAACTTCTAAATCTAGCTCTTTA 788163 i-i ii --- iv iv vi iivv v ii v v HERVK22#LTR/E 4601 GGGGGAA-TATGAGTAAGGACCCTGCAACACTATTGGCACAAGCCTTATT 4649 chr5qtel1M 788164 TACTATTAACTTCTTGATTTT---TGACAAA 788191 iv i i i v --- i HERVK22#LTR/E 4650 TACCCTTAATTTTTTAAATTTAGATGATAAA 4680 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.11 CpG sites = 38, Kimura (unadjusted) = 43.03 Transitions / transversions = 0.81 (38/47) Gap_init rate = 0.06 (15 / 271), avg. gap size = 1.33 (20 / 15) 28 0.00 0.00 0.00 chr5qtel1M 790028 790054 (209946) (TCTG)n#Simple_repeat 1 27 (0) c_b265s251i1 10496 chr5qtel1M 790028 TCTGTCTGTCTGTCTGTCTGTCTGTCT 790054 (TCTG)n#Simpl 1 TCTGTCTGTCTGTCTGTCTGTCTGTCT 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 91 36.69 2.31 0.62 chr5qtel1M 791153 791629 (208371) (TC)n#Simple_repeat 1 485 (0) m_b265s252i7 10497 chr5qtel1M 791153 TCTCTTTAACTATATGTCTTTCCCTCTTTTTCACTGTTTCTTTTTCTCTC 791202 i vv v v v i i i i v v i i i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr5qtel1M 791203 TCT-TATTTATTTATTTATTTTACCTTGTTTCTTTCTCTCTCACACAGTC 791251 - v i v i v i v i iv ii v i i v v vv (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chr5qtel1M 791252 TGTCTCTTTCCCTCTTACTCTGTTCCTCTCTTTTTCTGTTTTTATATTTG 791301 v i i iv v ii i i v i i v v i v (TC)n#Simple_ 101 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 150 chr5qtel1M 791302 ACT-TTTTTCT-TTTTTCTTTCTTTCTTTCTCTCT-TCTCTCTCTCTCTC 791348 v - i i - i i i i i - (TC)n#Simple_ 151 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 200 chr5qtel1M 791349 ACATTCTATCTCCTTTTCTCTCATTCTGCT-TCTTTCT-TGTTTGCTCTC 791396 v vi v ii i vi - - i - v i - (TC)n#Simple_ 201 TCTCTCTCTCTCTCTCTCTCTCTCTCT-CTCTCTCTCTCTCTCT-CTCTC 248 chr5qtel1M 791397 CCTGGCTCTGTCTTTCTATCTGTCTCTTTTTCTGAATTACTCT-TTTTTC 791445 i vv v i v v i i vvv iv - i i (TC)n#Simple_ 249 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 298 chr5qtel1M 791446 TCTCTCTCTCTTTCT-TGACTC-CCCTAT-TCTCTGGCT-TCCCATCACT 791491 i - vv - i v - vv - i - v (TC)n#Simple_ 299 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TCTCT 347 chr5qtel1M 791492 CCATATTTCTGTCTCTTTCTCTCTCTGTCTCTCTATCTCACTATGGCTTG 791541 iv v i v i v v v v vv iv (TC)n#Simple_ 348 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 397 chr5qtel1M 791542 CTCTCTGACATTTTCTCACTTTTTCTATCAGTCTTTCTATTTGGCTCTTT 791591 vv vi i v i i v vv i v i vv i (TC)n#Simple_ 398 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 447 chr5qtel1M 791592 CTCTCTTTCAGACTCTGTATATCCCTCACTCTCTCTCT 791629 i vvv v v v i v (TC)n#Simple_ 448 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 485 Matrix = Unknown Transitions / transversions = 0.89 (64/72) Gap_init rate = 0.03 (14 / 476), avg. gap size = 1.00 (14 / 14) 17 4.94 0.00 0.00 chr5qtel1M 791629 791649 (208351) (T)n#Simple_repeat 1 21 (0) m_b265s252i8 10498 chr5qtel1M 791629 TTTTTTTTTTTTTTTGTTTTT 791649 v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTT 21 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 680 31.22 3.64 3.64 chr5qtel1M 792157 792678 (207322) L1PREC2_orf2#LINE/L1 2733 3254 (40) m_b265s551i6 10499 chr5qtel1M 792157 CTATAACAATTTAGTGTTTGACAAACC---CAAAGATCCTCACTTTTGGG 792203 i v i ii v i v --- i ivvv v --- L1PREC2_orf2# 2733 CTACAACCATCTGATCTTCGACAAAGCTGACAAAAACAAGCAAT---GGG 2779 chr5qtel1M 792204 ATAAGAATTCATTATTTGACAAAAATTGCTGGGATAACTGGAAATTAG-- 792251 iv i i vi ii i viv ---i -- L1PREC2_orf2# 2780 GAAAGGACTCCCTATTCAATAAATGGTGCTGGGATAACTGG---CTAGCC 2826 chr5qtel1M 792252 -TATGGCAGAA-ATTAGGCATGGACCCACACTTAATACCGTATACCAAGA 792299 - - - iiivv viv i v i i v i L1PREC2_orf2# 2827 ATATG-CAGAAGATTGAAACTGGACCCCTTCCTTACACCATATACAAAAA 2875 chr5qtel1M 792300 TAAGATCAAAATGGGTCCATGATTTAGACATAAAGAACGAGATTATAAAC 792349 v iv i i iv v i i ii ivv i i i v L1PREC2_orf2# 2876 TCAACTCAAGATGGATTAAAGACTTAAATGTAAAACCCAAAACTATAAAA 2925 chr5qtel1M 792350 AAATTGGAGGTACA---TAGG--ATAGTTTATCTCTCAGACTTGTGGAAG 792394 vvi i - --- -- --ii - -i v i- v L1PREC2_orf2# 2926 ACCCTGGAAG-ACAACCTAGGCAATA--CCAT-TCT-GGACATA-GGAAC 2969 chr5qtel1M 792395 AGGAAGAAATTT-GTGACTAAAGATGAACTAGAGACCATTATTG----AT 792439 i v i i -i -i i -- i i ii v iivi---- v L1PREC2_orf2# 2970 GGGCAAAGATTTCATGAC-GAAGACG--CCAAAAGCAATTGCAACAAAAG 3016 chr5qtel1M 792440 CACAAAATAGAAAATTTTGATTACATCAAATTAAAAAGCTTCTGTACAAA 792489 - v v v vv ivv i i i i - i L1PREC2_orf2# 3017 CA-AAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCAC-AG 3064 chr5qtel1M 792490 CAAAACTAA-TATAAACAAGATTAGA-AGGGAAGCAACAAACTGGGAAAA 792537 vv - v - v i - iv v v i v i L1PREC2_orf2# 3065 CAAAAGAAACTATCAAC-AGAGTAAACAGACAACCTACAGAATGGGAGAA 3113 chr5qtel1M 792538 CATCTTCACAGTTAAAGGTTCTGATAAAGGCCTCATTTCCAAAATATATA 792587 v ? ii iviv v vv i i v v iv v L1PREC2_orf2# 3114 AATNTTTGCAAACTATGCATCTGACAAAGGTCTAATATCCAGCATCTATA 3163 chr5qtel1M 792588 GAGAGCTGACTCTAATTTATAAGAAACAAAGCCATTCTCCAATTGATAAA 792637 ii i v vv v i v vvv ivvi v i v i L1PREC2_orf2# 3164 AGGAACTTAAACAAATTTACAAGAAAAAAACAAACAACCCCATTAAAAAG 3213 chr5qtel1M 792638 TGGTCAAAGGATATGAATAGACAATTTTCAGATGATGAAAT 792678 v i i v i v v v L1PREC2_orf2# 3214 TGGGCAAAGGACATGAACAGACACTTTTCAAAAGAAGACAT 3254 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.89 CpG sites = 83, Kimura (unadjusted) = 41.25 Transitions / transversions = 1.12 (83/74) Gap_init rate = 0.06 (29 / 521), avg. gap size = 1.31 (38 / 29) 547 30.51 1.46 0.72 chr5qtel1M 792443 792716 (207284) L1M1_orf2#LINE/L1 3019 3294 (0) m_b265s551i7 10499 chr5qtel1M 792443 AAAATAGAAAATTTTGATTACATCAAATTAAAAAGCTTCTGTACAAACAA 792492 i v v vv i i i - i L1M1_orf2#LIN 3019 AAAATGGACAAATGGGATCACATCAAGTTAAAAAGCTTCTGCAC-AGCAA 3067 chr5qtel1M 792493 AACTAAT-ATAAACAAGATTAGAAGGGAAGCAACAAACTGGGAAAACATC 792541 ivv i- v ii v ii iv v v i v i v v L1M1_orf2#LIN 3068 AGGAAACAATCAACAAAGTGAAGAGACAACCCACAGAATGGGAGAAAATA 3117 chr5qtel1M 792542 TTCACAGTTAAAGGTTCTGATAAAGGCCTCATTTCCAAAATATATAGAGA 792591 ii iviv vvvv i i vi v vv i ii L1M1_orf2#LIN 3118 TTTGCAAACTACCCATCTGACAAGGGATTAATAACCAGAATATATAAGGA 3167 chr5qtel1M 792592 GCTGACTCTAATTTATAAGAAACAAAGCC-ATTCTCCAATTGATAAATGG 792640 v vv v v i i - v i- vv i i v L1M1_orf2#LIN 3168 GCTCAAACAACTCTATAGGAAA-AAATCTAATAATCCGATTAAAAAATGG 3216 chr5qtel1M 792641 TCAAAGGATATGAATAGACAATTTTCAGATGATGAAATTGAAATCATTAC 792690 v i v v i i v v v vv viiv v L1M1_orf2#LIN 3217 GCAAAAGATCTGAATAGACATTTCTCAAAAGAAGACATACAAATGGCAAA 3266 chr5qtel1M 792691 CACTCATATGAAA--GTGTTCCAAATCA 792716 vv -- i v v L1M1_orf2#LIN 3267 CAGGCATATGAAAAGGTGCTCAACATCA 3294 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.74 CpG sites = 35, Kimura (unadjusted) = 39.33 Transitions / transversions = 0.73 (35/48) Gap_init rate = 0.02 (5 / 273), avg. gap size = 1.20 (6 / 5) 1751 28.64 1.60 1.11 chr5qtel1M 792580 793204 (206796) L1ME4c_3end#LINE/L1 12 639 (191) m_b265s551i8 10499 chr5qtel1M 792580 AATATATAGAGAGCTGACTCTAATTTATAAGAAACAAAGCCATTCTCCAA 792629 ? i v i v v v ? v v vv i L1ME4c_3end#L 12 ANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAAGACCCCAA 61 chr5qtel1M 792630 TTGATAAATGGTCAAAGGATATGAATAGACAATTTTCAGATGATGAAATT 792679 v v i i iv ? v v v L1ME4c_3end#L 62 TAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAGGAAATA 111 chr5qtel1M 792680 GAAATCATTACCACTCATATG--AAAGTGTTCCAAATCATTATTAATCAG 792727 v ? vi v v vv i -- i v vv ii v i L1ME4c_3end#L 112 CAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTAGTAATCAA 161 chr5qtel1M 792728 AGAAATGCAAATTAAGACAACTCTGAGATACCACTACACACCTGTCAGAT 792777 ii vv i vi i i i i L1ME4c_3end#L 162 AGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCTATTAAAT 211 chr5qtel1M 792778 TGGCTAAGATGACAGGAAAAAATAATGATG---AGTGTTGGAGGGGATGT 792824 i v i v---vi v i i i--- i i v i ? i L1ME4c_3end#L 212 TAGCAAAAATT---TAAAAAATTGATAATACCCAATGCTGGCGAGGNTGC 258 chr5qtel1M 792825 GGGAAAACTGGGACACTGATACATTGTTGGTGGAGCTGTGAACAGATCCA 792874 vi v ? v i vi? i iv i v L1ME4c_3end#L 259 GGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACA 308 chr5qtel1M 792875 ACCATTCT-GAGAGCAATCTGGAATTATGC-CCAAAAGTTATCAAACTGT 792922 v i - i i v v i i-i i ii v v L1ME4c_3end#L 309 ACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAAAATGT 358 chr5qtel1M 792923 ACATACCCTTTGATCCAGCAGTGTTTCTACTGGGCTTATACCCCAAGGAG 792972 v i i i viiv v vv v i i i L1ME4c_3end#L 359 TCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAA 408 chr5qtel1M 792973 ATACT---AAAGAAGGGAAAGGGACCTGTATGTGCCAAAATGTTTGTGGC 793019 v --- i i --- i ii v i ii v L1ME4c_3end#L 409 ATAATTCAAAAGAAGGAAAAAG---CTATATGCACGAAGATGTTCATTGC 455 chr5qtel1M 793020 AGCCCTGTTTGTAGTGGCTAGAAGCTGGAAACTGAGTGGCTGCCCATCAA 793069 vi i i i i v i ii vivv iiv i v L1ME4c_3end#L 456 AGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAA 505 chr5qtel1M 793070 TGGGAGAATGGTTGGGTAAATTGTGGTATATGAATGTTATGGGATATTAT 793119 i i ii i i v? iviv i L1ME4c_3end#L 506 TAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATATTAT 555 chr5qtel1M 793120 TGTTCTGTAAGAAATGACCAGCAAGATGAATACAGAGAAGCTTGGAGAGA 793169 vvvv ii v i iv vi v v v iiv v i v i iv L1ME4c_3end#L 556 GCAGCCATTAAAAATGATAATTATGAAGACTATGTAGCAACATGGAAAAT 605 chr5qtel1M 793170 ATTACATGAACTGATGCTAAGTGAAATGAGCAGAA 793204 i -i vv i i vi L1ME4c_3end#L 606 GTT-TATGATATAATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.10 CpG sites = 97, Kimura (unadjusted) = 37.42 Transitions / transversions = 1.21 (97/80) Gap_init rate = 0.02 (12 / 624), avg. gap size = 1.42 (17 / 12) 21 15.89 0.00 0.00 chr5qtel1M 793631 793665 (206335) (A)n#Simple_repeat 1 35 (0) m_b265s252i9 10500 chr5qtel1M 793631 AATAATAAAAAAAAAGTAAAAAAAAAAAAAAACAA 793665 v v iv v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 35 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 22 21.33 0.00 0.00 chr5qtel1M 794288 794331 (205669) (A)n#Simple_repeat 1 44 (0) m_b265s252i10 10501 chr5qtel1M 794288 AAAAAAAAAACTAAAAAAAACAACAACAACAAAAAAAACACAAA 794331 vv v v v v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 44 Matrix = Unknown Transitions / transversions = 0.00 (0/8) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 15 19.43 0.00 4.65 chr5qtel1M 795100 795144 (204856) (GAAAAG)n#Simple_repeat 1 43 (0) m_b265s252i11 10502 chr5qtel1M 795100 GAAGAGAAAACAGAAAAGTAGAACAGGAAAAGGATAAGAAAAAGG 795144 i i vi -- v v i (GAAAAG)n#Sim 1 GAAAAGGAAAAGGAAAAG--GAAAAGGAAAAGGAAAAGGAAAAGG 43 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.05 (2 / 44), avg. gap size = 1.00 (2 / 2) 225 21.17 19.08 2.63 chr5qtel1M 795271 795401 (204599) L1M1_orf2#LINE/L1 25 176 (3118) m_b265s551i9 10503 chr5qtel1M 795271 TTAATAATTTTAACTCTGAATGTGAATGGGATGAACTCTCCCATAAAAGG 795320 i --- vi i iv i v v -i L1M1_orf2#LIN 25 TCAATAAT---AACATTGAATGTAAATGGACTAAACTCTCCAATCAAA-A 70 chr5qtel1M 795321 GAAAAAGAA-AGCTGACTGGATTAGAAG-------CCAGT--TTTGTT-- 795358 v v i-i v v i i------- ? -- i -- L1M1_orf2#LIN 71 GACATAGAGTGGCTGAATGGATGAAAAAACAAGACCCANTGATCTGTTGC 120 chr5qtel1M 795359 -TACGAGAAACAC-TTTC------GAAG-----CATAGAGTAAATGTAAA 795395 - i -i ------i ----- v i vi L1M1_orf2#LIN 121 CTACAAGAAACACACTTCACCTATAAAGACACACATAGACTGAAAATAAA 170 chr5qtel1M 795396 GGGCTG 795401 v L1M1_orf2#LIN 171 GGGATG 176 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 25.67 CpG sites = 16, Kimura (unadjusted) = 25.67 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.09 (12 / 130), avg. gap size = 2.42 (29 / 12) 251 24.97 12.87 0.88 chr5qtel1M 795283 795383 (204617) L1MEj_5end#LINE/L1 2044 2156 (4) m_b265s551i10 10503 chr5qtel1M 795283 ACTCTGAATGTGAATGGGATGAACTCTCCCATAAAAGGGAAAAAGAAAG- 795331 v i iv i v -i v i vv - L1MEj_5end#LI 2044 ACACTAAATGTGAATGGACTGAATTCTCCCATTAAA-AGACAGAGACTGT 2092 chr5qtel1M 795332 CTGACTGGATTAGAAG-------CCAGTT-----TTGTTTACGAGAAACA 795369 v i i i i------- i -----i i L1MEj_5end#LI 2093 CAGATTGGGTTAAAAAACAAAACCCAGCTATATGCTGTTTACAAGAAACA 2142 chr5qtel1M 795370 CTTTCGAAGCATAG 795383 vi ii i v L1MEj_5end#LI 2143 CACTTAAAACAAAG 2156 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 31.34 CpG sites = 16, Kimura (unadjusted) = 31.34 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.04 (4 / 100), avg. gap size = 3.50 (14 / 4) 218 26.11 4.11 5.56 chr5qtel1M 796162 796234 (203766) MIRc#SINE/MIR 17 88 (180) m_b265s601i1 10504 chr5qtel1M 796162 AGTAGGCAGAGCAGTG-ATCTGGTTTCAGGAAAACCT--GTTCAAATCTG 796208 i iv v - ii vv i -- i i iv MIRc#SINE/MIR 17 AGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCC 66 chr5qtel1M 796209 AACTCTGCCTCAATTTCCTTAACTGT 796234 ii --- i v - i MIRc#SINE/MIR 67 GGCTCTGCC---ACTTAC-TAGCTGT 88 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.89 CpG sites = 12, Kimura (unadjusted) = 33.30 Transitions / transversions = 2.00 (12/6) Gap_init rate = 0.08 (6 / 72), avg. gap size = 1.17 (7 / 6) 364 28.24 6.87 0.00 chr5qtel1M 796211 796341 (203659) MIR#SINE/MIR 113 252 (10) m_b265s601i2 10504 chr5qtel1M 796211 CTCTGCCTCAATTTCCTTAACTGTTA--TGAGGATAAAAACAGCATTAAC 796258 v i i v v -- i v i i iiv MIR#SINE/MIR 113 CTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTAC 162 chr5qtel1M 796259 TCCAAAGAGTTGTTCTTAACATCAAAC-AGATAATATCTGTAAAATAGTT 796307 ii v i v v iv i i- v iv iiiv MIR#SINE/MIR 163 CTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATACATGTAAAGCGCTT 212 chr5qtel1M 796308 AGCACA--GCATAG----TAGCAAATGCTGCATAAATGTT 796341 v -- v i ---- i ii vv MIR#SINE/MIR 213 AGAACAGTGCCTGGCACATAGTAAGCGCTCAATAAATGTT 252 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.70 CpG sites = 21, Kimura (unadjusted) = 36.24 Transitions / transversions = 1.31 (21/16) Gap_init rate = 0.03 (4 / 130), avg. gap size = 2.25 (9 / 4) 616 18.03 3.25 0.79 chr5qtel1M 796398 796520 (203480) MIRb#SINE/MIR 113 238 (30) m_b265s601i3 10505 chr5qtel1M 796398 AACCTCTGTTTGCCTCAGTTTTTACATCTGTATATTCAGAGATAATAATA 796447 v vv iiv v v -i i MIRb#SINE/MIR 113 AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAAT-GGGGATAATAATA 161 chr5qtel1M 796448 TCTGCC----AGAGTGATTGTGAGGATCAAATGAGACAATGATTGTAAAG 796493 i i ---- i vi i i vv MIRb#SINE/MIR 162 CCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAG 211 chr5qtel1M 796494 AGTTTAGCACAGTGCCTGGCACCTAGT 796520 v i v MIRb#SINE/MIR 212 CGCTTAGCACAGTGCCTGGCACATAGT 238 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 20.74 CpG sites = 11, Kimura (unadjusted) = 20.74 Transitions / transversions = 1.00 (11/11) Gap_init rate = 0.02 (2 / 122), avg. gap size = 2.50 (5 / 2) 13 25.47 2.08 0.00 chr5qtel1M 797355 797376 (202624) (ACCCTA)n#Simple_repeat 1 23 (26) m_b265s252i12 10506 chr5qtel1M 797355 ACTCTAACCCTAACCCTAA-ATT 797376 i -vi (ACCCTA)n#Sim 1 ACCCTAACCCTAACCCTAACCCT 23 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.05 (1 / 21), avg. gap size = 1.00 (1 / 1) 35 2.76 0.00 0.00 chr5qtel1M 797377 797413 (202587) (CGCCTCC)n#Simple_repeat 1 37 (0) c_b265s251i2 10507 chr5qtel1M 797377 CGCCTCCCGACTCCCGCCTCCCGCCTCCCGCCTCCCG 797413 v (CGCCTCC)n#Si 1 CGCCTCCCGCCTCCCGCCTCCCGCCTCCCGCCTCCCG 37 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 13 25.47 2.08 0.00 chr5qtel1M 797414 797438 (202562) (ACCCTA)n#Simple_repeat 24 48 (1) m_b265s252i12 10508 chr5qtel1M 797414 ACTCGCCTCCTGACTCTAACCCTAA 797438 i vvvi i i (ACCCTA)n#Sim 24 ACCCTAACCCTAACCCTAACCCTAA 48 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 23 10.03 0.00 0.00 chr5qtel1M 797683 797715 (202285) (A)n#Simple_repeat 1 33 (0) m_b265s252i13 10509 chr5qtel1M 797683 AAAAAAAAAAAAAAAAAAAAAGAAAGAAAGAAA 797715 i i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 33 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 34 0.00 0.00 0.00 chr5qtel1M 798213 798241 (201759) (CA)n#Simple_repeat 1 29 (0) c_b265s251i3 10510 chr5qtel1M 798213 CACACACACACACACACACACACACACAC 798241 (CA)n#Simple_ 1 CACACACACACACACACACACACACACAC 29 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 22 10.06 10.91 1.67 chr5qtel1M 798492 798546 (201454) (AT)n#Simple_repeat 1 60 (0) m_b265s252i14 10511 chr5qtel1M 798492 ATATATA-ATA-ATATGTA-AAATATATATATGTA-ATA-ATATATAT-T 798535 - - i - v i - - - (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr5qtel1M 798536 ATCTGATAGAT 798546 v - v (AT)n#Simple_ 51 ATAT-ATATAT 60 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.13 (7 / 54), avg. gap size = 1.00 (7 / 7) 474 25.25 2.61 6.80 chr5qtel1M 798872 799024 (200976) MIRc#SINE/MIR 2 148 (120) m_b265s601i4 10512 chr5qtel1M 798872 GGGGTGGGGGGGTGCCACAGTGCCCAGAGCCCTGGATTTACAATCAGGAA 798921 i ii v v --- vvv v i iv i MIRc#SINE/MIR 2 GAGGCAGTGTGGTGC---AGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr5qtel1M 798922 CTTAACTTCAGAGGTTTAAATCCTGCCTCAGACACTTATCAGGTATGTCA 798971 ---i i ---i ii i i v v v ii v i v MIRc#SINE/MIR 49 ---GACCT---GGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGA 92 chr5qtel1M 798972 GCCTGGCCAAGTCACTCAAGTCTGTTT--GCCT--GTTTCCTCATCTGTA 799017 v i v i -i v i -- -- MIRc#SINE/MIR 93 CCTTGGGCAAGTCACTTAA-CCTCTCTGAGCCTCAGTTTCCTCATCTGTA 141 chr5qtel1M 799018 AAATGAG 799024 i MIRc#SINE/MIR 142 AAATGGG 148 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.15 CpG sites = 21, Kimura (unadjusted) = 31.31 Transitions / transversions = 1.40 (21/15) Gap_init rate = 0.08 (12 / 152), avg. gap size = 1.17 (14 / 12) 292 28.40 1.23 0.00 chr5qtel1M 799825 799905 (200095) C MIRc#SINE/MIR (184) 84 3 m_b265s601i5 10513 chr5qtel1M 799825 CTAGAGAGGTGCAGATCCAGGATTTCTACCTATGTCCTC-TGACTCAAAA 799873 vi vv v i i ivv i v i - v i C MIRc#SINE/MIR 84 CTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr5qtel1M 799874 TGTAGTGATCTTTCCCTTCCACCATACTGTCT 799905 vi v vi v i i C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTGCACCACACTGCCT 3 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.31 CpG sites = 11, Kimura (unadjusted) = 36.00 Transitions / transversions = 0.92 (11/12) Gap_init rate = 0.01 (1 / 80), avg. gap size = 1.00 (1 / 1) 18 4.77 0.00 0.00 chr5qtel1M 800341 800362 (199638) (AG)n#Simple_repeat 1 22 (0) m_b265s252i15 10514 chr5qtel1M 800341 AGAGAGAGAGAGAGAGAGAAAG 800362 i (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAG 22 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 302 27.16 17.59 2.83 chr5qtel1M 801170 801385 (198615) MIRc#SINE/MIR 19 265 (3) m_b265s601i6 10515 chr5qtel1M 801170 TGGATAGAG----AGCCTTGAA-TCAGGAAGACCTGACTTTTA-TCCTAT 801213 v ----i v i - iv iv - iiv MIRc#SINE/MIR 19 TGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGG 68 chr5qtel1M 801214 GTCAGAAACTTGCTA-CT-CAAGATTT-------ATCACTCCATTTC--- 801251 v v vv i - -iiv ii -------i iv ii --- MIRc#SINE/MIR 69 CTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCT 118 chr5qtel1M 801252 ---CCTCAGTTTCTTTATCTGTAAAAAGGAGGCAATAATAGCATCTAAGT 801298 --- i i v i --- ii i -- i MIRc#SINE/MIR 119 GAGCCTCAGTTTCCTCATCTGTAAAATGGGG---ATAATAATACCT--GC 163 chr5qtel1M 801299 CCTATAT-CCTC------TTAT-----GGATAAAATGAGATAATATTTAT 801336 iiv - ------ i ----- v i-- MIRc#SINE/MIR 164 CCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATG--TAT 211 chr5qtel1M 801337 ATG---GTGTATGATACATAGC-AGGTGCGATATAAATGCTAGCTATT-T 801381 i --- i iv vi v iv i- i v i iv v?i - MIRc#SINE/MIR 212 GTGAAAGCGCTTTGTAAACTGTAAAGTGCTATACAAATGTAAGGNGTTAT 261 chr5qtel1M 801382 TATT 801385 MIRc#SINE/MIR 262 TATT 265 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.89 CpG sites = 36, Kimura (unadjusted) = 35.27 Transitions / transversions = 1.71 (36/21) Gap_init rate = 0.10 (21 / 215), avg. gap size = 2.14 (45 / 21) 364 28.68 10.08 0.00 chr5qtel1M 801252 801380 (198620) MIR#SINE/MIR 118 259 (3) m_b265s601i7 10515 chr5qtel1M 801252 CCTCAGTTTCTTTATCTGTAAAAAGGAGGCAATAATAGCATCTAAGTCCT 801301 i i v i ii i i vv v MIR#SINE/MIR 118 CCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTCAT 167 chr5qtel1M 801302 A-TATCCTCTTATGGATAAAATGAGATAATATTTAT------------AT 801338 -vi iv iv iv v v iv i ------------ i MIR#SINE/MIR 168 AGGGTTGTTGTGAGGATTAAATGAGTTAATACATGTAAAGCGCTTAGAAC 217 chr5qtel1M 801339 GGTGTATGATACATAGCAGGTGCGATATAAATGCTAGCTATT 801380 i iv ii i i i vvv i MIR#SINE/MIR 218 AGTGCCTGGCACATAGTAAGCGCTCAATAAATGTTAGCTATT 259 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.91 CpG sites = 22, Kimura (unadjusted) = 37.18 Transitions / transversions = 1.47 (22/15) Gap_init rate = 0.02 (2 / 128), avg. gap size = 6.50 (13 / 2) 261 30.66 10.95 0.00 chr5qtel1M 801498 801634 (198366) L2a_3end#LINE/L2 356 507 (10) m_b265s601i8 10516 chr5qtel1M 801498 TTCTACATAGTTGCTGGTATATTGTGTG----ACCTGAC-AGTCTGTGAC 801542 i v v ii v v v ----v iv - vv i v L2a_3end#LINE 356 TTTTACTTATTTATTTGTTTATTGTCTGTCTCCCCCCACTAGAATGTAAG 405 chr5qtel1M 801543 CTCCATGAGAGCAGGGGATATTCCTTGCCTTCTTTA--GCT-----CCCG 801585 i iv v vii ii v i -- ----- i L2a_3end#LINE 406 CTCCATGAGGGCAGGGACTTTTGTCTGTTTTGTTCACTGCTGTATCCCCA 455 chr5qtel1M 801586 GGGCTTAGCCCATGGTCTGACATATCACAGGCACT---TAAATGTTTGCT 801632 v i vv vv i i i vii i --- i i L2a_3end#LINE 456 GCGCCTAGAACAGTGCCTGGCACATAGTAGGCGCTCAATAAATATTTGTT 505 chr5qtel1M 801633 GA 801634 L2a_3end#LINE 506 GA 507 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.89 CpG sites = 22, Kimura (unadjusted) = 40.11 Transitions / transversions = 1.10 (22/20) Gap_init rate = 0.04 (5 / 136), avg. gap size = 3.00 (15 / 5) 287 27.70 9.80 0.90 chr5qtel1M 801533 801634 (198366) L2b_3end#LINE/L2 346 456 (10) m_b265s601i9 10516 chr5qtel1M 801533 AGTCTGTGACCTCCATGAGAGCAGGGGATATTCCTTGCCTTCTTTA--GC 801580 v v i i ivii?vi - i v i -- L2b_3end#LINE 346 AGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTC-TGTCTTGTTCACCGC 394 chr5qtel1M 801581 T-----CCCGGGGCTTAGCCCATGGTCTGACATATCACAGGCACT---TA 801622 ----- i v i v v? i i i ivii i --- L2b_3end#LINE 395 TGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTA 444 chr5qtel1M 801623 AATGTTTGCTGA 801634 i i L2b_3end#LINE 445 AATATTTGTTGA 456 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.10 CpG sites = 19, Kimura (unadjusted) = 37.21 Transitions / transversions = 2.11 (19/9) Gap_init rate = 0.04 (4 / 101), avg. gap size = 2.75 (11 / 4) 283 28.41 4.55 0.00 chr5qtel1M 801721 801808 (198192) C MIR3#SINE/MIR (3) 205 114 m_b265s601i10 10517 chr5qtel1M 801721 TTATAGGGTCACA-AATG--ATAACTGAATGGGAACTACAAGGTCATGGA 801767 i ii i - -- v i i v v vvi i vv C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTA 156 chr5qtel1M 801768 GTGTA-CCCTCTCATTTTATAGATGGGAAAACTTAGATTCAG 801808 vi - i i i i v iii C MIR3#SINE/MIR 155 GTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAG 114 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.08 CpG sites = 16, Kimura (unadjusted) = 37.08 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.03 (3 / 87), avg. gap size = 1.33 (4 / 3) 40 31.76 0.00 4.52 chr5qtel1M 802704 802888 (197112) (AGACAG)n#Simple_repeat 1 177 (0) m_b265s252i16 10518 chr5qtel1M 802704 AGAGAGAGACAGACAAACAGACAGACACACACACACACACACACACGGAA 802753 v v v v v v v v v v v -- i (AGACAG)n#Sim 1 AGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGAC--AG 48 chr5qtel1M 802754 AAAAAAAGGGAGAAACAGAGATTCAGAAAAATAGGGAGAGACAGAGACTC 802803 i v i iv i -- i v v iv vv (AGACAG)n#Sim 49 AGACAGAGACAGAGACAGAGA--CAGAGACAGAGACAGAGACAGAGACAG 96 chr5qtel1M 802804 ACAGAGAGTCAGAGAGTGAAAATCAGAGTGAGAAAGAGAAAGAGACAGTG 802853 v v v vv i vvv vv v v -- (AGACAG)n#Sim 97 AGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACA--G 144 chr5qtel1M 802854 AGTCAGAGAGGCAAAGAGAAATACAGACACAGAGA 802888 v -- i v i v v (AGACAG)n#Sim 145 AGACAGAGA--CAGAGACAGAGACAGAGACAGAGA 177 Matrix = Unknown Transitions / transversions = 0.29 (10/34) Gap_init rate = 0.04 (8 / 184), avg. gap size = 1.00 (8 / 8) 19 12.06 0.00 0.00 chr5qtel1M 803416 803443 (196557) (T)n#Simple_repeat 1 28 (0) m_b265s252i17 10519 chr5qtel1M 803416 TTTTTCTTTTCTTTCTTTTTTTTTTTTT 803443 i i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 28 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 38 0.00 0.00 0.00 chr5qtel1M 803600 803634 (196366) (T)n#Simple_repeat 1 35 (0) c_b265s251i4 10520 chr5qtel1M 803600 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 803634 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 35 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 47 4.20 0.00 0.00 chr5qtel1M 804221 804269 (195731) (CT)n#Simple_repeat 1 49 (0) c_b265s251i5 10521 chr5qtel1M 804221 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTTCTCTCTATCTCTC 804269 i v (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 49 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 15 10.76 10.00 0.00 chr5qtel1M 805009 805048 (194952) (AAGAAT)n#Simple_repeat 1 44 (0) m_b265s252i18 10522 chr5qtel1M 805009 AAGAA-AAG-ATAGTAAT-AGAATAGGAA-AAGAATAAGAAAAA 805048 - - iv - i - v (AAGAAT)n#Sim 1 AAGAATAAGAATAAGAATAAGAATAAGAATAAGAATAAGAATAA 44 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.10 (4 / 39), avg. gap size = 1.00 (4 / 4) 229 22.97 12.87 0.88 chr5qtel1M 805177 805277 (194723) L1M1_orf2#LINE/L1 22 134 (3160) m_b265s551i11 10523 chr5qtel1M 805177 TTAGTAATTTTAACTCTGAATGTGAATGGGATGAACTCTCCGATAAAAGG 805226 vi vv vi i iv i i v -i L1M1_orf2#LIN 22 TTATCAATAATAACATTGAATGTAAATGGACTAAACTCTCCAATCAAA-A 70 chr5qtel1M 805227 GAAATAGAA-AGCTGACTGGATTAGAAG-------CCAGT--TTTGTT-- 805264 v i-i v v i i------- ? -- i -- L1M1_orf2#LIN 71 GACATAGAGTGGCTGAATGGATGAAAAAACAAGACCCANTGATCTGTTGC 120 chr5qtel1M 805265 -TACAAAAAAAACA 805277 - i v L1M1_orf2#LIN 121 CTACAAGAAACACA 134 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 28.24 CpG sites = 13, Kimura (unadjusted) = 28.24 Transitions / transversions = 1.30 (13/10) Gap_init rate = 0.06 (6 / 100), avg. gap size = 2.33 (14 / 6) 231 20.88 1.32 5.48 chr5qtel1M 805177 805252 (194748) L1M4c_5end#LINE/L1 2370 2442 (58) m_b265s551i12 10523 chr5qtel1M 805177 TTAGTAATTTTAACTCTGAATGTGAATGGGATGAACTCTCCGATAAAAGG 805226 i --- i i i iv i i v -i L1M4c_5end#LI 2370 TCAGTAATT---ACTTTAAATGTAAATGGATTAAACTCTCCAATCAAA-A 2415 chr5qtel1M 805227 GAAATAGA-AAGCTGACTGGATTAGAA 805252 v ? -vi ? v i L1M4c_5end#LI 2416 GACANAGATTGGCNGAATGGATTAAAA 2442 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 25.95 CpG sites = 10, Kimura (unadjusted) = 25.95 Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.07 (5 / 75), avg. gap size = 1.00 (5 / 5) 492 30.48 4.20 4.20 chr5qtel1M 806005 806456 (193544) L1M5_orf2#LINE/L1 2836 3287 (7) m_b265s551i13 10524 chr5qtel1M 806005 AAACTAAGCATTGACCCACACTTAACACCGTACACTAAGATAAGGTCAAA 806054 v i i?v i vi i v i v i v iv ? i L1M5_orf2#LIN 2836 AAAATGAANCTCGACCCCTACCTCACACCATACACAAAAATTAATTCNAG 2885 chr5qtel1M 806055 ATGGGTTCAT-GACCTAGGCATAAAGAATGAGATTATAAATAAATT--AG 806101 i - - iiii ii? i i i -- v -- L1M5_orf2#LIN 2886 ATGGAT-CATAGACCTAAATGTAAAAGNTAAAACTATAAA--ACTTCTAG 2932 chr5qtel1M 806102 AGGAA--CACAGGATAGTTTACCTCTCAGATCCGTGGAAGAGGAAGGAAT 806149 i -- i v i -- i - iviv v i?v v iii L1M5_orf2#LIN 2933 AAGAAAACATAGGAGAAT--ATCT-TCGTGACCTTGGGNTAGGCAAAGAT 2979 chr5qtel1M 806150 TTATGACCAAAGAAGAACTAGAGATCATTACTGATCACCAAATAGAAGAT 806199 v ---i v i vvi i i v i? --- i iv v i i L1M5_orf2#LIN 2980 TTCT---TAAACAGGACACAAAAAGCACNA---ACCATAAAAGAAAAAAT 3023 chr5qtel1M 806200 T-------TTGATTATATCAAATTGAAAAATTTTTGTATAAACAAAAG-T 806241 ------- v i ?i v v i i i- v?v -i L1M5_orf2#LIN 3024 TGATAAATTGGACTNCATCAAAATTAAAAACTTCTGC-TCNTCAAAAGAC 3072 chr5qtel1M 806242 AATGCAGACAAGATTAGAAGGGAAACAATAAACTGGGA--AAACATTTAT 806289 vi ivi v i v i v i v i i ? -- i ii L1M5_orf2#LIN 3073 ACCGTTAAGAAAATGAAAAGGCAAGCCACAGANTGGGAGAAAATATTTGC 3122 chr5qtel1M 806290 ACAGTCAAAGGTTCTGACAAAGGCCTCATTTCCAAAATATATAGAGAATT 806339 - ?v v vi - v i v i i i L1M5_orf2#LIN 3123 A-ANACATATAT-CTGACAAAGGACTCGTATCCAGAATATATAAAGAACT 3170 chr5qtel1M 806340 GACTCTAATTT-ATAAGAAA---TCAAGCCATTTTCCAATTGATAAATAG 806385 v- vi ? i- ? ---v i v ---i v? v i L1M5_orf2#LIN 3171 C-CTACAANTCAATAANAAAAAGACAAACAA---CCCAATANAAAAATGG 3216 chr5qtel1M 806386 TCAAAAGATATGAATAGACAATTCTTAGATGAAAAAATTGAAACTATTTC 806435 v iv i v vi i v i v ?v iviiivv L1M5_orf2#LIN 3217 GCAAAAGACTTGAACAGACACTTCACAAAAGAAGATATNCAAATGGCCAA 3266 chr5qtel1M 806436 TAGCCATATAAAAAGATGCTC 806456 iv i i L1M5_orf2#LIN 3267 TAAGCACATGAAAAGATGCTC 3287 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.40 CpG sites = 78, Kimura (unadjusted) = 42.09 Transitions / transversions = 1.44 (78/54) Gap_init rate = 0.06 (27 / 451), avg. gap size = 1.41 (38 / 27) 514 27.39 0.00 1.79 chr5qtel1M 806320 806490 (193510) L1ME3C_3end#LINE/L1 7 174 (696) m_b265s551i14 10524 chr5qtel1M 806320 TCCAAAATATATAGAGAATTGACTCTAATTTATAAGAAATCAAGCCATTT 806369 i i i vviv v iv v ii v i-- L1ME3C_3end#L 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAAACAGACAAC-- 54 chr5qtel1M 806370 TCCAATTGATAAATAGTCAAAAGATATGAATAGACAATTCTTAGATGAAA 806419 - v v i v i i vi v ii L1ME3C_3end#L 55 -CCAATAGAAAAATGGGCAAAAGATATGAACAGGCAATTCACAGAAGAGG 103 chr5qtel1M 806420 AAATTGAAACTATTTCTAGCCATATAAAAAGATGCTCCAAGCCATTATTA 806469 i?vi iviiivv iv i v vvi i v L1ME3C_3end#L 104 AAACNCGAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTA 153 chr5qtel1M 806470 ATCAGAGAAATGCAAATTAAA 806490 i L1ME3C_3end#L 154 ATCAGGGAAATGCAAATTAAA 174 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 34.00 CpG sites = 25, Kimura (unadjusted) = 34.92 Transitions / transversions = 1.19 (25/21) Gap_init rate = 0.02 (3 / 170), avg. gap size = 1.00 (3 / 3) 614 30.78 2.28 5.59 chr5qtel1M 806460 806810 (193190) L1MA5A_3end#LINE/L1 214 553 (491) m_b265s551i15 10524 chr5qtel1M 806460 GCCATTATTAATCAGAGAAATGCAAATTAAATGCAGAATGTTGGAGGGGC 806509 i i vv v --- -- -- - i v i v L1MA5A_3end#L 214 GCTATTATCAAAAAGACAAA---AAAT--AA--CA-AATGCTGGCGAGGA 255 chr5qtel1M 806510 TGTGGGAAAACAGGGACACTAATACATTATTGGTGGAATTGTGAATACAT 806559 i ii vi i v v i i i v i ivvi L1MA5A_3end#L 256 TGCGGAGAAAAGGGAACTCTTATACACTGTTGGTGGGAATGTAAACTAGT 305 chr5qtel1M 806560 CCAGCTATTCCGGAGAGCAATTTGGAACTATGTTCAAAAAGTTATCAAAC 806609 v i i vi i i v iv - vi ii - i L1MA5A_3end#L 306 ACAGCCACTATGGAGAACAGTATGGAGGT-TCCTCAAAAAACTA-CAAAT 353 chr5qtel1M 806610 TGTGCATACCCTTTGATCCAGCAGTGTCTCTACTGGGCTTATGTCCCAAA 806659 v vi - v v i vi v v v i v i L1MA5A_3end#L 354 AGAAC-TACCATATGATCCAGCAATCCCACTACTGGGCATTTATCCAAAG 402 chr5qtel1M 806660 GAGATCTTAAAGAA---GGTA-----AAGGGACCTGTTTGTGCAAGAATG 806701 ------ i ---i ----- i --i i ii vvvv L1MA5A_3end#L 403 GA------AAGGAAATCAGTATATCGAAGAGAC--ATCTGCACCCCCATG 444 chr5qtel1M 806702 TTTGTGGCAGGTCTCTTTATAGTGGCCAAAAACTGGAAACTGAGTGGATG 806751 i v vv v i i i i i vv v vivv i i L1MA5A_3end#L 445 TTTATTGCAGCACTATTCACAATAGCCAAGATATGGAATCAACCTAGGTG 494 chr5qtel1M 806752 TCCATCAATTGGAGAATGGCTGAATACATTGTGGTATATGAATATTATGG 806801 v iv iv v i v v v iv i iv L1MA5A_3end#L 495 TCCAACAACAGATGAATGGATAAAGAAAATGTGGTATATATACACAATGG 544 chr5qtel1M 806802 GATATTATT 806810 i i L1MA5A_3end#L 545 AATACTATT 553 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.76 CpG sites = 54, Kimura (unadjusted) = 40.27 Transitions / transversions = 1.12 (54/48) Gap_init rate = 0.06 (21 / 350), avg. gap size = 1.29 (27 / 21) 1011 27.19 0.64 1.61 chr5qtel1M 806496 806809 (193191) L1ME3G_3end#LINE/L1 238 548 (376) m_b265s551i16 10524 chr5qtel1M 806496 AATGTTGGAGGGGCTGTGGGAAAACAGGGACACTAATACATTATTGGTGG 806545 i v i v i i v v v i ii L1ME3G_3end#L 238 AGTGTTGGCGAGGGTGTGGGGAAACGGGTACTCTCATACACTGCTGGTGG 287 chr5qtel1M 806546 AATTGTGAATACATCCAGCTATTCCGGAGAGCAATTTGGAACTATGTTCA 806595 i v i vvi v i? ii i v v v viv L1ME3G_3end#L 288 GAGTGTAAATTGGTACAGCCNTTTTGGAGGGCAATTTGGCAGTATCTATT 337 chr5qtel1M 806596 AAAAGTTATCAAACTGTGCATACCCTTTGATCCAGCAGTGTCTCTACTGG 806645 v --- v i i i vi v v ? L1ME3G_3end#L 338 AAAATTTA---AAATGCGCATACCCTTTGACCCAGCAATTCCACTTCTNG 384 chr5qtel1M 806646 GCTTATGTCCCAAAGAGAT-CTTAAAGAAG-GTAAAGGGACCTGTTTGTG 806693 ?v v i i ? i - iiv v v - i v i --? iv i L1ME3G_3end#L 385 GNATCTATCCTANAGAAATACTCGCACATGTGCACAAGGA--NGCATGTA 432 chr5qtel1M 806694 CAAGAATGTTTGTGGCAGGTCTCTTTATAGTGGCCAAAAACTGGAAACTG 806743 i ii v vvi v i i i v i vi L1ME3G_3end#L 433 CAAGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAA 482 chr5qtel1M 806744 AGTGGATGTCCATCAATTGGAGAATGGCTGAATACATTGTGGTATATGAA 806793 vv ii v i i i v i vv L1ME3G_3end#L 483 CCTAAATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCA 532 chr5qtel1M 806794 TATTATGGGATATTAT 806809 i i i L1ME3G_3end#L 533 TACTATGGAATACTAT 548 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.51 CpG sites = 46, Kimura (unadjusted) = 35.09 Transitions / transversions = 1.21 (46/38) Gap_init rate = 0.02 (7 / 313), avg. gap size = 1.00 (7 / 7) 659 31.77 2.03 2.55 chr5qtel1M 806498 806891 (193109) L1MC4a_3end#LINE/L1 241 632 (1997) m_b265s551i17 10524 chr5qtel1M 806498 TGTTGGAGGGGCTGTGGGAAAACAGGGACACTAATACATTATTGGTGGAA 806547 v i i v v v ii i L1MC4a_3end#L 241 TGTTGGCGAGGCTGTGGGGAAACAGGCACTCTCATACATTGCTGGTGGGA 290 chr5qtel1M 806548 TTGTGAATACATCCAGCTATTCCGGAGAGCAATTTGGAACTATGTTCAAA 806597 v ii ?vvi v i iv ?i i v v v -i v v L1MC4a_3end#L 291 ATGCAAANTGGTACAACCCTTNTGGAGGGGAATTTGGCAATAT-CTAACA 339 chr5qtel1M 806598 AAGTTATCAAACTGTGCA--TACCCTTTGATCCAGCAGTGTCTCTACTGG 806645 ii - --- i -- i i vi v v i L1MC4a_3end#L 340 AAACTA-CA---TATGCATTTACCCTTTGACCCAGCAATCCCACTTCTAG 385 chr5qtel1M 806646 GCTTATGTCCCAAAG--AGATCTTAAAGAAG-GTAAAGGGACCTGTTTGT 806692 vv v ii ii -- v i iv v v -ii iv? v i-- i L1MC4a_3end#L 386 GAATTTACCCTGAAGATACACCTCCAACATGTACAAAATNACATA--TGC 433 chr5qtel1M 806693 GCAAGAATGTTTGTGGCAGGTCTCTTTATAGTGGCCAAAAACTGGAAACT 806742 i iv i ii v vvi v i i v v v i v L1MC4a_3end#L 434 ACAAGGTTATTCATTGCAGCATTGTTTGTAATTGCAAAATATTGGAAACA 483 chr5qtel1M 806743 GAGTGGATGTCCATCAATTGGAGAATGGCTGAATACATTGTGGTATATGA 806792 ivv ii i ?? v ? i v i i i vv L1MC4a_3end#L 484 ACCTAAATGCCCATNNATAGGAGANTGGTTGAATAAACTATGGTACATCC 533 chr5qtel1M 806793 ATATTATGGGATATTATTGTTCTGTAAGAAATGACCAGCAGGGTGATTTC 806842 i iv ii i vvvv i - -- vv iv i L1MC4a_3end#L 534 ACACAATGGAGTACTATGCAGCTGTAAAAAA-GA--ATGAGGAAGATCTC 580 chr5qtel1M 806843 -AGAAA--GGCCTGGAGAGACTTACACGAACTGATGATGAGTGAAATGAG 806889 - vi -- iiv v i v v vv iv v i vi L1MC4a_3end#L 581 TATGAACTGATATGGAGTGATTTCCAGGATATATTGTTAAGTGAAAAAAG 630 chr5qtel1M 806890 CA 806891 L1MC4a_3end#L 631 CA 632 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 42.97 CpG sites = 63, Kimura (unadjusted) = 42.97 Transitions / transversions = 1.07 (63/59) Gap_init rate = 0.04 (15 / 393), avg. gap size = 1.20 (18 / 15) 217 28.57 3.17 0.00 chr5qtel1M 807471 807533 (192467) MIR1_Amn#SINE/MIR 13 77 (153) m_b265s601i11 10525 chr5qtel1M 807471 GTAGCTGAGTGGGTAGATCAGTGACCTGGGTTCAGGAAAACCTG--TTCA 807518 i iiv i v v iv viiv i i -- ? MIR1_Amn#SINE 13 GTGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGAGACCTGGGTTCN 62 chr5qtel1M 807519 ATTCTGAGCTCTGCC 807533 ? ivi MIR1_Amn#SINE 63 ANTCCCGGCTCTGCC 77 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.04 CpG sites = 11, Kimura (unadjusted) = 38.78 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.02 (1 / 62), avg. gap size = 2.00 (2 / 1) 221 23.21 4.11 5.56 chr5qtel1M 807478 807550 (192450) MIRc#SINE/MIR 17 88 (180) m_b265s601i12 10525 chr5qtel1M 807478 AGTGGGTAGATCAGTG-ACCTGGGTTCAGGAAAACCT--GTTCAATTCTG 807524 iv v v - i iv i -- i v iv MIRc#SINE/MIR 17 AGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCC 66 chr5qtel1M 807525 AGCTCTGCCTCAATTTCCTTAACTGT 807550 i --- i v - i MIRc#SINE/MIR 67 GGCTCTGCC---ACTTAC-TAGCTGT 88 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 24.23 CpG sites = 9, Kimura (unadjusted) = 28.17 Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.08 (6 / 72), avg. gap size = 1.17 (7 / 6) 450 25.19 6.87 0.00 chr5qtel1M 807527 807657 (192343) MIR#SINE/MIR 113 252 (10) m_b265s601i13 10525 chr5qtel1M 807527 CTCTGCCTCAATTTCCTTAACTGTAA--TGAGGATAAAAACAGCACTCAC 807574 v i i v -- i v i i ii MIR#SINE/MIR 113 CTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTAC 162 chr5qtel1M 807575 TTCAGAGAGTTGTTCTTAACATCAAAC-AGATAATATCTGTAAAGTGCTT 807623 i v i v v iv i i- v iv i MIR#SINE/MIR 163 CTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATACATGTAAAGCGCTT 212 chr5qtel1M 807624 AGCACA--GCATAG----TAGCAAATGCCACATAAATGCT 807657 v -- v i ---- i ii ivv i MIR#SINE/MIR 213 AGAACAGTGCCTGGCACATAGTAAGCGCTCAATAAATGTT 252 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.20 CpG sites = 20, Kimura (unadjusted) = 31.46 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.03 (4 / 130), avg. gap size = 2.25 (9 / 4) 233 20.06 0.00 5.45 chr5qtel1M 807714 807771 (192229) MIR#SINE/MIR 106 160 (102) m_b265s601i14 10526 chr5qtel1M 807714 AACCTCTGTTTGCCTCAGTTTTTACATCTATAAATTCAGAGATAATAGCA 807763 v v iiv i v -i i -- MIR#SINE/MIR 106 AACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAAT-GGGGATAATA--A 152 chr5qtel1M 807764 CAGTGCCT 807771 i i MIR#SINE/MIR 153 TAGTACCT 160 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 23.75 CpG sites = 7, Kimura (unadjusted) = 23.75 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.05 (3 / 57), avg. gap size = 1.00 (3 / 3) 16 11.69 0.00 0.00 chr5qtel1M 809123 809150 (190850) (ATAC)n#Simple_repeat 1 28 (0) m_b265s252i19 10527 chr5qtel1M 809123 ATACATACATGCATACACACATAAATAC 809150 i i v (ATAC)n#Simpl 1 ATACATACATACATACATACATACATAC 28 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 390 21.19 5.94 1.90 chr5qtel1M 809151 809251 (190749) Charlie7a#DNA/hAT-Charlie 167 271 (1) m_b265s502i0 10528 chr5qtel1M 809151 ACACATATATAATGTATAAATAAGCA------CACACATTAGATATACAT 809194 ii v ii ------ i i i ivi i Charlie7a#DNA 167 ACATGTATATAATTTATAAATAAATAAATATACATATATTGGGGGTGCAT 216 chr5qtel1M 809195 ATTCAAAAATGTTTTACTTATAGAGGTGAATGTGATCAAAACAGTTAGGA 809244 ii v v i v -- v v Charlie7a#DNA 217 GCTCAAAAATTTTTTACTGATAGGGGTGCA--TGATCAAAAAAGTTTGGA 264 chr5qtel1M 809245 GACTACT 809251 i Charlie7a#DNA 265 GACCACT 271 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 25.62 CpG sites = 14, Kimura (unadjusted) = 25.62 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.03 (3 / 100), avg. gap size = 2.67 (8 / 3) 424 30.16 1.43 2.90 chr5qtel1M 809253 809392 (190608) C MIR3#SINE/MIR (37) 171 34 m_b265s601i15 10529 chr5qtel1M 809253 CCTTCGAGATCATCT-GTTCTACCCTCTCCTCACTTTATAGATGAGAAAA 809301 v - i v --- i i i C MIR3#SINE/MIR 171 CCTTAGAGATCATCTAGTCCAACCC---CCTCATTTTACAGATGAGGAAA 125 chr5qtel1M 809302 CATAGACCCAAGAAGGTTAACTTAATTAATTCAAGATCACTCAGGTAATA 809351 vv i iii v v v v -iii i v v? i v C MIR3#SINE/MIR 124 CTGAGGCCCAGAGAGGTGAAGTGACTT-GCCCAAGGTCACACAGCNAGTT 76 chr5qtel1M 809352 GCCATCAGAGTTAGGATTTAAACTCAGATCCTCT-AGTCCTA 809392 iviiv iii i vi i i ii - v i C MIR3#SINE/MIR 75 AGTGGCAGAGCCGGGACTAGAACCCAGGTCTCCTGACTCCCA 34 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.12 CpG sites = 26, Kimura (unadjusted) = 40.57 Transitions / transversions = 1.73 (26/15) Gap_init rate = 0.04 (6 / 139), avg. gap size = 1.00 (6 / 6) 476 33.33 0.75 0.75 chr5qtel1M 809279 809411 (190589) C MIRb#SINE/MIR (115) 153 21 m_b265s601i16 10529 chr5qtel1M 809279 TCCTCACTTTATAGATGAGAAAACATAGACCCAAGAAGGTTAACTTAATT 809328 i i i i vv i i iii -v i C MIRb#SINE/MIR 153 TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAA-GTAACT 105 chr5qtel1M 809329 AATTCAAGATCACTCAGGTAATAGCCATCAGAGTTAGGATTTAAACTCAG 809378 viii i v v i iviiv iii ii i C MIRb#SINE/MIR 104 TGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAG 55 chr5qtel1M 809379 ATCC-TCTAGTCCTAAAGCCAGTATTTTTCCCAC 809411 i i- iiii i v ii i i C MIRb#SINE/MIR 54 GTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCAC 21 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 45.65 CpG sites = 35, Kimura (unadjusted) = 49.29 Transitions / transversions = 3.89 (35/9) Gap_init rate = 0.02 (2 / 132), avg. gap size = 1.00 (2 / 2) 396 26.62 5.92 11.03 chr5qtel1M 809508 809659 (190341) C MIRc#SINE/MIR (119) 149 5 m_b265s601i17 10530 chr5qtel1M 809508 CCTCATTTCACAGAGGAGGAAACATATGACT---------TAAGTAACTT 809548 i i v - iv i --------- i C MIRc#SINE/MIR 149 CCCCATTTTACAGATGAGGAAAC-TGAGGCTCAGAGAGGTTAAGTGACTT 101 chr5qtel1M 809549 ACCCAAAGTAACACAGTGAGTGAGTGTCTAAGGTCAGATTTGGACTGATG 809598 i i v iv i v - ii i i----- --i C MIRc#SINE/MIR 100 GCCCAAGGTCACACAGCTAGTAAGTGGC-AGAGCCG-----GGACT--CG 59 chr5qtel1M 809599 AACATAAGTCTTCCTAGTTCCAAACGAATGCTCAGTACTATTTTCCCTAT 809648 vi i iii ------ ii i v i v ii C MIRc#SINE/MIR 58 AACCCAGGTCTTCCTGACTCCAA------GTCCAGTGCTCTTTCCACTGC 15 chr5qtel1M 809649 ATCTACAGTAC 809659 - i v i C MIRc#SINE/MIR 14 A-CCACACTGC 5 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.25 CpG sites = 27, Kimura (unadjusted) = 34.66 Transitions / transversions = 3.00 (27/9) Gap_init rate = 0.11 (17 / 151), avg. gap size = 1.47 (25 / 17) 663 24.23 4.76 1.73 chr5qtel1M 809708 809875 (190125) C MIRb#SINE/MIR (39) 229 57 m_b265s601i18 10531 chr5qtel1M 809708 CAAATAGTGTGCTAAGTGCTTTAAAATTATTATCTCATTTGATCCTCACA 809757 iii v i v vvi i C MIRb#SINE/MIR 229 CAGGCACTGTGCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACA 180 chr5qtel1M 809758 ACTATCCTGGCAGTTAGATGCTGTGGTTACCCCCATTTTACAACCAAGGA 809807 v i vv v i ii ---i i ivii C MIRb#SINE/MIR 179 ACAACCCTGCGAGGTAGGTATT---ATTATCCCCATTTTACAGATGAGGA 133 chr5qtel1M 809808 AACTGAGG--CAAAGGGGTTAAGTGACTGGCCCAGCTTCATCCAGATAGT 809855 -- i i i v ivv iv v C MIRb#SINE/MIR 132 AACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGT 83 chr5qtel1M 809856 ------CTGAGGCTGGGTTTGAACTC 809875 ------ v v v i i i C MIRb#SINE/MIR 82 AAGTGGCAGAGCCGGGATTCGAACCC 57 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.08 CpG sites = 23, Kimura (unadjusted) = 29.82 Transitions / transversions = 1.35 (23/17) Gap_init rate = 0.03 (5 / 167), avg. gap size = 2.20 (11 / 5) 196 16.67 0.00 0.00 chr5qtel1M 810113 810142 (189858) MIRc#SINE/MIR 170 199 (69) m_b265s601i19 10532 chr5qtel1M 810113 TACCTCATAGGGTTGTTATGGAGATCAGAT 810142 i i ii i MIRc#SINE/MIR 170 TACCTCACAGGGTTGTTGTGAGGATCAAAT 199 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 20.27 CpG sites = 5, Kimura (unadjusted) = 20.27 Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 13 17.64 0.00 3.03 chr5qtel1M 810478 810511 (189489) (GGGTG)n#Simple_repeat 1 33 (0) m_b265s252i20 10533 chr5qtel1M 810478 GGGTTGGGTGAAGGTGGGATGGAGTGGGGTTGGG 810511 v -i i i v (GGGTG)n#Simp 1 GGGTGGGGTG-GGGTGGGGTGGGGTGGGGTGGGG 33 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 50 2.17 0.00 0.00 chr5qtel1M 811588 811634 (188366) (AC)n#Simple_repeat 1 47 (0) c_b265s251i6 10534 chr5qtel1M 811588 ACACATACACACACACACACACACACACACACACACACACACACACA 811634 i (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACA 47 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 491 20.85 0.00 6.60 chr5qtel1M 812821 812933 (187067) C MIRc#SINE/MIR (153) 115 10 m_b265s601i20 10535 chr5qtel1M 812821 GGGGTTAAGTGACTTTCCCAGGGTCACACAGCTAAGAAGTGTTAAGTGTC 812870 i v i i------- v C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGC 73 chr5qtel1M 812871 TGAGGCCAGATTGGAACTCAGGTCCTCCTGACTTCAGGACTGGTGCTCTG 812920 v v vi i v i i i i v ii v C MIRc#SINE/MIR 72 AGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTT 23 chr5qtel1M 812921 ACCACTGAGCCAC 812933 v vi C MIRc#SINE/MIR 22 TCCACTGCACCAC 10 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 24.57 CpG sites = 12, Kimura (unadjusted) = 24.57 Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.06 (7 / 112), avg. gap size = 1.00 (7 / 7) 249 34.11 13.18 0.00 chr5qtel1M 816469 816597 (183403) MIRc#SINE/MIR 3 148 (120) m_b266s601i0 10536 chr5qtel1M 816469 AGACGATGT--TGCAGTAGATAGACTAGTAGGCCTTAAGAAATGAAGACC 816516 i ii -- i v vi v i i i vi vv v MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chr5qtel1M 816517 TGAGTTTTAATCTCAACTCAGAAACTTGATAG----------TCAAGCAA 816556 i iv i i ii v vv iv ---------- iii MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 102 chr5qtel1M 816557 G-----GGGTCTCTGTTTATCTCAGTTACTTGCTCTGTAAAATGGG 816597 -----viii v vvii v i vv MIRc#SINE/MIR 103 GTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 44.08 CpG sites = 25, Kimura (unadjusted) = 47.00 Transitions / transversions = 1.32 (25/19) Gap_init rate = 0.02 (3 / 128), avg. gap size = 5.67 (17 / 3) 203 30.18 7.48 5.33 chr5qtel1M 819044 819190 (180810) C MIRc#SINE/MIR (37) 231 82 m_b266s601i1 10537 chr5qtel1M 819044 AATTTCTAATGAGCTTTCTAC-TAAAATA---CATTAGATTCTTACAGTA 819089 i vi v v - - v v --- v i i ii C MIRc#SINE/MIR 231 AGTTTACAAAGCGCTTTC-ACATACATTATCTCATTTGATCCTCACAACA 183 chr5qtel1M 819090 AGCCTGTGACAATA--CAGA--AAGTGCCTTCATTCTCACTGTGTGCCCA 819135 v -ii -- i-- i iiiv i i i i v i---- C MIRc#SINE/MIR 182 ACCCTGTGA-GGTAGGCAGGGCAGGTATTATTATCCCCATTTTA----CA 138 chr5qtel1M 819136 GGTCAGGCCAAC---AGCTCAGAATGGTTGAGTGAGCTGAACCAAATTCC 819182 i v -v ---i iv i - viv iv v C MIRc#SINE/MIR 137 GATGAGG-AAACTGAGGCTCAGAGAGGTTAAGTGA-CTTGCCCAAGGTCA 90 chr5qtel1M 819183 AGCAGCTA 819190 vi C MIRc#SINE/MIR 89 CACAGCTA 82 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.90 CpG sites = 25, Kimura (unadjusted) = 39.90 Transitions / transversions = 1.47 (25/17) Gap_init rate = 0.09 (13 / 146), avg. gap size = 1.46 (19 / 13) 12 11.26 6.90 0.00 chr5qtel1M 819296 819324 (180676) (TTTTA)n#Simple_repeat 1 31 (0) m_b266s252i0 10538 chr5qtel1M 819296 TTTAATTTTA-TTTATTTT-TTGTATATTAT 819324 v - - v v (TTTTA)n#Simp 1 TTTTATTTTATTTTATTTTATTTTATTTTAT 31 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.07 (2 / 28), avg. gap size = 1.00 (2 / 2) 374 30.53 1.89 3.18 chr5qtel1M 821249 821407 (178593) MIRb#SINE/MIR 43 199 (69) m_b266s601i2 10539 chr5qtel1M 821249 AGTCATAATGTACTCGAGTTTAAATTAGGCCTCAAACAGTTACTAACTGT 821298 -i iiv ii i ii ivv v viv v i MIRb#SINE/MIR 43 AGTCA-GACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGT 91 chr5qtel1M 821299 ATACCCCGTGGTAAGTCAATTAACC-CTGTTTGCCTTAGTTTCCTCAACT 821347 i iv ivv i i v - v vv i v MIRb#SINE/MIR 92 GTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCT 141 chr5qtel1M 821348 CTTAAATGGGGATAAAAGTATA-ACCTCAAGTGGAAGGTTAATATG-GCA 821395 v v v i iv- ---- v i iv i - v MIRb#SINE/MIR 142 GTAAAATGGGGATAATAATACCTACCTC----GCAGGGTTGTTGTGAGGA 187 chr5qtel1M 821396 TAAATTGACATA 821407 v v v MIRb#SINE/MIR 188 TTAAATGAGATA 199 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.37 CpG sites = 22, Kimura (unadjusted) = 39.53 Transitions / transversions = 0.88 (22/25) Gap_init rate = 0.05 (8 / 158), avg. gap size = 1.00 (8 / 8) 386 29.57 0.87 0.00 chr5qtel1M 821259 821373 (178627) MIR#SINE/MIR 45 160 (102) m_b266s601i3 10539 chr5qtel1M 821259 TACTCGAGTTTAAATTAGGCCTCAAACAGTTACTAACTGTATACCCCGTG 821308 i ii i ii ivv v viv v i i iv ivv MIR#SINE/MIR 45 TGCCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 94 chr5qtel1M 821309 GTAAGTCAATTAACC-CTGTTTGCCTTAGTTTCCTCAACTCTTAAATGGG 821357 i i v - v v i v v v MIR#SINE/MIR 95 GCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGG 144 chr5qtel1M 821358 GATAAAAGTATAACCT 821373 v i vv MIR#SINE/MIR 145 GATAATAATAGTACCT 160 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.40 CpG sites = 16, Kimura (unadjusted) = 37.91 Transitions / transversions = 0.89 (16/18) Gap_init rate = 0.01 (1 / 114), avg. gap size = 1.00 (1 / 1) 263 30.98 2.10 0.69 chr5qtel1M 821983 822125 (177875) L1ME4c_3end#LINE/L1 495 639 (191) m_b266s551i0 10540 chr5qtel1M 821983 ATGCCCATCAACGGGAGAATGGTTGGGTAAATTGTGGTATATGAATGTTA 822032 i v ii i ii i i v? iviv L1ME4c_3end#L 495 ATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGA 544 chr5qtel1M 822033 TGGATTATTGTTCTG---TAAGAAATGACCAGGAGGATGAATACAGAGAG 822079 v i v v --- v i iv vv v v v iiv vi L1ME4c_3end#L 545 TGGAATATTATGCAGCCATTAAAAATGATAATTATGAAGACTATGTAGCA 594 chr5qtel1M 822080 GCTTGGAGAGACTTATATGAACTGATGCTAAGTGAAATGAGCAGAA 822125 i v i ivv - vv i i vi L1ME4c_3end#L 595 ACATGGAAAATGTT-TATGATATAATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.73 CpG sites = 22, Kimura (unadjusted) = 40.91 Transitions / transversions = 1.00 (22/22) Gap_init rate = 0.01 (2 / 142), avg. gap size = 2.00 (4 / 2) 12 5.48 0.00 0.00 chr5qtel1M 823938 823956 (176044) (GTG)n#Simple_repeat 1 19 (0) m_b266s252i1 10541 chr5qtel1M 823938 GTGGTGGTGGTGGTGGGGG 823956 v (GTG)n#Simple 1 GTGGTGGTGGTGGTGGTGG 19 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 264 20.65 11.24 2.06 chr5qtel1M 825895 825983 (174017) C MIR3#SINE/MIR (28) 180 84 m_b266s601i4 10542 chr5qtel1M 825895 TAGAAAGTCCCTTCAGAATTCA-AGAATCCAACTCCCTTCAATTTCCAGA 825943 i i vv - iv -vv i i - v v C MIR3#SINE/MIR 180 TGGAAGGGACCTT-AGAGATCATCTAGTCCAACCCCCT-CATTTTACAGA 133 chr5qtel1M 825944 --AGGAAAC--AAGCACAGAGA-----AGCGATTTGTTCAAGGTCACAC 825983 -- -- i v ----- i i ii C MIR3#SINE/MIR 132 TGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACAC 84 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 24.50 CpG sites = 10, Kimura (unadjusted) = 24.50 Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.07 (6 / 88), avg. gap size = 2.00 (12 / 6) 36 5.27 0.00 0.00 chr5qtel1M 826219 826258 (173742) (TA)n#Simple_repeat 1 40 (0) c_b266s251i0 10543 chr5qtel1M 826219 TATATATATATATATATATATATATATATACATACATATA 826258 i i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATA 40 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 17 0.00 0.00 0.00 chr5qtel1M 826259 826277 (173723) (CA)n#Simple_repeat 1 19 (0) m_b266s252i2 10544 chr5qtel1M 826259 CACACACACACACACACAC 826277 (CA)n#Simple_ 1 CACACACACACACACACAC 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 15 13.87 0.00 0.00 chr5qtel1M 826278 826301 (173699) (T)n#Simple_repeat 1 24 (0) m_b266s252i3 10545 chr5qtel1M 826278 TTTTTTTTAGGTTTTTTTTTTTTT 826301 vvv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTT 24 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 1074 29.24 3.10 4.61 chr5qtel1M 826723 827206 (172794) C L1ME5_3end#LINE/L1 (274) 667 191 m_b266s551i1 10546 chr5qtel1M 826723 ATAGTATTGTTGTTGAAGTATATAATAATCTC---CTGGTTCT-GCTCAT 826768 i ------- - ?-- --- v -i iv C L1ME5_3end#LI 667 ATGGTATTGT-------GT-TATAN--ATCTCATTCTGTTTCTTACTTTT 628 chr5qtel1M 826769 TTCACTCAACTTCA-GTTGGTTTAAG-TCTCTCTAGG--GCTTTCTGAAA 826814 i vii - -- - iv i v -- v v v - C L1ME5_3end#LI 627 TTCACTCAGCACTATGTT--TTTAAGATCCATCCATGTTGCTATGTGTA- 581 chr5qtel1M 826815 TTATCTTGCTGGTCATTTCTTACAGAAAAATAACATTCCATAATATTCAA 826864 -i v iiv iii v v vviv ii i ii i v v C L1ME5_3end#LI 580 -CATCTAGTCCGTTGCTTCTAACTGCTGCATAGTACTCCATGGTGTGCAT 532 chr5qtel1M 826865 ATACCACAATTTATTCAGCCATTCTCCAACTGATGGGCATCCACTCAGTT 826914 vi v iii v i v v i i vviv ii C L1ME5_3end#LI 531 CCACCACATTTTACCTATCCACTCTCCCAGTGATGGACACCCAGGTTGCC 482 chr5qtel1M 826915 TCCAGTTTCTGGCCACTACAAACAGGGTTGCCACATACATTTTTGCACAT 826964 ii i iv i iv i v iiv ii i i C L1ME5_3end#LI 481 TCCAACTCCCCGCCACCACAAACAACGCTGCAATGAACATCCTCGTACAT 432 chr5qtel1M 826965 ACAGGTCCCTTTCC---CTTCTTTAAGA-TCTCTTTGGGATATAAGCCCA 827010 ---- i vi--- i v v i - i vi C L1ME5_3end#LI 431 ----GTCCCCTTATGGACCTGTGTGAGAATTTCTTTGGGATATATACCCA 386 chr5qtel1M 827011 GTAGTAACACTGCTGGATCAAAGGGTATGCAGTTTGATAATTT-TTTGAC 827059 v iiiv i i v - --- v v- C L1ME5_3end#LI 385 GGAGCGGAATTGCTGGGTCATAGGGTATGC-GT---ATACTTAATTTGAC 340 chr5qtel1M 827060 CA--TATTTCCAAATTGTTCTCCAGAATGGTTGGATGTATTCACAATTCC 827107 i -- i v i i i v ivvi ii v i C L1ME5_3end#LI 339 TAAGTACTGCCAGATTGCTCTCCAGAATGGCTGCACCAGTCTACACTCCC 290 chr5qtel1M 827108 ACCCACAATGTATGAGTGTCCCAGTTTTCCCACATCCCCTCCAACATTCC 827157 vi i i v i vi ? i i v i iv C L1ME5_3end#LI 289 ACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATCCTCGCCAACACTTG 240 chr5qtel1M 827158 GCATTATCCTTCCCTGTCATTCTAGCCAATCTAACAGGTGTGTAGTGGT 827206 vv ii v v i v i i iv i C L1ME5_3end#LI 239 GCATTATCCAGCTTTCTAATTTTTGCCAGTCTAATAGGTGTAAAGTGAT 191 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.62 CpG sites = 81, Kimura (unadjusted) = 38.39 Transitions / transversions = 1.50 (81/54) Gap_init rate = 0.06 (31 / 483), avg. gap size = 1.19 (37 / 31) 12 11.51 3.33 3.33 chr5qtel1M 829288 829317 (170683) (AATTA)n#Simple_repeat 1 30 (0) m_b266s252i4 10547 chr5qtel1M 829288 AATTAAATTAGA-GAAATGAAACTTAAATTA 829317 i -v v - (AATTA)n#Simp 1 AATTAAATTAAATTAAATTAAA-TTAAATTA 30 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.07 (2 / 29), avg. gap size = 1.00 (2 / 2) 228 17.15 0.00 8.51 chr5qtel1M 829367 829417 (170583) L2a_3end#LINE/L2 383 429 (88) m_b266s601i5 10548 chr5qtel1M 829367 GTCTTTCCTCAAGGGAATGTAAGCTCCTTGGGGGCAGGGCCTGACTTTTG 829416 ii i vvi v i ---- L2a_3end#LINE 383 GTCTCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGG----GACTTTTG 428 chr5qtel1M 829417 T 829417 L2a_3end#LINE 429 T 429 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 19.60 CpG sites = 5, Kimura (unadjusted) = 19.60 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.08 (4 / 50), avg. gap size = 1.00 (4 / 4) 420 26.59 0.00 9.09 chr5qtel1M 830194 830313 (169687) C MIRc#SINE/MIR (155) 113 4 m_b266s601i6 10549 chr5qtel1M 830194 GGTTAAGTGACTTACACAGAGTCACACAGCTAGGAAGTGTTGAGTGTCTG 830243 i v ii ------- i v v C MIRc#SINE/MIR 113 GGTTAAGTGACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGCAG 71 chr5qtel1M 830244 AGGCCAGATTTTAACTCAAGTTCTCCTGAGTTCAGGGCTGGCCCTCTCTC 830293 v vi i iv i i ii v i i v ii iv i C MIRc#SINE/MIR 70 AGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTC 21 chr5qtel1M 830294 TACTGCATCACCTAGCTGCC 830313 i i ---i C MIRc#SINE/MIR 20 CACTGCACCAC---ACTGCC 4 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.49 CpG sites = 20, Kimura (unadjusted) = 33.95 Transitions / transversions = 2.22 (20/9) Gap_init rate = 0.08 (10 / 119), avg. gap size = 1.00 (10 / 10) 243 24.99 5.33 3.95 chr5qtel1M 830416 830490 (169510) MIRb#SINE/MIR 78 153 (115) m_b266s601i7 10550 chr5qtel1M 830416 CACTTAATGGCTGTGTGACCCTGGGCAAACTCCTGGACACCT----GTCT 830461 v i i ii v vi vi ---- i MIRb#SINE/MIR 78 CACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCT 127 chr5qtel1M 830462 CACTGTTCTCAGCTTATGTAAACTGAAGA 830490 v v i v --- v ii MIRb#SINE/MIR 128 CAGTTTCCTCATC---TGTAAAATGGGGA 153 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.91 CpG sites = 10, Kimura (unadjusted) = 30.91 Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.05 (4 / 74), avg. gap size = 1.75 (7 / 4) 317 31.21 0.00 6.80 chr5qtel1M 831759 831868 (168132) C MIRc#SINE/MIR (155) 113 11 m_b266s601i8 10551 chr5qtel1M 831759 GGTGAGGTAGCTAGGTCTAAGTGTCACAGCTAGCAAGGGTTAAGTGTCTG 831808 v i ii v vi v i vv ------- v v C MIRc#SINE/MIR 113 GGTTAAGTGACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGCAG 71 chr5qtel1M 831809 AGACCAGATTTGAACTCAGGTCTTCCTGATTTCAGGGCTGGTGTTCAGTT 831858 v vi i i i i i i v ii i vv i C MIRc#SINE/MIR 70 AGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTC 21 chr5qtel1M 831859 CACCTTACCA 831868 ivi C MIRc#SINE/MIR 20 CACTGCACCA 11 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.48 CpG sites = 18, Kimura (unadjusted) = 41.15 Transitions / transversions = 1.29 (18/14) Gap_init rate = 0.06 (7 / 109), avg. gap size = 1.00 (7 / 7) 16 0.00 0.00 0.00 chr5qtel1M 832571 832587 (167413) (A)n#Simple_repeat 1 17 (0) m_b266s252i5 10552 chr5qtel1M 832571 AAAAAAAAAAAAAAAAA 832587 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 22 15.32 0.00 0.00 chr5qtel1M 835776 835812 (164188) (G)n#Simple_repeat 1 37 (0) m_b266s252i6 10553 chr5qtel1M 835776 GGGGGGGAGGGGGGACGGGGGGGAGGGGGGGAGGGGG 835812 i iv i i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 37 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 18 12.55 2.04 6.38 chr5qtel1M 837131 837179 (162821) (ACACAT)n#Simple_repeat 1 47 (0) m_b266s252i7 10554 chr5qtel1M 837131 ACATATAAATCATACACATACACATATACATAACAGATCAAACATA-ACA 837179 i v - i - v - v - (ACACAT)n#Sim 1 ACACATACA-CATACACATACACATACACAT-ACACAT-ACACATACACA 47 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.08 (4 / 48), avg. gap size = 1.00 (4 / 4) 14 4.49 0.00 4.17 chr5qtel1M 838911 838935 (161065) (CAAA)n#Simple_repeat 1 24 (0) m_b266s252i8 10555 chr5qtel1M 838911 CAACCAAACCAAACAAACAAACAAA 838935 v - (CAAA)n#Simpl 1 CAAACAAA-CAAACAAACAAACAAA 24 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 260 24.56 0.00 0.00 chr5qtel1M 842383 842439 (157561) C HERVK14#LTR/ERVK (989) 5107 5051 m_b266s701i0 10556 chr5qtel1M 842383 GGAATCCACACAGGTGTGTGGCTGTCCTGTGGAAAGACACAAGCATATCC 842432 v i iiiv ii viv i v C HERVK14#LTR/E 5107 GGCACCCACACAGGCACCTGATTGTCACCTGGAGAGACACAAGCAAATCC 5058 chr5qtel1M 842433 TCTGCCC 842439 v C HERVK14#LTR/E 5057 TCTTCCC 5051 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 30.29 CpG sites = 8, Kimura (unadjusted) = 30.29 Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0) 618 30.30 6.12 2.82 chr5qtel1M 843330 843672 (156328) C HERVK#LTR/ERVK (2361) 5175 4822 m_b266s701i1 10557 chr5qtel1M 843330 TTGAACCTTAAGCATTTGATTAGTTCTTTCTACTATGGCTTGTCCTTGAG 843379 i i i ii iv v i i C HERVK#LTR/ERV 5175 TTGAGCTTTGAGTGTTCTATTAGTTCTTTCAACTATGGCCTGTCCTTGGG 5126 chr5qtel1M 843380 GGTTATAGGGAATGCCAATATTATGTG-AATTATGGA---ATTTAGAGCA 843425 ii i v vi vv - v vv --- ---- C HERVK#LTR/ERV 5125 AATTATAAGGAATTCCTGTTGTATGTGTAATTTTCCACTGATTTA----A 5080 chr5qtel1M 843426 AAAATCAGAAAAGGCTTTAGAAGTATATGCAGGCCCATTATCTGTTTTGA 843475 i v ivvii ? vv vvi v v i v i C HERVK#LTR/ERV 5079 GAATTTTTGGAANGCTTTACTACAGTATCCTGGCCCATTGTCAGTTTTAA 5030 chr5qtel1M 843476 TACCTTTTGGCATTCCCATAATAGAAAAGCAAAGAAATAAATG--TTGCA 843523 vii i v i i i v i iiv -- vi C HERVK#LTR/ERV 5029 TTTTTTCTGGAACTCCCATGACAGCAAAACAAGATAATAAATGTTTTTTA 4980 chr5qtel1M 843524 ACACATCTTTAAAGGG--TTCACTGGTCCTTGGGGAGGCGACAATAT--A 843569 ---- vvi vi-- v iv -- vii vi v v -- C HERVK#LTR/ERV 4979 ACA----TGGGAAGTACTTTCTCCTGTC--TGGCAGGTTGCCCATATGAA 4936 chr5qtel1M 843570 GTGGGAGAATGTGTCCACAGTACCACG--TAAATAA---------GAACG 843608 i v iv v i v v vv i --i ? i ---------i i C HERVK#LTR/ERV 4935 ATGTGAATAAGTATCAACTGTTACATGGACANATGACAATCTTCCAAATG 4886 chr5qtel1M 843609 ATGAGATATGTGTAACGTCCAATTGCCAGAGATCATTAGCTCTTAGACCT 843658 v iv i i i i v v ivv vv vi C HERVK#LTR/ERV 4885 AAGGTACATGCGTGACATCCATTTGCCATAACGCATTAGGACACAGACCT 4836 chr5qtel1M 843659 TTGGGATTTACTCC 843672 i v C HERVK#LTR/ERV 4835 CTGGGATTAACTCC 4822 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.23 CpG sites = 51, Kimura (unadjusted) = 39.73 Transitions / transversions = 1.02 (51/50) Gap_init rate = 0.05 (17 / 342), avg. gap size = 1.82 (31 / 17) 366 23.38 0.00 0.00 chr5qtel1M 844927 845003 (154997) C HERVK#LTR/ERVK (2361) 5175 5099 m_b266s701i2 10558 chr5qtel1M 844927 TTGAACCTTAAGCATTTGATTAGTTCTTTCTACTATGGCTTGTCCTTGAG 844976 i i i ii iv v i i C HERVK#LTR/ERV 5175 TTGAGCTTTGAGTGTTCTATTAGTTCTTTCAACTATGGCCTGTCCTTGGG 5126 chr5qtel1M 844977 GGTTATAGGGAATGCCAATATTATGTG 845003 ii i v vi vv C HERVK#LTR/ERV 5125 AATTATAAGGAATTCCTGTTGTATGTG 5099 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 28.92 CpG sites = 12, Kimura (unadjusted) = 28.92 Transitions / transversions = 2.00 (12/6) Gap_init rate = 0.00 (0 / 76), avg. gap size = 0.0 (0 / 0) 17 8.85 0.00 0.00 chr5qtel1M 848980 849003 (150997) (AG)n#Simple_repeat 1 24 (0) m_b266s252i10 10559 chr5qtel1M 848980 AGAGAGAGAGACAGAAAGAGAGAG 849003 v i (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAG 24 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 18 7.52 3.57 0.00 chr5qtel1M 849346 849373 (150627) (AT)n#Simple_repeat 1 29 (0) m_b266s252i11 10560 chr5qtel1M 849346 ATATAGACATATATATATATATATA-ATA 849373 v i - (AT)n#Simple_ 1 ATATATATATATATATATATATATATATA 29 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 15 0.00 0.00 0.00 chr5qtel1M 850101 850117 (149883) (AT)n#Simple_repeat 1 17 (0) m_b266s252i12 10561 chr5qtel1M 850101 ATATATATATATATATA 850117 (AT)n#Simple_ 1 ATATATATATATATATA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 12 16.27 6.98 2.22 chr5qtel1M 850247 850289 (149711) (GAAGCA)n#Simple_repeat 1 45 (0) m_b266s252i13 10562 chr5qtel1M 850247 GAGGCTGAAG-A-AAGCAGAAGCAGGAGCA-AAGGACAAAGCTGAA 850289 i v - - i - v -i v (GAAGCA)n#Sim 1 GAAGCAGAAGCAGAAGCAGAAGCAGAAGCAGAAGCA-GAAGCAGAA 45 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.10 (4 / 42), avg. gap size = 1.00 (4 / 4) 12 11.68 10.81 0.00 chr5qtel1M 850255 850291 (149709) (AGAAAGC)n#Simple_repeat 1 41 (0) m_b266s252i14 10562 chr5qtel1M 850255 AGAAAGCAG-AAGCAG-GAGC--AAAGGACAAAGCTGAAAG 850291 - -i -- v v v (AGAAAGC)n#Si 1 AGAAAGCAGAAAGCAGAAAGCAGAAAGCAGAAAGCAGAAAG 41 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.08 (3 / 36), avg. gap size = 1.33 (4 / 3) 1376 29.57 2.38 2.76 chr5qtel1M 850548 851093 (148907) C L1ME4c_3end#LINE/L1 (275) 555 12 m_b266s551i2 10563 chr5qtel1M 850548 ATAATATTCCATAACATTCATATACCACAATTTACCCAACCATTCTCCAG 850597 vivi ?v i i ii i vi C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chr5qtel1M 850598 TTGATGGGCATCCAT-TCATTTTAAAGTTTCTAGCCACTATGAGCAGGGC 850646 v i ii v- ii iv - i v i i i ii iv C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAA-TTTTTCGCTATTATAAATAACGC 457 chr5qtel1M 850647 TGCCACAAACATTTTGGCCCATACAGGTCCCTTTCCCTTCTTT---AGTA 850693 v ii i v iv i --- i i --- v C L1ME4c_3end#L 456 TGCAATGAACATCTTCGTGCATATAG---CTTTTTCCTTCTTTTGAATTA 410 chr5qtel1M 850694 TCTCTTTGGGGTTTATAAG--CCCAGTAGTAGTACTGCTGGATCAAAGTG 850741 i i i ---- i-- v i v i i i v C L1ME4c_3end#L 409 TTTCCTTAGG----ATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGG 364 chr5qtel1M 850742 AATGCACAGTTTGATAATTTTTTGGGCATAATTCCAGATTGCTCTCCAGA 850791 v v v v iii i vivi i v v i i i C L1ME4c_3end#L 363 TATGAACATTTTTATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAA 314 chr5qtel1M 850792 ATGGTTGGATTCGTTCACAACTTCACCAACAATGCATCAACATCCTGGTT 850841 v v iivi i ?ivi i i v i?i v ii C L1ME4c_3end#L 313 AGGGTTGTACCAATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTT 264 chr5qtel1M 850842 TTCCTGCATCCCCTCCAACATT---CATCATTATTTTTTCCTGTCATCTT 850888 iv i ? i v i ---i i i v iv---v i C L1ME4c_3end#L 263 TCACCGCANCCTCGCCAGCATTGGGTATTATCAATTTTTTA---AATTTT 217 chr5qtel1M 850889 AGCCAATCTGACAGGTGTGTAGTGGTATCTTAGAGTTGTCTTAATTTGTG 850938 v i i i i i iv i i vv ii ii C L1ME4c_3end#L 216 TGCTAATTTAATAGGCGTAAAATGGTATCTCATTGTTGCTTTAATTTGCA 167 chr5qtel1M 850939 TTTCTCTGATCAATAGTGATTTGGAACACTCTTTCATATGAGTGGAAATA 850988 i i v i vv v i i i i vv vvv iv C L1ME4c_3end#L 166 TTTCTTTGATTACTAGCGAGGTTGAACATTTTTCCATGTGTTTGTTTACT 117 chr5qtel1M 850989 GTTTCAATTTCATCATCTGAAAATAGTCTGTTCATATCCTTTGACCATTT 851038 i? vv v v ? vi v i v C L1ME4c_3end#L 116 ANTTGTATTTCCTCTTNTGTGAATTGTCTGTTCATGTCCTTTGCCCATTT 67 chr5qtel1M 851039 ATCAATTGGAGAACGGCCTGA----TTTCTTATAAATTAGAGTCAATTCT 851084 v i---- v i ---- v v i v ii C L1ME4c_3end#L 66 ATCTATTGGG----GTCTTGATNTTTTTCTTATCAATTTGAATGAGCTCT 21 chr5qtel1M 851085 CTATATATT 851093 i ? C L1ME4c_3end#L 20 TTATATANT 12 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.96 CpG sites = 96, Kimura (unadjusted) = 39.59 Transitions / transversions = 1.57 (96/61) Gap_init rate = 0.04 (20 / 545), avg. gap size = 1.40 (28 / 20) 447 31.22 5.07 5.24 chr5qtel1M 850955 851566 (148434) C L1M5_orf2#LINE/L1 (0) 3294 2684 m_b266s551i3 10563 chr5qtel1M 850955 TGATTTGGAACACTCTTTCATATG---AGTGGAAATAGTTTCAATTTCAT 851001 ?v v i iii i --- v vv --- v? v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCAT---TTGNATATCTT 3248 chr5qtel1M 851002 CATCTGAAAATAGTCTGTTCATATCCTTTGACCATTTATCAATTGGA--G 851049 v i vi vv vi i v v ?v i-- C L1M5_orf2#LIN 3247 CTTTTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTG 3198 chr5qtel1M 851050 AACGGCCTGATTTCTTA-TAAATTAGAGTCAATTCTCTATATATTTTGGA 851098 vvi v i -- ? - i ? iv -v i i i C L1M5_orf2#LIN 3197 TTTGTCTT--TTTNTTATTGANTTGTAG-GAGTTCTTTATATATTCTGGA 3151 chr5qtel1M 851099 AATGAGGCCTTTATGAAGAACCTTTAACCATGAAAATATTT--TCCCAGT 851146 v i v i v iiv iv v ---?v v -- ? C L1M5_orf2#LIN 3150 TACGAGTCCTTTGTCAGATATATGT---NTTGCAAATATTTTCTCCCANT 3104 chr5qtel1M 851147 TTGTTGTTTCCCCTCTAATCTTGTTTGCGTTAGTTTTGTTTGTACAAAGG 851196 i v i v i i v i v vi v ivi vvv? vi i i C L1M5_orf2#LIN 3103 CTGTGGCTTGCCTTTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAG 3054 chr5qtel1M 851197 CTTTTTAATTTGATATAATCAA-------AATTTTCTATTTTGTGATCAA 851239 i v v i? i v ------- i v i i --- C L1M5_orf2#LIN 3053 TTTTTAATTTTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGGT--- 3007 chr5qtel1M 851240 TAATGATCTCTAGTTCATCTTTGGTCACAAATTTCTTCCTCCTCCACAAG 851289 ?i v i i ivv v v i--- v i i v v?i - i C L1M5_orf2#LIN 3006 TNGTGCTTTTTGTGTCCTGTTTA---AGAAATCTTTGCCTANCCCA-AGG 2961 chr5qtel1M 851290 TCTGAGAGGTAAACTGCCCTATG--TTCCTCT--AATTTATTTATAATCT 851335 vvii i vv -- -- i -- v -- i i C L1M5_orf2#LIN 2960 TCACGAAGATATTCT--CCTATGTTTTCTTCTAGAAGT--TTTATAGTTT 2915 chr5qtel1M 851336 TATTCTTTATGCCTAAATC-ATGGACCTATTTAGATTTTATCTTGATATA 851384 ?ii iiii ii - - i i i ? v v i vi i C L1M5_orf2#LIN 2914 TANCTTTTACATTTAGGTCTAT-GATCCATCTNGAATTAATTTTTGTGTA 2866 chr5qtel1M 851385 CGGTGTTAAGTGTGGGTCCATGCCTAGTTTCTGCCATGCTAATTTCCAGT 851434 i v i iv v v?iii v i v iivi v i C L1M5_orf2#LIN 2865 TGGTGTGAGGTAGGGGTCGAGNTTCATTTTTTTCCATATGGATATCCAAT 2816 chr5qtel1M 851435 TTTCCCAGCAGTTTTTGTCAATTAATGA--ATTCTTATCCCA--AAACTT 851480 v i viv ii -- v -- i vi --i - C L1M5_orf2#LIN 2815 TGTTCCAGCACCATTTGTTGA--AAAGACTATCCTTTCCCCACTGAA-TT 2769 chr5qtel1M 851481 GGGATCTTTGG---GTTTGTCAAACACTAGATTGCTATAGTTG-ACAATT 851526 ---- ? ---v v ii i? v? i vv -iiiiv C L1M5_orf2#LIN 2768 G----CNTTGGCACCTTTGTCAAAAATCAANTGNCCATATATGTGTGGGT 2723 chr5qtel1M 851527 TTGTCTTGTGAAC---CTAACCTATTCCACTGATCAACTATTT 851566 i i - v i --- vi i i --- C L1M5_orf2#LIN 2722 CTAT-TTCTGGACTCTCTATTCTGTTCCATTGAT---CTATTT 2684 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 42.42 CpG sites = 100, Kimura (unadjusted) = 43.05 Transitions / transversions = 1.23 (100/81) Gap_init rate = 0.07 (45 / 611), avg. gap size = 1.40 (63 / 45) 526 33.07 3.98 4.18 chr5qtel1M 850994 851520 (148480) C L1P3_orf2#LINE/L1 (39) 3255 2730 m_b266s551i4 10563 chr5qtel1M 850994 AATTTCATCATCTGAAAATAGTCTGTTCATATCCTTTGACCATTTATCAA 851043 v v v i i vv i v i v ii C L1P3_orf2#LIN 3255 AATGTCTTCTTTTGAGAAGTGTCTGTTCATATCCTTCGCCCACTTTTTGA 3206 chr5qtel1M 851044 TTGGAGAACGGCCTGATTT---CTTATAAATTAGAGTCAATTCTCTATAT 851090 - i --iv ii v --- i v vv v i ii i v C L1P3_orf2#LIN 3205 T-GGGG--TTGTTTGTTTTTTTCTTGTAAATTTGTTTAAGTTCCTTGTAG 3159 chr5qtel1M 851091 ATTTTGGAAATGAGGCCTTTAT--GAAGAACCTTTAACCATGAAAATATT 851138 i v v v i -- v i --- vi iiiii v C L1P3_orf2#LIN 3158 ATTCTGGATATTAGCCCTTTGTCAGATGGA---TAGATTGCAAAAATTTT 3112 chr5qtel1M 851139 TTCCCAGTTTGTTGTTTCCCCTCTAATCTTGTTTGCGTTAGTTTTGTTTG 851188 i v i v v v ivi v iii v --- v iv C L1P3_orf2#LIN 3111 CTCCCATTCTGTAGGTTGCCTGTTCACTCTGAT---GATAGTTTCTTTTG 3065 chr5qtel1M 851189 ---TACAAAGGCTTTTTAATTTGATATAATCAAAATTTTCTATTTTG--- 851232 --- i i i i i i vvi vv v v v --- C L1P3_orf2#LIN 3064 CTGTGCAGAAGCTCTTTAGTTTAATTAGATCCCATTTGTCAATTTTGGCT 3015 chr5qtel1M 851233 -TGATCAATAATGATCTCTAGTTCATCTTTGGTCACAAATTTCTTCCTCC 851281 - vi iivi v v i - i --i - i ii v ii v i v C L1P3_orf2#LIN 3014 TTTGTTGCCATTGCTTT-TGGT--GT-TTTAGTCATGAAGTCTTTGCCCA 2969 chr5qtel1M 851282 TCCACAAGTC-TGAGAGGTAAACTGCCCTATGTT--CCTCTAATTTATTT 851328 v vi v - iv --i - v -- i ivv v C L1P3_orf2#LIN 2968 TGCCTATGTCCTGAATGGTA--TTGCC-TAGGTTTTCTTCTAGGGTTTTT 2922 chr5qtel1M 851329 ATAATCTTATTCTTTATGCCTAAATCATGGACCTATTTAGATTTTATCTT 851378 ii i vvii i ii i v vi i i i v v v i C L1P3_orf2#LIN 2921 ATGGTTTTAGGTCTTACGTTTAAGTCTTTAATCCATCTTGAGTTAATTTT 2872 chr5qtel1M 851379 GATATACGGTGTTAAGTGTGGGTCCATGCCTAGTTT-CTGC-CATG-CTA 851425 vi v v i viv vviii - -i - C L1P3_orf2#LIN 2871 TGTATAAGGTGTAAGGAAGGGGTCCAGTTTCAGTTTTCTGCATATGGCTA 2822 chr5qtel1M 851426 ATTTCCAGTTTTCCCAGCAGTTTTTGTCAATTAATGAATTCTTATCCCAA 851475 i--- i viv i i v iv i vi v C L1P3_orf2#LIN 2821 G---CCAGTTTTCCCAACACCATTTATTAAATAGGGAATCCTTTCCCCAT 2775 chr5qtel1M 851476 AACTTGGGATCTTTG---GGTTTGTCAAACACTAGATTGCTATAGTTG 851520 vi --- i --- v ii v i i v C L1P3_orf2#LIN 2774 TGCTTG---TTTTTGTCAGGTTTGTCAAAGATCAGATGGTTGTAGATG 2730 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 44.05 CpG sites = 92, Kimura (unadjusted) = 44.77 Transitions / transversions = 1.23 (92/75) Gap_init rate = 0.06 (32 / 526), avg. gap size = 1.34 (43 / 32) 338 24.74 6.19 0.00 chr5qtel1M 854315 854411 (145589) C L2a_3end#LINE/L2 (8) 509 407 m_b267s601i0 10564 chr5qtel1M 854315 ATTCAACACTTATT-ATTGAGTGCCTACTCTATACCAGACATTATGATAA 854363 vv - i v i i i i i vv i C L2a_3end#LINE 509 ATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAG 460 chr5qtel1M 854364 GGGCTGGATATACAA-AATCA--AAAACAA--AACAGTCCCTGCCGTTGA 854408 v iv i- i v -- i-- v v iiv C L2a_3end#LINE 459 GCGCTGGGGATACAGCAGTGAACAAAACAGACAAAAGTCCCTGCCCTCAT 410 chr5qtel1M 854409 GGA 854411 C L2a_3end#LINE 409 GGA 407 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.97 CpG sites = 13, Kimura (unadjusted) = 30.45 Transitions / transversions = 1.18 (13/11) Gap_init rate = 0.04 (4 / 96), avg. gap size = 1.50 (6 / 4) 14 12.16 0.00 0.00 chr5qtel1M 854952 854978 (145022) (CATGC)n#Simple_repeat 1 27 (0) m_b267s252i2 10565 chr5qtel1M 854952 CATGCCAGGCTATGCCATGCTATGCCA 854978 v i i (CATGC)n#Simp 1 CATGCCATGCCATGCCATGCCATGCCA 27 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 302 35.91 1.27 6.00 chr5qtel1M 856078 856234 (143766) MamSINE1#SINE/tRNA-RTE 27 176 (114) m_b267s601i1 10566 chr5qtel1M 856078 TAGAGCATAATTCTATCGAGGCCAAGATTATAGGTTCAAAGTCTTTGCAA 856127 iii v vi i i ii i vvi iv iii MamSINE1#SINE 27 TAGAGCACGGTGCTAATGAGGCCAAGGTCACGGGTTCGATCCCCGTGTGG 76 chr5qtel1M 856128 GCCATTTAGTTTTCATCAGAAAAATGGAATCCTTAG-CCACTCCTACCTA 856176 v i vv v vvvv --- vi - ii v -- MamSINE1#SINE 77 GCCAGTTAGCTTTGCTCTGTTCCATGG---CCACAGACTGCACC--CCTA 121 chr5qtel1M 856177 ACACCAGTCAGATAATCTTAT-TTTGTGTGTCCTAGGTAGCCACAAAAGA 856225 v i -ivi iii-vv i i v v --- ii i MamSINE1#SINE 122 ACCCCAGCCAG-CCGTCTCGCAAATGCGTGCCGTTGGT---CACAAGGGG 167 chr5qtel1M 856226 GCCTGACAG 856234 v i i MamSINE1#SINE 168 GACCGGCAG 176 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.21 CpG sites = 31, Kimura (unadjusted) = 50.74 Transitions / transversions = 1.41 (31/22) Gap_init rate = 0.07 (11 / 156), avg. gap size = 1.00 (11 / 11) 18 12.17 0.00 0.00 chr5qtel1M 857530 857556 (142444) (T)n#Simple_repeat 1 27 (0) m_b267s252i3 10567 chr5qtel1M 857530 TTTTTTTTTTTTTGTTTGTTTGTTTTT 857556 v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTT 27 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 13 4.76 0.00 4.35 chr5qtel1M 859372 859395 (140605) (CCCT)n#Simple_repeat 1 23 (0) m_b267s252i4 10568 chr5qtel1M 859372 CCCTCCCTCCCTCCACCCCCTCCC 859395 - i (CCCT)n#Simpl 1 CCCTCCCTCCCTCC-CTCCCTCCC 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 584 17.55 3.10 7.26 chr5qtel1M 859901 860029 (139971) C MIRc#SINE/MIR (142) 126 3 m_b267s601i2 10569 chr5qtel1M 859901 TGAGGCAATTAG---GGTTAAGTGACTTGCCCAGGGTCACACAGCTAGGA 859947 -- i --- i v C MIRc#SINE/MIR 126 TGAGGC--TCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTA 79 chr5qtel1M 859948 AGTGTTAAGTTTCTGAGCCCAGATTTGAACTCAAGTTCTCCTGACTTCAA 859997 vi ------- vi i i i i ii i C MIRc#SINE/MIR 78 AGTGGCA-------GAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAA 36 chr5qtel1M 859998 GGCTTGTCCTCTATCCATTGCACCAC-CTACCT 860029 v iv v v i - i C MIRc#SINE/MIR 35 GTCCAGTGCTCTTTCCACTGCACCACACTGCCT 3 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 19.30 CpG sites = 14, Kimura (unadjusted) = 20.34 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.09 (11 / 128), avg. gap size = 1.18 (13 / 11) 17 26.94 1.82 0.00 chr5qtel1M 862149 862203 (137797) (TATGTA)n#Simple_repeat 1 56 (0) m_b267s252i5 10570 chr5qtel1M 862149 TATGTGTGTGTGTGTGTACAGGTATATCCACAAG-ATATGTACATGTGTA 862197 i i i i i v vi i v - i i (TATGTA)n#Sim 1 TATGTATATGTATATGTATATGTATATGTATATGTATATGTATATGTATA 50 chr5qtel1M 862198 TGTATA 862203 (TATGTA)n#Sim 51 TGTATA 56 Matrix = Unknown Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1) 18 15.40 0.00 0.00 chr5qtel1M 862663 862698 (137302) (TGCTGGA)n#Simple_repeat 1 36 (0) m_b267s252i6 10571 chr5qtel1M 862663 TGCTGGAGGCTGTATGCTAGATGCAGCATGCTGGAT 862698 v v i v v (TGCTGGA)n#Si 1 TGCTGGATGCTGGATGCTGGATGCTGGATGCTGGAT 36 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 13 23.23 0.00 8.00 chr5qtel1M 863787 863840 (136160) (CCCTT)n#Simple_repeat 1 50 (0) m_b267s252i7 10572 chr5qtel1M 863787 CCCATCCCTTCCCTCTCTTTCTCCTCTTCTTGTCCTTCCTTTCCCTGTCC 863836 v ii i - - i i vi i - (CCCTT)n#Simp 1 CCCTTCCCTTCCCTTCCCTTC-CCT-TCCCTTCCCTTCCCTTCCCT-TCC 47 chr5qtel1M 863837 TCTT 863840 - (CCCTT)n#Simp 48 -CTT 50 Matrix = Unknown Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.08 (4 / 53), avg. gap size = 1.00 (4 / 4) 488 22.01 1.64 6.90 chr5qtel1M 864786 864907 (135093) C MIRc#SINE/MIR (140) 128 13 m_b267s601i3 10573 chr5qtel1M 864786 ACTGAG--TCAATTGGGGTTAAGTGAGTTGGCCAGAGTCACACAGCTAGG 864833 -- iv- i v v ii - C MIRc#SINE/MIR 128 ACTGAGGCTCAGA-GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG- 81 chr5qtel1M 864834 CAGTGCTAAGTGTCAGAGGCCAGATTTGAACCCAGGGCCTCCTAACTTCA 864883 ------ v v vi i i v i i i C MIRc#SINE/MIR 80 ------TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCA 37 chr5qtel1M 864884 ATGCTGATGCTCTATCTACTGTAC 864907 vv iii v i i C MIRc#SINE/MIR 36 AGTCCAGTGCTCTTTCCACTGCAC 13 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.23 CpG sites = 15, Kimura (unadjusted) = 26.43 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.07 (9 / 121), avg. gap size = 1.11 (10 / 9) 229 29.70 2.91 1.92 chr5qtel1M 864923 865025 (134975) L1ME3C_3end#LINE/L1 446 549 (321) m_b267s551i2 10574 chr5qtel1M 864923 TTGCATCAGTCTTTATGGTGGTTAAGAACTGGAAATTCAG---GGATGCT 864969 v v v i ii i iv i i -- i---ii ii L1ME3C_3end#L 446 TTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAA--CAACCTAAATGTC 493 chr5qtel1M 864970 CATCAAATGGAAAATGAGTGAACAAATTGTGGTATGTGCTTGTGATGGCA 865019 vv i ii i i i v v iii v L1ME3C_3end#L 494 CATCAACAGGAGAATGGATAAATAAATTGTGGTATATTCATACAATGGAA 543 chr5qtel1M 865020 TACTAT 865025 L1ME3C_3end#L 544 TACTAT 549 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.29 CpG sites = 21, Kimura (unadjusted) = 40.06 Transitions / transversions = 2.33 (21/9) Gap_init rate = 0.03 (3 / 102), avg. gap size = 1.67 (5 / 3) 254 28.57 3.23 2.13 chr5qtel1M 864934 865026 (134974) L1ME2z_3end#LINE/L1 460 553 (638) m_b267s551i3 10574 chr5qtel1M 864934 TTTATGGTGGTTAAGAACTGGAAAT---TCAGGGATGCTCATCAAATGGA 864980 i ii i ii i i---i -- ii vv L1ME2z_3end#L 460 TTCATAATAGCCAAAAACTGGAAACAGCCCAGG--TGTCCATCAACAGGA 507 chr5qtel1M 864981 AAATGAGTGAACAAATTGTGGTATGTGCTTGTGATGGCATACTATT 865026 i ii i i i v v iii v i L1ME2z_3end#L 508 GAATGGATAAACAAACTGTGGTATATTCATACAATGGAATACTACT 553 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.24 CpG sites = 21, Kimura (unadjusted) = 39.24 Transitions / transversions = 4.20 (21/5) Gap_init rate = 0.03 (3 / 92), avg. gap size = 1.67 (5 / 3) 21 26.39 1.32 2.67 chr5qtel1M 865504 865579 (134421) (ATCT)n#Simple_repeat 1 75 (0) m_b267s252i8 10575 chr5qtel1M 865504 ATCT-TCTCTGTCTCTGTCTCTGTCTTTGTCTAAGTCTATCCCTCTATCC 865552 - v v v i v v v i i - - iv i (ATCT)n#Simpl 1 ATCTATCTATCTATCTATCTATCTATCTATCT-A-TCTATCTATCTATCT 48 chr5qtel1M 865553 ATTCCTCTATCTATCTATCTATCTGTC 865579 iiv i (ATCT)n#Simpl 49 ATCTATCTATCTATCTATCTATCTATC 75 Matrix = Unknown Transitions / transversions = 1.00 (8/8) Gap_init rate = 0.04 (3 / 75), avg. gap size = 1.00 (3 / 3) 44 2.33 0.00 0.00 chr5qtel1M 865580 865623 (134377) (CAT)n#Simple_repeat 1 44 (0) c_b267s251i0 10576 chr5qtel1M 865580 CATCATCATCATCATCATCATCATCATTATCATCATCATCATCA 865623 i (CAT)n#Simple 1 CATCATCATCATCATCATCATCATCATCATCATCATCATCATCA 44 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 613 21.02 0.63 9.66 chr5qtel1M 866264 866421 (133579) MIRc#SINE/MIR 2 146 (122) m_b267s601i4 10577 chr5qtel1M 866264 GGGGCAGTGAGGTGGTGCCGTAGTGCAAAGAGCCCTGGGCTTGGAATCAG 866313 i --- --- v v i i MIRc#SINE/MIR 2 GAGGCAGTG---TGGTGC---AGTGGAAAGAGCACTGGACTTGGAGTCAG 45 chr5qtel1M 866314 GAAGACTCAATTTCATGAATTCAAATTTTACCTCATATATTTACTGGGTG 866363 iiiiv -- i i viii i i ------ i i v MIRc#SINE/MIR 46 GAAGACCTGGGTTC--GAGTCCCGGCTCTGCC------ACTTACTAGCTG 87 chr5qtel1M 866364 TGTGAACTTGACCAAGTCACTCGACC-CTGTTTGCCTCACTTTCCTCATC 866412 v iv ii - v vv v MIRc#SINE/MIR 88 TGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATC 137 chr5qtel1M 866413 TGTAAAATG 866421 MIRc#SINE/MIR 138 TGTAAAATG 146 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.00 CpG sites = 19, Kimura (unadjusted) = 24.94 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.10 (15 / 157), avg. gap size = 1.00 (15 / 15) 28 0.00 0.00 0.00 chr5qtel1M 867699 867725 (132275) (T)n#Simple_repeat 1 27 (0) c_b267s251i1 10578 chr5qtel1M 867699 TTTTTTTTTTTTTTTTTTTTTTTTTTT 867725 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTT 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 452 23.61 3.12 7.32 chr5qtel1M 868676 868803 (131197) MIRc#SINE/MIR 24 146 (122) m_b267s601i5 10579 chr5qtel1M 868676 AGAGCCCTGGGTTTGGAATCAGGAATACTCAATGCCAGAGATTTAAATCC 868725 v ii i v i--- ----- i ii i MIRc#SINE/MIR 24 AGAGCACTGGACTTGGAGTCAGGAAGACC---TG-----GGTTCGAGTCC 65 chr5qtel1M 868726 TGCCTCAGACACTTATCATGTATGTCATCCTGGTCAAGTCACTCAAGCCT 868775 i v v v ii vv i v i i v i - MIRc#SINE/MIR 66 CGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAA-CCT 114 chr5qtel1M 868776 GTTTGCGT----GTTTCCTCATCTGTAAAATG 868803 v i v i---- MIRc#SINE/MIR 115 CTCTGAGCCTCAGTTTCCTCATCTGTAAAATG 146 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.36 CpG sites = 17, Kimura (unadjusted) = 28.86 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.08 (10 / 127), avg. gap size = 1.30 (13 / 10) 18 29.11 0.00 2.94 chr5qtel1M 870092 870161 (129839) (AAAAT)n#Simple_repeat 1 68 (0) m_b267s252i9 10580 chr5qtel1M 870092 AAAATAAAATCAAACCAGTAAAAAAATAAAAAGAGAGAAAACAAAATAAA 870141 - vi -v v vi i v i (AAAAT)n#Simp 1 AAAATAAAAT-AAAATA-AAATAAAATAAAATAAAATAAAATAAAATAAA 48 chr5qtel1M 870142 ATGCAAGCAAACAACAAAAA 870161 iv vv i v v (AAAAT)n#Simp 49 ATAAAATAAAATAAAATAAA 68 Matrix = Unknown Transitions / transversions = 0.60 (6/10) Gap_init rate = 0.03 (2 / 69), avg. gap size = 1.00 (2 / 2) 302 26.65 17.41 1.15 chr5qtel1M 870926 871149 (128851) MIRc#SINE/MIR 6 265 (3) m_b267s601i6 10581 chr5qtel1M 870926 CAGTGAATTTCATGTGGATAGAG----AGCCTTGAA-TCAGGAAGACCTG 870970 viv v - v ----i v i - MIRc#SINE/MIR 6 CAGTGTGGTGCA-GTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTG 54 chr5qtel1M 870971 ACTTTTA-TCCTA----TGTCAGAAACTA----------CT----CAAG- 871000 iv iv - ii---- i vvv ---------- ---- - MIRc#SINE/MIR 55 GGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGT 104 chr5qtel1M 871001 -ATTTAGGACCTTTTTTTCCCTCAGTTTCTTTATCTGTAAAAAGGATGTA 871049 - i -- i i vvv i i v ivi MIRc#SINE/MIR 105 CACTTA--ACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATA 152 chr5qtel1M 871050 ATAATA---G---TATCTAAATC-CTGTGTTCTTTTGTGGATAAAATGAG 871092 --- --- ii vv - v v v v v v MIRc#SINE/MIR 153 ATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAG 202 chr5qtel1M 871093 GT-ATTTATATG---GTGCATGATACATAGC-AGGTGTGATATAAATGCT 871137 i - v i --- i v vi v iv i- i iv i iv MIRc#SINE/MIR 203 ATAATGTATGTGAAAGCGCTTTGTAAACTGTAAAGTGCTATACAAATGTA 252 chr5qtel1M 871138 AGCTATT-TTATT 871149 v?i - MIRc#SINE/MIR 253 AGGNGTTATTATT 265 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.38 CpG sites = 28, Kimura (unadjusted) = 33.44 Transitions / transversions = 0.90 (28/31) Gap_init rate = 0.08 (18 / 223), avg. gap size = 2.33 (42 / 18) 406 26.28 11.68 0.00 chr5qtel1M 871008 871144 (128856) MIR#SINE/MIR 107 259 (3) m_b267s601i7 10581 chr5qtel1M 871008 ACCTTTTTTTCCCTCAGTTTCTTTATCTGTAAAAAGGATGTAATAATAGT 871057 i i v v i i v ivi MIR#SINE/MIR 107 ACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGT 156 chr5qtel1M 871058 ATCTAAATCCT-GTGTTCTTTTGTGGATAAAATGAG-------------- 871092 i vv v - v v v v v -------------- MIR#SINE/MIR 157 ACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATACATGTAAA 206 chr5qtel1M 871093 GTATTTAT-ATGGTGCATGATACATAGCAGGTGTGATATAAATGCTAGCT 871141 iii v- ii v ii i i i ivvv i MIR#SINE/MIR 207 GCGCTTAGAACAGTGCCTGGCACATAGTAAGCGCTCAATAAATGTTAGCT 256 chr5qtel1M 871142 ATT 871144 MIR#SINE/MIR 257 ATT 259 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.53 CpG sites = 19, Kimura (unadjusted) = 32.79 Transitions / transversions = 1.12 (19/17) Gap_init rate = 0.02 (3 / 136), avg. gap size = 5.33 (16 / 3) 220 34.48 8.05 0.00 chr5qtel1M 871301 871387 (128613) L2a_3end#LINE/L2 400 493 (24) m_b267s601i8 10582 chr5qtel1M 871301 TGTCACCTCCATGAGAGCAGGGGATGTTACTTGCCTTCTTTA--GCT--- 871345 v v i iv v iii ii v i -- --- L2a_3end#LINE 400 TGTAAGCTCCATGAGGGCAGGGACTTTTGTCTGTTTTGTTCACTGCTGTA 449 chr5qtel1M 871346 --CCTGGTGCTTAGCCCATGGTCTGACATATCACAGACACTTAA 871387 -- ii i i vv vv i i i vii i i i L2a_3end#LINE 450 TCCCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGGCGCTCAA 493 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.64 CpG sites = 20, Kimura (unadjusted) = 49.28 Transitions / transversions = 2.00 (20/10) Gap_init rate = 0.03 (3 / 86), avg. gap size = 2.33 (7 / 3) 281 26.44 5.75 0.00 chr5qtel1M 871396 871482 (128518) C MIR3#SINE/MIR (3) 205 114 m_b267s601i9 10583 chr5qtel1M 871396 TTATAGGGTCACA-AATG--ATAACTGGATGAGAACTACAAGGTCATGGA 871442 i ii i - -- v i v i v vvi i vv C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTA 156 chr5qtel1M 871443 GTGTA-CCCTCTCATTTTATAGATG-GGAAACTTAGATTCAG 871482 vi - i i - v iii C MIR3#SINE/MIR 155 GTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAG 114 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.49 CpG sites = 14, Kimura (unadjusted) = 33.49 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.05 (4 / 86), avg. gap size = 1.25 (5 / 4) 43 0.00 0.00 0.00 chr5qtel1M 872390 872426 (127574) (AC)n#Simple_repeat 1 37 (0) c_b267s251i2 10584 chr5qtel1M 872390 ACACACACACACACACACACACACACACACACACACA 872426 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACA 37 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 15 10.11 6.25 0.00 chr5qtel1M 872837 872868 (127132) (TTTC)n#Simple_repeat 1 34 (0) m_b267s252i10 10585 chr5qtel1M 872837 TTTCTTACTTT-TTT-TTTTTTTCTTTCTCTCTT 872868 v - - i i (TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 34 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.06 (2 / 31), avg. gap size = 1.00 (2 / 2) 14 4.94 0.00 0.00 chr5qtel1M 873269 873289 (126711) (ATT)n#Simple_repeat 1 21 (0) m_b267s252i11 10586 chr5qtel1M 873269 ATTATTATTATTATTATTTTT 873289 v (ATT)n#Simple 1 ATTATTATTATTATTATTATT 21 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 23 18.80 0.00 0.00 chr5qtel1M 874256 874298 (125702) (T)n#Simple_repeat 1 43 (0) m_b267s252i12 10587 chr5qtel1M 874256 TTTTTTTTTTTTCTTTTTTTTTTTTACTTTTTCTATCTTTCTT 874298 i vi i v i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 43 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 29 30.90 2.31 1.53 chr5qtel1M 875970 876099 (123901) (TCTC)n#Simple_repeat 1 131 (0) m_b267s252i13 10588 chr5qtel1M 875970 TCTCTGTCTGTC-CTGCTAAGTCTCTCTCTTTCTTGCTTACACTATAT-T 876017 v v - - vvv i iv iv v v v - (TCTC)n#Simpl 1 TCTCTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 49 chr5qtel1M 876018 CCCTCTCTAGCTCTGTCTATCTCTCTGTTTCTCTCAACT-TCTCTTTCTT 876066 i vv v v v i -v - i i (TCTC)n#Simpl 50 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TCTCTCTCTCTCTC 98 chr5qtel1M 876067 TATCACTTTTTGTTTCCCTCTCTTGCTCTCTCT 876099 v v i i v i i iv (TCTC)n#Simpl 99 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 131 Matrix = Unknown Transitions / transversions = 0.60 (12/20) Gap_init rate = 0.04 (5 / 129), avg. gap size = 1.00 (5 / 5) 20 13.69 0.00 0.00 chr5qtel1M 876462 876493 (123507) (A)n#Simple_repeat 1 32 (0) m_b267s252i14 10589 chr5qtel1M 876462 AAAAAAAAAAAAAAACCTAAAAGAAAAAAAAA 876493 vvv i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 32 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 15 5.48 0.00 0.00 chr5qtel1M 877738 877756 (122244) (A)n#Simple_repeat 1 19 (0) m_b267s252i15 10590 chr5qtel1M 877738 AAAAAAAAAAAAAAATAAA 877756 v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAA 19 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 21 0.00 0.00 0.00 chr5qtel1M 878455 878477 (121523) (T)n#Simple_repeat 1 23 (0) m_b267s252i16 10591 chr5qtel1M 878455 TTTTTTTTTTTTTTTTTTTTTTT 878477 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTT 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 1470 27.47 0.36 1.66 chr5qtel1M 879029 879576 (120424) C L1ME3G_3end#LINE/L1 (377) 547 7 m_b267s551i4 10592 chr5qtel1M 879029 TAATATTCCATAATTTTCATATACCACAATTTATTCAGCCATTCTCCAAC 879078 i i v vv i i i i v i C L1ME3G_3end#L 547 TAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTAT 498 chr5qtel1M 879079 TGATGGACATCCATTCAGTTTCCAGTTTCTAGCCACTACAAAAAGGGCTG 879128 ii vviv i i v i i v iv C L1ME3G_3end#L 497 TGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCTG 448 chr5qtel1M 879129 CCACAAACATTCGTGCACATACAGGTCCCTTTCC-CTTCTTT-ATAATCT 879176 v ii i v i i ?-- i v v - v v vi- vv i C L1ME3G_3end#L 447 CAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATTT 400 chr5qtel1M 879177 CTTTGGGATATAATCCCAGTAGTAACACTGCTGGATCAAAGGGTATGCAC 879226 ? i v v? ? v iiv i i i C L1ME3G_3end#L 399 CTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGC 350 chr5qtel1M 879227 AGTTTGATAACTTTTTGAGCATAGTTCCAAACTACTCTCCAAAATGGTTG 879276 v i -- i vvv - v v i i i ? i C L1ME3G_3end#L 349 ATTTTAA--ATTTTAATAG-ATACTGCCAAATTGCCCTCCAAAANGGCTG 303 chr5qtel1M 879277 GATTCGTTCACAACTCCACCAACAATGCATCAATGTCCCAGTTTTCCCGC 879326 v iivi i vii i i i v iv v v i i C L1ME3G_3end#L 302 TACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCAC 253 chr5qtel1M 879327 ATCCCCTCCAACAATCATCATTATTTTTTCCTGTCATCTTAGCCAATCTG 879376 i i v v ?ivi ivv?iii vvv i v C L1ME3G_3end#L 252 ACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATCTG 203 chr5qtel1M 879377 ACAGGTGTGTAGTGGTATCTTAGAGTTGTCTTAATTTGCATTTCTCTGAT 879426 ii viv i i vv i i C L1ME3G_3end#L 202 ATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGAT 153 chr5qtel1M 879427 TAATAATGACTTGGAGCATCTTTTCATATGACTAGAAATAGTTTCAATTT 879476 v i vv v vi vviiivi vv C L1ME3G_3end#L 152 TACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGTATTT 103 chr5qtel1M 879477 CTTCATCTGAGAATTGTCTGTTCATATCCTTTGACCATTTTTCAATTGGA 879526 i v v i v v i C L1ME3G_3end#L 102 CCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGGG 53 chr5qtel1M 879527 GAATGGCTTGATTTTTTATAAATTAGAGTTAATTCTCTATATATTTTGGA 879576 v-- v -- i vi v vivv i i i C L1ME3G_3end#L 52 T--TGTCTT--TTTCTTATTGATTTGTAGGAGTTCTTTATATATTCTGGA 7 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.70 CpG sites = 78, Kimura (unadjusted) = 35.29 Transitions / transversions = 1.11 (78/70) Gap_init rate = 0.02 (11 / 547), avg. gap size = 1.00 (11 / 11) 5088 30.00 2.18 2.18 chr5qtel1M 879433 882689 (117311) C L1M5_orf2#LINE/L1 (0) 3294 38 m_b267s551i5 10592 chr5qtel1M 879433 TGACTTGGAGCATCTTTTCATATGACTAGAAATAGTTTCAATTTCTTCAT 879482 ?v v i vi vviiivi v? v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr5qtel1M 879483 CTGAGAATTGTCTGTTCATATCCTTTGACCATTTTTCAATTGGA--GAAT 879530 i v v vi i v ?v i-- vv C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTT 3195 chr5qtel1M 879531 GGCTTGATTTTTTAT-AAATTAGAGTTAATTCTCTATATATTTTGGAAAT 879579 v -- ? -i ? iv v- i i i v i C L1M5_orf2#LIN 3194 GTCTT--TTTNTTATTGANTTGTAGG-AGTTCTTTATATATTCTGGATAC 3148 chr5qtel1M 879580 GAGGCCTTTATCAGA-ACCTTTGACTGTAAAAATATTTTCCCAGTTTATT 879628 v i - iv v ?-i i v v i ? i i v C L1M5_orf2#LIN 3147 GAGTCCTTTGTCAGATATATGTN-TTGCAAATATTTTCTCCCANTCTGTG 3099 chr5qtel1M 879629 GCTTCCCTTCTAATCTTGTCTGCATTAGTTTTGTTTGTACAAAAACTTTT 879678 v i v i v ivi iv ivi vvv? vi i ii C L1M5_orf2#LIN 3098 GCTTGCCTTTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTTT 3049 chr5qtel1M 879679 CAGTTTGGTATAATCGAA-------ATTTTCTATTTTGTGATCAGTAATG 879721 v v i i? i v ------- i v i i i? i--- C L1M5_orf2#LIN 3048 AATTTTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGGTTNGTG--- 3002 chr5qtel1M 879722 ATCTCTAGTTCTGCTTTGGTCATAAAGACCTTCCCCT-TCCACAGGTCTG 879770 -- i -- v iii v i - i i i iv -? vv vv C L1M5_orf2#LIN 3001 --CTTT--TTGTGTCCTGTTTA-AGAAATCTTTGCCTANCCCAAGGTCAC 2957 chr5qtel1M 879771 AGAGGTAAACTATCCTATGTT--CCTCTAATTTATTAATAATTTCATTCT 879818 ii i --i v -- i ivvvv v i i ?ii C L1M5_orf2#LIN 2956 GAAGATA--TTCTCCTATGTTTTCTTCTAGAAGTTTTATAGTTTTANCTT 2909 chr5qtel1M 879819 TTATGCCTAGGTC-ATGAACCCATTTTGACCTTATCTTGGTGTACGGCGT 879867 iiii - -i i ? vi v i v i i C L1M5_orf2#LIN 2908 TTACATTTAGGTCTATGA-TCCATCTNGAATTAATTTTTGTGTATGGTGT 2860 chr5qtel1M 879868 TAAGTATGGATCAATGCCTAGTTTCTGCCATATTAGTTTCCAATTTTCCC 879917 v i v i i v?iii v i v vii v v i C L1M5_orf2#LIN 2859 GAGGTAGGGGTCGAGNTTCATTTTTTTCCATATGGATATCCAATTGTTCC 2810 chr5qtel1M 879918 AGCAATTTTTATCAAACAGTAAGTTCTTATCCCAAAAGCTGGGAT-CTTT 879966 viv i ii v vvvi i vi ---- iiv - ? C L1M5_orf2#LIN 2809 AGCACCATTTGTTGAAAAGACTATCCTTTCCCCA----CTGAATTGCNTT 2764 chr5qtel1M 879967 GGG---TTTGTCAAAGACTAGGTTGCTATATTTGT-TGACTGTTTTATCC 880012 v--- i ii i? v? i v - --- v i ii C L1M5_orf2#LIN 2763 GGCACCTTTGTCAAAAATCAANTGNCCATATATGTGTG---GGTCTATTT 2717 chr5qtel1M 880013 CTTGAAC---CTAATCTATTCCACTGATCAACTAATCTATTCCTTA-GCC 880058 - i --- v i i v i vi - - C L1M5_orf2#LIN 2716 CT-GGACTCTCTATTCTGTTCCATTGATCTATTTGTCTAT-CCTTACGCC 2669 chr5qtel1M 880059 AATACCAAATAGTTTTGGTAACTGCTGCTCTATAATATAATTTT-AGATC 880107 v iv i i v iv i - i i - ? C L1M5_orf2#LIN 2668 AATACCACACTGTCTTGATTACTGTAGCTTTATAATA-AGTCTTGANATC 2620 chr5qtel1M 880108 TGGTACAGCTAAG-CCACCATCATTTGATTTT-TTTTTCATTAATTCCCT 880155 ? vv - - v v - v i - v-i vii C L1M5_orf2#LIN 2619 NGGTAGTG-TAAGTCCTCCAAC-TTTGTTCTTCTTTTTCAA-GATTGTTT 2573 chr5qtel1M 880156 TGAA-ATTCTTGACCTTTTGTTTTTCCATATGAACTTTGTTGTTATTTTT 880204 iv- ? ii i iv i i ivvi i vi v C L1M5_orf2#LIN 2572 TGGCTATTCTNGGTCCTTTGCATTTCCATATAAATTTTAGAATCAGCTTG 2523 chr5qtel1M 880205 TCTAGGTCATTAAAATAGTTTTTTGGGAGTCTGATTGGTATAGCGCTAAA 880254 v vv vvi v iii vi v i v v ii i C L1M5_orf2#LIN 2522 TCAATTTCTACAAAAAAACCTGCTGGGATTTTGATTGGGATTGCATTGAA 2473 chr5qtel1M 880255 TAAATAGATTAGTTTAGGTAATATTGTCATCTTTATTATATTTGCTCGCC 880304 vv i i i v iv v ? iv viv vi C L1M5_orf2#LIN 2472 TCTATAGATCAATTTGGGGAGAATTGACATCTTNACAATATTGAGTCTTC 2423 chr5qtel1M 880305 CTATCCAAGAGCATTTAATATTTTTCCAATTGGTTAGATCAGACTTAATT 880354 v v i vvv i i v iv i vvvi C L1M5_orf2#LIN 2422 CAATCCATGAACATGGTATATCTCTCCATTTATTTAGGTCTTCTTTAATT 2373 chr5qtel1M 880355 TGTGTGAAAAGTGGTCTGTAATTTTGCTCATAAAGTTTCTG---ATTTTC 880401 v v v iv i v i i vvvii ? v ii --- ? - C L1M5_orf2#LIN 2372 TCTCTCAGCAATGTTTTGTAGTTTTCAGTGTANAGGTCTTGCACATNTT- 2324 chr5qtel1M 880402 CCTTGGCAGATAGATTCCTAAATATTTTATATTATCAGTAGTTACTTTAA 880451 -- vi vv i ? i v iv vv i i v C L1M5_orf2#LIN 2323 --TTGTTAGATTTATTCCTAAGTATTTNATGTTTTTTGATGCTATTGTAA 2276 chr5qtel1M 880452 ATGGAATTTCTCTTTGTAACTCTGACTGTTGGATT--TTGTTAGTGATAT 880499 v vi i ?-- v i v i v ivi -- iv ii C L1M5_orf2#LIN 2275 ATGGTATTGTTTTTN--AAATTTCATTTTCCAATTGTTTGTTGCTAGTAT 2228 chr5qtel1M 880500 ATAAGAATGCTGATGACTTATGTGGGTTTATTTTATAACCAGCAACTTTG 880549 ii i viv i v ivi v ii i v ? i i C L1M5_orf2#LIN 2227 ATAGAAATACAATTGATTTTTGTATATTGACCTTGTATCCNGCGACCTTG 2178 chr5qtel1M 880550 CTAAAGTTGTGGATTATTTCTAATAACTTTTTAGCAGAATCTCTGGGGTT 880599 v iiivv v i ii ? v i v i ? i C L1M5_orf2#LIN 2177 CTAAATTCACTTATTAGTTCTAGTAGTTTNTTTGTAGATTCTTTNGGATT 2128 chr5qtel1M 880600 CTCTAAGTATACCATCATGTCATCGGCAAAGAGTGATAATTTGGCTTCCT 880649 i v ? v v i v i? i i vii i C L1M5_orf2#LIN 2127 TTCTACGTANACAATCATGTCATCTGCGAATAANGACAGTTTTATTTCTT 2078 chr5qtel1M 880650 CATTGCCTATTCTTATTCCTTTAATCTCTTTCTCAGCTCTTATTGCTATA 880699 v v v ii v v i i vvvi vv i C L1M5_orf2#LIN 2077 CCTTTCCAATCTTTATGCCTTTTATTTCTTTTTCTTGCCTTATTGCACTG 2028 chr5qtel1M 880700 GCTAGCGTTTCTAATACAATATTAAATAGTAACGGTGATAGTGGGCAACC 880749 viii i i i i v ii ? i i v C L1M5_orf2#LIN 2027 GCTAGGACCTCCAGTACAATGTTGAATAGAAGTGGTGANAGCGGACATCC 1978 chr5qtel1M 880750 TTGTTTCACTCCAGATCTTATTGGGAATGGTTGCAGTTTGTCTCCATTAC 880799 i iii v vv v v? v ? v v v C L1M5_orf2#LIN 1977 TTGTCTTGTTCCCGATCTTAGGGGGAAAGCNTTCAGTNTTTCACCATTAA 1928 chr5qtel1M 880800 ATATGATGCTTACTGATGGTTTTAAATAGATGCTGCTGATTATTTTAAGG 880849 i i ?i vv vvi ivi v i vv i C L1M5_orf2#LIN 1927 GTATGATGTTNGCTGTAGGTTTTTCGTAGATGCCCTTTATCAGGTTGAGG 1878 chr5qtel1M 880850 AAAAGTCCATTTATTCCTATACTCTCAAGTGTTTTTAATAGGAATGGATG 880899 ivvi v i vvi viii v vi v i C L1M5_orf2#LIN 1877 AAGTTCCCTTCTATTCCTAGTTTGCTGAGAGTTTTTATCATGAATGGGTG 1828 chr5qtel1M 880900 TTGGATTTTATCAAATGCTTTTTCTGCATCTATTGAGATGATCATATGGT 880949 i i i C L1M5_orf2#LIN 1827 TTGAATTTTGTCAAATGCTTTTTCTGCATCTATTGAGATGATCATATGAT 1778 chr5qtel1M 880950 TTTTGTTAATTTGGT-TATTAACATGGCCAATTATATTGATAGTTTTCCT 880998 v iv- iv - i i iv i v v i v C L1M5_orf2#LIN 1777 TTTTCTCC-TTTATTCTGTTAATATGGTGAATTACATTGATTGATTTTCG 1729 chr5qtel1M 880999 AATATTGAACCAGCCCTGCATTCCTGGTATAAATCCTACTTGATCATAGT 881048 i i i i v i i i ii C L1M5_orf2#LIN 1728 AATGTTAAACCAACCTTGCATTCCTGGGATAAACCCCACTTGGTCATGAT 1679 chr5qtel1M 881049 GTATTATCTTGGAGATGATTTTCTGTAGTCTTTTTGCTAATATCTTATTT 881098 i vvvv ivv v v v vv i i ? C L1M5_orf2#LIN 1678 GTATTATCCTTTTTATATATTGCTGGATTCGATTTGCTAATATTTTGTTN 1629 chr5qtel1M 881099 AAGATTTTAGCATCAATATTCATTAGGGAGATTGGTCTATAATTTTCTTT 881148 i v v i v v i C L1M5_orf2#LIN 1628 AGGATTTTTGCATCTATGTTCATGAGGGATATTGGTCTGTAATTTTCTTT 1579 chr5qtel1M 881149 CTCTGT--TTTCAGCCTACCTGGTTTAGGTATCAGTACCATGTCTGTGTC 881196 iii -- v --ii ii ? v vii? iiv iv C L1M5_orf2#LIN 1578 TCTTGTAATGTC--TTTGTCNGGTTTTGGTATCAGGGTNATGCTGGCCTC 1531 chr5qtel1M 881197 ATAGAAGGAATTTGGTAGGACTCCTTCATTCCCTATTTTATCAAATAATT 881246 i v i v v vii i v ii v vi v i C L1M5_orf2#LIN 1530 ATAAAATGAGTTGGGAAGTGTTCCCTCTTTTTCTATTTTCTGGAAGAGTT 1481 chr5qtel1M 881247 TATATAGCATTGGGGCCAATTGTTCTTTAAATGTTTGGTAAAATTCACAT 881296 i i iv viii v v i i vv C L1M5_orf2#LIN 1480 TGTGTAAGATTGGTATTATTTCTTCCTTAAATGTTTGGTAGAATTCACCA 1431 chr5qtel1M 881297 GTAAATCCATCTGGTCCTGGGGATTTTTTCTTAGGGAGTTGTTTAATTGC 881346 i v v i v i iv i i v v i C L1M5_orf2#LIN 1430 GTGAAGCCATCTGGGCCTGGAGTTTTCTTTGTGGGAAGGTTTTTAATTAC 1381 chr5qtel1M 881347 CTGTTCTATTTCTTTTTCTGAAATGGGACTATTCAAGCAATTTACTTCCT 881396 vvi v vviv v i i iiivv i i i C L1M5_orf2#LIN 1380 AAATTCAATTTCTTTAATAGATATAGGGCTATTCAGATTTTCTATTTCTT 1331 chr5qtel1M 881397 CCTCTGTTAGTCTGGGAAGTCTATATTTTTGGAGGTAGTCATCCATTTCA 881446 i v? i i v v i?i i i vi v v ii C L1M5_orf2#LIN 1330 CTTGNGTCAGTTTTGGTAANTTGTGTTTTTCAAGGAATTTGTCCATTTCA 1281 chr5qtel1M 881447 CTTAGGTTATCAAATTTATTGGCATAAAGTTGAGCAAAATAACTCCTTAT 881496 ii i ? vv v viii C L1M5_orf2#LIN 1280 TCTAAGTTNTCAAATTTATTGGCATAAAGTTGTTCATAATATTCTCTTAT 1231 chr5qtel1M 881497 TATTTCTCTAATTTCCTCTTCATTGGTGGAAAGTTCTCCCTTTTCATTTT 881546 iii i v ivivvv iv i vi vv i ii C L1M5_orf2#LIN 1230 TATCCTTTTAATGTCTGTAGGATCTGTAGTGATGTCTCCTTTTTCATTCC 1181 chr5qtel1M 881547 TAAGACTACTAATTTCATTTTCCTCCCTCCTTTTTCTAATCAGATTTACC 881596 i v i iv vvv i i i ii ii i vi ?i i C L1M5_orf2#LIN 1180 TGATATTGGTAATTTGTGTCTTCTCTCTTTTTTTCTTGATCAGTCTNGCT 1131 chr5qtel1M 881597 AAAGGCTTATCTATTTTATTGGCTTTTTCATAGAACCAACTCTTAGTTTT 881646 i i v iii v i i i i i C L1M5_orf2#LIN 1130 AGAGGTTTATCAATTTTATTGATCTTTTCAAAGAACCAGCTTTTGGCTTC 1081 chr5qtel1M 881647 ATTAATTAGTTCAATAGTTTTTTTACTTTCAATATTTTTAATTTCTCCTT 881696 i i vvi v v ? ? ii v v iv i v i C L1M5_orf2#LIN 1080 GTTGATTTTCTCTATTGTNTNTTTGTTTTCTATTTCATTGATTTCTGCTC 1031 chr5qtel1M 881697 TTAATTTTAGAATTTCCAATTTAGTATTTGATTGGGGGTTTTTAATTTGG 881746 vi vv vvii vv i ?v v --- v C L1M5_orf2#LIN 1030 TTATCTTTATTATTTCCTTCCTTCTACTTNCTTTGGG---TTTAATTTGC 984 chr5qtel1M 881747 ---TCTTTTTTTAGTTTTTTTAGTTGCAAGCCCAATTCATTAATCTT--T 881791 --- i i i v v v ii iv i i --v C L1M5_orf2#LIN 983 TCTTCTTTTTCTAGCTTCTTAAGGTGGAAGCTTAGATCATTGATTTTAAG 934 chr5qtel1M 881792 TCTTTC-TCTGTTTTATTCAAGTAAGCCTCTAAGGATATAAAATTCCCTC 881840 i - v i --- vi ? v i ? v v C L1M5_orf2#LIN 933 CCTTTCTTCTTTTCTA---ATATANGCATTTAANGCTATAAATTTCCCTC 887 chr5qtel1M 881841 TTATTACCGCTTTGGCTGCATCCCACAAATTTTGGTATGATGTCTCATCA 881890 v vi i i i v v iv C L1M5_orf2#LIN 886 TAAGCACTGCTTTAGCTGCATCCCACAAATTTTGATATGTTGTATTTTCA 837 chr5qtel1M 881891 TTGTCATTATCTTGAGTGAAATTATTAATTGTATCTATAATTTGCTGCTT 881940 ? vvv v iviv v vi viv?i i i vi vi C L1M5_orf2#LIN 836 TTNTCATTCAGTTCAAAATATTTTCTAATTTCCNTTGTGATTTCTTCTTT 787 chr5qtel1M 881941 CACCCAATCATTCTTTA-AGATGAGATTGTTTAGTTTCCAATTACTTTTT 881989 v vvvi v - ii v - i v -- v C L1M5_orf2#LIN 786 GACCCATGGGTTATTTAGAAGTGTG-TTGTTTAATTTCCAAATA--TTTG 740 chr5qtel1M 881990 GGTCTATTTCCCCCTAACTTTTTGTTGAATGTAGTTTTT------ATTGC 882033 vv - ivv? v -- - ii i ------ v C L1M5_orf2#LIN 739 GGGAT-TTTCTAGNTATCTTTTTGTT--AT-TGATTTCTAATTTAATTCC 694 chr5qtel1M 882034 ATCATGATCTGAAAAGAAAGCATTTACTATTTCTGCTTTCTTGCATTTAA 882083 ii i v i v v viv v iv viiii i ?iv - C L1M5_orf2#LIN 693 ATTGTGGTCAGAGAACATACTCTGTATGATTTCAATCCTTTNAAATTTA- 645 chr5qtel1M 882084 TTTTGAG----GTCTTTATGTCCTAATATATGGTCAATTTTTGAATAGGT 882129 -- ---- - v i i? v i v v v v C L1M5_orf2#LIN 644 --TTGAGACTTGT-TTTATGGCCCAGNATATGGTCTATCTTGGTAAATGT 598 chr5qtel1M 882130 TCCATGAACTGCTGAGAAGAAAGTATATTCC-CTTCTATCTCCATTCAAT 882178 vi vvi i v i i- ?vi i - vvi v? i C L1M5_orf2#LIN 597 TCCATGTGCACTTGAAAAGAATGTGTATTCTGCNGTTGT-TGGGTGNAGT 549 chr5qtel1M 882179 TTTCTCCAAAGATCCAACATACCTAATT--TTTCTAATATTCTATTTACT 882226 v vi vi v vi vii v i -- vv i i -- i i vv C L1M5_orf2#LIN 548 GTTCTATAAATGTCAATTAGGTCAAGTTGGTTGATAGTGT--TGTTCAAA 501 chr5qtel1M 882227 TCTTTAAT-TTCTTTCTTATTTGTTTTGTG-GTTTGATTTGTCTAATT-C 882273 iv - i v v -- v-ii v i i - - C L1M5_orf2#LIN 500 TCTTCTATATCCTTACTGATT--TTTTGTCTACTTGTTCTATC-AATTAC 454 chr5qtel1M 882274 TGAGAGTGCAAGGTTGAGATCTCCTACTATTACAGTTTTG---TTGTCTA 882320 v v?iv i i ? --- i v --- C L1M5_orf2#LIN 453 TGAGAGAGGNGTGTTAAAATCTCCNACTAT---AATTGTGGATTTGTCTA 407 chr5qtel1M 882321 TTTCTTCTTGCAACTCTCTTAACTTCTCCTTTAGGAAGTTGAGTGCCATA 882370 i vi ii v i ii i v i v v v viiv iv i C L1M5_orf2#LIN 406 TTTCTCCTTTTAGTTCTGTCAGTTTTTGCTTCATGTATTTTGAAGCTCTG 357 chr5qtel1M 882371 CCACTTGGTGCATATATGTTTAATATTGATATTGCTTCGTTGTTTATGCT 882420 ii i v i ii iv v vv - v v vviv C L1M5_orf2#LIN 356 TTATTAGGTGCATACACATTTAGGATTGTTATGTCTTC-TTGATGAATTG 308 chr5qtel1M 882421 ACCC-TTTAGCAGGATGTAGTTTCCTTCCTTATCTCTTTTAATTAGATCA 882469 - v vv v i v i i vv --- -- C L1M5_orf2#LIN 307 ACCCTTTTATCATTATGAAATGTCCCTCTTTATCTCTGGTAAT---AT-- 263 chr5qtel1M 882470 ATTTTTACTTT------TGCTTGATCTGAGATAAGGATGGCTACCCCTGC 882513 - i i i ------ i vi v v iv i i ? v C L1M5_orf2#LIN 262 -TTCTTGCCTTGAAGTCTACTTTGTCTGATATTAATATAGCCACNCCAGC 214 chr5qtel1M 882514 TTT-TTTGACTTCACCTGAAGCATAATAGATTTTGCTCCAGCCTTTTACC 882562 - vi? viiv v-v ii v i vi v i C L1M5_orf2#LIN 213 TTTCTTTTGNTTAGTGTT-TGCATGGTATATCTTTTTCCATCCTTTTACT 165 chr5qtel1M 882563 TTTACTCTATATGTATCCCCCTGCTTTAAATGTGTTTCTTGTAAACAACA 882612 i vi ? v i iiiv ii v i i i i i C L1M5_orf2#LIN 164 TTCAACCTNTCTGTGTCTTTATATTTAAAGTGCGTCTCTTGTAGACAGCA 115 chr5qtel1M 882613 TATTGTAGGGTTCTGACTTTTGATCCAGTCTG-CTATCTGCCTCCTCTTT 882661 v v ii vi v - v - iv i v C L1M5_orf2#LIN 114 TATAGTTGGGTCTTGTTTTTTTATCCAGTCTGACAATCT-CTGCCTTTTA 66 chr5qtel1M 882662 ATGGGGGAGTTCATCCCATTCACATTTA 882689 v i v i v? i C L1M5_orf2#LIN 65 ATTGGAGTGTTTAGNCCATTTACATTTA 38 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.50 CpG sites = 512, Kimura (unadjusted) = 40.04 Transitions / transversions = 1.15 (512/444) Gap_init rate = 0.03 (107 / 3256), avg. gap size = 1.33 (142 / 107) 397 20.68 5.33 3.27 chr5qtel1M 882578 882727 (117273) C L1MEh_5end#LINE/L1 (1) 2234 2082 m_b267s551i6 10592 chr5qtel1M 882578 TCCCCCTGCTTTAAATGTGTTTCTTGTAAACAACATATTGTAGGGTTCTG 882627 ii? i i i i i v i i C L1MEh_5end#LI 2234 TCCTTNTGTTTTAAGTGTGTCTCTTGTAGACAGCATATTGTTGGATTTTG 2185 chr5qtel1M 882628 ACTTTTGATCCAGTCTGCT-ATCTGCCTCCTCTTTATGGGGGAGTTCATC 882676 vi ?i i v?- - ivi i v v v i v C L1MEh_5end#LI 2184 TTTTTNAATCCAATCTGANAATCT-CTGTCTTTTAATTGGTGAGTTTAAC 2136 chr5qtel1M 882677 CCATTCACATTTACGGTTAGAATTACTAA---ATCTG----TATTTCCTG 882719 i --- iv i?--- i? ---- - C L1MEh_5end#LI 2135 CCATTTACATTTA---TTGTAATTACTGNTATATTNGGACTTATTT-CTG 2090 chr5qtel1M 882720 CCATCCTA 882727 i C L1MEh_5end#LI 2089 CCATCTTA 2082 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 26.09 CpG sites = 21, Kimura (unadjusted) = 26.09 Transitions / transversions = 2.33 (21/9) Gap_init rate = 0.05 (8 / 149), avg. gap size = 1.62 (13 / 8) 289 25.05 5.20 7.69 chr5qtel1M 882584 882756 (117244) C L1MEd_5end#LINE/L1 (7) 2217 2049 m_b267s551i7 10592 chr5qtel1M 882584 TGCTTTAAATGTGTTTCTTGTAAACAACATATTGTAGGGTTCTGACTTTT 882633 i ii i i v iv i ivvvi C L1MEd_5end#LI 2217 TGTTTTAGGTGTGTCTCTTGTAAACAGCATATAGCTGGATTTGTTTTTTT 2168 chr5qtel1M 882634 GATCCAGTCTG-CTATCTGCCTCCTCTTTATGGGGGAGTTCATCCCATTC 882682 i i - v - ivi i v iv ? i vi i C L1MEd_5end#LI 2167 AATCCAATCTGACAATCT-CTGTCTTTTAACTGGNGAGTTTAGTCCATTT 2119 chr5qtel1M 882683 ACATTTACGGTTAGAATTACTAA---ATCTGTAT---TTCCTGCCATCCT 882726 --- ivi i --- i v --- i i i C L1MEd_5end#LI 2118 ACATTTA---TTGTGATTACTGATATATTTGGATTTATTTCTACCATCTT 2072 chr5qtel1M 882727 AATAACCCCAGATTGTGCTT--TACTTATTCT 882756 v --------- -- i i C L1MEd_5end#LI 2071 ATT---------TTGTGCTTTCTATTTGTTCT 2049 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 31.82 CpG sites = 27, Kimura (unadjusted) = 31.82 Transitions / transversions = 2.08 (27/13) Gap_init rate = 0.10 (17 / 172), avg. gap size = 1.29 (22 / 17) 14 30.68 0.00 0.00 chr5qtel1M 885759 885807 (114193) (GAAAAG)n#Simple_repeat 1 49 (0) m_b267s252i17 10593 chr5qtel1M 885759 GAAGAGAAAACAGAAGTAGAACAGGAAAAGGATAAGAAAAAGGGGAAGG 885807 i i vi ivi v v i ii (GAAAAG)n#Sim 1 GAAAAGGAAAAGGAAAAGGAAAAGGAAAAGGAAAAGGAAAAGGAAAAGG 49 Matrix = Unknown Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 225 19.78 1.25 5.19 chr5qtel1M 885929 886008 (113992) L1M4c_5end#LINE/L1 2370 2446 (54) m_b267s551i8 10594 chr5qtel1M 885929 TTAGTAATTTTAACTATGAATGTGAATGGGATGAACTCTCCCATAAAAGG 885978 i --- v i i iv i v v -i L1M4c_5end#LI 2370 TCAGTAATT---ACTTTAAATGTAAATGGATTAAACTCTCCAATCAAA-A 2415 chr5qtel1M 885979 GAAACAGA-TAGCTGACTGGATTAGAAACCA 886008 v ? - i ? v i v L1M4c_5end#LI 2416 GACANAGATTGGCNGAATGGATTAAAAAACA 2446 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 23.85 CpG sites = 8, Kimura (unadjusted) = 23.85 Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.06 (5 / 79), avg. gap size = 1.00 (5 / 5) 26 13.49 0.00 0.00 chr5qtel1M 886020 886060 (113940) (A)n#Simple_repeat 1 41 (0) m_b267s252i19 10595 chr5qtel1M 886020 AAAAACAAAAAACAAAAAACAAAAACAAAACAAAAAAAAAA 886060 v v v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 41 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 207 26.30 3.30 8.05 chr5qtel1M 886851 886941 (113059) MIRc#SINE/MIR 2 88 (180) m_b267s601i10 10596 chr5qtel1M 886851 GAGACATTTAGGTAGCTGAGTGGGCAGAGCAGTG-ACCTGGTTTCAGGAA 886899 i v vv - -- iv v - i vv MIRc#SINE/MIR 2 GAGGCAGTGTGGT-GC--AGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr5qtel1M 886900 AACCT--GTTCAAATCTGAATTCTTCCTTAATTTCCTTAACTGT 886941 i -- i i iviii v --- i v - i MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCC---ACTTAC-TAGCTGT 88 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.26 CpG sites = 12, Kimura (unadjusted) = 32.74 Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.10 (9 / 90), avg. gap size = 1.11 (10 / 9) 469 25.20 6.30 0.00 chr5qtel1M 886923 887049 (112951) MIR#SINE/MIR 118 252 (10) m_b267s601i11 10596 chr5qtel1M 886923 CCTTAATTTCCTTAACTGTTA--TGAGGATAAAAACAGCACTCACTTCAG 886970 i i i v v -- i v i i ii i v MIR#SINE/MIR 118 CCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTCAT 167 chr5qtel1M 886971 AGAGTTGTTCTTAGCATCAAATGAGATAATATCTGTAAAGTGCTTAGCAC 887020 i v v v i v iv i v MIR#SINE/MIR 168 AGGGTTGTTGTGAGGATTAAATGAGTTAATACATGTAAAGCGCTTAGAAC 217 chr5qtel1M 887021 A--GCATAG----TAGCAAATGCCACATAAATGCT 887049 -- v i ---- i ii ivv i MIR#SINE/MIR 218 AGTGCCTGGCACATAGTAAGCGCTCAATAAATGTT 252 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.09 CpG sites = 19, Kimura (unadjusted) = 31.40 Transitions / transversions = 1.46 (19/13) Gap_init rate = 0.02 (3 / 126), avg. gap size = 2.67 (8 / 3) 583 19.34 1.63 3.31 chr5qtel1M 887106 887228 (112772) MIRb#SINE/MIR 113 233 (35) m_b267s601i12 10597 chr5qtel1M 887106 AACCTGTTTG--CCTCAGTTTTTACATCTATAAATTCAGAGATAATAGCA 887153 v i -- iiv i v -i i i-- MIRb#SINE/MIR 113 AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAAT-GGGGATAATAA-- 159 chr5qtel1M 887154 GTACCTATCTGCCAGAATGATTGTGAGGATCAAATGAGACAATAATTGTA 887203 - i vv ii vi i i ivv MIRb#SINE/MIR 160 -TACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTA 208 chr5qtel1M 887204 AAGAGCTTAGCACAGTGCCTGGCAC 887228 v MIRb#SINE/MIR 209 AAGCGCTTAGCACAGTGCCTGGCAC 233 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 22.72 CpG sites = 14, Kimura (unadjusted) = 22.72 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.04 (5 / 122), avg. gap size = 1.20 (6 / 5) 30 0.00 0.00 0.00 chr5qtel1M 888375 888400 (111600) (CA)n#Simple_repeat 1 26 (0) c_b268s251i0 10598 chr5qtel1M 888375 CACACACACACACACACACACACACA 888400 (CA)n#Simple_ 1 CACACACACACACACACACACACACA 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 287 23.69 6.00 2.91 chr5qtel1M 888402 888501 (111499) Charlie7a#DNA/hAT-Charlie 169 271 (1) m_b268s502i0 10599 chr5qtel1M 888402 ATATATAAAACTTATAAATAAGCA------CACACATCAGAGATACATGT 888445 i v i ii ------ i i ii i i i i Charlie7a#DNA 169 ATGTATATAATTTATAAATAAATAAATATACATATATTGGGGGTGCATGC 218 chr5qtel1M 888446 TCAAAAATGTTTTACCGATAGAAGCAAATGTGATCAAAACAAGTTAGGAG 888495 v i ii iiv -- - v Charlie7a#DNA 219 TCAAAAATTTTTTACTGATAGGGGTGCA--TGATCAAAA-AAGTTTGGAG 265 chr5qtel1M 888496 ACTGCT 888501 ii Charlie7a#DNA 266 ACCACT 271 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 30.52 CpG sites = 19, Kimura (unadjusted) = 30.52 Transitions / transversions = 4.75 (19/4) Gap_init rate = 0.04 (4 / 99), avg. gap size = 2.25 (9 / 4) 500 32.09 0.62 3.82 chr5qtel1M 888503 888664 (111336) C MIR3#SINE/MIR (37) 171 15 m_b268s601i1 10600 chr5qtel1M 888503 CCTTAGAGATCATCTATTCTGCTCTCCTCCTCACTTTATAGATGAGAAAA 888552 v iiv--- i i i i C MIR3#SINE/MIR 171 CCTTAGAGATCATCTAGTCCAA---CCCCCTCATTTTACAGATGAGGAAA 125 chr5qtel1M 888553 CATAGACCCAAGAAGGTTAACTTAATTTACCCAAGACCACTCAGGTAATA 888602 vv i iii v -v i i i ii v v? i v C MIR3#SINE/MIR 124 CTGAGGCCCAGAGAGGTGAA-GTGACTTGCCCAAGGTCACACAGCNAGTT 76 chr5qtel1M 888603 GCCGTCAGAGTTAGGATTTAAACTCAGATGCTCTGG-TCCCAAAGCCAGT 888651 ivi v iii i vi i i vii i- -- i v C MIR3#SINE/MIR 75 AGTGGCAGAGCCGGGACTAGAACCCAGGTCTCCTGACTCCC--AGTCCGT 28 chr5qtel1M 888652 ATTTTTCCCACTC 888664 ii i ii ii C MIR3#SINE/MIR 27 GCTCTCTCTGCTC 15 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.02 CpG sites = 36, Kimura (unadjusted) = 45.45 Transitions / transversions = 2.57 (36/14) Gap_init rate = 0.04 (7 / 161), avg. gap size = 1.00 (7 / 7) 542 30.08 0.75 0.75 chr5qtel1M 888530 888663 (111337) C MIRb#SINE/MIR (115) 153 20 m_b268s601i2 10600 chr5qtel1M 888530 TCCTCACTTTATAGATGAGAAAACATAGACCCAAGAAGGTTAACTTAATT 888579 i i i i vv i i iii v - i C MIRb#SINE/MIR 153 TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGT-AACT 105 chr5qtel1M 888580 TACCCAAGACCACTCAGGTAATAGCCGTCAGAGTTAGGATTTAAACTCAG 888629 i ii v v i ivi v iii ii i C MIRb#SINE/MIR 104 TGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAG 55 chr5qtel1M 888630 ATGC-TCTGGTCCCAAAGCCAGTATTTTTCCCACT 888663 i vi- iii v ii i i C MIRb#SINE/MIR 54 GTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACT 20 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.67 CpG sites = 31, Kimura (unadjusted) = 41.80 Transitions / transversions = 3.44 (31/9) Gap_init rate = 0.02 (2 / 133), avg. gap size = 1.00 (2 / 2) 402 26.41 5.26 10.34 chr5qtel1M 888759 888910 (111090) C MIRc#SINE/MIR (119) 149 5 m_b268s601i3 10601 chr5qtel1M 888759 CCTCATTTCACAGAGGAGGAAAC--AAGT-----GAC-TTAAGTAACTTA 888800 i i v -- i i----- v- i i C MIRc#SINE/MIR 149 CCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTG 100 chr5qtel1M 888801 CCCAAAGTAACACAGTGAGTGAGTGTCTAAGGTCAGATTTGGACTGATGA 888850 i v iv i v - ii i i----- --i C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGGC-AGAGCCG-----GGACT--CGA 58 chr5qtel1M 888851 ACATAAGTCTTCCTAGTTCCAAACTAATGCTCAGTACTATTTTCCCTATA 888900 vi i iii ------ ii i v i v ii C MIRc#SINE/MIR 57 ACCCAGGTCTTCCTGACTCCAA------GTCCAGTGCTCTTTCCACTGCA 14 chr5qtel1M 888901 TCTACAGTAC 888910 - i v i C MIRc#SINE/MIR 13 -CCACACTGC 5 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.94 CpG sites = 27, Kimura (unadjusted) = 34.32 Transitions / transversions = 3.00 (27/9) Gap_init rate = 0.12 (18 / 151), avg. gap size = 1.28 (23 / 18) 616 23.58 7.32 1.73 chr5qtel1M 888959 889122 (110878) C MIRb#SINE/MIR (39) 229 57 m_b268s601i4 10602 chr5qtel1M 888959 CAAATAGTGTGCTAAGCGCTTTACA---ATTATCTCATTTGATCCTCACA 889005 iii v --- i C MIRb#SINE/MIR 229 CAGGCACTGTGCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACA 180 chr5qtel1M 889006 GCTATC-TGGTAGTTAGATGCTGTGGTTACCCCCATTTTACAATCAAGGA 889054 i v i - vv v i ii i --- i ivii C MIRb#SINE/MIR 179 ACAACCCTGCGAGGTAGGTATTAT---TATCCCCATTTTACAGATGAGGA 133 chr5qtel1M 889055 AATTGAGG--CAAAGGGGTTAAGTGACTGGCTCAGCTTCATCCAGATAGT 889102 i -- i i i v i ivv iv v C MIRb#SINE/MIR 132 AACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGT 83 chr5qtel1M 889103 ------CTGAGGCTGGGTTTGAACTC 889122 ------ v v v i i i C MIRb#SINE/MIR 82 AAGTGGCAGAGCCGGGATTCGAACCC 57 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.19 CpG sites = 24, Kimura (unadjusted) = 29.09 Transitions / transversions = 1.71 (24/14) Gap_init rate = 0.04 (7 / 163), avg. gap size = 2.14 (15 / 7) 196 16.67 0.00 0.00 chr5qtel1M 889346 889375 (110625) MIRc#SINE/MIR 170 199 (69) m_b268s601i5 10603 chr5qtel1M 889346 TACCTCATAGGGTTGTTATGGAGATCAGAT 889375 i i ii i MIRc#SINE/MIR 170 TACCTCACAGGGTTGTTGTGAGGATCAAAT 199 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 20.27 CpG sites = 5, Kimura (unadjusted) = 20.27 Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 38 2.78 0.00 0.00 chr5qtel1M 890797 890833 (109167) (AC)n#Simple_repeat 1 37 (0) c_b268s251i1 10604 chr5qtel1M 890797 ACACACACACACACACACACACACACACACATACACA 890833 i (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACA 37 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 332 31.63 6.22 4.72 chr5qtel1M 891572 891780 (108220) L3#LINE/CR1 3882 4093 (6) m_b268s601i6 10605 chr5qtel1M 891572 GGC-CAATCTGGGGAA-ATCTTTCTAACAATTGGAGATATGCTAACGTGG 891619 - v ii - v ii v i v v vi L3#LINE/CR1 3882 GGCTCAATATAAGGAAGAACTTTCTAACAATCAGAGCTGTCCAAAAATGG 3931 chr5qtel1M 891620 AA-------CTTGGAGAAGCTGTAGGATCCTCCTGCCTAGAGATTTTTTA 891662 ------- i v ? i iv ii v i v vv i i- v i L3#LINE/CR1 3932 AATGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGTCACTGGAGG-TGTTCA 3980 chr5qtel1M 891663 ATCAGAGCAGAGATGACAGTTTGCTAAGCATATAATGTTGATGGGATTGT 891712 v vvvi vii ii i v i -- v v vi L3#LINE/CR1 3981 AGCAGAGGCTGGATGACCACTTGTCAGGGATGT--TGTAGAAGGGATTCC 4028 chr5qtel1M 891713 TATTTTGTCACTGTTATATTGGATTAGATAG---TTGAGGTCATCTAACC 891759 iiv --iv vv vi i ii---i i -i ---- L3#LINE/CR1 4029 TGCATTG--GATGGGAGGTTGGACTAGATGACCTCTAAGGTC-CCT---- 4071 chr5qtel1M 891760 TCTGATTCTGAGATT-TGTGAT 891780 ii i - L3#LINE/CR1 4072 TCCAACTCTGAGATTCTGTGAT 4093 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.62 CpG sites = 36, Kimura (unadjusted) = 42.62 Transitions / transversions = 1.33 (36/27) Gap_init rate = 0.07 (15 / 208), avg. gap size = 1.53 (23 / 15) 14 11.61 4.88 4.88 chr5qtel1M 891965 892005 (107995) (CTTGTT)n#Simple_repeat 1 41 (0) m_b268s252i0 10606 chr5qtel1M 891965 CTTG-TCAT-TTCTTATTCTTGAGTTCTTGTTGTTGTTGTTGT 892005 - v - i -- v v (CTTGTT)n#Sim 1 CTTGTTCTTGTTCTTGTTCTT--GTTCTTGTTCTTGTTCTTGT 41 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.10 (4 / 40), avg. gap size = 1.00 (4 / 4) 506 23.77 0.00 6.14 chr5qtel1M 892015 892135 (107865) C MIRc#SINE/MIR (153) 115 2 m_b268s601i7 10607 chr5qtel1M 892015 GGGGTTAAGTGACTTTCCCAGAGTCACACAGCTAGGAAGTGTTAAGTGTC 892064 i v ii ------- v C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGC 73 chr5qtel1M 892065 TGAGGTCAGATTTGAACTCAGGTCTTCCTGACTTCAGGGCTGGTTCTCTA 892114 v vivi i i i i i v ii v v C MIRc#SINE/MIR 72 AGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTT 23 chr5qtel1M 892115 TCCACTGAGCCATCTAGCTTC 892135 vi iviv i C MIRc#SINE/MIR 22 TCCACTGCACCACACTGCCTC 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.56 CpG sites = 16, Kimura (unadjusted) = 29.04 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.06 (7 / 120), avg. gap size = 1.00 (7 / 7) 361 37.42 0.57 4.79 chr5qtel1M 892204 892377 (107623) C MIRc#SINE/MIR (87) 181 15 m_b268s601i8 10608 chr5qtel1M 892204 CCCTGTGCAGTGGTTATAACAGGTGTTCTTATTGCCAGTTTATAG-TTAG 892252 vi i vi vii i v iv v i - v C MIRc#SINE/MIR 181 CCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAG 132 chr5qtel1M 892253 GAAACTGAGTTTGAGAGCCATCAACTGCCACACTGAGGAATTAAACGATA 892302 vi v vvi i v v vii iv i -------- vi C MIRc#SINE/MIR 131 GAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAG--------GTCA 90 chr5qtel1M 892303 CGCACTGAAGAAATATCAGGGGCAGGATTTGAATCCAGGCTGTTCTGACT 892352 i viv iv i iv i v i i i i iiv i C MIRc#SINE/MIR 89 CACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACT 40 chr5qtel1M 892353 CCAGGACTACTAGGCTATCTGCTAC 892377 i v i v ivv v ii i C MIRc#SINE/MIR 39 CCAAGTCCAGTGCTCTTTCCACTGC 15 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 51.19 CpG sites = 35, Kimura (unadjusted) = 53.73 Transitions / transversions = 1.30 (35/27) Gap_init rate = 0.05 (9 / 173), avg. gap size = 1.00 (9 / 9) 267 26.58 1.25 1.25 chr5qtel1M 893473 893552 (106448) C MIRc#SINE/MIR (19) 249 170 m_b268s601i9 10609 chr5qtel1M 893473 ATTTCTAAGGCAATTTAAGTTTTGCAAAGTACTTT-ACAGGTATTAATTC 893521 v vi v viv i ii - vii vi C MIRc#SINE/MIR 249 ATTTGTATAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATCTC 200 chr5qtel1M 893522 ATTTGATTCTCACAAACAAATCTGGAAGATA 893552 i - vi vi i C MIRc#SINE/MIR 199 ATTTGATCCTCAC-AACAACCCTGTGAGGTA 170 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.38 CpG sites = 12, Kimura (unadjusted) = 33.50 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.03 (2 / 79), avg. gap size = 1.00 (2 / 2) 244 31.32 1.96 4.00 chr5qtel1M 895764 895916 (104084) L1ME3E_3end#LINE/L1 72 221 (768) m_b268s551i0 10610 chr5qtel1M 895764 GATAAATGAAACGAATGGGCATTTTTTCAAGGAAAAAAAAAACA-AAATA 895812 ii v v i ii --- vi i ii - -i i L1ME3E_3end#L 72 GGCAAAAGACATGAACAGGCATTT---CACAGAAGAGGAAA-CACGAATG 117 chr5qtel1M 895813 ATTTATAGTCATATGTAAGAAAAGGCTCTAGATCATCGTTGATTAG--AT 895860 iiiv iv -- i i v v vv iiv i i -- v L1ME3E_3end#L 118 GCCAATAAACATATG--AAAAGATGCTCAACCTCATTAGTAATCAGGGAA 165 chr5qtel1M 895861 ATGTAGACTAAAATTACCTTGGTATACCATTTTACACCTACCAAATTAGC 895910 i i i ii vv iv i i i L1ME3E_3end#L 166 ATGCAAATTAAAACCACAATGAGATACCATTTTACACCCACCAGATTGGC 215 chr5qtel1M 895911 TGAAAT 895916 vi L1ME3E_3end#L 216 AAAAAT 221 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.53 CpG sites = 31, Kimura (unadjusted) = 42.80 Transitions / transversions = 2.07 (31/15) Gap_init rate = 0.05 (8 / 152), avg. gap size = 1.12 (9 / 8) 229 23.58 0.00 4.41 chr5qtel1M 895857 895927 (104073) L1MC5a_3end#LINE/L1 162 229 (2548) m_b268s551i1 10610 chr5qtel1M 895857 AGATATGTAGACTAAAATTACCTTGGTATACCATTTTACACCTACCAAAT 895906 v i i i i vi iv iv i i L1MC5a_3end#L 162 AGAAATGCAAATTAAAACTACACTGAGATACCATTTCTCACCTATCAGAT 211 chr5qtel1M 895907 TAGCTGAAATAATCTAAAGGT 895927 i -- - i i L1MC5a_3end#L 212 TGGC--AAA-AATCCAAAAGT 229 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 29.66 CpG sites = 12, Kimura (unadjusted) = 29.66 Transitions / transversions = 3.00 (12/4) Gap_init rate = 0.04 (3 / 70), avg. gap size = 1.00 (3 / 3) 30 0.00 5.71 0.00 chr5qtel1M 896179 896213 (103787) (TATT)n#Simple_repeat 1 37 (0) c_b268s251i2 10611 chr5qtel1M 896179 TATTT-TTTATTT-TTTATTTATTTATTTATTTATTT 896213 - - (TATT)n#Simpl 1 TATTTATTTATTTATTTATTTATTTATTTATTTATTT 37 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 507 21.80 0.82 6.03 chr5qtel1M 896216 896337 (103663) C MIRc#SINE/MIR (140) 128 13 m_b268s601i10 10609 chr5qtel1M 896216 ACTGAGAC-AATTGGGGTTAAGTGAGTTGGCCAGAGTCACACAGCTAGGC 896264 i -v vv i v v ii -- C MIRc#SINE/MIR 128 ACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG-- 81 chr5qtel1M 896265 AGTGCTAAGTGTCAGAGGCCAGATTTGAACCCAGGGCCTCCTAACTTCAG 896314 ----- v v vi i i v i i i i C MIRc#SINE/MIR 80 -----TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAA 36 chr5qtel1M 896315 GGCTGGTGCTCTATCCACTGTAC 896337 v ii v i C MIRc#SINE/MIR 35 GTCCAGTGCTCTTTCCACTGCAC 13 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.85 CpG sites = 14, Kimura (unadjusted) = 26.02 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.07 (8 / 121), avg. gap size = 1.00 (8 / 8) 271 29.71 1.94 1.94 chr5qtel1M 896355 896457 (103543) L1ME2z_3end#LINE/L1 451 553 (638) m_b268s551i2 10612 chr5qtel1M 896355 GCAGCAGTCTTTATGGTGGTTAAGAACTGGAAAT--TTCAGGGATGCTCA 896402 vv v i ii i ii i i--ii -- ii L1ME2z_3end#L 451 GCAGCTTTATTCATAATAGCCAAAAACTGGAAACAGCCCAGG--TGTCCA 498 chr5qtel1M 896403 TCAAATGGAAAATGAGTGAACAAATTGTGGTATGTGCTTGTGATGGCATA 896452 vv i ii i i i v v iii v L1ME2z_3end#L 499 TCAACAGGAGAATGGATAAACAAACTGTGGTATATTCATACAATGGAATA 548 chr5qtel1M 896453 CTATT 896457 i L1ME2z_3end#L 549 CTACT 553 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.48 CpG sites = 22, Kimura (unadjusted) = 40.48 Transitions / transversions = 2.75 (22/8) Gap_init rate = 0.03 (3 / 102), avg. gap size = 1.33 (4 / 3) 21 14.18 0.00 0.00 chr5qtel1M 896932 896970 (103030) (TCTA)n#Simple_repeat 1 39 (0) m_b268s252i2 10613 chr5qtel1M 896932 TCTGTCTCTCTGTCTATCCCTCTATCTATCTATCTATCT 896970 i v i iv (TCTA)n#Simpl 1 TCTATCTATCTATCTATCTATCTATCTATCTATCTATCT 39 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 26 0.00 0.00 0.00 chr5qtel1M 896971 896995 (103005) (ATC)n#Simple_repeat 1 25 (0) c_b268s251i3 10614 chr5qtel1M 896971 ATCATCATCATCATCATCATCATCA 896995 (ATC)n#Simple 1 ATCATCATCATCATCATCATCATCA 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 532 21.46 6.99 5.52 chr5qtel1M 897648 897790 (102210) MIRc#SINE/MIR 2 146 (122) m_b268s601i11 10615 chr5qtel1M 897648 GGGGCAGTGAGGTG--GTG-------CCCTGGGCTTGGAATCAGGAAGAC 897688 i v -- ------- v i i MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr5qtel1M 897689 TCAATTTCATGAATTCAAATTTTACCTCATATATTTACTGGGTGTGTGAA 897738 iiiiv -- i i viii i i ------ i i v v MIRc#SINE/MIR 52 CTGGGTTC--GAGTCCCGGCTCTGCC------ACTTACTAGCTGTGTGAC 93 chr5qtel1M 897739 CTTGACCAAGTCACTCGACC-CTGTTTGCCTCAGTTTCCTCATCTGTAAA 897787 iv ii - v vv MIRc#SINE/MIR 94 CTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAA 143 chr5qtel1M 897788 ATG 897790 MIRc#SINE/MIR 144 ATG 146 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.95 CpG sites = 19, Kimura (unadjusted) = 25.98 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.08 (11 / 142), avg. gap size = 1.64 (18 / 11) 257 12.20 0.00 0.00 chr5qtel1M 898397 898437 (101563) MIRc#SINE/MIR 75 115 (153) m_b268s601i12 10616 chr5qtel1M 898397 CACTTCCTAGTTGTGTGACCCTGGGCATGTCACTTAACCCC 898437 v i i v i MIRc#SINE/MIR 75 CACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 13.42 CpG sites = 3, Kimura (unadjusted) = 13.42 Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 16 19.22 0.00 0.00 chr5qtel1M 898444 898479 (101521) (AGAA)n#Simple_repeat 1 36 (0) m_b268s252i3 10617 chr5qtel1M 898444 AGATAGAAAGAAAGAAGGAAGGAAGGAAGGAAATAA 898479 v i i i i v (AGAA)n#Simpl 1 AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAA 36 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 12 26.73 1.96 1.96 chr5qtel1M 898833 898883 (101117) (CCAAGAA)n#Simple_repeat 1 51 (0) m_b268s252i4 10618 chr5qtel1M 898833 CCTAGAACCAATACACTTAGCAAGAGGTACCCA-AACCTAGAACCAAGAA 898881 v v - iv v vv i v v - v (CCAAGAA)n#Si 1 CCAAGAACCAAGA-ACCAAGAACCAAGAACCAAGAACCAAGAACCAAGAA 49 chr5qtel1M 898882 CC 898883 (CCAAGAA)n#Si 50 CC 51 Matrix = Unknown Transitions / transversions = 0.22 (2/9) Gap_init rate = 0.04 (2 / 50), avg. gap size = 1.00 (2 / 2) 371 31.57 0.00 6.67 chr5qtel1M 900640 900751 (99249) MIRc#SINE/MIR 11 115 (153) m_b268s601i13 10619 chr5qtel1M 900640 TGGTATAGTGGATAGAGCAGCATCCCTGAAGTCAGGAGAATCCAAATTCA 900689 ii v viivv i i ii i iiii i MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr5qtel1M 900690 ATTCCAGACTGAGACAGTTAATACATACTAGCTGTGTGACGCTGGACACA 900739 v v i -------i ivi v vi i vi MIRc#SINE/MIR 61 AGTCCCGGCT-------CTGCCACTTACTAGCTGTGTGACCTTGGGCAAG 103 chr5qtel1M 900740 CCACTTAACCCC 900751 i i MIRc#SINE/MIR 104 TCACTTAACCTC 115 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.59 CpG sites = 23, Kimura (unadjusted) = 43.39 Transitions / transversions = 2.30 (23/10) Gap_init rate = 0.06 (7 / 111), avg. gap size = 1.00 (7 / 7) 1957 28.18 1.08 2.05 chr5qtel1M 901030 901768 (98232) L1M4_orf2#LINE/L1 1296 2027 (1267) m_b268s551i3 10620 chr5qtel1M 901030 CCTACAAAAATATAGGCTTCCCAGATTATCAGAGGAGGAAGTAAATTGCT 901079 v i i i ii v v i i iv vv i i i i vviii L1M4_orf2#LIN 1296 CCTAGAAAGACACAAACTACCGAAACTGACTCAAGAAGAAATAGAAAATC 1345 chr5qtel1M 901080 TAAATACTCCCATTTCAGAAAAAGAAATAGAACAAGTCATTAATCAACTC 901129 i vv i vv iiv i v iv v i vv i L1M4_orf2#LIN 1346 TGAATAGACCTATAACAAGTAAAGAGATTGAATTAGTAATCAAAAAACTT 1395 chr5qtel1M 901130 CCTAAAAAAAAAAAAAAAAAATCCCCAGGACCAGATGGATTTACATGTGA 901179 i v i i--------- ? v i vv L1M4_orf2#LIN 1396 CCCACAAAGAAAAG---------CCCAGGNCCAGATGGCTTCACTGGTGA 1436 chr5qtel1M 901180 ATTCTACTAAACATTCAAAGAACAATTAGTCCCAATGCTTTACAAACTGT 901229 i i v iiv v i v L1M4_orf2#LIN 1437 ATTCTACCAAACATTTAAAGAAGAATTAACACCAATCCTTCACAAACTCT 1486 chr5qtel1M 901230 TTGAAAAAATAGGGAATGAAGGAGTCCTACCAAATTCCTTTTATGACACA 901279 iv iii v i iiv v v i v i vi v L1M4_orf2#LIN 1487 TCCAAAAAATAGAAGAGGAGGGAACACTTCCCAACTCATTCTATGAGGCC 1536 chr5qtel1M 901280 GACATGGTACTGATACCTAAACCAGGTAGGTTGAAAACA-------GAAA 901322 iii viiv v ii ----- i -------i L1M4_orf2#LIN 1537 AGTATTACCCTGATACCAAAACCAGACA-----AAGACATCACAAGAAAA 1581 chr5qtel1M 901323 GAAAATTATAGACCAATCTCCCTAATGAATATTGATGCTAAAATCTTATA 901372 i i v v v v i vv L1M4_orf2#LIN 1582 GAAAACTACAGACCAATATCCCTTATGAATATAGATGCAAAAATCCTCAA 1631 chr5qtel1M 901373 TAAAATATTTGCAAAAAGACTATAGAAAACCATCCCCAGGATAATACACC 901422 i i v vv v vi v vvi vvvv v L1M4_orf2#LIN 1632 CAAAATACTAGCAAACCGAATCCAGCAACATATAAAAAGGATTATACACC 1681 chr5qtel1M 901423 ACAATCAAGTAGAATTTATACCAGGAATTCAGGGCTGGTTCAATATTAGG 901472 ii i i i v v i i i ?v i L1M4_orf2#LIN 1682 ATGACCAAGTGGGATTTATCCCAGGAATGCAAGGTTGGTTCAACATNCGA 1731 chr5qtel1M 901473 AAAACTATCAGTATAATTGACCATATTAAT-TAACAAATTAACAAAAACC 901521 v v i i vv -v i v-i L1M4_orf2#LIN 1732 AAATCAATCAATGTAATACACCATATTAATAGAATAAAG-GACAAAAACC 1780 chr5qtel1M 901522 ATACGATCATCTCAATAGATGCAGAAAAAGCATTTGATAAAATCCAACAT 901571 i i i i i L1M4_orf2#LIN 1781 ACATGATCATCTCAATAGACGCAGAAAAAGCATTTGACAAAATCCAACAC 1830 chr5qtel1M 901572 CCATTCCTATTAAAAACACTTGAGAGTATAGGAATAAATGGACTTTTCCT 901621 v v iv ii v ivv i v ivvi L1M4_orf2#LIN 1831 CCTTTCATGATAAAAACACTCAACAAACTAGGAATAGAAGGGAACTTCCT 1880 chr5qtel1M 901622 TAAAATAATCAGTAGCATCTATTTAAAACCAGCAATAAGAATCATATGTA 901671 i vv i v ivi ivv vi iiv iv iv L1M4_orf2#LIN 1881 CAACCTGATAAAGGGCATCTACGAAAAACCCACAGCTAACATCATACTTA 1930 chr5qtel1M 901672 ATGGGGACAAACTGCAACCATTCCCAATAAGATCAGGAGTGAAACAAGGT 901721 v v i v ?v v vv iii i v L1M4_orf2#LIN 1931 ATGGTGAAAGACTGAANGCTTTCCCCCTAAGATCAGGAACAAGACAAGGA 1980 chr5qtel1M 901722 TGCCCACTATCACCGTTACTATTTAATATTGTATTAGAAATGCTAGC 901768 i i v i ii v i i i i ii v L1M4_orf2#LIN 1981 TGTCCGCTCTCGCCACTTCTATTCAACATTGTACTGGAGGTTCTAGC 2027 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.24 CpG sites = 109, Kimura (unadjusted) = 36.12 Transitions / transversions = 1.15 (109/95) Gap_init rate = 0.02 (17 / 738), avg. gap size = 1.35 (23 / 17) 360 31.48 2.84 3.82 chr5qtel1M 901772 902088 (97912) L1MC5a_3end#LINE/L1 324 637 (2140) m_b268s551i5 10620 chr5qtel1M 901772 AATTTGGAATTATGCTCAAAAAGTTATCAAACTGTGCAT--ATCCTTTGA 901819 v v - viv i - --- i -- i L1MC5a_3end#L 324 AATTTGGCAATAT-CTAGCAAAATTA-CA---TATGCATTTACCCTTTGA 368 chr5qtel1M 901820 TCCAGCACTGTTACTTACTACTG-TATATCCCAAAGAGA---TCATAAAG 901865 i v vii - vvi- v i v --- ?ii i L1MC5a_3end#L 369 CCCAGCAATCCCACTT-CTAGGAATCTATCCCGAAGATACACTNGCAAAA 417 chr5qtel1M 901866 AAGGGAAAGGGACCTGTATGTGCAAGAATGTTTGTGGCAGGTCTCTTTGT 901915 viv ? - -- ii iv i ii v vvi v L1MC5a_3end#L 418 ATACGAAANG-AC--GTATGCACAAGGTTATTCATTGCAGCATTATTTGT 464 chr5qtel1M 901916 AGTGGCCAGAAACTGGAAACTGAGTGGATGCCCATCCATTGGAGAATGGC 901965 i i v i i vivviii i v v i v i L1MC5a_3end#L 465 AATAGCAAAAGACTGGAAACAACCCAAATGTCCATCAATAGGGGACTGGT 514 chr5qtel1M 901966 TGAATAAATTGTGGTATATGGATATTATGGAATGTTATTGTTCTGTAAGA 902015 i i i vv i iv i ii vvvv i L1MC5a_3end#L 515 TGAATAAACTATGGTACATCCACACAATGGAGTACTATGCAGCTGTAAAA 564 chr5qtel1M 902016 AATGATCAACAGGATGATTTC---AGAAAGGCCTGGAGAGACTTACACGA 902062 ivi ---v v i --- v vv ?iv v ii v v L1MC5a_3end#L 565 AGGAAT---GAGGAAGATCTCTATATACTGNTATGGAGTGATCTCCAGGA 611 chr5qtel1M 902063 ACTGATGCTGAGTGAAACGAGCAGGG 902088 vv iv i i vi i L1MC5a_3end#L 612 TATATTGTTAAGTGAAAAAAGCAAGG 637 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.62 CpG sites = 51, Kimura (unadjusted) = 42.20 Transitions / transversions = 1.13 (51/45) Gap_init rate = 0.05 (16 / 316), avg. gap size = 1.31 (21 / 16) 522 25.24 3.02 4.37 chr5qtel1M 901772 902003 (97997) L1ME3F_3end#LINE/L1 324 552 (438) m_b268s551i4 10620 chr5qtel1M 901772 AATTTGGAATTATGCTCAAAAAGTTATCAAAC-TGTGCATATCCTTTGAT 901820 v - iv i--- - vi i vi i L1ME3F_3end#L 324 AATTTGGCATTAT-CTCGTAAAGTTG---AACATTCGCATACCCTACGAC 369 chr5qtel1M 901821 CCAGCACTGTTACTTACTACTGTATATCCCAAAGAGA---TCATAAAGAA 901867 v vii i- v- v v --- v iv v v L1ME3F_3end#L 370 CCAGCAATTCCACTC-CTAG-GTATATACCCAAGAGAAACTCTTGCACAT 417 chr5qtel1M 901868 GGGAA--AGG-GACCTGTATGTGCAAGAATGTTTGTGGCAGGTCTCTTTG 901914 v v -- - ---- i ii i vv v i L1ME3F_3end#L 418 GTGCACCAGGAGAC----ATGTACAAGAATGTTCATAGCAGCACTGTTCG 463 chr5qtel1M 901915 TAGTGGCCAGAAACTGGAAACTGAGTGGATGCCCATCCATTGGAGAATGG 901964 i i v i vivviii i v iv L1ME3F_3end#L 464 TAATAGCAAAAAACTGGAAACAACCCAAATGTCCATCGACAGGAGAATGG 513 chr5qtel1M 901965 CTGAATAAATTGTGGTATATGGATATTATGGAATGTTAT 902003 v i vv i iv i L1ME3F_3end#L 514 ATAAATAAATTGTGGTATATTCACACAATGGAATATTAT 552 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 28.50 CpG sites = 28, Kimura (unadjusted) = 31.04 Transitions / transversions = 1.00 (28/28) Gap_init rate = 0.06 (14 / 231), avg. gap size = 1.21 (17 / 14) 15 5.56 0.00 0.00 chr5qtel1M 902553 902571 (97429) (A)n#Simple_repeat 1 19 (0) m_b268s252i5 10621 chr5qtel1M 902553 AAAAAAAAAAAAAAAGAAA 902571 i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAA 19 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 297 33.61 3.14 3.41 chr5qtel1M 902856 903237 (96763) L1MA10_3end#LINE/L1 264 644 (437) m_b268s551i7 10622 chr5qtel1M 902856 AACTGGGACACTGATGTGTTGTTGGTGGAACTGTGAAGGAATCCAACCAC 902905 ?? i v vi iiii i v i ?vii v i L1MA10_3end#L 264 AANNGGAACCCTTGTACACTGTTGGTGGGAATGTAAANTGGTGCAGCCAC 313 chr5qtel1M 902906 TCTGGGGAGCAATTTGGAACTATCCTCAAAAAGTTTTCAAATTGTGCATA 902955 v ii i i v iv - i- vv v vi - L1MA10_3end#L 314 TATGGAAAACAGTATGGAGGT-TCCTCAAAAAA-TTAAAAATAGAAC-TA 360 chr5qtel1M 902956 CCCTTTGATCCAGCAGTGTTTCTCCTGGCATTATATCTCAGAGATCTTAA 903005 v v i viiv i vvv iv i vi v L1MA10_3end#L 361 CCATATGATCCAGCAATCCCACTTCTGGGTATATATCCAAAAGAATTGAA 410 chr5qtel1M 903006 AGGAGGG----AAAGGGATCCACATGTACAAAAATGTTTGTGGCAGCCCT 903051 vv i----i i -- iv i vvvv ii v - v L1MA10_3end#L 411 ATCAGGATCTCGAAGAGAT--ATCTGCACTCCCATGTTCATTGCAG-CAT 457 chr5qtel1M 903052 TTTTTGTAGTGGCAAGAAAGTGGAAACTGAGTGGATGCCCATCAGTTGCA 903101 v iii i i v ii vi vivv ii i iiiv vv L1MA10_3end#L 458 TATTCACAATAGCCAAGATATGGAAACAACCTAAATGTCCATCGACGGAT 507 chr5qtel1M 903102 GAATGGCTGAATAAATTTTGGCATATGAATGTTTTGGGATATTATTGTTC 903151 v i v v v i iv iivv i vvv L1MA10_3end#L 508 GAATGGATAAAGAAAATGTGGTATATACATACAATGGAATATTATTCAGC 557 chr5qtel1M 903152 TTTAAGAAATGACAAGAAGGA-----TG--ATTTCAGAGAGGCCCGGAGA 903194 i i ------ ----- -- vv v -i vi vi L1MA10_3end#L 558 CTTAAAA------AAGAAGGAAATCCTGCCATTTGCGACA-ACATGGATG 600 chr5qtel1M 903195 GACCTACCTGAACTGATGCTGAGTGAAATAAG-CAGAACCAGAA 903237 i ivvv vv v i - ?vv L1MA10_3end#L 601 AACCTGGAGGACATTATGCTAAGTGAAATAAGCCAGNCACAGAA 644 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 44.45 CpG sites = 61, Kimura (unadjusted) = 45.93 Transitions / transversions = 0.97 (61/63) Gap_init rate = 0.04 (17 / 381), avg. gap size = 1.47 (25 / 17) 630 29.23 1.72 2.42 chr5qtel1M 902856 903146 (96854) L1ME3C_3end#LINE/L1 261 549 (321) m_b268s551i6 10622 chr5qtel1M 902856 AACTGGGACACTGATGTGTTGTTGGTGGAACTGTGAAGGAATCCAACCAC 902905 v i v v iiii i i v i vvii v L1ME3C_3end#L 261 AACGGGAACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTACAACCAC 310 chr5qtel1M 902906 TCTGGGGAGCAATTTGGAACTATCCTCAAAAAGTTTTCAAATTGTGCATA 902955 i i v v - viv -- v iv i L1ME3C_3end#L 311 TTTGGAGAGCAATTTGGCAATAT-CTAGTAAAG--TTGAAGATGCGCATA 357 chr5qtel1M 902956 CCCTTTGATCCAGCAGTGTTTCTCCT-GGCATTATATCTCAGAGA---TC 903001 vi i i viiv - i - i ii --- L1ME3C_3end#L 358 CCCTACGACCCAGCAATTCCACTCCTAGGTA-TATACCCTAGAGAAACTC 406 chr5qtel1M 903002 TTAAAGGAG-GGAAAGGGATCCACATGTACAAAAATGTTTGTGGCAGCCC 903050 iiv v v - v v i --v i ii v - v L1ME3C_3end#L 407 TCGCACGTGTGCACAAGGA--GACATGTACAAGAATGTTCATTGCAG-CA 453 chr5qtel1M 903051 TTTTTTGTAGTGGCAAGAAAGTGGAAACTGAGTGGATGCCCATCAGTTGC 903100 v i i i i v vivv ii i iiv v L1ME3C_3end#L 454 TTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCAACAGG 503 chr5qtel1M 903101 AGAATGGCTGAATAAATTTTGGCATATGAATGTTTTGGGATATTAT 903146 v i v i vv iivv i i L1ME3C_3end#L 504 AGAATGGATAAATAAATTGTGGTATATTCATACAATGGAATACTAT 549 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.49 CpG sites = 46, Kimura (unadjusted) = 37.82 Transitions / transversions = 1.24 (46/37) Gap_init rate = 0.03 (10 / 290), avg. gap size = 1.20 (12 / 10) 316 33.06 11.29 0.00 chr5qtel1M 904362 904485 (95515) MIRc#SINE/MIR 11 148 (120) m_b268s601i14 10623 chr5qtel1M 904362 TGGTGCAGTAGATAGACTAGTAGGCCTTAAGACATGAAGACCAGAGTTTT 904411 i v vi v i i i vi v v v i iv MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr5qtel1M 904412 AATCTCAACTCAGAAACTTGATAGTCA---------AGCCAAGGC----- 904447 i i ii v vv iv iii---------i v v ----- MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTA 110 chr5qtel1M 904448 GTCTCTGTTTATCTCAGTTTCTTTCTCTGTAAAATGGG 904485 ii v vvii i iv MIRc#SINE/MIR 111 ACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.96 CpG sites = 23, Kimura (unadjusted) = 44.87 Transitions / transversions = 1.28 (23/18) Gap_init rate = 0.02 (2 / 123), avg. gap size = 7.00 (14 / 2) 180 27.01 9.79 6.80 chr5qtel1M 904533 904675 (95325) L2a_3end#LINE/L2 335 481 (36) m_b268s601i15 10624 chr5qtel1M 904533 CACTATCTGGTCCATAGTGGGT-TTCCACCTAGTGGTTTGT--GTTGTCA 904579 i i-- v ivi - ii i v vi --i v L2a_3end#LINE 335 CACCATCTGA--CATACTATATATTTTACTTATTTATTTGTTTATTGTCT 382 chr5qtel1M 904580 GTC-----CCACCAGTCTGTGATCTCCATAGGAGCAGGGACACCCTTTGC 904624 ----- i vv i v ii i --- i - L2a_3end#LINE 383 GTCTCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGA---CTTTTG- 428 chr5qtel1M 904625 AACTCTCTTTTGGTTCCTAC---ATACCAAG-GCCT--GACATGTATCAG 904668 --- v v iv i --- v v - --i - ii v L2a_3end#LINE 429 ---TCTGTTTTGTTCACTGCTGTATCCCCAGCGCCTAGAACA-GTGCCTG 474 chr5qtel1M 904669 GTTCATA 904675 iv L2a_3end#LINE 475 GCACATA 481 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.37 CpG sites = 21, Kimura (unadjusted) = 34.37 Transitions / transversions = 1.40 (21/15) Gap_init rate = 0.11 (16 / 142), avg. gap size = 1.50 (24 / 16) 205 29.63 7.94 6.25 chr5qtel1M 904562 904687 (95313) L2c_3end#LINE/L2 341 468 (10) m_b268s601i16 10624 chr5qtel1M 904562 TAGTGGTTTGTGT---TGTCAGTC----CCACCAGTCTGTGATCTCCATA 904604 i v i v --- v ---- i v v v i L2c_3end#LINE 341 TAATTGTCTGTTTACNTGTCTGTCTCCTCCACTAGACTGTGAGCTCCTTG 390 chr5qtel1M 904605 GGAGCAGGGACACCCTTTGCAACTCTCTTTTGGTTCCTACATACCAAGGC 904654 i i -- v v viv i vii vv ------ iv L2c_3end#LINE 391 AGGGCAGGG--ACCGTGTCTTATTCATCTTTGTATCC------CCAGCGC 432 chr5qtel1M 904655 CTGACATGTATCAGGTTC---ATAAATGCTTCTTAA 904687 i ii vi iv --- i v i L2c_3end#LINE 433 CTGGCACATAGTAGGCGCTCAATAAATGTTTGTTGA 468 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.95 CpG sites = 18, Kimura (unadjusted) = 38.31 Transitions / transversions = 1.06 (18/17) Gap_init rate = 0.09 (11 / 125), avg. gap size = 1.64 (18 / 11) 293 33.73 1.20 0.00 chr5qtel1M 904697 904779 (95221) C MIRc#SINE/MIR (184) 84 1 m_b268s601i17 10625 chr5qtel1M 904697 CTAAGAAAGAGCGGTGCTAGAATATCAACCCATGTCTTC-TGAGTTCAAA 904745 iv ivi i v ii i iviv v - v i i C MIRc#SINE/MIR 84 CTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr5qtel1M 904746 TGTAGGGATCTTTCCATTATACCATGCTGCCTTG 904779 vi v v i ii ii i C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTGCACCACACTGCCTCG 1 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.24 CpG sites = 18, Kimura (unadjusted) = 47.29 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.01 (1 / 82), avg. gap size = 1.00 (1 / 1) 387 32.33 0.61 5.13 chr5qtel1M 908538 908700 (91300) MIR#SINE/MIR 34 189 (73) m_b268s601i18 10626 chr5qtel1M 908538 TGGAGATAGACATAATGTACCCAAGTTTTAATTAAGCCTCGAACAGTTAC 908587 vi ------ i iii iv ivv v viv v MIR#SINE/MIR 34 TGGAGCCAGAC------TGCCTGGGTTCGAATCCCGGCTCTGCCACTTAC 77 chr5qtel1M 908588 TAACTGTATACCCCTTGCTAAATCAATTAAACCTCAGTTTGCTTTAATTT 908637 i i iv i v vi i i v - vv v i i i MIR#SINE/MIR 78 TAGCTGTGTGACCTTGGGCAAGTTACTTAA-CCTCTCTGTGCCTCAGTTT 126 chr5qtel1M 908638 CCTCACCTCTTTAAGTGGGGATAACATTATCACCTAACTTGGAAGGTTAA 908687 i v v- i i v vi v iiv i iv MIR#SINE/MIR 127 CCTCATCTGTA-AAATGGGGATAATAATAGTACCTACCTCATAGGGTTGT 175 chr5qtel1M 908688 TATGA-CATTAAAT 908700 i -v MIR#SINE/MIR 176 TGTGAGGATTAAAT 189 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.00 CpG sites = 27, Kimura (unadjusted) = 43.14 Transitions / transversions = 1.17 (27/23) Gap_init rate = 0.06 (9 / 162), avg. gap size = 1.00 (9 / 9) 17 37.36 0.00 0.00 chr5qtel1M 908901 908961 (91039) (AT)n#Simple_repeat 1 61 (0) m_b268s252i6 10627 chr5qtel1M 908901 ATATATATACACACACACAAATATAGATAAGCATGCATATACATATGTAA 908950 i i i i i v v vii ii i i v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr5qtel1M 908951 ATGTATATGTA 908961 i i (AT)n#Simple_ 51 ATATATATATA 61 Matrix = Unknown Transitions / transversions = 3.25 (13/4) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 224 33.33 3.81 0.00 chr5qtel1M 909333 909437 (90563) L3#LINE/CR1 3980 4088 (11) m_b268s601i19 10628 chr5qtel1M 909333 AAGGAAAACCTGCTTGAGCAATTTTCAGAGCT-TTGGA-AATAAATT--T 909378 v i iv vv v v v i v - v - vii -- L3#LINE/CR1 3980 AAGCAGAGGCTGGATGACCACTTGTCAGGGATGTTGTAGAAGGGATTCCT 4029 chr5qtel1M 909379 GTGTCCAAGTAGAGGTTAGACAACATAACCTCTGAGATTAGTTCCATGTC 909428 ii ivi vvi i v v i i i ivv vv L3#LINE/CR1 4030 GCATTGGATGGGAGGTTGGACTAGATGACCTCTAAGGTCCCTTCCAACTC 4079 chr5qtel1M 909429 TGAGATGCT 909437 v L3#LINE/CR1 4080 TGAGATTCT 4088 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.32 CpG sites = 15, Kimura (unadjusted) = 44.32 Transitions / transversions = 0.75 (15/20) Gap_init rate = 0.03 (3 / 104), avg. gap size = 1.33 (4 / 3) 470 22.67 6.25 2.00 chr5qtel1M 909825 909968 (90032) C MIR3#SINE/MIR (7) 201 52 m_b268s601i20 10629 chr5qtel1M 909825 AAAATCATGAGATGT-AGAGCTGGAAGTCCCTTCTGAATTCA-AGAATCC 909872 i iii - vvv i iv iv -vv i C MIR3#SINE/MIR 201 AGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCC 152 chr5qtel1M 909873 AACCCCCTTCAGTTTCCAGA--AGGAAACTGAAGCACAGA-----GAAGG 909915 - v v -- i v ----- v C MIR3#SINE/MIR 151 AACCCCCT-CATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGT 103 chr5qtel1M 909916 GATTTGCTCAAAGGTCACACAATTTGTGAGTGTCAGAGTCAGTTCCTGGA 909965 i i - ii?v v v i i -vv i C MIR3#SINE/MIR 102 GACTTGCCC-AAGGTCACACAGCNAGTTAGTGGCAGAGCCGG-GACTAGA 55 chr5qtel1M 909966 ACC 909968 C MIR3#SINE/MIR 54 ACC 52 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.51 CpG sites = 16, Kimura (unadjusted) = 27.48 Transitions / transversions = 1.00 (16/16) Gap_init rate = 0.05 (7 / 143), avg. gap size = 1.71 (12 / 7) 20 16.89 0.00 0.00 chr5qtel1M 914630 914663 (85337) (A)n#Simple_repeat 1 34 (0) m_b268s252i7 10630 chr5qtel1M 914630 AATAAAAAAAAAAAAAAGAAAGAAAGAAAGAAAA 914663 v i i i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 34 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 19 8.18 0.00 0.00 chr5qtel1M 914867 914892 (85108) (C)n#Simple_repeat 1 26 (0) m_b268s252i8 10631 chr5qtel1M 914867 CCCCCAACCCCCCCCCCCCCCCCCCC 914892 vv (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCC 26 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 284 33.91 4.93 3.43 chr5qtel1M 915487 915831 (84169) L1MD_orf2#LINE/L1 1896 2245 (1049) m_b268s551i8 10632 chr5qtel1M 915487 CATTCATAAAAACATTTATCTAAAACTAAAAGCATCACATAAAATGGGGT 915536 ii i ----- i v i --- i ivv v v L1MD_orf2#LIN 1896 CATCTACAAAAA-----ACCTACAGCTAA---CATCATACTTAATGGTGA 1937 chr5qtel1M 915537 CATATTAGAAACTTTTCCAATAAATGCAGAAGTAAAGCAAGGATGATTAC 915586 v v i ii vi i vv ivv i i ii i viii L1MD_orf2#LIN 1938 AAGACTGAATGCTTTCCCCCTAAGATCGGGAACAAGGCAAGGATGTCCGC 1987 chr5qtel1M 915587 TCTCCTCACTCTT-------------CTGGAAATGCTAGCAA---TAACA 915620 vi ------------- i v v ---i i L1MD_orf2#LIN 1988 TCTCACCACTCTTATTCAACATAGTACTGGAAGTTCTAGCCAGTGCAATA 2037 chr5qtel1M 915621 ACACAAGAGAAAGGAAA-GAAAGTAATAAAGACAGGTAAAGATCAACTCA 915669 vi - -i vv v iv v i vv v v L1MD_orf2#LIN 2038 AGGCAAGA-AAAGGAAATAAAAGGCATACAGATTGGAAAGGAAGAAATAA 2086 chr5qtel1M 915670 AACTATCCCCGTTTGTTGATGAGAGGATGCTTTACTTGGACAAACCAAGG 915719 i ii iv v v vv i v i v v v i L1MD_orf2#LIN 2087 AACTGTCCCTATTTGCAGATGACATGATTGTCTACGTAGAAAATCCCAAG 2136 chr5qtel1M 915720 GAGTCAGCAGAGACACCAATTCAGGTAGTTATTAATTTATGCAAAGCTGC 915769 i vi i i v ivv vv iv i v v i v vv i ii L1MD_orf2#LIN 2137 GAATCTACAAAAAAACTCCTAGAACTAATAAGTGAGTTCAGCAAGGTCGC 2186 chr5qtel1M 915770 AGGATATATAGTGAATTGCCCTAAATTAAGAGCATTTCTAGGAAATAGTA 915819 i vii ? ivvv vv i vv i v--- v L1MD_orf2#LIN 2187 AGGATACAAGATNAACATACAAAAATCAATTGTATTTCTAT---ATACTA 2233 chr5qtel1M 915820 ACAAAGTACACG 915831 i v v L1MD_orf2#LIN 2234 GCAATGAACACG 2245 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 44.27 CpG sites = 54, Kimura (unadjusted) = 45.94 Transitions / transversions = 0.92 (54/59) Gap_init rate = 0.04 (15 / 344), avg. gap size = 1.93 (29 / 15) 332 30.73 7.02 4.23 chr5qtel1M 915487 915785 (84215) L1MC_orf2#LINE/L1 1896 2202 (1092) m_b268s551i9 10632 chr5qtel1M 915487 CATTCATAAAAACATTTATCTAAAACTAAAAGCATCACATAAAATGGGGT 915536 ii i ----- i v i --- i ivv v v L1MC_orf2#LIN 1896 CATCTACAAAAA-----ACCTACAGCTAA---CATCATACTTAATGGTGA 1937 chr5qtel1M 915537 CATATTAGAAACTTTTCCAATAAATGCAGAAGTAAAGCAAGGATGATTAC 915586 v v i ? i i iv ivv i ii i viiv L1MC_orf2#LIN 1938 GAAACTNGAAGCTTTCCCGCTAAGATCAGGAACAAGGCAAGGATGTCCCC 1987 chr5qtel1M 915587 TCTCCTCACTCTT-------------CTGGAAATGCTAGC-AAT--AACA 915620 vi i ------------- i v - -- i L1MC_orf2#LIN 1988 TCTCACCACTCCTTTTCAACATCGTACTGGAAGTCCTAGCTAATGCAATA 2037 chr5qtel1M 915621 ACACAAGAGAAAGGAAA-GAAAGTAATAAAGACAGGTAAAGATCAACTCA 915669 v - -i vv v iv v i vv v v L1MC_orf2#LIN 2038 AGACAAGA-AAAGGAAATAAAAGGTATACAGATTGGGAAGGAAGAAATAA 2086 chr5qtel1M 915670 AACTATCCCCGTTTGTTGATGAGAGGATGCTTTACTTGGACAAACCAAGG 915719 i iii i iv v v vv i iv i v v i ii L1MC_orf2#LIN 2087 AACTGTCTTTGTTCGCAGATGACATGATTGTCTATGTAGAAAATCCGAAA 2136 chr5qtel1M 915720 GAGTCAGCAGAGACACCAATTCAGGTAGTTATTAAT---TTAT-GCAAAG 915765 i ii i i ---- i vv v ii v v--- - i L1MC_orf2#LIN 2137 GAATCGACAAAAA----AACTCCTGGAACTAATAAGCGATTATAGCAAGG 2182 chr5qtel1M 915766 CTGCAGGATATATAGTGAAT 915785 i i vi v L1MC_orf2#LIN 2183 TTGCAGGATACAAGGTTAAT 2202 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.38 CpG sites = 49, Kimura (unadjusted) = 40.76 Transitions / transversions = 1.26 (49/39) Gap_init rate = 0.06 (19 / 298), avg. gap size = 1.79 (34 / 19) 241 33.31 9.86 0.92 chr5qtel1M 915519 916015 (83985) L1PREC2_orf2#LINE/L1 1920 2460 (834) m_b268s551i11 10632 chr5qtel1M 915519 CATCACATAAAATGGGGTCATATTAGAAACTTTTCCAATAAATGCAGAAG 915568 i ivi vvv vii i i v i vv i vi v ivi L1PREC2_orf2# 1920 CATCATACTGAATGGGCAAAAGCTGGAAGCATTCCCCTTGAAAACCGGCA 1969 chr5qtel1M 915569 TAAAGCAAGGATGATTACTCTCCTCACTC---TTC----------TGGAA 915605 i ii viiv vi --- ---------- L1PREC2_orf2# 1970 CAAGACAAGGATGCCCTCTCTCACCACTCCTATTCAACATAGTATTGGAA 2019 chr5qtel1M 915606 ATGCTAGCAATAACAA-CA--CAAGAGAAAGGAAAGAAAGTAATAAAGAC 915652 i v i v v i - -- i vi i vv vv i i L1PREC2_orf2# 2020 GTCCTGGCCAGAGCAATCAGGCAAGAGAAAGAAATAAAGGGCATCCAAAT 2069 chr5qtel1M 915653 AGGTAAAGATCAACTCAAACTATCCCCGTTTGTTGATGAGAGGATGCTTT 915702 v i vv v i iv i v v v v L1PREC2_orf2# 2070 AGGAAGAGAGGAAGTCAAACTATCCCTGTTTGCAGACGACATGATTCTAT 2119 chr5qtel1M 915703 ACTTGGACAAACCAAGGGAGTCAG--CAGAGACACCAATTCAGGTAGTTA 915750 ii i v v v vi vv i -- i ii v -- ? v ii v L1PREC2_orf2# 2120 ATCTAGAAAACCCCATAGTCTCGGCCCAAAAGCTCC--TTNAGCTGATAA 2167 chr5qtel1M 915751 TTAATTTATGCAAAGCTGCAGGATATATAGTGAATTGCCCTAAATTAAGA 915800 vi i vv i v i v i v vvv vv i vv L1PREC2_orf2# 2168 ACAACTTCAGCAAAGTTTCAGGATACAAAATCAATGTACAAAAATCACTA 2217 chr5qtel1M 915801 GCATTTCTAGGAAATAGTAACA---AAGTACACGAAT--AATTGAGA--G 915843 i viv vi ii --- i- iv ii-- iii -- L1PREC2_orf2# 2218 GCATTCCTATACACCAACAACAGCCAAGC-CGAGAGCCAAATCAGGAACG 2266 chr5qtel1M 915844 AAATCCCA------------ACAAATA-AGTAAAATATGCAG----ACAG 915876 v ------------ v - i ivi ---- L1PREC2_orf2# 2267 CAATCCCATTCACAATTGCCACAAAAAGAATAAAATACCTAGGAATACAG 2316 chr5qtel1M 915877 C-ATCTAGGAA--TTAAAGAGTTGTATAAATTCTATTGCAAAGCAATCCT 915923 - v i i -- v vi v i vvvvv i i v v L1PREC2_orf2# 2317 CTAACCAGGGAGGTGAAAGATCTCTACAATGAGAATTACAAAACACTGCT 2366 chr5qtel1M 915924 TAAAGAAATGCAG-GACAACCTAAA-AGGTAGAGGAATCTTCAGTGCTCA 915971 i - - ii vi - ii i ii iv vi L1PREC2_orf2# 2367 CAAAGAAAT-CAGAGATGACACAAACAAATGGAAAAACATTCCATGCTCA 2415 chr5qtel1M 915972 TGACTAGGTTGTGTCAACATAATAAAAATAGCAAATAC--CCCAAA 916015 iv vv vi i vi v i -v -- L1PREC2_orf2# 2416 TGGATAGGAAGAATCAATATCGTTAAAATGGC-CATACTGCCCAAA 2460 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 43.52 CpG sites = 83, Kimura (unadjusted) = 44.97 Transitions / transversions = 1.02 (83/81) Gap_init rate = 0.04 (21 / 496), avg. gap size = 2.57 (54 / 21) 334 31.62 8.12 0.47 chr5qtel1M 915519 915715 (84285) L1PB_orf2#LINE/L1 1920 2131 (1163) m_b268s551i10 10632 chr5qtel1M 915519 CATCACATAAAATGGGGTCATATTAGAAACTTTTCCAATAAATGCAGAAG 915568 ? i ivi vv vi ii i v i vv i ivi v i i L1PB_orf2#LIN 1920 CATNATACTGAATGGGGAAAAGTTGAAAGCATTCCCCCTGAGAACTGGAA 1969 chr5qtel1M 915569 TAAAGCAAGGATGATTACTCTCCTCACTCTT-------------CTGGAA 915605 i ii vii vi ii ------------- L1PB_orf2#LIN 1970 CAAGACAAGGATGCCCACTCTCACCACTTCTNTTCAACATAGTACTGGAA 2019 chr5qtel1M 915606 ATGCTAGCAATAACAAC---ACAAGAGAAAGGAAAGAAAGTAATAAAGAC 915652 i v v v i i--- i vi i vv vv i i L1PB_orf2#LIN 2020 GTCCTAGCCAGAGCAATCAGACAAGAGAAAGAAATAAAGGGCATCCAAAT 2069 chr5qtel1M 915653 AGGTAAAGATCAACTCAAACTATCCCCGTTTGTTGATGAGAGGATGCTTT 915702 v vv v i v i i v v vv ? L1PB_orf2#LIN 2070 CGGTAAAGAGGAAGTCAAACTGTCGCTGTTTGCTGATGATATGATCGTNT 2119 chr5qtel1M 915703 ACTTGGACAAACC 915715 i i - L1PB_orf2#LIN 2120 ACCTAGA-AAACC 2131 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 42.66 CpG sites = 34, Kimura (unadjusted) = 42.66 Transitions / transversions = 1.21 (34/28) Gap_init rate = 0.02 (3 / 196), avg. gap size = 5.67 (17 / 3) 247 27.57 7.48 8.49 chr5qtel1M 916082 916188 (83812) MIRc#SINE/MIR 45 150 (118) m_b268s601i21 10633 chr5qtel1M 916082 GGAAGACCTTAGCTTACAAGAAGCCTCAA----GACACTTAATGGCTGTG 916127 vi i ii----- i i ii---- v v i MIRc#SINE/MIR 45 GGAAGACCTGGGTTCG-----AGTCCCGGCTCTGCCACTTACTAGCTGTG 89 chr5qtel1M 916128 TGACCTTGGGCAAACTCCTGGACACCT----GTCTCTGTGTTCTCAAGTA 916173 iiiv vi vi ---- i v v i -- - MIRc#SINE/MIR 90 TGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCA--T- 136 chr5qtel1M 916174 ACTGTAAACTGAAGA 916188 - v ii MIRc#SINE/MIR 137 -CTGTAAAATGGGGA 150 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.35 CpG sites = 18, Kimura (unadjusted) = 35.81 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.10 (11 / 106), avg. gap size = 1.55 (17 / 11) 252 22.22 5.26 5.26 chr5qtel1M 916113 916188 (83812) MIRb#SINE/MIR 78 153 (115) m_b268s601i22 10633 chr5qtel1M 916113 CACTTAATGGCTGTGTGACCTTGGGCAAACTCCTGGACACCT----GTCT 916158 v i ii v vi vi ---- i MIRb#SINE/MIR 78 CACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCT 127 chr5qtel1M 916159 CTGTGTTCTCAAGTAACTGTAAACTGAAGA 916188 v v i -- -- v ii MIRb#SINE/MIR 128 CAGTTTCCTCA--T--CTGTAAAATGGGGA 153 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.73 CpG sites = 9, Kimura (unadjusted) = 26.73 Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.07 (5 / 75), avg. gap size = 1.60 (8 / 5) 25 11.88 0.00 0.00 chr5qtel1M 917339 917375 (82625) (A)n#Simple_repeat 1 37 (0) m_b268s252i9 10634 chr5qtel1M 917339 AAAAAAAAAAAAAAAAAAAAAAAAGGAAGAAAATAAA 917375 ii i v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 37 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 321 24.18 0.00 11.36 chr5qtel1M 917542 917639 (82361) C MIRc#SINE/MIR (179) 89 2 m_b268s601i23 10635 chr5qtel1M 917542 CACAGCTAGCAAGTATTAAGTGTCCGAGGTCAGTTTTGAACTCAGTTCCT 917591 ------- v v vivi vi i i v i C MIRc#SINE/MIR 89 CACAGCTAG-------TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTT 47 chr5qtel1M 917592 CCTGACTTCAGGGCTGGTGCTCTGTCCACTGTACCATCTAGCTGCCTC 917639 i i v ii v i i---i C MIRc#SINE/MIR 46 CCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC---ACTGCCTC 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.21 CpG sites = 13, Kimura (unadjusted) = 29.43 Transitions / transversions = 1.62 (13/8) Gap_init rate = 0.10 (10 / 97), avg. gap size = 1.00 (10 / 10) 180 27.59 5.56 10.83 chr5qtel1M 917835 917960 (82040) X24_LINE#LINE/L2 156 275 (39) m_b268s601i24 10636 chr5qtel1M 917835 CAAAGTGTCCAAAGTGACTCCATTTTGTCAAGCTCCTCCAT---CTGGTC 917881 i ------ ii v i i v - vi ---i v X24_LINE#LINE 156 CAAGGTGT------TGACTTTAATCTATAAAGC-CCTATATGGTTTGGGC 198 chr5qtel1M 917882 CCTGGCCTTTACCTCAGAGACCACTGCCCCCACCCTTTATAGGGGAACA- 917930 --- i i i -- i i v ? ii vv vv i- X24_LINE#LINE 199 CCTGG---TTACCTTAGAGATCGC--CTCTCTCCCTNTGCACCGTCACGG 243 chr5qtel1M 917931 -AATGAAGCAACAGCTAAA--GCTCTTACTAAC 917960 - vi - v ii-- i i X24_LINE#LINE 244 CAATTGAG-ATCAGCTAGGATGCTCCTGCTAAC 275 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.98 CpG sites = 20, Kimura (unadjusted) = 35.85 Transitions / transversions = 1.82 (20/11) Gap_init rate = 0.14 (17 / 125), avg. gap size = 1.18 (20 / 17) 16 13.75 10.20 0.00 chr5qtel1M 918400 918448 (81552) (CCCTCT)n#Simple_repeat 1 54 (0) m_b268s252i10 10637 chr5qtel1M 918400 CCCCCTCCCTCTCTTTCT-CCTCTTCTTCT-CC-CT-CCTCTCCCTGT-C 918444 i ii - i i - - - v - (CCCTCT)n#Sim 1 CCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCC 50 chr5qtel1M 918445 CTCT 918448 (CCCTCT)n#Sim 51 CTCT 54 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.10 (5 / 48), avg. gap size = 1.00 (5 / 5) 28 0.00 0.00 0.00 chr5qtel1M 918740 918766 (81234) (G)n#Simple_repeat 1 27 (0) c_b268s251i4 10638 chr5qtel1M 918740 GGGGGGGGGGGGGGGGGGGGGGGGGGG 918766 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGG 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 14 27.30 2.56 5.26 chr5qtel1M 920588 920665 (79335) (GAAA)n#Simple_repeat 1 76 (0) m_b268s252i11 10639 chr5qtel1M 920588 GAAAG-AAGAATCAGAATAAAAGGAAAAAAAATGAGAAAGCAAAAAACAA 920636 - -- - i i i ivi - i vi (GAAA)n#Simpl 1 GAAAGAAAGAA--AGAA-AGAAAGAAAGAAAGAAAGAAAG-AAAGAAAGA 46 chr5qtel1M 920637 AACAAACAAACAAA-CAAGAAAAAGTGAAA 920665 v v v -v i iv (GAAA)n#Simpl 47 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 76 Matrix = Unknown Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.08 (6 / 77), avg. gap size = 1.00 (6 / 6) 20 3.42 0.00 3.23 chr5qtel1M 921167 921198 (78802) (TTTATT)n#Simple_repeat 1 31 (0) m_b268s252i12 10640 chr5qtel1M 921167 TTTTTTTTTATTTTTATTTTTATTTTTTATTT 921198 v - (TTTATT)n#Sim 1 TTTATTTTTATTTTTATTTTTA-TTTTTATTT 31 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 15 5.48 0.00 0.00 chr5qtel1M 921465 921483 (78517) (T)n#Simple_repeat 1 19 (0) m_b268s252i14 10641 chr5qtel1M 921465 TTTGTTTTTTTTTTTTTTT 921483 v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 397 24.87 2.90 6.77 chr5qtel1M 922064 922201 (77799) MIRc#SINE/MIR 16 148 (120) m_b268s601i25 10642 chr5qtel1M 922064 CAGTGTCCAGAGCCCTGCCTTTGCACTCAGGAATACTCAATGCCAGAGGT 922113 vvv v vvi v v v i--- ----- MIRc#SINE/MIR 16 CAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC---TG-----GGT 57 chr5qtel1M 922114 TTAAATCCTGCCTCAGACACTTATCGGGTATGTCAGCCTGGCCAAGTCAC 922163 ii i i v v v iii v i v v i v MIRc#SINE/MIR 58 TCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCAC 107 chr5qtel1M 922164 TCAAGCTTGTTT--GCCT--GTTTCCTCATCTGTAAAATGAG 922201 i - i v i -- -- i MIRc#SINE/MIR 108 TTAA-CCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.04 CpG sites = 15, Kimura (unadjusted) = 30.30 Transitions / transversions = 0.88 (15/17) Gap_init rate = 0.08 (11 / 137), avg. gap size = 1.18 (13 / 11) 182 24.10 17.05 0.98 chr5qtel1M 922935 923022 (76978) L2#LINE/L2 2548 2649 (433) m_b268s601i26 10643 chr5qtel1M 922935 CCTAAAGTTTTGGAGTT---CTAGGCTC-TCTCCTTTTT-----CCCCAC 922975 v iii i--- v i - i i i----- L2#LINE/L2 2548 CCAAAAACCTTGGAGTCATCCTTGACTCCTCTCTTTCTCTCACACCCCAC 2597 chr5qtel1M 922976 CTACTATTCATAAGCCA--CTTGTGGAGTTCTAC----AAAATATATTCA 923019 v v v i v v -- i v - i ---- i L2#LINE/L2 2598 ATCCAATCCATCAGCAAATCCTGTCG-GCTCTACCTTCAAAATATATCCA 2646 chr5qtel1M 923020 TAA 923022 v L2#LINE/L2 2647 GAA 2649 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.64 CpG sites = 12, Kimura (unadjusted) = 29.64 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.07 (6 / 87), avg. gap size = 2.67 (16 / 6) 18 4.77 0.00 0.00 chr5qtel1M 923104 923125 (76875) (AG)n#Simple_repeat 1 22 (0) m_b268s252i15 10644 chr5qtel1M 923104 AGAGAGAGAGAAAGAGAGAGAG 923125 i (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAG 22 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 42 32.78 1.84 0.00 chr5qtel1M 923286 923303 (76697) (AG)n#Simple_repeat 1 18 (148) m_b268s252i16 10645 chr5qtel1M 923286 AGAGAGAGACAGACAAAG 923303 v v i (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAG 18 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 54 0.00 0.00 0.00 chr5qtel1M 923304 923349 (76651) (AC)n#Simple_repeat 1 46 (0) c_b268s251i5 10646 chr5qtel1M 923304 ACACACACACACACACACACACACACACACACACACACACACACAC 923349 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACAC 46 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 42 32.78 1.84 0.00 chr5qtel1M 923350 923493 (76507) (AG)n#Simple_repeat 19 165 (1) m_b268s252i16 10647 chr5qtel1M 923350 G-GAGTAAGAAAAAGTGAGAAACAGAGATTCTGAAAAATAGGGAGAGACA 923398 - vi i i v i v vvvv i i v i v (AG)n#Simple_ 19 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 68 chr5qtel1M 923399 GAGCAAGAGTCACAGAGAGCCAGAGAGTGA-AAAAAGAGAAGGAGAGAGA 923447 vi vv v vv v - i i ii (AG)n#Simple_ 69 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 118 chr5qtel1M 923448 CAGAGTGAGTCAGAGAGGCAAAGAGAAATACAGACACAGAGA-AGAG 923493 v v vv iv i i v v v v - (AG)n#Simple_ 119 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 165 Matrix = Unknown Transitions / transversions = 0.60 (15/25) Gap_init rate = 0.02 (3 / 143), avg. gap size = 1.00 (3 / 3) 43 0.00 0.00 0.00 chr5qtel1M 925179 925215 (74785) (TG)n#Simple_repeat 1 37 (0) c_b269s251i0 10648 chr5qtel1M 925179 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 925215 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 37 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 224 38.40 0.80 0.00 chr5qtel1M 927172 927296 (72704) L2d2_3end#LINE/L2 137 262 (293) m_b269s601i0 10649 chr5qtel1M 927172 CCCAAATCAGTCTCCACACCAGGAACACACTCTGCCTTCAGCTCCAGCTC 927221 i vii iv i v i v ii v iiv vv v v L2d2_3end#LIN 137 CTCACGCCGTTCCCCCCGCCTGGAATGCCCTTCCCCTTCCTCTCCACCTA 186 chr5qtel1M 927222 TTGAAGTCCCTGGTTTCCTTCCAGATTCACTTCAAATTCTGCTGCCAGCA 927271 iv i ivvviv v iii vi ? ii iv vv i L2d2_3end#LIN 187 TCCAAATCCTACCCATCCTTCAAGGCCCAGCTCAAATNCCACCTCCTCCG 236 chr5qtel1M 927272 GGAAGCCTTTCCTG-CTCCTTCAGTC 927296 v i - iv i i L2d2_3end#LIN 237 TGAAGCCTTCCCTGACCACTCCAGCC 262 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 49.64 CpG sites = 26, Kimura (unadjusted) = 56.37 Transitions / transversions = 1.18 (26/22) Gap_init rate = 0.01 (1 / 124), avg. gap size = 1.00 (1 / 1) 223 24.19 3.17 1.56 chr5qtel1M 927287 927349 (72651) C L2c_3end#LINE/L2 (2) 476 413 m_b269s601i1 10650 chr5qtel1M 927287 TCCTTCAGTCAATAAGCTTTTATTAAGTAGCTGAAGATGTTCCAGGCCCT 927336 v v i i v i i- iv vv v v C L2c_3end#LINE 476 TCATTCATTCAACAAACATTTATTGAGC-GCCTACTATGTGCCAGGCGCT 428 chr5qtel1M 927337 GGGGATGT--AGATG 927349 ii-- C L2c_3end#LINE 427 GGGGATACAAAGATG 413 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.17 CpG sites = 7, Kimura (unadjusted) = 29.38 Transitions / transversions = 0.88 (7/8) Gap_init rate = 0.03 (2 / 62), avg. gap size = 1.50 (3 / 2) 672 29.54 6.79 0.43 chr5qtel1M 927995 928215 (71785) MIRb#SINE/MIR 27 261 (7) m_b269s601i2 10651 chr5qtel1M 927995 AGAGTGCTGGGCCTGGAGCAGGAGAGGCCCAAGTTTGGATCTGCCCTCAG 928044 ii v vii ivi v i iii i i ivvv v MIRb#SINE/MIR 27 AGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTCTG 76 chr5qtel1M 928045 GAATTTACTAGCTGTGTGACCCAGAGCAAATCATTTATTCTCTCTCTGCC 928094 vv i iv i i i i vi vv MIRb#SINE/MIR 77 CCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCC 126 chr5qtel1M 928095 TCAATTTCCTGAAATGTAAAATGG--------ATCCCCATCTCATAGGGA 928136 i v vv -------- v i i ii v MIRb#SINE/MIR 127 TCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTACCTCGCAGGGT 176 chr5qtel1M 928137 GGTTCTGAGAATC-ATTGAGATA------GTAAAACACTTAGCACAGTGC 928179 v v i i- v ------ i i MIRb#SINE/MIR 177 TGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAGTGC 226 chr5qtel1M 928180 TTGGCCTGGGGGGAAGCGCCTCATGAATGCTTGTTC 928215 i vi-ivi v iiv i v v i MIRb#SINE/MIR 227 CTGGCAC-ATAGTAAGCGCTCAATAAATGGTAGCTC 261 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.25 CpG sites = 37, Kimura (unadjusted) = 38.49 Transitions / transversions = 1.32 (37/28) Gap_init rate = 0.02 (4 / 220), avg. gap size = 4.00 (16 / 4) 414 19.97 9.35 6.29 chr5qtel1M 930998 931136 (68864) MIRc#SINE/MIR 4 146 (122) m_b269s601i3 10652 chr5qtel1M 930998 GGTAG-GTGACACAGTAGAGAGA--------CCTTGAG-CAGGAAGACTA 931037 i - iii i i -------- i v - -- MIRc#SINE/MIR 4 GGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC-- 51 chr5qtel1M 931038 CTATTTTTGA-TCTAGAATGTGGCCCCAGGCACTTACTAGCTGTGTTACC 931086 ivv i - i------i i i- v v MIRc#SINE/MIR 52 CTGGGTTCGAGTCC------CGGCTCT-GCCACTTACTAGCTGTGTGACC 94 chr5qtel1M 931087 CTGGGCAAGTCACTTAACC-CTGTTTGCCTCAGCTTCATCAATTG-AAAA 931134 i - v vv i v vi - MIRc#SINE/MIR 95 TTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAA 144 chr5qtel1M 931135 TG 931136 MIRc#SINE/MIR 145 TG 146 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 21.68 CpG sites = 16, Kimura (unadjusted) = 23.69 Transitions / transversions = 1.60 (16/10) Gap_init rate = 0.11 (15 / 138), avg. gap size = 1.47 (22 / 15) 28 0.00 0.00 0.00 chr5qtel1M 931934 931960 (68040) (TTTG)n#Simple_repeat 1 27 (0) c_b269s251i1 10653 chr5qtel1M 931934 TTTGTTTGTTTGTTTGTTTGTTTGTTT 931960 (TTTG)n#Simpl 1 TTTGTTTGTTTGTTTGTTTGTTTGTTT 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 373 29.56 0.84 6.19 chr5qtel1M 931977 932095 (67905) C MIRc#SINE/MIR (153) 115 3 m_b269s601i4 10654 chr5qtel1M 931977 GGGATTAAGCGACTTGCCCAGAGTCACACAGCCAGGAGGTGTTAAATGTC 932026 i i i ii i ------- i v C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGC 73 chr5qtel1M 932027 CGAGGTAAGATTTGAACTGGGGACCCCCTGACTTCAGGACTGGCGCTCTA 932076 v viii i i ivi v ii i i v ii i v C MIRc#SINE/MIR 72 AGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTT 23 chr5qtel1M 932077 TTCCCTGCGTCAC-CTGGCT 932095 i v ii - v C MIRc#SINE/MIR 22 TCCACTGCACCACACTGCCT 3 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.60 CpG sites = 24, Kimura (unadjusted) = 39.94 Transitions / transversions = 2.67 (24/9) Gap_init rate = 0.07 (8 / 118), avg. gap size = 1.00 (8 / 8) 16 0.00 0.00 0.00 chr5qtel1M 934673 934689 (65311) (T)n#Simple_repeat 1 17 (0) m_b269s252i0 10655 chr5qtel1M 934673 TTTTTTTTTTTTTTTTT 934689 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTT 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 31 21.54 4.55 1.10 chr5qtel1M 935655 935742 (64258) (AT)n#Simple_repeat 1 91 (0) m_b269s252i1 10656 chr5qtel1M 935655 ATCTATA-ATATACTTTTTATACATA-AGATATATCT-TATCTTAAGATA 935701 v - - v v i - v v - v vv v (AT)n#Simple_ 1 ATATATATATATA-TATATATATATATATATATATATATATATATATATA 49 chr5qtel1M 935702 TATCT-TATATCTTTATACATATATATATATATATAATTATA 935742 v - v v i vv (AT)n#Simple_ 50 TATATATATATATATATATATATATATATATATATATATATA 91 Matrix = Unknown Transitions / transversions = 0.14 (2/14) Gap_init rate = 0.06 (5 / 87), avg. gap size = 1.00 (5 / 5) 369 28.57 14.29 0.00 chr5qtel1M 937064 937175 (62825) C MIRc#SINE/MIR (140) 128 1 m_b269s601i5 10657 chr5qtel1M 937064 ACTGAGACTCAGTTAAGTTAAATTACTTTCCCAAGACTACA--------- 937104 i vv i i v v iii --------- C MIRc#SINE/MIR 128 ACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTA 79 chr5qtel1M 937105 ----GCAGTACTGGAATTTCAGCCT--GTTTTC-TGAGTCCAAATGTAGG 937147 ---- vi i i i iv i i-- i - v i vi v C MIRc#SINE/MIR 78 AGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGT 29 chr5qtel1M 937148 GATCTTTCCATTATACCATGCTGCCTTG 937175 v i ii ii i C MIRc#SINE/MIR 28 GCTCTTTCCACTGCACCACACTGCCTCG 1 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.37 CpG sites = 22, Kimura (unadjusted) = 37.82 Transitions / transversions = 2.20 (22/10) Gap_init rate = 0.04 (4 / 111), avg. gap size = 4.00 (16 / 4) 12 16.86 2.86 2.86 chr5qtel1M 939443 939477 (60523) (AAC)n#Simple_repeat 1 35 (0) m_b269s252i2 10658 chr5qtel1M 939443 AAAAACAACAACAATAATAA-AACAAATACAGACAA 939477 v i i - vv - (AAC)n#Simple 1 AACAACAACAACAACAACAACAACAACAACA-ACAA 35 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 41 0.00 0.00 0.00 chr5qtel1M 940247 940281 (59719) (AT)n#Simple_repeat 1 35 (0) c_b269s251i2 10659 chr5qtel1M 940247 ATATATATATATATATATATATATATATATATATA 940281 (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATA 35 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 13 4.76 0.00 4.35 chr5qtel1M 941347 941370 (58630) (GGGA)n#Simple_repeat 1 23 (0) m_b269s252i3 10660 chr5qtel1M 941347 GGGAGGGGGTGGAGGGAGGGAGGG 941370 i - (GGGA)n#Simpl 1 GGGAGGGAG-GGAGGGAGGGAGGG 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 316 34.68 4.03 0.00 chr5qtel1M 942347 942470 (57530) MIR#SINE/MIR 52 180 (82) m_b269s601i6 10661 chr5qtel1M 942347 GTTTAAATTAAGCCTTGAACAGTTATTAACTGTATACTCTTTGGAAAGCC 942396 ii ivv v iviv v i i i ivi v v ii MIR#SINE/MIR 52 GTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTT 101 chr5qtel1M 942397 AATTAAAAC-----TGCCTGAGTTTCCTCACCTCTTAAGTGGGGATAACA 942441 v vvi----- v i v v i i MIR#SINE/MIR 102 ACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATA 151 chr5qtel1M 942442 GTATCAACTAACTTGGAAGGTTAATATGA 942470 i vi v v iiv i iv i MIR#SINE/MIR 152 ATAGTACCTACCTCATAGGGTTGTTGTGA 180 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 46.03 CpG sites = 23, Kimura (unadjusted) = 47.73 Transitions / transversions = 1.15 (23/20) Gap_init rate = 0.01 (1 / 123), avg. gap size = 5.00 (5 / 1) 16 30.60 2.94 0.00 chr5qtel1M 942664 942731 (57269) (TACA)n#Simple_repeat 1 70 (0) m_b269s252i4 10662 chr5qtel1M 942664 TACATAGAAACATGCATAGAT--ATACATACACATCTCTATACATGCAAA 942711 v v i v -- i iv vi i v (TACA)n#Simpl 1 TACATACATACATACATACATACATACATACATACATACATACATACATA 50 chr5qtel1M 942712 AATATAATTATGCATACATA 942731 v i vvi i (TACA)n#Simpl 51 CATACATACATACATACATA 70 Matrix = Unknown Transitions / transversions = 0.89 (8/9) Gap_init rate = 0.01 (1 / 67), avg. gap size = 2.00 (2 / 1) 225 33.33 3.81 0.00 chr5qtel1M 943150 943254 (56746) L3#LINE/CR1 3980 4088 (11) m_b269s601i7 10663 chr5qtel1M 943150 AAGAAAAACCTGCTTGAGCAACTTTCAGAGCT-TTGTA-AATAAATTCAT 943197 v i iv vv v vi v i v - - vii v L3#LINE/CR1 3980 AAGCAGAGGCTGGATGACCACTTGTCAGGGATGTTGTAGAAGGGATTCCT 4029 chr5qtel1M 943198 G--TCCAAGTAGAGGTTAGACAAAATAACCTCTGAGATTAGTTCCATGTC 943245 -- ivi vvi i v i i i i ivv vv L3#LINE/CR1 4030 GCATTGGATGGGAGGTTGGACTAGATGACCTCTAAGGTCCCTTCCAACTC 4079 chr5qtel1M 943246 TGTGATGCT 943254 v v L3#LINE/CR1 4080 TGAGATTCT 4088 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.32 CpG sites = 15, Kimura (unadjusted) = 44.32 Transitions / transversions = 0.75 (15/20) Gap_init rate = 0.03 (3 / 104), avg. gap size = 1.33 (4 / 3) 323 30.59 6.00 1.92 chr5qtel1M 943629 943778 (56222) C MIR3#SINE/MIR (7) 201 46 m_b269s601i8 10664 chr5qtel1M 943629 AAAATCATGAAATAT-GGAGCCAAAATTCCCTTCAGAATTCAGG-AATCC 943676 i ii i -i iii vvvv i i iv vv- i C MIR3#SINE/MIR 201 AGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCC 152 chr5qtel1M 943677 AATCCTCTTCAATTTCCAGA--AGGGAACTGAAGTACAGAG----GAGG- 943719 i i - v v -- i i iv ---- i - C MIR3#SINE/MIR 151 AACCCCCT-CATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGT 103 chr5qtel1M 943720 GATTTACTCAAAGGTCACACCATTTTTAAGTGTCAGAGTCAGCTCCTGGA 943769 i i i - vii?vv v v i i -vv i C MIR3#SINE/MIR 102 GACTTGCCC-AAGGTCACACAGCNAGTTAGTGGCAGAGCCGG-GACTAGA 55 chr5qtel1M 943770 ACCGTGGTC 943778 vv C MIR3#SINE/MIR 54 ACCCAGGTC 46 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.66 CpG sites = 26, Kimura (unadjusted) = 40.84 Transitions / transversions = 1.37 (26/19) Gap_init rate = 0.05 (8 / 149), avg. gap size = 1.50 (12 / 8) 19 0.00 0.00 0.00 chr5qtel1M 946464 946484 (53516) (T)n#Simple_repeat 1 21 (0) m_b269s252i5 10665 chr5qtel1M 946464 TTTTTTTTTTTTTTTTTTTTT 946484 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTT 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 20 4.35 0.00 0.00 chr5qtel1M 947838 947861 (52139) (A)n#Simple_repeat 1 24 (0) m_b269s252i6 10666 chr5qtel1M 947838 AAAAAAAAAAAAAAAAAGAAAAAA 947861 i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAA 24 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 11 17.73 5.00 2.44 chr5qtel1M 947904 947943 (52057) (ATGAAAA)n#Simple_repeat 1 41 (0) m_b269s252i7 10667 chr5qtel1M 947904 ATG-AAAAT-TAAATTGAAAAATGAAATTTAAAACATTGAAA 947943 - -v v vv i - v (ATGAAAA)n#Si 1 ATGAAAAATGAAAAATGAAAAATGAAAAATGAAA-AATGAAA 41 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.08 (3 / 39), avg. gap size = 1.00 (3 / 3) 360 30.08 5.96 4.23 chr5qtel1M 948701 949002 (50998) L1MC_orf2#LINE/L1 1896 2202 (1092) m_b269s551i0 10668 chr5qtel1M 948701 CATTCATAAAAACATTTATCTAAAACTAAAAGCATCACATGAAATGGGGT 948750 ii i ----- i v i --- i ivv v v L1MC_orf2#LIN 1896 CATCTACAAAAA-----ACCTACAGCTAA---CATCATACTTAATGGTGA 1937 chr5qtel1M 948751 TATATTAGAAACTTTCCCAATAAATGCAGAAGTAAAGCAAGGATGATTAC 948800 v v i ? i iv ivv i ii i viiv L1MC_orf2#LIN 1938 GAAACTNGAAGCTTTCCCGCTAAGATCAGGAACAAGGCAAGGATGTCCCC 1987 chr5qtel1M 948801 TCCCCCCACTCTT-------------CTAGAAATGCTAGC-AATAACAAT 948836 i v i ------------- i i v - -i L1MC_orf2#LIN 1988 TCTCACCACTCCTTTTCAACATCGTACTGGAAGTCCTAGCTAAT-GCAAT 2036 chr5qtel1M 948837 GACACAAGAGAAAGGAAAGAAA--GTACTAAAGACGGGTAAAGAACTACT 948884 i v - v -- - v iv v i vv v L1MC_orf2#LIN 2037 AAGACAAGA-AAAGGAAATAAAAGGTA-TACAGATTGGGAAGGAAGAAAT 2084 chr5qtel1M 948885 CTAACTATCCCTGTTTGCTGATGAGAGGATGCTTTACTTGGACAAACCAA 948934 vv i ii i v v v vv i iv i v v i L1MC_orf2#LIN 2085 AAAACTGTCTTTGTTCGCAGATGACATGATTGTCTATGTAGAAAATCCGA 2134 chr5qtel1M 948935 GGGAGTCAGCAGAGACA-TCAACTGAAATAATTAATAGTTTAT-GCAATA 948982 ii i ii i i v - -- i iv v vv v - vi L1MC_orf2#LIN 2135 AAGAATCGACAAAAAAACTC--CTGGAACTAATAAGCGATTATAGCAAGG 2182 chr5qtel1M 948983 CTGCATGATACAGAGTGAAT 949002 i v ii v L1MC_orf2#LIN 2183 TTGCAGGATACAAGGTTAAT 2202 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.08 CpG sites = 46, Kimura (unadjusted) = 39.35 Transitions / transversions = 1.12 (46/41) Gap_init rate = 0.06 (18 / 301), avg. gap size = 1.72 (31 / 18) 269 25.14 11.76 6.40 chr5qtel1M 949279 949397 (50603) MIRc#SINE/MIR 19 143 (125) m_b269s601i9 10669 chr5qtel1M 949279 TAGAAAGAGGG-TGATCTTGG-----GGAAGACCTTAGCTTACAAGAAGC 949322 i vi- iv ----- vi i ii----- i MIRc#SINE/MIR 19 TGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG-----AGT 63 chr5qtel1M 949323 CTCAA----GACCCTTAATGGCTGTGTGACCCTGGGCAAACTCCTACACA 949368 i ii---- v v v i i iiiv vv v MIRc#SINE/MIR 64 CCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACC 113 chr5qtel1M 949369 TCT----GTCTCAGTTTTCTCAACTCATGTAAA 949397 ---- i i -- - MIRc#SINE/MIR 114 TCTCTGAGCCTCAGTTTCCTCA--TC-TGTAAA 143 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.88 CpG sites = 18, Kimura (unadjusted) = 31.72 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.10 (12 / 118), avg. gap size = 1.83 (22 / 12) 232 21.72 5.56 4.11 chr5qtel1M 949339 949410 (50590) MIR1_Amn#SINE/MIR 86 158 (72) m_b269s601i10 10669 chr5qtel1M 949339 GCTGTGTGACCCTGGGCAAACTCCTACACATCT----GTCTCAGTTTTCT 949384 ? i iiiv v? v ---- i i MIR1_Amn#SINE 86 GCTGNGTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCT 135 chr5qtel1M 949385 CAACTCATGTAAACTTAAGAACATGA 949410 -- - v vii vv MIR1_Amn#SINE 136 CA--TC-TGTAAAATGGGGATAATGA 158 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.89 CpG sites = 8, Kimura (unadjusted) = 26.89 Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.06 (4 / 71), avg. gap size = 1.75 (7 / 4) 363 21.94 1.96 10.64 chr5qtel1M 950711 950812 (49188) C MIRc#SINE/MIR (173) 95 2 m_b269s601i11 10670 chr5qtel1M 950711 AAGTGACACAGCTAGCAAGTGTTAAATATTTGAGGCCAGATTTGAACTCG 950760 i v i vi ------- v vi i i i i C MIRc#SINE/MIR 95 AGGTCACACAGCTAGTAAGTGGCA-------GAGCCGGGACTCGAACCCA 53 chr5qtel1M 950761 GGTCCTCCTGACTTCAGGGCTGGTGCTG--TCCACTGTACCACCTAACTG 950808 i i i v ii v-- i --- C MIRc#SINE/MIR 52 GGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC---ACTG 6 chr5qtel1M 950809 CCTC 950812 C MIRc#SINE/MIR 5 CCTC 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.03 CpG sites = 14, Kimura (unadjusted) = 26.56 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.11 (11 / 101), avg. gap size = 1.09 (12 / 11) 17 26.31 0.00 0.00 chr5qtel1M 955714 955754 (44246) (AA)n#Simple_repeat 1 41 (0) m_b269s252i8 10671 chr5qtel1M 955714 AAAAAAAAAAACAGGAGAAAGCAAAAAAAAACCAAGAAAAA 955754 v ii i iv vv i (AA)n#Simple_ 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 41 Matrix = Unknown Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 19 18.24 2.27 0.00 chr5qtel1M 960111 960154 (39846) (AATTT)n#Simple_repeat 1 45 (0) m_b269s252i9 10672 chr5qtel1M 960111 AATTT-TTTTATTTTAATTTAATTTCATTTAAATGATTTTAAATT 960154 -v v v v v v v (AATTT)n#Simp 1 AATTTAATTTAATTTAATTTAATTTAATTTAATTTAATTTAATTT 45 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.02 (1 / 43), avg. gap size = 1.00 (1 / 1) 27 25.35 0.00 0.00 chr5qtel1M 960518 960587 (39413) (AAA)n#Simple_repeat 1 70 (0) m_b269s252i10 10673 chr5qtel1M 960518 AAAGAAGAATCAGAACAAAAGGAAAAAAAAAAAACACAAGAAAATAATAA 960567 i i vv i v ii v v i v v (AAA)n#Simple 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr5qtel1M 960568 AAAAAAAAAAACAAGAAAAA 960587 v i (AAA)n#Simple 51 AAAAAAAAAAAAAAAAAAAA 70 Matrix = Unknown Transitions / transversions = 0.88 (7/8) Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0) 486 20.15 4.88 3.20 chr5qtel1M 961988 962110 (37890) MIRc#SINE/MIR 24 148 (120) m_b269s601i12 10674 chr5qtel1M 961988 AGAGCCCTGGCTTTGGAATCAGGAA--CTTGAGAGGTTGAAATCCTGCCT 962035 v vi i -- i --- vi i i v MIRc#SINE/MIR 24 AGAGCACTGGACTTGGAGTCAGGAAGACCTG---GGTTCGAGTCCCGGCT 70 chr5qtel1M 962036 CAGACACTTATCGGATGTGTCAGCCTGGCCAAGTCACTCAAGCCTGTTT- 962084 v v iii v v v i v i - v i - MIRc#SINE/MIR 71 CTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAA-CCTCTCTG 119 chr5qtel1M 962085 -GCCT--GTTTCCTCATCTGTAAAATGAG 962110 - -- i MIRc#SINE/MIR 120 AGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 21.58 CpG sites = 13, Kimura (unadjusted) = 23.73 Transitions / transversions = 1.18 (13/11) Gap_init rate = 0.07 (8 / 122), avg. gap size = 1.25 (10 / 8) 387 27.83 7.83 0.00 chr5qtel1M 962910 963024 (36976) C MIRc#SINE/MIR (142) 126 3 m_b270s601i1 10675 chr5qtel1M 962910 TGAGAGCCAGTTAATTGAAATTACTTGTCCAAGGCCAGAGAG---GCA-- 962954 ivi vv iv v i v i i v v --- i -- C MIRc#SINE/MIR 126 TGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAG 77 chr5qtel1M 962955 ---CAGAACCAGGATTTCTACCCATGTCCTCTT-ACTCAAAATCTAGTGA 963000 --- i i i ivv v i i - v i i v C MIRc#SINE/MIR 76 TGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGC 27 chr5qtel1M 963001 TCTTTCCCTTGCACCATACTGTCT 963024 vi i i C MIRc#SINE/MIR 26 TCTTTCCACTGCACCACACTGCCT 3 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.81 CpG sites = 18, Kimura (unadjusted) = 35.50 Transitions / transversions = 1.29 (18/14) Gap_init rate = 0.04 (4 / 114), avg. gap size = 2.25 (9 / 4) 17 17.24 0.00 2.50 chr5qtel1M 964433 964473 (35527) (TTTCTT)n#Simple_repeat 1 40 (0) m_b270s252i0 10676 chr5qtel1M 964433 TTTCTTTTTTTTTTTCTTTTTGCAATTCTTCTTCTCTTTTC 964473 i vivv i - (TTTCTT)n#Sim 1 TTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCT-TTTTC 40 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 524 26.80 11.91 3.14 chr5qtel1M 964533 964767 (35233) MIRb#SINE/MIR 14 268 (0) m_b270s601i2 10677 chr5qtel1M 964533 TGGTACAGTGGCTTGCCCATGGATAGAGCCTTC-AGTCAGGAAGACCTGA 964581 i vvv vv i ----- i v- iv i MIRb#SINE/MIR 14 TGGTGCAGTGGAAAGAGCACGG-----GCTTTGGAGTCAGACAGACCTGG 58 chr5qtel1M 964582 GTTTTAATCCCATGTCAGAAACGTGCTAGTCAAG---CTTTAGG------ 964622 iv ivv v vv v i iiiv --- i i ------ MIRb#SINE/MIR 59 GTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTT 108 chr5qtel1M 964623 -----ACCTCTGTTTCCCTCAGTTTCTTCATCTGTAAAATGGATGTAATA 964667 ----- v vvv i i---i MIRb#SINE/MIR 109 ACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG---GATA 155 chr5qtel1M 964668 ATAACAACTAAGTC-CTGTGTTCTCTTGTGAATAAAATGAGATAAT--AT 964714 i v vv - v v v iv v i v -- MIRb#SINE/MIR 156 ATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCAT 205 chr5qtel1M 964715 TTA----------TACAGTGCATGATACTTAGCAGGTGCTATATAAATGC 964754 v ----------i v ii v i i i vv v MIRb#SINE/MIR 206 GTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAAATGG 255 chr5qtel1M 964755 TAGCTATTTTATT 964767 v v MIRb#SINE/MIR 256 TAGCTCTATTATT 268 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.86 CpG sites = 25, Kimura (unadjusted) = 33.35 Transitions / transversions = 0.69 (25/36) Gap_init rate = 0.06 (15 / 234), avg. gap size = 2.40 (36 / 15) 325 25.84 4.49 0.00 chr5qtel1M 965418 965506 (34494) C MIR3#SINE/MIR (2) 206 114 m_b270s601i3 10678 chr5qtel1M 965418 ATTATAGAATCACGGATGATCA---CTGGAAGGGACCTACAAGGCCATGG 965464 i ii vvi --- vvi ii vv C MIR3#SINE/MIR 206 ATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCT 157 chr5qtel1M 965465 AGTGCA-CCCCCTAATTTTCTAGATGGGGAAATTTAGTTTCAG 965506 v - v vi i i v vii C MIR3#SINE/MIR 156 AGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAG 114 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.08 CpG sites = 12, Kimura (unadjusted) = 32.08 Transitions / transversions = 1.09 (12/11) Gap_init rate = 0.02 (2 / 88), avg. gap size = 2.00 (4 / 2) 17 0.00 4.76 0.00 chr5qtel1M 966175 966195 (33805) (AG)n#Simple_repeat 1 22 (0) m_b270s252i1 10679 chr5qtel1M 966175 AGAGAGAGAGA-AGAGAGAGAG 966195 - (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAG 22 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.05 (1 / 20), avg. gap size = 1.00 (1 / 1) 55 0.00 0.00 0.00 chr5qtel1M 966372 966418 (33582) (AC)n#Simple_repeat 1 47 (0) c_b270s251i0 10680 chr5qtel1M 966372 ACACACACACACACACACACACACACACACACACACACACACACACA 966418 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACA 47 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 129 31.58 2.11 2.29 chr5qtel1M 967068 967636 (32364) (AGAAAG)n#Simple_repeat 1 568 (0) m_b270s252i2 10681 chr5qtel1M 967068 AGAAAGAGAGAGAAAAAGAGGCAGAAAGACAGAAACAGTGAGAGAGGAAG 967117 i i iv i i v v vi iii (AGAAAG)n#Sim 1 AGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAG 50 chr5qtel1M 967118 CCAACAGATTGAGAGAGAAGCAAAGA-CATGATTAAAAGAAATAGAGTGA 967166 -v v vv i - - -v v vv i v iv (AGAAAG)n#Sim 51 -AAAGAGAAAGAGAAAG-AG-AAAGAGAAAGAGAAAGAGAAAGAGAAAGA 97 chr5qtel1M 967167 AAAAAAGACAGAGATAGAACCAGAGACAGAG--AGAGCAAGACAAATGA- 967213 i i v v ivv v -- v v - - (AGAAAG)n#Sim 98 GAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAA-GAG 146 chr5qtel1M 967214 ACAG-GAAAGATAAAGATAGTGCCAGATGGAGAGGGAGAAAGAGAAAGAG 967262 v - v v iv -- vi ii (AGAAAG)n#Sim 147 AAAGAGAAAGAGAAAGAGAAAG--AGAAAGAGAAAGAGAAAGAGAAAGAG 194 chr5qtel1M 967263 AAAGAGAGAGGGCTGGGGGAGGGAGAAGGGGGGAAGAGAGACAGAGAGAG 967312 i i -vii i ii -i i i i v i (AGAAAG)n#Sim 195 AAAGAGAAAGAG-AAAGAGAAAGAGAA-AGAGAAAGAGAAAGAGAAAGAG 242 chr5qtel1M 967313 AGACAGAAAGAGAAAGAGATACAGACAGAGAGAGATGTAGACAGTGAGAT 967362 i v v v v i - - i v vi v (AGAAAG)n#Sim 243 AAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGA-G-AAAGAGAAAGAG 290 chr5qtel1M 967363 AGAAAGAAAGATAAAGAGACAGAAACAGTGAGACAGAGAGAGACAGAACC 967412 i i v v i v v i v i v ivv (AGAAAG)n#Sim 291 AAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAA 340 chr5qtel1M 967413 AGAGCTAGAGAGATA-AGAGTGAAGAAAAAAGAGAAAG-GAAAGA-AAGG 967459 vv i v - i v ii i - - i (AGAAAG)n#Sim 341 AGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAG 390 chr5qtel1M 967460 AAGTGCCAGATAGAGAAGGAGGGAGGAGGGGAGAGACACAGAGAGAGAAA 967509 - vivv v i - i i - ii v v i (AGAAAG)n#Sim 391 -AGAAAGAGAAAGAGAAAGA-GAAAGA-GAAAGAGAAAGAGAAAGAGAAA 437 chr5qtel1M 967510 GAGAAAGAGCCAGAGCCAGAGAGATAGTGAGATAGCCAGAAAGACAGACA 967559 vv vv i v vi v ivv v i v (AGAAAG)n#Sim 438 GAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGA 487 chr5qtel1M 967560 ATGAGAGAGACAGAGACAGAACCAGAACTAGACAGAGCAAGACAGAGTGA 967609 ivi i v i v vv vv v v v i v (AGAAAG)n#Sim 488 GAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGA 537 chr5qtel1M 967610 AGAAGAAAGAGAAAG-G--AGAGAAAG-GAA 967636 ii - -- - (AGAAAG)n#Sim 538 AAGAGAAAGAGAAAGAGAAAGAGAAAGAGAA 568 Matrix = Unknown Transitions / transversions = 0.87 (65/75) Gap_init rate = 0.04 (23 / 568), avg. gap size = 1.09 (25 / 23) 501 29.06 2.04 8.70 chr5qtel1M 967968 968163 (31837) MIRb#SINE/MIR 4 187 (81) m_b270s601i4 10682 chr5qtel1M 967968 AGAGATAGCTAGGTGGTGCAGTGGAAAGAGTTCTGAGTCTGGACTCAGGA 968017 i ii --- iv v iv i v iv MIRb#SINE/MIR 4 AGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGAC 50 chr5qtel1M 968018 AGATTCATCTATGTGAGTTCAAATTCGGCCTCAGATATTTAGGAGTTGTG 968067 ii-------- i i i v v v vi i vv i MIRb#SINE/MIR 51 AGACC--------TGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTG 92 chr5qtel1M 968068 AGACTTTAGATAAGACACTTTTAACC-CTATTTACCTCAGTTTCCTCATC 968116 v i i ii vi -- - v vvi MIRb#SINE/MIR 93 TGACCTTGGGCAAGTTAC--TTAACCTCTCTGAGCCTCAGTTTCCTCATC 140 chr5qtel1M 968117 TATACAATGAGCTAGAGAAGGATTCCAGTC---CAGTATCTTTGTGAAGA 968163 i v i --- v vi v vii --- vi iv i MIRb#SINE/MIR 141 TGTAAAATGGG---GATAATAATACCTACCTCGCAGGGTTGTTGTGAGGA 187 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.37 CpG sites = 29, Kimura (unadjusted) = 37.27 Transitions / transversions = 1.26 (29/23) Gap_init rate = 0.09 (18 / 195), avg. gap size = 1.11 (20 / 18) 550 25.48 0.68 7.19 chr5qtel1M 967980 968127 (31873) MIRc#SINE/MIR 10 148 (120) m_b270s601i5 10682 chr5qtel1M 967980 GTGGTGCAGTGGAAAGAGTTCTGAGTCTGGACTCAGGAAGATTCATCTAT 968029 iv iiii v ii------- MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC------- 52 chr5qtel1M 968030 GTGAGTTCAAATTCGGCCTCAGATATTTAGGAGTTGTGAGACTTTAGATA 968079 - i i i i v v v vi i vv i v i i ii MIRc#SINE/MIR 53 -TGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 101 chr5qtel1M 968080 AGACACTTTTAACC-CTATTTACCTCAGTTTCCTCATCTATACAATGAG 968127 v -- - v vvi i v i MIRc#SINE/MIR 102 AGTCAC--TTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.61 CpG sites = 21, Kimura (unadjusted) = 31.70 Transitions / transversions = 1.50 (21/14) Gap_init rate = 0.07 (11 / 147), avg. gap size = 1.00 (11 / 11) 25 11.17 3.85 3.85 chr5qtel1M 968306 968357 (31643) (AG)n#Simple_repeat 1 52 (0) m_b270s252i3 10683 chr5qtel1M 968306 AGGGAGAGAGAG-GAGAGAGAGAGAGCACGAGGTATA-AGTGAGAGAGAG 968353 i - - - iv v - v (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAG-A-GAGAGAGAGAGAGAGAGAGAG 48 chr5qtel1M 968354 AGAG 968357 (AG)n#Simple_ 49 AGAG 52 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.08 (4 / 51), avg. gap size = 1.00 (4 / 4) 202 31.59 4.04 7.29 chr5qtel1M 968600 968698 (31302) C MamRTE1#LINE/RTE-BovB (2223) 1589 1494 m_b270s601i6 10684 chr5qtel1M 968600 TAATTTATTCCC-TCAATGACCCACACTGGGTGAGGTCGTTTGATAGCAC 968648 i v i i - -- viiv - iv ? i i C MamRTE1#LINE/ 1589 TGAGTCATTCTCATCAA--ACCAGTTCTGG-TGGCGTCGTTTNACAGCGC 1543 chr5qtel1M 968649 CCA---CTTTGGAGACCACTTGTAGCATAAATGGTGACTTGGAGGAACAC 968695 --- vi iv i ii i ----i? i i iiv i i ? i C MamRTE1#LINE/ 1542 CCACAGCGCTGATGGCTGCCTG----GNAGACGGCATCTCGGAGAANCGC 1497 chr5qtel1M 968696 CCA 968698 C MamRTE1#LINE/ 1496 CCA 1494 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.16 CpG sites = 22, Kimura (unadjusted) = 46.83 Transitions / transversions = 3.14 (22/7) Gap_init rate = 0.09 (9 / 98), avg. gap size = 1.22 (11 / 9) 334 24.35 25.22 0.00 chr5qtel1M 969131 969245 (30755) MIRc#SINE/MIR 3 146 (122) m_b270s601i7 10685 chr5qtel1M 969131 AGGTAG-GTGATACAGTGAGTAGAGTGCTTGGCCTAGGGTCAGAGAGAC- 969178 i - i i iiv ii v i i i i ii - MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chr5qtel1M 969179 -------------------TGC---TTACT----GTGTGACCCTGGGCAA 969202 ------------------- --- ---- i MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 102 chr5qtel1M 969203 AATATCTAATCCTGCTT-GCCTCAGTTTTTTCATCTGTAAAATG 969245 ivi ii i iiv v- ii MIRc#SINE/MIR 103 GTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATG 146 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.58 CpG sites = 23, Kimura (unadjusted) = 31.58 Transitions / transversions = 4.60 (23/5) Gap_init rate = 0.05 (6 / 114), avg. gap size = 4.83 (29 / 6) 349 20.90 1.49 0.00 chr5qtel1M 969179 969245 (30755) MIR#SINE/MIR 75 142 (120) m_b270s601i8 10685 chr5qtel1M 969179 TGCTTACTGTGTGACCCTGGGCAAAATATCTAATCCTGCT-TGCCTCAGT 969227 i vi i iv ii i iiv - MIR#SINE/MIR 75 TACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGT 124 chr5qtel1M 969228 TTTTTCATCTGTAAAATG 969245 ii MIR#SINE/MIR 125 TTCCTCATCTGTAAAATG 142 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.70 CpG sites = 11, Kimura (unadjusted) = 25.70 Transitions / transversions = 3.67 (11/3) Gap_init rate = 0.02 (1 / 66), avg. gap size = 1.00 (1 / 1) 345 23.19 1.18 3.61 chr5qtel1M 969180 969264 (30736) MIR1_Amn#SINE/MIR 82 164 (66) m_b270s601i9 10685 chr5qtel1M 969180 GCTTACTGTGTGACCCTGGGCAAAATATCTAATCCTGCT-TGCCTCAGTT 969228 i?i ? i ivi ii ? i iiv -? MIR1_Amn#SINE 82 GCCNGCTGNGTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTT 131 chr5qtel1M 969229 TTTTCATCTGTAAAATGAACTGGAGAAAGAAATTGA 969264 ii i--- v v v i MIR1_Amn#SINE 132 TCCTCATCTGTAAAATGG---GGATAATGATACTGA 164 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.93 CpG sites = 14, Kimura (unadjusted) = 30.93 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.05 (4 / 84), avg. gap size = 1.00 (4 / 4) 361 22.31 5.66 2.75 chr5qtel1M 969298 969403 (30597) EuthAT-N1#DNA/hAT-Tip100 117 225 (110) m_b270s502i0 10686 chr5qtel1M 969298 ATTTACATGATGCTGACAGCTTTTGCTGTCTTTCAGCAAACTAGAAACAA 969347 ---i viv vv i ivv EuthAT-N1#DNA 117 ATTTACATG---TTGACAGCACATGCACTCCTTCAGCAGCGTAGAAACAA 163 chr5qtel1M 969348 C--AATTTAACGCCTGGTTAGTAAGAA----TAGTTAAAATTGATAGGTA 969391 -- ii i i i i ---- v iv v EuthAT-N1#DNA 164 CTGAGCTTAGCACCTAGTTAGCAAGAATAATTAGTTAAAATAGGAAGCTA 213 chr5qtel1M 969392 CTAGATGGCATG 969403 i ii EuthAT-N1#DNA 214 CCAGATGGCGCG 225 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 24.40 CpG sites = 14, Kimura (unadjusted) = 27.06 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.05 (5 / 105), avg. gap size = 1.80 (9 / 5) 323 27.43 11.50 0.00 chr5qtel1M 969929 970041 (29959) C MIRc#SINE/MIR (140) 128 3 m_b270s601i10 10687 chr5qtel1M 969929 ACTGAGACCCAGTAAATTTAAATCACTTTTTCAAG---AC-CAG-TGGTA 969973 i i vi iv i v vii --- - - i C MIRc#SINE/MIR 128 ACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTA 79 chr5qtel1M 969974 -----CAGAATCAGAAATTCAACTCATGTC---CCGACTCCAATTCAAGT 970015 ----- ii i i v iv i v --- i v v C MIRc#SINE/MIR 78 AGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGT 29 chr5qtel1M 970016 GAACTTTCCACTCCATCATGTTGCCT 970041 vv v i iii C MIRc#SINE/MIR 28 GCTCTTTCCACTGCACCACACTGCCT 3 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.40 CpG sites = 19, Kimura (unadjusted) = 35.18 Transitions / transversions = 1.58 (19/12) Gap_init rate = 0.04 (5 / 112), avg. gap size = 2.60 (13 / 5) 27 0.00 0.00 0.00 chr5qtel1M 970357 970382 (29618) (T)n#Simple_repeat 1 26 (0) c_b270s251i1 10688 chr5qtel1M 970357 TTTTTTTTTTTTTTTTTTTTTTTTTT 970382 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 233 29.27 0.00 0.00 chr5qtel1M 970725 970806 (29194) C L1PA4_3end#LINE/L1 (332) 570 489 m_b270s551i0 10689 chr5qtel1M 970725 ATCATTTCTTATAGAACAATAATATTCCATAATGTTCATATGCCATAACT 970774 i i vvvv i ii vi i i vi C L1PA4_3end#LI 570 ATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCACATTT 521 chr5qtel1M 970775 TCTTCAGCCATTCTCCAACTGTTGGGCATCTG 970806 v v v viv i i i C L1PA4_3end#LI 520 TCTTAATCCAGTCTATCATTGTTGGACATTTG 489 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.81 CpG sites = 13, Kimura (unadjusted) = 37.81 Transitions / transversions = 1.18 (13/11) Gap_init rate = 0.00 (0 / 81), avg. gap size = 0.0 (0 / 0) 235 24.59 0.00 0.00 chr5qtel1M 970743 970803 (29197) C L1ME3G_3end#LINE/L1 (376) 548 488 m_b270s551i1 10689 chr5qtel1M 970743 ATAATATTCCATAATGTTCATATGCCATAACTTCTTCAGCCATTCTCCAA 970792 i i i vv i i v i i i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr5qtel1M 970793 CTGTTGGGCAT 970803 i v i C L1ME3G_3end#L 498 TTGATGGACAT 488 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 30.84 CpG sites = 10, Kimura (unadjusted) = 30.84 Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 15 5.56 0.00 0.00 chr5qtel1M 971279 971297 (28703) (T)n#Simple_repeat 1 19 (0) m_b270s252i4 10690 chr5qtel1M 971279 TTTTCTTTTTTTTTTTTTT 971297 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 23 9.78 0.00 0.00 chr5qtel1M 971431 971463 (28537) (T)n#Simple_repeat 1 33 (0) m_b270s252i5 10691 chr5qtel1M 971431 TTTCTTTTTTTTTTTTTTTTTCTTTTTTTATTT 971463 i i v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 33 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 1048 27.92 2.93 3.65 chr5qtel1M 971922 972501 (27499) C L1MC4a_3end#LINE/L1 (1997) 632 57 m_b270s551i2 10692 chr5qtel1M 971922 TGCTCATTTCACTCAGCATCAGTTCGTGTAAGTCTCTCCAGGCC--TTTC 971969 iv i i vi vv v v i v vii -- iv C L1MC4a_3end#L 632 TGCTTTTTTCACTTAACAATATATCCTGGAAATCACTCCATATCAGTTCA 583 chr5qtel1M 971970 T-GAAATCATCCTGTTGGTCATTTCTTACAGA-ACAGTAATATTCCATAA 972017 - i v vv -- - i v-i - i i vi C L1MC4a_3end#L 582 TAGAGATCTTCCTCAT--TC-TTTTTTACAGCTGCA-TAGTACTCCATTG 537 chr5qtel1M 972018 TTTTCATATACCACAATTTATTCAACCATTCTCCAACTGATGGACATCCA 972067 v vv i i i ? v i?? i ii C L1MC4a_3end#L 536 TGTGGATGTACCATAGTTTATTCAACCANTCTCCTATNNATGGGCATTTA 487 chr5qtel1M 972068 TTCAGTTTCCAGTTTTTAGCCACTGCAAAAAGGGCTGCCACAAACATTCG 972117 vviv i v v v i i v iv v ii i vi v C L1MC4a_3end#L 486 GGTTGTTTCCAATATTTTGCAATTACAAACAATGCTGCAATGAATAACCT 437 chr5qtel1M 972118 TGCACATACAGGTCCCTTTCC-CTTCTT-----TATAATCTCTTTGGGAT 972161 ii i-- ?vi vi- v v ----- i --- ii i C L1MC4a_3end#L 436 TGTGCATAT--GTNATTTTGTACATGTTGGAGGTGTA---TCTTCAGGGT 392 chr5qtel1M 972162 ATAATCCCAGTAGTAACACTGCTGGATCAAAGGGTA--TGCACAGTTTGA 972209 v v i v iiv i i -- i --- - C L1MC4a_3end#L 391 AAATTCCTAGAAGTGGGATTGCTGGGTCAAAGGGTAAATGCATA---TG- 346 chr5qtel1M 972210 TAACTTTTTGAGCATAGTTCCAAACTGCTCTCCAAAATGGTTGGATTCGT 972259 ii v v - v v i v i ? v v iiv? C L1MC4a_3end#L 345 TAGTTTTGTTAG-ATATTGCCAAATTCCCCTCCANAAGGGTTGTACCANT 297 chr5qtel1M 972260 TCACAACTCCACCAACAATGCATCAATGTCCCAGTTTTCCCGCATCCCCT 972309 ii vii i i v iv v v i i v i v C L1MC4a_3end#L 296 TTGCATTCCCACCAGCAATGTATGAGAGTGCCTGTTTCCCCACAGCCTCG 247 chr5qtel1M 972310 CCAACAATCATCATTATTTTTTC---CTGTC--ATCTTAGCCAATCTGAC 972354 i----- v i v v --- v i-- i v i C L1MC4a_3end#L 246 CCAACAG-----AGTGTGTTGTCAAACTTTTGAATTTTTGCCAATCTGAT 202 chr5qtel1M 972355 AGGTGTGTAGTGGTATCTTAGAGTTGTCTTAATTTGCATTTCTCTGATTA 972404 v v i i v v i v C L1MC4a_3end#L 201 AGGTGAGAAATGGTATCTCAGTGTAGTTTTAATTTGCATTTCTCTTATTA 152 chr5qtel1M 972405 ATAATGACTTGGAGCATCTTTTTATATGACTAGAAATAGTTTCAATTTCT 972454 vv i vv v i i vi iiiiivi ?v ? C L1MC4a_3end#L 151 TGAGTGAGGTTGAACATCTTTTCATATGTTTAAGGGCCATTTNTATNTCT 102 chr5qtel1M 972455 TCATCTGAGAATTGTCTGTTCATATCCTTTGACCATTTTTCAATTGG 972501 -- i v i i v v i C L1MC4a_3end#L 101 T--TTTGTGAATTGTCTGTTCATGTCTTTTGCCCATTTTTCTATCGG 57 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.85 CpG sites = 83, Kimura (unadjusted) = 36.13 Transitions / transversions = 1.14 (83/73) Gap_init rate = 0.05 (29 / 579), avg. gap size = 1.31 (38 / 29) 1461 27.47 0.36 1.66 chr5qtel1M 972005 972552 (27448) C L1ME3G_3end#LINE/L1 (377) 547 7 m_b270s551i3 10692 chr5qtel1M 972005 TAATATTCCATAATTTTCATATACCACAATTTATTCAACCATTCTCCAAC 972054 i i v vv i i i v i C L1ME3G_3end#L 547 TAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTAT 498 chr5qtel1M 972055 TGATGGACATCCATTCAGTTTCCAGTTTTTAGCCACTGCAAAAAGGGCTG 972104 ii vviv i v i i i v iv C L1ME3G_3end#L 497 TGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCTG 448 chr5qtel1M 972105 CCACAAACATTCGTGCACATACAGGTCCCTTTCC-CTTCTTT-ATAATCT 972152 v ii i v i i ?-- i v v - v v vi- vv i C L1ME3G_3end#L 447 CAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATTT 400 chr5qtel1M 972153 CTTTGGGATATAATCCCAGTAGTAACACTGCTGGATCAAAGGGTATGCAC 972202 ? i v v? ? v iiv i i i C L1ME3G_3end#L 399 CTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGC 350 chr5qtel1M 972203 AGTTTGATAACTTTTTGAGCATAGTTCCAAACTGCTCTCCAAAATGGTTG 972252 v i -- i vvv - v v i i ? i C L1ME3G_3end#L 349 ATTTTAA--ATTTTAATAG-ATACTGCCAAATTGCCCTCCAAAANGGCTG 303 chr5qtel1M 972253 GATTCGTTCACAACTCCACCAACAATGCATCAATGTCCCAGTTTTCCCGC 972302 v iivi i vii i i i v iv v v i i C L1ME3G_3end#L 302 TACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCAC 253 chr5qtel1M 972303 ATCCCCTCCAACAATCATCATTATTTTTTCCTGTCATCTTAGCCAATCTG 972352 i i v v ?ivi ivv?iii vvv i v C L1ME3G_3end#L 252 ACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATCTG 203 chr5qtel1M 972353 ACAGGTGTGTAGTGGTATCTTAGAGTTGTCTTAATTTGCATTTCTCTGAT 972402 ii viv i i vv i i C L1ME3G_3end#L 202 ATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGAT 153 chr5qtel1M 972403 TAATAATGACTTGGAGCATCTTTTTATATGACTAGAAATAGTTTCAATTT 972452 v i vv v i vi vviiivi vv C L1ME3G_3end#L 152 TACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGTATTT 103 chr5qtel1M 972453 CTTCATCTGAGAATTGTCTGTTCATATCCTTTGACCATTTTTCAATTGGA 972502 i v v i v v i C L1ME3G_3end#L 102 CCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGGG 53 chr5qtel1M 972503 GAATGGCTTGATTTTTTATAAATTAGAGTTAATTCTCTCTATATTTTGGA 972552 v-- v -- i vi v vivv i i v i C L1ME3G_3end#L 52 T--TGTCTT--TTTCTTATTGATTTGTAGGAGTTCTTTATATATTCTGGA 7 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.67 CpG sites = 77, Kimura (unadjusted) = 35.25 Transitions / transversions = 1.08 (77/71) Gap_init rate = 0.02 (11 / 547), avg. gap size = 1.00 (11 / 11) 4200 29.66 1.79 1.71 chr5qtel1M 972409 974748 (25252) C L1M5_orf2#LINE/L1 (0) 3294 953 m_b270s551i4 10692 chr5qtel1M 972409 TGACTTGGAGCATCTTTTTATATGACTAGAAATAGTTTCAATTTCTTCAT 972458 ?v v i i vi vviiivi v? v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr5qtel1M 972459 CTGAGAATTGTCTGTTCATATCCTTTGACCATTTTTCAATTGGA--GAAT 972506 i v v vi i v ?v i-- vv C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTT 3195 chr5qtel1M 972507 GGCTTGATTTTTTAT-AAATTAGAGTTAATTCTCTCTATATTTTGGAAAT 972555 v -- ? -i ? iv v- i i v i v i C L1M5_orf2#LIN 3194 GTCTT--TTTNTTATTGANTTGTAGG-AGTTCTTTATATATTCTGGATAC 3148 chr5qtel1M 972556 GAGGCCTTTATCAGA-ACCTTTGGCTGTAAAAATATTTTCCCAGTTTATT 972604 v i - iv v ?-i i v v i ? i i v C L1M5_orf2#LIN 3147 GAGTCCTTTGTCAGATATATGTN-TTGCAAATATTTTCTCCCANTCTGTG 3099 chr5qtel1M 972605 GCTTCCCTTCTAATCTTGTCTGCATTAGTTTTGTTTGTACAAAAACTTTT 972654 v i v i v ivi iv ivi vvv? vi i ii C L1M5_orf2#LIN 3098 GCTTGCCTTTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTTT 3049 chr5qtel1M 972655 CAGTTTGGTAGAATCGAA-------ATTTTCTATTTTGTGATCAGTAATG 972697 v v i i? i v ------- i v i i i? i--- C L1M5_orf2#LIN 3048 AATTTTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGGTTNGTG--- 3002 chr5qtel1M 972698 ATCTCTAGTTCTGCTTTGGTCATAAAGACCTTCCCCT-TCCACAGGTCTG 972746 -- i -- v iii v i - i i i iv -? vv vv C L1M5_orf2#LIN 3001 --CTTT--TTGTGTCCTGTTTA-AGAAATCTTTGCCTANCCCAAGGTCAC 2957 chr5qtel1M 972747 AGAGGTAAACTATCCTATGTT--CCTCTAATTTATTAATAATTTCATTCT 972794 ii i --i v -- i ivvvv v i i ?ii C L1M5_orf2#LIN 2956 GAAGATA--TTCTCCTATGTTTTCTTCTAGAAGTTTTATAGTTTTANCTT 2909 chr5qtel1M 972795 TTATGCCTAGGTC-ATGAACCCATTTTGACCTTATCTTAGTGTACGACGT 972843 iiii - -i i ? vi v i v i ii C L1M5_orf2#LIN 2908 TTACATTTAGGTCTATGA-TCCATCTNGAATTAATTTTTGTGTATGGTGT 2860 chr5qtel1M 972844 TAAGTATGGATCAATGCCTAGTTTCTGCCATATTAGTTTCCAATTTTCCC 972893 v i v i i v?iii v i v vii v v i C L1M5_orf2#LIN 2859 GAGGTAGGGGTCGAGNTTCATTTTTTTCCATATGGATATCCAATTGTTCC 2810 chr5qtel1M 972894 AGCA--ATTTTTTTCAAACAGTAAGTTCTTATCCCAAAAGCTGGGATT-- 972939 -- v vv v v -- i vi ---- i- -- C L1M5_orf2#LIN 2809 AGCACCATTTGTTGAAAAGACTA--TCCTTTCCCCA----CTGA-ATTGC 2767 chr5qtel1M 972940 TTTGGG---TTTGTCAAAGACTAGGTTGCTATATTTGT-TGACTGTTTTA 972985 ? v--- i ii i? v? i v - --- v i C L1M5_orf2#LIN 2766 NTTGGCACCTTTGTCAAAAATCAANTGNCCATATATGTGTG---GGTCTA 2720 chr5qtel1M 972986 TCCCTTGAAC---CTAATCTATTCCACTGATCAACTTATCTATTCCTTA- 973031 ii - i --- v i i v i i - - C L1M5_orf2#LIN 2719 TTTCT-GGACTCTCTATTCTGTTCCATTGATCTATTTGTCTAT-CCTTAC 2672 chr5qtel1M 973032 GCCAATACCAAATAGTTTTGGTAACTGCTGCTCTATAATATAATTTT-AG 973080 v iv i i v iv i - i i - ? C L1M5_orf2#LIN 2671 GCCAATACCACACTGTCTTGATTACTGTAGCTTTATAATA-AGTCTTGAN 2623 chr5qtel1M 973081 ATCTGGTCAGCTAAG-CCACCATCATTTGATTTT-TTTTTCATTAATTCC 973128 ? vivv - v v - v i - v-i vi C L1M5_orf2#LIN 2622 ATCNGGTAGTGTAAGTCCTCCAAC-TTTGTTCTTCTTTTTCAA-GATTGT 2575 chr5qtel1M 973129 CTTGAA-ATTCTTGACCTTTTGTTTTTCCATATGAACTTTGTTGTTATTT 973177 i iv- ? ii i iv i i ivvi i vi C L1M5_orf2#LIN 2574 TTTGGCTATTCTNGGTCCTTTGCATTTCCATATAAATTTTAGAATCAGCT 2525 chr5qtel1M 973178 TTTCTAGGTC-ATTAAAATAGTTTTTGGGAGTCTGATTGGTATAGCGCTA 973226 v v vv - iv v vi vi v i v v ii i C L1M5_orf2#LIN 2524 TGTCAATTTCTACAAAAAAACCTGCTGGGATTTTGATTGGGATTGCATTG 2475 chr5qtel1M 973227 AATAAATAGATTAGTTTAGGTAATATTGTCATCTTTATTATATTTGCTCG 973276 vv i i i v iv v ? iv viv v C L1M5_orf2#LIN 2474 AATCTATAGATCAATTTGGGGAGAATTGACATCTTNACAATATTGAGTCT 2425 chr5qtel1M 973277 CCCTATCCAAGAGCATTTAATATTTTTCCAATTGGTTAGATCAGACTTAA 973326 i v v i vvv i i v iv i vvvi C L1M5_orf2#LIN 2424 TCCAATCCATGAACATGGTATATCTCTCCATTTATTTAGGTCTTCTTTAA 2375 chr5qtel1M 973327 TTT-TGTGAAAAGTGGTCTGTAATTTTGCTCATAAAGTTTCTGATTTTCC 973375 - v v iv i v i i vvvii ? v ii vviv ?i C L1M5_orf2#LIN 2374 TTTCTCTCAGCAATGTTTTGTAGTTTTCAGTGTANAGGTCTTGCACATNT 2325 chr5qtel1M 973376 TTTGGCAGATAGATTCCTAAATATTTTATATTATCAGTAGTTACTTTAAA 973425 vi vv i ? i v iv vv i i v C L1M5_orf2#LIN 2324 TTTGTTAGATTTATTCCTAAGTATTTNATGTTTTTTGATGCTATTGTAAA 2275 chr5qtel1M 973426 TGGAATTTCTCTTTGTAACTCTGACTGTTGGATT--TTGTTAGTGATATA 973473 v vi i ?-- v i v i v ivi -- iv ii C L1M5_orf2#LIN 2274 TGGTATTGTTTTTN--AAATTTCATTTTCCAATTGTTTGTTGCTAGTATA 2227 chr5qtel1M 973474 TAAGAATGCTGATGACTTATGTGGGTTTATTTTATAACCAGCAACTTTGC 973523 ii i viv i v ivi v ii i v ? i i C L1M5_orf2#LIN 2226 TAGAAATACAATTGATTTTTGTATATTGACCTTGTATCCNGCGACCTTGC 2177 chr5qtel1M 973524 TAAAGTTGTGGATTATTTCTAATAACTTTTTAGCAGAATCTCTTGGGTTC 973573 v iiivv v i ii ? v i v i ? i i C L1M5_orf2#LIN 2176 TAAATTCACTTATTAGTTCTAGTAGTTTNTTTGTAGATTCTTTNGGATTT 2127 chr5qtel1M 973574 TCTAAGTATACCATCATGTCATCGGCAAAGAGTGATAATTTGGCTTCCTC 973623 v ? v v i v i? i i vii i C L1M5_orf2#LIN 2126 TCTACGTANACAATCATGTCATCTGCGAATAANGACAGTTTTATTTCTTC 2077 chr5qtel1M 973624 ATTGCCTATTCTTATTCCTTTAATCTCTTTCTCAGCTCTTATTGCTATAG 973673 v v v ii v v i i vvvi vv i C L1M5_orf2#LIN 2076 CTTTCCAATCTTTATGCCTTTTATTTCTTTTTCTTGCCTTATTGCACTGG 2027 chr5qtel1M 973674 CTAGCGTTTCTAATACAATATTAAATAGTAATGGTGATAGTGGGCAACCT 973723 viii i i i i v i ? i i v C L1M5_orf2#LIN 2026 CTAGGACCTCCAGTACAATGTTGAATAGAAGTGGTGANAGCGGACATCCT 1977 chr5qtel1M 973724 TGTTTCACTCCAGATCTTATTGGGAATGGTTGCAGTTTGTCTCCATTACA 973773 i iii v vv v v? v ? v v vi C L1M5_orf2#LIN 1976 TGTCTTGTTCCCGATCTTAGGGGGAAAGCNTTCAGTNTTTCACCATTAAG 1927 chr5qtel1M 973774 TATGATGCTTACTGATGGTTTTAAATAGATGCTGCTGATTATTTTAAGGA 973823 i ?i vv vvi ivi v i vv i C L1M5_orf2#LIN 1926 TATGATGTTNGCTGTAGGTTTTTCGTAGATGCCCTTTATCAGGTTGAGGA 1877 chr5qtel1M 973824 AAAGTCCATTTATTCCTATACTCTCAAGTGTTTTTAATAGGAATGGATGT 973873 ivvi v i vvi viii v vi v i C L1M5_orf2#LIN 1876 AGTTCCCTTCTATTCCTAGTTTGCTGAGAGTTTTTATCATGAATGGGTGT 1827 chr5qtel1M 973874 TGGATTTTATCAAATGCTTTTTCTGTATCTATTGAGATGATCATATGGTT 973923 i i i i C L1M5_orf2#LIN 1826 TGAATTTTGTCAAATGCTTTTTCTGCATCTATTGAGATGATCATATGATT 1777 chr5qtel1M 973924 TTTGTTAATTTGGT-TATTAACATGGCCAATTATATTGATAGTTTTCCTA 973972 v iv- iv - i i iv i v v i v C L1M5_orf2#LIN 1776 TTTCTCC-TTTATTCTGTTAATATGGTGAATTACATTGATTGATTTTCGA 1728 chr5qtel1M 973973 ATATTGAACCAGCCCTGCATTCCTGGTATAAA-TCTACTTGATCATAGTG 974021 i i i i v -i i i ii C L1M5_orf2#LIN 1727 ATGTTAAACCAACCTTGCATTCCTGGGATAAACCCCACTTGGTCATGATG 1678 chr5qtel1M 974022 TATTATCCTGGAGATGACTTTCTGTAGTCTTTTTGCTAATATCTTATTTA 974071 vvvv ivv v v v vv i i ? C L1M5_orf2#LIN 1677 TATTATCCTTTTTATATATTGCTGGATTCGATTTGCTAATATTTTGTTNA 1628 chr5qtel1M 974072 AGATTTTAGCATCAATATTCATTAGGGAGATTGGTCTATAATTTTCTTTC 974121 i v v i v v i i C L1M5_orf2#LIN 1627 GGATTTTTGCATCTATGTTCATGAGGGATATTGGTCTGTAATTTTCTTTT 1578 chr5qtel1M 974122 TCTGT--TTTCAGCCTACCTGGTTTAGGTATCAGTACCATGTCTGTGTCA 974169 ii -- v --ii ii ? v vii? iiv iv C L1M5_orf2#LIN 1577 CTTGTAATGTC--TTTGTCNGGTTTTGGTATCAGGGTNATGCTGGCCTCA 1530 chr5qtel1M 974170 TAGAAGGAATTTGGTAGGACTCCTTCATTCCCTATTTTAATCAAATAATT 974219 i v i v v vii i v ii -v vi v i C L1M5_orf2#LIN 1529 TAAAATGAGTTGGGAAGTGTTCCCTCTTTTTCTATTTT-CTGGAAGAGTT 1481 chr5qtel1M 974220 TATATAGCATTGGGGCCAATTGTTCTTTAAATGTTTGGTAAAATTCACAT 974269 i i iv viii v v i i vv C L1M5_orf2#LIN 1480 TGTGTAAGATTGGTATTATTTCTTCCTTAAATGTTTGGTAGAATTCACCA 1431 chr5qtel1M 974270 GTAAATCCATCTGGTCCTGGGGATTTTTTTCTTAGGGAGTTGTTTAATTG 974319 i v v i - i iv i i v v i C L1M5_orf2#LIN 1430 GTGAAGCCATCTGGGCCTGGAG-TTTTCTTTGTGGGAAGGTTTTTAATTA 1382 chr5qtel1M 974320 CCTGTTCTATTTCTTTTTCTGAAATGGGACTATTCAAGCAATTTACTTCC 974369 vvi v vviv v i i iiivv i i i C L1M5_orf2#LIN 1381 CAAATTCAATTTCTTTAATAGATATAGGGCTATTCAGATTTTCTATTTCT 1332 chr5qtel1M 974370 TCCTCTGTTAGTCTGGGAAGTCTGTATTTTTGGAGGTAGTCATCCATTTC 974419 i v? i i v v i?i i vi v v ii C L1M5_orf2#LIN 1331 TCTTGNGTCAGTTTTGGTAANTTGTGTTTTTCAAGGAATTTGTCCATTTC 1282 chr5qtel1M 974420 ACTTAGGTTATCAAATTTATTGGCATAAAGCTGAGCAAAATAACTCCTTA 974469 ii i ? i vv v viii C L1M5_orf2#LIN 1281 ATCTAAGTTNTCAAATTTATTGGCATAAAGTTGTTCATAATATTCTCTTA 1232 chr5qtel1M 974470 TTATTTCTCTAATTTCCTCTTCATTGGTGGAAAGTTCTCCCTTTTCATTT 974519 iii i v ivivvv iv i vi vv i i C L1M5_orf2#LIN 1231 TTATCCTTTTAATGTCTGTAGGATCTGTAGTGATGTCTCCTTTTTCATTC 1182 chr5qtel1M 974520 TTAAGACTACTAATTTCATTTTCCTCCCTCTTTTTTCTAATCAGATTTAC 974569 i i v i iv vvv i i i i ii i vi ?i C L1M5_orf2#LIN 1181 CTGATATTGGTAATTTGTGTCTTCTCTCTTTTTTTCTTGATCAGTCTNGC 1132 chr5qtel1M 974570 CAAAGGCTTATCTATTTTATTGGCTTTTTCATAGAACCAACTCTTAGTTT 974619 i i i v iii v i i i i C L1M5_orf2#LIN 1131 TAGAGGTTTATCAATTTTATTGATCTTTTCAAAGAACCAGCTTTTGGCTT 1082 chr5qtel1M 974620 TATTAATTAGTTCAATAGCTTTTTTACTTTCAATATTTTTAATTTCTCCT 974669 ii i vvi v v i? ? ii v v iv i v C L1M5_orf2#LIN 1081 CGTTGATTTTCTCTATTGTNTNTTTGTTTTCTATTTCATTGATTTCTGCT 1032 chr5qtel1M 974670 TTTAATTTTAGAATTTCCAATTTAGTATTTGATTGGGGGTTTTTAATTTG 974719 i vi vv vvii vv i ?v v --- C L1M5_orf2#LIN 1031 CTTATCTTTATTATTTCCTTCCTTCTACTTNCTTTGGG---TTTAATTTG 985 chr5qtel1M 974720 G---TCTTTTTTTAGTTTTTTTAGTTGCAAGC 974748 v--- i i i v v v C L1M5_orf2#LIN 984 CTCTTCTTTTTCTAGCTTCTTAAGGTGGAAGC 953 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.84 CpG sites = 372, Kimura (unadjusted) = 39.51 Transitions / transversions = 1.20 (372/310) Gap_init rate = 0.03 (64 / 2339), avg. gap size = 1.28 (82 / 64) 17 23.93 2.04 0.00 chr5qtel1M 976022 976070 (23930) (CAAA)n#Simple_repeat 1 50 (0) m_b270s252i6 10693 chr5qtel1M 976022 CAAAAAAAAAAAGAAAAAAAGAAATAAACAAAGAAA-AGCCTAACAAACA 976070 v v v v v i v - iv v (CAAA)n#Simpl 1 CAAACAAACAAACAAACAAACAAACAAACAAACAAACAAACAAACAAACA 50 Matrix = Unknown Transitions / transversions = 0.25 (2/8) Gap_init rate = 0.02 (1 / 48), avg. gap size = 1.00 (1 / 1) 22 15.51 0.00 0.00 chr5qtel1M 976023 976058 (23942) (A)n#Simple_repeat 1 36 (0) m_b270s252i7 10693 chr5qtel1M 976023 AAAAAAAAAAAGAAAAAAAGAAATAAACAAAGAAAA 976058 i i v v i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 36 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 195 34.89 6.06 4.48 chr5qtel1M 976254 976385 (23615) C MIRc#SINE/MIR (52) 216 83 m_b270s601i11 10694 chr5qtel1M 976254 TTCATGCACAGTTA---CACTGGAACTTTATAATAAACCTGTGACA---A 976297 iii - --- i v v i i i i v vi---i C MIRc#SINE/MIR 216 TTCACATACA-TTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGG 168 chr5qtel1M 976298 CAGAGGAAGTGCTTTCATTCTCATTAGGTCCACAACTCAGGTCATCA--G 976345 i v i ii v i i i ----ii iv v vv iii-- C MIRc#SINE/MIR 167 CAGGGCAGGTATTATTATCCCCATT----TTACAGATGAGGAAACTGAGG 122 chr5qtel1M 976346 CTGAAAATGGCCAAGTGACTTGACCCAAATCTCAGCAGCT 976385 v i iv ii v v ii v - C MIRc#SINE/MIR 121 CTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACA-CAGCT 83 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 50.10 CpG sites = 29, Kimura (unadjusted) = 50.10 Transitions / transversions = 1.93 (29/15) Gap_init rate = 0.07 (9 / 131), avg. gap size = 1.56 (14 / 9) 352 26.65 19.90 1.78 chr5qtel1M 977815 978005 (21995) MIRc#SINE/MIR 18 242 (26) m_b270s601i12 10695 chr5qtel1M 977815 GTGGAAAGGGC------CTTGAA-TCAGGAAGACAGAGGTTTTAATCCCA 977857 i ------ i - vvi iv i i MIRc#SINE/MIR 18 GTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCG 67 chr5qtel1M 977858 CCTCAGAAACTTGCT-GTTATAGGACCT-----------------CTGTT 977889 v v vv i - i i iv ----------------- v i MIRc#SINE/MIR 68 GCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTC 117 chr5qtel1M 977890 TGA--TTCCTTTTCTTTGTCTGTAATATATGCATAATAATAGCAGCTAAG 977937 --i vv i ii v iv v v v ivv MIRc#SINE/MIR 118 TGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTG 167 chr5qtel1M 977938 T---CCTCA---GATTCTCATGAGGATAAAATAAGACAATGCAGAGTATG 977981 i--- --- i v ii v i i i --- i MIRc#SINE/MIR 168 CCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTA---TGTG 214 chr5qtel1M 977982 A---CACATAG--AGCTGTATAAATGCTA 978005 --- i v v -- i - i MIRc#SINE/MIR 215 AAAGCGCTTTGTAAACTGTA-AAGTGCTA 242 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.28 CpG sites = 28, Kimura (unadjusted) = 33.69 Transitions / transversions = 1.27 (28/22) Gap_init rate = 0.07 (13 / 190), avg. gap size = 3.23 (42 / 13) 204 38.24 7.35 0.00 chr5qtel1M 978136 978271 (21729) L2b_3end#LINE/L2 320 465 (1) m_b270s601i13 10696 chr5qtel1M 978136 CTGCTGGCATAT-TGTCTGCCCTGCCATTCTGTGACCTTCAGGAGAGTGG 978184 ? vi i - v ii i vv v i iv i ii L2b_3end#LINE 320 CTGNTTACATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAG 369 chr5qtel1M 978185 AGG--ATGTC--CCTTAGAC-TCTTTATGTTCCTGGTATTCAGCCCAGAA 978229 i i--i? --i ivv -i vi i i i ii iiiii v ?i L2b_3end#LINE 370 GGACCGNGTCTGTCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNG 419 chr5qtel1M 978230 -CTGCCATGTAGAAGGCACT---TAAGTGTTTACTGACTAGAAGAA 978271 - v iii v i --- i i ii v ii v L2b_3end#LINE 420 CCTGGCACACAGTAGGCGCTCAGTAAATATTTGTTGAATGAATGAA 465 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 54.43 CpG sites = 38, Kimura (unadjusted) = 62.37 Transitions / transversions = 2.71 (38/14) Gap_init rate = 0.04 (6 / 135), avg. gap size = 1.67 (10 / 6) 256 24.99 5.88 1.12 chr5qtel1M 978363 978447 (21553) C MIR3#SINE/MIR (5) 203 115 m_b270s601i14 10697 chr5qtel1M 978363 ATAGCATCCCAGA-TG--AGCACTAGAAGGGACC-TACAGGTCCATGGAG 978408 v vi - -- vi i - v i - vv C MIR3#SINE/MIR 203 ATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGAT-CATCTAG 155 chr5qtel1M 978409 TGCAACCTTCTCCTTTCATAGATG-GAAAAATGAGATTCA 978447 v ii v i i - i v iii C MIR3#SINE/MIR 154 TCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCA 115 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.98 CpG sites = 12, Kimura (unadjusted) = 30.98 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.06 (5 / 84), avg. gap size = 1.20 (6 / 5) 447 30.27 10.42 1.92 chr5qtel1M 979082 979273 (20727) MIRc#SINE/MIR 2 209 (59) m_b270s601i15 10698 chr5qtel1M 979082 GAGCCAGTA--GTACAGTGCA--GAGTTCTGGGCATATCTTCAGGTATAC 979127 v i-- i v -- iv i v ivvv v v MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr5qtel1M 979128 CCGAGTTTGAATTAAGCCTTGGACAGTTACT----GTGTACCTCTGGGCA 979173 i i i i ivv v iv v v ---- iv ii MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 101 chr5qtel1M 979174 AGTCAATTAAACTCTGTTAGTTTGTCTCAGTTTCCTCAACTG------AG 979217 v v v v ---- i v ------i MIRc#SINE/MIR 102 AGTCACTTAACCTCTCTGA----GCCTCAGTTTCCTCATCTGTAAAATGG 147 chr5qtel1M 979218 GAATAACAATATA------ACCTAACTTGGAAAGTTAAGATGAGGATAAA 979261 i i iv------i v iiv ii ivvi v MIRc#SINE/MIR 148 GGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAA 197 chr5qtel1M 979262 GTGATACAATAT 979273 i v i i MIRc#SINE/MIR 198 ATGAGATAATGT 209 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.54 CpG sites = 29, Kimura (unadjusted) = 39.41 Transitions / transversions = 1.04 (29/28) Gap_init rate = 0.05 (9 / 191), avg. gap size = 2.67 (24 / 9) 15 23.53 2.22 0.00 chr5qtel1M 979451 979495 (20505) (TACA)n#Simple_repeat 1 46 (0) m_b270s252i8 10699 chr5qtel1M 979451 TACATAGAAATATATATACATATATAAATA-ATAAATACACACGTA 979495 v v i i i v - v i i (TACA)n#Simpl 1 TACATACATACATACATACATACATACATACATACATACATACATA 46 Matrix = Unknown Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 231 24.69 9.30 1.08 chr5qtel1M 980335 980420 (19580) C MIR3#SINE/MIR (24) 184 92 m_b270s601i16 10700 chr5qtel1M 980335 GGGCTGAAAGCCCCTTTAGAAGTAA-AGAGTCCAACCCCCTTAAGTTTAT 980383 i i vvv i ii v -vv i -v i C MIR3#SINE/MIR 184 GAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCA-TTTTAC 136 chr5qtel1M 980384 AG--GAGGAAAGTGAAACACAGAGA--TGG---GATTTGCCAAA 980420 -- v ii v -- i--- i v C MIR3#SINE/MIR 135 AGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAA 92 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.32 CpG sites = 11, Kimura (unadjusted) = 30.32 Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.06 (5 / 85), avg. gap size = 1.80 (9 / 5) 314 27.94 8.02 0.57 chr5qtel1M 981615 981938 (18062) L1M5_orf2#LINE/L1 827 1174 (2120) m_b270s551i5 10701 chr5qtel1M 981615 TAAAAGAAAATGATTAAACAATAACCCAAAATTTCTTGGGTTGAGCTAAA 981664 i v ? vv v i vvi v v i vv L1M5_orf2#LIN 827 TGAATGANAATGAAAATACAACATATCAAAATTTGTGGGATGCAGCTAAA 876 chr5qtel1M 981665 GCAGTCCTCAGAGGGAGA--AACAGATTTACTAT-CACACATTAAGAAAA 981711 v i i --v i v? v- - ?i i ii i L1M5_orf2#LIN 877 GCAGTGCTTAGAGGGAAATTTATAGCNTTAA-ATGCNTATATTAGAAAAG 925 chr5qtel1M 981712 AAGAAAG-----AGATTAAT----TAAATATGCACTATAAAAAACTAGAA 981752 ----- i i ---- iiv v iv i i L1M5_orf2#LIN 926 AAGAAAGGCTTAAAATCAATGATCTAAGCTTCCACCTTAAGAAGCTAGAA 975 chr5qtel1M 981753 AAATAAATG---AGTAAATACAAAATAAGTACAAAAGACAAGATATTAAA 981799 v iv --- v iv i? v iii vi i v L1M5_orf2#LIN 976 AAAGAAGAGCAAATTAAACCCAAAGNAAGTAGAAGGAAGGAAATAATAAA 1025 chr5qtel1M 981800 ATTAGAAG--GAAAATAGAAAAATTGGAAATAAAAAAATAAAAATGAGA- 981846 iv ii -- vi ivi v i i ? ? i v iv i - L1M5_orf2#LIN 1026 GATAAGAGCAGAAATCAATGAAATAGAAAACAAANANACAATAGAGAAAA 1075 chr5qtel1M 981847 --AATGGAACTAAAAATGGCTTCTTTGAAATGATTCGTAAAATGGAGAAA 981894 -- i i i i iiv v v ivi v v- L1M5_orf2#LIN 1076 TCAACGAAGCCAAAAGCTGGTTCTTTGAAAAGATCAATAAAATTGAT-AA 1124 chr5qtel1M 981895 ACCCTTAGCTAATCTGATCA--AAAGGAAGAGAG----CACAAAATCCCA 981938 ii ? iv -- ii ---- v v L1M5_orf2#LIN 1125 ACCTCTAGCNAGACTGATCAAGAAAAAAAGAGAGAAGACACAAATTACCA 1174 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.27 CpG sites = 51, Kimura (unadjusted) = 36.79 Transitions / transversions = 1.31 (51/39) Gap_init rate = 0.04 (12 / 323), avg. gap size = 2.33 (28 / 12) 246 26.73 7.25 4.23 chr5qtel1M 982208 982414 (17586) L1M1_orf2#LINE/L1 1545 1757 (1537) m_b270s551i6 10702 chr5qtel1M 982208 CCTAAAACTGAAACCAAGGAAAGTC----CAGAGACAGAAAATTACAAGT 982253 i v ii iiv v ---- i i v i i i L1M1_orf2#LIN 1545 CCTGATACCAAAACCAGACAAAGACACATCAAAAAAAGAAAACTACAGGC 1594 chr5qtel1M 982254 CAAAG-----AATAAATATTGTCTCCTCACTCCAATTTTAAACAAAGTCC 982298 vi-----i i -v v vv ---- ii v i v L1M1_orf2#LIN 1595 CAATATCTCTGATGAATATTG-ATGCAAA----AATCCTCAACAAAATAC 1639 chr5qtel1M 982299 TATCAAAC--AA--CCACAATAAATTATCTAAGAAACCATTTATTATAAT 982344 v -- -- v v --- i i i i i i i L1M1_orf2#LIN 1640 TAGCAAACCGAATTCAACAATACATTA---AAAAGATCATTCATCATGAC 1686 chr5qtel1M 982345 CAAATGGGATTTCTACCAGGTATGGAAGAATATTTCAACATTAGGAAAA- 982393 i v v ? v v i iv - v v - L1M1_orf2#LIN 1687 CAAGTGGGATTTATCCCNGGGATGCAAGGATGGTTCAACA-TACGCAAAT 1735 chr5qtel1M 982394 -AATGAATATAATTAATCACAT 982414 - v i i vv i L1M1_orf2#LIN 1736 CAATCAATGTGATACATCATAT 1757 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 33.90 CpG sites = 29, Kimura (unadjusted) = 33.90 Transitions / transversions = 1.21 (29/24) Gap_init rate = 0.07 (15 / 206), avg. gap size = 1.60 (24 / 15) 16 9.71 0.00 0.00 chr5qtel1M 982592 982613 (17387) (T)n#Simple_repeat 1 22 (0) m_b270s252i10 10703 chr5qtel1M 982592 TTTTCATTTTTTTTTTTTTTTT 982613 iv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTT 22 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 13 4.76 0.00 4.35 chr5qtel1M 982698 982721 (17279) (CCCT)n#Simple_repeat 1 23 (0) m_b270s252i11 10704 chr5qtel1M 982698 CCCTCCCTCCCTCCACCCCCTCCC 982721 - i (CCCT)n#Simpl 1 CCCTCCCTCCCTCC-CTCCCTCCC 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 343 30.16 3.36 2.50 chr5qtel1M 985569 985687 (14313) MIRb#SINE/MIR 143 262 (6) m_b270s601i17 10705 chr5qtel1M 985569 TAAAATAGGGATAATAATATTTACTTAACAGGTTTGGTATGAGGACATGG 985618 i ii i vi v v i ivvii MIRb#SINE/MIR 143 TAAAATGGGGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAA 192 chr5qtel1M 985619 GGAGCTACTG---ATAAGGTGCTTTAAACAA-GTCTGGCACTTAGTAGGT 985664 v v v ---i i i viv i- i v i i MIRb#SINE/MIR 193 TGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGC 242 chr5qtel1M 985665 GCCTTATAATAGATGCCAGTTTT 985687 i---i i vi i i MIRb#SINE/MIR 243 GCT---CAATAAATGGTAGCTCT 262 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.00 CpG sites = 23, Kimura (unadjusted) = 40.45 Transitions / transversions = 1.92 (23/12) Gap_init rate = 0.04 (5 / 118), avg. gap size = 1.40 (7 / 5) 13 20.41 3.57 5.45 chr5qtel1M 989375 989430 (10570) (ATTACT)n#Simple_repeat 1 55 (0) m_b270s252i12 10706 chr5qtel1M 989375 ATTACTCTGTCCTACT-CTATAGGCATTACTCATTACT-TTAGCTATTAC 989422 v - v i - vivi - - - (ATTACT)n#Sim 1 ATTACTAT-TACTATTACTATTACTATTACT-ATTACTATTA-CTATTAC 47 chr5qtel1M 989423 TTTTATTA 989430 v i (ATTACT)n#Sim 48 TATTACTA 55 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.09 (5 / 55), avg. gap size = 1.00 (5 / 5) 278 29.43 10.88 0.62 chr5qtel1M 989558 989704 (10296) L2a_3end#LINE/L2 356 517 (0) m_b270s601i18 10707 chr5qtel1M 989558 TTCTACCTCATTGTTGGTGTATTGTCTA-----CCCCACCAATCTGTGAA 989602 i i vv i v v i----- i ivv i i L2a_3end#LINE 356 TTTTACTTATTTATTTGTTTATTGTCTGTCTCCCCCCACTAGAATGTAAG 405 chr5qtel1M 989603 CTCCATA--GGAAGGGG----TGTCACTTGCATCTCCTTTTG-ATCCTGA 989645 i-- v i---- vv vii iiv vi - iv L2a_3end#LINE 406 CTCCATGAGGGCAGGGACTTTTGTCTGTTTTGTTCACTGCTGTATCCCCA 455 chr5qtel1M 989646 -TGCTTAGCCCAGGGCCTGGCATTTCCTAGGCACT---TAAATATTTGCT 989691 -i i vv v iv vv i --- i L2a_3end#LINE 456 GCGCCTAGAACAGTGCCTGGCACATAGTAGGCGCTCAATAAATATTTGTT 505 chr5qtel1M 989692 GACTTGAAGAAAT 989704 v- vi L2a_3end#LINE 506 GAA-TGAATGAAT 517 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.76 CpG sites = 22, Kimura (unadjusted) = 37.94 Transitions / transversions = 1.05 (22/21) Gap_init rate = 0.05 (7 / 146), avg. gap size = 2.43 (17 / 7) 335 24.36 8.80 1.49 chr5qtel1M 989580 989704 (10296) L2b_3end#LINE/L2 333 466 (0) m_b270s601i19 10707 chr5qtel1M 989580 TGTCTACCCCACCAATCTGTGAACTCCAT--AGGAAGGG---GTGTC--A 989622 v i iv i i --i v --- ? --v L2b_3end#LINE 333 TGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGT 382 chr5qtel1M 989623 CTTGCATCTCCTTTTGATCCTGA-TGCTTAGCCCAGGGCCTGGCATTTCC 989671 i- v vi vv iv -i i v ? ivivv L2b_3end#LINE 383 CTTGT-TCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAG 431 chr5qtel1M 989672 TAGGCACT---TAAATATTTGCTGACTTGAAGAAAT 989704 i --- i v- vi L2b_3end#LINE 432 TAGGCGCTCAGTAAATATTTGTTGAA-TGAATGAAT 466 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.94 CpG sites = 15, Kimura (unadjusted) = 30.38 Transitions / transversions = 1.00 (15/15) Gap_init rate = 0.06 (7 / 124), avg. gap size = 1.86 (13 / 7) 391 22.09 3.49 0.00 chr5qtel1M 989784 989869 (10131) C MIR3#SINE/MIR (5) 203 115 m_b270s601i20 10708 chr5qtel1M 989784 ATAGGATCATAGATGATCA---CTGGAAAGGACCTACTAGGCCATAGAGT 989830 i vvi --- i vvv ii vv C MIR3#SINE/MIR 203 ATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGT 154 chr5qtel1M 989831 GCAACCCCCTCATTTTACAGATAGGGAAATTTAGATCCA 989869 v ii i v ii C MIR3#SINE/MIR 153 CCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCA 115 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.44 CpG sites = 10, Kimura (unadjusted) = 26.44 Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.01 (1 / 85), avg. gap size = 3.00 (3 / 1) 16 15.91 0.00 0.00 chr5qtel1M 989893 989920 (10080) (A)n#Simple_repeat 1 28 (0) m_b270s252i13 10709 chr5qtel1M 989893 AAAAAAAAAAAAAAAAATTGAAAAAGAA 989920 vvi i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA 28 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 24 29.37 0.00 0.00 chr5qtel1M 990503 990577 (9423) (AAAA)n#Simple_repeat 1 75 (0) m_b270s252i14 10710 chr5qtel1M 990503 AAAAGAAAAAAAAACAATAAAAAGAAGAAAAAAGAGAAAGGAAAAAAAAA 990552 i v v i i i i ii (AAAA)n#Simpl 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr5qtel1M 990553 GCAAGCAAGCAAACAACAACAAAAA 990577 iv iv iv v v v (AAAA)n#Simpl 51 AAAAAAAAAAAAAAAAAAAAAAAAA 75 Matrix = Unknown Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.00 (0 / 74), avg. gap size = 0.0 (0 / 0) 517 33.19 0.98 2.99 chr5qtel1M 990967 991171 (8829) MIRb#SINE/MIR 1 201 (67) m_b270s601i21 10711 chr5qtel1M 990967 CAGAAGGGGAGATGGTAGTATAATAAAGAGAAACCCAGGCCT-AGAATCA 991015 i v v-- i ii i ii i i- v i i -i i MIRb#SINE/MIR 1 CAGAGGGGCAGC--GTGGTGCAGTGGAAAGAG-CACGGGCTTTGGAGTCA 47 chr5qtel1M 991016 GAAGTGCTTGAGTTGAAATCAAGCTTCAGACAATTTCTAGCTCTGTACCC 991065 vivi i i vi vv vi v v v v v iv MIRb#SINE/MIR 48 GACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACC 97 chr5qtel1M 991066 CTTGGCACAT-ATTTAAAGTCTCTTTGCCTTAGTTTCCTCGACTCTTAAA 991114 i v vi - i vv vv i iv v v MIRb#SINE/MIR 98 TTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAA 147 chr5qtel1M 991115 TGGAGAGAATAATATCAATTAAATTGGAAGGTTATTATGAAGACAAGGTA 991164 i v i --- vv i v i i i i iv ii i MIRb#SINE/MIR 148 TGGGGATAATAATACC---TACCTCGCAGGGTTGTTGTGAGGATTAAATG 194 chr5qtel1M 991165 ACATAAT 991171 v MIRb#SINE/MIR 195 AGATAAT 201 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.19 CpG sites = 36, Kimura (unadjusted) = 44.90 Transitions / transversions = 1.20 (36/30) Gap_init rate = 0.04 (8 / 204), avg. gap size = 1.00 (8 / 8) 46 0.00 0.00 0.00 chr5qtel1M 992046 992084 (7916) (TG)n#Simple_repeat 1 39 (0) c_b270s251i2 10712 chr5qtel1M 992046 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 992084 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 39 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 225 28.57 2.86 0.00 chr5qtel1M 996494 996563 (3437) C MIRc#SINE/MIR (7) 261 190 m_b270s601i22 10713 chr5qtel1M 996494 ATAATAGCTTATGTTCATATGACCCTTTGT-GTTTACAAAGTGTTTT-GT 996541 i?v ii ii ii v ii- i i -ii C MIRc#SINE/MIR 261 ATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCGCTTTCAC 212 chr5qtel1M 996542 ATATATCAACTCATTTAATTCT 996563 i i v i i C MIRc#SINE/MIR 211 ATACATTATCTCATTTGATCCT 190 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.96 CpG sites = 17, Kimura (unadjusted) = 40.69 Transitions / transversions = 5.67 (17/3) Gap_init rate = 0.03 (2 / 69), avg. gap size = 1.00 (2 / 2) 16 0.00 0.00 0.00 chr5qtel1M 998884 998900 (1100) (T)n#Simple_repeat 1 17 (0) m_b270s252i16 10714 chr5qtel1M 998884 TTTTTTTTTTTTTTTTT 998900 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTT 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 14 29.03 1.67 1.67 chr5qtel1M 998884 998943 (1057) (TTTTTA)n#Simple_repeat 1 60 (0) m_b270s252i15 10715 chr5qtel1M 998884 TTTTTTTTTTTTTTTTTACATTAAGTATT-TTTTAATATTAAGTACCTGT 998932 v v iv v v v - v v v - vii i (TTTTTA)n#Sim 1 TTTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTTA-TTTTTAT 49 chr5qtel1M 998933 TTTTATTTTTA 998943 (TTTTTA)n#Sim 50 TTTTATTTTTA 60 Matrix = Unknown Transitions / transversions = 0.40 (4/10) Gap_init rate = 0.03 (2 / 59), avg. gap size = 1.00 (2 / 2) 395 27.31 0.79 4.10 chr6ptel1M 76 201 (999799) C MIR#SINE/MIR (64) 198 77 m_b271s601i0 10716 chr6ptel1M 76 TATTATGTCACTTTGATC-TCATCTTAACATTTCAAGTCAGGTGATATTG 124 vv - i - ivvi vi vii vi iv i C MIR#SINE/MIR 198 TATTAACTCA-TTTAATCCTCACAACAACCCTATGAGGTAGGTACTATTA 150 chr6ptel1M 125 TTATCCCTATTTCAGAGTTGAGGAAACTGAGGGAAACAAACAGAATTTAA 174 i i v v ---- v v iv C MIR#SINE/MIR 149 TTATCCCCATTTTACAGATGAGGAAACTGAGG----CACAGAGAGGTTAA 104 chr6ptel1M 175 TTGATTTGCCCAGAGGTACACAGTTAG 201 v i i ii vi i C MIR#SINE/MIR 103 GTAACTTGCCCAAGGTCACACAGCTAG 77 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.49 CpG sites = 18, Kimura (unadjusted) = 34.49 Transitions / transversions = 1.20 (18/15) Gap_init rate = 0.05 (6 / 125), avg. gap size = 1.00 (6 / 6) 364 24.98 5.47 3.05 chr6ptel1M 96 223 (999777) C MIR1_Amn#SINE/MIR (41) 189 59 m_b271s601i1 10716 chr6ptel1M 96 ATCTTAA--CATTT--CAAGTCAGGTGA-TATTGTTATCCCTATTTCAGA 140 i -- i -- ivv v - ii i i v C MIR1_Amn#SINE 189 ATCTCAAAGCACTTTACAAAGGAGGTCAGTATCATTATCCCCATTTTACA 140 chr6ptel1M 141 GTTGAGGAAACTGAGGGAAACAAACAGAATTTAATTGATTTGCCCAGAGG 190 v ---- ?v v iv ? v i ii v C MIR1_Amn#SINE 139 GATGAGGAAACTGAGG----CNCAGAGAGGTNAAGTGACTTGCCCAAGGT 94 chr6ptel1M 191 TACACAGTTAGCCACC--CAGGTTTGGGATCAGAA 223 i ? i?i ? vi-- ivii ?i? C MIR1_Amn#SINE 93 CACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAA 59 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.29 CpG sites = 19, Kimura (unadjusted) = 33.61 Transitions / transversions = 1.58 (19/12) Gap_init rate = 0.06 (8 / 127), avg. gap size = 1.38 (11 / 8) 19 13.65 3.85 3.85 chr6ptel1M 713 764 (999236) (TATGAA)n#Simple_repeat 1 52 (0) m_b271s252i0 10717 chr6ptel1M 713 TATGAATAT-TTCATGAATATGAAAGATGAAATATGAATATG-TGATGAA 760 -vvi - v - -vv (TATGAA)n#Sim 1 TATGAATATGAATATGAATATG-AATATG-AATATGAATATGAATATGAA 48 chr6ptel1M 761 TATG 764 (TATGAA)n#Sim 49 TATG 52 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.08 (4 / 51), avg. gap size = 1.00 (4 / 4) 311 25.10 12.69 4.86 chr6ptel1M 776 909 (999091) C MIRc#SINE/MIR (111) 157 14 m_b271s601i2 10718 chr6ptel1M 776 ATTATCATGCCCATTTTACAGATAAAGAAACTGAATCTAACTAAGGTCCT 825 i v i i iv v vvi ivv C MIRc#SINE/MIR 157 ATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAA 108 chr6ptel1M 826 ATAACTTGACTTGCAAGGTT------CT---------CAG-GTC-GGATT 858 i i v --- i------ --------- - i - i C MIRc#SINE/MIR 107 GTGACTTGCC---CAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACT 61 chr6ptel1M 859 AGAAACCTGGGCTTCCTGATTCAAGGCCCTATCCACATTCTATCCACTGT 908 v v v v i v i i vi v ---- v i C MIRc#SINE/MIR 60 CGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGC----TCTTTCCACTGC 15 chr6ptel1M 909 A 909 C MIRc#SINE/MIR 14 A 14 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.99 CpG sites = 16, Kimura (unadjusted) = 30.99 Transitions / transversions = 1.00 (16/16) Gap_init rate = 0.08 (11 / 133), avg. gap size = 2.18 (24 / 11) 18 4.77 0.00 0.00 chr6ptel1M 965 986 (999014) (A)n#Simple_repeat 1 22 (0) m_b271s252i1 10719 chr6ptel1M 965 AAAAAAAAAAAAAAAAAAAGAA 986 i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAA 22 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 23 0.00 0.00 0.00 chr6ptel1M 1066 1090 (998910) (A)n#Simple_repeat 1 25 (0) m_b271s252i2 10720 chr6ptel1M 1066 AAAAAAAAAAAAAAAAAAAAAAAAA 1090 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAA 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 36 2.92 0.00 0.00 chr6ptel1M 2395 2429 (997571) (TG)n#Simple_repeat 1 35 (0) c_b271s251i0 10721 chr6ptel1M 2395 TGTGAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 2429 v (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 35 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 16 14.85 0.00 5.13 chr6ptel1M 2446 2486 (997514) (TTTTCT)n#Simple_repeat 1 39 (0) m_b271s252i3 10722 chr6ptel1M 2446 TTTGCTTTATTGTTTGCTCTTTTCTTTTTCTTTTTTCTTTT 2486 v v iv v - - (TTTTCT)n#Sim 1 TTTTCTTTTTCTTTTTCT-TTTTCTTTTTC-TTTTTCTTTT 39 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 319 33.88 0.83 0.00 chr6ptel1M 5523 5643 (994357) L1ME3G_3end#LINE/L1 427 548 (376) m_b271s551i0 10723 chr6ptel1M 5523 CATGTGCAGAAATGTTT-CTGCAACCCTGTTTGTAGTGGCAAGAAACTGG 5571 i iii i-i i vi i i i i i L1ME3G_3end#L 427 CATGTACAAGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGG 476 chr6ptel1M 5572 AAACTGAGTGGATGCCCATTAATTGAAGAATGACCGAATAAGTTATAGCA 5621 vivv ii i i v ii iiii i i i L1ME3G_3end#L 477 AAACAACCTAAATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGTA 526 chr6ptel1M 5622 CACGAATGTTATAGAATGTTAT 5643 i ivv ii i ii L1ME3G_3end#L 527 TATCCATACTATGGAATACTAT 548 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 49.51 CpG sites = 34, Kimura (unadjusted) = 51.43 Transitions / transversions = 4.86 (34/7) Gap_init rate = 0.01 (1 / 120), avg. gap size = 1.00 (1 / 1) 17 4.94 0.00 0.00 chr6ptel1M 6143 6163 (993837) (TA)n#Simple_repeat 1 21 (0) m_b271s252i4 10724 chr6ptel1M 6143 TATAAATATATATATATATAT 6163 v (TA)n#Simple_ 1 TATATATATATATATATATAT 21 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 284 36.63 2.30 1.14 chr6ptel1M 7004 7177 (992823) L2#LINE/L2 2384 2559 (523) m_b271s601i3 10725 chr6ptel1M 7004 TCATATATCCTAGTACTT---CTACATTTTCAATTAGGTAATTCATAGAT 7050 i v v i i --- v i i v i i ivi v ii L2#LINE/L2 2384 TCGTATATCCAACTGCCTACTCGACATCTCCACTTGGATGTCTAATAGGC 2433 chr6ptel1M 7051 ATCTCAAACTTATCACATCCAAAACAAAACCTATTAACTTCCAGC-CAAA 7099 v ii vi iiv v v vv - L2#LINE/L2 2434 ATCTCAAACTTAACATGTCCAAAACTGAACTCCTGATCTTCCCCCTCAAA 2483 chr6ptel1M 7100 TCATATCCCTCTTCCAAATATCCATATTTCAGTTGAAGGTACCACCACAT 7149 i - iii iiv iviv vi i ?i v i v v i-i L2#LINE/L2 2484 CC-TGCTCCTCCCGCAGTCTTCCCCATCTCAGTNAATGGCAACTCCAT-C 2531 chr6ptel1M 7150 CACCCAATAACCCAAACTGACAATCCTG 7177 vi i vi i ii ii v i i L2#LINE/L2 2532 CTTCCAGTTGCTCAGGCCAAAAACCTTG 2559 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 51.36 CpG sites = 40, Kimura (unadjusted) = 53.94 Transitions / transversions = 1.74 (40/23) Gap_init rate = 0.02 (4 / 173), avg. gap size = 1.50 (6 / 4) 295 29.00 5.49 1.17 chr6ptel1M 8766 8929 (991071) PRIMAX-int#LTR/ERV1 3009 3179 (923) m_b271s701i0 10726 chr6ptel1M 8766 TTCAGTCCAACAAGCTGAACTCAGGGCGGTAAC-CAGGCTCATCAGTTAA 8814 ii ? v?vi ?v ? -?i iii v ii PRIMAX-int#LT 3009 TTCAGCTCAACAAGCNGAACTANTAGCNTTNACTNGGGCCTGTCACTTGG 3058 chr6ptel1M 8815 GAAAAG--ACAACAGGATGAATACCTATGCCCAGAGCAGGTATGCCTTTG 8862 v -- ? v --iv ii i vv v i i i PRIMAX-int#LT 3059 CAAAAGGAANAACTG--CTAATATTTATACGGACAGTAGATATGCTTTTG 3106 chr6ptel1M 8863 GAATAGCCC-TGACTTTAGGATTCTAGTGAAACATCAGGGACT-----CC 8906 ii i i - i i i v vv vvii ii ----- PRIMAX-int#LT 3107 GGGTGGTCCATGATTTTGGAATGCTATGGAAACAAAGAGGGTTCTTNACC 3156 chr6ptel1M 8907 TCCTCAGGATAATCCATTAGAAA 8929 i v vi ? i PRIMAX-int#LT 3157 TCTTCTGGTCAATCCATNAAAAA 3179 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.53 CpG sites = 30, Kimura (unadjusted) = 40.53 Transitions / transversions = 1.76 (30/17) Gap_init rate = 0.04 (6 / 163), avg. gap size = 1.83 (11 / 6) 287 29.94 2.23 1.10 chr6ptel1M 9485 9663 (990337) ERV24_Prim#LTR/ERV1 4987 5167 (2408) m_b271s701i1 10727 chr6ptel1M 9485 GGCCAGTTTCCTCTCCCAGATGTTCCCTTTCAAAGC-TGGCAGAAGGGTC 9533 i v i v v v- i i i- i?v i i ERV24_Prim#LT 4987 GGTCATTTTCCTTTACCAGAAGG-CCCTTTCGAGGTATGGCAANTGGATT 5035 chr6ptel1M 9534 TTCATTCAATTGCCAGCTGCCCATCGTTCCAAATATGCTTTGGGGATGCT 9583 - ii iv vv ? vv v v i i i i ? v? v ERV24_Prim#LT 5036 TT-ATTCAGCTGCCGCCATCNCAAGGATACGAGTATGTTCTNGTNATGGT 5084 chr6ptel1M 9584 CTGTACACTTTCCTGGTGGGTGGCAGAATTCCCAT-CATATT-GCCACAG 9631 i iii iiiv i v v i ? - v vv- ? i ERV24_Prim#LT 5085 TTGTATGTTTTCTCATTGGGTAGAAGCATTTCCNTGCAGAAGAGCNACGG 5134 chr6ptel1M 9632 CCTC-TCAGGTAACAAAATCCTTTTAGAAAAAA 9663 i-v vviii i ? ERV24_Prim#LT 5135 CCTTAGCAGTAGGTAAAATTCTNTTAGAAAAAA 5167 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.41 CpG sites = 30, Kimura (unadjusted) = 41.38 Transitions / transversions = 1.30 (30/23) Gap_init rate = 0.03 (6 / 178), avg. gap size = 1.00 (6 / 6) 261 30.58 0.83 0.00 chr6ptel1M 9697 9817 (990183) L1ME3F_3end#LINE/L1 452 573 (417) m_b271s551i1 10728 chr6ptel1M 9697 CAGCTCTTTGTGCAGTCGTAAAGAACTGGAAAATAAGTACATGTCTATTG 9746 v v vi i i v i i vv vvi v i i L1ME3F_3end#L 452 CAGCACTGTTCGTAATAGCAAAAAACTGGAAACAACCCAAATGTCCATCG 501 chr6ptel1M 9747 ATTTTGGAATGGCCAAACAAACTGTGGTACATGAAGGCAATGAAATATTA 9796 ivvvi vi i i i vv vi i L1ME3F_3end#L 502 ACAGGAGAATGGATAAATAAATTGTGGTATATTCACACAATGGAATATTA 551 chr6ptel1M 9797 TCGTTCTGTGAAAATG-ATGAA 9817 vvvv v - L1ME3F_3end#L 552 TACAGCAGTGAAAATGAATGAA 573 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.89 CpG sites = 16, Kimura (unadjusted) = 39.47 Transitions / transversions = 0.76 (16/21) Gap_init rate = 0.01 (1 / 120), avg. gap size = 1.00 (1 / 1) 266 23.90 7.44 3.17 chr6ptel1M 9753 9873 (990127) L1MC2_3end#LINE/L1 508 633 (458) m_b271s551i2 10728 chr6ptel1M 9753 GAATGGCCAAACAAACTGTGGTACATGAAGGCAATGAAATATTATCGTTC 9802 vi vv vi i --- L1MC2_3end#LI 508 GAATGGATAAACAAACTGTGGTACATCCATACAATGGAATATTA---TTC 554 chr6ptel1M 9803 TGTGAAAATGATGAATGAG----CAAGTTTTGGAAAGGCCTGGAG----- 9843 v i v vi vi ---- iivi i i v ----- L1MC2_3end#LI 555 AGCGATAAAAAGAAATGAGCTATCAAGCCACGAAAAGACATGGAGGAACC 604 chr6ptel1M 9844 TTACATGACCTGATGCTGAGCCAAAGAAGC 9873 v - v iv i iv L1MC2_3end#LI 605 TTAAATG-CATATTGCTAAGTGAAAGAAGC 633 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 26.73 CpG sites = 14, Kimura (unadjusted) = 29.07 Transitions / transversions = 1.00 (14/14) Gap_init rate = 0.05 (6 / 120), avg. gap size = 2.17 (13 / 6) 12 16.34 2.78 2.78 chr6ptel1M 10704 10739 (989261) (ATGCCAG)n#Simple_repeat 1 36 (0) m_b271s252i5 10729 chr6ptel1M 10704 ATCCCAGATGGGCA-ATACCATCTGCCAGATGCCAGA 10739 v - v - i vv (ATGCCAG)n#Si 1 ATGCCAGAT-GCCAGATGCCAGATGCCAGATGCCAGA 36 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 18 0.00 0.00 0.00 chr6ptel1M 14170 14189 (985811) (A)n#Simple_repeat 1 20 (0) m_b271s252i6 10730 chr6ptel1M 14170 AAAAAAAAAAAAAAAAAAAA 14189 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAA 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 246 29.77 9.86 0.65 chr6ptel1M 17305 17446 (982554) MIR3#SINE/MIR 52 206 (2) m_b271s601i4 10731 chr6ptel1M 17305 GGTTCAAGAGCTGACTCTGTCAGAAA---GCC-TATGACCTTTGTGCAAA 17350 v vv i i i vv --- i- i v - i MIR3#SINE/MIR 52 GGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGG-GCAAG 100 chr6ptel1M 17351 TCCCTTC-----TCTGTGTTTCTGTTT-CTTAT-TGTAAATTGGAGGAGT 17393 v ----- v ii v - i - v ii i MIR3#SINE/MIR 101 TCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGT 150 chr6ptel1M 17394 TGAGCTCTTTCCT-TCTGAAGGATCTTTCAGCCCC-ACATCTTCTGACTT 17441 ii vvv vv - i i vvi i i i- ii v i i MIR3#SINE/MIR 151 TGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTC 200 chr6ptel1M 17442 T-TGAT 17446 - MIR3#SINE/MIR 201 TATGAT 206 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.75 CpG sites = 24, Kimura (unadjusted) = 38.93 Transitions / transversions = 1.33 (24/18) Gap_init rate = 0.06 (9 / 141), avg. gap size = 1.67 (15 / 9) 353 30.25 2.07 4.23 chr6ptel1M 18448 18592 (981408) C MIRb#SINE/MIR (67) 201 60 m_b271s601i5 10732 chr6ptel1M 18448 ATTATGTCACTTTAACCTGATCTTAATATTTCACGTCAGGT-GATATTGT 18496 v - i i-- vi i vii -i iv - i i C MIRb#SINE/MIR 201 ATTATCTCA-TTTAATCC--TCACAACAACCC-TGCGAGGTAGGTATTAT 156 chr6ptel1M 18497 TGTCCCTATTTCAGAGTTGAGGAAACAGGAAAACAAACAGAATTTAATTG 18546 i i i v v v -- ii vv v iv v i C MIRb#SINE/MIR 155 TATCCCCATTTTACAGATGAGGAAACTG--AGGCTCAGAGAGGTTAAGTA 108 chr6ptel1M 18547 ATTTGCCCAGAGGTACACAGTTAGTAACT--CAGGTTAGGGATCAGAA 18592 i ii vi i v -- iviv iv C MIRb#SINE/MIR 107 ACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAA 60 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.67 CpG sites = 25, Kimura (unadjusted) = 39.90 Transitions / transversions = 1.47 (25/17) Gap_init rate = 0.06 (8 / 144), avg. gap size = 1.12 (9 / 8) 355 28.30 1.85 1.85 chr6ptel1M 18485 18592 (981408) C MIR#SINE/MIR (102) 160 53 m_b271s601i6 10732 chr6ptel1M 18485 AGGTGATATTGTTGTCCCTATTTCAGAGTTGAGGAAACAGGAAAACAAAC 18534 iv i i i i v v v -- ii v v C MIR#SINE/MIR 160 AGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTG--AGGCACAG 113 chr6ptel1M 18535 AGAATTTAATTGATTTGCCCAGAGGTACACAGTTAGTAACT--CAGGTTA 18582 iv v i i ii vi i v -- iviv C MIR#SINE/MIR 112 AGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCC 63 chr6ptel1M 18583 GGGATCAGAA 18592 iv C MIR#SINE/MIR 62 GGGATTCGAA 53 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.33 CpG sites = 17, Kimura (unadjusted) = 36.33 Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.03 (3 / 107), avg. gap size = 1.33 (4 / 3) 185 24.94 9.21 5.06 chr6ptel1M 18529 18604 (981396) C OldhAT1#DNA/hAT-Ac (506) 2336 2258 m_b271s601i7 10733 chr6ptel1M 18529 ACAAACAGAATTTAATTGATTTGCCCAGAGGTACACA-------GTTAGT 18571 v i v i v -- vi i v - i------- vi i C OldhAT1#DNA/h 2336 ACCAGCAGCACTGAA--GATGCGCTCTGAG-TACACGCTGGATGGTGGGC 2290 chr6ptel1M 18572 AACTCAGGTTAGGGATCAGAAGTTTCTGCCAGA 18604 - i v v i i C OldhAT1#DNA/h 2289 AACTCAGGT-AGAGAACAGCAATTTTTGCCAGA 2258 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.97 CpG sites = 10, Kimura (unadjusted) = 30.91 Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.07 (5 / 75), avg. gap size = 2.20 (11 / 5) 268 22.53 25.00 1.74 chr6ptel1M 19547 19686 (980314) C MIR#SINE/MIR (3) 259 88 m_b271s601i8 10734 chr6ptel1M 19547 AACAGGTAGCATTTATACAGC-C---CTGTGTGCCA-----TGTTCTA-- 19585 i v i vv - --- i ----- -- C MIR#SINE/MIR 259 AATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAG 210 chr6ptel1M 19586 -----------CATTGTCTTATTTCATCTTCATGAGAACCA---GAGG-- 19619 -----------i iv i v i ii v v--- -- C MIR#SINE/MIR 209 CGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGGTA 160 chr6ptel1M 19620 ------ATT--TATGTCCATTTTACAGATAAAGAAACTGAATCTAACAAA 19661 ------ -- vi i i iv vv v i C MIR#SINE/MIR 159 GGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGA 110 chr6ptel1M 19662 GGTCCTATAACTTGACTTGCAAGGT 19686 ivvi v --- C MIR#SINE/MIR 109 GGTTAAGTAACTTGCC---CAAGGT 88 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.19 CpG sites = 16, Kimura (unadjusted) = 27.19 Transitions / transversions = 1.07 (16/15) Gap_init rate = 0.08 (11 / 139), avg. gap size = 3.45 (38 / 11) 367 25.48 16.57 4.79 chr6ptel1M 19584 19752 (980248) C MIRb#SINE/MIR (64) 204 17 m_b271s601i9 10734 chr6ptel1M 19584 TACATTGTCTTATTTCATCTTCATGAGAACCA---GAGG-----ATT--T 19623 i i i v i ii v v--- ----- -- C MIRb#SINE/MIR 204 TGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATT 155 chr6ptel1M 19624 ATGTCCATTTTACAGATAAAGAAACTGAATCTAACAAAGGTCCTATAACT 19673 vi i i iv v v i ivvi C MIRb#SINE/MIR 154 ATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACT 105 chr6ptel1M 19674 TGACTTGCAAGGTT------CT-----------GAGGTGGGAATAAAACC 19706 v --- i------ ----------- vi v vi C MIRb#SINE/MIR 104 TGCC---CAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACC 58 chr6ptel1M 19707 CTGGGCTTCCTGA-TTCAAGGCCCTACCCCACATTCTATCCACTGTA 19752 v v vi - i i ------ iiii v i C MIRb#SINE/MIR 57 CAGGTCTGTCTGACTCCAAAG------CCCGTGCTCTTTCCACTGCA 17 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.27 CpG sites = 24, Kimura (unadjusted) = 32.04 Transitions / transversions = 1.41 (24/17) Gap_init rate = 0.09 (15 / 168), avg. gap size = 2.47 (37 / 15) 17 4.30 0.00 0.00 chr6ptel1M 19898 19921 (980079) (TAAA)n#Simple_repeat 1 24 (0) m_b271s252i7 10735 chr6ptel1M 19898 TAAAAAAATAAATAAATAAATAAA 19921 v (TAAA)n#Simpl 1 TAAATAAATAAATAAATAAATAAA 24 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 14 26.68 2.04 0.00 chr6ptel1M 21267 21315 (978685) (TTTC)n#Simple_repeat 1 50 (0) m_b271s252i8 10736 chr6ptel1M 21267 TTGCTTTATTGTTTGCTTT-TTTCTTTGTTTGTTTGTTTCTCTTTTTTTT 21315 v v vi v - v v v i i i (TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 50 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.02 (1 / 48), avg. gap size = 1.00 (1 / 1) 267 30.57 9.84 5.49 chr6ptel1M 23401 23715 (976285) L1MC5_3end#LINE/L1 225 552 (2142) m_b271s551i3 10737 chr6ptel1M 23401 AAAGTTTCTCAACATAAGCAATGTGGAAAGGCTTTTGGGACAAACACAGA 23450 vv vv vi - vi v v -- -i v L1MC5_3end#LI 225 AAAGTTTGACAACATACTCTGT-TGGCGAGGCTGTGGGGA--AACA-GGC 270 chr6ptel1M 23451 ACGCTAATGTATTGTTGGTGGAATTATGAAAGGATCTAACCATTCTATGC 23500 v v ii i i v iii v i vi --i - L1MC5_3end#LI 271 ACTCTCATACATTGCTGGTGGGAATGCAAAATGGTACAACC--CCTATG- 317 chr6ptel1M 23501 CCAAAGGGTAAT--------------CAAAAG-----GTGTAT--AGCCT 23529 ---i v -------------- v-----i i -- v L1MC5_3end#LI 318 ---GAGGGGAATTTGGCAATATCTAGCAAAATTACATATGCATTTACCCT 364 chr6ptel1M 23530 TTGAACTAGCAAT---GTTTCTACTGGACT-TATTTGCCAAAGAGAT--- 23572 v i ---ii -- v - i-- v i--- L1MC5_3end#LI 365 TTGACCCAGCAATCCCACTTCTA--GGAATCTATC--CCAAAGATACACT 410 chr6ptel1M 23573 -CCAAAAGGAAGGAAAGGGACCCAGATGTGCAGAAATGTTT-CTGCAGCC 23620 -v iv v i i---- iv ii iiiv i i-i v L1MC5_3end#LI 411 GGCAAAAATACGAAAAGA----CGTATGCACAAGGCTATTCATTGCAGCA 456 chr6ptel1M 23621 CTGTTTGTAGTGGCAAGAAACTGGAAACTGACTGGATGCCCATCAGCCGG 23670 i i i i i viv iii i iiv L1MC5_3end#LI 457 CTATTTGTAATAGCAAAAGACTGGAAACAACCCAAATGTCCATCAATAGG 506 chr6ptel1M 23671 GAGAT-GCTAAATAAGTTATAGCACATTAATGTTATGGAATATTAT 23715 iiv - i i ii i i iv iiiv i i L1MC5_3end#LI 507 GGACTGGTTGAATAAACTATGGTACATCCACACAATGGAGTACTAT 552 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.02 CpG sites = 59, Kimura (unadjusted) = 41.23 Transitions / transversions = 1.84 (59/32) Gap_init rate = 0.09 (27 / 314), avg. gap size = 1.81 (49 / 27) 405 29.84 4.85 2.59 chr6ptel1M 23504 23730 (976270) L1ME4c_3end#LINE/L1 342 573 (257) m_b271s551i4 10737 chr6ptel1M 23504 AAGGGTAATCAAAAGGTGTATAGCCTTTGAACTAGCAATGTTTCTACTGG 23553 i iv v v vi v v i i viiv v L1ME4c_3end#L 342 AAGAGCCATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGG 391 chr6ptel1M 23554 --ACTTATTTGCCAAAGAGAT---CCAAAAGGAAGGAAAGGGACCCAGAT 23598 -- i i-- i i i ---i - ii -- i v L1ME4c_3end#L 392 GAATTTATC--CTAAGGAAATAATTCAAAAG-AAGGAAAAAG--CTATAT 436 chr6ptel1M 23599 GTGCAGAAATGTTT-CTGCAGCCCTGTTTGTAGTGGCAAGAAACTGGAAA 23647 ii ii i i-i vi i i i i i i i L1ME4c_3end#L 437 GCACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAA 486 chr6ptel1M 23648 CTGACTGGATGCCCATCAGCCGGGAGATG-CTAAATAAGTTATAGCACAT 23696 viv ii i v iiv ii -i i i i i L1ME4c_3end#L 487 CAACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACAT 536 chr6ptel1M 23697 TAATGTTATGGAATATTAT----TCTTTAAAGAATGAT 23730 i? iviv ----i v - L1ME4c_3end#L 537 CNACTCGATGGAATATTATGCAGCCATTAAA-AATGAT 573 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.49 CpG sites = 48, Kimura (unadjusted) = 40.98 Transitions / transversions = 2.67 (48/18) Gap_init rate = 0.05 (11 / 226), avg. gap size = 1.55 (17 / 11) 12 35.32 0.00 0.00 chr6ptel1M 27263 27319 (972681) (TTTTTT)n#Simple_repeat 1 57 (0) m_b271s252i9 10738 chr6ptel1M 27263 TTTTGTTGTTGTTTACTTGCTTTTCTCTTTCTCAGGTTTTTTTTTTTTTT 27312 v v v vi vi i i i ivvv (TTTTTT)n#Sim 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr6ptel1M 27313 CATTTTT 27319 iv (TTTTTT)n#Sim 51 TTTTTTT 57 Matrix = Unknown Transitions / transversions = 0.78 (7/9) Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0) 675 31.08 1.93 2.15 chr6ptel1M 28904 29370 (970630) C L1MC4a_3end#LINE/L1 (1997) 632 167 m_b271s551i5 10739 chr6ptel1M 28904 TGCTTATTTCACTCAGCATCAGTTCGTGTAAGTCTCTCCAGGCC--TTTC 28951 v i i vi vv v v i v vii -- iv C L1MC4a_3end#L 632 TGCTTTTTTCACTTAACAATATATCCTGGAAATCACTCCATATCAGTTCA 583 chr6ptel1M 28952 T-GAAATCCTCCTGCTGGTCCTTTCTTACAGAACAATAATATTCCATAAC 29000 - i i v---i i i vvvv i i vii C L1MC4a_3end#L 582 TAGAGATCTTCCTC---ATTCTTTTTTACAGCTGCATAGTACTCCATTGT 536 chr6ptel1M 29001 ATTCATACACCACAATTTGTTCAGCCATTCTCCAATTAATGGGCATCCAT 29050 i vv ii i i i i ? v ?? ii v C L1MC4a_3end#L 535 GTGGATGTACCATAGTTTATTCAACCANTCTCCTATNNATGGGCATTTAG 486 chr6ptel1M 29051 TCACTTTCCAGTTTCTGGCCACTACAAAGAGGGCTGCCACAAAC-ATTTT 29099 vivv i v i v v i v iv v ii i- ii C L1MC4a_3end#L 485 GTTGTTTCCAATATTTTGCAATTACAAACAATGCTGCAATGAATAACCTT 436 chr6ptel1M 29100 G-GCATATACAGGTCCCTTTCC-CTTCTTTGA--TATCTCTTTGGGATAT 29145 - ---- ?vi vi- v v v -- i v ii i v C L1MC4a_3end#L 435 GTGCATAT----GTNATTTTGTACATGTTGGAGGTGTATCTTCAGGGTAA 390 chr6ptel1M 29146 A-GCCCAGAAGTAACACTGCTGGATCAAAGGGTATGGCCAGTTTGATAAC 29194 -v i iiv i i vivv - v - ii C L1MC4a_3end#L 389 ATTCCTAGAAGTGGGATTGCTGGGTCAAAGGGTAAATGCA-TATG-TAGT 342 chr6ptel1M 29195 TTTTTGAGCATAGTTCCAAACTGCTCTCCAGAATGGTTGGATATATTCAC 29244 v v - v v i v i ? v v ivv? ii C L1MC4a_3end#L 341 TTTGTTAG-ATATTGCCAAATTCCCCTCCANAAGGGTTGTACCANTTTGC 293 chr6ptel1M 29245 AATTCTACCAACAGTGTATTAGTGTCCCTGTTTTCCCACATCCCCTCCAA 29294 v i i i i v v v i v i v C L1MC4a_3end#L 292 ATTCCCACCAGCAATGTATGAGAGTGCCTGTTTCCCCACAGCCTCGCCAA 243 chr6ptel1M 29295 CATTCTGCATTATCTTTCCCTGTCATTCTAGCCATTCTGACAGGTATGTA 29344 vvv ii i vvv ii vvv i v v i iv v C L1MC4a_3end#L 242 CAGAGTGTGTTGTCAAACTTTTGAATTTTTGCCAATCTGATAGGTGAGAA 193 chr6ptel1M 29345 GTGGTATCTCAGAGTTGTCTTAGTTT 29370 i v v i i C L1MC4a_3end#L 192 ATGGTATCTCAGTGTAGTTTTAATTT 167 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.41 CpG sites = 71, Kimura (unadjusted) = 41.41 Transitions / transversions = 1.00 (71/71) Gap_init rate = 0.04 (17 / 466), avg. gap size = 1.12 (19 / 17) 944 28.69 0.78 1.31 chr6ptel1M 28986 29370 (970630) C L1ME3G_3end#LINE/L1 (376) 548 166 m_b271s551i6 10739 chr6ptel1M 28986 ATAATATTCCATAACATTCATACACCACAATTTGTTCAGCCATTCTCCAA 29035 i ii vv i i i i i i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr6ptel1M 29036 TTAATGGGCATCCATTCACTTTCCAGTTTCTGGCCACTACAAAGAGGGCT 29085 i i ii vvivv i i v i i v iv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr6ptel1M 29086 GCCACAAACATTTTGGCATATACAGGTCCCTTTCC-CTTCTTTGA-TATC 29133 v ii ii v i i i ?-- i v v - v v vi - i C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATT 401 chr6ptel1M 29134 TCTTTGGGATATA-GCCCAGAAGTAACACTGCTGGATCAAAGGGTATGGC 29182 ? i v -? ? iiv i i vv C L1ME3G_3end#L 400 TCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCG 351 chr6ptel1M 29183 CAGTTTGATAACTTTTTGAGCATAGTTCCAAACTGCTCTCCAGAATGGTT 29232 v i -- i vvv - v v i i i ? i C L1ME3G_3end#L 350 CATTTTAA--ATTTTAATAG-ATACTGCCAAATTGCCCTCCAAAANGGCT 304 chr6ptel1M 29233 GGATATATTCACAATTCTACCAACAGTGTATTAGTGTCCCTGTTTTCCCA 29282 v ivv i v i i i v v v i i C L1ME3G_3end#L 303 GTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCA 254 chr6ptel1M 29283 CATCCCCTCCAACATTCTGCATTATCTTTCCCTGTCATTCTAGCCATTCT 29332 i i v i ?vii vv? ii vvv i v v C L1ME3G_3end#L 253 CACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATCT 204 chr6ptel1M 29333 GACAGGTATGTAGTGGTATCTCAGAGTTGTCTTAGTTT 29370 ii iviv i vv i i C L1ME3G_3end#L 203 GATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTT 166 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.04 CpG sites = 62, Kimura (unadjusted) = 37.92 Transitions / transversions = 1.32 (62/47) Gap_init rate = 0.02 (8 / 384), avg. gap size = 1.00 (8 / 8) 371 20.00 1.33 0.00 chr6ptel1M 29581 29655 (970345) C MIR#SINE/MIR (118) 144 69 m_b271s601i10 10740 chr6ptel1M 29581 CTCATTTTACAAATGAGGAAACTGAGGCAAACAG-GGTAAAGTGACCTGA 29629 i i v v - v i i v C MIR#SINE/MIR 144 CCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGC 95 chr6ptel1M 29630 CCAGGTTCTCATACCTAGTAATTAGC 29655 i v v i v v i C MIR#SINE/MIR 94 CCAAGGTCACACAGCTAGTAAGTGGC 69 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 23.36 CpG sites = 7, Kimura (unadjusted) = 23.36 Transitions / transversions = 0.88 (7/8) Gap_init rate = 0.01 (1 / 74), avg. gap size = 1.00 (1 / 1) 15 15.27 5.26 0.00 chr6ptel1M 31467 31504 (968496) (TACATA)n#Simple_repeat 1 40 (0) m_b271s252i10 10741 chr6ptel1M 31467 TACACACACACATATATATACATATAC--ATACATACACA 31504 i i i i -- i (TACATA)n#Sim 1 TACATATACATATACATATACATATACATATACATATACA 40 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.03 (1 / 37), avg. gap size = 2.00 (2 / 1) 17 28.03 0.00 0.00 chr6ptel1M 31468 31508 (968492) (AC)n#Simple_repeat 1 41 (0) m_b271s252i11 10741 chr6ptel1M 31468 ACACACACACATATATATACATATACATACATACACACTCA 31508 i i i i i i i i v (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACA 41 Matrix = Unknown Transitions / transversions = 8.00 (8/1) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 378 31.95 0.70 5.88 chr6ptel1M 32048 32190 (967810) MIRc#SINE/MIR 11 146 (122) m_b271s601i11 10742 chr6ptel1M 32048 TGGTGGCAGTGGCTAGAGAATGCTGGGCCTGGAGTCCAAAAGACTCATCC 32097 - -- i iii i i vii ----- MIRc#SINE/MIR 11 TGGTG-CAGTGG--AAAGAGCACTGGACTTGGAGTCAGGAAGAC-----C 52 chr6ptel1M 32098 CAAGTTTCAATCTGGTCTCAGACCCTAACTAGCTTGGTGACTCATGGTAA 32147 iii iv i iv v v v v v vv iivv i MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 102 chr6ptel1M 32148 GTATATTAATTCTCCTG-GCTTCAGTTTCCCTGTTTGTAAAGTG 32190 vvv iiiii - i iii i i MIRc#SINE/MIR 103 GTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATG 146 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.22 CpG sites = 28, Kimura (unadjusted) = 43.60 Transitions / transversions = 1.87 (28/15) Gap_init rate = 0.06 (9 / 142), avg. gap size = 1.00 (9 / 9) 13 18.27 2.63 0.00 chr6ptel1M 32733 32761 (967239) (TGTA)n#Simple_repeat 1 30 (9) m_b271s252i12 10743 chr6ptel1M 32733 TGTGTTTAT-TATTTATGTATGTATGTGTG 32761 i v - v i (TGTA)n#Simpl 1 TGTATGTATGTATGTATGTATGTATGTATG 30 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1) 29 0.00 0.00 0.00 chr6ptel1M 32762 32786 (967214) (TA)n#Simple_repeat 1 25 (0) c_b271s251i1 10744 chr6ptel1M 32762 TATATATATATATATATATATATAT 32786 (TA)n#Simple_ 1 TATATATATATATATATATATATAT 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 396 23.13 13.64 1.74 chr6ptel1M 33572 33725 (966275) C MIR#SINE/MIR (3) 259 88 m_b271s601i12 10745 chr6ptel1M 33572 AATAGGTAGCATTTATACAAC-C---CTGTGTGCCA-----TGCTCT--G 33610 v i vv i - --- i ----- i -- C MIR#SINE/MIR 259 AATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAG 210 chr6ptel1M 33611 CGT------TGTCTTATTTCAT----TCCTCATGAGATCCAGAGGACTTA 33650 i------ v vi ---- ii v v vv v vv C MIR#SINE/MIR 209 CGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGGTA 160 chr6ptel1M 33651 AGTACTATTATTATGCCCATTTTACACATAAAGAAACTGAATCTAACAGA 33700 i v v i i iv vv v C MIR#SINE/MIR 159 GGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGA 110 chr6ptel1M 33701 GGTCCTATAACTTGACTTGCAAGGT 33725 ivvi v --- C MIR#SINE/MIR 109 GGTTAAGTAACTTGCC---CAAGGT 88 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.76 CpG sites = 14, Kimura (unadjusted) = 27.76 Transitions / transversions = 0.67 (14/21) Gap_init rate = 0.06 (9 / 153), avg. gap size = 2.67 (24 / 9) 370 27.58 9.89 6.38 chr6ptel1M 33609 33790 (966210) C MIRb#SINE/MIR (64) 204 17 m_b271s601i13 10745 chr6ptel1M 33609 TGCGTTGTCTTATTTCATTCCTCATGAGATCCAGAGGACTTAAGTACTAT 33658 i i i v - ii v v vviv vv i --- C MIRb#SINE/MIR 204 TGCATTATCTCATTTAAT-CCTCACAACAACCCTGCGAGGTAGGTA---T 159 chr6ptel1M 33659 TATTATGCCCATTTTACACATAAAGAAACTGAATCTAACAGAGGTCCTAT 33708 v v i i iv v v ivvi C MIRb#SINE/MIR 158 TATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGT 109 chr6ptel1M 33709 AACTTGACTTGCAAGGTT-CTCAG---GT-------------GGGATTAA 33741 v --- i- v --- ------------- vi C MIRb#SINE/MIR 108 AACTTGCC---CAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCG 62 chr6ptel1M 33742 AACTCTGGGTTTCCTGA-TTCAAGGCCCTATCCACATTCTATCCATTGTA 33790 i v vi vi - i i ----- iiii v i i C MIRb#SINE/MIR 61 AACCCAGGTCTGTCTGACTCCAAAGC-----CCGTGCTCTTTCCACTGCA 17 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.23 CpG sites = 25, Kimura (unadjusted) = 35.03 Transitions / transversions = 1.14 (25/22) Gap_init rate = 0.09 (16 / 181), avg. gap size = 1.88 (30 / 16) 26 11.82 0.00 0.00 chr6ptel1M 33934 33971 (966029) (A)n#Simple_repeat 1 38 (0) m_b271s252i13 10746 chr6ptel1M 33934 AAAAAAAAAAAAAAAAAAGAAAGAAAGAAAAAAGAAAA 33971 i i i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 38 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 487 31.33 3.46 1.70 chr6ptel1M 35585 35873 (964127) L1ME4c_3end#LINE/L1 262 555 (275) m_b271s551i7 10747 chr6ptel1M 35585 GAAACCTGGGACACTAATGCATTGTTGGTGGAGTTGTGAACAGATCCAAC 35634 - v ? v i i vi? i iv i v L1ME4c_3end#L 262 GAAAC-TGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACAAC 310 chr6ptel1M 35635 CATTCTGTTGAGCAATATGGAACTATGCCCAAAGGGCAATCAAAAGGTGC 35684 v i vvi v v v i iviv i v v v v L1ME4c_3end#L 311 CCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAAAATGTTC 360 chr6ptel1M 35685 ATAACCTTTGAACTAGCAATGTTTCTGCTGGG--CTTATTTGCCAGAGA- 35731 v v i i viiv v --i i-- i ii - L1ME4c_3end#L 361 ATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATC--CTAAGGAA 408 chr6ptel1M 35732 ----TCCGAAAGGAGGGAAAGGACCCACA-GAACAGAAATGTTT-CTGCA 35775 ---- i i i i i -- i i - v ii i i-i L1ME4c_3end#L 409 ATAATTCAAAAGAAGGAAAAAG--CTATATGCACGAAGATGTTCATTGCA 456 chr6ptel1M 35776 GCTGTATTTGTAGTGGCAAGAAACTGCAAACTGAGTGGATGTCCATCAGC 35825 vv i i i i i i v vivv ii v ii L1ME4c_3end#L 457 GCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAAT 506 chr6ptel1M 35826 TGGGAAATA-CTGAATAAGTTATAGTACATTAATGTTGTGTAATATTAT 35873 v i i-i i i i i i? ivivi v L1ME4c_3end#L 507 AGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATATTAT 555 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.28 CpG sites = 55, Kimura (unadjusted) = 42.85 Transitions / transversions = 1.62 (55/34) Gap_init rate = 0.04 (11 / 288), avg. gap size = 1.36 (15 / 11) 19 18.94 0.00 0.00 chr6ptel1M 37225 37260 (962740) (A)n#Simple_repeat 1 36 (0) m_b271s252i14 10748 chr6ptel1M 37225 AAAACCAAAAAAATGGAAAAAAAAAAAAAAGAAAAA 37260 vv vii i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 36 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 296 20.25 0.00 2.38 chr6ptel1M 37640 37725 (962275) L1MEh_5end#LINE/L1 2134 2217 (18) m_b271s551i8 10749 chr6ptel1M 37640 GGGTTAATAACTCTCCCATAAAATGTAAGTGAATAGCAGATTGGATTAAA 37689 -- v v v v vv v v ?v ? L1MEh_5end#LI 2134 GGGTTAA--ACTCACCAATTAAAAGACAGAGATTNTCAGATTGGATTNAA 2181 chr6ptel1M 37690 AGCCAAAATCCTACAATATGTTGTTTCCAAGAAGCA 37725 iv v i i v ii L1MEh_5end#LI 2182 AAACAAAATCCAACAATATGCTGTCTACAAGAGACA 2217 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 24.28 CpG sites = 5, Kimura (unadjusted) = 24.28 Transitions / transversions = 0.42 (5/12) Gap_init rate = 0.02 (2 / 85), avg. gap size = 1.00 (2 / 2) 743 29.10 4.20 7.76 chr6ptel1M 38045 38830 (961170) L1M5_orf2#LINE/L1 2535 3294 (0) m_b272s551i1 10750 chr6ptel1M 38045 AAAATTCATAAGGAAGAACAAAAGGTCAAGAAT-TTCAAGAGAA-CTAAT 38092 i v ivi i ii ? -vi i v - -- L1M5_orf2#LIN 2535 AAAATTTATATGGAAATGCAAAGGACCNAGAATAGCCAAAACAATCT--T 2582 chr6ptel1M 38093 GAAAAAAAAAAATCAAA--TGAAGGCAGCCTAGCTTTGCCTAATCT-AAA 38139 i i - -- i --i i - vi i ?i ? - i L1M5_orf2#LIN 2583 GAAAAAGAAGAA-CAAAGTTGGAGG--ACTTA-CACTACCNGATNTCAAG 2628 chr6ptel1M 38140 ACTATATTATAAAGCAGCAGTCACCAAAACCATTTGGTATTGG-ATAAGA 38188 - vi v i i vi v -i - L1M5_orf2#LIN 2629 ACT-TATTATAAAGCTACAGTAATCAAGACAGTGTGGTATTGGCGTAAG- 2676 chr6ptel1M 38189 AATAGACTAGTTGATCAGTGGAATAGATTA---AGTTCACAGGTCAAAAT 38235 i v i v i i v --- i ------i L1M5_orf2#LIN 2677 GATAGACAAATAGATCAATGGAACAGAATAGAGAGTCCA------GAAAT 2720 chr6ptel1M 38236 AG--TCA-ACAACTATAGCAATCTAGTGTTTGACAAA----CCAAAGATC 38278 --i - vv i ?v ?i ii v ---- ? --- L1M5_orf2#LIN 2721 AGACCCACACATATATGGNCANTTGATTTTTGACAAAGGTGCCAANG--- 2767 chr6ptel1M 38279 CCAACTT-TTGGGATAAAAATTCACTATTTGACAAAAACTACTGGGAAAA 38327 - i i-v iv ii vvv v ii viv i i v L1M5_orf2#LIN 2768 -CAATTCAGTGGGGAAAGGATAGTCTTTTCAACAAATGGTGCTGGAACAA 2816 chr6ptel1M 38328 CTGGAAATTAGTATGGCAGAAACTAGGCATGGATCC--ACATGATACCGT 38375 i v ivi v i v iii?v v i -- v v i i L1M5_orf2#LIN 2817 TTGGATATCCATATGGAAAAAAATGAANCTCGACCCCTACCTCACACCAT 2866 chr6ptel1M 38376 ACATCAAGATAAGATCAAAATGGGTTCAT-GATTTAGGCATAAAGAATGA 38424 iv i v iv ? i i- - ii iiii ii? i L1M5_orf2#LIN 2867 ACACAAAAATTAATTCNAGATGGA-TCATAGACCTAAATGTAAAAGNTAA 2915 chr6ptel1M 38425 GATTATAAATAAATT---GGAG-GAACATAGGATAGTTTACCTTTCAGAC 38470 i i -- v --- i -i v i-- i ivv L1M5_orf2#LIN 2916 AACTATAA--AACTTCTAGAAGAAAACATAGGAGAA--TATCTTCGTGAC 2961 chr6ptel1M 38471 TTGTGGAGGAGGTAGAAATTTGTGACCAAAGAAGA-ACTAAAGTTCATTA 38519 i - i?v i i i v ---i v i - v ---- vi L1M5_orf2#LIN 2962 CT-TGGGNTAGGCAAAGATTTCT---TAAACAGGACACAAAA----AGCA 3003 chr6ptel1M 38520 TTGATCACAAGACAGAAAAT-------TTTGATTACATCAAATTAAAAAG 38562 i?i i i i v i ------- v i ? v v i L1M5_orf2#LIN 3004 CNAACCATAAAAGAAAAAATTGATAAATTGGACTNCATCAAAATTAAAAA 3053 chr6ptel1M 38563 CTTTTGTACAAACAAAACCAATGCAGACAAAATCAGAAGGGAAGCAATAA 38612 i iv ?vvv iv vi ivi v v i v v i i L1M5_orf2#LIN 3054 CTTCTGCTCNTCAAAAGACACCGTTAAGAAAATGAAAAGGCAAGCCACAG 3103 chr6ptel1M 38613 AATGGGAAAATATTTTTACATTTACA-GGATCTGATAAAAGCCTCATTTC 38661 ? i v v i -v? -iv i i v i v L1M5_orf2#LIN 3104 ANTGGGAGAAAATATTTGCA-ANACATATATCTGACAAAGGACTCGTATC 3152 chr6ptel1M 38662 CAAAACATATTTGACTCTAATAATTGACTCTAACTTTAAGAAAATAATTT 38711 i i -------- vi --- --- -------- i ? i L1M5_orf2#LIN 3153 CAGAATATA--------TAAAGA---ACTC---CT--------ACAANTC 3180 chr6ptel1M 38712 AATAATTTAAGAAATTAAGCCATTCTCCAATTGATAAATGGTCAAAGAAT 38761 --? i ivi i v ---i v? v v ii i L1M5_orf2#LIN 3181 AATAA--NAAAAAGACAAACAA---CCCAATANAAAAATGGGCAAAAGAC 3225 chr6ptel1M 38762 ATGAACAGACAATTTTCATAAGATGAAATTGAAACTATTTCTAGCCATAT 38811 v v iv v v v ?v iviiivv iv i L1M5_orf2#LIN 3226 TTGAACAGACACTTCACAAAAGAAGATATNCAAATGGCCAATAAGCACAT 3275 chr6ptel1M 38812 GAAAATATGCTCCAAGTCA 38830 v v v? L1M5_orf2#LIN 3276 GAAAAGATGCTCAACNTCA 3294 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.25 CpG sites = 125, Kimura (unadjusted) = 39.21 Transitions / transversions = 1.45 (125/86) Gap_init rate = 0.10 (76 / 785), avg. gap size = 1.21 (92 / 76) 1406 30.80 1.03 1.20 chr6ptel1M 38736 39320 (960680) L1ME4c_3end#LINE/L1 56 639 (191) m_b272s551i2 10750 chr6ptel1M 38736 CTCCAATTGATAAATGGTCAAAGAATATGAACAGACAATTTTCATAAGAT 38785 i v v i i iv ? v L1ME4c_3end#L 56 CCCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAG 105 chr6ptel1M 38786 GAAATTGAAACTATTTCTAGCCATATGAAAATATGCTCCAAGTCATTATT 38835 vv ?ivi vvvi iv i i v i v vv ii v L1ME4c_3end#L 106 GAAATACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTAGT 155 chr6ptel1M 38836 AATCAGAGAAATGCAAATTAAGACAATTCTGAGATACCATTATACACCTG 38885 i ii ivv v i i L1ME4c_3end#L 156 AATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCTA 205 chr6ptel1M 38886 TCAGATTGGCTAAGAGGACAGGAAAAGATAGTGAGGAATGTTGGAGGGGA 38935 i i i v i vvvv ii vv i ivvv i v i ? L1ME4c_3end#L 206 TTAAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGCTGGCGAGGN 255 chr6ptel1M 38936 TCCAGGAAACCTGGGACACTGATGCATTGTTGGTGGAGTTGTGAACAGAT 38985 v i vi v v ? v i i vi? i iv i L1ME4c_3end#L 256 TGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGT 305 chr6ptel1M 38986 CAAACCATTCTGGAGAGCAATTCGGAACTATGCTCAAAAAGTTATCAAAC 39035 vv v i i i v v i iviv i ii v v L1ME4c_3end#L 306 ACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAAAA 355 chr6ptel1M 39036 TGTGCATACCCTTTGATCCAGCAGTGATACTACTGGGCTTATATCCCAAA 39085 v i i i vvi v vv v i i L1ME4c_3end#L 356 TGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAG 405 chr6ptel1M 39086 AAGAT-ATT--AAAGAAGGGAAAGGGACCCGAACGTGCAAAAATGTTTGT 39132 i i - -- i i --- iiv i ii i i ii L1ME4c_3end#L 406 GAAATAATTCAAAAGAAGGAAAAAG---CTATATGCACGAAGATGTTCAT 452 chr6ptel1M 39133 CGCATCCCATTTTGTAGTGGCTAGAAACTGGAAAATGAA--TGGATGCCC 39180 i v vivv i i i v i i --v -- ii i L1ME4c_3end#L 453 TGCAGCGTTATTTATAATAGCGAAAAATTGGAAA--CAACCTAAATGTCC 500 chr6ptel1M 39181 ATCCATTGGAGAATGGTTGGGTAAATTGTGGTATATGAATGTTATGGAAT 39230 v v v i ii i i v? iviv L1ME4c_3end#L 501 AACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAAT 550 chr6ptel1M 39231 ATTAT-TATTCTGTAAGAAATGTCCAGCAGGATGAATACAGAGAAGCTTG 39279 -i vi vv - viv vi v v v iiv v i v L1ME4c_3end#L 551 ATTATGCAGCCATTAA-AAATGATAATTATGAAGACTATGTAGCAACATG 599 chr6ptel1M 39280 GAGAGAATTACATGAACTGATGCTAAGTGAAATGAGCAGAA 39320 i ivi -i vv i i vi L1ME4c_3end#L 600 GAAAATGTT-TATGATATAATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.27 CpG sites = 96, Kimura (unadjusted) = 41.05 Transitions / transversions = 1.17 (96/82) Gap_init rate = 0.02 (11 / 584), avg. gap size = 1.18 (13 / 11) 17 12.00 2.63 2.63 chr6ptel1M 39738 39775 (960225) (ATAAAA)n#Simple_repeat 1 38 (0) m_b272s252i1 10751 chr6ptel1M 39738 ATAATAATAAAAAAAATAAATAAAAAT-AAGATAAACAT 39775 v v - - i v (ATAAAA)n#Sim 1 ATAAAAATAAAAATAA-AAATAAAAATAAAAATAAAAAT 38 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 437 24.69 8.77 0.54 chr6ptel1M 42776 42946 (957054) ERV24B_Prim#LTR/ERV1 4305 4489 (3124) m_b272s701i0 10752 chr6ptel1M 42776 CTCCCAGATGGCCA-TTCAGCCTAACAAGCTAAACTGTAGGCA------- 42817 i -i -? i i vi i ?vv? ?------- ERV24B_Prim#L 4305 CTTCCAGA-AGCCACNTCGGCCCAACAAGCAGAATTNATNGCNTTNACCA 4353 chr6ptel1M 42818 -AGCTCATCAGTTAAGAAAAGGTAAAAGGATGAATATCTACACCCAGAGC 42866 - ii ? iiv? v ? vviiv i i vv v ERV24B_Prim#L 4354 GAGCTTGTCANTTGGCNAAAGGAANAACTGCTAATATTTATACAGACAGC 4403 chr6ptel1M 42867 AGGTGTGCCTTTGGAGTAG-CTGTGACTTTAGGGTGCTAGGGAAAC-ATC 42914 i i i - ii i i ii v - vv ERV24B_Prim#L 4404 AGATATGCTTTTGGAGTAGCCCATGATTTTGGAATGCTATGGAAACAAAG 4453 chr6ptel1M 42915 AGGACTT----CCTCCTCAGGACAGTCCATTAAAAA 42946 ?i ---- i v ? ii ? ERV24B_Prim#L 4454 AGGNTTTCTNACCTCTTCTGGNCAACCCATNAAAAA 4489 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 32.43 CpG sites = 27, Kimura (unadjusted) = 33.41 Transitions / transversions = 1.80 (27/15) Gap_init rate = 0.04 (7 / 170), avg. gap size = 2.29 (16 / 7) 370 29.01 9.04 0.99 chr6ptel1M 42786 42973 (957027) PRIMAX-int#LTR/ERV1 3004 3206 (896) m_b272s701i1 10752 chr6ptel1M 42786 GCCA-TTCAGCCTAACAAGCTAAACTGTAGGCA--------AGCTCATCA 42826 - ii ?i i?vi ?--------i iii PRIMAX-int#LT 3004 GCCANTTCAGCTCAACAAGCNGAACTANTAGCNTTNACTNGGGCCTGTCA 3053 chr6ptel1M 42827 GTTAAGAAAAGGTAAAAGGATGAATATCTACACCCAGAGCAGGTGTGCCT 42876 v iiv v ? vviiv i i vv v i i i i PRIMAX-int#LT 3054 CTTGGCAAAAGGAANAACTGCTAATATTTATACGGACAGTAGATATGCTT 3103 chr6ptel1M 42877 TTGGAGTAG-CTGTGACTTTAGGGTGCTAGGGAAACATCAGGA-----CT 42920 i i - ii i i ii v -- i ----- PRIMAX-int#LT 3104 TTGGGGTGGTCCATGATTTTGGAATGCTATGGAAACA--AAGAGGGTTCT 3151 chr6ptel1M 42921 T--CCTCCTCAGGACAGTCCATTAAAAACAAAAAACAAGGATCTCAACTA 42968 -- i v v i ? iii v v ?vivv? v PRIMAX-int#LT 3152 TNACCTCTTCTGGTCAATCCATNAAAAATGGACATCNTATTNCACAACTA 3201 chr6ptel1M 42969 TTAGA 42973 i PRIMAX-int#LT 3202 CTAGA 3206 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.34 CpG sites = 35, Kimura (unadjusted) = 40.34 Transitions / transversions = 1.84 (35/19) Gap_init rate = 0.04 (7 / 187), avg. gap size = 2.71 (19 / 7) 473 29.11 3.80 0.00 chr6ptel1M 42816 42973 (957027) PRIMA4-int#LTR/ERV1 4805 4968 (3302) m_b272s701i2 10752 chr6ptel1M 42816 CAAGCTCATCAGTTAAGAAAAGGTAAAAGGATGAATATCTACACCCAGAG 42865 i ii i iiv ii iivvii i i iv v PRIMA4-int#LT 4805 CGAGCTTGTCAATTGGCAAAAGACAAGGCTGCGAACATTTACACTGACAG 4854 chr6ptel1M 42866 CAGGTGTGCCTTTGGAGTAGCT-GTGACTTTAGGGTGCTAGGGAAACAT- 42913 v v i ? i v -i i i v v v- PRIMA4-int#LT 4855 CCGCTATGCNTTTGGGGTTGCTCATGACTTTGGGATGCTATGGAAAGAGA 4904 chr6ptel1M 42914 CAGGAC--TT--CCTCCTCAGGACAGTCCATTAAAAACAAAAAACAAGGA 42959 v i-- -- i ii v iii v v PRIMA4-int#LT 4905 GAGGATATTTAACCTCCTCAGGGCAACCCATAAAAAATGGACAACAAGTA 4954 chr6ptel1M 42960 TCTCAACTATTAGA 42973 vv i i PRIMA4-int#LT 4955 TCAGAGCTGTTAGA 4968 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.43 CpG sites = 29, Kimura (unadjusted) = 38.58 Transitions / transversions = 1.71 (29/17) Gap_init rate = 0.03 (4 / 157), avg. gap size = 1.50 (6 / 4) 344 28.05 0.61 0.00 chr6ptel1M 43000 43163 (956837) C HERVK14C#LTR/ERVK (4386) 3048 2884 m_b272s701i3 10753 chr6ptel1M 43000 TTTTTTCTTTATACCAAGTACAGGGGAGTTTCATGGGCTAGTTGTTTCCT 43049 ? vv ii v ? i i ? ivv iv vvv C HERVK14C#LTR/ 3048 TTTTTTCTTNATTACAAACACTGGNGAATTCCANGGAGAAAATGTGGGCT 2999 chr6ptel1M 43050 CGGTATGTCCTAATTCTAATTGTTCTTGTACTAATTGATGTAGTGCGGCT 43099 ?i i vv? vv vv iv vv i C HERVK14C#LTR/ 2998 CNATGTGTCCTTTNTCTAATTGTTCTTTGACTAATTCCTGTAAGGCCCCC 2949 chr6ptel1M 43100 ATTTTCTCTTTGGACAGGGTTCATTGCTCCACTCATACTGGTGTGCTGGT 43149 v i i vi ?? v vi i ? ? i v ? ?v viv C HERVK14C#LTR/ 2948 AGTTTTTCCTGAGNNAGCGGCCACTGNTCNACCCAAACNGGNTTTTGGGT 2899 chr6ptel1M 43150 AGT-CATTTTTAGAG 43163 v? - v i C HERVK14C#LTR/ 2898 CNTCCATTTTAAGGG 2884 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.82 CpG sites = 18, Kimura (unadjusted) = 38.82 Transitions / transversions = 0.64 (18/28) Gap_init rate = 0.01 (1 / 163), avg. gap size = 1.00 (1 / 1) 12 22.42 0.00 2.70 chr6ptel1M 46828 46865 (953135) (AATA)n#Simple_repeat 1 37 (0) m_b272s252i2 10754 chr6ptel1M 46828 AATAAATAAATTTACTAGAGAAATAAAGAGAAAAATAA 46865 - v v i v v i v (AATA)n#Simpl 1 AATAAATAAA-TAAATAAATAAATAAATAAATAAATAA 37 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 19 27.80 0.00 0.00 chr6ptel1M 49343 49398 (950602) (TTT)n#Simple_repeat 1 56 (0) m_b272s252i3 10755 chr6ptel1M 49343 TTTTGTTGTTGTTTATTTGCTTTTCCCTTTCTTGTTTTTTTTTTATTTTT 49392 v v v v vi iii i v v (TTT)n#Simple 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr6ptel1M 49393 ATTTTT 49398 v (TTT)n#Simple 51 TTTTTT 56 Matrix = Unknown Transitions / transversions = 0.62 (5/8) Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0) 19 0.00 0.00 0.00 chr6ptel1M 50450 50470 (949530) (T)n#Simple_repeat 1 21 (0) m_b272s252i4 10756 chr6ptel1M 50450 TTTTTTTTTTTTTTTTTTTTT 50470 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTT 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 377 26.30 3.45 10.43 chr6ptel1M 50963 51136 (948864) C MIRb#SINE/MIR (81) 187 25 m_b272s601i0 10757 chr6ptel1M 50963 TCTTGGCAACGATCCTG-GAG-TAGTTTGTTATTTCCTTCTTTGGCTCAT 51010 i vi i i - - v -i vi -------- i C MIRb#SINE/MIR 187 TCCTCACAACAACCCTGCGAGGTAGGT-ATTATTATC--------CCCAT 147 chr6ptel1M 51011 TTTA-AAATGAGGAAACTGAGGCTAAAAG-GGTGAAGTGACTTGACCAGG 51058 - i v i - v i v i C MIRb#SINE/MIR 146 TTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAG 97 chr6ptel1M 51059 TTCCCATGCCTAGTAATTAT--GAGACTAGATTTGAACTCATGAAGCTGA 51106 v v iiv v iv-- v vi i i v --v - C MIRb#SINE/MIR 96 GTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGG--TCTG- 50 chr6ptel1M 51107 AACTTCCTGATTGCAAGCTCTATGCACTTT 51136 -----i i v ivi ii v C MIRb#SINE/MIR 49 -----TCTGACTCCAAAGCCCGTGCTCTTT 25 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.69 CpG sites = 23, Kimura (unadjusted) = 32.69 Transitions / transversions = 1.28 (23/18) Gap_init rate = 0.13 (22 / 173), avg. gap size = 1.05 (23 / 22) 431 23.63 3.05 6.30 chr6ptel1M 51006 51136 (948864) C MIRc#SINE/MIR (120) 148 22 m_b272s601i1 10757 chr6ptel1M 51006 CTCATTTTA-AAATGAGGAAACTGAGGCTAAAAG-GGTGAAGTGACTTGA 51053 i - i v i - v v C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr6ptel1M 51054 CCAGGTTCCCATGCCTAGTAATTAT--GAGACTAGATTTGAACTCATGAA 51101 i v v iiv v iv-- v vi i i i ---- C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCC----A 53 chr6ptel1M 51102 GCTGAAACTTCCTGATTGCAAGCTCTATGCACTTT 51136 v ---- i v ii vi v C MIRc#SINE/MIR 52 GGT----CTTCCTGACTCCAAGTCCAGTGCTCTTT 22 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.47 CpG sites = 15, Kimura (unadjusted) = 28.59 Transitions / transversions = 1.07 (15/14) Gap_init rate = 0.08 (11 / 130), avg. gap size = 1.09 (12 / 11) 31 0.00 0.00 0.00 chr6ptel1M 51729 51757 (948243) (T)n#Simple_repeat 1 29 (0) c_b272s251i0 10758 chr6ptel1M 51729 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 51757 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 300 31.60 6.75 1.20 chr6ptel1M 52098 52334 (947666) C L1ME1_3end#LINE/L1 (267) 659 410 m_b272s551i3 10759 chr6ptel1M 52098 ATACA--ATGT--TTTCTTATTTCTG--TTCTT---CTCACCCTTCTGTA 52138 -- -- i i i v -- --- v v vv ?- C L1ME1_3end#LI 659 ATACAGTATGTANTCTTTTGTGTCTGGCTTCTTTCACTCAGCATAATGN- 611 chr6ptel1M 52139 TTTTGACTAGTCTTTCCATGTTTTTCTAAA-ATCTGTAGTTCATTC--TT 52185 --ii iiv v viivi- v i -- C L1ME1_3end#LI 610 TTTTGA--GATTCATCCATGTTGTTGCGTGTATCAGTAGTTCGTTCCTTT 563 chr6ptel1M 52186 ATATCAC--AGTAGTATTTCAGCATATACTTGTACCACAACTTGTGTGAT 52233 v ii -- i vii ivv i i v ivi C L1ME1_3end#LI 562 TTATTGCTGAGTAGTATTCCATTGTATGGATATACCACAATTTGTTTATC 513 chr6ptel1M 52234 CGTTC-CCAGGTGACAGGCAACTCTCCTATTTCTAGTTCTTAGCCACCAC 52282 i - ? v ii i vi vvvi i i i i i ii C L1ME1_3end#LI 512 CATTCACCNGTTGATGGACATTTGGGTTGTTTCCAGTTTTTGGCTATTAC 463 chr6ptel1M 52283 AAAGAGTACAGCTACAAACATTTTTGAGCATGTTTTTCTACACACA-ATG 52331 i v ivi v ii iv vi v i v iiiv - C L1ME1_3end#LI 462 GAATAAAGCTGCTATGAACATTCGTGTACAAGTCTTTGTGTGGACATATG 413 chr6ptel1M 52332 TTT 52334 C L1ME1_3end#LI 412 TTT 410 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.99 CpG sites = 45, Kimura (unadjusted) = 43.16 Transitions / transversions = 1.55 (45/29) Gap_init rate = 0.05 (12 / 236), avg. gap size = 1.58 (19 / 12) 411 29.67 3.85 0.00 chr6ptel1M 52153 52334 (947666) C L1MC4_3end#LINE/L1 (2191) 598 410 m_b272s551i4 10759 chr6ptel1M 52153 TCCATGTTTTTCTA-AAATCTGTAGTTCATTC--TTATATCAC--AGTAG 52197 ? vii-i? v -- v i -- C L1MC4_3end#LI 598 TCCATGTTNTTGCGTGNATCAGTAGTTCATTCCTTTTTATCGCTGAGTAG 549 chr6ptel1M 52198 TATTTCAGCATATACTTGTACCACAACTTGTGTGATCGTTC-CCAGGTGA 52246 i vii ivv ii v ivi i - v v C L1MC4_3end#LI 548 TATTCCATTGTATGGATGTACCACAGTTTGTTTATCCATTCACCTGTTGA 499 chr6ptel1M 52247 CAGGCAACTCTCCTATTTCTAGTTCTTAGCCACCACAAAGAGTACAGCTA 52296 vi i v ?vvi i i ? i i ? ii ii v ivi v C L1MC4_3end#LI 498 AGGACATCTNGGTTGTTTCCAGNTTTTGGCNATTATGAATAAAGCTGCTA 449 chr6ptel1M 52297 CAAACATTTTTGAGCATGTTTTTCTACACACA-ATGTTT 52334 i iv vi v v iiiv - ? C L1MC4_3end#LI 448 TAAACATTCGTGTACAGGTTTTTGTGTGGACATANGTTT 410 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.71 CpG sites = 32, Kimura (unadjusted) = 40.73 Transitions / transversions = 1.45 (32/22) Gap_init rate = 0.03 (5 / 181), avg. gap size = 1.40 (7 / 5) 358 32.26 4.67 2.28 chr6ptel1M 52356 52612 (947388) C L1ME5_3end#LINE/L1 (611) 330 68 m_b272s551i5 10759 chr6ptel1M 52356 CCAAAGGGCTCTGCGAAATGGTTATTTCATATTATAATTCCCACCAACAA 52405 i vv v ii i iivi vvi i -i i i C L1ME5_3end#LI 330 CCAGATTGCTCTCCAGAATGGCTGCACCAGTCTACA-CTCCCACCAGCAG 282 chr6ptel1M 52406 TT-------GTCTCTCAGTTTTTCCACATCCTCTTCAACATTTATCACTT 52448 v------- ii --i ? ii vi i iv -- C L1ME5_3end#LI 281 TGCATGAGGGTTCCT--ATNTCCCCACATCCTCGCCAACACTTGGCA--T 236 chr6ptel1M 52449 TCCCCATCTATCT--TTTTAGACAATCTGGTAGGAGTAAAATGATATTTC 52496 vi v v -- v v i ii v i i C L1ME5_3end#LI 235 TATCCAGCTTTCTAATTTTTGCCAGTCTAATAGGTGTAAAGTGATATCTC 186 chr6ptel1M 52497 CAAGTACTATTAATATGAATTTCTATGATCTGTAACGATCTAGAGCGT-T 52545 vvv vv v v v v ivv i vi v i - C L1ME5_3end#LI 185 ATTGTTGTTTTAATTTGCATTTCTCTGATTACTAATGAGTTTGAGCATCT 136 chr6ptel1M 52546 TTAAAAAAACATGACTATCCTTTC-GGTTTCTTCTTTGAAAAACTGTC-A 52593 i vv v vi v -i v - i iviv i i -i C L1ME5_3end#LI 135 CTTCATATGCTTG-TTAGCCTTTCGGGTTTCCTCTTCTGTAAATTGCCTG 87 chr6ptel1M 52594 TTCATTTCACTTGTTCGTT 52612 v vi ii i C L1ME5_3end#LI 86 TTCATATCCTTTGCCCATT 68 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 43.32 CpG sites = 43, Kimura (unadjusted) = 43.32 Transitions / transversions = 1.13 (43/38) Gap_init rate = 0.04 (11 / 256), avg. gap size = 1.64 (18 / 11) 392 30.68 3.65 1.53 chr6ptel1M 52356 52547 (947453) C L1ME2_3end#LINE/L1 (581) 330 135 m_b272s551i6 10759 chr6ptel1M 52356 CCAAAGGGCTCTGCGAAATGGTTATTTCATATTATAATTCCCACCAACAA 52405 v? i i v i i i vi v i -i i C L1ME2_3end#LI 330 CCAAACNGTTTTCCAAAGTGGTTGTACCATTTTACA-CTCCCACCAGCAA 282 chr6ptel1M 52406 T-TGTC----TCTCAGTTTTTCCACATCCTCTTCAACATTTATCACTTTC 52450 - i v---- ii vi vi ivi -- v C L1ME2_3end#LI 281 TGTATGAGAGTTCCAGTTGCTCCACATCCTCGCCAACATTTGGTA--TTG 234 chr6ptel1M 52451 CCCATCTATCT--TTTTAGACAATCTGGTAGGAGTAAAATGATATTTCCA 52498 i vi v i -- v v i i v i? i i i vv C L1ME2_3end#LI 233 TCAGTCTTTTTAATTTTAGCCATTCTAGTGGGTGTGNAGTGGTATCTCAT 184 chr6ptel1M 52499 AGTACTATTAATATGAATTTCTATGATCTGTAACGATCTAGAGCGTTTT 52547 v iv v v v iv vvv i v v iii C L1ME2_3end#LI 183 TGTGGTTTTAATTTGCATTTCCCTGATGACTAATGATGTTGAGCACCTT 135 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.83 CpG sites = 31, Kimura (unadjusted) = 40.83 Transitions / transversions = 1.15 (31/27) Gap_init rate = 0.03 (6 / 191), avg. gap size = 1.67 (10 / 6) 13 30.78 0.00 4.55 chr6ptel1M 52736 52804 (947196) (CTTTC)n#Simple_repeat 1 66 (0) m_b272s252i5 10760 chr6ptel1M 52736 CTTTCTTTTACTCTCCTATTCCTAATTTTACCCAGTCCTTTAAATTCCCA 52785 i v i - -v ii vi vv -vv i v (CTTTC)n#Simp 1 CTTTCCTTTCCTTTCCT-TTCCT-TTCCTTTCCTTTCCTTT-CCTTTCCT 47 chr6ptel1M 52786 TTCCTTACCTTTTCTTTCC 52804 v i (CTTTC)n#Simp 48 TTCCTTTCCTTTCCTTTCC 66 Matrix = Unknown Transitions / transversions = 0.78 (7/9) Gap_init rate = 0.04 (3 / 68), avg. gap size = 1.00 (3 / 3) 240 11.37 0.00 2.27 chr6ptel1M 53112 53156 (946844) C DNM1r#Unknown (2116) 2546 2503 m_b272s502i0 10761 chr6ptel1M 53112 TACACACACGTATATATACATATATAATACACACATATGCACATA 53156 i ? i i - ii C DNM1r#Unknown 2546 TATANATACGTATATATACACATAT-ATACACACATACACACATA 2503 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 13.23 CpG sites = 5, Kimura (unadjusted) = 13.23 Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 257 35.71 0.71 0.71 chr6ptel1M 55543 55683 (944317) C L1ME2z_3end#LINE/L1 (625) 566 426 m_b272s551i7 10762 chr6ptel1M 55543 CTTCTTATAGCACAGTAATATTCCATTATAATCTTGTACCACAACTTGTG 55592 i v vv i i vvvv i ii v C L1ME2z_3end#L 566 CTTTTTATTGCTGAGTAGTATTCCATTGTATGAATATACCACAGTTTGTT 517 chr6ptel1M 55593 TGATAGCTCCCCAGGTGACAGGCAACTCTCCAATTTCTAGTTCTTAGCCA 55642 ivivii i v v ii i v vvv vi i i i i C L1ME2z_3end#L 516 TATCCATTCTCCTGTTGATGGACACCTGGGCTGTTTCCAGTTTTTGGCTA 467 chr6ptel1M 55643 GCAC-AATGAGTGCAGCTACAAACATTTTTGAGGGAGTTTTT 55683 vi i- i i- v ii i vivi i C L1ME2z_3end#L 466 TTATGAATAAA-GCTGCTATGAACATTCTTGTACAAGTCTTT 426 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 50.46 CpG sites = 29, Kimura (unadjusted) = 50.46 Transitions / transversions = 1.38 (29/21) Gap_init rate = 0.01 (2 / 140), avg. gap size = 1.00 (2 / 2) 431 27.74 3.95 2.22 chr6ptel1M 55716 55892 (944108) C L1ME3Cz_3end#LINE/L1 (664) 333 154 m_b272s551i8 10762 chr6ptel1M 55716 GGTATGGCCAAAGGACTCTGTAAAATGGTTGCTTCATTTTACAATTCCCA 55765 i v vvi vi i ivi v -i C L1ME3Cz_3end# 333 GATATTGCCAAATTGCTCTCCAAAGTGGTTGTACCAATTTACA-CTCCCA 285 chr6ptel1M 55766 CCAACAAT---TAATTGTCTCTCAATTTCTCCACATGTTCTTCAACGTTT 55812 i i --- i vv - i i- vi vi ii C L1ME3Cz_3end# 284 CCAGCAGTGTATGAGAGT-TCCCG-TTTCTCCACATCCTCGCCAACACTT 237 chr6ptel1M 55813 GTTACTTTC----TTCTATCCTTTTAGACAATCTGGTCAGAGTAAAATGA 55858 v i v ---- i vvi - v i vi v i i C L1ME3Cz_3end# 236 GGTATTGTCAGACTTTTAAATTTTT-GCCAATCTGATGGGTGTGAAATGG 188 chr6ptel1M 55859 TATTTTCAGGTAGTTTTAATATGAATTTCTCTGA 55892 i ivvv ? v v i C L1ME3Cz_3end# 187 TATCTCATTGTNGTTTTAATTTGCATTTCCCTGA 154 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 34.60 CpG sites = 26, Kimura (unadjusted) = 35.51 Transitions / transversions = 1.18 (26/22) Gap_init rate = 0.03 (6 / 176), avg. gap size = 1.83 (11 / 6) 405 29.83 3.61 1.52 chr6ptel1M 55722 55915 (944085) C L1ME2_3end#LINE/L1 (580) 331 134 m_b272s551i9 10762 chr6ptel1M 55722 GCCAAAGGACTCTGTAAAATGGTTGCTTCATTTTACAATTCCCACCAACA 55771 v?ii i vi i ivi -i i C L1ME2_3end#LI 331 GCCAAACNGTTTTCCAAAGTGGTTGTACCATTTTACA-CTCCCACCAGCA 283 chr6ptel1M 55772 AT---TAATTGTCTCTCAATTTCTCCACATGTTCTTCAACGTTTGTTACT 55818 --- i vv - - i v vi vi i v i C L1ME2_3end#LI 282 ATGTATGAGAGT-TC-CAGTTGCTCCACATCCTCGCCAACATTTGGTATT 235 chr6ptel1M 55819 TTC---TTCTATCCTTTTAGACAATCTGGTCAGAGTAAAATGATATTTTC 55865 v ---i i v vv v v i vi v i? i i i iv C L1ME2_3end#LI 234 GTCAGTCTTTTTAATTTTAGCCATTCTAGTGGGTGTGNAGTGGTATCTCA 185 chr6ptel1M 55866 AGGTAGTTTTAATATGAATTTCTCTGACCTTTGATGATCTAGA-TACTTT 55914 vv i v v i ivvi i v v -i i C L1ME2_3end#LI 184 TTGTGGTTTTAATTTGCATTTCCCTGATGACTAATGATGTTGAGCACCTT 135 chr6ptel1M 55915 T 55915 C L1ME2_3end#LI 134 T 134 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.38 CpG sites = 31, Kimura (unadjusted) = 39.38 Transitions / transversions = 1.19 (31/26) Gap_init rate = 0.03 (6 / 193), avg. gap size = 1.67 (10 / 6) 369 30.23 11.17 2.05 chr6ptel1M 56311 56489 (943511) C MIRc#SINE/MIR (60) 208 14 m_b272s601i2 10763 chr6ptel1M 56311 CATTGTCTTATTTCATCCTCAAGAGAACC-----AGA-AGACTTAGTTGC 56354 i i v vi v ----- i- i vvi iv v C MIRc#SINE/MIR 208 CATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGG 159 chr6ptel1M 56355 TATTATTATGCCCATTTTATAGATAAAGAAATTGAATCTAACAGAGGTCC 56404 v i i i i iv v v iv C MIRc#SINE/MIR 158 TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTA 109 chr6ptel1M 56405 TATAACTTGAC-----TTGCAATGCTCTCAGGT-------CTGAG--TAA 56440 vi i v ----- ii vv vvi i ------- i i -- vi C MIRc#SINE/MIR 108 AGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCG 59 chr6ptel1M 56441 AACTCTGGGCTTCCTGATTCAAGGCCCTATCCACATTCTATCCACTGTA 56489 i v v i v i i vi v ---- v i C MIRc#SINE/MIR 58 AACCCAGGTCTTCCTGACTCCAAGTCCAGTGC----TCTTTCCACTGCA 14 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.61 CpG sites = 28, Kimura (unadjusted) = 39.49 Transitions / transversions = 1.12 (28/25) Gap_init rate = 0.05 (9 / 178), avg. gap size = 2.67 (24 / 9) 15 5.56 0.00 0.00 chr6ptel1M 57969 57987 (942013) (A)n#Simple_repeat 1 19 (0) m_b272s252i6 10764 chr6ptel1M 57969 AAAAAAAAAAAAAAAAGAA 57987 i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAA 19 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 224 31.19 3.88 3.08 chr6ptel1M 58318 58446 (941554) MIRc#SINE/MIR 83 212 (56) m_b272s601i3 10765 chr6ptel1M 58318 AGCTGCTGGGAT-TTGGGCAGAGTCACTCAGCCATCCTGAGCTT--ATGA 58364 - v i- - i i vii i --i vv MIRc#SINE/MIR 83 AGCTG-TGTGACCTTGGGCA-AGTCACTTAACCTCTCTGAGCCTCAGTTT 130 chr6ptel1M 58365 CCTCAGTTGTGCACCTAAGGAAAATGAAGGCACTCTCTGTGT-TGTCACA 58413 vi iv v- ii v - vi viv i iv -iv MIRc#SINE/MIR 131 CCTCATCTGTAAAA-TGGGGATAAT-AATACCTGCCCTGCCTACCTCACA 178 chr6ptel1M 58414 GG-TTATTGTGAGATTCGACTGTAATGGTGCATG 58446 - i iv i v vi ii i MIRc#SINE/MIR 179 GGGTTGTTGTGAGGATCAAATGAGATAATGTATG 212 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 41.65 CpG sites = 23, Kimura (unadjusted) = 41.65 Transitions / transversions = 1.44 (23/16) Gap_init rate = 0.06 (8 / 128), avg. gap size = 1.12 (9 / 8) 18 4.77 0.00 0.00 chr6ptel1M 58588 58609 (941391) (TG)n#Simple_repeat 1 22 (0) m_b272s252i7 10766 chr6ptel1M 58588 TGTATGTGTGTGTGTGTGTGTG 58609 i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTG 22 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 19 25.78 0.00 0.00 chr6ptel1M 58623 58677 (941323) (TTTTTTT)n#Simple_repeat 1 55 (0) m_b272s252i8 10767 chr6ptel1M 58623 TTTGTTTTATTGTTTTCAGTTTTCTTTTACTTTAATCTTTTTTTTTTTTT 58672 v v v ivv i vi vv i (TTTTTTT)n#Si 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr6ptel1M 58673 TTTTT 58677 (TTTTTTT)n#Si 51 TTTTT 55 Matrix = Unknown Transitions / transversions = 0.50 (4/8) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 266 30.67 0.94 9.69 chr6ptel1M 59698 59910 (940090) L1MA8_3end#LINE/L1 216 411 (627) m_b272s551i10 10768 chr6ptel1M 59698 TATTTTAAAGAAGAAGAAAAACCCAACATGTAACCAATGT-GGAAAGGTT 59746 v v i v i --------- v i - vi v L1MA8_3end#LI 216 TATTATCAAAAAGACGAAAGA---------TAACAAGTGTTGGCGAGGAT 256 chr6ptel1M 59747 TTTAGGGGAAAACCTGCAACACTAATGCATTATTGGTGCAGTTGTGAACA 59796 v -- i v-- v v viii i i viiv i iv L1MA8_3end#LI 257 GT--GGAGAAAAG--GGAACCCTTGCACACTGTTGGTGGGAATGTAAATT 302 chr6ptel1M 59797 GATCCAACCATTCTGGAGAGCAATTTGGAACTATGCCCAAAGGGTTATCA 59846 ii v i v i i i v iv - v i iii --- L1MA8_3end#LI 303 AGTACAGCCATTATGGAAAACAGTATGGAGGT-TCCTCAAAAAATTA--- 348 chr6ptel1M 59847 AAAGCTGCA-TACCCTTTGATCCAGCAATATTTCTACTGGGGTTATATGC 59895 iiv v - v v viiv vv - L1MA8_3end#LI 349 AAAATAGAACTACCATATGATCCAGCAATCCCACTACTGGGTATATAT-C 397 chr6ptel1M 59896 CAGAAAGAACTTAAA 59910 - i v v L1MA8_3end#LI 398 CA-AAGGAAATGAAA 411 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.73 CpG sites = 30, Kimura (unadjusted) = 39.57 Transitions / transversions = 1.03 (30/29) Gap_init rate = 0.10 (21 / 212), avg. gap size = 1.00 (21 / 21) 735 31.97 0.93 1.88 chr6ptel1M 59728 60049 (939951) L1ME4c_3end#LINE/L1 237 555 (275) m_b272s551i11 10768 chr6ptel1M 59728 TAACCAATG-TGGAAAGGTTTTTAGGGGAAAACCTGCAACACTAATGCAT 59776 v - vi ? vi-- v -- vv ? v i L1ME4c_3end#L 237 TACCCAATGCTGGCGAGGNTGC--GGTGAAA--CTGGTACNCTCATACAT 282 chr6ptel1M 59777 TATTGGTGCAGTTGTGAACAGATCCAACCATTCTGGAGAGCAATTTGGAA 59826 ii vvi? i iv i v v i i v L1ME4c_3end#L 283 TGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGGCA 332 chr6ptel1M 59827 CTATGCCCAAAGGGTTATCAAAAGCTGCATACCCTTTGATCCAGCAATAT 59876 v i iviv i ii v vv v i i vi L1ME4c_3end#L 333 ATACGTATCAAGAGCCATAAAAATGTTCATACCCTTTGACCCAGTAATTC 382 chr6ptel1M 59877 TTCTACTGGGGTTATATGCCA--GAAAGAACTTAAAGGGGGGAAAGGGAC 59924 iv v iv v v i -- v i i i ii ii -- L1ME4c_3end#L 383 CACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAAGAAGGAAAAAG-- 430 chr6ptel1M 59925 CCACATGTGCAAAAATATTTGTGGCAGCCCTGTTAGTAGTGGCAAGAAAT 59974 i i ii i i i ii v vi i vi i i i i L1ME4c_3end#L 431 CTATATGCACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAAT 480 chr6ptel1M 59975 TGGAAACTGAGTGGAAGCCCATCAGCTGGGGAATGGCTGAATAAGTCATA 60024 vivv ii v i v iiv i i i i i i L1ME4c_3end#L 481 TGGAAACAACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATG 530 chr6ptel1M 60025 GCACATGAAGGTTGTGGAATATTAT 60049 i v? vvivi L1ME4c_3end#L 531 GTACATCNACTCGATGGAATATTAT 555 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.55 CpG sites = 61, Kimura (unadjusted) = 44.03 Transitions / transversions = 1.52 (61/40) Gap_init rate = 0.02 (8 / 321), avg. gap size = 1.12 (9 / 8) 363 25.19 10.00 0.76 chr6ptel1M 60698 60817 (939183) L2d2_3end#LINE/L2 422 552 (3) m_b272s601i4 10769 chr6ptel1M 60698 TTGTCTTCCATGTTAAATTGTAAGCTTTTTG-GGCTAGGG--CTTGTCTC 60744 i vvii i ii - vi -- v i L2d2_3end#LIN 422 TTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTT 471 chr6ptel1M 60745 CTGCCTTTTTTGTAACCCT---------TAACACAGTGCCTGGTGCATTG 60785 v i - i v i--------- i v ii iv L2d2_3end#LIN 472 ATAC-TTCTTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAG 520 chr6ptel1M 60786 TAGGAGCTTAATAAATACTAATTGAATTGTTT 60817 v i i vi v v L2d2_3end#LIN 521 TAGGCGCTCAATAAATATTTGTTGATTTGATT 552 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.45 CpG sites = 18, Kimura (unadjusted) = 31.45 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.03 (4 / 119), avg. gap size = 3.25 (13 / 4) 336 21.59 4.49 1.09 chr6ptel1M 61199 61287 (938713) C L1MC1_3end#LINE/L1 (862) 218 127 m_b272s551i12 10770 chr6ptel1M 61199 TTGTCCAATTTGAGAGGTGTGTAGTAATA---CATCAGTGTCTTAATTTG 61245 v v i i v ii --- iiv i C L1MC1_3end#LI 218 TTGGCCATTCTAATAGGTGTGTAGTGGTATCTCATTGTTGTTTTAATTTG 169 chr6ptel1M 61246 TATTTTTCTGATCA-ATGGTAATTTGAAGCATCTTTTCATATG 61287 i ii v - i- i v i C L1MC1_3end#LI 168 CATTTCCCTGATGACATA-TGATGTGGAGCATCTTTTCATATG 127 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 26.26 CpG sites = 13, Kimura (unadjusted) = 26.26 Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.03 (3 / 88), avg. gap size = 1.67 (5 / 3) 277 29.29 3.03 0.00 chr6ptel1M 61203 61301 (938699) C L1MC5_3end#LINE/L1 (2480) 214 113 m_b272s551i13 10770 chr6ptel1M 61203 CCAATTTGAGAGGTGTGTAGTAATACATCAGTGT---CTTAATTTGTATT 61249 i v v v i ii iv ---i i C L1MC5_3end#LI 214 CCAATCTGATAGGTGAGAAATGGTATCTCAGTGTAGTTTTAATTTGCATT 165 chr6ptel1M 61250 TTTCTGATCAATGGTAATTTGAAGCATCTTTTCATATGAATAGAAACAGT 61299 i v i vvi ii vv vi ?v ii i vi C L1MC5_3end#LI 164 TCTCTTATTATGAGCGAGGTTGAGCATCTTTTCATATGNTTAAGAGCCAT 115 chr6ptel1M 61300 TT 61301 C L1MC5_3end#LI 114 TT 113 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.82 CpG sites = 17, Kimura (unadjusted) = 38.71 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.01 (1 / 98), avg. gap size = 3.00 (3 / 1) 25 15.07 0.00 2.22 chr6ptel1M 62123 62168 (937832) (TA)n#Simple_repeat 1 45 (0) m_b272s252i10 10771 chr6ptel1M 62123 TATATATGAATCCTATATATATATATTGAGATATATATATATATAT 62168 iv -v vv v (TA)n#Simple_ 1 TATATATATAT-ATATATATATATATATATATATATATATATATAT 45 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1) 191 23.56 16.67 0.96 chr6ptel1M 62446 62535 (937465) MIRb#SINE/MIR 50 153 (115) m_b272s601i5 10772 chr6ptel1M 62446 CACACCTGC-CTCGATATTCTTTTTCAGACATTTTTTAGCTGTCT---CC 62491 v v-i - i ivvi v v i vi v --- i MIRb#SINE/MIR 50 CAGACCTGGGTTCGA-ATCCCGGCTCTGCCACTTACTAGCTGTGTGACCT 98 chr6ptel1M 62492 TGGGC----TA---AACC---CTGAATCTCAGTTTCCCC-TTTGGAAAAT 62530 ---- --- --- ii i - i v MIRb#SINE/MIR 99 TGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAAT 148 chr6ptel1M 62531 GAGGA 62535 i MIRb#SINE/MIR 149 GGGGA 153 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.23 CpG sites = 12, Kimura (unadjusted) = 28.81 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.08 (7 / 89), avg. gap size = 2.29 (16 / 7) 321 22.78 5.06 0.00 chr6ptel1M 62501 62579 (937421) MIR3#SINE/MIR 112 194 (14) m_b272s601i7 10772 chr6ptel1M 62501 CCCTGAATCTCAGTTTCCCC-TTTGGAAAATGAGGAGGTTGGACTCCATG 62549 i iii i - i v i vv MIR3#SINE/MIR 112 CTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATG 161 chr6ptel1M 62550 ACTTTTTATCTCCCTTCCAG---TGACCATCTA 62579 ii i v vv --- vv MIR3#SINE/MIR 162 ATCTCTAAGGTCCCTTCCAGCTCTGACATTCTA 194 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.54 CpG sites = 10, Kimura (unadjusted) = 27.54 Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.03 (2 / 78), avg. gap size = 2.00 (4 / 2) 27 0.00 0.00 0.00 chr6ptel1M 62638 62666 (937334) (A)n#Simple_repeat 1 29 (0) m_b272s252i11 10773 chr6ptel1M 62638 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA 62666 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA 29 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 13 12.75 5.56 2.70 chr6ptel1M 63837 63872 (936128) (GAAAT)n#Simple_repeat 1 37 (0) m_b272s252i12 10774 chr6ptel1M 63837 GAAATG-AATGAAATTGCAA-GCAATGAAATGGAAAGA 63872 - - v - v i v (GAAAT)n#Simp 1 GAAATGAAATGAAA-TGAAATGAAATGAAATGAAATGA 37 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.09 (3 / 35), avg. gap size = 1.00 (3 / 3) 599 21.26 4.57 0.55 chr6ptel1M 67115 67289 (932711) ERV24B_Prim#LTR/ERV1 4308 4489 (3124) m_b272s701i4 10775 chr6ptel1M 67115 CCAGATGGCCA-TTCAGCCCAAAAAGCTGAACTCATTGCAGTAGCCAG-G 67162 -i -? i v v i ? ? ?v ?i - ERV24B_Prim#L 4308 CCAGA-AGCCACNTCGGCCCAACAAGCAGAATTNATNGCNTTNACCAGAG 4356 chr6ptel1M 67163 CTCGTCAGTTAAGAAAAGGCCAAAGGATGAATACTTACGCCTAGAGCAGG 67212 i ? iiv? vv? vviiv i ii vv v i ERV24B_Prim#L 4357 CTTGTCANTTGGCNAAAGGAANAACTGCTAATATTTATACAGACAGCAGA 4406 chr6ptel1M 67213 TATGCCTTTGGAGTAGCCC-TGACTTTAGGGTGCTAAGGAAACATCAGGG 67261 i - i i ii v vvii ERV24B_Prim#L 4407 TATGCTTTTGGAGTAGCCCATGATTTTGGAATGCTATGGAAACAAAGAGG 4456 chr6ptel1M 67262 CTT-----CCTCTTCAGGACAATCCATTAAAAA 67289 ? ----- v ? i ? ERV24B_Prim#L 4457 NTTTCTNACCTCTTCTGGNCAACCCATNAAAAA 4489 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 26.60 CpG sites = 21, Kimura (unadjusted) = 27.45 Transitions / transversions = 1.31 (21/16) Gap_init rate = 0.03 (5 / 174), avg. gap size = 1.80 (9 / 5) 369 31.82 1.13 0.56 chr6ptel1M 67801 67977 (932023) ERV24_Prim#LTR/ERV1 4990 5167 (2408) m_b272s701i5 10775 chr6ptel1M 67801 CAGTTTCCTCTCCCAGATGTTCCCTTTCAAACCTGGCAGAAGGGTCTTCA 67850 v i v v vi i iv iiiv i?v i i - ERV24_Prim#LT 4990 CATTTTCCTTTACCAGAAGGCCCTTTCGAGGTATGGCAANTGGATTTT-A 5038 chr6ptel1M 67851 TTCAATTGCCAGCTGCCCATGGTTCCAAATATGCTTTGGGGATGGTCTGT 67900 ii iv vv ? v v v i i i i ? v? i ERV24_Prim#LT 5039 TTCAGCTGCCGCCATCNCAAGGATACGAGTATGTTCTNGTNATGGTTTGT 5088 chr6ptel1M 67901 ATACTTTCCCGCTGGTTGGCAGAGTTCCCCT-CATATT-GCCACAGCCTC 67948 ii i ii v i v vi i ? - v vv- ? i i ERV24_Prim#LT 5089 ATGTTTTCTCATTGGGTAGAAGCATTTCCNTGCAGAAGAGCNACGGCCTT 5138 chr6ptel1M 67949 TGGGGTAGCAAAGATCTTTTTAGAAAAAA 67977 v vi vv i ii ? ERV24_Prim#LT 5139 AGCAGTAGGTAAAATTCTNTTAGAAAAAA 5167 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.87 CpG sites = 32, Kimura (unadjusted) = 45.13 Transitions / transversions = 1.33 (32/24) Gap_init rate = 0.02 (3 / 176), avg. gap size = 1.00 (3 / 3) 271 30.58 0.83 0.00 chr6ptel1M 68010 68130 (931870) L1ME3F_3end#LINE/L1 452 573 (417) m_b272s551i14 10776 chr6ptel1M 68010 CAGCTCTTTGTGCAGTTGTAAAGAACTGGAAAATAAGTACCTGTCTGTTG 68059 v v vi i i v i i vv vvi vv ii i L1ME3F_3end#L 452 CAGCACTGTTCGTAATAGCAAAAAACTGGAAACAACCCAAATGTCCATCG 501 chr6ptel1M 68060 ATTTTAGAATGGCCCAACAAATTGTGGTAAATGAAGGCAATGGAATATTA 68109 ivvv viv i v vv vi L1ME3F_3end#L 502 ACAGGAGAATGGATAAATAAATTGTGGTATATTCACACAATGGAATATTA 551 chr6ptel1M 68110 TTGTTCTGTGAAAATG-ATGAA 68130 vvvv v - L1ME3F_3end#L 552 TACAGCAGTGAAAATGAATGAA 573 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.82 CpG sites = 13, Kimura (unadjusted) = 39.29 Transitions / transversions = 0.54 (13/24) Gap_init rate = 0.01 (1 / 120), avg. gap size = 1.00 (1 / 1) 248 30.93 4.81 3.16 chr6ptel1M 68027 68213 (931787) L1ME3D_3end#LINE/L1 468 657 (332) m_b272s551i15 10776 chr6ptel1M 68027 GTAAAGAACTGGAAAATAAGTACCTGTCTGTTGATTTTAGAATGGCCCAA 68076 i i vv vvi vv ii ii ivv viv L1ME3D_3end#L 468 GCAAAAAACTGGAAACAACCCAAATGTCCATCAACAGTAGAATGGATAAA 517 chr6ptel1M 68077 CAAATTGTGGTAAATGAAGGCAATGGAATATTATTGTTCTGTGAAAATG- 68125 i v vv vi i vvvv v - L1ME3D_3end#L 518 TAAATTGTGGTATATTCATACAATGGAATACTATACAGCAGTGAAAATGA 567 chr6ptel1M 68126 ATGAATGA-----GCAAGTTTTGGAAAGGGCTGGAGTTACATGACCTGAT 68170 iv -----i v iv i-i v v v i vi vv vi v i L1ME3D_3end#L 568 ATGAACTACAGCTACACGCATC-AACATGGATGAATCTCAAAAACATAAT 616 chr6ptel1M 68171 GTTGAGCCAAACAAGCAGACC-CAGAAG--TACATTGTACACAGTA 68213 v v iii - -- ----- L1ME3D_3end#L 617 GTTGAGCGAAAAAAGCAAGTCGCAGAAGAATACAT-----ACAGTA 657 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.08 CpG sites = 24, Kimura (unadjusted) = 40.08 Transitions / transversions = 0.75 (24/32) Gap_init rate = 0.05 (10 / 186), avg. gap size = 1.50 (15 / 10) 251 28.14 1.01 3.09 chr6ptel1M 69132 69230 (930770) MER52-int#LTR/ERV1 6831 6927 (164) m_b272s701i6 10777 chr6ptel1M 69132 TGCTCATATTAGGTCCTTGCGTTTTCAAATTGCTCATGAGATTTGTTTCT 69181 i ? v v i vi i vi v ii i i MER52-int#LTR 6831 TACNCATATTTGGTCCATGCATACTTAACCTCCTTGTAAAATTTGTTTCT 6880 chr6ptel1M 69182 TCTAGGCTACAAGCTG-CAAACTTCCAACTTCTCCTGCAACCCGGGAACC 69230 v v v i ii- - vivv v i-- i MER52-int#LTR 6881 TCTCGCCTAGAGGCCATCAAAC-TCCAAACGGTCATGCAACT--GGAGCC 6927 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 34.79 CpG sites = 15, Kimura (unadjusted) = 36.46 Transitions / transversions = 1.25 (15/12) Gap_init rate = 0.04 (4 / 98), avg. gap size = 1.00 (4 / 4) 256 21.79 4.94 3.66 chr6ptel1M 69359 69439 (930561) MER50-int#LTR/ERV1 7118 7199 (6) m_b272s701i7 10777 chr6ptel1M 69359 CAGCAGGAAGTAGATACAGAAGACTTGAGACCACAGACCCTTTT-CCAAA 69407 i v --- viv v v - v MER50-int#LTR 7118 CAGCAGGAAGCAGTTACAGAAGACT---GACCTTCGTCCATTTTCCCCAA 7164 chr6ptel1M 69408 AGAATTTGTGTTT---ATTGTTTGAGGGGGAGATG 69439 v v i --- i v vii i MER50-int#LTR 7165 AGAATTGGGGTCTTGGACTCTTGAGGGGGGAAATG 7199 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 25.79 CpG sites = 7, Kimura (unadjusted) = 25.79 Transitions / transversions = 0.70 (7/10) Gap_init rate = 0.06 (5 / 80), avg. gap size = 1.40 (7 / 5) 12 28.17 1.89 1.89 chr6ptel1M 71701 71753 (928247) (GGGA)n#Simple_repeat 1 53 (0) m_b272s252i13 10778 chr6ptel1M 71701 GGGTGGAGGGGAGGCAGGGAGGCAGAGGACACTGGG-GGGTGGGAGGGGG 71749 v ii v v - vivv - v i (GGGA)n#Simpl 1 GGGAGGGAGGGAGGGAGGGAGGGAG-GGAGGGAGGGAGGGAGGGAGGGAG 49 chr6ptel1M 71750 AGAG 71753 i (GGGA)n#Simpl 50 GGAG 53 Matrix = Unknown Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.00 (2 / 2) 17 12.53 0.00 0.00 chr6ptel1M 72711 72736 (927264) (AC)n#Simple_repeat 1 26 (0) m_b272s252i14 10779 chr6ptel1M 72711 ACAGACAAGCACACACACACACACAC 72736 v vi (AC)n#Simple_ 1 ACACACACACACACACACACACACAC 26 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 237 31.19 9.86 0.65 chr6ptel1M 75027 75168 (924832) MIR3#SINE/MIR 52 206 (2) m_b273s601i0 10780 chr6ptel1M 75027 GGTTCAAGAGCTGACTCTGTCAGAAA---GCC-TACGACCTTTGTGCAAA 75072 v vv i i i vv --- i- ii v - i MIR3#SINE/MIR 52 GGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGG-GCAAG 100 chr6ptel1M 75073 TCCCTTC-----TCTGTGTTTCCGTTTCTTC--TTGTAAATTGGAGGAGT 75115 v ----- v ii v i --i v ii i MIR3#SINE/MIR 101 TCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGT 150 chr6ptel1M 75116 TGAGCTCTTTCCT-TCTGAAGGATCTTTCAGCCCC-ACATCTTTTGACTT 75163 ii vvv vv - i i vvi i i i- ii v i i MIR3#SINE/MIR 151 TGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTC 200 chr6ptel1M 75164 T-TGAT 75168 - MIR3#SINE/MIR 201 TATGAT 206 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 40.42 CpG sites = 26, Kimura (unadjusted) = 41.67 Transitions / transversions = 1.44 (26/18) Gap_init rate = 0.06 (8 / 141), avg. gap size = 1.88 (15 / 8) 353 28.57 2.52 3.16 chr6ptel1M 76595 76753 (923247) C MIR#SINE/MIR (31) 231 74 m_b273s601i1 10781 chr6ptel1M 76595 ATGTGC-AATCATCTTTTTAAGTACAACAAA-ATATTATGTCACTTTAAT 76642 - iv iiv i ii vvi v -i vv - C MIR#SINE/MIR 231 ATGTGCCAGGCACTGTTCTAAGCGCTTTACATGTATTAACTCA-TTTAAT 183 chr6ptel1M 76643 CTCATCTTAACATTTCAA--AGTTAGGTAATATTGTTATCCCCATTTCAG 76690 i-- vi vii v -- v v i i v C MIR#SINE/MIR 182 CC--TCACAACAACCCTATGAGGTAGGTACTATTATTATCCCCATTTTAC 135 chr6ptel1M 76691 AGTTGAGGAAAAAGGAAAACAAACAGAATTTAATTGACTTGCCCAGAAGT 76740 v vv -- ii v v iv v i iiivi C MIR#SINE/MIR 134 AGATGAGGAAACTG--AGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTC 87 chr6ptel1M 76741 ACACAGATAGTAA 76753 v C MIR#SINE/MIR 86 ACACAGCTAGTAA 74 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.27 CpG sites = 22, Kimura (unadjusted) = 36.39 Transitions / transversions = 1.00 (22/22) Gap_init rate = 0.05 (8 / 158), avg. gap size = 1.12 (9 / 8) 344 31.17 10.80 1.56 chr6ptel1M 77769 77944 (922056) C MIRb#SINE/MIR (64) 204 13 m_b273s601i2 10782 chr6ptel1M 77769 TGCATTGTCTTATTTCATCCTCATGAGAAGCAGAGGACTTAAGTGCTATT 77818 i i v ii v v vviv vv i ii C MIRb#SINE/MIR 204 TGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATT 155 chr6ptel1M 77819 ATTAAACCAATTTTACAGATAAAGCAACTGAATCTAACAGAGATCCTATA 77868 i--- v i i v iv v v i ivvi C MIRb#SINE/MIR 154 ATC---CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTA 108 chr6ptel1M 77869 ACTTG--------------ACTTGAAAGGTTTTGAGATGGGATTAAAACC 77904 --------------i v v vvviv vi vi C MIRb#SINE/MIR 107 ACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACC 58 chr6ptel1M 77905 CTGGGCTTCCAGACT-CAAGGCC----CTATTCACATTCTACCAC 77944 v v vi v - i ---- v iv i vi C MIRb#SINE/MIR 57 CAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCACCAC 13 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.76 CpG sites = 24, Kimura (unadjusted) = 40.62 Transitions / transversions = 0.80 (24/30) Gap_init rate = 0.03 (6 / 175), avg. gap size = 3.67 (22 / 6) 201 33.30 6.47 2.78 chr6ptel1M 79137 79275 (920725) MIRc#SINE/MIR 88 231 (37) m_b273s601i3 10783 chr6ptel1M 79137 TGGGATTTGGATCACGTCACTCAGCCATTCTGAGCT--GGTGACCTAAGT 79184 v ii v iv v i i vi i--i vv v vi MIRc#SINE/MIR 88 TGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATC 137 chr6ptel1M 79185 TGTGCACCTAAGGAGGCTGATGGCACT--CTCTGTGT-TGTCACAGA-TT 79230 iv ---- v i v i iii i-- i iv -iv i- MIRc#SINE/MIR 138 TGTAAA----ATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTT 183 chr6ptel1M 79231 ATTGTGAGGTTCCACTGAGAT--TGTGCGTGAAA-CTCCTTAGAAATT 79275 i v v v -- ii - v i iv i MIRc#SINE/MIR 184 GTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTTTGTAAACT 231 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 45.58 CpG sites = 26, Kimura (unadjusted) = 45.58 Transitions / transversions = 1.37 (26/19) Gap_init rate = 0.07 (10 / 138), avg. gap size = 1.30 (13 / 10) 33 5.72 0.00 0.00 chr6ptel1M 79380 79416 (920584) (TG)n#Simple_repeat 1 37 (0) c_b273s251i0 10784 chr6ptel1M 79380 TGTGTGTATGTGTGTGTGTGTGTGTATGTGTGTGTGT 79416 i i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 37 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 14 18.37 5.88 1.89 chr6ptel1M 79438 79488 (920512) (CTTTATT)n#Simple_repeat 1 53 (0) m_b273s252i0 10785 chr6ptel1M 79438 CTTTATT-GTT-TGCTATTTTCTTTCCTTCTTTCTT-TTTATTTTTTATT 79484 -v - v v v -v v - i (CTTTATT)n#Si 1 CTTTATTCTTTATTCTTTATTCTTT-ATTCTTTATTCTTTATTCTTTATT 49 chr6ptel1M 79485 TTTT 79488 i (CTTTATT)n#Si 50 CTTT 53 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.08 (4 / 50), avg. gap size = 1.00 (4 / 4) 17 27.80 0.00 0.00 chr6ptel1M 79439 79490 (920510) (TTTT)n#Simple_repeat 1 52 (0) m_b273s252i1 10785 chr6ptel1M 79439 TTTATTGTTTGCTATTTTCTTTCCTTCTTTCTTTTTATTTTTTATTTTTT 79488 v v vi v i ii i i v v (TTTT)n#Simpl 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr6ptel1M 79489 TT 79490 (TTTT)n#Simpl 51 TT 52 Matrix = Unknown Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 521 34.44 4.33 1.74 chr6ptel1M 81061 81453 (918547) L1ME4c_3end#LINE/L1 237 639 (191) m_b273s551i0 10786 chr6ptel1M 81061 TAACCAATG-TGGAAAGGCTTTTGTGGGAAACCTGGGACACTAATGTATT 81109 v - vi ? --- i vi v v ? v ii L1ME4c_3end#L 237 TACCCAATGCTGGCGAGGNT---GCGGTGAAACTGGTACNCTCATACATT 283 chr6ptel1M 81110 GTTAGGAGACTTGTAAACAGATCCGACCATTCTGCCGAGCAATGTGGAAA 81159 i i vi vv? iv i v i v i vvi v v L1ME4c_3end#L 284 GCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGGCAA 333 chr6ptel1M 81160 TATGGCCAAAGGGTAATCAAGAGGTGCATAGCCTTTGAACTAGCAATGTT 81209 i vviv i iv v i v v v v i i vii L1ME4c_3end#L 334 TACGTATCAAGAGCCATAAAAATGTTCATACCCTTTGACCCAGTAATTCC 383 chr6ptel1M 81210 TCTACTGGG--CTTATT------------TGCCAAAGGAGGGAAAAGGAC 81245 v v --i i------------ v v i i --- L1ME4c_3end#L 384 ACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAAGAAGGAAAAAG--- 430 chr6ptel1M 81246 CCACATGTGCAGACATGTTT-CTGCAGCCCTGTTTGTACTGGGAAGAAAC 81294 i i ii ii v i-i vi i i v i vi i i L1ME4c_3end#L 431 CTATATGCACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAAT 480 chr6ptel1M 81295 TGGAAACTGACTGGATGCCCATCAGCTGGGAAATGCTGAA-TAAGTCATA 81343 viv ii i v iiv i v v - i i i L1ME4c_3end#L 481 TGGAAACAACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATG 530 chr6ptel1M 81344 GCACATTGATGTTGTGGAATATTATTGTTCTATAAGGAATGATCAGCAGG 81393 i i? ivivi vvvv i v ii v vi v L1ME4c_3end#L 531 GTACATCNACTCGATGGAATATTATGCAGCCATTAAAAATGATAATTATG 580 chr6ptel1M 81394 ATGATTCCAGAGATGCCTGGAGAGACCTACATGAATTGATGCAAAGTGAA 81443 v i viiv vvi v - i iv vi vv i iv L1ME4c_3end#L 581 AAGACTATGTAGCAACATGGA-AAATGTTTATGATATAATGTTAAGTGAA 629 chr6ptel1M 81444 GTGAGCAGAA 81453 ivi L1ME4c_3end#L 630 AAAAGCAGAA 639 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 45.05 CpG sites = 71, Kimura (unadjusted) = 47.99 Transitions / transversions = 1.15 (71/62) Gap_init rate = 0.03 (12 / 392), avg. gap size = 2.00 (24 / 12) 11 20.23 2.94 0.00 chr6ptel1M 81941 81974 (918026) (TATGCC)n#Simple_repeat 1 35 (0) m_b273s252i2 10787 chr6ptel1M 81941 TATGTCTGT-CCTTTGCTTCTGCCTATGCATATGC 81974 i i - v i v v (TATGCC)n#Sim 1 TATGCCTATGCCTATGCCTATGCCTATGCCTATGC 35 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 245 29.61 5.80 2.10 chr6ptel1M 88397 88534 (911466) C L1ME2z_3end#LINE/L1 (625) 566 424 m_b273s551i1 10788 chr6ptel1M 88397 CTTCTTATAGCACAGTAGTATTCCATTATAATCTTGTACCACAACGTGTG 88446 i v vv i vvvv i iiv v C L1ME2z_3end#L 566 CTTTTTATTGCTGAGTAGTATTCCATTGTATGAATATACCACAGTTTGTT 517 chr6ptel1M 88447 ATAGC---TCCCCAGGTGACAGGCAACT---CTCAATTTCTAGTTCTTAG 88490 - v --- i v v ii i v --- --i i i i C L1ME2z_3end#L 516 -TATCCATTCTCCTGTTGATGGACACCTGGGCT--GTTTCCAGTTTTTGG 470 chr6ptel1M 88491 CCAGCAC-AAGAGTGCAGCTATAAACATTTTAGTG-AAGTTTTTCT 88534 i vi i- v iv v i i v i- i i C L1ME2z_3end#L 469 CTATTATGAATAAAGCTGCTATGAACATTCTTGTACAAGTCTTTTT 424 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.49 CpG sites = 22, Kimura (unadjusted) = 38.49 Transitions / transversions = 1.22 (22/18) Gap_init rate = 0.05 (7 / 137), avg. gap size = 1.57 (11 / 7) 268 27.80 5.93 1.42 chr6ptel1M 88568 88702 (911298) C L1ME3Cz_3end#LINE/L1 (670) 327 187 m_b273s551i2 10789 chr6ptel1M 88568 GCCAAAGGACTCTCCAAAATGGTTTTTC--ATTTACAATTCCACCTACAA 88615 vvi i v v -- v i vi i C L1ME3Cz_3end# 327 GCCAAATTGCTCTCCAAAGTGGTTGTACCAATTTACACTCCCACCAGCAG 278 chr6ptel1M 88616 TTAATTAT--CTCTCAATTTCTCCACATGCTCTTCAACGTTTGTCACTTT 88663 vv v v--i i i- v vi ii vi i v C L1ME3Cz_3end# 277 TGTATGAGAGTTCCCG-TTTCTCCACATCCTCGCCAACACTTGGTATTGT 229 chr6ptel1M 88664 ----CTTCTATCCTTTTAGACAATCTGGTCGGAGGGAAATTGT 88702 ---- i vvi - v i v v v v C L1ME3Cz_3end# 228 CAGACTTTTAAATTTTT-GCCAATCTGATGGGTGTGAAATGGT 187 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.79 CpG sites = 16, Kimura (unadjusted) = 34.90 Transitions / transversions = 0.76 (16/21) Gap_init rate = 0.04 (5 / 134), avg. gap size = 2.00 (10 / 5) 13 29.29 1.16 7.41 chr6ptel1M 90549 90634 (909366) (TTCT)n#Simple_repeat 1 81 (0) m_b273s252i3 10790 chr6ptel1M 90549 TTCTATCTTATTTTTACTCCTTACTTTCTTTATTAGCTTCTCCTT-TTAC 90597 v - i vi i v v -v - i - v (TTCT)n#Simpl 1 TTCTTTCTT-TCTTTCTTTCTTTCTTTCTTTCTT-TCTT-TCTTTCTTTC 47 chr6ptel1M 90598 TCTCTCCCTGCTACTTTCTTTCTCCCTCTTATTCCTT 90634 i ii -- v ii - v i (TTCT)n#Simpl 48 TTTCTTTCT--TTCTTTCTTTCTTTCT-TTCTTTCTT 81 Matrix = Unknown Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.08 (7 / 85), avg. gap size = 1.00 (7 / 7) 260 26.67 0.00 0.00 chr6ptel1M 90979 91038 (908962) C DNM1r#Unknown (2130) 2532 2473 m_b273s502i0 10791 chr6ptel1M 90979 TATACACACACACACGTATATACATACATATACATACGCACATATACACA 91028 i i i ii i i i ii i i C DNM1r#Unknown 2532 TATACACATATATACACACATACACACATATACACACATATATACACACA 2483 chr6ptel1M 91029 CATATGTGAC 91038 i i i i C DNM1r#Unknown 2482 TACACGTGGC 2473 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 34.99 CpG sites = 16, Kimura (unadjusted) = 38.11 Transitions / transversions = 1.00 (16/0) Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0) 352 24.76 6.03 2.50 chr6ptel1M 91370 91485 (908515) C MIRb#SINE/MIR (46) 222 103 m_b273s601i4 10792 chr6ptel1M 91370 TGTGCCATGCTCTT------CATTGTCTTATTTCATCCTCAAGAGAACCA 91413 i v v ------ i i v vi v v C MIRb#SINE/MIR 222 TGTGCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCC 173 chr6ptel1M 91414 GAGGACTTAGTTGCTATTATTATGCCCATTTTATAGAT-AAGAAATTGAA 91462 viv ---i v v v i - i i i C MIRb#SINE/MIR 172 TGCGA---GGTAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAG 126 chr6ptel1M 91463 TCTAACAGAGGTCCTATAACTTG 91485 v v v ivvi C MIRb#SINE/MIR 125 GCTCAGAGAGGTTAAGTAACTTG 103 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.17 CpG sites = 12, Kimura (unadjusted) = 30.17 Transitions / transversions = 0.75 (12/16) Gap_init rate = 0.04 (5 / 115), avg. gap size = 2.00 (10 / 5) 329 27.97 13.48 3.59 chr6ptel1M 91384 91561 (908439) C MIRc#SINE/MIR (60) 208 14 m_b273s601i5 10792 chr6ptel1M 91384 CATTGTCTTATTTCATCCTCAAGAGAACCA---GAGG---ACTTAGTTGC 91427 i i v vi v v--- ---i vvi iv v C MIRc#SINE/MIR 208 CATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGG 159 chr6ptel1M 91428 TATTATTATGCCCATTTTATAGAT-AAGAAATTGAATCTAACAGAGGTCC 91476 v i - i i iv v v iv C MIRc#SINE/MIR 158 TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTA 109 chr6ptel1M 91477 TATAACTTGACTTGCAATGTT------CT---------CAGGTCTGAG-- 91509 vi i v --- v i------ --------- iv i i -- C MIRc#SINE/MIR 108 AGTGACTTGCC---CAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGAC 62 chr6ptel1M 91510 TAAAACTCTGGGCTTCCTGATTCAAGGCCCTATCCACATTCTATCCACTG 91559 vi i v v i v i i vi v ---- v C MIRc#SINE/MIR 61 TCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGC----TCTTTCCACTG 16 chr6ptel1M 91560 TA 91561 i C MIRc#SINE/MIR 15 CA 14 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.78 CpG sites = 24, Kimura (unadjusted) = 35.56 Transitions / transversions = 1.00 (24/24) Gap_init rate = 0.07 (13 / 177), avg. gap size = 2.38 (31 / 13) 21 0.00 0.00 0.00 chr6ptel1M 93305 93327 (906673) (TG)n#Simple_repeat 1 23 (0) m_b273s252i4 10793 chr6ptel1M 93305 TGTGTGTGTGTGTGTGTGTGTGT 93327 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGT 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 19 18.70 1.67 5.17 chr6ptel1M 93340 93399 (906601) (TTTCT)n#Simple_repeat 1 58 (0) m_b273s252i5 10794 chr6ptel1M 93340 TTTGTTTTATTGTTTTCAGTTTTCTTTTCTTTTAATCTTTCTTTTTTTTT 93389 v v v i ivv -v - - i (TTTCT)n#Simp 1 TTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTT-CT-TTTC-TTTTCTTT 47 chr6ptel1M 93390 TCTTTT-TTTT 93399 - (TTTCT)n#Simp 48 TCTTTTCTTTT 58 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.07 (4 / 59), avg. gap size = 1.00 (4 / 4) 254 31.68 2.19 6.86 chr6ptel1M 94021 94203 (905797) L1PA12_3end#LINE/L1 237 411 (504) m_b273s551i3 10795 chr6ptel1M 94021 TAATCAATG-TGGAAAGGTTTTTAGGAGGAAATCTGTGACACTAATGCAT 94069 ivi - vi v -- i v-- vi i v? i i L1PA12_3end#L 237 TAACAGATGCTGGCGAGGTTGT--GGAGAAAAA--GGAACGCTTNTACAC 282 chr6ptel1M 94070 TATTGGTGAAGTTGTGAACAGATCCAACCATTCTGGAGAGCAATTTGGAA 94119 i iiiv i ivii i v iii i v -- L1PA12_3end#L 283 TGTTGGTGGGAGTGTAAATTAGTTCAACCATTGTGGAAGACAGTGTGG-- 330 chr6ptel1M 94120 CTATGCC-CAAAGGGTTATCAAAAG-CTG-CATACCCTTTGATCTAGTGG 94166 v v - ---- i v - v -v v i i i iii L1PA12_3end#L 331 CGATTCCTCAAAG----ACCTAAAGACAGAAATACCATTCGACCCAGCAA 376 chr6ptel1M 94167 TGTTTCTACTGGGCTTATATGCCAAAGAGAATTTAAA 94203 viivi -- i v ii v L1PA12_3end#L 377 TCCCATTACTGGG--TATATACCCAAAGGAATATAAA 411 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.97 CpG sites = 34, Kimura (unadjusted) = 43.16 Transitions / transversions = 1.70 (34/20) Gap_init rate = 0.09 (16 / 182), avg. gap size = 1.00 (16 / 16) 719 32.88 0.68 1.02 chr6ptel1M 94048 94342 (905658) L1ME4c_3end#LINE/L1 262 555 (275) m_b273s551i4 10795 chr6ptel1M 94048 GAAATCTGTGACACTAATGCATTATTGGTGAAGTTGTGAACAGATCCAAC 94097 - vv ? v i ii ivi? i iv i v L1ME4c_3end#L 262 GAAA-CTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACAAC 310 chr6ptel1M 94098 CATTCTGGAGAGCAATTTGGAACTATGCCCAAAGGGTTATCAAAAGCTGC 94147 v i i v v i iviv i ii v vv v L1ME4c_3end#L 311 CCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAAAATGTTC 360 chr6ptel1M 94148 ATACCCTTTGATCTAGTGGTGTTTCTACTGGGCTTATATGCCAAAGAG-- 94195 i i ii viiv v vv v v i i i-- L1ME4c_3end#L 361 ATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAAT 410 chr6ptel1M 94196 AATTTAAAGGAGGGAATGGGACCCACATTTGCAAAAATGTTTGTGGCAGC 94245 i i i --ii v i i vii i i ii v L1ME4c_3end#L 411 AATTCAAAAGAAGGAA--AAAGCTATATGCACGAAGATGTTCATTGCAGC 458 chr6ptel1M 94246 CATGTTTGTGGAGGCAAGAAACTGGAAACTGAGTGGATGCCCATCAGCTG 94295 vv i i iivi i i i vivv ii i v iiv L1ME4c_3end#L 459 GTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAG 508 chr6ptel1M 94296 GGGAATGGCTGAATAAGTCATAGCACATGAATGCTATGGAATATTAT 94342 i i i i i i i v? iv v L1ME4c_3end#L 509 GGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATATTAT 555 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 43.98 CpG sites = 60, Kimura (unadjusted) = 45.97 Transitions / transversions = 1.67 (60/36) Gap_init rate = 0.01 (4 / 294), avg. gap size = 1.25 (5 / 4) 379 25.84 10.26 0.78 chr6ptel1M 94991 95107 (904893) L2d2_3end#LINE/L2 422 549 (6) m_b273s601i6 10796 chr6ptel1M 94991 TTGTCTTCCATGTTAAATTGTAAGCTATTTG--GGTAAGGGCT-TGTCTC 95037 i vvii i vi -- i i i i- i L2d2_3end#LIN 422 TTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTT 471 chr6ptel1M 95038 CTGCCTTTTTTGTATCCCT---------TAACACAGTGCCTGGTGCATTG 95078 v i - i i--------- i v ii iv L2d2_3end#LIN 472 ATAC-TTCTTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAG 520 chr6ptel1M 95079 TAGGAGCCTAATAAATACTGATTGAATTG 95107 v ii i vi v L2d2_3end#LIN 521 TAGGCGCTCAATAAATATTTGTTGATTTG 549 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.18 CpG sites = 21, Kimura (unadjusted) = 33.18 Transitions / transversions = 2.33 (21/9) Gap_init rate = 0.03 (4 / 116), avg. gap size = 3.25 (13 / 4) 355 21.11 2.20 1.09 chr6ptel1M 95471 95561 (904439) C L1MC1_3end#LINE/L1 (862) 218 127 m_b273s551i5 10797 chr6ptel1M 95471 TTGTCCAATTTGAGAGGTGTGTAGTAATACATCAGGGT-GTCTTAATTTG 95519 v v i i v ii iv vv - i C L1MC1_3end#LI 218 TTGGCCATTCTAATAGGTGTGTAGTGGTATCTCATTGTTGTTTTAATTTG 169 chr6ptel1M 95520 CATTTTTCTGATCA-ATGGTAATTTGAAGCATCTTTTCATATG 95561 ii v - i- i v i C L1MC1_3end#LI 168 CATTTCCCTGATGACATA-TGATGTGGAGCATCTTTTCATATG 127 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 25.17 CpG sites = 11, Kimura (unadjusted) = 25.17 Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.03 (3 / 90), avg. gap size = 1.00 (3 / 3) 32 21.31 0.00 0.00 chr6ptel1M 96391 96455 (903545) (T)n#Simple_repeat 1 65 (0) m_b273s252i6 10798 chr6ptel1M 96391 TTTCTTTCTTTTTTTTTTTTTTTTTTTTGCTCAATCATTTTTCTTTTTTT 96440 i i vi ivv iv i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr6ptel1M 96441 TTTTTTATTTTATTT 96455 v v (T)n#Simple_r 51 TTTTTTTTTTTTTTT 65 Matrix = Unknown Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0) 1148 26.95 5.19 5.00 chr6ptel1M 96874 97412 (902588) C L1ME5_3end#LINE/L1 (274) 667 128 m_b273s551i6 10799 chr6ptel1M 96874 ATAGTATTGTTGTTGAAGTATAATGATCTC---CTGGTCCT-GCTCATTT 96919 i - ----- ?-- --- v i -i iv C L1ME5_3end#LI 667 ATGGTATTGT-GTT-----ATAN--ATCTCATTCTGTTTCTTACTTTTTT 626 chr6ptel1M 96920 CACTCAGCATCA-GTTCATGTAAG-TCTCTCCAGGC--CTTTCTGAAATT 96965 ii - -- v - iv v i-- v v v --i C L1ME5_3end#LI 625 CACTCAGCACTATGTT--TTTAAGATCCATCCATGTTGCTATGTGTA--C 580 chr6ptel1M 96966 ATCCTGTTGGTCATTTCTTACAGA-ACAGTAATATTCCATAATATTCATA 97014 iv iv iii v v v-i - i i ii i v v C L1ME5_3end#LI 579 ATCTAGTCCGTTGCTTCTAACTGCTGCA-TAGTACTCCATGGTGTGCATC 531 chr6ptel1M 97015 TACCACAATTTATTCAGCCATTCTCCAACTGATGGACATCCA--TTCAGT 97062 i v iii v i v v i -- -- i C L1ME5_3end#LI 530 CACCACATTTTACCTATCCACTCTCCCAGTGATGGACACCCAGGTT--GC 483 chr6ptel1M 97063 TTCCGGTT--TTACCACTACAA--AGGGCTGCCACAAACATTCGTGCACA 97108 i iii --iii i -- iv v ii i vi i C L1ME5_3end#LI 482 CTCCAACTCCCCGCCACCACAAACAACGCTGCAATGAACATCCTCGTACA 433 chr6ptel1M 97109 TACGGTCCCTTT----CCCTTCTTTATAATCTCTTTGGGATATAATCCCA 97154 --- i ----v viv v v i vv C L1ME5_3end#LI 432 T---GTCCCCTTATGGACCTGTGTGAGAATTTCTTTGGGATATATACCCA 386 chr6ptel1M 97155 GTAGTAACACTGCTGGATCA-AGGGTATGCACA-GTTTGA--TGACTTTT 97200 v iiiv i i - ii -ii i -- --- C L1ME5_3end#LI 385 GGAGCGGAATTGCTGGGTCATAGGGTATGCGTATACTTAATTTGAC---T 339 chr6ptel1M 97201 GAGCATAGTTCAAACTACTCT-CAAAATGGTTGGATTCGTTCACACT-CC 97248 i i iv -i i i i - i i v iiv ii - C L1ME5_3end#LI 338 AAGTACTG-CCAGATTGCTCTCCAGAATGGCTGCACCAGTCTACACTCCC 290 chr6ptel1M 97249 ACCAACAATGCATCAATGTCCCAGTTTTCCCACATCCCCTCCAACAATCA 97298 i i v iv i vi ? i i v v ii C L1ME5_3end#LI 289 ACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATCCTCGCCAACACTTG 240 chr6ptel1M 97299 TCATTATT---TTTTCCTGTCATCTTAGCCAATCTGACAGGTGTGTAGTG 97345 v i---i --- v i v i i i iv C L1ME5_3end#LI 239 GCATTATCCAGCTTTC---TAATTTTTGCCAGTCTAATAGGTGTAAAGTG 193 chr6ptel1M 97346 GTATCTTAGAGTTGTCTTAATTTGCATTTCTCTAATTAATAATGACTTTG 97395 i i vv i i v v C L1ME5_3end#LI 192 ATATCTCATTGTTGTTTTAATTTGCATTTCTCTGATTACTAATGAGTTTG 143 chr6ptel1M 97396 GGTCACTTTCTTTACAT 97412 i - - i i i C L1ME5_3end#LI 142 AG-CA-TCTCTTCATAT 128 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.56 CpG sites = 91, Kimura (unadjusted) = 34.90 Transitions / transversions = 1.94 (91/47) Gap_init rate = 0.08 (43 / 538), avg. gap size = 1.28 (55 / 43) 285 29.12 10.94 0.71 chr6ptel1M 97691 97818 (902182) MIRb#SINE/MIR 13 153 (115) m_b273s601i7 10800 chr6ptel1M 97691 GTTGTCCAGAGGTTAGAGCAAGAGATA-GAAGATTAACA--CCTGCCTTG 97737 v v v vv v i v v- i vivi -- vv v MIRb#SINE/MIR 13 GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTC 62 chr6ptel1M 97738 ATATTCTTTTTCAGACATTTCTTAGCTGTA-GACTCCTGGGCAA------ 97780 iv i ivvi v v i vi i- - i ------ MIRb#SINE/MIR 63 GAATCCCGGCTCTGCCACTTACTAGCTGTGTGAC-CTTGGGCAAGTTACT 111 chr6ptel1M 97781 -AACC---CTGAATCTCAGTTTTCCCATTTGTAAAATGAGGA 97818 - --- ii i i i i MIRb#SINE/MIR 112 TAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGA 153 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.83 CpG sites = 18, Kimura (unadjusted) = 37.26 Transitions / transversions = 0.95 (18/19) Gap_init rate = 0.06 (7 / 127), avg. gap size = 2.14 (15 / 7) 372 20.57 13.59 0.86 chr6ptel1M 97760 97862 (902138) MIR3#SINE/MIR 79 194 (14) m_b273s601i8 10800 chr6ptel1M 97760 TAGCTGTA-GACTCCTGGGCAAA-------ACC---CTGAATCTCAGTTT 97798 ? i- - i i------- --- iii MIR3#SINE/MIR 79 TNGCTGTGTGAC-CTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTT 127 chr6ptel1M 97799 TCCCATTTGTAAAATGAGGAGGTTGGACTCCATGGCTTTTTATTTCCCTT 97848 i i i i vv iii i v vv MIR3#SINE/MIR 128 CCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTT 177 chr6ptel1M 97849 CCAG---TGACCATCTA 97862 --- vv MIR3#SINE/MIR 178 CCAGCTCTGACATTCTA 194 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 25.00 CpG sites = 14, Kimura (unadjusted) = 25.00 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.05 (5 / 102), avg. gap size = 3.00 (15 / 5) 1572 30.87 2.83 2.03 chr6ptel1M 98534 99558 (900442) PRIMA41-int#LTR/ERV1 3111 4143 (3613) m_b273s701i0 10801 chr6ptel1M 98534 AAATAGACTCTTCCGTGTGGGACCAGGGCATTCCTGGGAGAGCCACGCAT 98583 i i ii ??? v vv ivi v ? i ??iiv i PRIMA41-int#L 3111 AAGTAAATCCTNNNGTTTGGGACACGGAGGTTCCGGGNAAAGCNNTAAAC 3160 chr6ptel1M 98584 GCCACTCCAGCCCTTATCAGACTAAGGGATCCTAGTGT-ATTTCCTCATA 98632 iiv i ii v? vi v i --- ii -v?? v i ? i PRIMA41-int#L 3161 GTTCCCCCAGTTCGNATCCAACTTAAG---CCCGGTGTTCNNTACCCNTG 3207 chr6ptel1M 98633 G--GTGCCAATACCCAATTAAGCGGGAAGATAGGATAGGCC-TGCAGCCT 98679 -- v v v- vvv?i ii v vi vv- v i PRIMA41-int#L 3208 GAAGAGACAATACCCT-TTAAGGCCNGAGGCACGAGGGGGGATCCAGCCC 3256 chr6ptel1M 98680 TTAATTGACAACTTCCTTAAATTCTAACTCCTGATTCCCTGCAACTCCCC 98729 i v v? v i vv vivi?i vi i vv i? v PRIMA41-int#L 3257 CTAATAGCNAAGTTTCTGCAATATGGNTTATTAAGGCCCTGTNAGTCCCC 3306 chr6ptel1M 98730 TTGTAATACTCCGATTCTTTCTGTCAGAAAGCCAAATGGAGATTACCGGG 98779 i ? ii ?i ? i i i ? v iv PRIMA41-int#L 3307 TTGTAATACCCCNATCTTNCCNGTTAAAAAGCCAAATGGGGANTACAGAT 3356 chr6ptel1M 98780 TAGTGCAGGATCTTAGGGCAATAAATGAAGCGGTTGTACCAATCCATCCC 98829 v v i i ?? ?i v i ? i v v ? i ? PRIMA41-int#L 3357 TTGTTCAAGACCTNNGGGCNGTTAATGAGGCNGTCGTTCCCATNCACCCN 3406 chr6ptel1M 98830 ATAGTAGCCAACCCATATACAATTCTCAAACAAATTCCTGGGAATACAGG 98879 ?v i v i i? vi vivv ii i ? i i ?ii PRIMA41-int#L 3407 ATAGTNCCCAATCCTTACACGNTGTTAGCCCAGGTCCCNGGGGATGCNAA 3456 chr6ptel1M 98880 ATGGTTTTCCACCCTGGACCTTAAAGACGC---CTTTTTCTGTATCCCTC 98926 v iv vii?i i ? i i ---i ? i ii vv PRIMA41-int#L 3457 TTGGTTCACAGTNTTAGACCTNAAGGATGCTTTTTTTTTNTGCATTTCAG 3506 chr6ptel1M 98927 TGCCTGAGGACTCGAGATTGCTTTTTGCCTTTCAATGGGCTAAACCAGGG 98976 i vivv? i ?vi ?vv ? i v i i v ?? i PRIMA41-int#L 3507 TACACCCNGATTCNCAATNTATNTTTGCTTTTGAATGGACTGATCCNNGA 3556 chr6ptel1M 98977 GAAC--TTC--CCCATTAACTAACTTGGACTGTATTGCCCCAGGGCTTTC 99022 v ?i-- -- ?iv i i i v vi v ? v PRIMA41-int#L 3557 TANTCATTCGGCNTCTCAATTAACCTGGACAGTCCTTCCCCAGGGNTTTA 3606 chr6ptel1M 99023 AGGACAGCCCACATTTATTCAGCCAAGCCCTAGCTAAAGATCTGTGGGAC 99072 i v i ? ii vv v ?i i ? vi iv i v PRIMA41-int#L 3607 GGGACAGCCCCCATCTNTTTGGAAATGCNTTGGCNAAAGAATTAAGGAAG 3656 chr6ptel1M 99073 CTTAATCTGTCTAGCAGTAGTCTTATACAATATGTGGATGATATATTACT 99122 vv vi vv vi i?v v v iv i ?v PRIMA41-int#L 3657 CTACAGTTGAATAGGGGCNCTATTATTCAATATGTGGATGACTTGTTNAT 3706 chr6ptel1M 99123 TTGCAG-CCGACCAGAGAGGAGTCTTGGATAGCG--GCCACAAAGACCTT 99169 ?vi - ? i i i -- i ivi--i iv vi?i PRIMA41-int#L 3707 TNCTAGCCCNACTAAAGAAGA--CTCGGATAAAAATACCATTAAGTTNCT 3754 chr6ptel1M 99170 AAACCTTCTAGC--CTCATGGGGGTACAGGGTCTCCCTGCCAAAGGCCCA 99217 ii i i v-- v i-- i ? ? i vv PRIMA41-int#L 3755 AAATTTCCTGGGAACTAAC--GGGTATAGGGTNTCNCCGCACAAGGCCCA 3802 chr6ptel1M 99218 CATTGCCCGCCTGTCA----GTCAAATATTTGGGTCACAATCTCACCCCC 99263 v -i ?i --- ---- i vi iv? v i PRIMA41-int#L 3803 GATT-TCNAC---TCAAAAGGTTAAATATTTGGGATACGTNCTAACCCCT 3848 chr6ptel1M 99264 ACCTCTCGATCTCTAA-CTGAGGAGAGGAAACAGGTTATTTTAAGCCTCC 99312 iv?v i iv v? i- iv?i i? i v ii i ii??? PRIMA41-int#L 3849 GGNACCCGGGCANTAGCCCCNAGAANGAAAAGAGGCCATCTTGGNNNTCC 3898 chr6ptel1M 99313 CAGATTCTGCC---TCAAAAAGGCAATTGAGAACCTTTCTTGGCATAGAT 99359 i ?i -- ---i i -i ii ? ii i i v v i v? PRIMA41-int#L 3899 CGGANCC--CCAGACCAAGAA-ACAGCTGNGGGCTTTTTTGGGAATGGCN 3945 chr6ptel1M 99360 GGTTTCTGCAGGATCTAGATTCCTAATTTTGGGATTATTGCCAGACCCCT 99409 v v?vv?v i i ? iiiv v? v ? ii ii PRIMA41-int#L 3946 GGATTCTGCTNTTNATGGGTNCCCGGATTTGGGCNTATAGCNAAGCCTTT 3995 chr6ptel1M 99410 CTACGATTCTGTTCAAGGTCCTGA--TAACCTTCCTCTTGAATGGGGACT 99457 v i vv v vv vv v -- i ? -- - ? - iv PRIMA41-int#L 3996 ATATGAGGCTCTAAAAGGAGCGGACGTGANC--CCT-TNGAAT-GGGATA 4041 chr6ptel1M 99458 GGA---GCAGGTCAAGGCTTTTAAAACCCTGAAAGCCAAACTGACCTCTG 99504 ? --- iiv - ?i v ? vv ivv? v PRIMA41-int#L 4042 GNAACTGCAAAAC-ANACTTTTAATACCCTNAAAGAGAAACTGGGANCAG 4090 chr6ptel1M 99505 CTCCTGTTCTTGCCCTGCCTAACTTACAGAAACCTTTCACTCTGTTTGTG 99554 ? iii v vv? v i ? ?v ? i ? iv i i v - PRIMA41-int#L 4091 CTCCNGCCTTGGGANTCCCCAANTTNGANAAGCCNTTTCCTTTATGTG-G 4139 chr6ptel1M 99555 TTGA 99558 i PRIMA41-int#L 4140 CTGA 4143 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 43.67 CpG sites = 173, Kimura (unadjusted) = 45.71 Transitions / transversions = 1.26 (173/137) Gap_init rate = 0.03 (35 / 1024), avg. gap size = 1.43 (50 / 35) 2043 27.65 2.64 2.41 chr6ptel1M 100107 100977 (899023) PRIMA41-int#LTR/ERV1 4135 5007 (2749) m_b273s701i1 10801 chr6ptel1M 100107 TGTAGATGAGAGGCATGGACAGGCGTTGGGAGTCCTTACTTA---GCTTC 100153 i v i ii v i- v vi v ?i ii --- -- PRIMA41-int#L 4135 TGTGGCTGAAAAACAAGGG-ACGCCCTGGGTGTCCTNGCCCAAAGGCT-- 4181 chr6ptel1M 100154 TAGGGCCCGACCCCAGACCCGTGGCTTATTTTTCAAAGAAACTAGACTCA 100203 -- vvvv i v v ? v v i ivi PRIMA41-int#L 4182 --GGGAAATATCCCCGACCAGTGGCNTATTTTTCTAAGCAGCTAGACCAG 4229 chr6ptel1M 100204 GTCTCCCTAGGGTGGCCTTCCTATCTCAG------AGCTGCCACAGCCCT 100247 vv ?iii ?vvv ii ? ------? ? ? v i PRIMA41-int#L 4230 GTGGCNTCGGGGTGGCCNGGATGCCTNAGGGCNGTNGCNGCNACCGCTCT 4279 chr6ptel1M 100248 GTTAATTGAGGAAACCTCCAAACTGACTCTGGGTCAGCCATTAGAGGTTT 100297 ? ii v ? i vvi ? ?i v i v?i PRIMA41-int#L 4280 NTTGGTAGANGAAGCCAGTAAACTNACNTTGGGACAACANCTAGAGGTTT 4329 chr6ptel1M 100298 TAACCCCACATAGAGTCCAAAGCATTTTAGAAGCCAAAGGGCATCAGTGA 100347 i ? ivi v ii vi ii ? i i i PRIMA41-int#L 4330 TGACCCCNCACCAAGTACAGGGGGTCCTAGAAGCNAAAGGACACCAGTGG 4379 chr6ptel1M 100348 CTCTCAAGTGGGAGGCTTACT-AAGTACCAGGCTCTACTGCTGGATACCC 100396 ? vv i - vi? - i i i ?i i i PRIMA41-int#L 4380 NTGACAGG-GGGACANTTACTNAAATATCAGGCTTTNTTGCTAGACACCC 4428 chr6ptel1M 100397 CTGACCTGTCCCTCCAAGTCTGTCGCACTTTAAATCCTGCCACTCTTCTC 100446 - iv iv i iv v i iv i i v i ii? i v PRIMA41-int#L 4429 C-GATGTAACTCTTAAAGTATGCCAAACTTTGAACCCAGCTACCTNTTTG 4477 chr6ptel1M 100447 CCTGACGTCTCTCAATCAGAAGAGATTGTCCATAATTGTATGGAAGTTAT 100496 ? v-- i v iv vvvv ii i ---- iv PRIMA41-int#L 4478 CCNGAA--CCCACAGGCACCCTAGATCATTC----TTGTATACAAGTTAT 4521 chr6ptel1M 100497 AGACTCAGTCCACTCCAGCAGACCTGACTTAAATGACACCCCCCTTGAGA 100546 i viv i ii ? i v v iivv v v PRIMA41-int#L 4522 GGAGCAAATTTACTCCAGCNGGCCGGACTTAAAGGATGAGCCCCTAGATA 4571 chr6ptel1M 100547 ACCCAGATGGGGAGTGGTTCACAGATGGGTCTAGCTTTCTCGAGAAGGGG 100596 i v v vi i i ivv v vv v? i PRIMA41-int#L 4572 ATCCCGAGGTAGAATGGTTTACAGATGGAAGTAGCTTTGTGCACNAGGGA 4621 chr6ptel1M 100597 GAGAGAAAGATGGGCTATGCTGTGGT--GTCTCTTTGCGG-CATCTTGGA 100643 i v ii? v ? -- i vviv? v -? --- PRIMA41-int#L 4622 AACAGAAAGGCNGGGTATGCTGTNGTTAGCCAACANGAGGTNATC---GA 4668 chr6ptel1M 100644 GGCCAAACCATTGCCTCCTGGCACCTCTGCACAGAAATCAGAGCTCATGG 100693 ?? iv v i vv vv? v v i iv i ii v ? PRIMA41-int#L 4669 GGCNNAGGCCTTACCGGCTTCNACCTCAGCTCAAAAGGCGGAATTAATNG 4718 chr6ptel1M 100694 CATTAACCAGAGCGTTAGAACTTGGGAAGAGGG--TGAGAGTCAACATCT 100741 vi ? ii i vi ?v - - i-- i ? PRIMA41-int#L 4719 CTCTNATTAGGGCCCTNCAA-TTGGGAA-AGGACTTAAGAGTCAACATNT 4766 chr6ptel1M 100742 ACACGGACTCCAAATATGCTTTCCATATCTTCCATGCTCATGGAGCTATT 100791 ? v i i ?? i vvi vi v? i ? PRIMA41-int#L 4767 NCACTGATTCCAAGTATGNNTTTCTGGTGCTCCATGCTCATGCNGCCATN 4816 chr6ptel1M 100792 TGAAAAGAAAGGGGCTTGTTGACAGCAAAAAACTCTCCCATTAAACATGA 100841 i i ? vi ?i i ? v iii? i v v PRIMA41-int#L 4817 TGGAAGGAANGGGGACTNCTAACNGCTAAGGGNTCCCCCATAAAACATCA 4866 chr6ptel1M 100842 GGGAGAAATTCTGCACCTATTGCAAGCTGTTCATGAGCCTAGAGAGAT-- 100889 vvv v i ? iv v i?vvv i ii ii -- PRIMA41-int#L 4867 CTCAGAAATTCTGAATCTNTTAGATGCTGTTTNGCTGCCCAAGGAAGTAG 4916 chr6ptel1M 100890 CTGTCATTC--TGTAAAGGGCACC--GGAGGGGACATTCACC-TCAGGCT 100934 ? ? -- i i i i --ii - i ?i- ? -- PRIMA41-int#L 4917 CNGTNATTCATTGCAGAGGACATCAAAAAGGGGAC-TCCANTGTNA--CT 4963 chr6ptel1M 100935 AAGGGAAAC-AGCTGGCAGACTTAGCTGCTAAGTCTGCTGCCTT 100977 -vv ? v? v v i v v PRIMA41-int#L 4964 AAGGGAAACTCCCTNGCAGACGNAGCAGCTAAGGCCGCAGCATT 5007 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.38 CpG sites = 128, Kimura (unadjusted) = 38.02 Transitions / transversions = 1.20 (128/107) Gap_init rate = 0.04 (32 / 870), avg. gap size = 1.38 (44 / 32) 456 25.28 3.93 6.73 chr6ptel1M 101179 101407 (898593) HERV4_I#LTR/ERV1 5013 5235 (1304) m_b273s701i2 10801 chr6ptel1M 101179 TGGGGAGAAATGCTCTCCATTCCCTGGTGAAACACGTT-TTCAC-GGGCC 101226 i ivi vvv v - v i - i- HERV4_I#LTR/E 5013 TGGGGAGAGATGCCACCCTGGCCATGGT-AAACAGGCTCTTCATTGGGCC 5061 chr6ptel1M 101227 --ACA-AGCT-GGGAGGAACACTCAAACAGGTGTGCCAGTTCTGCCCAGT 101272 -- v- -v v ----- i i v i ivi i v HERV4_I#LTR/E 5062 TAACTTAGCTTCGGTGG-----TTAAGCAGGTCTGTCAAGCCTGCTCACT 5106 chr6ptel1M 101273 CTGTGC-CTAGGTAA--ATCCTGAGGGAGCTGTTAAGCCCCCACCTCTCC 101319 v - --- -- i -- i i ---- iviv v vv HERV4_I#LTR/E 5107 GTGTGCACT---TAACAACCC--AGGAAAC----AAAATGCCTCCTCTAA 5147 chr6ptel1M 101320 TGAAGGCAGTCCAGAGGAGAGGCACATACCCTGGTGAGGATTGGCAGCTA 101369 ii iv v v v v i i ii HERV4_I#LTR/E 5148 TAGAACCAGTCCAGAGGAGAGGAACTTACCCAGGGGAAGACTGGCAATTA 5197 chr6ptel1M 101370 GACTTCACACATATGCCCCCTTGTAAAGGGTTTAAGTT 101407 v vv i i i vi HERV4_I#LTR/E 5198 GACTTCACCCATATGCCAGCTTGCAGAGGATACAAGTT 5235 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 31.05 CpG sites = 27, Kimura (unadjusted) = 31.05 Transitions / transversions = 1.00 (27/27) Gap_init rate = 0.10 (22 / 228), avg. gap size = 1.09 (24 / 22) 476 32.13 1.79 0.89 chr6ptel1M 101916 102138 (897862) MER66-int#LTR/ERV1 6043 6267 (409) m_b273s701i3 10801 chr6ptel1M 101916 TTTGCCAATGAAACGGCTCATTCTTTGAGGGAGATTCAGGAATCTCTAGA 101965 v vii v i v vv v i i ii i i i MER66-int#LTR 6043 TTAGCCACCAACACAGGTCAGGCATTAAAGGGAATTCAAGAGTCCCTAGA 6092 chr6ptel1M 101966 CTCTT-GGCTAACATGGTTTTGGATAATCGAATGGCTTTAGATTATCTTC 102014 - v ii i i v iv v i v i - v MER66-int#LTR 6093 CTCTTTGGCAAATGTAGTTCTCGATAACAGACTAGCGTTGGATTAT-TTA 6141 chr6ptel1M 102015 TTACCTCCAGC--GGAGGTGTCTGTGCTCTAGTCAACACCTCTTGCTGCA 102062 i v v- i -- v v vv vi i i vvv i MER66-int#LTR 6142 CTAGCTG-AACAAGGTGGAGTCTGTGCAGTTATTAATAAAACCTGCTGCA 6190 chr6ptel1M 102063 TGTATATTAACAACTCAAGGAAAGTTGAGCTGTGCACAGAAAGAATCTTA 102112 ii vi iv i v vvi ivv ii vv MER66-int#LTR 6191 CATATATTAACAACTCTGGACAGGTTGAGGTTAACATTCAAAAGATCTAT 6240 chr6ptel1M 102113 CAGAAGGTTGCCTGGATACA-AGACAT 102138 v v i i i v - i MER66-int#LTR 6241 GAGCAAGCTACCTGGTTACATAGATAT 6267 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 42.62 CpG sites = 36, Kimura (unadjusted) = 42.62 Transitions / transversions = 1.03 (36/35) Gap_init rate = 0.02 (5 / 222), avg. gap size = 1.20 (6 / 5) 264 17.74 1.59 1.59 chr6ptel1M 102458 102520 (897480) HERV35I#LTR/ERV1 6828 6890 (28) m_b273s701i4 10801 chr6ptel1M 102458 CGACCATTTCCAGCAGGAAGTAGCTACAGAAGACTCAGATCACCGACCCT 102507 i v v i v - v vi i HERV35I#LTR/E 6828 CAACCCTGTTCAGCAGGAAGTAGCTTCAGAAGA-TGAGATCTTCGGCCCT 6876 chr6ptel1M 102508 TT-TCCAAAAGAAT 102520 - vv HERV35I#LTR/E 6877 TTCTCCTTAAGAAT 6890 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 20.25 CpG sites = 4, Kimura (unadjusted) = 20.25 Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.03 (2 / 62), avg. gap size = 1.00 (2 / 2) 324 17.94 4.94 3.66 chr6ptel1M 102468 102548 (897452) MER50-int#LTR/ERV1 7118 7199 (6) m_b273s701i5 10801 chr6ptel1M 102468 CAGCAGGAAGTAGCTACAGAAGACTCAGATCACCGACCCTTTT-CCAAAA 102516 i i -- i vi v v - v MER50-int#LTR 7118 CAGCAGGAAGCAGTTACAGAAGACT--GACCTTCGTCCATTTTCCCCAAA 7165 chr6ptel1M 102517 GAATTTGTATTT---ATTGCTTGAGGGGGGAGATG 102548 v vi i --- i - i MER50-int#LTR 7166 GAATTGGGGTCTTGGACT-CTTGAGGGGGGAAATG 7199 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 20.74 CpG sites = 8, Kimura (unadjusted) = 20.74 Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.06 (5 / 80), avg. gap size = 1.40 (7 / 5) 20 13.96 0.00 0.00 chr6ptel1M 102723 102754 (897246) (C)n#Simple_repeat 1 32 (0) m_b273s252i7 10802 chr6ptel1M 102723 CCCCCCCCCCCCTCCTCCCCACCTCCCCCCCC 102754 i i v i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 32 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 15 19.61 0.00 0.00 chr6ptel1M 104288 104316 (895684) (C)n#Simple_repeat 1 29 (0) m_b273s252i8 10803 chr6ptel1M 104288 CCCTCCTCCCCCCCCCCCACCACCACCCC 104316 i i v v v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC 29 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 386 27.68 4.49 0.54 chr6ptel1M 105472 105649 (894351) ERV24B_Prim#LTR/ERV1 4305 4489 (3124) m_b273s701i6 10804 chr6ptel1M 105472 CTCCCAGATGGCCA-TTCAGGCCAACAAGCTGAACTTGGGGCAGCAGCTA 105520 i -i -? i v v i ?iv? ?vi?i i ERV24B_Prim#L 4305 CTTCCAGA-AGCCACNTCGGCCCAACAAGCAGAATTNATNGCNTTNACCA 4353 chr6ptel1M 105521 G-GCTAGTCAGTTAAGAAAAGACAAAAGGATGAATATCTGCACCCAGAGC 105569 - v ? iiv? iv ? vviiv i ii vv v ERV24B_Prim#L 4354 GAGCTTGTCANTTGGCNAAAGGAANAACTGCTAATATTTATACAGACAGC 4403 chr6ptel1M 105570 CAGGATGCCTTTGGAGTAGCCT-TGACTTTTGGGTGGTAGGGAAACATCA 105618 viiv i i- i v ii v v vvi ERV24B_Prim#L 4404 AGATATGCTTTTGGAGTAGCCCATGATTTTGGAATGCTATGGAAACAAAG 4453 chr6ptel1M 105619 GGGCCT-----CCTCTTCAGGACAGTCCATTAAAAA 105649 i ?i ----- v ? ii ? ERV24B_Prim#L 4454 AGGNTTTCTNACCTCTTCTGGNCAACCCATNAAAAA 4489 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.46 CpG sites = 28, Kimura (unadjusted) = 38.46 Transitions / transversions = 1.33 (28/21) Gap_init rate = 0.03 (5 / 177), avg. gap size = 1.80 (9 / 5) 250 21.56 7.69 3.16 chr6ptel1M 106434 106524 (893476) L1MC1_3end#LINE/L1 505 599 (481) m_b273s551i7 10805 chr6ptel1M 106434 GGGGAATGGCCAAATAACTTGTGATGCATGAAGGCGATGCAATATTATTC 106483 v vi vi i i vv i i v L1MC1_3end#LI 505 GGTGAATGGATAAATAAACTGTGGTACATCCAGACAATGGAATATTATTC 554 chr6ptel1M 106484 TG---TAAAAATGATGAATGAG----CAAGTTTTGGAAAGGCCTGGAG 106524 v --- - -- ---- iiv i i v L1MC1_3end#LI 555 AGCGCTAAAAA-GA--AATGAGCTATCAAGCCATGAAAAGACATGGAG 599 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 25.71 CpG sites = 10, Kimura (unadjusted) = 25.71 Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.06 (5 / 90), avg. gap size = 2.00 (10 / 5) 11 32.62 4.35 0.00 chr6ptel1M 106729 106797 (893203) (CTGTTTT)n#Simple_repeat 1 72 (0) m_b273s252i9 10806 chr6ptel1M 106729 CTGTGTTCTCTTTTTTCTTTT-TGTTTTTTGATCTCT-TCAATGGTTTTG 106776 v v i v - i v i - ivviv v (CTGTTTT)n#Si 1 CTGTTTTCTGTTTTCTGTTTTCTGTTTTCTGTTTTCTGTTTTCTGTTTTC 50 chr6ptel1M 106777 CACTTT-TGCTCTCTGTTTTCT 106797 iii - i i (CTGTTTT)n#Si 51 TGTTTTCTGTTTTCTGTTTTCT 72 Matrix = Unknown Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.04 (3 / 68), avg. gap size = 1.00 (3 / 3) 40 0.00 0.00 0.00 chr6ptel1M 109329 109362 (890638) (AC)n#Simple_repeat 1 34 (0) c_b273s251i1 10807 chr6ptel1M 109329 ACACACACACACACACACACACACACACACACAC 109362 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACAC 34 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 203 30.11 5.38 0.00 chr6ptel1M 112794 112886 (887114) MIR3#SINE/MIR 109 206 (2) m_b274s601i0 10808 chr6ptel1M 112794 CTTCTCTGTGTTTCTGTTTCTTC--CTGAAAATTGGAGGGGTTGAACTCT 112841 i v ii v i -- v v ii i vv MIR3#SINE/MIR 109 CCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAG 158 chr6ptel1M 112842 TTCCT-TCTGAAGGATCTTTCAGC-CCGACATCTTCTGACTTT-TGAT 112886 v vv - i i vvi i - i ii v i i - MIR3#SINE/MIR 159 ATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTATGAT 206 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.50 CpG sites = 16, Kimura (unadjusted) = 39.50 Transitions / transversions = 1.33 (16/12) Gap_init rate = 0.04 (4 / 92), avg. gap size = 1.25 (5 / 4) 15 10.32 0.00 6.06 chr6ptel1M 113304 113338 (886662) (TTTCCT)n#Simple_repeat 1 33 (0) m_b274s252i0 10809 chr6ptel1M 113304 TTTCCTTTTCCTTTTCCTTTCAACTCCTTCCTTTT 113338 -vv -i (TTTCCT)n#Sim 1 TTTCCTTTTCCTTTTCCTTT-TCCT-TTTCCTTTT 33 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 352 30.00 1.79 1.79 chr6ptel1M 113937 114048 (885952) C MIR#SINE/MIR (98) 164 53 m_b274s601i1 10810 chr6ptel1M 113937 AGTTAGGTGATATTGTTATCCCTATTTCAGAGTTGAGGAAACAGGAAAAC 113986 v iv i i i v v v iiiv C MIR#SINE/MIR 164 AGGTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCAC 115 chr6ptel1M 113987 AATCAGAATTTAGTTGACTTGCCCAGAGGTACACAGTTAATAACC--CAA 114034 i-- iv iv i ii vi i i vi-- i C MIR#SINE/MIR 114 AG--AGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAG 67 chr6ptel1M 114035 ATTTGGGATCAGAA 114048 vii iv C MIR#SINE/MIR 66 AGCCGGGATTCGAA 53 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.33 CpG sites = 21, Kimura (unadjusted) = 39.91 Transitions / transversions = 1.75 (21/12) Gap_init rate = 0.03 (3 / 111), avg. gap size = 1.33 (4 / 3) 209 34.65 7.09 0.00 chr6ptel1M 114738 114864 (885136) C L2b_3end#LINE/L2 (10) 456 321 m_b274s601i2 10811 chr6ptel1M 114738 TCAGTAAACAGTTA---AGGGCCTGCTACAGGGCAG-CCCTGGGCTAAAT 114783 ii i v --- v i iiiv v - ? v iii C L2b_3end#LINE 456 TCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGC 407 chr6ptel1M 114784 AGCAGGAA--CAGAAAGAGATGTGAGGGACAT--CCCCTGTTCTCCTGGA 114829 ivii i -- viivii iiv vi ?i--i ii vi C L2b_3end#LINE 406 GCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGGA 357 chr6ptel1M 114830 GGTCACAGACTGGTGGGGCAGACA-ATATGCCAGCA 114864 v v i v - i iv ? C L2b_3end#LINE 356 GCTCACAGTCTAGTGGGGGAGACAGACATGTAANCA 321 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 44.57 CpG sites = 29, Kimura (unadjusted) = 51.35 Transitions / transversions = 1.93 (29/15) Gap_init rate = 0.04 (5 / 126), avg. gap size = 1.80 (9 / 5) 378 29.45 9.43 1.75 chr6ptel1M 115033 115191 (884809) C MIRb#SINE/MIR (64) 204 34 m_b274s601i3 10812 chr6ptel1M 115033 TGCATTGTCTTATTTCATCCTCATGAAAACCAGAGGATTTAGGTGCTATT 115082 i i v ii v vviv vv ii C MIRb#SINE/MIR 204 TGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATT 155 chr6ptel1M 115083 ATTAAACCCATTTTCCAGATAAAGATACTGAATCTAACCGAGGTCCTATA 115132 i--- v i i v iv v vv ivvi C MIRb#SINE/MIR 154 ATC---CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTA 108 chr6ptel1M 115133 ACTTGAC-----TTGCAAAGTT---------CTGAGGTGGGAACAAAACC 115168 v ----- ii v i --------- v vi vivi C MIRb#SINE/MIR 107 ACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACC 58 chr6ptel1M 115169 CTGGGCTTCCTGA-TTCAAGGCCC 115191 v v vi - i i C MIRb#SINE/MIR 57 CAGGTCTGTCTGACTCCAAAGCCC 34 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.81 CpG sites = 22, Kimura (unadjusted) = 37.82 Transitions / transversions = 0.92 (22/24) Gap_init rate = 0.04 (6 / 158), avg. gap size = 3.00 (18 / 6) 20 7.86 0.00 0.00 chr6ptel1M 116662 116688 (883312) (TG)n#Simple_repeat 1 27 (0) m_b274s252i1 10813 chr6ptel1M 116662 TGTGAGTGAGTGTGTGTGTGTGTGTGT 116688 v v (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGT 27 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 13 21.18 2.63 0.00 chr6ptel1M 116708 116745 (883255) (TTTC)n#Simple_repeat 1 39 (0) m_b274s252i2 10814 chr6ptel1M 116708 TTGCTTTATTGTTTGCTCT-TTTCTTTCTTTCTTTTTTT 116745 v v vi v i - i (TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT 39 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 247 33.38 1.23 4.43 chr6ptel1M 118847 119009 (880991) L1PA14_3end#LINE/L1 237 394 (514) m_b274s551i0 10815 chr6ptel1M 118847 TAACCAATG-TGGAAAGGCTTTTGGGGGAAACCTGGGATGCTAATGTATT 118895 vi - vi - vi i i v-- i ii v ii i L1PA14_3end#L 237 TAACAGATGCTGGCGAGG-TTGCGGAGAAAAG--GGAACACTTATACACT 283 chr6ptel1M 118896 ATTGGTGGAGTTGTGAACGGATCCAACCATTCTGCCAAGCAATATGGAGC 118945 i iiv i ivii i v vv i v v L1PA14_3end#L 284 GTTGGTGGGAGTGTAAATTAGTTCAACCATTGTGGAAAGCAGTATGGCGA 333 chr6ptel1M 118946 TATGCCCAAAGGGCTATTAAAAGGTGCATAGCCTTTTTA-CTAGCAATGT 118994 - v i i --- vv v ivi v iv - i vi L1PA14_3end#L 334 T-TCCTCAAAGAGC---TAAAAGCAGAACTACCATTCGACCCAGCAATCC 379 chr6ptel1M 118995 TTCTACTGGGCTTAT 119009 ivi iv L1PA14_3end#L 380 CATTACTGGGTATAT 394 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 42.05 CpG sites = 30, Kimura (unadjusted) = 45.57 Transitions / transversions = 1.36 (30/22) Gap_init rate = 0.06 (9 / 162), avg. gap size = 1.00 (9 / 9) 404 33.51 2.62 4.98 chr6ptel1M 118870 119136 (880864) L1ME5_3end#LINE/L1 259 519 (422) m_b274s551i1 10815 chr6ptel1M 118870 GGGGAAACCTGGGATGCTAATGTATTATTGGTGGAGTTGTGAACGGATCC 118919 ? iv- i iv v i i ii iiv ii v i v L1ME5_3end#LI 259 GGGGANATA-GGAACCCTCATGCACTGCTGGTGGGAGTGTAGACTGGTGC 307 chr6ptel1M 118920 AACCATTCTGCCAAGCAATATGGAGCTA--TGCCCAAAGGGCTATTAAA- 118966 i vvi v viv -- ivi ------ i- L1ME5_3end#LI 308 AGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAA------ATTAAGT 351 chr6ptel1M 118967 AGGTGCATAGCCTTTTTACTAGCAATGTTTCTACTGGGCTTATTTGCCAA 119016 vii v v vvv i viiv v iv v v L1ME5_3end#LI 352 ATACGCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATATCCCAA 401 chr6ptel1M 119017 AGAGATCCTAAAGGAGG---GAAAGGGATCCACAGGTGCAGAAATGTTT- 119062 i i v viv ---iv i--- v i iiii i- L1ME5_3end#LI 402 AGAAATTCTCACACAGGTCCATAAGGGG---ACATGTACGAGGATGTTCA 448 chr6ptel1M 119063 CTGCAGCTCTGTTTGTAGTGGCAAGTTACTGGACACTGACTGGATGCCCA 119112 i vi i ii vvii vi viv i i L1ME5_3end#LI 449 TTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGGGTGTCCA 498 chr6ptel1M 119113 TCAGTTGGGAGATGCTGAATAAGT 119136 -i --v i i L1ME5_3end#LI 499 TCA-CTGGGAGA--GTGGATAGGT 519 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 43.15 CpG sites = 49, Kimura (unadjusted) = 46.09 Transitions / transversions = 1.36 (49/36) Gap_init rate = 0.06 (17 / 266), avg. gap size = 1.18 (20 / 17) 274 24.39 2.41 1.19 chr6ptel1M 119064 119146 (880854) L1MC4a_3end#LINE/L1 448 531 (2098) m_b274s551i2 10815 chr6ptel1M 119064 TGCAGCTCTGTTTGTAGTGGCAAGTTACTGGACACTGACTGGATGCCCAT 119113 vi i v iv i v viv ii L1MC4a_3end#L 448 TGCAGCATTGTTTGTAATTGCAAAATATTGGAAACAACCTAAATGCCCAT 497 chr6ptel1M 119114 CAGTTGGGAGAT--GCTGAATAAGTTATAGCACAT 119146 ??i- i ?-- i ii i i L1MC4a_3end#L 498 NNA-TAGGAGANTGGTTGAATAAACTATGGTACAT 531 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 32.26 CpG sites = 14, Kimura (unadjusted) = 32.26 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.02 (2 / 82), avg. gap size = 1.50 (3 / 2) 395 33.52 0.00 2.13 chr6ptel1M 119564 119755 (880245) ERV24_Prim#LTR/ERV1 4987 5174 (2401) m_b274s701i0 10816 chr6ptel1M 119564 GGCCAGTTTCCTCTCTCAGATGCTCCCTTTCAAACCTGGTAGAGGGACTT 119613 i v i vi v vi i iv iiiv i i?v i ERV24_Prim#LT 4987 GGTCATTTTCCTTTACCAGAAGGCCCTTTCGAGGTATGGCAANTGGATTT 5036 chr6ptel1M 119614 CATTCAATTGCCACCTGCCCATGATTCCAAATATGCTTTGGGGATGGTCT 119663 i ii i vv ? v iv v i i i i ? v? i ERV24_Prim#LT 5037 TATTCAGCTGCCGCCATCNCAAGGATACGAGTATGTTCTNGTNATGGTTT 5086 chr6ptel1M 119664 GTACACTTTCCCGATGGGTGGCAGAGTTCCCCAGAGTTCATCAGAGCCAC 119713 iii i iv i v vi i ?---- v vv ? ERV24_Prim#LT 5087 GTATGTTTTCTCATTGGGTAGAAGCATTTCCN----TGCAGAAGAGCNAC 5132 chr6ptel1M 119714 AGGCTCTGGGCTAGCAAAAATCATCTTAGAAAAAAACATTTC 119755 i v iv viv vv iv ? vi i ERV24_Prim#LT 5133 GGCCTTAGCAGTAGGTAAAATTCTNTTAGAAAAAATTATTCC 5174 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 44.24 CpG sites = 36, Kimura (unadjusted) = 48.45 Transitions / transversions = 1.33 (36/27) Gap_init rate = 0.02 (4 / 191), avg. gap size = 1.00 (4 / 4) 227 24.59 0.00 0.00 chr6ptel1M 119821 119881 (880119) L1MC1_3end#LINE/L1 493 553 (527) m_b274s551i3 10815 chr6ptel1M 119821 TGTCTGTCTGTTGGGGAATGGCCAAACAACTTGTGGTACTTGAAGACCAA 119870 iv v v v vi i vi v vv v v L1MC1_3end#LI 493 TGTCCTTCAGTAGGTGAATGGATAAATAAACTGTGGTACATCCAGACAAT 542 chr6ptel1M 119871 GGAATATTATT 119881 L1MC1_3end#LI 543 GGAATATTATT 553 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 29.84 CpG sites = 4, Kimura (unadjusted) = 29.84 Transitions / transversions = 0.36 (4/11) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 46 5.92 0.00 0.00 chr6ptel1M 123121 123173 (876827) (AC)n#Simple_repeat 1 53 (0) c_b274s251i0 10817 chr6ptel1M 123121 ACACACACACACACACACACAAACACACACACACACACAGAGACACACAC 123170 v v v (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50 chr6ptel1M 123171 ACA 123173 (AC)n#Simple_ 51 ACA 53 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 462 24.69 0.75 6.30 chr6ptel1M 124785 124918 (875082) C MIRc#SINE/MIR (120) 148 22 m_b274s601i4 10818 chr6ptel1M 124785 CTCATTTTACAAATGAGGAAACTGAGGCAAAGAG-GGTGAAGTGACTTGA 124833 i i vv - v v C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr6ptel1M 124834 CCAGGTTCCCATACCTAGTAATTATATGAGAGTAGATTTCAACTCATGAA 124883 i v v i v --i ivv iv i----i -- C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAA--GTGGCAGAGCCGG----GACTC--GAA 57 chr6ptel1M 124884 GCTATATCTTCTTGATTGCAAGCTCTATGCACTTT 124918 v i vi i i v ii vi v C MIRc#SINE/MIR 56 CCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTT 22 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.14 CpG sites = 16, Kimura (unadjusted) = 30.14 Transitions / transversions = 1.07 (16/15) Gap_init rate = 0.07 (9 / 133), avg. gap size = 1.00 (9 / 9) 16 15.84 0.00 2.78 chr6ptel1M 125191 125227 (874773) (ATTT)n#Simple_repeat 1 36 (0) m_b274s252i3 10819 chr6ptel1M 125191 ATTAATTTATTTAATTACTGATTTATTTCATTTTTTT 125227 v v i v - v (ATTT)n#Simpl 1 ATTTATTTATTTATTTATTTATTTATTT-ATTTATTT 36 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 12 22.45 0.00 2.70 chr6ptel1M 125192 125229 (874771) (TTATT)n#Simple_repeat 1 37 (0) m_b274s252i4 10819 chr6ptel1M 125192 TTAATTTATTTAATTACTGATTTATTTCATTTTTTTTT 125229 v v -i iv i v (TTATT)n#Simp 1 TTATTTTATTTTATT-TTATTTTATTTTATTTTATTTT 37 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 296 35.94 0.00 0.00 chr6ptel1M 128972 129099 (870901) C L1ME2z_3end#LINE/L1 (638) 553 426 m_b274s551i4 10820 chr6ptel1M 128972 AGTAGTATTCCATCATAATCTTATATGACAACTTGTGTGATCATTCTCCA 129021 ii vvvv iv ii v ivi v C L1ME2z_3end#L 553 AGTAGTATTCCATTGTATGAATATACCACAGTTTGTTTATCCATTCTCCT 504 chr6ptel1M 129022 GGTGACAGGATTCTCTGCAATTTCTAGTTCTTAGCCACCAGAAAGAGTGC 129071 v ii ivvi vv vi i i i i ii vi v iv C L1ME2z_3end#L 503 GTTGATGGACACCTGGGCTGTTTCCAGTTTTTGGCTATTATGAATAAAGC 454 chr6ptel1M 129072 AGCTACAAACATTTTTGAGTGAGTTTTT 129099 v ii i viii i C L1ME2z_3end#L 453 TGCTATGAACATTCTTGTACAAGTCTTT 426 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 51.04 CpG sites = 27, Kimura (unadjusted) = 51.04 Transitions / transversions = 1.42 (27/19) Gap_init rate = 0.00 (0 / 127), avg. gap size = 0.0 (0 / 0) 248 27.76 6.04 3.27 chr6ptel1M 129178 129326 (870674) C L1HS_3end#LINE/L1 (614) 288 136 m_b274s551i5 10821 chr6ptel1M 129178 CCAACAAT-TAATTATCTCTCAATTTTTCCATATCCTCTTCAACATTTGT 129226 i - vvi v ii v i ii i i ii C L1HS_3end#LIN 288 CCAACAGTGTAAAAGTGTTCCTATTTCTCCGCATCCTCTCCAGCACCTGT 239 chr6ptel1M 129227 CATTTTCC--CTTTCTATTCTTTTAGATAATCTTATTGGAGTAACATGAT 129274 ii i i-- i v vv -- vi v v i v i v C L1HS_3end#LIN 238 TGTTTCCTGACTTTTTAATGATT--GCCATTCTAACTGGTGTGAGATGAT 191 chr6ptel1M 129275 ATTTCCAAGTA---TTAATATGAATTTCTCTGAT--CTA-TGATGATCTA 129318 i vv i--- i v v -- i - --- C L1HS_3end#LIN 190 ATCTCATAGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGAT--- 144 chr6ptel1M 129319 GAGCCTTT 129326 v C L1HS_3end#LIN 143 GAGCATTT 136 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 34.40 CpG sites = 23, Kimura (unadjusted) = 35.50 Transitions / transversions = 1.35 (23/17) Gap_init rate = 0.07 (10 / 148), avg. gap size = 1.40 (14 / 10) 289 28.17 6.53 5.47 chr6ptel1M 129197 129395 (870605) C L1MB1_3end#LINE/L1 (647) 268 68 m_b274s551i6 10821 chr6ptel1M 129197 CAATTTTTCCATATCCTCTTCAACATTTGTCATTTTCCCTTTCTATTCTT 129246 i i vi i i i------ i i C L1MB1_3end#LI 268 CAATTTCTCCACATCCTCGCCAACACTTGTTATTTTT------TGTTTTT 225 chr6ptel1M 129247 TTAGATAAT-------CTTATTGGAGTAACATGATATTTCCA----AGTA 129285 - ------- v iv v i vi i - ----i v C L1MB1_3end#LI 224 TT-GATAATAGCCATCCTAACAGGTGTGAGGTGATATCTC-ATTGTGGTT 177 chr6ptel1M 129286 TTAATATGAATTTCTCTGATCTATGATGATCTAGAGC--CTTTTAAAAAC 129333 i v v i vvv ii v v -- v ---i C L1MB1_3end#LI 176 TTGATTTGCATTTCCCTGATGATTAGTGATGTTGAGCATCTTTTCA---T 130 chr6ptel1M 129334 ATAACTATAAATTATCTTGATTTCTTCTTTGAAAAACTGTCCATTCATTT 129383 v i viiii i vv v i i v i vv C L1MB1_3end#LI 129 ATACCTGTTGGCCATTTGTATGTCTTCTTTGGAGAAATGTCTATTCAAGT 80 chr6ptel1M 129384 CATTTATTCATT 129395 v iii C L1MB1_3end#LI 79 CCTTTGCCCATT 68 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.14 CpG sites = 30, Kimura (unadjusted) = 36.14 Transitions / transversions = 1.30 (30/23) Gap_init rate = 0.07 (14 / 198), avg. gap size = 1.71 (24 / 14) 261 19.61 0.00 0.00 chr6ptel1M 129883 129933 (870067) C DNM1r#Unknown (2137) 2525 2475 m_b274s502i0 10822 chr6ptel1M 129883 ATACACACACACATATATACATATACATACATACATATACACACATATGT 129932 i i i i i i i i i i C DNM1r#Unknown 2525 ATATATACACACATACACACATATACACACATATATACACACATACACGT 2476 chr6ptel1M 129933 G 129933 C DNM1r#Unknown 2475 G 2475 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 22.07 CpG sites = 10, Kimura (unadjusted) = 24.89 Transitions / transversions = 1.00 (10/0) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 17 16.14 0.00 0.00 chr6ptel1M 130343 130371 (869629) (T)n#Simple_repeat 1 29 (0) m_b274s252i5 10823 chr6ptel1M 130343 TTTTCTTTCTTTCTTTTTTCTTTTTTTTT 130371 i i i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 18 6.46 6.06 0.00 chr6ptel1M 130344 130376 (869624) (TTTC)n#Simple_repeat 1 35 (0) m_b274s252i6 10823 chr6ptel1M 130344 TTTCTTTCTTTCTTT-TTTCTTT-TTTTTTCCTTT 130376 - - i i (TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT 35 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.06 (2 / 32), avg. gap size = 1.00 (2 / 2) 369 31.19 1.40 5.84 chr6ptel1M 130459 130601 (869399) MIRc#SINE/MIR 10 146 (122) m_b274s601i5 10824 chr6ptel1M 130459 GTGGTGGCAGTGGCTAGAGAATGCTGGGCCTGGAGTCCAAAAGACTCATC 130508 - -- i iii i i vii ----- MIRc#SINE/MIR 10 GTGGTG-CAGTGG--AAAGAGCACTGGACTTGGAGTCAGGAAGAC----- 51 chr6ptel1M 130509 CTAAATTTCAATCTGGTCTCAGAC-CTAACTAGCTTGGTGACCCACAATA 130557 iii iv i iv v v v - v vv ivviii MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 101 chr6ptel1M 130558 AGTATATTAATTCTCCTG-GCCTCCGTTTCCCTGTCTGCAAAATG 130601 vvv iiiii - v iii i MIRc#SINE/MIR 102 AGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATG 146 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 40.72 CpG sites = 27, Kimura (unadjusted) = 42.06 Transitions / transversions = 1.80 (27/15) Gap_init rate = 0.07 (10 / 142), avg. gap size = 1.00 (10 / 10) 226 33.27 14.06 1.39 chr6ptel1M 131197 131388 (868612) C L3#LINE/CR1 (46) 4053 3838 m_b274s601i6 10825 chr6ptel1M 131197 CTTATCCAACCCATTCC--CTGAAACCAGAAGCCTTTCTGCAACA-ACCT 131243 vi -- i -- ii vi vi v i i -v C L3#LINE/CR1 4053 CTAGTCCAACC--TCCCATCCAATGCAGGAATCCCTTCTACAACATCCCT 4006 chr6ptel1M 131244 GAAAATTAATCA----GTTTCGATGTGAAGATCCCCAG-GATCAGAGG-- 131286 v v ii ---- ii viiv v i i - ivi ii -- C L3#LINE/CR1 4005 GACAAGTGGTCATCCAGCCTCTGCTTGAACACCTCCAGTGACGGGGAGCT 3956 chr6ptel1M 131287 -----------AATGCAGCCCATTGCATGTTGGGGCATCTCCAATGGTTA 131325 -----------i v v v v i v ii v C L3#LINE/CR1 3955 CACTACCTCNCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGATTGTTA 3906 chr6ptel1M 131326 TAG----CTGACCTTCTACAGAAATGATG-CTGCGTTCATCTAAGTCCC- 131369 v i---- v- v iv ivi vi- v i v v v i - C L3#LINE/CR1 3905 GAAAGTTCTT-CCTTATATTGAGCCGAAATCTGCCTCCCTGTAACTTCCA 3857 chr6ptel1M 131370 CCTTTTATTTCTAGTTCTG 131388 iv iv i C L3#LINE/CR1 3856 CCCATTGGTCCTAGTTCTG 3838 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 42.31 CpG sites = 34, Kimura (unadjusted) = 45.16 Transitions / transversions = 1.17 (34/29) Gap_init rate = 0.06 (12 / 191), avg. gap size = 2.50 (30 / 12) 254 24.98 5.13 2.50 chr6ptel1M 131451 131528 (868472) Charlie1#DNA/hAT-Charlie 28 107 (2674) m_b274s502i1 10826 chr6ptel1M 131451 ACCTCTCATGGTCACCAAGACCACAAGTCAGGAAGTATGTAAGTTCAAAG 131500 i viv v i vi--v ii vi ii v i Charlie1#DNA/ 28 ACCCCTGGGGGTCCCCGAGACCCT--TTCAGGGGGTCCGCGAGGTCAAAA 75 chr6ptel1M 131501 CTATTTCC-TAATAATACTAAAA---TATTTG 131528 i - i --- Charlie1#DNA/ 76 CTATTTTCATAATAATACTAAGACGTTATTTG 107 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 25.43 CpG sites = 12, Kimura (unadjusted) = 31.29 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.05 (4 / 77), avg. gap size = 1.50 (6 / 4) 243 22.44 0.00 3.45 chr6ptel1M 131584 131643 (868357) DNM1r#Unknown 2489 2546 (2116) m_b274s502i2 10827 chr6ptel1M 131584 TATATATGTAAATGTGTATGTGTGTGTGTGTGTGTGTATATATAAATACA 131633 i-- i i i i i i v i DNM1r#Unknown 2489 TATATATGTG--TGTATATGTGTGTATGTGTGTATATATGTGTATATATA 2536 chr6ptel1M 131634 CACACATACA 131643 ii i? i DNM1r#Unknown 2537 CGTATNTATA 2546 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 27.02 CpG sites = 12, Kimura (unadjusted) = 29.76 Transitions / transversions = 12.00 (12/1) Gap_init rate = 0.03 (2 / 59), avg. gap size = 1.00 (2 / 2) 778 19.27 10.11 2.80 chr6ptel1M 131666 131932 (868068) Charlie1#DNA/hAT-Charlie 2410 2695 (86) m_b274s502i3 10828 chr6ptel1M 131666 TATACTTCAACCAAGAGAACATATTGAAACAATCTGAATATAGAAACAGT 131715 i v i v ivi ii i v Charlie1#DNA/ 2410 TATACTTCAACCAAAACAACATATCGCAACAGATTGAATGCAGAAGCAGA 2459 chr6ptel1M 131716 TATGATAATCCAATGTTCTTCCATTAACCTAGATAATAAAGAGATTTGCA 131765 v iivv i v i i v Charlie1#DNA/ 2460 TATGAGAATCCAGCTGTCTTCTATTAAGCCAGACATTAAAGAGATTTGCA 2509 chr6ptel1M 131766 AAAATATGTAAAACAATGCCA---TTCTCAC-------TTTTTTTTTAGA 131805 -- --- ------- v i Charlie1#DNA/ 2510 AAA--ATGTAAAACAATGCCACTCTTCTCACTAAATTTTTTTGTTTTGGA 2557 chr6ptel1M 131806 A---ATAA--AATTTTCATA------------TTATGTTAACACATACTA 131838 --- i-- v ------------ ii v i Charlie1#DNA/ 2558 AAATATAGTTATTTTTCATAAAAATATGTTATTTATGTTAACATGTAATG 2607 chr6ptel1M 131839 GGTTTATTATTTATTATATACAAATGAATTTATAAATACATATTTAAAGT 131888 - --- vi v -- v v i Charlie1#DNA/ 2608 GGTTTATTA-TTATT---TTTAAATGAATTAATAAAT--ATTTTAAAAAT 2651 chr6ptel1M 131889 TATTCCATTTTTAGAGATAATAAGGTAAATATTAGTATATGTAA 131932 vi vi v vvvv v iii v i Charlie1#DNA/ 2652 TTCTCAGTTTTAATTTCTAATACGGTAAATATCGATAGATATAA 2695 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 21.43 CpG sites = 25, Kimura (unadjusted) = 22.46 Transitions / transversions = 1.00 (25/25) Gap_init rate = 0.05 (13 / 266), avg. gap size = 2.69 (35 / 13) 250 18.52 5.56 0.00 chr6ptel1M 131934 131987 (868013) C MER63C#DNA/hAT-Tip100 (0) 930 874 m_b274s502i4 10829 chr6ptel1M 131934 CAGGGGTATTCTGATAAATGTTTAATAACTGGTTCTCT--GCAAAGACAT 131981 v i v i i i i -- v i v C MER63C#DNA/hA 930 CAGTGGTGTGCTGGTAAATGTTTAACAACCGGCTCTCTGGGGAAAAAAAT 881 chr6ptel1M 131982 G-ATGTA 131987 - C MER63C#DNA/hA 880 GTATGTA 874 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 19.26 CpG sites = 6, Kimura (unadjusted) = 21.58 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.04 (2 / 53), avg. gap size = 1.50 (3 / 2) 339 23.75 0.00 0.00 chr6ptel1M 131976 132055 (867945) C MER63D#DNA/hAT-Tip100 (587) 474 395 m_b274s502i5 10829 chr6ptel1M 131976 AGACATGATGTACTTTTAAGTTGTATTTCAATTAAAAACTTTTTTTCCAT 132025 i iii vv i vv vv v i C MER63D#DNA/hA 474 AGACACGACACACTTTTAAGTTTAATCTGCATTATTAACATTTTCTCCAT 425 chr6ptel1M 132026 CTCTTTCTTGAGTTTAAGCAATCAGCAAAA 132055 v i i ii i C MER63D#DNA/hA 424 CACTTTCTTAAGTCTAGACAATCAACAAAA 395 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 27.31 CpG sites = 11, Kimura (unadjusted) = 29.08 Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.00 (0 / 79), avg. gap size = 0.0 (0 / 0) 328 22.61 13.82 2.94 chr6ptel1M 132283 132405 (867595) L2a_3end#LINE/L2 380 515 (2) m_b274s601i7 10830 chr6ptel1M 132283 TTTGTCTACATCCCTATTAGGAATGGAAGTTCCCTAAAGGGAGAGACTTT 132332 i v -- i i - v i v i i v i L2a_3end#LINE 380 TCTGTCTCC--CCCCACTAG-AATGTAAGCTCCATGAGGGCAGGGACTTT 426 chr6ptel1M 132333 T---TGTTTCAACTCATTAGT-TA---ACATCACC---AACAG------- 132365 --- ii-i i iv - ---v v i --- ------- L2a_3end#LINE 427 TGTCTGTTTTG-TTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGG 475 chr6ptel1M 132366 CACACAGTAGGAGCTTAATAAACATTTGTTAAGTTAATGA 132405 i v i i i i v L2a_3end#LINE 476 CACATAGTAGGCGCTCAATAAATATTTGTTGAATGAATGA 515 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 26.65 CpG sites = 18, Kimura (unadjusted) = 27.85 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.07 (9 / 122), avg. gap size = 2.33 (21 / 9) 21 4.17 0.00 0.00 chr6ptel1M 132886 132910 (867090) (A)n#Simple_repeat 1 25 (0) m_b274s252i7 10831 chr6ptel1M 132886 AAAAAAAAAAAAAAAAAAAAAAGAA 132910 i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAA 25 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 20 15.86 0.00 0.00 chr6ptel1M 134352 134386 (865614) (TA)n#Simple_repeat 1 35 (0) m_b274s252i9 10832 chr6ptel1M 134352 TATATGTACTTTTAAATATATATATATATATATAT 134386 i iv v v (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATAT 35 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 16 29.94 0.00 3.12 chr6ptel1M 134352 134417 (865583) (TATATG)n#Simple_repeat 1 64 (0) m_b274s252i8 10833 chr6ptel1M 134352 TATATGTACTTTTAAATATATATATATATATATATGTGTGTGTGTGTATA 134401 iv v v i i i i i i i i (TATATG)n#Sim 1 TATATGTATATGTATATGTATATGTATATGTATATGTATATGTATATGTA 50 chr6ptel1M 134402 CCATTGTATTTGAATA 134417 -i - v v (TATATG)n#Sim 51 -TA-TGTATATGTATA 64 Matrix = Unknown Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.03 (2 / 65), avg. gap size = 1.00 (2 / 2) 184 26.54 0.00 2.04 chr6ptel1M 134626 134675 (865325) C MIR3#SINE/MIR (0) 208 160 m_b274s601i8 10834 chr6ptel1M 134626 GAGTCAAAAAATCACAGAATAATGGAACTGGAAGGGGTCCTAGAACATCA 134675 i v i i ivii i ii i i- C MIR3#SINE/MIR 208 GAATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAG-ATCA 160 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.78 CpG sites = 11, Kimura (unadjusted) = 35.78 Transitions / transversions = 5.50 (11/2) Gap_init rate = 0.02 (1 / 49), avg. gap size = 1.00 (1 / 1) 17 0.00 0.00 0.00 chr6ptel1M 135271 135289 (864711) (T)n#Simple_repeat 1 19 (0) m_b274s252i10 10835 chr6ptel1M 135271 TTTTTTTTTTTTTTTTTTT 135289 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 262 25.61 10.98 0.00 chr6ptel1M 135331 135412 (864588) MIR3#SINE/MIR 23 113 (95) m_b274s601i9 10836 chr6ptel1M 135331 AGAGT-CAGCCTGGGAACCAGGAAGCCTGGGTTTCAGACCTAATTC---- 135375 i- i v ii ii ii v iiii ---- MIR3#SINE/MIR 23 AGAGCACGGACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCC 72 chr6ptel1M 135376 -CT-ACTGGCAGTGCCACC-TGAGTAAGCCACTT-ACTTCT 135412 - - ? v iv - i i i - i MIR3#SINE/MIR 73 ACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCT 113 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.03 CpG sites = 17, Kimura (unadjusted) = 34.26 Transitions / transversions = 4.25 (17/4) Gap_init rate = 0.07 (6 / 81), avg. gap size = 1.50 (9 / 6) 287 30.29 4.00 0.97 chr6ptel1M 135843 135942 (864058) C MIRc#SINE/MIR (82) 186 84 m_b274s601i10 10837 chr6ptel1M 135843 AACAACACAGTGAAGTAG-CTGGGCTGACCATTAGCGTTTTCCCTTTACA 135891 v v i - v v ii- vii iii vi C MIRc#SINE/MIR 186 AACAACCCTGTGAGGTAGGCAGGGCAGGT-ATTATTATCCCCATTTTACA 138 chr6ptel1M 135892 AAAAAGGAAACTGAAACCCAGAGACACTG---GACCTGCCCATGCTTGCA 135938 i vi ii i vii i--- i v v ii C MIRc#SINE/MIR 137 GATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACA 88 chr6ptel1M 135939 CAGC 135942 C MIRc#SINE/MIR 87 CAGC 84 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 40.81 CpG sites = 20, Kimura (unadjusted) = 40.81 Transitions / transversions = 2.00 (20/10) Gap_init rate = 0.03 (3 / 99), avg. gap size = 1.67 (5 / 3) 588 33.61 0.38 2.69 chr6ptel1M 136639 136904 (863096) HERV4_I#LTR/ERV1 1007 1266 (5273) m_b274s701i1 10838 chr6ptel1M 136639 TCTCTTCCATCCCTAGAGATTCTCCATTGGGCTATCTCTTAAGAAATAGG 136688 v -- --- i ii v iiv i v ivv v HERV4_I#LTR/E 1007 TCTATTCCA--CCT---GATTCCCCGCTTGGCTGCATCCTCAACCATTGG 1051 chr6ptel1M 136689 AACAAATTTGGCTTAAAAGACTTAAAATCGAAAAGGT-TCATCCATTTTT 136737 iv i iivi vi ii ii-v v - v iiv i HERV4_I#LTR/E 1052 AATCAATTTGACCCTGACAATCTAAGG-AGAAAACGTNTGATTTTTTTCT 1100 chr6ptel1M 136738 GTAATTACTGTCTGGCCTGAGTATAAGTTAGACAACCATGAGGCATGGCC 136787 i - i iv ? ? i i?? i v ivv v HERV4_I#LTR/E 1101 GCAAT-ACTGTTTGGCCCCANTATNAGCTGNNCAGCCAGGAACAATGGGC 1149 chr6ptel1M 136788 AGTTAATGTCTCTATCAATTTCATTACTATTAGAGAATTGGACTTGTTTT 136837 i i vivviv i viivi i ivviv i i i HERV4_I#LTR/E 1150 GGTCAATGGTAGCCTTAATTATGACACCATCCTGCAATTAGACCTATTTT 1199 chr6ptel1M 136838 GCAAGAAACAAGAGAAATGGATGGAAATTCCTTATATCCAGGACTTCATG 136887 ii i iv vii i v i v v HERV4_I#LTR/E 1200 GCAAGAGGCAGGGCAAATGGTCAGAAATCCCATATGTACAGGCCTTCATG 1249 chr6ptel1M 136888 GTCCTTTCCCAGAATCC 136904 i v v i i HERV4_I#LTR/E 1250 GCCCTATACCAAAACCC 1266 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 45.88 CpG sites = 52, Kimura (unadjusted) = 47.41 Transitions / transversions = 1.49 (52/35) Gap_init rate = 0.03 (8 / 265), avg. gap size = 1.00 (8 / 8) 36 2.70 0.00 0.00 chr6ptel1M 137204 137241 (862759) (CCT)n#Simple_repeat 1 38 (0) c_b274s251i1 10839 chr6ptel1M 137204 CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTTCTCCTCC 137241 i (CCT)n#Simple 1 CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC 38 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 26 13.32 0.00 3.92 chr6ptel1M 137242 137294 (862706) (ACC)n#Simple_repeat 1 51 (0) m_b274s252i11 10840 chr6ptel1M 137242 ACCACCACCCACCACCACCACCACCACCATCACTCACTCCCTCCACCCCC 137291 - i - iv v v (ACC)n#Simple 1 ACCACCA-CCACCACCACCACCACCACCACCAC-CACCACCACCACCACC 48 chr6ptel1M 137292 TCC 137294 v (ACC)n#Simple 49 ACC 51 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.00 (2 / 2) 408 27.97 8.47 0.00 chr6ptel1M 137986 138103 (861897) L2d2_3end#LINE/L2 422 549 (6) m_b274s601i11 10841 chr6ptel1M 137986 TTGTCTTCCTTGTTAAATTATAAGCTTTTTGAGGCTAGGGTTTGTCTCTT 138035 i ivii i i ii vi viii v L2d2_3end#LIN 422 TTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTT 471 chr6ptel1M 138036 GC-CTTTTTTGTATCCCT---------TAACACAGTGCCTGGTGCATATT 138075 ii- i i--------- i v ii i v L2d2_3end#LIN 472 ATACTTCTTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAGT 521 chr6ptel1M 138076 AAGAGCTTAATAAATACTGATTGAATTG 138103 i v i i vi v L2d2_3end#LIN 522 AGGCGCTCAATAAATATTTGTTGATTTG 549 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.13 CpG sites = 24, Kimura (unadjusted) = 37.13 Transitions / transversions = 2.67 (24/9) Gap_init rate = 0.02 (2 / 117), avg. gap size = 5.00 (10 / 2) 354 21.11 2.20 1.09 chr6ptel1M 138489 138579 (861421) C L1MC1_3end#LINE/L1 (862) 218 127 m_b274s551i7 10842 chr6ptel1M 138489 TTGTCCAATTTGAGAGGTGTGTAGTAATACATCAGAGT-GTCTTAATTTG 138537 v v i i v ii iv vv - i C L1MC1_3end#LI 218 TTGGCCATTCTAATAGGTGTGTAGTGGTATCTCATTGTTGTTTTAATTTG 169 chr6ptel1M 138538 CATTTTTCTGATCA-ATGGTAATTTGAAGCATCTTTTCATATG 138579 ii v - i- i v i C L1MC1_3end#LI 168 CATTTCCCTGATGACATA-TGATGTGGAGCATCTTTTCATATG 127 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 25.17 CpG sites = 11, Kimura (unadjusted) = 25.17 Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.03 (3 / 90), avg. gap size = 1.00 (3 / 3) 277 27.82 15.04 0.00 chr6ptel1M 144421 144553 (855447) PRIMA4-int#LTR/ERV1 4804 4956 (3314) m_b274s701i2 10843 chr6ptel1M 144421 CCAGGCTGGTCAGTTAAGAAAAGACAAAGG-ATGAATATCTGCACCCAGA 144469 ii v i iiv i v-ii i i i iv v PRIMA4-int#LT 4804 CCGAGCTTGTCAATTGGCAAAAGACAAGGCTGCGAACATTTACACTGACA 4853 chr6ptel1M 144470 GC-------------AGGTAGCCC-TGACTTTAGGGTGCTAGGGAAACAT 144505 -------------i v i - i i v v v PRIMA4-int#LT 4854 GCCGCTATGCNTTTGGGGTTGCTCATGACTTTGGGATGCTATGGAAAGAG 4903 chr6ptel1M 144506 -TAGGACCT----CCTCCTCAGGACAATCCATTAAAAACCAAAAACAGGG 144550 -v iv ---- i i v ivi v i v PRIMA4-int#LT 4904 AGAGGATATTTAACCTCCTCAGGGCAACCCATAAAAAATGGACAACAAGT 4953 chr6ptel1M 144551 ATC 144553 PRIMA4-int#LT 4954 ATC 4956 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.33 CpG sites = 22, Kimura (unadjusted) = 35.70 Transitions / transversions = 1.47 (22/15) Gap_init rate = 0.04 (5 / 132), avg. gap size = 4.00 (20 / 5) 368 32.40 1.11 0.55 chr6ptel1M 145074 145253 (854747) ERV24_Prim#LTR/ERV1 4987 5167 (2408) m_b274s701i3 10843 chr6ptel1M 145074 GGCCACTTTCCTCTCCCAGATGTTCCCTTTCAAACCTGACAGAAGGACCT 145123 i i i v v vi i iv iiiv i i?v ii ERV24_Prim#LT 4987 GGTCATTTTCCTTTACCAGAAGGCCCTTTCGAGGTATGGCAANTGGATTT 5036 chr6ptel1M 145124 TCATTCAATTGCCAGCTGCCCGTGGTTCCAAATATGCTTTGGGGATGGTC 145173 - ii iv vv ? iv v v i i i i ? v? i ERV24_Prim#LT 5037 T-ATTCAGCTGCCGCCATCNCAAGGATACGAGTATGTTCTNGTNATGGTT 5085 chr6ptel1M 145174 TGTATACTTTCCCGCTGGGTGGCAAAGTTCCCCT-CATATT-GCCACAGC 145221 ii i ii i v ivi i ? - v vv- ? i ERV24_Prim#LT 5086 TGTATGTTTTCTCATTGGGTAGAAGCATTTCCNTGCAGAAGAGCNACGGC 5135 chr6ptel1M 145222 CTCTGGGCTAGCAAAAATCCTCTTAGAAAAAA 145253 iv viv vv i ? ERV24_Prim#LT 5136 CTTAGCAGTAGGTAAAATTCTNTTAGAAAAAA 5167 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 42.32 CpG sites = 35, Kimura (unadjusted) = 46.68 Transitions / transversions = 1.52 (35/23) Gap_init rate = 0.02 (3 / 179), avg. gap size = 1.00 (3 / 3) 288 32.30 0.00 2.36 chr6ptel1M 145283 145412 (854588) L1ME1_3end#LINE/L1 449 575 (351) m_b274s551i8 10844 chr6ptel1M 145283 TGGCAGCTCTTTGTGCAGTCATAAAGAACTGGAAAATAAGTAGATGTCTA 145332 i i v vi i i viiv i vv vvi i i L1ME1_3end#LI 449 TAGCAGCTTTATTCGTAATAGCCAAAAACTGGAAACAACCCAAATGTCCA 498 chr6ptel1M 145333 TCGATTGGGGAATGGAGGAACAACTTGTGGTTCATGAAAGCAATGAAATG 145382 i i? v vi v vi vv vi i -- L1ME1_3end#LI 499 TCAACNGGTGAATGGATAAACAAATTGTGGTATATCCATACAATGGAA-- 546 chr6ptel1M 145383 TTATTGCTCTGTAAAAATAAGGAATGGGCT 145412 - i i v i v v i ii L1ME1_3end#LI 547 -TACTACTCAGCAATAAAAAGGAACGAACT 575 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.05 CpG sites = 23, Kimura (unadjusted) = 43.87 Transitions / transversions = 1.28 (23/18) Gap_init rate = 0.02 (3 / 129), avg. gap size = 1.00 (3 / 3) 13 14.17 3.23 0.00 chr6ptel1M 146734 146764 (853236) (GGGCTG)n#Simple_repeat 1 32 (0) m_b274s252i12 10845 chr6ptel1M 146734 GGGATGGGGCT-GGGCAAGGGATGGGGCTGGG 146764 v - vi v (GGGCTG)n#Sim 1 GGGCTGGGGCTGGGGCTGGGGCTGGGGCTGGG 32 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.03 (1 / 30), avg. gap size = 1.00 (1 / 1) 16 19.09 0.00 0.00 chr6ptel1M 148955 148984 (851016) (AC)n#Simple_repeat 1 30 (0) m_b275s252i0 10846 chr6ptel1M 148955 ACAGACAGATATACACACGCACACACACAC 148984 v v i i i (AC)n#Simple_ 1 ACACACACACACACACACACACACACACAC 30 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 15 0.00 0.00 0.00 chr6ptel1M 150853 150869 (849131) (TC)n#Simple_repeat 1 17 (0) m_b275s252i1 10847 chr6ptel1M 150853 TCTCTCTCTCTCTCTCT 150869 (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCT 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 292 25.93 8.49 1.77 chr6ptel1M 152025 152130 (847870) MIR3#SINE/MIR 85 197 (11) m_b275s601i0 10848 chr6ptel1M 152025 TATGACCTTTGGGCAAATCCCTTC-----TTTGTGTTTCAGTTTCTTC-- 152067 i - i v ----- i v ii i -- MIR3#SINE/MIR 85 TGTGACCTT-GGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCAT 133 chr6ptel1M 152068 CTGTAAATTGGAAGGGGTTGAACT-CATTCCTTCTGAAGGATCTTTCAGC 152116 v - i i -v vvii i i vvi i MIR3#SINE/MIR 134 CTGTAAAAT-GAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGC 182 chr6ptel1M 152117 CCC-ACATCTTCTGA 152130 i i- ii v MIR3#SINE/MIR 183 TCTGACATTCTATGA 197 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.09 CpG sites = 18, Kimura (unadjusted) = 33.09 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.06 (6 / 105), avg. gap size = 1.83 (11 / 6) 11 13.59 2.78 5.71 chr6ptel1M 152542 152577 (847423) (CCTTT)n#Simple_repeat 1 35 (0) m_b275s252i2 10849 chr6ptel1M 152542 CCTTTCCTTTTCCTTTTCCTGTCAACTCC-TTCCTTT 152577 - - v vvi - (CCTTT)n#Simp 1 CCTTTCC-TTTCC-TTTCCTTTCCTTTCCTTTCCTTT 35 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.09 (3 / 35), avg. gap size = 1.00 (3 / 3) 355 34.03 1.37 1.37 chr6ptel1M 153130 153275 (846725) C MIR#SINE/MIR (64) 198 53 m_b275s601i1 10850 chr6ptel1M 153130 TATTATGTCCTTTTAACCTCATCTTAACATTTCAAGTCAGGTGACATTGT 153179 vv v v v ivvi vi vii vi ivi i C MIR#SINE/MIR 198 TATTAACTCATTTAATCCTCACAACAACCCTATGAGGTAGGTACTATTAT 149 chr6ptel1M 153180 TATCCCCATTTCAGAGTTGAGGAAACAGGAAAACAATCAGAATTTCATTG 153229 i v v v iiiv i-- iv v v i C MIR#SINE/MIR 148 TATCCCCATTTTACAGATGAGGAAACTGAGGCACAG--AGAGGTTAAGTA 101 chr6ptel1M 153230 ACTTACCCAGAGGTACACAGTTAGCAACC--CAGGTTTGGGATCAGAA 153275 i ii vi i i vi-- ivii iv C MIR#SINE/MIR 100 ACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAA 53 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 45.33 CpG sites = 27, Kimura (unadjusted) = 46.63 Transitions / transversions = 1.23 (27/22) Gap_init rate = 0.02 (3 / 145), avg. gap size = 1.33 (4 / 3) 249 32.00 9.60 0.00 chr6ptel1M 153877 154001 (845999) C L2b_3end#LINE/L2 (1) 465 329 m_b275s601i2 10851 chr6ptel1M 153877 TTCTTCTAGTCAGAAAATA---ATTAGGGGCCTGCTACATGGCAGTCTTT 153923 v ii v iv --- i ii v i iii v v ?i C L2b_3end#LINE 465 TTCATTCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCT 416 chr6ptel1M 153924 G-GCTAAACACCGGGAACACAAAGA--GATGTGAGGGACATCG--CCTGT 153968 - ii i i i i iv i--i iiv vi ?iv -- i C L2b_3end#LINE 415 GTGCTAGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGC 366 chr6ptel1M 153969 CCTGATGGAGGTCACAG---AGT-GGCGAGGCAGACA 154001 v i v --- - v i C L2b_3end#LINE 365 CCTCACGGAGCTCACAGTCTAGTGGGGGAGACAGACA 329 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 40.68 CpG sites = 27, Kimura (unadjusted) = 45.28 Transitions / transversions = 2.08 (27/13) Gap_init rate = 0.05 (6 / 124), avg. gap size = 2.00 (12 / 6) 419 30.99 7.69 4.26 chr6ptel1M 154173 154354 (845646) C MIRb#SINE/MIR (64) 204 17 m_b275s601i3 10852 chr6ptel1M 154173 TGCATTGTCTTATTTCATCCTCATGAGAACCAGAGGACTTAGGTGCTATT 154222 i i v ii v vviv vv --- C MIRb#SINE/MIR 204 TGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGT---ATT 158 chr6ptel1M 154223 ACTATGTCCATTTTACAGATAAAGAAACTGAATCTAACACAGGTCCTATC 154272 i vi i i iv v v v ivvi v C MIRb#SINE/MIR 157 ATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTA 108 chr6ptel1M 154273 ACTTG-----AATTGCAAGGTT---------CTGAGGTGGGATTAAAACC 154308 -----ii ii vi i --------- v vi vi C MIRb#SINE/MIR 107 ACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACC 58 chr6ptel1M 154309 CTGGGCTTCTTGATTCAAGGCCCTAACCCACATTCTATCCACTGTA 154354 v v vii i v i----- i iiii v i C MIRb#SINE/MIR 57 CAGGTCTGTCTGACTCCAA-----AGCCCGTGCTCTTTCCACTGCA 17 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.12 CpG sites = 30, Kimura (unadjusted) = 41.03 Transitions / transversions = 1.25 (30/24) Gap_init rate = 0.06 (10 / 181), avg. gap size = 2.20 (22 / 10) 16 0.00 0.00 0.00 chr6ptel1M 154498 154514 (845486) (A)n#Simple_repeat 1 17 (0) m_b275s252i3 10853 chr6ptel1M 154498 AAAAAAAAAAAAAAAAA 154514 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 20 16.66 0.00 0.00 chr6ptel1M 155266 155299 (844701) (A)n#Simple_repeat 1 34 (0) m_b275s252i4 10854 chr6ptel1M 155266 AAATACAAAAAAAAAAAAACAAAAACAAAAACAA 155299 v v v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 34 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 38 0.00 0.00 0.00 chr6ptel1M 155860 155892 (844108) (GT)n#Simple_repeat 1 33 (0) c_b275s251i0 10855 chr6ptel1M 155860 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 155892 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 33 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 17 22.79 0.00 0.00 chr6ptel1M 155913 155948 (844052) (T)n#Simple_repeat 1 36 (0) m_b275s252i5 10856 chr6ptel1M 155913 TTTATTGTTTGCTCTTTTCTTTCTTTTTTTTTTTTT 155948 v v vi i i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 36 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 601 33.22 2.83 2.51 chr6ptel1M 157712 158029 (841971) L1ME4c_3end#LINE/L1 237 555 (275) m_b275s551i0 10857 chr6ptel1M 157712 TAACCAATG-TGGAAAGGCTTTTGGGGGAAACCTGGGATGCTAATGTATT 157760 v - vi ? --- v vi v v i? v ii L1ME4c_3end#L 237 TACCCAATGCTGGCGAGGNT---GCGGTGAAACTGGTACNCTCATACATT 283 chr6ptel1M 157761 ATTGGTGGGATTATGAACGGATCCAATCATTCTGTCAAGCAATGTGGAAC 157810 ii v ? i i iv i v i v i vv v v v L1ME4c_3end#L 284 GCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGGCAA 333 chr6ptel1M 157811 TATGC-CCAACGACTATCAAAAGGTACATATCCTTTGCTCTAGCAATGTT 157859 i i-i vii i v v v i vi i i vii L1ME4c_3end#L 334 TACGTATCAAGAGCCATAAAAATGTTCATACCCTTTGACCCAGTAATTCC 383 chr6ptel1M 157860 TCTCCTGGG--CTTATTTGCCAAAGAGAT---CCTAAAGGAGTAAAAGGG 157904 v i --i i-- i i i ---i v i v i - L1ME4c_3end#L 384 ACTTCTGGGAATTTATC--CTAAGGAAATAATTCAAAAGAAGGAAAAAG- 430 chr6ptel1M 157905 ACCCACAGGTGCAGAAATGTTT-CTCCAGCCGTATTTGTAGTGGCAAGAA 157953 -- i i v ii ii i i-i v vv i i i i i L1ME4c_3end#L 431 --CTATATGCACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAA 478 chr6ptel1M 157954 ATTGGAAATTGAGTGGATGCCCATCAGCTGGGAAAT-ACTGAATAAGTTA 158002 ivivv ii i v iiv i -ii i i i L1ME4c_3end#L 479 ATTGGAAACAACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTA 528 chr6ptel1M 158003 TAGCACATTAATGTTGTGGAATATTAT 158029 i i i? ivivi L1ME4c_3end#L 529 TGGTACATCNACTCGATGGAATATTAT 555 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 44.05 CpG sites = 67, Kimura (unadjusted) = 47.25 Transitions / transversions = 1.86 (67/36) Gap_init rate = 0.04 (14 / 317), avg. gap size = 1.21 (17 / 14) 238 35.64 4.72 4.72 chr6ptel1M 157758 158075 (841925) L1PB1_3end#LINE/L1 281 598 (300) m_b275s551i1 10857 chr6ptel1M 157758 ATTATTGGTGGGATTATGAACGGATCCAATCATTCTGTCAAGCAATGTGG 157807 i ii v i i vii v i i v vv i i L1PB1_3end#LI 281 ACTGCTGGTGGGAATGTAAACTAGTACAACCACTATGGAAAACAGTGTGG 330 chr6ptel1M 157808 AACTATGCCCAACGACTATCAAAAGGTACA--TATCCTTTGCTCTAGCAA 157855 iv - v ii v -- ii - v -- i v v i L1PB1_3end#LI 331 AGAT-TCCTTAAAGA--ACTAAAA-GTAGAACTACCATTTGATCCAGCAA 376 chr6ptel1M 157856 TGTTTCTCCTGGGCTTATTTGCC-------AAAGAGATC-CTAAAGGAGT 157897 viiv v -- i i ------- ii -i v v -- L1PB1_3end#LI 377 TCCCACTACTGGG--TATCTACCCAGAGGAAAAGAAGTCATTATACGA-- 422 chr6ptel1M 157898 AAAAGGGACCCACAGGTGCAGAAATGTTTCT-CCAGCCGTATTTGTAGTG 157946 iv iii vii ---- v -v vvv i i i v L1PB1_3end#LI 423 AAAAGATACTTGCACACGC----ATGTTTATAGCAGCACAATTCGCAATT 468 chr6ptel1M 157947 GCAAGAAATTGGAAATTGAGTGGATGCCCATCAGCTGGGAAATAC-TGAA 157995 i vv viv vviii iiiiivi i iv- i L1PB1_3end#LI 469 GCAAAAATATGGAACCAGCCCAAATGCCCATCAATCAACGAGTGGATAAA 518 chr6ptel1M 157996 TAAGTTATAGCACATTAATGTTGTGGAATATTATTACTCTAT---AAGGA 158042 v i? i i i i vv iiii i i vvv i --- L1PB1_3end#LI 519 GAAANTGTGGTATATATATACCATGGAATACTACTCAGCCATAAAAAGGA 568 chr6ptel1M 158043 GTGATCAGCAAGATGATTCCACAGAGGCCTGGA 158075 i -- ?i vivv - i v i L1PB1_3end#LI 569 ATGA--ANTAATGGCATT-CGCAGCGACCTGGA 598 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 48.43 CpG sites = 65, Kimura (unadjusted) = 51.17 Transitions / transversions = 1.51 (65/43) Gap_init rate = 0.07 (21 / 317), avg. gap size = 1.43 (30 / 21) 16 23.41 8.33 0.00 chr6ptel1M 158389 158448 (841552) (TA)n#Simple_repeat 1 65 (0) m_b275s252i6 10858 chr6ptel1M 158389 TATAAATATGTATGCATATAT-TGGATTTA-AGATATATAT-TTTACA-A 158434 v i ii - iv v - v - v i - (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr6ptel1M 158435 TGTTTA-ATATATAT 158448 i v - (TA)n#Simple_ 51 TATATATATATATAT 65 Matrix = Unknown Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.08 (5 / 59), avg. gap size = 1.00 (5 / 5) 13 27.69 1.85 1.85 chr6ptel1M 159140 159193 (840807) (TTCTTT)n#Simple_repeat 1 54 (0) m_b275s252i7 10859 chr6ptel1M 159140 TTCTTTTTCTTTTT-TTTTCCTCATGGCTTTTACCTTGTGTTAGGATTTT 159188 - i -v vv v i v v vvvv (TTCTTT)n#Sim 1 TTCTTTTTCTTTTTCTTTTTCT-TTTTCTTTTTCTTTTTCTTTTTCTTTT 49 chr6ptel1M 159189 TCTTT 159193 (TTCTTT)n#Sim 50 TCTTT 54 Matrix = Unknown Transitions / transversions = 0.20 (2/10) Gap_init rate = 0.04 (2 / 53), avg. gap size = 1.00 (2 / 2) 11 21.55 2.50 2.50 chr6ptel1M 164205 164244 (835756) (CTTCAAA)n#Simple_repeat 1 40 (0) m_b275s252i8 10860 chr6ptel1M 164205 CTTCAAACTTCATCACTGC-CTGATGAAACTTCAAACTTCA 164244 -v v -vvvv v (CTTCAAA)n#Si 1 CTTCAAACTTCA-AACTTCAAACTTCAAACTTCAAACTTCA 40 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 261 27.37 3.06 3.06 chr6ptel1M 164253 164350 (835650) C L1MD_orf2#LINE/L1 (2830) 464 367 m_b275s551i2 10861 chr6ptel1M 164253 CTATCTAGTTCTGAGAAGGCAAGGTTGAGATCTGCCACTACTAGAGTTGT 164302 v v v ii viiv ii - -- v i C L1MD_orf2#LIN 464 CTATCAATTGCTGAGAGAGGGGTGTTGAAGTCT-CCA--ACTATAATTGT 418 chr6ptel1M 164303 G---CTGTCTATTTCTTCTTGCAGCTCTCTTAACTTCTCCTTTAGGAATT 164349 ---i i v i v i ii i v i v v C L1MD_orf2#LIN 417 GGATTTGTCTATTTCTCCTTTCAGTTCTATCAGTTTTTGCTTCACGTATT 368 chr6ptel1M 164350 T 164350 C L1MD_orf2#LIN 367 T 367 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 34.83 CpG sites = 15, Kimura (unadjusted) = 34.83 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.04 (4 / 97), avg. gap size = 1.50 (6 / 4) 1225 27.14 4.35 4.53 chr6ptel1M 164958 165532 (834468) L1ME5_3end#LINE/L1 87 660 (281) m_b275s551i3 10862 chr6ptel1M 164958 CAGACAATTTTCAGATGATGAAATT-GAAA--CTATTTCTACCCATATGA 165004 i v v v ii- -- ---vi vv L1ME5_3end#LI 87 CAGGCAATTTACAGAAGAGGAAACCCGAAAGGCTA---ACAAGCATATGA 133 chr6ptel1M 165005 AAAGGTGTTCTAAATCATTATTGATCAGATAAATGCAAATTAAGACAATT 165054 i i i v v v i v i iv L1ME5_3end#LI 134 AGAGATGCTCAAACTCATTAGTAATCAGAGAAATGCAAATTAAAACAACA 183 chr6ptel1M 165055 CTGAGATACCACTACACACCTCTAAGATTGGCTAAAATGATAGGAAA--A 165102 v i vi v v i v -- i i--i L1ME5_3end#LI 184 ATGAGATATCACTTTACACCTATTAGACTGGCAAAAAT--TAGAAAGCTG 231 chr6ptel1M 165103 GATGATG---AATGTTGGAGGGAATGTGGGAAAACTCGGGCACTAATTCA 165149 i --- i v i i i ? ivv ii v v v L1ME5_3end#LI 232 GATAATGCCAAGTGTTGGCGAGGATGTGGGGANATAGGAACCCTCATGCA 281 chr6ptel1M 165150 TTGTTGGTGG-AGTTTTGAATGGATCCAACCATTCTGGAGAGCAATTTGG 165198 i i - v v v - v i i L1ME5_3end#LI 282 CTGCTGGTGGGAGTGTAGACTGG-TGCAGCCATTCTGGAGAGCAATCTGG 330 chr6ptel1M 165199 AACTA--TAGTCAAA--AAGTTATCAAACTGTGCATAACCTTTGATCCAG 165244 v v -- -- - --- --- v v i L1ME5_3end#LI 331 CAGTACTTAGTCAAATTAAGT-AT---AC---GCATACCCTATGACCCAG 373 chr6ptel1M 165245 CAGTGCTACTACTGGGCTTATACCCCAAAGAGATATTAAGGAAG----AG 165290 i v ii v iv i i vi v viv ---- v L1ME5_3end#LI 374 CAATTCCGCTCCTGGGTATATATCCCAAAGAAATTCTCACACAGGTCCAT 423 chr6ptel1M 165291 AAAGGGACCCATATGTGCAAAAATGTTTGTGGCAGCCCTTTTTGTATTGC 165340 i ---- i i ii ii v vi v iv - L1ME5_3end#LI 424 AAGGGGAC----ATGTACGAGGATGTTCATTGCAGCGTTGTTTGTGGTG- 468 chr6ptel1M 165341 TAGAAACAGTGAAATGGAATGTGAA-TGGATGCCCATCAATTGGAGAATG 165389 -----i i v iv i- ii v- i i v v i L1ME5_3end#LI 469 -----GCGGGGAGTTGGAG-GCAACCTGGGTGTCCATCACTGGGAGAGTG 512 chr6ptel1M 165390 GTTGGGTAAATTGTGGTATCTGAATGTTTTGGAATATTATTGTTCTATAA 165439 v i v ivv v iiiiv i i vvvv vi v L1ME5_3end#LI 513 GATAGGTAAAATGTGGTGGATGCACACCATGGAGTACTATGCAGCAGTTA 562 chr6ptel1M 165440 GAAATGACCAGCAGGATGAATACAGAGAGGATTGGAGAGA-CTTACGTGA 165488 iii vii vi v i v viivv vi - vi-- L1ME5_3end#LI 563 GAAGCAACGGACTAGATGTACACATAGCAACATGGATGGATCTTAAA--A 610 chr6ptel1M 165489 AC-TGATGCTGAGTGAAATAAGC-AGAACCAG---GAGATC-ATTACACA 165532 - ii v i- v --- ?- v L1ME5_3end#LI 611 ACATAGTGCTGAGTGAAAAAAGTAAGAAACAGAATGAGATNTATAACACA 660 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.45 CpG sites = 78, Kimura (unadjusted) = 34.32 Transitions / transversions = 1.10 (78/71) Gap_init rate = 0.07 (40 / 574), avg. gap size = 1.27 (51 / 40) 18 15.04 5.41 0.00 chr6ptel1M 165785 165821 (834179) (TA)n#Simple_repeat 1 39 (0) m_b275s252i9 10863 chr6ptel1M 165785 TATAAATATGTATATATATATAT-TGTATTTA-ACATAT 165821 v i - i v - i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATAT 39 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 47 2.27 0.00 0.00 chr6ptel1M 168300 168344 (831656) (CA)n#Simple_repeat 1 45 (0) c_b275s251i1 10864 chr6ptel1M 168300 CACACATACACACACACACACACACACACACACACACACACACAC 168344 i (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACAC 45 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 13 12.82 0.00 10.53 chr6ptel1M 170336 170377 (829623) (TTTCAT)n#Simple_repeat 1 38 (0) m_b275s252i10 10865 chr6ptel1M 170336 TTTAATTAATCATTTTCATTTTCCTTTACAAATTTATCATTT 170377 v -v v v -- - (TTTCAT)n#Sim 1 TTTCATT-TTCATTTTCATTTTCATTTTC--ATTT-TCATTT 38 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.10 (4 / 41), avg. gap size = 1.00 (4 / 4) 248 25.71 7.69 2.75 chr6ptel1M 171411 171514 (828486) MIR3#SINE/MIR 85 193 (15) m_b275s601i4 10866 chr6ptel1M 171411 TATGACCTTGAAGCGAATCCCTTC-----TCTGTGTTTCAGTTTTTTC-- 171453 i i- i i v ----- v ii ii -- MIR3#SINE/MIR 85 TGTGACCTTGG-GCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCAT 133 chr6ptel1M 171454 CAGTAAATTGGAGGGGGTTGGACTCTTTCCT-TCTGAAGGATCTTTCAGC 171502 v v - vvv vv - i i vvi i MIR3#SINE/MIR 134 CTGTAAAAT-GAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGC 182 chr6ptel1M 171503 TCTATGTATTCT 171514 i-ii MIR3#SINE/MIR 183 TCTG-ACATTCT 193 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.18 CpG sites = 15, Kimura (unadjusted) = 32.18 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.06 (6 / 103), avg. gap size = 1.83 (11 / 6) 15 10.32 0.00 6.06 chr6ptel1M 171945 171979 (828021) (TTTCCT)n#Simple_repeat 1 33 (0) m_b275s252i11 10867 chr6ptel1M 171945 TTTCCTTTTCCTTTTCCTTTCAACTCCTTCCTTTT 171979 -vv -i (TTTCCT)n#Sim 1 TTTCCTTTTCCTTTTCCTTT-TCCT-TTTCCTTTT 33 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 256 16.61 0.00 16.18 chr6ptel1M 172358 172416 (827584) DNM1r#Unknown 2479 2526 (2136) m_b275s502i0 10868 chr6ptel1M 172358 TGTATGTATGCATATTTATGTGTGTTTATTATTCATTAATGTGTATGTGT 172407 i i -- v ---------i DNM1r#Unknown 2479 TGTATGTGTGTATAT--ATGTGTGTATAT---------GTGTGTATGTGT 2517 chr6ptel1M 172408 GTATATATA 172416 i DNM1r#Unknown 2518 GTATATATG 2526 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 17.74 CpG sites = 10, Kimura (unadjusted) = 19.92 Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.19 (11 / 58), avg. gap size = 1.00 (11 / 11) 36 2.94 0.00 0.00 chr6ptel1M 172417 172451 (827549) (TG)n#Simple_repeat 1 35 (0) c_b275s251i2 10869 chr6ptel1M 172417 TGTGTGTGTGTGTGTGTGTGTGTGTGTATGTGTGT 172451 i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 35 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 256 16.61 0.00 16.18 chr6ptel1M 172452 172470 (827530) DNM1r#Unknown 2527 2545 (2117) m_b275s502i0 10868 chr6ptel1M 172452 ACACATACATATATATATA 172470 ii i i ii ? DNM1r#Unknown 2527 GTATATATACGTATNTATA 2545 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 17.74 CpG sites = 10, Kimura (unadjusted) = 19.92 Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 325 28.67 5.60 2.33 chr6ptel1M 172648 172772 (827228) C MIRb#SINE/MIR (80) 188 60 m_b275s601i5 10870 chr6ptel1M 172648 ATCTTCACATTTCAAGCC----AGGT-GATATTCCTATCCCCATTTCATT 172692 i v-- v ---- - i vi i iv C MIRb#SINE/MIR 188 ATCCTCACAA--CAACCCTGCGAGGTAGGTATTATTATCCCCATTTTACA 141 chr6ptel1M 172693 GTTGAGGAAATAGGAAACAAACAGAATTTAATTGACTTGCCCAGAGGTAC 172742 v i-v ii vv v iv v i ii vi C MIRb#SINE/MIR 140 GATGAGGAAAC-TGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCAC 92 chr6ptel1M 172743 ACAGTTAGCAACC--CAGGTTTGGGATCAGAA 172772 i i vi-- ivii iv C MIRb#SINE/MIR 91 ACAGCTAGTAAGTGGCAGAGCCGGGATTCGAA 60 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.70 CpG sites = 20, Kimura (unadjusted) = 37.02 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.05 (6 / 124), avg. gap size = 1.67 (10 / 6) 339 30.19 1.87 0.93 chr6ptel1M 172666 172772 (827228) C MIR#SINE/MIR (102) 160 53 m_b275s601i6 10870 chr6ptel1M 172666 AGGTGATATTCCTATCCCCATTTCATTGTTGAGGAAATAGGAAACAAACA 172715 iv vi i iv v i-v ii v v C MIR#SINE/MIR 160 AGGTACTATTATTATCCCCATTTTACAGATGAGGAAAC-TGAGGCACAGA 112 chr6ptel1M 172716 GAATTTAATTGACTTGCCCAGAGGTACACAGTTAGCAACC--CAGGTTTG 172763 iv v i ii vi i i vi-- ivii C MIR#SINE/MIR 111 GAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 62 chr6ptel1M 172764 GGATCAGAA 172772 iv C MIR#SINE/MIR 61 GGATTCGAA 53 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.23 CpG sites = 19, Kimura (unadjusted) = 39.84 Transitions / transversions = 1.46 (19/13) Gap_init rate = 0.02 (2 / 106), avg. gap size = 1.50 (3 / 2) 383 29.76 9.34 5.85 chr6ptel1M 173713 173894 (826106) C MIRb#SINE/MIR (64) 204 17 m_b275s601i7 10871 chr6ptel1M 173713 TGCATTGTCTTATTTCATTCTCATGAGAACCAGAGGATTTAAGTGCTATC 173762 i i v i ii v vviv vv i --- i C MIRb#SINE/MIR 204 TGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGT---ATT 158 chr6ptel1M 173763 ATTATGTCCATTTTACAGATAAAGAAACTGAATCTAACAGAAGTCCTATA 173812 vi i i iv v v i ivvi C MIRb#SINE/MIR 157 ATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTA 108 chr6ptel1M 173813 ACTTGACTTGCAAGGTT------CTG--AGGTGGAAAAA---------AA 173845 v --- i------ i-- i v i i---------i C MIRb#SINE/MIR 107 ACTTGCC---CAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGA 61 chr6ptel1M 173846 ATCCTGGGCTTCCTGATTCAAGGCCCTAACCCACATTCTATCCACTGTA 173894 i v v vi i v i----- i iiii v i C MIRb#SINE/MIR 60 ACCCAGGTCTGTCTGACTCCAA-----AGCCCGTGCTCTTTCCACTGCA 17 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.33 CpG sites = 31, Kimura (unadjusted) = 39.31 Transitions / transversions = 1.55 (31/20) Gap_init rate = 0.08 (14 / 181), avg. gap size = 2.00 (28 / 14) 12 22.45 0.00 2.70 chr6ptel1M 174865 174902 (825098) (AATAG)n#Simple_repeat 1 37 (0) m_b275s252i12 10872 chr6ptel1M 174865 AATAGAAAAAAATAGAATTGAATGAGATCAGCATGGAA 174902 v i v - vi v i (AATAG)n#Simp 1 AATAGAATAGAATAGAATAGAAT-AGAATAGAATAGAA 37 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 13 18.17 0.00 0.00 chr6ptel1M 175348 175378 (824622) (TATGTG)n#Simple_repeat 1 31 (0) m_b275s252i13 10873 chr6ptel1M 175348 TATGTGCATGAGTAAGTGTATGTTTGTGTGT 175378 i v v v i (TATGTG)n#Sim 1 TATGTGTATGTGTATGTGTATGTGTATGTGT 31 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 232 32.70 4.76 3.53 chr6ptel1M 176781 176948 (823052) L1PA12_3end#LINE/L1 237 406 (509) m_b275s551i4 10874 chr6ptel1M 176781 TAACCAATG-TGGAAAGGCTTTTGGGGGAAACCTGGGACACTTCT----- 176824 vi - vi - v i i v-- i i ? ----- L1PA12_3end#L 237 TAACAGATGCTGGCGAGG-TTGTGGAGAAAAA--GGAACGCTTNTACACT 283 chr6ptel1M 176825 --TGGTGGAATTGTGAACTGATCCAACCATTCTGTTAAGCAATGTGGAAC 176872 -- i v i i ii i v vv ii i -- L1PA12_3end#L 284 GTTGGTGGGAGTGTAAATTAGTTCAACCATTGTGGAAGACAGTGTGG--C 331 chr6ptel1M 176873 TATGCCCAACAGCCATCAAAAGGTGCATAGCTTTTGAACTAGCAATGTTT 176922 v v iv v v v v i viviv v v i v i viiv L1PA12_3end#L 332 GATTCCTCAAAGACCTAAAGACAGAAATACCATTCGACCCAGCAATCCCA 381 chr6ptel1M 176923 CTACTGGGCTTATTTGCCAAAGAGAT 176948 i iv vi- ii L1PA12_3end#L 382 TTACTGGGTATATAC-CCAAAGGAAT 406 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.00 CpG sites = 28, Kimura (unadjusted) = 44.27 Transitions / transversions = 1.12 (28/25) Gap_init rate = 0.05 (9 / 167), avg. gap size = 1.56 (14 / 9) 442 30.33 4.28 6.35 chr6ptel1M 176806 177062 (822938) L1ME5_3end#LINE/L1 268 519 (422) m_b275s551i5 10874 chr6ptel1M 176806 GGAAACCTGGGACACTTCTTGGTGGAATTGTGAACTGATCCAACCATTCT 176855 v vivi v - i v ii i v i L1ME5_3end#LI 268 GGAACCCTCATGCACTGCT-GGTGGGAGTGTAGACTGGTGCAGCCATTCT 316 chr6ptel1M 176856 GTTAAGCAATGTGGAACTA--TGCCCAACAGCCATCAAA-AGGTGCATAG 176902 vvi v v v -- ivi ----- i i- vii v L1ME5_3end#LI 317 GGAGAGCAATCTGGCAGTACTTAGTCAA-----ATTAAGTATACGCATAC 361 chr6ptel1M 176903 CTTTTGAACTAGCAATGTTTCTACTGGGCTTATTTGCCAAAGAGATCTTA 176952 i v v i viiv v iv v v i ii v L1ME5_3end#LI 362 CCTATGACCCAGCAATTCCGCTCCTGGGTATATATCCCAAAGAAATTCTC 411 chr6ptel1M 176953 AAGGAGG---GAAAGGGACCCACAGGTGCAGAAATGTTT-CTGCAGCCCT 176998 viv ---iv i--- v i iiii i-i vi L1ME5_3end#LI 412 ACACAGGTCCATAAGGGG---ACATGTACGAGGATGTTCATTGCAGCGTT 458 chr6ptel1M 176999 GTTTGTTGTGGCAAGAAACTGG----AAACTGAGTGTATGCCCATCATCT 177044 v ii i ii ---- v i ---- - L1ME5_3end#LI 459 GTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGGGTGT----CCATCA-CT 503 chr6ptel1M 177045 GGGAACTACTGAATAAGT 177062 i-- v i i L1ME5_3end#LI 504 GGGAG--AGTGGATAGGT 519 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.08 CpG sites = 42, Kimura (unadjusted) = 39.86 Transitions / transversions = 1.35 (42/31) Gap_init rate = 0.08 (21 / 256), avg. gap size = 1.29 (27 / 21) 309 29.81 5.20 1.11 chr6ptel1M 177481 177653 (822347) ERV24_Prim#LTR/ERV1 4987 5166 (2409) m_b275s701i0 10875 chr6ptel1M 177481 GGCCAGTTTCCTCTCCCAGGTGTTCCCTTTCAAA------CAGAGGGACT 177524 i v i v iv v- i i------ i?v i ERV24_Prim#LT 4987 GGTCATTTTCCTTTACCAGAAGG-CCCTTTCGAGGTATGGCAANTGGATT 5035 chr6ptel1M 177525 TCATTCAATTGCCAGCTGCCCATGATTCCAAATATGCTCTGG-GATGGTT 177573 i ii iv vv ? v iv v i i i ? -? ERV24_Prim#LT 5036 TTATTCAGCTGCCGCCATCNCAAGGATACGAGTATGTTCTNGTNATGGTT 5085 chr6ptel1M 177574 TGTACACTTTCCTGCTGGGTGGCAGAGTTCTTCCT-CATACT-GTCACAG 177621 iii iiii i v vi - i ? - v vv- i? i ERV24_Prim#LT 5086 TGTATGTTTTCTCATTGGGTAGAAGCATT-TCCNTGCAGAAGAGCNACGG 5134 chr6ptel1M 177622 CCTGTGGGCTAGTAAAAATCCTCTTAGAAAAA 177653 vv viv vv i ? ERV24_Prim#LT 5135 CCTTAGCAGTAGGTAAAATTCTNTTAGAAAAA 5166 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.15 CpG sites = 29, Kimura (unadjusted) = 41.26 Transitions / transversions = 1.32 (29/22) Gap_init rate = 0.03 (6 / 172), avg. gap size = 1.83 (11 / 6) 254 33.33 2.05 1.36 chr6ptel1M 177684 177829 (822171) L1MC3_3end#LINE/L1 452 598 (1934) m_b275s551i6 10876 chr6ptel1M 177684 CAGCCCTTTTTTTGGTCACAAAGAACTGAA--CAATAAATATGTATCTGT 177731 ii v iv ii i v i i -- iv v -- iv L1MC3_3end#LI 452 CAGCTTTATTCATAATCGCCAAAAACTGGAAGCAACCAAGATGT--CCTT 499 chr6ptel1M 177732 CTATTTGGGAATGGCCAGACAAGCTGTGGTATATGAAGGCAATAGAATAT 177781 v vv v vi i i i vv vi i L1MC3_3end#LI 500 CAATAGGTGAATGGATAAACAAACTGTGGTACATCCATACAATGGAATAT 549 chr6ptel1M 177782 TATTGTTCTGTAAAAAT-GATGAACAAGCTGGTTTTGAAAAGGCCTGGA 177829 vvv vi v-i i v v vi iivi i v L1MC3_3end#LI 550 TATTCAGCGATAAAAAGAAATGAGCTATCAAGCCACGAAAAGACATGGA 598 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 42.35 CpG sites = 24, Kimura (unadjusted) = 44.79 Transitions / transversions = 1.00 (24/24) Gap_init rate = 0.03 (4 / 145), avg. gap size = 1.25 (5 / 4) 378 28.51 1.26 7.33 chr6ptel1M 180866 181024 (818976) C MIRb#SINE/MIR (117) 151 2 m_b275s601i9 10877 chr6ptel1M 180866 CTCATTTTACAAATGAAGAAACTGAGG--CAAACAGGATGAAGTGACTTC 180913 i i i -- i v - v i v C MIRb#SINE/MIR 151 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGG-TTAAGTAACTTG 103 chr6ptel1M 180914 ACCAGGTTCCCATACCTAGTAATTATATGAGACTGGATTTGAACACATGA 180963 v i v v i v v ivvv v v i v v - C MIRb#SINE/MIR 102 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGG- 54 chr6ptel1M 180964 AGCTGAATCTTCCTGATTGCAAGCTCTATGCCCTTCCCCCTCCCACCCCC 181013 ------- vi i v ivi ii i i v v --v v C MIRb#SINE/MIR 53 -------TCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGC--ACCAC 13 chr6ptel1M 181014 CCTACCCCCCT 181024 v i i C MIRb#SINE/MIR 12 GCTGCCCCTCT 2 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.73 CpG sites = 19, Kimura (unadjusted) = 35.87 Transitions / transversions = 0.83 (19/23) Gap_init rate = 0.08 (12 / 158), avg. gap size = 1.08 (13 / 12) 445 25.48 1.44 6.82 chr6ptel1M 180866 181004 (818996) C MIRc#SINE/MIR (120) 148 17 m_b275s601i8 10877 chr6ptel1M 180866 CTCATTTTACAAATGAAGAAACTGAGG--CAAACAGGATGAAGTGACTTC 180913 i i i -- i v - v v C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGG-TTAAGTGACTTG 100 chr6ptel1M 180914 ACCAGGTTCCCATACCTAGTAATTATATGAGACTGGATTTGAACACATGA 180963 v i v v i v v ivvv v v i i v v - C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGG- 51 chr6ptel1M 180964 AGCTGAATCTTCCTGATTGCAAGCTCTATGCCCTTCCCCCT 181004 ------- i v ii vi i i v C MIRc#SINE/MIR 50 -------TCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACT 17 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.06 CpG sites = 15, Kimura (unadjusted) = 31.15 Transitions / transversions = 0.83 (15/18) Gap_init rate = 0.07 (10 / 138), avg. gap size = 1.10 (11 / 10) 281 27.41 4.78 8.78 chr6ptel1M 181749 182020 (817980) C L1MA3_3end#LINE/L1 (723) 329 68 m_b275s551i7 10878 chr6ptel1M 181749 CACACTAGTACTCCATCATAATCTTGTACCACAGCATTTTCCAATTCCCA 181798 v - v vi ii -- i ---- v -- C L1MA3_3end#LI 329 CAAACT-GTTCTCCATAGTGGT--TGTACTA----ATTTAC--ATTCCCA 289 chr6ptel1M 181799 CCAACACT-TA--ACTGTTAACTCAATTTTTCCACATCCTTTTCAACATT 181845 v - -- vv vv --- i ivi i C L1MA3_3end#LI 288 CCAACAGTGTACGAGGGTTCCCT---TTTCTCCACATCCTCGCCAGCATT 242 chr6ptel1M 181846 TGTCACTTTCCCCTTCTGTCTTTT---TAGA---CAATCTGGTTGGAGTA 181889 i -- v ---- --- i --- v i iii i i C L1MA3_3end#LI 241 TGTTA--TTGC----CTGTCTTTTGGATAAAAGCCATTTTAACTGGGGTG 198 chr6ptel1M 181890 AAATGATATTTTCAGGTACTTTCAATGTGAATTTCCCTGATCTATGATGA 181939 i i ivvv v ii v v i vvvii C L1MA3_3end#LI 197 AGATGATATCTCATTGTAGTTTTGATTTGCATTTCTCTGATGATCAATGA 148 chr6ptel1M 181940 TCTAGAG---CTTTTTAAAAACATGAATATAAATTCTTTTG-ATTTCTTC 181985 v v --- i v v v -- v i---i v - v C L1MA3_3end#LI 147 TGTTGAGCACCTTTTCATATACCTG--TTTG---CCATTTGTATGTCTTC 103 chr6ptel1M 181986 TTTGAAAAACTGTCCATTCATTTTATCTATCCATT 182020 vi i v i vv iv i ii C L1MA3_3end#LI 102 TTTTGAGAAATGTCTATTCAGATCTTTTGCCCATT 68 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.72 CpG sites = 34, Kimura (unadjusted) = 34.32 Transitions / transversions = 1.00 (34/34) Gap_init rate = 0.11 (29 / 271), avg. gap size = 1.24 (36 / 29) 377 28.01 5.81 6.69 chr6ptel1M 181780 182020 (817980) C L1MB8_3end#LINE/L1 (619) 306 68 m_b275s551i8 10878 chr6ptel1M 181780 CAGCATTTTCCAATTCCCACCAACACT---TAACTGTTAACTCAATTTTT 181826 v v - i v --- i vv ---i i C L1MB8_3end#LI 306 CACCATTTTACA-TTCCCACCAGCAGTGTATGAGGGTT---CCAATTTCT 261 chr6ptel1M 181827 CCACATCCTTTTCAACATTTGTCACTTTCCCCTTCTGTCTTTTT------ 181870 ivi i i i v ------ ------ C L1MB8_3end#LI 260 CCACATCCTCGCCAACACTTGTTATTATC------TGTCTTTTTGATTAT 217 chr6ptel1M 181871 AGACAATCTGGTTGGAGTAAAATGATATTTTCAGGTACTTTCAATGTGAA 181920 v vi i v v i i i i ivvv iv ii v v C L1MB8_3end#LI 216 AGCCATCCTAGTGGGTGTGAAGTGGTATCTCATTGTGGTTTTGATTTGCA 167 chr6ptel1M 181921 TTTCCCTGAT--CTATGATGATCTAGAG---CTTTTTAAAAACATGAATA 181965 -- -- v v --- i---- ii vv C L1MB8_3end#LI 166 TTTCCCTGATGACTA--ATGATGTTGAGCATCTTTTC----ATGTGCTTA 123 chr6ptel1M 181966 TAAATTCTTTTGATTTCTTCTTTGAAAAACTGTCCATTCATTTTATCTAT 182015 viiiiv vv v i i v i vv iv i ii C L1MB8_3end#LI 122 TTGGCCATTTGTATATCTTCTTTGGAGAAATGTCTATTCAGATCCTTTGC 73 chr6ptel1M 182016 CCATT 182020 C L1MB8_3end#LI 72 CCATT 68 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 34.88 CpG sites = 33, Kimura (unadjusted) = 35.57 Transitions / transversions = 1.10 (33/30) Gap_init rate = 0.08 (20 / 240), avg. gap size = 1.50 (30 / 20) 237 19.15 0.00 0.00 chr6ptel1M 182564 182610 (817390) C DNM1r#Unknown (2140) 2522 2476 m_b275s502i1 10879 chr6ptel1M 182564 TGTACACACACACACACATATATATATATATATATATACATATACAT 182610 i i i i i i i i i C DNM1r#Unknown 2522 TATACACACATACACACATATACACACATATATACACACATACACGT 2476 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 21.13 CpG sites = 9, Kimura (unadjusted) = 24.14 Transitions / transversions = 1.00 (9/0) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 378 27.39 5.67 4.20 chr6ptel1M 183155 183295 (816705) MIR3#SINE/MIR 2 144 (64) m_b275s601i10 10880 chr6ptel1M 183155 TGGCAG--TGGCT----AGAGAATGC-CGGGCCTGGAGTCCAAAAGACTC 183197 -- ---- iv - i iv - ii -- MIR3#SINE/MIR 2 TGGCAGAGTGGCTGAGCAGAGAGAGCACGGACTGGGAGTC-AGGAGAC-- 48 chr6ptel1M 183198 ATCCCAAGTTTCAATCTGGTCTCAGACCCTAACTAGCTTGGTGACCCACG 183247 --- iii ii i iv v v v v ? vv ivv MIR3#SINE/MIR 49 ---CTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGG 95 chr6ptel1M 183248 GTAACT-ATATTAATTCTCTTGGCCTCAGTTTCCCTGTCTACAAAATGA 183295 i v - iv i vi v iii ii MIR3#SINE/MIR 96 GCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGA 144 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.35 CpG sites = 22, Kimura (unadjusted) = 35.35 Transitions / transversions = 1.47 (22/15) Gap_init rate = 0.07 (10 / 140), avg. gap size = 1.40 (14 / 10) 198 32.76 14.35 2.49 chr6ptel1M 183846 184061 (815939) C L3#LINE/CR1 (21) 4078 3838 m_b275s601i11 10881 chr6ptel1M 183846 AGCTGCAAGAAACT---GAGATTCATCAAATAGGAGAACAACTTATCCAA 183892 i v ii i--- i - --- vvv vv ii C L3#LINE/CR1 4078 AGTTGGAAGGGACCTTAGAGGT-CATC---TAGTCCAACCTCCCATCCAA 4033 chr6ptel1M 183893 CCCA--AACCCTGTGCTACAACA-ACCTGAAAATTAATCACTT----TCA 183935 iv -- i iv - -v v v ii iii---- v C L3#LINE/CR1 4032 TGCAGGAATCCCTT-CTACAACATCCCTGACAAGTGGTCATCCAGCCTCT 3984 chr6ptel1M 183936 ATGTGAAGATCCCCAGGATCAGAGAGAT--------------GCAGCCCA 183971 iiv v i i viv i i v -------------- C L3#LINE/CR1 3983 GCTTGAACACCTCCAGTGACGGGGAGCTCACTACCTCNCGAGGCAGCCCA 3934 chr6ptel1M 183972 CTGCATGTTGGGGCATCTCCAATGGTTATAG----CTGACCTTCTACAGA 184017 i v v v i v ii v v i---- v- v iv C L3#LINE/CR1 3933 TTCCATTTTTGGACAGCTCTGATTGTTAGAAAGTTCTT-CCTTATATTGA 3885 chr6ptel1M 184018 AATGATG-CTGCCTTCATCTAAGT--CTCCCGTTATTTCCAGTTCTG 184061 ivi vi- i v v v -- v i iv i i C L3#LINE/CR1 3884 GCCGAAATCTGCCTCCCTGTAACTTCCACCCATTGGTCCTAGTTCTG 3838 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 42.40 CpG sites = 36, Kimura (unadjusted) = 44.09 Transitions / transversions = 1.09 (36/33) Gap_init rate = 0.07 (14 / 215), avg. gap size = 2.64 (37 / 14) 18 0.00 0.00 0.00 chr6ptel1M 184404 184423 (815577) (A)n#Simple_repeat 1 20 (0) m_b275s252i14 10882 chr6ptel1M 184404 AAAAAAAAAAAAAAAAAAAA 184423 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAA 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 13 30.16 1.35 4.17 chr6ptel1M 184580 184653 (815347) (AAAGA)n#Simple_repeat 1 72 (0) m_b275s252i15 10883 chr6ptel1M 184580 AAAGAAAATTAAAAGAAAAGTGGGGAAAGGGAACAAGAACATGGTAGAAA 184629 -v viii -i - v viiv (AAAGA)n#Simp 1 AAAGAAAA-GAAAAGAAAAGAAAAGAAA-AGAA-AAGAAAAGAAAAGAAA 47 chr6ptel1M 184630 AGTTTAGAAAAGGAAA-CACAGAAA 184653 vvv i -v v (AAAGA)n#Simp 48 AGAAAAGAAAAGAAAAGAAAAGAAA 72 Matrix = Unknown Transitions / transversions = 0.70 (7/10) Gap_init rate = 0.05 (4 / 73), avg. gap size = 1.00 (4 / 4) 12 16.57 0.00 0.00 chr6ptel1M 185621 185647 (814353) (TTTG)n#Simple_repeat 1 27 (0) m_b275s252i16 10884 chr6ptel1M 185621 TTTGTTCGTTTATTTGTTTTTTTCTTT 185647 i i v v (TTTG)n#Simpl 1 TTTGTTTGTTTGTTTGTTTGTTTGTTT 27 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 12 31.51 0.00 0.00 chr6ptel1M 185837 185883 (814117) (TATAAA)n#Simple_repeat 1 47 (0) m_b276s252i1 10885 chr6ptel1M 185837 TATATATGTAATCTTAAATATAAATATGTATACGTATATATGTATAA 185883 v i viv iv iiv vi (TATAAA)n#Sim 1 TATAAATATAAATATAAATATAAATATAAATATAAATATAAATATAA 47 Matrix = Unknown Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 180 25.00 2.04 2.04 chr6ptel1M 186133 186181 (813819) C MIR3#SINE/MIR (0) 208 160 m_b276s601i0 10886 chr6ptel1M 186133 GAGTCA-AAAATCACAGAATAATGGAACTGGAAGGGGTCCTAGAACATCA 186181 i - i i ivii i ii i i- C MIR3#SINE/MIR 208 GAATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAG-ATCA 160 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 33.68 CpG sites = 11, Kimura (unadjusted) = 33.68 Transitions / transversions = 11.00 (11/1) Gap_init rate = 0.04 (2 / 48), avg. gap size = 1.00 (2 / 2) 195 15.70 3.70 5.66 chr6ptel1M 186357 186410 (813590) C MIR3#SINE/MIR (6) 202 150 m_b276s601i1 10887 chr6ptel1M 186357 TAGAA-CATACAATGTCAGCA-TGGAAGGACCCTAAGAATCATTATCTTA 186404 - v vi- iv v i-- i - C MIR3#SINE/MIR 202 TAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAG--ATCATC-TA 156 chr6ptel1M 186405 GTCCAA 186410 C MIR3#SINE/MIR 155 GTCCAA 150 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 17.68 CpG sites = 4, Kimura (unadjusted) = 17.68 Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.09 (5 / 53), avg. gap size = 1.00 (5 / 5) 271 19.38 10.29 1.35 chr6ptel1M 186658 186725 (813275) MIRc#SINE/MIR 120 193 (75) m_b276s601i2 10888 chr6ptel1M 186658 AGCTTCAGCTCCCTC-TCTGTAAAACAG------TAATACTTGCCTCTAC 186700 i i i - ii ------ i - i MIRc#SINE/MIR 120 AGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCC-CTGC 168 chr6ptel1M 186701 CTCCCTCCCTGGGGTGTTAGGAGGA 186725 v v v v iv MIRc#SINE/MIR 169 CTACCTCACAGGGTTGTTGTGAGGA 193 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 22.84 CpG sites = 8, Kimura (unadjusted) = 22.84 Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.04 (3 / 67), avg. gap size = 2.67 (8 / 3) 21 16.12 0.00 0.00 chr6ptel1M 186765 186799 (813201) (T)n#Simple_repeat 1 35 (0) m_b276s252i2 10889 chr6ptel1M 186765 TTGTTTTTTTTTGTTTTTTGTTTTTTGGTTTTTTT 186799 v v v vv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 35 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 15 25.34 1.89 1.89 chr6ptel1M 188264 188316 (811684) (GGGA)n#Simple_repeat 1 53 (0) m_b276s252i3 10890 chr6ptel1M 188264 GGGTGGAGGGGAGGCAGGGAGGCAGAGGACACTGGG-GGGTGGGAGGGAG 188312 v ii v v - vivv - v (GGGA)n#Simpl 1 GGGAGGGAGGGAGGGAGGGAGGGAG-GGAGGGAGGGAGGGAGGGAGGGAG 49 chr6ptel1M 188313 AGAG 188316 i (GGGA)n#Simpl 50 GGAG 53 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.00 (2 / 2) 44 0.00 2.44 0.00 chr6ptel1M 189272 189312 (810688) (AC)n#Simple_repeat 1 42 (0) c_b276s251i0 10891 chr6ptel1M 189272 ACACAC-CACACACACACACACACACACACACACACACACAC 189312 - (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACAC 42 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 208 29.43 8.77 1.64 chr6ptel1M 190484 190597 (809403) MIR3#SINE/MIR 85 206 (2) m_b276s601i3 10892 chr6ptel1M 190484 TATGACTTTGGGGCAAATCCCTTC-----TCTGTATTTCAGTTTTTTC-- 190526 i i - i v ----- viii ii -- MIR3#SINE/MIR 85 TGTGACCTTGGG-CAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCAT 133 chr6ptel1M 190527 CAGTAATTTGGAGGGGGTTGAGCTCTTTCCT-TCTGAAGGATCTTTCAGC 190575 v vv - ii vvv vv - i i vvi i MIR3#SINE/MIR 134 CTGTAAAAT-GAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGC 182 chr6ptel1M 190576 CCC-ACATCTTCTGACTTT-TGAT 190597 i i- ii v i i - MIR3#SINE/MIR 183 TCTGACATTCTATGATTCTATGAT 206 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 38.65 CpG sites = 20, Kimura (unadjusted) = 38.65 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.06 (7 / 113), avg. gap size = 1.71 (12 / 7) 15 10.32 0.00 6.06 chr6ptel1M 191010 191044 (808956) (TTTCCT)n#Simple_repeat 1 33 (0) m_b276s252i4 10893 chr6ptel1M 191010 TTTCCTTTTCCTTTTCCTTTCAACTCCTTCCTTTT 191044 -vv -i (TTTCCT)n#Sim 1 TTTCCTTTTCCTTTTCCTTT-TCCT-TTTCCTTTT 33 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 20 32.62 2.59 2.59 chr6ptel1M 191382 191497 (808503) (ATATAT)n#Simple_repeat 1 116 (0) m_b276s252i5 10894 chr6ptel1M 191382 ATAAATAGAAATATGGATAGTGTAATTTTACATACATATCCATATGTATG 191431 v v v iv - i vv v i i vi i i (ATATAT)n#Sim 1 ATATATATATATATATATA-TATATATATATATATATATATATATATATA 49 chr6ptel1M 191432 TGTATTTATGTGTGTGAGTCTGTGTATAT-TATA-ATATACAT-TATTAA 191478 i v i i i - - v i i - - i - vv (ATATAT)n#Sim 50 TATATATATATATAT-A-TATATATATATATATATATATATATATATATA 97 chr6ptel1M 191479 TGTATATATATATTTCTAT 191497 i v v (ATATAT)n#Sim 98 TATATATATATATATATAT 116 Matrix = Unknown Transitions / transversions = 1.07 (15/14) Gap_init rate = 0.05 (6 / 115), avg. gap size = 1.00 (6 / 6) 15 25.43 5.88 1.41 chr6ptel1M 191424 191491 (808509) (TATG)n#Simple_repeat 1 71 (0) m_b276s252i6 10895 chr6ptel1M 191424 TATGTATG--TGTATTTATGTGTGTGAGTCTGTGTATAT-TATAATATAC 191470 -- v i iv v i i - -i ii (TATG)n#Simpl 1 TATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTAT-GTATGT 49 chr6ptel1M 191471 AT-TATTAATGTATATATATAT 191491 - vv i i (TATG)n#Simpl 50 ATGTATGTATGTATGTATGTAT 71 Matrix = Unknown Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.06 (4 / 67), avg. gap size = 1.25 (5 / 4) 20 32.62 2.59 2.59 chr6ptel1M 191382 191497 (808503) (ATATAT)n#Simple_repeat 1 116 (0) m_b276s252i5 10894 chr6ptel1M 191382 ATAAATAGAAATATGGATAGTGTAATTTTACATACATATCCATATGTATG 191431 v v v iv - i vv v i i vi i i (ATATAT)n#Sim 1 ATATATATATATATATATA-TATATATATATATATATATATATATATATA 49 chr6ptel1M 191432 TGTATTTATGTGTGTGAGTCTGTGTATAT-TATA-ATATACAT-TATTAA 191478 i v i i i - - v i i - - i - vv (ATATAT)n#Sim 50 TATATATATATATAT-A-TATATATATATATATATATATATATATATATA 97 chr6ptel1M 191479 TGTATATATATATTTCTAT 191497 i v v (ATATAT)n#Sim 98 TATATATATATATATATAT 116 Matrix = Unknown Transitions / transversions = 1.07 (15/14) Gap_init rate = 0.05 (6 / 115), avg. gap size = 1.00 (6 / 6) 410 30.07 2.07 1.37 chr6ptel1M 191657 191801 (808199) C MIR#SINE/MIR (64) 198 53 m_b276s601i4 10896 chr6ptel1M 191657 TATTATGTCACTTTAACCTCATCTTAACATTTAAAGTTAGGTGATATTGT 191706 vv i v v ivvi vi vvi v iv i C MIR#SINE/MIR 198 TATTAACTCATTTAATCCTCACAACAACCCTATGAGGTAGGTACTATTAT 149 chr6ptel1M 191707 TATCCCCATTTCATTGTTGAGGAAACAG-GAAACAATCAGAATTTAATTG 191755 i iv v v - iv i-- iv v i C MIR#SINE/MIR 148 TATCCCCATTTTACAGATGAGGAAACTGAGGCACAG--AGAGGTTAAGTA 101 chr6ptel1M 191756 ACTTGCCCAGAGGTACACAGTTAATAACC--CAGATTTGGGATCAGAA 191801 ii vi i i vi-- vii iv C MIR#SINE/MIR 100 ACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAA 53 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 37.86 CpG sites = 22, Kimura (unadjusted) = 39.00 Transitions / transversions = 1.05 (22/21) Gap_init rate = 0.03 (4 / 144), avg. gap size = 1.25 (5 / 4) 186 30.98 7.48 6.48 chr6ptel1M 192495 192601 (807399) C L2c_3end#LINE/L2 (10) 468 361 m_b276s601i5 10897 chr6ptel1M 192495 TCAGAAAATA---ATTAAGAGCCT-----GGGCTAAACACCAGCAGCACA 192536 iv i --- i v ----- v i ii i ii viii C L2c_3end#LINE 468 TCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGATACA 419 chr6ptel1M 192537 AAGAGATGTAAGGGACATCCCCTGCCCTCATGAAGGTCCCCTGCCACAGA 192586 vivi iv ivi v i ----- -- v C L2c_3end#LINE 418 AAGATGAATAAGACACGGTCCCTGCCCTCAAGGAG-----CT--CACAGT 376 chr6ptel1M 192587 CTGGTGGGGCAGACA 192601 i i v C L2c_3end#LINE 375 CTAGTGGAGGAGACA 361 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 38.33 CpG sites = 20, Kimura (unadjusted) = 41.88 Transitions / transversions = 1.82 (20/11) Gap_init rate = 0.08 (9 / 106), avg. gap size = 1.67 (15 / 9) 406 29.72 13.26 1.49 chr6ptel1M 192781 192961 (807039) C MIRc#SINE/MIR (58) 210 9 m_b276s601i6 10898 chr6ptel1M 192781 TGCATTGTCTTATTTCATCCTCATGAGAATCAGAGAATTTAGGT---GCA 192827 i i i v ii v i vvivi vv i--- C MIRc#SINE/MIR 210 TACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCA 161 chr6ptel1M 192828 ---ATTATTATGCCCATTTTACAGGTAAAGAAACTGAATCTAACATAGGT 192874 --- v i i i iv v v v C MIRc#SINE/MIR 160 GGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGT 111 chr6ptel1M 192875 CCTATAACTTGATTTTCAAGGTT------CT-----------GAGGTGGG 192907 ivvi i ---ii i------ ----------- vi C MIRc#SINE/MIR 110 TAAGTGACTTG---CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGG 64 chr6ptel1M 192908 AATAAAATCTTGGGCTTCCTGACTCAAGGCCCTATCCACATTCTA-TCCA 192956 v vi i iv v v i i vi v v v i - v C MIRc#SINE/MIR 63 ACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCA 14 chr6ptel1M 192957 CCATA 192961 i C MIRc#SINE/MIR 13 CCACA 9 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 36.78 CpG sites = 28, Kimura (unadjusted) = 38.60 Transitions / transversions = 1.12 (28/25) Gap_init rate = 0.04 (8 / 180), avg. gap size = 3.38 (27 / 8) 15 5.56 0.00 0.00 chr6ptel1M 193109 193127 (806873) (A)n#Simple_repeat 1 19 (0) m_b276s252i7 10899 chr6ptel1M 193109 AAAAAAAAAGAAAAAAAAA 193127 i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAA 19 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 26 8.39 0.00 2.56 chr6ptel1M 194430 194469 (805531) (AT)n#Simple_repeat 1 39 (0) m_b276s252i8 10900 chr6ptel1M 194430 ATATATATATATATATATGAGTTTTATATATATATATATA 194469 - vv v (AT)n#Simple_ 1 ATATATATATATATATAT-ATATATATATATATATATATA 39 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1) 38 6.82 0.00 0.00 chr6ptel1M 194470 194515 (805485) (TG)n#Simple_repeat 1 46 (0) c_b276s251i1 10901 chr6ptel1M 194470 TGTGTGTGTGTGTGTGTGTCTGTTTGTGTGTGTATGTGTGTGTGTG 194515 v v i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 46 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 12 4.30 8.33 0.00 chr6ptel1M 194546 194569 (805431) (TCTTT)n#Simple_repeat 1 26 (0) m_b276s252i9 10902 chr6ptel1M 194546 TCTTTTC-TTTC-TTTCTTTTGTTTT 194569 - - v (TCTTT)n#Simp 1 TCTTTTCTTTTCTTTTCTTTTCTTTT 26 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.09 (2 / 23), avg. gap size = 1.00 (2 / 2) 506 32.58 7.35 2.51 chr6ptel1M 197091 197471 (802529) L1ME4c_3end#LINE/L1 241 639 (191) m_b276s551i0 10903 chr6ptel1M 197091 CAATG-TGGAAAGGCTTTTGGGGGAAACCTGGGATGCTAATGTATTATTG 197139 - vi ? --- v vi v v i? v ii ii L1ME4c_3end#L 241 CAATGCTGGCGAGGNT---GCGGTGAAACTGGTACNCTCATACATTGCTG 287 chr6ptel1M 197140 GTGGAAATGTGAACGGATCCAACT------------AATTCTGTCACC-- 197175 v ? i iv i v i------------ - v vi-- L1ME4c_3end#L 288 GTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGCAATT-TGGCAATAC 336 chr6ptel1M 197176 ----CAACAGCTATCAAAAGGTGCATAGCCTTTGAACTAGCAATGCTTCT 197221 ---- v i v v v v v i i v iv L1ME4c_3end#L 337 GTATCAAGAGCCATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACT 386 chr6ptel1M 197222 ACTGGG--CTTATTTGCCAAAGAGAT---CCAAAAGGAGGGAAAAGGACC 197266 v --i i-- i i i ---i i i --- L1ME4c_3end#L 387 TCTGGGAATTTATC--CTAAGGAAATAATTCAAAAGAAGGAAAAAG---C 431 chr6ptel1M 197267 CACATGTGCAGAAATGTTT-CTGCAGCCCTGTTTGTAGTGGCAAGAAACT 197315 i i ii ii i i-i vi i i i i i i i L1ME4c_3end#L 432 TATATGCACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATT 481 chr6ptel1M 197316 GAAAACAG--TGGATGCCCATCATCTGGGAAATGCTGAA-TAAGTAATAG 197362 i i-- ii i v viv i v v - i v i L1ME4c_3end#L 482 GGAAACAACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGG 531 chr6ptel1M 197363 CACATTAATGTTGTGGAATATTGTTGTTCTATAAGGAATGATCAGCAGGA 197412 i i? ivivi i vvvv i v ii v vi v L1ME4c_3end#L 532 TACATCNACTCGATGGAATATTATGCAGCCATTAAAAATGATAATTATGA 581 chr6ptel1M 197413 TGATTCCAGAGACGCCTTGAGAGACCTACATGAACTGATGCAAAGTGAAG 197462 v i viiv - iv v ii i iv vi vv i iv i L1ME4c_3end#L 582 AGACTATGTAG-CAACATGGAAAATGTTTATGATATAATGTTAAGTGAAA 630 chr6ptel1M 197463 TGAGCAGAA 197471 vi L1ME4c_3end#L 631 AAAGCAGAA 639 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 43.15 CpG sites = 73, Kimura (unadjusted) = 45.18 Transitions / transversions = 1.52 (73/48) Gap_init rate = 0.05 (19 / 380), avg. gap size = 2.00 (38 / 19) 366 31.84 1.10 1.10 chr6ptel1M 197781 197961 (802039) ERV24_Prim#LTR/ERV1 4987 5167 (2408) m_b276s701i0 10904 chr6ptel1M 197781 GGCCAGTTTCCTCTCCCAGATGCTCCTTTTCAAACCTGGCAAAGGGTCTT 197830 i v i v v vi iv iiiv ?v vi ERV24_Prim#LT 4987 GGTCATTTTCCTTTACCAGAAGGCCCTTTCGAGGTATGGCAANTGGATTT 5036 chr6ptel1M 197831 CATTCAATTGCCAGCTGCCCATGGTTCTAAATATGCTTTGGGGATGGTCT 197880 i ii iv vv ? v v vii i i i ? v? i ERV24_Prim#LT 5037 TATTCAGCTGCCGCCATCNCAAGGATACGAGTATGTTCTNGTNATGGTTT 5086 chr6ptel1M 197881 GTACACTTTCATGTTGGTTGGCAGAGTTCCCCTGTCATCCTGGCATAGGC 197930 iii vii v i v vi i ? - vvvvi ?vv ERV24_Prim#LT 5087 GTATGTTTTCTCATTGGGTAGAAGCATTTCCNTG-CAGAAGAGCNACGGC 5135 chr6ptel1M 197931 TCTGGGC--TAGCAAAAATCCTCTTAGAAAAAA 197961 - vi -- vv i ? ERV24_Prim#LT 5136 -CTTAGCAGTAGGTAAAATTCTNTTAGAAAAAA 5167 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 41.35 CpG sites = 29, Kimura (unadjusted) = 44.50 Transitions / transversions = 1.04 (29/28) Gap_init rate = 0.02 (3 / 180), avg. gap size = 1.33 (4 / 3) 240 26.43 2.25 2.25 chr6ptel1M 198026 198114 (801886) L1MC3_3end#LINE/L1 465 553 (1979) m_b276s551i1 10905 chr6ptel1M 198026 AGTCACAAAGAACTGAA--CAATAAATATGTGTCTGTCTATTGGGGAATG 198073 i i v i i -- iv v -- iv v v v L1MC3_3end#LI 465 AATCGCCAAAAACTGGAAGCAACCAAGATGT--CCTTCAATAGGTGAATG 512 chr6ptel1M 198074 GCCAGACAAGTTGTGGTACTTGAAGTCAATGGAATATTATT 198114 vi i ii v vv vv L1MC3_3end#LI 513 GATAAACAAACTGTGGTACATCCATACAATGGAATATTATT 553 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 31.08 CpG sites = 10, Kimura (unadjusted) = 32.72 Transitions / transversions = 0.77 (10/13) Gap_init rate = 0.03 (3 / 88), avg. gap size = 1.33 (4 / 3) 23 14.04 2.13 0.00 chr6ptel1M 198385 198431 (801569) (TTTCTT)n#Simple_repeat 1 48 (0) m_b276s252i10 10906 chr6ptel1M 198385 TTTCGTTTTCTTTCTCATTTT-TTTTTCTTTTTGATTTTATTTTTCTT 198431 v i v - vv v (TTTCTT)n#Sim 1 TTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTT 48 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.02 (1 / 46), avg. gap size = 1.00 (1 / 1) 55 0.00 0.00 0.00 chr6ptel1M 198478 198524 (801476) (AT)n#Simple_repeat 1 47 (0) c_b276s251i2 10907 chr6ptel1M 198478 ATATATATATATATATATATATATATATATATATATATATATATATA 198524 (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATA 47 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 192 30.77 9.23 0.00 chr6ptel1M 198905 198969 (801031) OldhAT1#DNA/hAT-Ac 1313 1383 (1459) m_b276s601i7 10908 chr6ptel1M 198905 ATCTGTGGCCACTCTGC----TCCATCAGAGTTGGAAGAACTCTTGCTCA 198950 v i ?---- ii ii iii i ii vi ? OldhAT1#DNA/h 1313 ATCTGTGGACACTTTGNCCATTCTGTCAAGGCCAGAAAAATCCTGACTNA 1362 chr6ptel1M 198951 ACAACAATAAAAAA--AACTT 198969 i vi ii i -- OldhAT1#DNA/h 1363 GCTGCAGCAAGAAAACAACTT 1383 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 46.75 CpG sites = 17, Kimura (unadjusted) = 46.75 Transitions / transversions = 5.67 (17/3) Gap_init rate = 0.03 (2 / 64), avg. gap size = 3.00 (6 / 2) 941 30.05 2.05 3.29 chr6ptel1M 199813 200397 (799603) HERVK14C#LTR/ERVK 2845 3422 (4012) m_b276s701i1 10909 chr6ptel1M 199813 TTTTTAGGCAAGGCTGCTGTTCAAGGCCTGCCAACACTTTCATCTGTTTC 199862 viv ii v -- - iv? ------ i i HERVK14C#LTR/ 2845 TTTTTAGGGGCGGCCACTGTTGA--GCCT-CCAGANC------CTATTCC 2885 chr6ptel1M 199863 TATCCAATGGAGAACTGATCCACCAGTGTGGATAGAACAGTGGCCCTTAG 199912 iv vv ?i iv vvv? ? v i ? ? vi ?? HERVK14C#LTR/ 2886 CTTAAAATGGANGACCCAAAANCCNGTTTGGGTNGANCAGTGGCCGCTNN 2935 chr6ptel1M 199913 GTAGCGATAAAATTCAGGCCTTATTAGATATT-GTACAGGAATAACTTGA 199961 v viv v v vvi -i iv - vv i i i v HERVK14C#LTR/ 2936 CTCAGGAAAAACTGGGGGCCTTA-CAGGAATTAGTCAAAGAACAATTAGA 2984 chr6ptel1M 199962 TCAAGGACACTTACAACCTTCTATAAGTCCTTGGAATTATCCTGTATTTG 200011 ?v v ?v i iv vv vvv ? v? v i HERVK14C#LTR/ 2985 NAAAGGACACATNGAGCCCACATTTTCTCCNTGGAATTCNCCAGTGTTTG 3034 chr6ptel1M 200012 TTGTAAGAAAGAAATCTGGAAAATGGAGGATCTTCACTGATTTAAGAAAA 200061 vi ? ii i i v i v ? vi v i i v ivv HERVK14C#LTR/ 3035 TAATNAAGAAAAAATCCGGCAGATGGCGNATGCTAACCGACTTACGAGCC 3084 chr6ptel1M 200062 GTAAATGAACAG--ATGGAAACTATGAGGACTCTTCAGCCCTGACTTCCA 200109 v -- -- ?v v ? i i ? v vv i v ? HERVK14C#LTR/ 3085 GTCAATG--CAGTCATNCAACCNATGGGGGCNCTGCAGCCAGGGCTGCCN 3132 chr6ptel1M 200110 TCTTCTACTCAGTTACCTAGAGAATGGCCTTTTTGGGTTGTAGACATTAA 200159 ii ii ivv v v v ? vvvi i iv v HERVK14C#LTR/ 3133 TCCCCCGCCATGATTCCTAGAGACTGGCCNTTAATAGTTATAGATTTGAA 3182 chr6ptel1M 200160 GGATTGTTTCTATTCTATTCCTTTAGATAAGGAGGATATGAAAAGATTTG 200209 i i v v i vvi vv? v vi i HERVK14C#LTR/ 3183 GGACTGCTTCTTTACTATTCCTCTAGCAGAGCCNGATTTTGAAAAATTTG 3232 chr6ptel1M 200210 CCTTTTCAGTGCCCAGCGTTAAC--TTAGCTGAGCCTTATAA-AAGAGAT 200256 i v vi v iivii v --iv -- i -?ii i-v ?v HERVK14C#LTR/ 3233 CTTTTACTATTCCTGCTATGAACAACAAG--GAACC-NGCAGCCAGNTAT 3279 chr6ptel1M 200257 GAATGGACAGTTTTGCCACAGGA-ATGAAAAATAGCTCTACTCTGTGTCA 200305 v v v ? i i- vvi ii ? ?v v HERVK14C#LTR/ 3280 CATTGGAAAGTNTTGCCGCAGGGCATGTTGAATAGTCCNACNATTTGTCA 3329 chr6ptel1M 200306 AATGTATGTTGCTAGTGCTCTTCA----GTAAGAAAAGCATTTCCAAAAG 200351 iv ? v vv?iv v ---- ? i vvvi i vv HERVK14C#LTR/ 3330 AACTTNTGTGGGGNAGGCTATTCAACCTGTNAGAGATCAGTTTCCAGATT 3379 chr6ptel1M 200352 TG-ATGTTATTACATTATATGGATGATATATTGGGATGTGCACCTGA 200397 i?- i i - i ---? iv i HERVK14C#LTR/ 3380 CNTATATCATT-CATTATATGGATGACATATT---NTGTGCGGCCGA 3422 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.63 CpG sites = 75, Kimura (unadjusted) = 41.48 Transitions / transversions = 0.79 (75/95) Gap_init rate = 0.04 (26 / 584), avg. gap size = 1.19 (31 / 26) 1134 28.99 8.30 2.22 chr6ptel1M 199884 200606 (799394) HERVK14#LTR/ERVK 2660 3425 (2671) m_b276s701i2 10909 chr6ptel1M 199884 ACCAGTGTGGATAGAACAGTGGCC-CTTAGGTAGCGATAAAATTCAGGCC 199932 i v i i i i - v iii - v v vv i HERVK14#LTR/E 2660 ACCGGTTTGGGTGGAGCAATGGCCGCTGAAACAG-GAAAAACTGGAGGCT 2708 chr6ptel1M 199933 TTATTAGATATTGTACAGGAATAACTTGATCAAGGACACTTACAACCTTC 199982 vv vv v i i i vv vv i iv v i v HERVK14#LTR/E 2709 TTAAAAGAACTGGTGCAGGAACAATTGCAAAAGGGACATATAGAGCCTAC 2758 chr6ptel1M 199983 TATAAGTCCTTGGAATTATCCTGTATTTGTTG-TAAGAAAGAAATCTGGA 200031 v vvvi v ii- - v i HERVK14#LTR/E 2759 TTTCTCCCCTTGGAATTCTCCTGTATTTGTCATTAAGAAA-AAATCAGGG 2807 chr6ptel1M 200032 AAATGGAGGATCTTCACTGATTTAAGAAAAGTAAATGAACAGATGGAAAC 200081 i v v v iivv v vvvv vv v HERVK14#LTR/E 2808 AAATGGAGAATGTTAACAGATTTAAGGGCTGTTAATGCTGTGATTCAACC 2857 chr6ptel1M 200082 TATGAGGACTCTTCAGCCCTGACTTCCATCTTCTACTCAGTTACCTAGAG 200131 i i vi v v i vv i v v ii v vvv v v v i v HERVK14#LTR/E 2858 CATGGGTGCACTGCAACCAGGGCTGCCCTCCCCAACAATGATCCCAAAAT 2907 chr6ptel1M 200132 AATGGCCTTTTTGGGTTGTAGACATTAAGGATTGTTTCTATTCTATTCCT 200181 v i ivvi vi iv v i i v v i HERVK14#LTR/E 2908 ACTGGCCTCTCATAGTGATAGATCTAAAGGATTGCTTTTTTACCATTCCT 2957 chr6ptel1M 200182 TTAGATAAGGAGGA-TATGAAAAGATTTGCCTTTTCAGTGCCCAGCGTTA 200230 v ivvv i - - i v v v iv i v HERVK14#LTR/E 2958 TTAGCTGCCCAAGATTATGAAAA-ATTTGCTTTTACTGTTCCCGCCATAA 3006 chr6ptel1M 200231 ACTTAGCTGAGCCTTATAAAAGAGATG--AATGGACAGTTTTGCCAC-AG 200277 -- iivi vvii vvii v i-- v v vi i - HERVK14#LTR/E 3007 A--TAATAAAGAACCAGCGGACAGATACCATTGGAAAGTACTACCACAAG 3054 chr6ptel1M 200278 GAATGAAAAATAGCTCTACTCTGTGTCAAATGTATGTTGCTAGTGCTCTT 200327 v vv i v v v iv i vv iv v HERVK14#LTR/E 3055 GCATGCTAAATAGCCCGACTATTTGTCAAACTTATGTCGGGAAAGCTATT 3104 chr6ptel1M 200328 ----CAGTAAGAAAAGCATTTCCAAAAGTG--ATGTTATTACATTATATG 200371 ---- v i - v iv i -- i i- i HERVK14#LTR/E 3105 AAGCCAGTTAGAGAA-CAGTTTAAAAAATGTTATATTATC-CATTACATG 3152 chr6ptel1M 200372 GATGATATATTGGGATGTGCACCTGA------GGA--------------- 200400 vi --- v ------ --------------- HERVK14#LTR/E 3153 GATGATATTCTG---TGTGCAGCTGAAACTAGGGAAGAATTGATGTTGTG 3199 chr6ptel1M 200401 --ACAAATA-TTAGAA---GC-----ATGTCAC----------ATAGCTC 200429 -- i - --- ----- ivi ---------- i HERVK14#LTR/E 3200 CTACAAACAGTTAGAAAAGGCTGTAAATGCGGCAGGGTTAATTATAGCCC 3249 chr6ptel1M 200430 CAGAAAAAATTCAAAGACATGCTCCTTTTCAATATTTAGGATATGAA-GT 200478 v v i vviv i i i - - HERVK14#LTR/E 3250 CCGATAAAATCCAAACTTCTACTCCCTTTCAATATCTAGGA-ATGAAGGT 3298 chr6ptel1M 200479 ATATCCTAAGGTGCTTACATTA-----CAAAAACTTCCCTTAAGAACAGA 200523 v v -- i --- ----- iv vvv vv v HERVK14#LTR/E 3299 AGAAC--AAAGTGCT---ATTAAGCCTCAAAAGGTTCAAATTCGAAGAGA 3343 chr6ptel1M 200524 GAAGCTAAACACCTTAAATGACTTTCAGAAATAGATAAGGAGATATGCAA 200573 v vi v i i i -v v i vv v HERVK14#LTR/E 3344 TAATTTAAAAACCTTAAATGATTTCCAAAAAT-TATTAGGAGACATTAAT 3392 chr6ptel1M 200574 TGGATGCGGCCAGTGTTAGGCCTGACTACCTAT 200606 v v iiv v vv HERVK14#LTR/E 3393 TGGATTCGTCCAACTTTAGGCATTCCTACCTAT 3425 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 35.73 CpG sites = 82, Kimura (unadjusted) = 36.80 Transitions / transversions = 0.67 (82/123) Gap_init rate = 0.05 (33 / 722), avg. gap size = 2.33 (77 / 33) 306 27.03 5.11 5.56 chr6ptel1M 200420 200654 (799346) HERVK11D#LTR/ERVK 3671 3904 (3848) m_b276s701i3 10909 chr6ptel1M 200420 CACATAGCTCCAGAAAAAATTCAA--AGACATGCTCCTTTTCAATATTTA 200467 v v v -- v -- vi i HERVK11D#LTR/ 3671 CACATCGCTCCTGATAAAATTCAACAAGCCA--CTCCTTTTCTGTACTTA 3718 chr6ptel1M 200468 GGATATGAAGTATATCCTAAGGT-GCTTACATTA-----CAAAAACTTCC 200511 - v i- v--- v - i- ----- v i v HERVK11D#LTR/ 3719 GGA-ATGCAGC-TAG---AAGCTCGCTC-CATTAAGCCCCAAAAAGTCCA 3762 chr6ptel1M 200512 CTTAAGAACAGAGAAGCTAAACACCTTAAATGACTTTCAGAAATAGATAA 200561 vi vv v v v vi i i -v iv HERVK11D#LTR/ 3763 ACTTCGTACTGACAATTTAAACACCTTAAATGATTTTCAAAAAT-TACTA 3811 chr6ptel1M 200562 GGAGATATGCAATGGATGC-GGCCAGTGTTAGGCCTGACTACCTAT-CA- 200608 v i - viviv - i iivi v vv i - - HERVK11D#LTR/ 3812 GGTGACAT-CAATTATCTCAGACCAACCCTAGGCATCCCTACTTATGCAT 3860 chr6ptel1M 200609 -ATTGCAACTGTTATATGACATTTTAATGAAAGACAGTGCTTTAAAC 200654 - iv v i --- v i viiii i vv v HERVK11D#LTR/ 3861 TATCTCATCTATT---TGCCACTTTATCAGGAGATACAGATTTAAAC 3904 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 33.64 CpG sites = 26, Kimura (unadjusted) = 33.64 Transitions / transversions = 0.76 (26/34) Gap_init rate = 0.09 (20 / 234), avg. gap size = 1.25 (25 / 20) 41 0.00 2.56 0.00 chr6ptel1M 201399 201437 (798563) (TA)n#Simple_repeat 1 40 (0) c_b276s251i3 10910 chr6ptel1M 201399 TATA-ATATATATATATATATATATATATATATATATATA 201437 - (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATA 40 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.03 (1 / 38), avg. gap size = 1.00 (1 / 1) 12 18.27 5.41 0.00 chr6ptel1M 201561 201597 (798403) (ATAAGT)n#Simple_repeat 1 39 (0) m_b276s252i11 10911 chr6ptel1M 201561 ATATGTTAAAGTATAAGT-TAAATACAA-TATATGTATA 201597 v vv - i i - v (ATAAGT)n#Sim 1 ATAAGTATAAGTATAAGTATAAGTATAAGTATAAGTATA 39 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 509 28.48 4.75 3.66 chr6ptel1M 201926 202304 (797696) HERVK14C#LTR/ERVK 4729 5111 (2323) m_b276s701i4 10909 chr6ptel1M 201926 AACCTTTGTGGTTTGAGACCCAATGAATTTTGGCAAATGGATGTGATTCA 201975 i?i v v iv? i ?vii ? i ? ii HERVK14C#LTR/ 4729 AACCCNCGAGGATTGGCNCCTAATNCGCTNTGGCAAATGGACGTNACCCA 4778 chr6ptel1M 201976 TTATAAATCT-TTTGGTCGTCTGTCTTTTATCTATGTTGTGGTAGACCCT 202024 -i vv ?i- vviv ? ? vii i ?iiv iv i HERVK14C#LTR/ 4779 T-GTACCTNCATTTGGGAAACTNTCNTACGTCCATGTNACTGTAGATACC 4827 chr6ptel1M 202025 TTTTCAGGATTCACTTTT-----GCAA--TACCAGCAGCAGAAGAGACAG 202067 ----- i v----- ? -- i -- i i? i ? HERVK14C#LTR/ 4828 TTTTC-----TCATTTTGTNTGGGCNACTTGCCA--AACAGGNGAGGCNG 4870 chr6ptel1M 202068 CC-CAAGTGGTCACTGA-ATTCCTTATCCAAGCAAATGCAATTATGGGTG 202115 i- vv v v vv - ivi v viviv--i ?i i ii HERVK14C#LTR/ 4871 CTGCTCGTGTTAAAAGACATTTGCTTTCCTGTTT--CGCNGTCATGGGCA 4918 chr6ptel1M 202116 TGTCACAAGCAATAAAAACAGATAATGGACCTGCATATACTTCTAAACAT 202165 vi iv? v ? i v v vv i?? vv ?-i HERVK14C#LTR/ 4919 TTCCACAAAANATTAAAACNGACAATGGCCCAGGCTACNNTAGTAAAN-C 4967 chr6ptel1M 202166 TTTGCACACTTTTGTGCACACAGTATAAGATTTTACACACTACTGGCATA 202215 i? ?i v iv v - i iv? v vv ? ? v HERVK14C#LTR/ 4968 TTTANANGCGTTCCTTCA-ACAATGGNACATTAAACACANTACTGGNATC 5016 chr6ptel1M 202216 CCTTTTAATCCACAAGGACAGGCAATAGTAGAGAGGAG--AAACAGACAT 202263 i v i v ? i v v v - v -- v ii v HERVK14C#LTR/ 5017 CCCTATAATTCTCAAGGNCAAGCCATTGTTGA-ACGAGCTAATCGAACCT 5065 chr6ptel1M 202264 TAAGATGCTC--CTCCAAAAACAAA----AGAAAGGGGGAGCCACAG 202304 i -? --i v ---- i i v HERVK14C#LTR/ 5066 TAAAA-NCTCAATTACAAAAACAAAAGACAGAAGGGGGGAACCAGAG 5111 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 36.97 CpG sites = 53, Kimura (unadjusted) = 39.89 Transitions / transversions = 1.04 (53/51) Gap_init rate = 0.06 (22 / 378), avg. gap size = 1.45 (32 / 22) 475 29.72 6.44 4.45 chr6ptel1M 201935 202353 (797647) HERVK#LTR/ERVK 4837 5263 (2273) m_b276s701i5 10909 chr6ptel1M 201935 GGTTTGAGACCCAATGAATTTTGGCAAATGGATGTGATTCATTATAAAT- 201983 i v v i vi v v iv -i vv - HERVK#LTR/ERV 4837 GGTCTGTGTCCTAATGCGTTATGGCAAATGGATGTCACGCAT-GTACCTT 4885 chr6ptel1M 201984 CTTTTGGTCGTCTGTCTTTTATCTATGTTGTGGTAGACCCTTTTTCAGGA 202033 v vv vi v ? i i viii v iv v viv HERVK#LTR/ERV 4886 CATTTGGAAGATTGTCATNTGTCCATGTAACAGTTGATACTTATTCACAT 4935 chr6ptel1M 202034 TTCACTTTTGCAA--TACCAG-CAGCAGAAGAGACAGCCCAAGTGGTCAC 202080 iv vv -- i - v iiv vv -- v v v HERVK#LTR/ERV 4936 TTCATATGGGCAACCTGCCAGACAGGAGAAAGTACTTCCCA--TGTTAAA 4983 chr6ptel1M 202081 TGA-ATTCCTTATCCAAGCAAATGCAATTATGGGTGTGTCACAAGCAATA 202129 vi - iv iviviv-- vi i v vi v iv v HERVK#LTR/ERV 4984 AAACATTTATTATCTTGTTT--TGCTGTCATGGGAGTTCCAGAAAAAATT 5031 chr6ptel1M 202130 AAAACAGATAATGGACCTGCATATACTTCTAAA-CATTTTGCACACTTTT 202178 v i i v v ivv vv - ? iiiv v i i HERVK#LTR/ERV 5032 AAAACTGACAATGGGCCAGGATACTGTAGTAAAGCNTTCCAAAAATTCTT 5081 chr6ptel1M 202179 GTGCACACAGTATAAGATTTTACACACTACTGGCATACCTTTTAATCCAC 202228 i--- vv iv i vi i v v v v v i v HERVK#LTR/ERV 5082 A---AATCAGTGGAAAATTACACATACAACAGGAATTCCTTATAATTCCC 5128 chr6ptel1M 202229 AAGGACAGGCAATAGTAGAGAGGAGAAACAG-ACATTAAGATGCTCCTCC 202277 v v i i vv i - i v i - ---- HERVK#LTR/ERV 5129 AAGGACAGGCCATAGTTGAAAGAACTAATAGAACACTCAAA-GCT----C 5173 chr6ptel1M 202278 AA------AAACAAAAGAAAGGGGGAGCCACAG--------GTAACCCT- 202312 ------ ii -- -------- ? v - HERVK#LTR/ERV 5174 AATTGGTTAAACAAAAAGAAGGGGGAG--ACAGTAAGGAGTGTANCACTC 5221 chr6ptel1M 202313 -----ATAGAACTTTTAAATTTAGCTCTTTATACTATTAACTTCTT 202353 ----- iv --- i v i - v i HERVK#LTR/ERV 5222 CCCAGATGCAACTT---AATCTAGCACTCTATACT-TTAAATTTTT 5263 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 37.65 CpG sites = 51, Kimura (unadjusted) = 38.43 Transitions / transversions = 0.75 (51/68) Gap_init rate = 0.07 (29 / 418), avg. gap size = 1.59 (46 / 29) 575 31.17 3.29 3.97 chr6ptel1M 201944 202247 (797753) HERVK11#LTR/ERVK 4978 5279 (2674) m_b276s701i6 10909 chr6ptel1M 201944 CCCAATGAATTTTGGCAAATGGATGTGATTCATTATAAATCTTTTGGTCG 201993 i ?v v i vv iv i iv HERVK11#LTR/E 4978 CCTAATGNTTTATGGCAAATGGATGTGACTCATGTTAGCTCCTTTGGCAG 5027 chr6ptel1M 201994 TCTGTCTTTTATCTATGTTGTGGTAGACCCTTTTTCAGGATTCACTTTTG 202043 v ? v v i vi viv iv i i v i ii vv HERVK11#LTR/E 5028 ACTNTCATATGTGCATGTTTCTGTAGATACCTTCTCAGGTTTTATCTGGG 5077 chr6ptel1M 202044 CAA--TACC-AGCAGCAGAAGAGACAGCCCAAGT----GGTCA-CTGAAT 202085 v -- i - i vi iv i v ----iiv - v HERVK11#LTR/E 5078 CTACTTGCCAAACAGGGGAAGGCACGGCCCATGTTAAAAAACATCTGTAT 5127 chr6ptel1M 202086 TCCTTATCCAAGCAAATGCAATTATGGGTGTGTCACAAGCAATAAAAACA 202135 i vv i-------- i vv vi i vvv i HERVK11#LTR/E 5128 TCTTGCTT--------TGCAGTTATGGGGCTTCCATATCAAATAAAGACA 5169 chr6ptel1M 202136 GATAATGGACCTGCATATACTTCTAAACATTTTGCACACT--TTTGTGCA 202183 i i vv v ii vv ivv --- i -- i HERVK11#LTR/E 5170 GACAACGCCCCTGGATATGTTAGTAAGGCTTTTG---ATTTATTTATGCA 5216 chr6ptel1M 202184 CACAGTATAAGATTTTACACACTACTGGCATACCTTTTAATCCACAAGGA 202233 - iviii iv i i i v v vi v i HERVK11#LTR/E 5217 -ACAGTGGGGAATTTCCCATATTACCGGAATCCCTTACAATCCTCAGGGA 5265 chr6ptel1M 202234 CAGGCAATAGTAGA 202247 vi i i HERVK11#LTR/E 5266 CAGGCTGTGGTGGA 5279 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.59 CpG sites = 47, Kimura (unadjusted) = 41.34 Transitions / transversions = 1.07 (47/44) Gap_init rate = 0.06 (17 / 303), avg. gap size = 1.29 (22 / 17) 235 35.93 2.83 2.83 chr6ptel1M 204194 204299 (795701) C L2d2_3end#LINE/L2 (17) 538 433 m_b276s601i8 10912 chr6ptel1M 204194 ACATTTATTAAACACCTGCTGGATACAGATCATGATGCTAGCCACCAAGA 204243 i i i i i vi i iiv ivi v i iiv i C L2d2_3end#LIN 538 ATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGTGG 489 chr6ptel1M 204244 GGG--ACAGAAAACCTGGATGCACCAGGGCATCTGTCCT-AGAGAGGTAA 204290 -- i i --- v iviv v ivi i - ii v v C L2d2_3end#LIN 488 GGGATACAAAGAA---GTATAAGACATGGTCCCTGCCCTCAAGGAGCTTA 442 chr6ptel1M 204291 CACTCTAGT 204299 v C L2d2_3end#LIN 441 CAATCTAGT 433 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 48.01 CpG sites = 24, Kimura (unadjusted) = 52.13 Transitions / transversions = 1.85 (24/13) Gap_init rate = 0.05 (5 / 105), avg. gap size = 1.20 (6 / 5) 13 26.36 1.72 3.51 chr6ptel1M 205064 205121 (794879) (GGGGA)n#Simple_repeat 1 57 (0) m_b276s252i12 10913 chr6ptel1M 205064 GGGGGGGGGAGGGGAGATCCCTGTGATGGCCTGGG-GAGGAGGGGCAGGG 205112 i -vvvvv v v vvv - i - (GGGGA)n#Simp 1 GGGGAGGGGAGGGGAG-GGGAGGGGAGGGGAGGGGAGGGGAGGGG-AGGG 48 chr6ptel1M 205113 GAGGGGAGG 205121 (GGGGA)n#Simp 49 GAGGGGAGG 57 Matrix = Unknown Transitions / transversions = 0.20 (2/10) Gap_init rate = 0.05 (3 / 57), avg. gap size = 1.00 (3 / 3) 16 18.85 0.00 0.00 chr6ptel1M 205515 205550 (794450) (GCGG)n#Simple_repeat 1 36 (0) m_b276s252i13 10914 chr6ptel1M 205515 GCGGACGGGCCCGCGGGCGGGCAGGGGCGCGGGCGG 205550 i vv i v v (GCGG)n#Simpl 1 GCGGGCGGGCGGGCGGGCGGGCGGGCGGGCGGGCGG 36 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 294 29.56 2.19 11.11 chr6ptel1M 206536 206672 (793328) MIR#SINE/MIR 87 212 (50) m_b276s601i9 10915 chr6ptel1M 206536 GACTTTGAGC---TTATCCCCAACTTCAGCCTGTCCTAGTTTGCTCATCT 206582 i i --- -- ii i vviv i ii v MIR#SINE/MIR 87 GACCTTGGGCAAGTTA--CTTAACCTCTCTGTGCCTCAGTTTCCTCATCT 134 chr6ptel1M 206583 CCGAAGTGGGGAGAATTCGAGCACCCGCCTCCCAGGGTTGTTGCAAAGTC 206632 vii i v vvv i ii vi ii i -- MIR#SINE/MIR 135 GTAAAATGGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGG-- 182 chr6ptel1M 206633 ACATTAAGAAAACGTTTATGCAGGCTTTTGCAAATCGCTT 206672 -- ivi -- v i ------ i v MIR#SINE/MIR 183 --ATTAAATGA--GTTAATACA------TGTAAAGCGCTT 212 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 38.60 CpG sites = 23, Kimura (unadjusted) = 38.60 Transitions / transversions = 1.77 (23/13) Gap_init rate = 0.11 (15 / 136), avg. gap size = 1.13 (17 / 15) 247 27.59 0.00 0.00 chr6ptel1M 207218 207275 (792725) MIR3#SINE/MIR 107 164 (44) m_b276s601i10 10916 chr6ptel1M 207218 CATTTCTCTCGCTTTCAGTTTCTTCCCTTGTTAAATAAAGGGGTTGGACA 207267 ii v vii i vii v i i v MIR3#SINE/MIR 107 CACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACT 156 chr6ptel1M 207268 AGCTCATC 207275 v v MIR3#SINE/MIR 157 AGATGATC 164 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 35.10 CpG sites = 9, Kimura (unadjusted) = 35.10 Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0) 453 27.67 6.77 2.16 chr6ptel1M 207538 207670 (792330) MIRc#SINE/MIR 19 157 (111) m_b276s601i11 10917 chr6ptel1M 207538 TGAAACAGAGCACTGACC-----GTTAAAACG--CCAGGTT--AATCCCA 207578 i - iv ----- i ii v -- ii -- i i MIRc#SINE/MIR 19 TGGAA-AGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCG 67 chr6ptel1M 207579 CTTCTGTTGCTTACTAGTTATGGAAGCTTGGACAATAATCATTTTACCTT 207628 vi iii i i vi v i --i i v i MIRc#SINE/MIR 68 GCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA--GTCACTTAACCTC 115 chr6ptel1M 207629 TGTGGAATTCAGTCTCCACATCTGTCCAATGAGGATAATAAT 207670 v iivi i v vv i MIRc#SINE/MIR 116 TCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAAT 157 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 35.02 CpG sites = 25, Kimura (unadjusted) = 36.31 Transitions / transversions = 2.27 (25/11) Gap_init rate = 0.05 (6 / 132), avg. gap size = 2.00 (12 / 6) 312 28.57 13.33 0.00 chr6ptel1M 207769 207873 (792127) C MIRb#SINE/MIR (70) 198 80 m_b276s601i12 10918 chr6ptel1M 207769 ATCTTACTTGATCTTCGCAACAACTCT--GAAGTAGA-------AGCCCC 207809 i i i i i i -- i i------- v C MIRb#SINE/MIR 198 ATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATTATCCCC 149 chr6ptel1M 207810 ATTTTATAGATGGGAAAATGGA----TAGATAGGTCATCCGACTGGTCCA 207855 i i i iv ----i v i vvii v i C MIRb#SINE/MIR 148 ATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCA 99 chr6ptel1M 207856 GCGTCATCCC-CCAATAAG 207873 iv iv v- i i C MIRb#SINE/MIR 98 AGGTCACACAGCTAGTAAG 80 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 37.95 CpG sites = 21, Kimura (unadjusted) = 37.95 Transitions / transversions = 2.33 (21/9) Gap_init rate = 0.04 (4 / 104), avg. gap size = 3.50 (14 / 4) 212 25.00 3.33 0.00 chr6ptel1M 208285 208344 (791656) C MIRb#SINE/MIR (156) 112 51 m_b276s601i13 10919 chr6ptel1M 208285 AAAGAACTTGCTCACCGTCACAGTGATAGTAAAT-CCTGAGCTGAG-TTG 208332 iv i vv vv v i -v v i i - v C MIRb#SINE/MIR 112 AAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTC 63 chr6ptel1M 208333 GAACCCAGGCCT 208344 i C MIRb#SINE/MIR 62 GAACCCAGGTCT 51 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 28.20 CpG sites = 6, Kimura (unadjusted) = 30.46 Transitions / transversions = 0.67 (6/9) Gap_init rate = 0.03 (2 / 59), avg. gap size = 1.00 (2 / 2) 562 19.18 1.79 6.88 chr6ptel1M 209125 209292 (790708) Charlie4a#DNA/hAT-Charlie 343 502 (6) m_b276s502i0 10920 chr6ptel1M 209125 TTTTTTTTTTTAACAATATTTTGATCATTGTGTTTATTATTATAAAGTGA 209174 v? --- v i i --i v -v i Charlie4a#DNA 343 TTTGNTTTTTTAA---TATTTTGATAACTGTATTT--CAATATAA-TTGG 386 chr6ptel1M 209175 TTTCATTTGTAATCCTGTGTATTTTTCTTTAATAACTTAAAAATGTAATT 209224 v i vi vvv i ii v Charlie4a#DNA 387 TTTCCTTTGTAATCCTATGTATTTTATTTTATGCATTTAAAAACATTATT 436 chr6ptel1M 209225 CTG---AGGAGTCTCTAGGCTTCCCCAGTCTGCCATGGGGAGGAGGTCCA 209271 --- i iv v v ----- i i Charlie4a#DNA 437 CTGAGAAGGGGTCCATAGGCTTCACCAGACTGCCA-----AAGGGGTCCA 481 chr6ptel1M 209272 TGTCATGAAAAAGGTTGAGAA 209292 v ii i Charlie4a#DNA 482 TGGCACAAAAAAGGTTAAGAA 502 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 22.41 CpG sites = 16, Kimura (unadjusted) = 22.41 Transitions / transversions = 1.14 (16/14) Gap_init rate = 0.07 (12 / 167), avg. gap size = 1.17 (14 / 12) 494 23.09 0.75 6.30 chr6ptel1M 209597 209730 (790270) MIRc#SINE/MIR 2 128 (140) m_b276s601i14 10921 chr6ptel1M 209597 GGGGCAGCTGGATGGCACAGTGAATAGAGAACCAGCCCTGAAGTCAGGAG 209646 i - -- ii i v v ii v i i i MIRc#SINE/MIR 2 GAGGCAG-TG--TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr6ptel1M 209647 GACCTGAATTCAATTCTGGCCTCAGACACAATGCTTTCTAGCTGTGTGAC 209696 ii i v iv v v v ----- v MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCCA-----CTTACTAGCTGTGTGAC 93 chr6ptel1M 209697 TCTGGGCAAGCCACTTAACCCCAATT-GCCTCAGT 209730 ii i i vv v- MIRc#SINE/MIR 94 CTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGT 128 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 26.88 CpG sites = 17, Kimura (unadjusted) = 28.00 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.07 (9 / 133), avg. gap size = 1.00 (9 / 9) 198 17.14 0.00 0.00 chr6ptel1M 209747 209781 (790219) C MIR3#SINE/MIR (9) 199 165 m_b276s601i15 10922 chr6ptel1M 209747 AAACATAGAATGTTGGAGCTGGAGGGAACCTTTGA 209781 v ii i i v C MIR3#SINE/MIR 199 AATCATAGAATGTCAGAGCTGGAAGGGACCTTAGA 165 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 19.86 CpG sites = 4, Kimura (unadjusted) = 19.86 Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 478 21.59 10.60 1.83 chr6ptel1M 209817 209967 (790033) C Charlie4a#DNA/hAT-Charlie (1) 507 344 m_b276s502i1 10923 chr6ptel1M 209817 AGAGGCTCTTATTCTTTTTTTGTACC-TGACAATGTCTTGACAGTCTTCA 209865 i i vi - i - i- vivii i vvv C Charlie4a#DNA 507 AGGGGTTCTTAACCTTTTTT-GTGCCATGG-ACCCCTTTGGCAGTCTGGT 460 chr6ptel1M 209866 GAAGCCGCTAGACCCCCTTCTCAGA--------------TCCATAGA-CA 209900 vv i - -------------- v i -i C Charlie4a#DNA 459 GAAGCCTATGGACCCC-TTCTCAGAATAATGTTTTTAAATGCATAAAATA 411 chr6ptel1M 209901 AAATATATAGGATTACAAAGGAAACCGATTACACTGATGTATGGTTTTCA 209950 i i i i vi ii v C Charlie4a#DNA 410 AAATACATAGGATTACAAAGGAAACCAATTATATTGAAATACAGTTATCA 361 chr6ptel1M 209951 TAATATTGAAAAAACAA 209967 v i ? C Charlie4a#DNA 360 AAATATTAAAAAANCAA 344 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 26.28 CpG sites = 20, Kimura (unadjusted) = 26.28 Transitions / transversions = 1.67 (20/12) Gap_init rate = 0.04 (6 / 150), avg. gap size = 3.17 (19 / 6) 236 33.10 0.00 7.59 chr6ptel1M 209968 210052 (789948) C MIR3#SINE/MIR (22) 186 108 m_b276s601i16 10924 chr6ptel1M 209968 CAAAAATGAAGGATATTTTGGAGATTATCAAATTCAATCCCATTCTCTTA 210017 i iv i i iv ii i i v i i i v iv i C MIR3#SINE/MIR 186 CAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTA 137 chr6ptel1M 210018 TAGAACTCCCTCTGTAAACTGAGACCCAAAGAGAT 210052 i ------ vv v i i i C MIR3#SINE/MIR 136 CAGA------TGAGGAAACTGAGGCCCAGAGAGGT 108 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 46.36 CpG sites = 18, Kimura (unadjusted) = 46.36 Transitions / transversions = 2.25 (18/8) Gap_init rate = 0.07 (6 / 84), avg. gap size = 1.00 (6 / 6) 809 26.44 4.72 7.69 chr6ptel1M 210127 210380 (789620) C MIRc#SINE/MIR (20) 248 2 m_b276s601i17 10925 chr6ptel1M 210127 TTTATATAGTGCTT-AAAGTTGCCAAAGCTATTTATATTTATTTATTTAC 210175 i ii - v vv -------ii -- i iv C MIRc#SINE/MIR 248 TTTGTATAGCACTTTACAGTTTACAAAGC-------GCTT--TCACATAC 208 chr6ptel1M 210176 AT-ATCTCATTTGTTCTTTGCAATAGCTCTGTGAGGTGAGTAGAATGGAT 210224 - v i ii i i i ii i iiii i C MIRc#SINE/MIR 207 ATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGT 158 chr6ptel1M 210225 ATTATTATTATTATTATTTTGCTGAGGCAATT----------GGGGTTAA 210264 ivii v viv v v i ---------- i C MIRc#SINE/MIR 157 ATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAA 108 chr6ptel1M 210265 ATAACTTGCCCAGGGTCACACAGGTAGGAAGTGTTAAGCATCTGAGATCA 210314 i i i v v ---- --- vivi C MIRc#SINE/MIR 107 GTGACTTGCCCAAGGTCACACAGCTAGTAAGTG----GCA---GAGCCGG 65 chr6ptel1M 210315 GATTTGAACTCAGGTCCTCCTGACTTCAGAGCTGGTGCTCTATCCATGGC 210364 i i i i i iiv ii v iv C MIRc#SINE/MIR 64 GACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGC 15 chr6ptel1M 210365 ACCACCTAACTGTCCC 210380 --- i i C MIRc#SINE/MIR 14 ACCAC---ACTGCCTC 2 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 32.10 CpG sites = 44, Kimura (unadjusted) = 34.15 Transitions / transversions = 2.44 (44/18) Gap_init rate = 0.09 (22 / 253), avg. gap size = 1.41 (31 / 22) 326 23.26 5.81 0.00 chr6ptel1M 210378 210463 (789537) C MIR#SINE/MIR (91) 171 81 m_b276s601i18 10922 chr6ptel1M 210378 CCCTAGAA--TGAATGTTATTATTATGCCCATTTTTCAGATGAGGAACTT 210425 vi -- iii ii v v vi C MIR#SINE/MIR 171 CCCTATGAGGTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACT 122 chr6ptel1M 210426 GAGGT-CA-AGA-CTCAAGTGACTTGCCCATGTCCAAATAG 210463 i- - -v i i v vi v i C MIR#SINE/MIR 121 GAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAG 81 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 28.41 CpG sites = 12, Kimura (unadjusted) = 28.41 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.05 (4 / 85), avg. gap size = 1.25 (5 / 4) 451 20.49 9.02 0.00 chr6ptel1M 210393 210514 (789486) C MIRc#SINE/MIR (110) 158 26 m_b276s601i19 10922 chr6ptel1M 210393 TATTATTATGCCCATTTTTCAGATGAGGAACTTGAGG-TCA-AGA-CTCA 210439 v v vi - - -v i C MIRc#SINE/MIR 158 TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTA 109 chr6ptel1M 210440 AGTGACTTGCCC-ATGTC---CAAATAGTA--TGG--GGACTTTTTTTTC 210481 - v --- iv -- -- ii ivvvvi iv C MIRc#SINE/MIR 108 AGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCG 59 chr6ptel1M 210482 AACTCAAGTCTTCCTGAATCCAAGTCTGGTACT 210514 i i v ii i C MIRc#SINE/MIR 58 AACCCAGGTCTTCCTGACTCCAAGTCCAGTGCT 26 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 22.04 CpG sites = 13, Kimura (unadjusted) = 24.14 Transitions / transversions = 1.08 (13/12) Gap_init rate = 0.06 (7 / 121), avg. gap size = 1.57 (11 / 7) 19 4.50 0.00 0.00 chr6ptel1M 210923 210945 (789055) (A)n#Simple_repeat 1 23 (0) m_b276s252i14 10926 chr6ptel1M 210923 AAAAAAAAAAAAAAACAAAAAAA 210945 v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAA 23 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 463 26.97 19.72 0.79 chr6ptel1M 211307 211519 (788481) C MIRc#SINE/MIR (2) 266 14 m_b276s601i20 10927 chr6ptel1M 211307 TAGTAATCATCAATCTCATTTCTAGATCACCTCAAAGTTGACAAAATGCT 211356 i v i?vv iv v v v i i v v ii C MIRc#SINE/MIR 266 TAATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCGCT 217 chr6ptel1M 211357 TCC-----------CTCAC----------CAACAGTTCTTCATGGTAGGG 211385 i ----------- i---------- iii viiv v C MIRc#SINE/MIR 216 TTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGC 167 chr6ptel1M 211386 AGTACACTTGTTATTATCC----TTTACAGATGAGGAAACTGAGGCCCAA 211431 vi vv i ---- i i C MIRc#SINE/MIR 166 AGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAG 117 chr6ptel1M 211432 AGACATAATATAATTTGGCCAAGGGCAAAGAGTGCCAGTA------AGAG 211475 vi v vi i i v v v v -- i ------ C MIRc#SINE/MIR 116 AGAGGTTAAGTGACTTGCCCAAGGTCACACA--GCTAGTAAGTGGCAGAG 69 chr6ptel1M 211476 TTAGGGCATGAACCCA---CT------CTCCA--CCCAGAAATCTTTTCA 211514 iii i vi --- ------ --i viv i C MIRc#SINE/MIR 68 CCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCA 19 chr6ptel1M 211515 CTTCA 211519 v C MIRc#SINE/MIR 18 CTGCA 14 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 32.02 CpG sites = 31, Kimura (unadjusted) = 34.27 Transitions / transversions = 1.19 (31/26) Gap_init rate = 0.04 (9 / 212), avg. gap size = 4.89 (44 / 9) 892 23.54 4.80 3.15 chr6ptel1M 211660 211909 (788091) MIRb#SINE/MIR 15 268 (0) m_b276s601i21 10928 chr6ptel1M 211660 GATACAGCGGATGGAACAGAGGATGTAGAGTCAAGAAGATGTGAAATCAG 211709 i i i vi i vi v v i iiv iv iiv ii MIRb#SINE/MIR 15 GGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCGA 64 chr6ptel1M 211710 ATCTAGCTTCTG--A--TACTAG-TGTGTGAATTTGGGCAAGTCAGTTAA 211754 iv vi -- -- - vi i v MIRb#SINE/MIR 65 ATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAA 114 chr6ptel1M 211755 CCTCTCTCTGCCTTGGTTTCCTTATCTGTAAAATGGGGGATAATAATGGG 211804 vv ii i - --- MIRb#SINE/MIR 115 CCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAAT-GGGGATAATAAT--- 160 chr6ptel1M 211805 GATAATACTCCTTCAGGAATATTTTGAGGTTCAGATGAGATA---TCTGT 211851 - i-v - iiv iv i v v i i ---iv MIRb#SINE/MIR 161 -AC-CTAC-CTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCATGT 207 chr6ptel1M 211852 AAAGCACTCAGCACAGTGTCTGGCACATAGCAGATACT--ATATAATGGT 211899 i i i i iiii -- - MIRb#SINE/MIR 208 AAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATA-AATGGT 256 chr6ptel1M 211900 TG--CTATTATT 211909 v -- MIRb#SINE/MIR 257 AGCTCTATTATT 268 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 26.09 CpG sites = 37, Kimura (unadjusted) = 29.10 Transitions / transversions = 1.85 (37/20) Gap_init rate = 0.06 (14 / 249), avg. gap size = 1.43 (20 / 14) 247 31.59 5.83 2.42 chr6ptel1M 212298 212417 (787583) C MIRc#SINE/MIR (142) 126 3 m_b276s601i22 10929 chr6ptel1M 212298 TGGGACT--GACAGGTTAAGAGGCCTTCCCAGAGTCACACAGCACTTCTG 212345 i i -- v v i i v ii -- vv i C MIRc#SINE/MIR 126 TGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAG--CTAGTA 79 chr6ptel1M 212346 TATGAAAGAGGT-GGACTCTTTCCCAGATTTTCCTAAGGCACAAAGCTAG 212394 vi iv vi- vvv i i i vv - iv i C MIRc#SINE/MIR 78 AGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTC-CAAGTCCAG 30 chr6ptel1M 212395 ----CTAGCTACTCTACCAAGCTGCTT 212417 ---- vv i vi vi i C MIRc#SINE/MIR 29 TGCTCTTTCCACTGCACCACACTGCCT 3 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 40.30 CpG sites = 19, Kimura (unadjusted) = 41.76 Transitions / transversions = 1.06 (19/18) Gap_init rate = 0.05 (6 / 119), avg. gap size = 1.67 (10 / 6) 208 31.51 1.37 0.00 chr6ptel1M 213380 213452 (786548) C L2c_3end#LINE/L2 (54) 424 351 m_b276s601i23 10930 chr6ptel1M 213380 GACGCAACAAAAAGCAAAAC-CTGTCCCTGCTCTAAAGAAGCTGATACTC 213428 ii vi vi ii i - v i v i v i v C L2c_3end#LINE 424 GATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTC 375 chr6ptel1M 213429 TACTGAAGGAGTCAAACCGGCAGA 213452 v i v i v? i i C L2c_3end#LINE 374 TAGTGGAGGAGACAGACANGTAAA 351 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 43.26 CpG sites = 14, Kimura (unadjusted) = 43.26 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.01 (1 / 72), avg. gap size = 1.00 (1 / 1) 221 29.83 10.43 6.72 chr6ptel1M 214176 214290 (785710) MIRc#SINE/MIR 20 138 (130) m_b276s601i24 10931 chr6ptel1M 214176 GGAAACAGGGCTAGCCCTGGGGTGAGCACCGGAAGGGGAGCTGGGCTTGG 214225 v vi i v i i ----- v --- v i i i MIRc#SINE/MIR 20 GGAAAGAGCACTGGACTTGGAGT-----CAGGAAG---ACCTGGGTTCGA 61 chr6ptel1M 214226 ATCCCGGCTCTGGAGCTCGCTGCGCGTTTGACTTTGGACA---------- 214265 i vvi ii ivvi v i i ---------- MIRc#SINE/MIR 62 GTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAA 111 chr6ptel1M 214266 --CCTCTAGACCTTAGTTTCCTTAACT 214290 --i iii i i v MIRc#SINE/MIR 112 CCTCTCTGAGCCTCAGTTTCCTCATCT 138 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 38.31 CpG sites = 21, Kimura (unadjusted) = 39.95 Transitions / transversions = 1.91 (21/11) Gap_init rate = 0.09 (10 / 114), avg. gap size = 2.00 (20 / 10) 19 23.70 3.03 1.49 chr6ptel1M 216921 216986 (783014) (GAGGGGA)n#Simple_repeat 1 67 (0) m_b276s252i15 10932 chr6ptel1M 216921 GAGTGGAGTGGGCGTGAGGGGTAAGGGGAGAGGGGA-A-GGGAAAGGGGA 216968 v v - v vi - - i (GAGGGGA)n#Si 1 GAGGGGAGAGGG-GAGAGGGGAGAGGGGAGAGGGGAGAGGGGAGAGGGGA 49 chr6ptel1M 216969 TGGAAGAATGGGGAGTGG 216986 vi ii iv v (GAGGGGA)n#Si 50 GAGGGGAGAGGGGAGAGG 67 Matrix = Unknown Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.05 (3 / 65), avg. gap size = 1.00 (3 / 3) 188 19.08 15.58 4.71 chr6ptel1M 217225 217301 (782699) MIR3#SINE/MIR 100 184 (24) m_b276s601i25 10933 chr6ptel1M 217225 GTCACTCGTCAGTCTCCTTA--CCTCAGTGTCCTTCAT-TGTAAAATGAG 217271 -- -i ii i-- v - - MIR3#SINE/MIR 100 GTCACT--TCA-CCTCTCTGGGCCTCAGTTTCCT-CATCTGTAAAATGAG 145 chr6ptel1M 217272 ------GAACT---CGATCTCCTAGGTCCTTTTGAACCC 217301 ------ i ---i iv i iv i i MIR3#SINE/MIR 146 GGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTC 184 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 23.11 CpG sites = 11, Kimura (unadjusted) = 23.11 Transitions / transversions = 3.67 (11/3) Gap_init rate = 0.11 (8 / 76), avg. gap size = 2.00 (16 / 8) 220 29.69 0.00 0.00 chr6ptel1M 217397 217460 (782540) C MIRc#SINE/MIR (136) 132 69 m_b276s601i26 10934 chr6ptel1M 217397 GGAAACTGAGGCCCAGAGAAAGATGGTGCCTTGCTCGAAGTCATAGAGGT 217446 i iivvvi v i i i i v v C MIRc#SINE/MIR 132 GGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCT 83 chr6ptel1M 217447 AGTAGCTGAAGGAG 217460 iv ivi C MIRc#SINE/MIR 82 AGTAAGTGGCAGAG 69 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 38.82 CpG sites = 11, Kimura (unadjusted) = 38.82 Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0) 240 24.53 0.00 0.00 chr6ptel1M 217397 217449 (782551) C MIR3#SINE/MIR (79) 129 77 m_b276s601i27 10934 chr6ptel1M 217397 GGAAACTGAGGCCCAGAGAAAGATGGTGCCTTGCTCGAAGTCATAGAGGT 217446 iivivi v i i i i v v? C MIR3#SINE/MIR 129 GGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGCN 80 chr6ptel1M 217447 AGT 217449 C MIR3#SINE/MIR 79 AGT 77 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 31.20 CpG sites = 8, Kimura (unadjusted) = 31.20 Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 362 29.77 5.34 0.00 chr6ptel1M 217541 217671 (782329) C UCON86#LINE/L2 (218) 464 327 m_b276s502i2 10935 chr6ptel1M 217541 ATCTGTTTTCTGCTGAGATTTGGAAGAGAACACAGGATCAGT-AGGC--A 217587 v i ?v v i iiii iiv ii ii - -- C UCON86#LINE/L 464 ATGTATTTTNAGATGAGATTTGAAAAGAGATGGAGAGTCGATGAGGCGGA 415 chr6ptel1M 217588 GAAATGCTAAAAGGGTTTTCCAGATGGCAGGGACTGC---TGAGAAATTT 217634 i i vii v v ii ---v ivi C UCON86#LINE/L 414 GAGATACAGGAAGGCTGTTCCAGATGGCAGGAGCTGCAGAGGAGAAGGCT 365 chr6ptel1M 217635 CTTACACC-ATAGGGGCAAGATTGTGTGGTCAGACAGA 217671 ii i - i v i ivvi C UCON86#LINE/L 364 CTCGCGCCAACAGCGGCGAGATTGTGTGAAGGGACAGA 327 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 35.06 CpG sites = 27, Kimura (unadjusted) = 40.53 Transitions / transversions = 2.25 (27/12) Gap_init rate = 0.03 (4 / 130), avg. gap size = 1.75 (7 / 4) 28 0.00 0.00 0.00 chr6ptel1M 217782 217808 (782192) (T)n#Simple_repeat 1 27 (0) c_b276s251i4 10936 chr6ptel1M 217782 TTTTTTTTTTTTTTTTTTTTTTTTTTT 217808 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTT 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 345 32.09 13.43 0.00 chr6ptel1M 218382 218515 (781485) MIRb#SINE/MIR 2 153 (115) m_b276s601i28 10937 chr6ptel1M 218382 AAAGGGTTAGT-TGGTGTGGTAGAA----CA-----TCTGGAG------A 218415 i vi i- ii i ---- ----- i ------ MIRb#SINE/MIR 2 AGAGGGGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACA 51 chr6ptel1M 218416 GAGCTGGATTCAAACACTACTTCTGACATTGACTTGCTATTAGATTCTAG 218465 v i i iv iivi v i v v i vv iii i MIRb#SINE/MIR 52 GACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 101 chr6ptel1M 218466 GCAACTCACTCAACCT--CTAAGCTGTAGTTTCTTTACCTACAAAAAGAA 218513 v i i -- i ivi i i i ii v ii MIRb#SINE/MIR 102 GCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 151 chr6ptel1M 218514 GA 218515 MIRb#SINE/MIR 152 GA 153 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 40.65 CpG sites = 31, Kimura (unadjusted) = 45.11 Transitions / transversions = 2.58 (31/12) Gap_init rate = 0.04 (5 / 133), avg. gap size = 3.60 (18 / 5) 415 36.84 1.50 0.00 chr6ptel1M 218414 218546 (781454) MIR3#SINE/MIR 44 178 (30) m_b276s601i29 10937 chr6ptel1M 218414 GAGAGCTGGATTCAAACACTACTTCTGACATTGACTTGCTATTAGATTCT 218463 v i v iiv iivi v i i ? i vv iii MIR3#SINE/MIR 44 GAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTT 93 chr6ptel1M 218464 AGGCAACTCACTCAACCT--CTAAGCTGTAGTTTCTTTACCTACAAAAAG 218511 i v iv -- ii ivi i i i ii v MIR3#SINE/MIR 94 GGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATG 143 chr6ptel1M 218512 AAGAGATTGAATTAAGGGACTCCCAAGGATCTTTC 218546 i i i i i iiv iii i vi i MIR3#SINE/MIR 144 AGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTC 178 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 55.03 CpG sites = 36, Kimura (unadjusted) = 57.12 Transitions / transversions = 2.77 (36/13) Gap_init rate = 0.01 (1 / 132), avg. gap size = 2.00 (2 / 1) 27 14.91 5.00 0.00 chr6ptel1M 218817 218876 (781124) (CAA)n#Simple_repeat 1 63 (0) m_b276s252i16 10938 chr6ptel1M 218817 CAA-AAAAACACCAA-AA-AACCAAAAGAACAACAACAACCACAACAAAA 218863 - v v - - v v v v v (CAA)n#Simple 1 CAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACA 50 chr6ptel1M 218864 CCAACAACAACAA 218876 v (CAA)n#Simple 51 ACAACAACAACAA 63 Matrix = Unknown Transitions / transversions = 0.00 (0/8) Gap_init rate = 0.05 (3 / 59), avg. gap size = 1.00 (3 / 3) 577 33.82 3.60 3.23 chr6ptel1M 218945 219222 (780778) L3#LINE/CR1 3780 4058 (41) m_b276s601i30 10939 chr6ptel1M 218945 ATCTGAAAG--TATCATCTGAAAGAGGGATTTGATCTATTCCACTTGTTC 218992 i i -- i v i v ii iiiv vii L3#LINE/CR1 3780 ATTTGAAGGGCTGTCATGTGGAAGAGGGATTAGACTTATTCTGTGTGGCT 3829 chr6ptel1M 218993 CCACATGGTATAATGAAAAGCACTCGA-GGCAATGAGCAGAGAAGCATAT 219041 v v i v iv ii v v v i- v i v - i i v L3#LINE/CR1 3830 CCAGAGGGCAGAACTAGGACCAATGGGTGGAAGTTA-CAGGGAGGCAGAT 3878 chr6ptel1M 219042 TTCAGCTTGATTTAAGGAAAAGAAATCCTAAC-GT--GAGACATCC-AAA 219087 i ii v i - vv i -i -- vii - L3#LINE/CR1 3879 TTCGGCTCAATATAAGGAAGA-ACTTTCTAACAATCAGAGCTGTCCAAAA 3927 chr6ptel1M 219088 TTTAAATGGGCTGTCTTGGGGAGCAGTGGATTCTTTCCTCATCTAACCCT 219137 v vi i i ? ii i iii -ii v - i----- L3#LINE/CR1 3928 ATGGAATGGGCTGCCTCGNGAGGTAGTGAGCTC-CCCGTCA-CTG----- 3970 chr6ptel1M 219138 AAGGTCATCATATGCAGGCTAGACGACCATTTCCTGAGTACGTTGTTGAA 219187 i vv viiiv i i i viiii v i v L3#LINE/CR1 3971 GAGGTGTTCAAGCAGAGGCTGGATGACCACTTGTCAGGGATGTTGTAGAA 4020 chr6ptel1M 219188 -AGATTCTAGC--TCAACCACTGGCTGGACTAGATGGC 219222 -i iv -- vi ivivv i i L3#LINE/CR1 4021 GGGATTCCTGCATTGGATGGGAGGTTGGACTAGATGAC 4058 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 46.17 CpG sites = 58, Kimura (unadjusted) = 47.66 Transitions / transversions = 1.76 (58/33) Gap_init rate = 0.06 (16 / 277), avg. gap size = 1.19 (19 / 16) 424 21.41 14.18 0.62 chr6ptel1M 219293 219433 (780567) C MIR3#SINE/MIR (13) 195 36 m_b276s601i31 10940 chr6ptel1M 219293 ATAAAAT---AGGCTTGGAAGGAAACTTGGAGATCATCAAGTCCAATCCT 219339 i --- ivi i v i v i i C MIR3#SINE/MIR 195 ATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCC 146 chr6ptel1M 219340 CTAGTTTTACACATTAGGAAGATGAGTCCCAG-GCAGTGAA-TAAC-TGC 219386 vi v v iv v - vi - i - C MIR3#SINE/MIR 145 CTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGC 96 chr6ptel1M 219387 T-----TCACA----AAGTTA----CAAAAGCCAGCACT-GAAGACAGAC 219422 i----- ----? ---- - i i v - vv ii C MIR3#SINE/MIR 95 CCAAGGTCACACAGCNAGTTAGTGGC-AGAGCCGGGACTAGAACCCAGGT 47 chr6ptel1M 219423 CTCTGGACTCC 219433 iv C MIR3#SINE/MIR 46 CTCCTGACTCC 36 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 24.84 CpG sites = 17, Kimura (unadjusted) = 25.81 Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.06 (9 / 140), avg. gap size = 2.33 (21 / 9) 769 30.20 6.53 0.00 chr6ptel1M 220636 220880 (779120) C MIRc#SINE/MIR (1) 267 7 m_b276s601i32 10941 chr6ptel1M 220636 ATCATAATAATATCTAACACTTATATGGCTCTTTAAGGATTGTAGAACCC 220685 v i?i v i i i v vi v ii i i v C MIRc#SINE/MIR 267 ATAATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCGC 218 chr6ptel1M 220686 TTT-ATAGAGGTCATGTCCCTCCATCTTTTCAACAGTCCTGGGAGGT--- 220731 - i v vi i v vi iv i iv ii v --- C MIRc#SINE/MIR 217 TTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGG 168 chr6ptel1M 220732 ---GGTTGTTATTATTATCCCTATTTCATAAATGAATAAATTGAGACTGA 220778 --- iv v i i i i iv i i v C MIRc#SINE/MIR 167 CAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCA 118 chr6ptel1M 220779 GAAAGGTTCAATCATTTTCTTAGAGCCACACAGCTACTAAATGTCTGAGG 220828 i v i v i v ii ii i v i v v v C MIRc#SINE/MIR 117 GAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGC 68 chr6ptel1M 220829 CAGGATTTGAATTCAGGTCT------CTACAACTCC--CACTTCTGCCAC 220870 i i i ii ------ v v --ii ii v C MIRc#SINE/MIR 67 CGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCAC 18 chr6ptel1M 220871 T-TACCTCACT 220880 -i v C MIRc#SINE/MIR 17 TGCACCACACT 7 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 38.93 CpG sites = 46, Kimura (unadjusted) = 40.36 Transitions / transversions = 1.64 (46/28) Gap_init rate = 0.02 (6 / 244), avg. gap size = 2.67 (16 / 6) 276 28.82 8.57 0.88 chr6ptel1M 220921 221025 (778975) MIR3#SINE/MIR 87 199 (9) m_b276s601i33 10942 chr6ptel1M 220921 TGAATTTGAAGAA-CCACTTGGACCTAAATAGCCCTCAGTGTCCTCATCT 220969 vi iiv -i v- vvv i v v MIR3#SINE/MIR 87 TGACCTTGGGCAAGTCACTTC-ACCTCTCTGGGCCTCAGTTTCCTCATCT 135 chr6ptel1M 220970 GCCACTAGGAGGGATTAGACTAGATGGTCTCCA------CTTCGAA--CT 221011 iv vvv ii i i i i ------ v i-- MIR3#SINE/MIR 136 GTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCT 185 chr6ptel1M 221012 GAAATCTTGTGATT 221025 v ii i MIR3#SINE/MIR 186 GACATTCTATGATT 199 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 37.04 CpG sites = 16, Kimura (unadjusted) = 37.04 Transitions / transversions = 1.14 (16/14) Gap_init rate = 0.04 (4 / 104), avg. gap size = 2.50 (10 / 4) 185 26.84 0.00 11.76 chr6ptel1M 221160 221235 (778765) MIRb#SINE/MIR 12 79 (189) m_b276s601i34 10943 chr6ptel1M 221160 CGTGGTGTATGGCTGAAAGAGCTCGGGATTTGGCCAGAGAAGCAAGGCTG 221209 i -- iv v v -- vv ii iiv MIRb#SINE/MIR 12 CGTGGTGCA--GTGGAAAGAGCACGGGCTTTGG--AGTCAGACAGACCTG 57 chr6ptel1M 221210 GAGTCATCCCAATCCTGGCTCCACCA 221235 iv i---- i ii MIRb#SINE/MIR 58 GGTTCG----AATCCCGGCTCTGCCA 79 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.15 CpG sites = 11, Kimura (unadjusted) = 33.56 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.11 (8 / 75), avg. gap size = 1.00 (8 / 8) 328 25.56 11.11 0.00 chr6ptel1M 221610 221699 (778301) C MIR3#SINE/MIR (77) 131 32 m_b276s601i35 10944 chr6ptel1M 221610 GAGGAAAC--AGGCCCAAA-AGGTAGAGT-ACTTACCTGAGATTACA--- 221652 -- i - ii - i ii i i --- C MIR3#SINE/MIR 131 GAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAG 82 chr6ptel1M 221653 ---GTCAAAGTCAGAGGTGGAATTTGTACCCAGATCCTTTGACTCCCAAT 221699 --- i iv v vi i i v v i iii i C MIR3#SINE/MIR 81 CNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGTCTCCTGACTCCCAGT 32 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 31.54 CpG sites = 18, Kimura (unadjusted) = 33.34 Transitions / transversions = 3.60 (18/5) Gap_init rate = 0.06 (5 / 89), avg. gap size = 2.00 (10 / 5) 542 22.96 1.14 7.93 chr6ptel1M 222754 222928 (777072) L2d2_3end#LINE/L2 346 509 (46) m_b276s601i36 10945 chr6ptel1M 222754 TGACATCTCTCTTATAGTATTGTCATGTATTGCTATTTAACCATTGTATT 222803 ii -- i v v i i viv L2d2_3end#LIN 346 TGACATCTCTTCTAT--TGTTGTCTTGAACTGTTATTTAAATCTTGTATT 393 chr6ptel1M 222804 ATCTTTTA-TTTTGCCTGTGTGCATATACTTGCTGTTCTCTAGTCCTCCT 222852 i iv -i v vi vi i - ------ ---- i v L2d2_3end#LIN 394 GTTATTTAACTTTTCACGTGTTTATGT-CTTG------TCT----CCCCA 432 chr6ptel1M 222853 ACTAGATTATAAGCTC-TTGTAGGCAGGGACTTTGTTTCATAAATTTCTG 222901 i - vi iv i i vv i i L2d2_3end#LIN 433 ACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACTTCTTTG 482 chr6ptel1M 222902 TTTCCCTCTCAGCACCTAGCACAGTGC 222928 v i v i L2d2_3end#LIN 483 TATCCCCCACAGCGCCTAGCACAGTGC 509 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 26.05 CpG sites = 22, Kimura (unadjusted) = 27.76 Transitions / transversions = 1.47 (22/15) Gap_init rate = 0.09 (15 / 174), avg. gap size = 1.00 (15 / 15) 237 31.04 2.25 2.25 chr6ptel1M 224067 224155 (775845) C L2d2_3end#LINE/L2 (332) 223 135 m_b277s601i1 10946 chr6ptel1M 224067 ATTTGAGCTGGATTTTGAAGGA-GGCTAGGAACTCTAGG-AGGCAGAAAT 224114 iii - v -- i i i- ii i v C L2d2_3end#LIN 223 ATTTGAGCTGGGCCTTGAAGGATGGGTAGGA--TTTGGATAGGTGGAGAG 176 chr6ptel1M 224115 AAGGAGCGAGAGGATTCCAGTCTGGAGGACTGTCATATGCA 224155 i i i vi i v v v i vi v i iv C L2d2_3end#LIN 175 GAAGGGGAAGGGCATTCCAGGCGGGGGGAACGGCGTGAGCA 135 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 38.10 CpG sites = 18, Kimura (unadjusted) = 42.21 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.05 (4 / 88), avg. gap size = 1.00 (4 / 4) 226 26.56 7.50 1.18 chr6ptel1M 226113 226192 (773808) L2a_3end#LINE/L2 412 496 (21) m_b277s601i2 10947 chr6ptel1M 226113 GAAGGTAGGGGCT---GTTTGGTTT--TTACTCTTGGCTCTCCAGCACCT 226157 i i i --- i v -- i vi vv i i L2a_3end#LINE 412 GAGGGCAGGGACTTTTGTCTGTTTTGTTCACTGCTGTATCCCCAGCGCCT 461 chr6ptel1M 226158 CGCAGAGCGCCTGGCAGACAGGACAC-CTCGAATAA 226192 v v v i v i v vi - - L2a_3end#LINE 462 AGAACAGTGCCTGGCACATAGTAGGCGCTC-AATAA 496 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 31.38 CpG sites = 11, Kimura (unadjusted) = 33.26 Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.05 (4 / 79), avg. gap size = 1.75 (7 / 4) 184 28.31 0.00 4.35 chr6ptel1M 228718 228765 (771235) C L2b_3end#LINE/L2 (0) 466 421 m_b277s601i3 10948 chr6ptel1M 228718 ATTTGTTTCTTCAGCAAATATTTATTAGGCATCTCCTGGGTTCACCAG 228765 ii iv i i ii ii v v --i C L2b_3end#LINE 466 ATTCATTCATTCAACAAATATTTACTGAGCGCCTACTGTGT--GCCAG 421 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 34.38 CpG sites = 10, Kimura (unadjusted) = 38.15 Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.04 (2 / 47), avg. gap size = 1.00 (2 / 2) 306 31.79 1.05 2.53 chr6ptel1M 228889 229114 (770886) (AGG)n#Simple_repeat 1 224 (1001) m_b277s252i0 10949 chr6ptel1M 228889 AGGAAGAGGAAGAGGAGGAGGAAGA-GAGGAAGGAAGAGGAGGAGGAAGA 228937 i i i - - i i (AGG)n#Simple 1 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGG-AGGAGGAGGAGGAGGAGGA 49 chr6ptel1M 228938 GTGGTAATAGTAGTAGTAGTAGTAGTAGGAATAATAGATGTTGTAGTAGT 228987 vi v iv v v v v v v iv iv iv vv v v v (AGG)n#Simple 50 GGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGG 99 chr6ptel1M 228988 AGTGGGAGGAAGAATAGTGTAGAGGTAGGAGAAGGAGGAGGAAGAGGAGG 229037 vi i iv - vi - i i (AGG)n#Simple 100 AGGAGGAGGAGGAGGAG-GAGGAGG-AGGAGGAGGAGGAGGAGGAGGAGG 147 chr6ptel1M 229038 AGTGGCAATAGTAGTAGGAAGAGGAGAAGAAAGAGGAAGAGAAGGAATGG 229087 vi v iv v v i i i i i i ivi (AGG)n#Simple 148 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG 197 chr6ptel1M 229088 TAGTAGGAGGAACAGTGTAGAGG-CGAT 229114 v v iv - vi -v v (AGG)n#Simple 198 GAGGAGGAGGAGGAG-GAGGAGGAGGAG 224 Matrix = Unknown Transitions / transversions = 0.88 (28/32) Gap_init rate = 0.03 (6 / 225), avg. gap size = 1.00 (6 / 6) 26 0.00 0.00 0.00 chr6ptel1M 229115 229139 (770861) (AGG)n#Simple_repeat 1 25 (0) c_b277s251i0 10950 chr6ptel1M 229115 AGGAGGAGGAGGAGGAGGAGGAGGA 229139 (AGG)n#Simple 1 AGGAGGAGGAGGAGGAGGAGGAGGA 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 306 31.79 1.05 2.53 chr6ptel1M 229140 230155 (769845) (AGG)n#Simple_repeat 225 1224 (1) m_b277s252i0 10951 chr6ptel1M 229140 A-AAAGAGGAGTGGCAATAATAGTAGTAGGAAGAACAGTGTAGAAGTAGT 229188 -i i vi v iv iv v v i iv - - i v v (AGG)n#Simple 225 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG-G-AGGAGGAGG 272 chr6ptel1M 229189 AGTAGTAGTAGTAGGAGGAGGAGTGGTAATAGGAGGCATAATAACAGTGA 229238 v v v v vi v iv - vi vi -i v i (AGG)n#Simple 273 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGG-AGGAGGA-GGAGG 320 chr6ptel1M 229239 AGAAGTAGGAGTTGGAGGAGGAGGAACAGGAGGAGAAGTAGTAGTAGGAG 229288 i v vv iv i v v v (AGG)n#Simple 321 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG 370 chr6ptel1M 229289 GAGGAACAGTGA-TAATAGTAGCAGTAGTAGGAATAGTAGGA-GAGATAG 229336 iv - -v iv v v v v iv v - -v (AGG)n#Simple 371 GAGGAGGAG-GAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG-GAG 418 chr6ptel1M 229337 TAGAAGTAGGAGGAGGAAGAGTGGTAGTAGAAGGAGGAGGATGAATAGTG 229386 v i v i vi v v i v iv - (AGG)n#Simple 419 GAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG-G 467 chr6ptel1M 229387 TAGAGGCAGTAGGGGGAGGAGGAGAAGGAGGAGGAGGAAGAGGAGGAGTG 229436 vi - v i i i vi (AGG)n#Simple 468 AGGAGG-AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA 516 chr6ptel1M 229437 GTAATAGTAGGA-GAGGAGGAACAGTGTAGAGGTACTAGAAGAAGGAGGA 229485 v iv v - iv - vi - vv i i (AGG)n#Simple 517 GGAGGAGGAGGAGGAGGAGGAGGAG-GAGGAGG-AGGAGGAGGAGGAGGA 564 chr6ptel1M 229486 GGAGAAAGAGGAGGAGGAGGAGTGGTAATAGGAGGA-GAGGAGGAACAGT 229534 i i vi v iv - iv - (AGG)n#Simple 565 GGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG- 613 chr6ptel1M 229535 GTAGGGGTACTAGGAGAAGGAGGAGGAGAAAGAGGAGGAGGAGGAGTGGT 229584 - i v vv i i i vi v (AGG)n#Simple 614 G-AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGG 662 chr6ptel1M 229585 AATAGTAGGA-GAGGAGGAACAGTGTAGAGGTACTAGAAGAAGGAGGAGG 229633 iv v - iv - vi - vv i i (AGG)n#Simple 663 AGGAGGAGGAGGAGGAGGAGGAG-GAGGAGG-AGGAGGAGGAGGAGGAGG 710 chr6ptel1M 229634 AGAAAGAGGAGGAGGAGGAGTGGTAATAGGAGGA-GAGGAGGAACAGTGT 229682 i i vi v iv - iv - - (AGG)n#Simple 711 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG-G- 758 chr6ptel1M 229683 AGGGGTACTAGGAGAAGGAGGAGGAGAAAGAGGAGGAGGAGGAGTGGTAA 229732 i v vv i i i vi v i (AGG)n#Simple 759 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG 808 chr6ptel1M 229733 TAGGAGGAGGAACACTATAGAGGCAATAGGAGAAGAAGGAGGAGGAACAG 229782 v iv vv -i - iv i i iv (AGG)n#Simple 809 GAGGAGGAGGAGGAGGA-GGAGG-AGGAGGAGGAGGAGGAGGAGGAGGAG 856 chr6ptel1M 229783 TGTAGAGGTAATAGGAAAAGGAGGAGGAAGAAGAGGGGGGCTAGTAGTAA 229832 - vi - iv ii i i i ivv v v i (AGG)n#Simple 857 -GAGGAGG-AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG 904 chr6ptel1M 229833 TATTAGTAGTAGTAGGAACAGTGTAGAAGTAGTAGGAGAAGGAGG-GGAG 229881 v vv v v v iv - - i v v i - (AGG)n#Simple 905 GAGGAGGAGGAGGAGGAGGAG-G-AGGAGGAGGAGGAGGAGGAGGAGGAG 952 chr6ptel1M 229882 GAGGAACAGTATAGAGGCACTAGGAGGAGGAGGAAGAGGAGGAGATGGAG 229931 iv v -i - vv i iv (AGG)n#Simple 953 GAGGAGGAGGA-GGAGG-AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG 1000 chr6ptel1M 229932 GAGGAGGACAACAAGGAGGAGTAGGAATAGTAGGA-GAGGTAGGAGGAGG 229980 vi vi v iv v - - (AGG)n#Simple 1001 GAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGG-AGGAGGAGG 1049 chr6ptel1M 229981 AGGAGGAAGAGTGGAAATAGGAGGAGGAATAGTGTAGAGGTAGTAGGA-G 230029 i vi i iv iv - vi - v - (AGG)n#Simple 1050 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG-GAGGAGG-AGGAGGAGG 1097 chr6ptel1M 230030 AAGAAGAGGAAGAAGAGGAGTGGTAATAGTAGTAACAGGAGGAGTAGACA 230079 i i i i vi v iv v v iv v ivi (AGG)n#Simple 1098 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG 1147 chr6ptel1M 230080 TAGTAGACGTAGTAGTAGTAGAAAGAAAACAAAGAGTAGGAGGAAGAATA 230129 v v iv v v v v i i ii vi i v i iv (AGG)n#Simple 1148 GAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA 1197 chr6ptel1M 230130 GAAGGAGGA-AAAGAGCAGGAGGAAGA 230155 i -i i v i (AGG)n#Simple 1198 GGAGGAGGAGGAGGAGGAGGAGGAGGA 1224 Matrix = Unknown Transitions / transversions = 0.86 (114/132) Gap_init rate = 0.04 (38 / 1015), avg. gap size = 1.00 (38 / 38) 266 39.34 1.64 0.00 chr6ptel1M 230193 230314 (769686) MIRc#SINE/MIR 4 127 (141) m_b277s601i4 10952 chr6ptel1M 230193 GGTAATTCAGTATAATGGGAAAATGGCAAGTCTCAGAGTCAGGATGACCT 230242 i i vii ii i i i vvi vi v ii v MIRc#SINE/MIR 4 GGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCT 53 chr6ptel1M 230243 GAGATCAAGTTCTGCCTCAGATATCTG--GGCAGAGGGACTTGGGGTATG 230290 i v i i i v v vi ii i--i v v v i v i v MIRc#SINE/MIR 54 GGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAG 103 chr6ptel1M 230291 TCATGTATCCCTTCTGTAATTCAG 230314 iv v ii vivi MIRc#SINE/MIR 104 TCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 55.35 CpG sites = 29, Kimura (unadjusted) = 59.20 Transitions / transversions = 1.53 (29/19) Gap_init rate = 0.01 (1 / 121), avg. gap size = 2.00 (2 / 1) 198 36.00 0.00 0.00 chr6ptel1M 231745 231819 (768181) C MIR3#SINE/MIR (23) 185 111 m_b277s601i5 10953 chr6ptel1M 231745 AGTGCAAAAAGGGATGTTGGGGTTTACCTGATCCAACTTCCACATTTTAG 231794 v vii iv i i v i i ii ii v v C MIR3#SINE/MIR 185 AGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTAC 136 chr6ptel1M 231795 CCATGGAGCAAAGGAGGTCAAGTGA 231819 vv ii v vv i v v C MIR3#SINE/MIR 135 AGATGAGGAAACTGAGGCCCAGAGA 111 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 50.20 CpG sites = 14, Kimura (unadjusted) = 50.20 Transitions / transversions = 1.08 (14/13) Gap_init rate = 0.00 (0 / 74), avg. gap size = 0.0 (0 / 0) 228 29.76 21.43 0.00 chr6ptel1M 232014 232097 (767903) MIRc#SINE/MIR 84 185 (83) m_b277s601i6 10954 chr6ptel1M 232014 GTTGTTTGACCTTGAACAA------TAAGCCATTTAAGCCTC-------- 232049 i v ii ------ v iv i i -------- MIRc#SINE/MIR 84 GCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCT 133 chr6ptel1M 232050 ----TGTAAAATGGGAATAGTAATGCTTATCCTCTCCATTACTTAGGATT 232095 ---- i i i i ii vi i iiv vi i MIRc#SINE/MIR 134 CATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTT 183 chr6ptel1M 232096 AT 232097 i MIRc#SINE/MIR 184 GT 185 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 40.95 CpG sites = 19, Kimura (unadjusted) = 40.95 Transitions / transversions = 3.17 (19/6) Gap_init rate = 0.04 (3 / 83), avg. gap size = 6.00 (18 / 3) 376 26.01 14.83 4.35 chr6ptel1M 232207 232415 (767585) C MIRc#SINE/MIR (1) 267 38 m_b277s601i7 10955 chr6ptel1M 232207 ATAATGATGAGATCGAGCATTCATGAAGTGCCTTAAGTTTTGCAGAGTAT 232256 i i v?i vvi ii iv ii i viv i i iii C MIRc#SINE/MIR 267 ATAATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCGC 218 chr6ptel1M 232257 TCCTCACAAGGACTATGTTTTATCATTTCATCCCCACTAAAAACTCGGGG 232306 i- ----- ii v v v i - v i v v C MIRc#SINE/MIR 217 TT-TCACA-----TACATTATCTCATTTGATCCTCAC-AACAACCCTGTG 175 chr6ptel1M 232307 AGGTAGG------AGCTATTATTATCCCAGCTTTA--GTTCGAGGA---- 232344 ------ v vii -- v - ---- C MIRc#SINE/MIR 174 AGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGAT-GAGGAAACT 126 chr6ptel1M 232345 --GGC----AGAGGTGAAG--A-TCACGCAGGATCACACAGGTAGGAAGT 232385 -- ---- v -- - ii v i i v v C MIRc#SINE/MIR 125 GAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGT 76 chr6ptel1M 232386 ------GTTGGGCTTCCCACCTCCAGGT----CTGACTCC 232415 ------ ii vi vv -- ---- C MIRc#SINE/MIR 75 GGCAGAGCCGGGACTCGAAC--CCAGGTCTTCCTGACTCC 38 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 31.41 CpG sites = 30, Kimura (unadjusted) = 33.02 Transitions / transversions = 1.36 (30/22) Gap_init rate = 0.09 (19 / 208), avg. gap size = 2.16 (41 / 19) 281 31.18 5.45 0.87 chr6ptel1M 232442 232551 (767449) Charlie23a#DNA/hAT-Charlie 224 338 (1) m_b277s502i0 10956 chr6ptel1M 232442 TTAGATATTCTCTCAATTCATGAAGAACGATCATACAATCACT------T 232485 vi i iv i i v vii vvi ii ------ Charlie23a#DN 224 TTATGTATTTTCTCAATCAACGGATACTAAAAGTACAACTACTATCATGT 273 chr6ptel1M 232486 GGGAATCAATGTCATTTTGTGAATTTAAAAAGGGACCTTTACATTCAAAA 232535 i vii vv v vv ii i i i i i Charlie23a#DN 274 GGGGATCCGCGAAATTTTTTGACGTTAAAAAGGGGTCCTCATACTCGAAA 323 chr6ptel1M 232536 AAGTTTGGGAACCATT 232551 i - i Charlie23a#DN 324 AGG-TTGGGAACCACT 338 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 35.90 CpG sites = 22, Kimura (unadjusted) = 42.27 Transitions / transversions = 1.83 (22/12) Gap_init rate = 0.02 (2 / 109), avg. gap size = 3.50 (7 / 2) 212 26.60 7.69 11.44 chr6ptel1M 232815 233022 (766978) C MIR3#SINE/MIR (6) 202 2 m_b277s601i8 10957 chr6ptel1M 232815 TGGAGTCAGAG---GTCAGAGTTGGACTCTGAGGGAGCCATTTAGATCTT 232861 i i v --- i ----- - v vv v C MIR3#SINE/MIR 202 TAGAATCATAGAATGTCAGAGCTGGA-----AGGGA-CCTTAGAGATCAT 159 chr6ptel1M 232862 TCTCAGTCTAGCTTTCCCCCT---CAG--GAGGAAAC--AGGCCCAGTGA 232904 - - i i iii i vi --- -- -- v C MIR3#SINE/MIR 158 -CT-AGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGA 111 chr6ptel1M 232905 GGTTTGGTGATGAGCTCCAAGGGTCAGAACTGGAACTCATACCCAG--GG 232952 vvi ivv - - ----------- i v ? --i C MIR3#SINE/MIR 110 GGTGAAGTGACTTGC-CCAA-GGTCA-----------CACAGCNAGTTAG 74 chr6ptel1M 232953 CTCCAAATCCAGGACGGTAGAG-CCAGCCCCGCTAGCTCC--ATCCGGG- 232998 ivv i v i -- i- vi iv ii --i v - C MIR3#SINE/MIR 73 TGGCAGAGCCGGGAC--TAGAACCCAGGTCTCCTGACTCCCAGTCCGTGC 26 chr6ptel1M 232999 TCTTTGTTCCCAGACGCCCTGCTA 233022 i v v i v i i i C MIR3#SINE/MIR 25 TCTCTCTGCTCAGCCACTCTGCCA 2 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 32.75 CpG sites = 28, Kimura (unadjusted) = 33.58 Transitions / transversions = 1.33 (28/21) Gap_init rate = 0.15 (31 / 207), avg. gap size = 1.26 (39 / 31) 278 29.72 7.26 2.31 chr6ptel1M 233036 233159 (766841) MIR3#SINE/MIR 59 188 (20) m_b277s601i9 10958 chr6ptel1M 233036 GTCCCAGCTCGGACGTGATTTAGGCCGTGGGGCC--GGG------ACTTT 233077 i v v iiv vi ? - i v i -- ------ i MIR3#SINE/MIR 59 GTCCCGGCTCTGCCACTAACTNG-CTGTGTGACCTTGGGCAAGTCACTTC 107 chr6ptel1M 233078 TGCTCTGCGTCCCTCAGTTTCTTCCCACATTAAATGAGAGAAGTGAATTA 233127 vv vi vv i vivii v i iiv i i MIR3#SINE/MIR 108 ACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTA 157 chr6ptel1M 233128 GAGCAGATCTTTCGGGTCCC-TCCAGTTCTGAC 233159 v-- i vi - i MIR3#SINE/MIR 158 GAT--GATCTCTAAGGTCCCTTCCAGCTCTGAC 188 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 37.80 CpG sites = 20, Kimura (unadjusted) = 39.18 Transitions / transversions = 1.25 (20/16) Gap_init rate = 0.05 (6 / 123), avg. gap size = 2.00 (12 / 6) 207 30.00 2.86 0.00 chr6ptel1M 233604 233673 (766327) MIRc#SINE/MIR 77 148 (120) m_b277s601i10 10959 chr6ptel1M 233604 CTTCTTAGGGACGTGCCCCTAGA-AAGTCGCTTAGTTTCTCTCAGC-TCC 233651 vi vvii v i i i- i iii v - v MIRc#SINE/MIR 77 CTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCA 126 chr6ptel1M 233652 CTTTACCCCTCTGCAAAATGGG 233673 v v i v i MIRc#SINE/MIR 127 GTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 39.31 CpG sites = 12, Kimura (unadjusted) = 39.31 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.03 (2 / 69), avg. gap size = 1.00 (2 / 2) 535 25.19 5.93 0.00 chr6ptel1M 233709 233843 (766157) MIRc#SINE/MIR 99 241 (27) m_b277s601i11 10960 chr6ptel1M 233709 GCAAGTCACTTAGTTTCTCTCAGCCTTGCTTTACTCCTCTGCAAAATGGA 233758 iii v iiv v v i i MIRc#SINE/MIR 99 GCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 chr6ptel1M 233759 GATAA----ACCAGCTTTG---ATCTCACAGGATTACTGGGAAGTTCACA 233801 ---- v ii --- i i ii v i v v MIRc#SINE/MIR 149 GATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAA 198 chr6ptel1M 233802 TGAGACAACGTCTGC-AAAGTTTTGTGTTTACCTTAAAGTGCT 233843 i i v i- ivi v vv iv MIRc#SINE/MIR 199 TGAGATAATGTATGTGAAAGCGCTTTGTAAACTGTAAAGTGCT 241 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.25 CpG sites = 20, Kimura (unadjusted) = 31.35 Transitions / transversions = 1.43 (20/14) Gap_init rate = 0.02 (3 / 134), avg. gap size = 2.67 (8 / 3) 305 25.34 8.15 3.55 chr6ptel1M 234040 234174 (765826) MIR3#SINE/MIR 65 205 (3) m_b277s601i12 10961 chr6ptel1M 234040 GCTCTCCCA-GAACT-GCCATGGAGCTGACCCTGC-TGAGCCACTTC-CC 234085 v -v - ii ---- i v-ii i - MIR3#SINE/MIR 65 GCTCTGCCACTAACTNGCTGTG----TGACCTTGGGCAAGTCACTTCACC 110 chr6ptel1M 234086 TTTCCAGGTCCTCAGTTTCCTCAGCTGTAAAAGGAAG-----AGACTCGA 234130 i ii - v v i -----i v MIR3#SINE/MIR 111 TCTCTGGG-CCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGA 159 chr6ptel1M 234131 GGA-CCCGAAAGACCCTTATA-CTTTGAATCTCTGAGCTTCCGTGA 234174 v - i v i v vi - i vvi iv v ii MIR3#SINE/MIR 160 TGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTATGA 205 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 31.61 CpG sites = 19, Kimura (unadjusted) = 31.61 Transitions / transversions = 1.36 (19/14) Gap_init rate = 0.09 (12 / 134), avg. gap size = 1.33 (16 / 12) 322 26.80 4.12 0.00 chr6ptel1M 234611 234707 (765293) L3#LINE/CR1 3670 3770 (329) m_b277s601i13 10962 chr6ptel1M 234611 GATGG--AGGGGACTGCAGACCATGTCCTACGAGAATCGGTTGAAGGGAA 234658 -- i v v i v i i v i v L3#LINE/CR1 3670 GATGGTGAAGGGTCTGGAAACCATGTCATATGAGGAACGGTTGAAGGAAC 3719 chr6ptel1M 234659 GAGGAAGATTTGGCTT--AAAAAAGAAGAGTTAAAGGAGTCATAACTGTT 234706 vi i vi i i -- i i v i v i iv i L3#LINE/CR1 3720 TGGGGATGTTTAGCCTGGAGAAGAGAAGACTTAGAGGAGACATGATAGCT 3769 chr6ptel1M 234707 G 234707 L3#LINE/CR1 3770 G 3770 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 34.14 CpG sites = 16, Kimura (unadjusted) = 34.14 Transitions / transversions = 1.60 (16/10) Gap_init rate = 0.02 (2 / 96), avg. gap size = 2.00 (4 / 2) 617 24.73 12.31 0.46 chr6ptel1M 234730 234924 (765076) MIRc#SINE/MIR 49 266 (2) m_b277s601i14 10963 chr6ptel1M 234730 GACCTGGAGTTCAAATGTGGCCTCAGATATTTAGCAGTTATGT--CTTTG 234777 - i i viv v v vi i vi i i -- i MIRc#SINE/MIR 49 GACCTGG-GTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTG 97 chr6ptel1M 234778 AGCAAGTTAC--AACCTCTTCCTGCCTCAGTTTTCTCATCTGTAAAATGG 234825 i i -- iivv i MIRc#SINE/MIR 98 GGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGG 147 chr6ptel1M 234826 GGACAATAATGGCT------CCTATTTTGCAGTGTTGTTGTG-----CAA 234864 i iv ------ ii ii v ----- MIRc#SINE/MIR 148 GGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAA 197 chr6ptel1M 234865 AT---ACCACTTAT---ACAGCACTTTATAAACCTTC---TGCTACATAA 234905 --- iv iv --- v i i iv v--- i i MIRc#SINE/MIR 198 ATGAGATAATGTATGTGAAAGCGCTTTGTAAACTGTAAAGTGCTATACAA 247 chr6ptel1M 234906 ATCCCAGCTATTATTAGTA 234924 viv v?i v MIRc#SINE/MIR 248 ATGTAAGGNGTTATTATTA 266 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.41 CpG sites = 29, Kimura (unadjusted) = 30.94 Transitions / transversions = 1.53 (29/19) Gap_init rate = 0.04 (8 / 194), avg. gap size = 3.12 (25 / 8) 272 33.31 5.08 3.33 chr6ptel1M 234933 235050 (764950) L3#LINE/CR1 3761 3880 (219) m_b277s601i15 10962 chr6ptel1M 234933 ATTATTACTATCTTCAAATACCCGAGGAGTTGTTATGGAGAAGAATGATG 234982 v vi i iii i i i i vi iv - L3#LINE/CR1 3761 ATGATAGCTGTCTTCAAATATTTGAAGGGCTGTCATGTGGAAGAGGGAT- 3809 chr6ptel1M 234983 GTATGGGTGTCATTTGCATG----CAAAGGAAAGAAGGAGCACAAAT--A 235026 --- i iiv vv i ii ---- i iv vv v v --i L3#LINE/CR1 3810 ---TAGACTTATTCTGTGTGGCTCCAGAGGGCAGAACTAGGACCAATGGG 3856 chr6ptel1M 235027 CAGAGGTCATAGGAAGGCAGATTT 235050 ii i i i i L3#LINE/CR1 3857 TGGAAGTTACAGGGAGGCAGATTT 3880 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 47.12 CpG sites = 26, Kimura (unadjusted) = 47.12 Transitions / transversions = 2.17 (26/12) Gap_init rate = 0.05 (6 / 117), avg. gap size = 1.67 (10 / 6) 302 23.97 10.53 1.20 chr6ptel1M 235359 235434 (764566) C MIRb#SINE/MIR (100) 168 86 m_b277s601i16 10964 chr6ptel1M 235359 AGGTGAAGTACAGTTACCTCCATTTTGTAGATGGGGAAACTGAGATTGCA 235408 - i ivi i i ii i ii vvi C MIRb#SINE/MIR 168 AGGT-AGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAG 120 chr6ptel1M 235409 AGAG--------ACTGCCTCAAGGTCACACAACT 235434 -------- vv i i C MIRb#SINE/MIR 119 AGAGGTTAAGTAACTTGCCCAAGGTCACACAGCT 86 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.24 CpG sites = 13, Kimura (unadjusted) = 30.24 Transitions / transversions = 2.60 (13/5) Gap_init rate = 0.03 (2 / 75), avg. gap size = 4.50 (9 / 2) 301 34.54 8.90 4.52 chr6ptel1M 235545 235735 (764265) C L2b_3end#LINE/L2 (1) 465 267 m_b277s601i17 10965 chr6ptel1M 235545 TCTACTCACTTAGTAAGCGTTTACTAAATGCCTACTCTG---------CT 235585 ii i i i ii iii i ii v --------- C L2b_3end#LINE 465 TTCATTCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCT 416 chr6ptel1M 235586 GTGCTAAGTGCTGGCATCACAAT--TGAG-AAG-CAAAGGCAGTCCCCGA 235631 i i vivi ii-- i- - i v? i i v C L2b_3end#LINE 415 GTGCTAGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGC 366 chr6ptel1M 235632 TCTCCAGGAGTTCCCA----AGTGGGAGAGGACAAGTGCTTTGTGAGACA 235677 i vv i v ---- i - iiiiiv vi?v - C L2b_3end#LINE 365 CCTCACGGAGCTCACAGTCTAGTGGGGGA-GACAGACATGTAANCAGAC- 318 chr6ptel1M 235678 AAATGGAGTTAATCCACAGAGGGAAGGTACCAGTTTTAAGGAGATTCTGG 235727 - ?i--- i v v v i vv ---i ii i iii v i C L2b_3end#LINE 317 -AATNA---TAACCCAGAGTGGCAGGGTAGGA---CTGGGGGGGCCCAGA 275 chr6ptel1M 235728 AAAGGGTG 235735 ii i C L2b_3end#LINE 274 GGAGGGCG 267 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 46.16 CpG sites = 46, Kimura (unadjusted) = 52.21 Transitions / transversions = 2.71 (46/17) Gap_init rate = 0.07 (14 / 190), avg. gap size = 1.86 (26 / 14) 307 33.31 5.83 2.42 chr6ptel1M 235545 235664 (764336) C L2c_3end#LINE/L2 (1) 477 354 m_b277s601i18 10965 chr6ptel1M 235545 TCTACTCACTTAGTAAGCGTTTACTAAATGCCTACTCTGCTGTGCTAAGT 235594 ii i i i ii i i i i ii ---v i i i C L2c_3end#LINE 477 TTCATTCATTCAACAAACATTTATTGAGCGCCTACT---ATGTGCCAGGC 431 chr6ptel1M 235595 GCTGGCATCACAATTGAGAAGCAAAGGCAGTCCCCGATCTCCAGGAGTTC 235644 vivi vviv vv i vi i i vi v i C L2c_3end#LINE 430 GCTGGGGATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTC 381 chr6ptel1M 235645 CCA----AGTGGGAGAG---GACAAGT 235664 v ---- ii --- ? C L2c_3end#LINE 380 ACAGTCTAGTGGAGGAGACAGACANGT 354 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 42.75 CpG sites = 27, Kimura (unadjusted) = 47.87 Transitions / transversions = 2.25 (27/12) Gap_init rate = 0.04 (5 / 119), avg. gap size = 2.00 (10 / 5) 420 27.26 4.76 2.67 chr6ptel1M 237296 237442 (762558) L2a_3end#LINE/L2 366 515 (2) m_b277s601i19 10966 chr6ptel1M 237296 TTTTCTGTTTCCTTTTCTGTTATTTTCCTCTGTAGCGAGTAACCTCTTTG 237345 v i v- v i-- ii i vv viv v iv L2a_3end#LINE 366 TTATTTGTTTA-TTGTCTGTC--TCCCCCCACTAGAATGTAAGCTCCATG 412 chr6ptel1M 237346 AGAGTAGAGACTAAT-TCT-TTTTA---AAT--TATATCCCCAGCACTTA 237388 i i i vv - - i--- v -- i i i L2a_3end#LINE 413 AGGGCAGGGACTTTTGTCTGTTTTGTTCACTGCTGTATCCCCAGCGCCTA 462 chr6ptel1M 237389 GAACAACACCTGGCATATAGTAAGTATTTAATAAATGTTTATTGGATTGA 237438 iii i i iii i i i i - L2a_3end#LINE 463 GAACAGTGCCTGGCACATAGTAGGCGCTCAATAAATATTTGTTGAA-TGA 511 chr6ptel1M 237439 AGGA 237442 v L2a_3end#LINE 512 ATGA 515 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 32.95 CpG sites = 26, Kimura (unadjusted) = 35.32 Transitions / transversions = 2.00 (26/13) Gap_init rate = 0.05 (8 / 146), avg. gap size = 1.38 (11 / 8) 181 36.58 6.75 5.42 chr6ptel1M 237438 237473 (762527) C L2#LINE/L2 (83) 2999 2970 m_b277s601i20 10965 chr6ptel1M 237438 AAGGAGGTCAATGTCCCCAAACCACAGGTGTATGTA 237473 i i vv iii v iv ----- - C L2#LINE/L2 2999 AAGGAGGCCAGTGTGGCTGGAGCGGAG-----TG-A 2970 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 52.42 CpG sites = 57, Kimura (unadjusted) = 55.57 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.17 (6 / 35), avg. gap size = 1.00 (6 / 6) 34 9.33 0.00 0.00 chr6ptel1M 237474 237520 (762480) (TG)n#Simple_repeat 1 47 (0) c_b277s251i1 10967 chr6ptel1M 237474 TGTGTGTGTGTATGTATGTATGTATGTGTGTGTGTGTGTGTGTGTGT 237520 i i i i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 47 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 181 36.58 6.75 5.42 chr6ptel1M 237521 237720 (762280) C L2#LINE/L2 (113) 2969 2761 m_b277s601i20 10965 chr6ptel1M 237521 TGGGGAGGGAGGGTG-TAAGGTATAAAAAGATTAGAAAGGTTA-GGAGGA 237568 i i - i - i iv i --- i i i v - i C L2#LINE/L2 2969 CGAGG-GGGAGAGTGGTAGGAGATGA---GGTCAGAGAGGTAACGGGGGA 2924 chr6ptel1M 237569 T-GGGTTATGAAGGG--TTATGA---ATTCAGAGGATTTTAG----GATC 237608 i-i i i v -- i ii--- vvi i i ----v ii C L2#LINE/L2 2923 CCAGATCATGTAGGGCCTTGTAGGCCATTGTAAGGACTTTGGCTTTTACT 2874 chr6ptel1M 237609 CTATAGAAGTT----AGTCACCAGATCACATTGAGGAGAAAGATGATGTG 237654 ivivi v ---- i iii vviiv v iiii ii C L2#LINE/L2 2873 CTGAGTGAGATGGGAAGCCATTGGAGGGTTTTGAGCAGAGGAGTGACATG 2824 chr6ptel1M 237655 GTCAGAGCTGTGCTTTAGGAAGCTCTTTTCGGCAGCTGTGTGAAGAAAGT 237704 i v vi ii i ii i v vi ii v vi --- C L2#LINE/L2 2823 ATCTGACTTACGTTTTAAAAGGATCACTCTGGCTGCTGTGTTGAGAA--- 2777 chr6ptel1M 237705 CAGAATGGAGAGGTGC 237720 i v ? i v C L2#LINE/L2 2776 TAGACTGNAGGGGGGC 2761 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 52.42 CpG sites = 57, Kimura (unadjusted) = 55.57 Transitions / transversions = 2.43 (51/21) Gap_init rate = 0.07 (14 / 199), avg. gap size = 1.64 (23 / 14) 184 27.70 3.07 15.86 chr6ptel1M 237717 237879 (762121) MIR1_Amn#SINE/MIR 13 157 (73) m_b277s601i21 10968 chr6ptel1M 237717 GTGCTCTGGGGTTGGATAAGAGGCTCTG---TAGGATTTGAGAGAGACCT 237763 v i --- - - v --- i i i i -- MIR1_Amn#SINE 13 GTGGTCTAG---TGGATA-GAG-CACTGGACTGGGACTCGGGAGA--CCT 55 chr6ptel1M 237764 GGCACATAGTA--GGCCCTTAATGAACATTTGTTGATTGATTGATAGGAG 237811 vviv? ? v-- i -----iv i ? ii?ii ?v i----- MIR1_Amn#SINE 56 GGGTTCNANTCCCGGCTCT-----GCCACTNGCCNGCTGNGTGAC----- 95 chr6ptel1M 237812 CTTGGGCAAGTCTCTCCATGTCTCTGAGATCCAGTTGCTTCTGGGATTTA 237861 v i? iv ? vii v i ---- i i MIR1_Amn#SINE 96 CTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTC----ATCTG 141 chr6ptel1M 237862 GAAATCATGGAGGGAGTG 237879 v -- i iv i MIR1_Amn#SINE 142 TAAA--ATGGGGATAATG 157 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 36.04 CpG sites = 24, Kimura (unadjusted) = 37.29 Transitions / transversions = 1.71 (24/14) Gap_init rate = 0.15 (25 / 162), avg. gap size = 1.12 (28 / 25) 190 22.86 0.00 0.00 chr6ptel1M 237761 237795 (762205) MIR#SINE/MIR 222 256 (6) m_b277s601i22 10968 chr6ptel1M 237761 CCTGGCACATAGTAGGCCCTTAATGAACATTTGTT 237795 i v i i ii v i MIR#SINE/MIR 222 CCTGGCACATAGTAAGCGCTCAATAAATGTTAGCT 256 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 28.58 CpG sites = 6, Kimura (unadjusted) = 28.58 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 326 23.26 1.53 14.66 chr6ptel1M 237809 237939 (762061) MIR3#SINE/MIR 88 203 (5) m_b277s601i24 10968 chr6ptel1M 237809 GAGCTTGGGCAAGTCTCTCCATGTCTCTGAGATCCAGTTGCTTCTGGGAT 237858 v v i iv i vii v i ---- MIR3#SINE/MIR 88 GACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTC----AT 133 chr6ptel1M 237859 TTAGAAATCATGGAGGGAGTGTACGTGGCTGCACTAAATGCTCTCTGAGG 237908 i iv -- - i ----- ---- i v i MIR3#SINE/MIR 134 CTGTAAA--AT-GAGGGGGT-----TGG----ACTAGATGATCTCTAAGG 171 chr6ptel1M 237909 T-TCTTGCAGCTTCAA-ATACTGTGATCACTAT 237939 -i v iii - v i i- MIR3#SINE/MIR 172 TCCCTTCCAGCTCTGACATTCTATGATT-CTAT 203 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 27.97 CpG sites = 17, Kimura (unadjusted) = 27.97 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.15 (19 / 130), avg. gap size = 1.00 (19 / 19) 294 11.90 0.00 0.00 chr6ptel1M 237765 237806 (762194) L2d_3end#LINE/L2 472 513 (3) m_b277s601i23 10969 chr6ptel1M 237765 GCACATAGTAGGCCCTTAATGAACATTTGTTGATTGATTGAT 237806 v i i i i L2d_3end#LINE 472 GCACATAGTAGGCGCTCAATAAATACTTGTTGATTGATTGAT 513 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 13.28 CpG sites = 4, Kimura (unadjusted) = 13.28 Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 184 27.70 3.07 15.86 chr6ptel1M 237717 237879 (762121) MIR1_Amn#SINE/MIR 13 157 (73) m_b277s601i21 10968 chr6ptel1M 237717 GTGCTCTGGGGTTGGATAAGAGGCTCTG---TAGGATTTGAGAGAGACCT 237763 v i --- - - v --- i i i i -- MIR1_Amn#SINE 13 GTGGTCTAG---TGGATA-GAG-CACTGGACTGGGACTCGGGAGA--CCT 55 chr6ptel1M 237764 GGCACATAGTA--GGCCCTTAATGAACATTTGTTGATTGATTGATAGGAG 237811 vviv? ? v-- i -----iv i ? ii?ii ?v i----- MIR1_Amn#SINE 56 GGGTTCNANTCCCGGCTCT-----GCCACTNGCCNGCTGNGTGAC----- 95 chr6ptel1M 237812 CTTGGGCAAGTCTCTCCATGTCTCTGAGATCCAGTTGCTTCTGGGATTTA 237861 v i? iv ? vii v i ---- i i MIR1_Amn#SINE 96 CTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTC----ATCTG 141 chr6ptel1M 237862 GAAATCATGGAGGGAGTG 237879 v -- i iv i MIR1_Amn#SINE 142 TAAA--ATGGGGATAATG 157 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 36.04 CpG sites = 24, Kimura (unadjusted) = 37.29 Transitions / transversions = 1.71 (24/14) Gap_init rate = 0.15 (25 / 162), avg. gap size = 1.12 (28 / 25) 190 22.86 0.00 0.00 chr6ptel1M 237761 237795 (762205) MIR#SINE/MIR 222 256 (6) m_b277s601i22 10968 chr6ptel1M 237761 CCTGGCACATAGTAGGCCCTTAATGAACATTTGTT 237795 i v i i ii v i MIR#SINE/MIR 222 CCTGGCACATAGTAAGCGCTCAATAAATGTTAGCT 256 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 28.58 CpG sites = 6, Kimura (unadjusted) = 28.58 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 326 23.26 1.53 14.66 chr6ptel1M 237809 237939 (762061) MIR3#SINE/MIR 88 203 (5) m_b277s601i24 10968 chr6ptel1M 237809 GAGCTTGGGCAAGTCTCTCCATGTCTCTGAGATCCAGTTGCTTCTGGGAT 237858 v v i iv i vii v i ---- MIR3#SINE/MIR 88 GACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTC----AT 133 chr6ptel1M 237859 TTAGAAATCATGGAGGGAGTGTACGTGGCTGCACTAAATGCTCTCTGAGG 237908 i iv -- - i ----- ---- i v i MIR3#SINE/MIR 134 CTGTAAA--AT-GAGGGGGT-----TGG----ACTAGATGATCTCTAAGG 171 chr6ptel1M 237909 T-TCTTGCAGCTTCAA-ATACTGTGATCACTAT 237939 -i v iii - v i i- MIR3#SINE/MIR 172 TCCCTTCCAGCTCTGACATTCTATGATT-CTAT 203 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 27.97 CpG sites = 17, Kimura (unadjusted) = 27.97 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.15 (19 / 130), avg. gap size = 1.00 (19 / 19) 229 22.77 0.00 7.55 chr6ptel1M 238184 238240 (761760) C L2d_3end#LINE/L2 (3) 513 461 m_b277s601i25 10970 chr6ptel1M 238184 ATCAATTAACCAACAATAAAACATTTATTAAGCACCTAGTACATTCTAGG 238233 i i ----ii i i v ii v vi C L2d_3end#LINE 513 ATCAATCAATCAACAA----GTATTTATTGAGCGCCTACTATGTGCTCAG 468 chr6ptel1M 238234 CACTGTG 238240 C L2d_3end#LINE 467 CACTGTG 461 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 25.50 CpG sites = 9, Kimura (unadjusted) = 28.23 Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.07 (4 / 56), avg. gap size = 1.00 (4 / 4) 208 27.78 0.00 0.00 chr6ptel1M 238334 238387 (761613) C MIRc#SINE/MIR (0) 268 215 m_b277s601i26 10971 chr6ptel1M 238334 AATCCTAACAATTGCTAACGTTTGTAGAGTGCTTTAAAGTTTATAAAATG 238383 vv i i?v v i v ii v i ii C MIRc#SINE/MIR 268 AATAATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCG 219 chr6ptel1M 238384 CCTT 238387 i C MIRc#SINE/MIR 218 CTTT 215 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 33.56 CpG sites = 9, Kimura (unadjusted) = 36.57 Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 21 18.67 3.57 7.41 chr6ptel1M 238450 238533 (761467) (TAA)n#Simple_repeat 1 81 (0) m_b277s252i1 10972 chr6ptel1M 238450 TAATAATATATGTGTATATAGTATTAATATATAGTATGTAATTATTAT-A 238498 - -vi - i v - i -i v v - (TAA)n#Simple 1 TAATAATA-AT-AATA-ATAATAATAATA-ATAATA-ATAATAATAATAA 45 chr6ptel1M 238499 TAATGTGTAAT-ATAATAGT-ATATTAATAATAATAA 238533 -vi - i - v (TAA)n#Simple 46 TAAT-AATAATAATAATAATAATAATAATAATAATAA 81 Matrix = Unknown Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.11 (9 / 83), avg. gap size = 1.00 (9 / 9) 354 30.52 14.81 1.17 chr6ptel1M 239300 239677 (760323) C L1ME3G_3end#LINE/L1 (404) 520 92 m_b277s551i0 10973 chr6ptel1M 239300 AATTTTTTCAGCCATTCCCCAGATGATGGGCATCTACACTATTTCCCATC 239349 v i i viv i i vii i v i C L1ME3G_3end#L 520 AATTTATTTAACCATTCCCCTATTGATGGACATTTAGGTTGTTTCCAATT 471 chr6ptel1M 239350 TTT-GCTATCAGAGAAAACATGGTAAT--ACATGCTTGGACGTGTGTA-- 239394 - i v i v iiiv i -- v v i i? v-- C L1ME3G_3end#L 470 TTTCGCTATTACAAACAATGCTGCAATGAACATCCTTGTACATGCNTCCT 421 chr6ptel1M 239395 -GAGTCTCTTTGAG-GTGTTTCCTTAG---------CCAGGAG----ATC 239429 - v iviv v v - i i? --------- ? i ---- i C L1ME3G_3end#L 420 TGTGCACATGTGCGAGTATTTCTNTAGGATAGATNCCNAGAAGTGGAATT 371 chr6ptel1M 239430 TCTGGATCAAAGAATATGGACACATTCT--CTTTTGGT--ATAATTTCAA 239475 v i ii -- i i --v ii -- v vi C L1ME3G_3end#L 370 GCTGGGTCAAAGGGTATG--CGCATTTTAAATTTTAATAGATACTGCCAA 323 chr6ptel1M 239476 ACCGCTTTCCAGAATTCACCG-GCCATTTGACAGCTTCACCA-------A 239517 ii ii i -?vi i -i v v viii ------- C L1ME3G_3end#L 322 ATTGCCCTCCAAAA-NGGCTGTACCAATTTACACTCCCACCAGCAGTGTA 274 chr6ptel1M 239518 T-AGGGCACTTGTCTTTCCACAGTCTCTCCCAT-CTGGTTGCTTTCCCCT 239565 - i i ii i ii vi v v i- ? v ii v vv?i C L1ME3G_3end#L 273 TGAGAGTACCCGTTTCCCCACACCCTCGCCAACACTNGATATTATCAANC 224 chr6ptel1M 239566 TTTTACACT-----CAA-------GGTGAAA-----TATCCAA--GTCGT 239596 v i ----- ------- ----- iv -- i C L1ME3G_3end#L 223 TTTTAAATTTTTGCCAATCTGATGGGTGAAAAATGGTATCTCATTGTTGT 174 chr6ptel1M 239597 TTGCATTTCTGTTTCTT---TTACTAGCGATTTTGAGCAGTTTATCGTAT 239643 vv vii ii--- i vv vi v i C L1ME3G_3end#L 173 TTTAATTTGCATTTCCCTGATTACTAGTGAGGTTGAGCATCTTTTCATAT 124 chr6ptel1M 239644 GGTTGTTAATAGTGTGTAATTCTTCTTGTCTGTG 239677 v i iiivi v v i -- C L1ME3G_3end#L 123 GTTTATTGGCCATTTGTATTTCCTCT--TCTGTG 92 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 40.67 CpG sites = 70, Kimura (unadjusted) = 41.65 Transitions / transversions = 1.59 (70/44) Gap_init rate = 0.06 (23 / 377), avg. gap size = 2.65 (61 / 23) 182 24.39 0.00 0.00 chr6ptel1M 239744 239784 (760216) L2d_3end#LINE/L2 476 516 (0) m_b277s601i27 10974 chr6ptel1M 239744 ATAGCAGGTGCTTAATAATTTCTTGTTTCCTGATTGACTAA 239784 i i i v v vvi i i L2d_3end#LINE 476 ATAGTAGGCGCTCAATAAATACTTGTTGATTGATTGATTGA 516 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 26.69 CpG sites = 6, Kimura (unadjusted) = 30.16 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 712 31.23 7.66 0.68 chr6ptel1M 240379 240652 (759348) 7SLRNA#SINE/Alu 22 314 (6) m_b277s502i1 10975 chr6ptel1M 240379 CTGTAGTCCCAGATGC-AGGAAGATTGAGGCTGGTAAA----TTGA---- 240419 v i -v i ii v vii ---- ---- 7SLRNA#SINE/A 22 CTGTAGTCCCAGCTACTCGGGAGGCTGAGGCGGGAGGATCGCTTGAGCCC 71 chr6ptel1M 240420 --GAGTTCAGAGCTA---------AAGCCAGTTGGGCGCCCATACGAAGT 240458 -- v i i--------- v ii i i i ii v 7SLRNA#SINE/A 72 AGGAGTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCCGCACTAAGT 121 chr6ptel1M 240459 TCAGGACCAATATGGTGAGTCACCAGAAGCACAGG-CCAACAGGCTACCA 240507 i v i viiv i i ivi - v i i v 7SLRNA#SINE/A 122 TCGGCATCAATATGGTGACCTCCCGGGAGCGGGGGACCACCAGGTTGCCT 171 chr6ptel1M 240508 AAGAAGGGGTAAGTTAGCCCAGATCAGAAAAATGGAAGAGTTTAAAGCTT 240557 i i iiii i i -- i iv v i i i 7SLRNA#SINE/A 172 AAGGAGGGGTGAACCGGCCCAGGTCGG--AAACGGAGCAGGTCAAAACTC 219 chr6ptel1M 240558 CCATTCTCATCAGTATTGGACTCAGACCTGTGACTAGCCACCATACTTCC 240607 i v v v iv ivi v iii i v 7SLRNA#SINE/A 220 CCGTGCTGATCAGTAGTGGGATCGCGCCTGTGAATAGCCACTGCACTCCA 269 chr6ptel1M 240608 TTTTGGAGGAGACAGGGAGACTAAGTCTCCAAATAAAATAAGAAA 240652 vii ivi v i v ivv iv v v i 7SLRNA#SINE/A 270 GCCTGGGCAACATAGCGAGACCCCGTCTCTTAAAAAAAAAAAAAA 314 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 34.65 CpG sites = 54, Kimura (unadjusted) = 42.24 Transitions / transversions = 1.74 (54/31) Gap_init rate = 0.03 (8 / 273), avg. gap size = 2.88 (23 / 8) 254 30.65 0.79 1.60 chr6ptel1M 241098 241223 (758777) C MARNA#DNA/TcMar-Mariner (133) 453 329 m_b277s502i2 10976 chr6ptel1M 241098 GGTGCTGCCATTGCTTTGAGCAGTCTGGTGCCATGTTTCTGTTATGTTCT 241147 i ivi i v i v viv v v i i vv vvi C MARNA#DNA/TcM 453 GATGCTGCCATTGCTCAAAACATTTTTGGAACTTCTCTTTGGAATTGCCT 404 chr6ptel1M 241148 CCAGATCCTCAGGCACATTCTTTTGGGGATCTCCTTTATTGTGCCAAAT- 241196 i v vv -- i v iv v v - C MARNA#DNA/TcM 403 TCAGAGCCTGCGGCACATTCTTTT--GAATATCCTCAATGGTGGCAAATC 356 chr6ptel1M 241197 TATATCCTTCGAGTGAATATTTGATTT 241223 vii i v viv C MARNA#DNA/TcM 355 TTCGTCCTTTGAGGGTGGATTTGATTT 329 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 38.14 CpG sites = 16, Kimura (unadjusted) = 39.55 Transitions / transversions = 0.73 (16/22) Gap_init rate = 0.02 (3 / 125), avg. gap size = 1.00 (3 / 3) 38 2.43 0.00 2.33 chr6ptel1M 241373 241416 (758584) (TTAT)n#Simple_repeat 1 43 (0) c_b277s251i2 10977 chr6ptel1M 241373 TTATTTATTTATTTATTTATTTATTTATTTTTTTTATTTATTTA 241416 - v (TTAT)n#Simpl 1 TTATTTATTTATTTATTTATTTATTTA-TTTATTTATTTATTTA 43 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.02 (1 / 43), avg. gap size = 1.00 (1 / 1) 16 9.71 0.00 0.00 chr6ptel1M 241504 241525 (758475) (C)n#Simple_repeat 1 22 (0) m_b277s252i2 10978 chr6ptel1M 241504 CCCCCCCCCCCACCCCCTCCCC 241525 v i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCC 22 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 483 31.32 1.49 1.49 chr6ptel1M 241883 242083 (757917) C L1MD1_3end#LINE/L1 (356) 633 433 m_b277s551i1 10979 chr6ptel1M 241883 GCTCATTTCACTCAGCATCAGTTCGTGTAAGTCTCTCCAGGCCTTTCTGA 241932 iv v v iiv v ii iiv iiv vi v C L1MD1_3end#LI 633 GCTTTTTTCACTCAGCATAATTCTCTGGAGATTCATCCAGGTTGTTGCGT 584 chr6ptel1M 241933 A-ATCATCCTGTTGGTCATTTCTTACAGAACAGTAATATTCCATAATTTT 241981 i- viv- v ivi i iv vvv i ii v v C L1MD1_3end#LI 583 GTATCAATA-GTTCGTTCCTTTTTATTGCTGAGTAGTATTCCATGGTATG 535 chr6ptel1M 241982 CATATACCACAATTTATTCAGCCATTCTCCAACTGATGGACATCCA--TT 242029 v i i i i i v vii v ii-- C L1MD1_3end#LI 534 GATGTACCACAGTTTGTTTAACCATTCACCCGTTGAAGGACATCTGGGTT 485 chr6ptel1M 242030 CAGTTTCCAGTTTCTAGCCACTACAAAAAGGGCTGCCACAAACATTCGTG 242079 -- i i i i i v ii i i C L1MD1_3end#LI 484 --GTTTCCAGTTTTTGGCTATTACGAATAAAGCTGCTATAAACATTCGTG 437 chr6ptel1M 242080 CACA 242083 i C L1MD1_3end#LI 436 TACA 433 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.42 CpG sites = 38, Kimura (unadjusted) = 42.11 Transitions / transversions = 1.58 (38/24) Gap_init rate = 0.03 (5 / 200), avg. gap size = 1.20 (6 / 5) 500 22.68 1.65 1.65 chr6ptel1M 241963 242083 (757917) C L1ME1_3end#LINE/L1 (373) 553 433 m_b277s551i2 10979 chr6ptel1M 241963 AGTAATATTCCATAATTTTCATATACCACAATTTATTCAGCCATTCTCCA 242012 i vi v vv i i v v ? C L1ME1_3end#LI 553 AGTAGTATTCCATTGTATGGATATACCACAATTTGTTTATCCATTCACCN 504 chr6ptel1M 242013 ACTGATGGACATCC--ATTCAGTTTCCAGTTTCTAGCCACTACAAAAAGG 242060 ii ii--i -- i i i i i v ii C L1ME1_3end#LI 503 GTTGATGGACATTTGGGTT--GTTTCCAGTTTTTGGCTATTACGAATAAA 456 chr6ptel1M 242061 GCTGCCACAAACATTCGTGCACA 242083 i ii i C L1ME1_3end#LI 455 GCTGCTATGAACATTCGTGTACA 433 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 27.31 CpG sites = 20, Kimura (unadjusted) = 28.56 Transitions / transversions = 2.86 (20/7) Gap_init rate = 0.03 (3 / 120), avg. gap size = 1.33 (4 / 3) 298 27.15 4.88 1.18 chr6ptel1M 242089 242170 (757830) C MIR3#SINE/MIR (42) 166 82 m_b277s601i28 10980 chr6ptel1M 242089 GGGACCACTTATTTAAACCCCCATCATTTTACTGATATGGAAATTGAGGT 242138 i i ii v iv - v iv i i C MIR3#SINE/MIR 166 GAGATCATCTAGTCCAACCCCC-TCATTTTACAGATGAGGAAACTGAGGC 118 chr6ptel1M 242139 GCTGAAAGG----GTAACTTGTCCCTAGTCCCATAG 242170 v v i ---- i i vvi v i C MIR3#SINE/MIR 117 CCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAG 82 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 34.57 CpG sites = 13, Kimura (unadjusted) = 34.57 Transitions / transversions = 1.44 (13/9) Gap_init rate = 0.02 (2 / 81), avg. gap size = 2.50 (5 / 2) 251 25.33 9.33 0.00 chr6ptel1M 242113 242187 (757813) C MIR#SINE/MIR (120) 142 61 m_b277s601i29 10980 chr6ptel1M 242113 CATTTTACTGATATGGAAATTGAGGTGCTGAAAGG----GTAACTTGTCC 242158 v iv i ii v i ---- i C MIR#SINE/MIR 142 CATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCC 93 chr6ptel1M 242159 CTAGTCCCATAGGCAAAAAGT--CA-AGCTGG 242187 vvi v i vi iv -- - i C MIR#SINE/MIR 92 AAGGTCACACAGCTAGTAAGTGGCAGAGCCGG 61 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.58 CpG sites = 11, Kimura (unadjusted) = 31.54 Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.04 (3 / 74), avg. gap size = 2.33 (7 / 3) 285 28.79 15.79 1.73 chr6ptel1M 242356 242507 (757493) MIR3#SINE/MIR 18 190 (18) m_b277s601i30 10981 chr6ptel1M 242356 CAGAGAAAGCAGCTGTCTGAGAG--GGGAGACATCGAGGTGGGAGTCTGG 242403 i - v v i --i -- vi vvv iv MIR3#SINE/MIR 18 CAGAGAGAGCA-CGGACTGGGAGTCAGGAGAC--CTGGGTTCTAGTCCCG 64 chr6ptel1M 242404 GCTCTGCTG--AGC--ACTGGGTGGCTGTGGAC-------------TCTC 242436 ii-- i --i v i iv i ------------- MIR3#SINE/MIR 65 GCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTC 114 chr6ptel1M 242437 AGGCTGTCACATCCCTCGTCTGTGA--TAAGAAGGT-AGATTCAATCATC 242483 v viv vv i i i -- i ii -i i vi v MIR3#SINE/MIR 115 TGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATC 164 chr6ptel1M 242484 TTTAAAATCA--TCCAGTTCTGACAT 242507 i ii v-- i MIR3#SINE/MIR 165 TCTAAGGTCCCTTCCAGCTCTGACAT 190 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 37.57 CpG sites = 26, Kimura (unadjusted) = 37.57 Transitions / transversions = 1.53 (26/17) Gap_init rate = 0.07 (10 / 151), avg. gap size = 2.70 (27 / 10) 297 26.92 16.38 0.75 chr6ptel1M 242839 242954 (757046) MIRb#SINE/MIR 20 153 (115) m_b277s601i31 10982 chr6ptel1M 242839 AATGGAAATATCAGTGCTTTTTGACTCAAA--AATCTGGGTTCAAATCCT 242886 i v v vv vi v v i --i i i i MIRb#SINE/MIR 20 AGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCGAATCCC 69 chr6ptel1M 242887 ACCTTTGACACTTGACCAG-TGTGT--TCTTG-------------ACC-C 242919 iv i v - i - --i ------------- - MIRb#SINE/MIR 70 GGCTCTGCCACTT-ACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTC 118 chr6ptel1M 242920 CCTGGGTTTCAGGCCCCTTTTCTGTAAAATGAGAA 242954 i i ii vii iv i i MIRb#SINE/MIR 119 TCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGA 153 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 31.73 CpG sites = 20, Kimura (unadjusted) = 34.61 Transitions / transversions = 1.82 (20/11) Gap_init rate = 0.05 (6 / 115), avg. gap size = 3.33 (20 / 6) 414 25.16 15.44 0.64 chr6ptel1M 242861 242996 (757004) MIR3#SINE/MIR 37 192 (16) m_b277s601i32 10982 chr6ptel1M 242861 GACTCAAAA-ATCTGGGTTCAAATCCTACCTTTGACACT---TGACCAGT 242906 v ii - i v i iiv i v --- ?i i- MIR3#SINE/MIR 37 GAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCT-GT 85 chr6ptel1M 242907 GTGTTCTTG-------------ACCCC-CTGGGTTTCAGGCCCCTTTTCT 242942 vi ------------- i - ii vii iv MIR3#SINE/MIR 86 GTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCT 135 chr6ptel1M 242943 GTAAAATGAGAAGCTTGGACTGGATGATCTCTGAG--TCCTTTTAACTCC 242990 ii v i i --i ii i i MIR3#SINE/MIR 136 GTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCT 185 chr6ptel1M 242991 -ATATTC 242996 - i MIR3#SINE/MIR 186 GACATTC 192 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 31.53 CpG sites = 26, Kimura (unadjusted) = 32.87 Transitions / transversions = 3.25 (26/8) Gap_init rate = 0.05 (7 / 135), avg. gap size = 3.14 (22 / 7) 443 20.69 0.00 18.26 chr6ptel1M 243258 243393 (756607) C MER63D#DNA/hAT-Tip100 (596) 465 351 m_b277s502i3 10983 chr6ptel1M 243258 ACATCTTTAAGTTTAATCCATATGATCAGCATTTCCTACATTACTTTCTT 243307 ii iii v i i i v i C MER63D#DNA/hA 465 ACACTTTTAAGTTTAATCTGCATTATTAACATTTTCTCCATCACTTTCTT 416 chr6ptel1M 243308 TATAAATAAATAAATAAAAAAGTCTAAATAATCACCAAAATAATAAATCA 243357 ------------------- i i v i C MER63D#DNA/hA 415 -------------------AAGTCTAGACAATCAACAAAACAATAAATCA 385 chr6ptel1M 243358 AGCTCTAATTTGTGGTGTTATAGCCAGTTTCTGAGG 243393 i i i i - - ii i v C MER63D#DNA/hA 384 AGCCCTGATTTGTAGCGTT-T-GCCGATTTCCGTGG 351 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 20.96 CpG sites = 19, Kimura (unadjusted) = 24.53 Transitions / transversions = 4.75 (19/4) Gap_init rate = 0.16 (21 / 135), avg. gap size = 1.00 (21 / 21) 311 32.11 2.21 6.11 chr6ptel1M 243621 243756 (756244) C MIR3#SINE/MIR (1) 207 77 m_b277s601i33 10984 chr6ptel1M 243621 AAATATAGGGT-ATAGAATTTTGCTGCTGAAAGGGTCCTTGAACGTAACC 243669 vi ii - v iivv i v ii vi v i C MIR3#SINE/MIR 207 AATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATC 158 chr6ptel1M 243670 TGACCCACTGCCAAACCCCATCATTCTGCAGCTGAGTGCATCGAGGCCT- 243718 iii ------- v i i v viv ii i- C MIR3#SINE/MIR 157 TAGTCCA-------ACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCA 115 chr6ptel1M 243719 GAGTGA-GAAATGATCCATTCAAGGTCCCAGCAGCAAAT 243756 v i- i iiiiii v - ? i C MIR3#SINE/MIR 114 GAGAGGTGAAGTGACTTGCCCAAGGTCACA-CAGCNAGT 77 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 44.91 CpG sites = 28, Kimura (unadjusted) = 44.91 Transitions / transversions = 2.15 (28/13) Gap_init rate = 0.08 (11 / 135), avg. gap size = 1.00 (11 / 11) 277 34.11 6.20 0.00 chr6ptel1M 243759 243887 (756113) C MIRc#SINE/MIR (17) 251 115 m_b277s601i34 10985 chr6ptel1M 243759 ACATTTGTG-AGCTCTTTATCATTT-CAGAGC------AAATCTCTCCTC 243800 i- v ivi - i ------ v viv iv C MIRc#SINE/MIR 251 ACATTTGTATAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATC 202 chr6ptel1M 243801 TCTTTTTACTCTCACACCATCGGGATTCGGCAGGCAGGACAGTTGTGACC 243850 v v ii v v vvvi vv i i v i v ii C MIRc#SINE/MIR 201 TCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATT 152 chr6ptel1M 243851 GTTCTCCTGCTATGGATGGAGAGGCTGAGGCTCTGAG 243887 i i i v vi ii ii ii v C MIRc#SINE/MIR 151 ATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAG 115 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 46.73 CpG sites = 24, Kimura (unadjusted) = 46.73 Transitions / transversions = 1.20 (24/20) Gap_init rate = 0.02 (3 / 128), avg. gap size = 2.67 (8 / 3) 210 21.19 4.08 8.51 chr6ptel1M 244890 244987 (755013) MIR#SINE/MIR 46 139 (123) m_b277s601i35 10986 chr6ptel1M 244890 GCCCGGGCTCGCAAATCCAGCCTCAGACA-TTCCCAGTCCCAGTCCCAGT 244938 i i -- v v v v - v i --- v viv -- MIR#SINE/MIR 46 GCCTGGGTTCG--AATCCCGGCTCTGCCACTTACTAG---CTGTGTGA-- 88 chr6ptel1M 244939 CCCTGGGTGAGACGCTTCACCTGCT---TGCCTCAGTTTCCTCATCTGTA 244985 i ii vii v - --- MIR#SINE/MIR 89 CCTTGGGCAAGTTACTTAACCT-CTCTGTGCCTCAGTTTCCTCATCTGTA 137 chr6ptel1M 244986 AA 244987 MIR#SINE/MIR 138 AA 139 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 24.92 CpG sites = 9, Kimura (unadjusted) = 24.92 Transitions / transversions = 0.90 (9/10) Gap_init rate = 0.10 (10 / 97), avg. gap size = 1.20 (12 / 10) 260 16.33 4.08 0.00 chr6ptel1M 244939 244987 (755013) MIR3#SINE/MIR 90 140 (68) m_b277s601i36 10986 chr6ptel1M 244939 CCCTGGGTGAGACGCTTCACCTGCTTG--CCTCAGTTTCCTCATCTGTAA 244986 i ii v i vii -- MIR3#SINE/MIR 90 CCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAA 139 chr6ptel1M 244987 A 244987 MIR3#SINE/MIR 140 A 140 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 18.95 CpG sites = 6, Kimura (unadjusted) = 18.95 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.02 (1 / 48), avg. gap size = 2.00 (2 / 1) 246 29.22 22.95 0.90 chr6ptel1M 245603 245785 (754215) MIRc#SINE/MIR 19 241 (27) m_b277s601i37 10987 chr6ptel1M 245603 TGGAAGGGGC-TTGGAGGTACAAGTTGGGAACATCTTGCTAC-AGTTCTG 245650 i i -i vv i-i ii v i v v v - i i MIRc#SINE/MIR 19 TGGAAAGAGCACTGGACTTG-GAGTCAGGAAGACCTGGGTTCGAGTCCCG 67 chr6ptel1M 245651 CCTCAGATGCTT-----CTATGTGACCCCGAG--------------TCTC 245681 v v vii ----- i ii i -------------- MIRc#SINE/MIR 68 GCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTC 117 chr6ptel1M 245682 --AGGCTCAGTTTCTTTTTATGTTAAAGGAGGAGGACAATA---GCCCTG 245726 -- v i iv v v v i vi i --- MIRc#SINE/MIR 118 TGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTG 167 chr6ptel1M 245727 ---GTCTTCCAGAGTCACGGGGAAGATCA------------T-TGTGCAA 245760 ---ii iv i iiiv v i ------------ - - MIRc#SINE/MIR 168 CCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTG-AA 216 chr6ptel1M 245761 AGGGCTTTGCAAACCTTAGACTGCT 245785 v i iv i v MIRc#SINE/MIR 217 AGCGCTTTGTAAACTGTAAAGTGCT 241 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 37.38 CpG sites = 32, Kimura (unadjusted) = 38.31 Transitions / transversions = 1.52 (32/21) Gap_init rate = 0.06 (11 / 182), avg. gap size = 4.00 (44 / 11) 217 35.05 5.15 0.00 chr6ptel1M 245893 245989 (754011) MIRc#SINE/MIR 19 120 (148) m_b277s601i38 10988 chr6ptel1M 245893 TGGATAAAGTGCCAGACTTGGAATCAGTAAGACCTGAGCAGCTATTCTGG 245942 v i ii ii i v i ivvvvi i i MIRc#SINE/MIR 19 TGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGG 68 chr6ptel1M 245943 GTCT-CAGTTTACTTA-TATATAAAGTGGGGATGATCAC---ACCTCCCT 245987 v - vii vi- i i i vv v vvii --- i MIRc#SINE/MIR 69 CTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCT 118 chr6ptel1M 245988 GA 245989 MIRc#SINE/MIR 119 GA 120 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 47.14 CpG sites = 20, Kimura (unadjusted) = 49.19 Transitions / transversions = 1.43 (20/14) Gap_init rate = 0.03 (3 / 96), avg. gap size = 1.67 (5 / 3) 312 25.00 0.00 0.00 chr6ptel1M 245938 246001 (753999) MIRb#SINE/MIR 119 182 (86) m_b277s601i39 10988 chr6ptel1M 245938 TCTGGGTCTCAGTTTACTTATATATAAAGTGGGGATGATCACACCTCCCT 245987 i i v i v i i i v i v MIRb#SINE/MIR 119 TCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTACCT 168 chr6ptel1M 245988 GAAAGAATTGTTGT 246001 viv ii MIRb#SINE/MIR 169 CGCAGGGTTGTTGT 182 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 28.94 CpG sites = 10, Kimura (unadjusted) = 31.26 Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0) 16 21.33 0.00 0.00 chr6ptel1M 246102 246134 (753866) (T)n#Simple_repeat 1 33 (0) m_b277s252i3 10989 chr6ptel1M 246102 TTTTTTTTTAATTTTTAAATTTTTTTTTTATTT 246134 vv vvv v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 33 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 505 29.22 0.65 0.65 chr6ptel1M 246425 246579 (753421) C MIR3#SINE/MIR (29) 179 25 m_b277s601i40 10990 chr6ptel1M 246425 GGCAGAGAACTTAGAGGCCATGGAGTCAGTCCCCTTCATTTTACAGCTAA 246474 v i v ii vv viv i v i C MIR3#SINE/MIR 179 GGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGA 130 chr6ptel1M 246475 GGAACCTGAGGCCTTATGAGGTCAACTGACTTATCAAGAGGCACAGAGGT 246524 v iviv v v ii v ii v v v? C MIR3#SINE/MIR 129 GGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGCN 80 chr6ptel1M 246525 AGTGAGTGTCTAAGGCATGATTTGCACTCAAGTCTCACTGA-TAGCAAGC 246573 v v vi v iv i v v i i - - vv iv C MIR3#SINE/MIR 79 AGTTAGTGGCAGAGCCGGGACTAGAACCCAGGTCTC-CTGACTCCCAGTC 31 chr6ptel1M 246574 AGTGCT 246579 v C MIR3#SINE/MIR 30 CGTGCT 25 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 36.42 CpG sites = 18, Kimura (unadjusted) = 37.41 Transitions / transversions = 0.67 (18/27) Gap_init rate = 0.01 (2 / 154), avg. gap size = 1.00 (2 / 2) 273 27.17 15.22 0.00 chr6ptel1M 246595 246686 (753314) C MIR3#SINE/MIR (32) 176 71 m_b277s601i41 10991 chr6ptel1M 246595 AGAGGACTTGGATGTCACTTTGTCCAACTCCTTCATTTTACTGAT----- 246639 i iv i vi ii v i i v ----- C MIR3#SINE/MIR 176 AGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGA 127 chr6ptel1M 246640 --------CTCAGAGAGAGCAAGTGA-TAGCCCAAAGTGCCTTAGTAAGT 246680 -------- i ivv - v i vv vi i? C MIR3#SINE/MIR 126 AACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGCNAGT 77 chr6ptel1M 246681 TACTAG 246686 v i C MIR3#SINE/MIR 76 TAGTGG 71 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 34.90 CpG sites = 14, Kimura (unadjusted) = 34.90 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.03 (3 / 91), avg. gap size = 4.67 (14 / 3) 354 31.79 12.90 0.57 chr6ptel1M 246741 246895 (753105) MIRc#SINE/MIR 13 186 (82) m_b277s601i42 10992 chr6ptel1M 246741 GTGTAGGGGAAGGAGCTGGTGCTTTTGGAG-----AAGATCTGGGT---- 246781 i v i -iv vvi ----- i ---- MIRc#SINE/MIR 13 GTGCAGTGGAAAGAGC-ACTGGACTTGGAGTCAGGAAGACCTGGGTTCGA 61 chr6ptel1M 246782 --CCTGTCTC--------ACTGGCTGTATGACTCAATACAAATTAATGAG 246821 -- i v -------- i i iivivi i i v v i MIRc#SINE/MIR 62 GTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAA 111 chr6ptel1M 246822 CATCTTTGTGCCTCAATAACCCCATCTGCAAAATCAGAATCCTGAAACCT 246871 v i v i vv i i vi i vv i v MIRc#SINE/MIR 112 CCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCT 161 chr6ptel1M 246872 AGTA-ACCTACTTCATAGATTTATT 246895 iviv-i i i iv i MIRc#SINE/MIR 162 GCCCTGCCTACCTCACAGGGTTGTT 186 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 41.66 CpG sites = 29, Kimura (unadjusted) = 42.83 Transitions / transversions = 1.45 (29/20) Gap_init rate = 0.04 (6 / 154), avg. gap size = 3.50 (21 / 6) 376 29.95 1.64 4.20 chr6ptel1M 246774 246895 (753105) MIR#SINE/MIR 58 176 (86) m_b277s601i43 10992 chr6ptel1M 246774 ATCTGGGTCCTGTC--TCACTGGCTGTATGACTCAATACAAATTAATGAG 246821 iv ii i -- i i i iivivi i v v i MIR#SINE/MIR 58 ATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAA 107 chr6ptel1M 246822 CATCTTTGTGCCTCAATAACCCCATCTGCAAAATCAGAATCCTGAAACCT 246871 v i i vv i i vi i vv i ---- MIR#SINE/MIR 108 CCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAA----T 153 chr6ptel1M 246872 AGTAACCTACTTCATAGATTTATT 246895 - i iv i MIR#SINE/MIR 154 AGT-ACCTACCTCATAGGGTTGTT 176 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 39.97 CpG sites = 23, Kimura (unadjusted) = 39.97 Transitions / transversions = 1.92 (23/12) Gap_init rate = 0.05 (6 / 121), avg. gap size = 1.17 (7 / 6) 209 31.33 5.00 1.61 chr6ptel1M 247990 248109 (751891) C MIRb#SINE/MIR (141) 127 4 m_b277s601i44 10993 chr6ptel1M 247990 AAGCACCGAGAGGTTCAGTGACTACTCTTAGGTCGGCCAGCGAG-GAGTC 248038 i v v v i vvi iv ivv v -i v C MIRb#SINE/MIR 127 AGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTG 78 chr6ptel1M 248039 TCAGAAGTAGGGCT---ACCCA-GCCTTTCTCACTCCAGCACTCAT-CTC 248083 v ivii ii --- - i v v ivi i i - C MIRb#SINE/MIR 77 GCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTC 28 chr6ptel1M 248084 TGTCCGTTCTGCCCCTCACAGCCCCT 248109 v i-- v v i v C MIRb#SINE/MIR 27 TTTCCA--CTGCACCACGCTGCCCCT 4 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 36.84 CpG sites = 18, Kimura (unadjusted) = 41.09 Transitions / transversions = 0.95 (18/19) Gap_init rate = 0.05 (6 / 119), avg. gap size = 1.33 (8 / 6) 15 12.15 2.50 5.13 chr6ptel1M 249921 249960 (750040) (CTCTT)n#Simple_repeat 1 39 (0) m_b277s252i4 10994 chr6ptel1M 249921 CTTTTC-CTTCTCTTCTCTTCTCCTCCTCTTCATGCTCTCT 249960 i - - i - vi (CTCTT)n#Simp 1 CTCTTCTCTTCTCTTCTCTTCT-CTTCTCTTC-TCTTCTCT 39 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.08 (3 / 39), avg. gap size = 1.00 (3 / 3) 15 24.12 0.00 0.00 chr6ptel1M 250287 250320 (749680) (CT)n#Simple_repeat 1 34 (0) m_b277s252i5 10995 chr6ptel1M 250287 CTCTCTCTAATTGTTTCTTTCTCACTCTCTCTCT 250320 vvi v i i v (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 34 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 220 28.30 0.00 0.00 chr6ptel1M 250862 250914 (749086) C L2d_3end#LINE/L2 (0) 516 464 m_b277s601i45 10996 chr6ptel1M 250862 TTGACCAAACAATCAATAAACATTTATTGAGCGCCTATTCTATTCCAGAC 250911 ii i v i ii i v i v ivii C L2d_3end#LINE 516 TCAATCAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGC 467 chr6ptel1M 250912 ACT 250914 C L2d_3end#LINE 466 ACT 464 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 37.81 CpG sites = 11, Kimura (unadjusted) = 37.81 Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 272 27.12 0.00 0.00 chr6ptel1M 250871 250929 (749071) C L2a_3end#LINE/L2 (7) 510 452 m_b277s601i46 10996 chr6ptel1M 250871 CAATCAATAAACATTTATTGAGCGCCTATTCTATTCCAGACACTAGCCAT 250920 v i i i v i v i ivi vv C L2a_3end#LINE 510 CATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTA 461 chr6ptel1M 250921 GGTATTGGG 250929 iii C L2a_3end#LINE 460 GGCGCTGGG 452 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 31.79 CpG sites = 10, Kimura (unadjusted) = 34.74 Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.0 (0 / 0) 296 33.59 2.56 4.58 chr6ptel1M 251226 251381 (748619) MIR3#SINE/MIR 40 192 (16) m_b277s601i47 10997 chr6ptel1M 251226 TCCAAAGACCTGTAT-AGAGTTTCTGATTTACCTCTAATTCAGCTTTTTG 251274 vii vi -vv ii v v i i v i ?- v v MIR3#SINE/MIR 40 TCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTN-GCTGTGTG 88 chr6ptel1M 251275 ACCTTTGAGCCTTAGGAG-CATTTTGACCCTCTGGCCTTTAGTCTCCTAG 251323 - i -----i - i iiv i v i i i vi MIR3#SINE/MIR 89 ACCTT-GGGC-----AAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCA 132 chr6ptel1M 251324 GC-ATGAAATGAGAAATCTGCACCAGAAGATCTGAGAAATCCCCT-CAGC 251371 v -i i iiivi v i v vvi ii i - MIR3#SINE/MIR 133 TCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGC 182 chr6ptel1M 251372 TGGGACATCC 251381 vv i MIR3#SINE/MIR 183 TCTGACATTC 192 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 46.76 CpG sites = 30, Kimura (unadjusted) = 46.76 Transitions / transversions = 1.50 (30/20) Gap_init rate = 0.07 (11 / 155), avg. gap size = 1.00 (11 / 11) 424 19.08 5.31 7.21 chr6ptel1M 251880 251992 (748008) MIRc#SINE/MIR 38 148 (120) m_b277s601i48 10998 chr6ptel1M 251880 GGAATCAGAAAGCCTCAGCTCCTGAGTTAAAATCTGGCCTCAG--AC--A 251925 i i v ------- i vi i iv v v -- -- MIRc#SINE/MIR 38 GGAGTCAGGAAGAC-------CTGGGTTCGAGTCCCGGCTCTGCCACTTA 80 chr6ptel1M 251926 CTAGCTGTGTGAGCCCGGGCAAGTCACTTATTCCTGTTT--GCCTCAGAT 251973 v ii -v v i -- v MIRc#SINE/MIR 81 CTAGCTGTGTGACCTTGGGCAAGTCACTTA-ACCTCTCTGAGCCTCAGTT 129 chr6ptel1M 251974 TTCTCATCTGTAAAATGAG 251992 i i MIRc#SINE/MIR 130 TCCTCATCTGTAAAATGGG 148 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 20.99 CpG sites = 11, Kimura (unadjusted) = 22.20 Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.10 (11 / 112), avg. gap size = 1.27 (14 / 11) 425 19.35 5.38 0.00 chr6ptel1M 251900 251992 (748008) MIR#SINE/MIR 47 144 (118) m_b277s601i49 10998 chr6ptel1M 251900 CCTGAGTTAAAATCTGGCCTCAG--AC--ACTAGCTGTGTGAGCCCGGGC 251945 i vi iv v v -- -- v ii MIR#SINE/MIR 47 CCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGC 96 chr6ptel1M 251946 AAGTCACTTATTC-CTGTTTGCCTCAGATTTCTCATCTGTAAAATGAG 251992 i vi - v v v i i MIR#SINE/MIR 97 AAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGG 144 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 21.18 CpG sites = 9, Kimura (unadjusted) = 22.53 Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.03 (3 / 92), avg. gap size = 1.67 (5 / 3) 242 28.10 8.41 3.57 chr6ptel1M 252084 252190 (747810) C L2c_3end#LINE/L2 (16) 462 351 m_b277s601i50 10996 chr6ptel1M 252084 AACATTTCTTGAATGCCTTTTATATTCTCGGCACCTTGCTAAGTTATAAA 252133 v ii vi i v iv i -- --ii v i C L2c_3end#LINE 462 AACATTTATTGAGCGCCTACTATGTGCCAGGCGC--TG--GGGATACAAA 417 chr6ptel1M 252134 AGCCAGCAAGACA--GCTTCTGCCCTCA--GA-TT--CTGTCT-GTAGAG 252175 iiiv ii -- iii -- -i -- v - i C L2c_3end#LINE 416 GATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAGTGGAG 367 chr6ptel1M 252176 AAGAC-GGCACATAAA 252190 i - i ?i C L2c_3end#LINE 366 GAGACAGACANGTAAA 351 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 34.94 CpG sites = 22, Kimura (unadjusted) = 38.35 Transitions / transversions = 3.14 (22/7) Gap_init rate = 0.09 (10 / 106), avg. gap size = 1.30 (13 / 10) 595 33.33 4.50 4.04 chr6ptel1M 252472 252915 (747085) L1MC5a_3end#LINE/L1 191 636 (2141) m_b277s551i4 10999 chr6ptel1M 252472 ATCACTTCATGCCTCTCAGATTGGCTGAGATGACAAGAAGATAATGACGG 252521 i i vii v vi i v- i ivv i ii iv L1MC5a_3end#L 191 ACCATTTCTCACCTATCAGATTGGCAAAAATC-CAAAAGTTTGACAACAT 239 chr6ptel1M 252522 A---TGTTGGAGGGGATGTGGGAAAACTGGAACACTGATGCATTGTCGGT 252568 --- v i v i v v v v i ii L1MC5a_3end#L 240 ACTCTGTTGGCGAGGCTGTGGGGAAACAGGCACTCTCATACATTGCTGGT 289 chr6ptel1M 252569 GGAACTATGAACTGTCGTCATTC---TGGAGGGCAATCTGG-AAT-TGTA 252613 i v iii v viiiv ii --- v i - - v L1MC5a_3end#L 290 GGGAATGCAAAATGGTACAACCCCTATGGAGGGGAATTTGGCAATATCTA 339 chr6ptel1M 252614 CCCAAAGGGCCATCAAACTGTGCAC--ACCCTTTGATCCAGCAGTGTCAC 252661 v v ------ i v - i i-- i i vi L1MC5a_3end#L 340 GCAAAA------TTACA-TATGCATTTACCCTTTGACCCAGCAATCCCAC 382 chr6ptel1M 252662 TACTGGGCTTATATCCCAAAGAGATCTTA--AAGGAGGGAAAGGGACCTG 252709 v i vv v i v ivi ?-- ii vivi i? -- L1MC5a_3end#L 383 TTCTAGGAATCTATCCCGAAGATACACTNGCAAAAATACGAAANGAC--G 430 chr6ptel1M 252710 TATGTGCAGAAGTGTTTGTGGTAGCCCTTTTTGCAGTGGCAAGGAACTGG 252759 ii iiiv i ii v i vi v i i i iii L1MC5a_3end#L 431 TATGCACAAGGTTATTCATTGCAGCATTATTTGTAATAGCAAAAGACTGG 480 chr6ptel1M 252760 AAACTGAGTGGATGCCCATCAATTAGAGAATGGCTGAATAAATTGTGGTA 252809 vivviii i vi i v i i i L1MC5a_3end#L 481 AAACAACCCAAATGTCCATCAATAGGGGACTGGTTGAATAAACTATGGTA 530 chr6ptel1M 252810 TATGAATGTTGTGGAATATTAT-----TGTTCAGTAAGAAATGACCAGCA 252854 i vv iiivi i i ----- -- iv i ------ L1MC5a_3end#L 531 CATCCACACAATGGAGTACTATGCAGCTGT--AAAAAGGAATG------A 572 chr6ptel1M 252855 GGAGGATTTC---AGAAAGGCCTGGAGAGATTTACACGAACTGATGCTGA 252901 i i --- v vv ?iv v i v v vv iv i i L1MC5a_3end#L 573 GGAAGATCTCTATATACTGNTATGGAGTGATCTCCAGGATATATTGTTAA 622 chr6ptel1M 252902 GTGAACTGAGCAGG 252915 vvi i L1MC5a_3end#L 623 GTGAAAAAAGCAAG 636 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 45.49 CpG sites = 86, Kimura (unadjusted) = 46.41 Transitions / transversions = 1.54 (86/56) Gap_init rate = 0.06 (26 / 443), avg. gap size = 1.46 (38 / 26) 951 29.97 4.17 3.59 chr6ptel1M 252472 252831 (747169) L1ME5_3end#LINE/L1 191 552 (389) m_b277s551i3 10999 chr6ptel1M 252472 ATCACTTCATGCCTCTCAGATTGGCTGAGATGACAAGA--AGATAATGAC 252519 i ii v i i vi i v v ii--i v L1ME5_3end#LI 191 ATCACTTTACACCTATTAGACTGGCAAAAATTAGAAAGCTGGATAATGCC 240 chr6ptel1M 252520 GGATGTTGGAGGGGATGTGGGAAAACTGGAACACTGATGCATTGTCGGTG 252569 iii v i i ? iv v v i ii L1ME5_3end#LI 241 AAGTGTTGGCGAGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTG 290 chr6ptel1M 252570 GAACTATGAACTG---TCGTCATTCTGGAGGGCAATCTGGAATTGTACCC 252616 i v i ii ---iv i i v -- ii L1ME5_3end#LI 291 GGAGTGTAGACTGGTGCAGCCATTCTGGAGAGCAATCTGGCA--GTACTT 338 chr6ptel1M 252617 AAAGGGCCATCAAACT--GT----GCACACCCTTTGATCCAGCAGTGTCA 252660 i------- i -- ---- i v i i vi i L1ME5_3end#LI 339 AG-------TCAAATTAAGTATACGCATACCCTATGACCCAGCAATTCCG 381 chr6ptel1M 252661 CTACTGGGCTTATATCCCAAAGAGATCTTAAAGGAGG----GAAAGGGAC 252706 v iv i ii v viv ----v i L1ME5_3end#LI 382 CTCCTGGGTATATATCCCAAAGAAATTCTCACACAGGTCCATAAGGGGAC 431 chr6ptel1M 252707 CTGTATGTGCAGAAGTGTTTGTGGTAGCCCTTTTTGCAGTGGCAAGGAAC 252756 v i --- i - ii v i vi v ii ii ii L1ME5_3end#LI 432 ATGTACG---AGGA-TGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGT 477 chr6ptel1M 252757 TGGAAACTGAGTGGATGCCCATCAATTAGAGAATGGCTGAATAAATTGTG 252806 ii vivv i i v vi i v iii v L1ME5_3end#LI 478 TGGAGGCAACCTGGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTG 527 chr6ptel1M 252807 GTATATGAATGTTGTGGAATATTAT 252831 iv v iiiii i i L1ME5_3end#LI 528 GTGGATGCACACCATGGAGTACTAT 552 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 38.98 CpG sites = 71, Kimura (unadjusted) = 40.53 Transitions / transversions = 2.15 (71/33) Gap_init rate = 0.05 (18 / 359), avg. gap size = 1.56 (28 / 18) 352 10.91 0.00 0.00 chr6ptel1M 253479 253533 (746467) C Charlie4#DNA/hAT-Charlie (3234) 144 90 m_b277s502i4 11000 chr6ptel1M 253479 ATTCATGATTAAAGGAAATGCTAAATTTCACTTAAAGGTCAATGAAAATA 253528 i i v i i i C Charlie4#DNA/ 144 ATTCATAATTGAAGGAAATGCTAAATTTCAGTTAGAGGTTAGTGAAAATA 95 chr6ptel1M 253529 AAGAT 253533 C Charlie4#DNA/ 94 AAGAT 90 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 12.08 CpG sites = 5, Kimura (unadjusted) = 12.08 Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 297 10.42 0.00 0.00 chr6ptel1M 253599 253646 (746354) C Charlie4#DNA/hAT-Charlie (3241) 137 90 m_b277s502i5 11000 chr6ptel1M 253599 ATTAAAGGAAATGCTAAATTTCACTTAGAGGTCATGGAAAATAAAGAT 253646 i v i vv C Charlie4#DNA/ 137 ATTGAAGGAAATGCTAAATTTCAGTTAGAGGTTAGTGAAAATAAAGAT 90 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 11.22 CpG sites = 2, Kimura (unadjusted) = 11.22 Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 181 29.95 1.97 16.54 chr6ptel1M 254236 254387 (745613) C MIR3#SINE/MIR (60) 148 16 m_b277s601i51 11001 chr6ptel1M 254236 CCCCTCATGTTACAGATGAGT-AACCGGGTTCTATAGCAACCAAAGGTGG 254284 v v- i i vi i v viiiv -- i C MIR3#SINE/MIR 148 CCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAA--GTGA 101 chr6ptel1M 254285 CAGACCCAAGGTTCAGACACTTTCCGCTGAACCACACTCATGGTTACTCA 254334 vvi i--- --------- i ? -ii vi ----- C MIR3#SINE/MIR 100 CTTGCCCAAGGTC---ACAC---------AGCNA-GTTAGTGG-----CA 69 chr6ptel1M 254335 -AGTTATTGCATTTGAACTCAGGACTTCTTACTCCGTGTCC-TGCACTCT 254382 - iii-- v i v i v i v vv - v C MIR3#SINE/MIR 68 GAGCCG--GGACTAGAACCCAGGTCTCCTGACTCCCAGTCCGTGCTCTCT 21 chr6ptel1M 254383 TGGCT 254387 iv C MIR3#SINE/MIR 20 CTGCT 16 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 36.81 CpG sites = 21, Kimura (unadjusted) = 38.21 Transitions / transversions = 1.24 (21/17) Gap_init rate = 0.17 (25 / 151), avg. gap size = 1.00 (25 / 25) 416 22.83 5.43 0.00 chr6ptel1M 254936 255027 (744973) C L3#LINE/CR1 (4) 4095 3999 m_b277s601i52 11002 chr6ptel1M 254936 GAATCACAGAATTTCAGAGTTTGAGGAGACCTCAGAAGCCATCTGATTGG 254985 i v i i i i i ii ivi C L3#LINE/CR1 4095 GAATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCA 4046 chr6ptel1M 254986 ACC-CTAATTCAA-GCAGGAAACTCCT---CAATATTCCTGAGAAGT 255027 - iv i - v i i --- i i v C L3#LINE/CR1 4045 ACCTCCCATCCAATGCAGGAATCCCTTCTACAACATCCCTGACAAGT 3999 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 28.60 CpG sites = 16, Kimura (unadjusted) = 28.60 Transitions / transversions = 3.20 (16/5) Gap_init rate = 0.03 (3 / 91), avg. gap size = 1.67 (5 / 3) 264 19.97 14.47 1.16 chr6ptel1M 255030 255105 (744895) MIRc#SINE/MIR 15 100 (168) m_b277s601i53 11003 chr6ptel1M 255030 GCAGTGAAA------CTGGACTTGGAAT---GAGTACCTGGATTCAAGTG 255070 i ------ i --- iv i i v MIRc#SINE/MIR 15 GCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTC 64 chr6ptel1M 255071 CTGG--ATACTTCTTGCTCTCTGTGTGACCTCTGGGC 255105 i --v i iv i vv - MIRc#SINE/MIR 65 CCGGCTCTGCCACTTACTAGCTGTGTGACCT-TGGGC 100 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 20.23 CpG sites = 9, Kimura (unadjusted) = 23.64 Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.05 (4 / 75), avg. gap size = 3.00 (12 / 4) 281 23.08 14.29 0.00 chr6ptel1M 255852 255942 (744058) L2b_3end#LINE/L2 268 371 (95) m_b277s601i54 11004 chr6ptel1M 255852 GCCTTCCCCTG------CCTGTTCCTAGCTTGCCATTTTAAATT-TCCTT 255894 i i ------ iiv v i i i iii - ?v L2b_3end#LINE 268 GCCCTCCTCTGGGCCCCCCCAGTCCTACCCTGCCACTCTGGGTTATNATT 317 chr6ptel1M 255895 TTATGGGT---TATCT---TCCCCCACTAGAATGTAAGCTCCTTAAGGGC 255938 v v ?v --- i --- v i v i L2b_3end#LINE 318 GTCTGNTTACATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGC 367 chr6ptel1M 255939 AGGG 255942 L2b_3end#LINE 368 AGGG 371 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.02 CpG sites = 13, Kimura (unadjusted) = 29.02 Transitions / transversions = 1.62 (13/8) Gap_init rate = 0.04 (4 / 90), avg. gap size = 3.25 (13 / 4) 292 20.00 1.39 2.82 chr6ptel1M 255871 255942 (744058) L2c_3end#LINE/L2 329 399 (79) m_b277s601i55 11004 chr6ptel1M 255871 TAGCTTGCCATTTTAAATTTCCTTTTATGGGT-TATCTTCCCCCACTAGA 255919 i i- v v v iv i?v - i - i L2c_3end#LINE 329 TAACTTGT-ATTGTAATTGTCTGTTTACNTGTCTGTCT-CCTCCACTAGA 376 chr6ptel1M 255920 ATGTAAGCTCCTTAAGGGCAGGG 255942 v i i L2c_3end#LINE 377 CTGTGAGCTCCTTGAGGGCAGGG 399 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 23.97 CpG sites = 8, Kimura (unadjusted) = 23.97 Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.04 (3 / 71), avg. gap size = 1.00 (3 / 3) 322 16.67 6.06 0.00 chr6ptel1M 255880 255945 (744055) L2a_3end#LINE/L2 355 424 (93) m_b277s601i56 11004 chr6ptel1M 255880 ATTTTAA--ATTTCCTT--TTATGGGTTATCTTCCCCCACTAGAATGTAA 255925 v-- vi -- v vi i i L2a_3end#LINE 355 ATTTTACTTATTTATTTGTTTATTGTCTGTCTCCCCCCACTAGAATGTAA 404 chr6ptel1M 255926 GCTCCTTAAGGGCAGGGTCT 255945 v i v L2a_3end#LINE 405 GCTCCATGAGGGCAGGGACT 424 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 18.90 CpG sites = 5, Kimura (unadjusted) = 18.90 Transitions / transversions = 0.83 (5/6) Gap_init rate = 0.03 (2 / 65), avg. gap size = 2.00 (4 / 2) 262 12.52 1.69 5.26 chr6ptel1M 255902 255960 (744040) L2d_3end#LINE/L2 380 436 (80) m_b277s601i57 11004 chr6ptel1M 255902 TTATCTTCCCCCACTAGAATGTAAGCTCCTTAAGGGCAGGGTCTAATG-C 255950 i - v v i v i- - L2d_3end#LINE 380 TTGTCT-CCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACC-ATGTC 427 chr6ptel1M 255951 TTAGTGCTCT 255960 - i ? L2d_3end#LINE 428 TTA-TACTNT 436 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 14.04 CpG sites = 4, Kimura (unadjusted) = 14.04 Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.07 (4 / 58), avg. gap size = 1.00 (4 / 4) 345 33.47 8.06 5.24 chr6ptel1M 256184 256369 (743631) C MIR3#SINE/MIR (14) 194 4 m_b277s601i58 11005 chr6ptel1M 256184 TAAAACGATGGAGCTGAACTGGGTCAGAGAATTCCAGATCACAGAGTCTA 256233 i i vii i vv ii ------ vv ivv i C MIR3#SINE/MIR 194 TAGAATGTCAGAGCTGGAAGGGACC------TTAGAGATCATCTAGTCCA 151 chr6ptel1M 256234 GCTAGTGCTCTCCTTTTACAGAGGAGGAAACCT--GTTTGGAGAGG---- 256277 i i---- i v v iv-- iiii ---- C MIR3#SINE/MIR 150 ACC----CCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAA 105 chr6ptel1M 256278 ---ACTCACCCAAGGTGACATGGAGAATAGATGACAGAGCCATTATTTCA 256324 --- ii v ii v? i vii i ivv i vv C MIR3#SINE/MIR 104 GTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGA 55 chr6ptel1M 256325 GCCCTG----TCTGA-TCCCAAATTATGCCTTCTTTGCTTCG-GATTCTG 256368 i v ----i - iviii ii i iv -v i C MIR3#SINE/MIR 54 ACCCAGGTCTCCTGACTCCCAGTCCGTGCTCTCTCTGCTCAGCCACTCTG 5 chr6ptel1M 256369 C 256369 C MIR3#SINE/MIR 4 C 4 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 44.89 CpG sites = 38, Kimura (unadjusted) = 47.26 Transitions / transversions = 1.81 (38/21) Gap_init rate = 0.09 (16 / 185), avg. gap size = 1.56 (25 / 16) 369 32.12 10.95 0.00 chr6ptel1M 256242 256378 (743622) C MIRb#SINE/MIR (115) 153 2 m_b277s601i59 11005 chr6ptel1M 256242 TCTCC-TTTTACAGAGGAGGAAACCT--GTTTGGAGAGG-------ACTC 256281 i - v iv-- i ii ------- i C MIRb#SINE/MIR 153 TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTT 104 chr6ptel1M 256282 ACCCAAGGTGACATGGAGAATAGATGACAGAGCCATTATT-----TCAGC 256326 i v ii vv i ii i ivv -----i v C MIRb#SINE/MIR 103 GCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGG 54 chr6ptel1M 256327 CCTGTCTGATCCCAAATTATGCCTTCTTTGCTTCGGATTCTGCTGCCTTT 256376 i ii vivi ivi v vii v iivi ii C MIRb#SINE/MIR 53 TCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCACCACGCTGCCCCT 4 chr6ptel1M 256377 CT 256378 C MIRb#SINE/MIR 3 CT 2 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 40.18 CpG sites = 29, Kimura (unadjusted) = 44.23 Transitions / transversions = 1.93 (29/15) Gap_init rate = 0.03 (4 / 136), avg. gap size = 3.75 (15 / 4) 185 29.04 1.56 3.17 chr6ptel1M 257032 257095 (742905) C MIR3#SINE/MIR (27) 181 119 m_b277s601i60 11006 chr6ptel1M 257032 CTTGAAAGGGCTGGAGTGATCACCTAGTCTGGCCTCCGATT-TTTTACTG 257080 v i i ivv v i iii i -- i- v C MIR3#SINE/MIR 181 CTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCC--TCATTTTACAG 134 chr6ptel1M 257081 TGGAGGACACTGAAG 257095 vv v i C MIR3#SINE/MIR 133 ATGAGGAAACTGAGG 119 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 37.50 CpG sites = 10, Kimura (unadjusted) = 37.50 Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.05 (3 / 63), avg. gap size = 1.00 (3 / 3) 474 23.94 8.45 0.00 chr6ptel1M 257164 257305 (742695) Charlie4#DNA/hAT-Charlie 3225 3378 (0) m_b277s502i6 11007 chr6ptel1M 257164 ATATTTTGATGA-----TTTCAGTATAGCTGGGTTCCTTTGTAAATCTTT 257208 i ----- i ii v vi v Charlie4#DNA/ 3225 ATATTTTGATAACTATATTTCAATATAATTGGTTTCCTTTGTAATCCTAT 3274 chr6ptel1M 257209 CTA-TTTATCTTGTGCAGCT-AAGACATTATTCTG---AGGAGTTCACAT 257253 v - i i vi - i --- i i i v Charlie4#DNA/ 3275 GTATTTTATTTTATGCATTTAAAAACATTATTCTGAGAAGGGGTCCATAG 3324 chr6ptel1M 257254 GCTTCGCTGCATGAACAAAGGGATACAGGGCATTAAAAAAGTT--GAGTC 257301 i iiv iviv i v v iv i -- ii Charlie4#DNA/ 3325 GCTTCACCAGACTGCCAAAGGGGTCCATGGCACAAAAAAGGTTAAGAACC 3374 chr6ptel1M 257302 CCTG 257305 Charlie4#DNA/ 3375 CCTG 3378 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 29.70 CpG sites = 22, Kimura (unadjusted) = 29.70 Transitions / transversions = 1.83 (22/12) Gap_init rate = 0.04 (5 / 141), avg. gap size = 2.40 (12 / 5) 187 27.80 2.67 4.05 chr6ptel1M 257703 257777 (742223) C MIRc#SINE/MIR (77) 191 118 m_b277s601i61 11008 chr6ptel1M 257703 CTGACAACAATCCT-TGAGGCAGGGGGTACAAGGATTCATTGTTACCTAC 257751 v i - i vi vi i v - i i- i i C MIRc#SINE/MIR 191 CTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATT-ATTATC-CCCAT 144 chr6ptel1M 257752 ATTTA-AAATGGTGCACTTGAGTCTCA 257777 - - i iv v vi v C MIRc#SINE/MIR 143 -TTTACAGATGAGGAAACTGAGGCTCA 118 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 35.67 CpG sites = 12, Kimura (unadjusted) = 35.67 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.07 (5 / 74), avg. gap size = 1.00 (5 / 5) 577 27.60 4.50 3.98 chr6ptel1M 257778 257977 (742023) C MIRc#SINE/MIR (32) 236 36 m_b277s601i62 11009 chr6ptel1M 257778 TTTAAACATTTCAAAGAAGTTT-ATACATATGGTCTTATTTGAGCCTGAC 257826 v vv v viv - i i i vi i v v C MIRc#SINE/MIR 236 TTTACAGTTTACAAAGCGCTTTCACATACATTATCTCATTTGATCCTCAC 187 chr6ptel1M 257827 GGCTACCCTGTGAGATGGGCAC--TAGAGTATTATTCTCTGTATTTTACA 257874 ii v i i v--i - v ivi C MIRc#SINE/MIR 186 AACAACCCTGTGAGGTAGGCAGGGCAG-GTATTATTATCCCCATTTTACA 138 chr6ptel1M 257875 GACAAAGAAACCGAGGCTAAGCAAGTTTAAGTGGTTCTTTTGTGGTCA-A 257923 ii i i v vi v ii iviiiiv - C MIRc#SINE/MIR 137 GATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACA 88 chr6ptel1M 257924 TAGATAGT--GT--CCAAGGCAGGACTTGAACTCACGCAAGATTTCTTCC 257969 i v -- -- vi v i i i v ------- C MIRc#SINE/MIR 87 CAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGG-------TCTTCC 45 chr6ptel1M 257970 TG-CTTCAA 257977 - i C MIRc#SINE/MIR 44 TGACTCCAA 36 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 32.84 CpG sites = 31, Kimura (unadjusted) = 35.28 Transitions / transversions = 1.41 (31/22) Gap_init rate = 0.07 (14 / 199), avg. gap size = 1.21 (17 / 14) 227 22.47 10.53 6.33 chr6ptel1M 258399 258474 (741526) MIR3#SINE/MIR 109 187 (21) m_b277s601i63 11010 chr6ptel1M 258399 CCTCGTTGGACC---GTGTTCTC---TGTAAA-TAAGGAGGTCGGA-TAG 258440 vi i --- v i --- - i i i - MIR3#SINE/MIR 109 CCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAG 158 chr6ptel1M 258441 ACTTCATGACTTCTAAGGGACTTTCCAACTCCAA 258474 ----- ii vv i i ii MIR3#SINE/MIR 159 A-----TGATCTCTAAGGTCCCTTCCAGCTCTGA 187 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 28.06 CpG sites = 12, Kimura (unadjusted) = 28.06 Transitions / transversions = 3.00 (12/4) Gap_init rate = 0.12 (9 / 75), avg. gap size = 1.44 (13 / 9) 60 4.78 0.00 0.00 chr6ptel1M 258536 258600 (741400) (GT)n#Simple_repeat 1 65 (0) c_b277s251i3 11011 chr6ptel1M 258536 GTGTGTGAGTGTGTGAGTGTGTGTGAGTGTGTGTGTGTGTGTGTGTGTGT 258585 v v v (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50 chr6ptel1M 258586 GTGTGTGTGTGTGTG 258600 (GT)n#Simple_ 51 GTGTGTGTGTGTGTG 65 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0) 184 34.53 4.46 1.74 chr6ptel1M 258895 259006 (740994) C MIR3#SINE/MIR (1) 207 93 m_b277s601i64 11012 chr6ptel1M 258895 AATCCTAGA-CCAAAGAATGTTGGAGACTGAACAGATCTGAGAGACAA-- 258941 v -i v ii viv vi i v iv -- C MIR3#SINE/MIR 207 AATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATC 158 chr6ptel1M 258942 -ATTCCAACTACCTGTTTTTTAAAGATGA-ACATTTGGGACTCAAAAAAA 258989 - v iv -iv v -iv vi i i i - i i i C MIR3#SINE/MIR 157 TAGTCCAACCCCCT-CATTTTACAGATGAGGAAACTGAGGCCC-AGAGAG 110 chr6ptel1M 258990 ATCCAATGAATTATCTA 259006 i vv i v ii i C MIR3#SINE/MIR 109 GTGAAGTGACTTGCCCA 93 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 48.02 CpG sites = 22, Kimura (unadjusted) = 48.02 Transitions / transversions = 1.38 (22/16) Gap_init rate = 0.05 (6 / 111), avg. gap size = 1.17 (7 / 6) 239 34.66 4.81 4.31 chr6ptel1M 259238 259445 (740555) CR1-3_Croc#LINE/CR1 2588 2796 (809) m_b277s551i5 11013 chr6ptel1M 259238 GTTCTTGGTTTCACAGCTGTTTTCTGAAAGGACATTAATAAGCAGGAGAG 259287 v i i ----- ivi i vi v ivi CR1-3_Croc#LI 2588 GTTCTGGGCTCCACA-----TTTTAAAAAGGACGTGGAGAAGTTAGAGAG 2632 chr6ptel1M 259288 GA---AGTAGCTG-------AGATAATGAAGGGACTTGACATTGTGCCAA 259327 i--- vi v ------- i i vi v viviiv i v CR1-3_Croc#LI 2633 GGTCCAGAGGCGGGCAACAAAGATGATAAAGGGCTTGGAAGGCAAGTCAT 2682 chr6ptel1M 259328 ATGAAGATTGGTTTGAAGGAGCTAGGTATATTGAGCCAGGAGAAAGGAAG 259377 i i vv i - i i v iv vi i iv CR1-3_Croc#LI 2683 ACGAGGAGAGGCT-GAAGGAGCTAGGCATGTTCAGCTTGCGGAAAAGGCG 2731 chr6ptel1M 259378 ACTTAGTGGAGACTTATTAGCCATCTTTGAGCATTGCAAGAGTTGCTGTC 259427 vi v v i v iv vi ii ii i vv i--- i CR1-3_Croc#LI 2732 CTTAAGAGGGGACATGATAGCAGTCTTCAAATACTTGAAGG---GCTGCC 2778 chr6ptel1M 259428 ATGAAGAATAATGATAGC 259445 i v iv v CR1-3_Croc#LI 2779 ATAAAGAAGAGGGAAAGC 2796 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 45.21 CpG sites = 39, Kimura (unadjusted) = 48.09 Transitions / transversions = 1.30 (39/30) Gap_init rate = 0.05 (11 / 207), avg. gap size = 1.73 (19 / 11) 187 32.09 1.59 8.47 chr6ptel1M 260803 260928 (739072) L2d2_3end#LINE/L2 164 281 (274) m_b278s601i2 11014 chr6ptel1M 260803 CCTGTCCCCTTCCTGCCACATTGCTCATTGGAAGCCTACCCAGCCTTTGA 260852 iv vi - --- ii ivi v v ii L2d2_3end#LIN 164 CCCTTCCCCTTCCTCTC-CA---CCTATCCAAATCCTACCCATCCTTCAA 209 chr6ptel1M 260853 AATCCAGCTCAAATCCTACTT--TCTAGGAAATCCACCCTAATGTCCCCT 260900 iii ? i i -- iiv ii iv i --- v L2d2_3end#LIN 210 GGCCCAGCTCAAATNCCACCTCCTCCGTGAAGCCTTCCCTGA---CCACT 256 chr6ptel1M 260901 TACACAACCATAAACAATCACTCTTTCC 260928 i--- i vv? iii v ii L2d2_3end#LIN 257 C---CAGCCCGNAGTGATCTCTCCCTCC 281 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 43.66 CpG sites = 26, Kimura (unadjusted) = 45.58 Transitions / transversions = 2.36 (26/11) Gap_init rate = 0.09 (11 / 125), avg. gap size = 1.09 (12 / 11) 223 31.43 2.22 4.55 chr6ptel1M 260803 260892 (739108) L2d_3end#LINE/L2 164 251 (265) m_b278s601i1 11014 chr6ptel1M 260803 CCTGTCCCCTTCCTGCCACATTGCTCATTGGAAGCCTACCCAGCCTTTGA 260852 iv vi v vi iii ---- v v ii L2d_3end#LINE 164 CCCTTCCCCTTCCTCTCTCTCTATCCA----AATCCTACCCATCCTTCAA 209 chr6ptel1M 260853 AATCCAGCTCAAATCCTACTT--TCTAGGAAATCCACCCTAA 260892 iii i i i -- i v ii iv i L2d_3end#LINE 210 GGCCCAGCTCAAGTCCCACCTCCTCCACGAAGCCTTCCCTGA 251 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 43.42 CpG sites = 19, Kimura (unadjusted) = 43.42 Transitions / transversions = 2.38 (19/8) Gap_init rate = 0.06 (5 / 89), avg. gap size = 1.20 (6 / 5) 623 26.01 5.77 5.36 chr6ptel1M 260945 261204 (738796) C MIRb#SINE/MIR (1) 267 7 m_b278s601i3 11015 chr6ptel1M 260945 ATAATA-AG-TACTAGTAGTT-AGCAATTATAACATCCTAAGC--TTTGC 260989 - - i v vi - iv iv ii v i i -- v C MIRb#SINE/MIR 267 ATAATAGAGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGC 218 chr6ptel1M 260990 AAAGAATTTT-TATACTATTATCTCATT-AACTTTC-TGACAACCCTG-G 261035 v vii -i i - - iii -ii - C MIRb#SINE/MIR 217 TAAGCGCTTTACATGC-ATTATCTCATTTAATCCTCACAACAACCCTGCG 169 chr6ptel1M 261036 ATATAAGTGCTATTATTTTTCTTATTCCCATTTTACAGATGAGGAAACTG 261085 vi i --- ------ i C MIRb#SINE/MIR 168 AGGTAGGT---ATTATT------ATCCCCATTTTACAGATGAGGAAACTG 128 chr6ptel1M 261086 AAGCAGACAGAAGTTGCATGACTTGGCTAGTATCACCCAGTTCCTTAAGT 261135 i vv v i ivi i v i ivi v i -vv C MIRb#SINE/MIR 127 AGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCT-AGTAAGT 79 chr6ptel1M 261136 GTCTGAGATGGGATATG-----AGGTCAGT-TGACATGAGGGCCAGGGCT 261179 v v vi vi ----- v - viv ii v v C MIRb#SINE/MIR 78 GGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCT 29 chr6ptel1M 261180 CTTTCCACTGTGCCTCCTTGCTGCC 261204 ii v --- C MIRb#SINE/MIR 28 CTTTCCACTGCACCAC---GCTGCC 7 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.14 CpG sites = 36, Kimura (unadjusted) = 32.54 Transitions / transversions = 1.29 (36/28) Gap_init rate = 0.09 (24 / 259), avg. gap size = 1.21 (29 / 24) 628 30.38 5.63 1.67 chr6ptel1M 260970 261200 (738800) C MIRc#SINE/MIR (24) 244 5 m_b278s601i4 11015 chr6ptel1M 260970 TATAACATCCTAAGCTTTGCAAAGAATTTTTATAC-TATTATCTCATT-- 261016 i iii viv i vii i i i-i -- C MIRc#SINE/MIR 244 TATAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATCTCATTTG 195 chr6ptel1M 261017 AACTTTCTGACAACCCTG-GATATAAGT---GCTATTATTTTTCTTATTC 261062 v i ivii - vi i i--- viv ---v i C MIRc#SINE/MIR 194 ATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATT---ATTATCC 148 chr6ptel1M 261063 CCATTTTACAGATGAGGAAACTGAAGCAGACAGAAGTTGCATGACTTGGC 261112 i vv v i ivi v C MIRc#SINE/MIR 147 CCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCC 98 chr6ptel1M 261113 TAGTATCACCCAGTTCCTTAAGTGTCTGAGATGGGATATGAGGTCAG--- 261159 i ivi v i -vv v v vi ivi ivi --- C MIRc#SINE/MIR 97 CAAGGTCACACAGCT-AGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTC 49 chr6ptel1M 261160 ---TTGACATGAGGGCCAGGGCTCTTTCCACTGTGCCTCCTTGC 261200 ---i viv i v v ii v vi C MIRc#SINE/MIR 48 TTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTGC 5 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.85 CpG sites = 40, Kimura (unadjusted) = 40.09 Transitions / transversions = 1.38 (40/29) Gap_init rate = 0.04 (10 / 230), avg. gap size = 1.70 (17 / 10) 368 29.74 2.61 3.51 chr6ptel1M 261589 261703 (738297) C MIRc#SINE/MIR (153) 115 2 m_b278s601i5 11016 chr6ptel1M 261589 GAGCTCCAGTGACTTGCCCAGAGCTCTAAAGCTAGAATGTGTTAGAAGCA 261638 v iv ii iivi v v v vi iv i C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 66 chr6ptel1M 261639 ACACTTGAGCCCAGTAAAGTCTTCCTAGGTCTAAGTCA---GCTCTATCC 261685 iv i i ---- iiv i v--- v C MIRc#SINE/MIR 65 GGACTCGAACCCAG----GTCTTCCTGACTCCAAGTCCAGTGCTCTTTCC 20 chr6ptel1M 261686 ACAACACTATGCTGTCTC 261703 vi i ii i C MIRc#SINE/MIR 19 ACTGCACCACACTGCCTC 2 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.12 CpG sites = 20, Kimura (unadjusted) = 39.13 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.04 (5 / 114), avg. gap size = 1.40 (7 / 5) 17 23.60 5.41 2.63 chr6ptel1M 261790 261863 (738137) (TACA)n#Simple_repeat 1 76 (0) m_b278s252i0 11017 chr6ptel1M 261790 TACATATATACATACATGTGGCACATACAGACATATATATGTACACATAT 261839 i -vvii v i ii i i (TACA)n#Simpl 1 TACATACATACATACAT-ACATACATACATACATACATACATACATACAT 49 chr6ptel1M 261840 ATGATA-ATA-ATA-ATA-AAGCATACA 261863 -v - - - - vi (TACA)n#Simpl 50 A-CATACATACATACATACATACATACA 76 Matrix = Unknown Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.08 (6 / 73), avg. gap size = 1.00 (6 / 6) 245 18.52 5.56 0.00 chr6ptel1M 262155 262208 (737792) CR1-3_Croc#LINE/CR1 3544 3600 (5) m_b278s551i1 11018 chr6ptel1M 262155 AGGAATTTGGACCAGATGAC-TC-AAAGGTCCCTTCCAGCCTGGATTC-C 262201 iiv i - -ii iviv - CR1-3_Croc#LI 3544 AGGGGGTTGGACTAGATGACCTCTGGAGGTCCCTTCCAGCCCTACTTCTC 3593 chr6ptel1M 262202 TATGATT 262208 CR1-3_Croc#LI 3594 TATGATT 3600 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 21.85 CpG sites = 7, Kimura (unadjusted) = 21.85 Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.06 (3 / 53), avg. gap size = 1.00 (3 / 3) 466 23.80 7.09 0.74 chr6ptel1M 262224 262350 (737650) MIR3#SINE/MIR 73 207 (1) m_b278s601i6 11019 chr6ptel1M 262224 ACTAACTAGCTGGATAAATTTGGGCAAAATTACATAACCTTTCTAAGATT 262273 ? vi i vi i- i v v i ii vi MIR3#SINE/MIR 73 ACTAACTNGCTGTGTGACCTTGGGCAAG-TCACTTCACCTCTCTGGGCCT 121 chr6ptel1M 262274 --GTTTCCCCATCTGGCAAATGAAGGGTTAGAACTACATGATCTTTAA-- 262319 -- i vv i v v i v i -- MIR3#SINE/MIR 122 CAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGG 171 chr6ptel1M 262320 -----TCTAGCTCAAAAATTCAATAATTTTATGATT 262350 ----- i vi v v i i MIR3#SINE/MIR 172 TCCCTTCCAGCTCTGACATTCTATGATTCTATGATT 207 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.41 CpG sites = 17, Kimura (unadjusted) = 29.41 Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.02 (3 / 126), avg. gap size = 3.33 (10 / 3) 16 0.00 0.00 0.00 chr6ptel1M 262383 262399 (737601) (T)n#Simple_repeat 1 17 (0) m_b278s252i1 11020 chr6ptel1M 262383 TTTTTTTTTTTTTTTTT 262399 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTT 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 15 5.56 0.00 0.00 chr6ptel1M 262516 262534 (737466) (C)n#Simple_repeat 1 19 (0) m_b278s252i2 11021 chr6ptel1M 262516 CCCCCCCCCCCCCCCTCCC 262534 i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCC 19 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 1590 25.95 3.67 3.34 chr6ptel1M 262890 263515 (736485) C L1ME4a_3end#LINE/L1 (232) 639 12 m_b278s551i2 11022 chr6ptel1M 262890 CCTGCTCATTTCACTCAGCATCAGTTCATGTAAGTCTCTCCAGGCCTTTC 262939 iv i i i vv vivi i ii v i v - C L1ME4a_3end#L 639 CCTGCTTTTTTCACTTAACATTATATCATGAGCATTTTCCCATGTCATT- 591 chr6ptel1M 262940 TGAAATCATCCTGTTGG-----TCATTTCTTACAGA-ACAGTAATATTCC 262983 -- - i - i i----- ? i v ii v-i - C L1ME4a_3end#L 590 --AAAT-ATTCT-TCGAAAACATNATTTTTAATGGCTGCA-TAATATTCC 546 chr6ptel1M 262984 ATAATTTTCATATACCACAATTTATTCAACCATTCTCCAACTGATGGACA 263033 v? v vv i i i ? i v i v C L1ME4a_3end#L 545 ATTNTATGGATGTACCATAATTTATTTAACCANTCCCCTATTGTTGGACA 496 chr6ptel1M 263034 TCCA--TTCAGTTTCCAGTTTTTAGCCACTACAAAAAGGGCTGCCACAAA 263081 ii -- -- i v i i i v iv v ii C L1ME4a_3end#L 495 TTTAGGTT--GTTTCCAATTTTTCGCTATTATAAATAATGCTGCGATGAA 448 chr6ptel1M 263082 CATTCGTGCACATACAGGTCCCTTTCC-CTTCTTT-ATAATCTCTTTGGG 263129 i v i v -- ii v ? - v i - v i i i C L1ME4a_3end#L 447 CATCCTTGTACATAAA--TCTTTGTNCACATCTCTGATTATTTCCTTAGG 400 chr6ptel1M 263130 ATATAATCCCAGTAGTAACACTGCTGGATCAAAGGGTATGCACAGTTTGA 263179 v v i v iiv i i i ? v v C L1ME4a_3end#L 399 ATAAATTCCTAGAAGTGGAATTACTGGGTCAAAGGGTATGNACATTTTTA 350 chr6ptel1M 263180 TAACTTTTTGA-GCATAGTTCCAAACTACTCTCCAAAATGGTTGGATTCG 263228 - ivi -i v v i i i i v v iivi C L1ME4a_3end#L 349 -AGGCTTTTGATACATATTGCCAAATTGCCCTCCAGAAAGGTTGTACCAA 301 chr6ptel1M 263229 TTCACAACTCCACCAACAATGAATCAATGTCCCAGTTTTCCCACATCCCC 263278 i vii i i v v iv v v i? i i C L1ME4a_3end#L 300 TTTACACTCCCACCAGCAGTGTATGAGAGTGCCCGTTTCNCCACACCCTC 251 chr6ptel1M 263279 TCCAACA------ATCATCATTATTTTTTCCTGTCATCTTAGCCAATCTG 263322 v ------ i -- i vv---- v i C L1ME4a_3end#L 250 GCCAACACTGGGTATTATCA--ATCTTTTAA----ATCTTTGCCAATTTG 207 chr6ptel1M 263323 ACAGGTGTGTAGTGGTATCTTAGAGTTGTCTTAATTTGCATTTCTCTGAT 263372 i viv i i vv i i C L1ME4a_3end#L 206 ATAGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCTTTGAT 157 chr6ptel1M 263373 --ATAATGACTTGGAGCATCTTTTCATATGACTAGAAATAGTTTCAATTT 263420 --v i vv v i ? vi vviiivi vv C L1ME4a_3end#L 156 TACTAGTGAGGTTGAACATNTTTTCATATGTTTATTGGCCATTTGTATTT 107 chr6ptel1M 263421 CTTCATCTGAGAATTGTCTGTTCATATCCTTTGACCATTTTTCAATTGGA 263470 v i v i v v i C L1ME4a_3end#L 106 CTTCTTTTGTGAATTGTCTGTTCATGTCCTTTGCCCATTTTTCTATTGGG 57 chr6ptel1M 263471 GAAT--GGCTTGATTTTTTATAAATTAG--AGTTAATTCTCTATATATT 263515 vi -- v -- i vi v -- -- ii i C L1ME4a_3end#L 56 GTGTTCGTCTT--TTTCTTATTGATTTGTAAG--AGCTCTTTATATATT 12 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 32.69 CpG sites = 89, Kimura (unadjusted) = 32.95 Transitions / transversions = 1.31 (89/68) Gap_init rate = 0.05 (31 / 625), avg. gap size = 1.42 (44 / 31) 1667 25.66 1.82 2.76 chr6ptel1M 262975 263523 (736477) C L1ME3G_3end#LINE/L1 (377) 547 4 m_b278s551i3 11022 chr6ptel1M 262975 TAATATTCCATAATTTTCATATACCACAATTTATTCAACCATTCTCCAAC 263024 i i v vv i i i v i C L1ME3G_3end#L 547 TAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTAT 498 chr6ptel1M 263025 TGATGGACATCCA--TTCAGTTTCCAGTTTTTAGCCACTACAAAAAGGGC 263072 ii -- -- i v i i v iv C L1ME3G_3end#L 497 TGATGGACATTTAGGTT--GTTTCCAATTTTTCGCTATTACAAACAATGC 450 chr6ptel1M 263073 TGCCACAAACATTCGTGCACATACAGGTCCCTTTCC-CTTCTTT-ATAAT 263120 v ii i v i i ?-- i v v - v v vi- vv C L1ME3G_3end#L 449 TGCAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTAT 402 chr6ptel1M 263121 CTCTTTGGGATATAATCCCAGTAGTAACACTGCTGGATCAAAGGGTATGC 263170 i ? i v v? ? v iiv i i C L1ME3G_3end#L 401 TTCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGC 352 chr6ptel1M 263171 ACAGTTTGATAACTTTTTGAGCATAGTTCCAAACTACTCTCCAAAATGGT 263220 i v --- v viviv v v i i i ? i C L1ME3G_3end#L 351 GCATTT---TAAATTTTAATAGATACTGCCAAATTGCCCTCCAAAANGGC 305 chr6ptel1M 263221 TGGATTCGTTCACAACTCCACCAACAATGAATCAATGTCCCAGTTTTCCC 263270 v iivi i vii i i v v iv v v i C L1ME3G_3end#L 304 TGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCC 255 chr6ptel1M 263271 ACATCCCCTCCAACAATCATCATTAT----TTTTTCCTGTCATCTTAGCC 263316 i i v v ?ivi ----i v----v i v C L1ME3G_3end#L 254 ACACCCTCGCCAACACTNGATATTATCAANCTTTTA----AATTTTTGCC 209 chr6ptel1M 263317 AATCTGACAGGTGTGTAGTGGTATCTTAGAGTTGTCTTAATTTGCATTTC 263366 ii viv i i vv i C L1ME3G_3end#L 208 AATCTGATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTC 159 chr6ptel1M 263367 TCTGAT--ATAATGACTTGGAGCATCTTTTCATATGACTAGAAATAGTTT 263414 i --v i vv v vi vviiivi C L1ME3G_3end#L 158 CCTGATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTT 109 chr6ptel1M 263415 CAATTTCTTCATCTGAGAATTGTCTGTTCATATCCTTTGACCATTTTTCA 263464 vv i v v i v v C L1ME3G_3end#L 108 GTATTTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCT 59 chr6ptel1M 263465 ATTGGAGAATGGCTTGATTTTTTATAAATTAGAGTTAATTCTCTATATAT 263514 iv-- v -- i vi v vivv i i C L1ME3G_3end#L 58 ATTGGGT--TGTCTT--TTTCTTATTGATTTGTAGGAGTTCTTTATATAT 13 chr6ptel1M 263515 TTTGGAAAT 263523 i v C L1ME3G_3end#L 12 TCTGGATAT 4 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 31.64 CpG sites = 70, Kimura (unadjusted) = 32.20 Transitions / transversions = 1.04 (70/67) Gap_init rate = 0.04 (20 / 548), avg. gap size = 1.25 (25 / 20) 543 27.97 2.97 2.97 chr6ptel1M 263384 263652 (736348) C L1M3_orf2#LINE/L1 (7) 3281 3013 m_b278s551i4 11022 chr6ptel1M 263384 GAGCATCTTTTCATATGACTAGAAATAGTTTCAATTTCTTCATCTGAGAA 263433 iv ivviiivi vv v v iv C L1M3_orf2#LIN 3281 GAGCATCTTTTCATATACCTGTTGGCCATTTGTATGTCTTCTTTGGAGAA 3232 chr6ptel1M 263434 TTGTCTGTTCATATCCTTTGACCATTTTTCAATTGGAGAATGGCTTGATT 263483 v i vi v ? i ivv --- v C L1M3_orf2#LIN 3231 ATGTCTATTCAGGTCCTTTGCCCATTTTTNAATCGGGTTAT---TTGTTT 3185 chr6ptel1M 263484 TTTTATAAATTAGAGTT-----AATTCTCTATATATTTTGGAAATGAGGC 263528 ii-v - ----- i ii v v iv C L1M3_orf2#LIN 3184 TTTTGC-TATT-GAGTTGTANGAGTTCCTTATATATTTTGGATATTAACC 3137 chr6ptel1M 263529 CTTTATCAGAACCTTTGACTGTAAAAATATTTTCCCAGTTTATTGCTTCC 263578 i vviv v vi i v v i v iii v v v C L1M3_orf2#LIN 3136 CCTTATCAGATATATGGTTTGCAAATATTTTCTCCCATTCCGTAGGTTGC 3087 chr6ptel1M 263579 CTTCTAATCTTGTCTGCATTAGTTTTGTT---TGTACAAAAACTTTTCAG 263625 i v iii - - - iv --- i i i i C L1M3_orf2#LIN 3086 CTTTTCACTCTGT-TG-ATT-GTTTCCTTTGCTGTGCAGAAGCTTTTTAG 3040 chr6ptel1M 263626 TTTGGTATAATCGAAATTTTCTATTTT 263652 i i i vv v v C L1M3_orf2#LIN 3039 TTTGATGTAGTCCCACTTGTCTATTTT 3013 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 34.36 CpG sites = 37, Kimura (unadjusted) = 35.61 Transitions / transversions = 1.03 (37/36) Gap_init rate = 0.04 (10 / 268), avg. gap size = 1.60 (16 / 10) 293 19.21 7.41 8.41 chr6ptel1M 263976 264083 (735917) MIR#SINE/MIR 110 216 (46) m_b278s601i8 11023 chr6ptel1M 263976 TCTCTGGCCCTCAGTTTTTCCACCTGAAAAAGGGGCCTAATAATACTTGT 264025 vv iii i v v vv --- MIR#SINE/MIR 110 TCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATA---GT 156 chr6ptel1M 264026 ACTGA------AGGGATGTTTTTAGAATTAAATGAGAATCAA-ACCAAGA 264068 iv ------ v v v i -- i - ---- MIR#SINE/MIR 157 ACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAG--TTAATAC----A 200 chr6ptel1M 264069 TATAAA-TGCTTAGAA 264083 i -i MIR#SINE/MIR 201 TGTAAAGCGCTTAGAA 216 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 21.01 CpG sites = 9, Kimura (unadjusted) = 22.26 Transitions / transversions = 0.90 (9/10) Gap_init rate = 0.11 (12 / 107), avg. gap size = 1.42 (17 / 12) 346 25.93 0.00 0.00 chr6ptel1M 263976 264056 (735944) MIRb#SINE/MIR 117 197 (71) m_b278s601i7 11023 chr6ptel1M 263976 TCTCTGGCCCTCAGTTTTTCCACCTGAAAAAGGGGCCTAATAATACTTGT 264025 iv iii i v v vv i ii MIRb#SINE/MIR 117 TCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTAC 166 chr6ptel1M 264026 ACTGAAGGGATGTTTTTAGAATTAAATGAGA 264056 vii v v v v i MIRb#SINE/MIR 167 CTCGCAGGGTTGTTGTGAGGATTAAATGAGA 197 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.42 CpG sites = 11, Kimura (unadjusted) = 32.22 Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.00 (0 / 80), avg. gap size = 0.0 (0 / 0) 439 31.75 0.00 5.70 chr6ptel1M 264079 264245 (735755) C MIR3#SINE/MIR (14) 194 37 m_b278s601i9 11024 chr6ptel1M 264079 TAGAAAATTTGAGCTGGAAAGGACATTACTGTGGGGGTAATGTTACTGGA 264128 vi iv i v ----- i i v v viiivi C MIR3#SINE/MIR 194 TAGAATGTCAGAGCTGGAAGGGACCTTA-----GAGATCATCTAGTCCAA 150 chr6ptel1M 264129 CTCTTAGACTCTACAAATGAGGAGACTCACACCTAGAGAGTTGAAAGTGT 264178 i iivv i i i i v vi i v - v C MIR3#SINE/MIR 149 CCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTG-AAGTGA 101 chr6ptel1M 264179 CTTGTTCAAGATCACACCAACCAGTACCTAGCAGAGTTATGGGATCTGAA 264228 ii i - i ? vvv i i--i iiv C MIR3#SINE/MIR 100 CTTGCCCAAGGTCACA-CAGCNAGTTAGTGGCAGAGC--CGGGACTAGAA 54 chr6ptel1M 264229 TCAAGGTCATCTTATTC 264245 i v vi v i C MIR3#SINE/MIR 53 CCCAGGTCTCCTGACTC 37 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 41.82 CpG sites = 30, Kimura (unadjusted) = 42.97 Transitions / transversions = 1.50 (30/20) Gap_init rate = 0.05 (9 / 166), avg. gap size = 1.00 (9 / 9) 370 33.00 0.58 4.85 chr6ptel1M 264096 264267 (735733) C MIR1_Amn#SINE/MIR (46) 184 20 m_b278s601i10 11024 chr6ptel1M 264096 AAAGGACATTACTGTGGGGGT-AATGTTACTGGACTCTTAGACTCTACAA 264144 v v viv i - i i i i ivv i ---- i i i C MIR1_Amn#SINE 184 AAAGCACTTTACAAAGGAGGTCAGTATCATTATCCCC----ATTTTACAG 139 chr6ptel1M 264145 ATGAGGAGACTCACACCTAGAGAGTTGAAAGTGTCTTGTTCAAGATCACA 264194 i v vi ?i v -? v ii i - C MIR1_Amn#SINE 138 ATGAGGAAACTGAGGCNCAGAGAGGT-NAAGTGACTTGCCCAAGGTCAC- 91 chr6ptel1M 264195 CCAACCAGTACCTAGCAGAGTTATGGGATCTGAATCAAGGTCATCTTATT 264244 ? i ?i i?vv i i--i ?i? i v vi iv v C MIR1_Amn#SINE 90 NCAGCNGGCNAGTGGCAGAGC--CGGGANTNGAACCCAGGTCTCCCGAGT 43 chr6ptel1M 264245 CTAAATGTAGTGTATTTCCCATT 264267 iv i vi ivi vi i C MIR1_Amn#SINE 42 CCCAGTCCAGTGCTCTATCCACT 20 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 45.92 CpG sites = 34, Kimura (unadjusted) = 48.46 Transitions / transversions = 1.70 (34/20) Gap_init rate = 0.05 (9 / 171), avg. gap size = 1.00 (9 / 9) 441 29.16 1.52 3.88 chr6ptel1M 264136 264267 (735733) C MIRc#SINE/MIR (123) 145 17 m_b278s601i11 11024 chr6ptel1M 264136 ACTCTACAAATGAGGAGACTCACACCTAGAGA-GTTGAAAGTGTCTTGTT 264184 i i i i v vi ii - -- v ii C MIRc#SINE/MIR 145 ATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTT--AAGTGACTTGCC 98 chr6ptel1M 264185 CAAGATCACACCAACCAGTACCTAGCAGAGTTATGGGATCTGAATCAAGG 264234 i - i i vv i i--i iii i v C MIRc#SINE/MIR 97 CAAGGTCACA-CAGCTAGTAAGTGGCAGAGC--CGGGACTCGAACCCAGG 51 chr6ptel1M 264235 TCATCTT-ATTCTAAATGTAGTGTATTTCCCATT 264267 v i - i i i vi ivi i i C MIRc#SINE/MIR 50 TCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACT 17 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.85 CpG sites = 28, Kimura (unadjusted) = 39.67 Transitions / transversions = 3.11 (28/9) Gap_init rate = 0.05 (7 / 131), avg. gap size = 1.00 (7 / 7) 485 19.83 8.62 0.00 chr6ptel1M 264336 264451 (735549) C MER63D#DNA/hAT-Tip100 (590) 471 346 m_b278s502i0 11025 chr6ptel1M 264336 CATGAGACACTT--AAATTTTACCTACATTATAAAATTCTTTTCCATCA- 264382 i v -- i v i i v vv i i - C MER63D#DNA/hA 471 CACGACACACTTTTAAGTTTAATCTGCATTATTAACATTTTCTCCATCAC 422 chr6ptel1M 264383 -TGATTAAGTCTAGACAATCAATAA------AAACCAGGCCCAGCTCTGT 264425 - vv i ------ i i v v i C MER63D#DNA/hA 421 TTTCTTAAGTCTAGACAATCAACAAAACAATAAATCAAGCCCTGATTTGT 372 chr6ptel1M 264426 AGCATTTGCTGATTTCCAAGGTGTAA 264451 i i iv C MER63D#DNA/hA 371 AGCGTTTGCCGATTTCCGTGGTGTAA 346 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 19.00 CpG sites = 13, Kimura (unadjusted) = 23.31 Transitions / transversions = 1.30 (13/10) Gap_init rate = 0.03 (4 / 115), avg. gap size = 2.50 (10 / 4) 261 32.86 0.00 0.00 chr6ptel1M 264550 264619 (735381) MIRc#SINE/MIR 101 170 (98) m_b278s601i12 11026 chr6ptel1M 264550 AAGTTGTTTGCTTTCTTCAAGCCTTAGTTTACCATTTTGTAAAATGAGGA 264599 iii ivii iii i v ivv i i MIRc#SINE/MIR 101 AAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGA 150 chr6ptel1M 264600 GGATGATACCTGTGCTACCT 264619 vi i iv i MIRc#SINE/MIR 151 TAATAATACCTGCCCTGCCT 170 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 47.07 CpG sites = 17, Kimura (unadjusted) = 47.07 Transitions / transversions = 2.83 (17/6) Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0) 17 8.91 0.00 0.00 chr6ptel1M 265440 265463 (734537) (T)n#Simple_repeat 1 24 (0) m_b278s252i3 11027 chr6ptel1M 265440 TTTGTTTTTTTTTGTTTTTTTTTT 265463 v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTT 24 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 44 0.00 0.00 0.00 chr6ptel1M 265465 265502 (734498) (GT)n#Simple_repeat 1 38 (0) c_b278s251i0 11028 chr6ptel1M 265465 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 265502 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 38 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 232 29.63 0.00 0.00 chr6ptel1M 265923 265976 (734024) C MIRc#SINE/MIR (207) 61 8 m_b278s601i13 11029 chr6ptel1M 265923 TTGAACCCAAGTCTTTTAGACTCCAAACCCAATGCTCCCTTTACTTTGCC 265972 i i iiv ii i ii ii vii C MIRc#SINE/MIR 61 TCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACC 12 chr6ptel1M 265973 AGAC 265976 v C MIRc#SINE/MIR 11 ACAC 8 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.97 CpG sites = 13, Kimura (unadjusted) = 41.45 Transitions / transversions = 4.33 (13/3) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 744 20.12 2.44 0.00 chr6ptel1M 266125 266288 (733712) Charlie4a#DNA/hAT-Charlie 340 507 (1) m_b278s502i1 11030 chr6ptel1M 266125 AGATTTGTTTTTGTACTCTTTGGATAAAGAGATTTCAATATGACTACCTT 266174 i ? v v v v vviv i i ivi Charlie4a#DNA 340 AAATTTGNTTTTTTAATATTTTGATAACTGTATTTCAATATAATTGGTTT 389 chr6ptel1M 266175 GCTTTGTAATCCT--GTATTTTATTTGATGCAGTTGAAAATGTTATTCTG 266222 v -- v v i ii Charlie4a#DNA 390 CCTTTGTAATCCTATGTATTTTATTTTATGCATTTAAAAACATTATTCTG 439 chr6ptel1M 266223 ACAAGGGGACCATA-GTTTCACTACACTGTAAAAGGGGTCTATCACAC-A 266270 v v - i i v iv i vi - Charlie4a#DNA 440 AGAAGGGGTCCATAGGCTTCACCAGACTGCCAAAGGGGTCCATGGCACAA 489 chr6ptel1M 266271 AAAAGGTTAAGGATGCCT 266288 i iv Charlie4a#DNA 490 AAAAGGTTAAGAACCCCT 507 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 23.73 CpG sites = 16, Kimura (unadjusted) = 23.73 Transitions / transversions = 0.94 (16/17) Gap_init rate = 0.02 (3 / 163), avg. gap size = 1.33 (4 / 3) 304 20.33 0.00 3.12 chr6ptel1M 267390 267455 (732545) DNM1r#Unknown 2482 2545 (2117) m_b278s502i2 11031 chr6ptel1M 267390 ATGTACATATATATGCATGTGTATATGTGTATGTATATATTCATATGTGT 267439 iii ii i i i i -- DNM1r#Unknown 2482 ATGTGTGTATATATGTGTGTATATGTGTGTATGTGTGTAT--ATATGTGT 2529 chr6ptel1M 267440 ATGTACACACATGTAT 267455 i i ii ? DNM1r#Unknown 2530 ATATATACGTATNTAT 2545 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 24.24 CpG sites = 13, Kimura (unadjusted) = 26.61 Transitions / transversions = 1.00 (13/0) Gap_init rate = 0.03 (2 / 65), avg. gap size = 1.00 (2 / 2) 240 23.73 0.00 6.94 chr6ptel1M 267395 267471 (732529) DNM1r#Unknown 2475 2546 (2116) m_b278s502i3 11031 chr6ptel1M 267395 CATATATATGCATGTGTATATGTGTATGTATATATTCATATGTGTATGTA 267444 ii i ii i -- i vii -- DNM1r#Unknown 2475 CACGTGTATGTGTGTATATATGTG--TGTATATGTGTGTATGTG--TGTA 2520 chr6ptel1M 267445 CACACATGTATGTTATATGTGTGTATA 267471 i i ii i- i i ? DNM1r#Unknown 2521 TATATGTGTATA-TATACGTATNTATA 2546 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 27.20 CpG sites = 16, Kimura (unadjusted) = 31.97 Transitions / transversions = 16.00 (16/1) Gap_init rate = 0.07 (5 / 76), avg. gap size = 1.00 (5 / 5) 259 20.86 0.00 12.33 chr6ptel1M 267405 267486 (732514) DNM1r#Unknown 2475 2547 (2115) m_b278s502i4 11031 chr6ptel1M 267405 CATGTGTATATGTGTATGTATATATTCATATGTGTATGTACACACATGTA 267454 i i i i i vi i -------- i DNM1r#Unknown 2475 CACGTGTATGTGTGTATATATGTGTGTATATGTGTGT--------ATGTG 2516 chr6ptel1M 267455 TGTTATATGTGTGTATACATATATGTGTACAG 267486 - i i ii i ? i DNM1r#Unknown 2517 TGT-ATATATGTGTATATATACGTATNTATAG 2547 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 22.24 CpG sites = 14, Kimura (unadjusted) = 26.48 Transitions / transversions = 14.00 (14/1) Gap_init rate = 0.11 (9 / 81), avg. gap size = 1.00 (9 / 9) 245 27.53 10.00 3.12 chr6ptel1M 267954 268073 (731927) L2c_3end#LINE/L2 349 476 (2) m_b278s601i14 11032 chr6ptel1M 267954 TATTTACATG-CTGTC----ACATTAGAATGTGAGC-----AAGAACAGT 267993 i ? - ----v i v -----i ii v L2c_3end#LINE 349 TGTTTACNTGTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGG 398 chr6ptel1M 267994 GATT-TGACTTTTATGACCCTGGTACTTTGCACAAAACCCA-CACATAAT 268041 ii- v v - v i i v --- v v ivi ii- i L2c_3end#LINE 399 GACCGTGTCTTAT-TCATCTTTGTA---TCCCCAGCGCCTGGCACATAGT 444 chr6ptel1M 268042 AAGTGCTTAATAAATGTTTATTAACAGACTGA 268073 i i i i i vv v L2c_3end#LINE 445 AGGCGCTCAATAAATGTTTGTTGAATGAATGA 476 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.66 CpG sites = 19, Kimura (unadjusted) = 35.71 Transitions / transversions = 1.46 (19/13) Gap_init rate = 0.08 (9 / 119), avg. gap size = 1.78 (16 / 9) 670 35.03 2.08 0.59 chr6ptel1M 268479 268814 (731186) C L2#LINE/L2 (493) 2589 2249 m_b278s601i15 11033 chr6ptel1M 268479 TGAGCAAGAGGGAGGAGTTGAGGATGATACCAAGCTGCAGATCCCATAGA 268528 vi i i ii iv v vivviv iiviv C L2#LINE/L2 2589 TGAGAGAAAGAGAGGAGTCAAGGATGACTCCAAGGTTTTTGGCCTGAGCA 2540 chr6ptel1M 268529 ACTAGAAGGATTGGTGATGCCCTTGGCAGAAATAGAAAAGTTAGAAAGAT 268578 i - v v v ?i v i i ii viv vii v C L2#LINE/L2 2539 ACTGGAAGGAT-GGAGTTGCCATTNACTGAGATGGGGAAGACTGCGGGAG 2491 chr6ptel1M 268579 GGATGGTCTTTTGAGGAAAGATAATGAGTTCTGCTTTGGATATGGTGACT 268628 iiii vi vv i i v v v i i v i v C L2#LINE/L2 2490 GAGCAGGTTTGAGGGGGAAGATCAGGAGTTCAGTTTTGGACATGTTAAGT 2441 chr6ptel1M 268629 TTGACACGCTTGGAAGGTATCTAGGTGGAGATGCCCA-TAGGAAGTTCAT 268677 v i i ivv ii i i i v - v viv C L2#LINE/L2 2440 TTGAGATGCCTATTAGACATCCAAGTGGAGATGTCGAGTAGGCAGTTGGA 2391 chr6ptel1M 268678 AACATAATCCTGGAGCTCTTGAGAAAGATTAGAGCTGGATGGTG-AGATA 268726 v i ii vi i vv i i i iv i - i i- i v C L2#LINE/L2 2390 TATACGAGTCTGGAGTTCAGGGGAGAGGTCCGGGCTGGA-GATATAAATT 2342 chr6ptel1M 268727 TGGGAGTCTT--GCTTAGAGATAA---TTGAATTCATGGGAGCTGATGAG 268771 v -- v v ii--- i vi i viv C L2#LINE/L2 2341 TGGGAGTCATCAGCATATAGATGGTATTTAAAGCCATGAGACTGGATGAG 2292 chr6ptel1M 268772 ATCATGAAGAGAGAGGATATAAAGCAAGGAGAGAAAATGCCCA 268814 iv? i v ii i i vvi i i v i C L2#LINE/L2 2291 ATCACCNAGGGAGTGAGTGTAGATAGAGAAGAGAAGAGGTCCA 2249 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 48.20 CpG sites = 68, Kimura (unadjusted) = 49.48 Transitions / transversions = 1.39 (68/49) Gap_init rate = 0.02 (6 / 335), avg. gap size = 1.50 (9 / 6) 333 29.52 4.17 9.65 chr6ptel1M 269318 269437 (730563) MIRc#SINE/MIR 2 115 (153) m_b278s601i17 11034 chr6ptel1M 269318 GGGGCAGCTAAATGATGCAGTGGATAGAGCACCAGCTCTGACATCAGGAG 269367 i i---i i v ii vii ivi i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr6ptel1M 269368 AACCTAAGTTCAAATATGTTCTCAGACACT-TAACACTTACTAGCTATGT 269416 i ii i i----- i i --- - iv i MIRc#SINE/MIR 49 GACCTGGGTTCGAG-----TCCCGG---CTCTGCCACTTACTAGCTGTGT 90 chr6ptel1M 269417 AATCCTAG----ATCACATAACTCC 269437 i i i i ----i v ii MIRc#SINE/MIR 91 GACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.90 CpG sites = 27, Kimura (unadjusted) = 41.37 Transitions / transversions = 5.40 (27/5) Gap_init rate = 0.11 (13 / 119), avg. gap size = 1.23 (16 / 13) 357 26.35 0.93 11.34 chr6ptel1M 269318 269424 (730576) MIRb#SINE/MIR 5 101 (167) m_b278s601i16 11034 chr6ptel1M 269318 GGGGCAGCTAAATGATGCAGTGGATAGAGCACCAGCTCTGACATCAGGAG 269367 ---i i v vi i ivi ivi MIRb#SINE/MIR 5 GGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACA 51 chr6ptel1M 269368 AACCTAAGTTCAAATATGTTCTCAGACACT-TAACACTTACTAGCTATGT 269416 i ii i ----- i i --- - iv i MIRb#SINE/MIR 52 GACCTGGGTTCGAA-----TCCCGG---CTCTGCCACTTACTAGCTGTGT 93 chr6ptel1M 269417 AATCCTAG 269424 i i i i MIRb#SINE/MIR 94 GACCTTGG 101 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.34 CpG sites = 20, Kimura (unadjusted) = 34.38 Transitions / transversions = 4.00 (20/5) Gap_init rate = 0.11 (12 / 106), avg. gap size = 1.00 (12 / 12) 15 24.19 3.23 3.23 chr6ptel1M 269607 269668 (730332) (TGTTTA)n#Simple_repeat 1 62 (0) m_b278s252i4 11035 chr6ptel1M 269607 TGATTATG-TAATTTTCTAT-TTTATGCTTACCTTTATTATTTATGATTA 269654 v - v v - - i iv - i v (TGTTTA)n#Sim 1 TGTTTATGTTTATGTT-TATGTTTATGTTTATGTTTA-TGTTTATGTTTA 48 chr6ptel1M 269655 TATCTTTATTTATG 269668 i i v i (TGTTTA)n#Sim 49 TGTTTATGTTTATG 62 Matrix = Unknown Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.07 (4 / 61), avg. gap size = 1.00 (4 / 4) 580 28.28 12.22 0.81 chr6ptel1M 270317 270537 (729463) MIRc#SINE/MIR 23 268 (0) m_b278s601i18 11036 chr6ptel1M 270317 AAGAGCAGTGGACTCAAGAGTCAGGAAGACTTGGGTTCAAAAGGAGCCTT 270366 v ii- i i ivvvv v i MIRc#SINE/MIR 23 AAGAGCACTGGACTTG-GAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTC 71 chr6ptel1M 270367 AGACACTCACTAGTTGTGCAAACCCAGGCAAATCACCTAACCTCTCT--- 270413 v v i i ii v iii i i --- MIRc#SINE/MIR 72 TGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAG 121 chr6ptel1M 270414 -----GTTTGCTTCA-CTGCCAATTA-------------CTGCAATAGCT 270444 ----- - i - iv v i------------- vv iv MIRc#SINE/MIR 122 CCTCAGTTT-CCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCT 170 chr6ptel1M 270445 ACCTCCTAG---TATTGTGAGGTCCAAATGAGACAATA-ATGGATAAGCA 270490 vi --- i vi i i- viv i MIRc#SINE/MIR 171 ACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCG 220 chr6ptel1M 270491 CTTCTCCAGCCTTAAGACATTATGTAAATA-GAGCTATTATTATTATT 270537 iviv i iv iiiii ii i-i v?i MIRc#SINE/MIR 221 CTTTGTAAACTGTAAAGTGCTATACAAATGTAAGGNGTTATTATTATT 268 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.65 CpG sites = 40, Kimura (unadjusted) = 37.18 Transitions / transversions = 1.82 (40/22) Gap_init rate = 0.04 (9 / 220), avg. gap size = 3.22 (29 / 9) 627 25.19 1.36 2.76 chr6ptel1M 270763 270909 (729091) C MIRc#SINE/MIR (122) 146 2 m_b278s601i19 11037 chr6ptel1M 270763 CGTTTTACAGATGAGGAAACTGAAGC--AAAAAGGTTTAAGTGGCTTGCC 270810 i i -- i i - i C MIRc#SINE/MIR 146 CATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTT-AAGTGACTTGCC 98 chr6ptel1M 270811 CAGGGTCACACAATTAGGAAGTATCTGAGGTTAGATTTGACATTAATTCT 270860 i ii v iv v vivi i i vvii iv C MIRc#SINE/MIR 97 CAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCT 48 chr6ptel1M 270861 TCCTGATTTCAAGCCTACAGTTCTCTCCACTGGGTCACCTAATTGTCTC 270909 i i i i vv i i --- vv i i C MIRc#SINE/MIR 47 TCCTGACTCCAAGTCCAGTGCTCTTTCCACTG---CACCACACTGCCTC 2 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.67 CpG sites = 24, Kimura (unadjusted) = 31.79 Transitions / transversions = 2.00 (24/12) Gap_init rate = 0.03 (5 / 146), avg. gap size = 1.20 (6 / 5) 240 29.82 8.12 3.59 chr6ptel1M 271006 271165 (728835) C L1MB5_3end#LINE/L1 (631) 290 124 m_b278s551i5 11038 chr6ptel1M 271006 CACCAACAATGCTATCAGCATTCTGACTTCTCAA-AGCCCTGCCCACATA 271054 i - iv vi ii i v - v ii v iv C L1MB5_3end#LI 290 CACCAGCAATG-TACGAGGGTTCCAATTTCTCCACATCCTCGCCAACACT 242 chr6ptel1M 271055 GGCCATTTCTTTTTTTGTTATTTTTGGTCATTTGATTTGATGAGAGTGAA 271104 v ii iiiv v v v i i ii---- ii i v C L1MB5_3end#LI 241 TGTTATTTTCCGTTTTTTTAATTATAGCCATCC----TAGTGGGTGTGAA 196 chr6ptel1M 271105 AGAGAA----A----GGTTTT----TGTATTTCTCTTATTATTAATTATT 271142 ivi v ---- ---- ---- i i v v i v v C L1MB5_3end#LI 195 GTGGTATCTCATTGTGGTTTTGATTTGCATTTCCCTAATGACTAATGATG 146 chr6ptel1M 271143 TGGAGCATTTGTTTCATGTGCTT 271165 v i - C L1MB5_3end#LI 145 TTGAGCATCT-TTTCATGTGCTT 124 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 35.98 CpG sites = 27, Kimura (unadjusted) = 39.21 Transitions / transversions = 1.42 (27/19) Gap_init rate = 0.06 (10 / 159), avg. gap size = 1.90 (19 / 10) 19 11.70 0.00 0.00 chr6ptel1M 271200 271227 (728773) (T)n#Simple_repeat 1 28 (0) m_b278s252i5 11039 chr6ptel1M 271200 TTTTTTTTTTTTTTTTTTTAAATTTTTT 271227 vvv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 28 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 366 36.05 2.72 0.00 chr6ptel1M 271453 271599 (728401) MIRc#SINE/MIR 21 171 (97) m_b278s601i20 11040 chr6ptel1M 271453 GAAAAATTATTGGACTTGGAA-CGAGAAGACTTAGGTCTGAAGCTTGGTT 271501 i vi i i- ii i i ii iv ii i MIRc#SINE/MIR 21 GAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCT 70 chr6ptel1M 271502 CTGCTCCTTAC-AACT-TATGACTGTGGGCACCTTATTGGTCCTCCTAGG 271549 iv - i - i iv vv i i viv iiv i MIRc#SINE/MIR 71 CTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGA 120 chr6ptel1M 271550 GCATCAGTCTGTGTACATGGAAGATGCAG-TAGCACTACATGATCTCTCT 271598 v i vivi iv v i vi - ii v v vi vi MIRc#SINE/MIR 121 GCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCT 170 chr6ptel1M 271599 A 271599 MIRc#SINE/MIR 171 A 171 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 49.37 CpG sites = 34, Kimura (unadjusted) = 52.28 Transitions / transversions = 1.79 (34/19) Gap_init rate = 0.03 (4 / 146), avg. gap size = 1.00 (4 / 4) 15 16.57 0.00 0.00 chr6ptel1M 272023 272049 (727951) (TA)n#Simple_repeat 1 27 (0) m_b278s252i7 11041 chr6ptel1M 272023 TATATATGTATATCTATATCTATGTAT 272049 i v v i (TA)n#Simple_ 1 TATATATATATATATATATATATATAT 27 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 11 11.26 6.90 0.00 chr6ptel1M 272025 272053 (727947) (TATATG)n#Simple_repeat 1 31 (0) m_b278s252i8 11041 chr6ptel1M 272025 TATATGTATATCTATA--TCTATGTATTTGT 272053 v -- v v (TATATG)n#Sim 1 TATATGTATATGTATATGTATATGTATATGT 31 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.04 (1 / 28), avg. gap size = 2.00 (2 / 1) 13 27.09 0.00 2.22 chr6ptel1M 272021 272066 (727934) (TCTA)n#Simple_repeat 1 45 (0) m_b278s252i6 11042 chr6ptel1M 272021 TCTATATATGTATATCTATATCTATGTATTTGTCTCTCTGATCAAT 272066 v v v v v v i i v - v (TCTA)n#Simpl 1 TCTATCTATCTATCTATCTATCTATCTATCTATCTATCT-ATCTAT 45 Matrix = Unknown Transitions / transversions = 0.25 (2/8) Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1) 489 21.79 3.68 2.17 chr6ptel1M 272145 272280 (727720) C Charlie1a#DNA/hAT-Charlie (0) 1455 1318 m_b278s502i5 11043 chr6ptel1M 272145 CAGTGGTTCTCAAA-TTTTTGTTCTCAGTA--TCTTCATGTTGTTAAAAA 272191 i - v v --i i iii v - C Charlie1a#DNA 1455 CAGCGGTTCTCAAACTTTTTGGTCTCAGGACCCCTTTACACTCTT-AAAA 1407 chr6ptel1M 272192 ATTATCAAGGATCTTTCAAAGAGTTTTTGTTCACATGGATTATATTTATA 272241 ii i --i i i ii i i v C Charlie1a#DNA 1406 ATTATTGAGGACC--CCAAAGAGCTTTTGTTTATGTGGGTTATATCTATC 1359 chr6ptel1M 272242 GCTAGTTACTATATGAGAAATAAAAA--AAAAGATTTTGAA 272280 v v i v v --i i i v C Charlie1a#DNA 1358 GATATTTACCATATTAGAAATTAAAACTGAGAAATTTTTAA 1318 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 25.55 CpG sites = 20, Kimura (unadjusted) = 26.61 Transitions / transversions = 2.22 (20/9) Gap_init rate = 0.04 (6 / 135), avg. gap size = 1.33 (8 / 6) 406 25.61 0.00 1.22 chr6ptel1M 272266 272348 (727652) C Charlie1b#DNA/hAT-Charlie (441) 82 1 m_b278s502i6 11043 chr6ptel1M 272266 AAAAAAGATTTTGAATTTGTAGACCCTCTGAAAGGGTTTCAGAGACCCCA 272315 v - vi i ii i i i i v C Charlie1b#DNA 82 AAAATAG-TTTTGACCTCGCGGACCCCCTGAAAGGGTCTCGGGGACCCCC 34 chr6ptel1M 272316 ACAATTCTTTGGACTACACTTTGAGGACCACTG 272348 viiv iii i i i C Charlie1b#DNA 33 AGGGGTCCCCGGACCACACTTTGAGAACCGCTG 1 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 23.95 CpG sites = 16, Kimura (unadjusted) = 33.25 Transitions / transversions = 3.20 (16/5) Gap_init rate = 0.01 (1 / 82), avg. gap size = 1.00 (1 / 1) 249 17.78 0.00 0.00 chr6ptel1M 272452 272496 (727504) C EutTc1-N2#DNA/TcMar-Tc1 (333) 45 1 m_b278s502i7 11044 chr6ptel1M 272452 AATTATGAAAGCTTAATCCTGCACTAACACATTTAGGACACCTTG 272496 i v vv v v i i C EutTc1-N2#DNA 45 AGTTATTAAAGCTTAAAACTGCACTAAGACTTTTGGGACACCCTG 1 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 20.30 CpG sites = 3, Kimura (unadjusted) = 20.30 Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 410 30.18 4.49 5.08 chr6ptel1M 272564 272741 (727259) MIR3#SINE/MIR 22 198 (10) m_b278s601i21 11045 chr6ptel1M 272564 GAAAGCACGA--TGGA--TTTGGAG-TCTGAATTATGGATCCCACTTCTC 272608 i i-- i-- iv -i ii v i - ivi v MIR3#SINE/MIR 22 GAGAGCACGGACTGGGAGTCAGGAGACCTGGGTTCTAG-TCCCGGCTCTG 70 chr6ptel1M 272609 ACACTTCTTACCCTTGAAACTTTGGACATCTCACTTC--CTCTTTGGCCC 272656 v vvi ?v iv vi i i vv -- i v MIR3#SINE/MIR 71 CCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCC 120 chr6ptel1M 272657 TAAATGTCCTTTTCTATAAAATGGTGGTGGAATGAGGTTAGGCCAAATGA 272706 v i v iv i -------- v i i i i i MIR3#SINE/MIR 121 TCAGTTTCCTCATCTGTAAAATG--------AGGGGGTTGGACTAGATGA 162 chr6ptel1M 272707 TCTCTGGGGTCCC-TCTACCTTAAAAATTATATAAT 272741 ii - i v ivi v v i MIR3#SINE/MIR 163 TCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGAT 198 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.07 CpG sites = 30, Kimura (unadjusted) = 40.09 Transitions / transversions = 1.43 (30/21) Gap_init rate = 0.08 (14 / 177), avg. gap size = 1.21 (17 / 14) 295 27.69 0.00 0.00 chr6ptel1M 273584 273648 (726352) C L2d2_3end#LINE/L2 (71) 484 420 m_b278s601i22 11046 chr6ptel1M 273584 TGCAGATAAACATAAGACACGGTCTCTGCCCTAGACGAACTTATAATCTA 273633 i i v ii i i vi v i i C L2d2_3end#LIN 484 TACAAAGAAGTATAAGACATGGTCCCTGCCCTCAAGGAGCTTACAATCTA 435 chr6ptel1M 273634 GCTAGGACAATAAGA 273648 i i ivi i C L2d2_3end#LIN 434 GTTGGGGAGACAAGA 420 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.18 CpG sites = 14, Kimura (unadjusted) = 37.18 Transitions / transversions = 3.50 (14/4) Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0) 315 35.05 5.14 10.10 chr6ptel1M 273595 273905 (726095) C L2d_3end#LINE/L2 (85) 431 135 m_b278s601i23 11046 chr6ptel1M 273595 ATAAGACACGGTCTCTGCCCTAGACGAACTTATAATCTAGCTAGGACAAT 273644 i i vi v i i i i ivi i C L2d_3end#LINE 431 ATAAGACATGGTCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGGAGAC 382 chr6ptel1M 273645 AAGA-----------GAAGCAGAT-GATAATATTCCAAGTCTGCTTAT-T 273681 ----------- i iv - v i v v v v iv -v C L2d_3end#LINE 381 AAGACTAACACACATGAAACAATTAGAGAACAATACAAGACAGTATATAA 332 chr6ptel1M 273682 CTAAATGTGATA-TGAAGAATATTAGCAATAAGGGCTACTGGAATTTAGA 273730 i i iv v - vivii ivii v v iv i i C L2d_3end#LINE 331 TTAAGTGCTAAATTGCGTGGTACAGACTATAAGTGCTATAGGAGTTCAGA 282 chr6ptel1M 273731 GGAGAG-GAGGTACTTCTGCATTGGAATAAGATAGATTAGACAAGACCAC 273779 i i - i vvv v vii i ------ i i iv i iv C L2d_3end#LINE 281 GAAGGGAGAGATCAGTGTGGGCTGGAGT------GGTCAGGGAAGGCTTC 238 chr6ptel1M 273780 AT-AAAAAGGCAGCATTTAACATGGGGACACTTGAAGAGGGAGAAGTATT 273828 i -i ii ii v i i vv -- - iiv i v v C L2d_3end#LINE 237 GTGGAGGAGGTGGGACTTGAGCTGGG--C-CTTGAAGGATGGGTAGGATT 191 chr6ptel1M 273829 ATCATAGGGGGAAATGGGGTCAAATTTTGGAGGGTGAAGTCAAGAATGTA 273878 vvv i i i -------------- i v ---- --- i C L2d_3end#LINE 190 TGGATAGAGAGAGA--------------GGAAGGGGAAG----G---GCA 162 chr6ptel1M 273879 CTCTAGATGGAAGGAATGGCCTGAGTA 273905 i i ii ii i v i C L2d_3end#LINE 161 TTCCAGGCGGGGGGAACGGCGTGAGCA 135 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 46.49 CpG sites = 61, Kimura (unadjusted) = 49.36 Transitions / transversions = 1.65 (61/37) Gap_init rate = 0.12 (36 / 310), avg. gap size = 1.28 (46 / 36) 184 17.95 2.56 0.00 chr6ptel1M 273960 273998 (726002) C MIR3#SINE/MIR (6) 202 163 m_b278s601i24 11047 chr6ptel1M 273960 TAGAATTAT-GAATGCATGAGCTAGAAGGGTCCTTAGAAA 273998 i - ivv i v i C MIR3#SINE/MIR 202 TAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGA 163 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 20.74 CpG sites = 4, Kimura (unadjusted) = 20.74 Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.03 (1 / 38), avg. gap size = 1.00 (1 / 1) 263 19.02 8.05 3.30 chr6ptel1M 274118 274204 (725796) C MIR1_Amn#SINE/MIR (112) 118 28 m_b278s601i25 11048 chr6ptel1M 274118 AGAGG-GAACTGAAGCTT---CAGGGTCACTCAATGGGTGAGTGGCAGAA 274163 -? v -- --- i ? ii? i? i C MIR1_Amn#SINE 118 AGAGGTNAAGTGA--CTTGCCCAAGGTCACNCAGCNGGCNAGTGGCAGAG 71 chr6ptel1M 274164 ACAGGACTAAAGGCTGTGTCCGCCC---TCACAGTCCAGTGCTC 274204 v i ? ?i iv iiv i- --- v C MIR1_Amn#SINE 70 CCGGGANTNGAACCCAGGTCT-CCCGAGTCCCAGTCCAGTGCTC 28 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 22.94 CpG sites = 11, Kimura (unadjusted) = 24.67 Transitions / transversions = 2.20 (11/5) Gap_init rate = 0.07 (6 / 86), avg. gap size = 1.67 (10 / 6) 346 26.50 4.83 6.29 chr6ptel1M 275599 275743 (724257) C MIR3#SINE/MIR (64) 144 2 m_b278s601i26 11047 chr6ptel1M 275599 TCATTTTGTAGACGAGGGA-CTGAGGCAAACAG-GGTGAAGTGACTTGCC 275646 ii i i - vv v - C MIR3#SINE/MIR 144 TCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCC 95 chr6ptel1M 275647 CAGGATCAAACTGCTGGTAAAGGTCTAAGGCTGGATTTGAACTCAAGAAA 275696 i i v v ?i v iv v vi v v i v i ------ C MIR3#SINE/MIR 94 CAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCC------ 51 chr6ptel1M 275697 AGAAGACTTCCCAAGT-CCAGACCCTGGCCTCCCTG---AG-CATTCTGG 275741 --- iii ii v - v v vi i --- - i v C MIR3#SINE/MIR 50 ---AGGTCTCCTGACTCCCAGTCCGTGCTCTCTCTGCTCAGCCACTCTGC 4 chr6ptel1M 275742 CA 275743 C MIR3#SINE/MIR 3 CA 2 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.42 CpG sites = 19, Kimura (unadjusted) = 33.42 Transitions / transversions = 1.12 (19/17) Gap_init rate = 0.10 (14 / 144), avg. gap size = 1.14 (16 / 14) 374 24.47 2.13 0.00 chr6ptel1M 275600 275693 (724307) C MIR#SINE/MIR (120) 142 47 m_b278s601i27 11047 chr6ptel1M 275600 CATTTTGTAGACGAGGGA-CTGAGGCAAACAG-GGTGAAGTGACTTGCCC 275647 ii i i - v v - v i C MIR#SINE/MIR 142 CATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCC 93 chr6ptel1M 275648 AGGATCAAACTGCTGGTAAAGGTCTAAGGCTGGATTTGAACTCAAG 275693 i i v v i iv v vi v v i i i C MIR#SINE/MIR 92 AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGG 47 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.60 CpG sites = 13, Kimura (unadjusted) = 30.12 Transitions / transversions = 1.30 (13/10) Gap_init rate = 0.02 (2 / 93), avg. gap size = 1.00 (2 / 2) 282 29.64 8.40 0.78 chr6ptel1M 276353 276471 (723529) C MIR3#SINE/MIR (63) 145 18 m_b278s601i29 11049 chr6ptel1M 276353 CTCATCTTACAGGTGAGGAAACTAAGACCAA--------CAGTGACTAGC 276394 i i i i v --------v v C MIR3#SINE/MIR 145 CTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGC 96 chr6ptel1M 276395 CTCGGATCACTTGGATAGCAAGTGTCTGAGGTCAGATTTGAACTCAGGGC 276444 ivi i vii v? iv v v vivi i v i v C MIR3#SINE/MIR 95 CCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGTC 46 chr6ptel1M 276445 ATGAGACCTCCTAG-CTTTGC-CACTCTG 276471 vivv - i - iv - v C MIR3#SINE/MIR 45 TCCTGA-CTCCCAGTCCGTGCTCTCTCTG 18 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.89 CpG sites = 17, Kimura (unadjusted) = 38.58 Transitions / transversions = 0.94 (17/18) Gap_init rate = 0.03 (4 / 118), avg. gap size = 2.75 (11 / 4) 307 24.44 8.89 0.00 chr6ptel1M 276353 276442 (723558) C MIR1_Amn#SINE/MIR (80) 150 53 m_b278s601i28 11049 chr6ptel1M 276353 CTCATCTTACAGGTGAGGAAACTAAGAC-CA-------ACAGTGACTAGC 276394 i i i i i - -------?v v C MIR1_Amn#SINE 150 CCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGC 101 chr6ptel1M 276395 CTCGGATCACTTGGATAGCAAGTGTCTGAGGTCAGATTTGAACTCAGG 276442 ivi i ?ii v?i ? v v vivi ? ? i C MIR1_Amn#SINE 100 CCAAGGTCACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAACCCAGG 53 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.42 CpG sites = 14, Kimura (unadjusted) = 33.26 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.02 (2 / 89), avg. gap size = 4.00 (8 / 2) 366 27.42 8.06 0.00 chr6ptel1M 276409 276532 (723468) MIR#SINE/MIR 6 139 (123) m_b278s601i30 11050 chr6ptel1M 276409 ATAGCA-AGTGTCTGAGGTCA---GATTTGAACTCAGG--GCATGAGACC 276452 - vi i iv --- v i i vi i-- v i vi MIR#SINE/MIR 6 ATAGCATAGTGGTTAAGAGCACGGGCTCTGGAGCCAGACTGCCTGGGTTC 55 chr6ptel1M 276453 ---TCCTAGCTTTGCCACTCTGTAGCTGTGTAGTCTTGGGTAA-TCACGT 276498 --- ii i ivv iii i - i v MIR#SINE/MIR 56 GAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTT 105 chr6ptel1M 276499 CACCTCACAGAGCCTCAGTTGCCTCATCTACAAA 276532 v v v v v ii MIR#SINE/MIR 106 AACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAA 139 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.58 CpG sites = 20, Kimura (unadjusted) = 34.99 Transitions / transversions = 1.43 (20/14) Gap_init rate = 0.04 (5 / 123), avg. gap size = 2.00 (10 / 5) 465 28.57 4.51 0.00 chr6ptel1M 276427 276559 (723441) MIR3#SINE/MIR 29 167 (41) m_b278s601i31 11050 chr6ptel1M 276427 CAGATTTGAACTCAGGG--CATGAGACCT---CCTAGCTTTGCCACTCTG 276471 i i v i v i-- v i vi --- ii i vvv MIR3#SINE/MIR 29 CGGACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAAC 78 chr6ptel1M 276472 TAGCTGTGTAGTCTTGGGTAA-TCACGTCACCTCACAGAGCCTCAGTTGC 276520 ? iii i - v v v i v MIR3#SINE/MIR 79 TNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTC 128 chr6ptel1M 276521 CTCATCTACAAATTAAATATGTTGAATTAGAAGAGCTTT 276559 ii v i iviv i i v v i MIR3#SINE/MIR 129 CTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCT 167 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.68 CpG sites = 22, Kimura (unadjusted) = 37.25 Transitions / transversions = 1.38 (22/16) Gap_init rate = 0.02 (3 / 132), avg. gap size = 2.00 (6 / 3) 27 0.00 0.00 0.00 chr6ptel1M 277511 277536 (722464) (T)n#Simple_repeat 1 26 (0) c_b278s251i1 11051 chr6ptel1M 277511 TTTTTTTTTTTTTTTTTTTTTTTTTT 277536 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 15 13.67 0.00 0.00 chr6ptel1M 277632 277655 (722345) (C)n#Simple_repeat 1 24 (0) m_b278s252i9 11052 chr6ptel1M 277632 CCCCACCCCCCCCACCCCCTCCCC 277655 v v i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCC 24 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 337 23.19 4.83 4.83 chr6ptel1M 278013 278157 (721843) C L1MC1_3end#LINE/L1 (447) 633 489 m_b278s551i6 11053 chr6ptel1M 278013 GCTCATTTCACTTAGCATCAGTTCGTGTAAGTCTC-TCCAGGCCTTTCTG 278061 iv i vi - v i v i - v i --- C L1MC1_3end#LI 633 GCTTCTTTCACTTAGTAATA-TGCATTTAAGTTTCCTCCATGTCTTT--- 588 chr6ptel1M 278062 AAATCAT--CCTGTTGG-TCATTTCTTAC-AGAAC--AGTAATATTCCAT 278105 --- -- i v i - vi- vi -- i C L1MC1_3end#LI 587 ---TCATGGCTTGATAGCTCATTTCTTTTTAGCGCTGAATAATATTCCAT 541 chr6ptel1M 278106 AATTTTCATATACCACAATTTATTCAGCCATTCTCCAACTGATGGACATC 278155 vi i vv i i i v v v v C L1MC1_3end#LI 540 TGTCTGGATGTACCACAGTTTATTTATCCATTCACCTACTGAAGGACATC 491 chr6ptel1M 278156 CT 278157 i C L1MC1_3end#LI 490 TT 489 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 27.06 CpG sites = 17, Kimura (unadjusted) = 28.06 Transitions / transversions = 1.13 (17/15) Gap_init rate = 0.08 (12 / 144), avg. gap size = 1.17 (14 / 12) 223 32.06 0.00 7.69 chr6ptel1M 279082 279179 (720821) C L2c_3end#LINE/L2 (1) 477 387 m_b278s601i32 11054 chr6ptel1M 279082 TCCAGTCAGGCAACAAACCTGCATTGTGCCCTCGCTCTACGTCAGGCACC 279131 i v vv v vi v v iii v ii i i i C L2c_3end#LINE 477 TTCATTCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCT 428 chr6ptel1M 279132 AGGGCAGAGATACAAGGAAAGGCAAAAGACACAATTCCTGTCCCTAAG 279179 i ----- -- i v v v ii i i ii C L2c_3end#LINE 427 GGG-----GATACAA--AGATGAATAAGACACGGTCCCTGCCCTCAAG 387 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.32 CpG sites = 18, Kimura (unadjusted) = 43.25 Transitions / transversions = 1.64 (18/11) Gap_init rate = 0.07 (7 / 97), avg. gap size = 1.00 (7 / 7) 203 31.88 4.35 0.00 chr6ptel1M 279388 279456 (720544) L2d2_3end#LINE/L2 446 517 (38) m_b278s601i33 11055 chr6ptel1M 279388 CTCCTCGAGGAGAGGGCTCATCTTTTGACTTTCTTTTTACCCC---TGGC 279434 i iv vi v i ivvi v i ---ii L2d2_3end#LIN 446 CTCCTTGAGGGCAGGGACCATGTCTTATACTTCTTTGTATCCCCCACAGC 495 chr6ptel1M 279435 ACTTAGCAGAATTCCTGGTACA 279456 i i v i v v i L2d2_3end#LIN 496 GCCTAGCACAGTGCCTTGCACA 517 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 40.36 CpG sites = 13, Kimura (unadjusted) = 42.94 Transitions / transversions = 1.44 (13/9) Gap_init rate = 0.01 (1 / 68), avg. gap size = 3.00 (3 / 1) 284 26.92 7.14 7.14 chr6ptel1M 279519 279630 (720370) C MIRc#SINE/MIR (120) 148 37 m_b278s601i34 11056 chr6ptel1M 279519 CTCATCTTACAGGTGAGGGAAACTAAGAC-CAAC-------AGTGACTAG 279560 i i i - i i - iv------- v C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGG-AAACTGAGGCTCAGAGAGGTTAAGTGACTTG 100 chr6ptel1M 279561 CCTCGGATCACTCGGATAGCAAGTGTCTGAGGTCAGATTTGAACTCAGGG 279610 ivi i v i v i v v vivi i i i v C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGT 50 chr6ptel1M 279611 CATGAGACCTCCTGCCTCCA 279630 ------- i v C MIRc#SINE/MIR 49 -------CTTCCTGACTCCA 37 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.32 CpG sites = 17, Kimura (unadjusted) = 34.28 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.09 (10 / 111), avg. gap size = 1.60 (16 / 10) 290 23.32 8.79 1.02 chr6ptel1M 279519 279609 (720391) C MIR1_Amn#SINE/MIR (80) 150 53 m_b278s601i35 11056 chr6ptel1M 279519 CTCATCTTACAGGTGAGGGAAACTAAGAC-CA-------ACAGTGACTAG 279560 i i i - i i - -------?v v C MIR1_Amn#SINE 150 CCCATTTTACAGATGAGG-AAACTGAGGCNCAGAGAGGTNAAGTGACTTG 102 chr6ptel1M 279561 CCTCGGATCACTCGGATAGCAAGTGTCTGAGGTCAGATTTGAACTCAGG 279609 ivi i ? i v?i ? v v vivi ? ? i C MIR1_Amn#SINE 101 CCCAAGGTCACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAACCCAGG 53 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.45 CpG sites = 13, Kimura (unadjusted) = 31.22 Transitions / transversions = 1.62 (13/8) Gap_init rate = 0.03 (3 / 90), avg. gap size = 3.00 (9 / 3) 16 17.50 0.00 3.03 chr6ptel1M 279687 279720 (720280) (TC)n#Simple_repeat 1 33 (0) m_b278s252i11 11057 chr6ptel1M 279687 TCTTTCTCTATCATCTCTCTATCTCTAGCTCTCT 279720 i v - v vv (TC)n#Simple_ 1 TCTCTCTCTCTC-TCTCTCTCTCTCTCTCTCTCT 33 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 20 25.76 1.27 3.90 chr6ptel1M 279682 279760 (720240) (CTATCT)n#Simple_repeat 1 77 (0) m_b278s252i10 11058 chr6ptel1M 279682 CTATGTCTTTCTCTATC-ATCTCTCTATCTCTAGCTCTCTGATTGAGTCT 279730 v v -v v v v -v iv - (CTATCT)n#Sim 1 CTATCTCTATCTCTATCTCTATCTCTATCTCTATCTCTAT-CTCTA-TCT 48 chr6ptel1M 279731 CTGTCTATAGCCATGTCTCTAATCTATATC 279760 i v v iv i - v (CTATCT)n#Sim 49 CTATCTCTATCTCTATCTCT-ATCTCTATC 77 Matrix = Unknown Transitions / transversions = 0.33 (4/12) Gap_init rate = 0.05 (4 / 78), avg. gap size = 1.00 (4 / 4) 229 25.27 7.95 1.06 chr6ptel1M 280310 280397 (719603) C L3#LINE/CR1 (81) 4018 3925 m_b278s601i36 11059 chr6ptel1M 280310 CTGTGACATC--TGACAAGTGGCCACCCAATGGTCTA--TGG--GCTTCC 280353 iii -- i i ii-v i-- i--i i C L3#LINE/CR1 4018 CTACAACATCCCTGACAAGTGGTCATCCAGC-CTCTGCTTGAACACCTCC 3970 chr6ptel1M 280354 AGGGA-GGGGGCCTCCCTTTCTCCCGAGACAGCACCTTCCACTTT 280397 v - iv v vi ? i v v i C L3#LINE/CR1 3969 AGTGACGGGGAGCTCACTACCTCNCGAGGCAGCCCATTCCATTTT 3925 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.57 CpG sites = 15, Kimura (unadjusted) = 32.57 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.06 (5 / 87), avg. gap size = 1.60 (8 / 5) 26 39.50 1.32 1.99 chr6ptel1M 281349 281500 (718500) (GT)n#Simple_repeat 1 151 (0) m_b278s252i12 11060 chr6ptel1M 281349 GTGTGTGTGAATGTGTGTTTATATGCTTGTGTGTGGGTGCAT-TCATTGC 281397 vi v i i iv v ii - vvv i (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50 chr6ptel1M 281398 ATGCGTGCGAATGCATGTGCCTGTATATGGGTGCATGTGT-TGTATGAGC 281446 i i i vi ii iv i i v ii - i v i (GT)n#Simple_ 51 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 100 chr6ptel1M 281447 ACACACGTGTGTATGTGTGTAGATGTGTGTATCGTGTGAGTGCACGTGTG 281496 iiiiii i - - i - v iii (GT)n#Simple_ 101 GTGTGTGTGTGTGTGTGTGT-G-TGTGTGTGT-GTGTGTGTGTGTGTGTG 147 chr6ptel1M 281497 TGTG 281500 (GT)n#Simple_ 148 TGTG 151 Matrix = Unknown Transitions / transversions = 2.58 (31/12) Gap_init rate = 0.03 (5 / 151), avg. gap size = 1.00 (5 / 5) 285 32.90 0.81 6.84 chr6ptel1M 281585 281708 (718292) MIR3#SINE/MIR 61 177 (31) m_b278s601i37 11061 chr6ptel1M 281585 CCTGACTCTAAGGCTGACTGATTACGTGACTTCAGGAGGGGGGCAAATCC 281634 i i ivvi i ?ii ii i i------- i v MIR3#SINE/MIR 61 CCCGGCTCTGCCACTAACTNGCTGTGTGACCTT-------GGGCAAGTCA 103 chr6ptel1M 281635 TCTTGATCTCTGTGATCCTCAGTTTCTTTACCCACAAAAT-CCAGGGTTA 281683 - v i v iv i i i iii -vvi i MIR3#SINE/MIR 104 -CTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTG 152 chr6ptel1M 281684 GCCTACAAGATGGTTGTGGTCCCTT 281708 v v v vvi iv MIR3#SINE/MIR 153 GACTAGATGATCTCTAAGGTCCCTT 177 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 44.04 CpG sites = 24, Kimura (unadjusted) = 45.71 Transitions / transversions = 1.71 (24/14) Gap_init rate = 0.07 (9 / 123), avg. gap size = 1.00 (9 / 9) 237 33.01 13.50 3.35 chr6ptel1M 281888 282050 (717950) C MIR3#SINE/MIR (10) 198 20 m_b278s601i38 11062 chr6ptel1M 281888 ATAATAGA--GCCAGAGATTTAAAAGCATAGATCTCAAAGACCTTCCACG 281935 v -- i --i ii ---i i i i i v i vv C MIR3#SINE/MIR 198 ATCATAGAATGTCAGAG--CTGGAAG---GGACCTTAGAGATCATCTAGT 154 chr6ptel1M 281936 TCATCTTTCTCATTTTATGGGCAAGGAAATGGAAGCCTA-AGGGACTTAG 281984 i v iii ii iii iv i i - i iivv C MIR3#SINE/MIR 153 CCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAG 104 chr6ptel1M 281985 TGA--TGTTT----TCACA-AGTA--TTATGTGGT-------GAATTTGA 282018 -- iii---- - i?-- - i------- i i v C MIR3#SINE/MIR 103 TGACTTGCCCAAGGTCACACAGCNAGTTA-GTGGCAGAGCCGGGACTAGA 55 chr6ptel1M 282019 ACACAGATCTTTTGCCTTCAAA---ATGTTCTTTC 282050 v i ii v i v i---i i i C MIR3#SINE/MIR 54 ACCCAGGTCTCCTGACTCCCAGTCCGTGCTCTCTC 20 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 47.34 CpG sites = 40, Kimura (unadjusted) = 48.72 Transitions / transversions = 3.33 (40/12) Gap_init rate = 0.09 (14 / 162), avg. gap size = 2.00 (28 / 14) 288 31.06 15.91 0.00 chr6ptel1M 281942 282073 (717927) C MIRb#SINE/MIR (115) 153 1 m_b278s601i39 11062 chr6ptel1M 281942 TTCTCATTTTATGGGCAAGGAAATGGAAGCCTA-AGGGACTTAGTGA--T 281988 i i ii iii iv i ii - i ii v i -- C MIRb#SINE/MIR 153 TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTT 104 chr6ptel1M 281989 GTTT----TCACA-AG-TATTATGTGGT-------GAATTTGAACACAGA 282025 iii---- - - v v i------- i i v i C MIRb#SINE/MIR 103 GCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGG 54 chr6ptel1M 282026 TCT-TTTGCCTTCAAAA----TGTTCTTTCCAAAGCACTCTATTGCCCCC 282070 - i v i i---- i vv iviii i C MIRb#SINE/MIR 53 TCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCACCACGCTGCCCCT 4 chr6ptel1M 282071 TTG 282073 i C MIRb#SINE/MIR 3 CTG 1 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 40.81 CpG sites = 32, Kimura (unadjusted) = 43.93 Transitions / transversions = 3.56 (32/9) Gap_init rate = 0.06 (8 / 131), avg. gap size = 2.62 (21 / 8) 242 29.21 25.84 0.00 chr6ptel1M 282179 282267 (717733) L3#LINE/CR1 3962 4073 (26) m_b278s601i40 11063 chr6ptel1M 282179 CTGACACTGGAAATGCTCAAGCAAAATCTAAATGACGCCTCATCACAGAT 282228 i v ii i i iv ii vv ii vi L3#LINE/CR1 3962 CCGTCACTGGAGGTGTTCAAGCAGAGGCTGGATGACCACTTGTCAGGGAT 4011 chr6ptel1M 282229 ATCATA-----------------------GAGATTGGGCTAGACCATCTC 282255 i ii ----------------------- i i iv i L3#LINE/CR1 4012 GTTGTAGAAGGGATTCCTGCATTGGATGGGAGGTTGGACTAGATGACCTC 4061 chr6ptel1M 282256 CAAAGTCCCTTC 282267 i i L3#LINE/CR1 4062 TAAGGTCCCTTC 4073 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.94 CpG sites = 20, Kimura (unadjusted) = 39.99 Transitions / transversions = 3.33 (20/6) Gap_init rate = 0.01 (1 / 88), avg. gap size = 23.00 (23 / 1) 457 24.90 1.26 16.67 chr6ptel1M 283022 283180 (716820) MIRc#SINE/MIR 8 145 (123) m_b278s601i41 11064 chr6ptel1M 283022 GTGTGGTGCAGTGATTAGAATGCTGGGCCTGGAGTTAGGAAGAACATTAG 283071 ivv iii i i i ------- MIRc#SINE/MIR 8 GTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA------- 50 chr6ptel1M 283072 GAAGAACCCCATGTTCTGGGGTTCAAATCT-GACTGCAGACACTTGGGAC 283120 --------------- iv i i i- i - v v ivv v MIRc#SINE/MIR 51 ---------------CCTGGGTTCGAGTCCCGGCT-CTGCCACTTACTAG 84 chr6ptel1M 283121 TTGTGGGATCCTGAGCAAATCACTTTACCCTGCTG-GCCTCAGTTTCCTT 283169 i v i i i i v iiv - i MIRc#SINE/MIR 85 CTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTC 134 chr6ptel1M 283170 ATCTATAAAAT 283180 i MIRc#SINE/MIR 135 ATCTGTAAAAT 145 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.22 CpG sites = 22, Kimura (unadjusted) = 30.32 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.16 (25 / 158), avg. gap size = 1.00 (25 / 25) 52 23.16 3.03 0.00 chr6ptel1M 283484 283615 (716385) (TA)n#Simple_repeat 1 136 (0) m_b278s252i13 11065 chr6ptel1M 283484 TATATATATATGTATATATACACACACACATATATATA-ATTTA-AAATA 283531 i i i i i i - v - v (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr6ptel1M 283532 TATACATGCATCTATTTATATGTATATATATATA-ATTTATTTATA-ATA 283579 i ii v v i - v v - (TA)n#Simple_ 51 TATATATATATATATATATATATATATATATATATATATATATATATATA 100 chr6ptel1M 283580 TATATGTGCACATATATTTATATTTCAACATATTTA 283615 i ii i v v vv i v (TA)n#Simple_ 101 TATATATATATATATATATATATATATATATATATA 136 Matrix = Unknown Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.03 (4 / 131), avg. gap size = 1.00 (4 / 4) 337 29.15 8.75 4.76 chr6ptel1M 283647 283909 (716091) L3#LINE/CR1 3687 3959 (140) m_b278s601i42 11066 chr6ptel1M 283647 AAATCAC-TCACAAGTGAGGGTAACTGCTTAAGGGACACAAAAGCATGTA 283695 i i- i -- -- v i v i v---ii v v L3#LINE/CR1 3687 AAACCATGTCATA--TGAGG--AACGGTTGAAGGAACT---GGGGATGTT 3729 chr6ptel1M 283696 -AACCTGGAACGTGGAAACCTTGGAAGGGACAGGA-AGCGGTCTTCACAA 283743 - i ivivi iv i i i v - v v v L3#LINE/CR1 3730 TAGCCTGGAGAAGAGAAGACTTAGAGGAGACATGATAGCTGTCTTCAAAT 3779 chr6ptel1M 283744 AGTTAAAGGAATATCATGTGGAAGAGAGATTCCATTTGTTCCCCTTGA-T 283792 v i iv i i vv i i iviv i- L3#LINE/CR1 3780 ATTTGAAGGGCTGTCATGTGGAAGAGGGATTAGACTTATTCTGTGTGGCT 3829 chr6ptel1M 283793 GTAAAAGGCAG--CCATGACCCTGTGAGGAGGCAGCTACCT---GGCAGA 283837 vi i i -- i v v-i - v v i vv--- L3#LINE/CR1 3830 CCAGAGGGCAGAACTAGGACCA-ATG-GGTGGAAGTTACAGGGAGGCAGA 3877 chr6ptel1M 283838 TGTGTGGC-CAA-GTAGG-----------TAACAATACCCAGCGATGTCC 283874 - vi - -i i ----------- --- v v L3#LINE/CR1 3878 T-TTCGGCTCAATATAAGGAAGAACTTTCTAACAAT---CAGAGCTGTCC 3923 chr6ptel1M 283875 CACAGTACAAC-GGCTGCTTCGGGACATCCTGGGCT 283909 v v i iv i- i ? vi vv i L3#LINE/CR1 3924 AAAAATGGAATGGGCTGCCTCGNGAGGTAGTGAGCT 3959 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.19 CpG sites = 39, Kimura (unadjusted) = 37.85 Transitions / transversions = 1.15 (39/34) Gap_init rate = 0.09 (23 / 262), avg. gap size = 1.57 (36 / 23) 192 24.32 0.00 0.00 chr6ptel1M 284232 284268 (715732) L2d_3end#LINE/L2 396 432 (84) m_b278s601i43 11067 chr6ptel1M 284232 ACTGGAAACTCTCTGAGGGCTGGGATTATGTCTCATA 284268 i v i ii v ii i L2d_3end#LINE 396 ATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATA 432 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.18 CpG sites = 7, Kimura (unadjusted) = 31.18 Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 64 1.72 0.00 0.00 chr6ptel1M 284274 284332 (715668) (CA)n#Simple_repeat 1 59 (0) c_b278s251i2 11068 chr6ptel1M 284274 CACACACACACACACACACACACACACACACACACACACACACACACACA 284323 (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 chr6ptel1M 284324 CACTCACAC 284332 v (CA)n#Simple_ 51 CACACACAC 59 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.0 (0 / 0) 185 18.44 7.58 1.43 chr6ptel1M 284588 284653 (715347) MIRc#SINE/MIR 159 228 (40) m_b278s601i44 11064 chr6ptel1M 284588 CCTCCCCTTCC--CCTC-CAGGCTTGTTGTGA-GAGCTAATGAGACAGGG 284633 v v -- - v - v v i iv MIRc#SINE/MIR 159 CCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATG 208 chr6ptel1M 284634 TGTTTG-AAGCTCTCCTGTAA 284653 i v - v -i MIRc#SINE/MIR 209 TATGTGAAAGCGCT-TTGTAA 228 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 21.19 CpG sites = 4, Kimura (unadjusted) = 21.19 Transitions / transversions = 0.50 (4/8) Gap_init rate = 0.08 (5 / 65), avg. gap size = 1.20 (6 / 5) 397 25.49 3.92 0.00 chr6ptel1M 284951 285052 (714948) MIR#SINE/MIR 76 181 (81) m_b278s601i45 11069 chr6ptel1M 284951 ATTGGCTGCATTTCTCTGGGCAAACTTTTTAACCCCTCTCTGGC--AGTC 284998 i i ii vv ii ii vi i v v -- i MIR#SINE/MIR 76 ACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTT 125 chr6ptel1M 284999 TCCTCATCTGTGAAATGGGCTTAATAATAGAAATTGCTTCAT--GGTCAT 285046 i vv v vi i i -- ii MIR#SINE/MIR 126 TCCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTCATAGGGTTGT 175 chr6ptel1M 285047 TGTGAG 285052 MIR#SINE/MIR 176 TGTGAG 181 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.23 CpG sites = 17, Kimura (unadjusted) = 32.23 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.02 (2 / 101), avg. gap size = 2.00 (4 / 2) 15 14.38 0.00 0.00 chr6ptel1M 285277 285300 (714700) (T)n#Simple_repeat 1 24 (0) m_b278s252i14 11070 chr6ptel1M 285277 TTTTTTTCTTTTTCTTTTTCTTTT 285300 i i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTT 24 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 194 19.57 2.13 2.13 chr6ptel1M 285895 285941 (714059) C MIR3#SINE/MIR (4) 204 158 m_b278s601i46 11071 chr6ptel1M 285895 CACAGAATCAGGGAAATGGTAGCACTGGAAAGGACCTTGGA-ATCATC 285941 i vi - vi vi i i - C MIR3#SINE/MIR 204 CATAGAATCATAGAA-TGTCAGAGCTGGAAGGGACCTTAGAGATCATC 158 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 23.23 CpG sites = 6, Kimura (unadjusted) = 23.23 Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.04 (2 / 46), avg. gap size = 1.00 (2 / 2) 187 37.97 1.27 0.00 chr6ptel1M 286187 286265 (713735) MIRb#SINE/MIR 184 263 (5) m_b278s601i47 11072 chr6ptel1M 286187 AAGATCAAAT-AGATGCCGTGTGTGAGGCACCCAGCAAAGCATCCAGCAC 286235 i i - ivi ii i i i ii v iii ii MIRb#SINE/MIR 184 AGGATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCAC 233 chr6ptel1M 286236 ATACTCTGGGTTCAGTGAGTGCTTGTTCCA 286265 v vv v i i i i v v i i MIRb#SINE/MIR 234 ATAGTAAGCGCTCAATAAATGGTAGCTCTA 263 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 56.11 CpG sites = 22, Kimura (unadjusted) = 59.34 Transitions / transversions = 2.75 (22/8) Gap_init rate = 0.01 (1 / 78), avg. gap size = 1.00 (1 / 1) 1458 30.87 1.01 1.70 chr6ptel1M 287514 288106 (711894) C L1ME3B_3end#LINE/L1 (343) 646 58 m_b278s551i7 11073 chr6ptel1M 287514 TCTCCTG-GTCCTGCTCATTTCACTCAGCATCAGTTCTGTGAGTCTC-TC 287561 ii - i iv i i i vv i vi - C L1ME3B_3end#L 646 TCTTTTGTGTCTTGCTTCTTTCGCTCAACATTATGTTTGTGAGATTCATC 597 chr6ptel1M 287562 CAGGCCTTTCTGAAATCCTCCTGTTGGTCCTTTCTTACAGAACAATAATA 287611 v iiv vi vivvv viv v i v i i iv vvvv i C L1ME3B_3end#L 596 CATGTTGTTGCGTGTAGCTGTAGTTCGTTCATTTTCATTGCTGTATAGTA 547 chr6ptel1M 287612 TTTCATAACATTCATATACCACAATTTATTCAGCCATTCTCCAACTGATG 287661 i vii vv i v v vii C L1ME3B_3end#L 546 TTCCATTGTATGAATATACCACAATTTATTTATCCATTCTACTGTTGATG 497 chr6ptel1M 287662 GGCATCCACTCAGTTTCCAGTTTCTGGCCACTACAAAGAGGGCTGCCACA 287711 i iiivviv i? i i i v iv i ii C L1ME3B_3end#L 496 GACATTTGGGTTGTTTCCAGTTTTNGGCTATTACGAACAATGCTGCTATG 447 chr6ptel1M 287712 AACATTCATGCATATACAGGTC-CCT--TTCCCTTCTTTATG-ATCTCTC 287757 v ---- v ?- -- v v v v vi i -i i C L1ME3B_3end#L 446 AACATTCTTG----TACATGTNTCCTGGTGCACATGTGCACGCGTTTCTC 401 chr6ptel1M 287758 TGGGATATAAGCCCAGTAGTAATAACACTGCTGGATCAAAGGGTATGCAC 287807 i i vi --- v i iiv i i v ii C L1ME3B_3end#L 400 TAGGGTATATACC---TAGGAGTGGAATTGCTGGGTCATAGGGTATGCGT 354 chr6ptel1M 287808 AGTTTGATAACTTTTTGAGCATAGTTCCAAACTGCTCTCCAGAATGGCTG 287857 vi --i v?v - i v i i i i i C L1ME3B_3end#L 353 ATCTT--CAACTTTANTAG-ATAATGCCAAACTGTTTTCCAAAGTGGTTG 307 chr6ptel1M 287858 GATGTATCCACAATTCCACCAACAATGTATCAGTGTCCCTGTTTTCCCAC 287907 v ivv ii v i i i v v i i vii C L1ME3B_3end#L 306 TACCAATTTACACTCCCACCAGCAGTGTATGAGAGTTCCCGTTGCTCCAC 257 chr6ptel1M 287908 ATCCCCTCCAATATTCCGCATTATCTTTCCCTGTCATTCTAGCCAGTCTG 287957 i v i i iv i i vvv ii v?v i v ? C L1ME3B_3end#L 256 ATCCTCGCCAACACTTGGTATTGTCAGACTTTTNAATTTTTGCCANTCTG 207 chr6ptel1M 287958 ACAAGTGTGCAGTGGTATTTCACAGTTGTCTTAATTTGTGTTTCTCTGAT 288007 iiii i i iv v i ii i C L1ME3B_3end#L 206 GTGGGTGTGTAGTGGTATCTCATTGTGGTTTTAATTTGCATTTCCCTGAT 157 chr6ptel1M 288008 TAATAATGACTTGGAGCATCTTTTCATATGGCTAGAGATAGTTTCAATTT 288057 v vv v i vi vv iivi vi C L1ME3B_3end#L 156 TACTAATGAGGTTGAGCACCTTTTCATATGTTTATTGGCCATTTGGATTT 107 chr6ptel1M 288058 CTTCATCTGAGAATTGTCTGTTCATATCCTTTGACCATTTATCAATTGG 288106 i v i v v i vi i v v v C L1ME3B_3end#L 106 CCTCTTTTGTGAAGTGCCTGTTCAAGTCTTTTGCCCATTTTTCTATTGG 58 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.20 CpG sites = 101, Kimura (unadjusted) = 41.28 Transitions / transversions = 1.28 (101/79) Gap_init rate = 0.03 (15 / 592), avg. gap size = 1.07 (16 / 15) 1614 25.57 2.50 4.31 chr6ptel1M 287606 288124 (711876) C L1ME5_3end#LINE/L1 (389) 552 43 m_b278s551i8 11073 chr6ptel1M 287606 ATAATATTTCATAACATTCATATACCACAATTTATTCAGCCATTCTCCAA 287655 i i i iiii v vi v iii v i v C L1ME5_3end#LI 552 ATAGTACTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCA 503 chr6ptel1M 287656 CTGATGGGCATCCACTCAGTTTCCAGTTTCTGGCCACTACAAAGAGGGCT 287705 v i i vviv ii ii i iv i v iv C L1ME5_3end#LI 502 GTGATGGACACCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCT 453 chr6ptel1M 287706 GCCACAAACATTCATGCATATACAGGTCCCTTTC----CCTTCTTTATGA 287751 v ii i vi ---- v i v---- viv v vi C L1ME5_3end#LI 452 GCAATGAACATCCTCG----TACATGTCCCCTTATGGACCTGTGTGAGAA 407 chr6ptel1M 287752 TCTCTCTGGGATATAAGCCCAGTAGT--AATAACACTGCTGGATCAAAGG 287799 i i vi v i-- ----- i v C L1ME5_3end#LI 406 TTTCTTTGGGATATATACCCAGGAGCGGAAT-----TGCTGGGTCATAGG 362 chr6ptel1M 287800 GTATGCACAGTTTGATAACTT--TTTGAGCA--TAGTTCCAAACTGCTCT 287845 --- --- - -- vi -- v v i i C L1ME5_3end#LI 361 GTATGC---GT---ATA-CTTAATTTGACTAAGTACTGCCAGATTGCTCT 319 chr6ptel1M 287846 CCAGAATGGCTGGATGTATCCACAATTCCACCAACAATGTATCAGTGTCC 287895 v ivvi i v i i i i v v i C L1ME5_3end#LI 318 CCAGAATGGCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTC 269 chr6ptel1M 287896 CTGTTTTCCCACATCCCCTCCAATATTCCGCATTATCTTTCCCTGTCATT 287945 i ? i i v i i iv ivv ii v v C L1ME5_3end#LI 268 CTATNTCCCCACATCCTCGCCAACACTTGGCATTATCCAGCTTTCTAATT 219 chr6ptel1M 287946 CTAGCCAGTCTGACAAGTGTGCAGTGGTATTTCACAGTTGTCTTAATTTG 287995 i v i i i iv i i iv i C L1ME5_3end#LI 218 TTTGCCAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTG 169 chr6ptel1M 287996 TGTTTCTCTGATTAATAATGACTTGGAGCATCTTTTCATATGGCTAGAGA 288045 ii v v v i vi --- v C L1ME5_3end#LI 168 CATTTCTCTGATTACTAATGAGTTTGAGCATCTCTTCATATGCTT---GT 122 chr6ptel1M 288046 TAG--TTTCAA-TTTCTTCATCTGAGAATTGTCTGTTCATATCCTTTGAC 288092 -- ii- i v vi i v C L1ME5_3end#LI 121 TAGCCTTTCGGGTTTCCTCTTCTGTAAATTGCCTGTTCATATCCTTTGCC 72 chr6ptel1M 288093 CATTTATCAATTGGAGAATTAACCATCATTTT 288124 v v i -- -? i v C L1ME5_3end#LI 71 CATTTTTCTATTGGGG--TT-NCCGTCTTTTT 43 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 30.90 CpG sites = 75, Kimura (unadjusted) = 32.12 Transitions / transversions = 1.44 (75/52) Gap_init rate = 0.05 (28 / 518), avg. gap size = 1.25 (35 / 28) 390 28.44 9.16 0.70 chr6ptel1M 288226 288356 (711644) MIR#SINE/MIR 29 170 (92) m_b278s601i48 11074 chr6ptel1M 288226 GGCCC-GGAGCTAGAC---CTGAGTTCAAATCCTGCCTTAGGCACTTATC 288271 i - i --- i i i v iv v ii MIR#SINE/MIR 29 GGCTCTGGAGCCAGACTGCCTGGGTTCGAATCCCGGCTCTGCCACTTACT 78 chr6ptel1M 288272 AGCTCTGTATTCCTGGGTAAGC--CTGGATC------TGGCTCAGCTTTT 288313 v ivi i i i-- vi i ------ v i ii MIR#SINE/MIR 79 AGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCC 128 chr6ptel1M 288314 TCAGCTGTAAACAGAGGAAGAAGCATAGCATCTACCTCGTGAG 288356 v - vi i v vv i i i ii MIR#SINE/MIR 129 TCATCTGTAAA-ATGGGGATAATAATAGTACCTACCTCATAGG 170 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.92 CpG sites = 25, Kimura (unadjusted) = 37.50 Transitions / transversions = 2.08 (25/12) Gap_init rate = 0.04 (5 / 130), avg. gap size = 2.60 (13 / 5) 74 40.92 3.28 1.45 chr6ptel1M 289573 290182 (709818) (AC)n#Simple_repeat 1 621 (0) m_b278s252i15 11075 chr6ptel1M 289573 ACACACACACATACACACGCACACA-AAATACATACATACACATTCAGGC 289621 i i - v i i i iv vi (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50 chr6ptel1M 289622 A-ACACGCACAGACACACGTGTGGTAAATAGA-ATGCTCACACATATATT 289669 - i v -vvvvii v i v - ii v i i -i (AC)n#Simple_ 51 ACACACACACACACACAC-ACACACACACACACACACACACACACACA-C 98 chr6ptel1M 289670 ACAGAGACAGACTCACATGCACA-ACATGCATATGCACACATGCACACAC 289718 v v v v ii - ii i ii ii (AC)n#Simple_ 99 ACACACACACACACACACACACACACACACACACACACACACACACACAC 148 chr6ptel1M 289719 ACACATGGA-AGACACTCAGCACAGCACACATGCGCACACATTCACA-AT 289766 iiv - v v - - ii i iv - i (AC)n#Simple_ 149 ACACACACACACACACACA-CACA-CACACACACACACACACACACACAC 196 chr6ptel1M 289767 GCATGCACACACTCATGTAC-CGCACACATAGA-ATACACACAAACACGC 289814 i ii v iii - i i v - i v i (AC)n#Simple_ 197 ACACACACACACACACACACACACACACACACACACACACACACACACAC 246 chr6ptel1M 289815 ACATAC-CATGTGCACA-ATGCACATGCATACATATACACA-ATGCACAC 289861 i - iiii - ii ii i i i - ii (AC)n#Simple_ 247 ACACACACACACACACACACACACACACACACACACACACACACACACAC 296 chr6ptel1M 289862 TCACAAACACACACATTCAGCACA-ATATACATACATGCTTATACCCACA 289910 v v iv - - i i i ii vi i v (AC)n#Simple_ 297 ACACACACACACACACACA-CACACACACACACACACACACACACACACA 345 chr6ptel1M 289911 TGCACACA-ATATTCATGTGCACA-ACCCATACACACGTGTCTATATACA 289958 ii - i iv iiii - v i -vvv - i i (AC)n#Simple_ 346 CACACACACACACACACACACACACACACACACACAC-ACAC-ACACACA 393 chr6ptel1M 289959 TGCACACA-ACACACTGTATTCACACATAAATGCACA-ATTCATATACAT 290006 ii - -ii iv i v ii - iv i i i (AC)n#Simple_ 394 CACACACACACACAC-ACACACACACACACACACACACACACACACACAC 442 chr6ptel1M 290007 GCACGCACACATACCCACATGCACA-ACACACACATGTATGCACACATGC 290055 i i i v ii - iii ii ii (AC)n#Simple_ 443 ACACACACACACACACACACACACACACACACACACACACACACACACAC 492 chr6ptel1M 290056 CTAGATAGATGTGCTTGCTCACATGCCCACATGCACAGCCCTGA-ACACA 290104 vi v i v iiii vii v ii v ii - v vv - (AC)n#Simple_ 493 ACACACACACACACACACACACACACACACACACACA-CACACACACACA 541 chr6ptel1M 290105 CATGCACATATTCATACTTACACA-AAACACACATACATGCCCACACATG 290153 ii i iv i vi - v i ii v ii (AC)n#Simple_ 542 CACACACACACACACACACACACACACACACACACACACACACACACACA 591 chr6ptel1M 290154 GCCACATGCACA-ACCCGCACGCACATACA 290182 vv ii - v i i i (AC)n#Simple_ 592 CACACACACACACACACACACACACACACA 621 Matrix = Unknown Transitions / transversions = 2.44 (127/52) Gap_init rate = 0.05 (29 / 609), avg. gap size = 1.00 (29 / 29) 200 29.23 8.33 2.25 chr6ptel1M 290187 290270 (709730) C MIRc#SINE/MIR (48) 220 132 m_b278s601i49 11076 chr6ptel1M 290187 CACTTTCCCACAGACACTGCC--ATTTCATCCCCA-----GCCTGATAAG 290229 i -- v i ii -- v i -----i ivi i C MIRc#SINE/MIR 220 CGCTTTC--ACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAG 173 chr6ptel1M 290230 CAAGTCAAGGTAAATATTATTATCCCCAACTTAGAAACGAG 290270 vv v i i ii vi v i i C MIRc#SINE/MIR 172 GTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAG 132 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.78 CpG sites = 16, Kimura (unadjusted) = 38.88 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.05 (4 / 83), avg. gap size = 2.25 (9 / 4) 208 20.55 8.22 0.00 chr6ptel1M 290434 290506 (709494) MIR1_Amn#SINE/MIR 41 119 (111) m_b278s601i50 11077 chr6ptel1M 290434 GGACTCAGAGGTCCTGTGTTCAAACTGGGGCTCT----CTGGCCA-CTGT 290478 i ii v v ? ?iivv ---- ? ?- ? MIR1_Amn#SINE 41 GGACTCGGGAGACCTGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGN 90 chr6ptel1M 290479 GTGATGCTGGGCAAGCCTCCTGACC-CTC 290506 ivi i v i ? - MIR1_Amn#SINE 91 GTGACCTTGGGCAAGTCACTTNACCTCTC 119 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 25.06 CpG sites = 9, Kimura (unadjusted) = 27.11 Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.04 (3 / 72), avg. gap size = 2.00 (6 / 3) 215 22.50 0.00 0.00 chr6ptel1M 290878 290917 (709083) L2c_3end#LINE/L2 433 472 (6) m_b278s601i51 11078 chr6ptel1M 290878 CTGGCACATAGCGGGCATTTAACAAATGTTTCCTGACTGA 290917 ii ii i i vi v L2c_3end#LINE 433 CTGGCACATAGTAGGCGCTCAATAAATGTTTGTTGAATGA 472 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 24.56 CpG sites = 7, Kimura (unadjusted) = 28.18 Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 720 28.63 3.64 2.40 chr6ptel1M 290959 291205 (708795) MIRb#SINE/MIR 13 262 (6) m_b278s601i52 11079 chr6ptel1M 290959 GTGACCCAGTGGCTAGAGCACCGACTTTGGAGTCA---AGAGCCAAATTC 291005 iiv vv v i --- v iiii MIRb#SINE/MIR 13 GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTC 62 chr6ptel1M 291006 AAATGCACTCTCAGACACTCATGAGCTCCTGGATGCCTTT---CAAGTCA 291052 i v vvv v v i iv --- vi v i --- i MIRb#SINE/MIR 63 GAATCCCGGCTCTGCCACTTACTAGCT---GTGTGACCTTGGGCAAGTTA 109 chr6ptel1M 291053 CTTAACCTTTGACTG--CCTAAGTTTCCTCAACTGGAAAATGGGGTAAAA 291100 i -- -- v v v - v MIRb#SINE/MIR 110 CTTAACCTCT--CTGAGCCTCAGTTTCCTCATCTGTAAAATGGGG-ATAA 156 chr6ptel1M 291101 TAGCACTTATTTCTCAGAGTTAAGGTAAAGAGCAAGCAAGATGATATTTG 291150 ii i ii v i ivv i i vi iii i iiv MIRb#SINE/MIR 157 TAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCATG 206 chr6ptel1M 291151 GGAAGCACTAAG-ACTGCGCCTGGAACATAGTAGGTGCTATAAAAATGCT 291199 vi i v - v i v i i vv v v MIRb#SINE/MIR 207 TAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAAATGGT 256 chr6ptel1M 291200 TATTCT 291205 vii MIRb#SINE/MIR 257 AGCTCT 262 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.73 CpG sites = 37, Kimura (unadjusted) = 36.69 Transitions / transversions = 1.16 (37/32) Gap_init rate = 0.04 (10 / 246), avg. gap size = 1.50 (15 / 10) 237 26.07 5.26 3.09 chr6ptel1M 292102 292196 (707804) L2d_3end#LINE/L2 285 381 (135) m_b278s601i53 11080 chr6ptel1M 292102 GAATCCCTGCCTCACTTATTCTCCGAACTACACAATTAAGTGCTTGATGG 292151 ii iivv vv i v i i v ii i vi L2d_3end#LINE 285 GAACTCCTATAGCACTTATAGTCTGTACCACGCAATTTAGCACTTAATTA 334 chr6ptel1M 292152 TAAACTG----GT-TTGTTCTCTAGTTTCCTTATGTGTATGTTCAGTCTT 292196 v ---- - i vii i -- - L2d_3end#LINE 335 TATACTGTCTTGTATTGTTCTCTAATTGTTTCATGTG--TGTT-AGTCTT 381 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.35 CpG sites = 15, Kimura (unadjusted) = 33.02 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.05 (5 / 94), avg. gap size = 1.60 (8 / 5) 522 22.58 1.88 8.67 chr6ptel1M 292279 292438 (707562) C MIR1_Amn#SINE/MIR (80) 150 1 m_b278s601i55 11076 chr6ptel1M 292279 CTCATTTTACAGATGAGGAAACTGAGGCAAACAG-GGTTAAGTGACTTGT 292327 i ?v v - ? i C MIR1_Amn#SINE 150 CCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGC 101 chr6ptel1M 292328 TCAGGGTCACACAGCTAATGAGTGTGTAAGGCT-GGATTTGAGCTCAGGA 292376 i i ? ?iii? - i ii i- ? ? i i - C MIR1_Amn#SINE 100 CCAAGGTCACNCAGCNGGCNAGTG-GCAGAGCCGGGANTNGAACCCAGG- 53 chr6ptel1M 292377 AGATGAGTATTCCTGACTCTAGGCCCAGCGCTCTGTGCCCCATGGAGCCA 292426 --- -----i i v ivi i i i --- iviii C MIR1_Amn#SINE 52 ---T-----CTCCCGAGTCCCAGTCCAGTGCTCTAT---CCACTAGACCA 14 chr6ptel1M 292427 -ATTAGCTGCCTA 292438 - i iv v C MIR1_Amn#SINE 13 CACTGCCTCCCTA 1 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.82 CpG sites = 26, Kimura (unadjusted) = 29.99 Transitions / transversions = 3.71 (26/7) Gap_init rate = 0.10 (16 / 159), avg. gap size = 1.00 (16 / 16) 627 17.96 1.52 7.20 chr6ptel1M 292279 292410 (707590) C MIRc#SINE/MIR (120) 148 24 m_b278s601i54 11076 chr6ptel1M 292279 CTCATTTTACAGATGAGGAAACTGAGGCAAACAG-GGTTAAGTGACTTGT 292327 i vv v - i C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr6ptel1M 292328 TCAGGGTCACACAGCTAATGAGTGTGTAAGGCT-GGATTTGAGCTCAGGA 292376 i i i i - i ii i- i i i i -- C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTG-GCAGAGCCGGGACTCGAACCCAG-- 52 chr6ptel1M 292377 AGATGAGTATTCCTGACTCTAGGCCCAGCGCTCT 292410 ------ v i i i i C MIRc#SINE/MIR 51 ------GTCTTCCTGACTCCAAGTCCAGTGCTCT 24 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 19.23 CpG sites = 18, Kimura (unadjusted) = 21.35 Transitions / transversions = 4.50 (18/4) Gap_init rate = 0.08 (11 / 131), avg. gap size = 1.00 (11 / 11) 293 36.59 7.85 5.33 chr6ptel1M 292439 293024 (706976) C L3b_3end#LINE/CR1 (205) 1001 402 m_b278s601i57 11081 chr6ptel1M 292439 TTTCCCTCCTATGGAACCAAAAATGGTTTAT-CTGCAAT----ATCTTTT 292483 i i iv vv v - vvi i - i ----ii iv C L3b_3end#LINE 1001 TCTTCCTTATATCTAACCTAAA-TCCCTCATGCTGCAGTTTAAGCCCATT 953 chr6ptel1M 292484 TGTTCTTAATTTTGCCCTC--TAGAGCCAAGCAGAACAATTCAAC-CTAT 292530 vi i- i i -- i -- v v ii viv - ii C L3b_3end#LINE 952 TCCTCTTG-TTCTGTCCTCAGTGGAG--ATGGAGAACAGCTGGTCACCGT 906 chr6ptel1M 292531 GTTGCATTTGATCCCCTTTTACATATTTAAAGTCAGCAATCGTGTTTCTC 292580 vi vi iv i vv i i i i i v ? iv iiv i? i C L3b_3end#LINE 905 CCTCTACGTAATAACCCTTCATATACTTGAAGACNGTTATTAAGTCNCCC 856 chr6ptel1M 292581 A--AGTCTTTTCTTCTACAGGGTAAATATTGCC-GTTTTTTT--CCAGTG 292625 v-- i i v v i v v - ii -- ---- C L3b_3end#LINE 855 CTCAGCCTTCTCTTCTCCAGGCTGAATAATCCCAGTTCCTTTAACC---- 810 chr6ptel1M 292626 ATTCTCCTATGGCACCCCTCATTCCTCTCACTGCCCA-----ATGACCCT 292670 - ii ii i vv v iv i vv i vi ivi -----i vi i C L3b_3end#LINE 809 -TTTCCTCATAGGTCCCATTTTCCAGCCCTTTAATCATTTTTGTTGCTCT 761 chr6ptel1M 292671 CCTCTGGACAGTTTCTCAGAATTCT-----TCCC----AAAATGTAGCAA 292711 i -- i vi ? ----- ---- ? i ?iv C L3b_3end#LINE 760 CCTCTGAAC--TCTCTCCAANTTCTCCACGTCCCTTTTAAANTGTGGNGC 713 chr6ptel1M 292712 CCAGGATTAAGGGAGGAACCCTAGTTGTGCTTTTAATAGGGGGCAGTACA 292761 i i i iv vi v i i ? ? vii v vi v viv v C L3b_3end#LINE 712 CCAGAACTGAACGCAGTACTCCAGNTGNGGCCTGACCAGCGCAGAGTAGA 663 chr6ptel1M 292762 GATGAAATCTCACCATTTTTATT-TG--GACAATTGACATCTGTTAATGG 292808 vv i ??v viii i? - -- i i ?-- v v C L3b_3end#LINE 662 GCGGGANNATCACCTCCCTTGNTCTGTCGGCGATN--CTTCTGTTAATGC 615 chr6ptel1M 292809 AAGTCACAATCACAGGGGC--CTCTGG--GCTATCTCAGCA--GC----- 292847 ivi vi i vvi --i i -- iiiv - -- ----- C L3b_3end#LINE 614 AGCCCAAGATCGCATTAGCTTTTTTGGCAGCCGCGTC-GCACTGCTGACT 566 chr6ptel1M 292848 CATCCTGAATGCAAAGCTCTCCAAAACACACCGATCTTTTCTTTACACAC 292897 vi iiviivi iivv i v v v i -- i ii? C L3b_3end#LINE 565 CATATTGAGCTTGCGGTCAACTAAAACCCCCAGGTCTTT--TTCACATGN 518 chr6ptel1M 292898 ACTTTTGTCTAATTACTCATCACCTCAATCAGGAATACCCCAATCTGGAT 292947 i vi - ------ii i v -- ------- vi v i C L3b_3end#LINE 517 GCTGCTG-CTAA------GCCGCGTC--TC-------CCCCATCCTGTAC 484 chr6ptel1M 292948 TCTTATGGTTGA--GTCTGAA-GCAAATGTAGGGCTCT-TTTTTCTCCCT 292993 viii i ?--v i -v i i i i -iv v C L3b_3end#LINE 483 TCGCGCGATTGNTTTTTTGAACCCAAGTGCAGGACTTTACGTTTATCCCT 434 chr6ptel1M 292994 AGAAAGTTTTGCCTT-CTAGATTCAACACATC 293024 ivvi i iii -i i ? ii v i? C L3b_3end#LINE 433 GTTGAATTTCATCTTGTTGGNTTCGGCCCGNC 402 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 50.13 CpG sites = 126, Kimura (unadjusted) = 55.54 Transitions / transversions = 1.64 (126/77) Gap_init rate = 0.09 (52 / 585), avg. gap size = 1.50 (78 / 52) 818 34.96 4.61 0.00 chr6ptel1M 292439 292807 (707193) C L3#LINE/CR1 (200) 3899 3514 m_b278s601i56 11081 chr6ptel1M 292439 TTTCCCTCCTATGGAACCAAAAATGGTTTATCTGCAATATCTTT---TTG 292485 i i iv v i i viv ii vi i iv ivi--- C L3#LINE/CR1 3899 TCTTCCTTATATTGAGCCGAAATCTGCCTCCCTGTAACTTCCACCCATTG 3850 chr6ptel1M 292486 TTCTTAATTTTGCCCTCTAGAGCCAAGCAGAACAATTC-AACCTATGTTG 292534 v i i i i vi i v - i iv v v C L3#LINE/CR1 3849 GTCCTAGTTCTGCCCTCTGGAGCCACACAGAATAAGTCTAATCCCTCTTC 3800 chr6ptel1M 292535 CATTTGATCCCCTTTTACATATTTAAAGTCAGCAATCGTGTTTC-TC-AA 292582 iv ivv i i v i v v i i - - C L3#LINE/CR1 3799 CACATGACAGCCCTTCAAATATTTGAAGACAGCTATCATGTCTCCTCTAA 3750 chr6ptel1M 292583 GTCTTTTCTTCTACAGGGTAAATATTGCCGTTTTTTTCCAGTGATTCTCC 292632 i v v i iv iv ii v vi v i v C L3#LINE/CR1 3749 GTCTTCTCTTCTCCAGGCTAAACATCCCCAGTTCCTTCAACCGTTCCTCA 3700 chr6ptel1M 292633 TATGGCAC--CCCTCATTCCTCTCACTG-CCCAATGACCCTCCTCTGGA- 292678 i i--iiii vv ii ii- iii vi i - C L3#LINE/CR1 3699 TATGACATGGTTTCCAGACCCTTCACCATCCTGGTCGCTCTCCTCTGGAC 3650 chr6ptel1M 292679 ------CAGTTTCTCAGAATTCTTCCCAAAATGTAGCAACCAGGATTAAG 292722 ------ v ivi i i ii i iv i i i i C L3#LINE/CR1 3649 GCGCTCCAGTTTGTCAATGTCCCTCTTAAAATGTGGCGCCCAGAACTGAA 3600 chr6ptel1M 292723 GGAGGAACCCTAGTTGTGCTTTTAATAGGGGGCAGTACAGATGAAATCTC 292772 v viiv i i v v i v vi v viv vv i v v i C L3#LINE/CR1 3599 CGCAATACTCCAGATGTGGTCTGACCAGCGCAGAGTACAGCGGGACTATT 3550 chr6ptel1M 292773 ACCATTTTT-ATTTGGACAATTGACATCTGTTAATG 292807 viii -? i v vv v i C L3#LINE/CR1 3549 ACCTCCCTTGNTCTGGACACTATACTTCTATTAATG 3514 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 47.15 CpG sites = 77, Kimura (unadjusted) = 49.33 Transitions / transversions = 1.48 (77/52) Gap_init rate = 0.02 (9 / 368), avg. gap size = 1.89 (17 / 9) 203 28.68 6.56 5.69 chr6ptel1M 293035 293156 (706844) L2d_3end#LINE/L2 391 513 (3) m_b278s601i58 11082 chr6ptel1M 293035 ATTAGACTGT--GTTACTTGAGACGAGAGATGCTCTCTTGCCTTGTATTT 293082 i i -- i v ivv i ivv v iivi ? - L2d_3end#LINE 391 ACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACTNT-TTT 439 chr6ptel1M 293083 GTAGACGTCCATCCCTATGGC----AGCGCGGGTCTG-GTCCATTATAGG 293127 ? --- --- i ii ---- i i vv - iv vi L2d_3end#LINE 440 NT---CGT---TCCCCACAGCGCCTAGCACAGTGCTGAGCACATAGTAGG 483 chr6ptel1M 293128 TACG-AGTAAATATTTGTTGATTGATTAAT 293156 ii v- i i i L2d_3end#LINE 484 CGCTCAATAAATACTTGTTGATTGATTGAT 513 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.79 CpG sites = 21, Kimura (unadjusted) = 38.46 Transitions / transversions = 1.75 (21/12) Gap_init rate = 0.09 (11 / 121), avg. gap size = 1.36 (15 / 11) 289 35.85 6.42 4.04 chr6ptel1M 293590 293807 (706193) C L2d2_3end#LINE/L2 (312) 243 21 m_b278s601i59 11083 chr6ptel1M 293590 GGCTGTTATGGAGTATGTGGGAAACTGACTTGAAGTGAGTTTGAAAATAT 293639 - i i v v ? ------i iv i ii vi iv C L2d2_3end#LIN 243 GGCT-TCACGGAGGAGGTGGNA------TTTGAGCTGGGCCTTGAAGGAT 201 chr6ptel1M 293640 GGGTAGGAATTCACCAAGTAAAAGGGATGACTGAGAACATTCTGGGCATG 293689 v vivi i ii ii v ivvi ii ii iv C L2d2_3end#LIN 200 GGGTAGGATTTGGATAGGTGGAGAGGAAGGGGAAGGGCATTCCAGGCGGG 151 chr6ptel1M 293690 GGTATAGGATT--------GCATAGAGGACTGGGAAAACACACAATATGT 293731 v vv vv -------- ii --i ?i i viiii C L2d2_3end#LIN 150 GGGAACGGCGTGAGCAAAGGCGCAGAGG--CGGGAANGCGCAAGGCGTGT 103 chr6ptel1M 293732 TTAGGGAACAGAAAGTAG----GGTTGGCTGAAGCATTAAACTTGT-CAG 293776 ii i vi ---- v i ivviiii i -? C L2d2_3end#LIN 102 TCGGGGGACAGTGAGTAGACCAGTTTGGCTGGAGCGGAGGGTTCGTGNAG 53 chr6ptel1M 293777 AGAGATA-TATGAAAGAAGGCTATAAAGTTAG 293807 i ii - iv i v iv v? C L2d2_3end#LIN 52 GGGAATAGTGGGAGATAAGGCTGGAAAGGNAG 21 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 44.42 CpG sites = 49, Kimura (unadjusted) = 53.74 Transitions / transversions = 1.88 (49/26) Gap_init rate = 0.06 (13 / 217), avg. gap size = 1.77 (23 / 13) 17 3.96 3.85 0.00 chr6ptel1M 293834 293859 (706141) (CAA)n#Simple_repeat 1 27 (0) m_b278s252i16 11084 chr6ptel1M 293834 CAA-AACAACAACAACAACAACAAGAA 293859 - v (CAA)n#Simple 1 CAACAACAACAACAACAACAACAACAA 27 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.04 (1 / 25), avg. gap size = 1.00 (1 / 1) 41 21.79 0.00 2.08 chr6ptel1M 294587 294684 (705316) (AGGA)n#Simple_repeat 1 96 (0) m_b278s252i17 11085 chr6ptel1M 294587 AGGAATGGAAAGAAGGAGAAAAAGAGAGAAGGAAGGAGGAAATGAGGGAG 294636 - i iii i ii i i v i i (AGGA)n#Simpl 1 AGGAA-GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 49 chr6ptel1M 294637 GGAAGGAAGAAAGGAGGGAAAGAAGGAAGAAATGAAGGAAGGGAAGGA 294684 i i i i v - (AGGA)n#Simpl 50 GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA-GGAAGGA 96 Matrix = Unknown Transitions / transversions = 7.50 (15/2) Gap_init rate = 0.02 (2 / 97), avg. gap size = 1.00 (2 / 2) 509 21.37 14.73 2.07 chr6ptel1M 295352 295480 (704520) C MIRc#SINE/MIR (120) 148 4 m_b278s601i60 11086 chr6ptel1M 295352 CTCATTTTACAATTGAGGAAAGTGAGGC-----------AAGTGTCTTGC 295390 i iv v ----------- v C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr6ptel1M 295391 CCAGGGTTGCACAACTACTAAGAGTCTGAGGCTGAATTTGAATTCAGATC 295440 i ii i v v v v v v i i i ii i C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTC 49 chr6ptel1M 295441 TTCCTGACTCCAGATCCA--------TTTACTGAATCACATAGCTGCC 295480 ii -------- ii v i --- C MIRc#SINE/MIR 48 TTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACA---CTGCC 4 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 24.71 CpG sites = 17, Kimura (unadjusted) = 25.80 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.04 (5 / 128), avg. gap size = 4.40 (22 / 5) 353 30.70 5.26 0.00 chr6ptel1M 295826 295939 (704061) C L2d_3end#LINE/L2 (6) 510 391 m_b278s601i61 11087 chr6ptel1M 295826 AATTAACCAAAAAGTATT-ATCAAGTGTTTGCTCTGTGTCTGGCACTGGG 295874 i i v - ii i ii i v iiii v C L2d_3end#LINE 510 AATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTGTG 461 chr6ptel1M 295875 CTAAATGTTG-GGGAAAT--CAAGAAAG-GCAACA-ACCGTTCCTACCCT 295919 iii i - i i--? i ? -ii v - iv i i C L2d_3end#LINE 460 CTAGGCGCTGTGGGGAACGANAAAANAGTATAAGACATGGTCCCTGCCCT 411 chr6ptel1M 295920 CAAAAAGCTTATACTTTAAT 295939 ii i v i i C L2d_3end#LINE 410 CAAGGAGCTTACAATCTAGT 391 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.87 CpG sites = 29, Kimura (unadjusted) = 45.20 Transitions / transversions = 4.83 (29/6) Gap_init rate = 0.04 (5 / 113), avg. gap size = 1.20 (6 / 5) 218 9.68 0.00 0.00 chr6ptel1M 296070 296100 (703900) MIR3#SINE/MIR 164 194 (14) m_b278s601i62 11088 chr6ptel1M 296070 CTCTGAGGTCCCTTCAAGCTCTGACATTTTA 296100 i v i MIR3#SINE/MIR 164 CTCTAAGGTCCCTTCCAGCTCTGACATTCTA 194 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 10.46 CpG sites = 2, Kimura (unadjusted) = 10.46 Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 384 25.96 2.69 13.02 chr6ptel1M 297092 297277 (702723) MIR#SINE/MIR 15 183 (79) m_b279s601i2 11089 chr6ptel1M 297092 TGGTTGAACACATCGAGGTCTTGTAGGAACAAGAATGCCAAGGTTGGAAT 297141 i ivi - i v ---- i v v vi v MIR#SINE/MIR 15 TGGTTAAGAGCA-CGGGCTCT----GGAGCCAGACTGCCTGGGTTCGAAT 59 chr6ptel1M 297142 TAGGAGACCAGGGTTAGATTCTAGACACTTATTTGCTTTATGACCTTTTC 297191 ------- v ------i - v i v v i vvv MIR#SINE/MIR 60 -------CCCGG------CTCT-GCCACTTACTAGCTGTGTGACCTTGGG 95 chr6ptel1M 297192 TAAGCTCCTTTACCTCT--GTGCTGCAATTTTCCTATCCTTAAAATGGAG 297239 i i v v -- iv i i ii iv i MIR#SINE/MIR 96 CAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGG 145 chr6ptel1M 297240 ATGAT--TGG-ACTTCCTTCTAGATAGGGTTTTTGTTAGGA 297277 i -- i - i v i --- v v MIR#SINE/MIR 146 ATAATAATAGTACCTACCTC---ATAGGGTTGTTGTGAGGA 183 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.72 CpG sites = 22, Kimura (unadjusted) = 31.72 Transitions / transversions = 1.10 (22/20) Gap_init rate = 0.14 (25 / 185), avg. gap size = 1.08 (27 / 25) 333 28.49 4.94 8.97 chr6ptel1M 297137 297298 (702702) MIR1_Amn#SINE/MIR 41 196 (34) m_b279s601i3 11089 chr6ptel1M 297137 GGAATTAGGAGACCAGGGTTAGATTCTAGAC------ACTTATTTGCTTT 297180 v ii v v? ? iv i ------ ?iii? v? MIR1_Amn#SINE 41 GGACTCGGGAGACCTGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGN 90 chr6ptel1M 297181 ATGACCTTTTCTAAGCTCCTTTACCTCT--GTGCTGCAATTTTCCTATCC 297228 i vvvi iiv ? -- ? iv i i ii i MIR1_Amn#SINE 91 GTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCT 140 chr6ptel1M 297229 TTAAAATGGAGATGATTGGACTTCCTTCTAGATAGGGTTTTTGTTAGGAA 297278 v i i viv vv i ----------i ---- MIR1_Amn#SINE 141 GTAAAATGGGGATAATGATACTGACCTC----------CTTTGT----AA 176 chr6ptel1M 297279 AGTACTTTGAAAACTTCTAA 297298 i i v v i MIR1_Amn#SINE 177 AGTGCTTTGAGATCTACTGA 196 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.80 CpG sites = 25, Kimura (unadjusted) = 39.13 Transitions / transversions = 1.47 (25/17) Gap_init rate = 0.10 (16 / 161), avg. gap size = 1.38 (22 / 16) 29 0.00 0.00 0.00 chr6ptel1M 297473 297497 (702503) (CT)n#Simple_repeat 1 25 (0) c_b279s251i0 11090 chr6ptel1M 297473 CTCTCTCTCTCTCTCTCTCTCTCTC 297497 (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTC 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 36 0.00 0.00 0.00 chr6ptel1M 297501 297531 (702469) (AC)n#Simple_repeat 1 31 (0) c_b279s251i1 11091 chr6ptel1M 297501 ACACACACACACACACACACACACACACACA 297531 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACA 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 201 35.16 5.49 0.00 chr6ptel1M 297718 297808 (702192) C L2d2_3end#LINE/L2 (49) 506 411 m_b279s601i4 11092 chr6ptel1M 297718 CTATGCTAGGAATTGGAAGAAGTACA---AAGTACAAGTCAT-ATACAGG 297763 i vii vii iii --- i v -i v vv C L2d2_3end#LIN 506 CTGTGCTAGGCGCTGTGGGGGATACAAAGAAGTATAAGACATGGTCCCTG 457 chr6ptel1M 297764 CTACCAAGGATCTTGCCATCT-GATAGAGGGATAAAGTACAAATAC 297808 ivi v i v - v i i i i iii i i C L2d2_3end#LIN 456 CCCTCAAGGAGCTTACAATCTAGTTGGGGAGACAAGACATAAACAC 411 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 48.83 CpG sites = 22, Kimura (unadjusted) = 51.20 Transitions / transversions = 2.20 (22/10) Gap_init rate = 0.03 (3 / 90), avg. gap size = 1.67 (5 / 3) 223 36.30 12.05 2.42 chr6ptel1M 298220 298634 (701366) L2#LINE/L2 1927 2380 (702) m_b279s601i5 11093 chr6ptel1M 298220 CCTATTCTCTTCT--ACTTCTTACAGTTGAGCTTCAGGGCCCATCACTCT 298267 i ii -- iivi v i iii iv vv i i L2#LINE/L2 1927 CCCATTCTCTCTTGAACCCACTCCAATCAGGCTTTCGTCCCCACCACTCC 1976 chr6ptel1M 298268 GATGAATCTGTTCTCTAAAAGATTATTAGTGATGTTATAATTAATAAGTC 298317 ivi v i ivvv i i ii i iv ivvvi iv i L2#LINE/L2 1977 ACCGAAACTGCTCTTGTCAAGGTCACCAATGACCTCCACGTTGCTAAATC 2026 chr6ptel1M 298318 TAATAACCT-TTATT--TTCTCATCCTCCTTGGTCATCCTGTAGCTTTAA 298364 i iii v- v i-- i i v ii v?i v i v vi L2#LINE/L2 2027 CAATGGTCAATTCTCAGTCCTCATCTTACTTGACCTNTCAGCAGCATTTG 2076 chr6ptel1M 298365 AAACATGTGA---------CCTTCTT----------CCCCAC-------- 298387 v vv --------- ---------- ii -------- L2#LINE/L2 2077 ACACAGTTGATCACTCCCTCCTTCTTGAAACACTTTCTTCACTTGGCTTC 2126 chr6ptel1M 298388 CAGAATAT---GCTCT-------TTCTTTTTGGCTCCCTGAT-GCTTCTA 298426 i i i---i ------- i ii iv v ii- i - L2#LINE/L2 2127 CAGGACACCACACTCTCCTGGTTTTCCTCCTACCTCACTGGCCGCTCCT- 2175 chr6ptel1M 298427 TCTC-TTCTTACATTCTG--TCATCACCCATCTCCC-ATTCCCTAAATGT 298472 -v iviv v -- v - i -ivi i ? i L2#LINE/L2 2176 TCTCAGTCTCCTTTGCTGGTTCCTC-CTCATCTCCCCGACCTCTNAACGT 2224 chr6ptel1M 298473 GGGGGTTTCCCAAGGCTCTATCTCAGGCTCTCTTATTTCTTTCCCATGGA 298522 v i vi i vi iiv vi --i ii i vv L2#LINE/L2 2225 TGGAGTGCCCCAGGGCTCAGTCCTTGGACCTCTT--CTCTTCTCTATCTA 2272 chr6ptel1M 298523 AATCGTATCTGTTCCTT--TTAGTTCAGTTTTCA-TCTCTTGGGTTCAGT 298569 v i---- vv i ?-- v vi --- i - v v i iv L2#LINE/L2 2273 CAC----TCACTCCCTNGGTGATCTCA---TCCAGTCTCATGGCTTTAAA 2315 chr6ptel1M 298570 TACGATCTCAGCACAGATGTCACCTAAATTTACATATCAAAACCTAATAT 298619 v vviii v v v i i v v iv vi iv L2#LINE/L2 2316 TACCATCTATATGCTGATGACTCCCAAATTTATATCTCCAGCCCGGACCT 2365 chr6ptel1M 298620 CTCTCTAGAACTCTA 298634 i iv i L2#LINE/L2 2366 CTCCCCTGAACTCCA 2380 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 50.58 CpG sites = 87, Kimura (unadjusted) = 52.69 Transitions / transversions = 1.45 (87/60) Gap_init rate = 0.06 (25 / 414), avg. gap size = 2.44 (61 / 25) 375 29.55 13.48 3.06 chr6ptel1M 298759 298936 (701064) C L3#LINE/CR1 (7) 4092 3897 m_b279s601i6 11094 chr6ptel1M 298759 TCACAAAATCTCATTGCTGAGAAGGACTT--------ATCGGGTCCAATC 298800 i vv i ii i i -------- vi i C L3#LINE/CR1 4092 TCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCAACC 4043 chr6ptel1M 298801 TTTACATGAA---CAAGAGCCTGCTGAATTATACACCATCC-----AAAT 298842 ii- vv --- i ii i- ---- v v ----- i C L3#LINE/CR1 4042 TCC-CATCCAATGCAGGAATCC-CT----TCTACAACATCCCTGACAAGT 3999 chr6ptel1M 298843 AGTCACCCACCTCCTACTGGAA-GCCTCCAATGCAAGTGAACTCACTAC- 298890 i i v ii i v -i i vvi v i - C L3#LINE/CR1 3998 GGTCATCCAGCCTCTGCTTGAACACCTCCAGTGACGGGGAGCTCACTACC 3949 chr6ptel1M 298891 ------GACTTCCCATTTTACTTCTGAATAGTTCTAACTGTTAACAAGTT 298934 ------ i vv ii i i i i i i i iv C L3#LINE/CR1 3948 TCNCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGATTGTTAGAAAGTT 3899 chr6ptel1M 298935 TT 298936 i C L3#LINE/CR1 3898 CT 3897 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.99 CpG sites = 36, Kimura (unadjusted) = 40.03 Transitions / transversions = 2.40 (36/15) Gap_init rate = 0.07 (12 / 177), avg. gap size = 2.50 (30 / 12) 198 33.34 0.00 1.75 chr6ptel1M 299048 299105 (700895) L2d2_3end#LINE/L2 489 545 (10) m_b279s601i7 11095 chr6ptel1M 299048 CCACATTCTTCTAGCTTGATGCCTTACATATGGCAAATATTGAATAAATG 299097 v- vi viii i i ii i iiiii v i L2d2_3end#LIN 489 CCACAG-CGCCTAGCACAGTGCCTTGCACACAGTAGGCGCTCAATAAATA 537 chr6ptel1M 299098 TTTGTTGA 299105 L2d2_3end#LIN 538 TTTGTTGA 545 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 44.99 CpG sites = 15, Kimura (unadjusted) = 49.16 Transitions / transversions = 3.75 (15/4) Gap_init rate = 0.02 (1 / 57), avg. gap size = 1.00 (1 / 1) 193 31.30 7.79 10.97 chr6ptel1M 299283 299526 (700474) L2c_3end#LINE/L2 26 262 (216) m_b279s601i8 11093 chr6ptel1M 299283 TCTGTAGCCTC-TCTTCTTT-CTTTCATT-TAGCACACTAT---TCAGCC 299326 vi - i ii- ii v i- v v ---i L2c_3end#LINE 26 TCTCCAGCCTCATCTCCTCCACTCCCCTCCTCGCCCACTATGCTCCAGCC 75 chr6ptel1M 299327 AGATCTAATTTTTATGACATCCCCCAAACAGATCTTCTGTTTATT--TGA 299374 v iiv i ?i - - i vii v- v iv -- v L2c_3end#LINE 76 ACACTGAACTNCT-TG-CATTCCCCAAACACGCCG-CAGTTCTTTCCTGC 122 chr6ptel1M 299375 TTCAATGTCTTTGT--------TTCCCCTAGGCTGAAAATGTTCCTCTCT 299416 i vi? i i-------- iiv v i - i i i i L2c_3end#LINE 123 CTCCGNGCCTTTGCACATGCTGTTCCCTCTGCCTGGAA-TGCTCTTCCCC 171 chr6ptel1M 299417 TTCTCTGCTTCCT---TAATTCTCAGTCTTAAGCTATTGAAAAGCATTCT 299463 iiii v iv --- i ----------- i ------ i L2c_3end#LINE 172 CCTCCTTCCACCTGGCTAACTC-----------CTACT------CATCCT 204 chr6ptel1M 299464 GTTCTTCATGGAACAGCTCAGAGGCTACCTCCTTCATGAAGCCATCTCTG 299513 ----- v ?vv v ii i iv v i L2c_3end#LINE 205 -----TCAAGNCTCAGCTCAGATGTCACCTCCTCCGGGAAGCCTTCCCTG 249 chr6ptel1M 299514 ATCAATCAAATTT 299526 i vvi i?i L2c_3end#LINE 250 ACCCCCCAAGNCT 262 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 40.82 CpG sites = 44, Kimura (unadjusted) = 43.40 Transitions / transversions = 1.83 (44/24) Gap_init rate = 0.14 (33 / 243), avg. gap size = 1.36 (45 / 33) 255 32.88 4.98 12.23 chr6ptel1M 299320 299520 (700480) L2d2_3end#LINE/L2 70 257 (298) m_b279s601i9 11093 chr6ptel1M 299320 TTCAGCCAGATCTAATTTTTATGAC-ATCCCCCAAACAGATCTTCTGTTT 299368 i i - ii i vi- v -i i vii vi i? L2d2_3end#LIN 70 TCCAGCCAAA-CTGGTCTAC-TCACTGTCCCCCGAACACGCCTTGCGCNT 117 chr6ptel1M 299369 ATTTGATTCAATGTCTTTGTT--------TCCCCTAGGCTGAAAATGTTC 299410 viii vi vii i i -------- iv v i - ii L2d2_3end#LIN 118 TCCCGCCTCTGCGCCTTTGCTCACGCCGTTCCCCCCGCCTGGAA-TGCCC 166 chr6ptel1M 299411 CTCTCTTTCTCTGCTTC-CTTAATTCTCAGTCTTAAGCTATTGAAAAGCA 299459 i i i - - i - i -- iv i i --------------- L2d2_3end#LIN 167 TTCCCCTTC-CT-CTCCACCTA--TCCAAATCCTA--------------- 197 chr6ptel1M 299460 TTCTGTTCTTCATGGAACAGCTCAGAGGCTACCTCCTTCATGAAGCCATC 299509 -i ii i v vv i v? i i i v L2d2_3end#LIN 198 -CCCATCCTTCAAGGCCCAGCTCAAATNCCACCTCCTCCGTGAAGCCTTC 246 chr6ptel1M 299510 TCTGATCAATC 299520 i i v L2d2_3end#LIN 247 CCTGACCACTC 257 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 40.36 CpG sites = 42, Kimura (unadjusted) = 47.00 Transitions / transversions = 2.62 (42/16) Gap_init rate = 0.13 (26 / 200), avg. gap size = 1.27 (33 / 26) 19 26.05 2.70 2.70 chr6ptel1M 299533 299606 (700394) (TATA)n#Simple_repeat 1 74 (0) m_b279s252i0 11096 chr6ptel1M 299533 TATTTAT-TCTATATATGTATACATAT-TGGAAATACATACACTCATATA 299580 v - v i i - iv v i i - - (TATA)n#Simpl 1 TATATATATATATATATATATATATATATATATATATATATA-T-ATATA 48 chr6ptel1M 299581 CATATGTGTATACATGTATGTATATA 299606 i i i i i i (TATA)n#Simpl 49 TATATATATATATATATATATATATA 74 Matrix = Unknown Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.05 (4 / 73), avg. gap size = 1.00 (4 / 4) 515 23.76 4.73 6.16 chr6ptel1M 299618 299765 (700235) MIRc#SINE/MIR 3 148 (120) m_b279s601i10 11097 chr6ptel1M 299618 AGTCAG-GTGATATACTGGATAGA---CTAGTCCTGGGGTCAA-AAGATT 299662 v - i ii v v --- i v i i i- i- MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC- 51 chr6ptel1M 299663 CATCTAACTGAGTTCAAATCCAGCCTTAAGCATTTACTAGCTGTGTAACT 299712 ------- i i i v v iviv i i i MIRc#SINE/MIR 52 -------CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACC 94 chr6ptel1M 299713 CTAGGCATATCATTTAATCCTGTTTGA--CTCAGGTTCCTCATCTGTAAA 299760 i i vi i - v i -- v MIRc#SINE/MIR 95 TTGGGCAAGTCACTTAA-CCTCTCTGAGCCTCAGTTTCCTCATCTGTAAA 143 chr6ptel1M 299761 ATGAG 299765 i MIRc#SINE/MIR 144 ATGGG 148 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.43 CpG sites = 22, Kimura (unadjusted) = 29.49 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.09 (13 / 147), avg. gap size = 1.23 (16 / 13) 335 33.75 6.03 2.93 chr6ptel1M 299880 300111 (699889) C L2d2_3end#LINE/L2 (247) 308 70 m_b279s601i11 11092 chr6ptel1M 299880 AGACAAGACAAATAC-ATAGG-GTTCTGGGGGGATTGGAGAACACTAGCA 299927 --i ? i - - v i i iv-i v ?vvi C L2d2_3end#LIN 308 AGACAA--TAANTGCTATAGGAGTTCAGAGGAGGG-AGAGATCACTNCGG 262 chr6ptel1M 299928 GTTGGGGGAATTAGGAAAGACTTCATGTAACAGATGATGCTTGAGCCGAA 299977 i i vii i i i i v iv i i?ii i ii C L2d2_3end#LIN 261 GCTGGAGTGGTCAGGGAAGGCTTCACGGAGGAGGTGGNATTTGAGCTGGG 212 chr6ptel1M 299978 TTTTGATTAA-AGATGGAATTCTAAGAGGTGAAGACAAAGAGGGAGTGGA 300026 ii vvi -i i i i ivi v i vi i i v v C L2d2_3end#LIN 211 CCTTGAAGGATGGGTAGGATTTGGATAGGTGGAGAGGAAGGGGAAGGGCA 162 chr6ptel1M 300027 TTCT-GGCCCTGAGACAGGCA-GGGCAAAGCCACACAGGAGACAGAAAAT 300074 i- vvv i vv i- i v i --- i - ii ? C L2d2_3end#LIN 161 TTCCAGGCGGGGGGAACGGCGTGAGCAAAGGCGCA---GAGGC-GGGAAN 116 chr6ptel1M 300075 GTGAAAGA------TGAGGAATAG-GA--AGGTCATTTTGTCTGGA 300111 i v i------i i i i - -- ii v v C L2d2_3end#LIN 115 GCGCAAGGCGTGTTCGGGGGACAGTGAGTAGACCAGTTTGGCTGGA 70 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 44.78 CpG sites = 52, Kimura (unadjusted) = 49.40 Transitions / transversions = 2.17 (52/24) Gap_init rate = 0.06 (15 / 231), avg. gap size = 1.40 (21 / 15) 18 0.00 0.00 0.00 chr6ptel1M 300678 300697 (699303) (T)n#Simple_repeat 1 20 (0) m_b279s252i1 11098 chr6ptel1M 300678 TTTTTTTTTTTTTTTTTTTT 300697 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTT 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 14 13.88 6.06 0.00 chr6ptel1M 300745 300777 (699223) (TGT)n#Simple_repeat 1 35 (0) m_b279s252i2 11099 chr6ptel1M 300745 TGTT-TTGTTGTTATTGTTGTT-TTACTATTGTTG 300777 - i - ii i (TGT)n#Simple 1 TGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTG 35 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.06 (2 / 32), avg. gap size = 1.00 (2 / 2) 207 23.53 7.84 0.00 chr6ptel1M 300886 300936 (699064) C MIRc#SINE/MIR (158) 110 56 m_b279s601i12 11100 chr6ptel1M 300886 TAAGTGACTTGGCCAAAACCATA----TTGAAAATGTCAGAGGTGGGACT 300931 v iii i ---- v v i v vi C MIRc#SINE/MIR 110 TAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACT 61 chr6ptel1M 300932 TGAAC 300936 i C MIRc#SINE/MIR 60 CGAAC 56 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 23.43 CpG sites = 7, Kimura (unadjusted) = 28.76 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.02 (1 / 50), avg. gap size = 4.00 (4 / 1) 589 21.86 6.90 5.34 chr6ptel1M 300990 301192 (698808) MIRc#SINE/MIR 4 209 (59) m_b279s601i13 11101 chr6ptel1M 300990 GGCAAGTGTGAGAATAGTAGAGAGAACTCTGC-CTTCGAGTCAG-AAGAC 301037 - - vii i i i v v- v - MIRc#SINE/MIR 4 GGCA-GTGTG-GTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr6ptel1M 301038 CTGGATTCGAATCCAGA-TCTTCGAGCTGTAACTATCC-TGTGATTT--A 301083 i i v i- v v vi --- v i- ii --i MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTT---ACTAGCTGTGTGACCTTGG 98 chr6ptel1M 301084 ACAAGTCATT--ATGTCTC--ATCCCGAGTTTGACATGGAGCATTTGGTA 301129 i i -- iv -- v iv -- v ---- i vv MIRc#SINE/MIR 99 GCAAGTCACTTAACCTCTCTGAGCCTCAGTTT--CCT----CATCTGTAA 142 chr6ptel1M 301130 AATGG----AATAACACCTGCCCTGCCTTCCTCACAGGGATATTGTGCAA 301175 ---- i v v i vii MIRc#SINE/MIR 143 AATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGG 192 chr6ptel1M 301176 ATCAACTGAGATAATAT 301192 v i MIRc#SINE/MIR 193 ATCAAATGAGATAATGT 209 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 26.18 CpG sites = 23, Kimura (unadjusted) = 26.18 Transitions / transversions = 1.21 (23/19) Gap_init rate = 0.09 (19 / 202), avg. gap size = 1.32 (25 / 19) 62 17.69 2.82 5.20 chr6ptel1M 301338 301514 (698486) (AGGA)n#Simple_repeat 1 173 (0) m_b279s252i3 11102 chr6ptel1M 301338 AGGAAGG-AGGGAGGCAGAGACAGGGAGAGATGGAAGGAAGGAAGGGAGG 301386 - i v - - i - v i (AGGA)n#Simpl 1 AGGAAGGAAGGAAGGAAG-GA-AGGAAG-GAAGGAAGGAAGGAAGGAAGG 47 chr6ptel1M 301387 AAGGAAAGAAGGACGAGATGGAAGGAAGGAAGGAAAGAAGGAGGGAAGGG 301436 i v - v i i - (AGGA)n#Simpl 48 AAGGAAGGAAGGAAG-GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA-GG 95 chr6ptel1M 301437 AGAGCAGAGGAA--AAGAGAAGAGAAGGGAAGATTTAGAGAAGG-AGGAA 301483 - v - -- - - i i vvv ii - (AGGA)n#Simpl 96 A-AGGA-AGGAAGGAAG-GAAG-GAAGGAAGGAAGGAAGGAAGGAAGGAA 141 chr6ptel1M 301484 GGAGGGACAGAGGGAAGGAA-AAAGGGAGCAA 301514 i vi i -i i v (AGGA)n#Simpl 142 GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 173 Matrix = Unknown Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.07 (13 / 176), avg. gap size = 1.08 (14 / 13) 240 30.43 1.45 0.00 chr6ptel1M 301882 301950 (698050) MIR3#SINE/MIR 85 154 (54) m_b279s601i14 11103 chr6ptel1M 301882 TGTGACTTTGGAAGAGTCCTTTC-CCTCACTTGCCTTCAGTTTTCTCACA 301930 i ivi vi - v v v i i iv MIR3#SINE/MIR 85 TGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATC 134 chr6ptel1M 301931 GGGAAAACAAAGGGCCTGAA 301950 v v ii i vi i MIR3#SINE/MIR 135 TGTAAAATGAGGGGGTTGGA 154 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 40.09 CpG sites = 12, Kimura (unadjusted) = 40.09 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.01 (1 / 68), avg. gap size = 1.00 (1 / 1) 325 35.00 8.06 3.87 chr6ptel1M 302347 302768 (697232) L2b_3end#LINE/L2 10 448 (18) m_b279s601i15 11104 chr6ptel1M 302347 CTGGCCCTTCCCATCTTTCCA-----ATTTTCTTCCACCCTACTCCTCCC 302391 iv i- i i i----- i i v i v i i v i L2b_3end#LINE 10 CTGGCCCCGCT-ACCTCTCCGGCCTCATCTCCTACCACTCTCCCCTTGCT 58 chr6ptel1M 302392 CAAATTGTCTTCAGAT---CTGGACCACTGG-TGGTGCTGGCACAC---- 302433 vvi - i vi--- v iv v - v v v v ---- L2b_3end#LINE 59 CACTCTG-CTCCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACACGCCA 107 chr6ptel1M 302434 TGCTGACTC-----TTAGCATTTTGTTGTCTA-TGTTCCA-CTGA-TGAA 302475 ? v? ----- i viii vviii? i- v- v- i L2b_3end#LINE 108 NGCTCNCTCCCGCCTCAGGGCCTTTGCACNTGCTGTTCCCTCTGCCTGGA 157 chr6ptel1M 302476 ATCTTTCCTCCCCGCCCCCCC-CCTTGCTACCTCCTGATT-TCCTTCACT 302523 - vii i i i ii - v i v iv i- v- L2b_3end#LINE 158 A-CGCCCTTCCCCACCTCTTCGCCTGGCCAACTCCTACTCATCCTTCAG- 205 chr6ptel1M 302524 TGTTTCAGTCCAGTGGAAAAATCACTTTCTACAAGACACCTTTCCCAGTT 302573 - i ii ----- vi i i v ii vi i i --- v L2b_3end#LINE 206 -GTCTCAGCTCA-----AATGTCACCTCCTCCGGGAAGCCCTCCC---TG 246 chr6ptel1M 302574 ATCCTTC---CC---TCTGGAACTCCCCCCAAAGTGCTCC-AGATATCTC 302616 i ii --- --- v vi i i i vii iv i - viv vi L2b_3end#LINE 247 ACCCCCCAGGCCGGGTCAGGCGCCCTCCTCTGGGCCCCCCCAGTCCTACC 296 chr6ptel1M 302617 TTGTATACCCATGGTTATC--TGTATG-TTAT-TCTCCACTCCACCCCCA 302662 i i-i i vv ?-- v - i- v ii- i- L2b_3end#LINE 297 CTGC-CACTCTGGGTTATNATTGTCTGNTTACATGTCTG-TCT-CCCCCA 343 chr6ptel1M 302663 TGTGACTCTTAGTTCCTTGACAACAGAGACACAATTCTTTTGGGATTATT 302712 ivv v v i v vii i - i?v v ivv v i ii L2b_3end#LINE 344 CTAGACTGTGAGCTCCGTGAGGGCAGGGAC-CGNGTCTGTCTTGTTCACC 392 chr6ptel1M 302713 TTCATATCCCCAGGACTTAGTATAGAACCTGGCACACAGAAGGTGCCTAA 302762 viii vi i i i ?i v i ii i L2b_3end#LINE 393 GCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAG 442 chr6ptel1M 302763 TAAATA 302768 L2b_3end#LINE 443 TAAATA 448 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 46.76 CpG sites = 88, Kimura (unadjusted) = 50.84 Transitions / transversions = 1.63 (88/54) Gap_init rate = 0.08 (33 / 421), avg. gap size = 1.55 (51 / 33) 328 33.62 0.00 2.99 chr6ptel1M 302631 302768 (697232) L2a_3end#LINE/L2 366 499 (18) m_b279s601i16 11104 chr6ptel1M 302631 TTATCTGTATGTTATTCTCCACTCCACCCCCATGTGACTCTTAGTTCCTT 302680 i --- v ii- iv ivv v v v i v L2a_3end#LINE 366 TTATTTGT---TTATTGTCTG-TCTCCCCCCACTAGAATGTAAGCTCCAT 411 chr6ptel1M 302681 GACAACAGAGACACAATTCTTTTGGGATTATTTTCATATCCCCAGGACTT 302730 vii i vivvv v vv v i i viii vi i L2a_3end#LINE 412 GAGGGCAGGGACTTTTGTCTGTTTTGTTCACTGCTGTATCCCCAGCGCCT 461 chr6ptel1M 302731 AGTATAGAACCTGGCACACAGAAGGTGCCTAATAAATA 302768 v i vi i v i ii L2a_3end#LINE 462 AGAACAGTGCCTGGCACATAGTAGGCGCTCAATAAATA 499 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 42.70 CpG sites = 23, Kimura (unadjusted) = 45.36 Transitions / transversions = 1.05 (23/22) Gap_init rate = 0.03 (4 / 137), avg. gap size = 1.00 (4 / 4) 261 37.07 9.94 1.14 chr6ptel1M 302776 302936 (697064) C MIRc#SINE/MIR (75) 193 19 m_b279s601i17 11105 chr6ptel1M 302776 TCTTTATAGCAGTTCTATGAGAAGAGTAATGT--GTAATGGTTAGCCATG 302823 i i i i iii i ivii i iv i-- - vi v vii C MIRc#SINE/MIR 193 TCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTA-TTATTATCCCCA 145 chr6ptel1M 302824 TTTTACAGATAATG---------CTTAGAGG----AAGTGCCTCAGCAGA 302860 i v --------- i i---- v iiv vi C MIRc#SINE/MIR 144 TTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAA 95 chr6ptel1M 302861 GGTCATACATTCAGCTGCTGTTAGAGTTGAAACTGGAATCCAGATCTTTG 302910 i vii iviv vi ii ii v i i iv C MIRc#SINE/MIR 94 GGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCC 45 chr6ptel1M 302911 T-ACTCAGGAGTTCAGAACCCGGTCCA 302936 - -vi i vi i vv C MIRc#SINE/MIR 44 TGACTC-CAAGTCCAGTGCTCTTTCCA 19 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 54.08 CpG sites = 40, Kimura (unadjusted) = 55.56 Transitions / transversions = 2.11 (40/19) Gap_init rate = 0.04 (6 / 160), avg. gap size = 3.00 (18 / 6) 226 30.46 16.67 2.72 chr6ptel1M 303051 303212 (696788) C L3#LINE/CR1 (4) 4095 3912 m_b279s601i18 11106 chr6ptel1M 303051 GAATCACAGCAGGTGAGAGTGAGAA-GGAGCTCAGAGG-CATCCAGTTTA 303098 v vv v vi - v i - i ii C L3#LINE/CR1 4095 GAATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCA 4046 chr6ptel1M 303099 ACTT-------GAGGGGGACCAAGAATACCCTGGAAGTGATCCCCAGCAA 303141 i -------i v ----- i v i vv vivv iii C L3#LINE/CR1 4045 ACCTCCCATCCAATG-----CAGGAATCCCTTCTACAACATCCCTGACAA 4001 chr6ptel1M 303142 AGGGTCA-----CCTTT----------CTC---TGAGAGGACACCAACTT 303173 iv ----- i ---------- --- vi ivi iv v C L3#LINE/CR1 4000 GTGGTCATCCAGCCTCTGCTTGAACACCTCCAGTGACGGGGAGCTCACTA 3951 chr6ptel1M 303174 CTTCCTGAGGCAGATCCCTCCATTTGTAGACAGATTTAA 303212 i ?i vi vi v i v i i C L3#LINE/CR1 3950 CCTCNCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGA 3912 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.29 CpG sites = 26, Kimura (unadjusted) = 40.44 Transitions / transversions = 1.18 (26/22) Gap_init rate = 0.07 (11 / 161), avg. gap size = 2.91 (32 / 11) 360 32.42 3.97 1.95 chr6ptel1M 303434 303584 (696416) C MIRc#SINE/MIR (110) 158 5 m_b279s601i19 11107 chr6ptel1M 303434 TGTTGTTATTCCCATTTGGCAGATGGGGAAGCTAAAGCTT---GAAGTTG 303480 i i i vi i i i i i--- i i C MIRc#SINE/MIR 158 TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTA 109 chr6ptel1M 303481 AGTGTCTTGGCC-ATGTCATATATTTGGTGAGTGTGGGTGCATCCTGTTC 303529 v v - v i i vi i i --- iiv v v vv C MIRc#SINE/MIR 108 AGTGACTTGCCCAAGGTCACACAGCTAGTAAGT---GGCAGAGCCGGGAC 62 chr6ptel1M 303530 T-GAATCTAGGGACCCCAG-CTCCCAGTTCAGTCTTTTTGCTATGATCCT 303577 - i i vvii v - v i vi i v i iviiv i C MIRc#SINE/MIR 61 TCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACC 12 chr6ptel1M 303578 ACACTGC 303584 C MIRc#SINE/MIR 11 ACACTGC 5 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 44.40 CpG sites = 30, Kimura (unadjusted) = 44.40 Transitions / transversions = 1.67 (30/18) Gap_init rate = 0.05 (7 / 150), avg. gap size = 1.29 (9 / 7) 210 33.41 1.05 5.49 chr6ptel1M 303751 303845 (696155) MIRc#SINE/MIR 123 213 (55) m_b279s601i20 11108 chr6ptel1M 303751 CTTAGTTTCCTCATTGCCATCTATGATGAGGTTA-CGCTGACTGTGGCAC 303799 i i---- v vi i v -iiv iv ivvii MIRc#SINE/MIR 123 CTCAGTTTCCTCATC----TGTAAAATGGGGATAATAATACCTGCCCTGC 168 chr6ptel1M 303800 TCACTTTGCAGGATTACTGTGATAATCAAATGAAAGCATAGTATGT 303845 ii i ii i ii vi i vv - MIRc#SINE/MIR 169 CTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAAT-GTATGT 213 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 46.83 CpG sites = 20, Kimura (unadjusted) = 46.83 Transitions / transversions = 2.00 (20/10) Gap_init rate = 0.06 (6 / 94), avg. gap size = 1.00 (6 / 6) 506 14.00 12.00 0.00 chr6ptel1M 303903 304002 (695998) MIR3#SINE/MIR 34 145 (63) m_b279s601i21 11109 chr6ptel1M 303903 TGGGAGTT-GGAGACCTGAGTTCCAACTCTGGC-CTG---------AGCT 303941 i- i i iii i - ---------? MIR3#SINE/MIR 34 TGGGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCT 83 chr6ptel1M 303942 GGGTGACCTTGGGCAAATCACTT-ACCACTGTTTGCCTCAGTTTCCTCAT 303990 v i - v v vv MIR3#SINE/MIR 84 GTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCAT 133 chr6ptel1M 303991 CTATAAAATGAG 304002 i MIR3#SINE/MIR 134 CTGTAAAATGAG 145 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 14.71 CpG sites = 9, Kimura (unadjusted) = 15.88 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.04 (4 / 99), avg. gap size = 3.00 (12 / 4) 13 8.53 4.00 0.00 chr6ptel1M 304264 304288 (695712) (ATCAG)n#Simple_repeat 1 26 (0) m_b279s252i4 11110 chr6ptel1M 304264 ATCAGATCAGATCAGATAATAT-AGA 304288 v v - (ATCAG)n#Simp 1 ATCAGATCAGATCAGATCAGATCAGA 26 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 26 32.34 0.00 2.06 chr6ptel1M 304727 304825 (695175) (TACTAC)n#Simple_repeat 1 97 (0) m_b279s252i5 11111 chr6ptel1M 304727 TACTATTTACTACTGCTGCTGCTAATACTGTTGGGGCTACTGGCTGCTGC 304776 -i i i i v ii ivvi -i i i (TACTAC)n#Sim 1 TACTA-CTACTACTACTACTACTACTACTACTACTACTACT-ACTACTAC 48 chr6ptel1M 304777 TATTGTTGCTGCTCATACTACTACTATTATTACTACTTCTACTACTACT 304825 i ii i i vv i i v (TACTAC)n#Sim 49 TACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACT 97 Matrix = Unknown Transitions / transversions = 3.00 (18/6) Gap_init rate = 0.02 (2 / 98), avg. gap size = 1.00 (2 / 2) 22 26.14 0.00 1.61 chr6ptel1M 304763 304825 (695175) (CTA)n#Simple_repeat 1 62 (0) m_b279s252i7 11111 chr6ptel1M 304763 CTACTGGCTGCTGCTATTGTTGCTGCTCATACTACTACTATTATTACTAC 304812 -i i i i ii i i vv i i (CTA)n#Simple 1 CTACT-ACTACTACTACTACTACTACTACTACTACTACTACTACTACTAC 49 chr6ptel1M 304813 TTCTACTACTACT 304825 v (CTA)n#Simple 50 TACTACTACTACT 62 Matrix = Unknown Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.02 (1 / 62), avg. gap size = 1.00 (1 / 1) 18 25.69 0.00 1.89 chr6ptel1M 304736 304789 (695211) (CTG)n#Simple_repeat 1 53 (0) m_b279s252i6 11112 chr6ptel1M 304736 CTACTGCTGCTGCTAATACTGTTGGGGCTACTGGCTGCTGCTATTGTTGC 304785 i iv i i vv i - ii i (CTG)n#Simple 1 CTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT-GCTGCTGCTGCTGCTGC 49 chr6ptel1M 304786 TGCT 304789 (CTG)n#Simple 50 TGCT 53 Matrix = Unknown Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.02 (1 / 53), avg. gap size = 1.00 (1 / 1) 26 32.34 0.00 2.06 chr6ptel1M 304727 304825 (695175) (TACTAC)n#Simple_repeat 1 97 (0) m_b279s252i5 11111 chr6ptel1M 304727 TACTATTTACTACTGCTGCTGCTAATACTGTTGGGGCTACTGGCTGCTGC 304776 -i i i i v ii ivvi -i i i (TACTAC)n#Sim 1 TACTA-CTACTACTACTACTACTACTACTACTACTACTACT-ACTACTAC 48 chr6ptel1M 304777 TATTGTTGCTGCTCATACTACTACTATTATTACTACTTCTACTACTACT 304825 i ii i i vv i i v (TACTAC)n#Sim 49 TACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACT 97 Matrix = Unknown Transitions / transversions = 3.00 (18/6) Gap_init rate = 0.02 (2 / 98), avg. gap size = 1.00 (2 / 2) 22 26.14 0.00 1.61 chr6ptel1M 304763 304825 (695175) (CTA)n#Simple_repeat 1 62 (0) m_b279s252i7 11111 chr6ptel1M 304763 CTACTGGCTGCTGCTATTGTTGCTGCTCATACTACTACTATTATTACTAC 304812 -i i i i ii i i vv i i (CTA)n#Simple 1 CTACT-ACTACTACTACTACTACTACTACTACTACTACTACTACTACTAC 49 chr6ptel1M 304813 TTCTACTACTACT 304825 v (CTA)n#Simple 50 TACTACTACTACT 62 Matrix = Unknown Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.02 (1 / 62), avg. gap size = 1.00 (1 / 1) 330 27.06 3.53 0.00 chr6ptel1M 304826 304910 (695090) MIR3#SINE/MIR 120 207 (1) m_b279s601i22 11113 chr6ptel1M 304826 CCCATTTTCCTCATCCATCAAATGAAGAGATTAGACCCGATGAATTCT-- 304873 i v ii v i i i i iv vi -- MIR3#SINE/MIR 120 CTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAA 169 chr6ptel1M 304874 GTTCTTTTCCAGTTCTAATGTGCCATAATTCTA-GATT 304910 v ii i i ii v i i - MIR3#SINE/MIR 170 GGTCCCTTCCAGCTCTGACATTCTATGATTCTATGATT 207 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.60 CpG sites = 17, Kimura (unadjusted) = 35.60 Transitions / transversions = 2.83 (17/6) Gap_init rate = 0.02 (2 / 84), avg. gap size = 1.50 (3 / 2) 21 11.78 0.00 2.56 chr6ptel1M 305288 305327 (694673) (TTTC)n#Simple_repeat 1 39 (0) m_b279s252i8 11114 chr6ptel1M 305288 TTTCTTTCTTTCTTTCCTTCCTTCCTTCCTTTCTTTTTTT 305327 - i i i i (TTTC)n#Simpl 1 TTTCTTTCTTTCTTT-CTTTCTTTCTTTCTTTCTTTCTTT 39 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1) 684 32.72 1.81 1.50 chr6ptel1M 305761 306092 (693908) C L1ME4c_3end#LINE/L1 (191) 639 307 m_b279s551i0 11115 chr6ptel1M 305761 TTCTGCTCACTTCACTCAGCATCAGTTCATGAAAGTCTCTCCAGGTCTCT 305810 ivi i i i vv i vi i - v iv C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATAAACATTT-TCCATGTTGCT 591 chr6ptel1M 305811 TTAAAATCTCC-TCCTGATCACTTCTTGTAGAACAATAATATTCTAAAAC 305859 vi v i i - vv v i i vi i vvvv i vviv C L1ME4c_3end#L 590 ACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCGA 541 chr6ptel1M 305860 ATTCATATACTATAATTTATTCAGCCATTTCCCAGCTGATGGGCATCCAC 305909 i ?v i i i i i i vii v i ii v C L1ME4c_3end#L 540 GTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAG 491 chr6ptel1M 305910 TCAGTTTCCAGTTTCTTGCCACTACAAAGAGGACTGCCACAAACATTTCT 305959 viv i i i i i i v ivi v ii i ii C L1ME4c_3end#L 490 GTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTC 441 chr6ptel1M 305960 GCACATGTGAGTCCCTCTTTCCTCCTT---AAG-ATCTCTTTGGGATATA 306005 ii i - --- i i --- v- i i i v C L1ME4c_3end#L 440 GTGCATAT-AG---CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAA 395 chr6ptel1M 306006 GGCCCAGTAGAAACACTGCTTGGCCAAAGGGTATGTACATTTTGATACCC 306055 vv v viiv i i v i v v iv i C L1ME4c_3end#L 394 TTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCT 345 chr6ptel1M 306056 TTTGG-GCATAGTTCCAAATTGCTCTCCAGAATGGTTG 306092 i i-i i v v i i v C L1ME4c_3end#L 344 CTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTG 307 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 42.11 CpG sites = 65, Kimura (unadjusted) = 44.95 Transitions / transversions = 1.55 (65/42) Gap_init rate = 0.03 (9 / 331), avg. gap size = 1.22 (11 / 9) 315 18.97 20.93 1.96 chr6ptel1M 306534 306662 (693338) C Charlie4#DNA/hAT-Charlie (14) 3364 3212 m_b279s502i0 11116 chr6ptel1M 306534 CTTTTGTATGTCATTAACTGTTTTGGCAGCCTGGTGAATCCCCTGTATTC 306583 v i i vi ivi i v iv v ii C Charlie4#DNA/ 3364 CTTTTTTGTGCCATGGACCCCTTTGGCAGTCTGGTGAAGCCTATGGACCC 3315 chr6ptel1M 306584 TTTAT----ATAATGTTATTAAATACATCAAATA---------GGATTAC 306620 i v ---- v i v --------- C Charlie4#DNA/ 3314 CTTCTCAGAATAATGTTTTTAAATGCATAAAATAAAATACATAGGATTAC 3265 chr6ptel1M 306621 TAA------------TAATGAAATA--GTTATCAAACTATTTATAAAAAT 306656 v ------------ v -- v -- i C Charlie4#DNA/ 3264 AAAGGAAACCAATTATATTGAAATATAGTTATCAAAATATT--TAAAAAC 3217 chr6ptel1M 306657 GAAATT 306662 - C Charlie4#DNA/ 3216 -AAATT 3212 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 22.11 CpG sites = 12, Kimura (unadjusted) = 22.11 Transitions / transversions = 1.00 (12/12) Gap_init rate = 0.05 (7 / 128), avg. gap size = 4.29 (30 / 7) 413 31.35 4.64 4.64 chr6ptel1M 307276 307469 (692531) C MIR3#SINE/MIR (3) 205 12 m_b279s601i23 11117 chr6ptel1M 307276 TCACAGGATCATGGA--TTTAGAACTAAAAGAGACCTCAGAGATGATCT- 307322 i i i --v i i ii i i v - C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTA 156 chr6ptel1M 307323 GTTGTATGTTGTCCCTTTCTAGATTGGGAAGCTAAGGCCAAGGGAACTTA 307372 ivv iviiv vi vi vi i i v i iv v C MIR3#SINE/MIR 155 GTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGA 106 chr6ptel1M 307373 ACTGACTTACTTGCCCAAAGTTCTCCCCTTGGT--GTGG-AGAGAAGGG- 307418 v ---- i iviv vvi?i -- - vv - C MIR3#SINE/MIR 105 AGTG----ACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGA 60 chr6ptel1M 307419 TGGGAATCCAGCTTCTCTGACTGGATTCC--TCTATGCTCTCCTCAGTTT 307466 ivi i v iii ---- i -- ii - v i i C MIR3#SINE/MIR 59 CTAGAACCCAGGTCTCCTGAC----TCCCAGTCCGTGCTCT-CTCTGCTC 15 chr6ptel1M 307467 AGC 307469 C MIR3#SINE/MIR 14 AGC 12 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 41.49 CpG sites = 36, Kimura (unadjusted) = 42.59 Transitions / transversions = 1.64 (36/22) Gap_init rate = 0.08 (15 / 193), avg. gap size = 1.20 (18 / 15) 214 34.78 11.96 0.00 chr6ptel1M 307523 307614 (692386) C L3#LINE/CR1 (25) 4074 3972 m_b279s601i24 11118 chr6ptel1M 307523 GAGAAGTACCTTAGAAATCA----GT------TTTCATCCAAT-TGAAAA 307561 ii i v ii ---- ------ ii -iiii C L3#LINE/CR1 4074 GGAAGGGACCTTAGAGGTCATCTAGTCCAACCTCCCATCCAATGCAGGAA 4025 chr6ptel1M 307562 TTCACTCCATGACATCACTAACAAGTAATCCTTTACTTTCTGACTGAGCA 307611 i vi i ii v i ii v ii vii vi i C L3#LINE/CR1 4024 TCCCTTCTACAACATCCCTGACAAGTGGTCATCCAGCCTCTGCTTGAACA 3975 chr6ptel1M 307612 GCT 307614 v C L3#LINE/CR1 3974 CCT 3972 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 52.45 CpG sites = 25, Kimura (unadjusted) = 52.45 Transitions / transversions = 3.57 (25/7) Gap_init rate = 0.03 (3 / 91), avg. gap size = 3.67 (11 / 3) 368 25.00 0.00 0.00 chr6ptel1M 308642 308717 (691283) C MIRb#SINE/MIR (81) 187 112 m_b279s601i25 11119 chr6ptel1M 308642 TTCTCACAACAACCTTGTGGTACAAGTATTATTGCCCCATTTTTAGTGAT 308691 i i i ivii i ii vv vv C MIRb#SINE/MIR 187 TCCTCACAACAACCCTGCGAGGTAGGTATTATTATCCCCATTTTACAGAT 138 chr6ptel1M 308692 AAGGAAACTAAAACTCAGAGAGTTTA 308717 i i ii v C MIRb#SINE/MIR 137 GAGGAAACTGAGGCTCAGAGAGGTTA 112 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.62 CpG sites = 13, Kimura (unadjusted) = 31.62 Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.00 (0 / 75), avg. gap size = 0.0 (0 / 0) 199 22.58 11.29 0.00 chr6ptel1M 308758 308819 (691181) C MIRc#SINE/MIR (107) 161 93 m_b279s601i26 11120 chr6ptel1M 308758 AGAGATTATT-TTCTTATTTTATAGATGAGGAAAGTG------ATAGAAG 308800 iv - i ii i v ------ v i C MIRc#SINE/MIR 161 AGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGG 112 chr6ptel1M 308801 TTAAATGACTTATACAAAG 308819 i iiv i C MIRc#SINE/MIR 111 TTAAGTGACTTGCCCAAGG 93 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.93 CpG sites = 10, Kimura (unadjusted) = 27.93 Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.03 (2 / 61), avg. gap size = 3.50 (7 / 2) 252 11.11 0.00 0.00 chr6ptel1M 309358 309388 (690612) C L3#LINE/CR1 (12) 4087 4057 m_b279s601i27 11121 chr6ptel1M 309358 GAATCTCAGAGTTGGAAGGGACCTCAGAAGC 309388 i i i C L3#LINE/CR1 4087 GAATCTCAGAGTTGGAAGGGACCTTAGAGGT 4057 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 12.98 CpG sites = 4, Kimura (unadjusted) = 12.98 Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 56 0.00 0.00 0.00 chr6ptel1M 309389 309436 (690564) (TA)n#Simple_repeat 1 48 (0) c_b279s251i2 11122 chr6ptel1M 309389 TATATATATATATATATATATATATATATATATATATATATATATATA 309436 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATA 48 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 278 31.51 14.79 2.43 chr6ptel1M 309580 309836 (690164) C L3#LINE/CR1 (65) 4034 3747 m_b279s601i28 11123 chr6ptel1M 309580 AGTGAAGGAAATCTCCCTTCCTC--CACCCCTGGCGATTGGTCATCGGGG 309627 i v --- iv -- i i i v vi v C L3#LINE/CR1 4034 AATGCAGGAA---TCCCTTCTACAACATCCCTGACAAGTGGTCATCCAGC 3988 chr6ptel1M 309628 CTCCACA-GAA-------AGTTACCTGGG--------CCTCTCCAGGCAG 309661 ii v- ------- v vv i-------- ? v C L3#LINE/CR1 3987 CTCTGCTTGAACACCTCCAGTGACGGGGAGCTCACTACCTCNCGAGGCAG 3938 chr6ptel1M 309662 CCCATTCTCCTTCTGGATAGCCCTAATTTTCAGGAAGCTTTTCTGCATAT 309711 ivi i i i i v i i i i ivi C L3#LINE/CR1 3937 CCCATTCCATTTTTGGACAGCTCTGATTGTTAGAAAGTTCTTCCTTATAT 3888 chr6ptel1M 309712 ----CCAGTATCTGTTCTACCCCAGTGTCT--CACCACACC-GTCCCA-- 309752 ---- iiv -i -- v iv -- - ii- i -- C L3#LINE/CR1 3887 TGAGCCGAAATCTG-CCT--CCCTGTAACTTCCACC-CATTGGTCCTAGT 3842 chr6ptel1M 309753 -----CCTCCAAGACCAGGCAGGACACATGCAAATGCTCTTTCTCAT--- 309794 ----- iiiii vi i i vi vi viv i v --- C L3#LINE/CR1 3841 TCTGCCCTCTGGAGCCACACAGAATAAGTCTAATCCCTCTTCCACATGAC 3792 chr6ptel1M 309795 ---CCTTTTTATATTCAAAATTAACCTCCCTGTTCCCTTAAAGTC 309836 --- ivv ii ivi i ivi v ii iv C L3#LINE/CR1 3791 AGCCCTTCAAATATTTGAAGACAGCTATCATGTCTCCTCTAAGTC 3747 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 42.53 CpG sites = 51, Kimura (unadjusted) = 43.29 Transitions / transversions = 1.82 (51/28) Gap_init rate = 0.06 (16 / 256), avg. gap size = 2.81 (45 / 16) 281 35.37 1.63 5.78 chr6ptel1M 309876 310181 (689819) L1ME4c_3end#LINE/L1 346 639 (191) m_b279s551i1 11124 chr6ptel1M 309876 GTCATAAAACTGCGCATGTACCTTTTCAACCAGCAATATTGTTTC--AGT 309923 i v iv -- i v v i viiii --i v L1ME4c_3end#L 346 GCCATAAAAATGTTCAT--ACCCTTTGACCCAGTAATTCCACTTCTGGGA 393 chr6ptel1M 309924 CTGTATCCCAAAGAGATA-TTAAAAAGCGGGGGTGGGGGAGGGAAGGACC 309972 v v i i i - v ------------ i ii v L1ME4c_3end#L 394 ATTTATCCTAAGGAAATAATTCAAAAG------------AAGGAAAAAGC 431 chr6ptel1M 309973 TGCTTGTAACAAAAATATTTATAGCAGCTCTTTTTGCGGTGGCTGAGAAT 310022 iiv i - i i i i v vi v iiii i vi i L1ME4c_3end#L 432 TATATGCA-CGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAAT 480 chr6ptel1M 310023 TAGAAACTGAGGAGATGTCCTGAAATTAGGGAATGGCTAAACAAGTTATG 310072 i vivvv i viv vi i ii i L1ME4c_3end#L 481 TGGAAACAACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATG 530 chr6ptel1M 310073 TTATAT-GATTGTAATGCAATATATTTTTGTTGTAAGAAATGACAAGCAA 310121 v i -? i -ii v vv viv iii v i i vi v L1ME4c_3end#L 531 GTACATCNACT-CGATGGAATATTATGCAGCCATTAAAAATGATAATTAT 579 chr6ptel1M 310122 GATGATTTCAGAA-AACCTGGAAAGACTTACATGAACTGATGCAAAGTGA 310170 v i viiv i- v ivv -i vv i iv L1ME4c_3end#L 580 GAAGACTATGTAGCAACATGGAAAATGTT-TATGATATAATGTTAAGTGA 628 chr6ptel1M 310171 AGTGAGAAGAA 310181 ivi v L1ME4c_3end#L 629 AAAAAGCAGAA 639 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 48.47 CpG sites = 60, Kimura (unadjusted) = 49.95 Transitions / transversions = 1.43 (60/42) Gap_init rate = 0.07 (21 / 305), avg. gap size = 1.05 (22 / 21) 333 29.52 1.01 8.06 chr6ptel1M 309880 310078 (689922) L1ME3G_3end#LINE/L1 344 529 (395) m_b279s551i2 11124 chr6ptel1M 309880 TAAAACTGCGCATGTACCTTTTCAACCAGCAATATTGTTTC--AGTCTGT 309927 - -- i v v viiii --i ?v v L1ME3G_3end#L 344 TAAAA-TGCGCAT--ACCCTTTGACCCAGCAATTCCACTTCTNGGNATCT 390 chr6ptel1M 309928 ATCCCAAAGAGATATTAAAAAGCGGGGGTGGGGGAGGGAAGGACCTGCTT 309977 i ? i i ------ vivi v vi---v ?-- v L1ME3G_3end#L 391 ATCCTANAGAAATACT------CGCACATGTGCA---CAAGGAN--GCAT 429 chr6ptel1M 309978 GTAACAAAAATATTTATAGCAGCTCTTTTTGCGGTGGCTGAGAATTAGAA 310027 - ii i i v vi v iii i vi i i L1ME3G_3end#L 430 GTA-CAAGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAA 478 chr6ptel1M 310028 ACTGAGGAGATGTCCTGAAATTAGGGAATGGCTAAACAAGTTATGTTATA 310077 vivvv i vvv vi i i i v L1ME3G_3end#L 479 ACAACCTAAATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGTATA 528 chr6ptel1M 310078 T 310078 L1ME3G_3end#L 529 T 529 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.89 CpG sites = 30, Kimura (unadjusted) = 38.89 Transitions / transversions = 1.25 (30/24) Gap_init rate = 0.08 (16 / 198), avg. gap size = 1.06 (17 / 16) 301 33.05 0.00 0.85 chr6ptel1M 309975 310093 (689907) L1ME2z_3end#LINE/L1 431 548 (643) m_b279s551i3 11124 chr6ptel1M 309975 CTTGTAACAAAAATATTTATAGCAGCTCTTTTTGCGGTGGCTGAGAATTA 310024 - i i i i v iiiii i ii i i i L1ME2z_3end#L 431 CTTGTA-CAAGAATGTTCATAGCAGCTTTATTCATAATAGCCAAAAACTG 479 chr6ptel1M 310025 GAAACTGAGGAGATGTCCTGAAATTAGGGAATGGCTAAACAAGTTATGTT 310074 v vvv i vvv ivi i v ii i v L1ME2z_3end#L 480 GAAACAGCCCAGGTGTCCATCAACAGGAGAATGGATAAACAAACTGTGGT 529 chr6ptel1M 310075 ATATGATTGTAATGCAATA 310093 vvv ii v L1ME2z_3end#L 530 ATATTCATACAATGGAATA 548 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 45.50 CpG sites = 24, Kimura (unadjusted) = 45.50 Transitions / transversions = 1.60 (24/15) Gap_init rate = 0.01 (1 / 118), avg. gap size = 1.00 (1 / 1) 62 37.73 0.78 1.18 chr6ptel1M 310376 310631 (689369) (CCTC)n#Simple_repeat 1 255 (0) m_b279s252i9 11125 chr6ptel1M 310376 CCTCCCTCCCTCTCTTCCTTCCTTCCTTCCTTCTTCCCTCTCTCCCACCC 310425 i i i i i i i i v (CCTC)n#Simpl 1 CCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCC 50 chr6ptel1M 310426 TCCTTTCCTTCCTTCCTTTTCCCCTTTTTCTTTAGTTCTTTCCCTCCCCC 310475 i i i i iiii iii ii vvi ii i (CCTC)n#Simpl 51 TCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTC 100 chr6ptel1M 310476 CCTCTCTTCTTTCTTTCCTTTCT-TTTCCCTTCCCTTCCTTCTTCCCTCC 310524 i i i i i i ii -ii - i i i (CCTC)n#Simpl 101 CCTCCCTCCCTCCCTCCCTCCCTCCCTCCC-TCCCTCCCTCCCTCCCTCC 149 chr6ptel1M 310525 CTTTCTTTCTCCCTCTCTTTCTTCCTCCCTCCCTCCCTTCCTCTTTTCTT 310574 ii ii i ii i i -ii ii (CCTC)n#Simpl 150 CTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTC-CCTCCC 198 chr6ptel1M 310575 TCCCT-TCTTTCTCATTTAGTTCTTTCCCACCTTCCCTTCCTCCCTCCCT 310623 -i ii -ii vvi ii v i i (CCTC)n#Simpl 199 TCCCTCCCTCCCTC-CCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCT 247 chr6ptel1M 310624 CCCTTCCT 310631 i (CCTC)n#Simpl 248 CCCTCCCT 255 Matrix = Unknown Transitions / transversions = 10.33 (62/6) Gap_init rate = 0.02 (5 / 255), avg. gap size = 1.00 (5 / 5) 586 16.19 3.81 0.00 chr6ptel1M 310634 310738 (689262) MIRc#SINE/MIR 40 148 (120) m_b279s601i29 11126 chr6ptel1M 310634 AATCAGGAAGATCTGAGTTCAA-TCCAGCCTCAGATTCTTACTAGCT-TG 310681 i i i i - v v v viv - MIRc#SINE/MIR 40 AGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTG 89 chr6ptel1M 310682 TGACCCTGGACAAGTCACTTAATCTGTT--AGCTTCAGTTTCCTCATCTG 310729 i i i v i-- i MIRc#SINE/MIR 90 TGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTG 139 chr6ptel1M 310730 TAAAATGAG 310738 i MIRc#SINE/MIR 140 TAAAATGGG 148 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 17.39 CpG sites = 11, Kimura (unadjusted) = 18.54 Transitions / transversions = 1.83 (11/6) Gap_init rate = 0.03 (3 / 104), avg. gap size = 1.33 (4 / 3) 478 12.75 6.42 6.42 chr6ptel1M 310646 310754 (689246) MIR#SINE/MIR 48 156 (106) m_b279s601i30 11126 chr6ptel1M 310646 CTGAGTTC-AATCCAGCCTCAGATTCTTACTAGCT-TGTGACCCTGGACA 310693 i - v v v viv - i i MIR#SINE/MIR 48 CTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 97 chr6ptel1M 310694 AGTCACTTAA----TCTGTTAGCTTCAGTTTCCTCATCTGTAAAATGAGC 310739 i ---- -- i ----- MIR#SINE/MIR 98 AGTTACTTAACCTCTCTGT--GCCTCAGTTTCCTCATCTGTAAAA----- 140 chr6ptel1M 310740 TGGAAATAA-AATAGT 310754 ii - MIR#SINE/MIR 141 TGGGGATAATAATAGT 156 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 14.11 CpG sites = 8, Kimura (unadjusted) = 14.11 Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.10 (11 / 108), avg. gap size = 1.27 (14 / 11) 210 28.30 1.89 0.00 chr6ptel1M 310844 310896 (689104) C L2d2_3end#LINE/L2 (90) 465 412 m_b279s601i31 11127 chr6ptel1M 310844 TGGCCCTTACTTCAAAGGAACACAGAATTTAGTT-GGGAGATAAGACATG 310892 i i i iiiv i vi v i - i i C L2d2_3end#LIN 465 TGGTCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGGAGACAAGACATA 416 chr6ptel1M 310893 CACA 310896 v C L2d2_3end#LIN 415 AACA 412 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.81 CpG sites = 11, Kimura (unadjusted) = 37.81 Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.02 (1 / 52), avg. gap size = 1.00 (1 / 1) 214 29.88 2.27 1.12 chr6ptel1M 310929 311016 (688984) C MIRb#SINE/MIR (65) 203 115 m_b279s601i32 11128 chr6ptel1M 310929 GCACTCTCTCACTGGACTCTCATAA-GCCCCTAGCAATGCCAGGATTAGT 310977 i v i vi ii i -iv - i v ivi v v C MIRb#SINE/MIR 203 GCATTATCTCATTTAATCCTCACAACAACCCT-GCGAGGTAGGTATTATT 155 chr6ptel1M 310978 AGCTCACCTTTACAGTAGAGGAAACAAAGGC-CAGAGAGG 311016 v i vvi vv vi - C MIRb#SINE/MIR 154 ATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGG 115 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.77 CpG sites = 13, Kimura (unadjusted) = 38.61 Transitions / transversions = 1.00 (13/13) Gap_init rate = 0.03 (3 / 87), avg. gap size = 1.00 (3 / 3) 198 34.33 7.46 4.35 chr6ptel1M 311138 311271 (688729) MIRc#SINE/MIR 2 139 (129) m_b279s601i33 11129 chr6ptel1M 311138 GAAGCAGTTGTGGCGAGGGCCGCTGGAAGAAGTTTTAGGTATG-ACTTTG 311186 i - i vi ----- ii ivi i iiv - v iv MIRc#SINE/MIR 2 GAGGCAGT-GTGGTGCAG-----TGGAAAGAGCACTGGACTTGGAGTCAG 45 chr6ptel1M 311187 GAAG-CCCAAGTTAGGATTTCACATAATTCATTTACTCCCTGTGTGTCCT 311235 - iii v ii ii ivv vvvi i vv v MIRc#SINE/MIR 46 GAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCT 95 chr6ptel1M 311236 ----CAAGTTCC--GATCTCTCCA--CCTCAATACCCTCATCTG 311271 ---- iv --i i ii-- i vi MIRc#SINE/MIR 96 TGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTG 139 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 46.94 CpG sites = 28, Kimura (unadjusted) = 48.53 Transitions / transversions = 1.75 (28/16) Gap_init rate = 0.08 (11 / 133), avg. gap size = 1.45 (16 / 11) 244 28.33 1.67 0.00 chr6ptel1M 312473 312532 (687468) tRNA-Arg-AGG#tRNA 7 67 (9) m_b279s502i1 11130 chr6ptel1M 312473 GTGGCTCAGTGCACAAAGCACTGGC-TCTAGATTCAGAGGCTGTAGGTTC 312521 ii i v i i - ivi vi i ii i tRNA-Arg-AGG# 7 GTGGCCTAATGGATAAGGCACTGGCCTCCTAAGCCAGGGATTGTGGGTTC 56 chr6ptel1M 312522 AAATCCCACCT 312532 i i tRNA-Arg-AGG# 57 GAGTCCCACCT 67 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 35.98 CpG sites = 14, Kimura (unadjusted) = 38.99 Transitions / transversions = 4.67 (14/3) Gap_init rate = 0.02 (1 / 59), avg. gap size = 1.00 (1 / 1) 189 31.67 3.33 0.00 chr6ptel1M 312591 312650 (687350) MIR3#SINE/MIR 119 180 (28) m_b279s601i34 11131 chr6ptel1M 312591 CCTCATTCTTGTGAACTGTAAAATAAATGGATTGGATT--ATGGCTTCTG 312638 v i iv v v i iv i i -- iii i MIR3#SINE/MIR 119 CCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTA 168 chr6ptel1M 312639 TAGTCTCTTCTA 312650 vi i i MIR3#SINE/MIR 169 AGGTCCCTTCCA 180 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 43.69 CpG sites = 13, Kimura (unadjusted) = 43.69 Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.02 (1 / 59), avg. gap size = 2.00 (2 / 1) 30 0.00 0.00 0.00 chr6ptel1M 313285 313310 (686690) (TG)n#Simple_repeat 1 26 (0) c_b279s251i3 11132 chr6ptel1M 313285 TGTGTGTGTGTGTGTGTGTGTGTGTG 313310 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTG 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 324 27.38 2.38 0.00 chr6ptel1M 313380 313463 (686537) C MIRc#SINE/MIR (105) 163 78 m_b279s601i35 11133 chr6ptel1M 313380 GCAAATGTTATTATGATTATTTTTTAGCTGAGGAGAC--AGGATCACGGG 313427 ii i vvii vi v i -- v vi i C MIRc#SINE/MIR 163 GCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGA 114 chr6ptel1M 313428 GGTTAAATTGCTTGATCAAAGTCATACAACTAGTAA 313463 i vi vi i i i C MIRc#SINE/MIR 113 GGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAA 78 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.39 CpG sites = 15, Kimura (unadjusted) = 35.39 Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.01 (1 / 83), avg. gap size = 2.00 (2 / 1) 208 33.90 9.73 0.81 chr6ptel1M 313933 314045 (685955) L2b_3end#LINE/L2 334 456 (10) m_b279s601i36 11134 chr6ptel1M 313933 GTC-CTCCCTTTAGACTGT--GCTTCTCAGGGGCAGGA-------TTCTC 313972 - i vi -- i viii i-------i v L2b_3end#LINE 334 GTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTC 383 chr6ptel1M 313973 CAGCTC-TCTCTGCATCTCAGACATTTATCTCAGCACCTGGGACAGAGAA 314021 iv i -i v i i vii iii v v ?i v v v L2b_3end#LINE 384 TTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTA 433 chr6ptel1M 314022 GGTACTTAAATTAACATTTTCTGA 314045 ii i- i v i vi L2b_3end#LINE 434 GGCGCTC-AGTAAATATTTGTTGA 456 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 44.78 CpG sites = 25, Kimura (unadjusted) = 48.59 Transitions / transversions = 1.92 (25/13) Gap_init rate = 0.04 (5 / 112), avg. gap size = 2.40 (12 / 5) 222 32.53 6.02 0.00 chr6ptel1M 314119 314201 (685799) C L2c_3end#LINE/L2 (34) 444 357 m_b279s601i37 11135 chr6ptel1M 314119 ACTCTGTTCTGGGTGCTGGGTATACAAAGAC--ATGAAACA--ATCTCTA 314164 v v ii i v i-- i i --i i i C L2c_3end#LINE 444 ACTATGTGCCAGGCGCTGGGGATACAAAGATGAATAAGACACGGTCCCTG 395 chr6ptel1M 314165 -TCTCAAGAAGTGAATGTTCCTTCAAAGGAGACACACA 314201 -i i ivv iiv ivviii v C L2c_3end#LINE 394 CCCTCAAGGAGCTCACAGTCTAGTGGAGGAGACAGACA 357 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 42.86 CpG sites = 18, Kimura (unadjusted) = 45.17 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.04 (3 / 82), avg. gap size = 1.67 (5 / 3) 239 33.33 6.25 6.25 chr6ptel1M 314249 314504 (685496) C L2c_3end#LINE/L2 (111) 367 112 m_b279s601i38 11127 chr6ptel1M 314249 GGAAATAAAGCTGCAAACACATATTTATAAGTACAC----ACGGCATGGA 314294 i i i vv? i v i v i - v---- i -- iii C L2c_3end#LINE 367 GGAGACAGACANGTAAACAGACAATTACAA-TACAAGTTAATG--ATAAG 321 chr6ptel1M 314295 TACCAGCAATAGAAGATATATACAT----CTATGATAGTTTGAAATGGAG 314340 i i -i i i - v v---- iv iviii -- C L2c_3end#LINE 320 TGCTA-TAATGGGAG-TATAGACAGGGTGCTATGGGAGCACAGA--GGAG 275 chr6ptel1M 314341 GACAC-TAGG---AACTGGGGGAATCAGGAAAGGCATC----AGGTCGCC 314382 i - i---i? v ii i v ---- vv -- C L2c_3end#LINE 274 GGCACCTAGACTAGNCTTGGGGGGTCAGGGAAGGCTTCCCGGAGGAGG-- 227 chr6ptel1M 314383 TTTGATACTTGAACTGTGTTTTGGCGGAAGAGAAGGATTCACTGAGACTG 314432 -- i ii i v ?i iv v v v i viv iiv C L2c_3end#LINE 226 --TGACATCTGAGCTGAGNCTTGAAGGATGAGTAGGAGTTAGCCAGGTGG 179 chr6ptel1M 314433 ACACAGGATCAGGCAGTGTCTTCCAGATGATGGAGACATCCAGTGCAAAG 314482 viv i--i v v iv iiiiv ii v vv C L2c_3end#LINE 178 AAGGAGGG--GGGAAGAGCATTCCAGGCAGAGGGAACAGCATGTGCAAAG 131 chr6ptel1M 314483 CCATGGCGTGCCAAGGTAAGAA 314504 v ?i v - -- v C L2c_3end#LINE 130 GCNCGGAG-GC--AGGAAAGAA 112 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 46.01 CpG sites = 47, Kimura (unadjusted) = 46.83 Transitions / transversions = 1.42 (47/33) Gap_init rate = 0.08 (21 / 255), avg. gap size = 1.52 (32 / 21) 228 35.38 7.58 0.89 chr6ptel1M 314320 314530 (685470) C L2d2_3end#LINE/L2 (259) 296 72 m_b279s601i39 11127 chr6ptel1M 314320 CTATGATAGTTTGAA--ATGGAG-GA-CACTAGGAACTGGGGGAATCAGG 314365 iiv iii -- v - - ?v ii i vii C L2d2_3end#LIN 296 CTATAGGAGTTCAGAGGAGGGAGAGATCACTNCGGGCTGGAGTGGTCAGG 247 chr6ptel1M 314366 AAAGGCATCAGGTCGCCTTTGATACTTGAACTGTGTTTTGGCGGAAGAGA 314415 i v v vv vvvv i? i i v ii iv v i v C L2d2_3end#LIN 246 GAAGGCTTCACGGAGGAGGTGGNATTTGAGCTGGGCCTTGAAGGATGGGT 197 chr6ptel1M 314416 AGGATTCACTGAGACTGACACAGGATCAGGCAGTGTCTTCCAGATGATGG 314465 iivvv i- i- v vvi v v iv ii iv C L2d2_3end#LIN 196 AGGATTTGGATAGG-TGG-AGAGGAAGGGGAAGGGCATTCCAGGCGGGGG 149 chr6ptel1M 314466 AGACATCCAGTGCAAAGCCAT---GGCG----TGC-CAAGGTA----AGA 314503 ii iv vv v v ii--- ----? - ii----v i C L2d2_3end#LIN 148 GAACGGCGTGAGCAAAGGCGCAGAGGCGGGAANGCGCAAGGCGTGTTCGG 99 chr6ptel1M 314504 AGGACCCGGAGAAGGACAGTTTGGCTG 314530 i vvv v iv C L2d2_3end#LIN 98 GGGACAGTGAGTAGACCAGTTTGGCTG 72 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 46.08 CpG sites = 37, Kimura (unadjusted) = 49.83 Transitions / transversions = 1.00 (37/37) Gap_init rate = 0.04 (9 / 210), avg. gap size = 2.00 (18 / 9) 478 28.61 1.37 4.23 chr6ptel1M 314632 314777 (685223) C MIRc#SINE/MIR (124) 144 3 m_b279s601i40 11136 chr6ptel1M 314632 TTTTATAGATGGGGAAGCTGAGGCAAACAG-GGTTAAGTATCTTGCCCAA 314680 i i i vv v - iv C MIRc#SINE/MIR 144 TTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAA 95 chr6ptel1M 314681 GGTCATGCAGCAAGTGAGCATCTGAAACTAGGTTTGAATTTAGGAAGATT 314730 ii v i iiv v iv vi ii i iii --- vi C MIRc#SINE/MIR 94 GGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAG---GTCT 48 chr6ptel1M 314731 TCCTTACTCCAGGCCTGGCGTTCTGTGCACTATAGTGCCAC-CTCCCT 314777 v i i ii i i v v ii --- - v C MIRc#SINE/MIR 47 TCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCA---CCACACTGCCT 3 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.26 CpG sites = 26, Kimura (unadjusted) = 37.46 Transitions / transversions = 1.86 (26/14) Gap_init rate = 0.06 (8 / 145), avg. gap size = 1.00 (8 / 8) 340 36.26 1.17 4.85 chr6ptel1M 314945 315115 (684885) C MIR3#SINE/MIR (23) 185 21 m_b279s601i41 11137 chr6ptel1M 314945 AGACCTAGAAGGGACTTTGGAAGAACCATC-AATCTAATCTGCTTACTTG 314993 v i i i --i i - i i i iv i i v C MIR3#SINE/MIR 185 AGAGCTGGAAGGGACCTTAGA--GATCATCTAGTCCAACCCCCTCATTTT 138 chr6ptel1M 314994 CTTAATGAGACAAGT-ACATAGAAAGAGTTTAAGTGATTTTGCCAAGATC 315042 vivi iv v - viivv i v v i vv i C MIR3#SINE/MIR 137 ACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTC 88 chr6ptel1M 315043 GCACAGTCTAGGAAGTATTAAAATTGGAGCTTAAAGCCTGGTTCTCTATC 315092 i - ? vv ivi i iii ii vi v v iii iv C MIR3#SINE/MIR 87 ACACAG-CNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGTCTCCTGAC 39 chr6ptel1M 315093 CACCCATCCACCCAGTGCTCTTT 315115 iv vi ----- i C MIR3#SINE/MIR 38 TCCCAGTCC-----GTGCTCTCT 21 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 51.17 CpG sites = 36, Kimura (unadjusted) = 52.50 Transitions / transversions = 1.57 (36/23) Gap_init rate = 0.06 (10 / 170), avg. gap size = 1.00 (10 / 10) 223 35.80 6.17 0.00 chr6ptel1M 316049 316129 (683871) C MIRc#SINE/MIR (144) 124 39 m_b279s601i42 11138 chr6ptel1M 316049 AAGCTCAGAAAGT---AGAAATCTGCCT--GTTCCCATGGCTAATGAACC 316093 i i v--- vi ii i-- v v ii i i iiv C MIRc#SINE/MIR 124 AGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTG 75 chr6ptel1M 316094 ACAGAGCTGAGGATCACACCCAAGTTTTTGTAACTC 316129 i i i iv iv i i iv i C MIRc#SINE/MIR 74 GCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTC 39 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 48.03 CpG sites = 21, Kimura (unadjusted) = 53.52 Transitions / transversions = 2.62 (21/8) Gap_init rate = 0.03 (2 / 80), avg. gap size = 2.50 (5 / 2) 395 21.35 0.00 0.00 chr6ptel1M 316417 316505 (683495) Charlie4a#DNA/hAT-Charlie 356 444 (64) m_b279s502i2 11139 chr6ptel1M 316417 TACTTTGATAACTGTATTTCATTATGATTAATATTCTTTGTAATGCTATA 316466 i v i ii v i v i Charlie4a#DNA 356 TATTTTGATAACTGTATTTCAATATAATTGGTTTCCTTTGTAATCCTATG 405 chr6ptel1M 316467 TGTTTTATTTTGGGCCTTTAAAAGAATCATTTGAAGAAG 316505 i iv v iv i ivi Charlie4a#DNA 406 TATTTTATTTTATGCATTTAAAAACATTATTCTGAGAAG 444 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 25.69 CpG sites = 12, Kimura (unadjusted) = 25.69 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.00 (0 / 88), avg. gap size = 0.0 (0 / 0) 392 21.51 8.33 3.17 chr6ptel1M 316652 316771 (683229) C Charlie4a#DNA/hAT-Charlie (379) 129 4 m_b279s502i3 11116 chr6ptel1M 316652 ACATTCCTAAATAATTGAAAACAGGGTTAAGTTTCAGTTAGAGTTTAGTG 316701 ---- iiv iv i i v C Charlie4a#DNA 129 ACATTC----ATAATTGAAGGAAATGCTAAATTTCAGTTAGAGGTTAGTG 84 chr6ptel1M 316702 -AAATTGAGATGGAA-TTTTTTCTCTTTCCACATTCTAAGA-CCCCTGAA 316748 - vi v - i iv vi vvi - C Charlie4a#DNA 83 AAAATAAAGATGTAATTTTTTTCCCCATCCAAGTTCACGGACCCCCTGAA 34 chr6ptel1M 316749 ATCTA-------GCCCTAGATTAAGACCTC 316771 v -------i i i v i C Charlie4a#DNA 33 TTCTATCCACGGACCCCAGGTTAAGAACCC 4 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 24.59 CpG sites = 14, Kimura (unadjusted) = 25.75 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.07 (8 / 119), avg. gap size = 1.75 (14 / 8) 16 19.09 0.00 0.00 chr6ptel1M 316851 316880 (683120) (T)n#Simple_repeat 1 30 (0) m_b279s252i10 11140 chr6ptel1M 316851 TTTTTTTCTTTCTTTTTTTTCTTGTTATTT 316880 i i i v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 30 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 322 34.94 5.12 3.09 chr6ptel1M 318661 318914 (681086) C L2d2_3end#LINE/L2 (295) 260 2 m_b279s601i43 11141 chr6ptel1M 318661 CTGAAGGGGGATTGGGAAAGGTTTCATGTAGAAGGTTGTACTGGAGATGA 318710 i v -- ii i i i v i v ? i v v i C L2d2_3end#LIN 260 CTGGAGTGG--TCAGGGAAGGCTTCACGGAGGAGGTGGNATTTGAGCTGG 213 chr6ptel1M 318711 AACCTGAAGAAAACTAGG--GGCTCTGAA-AAGCGGCGGTTCAGTAGA-- 318755 iv i i --- i -- v i i - i i v ivvv vi -- C L2d2_3end#LIN 212 GCCTTGAAGGA---TGGGTAGGATTTGGATAGGTGGAGAGGAAGGGGAAG 166 chr6ptel1M 318756 -TCATTCCAGGCGTGGAGGACAACAGATGCAAAGATTTAGAGGTGGG-AG 318803 -v v i i ii iviv iivi i - ? C L2d2_3end#LIN 165 GGCATTCCAGGCGGGGGGAACGGCGTGAGCAAAGGCGCAGAGGCGGGAAN 116 chr6ptel1M 318804 GTGGA--GCATCCTGGAAGGAGCAGTAAGCAGATCAG-GCGGCTGGACTA 318850 i v -- i vi v ii - i i i -vi --i C L2d2_3end#LIN 115 GCGCAAGGCGTGTTCGGGGGA-CAGTGAGTAGACCAGTTTGGCTGGA--G 69 chr6ptel1M 318851 TTAAAAA---GTGTATGGGAGTAGTGTCTAAGAAAACTACAAAAGCAGAA 318897 ivi iii--- ? v i vvvi v ii iv i ? iv C L2d2_3end#LIN 68 CGGAGGGTTCGTGNAGGGGAATAGTGGGAGATAAGGCTGGAAAGGNAGGT 19 chr6ptel1M 318898 AGGGCTCAGCTTGGGGA 318914 v vi v i v C L2d2_3end#LIN 18 TGGGGCCAGATCGTGGA 2 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 43.37 CpG sites = 53, Kimura (unadjusted) = 50.67 Transitions / transversions = 1.61 (53/33) Gap_init rate = 0.06 (16 / 253), avg. gap size = 1.31 (21 / 16) 387 30.48 5.49 2.67 chr6ptel1M 318666 318847 (681153) C L2b_3end#LINE/L2 (213) 253 67 m_b279s601i44 11141 chr6ptel1M 318666 GGGGGATTGGGAAAGGTTTCATGTAGAAGGTTGTACTGGAGATGAAACCT 318715 i ii i i i vi v i vii i v v i C L2b_3end#LINE 253 GGGGGGTCAGGGAGGGCTTCCCGGAGGAGGTGACATTTGAGCTGAGACCT 204 chr6ptel1M 318716 GAAGAA-AACTAGG----GGCTCTGAAAAGCGGCGGTTCAGTAGATCATT 318760 i -i v ---- ivv vi v i ---i v iv i C L2b_3end#LINE 203 GAAGGATGAGTAGGAGTTGGCCAGGCGAAGAGGTGG---GGAAGGGCGTT 157 chr6ptel1M 318761 CCAGGCGTGGAGGACAACAGATGCAAAGATTTAGAGGTGGGAGGTGGAGC 318810 ivi i i i ?i iiiiv i --? C L2b_3end#LINE 156 CCAGGCAGAGGGAACAGCANGTGCAAAGGCCCTGAGGCGGGAG--NGAGC 109 chr6ptel1M 318811 AT--CCTG--GAAGGAGCAGTAAGCAGATCAG-GCGGCTGGA 318847 ? -- v --vi i i v ii - i C L2b_3end#LINE 108 NTGGCGTGTTCGAGGAACAGCAAGGAGGCCAGTGTGGCTGGA 67 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.30 CpG sites = 37, Kimura (unadjusted) = 42.45 Transitions / transversions = 2.18 (37/17) Gap_init rate = 0.06 (10 / 181), avg. gap size = 1.50 (15 / 10) 381 27.94 3.79 8.42 chr6ptel1M 319323 319533 (680467) C MIR#SINE/MIR (11) 251 50 m_b279s601i45 11142 chr6ptel1M 319323 ACAGTTATTG--TGATTATTAATGATTGCCAG-CATT--TATATAGTTCT 319367 v --i v i - -- - i -- v - iv C MIR#SINE/MIR 251 ACATTTATTGAGCGCTTACTA-TG--TGCCAGGCACTGTTCTA-AGCGCT 206 chr6ptel1M 319368 TTACAAATATCCAATAAACACTATGTCATTTTTGTTAATAACCC-AGGAA 319416 vi i----- v - v v ii iii- i - v i C MIR#SINE/MIR 205 TTACATGTATT-----AACTC-ATTTAATCCTCAC-AACAACCCTATGAG 163 chr6ptel1M 319417 CTCGGTGCCCTTAAAATGGGGACACCATTTTACAGATGAGGAAAC-AAGG 319465 v v i iv vv ----- v -i C MIR#SINE/MIR 162 GTAGGTACTATTATTAT-----CCCCATTTTACAGATGAGGAAACTGAGG 118 chr6ptel1M 319466 T-CAAAAAGATGAATTCACTTTCTCAGGGTGATATAGCCAGGAAATATTG 319514 i- i i i v v v v i i v i i i v i ivi- C MIR#SINE/MIR 117 CACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGC- 69 chr6ptel1M 319515 GGAGCTGGGATTTGAACTC 319533 i i i i C MIR#SINE/MIR 68 AGAGCCGGGATTCGAACCC 50 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.49 CpG sites = 32, Kimura (unadjusted) = 35.72 Transitions / transversions = 1.45 (32/22) Gap_init rate = 0.11 (23 / 210), avg. gap size = 1.09 (25 / 23) 382 24.99 2.15 1.06 chr6ptel1M 319441 319533 (680467) C MIRb#SINE/MIR (118) 150 57 m_b279s601i46 11142 chr6ptel1M 319441 CCATTTTACAGATGAGGAAAC-AAGG-TCAAAAAGATGAATTCACTTTCT 319488 -i - i i i v v v v i C MIRb#SINE/MIR 150 CCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCC 101 chr6ptel1M 319489 CAGGGTGATATAGCCAGGAAATATTGGGAGCTGGGATTTGAACTC 319533 i v i i i v i ivi-i i i i C MIRb#SINE/MIR 100 CAAGGTCACACAGCTAGTAAGTGGC-AGAGCCGGGATTCGAACCC 57 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.42 CpG sites = 16, Kimura (unadjusted) = 31.70 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.03 (3 / 92), avg. gap size = 1.00 (3 / 3) 21 13.40 0.00 0.00 chr6ptel1M 319658 319690 (680310) (A)n#Simple_repeat 1 33 (0) m_b279s252i11 11143 chr6ptel1M 319658 AACAAAAAAACAAAAACAAAAAAAAAAAAACAA 319690 v v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 33 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 514 25.16 3.85 0.62 chr6ptel1M 319866 320021 (679979) C Charlie4#DNA/hAT-Charlie (2) 3376 3216 m_b279s502i4 11144 chr6ptel1M 319866 GGGGTGGTTAACCTTTTTGATGTCA-GAAATGCTTCAGAGATCTGGGAAC 319914 vv vi i - i viv ii vii vi v C Charlie4#DNA/ 3376 GGGGTTCTTAACCTTTTTTGTGCCATGGACCCCTTTGGCAGTCTGGTGAA 3327 chr6ptel1M 319915 GCTTATG--TGCTTTCTCAGAA--GCATTTTTAAATGCATTAACATAGAA 319960 i --iv i --iii - v i C Charlie4#DNA/ 3326 GCCTATGGACCCCTTCTCAGAATAATGTTTTTAAATGCAT-AAAATAAAA 3278 chr6ptel1M 319961 CACA-AGAATCACAAAGGTTACTCATTATTTTGTAACTCAGTTATCAAAA 320009 i - i i vv iv v v ivi C Charlie4#DNA/ 3277 TACATAGGATTACAAAGGAAACCAATTATATTGAAATATAGTTATCAAAA 3228 chr6ptel1M 320010 TATTTCAAAACA 320021 v C Charlie4#DNA/ 3227 TATTTAAAAACA 3216 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 31.20 CpG sites = 22, Kimura (unadjusted) = 31.20 Transitions / transversions = 1.29 (22/17) Gap_init rate = 0.03 (5 / 155), avg. gap size = 1.40 (7 / 5) 238 28.21 11.54 0.00 chr6ptel1M 320371 320448 (679552) C MIRc#SINE/MIR (75) 193 107 m_b279s601i47 11145 chr6ptel1M 320371 TCCTCACAACAGACCTGGGAGGTAGGCAGTATGACTAAAGGTAGTCCCAT 320420 iv v viiiiv vviv vi C MIRc#SINE/MIR 193 TCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCAT 144 chr6ptel1M 320421 TT---------AGAAGCTGAGGCTCAGAAGAATGAAG 320448 ---------i i iiii v C MIRc#SINE/MIR 143 TTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAG 107 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.33 CpG sites = 13, Kimura (unadjusted) = 36.33 Transitions / transversions = 1.44 (13/9) Gap_init rate = 0.01 (1 / 77), avg. gap size = 9.00 (9 / 1) 303 32.75 0.00 4.95 chr6ptel1M 320474 320579 (679421) C L3#LINE/CR1 (69) 4030 3930 m_b279s601i48 11146 chr6ptel1M 320474 CAGGCATCTCCTCTTGTCAATGCAATCTTCAACGAATGGTGATTTAGCCT 320523 v i i v-- i--- iiii i i v ii C L3#LINE/CR1 4030 CAGGAATCCCTTCTA--CAAC---ATCCCTGACAAGTGGTCATCCAGCCT 3986 chr6ptel1M 320524 CTACTAGAAGACCTTTAATGATCAAGAACCCACTCCCTGCAGAAGCTGTC 320573 i v v ii i ivii i i v v?v i v i C L3#LINE/CR1 3985 CTGCTTGAACACCTCCAGTGACGGGGAGCTCACTACCTCNCGAGGCAGCC 3936 chr6ptel1M 320574 CATCCC 320579 i C L3#LINE/CR1 3935 CATTCC 3930 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 44.62 CpG sites = 23, Kimura (unadjusted) = 46.63 Transitions / transversions = 2.30 (23/10) Gap_init rate = 0.05 (5 / 105), avg. gap size = 1.00 (5 / 5) 469 23.81 0.00 1.90 chr6ptel1M 320594 320700 (679300) MIRc#SINE/MIR 32 136 (132) m_b279s601i49 11147 chr6ptel1M 320594 GGCCTTCGGAGTCAGGAATTCCTGATTTCAAATTCCAGCTCAGACACTTA 320643 v - vv iv i i i i v v MIRc#SINE/MIR 32 GGACTT-GGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTA 80 chr6ptel1M 320644 TTAGTTATGTGATCCTGGGCAAGTCATATAAATTCTACCTGCCTCAGTTT 320693 i i i i i iv vi vivv MIRc#SINE/MIR 81 CTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTT 130 chr6ptel1M 320694 ACCTTAT 320700 - i MIRc#SINE/MIR 131 -CCTCAT 136 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 26.44 CpG sites = 14, Kimura (unadjusted) = 29.09 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.02 (2 / 106), avg. gap size = 1.00 (2 / 2) 438 24.55 7.98 6.84 chr6ptel1M 320601 320788 (679212) MIR1_Amn#SINE/MIR 41 230 (0) m_b279s601i50 11147 chr6ptel1M 320601 GGAGTCAGGAATTCCTGATTTCAAATTCCAGCTCAGACACTTATTAGTTA 320650 v i iv- iv ? ? i i v v ?iii? i i MIR1_Amn#SINE 41 GGACTCGGGAGA-CCTGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTG 89 chr6ptel1M 320651 TGTGATCCTGGGCAAGTCATATAAATTCTACCTGCCTCAGTTTACCTTAT 320700 ? i i iv ? vi viv? - i MIR1_Amn#SINE 90 NGTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTT-CCTCAT 138 chr6ptel1M 320701 ----AGAATTATTGCCGAGGATCAAATGA----GACAATATTTGTAAAGT 320742 ---- i ------- i -- ---- vviv MIR1_Amn#SINE 139 CTGTAAAAT-------GGGGAT--AATGATACTGACCTCCTTTGTAAAGT 179 chr6ptel1M 320743 GCTTCATAAACCT-------AAAGATGCTGCATACATGCTAATTATTTAT 320785 ii- i i ------- ii i viv iv - MIR1_Amn#SINE 180 GCTTTG-AGATCTACTGATGAAAAGTGCTACATAAGAGCTAGGTA-TTAT 227 chr6ptel1M 320786 TAT 320788 MIR1_Amn#SINE 228 TAT 230 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.56 CpG sites = 28, Kimura (unadjusted) = 32.38 Transitions / transversions = 1.87 (28/15) Gap_init rate = 0.09 (16 / 187), avg. gap size = 1.75 (28 / 16) 190 32.59 0.00 15.04 chr6ptel1M 320791 320920 (679080) C L3#LINE/CR1 (203) 3896 3784 m_b279s601i51 11146 chr6ptel1M 320791 TCCTTAGACCCAGCCTAAATAAGCTTCTCCATAACCTCAGTTCATTATCT 320840 v iiv v vv i i ii i viii ivii C L3#LINE/CR1 3896 TCCTTATATTGAGCCGAAATCTGCCTCCCTGTAACTTCCACCCATTGGTC 3847 chr6ptel1M 320841 CTCTTTGTGCCCTTTGAGAGCAAGTGGAACAGGACAAGGGTTTTTTTTTT 320890 vv v i - v ----v i i -- i vv iii C L3#LINE/CR1 3846 CTAGTTCTGCCCTCTG-GAGCCA----CACAGAATAA--GTCTAATCCCT 3804 chr6ptel1M 320891 TTTTTTTTTGCCCCCACATGACAACCCTTC 320920 i ---------- i C L3#LINE/CR1 3803 CTT----------CCACATGACAGCCCTTC 3784 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 43.12 CpG sites = 22, Kimura (unadjusted) = 43.12 Transitions / transversions = 1.57 (22/14) Gap_init rate = 0.13 (17 / 129), avg. gap size = 1.00 (17 / 17) 462 25.94 0.85 4.42 chr6ptel1M 320951 321067 (678933) C MIRc#SINE/MIR (153) 115 3 m_b279s601i52 11145 chr6ptel1M 320951 GGGATTAAGTGACTTGTGCAGGGTCACACAGCTTTCTTAAATGTTAAGTG 321000 i i iv i --vv i vi --- C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCT--AGTAAGTGGCA---G 71 chr6ptel1M 321001 AGGCCAGATTTGAACTCAGGTCCTCCTGATTTCAGGGTTGATGCTCTATC 321050 v vi i i i i i i i viiii v C MIRc#SINE/MIR 70 AGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTC 21 chr6ptel1M 321051 CACTACACCA-ACTAGCT 321067 i - iv C MIRc#SINE/MIR 20 CACTGCACCACACTGCCT 3 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.74 CpG sites = 20, Kimura (unadjusted) = 33.15 Transitions / transversions = 2.22 (20/9) Gap_init rate = 0.05 (6 / 116), avg. gap size = 1.00 (6 / 6) 212 32.70 10.57 3.03 chr6ptel1M 321149 321271 (678729) C L3#LINE/CR1 (437) 3662 3531 m_b279s601i53 11148 chr6ptel1M 321149 CTCTACTCTGGACATGCTT--ATTTGGCAACTTACTTCCCAAAA-GACGT 321195 v ii i--i v iv v i ii - vv i C L3#LINE/CR1 3662 CTCTCCTCTGGACGCGCTCCAGTTTGTCAATGTCCCTCTTAAAATGTGGC 3613 chr6ptel1M 321196 ACCCAGAAGTTAGCGCGGTGTTGAACCTGTAAT-TGAAGCACCAGCACAG 321244 i v v i ii ii vv vv ii - ---- i C L3#LINE/CR1 3612 GCCCAGAACTGAACGCAATACTCCAGATGTGGTCTG----ACCAGCGCAG 3567 chr6ptel1M 321245 AATGCCTCAG---------CTCCCTCATTCTGAGCA 321271 i i vv i --------- ii? ii C L3#LINE/CR1 3566 AGTACAGCGGGACTATTACCTCCCTTGNTCTGGACA 3531 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.99 CpG sites = 25, Kimura (unadjusted) = 45.86 Transitions / transversions = 1.79 (25/14) Gap_init rate = 0.07 (8 / 122), avg. gap size = 2.12 (17 / 8) 228 31.33 8.01 10.98 chr6ptel1M 321469 321805 (678195) C L3#LINE/CR1 (664) 3435 3108 m_b279s601i54 11148 chr6ptel1M 321469 CTCAAATCTTTTTC--TTGACACTCCTTTTCTAGTCAGGCTC-CTTGGCC 321515 ii ii --v - v vi v- i iii - ivii C L3#LINE/CR1 3435 CCTAGGTCTTTTTCACGTGA-ACTGCTGCTA-AGCCAGATCCTCTCCATC 3388 chr6ptel1M 321516 CTGGATTTGCATAATTAACTCCCTGGAC-TAAA----GAACTTTGCCTTT 321560 v i iii i i i iii i - ---- i i v C L3#LINE/CR1 3387 CTGTACTTGTGCAGTTGATTTTTTGAACCTAAATGCAGGACTTTACATTT 3338 chr6ptel1M 321561 ATTTCTGTTACACGTCAGATCATCGCATTCCCTCCCGCCATCATTGTAGC 321610 ii v iv vv ii i -i i vv --- i vi C L3#LINE/CR1 3337 ATCCCTGTTAAATTTCATCTTGTTG-GTTTCGGCCC---ATCGTTCCAGC 3292 chr6ptel1M 321611 CAGCTGAGAT---TTGGAGTAGGGGGTCTCGGAAACGTCATCTGACAAAT 321657 v ii --- v i vvv iv ------- ii? iv C L3#LINE/CR1 3291 CTGTCGAGATCNTTTTGAATCTTGATTCT-------GTCATCCANCGTAT 3249 chr6ptel1M 321658 T--CTCTTCTTTTC---TTGGTGTTGTCTGCAAA--TGAT-AGTATGTGA 321699 -- v i i ii --- v ii -- - i --- C L3#LINE/CR1 3248 TAGCTATCCCTCCCAGCTTTGTGTCATCTGCAAATTTGATAAGCATG--- 3202 chr6ptel1M 321700 CTCCCCATG--CTCATCTGGACTGCAGTAGTTTTATCAGTCACAAATCTG 321747 iii i --i ------- -- -- i iii - v --- C L3#LINE/CR1 3201 CCTTCTATGTCTTCATC-------CA--AG--TCATTGAT-AAAAAT--- 3167 chr6ptel1M 321748 CTAGGTGGAACTGCGCAGGGTC--CGAC-GTGCC---TGACACCTCTACT 321791 ---- v v vi i --v - v --- i - v i C L3#LINE/CR1 3166 ----GTTGAACAGGACAGGGCCAAGGACAGAGCCCTGTGGCA-CGCCACT 3122 chr6ptel1M 321792 AGAGACTTCTCTCC 321805 i i C L3#LINE/CR1 3121 AGAGACCTCCCTCC 3108 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 41.11 CpG sites = 64, Kimura (unadjusted) = 42.98 Transitions / transversions = 2.13 (64/30) Gap_init rate = 0.15 (49 / 336), avg. gap size = 1.29 (63 / 49) 331 22.07 4.59 8.57 chr6ptel1M 321963 322071 (677929) C MIRc#SINE/MIR (141) 127 23 m_b279s601i55 11149 chr6ptel1M 321963 CTGAGGCAATTGGAG---TCAAGTGACTTTCCCAGGGTCACACC-CTAGG 322008 -- ii --- i v i v- v C MIRc#SINE/MIR 127 CTGAGGC--TCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGT 80 chr6ptel1M 322009 AAGTGTTAAATGTCTGAGGTCACATTTGAACTCAGGTCCTCCTGACTTCA 322058 vi i - i --i ---- i i i i i C MIRc#SINE/MIR 79 AAGTGGCAGA-GCC--GGG----ACTCGAACCCAGGTCTTCCTGACTCCA 37 chr6ptel1M 322059 GGACCGAT-CTCCT 322071 i v ii - i C MIRc#SINE/MIR 36 AGTCCAGTGCTCTT 23 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 24.48 CpG sites = 17, Kimura (unadjusted) = 27.35 Transitions / transversions = 3.40 (17/5) Gap_init rate = 0.11 (12 / 108), avg. gap size = 1.17 (14 / 12) 255 27.12 2.68 4.55 chr6ptel1M 322239 322350 (677650) MIRc#SINE/MIR 96 205 (63) m_b279s601i56 11150 chr6ptel1M 322239 TGGACAAAGTCATTTCATTTCGCTTGGCCTCCATCATCTTATCTGTAGAA 322288 i - i v ii v vi vi ivi i i MIRc#SINE/MIR 96 TGGGCAA-GTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAA 144 chr6ptel1M 322289 TGGGCATAAT-ATAACT-CATTGGAT-CCCCAGAGTATTGTATGTGGCAA 322335 v - v - vi vv - i v vi - -- i MIRc#SINE/MIR 145 TGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGT-TGTG--AG 191 chr6ptel1M 322336 GCTGCAAAAGAGACA 322350 v - v i MIRc#SINE/MIR 192 GAT-CAAATGAGATA 205 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.07 CpG sites = 15, Kimura (unadjusted) = 34.07 Transitions / transversions = 1.07 (15/14) Gap_init rate = 0.07 (8 / 111), avg. gap size = 1.00 (8 / 8) 21 29.48 2.08 3.16 chr6ptel1M 322777 322872 (677128) (GGC)n#Simple_repeat 1 95 (0) m_b279s252i12 11151 chr6ptel1M 322777 GGTGGCGGGAGGCGGGCTG-GGAGG-GGCCGGAGCGGATGCAGCAGGGGC 322824 i - v - v - v - v vi vv i i v (GGC)n#Simple 1 GGCGGC-GGCGGC-GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC 48 chr6ptel1M 322825 GTGTGACTGCACTGGTGTCGGCGGGAGCGGCGGCGGCGGCGGCGGCGG 322872 - i i v ivi i v vi (GGC)n#Simple 49 G-GCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGG 95 Matrix = Unknown Transitions / transversions = 0.83 (10/12) Gap_init rate = 0.05 (5 / 95), avg. gap size = 1.00 (5 / 5) 17 15.32 2.70 0.00 chr6ptel1M 322845 322881 (677119) (GCGGCA)n#Simple_repeat 1 38 (0) m_b279s252i13 11152 chr6ptel1M 322845 GCGGGAGCGGCGGCGGCGGCGGCGGCGG-AGCAGCAGC 322881 v i i i - i (GCGGCA)n#Sim 1 GCGGCAGCGGCAGCGGCAGCGGCAGCGGCAGCGGCAGC 38 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 37 0.00 0.00 0.00 chr6ptel1M 323107 323140 (676860) (C)n#Simple_repeat 1 34 (0) c_b279s251i4 11153 chr6ptel1M 323107 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 323140 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 34 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 43 7.86 0.00 0.00 chr6ptel1M 323545 323599 (676401) (GT)n#Simple_repeat 1 55 (0) c_b279s251i5 11154 chr6ptel1M 323545 GTGTGTGTGCGTGTGTGTGTGTGCGCGTATGTGTGTGTGTGTGTGTGTGT 323594 i i i i (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50 chr6ptel1M 323595 GTGTG 323599 (GT)n#Simple_ 51 GTGTG 55 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 27 21.98 4.17 3.09 chr6ptel1M 323702 323797 (676203) (CGGGCG)n#Simple_repeat 1 97 (0) m_b279s252i14 11155 chr6ptel1M 323702 CGGGAGCCGGCGGGAGGGCCGGGC-CGGG-G-GGG-GGGGGCGCGGGGCC 323747 v v v - vv - - - - v vv (CGGGCG)n#Sim 1 CGGGCGCGGGCGCG-GGCGCGGGCGCGGGCGCGGGCGCGGGCGCGGGCGC 49 chr6ptel1M 323748 GGGAGTGGGGTGCGGGGCCGGGAGTAGGGCGCGGGCCCGGGCCCGGGCGC 323797 v -v i vv v -v v v (CGGGCG)n#Sim 50 GGGCG-CGGGCGCGGGCGCGGGCG-CGGGCGCGGGCGCGGGCGCGGGCGC 97 Matrix = Unknown Transitions / transversions = 0.06 (1/16) Gap_init rate = 0.07 (7 / 95), avg. gap size = 1.00 (7 / 7) 20 23.50 0.00 5.88 chr6ptel1M 323736 323807 (676193) (GGGCCC)n#Simple_repeat 1 68 (0) m_b279s252i15 11155 chr6ptel1M 323736 GGGCGCGGGGCCGGGAGTGGGGTGCGGGGCCGGGAGTAGGGCGCGGGCCC 323785 v v -viv iv v -viv v (GGGCCC)n#Sim 1 GGGCCCGGGCCCGGG-CCCGGGCCCGGGCCCGGG-CCCGGGCCCGGGCCC 48 chr6ptel1M 323786 GGGCCCGGGCGCCCCGGCCCGG 323807 - - v (GGGCCC)n#Sim 49 GGGCCC-GG-GCCCGGGCCCGG 68 Matrix = Unknown Transitions / transversions = 0.30 (3/10) Gap_init rate = 0.06 (4 / 71), avg. gap size = 1.00 (4 / 4) 62 1.78 0.00 0.00 chr6ptel1M 324055 324111 (675889) (TG)n#Simple_repeat 1 57 (0) c_b279s251i6 11156 chr6ptel1M 324055 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 324104 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr6ptel1M 324105 TCTGTGT 324111 v (TG)n#Simple_ 51 TGTGTGT 57 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0) 21 4.00 0.00 0.00 chr6ptel1M 325043 325068 (674932) (TG)n#Simple_repeat 1 26 (0) m_b279s252i16 11157 chr6ptel1M 325043 TGTGTGTGTGTGTGTGTGTGTGTATG 325068 i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTG 26 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 435 29.72 2.33 4.14 chr6ptel1M 325214 325385 (674615) MIR3#SINE/MIR 33 201 (7) m_b279s601i57 11158 chr6ptel1M 325214 CTGGGATTCTGG-GACTTGGGTTCAAATTCCAGTTGGGCTGCTTGGGATC 325262 v v - i v i i i i vv ii vivv?v MIR3#SINE/MIR 33 CTGGGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGC 82 chr6ptel1M 325263 TCTGTGACCTTAGGGCTGTCATTTCA--TGTGTGGCTCTCAGTTTCTTCA 325310 v i vvv i -- v v vi i MIR3#SINE/MIR 83 TGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCA 132 chr6ptel1M 325311 TCTGTAAAAATAAGGTAGATCACGCTCATGTAGCCAACCTCCAAGGTCAC 325360 - i -i i iivi ----- vii i i v MIR3#SINE/MIR 133 TCTGT-AAAATGAGG-GGGTTGGAC-----TAGATGATCTCTAAGGTCCC 175 chr6ptel1M 325361 TTTCAGTTCTAA-AGCCTGTGACCCT 325385 i i i - vi i ii MIR3#SINE/MIR 176 TTCCAGCTCTGACATTCTATGATTCT 201 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.23 CpG sites = 29, Kimura (unadjusted) = 39.27 Transitions / transversions = 1.45 (29/20) Gap_init rate = 0.06 (10 / 171), avg. gap size = 1.10 (11 / 10) 180 12.50 3.12 0.00 chr6ptel1M 325758 325789 (674211) C L3b_3end#LINE/CR1 (618) 588 556 m_b279s601i58 11159 chr6ptel1M 325758 GCA-CCGCTTGACACTGCTGACTCATACTGAGC 325789 - v vi i C L3b_3end#LINE 588 GCAGCCGCGTCGCACTGCTGACTCATATTGAGC 556 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 10.37 CpG sites = 2, Kimura (unadjusted) = 13.72 Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 12 21.98 2.70 0.00 chr6ptel1M 326214 326250 (673750) (TTTAAAA)n#Simple_repeat 1 38 (0) m_b279s252i17 11160 chr6ptel1M 326214 TTTAAAAAATAATAATT-GTATTTAAAATTTATAATTT 326250 vv v v -iv v (TTTAAAA)n#Si 1 TTTAAAATTTAAAATTTAAAATTTAAAATTTAAAATTT 38 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 243 22.22 0.00 0.00 chr6ptel1M 326292 326336 (673664) C MIRc#SINE/MIR (97) 171 127 m_b279s601i59 11161 chr6ptel1M 326292 TAGGTAAAGTAAATATTATTGTCCCCATTTGACAGATGAATAAAC 326336 i ii i ii i v iv C MIRc#SINE/MIR 171 TAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAAC 127 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.87 CpG sites = 8, Kimura (unadjusted) = 27.87 Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 336 32.55 5.95 3.70 chr6ptel1M 326849 327033 (672967) C MIR3#SINE/MIR (6) 202 14 m_b279s601i60 11162 chr6ptel1M 326849 TAGAAGTATAGGAAAAAAAGTTAGAGCCAACAGG--CCTTAGAAATCATC 326896 vi ----- v i iiiv -- i C MIR3#SINE/MIR 202 TAGAATCATAG-----AATGTCAGAGCTGGAAGGGACCTTAGAGATCATC 158 chr6ptel1M 326897 TTAGCCAAATCTCACATTTTTC---TTAGGCAAAATAAATACTATCTTTG 326943 viv vi i v v --- v - v i ivv i vvvvv C MIR3#SINE/MIR 157 TAGTCCAACCCCCTCATTTTACAGATGAGG-AAACTGAGGCCCAGAGAGG 109 chr6ptel1M 326944 TACA-TGAATTGCTTGATATCATCCTATGAGTTAGGAGCAAAGTGAAGAC 326992 iv - v iii vi iv vii? vi i ivii C MIR3#SINE/MIR 108 TGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGAC 59 chr6ptel1M 326993 TGGAATTCCA----TCATGACTTCCGGTCC-TGCCCTTTCTTTTCA 327033 i -i ---- v i i - i i vi C MIR3#SINE/MIR 58 TAGAA-CCCAGGTCTCCTGACTCCCAGTCCGTGCTCTCTCTGCTCA 14 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 43.18 CpG sites = 32, Kimura (unadjusted) = 44.21 Transitions / transversions = 1.23 (32/26) Gap_init rate = 0.07 (12 / 184), avg. gap size = 1.50 (18 / 12) 364 28.98 7.46 2.13 chr6ptel1M 327621 327754 (672246) C L2a_3end#LINE/L2 (10) 507 367 m_b279s601i61 11163 chr6ptel1M 327621 TCAACAAACATTTATTAAGTGTTTATTACTTGCCAGGCACAGCATTAGGT 327670 i i i ii i iv v ivi i C L2a_3end#LINE 507 TCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGC 458 chr6ptel1M 327671 ACTGGTGATAAAAATACAATGAATGAAAC-------AATCCTAGCTCAGG 327713 i v v ---i i ii ------- i iv i vvi C L2a_3end#LINE 457 GCTGGGGATACA---GCAGTGAACAAAACAGACAAAAGTCCCTGCCCTCA 411 chr6ptel1M 327714 AGGAACTGTTATTTTAAT--AGGGAGACA-AGAATATACACATA 327754 v i vvi i i --i - v v v C L2a_3end#LINE 410 TGGAGCTTACATTCTAGTGGGGGGAGACAGACAATAAACAAATA 367 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.39 CpG sites = 24, Kimura (unadjusted) = 38.07 Transitions / transversions = 1.71 (24/14) Gap_init rate = 0.05 (6 / 133), avg. gap size = 2.17 (13 / 6) 13 26.25 0.00 2.17 chr6ptel1M 327796 327842 (672158) (TAAAA)n#Simple_repeat 1 46 (0) m_b279s252i18 11164 chr6ptel1M 327796 TACAATAGAATAAATAAAAATGAAGATAAAATAGCTTAATAGAAAAT 327842 v i vv - i ivv v v (TAAAA)n#Simp 1 TAAAATAAAATAAAATAAAAT-AAAATAAAATAAAATAAAATAAAAT 46 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.02 (1 / 46), avg. gap size = 1.00 (1 / 1) 206 31.38 6.45 2.33 chr6ptel1M 328167 328290 (671710) L2a_3end#LINE/L2 333 461 (56) m_b279s601i62 11165 chr6ptel1M 328167 ACCACCCCCACACATACACTCAATTTTCACTTAAATTTTCTTTTATGGAT 328216 i vi vv vv vv - vv v iv v vi L2a_3end#LINE 333 ATCACCATCTGACATACTATATATTTT-ACTTATTTATTTGTTTATTGTC 381 chr6ptel1M 328217 TGCCTGCTTCCATTAGAATGTAAGTTCTGTGGGAGTA------TATGTTT 328260 i v ii i i ii i i i ------ v i L2a_3end#LINE 382 TGTCTCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTCT 431 chr6ptel1M 328261 GTATTTGTATCCCTA--GTATTTCAAAGGTCT 328290 - - v i-- ii v iv i L2a_3end#LINE 432 GT-TTTGT-TCACTGCTGTATCCCCAGCGCCT 461 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 41.46 CpG sites = 20, Kimura (unadjusted) = 41.46 Transitions / transversions = 1.11 (20/18) Gap_init rate = 0.04 (5 / 123), avg. gap size = 2.20 (11 / 5) 258 37.26 8.60 1.89 chr6ptel1M 328398 329141 (670859) C L2#LINE/L2 (1317) 1765 973 m_b279s601i63 11166 chr6ptel1M 328398 GGAAACAAACCAATAGGAAGGGAGAAGTTGAAGATCCAAGAGAAAGAAGT 328447 i ii v i ii i i v v i i i v C L2#LINE/L2 1765 GGGAATGATCCAGTAGAGAGGGAAAAATTGATGATGCAGGAGAGAGAGGG 1716 chr6ptel1M 328448 GA---TTCCATGAAG--ATGGCAATCTATAGGAAAAACAGGATCAAA--- 328489 --- v - i -- v vv vvi vi i vi vii --- C L2#LINE/L2 1715 GAGAATTGC-TGGAGCGATGTCCTTGAGTAGGCGAGAGGGGATGGGATCT 1667 chr6ptel1M 328490 AGTAT----GTGAAGAGGCTTTAGC-TCGGCCAGGAGAAAGGAATCTTTT 328534 ii---- i i -- i - ii vi v v -ivv i C L2#LINE/L2 1666 AGTGCACAAGTGGAGGGG--TTGGCCTTAGATAGGAGCACGGA-CAGTTC 1620 chr6ptel1M 328535 GTTTTCAGAGACTAAGGGAAAGGAAAAGAA-GTGGGGAATGATGTCGAGA 328583 i iivi vi viii i v i v - v vv iv iv C L2#LINE/L2 1619 ATCCGTAGTAACAGGAGGGAAGGCAGAGTATGTGGGCACAGATGCAGGTA 1570 chr6ptel1M 328584 GGTTTTGCAG----GGAAGAGAGGGGGAGCAGAAGTGGTTCATGGGGAAT 328629 vv- i ---- vi v i i ??v ii v-i v vv -- C L2#LINE/L2 1569 GGTGG-GTAGATGTGGTGGTGGGAGNNTGTGGAAGTT-CTCTTCTG--AT 1524 chr6ptel1M 328630 GACCTCTATTTTCT--ATCATGTAGGATGCAAAAT----ATTTGAGAGAA 328673 vi i --i v vi v ii ---- vi vi C L2#LINE/L2 1523 TGCTTCTATTTTCTCAGTGAAATAGGAAGCAAGGTCATCAGCTGAGAGTG 1474 chr6ptel1M 328674 GGGA-AGAGGAAAATAAG--GGAGGATTGAGGATAGAAGAGAAGGTTTCT 328720 i - i ii viv -- v v i v vv C L2#LINE/L2 1473 AGGATAGGGGAGGAGGTGTTGGAGGTTTGAGGAGAGAGGAGAAGGTGTGA 1424 chr6ptel1M 328721 AATAGTC-TCTATTTAGAATGAATTAGAAAACCACTTAAGGAAA---AAT 328766 - -vv i iivv vi ivivi i --- i C L2#LINE/L2 1423 AATAGTCGTCTA-GGAGAGTGGGAGAGTGAATGGACTAGGGAAATGTAGT 1375 chr6ptel1M 328767 AGGATTTTTTTGCTACGGTGAAGCTCAAGTTAAAGTTAGGTAACGTGAAT 328816 ? viivv vi iv i i vi v v i i ? vviv i C L2#LINE/L2 1374 ANGATTGCCGGGCAGCATTAAGGGCCCACTTGAGGTTNGTGGTCATGAAT 1325 chr6ptel1M 328817 TTATTGTG-TACT-GTTAGCACAATTTTATGAATTCCTCTAGCACTATTT 328864 vv -v i- i iii v i vv i i vvii i C L2#LINE/L2 1324 TTAAAGTGAGACCAGTCAGCATGGTTGTGTGTTTTTCTCCAGCCACGTTC 1275 chr6ptel1M 328865 AATAATACACCAAAAAGAACAGAGGTGGTAGATGGTGGGGATTATCCAGA 328914 iivii? ivvviv i vi i vv ii vi v iv v i C L2#LINE/L2 1274 AGCTGCNCGGGTGCAGGCGCGGAGTAGGCGGAGAGTTGGATTTAACCAGG 1225 chr6ptel1M 328915 GACGAGG-TTTGCCAAGGGACGAACAGC--AATGAAAGGTGATGAAGATA 328961 vi ? - i v - v ii -- ii i iv ivv iv C L2#LINE/L2 1224 GTTGNGGTTTTGCCAGGCGA-GTACGACGAAGCGAGAGAGGGGCAAGGGA 1176 chr6ptel1M 328962 TTCAATAGTAGATGACAGCGTAGAGTTGA-----ATTGGCTA---ATTGT 329003 v ii vi v - iv v v v v ----- ? i i --- v v C L2#LINE/L2 1175 GTTGAGGGTATATG-CAAGGGAGTGATTATAATGATNGACCATGGAATCT 1127 chr6ptel1M 329004 AAGTTGAGACTGGGAGGAGAGTGAG--CA--GGGAGGATGATTTGAGAAA 329049 i - iivi ii -- --i i i --- i v C L2#LINE/L2 1126 AAGCTG-GGTAAGGAGGGAAGTGAGGACATGAGGGGGGTGA---GGGACA 1081 chr6ptel1M 329050 G-AAACAAGTGAT-GGA-----GCATTAAAGATCTTTATTAGGGTGAGGA 329092 -i v i i - ----- v ii i iivi vi vi i C L2#LINE/L2 1080 GTGAAAAGGTGGTAGGATCAATGGATTGGAGGTCCCGGTGGGGTCGAAGA 1031 chr6ptel1M 329093 ATAGCT----TTAGG-----AAAGGGAGAAAGAGAGAATGACTGGAGGTT 329133 v i ---- ii ----- i vi vvi v iv v C L2#LINE/L2 1030 ATTGTTGGAGTCGGGGTACTAGAGGGAGTGAGCTGGAAAGATAGGAGGTG 981 chr6ptel1M 329134 ACGGTCAG 329141 ii C L2#LINE/L2 980 GTGGTCAG 973 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 50.53 CpG sites = 153, Kimura (unadjusted) = 54.41 Transitions / transversions = 1.29 (153/119) Gap_init rate = 0.06 (41 / 743), avg. gap size = 1.93 (79 / 41) 15 23.85 4.08 0.00 chr6ptel1M 329215 329263 (670737) (AGT)n#Simple_repeat 1 51 (0) m_b279s252i19 11167 chr6ptel1M 329215 AGTAGT-GT-GGAGAAGTATTACTACTACTAGTAGTAGCAGCAGCAGCAG 329262 - - v v v v v v i i i i (AGT)n#Simple 1 AGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAG 50 chr6ptel1M 329263 T 329263 (AGT)n#Simple 51 T 51 Matrix = Unknown Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.04 (2 / 48), avg. gap size = 1.00 (2 / 2) 476 29.27 16.11 1.24 chr6ptel1M 329301 329331 (670669) C MIRc#SINE/MIR (17) 251 221 m_b279s601i64 11168 chr6ptel1M 329301 ACATTTATATATTGCTTTATGGTTGACAAAG 329331 i vii ii v C MIRc#SINE/MIR 251 ACATTTGTATAGCACTTTACAGTTTACAAAG 221 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.73 CpG sites = 47, Kimura (unadjusted) = 40.51 Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 46 4.35 0.00 0.00 chr6ptel1M 329332 329379 (670621) (CA)n#Simple_repeat 1 48 (0) c_b279s251i7 11169 chr6ptel1M 329332 CACACACACACACACACACACACACACACACACACACATGCACACACA 329379 ii (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACA 48 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 476 29.27 16.11 1.24 chr6ptel1M 329380 329558 (670442) C MIRc#SINE/MIR (48) 220 11 m_b279s601i64 11168 chr6ptel1M 329380 ---TTCA---------TTTCACTGGATCCTTACAACAATCCTATAAAGTT 329417 --- --------- i i v i i i i i - C MIRc#SINE/MIR 220 GCTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGT- 172 chr6ptel1M 329418 AGGC-----------TGTT----TGGTTTTACAGATGCAGAAAGGGAGGT 329452 ----------- i ----ivi vi vv i C MIRc#SINE/MIR 171 AGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGC 122 chr6ptel1M 329453 T--AAGAGATCAAATGCATTT--TCAGGATCACA-AATTAGTAAGTGTCT 329497 --i i i i - i --i i i - ii v v C MIRc#SINE/MIR 121 TCAGAGAGGTTAAGTG-ACTTGCCCAAGGTCACACAGCTAGTAAGTGGCA 73 chr6ptel1M 329498 AAAGCAGAATTAAAATTCAGATCTCCTTGATT--AATCTCTGGCACCTTA 329545 i iv i i i vi ii i i i i -- -v ii ii ii v C MIRc#SINE/MIR 72 GAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAA-GTCCAGTGCTCTT 24 chr6ptel1M 329546 TCCACCACACAAC 329558 ii v C MIRc#SINE/MIR 23 TCCACTGCACCAC 11 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.73 CpG sites = 47, Kimura (unadjusted) = 40.51 Transitions / transversions = 3.50 (42/12) Gap_init rate = 0.06 (11 / 178), avg. gap size = 3.36 (37 / 11) 374 35.52 5.42 4.17 chr6ptel1M 329568 329899 (670101) C L2#LINE/L2 (2232) 850 515 m_b279s601i65 11166 chr6ptel1M 329568 AGGAGAATGAGCAATTGGGAGATCAGAAAATTTGA-GGATATATTAACTT 329616 ivii v i i ii iiv v - -i iv v C L2#LINE/L2 850 AGGAGGTCAAGGAACTGAGAGGCCAGGGTATTGGAAGGAT-CATCTACGT 802 chr6ptel1M 329617 GAATATTGGAGTCTCCTAGTATAAAAGCAGGGATTAGGAAAGAGAGAAAG 329666 i i i v v v v vii ii viv vvi iv C L2#LINE/L2 801 GGATATTGAAATCACCAAGAATTATGACAGGAGTAGTGTTGGAGAGAGTG 752 chr6ptel1M 329667 GCTGTGAACCAGGGGCTGAACTCCTCAAGAAAAGAGGGAGAATGATT--G 329714 i v i i i v i i v i i ii-- C L2#LINE/L2 751 ACAGTGAGCCAGGAGCTAAAATCTTCAAGGAATGAGGGGGAGTGACCCGG 702 chr6ptel1M 329715 GGGTCTGGAACATGGGAACTACCATGTTTTGAATA--GAATGG-AAAATT 329761 i - v v ivvi v v v --vv ii -- ii - v i i C L2#LINE/L2 701 AGGTC-GGTAGATGACTGCAACAAGG--AGGGGTAGCGGGTGGTATAGTC 655 chr6ptel1M 329762 TGAATCATGTGAACTTCAGAGGAGAGGTTGCCAATTT--------ACGGC 329803 - v ii iv i vv i -----i -------- v v C L2#LINE/L2 654 TG-ATGACATGAGATTCAAAGCTGGGGT-----GTTTTAGGGAGGAGGGA 611 chr6ptel1M 329804 CGTAGA---GTTAGGAAGTGGCAGTAGGCAACAAGAAGTTTTTCCGCTCC 329850 v v --- iv i i ii v i i vvivi ii i C L2#LINE/L2 610 GGGAGAATGGTCTGGAAGCGGCAATGAGGAGCAAGGAGGACACCTACCCC 561 chr6ptel1M 329851 ATCTCCAACACCAGTTG-ACTAGAGATGCAGGAATATCAGAAATGAGCTA 329899 i ivv v - v i ? ii i---- vv i C L2#LINE/L2 560 ACCTCCAGGCCCAGTGGTACGAGGGNTGTGGGAG----AGAAAACAGCCA 515 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 49.60 CpG sites = 65, Kimura (unadjusted) = 50.24 Transitions / transversions = 1.35 (65/48) Gap_init rate = 0.06 (21 / 331), avg. gap size = 1.52 (32 / 21) 289 31.67 5.85 5.85 chr6ptel1M 330527 330697 (669303) L3#LINE/CR1 3901 4071 (28) m_b279s601i66 11170 chr6ptel1M 330527 CTCCCTCATAATTAGAGCAATCCAAAGCTGTAATGGGATGCTTTCAGGAC 330576 ii v i i vi iv v v i iv? iiv L3#LINE/CR1 3901 CTTTCTAACAATCAGAGCTGTCCAAAAATGGAATGGGCTGCCTCGNGAGG 3950 chr6ptel1M 330577 CAGTGAGTTCAACTTCAGCAACAGCTCTTTAAGCTGGACCTGGTTGAC-- 330624 i i vv v - viv v v i v iiv v -- L3#LINE/CR1 3951 TAGTGAGCTCCCCGTCA-CTGGAGGTGTTCAAGCAGAGGCTGGATGACCA 3999 chr6ptel1M 330625 ----TTAGGGTTGGACTCTTTGGAGAAGAGTTTCTTT--TTGG--GGCAG 330666 ---- i v ------ v i v i v-- -- v L3#LINE/CR1 4000 CTTGTCAGGGATG------TTGTAGAAGGGATTCCTGCATTGGATGGGAG 4043 chr6ptel1M 330667 GGCTTGGATCAGATAGTCACTGACAGTTTCT 330697 -- ii iii v i -i ii L3#LINE/CR1 4044 G--TTGGACTAGATGACCTCTAA-GGTCCCT 4071 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 41.41 CpG sites = 28, Kimura (unadjusted) = 42.51 Transitions / transversions = 1.22 (28/23) Gap_init rate = 0.08 (14 / 170), avg. gap size = 1.43 (20 / 14) 196 23.91 2.17 0.00 chr6ptel1M 330868 330913 (669087) C MIR3#SINE/MIR (38) 170 124 m_b279s601i67 11171 chr6ptel1M 330868 CTTA-AGACTATCTAGTCCAGTTTCCTTATTTTAGATATCAAGAAAC 330913 - ii iiii i v v v i C MIR3#SINE/MIR 170 CTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAAC 124 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.13 CpG sites = 8, Kimura (unadjusted) = 30.13 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1) 357 31.49 4.64 3.27 chr6ptel1M 330998 331148 (668852) MIRc#SINE/MIR 1 153 (115) m_b279s601i68 11172 chr6ptel1M 330998 CAAGACAGTGGAGTG---TGGGATTAGCATGGTATGGTGGAAAGGTAGAA 331044 i i vi --- i vv iv v iv- -- vi i MIRc#SINE/MIR 1 CGAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACT-TGGA--GTCAGGA 47 chr6ptel1M 331045 AGAGACCTGGGCTGAAGTTCTGGTCTGGCCACTAACTGTTCGTGCCATCT 331094 -- i vi i i iiiv v ivii iv i MIRc#SINE/MIR 48 AGA--CCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCT 95 chr6ptel1M 331095 TGAAAAAGACACTTA---TCTGTGGGTCTCAGTTTCTTCATAT-CAAGAT 331140 iiv v --- v i i i v -i i MIRc#SINE/MIR 96 TGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAAT 145 chr6ptel1M 331141 TGAAATAA 331148 v ii MIRc#SINE/MIR 146 GGGGATAA 153 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.01 CpG sites = 29, Kimura (unadjusted) = 42.67 Transitions / transversions = 1.71 (29/17) Gap_init rate = 0.05 (8 / 150), avg. gap size = 1.50 (12 / 8) 380 31.42 8.51 0.66 chr6ptel1M 331044 331184 (668816) MIR3#SINE/MIR 42 193 (15) m_b279s601i69 11172 chr6ptel1M 331044 AAGAGACCTGGGCTGAAGTTCTGGTCTGGCCACTAACTGTTCGTGCCATC 331093 i i vv i i iiiv ?vii iv i MIR3#SINE/MIR 42 AGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACC 91 chr6ptel1M 331094 TTGAAAAAGACACTT---ATCTGTGGGTCTCAGTTTCTTCAT-------A 331133 iiv v ---v v i i ------- MIR3#SINE/MIR 92 TTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAA 141 chr6ptel1M 331134 TCA--AGATTGAAATAAATCCCATCCAGGGCCCTTTGTGGTTCTGATGAT 331181 v --i i i v i vviv i i i i vii i i- MIR3#SINE/MIR 142 TGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGAC-AT 190 chr6ptel1M 331182 TTT 331184 i MIR3#SINE/MIR 191 TCT 193 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 41.97 CpG sites = 29, Kimura (unadjusted) = 43.32 Transitions / transversions = 1.93 (29/15) Gap_init rate = 0.03 (4 / 140), avg. gap size = 3.25 (13 / 4) 232 27.56 8.63 3.42 chr6ptel1M 331639 331777 (668223) L1MB2_3end#LINE/L1 408 553 (365) m_b279s551i4 11173 chr6ptel1M 331639 GAAAGCAAGGGGATAGGAGGGAAAT--GCACTCTCATGT-----GCAGCC 331681 - vv v i i v -- v i ----- v L1MB2_3end#LI 408 GAAAGCA-GGGTCTCGAAGAGATATTTGCACACCCATGTTCATAGCAGCA 456 chr6ptel1M 331682 CTTTTTGTAGTGGCAAGGAACTGGAAAC----CGAGTGATGTCCATCAGT 331727 i v iii i i v i iv i ---- i --- - v L1MB2_3end#LI 457 TTATTCACAATAGCCAAGAGGTGGAAGCAACCCAAGTG---TCCATC-GA 502 chr6ptel1M 331728 TAGA-GAATGGCTGGATAAATTATGGTATATTAATGTTATGGAATATTCT 331776 ii - v ii i v i vv iiv v L1MB2_3end#LI 503 CGGATGAATGGATAAACAAAATGTGGTATATACATACAATGGAATATTAT 552 chr6ptel1M 331777 T 331777 L1MB2_3end#LI 553 T 553 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.88 CpG sites = 21, Kimura (unadjusted) = 35.18 Transitions / transversions = 1.31 (21/16) Gap_init rate = 0.07 (9 / 138), avg. gap size = 1.89 (17 / 9) 266 30.05 7.41 1.40 chr6ptel1M 331656 331790 (668210) L1MA4A_3end#LINE/L1 424 566 (484) m_b279s551i5 11173 chr6ptel1M 331656 AGGGAAA--TGCACTCTCATGT-----GCAGCCCTTTTTGTAGTGGCAAG 331698 v -- i ----- v v iii i i i L1MA4A_3end#L 424 AGGGATACCTGCACTCCCATGTTTATTGCAGCACTATTCACAATAGCAAA 473 chr6ptel1M 331699 GAACTGGAA---ACCGAGTGATGTCCATCAGTTAGAGAATGGCTGGATAA 331745 vv --- v i--i iiviiv v ii v L1MA4A_3end#L 474 GATATGGAATCAACCTAA--GTGTCCATCAACGGATGAATGGATAAAGAA 521 chr6ptel1M 331746 ATTATGGTATATTAATGTTATGGAATATTCTTATTCTATAAGAAA 331790 v i vv iiiv i v vvv i i L1MA4A_3end#L 522 AATGTGGTATATATACACAATGGAATACTATTCGGCCATAAAAAA 566 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.02 CpG sites = 22, Kimura (unadjusted) = 39.27 Transitions / transversions = 1.22 (22/18) Gap_init rate = 0.04 (5 / 134), avg. gap size = 2.40 (12 / 5) 242 29.53 7.73 3.98 chr6ptel1M 331663 331856 (668144) L1MA10_3end#LINE/L1 433 633 (448) m_b279s551i6 11173 chr6ptel1M 331663 TGCACTCTCATGT-----GCAGCCCTTTTTGTAGTGGCAAGGAACTGGAA 331707 i ----- vi v iii i i v i vv L1MA10_3end#L 433 TGCACTCCCATGTTCATTGCAGCATTATTCACAATAGCCAAGATATGGAA 482 chr6ptel1M 331708 ACCGAGTGA-TGTCCATCAGTTAGA-GAATGGCTGGATAAATTATGGTAT 331755 vivv i - - vii - v ii v v i L1MA10_3end#L 483 ACAACCTAAATGTCCATC-GACGGATGAATGGATAAAGAAAATGTGGTAT 531 chr6ptel1M 331756 ATTAATGTTATGGAATATTCTT-ATTCTATAAGAAACGATCAGCAGGA-- 331802 vv iiv v - vi - i ------ v -- L1MA10_3end#L 532 ATACATACAATGGAATATTATTCAGCCT-TAAAAA------AGAAGGAAA 574 chr6ptel1M 331803 ---TG--ATTTCCTAGAGCCTGGAGAGACTTATAGGAACTGATGCTTGGT 331847 --- -- v v v i v vii i iv vv v vi L1MA10_3end#L 575 TCCTGCCATTTGCGACAACATGGATGAACCTGGAGGACATTATGCTAAGT 624 chr6ptel1M 331848 GAAGTGAGC 331856 i i L1MA10_3end#L 625 GAAATAAGC 633 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.07 CpG sites = 27, Kimura (unadjusted) = 38.02 Transitions / transversions = 0.96 (27/28) Gap_init rate = 0.08 (15 / 193), avg. gap size = 1.53 (23 / 15) 411 25.00 0.95 0.95 chr6ptel1M 331670 331774 (668226) L1ME3G_3end#LINE/L1 442 546 (378) m_b279s551i7 11173 chr6ptel1M 331670 TCATGTGCAGCCCTTTTTGTAGTGGCAAGGAACTGGAAACCGAGTGA-TG 331718 - vi v i i i ii i vivv i - L1ME3G_3end#L 442 TCAT-TGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATG 490 chr6ptel1M 331719 TCCATCAGTTAGAGAATGGCTGGATAAATTATGGTATATTAATGTTATGG 331768 i vi i i ii iv ii L1ME3G_3end#L 491 TCCATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGG 540 chr6ptel1M 331769 AATATT 331774 i L1ME3G_3end#L 541 AATACT 546 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 30.45 CpG sites = 19, Kimura (unadjusted) = 31.96 Transitions / transversions = 2.71 (19/7) Gap_init rate = 0.02 (2 / 104), avg. gap size = 1.00 (2 / 2) 268 30.62 3.51 2.61 chr6ptel1M 331676 331789 (668211) L1MB7_3end#LINE/L1 451 565 (366) m_b279s551i8 11173 chr6ptel1M 331676 GCAGCCCTTTTTGTAGTGGCAAGGAACTGGAAAC----CGAGTGATGTCC 331721 vi v ii i i v ii v ---- i --- L1MB7_3end#LI 451 GCAGCATTATTCATAATAGCCAAAAAGTGGAAACAACCCAA---ATGTCC 497 chr6ptel1M 331722 ATCAGTTAGAGAATGGCTGGATAAATTATGGTATATTAATGTTATGGAAT 331771 ii iiv v ii i v i iv iiv L1MB7_3end#LI 498 ATCAACTGATGAATGGATAAACAAAATGTGGTATATCCATACAATGGAAT 547 chr6ptel1M 331772 ATTCTTATTCTATAAGAA 331789 v vvv i i L1MB7_3end#LI 548 ATTATTCGGCCATAAAAA 565 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.88 CpG sites = 21, Kimura (unadjusted) = 40.88 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.04 (4 / 113), avg. gap size = 1.75 (7 / 4) 280 24.59 1.64 0.00 chr6ptel1M 332390 332450 (667550) MIR3#SINE/MIR 143 204 (4) m_b279s601i70 11174 chr6ptel1M 332390 GAAAGGCTTGGATTAAATGATCTTTAATATCTCTTCCAGTTTAAACATGC 332439 ii v i i i vi i i ivi v MIR3#SINE/MIR 143 GAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTC 192 chr6ptel1M 332440 TGT-ATTCTATG 332450 i - MIR3#SINE/MIR 193 TATGATTCTATG 204 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.29 CpG sites = 11, Kimura (unadjusted) = 31.29 Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.02 (1 / 60), avg. gap size = 1.00 (1 / 1) 322 26.22 0.00 4.67 chr6ptel1M 332811 332922 (667078) Charlie4#DNA/hAT-Charlie 34 140 (3238) m_b279s502i5 11175 chr6ptel1M 332811 AACGAATTCATAGCTAGATTTCAGGGTTTCTATGAACTTAAAAGTAGAAA 332860 v ii i i i v v vv ii ii v -i Charlie4#DNA/ 34 AAGGGGTCCGTGGATAGAATTCAGGGGGTCCGTGAACTTGGATG-GGAAA 82 chr6ptel1M 332861 ATATTTCATATGTATTTTCACTGAACTCTTAACTGAAATAAACCATCATC 332910 v v v v i v - ---ii v i Charlie4#DNA/ 83 AAATTACATCTTTATTTTCACTAACCTC-TAACTGAAAT---TTAGCATT 128 chr6ptel1M 332911 TCCTCCCATTAT 332922 i v Charlie4#DNA/ 129 TCCTTCAATTAT 140 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 29.77 CpG sites = 15, Kimura (unadjusted) = 32.66 Transitions / transversions = 1.15 (15/13) Gap_init rate = 0.05 (5 / 111), avg. gap size = 1.00 (5 / 5) 274 35.60 3.01 0.74 chr6ptel1M 333451 333583 (666417) C L3#LINE/CR1 (222) 3877 3742 m_b279s601i71 11176 chr6ptel1M 333451 TTTTCCTCCTTATAATTTCTATTCAT--GACTTTGTTCTTCCTGATGAAG 333498 i v i i i i ii -- v i v v ivv i C L3#LINE/CR1 3877 TCTGCCTCCCTGTAACTTCCACCCATTGGTCCTAGTTCTGCCCTCTGGAG 3828 chr6ptel1M 333499 ACCATGCAGAACTAGCTAAATTTCACTTGCTCACAAGTGGTTTTCTGATA 333548 - ii iv iiv ii v v v ii vv vii vi C L3#LINE/CR1 3827 -CCACACAGAATAAGTCTAATCCCTCTTCCACATGACAGCCCTTCAAATA 3779 chr6ptel1M 333549 TTTAAAGGCAATAGTCTCG--TCCTCTAAGACTTCCC 333583 i i iivi vi -- v i C L3#LINE/CR1 3778 TTTGAAGACAGCTATCATGTCTCCTCTAAGTCTTCTC 3742 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 50.83 CpG sites = 29, Kimura (unadjusted) = 50.83 Transitions / transversions = 1.61 (29/18) Gap_init rate = 0.02 (3 / 132), avg. gap size = 1.67 (5 / 3) 355 29.70 5.94 0.00 chr6ptel1M 334021 334121 (665879) C MIRc#SINE/MIR (79) 189 83 m_b280s601i1 11177 chr6ptel1M 334021 CACAACAGCTTTGTTAAGTAGATTGTACAGGTATTAACCTCCTCATTTTC 334070 i ii v i iiv vi viv i v C MIRc#SINE/MIR 189 CACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTA 140 chr6ptel1M 334071 CTGATGGGTAAACTGAG---CAAAGG---CAAGTGAGTCGTTCAGGGTTA 334114 v i v --- i i---i v i ii i i C MIRc#SINE/MIR 139 CAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCA 90 chr6ptel1M 334115 TATAACT 334121 i i i C MIRc#SINE/MIR 89 CACAGCT 83 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 40.06 CpG sites = 21, Kimura (unadjusted) = 40.06 Transitions / transversions = 2.33 (21/9) Gap_init rate = 0.02 (2 / 100), avg. gap size = 3.00 (6 / 2) 211 15.98 7.55 5.56 chr6ptel1M 334242 334294 (665706) MIR3#SINE/MIR 91 144 (64) m_b280s601i2 11178 chr6ptel1M 334242 CTTGGGCAAAGCACTTCACAATCTCT-TGGACTTCACTTTCCTTACC--- 334287 iv --- - i i v i i --- MIR3#SINE/MIR 91 CTTGGGCAAGTCACTTCAC---CTCTCTGGGCCTCAGTTTCCTCATCTGT 137 chr6ptel1M 334288 AAGATGA 334294 i MIR3#SINE/MIR 138 AAAATGA 144 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 18.51 CpG sites = 6, Kimura (unadjusted) = 18.51 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.10 (5 / 52), avg. gap size = 1.40 (7 / 5) 23 31.51 2.13 0.00 chr6ptel1M 334381 334474 (665526) (TCTC)n#Simple_repeat 1 96 (0) m_b280s252i0 11179 chr6ptel1M 334381 TCCCTCTTTTTCT-TCCTTCTCTCGCTCCCTTCCTCCCAATCCCT-TCTC 334428 i i i - ii v i ii i vv i - (TCTC)n#Simpl 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr6ptel1M 334429 TCTTTCTGTCTCTGACTCTACCTCTCTGGCTCTGTCACTGTCTCTC 334474 i v vv vi vv v v v (TCTC)n#Simpl 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 96 Matrix = Unknown Transitions / transversions = 1.00 (12/12) Gap_init rate = 0.02 (2 / 93), avg. gap size = 1.00 (2 / 2) 431 28.91 8.61 6.43 chr6ptel1M 334490 334733 (665267) C L2c_3end#LINE/L2 (6) 472 224 m_b280s601i3 11180 chr6ptel1M 334490 TCATCTGAAAAACATTTATTAATCATCTACCATGTGCTGAGCATTAAGCC 334539 iii v i v ii i iii ----- - C L2c_3end#LINE 472 TCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGC-----GC- 429 chr6ptel1M 334540 ACATGGTAGAGATTCAAAAGAGGCAAAAGACAGGAGCCCTTACCCTCAAG 334589 ------ i i v - v v v v - i i i C L2c_3end#LINE 428 ------TGGGGATACAAA-GATGAATAAGACACG-GTCCCTGCCCTCAAG 387 chr6ptel1M 334590 GAATGCATAATCTAATGGGGAAGACA-ACAAGCAGATTCATATTTACAA- 334637 iiv i i i i i - ? i i ivv i v - C L2c_3end#LINE 386 GAGCTCACAGTCTAGTGGAGGAGACAGACANGTAAACAGACAATTACAAT 337 chr6ptel1M 334638 ACAAGTT-ATAACCAG-GATATGA------TATGGAGGGAATAACCAAGA 334679 - i iv - v i ------ i vi ii -i i v i C L2c_3end#LINE 336 ACAAGTTAATGATAAGTGCTATAATGGGAGTATAGACAGGGT-GCTATGG 288 chr6ptel1M 334680 GAG------GGAAGGCA-CTAGAATGAACT----GGGTTTGAAAACAACT 334718 ------ i - v ii? ---- iv ii -ii C L2c_3end#LINE 287 GAGCACAGAGGAGGGCACCTAGACTAGNCTTGGGGGGTCAGGGAA-GGCT 239 chr6ptel1M 334719 TCGTTGAGAAGATGA 334733 viv i i C L2c_3end#LINE 238 TCCCGGAGGAGGTGA 224 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.69 CpG sites = 47, Kimura (unadjusted) = 39.26 Transitions / transversions = 2.47 (47/19) Gap_init rate = 0.10 (24 / 243), avg. gap size = 1.54 (37 / 24) 23 8.10 0.00 4.88 chr6ptel1M 334782 334824 (665176) (TCTCTG)n#Simple_repeat 1 41 (0) m_b280s252i2 11181 chr6ptel1M 334782 TCTCTGTCTCTGTCTCTGGGTGTCTGTCTCTGTCTCTCTTTCT 334824 -- v v i (TCTCTG)n#Sim 1 TCTCTGTCTCTGTCTCT--GTCTCTGTCTCTGTCTCTGTCTCT 41 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.00 (2 / 2) 543 18.09 0.00 9.43 chr6ptel1M 335123 335238 (664762) MIRc#SINE/MIR 10 115 (153) m_b280s601i4 11182 chr6ptel1M 335123 GTGGTGCAGTGGATAGAGCACCAGCCCTTGAAGTCAGGAGAATCTGAGTT 335172 v ii v - i ii i i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGAC-TTGGAGTCAGGAAGACCTGGGTT 58 chr6ptel1M 335173 CAAATCTTGTCTCAGACACTTAACACTCCTTAGCTGTGTGTGACCCTGGG 335222 i i ii v v v -------i -- i MIRc#SINE/MIR 59 CGAGTCCCGGCTCTGCCACTTA-------CTAGC--TGTGTGACCTTGGG 99 chr6ptel1M 335223 CAAGTCACTTAACCCC 335238 i MIRc#SINE/MIR 100 CAAGTCACTTAACCTC 115 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 18.72 CpG sites = 14, Kimura (unadjusted) = 21.13 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.09 (10 / 115), avg. gap size = 1.00 (10 / 10) 284 23.61 3.23 4.35 chr6ptel1M 335617 335709 (664291) MIRc#SINE/MIR 177 268 (0) m_b280s601i5 11182 chr6ptel1M 335617 CAGGGTTGGTGGAAGGATCCAATGACATCATCAGTGTATGT-AAAGCATT 335665 v vi v v ---- i - ii MIRc#SINE/MIR 177 CAGGGTTGTTGTGAGGATCAAATGAGAT----AATGTATGTGAAAGCGCT 222 chr6ptel1M 335666 TTATAACCTA-AAAGCACCATAT-AATAGGAAGTATTATTTTTATT 335709 i v i- ii i i- ivi i ?i v MIRc#SINE/MIR 223 TTGTAAACTGTAAAGTGCTATACAAATGTAAGGNGTTATTATTATT 268 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.01 CpG sites = 14, Kimura (unadjusted) = 29.68 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.08 (7 / 92), avg. gap size = 1.00 (7 / 7) 451 28.08 0.00 0.88 chr6ptel1M 335755 335869 (664131) C MIR3#SINE/MIR (3) 205 92 m_b280s601i6 11183 chr6ptel1M 335755 TCATAGAATCTTAGAAGGTTAGAGCTAGATTAGTTCTTTAGAAATGATCT 335804 v v i i vvi vi - i v C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTT-AGAGATCATCT 157 chr6ptel1M 335805 TGTCCTACCCCCTCATTTTCCTGGGGAGGAAACTGAGGCTTGAATGGGGA 335854 v v v v iv iiii vi vi C MIR3#SINE/MIR 156 AGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTG 107 chr6ptel1M 335855 AAATCATTCATTCAA 335869 i v i iiii C MIR3#SINE/MIR 106 AAGTGACTTGCCCAA 92 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.91 CpG sites = 18, Kimura (unadjusted) = 35.91 Transitions / transversions = 1.29 (18/14) Gap_init rate = 0.01 (1 / 114), avg. gap size = 1.00 (1 / 1) 247 30.68 4.17 10.76 chr6ptel1M 335858 336025 (663975) C L2c_3end#LINE/L2 (2) 476 319 m_b280s601i8 11184 chr6ptel1M 335858 TCATTCATTCAACAG----TTATTAAA-GCCTAGTGTGAGGAAGGCACAG 335902 i---- i i- v i ------------ C L2c_3end#LINE 476 TCATTCATTCAACAAACATTTATTGAGCGCCTACTATG------------ 439 chr6ptel1M 335903 TGCCTGGCTCTGCTTACATAGGGATGA-CATGACACTGATTTTTCTCTCA 335951 v v vvv i i ii -i v v viii v i C L2c_3end#LINE 438 TGCCAGGCGCTGGGGATACAAAGATGAATAAGACACGGTCCCTGCCCTCA 389 chr6ptel1M 335952 AGCATCTTATGATCCATTGGTGGCAGCCACAATTATACAAACAGCCATAG 336001 v v i iii i v v - -- ivi ?ii -- i i C L2c_3end#LINE 388 AGGAGCTCACAGTCTAGTGGAGG-AG--ACAGACANGTAAACAG--ACAA 344 chr6ptel1M 336002 CTATAATAT-AGTATATAATAAATG 336025 i i i- vv i i C L2c_3end#LINE 343 TTACAATACAAGTTAATGATAAGTG 319 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 41.08 CpG sites = 29, Kimura (unadjusted) = 41.08 Transitions / transversions = 1.71 (29/17) Gap_init rate = 0.13 (21 / 167), avg. gap size = 1.14 (24 / 21) 277 30.41 7.09 2.03 chr6ptel1M 335858 335998 (664002) C L2b_3end#LINE/L2 (2) 464 317 m_b280s601i7 11184 chr6ptel1M 335858 TCATTCATTCAACAG----TTATTAAA-GCCTAGTGTGAGGAAGGCACAG 335902 i---- i i i- v v vv ? v C L2b_3end#LINE 464 TCATTCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTG 415 chr6ptel1M 335903 TGCCTGGCTCTGCTTACATAGGGATG-ACATGACA---CTGATTTTT-CT 335947 iv v vvv i i v i - v ---?i i iii - i C L2b_3end#LINE 414 TGCTAGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCC 365 chr6ptel1M 335948 CTCAAGCATCTTATGATCCATTGGTGGCAGCCACAATTATACAAACAGCC 335997 v v v i iii i v - v -- ivi ii ? v C L2b_3end#LINE 364 CTCACGGAGCTCACAGTCTAGTGG-GGGAG--ACAGACATGTAANCAGAC 318 chr6ptel1M 335998 A 335998 C L2b_3end#LINE 317 A 317 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.83 CpG sites = 23, Kimura (unadjusted) = 41.10 Transitions / transversions = 1.21 (23/19) Gap_init rate = 0.06 (8 / 140), avg. gap size = 1.62 (13 / 8) 13 25.68 2.17 0.00 chr6ptel1M 336030 336075 (663925) (ATGTAAT)n#Simple_repeat 1 47 (0) m_b280s252i3 11185 chr6ptel1M 336030 ATGTAGTAAG-CATATGTTATATATCCTATGAAATATATATTATGTA 336075 i v -v v i vv v i v (ATGTAAT)n#Si 1 ATGTAATATGTAATATGTAATATGTAATATGTAATATGTAATATGTA 47 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1) 732 33.92 9.68 0.74 chr6ptel1M 336404 336899 (663101) C L2#LINE/L2 (218) 2864 2325 m_b280s601i9 11184 chr6ptel1M 336404 GAAGGGGAGTACTTAAATGTTTTTGGTTAGTGGAATAATATGATGTAAGT 336453 v i ivv ii v v ivi v i i i v i v C L2#LINE/L2 2864 GATGGGAAGCCATTGGAGGGTTTTGAGCAGAGGAGTGACATGATCTGACT 2815 chr6ptel1M 336454 AATTCATCTGGAAAGACCATT--GAGT-CAGTGTGAGGGATGGAATAGAG 336500 v ivi- i ii i i i -- iv - v vii i i v i? C L2#LINE/L2 2814 TACGT-TTTAAAAGGATCACTCTGGCTGCTGTGTTGAGAATAGACTGNAG 2766 chr6ptel1M 336501 AAGGGGCAAAT-TGGAAGAATGAAGATCAGTTAAGAGGACATTACAGTAG 336549 i- iv- v v i i i vi i i C L2#LINE/L2 2765 G-GGGGCAAGGGTGGAAGCAGGGAGACCAGTTAGGAGGCTATTGCAGTAA 2717 chr6ptel1M 336550 TCCAGACAAGAAATGGTATGGACTCAAACTCTAGTGG-------AGAGGC 336592 i i i i ivv i iii ivvi -------i i C L2#LINE/L2 2716 TCCAGGCGAGAGATGATGGTGGCTTGGACCAGGGTGGTGGCAGTGGAGGT 2667 chr6ptel1M 336593 AG------------GGAT---GGATACA-----AAGGCAATG-----AGG 336617 i ------------ --- i ----- i iv ----- C L2#LINE/L2 2666 GGTGAGAAGTGGTCGGATTCTGGATATATTTTGAAGGTAGAGCCGACAGG 2617 chr6ptel1M 336618 ATTTGGCCCCTGATTATATGTATGGGGTGAGCAAGAAGGAAGAGTCAAAC 336667 vivviv iv iv v vi i ii i iv C L2#LINE/L2 2616 ATTTGCTGATGGATTGGATGTGGGGTGTGAGAGAAAGAGAGGAGTCAAGG 2567 chr6ptel1M 336668 AGCTCTCCAAGATTATTTGTCTGGGTACCTGGGAAGGATGGCAGTT-TAG 336716 vvv i v v i i i v - - -ivi C L2#LINE/L2 2566 ATGACTCCAAGGTTTTTGGCCTGAGCAACTGG-AAGGATGG-AGTTGCCA 2519 chr6ptel1M 336717 TGAACAGAAATGAAGGAG-TTGAAGGAGG--CAGGGTTG-GAGAAAAGAC 336762 v? v i ii i -i vi -- v - i ii i C L2#LINE/L2 2518 TTNACTGAGATGGGGAAGACTGCGGGAGGAGCAGGTTTGAGGGGGAAGAT 2469 chr6ptel1M 336763 GGTGAGTTCAATTTTAAATAGGTTGAGTTGGAGAAGTTGGCAGGACAGCC 336812 viv i ii i v i v v iiviivi v C L2#LINE/L2 2468 CAGGAGTTCAGTTTTGGACATGTTAAGTTTGAGATGCCTATTAGACATCC 2419 chr6ptel1M 336813 ACGTGGAACTATCCAGCAGATAGTTGCAAGCACA-----GGAGTTTTGGG 336857 v iv i v i ii v vii i----- iv C L2#LINE/L2 2418 AAGTGGAGATGTCGAGTAGGCAGTTGGATATACGAGTCTGGAGTTCAGGG 2369 chr6ptel1M 336858 GAGAAACAGAGGCTAGAGAAAT-GATTTGAAAATTA-CGGCATA 336899 iiivvi i v -i ii i i - i C L2#LINE/L2 2368 GAGAGGTCCGGGCTGGAGATATAAATTTGGGAGTCATCAGCATA 2325 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 45.85 CpG sites = 106, Kimura (unadjusted) = 47.88 Transitions / transversions = 1.74 (106/61) Gap_init rate = 0.04 (19 / 495), avg. gap size = 2.74 (52 / 19) 362 32.02 3.82 2.52 chr6ptel1M 336903 337059 (662941) C MIR3#SINE/MIR (27) 181 23 m_b280s601i10 11186 chr6ptel1M 336903 CTGAAAGGA---TTGGAATGATTCATACAGTCTAGCCCAGTCACTTTACA 336949 i i--- i -- - vi i i vv i C MIR3#SINE/MIR 181 CTGGAAGGGACCTTAGA--GAT-CATCTAGTCCAACCCCCTCATTTTACA 135 chr6ptel1M 336950 AATGA-GAATCTAAGACCCAGGGAGTTT--GTGACTTGGTGAAAGTCATA 336996 i - v i i i v v-- viv i i C MIR3#SINE/MIR 134 GATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACA 85 chr6ptel1M 336997 TGAGTAGTAAGTCACACGGCAGGAACTTGAATATGTATTTTTTGATAACA 337046 iiiv? v vi vi v i v iviivi i ii ivv v C MIR3#SINE/MIR 84 CAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGTCTCCTGACTCCC 35 chr6ptel1M 337047 AATGCAGTGCTCT 337059 i - v C MIR3#SINE/MIR 34 AGT-CCGTGCTCT 23 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 43.63 CpG sites = 29, Kimura (unadjusted) = 43.63 Transitions / transversions = 1.45 (29/20) Gap_init rate = 0.04 (7 / 156), avg. gap size = 1.43 (10 / 7) 472 28.98 3.60 0.70 chr6ptel1M 336941 337079 (662921) C MIRc#SINE/MIR (122) 146 4 m_b280s601i11 11186 chr6ptel1M 336941 CACTTTACAAATGAG-AATCTAAGACCCAGGGAGTTT--GTGACTTGGTG 336987 i i - v i i i i v -- viv C MIRc#SINE/MIR 146 CATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCC 97 chr6ptel1M 336988 AAAGTCATATGAGTAGTAAGTCACACGGCAGGAACTTGAA--TATGTATT 337035 i i iiiv vi vi v i i --i v -i C MIRc#SINE/MIR 96 AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGT-CT 48 chr6ptel1M 337036 TTTTGATAACAAATGCAGTGCTCTAATCACTGCACCATGCTTCC 337079 ii ivv i v vvi ii v C MIRc#SINE/MIR 47 TCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTGCC 4 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.75 CpG sites = 25, Kimura (unadjusted) = 37.97 Transitions / transversions = 1.67 (25/15) Gap_init rate = 0.03 (4 / 138), avg. gap size = 1.50 (6 / 4) 191 21.74 4.35 0.00 chr6ptel1M 337863 337908 (662092) L3#LINE/CR1 4045 4092 (7) m_b280s601i12 11187 chr6ptel1M 337863 TTAGACTAGGTAAACTCTAAGGT-CCTTCCATCTTTTAG-TCCCATGA 337908 i i i v - v i v - i ii L3#LINE/CR1 4045 TTGGACTAGATGACCTCTAAGGTCCCTTCCAACTCTGAGATTCTGTGA 4092 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 26.56 CpG sites = 7, Kimura (unadjusted) = 26.56 Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.04 (2 / 45), avg. gap size = 1.00 (2 / 2) 332 29.26 7.45 2.37 chr6ptel1M 338774 338934 (661066) C MIRc#SINE/MIR (16) 252 84 m_b280s601i13 11188 chr6ptel1M 338774 TGCATTT-TATAGCTTCACTTTG-GGCTGGCAGAGGAATCTCCTAGATAT 338821 i - --- i-i i vi i viv i vi v i C MIRc#SINE/MIR 252 TACATTTGTATAGC---ACTTTACAGTTTACAAAGCGCTTTCACATACAT 206 chr6ptel1M 338822 GATCTCATT--ATTTT-ATCACAACCCTTTAAGGTGGGTCAGGCAGGTAT 338868 v -- ii - iv v i i ivi C MIRc#SINE/MIR 205 TATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTAT 156 chr6ptel1M 338869 TATAAGTCCTC--TTTATAGGTGTGGAAA-GAAAGTTTTGAGGGGT---G 338912 v - i -- i i v -vi i i iv i --- C MIRc#SINE/MIR 155 TATTA-TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAG 107 chr6ptel1M 338913 AGATTTCCCTGAGATT-CTCAGC 338934 v i v ii i i- v C MIRc#SINE/MIR 106 TGACTTGCCCAAGGTCACACAGC 84 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.69 CpG sites = 30, Kimura (unadjusted) = 38.79 Transitions / transversions = 1.88 (30/16) Gap_init rate = 0.07 (12 / 160), avg. gap size = 1.33 (16 / 12) 224 20.87 7.14 4.17 chr6ptel1M 339022 339091 (660909) C L2b_3end#LINE/L2 (1) 465 394 m_b280s601i14 11189 chr6ptel1M 339022 TTCATTGTCACCTCAGCAAATATTTACTCAGTGTCTA---TGTACAAGAC 339068 -- i- i v i i --- i v i C L2b_3end#LINE 465 TTCATT--CAT-TCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGC 419 chr6ptel1M 339069 CC--TGCTAGGAGGTGAAGCTCCAG 339091 ? -- v v ii v v C L2b_3end#LINE 418 NCTGTGCTAGGCGCTGGGGATACAG 394 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 23.29 CpG sites = 8, Kimura (unadjusted) = 25.29 Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.07 (5 / 69), avg. gap size = 1.60 (8 / 5) 228 31.51 2.74 0.00 chr6ptel1M 339330 339402 (660598) C MIRc#SINE/MIR (31) 237 163 m_b280s601i15 11190 chr6ptel1M 339330 CTTTATGGTC-ACAAAATGGTCGTGCAT-CTTTATCTCAGTTAATCTTGC 339377 ii i- ii v ivii - v v i i vv C MIRc#SINE/MIR 237 CTTTACAGTTTACAAAGCGCTTTCACATACATTATCTCATTTGATCCTCA 188 chr6ptel1M 339378 CAGCAGACTTATGGGATAGGCAGGG 339402 i iv i i i i C MIRc#SINE/MIR 187 CAACAACCCTGTGAGGTAGGCAGGG 163 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 40.95 CpG sites = 16, Kimura (unadjusted) = 43.53 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.03 (2 / 72), avg. gap size = 1.00 (2 / 2) 364 29.46 1.79 0.00 chr6ptel1M 340512 340623 (659377) MARNA#DNA/TcMar-Mariner 201 314 (272) m_b280s502i1 11191 chr6ptel1M 340512 CCACCCAAGAAAATCATTCTCAGTGCTTTATATTCGTGTCTTA-TTTTGA 340560 v v v i v iiii i - MARNA#DNA/TcM 201 CCACACAAGAAAATCAGTCTCATTACTTTATAGTCACACCTCATTTTTGA 250 chr6ptel1M 340561 CC-AAGTTGTTATTCCTCCATTGAATTGTACATTTTATTCACTAGACTGG 340609 - iv iv v i vii vi iiiv ii i v MARNA#DNA/TcM 251 CCNAAAATAGTATTACCCAGCTTGATCACCCACCTTATTCACCAGACTTG 300 chr6ptel1M 340610 ACTTTAAATGACTT 340623 i iii MARNA#DNA/TcM 301 GCTCCGAATGACTT 314 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.52 CpG sites = 22, Kimura (unadjusted) = 39.24 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.02 (2 / 111), avg. gap size = 1.00 (2 / 2) 23 21.41 0.00 0.00 chr6ptel1M 341117 341161 (658839) (AC)n#Simple_repeat 1 45 (0) m_b280s252i4 11192 chr6ptel1M 341117 ACACACACACACACACACATATGTATACACACACACATAAATACA 341161 i iii i i v i (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACA 45 Matrix = Unknown Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 401 33.75 6.86 1.24 chr6ptel1M 341170 341475 (658525) C L1ME4c_3end#LINE/L1 (442) 388 66 m_b280s551i0 11193 chr6ptel1M 341170 GAACTGGGGTGTCTAGATCAAAGGGCTTGGATGTTTTGATCACTTTTTTT 341219 v ii vv i i iv i ii v vi i vv C L1ME4c_3end#L 388 GAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTCTTGAT 339 chr6ptel1M 341220 GGCGTAACTCCAGATTGTTTTCCAAAAAGTATGGATCACTTCATGGCCCT 341269 i- viv i i i vv v i v i ii?iv i C L1ME4c_3end#L 338 A-CGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACANTGCC 290 chr6ptel1M 341270 ACCAACAATTCATTAGTGTGCCTACCTC-CCGT---CTGCCTAACACTGT 341315 i vi v ? i viii - i--- vv i i i v C L1ME4c_3end#L 289 ACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGCATTGG 240 chr6ptel1M 341316 ----------TTTTTT---TTTTTTCCAGTTTGTTGGATATAAGCTAAAA 341352 ---------- --- v i i iv i iii iv iiv C L1ME4c_3end#L 239 GTATTATCAATTTTTTAAATTTTTGCTAATTTAATAGGCGTAAAATGGTA 190 chr6ptel1M 341353 TTTTAGAGTTTCTTTAATTTGCATTTTTCTCATTATTATTCTTTATTTGG 341402 i i vv v i i v i viv--- vv v C L1ME4c_3end#L 189 TCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACTAGCG---AGGTTG 143 chr6ptel1M 341403 AGCAGCCTTTCATATGGTTGGTTACAATTTGCAATTTTTCTTTTGAGAAT 341452 i vii i i v v v ? i v ii ? v C L1ME4c_3end#L 142 AACATTTTTCCATGTGTTTGTTTACTANTTGTATTTCCTCTTNTGTGAAT 93 chr6ptel1M 341453 ----TATTTATATCCTCTTACCACTTA 341475 ---- i i i i vv i C L1ME4c_3end#L 92 TGTCTGTTCATGTCCTTTGCCCATTTA 66 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 46.12 CpG sites = 60, Kimura (unadjusted) = 47.50 Transitions / transversions = 1.43 (60/42) Gap_init rate = 0.03 (9 / 305), avg. gap size = 2.78 (25 / 9) 632 21.92 2.65 3.33 chr6ptel1M 341476 341626 (658374) MARNA#DNA/TcMar-Mariner 303 452 (134) m_b280s502i2 11194 chr6ptel1M 341476 TCTGAATGACTTTTGGCTGCTTCCCAGAAATCAAATCTGGCCTCGAACAA 341525 i i - i iiv i vi MARNA#DNA/TcM 303 TCCGAATGACTTTTGGCTGTTTCC-AAAAATCAAATCCACCCTCAAAGGA 351 chr6ptel1M 341526 CAAAGATTTGCCATCACTGAGGAGATTAAAAAGAATGTGCCAAAAGTTCT 341575 i i i v v iv i i MARNA#DNA/TcM 352 CGAAGATTTGCCACCATTGAGGATATTCAAAAGAATGTGCCGCAGGCTCT 401 chr6ptel1M 341576 GCAGGCCATTTCCCCAAAGGAGA----CTGGACATGTCACAAGCAATGAG 341621 v v --- - ---- iii v ivii iv MARNA#DNA/TcM 402 GAAGGCAATT---CCAAA-GAGAAGTTCCAAAAATGTTTTGAGCAATGGC 447 chr6ptel1M 341622 AATAT 341626 ii MARNA#DNA/TcM 448 AGCAT 452 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 23.92 CpG sites = 22, Kimura (unadjusted) = 26.77 Transitions / transversions = 2.20 (22/10) Gap_init rate = 0.04 (6 / 150), avg. gap size = 1.50 (9 / 6) 342 25.85 0.00 1.12 chr6ptel1M 341795 341884 (658116) C MARNA#DNA/TcMar-Mariner (450) 136 48 m_b280s502i3 11195 chr6ptel1M 341795 GTATGATTAGAATAAGTGCACAGTCTCCCGTCAGGACAACTTTGAAATGA 341844 i vi i i i ivviv v i- C MARNA#DNA/TcM 136 GCATCGTTGGAATAAGTGTACAGCCTCCCAAGGTGACTACTTTGAAG-GA 88 chr6ptel1M 341845 GAATACTCTTTTGGATGACAAAGTACTGGTCTATTTATTT 341884 v i v vvv v v i i C MARNA#DNA/TcM 87 CAACACTCATTTGGATGTATAAGTTCTGGTGTGTTTGTTT 48 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 30.31 CpG sites = 11, Kimura (unadjusted) = 31.92 Transitions / transversions = 0.92 (11/12) Gap_init rate = 0.01 (1 / 89), avg. gap size = 1.00 (1 / 1) 191 23.26 2.33 0.00 chr6ptel1M 341913 341955 (658045) C MIR3#SINE/MIR (6) 202 159 m_b280s601i16 11196 chr6ptel1M 341913 TGGAATTTTAAAATGTCAGAGCCAGAAGAGACCCT-GAAAACAT 341955 i iv i ii i i - i v C MIR3#SINE/MIR 202 TAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCAT 159 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.56 CpG sites = 8, Kimura (unadjusted) = 29.56 Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.02 (1 / 42), avg. gap size = 1.00 (1 / 1) 202 8.82 8.82 0.00 chr6ptel1M 341995 342028 (657972) C MIR3#SINE/MIR (15) 193 157 m_b280s601i17 11197 chr6ptel1M 341995 AGAATGCCAG---TGGACGGGACCTTAGGGATCATCT 342028 i --- v i C MIR3#SINE/MIR 193 AGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCT 157 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 9.47 CpG sites = 2, Kimura (unadjusted) = 9.47 Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.03 (1 / 33), avg. gap size = 3.00 (3 / 1) 343 32.84 0.79 4.07 chr6ptel1M 342084 342210 (657790) C Tigger19b#DNA/TcMar-Tigger (44) 506 384 m_b280s601i18 11198 chr6ptel1M 342084 GTGAAGAATCCCAAATAGCACACAGCACTAAAGCCATTTATTTCTATTTG 342133 i v v ii iv i iiv v ii ---- C Tigger19b#DNA 506 GTGGATAATCCAAAACGGCGGATAATCCAAAAATCATTTAT----ATTTG 461 chr6ptel1M 342134 GCTGCTGAGTGATTTTTCACACTCGTGTTTAAACA-AGGTGTATACAGTG 342182 viv i vv iii iiii i i -i i viii C Tigger19b#DNA 460 GCTTTGGAATGTGTTTTTGTACTTACATTTGAATATGGGTGTGTCTGATG 411 chr6ptel1M 342183 TTTTGGGAAGTTCACAGCACTTTGAGCA 342210 i - i ii i C Tigger19b#DNA 410 TTCTGGGAA-TTCACAACACTTCAAACA 384 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 43.59 CpG sites = 30, Kimura (unadjusted) = 47.12 Transitions / transversions = 3.00 (30/10) Gap_init rate = 0.05 (6 / 126), avg. gap size = 1.00 (6 / 6) 239 29.17 4.00 4.00 chr6ptel1M 342905 343004 (656996) MIR3#SINE/MIR 103 202 (6) m_b280s601i19 11199 chr6ptel1M 342905 ACTT-ACCTCCTCAG--CTCAGTCTGCTCATCTAT-AAATGCAGGATTGA 342950 - iiii -- i v i - vi iv vi MIR3#SINE/MIR 103 ACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTG 152 chr6ptel1M 342951 GACTTGTTGCCTTTTCAGGACTCTGAGATCTAACTTTGTGATCCTATGAT 343000 v v vii i v v i ---- i i i vv i MIR3#SINE/MIR 153 GACTAGATGATCTCTAAGGTCCCT----TCCAGCTCTGACATTCTATGAT 198 chr6ptel1M 343001 TCTA 343004 MIR3#SINE/MIR 199 TCTA 202 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.13 CpG sites = 17, Kimura (unadjusted) = 38.13 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.07 (7 / 99), avg. gap size = 1.14 (8 / 7) 671 27.76 8.47 0.79 chr6ptel1M 343573 343808 (656192) MIRc#SINE/MIR 13 266 (2) m_b280s601i20 11200 chr6ptel1M 343573 GTGCAG--AATATAGTGCTTAACTTGGACCCAGCAA--------TTCAAA 343612 --i v v ii vi vi v -------- i i MIRc#SINE/MIR 13 GTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAG 62 chr6ptel1M 343613 TCCTGCCTCAGGTACTAATTAGCCATGCAACCTGCTGCAAGTGTCA-TTA 343661 i v v vi v i ii ii vvv -- - MIRc#SINE/MIR 63 TCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGT--CACTTA 110 chr6ptel1M 343662 TCCTGTCTG--CCTCAGTTTCTTTAATTGTAAAACAGGAATACTGTTA-- 343707 v v -- i i vi ii i v iv -- MIRc#SINE/MIR 111 ACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACC 160 chr6ptel1M 343708 -GC---ACCTACCTCCCGGGATTATTGTGAGGATAAGATGAAAGAATATT 343753 - ---i v i i i v i i v i v MIRc#SINE/MIR 161 TGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTA 210 chr6ptel1M 343754 TGT-AAAGCACTTTTCAAGCCTTAAAGCACTGTGCAAATGCTAGCTATTA 343802 - i vi i iv ii i i iv v?i MIRc#SINE/MIR 211 TGTGAAAGCGCTTTGTAAACTGTAAAGTGCTATACAAATGTAAGGNGTTA 260 chr6ptel1M 343803 TCAATA 343808 i v MIRc#SINE/MIR 261 TTATTA 266 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.82 CpG sites = 39, Kimura (unadjusted) = 35.87 Transitions / transversions = 1.50 (39/26) Gap_init rate = 0.04 (10 / 235), avg. gap size = 2.20 (22 / 10) 269 24.66 11.76 4.59 chr6ptel1M 344569 344670 (655330) L3#LINE/CR1 3912 4020 (79) m_b280s601i21 11201 chr6ptel1M 344569 TCAGAGCTGTAGCC---ACTGAACTACCTAGCTGCCT--TAAGGTAGTAA 344613 -- --- v i v i---i --?i i L3#LINE/CR1 3912 TCAGAGCTGT--CCAAAAATGGAATG---GGCTGCCTCGNGAGGTAGTGA 3956 chr6ptel1M 344614 GCTCCTTGTCAC---AGGTGTTCTTGAAAAGAC----TGATCATCTGTCA 344656 ii --- vv v i i ---- i ii L3#LINE/CR1 3957 GCTCCCCGTCACTGGAGGTGTTCAAGCAGAGGCTGGATGACCACTTGTCA 4006 chr6ptel1M 344657 AAATTATTCTTGAA 344670 iiiv i v v L3#LINE/CR1 4007 GGGATGTTGTAGAA 4020 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.93 CpG sites = 16, Kimura (unadjusted) = 31.51 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.09 (9 / 101), avg. gap size = 1.89 (17 / 9) 409 29.25 2.83 0.00 chr6ptel1M 345291 345396 (654604) C MIRc#SINE/MIR (150) 118 10 m_b280s601i22 11202 chr6ptel1M 345291 AGTGAAGGTAAGTGACTTTCC---AGTCACACACCTAGTAAGTGTTTGAG 345337 v i v v ---i v viv C MIRc#SINE/MIR 118 AGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAG 69 chr6ptel1M 345338 GTTGGACTTGAATTCAGAGGTTCCTAACCTTAAGTTCAGCAGTTTATCCA 345387 viv i ii ivv i iii i iiv i v C MIRc#SINE/MIR 68 CCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCA 19 chr6ptel1M 345388 TTGAGCCAC 345396 i vi C MIRc#SINE/MIR 18 CTGCACCAC 10 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.99 CpG sites = 18, Kimura (unadjusted) = 38.05 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.01 (1 / 105), avg. gap size = 3.00 (3 / 1) 363 30.28 15.79 0.65 chr6ptel1M 346183 346315 (653685) MIR3#SINE/MIR 15 167 (41) m_b280s601i23 11203 chr6ptel1M 346183 GATCAGGGAGAACCCAGCCCAGGCAATCAGTCAACATGGAGTCTGGTCAT 346232 v i i v i v ii - i vvi v iv i vi MIR3#SINE/MIR 15 GAGCAGAGAGAGCACGGACTGGG-AGTCAGGAGACCTGGGTTCTAGTCCC 63 chr6ptel1M 346233 GGCTCTGTCA----------GGGGAATCCCGAGTAAATCATTTT--TTCT 346270 i ---------- v vi i ii i i i i i--i MIR3#SINE/MIR 64 GGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCT 113 chr6ptel1M 346271 TTGGATCTCAGTTTTCTCATCTGCAAA---------TTGGACTAGGAGCT 346311 i ii i i --------- iv v MIR3#SINE/MIR 114 CTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGAT 163 chr6ptel1M 346312 TTCT 346315 i MIR3#SINE/MIR 164 CTCT 167 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.48 CpG sites = 28, Kimura (unadjusted) = 41.21 Transitions / transversions = 2.33 (28/12) Gap_init rate = 0.03 (4 / 132), avg. gap size = 5.50 (22 / 4) 28 0.00 0.00 0.00 chr6ptel1M 346403 346429 (653571) (TACAA)n#Simple_repeat 1 27 (0) c_b280s251i0 11204 chr6ptel1M 346403 TACAATACAATACAATACAATACAATA 346429 (TACAA)n#Simp 1 TACAATACAATACAATACAATACAATA 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 215 26.13 2.86 12.50 chr6ptel1M 347255 347359 (652641) L2c_3end#LINE/L2 382 477 (1) m_b280s601i24 11205 chr6ptel1M 347255 AACTTCTTATGGATGGGGAC--TGTCTTTTGCATCTTTTTGTATCCCCGT 347302 i i iv iii -- v v -- -- L2c_3end#LINE 382 AGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTT--GTATCCCC-- 427 chr6ptel1M 347303 GGCTTAGTCCATCTGTCACAAATGAAGTGATTAATAAATA-TTATCAAAT 347351 ----- -- ii v v vv i i v i i- i ii L2c_3end#LINE 428 -----AG--CGCCTGGCACATAGTAGGCGCTCAATAAATGTTTGTTGAAT 470 chr6ptel1M 347352 AGAATTAA 347359 - v L2c_3end#LINE 471 -GAATGAA 477 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.33 CpG sites = 15, Kimura (unadjusted) = 32.56 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.13 (14 / 104), avg. gap size = 1.07 (15 / 14) 229 30.75 5.56 3.64 chr6ptel1M 347363 347470 (652530) MIRc#SINE/MIR 22 131 (137) m_b280s601i25 11206 chr6ptel1M 347363 AACGAGACGCTGAATTTGGAGTCAAG--GGTATGGGATTGAATTTTGACT 347410 v - i i i i -- iiv v i i iii i MIRc#SINE/MIR 22 AAAGAG-CACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCT 70 chr6ptel1M 347411 TGACTACTTTCCTCACAGTG--GCTTTGAAGGCA--TCACTTATTGCCTC 347456 ivi i -v vi v --i i -- -- vivi MIRc#SINE/MIR 71 CTGCCACTT-ACTAGCTGTGTGACCTTG--GGCAAGTCACTTAACCTCTC 117 chr6ptel1M 347457 GTAGCCTCCGTTTC 347470 vv v MIRc#SINE/MIR 118 TGAGCCTCAGTTTC 131 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.87 CpG sites = 20, Kimura (unadjusted) = 41.22 Transitions / transversions = 1.67 (20/12) Gap_init rate = 0.07 (7 / 107), avg. gap size = 1.43 (10 / 7) 290 23.92 9.52 3.76 chr6ptel1M 347988 348113 (651887) MIR1_Amn#SINE/MIR 48 180 (50) m_b280s601i26 11207 chr6ptel1M 347988 GGAGTAGCTGAGTTTGAATCC------TGCCAACGGT-GACTGCATGACT 348030 - v i i? ? ------ vi? i-?i ?i i MIR1_Amn#SINE 48 GGAG-ACCTGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACC 96 chr6ptel1M 348031 CTAGGGAAGTC--TGCATCTCTCTCT--CTCAGGTTTCCCCATCTGTAAA 348076 i i v -- v? i v?-- - i MIR1_Amn#SINE 97 TTGGGCAAGTCACTTNACCTCTCTGNGCCTCAG-TTTCCTCATCTGTAAA 145 chr6ptel1M 348077 ATAAACATAACCATCGCATCGG-CTCCCTTGGAAGATG 348113 iiiv iv --- ii i- i v ii MIR1_Amn#SINE 146 ATGGGGATAATGAT---ACTGACCTCCTTTGTAAAGTG 180 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.65 CpG sites = 21, Kimura (unadjusted) = 32.65 Transitions / transversions = 2.62 (21/8) Gap_init rate = 0.08 (10 / 125), avg. gap size = 1.70 (17 / 10) 313 21.77 17.86 1.54 chr6ptel1M 348693 348804 (651196) MIRc#SINE/MIR 25 154 (114) m_b280s601i27 11208 chr6ptel1M 348693 GGGTGCTGGACTTGGAGCCGGGAAGCCACAAGTTTGAA------CACTGC 348736 i ii i i v viii i i------ v MIRc#SINE/MIR 25 GAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGC 74 chr6ptel1M 348737 CACAGACT--CTT-----CCT-------ATCTCTTAACCTCTCTCAGTCC 348772 vv -- v----- -------i v v -- MIRc#SINE/MIR 75 CACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAG--C 122 chr6ptel1M 348773 CTCAGTTTCCTCCTCTGTAAGGTGGGCACAAT 348804 v ii v i MIRc#SINE/MIR 123 CTCAGTTTCCTCATCTGTAAAATGGGGATAAT 154 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 24.97 CpG sites = 14, Kimura (unadjusted) = 26.21 Transitions / transversions = 1.40 (14/10) Gap_init rate = 0.05 (6 / 111), avg. gap size = 3.67 (22 / 6) 49 5.78 0.00 0.00 chr6ptel1M 350185 350239 (649761) (TA)n#Simple_repeat 1 55 (0) c_b280s251i1 11209 chr6ptel1M 350185 TATATATATATATATATATATATATACATATATACATATATATATATATA 350234 i i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr6ptel1M 350235 CATAT 350239 i (TA)n#Simple_ 51 TATAT 55 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 467 21.29 1.89 18.03 chr6ptel1M 350255 350466 (649534) L2c_3end#LINE/L2 293 475 (3) m_b280s601i28 11210 chr6ptel1M 350255 GCATCGCTGTTTATATACTTACATGTAGAATGCTCATCATTATTAACATA 350304 i - i -- iv - v iii i --- --- L2c_3end#LINE 293 GCACC-CTGTCTATA--CTCCCAT-TATAGCACTTATCATTA---AC--- 332 chr6ptel1M 350305 TTGTAGTGTAGAATGTGCATAATTGTTTACACATCC--CCCCTCACCCCG 350352 v - v ------i ?ii i-- i vv iv L2c_3end#LINE 333 TTGTATTGTA-ATTGT------CTGTTTACNTGTCTGTCTCCTCCACTAG 375 chr6ptel1M 350353 ACTCTGAGGTCCTTGACG-CAGGGACTGTCTGACTCTTGCTTGT-TTTGT 350400 v v v - i -- -- ii ii - L2c_3end#LINE 376 ACTGTGAGCTCCTTGAGGGCAGGGACCGT--G--TCTTATTCATCTTTGT 421 chr6ptel1M 350401 ATCCCCAGAGCTTAGCCCAGTGCCTGGCACATAGTAGGCACTTAATAAAT 350450 ------------ i i i L2c_3end#LINE 422 ATC------------CCCAGCGCCTGGCACATAGTAGGCGCTCAATAAAT 459 chr6ptel1M 350451 ACTTGCTGGCTGACTG 350466 ii i iv v L2c_3end#LINE 460 GTTTGTTGAATGAATG 475 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 22.76 CpG sites = 25, Kimura (unadjusted) = 25.03 Transitions / transversions = 2.08 (25/12) Gap_init rate = 0.17 (36 / 211), avg. gap size = 1.03 (37 / 36) 505 26.69 5.00 2.16 chr6ptel1M 350287 350466 (649534) L2a_3end#LINE/L2 330 514 (3) m_b280s601i29 11210 chr6ptel1M 350287 CTCATCATTAT-TAACATATTGTAGTGTAGAATGTGCATAATTGTTTAC- 350334 i ii - i i i - i vvv iv iiv v i- L2a_3end#LINE 330 CTTATCACCATCTGACATACTATA-TATTTTACTTATTTATTTGTTTATT 378 chr6ptel1M 350335 --ACATCCCCCCTCACCCCGACTCTGAGGTCCTTGACG-CAGGGACT--- 350378 --vii i i iv- v v i v v v - --- L2a_3end#LINE 379 GTCTGTCTCCCCCCACTA-GAATGTAAGCTCCATGAGGGCAGGGACTTTT 427 chr6ptel1M 350379 GTCTGACTCTTGCTTGTT-TTGTATCCCCAGAGCTTAGCCCAGTGCCTGG 350427 -- i i iii -i v i vv L2a_3end#LINE 428 GTCTG--TTTTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGG 475 chr6ptel1M 350428 CACATAGTAGGCACTTAATAAATACTTGCTGGCTGACTG 350466 i i i i iv v L2a_3end#LINE 476 CACATAGTAGGCGCTCAATAAATATTTGTTGAATGAATG 514 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.09 CpG sites = 29, Kimura (unadjusted) = 33.99 Transitions / transversions = 1.61 (29/18) Gap_init rate = 0.05 (9 / 179), avg. gap size = 1.44 (13 / 9) 532 20.57 5.04 2.10 chr6ptel1M 350328 350466 (649534) L2b_3end#LINE/L2 321 463 (3) m_b280s601i30 11210 chr6ptel1M 350328 TGTTTACACATC---CCCCCTCACCCCGACTCTGAGGTCCTTGACG-CAG 350373 ? ii --- i i iv- v v v v - L2b_3end#LINE 321 TGNTTACATGTCTGTCTCCCCCACTA-GACTGTGAGCTCCGTGAGGGCAG 369 chr6ptel1M 350374 GGAC--TGTCTGACTCTTGCTTGTT-TTGTATCCCCAGAGCTTAGCCCAG 350420 --? -- i iiii-i v i v L2b_3end#LINE 370 GGACCGNGTCTG--TCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAG 417 chr6ptel1M 350421 TGCCTGGCACATAGTAGGCACTTAATAAATACTTGCTGGCTGACTG 350466 ? i i i i i i iv v L2b_3end#LINE 418 NGCCTGGCACACAGTAGGCGCTCAGTAAATATTTGTTGAATGAATG 463 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 23.39 CpG sites = 19, Kimura (unadjusted) = 25.44 Transitions / transversions = 2.11 (19/9) Gap_init rate = 0.05 (7 / 138), avg. gap size = 1.43 (10 / 7) 516 34.77 8.29 3.05 chr6ptel1M 350477 351007 (648993) L2#LINE/L2 2283 2840 (242) m_b280s601i31 11211 chr6ptel1M 350477 CTTAGTCAGCTTGTCAGCTCTCGTGGATTTAA-TGCCTTTGTCTGTGCTG 350525 ?i v v ii viv i v - i v i- v i L2#LINE/L2 2283 CTNGGTGATCTCATCCAGTCTCATGGCTTTAAATACCATC-TATATGCTG 2331 chr6ptel1M 350526 ACAATTTTCATAT--GGATCTCTGGTTCCCCACCCTCTCC---GACCTCT 350570 ii i ii v --iv ii -- viv --- v i L2#LINE/L2 2332 ATGACTCCCAAATTTATATCTCCAG--CCCGGACCTCTCCCCTGAACTCC 2379 chr6ptel1M 350571 GG-CTCCT---TTCAGCTATCT------CA----CACT-GGATGGCCAGT 350605 i - v --- i i ii ------ ---- - v i i L2#LINE/L2 2380 AGACTCGTATATCCAACTGCCTACTCGACATCTCCACTTGGATGTCTAAT 2429 chr6ptel1M 350606 GGACATATTAAACTCAACTTGTACAAAGCCAAACTCGTTATCTTCCCTGG 350655 i i v i i v v i ii v v ivv L2#LINE/L2 2430 AGGCATCTCAAACTTAACATGTCCAAAACTGAACTCCTGATCTTCCCCCT 2479 chr6ptel1M 350656 GCACCCAGCGTTTCCTCTGTA-CCTTCCCTCTCCATTACTGCTAAGGGCA 350704 vv v v -- i ii i i -i ---- iv v i? v L2#LINE/L2 2480 CAAACCTGC--TCCTCCCGCAGTCTTCC----CCATCTCAGTNAATGGCA 2523 chr6ptel1M 350705 ACGTGCTCCTCCTGGTCCCTCAGGCTCACAGCCTAGGAGTCGACCTCGGT 350754 vivv i ii iv iv v i v iv i ii L2#LINE/L2 2524 ACTCCATCCTTCCAGTTGCTCAGGCCAAAAACCTTGGAGTCATCCTTGAC 2573 chr6ptel1M 350755 TC--------CTCTCACCCTCCACAT--GATC----------TCCTGGCG 350784 -------- v i --i ---------- v L2#LINE/L2 2574 TCCTCTCTTTCTCTCACACCCCACATCCAATCCATCAGCAAATCCTGTCG 2623 chr6ptel1M 350785 ATTTTGCCGCTGGGGCCTCTTTCCTGTACTC--TTACTTCTCTCCTTTGA 350832 ii i i viiiiii-- v v v v ii --ii v viivv L2#LINE/L2 2624 GCTCTACCTTCAAAA--TATATCCAGAATCCGACCACTTCTCACCACCTC 2671 chr6ptel1M 350833 CACTGCCACAGTTCCAGCCCTAACCCTCCCACTCGTTACCTCCAGCCTGG 350882 viii ii i v i----- - i i i iv L2#LINE/L2 2672 CACTGCCACCACCCTGGTCCAAG-----CCAC-CATCATCTCTCGCCTGG 2715 chr6ptel1M 350883 GCTGTTGCAGCAGCCTCCTTCCGAGTCTGCCGGACTCAGGTCTCTCTCCG 350932 ii ii ii vv vi v v vi vivi iv i v L2#LINE/L2 2716 ATTACTGCAATAGCCTCCTAACTGGTCTCCCTGCTTCCACCCTTGCCCCC 2765 chr6ptel1M 350933 CTTCAGTCCACCCCCAGCTCAGCCACCCGAGTGATTTTCCTAAAGCACGG 350982 ? i ii i i v vi v ii ii i iiii L2#LINE/L2 2766 CTNCAGTCTATTCTCAACACAGCAGCCAGAGTGATCCTTTTAAAACGTAA 2815 chr6ptel1M 350983 ATCTGACCGGGAGCCTCCTCTGCTC 351007 i v i iv vvv L2#LINE/L2 2816 GTCAGATCATGTCACTCCTCTGCTC 2840 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 48.84 CpG sites = 111, Kimura (unadjusted) = 49.65 Transitions / transversions = 1.63 (111/68) Gap_init rate = 0.06 (30 / 530), avg. gap size = 2.03 (61 / 30) 199 23.71 9.76 2.27 chr6ptel1M 351541 351622 (648378) MamRTE1#LINE/RTE-BovB 706 793 (3019) m_b280s601i32 11212 chr6ptel1M 351541 AGCTCA--GAGACAGAAGCTGGCTTAGCCTTCCTTGAGGAAGAGTATTCC 351588 -- iv i ? vv - vv iii v MamRTE1#LINE/ 706 AGCTCACGGAGACAGGTGCCGGNTACGCCTT-CTTCTGGAGAGGTCTTCC 754 chr6ptel1M 351589 CTCTGCCAAAGC--CGG-TC---GGCACCTTCTTTGTAGT 351622 -i i -- - --- ii vv i i MamRTE1#LINE/ 755 CTCT-TCAGAGCGACGGCTCTCAGGCGTCAGCTTTGCAAT 793 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 25.99 CpG sites = 11, Kimura (unadjusted) = 29.54 Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.07 (6 / 81), avg. gap size = 1.67 (10 / 6) 226 27.26 11.61 5.04 chr6ptel1M 351622 351733 (648267) C MIR#SINE/MIR (123) 139 21 m_b280s601i33 11213 chr6ptel1M 351622 TTTACAGGGTGAGGGTTTTCTAGAGTACAGAGGGGTTAAG---------- 351661 i- ivv-- iii i i ---------- C MIR#SINE/MIR 139 TTTACAGA-TGAGGAAA--CTGAGGCACAGAGAGGTTAAGTAACTTGCCC 93 chr6ptel1M 351662 -GGATCATACAACCAGTTTGTGTCAGAGGTGGGGAATCTTAATCCCAGAT 351710 -i i i i i vv v vi -- - ii v ii C MIR#SINE/MIR 92 AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGG--AT-TCGAACCCAGGC 46 chr6ptel1M 351711 GTTCTGGC-CCAAAGCCAG-ACTCT 351733 iv - i v -i C MIR#SINE/MIR 45 AGTCTGGCTCCAGAGCCCGTGCTCT 21 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.45 CpG sites = 20, Kimura (unadjusted) = 35.67 Transitions / transversions = 2.22 (20/9) Gap_init rate = 0.09 (10 / 111), avg. gap size = 1.90 (19 / 10) 242 28.98 1.27 3.90 chr6ptel1M 351663 351741 (648259) C MIR3#SINE/MIR (117) 91 15 m_b280s601i34 11213 chr6ptel1M 351663 GATCATACAACCAGTTTGTGTCAGAGGTGGGGAATCTTAATCCCAGATGT 351712 i i i ? v v vi i--- vi v i v C MIR3#SINE/MIR 91 GGTCACACAGCNAGTTAGTGGCAGAGCCGGGA---CTAGAACCCAGGTCT 45 chr6ptel1M 351713 TCTGGC-CCAAAGCCAGACTCTCTCTGCCC 351741 i i - v iv ivi i C MIR3#SINE/MIR 44 CCTGACTCCCAGTCCGTGCTCTCTCTGCTC 15 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.98 CpG sites = 13, Kimura (unadjusted) = 38.29 Transitions / transversions = 1.44 (13/9) Gap_init rate = 0.05 (4 / 78), avg. gap size = 1.00 (4 / 4) 260 27.17 9.29 8.81 chr6ptel1M 351831 352056 (647944) CR1-3_Croc#LINE/CR1 2732 2958 (647) m_b280s551i1 11214 chr6ptel1M 351831 CTGAAGAGAGAGTATGATCAAGT-GTCGGCAGGTATTGGAAGGGCGGCCA 351879 v i iii -- i- vv ii i v v CR1-3_Croc#LI 2732 CTTAAGAGGGGACATGAT--AGCAGTCTTCAAATACTTGAAGGGCTGCCA 2779 chr6ptel1M 351880 CACGGAAGAGGGATCAGACTTGCTC-CGCTTGGCTG--GAGAGGACACTG 351926 i vi vviv i vi - v - -- ---- CR1-3_Croc#LI 2780 TAAAGAAGAGGGAAAGCACCTTTTCTCTCTT-GCTGCAGAGAGGA----G 2824 chr6ptel1M 351927 G--GCAGGCGCAATCAGTTTAAATTGTAG------------AGATTCGGG 351962 -- i i - viv v i i ------------ - i CR1-3_Croc#LI 2825 GACGCGGAC-CAATGGCTTGAAGTTGCAGCAAAGTAGGTTTAGATT-GGA 2872 chr6ptel1M 351963 TTTCTGCTTGAAAAGCTCCTTCTCCGTTACAACTGTCTGAAAGTGAAATG 352012 v i --- i i v i v v vv iv i i CR1-3_Croc#LI 2873 TATCCG---GAAAAACTTCTTCACTGTTAGAACAGTGAGGCAGTGGAATA 2919 chr6ptel1M 352013 GGATGCTCTGTGAGCCGGGGAAACT---CATTCTCCATCACTGGAAG 352056 iv -------- ii ii ---v i i CR1-3_Croc#LI 2920 GACTGC--------CTAGGGAAGTTGTGGACTCTCCATCACTGGAGG 2958 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.09 CpG sites = 33, Kimura (unadjusted) = 34.60 Transitions / transversions = 1.43 (33/23) Gap_init rate = 0.12 (26 / 225), avg. gap size = 1.58 (41 / 26) 258 23.16 11.54 4.50 chr6ptel1M 352356 352459 (647541) MIRc#SINE/MIR 18 128 (140) m_b280s601i35 11215 chr6ptel1M 352356 GTGGAAAGACCATTGA---TACCGTTATGGGAG---CGGG---AGGTCCT 352396 v i i--- ivv i - i ---i ---ii i MIRc#SINE/MIR 18 GTGGAAAGAGCACTGGACTTGGAGTCA-GGAAGACCTGGGTTCGAGTCCC 66 chr6ptel1M 352397 AAAGCTTGGCTACTTACACCATCTATGTGATCTTGGGAAAGTCACTTG-- 352444 i-- iv i --i v i i v i-- MIRc#SINE/MIR 67 G--GCTCTGCCACTTAC--TAGCTGTGTGACCTTGGGCAAGTCACTTAAC 112 chr6ptel1M 352445 CTCTCTGGG-CTCAGT 352459 i - MIRc#SINE/MIR 113 CTCTCTGAGCCTCAGT 128 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 25.99 CpG sites = 17, Kimura (unadjusted) = 29.11 Transitions / transversions = 2.83 (17/6) Gap_init rate = 0.10 (10 / 103), avg. gap size = 1.70 (17 / 10) 370 26.09 19.13 0.00 chr6ptel1M 354394 354508 (645492) C MIRc#SINE/MIR (18) 250 114 m_b280s601i36 11216 chr6ptel1M 354394 CATTTACATAACTCATTACGGTTCACAAAGTGCTTTC------------- 354430 ii i v v i i i ------------- C MIRc#SINE/MIR 250 CATTTGTATAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATCT 201 chr6ptel1M 354431 ---------CTCAGAACCATCTTGGGAAGTAGATCACGCCAGTTTTATGA 354471 --------- v v i i v i iiviv vi v v C MIRc#SINE/MIR 200 CATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTA 151 chr6ptel1M 354472 TTCCCACTTTAAAGACTGGGAAACTAAGGCTCAGAGA 354508 i i v ivi i C MIRc#SINE/MIR 150 TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGA 114 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.54 CpG sites = 18, Kimura (unadjusted) = 32.86 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.02 (2 / 114), avg. gap size = 11.00 (22 / 2) 252 24.22 0.00 3.23 chr6ptel1M 354459 354522 (645478) C MIR1_Amn#SINE/MIR (65) 165 104 m_b280s601i37 11216 chr6ptel1M 354459 GCCAGTTTTATGATTCCCACTTTAAAGACTGGGAAACTAAGGCTCAGAGA 354508 i v i v i i v ivi i ? - C MIR1_Amn#SINE 165 GTCAGTATCATTATCCCCATTTTACAGATGAGGAAACTGAGGCNCAGAG- 117 chr6ptel1M 354509 CATATGAAATGATT 354522 - vi ? i i C MIR1_Amn#SINE 116 -AGGTNAAGTGACT 104 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.51 CpG sites = 10, Kimura (unadjusted) = 31.51 Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.03 (2 / 63), avg. gap size = 1.00 (2 / 2) 424 25.00 9.62 0.00 chr6ptel1M 354688 354791 (645209) MIRc#SINE/MIR 30 143 (125) m_b280s601i38 11217 chr6ptel1M 354688 CTGGACTTGGAGTCAGGAAGCCCTGGGTTCAAACTCCACCTCATACACTA 354737 v i iii iv vvv v MIRc#SINE/MIR 30 CTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTT 79 chr6ptel1M 354738 AATAACCGTATGAT----AATAGGTCA------TTCTCCAGACCTCAGTT 354777 v i i i i----iii i ------i iiii MIRc#SINE/MIR 80 ACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTT 129 chr6ptel1M 354778 TCCTCTTCTGTAAA 354791 v MIRc#SINE/MIR 130 TCCTCATCTGTAAA 143 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.77 CpG sites = 18, Kimura (unadjusted) = 31.68 Transitions / transversions = 2.25 (18/8) Gap_init rate = 0.02 (2 / 103), avg. gap size = 5.00 (10 / 2) 538 28.42 6.01 3.82 chr6ptel1M 355461 355793 (644207) L1ME4c_3end#LINE/L1 300 639 (191) m_b280s551i2 11218 chr6ptel1M 355461 ATTGGTCT--CCATTCTGGATAGTAATCTGGAGTTATGCCCAAAGGGCTA 355508 vi-- v i v i i viv i iviv i i L1ME4c_3end#L 300 ATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCA 349 chr6ptel1M 355509 TAAAACTCTGCATACCCTTTGACCCTGCAGCACCATTACTGGATCTGTAT 355558 v v v v i iiv i v ivv v L1ME4c_3end#L 350 TAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTAT 399 chr6ptel1M 355559 CCCAAGGAAATCATC--AAGGAGGGAAAAGGCCCCACACATGCA--AAAA 355604 i v i-- i i i ----i i -- i L1ME4c_3end#L 400 CCTAAGGAAATAATTCAAAAGAAGGAAAAAGC----TATATGCACGAAGA 445 chr6ptel1M 355605 TGT---TTGCAGCAGTTTTTGTGTAATAGCAAAGGACTGGGAAAGGAGTG 355651 --- - v - i i ii i i viivv i L1ME4c_3end#L 446 TGTTCATTGCAGC-GTTATT-TATAATAGCGAAAAATTGGAAACAACCTA 493 chr6ptel1M 355652 GATGCCCATCCATTGGGAAATGGCTGGAGAA---GTGGTACATGAAGGTT 355698 i i v v v i i iiiv ---i v? vviv L1ME4c_3end#L 494 AATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCG 543 chr6ptel1M 355699 ATGAAATATTAGTGT-TTTATAAGAAATGATG-----GACAAGCTAATTA 355742 i - i-vii v i i----- - ii -- i L1ME4c_3end#L 544 ATGGAATATTA-TGCAGCCATTAAAAATGATAATTATGA-AGACTA--TG 589 chr6ptel1M 355743 TAGAAAGGCCTGGAAAGATTTACATGAACTAA-GCTAAGCG-AACAAGCA 355790 v -- v - v vi vv - i i - v L1ME4c_3end#L 590 TAGCAA--CATGGAAA-ATGTTTATGATATAATGTTAAGTGAAAAAAGCA 636 chr6ptel1M 355791 GAA 355793 L1ME4c_3end#L 637 GAA 639 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 35.30 CpG sites = 53, Kimura (unadjusted) = 36.82 Transitions / transversions = 1.39 (53/38) Gap_init rate = 0.07 (22 / 332), avg. gap size = 1.50 (33 / 22) 505 28.70 0.71 2.92 chr6ptel1M 356207 356346 (643654) L3#LINE/CR1 3917 4053 (46) m_b280s601i39 11219 chr6ptel1M 356207 GCTAGTCAGAAAGAAATTGTGTTGTTGAGGTCAGGAGTTAGTGAGTTCCT 356256 ivi i vii v v i ii---- i? v i i L3#LINE/CR1 3917 GCTGTCCAAAAATGGAATGGGCTGCC----TCGNGAGGTAGTGAGCTCCC 3962 chr6ptel1M 356257 TGATACTAGAGTTATTCAAGGACAGTCTGAATGAGCACTTGTCAGCAATG 356306 i vi i v i v v v i v vi L3#LINE/CR1 3963 CGTCACTGGAGGTGTTCAAGCAGAGGCTGGATGACCACTTGTCAGGGATG 4012 chr6ptel1M 356307 TTATAGAGGAGATTCCTACCTTGAATAGG-GCTTGAACAAG 356346 i i i i v i i - v i v L3#LINE/CR1 4013 TTGTAGAAGGGATTCCTGCATTGGATGGGAGGTTGGACTAG 4053 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.27 CpG sites = 24, Kimura (unadjusted) = 37.71 Transitions / transversions = 1.60 (24/15) Gap_init rate = 0.04 (5 / 139), avg. gap size = 1.00 (5 / 5) 399 28.97 1.87 0.00 chr6ptel1M 356518 356624 (643376) L3#LINE/CR1 3990 4098 (1) m_b280s601i40 11220 chr6ptel1M 356518 TGGATAACCATTAGTTGGAAATAGGTCAGAGAAAATTCCTCC-TTAGTCT 356566 i i v ii ii ivvvi iiii v - i viv L3#LINE/CR1 3990 TGGATGACCACTTGTCAGGGATGTTGTAGAAGGGATTCCTGCATTGGATG 4039 chr6ptel1M 356567 TGAG-TTGGATTAGATGCCCTTTGAGGTTTCTTCCAACTTTGACATTCTG 356615 v - i v i i ii i v L3#LINE/CR1 4040 GGAGGTTGGACTAGATGACCTCTAAGGTCCCTTCCAACTCTGAGATTCTG 4089 chr6ptel1M 356616 TGATTCTGT 356624 i L3#LINE/CR1 4090 TGATTCTAT 4098 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.45 CpG sites = 21, Kimura (unadjusted) = 38.45 Transitions / transversions = 2.10 (21/10) Gap_init rate = 0.02 (2 / 106), avg. gap size = 1.00 (2 / 2) 321 37.80 4.76 4.27 chr6ptel1M 356740 356949 (643051) MIRc#SINE/MIR 1 211 (57) m_b280s601i41 11221 chr6ptel1M 356740 CAAGATAGTATA-TGTTGTGTGATATGCTTTGTATTTAAAAAATTAGAAA 356788 i ii i i- iv vi viv vi v i ii i-- i i MIRc#SINE/MIR 1 CGAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAG--TCAGGAA 48 chr6ptel1M 356789 AAC-TGGGCTTGAGATAAAGTTCCATCACTTATCAGTCTTGTGATATTAA 356837 i - i i vivvi i iii ii iiv iv ii MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 98 chr6ptel1M 356838 GCGAGTTACTCACATGTTCCCCTTGACCTTTTAATTTTTTCACATTTAAA 356887 i i i v----i i ii v -i i i ii iv v MIRc#SINE/MIR 99 GCAAGTCACTTAA----CCTCTCTGAGC-CTCAGTTTCCTCATCTGTAAA 143 chr6ptel1M 356888 AAGGGGTCAATTCTATTTGC-------ATTTAACAGAATTTTGTCATGAG 356930 v vi vv ii ------- ii v ii-- ii MIRc#SINE/MIR 144 ATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGG--TTGTTGTGAG 191 chr6ptel1M 356931 GGTC-AATGTGATAGTGTAT 356949 i - v i MIRc#SINE/MIR 192 GATCAAATGAGATAATGTAT 211 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 54.88 CpG sites = 55, Kimura (unadjusted) = 58.60 Transitions / transversions = 2.62 (55/21) Gap_init rate = 0.06 (13 / 209), avg. gap size = 1.46 (19 / 13) 22 20.47 0.00 3.85 chr6ptel1M 357091 357144 (642856) (GA)n#Simple_repeat 1 52 (0) m_b280s252i5 11222 chr6ptel1M 357091 GAGAGAGACACACAAAGAAAGAGAGACGCAGAGACAGAGAGACAGAGACA 357140 v v v i i - - v v v (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGA-G-AGAGAGAGAGAGAGAGAGAGA 48 chr6ptel1M 357141 AAGA 357144 i (GA)n#Simple_ 49 GAGA 52 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.04 (2 / 53), avg. gap size = 1.00 (2 / 2) 46 3.95 1.92 0.00 chr6ptel1M 357993 358044 (641956) (AT)n#Simple_repeat 1 53 (0) c_b280s251i2 11223 chr6ptel1M 357993 ATATATATATATATATATATTTATACAT-TATATATATATATATATATAT 358041 v i - (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr6ptel1M 358042 ATA 358044 (AT)n#Simple_ 51 ATA 53 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.02 (1 / 51), avg. gap size = 1.00 (1 / 1) 29 5.92 7.55 0.00 chr6ptel1M 358253 358305 (641695) (GTTGTT)n#Simple_repeat 1 57 (0) m_b280s252i6 11224 chr6ptel1M 358253 GTTTTTGTTGTTGTTGTTGTTGTTGTTTTTGTT-TTGTT-TTGTT-TT-T 358298 v v - - - - (GTTGTT)n#Sim 1 GTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGT 50 chr6ptel1M 358299 TGTTTTT 358305 v (GTTGTT)n#Sim 51 TGTTGTT 57 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.08 (4 / 52), avg. gap size = 1.00 (4 / 4) 389 31.79 3.37 2.79 chr6ptel1M 358356 358533 (641467) MIR1_Amn#SINE/MIR 5 183 (47) m_b280s601i43 11225 chr6ptel1M 358356 GAGGCAAGAGTGGGGCAGAAGA-AGAATGCTGCATTTGGAGTCCCAAGAC 358404 - v vvi vi - iii v i v v vvi MIR1_Amn#SINE 5 GAGGCA-GTGTGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGAGAC 53 chr6ptel1M 358405 CCAAATTCAAATCCTAACTCTGTTACTA-CCTG----GAGGTTTTTGGTA 358449 iiii ? ? iii ii ?- ? ---- v iii v i MIR1_Amn#SINE 54 CTGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCA 103 chr6ptel1M 358450 ATGTCACTTATTCTCTCTGGGCCTGAGGTTTTACCTTGGTAAAAGGAGAA 358499 - ?vi ? v v iiv v iv v i i MIR1_Amn#SINE 104 A-GTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGGA 152 chr6ptel1M 358500 TATCAATCAGCAAACCCGCATTTATCAAGTGTTT 358533 vii --i vi i- v i v i MIR1_Amn#SINE 153 TAATGAT--ACTGACCT-CCTTTGTAAAGTGCTT 183 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 43.82 CpG sites = 33, Kimura (unadjusted) = 45.07 Transitions / transversions = 1.50 (33/22) Gap_init rate = 0.05 (8 / 177), avg. gap size = 1.38 (11 / 8) 457 28.85 4.64 1.28 chr6ptel1M 358356 358506 (641494) MIRc#SINE/MIR 2 157 (111) m_b280s601i42 11225 chr6ptel1M 358356 GAGGCAAGAGTGGGGCAGAAGAA-GAATGCTGCATTTGGAGTCCC-AAGA 358403 - v v vi - iii v i vv- MIRc#SINE/MIR 2 GAGGCA-GTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA 50 chr6ptel1M 358404 CCCAAATTCAAATCCTAACTCTG----TTACTACCTG-GAGGTTTTTGGT 358448 iiii i i iii ---- v - v iii v i MIRc#SINE/MIR 51 CCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGC 100 chr6ptel1M 358449 AATGTCACTTATTCTCTCTGGGCCTGAGGTTTTACCTTGGTAAAAGGAGA 358498 - vi i v v iiv v iv v i i MIRc#SINE/MIR 101 AA-GTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGG 149 chr6ptel1M 358499 ATATCAAT 358506 vi MIRc#SINE/MIR 150 ATAATAAT 157 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.25 CpG sites = 26, Kimura (unadjusted) = 37.57 Transitions / transversions = 1.53 (26/17) Gap_init rate = 0.04 (6 / 150), avg. gap size = 1.50 (9 / 6) 311 31.97 2.97 4.00 chr6ptel1M 358502 358602 (641398) C L2b_3end#LINE/L2 (6) 460 361 m_b280s601i44 11226 chr6ptel1M 358502 TCAATCAGCAAACCCGCATTTATCAAGTGTTTACTATGTGCCAGGCACTG 358551 v i i---- iii i ii i ? C L2b_3end#LINE 460 TCATTCAACAAAT----ATTTACTGAGCGCCTACTGTGTGCCAGGCNCTG 415 chr6ptel1M 358552 TGCCAA--ATTGAGGATGTAAAGAAGGGCAAAAAAACCACAG-CCCTGTT 358598 i i--ii i ii iv iv ii i v iv ? i - ii C L2b_3end#LINE 414 TGCTAGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCC 365 chr6ptel1M 358599 CTTA 358602 i C L2b_3end#LINE 364 CTCA 361 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 41.95 CpG sites = 26, Kimura (unadjusted) = 48.60 Transitions / transversions = 5.20 (26/5) Gap_init rate = 0.06 (6 / 100), avg. gap size = 1.17 (7 / 6) 237 28.56 5.17 3.39 chr6ptel1M 358599 358714 (641286) MIRc#SINE/MIR 123 240 (28) m_b280s601i45 11227 chr6ptel1M 358599 CTTAGTTTCTTTATC-ATAAAATGGTGATAGTGAAATTT---CTGAAATT 358644 i i i -i v i i v ii --- ---ii MIRc#SINE/MIR 123 CTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTG---CC 169 chr6ptel1M 358645 TAACT-GGGGGATTTTTGTGAAGGTGAAACGAGATACTATAT-TTAAAAT 358692 v -ivi i v i i v i v i - v ii MIRc#SINE/MIR 170 TACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGC 219 chr6ptel1M 358693 AATTTGCAAAGCAGTAAAGGGC 358714 iv i - v v MIRc#SINE/MIR 220 GCTTTGTAAA-CTGTAAAGTGC 240 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.85 CpG sites = 21, Kimura (unadjusted) = 37.52 Transitions / transversions = 1.91 (21/11) Gap_init rate = 0.07 (8 / 115), avg. gap size = 1.25 (10 / 8) 240 37.49 3.31 0.81 chr6ptel1M 358785 358905 (641095) C MIRc#SINE/MIR (143) 125 2 m_b280s601i46 11228 chr6ptel1M 358785 GGGGCT-AGTAAGG--AAATACCTTGCCCAGGGTC-CCTTGCCAGTAGGC 358830 i - vi -- i iv i - viv i i i C MIRc#SINE/MIR 125 GAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGT 76 chr6ptel1M 358831 ACTCGGAGGCAGATCTTAACCCCAGGCCTTCTTAGCTTGGAAATCAGCTC 358880 i-v i v i iv ii v i i ii ivi ivi iv C MIRc#SINE/MIR 75 G-GCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGC 27 chr6ptel1M 358881 TCTGTCTTCTAGGTCATGTTGCCTC 358905 v iv ivii iii C MIRc#SINE/MIR 26 TCTTTCCACTGCACCACACTGCCTC 2 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 52.67 CpG sites = 31, Kimura (unadjusted) = 56.81 Transitions / transversions = 2.21 (31/14) Gap_init rate = 0.03 (4 / 120), avg. gap size = 1.25 (5 / 4) 481 27.32 2.65 5.44 chr6ptel1M 359120 359270 (640730) C MIRc#SINE/MIR (120) 148 2 m_b280s601i47 11229 chr6ptel1M 359120 CTCATTTTACAAACAAGAAAACTGAGGC--AAACAGGATTCAGCCACTTG 359167 i i ii i -- i v - v iv C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGG-TTAAGTGACTTG 100 chr6ptel1M 359168 TCCTGAATCACATGGCAATTAAGTGTCTGAGGTCAGATTT-AACTCAGAA 359216 i viii ii v v v v vivi i i- i i- C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGG- 51 chr6ptel1M 359217 AGTTAATCTTCCTGACTTCAGGCCCTGTACTCTATCCACTGTGCCAC-CT 359265 ------ i i i v i v ii - C MIRc#SINE/MIR 50 ------TCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACT 7 chr6ptel1M 359266 AACTC 359270 iv C MIRc#SINE/MIR 6 GCCTC 2 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.07 CpG sites = 26, Kimura (unadjusted) = 35.32 Transitions / transversions = 2.00 (26/13) Gap_init rate = 0.07 (11 / 150), avg. gap size = 1.09 (12 / 11) 343 27.37 1.05 0.00 chr6ptel1M 359764 359858 (640142) L1ME2z_3end#LINE/L1 438 533 (658) m_b280s551i3 11230 chr6ptel1M 359764 AAGAAT-TGCCTCACAGGTCTCTTTGTAGTGGCCAGAAACTGGAAAGTGA 359812 - v v vi v i v ii i i i vv v L1ME2z_3end#L 438 AAGAATGTTCATAGCAGCTTTATTCATAATAGCCAAAAACTGGAAACAGC 487 chr6ptel1M 359813 GTAGATGCCCATCAATTGGAGAATGGCTGAATAAACTGCGGCATAT 359858 vi i i iv v i i i i L1ME2z_3end#L 488 CCAGGTGTCCATCAACAGGAGAATGGATAAACAAACTGTGGTATAT 533 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 34.83 CpG sites = 15, Kimura (unadjusted) = 34.83 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.01 (1 / 94), avg. gap size = 1.00 (1 / 1) 54 6.68 0.00 0.00 chr6ptel1M 359865 359928 (640072) (TA)n#Simple_repeat 1 64 (0) c_b280s251i3 11231 chr6ptel1M 359865 TATATATATGTATATGTATATATATATATGTGTATATATATATATATATA 359914 i i i i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr6ptel1M 359915 TATATATATATATA 359928 (TA)n#Simple_ 51 TATATATATATATA 64 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0) 284 28.77 8.66 1.47 chr6ptel1M 360730 360856 (639144) L2d2_3end#LINE/L2 420 555 (0) m_b280s601i48 11232 chr6ptel1M 360730 TCTTGGTTGTTCCA--TACATTATAAACTTTTCAAGGGCTGAAAC----T 360773 vi -ii -- v i i ii ii v ii ---- L2d2_3end#LIN 420 TCTTGTCT-CCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGT 468 chr6ptel1M 360774 TTTA-ACTAGA--GTTTCCTGCCCCAGTGCCTAGTACAGTGCCATACTGC 360820 i - vvv-- v i- v i i v i vvv L2d2_3end#LIN 469 CTTATACTTCTTTGTATCCC-CCACAGCGCCTAGCACAGTGCCTTGCACA 517 chr6ptel1M 360821 TAATAGGTGACAAATAAAGATTTGTGG--TTGATTTGA 360856 i i i viv v v -- L2d2_3end#LIN 518 CAGTAGGCGCTCAATAAATATTTGTTGATTTGATTTGA 555 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.56 CpG sites = 20, Kimura (unadjusted) = 37.10 Transitions / transversions = 1.25 (20/16) Gap_init rate = 0.06 (7 / 126), avg. gap size = 1.86 (13 / 7) 772 31.57 6.63 6.63 chr6ptel1M 361014 361420 (638580) L3#LINE/CR1 3536 3942 (157) m_b280s601i49 11233 chr6ptel1M 361014 AAAACAAGTAAAGTCAGAAGTCCTATAGTCCTCTGTCTTAGGGAGAGC-T 361062 i ? vi i - iv iiiv v ivi i vv v -i L3#LINE/CR1 3536 AGANCAAGGGAGGT-AATAGTCCCGCTGTACTCTGCGCTGGTCAGACCAC 3584 chr6ptel1M 361063 AGCAGAAGTA--------AGTTCCAGGCACCACATTTTAGGAAGGACTTT 361104 v v i -------- ii i i i v L3#LINE/CR1 3585 ATCTGGAGTATTGCGTTCAGTTCTGGGCGCCACATTTTAAGAGGGACATT 3634 chr6ptel1M 361105 GACAAACTAGAAGGTATCCTGGAGATGATGAGTAGGATGTGAAAAGAATT 361154 i iv ii v ii viii vi vvi i ivi L3#LINE/CR1 3635 GACAAACTGGAGCGCGTCCAGAGGAGAGCGACCAGGATGGTGAAGGGTCT 3684 chr6ptel1M 361155 GGGGACCATACCTTGTGAGTGAGGGCTGGTTAGAGAACTTCAAGATGTCT 361204 ii ii v ----i ivi ii i vi vii i L3#LINE/CR1 3685 GGAAACCATGTCAT----ATGAGGAACGGTTGAAGGAACTGGGGATGTTT 3730 chr6ptel1M 361205 AGTCTGGGGGTGAGGGAGTGGAGAAAGAGGAAGAC--AGAAGAGGGACAC 361252 i i --------------- - -- i -- i L3#LINE/CR1 3731 AGCCTGGAG---------------AAGA-GAAGACTTAGAGGA--GACAT 3762 chr6ptel1M 361253 GGTTATTTTCTTTAAAAAAAACTTGGAAAACTGTCCAGGGGGAA----CA 361298 i vii v i--- v i i iii - v v ----v L3#LINE/CR1 3763 GATAGCTGTCTTC---AAATATTTGAAGGGCTGT-CATGTGGAAGAGGGA 3808 chr6ptel1M 361299 TTAGACT--TTCT---TGGTATTAGAAGGCATA------ATCAAAGGATA 361337 -- --- ivii i v ------ i v i i L3#LINE/CR1 3809 TTAGACTTATTCTGTGTGGCTCCAGAGGGCAGAACTAGGACCAATGGGTG 3858 chr6ptel1M 361338 GAACTTGTGAGGAGGCAAATTTCCCTTCAAGTTAAGGAAGAACTTTTTAA 361387 v iiii i vvi vv i L3#LINE/CR1 3859 GAAGTTACAGGGAGGCAGATTTCGGCTCAATATAAGGAAGAACTTTCTAA 3908 chr6ptel1M 361388 TCATGAG-GATGTCTAGAATCAGAATGAACAGCC 361420 iv v - v i i vii ii v L3#LINE/CR1 3909 CAATCAGAGCTGTCCAAAAATGGAATGGGCTGCC 3942 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 40.31 CpG sites = 79, Kimura (unadjusted) = 43.32 Transitions / transversions = 1.93 (79/41) Gap_init rate = 0.09 (35 / 406), avg. gap size = 1.54 (54 / 35) 17 22.79 0.00 0.00 chr6ptel1M 361755 361790 (638210) (T)n#Simple_repeat 1 36 (0) m_b280s252i7 11234 chr6ptel1M 361755 TTTTTTGTTTTTTCTTTTTGTGTTTTTTCCCTTTTT 361790 v i v v iii (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 36 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 665 28.38 3.88 1.26 chr6ptel1M 362158 362389 (637611) MIRc#SINE/MIR 31 268 (0) m_b280s601i50 11235 chr6ptel1M 362158 TGGACCTGAAGTTAGCAAGAGTTGAGTTCAGACCTTGCCTCAAAAACACT 362207 i i i v vi i iiii ii v viv-- MIRc#SINE/MIR 31 TGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGC--CACT 78 chr6ptel1M 362208 TACCA-CTGTGAGGCACTGGAAAAGAAACTTAACTTCTCTTTGCCTCAGT 362256 i - v i vi iv vv i vv MIRc#SINE/MIR 79 TACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGT 128 chr6ptel1M 362257 TTCCTCATCTGAAATATGGTGATCAGGTT--CTAACCTGTCT---CCA-A 362300 v v v v viv -- iv i ---i - MIRc#SINE/MIR 129 TTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACA 178 chr6ptel1M 362301 GGCTTCTTGTGAGGATCATATGTGAGGATCT-TGT-AAAGTACTATGCAA 362348 v v v v vi v - - ii v i MIRc#SINE/MIR 179 GGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTTTGTAA 228 chr6ptel1M 362349 ATCATAAAGCACTAATTTGAATGCTAGATATTGTCATTATT 362389 iii ii - vii iv i?i i i MIRc#SINE/MIR 229 ACTGTAAAGTGCT-ATACAAATGTAAGGNGTTATTATTATT 268 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.53 CpG sites = 37, Kimura (unadjusted) = 36.70 Transitions / transversions = 1.32 (37/28) Gap_init rate = 0.04 (9 / 231), avg. gap size = 1.33 (12 / 9) 449 27.02 1.44 6.82 chr6ptel1M 363498 363636 (636364) MIRc#SINE/MIR 13 144 (124) m_b280s601i51 11236 chr6ptel1M 363498 GCACAGCAGATAGAGCGTAGGGCCTGGAGTCAGGAACACTCATCTTCCTT 363547 ii ii v iiv i i v -------- v MIRc#SINE/MIR 13 GTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC--------CTG 54 chr6ptel1M 363548 CGCTCAAATCTGGCCTCTGACACTAACTAGTTGTGTGGTCCTGGGCAAGT 363597 v i i i iv v v v i ii i MIRc#SINE/MIR 55 GGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGT 104 chr6ptel1M 363598 CACCTCATCCTGTTT--GTTCCAGTTTCTGCATCTTTAAAA 363636 i v - v i -- iii iv v MIRc#SINE/MIR 105 CACTTAA-CCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAA 144 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.21 CpG sites = 22, Kimura (unadjusted) = 34.43 Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.07 (10 / 138), avg. gap size = 1.10 (11 / 10) 352 19.32 18.18 1.96 chr6ptel1M 364417 364548 (635452) MIRc#SINE/MIR 115 267 (1) m_b280s601i52 11236 chr6ptel1M 364417 CTTTGAGTCTCAGATTGACTCATTTGTAAAAGTGGAGTTAATAAGACTTG 364466 i i - vv i - i v v i MIRc#SINE/MIR 115 CTCTGAGCCTCAG-TTTCCTCATCTGTAAAA-TGGGGATAATAATACCTG 162 chr6ptel1M 364467 -------------ACAGGGCAGTTGTGAG-----ACTGACATAATGCGGT 364498 ------------- iv ----- v v ii- MIRc#SINE/MIR 163 CCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTA-T 211 chr6ptel1M 364499 GTGAA-GCACTTTGAAGGCTTGAAAGTGCCATGAAAAT-----CCGTTAT 364542 - i v ii vv i iv -----v? MIRc#SINE/MIR 212 GTGAAAGCGCTTTGTAAACTGTAAAGTGCTATACAAATGTAAGGNGTTAT 261 chr6ptel1M 364543 TATTAT 364548 MIRc#SINE/MIR 262 TATTAT 267 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 21.81 CpG sites = 13, Kimura (unadjusted) = 22.80 Transitions / transversions = 1.08 (13/12) Gap_init rate = 0.05 (7 / 131), avg. gap size = 3.86 (27 / 7) 195 23.98 6.73 7.77 chr6ptel1M 365374 365477 (634523) MIR1_Amn#SINE/MIR 21 123 (107) m_b280s601i53 11237 chr6ptel1M 365374 GTGGGCAGACCACTAGCCT----CTGGGGAGGAATTTGGGGGTTCCAATC 365419 ii v i v ---- v -- ii -- ? ? MIR1_Amn#SINE 21 GTGGATAGAGCACTGGACTGGGACTCGGGAG--ACCTGGG--TTCNANTC 66 chr6ptel1M 365420 CTGCTTCAGACACTTGTTGGCTGTGTGATTCTCCCTGAG---ATCAGTAC 365466 i vi v v ? ii? ? ---- i i ---i v v? MIR1_Amn#SINE 67 CCGGCTCTGCCACTNGCCNGCTGNGTGA----CCTTGGGCAAGTCACTTN 112 chr6ptel1M 365467 CCTTCCCTGGG 365477 v i i ? MIR1_Amn#SINE 113 ACCTCTCTGNG 123 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.82 CpG sites = 14, Kimura (unadjusted) = 32.52 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.10 (10 / 103), avg. gap size = 1.50 (15 / 10) 210 29.09 20.91 0.00 chr6ptel1M 365409 365518 (634482) MIR3#SINE/MIR 51 183 (25) m_b280s601i54 11237 chr6ptel1M 365409 GGGTTCCAATCCTGCTTCAGACACTTGTTGGCTGTGTGATT--------- 365449 i i i vi v v vii ? ii--------- MIR3#SINE/MIR 51 GGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAG 100 chr6ptel1M 365450 ---------CTCCCTGAGA-TCAGTACCCTTCCCTGGGAAGGGAGGGG-T 365488 --------- i i v- vi ivi vi iv - MIR3#SINE/MIR 101 TCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGT 150 chr6ptel1M 365489 TAGATTGGAC---TTCTCAGCTCCCTTCCAACT 365518 i i i i---i v v i MIR3#SINE/MIR 151 TGGACTAGATGATCTCTAAGGTCCCTTCCAGCT 183 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.35 CpG sites = 21, Kimura (unadjusted) = 38.94 Transitions / transversions = 1.91 (21/11) Gap_init rate = 0.05 (5 / 109), avg. gap size = 4.60 (23 / 5) 653 23.18 2.88 0.70 chr6ptel1M 366007 366145 (633855) C MIRc#SINE/MIR (120) 148 7 m_b280s601i55 11238 chr6ptel1M 366007 CTCATTTTACAGATGAGAAAACTGAG--TCAAACAGGGTTAAGTGACTTG 366054 i i -- i v - C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGG-TTAAGTGACTTG 100 chr6ptel1M 366055 CCCAAGATCACATGGCTACTAAATATCTGAGATCAGATGTTAATTCAGAT 366104 i ii v i iv v vivi iviv ii i C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGT 50 chr6ptel1M 366105 TTTCCTGACT--AGGCTCAGTGCTCTATCTGCTGTACCACCCT 366145 i -- i ii v ii i v C MIRc#SINE/MIR 49 CTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACT 7 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 26.64 CpG sites = 22, Kimura (unadjusted) = 28.74 Transitions / transversions = 2.20 (22/10) Gap_init rate = 0.02 (3 / 138), avg. gap size = 1.67 (5 / 3) 242 31.49 2.68 3.60 chr6ptel1M 366264 366375 (633625) C MIR3#SINE/MIR (21) 187 77 m_b280s601i56 11239 chr6ptel1M 366264 TCAGAGTCAGAAGGAATCAAAGAGACCATCCAGGCTGAGCTCCCTGATTT 366313 iii i i vv i i v i- i i v C MIR3#SINE/MIR 187 TCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCC-AACCCCCTCATTT 139 chr6ptel1M 366314 TACAGCTG-GTCCTCTGAAGCTCACTCAAGAAG-GCTGTTCCTTGACTAA 366361 v - vvvv i i ---i i - vv vv v i C MIR3#SINE/MIR 138 TACAGATGAGGAAACTGAGGCCCA---GAGAGGTGAAGTGACTTGCCCAA 92 chr6ptel1M 366362 GATAGCAT-GTGAGT 366375 i vi i- i? C MIR3#SINE/MIR 91 GGTCACACAGCNAGT 77 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 42.42 CpG sites = 19, Kimura (unadjusted) = 42.42 Transitions / transversions = 1.27 (19/15) Gap_init rate = 0.06 (7 / 111), avg. gap size = 1.00 (7 / 7) 388 30.58 10.17 2.09 chr6ptel1M 366593 366769 (633231) C MIRc#SINE/MIR (75) 193 3 m_b280s601i57 11240 chr6ptel1M 366593 TCTTCCTAATAACCCTGTGAGATAG--AGCGAGAGAATTA--------AG 366632 i vi i i -- v vii v -------- v C MIRc#SINE/MIR 193 TCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCAT 144 chr6ptel1M 366633 T--ACGGAGAAATAAACATATACTGGGAAATGTTCAATAATTTGCTCAAG 366680 -- i vi iv vv vi vi i v v i i i i C MIRc#SINE/MIR 143 TTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAG 94 chr6ptel1M 366681 GCCTCCCACCTAGCAAGTCTGACAGAGCTGGGACTCATGCTCTAG--TTC 366728 i v v v i -- i i ivi i vi -- C MIRc#SINE/MIR 93 GTCACACAGCTAGTAAGT--GGCAGAGCCGGGACTCGAACCCAGGTCTTC 46 chr6ptel1M 366729 CTAGTTC--AGT--ATTCCTTCTTCTACTGCATCAGTCAGTACCT 366769 iii -- -- v v ii i i -- v i C MIRc#SINE/MIR 45 CTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCA--CACTGCCT 3 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.75 CpG sites = 32, Kimura (unadjusted) = 40.75 Transitions / transversions = 1.52 (32/21) Gap_init rate = 0.06 (10 / 176), avg. gap size = 2.20 (22 / 10) 331 19.64 0.00 0.00 chr6ptel1M 367069 367124 (632876) C U6#snRNA (51) 56 1 m_b280s502i4 11241 chr6ptel1M 367069 TGTTAATCTTCTCTGTATTGTTTCACTTTAAACATATGCGCTACCAAAGG 367118 i i i v v ii i i i v C U6#snRNA 56 TGCTAATCTTCTCTGTATCGTTCCAATTTTAGTATATGTGCTGCCGAAGC 7 chr6ptel1M 367119 GAGCAC 367124 C U6#snRNA 6 GAGCAC 1 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 18.91 CpG sites = 8, Kimura (unadjusted) = 23.55 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0) 218 27.13 1.64 3.33 chr6ptel1M 367664 367724 (632276) C L3#LINE/CR1 (6) 4093 4034 m_b280s601i58 11242 chr6ptel1M 367664 ATCATAGAATTTTAGAGTTGAAAAGAACC-TGGAGGTTCCCCCACTCACA 367712 i i i i i i - i - vi i v - C L3#LINE/CR1 4093 ATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGG-TCATCTAGTC-CA 4046 chr6ptel1M 367713 ATGTCTTATCTA 367724 iv ii i C L3#LINE/CR1 4045 ACCTCCCATCCA 4034 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.50 CpG sites = 13, Kimura (unadjusted) = 36.50 Transitions / transversions = 4.33 (13/3) Gap_init rate = 0.05 (3 / 60), avg. gap size = 1.00 (3 / 3) 563 25.46 3.59 3.59 chr6ptel1M 368441 368607 (631393) MIRc#SINE/MIR 31 197 (71) m_b280s601i59 11243 chr6ptel1M 368441 TGGGCATTGGAG--AAGGGGACCCGTGTCCGATGCAAGTCCAGATTCTGC 368488 i - -- i ii i v i ----- v ii MIRc#SINE/MIR 31 TGGAC-TTGGAGTCAGGAAGACCTGGGTTCGA-----GTCCCGGCTCTGC 74 chr6ptel1M 368489 TACTCGCTGGCACTGTGACTAAGGCCAAGCCATTTGATCTCT-TG-GTCT 368536 i ii i vv ivv v i i i i - - i MIRc#SINE/MIR 75 CACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCT 124 chr6ptel1M 368537 CAGTTTCTTCATTTGTCAAGTGGGGATAATAACATTTGCATTCTCTACCT 368586 i i v i i ii vi vi MIRc#SINE/MIR 125 CAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCT 174 chr6ptel1M 368587 -ATAGGGTT-TGGGGAAGATTAA 368607 - i - v v i i MIRc#SINE/MIR 175 CACAGGGTTGTTGTGAGGATCAA 197 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.56 CpG sites = 29, Kimura (unadjusted) = 32.56 Transitions / transversions = 2.42 (29/12) Gap_init rate = 0.07 (11 / 166), avg. gap size = 1.09 (12 / 11) 329 26.42 5.36 5.36 chr6ptel1M 369180 369291 (630709) MIRc#SINE/MIR 2 113 (155) m_b280s601i60 11244 chr6ptel1M 369180 GAGGCAGCCTGGTAAAGTCGGTAAAGC------CTTGGAGTCAGGGAGAT 369223 iv iv v iv i ------ i i MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr6ptel1M 369224 CAGGGTTTAAGTCTTGTCCCTGACATATTCCTGCTGGCAAGACATATTTC 369273 v ii ii v i v iv v iv - iiv v ----- MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCT-GTGTGACCT----- 95 chr6ptel1M 369274 TGGGCAAGTCACTTAGCC 369291 i MIRc#SINE/MIR 96 TGGGCAAGTCACTTAACC 113 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.26 CpG sites = 16, Kimura (unadjusted) = 33.23 Transitions / transversions = 1.33 (16/12) Gap_init rate = 0.06 (7 / 111), avg. gap size = 1.71 (12 / 7) 207 28.85 3.97 11.97 chr6ptel1M 369182 369307 (630693) MIR3#SINE/MIR 3 119 (89) m_b280s601i61 11244 chr6ptel1M 369182 GGCAGCCTGGTAAAGTCGGTAAAGC-----CTTGGAGTCAGGGAGATCAG 369226 vv ivi iv iv i ----- v - i v MIR3#SINE/MIR 3 GGCAGAGTGGCTGAGCAGAGAGAGCACGGACTGGGAGTCAGG-AGACCTG 51 chr6ptel1M 369227 GGTTTAAGTCTTGTCCCTGACATATTCCTGCTGGCAAGACATATTTCTGG 369276 iv ii v i v ivvv i? -iiv v ----- MIR3#SINE/MIR 52 GGTTCTAGTCCCGGCTCTGCCACTAACTNGCTG-TGTGACCT-----TGG 95 chr6ptel1M 369277 GCAAGTCACTTAGCCAGTCAATGCTCTGGGC 369307 ------- viv MIR3#SINE/MIR 96 GCAAGTCACT-------TCACCTCTCTGGGC 119 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.29 CpG sites = 15, Kimura (unadjusted) = 36.68 Transitions / transversions = 0.88 (15/17) Gap_init rate = 0.12 (15 / 125), avg. gap size = 1.27 (19 / 15) 576 29.98 10.38 0.86 chr6ptel1M 369917 370128 (629872) C L3#LINE/CR1 (11) 4088 3857 m_b280s601i62 11245 chr6ptel1M 369917 AGAATCTCCAGAGTTGGACAAA--CTCAGGGATCACCTGGTCTAACCT-- 369962 - viii-- i i i i i i -- C L3#LINE/CR1 4088 AGAATCTC-AGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCAACCTCC 4040 chr6ptel1M 369963 -----GGAGAAGGAAGCTCTTCTCTGACACGTCTGAGAAATGGTCATCAA 370007 -----iiv v v i vii ivi v i v C L3#LINE/CR1 4039 CATCCAATGCAGGAATCCCTTCTACAACATCCCTGACAAGTGGTCATCCA 3990 chr6ptel1M 370008 GGAGCTGTT------------GTGACGGGTGATTCACTATCTATCAAAGC 370045 vvv i ------------ viii i v? i i C L3#LINE/CR1 3989 GCCTCTGCTTGAACACCTCCAGTGACGGGGAGCTCACTACCTCNCGAGGC 3940 chr6ptel1M 370046 ATCCCATTCGCCTTCTGAACAGTCCTAAGCATGGGGAGGGTACTTCATTA 370095 v vvi i i ii i vii vi i i v - v C L3#LINE/CR1 3939 AGCCCATTCCATTTTTGGACAGCTCTGATTGTTAGAAAGTT-CTTCCTTA 3891 chr6ptel1M 370096 AACTAAATGGAAATCTGCCTTCCTGT-GCTTCCA 370128 v i i iiv i -i C L3#LINE/CR1 3890 TATTGAGCCGAAATCTGCCTCCCTGTAACTTCCA 3857 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.48 CpG sites = 41, Kimura (unadjusted) = 40.33 Transitions / transversions = 1.86 (41/22) Gap_init rate = 0.03 (7 / 211), avg. gap size = 3.43 (24 / 7) 284 34.75 4.42 6.18 chr6ptel1M 370927 371107 (628893) MIRc#SINE/MIR 9 186 (82) m_b281s601i1 11246 chr6ptel1M 370927 TGTGGGATAGTGGCCATATCATTGAACATGGAA-GGGGAAGACCAATGTT 370975 vii vv v v i i v i-vi viv MIRc#SINE/MIR 9 TGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTT 58 chr6ptel1M 370976 CTTGTCTTGGGCCTGTCACGTATTGACAAAATAATTTAACTATAGGTCTA 371025 vv ii vi i v i ii ---- i- v i iv i i--- MIRc#SINE/MIR 59 CGAGTCCCGGCTCTGCCACTTACTAGC----TG-TGTGACCTTGGGC--- 100 chr6ptel1M 371026 TATGTAAAGTAAC-------AACTTCACTTTCATCATCTGTGATTTAGGA 371068 - v v vv ------- i i v v i vv i - MIRc#SINE/MIR 101 -AAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG- 148 chr6ptel1M 371069 TAGCAATATTACTTGTATTGACTTCCTCCCAGGATTATT 371107 -iii v i ivi v v v i i MIRc#SINE/MIR 149 -GATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTT 186 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 46.57 CpG sites = 31, Kimura (unadjusted) = 47.68 Transitions / transversions = 1.11 (31/28) Gap_init rate = 0.07 (13 / 180), avg. gap size = 1.46 (19 / 13) 21 5.20 7.50 0.00 chr6ptel1M 371314 371353 (628647) (TTATTAT)n#Simple_repeat 1 43 (0) m_b281s252i1 11247 chr6ptel1M 371314 TTATAATTTATTA-TTATAATTTA-T-TTTATTATTTATTATT 371353 v - v - - (TTATTAT)n#Si 1 TTATTATTTATTATTTATTATTTATTATTTATTATTTATTATT 43 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.08 (3 / 39), avg. gap size = 1.00 (3 / 3) 192 28.66 0.00 5.36 chr6ptel1M 371424 371482 (628518) L2a_3end#LINE/L2 460 515 (2) m_b281s601i2 11248 chr6ptel1M 371424 CTTAAACAATTCTTGGCACATGGCAGGTGCTTAATGTTCATTAACTATTG 371473 vi i v i i i i i i--- v vi i L2a_3end#LINE 460 CTAGAACAGTGCCTGGCACATAGTAGGCGCTCAATA---AATATTTGTTG 506 chr6ptel1M 371474 ACTGACTGA 371482 v v L2a_3end#LINE 507 AATGAATGA 515 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.32 CpG sites = 10, Kimura (unadjusted) = 37.24 Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.05 (3 / 58), avg. gap size = 1.00 (3 / 3) 230 15.38 2.56 0.00 chr6ptel1M 371494 371532 (628468) MIRc#SINE/MIR 168 207 (61) m_b281s601i3 11243 chr6ptel1M 371494 CCT-CCTCATAGGGTTGTTGTGAAAGTCAAGTTAGATAAT 371532 - i iii i v MIRc#SINE/MIR 168 CCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAAT 207 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 17.88 CpG sites = 5, Kimura (unadjusted) = 17.88 Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.03 (1 / 38), avg. gap size = 1.00 (1 / 1) 320 34.56 1.77 2.68 chr6ptel1M 371844 371956 (628044) MIRb#SINE/MIR 9 120 (148) m_b281s601i4 11249 chr6ptel1M 371844 CAGTCATGGTGTAGTTGGGATGGAGC--TAGCTTCAAAGTCAGGAAGACT 371891 - i i -- vi --vi iii iv i MIRb#SINE/MIR 9 CAG-CGTGGTGCAGT--GGAAAGAGCACGGGCTTTGGAGTCAGACAGACC 55 chr6ptel1M 371892 TGAATTCAAACCTTGTCTCTGATAAATACTGTCTATATGATTATAAGTAA 371941 ii i i ii v vi vv iv i i iiv ii i MIRb#SINE/MIR 56 TGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 105 chr6ptel1M 371942 GTTATTGAAATTTTC 371956 i v vi i MIRb#SINE/MIR 106 GTTACTTAACCTCTC 120 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.60 CpG sites = 27, Kimura (unadjusted) = 50.27 Transitions / transversions = 2.45 (27/11) Gap_init rate = 0.04 (4 / 112), avg. gap size = 1.25 (5 / 4) 918 29.04 3.41 4.16 chr6ptel1M 371962 372518 (627482) L1MC1_3end#LINE/L1 81 633 (447) m_b281s551i0 11250 chr6ptel1M 371962 CCTGAACAGACAATTCTCAGAAGAAGAAATTGAAACTATTTCTAGTCATA 372011 ? vi v vi v vv i iviivvv iv L1MC1_3end#LI 81 CCTNAACAGACACCTCACCAAAGAAGATATACAGATGGCAAATAAGCATA 130 chr6ptel1M 372012 TGAAAAGATGCTCCAAGTCATTAT-TAATCAGAGAAATGCAAATTAAGAC 372060 vi - - v i i L1MC1_3end#LI 131 TGAAAAGATGCTCCACATCA-TATGTCATCAGGGAAATGCAAATTAAAAC 179 chr6ptel1M 372061 AACTCTAAGATACCACTACACATCTGTCAGATTGGCTAAGATGACAGGAA 372110 vv i i i i v i i -- vi L1MC1_3end#LI 180 AACAATGAGATACCACTACACACCTATTAGAATGGCCAAAAT--CCAGAA 227 chr6ptel1M 372111 AA--AATAATGATGATTGTTGGAGGGGATGCGGGAAAACTGGGACATTGA 372158 v --i i iivii v i v i i iiv v i vi v L1MC1_3end#LI 228 CACTGACAACACCAAATGCTGGCGAGGATGTGGAGCAACAGGAACTCTCA 277 chr6ptel1M 372159 TGCATTGTTGGTGGAGTTGTGAATGAATCCAACCATTTTGGAGAGCAGTT 372208 v i iiv ii vvii v i i iii L1MC1_3end#LI 278 TTCATTGCTGGTGGGAATGCAAAATGGTACAGCCACTTTGGAAGACAGTT 327 chr6ptel1M 372209 TGGAACTATGCTCA-AAAAGTTATCAAACTGTGCATACCCTTTGATCCAG 372257 v v - v i - v v v v v --- v vi L1MC1_3end#LI 328 TGGCAGT-TTCTTACAAAACTAAACATACTCT---TACCATACGATCCAG 373 chr6ptel1M 372258 CAGTGTTACTAC-TGGGATTTATATCCCAAAGAGATTATAAA-----GAA 372301 i vvii v - v --- iii iv ----- vv L1MC1_3end#LI 374 CAATCGCGCTCCTTGGTATTTA---CCCAAAGGAGTTGAAAACTTATGTC 420 chr6ptel1M 372302 GGGAAAGGGACCTGTATGTGCACGAATGTTTGTGGCAGCCCTTTTTGTAG 372351 viv v iii i ---- i i i ii v ii i L1MC1_3end#LI 421 CACACAAAAACCTGCA----CACGGATGTTTATAGCAGCTTTATTCATAA 466 chr6ptel1M 372352 TGGCTAGAAACTGGAAACTGAAT--GGATGTCCATCAGTTGGAGAATGGC 372399 v i i vi i -- i--i v v v v L1MC1_3end#LI 467 TTGCCAAAACTTGGAAGC--AACCAAGATGTCCTTCAGTAGGTGAATGGA 514 chr6ptel1M 372400 TGAATAAATTGTGGTATATGAAAATTATGGAATATTACT--GTTCT-GTA 372446 i i i vv i iv i -- iv -iv L1MC1_3end#LI 515 TAAATAAACTGTGGTACATCCAGACAATGGAATATTATTCAGCGCTAAAA 564 chr6ptel1M 372447 AGAAATGA-CCAACAGG--ATGATTTCAGAAAGGCCTGGA-GAGACTTAC 372492 - i v i -- ------ i v - i v L1MC1_3end#LI 565 AGAAATGAGCTATCAAGCCATGA------AAAGACATGGAGGAAACTTAA 608 chr6ptel1M 372493 ACGAACTGATGCTGAGTGAAATGAGC 372518 i v - iv i i vi L1MC1_3end#LI 609 ATGCA-TATTACTAAGTGAAAGAAGC 633 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.67 CpG sites = 87, Kimura (unadjusted) = 37.62 Transitions / transversions = 1.28 (87/68) Gap_init rate = 0.06 (34 / 556), avg. gap size = 1.24 (42 / 34) 1275 27.77 1.69 2.56 chr6ptel1M 371964 372436 (627564) L1ME3Cz_3end#LINE/L1 79 547 (450) m_b281s551i1 11250 chr6ptel1M 371964 TGAACAGACAATTCTCAGAAGAAGAAATTGAAACTATTTCTAGTCATATG 372013 i v i iivi iviiivv iv L1ME3Cz_3end# 79 TGAACAGGCAATTCACAGAAGAGGAAACCCGAATGGCCAATAAACATATG 128 chr6ptel1M 372014 AAAAGATGCTCCAAGTCATTATTAATCAGAGAAATGCAAATTAAGACAAC 372063 v vv i v i i ? L1ME3Cz_3end# 129 AAAAGATGCTCAACCTCACTAGTAATCAGGGAAATGCAAATTAAAACNAC 178 chr6ptel1M 372064 TCTAAGATACCACTACACATCTGTCAGATTGGCTAAGATGACAGGAAAAA 372113 vv i i v i ii v i v----v i L1ME3Cz_3end# 179 AATGAGATACCATTTCACACCCATCAGATTGGCAAAAATT----TAAAAG 224 chr6ptel1M 372114 ----ATAATGATGATTGTTGGAGGGGATGCGGGAAAACTGGGACATTGAT 372159 ---- i ivii v v i i ii v i vi v L1ME3Cz_3end# 225 TCTGACAATACCAAGTGTTGGCGAGGATGTGGAGAAACGGGAACTCTCAT 274 chr6ptel1M 372160 GCATTGTTGGTGGAGTTGTGAATGAATCCAACCATTTTGGAGAGCAGTTT 372209 i i i iiv i vii v i i L1ME3Cz_3end# 275 ACACTGCTGGTGGGAGTGTAAATTGGTACAACCACTTTGGAGAGCAATTT 324 chr6ptel1M 372210 GGAACTATGCTCAAAAAGTTATCAAACTGTGCATACCCTTTGATCCAGCA 372259 v v - viv i-- iv i vi i L1ME3Cz_3end# 325 GGCAATAT-CTAGTAAAGTTG--AAGATGCGCATACCCTACGACCCAGCA 371 chr6ptel1M 372260 GTGTTACTACTGGGATTTATATCCCAAAGAGATTAT-AAAGAAGGG---A 372305 i vii v i - v i i i i i v -iv v v v --- L1ME3Cz_3end# 372 ATTCCACTTCTAGG-TATATACCCTAGAGAAACTCTCGCACATGTGCACA 420 chr6ptel1M 372306 AAGGGACCTGTATGTGCACGAATGTTTGTGGCAGCCCTTTTTGTAGTGGC 372355 i i ---- i v i ii v vi v i i L1ME3Cz_3end# 421 AGGAGAC----ATGTACAAGGATGTTCATTGCAGCATTGTTTGTAATAGC 466 chr6ptel1M 372356 TAGAAACTGGAAACTGAATGGATGTCCATCAGTTGGAGAATGGCTGAATA 372405 v i i vivv ii i v i v i L1ME3Cz_3end# 467 GAAAAATTGGAAACAACCTAAATGTCCATCAATAGGGGAATGGATAAATA 516 chr6ptel1M 372406 AATTGTGGTATATGAAAATTATGGAATATTA 372436 vv v iv i L1ME3Cz_3end# 517 AATTGTGGTATATTCATACAATGGAATACTA 547 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.27 CpG sites = 75, Kimura (unadjusted) = 35.66 Transitions / transversions = 1.42 (75/53) Gap_init rate = 0.03 (15 / 472), avg. gap size = 1.33 (20 / 15) 17 15.26 0.00 0.00 chr6ptel1M 372984 373012 (626988) (A)n#Simple_repeat 1 29 (0) m_b281s252i2 11251 chr6ptel1M 372984 AAATAAAAAAAAATTAAAAAAAAAAGAAA 373012 v vv i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA 29 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 33 5.72 0.00 0.00 chr6ptel1M 373049 373085 (626915) (TG)n#Simple_repeat 1 37 (0) c_b281s251i0 11252 chr6ptel1M 373049 TGTGTGTATGTGTGTGTGTGTATGTGTGTGTGTGTGT 373085 i i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 37 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 15 5.56 0.00 0.00 chr6ptel1M 373170 373188 (626812) (AC)n#Simple_repeat 1 19 (0) m_b281s252i3 11253 chr6ptel1M 373170 ACACACATACACACACACA 373188 i (AC)n#Simple_ 1 ACACACACACACACACACA 19 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 15 21.30 2.22 2.22 chr6ptel1M 374069 374113 (625887) (TGT)n#Simple_repeat 1 45 (0) m_b281s252i4 11254 chr6ptel1M 374069 TGATGTT-TTGAATGATGTTTTTGTTGTTATTGTTATTATTGTGGT 374113 v - -v v v i i i v (TGT)n#Simple 1 TGTTGTTGTTG-TTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGT 45 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.05 (2 / 44), avg. gap size = 1.00 (2 / 2) 11 16.86 2.86 2.86 chr6ptel1M 374086 374120 (625880) (TTGTTA)n#Simple_repeat 1 35 (0) m_b281s252i5 11254 chr6ptel1M 374086 TTTTTGTTGTTATTGTTATTATT-GTGGTATATGTT 374120 v i i -v v - (TTGTTA)n#Sim 1 TTGTTATTGTTATTGTTATTGTTATTGTTAT-TGTT 35 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 16 20.34 2.86 0.00 chr6ptel1M 374286 374320 (625680) (AT)n#Simple_repeat 1 36 (0) m_b281s252i6 11255 chr6ptel1M 374286 ATATATAAATGTACACACACATAT-TATATATATAT 374320 v i i i i i - (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATAT 36 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 73 0.00 2.13 5.49 chr6ptel1M 374413 374506 (625494) (TTTC)n#Simple_repeat 1 91 (0) c_b281s251i1 11256 chr6ptel1M 374413 TTTCTTTTCTTTTCTTTTCCTTTCCTTTC-TT-TTTCTTTCTTTCTTTCT 374460 - - - - - - - (TTTC)n#Simpl 1 TTTC-TTTC-TTTC-TTT-CTTT-CTTTCTTTCTTTCTTTCTTTCTTTCT 45 chr6ptel1M 374461 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT 374506 (TTTC)n#Simpl 46 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT 91 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.08 (7 / 93), avg. gap size = 1.00 (7 / 7) 509 25.46 10.46 2.42 chr6ptel1M 374777 374929 (625071) C MIRb#SINE/MIR (102) 166 2 m_b281s601i5 11257 chr6ptel1M 374777 GCAGTTCTTGTGATCTCCA------AGCTGAGAAAATAACTGAGGATCAG 374820 i v v i v i ------ v i --- v C MIRb#SINE/MIR 166 GTAGGTATTATTATCCCCATTTTACAGATGAGGAAA---CTGAGGCTCAG 120 chr6ptel1M 374821 AGAAATGAAGAGATATGTTCAAAGTCAGATAGCTAGTAAAAAGTCAGAG- 374869 ii v vi iv ii i v i ivi - - C MIRb#SINE/MIR 119 AGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGG-CAGAGC 71 chr6ptel1M 374870 TGGGATTTGAGC---------TTTGACTCCAAGATGTGTGGTCTTTCCAC 374910 i i i --------- i iiivi v C MIRb#SINE/MIR 70 CGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCAC 21 chr6ptel1M 374911 TTTACCACACTGCCACTCT 374929 vi i v C MIRb#SINE/MIR 20 TGCACCACGCTGCCCCTCT 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.13 CpG sites = 24, Kimura (unadjusted) = 32.11 Transitions / transversions = 1.71 (24/14) Gap_init rate = 0.05 (7 / 152), avg. gap size = 2.86 (20 / 7) 24 23.61 2.99 1.47 chr6ptel1M 375077 375143 (624857) (TA)n#Simple_repeat 1 68 (0) m_b281s252i7 11258 chr6ptel1M 375077 TATATATACATATAGCTATAAACTATATTCAT-TATATATGGA-ATATAT 375124 i vv v - vi - iv - (TA)n#Simple_ 1 TATATATATATATATATATATA-TATATATATATATATATATATATATAT 49 chr6ptel1M 375125 ATACACACACATATATGTA 375143 i i i i i (TA)n#Simple_ 50 ATATATATATATATATATA 68 Matrix = Unknown Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.05 (3 / 66), avg. gap size = 1.00 (3 / 3) 384 30.68 7.79 6.87 chr6ptel1M 375163 375393 (624607) C MIR#SINE/MIR (0) 262 30 m_b281s601i6 11259 chr6ptel1M 375163 AGTAATAACTAACATTTATATAGTAATGTATATATTTATATGGTATTGGG 375212 i i vv iiv - i- v iivv i i -- C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCT-TAC-TATGTGCCAGGCACTG-- 217 chr6ptel1M 375213 GAGAGGTTTGCAAAGCACTTCACAGATATGACTTCATTTTATCCTGGGA- 375261 -------- v v i i vi v vi v viv - C MIR#SINE/MIR 216 --------TTCTAAGCGCTTTACATGTATTAACTCATTTAATCCTCACAA 175 chr6ptel1M 375262 ------TATA--GTAAGTA--ATTATTATAGAC-TTTTAAAGATGAAGAA 375300 ------ i-- i -- vvv - v i C MIR#SINE/MIR 174 CAACCCTATGAGGTAGGTACTATTATTATCCCCATTTTACAGATGAGGAA 125 chr6ptel1M 375301 ATTGAGGAAGGCAGCATTTAAGTGCCTTACCTAGAATCAATCACACAGCT 375350 i v viv viv iv i i i----ii C MIR#SINE/MIR 124 ACTGAGGCACAGAGAGGTTAAGTAACTTGCCCAA----GGTCACACAGCT 79 chr6ptel1M 375351 AATAA-TAGTCTGGCCTGGGTTCAGGTCT-----TTCTGATTCCAGAGC 375393 i - i ivvi v i iiii i-----v ii C MIR#SINE/MIR 78 AGTAAGTGGCAGAGCCGGGATTCGAACCCAGGCAGTCTGGCTCCAGAGC 30 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.14 CpG sites = 38, Kimura (unadjusted) = 40.60 Transitions / transversions = 1.36 (38/28) Gap_init rate = 0.10 (22 / 230), avg. gap size = 1.55 (34 / 22) 413 30.15 12.68 3.45 chr6ptel1M 375193 375405 (624595) C MIRc#SINE/MIR (16) 252 21 m_b281s601i7 11259 chr6ptel1M 375193 TATATTTATATGGTATTGGGGAGAGGTTTGCAAAGCACTT-CACAGATAT 375241 i i i i i vviv --- i i - v i C MIRc#SINE/MIR 252 TACATTTGTATAGCACTTTACAG---TTTACAAAGCGCTTTCACATACAT 206 chr6ptel1M 375242 GACTTCATTTTATCCT----------------GG--GATATAGTAAGTAA 375273 v ii v ---------------- -- ii vi i i - C MIRc#SINE/MIR 205 TATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTA- 157 chr6ptel1M 375274 TTATTATAGAC-TTTTAAAGATGAAGAAATTGAGGAAGGCAGCATTTAAG 375322 vvv - v i i vvviv viv C MIRc#SINE/MIR 156 TTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAG 107 chr6ptel1M 375323 TGCCTTACCTAGAATCAATCACACAGCTAATA------ATAGTCTGGCCT 375366 v i i i----ii i ------ v i v v C MIRc#SINE/MIR 106 TGACTTGCCCAA----GGTCACACAGCTAGTAAGTGGCAGAGCCGGGACT 61 chr6ptel1M 375367 -GGGTTCAGGTCTTTCTGATTCCAGAGCTATGACTATTTC 375405 - iiii i i iiv i vvi v C MIRc#SINE/MIR 60 CGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTC 21 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.13 CpG sites = 37, Kimura (unadjusted) = 39.97 Transitions / transversions = 1.48 (37/25) Gap_init rate = 0.07 (14 / 212), avg. gap size = 2.50 (35 / 14) 43 0.00 0.00 0.00 chr6ptel1M 375463 375499 (624501) (AC)n#Simple_repeat 1 37 (0) c_b281s251i2 11260 chr6ptel1M 375463 ACACACACACACACACACACACACACACACACACACA 375499 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACA 37 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 12 3.99 7.14 3.45 chr6ptel1M 376022 376049 (623951) (AGGA)n#Simple_repeat 1 29 (0) m_b281s252i8 11261 chr6ptel1M 376022 AGGAAGAGAGGGAAGGAA--AAGGAAGGAA 376049 - i -- (AGGA)n#Simpl 1 AGGAAG-GAAGGAAGGAAGGAAGGAAGGAA 29 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.07 (2 / 27), avg. gap size = 1.50 (3 / 2) 15 5.48 0.00 0.00 chr6ptel1M 376712 376730 (623270) (T)n#Simple_repeat 1 19 (0) m_b281s252i9 11262 chr6ptel1M 376712 TTGTTTTTTTTTTTTTTTT 376730 v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 13 10.69 3.12 3.12 chr6ptel1M 377158 377189 (622811) (TCCTT)n#Simple_repeat 1 32 (0) m_b281s252i10 11263 chr6ptel1M 377158 TCCATCCCTTTCCTTTCCTTGTCATTT-CTTTC 377189 v i - v - (TCCTT)n#Simp 1 TCCTTTCCTTTCCTTTCCTT-TCCTTTCCTTTC 32 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.06 (2 / 31), avg. gap size = 1.00 (2 / 2) 49 0.00 0.00 0.00 chr6ptel1M 377513 377554 (622446) (GT)n#Simple_repeat 1 42 (0) c_b281s251i3 11264 chr6ptel1M 377513 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 377554 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 42 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 275 31.50 11.02 0.00 chr6ptel1M 378102 378228 (621772) MIRb#SINE/MIR 12 152 (116) m_b281s601i8 11265 chr6ptel1M 378102 CATGATGTAGTAGTAAAAG----GCCTGTGGAATTAGG-AGATAAGTATT 378146 i i i i v i ---- v v i i i- ivv vi MIRb#SINE/MIR 12 CGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTT 61 chr6ptel1M 378147 CTAATCCTCACTCTGCTTCTAATTA-C----TGACCTTGGATGACTT--T 378189 v ivi iv v i - ---- iii v -- MIRb#SINE/MIR 62 CGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACT 111 chr6ptel1M 378190 TTCCCTCTTTAGACCT--GTTTTCTGCTCTTTAGAATGAGG 378228 vv i iii -- i vv v i i MIRb#SINE/MIR 112 TAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGG 152 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.53 CpG sites = 24, Kimura (unadjusted) = 42.31 Transitions / transversions = 1.50 (24/16) Gap_init rate = 0.05 (6 / 126), avg. gap size = 2.33 (14 / 6) 262 32.64 11.11 0.00 chr6ptel1M 378104 378247 (621753) MIRc#SINE/MIR 11 170 (98) m_b281s601i9 11265 chr6ptel1M 378104 TGATGTAGTAGTAAAAGGCCTG----TGGAATTAGGA-GATAAGTATTCT 378148 i i i v i vv ---- i i - ivv vi v MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr6ptel1M 378149 AATCCTCACTCTGCTTCTAATTA-C----TGACCTTGGATGACT--TTTT 378191 i ivi iv v i - ---- iii v --i v MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTA 110 chr6ptel1M 378192 CCCTCTTTAGACCT--GTTTTCTGCTCTTTAGAATGAGGG-AATGGGA-C 378237 v i iii -- i vv v i i i- iiv - MIRc#SINE/MIR 111 ACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACC 160 chr6ptel1M 378238 TGCCTGGTCT 378247 iv i MIRc#SINE/MIR 161 TGCCCTGCCT 170 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.40 CpG sites = 29, Kimura (unadjusted) = 44.71 Transitions / transversions = 1.61 (29/18) Gap_init rate = 0.06 (8 / 143), avg. gap size = 2.00 (16 / 8) 479 27.70 6.04 0.64 chr6ptel1M 378120 378268 (621732) MIR3#SINE/MIR 30 186 (22) m_b281s601i10 11265 chr6ptel1M 378120 GGCCTGTGGAATTAGGAGATAAGTATTCTAATCCTCACTCTGCTTCTAAT 378169 v - i i ivv vi i ivi iv i MIR3#SINE/MIR 30 GGACTG-GGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAAC 78 chr6ptel1M 378170 TA-CTG----ACCTTGGATGACTT-TTTC-CCTCTTTAGACCT--GTTTT 378210 ?- ---- iii v i-i - i i i -- i MIR3#SINE/MIR 79 TNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTC 128 chr6ptel1M 378211 CTGCTCTTTAGAATGAGGGAATGGGACTGCCTGGTCTCCAAGATGCTTTC 378260 vv v i ii v ivv i i i v i MIR3#SINE/MIR 129 CTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTC 178 chr6ptel1M 378261 CAGTTCTG 378268 i MIR3#SINE/MIR 179 CAGCTCTG 186 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.21 CpG sites = 27, Kimura (unadjusted) = 36.33 Transitions / transversions = 1.93 (27/14) Gap_init rate = 0.04 (6 / 148), avg. gap size = 1.67 (10 / 6) 768 37.06 5.57 1.20 chr6ptel1M 378491 379047 (620953) L2#LINE/L2 2502 3082 (0) m_b281s601i11 11266 chr6ptel1M 378491 TTTCCTGCTTTGGTCAAGGGCATCAACGTACTTCCAG--GTTATGGGCTT 378538 i iiii ii ? v v vv i v -- i -ii iv L2#LINE/L2 2502 TTCCCCATCTCAGTNAATGGCAACTCCATCCTTCCAGTTGCT-CAGGCCA 2550 chr6ptel1M 378539 GAAACTTTAGA---ATCCTCAAGCCCTCCCTCTCTCTTATCCCACAGATC 378585 i i i --- ii vi i i i iv v v L2#LINE/L2 2551 AAAACCTTGGAGTCATCCTTGACTCCTCTCTTTCTCTCACACCCCACATC 2600 chr6ptel1M 378586 CAGACAGTTGCCAAATCTTGCTTTTTTCTCCCTCCACAACATTCCTTGCA 378635 iv vi iiv i - ivvi v i v i vi iv v L2#LINE/L2 2601 CAATCCATCAGCAAATCCTG-TCGGCTCTACCTTCAAAATATATCCAGAA 2649 chr6ptel1M 378636 TT-GTCCATTTCTCTCTGCTCCCAGGATCACCACCTTAATTCAGACACAT 378684 i- v i v ii ii vvii i ii i ii - - L2#LINE/L2 2650 TCCGACCACTTCTCACCACCTCCACTGCCACCACCCTGGTCCAAGC-CA- 2697 chr6ptel1M 378685 AACCTTTTTTTCCCCCCTGAAATAGTGCAATAGCCTG-TAATTGGTT--C 378731 -- v iv i i v i v v v- i i-- L2#LINE/L2 2698 --CCATCATCTCTCGCCTGGATTACTGCAATAGCCTCCTAACTGGTCTCC 2745 chr6ptel1M 378732 CTGACTCAAGTCTT--CTCACTCCATCATTTTCCTAA---AGTAGC-AAA 378775 vi v vi -- i v ? viv v ii --- i - i L2#LINE/L2 2746 CTGCTTCCACCCTTGCCCCCCTNCAGTCTATTCTCAACACAGCAGCCAGA 2795 chr6ptel1M 378776 GTGATTTTCCTAACATGCAAATATGATCACGCCACTCCTCTACTTAATAA 378825 ii ii v i i i vv i i i i v v L2#LINE/L2 2796 GTGATCCTTTTAAAACGTAAGTCAGATCATGTCACTCCTCTGCTCAAAAC 2845 chr6ptel1M 378826 ATTTCAGCACCTCTCAATTCCCTTTAGAATAAAATATAAAATCCTCACTT 378875 vi i iiiv ii v ii vi i i vvi i i vv L2#LINE/L2 2846 CCTCCAATGGCTTCCCATCTCACTCAGAGTAAAAGCCAAAGTCCTTACAA 2895 chr6ptel1M 378876 TGGCTTTTAAAGTTCT--TTAGTCT-GCCCCCAACCATGTTTCTAGCCTG 378922 i vi i ii --v ii - i viii iv i ii v L2#LINE/L2 2896 TGGCCTACAAGGCCCTACATGATCTGGTCCCCCGTTACCTCTCTGACCTC 2945 chr6ptel1M 378923 GTTGTATATTACTCCTTTCTTAGTGCTCTCTAGTCTGGCTAAACTCAC-- 378970 i iviv ii iiii i v iv v iiv ii i v vi -- L2#LINE/L2 2946 ATCTCCTACCACTCTCCCCCTCGCTCACTCCGCTCCAGCCACACTGGCCT 2995 chr6ptel1M 378971 CCTTCCTGT--CTTG-ACACTC---AC-TGTTCACCCTTT---GTCTTTG 379010 v -- i - v ---i -i i v v i i--- i L2#LINE/L2 2996 CCTTGCTGTTCCTCGAACACGCCAGGCACGCTCCCGCCTCAGGGCCTTTG 3045 chr6ptel1M 379011 C-CTTGTCTGTGCCCTTTTCCCAGAATTCACCTCTCTC 379047 - - v i v ii iv v i i i L2#LINE/L2 3046 CACTTG-CTGTTCCCTCTGCCTGGAACGCTCTTCCCCC 3082 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 52.27 CpG sites = 133, Kimura (unadjusted) = 55.22 Transitions / transversions = 1.87 (133/71) Gap_init rate = 0.04 (24 / 556), avg. gap size = 1.58 (38 / 24) 325 32.50 6.70 10.27 chr6ptel1M 378896 379358 (620642) L2b_3end#LINE/L2 9 456 (10) m_b281s601i12 11266 chr6ptel1M 378896 TCTGCCCCCAACCATGTTTCTAGCCTGGTTGTATATTACTCCTTTCTTAG 378945 v i- i iv i ii vi iviv ii iiii - L2b_3end#LINE 9 TCTGGCCCCG-CTACCTCTCCGGCCTCATCTCCTACCACTCTCCCCTT-G 56 chr6ptel1M 378946 TGCTCTCTAGTCTGGCTAAACTCACC--CTTCCTGT--CTTGA-CACTCA 378990 iv v iv ii i v vi -- v -- i - v v L2b_3end#LINE 57 CTCACTCTGCTCCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACACGCC 106 chr6ptel1M 378991 CTGTTCAC-----CCTT--TGTCTTTGC-CTTGTCTGTGCCCTTTTCCCA 379032 v? i ? ----- i--v i - ? - v i v ii L2b_3end#LINE 107 ANGCTCNCTCCCGCCTCAGGGCCTTTGCACNTG-CTGTTCCCTCTGCCTG 155 chr6ptel1M 379033 GAATTCACCTCTCTCTCACCTCCTCCTCTTAGG---ATTTCTCCTTCTC- 379078 -- i ii i - i vi -- --- i i v iv - L2b_3end#LINE 156 GAA--CGCCCTTCCC-CACCTCTTCGCCT--GGCCAACTCCTACTCATCC 200 chr6ptel1M 379079 TTCAGTACTTAGCTCACATGCCACTCTCAACATGGAGCCTTTCCTGATCT 379128 vv i v i iii vv iv i i i - i L2b_3end#LINE 201 TTCAGGTCTCAGCTCAAATGTCACCTCCTCCGGGAAGCCCTCCCTGA-CC 249 chr6ptel1M 379129 CTTTAGGTAGTAGCATGGTCCCCCCACCT---CCACCCCAA-ATTACCTT 379174 iii iv viv - iv i vi --- v i-vi i L2b_3end#LINE 250 CCCCAGGCCGGGTCA-GGCGCCCTCCTCTGGGCCCCCCCAGTCCTACCCT 298 chr6ptel1M 379175 G--AATTTGTTTTGCAGATACTTGTAGATGGAGATGT-TGTGCTGTCCC- 379220 -- v i vv ---- ?v vvi?vv v - - vi - L2b_3end#LINE 299 GCCACTCTGGGTT----ATNATTGTCTGNTTACATGTCTGT-CTCCCCCA 343 chr6ptel1M 379221 --AG---GTATGCTCTTTGAGGGCGCGGACAGTTTCATTTGTTTTTTTTG 379265 -- --- iv iv iv v ----------------? L2b_3end#LINE 344 CTAGACTGTGAGCTCCGTGAGGGCAGGGACCG----------------NG 377 chr6ptel1M 379266 TTTGTTTGTTTGTTTTTTGTTTTTGTTTTTGAATATTTAGTGCTT-GCAT 379314 i ---i ivii ---i ------ viii i i - i L2b_3end#LINE 378 TCTGT---CTTGTTCACCG---CTGT------ATCCCCAGCGCCTAGCAC 415 chr6ptel1M 379315 AGTGCCTGGTACTTAATAGGTGTTTCATAAATACTTTTGGTTGA 379358 ? i vi i i i ivi i --- L2b_3end#LINE 416 AGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTT---GTTGA 456 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.79 CpG sites = 84, Kimura (unadjusted) = 45.35 Transitions / transversions = 1.65 (84/51) Gap_init rate = 0.13 (62 / 462), avg. gap size = 1.24 (77 / 62) 447 25.44 9.81 6.33 chr6ptel1M 379482 379695 (620305) C L2d2_3end#LINE/L2 (53) 502 282 m_b281s601i13 11267 chr6ptel1M 379482 GCTAAGTGCTCTGGGGCTTGCAAAAGGATCTAAG------------CTCT 379519 i i v vv i iiii v ------------ i C L2d2_3end#LIN 502 GCTAGGCGCTGTGGGGGATACAAAGAAGTATAAGACATGGTCCCTGCCCT 453 chr6ptel1M 379520 CAAGGAGTTTATAATGCAGATGAATGATTAAAAAAAAGATATAAACCCAT 379569 i i vi v ii------i i v i v i C L2d2_3end#LIN 452 CAAGGAGCTTACAATCTAGTTGGG------GAGACAAGACATAAACACGT 409 chr6ptel1M 379570 GAAAATATAAATAACAACACAAA----GAAT--CAGTTCTGGAGACAGCA 379613 vv i i----i -- --i i C L2d2_3end#LIN 408 GAAAAGTTAAATAACAATACAAGATTTAAATAACAGTTC--AAGACAACA 361 chr6ptel1M 379614 GCAGATGAGCCAACCACCAGGCAGAGGCACGTGACTAATTGCCCAG-GAG 379662 ii v vi-ii v --- i i i v i- i C L2d2_3end#LIN 360 ATAGAAGAGAT-GTCACAAGGCA---GTACATGATTAATTGCCAAATGAA 315 chr6ptel1M 379663 GGATCCAGAC--TAATTGCTATAGATCAGGTCAGA 379695 v i v -- ? i-- v C L2d2_3end#LIN 314 TGGTACAGACAATAANTGCTATAGG--AGTTCAGA 282 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.98 CpG sites = 34, Kimura (unadjusted) = 32.54 Transitions / transversions = 2.00 (34/17) Gap_init rate = 0.09 (19 / 213), avg. gap size = 1.84 (35 / 19) 242 37.60 0.74 1.49 chr6ptel1M 380119 380253 (619747) C L2d2_3end#LINE/L2 (268) 287 154 m_b281s601i14 11267 chr6ptel1M 380119 TTCAAAAGAGAGAGAGAATGAGCTAATCACTGAGGATCTCAAGAATGGCT 380168 i i i - v - ?vvvi ii vvv i i v C L2d2_3end#LIN 287 TTCAGAGGAGGGAGAGA-TCA-CTNCGGGCTGGAGTGGTCAGGGAAGGCT 240 chr6ptel1M 380169 TCATGTAGAAGATAGCTCCAGAACTGTACTTTGAAAGGAGTGAGGGATTC 380218 i v i i i ?viiv i vi i i iv v vi i C L2d2_3end#LIN 239 TCACGGAGGAGGTGGNATTTGAGCTGGGCCTTGAAGGATGGGTAGGATTT 190 chr6ptel1M 380219 TCCCAGGC-GAGATGAAGAGATTGCATATTTCAGGC 380253 vvvi i- v i ivv vii i C L2d2_3end#LIN 189 GGATAGGTGGAGAGGAAGGGGAAGGGCATTCCAGGC 154 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 53.81 CpG sites = 28, Kimura (unadjusted) = 55.48 Transitions / transversions = 1.27 (28/22) Gap_init rate = 0.02 (3 / 134), avg. gap size = 1.00 (3 / 3) 241 32.42 20.62 1.62 chr6ptel1M 380637 381053 (618947) C L2#LINE/L2 (28) 3054 2560 m_b281s601i15 11267 chr6ptel1M 380637 CAGCAAGGGCCAAGGCACTGAGATAGAGA------TGGAGTAT--GAGAA 380678 v v v iii iii------ v i -- i C L2#LINE/L2 3054 CAGCAAGTGCAAAGGCCCTGAGGCGGGAGCGTGCCTGGCGTGTTCGAGGA 3005 chr6ptel1M 380679 AGAGC-------------TCGCTGG--TGGGATGGTTTAGG-----AATA 380708 v ------------- v --i ii iviv ----- i i C L2#LINE/L2 3004 ACAGCAAGGAGGCCAGTGTGGCTGGAGCGGAGTGAGCGAGGGGGAGAGTG 2955 chr6ptel1M 380709 GTCACTAGATAATATAGAATATAGAATAGAAAGCTGGATTATGAAGGGTC 380758 - vv i vi vii v viv ii iiii ii i v i C L2#LINE/L2 2954 GT-AGGAGATGAGGTCAGAGAGGTAACGGGGGACCAGATCATGTAGGGCC 2906 chr6ptel1M 380759 TTAAATGTCAA-ATGAGAATTTTAATTTTCCTTTT-------ATAGACAG 380800 iv v i v-i i i i iii ivi i ------- i iv C L2#LINE/L2 2905 TTGTAGGCCATTGTAAGGACTTTGGCTTTTACTCTGAGTGAGATGGGAAG 2856 chr6ptel1M 380801 CCATTGAAGATGGTT----ATAGGGGAGTTTCACAAGTCAGATCTATGGT 380846 i -- ----ii i vv ii - v ii i v C L2#LINE/L2 2855 CCATTGGAG--GGTTTTGAGCAGAGGAGTGACATGA-TCTGACTTACGTT 2809 chr6ptel1M 380847 TTAGAAGTAACAATTTTGTCTG--GTG--GAGGATGGATT-CAGGAAGGC 380891 i v v -i i v -- -- i i i -? ii C L2#LINE/L2 2808 TTAAAAGGATCA-CTCTGGCTGCTGTGTTGAGAATAGACTGNAGGGGGGC 2760 chr6ptel1M 380892 ACATAATGGATGCAAGAAGA---GTCTGGA------TGCGGTAATTAGGG 380932 - vii v i i --- iv ------ i ivi C L2#LINE/L2 2759 A-AGGGTGGAAGCAGGGAGACCAGTTAGGAGGCTATTGCAGTAATCCAGG 2711 chr6ptel1M 380933 CTGG-GATGTATG---------AGTAGGGAGAAGGGACT--AGGTG-TGA 380969 vi - - --------- vi v iv v v -- - C L2#LINE/L2 2710 CGAGAGATG-ATGGTGGCTTGGACCAGGGTGGTGGCAGTGGAGGTGGTGA 2662 chr6ptel1M 380970 GA--------GATGTTAG---------GAAGGTAGAAGTAGCATGATTTA 381002 -------- vi i --------- iviii v - C L2#LINE/L2 2661 GAAGTGGTCGGATTCTGGATATATTTTGAAGGTAGAGCCGACAGGATTT- 2613 chr6ptel1M 381003 GCTACTG-ACCAGAAATGGGG-GTGAAAGAGAAGAAAGAGTCAAGAATGA 381050 iv - iii vi - i i iii i i C L2#LINE/L2 2612 GCTGATGGATTGGATGTGGGGTGTGAGAGAAAGAGAGGAGTCAAGGATGA 2563 chr6ptel1M 381051 CTC 381053 C L2#LINE/L2 2562 CTC 2560 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.47 CpG sites = 90, Kimura (unadjusted) = 45.46 Transitions / transversions = 2.09 (90/43) Gap_init rate = 0.07 (29 / 416), avg. gap size = 3.24 (94 / 29) 12 7.67 6.67 3.23 chr6ptel1M 381347 381376 (618624) (TTTG)n#Simple_repeat 1 31 (0) m_b281s252i11 11268 chr6ptel1M 381347 TTTG-TTGTTTGCTTGCTT-TTTGTTTTGTTT 381376 - i i - - (TTTG)n#Simpl 1 TTTGTTTGTTTGTTTGTTTGTTTG-TTTGTTT 31 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.10 (3 / 29), avg. gap size = 1.00 (3 / 3) 445 28.09 13.44 0.48 chr6ptel1M 381895 382080 (617920) C MIRc#SINE/MIR (2) 266 57 m_b281s601i16 11269 chr6ptel1M 381895 TAATAATAACAGCCAGAATTTCTGTAGTGTTTTGAGTTTTGCAAAATACC 381944 ?v iviv v i iii iviv i iii i C MIRc#SINE/MIR 266 TAATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCGCT 217 chr6ptel1M 381945 TTGCAAATA---TATCTCATATGATCCTCACAGTGGCCTAGGGAG--AGG 381989 - v --- v iiii iv v -- C MIRc#SINE/MIR 216 TT-CACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGG 168 chr6ptel1M 381990 -GGGATA---ATTATTATCCACACTTTACAGATGAAAAAA-TCATGC--- 382031 -i ii --- v i ii - v v --- C MIRc#SINE/MIR 167 CAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCA 118 chr6ptel1M 382032 ----ATTTAA--------CCCAAGGTCACAGAGCTAATAAGAATCTGGGT 382069 ----iv -------- v i viv v i i C MIRc#SINE/MIR 117 GAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGC 68 chr6ptel1M 382070 TTAGATTTGAA 382080 ivi i i C MIRc#SINE/MIR 67 CGGGACTCGAA 57 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.02 CpG sites = 33, Kimura (unadjusted) = 36.77 Transitions / transversions = 1.74 (33/19) Gap_init rate = 0.04 (8 / 185), avg. gap size = 3.25 (26 / 8) 418 31.37 3.87 1.26 chr6ptel1M 383003 383157 (616843) MIRb#SINE/MIR 17 175 (93) m_b281s601i17 11270 chr6ptel1M 383003 TGTAATATGAAGAGTGCTCACTCTGGAGTCAGA-AGATCCAGGGCTTGT- 383050 i i ivi ii vvi i - - v i i v- MIRb#SINE/MIR 17 TGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGA-CCTGGGTTCGAA 65 chr6ptel1M 383051 TCCTACCACTGGCATTTACTGCTTTTGTGACTTTGGCTAGATCATTTTAC 383100 iiv v v i ivi v i vi ii i i v MIRb#SINE/MIR 66 TCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAAC 115 chr6ptel1M 383101 TTTTCTAACCCTCAATTTCCTCAGCCAT-AAATGAAGA-GGT--TATCTA 383146 i i i v i v ii - ii -ii -- i MIRb#SINE/MIR 116 CTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTA 165 chr6ptel1M 383147 CAGTCTCAGGG 383157 -v v MIRb#SINE/MIR 166 C-CTCGCAGGG 175 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.33 CpG sites = 32, Kimura (unadjusted) = 42.87 Transitions / transversions = 2.00 (32/16) Gap_init rate = 0.05 (7 / 154), avg. gap size = 1.14 (8 / 7) 433 32.82 0.78 0.78 chr6ptel1M 383013 383141 (616859) MIR3#SINE/MIR 23 151 (57) m_b281s601i18 11270 chr6ptel1M 383013 AGAGTGCTCACTCTGGAGTCAGAAGATCCAGGGCTTGTTCCTACCACTGG 383062 ii vv v- i i ii vii iv iiv v v MIR3#SINE/MIR 23 AGAGCACGGACTG-GGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGC 71 chr6ptel1M 383063 CATTTACTGCTTTTGTGACTTTGGCTAGATCATTTTACTTTTCTAACCCT 383112 i v ?vi v i vi ii i i i i iiv MIR3#SINE/MIR 72 CACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCT 121 chr6ptel1M 383113 CAATTTCCTCAGCCAT-AAATGAAGAGGTT 383141 i v ii - i i MIR3#SINE/MIR 122 CAGTTTCCTCATCTGTAAAATGAGGGGGTT 151 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.56 CpG sites = 28, Kimura (unadjusted) = 46.28 Transitions / transversions = 2.00 (28/14) Gap_init rate = 0.02 (2 / 128), avg. gap size = 1.00 (2 / 2) 23 15.81 0.00 2.33 chr6ptel1M 383284 383327 (616673) (AC)n#Simple_repeat 1 43 (0) m_b281s252i12 11271 chr6ptel1M 383284 ACACACCCACACACCTACACCCACACCCTACACACACATACACA 383327 v vi v v - i (AC)n#Simple_ 1 ACACACACACACACACACACACACACAC-ACACACACACACACA 43 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.02 (1 / 43), avg. gap size = 1.00 (1 / 1) 359 27.96 12.24 3.29 chr6ptel1M 383542 383737 (616263) MIRc#SINE/MIR 14 226 (42) m_b281s601i19 11272 chr6ptel1M 383542 TGCAGTGGAAAGTGACCTGGATGGGGAGTCAG------CTG----C---T 383578 v vv ivv ------ ---- --- MIRc#SINE/MIR 14 TGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGT 63 chr6ptel1M 383579 CCCACCTC--CCAATCTTA-TACCTTCGGTGACCTCTG-------ACTTT 383618 iv -- -- - v vi - iv ------- v MIRc#SINE/MIR 64 CCCGGCTCTGCCA--CTTACTAGCTGTG-TGACCTTGGGCAAGTCACTTA 110 chr6ptel1M 383619 TCCTTGGTGAGTCTCATTTTTCTCAGTGACAAAATGGAGATGATAATAGC 383668 v ivv i v i vivii i i v MIRc#SINE/MIR 111 ACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACC 160 chr6ptel1M 383669 AACAGCATCTGTTTCACAAGAATATTGGTAGACTCAAAGGAGATCATTTG 383718 vi vviii iii i iv i vv iv v v v i MIRc#SINE/MIR 161 TGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTA 210 chr6ptel1M 383719 AAGCTGTG-AAGCTCTCTGT 383737 ---- - v i MIRc#SINE/MIR 211 ----TGTGAAAGCGCTTTGT 226 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.59 CpG sites = 25, Kimura (unadjusted) = 35.40 Transitions / transversions = 0.89 (25/28) Gap_init rate = 0.07 (14 / 195), avg. gap size = 2.21 (31 / 14) 199 24.20 0.00 7.41 chr6ptel1M 384373 384430 (615570) MIRb#SINE/MIR 87 140 (128) m_b281s601i20 11273 chr6ptel1M 384373 GCTGTGTGACCTTGGATAGTTGGATACTTTAAGGTTTCCAAAGCACAGTC 384422 ii iv --- - vv i ii iv v i MIRb#SINE/MIR 87 GCTGTGTGACCTTGGGCAAGT---TAC-TTAACCTCTCTGAGCCTCAGTT 132 chr6ptel1M 384423 TCCTCATC 384430 MIRb#SINE/MIR 133 TCCTCATC 140 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.74 CpG sites = 8, Kimura (unadjusted) = 29.74 Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.07 (4 / 57), avg. gap size = 1.00 (4 / 4) 409 33.72 4.17 1.16 chr6ptel1M 385209 385376 (614624) MIR3#SINE/MIR 34 206 (2) m_b281s601i21 11274 chr6ptel1M 385209 TGGAAATCAGGAGAGGAAGGTCCAGGCATCAGCTCTGCTATTCCCCTTCT 385258 i i vvvi i vi ivi i i i vv i?v MIR3#SINE/MIR 34 TGGGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCT 83 chr6ptel1M 385259 GTATGATCCTCAGGCAAGGTACTTCCCTGCTCTGAGAC----TTCCCAGC 385304 i - ii vi v iv i v ---- i vvv MIR3#SINE/MIR 84 GTGTGA-CCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCA 132 chr6ptel1M 385305 TCTGAGAAATAAGCAAGGTTGGGCTAGGTTTTCTCAAAAAGAGTTTTCAA 385354 vi i -ii i i vv v iivvvi i i MIR3#SINE/MIR 133 TCTGTAAAATGAG-GGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAG 181 chr6ptel1M 385355 ATCTG---TCTTATGATATTATGAT 385376 v --- ii vi MIR3#SINE/MIR 182 CTCTGACATTCTATGATTCTATGAT 206 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.55 CpG sites = 32, Kimura (unadjusted) = 46.70 Transitions / transversions = 1.33 (32/24) Gap_init rate = 0.02 (4 / 167), avg. gap size = 2.25 (9 / 4) 575 31.69 6.95 3.75 chr6ptel1M 385434 385692 (614308) MIRb#SINE/MIR 2 268 (0) m_b281s601i22 11275 chr6ptel1M 385434 AGAGGGGCAACAATGTTGGGCAATGGATACATAGCTCTGGGTCTGGAATC 385483 i --- v v i --v v v v v i i MIRb#SINE/MIR 2 AGAGGGGCAGC---GTGGTGCAGTGGA--AAGAGCACGGGCTTTGGAGTC 46 chr6ptel1M 385484 GGGAAGAGCCGAGTTCAAATTCAGCCTTAAACATTTACTAACTGCTTGGC 385533 i iv v i i i i v v iviv i i iv i MIRb#SINE/MIR 47 AGACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGAC 96 chr6ptel1M 385534 CCTTCATGAGTCACTTAAAATTCCTGAAT---------------TGTAAA 385568 i vviii i vv ii ii--------------- MIRb#SINE/MIR 97 CTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAA 146 chr6ptel1M 385569 A--AACTTAATAGCATCCATATCCTAGGGTT-TTGTGAGGTTCGTGAAAT 385615 --iivv ii i i iv vi - ---i v MIRb#SINE/MIR 147 ATGGGGATAATAATACCTACCTCGCAGGGTTGTTGTGAGG---ATTAAAT 193 chr6ptel1M 385616 GAAATAATAATTGTAAAGCACTTAGCATACTATGTGAGACATCTGTAAGT 385665 i ivv i i v iiv iv v- i MIRb#SINE/MIR 194 GAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATA-GTAAGC 242 chr6ptel1M 385666 GCTATGTAAATATGGACTGCTATTATT 385692 vvi ivvii - MIRb#SINE/MIR 243 GCTCAATAAATGGTAGCT-CTATTATT 268 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.43 CpG sites = 46, Kimura (unadjusted) = 42.56 Transitions / transversions = 1.39 (46/33) Gap_init rate = 0.05 (13 / 258), avg. gap size = 2.15 (28 / 13) 255 29.73 0.00 1.35 chr6ptel1M 386745 386819 (613181) C L2b_3end#LINE/L2 (3) 463 390 m_b281s601i23 11276 chr6ptel1M 386745 CATTAATTCAACAGACATTTCCTAAGTTCCTGCTCTGTACAAGGATCAGT 386794 v i i v i iv i v i v v? v C L2b_3end#LINE 463 CATTCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGT 414 chr6ptel1M 386795 GCTGGGCATGTGACGGTCAAGTGGT 386819 i ii- iv i vv i C L2b_3end#LINE 413 GCTAGGCGC-TGGGGATACAGCGGT 390 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.87 CpG sites = 12, Kimura (unadjusted) = 39.35 Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.01 (1 / 74), avg. gap size = 1.00 (1 / 1) 58 1.89 0.00 0.00 chr6ptel1M 387212 387265 (612735) (GA)n#Simple_repeat 1 54 (0) c_b281s251i4 11277 chr6ptel1M 387212 GAGAAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 387261 i (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr6ptel1M 387262 GAGA 387265 (GA)n#Simple_ 51 GAGA 54 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 416 31.31 6.01 0.52 chr6ptel1M 387367 387549 (612451) MIR3#SINE/MIR 16 208 (0) m_b281s601i24 11278 chr6ptel1M 387367 AGTAGAAAGGGTGCTGGTTCTGAAGTCATAGCATGTGAACT-TAG----A 387411 i i i ii v ii v- i viiv iv iii - ----i MIR3#SINE/MIR 16 AGCAGAGAGAGCACGGACTG-GGAGTCAGGAGACCTGGGTTCTAGTCCCG 64 chr6ptel1M 387412 ATTCTGCCTCT--CTC-CTGGATGATGTTGGGCAAGTCACATGATTT-TC 387457 ii v -- ?- vi iv v v ii - MIR3#SINE/MIR 65 GCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTC 114 chr6ptel1M 387458 TGGGCCTGAGATTCTTCA-CTGTGTACTTAGGGA-TTGGACTAGCTAACC 387505 v v i - iv v v i- v i i MIR3#SINE/MIR 115 TGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATC 164 chr6ptel1M 387506 TATAAGATCTCTTTTTGCGCTCTAAATGTACGATTCCATGAGTC 387549 v i i iiv v vvv v v i i v MIR3#SINE/MIR 165 TCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTATGATTC 208 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.95 CpG sites = 32, Kimura (unadjusted) = 41.92 Transitions / transversions = 1.28 (32/25) Gap_init rate = 0.04 (8 / 182), avg. gap size = 1.50 (12 / 8) 49 0.00 0.00 0.00 chr6ptel1M 387570 387611 (612389) (CT)n#Simple_repeat 1 42 (0) c_b281s251i5 11279 chr6ptel1M 387570 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 387611 (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 42 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 40 31.74 3.19 2.11 chr6ptel1M 387613 387800 (612200) (TCTT)n#Simple_repeat 1 190 (0) m_b281s252i13 11280 chr6ptel1M 387613 TCTTTGTTTCCGTCTCTGTTTTTGTCTGTCTCTCCCTCTTTCTTCCAACC 387662 v iv i v i v v i ii i --ii (TCTT)n#Simpl 1 TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC--TT 48 chr6ptel1M 387663 TCTTTCTCTC-TGCTATCCTCCCCCCTTCTCTGTCGTT-TCCCTTTACTC 387710 i - v v i i iii - v v - ii vi i (TCTT)n#Simpl 49 TCTTTCTTTCTTTCTTTCTTTCTTTCTT-TCTTTCTTTCTTTCTTTCTTT 97 chr6ptel1M 387711 CTTCCTTACCTCTCTTTCTCTCCCTCCCTCCCTCTTTCCTTCTTTC--TC 387758 i -i i i ii ii ii i -- (TCTT)n#Simpl 98 CTTTCTT-TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC 146 chr6ptel1M 387759 TTTCTCTCTCTCTTTCTTTGTTTC--TCTTTCTCTCTATCTTTC 387800 i i v -- i v (TCTT)n#Simpl 147 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC 190 Matrix = Unknown Transitions / transversions = 2.75 (33/12) Gap_init rate = 0.04 (8 / 187), avg. gap size = 1.25 (10 / 8) 19 15.29 4.55 0.00 chr6ptel1M 388009 388052 (611948) (GTT)n#Simple_repeat 1 46 (0) m_b281s252i14 11281 chr6ptel1M 388009 GTTGTT-TTGTTGTTGTTGTTG-GGTTTTGGTGGTGGTTTTTGTTG 388052 - -v v v v v v (GTT)n#Simple 1 GTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTG 46 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2) 234 28.75 6.25 0.00 chr6ptel1M 388075 388154 (611846) MIRb#SINE/MIR 19 103 (165) m_b281s601i25 11282 chr6ptel1M 388075 CAGTAGAA---GCAGGGAATTTGTAGTCAAA-GGTCCAAGATTTGAATCC 388120 i --- v iv v i -i v vi i i MIRb#SINE/MIR 19 CAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCGAATCC 68 chr6ptel1M 388121 AGGGTCTCCTACCTCCT-GCCTCATGACCTCGGGC 388154 v v v i i v - ivii i MIRb#SINE/MIR 69 CGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGC 103 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.08 CpG sites = 13, Kimura (unadjusted) = 37.08 Transitions / transversions = 1.30 (13/10) Gap_init rate = 0.04 (3 / 79), avg. gap size = 1.67 (5 / 3) 226 37.64 9.59 3.56 chr6ptel1M 390668 390959 (609041) C MamTip2b#DNA/hAT-Tip100 (91) 358 50 m_b281s601i26 11283 chr6ptel1M 390668 GCTTTTGACTTCATTTCAGCCTCCTTCTCCCCAGTCCTAGCTCCCCTCTT 390717 iiv ii viiiv ?i ii vi vv i iv iv i C MamTip2b#DNA/ 358 GCTCCAGACCCCTCCCGANTCTCCCCCTCCCCCATCAAAACTTACCCGTC 309 chr6ptel1M 390718 CCCTCTTGCCTTATCACAGGGTCTTGTTCTCAGCTGATT------TTTTT 390761 iv v iv v vi v i i i --- v i?------i vv C MamTip2b#DNA/ 308 CTGTGTCCCATTCCCTCAGGGCCCTGCT---AGGTGACNGGNNAGCTAAT 262 chr6ptel1M 390762 TTTTTTTACTAATTCTTGATGAAGT---AGTGGCTGATATCTACTCATGG 390808 i vv vv vi v i i --- i vivi i vv C MamTip2b#DNA/ 261 CTGATAAACTAATTCACGCTAAGGTGTTAATGGCTGATAATGGCTTAATG 212 chr6ptel1M 390809 TGTTATCC--AAGAGATACTATAATTG------AACACGAACCTT-TGAA 390849 i --vvv i vi v ------ viii - ii C MamTip2b#DNA/ 211 TGTTACCCCTCCCAGGTAACATATTTGCATTTTAACAGAGGCCTTCTAGA 162 chr6ptel1M 390850 GACTGGAATGTCTTTGAGACTCAGAGGAATGTTCTTTAATGAGGGACCTT 390899 --- i ---i i i -v i iv ivv C MamTip2b#DNA/ 161 GAC---AATGCCTT---AACCCAAAGGAATG-ACTCTAATGGTGGGAATT 119 chr6ptel1M 390900 TTAAACA--GT-GCAAGCC----AGAGAG---CTTTCAGACAAGGGTCCT 390939 i ii -- i- i ----i i ---i vi i i vv i C MamTip2b#DNA/ 118 TCAGGCACCGCGGCAGGCCGGTGGGGGAGATATTTTGGGGCAGGGGGGCC 69 chr6ptel1M 390940 TGTTAAGCTTCTCCCAGGTC 390959 - vi vi i i ii C MamTip2b#DNA/ 68 T-TTCGGCGCCCCTCAAATC 50 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 51.98 CpG sites = 64, Kimura (unadjusted) = 55.95 Transitions / transversions = 1.52 (64/42) Gap_init rate = 0.07 (20 / 291), avg. gap size = 1.95 (39 / 20) 424 31.66 7.59 8.05 chr6ptel1M 390728 390964 (609036) C MamTip2#DNA/hAT-Tip100 (16) 289 54 m_b281s601i27 11283 chr6ptel1M 390728 TTATCACAGGGTCTTGTTCTCAGCTGATTTTTTTTTTTTTTACTAATTCT 390777 vi ? i i iii v iv-------- i i C MamTip2#DNA/h 289 TTCCCNCAGGGCCTTGCTCTCAGCTAGCTGTCA--------ACTAATCCC 248 chr6ptel1M 390778 TGATGAAGTAGTGGCTGATATCTACTCATGGTGTTA----TCCAAGAGAT 390823 i v i i iv i vivi i v ---- v i i C MamTip2#DNA/h 247 CGCTAAGGTGTTAGCTGATAATGGCTTAAGGTGTTACCCCTCCCAGGGGT 198 chr6ptel1M 390824 ACT-ATAATTGAACACGA-ACCTTTGAAGACTGGAATGTCTTTGAGACTC 390871 i -ii v v i v i- iii i iii v i ii i C MamTip2#DNA/h 197 ATTTGCATTTTAATAGGGGACTCCTGGAGACCAAAAAGCCTTCAAGACCC 148 chr6ptel1M 390872 AGAGGAATG-TTCTTTAATGAGGGACCTTTTAAACA--GTG-CAAGC--- 390914 i -v i iv -v i ii -- - i --- C MamTip2#DNA/h 147 AAAGGAATGAATCTCTAATGGTGGA-ATTTCAGGCACCGTGACAGGCGGA 99 chr6ptel1M 390915 -CAGAGAG---CTTTCAGACAAGGGTCCTTGTTAAGCTTCTCCCAG-GTC 390959 -vi ---i vi i i --------- i - i - i C MamTip2#DNA/h 98 TGGGAGAGATATTTTGGGGCAGGGG---------AGCCT-TCCCGGCGCC 59 chr6ptel1M 390960 TCTCA 390964 i C MamTip2#DNA/h 58 CCTCA 54 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.97 CpG sites = 51, Kimura (unadjusted) = 44.79 Transitions / transversions = 2.83 (51/18) Gap_init rate = 0.12 (29 / 236), avg. gap size = 1.28 (37 / 29) 27 8.35 3.92 0.00 chr6ptel1M 391282 391332 (608668) (AGAGAC)n#Simple_repeat 1 53 (0) c_b281s251i6 11284 chr6ptel1M 391282 AGAGACAGAGACAGAGAGAGACAAAGAGACA-ATA-AGAGACAGAGACAG 391329 v v v - v - (AGAGAC)n#Sim 1 AGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAG 50 chr6ptel1M 391330 AGA 391332 (AGAGAC)n#Sim 51 AGA 53 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.04 (2 / 50), avg. gap size = 1.00 (2 / 2) 189 29.74 2.60 3.95 chr6ptel1M 391623 391699 (608301) MIR3#SINE/MIR 110 185 (23) m_b281s601i28 11285 chr6ptel1M 391623 CTCTCTGA-CTCCGCTTTCCTGCAT-TGCAAACCACAGAGATTGGGGGAG 391670 i- ii iv - - i viivi i i ivv MIR3#SINE/MIR 110 CTCTCTGGGCCTCAGTTTCCT-CATCTGTAAAATGAGGGGGTTGGACTAG 158 chr6ptel1M 391671 ATGAGCCTTGAGATCCCTTCTAAGGCTCT 391699 v ii i i i -- MIR3#SINE/MIR 159 ATGATCTCTAAGGTCCCTTCCA--GCTCT 185 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.45 CpG sites = 16, Kimura (unadjusted) = 40.45 Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.07 (5 / 76), avg. gap size = 1.00 (5 / 5) 284 23.04 18.18 6.72 chr6ptel1M 393113 393233 (606767) MIRc#SINE/MIR 16 149 (119) m_b281s601i29 11286 chr6ptel1M 393113 CAGTGGA--GAGTAT--GACACAGAGGTAGGTAGATTCATCTTCCTGAGT 393158 -- i i-- vii vi v -------- i MIRc#SINE/MIR 16 CAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA--------CCTGGGT 57 chr6ptel1M 393159 TTAAATCCTGCCTCAGACACTTACTTAGCTGTATGA-------------- 393194 ii i i v v v - i -------------- MIRc#SINE/MIR 58 TCGAGTCCCGGCTCTGCCACTTAC-TAGCTGTGTGACCTTGGGCAAGTCA 106 chr6ptel1M 393195 ---AACC-CTATTTACCTCAGTTTCCTCATTTGTAAGAAGAAG 393233 --- - v vvi i i v ii MIRc#SINE/MIR 107 CTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGG 149 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.77 CpG sites = 16, Kimura (unadjusted) = 28.42 Transitions / transversions = 1.60 (16/10) Gap_init rate = 0.12 (14 / 120), avg. gap size = 2.21 (31 / 14) 295 20.20 21.18 0.98 chr6ptel1M 393149 393233 (606767) MIR#SINE/MIR 44 145 (117) m_b281s601i30 11286 chr6ptel1M 393149 CTTCCTGAGTTTAAATCCTGCCTCAGACACTTACTTAGCTGTATGA---- 393194 v i ii i v v v - i ---- MIR#SINE/MIR 44 CTGCCTGGGTTCGAATCCCGGCTCTGCCACTTAC-TAGCTGTGTGACCTT 92 chr6ptel1M 393195 -------------AACC-CTATTTACCTCAGTTTCCTCATTTGTAAGAAG 393230 ------------- - v v i i i v MIR#SINE/MIR 93 GGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATG 142 chr6ptel1M 393231 AAG 393233 ii MIR#SINE/MIR 143 GGG 145 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 20.72 CpG sites = 10, Kimura (unadjusted) = 23.95 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.05 (4 / 84), avg. gap size = 4.75 (19 / 4) 222 20.53 20.00 2.56 chr6ptel1M 393152 393251 (606749) MIR1_Amn#SINE/MIR 53 169 (61) m_b281s601i31 11286 chr6ptel1M 393152 CCTGAGTTTAAATCCTGCCTCAGACACTTACTTAGCTGTATGA------- 393194 i i? ? i v v v ?i i?- ?i ------- MIR1_Amn#SINE 53 CCTGGGTTCNANTCCCGGCTCTGCCACTNGCCN-GCTGNGTGACCTTGGG 101 chr6ptel1M 393195 ----------AACC-CTATTTACCTCAGTTTCCTCATTTGTAAGAAGAAG 393233 ----------? - v v?i i i v ii MIR1_Amn#SINE 102 CAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGG 151 chr6ptel1M 393234 CAAATGGCAAACTG--CTCC 393251 vv -- v -- MIR1_Amn#SINE 152 ATAATG--ATACTGACCTCC 169 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.19 CpG sites = 11, Kimura (unadjusted) = 26.69 Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.07 (7 / 99), avg. gap size = 3.29 (23 / 7) 240 17.95 0.00 0.00 chr6ptel1M 393685 393723 (606277) L2c_3end#LINE/L2 428 466 (12) m_b281s601i32 11287 chr6ptel1M 393685 AGTGCCTGGCACATAGTCAGTGCTTACTAAATGCTTGTT 393723 i vi i i v i L2c_3end#LINE 428 AGCGCCTGGCACATAGTAGGCGCTCAATAAATGTTTGTT 466 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 14.83 CpG sites = 5, Kimura (unadjusted) = 21.09 Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 222 20.44 0.00 4.08 chr6ptel1M 393721 393771 (606229) L2d_3end#LINE/L2 465 513 (3) m_b281s601i33 11287 chr6ptel1M 393721 GTTCTCAGCATTAGTACTAAGTGCTTACTAAATGCTTGTTGATTGATTGA 393770 v v i--i v i i i v i L2d_3end#LINE 465 GTGCTGAGCAC--ATAGTAGGCGCTCAATAAATACTTGTTGATTGATTGA 512 chr6ptel1M 393771 T 393771 L2d_3end#LINE 513 T 513 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 21.57 CpG sites = 6, Kimura (unadjusted) = 24.22 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.04 (2 / 50), avg. gap size = 1.00 (2 / 2) 401 32.03 4.35 6.67 chr6ptel1M 393822 394005 (605995) MIRc#SINE/MIR 14 193 (75) m_b281s601i34 11288 chr6ptel1M 393822 TGCACTGAGAGAGAGCATCAGATGAAGCACATTTTAGTCAG-AAGGCCTG 393870 v - i iii i-------- vv - i MIRc#SINE/MIR 14 TGCAGTG-GAAAGAGCACTGGAC--------TTGGAGTCAGGAAGACCTG 54 chr6ptel1M 393871 G-TTTGAA-----ATTCTGACACTTGATGGCTATTTATTGCCCTCAGATG 393914 - i i-----ii v iv i i v --- v ii iii MIRc#SINE/MIR 55 GGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGT---GACCTTGGGCA 101 chr6ptel1M 393915 AGACACCTTTCCCATCTGAACCTCCATTTCTTCATCTATAAAAATGGAAA 393964 v i vv iv i vi i i vv i v MIRc#SINE/MIR 102 AGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGAT 151 chr6ptel1M 393965 GATAATG-CTGTTCTACTTGTATTATAGGGATGTGGGGAGAA 394005 i i- ii i i iiv i i v v v i MIRc#SINE/MIR 152 AATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGA 193 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.79 CpG sites = 36, Kimura (unadjusted) = 43.89 Transitions / transversions = 1.89 (36/19) Gap_init rate = 0.09 (16 / 183), avg. gap size = 1.25 (20 / 16) 274 35.97 0.00 0.88 chr6ptel1M 394799 394913 (605087) L2c_3end#LINE/L2 364 477 (1) m_b281s601i35 11289 chr6ptel1M 394799 CTCCCTCAGCAATATGTAAAATCCATAAAGGAAAGGACCATTTCATTTAC 394848 ii vi ivv i iv v i i v i i v v v v L2c_3end#LINE 364 CTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTC 413 chr6ptel1M 394849 ATCTTGTTTTTTCCAGCACCTTGCCCATAGTGGTTGCTTCATAATTCCTT 394898 vv v ii i v v i vi iv v vi L2c_3end#LINE 414 ATCTTTGTATCCCCAGCGCCTGGCACATAGTAGGCGCTCAATAAATGTTT 463 chr6ptel1M 394899 ATTATGTGATACGAA 394913 i ivi - i L2c_3end#LINE 464 GTTGAATGA-ATGAA 477 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.11 CpG sites = 21, Kimura (unadjusted) = 50.05 Transitions / transversions = 1.05 (21/20) Gap_init rate = 0.01 (1 / 114), avg. gap size = 1.00 (1 / 1) 190 33.33 0.00 0.00 chr6ptel1M 395244 395291 (604709) L2d_3end#LINE/L2 464 511 (5) m_b281s601i36 11289 chr6ptel1M 395244 AATGCTTGACATATAATAAGTACTTAATAAGTGCATGTTGACTAACTG 395291 i vii i i i ii i i i v i i i L2d_3end#LINE 464 AGTGCTGAGCACATAGTAGGCGCTCAATAAATACTTGTTGATTGATTG 511 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.95 CpG sites = 14, Kimura (unadjusted) = 51.22 Transitions / transversions = 7.00 (14/2) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 222 30.09 15.93 0.00 chr6ptel1M 395436 395548 (604452) C MIRc#SINE/MIR (50) 218 88 m_b281s601i37 11290 chr6ptel1M 395436 CTTTGACATT--TTAATCCATTTGTCCTTCATAATTCCCCTATAATGCAG 395483 v v-- vii vi i i ivv i i v i C MIRc#SINE/MIR 218 CTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAG 169 chr6ptel1M 395484 CCAG------TATCATGATTCTCAACTTAAAGATGAGAAAACAGAAACCC 395527 v ------ i v i i vi v i v ii i C MIRc#SINE/MIR 168 GCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC 119 chr6ptel1M 395528 ----------ATTGACCTCCCCAAGTTTACA 395548 ---------- v i v v i C MIRc#SINE/MIR 118 AGAGAGGTTAAGTGACTTGCCCAAGGTCACA 88 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.37 CpG sites = 19, Kimura (unadjusted) = 39.37 Transitions / transversions = 1.27 (19/15) Gap_init rate = 0.03 (3 / 112), avg. gap size = 6.00 (18 / 3) 243 33.73 0.00 0.00 chr6ptel1M 395446 395528 (604472) C MIR#SINE/MIR (66) 196 114 m_b281s601i38 11290 chr6ptel1M 395446 TTAATCCATTTGTCCTTCATAATTCCCCTATAATGCAGCCAGTATCATGA 395495 ii ivi i i ivv i v i vi v i v C MIR#SINE/MIR 196 TTAACTCATTTAATCCTCACAACAACCCTATGAGGTAGGTACTATTATTA 147 chr6ptel1M 395496 TTCTCAACTTAAAGATGAGAAAACAGAAACCCA 395528 i i vi v i v ii v C MIR#SINE/MIR 146 TCCCCATTTTACAGATGAGGAAACTGAGGCACA 114 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 46.76 CpG sites = 17, Kimura (unadjusted) = 46.76 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.00 (0 / 82), avg. gap size = 0.0 (0 / 0) 354 30.16 3.39 1.67 chr6ptel1M 395623 395740 (604260) C MIRc#SINE/MIR (67) 201 82 m_b281s601i39 11291 chr6ptel1M 395623 TCATTTCATCTTTCCAACAACTTGCTGAATGGTGCTTGGGAGAAGTATTA 395672 v i iv iivv -- ivvii iv i C MIRc#SINE/MIR 201 TCATTTGATCCTCACAACAACCCTGTGA--GGTAGGCAGGGCAGGTATTA 154 chr6ptel1M 395673 GAAAACATATTTTATAGGTGAGCAAACTGAAGCCCGGAGAGACT--GTCG 395720 vv vv vi i i v i i i ii -- vi C MIRc#SINE/MIR 153 TTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGA 104 chr6ptel1M 395721 CC--CCCGAGGTCATACAGCTA 395740 i-- i i C MIRc#SINE/MIR 103 CTTGCCCAAGGTCACACAGCTA 82 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.87 CpG sites = 21, Kimura (unadjusted) = 39.87 Transitions / transversions = 1.50 (21/14) Gap_init rate = 0.03 (4 / 117), avg. gap size = 1.50 (6 / 4) 213 28.32 0.00 1.89 chr6ptel1M 395851 395904 (604096) C L2a_3end#LINE/L2 (9) 508 456 m_b281s601i40 11292 chr6ptel1M 395851 TTCAACATGCATTTATTAAGTACTTAACTACCTGCCAGACACTGTGATGA 395900 vii i ii i - iv i vv ii C L2a_3end#LINE 508 TTCAACAAATATTTATTGAGCGCCTA-CTATGTGCCAGGCACTGTTCTAG 460 chr6ptel1M 395901 GCAC 395904 i C L2a_3end#LINE 459 GCGC 456 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.23 CpG sites = 11, Kimura (unadjusted) = 37.81 Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.02 (1 / 53), avg. gap size = 1.00 (1 / 1) 540 34.77 11.91 0.32 chr6ptel1M 396427 396703 (603297) L3#LINE/CR1 3791 4099 (0) m_b281s601i41 11293 chr6ptel1M 396427 TGATATGGAAAAGAGGGACTGTATATATT-----TGGCTCCTTAAGGAAG 396471 vi vii i iv iv ----- vv i v L3#LINE/CR1 3791 TGTCATGTGGAAGAGGGATTAGACTTATTCTGTGTGGCTCCAGAGGGCAG 3840 chr6ptel1M 396472 AAC-AGCAACTATGGAGTGACATTTCAGGAAGATAGATGTCTCATGAATA 396520 - v v v ivv vi v i ii v vvv v L3#LINE/CR1 3841 AACTAGGACCAATGGGTGGAAGTTACAGGGAGGCAGATTTCGGCTCAATA 3890 chr6ptel1M 396521 TAAGGAAGAACTTCCTGGCAGTTGGAGCTATTCCACAAGGGAAAGATTTG 396570 i ii i ii i i v v v v ivi L3#LINE/CR1 3891 TAAGGAAGAACTTTCTAACAATCAGAGCTGTCCAAAAATGGAATGGGCTG 3940 chr6ptel1M 396571 CTTTACAAACT-GTGAACTTCCCATTACTTGTAGTTGTT-----AAAGAT 396614 i ii?i iv - i i i i - v v ----- i ii L3#LINE/CR1 3941 CCTCGNGAGGTAGTGAGCTCCCCGTCAC-TGGAGGTGTTCAAGCAGAGGC 3989 chr6ptel1M 396615 TG--------CTTATCAGCAATGTCATATGCAGATTTTTTTCACCAAGCC 396656 -------- i vi ii vivi iv ii v iiiiiiv L3#LINE/CR1 3990 TGGATGACCACTTGTCAGGGATGTTGTAGAAGGGATTCCTGCATTGGATG 4039 chr6ptel1M 396657 AA-----GGAATAAATGATC--------CTTTTCCAACTGTAAAATTCTC 396693 ii----- v i i -------- ii v i i v L3#LINE/CR1 4040 GGAGGTTGGACTAGATGACCTCTAAGGTCCCTTCCAACTCTGAGATTCTG 4089 chr6ptel1M 396694 TGGTTGTGTC 396703 i v i L3#LINE/CR1 4090 TGATTCTATC 4099 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 47.74 CpG sites = 59, Kimura (unadjusted) = 49.30 Transitions / transversions = 1.59 (59/37) Gap_init rate = 0.03 (8 / 276), avg. gap size = 4.25 (34 / 8) 13 14.60 0.00 6.25 chr6ptel1M 397291 397324 (602676) (TTA)n#Simple_repeat 1 32 (0) m_b281s252i15 11294 chr6ptel1M 397291 TTATTTATTATAAATATTATTTATAATTATTGTT 397324 - v v - v i (TTA)n#Simple 1 TTA-TTATTATTATTATTA-TTATTATTATTATT 32 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2) 635 24.99 8.29 0.45 chr6ptel1M 397325 397529 (602471) C MIRc#SINE/MIR (0) 268 48 m_b281s601i42 11295 chr6ptel1M 397325 AACAATAATAAG----TAGATTTAATATGATATGTTAAGGTTTTCAAAAC 397370 i v---- v i- iii iv vi v i C MIRc#SINE/MIR 268 AATAATAATAACNCCTTACATTTG-TATAGCACTTTACAGTTTACAAAGC 220 chr6ptel1M 397371 CCTTT---ACACAT-ATCTCAGTTTATCTTCCCAACAACCCTGGGAGGTA 397416 v --- i - v v i v v C MIRc#SINE/MIR 219 GCTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTA 170 chr6ptel1M 397417 GT----GC---TGCTATTATTCTCATTTTATAGGTGATAAATCTAAGGCA 397459 v---- --- ii i i i i vi v i v C MIRc#SINE/MIR 169 GGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCT 120 chr6ptel1M 397460 GACAGAGGTTAAGTGACTTGTCCAGTGT-AAACAGCTAGTAAGAATCTGA 397508 v v i iv - v viv v C MIRc#SINE/MIR 119 CAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGA 70 chr6ptel1M 397509 -TTTGGATTTGATTCCATTTCT 397529 -iiv i i vi vv C MIRc#SINE/MIR 69 GCCGGGACTCGAACCCAGGTCT 48 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.33 CpG sites = 26, Kimura (unadjusted) = 30.73 Transitions / transversions = 1.04 (26/25) Gap_init rate = 0.04 (8 / 204), avg. gap size = 2.25 (18 / 8) 656 24.07 3.70 0.00 chr6ptel1M 397363 397524 (602476) C MIR#SINE/MIR (46) 216 49 m_b281s601i43 11295 chr6ptel1M 397363 TTCAAAACCCTTTACACATAT---CTCAGTTTATCTTCCCAACAACCCTG 397409 v i v ii --- v v i v i C MIR#SINE/MIR 216 TTCTAAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTA 167 chr6ptel1M 397410 GGAGGTAG-TGCTGCTATTATTCTCATTTTATAGGTGATAAATCTAAGGC 397458 v - i ii i i i i vi v i C MIR#SINE/MIR 166 TGAGGTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGC 117 chr6ptel1M 397459 AGACAGAGGTTAAGTGACTTGTCCAGTGT-AAACAGCTAGTAAGAATCTG 397507 v v i i iv - v viv v C MIR#SINE/MIR 116 ACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAG 67 chr6ptel1M 397508 A-TTTGGATTTGATTCCA 397524 -iiv i vi C MIR#SINE/MIR 66 AGCCGGGATTCGAACCCA 49 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.76 CpG sites = 22, Kimura (unadjusted) = 29.51 Transitions / transversions = 1.29 (22/17) Gap_init rate = 0.02 (4 / 161), avg. gap size = 1.50 (6 / 4) 620 23.52 5.26 1.52 chr6ptel1M 397367 397556 (602444) C MIRb#SINE/MIR (52) 216 20 m_b281s601i44 11295 chr6ptel1M 397367 AAACCCTTTACA--CAT-ATCTCAGTTTATCTTCCCAACAACCCTGGGAG 397413 i v -- - v v i v v C MIRb#SINE/MIR 216 AAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAG 167 chr6ptel1M 397414 GTAGTGCTGCTATTATTCTCATTTTATAGGTGATAAATCTAAGGCAGACA 397463 - - ii i i i i vi v i vv v C MIRb#SINE/MIR 166 GTAG-G-TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGA 119 chr6ptel1M 397464 GAGGTTAAGTGACTTGTCCAGTGT-AAACAGCTAGTAAGAATCTGA-TTT 397511 i i iv - v viv v -iiv C MIRb#SINE/MIR 118 GAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 69 chr6ptel1M 397512 GGATTTGATTCCATTTCTAGTATG-CTTTAA---CTGT-CTCATCTCACT 397556 i vi vv - v - ii --- i - v ii C MIRb#SINE/MIR 68 GGATTCGAACCCAGGTCT-GTCTGACTCCAAAGCCCGTGCTCTTTCCACT 20 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.34 CpG sites = 23, Kimura (unadjusted) = 28.54 Transitions / transversions = 1.10 (23/21) Gap_init rate = 0.05 (10 / 189), avg. gap size = 1.30 (13 / 10) 385 30.82 17.48 4.10 chr6ptel1M 397561 397949 (602051) L3#LINE/CR1 3324 3762 (337) m_b281s601i45 11296 chr6ptel1M 397561 AATTTATTAGGGAATAAATACAAAGTTCTAAATTT----TATAAAATTTA 397606 vi - ii i iv ---- vv v i L3#LINE/CR1 3324 AATTTAACAGGGA-TAAATGTAAAGTCCTGCATTTAGGTTCAAAAAATCA 3372 chr6ptel1M 397607 AGTATGTAG---CAGGAAAGGGAGAA--------AG-AACAGTTAATATG 397644 v iiii i--- vi i i -------- - i v ii L3#LINE/CR1 3373 ACTGCACAAGTACAGGATGGAGAGGATCTGGCTTAGCAGCAGTTCACGTG 3422 chr6ptel1M 397645 AAA----TCTGCAAATTTGAGTGAACTACAAATTCAATATGAGTCAGAAA 397690 ----i iviii v vi ii ii i iv i L3#LINE/CR1 3423 AAAAAGACCTAGGGGTTTTAGTTGACCGCAAGCTCAATATGAGCCAACAG 3472 chr6ptel1M 397691 TGAAAAGAAAAAAATTGGCT-CCAAAC--TCTAAGGTTATCTT----TGC 397733 vi v -------- - v--v v iv ---- L3#LINE/CR1 3473 TGTGATG--------TGGCTGCCAAAAAAGCTAATGCAATCTTAGGCTGC 3514 chr6ptel1M 397734 --CAAGAGAAGGAGATGAAGCATCTGGCACAAAGGTGA-AATGG------ 397774 --i v ---- iv ii ii v? i v i- i ------ L3#LINE/CR1 3515 ATTAATAGAAG----TATAGTGTCCAGANCAAGGGAGGTAATAGTCCCGC 3560 chr6ptel1M 397775 ------ATGCGCCAGTTGGGC------TGATGTATTTTAGTCAGTTATCA 397812 ------v ii ii i ------ iv viiv v vi L3#LINE/CR1 3561 TGTACTCTGCGCTGGTCAGACCACATCTGGAGTATTGCGTTCAGTTCTGG 3610 chr6ptel1M 397813 GCACAGTATTTTA-GACACAGGACATTGCCAAGCAGGACCAAACCCAGAG 397861 i vii - ---i v i v v ivii L3#LINE/CR1 3611 GCGCCACATTTTAAGA---GGGACATTGACAAACTGGAGCGCGTCCAGAG 3657 chr6ptel1M 397862 ----GTGACGAGGATGAGCAAAGAATG-AGAGATCTTCTCATACAAAGAA 397906 ---- i v - ii ii v-i i i v v ii i L3#LINE/CR1 3658 GAGAGCGACCAGGATG-GTGAAGGGTCTGGAAACCATGTCATATGAGGAA 3706 chr6ptel1M 397907 AG-----------TGGGAATGTTTTAGCCTAAAGAATCAAAGAT---GAG 397942 v ----------- i - ii vvi i--- L3#LINE/CR1 3707 CGGTTGAAGGAACTGGGGATG-TTTAGCCTGGAGAAGAGAAGACTTAGAG 3755 chr6ptel1M 397943 GGGACAT 397949 i L3#LINE/CR1 3756 GAGACAT 3762 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.58 CpG sites = 75, Kimura (unadjusted) = 42.12 Transitions / transversions = 1.88 (75/40) Gap_init rate = 0.09 (35 / 388), avg. gap size = 2.46 (86 / 35) 429 26.13 7.53 8.28 chr6ptel1M 397989 398134 (601866) MIRc#SINE/MIR 2 146 (122) m_b281s601i46 11297 chr6ptel1M 397989 GGGGCAGCTACATGGCAAAGGGAATAGGGTGCTGGGCCTGGAGCCAGAAA 398038 i i---i iiv v i v i ii i i i i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr6ptel1M 398039 GATTCTTCTTTATGAGTTCAAATACAAATTCAGGCACTTACTAGTTGTGT 398088 ii-------- i i i v viii v v i MIRc#SINE/MIR 49 GACC--------TGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGT 90 chr6ptel1M 398089 GATCCTGGGCAAGTCACTTAAACCTGTTTG-----------CCTCATGTG 398127 i i - v i ----------- v MIRc#SINE/MIR 91 GACCTTGGGCAAGTCACTTAA-CCTCTCTGAGCCTCAGTTTCCTCATCTG 139 chr6ptel1M 398128 TAAAGTG 398134 i MIRc#SINE/MIR 140 TAAAATG 146 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.57 CpG sites = 26, Kimura (unadjusted) = 33.98 Transitions / transversions = 2.89 (26/9) Gap_init rate = 0.09 (13 / 145), avg. gap size = 1.77 (23 / 13) 15 8.91 0.00 0.00 chr6ptel1M 398212 398235 (601765) (ACA)n#Simple_repeat 1 24 (0) m_b281s252i16 11298 chr6ptel1M 398212 ACAACAACAACAACAAAAAAAACA 398235 v v (ACA)n#Simple 1 ACAACAACAACAACAACAACAACA 24 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 510 29.33 12.88 1.94 chr6ptel1M 398472 398704 (601296) L3#LINE/CR1 3750 4007 (92) m_b281s601i47 11296 chr6ptel1M 398472 TTAGAGGAAAT--------TATCATCTGATATTTGTTTAGCTGTGATGAG 398513 i i-------- i v vi vvvi v v L3#LINE/CR1 3750 TTAGAGGAGACATGATAGCTGTCTTCAAATATTTGAAGGGCTGTCATGTG 3799 chr6ptel1M 398514 GAAGAAGGACTCAGTTTTTTCTGCCTGGCCAACCTGAGAGTGTAGAACTG 398563 i i viii v iv i-- -- v i i L3#LINE/CR1 3800 GAAGAGGGATTAGACTTATTCTGTGTGGCT--CC--AGAGGGCAGAACTA 3845 chr6ptel1M 398564 GTACCAATGTGGGGAAATTTCTGAGAGGCTCATTTTGACTTGATAAAATG 398613 v v v i v v i vv i i ii v v L3#LINE/CR1 3846 GGACCAATGGGTGGAAGTTACAGGGAGGCAGATTTCGGCTCAATATAAGG 3895 chr6ptel1M 398614 AACAGTTTCCTAGAACTAAGAGTT---------------------TCTCA 398642 v ii i iv v v i ---------------------i i L3#LINE/CR1 3896 AAGAACTTTCTAACAATCAGAGCTGTCCAAAAATGGAATGGGCTGCCTCG 3945 chr6ptel1M 398643 GGTATTACTTAGATCCCCATCAATGGGGGGTCTAGAAGC-GATGCTAAAT 398691 ? viv v v v i v - i v vv - v ii L3#LINE/CR1 3946 NGAGGTAGTGAGCTCCCCGTCACT-GGAGGTGTTCAAGCAGAGGCTGGAT 3994 chr6ptel1M 398692 GATCACTTGTCAG 398704 i L3#LINE/CR1 3995 GACCACTTGTCAG 4007 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.86 CpG sites = 33, Kimura (unadjusted) = 37.94 Transitions / transversions = 0.97 (33/34) Gap_init rate = 0.03 (8 / 232), avg. gap size = 4.38 (35 / 8) 217 35.75 1.53 3.91 chr6ptel1M 399254 399384 (600616) C MIR#SINE/MIR (49) 213 86 m_b281s601i48 11299 chr6ptel1M 399254 TGAATATTCTATATTTACTTTATTTCATTTGATCC-AATATTAATCCTTT 399302 i iiii i i v -- vi i -v i vi i v C MIR#SINE/MIR 213 TAAGCGCTTTACATGTA--TTAACTCATTTAATCCTCACAACAACCCTAT 166 chr6ptel1M 399303 GCAGAAAGTCATACAGATATTATCCCTATTT-GTAAAGGAGGAATATGTG 399351 vi v i vv i--- i -ii i v vv v C MIR#SINE/MIR 165 GAGGTAGGTACTAT---TATTATCCCCATTTTACAGATGAGGAAACTGAG 119 chr6ptel1M 399352 GCCCTGAAAGAAGAAATGCCTTGTCAAAAATCA 399384 v v i ivv i iv i v ii C MIR#SINE/MIR 118 GCACAGAGAGGTTAAGTAACTTGCCCAAGGTCA 86 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 48.64 CpG sites = 26, Kimura (unadjusted) = 50.42 Transitions / transversions = 1.37 (26/19) Gap_init rate = 0.05 (7 / 130), avg. gap size = 1.00 (7 / 7) 301 32.76 4.31 0.00 chr6ptel1M 399269 399384 (600616) C MIRc#SINE/MIR (58) 210 90 m_b281s601i49 11299 chr6ptel1M 399269 TACTTTATTTCATTTGATCC-AATATTAATCCTTTGCAGAAAGTCATACA 399317 v i -v i vi i v vi v i ivivi C MIRc#SINE/MIR 210 TACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCA 161 chr6ptel1M 399318 GATATTAT---CCCTATTT-GTAAAGGAGGAATATGTGGCCCTGAAAGAA 399363 i --- i -ii i v vv v i v i iv C MIRc#SINE/MIR 160 GGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGT 111 chr6ptel1M 399364 GAAATGCCTTGTCAAAAATCA 399384 v i v i v ii C MIRc#SINE/MIR 110 TAAGTGACTTGCCCAAGGTCA 90 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.20 CpG sites = 21, Kimura (unadjusted) = 44.20 Transitions / transversions = 1.24 (21/17) Gap_init rate = 0.03 (3 / 115), avg. gap size = 1.67 (5 / 3) 391 26.00 2.00 0.00 chr6ptel1M 399561 399660 (600340) C MIR3#SINE/MIR (25) 183 82 m_b281s601i50 11300 chr6ptel1M 399561 AGCAGGAAGGATGCTGAGTGACTGTGGAGTCCA-CCTCCATATTTTAGCA 399609 v ivv v v iii vv - i vi vvi C MIR3#SINE/MIR 183 AGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAG 134 chr6ptel1M 399610 ATGAGGAAATTGAGGTTCAGTGAGCTAAAGTGATTTGCTCAA-GTCATAC 399658 i ii v v i i i - i C MIR3#SINE/MIR 133 ATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACAC 84 chr6ptel1M 399659 AG 399660 C MIR3#SINE/MIR 83 AG 82 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.40 CpG sites = 14, Kimura (unadjusted) = 32.40 Transitions / transversions = 1.17 (14/12) Gap_init rate = 0.02 (2 / 99), avg. gap size = 1.00 (2 / 2) 427 27.89 10.26 1.18 chr6ptel1M 399667 399822 (600178) C MIR3#SINE/MIR (24) 184 15 m_b281s601i51 11301 chr6ptel1M 399667 GAGCTAGAAAGGAACTTAGGG-CCTTCTATTCAAACACTGTCAATT---- 399711 i i v i -i v v v v iv v ---- C MIR3#SINE/MIR 184 GAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACA 135 chr6ptel1M 399712 ---GAG-AAATTAAGACCTAAAGA----AACTGACTTCCCTGAGAAGTCA 399753 --- - i i i i i ---- v v ii -- C MIR3#SINE/MIR 134 GATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAG--GTCA 87 chr6ptel1M 399754 TATA-TAGATAAGTAGCAGAGTCTTTATTTGAACCCAAGTCTTCTGATTC 399802 i i -i?ii v i i vvv i v i i i C MIR3#SINE/MIR 86 CACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGTCTCCTGACTC 37 chr6ptel1M 399803 TAAGTCAGTA-TCTC-CTATTC 399822 iv v i- - ii C MIR3#SINE/MIR 36 CCAGTCCGTGCTCTCTCTGCTC 15 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.45 CpG sites = 27, Kimura (unadjusted) = 36.45 Transitions / transversions = 1.69 (27/16) Gap_init rate = 0.06 (10 / 155), avg. gap size = 1.80 (18 / 10) 220 25.93 4.71 4.71 chr6ptel1M 400060 400144 (599856) C MIRc#SINE/MIR (89) 179 95 m_b281s601i52 11302 chr6ptel1M 400060 CTGAGAGGCACTGACAAG--AGATAATATTATCCCTATTTTGTAAAGGAC 400107 v i -- i i -- i v i ii i v v C MIRc#SINE/MIR 179 CTGTGAGGTA--GGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAG 132 chr6ptel1M 400108 GAATATGTAGCTCTAAAAGAGG--AACTGTCTTGTCAAA 400144 vv vi -- i -- v v i v C MIRc#SINE/MIR 131 GAAACTGAGGCTC--AGAGAGGTTAAGTGACTTGCCCAA 95 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.22 CpG sites = 11, Kimura (unadjusted) = 32.22 Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.07 (6 / 84), avg. gap size = 1.33 (8 / 6) 332 32.82 4.44 0.71 chr6ptel1M 400318 400452 (599548) MIRc#SINE/MIR 112 251 (17) m_b281s601i53 11303 chr6ptel1M 400318 CTTCCCTGAATCTTGGTGCCTTCATCTCTGGGATGGG-ATATCAATACGG 400366 i i ii ii vi i v iii - vi vv MIRc#SINE/MIR 112 CCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCT 161 chr6ptel1M 400367 GATTTGCCCACTGTTGCTGAGTTACTGAGAAGATCAAATGAGATA---TA 400413 vii i i- ii v i ii v i --- MIRc#SINE/MIR 162 GCCCTGCCTACC-TCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTA 210 chr6ptel1M 400414 C-TGGGTTCTATTTAT-AACTGTAAAATACTACTTAACTGT 400452 i- iivv vv i - i i ivi v MIRc#SINE/MIR 211 TGTGAAAGCGCTTTGTAAACTGTAAAGTGCTATACAAATGT 251 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 46.03 CpG sites = 30, Kimura (unadjusted) = 46.03 Transitions / transversions = 2.14 (30/14) Gap_init rate = 0.04 (5 / 134), avg. gap size = 1.40 (7 / 5) 15 16.01 0.00 5.41 chr6ptel1M 400736 400774 (599226) (TAA)n#Simple_repeat 1 37 (0) m_b281s252i17 11304 chr6ptel1M 400736 TATTATTAATAATTATTATTAATAATTAATAATAAAAAT 400774 v v - v v - v (TAA)n#Simple 1 TAATAATAATAA-TAATAATAATAA-TAATAATAATAAT 37 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2) 34 26.49 5.21 4.66 chr6ptel1M 401428 401619 (598381) (TCCT)n#Simple_repeat 1 193 (0) m_b281s252i18 11305 chr6ptel1M 401428 TCCCTCCTTCCTGTCTGTTCTGGTTCTTGCTTGCTT-GTTTCTT-GTTCC 401475 i - -v -vv i v v -v i -v (TCCT)n#Simpl 1 TCCTTCCTTCCT-TC-CTTC-CTTCCTTCCTTCCTTCCTTCCTTCCTTCC 47 chr6ptel1M 401476 TTTTTTCTGTTCTTCC-TCCTT-TATCTTTCCTTCCTT-CTCCTTTCCCT 401522 ii iv i - -iv i - i i - (TCCT)n#Simpl 48 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT-CCT 96 chr6ptel1M 401523 TCTTCCCTTCCCTTCCTTGTTTTTTTTCCTTTCTCCCTTCCTTTCCCCCA 401572 i i - -ii ii i i - ii v (TCCT)n#Simpl 97 TCCTTCCTT-CCTTCCTT-CCTTCCTTCCTTCCTTCCTTCC-TTCCTTCC 143 chr6ptel1M 401573 TTCTTTTC-CCCTTCTCTT-C-TCCCTCTTTCTCTT--TTTCTTCCTTTC 401617 i i -i - - - i i - -- i i (TCCT)n#Simpl 144 TTCCTTCCTTCCTTC-CTTCCTTCCTTCCTTC-CTTCCTTCCTTCCTTCC 191 chr6ptel1M 401618 TT 401619 (TCCT)n#Simpl 192 TT 193 Matrix = Unknown Transitions / transversions = 2.80 (28/10) Gap_init rate = 0.09 (18 / 191), avg. gap size = 1.06 (19 / 18) 12 14.69 3.33 0.00 chr6ptel1M 402523 402552 (597448) (ATTAAA)n#Simple_repeat 1 31 (0) m_b281s252i19 11306 chr6ptel1M 402523 ATT-AATTTAAAAATAAAATCAAATTTAAAA 402552 - v v i v (ATTAAA)n#Sim 1 ATTAAAATTAAAATTAAAATTAAAATTAAAA 31 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 214 31.61 5.00 1.94 chr6ptel1M 402908 403007 (596993) C L2a_3end#LINE/L2 (20) 497 395 m_b281s601i54 11307 chr6ptel1M 402908 TTCATTAAATACCTACTATGACCAAGGCACTGTCCATGGAAAGCATGAAG 402957 i i iii vv v i - i iviviiv i v C L2a_3end#LINE 497 TTTATTGAGCGCCTACTATGTGCCAGGCACTGTTC-TAGGCGCTGGGGAT 449 chr6ptel1M 402958 ACAA----AAACAAAA-AGGAAACAATCACTGCCCCTCTGGTAGCTTAGA 403002 i----i - iv v i v iiv - v C L2a_3end#LINE 448 ACAGCAGTGAACAAAACAGACAAAAGTCCCTGCCCTCATGG-AGCTTACA 400 chr6ptel1M 403003 GTCTA 403007 v C L2a_3end#LINE 399 TTCTA 395 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.63 CpG sites = 18, Kimura (unadjusted) = 42.36 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.04 (4 / 99), avg. gap size = 1.75 (7 / 4) 206 32.39 2.21 6.92 chr6ptel1M 403280 403415 (596585) MIRc#SINE/MIR 9 138 (130) m_b281s601i55 11308 chr6ptel1M 403280 TGTGATGCACTGGA--GGACAGTTGTCTAGAGGGGGGTCCAGGAGAATTC 403327 i v -- ii v v v ----v i vi i --i MIRc#SINE/MIR 9 TGTGGTGCAGTGGAAAGAGCACTGGACT----TGGAGTCAGGAAGA--CC 52 chr6ptel1M 403328 TGAATCAGGAGCCCAAGATCTGAGTCTGTCCTTGCTATG-GGTCTTTATC 403376 ii iv - i vi v vvv - v v i - ii viv MIRc#SINE/MIR 53 TGGGTTCG-AGTCCCGGCTCTGCCACT-TACTAGCTGTGTGACCTTGGGC 100 chr6ptel1M 403377 AAGGTCAGTTCACTTCTCTGGGTCTTAGTATTTTCATCT 403415 - v v i i i i v ii MIRc#SINE/MIR 101 AAG-TCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCT 138 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.77 CpG sites = 22, Kimura (unadjusted) = 43.15 Transitions / transversions = 1.16 (22/19) Gap_init rate = 0.08 (11 / 135), avg. gap size = 1.09 (12 / 11) 208 30.89 0.89 4.63 chr6ptel1M 403304 403415 (596585) MIR1_Amn#SINE/MIR 33 140 (90) m_b281s601i56 11308 chr6ptel1M 403304 CTAGAGGGGGGTCCAGGAGAATTCTGAATCAGGAGCCCAAGATCTGAGTC 403353 i vv iii i --i ii iv?i?v i- v vvv MIR1_Amn#SINE 33 CTGGACTGGGACTCGGGAGA--CCTGGGTTCNANTCCCG-GCTCTGCCAC 79 chr6ptel1M 403354 TGTCCTTGCTATG-GGTCTTTATCAAGGTCAGTTCACTTCTCTGGGTCTT 403402 ?v ?- i? - ii viv - v ? i ? i i MIR1_Amn#SINE 80 TNGCCN-GCTGNGTGACCTTGGGCAAG-TCACTTNACCTCTCTGNGCCTC 127 chr6ptel1M 403403 AGTATTTTCATCT 403415 v ii MIR1_Amn#SINE 128 AGTTTCCTCATCT 140 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.59 CpG sites = 20, Kimura (unadjusted) = 45.28 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.05 (6 / 111), avg. gap size = 1.00 (6 / 6) 314 29.31 9.33 4.46 chr6ptel1M 403329 403478 (596522) MIR3#SINE/MIR 37 193 (15) m_b281s601i57 11308 chr6ptel1M 403329 GAATCAGGAGCCCAAGAT-------CTGAGTCTGTC-----CTTGCTATG 403366 i v vi i ------- i iv i ----- ? i MIR3#SINE/MIR 37 GAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTG 86 chr6ptel1M 403367 -GGTCTTTATCAAGGTCAGTTCACTTCTCTGGGTCTTAGTATTTTCATCT 403415 - ii viv - v i i i v ii MIR3#SINE/MIR 87 TGACCTTGGGCAAG-TCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCT 135 chr6ptel1M 403416 -TACTATAAATAAGATGTGGTTGGACTGCATTGTCTGTGTGACCATTTCT 403464 - ---- i -- v iv vi v iv ii vi i MIR3#SINE/MIR 136 GTA----AAATGAG--GGGGTTGGACTAGATGATCTCTAAGGTCCCTTCC 179 chr6ptel1M 403465 GCTTTTGATGTTCT 403478 ivi i ii MIR3#SINE/MIR 180 AGCTCTGACATTCT 193 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.21 CpG sites = 28, Kimura (unadjusted) = 39.45 Transitions / transversions = 2.00 (28/14) Gap_init rate = 0.07 (11 / 149), avg. gap size = 1.91 (21 / 11) 313 24.52 1.18 8.86 chr6ptel1M 403723 403807 (596193) C MIRc#SINE/MIR (141) 127 49 m_b281s601i58 11309 chr6ptel1M 403723 CTGAGGC-AATTGGGGTTAAATGATTTGCCTAGGGTCACACAACTAGGAT 403771 -v vv i i i i i i --- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG--- 81 chr6ptel1M 403772 GCATTAAGTATCTGAGGCTAGATTTGAACTCAGATC 403807 ---- iv v v vi i i i i C MIRc#SINE/MIR 80 ----TAAGTGGCAGAGCCGGGACTCGAACCCAGGTC 49 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.39 CpG sites = 12, Kimura (unadjusted) = 30.27 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.10 (8 / 84), avg. gap size = 1.00 (8 / 8) 252 28.54 8.00 1.89 chr6ptel1M 403807 403906 (596094) C MamTip2#DNA/hAT-Tip100 (101) 204 99 m_b281s601i59 11310 chr6ptel1M 403807 CAGGAATATTTGCATTTTAA-AGAG------TGGCAAGGGGAAGATGATC 403849 ii - i ------ -- ivv i v vii C MamTip2#DNA/h 204 CAGGGGTATTTGCATTTTAATAGGGGACTCCTGG--AGACCAAAAAGCCT 157 chr6ptel1M 403850 TGAA-ATACAAAATAACAAAGCTCTAATGGTAGAATTTCAGCCATCATGG 403898 v - iv iv ii v i v i i i C MamTip2#DNA/h 156 TCAAGACCCAAAGGAATGAATCTCTAATGGTGGAATTTCAGGCACCGTGA 107 chr6ptel1M 403899 TACCTGGA 403906 i vvi C MamTip2#DNA/h 106 CAGGCGGA 99 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.80 CpG sites = 17, Kimura (unadjusted) = 37.09 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.05 (5 / 99), avg. gap size = 2.00 (10 / 5) 201 29.15 9.40 3.23 chr6ptel1M 403812 403928 (596072) C MamTip2b#DNA/hAT-Tip100 (258) 191 68 m_b281s601i60 11310 chr6ptel1M 403812 ATATTTGCATTTTAA-AGAGTGGCAAGGGGAAGATGAT-CTGAAATACAA 403859 - -- vvvvvii ii - ivv iv C MamTip2b#DNA/ 191 ATATTTGCATTTTAACAGAG--GCCTTCTAGAGACAATGCCTTAACCCAA 144 chr6ptel1M 403860 AATAACAAAGCTCTAATGGTAG-AATTTCAGCCATCATGGTA--CC--TG 403904 iv ii -- i - v i ii i -- -- C MamTip2b#DNA/ 143 AGGAATGA--CTCTAATGGTGGGAATTTCAGGCACCGCGGCAGGCCGGTG 96 chr6ptel1M 403905 G----AATATTTATGGTTAAGGAGACTT 403928 ----i vv vi i i i i C MamTip2b#DNA/ 95 GGGGAGATATTTTGGGGCAGGGGGGCCT 68 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.28 CpG sites = 20, Kimura (unadjusted) = 38.19 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.09 (10 / 116), avg. gap size = 1.50 (15 / 10) 196 26.39 4.59 9.62 chr6ptel1M 404692 404800 (595200) MIRc#SINE/MIR 105 208 (60) m_b281s601i61 11311 chr6ptel1M 404692 CACTTCACCCAGTCTG--CCTCAGTTTCCTCATATGTAACTTGAGCTGAG 404739 v iv- -- v vv ---- i MIRc#SINE/MIR 105 CACTTAACCTC-TCTGAGCCTCAGTTTCCTCATCTGTAAAATG----GGG 149 chr6ptel1M 404740 AAAGAAATAGTAATCCTTC---CCTCCCAGAATCTTTGATAAGAATATTC 404786 v iv vivii v --- v ii iv - i i ---- MIRc#SINE/MIR 150 ATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTG-TGAGGAT---- 194 chr6ptel1M 404787 CAAATGAAACTATG 404800 i iv MIRc#SINE/MIR 195 CAAATGAGATAATG 208 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.66 CpG sites = 13, Kimura (unadjusted) = 32.66 Transitions / transversions = 1.00 (13/13) Gap_init rate = 0.11 (12 / 108), avg. gap size = 1.25 (15 / 12) 214 18.72 9.30 6.82 chr6ptel1M 404692 404777 (595223) MIR3#SINE/MIR 102 189 (19) m_b281s601i62 11311 chr6ptel1M 404692 CACTTCACCCAGTCTG--CCTCAGTTTCCTCATATGTAACTTGAGCTGAG 404739 iv- -- v vv -- i MIR3#SINE/MIR 102 CACTTCACCTC-TCTGGGCCTCAGTTTCCTCATCTGTAAAATGAG--GGG 148 chr6ptel1M 404740 AAAGAAATAG-TAATC-CT----TCCCTCCCAGAATCTTTGATA 404777 ivv i v - i - ---- i --- i i MIR3#SINE/MIR 149 GTTGGACTAGATGATCTCTAAGGTCCCTTCCAG---CTCTGACA 189 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 21.76 CpG sites = 8, Kimura (unadjusted) = 21.76 Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.12 (10 / 85), avg. gap size = 1.40 (14 / 10) 217 25.91 0.00 18.75 chr6ptel1M 404707 404801 (595199) MIRb#SINE/MIR 124 203 (65) m_b281s601i63 11311 chr6ptel1M 404707 GCCTCAGTTTCCTCATATGTAACTTGAGCTGAGAAAGAAATAGTAATCCT 404756 v vv ---------- ii i v i MIRb#SINE/MIR 124 GCCTCAGTTTCCTCATCTGTAAAATG----------GGGATAATAATACC 163 chr6ptel1M 404757 TCCCTCCCAGAATCTTTGATAAGAATATTCCAAATGAAACTATGC 404801 v v ii iv - i i ----i i iv MIRb#SINE/MIR 164 TACCTCGCAGGGTTGTTG-TGAGGAT----TAAATGAGATAATGC 203 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.12 CpG sites = 12, Kimura (unadjusted) = 31.12 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.16 (15 / 94), avg. gap size = 1.00 (15 / 15) 630 24.88 0.99 0.99 chr6ptel1M 404815 405017 (594983) L1ME3G_3end#LINE/L1 345 547 (377) m_b281s551i2 11312 chr6ptel1M 404815 AAACTGTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGATTATATCC 404864 v i i i vii v ? ?v v L1ME3G_3end#L 345 AAAATGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCC 394 chr6ptel1M 404865 CAAAGAGATTAT-AAAGAAG-GGAAAGGGACCTGTATGTGCATGAATGTT 404912 i ? i vv -iv v v - v v i --? i i v i L1ME3G_3end#L 395 TANAGAAATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTT 442 chr6ptel1M 404913 TGTGGCAGCCCTGTTTGTAGTGGCTAAAAACTGGAAACTGAATGGATGTC 404962 ii v vi i i v i vivv ii L1ME3G_3end#L 443 CATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTC 492 chr6ptel1M 404963 CATCAGTTGGAGAATGGCTGAATAAATTGTGGTATATGAATATTATGGAA 405012 i v i i i i vv i L1ME3G_3end#L 493 CATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAA 542 chr6ptel1M 405013 TATTA 405017 i L1ME3G_3end#L 543 TACTA 547 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 30.03 CpG sites = 28, Kimura (unadjusted) = 31.52 Transitions / transversions = 1.27 (28/22) Gap_init rate = 0.02 (4 / 202), avg. gap size = 1.00 (4 / 4) 352 29.96 3.62 3.25 chr6ptel1M 404825 405100 (594900) L1MC4a_3end#LINE/L1 356 632 (1997) m_b281s551i3 11312 chr6ptel1M 404825 TACCCTTTGATCCAGCAGTGTTACTACTGGGATTATATCCCAAAGAGATT 404874 i i vii v i v v i ii --- L1MC4a_3end#L 356 TACCCTTTGACCCAGCAATCCCACTTCTAGGAATTTACCCTGAAGA---T 402 chr6ptel1M 404875 ATA-----AAGAAG-GGAAAGGGACCTGTATGTGCATGAATGTTTGTGGC 404918 i ----- v v -iv iv? --i ii v iv i ii v L1MC4a_3end#L 403 ACACCTCCAACATGTACAAAATNAC--ATATGCACAAGGTTATTCATTGC 450 chr6ptel1M 404919 AGCCCTGTTTGTAGTGGCTAAAAACTGGAAACTGAATGGATGTCCATCAG 404968 vi i v v v i vivv ii i ??i L1MC4a_3end#L 451 AGCATTGTTTGTAATTGCAAAATATTGGAAACAACCTAAATGCCCATNNA 500 chr6ptel1M 404969 TTGGAGAATGGCTGAATAAATTGTGGTATATGAATATTATGGAATATTAC 405018 v ? i i i i vv i iv i i - L1MC4a_3end#L 501 TAGGAGANTGGTTGAATAAACTATGGTACATCCACACAATGGAGTACTA- 549 chr6ptel1M 405019 TGT-TCTGTAAGAAATGACCAACAGGATGATTTC-AGAAA--GGCCTGGA 405064 i-v i - -- vv v i - vi -- iiv L1MC4a_3end#L 550 TGCAGCTGTAAAAAA-GA--ATGAGGAAGATCTCTATGAACTGATATGGA 596 chr6ptel1M 405065 GAGACTTACACGAACTGATGCTGAGTGAAATGAGCA 405100 v i v v vv iv i i vi L1MC4a_3end#L 597 GTGATTTCCAGGATATATTGTTAAGTGAAAAAAGCA 632 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.98 CpG sites = 45, Kimura (unadjusted) = 39.98 Transitions / transversions = 1.29 (45/35) Gap_init rate = 0.05 (14 / 275), avg. gap size = 1.36 (19 / 14) 362 26.56 4.48 4.48 chr6ptel1M 404899 405099 (594901) L1MC1_3end#LINE/L1 433 633 (447) m_b281s551i5 11312 chr6ptel1M 404899 TGTGCATGAATGTTTGTGGCAGCCCTGTTTGTAGTGGCTAAAAACTGGAA 404948 ii i i i i ii i ii i v i vi L1MC1_3end#LI 433 TGCACACGGATGTTTATAGCAGCTTTATTCATAATTGCCAAAACTTGGAA 482 chr6ptel1M 404949 ACTGAAT--GGATGTCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTA 404996 i -- i--i v v v v i i L1MC1_3end#LI 483 GC--AACCAAGATGTCCTTCAGTAGGTGAATGGATAAATAAACTGTGGTA 530 chr6ptel1M 404997 TATGAATATTATGGAATATTACT--GTTCT-GTAAGAAATGA-CCAACAG 405042 i vv v iv i -- iv -iv - i v i L1MC1_3end#LI 531 CATCCAGACAATGGAATATTATTCAGCGCTAAAAAGAAATGAGCTATCAA 580 chr6ptel1M 405043 G--ATGATTTCAGAAAGGCCTGGA-GAGACTTACACGAACTGATGCTGAG 405089 -- ------ i v - i v i v - iv i i L1MC1_3end#LI 581 GCCATGA------AAAGACATGGAGGAAACTTAAATGCA-TATTACTAAG 623 chr6ptel1M 405090 TGAAATGAGC 405099 vi L1MC1_3end#LI 624 TGAAAGAAGC 633 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 32.32 CpG sites = 33, Kimura (unadjusted) = 33.96 Transitions / transversions = 1.83 (33/18) Gap_init rate = 0.07 (15 / 200), avg. gap size = 1.20 (18 / 15) 403 26.73 0.00 2.29 chr6ptel1M 404899 405032 (594968) L1MB8_3end#LINE/L1 433 563 (362) m_b281s551i4 11312 chr6ptel1M 404899 TGTGCATGAATGTTTGTGGCAGCCCTGTTTGTAGTGGCTAAAAACTGGAA 404948 i i ii i vi i ii i i i v L1MB8_3end#LI 433 TGTACACGAATGTTCATAGCAGCATTATTCATAATAGCCAAAAAGTGGAA 482 chr6ptel1M 404949 ACTGAATGGATGTCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATA 404998 vivviii ii iv v i v L1MB8_3end#LI 483 ACAACCCAAATGTCCATCAACTGATGAATGGATAAATAAAATGTGGTATA 532 chr6ptel1M 404999 TGAATATTATGGAATATTACTGTTCTGTAAGAAA 405032 vv iv --- v i v L1MB8_3end#LI 533 TCCATACAATGGAATATTA---TTCGGCAATAAA 563 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 32.89 CpG sites = 22, Kimura (unadjusted) = 34.09 Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.02 (3 / 133), avg. gap size = 1.00 (3 / 3) 205 11.11 2.78 0.00 chr6ptel1M 406026 406061 (593939) MIR3#SINE/MIR 165 201 (7) m_b281s601i64 11313 chr6ptel1M 406026 TCCAAGGTCCCTTC-AGCACTGACAGTCTGTGATTCT 406061 i - v v i MIR3#SINE/MIR 165 TCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCT 201 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 12.06 CpG sites = 2, Kimura (unadjusted) = 12.06 Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) 277 22.59 14.81 1.64 chr6ptel1M 406716 406823 (593177) MIRc#SINE/MIR 36 157 (111) m_b281s601i65 11314 chr6ptel1M 406716 TTAGATTCAG--AGACTTGGGTTCGA--CCTGGCTGTGCC---CACAA-- 406756 i v -- i -- i v ---i v -- MIRc#SINE/MIR 36 TTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGC 85 chr6ptel1M 406757 -GTGTGACTTTCAAGAAGC--CTT---TTCTC-GGGCTTCAGTTGTGTAC 406799 - i viiv i-- ---i - i i viv vv MIRc#SINE/MIR 86 TGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCA 135 chr6ptel1M 406800 TCTGTAAATAAGAGAGATAATAAT 406823 -- vi i MIRc#SINE/MIR 136 TCTGTAA--AATGGGGATAATAAT 157 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.12 CpG sites = 14, Kimura (unadjusted) = 27.42 Transitions / transversions = 1.40 (14/10) Gap_init rate = 0.09 (10 / 107), avg. gap size = 1.80 (18 / 10) 181 18.18 0.00 0.00 chr6ptel1M 406909 406941 (593059) C MIR#SINE/MIR (119) 143 111 m_b281s601i66 11315 chr6ptel1M 406909 CCATTTTACAGAGAGGGAGACTGATTCACAGAG 406941 vii i vv C MIR#SINE/MIR 143 CCATTTTACAGATGAGGAAACTGAGGCACAGAG 111 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 20.94 CpG sites = 3, Kimura (unadjusted) = 20.94 Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 310 25.46 8.77 8.14 chr6ptel1M 407267 407437 (592563) C MIR1_Amn#SINE/MIR (1) 229 58 m_b281s601i67 11316 chr6ptel1M 407267 TACTAATAACTGGTGTTCATATGGCACTTTAAA--AACACGATCTC---- 407310 v v i ivi i i i vv -- ii - ---- C MIR1_Amn#SINE 229 TAATAATACCTAGCTCTTATGTAGCACTTTTCATCAGTA-GATCTCAAAG 181 chr6ptel1M 407311 --CTTTAGTGAGCCTGTGAGG-CAATTCTGCTATTCTCCAGATTGTACAG 407357 -- vvi ----- - i viiii i i --- v C MIR1_Amn#SINE 180 CACTTTACAAAG-----GAGGTCAGTATCATTATCCCC---ATTTTACAG 139 chr6ptel1M 407358 AGGAGGAAACTGAGAATCAGCTCACATTGATTAAGTGACTTG-CCAACAT 407406 v ----- ? v vv i ? - vi C MIR1_Amn#SINE 138 ATGAGGAAACTGAG-----GCNCAGAGAGGTNAAGTGACTTGCCCAAGGT 94 chr6ptel1M 407407 CA-----CAAACTAGAGGAGGAGTCAGGATTCAAAC 407437 ----- ?ii ? v vi i i ? ?i C MIR1_Amn#SINE 93 CACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAAC 58 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.50 CpG sites = 24, Kimura (unadjusted) = 33.52 Transitions / transversions = 1.50 (24/16) Gap_init rate = 0.12 (20 / 170), avg. gap size = 1.45 (29 / 20) 395 23.35 10.14 4.49 chr6ptel1M 407290 407437 (592563) C MIRb#SINE/MIR (54) 214 59 m_b281s601i68 11316 chr6ptel1M 407290 GCACTTTAAAAACACGATCTCCTTTAGT---------GAGCCTGTGAGGC 407330 i v vi iv v i ---------i v i i C MIRb#SINE/MIR 214 GCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGT 165 chr6ptel1M 407331 AATTCTGCTATTCTCCAGATTGTACAGAGGAGGAAACTGAGAATCAGCTC 407380 iv v -- v vv v v ----- C MIRb#SINE/MIR 164 AGGTAT--TATTATCCCCATTTTACAGATGAGGAAACTGAG-----GCTC 122 chr6ptel1M 407381 ACATTGATTAAGTGACTTG-CCAACATCACA-AACTAG--AGGAG--GAG 407424 v vv i i - vi - i -- vi -- C MIRb#SINE/MIR 121 AGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAG 72 chr6ptel1M 407425 TCAGGATTCAAAC 407437 i i i C MIRb#SINE/MIR 71 CCGGGATTCGAAC 59 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.48 CpG sites = 16, Kimura (unadjusted) = 28.25 Transitions / transversions = 0.94 (16/17) Gap_init rate = 0.08 (12 / 147), avg. gap size = 1.83 (22 / 12) 243 31.46 2.25 0.00 chr6ptel1M 407922 408010 (591990) L2d2_3end#LINE/L2 180 270 (285) m_b282s601i2 11317 chr6ptel1M 407922 CTATCTGTCAAAATGCCTCCTTTCCTTTAAGGTCTAATTCAGGTACT-TA 407970 i i i v v iv iv i i i ii ii ? i-iv L2d2_3end#LIN 180 CCACCTATCCAAATCCTACCCATCCTTCAAGGCCCAGCTCAAATNCCACC 229 chr6ptel1M 407971 TCTTGCAAGAAACATTCCCTGACCTC-CCAGCTGGCAGTGA 408010 i v iv i v v - iv ? L2d2_3end#LIN 230 TCCTCCGTGAAGCCTTCCCTGACCACTCCAGCCCGNAGTGA 270 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 42.00 CpG sites = 18, Kimura (unadjusted) = 44.15 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.02 (2 / 88), avg. gap size = 1.00 (2 / 2) 21 14.50 1.64 6.90 chr6ptel1M 408245 408305 (591695) (CTTTCC)n#Simple_repeat 1 58 (0) m_b282s252i0 11318 chr6ptel1M 408245 CTTGCCTCTCTTCCCTTTTCCCCTTTCCCATT-TCTTTCCCTTTCTCTTT 408293 v - - - - v -i i (CTTTCC)n#Sim 1 CTTTCC-CT-TTCCC-TTT-CCCTTTCCCTTTCCCTTTCCCTTTCCCTTT 46 chr6ptel1M 408294 CCATTCTCCTTT 408305 v ii (CTTTCC)n#Sim 47 CCCTTTCCCTTT 58 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.08 (5 / 60), avg. gap size = 1.00 (5 / 5) 278 20.37 0.00 0.00 chr6ptel1M 408308 408361 (591639) C L2d_3end#LINE/L2 (4) 512 459 m_b282s601i3 11319 chr6ptel1M 408308 TCAATCAACAAACATGTAGTTACTGAGCATTTACTATGTGCTGGGTACTG 408357 iv v v i iii vi i C L2d_3end#LINE 512 TCAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTG 463 chr6ptel1M 408358 TGCT 408361 C L2d_3end#LINE 462 TGCT 459 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 21.84 CpG sites = 7, Kimura (unadjusted) = 24.28 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 12 0.00 5.26 0.00 chr6ptel1M 409044 409062 (590938) (ATC)n#Simple_repeat 1 20 (0) m_b282s252i2 11320 chr6ptel1M 409044 ATCATCAT-ATCATCATCAT 409062 - (ATC)n#Simple 1 ATCATCATCATCATCATCAT 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.06 (1 / 18), avg. gap size = 1.00 (1 / 1) 423 20.00 1.05 0.00 chr6ptel1M 409200 409294 (590706) MIR#SINE/MIR 49 144 (118) m_b282s601i4 11321 chr6ptel1M 409200 TGAATTCAAATCCAGCCACGGACACTTACTAGCTGTGTGACCCAGGGCAA 409249 ii i v v v v v iv MIR#SINE/MIR 49 TGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 98 chr6ptel1M 409250 GTCACTTAACCT-TTTCTGCCTCTGTTTCCTCCTCTTTCAGATGAG 409294 i - i v v v v v i i MIR#SINE/MIR 99 GTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGG 144 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 22.00 CpG sites = 8, Kimura (unadjusted) = 23.30 Transitions / transversions = 0.73 (8/11) Gap_init rate = 0.01 (1 / 94), avg. gap size = 1.00 (1 / 1) 225 28.12 10.42 0.00 chr6ptel1M 409830 409925 (590075) C MIR3#SINE/MIR (66) 142 37 m_b282s601i5 11322 chr6ptel1M 409830 ATTTTACAGA---AGTTACTGAGGTACTAAGTGGGCAAGTGCCTCGTTGA 409876 ---i vv iv vi v vv v i iiv C MIR3#SINE/MIR 142 ATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCA 93 chr6ptel1M 409877 AGGGCAGATAGC----TAGTGACAGAGCTAGAA--AG-CTCCAAAGCTCC 409919 v v i ---- i ii i -- -vi iiv C MIR3#SINE/MIR 92 AGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGTCTCC 43 chr6ptel1M 409920 TGACTC 409925 C MIR3#SINE/MIR 42 TGACTC 37 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.96 CpG sites = 14, Kimura (unadjusted) = 35.75 Transitions / transversions = 1.08 (14/13) Gap_init rate = 0.04 (4 / 95), avg. gap size = 2.50 (10 / 4) 294 30.10 14.29 0.00 chr6ptel1M 410008 410203 (589797) L3#LINE/CR1 3780 4003 (96) m_b282s601i6 11323 chr6ptel1M 410008 ATTCGAAGGGCTGTC--CTGGCAGA--GACTGGACCTTCTCTGCTTGGC- 410052 i --v v -- i i i vi iv - L3#LINE/CR1 3780 ATTTGAAGGGCTGTCATGTGGAAGAGGGATTAGACTTATTCTGTGTGGCT 3829 chr6ptel1M 410053 CCA-AGGACAAAAGTAGCAACAATGGG-GGAAGCTGCAGACA---AGATT 410097 - i i v v v - i i iv --- L3#LINE/CR1 3830 CCAGAGGGCAGAACTAGGACCAATGGGTGGAAGTTACAGGGAGGCAGATT 3879 chr6ptel1M 410098 GTATCTGGCTAGAAGGCTGCTGTTGTTCAGTGTCAGAGCTGTCCCGGAGT 410147 viiv viv v vv vvv vi v vvi vii i L3#LINE/CR1 3880 TCGGCTCAATATAAGGAAGAACTTTCTAACAATCAGAGCTGTCCAAAAAT 3929 chr6ptel1M 410148 GGAATGGGC------------------GCTTCTGGTCACCAGAGACCTTT 410179 ------------------ i iv ii iiv i L3#LINE/CR1 3930 GGAATGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGTCACTGGAGGTGTTC 3979 chr6ptel1M 410180 AGTCAGAGGCTCCACAATGACTTG 410203 iv vv ii iv L3#LINE/CR1 3980 AAGCAGAGGCTGGATGACCACTTG 4003 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 38.11 CpG sites = 30, Kimura (unadjusted) = 39.04 Transitions / transversions = 1.03 (30/29) Gap_init rate = 0.04 (7 / 195), avg. gap size = 4.00 (28 / 7) 478 30.49 12.23 1.18 chr6ptel1M 411191 411419 (588581) L3#LINE/CR1 3801 4054 (45) m_b282s601i7 11324 chr6ptel1M 411191 AAGAAAGATTAAATTTGTTCAGTCTTGCTCCAGAGGGTAGAACCAAAAGA 411240 ii i i i v v v i i ii vv L3#LINE/CR1 3801 AAGAGGGATTAGACTTATTCTGTGTGGCTCCAGAGGGCAGAACTAGGACC 3850 chr6ptel1M 411241 AATTGAAGAAAGTTACAAAGAA--AGA-----GTTTAGTATAAAGACATA 411283 v iv i ii i-- ----- i i i i viv L3#LINE/CR1 3851 AATGGGTGGAAGTTACAGGGAGGCAGATTTCGGCTCAATATAAGGAAGAA 3900 chr6ptel1M 411284 CTTCCCAATAAT---------------ATGAGATG---TGTTTTGGGGAG 411315 i i i --------------- ii --- ii i ? ii L3#LINE/CR1 3901 CTTTCTAACAATCAGAGCTGTCCAAAAATGGAATGGGCTGCCTCGNGAGG 3950 chr6ptel1M 411316 AGGTGAATGTTCCTCCTTCTTGAAGATCTTCCAAACAGAGGATGGACATC 411365 vi -- i i v ivi i i v - i v iiv L3#LINE/CR1 3951 TAGTGA--GCTCCCCGTCACTGGAGGTGTT-CAAGCAGAGGCTGGATGAC 3997 chr6ptel1M 411366 CACTTGTCAATACGGTTGCAGTGAGGATTCCTT--TTGGGTATGA-TTTA 411412 ivivv i vii v-- i iv -v i L3#LINE/CR1 3998 CACTTGTCAGGGATGTTGTAGAAGGGATTCCTGCATTGGATGGGAGGTTG 4047 chr6ptel1M 411413 GACTAGA 411419 L3#LINE/CR1 4048 GACTAGA 4054 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 40.86 CpG sites = 47, Kimura (unadjusted) = 41.68 Transitions / transversions = 2.14 (47/22) Gap_init rate = 0.04 (9 / 228), avg. gap size = 3.44 (31 / 9) 16 22.20 1.79 3.64 chr6ptel1M 412028 412083 (587917) (AATGAG)n#Simple_repeat 1 55 (0) m_b282s252i3 11325 chr6ptel1M 412028 AATAAAAATAAAATATGACCATGATAATGA-AATGAAGAATAAGAATCAG 412076 i i i i - vv v - - i v (AATGAG)n#Sim 1 AATGAGAATGAGA-ATGAGAATGAGAATGAGAATG-AGAATGAGAATGAG 48 chr6ptel1M 412077 AAGGAGA 412083 v (AATGAG)n#Sim 49 AATGAGA 55 Matrix = Unknown Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.05 (3 / 55), avg. gap size = 1.00 (3 / 3) 251 26.37 12.09 0.00 chr6ptel1M 412807 412897 (587103) C L3#LINE/CR1 (83) 4016 3915 m_b282s601i8 11326 chr6ptel1M 412807 ATAACTTCCCAAGCAAATAGTTATTCAGACCCTGCG-GAAGAC-TACAGT 412854 i v vii i i i i v i v- v - v C L3#LINE/CR1 4016 ACAACATCCCTGACAAGTGGTCATCCAGCCTCTGCTTGAACACCTCCAGT 3967 chr6ptel1M 412855 GACAGGAAACTTCCTGCCTCT---------CCATTTCAGATTCGGACAGC 412895 i i i iv i ?--------- i vv i C L3#LINE/CR1 3966 GACGGGGAGCTCACTACCTCNCGAGGCAGCCCATTCCATTTTTGGACAGC 3917 chr6ptel1M 412896 TC 412897 C L3#LINE/CR1 3916 TC 3915 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 32.24 CpG sites = 15, Kimura (unadjusted) = 33.98 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.03 (3 / 90), avg. gap size = 3.67 (11 / 3) 247 19.23 1.92 0.00 chr6ptel1M 413032 413083 (586917) C MIRc#SINE/MIR (204) 64 12 m_b282s601i9 11327 chr6ptel1M 413032 GACTTGGACCCAGGCCTTC-TGAATCCAAGTGCATCATTCTTTCCACTAC 413080 i i i - v v viii i C MIRc#SINE/MIR 64 GACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGC 15 chr6ptel1M 413081 ACC 413083 C MIRc#SINE/MIR 14 ACC 12 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 20.35 CpG sites = 7, Kimura (unadjusted) = 22.86 Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.02 (1 / 51), avg. gap size = 1.00 (1 / 1) 307 31.37 2.16 5.97 chr6ptel1M 413627 413765 (586235) C MIR3#SINE/MIR (37) 171 38 m_b282s601i10 11328 chr6ptel1M 413627 CTTTAGAGACCATTTAGTCCAATCCCATTTTTTTTTCCAAAGGTAAAGAA 413676 i i i i v iv ---- v i i i C MIR3#SINE/MIR 171 CCTTAGAGATCATCTAGTCCAACCCCCTCATTTT----ACAGATGAGGAA 126 chr6ptel1M 413677 ACTAAGTTCATGAGAATAGAAATCAGTTGACTAAGGTCCCATGACTAGTC 413726 i vi vv ivv i v v v i v iii ? i C MIR3#SINE/MIR 125 ACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGCNAGTT 76 chr6ptel1M 413727 ATTTGTAGAA--GGGATGGTTTGAAGCTCAGG-GTTCTGATT 413765 v v i i-- ----i ii i i -v i i C MIR3#SINE/MIR 75 AGTGGCAGAGCCGGGA----CTAGAACCCAGGTCTCCTGACT 38 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 42.78 CpG sites = 26, Kimura (unadjusted) = 42.78 Transitions / transversions = 1.73 (26/15) Gap_init rate = 0.07 (10 / 138), avg. gap size = 1.10 (11 / 10) 357 24.05 7.27 1.72 chr6ptel1M 414782 414891 (585109) MIRc#SINE/MIR 131 246 (22) m_b282s601i11 11329 chr6ptel1M 414782 CCATATCTGAGAAATGGGGATA--AGGACCCATTCTACCCCTCCCCCATG 414829 vi vi -- iv iiii i-- v i ii MIRc#SINE/MIR 131 CCTCATCTGTAAAATGGGGATAATAATACCTGCCCTG--CCTACCTCACA 178 chr6ptel1M 414830 GGATTTTTGTGAGGAT----TGAAATAA--TATGTGAAAGTACTTTGTAA 414873 i v ---- i -- ii MIRc#SINE/MIR 179 GGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTTTGTAA 228 chr6ptel1M 414874 AATGTATAAAACTATATA 414891 v v ivi i MIRc#SINE/MIR 229 ACTGTAAAGTGCTATACA 246 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 28.63 CpG sites = 18, Kimura (unadjusted) = 30.17 Transitions / transversions = 2.25 (18/8) Gap_init rate = 0.05 (5 / 109), avg. gap size = 2.00 (10 / 5) 489 13.04 9.78 0.00 chr6ptel1M 416107 416198 (583802) Charlie4a#DNA/hAT-Charlie 352 452 (56) m_b282s502i0 11330 chr6ptel1M 416107 TTAATATTTTG---------TTTCACTACAATTGGTTTTCTTGGTAATCC 416147 --------- v i i v Charlie4a#DNA 352 TTAATATTTTGATAACTGTATTTCAATATAATTGGTTTCCTTTGTAATCC 401 chr6ptel1M 416148 TATGCATTTTATTGTATGCATTTAACAATATTATTCTGAGAAACAGCCCA 416197 i v v i ivi i Charlie4a#DNA 402 TATGTATTTTATTTTATGCATTTAAAAACATTATTCTGAGAAGGGGTCCA 451 chr6ptel1M 416198 T 416198 Charlie4a#DNA 452 T 452 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 14.44 CpG sites = 7, Kimura (unadjusted) = 14.44 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.01 (1 / 91), avg. gap size = 9.00 (9 / 1) 195 26.79 0.00 0.00 chr6ptel1M 416255 416310 (583690) MIRc#SINE/MIR 212 267 (1) m_b282s601i12 11331 chr6ptel1M 416255 GTGGAAGCCCATTGTTAACTGTAAAATGTCATATGAATATAAGTTCCTGT 416304 i v v v i ii ii i v?vi i MIRc#SINE/MIR 212 GTGAAAGCGCTTTGTAAACTGTAAAGTGCTATACAAATGTAAGGNGTTAT 261 chr6ptel1M 416305 TAGTAT 416310 v MIRc#SINE/MIR 262 TATTAT 267 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 34.82 CpG sites = 9, Kimura (unadjusted) = 34.82 Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0) 217 34.90 0.88 9.52 chr6ptel1M 416447 416560 (583440) L2d2_3end#LINE/L2 440 544 (11) m_b282s601i13 11332 chr6ptel1M 416447 TGTATGCTCCTTAAGT-CAGGATCTGTTTTTTGTATTCCCCATCTCATCT 416495 v i v- iv ii v i i i ---------- L2d2_3end#LIN 440 TGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACT----------TCT 479 chr6ptel1M 416496 TTGTATTCTACATGAAACCTAATACAGGATCCTACACACAATAGAAATTC 416545 i iv iiivi ii vii i i i ivii L2d2_3end#LIN 480 TTGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAGTAGGCGCTC 529 chr6ptel1M 416546 ACTGCCTGTTTGTTG 416560 v ivv i L2d2_3end#LIN 530 AATAAATATTTGTTG 544 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 46.08 CpG sites = 25, Kimura (unadjusted) = 50.10 Transitions / transversions = 2.27 (25/11) Gap_init rate = 0.10 (11 / 113), avg. gap size = 1.00 (11 / 11) 351 24.00 0.00 0.00 chr6ptel1M 416836 416910 (583090) MIRc#SINE/MIR 113 187 (81) m_b282s601i14 11333 chr6ptel1M 416836 CTGTCTGAACCTGAAATTCCTCCTTTGTAAAATGGAGATACTAACATTTG 416885 v i v iv v i i v i ii MIRc#SINE/MIR 113 CTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTG 162 chr6ptel1M 416886 CTCTACCTAACTTAAAGGGTTATTG 416910 i i v i v i MIRc#SINE/MIR 163 CCCTGCCTACCTCACAGGGTTGTTG 187 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 29.61 CpG sites = 11, Kimura (unadjusted) = 29.61 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.00 (0 / 74), avg. gap size = 0.0 (0 / 0) 21 13.05 9.86 2.63 chr6ptel1M 416935 417005 (582995) (CCTCTT)n#Simple_repeat 1 76 (0) m_b282s252i4 11334 chr6ptel1M 416935 CCTACTTCTCCTTCC-CTTACTCTT-C-C-TCCTCTCCCTCATCCTCTAT 416980 - ii - v - - - i v - (CCTCTT)n#Sim 1 CCT-CTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCT-T 48 chr6ptel1M 416981 ACTC--CCTC-CCCCCTTCCTCTTCCTC 417005 v -- -i i (CCTCTT)n#Sim 49 CCTCTTCCTCTTCCTCTTCCTCTTCCTC 76 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.11 (8 / 70), avg. gap size = 1.12 (9 / 8) 510 28.39 3.68 0.60 chr6ptel1M 420237 420399 (579601) C MIRc#SINE/MIR (64) 204 37 m_b282s601i15 11335 chr6ptel1M 420237 ATCTGATTGGATTCTCA-----ACCCTGGGTTGGGAGGTAGGAT-GCTAT 420280 v v i ----- v v- v i ii- v C MIRc#SINE/MIR 204 ATCTCATTTGATCCTCACAACAACCCTGTGA-GGTAGGCAGGGCAGGTAT 156 chr6ptel1M 420281 TATTATTCCCATTTGATAGAGGAGGAAACTGAGGCAAACAGCATTTCAGT 420330 i v i v vv v viv v C MIRc#SINE/MIR 155 TATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGT 106 chr6ptel1M 420331 AATGCCCCTGGGGTCACAGAGCTAGTTAGTGACAGAGGCCACATCTGAAC 420380 i iviv iii v v i v viv iii C MIRc#SINE/MIR 105 GACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAAC 56 chr6ptel1M 420381 TCAGGGTTTTCCAATTCCA 420399 i vi i ii i C MIRc#SINE/MIR 55 CCAGGTCTTCCTGACTCCA 37 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 35.24 CpG sites = 24, Kimura (unadjusted) = 36.21 Transitions / transversions = 1.09 (24/22) Gap_init rate = 0.02 (3 / 162), avg. gap size = 2.33 (7 / 3) 230 28.95 12.28 0.00 chr6ptel1M 421543 421656 (578344) MIRb#SINE/MIR 40 167 (101) m_b282s601i16 11336 chr6ptel1M 421543 TGGAAGAAGACAGACTTGATTTTGGGTCCCCCTTATCTCATTTTC-AGCT 421591 ivv i iv i ii vvi v vi i v - MIRb#SINE/MIR 40 TGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCT 89 chr6ptel1M 421592 CTATCACCTTCA-TAA------TAA------TGAGCCTCTGTATCCCTAT 421628 v i v vi-i ------ ------ v v ii MIRb#SINE/MIR 90 GTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCAT 139 chr6ptel1M 421629 ATGTAGAATGGGTATAATTATATTTACC 421656 v i v v ii MIRb#SINE/MIR 140 CTGTAAAATGGGGATAATAATACCTACC 167 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 35.72 CpG sites = 17, Kimura (unadjusted) = 37.10 Transitions / transversions = 1.06 (17/16) Gap_init rate = 0.04 (4 / 113), avg. gap size = 3.50 (14 / 4) 201 23.16 0.00 6.15 chr6ptel1M 421610 421678 (578322) MIR1_Amn#SINE/MIR 120 184 (46) m_b282s601i17 11336 chr6ptel1M 421610 TGAGCCTCTGTATCCCTATATGTAGAATGGGTATAATTATATTTACCCTT 421659 ? v v ii v i v v i v - i MIR1_Amn#SINE 120 TGNGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATGATACTGA-CCTC 168 chr6ptel1M 421660 CTAGACTGAAAAGCACTTT 421678 ---i v ii MIR1_Amn#SINE 169 CT---TTGTAAAGTGCTTT 184 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 28.44 CpG sites = 8, Kimura (unadjusted) = 28.44 Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.06 (4 / 68), avg. gap size = 1.00 (4 / 4) 585 30.68 0.00 1.84 chr6ptel1M 421788 421953 (578047) C MIR3#SINE/MIR (9) 199 37 m_b282s601i18 11337 chr6ptel1M 421788 AATTATAGAATATTAGAATTGGAAAAAAAAACCATAGAAATCATCTATTC 421837 i i i ii iii --- v i v C MIR3#SINE/MIR 199 AATCATAGAATGTCAGAGCTGGAAGGGA---CCTTAGAGATCATCTAGTC 153 chr6ptel1M 421838 CTGTCTCCTCATTTTTCCAAAGAGAAAATTGAAGCCCCAAGAGGAAGAGA 421887 vii i v vi v i i i vi vii v C MIR3#SINE/MIR 152 CAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGT 103 chr6ptel1M 421888 AACTGGTTCAATATCATACAGTGAGATTCTGATGGACTTAGAACTAGAAC 421937 i v ii vi i i? v vv iii viii i C MIR3#SINE/MIR 102 GACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAAC 53 chr6ptel1M 421938 CTGGGTCTTCTGACTC 421953 ii i C MIR3#SINE/MIR 52 CCAGGTCTCCTGACTC 37 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 41.03 CpG sites = 35, Kimura (unadjusted) = 42.31 Transitions / transversions = 2.33 (35/15) Gap_init rate = 0.02 (3 / 165), avg. gap size = 1.00 (3 / 3) 314 34.40 2.40 0.00 chr6ptel1M 421843 421967 (578033) C MIRc#SINE/MIR (118) 150 23 m_b282s601i19 11337 chr6ptel1M 421843 TCCTCATTTTTCCAAAGAGAAAATTGAAGCCCCAAGAGGAAGAGAAACTG 421892 i v vi v i i i i vi vvi vi v C MIRc#SINE/MIR 150 TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTT 101 chr6ptel1M 421893 GTTCAATATCATACAGTGAGATTCTGATGGACTTAGAACTAGAACCTGGG 421942 ii vi i iv vvvv iii viii i v ii C MIRc#SINE/MIR 100 GCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGG 51 chr6ptel1M 421943 TCTT-CTGACTC--ACTCCAATACTGTT 421967 - -- v i i v C MIRc#SINE/MIR 50 TCTTCCTGACTCCAAGTCCAGTGCTCTT 23 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 46.03 CpG sites = 25, Kimura (unadjusted) = 47.76 Transitions / transversions = 1.39 (25/18) Gap_init rate = 0.02 (2 / 124), avg. gap size = 1.50 (3 / 2) 275 34.21 1.72 1.72 chr6ptel1M 421985 422100 (577900) C L2d2_3end#LINE/L2 (13) 542 427 m_b282s601i20 11338 chr6ptel1M 421985 ATAAATATTCATTAGATAGTTACTGAGTGCAGAGCACTGGGTGGCTGATG 422034 i i iiiiivi v ii -- viv ii C L2d2_3end#LIN 542 ACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTG--TGCTAGGCG 495 chr6ptel1M 422035 AGGTGGGGAATAGAAA--ACTATAAAGCCTGGCTATTACCCTCCTGGAGC 422082 vv i v -- v ii v iivi i vv C L2d2_3end#LIN 494 CTGTGGGGGATACAAAGAAGTATAAGACATGGTCCCTGCCCTCAAGGAGC 445 chr6ptel1M 422083 TTACGGTCCGATAGTGGA 422100 ii iii v v C L2d2_3end#LIN 444 TTACAATCTAGTTGGGGA 427 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 44.59 CpG sites = 25, Kimura (unadjusted) = 48.26 Transitions / transversions = 1.79 (25/14) Gap_init rate = 0.03 (3 / 115), avg. gap size = 1.33 (4 / 3) 211 35.20 2.36 1.56 chr6ptel1M 422472 422598 (577402) C L2d_3end#LINE/L2 (222) 294 167 m_b282s601i21 11338 chr6ptel1M 422472 ATGGGAAGTCTGAGCAAGGCAAGCTCATTTCCAGTTGACAAGAGTCAAGG 422521 i iv v v i vi v v vivi i i- ivi i C L2d_3end#LINE 294 ATAGGAGTTCAGAGAAGGGAGAGATCAGTGTGGGCTGG-AGTGGTCAGGG 246 chr6ptel1M 422522 AAGATTTCTTGCAGGAGGTAG--CTTTGGATACACTCTTGAAGAATGATT 422569 ii v v i -- vi v ivi - i iv C L2d_3end#LINE 245 AAGGCTTCGTGGAGGAGGTGGGACTTGAGCTGGGC-CTTGAAGGATGGGT 197 chr6ptel1M 422570 AAGAATTCAATGGAGGAAGA-CAGGAGGAA 422598 i v vi i ii -v i i C L2d_3end#LINE 196 AGGATTTGGATAGAGAGAGAGGAAGGGGAA 167 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 49.54 CpG sites = 26, Kimura (unadjusted) = 49.54 Transitions / transversions = 1.44 (26/18) Gap_init rate = 0.03 (4 / 126), avg. gap size = 1.25 (5 / 4) 212 29.75 4.65 2.27 chr6ptel1M 422513 422598 (577402) C L2c_3end#LINE/L2 (225) 253 166 m_b282s601i22 11338 chr6ptel1M 422513 GAGTCAAGGAAGATTTCTTGCAGGAGGTAGC-TTTGGATACACTCTTGAA 422561 i i ii ii v ii - i iiivv v? C L2c_3end#LINE 253 GGGTCAGGGAAGGCTTCCCGGAGGAGGTGACATCTGAGCTGAGNCTTGAA 204 chr6ptel1M 422562 GAATGATTAAGAATT---CAATGGAGGAAGACAGGAGGAA 422598 i v i i --- -- v ivi i C L2c_3end#LINE 203 GGATGAGTAGGAGTTAGCCA--GGTGGAAGGAGGGGGGAA 166 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 38.92 CpG sites = 18, Kimura (unadjusted) = 41.12 Transitions / transversions = 2.57 (18/7) Gap_init rate = 0.05 (4 / 85), avg. gap size = 1.50 (6 / 4) 255 29.71 11.38 1.48 chr6ptel1M 422679 422801 (577199) MIR3#SINE/MIR 61 195 (13) m_b282s601i23 11339 chr6ptel1M 422679 CTCAGCTTCTGCT--TAACTGAATGTGTGATTCT--------TATTTAAC 422718 i i - i-- ?iv iii --------i i v MIR3#SINE/MIR 61 CCCGGCT-CTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCAC 109 chr6ptel1M 422719 TACTTTAGGTTTTAGTCACC-CATCTCTAAAAGGAGGGGGTCAGATTAGA 422767 iv i i ii i iv - v v ii i MIR3#SINE/MIR 110 CTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGA 159 chr6ptel1M 422768 TCTTCTC--AGACACTCTTCCAATCTTAAC-TTCCAT 422801 vv -- ii- i iiii i - i MIR3#SINE/MIR 160 TGATCTCTAAGGT-CCCTTCCAGCTCTGACATTCTAT 195 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 40.10 CpG sites = 28, Kimura (unadjusted) = 41.68 Transitions / transversions = 3.50 (28/8) Gap_init rate = 0.06 (7 / 122), avg. gap size = 2.29 (16 / 7) 13 7.79 3.45 3.45 chr6ptel1M 423328 423356 (576644) (TCTCC)n#Simple_repeat 1 29 (0) m_b282s252i5 11340 chr6ptel1M 423328 TCT-CTTTCCTCTCCTCTCCTCTACTACTC 423356 - i v - (TCTCC)n#Simp 1 TCTCCTCTCCTCTCCTCTCCTCTCCT-CTC 29 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.07 (2 / 28), avg. gap size = 1.00 (2 / 2) 267 15.71 10.43 0.43 chr6ptel1M 423421 423631 (576369) HERVIP10FH#LTR/ERV1 777 1008 (4094) m_b282s701i0 11341 chr6ptel1M 423421 CTGGCAGAGA---GGAAGGA---G-AGAGAGAGACAAAAAAAGAGAAAGA 423463 i--- i --- - ii vi i i i HERVIP10FH#LT 777 CTGGCAGAGGCAGGGAAAGACCAGCAGAGAGGAAAGAGAGAAGAGAGAGA 826 chr6ptel1M 423464 GAGAGAGAAAAGACAGAGAGAG-GAGAGATAGAGAGAGAGAGAGATAGAG 423512 i i - - v i v HERVIP10FH#LT 827 GAGAGAGAGAGGA-AGAGAGAGAGAGAGAAAGAGAGAGAGAGGGAGAGAG 875 chr6ptel1M 423513 ATAGAGAGAGAGAGAGATAGAGATAGAGAGAG--AGAGAGAGAGAGAGAG 423560 v v i i vi i v -- ii v HERVIP10FH#LT 876 AGAGACAAAGAGGGAGTCAAAGAGAGAGAGAGGCAGAGAGAGGAAGAGAC 925 chr6ptel1M 423561 AGAGAGATAGAGAGAGAG--AGAGAGAGAGAGAGAG----------AGAG 423598 i i i -- ---------- i HERVIP10FH#LT 926 AGAGAGACAAAGAGGGAGTCAGAGAGAGAGAGAGAGACAGAAAGTCAAAG 975 chr6ptel1M 423599 AGAGAGAGAGAGAGAGAGAGAGAAGTAGTACAG 423631 i i v v HERVIP10FH#LT 976 AGAGAAAGAAAGAGAGAGATAGAAGTAGTAAAG 1008 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 18.01 CpG sites = 23, Kimura (unadjusted) = 18.01 Transitions / transversions = 2.30 (23/10) Gap_init rate = 0.04 (8 / 210), avg. gap size = 2.88 (23 / 8) 426 22.64 0.93 0.93 chr6ptel1M 424327 424433 (575567) C MIR#SINE/MIR (118) 144 38 m_b282s601i24 11342 chr6ptel1M 424327 CTCATTTTACAGATGAGAAACATGAGGGAAACAG-GCTTAAGTGACTTGC 424375 i i vv v v v - v i C MIR#SINE/MIR 144 CCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGC 95 chr6ptel1M 424376 CCAAGGTCACATAGCTAGTAAGTATATGAGGTCAGATTTGAATTGAGAGC 424425 i ivvv vivi i iiv - C MIR#SINE/MIR 94 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAG-GC 46 chr6ptel1M 424426 TGCCTGGC 424433 v i C MIR#SINE/MIR 45 AGTCTGGC 38 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 24.60 CpG sites = 11, Kimura (unadjusted) = 27.07 Transitions / transversions = 0.85 (11/13) Gap_init rate = 0.02 (2 / 106), avg. gap size = 1.00 (2 / 2) 198 27.89 0.00 3.28 chr6ptel1M 424504 424566 (575434) C MIRc#SINE/MIR (75) 193 133 m_b282s601i25 11343 chr6ptel1M 424504 TTCTCAAAACAATCCAGTGAGGTAGGTATCATAAATGTAATTTTCCCCCT 424553 i v i v i vvii ii i v v -- C MIRc#SINE/MIR 193 TCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCC-- 146 chr6ptel1M 424554 ATTTTGCTGATAA 424566 i v i C MIRc#SINE/MIR 145 ATTTTACAGATGA 133 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 35.74 CpG sites = 10, Kimura (unadjusted) = 35.74 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.03 (2 / 62), avg. gap size = 1.00 (2 / 2) 712 27.65 3.15 2.23 chr6ptel1M 424586 424807 (575193) C MIRc#SINE/MIR (27) 241 18 m_b282s601i26 11344 chr6ptel1M 424586 AGTATTTTAGAGTTTGCAAAGTGCTGT-ACACATATTGTGCTACTGGATC 424634 i i v i i v - i i i vii i v C MIRc#SINE/MIR 241 AGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATCTCATTTGATC 192 chr6ptel1M 424635 CTCACAATGATCCTGTTGGGT------GAAAATTATCATTCTCCCCATTG 424678 ii i vi ------ iv iv i v v C MIRc#SINE/MIR 191 CTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTT 142 chr6ptel1M 424679 TACAAATGAAGAAAGTGAGCCTGAGAAAGAGTCAGTGGAATTGCCCAGGC 424728 i i v v v i iv v - v i v C MIRc#SINE/MIR 141 TACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTG-ACTTGCCCAAGG 93 chr6ptel1M 424729 TTACACAATTTTTAAGTGTCTGGGGCAGGATTCAAACTCAGATCTTCCTT 424778 i ii vv v v i v i i i i i - C MIRc#SINE/MIR 92 TCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCC-T 44 chr6ptel1M 424779 AACTCTGATCCCATTATTCTCTTTTCCAC 424807 i ii vi v ii --- C MIRc#SINE/MIR 43 GACTCCAAGTCCAGTGCTC---TTTCCAC 18 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.38 CpG sites = 37, Kimura (unadjusted) = 35.58 Transitions / transversions = 1.61 (37/23) Gap_init rate = 0.03 (7 / 221), avg. gap size = 1.71 (12 / 7) 289 23.33 9.09 2.56 chr6ptel1M 425355 425464 (574536) C MIRb#SINE/MIR (53) 215 99 m_b282s601i27 11345 chr6ptel1M 425355 AGTGCTGTACA--CAGAATGTTACT-GATCCCTACAACAATCCAGTCCAG 425401 i v -- vv v i i -i ii i v ivvi C MIRb#SINE/MIR 215 AGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGG 166 chr6ptel1M 425402 TAGATGGATCATTATCTCCATTTTCCAGAAGA------TGAGGCTAAGAG 425445 i -- i i v v ------ v C MIRb#SINE/MIR 165 TAGGT--ATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAG 118 chr6ptel1M 425446 AGATTAGAATAGCTT-CCCA 425464 i - i i - C MIRb#SINE/MIR 117 AGGTTA-AGTAACTTGCCCA 99 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 25.96 CpG sites = 15, Kimura (unadjusted) = 28.58 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.06 (7 / 109), avg. gap size = 1.86 (13 / 7) 244 17.02 2.13 0.00 chr6ptel1M 426329 426375 (573625) C MIRc#SINE/MIR (104) 164 117 m_b282s601i28 11346 chr6ptel1M 426329 GGAAGGTGCTATTATCTCTATTTCACAGTTGAGAAAACTGAGG-TCAG 426375 v ii i i i v i - C MIRc#SINE/MIR 164 GGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAG 117 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 19.91 CpG sites = 6, Kimura (unadjusted) = 19.91 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.02 (1 / 46), avg. gap size = 1.00 (1 / 1) 34 10.56 5.33 2.60 chr6ptel1M 427512 427586 (572414) (TTGTT)n#Simple_repeat 1 77 (0) m_b282s252i6 11347 chr6ptel1M 427512 TTGTTATTGGGTTGTGTT-TTTT-TTTTGTGTTTG-TTTGTTTTGTTTTG 427558 - vv v - - - - (TTGTT)n#Simp 1 TTGTT-TTGTTTTGTTTTGTTTTGTTTTGT-TTTGTTTTGTTTTGTTTTG 48 chr6ptel1M 427559 TTTTGTTTTTCTTTG-TTTGGTTGGTTTT 427586 vi - v v (TTGTT)n#Simp 49 TTTTGTTTTGTTTTGTTTTGTTTTGTTTT 77 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.08 (6 / 74), avg. gap size = 1.00 (6 / 6) 555 29.34 5.38 2.17 chr6ptel1M 427676 427898 (572102) C MIRb#SINE/MIR (5) 263 34 m_b282s601i29 11348 chr6ptel1M 427676 TGGAG-TGCCATTTATGTAGCATTTATCAAAAGAAACAAG-AGTACACTG 427723 i - i vv ii ii viv v-- i - v iii i C MIRb#SINE/MIR 263 TAGAGCTACCATTTATTGAGCGCTTACTATGTGC--CAGGCACTGTGCTA 216 chr6ptel1M 427724 AAAGCAGTACAT---TTGTCTCACTTGATCCCCACAACAACTTTCTGCAA 427770 iv vv --- i i i i i-- i C MIRb#SINE/MIR 215 AGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACC--CTGCGA 168 chr6ptel1M 427771 TCAGGGCAATAAATAACTCCATTTTACAGTTGAGGAAACTGAGGCTGAGA 427820 vvvi i v v- v i v v C MIRb#SINE/MIR 167 GGTAGGTATTAT-TATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGA 119 chr6ptel1M 427821 GAGGTTAAGAGACTTGTCCAGAATCACATGAATGGTGAATAG------TT 427864 vi i iii iiiv i i i i ------iv C MIRb#SINE/MIR 118 GAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 69 chr6ptel1M 427865 GGATTTGGGCTCA-GTCTTCCTGGCTCCAAGTCCC 427898 i ii i - vi i iv C MIRb#SINE/MIR 68 GGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCC 34 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 35.82 CpG sites = 42, Kimura (unadjusted) = 38.94 Transitions / transversions = 1.91 (42/22) Gap_init rate = 0.05 (10 / 222), avg. gap size = 1.70 (17 / 10) 678 21.68 7.78 0.56 chr6ptel1M 427731 427897 (572103) C MIRc#SINE/MIR (58) 210 32 m_b282s601i30 11348 chr6ptel1M 427731 TACATTTGTCTCACTTGATCCCCACAACAACTTTCTGCAAT---CAGGGC 427777 -i i i ii v vii --- C MIRc#SINE/MIR 210 TACATT-ATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGC 162 chr6ptel1M 427778 A---ATAAATAACTCCATTTTACAGTTGAGGAAACTGAGGCTGAGAGAGG 427824 --- v v v i v v C MIRc#SINE/MIR 161 AGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGG 112 chr6ptel1M 427825 TTAAGAGACTTGTCCAGAATCACATGAATGGTGAATAG------TTGGAT 427868 v i iii iiiv i i i i ------iv i C MIRc#SINE/MIR 111 TTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGAC 62 chr6ptel1M 427869 TTGGGCTCA-GTCTTCCTGGCTCCAAGTCC 427897 i ii i - i C MIRc#SINE/MIR 61 TCGAACCCAGGTCTTCCTGACTCCAAGTCC 32 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 24.89 CpG sites = 26, Kimura (unadjusted) = 26.59 Transitions / transversions = 2.60 (26/10) Gap_init rate = 0.03 (5 / 166), avg. gap size = 2.80 (14 / 5) 292 18.70 4.07 0.00 chr6ptel1M 429498 429620 (570380) C HERVIP10FH#LTR/ERV1 (4105) 997 870 m_b282s701i1 11349 chr6ptel1M 429498 CTGTCTCTCTCTCTCTCTCTCTCTCTGTCTGTCTGTCTCTCTCTCTCTC- 429546 i i i i v v - C HERVIP10FH#LT 997 CTATCTCTCTCTTTCTTTCTCTCTTTGACTTTCTGTCTCTCTCTCTCTCT 948 chr6ptel1M 429547 ----CTTTGTCTCTGTCTCTCTGTCTCTCTCTCTCTCTGTCTGTCTCTCT 429592 ---- iiv i ii i v C HERVIP10FH#LT 947 CTGACTCCCTCTTTGTCTCTCTGTCTCTTCCTCTCTCTGCCTCTCTCTCT 898 chr6ptel1M 429593 CTCTGTCTCTGTATGTGTGTCTGTATCT 429620 i v iv v v v v v C HERVIP10FH#LT 897 CTTTGACTCCCTCTTTGTCTCTCTCTCT 870 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 21.67 CpG sites = 12, Kimura (unadjusted) = 21.67 Transitions / transversions = 1.09 (12/11) Gap_init rate = 0.02 (2 / 122), avg. gap size = 2.50 (5 / 2) 193 22.23 0.00 2.22 chr6ptel1M 430478 430523 (569477) C MIR3#SINE/MIR (22) 186 142 m_b282s601i31 11350 chr6ptel1M 430478 CAGAATATGAAGGCATCTTAGAGATTATCTAGGCTGAACCCCCCCA 430523 iivv v i i v i- i C MIR3#SINE/MIR 186 CAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCC-AACCCCCTCA 142 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 26.86 CpG sites = 6, Kimura (unadjusted) = 26.86 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1) 445 19.09 12.73 0.00 chr6ptel1M 430899 430954 (569046) C MER63D#DNA/hAT-Tip100 (604) 457 388 m_b282s502i1 11351 chr6ptel1M 430899 AAGTTTCATCTGCATCATTAACATTTTCTTAGTCACTTT----AGTCCAG 430944 v i ivi ---- i C MER63D#DNA/hA 457 AAGTTTAATCTGCATTATTAACATTTTCTCCATCACTTTCTTAAGTCTAG 408 chr6ptel1M 430945 CCAGTCCAC----------A 430954 v i v ---------- C MER63D#DNA/hA 407 ACAATCAACAAAACAATAAA 388 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 20.11 CpG sites = 10, Kimura (unadjusted) = 22.37 Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.04 (2 / 55), avg. gap size = 7.00 (14 / 2) 43 0.00 5.08 3.33 chr6ptel1M 430955 431013 (568987) (AAAC)n#Simple_repeat 1 60 (0) c_b282s251i0 11352 chr6ptel1M 430955 AAACAAACAAACAAACAAAACAAA-AAACAAA-AAACAAAACAAACAAAC 431002 - - - - (AAAC)n#Simpl 1 AAACAAACAAACAAAC-AAACAAACAAACAAACAAAC-AAACAAACAAAC 48 chr6ptel1M 431003 AAACAAA-AAAC 431013 - (AAAC)n#Simpl 49 AAACAAACAAAC 60 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.09 (5 / 58), avg. gap size = 1.00 (5 / 5) 445 19.09 12.73 0.00 chr6ptel1M 431014 431066 (568934) C MER63D#DNA/hAT-Tip100 (674) 387 335 m_b282s502i1 11351 chr6ptel1M 431014 CAAGCCCTAGTTTTTAGAGTTTGCTGATTTCTGGGGTATAAAACCTGCCT 431063 ii v v i i v i vv v v C MER63D#DNA/hA 387 CAAGCCCTGATTTGTAGCGTTTGCCGATTTCCGTGGTGTAAATACTCCCA 338 chr6ptel1M 431064 CCA 431066 C MER63D#DNA/hA 337 CCA 335 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 20.11 CpG sites = 10, Kimura (unadjusted) = 22.37 Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 62 0.00 0.00 0.00 chr6ptel1M 431501 431553 (568447) (TA)n#Simple_repeat 1 53 (0) c_b282s251i1 11353 chr6ptel1M 431501 TATATATATATATATATATATATATATATATATATATATATATATATATA 431550 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr6ptel1M 431551 TAT 431553 (TA)n#Simple_ 51 TAT 53 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 17 26.40 3.51 1.72 chr6ptel1M 432079 432135 (567865) (GA)n#Simple_repeat 1 58 (0) m_b282s252i7 11354 chr6ptel1M 432079 GAGAGAGAGAGTTGGGGGGGAGAAAAGGAGGGGGAG-GATACAGACA-AG 432126 -v i i i i ii i i - v v v - (GA)n#Simple_ 1 GAGAGAGAGAG-AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 49 chr6ptel1M 432127 AGAGAGAGA 432135 (GA)n#Simple_ 50 AGAGAGAGA 58 Matrix = Unknown Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.05 (3 / 56), avg. gap size = 1.00 (3 / 3) 21 15.62 3.92 0.00 chr6ptel1M 432146 432171 (567829) (AAGG)n#Simple_repeat 1 27 (26) m_b282s252i8 11354 chr6ptel1M 432146 AAGGGA-GAGGGAAGGAAGGAAGGAAG 432171 i - i (AAGG)n#Simpl 1 AAGGAAGGAAGGAAGGAAGGAAGGAAG 27 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.04 (1 / 25), avg. gap size = 1.00 (1 / 1) 54 0.00 0.00 0.00 chr6ptel1M 432172 432217 (567783) (GA)n#Simple_repeat 1 46 (0) c_b282s251i2 11355 chr6ptel1M 432172 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 432217 (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 46 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 21 15.62 3.92 0.00 chr6ptel1M 432218 432241 (567759) (AAGG)n#Simple_repeat 28 52 (1) m_b282s252i8 11356 chr6ptel1M 432218 AAGG-AGGTGGGAAGGCTGGAGGGA 432241 - vi vv i (AAGG)n#Simpl 28 AAGGAAGGAAGGAAGGAAGGAAGGA 52 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 210 24.44 21.11 0.00 chr6ptel1M 432365 432454 (567546) C MIRc#SINE/MIR (139) 129 21 m_b282s601i32 11357 chr6ptel1M 432365 AACCGAGGGCCACAGAGTTT--GTGGCTTGTCCAAGTTCA---------- 432402 i vi v v -- i i v ---------- C MIRc#SINE/MIR 129 AACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGT 80 chr6ptel1M 432403 ---TGG---AGTTTGGGTTTGAATTCAGGTTTTCTTC-CTCTGAGTCCAG 432445 --- --- iiv ii i ii i i v- ii C MIRc#SINE/MIR 79 AAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAG 30 chr6ptel1M 432446 TTCTCTTTC 432454 v C MIRc#SINE/MIR 29 TGCTCTTTC 21 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 27.42 CpG sites = 15, Kimura (unadjusted) = 30.70 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.06 (5 / 89), avg. gap size = 3.80 (19 / 5) 15 22.74 6.67 2.56 chr6ptel1M 433685 433759 (566241) (AGACAAA)n#Simple_repeat 1 78 (0) m_b282s252i9 11358 chr6ptel1M 433685 AGATCAAAAGACAAAA-AAAAAAAAATGAGGAAAAAAGCCCCAAG-CAAA 433732 - - v i vvi i v v vv - (AGACAAA)n#Si 1 AGA-CAAAAGACAAAAGACAAAAGACAAAAGACAAAAGACAAAAGACAAA 49 chr6ptel1M 433733 CAAACAATA-ACAACA-ACAAATG-CAAAA 433759 - i v - v - v - (AGACAAA)n#Si 50 -AGACAAAAGACAAAAGACAAAAGACAAAA 78 Matrix = Unknown Transitions / transversions = 0.40 (4/10) Gap_init rate = 0.09 (7 / 74), avg. gap size = 1.00 (7 / 7) 345 32.27 5.74 4.48 chr6ptel1M 433943 434273 (565727) C L1PB1_3end#LINE/L1 (269) 629 295 m_b282s551i0 11359 chr6ptel1M 433943 ATTCCACTTAGAAT--CAGTTCATGCAAGTCTCTCCAGGCCTCTCTG-GA 433989 i i --i i-- v v iv -- v - C L1PB1_3end#LI 629 ACTTCACTTAGAATAATAGTC--TCCAATTCCATCCAGG--TCGCTGCGA 584 chr6ptel1M 433990 AT-CAGCTTGTTCATCACTTCTTATAGAATGA-TAATATTCCATAGCATT 434037 - vii v? iv i - iv - i i i v C L1PB1_3end#LI 583 ATGCCATTANTTCATTCCTTTTTAT-GGCTGAGTAGTATTCCATGGTATA 535 chr6ptel1M 434038 CATACACTATCATTTATTCA-GCATTTCCCAACTGATGGGCAT-----CC 434081 i i i iv? v i -v i iviii i ----- i C L1PB1_3end#LI 534 TATATACCACANTTTCTTTATCCACTCGTTGATTGATGGGCATTTGGGCT 485 chr6ptel1M 434082 GTTTCTAGTTCCTTGCCAGTAGAAAAAGGGCTGCCACAAACATTTCTGCA 434131 v i vv ii v v ivi vv v i i viv ii C L1PB1_3end#LI 484 GGTTCCATATTTTTGCAATTGCGAATTGTGCTGCTATAAACATGCGTGTG 435 chr6ptel1M 434132 CATTTGGGTTCCTTTCCCTCCTTTAA-GATCTCTTT-----GGGATATAA 434175 ----i vi --i v v - ii -----v i v v C L1PB1_3end#LI 434 CA----AGTATCTTT--TTCGTATAATGACTTCTTTTCCTCTGGGTAGAT 391 chr6ptel1M 434176 ACCCAGGAGAAACACTGCTGGGTCAAAGGGTAGGCACAATTTAATAGTCC 434225 v viiv i i v vivi v -- i C L1PB1_3end#LI 390 ACCCAGTAGTGGGATTGCTGGATCAAATGGTAGTTCTACTTT--TAGTTC 343 chr6ptel1M 434226 TC--AGGCAGAGTTCCAAATGGCCTTGCAGAATGGCTGGATCAGTTCACA 434273 i-- --i vi v iv ii v v i i v ii i C L1PB1_3end#LI 342 TTTAAGG--AATCTCCACACTGTTTTCCATAGTGGTTGTACTAGTTTACA 295 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 42.21 CpG sites = 59, Kimura (unadjusted) = 43.95 Transitions / transversions = 1.37 (59/43) Gap_init rate = 0.07 (24 / 330), avg. gap size = 1.42 (34 / 24) 416 31.49 4.93 3.83 chr6ptel1M 433990 434273 (565727) C L1ME2_3end#LINE/L1 (330) 581 295 m_b282s551i1 11359 chr6ptel1M 433990 ATCAGCTTGTTCATCACTTCTTATAGAATGA-TAATATTCCATAGCATTC 434038 - v i iv i v v- - i v i vv C L1ME2_3end#LI 581 ATCAG-TAGTTCGTTCCTTTTTATTGC-TGAGTAGTATTCCATTGTATGA 534 chr6ptel1M 434039 ATACACTATCATTTATTCA-GCATTTCCCAACTGATGGGCAT-----CCG 434082 i i iv i i -v i? vii i -----ii C L1ME2_3end#LI 533 ATATACCACAATTTGTTTATCCATTCNCCTGTTGATGGACATTTGGGTTG 484 chr6ptel1M 434083 TTTCTAGTTCCTTGCCAGTAGAAAAAGGGCTGCCACAAACATTTCTGCAC 434132 i iivv i v vi v ii i ii i? i C L1ME2_3end#LI 483 TTTCCAGTTTTGGGCTATTATGAATAAAGCTGCTATGAACATTCNTGTAC 434 chr6ptel1M 434133 A------TTTGGGTTCCTTTCCCTCCTTTAAGATCTCTTTGGGATATAAA 434176 ------ v vv v v vii i v ---- -- i v v C L1ME2_3end#LI 433 AAGTCTTTTTGTGGACATATGTTTTCATT----TCTCTT--GGGTAAATA 390 chr6ptel1M 434177 CCCAGGAGAAACACTGCTGGGTCAAAGGGTAGGCACA-ATTTAATAGTCC 434225 i viiv i v iii -i i-v iv C L1ME2_3end#LI 389 CCTAGGAGTGGAATTGCTGGGTCATAGGGTAGGTGTATGTTTAAC-TTTA 341 chr6ptel1M 434226 TCAGGCAGAGTTCCAAATGGCCTTGCAGAATGGCTGGATCAGTTCACA 434273 v -- i v v i? ii v i i i v i v i C L1ME2_3end#LI 340 TAAG--AAACTGCCAAACNGTTTTCCAAAGTGGTTGTACCATTTTACA 295 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 42.23 CpG sites = 51, Kimura (unadjusted) = 42.91 Transitions / transversions = 1.46 (51/35) Gap_init rate = 0.06 (16 / 283), avg. gap size = 1.56 (25 / 16) 630 29.31 3.54 1.94 chr6ptel1M 434020 434273 (565727) C L1ME3G_3end#LINE/L1 (376) 548 291 m_b282s551i2 11359 chr6ptel1M 434020 ATAATATTCCATAGCATTCATACACTATCATTTATTCAGC-ATTTCCCAA 434068 i i vv i i v i i - i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr6ptel1M 434069 CTGATGGGCATCC-----GTTTCTAGTTCCTTGCCAGTAGAAAAAGGGCT 434113 i i ii----- i i ii i i v v v iv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr6ptel1M 434114 GCCACAAACATTTCTGCACATTTGGGTTCCTTTCCCTCCTTTAAGA---T 434160 v ii iii i --- v? viv v v v iv --- C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACAT---GCNTCCTTGTGCACATGTGCGAGTAT 402 chr6ptel1M 434161 CTCTTTGGGATATAAACCCAGGAGAAACACTGCTGGGTCAAAGGGTAGGC 434210 i ? i v v? ? i viiv i v C L1ME3G_3end#L 401 TTCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGC 352 chr6ptel1M 434211 ACAATTTAATAGTCCTCAGGCAGAGTTCCAAATGGCCTTGCAGAATGGCT 434260 i v -- i ii v viv v v v v i v i ? C L1ME3G_3end#L 351 GCATTTTA--AATTTTAATAGATACTGCCAAATTGCCCTCCAAAANGGCT 304 chr6ptel1M 434261 GGATCAGTTCACA 434273 v i i i C L1ME3G_3end#L 303 GTACCAATTTACA 291 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 37.82 CpG sites = 42, Kimura (unadjusted) = 39.20 Transitions / transversions = 1.35 (42/31) Gap_init rate = 0.03 (8 / 253), avg. gap size = 1.75 (14 / 8) 218 34.57 1.83 1.83 chr6ptel1M 434321 434429 (565571) C L3#LINE/CR1 (4) 4095 3987 m_b282s601i33 11360 chr6ptel1M 434321 GAACTGCAAACTCTCAGGAGTCCAAAGAGACCTCACCAGTCGTATGGTCC 434370 iii i v - ivi i i vvi i v i C L3#LINE/CR1 4095 GAATCACAGAATCTCAG-AGTTGGAAGGGACCTTAGAGGTCATCTAGTCC 4047 chr6ptel1M 434371 CACCTAT-ACCTGA-GCAAGAATCGTCTCCACGAGCGCCTCTGACGGATG 434418 v vi- i ii - i vii i i - ii i iii C L3#LINE/CR1 4046 AACCTCCCATCCAATGCAGGAATCCCTTCTACAA-CATCCCTGACAAGTG 3998 chr6ptel1M 434419 AGCATCCAGTC 434429 iv i C L3#LINE/CR1 3997 GTCATCCAGCC 3987 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 51.36 CpG sites = 28, Kimura (unadjusted) = 51.36 Transitions / transversions = 3.11 (28/9) Gap_init rate = 0.04 (4 / 108), avg. gap size = 1.00 (4 / 4) 254 20.90 7.95 2.15 chr6ptel1M 434444 434531 (565469) C L2b_3end#LINE/L2 (18) 448 356 m_b282s601i34 11361 chr6ptel1M 434444 TATTT-CTGAAATGCCTGCTGTGTGCTGGGCCACGTGCTAAGAGCTGGGG 434492 - i-i i ii ?vi i v C L2b_3end#LINE 448 TATTTACTGAG-CGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGGG 400 chr6ptel1M 434493 GTACAA----GAA-AAGCCA-ACGTGTGCCCCTGTTCTCGAGGAG 434531 i i---- - v - ?i - i ii iv C L2b_3end#LINE 399 ATACAGCGGTGAACAAGACAGACNCG-GTCCCTGCCCTCACGGAG 356 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 23.13 CpG sites = 14, Kimura (unadjusted) = 26.48 Transitions / transversions = 3.50 (14/4) Gap_init rate = 0.07 (6 / 87), avg. gap size = 1.50 (9 / 6) 283 27.92 10.95 0.66 chr6ptel1M 435462 435598 (564402) C MIRc#SINE/MIR (17) 251 101 m_b282s601i35 11362 chr6ptel1M 435462 ACATTTCTGTAGCATTTTA------GCAGAG-ACATTTGCATATATCAGC 435504 v i i ------i i -i v ii i i v C MIRc#SINE/MIR 251 ACATTTGTATAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATC 202 chr6ptel1M 435505 TTCTTTGGTCCTC-CTTC--CCTTGTAAGGTAA--AGCACAAACATTA-- 435547 iv i - vv -- i i i-- vi iii -- C MIRc#SINE/MIR 201 TCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATT 152 chr6ptel1M 435548 A-CCACATTTTACAGATGAAAAAAACCAAGACCAAGAAAATCTAAGTCAC 435596 - v - ii ii i iv i ivi v C MIRc#SINE/MIR 151 ATCCCCATTTTACAGATG-AGGAAACTGAGGCTCAGAGAGGTTAAGTGAC 103 chr6ptel1M 435597 TT 435598 C MIRc#SINE/MIR 102 TT 101 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 35.66 CpG sites = 27, Kimura (unadjusted) = 36.91 Transitions / transversions = 2.45 (27/11) Gap_init rate = 0.06 (8 / 136), avg. gap size = 2.00 (16 / 8) 370 29.10 11.94 0.00 chr6ptel1M 435606 435739 (564261) C MIRb#SINE/MIR (116) 152 3 m_b282s601i36 11363 chr6ptel1M 435606 CCTCATTTTATAAA-GAAGGAATTGAGGCCCAGAAAGGTACGGTGATTTT 435654 i i i - i i i i i vvi i i v C MIRb#SINE/MIR 152 CCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTG 103 chr6ptel1M 435655 TCCAGTGTTCCACAGGTAGT-------------GGGATTCAAAGACAAGT 435691 i iv iv v ------------- i vv i C MIRb#SINE/MIR 102 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGT 53 chr6ptel1M 435692 TT-TCTAACTTGAAA-CTCATCCTTTTTCCTTCGTACCAGCCTGCCTCTC 435739 i - i iv - i i v i vii i vv i C MIRb#SINE/MIR 52 CTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCACCACGCTGCCCCTC 3 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 36.04 CpG sites = 26, Kimura (unadjusted) = 38.58 Transitions / transversions = 2.00 (26/13) Gap_init rate = 0.03 (4 / 133), avg. gap size = 4.00 (16 / 4) 341 29.16 3.28 1.61 chr6ptel1M 436057 436178 (563822) L2b_3end#LINE/L2 335 458 (8) m_b282s601i37 11364 chr6ptel1M 436057 TCTTCCCCATTAGAATGTAAGCCCTTTGAGGGCAGAAATCATCTTTCTAC 436106 i i v i i iv ii i i?v i v - L2b_3end#LINE 335 TCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGT-C 383 chr6ptel1M 436107 TTTTTCCACGA-ATGTTCCCAGTCCTTATC---GTGCTTGGTACAAAGGA 436152 v vv v-i i i iv i v --- ? i i v v L2b_3end#LINE 384 TTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTA 433 chr6ptel1M 436153 AGTCCTCAGTGAATGGTTTATTGAAT 436178 i iv i -i i L2b_3end#LINE 434 GGCGCTCAGTAAAT-ATTTGTTGAAT 458 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.63 CpG sites = 22, Kimura (unadjusted) = 39.21 Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.03 (4 / 121), avg. gap size = 1.50 (6 / 4) 392 13.31 25.47 0.76 chr6ptel1M 437118 437223 (562777) C Charlie4a#DNA/hAT-Charlie (22) 486 355 m_b282s502i2 11365 chr6ptel1M 437118 TGTCACAGACCC---TGGTCAGTTTCATGAA--------ACCCCTACTCA 437156 i ii --- - i vi -------- v C Charlie4a#DNA 486 TGCCATGGACCCCTTTGG-CAGTCTGGTGAAGCCTATGGACCCCTTCTCA 438 chr6ptel1M 437157 CAGTA----TTTTAAACGCAGAGA------------GGATTACAAAGGAA 437190 v i ---- i v i ------------ C Charlie4a#DNA 437 GAATAATGTTTTTAAATGCATAAAATAAAATACATAGGATTACAAAGGAA 388 chr6ptel1M 437191 ACCAATTTTATTGAAATACAGTTAACAAAATAT 437223 v v C Charlie4a#DNA 387 ACCAATTATATTGAAATACAGTTATCAAAATAT 355 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 14.79 CpG sites = 8, Kimura (unadjusted) = 14.79 Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.05 (5 / 105), avg. gap size = 5.60 (28 / 5) 347 32.95 7.73 1.46 chr6ptel1M 437515 437708 (562292) C MIRc#SINE/MIR (52) 216 11 m_b282s601i38 11366 chr6ptel1M 437515 TTTACACAGAGAATCTCATCTGGTCCTTACCAGGATCCCAAGAAGTACAC 437564 i i v vv i i i v vi i iiv i vi C MIRc#SINE/MIR 216 TTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGC 167 chr6ptel1M 437565 TGGG------TTATTATCCCCA-TTTATAGATGTAGAAACCCAGTCTGAG 437607 v ------ - i vi iv v v C MIRc#SINE/MIR 166 AGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAG 117 chr6ptel1M 437608 -GAAGT---GTGCTGCTTGCTTGGGGTGTCCCAGGGAGTGTGT----GAG 437649 - i --- --i iiii vv v vv iv ---- C MIRc#SINE/MIR 116 AGAGGTTAAGTG--ACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAG 69 chr6ptel1M 437650 GCAAGATTCCCACTCAGGCCTTCTGTCTCTCTAAGCTTGGTACTGTTTCT 437699 v ii i vv i i i- vv i iiii i v i C MIRc#SINE/MIR 68 CCGGGACTCGAACCCAGGTCTTCC-TGACTCCAAGTCCAGTGCTCTTTCC 20 chr6ptel1M 437700 GCCATGCCA 437708 i iiii C MIRc#SINE/MIR 19 ACTGCACCA 11 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 44.42 CpG sites = 39, Kimura (unadjusted) = 45.42 Transitions / transversions = 1.62 (39/24) Gap_init rate = 0.04 (8 / 193), avg. gap size = 2.25 (18 / 8) 421 26.55 3.51 0.85 chr6ptel1M 438288 438401 (561599) C Charlie4a#DNA/hAT-Charlie (20) 488 372 m_b282s502i3 11367 chr6ptel1M 438288 TATGTCATGTGCTCCCTTCA-AGGCTGGTAAAGCCTCTGGGACCCCCTTC 438336 i i vi i i vi- v i v - i ii C Charlie4a#DNA 488 TGTGCCATGGACCCCTTTGGCAGTCTGGTGAAGCCTATGG-ACCCCTTCT 440 chr6ptel1M 438337 CAGAATCATGCTTTTAAGTATGTAAAACA---TACATTGAATTGCAGAGG 438383 v i i iii i --- v i i i C Charlie4a#DNA 439 CAGAATAATGTTTTTAAATGCATAAAATAAAATACATAGGATTACAAAGG 390 chr6ptel1M 438384 GTATTGATTATATTGAAA 438401 iv iii C Charlie4a#DNA 389 AAACCAATTATATTGAAA 372 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 34.96 CpG sites = 23, Kimura (unadjusted) = 34.96 Transitions / transversions = 3.29 (23/7) Gap_init rate = 0.03 (3 / 113), avg. gap size = 1.67 (5 / 3) 62 31.50 2.69 0.88 chr6ptel1M 438474 438696 (561304) (GAGA)n#Simple_repeat 1 227 (0) m_b282s252i10 11368 chr6ptel1M 438474 GAGAGAGAGGGAAAGAAAGAGAGAAAGCAGAGAGAGA-AGAGAGAAAAAA 438522 i i i i - - i i i (GAGA)n#Simpl 1 GAGAGAGAGAGAGAGAGAGAGAGAGAG-AGAGAGAGAGAGAGAGAGAGAG 49 chr6ptel1M 438523 AGAAACAG-GGGAGAGAGAGAGGGCTGAGGGAAGGAGTAAGGGAAAGAGA 438571 i v - i i -v i ii vi i i (GAGA)n#Simpl 50 AGAGAGAGAGAGAGAGAGAGAGAG-AGAGAGAGAGAGAGAGAGAGAGAGA 98 chr6ptel1M 438572 AAAGGAGAGGGAGAAAGGAAGGGA-AGAAGGAAAG-GAGGGAGGGAGAAG 438619 i ii i i ii i - ii i - i i ii (GAGA)n#Simpl 99 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 148 chr6ptel1M 438620 GAGGGAGAGAGAGGGAAGGAAGGAGGGAGGGA-AGA-AAAGAGAGGGAGG 438667 i i ii ii i i - - i i i (GAGA)n#Simpl 149 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 198 chr6ptel1M 438668 GAGGGAGGGAGGAAAAAAGAGGGAGAGAG 438696 i i ii i i i (GAGA)n#Simpl 199 GAGAGAGAGAGAGAGAGAGAGAGAGAGAG 227 Matrix = Unknown Transitions / transversions = 16.33 (49/3) Gap_init rate = 0.04 (8 / 222), avg. gap size = 1.00 (8 / 8) 21 16.71 0.00 7.02 chr6ptel1M 438766 438826 (561174) (TGTGTC)n#Simple_repeat 1 57 (0) m_b282s252i11 11369 chr6ptel1M 438766 TGTATATGTGTCTGTGTCTGTGCTCATGTGTGTATGTGTGCATGTCTGTG 438815 i v - - v i v -- (TGTGTC)n#Sim 1 TGTGTCTGTGTCTGTGTCTGTG-TC-TGTGTCTGTGTCTG--TGTCTGTG 46 chr6ptel1M 438816 CATGTGTGTGT 438826 iv v (TGTGTC)n#Sim 47 TCTGTGTCTGT 57 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.07 (4 / 60), avg. gap size = 1.00 (4 / 4) 349 27.96 1.68 0.83 chr6ptel1M 439024 439142 (560858) C MIR#SINE/MIR (118) 144 25 m_b282s601i39 11370 chr6ptel1M 439024 CTCATTTTACAGTTGAGTAATCTGAGGCAAACAGA-GTGAAGTAATTTG- 439071 i v v v v v - v i - C MIR#SINE/MIR 144 CCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGC 95 chr6ptel1M 439072 CCAGGGTCATCCAGTCAGGAATTACCTGAAGCTGGATTTGAACTCATGAA 439121 i iv ii v v iv v iv v i i v v C MIR#SINE/MIR 94 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGCA 45 chr6ptel1M 439122 GAATGGACCTTAGAAGCCATG 439142 vv - iii iv i C MIR#SINE/MIR 44 GTCTGG-CTCCAGAGCCCGTG 25 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 32.70 CpG sites = 15, Kimura (unadjusted) = 35.21 Transitions / transversions = 0.83 (15/18) Gap_init rate = 0.03 (3 / 118), avg. gap size = 1.00 (3 / 3) 412 34.17 2.52 0.62 chr6ptel1M 439122 439280 (560720) C MIR3#SINE/MIR (30) 178 17 m_b282s601i40 11371 chr6ptel1M 439122 GAATGGACCTTAGAAGCCATGTAATCAAACTTTCTCCTTTTACATTTGAG 439171 v iii v i v iii v vv C MIR3#SINE/MIR 178 GAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGAG 129 chr6ptel1M 439172 GAGATCAAGGCACAGAGAAGCTGAGGATTTTGCCTCAGGTCTCCTAGGTA 439221 i iii v i ivi vivi iv v vi v? C MIR3#SINE/MIR 128 GAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGCNA 79 chr6ptel1M 439222 GTCAG----AGAGGTGAGATTTGAGCTTAGTTCCTCTACCTCCAAATGGG 439267 i ---- vi i i v i ii v ii iv v i -vv C MIR3#SINE/MIR 78 GTTAGTGGCAGAGCCGGGACTAGAACCCAGGTCTCCTGACTCCCAGT-CC 30 chr6ptel1M 439268 GTGCTTTTTCCAC 439280 i i ii C MIR3#SINE/MIR 29 GTGCTCTCTCTGC 17 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 46.90 CpG sites = 33, Kimura (unadjusted) = 48.17 Transitions / transversions = 1.57 (33/21) Gap_init rate = 0.01 (2 / 158), avg. gap size = 2.50 (5 / 2) 327 32.43 2.63 2.63 chr6ptel1M 439153 439304 (560696) C MIR1_Amn#SINE/MIR (78) 152 1 m_b282s601i41 11371 chr6ptel1M 439153 TTCTCCTTTTACATTTGAGGAGATCAAGGCACAGAGAAGCTGAGGATTTT 439202 i i v vv i iii ? i i?i vivi C MIR1_Amn#SINE 152 TCCCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTT 103 chr6ptel1M 439203 GCCTCAGGTCTCCTAGGTAGTCAG----AGAGGTGAGATTTGAGCTTAGT 439248 iv v ?i v?i i? ---- vi i ? ? i ii v C MIR1_Amn#SINE 102 GCCCAAGGTCACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAACCCAGG 53 chr6ptel1M 439249 TCCTCTACCTCCAAATGGGGTGCTTTTTCCACCATACCTCCCCTACTTCC 439298 ii iivv v i vvi i v i v v ---- v C MIR1_Amn#SINE 52 TCTCCCGAGTCCCAGTCCAGTGCTCTATCCACTAGACCAC----ACTGCC 7 chr6ptel1M 439299 TGCCTA 439304 v C MIR1_Amn#SINE 6 TCCCTA 1 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 44.22 CpG sites = 28, Kimura (unadjusted) = 47.06 Transitions / transversions = 1.40 (28/20) Gap_init rate = 0.03 (5 / 151), avg. gap size = 1.60 (8 / 5) 269 19.72 1.41 0.00 chr6ptel1M 439568 439638 (560362) MIR1_Amn#SINE/MIR 79 150 (80) m_b282s601i42 11372 chr6ptel1M 439568 CTTGTGGGATGTTTGACCCTGGTTAAGTCACTTCACCGTGTT-TGCCTTG 439616 ? iv? v ?v i vi ? vivi -? ii MIR1_Amn#SINE 79 CTNGCCNGCTGNGTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCA 128 chr6ptel1M 439617 GTTTCCTCATCTCTAAAATGGG 439638 v MIR1_Amn#SINE 129 GTTTCCTCATCTGTAAAATGGG 150 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 25.11 CpG sites = 7, Kimura (unadjusted) = 25.11 Transitions / transversions = 1.00 (7/7) Gap_init rate = 0.01 (1 / 70), avg. gap size = 1.00 (1 / 1) 270 16.39 3.23 1.59 chr6ptel1M 439577 439638 (560362) MIR3#SINE/MIR 83 145 (63) m_b282s601i43 11372 chr6ptel1M 439577 TGTTTGACCCTGGTTAAGTCACTTCACCGTGTTTG--CCTTGGTTTCCTC 439624 v i vi - v i -- ii MIR3#SINE/MIR 83 TGTGTGACCTTGGGCAAGTCACTTCACC-TCTCTGGGCCTCAGTTTCCTC 131 chr6ptel1M 439625 ATCTCTAAAATGGG 439638 v i MIR3#SINE/MIR 132 ATCTGTAAAATGAG 145 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 18.73 CpG sites = 6, Kimura (unadjusted) = 18.73 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.03 (2 / 61), avg. gap size = 1.50 (3 / 2) 293 23.10 13.10 9.83 chr6ptel1M 440407 440574 (559426) C MIRc#SINE/MIR (76) 192 20 m_b282s601i44 11373 chr6ptel1M 440407 CCTCAGCAGCAGCCCTGTGGGATAGGCAGGG--------ATTGTTTTCAT 440448 - i i i i -------- i iii C MIRc#SINE/MIR 192 CCTCA-CAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCAT 144 chr6ptel1M 440449 TCGACAGATGAGGAAAGAGAGTCTGCAGGGGGGGGGGGGGGGGGAGCAGG 440498 iv vv v - i i ------------vi i C MIRc#SINE/MIR 143 TTTACAGATGAGGAAACTGAGGCT-CAGAGAGG------------TTAAG 107 chr6ptel1M 440499 GGACTTATTCAAGGTCATGC--------ATTGGC--GGTCAGGATT--AA 440536 v iii ii -------- v --i i i i -- C MIRc#SINE/MIR 106 TGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAA 57 chr6ptel1M 440537 CTCCCCAGG-ATTCCAGATTCTAAATCCAGAG-TCTTTCC 440574 --- -v v i i i v - C MIRc#SINE/MIR 56 ---CCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCC 20 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 27.89 CpG sites = 25, Kimura (unadjusted) = 28.87 Transitions / transversions = 2.50 (25/10) Gap_init rate = 0.14 (23 / 167), avg. gap size = 1.70 (39 / 23) 23 29.60 3.75 0.00 chr6ptel1M 440580 440659 (559341) (TC)n#Simple_repeat 1 83 (0) m_b282s252i12 11374 chr6ptel1M 440580 TCT-TCTCTCCCT-TCCATCTCCTTCCTTCTCCATCTC-CTCTCTTGCCT 440626 - i - iv ii ii iv - iv ii (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr6ptel1M 440627 TCTCTGCCTCCCCATCTCTGTCTCTCTCTCTCT 440659 vi i iv v (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 83 Matrix = Unknown Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.04 (3 / 79), avg. gap size = 1.00 (3 / 3) 331 31.86 1.45 2.19 chr6ptel1M 441112 441249 (558751) C MIR3#SINE/MIR (43) 165 29 m_b282s601i45 11375 chr6ptel1M 441112 AGACCCTTCAATCCAAATTCAGCATTTCCCTTCTTAGGAAATTGAGTCCC 441161 i v ii i vii vv iv vvv v i v C MIR3#SINE/MIR 165 AGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCC 116 chr6ptel1M 441162 AGAGTTGGAAAGTGACT--CCCAAAATCATACAGCAAACCGTGTGTGACA 441209 vv vi -- ii i ? --- vv i C MIR3#SINE/MIR 115 AGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGCNA---GTTAGTGGCA 69 chr6ptel1M 441210 AATCTGGGACAAGAACCAAGTTGATCTTACTTTCTATCTG 441249 i v i v v v vvi v ii vi i C MIR3#SINE/MIR 68 GAGCCGGGACTAGAACCCAGGTCTCCTGACTCCCAGTCCG 29 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 39.80 CpG sites = 20, Kimura (unadjusted) = 42.27 Transitions / transversions = 0.87 (20/23) Gap_init rate = 0.03 (4 / 137), avg. gap size = 1.25 (5 / 4) 358 30.68 3.82 4.49 chr6ptel1M 441256 441412 (558588) C L2a_3end#LINE/L2 (3) 514 359 m_b282s601i46 11376 chr6ptel1M 441256 CATTCAAACAGTAAATGAGCACTTAGTAAGCACTTACTGTGTGCCAGACA 441305 vv ii ---- i v i i i i i C L2a_3end#LINE 514 CATTCATTCAACAAAT----ATTTATTGAGCGCCTACTATGTGCCAGGCA 469 chr6ptel1M 441306 CTGCCCTAATGGGTACAGATAGAAGGAAAAAAAAAAAAAGCAAAACCAAT 441355 ii ivv v ivi v iviivi v v ii --- i C L2a_3end#LINE 468 CTGTTCTAGGCGCTGGGGATACAGCAGTGAACAAAACAGACAAA---AGT 422 chr6ptel1M 441356 CTTTGCCCTTA-AGAGCTCACATTTTAGTGGAGG-----AAATGACATAC 441399 ii i -i i i i ----- i ii i v C L2a_3end#LINE 421 CCCTGCCCTCATGGAGCTTACATTCTAGTGGGGGGAGACAGACAATAAAC 372 chr6ptel1M 441400 AAATAATTAGGTA 441412 v i C L2a_3end#LINE 371 AAATAAATAAGTA 359 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 40.63 CpG sites = 32, Kimura (unadjusted) = 41.86 Transitions / transversions = 2.29 (32/14) Gap_init rate = 0.06 (9 / 156), avg. gap size = 1.44 (13 / 9) 304 28.34 1.11 13.75 chr6ptel1M 441257 441436 (558564) C L2c_3end#LINE/L2 (0) 478 319 m_b282s601i47 11376 chr6ptel1M 441257 ATTCAAACAGTAAATGAGCACTTAGTAAGCACTTACTGTGTGCCAGACAC 441306 vv v v ii i i v i i i i i i C L2c_3end#LINE 478 ATTCATTCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGC 429 chr6ptel1M 441307 TGCCCTAATGGGTACAGATAGAAGGAAAAAAAAAAAAAGCAAAACCAATC 441356 -------- ---- v i vi v i ---- ---- ii C L2c_3end#LINE 428 TG--------GG----GATACAAAGATGAATAAGA----CA----CGGTC 399 chr6ptel1M 441357 TTTGCCCTTAAG-AGCTCACATTTTAGTGGAGGAAAT-GACATACAAATA 441404 ii i - v i i i- ?ii i C L2c_3end#LINE 398 CCTGCCCTCAAGGAGCTCACAGTCTAGTGGAGGAGACAGACANGTAAACA 349 chr6ptel1M 441405 ATTAGGTACATGAAACACGTTCAGCATCAGTG 441436 ivi iv -- v v v vv v C L2c_3end#LINE 348 GACAATTACA--ATACAAGTTAATGATAAGTG 319 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.15 CpG sites = 27, Kimura (unadjusted) = 36.20 Transitions / transversions = 1.59 (27/17) Gap_init rate = 0.13 (24 / 179), avg. gap size = 1.00 (24 / 24) 30 17.97 0.00 0.00 chr6ptel1M 443241 443293 (556707) (T)n#Simple_repeat 1 53 (0) m_b282s252i13 11377 chr6ptel1M 443241 TTTTCTTTTTTTTTTCCTTTTTTTTCTTTTCTTTCTTTCTTTCTTTTTTT 443290 i ii i i i i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr6ptel1M 443291 TTT 443293 (T)n#Simple_r 51 TTT 53 Matrix = Unknown Transitions / transversions = 1.00 (8/0) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 384 33.34 1.61 1.61 chr6ptel1M 443760 443945 (556055) C L1MD1_3end#LINE/L1 (356) 633 448 m_b282s551i3 11378 chr6ptel1M 443760 GCTCATTTCACTCAGCATCAGTTCGTGTAAGTCTCTCCAGGCCTTTCTGA 443809 iv v v iiv v ii iiv iiv vi v C L1MD1_3end#LI 633 GCTTTTTTCACTCAGCATAATTCTCTGGAGATTCATCCAGGTTGTTGCGT 584 chr6ptel1M 443810 A-ATCATCCTGTTGGTCATTTCTTACAGAACAGTAATATTCCATAATATT 443858 i- viv- v ivi i iv vvv i ii v C L1MD1_3end#LI 583 GTATCAATA-GTTCGTTCCTTTTTATTGCTGAGTAGTATTCCATGGTATG 535 chr6ptel1M 443859 CATATACCACAATTTATTCAGCCATTCTCCAGCTGATGGGCATCCA--TT 443906 v i i i i i v v i v i ii-- C L1MD1_3end#LI 534 GATGTACCACAGTTTGTTTAACCATTCACCCGTTGAAGGACATCTGGGTT 485 chr6ptel1M 443907 CAGTTTCCAGTTTCTAGCCACTATAAAAAGGGCTGTTGT 443945 -- i i i i ii v ii i i C L1MD1_3end#LI 484 --GTTTCCAGTTTTTGGCTATTACGAATAAAGCTGCTAT 448 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 43.96 CpG sites = 38, Kimura (unadjusted) = 46.17 Transitions / transversions = 1.65 (38/23) Gap_init rate = 0.03 (5 / 185), avg. gap size = 1.20 (6 / 5) 387 24.37 1.67 4.27 chr6ptel1M 443827 443946 (556054) C L1MB8_3end#LINE/L1 (362) 563 447 m_b282s551i4 11378 chr6ptel1M 443827 TTTCTTACAGAACAGTAATATTCCATAATATTCATATACCACAATTTATT 443876 v i v --- vi vv v C L1MB8_3end#LI 563 TTTATTGCCGAA---TAATATTCCATTGTATGGATATACCACATTTTATT 517 chr6ptel1M 443877 CAGCCATTCTCCAGCTGATGGGCATCC--ATTCAGTTTCCAGTTTCTAGC 443924 i v vi i i ii--i -- v i i C L1MB8_3end#LI 516 TATCCATTCATCAGTTGATGGACATTTGGGTT--GTTTCCACTTTTTGGC 469 chr6ptel1M 443925 CACTATAAAAAGGGCTGTTGTG 443946 i i i v iv i i C L1MB8_3end#LI 468 TATTATGAATAATGCTGCTATG 447 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 30.13 CpG sites = 17, Kimura (unadjusted) = 30.13 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.05 (6 / 119), avg. gap size = 1.17 (7 / 6) 462 27.05 0.00 1.64 chr6ptel1M 443840 443963 (556037) C L1ME2z_3end#LINE/L1 (638) 553 432 m_b282s551i5 11378 chr6ptel1M 443840 AGTAATATTCCATAATATTCATATACCACAATTTATTCAGCCATTCTCCA 443889 i vi vv i i i v v C L1ME2z_3end#L 553 AGTAGTATTCCATTGTATGAATATACCACAGTTTGTTTATCCATTCTCCT 504 chr6ptel1M 443890 GCTGATGGGCATCCATTCAGTTTCCAGTTTCTAGCCACTATAAAAAGGGC 443939 i i i iivv v i i i i i v ii C L1ME2z_3end#L 503 GTTGATGGACACCTGGGCTGTTTCCAGTTTTTGGCTATTATGAATAAAGC 454 chr6ptel1M 443940 TGTTGTGGGATCATTTTCATAAAA 443963 i i -- v i ii v C L1ME2z_3end#L 453 TGCTAT--GAACATTCTTGTACAA 432 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 34.94 CpG sites = 22, Kimura (unadjusted) = 34.94 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.02 (2 / 123), avg. gap size = 1.00 (2 / 2) 44 0.00 0.00 0.00 chr6ptel1M 446052 446091 (553909) (GAT)n#Simple_repeat 1 40 (0) c_b283s251i0 11379 chr6ptel1M 446052 GATGATGATGATGATGATGATGATGATGATGATGATGATG 446091 (GAT)n#Simple 1 GATGATGATGATGATGATGATGATGATGATGATGATGATG 40 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 484 27.65 8.65 0.89 chr6ptel1M 446094 446301 (553699) C MIRc#SINE/MIR (3) 265 42 m_b283s601i0 11380 chr6ptel1M 446094 AGTAACAATAGCTAGCAATTACAGAGTG-TTTAAAGTTTGCAAACCATTT 446142 i i i?v vi v ii v ii- v i v ii C MIRc#SINE/MIR 265 AATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCGCTT 216 chr6ptel1M 446143 T-ACAGACATT---TCATCTCATCCTCACAAC---CCTGAGAGTT----- 446180 - v --- i v --- v v ----- C MIRc#SINE/MIR 215 TCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCA 166 chr6ptel1M 446181 --GTTGCTATTATTATCCCTGTTCGA-AGCTGAAGAAACTTTGGCAAACA 446227 -- iv v ii iv - v i vv vv v C MIRc#SINE/MIR 165 GGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGA 116 chr6ptel1M 446228 GTTGGTAAAGGACTTGTCCAGAGTCATTCAGCTAAGAAATGTCCCAGAGT 446277 vv v iv i ii iv iv i v -- i C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGC--AGAGC 68 chr6ptel1M 446278 --AGATTTGAATTCAGATCTTCCTGA 446301 --i i i ii i C MIRc#SINE/MIR 67 CGGGACTCGAACCCAGGTCTTCCTGA 42 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.84 CpG sites = 31, Kimura (unadjusted) = 35.36 Transitions / transversions = 1.19 (31/26) Gap_init rate = 0.05 (10 / 207), avg. gap size = 2.00 (20 / 10) 326 28.36 2.90 2.90 chr6ptel1M 446186 446323 (553677) C MIR1_Amn#SINE/MIR (70) 160 23 m_b283s601i1 11380 chr6ptel1M 446186 TATTATTATCCCTGTTCGA-AGCTGAAGAAACTTTGGCAAACAGTTGGTA 446234 i ii iv - v i vv ?v v v- ? C MIR1_Amn#SINE 160 TATCATTATCCCCATTTTACAGATGAGGAAACTGAGGCNCAGAGA-GGTN 112 chr6ptel1M 446235 AAG-GACTTGTCCAGAGTCATTCAGCTAAGAAATGTCCCAGAGT--AGAT 446281 - i ii i? ?iiv? i --v i--i ? C MIR1_Amn#SINE 111 AAGTGACTTGCCCAAGGTCACNCAGCNGGCNAGTG--GCAGAGCCGGGAN 64 chr6ptel1M 446282 TTGAATTCAGATCTTCCTGAGCCTGGATGCATCACTTGATCC 446323 ? ii i - i i ivii v vii iv C MIR1_Amn#SINE 63 TNGAACCCAGGTC-TCCCGAGTCCCAGTCCAGTGCTCTATCC 23 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 38.61 CpG sites = 25, Kimura (unadjusted) = 39.99 Transitions / transversions = 1.92 (25/13) Gap_init rate = 0.05 (7 / 137), avg. gap size = 1.14 (8 / 7) 203 34.07 3.19 3.19 chr6ptel1M 446413 446506 (553494) MIRc#SINE/MIR 42 135 (133) m_b283s601i2 11381 chr6ptel1M 446413 TCAGGAGGATCAGGGTTCAGATCATTTCTTGAATGCTTGTGAACTG---G 446459 i i v iii vivv ivivii iiv i --- MIRc#SINE/MIR 42 TCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTG 91 chr6ptel1M 446460 ACTCTGGACGAGTCATTCAACCTCTCAGTACCCACAGAATTTCTTTA 446506 ii i i i i v - v v -- i i MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACCTCTCTG-AGCCTCAG--TTTCCTCA 135 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 44.15 CpG sites = 21, Kimura (unadjusted) = 48.57 Transitions / transversions = 2.10 (21/10) Gap_init rate = 0.04 (4 / 93), avg. gap size = 1.50 (6 / 4) 251 35.13 2.68 0.66 chr6ptel1M 446899 447047 (552953) L3#LINE/CR1 3943 4094 (5) m_b283s601i3 11382 chr6ptel1M 446899 TCATTAGGTACTAAATTACTCCTCACTGAAGGTCTTGATGCAAAGAGTTC 446948 i?v v i ii v i v i v v v i - i v L3#LINE/CR1 3943 TCGNGAGGTAGTGAGCTCCCCGTCACTGGAGGTGTTCAAGCAGAG-GCTG 3991 chr6ptel1M 446949 ATTGACCATTTGCTCTATATGTT--AATTATGCTTCTTAT-TTAAATATG 446995 iv i iivviv -- ivviv v i ii- ii iv L3#LINE/CR1 3992 GATGACCACTTGTCAGGGATGTTGTAGAAGGGATTCCTGCATTGGATGGG 4041 chr6ptel1M 446996 -GGATGGACTCGATGTCCTTTGAAGTCTTTTCCAATTCTCTAAGTCTTTG 447044 - v v v i i i ii i vvi v v L3#LINE/CR1 4042 AGGTTGGACTAGATGACCTCTAAGGTCCCTTCCAACTCTGAGATTCTGTG 4091 chr6ptel1M 447045 ATT 447047 L3#LINE/CR1 4092 ATT 4094 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 47.84 CpG sites = 28, Kimura (unadjusted) = 49.17 Transitions / transversions = 1.17 (28/24) Gap_init rate = 0.03 (4 / 148), avg. gap size = 1.25 (5 / 4) 17 0.00 0.00 0.00 chr6ptel1M 447559 447577 (552423) (T)n#Simple_repeat 1 19 (0) m_b283s252i0 11383 chr6ptel1M 447559 TTTTTTTTTTTTTTTTTTT 447577 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 554 26.17 15.99 3.37 chr6ptel1M 447880 448223 (551777) L1ME4c_3end#LINE/L1 12 397 (433) m_b283s551i3 11384 chr6ptel1M 447880 AATATATAAAGAATTGACTCAAATTCATAAGAAT----TCAAGGCATTTT 447925 ? ii v i v v---- i ----i L1ME4c_3end#L 12 ANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAAGAC----C 57 chr6ptel1M 447926 CCAAAGGATAAATGGTCAAAGGATAAGAACAGACAATTTTCAGATGAAGA 447975 vi v i v iv ? v i L1ME4c_3end#L 58 CCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAGGA 107 chr6ptel1M 447976 AAT-----TA--AAAC-----CAT---------TTC-----------TAG 447993 ----- -- ----- --------- ----------- i L1ME4c_3end#L 108 AATACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTAGTAA 157 chr6ptel1M 447994 TCAGAGAAATTCAAATTAAGACA------------TATCTGATGAACTTC 448031 i v ii ------------i i v i -- i v L1ME4c_3end#L 158 TCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACG--CCTA 205 chr6ptel1M 448032 TTAGATTGGCTATGATGACAGGAAA--AATAATGATTATTGTTGGGGGGG 448079 i i v vi v-i ii --i ivii v i v i L1ME4c_3end#L 206 TTAAATTAGCAAAAATT-TAAAAAATTGATAATACCCAATGCTGGCGAGG 254 chr6ptel1M 448080 GGTGTGTGGGAAAACTGGAACACTAATACATTATTGGTGGAGTTGTGAAC 448129 ---? i vi v ? v ii vi? i i L1ME4c_3end#L 255 ---NTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAAT 301 chr6ptel1M 448130 TGATCCAACCATTCTGGAGAGCAATTTAGAGCTGTGCCCAAGGGGCTATC 448179 i v v i i i viv ii iviv i i i v L1ME4c_3end#L 302 TGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATA 351 chr6ptel1M 448180 AAACTG--AATTTCCTTTGATTCCGTAGTGTCTCTATTTTT---AATTT 448223 v --v vi ii v i --- i i i --- L1ME4c_3end#L 352 AAAATGTTCATACCCTTTGACCCAGTAAT---TCCACTTCTGGGAATTT 397 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 32.62 CpG sites = 55, Kimura (unadjusted) = 34.06 Transitions / transversions = 1.72 (55/32) Gap_init rate = 0.07 (23 / 343), avg. gap size = 2.96 (68 / 23) 359 33.04 2.29 4.21 chr6ptel1M 448674 448891 (551109) C L1ME5_3end#LINE/L1 (304) 637 424 m_b283s551i4 11385 chr6ptel1M 448674 TCCTGCTCATTTCACTCAGCATCA-GTTCGTGTAAG-TCTCTCCAGGCTT 448721 i i iv ii - -- v - iv v i v C L1ME5_3end#LI 637 TCTTACTTTTTTCACTCAGCACTATGTT--TTTAAGATCCATCCATGTTG 590 chr6ptel1M 448722 CTCTGAAATCATCCTGCTGGTCATTTCTTACAGAACAATAATATTCCATA 448771 v vivv iv iiv iii v v vvvv i i i C L1ME5_3end#LI 589 CTATGTGTACATCTAGTCCGTTGCTTCTAACTGCTGCATAGTACTCCATG 540 chr6ptel1M 448772 ATATTCACATCCCATCAC---TTACTCAGCCATTCTCCAGCTGATGGGCA 448818 i i --i - i --- ii v i viv i C L1ME5_3end#LI 539 GTGT--GCAT-CCACCACATTTTACCTATCCACTCTCCCAGTGATGGACA 493 chr6ptel1M 448819 TCCACTCAGTTTCCAGCTTCTGGCCACTACAAAGAGGGCTGCCACAAACA 448868 i vviv ii i i iv i v iv v ii C L1ME5_3end#LI 492 CCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCTGCAATGAACA 443 chr6ptel1M 448869 TTTTTGCACATGGGGGTCCCTTT 448891 ii i i ---- i C L1ME5_3end#LI 442 TCCTCGTACAT----GTCCCCTT 424 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 44.43 CpG sites = 42, Kimura (unadjusted) = 45.34 Transitions / transversions = 1.56 (42/27) Gap_init rate = 0.06 (12 / 217), avg. gap size = 1.17 (14 / 12) 416 28.69 0.00 0.00 chr6ptel1M 448759 448880 (551120) C L1ME3A_3end#LINE/L1 (368) 552 431 m_b283s551i5 11385 chr6ptel1M 448759 ATAATATTCCATAATATTCACATCCCATCACTTACTCAGCCATTCTCCAG 448808 i vi i vv i v iv i i i v v v C L1ME3A_3end#L 552 ATAGTATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTACTG 503 chr6ptel1M 448809 CTGATGGGCATCCACTCAGTTTCCAGCTTCTGGCCACTACAAAGAGGGCT 448858 i i iiivvi? i ?? i i i v v C L1ME3A_3end#L 502 TTGATGGACATTTGGGTNGTTTCCAGTTTNNGGCTATTACGAATAGTGCT 453 chr6ptel1M 448859 GCCACAAACATTTTTGCACATG 448880 i ii i i C L1ME3A_3end#L 452 GCTATGAACATTCTTGTACATG 431 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 37.59 CpG sites = 23, Kimura (unadjusted) = 39.04 Transitions / transversions = 1.92 (23/12) Gap_init rate = 0.00 (0 / 121), avg. gap size = 0.0 (0 / 0) 13 22.22 5.56 1.79 chr6ptel1M 449326 449379 (550621) (TTTCTT)n#Simple_repeat 1 56 (0) m_b283s252i1 11386 chr6ptel1M 449326 TTTCTTTATCTTTATTC-CAATCTTTCAGTTTTAGGTTTT-TTTTT-TTT 449372 v - -ivv ivv vvv - - (TTTCTT)n#Sim 1 TTTCTTTTTCTTT-TTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTT 49 chr6ptel1M 449373 TTCTTTT 449379 (TTTCTT)n#Sim 50 TTCTTTT 56 Matrix = Unknown Transitions / transversions = 0.25 (2/8) Gap_init rate = 0.08 (4 / 53), avg. gap size = 1.00 (4 / 4) 15 5.56 0.00 0.00 chr6ptel1M 449361 449379 (550621) (T)n#Simple_repeat 1 19 (0) m_b283s252i2 11387 chr6ptel1M 449361 TTTTTTTTTTTTTTCTTTT 449379 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 194 35.10 6.06 0.72 chr6ptel1M 449708 449839 (550161) L2a_3end#LINE/L2 352 490 (27) m_b283s601i4 11388 chr6ptel1M 449708 TATACTTTGTTTACTTATTTACATAAATGT-TGTACTAATCAAATAGACC 449756 i ii i ii- v v - viivvi v v vi L2a_3end#LINE 352 TATATTTTACTTATTTATTTGT-TTATTGTCTGTCTCCCCCCACTAGAAT 400 chr6ptel1M 449757 GGAAGCTTCTTGAAGGTCAAGA--TTGGTTTGTTTTGCTTTCTT-----T 449799 v i v i ivii -- v i i iv v----- L2a_3end#LINE 401 GTAAGCTCCATGAGGGCAGGGACTTTTGTCTGTTTTGTTCACTGCTGTAT 450 chr6ptel1M 449800 CTTCAGTACCCAGCACAATGTCTTGCTCTTAGAAGGCATT 449839 ii ii i v i i v v v v ii L2a_3end#LINE 451 CCCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGGCGCT 490 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 46.13 CpG sites = 27, Kimura (unadjusted) = 49.30 Transitions / transversions = 1.42 (27/19) Gap_init rate = 0.03 (4 / 131), avg. gap size = 2.25 (9 / 4) 225 34.41 5.38 0.00 chr6ptel1M 449747 449839 (550161) L2d2_3end#LINE/L2 431 528 (27) m_b283s601i5 11388 chr6ptel1M 449747 CAAATAGACCGGAAGCTTCTTGAAGGTCAAGAT--TGGTTTGTTTTGCTT 449794 v ii v i i ivii i-- vi i vi v L2d2_3end#LIN 431 CAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACTTCTT 480 chr6ptel1M 449795 TCTTTCTTC---AGTACCCAGCACAATGTCTTGCTCTTAGAAGGCATT 449839 v v ii --- ii i i i v vi v ii L2d2_3end#LIN 481 TGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAGTAGGCGCT 528 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 44.40 CpG sites = 21, Kimura (unadjusted) = 48.93 Transitions / transversions = 1.91 (21/11) Gap_init rate = 0.02 (2 / 92), avg. gap size = 2.50 (5 / 2) 372 32.69 8.80 0.86 chr6ptel1M 449839 450054 (549946) C MIRc#SINE/MIR (26) 242 10 m_b283s601i6 11389 chr6ptel1M 449839 TAACACT--ACATTTTTCTGAGAGTTTT---ATAAAT-ATCTCTTTT--T 449880 i -- v v vi v i --- v - v -- C MIRc#SINE/MIR 242 TAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATCTCATTTGAT 193 chr6ptel1M 449881 TCTCAAAAAACAAAATGCTGAGG------AGGTAGATGCTTTTATTCCCA 449924 i v -- vvivv ------i i i ii v i C MIRc#SINE/MIR 192 CCTCACAA--CAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCA 145 chr6ptel1M 449925 TCTGACCAATGAGGAAACTAAGG--CAGACAGATAGAGTGACTTGTCTGG 449972 i v vi i -- v i vi i iii C MIRc#SINE/MIR 144 TTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAA 95 chr6ptel1M 449973 GGTCACATAAGCAGTAAATCTTTGAGGTCAAAGTTGAATTTAAGTTTTTG 450022 i ivi i vviv vivii v i iii i i iv C MIRc#SINE/MIR 94 GGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCC 45 chr6ptel1M 450023 GAACTGCAGGT--AGTGTTCTAT-TACTGTGTTAC 450054 vi v i -- i v -i iiii C MIRc#SINE/MIR 44 TGACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 43.06 CpG sites = 43, Kimura (unadjusted) = 44.81 Transitions / transversions = 1.59 (43/27) Gap_init rate = 0.05 (10 / 215), avg. gap size = 2.10 (21 / 10) 372 26.61 5.52 4.08 chr6ptel1M 449847 449991 (550009) C MIRb#SINE/MIR (43) 225 79 m_b283s601i7 11389 chr6ptel1M 449847 CATTTTTCTGAGAGTTTTATA---AATATCTCTTTT--TTCTCAAAAAAC 449891 i v v i v i i --- v v -- i ----- C MIRb#SINE/MIR 225 CACTGTGCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCA-----C 181 chr6ptel1M 449892 AA-AATGCTGAGGAGGTAGATGCTTTTATTCCCATCTGACCAATGAGGAA 449940 - iv v - i ii v i i v vi C MIRb#SINE/MIR 180 AACAACCCTGCG-AGGTAGGTATTATTATCCCCATTTTACAGATGAGGAA 132 chr6ptel1M 449941 ACTAAGG--CAGACAGATAGAGTGACTTGTCTGGGGTCACATAAGCAGTA 449988 i -- v i vi i i iii i ivi C MIRb#SINE/MIR 131 ACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTA 82 chr6ptel1M 449989 AAT 449991 i C MIRb#SINE/MIR 81 AGT 79 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 34.07 CpG sites = 24, Kimura (unadjusted) = 34.07 Transitions / transversions = 1.85 (24/13) Gap_init rate = 0.07 (10 / 144), avg. gap size = 1.40 (14 / 10) 226 22.41 1.72 0.00 chr6ptel1M 450175 450232 (549768) DNM1r#Unknown 2485 2543 (2119) m_b283s502i0 11390 chr6ptel1M 450175 TGCATGTATCTCTGTGTATATGTAT-TATATATGTATATATATATATACA 450223 ii i v v i - i i i i i DNM1r#Unknown 2485 TGTGTATATATGTGTGTATATGTGTGTATGTGTGTATATATGTGTATATA 2534 chr6ptel1M 450224 CACATATAT 450232 i i ? DNM1r#Unknown 2535 TACGTATNT 2543 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 26.49 CpG sites = 11, Kimura (unadjusted) = 29.15 Transitions / transversions = 5.50 (11/2) Gap_init rate = 0.02 (1 / 57), avg. gap size = 1.00 (1 / 1) 36 0.00 0.00 0.00 chr6ptel1M 450236 450266 (549734) (GT)n#Simple_repeat 1 31 (0) c_b283s251i1 11391 chr6ptel1M 450236 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 450266 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 13 10.30 2.86 5.88 chr6ptel1M 450321 450355 (549645) (TCATT)n#Simple_repeat 1 34 (0) m_b283s252i3 11392 chr6ptel1M 450321 TCATATC-TTTCATTTCATTTTATCTTCACATTCAT 450355 v - i - -v (TCATT)n#Simp 1 TCATTTCATTTCATTTCATTTCAT-TTCA-TTTCAT 34 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.09 (3 / 34), avg. gap size = 1.00 (3 / 3) 38 0.00 0.00 0.00 chr6ptel1M 450502 450534 (549466) (GT)n#Simple_repeat 1 33 (0) c_b283s251i2 11393 chr6ptel1M 450502 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 450534 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 33 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 309 28.45 5.34 0.73 chr6ptel1M 450896 451026 (548974) C MIR3#SINE/MIR (5) 203 67 m_b283s601i8 11394 chr6ptel1M 450896 ATAGAATCCTAGACTATCGGAGCTGGACGGCATCTGCGAGATTCTCTGTT 450945 v v i i v v i vv iv iv C MIR3#SINE/MIR 203 ATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGT 154 chr6ptel1M 450946 CCGACCCCCTCAGTCCGTAAATGAGGACGTTGCGGAGCGGCCAAGGAAAG 450995 i v iiii i vii v vv i vv i vi C MIR3#SINE/MIR 153 CCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAG 104 chr6ptel1M 450996 GGA----TCCA--GTC-CACTAGTGGGTTGGTGGCAGA 451026 v ----i -- - - i?i i C MIR3#SINE/MIR 103 TGACTTGCCCAAGGTCACAC-AGCNAGTTAGTGGCAGA 67 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 36.81 CpG sites = 20, Kimura (unadjusted) = 36.81 Transitions / transversions = 1.18 (20/17) Gap_init rate = 0.03 (4 / 130), avg. gap size = 2.00 (8 / 4) 256 26.40 0.00 1.39 chr6ptel1M 451132 451204 (548796) MIR3#SINE/MIR 114 185 (23) m_b283s601i9 11395 chr6ptel1M 451132 CTGGGTCTTGGGTTCCTTGTCTGTGCACTGAGGGTATCAGCCTGGATGGT 451181 i ii v ii iv v vi ii v i i MIR3#SINE/MIR 114 CTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGAT 163 chr6ptel1M 451182 TTCTAAGGGTTTCTTCCAGCTCT 451204 i - ii MIR3#SINE/MIR 164 CTCTAA-GGTCCCTTCCAGCTCT 185 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 34.39 CpG sites = 14, Kimura (unadjusted) = 34.39 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.01 (1 / 72), avg. gap size = 1.00 (1 / 1) 343 29.17 3.31 0.81 chr6ptel1M 451272 451392 (548608) C MamRTE1#LINE/RTE-BovB (7) 3805 3682 m_b283s601i10 11396 chr6ptel1M 451272 TTGTTACCGTTTGCATTGAAAGGTGTCCCTGTTGATGGTGTTTGTGATCT 451321 i ii v i i vi i v v ii i v iv C MamRTE1#LINE/ 3805 TCGTTGTCCTTCGTATTCGAAGATGACGCTACTGACGGTGATTGCTATCT 3756 chr6ptel1M 451322 GTGTGTGT--CTGTGTCTGAGAAAGACAGATGGATGACTAATGG-CCTTT 451368 i i--v v - v vi i ii - C MamRTE1#LINE/ 3755 ATGTGTGCGGGTGTGGCTGA-AAAGACCGATGCGTGACCAACAGTCCTTT 3707 chr6ptel1M 451369 CCACACCAAAT-TACCTGGAGACTG 451392 iivii-i v i C MamRTE1#LINE/ 3706 CCACACTGTGCACACGTGAAGACTG 3682 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 30.57 CpG sites = 23, Kimura (unadjusted) = 38.60 Transitions / transversions = 1.92 (23/12) Gap_init rate = 0.03 (4 / 120), avg. gap size = 1.25 (5 / 4) 21 4.17 0.00 0.00 chr6ptel1M 451915 451939 (548061) (A)n#Simple_repeat 1 25 (0) m_b283s252i4 11397 chr6ptel1M 451915 AAAAAAAAAAAAAAAAAAAAAAGAA 451939 i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAA 25 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 359 22.67 3.03 2.00 chr6ptel1M 452123 452221 (547779) C MIR#SINE/MIR (119) 143 44 m_b283s601i11 11398 chr6ptel1M 452123 CCATTTTACAGATGAGGAAACTGAGGCAAATTG-CATCAGGTGACTTGCC 452171 v vv -vi i i i C MIR#SINE/MIR 143 CCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCC 94 chr6ptel1M 452172 TAGGGTCACATGACTAGGAAG-GATTCACAGCT-GGATTTGAACTTGGGA 452219 i i iii v - i-- v i- i iii v C MIR#SINE/MIR 93 CAAGGTCACACAGCTAGTAAGTGG--CAGAGCCGGGATTCGAACCCAGGC 46 chr6ptel1M 452220 AG 452221 C MIR#SINE/MIR 45 AG 44 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 25.00 CpG sites = 15, Kimura (unadjusted) = 27.92 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.05 (5 / 98), avg. gap size = 1.00 (5 / 5) 277 32.67 0.98 0.98 chr6ptel1M 454108 454209 (545791) MIR3#SINE/MIR 104 205 (3) m_b283s601i12 11399 chr6ptel1M 454108 CTTTATCTCATTATATCTTAATGTCTTCATGTGTGAAGTGAGGGTGCCCA 454157 i i vi ivii i i v i v i i v iivi MIR3#SINE/MIR 104 CTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGG 153 chr6ptel1M 454158 TCTTGATGATCCTTAGGGTTCCCTTAAGCTCAGA-ATCCTGTGATTTCCA 454206 v v ii i i i iv v - i i - i MIR3#SINE/MIR 154 ACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGA-TTCTA 202 chr6ptel1M 454207 TGA 454209 MIR3#SINE/MIR 203 TGA 205 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 45.94 CpG sites = 23, Kimura (unadjusted) = 45.94 Transitions / transversions = 2.30 (23/10) Gap_init rate = 0.02 (2 / 101), avg. gap size = 1.00 (2 / 2) 275 28.72 9.57 0.00 chr6ptel1M 454481 454574 (545426) C L2c_3end#LINE/L2 (10) 468 366 m_b283s601i13 11400 chr6ptel1M 454481 TCAACAAGTACTTACTAAATGCCTGCTGTGTGCCA--------GAAAAAA 454522 ii i i i ii i i -------- i v v C L2c_3end#LINE 468 TCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGATACA 419 chr6ptel1M 454523 AAAATATGTGAG-CGCAATCCCTGCCCACCAGGCGCTCTCAGGCTAATGG 454571 i ivi i - i ii v v v v v i C L2c_3end#LINE 418 AAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAGTGG 369 chr6ptel1M 454572 GGG 454574 i C L2c_3end#LINE 368 AGG 366 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 34.65 CpG sites = 19, Kimura (unadjusted) = 38.27 Transitions / transversions = 2.38 (19/8) Gap_init rate = 0.02 (2 / 93), avg. gap size = 4.50 (9 / 2) 423 35.03 2.79 1.10 chr6ptel1M 454669 454847 (545153) C MIR3#SINE/MIR (7) 201 20 m_b283s601i14 11401 chr6ptel1M 454669 AGCATCAAAGGATAGTAAAACTGGAAGGCACTTTAGGAATCAACCAGTCC 454718 v v i ivi i i v i ii v i C MIR3#SINE/MIR 201 AGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCC 152 chr6ptel1M 454719 CAGCCCTTATTTTTACAGATGAGGAAATGGCAGATGGGAATCTTGAAATG 454768 v v i vv iv vi vivi ivvv i C MIR3#SINE/MIR 151 AACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTG 102 chr6ptel1M 454769 ACTTATCCATGTGCACACATG-----TAGTAAAAGAACAAAAGTTTGAAC 454813 ii v vv - ----- iiv i viiiii v C MIR3#SINE/MIR 101 ACTTGCCCAAGGTCACACA-GCNAGTTAGTGGCAGAGCCGGGACTAGAAC 53 chr6ptel1M 454814 CCAGGCTTTTCAACTCTAAATTCTGTGGTTTTCC 454847 ii iiii iv i- i v i ii C MIR3#SINE/MIR 52 CCAGGTCTCCTGACTCCCAG-TCCGTGCTCTCTC 20 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 47.24 CpG sites = 38, Kimura (unadjusted) = 49.53 Transitions / transversions = 1.58 (38/24) Gap_init rate = 0.02 (3 / 178), avg. gap size = 2.33 (7 / 3) 593 17.11 1.46 6.11 chr6ptel1M 454850 454986 (545014) MIRc#SINE/MIR 16 146 (122) m_b283s601i15 11402 chr6ptel1M 454850 CAGTTCATAGAGCACTGGACCTGAAGTC-GGAAGACTCATCTGACTGAGT 454898 vv v i i - -------- i MIRc#SINE/MIR 16 CAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC--------CTGGGT 57 chr6ptel1M 454899 TCAAATCCAACCTCAGAACTTTACTAGCTGTGTGACCCTGGGCAAGTCAC 454948 i i viv v vvvi i MIRc#SINE/MIR 58 TCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCAC 107 chr6ptel1M 454949 TTAACTCAGCTG-GCCTCAGTTTCCCCATCTGTAAAATG 454986 iivv - i MIRc#SINE/MIR 108 TTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATG 146 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 17.61 CpG sites = 11, Kimura (unadjusted) = 19.45 Transitions / transversions = 1.00 (11/11) Gap_init rate = 0.07 (10 / 136), avg. gap size = 1.00 (10 / 10) 188 32.05 2.53 1.25 chr6ptel1M 455217 455295 (544705) MIR3#SINE/MIR 109 188 (20) m_b283s601i16 11403 chr6ptel1M 455217 CCTTCCCCGATCTCGGGTTCCTTCTGCTCTAACATAACGATGCTGGATTA 455266 ii iv ii i v iv - v v i v iv i i MIR3#SINE/MIR 109 CCTCTCTGGGCCTCAGTTTCCTCAT-CTGTAAAATGAGGGGGTTGGACTA 157 chr6ptel1M 455267 AATAACCTCGAA--TCCCTTGCAGTTCCGAC 455295 i i i v -- v i i MIR3#SINE/MIR 158 GATGATCTCTAAGGTCCCTTCCAGCTCTGAC 188 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 43.85 CpG sites = 16, Kimura (unadjusted) = 43.85 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.03 (2 / 78), avg. gap size = 1.50 (3 / 2) 245 26.74 4.65 0.00 chr6ptel1M 458006 458091 (541909) C MIR3#SINE/MIR (61) 147 58 m_b283s601i17 11404 chr6ptel1M 458006 CCTTCATTACCCAGACCAGGAA-CTGGAGCC-AAAGCAGGGAAGTCGCTT 458053 i viv iv - ii - i vi v vi C MIR3#SINE/MIR 147 CCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTT 98 chr6ptel1M 458054 CTCCAAAGTCACT--GCAAGTTAAAGGCAAAACCAGGACT 458091 vi i v-- ? iv i i i C MIR3#SINE/MIR 97 GCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACT 58 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 32.68 CpG sites = 14, Kimura (unadjusted) = 34.52 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.04 (3 / 85), avg. gap size = 1.33 (4 / 3) 297 16.59 0.00 10.45 chr6ptel1M 458706 458779 (541221) MIRc#SINE/MIR 49 115 (153) m_b283s601i18 11405 chr6ptel1M 458706 GACCTAAGTTCAAATCCAGCCTCAGATCCTTAATACTTCCTAGTTGTGTG 458755 ii i i v v v -- ----- v i MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTG--CC-----ACTTACTAGCTGTGTG 91 chr6ptel1M 458756 ACCCTGGGCAAGTCACTTAACCCC 458779 i i MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 17.02 CpG sites = 7, Kimura (unadjusted) = 18.82 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.10 (7 / 73), avg. gap size = 1.00 (7 / 7) 261 17.02 2.13 0.00 chr6ptel1M 459682 459728 (540272) C MIR#SINE/MIR (12) 250 203 m_b283s601i19 11406 chr6ptel1M 459682 CATTTATTAGGCACCTACTG-GCGCCAGGCACTGTCCTAAGTGCTTTA 459728 ii i i i- i i i C MIR#SINE/MIR 250 CATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGCGCTTTA 203 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 15.31 CpG sites = 8, Kimura (unadjusted) = 20.81 Transitions / transversions = 1.00 (8/0) Gap_init rate = 0.02 (1 / 46), avg. gap size = 1.00 (1 / 1) 255 34.21 3.15 5.65 chr6ptel1M 462241 462367 (537633) C L2d2_3end#LINE/L2 (19) 536 413 m_b283s601i20 11407 chr6ptel1M 462241 ATTTATGAGGCACTTACTATATGTATGCAGAGCACAATACT-GGCACCG- 462288 vii i i ---- i ii vi i - i i - C L2d2_3end#LIN 536 ATTTATTGAGCGCCTACT----GTGTGCAAGGCACTGTGCTAGGCGCTGT 491 chr6ptel1M 462289 AGGGTATGCAAAGTCTAA--ATGAGATATAGTTCCCATCCTTGTGTAGTT 462336 i v i --- -- i i i i iii iiv v i C L2d2_3end#LIN 490 GGGGGATACAAAG---AAGTATAAGACATGGTCCCTGCCCTCAAGGAGCT 444 chr6ptel1M 462337 TAGGGATTGATAAAAGAGATAAGACACAAAC 462367 viivi ii viii i i C L2d2_3end#LIN 443 TACAATCTAGTTGGGGAGACAAGACATAAAC 413 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 47.75 CpG sites = 33, Kimura (unadjusted) = 51.52 Transitions / transversions = 4.12 (33/8) Gap_init rate = 0.08 (10 / 126), avg. gap size = 1.10 (11 / 10) 12 24.89 0.00 0.00 chr6ptel1M 462656 462689 (537311) (AGAAC)n#Simple_repeat 1 34 (0) m_b283s252i5 11408 chr6ptel1M 462656 AGAACAGAACAGAACAAAGTAGTATTGGACAGAA 462689 i ii v iv i (AGAAC)n#Simp 1 AGAACAGAACAGAACAGAACAGAACAGAACAGAA 34 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 382 29.30 10.00 0.87 chr6ptel1M 462973 463182 (536818) L3#LINE/CR1 3826 4054 (45) m_b283s601i21 11409 chr6ptel1M 462973 GGCTTGAGAGGGCAGAACTTCGATCAATGGGTAGGCGACATAAGAAGATA 463022 iv vv i i iv vi i i i ii L3#LINE/CR1 3826 GGCTCCAGAGGGCAGAACTAGGACCAATGGGTGGAAGTTACAGGGAGGCA 3875 chr6ptel1M 463023 GATTTCTGTTC-GTATAAGGATAA--TTTCTAA-----AGAAGTATCTGA 463064 v i -i vi -- ----- iv i ii L3#LINE/CR1 3876 GATTTCGGCTCAATATAAGGAAGAACTTTCTAACAATCAGAGCTGTCCAA 3925 chr6ptel1M 463065 ATGGAGAATGGTTTTCCT---GAAGTAGTGAGCTTACCTG-----GGATG 463106 vivi vi v --- i i- i ----- v L3#LINE/CR1 3926 AAATGGAATGGGCTGCCTCGNGAGGTAGTGAGCTC-CCCGTCACTGGAGG 3974 chr6ptel1M 463107 TCTGCAGGGAGATACAGTATGAACTCTTGCT---GATGACTGTATATTGA 463153 v v i v vi v v v v ii--- -i v vv i L3#LINE/CR1 3975 TGTTCAAGCAGAGGCTGGATGACCACTTGTCAGGGATG-TTGTAGAAGGG 4023 chr6ptel1M 463154 ATTATTAC-TTAGGCGTG-GGTTGAACTAGA 463182 vi i - i ii v - i L3#LINE/CR1 4024 ATTCCTGCATTGGATGGGAGGTTGGACTAGA 4054 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 37.35 CpG sites = 35, Kimura (unadjusted) = 38.14 Transitions / transversions = 1.35 (35/26) Gap_init rate = 0.05 (10 / 209), avg. gap size = 2.30 (23 / 10) 649 19.54 0.00 5.84 chr6ptel1M 463185 463347 (536653) C Charlie4a#DNA/hAT-Charlie (1) 507 354 m_b283s502i1 11410 chr6ptel1M 463185 AGGAGCTCTTAAACATTTTGTGTGTCACAGACCTCCTTTGGCAATCTAGC 463234 i i v - v i ii - i i - C Charlie4a#DNA 507 AGGGGTTCTTAACC-TTTTTTGTGCCATGGACC-CCTTTGGCAGTCTGG- 461 chr6ptel1M 463235 CTGATAAAGCATATCATCACCCCTTGTGAGAATTCTGTTTTTAAATTCAT 463284 ---- i v vi-- v v vv v C Charlie4a#DNA 460 ----TGAAGCCTATGG--ACCCCTTCTCAGAATAATGTTTTTAAATGCAT 417 chr6ptel1M 463285 AAAATAACATTCATAGGGTTCCAAAGGAAATCTATTATACAGAAGTACTG 463334 v v i v i v iv i v C Charlie4a#DNA 416 AAAATAAAATACATAGGATTACAAAGGAAACCAATTATATTGAAATACAG 367 chr6ptel1M 463335 TTACCAAAATCTT 463347 i v C Charlie4a#DNA 366 TTATCAAAATATT 354 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 22.65 CpG sites = 14, Kimura (unadjusted) = 22.65 Transitions / transversions = 0.88 (14/16) Gap_init rate = 0.06 (9 / 162), avg. gap size = 1.00 (9 / 9) 240 28.34 7.59 2.63 chr6ptel1M 463460 463604 (536396) C Plat_L3#LINE/CR1 (314) 3259 3108 m_b283s551i6 11411 chr6ptel1M 463460 TCCATATACTAGAGGTCAGTTATTATG-CACCAGGAAGTCT--TTTTCTC 463506 i v i v v - vvvv i -- i C Plat_L3#LINE/ 3259 TTCATATACTTGAAGACAGTTATTAAGTCACCCCTTAGCCTTCTCTTCTC 3210 chr6ptel1M 463507 TAGGCT-AACAGCCCTTATCTTTCAGTTGAACCTTTTATGATAAGATC-- 463553 i - i iv -- i -- v iv v i i -- C Plat_L3#LINE/ 3209 CAGGCTAAACAACCCCAA--TTCC--TTTAACCTTTCCTCATAGGACCTA 3164 chr6ptel1M 463554 ---TTGAACCTTCTCATCATCTTAGCTTTTCTTCCCTAAATA--CTCCAG 463598 --- iv v i i v i v iivi i ii iv-- C Plat_L3#LINE/ 3163 TTTTCCATCCCTTTAATCATTTTTGTCGCTCTTCTCTGGACCCTCTCCAG 3114 chr6ptel1M 463599 TTTGTC 463604 v C Plat_L3#LINE/ 3113 TTTCTC 3108 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.21 CpG sites = 22, Kimura (unadjusted) = 36.34 Transitions / transversions = 1.22 (22/18) Gap_init rate = 0.07 (10 / 144), avg. gap size = 1.50 (15 / 10) 16 0.00 0.00 0.00 chr6ptel1M 464055 464074 (535926) (TTG)n#Simple_repeat 1 20 (0) m_b283s252i6 11412 chr6ptel1M 464055 TTGTTGTTGTTGTTGTTGTT 464074 (TTG)n#Simple 1 TTGTTGTTGTTGTTGTTGTT 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 228 26.00 1.25 3.85 chr6ptel1M 464468 464547 (535453) Plat_L3#LINE/CR1 3183 3260 (313) m_b283s551i7 11413 chr6ptel1M 464468 TTGAAGGAATTGGAGAAATTT-GCTTTGAGAAGAAAAGGCTTAAGAGGGG 464516 i i vvi - i v i - i v Plat_L3#LINE/ 3183 TTAAAGGAATTGGGGTTGTTTAGCCTGGAGAAGAGAAGGC-TAAGGGGTG 3231 chr6ptel1M 464517 CCCCAACAGCACCATGTTTAGGTGTATGAAG 464547 v ii i -- ii v i i i Plat_L3#LINE/ 3232 ACTTAATA--ACTGTCTTCAAGTATATGAAG 3260 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 33.37 CpG sites = 14, Kimura (unadjusted) = 33.37 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.05 (4 / 79), avg. gap size = 1.00 (4 / 4) 40 0.00 0.00 0.00 chr6ptel1M 464720 464753 (535247) (GT)n#Simple_repeat 1 34 (0) c_b283s251i3 11414 chr6ptel1M 464720 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 464753 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 34 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 451 24.18 12.12 1.83 chr6ptel1M 465478 465675 (534325) C MIRc#SINE/MIR (0) 268 51 m_b283s601i22 11415 chr6ptel1M 465478 AATAATAATAATACCA-GTATTT--ATAGCACGT-AAAGCTTTTTTA-AA 465522 i? v-ii -- v - v ---- - C MIRc#SINE/MIR 268 AATAATAATAACNCCTTACATTTGTATAGCACTTTACAG----TTTACAA 223 chr6ptel1M 465523 AGAGCTTT-ACATGTATTCTCTAATTTGATTCTCACAGTATTTCTGTGGG 465571 v - ii v v i ii vii i C MIRc#SINE/MIR 222 AGCGCTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAG 173 chr6ptel1M 465572 ATGGAT---GC---TAATATTATCCTCATTTGCCA-ATAAGTAGACTGAG 465614 i i ii--- --- v i vv - i v i C MIRc#SINE/MIR 172 GTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAG 123 chr6ptel1M 465615 G----G------TAAGT-ACTTGCCTAAGGTCATATAATTAGGACGTATC 465653 ---- ------ - i i i ii v v iv C MIRc#SINE/MIR 122 GCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGC 73 chr6ptel1M 465654 AGAGGCTGGGTTGAGACCTAAG 465675 v v ii vii i i C MIRc#SINE/MIR 72 AGAGCCGGGACTCGAACCCAGG 51 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 29.53 CpG sites = 30, Kimura (unadjusted) = 30.30 Transitions / transversions = 1.76 (30/17) Gap_init rate = 0.08 (15 / 197), avg. gap size = 1.87 (28 / 15) 487 26.62 7.79 0.00 chr6ptel1M 465522 465675 (534325) C MIR#SINE/MIR (50) 212 47 m_b283s601i23 11415 chr6ptel1M 465522 AAGAGCTTTACATGTATTCTCTAATTTGATTCTCACAGTATTTCTGTGGG 465571 v vv v i i ii vii i i C MIR#SINE/MIR 212 AAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAG 163 chr6ptel1M 465572 ATGGATGCTAATATTATCCTCATTTGCCA-ATAAGTAGACTGAGG----G 465616 i i i i v i vv - i v i ---- C MIR#SINE/MIR 162 GTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAG 113 chr6ptel1M 465617 ------TAAGT-ACTTGCCTAAGGTCATATAATTAGGACGTATCAGAGGC 465659 ------ - i i i ii v v iv v C MIR#SINE/MIR 112 AGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCC 63 chr6ptel1M 465660 TGGGTTGAGACCTAAG 465675 v i vii i i C MIR#SINE/MIR 62 GGGATTCGAACCCAGG 47 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 32.95 CpG sites = 26, Kimura (unadjusted) = 33.97 Transitions / transversions = 1.73 (26/15) Gap_init rate = 0.03 (4 / 153), avg. gap size = 3.00 (12 / 4) 1746 28.11 1.43 1.75 chr6ptel1M 467060 467689 (532311) C L1ME4c_3end#LINE/L1 (191) 639 12 m_b283s551i8 11416 chr6ptel1M 467060 TTCTGCTCATTTCACTTAGCATCAGTTCATGTA-ATTTCTCTCCAAGCTT 467108 iv i i vv iv - --- v i v C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATAAACATTT---TCCATGTTG 593 chr6ptel1M 467109 CTCTGTATTCATCTTGCTGGTCATTTCTTACAGAACAATAATATTCCATA 467158 vii v v v iv vi i v ii vvvv v C L1ME4c_3end#L 592 CTACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATC 543 chr6ptel1M 467159 ACATTCATATACCACAATTTACCCAACCATTCTCCAATTGATGGGCAGCC 467208 ivi ?v i i ii i v v i vii C L1ME4c_3end#L 542 GAGTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTT 493 chr6ptel1M 467209 ACTCAGTTTCCAGCTTCTAGCCACTACAAACAGGGCTGCCACAAACAT-- 467256 vviv ii i v i i i i iv v ii -- C L1ME4c_3end#L 492 AGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCT 443 chr6ptel1M 467257 TCGTGCACATACAGGTCCCTTTCCCTTCTTT---AGTATCTCCTTGGGGT 467303 i --- -- i i --- v i i i C L1ME4c_3end#L 442 TCGTGCATATA---G--CTTTTTCCTTCTTTTGAATTATTTCCTTAGGAT 398 chr6ptel1M 467304 ATAAGCCCAGTAGAAACACTGCTGGATCAAAGGGTATGCACAGTTTGATA 467353 v vv v viiv i i i v v v i C L1ME4c_3end#L 397 AAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATG 348 chr6ptel1M 467354 ACTTTTTGGGCATAATTCCAGATTGCTCTCCAGAATGGTTGGATTCATTC 467403 i i vivi i v v i i i v v iiv i C L1ME4c_3end#L 347 GCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTT 298 chr6ptel1M 467404 ACAGCTCCACCAACAATGTATCAGTGTCCCAGTTTTCCCACATCCCCTCC 467453 ?iv i v ? v iv i ? i v C L1ME4c_3end#L 297 ACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCC 248 chr6ptel1M 467454 AACACT---CATCATTATTTTTTCCTGTCATCTTAGCCAATCTGACAGGT 467500 i i ---i i i v iv---v i v i i i i i C L1ME4c_3end#L 247 AGCATTGGGTATTATCAATTTTTTA---AATTTTTGCTAATTTAATAGGC 201 chr6ptel1M 467501 GTGTAGTGGTATCTCAGAGTTGTCTTAATTTGCATTTCTCTGATTAATAA 467550 iv i vv ii i v i C L1ME4c_3end#L 200 GTAAAATGGTATCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACTAG 151 chr6ptel1M 467551 TGATTTGGAATACTCTTTCATATGAGTGGTAATAATTTCAATTTCATCAT 467600 i vv v i i i i i vv v v iv ? vv v v C L1ME4c_3end#L 150 CGAGGTTGAACATTTTTCCATGTGTTTGTTTACTANTTGTATTTCCTCTT 101 chr6ptel1M 467601 CTGAAAATTGTCTGTTCATATCCTTTGACCATTTATCAATTGGAGAATGG 467650 ? vi i v v i vv v C L1ME4c_3end#L 100 NTGTGAATTGTCTGTTCATGTCCTTTGCCCATTTATCTATTGGGGTCTTG 51 chr6ptel1M 467651 CTTGGTTTCTTATAAATTAGAGTCAGCTCTCTATATATT 467689 v ?vv v v i v i ? C L1ME4c_3end#L 50 ATNTTTTTCTTATCAATTTGAATGAGCTCTTTATATANT 12 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.07 CpG sites = 91, Kimura (unadjusted) = 36.36 Transitions / transversions = 1.10 (91/83) Gap_init rate = 0.02 (15 / 629), avg. gap size = 1.33 (20 / 15) 1146 29.02 3.91 3.66 chr6ptel1M 467551 468394 (531606) C L1M5_orf2#LINE/L1 (0) 3294 2449 m_b283s551i9 11416 chr6ptel1M 467551 TGATTTGGAATACTCTTTCATATGAGTGGTAATAATTTCAATTTCATCAT 467600 ?v v ii iii i vv iv iiiv v? v v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr6ptel1M 467601 CTGAAAATTGTCTGTTCATATCCTTTGACCATTTATCAATTGGA--GAAT 467648 i vi v vi i v v ?v i-- vv C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTT 3195 chr6ptel1M 467649 GGCTTGGTTTCTTA-TAAATTAGAGTCAGCTCTCTATATATTTTGGAAAT 467697 v -- ? - i ? iv -v i i i v i C L1M5_orf2#LIN 3194 GTCTT--TTTNTTATTGANTTGTAG-GAGTTCTTTATATATTCTGGATAC 3148 chr6ptel1M 467698 GAGGCCTTTATCAGA-ACCTTTAACTGTGAAGATGTTTTCCCAGTTTGTT 467746 v i - iv v -?i ii v v i ? i v C L1M5_orf2#LIN 3147 GAGTCCTTTGTCAGATATATGT-NTTGCAAATATTTTCTCCCANTCTGTG 3099 chr6ptel1M 467747 GCTTCCCTTCTAATCTTGTTTACATTAGTTTTGTTTGTACAGAAGCTTTT 467796 v i v i v v iv ivi vvv? vi i C L1M5_orf2#LIN 3098 GCTTGCCTTTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTTT 3049 chr6ptel1M 467797 TAATTTGATGTAATCAA-------AATTTTCTATTTTGTGATCAATAATG 467839 v v ? i v ------- i v i i --- ?i C L1M5_orf2#LIN 3048 AATTTTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGGT---TNGTG 3002 chr6ptel1M 467840 GTCTCTAGTTCGTCTTTAGTCACAAATTTCTTCCTCTTCCACAAGTCTGA 467889 v i i ivv v v --- v i i v v?i - i vvi C L1M5_orf2#LIN 3001 CTTTTTGTGTCCTGTTTA---AGAAATCTTTGCCTANCCCA-AGGTCACG 2956 chr6ptel1M 467890 GAGATAAACTATCCTATG--TTCTTCCAATTTGTTTATAATCTCGTTCTT 467937 i -- i v -- i ivvvv i i ii?ii C L1M5_orf2#LIN 2955 AAGAT--ATTCTCCTATGTTTTCTTCTAGAAGTTTTATAGTTTTANCTTT 2908 chr6ptel1M 467938 TATGTCTAAATC-ATGGACCCATTTTGATCTTATCTTGGTATATGGTGTT 467986 ii i ii - - i i ? vi v i v i v C L1M5_orf2#LIN 2907 TACATTTAGGTCTAT-GATCCATCTNGAATTAATTTTTGTGTATGGTGTG 2859 chr6ptel1M 467987 AAGTGTGGGTCCATGCCTAATTTCTGCCATACTAATTTCCAGTTATCCCA 468036 i iv v v?iii v i v ivi v i i i C L1M5_orf2#LIN 2858 AGGTAGGGGTCGAGNTTCATTTTTTTCCATATGGATATCCAATTGTTCCA 2809 chr6ptel1M 468037 GCAGTTTTTGTCAAATAATGA--ATTCTTGTCCCA--AAAGTGAGGATCT 468082 viv ii - - -- i vi --i v ----- ? C L1M5_orf2#LIN 2808 GCACCATTTGTTGAA-AA-GACTATCCTTTCCCCACTGAATTG-----CN 2766 chr6ptel1M 468083 TTGG---GTTTGTCAAACACTAAATTGCTATAGTTGACTAT---TCTGTC 468126 ---v v ii ? v? i vv -- i --- i - C L1M5_orf2#LIN 2765 TTGGCACCTTTGTCAAAAATCAANTGNCCATATATG--TGTGGGTCTAT- 2719 chr6ptel1M 468127 TTGTGAAC---CTAACCTGTTCCACTGATCAACTAATCTATTTCTTA-GC 468172 v i --- vi i v i vi - i - C L1M5_orf2#LIN 2718 TTCTGGACTCTCTATTCTGTTCCATTGATCTATTTGTCTA-TCCTTACGC 2670 chr6ptel1M 468173 CAATACCAAATAGTTTTGGTGACTGCTGCTTTATAATATAGTTTT-AGAT 468221 v iv i i v iv - i - ? C L1M5_orf2#LIN 2669 CAATACCACACTGTCTTGATTACTGTAGCTTTATAATA-AGTCTTGANAT 2621 chr6ptel1M 468222 CAGGTACAGCTAGGCCACCTTCA--TTTGATTTTTTTTTTCATTAATTCT 468269 ? vv - i i-- i -- v i i -vi v C L1M5_orf2#LIN 2620 CNGGTAGTG-TAAGT--CCTCCAACTTTGTTCTTCTTTTTCA-AGATTGT 2575 chr6ptel1M 468270 TTTGA-GATTCTTGACCTTTTATTATTCCATATGAATTTTGTTGTTATTT 468318 i-v ? ii i iivv i ivvi i vi C L1M5_orf2#LIN 2574 TTTGGCTATTCTNGGTCCTTTGCATTTCCATATAAATTTTAGAATCAGCT 2525 chr6ptel1M 468319 TTTCTAGATC-ATTAAAATATTTTCTTGGATGTCTGATTGGTATAGCACT 468367 v v vv - iv v ii v v - i v v i C L1M5_orf2#LIN 2524 TGTCAATTTCTACAAAAAAACCTGCTGGGAT-TTTGATTGGGATTGCATT 2476 chr6ptel1M 468368 AAATAAATAGATTAGTTTAGGGAAAAT 468394 i vv i i i i C L1M5_orf2#LIN 2475 GAATCTATAGATCAATTTGGGGAGAAT 2449 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 38.04 CpG sites = 128, Kimura (unadjusted) = 38.67 Transitions / transversions = 1.19 (128/108) Gap_init rate = 0.06 (47 / 843), avg. gap size = 1.36 (64 / 47) 237 32.21 0.83 1.68 chr6ptel1M 468646 468765 (531235) C L1ME3E_3end#LINE/L1 (438) 551 433 m_b283s551i10 11417 chr6ptel1M 468646 ATAATATTTCATTCCATTCATATACCAGAACTTATTCAGCCATTCCCCAA 468695 i i vi vv v i i v i vi C L1ME3E_3end#L 551 ATAGTATTCCATTGTATGAATATACCACAATTTATTTATCCATTCTCCTG 502 chr6ptel1M 468696 CAAATGGGCATCCAACCAATGTCCAGAGTTTTGCCACAACAAAAAAAAGT 468745 ivi i iiiivivi v vv i iv v vi-- C L1ME3E_3end#L 501 TCGATGGACATTTGGGTTGTTTCCAGTTTTTTGCTATTACAAACAATG-- 454 chr6ptel1M 468746 CTGCTCCAGACATT-TTGTAC 468765 viii - C L1ME3E_3end#L 453 CTGCTATGAACATTCTTGTAC 433 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 41.89 CpG sites = 22, Kimura (unadjusted) = 43.42 Transitions / transversions = 1.38 (22/16) Gap_init rate = 0.03 (3 / 119), avg. gap size = 1.00 (3 / 3) 30 0.00 0.00 0.00 chr6ptel1M 468950 468975 (531025) (AC)n#Simple_repeat 1 26 (0) c_b283s251i4 11418 chr6ptel1M 468950 ACACACACACACACACACACACACAC 468975 (AC)n#Simple_ 1 ACACACACACACACACACACACACAC 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 330 34.81 1.89 0.62 chr6ptel1M 469550 469708 (530292) C MIRc#SINE/MIR (106) 162 2 m_b283s601i24 11419 chr6ptel1M 469550 CAAGGATTCTTGTCCCCCTCCTGCAAACAAGGCAGCGGTATCTGAGAAAG 469599 i v v i v ii i i ii v i v viv v i C MIRc#SINE/MIR 162 CAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAG 113 chr6ptel1M 469600 ATAAAAAAAAGTTGTCTAAAGCC-C-CAGCTAAGAGGTGCCAGAGCCAGG 469647 i v ivi v- i i i i - - iv i v i C MIRc#SINE/MIR 112 GTTAAGTGAC-TTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGG 64 chr6ptel1M 469648 ACTAGAACCCGGATC-TCCTGTATCCAACAACAAAGCTCTTTTTAACACA 469696 v i i - vv vvv iv ii vii C MIRc#SINE/MIR 63 ACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCA 14 chr6ptel1M 469697 TCATCTTTTCTC 469708 i ivi vi C MIRc#SINE/MIR 13 CCACACTGCCTC 2 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 47.35 CpG sites = 32, Kimura (unadjusted) = 48.60 Transitions / transversions = 1.39 (32/23) Gap_init rate = 0.03 (4 / 158), avg. gap size = 1.00 (4 / 4) 957 22.75 0.93 1.41 chr6ptel1M 469968 470181 (529819) C MIRb#SINE/MIR (23) 245 33 m_b283s601i25 11420 chr6ptel1M 469968 AGCACTTACCATGTGCCAGGCACTGTGCTAAGCATTTTACACTTCTTTTC 470017 i i ii iviv v C MIRb#SINE/MIR 245 AGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACATGCATTATC 196 chr6ptel1M 470018 TTATTTGAGCTTCACAACAGCCCTGGGAAGTAGGTGCTATTATTATCTCC 470067 i i v i i v i --- i C MIRb#SINE/MIR 195 TCATTTAATCCTCACAACAACCCTGCGAGGTAGGT---ATTATTATCCCC 149 chr6ptel1M 470068 ATTTTACAGTGGAGAAAACTGAGGCAAACAGAGATTAAGTGGCTTGTCCA 470117 vv i vv v i ii i C MIRb#SINE/MIR 148 ATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCA 99 chr6ptel1M 470118 GGATCACGCAGCCAACAAGTATCTAAGGCTGCATTTGCACTTATGTCTTC 470167 i i i i ii iv vi v v v i v ii v vi C MIRb#SINE/MIR 98 AGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGT 49 chr6ptel1M 470168 CTGACTCC--AGCCTG 470181 -- i C MIRb#SINE/MIR 48 CTGACTCCAAAGCCCG 33 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 25.12 CpG sites = 30, Kimura (unadjusted) = 27.75 Transitions / transversions = 1.67 (30/18) Gap_init rate = 0.02 (4 / 213), avg. gap size = 1.25 (5 / 4) 765 26.29 3.70 1.36 chr6ptel1M 469997 470212 (529788) C MIRc#SINE/MIR (45) 223 3 m_b283s601i26 11420 chr6ptel1M 469997 AAGCATTTT-ACACTTCTTTTCTTATTTGAGCTTCACAACAGCCCTGGGA 470045 ii - iviv v i v i i v C MIRc#SINE/MIR 223 AAGCGCTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGA 174 chr6ptel1M 470046 AGTAGGT---GC---TATTATTATCTCCATTTTACAGTGGAGAAAACTGA 470089 i i--- --- i vv i C MIRc#SINE/MIR 173 GGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGA 124 chr6ptel1M 470090 GGCAAACAGAGATTAAGTGGCTTGTCCAGGATCACGCAGCCAACAAGTAT 470139 vv v i i i i i i i ii iv C MIRc#SINE/MIR 123 GGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGG 74 chr6ptel1M 470140 CTAAGGCTGCATTTGCACTTATGTCTTCCTGACTCC-AGCCTGGCATTGT 470188 vi v v v i i v ii v - i ii iii v C MIRc#SINE/MIR 73 CAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCT 24 chr6ptel1M 470189 ATTCACAATACTACCTGACTGCCT 470212 v i vii i --- C MIRc#SINE/MIR 23 TTCCACTGCACCAC---ACTGCCT 3 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 32.01 CpG sites = 36, Kimura (unadjusted) = 33.48 Transitions / transversions = 1.80 (36/20) Gap_init rate = 0.03 (7 / 215), avg. gap size = 1.57 (11 / 7) 188 28.85 0.00 0.00 chr6ptel1M 470803 470854 (529146) C L3#LINE/CR1 (247) 3852 3801 m_b283s601i27 11421 chr6ptel1M 470803 TTGCTTTTAGTTCAGACCTCTGGGGTCGACCAGAACAAATCCAGTCCCGC 470852 v ii v v i i ivv i i i i v C L3#LINE/CR1 3852 TTGGTCCTAGTTCTGCCCTCTGGAGCCACACAGAATAAGTCTAATCCCTC 3803 chr6ptel1M 470853 TT 470854 C L3#LINE/CR1 3802 TT 3801 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 37.51 CpG sites = 9, Kimura (unadjusted) = 37.51 Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 227 22.23 0.00 2.22 chr6ptel1M 471477 471522 (528478) C L2c_3end#LINE/L2 (10) 468 424 m_b283s601i28 11422 chr6ptel1M 471477 TCAGCTAGCATTTATTAAACACCTACTATGTGCCAGACCATTAGGG 471522 i v i i i i i- ii i C L2c_3end#LINE 468 TCAACAAACATTTATTGAGCGCCTACTATGTGCCAGG-CGCTGGGG 424 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 22.08 CpG sites = 9, Kimura (unadjusted) = 28.56 Transitions / transversions = 9.00 (9/1) Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1) 241 25.00 5.88 0.00 chr6ptel1M 471582 471649 (528351) C L2d2_3end#LINE/L2 (59) 496 425 m_b283s601i29 11423 chr6ptel1M 471582 CGCTGTGGGTGACACAGAGATGAACAAGTCACGGTTCCTGTCCTAAAAGG 471631 v i i v v i v i i i v i i C L2d2_3end#LIN 496 CGCTGTGGGGGATACAAAGAAGTATAAGACATGGTCCCTGCCCTCAAGGA 447 chr6ptel1M 471632 GCTTGC--TTT--TTAGAGAGA 471649 i -- i -- i i C L2d2_3end#LIN 446 GCTTACAATCTAGTTGGGGAGA 425 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 31.77 CpG sites = 12, Kimura (unadjusted) = 31.77 Transitions / transversions = 2.40 (12/5) Gap_init rate = 0.03 (2 / 67), avg. gap size = 2.00 (4 / 2) 231 29.88 6.12 0.97 chr6ptel1M 471655 471752 (528248) L2a_3end#LINE/L2 395 497 (20) m_b283s601i30 11424 chr6ptel1M 471655 TGGAACGGGAACTCCA---GGAAAGGGACTTTTGTTTGGTTTGGTTTTTT 471701 i i vi i --- iv i - v ivi L2a_3end#LINE 395 TAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTCT-GTTTTGTTCACT 443 chr6ptel1M 471702 G--GTATCTCTCGCATCTAGCACAGAACTTGGATTAGGGTAGGTGA-CAA 471748 -- i iv ii v vi i vvi vi i v- L2a_3end#LINE 444 GCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGGCGCTCAA 493 chr6ptel1M 471749 CAAA 471752 i L2a_3end#LINE 494 TAAA 497 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 36.09 CpG sites = 18, Kimura (unadjusted) = 39.56 Transitions / transversions = 1.64 (18/11) Gap_init rate = 0.04 (4 / 97), avg. gap size = 1.75 (7 / 4) 604 22.66 5.47 0.00 chr6ptel1M 473221 473348 (526652) Charlie4#DNA/hAT-Charlie 6 140 (3238) m_b283s502i2 11425 chr6ptel1M 473221 GTTCTTAACTTGGGGCCCACAGACCCCGAAAAGCCTCCTGGGGAGACTTC 473270 i i i v ii vii v iv v Charlie4#DNA/ 6 GTTCTTAACCTGGGGTCCACGGACCCCCAAGGGGTCCGTGGATAGAATTC 55 chr6ptel1M 473271 AGGTGATTCACAAACTTAGATGGGAAAAAATCCCATCTTTAATTTCA--- 473317 v i i iii i iv v --- Charlie4#DNA/ 56 AGGGGGTCCGTGAACTTGGATGGGAAAAAATTACATCTTTATTTTCACTA 105 chr6ptel1M 473318 ----GTAGCTGAAATTTAATATTTTATTCAATTAT 473348 ----v i ii iv Charlie4#DNA/ 106 ACCTCTAACTGAAATTTAGCATTTCCTTCAATTAT 140 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 25.55 CpG sites = 19, Kimura (unadjusted) = 27.75 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.02 (2 / 127), avg. gap size = 3.50 (7 / 2) 291 16.40 3.12 4.76 chr6ptel1M 473333 473396 (526604) Charlie4a#DNA/hAT-Charlie 406 468 (40) m_b283s502i3 11426 chr6ptel1M 473333 TATTTTATTCAATTATTCATT--ACAACATCCTTCTGAGCAGGGATCCAC 473380 --- v -- v iv v i i Charlie4a#DNA 406 TATTTTATT---TTATGCATTTAAAAACATTATTCTGAGAAGGGGTCCAT 452 chr6ptel1M 473381 AGATTTCACCAGGCTG 473396 ii i Charlie4a#DNA 453 AGGCTTCACCAGACTG 468 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 18.73 CpG sites = 6, Kimura (unadjusted) = 18.73 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.06 (4 / 63), avg. gap size = 1.25 (5 / 4) 458 34.44 4.51 2.41 chr6ptel1M 473423 473666 (526334) C L3#LINE/CR1 (52) 4047 3799 m_b283s601i31 11427 chr6ptel1M 473423 CAATCTCTTCCCAAAGGC-TGAATCTC--CTACATCCTCCCTGAAATATT 473469 i iivi v v -v i -- v v v vi v C L3#LINE/CR1 4047 CAACCTCCCATCCAATGCAGGAATCCCTTCTACAACATCCCTGACAAGTG 3998 chr6ptel1M 473470 GTCAGCCAATCCCTCCTGACATACTTCCTGTAATGGAAACCTCACTACCT 473519 v ii i v viv i i v i i ii v C L3#LINE/CR1 3997 GTCATCCAGCCTCTGCTTGAACACCTCCAGTGACGGGGAGCTCACTACCT 3948 chr6ptel1M 473520 AACAAGAGGGCCCATCCCATTTCCAAACAAGTAT-----TTAGCGCCTCT 473564 v? i ivi i iiii iv v ----- vi----- C L3#LINE/CR1 3947 CNCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGATTGTTAGAA----- 3903 chr6ptel1M 473565 TAATTTTATTTTATTTT---TTAAAATCTGATTTCCCGTTATGGTCCTCA 473611 - i i vii v ---iii vi i i v ivvi vi v C L3#LINE/CR1 3902 -AGTTCTTCCTTATATTGAGCCGAAATCTGCCTCCCTGTAACTTCCACCC 3854 chr6ptel1M 473612 ATTGCTCTTAATTTTATCCTTTGGGACCAAGCATAACAAGTTTAATCCCT 473661 v i i i ii i ii vi v i i C L3#LINE/CR1 3853 ATTGGTCCTAGTTCTGCCCTCTGGAGCCACACAGAATAAGTCTAATCCCT 3804 chr6ptel1M 473662 CTGCC 473666 v C L3#LINE/CR1 3803 CTTCC 3799 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 45.98 CpG sites = 50, Kimura (unadjusted) = 48.57 Transitions / transversions = 1.56 (50/32) Gap_init rate = 0.04 (10 / 243), avg. gap size = 1.70 (17 / 10) 239 28.17 0.00 0.00 chr6ptel1M 474314 474384 (525616) C MIRb#SINE/MIR (8) 260 190 m_b283s601i32 11428 chr6ptel1M 474314 AGCTGACATTCATTTAGCACTCGCACTGTGTCCGGTCCTGGGTTAAGCAC 474363 iv i v i ii vv i v iv v i i C MIRb#SINE/MIR 260 AGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGC 211 chr6ptel1M 474364 TTTACAATAATAATCTCATTT 474384 vvv v C MIRb#SINE/MIR 210 TTTACATGCATTATCTCATTT 190 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 31.41 CpG sites = 9, Kimura (unadjusted) = 35.52 Transitions / transversions = 0.82 (9/11) Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0) 415 24.80 3.20 0.00 chr6ptel1M 475504 475628 (524372) C MIR3#SINE/MIR (34) 174 46 m_b283s601i33 11429 chr6ptel1M 475504 GGACCTTAGAGCCCATCAAGTTCAACCTCCTCATGTTACCAACGAGGAAA 475553 vi v i i v vi i C MIR3#SINE/MIR 174 GGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAA 125 chr6ptel1M 475554 CTGAGTCCCAGAGAGGCCAAGACCCTTGGCTGCGCTCCCACAGC----TG 475599 v iv vvv v iiv v v ---- i C MIR3#SINE/MIR 124 CTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTA 75 chr6ptel1M 475600 GTGGCCGAGGCGGAATCTGACGCCAAGTC 475628 v v i iiv vv i C MIR3#SINE/MIR 74 GTGGCAGAGCCGGGACTAGAACCCAGGTC 46 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 30.19 CpG sites = 13, Kimura (unadjusted) = 30.19 Transitions / transversions = 0.72 (13/18) Gap_init rate = 0.01 (1 / 124), avg. gap size = 4.00 (4 / 1) 283 25.23 5.41 0.00 chr6ptel1M 475531 475641 (524359) C MIR1_Amn#SINE/MIR (78) 152 36 m_b283s601i34 11429 chr6ptel1M 475531 TCCTCATGTTACCAACGAGGAAACTGAGTCCCAGAGAGGCCAAGACCCTT 475580 i v vi i v ? i? vvv C MIR1_Amn#SINE 152 TCCCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTT 103 chr6ptel1M 475581 GGCTGCGCTCCCACAGCTG----GTGGCCGAGGCGGAATCTGACGCCAAG 475626 v iiv v v ? ? ---- v v i ?i? vv i C MIR1_Amn#SINE 102 GCCCAAGGTCACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAACCCAGG 53 chr6ptel1M 475627 --TCCAGCATTCTAGTC 475641 -- v vi i i C MIR1_Amn#SINE 52 TCTCCCGAGTCCCAGTC 36 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.07 CpG sites = 12, Kimura (unadjusted) = 33.07 Transitions / transversions = 0.75 (12/16) Gap_init rate = 0.02 (2 / 110), avg. gap size = 3.00 (6 / 2) 251 25.99 9.09 2.86 chr6ptel1M 476409 476507 (523493) C MIR3#SINE/MIR (30) 178 74 m_b283s601i35 11430 chr6ptel1M 476409 GAAAAGACCTTAGAGATCATCTGCCTCAACTGCTTGATTTGTCAAAATAA 476458 ii ivii iv i v - vv i i C MIR3#SINE/MIR 178 GAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTT-TACAGATGA 130 chr6ptel1M 476459 AAAGGAACAGAGGTCCAGAGAGA-GAAG----CTGCCCTGGGC----TAG 476499 ii -- v i i- ----i vi i----i C MIR3#SINE/MIR 129 GGA--AACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAG 82 chr6ptel1M 476500 TTAGTTAG 476507 i? C MIR3#SINE/MIR 81 CNAGTTAG 74 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 34.12 CpG sites = 18, Kimura (unadjusted) = 34.12 Transitions / transversions = 2.57 (18/7) Gap_init rate = 0.06 (6 / 98), avg. gap size = 2.00 (12 / 6) 382 17.39 14.13 0.00 chr6ptel1M 477352 477443 (522557) MIRc#SINE/MIR 40 144 (124) m_b283s601i36 11431 chr6ptel1M 477352 AGCCAAGAAGAACTGAGTTCGAA--ACAG-------ACTT--TAGCCGTG 477390 i i v i i--v i ------- -- i MIRc#SINE/MIR 40 AGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTG 89 chr6ptel1M 477391 TGATCCCGGGCAAGTCACTTAACTTCTC--AGCCTCAGTTTCCATTTCTA 477438 i ii i -- viv i MIRc#SINE/MIR 90 TGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTG 139 chr6ptel1M 477439 TAAAA 477443 MIRc#SINE/MIR 140 TAAAA 144 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 19.03 CpG sites = 12, Kimura (unadjusted) = 20.42 Transitions / transversions = 3.00 (12/4) Gap_init rate = 0.04 (4 / 91), avg. gap size = 3.25 (13 / 4) 320 23.46 3.70 0.00 chr6ptel1M 477383 477463 (522537) MIR3#SINE/MIR 79 162 (46) m_b283s601i37 11431 chr6ptel1M 477383 TAGCCGTGTGATCCCGGGCAAGTCACTTAACTTCTC--AGCCTCAGTTTC 477430 ? i i ii v i --i MIR3#SINE/MIR 79 TNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTC 128 chr6ptel1M 477431 CATTTCTATAAAA-GAAGCGTGAAGATTGGATGA 477463 viv i - i v vvvi i i MIR3#SINE/MIR 129 CTCATCTGTAAAATGAGGGGGTTGGACTAGATGA 162 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 29.32 CpG sites = 12, Kimura (unadjusted) = 29.32 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.03 (2 / 80), avg. gap size = 1.50 (3 / 2) 23 0.00 0.00 0.00 chr6ptel1M 477470 477494 (522506) (A)n#Simple_repeat 1 25 (0) m_b283s252i7 11432 chr6ptel1M 477470 AAAAAAAAAAAAAAAAAAAAAAAAA 477494 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAA 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 39 26.86 2.56 3.23 chr6ptel1M 477950 478105 (521895) (CATACA)n#Simple_repeat 1 155 (0) m_b283s252i9 11433 chr6ptel1M 477950 CACACACATTCACACTCACAATACATACACACACACTCATGCACATACAT 477999 i v iv - i i i v i i (CATACA)n#Sim 1 CATACACATACACATACAC-ATACACATACACATACACATACACATACAC 49 chr6ptel1M 478000 TTACACATACACATACATGCATTTATAT-GA-ATACATACACTCATGCAC 478047 v -- vi i -v - i i v i (CATACA)n#Sim 50 ATACACATACACATACA--CATACACATACACATACACATACACATACAC 97 chr6ptel1M 478048 ATGCATTTACACACTCACACTTTCTCACACACATTC-CCT-CACATCCTC 478095 i iv - - v v v i v - v - v v (CATACA)n#Sim 98 ATACACATACACA-T-ACACATACACATACACATACACATACACATACAC 145 chr6ptel1M 478096 AGTCACACAC 478105 vv i (CATACA)n#Sim 146 ATACACATAC 155 Matrix = Unknown Transitions / transversions = 0.94 (16/17) Gap_init rate = 0.06 (9 / 155), avg. gap size = 1.00 (9 / 9) 218 22.24 14.66 3.10 chr6ptel1M 478229 478344 (521656) C L2d2_3end#LINE/L2 (23) 532 404 m_b283s601i38 11434 chr6ptel1M 478229 ATTAAGGACCTACTATGTGTCAGCC-CTGCACAAGG-GCTG---GGGATA 478273 i vi i iv v - ii v - --- C L2d2_3end#LIN 532 ATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGTGGGGGATA 483 chr6ptel1M 478274 CAAA-----AT----CA--GTCCCTGCTCTGGAGGGAATCCCAGTCCAGC 478312 ----- ---- -- i vi iiv iv i i i C L2d2_3end#LIN 482 CAAAGAAGTATAAGACATGGTCCCTGCCCTCAAGGAGCTTACAATCTAGT 433 chr6ptel1M 478313 T-GGGAGACAACACAGCGACAACCACGTGCAAA 478344 - v ---- i v v C L2d2_3end#LIN 432 TGGGGAGACAAGAC----ATAAACACGTGAAAA 404 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 25.77 CpG sites = 15, Kimura (unadjusted) = 27.01 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.10 (11 / 115), avg. gap size = 1.91 (21 / 11) 227 18.03 12.90 10.53 chr6ptel1M 478229 478321 (521679) C L2c_3end#LINE/L2 (23) 455 361 m_b283s601i39 11434 chr6ptel1M 478229 ATTAAGGACCTACTATGTGTCAGCCCTGCACAAGGGCTGGGGATACAAA- 478277 i vi i ---- ------ - C L2c_3end#LINE 455 ATTGAGCGCCTACTATGTGCCAG----GC------GCTGGGGATACAAAG 416 chr6ptel1M 478278 AT----------CAGTCCCTGCTCTGGAGGGAATCCCAGTCCAGCTG-GG 478316 ---------- i i vi iiv v i iv - C L2c_3end#LINE 415 ATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAGTGGAGG 366 chr6ptel1M 478317 AGACA 478321 C L2c_3end#LINE 365 AGACA 361 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 18.12 CpG sites = 10, Kimura (unadjusted) = 21.13 Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.14 (13 / 92), avg. gap size = 1.69 (22 / 13) 181 30.00 0.00 0.00 chr6ptel1M 478882 478941 (521059) C MIR3#SINE/MIR (52) 156 97 m_b283s601i40 11435 chr6ptel1M 478882 AGTCTGCCCGCCTTATTTTTCTGATGTGGAAACTGAGGTCTCGGGGGATT 478931 iiv v i v v v i iv i i i v C MIR3#SINE/MIR 156 AGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTG 107 chr6ptel1M 478932 AGGTGCCCTG 478941 i v i C MIR3#SINE/MIR 106 AAGTGACTTG 97 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 39.18 CpG sites = 10, Kimura (unadjusted) = 39.18 Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0) 380 21.22 1.80 6.60 chr6ptel1M 479290 479400 (520600) C MIRc#SINE/MIR (153) 115 10 m_b283s601i41 11436 chr6ptel1M 479290 GAGGCTAAGTGACTTGCC-AGGGTCACACAGCTAGTTCATGTTCAGTGTC 479338 i - i -------v v C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGT-------AAGTGGC 73 chr6ptel1M 479339 TGAGTCCAAATTTGAACT-GGCTCCTCCTGCCTCCAGGACCAGCACTCTA 479387 v i vii i i i-i v i v i v ii v C MIRc#SINE/MIR 72 AGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTT 23 chr6ptel1M 479388 ACCACTGCACCAC 479400 v C MIRc#SINE/MIR 22 TCCACTGCACCAC 10 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 23.98 CpG sites = 13, Kimura (unadjusted) = 25.27 Transitions / transversions = 1.44 (13/9) Gap_init rate = 0.08 (9 / 110), avg. gap size = 1.00 (9 / 9) 399 16.46 1.27 0.00 chr6ptel1M 479970 480048 (519952) C MIR#SINE/MIR (118) 144 65 m_b283s601i42 11437 chr6ptel1M 479970 CTCATTTTACAGATGAGGAAACTGAGGCAAACAG-GGTTAAATGACTTGT 480018 i v v - i i i C MIR#SINE/MIR 144 CCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGC 95 chr6ptel1M 480019 CCAGGATCACAGAGCTAGGAAGAGTCTGAG 480048 i i v v v v v C MIR#SINE/MIR 94 CCAAGGTCACACAGCTAGTAAGTGGCAGAG 65 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 18.63 CpG sites = 6, Kimura (unadjusted) = 18.63 Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.01 (1 / 78), avg. gap size = 1.00 (1 / 1) 267 22.45 0.00 0.00 chr6ptel1M 480074 480122 (519878) L2d2_3end#LINE/L2 507 555 (0) m_b283s601i43 11438 chr6ptel1M 480074 TGTCCTGCACACAGTAGGTGCTCAACAAATGCTTATCAATTCGACTTGA 480122 i i i i ii i ii i i L2d2_3end#LIN 507 TGCCTTGCACACAGTAGGCGCTCAATAAATATTTGTTGATTTGATTTGA 555 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 26.57 CpG sites = 11, Kimura (unadjusted) = 29.80 Transitions / transversions = 1.00 (11/0) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 427 25.12 1.60 7.63 chr6ptel1M 480691 480815 (519185) C MIRc#SINE/MIR (120) 148 31 m_b283s601i44 11439 chr6ptel1M 480691 CTCATTTTATGGAGGAGGAAACTGAGGC--AAACATGGTGAAGTGATTTG 480738 i ii v -- i v - v i C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGA-GGTTAAGTGACTTG 100 chr6ptel1M 480739 CCCAGAGTCACCCAGCTAAGAAATAGCTGAGGCTGGATTTGACCTTAGAA 480788 ii v iv i i v v v i i v ii i- C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGG- 51 chr6ptel1M 480789 AAAAGATTCTTCTTGGCTTCAGGTCTA 480815 ------- i i i i i C MIRc#SINE/MIR 50 -------TCTTCCTGACTCCAAGTCCA 31 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 30.33 CpG sites = 20, Kimura (unadjusted) = 31.66 Transitions / transversions = 2.22 (20/9) Gap_init rate = 0.08 (10 / 124), avg. gap size = 1.10 (11 / 10) 197 30.64 9.79 2.79 chr6ptel1M 480838 481072 (518928) C L2#LINE/L2 (587) 2495 2245 m_b283s601i45 11440 chr6ptel1M 480838 GAGTGGAG--GGTGTGAAGGGAAAGAT---AAATTCTGCTCTGGGTTTGT 480882 i v -- v i i ---i i v i i iiv C L2#LINE/L2 2495 GGGAGGAGCAGGTTTGAGGGGGAAGATCAGGAGTTCAGTTTTGGACATGT 2446 chr6ptel1M 480883 GAACTCTGAGACGGCTACAAGGGGGCCAGCTGGAAATACCCAAGAGACAA 480932 v v i i v iv iviv iv i ii v iv i i C L2#LINE/L2 2445 TAAGTTTGAGATGCCTATTAGACATCCAAGTGGAGATGTCGAGTAGGCAG 2396 chr6ptel1M 480933 ATTAAATA-ACGTAGGCTGGAGCTCAGGAGAAAGTTCTAGG-TAGAG--- 480977 - ii - - v i i i v ii - i --- C L2#LINE/L2 2395 -TTGGATATACG-AGTCTGGAGTTCAGGGGAGAGGTCCGGGCTGGAGATA 2348 chr6ptel1M 480978 -AGATCTGGGAGCCAGGAG-----AGATCTGGGAGTGTAGAG--ATGAGG 481019 - i i i vv ----- --- vi v i -- i C L2#LINE/L2 2347 TAAATTTGGGAGTCATCAGCATATAGAT---GGTATTTAAAGCCATGAGA 2301 chr6ptel1M 481020 GCTGAGGAGATTAGCAA-----TGAGCCTGGAAGGGGAAGAGAAACGTGG 481064 viv v i v ? ----- iv i vi i -- v C L2#LINE/L2 2300 CTGGATGAGATCACCNAGGGAGTGAGTGTAGATAGAGAAGAGAA--GAGG 2253 chr6ptel1M 481065 TTCCAGAA 481072 i v i C L2#LINE/L2 2252 TCCAAGGA 2245 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 40.36 CpG sites = 43, Kimura (unadjusted) = 41.23 Transitions / transversions = 1.59 (43/27) Gap_init rate = 0.06 (15 / 234), avg. gap size = 2.00 (30 / 15) 213 35.15 3.52 5.64 chr6ptel1M 481949 482147 (517853) L2b_3end#LINE/L2 187 381 (85) m_b284s601i4 11441 chr6ptel1M 481949 ATTCTCACCCATTCTTCAAAGCCCTGCCCAGCTACCACCTCCTCCACGAA 481998 i ii i i iiv i v i iv ii iv L2b_3end#LINE 187 ACTCCTACTCATCCTTCAGGTCTCAGCTCAAATGTCACCTCCTCCGGGAA 236 chr6ptel1M 481999 GCATTCCCTGATTTCCCTCC--TCCCACTCAGAAGCAATTTCTT---CCC 482043 vi --- i --v viv iv vv iiii --- L2b_3end#LINE 237 GCCCTCCCTGA---CCCCCCAGGCCGGGTCAGGCGCCCTCCTCTGGGCCC 283 chr6ptel1M 482044 CCTCTGACCTTCCCCA-CATTTTGTGTCTCTTACTGAACTTCCATAGTTA 482092 i v v v ii- i i v - v ? i ---- -- i? L2b_3end#LINE 284 CCCCAGTCCTACCCTGCCACTCTGGGT-TATNATTG----TC--TGNTTA 326 chr6ptel1M 482093 C-TGTGGATTGCAATCATGTGTACAGTAAGATTCCTGAGGGCGGCAACCA 482141 - vvi iv vvi i- iv v i v i v i vi i L2b_3end#LINE 327 CATGTCTGTCTCCCCCAC-TAGACTGTGAGCTCCGTGAGGGCAGGGACCG 375 chr6ptel1M 482142 TCTTTG 482147 ?v i L2b_3end#LINE 376 NGTCTG 381 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 48.34 CpG sites = 39, Kimura (unadjusted) = 50.55 Transitions / transversions = 1.44 (39/27) Gap_init rate = 0.08 (15 / 198), avg. gap size = 1.20 (18 / 15) 330 24.40 0.83 5.17 chr6ptel1M 481951 482071 (517929) L2d2_3end#LINE/L2 193 308 (247) m_b284s601i5 11441 chr6ptel1M 481951 TCTCACCCATTCTTCAAAGCCCTGCCCAGCTACCACCTCCTCCACGAAGC 482000 ii i i v i iv ? ii L2d2_3end#LIN 193 TCCTACCCATCCTTCAAGGCCCAGCTCAAATNCCACCTCCTCCGTGAAGC 242 chr6ptel1M 482001 ATTCCCTGATTTCCCTCCTCCCACTCAGAAGCAATTTCTTCCCCCTCTGA 482050 v ----- iv vi i - ? ii i i i L2d2_3end#LIN 243 CTTCCCTGA-----CCACTCCAGCCC-GNAGTGATCTCTCCCTCCTCTGA 286 chr6ptel1M 482051 CCTTCCCCA-CATTTTGTGTCT 482071 v i ivi - ? vv L2d2_3end#LIN 287 ACTCCTATAGCANTTATTGTCT 308 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 30.22 CpG sites = 19, Kimura (unadjusted) = 31.59 Transitions / transversions = 2.11 (19/9) Gap_init rate = 0.06 (7 / 120), avg. gap size = 1.00 (7 / 7) 298 28.82 16.95 1.97 chr6ptel1M 482565 482741 (517259) L3#LINE/CR1 2535 2737 (1362) m_b284s601i6 11442 chr6ptel1M 482565 GAGAACTCTTACCTGCCACTTTA---GCGTTCTTACCTCCTGGTCT-GAA 482610 i v i --- i --- v vvii v i i- v L3#LINE/CR1 2535 GAGAGCACCTA---GCCGCTTTAAATGAGTTCAAGTCTCCAGGCCCAGAC 2581 chr6ptel1M 482611 GAAT---ATCCCACGACACTGAGAGA--CTGCAGATCCAAATGCCGAACT 482655 --- v ii i --i vii vi v i L3#LINE/CR1 2582 GAATTACATCCCAGGGTACTGAAAGAACTTGCAGATGTGATCGCGGAACC 2631 chr6ptel1M 482656 CCTGCTCCTGATTTTTGAAAACTTCCTTG----GGAAGAG------GAAG 482695 v iivv i i i v iv vvi---- ------ L3#LINE/CR1 2632 GCTGTCGGTAATCTTTGAGAAATCACGGAGAACGGAAGAGGTGCCAGAAG 2681 chr6ptel1M 482696 ---------GGGCCGATG--ATCCCGATCTCTAGAAAGGGTGGAAGAGGT 482734 --------- vi --i ? v ?i i i -ii i i L3#LINE/CR1 2682 ACTGGAGACGGGCAAATGTNGTNCCTANTTTTAAAAAGGG-AAAAAAGAT 2730 chr6ptel1M 482735 GGATTCT 482741 L3#LINE/CR1 2731 GGATTCT 2737 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 34.53 CpG sites = 31, Kimura (unadjusted) = 38.38 Transitions / transversions = 1.63 (31/19) Gap_init rate = 0.07 (12 / 176), avg. gap size = 2.83 (34 / 12) 295 34.71 3.25 1.60 chr6ptel1M 483066 483188 (516812) MIRc#SINE/MIR 3 127 (141) m_b284s601i7 11443 chr6ptel1M 483066 AGGCA-TATAGCCTAATAGATAGAGGACCAGCCTTGAAGGGGGGAAGATG 483114 - i i ivi i i v v ii v i vvi iv MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chr6ptel1M 483115 TAAGTTCAAACCCTCCTTCTGACATAATGAC-AGCCATATAATC-TGGGC 483162 ii i ii ivvi v i-- v - ii i i i - MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCAC--TTACTAGCTGTGTGACCTTGGGC 100 chr6ptel1M 483163 GAGTTA-TCAATCTCTCAGAGGCACAG 483188 i i - i i v v v MIRc#SINE/MIR 101 AAGTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 46.37 CpG sites = 28, Kimura (unadjusted) = 49.78 Transitions / transversions = 2.00 (28/14) Gap_init rate = 0.05 (6 / 122), avg. gap size = 1.00 (6 / 6) 352 25.20 15.74 0.81 chr6ptel1M 484096 484203 (515797) MIRc#SINE/MIR 2 125 (143) m_b284s601i8 11444 chr6ptel1M 484096 GAGGCAGTGTGGTGCAGTGAACAGAGGCA----------------GAAGA 484129 i v - ---------------- MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAG-CACTGGACTTGGAGTCAGGAAGA 50 chr6ptel1M 484130 CACAGACTCAAGGGCTGTTTCTGATGCATGCTAGCTTTGTGACCCTCAGC 484179 vii ii i vv i vi vii v i v i vi MIRc#SINE/MIR 51 CCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGC 100 chr6ptel1M 484180 AAGTTA-TTAACCTTTCAGGGCCCC 484203 i - i v i i MIRc#SINE/MIR 101 AAGTCACTTAACCTCTCTGAGCCTC 125 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 28.88 CpG sites = 17, Kimura (unadjusted) = 31.66 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.03 (3 / 107), avg. gap size = 6.00 (18 / 3) 369 33.70 6.32 1.09 chr6ptel1M 485405 485578 (514422) C MIRc#SINE/MIR (83) 185 3 m_b284s601i9 11445 chr6ptel1M 485405 ACAACCCAG---GGTGGGGAAGGTGTG-ATTGCCACCTCCGTTTTCCAGA 485450 v --- i v i iiv - iii i i i v C MIRc#SINE/MIR 185 ACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGA 136 chr6ptel1M 485451 AGAGGAACCCAGGGCATCCACTTA---TAAATAGCTTGCCCACTGTCATA 485497 v v iii --i vvv --- i ii vv i C MIRc#SINE/MIR 135 TGAGGAAACTGAGGC--TCAGAGAGGTTAAGTGACTTGCCCAAGGTCACA 88 chr6ptel1M 485498 TAACTGGCTACTGTCCAAGGCTGTATTCCAACTCAGTCCTTCCCGATCCT 485547 i i i iv v v vi v v v i v i vi i ii i C MIRc#SINE/MIR 87 CAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCC 38 chr6ptel1M 485548 GGGTCTGGAGCTCTATCCACT----CTCGCTGCCT 485578 ii ii v v ---- v i C MIRc#SINE/MIR 37 AAGTCCAGTGCTCTTTCCACTGCACCACACTGCCT 3 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 46.68 CpG sites = 35, Kimura (unadjusted) = 46.68 Transitions / transversions = 1.52 (35/23) Gap_init rate = 0.03 (6 / 173), avg. gap size = 2.17 (13 / 6) 235 27.27 6.06 0.00 chr6ptel1M 486111 486176 (513824) MIR3#SINE/MIR 87 156 (52) m_b284s601i11 11446 chr6ptel1M 486111 TGCCTGTGGGCAA----CTCTGACTCTATGGGCCTCAATTTTCTCATTTC 486156 v iv ---- iiiv v i i i v MIR3#SINE/MIR 87 TGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTG 136 chr6ptel1M 486157 TAAAATGGGCTATTTGGATT 486176 i vviv i MIR3#SINE/MIR 137 TAAAATGAGGGGGTTGGACT 156 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 34.54 CpG sites = 10, Kimura (unadjusted) = 34.54 Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.02 (1 / 65), avg. gap size = 4.00 (4 / 1) 248 16.36 7.27 0.00 chr6ptel1M 486111 486165 (513835) MIR1_Amn#SINE/MIR 92 150 (80) m_b284s601i10 11446 chr6ptel1M 486111 TGCCTGTGGGCAACTC---TGAC-TCTATGGGCCTCAATTTTCTCATTTC 486156 v iv v --- ? - v ? i i i v MIR1_Amn#SINE 92 TGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTG 141 chr6ptel1M 486157 TAAAATGGG 486165 MIR1_Amn#SINE 142 TAAAATGGG 150 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 19.30 CpG sites = 4, Kimura (unadjusted) = 19.30 Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.04 (2 / 54), avg. gap size = 2.00 (4 / 2) 312 21.25 2.47 1.22 chr6ptel1M 486193 486273 (513727) C MIR1_Amn#SINE/MIR (80) 150 69 m_b284s601i13 11447 chr6ptel1M 486193 CCCACTTTAGAGATGAGAAAACTGAGGCTCATA-AAGTCAAGTAAGTTGC 486241 i v i ? v - i ? i v C MIR1_Amn#SINE 150 CCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGC 101 chr6ptel1M 486242 CCACAATCATCTGACCACTCCAGT-CCAGAGCC 486273 vii i?iii ?i-v ? -v C MIR1_Amn#SINE 100 CCAAGGTCACNCAGCNG-GCNAGTGGCAGAGCC 69 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 27.73 CpG sites = 11, Kimura (unadjusted) = 27.73 Transitions / transversions = 1.83 (11/6) Gap_init rate = 0.04 (3 / 80), avg. gap size = 1.00 (3 / 3) 318 17.24 1.72 0.00 chr6ptel1M 486193 486250 (513750) C MIRb#SINE/MIR (117) 151 93 m_b284s601i12 11447 chr6ptel1M 486193 CCCACTTTAGAGATGAGAAAACTGAGGCTCATA-AAGTCAAGTAAGTTGC 486241 i v i v - i i v C MIRb#SINE/MIR 151 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGC 102 chr6ptel1M 486242 CCACAATCA 486250 vii C MIRb#SINE/MIR 101 CCAAGGTCA 93 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 19.85 CpG sites = 6, Kimura (unadjusted) = 19.85 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.02 (1 / 57), avg. gap size = 1.00 (1 / 1) 245 23.08 0.00 0.00 chr6ptel1M 486670 486721 (513279) L3#LINE/CR1 3867 3918 (181) m_b284s601i14 11448 chr6ptel1M 486670 AGAGAGTCAAAACTGGGTTAAATATAAGGAAGAACTTCTTGACAATTAGA 486719 i v i vi v i v ii i i L3#LINE/CR1 3867 AGGGAGGCAGATTTCGGCTCAATATAAGGAAGAACTTTCTAACAATCAGA 3916 chr6ptel1M 486720 GC 486721 L3#LINE/CR1 3917 GC 3918 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 28.45 CpG sites = 8, Kimura (unadjusted) = 28.45 Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 336 36.45 0.00 0.00 chr6ptel1M 486741 486847 (513153) MIR3#SINE/MIR 87 193 (15) m_b284s601i15 11449 chr6ptel1M 486741 TGATTTGGGATAACTCATTGCTTTTCTCTGAGTGTCAGGCTCATGTTCTT 486790 ii v ii v i v vii i iv vi v vv v MIR3#SINE/MIR 87 TGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTG 136 chr6ptel1M 486791 TTAAGTAAAGGAGTTAACCCAAATAATCTTCAAAGTCCCTTCCAGCTCCA 486840 v i i i i iiv i i i ii i ii MIR3#SINE/MIR 137 TAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTG 186 chr6ptel1M 486841 ATTTTTT 486847 iv i MIR3#SINE/MIR 187 ACATTCT 193 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 53.72 CpG sites = 26, Kimura (unadjusted) = 53.72 Transitions / transversions = 2.00 (26/13) Gap_init rate = 0.00 (0 / 106), avg. gap size = 0.0 (0 / 0) 187 27.72 0.00 6.90 chr6ptel1M 486856 486917 (513083) L3#LINE/CR1 3887 3944 (155) m_b284s601i16 11448 chr6ptel1M 486856 AATATAAGGAAAAAATTCCTAATAGCCATAGCTGCCTGCCAACAGAGGCA 486905 i v i i ii v i--- - i v v L3#LINE/CR1 3887 AATATAAGGAAGAACTTTCTAACAATCAGAGCTGT---CCAA-AAATGGA 3932 chr6ptel1M 486906 GTGGATTCCTTC 486917 i ii v i L3#LINE/CR1 3933 ATGGGCTGCCTC 3944 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 36.05 CpG sites = 11, Kimura (unadjusted) = 36.05 Transitions / transversions = 2.20 (11/5) Gap_init rate = 0.07 (4 / 61), avg. gap size = 1.00 (4 / 4) 500 32.38 2.10 2.82 chr6ptel1M 487095 487380 (512620) L1MD1_3end#LINE/L1 372 655 (334) m_b284s551i0 11450 chr6ptel1M 487095 AGCAGTGTTACTACTGGGCTTATATCCCAAAGAGATTATAAAGAAGGG-- 487142 i vvi v v v i i v v vvv v v-- L1MD1_3end#LI 372 AGCAATTGCACTCCTGGGCATTTATCCCAGAGAAATGAAAACTTATGTTC 421 chr6ptel1M 487143 --AAAGGGACCTGTATGTGCACGAATGTTTGTGGCAGCCCTCTTTGTAGT 487190 -- v iii ---- i i ii v i i L1MD1_3end#LI 422 ACACAAAAACCTGTA----CACGAATGTTTATAGCAGCTTTATTCGTAAT 467 chr6ptel1M 487191 GGCTAGAAACTGGAAACTGAATGGATGTCCATCAGTTGGAGAATGGCTGA 487240 i i i vivvii v iiv v i i L1MD1_3end#LI 468 AGCCAAAAACTGGAAACAACCCAGATGTCCTTCAACGGGTGAATGGTTAA 517 chr6ptel1M 487241 ATAAATTGTGGTATATGAATATTATGGAATATTACTGTTCTGTAAGAAAT 487290 i i i vv ii i vvv vi i iv L1MD1_3end#LI 518 ACAAACTGTGGTACATCCATACCATGGAATACTACTCAGCAATAAAAAGG 567 chr6ptel1M 487291 GACCAACAGGATGAT-TTCAGAAAGGCCTGGAGAGACTTACACGAACTGA 487339 i v -viv -iv iv vii vii ii v vii v v L1MD1_3end#LI 568 AACGAAC-TATTGATACACGCAACAACCTGGATGAATCTCCAGAGAATTA 616 chr6ptel1M 487340 TGCTGAGTGAAATGAG-CAGGACCAAGAGATCATTATATACT 487380 vi - ivv i ---i i L1MD1_3end#LI 617 TGCTGAGTGAAAAAAGCCAATCCCAAAAG---GTTACATACT 655 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 41.49 CpG sites = 49, Kimura (unadjusted) = 43.40 Transitions / transversions = 1.20 (49/41) Gap_init rate = 0.04 (12 / 285), avg. gap size = 1.17 (14 / 12) 507 29.09 1.33 2.24 chr6ptel1M 487156 487380 (512620) L1ME1_3end#LINE/L1 433 655 (271) m_b284s551i1 11450 chr6ptel1M 487156 TGTGCACGAATGTTTGTGGCAGCCCTCTTTGTAGTGGCTAGAAACTGGAA 487205 i ii i ii v i i i i i L1ME1_3end#LI 433 TGTACACGAATGTTCATAGCAGCTTTATTCGTAATAGCCAAAAACTGGAA 482 chr6ptel1M 487206 ACTGAATGGATGTCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATA 487255 vivviii ii? v v i i L1ME1_3end#LI 483 ACAACCCAAATGTCCATCAACNGGTGAATGGATAAACAAATTGTGGTATA 532 chr6ptel1M 487256 TGAATATTATGGAATATTACTGTTCTGTAAGAAATGACCAACAGGATGAT 487305 vv iv i vvv vi i ivi v -viv L1ME1_3end#LI 533 TCCATACAATGGAATACTACTCAGCAATAAAAAGGAACGAAC-TACTGAT 581 chr6ptel1M 487306 -TTCAGAAAGGCCTGGA-GAGACTTACACGAACTGATGCTGAGTGAAATG 487353 -iv iv vii v - iv i v v?v i - vi L1ME1_3end#LI 582 ACACGCAACAACATGGATGAATCTCAAAANCATT-ATGCTGAGTGAAAGA 630 chr6ptel1M 487354 AGCAGGAC-CAAGAGATCATTATATACT 487380 vi - i --- ? i L1ME1_3end#LI 631 AGCCAGACACAAAAG---ANTACATACT 655 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 36.94 CpG sites = 37, Kimura (unadjusted) = 38.47 Transitions / transversions = 1.37 (37/27) Gap_init rate = 0.04 (8 / 224), avg. gap size = 1.00 (8 / 8) 272 32.64 4.61 3.25 chr6ptel1M 488289 488440 (511560) L3#LINE/CR1 3573 3726 (373) m_b284s601i17 11451 chr6ptel1M 488289 TGCTCAGATCACATAAAGACTAAGTTTC-TTCTGTTCTATCCTGTGCATG 488337 v i vvi v -- v - v ivv vvii v L3#LINE/CR1 3573 TGGTCAGACCACATCTGGAGTA--TTGCGTTCAGTTCTGGGCGCCACATT 3620 chr6ptel1M 488338 TTAGGGAAGGAAATTGTTAGACTGGAAAAC----AGGGAACAGTGGCCAG 488383 i - i v vi i ivi ---- i i v i i L3#LINE/CR1 3621 TTAAG-AGGGACATTGACAAACTGGAGCGCGTCCAGAGGAGAGCGACCAG 3669 chr6ptel1M 488384 GGTCGGATGTACA-TTTG-AAACCATTTCGTGAAAGAACTGCATGAAGGA 488431 i -- i v vi- i - v i ivi i vi vv L3#LINE/CR1 3670 GAT--GGTGAAGGGTCTGGAAACCATGTCATATGAGGAACGGTTGAAGGA 3717 chr6ptel1M 488432 ACTGAAGAT 488440 ii L3#LINE/CR1 3718 ACTGGGGAT 3726 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 40.32 CpG sites = 26, Kimura (unadjusted) = 43.89 Transitions / transversions = 1.18 (26/22) Gap_init rate = 0.06 (9 / 151), avg. gap size = 1.33 (12 / 9) 381 28.88 12.70 2.90 chr6ptel1M 488496 488684 (511316) C MIRc#SINE/MIR (40) 228 22 m_b284s601i18 11452 chr6ptel1M 488496 TTGCAAAGCTCTTTC---CACATAGTCTCCTTTGATTCTCA----AACC- 488537 i v ---i vi v i ---- - C MIRc#SINE/MIR 228 TTACAAAGCGCTTTCACATACATTATCTCATTTGATCCTCACAACAACCC 179 chr6ptel1M 488538 GGTGCATACAGTTTAGTACTGTGGGCATTATTTTCCCCATTTTACAGAT- 488586 v ----- v vi i vv ii i v - C MIRc#SINE/MIR 178 TGTG-----AGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATG 134 chr6ptel1M 488587 ----------GGTTTAGAATGGCTGAGTGACTCGACCAATGTCCCATA-- 488624 ---------- i i iv i i i v v v i -- C MIRc#SINE/MIR 133 AGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGC 84 chr6ptel1M 488625 ---TAAATGGTAGGGGTTGTATTTTTATCCAGTTATTCCCTGGGGCCAAA 488671 --- i i i viv v i ivv i v v - ivv i C MIRc#SINE/MIR 83 TAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTT-CCTGACTCCAAG 35 chr6ptel1M 488672 GTGAGTACGATTT 488684 viv i vv C MIRc#SINE/MIR 34 TCCAGTGCTCTTT 22 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 35.38 CpG sites = 27, Kimura (unadjusted) = 37.10 Transitions / transversions = 1.04 (27/26) Gap_init rate = 0.06 (12 / 188), avg. gap size = 2.50 (30 / 12) 199 32.74 7.96 0.00 chr6ptel1M 488680 488792 (511208) L3#LINE/CR1 3747 3868 (231) m_b284s601i19 11451 chr6ptel1M 488680 GATTTGGAGGGAGAATAA-AGCTGTCTTTAAGTGTTTCAAGAGTCTTTGT 488728 i i iiiv i - i i i v i iiv ii L3#LINE/CR1 3747 GACTTAGAGGAGACATGATAGCTGTCTTCAAATATTTGAAGGGCTGTCAT 3796 chr6ptel1M 488729 AGGTTAAAGGGATTGGTCACATTCTACCTAG-TCCATGGAG-AGAA--AA 488774 iv vv i i v vi iiv i - vi i - -- i L3#LINE/CR1 3797 GTGGAAGAGGGATTAGACTTATTCTGTGTGGCTCCAGAGGGCAGAACTAG 3846 chr6ptel1M 488775 GTC--AT--ATGGAAGTTAAAG 488792 v -- --i v L3#LINE/CR1 3847 GACCAATGGGTGGAAGTTACAG 3868 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 45.75 CpG sites = 25, Kimura (unadjusted) = 45.75 Transitions / transversions = 2.08 (25/12) Gap_init rate = 0.05 (6 / 112), avg. gap size = 1.50 (9 / 6) 374 29.48 13.69 1.06 chr6ptel1M 488788 488955 (511045) L3#LINE/CR1 3906 4094 (5) m_b284s601i20 11451 chr6ptel1M 488788 TAAAGATCAGAGTTGTCCAAAA-------------CCACTTGAGCCTAGT 488824 vi i ------------- v v? v- L3#LINE/CR1 3906 TAACAATCAGAGCTGTCCAAAAATGGAATGGGCTGCCTCGNGAGG-TAGT 3954 chr6ptel1M 488825 GAGCTCTCCATTAATAGAAGTCTATCAG-AGAAGTT-------CATTTGT 488866 i i i v i i v viv - i i ------- i L3#LINE/CR1 3955 GAGCTCCCCGTCACTGGAGGTGTTCAAGCAGAGGCTGGATGACCACTTGT 4004 chr6ptel1M 488867 TCAGAGAGGTCGTA-AAGACATTTTCTAATCAGAGAACTGTTCTAACCTG 488915 - i v i - iv iiivv ii viivv v ivi iv L3#LINE/CR1 4005 -CAGGGATGTTGTAGAAGGGATTCCTGCATTGGATGGGAGGTTGGACTAG 4053 chr6ptel1M 488916 ATATGTTCTGAGGTCC-TTCCAGCTCTGAAATTCTGTGATT 488955 ivvi i - i i L3#LINE/CR1 4054 ATGACCTCTAAGGTCCCTTCCAACTCTGAGATTCTGTGATT 4094 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 37.92 CpG sites = 29, Kimura (unadjusted) = 38.94 Transitions / transversions = 1.45 (29/20) Gap_init rate = 0.04 (7 / 167), avg. gap size = 3.57 (25 / 7) 241 27.35 29.93 0.53 chr6ptel1M 489527 489673 (510327) C MIR3#SINE/MIR (3) 205 16 m_b284s601i21 11453 chr6ptel1M 489527 TCATAGGATCACAGA-T-CCAGAACTGAAAGGGATGTCAGA-----TGTA 489569 i i - -i i i iv i ----- v C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTA 156 chr6ptel1M 489570 G------------------CACATAAGGAAACTGAGGCAGAGAGAGGGTA 489601 ------------------ v i vv vv C MIR3#SINE/MIR 155 GTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGA 106 chr6ptel1M 489602 AATGAC--ATCCA-----------------AATGACAGAGATAGCCTTTC 489632 i --ii ----------------- i i vii vvi vv C MIR3#SINE/MIR 105 AGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAG 56 chr6ptel1M 489633 AGACCAAGTTCCCTGACTGCAAATCCATTGCTCTTTCCACT 489673 iv i ii v v i i- i ii C MIR3#SINE/MIR 55 AACCCAGGTCTCCTGACTCCCAGTCCG-TGCTCTCTCTGCT 16 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 32.92 CpG sites = 25, Kimura (unadjusted) = 35.21 Transitions / transversions = 1.67 (25/15) Gap_init rate = 0.05 (7 / 146), avg. gap size = 6.43 (45 / 7) 374 24.78 17.70 0.00 chr6ptel1M 489571 489683 (510317) C MIRc#SINE/MIR (129) 139 7 m_b284s601i22 11453 chr6ptel1M 489571 CACATAAGGAAACTGAGGCAGAGAGAGGGTAAATGAC--ATCCAAA---- 489614 v i vv v i --ii i---- C MIRc#SINE/MIR 139 CAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCA 90 chr6ptel1M 489615 -------------TGACAGAGATAGCCTTTCAGACCAAGT-TCCCTGACT 489650 ------------- i vii vvi iv iv i - i C MIRc#SINE/MIR 89 CACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACT 40 chr6ptel1M 489651 GCAAATCCATTGCTCTTTCCACTGTCCCATACT 489683 v i v iv i C MIRc#SINE/MIR 39 CCAAGTCCAGTGCTCTTTCCACTGCACCACACT 7 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 27.95 CpG sites = 16, Kimura (unadjusted) = 30.63 Transitions / transversions = 1.33 (16/12) Gap_init rate = 0.04 (4 / 112), avg. gap size = 5.00 (20 / 4) 309 34.96 3.18 5.09 chr6ptel1M 489744 489963 (510037) L2d2_3end#LINE/L2 138 353 (202) m_b284s601i23 11454 chr6ptel1M 489744 TCATACCATTAGAACTTCAACCTAGGACATCCTGGACCTTCCCACCTAAT 489793 ii i v--- ii vi i i iii vvv ivi i vi L2d2_3end#LIN 138 TCACGCCGTTC---CCCCCGCCTGGAATGCCCTTCCCCTTCCTCTCCACC 184 chr6ptel1M 489794 CATCCAAATTTT--CCATGACTTTCAAGGCTCCTTTCAACTGTCACCTGC 489841 i ii -- -- i i vvi v ?i v L2d2_3end#LIN 185 TATCCAAATCCTACCCAT--CCTTCAAGGCCCAGCTCAAATNCCACCTCC 232 chr6ptel1M 489842 TCCAAGGAGATTTTCATTGTTTTTCC--CTGGTTGTTCACCATCTCTTCC 489889 iv i vi i v viiivi -- iv ?v v---- i L2d2_3end#LIN 233 TCCGTGAAGCCTTCCCTGACCACTCCAGCCCGNAGTG----ATCTCTCCC 278 chr6ptel1M 489890 TCCCCTGAATTCTTGTAGCATTCACCATTTATGTTCTTCATTTGCT--TT 489937 i i i i ? i iii i i iiiv vi-- L2d2_3end#LIN 279 TCCTCTGAACTCCTATAGCANTTATTGTCTGTACCATTCATTTGGCAATT 328 chr6ptel1M 489938 TATCGCAGTA-TGCCTCGTGGTCATTT 489963 v ii- - i i- i L2d2_3end#LIN 329 AATCAT-GTACTGCCTTGTGA-CATCT 353 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 47.74 CpG sites = 51, Kimura (unadjusted) = 52.06 Transitions / transversions = 2.32 (51/22) Gap_init rate = 0.07 (15 / 219), avg. gap size = 1.20 (18 / 15) 51 0.00 0.00 0.00 chr6ptel1M 490179 490224 (509776) (CTTC)n#Simple_repeat 1 46 (0) c_b284s251i0 11455 chr6ptel1M 490179 CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT 490224 (CTTC)n#Simpl 1 CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT 46 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 13 26.98 0.00 5.77 chr6ptel1M 490227 490281 (509719) (TTC)n#Simple_repeat 1 52 (0) m_b284s252i0 11456 chr6ptel1M 490227 TTCTTCTTCCTCCTCCTCTTATCCCTTCCTTCGTGCTCCTTTTTCTGTTG 490276 i i i v -i - - v i i vi v (TTC)n#Simple 1 TTCTTCTTCTTCTTCTTCTTCT-TCTT-CTTC-TTCTTCTTCTTCTTCTT 47 chr6ptel1M 490277 CTTCT 490281 (TTC)n#Simple 48 CTTCT 52 Matrix = Unknown Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.06 (3 / 54), avg. gap size = 1.00 (3 / 3) 235 30.88 0.00 1.47 chr6ptel1M 490567 490635 (509365) MIR3#SINE/MIR 118 185 (23) m_b284s601i24 11457 chr6ptel1M 490567 GCCTCAGCTTTCCCAGCCACTAAATGGGGAGGTAAGAGCAGCTGAGGCCC 490616 i i i v iiiv i i vi vi v vvi i MIR3#SINE/MIR 118 GCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCT 167 chr6ptel1M 490617 AAAGTCCCTTTCTAGCTCT 490635 i - i MIR3#SINE/MIR 168 AAGGTCCC-TTCCAGCTCT 185 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 41.91 CpG sites = 14, Kimura (unadjusted) = 41.91 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.01 (1 / 68), avg. gap size = 1.00 (1 / 1) 181 33.33 5.38 0.00 chr6ptel1M 492477 492569 (507431) MIR3#SINE/MIR 37 134 (74) m_b284s601i25 11458 chr6ptel1M 492477 GGGTGAGGAGGCC-GGGC----GGTCTGAATCGGACACCGATGAGCTCTG 492521 i v i - i---- vi i iv v v ii iv? v MIR3#SINE/MIR 37 GAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTG 86 chr6ptel1M 492522 GGATCCAGGGCAAGTCACTTTGCTGCCGTTTGCCACGGTTCCCTCATC 492569 v i iv ii iv iv vv v i i MIR3#SINE/MIR 87 TGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATC 134 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 43.95 CpG sites = 17, Kimura (unadjusted) = 45.95 Transitions / transversions = 1.21 (17/14) Gap_init rate = 0.02 (2 / 92), avg. gap size = 2.50 (5 / 2) 195 34.25 0.00 0.00 chr6ptel1M 492497 492569 (507431) MIR#SINE/MIR 61 133 (129) m_b284s601i26 11458 chr6ptel1M 492497 CTGAATCGGACACCGATGAGCTCTGGGATCCAGGGCAAGTCACTTTGCTG 492546 i iv v v iv iv v v i iv i vi iv MIR#SINE/MIR 61 CCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCT 110 chr6ptel1M 492547 CCGTTTGCCACGGTTCCCTCATC 492569 iv v v i i MIR#SINE/MIR 111 CTCTGTGCCTCAGTTTCCTCATC 133 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 43.92 CpG sites = 12, Kimura (unadjusted) = 46.35 Transitions / transversions = 0.92 (12/13) Gap_init rate = 0.00 (0 / 72), avg. gap size = 0.0 (0 / 0) 193 30.95 2.38 0.00 chr6ptel1M 492569 492652 (507348) MIRc#SINE/MIR 172 257 (11) m_b284s601i27 11458 chr6ptel1M 492569 CCTTGCTGGGCTGTTG-GGGGTTCCAGGGAGTTAAGGCACGT-AAAGCGC 492616 ii v i - i v v iv v v i i - MIRc#SINE/MIR 172 CCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGC 221 chr6ptel1M 492617 TTGGGAAACCTTGAAGCACAATAACCATGTGATGGG 492652 v v iv i ii v vvv i v ? MIRc#SINE/MIR 222 TTTGTAAACTGTAAAGTGCTATACAAATGTAAGGNG 257 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 40.90 CpG sites = 12, Kimura (unadjusted) = 40.90 Transitions / transversions = 0.86 (12/14) Gap_init rate = 0.02 (2 / 83), avg. gap size = 1.00 (2 / 2) 336 30.02 7.10 3.43 chr6ptel1M 493429 493597 (506403) MIR3#SINE/MIR 2 176 (32) m_b284s601i28 11459 chr6ptel1M 493429 TGGCACTGTGTGG-TGAACAGGGTGT---TGGACTTGACGTCAA-AGACC 493473 -- v - i i v v---i v iv i- MIR3#SINE/MIR 2 TGGCA--GAGTGGCTGAGCAGAGAGAGCACGGACTGGGAGTCAGGAGACC 49 chr6ptel1M 493474 TAGATTAAAAGCCTGCCTCAGATAC-AA---GCTGTGAGACTCTAGTCAG 493519 i i vv iv i v v vi - --- v ii i v i MIR3#SINE/MIR 50 TGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAA 99 chr6ptel1M 493520 GT--CTTAGCCTTCTCCCTAACCCTTTGTTCTCTCAGATATAAAAAGAGA 493567 -- --- vi i iiv iv ii vv i v i MIR3#SINE/MIR 100 GTCACTT---CACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGG 146 chr6ptel1M 493568 GGGCTGGAGCCAG-TGGTCTCCCAGGACTCT 493597 i - i - i iv v i MIR3#SINE/MIR 147 GGGTTGGA-CTAGATGATCTCTAAGGTCCCT 176 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 37.37 CpG sites = 28, Kimura (unadjusted) = 39.42 Transitions / transversions = 1.33 (28/21) Gap_init rate = 0.08 (13 / 168), avg. gap size = 1.38 (18 / 13) 364 30.44 6.11 2.21 chr6ptel1M 493436 493566 (506434) MIRc#SINE/MIR 13 148 (120) m_b284s601i29 11459 chr6ptel1M 493436 GTGTGGTGAACAGGGTGTTGGACTTGACGTCA--AAGACCTAGATTAAAA 493483 ii i v i iii iv -- i i vi i MIRc#SINE/MIR 13 GTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAG 62 chr6ptel1M 493484 GCCTGCCTCAG--A--TACAAGCTGTGAGACTCTAGTCAGGT--CTTAGC 493527 v i v v -- -- v v ii i v i -- i MIRc#SINE/MIR 63 TCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAAC 112 chr6ptel1M 493528 CTTCTCCCTAACCCTTTGTTCTCTCAGATATAAAAAGAG 493566 --- i i v iv ii vv i v i MIRc#SINE/MIR 113 ---CTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 38.09 CpG sites = 25, Kimura (unadjusted) = 40.83 Transitions / transversions = 1.79 (25/14) Gap_init rate = 0.05 (7 / 130), avg. gap size = 1.57 (11 / 7) 343 22.92 10.00 0.83 chr6ptel1M 495273 495382 (504618) L2d_3end#LINE/L2 380 499 (17) m_b284s601i30 11460 chr6ptel1M 495273 TTGCCTCC---ACTAGAATGTAAGCTCCTTGAAGGCAGGGGCTATGGCTT 495319 i --- v i i i v L2d_3end#LINE 380 TTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTT 429 chr6ptel1M 495320 -TCCTGTATTTCTCAG--CCCACA-----TAGCAATGAGTTTGGTATATA 495361 - v ? - ? iv-- ----- vv v i vi i i L2d_3end#LINE 430 ATACTNT-TTTNTCGTTCCCCACAGCGCCTAGCACAGTGCTGAGCACATA 478 chr6ptel1M 495362 TGAGGTGCCTATTAATTGCTT 495382 vv i ii v v i L2d_3end#LINE 479 GTAGGCGCTCAATAAATACTT 499 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 25.74 CpG sites = 13, Kimura (unadjusted) = 28.29 Transitions / transversions = 1.08 (13/12) Gap_init rate = 0.05 (5 / 109), avg. gap size = 2.40 (12 / 5) 330 24.02 2.60 16.18 chr6ptel1M 495396 495549 (504451) C MIR3#SINE/MIR (20) 188 53 m_b284s601i31 11461 chr6ptel1M 495396 GTTAAAGCTCAAAGGGATGTTAGAACACAGAATGTTGCCTACTTCATGTA 495445 i i vi iv ----- ------------ v C MIR3#SINE/MIR 188 GTCAGAGCTGGAAGGGACCTTAGA-----GA------------TCATCTA 156 chr6ptel1M 495446 GTCTAACTCCTTCCTTTTATATATATGGGGACACTGAGGTCAAAGAGCAG 495495 i i i v i v -- i v i -v - C MIR3#SINE/MIR 155 GTCCAACCCCCTCATTTTACAGAT--GAGGAAACTGAGGCC-CAGAG-AG 110 chr6ptel1M 495496 GTAAAG-GGCTTGTCCAGTGGCATTCAGCAAGAAGGCGGGCAGAGCTTG- 495543 i - i i iv v iv ? vvi i- iv - C MIR3#SINE/MIR 109 GTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGT-GGCAGAGCCGGG 61 chr6ptel1M 495544 --TAGAAC 495549 -- C MIR3#SINE/MIR 60 ACTAGAAC 53 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 27.87 CpG sites = 18, Kimura (unadjusted) = 28.95 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.16 (25 / 153), avg. gap size = 1.04 (26 / 25) 293 29.88 2.27 1.12 chr6ptel1M 495793 495880 (504120) MIR3#SINE/MIR 64 152 (56) m_b284s601i32 11462 chr6ptel1M 495793 GGCTCTGCAGCCAAGTTACAACGTGGCCCTGACCAAGTCCTTT--CCTCT 495840 vi i v ?i vii i i iv vi -- MIR3#SINE/MIR 64 GGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCT 113 chr6ptel1M 495841 CCATGTCTCAGTTTTCCTTCCTGGTAAAGTGAAGGGGCTG 495880 iiv i i iivi - i i i MIR3#SINE/MIR 114 CTGGGCCTCAGTTTCCTCATCT-GTAAAATGAGGGGGTTG 152 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 41.48 CpG sites = 19, Kimura (unadjusted) = 41.48 Transitions / transversions = 2.71 (19/7) Gap_init rate = 0.02 (2 / 87), avg. gap size = 1.50 (3 / 2) 307 28.45 5.88 4.35 chr6ptel1M 496416 496551 (503449) C MIRc#SINE/MIR (75) 193 56 m_b284s601i33 11463 chr6ptel1M 496416 TCTGCACAA-AAGCCTGAAAGATCGGAGGTGTGGATATTATATTTTGCCC 496464 iv - v vi i v vi v ii i -- v v C MIRc#SINE/MIR 193 TCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTAT--TATCCCC 146 chr6ptel1M 496465 ATTTTATAAA----GAAACTGAGGCT--GAGAGATTATTCAGTGATTGGC 496508 i i ---- -- i --- i v C MIRc#SINE/MIR 145 ATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTA---AGTGACTTGC 99 chr6ptel1M 496509 TC-AGGTCATGCTGAGGATTGGTGCTGGACCCTGGATCTTGGAC 496551 i - ii v vvii vi vii v v - i i C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGA-CTCGAAC 56 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 35.37 CpG sites = 21, Kimura (unadjusted) = 36.61 Transitions / transversions = 1.31 (21/16) Gap_init rate = 0.07 (10 / 135), avg. gap size = 1.40 (14 / 10) 301 30.60 17.91 0.00 chr6ptel1M 496548 496681 (503319) MIR3#SINE/MIR 30 187 (21) m_b284s601i34 11464 chr6ptel1M 496548 GGACTGG-AGGCATAAGCACTGGATTTTAGTTCT---TTTGCT------- 496586 - v vi vv i i i i--- i i------- MIR3#SINE/MIR 30 GGACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACT 79 chr6ptel1M 496587 --CCATGT--CTCTGACCAAATCCTTTCCAATTTCTGAACCTCA------ 496626 -- ii -- ii iv i vi vvv i ii ------ MIR3#SINE/MIR 80 NGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCC 129 chr6ptel1M 496627 -TATCT--AAAATGATGGGACTGTCCTAGATCATTCCCAAGATTCCTCTC 496673 -i -- v ii vv v ii i i i ii MIR3#SINE/MIR 130 TCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCC 179 chr6ptel1M 496674 AGCTCTAA 496681 i MIR3#SINE/MIR 180 AGCTCTGA 187 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 40.20 CpG sites = 28, Kimura (unadjusted) = 41.57 Transitions / transversions = 2.15 (28/13) Gap_init rate = 0.05 (7 / 133), avg. gap size = 3.43 (24 / 7) 17 22.52 0.00 0.00 chr6ptel1M 496766 496801 (503199) (A)n#Simple_repeat 1 36 (0) m_b284s252i2 11465 chr6ptel1M 496766 AAAGAGAAAAAACAAAAACAAAAACAAAAACCAAAA 496801 i i v v v vv (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 36 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 15 14.38 0.00 0.00 chr6ptel1M 496857 496880 (503120) (TG)n#Simple_repeat 1 24 (0) m_b284s252i3 11466 chr6ptel1M 496857 TGTGTGCACGTGTGTGTGTGTGTG 496880 iii (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTG 24 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 181 17.98 9.26 7.27 chr6ptel1M 496885 496938 (503062) C L2c_3end#LINE/L2 (222) 256 202 m_b284s601i35 11467 chr6ptel1M 496885 GGGGAGTCAGGAAAGGCTCCATCC-----AAGTAACCTTTGAGCTGAGTA 496929 i i i -- ----- i i v i -- C L2c_3end#LINE 256 GGGGGGTCAGGGAAGGCTTC--CCGGAGGAGGTGACATCTGAGCTGAG-- 211 chr6ptel1M 496930 AGTTGAAAG 496938 ?v i C L2c_3end#LINE 210 NCTTGAAGG 202 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 21.89 CpG sites = 7, Kimura (unadjusted) = 21.89 Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.09 (5 / 53), avg. gap size = 1.80 (9 / 5) 322 33.11 9.09 3.90 chr6ptel1M 497384 497603 (502397) C L2d_3end#LINE/L2 (267) 249 19 m_b284s601i36 11468 chr6ptel1M 497384 AGGCAAGGTTTCCTGTCAGAAGTGGCGTCTAAAATGGATTTGCAAAGCCA 497433 v i v vvi i viii i iv iii vv i vii C L2d_3end#LINE 249 AGGGAAGGCTTCGTGGAGGAGGTGGGACTTGAGCTGGGCCTTGAAGGATG 200 chr6ptel1M 497434 GGAAAG----GGATTGAG-GAGACAAGGGGGTCACACAGAAGGCATCCCA 497478 v i ---- v - vi i -------i i i C L2d_3end#LINE 199 GGTAGGATTTGGATAGAGAGAGAGGAAGGGG-------AAGGGCATTCCA 157 chr6ptel1M 497479 GGCCCAG--AATGGTCTGGGCAAAGGCTCACTGG-GGGGATTCAC----- 497520 vvi -- i iv i v vv - i v i ----- C L2d_3end#LINE 156 GGCGGGGGGAACGGCGTGAGCAAAGGCGCAGAGGCGGGAATGCGCAAGGC 107 chr6ptel1M 497521 ----TCCAAAAAC-GCCAGGGGCTCGGTATGGCTGGAGCAGAGG--TCCT 497563 ---- viiii - iv i i vi iv i i -- v C L2d_3end#LINE 106 GTGTTCGGGGGACAGTGAAGAGACCGGCCTGACTGGAGCGGAGGGTTCGT 57 chr6ptel1M 497564 GCTTAAGGGGGTAATGAGAGATGAGACTGGAAATGTAAAG 497603 --i i i i i i ? v ii C L2d_3end#LINE 56 GCT--GGGGAGTAGTGGGAGATAAGGCTGGANAGGTAGGG 19 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 42.81 CpG sites = 45, Kimura (unadjusted) = 46.46 Transitions / transversions = 1.80 (45/25) Gap_init rate = 0.08 (17 / 219), avg. gap size = 1.71 (29 / 17) 20 19.72 2.08 2.08 chr6ptel1M 498186 498233 (501767) (AT)n#Simple_repeat 1 48 (0) m_b284s252i4 11469 chr6ptel1M 498186 ATATATCAGATATATA-ATATATACATGTGAATATTTATCTATTTATAT 498233 - v - i i iv v v v (AT)n#Simple_ 1 ATATAT-ATATATATATATATATATATATATATATATATATATATATAT 48 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.04 (2 / 47), avg. gap size = 1.00 (2 / 2) 304 25.00 2.13 2.13 chr6ptel1M 498405 498498 (501502) MIR1_Amn#SINE/MIR 71 164 (66) m_b284s601i37 11470 chr6ptel1M 498405 CCCTAGCACCAAACCG-TGTGTGGCTCTGAACAGGCCACTTTATCCCCTC 498453 i iv i?iv ? - ? i ii ii i i ? - i MIR1_Amn#SINE 71 CTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGTCACTTNA-CCTCTC 119 chr6ptel1M 498454 TGGGCCTCAGTTCACCCATTTGTAAACTGGAGCCAAGTGA-GCTGA 498498 ? iv i i v i vi - -i MIR1_Amn#SINE 120 TGNGCCTCAGTTTCCTCATCTGTAAAATGGGGATAA-TGATACTGA 164 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 34.92 CpG sites = 18, Kimura (unadjusted) = 34.92 Transitions / transversions = 3.60 (18/5) Gap_init rate = 0.04 (4 / 93), avg. gap size = 1.00 (4 / 4) 309 27.50 1.23 1.23 chr6ptel1M 498405 498485 (501515) MIR3#SINE/MIR 66 146 (62) m_b284s601i38 11470 chr6ptel1M 498405 CCCTAGCACCAAACCG-TGTGTGGCTCTGAACAGGCCACTTTATCCCCTC 498453 i iv i vi? - i ii ii i i i - i MIR3#SINE/MIR 66 CTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCA-CCTCTC 114 chr6ptel1M 498454 TGGGCCTCAGTTCACCCATTTGTAAACTGGAG 498485 iv i i v ii MIR3#SINE/MIR 115 TGGGCCTCAGTTTCCTCATCTGTAAAATGAGG 146 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 37.96 CpG sites = 18, Kimura (unadjusted) = 37.96 Transitions / transversions = 4.50 (18/4) Gap_init rate = 0.03 (2 / 80), avg. gap size = 1.00 (2 / 2) 477 24.59 6.77 2.16 chr6ptel1M 499437 499569 (500431) C MIRc#SINE/MIR (120) 148 10 m_b284s601i39 11471 chr6ptel1M 499437 CTCGTTTGACAGGCGAGGAAACTGAGGC-AAGCAGAGCTAAGTGACATTT 499485 i i v ii -v viii i -- C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGAC--TT 101 chr6ptel1M 499486 GTGCCAGAGTCACACAGCTAGTAAGTGCCCGTGGCTAGATTTGAA----- 499530 i- ii v v v v vi i i ----- C MIRc#SINE/MIR 100 GC-CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAG 52 chr6ptel1M 499531 --TTTCCTAACT-CAATCCCAGGGCTCTATGCACTGTGCTAC 499569 --i i - vi v v v ii i C MIRc#SINE/MIR 51 GTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 29.50 CpG sites = 20, Kimura (unadjusted) = 30.64 Transitions / transversions = 1.67 (20/12) Gap_init rate = 0.05 (7 / 132), avg. gap size = 1.71 (12 / 7) 407 23.43 11.03 2.72 chr6ptel1M 500353 500488 (499512) MIRb#SINE/MIR 8 154 (114) m_b284s601i40 11472 chr6ptel1M 500353 GCAGCATGGTTCGGTGGAAAGGATA---GTTATTCCCAGACTTGGAGACA 500399 i v i iii --- i - ---i v ii v v MIRb#SINE/MIR 8 GCAGCGTGGTGCAGTGGAAAGAGCACGGGCT-TT---GGAGTCAGACAGA 53 chr6ptel1M 500400 CCTGGGG--GAA------CTCTGCCTTTGAC-AGTCGTG--ACCTGGGGC 500438 v-- ------ vi v - ii -- v MIRb#SINE/MIR 54 CCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGC 103 chr6ptel1M 500439 TGGCTAATTAATTTCCC-AAGCTTCAGATTCCTCATCTGTAAAATGGGAA 500487 vi i v ii i -i i v i MIRb#SINE/MIR 104 AAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGA 153 chr6ptel1M 500488 T 500488 MIRb#SINE/MIR 154 T 154 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 27.88 CpG sites = 20, Kimura (unadjusted) = 28.98 Transitions / transversions = 1.82 (20/11) Gap_init rate = 0.07 (10 / 135), avg. gap size = 1.90 (19 / 10) 326 29.28 4.11 4.11 chr6ptel1M 500410 500555 (499445) MIR#SINE/MIR 65 210 (52) m_b284s601i41 11472 chr6ptel1M 500410 CTCTGCCTTTGAC-AGTCGTG--ACCTGGGGCTGGCTAATTAATTTCCCA 500456 vi v - ii -- v vi i v ii i v MIR#SINE/MIR 65 CTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCT 114 chr6ptel1M 500457 A-GCTTCAGATTCCTCATCTGTAAAATGGGAATGTAGCTGTAGGAGCTAC 500505 i- i v i -- iivi v v MIR#SINE/MIR 115 GTGCCTCAGTTTCCTCATCTGTAAAATGGGGA--TAATAATAGTACCTAC 162 chr6ptel1M 500506 --CAGAAGATGGAAGGGAGGAAGTTTAGGATGAATGTGTGCTTGTTAAGT 500553 -- v i i v vv v --- -i i vvi i v v i MIR#SINE/MIR 163 CTCATAGGGTTGTTGTGAGGA---TTA-AATGAGTTAATACATGTAAAGC 208 chr6ptel1M 500554 AC 500555 i MIR#SINE/MIR 209 GC 210 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 36.53 CpG sites = 22, Kimura (unadjusted) = 37.81 Transitions / transversions = 1.16 (22/19) Gap_init rate = 0.07 (10 / 145), avg. gap size = 1.20 (12 / 10) 12 17.65 5.00 2.44 chr6ptel1M 500575 500614 (499386) (AGAGG)n#Simple_repeat 1 41 (0) m_b284s252i5 11473 chr6ptel1M 500575 AGAGGAGGTGAGTGGAGCAGGA-ACGGGAGCAG-GGAGAGGA 500614 iv v - - v i v - (AGAGG)n#Simp 1 AGAGGAGAGGAGAGGAG-AGGAGAGGAGAGGAGAGGAGAGGA 41 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.08 (3 / 39), avg. gap size = 1.00 (3 / 3) 717 27.96 2.69 0.00 chr6ptel1M 501154 501339 (498661) MIRc#SINE/MIR 10 200 (68) m_b284s601i42 11474 chr6ptel1M 501154 GTGGCACAGTACAGGGAGCCCTGGGCC-GGAGTTAGGAAGCACAGAGTTC 501202 ii iv ii v i i- i vv v i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr6ptel1M 501203 AAATGCCACCTCAGACACTTGTTAGCTAGGCCATTCTGGGAAGGTCACTT 501252 i i v iv v v ii iv iv iii v i MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTT 109 chr6ptel1M 501253 AACTCCTGTCTGCCTCAGTTTCCCCTCATGTAAAATAGAGATAAT-ATAA 501301 ii v vv i viv i i - v MIRc#SINE/MIR 110 AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAC 159 chr6ptel1M 501302 TGG---TATCTACTTCTCAGGGTTGTTCTGAGGATAAAATG 501339 iv --- ii i v v v MIRc#SINE/MIR 160 CTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATG 200 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 34.11 CpG sites = 30, Kimura (unadjusted) = 35.82 Transitions / transversions = 1.36 (30/22) Gap_init rate = 0.02 (3 / 185), avg. gap size = 1.67 (5 / 3) 296 28.54 3.40 7.04 chr6ptel1M 501813 501959 (498041) C MIRc#SINE/MIR (75) 193 52 m_b284s601i43 11475 chr6ptel1M 501813 TCCTGACCCCAGTCCTG-GATCTAGG-AGGGAATCCAAAGA--ATTATTC 501858 v vv ii - vv - ---- iiv -- i C MIRc#SINE/MIR 193 TCCTCACAACAACCCTGTGAGGTAGGCAGGG----CAGGTATTATTATCC 148 chr6ptel1M 501859 TAATTTTACAGACAGGGAAACTGAGGCCCTGAGAGTAGAAGGTGCTTGCC 501908 iv iii i v vvv vvi C MIRc#SINE/MIR 147 CCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCC 98 chr6ptel1M 501909 AGCTGTCACCTAGCAGGGACCTCAGT-GCAGAGCCTCTGACTTCCAACTC 501957 vivv vi vi ---- v - -- v ivi v i C MIRc#SINE/MIR 97 CAAGGTCACACAGCTAG----TAAGTGGCAGAGC--CGGGACTCGAACCC 54 chr6ptel1M 501958 AG 501959 C MIRc#SINE/MIR 53 AG 52 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 35.96 CpG sites = 17, Kimura (unadjusted) = 35.96 Transitions / transversions = 0.77 (17/22) Gap_init rate = 0.10 (14 / 146), avg. gap size = 1.07 (15 / 14) 305 27.54 0.93 5.83 chr6ptel1M 501852 501959 (498041) C MIRb#SINE/MIR (111) 157 55 m_b284s601i44 11475 chr6ptel1M 501852 ATTATTCTAATTTTACAGACAGGGAAACTGAGGCCCTGAGAGTAGAAGGT 501901 i iv iii i v vvv vv C MIRb#SINE/MIR 157 ATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTA 108 chr6ptel1M 501902 GCTTGCCAGCTGTCACCTAGCAGGGACCTCAGT-GCAGAGCCTCTGACTT 501950 i vivv vi vi ---- v - -- v iv C MIRb#SINE/MIR 107 ACTTGCCCAAGGTCACACAGCTAG----TAAGTGGCAGAGC--CGGGATT 64 chr6ptel1M 501951 CCAACTCAG 501959 v i C MIRb#SINE/MIR 63 CGAACCCAG 55 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 34.30 CpG sites = 12, Kimura (unadjusted) = 34.30 Transitions / transversions = 0.75 (12/16) Gap_init rate = 0.07 (7 / 107), avg. gap size = 1.00 (7 / 7) 344 20.72 1.10 4.55 chr6ptel1M 501852 501942 (498058) C MIR1_Amn#SINE/MIR (74) 156 69 m_b284s601i45 11475 chr6ptel1M 501852 ATTATTCTAATTTTACAGACAGGGAAACTGAGGCCCTGAGAGTAGAAGGT 501901 i iv iii ? v vv? vv C MIR1_Amn#SINE 156 ATTATCCCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTG 107 chr6ptel1M 501902 GCTTGCCAGCTGTCACCTAGCAGGGACCTCAGT-GCAGAGCC 501942 i vivv ?i ? ----i? - C MIR1_Amn#SINE 106 ACTTGCCCAAGGTCACNCAGCNGG----CNAGTGGCAGAGCC 69 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 26.17 CpG sites = 9, Kimura (unadjusted) = 26.17 Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.06 (5 / 90), avg. gap size = 1.00 (5 / 5) 186 21.95 4.88 0.00 chr6ptel1M 502145 502185 (497815) L3#LINE/CR1 2001 2043 (2056) m_b284s601i46 11476 chr6ptel1M 502145 CCATGGCCTGGGACTC--AAGGGAAAATGATTTAAGAGCATTG 502185 ? i -- i i i ii i vi? L3#LINE/CR1 2001 CCATGGCCNGAGACTCAAAAAGAAAGATGGCTCAAGAGGGNTG 2043 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 29.94 CpG sites = 8, Kimura (unadjusted) = 29.94 Transitions / transversions = 8.00 (8/1) Gap_init rate = 0.03 (1 / 40), avg. gap size = 2.00 (2 / 1) 239 35.55 11.59 2.23 chr6ptel1M 502737 502900 (497100) MIRb#SINE/MIR 26 204 (64) m_b284s601i47 11477 chr6ptel1M 502737 AAGACTTTGGGACCTGGCTTCAGA-AGATCTGGATTCAAATCCC--CCCC 502783 vivi vii vv - i i i -- i i MIRb#SINE/MIR 26 AAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTCT 75 chr6ptel1M 502784 AC--CTTATTAACTGGATG----------AGTC-CTTAG---CTTTGGGG 502817 i -- i i vi ---------- i- i--- i i v MIRb#SINE/MIR 76 GCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGC 125 chr6ptel1M 502818 CTCTGTTTCTTCAGCTGCAACAAGAGAAGCTGGCCACTCTGCGCTTTCCA 502867 v i v i v v i i -- iiiv iv i-ii i iv MIRb#SINE/MIR 126 CTCAGTTTCCTCATCTGTAAAATGGGGA--TAATAATACC-TACCTCGCA 172 chr6ptel1M 502868 AAATTGTCGCAAGGACGAAGCAAGGTCGATGCA 502900 iii i ii iv iii i -i MIRb#SINE/MIR 173 GGGTTGTTGTGAGGATTAAATGAGAT-AATGCA 204 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 49.16 CpG sites = 42, Kimura (unadjusted) = 53.41 Transitions / transversions = 2.80 (42/15) Gap_init rate = 0.06 (10 / 163), avg. gap size = 2.30 (23 / 10) 538 23.25 17.32 1.45 chr6ptel1M 502949 503127 (496873) MIRc#SINE/MIR 10 216 (52) m_b284s601i48 11478 chr6ptel1M 502949 GTGGTGCAATGATTGGTAGAGGGTCAGACCTGGAGTGGGGAAACCCCAAG 502998 i --- iv viiii i vi iv iii MIRc#SINE/MIR 10 GTGGTGCAGTG---GAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGG 56 chr6ptel1M 502999 GTCAAATCC-AGCTCTG----------GCTGAGTGACCCTAGACAAGTCA 503037 v i i -i ---------- v i i i MIRc#SINE/MIR 57 TTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCA 106 chr6ptel1M 503038 TCTAATCTTT-------TCAGTTAACTCATCTGTAAAATGGAGATAATAG 503080 ii i i ------- vv i i MIRc#SINE/MIR 107 CTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAA 156 chr6ptel1M 503081 TA---GGCCTG---ACCTCCCA-GATTATAATGAGG-T----TGAGA-GA 503117 --- v --- v - i i vi - ---- -i MIRc#SINE/MIR 157 TACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAA 206 chr6ptel1M 503118 TGCATGTAAA 503127 i i MIRc#SINE/MIR 207 TGTATGTGAA 216 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 27.48 CpG sites = 30, Kimura (unadjusted) = 29.16 Transitions / transversions = 2.73 (30/11) Gap_init rate = 0.07 (12 / 178), avg. gap size = 2.83 (34 / 12) 304 28.10 14.88 0.00 chr6ptel1M 503439 503559 (496441) C L2d2_3end#LINE/L2 (3) 552 414 m_b284s601i49 11479 chr6ptel1M 503439 AATGAAAGAAACAAGCATTTATTAGGTGCTTCCTATGTACAAAGCACTGT 503488 v vv ii ii i i v i i i C L2d2_3end#LIN 552 AATCAAATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGT 503 chr6ptel1M 503489 ACTA----CTGT---------AAAGTGG--TAAACCA--GTCTTTGCTGT 503521 i ---- --------- vi -- iv -- ii iv C L2d2_3end#LIN 502 GCTAGGCGCTGTGGGGGATACAAAGAAGTATAAGACATGGTCCCTGCCCT 453 chr6ptel1M 503522 AAAGGAAGTCACTTTCCAACAGGGGAGACAA-ACACAGA 503559 v iv i vv i iiv - i i C L2d2_3end#LIN 452 CAAGGAGCTTACAATCTAGTTGGGGAGACAAGACATAAA 414 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 35.23 CpG sites = 22, Kimura (unadjusted) = 36.60 Transitions / transversions = 1.83 (22/12) Gap_init rate = 0.04 (5 / 120), avg. gap size = 3.60 (18 / 5) 306 29.63 16.67 0.00 chr6ptel1M 503448 503555 (496445) C L2b_3end#LINE/L2 (12) 454 329 m_b284s601i50 11479 chr6ptel1M 503448 AACAAGCATTTATTAGGTGCTTCCTATGTACAAAGCACTGTACTA----C 503493 ii i ii i i v i i v i ? i ---- C L2b_3end#LINE 454 AACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGC 405 chr6ptel1M 503494 TG----TAAAGTGGTAAAC----------CAGTCTTTGCTGTAAAGGAAG 503529 ---- v i i ---------- i ii iv v v iv C L2b_3end#LINE 404 TGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGGAGC 355 chr6ptel1M 503530 TCACTTTCCAACAGGGGAGACAAACA 503555 vv i iii i C L2b_3end#LINE 354 TCACAGTCTAGTGGGGGAGACAGACA 329 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 35.74 CpG sites = 23, Kimura (unadjusted) = 40.68 Transitions / transversions = 2.56 (23/9) Gap_init rate = 0.03 (3 / 107), avg. gap size = 6.00 (18 / 3) 261 31.03 0.00 4.76 chr6ptel1M 503934 504021 (495979) MIR3#SINE/MIR 102 185 (23) m_b284s601i51 11480 chr6ptel1M 503934 CATCTCACCATGCTTTTGGGCCCCACGTTTCCCCCTCTGGCAGATGAGGA 503983 ii ---ii i i - i v vv i i MIR3#SINE/MIR 102 CACTTCACC---TCTCTGGGCCTCA-GTTTCCTCATCTGTAAAATGAGGG 147 chr6ptel1M 503984 AATTGGCCCAAATGGCCTCCGGGGTCCTGTCTACCTCT 504021 ii v i i ii iii iv i v MIR3#SINE/MIR 148 GGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCT 185 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 43.52 CpG sites = 20, Kimura (unadjusted) = 43.52 Transitions / transversions = 3.33 (20/6) Gap_init rate = 0.05 (4 / 87), avg. gap size = 1.00 (4 / 4) 232 30.88 0.00 0.00 chr6ptel1M 504120 504187 (495813) C L3#LINE/CR1 (118) 3981 3914 m_b284s601i52 11481 chr6ptel1M 504120 TTAAAGATCTCTCCCGAGGGGAAGCCCCGTGCTCCTGGAAGCAGCACTTT 504169 i v i ivvi v i i vv i ii ?v i v v C L3#LINE/CR1 3981 TTGAACACCTCCAGTGACGGGGAGCTCACTACCTCNCGAGGCAGCCCATT 3932 chr6ptel1M 504170 CCATTTCGGGACAGCTCT 504187 iv C L3#LINE/CR1 3931 CCATTTTTGGACAGCTCT 3914 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 41.33 CpG sites = 11, Kimura (unadjusted) = 41.33 Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0) 44 29.12 0.00 0.00 chr6ptel1M 504335 504460 (495540) (AGAG)n#Simple_repeat 1 126 (0) m_b284s252i7 11482 chr6ptel1M 504335 AGAAAGAAAGACACAGAGAGTGAGAAAGGCAGAGAAACAGAGAGAGTGAA 504384 i i v v v i iv i v v i (AGAG)n#Simpl 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr6ptel1M 504385 ACAGAGACAGAGAGAGGGAGAGGGAGACACAGACAGACACAGAGGGAGGA 504434 v v i i v v v v v i ii (AGAG)n#Simpl 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 100 chr6ptel1M 504435 AGGAAGAGAGAGGGAAAGGGAGGGAG 504460 ii i i i i (AGAG)n#Simpl 101 AGAGAGAGAGAGAGAGAGAGAGAGAG 126 Matrix = Unknown Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.00 (0 / 125), avg. gap size = 0.0 (0 / 0) 206 23.73 4.84 4.84 chr6ptel1M 505478 505539 (494461) MIR3#SINE/MIR 113 174 (34) m_b284s601i53 11483 chr6ptel1M 505478 TTTGAACCTCAATTTTCTCTTCTGTAAATT---GGAGTTGGATTTGACTG 505524 i ii i i v v --- i i v --- MIR3#SINE/MIR 113 TCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGA--- 159 chr6ptel1M 505525 TGAGTTCTAACGTTC 505539 vi v i MIR3#SINE/MIR 160 TGATCTCTAAGGTCC 174 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 29.34 CpG sites = 9, Kimura (unadjusted) = 29.34 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.07 (4 / 61), avg. gap size = 1.50 (6 / 4) 278 28.95 6.42 1.75 chr6ptel1M 506196 506304 (493696) MIR3#SINE/MIR 87 200 (8) m_b284s601i54 11484 chr6ptel1M 506196 TAACCTGGGGAAAGCC--CTGATTTTCAAAGGCCTCAGTTTCTTGATCTG 506243 i v v i --i v ii iivvi i v MIR3#SINE/MIR 87 TGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTG 136 chr6ptel1M 506244 -AATATAGAAGGGACTGGTTCAAGTAAGCTCCTGAGAT-CCTTCCGGCTC 506291 - v - i ii vii ii i v - i i - i MIR3#SINE/MIR 137 TAAAAT-GAGGGGGTTGGACTAGATGATCT-CTAAGGTCCCTTCCAGCTC 184 chr6ptel1M 506292 TG--GTTCTA-GATCC 506304 --i - i MIR3#SINE/MIR 185 TGACATTCTATGATTC 200 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 38.80 CpG sites = 22, Kimura (unadjusted) = 38.80 Transitions / transversions = 2.44 (22/9) Gap_init rate = 0.06 (7 / 108), avg. gap size = 1.29 (9 / 7) 311 24.41 8.63 8.63 chr6ptel1M 507827 507965 (492035) MIR#SINE/MIR 6 144 (118) m_b284s601i55 11485 chr6ptel1M 507827 ATGGCATAGTGGATGCAGTGC-CAGACTTGGGAGC-AGACTCATCTTCCT 507874 i v i- v - i i iv - v----- MIR#SINE/MIR 6 ATAGCATAGTGGTTA-AGAGCACGGGCTCTGGAGCCAGACTG-----CCT 49 chr6ptel1M 507875 GAACTAAAATTCAGTTTCCAAAGCTGCCTAACTAGCTAGCTAGCTTCTTG 507924 iii vi i v vi i--- ii i - ivv ii -- MIR#SINE/MIR 50 GGGTTCGAATCCCGGCTCT---GCCACTTA-CTAGCTGTGTGAC--CTTG 93 chr6ptel1M 507925 GGCAAG---CTTA-------TTTGCCTCTGTTTCCTCATCTGTAAAGTGA 507964 --- ------- v v i i MIR#SINE/MIR 94 GGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGG 143 chr6ptel1M 507965 G 507965 MIR#SINE/MIR 144 G 144 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 28.11 CpG sites = 20, Kimura (unadjusted) = 30.43 Transitions / transversions = 1.82 (20/11) Gap_init rate = 0.12 (16 / 138), avg. gap size = 1.50 (24 / 16) 229 26.09 1.45 0.00 chr6ptel1M 508118 508186 (491814) MIR1_Amn#SINE/MIR 82 151 (79) m_b284s601i56 11486 chr6ptel1M 508118 GCCAGCTCAGGCATCTGGGGCACACATCTGTATCTCTCTGGGTCTCAGTT 508167 ? v? vv i v viivv v? i ? i MIR1_Amn#SINE 82 GCCNGCTGNGTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTT 131 chr6ptel1M 508168 ACTTC-TCAGGAAAATGAGG 508186 v i - v v i MIR1_Amn#SINE 132 TCCTCATCTGTAAAATGGGG 151 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 34.61 CpG sites = 7, Kimura (unadjusted) = 34.61 Transitions / transversions = 0.64 (7/11) Gap_init rate = 0.01 (1 / 68), avg. gap size = 1.00 (1 / 1) 327 25.47 8.49 0.00 chr6ptel1M 508130 508235 (491765) MIR3#SINE/MIR 89 203 (5) m_b284s601i57 11486 chr6ptel1M 508130 ATCTGGGGCACACATCTGTATCTCTCTGGGTCTCAGTTACTTC-TCAGGA 508178 i v viivv vi i i v i - v v MIR3#SINE/MIR 89 ACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTA 138 chr6ptel1M 508179 AAATGAGG-----GAATCAGAGCATCTCTTA--TCCCTTCAAGCTCTGCT 508221 ----- i ii vv v -- v vi MIR3#SINE/MIR 139 AAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGAC 188 chr6ptel1M 508222 CTTCTCTG-CTCTAT 508235 v v -i MIR3#SINE/MIR 189 ATTCTATGATTCTAT 203 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 31.25 CpG sites = 12, Kimura (unadjusted) = 31.25 Transitions / transversions = 0.80 (12/15) Gap_init rate = 0.04 (4 / 105), avg. gap size = 2.25 (9 / 4) 213 32.38 4.76 5.48 chr6ptel1M 509773 509919 (490081) L2b_3end#LINE/L2 146 291 (175) m_b284s601i58 11487 chr6ptel1M 509773 CCTCCATATCTGGAATCTGCTCCCCCTCACTTCT--GCCTCATCAAATCC 509820 -- ii i-- i ii i i -- vii v L2b_3end#LINE 146 CCTC--TGCCTGGAAC--GCCCTTCCCCACCTCTTCGCCTGGCCAACTCC 191 chr6ptel1M 509821 TTAGCTTCATTCAAGGTTCAGCTTCAGTGTTACCTCCTAAATGAAGTCTT 509870 vvv v v i vi iv i i vviv i i L2b_3end#LINE 192 TACTCATCCTTCAGGTCTCAGCTCAAATGTCACCTCCTCCGGGAAGCCCT 241 chr6ptel1M 509871 CTCT--TCCCCCTTGCTAATTGTTGGTTGCTGCCCCCCCT---CACCCCC 509915 i --i vv iii-- ii vi -- i i --- v L2b_3end#LINE 242 CCCTGACCCCCCAGGCCGG--GTCAGGCGC--CCTCCTCTGGGCCCCCCC 287 chr6ptel1M 509916 AATC 509919 i L2b_3end#LINE 288 AGTC 291 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 39.15 CpG sites = 29, Kimura (unadjusted) = 44.55 Transitions / transversions = 1.81 (29/16) Gap_init rate = 0.08 (11 / 146), avg. gap size = 1.36 (15 / 11) 273 29.99 1.98 0.98 chr6ptel1M 509774 509874 (490126) L2d_3end#LINE/L2 148 249 (267) m_b284s601i59 11487 chr6ptel1M 509774 CTCCATATCTGGAATCTGCTCCCCCTCACTTCTGCCTC-ATC-AAATCCT 509821 i viii viv i i- i vi - - L2d_3end#LINE 148 CCCCCCGCCTGGAATGCCCTTCCCCTT-CCTCTCTCTCTATCCAAATCCT 196 chr6ptel1M 509822 TAGCTTCATTCAAGGTTCAGCTTCAGTGTTACCTCCTAAATGAAGTCTTC 509871 vvv v v ii iv vii vv i i L2d_3end#LINE 197 ACCCATCCTTCAAGGCCCAGCTCAAGTCCCACCTCCTCCACGAAGCCTTC 246 chr6ptel1M 509872 TCT 509874 i L2d_3end#LINE 247 CCT 249 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 35.81 CpG sites = 17, Kimura (unadjusted) = 39.27 Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.03 (3 / 100), avg. gap size = 1.00 (3 / 3) 21 18.91 1.72 3.51 chr6ptel1M 510001 510058 (489942) (TTGT)n#Simple_repeat 1 57 (0) m_b284s252i8 11488 chr6ptel1M 510001 TTTTTTGTTTGTTTGTTTGTTTGTTTTCTTTCTCATGGTT-TTTCTTTTT 510049 v - v v -v v - v v (TTGT)n#Simpl 1 TTGTTTGTTTGTTTGTTTGTTTG-TTTGTTTGT-TTGTTTGTTTGTTTGT 48 chr6ptel1M 510050 TTCCTTGTT 510058 vi (TTGT)n#Simpl 49 TTGTTTGTT 57 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.05 (3 / 57), avg. gap size = 1.00 (3 / 3) 261 32.42 5.36 0.85 chr6ptel1M 510256 510367 (489633) L2a_3end#LINE/L2 396 512 (5) m_b284s601i60 11487 chr6ptel1M 510256 AAAATGCTGGCTTCTTAAAGGGAGGAACTACTTA---GATTTGT-CTTTG 510301 i ivi i v i i v i -i i--- v - vi L2a_3end#LINE 396 AGAATGTAAGCTCCATGAGGGCAGGGACT-TTTGTCTGTTTTGTTCACTG 444 chr6ptel1M 510302 -TGTATTTCCAGAGC-TAAGCTAGTGCCCACGGTATAATAGTTGTTTAAT 510349 - ii v - iivi iivvii i vi i i L2a_3end#LINE 445 CTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGGCGCTCAAT 494 chr6ptel1M 510350 AAATACTTATTGAATTAA 510367 i i v L2a_3end#LINE 495 AAATATTTGTTGAATGAA 512 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 43.63 CpG sites = 25, Kimura (unadjusted) = 45.40 Transitions / transversions = 2.27 (25/11) Gap_init rate = 0.05 (5 / 111), avg. gap size = 1.40 (7 / 5) 225 31.17 3.75 3.75 chr6ptel1M 510913 510992 (489008) L3#LINE/CR1 3513 3592 (507) m_b284s601i61 11489 chr6ptel1M 510913 GTATTATTTGAAGCATAATTTCTGG--CGGGAGCAGAAGCAGTCCCATTC 510960 i v v i i v ii -- ii i vi v ii ii - L3#LINE/CR1 3513 GCATTAATAGAAGTATAGTGTCCAGANCAAGGGAGGTAATAGTCCCGCT- 3561 chr6ptel1M 510961 TTGGCTTCTGC-TTGATCAGATCACATCTGGAG 510992 -- vvi -i i i L3#LINE/CR1 3562 --GTACTCTGCGCTGGTCAGACCACATCTGGAG 3592 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 40.59 CpG sites = 17, Kimura (unadjusted) = 43.03 Transitions / transversions = 2.43 (17/7) Gap_init rate = 0.06 (5 / 79), avg. gap size = 1.20 (6 / 5) 272 26.49 1.30 6.85 chr6ptel1M 511070 511146 (488854) L3#LINE/CR1 3588 3660 (439) m_b284s601i62 11489 chr6ptel1M 511070 TAGAGTATTGTGTTCAGGTCTGCATGCCTCATTTTGTGAAGGGCATTGCC 511119 i i v vii v iv i i --- L3#LINE/CR1 3588 TGGAGTATTGCGTTCAGTTCTGGGCGCCACATTTTAAGAGGGACATT--- 3634 chr6ptel1M 511120 AGGGCAAACTCTAATAC-TTCAGAGAAG 511146 -- i vv iii - i i L3#LINE/CR1 3635 --GACAAACTGGAGCGCGTCCAGAGGAG 3660 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 27.40 CpG sites = 13, Kimura (unadjusted) = 33.95 Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.08 (6 / 76), avg. gap size = 1.00 (6 / 6) 210 29.06 1.37 5.71 chr6ptel1M 511100 511172 (488828) C AmnSINE2#SINE/tRNA-Deu (97) 261 192 m_b284s601i63 11490 chr6ptel1M 511100 ATTTTGTGAAGGGCATTGCCAGGGCAAACTCTAATACTTCAGAGAAGCAG 511149 iv iv --- i i iv iv vv i - C AmnSINE2#SINE 261 ATTCGGCCAAGGGCA---CCGGGGCAAACCCCTACTCTTACGAAAAGC-G 216 chr6ptel1M 511150 CCATGAGTTC-TTGAGGTCTACAC 511172 i i v - i v i i C AmnSINE2#SINE 215 CCACGGGATCTTTAATGTCCACGC 192 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 28.86 CpG sites = 12, Kimura (unadjusted) = 37.75 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.07 (5 / 72), avg. gap size = 1.00 (5 / 5) 472 22.35 0.74 7.87 chr6ptel1M 511461 511596 (488404) C MIRb#SINE/MIR (138) 130 4 m_b284s601i64 11491 chr6ptel1M 511461 CTGAGGC-AATTGGGGTTAAGTGACTTGCCAAGGGTCACACAGCCAGGAA 511509 -v vv i i v i i v C MIRb#SINE/MIR 130 CTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAA 81 chr6ptel1M 511510 GTGTTAAGTGTCTAAGGTCACATTTGAACTCAGGTCCTTATGACTTCAGG 511559 vi - v i --i ---- i i iv v i ii C MIRb#SINE/MIR 80 GTGGCA-GAGCC--GGG----ATTCGAACCCAGGTCTGTCTGACTCCAAA 38 chr6ptel1M 511560 GCTGGTGCTCTCCCCGCTGCTCCACCTAGCTGCCCCT 511596 iv ii i v --- C MIRb#SINE/MIR 37 GCCCGTGCTCTTTCCACTGCACCAC---GCTGCCCCT 4 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 24.71 CpG sites = 17, Kimura (unadjusted) = 26.89 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.08 (11 / 135), avg. gap size = 1.00 (11 / 11) 272 19.61 5.88 0.00 chr6ptel1M 512414 512464 (487536) C MIR3#SINE/MIR (47) 161 108 m_b284s601i65 11492 chr6ptel1M 512414 CACCTAGTCCAGCCTCTT---TTTACATATGAGTAGACTGAGGCTCAGGG 512460 i i i i --- v v i i i C MIR3#SINE/MIR 161 CATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAG 112 chr6ptel1M 512461 AGAT 512464 i C MIR3#SINE/MIR 111 AGGT 108 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 23.81 CpG sites = 8, Kimura (unadjusted) = 23.81 Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.02 (1 / 50), avg. gap size = 3.00 (3 / 1) 254 32.55 9.77 0.69 chr6ptel1M 512444 512576 (487424) MIRc#SINE/MIR 31 175 (93) m_b284s601i66 11493 chr6ptel1M 512444 TAGACTGAGGCTCAGGGAGATCC---TCCGACTCC-AGCTCCATTG-TTG 512488 i vi iv i i i--- i v -i iiiii- i MIRc#SINE/MIR 31 TGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTA 80 chr6ptel1M 512489 TT-GCCATGTGGGCTTCCTC----CATCTCATTTCTAAGAGCCTCAGTTT 512533 i - ii iv vvv ---- ii v ii vv MIRc#SINE/MIR 81 CTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTT 130 chr6ptel1M 512534 CCTCATCC---ACATAGGCATAACGATGCTTGCATTGCCTTGCCTC 512576 i--- v i v ii i i vi - i MIRc#SINE/MIR 131 CCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCC-TACCTC 175 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 44.24 CpG sites = 30, Kimura (unadjusted) = 45.75 Transitions / transversions = 2.31 (30/13) Gap_init rate = 0.05 (7 / 132), avg. gap size = 2.00 (14 / 7) 192 35.44 2.53 0.00 chr6ptel1M 513028 513106 (486894) C L3#LINE/CR1 (3) 4096 4016 m_b284s601i67 11494 chr6ptel1M 513028 AGAATTACATAACCTTAGAACAGGAAGGAACTTAAAAACCTCTCTAACCC 513077 i v i i iiv i i v i iviiv ii C L3#LINE/CR1 4096 AGAATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCC 4047 chr6ptel1M 513078 AA--TCCGTTCCTGAGCATAAATCTTCTCTA 513106 -- vv viv vi iii C L3#LINE/CR1 4046 AACCTCCCATCCAATGCAGGAATCCCTTCTA 4016 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 50.94 CpG sites = 18, Kimura (unadjusted) = 50.94 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.01 (1 / 78), avg. gap size = 2.00 (2 / 1) 35 24.37 1.14 0.00 chr6ptel1M 513302 513329 (486671) (TC)n#Simple_repeat 1 28 (61) m_b284s252i9 11495 chr6ptel1M 513302 TCTCCCTACCTCTCTCTCTCTCTCTCTC 513329 i vi (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTC 28 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 30 7.01 2.13 2.13 chr6ptel1M 513330 513376 (486624) (TA)n#Simple_repeat 1 47 (0) c_b284s251i1 11496 chr6ptel1M 513330 TATATATATATATACATATATATA-ACTATATATATGTATATCTATAT 513376 i - - i v (TA)n#Simple_ 1 TATATATATATATATATATATATATA-TATATATATATATATATATAT 47 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.04 (2 / 46), avg. gap size = 1.00 (2 / 2) 35 24.37 1.14 0.00 chr6ptel1M 513377 513435 (486565) (TC)n#Simple_repeat 29 88 (1) m_b284s252i9 11497 chr6ptel1M 513377 CTATC-CTCCCTCTCTCCATATATATATCCGTACCTCCCTCCCTCCCTCT 513425 v - i iv v v v v iv vi i i i (TC)n#Simple_ 29 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 78 chr6ptel1M 513426 CTCTCTCTCT 513435 (TC)n#Simple_ 79 CTCTCTCTCT 88 Matrix = Unknown Transitions / transversions = 0.88 (7/8) Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1) 43 4.55 0.00 0.00 chr6ptel1M 513437 513482 (486518) (TA)n#Simple_repeat 1 46 (0) c_b284s251i2 11498 chr6ptel1M 513437 TATATGTATGTATATATATATATATATATATATATATATATATATA 513482 i i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATA 46 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 14 8.33 0.00 3.70 chr6ptel1M 513528 513555 (486445) (CTACC)n#Simple_repeat 1 27 (0) m_b284s252i10 11499 chr6ptel1M 513528 CTACCCTACCCTATTCTACCCTACTCCT 513555 ii - (CTACC)n#Simp 1 CTACCCTACCCTACCCTACCCTAC-CCT 27 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 543 21.67 2.48 0.81 chr6ptel1M 514285 514405 (485595) MIRc#SINE/MIR 24 146 (122) m_b284s601i68 11500 chr6ptel1M 514285 AGAGCACTAGGCTTAAAATCAGGAAGACTTAGCTCTAAG-CCAGCCTCAG 514333 i i ii i i i v iii - v v v MIRc#SINE/MIR 24 AGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTG 73 chr6ptel1M 514334 ACACTTCCTAGCTGTGGGACCCTGGGCAAGGCACTTCACCCCATTT--GC 514381 v v v i v v i - i -- MIRc#SINE/MIR 74 CCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC-TCTGAGC 122 chr6ptel1M 514382 CTCATTTTCCTCCCCTGTACAATG 514405 v vi v MIRc#SINE/MIR 123 CTCAGTTTCCTCATCTGTAAAATG 146 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 24.62 CpG sites = 14, Kimura (unadjusted) = 25.85 Transitions / transversions = 1.17 (14/12) Gap_init rate = 0.03 (3 / 120), avg. gap size = 1.33 (4 / 3) 16 4.17 4.00 0.00 chr6ptel1M 515129 515153 (484847) (TGA)n#Simple_repeat 1 26 (0) m_b284s252i11 11501 chr6ptel1M 515129 TGA-GATGATGATGATGATGGTGATG 515153 - i (TGA)n#Simple 1 TGATGATGATGATGATGATGATGATG 26 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 480 28.93 2.33 3.53 chr6ptel1M 515411 515582 (484418) MIR3#SINE/MIR 12 181 (27) m_b284s601i69 11502 chr6ptel1M 515411 GCCGAGACCAGAGCTCACGG--CGGGC-TCGGGAGAACCCAGGTTC-AGA 515456 i vvv vv --i v- i - ii - v MIR3#SINE/MIR 12 GCTGAGCAGAGAGAGCACGGACTGGGAGTCAGGAGA-CCTGGGTTCTAGT 60 chr6ptel1M 515457 CCCTGGTTGGCTATTTATTCACTAGAAGACCTTGGACAAATCACTTCTCT 515506 v v iv i i v i ?i iviv i i v i MIR3#SINE/MIR 61 CCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACC 110 chr6ptel1M 515507 TGGAGGGGGGAGGTCAGTTTCTTTCTCTGTAAAATGTGAGGAAGTTCCAC 515556 vvvv vv--- i iv -- ii vv MIR3#SINE/MIR 111 TCTCTGGGCC---TCAGTTTCCTCATCTGTAAAATG--AGGGGGTTGGAC 155 chr6ptel1M 515557 TGAATGCTTTCTAAGGTCCTCTCCAG 515582 ii v i ii MIR3#SINE/MIR 156 TAGATGATCTCTAAGGTCCCTTCCAG 181 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 37.26 CpG sites = 24, Kimura (unadjusted) = 37.26 Transitions / transversions = 1.00 (24/24) Gap_init rate = 0.05 (9 / 171), avg. gap size = 1.11 (10 / 9) 17 14.91 2.70 0.00 chr6ptel1M 516912 516948 (483052) (TTGGTT)n#Simple_repeat 1 38 (0) m_b284s252i12 11503 chr6ptel1M 516912 TTGG-TTTGGGATCGGTTTTGATTTTGGTTTTGTTTTT 516948 - vv i i v (TTGGTT)n#Sim 1 TTGGTTTTGGTTTTGGTTTTGGTTTTGGTTTTGGTTTT 38 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 48 4.11 0.00 0.00 chr6ptel1M 518269 518318 (481682) (TG)n#Simple_repeat 1 50 (0) c_b284s251i3 11504 chr6ptel1M 518269 TGTGTGTGTGTGTGTGTGTGTATGTGTGTGTGTCTGTGTGTGTGTGTGTG 518318 i v (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 25 11.38 5.26 6.67 chr6ptel1M 518862 518937 (481063) (GAAGAG)n#Simple_repeat 1 75 (0) m_b285s252i0 11505 chr6ptel1M 518862 GAAGGGGAGGAGGAGGGGTGTAATAGAGAA-TGGAAGA--AAGA-GAAGA 518907 i i i i - - v - -v -- - (GAAGAG)n#Sim 1 GAAGAGGAAGAGGAAGAG-G-AAGAG-GAAGAGGAAGAGGAAGAGGAAGA 47 chr6ptel1M 518908 GGAAGATGAAGAGGAAGGAGAGAAGAGGAA 518937 v - - (GAAGAG)n#Sim 48 GGAAGAGGAAGAGGAA-GAG-GAAGAGGAA 75 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.11 (8 / 75), avg. gap size = 1.12 (9 / 8) 15 21.37 5.48 5.48 chr6ptel1M 518864 518936 (481064) (AGG)n#Simple_repeat 1 73 (0) m_b285s252i1 11505 chr6ptel1M 518864 AGG-GGAGGAGGAGG-GGTGTAATA-GAGAATGGAAGA-AAGAGAAGAGG 518909 - - v v iv - i - i -i - i (AGG)n#Simple 1 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA-GGAGGAGGAG-GAGGAGG 48 chr6ptel1M 518910 AAGATGAAGAGGAAGGAGAGAAGAGGA 518936 i v i - - i (AGG)n#Simple 49 AGGAGGAGGAGG-AGGAG-GAGGAGGA 73 Matrix = Unknown Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.11 (8 / 72), avg. gap size = 1.00 (8 / 8) 328 27.25 9.00 0.93 chr6ptel1M 519316 519415 (480585) MIRc#SINE/MIR 17 124 (144) m_b285s601i0 11506 chr6ptel1M 519316 AGTAGGAAAAGCACTGGATTTGGAATCAAG--GACCTTGGATTCAAATCT 519363 i i i i i i -- - i i i i MIRc#SINE/MIR 17 AGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC-TGGGTTCGAGTCC 65 chr6ptel1M 519364 TTGCTCTGGTTTTTATCAGCTG-GTAACGT--GAC-TGTCATTT---CTC 519406 iv vivi ii - i v -- i -v i --- MIRc#SINE/MIR 66 CGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 chr6ptel1M 519407 TCCAGACCT 519415 iiii MIRc#SINE/MIR 116 TCTGAGCCT 124 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 33.34 CpG sites = 22, Kimura (unadjusted) = 36.82 Transitions / transversions = 4.40 (22/5) Gap_init rate = 0.06 (6 / 99), avg. gap size = 1.67 (10 / 6) 18 0.00 0.00 0.00 chr6ptel1M 519487 519506 (480494) (AG)n#Simple_repeat 1 20 (0) m_b285s252i2 11507 chr6ptel1M 519487 AGAGAGAGAGAGAGAGAGAG 519506 (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAG 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 309 30.78 8.24 5.09 chr6ptel1M 520716 520982 (479018) C L2#LINE/L2 (715) 2367 2093 m_b285s601i1 11508 chr6ptel1M 520716 AGAAGTTCGAGCGGCATAGATAGGTTTGAGAATTATCTGCAGGGAGAAGA 520765 i i i v v v v ii i i i v viv v i C L2#LINE/L2 2367 AGAGGTCCGGGCTGGAGATATAAATTTGGGAGTCATCAGCATATAGATGG 2318 chr6ptel1M 520766 TAATGTAATCACTGAGGGCTGATGAGACCACCAAGTAA--GAG----GAG 520809 v vv v vv iviv i ? vi -- ---- v C L2#LINE/L2 2317 TATTTAAAGCCATGAGACTGGATGAGATCACCNAGGGAGTGAGTGTAGAT 2268 chr6ptel1M 520810 AGAGAGGAGAAGAGGTGC--------AGTTCTGGCGGATACTC--ACAGT 520849 i v -------- ii -- ii -- iv C L2#LINE/L2 2267 AGAGAAGAGAAGAGGTCCAAGGACTGAGCCCTG--GGGCACTCCAACGTT 2220 chr6ptel1M 520850 CAGTGGCC---AATATCTGGCGGAGCTCCAGCAAAGGAGACTGAAAGGCT 520896 ? v i ---i v vv v i-- i ---- C L2#LINE/L2 2219 NAGAGGTCGGGGAGATGAGGAGGAA--CCAGCAAAGGAGACTGAGA---- 2176 chr6ptel1M 520897 GGGAACAGCTGGGAAGACTGGCAGGAGCAGGTGGAAAG-GCCATATCATC 520945 i i i ii vi i- i v iv vvv i - ivi i v v C L2#LINE/L2 2175 AGGAGCGGCCAGTGAGG-TAGGAGGAAAACCAGGAGAGTGTGGTGTCCTG 2127 chr6ptel1M 520946 AAAGCCTA--GAGGAAAGTCATTATCATTAAGGAAGAGG 520982 i v -- i -i ---- i i i C L2#LINE/L2 2126 GAAGCCAAGTGAAGAAAGT-GTT----TCAAGAAGGAGG 2093 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 39.70 CpG sites = 43, Kimura (unadjusted) = 41.07 Transitions / transversions = 1.23 (43/35) Gap_init rate = 0.08 (21 / 266), avg. gap size = 1.71 (36 / 21) 468 35.19 9.95 4.30 chr6ptel1M 521909 523054 (476946) C L2#LINE/L2 (1024) 2058 851 m_b285s601i2 11508 chr6ptel1M 521909 CAAGAAAGGATGAGCATTGGGGAAAAGCCATAGGAGTAGGCA-------G 521951 v - v i i i vvii v v vi ------- C L2#LINE/L2 2058 CAAGTAAG-ATGAGGACTGAGAATTGACCATTGGATTTAGCAACGTGGAG 2010 chr6ptel1M 521952 ATCCTGGGCAACCTTGGAAAGAATGGATCCATTTGAATAGTTGAGGCAGC 522001 i v v ii iv iii v i iv v i i v i i iiv C L2#LINE/L2 2009 GTCATTGGTGACCTTGACAAGAGCAGTTTCGGTGGAGTGGTGGGGACGAA 1960 chr6ptel1M 522002 AGTCAGATAGCAGAGAGT-CAAAAGA--ATGAGAGAAACCTAGGCATCCG 522048 i v v v v i - i -- i i i--- v iv C L2#LINE/L2 1959 AGCCTGATTGGAGTGGGTTCAAGAGAGAATGGGAGGAG---AGGAATTGG 1913 chr6ptel1M 522049 AAGCACTAATTCTCAGG--ACTTCCTCAAGGAACTTAGCCATGAAGCGGA 522096 ii vii v v - i-- iii i ii v ii i v C L2#LINE/L2 1912 AGACAGCGAGTAT-AGACAACTCTTTCGAGGAGTTTTGCTGTAAAGGGGA 1864 chr6ptel1M 522097 ACAGAGATGGAGGATGGACGCTAGCAGGGATAAGCAGAG-CAAGGGAAGG 522145 i vivi ii vv i - iv ? ii i - iii C L2#LINE/L2 1863 GCAGAGAAATGGGGCGGTAGCTGG-AGGGGGANGTGGGGTCAAGGGAGAA 1815 chr6ptel1M 522146 -----GGGTTTTAAGACAGCGGAGAGAAATCTTTGCC--TTTA-AAGCAG 522187 ----- vv --- vv i ?viv v-- i- v v C L2#LINE/L2 1814 TTTTTGTTTTTTAA---AGATGGGAGAAATNACAGCATGTTTGTATGCTG 1768 chr6ptel1M 522188 ATGAG--TGAT---------AAGGAGGAGGCGAT-CTATAGGAGAG-GAG 522224 i -- --------- i ii ivi -v ii - C L2#LINE/L2 1767 ATGGGAATGATCCAGTAGAGAGGGAAAAATTGATGATGCAGGAGAGAGAG 1718 chr6ptel1M 522225 GCGATAAGGAGAAAAGAGGAGGCGA--TCTATAAA-AGTCGGGATAGAAT 522271 ------ vv vv ii -- iv i i- v i vi i C L2#LINE/L2 1717 G------GGAGAATTGCTGGAGCGATGTCCTTGAGTAGGCGAGAGGGGAT 1674 chr6ptel1M 522272 GTGATCACATGTGTATGTAAAAGGATTTGCCTT-GACAAGA--AGGGCCA 522318 v vvi iii v ii i i v - i i -- v v C L2#LINE/L2 1673 GGGATCTAGTGCACAAGTGGAGGGGTTGGCCTTAGATAGGAGCACGGACA 1624 chr6ptel1M 522319 CCTCCTC--TTGCAAGCAGGGATGAAGG-AGAGTTGGGGAAGACATCTGT 522365 vi v -- v i - iiv - vv v iiv vv i C L2#LINE/L2 1623 GTTCATCCGTAGTAA-CAGGAGGGAAGGCAGAGTATGTGGGCACAGATGC 1575 chr6ptel1M 522366 -GATGAGGAGGAGGGTGTA--AAAGGGACCTCTTTGTGAACCACGTCCTT 522412 - i ii vi vi i i--iiv ---v?? i -- vv ii C L2#LINE/L2 1574 AGGTAGGTGGGTAGATGTGGTGGTGGGA---GNNTGTGGA--AGTTCTCT 1530 chr6ptel1M 522413 TTTCATT-TTT---TTTTCCCAGCAAAAT-------AAGATTCTCAGCTG 522451 i v -i --- i ii ------- i iv C L2#LINE/L2 1529 TCTGATTGCTTCTATTTTCTCAGTGAAATAGGAAGCAAGGTCATCAGCTG 1480 chr6ptel1M 522452 AGGGAGCAAGG---GGAGGGGAGCTATGTGAAGCTTGAGGAGGACTTAAA 522498 -- ii --- i i v i vv i i iivvv i C L2#LINE/L2 1479 A--GAGTGAGGATAGGGGAGGAGGTGTTGGAGGTTTGAGGAGAGAGGAGA 1432 chr6ptel1M 522499 AGCTTTGGAAATGTTATGGTAGTGAATGGAATAGTAAGTTAATTGGAG-- 522546 v v i vv ii vvvi v i i v i i vi i i i -- C L2#LINE/L2 1431 AGGTGTGAAATAGTCGTCTAGGAGAGTGGGAGAGTGAATGGACTAGGGAA 1382 chr6ptel1M 522547 --------CGATTGCC--------TT----GCCCAAGAATGGGTGCAGGT 522576 --------? -------- ---- vvviv v ?vv C L2#LINE/L2 1381 ATGTAGTANGATTGCCGGGCAGCATTAAGGGCCCACTTGAGGTTNGTGGT 1332 chr6ptel1M 522577 GA-GAATTTGTGGTGGACCCAATAAATCCCACTTTGTGCTCTTC-CCTGT 522624 v - ivi iiv i v iivivii v i i - v i C L2#LINE/L2 1331 CATGAATTTAAAGTGAGACCAGTCAGCATGGTTGTGTGTTTTTCTCCAGC 1282 chr6ptel1M 522625 TCCATTCAACAGCATGCACTCA---GCAG-GTAGG-GAAGGGGGGGAGCA 522669 iv i i v ?i viiv --- i - - i i vv viv C L2#LINE/L2 1281 CACGTTCAGCTGCNCGGGTGCAGGCGCGGAGTAGGCGGAGAGTTGGATTT 1232 chr6ptel1M 522670 ATCCAAGGTTGGGA-TTTGCAGGGCATG-ATCATCAAG-GAGATA---AC 522713 v i ? i- vi iv - iv iv - v ---i C L2#LINE/L2 1231 AACCAGGGTTGNGGTTTTGCCAGGCGAGTACGACGAAGCGAGAGAGGGGC 1182 chr6ptel1M 522714 AAGGGGCTAGAGGACA-GTGTA--GATCTGGTT----TGGTTCACTGAAC 522756 iv v ii -i i -- ivv i ---- i ?v iiviv C L2#LINE/L2 1181 AAGGGAGTTGAGGGTATATGCAAGGGAGTGATTATAATGATNGACCATGG 1132 chr6ptel1M 522757 AGTC-AAGATGAGGAAGGGAGAAGAGTGTAAACTGTATAAGGGAGGC--- 522802 i - v i v - iii vii --- i i i--- C L2#LINE/L2 1131 AATCTAAGCTGGGTAA-GGAGGGAAGTGAGGAC---ATGAGGGGGGTGAG 1086 chr6ptel1M 522803 GGTCTAAGAAAGGATTG-AGGAGTTGAGGGATGGGAGTTCTCGATGAAGA 522851 v viv i i v - - ii v v v i i ii v C L2#LINE/L2 1085 GGACAGTGAAAAGGTGGTAGGA-TCAATGGATTGGAGGTCCCGGTGGGGT 1037 chr6ptel1M 522852 TGAGCAAGACTGGGAATTGTAAGGCAGTAGGAAAGACAGGATGCTAGGCA 522901 i iv vvv v i i --i i v --- iv viv i -- C L2#LINE/L2 1036 CGAAGAATTGTTGGAGTCG--GGGTACTAG---AGGGAGTGAGCTGG--A 994 chr6ptel1M 522902 TAGATTGGGAATTGTAAGGCAGAAGGAAAGATGGGATGCTAGACATCTCA 522951 v v iii v -i v ii ----- v v i--- C L2#LINE/L2 993 AAGATAGGAGGTGGT-GGTCAGAGAG-----TGGGATGCTTGAAATT--- 953 chr6ptel1M 522952 GAGTTCATGACCATGGCTGTGACCTGCTCTTGGGTGATGGCAAGATCAAG 523001 v i i-- v v - -- v i v - i i i v C L2#LINE/L2 952 GAGATTATGG--AGGGGT-TG--CAGTTATT-GGTAATGACAAGGTCTAG 909 chr6ptel1M 523002 AGTGTGACCATCCAGGA-----TGGCTGAGAT--GAAGGAGGAGGAGGAC 523044 i i --i ----- i -- iv vi iv C L2#LINE/L2 908 GGTATGACCAT--GGGAGTGAGTGGCTGAGGTAGGGTGGAGGACAAGATC 861 chr6ptel1M 523045 GTGGGGGGAG 523054 i v i C L2#LINE/L2 860 ATTGGAGGAG 851 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 47.54 CpG sites = 224, Kimura (unadjusted) = 50.17 Transitions / transversions = 1.38 (224/162) Gap_init rate = 0.08 (97 / 1145), avg. gap size = 1.71 (166 / 97) 65 15.23 0.00 0.85 chr6ptel1M 523163 523280 (476720) (TCTCTC)n#Simple_repeat 1 117 (0) m_b285s252i3 11509 chr6ptel1M 523163 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTTTCTGTCTC 523212 v i v (TCTCTC)n#Sim 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr6ptel1M 523213 TGCTGTCTCTGTCTGTCTCTGTCTCTCTTTCTCTCTCTGTCACTCTGTTT 523262 - v v v v i v v v i (TCTCTC)n#Sim 51 T-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 99 chr6ptel1M 523263 CTCCGTTTCTCTCTGTCT 523280 iv i v (TCTCTC)n#Sim 100 CTCTCTCTCTCTCTCTCT 117 Matrix = Unknown Transitions / transversions = 0.45 (5/11) Gap_init rate = 0.01 (1 / 117), avg. gap size = 1.00 (1 / 1) 495 23.02 0.00 9.65 chr6ptel1M 523295 523419 (476581) C MIRc#SINE/MIR (153) 115 2 m_b285s601i3 11510 chr6ptel1M 523295 GGGGTTAATTGACTTGCCCAGAGTTACACAGCTAGGAAGTGTTAAGTGTC 523344 i v ii i ------- v C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGC 73 chr6ptel1M 523345 AAGAGGTCAAATTTGAACTCAGGTCCTCCTGATTGCAGGGCTGATGCTCT 523394 - vivii i i i i i v i v iii C MIRc#SINE/MIR 72 A-GAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCT 24 chr6ptel1M 523395 ATCCACTGCGCCACCTAGCTGCCCC 523419 v i ---i i C MIRc#SINE/MIR 23 TTCCACTGCACCAC---ACTGCCTC 2 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 25.84 CpG sites = 19, Kimura (unadjusted) = 28.38 Transitions / transversions = 2.71 (19/7) Gap_init rate = 0.09 (11 / 124), avg. gap size = 1.00 (11 / 11) 16 14.83 0.00 5.13 chr6ptel1M 523722 523762 (476238) (TTTTA)n#Simple_repeat 1 39 (0) m_b285s252i4 11511 chr6ptel1M 523722 TTTTATTTTATTTTATTTTTTTCTCTTGGTAATTTCATTTT 523762 v i v -- v i (TTTTA)n#Simp 1 TTTTATTTTATTTTATTTTATTTTATT--TTATTTTATTTT 39 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 16 5.27 0.00 0.00 chr6ptel1M 524258 524277 (475723) (A)n#Simple_repeat 1 20 (0) m_b285s252i5 11512 chr6ptel1M 524258 AAAAAAAAAAAAAAAGAAAA 524277 i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAA 20 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 15 19.66 0.00 0.00 chr6ptel1M 524691 524719 (475281) (A)n#Simple_repeat 1 29 (0) m_b285s252i6 11513 chr6ptel1M 524691 AAAAAAACAAAAACAAAAGACAAAACAAA 524719 v v i v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA 29 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 321 28.05 2.44 0.00 chr6ptel1M 524895 524976 (475024) C MIRc#SINE/MIR (79) 189 106 m_b285s601i4 11514 chr6ptel1M 524895 CACATGAACCCTGTGGGATGTATAATGCAAGCGTTATTCTCCCCATTTTT 524944 vv i i ivii iv i ii v v C MIRc#SINE/MIR 189 CACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTA 140 chr6ptel1M 524945 CAGATGAGAGAACTAGGG--AAGAGTCATTAAGT 524976 ii ii --v vvi C MIRc#SINE/MIR 139 CAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGT 106 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 36.20 CpG sites = 14, Kimura (unadjusted) = 36.20 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.01 (1 / 81), avg. gap size = 2.00 (2 / 1) 59 0.00 0.00 0.00 chr6ptel1M 525095 525144 (474856) (GT)n#Simple_repeat 1 50 (0) c_b285s251i1 11515 chr6ptel1M 525095 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 525144 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 180 24.19 12.90 0.00 chr6ptel1M 525179 525240 (474760) MIR1_Amn#SINE/MIR 101 170 (60) m_b285s601i6 11516 chr6ptel1M 525179 GTAAGTCATTTAATCTC----AGCCTCAG-TTCTGGGTCTGTAAAGGGGA 525223 i i ? i ----? - ivvi iv i MIR1_Amn#SINE 101 GCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGG 150 chr6ptel1M 525224 CACATTGA---GGGCCTCCT 525240 v i v ---v i MIR1_Amn#SINE 151 GATAATGATACTGACCTCCT 170 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 31.12 CpG sites = 9, Kimura (unadjusted) = 31.12 Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.05 (3 / 61), avg. gap size = 2.67 (8 / 3) 199 17.02 14.89 0.00 chr6ptel1M 525179 525225 (474775) MIRc#SINE/MIR 99 152 (116) m_b285s601i5 11516 chr6ptel1M 525179 GTAAGTCATTTAATCTC----AGCCTCAG-TTCTGGGTCTGTAAA--GGG 525221 i i i ---- - ivvi -- MIRc#SINE/MIR 99 GCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 chr6ptel1M 525222 GACA 525225 i MIRc#SINE/MIR 149 GATA 152 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 19.91 CpG sites = 6, Kimura (unadjusted) = 19.91 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.07 (3 / 46), avg. gap size = 2.33 (7 / 3) 243 33.62 9.48 0.00 chr6ptel1M 525618 525733 (474267) C L2b_3end#LINE/L2 (12) 454 328 m_b285s601i7 11517 chr6ptel1M 525618 AATAAATATTT-CT---CATTTA---TGTGTTAGGCTCCAAACAGGGAAA 525660 i - --- iii --- ii ? iivi vi viv C L2b_3end#LINE 454 AACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGC 405 chr6ptel1M 525661 TGGAAATACAAAGATGAAAAA---AGACATGATCTTTATTCCCAGGAAGA 525707 ii iv i v --- ?i i ii iii i v i v C L2b_3end#LINE 404 TGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGGAGC 355 chr6ptel1M 525708 TTATAGT-TGGGGGGGGGGGCAGATAT 525733 i i - i v i i i C L2b_3end#LINE 354 TCACAGTCTAGTGGGGGAGACAGACAT 328 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 45.11 CpG sites = 30, Kimura (unadjusted) = 50.77 Transitions / transversions = 3.33 (30/9) Gap_init rate = 0.04 (5 / 115), avg. gap size = 2.20 (11 / 5) 218 26.97 15.04 1.56 chr6ptel1M 525661 525773 (474227) C L2c_3end#LINE/L2 (50) 428 301 m_b285s601i8 11517 chr6ptel1M 525661 TGGAAATACAAAGATGAAAAAAGACATGATCTTTATTCCCAGGAAGATTA 525710 ii v - i i ii iii i i i v i C L2c_3end#LINE 428 TGGGGATACAAAGATGAATAA-GACACGGTCCCTGCCCTCAAGGAGCTCA 380 chr6ptel1M 525711 TAGT-TGGGGGGGGGGGCAGATA--TAGATATGACATGGAC----CAA-- 525751 i - i v i i i i -- i i - vvv ---- -- C L2c_3end#LINE 379 CAGTCTAGTGGAGGAGACAGACANGTAAACA-GACAATTACAATACAAGT 331 chr6ptel1M 525752 ----GATAAGTACCATAA----AGAATAGA 525773 ---- i i ---- v C L2c_3end#LINE 330 TAATGATAAGTGCTATAATGGGAGTATAGA 301 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 34.30 CpG sites = 23, Kimura (unadjusted) = 35.82 Transitions / transversions = 3.29 (23/7) Gap_init rate = 0.07 (8 / 112), avg. gap size = 2.38 (19 / 8) 453 19.58 13.42 0.60 chr6ptel1M 525784 525932 (474068) C MIRc#SINE/MIR (0) 268 101 m_b285s601i9 11518 chr6ptel1M 525784 AATAATAGTCATGTTTATACATTTA---AG---TTTAATGTTTCCATACC 525827 i v i?ii - i--- --- vv v v v C MIRc#SINE/MIR 268 AATAATAATAACNCCT-TACATTTGTATAGCACTTTACAGTTTACAAAGC 220 chr6ptel1M 525828 -CTGTTATGTACATTAT---ATCTGATCC--ATA-CAGTCCTGTGAGATA 525870 - v i ii --- i -- i - ii i C MIRc#SINE/MIR 219 GCTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTA 170 chr6ptel1M 525871 GGT---TC---TATTATTATCCCCATTT-ACAGATGTGTAAACTGAGGCT 525913 i---v --- - v v C MIRc#SINE/MIR 169 GGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCT 120 chr6ptel1M 525914 CAGGGAAATAATGTGACTT 525932 i ii v v C MIRc#SINE/MIR 119 CAGAGAGGTTAAGTGACTT 101 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 23.22 CpG sites = 17, Kimura (unadjusted) = 23.22 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.07 (10 / 148), avg. gap size = 2.10 (21 / 10) 195 32.03 6.33 1.20 chr6ptel1M 526169 526247 (473753) C MIR3#SINE/MIR (50) 158 76 m_b285s601i10 11519 chr6ptel1M 526169 CTAACTCAACTCCCCTGGTTTGTAAGCGAGGGAAACTGAGACCCAGACAG 526218 iii i iiiv ii iii - i v C MIR3#SINE/MIR 158 CTAGTCCAACCCCCTCATTTTACAGATGAGG-AAACTGAGGCCCAGAGAG 110 chr6ptel1M 526219 GCCGA--GA---GTCCCAAATCACGCACCACGTT 526247 ivi -- --- i v ii i v ?v C MIR3#SINE/MIR 109 GTGAAGTGACTTGCCCAAGGTCACACAGCNAGTT 76 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 46.60 CpG sites = 19, Kimura (unadjusted) = 46.60 Transitions / transversions = 3.17 (19/6) Gap_init rate = 0.04 (3 / 78), avg. gap size = 2.00 (6 / 3) 332 28.73 17.68 1.91 chr6ptel1M 526269 526449 (473551) MIRc#SINE/MIR 2 210 (58) m_b285s601i11 11520 chr6ptel1M 526269 GAGACCGTGTGGTGT--TGGG----GCGGTGAGCTCAGAGCCAGGAAGA- 526311 i v i-- i---- iv ii ii i - MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr6ptel1M 526312 ---GGTAC---------TTCAGAGGCTCACTGCCCGCGGGACTGTGGACA 526349 --- v ---------i v vvi i iv i i v iv i MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 101 chr6ptel1M 526350 AGGCCCTTAGCTTGTCTCAGCCTTGGTTTCCCCACCTGTGGAATG----- 526394 v v i i v v ii i i ii ----- MIRc#SINE/MIR 102 AGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGAT 151 chr6ptel1M 526395 ---AAAACCAGCCTTGATTACCTACCTCAGA-----GCTGCGGGGCTCCA 526436 --- v v i ---- v ----- i i i v v MIRc#SINE/MIR 152 AATAATACCTGCCCTG----CCTACCTCACAGGGTTGTTGTGAGGATCAA 197 chr6ptel1M 526437 AGGAGTTAACATA 526449 v v ii MIRc#SINE/MIR 198 ATGAGATAATGTA 210 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 37.52 CpG sites = 31, Kimura (unadjusted) = 37.52 Transitions / transversions = 1.55 (31/20) Gap_init rate = 0.07 (12 / 180), avg. gap size = 3.00 (36 / 12) 593 20.14 12.50 0.00 chr6ptel1M 527127 527270 (472730) MIRc#SINE/MIR 86 247 (21) m_b285s601i12 11521 chr6ptel1M 527127 TGTGTGACTCTGGGCAAGACACTTCACCTCT----GCCTCATTTTCCTCA 527172 ii v v ---- v MIRc#SINE/MIR 86 TGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCA 135 chr6ptel1M 527173 TCTGTGAAATGGGAGCAATAATA---GCCCTGATT--CCCAC-------T 527210 i iii --- vi -- i ------- MIRc#SINE/MIR 136 TCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGT 185 chr6ptel1M 527211 TATAAGAATTAAGTG-GATAATATTTGT-AGAGCATTTTGCAGACCTTTA 527258 i i i i i - i v - i ii i i iv v MIRc#SINE/MIR 186 TGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTTTGTAAACTGTAA 235 chr6ptel1M 527259 TGTGCTATATAA 527270 v i MIRc#SINE/MIR 236 AGTGCTATACAA 247 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 23.32 CpG sites = 21, Kimura (unadjusted) = 24.27 Transitions / transversions = 2.62 (21/8) Gap_init rate = 0.04 (6 / 143), avg. gap size = 3.00 (18 / 6) 261 26.04 0.00 1.37 chr6ptel1M 527474 527547 (472453) Tigger9b#DNA/TcMar-Tigger 21 93 (531) m_b285s502i0 11522 chr6ptel1M 527474 CTTGGTTTCAGAACTGCAGATTTGTCCCAACATTATCGATTTATTAGGGA 527523 v v i - ii i iiv i v Tigger9b#DNA/ 21 CTTGTTTTGAAAAC-GCGAATTTGTTCCAACGCGATTGATATATTAGGGA 69 chr6ptel1M 527524 GCGTTTTTAGCAGAACTCAAACTT 527547 i iv v v v i i Tigger9b#DNA/ 70 ACAATTTGAGCATAACGCGAATTT 93 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 24.91 CpG sites = 11, Kimura (unadjusted) = 32.65 Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.01 (1 / 73), avg. gap size = 1.00 (1 / 1) 294 22.37 1.30 1.30 chr6ptel1M 527586 527662 (472338) Tigger9b#DNA/TcMar-Tigger 310 386 (238) m_b285s502i1 11523 chr6ptel1M 527586 CACC-CTTCCCAATCACCCACAAGCTATAGTTCTTCTGAAAACTCCCTTC 527634 - v v i ii iii i vi- i v Tigger9b#DNA/ 310 CACCACTTCACAATAACTCACAAGCTGCAACCCTTCCGACG-CCCACTTC 358 chr6ptel1M 527635 CACAGGGAAACTTGAGGTCTTTATCAAG 527662 i v v v Tigger9b#DNA/ 359 CACAAGCAAACTTCAGGTCTTTTTCAAG 386 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 23.49 CpG sites = 10, Kimura (unadjusted) = 27.04 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.03 (2 / 76), avg. gap size = 1.00 (2 / 2) 443 25.32 3.66 3.66 chr6ptel1M 527794 527957 (472043) Tigger9b#DNA/TcMar-Tigger 398 561 (63) m_b285s502i2 11524 chr6ptel1M 527794 TACTTGCTGTGATATTTATATATTTCTTGATGGGTTCGCATGTTCAAAGC 527843 i ii ii i i iviv vi vi i Tigger9b#DNA/ 398 TATTTATTGTAGTATTTATGTATTTCTTAACCATTTAACATGTGTAAAAC 447 chr6ptel1M 527844 CGTGCTATC-TCTTTAAATTCAGTCCCCA-CTTTTTTT---GTGTGTCAC 527888 i i - i -- vi i i - ---i Tigger9b#DNA/ 448 TGTGCTACCGTTTTTA--TTAGGTTCCTATCTTTTTTTTTNATGTGTCAC 495 chr6ptel1M 527889 TGAGAAAGTTTTTTAATATTATGTCCCCTCCTAACCAAAATTT-CCCATG 527937 vi v i i i ---- i vv v - i Tigger9b#DNA/ 496 TGACGAAGTTTTTGAGTGTTGTG----CCCCTAACCCCATTTTCCCCATA 541 chr6ptel1M 527938 AATCTTGTGGCTTTTATTAC 527957 ii i i i Tigger9b#DNA/ 542 AGCCCTGTGGTTTTTATTGC 561 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 31.63 CpG sites = 30, Kimura (unadjusted) = 32.65 Transitions / transversions = 3.00 (30/10) Gap_init rate = 0.06 (10 / 163), avg. gap size = 1.20 (12 / 10) 336 23.56 14.62 2.05 chr6ptel1M 528075 528204 (471796) C MIR#SINE/MIR (0) 262 117 m_b285s601i13 11525 chr6ptel1M 528075 AATAATAGCTCATGTTTATAGATTTAAGTTTA--ATGTTTC---CAC-GT 528118 v ii v ---iv i -- vi --- - C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGA---GCGCTTACTATGTGCCAGGCACTGT 216 chr6ptel1M 528119 CCTG------TTATGTACATTA---TATCTGATC--CAT-ACAGTCCTGC 528156 i i------ ii ii ---i i i -- i- ii ii C MIR#SINE/MIR 215 TCTAAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTAT 166 chr6ptel1M 528157 GAGATAGGTTCTATTATTAGCCTCA-TTTACAGATGGGTAAACTGAAGC 528204 i v v i - i v i C MIR#SINE/MIR 165 GAGGTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGC 117 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 29.93 CpG sites = 23, Kimura (unadjusted) = 29.93 Transitions / transversions = 3.29 (23/7) Gap_init rate = 0.09 (11 / 129), avg. gap size = 2.00 (22 / 11) 344 17.47 8.43 3.45 chr6ptel1M 528123 528205 (471795) C MIRb#SINE/MIR (59) 209 123 m_b285s601i14 11525 chr6ptel1M 528123 TTATGTACATTAT---ATCTGATCC--ATA-CAGTCCTGCGAGATAGGTT 528166 ii i --- i i -- i - ii i - C MIRb#SINE/MIR 209 TTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGT- 161 chr6ptel1M 528167 CTATTATTAGCCTCATTT-ACAGATGGGTAAACTGAAGCT 528205 -- v i - i v i C MIRb#SINE/MIR 160 --ATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCT 123 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 20.93 CpG sites = 12, Kimura (unadjusted) = 20.93 Transitions / transversions = 6.00 (12/2) Gap_init rate = 0.09 (7 / 82), avg. gap size = 1.43 (10 / 7) 215 26.27 14.18 6.25 chr6ptel1M 528644 528777 (471223) MIR1_Amn#SINE/MIR 3 146 (84) m_b285s601i15 11526 chr6ptel1M 528644 GGAAAGCAGCGTGGTTGTGGTTGAGTGGA-AGGGTGCTGGGACTAGGG-T 528691 i i ------ iv - i ii - i i- MIR1_Amn#SINE 3 GGGAGGCAG------TGTGGTCTAGTGGATAGAGCACT-GGACTGGGACT 45 chr6ptel1M 528692 CAGAGCACCAGGTTTCAAAT------TCTGTCAGCTGTTTAGTT---TGT 528732 i iiv v v ? ? ------ i - ?vii? i --- v MIR1_Amn#SINE 46 CGGGAGACCTGGGTTCNANTCCCGGCTCTGCCA-CTNGCCNGCTGNGTGA 94 chr6ptel1M 528733 CTGTAGGCAAGACTGTTTCATCT--------CTCAATTTTCTTGCCTGTA 528774 iv i v -ii ? i -------- i i iii MIR1_Amn#SINE 95 CCTTGGGCAAGTC-ACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTA 143 chr6ptel1M 528775 AAA 528777 MIR1_Amn#SINE 144 AAA 146 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 35.16 CpG sites = 25, Kimura (unadjusted) = 36.60 Transitions / transversions = 3.12 (25/8) Gap_init rate = 0.11 (14 / 133), avg. gap size = 2.00 (28 / 14) 231 33.05 11.92 1.81 chr6ptel1M 528660 528810 (471190) MIR3#SINE/MIR 9 174 (34) m_b285s601i16 11526 chr6ptel1M 528660 GTGGTTGAGTGGAAGGGTGCTGGGACTAGG-GTCAGAGCACCAGGTTTCA 528708 i ii - i v vv i - iiv v v v MIR3#SINE/MIR 9 GTGGCTGAGCAGA-GAGAGCACGGACTGGGAGTCAGGAGACCTGGGTTCT 57 chr6ptel1M 528709 AAT------TCTGTCAGCTGTTTAGTT-TGT--CTGTAGGCAAGACTGTT 528749 i ------ i - ivi ? i - -- iv i v -ii MIR3#SINE/MIR 58 AGTCCCGGCTCTGCCA-CTAACTNGCTGTGTGACCTTGGGCAAGTC-ACT 105 chr6ptel1M 528750 TCATCTCTC--------AATTTTCTTGCCTGTAAAACCATGTAGTCCAAC 528791 i -------- i i iii iv v vi ivi MIR3#SINE/MIR 106 TCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGAC 155 chr6ptel1M 528792 TCACTCATCTTGGAGATTC 528810 viv v ivi i i MIR3#SINE/MIR 156 TAGATGATCTCTAAGGTCC 174 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 46.31 CpG sites = 31, Kimura (unadjusted) = 46.31 Transitions / transversions = 1.72 (31/18) Gap_init rate = 0.05 (8 / 150), avg. gap size = 2.62 (21 / 8) 482 21.23 15.62 0.68 chr6ptel1M 528798 528925 (471075) C MIR3#SINE/MIR (2) 206 60 m_b285s601i17 11527 chr6ptel1M 528798 ATCTTGGAGATTCTAAAAT-TTAGAGCTGGAGG------------TCATC 528834 v i - iv i - i i ------------ C MIR3#SINE/MIR 206 ATCATAGA-ATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATC 158 chr6ptel1M 528835 TGATCCAACTCTCTCATTTTACAAATGAGGCAACAGAGACCTAGAGAGAG 528884 ii i i i v v i i iv C MIR3#SINE/MIR 157 TAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGT 108 chr6ptel1M 528885 AAAATTAATTGGCCAAGGTCGCAC-GC------GTGGCAGAGATGAGA 528925 i i v v v i - ------ vi i C MIR3#SINE/MIR 107 GAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGA 60 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 24.61 CpG sites = 18, Kimura (unadjusted) = 25.69 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.04 (5 / 127), avg. gap size = 4.20 (21 / 5) 279 33.03 1.90 9.18 chr6ptel1M 530263 530472 (469528) MIRc#SINE/MIR 3 198 (70) m_b285s601i18 11528 chr6ptel1M 530263 AAGAAATGTGGGGAAGAGGAGCGGGCTCTGGCCGCAAAGCCAG-AAGGGC 530311 i v i v v v iv i v v viii i - iv MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chr6ptel1M 530312 GGGGCCAGAGTTC-AGCTCTGCT-CTTGCCAGTAGCCCCAGCGTTTGAGG 530359 v iiv i -i i- i i iv iviv v -- - MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACC--TTG-GG 99 chr6ptel1M 530360 GGAGTCACTTCCCTTCCCTCAGGCCC-GTTTGCTCATCTGTAAGATGACA 530408 vi vv i i v v i - v i --- MIRc#SINE/MIR 100 CAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATG--- 146 chr6ptel1M 530409 GGGTAGAATGAGATGAACTCTAACTGCCTTCTGGGCACCACAGAATCATG 530458 - v i v ivvi i iv i --------- ii -- MIRc#SINE/MIR 147 GGG-ATAATAATACCTGCCCTGCCTACCT---------CACAGGGT--TG 184 chr6ptel1M 530459 CTGGGAACACCAAA 530472 i v iv i MIRc#SINE/MIR 185 TTGTGAGGATCAAA 198 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 43.38 CpG sites = 35, Kimura (unadjusted) = 44.33 Transitions / transversions = 1.25 (35/28) Gap_init rate = 0.11 (22 / 209), avg. gap size = 1.00 (22 / 22) 328 27.88 6.87 1.45 chr6ptel1M 530312 530442 (469558) MIR3#SINE/MIR 44 181 (27) m_b285s601i19 11528 chr6ptel1M 530312 GGGGCCAGAGTTC-AGCTCTGCTCTTGCCAGTAGCCC-CAGCGT----TT 530355 i i v i - ii i viii v i i?- v i ---- MIR3#SINE/MIR 44 GAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTT 93 chr6ptel1M 530356 GAGGGGAGTCACTTCCCTTCCCTCAGGCCC--GTTTGCTCATCTGTAAGA 530403 - vi v i i -i i-- v i MIR3#SINE/MIR 94 G-GGCAAGTCACTTCACCTCTCT-GGGCCTCAGTTTCCTCATCTGTAAAA 141 chr6ptel1M 530404 TGACAGGGTAGAATGAGATGAACTCTAA-CTGCCTTCTGG 530442 vi v i iv v -v v ii MIR3#SINE/MIR 142 TGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAG 181 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 35.28 CpG sites = 23, Kimura (unadjusted) = 36.57 Transitions / transversions = 1.77 (23/13) Gap_init rate = 0.05 (7 / 130), avg. gap size = 1.57 (11 / 7) 355 30.75 11.81 0.62 chr6ptel1M 530479 530622 (469378) MIRb#SINE/MIR 51 210 (58) m_b285s601i20 11529 chr6ptel1M 530479 AGAGCTGGGCTTCAAGTCTGCCTCTG--AC--ACGAACTGCGGGACTGTA 530524 v i iv vi i v -- -- v i i v iv i MIRb#SINE/MIR 51 AGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTG 100 chr6ptel1M 530525 GGGAAGC-----AGGCTCTCTGGGCTTCAGGTTCATTGTCTGTAAAATGG 530569 v i----- iv i i v v ii MIRb#SINE/MIR 101 GGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGG 150 chr6ptel1M 530570 G--------CACCCATCTCTTAGAGTTGCTGTAAAGCCACAATAAAAGTA 530611 --------i i i vi i i i i vivv i i - MIRb#SINE/MIR 151 GGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGA-TA 199 chr6ptel1M 530612 AAGAGTGCAAA 530622 v vi i MIRb#SINE/MIR 200 ATGCATGTAAA 210 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 38.66 CpG sites = 27, Kimura (unadjusted) = 41.10 Transitions / transversions = 1.59 (27/17) Gap_init rate = 0.03 (5 / 143), avg. gap size = 3.60 (18 / 5) 1055 31.48 3.85 1.25 chr6ptel1M 531127 531750 (468250) C L1ME4c_3end#LINE/L1 (187) 643 4 m_b285s551i0 11530 chr6ptel1M 531127 TGTAT-CTGCTCATTTCACTAAGCATCAGGTCATGT-CAGTCTCTTCAGG 531174 - iv v i i vi iv- v i -- v C L1ME4c_3end#L 643 TGTATTCTGCTTTTTTCACTTAACATTATATCATAAACATTTTC--CATG 596 chr6ptel1M 531175 CCTTTGTGAAATCTTTCTGTTGGTCATTTCTTACAGAACAATAATATTCC 531224 iivi iiiv i iv iv vi i v ii vvvv C L1ME4c_3end#L 595 TTGCTACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCC 546 chr6ptel1M 531225 ATAACATTCATATACCATAATTTATTCAGCCATTGTCCATCTGATGG-CA 531273 vivi ?v i i i i vi vvi v - C L1ME4c_3end#L 545 ATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACA 496 chr6ptel1M 531274 TT-ATCTCAATTTCCAGTTTCTTGCCACTACAAAAAGGGCTGCCACAAAC 531322 - vv ii- i i i i i i v iv v ii C L1ME4c_3end#L 495 TTTAGGTTG-TTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAAC 447 chr6ptel1M 531323 ATTTTTGCACATGTGGGTCCTTTTCAGTCCTTTAAG--ATCTCTTTAGGA 531370 i i ii i i -- i vv i i i-- i i C L1ME4c_3end#L 446 ATCTTCGTGCATATAG--CTTTTTCCTTCTTTTGAATTATTTCCTTAGGA 399 chr6ptel1M 531371 TACAGGCCCAATAAAGATACTGCTGGATTAAAAGGTAG------TTTCAT 531414 v vv iv iv iv i i i i i v------ i C L1ME4c_3end#L 398 TAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTAT 349 chr6ptel1M 531415 AGCCAATTGA-GCATAATTCCAAATTGCTCTCCAGAAGG-TTGGATTAGT 531462 i iv- -i i v v i i - v ii i C L1ME4c_3end#L 348 GGCTC-TTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAAT 300 chr6ptel1M 531463 TCCCAACTCCATCAATAATGCATCAGTGCCCCAATTTTCCCGCATCCCCT 531512 iv ?iv i ii i v ? iv i iv ? i v C L1ME4c_3end#L 299 TTACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCG 250 chr6ptel1M 531513 CCAACATTTATCATTATCTTTTCCTGTCACTTTAGCCAAAATGAGAAGGG 531562 i vivi vv ii vvv i v i vv i v i v C L1ME4c_3end#L 249 CCAGCATTGGGTATTATCAATTTTTTAAATTTTTGCTAATTTAATAGGCG 200 chr6ptel1M 531563 TGAAGTGATATCTTAAAGTTGTCTTAATTTGCATTTCTCTAATAAATAAT 531612 i i i i vv ii i i v v ii C L1ME4c_3end#L 199 TAAAATGGTATCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACTAGC 150 chr6ptel1M 531613 GATTTAGAACATTTTTATATG---------ACTAGAATTA-ATTACTTCA 531652 vv v vi --------- -- ? i- v i v C L1ME4c_3end#L 149 GAGGTTGAACATTTTTCCATGTGTTTGTTTACT--ANTTGTATTTCCTCT 102 chr6ptel1M 531653 CATGAAAAATTTCTGTTCCTATCCTTTGACCATTTATCAGTTGGAGAATG 531702 i? vi v v v i v vi i vv v C L1ME4c_3end#L 101 TNTGTGAATTGTCTGTTCATGTCCTTTGCCCATTTATCTATTGGGGTCTT 52 chr6ptel1M 531703 ACTTTTATTCTTATAAATTTGAGTCAATTCTCTATATATTTTAGAAAT 531750 iv ? v v i v ii i ? v? v C L1ME4c_3end#L 51 GATNTTTTTCTTATCAATTTGAATGAGCTCTTTATATANTANAGATAT 4 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 41.38 CpG sites = 110, Kimura (unadjusted) = 42.84 Transitions / transversions = 1.31 (110/84) Gap_init rate = 0.03 (18 / 623), avg. gap size = 1.78 (32 / 18) 2100 31.12 5.23 4.40 chr6ptel1M 531659 534835 (465165) C L1M5_orf2#LINE/L1 (55) 3239 38 m_b285s551i1 11530 chr6ptel1M 531659 AAATTTCTGTTCCTATCCTTTGACCATTTATCAGTTGGA--GAATGACTT 531706 i v vvi i v v ?vi i-- vv v C L1M5_orf2#LIN 3239 AAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTTGTCTT 3190 chr6ptel1M 531707 TTATTCTTATAAATTTGAGTCAATTCTCTATATATTTTAGAAATGAGGCC 531756 -- ? vi ? vivv i i i i v i v C L1M5_orf2#LIN 3189 TT--TNTTATTGANTTGTAGGAGTTCTTTATATATTCTGGATACGAGTCC 3142 chr6ptel1M 531757 TTTATCAGAAACTTTCAATGTAAACCTTTTCTCC-ACTTTTCTGCTTCCC 531805 i v iv vi?v i iv - ? i viv v C L1M5_orf2#LIN 3141 TTTGTCAGATATATGTNTTGCAAATATTTTCTCCCANTCTGTGGCTTGCC 3092 chr6ptel1M 531806 TTTCAATCTTGGCTCCATTGGTATTGTTTGTACA--AAAACTTTTTAATA 531853 iv i -- iv i- i iv v?v -- i v v C L1M5_orf2#LIN 3091 TTTTCATTTT--CTTAAC-GGTGTCTTTTGANGAGCAGAAGTTTTTAATT 3045 chr6ptel1M 531854 T-AATGTA----AACTTATCCATTTTGCATTTCATAATGTTCCATAGGGT 531898 -i ? ---- i v viv i ii ------ ? v i C L1M5_orf2#LIN 3044 TTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGGT------TNGTGC 3001 chr6ptel1M 531899 CTTTTG-GCCATA------AATTCCTTACTTCTCCTCAAATCTGAGAAGT 531941 i - i v i------ v i i i v? iv ii -iv - C L1M5_orf2#LIN 3000 TTTTTGTGTCCTGTTTAAGAAATCTTTGCCTANCCCAAGGTC-ACGAAG- 2953 chr6ptel1M 531942 AGACTATCCTTTGTT--CTTCTA--ATTTGCTGATAATATCACCCTTTAT 531987 v i v v -- -- v -- v i v i ? i i C L1M5_orf2#LIN 2952 ATATTCTCCTATGTTTTCTTCTAGAAGTT--TTATAGTTTTANCTTTTAC 2905 chr6ptel1M 531988 GTCTAAATC-ATGCCCCATTTTGACCATATCTTAGTATAGGATTTTAGGT 532036 i i ii - vi i ? vivv i v i v i v v C L1M5_orf2#LIN 2904 ATTTAGGTCTATGATCCATCTNGAATTAATTTTTGTGTATGGTGTGAGGT 2855 chr6ptel1M 532037 GTTAATCAGTGCTT--GTTTCTGCCACACTGTTTTTTTCCATTTTCCAAG 532084 ivvii - v ? --v i v i iv v v i-- v v i v C L1M5_orf2#LIN 2854 AGGGGTC-GAGNTTCATTTTTTTCCATATGGATATC--CAATTGTTCCAG 2808 chr6ptel1M 532085 CA--ATTTTTGGCAAATAGTGAGTTCTTATCTCA--GA---GCTTTTGTA 532127 -- v v v v v i-- i vi i -- --- ? v i C L1M5_orf2#LIN 2807 CACCATTTGTTGAAAAGACTA--TCCTTTCCCCACTGAATTGCNTTGGCA 2760 chr6ptel1M 532128 --TTTACCAAACACTA---GATTATATAGTCTTTGACTGT-TGTGTCT-- 532169 -- ii v ii --- ?ii --------- - v -- C L1M5_orf2#LIN 2759 CCTTTGTCAAAAATCAANTGNCCATATA---------TGTGTGGGTCTAT 2719 chr6ptel1M 532170 -TGTGAACT---TAACCTATTCCACTGGTGCACTACTCTCTTTTTTAGCC 532215 - v i --- vi i i i vi i vv v ii vv C L1M5_orf2#LIN 2718 TTCTGGACTCTCTATTCTGTTCCATTGATCTATTTGTCTATCCTTACGCC 2669 chr6ptel1M 532216 AGTAGTACCAAATGGTTTTGATGACTACTGCTTTATAATATTGTTTT-AG 532264 i --- v iv i v iiv v- i - ? C L1M5_orf2#LIN 2668 AATA---CCACACTGTCTTGATTACTGTAGCTTTATAATAA-GTCTTGAN 2623 chr6ptel1M 532265 GTCTGGTGCAGC-TAGGGAACCTTTA--TTTG--CATCTTTATCATTAAT 532309 i ? -- i- i v-- ii -- -- v v v-i C L1M5_orf2#LIN 2622 ATCNGGT--AGTGTAAGT--CCTCCAACTTTGTTCTTCTTTTTCAA-GAT 2578 chr6ptel1M 532310 TCTCTTGA-GATTCTTGACCTTTTGTTCTTATAGATGGATGTTACTATT- 532357 v i i-v ? ii i ivi vi v ii v vv i- C L1M5_orf2#LIN 2577 TGTTTTGGCTATTCTNGGTCCTTTGCATTTCCATATAAATTTTAGAATCA 2528 chr6ptel1M 532358 GTTTTTCTAACTCTATAAAGAA-TTTCTTGGCAGTTTGATCGGTATGGCA 532406 i v v vi i i -ii vi v v i v v C L1M5_orf2#LIN 2527 GCTTGTCAATTTCTACAAAAAAACCTGCTGGGATTTTGATTGGGATTGCA 2478 chr6ptel1M 532407 CTCAATAATTAGGTTAATTTAAGTAAAATTGTCATTTTTTTA-TATCAGA 532455 i v vvv i i ii v i v i ?vi - iiii C L1M5_orf2#LIN 2477 TTGAATCTATAGATCAATTTGGGGAGAATTGACATCTTNACAATATTGAG 2428 chr6ptel1M 532456 TCAGCCTACCCATGAGTACTTGATAT-TCT-TCCAATTGTTTAGATCT-- 532501 vv v i -- v i - - v i i -- C L1M5_orf2#LIN 2427 TCTTCCAATCCATGA--ACATGGTATATCTCTCCATTTATTTAGGTCTTC 2380 chr6ptel1M 532502 ---AATTCTGTGTGACAAGTGTTTTGTCATTGTGTTCA---TATAGTTCC 532545 --- iiviviii - vi --- --- ? v i C L1M5_orf2#LIN 2379 TTTAATTTCTCTCAGCAA-TGTTTTGTAGTT---TTCAGTGTANAGGTCT 2334 chr6ptel1M 532546 TGGCTTTGTCTTGGCAGGTAGGCTCC--AATGTTTTACATTGCCAACAGT 532593 vviv ? i vi i vvii -- i i ? ii viivivv i C L1M5_orf2#LIN 2333 TGCACATNTTTTGTTAGATTTATTCCTAAGTATTTNATGTTTTTTGATGC 2284 chr6ptel1M 532594 TATTTTAAATGGAATTTCTCTTT---CTGTATCTTGCTGCTGGACTTTGT 532640 v v vi i ?---i vi i v vii --- C L1M5_orf2#LIN 2283 TATTGTAAATGGTATTGTTTTTNAAATTTCATTTTCCAATTG---TTTGT 2237 chr6ptel1M 532641 TGGTAATATTTAGAAATGCCGATGATTTATGTGGATTTATTTTGTATGCT 532690 v i v i viv v iv v ii v ? C L1M5_orf2#LIN 2236 TGCTAGTATATAGAAATACAATTGATTTTTGTATATTGACCTTGTATCCN 2187 chr6ptel1M 532691 GCAACTTTGCTAAAGTTGTTAATTGTTTCTGGTAGTTTCTTTAGTTAATT 532740 i i v iii v iv i ? - vi C L1M5_orf2#LIN 2186 GCGACCTTGCTAAATTCACTTATTAGTTCTAGTAGTTTNTTT-GTAGATT 2138 chr6ptel1M 532741 CTCTAGGATTCTTTAAGTTTACCAATATATTAACTGCAAAGAATGATAAT 532790 i ? i i v v? v vi i i v i v ? i i C L1M5_orf2#LIN 2137 CTTTNGGATTTTCTACGTANACAATCATGTCATCTGCGAATAANGACAGT 2088 chr6ptel1M 532791 TTTGTTTCTTTATTATTTATTCTAATTCCTTCAATTT--TTTTCTTCCCT 532838 i iv viiv ii v v iv -- v C L1M5_orf2#LIN 2087 TTTATTTCTTCCTTTCCAATCTTTATGCCTTTTATTTCTTTTTCTTGCCT 2038 chr6ptel1M 532839 TTTTGCTAAAGCTAATATTCCTAATATGATACTGAATAGAAATGGTGATA 532888 v vvvi iv iii i i ii ii i ? C L1M5_orf2#LIN 2037 TATTGCACTGGCTAGGACCTCCAGTACAATGTTGAATAGAAGTGGTGANA 1988 chr6ptel1M 532889 GTGAGCAATCTGATCTTCTTGCAAAT------------GCTTTTAATTTA 532926 i ii vi vi v v vi ------------ ? i i ? v C L1M5_orf2#LIN 1987 GCGGACATCCTTGTCTTGTTCCCGATCTTAGGGGGAAAGCNTTCAGTNTT 1938 chr6ptel1M 532927 TCCCCATTACATATG-TGT--GCAGATAGTTTTAGATAGATGCTACTTAT 532973 v vi - -- v vvi vvi ivi C L1M5_orf2#LIN 1937 TCACCATTAAGTATGATGTTNGCTGTAGGTTTTTCGTAGATGCCCTTTAT 1888 chr6ptel1M 532974 CATTTTAAGGAAAGCTCCATTTATTCCCCTGCTCTTATGCTCTGTAGTGT 533023 vv i ivii v i ----- vv v v--- v C L1M5_orf2#LIN 1887 CAGGTTGAGGAAGTTCCCTTCTATTCC-----TAGTTTGCTG---AGAGT 1846 chr6ptel1M 533024 TTTTAATAGGGATGGGTGTTGGATTTTGTCAAATGATTTTTCTACATCTA 533073 vi v i i v i C L1M5_orf2#LIN 1845 TTTTATCATGAATGGGTGTTGAATTTTGTCAAATGCTTTTTCTGCATCTA 1796 chr6ptel1M 533074 ----------CATGGGATTTCTCT---TAGTTTTGATACTGACAGTCAAT 533110 ---------- iv i --- vi i v v - ii v C L1M5_orf2#LIN 1795 TTGAGATGATCATATGATTTTTCTCCTTTATTCTGTTAAT-ATGGTGAAT 1747 chr6ptel1M 533111 TATGCCAATAGTTGTCCTGATACTGAATCAGCCCTACATTCCTGGTCTAA 533160 iiiii v v v i vi ii i i i i i vv C L1M5_orf2#LIN 1746 TACATTGATTGATTTTCGAATGTTAAACCAACCTTGCATTCCTGGGATAA 1697 chr6ptel1M 533161 ATCCTACTTGGTCACA--GTATTATCCTGGTGATAAGTTGT--AATTTT- 533205 i i ii-- vv v vi i--i iv- C L1M5_orf2#LIN 1696 ACCCCACTTGGTCATGATGTATTATCCTTTTTATATATTGCTGGATTCGA 1647 chr6ptel1M 533206 TTTGTTAATATTTTATTTAAGGTTTTTGCATCAATATTCATTAGAGAAAT 533255 i i ? i i v i v i v C L1M5_orf2#LIN 1646 TTTGCTAATATTTTGTTNAGGATTTTTGCATCTATGTTCATGAGGGATAT 1597 chr6ptel1M 533256 TGGTATATAATTTTCTTTCTCTGTTTTGGCCTTATGTGGTTTAAATATCA 533305 v i iii vv v i i v? vii C L1M5_orf2#LIN 1596 TGGTCTGTAATTTTCTTTTCTTGTAATGTCTTTGTCNGGTTTTGGTATCA 1547 chr6ptel1M 533306 GCACCATATATCT-GTGTCACAGAAGGAATTTGGTAGGACTCCTTC---C 533351 vii? i--- - iv i i v i v v vii i ---i C L1M5_orf2#LIN 1546 GGGTNATG---CTGGCCTCATAAAATGAGTTGGGAAGTGTTCCCTCTTTT 1500 chr6ptel1M 533352 CCTATTTTTTCAAATAGTTACTATAGTATTGGAATTAATTATTTTTTAAA 533401 i i vi v vv i iv v v v ii C L1M5_orf2#LIN 1499 TCTATTTTCTGGAAGAGTTTGTGTAAGATTGGTATTATTTCTTCCTTAAA 1450 chr6ptel1M 533402 TGTTTTGGTAAAACTCACTTGTAAATCCATCTGACCTTGGAGATTTTTTC 533451 - i i iv i v iv i v i i C L1M5_orf2#LIN 1449 TG-TTTGGTAGAATTCACCAGTGAAGCCATCTGGGCCTGGAGTTTTCTTT 1401 chr6ptel1M 533452 TTAGGGAGTTCATTAATAGTTTTTCAATTTATTTTTCTTAACA-----AG 533496 v i i v iv ---- viv i v ii i ----- C L1M5_orf2#LIN 1400 GTGGGAAGGTTTTTAA----TTACAAATTCAATTTCTTTAATAGATATAG 1355 chr6ptel1M 533497 GACTATTTAAATTATTCCTTTCCTCTTCTGTTAACCTGGGGAATCTATAT 533546 i i i v iiv i v? i iii v v ?i i i C L1M5_orf2#LIN 1354 GGCTATTCAGATTTTCTATTTCTTCTTGNGTCAGTTTTGGTAANTTGTGT 1305 chr6ptel1M 533547 CTTTGAAAGTATTCAT-CATTTTACTTAGATTATCAGATTTATTGGCATA 533595 i v i v ii - i ii ii ? i C L1M5_orf2#LIN 1304 TTTTCAAGGAATTTGTCCATTTCATCTAAGTTNTCAAATTTATTGGCATA 1255 chr6ptel1M 533596 TAATTGGGCAAAGTA-GCTCTTAATTATTACTTTAATTTCTTCTTCATTG 533644 v i vv v i -v - ivi v vivvv iv C L1M5_orf2#LIN 1254 AAGTTGTTCATAATATTCTCTT-ATTATCCTTTTAATGTCTGTAGGATCT 1206 chr6ptel1M 533645 GTAATAAGTTCACGCTTTTCTTTTTTTTGATAATGGTAATTTGTTTTTTT 533694 i i vv v - - iv ii v v i i C L1M5_orf2#LIN 1205 GTAGTGATGTCTC-CTTTT-TCATTCCTGATATTGGTAATTTGTGTCTTC 1158 chr6ptel1M 533695 TTTGCTTTTTTTTCTAATCAAGTTAAGTAAAGGTTTATCTATTTTGTTTT 533744 i - ii i ivi ?iv i v i-- C L1M5_orf2#LIN 1157 TCT-CTTTTTTTCTTGATCAGTCTNGCTAGAGGTTTATCAATTTTA--TT 1111 chr6ptel1M 533745 GCT-TTTTTATAAAACCAACTTTTAGTTTTATTAGTTCAATAGTTTTTTT 533793 v - i v i i i i ii ii ivv -v v v ? C L1M5_orf2#LIN 1110 GATCTTTTCAAAGAACCAGCTTTTGGCTTCGTTGATTTTCT-CTATTGTN 1062 chr6ptel1M 533794 TTTTTACTTTCAGTTTTATTAATCTTCTTTTATATTTTCAGAATTTC--- 533840 ? ii vi i i i iivi iv i i vv --- C L1M5_orf2#LIN 1061 TNTTTGTTTTCTATTTCATTGATTTCTGCTCTTATCTTTATTATTTCCTT 1012 chr6ptel1M 533841 ----AAATTTGGCATTTGGGGTTTTTTAATTTG---TTCTTTTTCTAGCT 533883 ----vv i --?v ---- --- C L1M5_orf2#LIN 1011 CCTTCTACTT--NCTTTGGG----TTTAATTTGCTCTTCTTTTTCTAGCT 968 chr6ptel1M 533884 TTTTTAGTTGCATGCCCAATTCATTGATCTT--TTCTTTC-TCTATTTTA 533930 i v v v v ii iv i --vi - v i C L1M5_orf2#LIN 967 TCTTAAGGTGGAAGCTTAGATCATTGATTTTAAGCCTTTCTTCTTTTCTA 918 chr6ptel1M 533931 TTCAAGTAAGCATCTAGAGGTATAAAACTTTCCCTAAGAACTGCTTTGGC 533980 --- vi ? i i? v vi ii i v i C L1M5_orf2#LIN 917 ---ATATANGCATTTAANGCTATAAATTTCCCTCTAAGCACTGCTTTAGC 871 chr6ptel1M 533981 TATATCCCATA---TCTGGTACCTTGTCTCATTTTTGTCATTCTCTTGGA 534027 ii i --- i i iv v iv iv ? vv vi C L1M5_orf2#LIN 870 TGCATCCCACAAATTTTGATATGTTGTATTTTCATTNTCATTCAGTTCAA 821 chr6ptel1M 534028 TGAAATTATC-AATTGTTCCTTATAGTTTGTTGTTTCACCCACTCATTCT 534076 -i v v - - i ? i ii v v v ivvi v C L1M5_orf2#LIN 820 -AATATTTTCTAATT-TCCNTTGTGATTTCTTCTTTGACCCATGGGTTAT 773 chr6ptel1M 534077 TTAGGATTA----GATTAGTTTCCAATTAATTTTTGGTTTGTTTTTCC-- 534120 i v i---- v i --- v --v v i-- C L1M5_orf2#LIN 772 TTAGAAGTGTGTTGTTTAATTTCCA---AATATTTGG--GGATTTTCTAG 728 chr6ptel1M 534121 CTGACCTTTTATTACGTG-----TAACTTCATTGTATCCTAATCTGACAA 534165 ? iv i i i- ----- i v vi iv ii v --- C L1M5_orf2#LIN 727 NTATCTTTTTGTTAT-TGATTTCTAATTTAATTCCATTGTGGTCAG---A 682 chr6ptel1M 534166 GGATAAATT---TATTATTTCTGCCTTTCTTCATTTATCTGA---TTGTG 534209 i i v i --- v vii i i?vv - --- -- C L1M5_orf2#LIN 681 GAACATACTCTGTATGATTTCAATCCTTTNAAATTTAT-TGAGACTTG-- 635 chr6ptel1M 534210 AGGTTTTTATGCCCTAATACATGGTCAATTTTTTGTGTAGGTTCCATGTA 534259 ---- v i i? i v - i v iv v i C L1M5_orf2#LIN 634 ----TTTTATGGCCCAGNATATGGTCTA-TCTTGGTAAATGTTCCATGTG 590 chr6ptel1M 534260 CTACAGATAAAAAAGTAGTATCTTTCTTTCTGTCCCCATTCAATTTTCTC 534309 vviv v i v - ii v ?v - -ivvi v? i v v C L1M5_orf2#LIN 589 CACTTGAAAAGAATGT-GTATTCTGCNGT-TGT-TGGGTGNAGTGTTCTA 543 chr6ptel1M 534310 CAAAGATCTATTATACCTAATTTTTCTAAAATTCTATTTATCTCTTTAAC 534359 i vi v vii v i vv iv v i vi i i vv iv i C L1M5_orf2#LIN 542 TAAATGTCAATTAGGTCAAGTTGGTTGATAGTGTTGTTCAAATCTTCTAT 493 chr6ptel1M 534360 ATCTTTCTTTTTTATTTTGTGGTTTCACTTA-TCTAGC---TA-TAATAC 534404 --- vi v v -- ii i- v --- - i v v C L1M5_orf2#LIN 492 ATC---CTTACTGATTTTTTG--TCTACTTGTTCTATCAATTACTGAGAG 448 chr6ptel1M 534405 AGGGAAGTTAAGATCCCCCCACTAGTATAGTTTTG---CTGTCTAGTTCT 534451 ?iv i i ---- ? v i v ---i v C L1M5_orf2#LIN 447 AGGNGTGTTAAAATCTC----CNACTATAATTGTGGATTTGTCTATTTCT 402 chr6ptel1M 534452 TCTTGCAGTTCTCTTAATTTCTCCTCTAGGAATCTGGATGCAATACCACT 534501 i vi v i i i v ii v v i v v vv iii i C L1M5_orf2#LIN 401 CCTTTTAGTTCTGTCAGTTTTTGCTTCATGTATTTTGAAGCTCTGTTATT 352 chr6ptel1M 534502 TGGTGCATATATCTTTAGTATTGATATTACTTCATTATCTA-TGATACCT 534550 v i iv v v vv v v vv - i- C L1M5_orf2#LIN 351 AGGTGCATACACATTTAGGATTGTTATGTCTTCTTGATGAATTGAC-CCT 303 chr6ptel1M 534551 TTCAGCAAGATAGAGTTTCCTTTCTTATCTCTTTGCATTAGATCTATTTT 534600 i v vv ii i v i ii ----iv - v v i C L1M5_orf2#LIN 302 TTTATCATTATGAAATGTCCCTCTTTATCTCT----GGTA-ATATTTCTT 258 chr6ptel1M 534601 TCTTT------TACTTGTTCTGATATCAAAATCACTAATCCTTGCTTTTT 534644 v i ------ vv i v vi i v? -v i C L1M5_orf2#LIN 257 GCCTTGAAGTCTACTTTGTCTGATATTAATATAGCCACNCC-AGCTTTCT 209 chr6ptel1M 534645 TTTTTTTTTTTTAATTTCATCTGAAGCATAAAAGATTCTGATCCAGCTTT 534694 v? vv ---i -------- iiv v ii vv v i C L1M5_orf2#LIN 208 TTTGNTTAGT---GTTT--------GCATGGTATATCTTTTTCCATCCTT 170 chr6ptel1M 534695 TTACCTTTACTCTCTATGTATCTCTCAGCTTCAAATGTGTTTTT--TAAA 534742 i i vi ? v i i vvii v i i i i -- i C L1M5_orf2#LIN 169 TTACTTTCAACCTNTCTGTGTCTTTATATTTAAAGTGCGTCTCTTGTAGA 120 chr6ptel1M 534743 CATTTTATCTATGGCCCATTGTAGGATTCTGGCTTTTAATCGCGTCTGCT 534792 ----------- vi v v i ii vi v vv vi C L1M5_orf2#LIN 119 CA-----------GCATATAGTTGGGTCTTGTTTTTTTATCCAGTCTGAC 81 chr6ptel1M 534793 AGCTACTTCTGTTTTATGGGAGAGATCATTCCATTCCCATTCA 534835 iiiv v iv v v v v i v? iv i C L1M5_orf2#LIN 80 AATCTCTGCCTTTTAATTGGAGTGTTTAGNCCATTTACATTTA 38 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 41.57 CpG sites = 516, Kimura (unadjusted) = 42.16 Transitions / transversions = 1.20 (516/429) Gap_init rate = 0.07 (209 / 3176), avg. gap size = 1.47 (307 / 209) 13 28.32 7.14 1.12 chr6ptel1M 534957 535040 (464960) (CCCTTTC)n#Simple_repeat 1 89 (0) m_b285s252i7 11531 chr6ptel1M 534957 CCCCTCCCCCTTT---CTTATCCCTTTCCCCTTTTACTTCTGCCCTCCCT 535003 i i --- vi iv i i v ii - (CCCTTTC)n#Si 1 CCCTTTCCCCTTTCCCCTTTCCCCTTTCCCCTTTCCCCTTTCCCCTTTC- 49 chr6ptel1M 535004 TCAATTAGCC--TCCCC-CTCTCCTTTCTCCTTTCCCCTT 535040 i vv vv -- -i i i (CCCTTTC)n#Si 50 CCCTTTCCCCTTTCCCCTTTCCCCTTTCCCCTTTCCCCTT 89 Matrix = Unknown Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.05 (4 / 83), avg. gap size = 1.75 (7 / 4) 20 0.00 0.00 0.00 chr6ptel1M 535176 535197 (464803) (T)n#Simple_repeat 1 22 (0) m_b285s252i8 11532 chr6ptel1M 535176 TTTTTTTTTTTTTTTTTTTTTT 535197 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTT 22 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 226 44.37 0.66 0.00 chr6ptel1M 535446 535596 (464404) C L2#LINE/L2 (243) 2839 2688 m_b285s601i21 11533 chr6ptel1M 535446 AATAGGGAAGTG-CAGGCTCACACCTGTACTTTAGGAAACTCGATGTGCC 535494 ii i i - v v vv i iiii ii iiv iv v v C L2#LINE/L2 2839 AGCAGAGGAGTGACATGATCTGACTTACGTTTTAAAAGGATCACTCTGGC 2790 chr6ptel1M 535495 AGATGTATAACTGACAGATGAGAAAGGGATAAGACTTGAGAAAGAGCGAT 535544 v v i vivvi i ivi? ii ii iv v iiv i v i C L2#LINE/L2 2789 TGCTGTGTTGAGAATAGACTGNAGGGGGGCAAGGGTGGAAGCAGGGAGAC 2740 chr6ptel1M 535545 CTATTAGGAGGCTACTGAAATAGTCCCAATGGGAGGTATTAGAGATCTGA 535594 vi i v i i viii i i iv i v iii i C L2#LINE/L2 2739 CAGTTAGGAGGCTATTGCAGTAATCCAGGCGAGAGATGATGGTGGCTTGG 2690 chr6ptel1M 535595 AC 535596 C L2#LINE/L2 2689 AC 2688 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 71.86 CpG sites = 44, Kimura (unadjusted) = 76.51 Transitions / transversions = 1.91 (44/23) Gap_init rate = 0.01 (1 / 150), avg. gap size = 1.00 (1 / 1) 253 28.18 3.95 11.27 chr6ptel1M 535772 535923 (464077) MIR1_Amn#SINE/MIR 17 158 (72) m_b285s601i22 11534 chr6ptel1M 535772 TCTGGAAGGTAGAAAGCTTTGCTCGGAACCCGGAAGTTCCAGGTTCAGAT 535821 i vi i ivi vvi - i i i vi ii ?i? MIR1_Amn#SINE 17 TCTAGTGGATAGAGCACTGGACT-GGGACTCGGGAGACCTGGGTTCNANT 65 chr6ptel1M 535822 CT--GCTCT--TACACACCGGTAGCTTGACCCTAGGCAAGGATTTACTTA 535867 i-- --i v?i ? iv ?v i i --- i ? MIR1_Amn#SINE 66 CCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAG---TCACTTN 112 chr6ptel1M 535868 ATCTCCCAATCCCCTGGGCAGTT--CTCATAGACTGTAAGGTCGAATTGA 535915 i i vi?v i---- -- --- ----- v i MIR1_Amn#SINE 113 ACCTCTCTGNGCCT----CAGTTTCCTCAT---CTGTAA-----AATGGG 150 chr6ptel1M 535916 GAAAGTGA 535923 v i MIR1_Amn#SINE 151 GATAATGA 158 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 39.42 CpG sites = 26, Kimura (unadjusted) = 39.42 Transitions / transversions = 2.17 (26/12) Gap_init rate = 0.13 (19 / 151), avg. gap size = 1.16 (22 / 19) 181 18.92 2.70 0.00 chr6ptel1M 536165 536201 (463799) MIR3#SINE/MIR 165 202 (6) m_b285s601i23 11528 chr6ptel1M 536165 TCCAAAGCCTCTTTCAGCTCGGACCTTCTATG-TTCTA 536201 i i i i i v v - MIR3#SINE/MIR 165 TCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTA 202 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 22.46 CpG sites = 5, Kimura (unadjusted) = 22.46 Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 188 25.00 0.00 0.00 chr6ptel1M 536453 536492 (463508) MIR3#SINE/MIR 160 199 (9) m_b285s601i24 11535 chr6ptel1M 536453 TAAGTTCCAAGGTCCTTTCCAGCTCAGACAGTTTGTGTTT 536492 i vi i i v v i i v MIR3#SINE/MIR 160 TGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATT 199 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 31.12 CpG sites = 6, Kimura (unadjusted) = 31.12 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 19 23.14 5.95 2.30 chr6ptel1M 539715 539798 (460202) (CCGGGG)n#Simple_repeat 1 87 (0) m_b285s252i9 11536 chr6ptel1M 539715 CCGGGGCCGGGTCGACGGCAGCGGAACCGGGGCC-GGCCCGGAG-CGGGG 539762 -- v viv ii - v i - (CCGGGG)n#Sim 1 CCGGGGCCGGG--GCCGGGGCCGGGGCCGGGGCCGGGGCCGGGGCCGGGG 48 chr6ptel1M 539763 CCGGGGCCCTTTGAGGAACCGGGG-C-GGGCC-GGGCCG 539798 vvvvvv ii - - - (CCGGGG)n#Sim 49 CCGGGGCCGGGGCCGGGGCCGGGGCCGGGGCCGGGGCCG 87 Matrix = Unknown Transitions / transversions = 0.60 (6/10) Gap_init rate = 0.08 (7 / 83), avg. gap size = 1.00 (7 / 7) 15 10.76 10.00 0.00 chr6ptel1M 540628 540667 (459333) (CAGCGG)n#Simple_repeat 1 44 (0) m_b285s252i12 11537 chr6ptel1M 540628 CAGC-GCAGCAGCAGCGGCA-CGGC-GC-ACAGCGCCAGCGTCA 540667 - i - - -i v v (CAGCGG)n#Sim 1 CAGCGGCAGCGGCAGCGGCAGCGGCAGCGGCAGCGGCAGCGGCA 44 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.10 (4 / 39), avg. gap size = 1.00 (4 / 4) 181 20.51 2.56 0.00 chr6ptel1M 542019 542057 (457943) MIRc#SINE/MIR 112 151 (117) m_b285s601i25 11538 chr6ptel1M 542019 CCCCACTGAGCCTCAGCTTTCT-GTCTGTAGAGGGGGGAT 542057 i v i i -i i iv MIRc#SINE/MIR 112 CCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGAT 151 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 24.94 CpG sites = 6, Kimura (unadjusted) = 24.94 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.03 (1 / 38), avg. gap size = 1.00 (1 / 1) 194 35.06 0.00 0.00 chr6ptel1M 543371 543447 (456553) MIR3#SINE/MIR 56 132 (76) m_b285s601i26 11539 chr6ptel1M 543371 CTGGACTTGTTTCTAACATCCGCTAGCAGCGTGCCCTTGGGTAATTAAGT 543420 i v ii vi iv iivi ? v i v i v v v MIR3#SINE/MIR 56 CTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACT 105 chr6ptel1M 543421 TCATCTGCCTGGCCCTCCATTACGTCA 543447 i vi v vi v v MIR3#SINE/MIR 106 TCACCTCTCTGGGCCTCAGTTTCCTCA 132 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 46.41 CpG sites = 13, Kimura (unadjusted) = 48.85 Transitions / transversions = 0.93 (13/14) Gap_init rate = 0.00 (0 / 76), avg. gap size = 0.0 (0 / 0) 196 34.51 2.65 0.00 chr6ptel1M 543382 543494 (456506) MIR1_Amn#SINE/MIR 72 187 (43) m_b285s601i27 11539 chr6ptel1M 543382 TCTAACATCCGCTAGCAGCGTGCCCTTGGGTAATTAAGTTCATCTGCCTG 543431 iv ii? i? v ? v i v v v ? i vi MIR1_Amn#SINE 72 TCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGTCACTTNACCTCTCTG 121 chr6ptel1M 543432 GCCCTCCATTACGTCAGCCACCTCAGGAGGA-AAAGCCCTTG--CTCCCT 543478 ?v vi v v v iiivvv v i - v vivi -- i MIR1_Amn#SINE 122 NGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATGATACTGACCTCCTT 171 chr6ptel1M 543479 CTTAAGGTGCCATGAG 543494 iv i iv MIR1_Amn#SINE 172 TGTAAAGTGCTTTGAG 187 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 49.83 CpG sites = 18, Kimura (unadjusted) = 49.83 Transitions / transversions = 0.86 (18/21) Gap_init rate = 0.02 (2 / 112), avg. gap size = 1.50 (3 / 2) 23 7.52 2.08 6.52 chr6ptel1M 545154 545201 (454799) (TAT)n#Simple_repeat 1 46 (0) m_b285s252i13 11540 chr6ptel1M 545154 TATTATTATTATTA-TATATAATATAATATATTATTATTCTGTATTATT 545201 - - v v - v - (TAT)n#Simple 1 TATTATTATTATTATTAT-TATTATTAT-TATTATTATTAT-TATTATT 46 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.09 (4 / 47), avg. gap size = 1.00 (4 / 4) 35 21.14 0.00 0.00 chr6ptel1M 547192 547262 (452738) (A)n#Simple_repeat 1 71 (0) m_b285s252i14 11541 chr6ptel1M 547192 AAATAAAAAAAAAAGAGATCATAAAAAATAAAAAAATAAAATAATAAAAA 547241 v i i vv v v v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr6ptel1M 547242 ACAAAAATAAAAAAAATAAAA 547262 v v v (A)n#Simple_r 51 AAAAAAAAAAAAAAAAAAAAA 71 Matrix = Unknown Transitions / transversions = 0.18 (2/11) Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 chr6ptel1M 548645 548662 (451338) (T)n#Simple_repeat 1 18 (0) m_b285s252i15 11542 chr6ptel1M 548645 TTTTTTTTTTTTTTTTTT 548662 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTT 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 313 32.56 5.84 5.84 chr6ptel1M 550486 550622 (449378) MIRc#SINE/MIR 12 148 (120) m_b285s601i28 11543 chr6ptel1M 550486 GGCGCAGGTGATAGAACGCTGGA------GTCGGGAACACTCGTCTTGTA 550529 i vv v i i ------ i v i------- i MIRc#SINE/MIR 12 GGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC-------TG 54 chr6ptel1M 550530 AGTTCAAA-CCTGCCTTCCAACACTTAATGGCTATGGGCTCCCAGAGGGG 550578 i i i- i v - iiv v i i v vi iii ivii MIRc#SINE/MIR 55 GGTTCGAGTCCCGGCT-CTGCCACTTACTAGCTGTGTGACCTTGGGCAAG 103 chr6ptel1M 550579 TCATCTAACCCTTTTTAGC-TCACTTTCTTTCTCTGTAAAATGAG 550622 ii ii i v - v i iv i MIRc#SINE/MIR 104 TCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 42.58 CpG sites = 29, Kimura (unadjusted) = 45.60 Transitions / transversions = 2.23 (29/13) Gap_init rate = 0.08 (11 / 136), avg. gap size = 1.45 (16 / 11) 257 26.42 5.49 4.35 chr6ptel1M 551082 551172 (448828) C MIR3#SINE/MIR (0) 208 117 m_b285s601i29 11544 chr6ptel1M 551082 GAATCAATCAGGATCA--GAACG--AAGGTTGGCAGGAGCCT-GGAGACG 551126 --i i -- i -- ii i v ii -i iv C MIR3#SINE/MIR 208 GAATCA--TAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATC 161 chr6ptel1M 551127 ATTTTGTGTAAGTCCTTCATCTTTCAGATGAGGAAACCAAATGGCC 551172 i v vi vi i i v ii -- C MIR3#SINE/MIR 160 ATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGA--GGCC 117 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 34.50 CpG sites = 17, Kimura (unadjusted) = 34.50 Transitions / transversions = 2.83 (17/6) Gap_init rate = 0.08 (7 / 90), avg. gap size = 1.29 (9 / 7) 289 32.05 1.28 0.00 chr6ptel1M 553707 553784 (446216) MIRc#SINE/MIR 3 81 (187) m_b285s601i30 11545 chr6ptel1M 553707 AAGAAATGTGGGACAGTGGAAAACATGCTGGATTTGGAGTGAGGGC-ACT 553755 i v i vi iviii i v iv- i MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chr6ptel1M 553756 TGGGTCCAAATATCCGCCCTGCTCCTCAC 553784 i i i vi v i iv i MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCACTTAC 81 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 41.96 CpG sites = 17, Kimura (unadjusted) = 44.40 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.01 (1 / 77), avg. gap size = 1.00 (1 / 1) 288 22.54 1.41 0.00 chr6ptel1M 554402 554472 (445528) C HSAT5v1#Satellite (618) 5280 5209 m_b285s502i3 11546 chr6ptel1M 554402 ACACACGTACACACACACATACATGCACGCACACACACATACATGCGCGC 554451 ii i i ? ii i i i ii ii i C HSAT5v1#Satel 5280 ACACACGCGCACACACGCGTNCACACACACACACGCGCGCACGCGCGTGC 5231 chr6ptel1M 554452 ACACACACA-TACATGCGCGCA 554472 - i i C HSAT5v1#Satel 5230 ACACACACATTGCATGCACGCA 5209 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 14.29 CpG sites = 16, Kimura (unadjusted) = 30.55 Transitions / transversions = 1.00 (16/0) Gap_init rate = 0.01 (1 / 70), avg. gap size = 1.00 (1 / 1) 269 25.35 1.41 0.00 chr6ptel1M 554422 554492 (445508) C HSAT5v1#Satellite (618) 5280 5209 m_b285s502i4 11546 chr6ptel1M 554422 ACATGCACGCACACACACATACATGCGCGCACACACACATACATGCGCGC 554471 ii i i i ? ii i i i i ii ii i C HSAT5v1#Satel 5280 ACACACGCGCACACACGCGTNCACACACACACACGCGCGCACGCGCGTGC 5231 chr6ptel1M 554472 ACACACACA-TACATGCGCGCA 554492 - i i C HSAT5v1#Satel 5230 ACACACACATTGCATGCACGCA 5209 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 18.45 CpG sites = 18, Kimura (unadjusted) = 36.11 Transitions / transversions = 1.00 (18/0) Gap_init rate = 0.01 (1 / 70), avg. gap size = 1.00 (1 / 1) 287 23.94 1.41 0.00 chr6ptel1M 554442 554512 (445488) C HSAT5v1#Satellite (618) 5280 5209 m_b285s502i5 11546 chr6ptel1M 554442 ACATGCGCGCACACACACATACATGCGCGCACACACACATACATGCGCGC 554491 ii i i ? ii i i i i ii ii i C HSAT5v1#Satel 5280 ACACACGCGCACACACGCGTNCACACACACACACGCGCGCACGCGCGTGC 5231 chr6ptel1M 554492 ACACACACA-TACATGCGCGCA 554512 - i i C HSAT5v1#Satel 5230 ACACACACATTGCATGCACGCA 5209 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 18.24 CpG sites = 17, Kimura (unadjusted) = 33.25 Transitions / transversions = 1.00 (17/0) Gap_init rate = 0.01 (1 / 70), avg. gap size = 1.00 (1 / 1) 286 25.00 1.39 0.00 chr6ptel1M 554462 554533 (445467) C HSAT5v1#Satellite (618) 5280 5208 m_b285s502i6 11546 chr6ptel1M 554462 ACATGCGCGCACACACACATACATGCGCGCACACACACATACATGCGCGC 554511 ii i i ? ii i i i i ii ii i C HSAT5v1#Satel 5280 ACACACGCGCACACACGCGTNCACACACACACACGCGCGCACGCGCGTGC 5231 chr6ptel1M 554512 ACACACACA-TACATGCGCACAT 554533 - i i i C HSAT5v1#Satel 5230 ACACACACATTGCATGCACGCAT 5208 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 18.14 CpG sites = 18, Kimura (unadjusted) = 35.37 Transitions / transversions = 1.00 (18/0) Gap_init rate = 0.01 (1 / 71), avg. gap size = 1.00 (1 / 1) 229 31.09 1.32 2.67 chr6ptel1M 554704 554779 (445221) C MIR3#SINE/MIR (25) 183 109 m_b285s601i31 11547 chr6ptel1M 554704 AGCAGAAAGGGAGCTCAAAGATTATCGGCTCCAATTTTCTCTTCTCCCAG 554753 v i v i i i viv iiii v i iv C MIR3#SINE/MIR 183 AGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAG 134 chr6ptel1M 554754 TAGAGGGAACTT-GGCTAACAGAGAAG 554779 vv i v- i-- i C MIR3#SINE/MIR 133 ATGAGGAAACTGAGGCC--CAGAGAGG 109 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 41.63 CpG sites = 14, Kimura (unadjusted) = 41.63 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.04 (3 / 75), avg. gap size = 1.00 (3 / 3) 410 30.34 4.64 3.95 chr6ptel1M 554786 554936 (445064) C MIR3#SINE/MIR (23) 185 34 m_b285s601i32 11548 chr6ptel1M 554786 AGAGCTGG--GAGACCTCGGGGCCCCTCCAGTTTAGTC---TCATTTTAA 554830 -- i ii i vi v i ii ii --- v C MIR3#SINE/MIR 185 AGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTAC 136 chr6ptel1M 554831 AGATGAGGAAACAGAGACCCCCAGAGAAACAAAAT--TTTGAGTCCATGG 554878 v i-- iiii i --i -- i v C MIR3#SINE/MIR 135 AGATGAGGAAACTGAGG--CCCAGAGAGGTGAAGTGACTT--GCCCAAGG 90 chr6ptel1M 554879 CTATAGAGCTATGAAGTATGGCTTCCTTAGGATTAGAAGTCAGGTCTTCT 554928 ii i v ? vvv -- vvvviii i vi i C MIR3#SINE/MIR 89 TCACACAGCNAGTTAG--TGGCAGAGCCGGGACTAGAACCCAGGTCTCCT 42 chr6ptel1M 554929 GGCCCTCA 554936 i i i C MIR3#SINE/MIR 41 GACTCCCA 34 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 40.06 CpG sites = 30, Kimura (unadjusted) = 41.47 Transitions / transversions = 2.14 (30/14) Gap_init rate = 0.06 (9 / 150), avg. gap size = 1.44 (13 / 9) 253 24.59 13.11 0.00 chr6ptel1M 556077 556198 (443802) L2d_3end#LINE/L2 108 245 (271) m_b286s601i2 11549 chr6ptel1M 556077 CCTTGGTCCTTCACCTCTCTGCACTCTCACTG--GCTGTCTCTCCTGCCT 556124 vv v v vi i ii ii v-- i ii i i L2d_3end#LINE 108 CCTTGCGCATTCCCGCCTCTGCGCCTTTGCTCACGCCGTTCCCCCCGCCT 157 chr6ptel1M 556125 GGAGGG----TCCCCTTCCTCT-TCTCC-TCCAGGTT-------TCCTTC 556161 iv ---- - i- ii i------- L2d_3end#LINE 158 GGAATGCCCTTCCCCTTCCTCTCTCTCTATCCAAATCCTACCCATCCTTC 207 chr6ptel1M 556162 A-GTCTCAGCTAAAGTCCCTCCTTCTGCAGGAAGCCTT 556198 - v i v v i v v L2d_3end#LINE 208 AAGGCCCAGCTCAAGTCCCACCTCCTCCACGAAGCCTT 245 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 26.95 CpG sites = 18, Kimura (unadjusted) = 30.47 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.05 (6 / 121), avg. gap size = 2.67 (16 / 6) 453 32.37 0.00 0.72 chr6ptel1M 556316 556455 (443545) C MIRc#SINE/MIR (120) 148 10 m_b286s601i3 11550 chr6ptel1M 556316 CTCATCTTACCAATCAGAAAACTGAGGCAAACAGGGTTTGAAGAAGCTCG 556365 i i vi v i vv v i v - vii i C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTT-AAGTGACTTG 100 chr6ptel1M 556366 GCCAGGATCATACAGCTAGGAAGTGTCTGAGTCCATATTAGAACTTGGGG 556415 v i i i v v v i viv i v iii v C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGT 50 chr6ptel1M 556416 CTTCCCAATTCTGGGATCACTGCTCTGTGCACTCCAACAC 556455 ii i iii vi v v v v v C MIRc#SINE/MIR 49 CTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 43.29 CpG sites = 24, Kimura (unadjusted) = 43.29 Transitions / transversions = 1.14 (24/21) Gap_init rate = 0.01 (1 / 139), avg. gap size = 1.00 (1 / 1) 234 29.67 4.02 14.22 chr6ptel1M 556425 556648 (443352) L2c_3end#LINE/L2 265 468 (10) m_b286s601i4 11549 chr6ptel1M 556425 TCTGGGATCACTGCTCTGTGCACTC-CAACACCCCTTAGCTGCCTCTAAT 556473 i vv v v v i -i i ------ i v v L2c_3end#LINE 265 TCTAGGTGCCCTCCTCTGTGCTCCCATAGCACCC------TGTCTATACT 308 chr6ptel1M 556474 CTCAGTACCTTCCTTTTGAGAGGTTATCCTGT-TTGTACACATTCCCTGT 556522 i v ivviv v v ---- v i - --- vi L2c_3end#LINE 309 CCCATTATAGCACTTATCA----TTAACTTGTATTGTA---ATTGTCTGT 351 chr6ptel1M 556523 GAGCTT-----CCTCCCTCATTAGACACAGTG-GGGCTCACTCTGAGCAG 556566 vvi ? -----i ii i ---- - i vi vv i L2c_3end#LINE 352 TTACNTGTCTGTCTCCTCCACTAGAC----TGTGAGCTCCTTGAGGGCAG 397 chr6ptel1M 556567 AGGCTGT-TCTGGACTTTCTTTATGCCCTCAGCCCTTAATAGAGTTCCTG 556615 i i i - viviiv i ii i ---------- -- L2c_3end#LINE 398 GGACCGTGTCTTATTCATCTTTGTATCCCCAGC----------G--CCTG 435 chr6ptel1M 556616 GCACATAGTAGGTGCTTCATACAAGTTTGCTGA 556648 i iv v v i L2c_3end#LINE 436 GCACATAGTAGGCGCTCAATAAATGTTTGTTGA 468 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 36.35 CpG sites = 31, Kimura (unadjusted) = 38.02 Transitions / transversions = 1.19 (31/26) Gap_init rate = 0.15 (34 / 223), avg. gap size = 1.12 (38 / 34) 242 30.07 5.15 10.87 chr6ptel1M 556455 556648 (443352) L2b_3end#LINE/L2 273 456 (10) m_b286s601i5 11549 chr6ptel1M 556455 CCCCTTAGCTGCCTCTAATCTCAGTACCTT--CCTTTTGAGAGGTTATC- 556501 i vi i- i i i i--- i -- vi i --- ?- L2b_3end#LINE 273 CCTCTGGGCC-CCCCCAGTCC---TACCCTGCCACTCTG---GGTTATNA 315 chr6ptel1M 556502 CTGTTTGTACACATTCCCTGTGAGCTTCCTCCCTCATTAGACACAGTG-G 556550 i i ?vi vi - ------- i i ---- - L2b_3end#LINE 316 TTGTCTGNTTACATGTC-TGT-------CTCCCCCACTAGAC----TGTG 353 chr6ptel1M 556551 GGCTCACTCTGAGCAGAGGCTGT-TCTGGACTT-----TCTTTATGCCCT 556594 i vv vv i i i i ?- v- -----i vi i ii i L2b_3end#LINE 354 AGCTCCGTGAGGGCAGGGACCGNGTCTGT-CTTGTTCACCGCTGTATCCC 402 chr6ptel1M 556595 CAGCCCTTAATAGAGTTCCTGGCACATAGTAGGTGCTTCATACAAGTTTG 556644 v i ii v ?v i i ivi v vi L2b_3end#LINE 403 CAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTTG 452 chr6ptel1M 556645 CTGA 556648 i L2b_3end#LINE 453 TTGA 456 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 39.52 CpG sites = 36, Kimura (unadjusted) = 41.67 Transitions / transversions = 2.25 (36/16) Gap_init rate = 0.13 (25 / 193), avg. gap size = 1.20 (30 / 25) 281 30.74 5.79 3.23 chr6ptel1M 556528 556648 (443352) L2a_3end#LINE/L2 384 507 (10) m_b286s601i6 11549 chr6ptel1M 556528 TCCTCCCTCATTAGACACAGTG-GGGCTCACTCTGAGCAGAGGCTGTTCT 556576 ii i i ----i -ii vv vv i i i v v L2a_3end#LINE 384 TCTCCCCCCACTAGA----ATGTAAGCTCCATGAGGGCAGGGACTTTTGT 429 chr6ptel1M 556577 GGACTTTCTTTA-TGC-----CCTCAGCCCTTAATAGAGTTCCTGGCACA 556620 vvii v i - ----- i v i iv v v L2a_3end#LINE 430 CTGTTTTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACA 479 chr6ptel1M 556621 TAGTAGGTGCTTCATACAAGTTTGCTGA 556648 i iv v vi i L2a_3end#LINE 480 TAGTAGGCGCTCAATAAATATTTGTTGA 507 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 39.10 CpG sites = 20, Kimura (unadjusted) = 40.55 Transitions / transversions = 1.25 (20/16) Gap_init rate = 0.06 (7 / 120), avg. gap size = 1.57 (11 / 7) 300 29.67 4.40 0.00 chr6ptel1M 556561 556651 (443349) L2d2_3end#LINE/L2 454 548 (7) m_b286s601i7 11549 chr6ptel1M 556561 GAGCAGAGGC--TGTTCTGGACTTTCTT-TATGCCCT-CAGCCCTTAATA 556606 i i i -- ii iv ii - v i- v i ii L2d2_3end#LIN 454 GGGCAGGGACCATGTCTTATACTTCTTTGTATCCCCCACAGCGCCTAGCA 503 chr6ptel1M 556607 GAGTTCCTGGCACATAGTAGGTGCTTCATACAAGTTTGCTGACTT 556651 v v v i i iv v vi i i L2d2_3end#LIN 504 CAGTGCCTTGCACACAGTAGGCGCTCAATAAATATTTGTTGATTT 548 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 37.70 CpG sites = 18, Kimura (unadjusted) = 39.62 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.03 (3 / 90), avg. gap size = 1.33 (4 / 3) 406 29.05 0.00 6.61 chr6ptel1M 557443 557571 (442429) MIR3#SINE/MIR 79 199 (9) m_b286s601i8 11551 chr6ptel1M 557443 TGGCTGGGTCCCCTTGGGTGAGTAAGTGACTTTTTCTCTAGAGGCCTCCA 557492 ? v vv i---- v ivi vvi vi MIR3#SINE/MIR 79 TNGCTGTGTGACCTTGGGC----AAGTCACTTCACCTCTCTGGGCCTCAG 124 chr6ptel1M 557493 TTTCTCTAACTATAAAATTAAGGGGACTAAACAAGTTGATCTTTAAGGTT 557542 iii v i - i ii ii v v i i MIR3#SINE/MIR 125 TTTCCTCATCTGTAAAA-TGAGGGGGTTGGACTAGATGATCTCTAAGGTC 173 chr6ptel1M 557543 TCTGACTCCAAATCTACTATTTCATGATT 557571 i --- iv ivi ii MIR3#SINE/MIR 174 CCT---TCCAGCTCTGACATTCTATGATT 199 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 38.32 CpG sites = 22, Kimura (unadjusted) = 38.32 Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.06 (8 / 128), avg. gap size = 1.00 (8 / 8) 203 33.33 0.00 0.00 chr6ptel1M 557922 557978 (442022) MIR1_Amn#SINE/MIR 41 97 (133) m_b286s601i9 11552 chr6ptel1M 557922 GAACCTAGAAAACGTGGCTCTGGGTCCTGACCTTGCCGCTTACCAGCTGG 557971 i iii i i v v ii?i? i i ii i ?i ? ? MIR1_Amn#SINE 41 GGACTCGGGAGACCTGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGN 90 chr6ptel1M 557972 GTAACTT 557978 i i MIR1_Amn#SINE 91 GTGACCT 97 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 50.28 CpG sites = 17, Kimura (unadjusted) = 60.93 Transitions / transversions = 8.50 (17/2) Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0) 271 28.23 11.16 6.32 chr6ptel1M 558603 558844 (441156) C L2#LINE/L2 (218) 2864 2612 m_b286s601i10 11553 chr6ptel1M 558603 GATAAGAAACCACTGCAAAGGTTTATGGGGTTTTTGGCAGAAAAGTGAGA 558652 ii i i v ---------- vi ii v C L2#LINE/L2 2864 GATGGGAAGCCATTGGA----------GGGTTTTGAGCAGAGGAGTGACA 2825 chr6ptel1M 558653 GAATTGTACCCATTTATTAGTAAGACGGCATTAGCAGCTGT----AGAA- 558697 vi ivv ii iv v iv i ivi vi i v ---- - C L2#LINE/L2 2824 TGATCTGACTTACGTTTTAAAAGGATCACTCTGGCTGCTGTGTTGAGAAT 2775 chr6ptel1M 558698 AGACTGGAGA----CAAAG-TGACAGTGCAAAAAGGCTAGTCAGGAGGCT 558742 ? i---- i - iv -- iii i i i C L2#LINE/L2 2774 AGACTGNAGGGGGGCAAGGGTGGAAG--CAGGGAGACCAGTTAGGAGGCT 2727 chr6ptel1M 558743 ATT--AATAGT--AGCTGAGATAAGATGGGG--TTGG-TTAGG--GGTGA 558783 -- i i -- vi v v v -- -ii -- i C L2#LINE/L2 2726 ATTGCAGTAATCCAGGCGAGAGATGATGGTGGCTTGGACCAGGGTGGTGG 2677 chr6ptel1M 558784 CAGTG--GGAGGGGAGAA--GGT---ACCCTGGAGGTAAACCACCTGGAG 558826 -- v v -- --- ii vi ----vii i C L2#LINE/L2 2676 CAGTGGAGGTGGTGAGAAGTGGTCGGATTCTGGATATA----TTTTGAAG 2631 chr6ptel1M 558827 GTAAAAGAGACAGG-TTTG 558844 i ivv - C L2#LINE/L2 2630 GTAGAGCCGACAGGATTTG 2612 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 35.67 CpG sites = 41, Kimura (unadjusted) = 37.15 Transitions / transversions = 1.78 (41/23) Gap_init rate = 0.12 (29 / 241), avg. gap size = 1.48 (43 / 29) 18 13.41 0.00 0.00 chr6ptel1M 559074 559107 (440893) (GAGAGG)n#Simple_repeat 1 34 (0) m_b286s252i0 11554 chr6ptel1M 559074 GAGAGAGAAAGGGGGAGGGAGAAGGAGAGGGAGA 559107 i i i i (GAGAGG)n#Sim 1 GAGAGGGAGAGGGAGAGGGAGAGGGAGAGGGAGA 34 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 753 22.61 16.08 0.00 chr6ptel1M 559733 559931 (440069) C MIRc#SINE/MIR (20) 248 18 m_b286s601i11 11555 chr6ptel1M 559733 TCTATTTAGCACTTTAAGGATTGGAAAATG-TTTCACATACATTATCTCA 559781 i i v vi v iv ii - C MIRc#SINE/MIR 248 TTTGTATAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATCTCA 199 chr6ptel1M 559782 TCTGAGCCGTACATCGACC-----AAGGAGGTAGGG--ATTATTGTTATC 559824 i v vi v i ----- i v i --iv i C MIRc#SINE/MIR 198 TTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATC 149 chr6ptel1M 559825 CCCATTTTATAGATAAATAAACCAAGGCTGAGACAGGTGAAGTGTCTTGC 559874 i i iv ii v v v v C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr6ptel1M 559875 CCAGG----------------------GAGCCAGAACTTGAATCCGGAGC 559902 i ---------------------- i i i i i iv C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTC 49 chr6ptel1M 559903 TTCC-AACTCCAAGCCTAGCGAT-TTTCCAC 559931 -i i i i v - C MIRc#SINE/MIR 48 TTCCTGACTCCAAGTCCAGTGCTCTTTCCAC 18 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 25.52 CpG sites = 29, Kimura (unadjusted) = 27.63 Transitions / transversions = 1.81 (29/16) Gap_init rate = 0.03 (6 / 198), avg. gap size = 5.33 (32 / 6) 1157 31.48 7.04 3.67 chr6ptel1M 560148 560701 (439299) C L3#LINE/CR1 (509) 3590 3019 m_b286s601i12 11556 chr6ptel1M 560148 CCAGATGTTGGT--GACTAACCCAAAG------GGGAGCTCCAGCTTCCT 560189 - -- i i v i ------ vivii v i C L3#LINE/CR1 3590 CCAGATGT-GGTCTGACCAGCGCAGAGTACAGCGGGACTATTACCTCCCT 3542 chr6ptel1M 560190 GGGTCTGGACACCATG-TTCTCC--ATGCTGCCCAAGAGCCCATTTGTTT 560236 v ? i i- vi-- v i viv v i C L3#LINE/CR1 3541 TGNTCTGGACACTATACTTCTATTAATGCAGCCTAAGATTGCATTAGCTT 3492 chr6ptel1M 560237 TTAAACCGGTTGTCAAGCCACACCATTGAGTCATATTGGGCCTGCAGTCT 560286 ---ii iv i vii ii iv i i i - C L3#LINE/CR1 3491 TT---TTGGCAGCCACATCACACTGTTGGCTCATATTGAGCTTGCGGTC- 3446 chr6ptel1M 560287 TCAGAAACAAAACAAAGCAAATCT-------ATCAAGTGCT----AGCCG 560325 ---- vi vvv-i ii -------i v v ---- i C L3#LINE/CR1 3445 ----AACTAAAACCCC-TAGGTCTTTTTCACGTGAACTGCTGCTAAGCCA 3401 chr6ptel1M 560326 CACCTCCTCCATCTTGTACTTGTGAAGTTTATTTTTTGACTATTGGGTGC 560375 v i ii i v v vi-i iii C L3#LINE/CR1 3400 GATCCTCTCCATCCTGTACTTGTGCAGTTGATTTTTTGAAC-CTAAATGC 3352 chr6ptel1M 560376 AAGACTGTATATTTATCTTCTCTGGATTTCGTTTTCTGGGGGCCCACTCA 560425 i v i iiivi ii i i v v vvi vi i C L3#LINE/CR1 3351 AGGACTTTACATTTATCCCTGTTAAATTTCATCTTGTTGGTTTCGGCCCA 3302 chr6ptel1M 560426 GCCGGATTCTGGCTGGATGAGATCTGTTAGGCTC-TGACTCTGTGAGC-- 560472 v ---i ii iv vi ?v v iv - i v v -- C L3#LINE/CR1 3301 TC---GTTCCAGCCTGTCGAGATCNTTTTGAATCTTGATTCTGTCATCCA 3255 chr6ptel1M 560473 ------TGGCTGT---TCGTAACCCTGGGTCATCGTCACACTTAATCAAC 560513 ------ i i --- vi i ii v vv v i i v i C L3#LINE/CR1 3254 NCGTATTAGCTATCCCTCCCAGCTTTGTGTCATCTGCAAATTTGATAAGC 3205 chr6ptel1M 560514 A--CTTACTGAAGCCTTGGTCCAAGTCATTGATAAAAACGGCTGAACAGC 560561 -- i v - v i vi i- i v C L3#LINE/CR1 3204 ATGCCTTCT-ATGTCTTCATCCAAGTCATTGATAAAAAT-GTTGAACAGG 3157 chr6ptel1M 560562 ACAGTAGCAAAGGCAGA-TTCTGGGGTATTCTACTGGCAACC-CCCTCCG 560609 viv i i -ii v i iv i i vi - i C L3#LINE/CR1 3156 ACAGGGCCAAGGACAGAGCCCTGTGGCACGCCACTAGAGACCTCCCTCCA 3107 chr6ptel1M 560610 AGTCAACATAGAGCTGTTAAAGATTATC-TCTGGGTCTAGGCATCCGACC 560658 i ii v v ii vv vi i - i v v i i i C L3#LINE/CR1 3106 GGTTGACATCGATCCATTAATCAACACCTTTTGGGTATAGTCGTTCAACC 3057 chr6ptel1M 560659 GGTTGGTTCTGCATCCGCCTAACTGGCACTACTGTCCGGACCA 560701 i i i----i v i - i iii i v C L3#LINE/CR1 3056 AGCTA----CGAATCCACCTAACT-GTACTATCATCCAGCCCA 3019 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 40.54 CpG sites = 106, Kimura (unadjusted) = 42.93 Transitions / transversions = 1.71 (106/62) Gap_init rate = 0.06 (35 / 553), avg. gap size = 1.71 (60 / 35) 474 27.59 2.03 2.03 chr6ptel1M 560851 560998 (439002) C MIR1_Amn#SINE/MIR (69) 161 14 m_b286s601i13 11557 chr6ptel1M 560851 GTGTCCTTCTCTAGCTCATTTTACAGATGAGGAAACTGAGGCAAATAGCC 560900 i v v --- i ?v v vv C MIR1_Amn#SINE 161 GTATCATTATC---CCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAG 115 chr6ptel1M 560901 -TTAAGTAACTGGCCCAAGATCACACAGCTAGTAGATGTCTGAGGCTGAA 560949 - ? i v i ? ?i i?ii v v v v i C MIR1_Amn#SINE 114 GTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNAGTGGCAGAGCCGGGA 65 chr6ptel1M 560950 TCTGAACTCAGCTATTCGGACTCTC--TCTACTATGCTGCCCCTCAGATT 560997 ?i? i v v i v v i -- i v iiv ii vii ii C MIR1_Amn#SINE 64 NTNGAACCCAGGTCTCCCGAGTCCCAGTCCAGTGCTCTATCCACTAGACC 15 chr6ptel1M 560998 A 560998 C MIR1_Amn#SINE 14 A 14 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 37.38 CpG sites = 22, Kimura (unadjusted) = 37.38 Transitions / transversions = 1.22 (22/18) Gap_init rate = 0.03 (5 / 147), avg. gap size = 1.20 (6 / 5) 560 20.37 0.93 0.00 chr6ptel1M 560865 560972 (439028) C MIR#SINE/MIR (118) 144 36 m_b286s601i14 11557 chr6ptel1M 560865 CTCATTTTACAGATGAGGAAACTGAGGCAAATAGCC-TTAAGTAACTGGC 560913 i v v vv- v C MIR#SINE/MIR 144 CCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGC 95 chr6ptel1M 560914 CCAAGATCACACAGCTAGTAGATGTCTGAGGCTGAATCTGAACTCAGCTA 560963 i ii v v v v i ii i vi C MIR#SINE/MIR 94 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGCA 45 chr6ptel1M 560964 TTCGGACTC 560972 v v i C MIR#SINE/MIR 44 GTCTGGCTC 36 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 22.68 CpG sites = 10, Kimura (unadjusted) = 23.85 Transitions / transversions = 0.83 (10/12) Gap_init rate = 0.01 (1 / 107), avg. gap size = 1.00 (1 / 1) 212 23.53 25.00 0.00 chr6ptel1M 561144 561211 (438789) L3#LINE/CR1 3853 3937 (162) m_b286s601i15 11558 chr6ptel1M 561144 TAGATGGAAGTTAAAAGGCTGCAAATTT------------AGG-----TT 561176 i i v i vv i ------------ -----i L3#LINE/CR1 3853 TGGGTGGAAGTTACAGGGAGGCAGATTTCGGCTCAATATAAGGAAGAACT 3902 chr6ptel1M 561177 TCCCAATAATCTGAGCTGTCCAAAAGTAGGATGAG 561211 i i i v i i i i L3#LINE/CR1 3903 TTCTAACAATCAGAGCTGTCCAAAAATGGAATGGG 3937 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.66 CpG sites = 12, Kimura (unadjusted) = 29.66 Transitions / transversions = 3.00 (12/4) Gap_init rate = 0.03 (2 / 67), avg. gap size = 8.50 (17 / 2) 283 31.09 11.76 0.66 chr6ptel1M 561601 561736 (438264) MIR3#SINE/MIR 11 161 (47) m_b286s601i16 11559 chr6ptel1M 561601 GACTGCAGCAGAGA-----TGGAGTGGGAACATGCAGA--TGGG----AG 561639 i - -----i v iivv v -- ---- MIR3#SINE/MIR 11 GGCTG-AGCAGAGAGAGCACGGACTGGGAGTCAGGAGACCTGGGTTCTAG 59 chr6ptel1M 561640 TCCCAACTCTGGC-----CTCCTCCTGTGACCCTGGTCCCTTGACTTAAT 561684 ii v ----- ?viiv i v vvv v v i MIR3#SINE/MIR 60 TCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCAC 109 chr6ptel1M 561685 TCCTCTGGGCCTCAGTTTACTCTCCTATGAAGTCACAGAGCCAAGGTAAA 561734 ii v vi i i i v vi i iiiiiv i MIR3#SINE/MIR 110 CTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGA 159 chr6ptel1M 561735 TG 561736 MIR3#SINE/MIR 160 TG 161 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 39.16 CpG sites = 24, Kimura (unadjusted) = 41.74 Transitions / transversions = 1.33 (24/18) Gap_init rate = 0.04 (5 / 135), avg. gap size = 3.40 (17 / 5) 192 27.96 13.64 2.46 chr6ptel1M 561816 561925 (438075) AmnL2-1#LINE/L2 2344 2465 (148) m_b286s601i17 11560 chr6ptel1M 561816 CGTCATTG--GGGGGGGGAGTCTTTTTCAATCTGCAGGTTAAGCT----- 561858 i i -- v v i i i i -- v ivv i----- AmnL2-1#LINE/ 2344 CGCCACTGTTGGTGCGAGAGCCTTCTCC--TCTGCAGCTCCTGCCATCTG 2391 chr6ptel1M 561859 GACCCCCCTTCCCTGTGTTCCTTT--TTAATTAATTC---AG---TTTTC 561900 v vv - i ii ii--i v ii i --- v---? AmnL2-1#LINE/ 2392 GAACAGCCTTCC-TGTATCTCTCCGCCTCATCGACTCTCCATCTCNTTTC 2440 chr6ptel1M 561901 AAATCTCAAGGGAAAACACATCTTT 561925 ?vv i AmnL2-1#LINE/ 2441 AAATCTCANCTGAAAACATATCTTT 2465 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 33.81 CpG sites = 18, Kimura (unadjusted) = 37.03 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.07 (8 / 109), avg. gap size = 2.25 (18 / 8) 218 30.14 3.33 8.77 chr6ptel1M 562398 562517 (437483) MIR1_Amn#SINE/MIR 114 227 (3) m_b286s601i18 11561 chr6ptel1M 562398 CCTCACTAGGTATCAGTTTTTCCATC-ATGAAATGGGGATGA--AT-CTG 562443 v i? iv iii -i i i -- - MIR1_Amn#SINE 114 CCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATGATACTG 163 chr6ptel1M 562444 ATTTCCTGACTCATCACCCAGAGCTATTGAGAATGAAGTCCTATAGAAAG 562493 ii --- ii v --- v - viv --- iv ii MIR1_Amn#SINE 164 ACCTCCT---TTGTAA---AGTGCT-TTGAGATCTA---CTGATGAAAAG 203 chr6ptel1M 562494 TGCTGGGCAAAAGTGAACTAGTAT 562517 ivii i iv iv v MIR1_Amn#SINE 204 TGCTACATAAGAGCTAGGTATTAT 227 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 40.75 CpG sites = 22, Kimura (unadjusted) = 40.75 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.11 (13 / 119), avg. gap size = 1.08 (14 / 13) 197 23.08 0.00 1.92 chr6ptel1M 562616 562668 (437332) MIRc#SINE/MIR 215 266 (2) m_b286s601i19 11562 chr6ptel1M 562616 AAAGTCCTTTGCAAACCTTAAAGTTCTAATGCCAGTTCAAGCTGTTATTA 562665 iv i iv v - i v i vi v? MIRc#SINE/MIR 215 AAAGCGCTTTGTAAACTGTAAAGTGCT-ATACAAATGTAAGGNGTTATTA 263 chr6ptel1M 562666 TTA 562668 MIRc#SINE/MIR 264 TTA 266 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 25.82 CpG sites = 6, Kimura (unadjusted) = 28.47 Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.02 (1 / 52), avg. gap size = 1.00 (1 / 1) 184 25.58 4.65 0.00 chr6ptel1M 562952 562994 (437006) C MIR3#SINE/MIR (14) 194 150 m_b286s601i20 11563 chr6ptel1M 562952 TAGAATGTCAGCACTAGAAAGGACTT--GGGGTCATTCACTCAAA 562994 vi i i i -- i i ii v v C MIR3#SINE/MIR 194 TAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAA 150 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 32.91 CpG sites = 8, Kimura (unadjusted) = 32.91 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.02 (1 / 42), avg. gap size = 2.00 (2 / 1) 204 32.05 5.13 0.00 chr6ptel1M 563863 563940 (436060) C MIR3#SINE/MIR (7) 201 120 m_b286s601i21 11564 chr6ptel1M 563863 AGAACAAGAAAAC-TTACACTTAGAAGGGATCTCAAAGCCCATCAAATCC 563911 iv v i i- i v vi i i i i vi v i C MIR3#SINE/MIR 201 AGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCC 152 chr6ptel1M 563912 GA-TCCCTCTCTTTACAA--GAAGAGGCTGAG 563940 i -i vi i-- i ii C MIR3#SINE/MIR 151 AACCCCCTCATTTTACAGATGAGGAAACTGAG 120 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 45.01 CpG sites = 18, Kimura (unadjusted) = 45.01 Transitions / transversions = 2.57 (18/7) Gap_init rate = 0.04 (3 / 77), avg. gap size = 1.33 (4 / 3) 260 14.58 2.08 0.00 chr6ptel1M 563994 564041 (435959) MIR1_Amn#SINE/MIR 94 142 (88) m_b286s601i22 11565 chr6ptel1M 563994 ATCTTATG-AAATCATTTGGCCTTTCTGTGCCTCAGTTTCCTCATCTGT 564041 i iv - i i ?i i ? MIR1_Amn#SINE 94 ACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGT 142 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 17.72 CpG sites = 6, Kimura (unadjusted) = 17.72 Transitions / transversions = 6.00 (6/1) Gap_init rate = 0.02 (1 / 47), avg. gap size = 1.00 (1 / 1) 306 29.89 9.20 0.00 chr6ptel1M 564032 564118 (435882) MIRc#SINE/MIR 163 257 (11) m_b286s601i23 11566 chr6ptel1M 564032 CCTCATCTGTCTCATAGGATTG----GGAGATCAAATGAGA----GCACA 564073 iiii ii i i ---- ii ---- i ii MIRc#SINE/MIR 163 CCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATG 212 chr6ptel1M 564074 CAGGAGCCCTCTGCAATTTCTAAAGTGCTACACAAATGCAAAGAG 564118 iiii v i i vi v i i i ? MIRc#SINE/MIR 213 TGAAAGCGCTTTGTAAACTGTAAAGTGCTATACAAATGTAAGGNG 257 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 43.98 CpG sites = 23, Kimura (unadjusted) = 43.98 Transitions / transversions = 7.67 (23/3) Gap_init rate = 0.02 (2 / 86), avg. gap size = 4.00 (8 / 2) 228 28.33 6.80 3.97 chr6ptel1M 564698 564844 (435156) MIR3#SINE/MIR 4 154 (54) m_b286s601i24 11567 chr6ptel1M 564698 GCAG-GTGGACTGGGAAGAGCGAG---GCAATGGCAATCTGGAGACCCGG 564743 - - i v v --- v v v i v i MIR3#SINE/MIR 4 GCAGAGTGG-CTGAGCAGAGAGAGCACGGACTGGGAGTCAGGAGACCTGG 52 chr6ptel1M 564744 GTTCCCAAGGGGACCT--CCCTAGCAAAGACTCAAAGTGAGAC--TGGCC 564789 i-----i v i-- i iv vvi ?ivv v -- v MIR3#SINE/MIR 53 GTTCT-----AGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGC 97 chr6ptel1M 564790 AAGTCACACC--CTATATAGACCCAGGCTTCCTCCTCTCCAAAACGTGGG 564837 vi -- v v i i ivi i v vi i v MIR3#SINE/MIR 98 AAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGG 147 chr6ptel1M 564838 GGCTGGA 564844 i MIR3#SINE/MIR 148 GGTTGGA 154 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 35.18 CpG sites = 19, Kimura (unadjusted) = 36.28 Transitions / transversions = 0.90 (19/21) Gap_init rate = 0.08 (11 / 146), avg. gap size = 1.45 (16 / 11) 17 20.06 0.00 4.55 chr6ptel1M 565354 565399 (434601) (ACAC)n#Simple_repeat 1 44 (0) m_b286s252i1 11568 chr6ptel1M 565354 ACACACATCTGCACATACACACATACATACATGCACACACGCACAC 565399 - -i i i i ii i (ACAC)n#Simpl 1 ACACACA-C-ACACACACACACACACACACACACACACACACACAC 44 Matrix = Unknown Transitions / transversions = 1.00 (7/0) Gap_init rate = 0.04 (2 / 45), avg. gap size = 1.00 (2 / 2) 321 19.94 16.09 2.02 chr6ptel1M 565647 565733 (434267) C L5#LINE/RTE-X (538) 1725 1627 m_b286s551i0 11569 chr6ptel1M 565647 GGGCTCTGGGAAAGGTTAAGATTGACCAGGTAAATTG------------- 565683 i - i - i v ------------- C L5#LINE/RTE-X 1725 GAGCT-TAGGAAAGGT-AAGATTGACCAGGTAGAATGATCTACTGTGATC 1678 chr6ptel1M 565684 -CTTTTAATTCTTCTCCACCATCTGGAAAAATCTATCCCTAACGTAGTCA 565732 - v i vi ii i i vi vi i C L5#LINE/RTE-X 1677 ACTTTTAATTATCCTATACCGCCTGGAAAAATTTGTGTCTAAAATAGCCA 1628 chr6ptel1M 565733 G 565733 C L5#LINE/RTE-X 1627 G 1627 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 22.41 CpG sites = 12, Kimura (unadjusted) = 23.99 Transitions / transversions = 2.40 (12/5) Gap_init rate = 0.05 (4 / 86), avg. gap size = 4.00 (16 / 4) 204 34.97 9.09 0.00 chr6ptel1M 566128 566270 (433730) MIRc#SINE/MIR 37 192 (76) m_b286s601i25 11570 chr6ptel1M 566128 TGCAGCCAGTGGGCCCTGGGCTGCGGTCTCAGTTCTAGCTCTCGACAGCG 566177 v i vii v i vvi i i i iv v iivi v MIRc#SINE/MIR 37 TGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCT 86 chr6ptel1M 566178 GTGTGACAGGGGGCAGCTCGTTTAA-TGCCCTGAATCTGA-TTTCCTCAC 566225 vvv iv ii -iv i ii v - i MIRc#SINE/MIR 87 GTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCAT 136 chr6ptel1M 566226 -----AAACGGTGGGA-----ACTCACACTACC-ACCAGCCGGGGTGGTT 566264 ----- i v iv ----- iii v i - vvv i v MIRc#SINE/MIR 137 CTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTT 186 chr6ptel1M 566265 GTGAAG 566270 i MIRc#SINE/MIR 187 GTGAGG 192 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 47.25 CpG sites = 28, Kimura (unadjusted) = 48.62 Transitions / transversions = 1.27 (28/22) Gap_init rate = 0.04 (5 / 142), avg. gap size = 2.60 (13 / 5) 20 32.08 1.08 2.17 chr6ptel1M 566779 566871 (433129) (ATGTAT)n#Simple_repeat 1 92 (0) m_b286s252i2 11571 chr6ptel1M 566779 ATGTATTTTGGTGTGTGTATGTATATGTACATATGAGAAATATAAATATA 566828 v vvi i i i i - v vi vi - (ATGTAT)n#Sim 1 ATGTATATGTATATGTATATGTATATGTATATGT-ATATGTATATGTAT- 48 chr6ptel1M 566829 ATATATAACTATAT-TAAGAGTATATGTGTGTATGTATGTATAT 566871 i vv - viv i i i i (ATGTAT)n#Sim 49 ATGTATATGTATATGTATATGTATATGTATATGTATATGTATAT 92 Matrix = Unknown Transitions / transversions = 1.30 (13/10) Gap_init rate = 0.03 (3 / 92), avg. gap size = 1.00 (3 / 3) 26 25.54 1.28 2.60 chr6ptel1M 566796 566873 (433127) (TA)n#Simple_repeat 1 77 (0) m_b286s252i4 11571 chr6ptel1M 566796 TATGTATATGTACATATGAGAAATATAAATATA-ATATATAACTATATTA 566844 i i i - v v v - vv vv (TA)n#Simple_ 1 TATATATATATATATAT-ATATATATATATATATATATATATATATATAT 49 chr6ptel1M 566845 AGAGTATATGTGTGTATGTATGTATATAT 566873 v - i i i i i (TA)n#Simple_ 50 ATA-TATATATATATATATATATATATAT 77 Matrix = Unknown Transitions / transversions = 1.00 (8/8) Gap_init rate = 0.04 (3 / 77), avg. gap size = 1.00 (3 / 3) 257 23.47 1.49 4.62 chr6ptel1M 566882 566948 (433052) MIRc#SINE/MIR 3 67 (201) m_b286s601i26 11572 chr6ptel1M 566882 AGGCAGCTAGGTGGCTCAGTGCATGGAACATTGGGCCTAGAGTCAGAAAG 566931 i--- iv v vi i i i i i i MIRc#SINE/MIR 3 AGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAG 49 chr6ptel1M 566932 A-CTGAGTTCGTGTCTCG 566948 - i v i MIRc#SINE/MIR 50 ACCTGGGTTCGAGTCCCG 67 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.40 CpG sites = 11, Kimura (unadjusted) = 29.40 Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.06 (4 / 66), avg. gap size = 1.00 (4 / 4) 611 29.19 13.88 0.00 chr6ptel1M 568382 568590 (431410) MIRc#SINE/MIR 23 260 (8) m_b286s601i27 11573 chr6ptel1M 568382 AAGA-TGCTGGACTTGGTGACACAAAGATCTGAACTGAAATCCCGCCTCA 568430 -ii v v vi i iii vi i v v MIRc#SINE/MIR 23 AAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCT 72 chr6ptel1M 568431 GACATTTACTGGTTGTGTGACT--------GTCA--------------GC 568458 v i i i i-------- -------------- MIRc#SINE/MIR 73 GCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGC 122 chr6ptel1M 568459 CTCAGTTTCCTCATTTGTACAATGGGGACAATAACA---GC---ACCTAA 568502 i v i i --- ---i v MIRc#SINE/MIR 123 CTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTAC 172 chr6ptel1M 568503 CACGTGAGATTGCTGTGAATCCCAAATGGGAGAACATCCGAAAAAGGGTT 568552 v iiii i i ivvi i v ii vi vi v i MIRc#SINE/MIR 173 CTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCT 222 chr6ptel1M 568553 TTGTGGAGCTTGAGGTACTGCACGAATGTCAGCAATTA 568590 ii viv i i i ii i v v?i MIRc#SINE/MIR 223 TTGTAAACTGTAAAGTGCTATACAAATGTAAGGNGTTA 260 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 38.20 CpG sites = 41, Kimura (unadjusted) = 39.04 Transitions / transversions = 2.05 (41/20) Gap_init rate = 0.02 (5 / 208), avg. gap size = 5.80 (29 / 5) 265 23.81 4.76 0.00 chr6ptel1M 568696 568758 (431242) C L2c_3end#LINE/L2 (2) 476 411 m_b286s601i28 11574 chr6ptel1M 568696 TCAGTTGATCAGCAAACATT-ATGAAGTACCCATTACGTGGCAGTCACTG 568744 v iiv i - vi ii i i i v v i C L2c_3end#LINE 476 TCATTCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTG 427 chr6ptel1M 568745 GGGATAC--AGATGAA 568758 -- C L2c_3end#LINE 426 GGGATACAAAGATGAA 411 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 24.83 CpG sites = 10, Kimura (unadjusted) = 29.60 Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.03 (2 / 62), avg. gap size = 1.50 (3 / 2) 248 27.38 15.48 0.00 chr6ptel1M 569460 569543 (430457) MIRc#SINE/MIR 101 197 (71) m_b286s601i29 11572 chr6ptel1M 569460 AAGTCATTGCATTTTTCTAAGT-TCGATTTC------TGTAAGA-GAGGG 569501 i vv ii i i i- ii ------ i - i i MIRc#SINE/MIR 101 AAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGA 150 chr6ptel1M 569502 CGATAAT-CCTGCCTT----AACTCACAAGACTGTTGGGAAAATCAA 569543 ii - i ---- v i ii v ii MIRc#SINE/MIR 151 TAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAA 197 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 37.16 CpG sites = 19, Kimura (unadjusted) = 37.16 Transitions / transversions = 4.75 (19/4) Gap_init rate = 0.06 (5 / 83), avg. gap size = 2.60 (13 / 5) 17 30.56 3.45 3.45 chr6ptel1M 569819 569905 (430095) (TC)n#Simple_repeat 1 87 (0) m_b286s252i5 11575 chr6ptel1M 569819 TCTGCTCCTTCTGCTCTCCCCTTGTC-CTCCATTTCTCTTTCGC-CACAT 569866 - ii - i ii v - iv i i v - v - (TC)n#Simple_ 1 TCT-CTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-T 47 chr6ptel1M 569867 TTCTCTCTCTCCATCTCTCACGTTCTCTCTCCCCCT-TCT 569905 i iv v vi i i - (TC)n#Simple_ 48 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 87 Matrix = Unknown Transitions / transversions = 1.86 (13/7) Gap_init rate = 0.07 (6 / 86), avg. gap size = 1.00 (6 / 6) 245 36.05 0.96 3.96 chr6ptel1M 570214 570317 (429683) MIRc#SINE/MIR 17 117 (151) m_b286s601i30 11576 chr6ptel1M 570214 AGGAAAAAGAGCCCTGAATGTAAGATGAA-AAGATCTGAGTTCAAATCCT 570262 vii v i iv iiii v i- i i i i i MIRc#SINE/MIR 17 AGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCC 66 chr6ptel1M 570263 AACCCTTATATTTAATCATCTGAGTAAACCTGTAAAACAAGTCACCTATC 570312 ii i vvi i v - v v i v i ---ii i v MIRc#SINE/MIR 67 GGCTCTGCCACTTACT-AGCTGTGTGACCTTG---GGCAAGTCACTTAAC 112 chr6ptel1M 570313 CTTTC 570317 i MIRc#SINE/MIR 113 CTCTC 117 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 48.64 CpG sites = 25, Kimura (unadjusted) = 53.29 Transitions / transversions = 2.27 (25/11) Gap_init rate = 0.05 (5 / 103), avg. gap size = 1.00 (5 / 5) 374 12.50 7.81 0.00 chr6ptel1M 571527 571590 (428410) MIR3#SINE/MIR 77 145 (63) m_b286s601i31 11577 chr6ptel1M 571527 ACTAGCCGTGTGACCCTGAGCAGGTCACTTCAG---TCTG--TCTCAGTT 571571 ? i i i i v--- --i MIR3#SINE/MIR 77 ACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTT 126 chr6ptel1M 571572 TCCTCATTTGCAAAATGAG 571590 i i MIR3#SINE/MIR 127 TCCTCATCTGTAAAATGAG 145 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 14.40 CpG sites = 7, Kimura (unadjusted) = 14.40 Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.03 (2 / 63), avg. gap size = 2.50 (5 / 2) 185 28.39 3.12 6.45 chr6ptel1M 572254 572317 (427683) C MIRc#SINE/MIR (200) 68 7 m_b286s601i32 11578 chr6ptel1M 572254 CCAGGACTCAGACCTGGGCTCTCCC-ACTCCAAATTCAGCG-TGTTTCAA 572301 i ii ii iii i- i i i - v v C MIRc#SINE/MIR 68 CCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCA 19 chr6ptel1M 572302 ATGTTTACATCACACT 572317 ----i i i C MIRc#SINE/MIR 18 ----CTGCACCACACT 7 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 33.78 CpG sites = 15, Kimura (unadjusted) = 39.83 Transitions / transversions = 7.50 (15/2) Gap_init rate = 0.10 (6 / 63), avg. gap size = 1.00 (6 / 6) 236 25.90 13.76 0.81 chr6ptel1M 573596 573704 (426296) C L2c_3end#LINE/L2 (12) 466 344 m_b286s601i34 11579 chr6ptel1M 573596 AACAAGTCTTTATTAAGCATGCTCTCTGTGCCAGGCAGTGTGT-TAC-AT 573643 iiv i iiviv v iv v v- - v C L2c_3end#LINE 466 AACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGATACAAA 417 chr6ptel1M 573644 GCTGAG-GATACAGAGTC--------CAAGGACCTCAT--TCTAGTGGAA 573682 v i-i v vi -------- v i-- i C L2c_3end#LINE 416 GATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAGTGGAG 367 chr6ptel1M 573683 ACAAACAGCCATGTCA--AGACAA 573704 i- i v ? v -- C L2c_3end#LINE 366 G-AGACAGACANGTAAACAGACAA 344 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 28.52 CpG sites = 14, Kimura (unadjusted) = 32.51 Transitions / transversions = 1.00 (14/14) Gap_init rate = 0.06 (7 / 108), avg. gap size = 2.29 (16 / 7) 288 26.23 0.00 0.00 chr6ptel1M 573596 573656 (426344) C L2a_3end#LINE/L2 (12) 505 445 m_b286s601i33 11579 chr6ptel1M 573596 AACAAGTCTTTATTAAGCATGCTCTCTGTGCCAGGCAGTGTGTTACATGC 573645 i v i iiviv v v vi vii C L2a_3end#LINE 505 AACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGCGC 456 chr6ptel1M 573646 TGAGGATACAG 573656 i C L2a_3end#LINE 455 TGGGGATACAG 445 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 28.12 CpG sites = 9, Kimura (unadjusted) = 32.89 Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 234 16.67 4.17 0.00 chr6ptel1M 574102 574149 (425851) C MIR3#SINE/MIR (47) 161 112 m_b286s601i35 11580 chr6ptel1M 574102 CATCCAGTCCAACCGCCTTATTGCTCAGTGGAGGAAACTGA--CCCAGAG 574149 i v i viv vv -- C MIR3#SINE/MIR 161 CATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAG 112 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 18.85 CpG sites = 3, Kimura (unadjusted) = 18.85 Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.02 (1 / 47), avg. gap size = 2.00 (2 / 1) 12 18.86 2.63 2.63 chr6ptel1M 574220 574257 (425743) (GAGCACA)n#Simple_repeat 1 38 (0) m_b286s252i6 11581 chr6ptel1M 574220 GAGCCCCCAGCACAAGAGCACAGAGGGAAGAGC-CAGAG 574257 v vv - viv - (GAGCACA)n#Si 1 GAGCACAGAGCAC-AGAGCACAGAGCACAGAGCACAGAG 38 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 378 25.94 0.90 2.75 chr6ptel1M 574874 574984 (425016) C MIRb#SINE/MIR (156) 112 4 m_b286s601i37 11582 chr6ptel1M 574874 AAGTGACTTGCCCAAGGTCACACAGCTAGGACGCGTCTGAGACCAGATTT 574923 i v v i v v v vi i C MIRb#SINE/MIR 112 AAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTC 63 chr6ptel1M 574924 GGACTCA-GTCCTCCTGATGTCAGGGTTGGGGCTCTATCCCCTGCGCCCC 574972 i i - ivi ivi ii iiv v v v i v C MIRb#SINE/MIR 62 GAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCACCAC 13 chr6ptel1M 574973 CTAGCTGCCCCT 574984 --- C MIRb#SINE/MIR 12 ---GCTGCCCCT 4 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.91 CpG sites = 15, Kimura (unadjusted) = 32.27 Transitions / transversions = 1.15 (15/13) Gap_init rate = 0.04 (4 / 110), avg. gap size = 1.00 (4 / 4) 401 25.77 1.03 0.00 chr6ptel1M 574874 574970 (425030) C MIRc#SINE/MIR (159) 109 12 m_b286s601i36 11582 chr6ptel1M 574874 AAGTGACTTGCCCAAGGTCACACAGCTAGGACGCGTCTGAGACCAGATTT 574923 v v i v v v vi i i C MIRc#SINE/MIR 109 AAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTC 60 chr6ptel1M 574924 GGACTCA-GTCCTCCTGATGTCAGGGTTGGGGCTCTATCCCCTGCGCC 574970 i i - i ivi i viii v v v i C MIRc#SINE/MIR 59 GAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACC 12 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.62 CpG sites = 14, Kimura (unadjusted) = 32.14 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.01 (1 / 96), avg. gap size = 1.00 (1 / 1) 206 30.77 0.00 0.00 chr6ptel1M 575125 575202 (424798) C MIR1_Amn#SINE/MIR (148) 82 5 m_b286s601i38 11583 chr6ptel1M 575125 CTGGTGATTGAGCCAGGAAGTGACCCCCGGAGCTCGGGGTCCAAACCCAG 575174 ?i iiv i ?v? v v vvii v i v ii C MIR1_Amn#SINE 82 CNAGTGGCAGAGCCGGGANTNGAACCCAGGTCTCCCGAGTCCCAGTCCAG 33 chr6ptel1M 575175 CCCTCTCTCCACTACAACACAGTGTCTC 575202 iv v v v v i C MIR1_Amn#SINE 32 TGCTCTATCCACTAGACCACACTGCCTC 5 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 39.87 CpG sites = 11, Kimura (unadjusted) = 42.07 Transitions / transversions = 0.85 (11/13) Gap_init rate = 0.00 (0 / 77), avg. gap size = 0.0 (0 / 0) 390 20.69 5.75 0.00 chr6ptel1M 575472 575558 (424442) MIR#SINE/MIR 53 144 (118) m_b286s601i39 11584 chr6ptel1M 575472 TTCAAATCTGGCCTCAG--AC--ACTAGTTACATGACCCTGGCCAAGTCA 575517 i iv v v -- -- i iii i v i MIR#SINE/MIR 53 TTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTA 102 chr6ptel1M 575518 CTTAAT-TCTGTTTGCCTCGGTTTCCTCATCTGGAAAATGAG 575558 i- v v i v i MIR#SINE/MIR 103 CTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGG 144 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 23.13 CpG sites = 11, Kimura (unadjusted) = 24.66 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.03 (3 / 86), avg. gap size = 1.67 (5 / 3) 213 28.79 1.52 0.00 chr6ptel1M 576228 576293 (423707) C MIR3#SINE/MIR (52) 156 90 m_b286s601i40 11585 chr6ptel1M 576228 AGCCCAACCCCCTT-CCCTACAGAAGAGGAAACTGAATTGCAGGCAGGAG 576276 i i-iii v iviv iv v C MIR3#SINE/MIR 156 AGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTG 107 chr6ptel1M 576277 ATGCACCTTCCCTAAGG 576293 v iiv v i C MIR3#SINE/MIR 106 AAGTGACTTGCCCAAGG 90 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 37.25 CpG sites = 11, Kimura (unadjusted) = 37.25 Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.02 (1 / 65), avg. gap size = 1.00 (1 / 1) 733 25.48 0.64 0.00 chr6ptel1M 576348 576504 (423496) C MIR#SINE/MIR (22) 240 83 m_b286s601i41 11586 chr6ptel1M 576348 GTGCTTACTCTGTGCCAGGCTTTATGCTAAGAACTTCACAAAAATTATCT 576397 i v vi i v vi i viv v C MIR#SINE/MIR 240 GCGCTTACTATGTGCCAGGCACTGTTCTAAGCGCTTTACATGTATTAACT 191 chr6ptel1M 576398 CATTCGATCCTCACAGCA-CCTTGGGAGATGGACACTACTATTATCTCCA 576446 ii i - i iv i i ii i i C MIR#SINE/MIR 190 CATTTAATCCTCACAACAACCCTATGAGGTAGGTACTATTATTATCCCCA 141 chr6ptel1M 576447 TTCTACAGATGAGAAAACTGAGGCAGACAGAGGCGAAGTGGCATGCTCAG 576496 i i v v iv ii v i i C MIR#SINE/MIR 140 TTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCCAA 91 chr6ptel1M 576497 AACAACAC 576504 iiiv C MIR#SINE/MIR 90 GGTCACAC 83 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.39 CpG sites = 27, Kimura (unadjusted) = 32.35 Transitions / transversions = 2.08 (27/13) Gap_init rate = 0.01 (1 / 156), avg. gap size = 1.00 (1 / 1) 432 23.73 1.65 2.50 chr6ptel1M 576397 576517 (423483) C MIR1_Amn#SINE/MIR (34) 196 77 m_b286s601i42 11586 chr6ptel1M 576397 TCATTCGATCCTCACAGCACCTTG-GGAGATGGACACTACTATTATCTCC 576445 v v - v i i-ii iv v v ii i C MIR1_Amn#SINE 196 TCAGTAGATC-TCAAAGCACTTTACAAAGGAGGTCAGTATCATTATCCCC 148 chr6ptel1M 576446 ATTCTACAGATGAGAAAACTGAGGCAGACAGAGGCGAAGTGGCATGCTCA 576495 i i ?v v i? i v i C MIR1_Amn#SINE 147 ATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGCCCA 98 chr6ptel1M 576496 GAACAACACTCAGAAAGC-AGTG 576517 iiii-- ? v?i - C MIR1_Amn#SINE 97 AGGT--CACNCAGCNGGCNAGTG 77 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.66 CpG sites = 18, Kimura (unadjusted) = 30.66 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.04 (5 / 120), avg. gap size = 1.00 (5 / 5) 204 20.83 8.33 0.00 chr6ptel1M 577495 577542 (422458) MIRc#SINE/MIR 22 73 (195) m_b286s601i43 11587 chr6ptel1M 577495 AAATAGCACTG-ATTTGCAGTCAGGA---TCTGGTTTTGAAATCTGGCTC 577540 v - i v ---i v i ivi i MIRc#SINE/MIR 22 AAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTC 71 chr6ptel1M 577541 TG 577542 MIRc#SINE/MIR 72 TG 73 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 19.50 CpG sites = 6, Kimura (unadjusted) = 24.83 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.04 (2 / 47), avg. gap size = 2.00 (4 / 2) 236 26.98 3.88 8.06 chr6ptel1M 578151 578279 (421721) C L2c_3end#LINE/L2 (4) 474 351 m_b286s601i44 11588 chr6ptel1M 578151 ATTCATGCAAGAAGCAGTTTTTAAAGCTTTGCC-ACTGGGCCCGTGGCCA 578199 v v i v v i - --- - iv i----- C L2c_3end#LINE 474 ATTCATTCAACAAACATTTATTGA-GC---GCCTACTATGT-----GCCA 434 chr6ptel1M 578200 AGTGCTGGGTGCAAAAAGAGGCAAACGACA-GG---CTTCCCTCTTGGAG 578245 i i vii v v v v v - --- v vv C L2c_3end#LINE 433 GGCGCTGGGGATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAG 384 chr6ptel1M 578246 CTTACAATCTAGGGGGCAAAGCAGAACACACAAA 578279 i i v ivi ii - ?ii C L2c_3end#LINE 383 CTCACAGTCTAGTGGAGGAGACAG-ACANGTAAA 351 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 32.75 CpG sites = 16, Kimura (unadjusted) = 34.02 Transitions / transversions = 1.00 (16/16) Gap_init rate = 0.10 (13 / 128), avg. gap size = 1.15 (15 / 13) 32 0.00 0.00 0.00 chr6ptel1M 578579 578608 (421392) (G)n#Simple_repeat 1 30 (0) c_b286s251i0 11589 chr6ptel1M 578579 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 578608 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 30 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 19 31.25 0.00 0.00 chr6ptel1M 578978 579036 (420964) (GG)n#Simple_repeat 1 59 (0) m_b286s252i7 11590 chr6ptel1M 578978 GGGGGGGGGGGCGGGGGGGGCTGCAGGGGGCGCCGCCTGTAAGGGGGGCG 579027 v vv vi v vv vvv vii v (GG)n#Simple_ 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 50 chr6ptel1M 579028 GGGGGGGGG 579036 (GG)n#Simple_ 51 GGGGGGGGG 59 Matrix = Unknown Transitions / transversions = 0.25 (3/12) Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.0 (0 / 0) 18 25.08 0.00 3.45 chr6ptel1M 579403 579462 (420538) (GCCCC)n#Simple_repeat 1 58 (0) m_b286s252i9 11591 chr6ptel1M 579403 GCCCCGCCCCGCCCCGCCCCGTCCCACGTGCCGTTCCGAGCCGGCCTGCG 579452 - - iv ii vv v i v (GCCCC)n#Simp 1 GCCCCGCCCCGCCCCGCCCCG-CCC-CGCCCCGCCCCGCCCCGCCCCGCC 48 chr6ptel1M 579453 GGGCGCCGCC 579462 vv v (GCCCC)n#Simp 49 CCGCCCCGCC 58 Matrix = Unknown Transitions / transversions = 0.50 (4/8) Gap_init rate = 0.03 (2 / 59), avg. gap size = 1.00 (2 / 2) 317 31.87 0.00 1.10 chr6ptel1M 581173 581264 (418736) C MIRc#SINE/MIR (107) 161 71 m_b286s601i45 11592 chr6ptel1M 581173 AAGCATTATCATCTTCTTTTTATAGAGGAAGAAAGTGGATGCCAGAAAGG 581222 i i i ii v i v i v iivvi i C MIRc#SINE/MIR 161 AGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGG 112 chr6ptel1M 581223 GGAAATGACCTTGCCTATAGTTACTCAGTCATTAAATGGTAG 581264 vv i - i vi i v ii v i i C MIRc#SINE/MIR 111 TTAAGTGAC-TTGCCCAAGGTCACACAGCTAGTAAGTGGCAG 71 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 43.69 CpG sites = 19, Kimura (unadjusted) = 43.69 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.01 (1 / 91), avg. gap size = 1.00 (1 / 1) 23 7.94 2.38 2.38 chr6ptel1M 581921 581962 (418038) (TTATG)n#Simple_repeat 1 42 (0) m_b286s252i10 11593 chr6ptel1M 581921 TTTTGTT-TGTTATGTTATGTTATATTATATTATTGTTATGTT 581962 v - i i - (TTATG)n#Simp 1 TTATGTTATGTTATGTTATGTTATGTTATGTTA-TGTTATGTT 42 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.05 (2 / 41), avg. gap size = 1.00 (2 / 2) 224 27.48 5.71 9.90 chr6ptel1M 583190 583294 (416706) MIR3#SINE/MIR 108 208 (0) m_b286s601i46 11594 chr6ptel1M 583190 ATTTCCTTGGAAATCTCATTTCTCTC-TTTATAAAATGAGATGATTGGAT 583238 ii ii i--i v ii - i i iv i i MIR3#SINE/MIR 108 ACCTCTCTGGG--CCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGAC 155 chr6ptel1M 583239 TAGACAGTCTCT--GGTCCTTTTGA---CTGAATCTCGTTCTGTGAGATA 583283 iii -- i iv --- ---- i i ---- MIR3#SINE/MIR 156 TAGATGATCTCTAAGGTCCCTTCCAGCTCTGA----CATTCTATG----A 197 chr6ptel1M 583284 TTTTCTGGTTC 583294 i v i MIR3#SINE/MIR 198 TTCTATGATTC 208 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 37.39 CpG sites = 22, Kimura (unadjusted) = 37.39 Transitions / transversions = 5.50 (22/4) Gap_init rate = 0.12 (13 / 104), avg. gap size = 1.23 (16 / 13) 389 31.97 0.00 6.82 chr6ptel1M 583320 583460 (416540) MIR3#SINE/MIR 9 140 (68) m_b286s601i47 11595 chr6ptel1M 583320 GTGGCGGTCCAAAGAAGCAGCACCTTGTATGGGAAGAGTTGGGAGATCTG 583369 v vv i i-- --- v iv -- ii i MIR3#SINE/MIR 9 GTGGCTGAGCAGAGAG--AGCAC---GGACTGG--GAGTCAGGAGACCTG 51 chr6ptel1M 583370 GATTCTAATCCCAATCCCAATTCTGATGCCAATTGTGTGACCATGTGCAA 583419 i i iiii iiviv i -- i?ii v v MIR3#SINE/MIR 52 GGTTCTAGTCCCGGCTCTGCCACTAA--CTNGCTGTGTGACCTTGGGCAA 99 chr6ptel1M 583420 GTCCCCTAATTTGTTTGACTCTCAATTTCCTCTTCCATAAA 583460 v i v ii v i ivi i v ii MIR3#SINE/MIR 100 GTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAA 140 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 42.77 CpG sites = 28, Kimura (unadjusted) = 44.23 Transitions / transversions = 2.00 (28/14) Gap_init rate = 0.06 (9 / 140), avg. gap size = 1.00 (9 / 9) 436 28.68 0.76 1.54 chr6ptel1M 583355 583485 (416515) MIR1_Amn#SINE/MIR 42 171 (59) m_b286s601i48 11595 chr6ptel1M 583355 GAGTTGGGAGATCTGGATTCTAATCCCAATCCCAATTCTGATGCCAATTG 583404 v i i i ? ? iiii iiviv ?-- ?ii MIR1_Amn#SINE 42 GACTCGGGAGACCTGGGTTCNANTCCCGGCTCTGCCACTN--GCCNGCTG 89 chr6ptel1M 583405 TGTGACCATGTGCAAGTCCCCTAATTTGTTTGACTCTCAATTTCCTCTTC 583454 ? v v v i ? ii v i ?vi i v MIR1_Amn#SINE 90 NGTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATC 139 chr6ptel1M 583455 CAT-AAATGGGATTAATAATAACCATCTACTT 583485 ii - iv i viv i v MIR1_Amn#SINE 140 TGTAAAATGGGGATAATGATACTGACCTCCTT 171 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 37.78 CpG sites = 24, Kimura (unadjusted) = 40.65 Transitions / transversions = 1.85 (24/13) Gap_init rate = 0.02 (3 / 130), avg. gap size = 1.00 (3 / 3) 263 26.00 0.00 0.00 chr6ptel1M 583511 583560 (416440) C MIRc#SINE/MIR (143) 125 76 m_b286s601i49 11596 chr6ptel1M 583511 GAAACCCAAAGAGATCAAATGACTTGGTTAAAGTCACATAGCCAGTAAGT 583560 ii i i i i i vii i i i C MIRc#SINE/MIR 125 GAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGT 76 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 35.68 CpG sites = 12, Kimura (unadjusted) = 35.68 Transitions / transversions = 12.00 (12/1) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 18 32.25 1.41 1.41 chr6ptel1M 583989 584059 (415941) (AT)n#Simple_repeat 1 71 (0) m_b286s252i11 11597 chr6ptel1M 583989 ATGTATATACATATATGTTTAATTAAACACATATATCACATATAACTATG 584038 i i i v vv v i i - i vv i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATAT-ATATATATATATA 49 chr6ptel1M 584039 TAT-TCCATAGATAGACATATA 584059 - vi v v i (AT)n#Simple_ 50 TATATATATATATATATATATA 71 Matrix = Unknown Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.03 (2 / 70), avg. gap size = 1.00 (2 / 2) 441 27.56 9.52 2.79 chr6ptel1M 584128 584295 (415705) C MIRc#SINE/MIR (88) 180 2 m_b286s601i50 11598 chr6ptel1M 584128 CTTGTAATGTAAGT-GGTCAACATAATCATTATTCCTATTTTATAAATGA 584176 i i v i i- v i-i - i i i i i C MIRc#SINE/MIR 180 CCTGTGAGGTAGGCAGGGCAG-GTA-TTATTATCCCCATTTTACAGATGA 133 chr6ptel1M 584177 GGGCAGTGAGACTCTGAAAGGTTAAGTGATTTCTTTATGCTTGCATAACT 584226 iv v i v i i viii v v ii i i C MIRc#SINE/MIR 132 GGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCT 83 chr6ptel1M 584227 AATAACT---AAA----------GAACCGAGGTA-TCCTTACCCTAAGTC 584262 i v --- i ---------- v v- v i i C MIRc#SINE/MIR 82 AGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTC 33 chr6ptel1M 584263 CAGAATGCT-TTGCTACTAACCTACAACTGCATC 584295 -- - v i ivv i - v C MIRc#SINE/MIR 32 CAG--TGCTCTTTCCACTGCACCAC-ACTGCCTC 2 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 35.72 CpG sites = 29, Kimura (unadjusted) = 35.72 Transitions / transversions = 1.81 (29/16) Gap_init rate = 0.06 (10 / 167), avg. gap size = 2.10 (21 / 10) 292 26.45 9.30 3.30 chr6ptel1M 584353 584438 (415562) C L2a_3end#LINE/L2 (4) 513 423 m_b286s601i52 11599 chr6ptel1M 584353 ATCCATTAAATAATCAATATTTATGAAGTGTCTGCTGTGCATCAGGCATT 584402 i v i --- vi i i i i iii i C L2a_3end#LINE 513 ATTCATTCAACAA---ATATTTATTGAGCGCCTACTATGTGCCAGGCACT 467 chr6ptel1M 584403 GTATTAAGCACTAGGAATACAA--------AAAAGAGACCAAAG 584438 vi i i i i i-------- v v C L2a_3end#LINE 466 GTTCTAGGCGCTGGGGATACAGCAGTGAACAAAACAGACAAAAG 423 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 31.01 CpG sites = 17, Kimura (unadjusted) = 34.94 Transitions / transversions = 3.40 (17/5) Gap_init rate = 0.05 (4 / 85), avg. gap size = 2.75 (11 / 4) 301 27.99 0.00 4.41 chr6ptel1M 584353 584423 (415577) C L2b_3end#LINE/L2 (4) 462 395 m_b286s601i51 11599 chr6ptel1M 584353 ATCCATTAAATAATCAATATTTATGAAGTGTCTGCTGTGCATCAGGCATT 584402 i v i --- ivi i i i iii ?i C L2b_3end#LINE 462 ATTCATTCAACAA---ATATTTACTGAGCGCCTACTGTGTGCCAGGCNCT 416 chr6ptel1M 584403 GTATTAAGCACTAGGAATACA 584423 ii i i i i C L2b_3end#LINE 415 GTGCTAGGCGCTGGGGATACA 395 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 34.58 CpG sites = 17, Kimura (unadjusted) = 40.07 Transitions / transversions = 8.50 (17/2) Gap_init rate = 0.04 (3 / 70), avg. gap size = 1.00 (3 / 3) 198 30.26 27.63 0.00 chr6ptel1M 584842 585069 (414931) C L2d_3end#LINE/L2 (0) 516 226 m_b286s601i53 11600 chr6ptel1M 584842 TCAAT-AGTCATTTGACA--TTTTTATTAAGCACCTACTATGTGTCTAAC 584888 - i v ii -- v i i iii i C L2d_3end#LINE 516 TCAATCAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGC 467 chr6ptel1M 584889 ACTGAAGCAGCAACTGT--------ACAGAATACTAT------T--TTCT 584922 vivi vvi -------- ? i ? v ------ -- i i C L2d_3end#LINE 466 ACTGTGCTAGGCGCTGTGGGGAACGANAAAANAGTATAAGACATGGTCCC 417 chr6ptel1M 584923 TG------GGAATCTTGTGGTCTGGTTGCAAAGTCAAATTTAAGACACAT 584966 ------i i v iiii i vii v ivi v C L2d_3end#LINE 416 TGCCCTCAAGGAGCTTACAATCTAGTTGGGGAGACAAGACTAACACACAT 367 chr6ptel1M 584967 ---ACAA--GAAAAAAAATAGGAAA-AATGTATTA-TAAG---------- 584999 --- --ii i v vi i - i i v - ---------- C L2d_3end#LINE 366 GAAACAATTAGAGAACAATACAAGACAGTATATAATTAAGTGCTAAATTG 317 chr6ptel1M 585000 --------AGACAATAAAGGTTACA-------AAAGAA-TGAGAAGTCAG 585033 -------- v iv i i ------- i -v ii C L2d_3end#LINE 316 CGTGGTACAGACTATAAGTGCTATAGGAGTTCAGAGAAGGGAGAGATCAG 267 chr6ptel1M 585034 TATAGACTAATGTGGACAGAG-----TTCATGAAGGAACTG 585069 i i i iiv v i ----- i i iv C L2d_3end#LINE 266 TGTGGGCTGGAGTGGTCAGGGAAGGCTTCGTGGAGGAGGTG 226 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 39.18 CpG sites = 48, Kimura (unadjusted) = 41.60 Transitions / transversions = 2.29 (48/21) Gap_init rate = 0.06 (14 / 227), avg. gap size = 4.50 (63 / 14) 211 20.45 4.55 0.00 chr6ptel1M 584849 584892 (415108) C L2a_3end#LINE/L2 (6) 511 466 m_b286s601i54 11600 chr6ptel1M 584849 TCATTTGACA--TTTTTATTAAGCACCTACTATGTGTCTAACACTG 584892 ii -- v i i i vii C L2a_3end#LINE 511 TCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTG 466 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 21.87 CpG sites = 7, Kimura (unadjusted) = 24.98 Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.02 (1 / 43), avg. gap size = 2.00 (2 / 1) 224 18.18 2.27 0.00 chr6ptel1M 585103 585146 (414854) MIR3#SINE/MIR 157 201 (7) m_b286s601i55 11601 chr6ptel1M 585103 AAATAATCCCTATGGTCTCTTCCAGGTCTAACATTCTA-GCTTCT 585146 i i i v i v i - v MIR3#SINE/MIR 157 AGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCT 201 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 21.18 CpG sites = 5, Kimura (unadjusted) = 21.18 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.02 (1 / 43), avg. gap size = 1.00 (1 / 1) 31 20.29 0.00 0.00 chr6ptel1M 585945 586009 (413991) (CTCCC)n#Simple_repeat 1 65 (0) m_b286s252i12 11602 chr6ptel1M 585945 CTCCCCTCCCCTCCCCGCCCTTCCCCTCCCCTCTTTTCCTTTCCCCTCCT 585994 v i iii ii i (CTCCC)n#Simp 1 CTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCC 50 chr6ptel1M 585995 CTCCTCTCTTCTCCC 586009 i ii (CTCCC)n#Simp 51 CTCCCCTCCCCTCCC 65 Matrix = Unknown Transitions / transversions = 10.00 (10/1) Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0) 288 32.22 2.44 4.13 chr6ptel1M 586120 586242 (413758) MIRb#SINE/MIR 41 161 (107) m_b286s601i56 11603 chr6ptel1M 586120 GGAATAAGAACTCAG-CTTAAAGTTGGATCCTGGTTCTAAAATTTAATAG 586168 i v --- - i iiiv i i i i ivv i v MIRb#SINE/MIR 41 GGAGTCAGA---CAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAG 87 chr6ptel1M 586169 CTGCAGGAATGTGGGCAAAGAAGTT--CCCCCTTGGGCCTTAGTTTCTTC 586216 iiv viv ivv v -- i ii i i i MIRb#SINE/MIR 88 CTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTC 137 chr6ptel1M 586217 TTGCCTAAAGATGTAGATTAATAATA 586242 v viv - vi - MIRb#SINE/MIR 138 ATCTGTAAA-ATGGGGAT-AATAATA 161 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 40.65 CpG sites = 23, Kimura (unadjusted) = 43.72 Transitions / transversions = 1.53 (23/15) Gap_init rate = 0.06 (7 / 122), avg. gap size = 1.14 (8 / 7) 298 33.64 1.79 1.79 chr6ptel1M 586134 586245 (413755) MIR#SINE/MIR 46 157 (105) m_b286s601i57 11603 chr6ptel1M 586134 GCTTAAAGTTGGATCCTGGTTCTAAAATTTAATAGCTGCAGGAATGTGGG 586183 i iiiv i i i i ivv i v iiv viv MIR#SINE/MIR 46 GCCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGG 95 chr6ptel1M 586184 CAAAGAAGTT--CCCCCTTGGGCCTTAGTTTCTTCTTGCCTAAAGATGTA 586231 ivv v -- i ii v i i v viv - vi MIR#SINE/MIR 96 CAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAA-ATGGG 144 chr6ptel1M 586232 GATTAATAATAATA 586245 - i MIR#SINE/MIR 145 GAT-AATAATAGTA 157 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 42.98 CpG sites = 22, Kimura (unadjusted) = 46.39 Transitions / transversions = 1.47 (22/15) Gap_init rate = 0.03 (3 / 111), avg. gap size = 1.33 (4 / 3) 750 29.28 0.55 0.00 chr6ptel1M 586285 586465 (413535) C MIRb#SINE/MIR (53) 215 34 m_b286s601i58 11604 chr6ptel1M 586285 AGTGCTCTGTATGTAACATCTTGTTTGATCCTCACAGCAATCTTGCAAGG 586334 i i ii i vi ii i i i i i C MIRb#SINE/MIR 215 AGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGG 166 chr6ptel1M 586335 AATGATTCATTATCCCTGTTTTATAGATGAGGAAACCAAGGCACAGAGTA 586384 v v vv i ii i ii v vi C MIRb#SINE/MIR 165 TAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAG 116 chr6ptel1M 586385 TTTAAGTGACTTGCTTGGGATCACGCTGCCAATAAATGTCTGAGGCAGGA 586434 v i iiii i i v i i i v v v i C MIRb#SINE/MIR 115 GTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGA 66 chr6ptel1M 586435 TTTCAATGTGGGCCTTGGTGACTCC-AAGCCC 586465 iv ivii i vvv - C MIRb#SINE/MIR 65 TTCGAACCCAGGTCTGTCTGACTCCAAAGCCC 34 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 35.27 CpG sites = 36, Kimura (unadjusted) = 39.04 Transitions / transversions = 2.12 (36/17) Gap_init rate = 0.01 (1 / 180), avg. gap size = 1.00 (1 / 1) 215 35.81 2.33 11.68 chr6ptel1M 586501 586715 (413285) MIR1_Amn#SINE/MIR 34 230 (0) m_b286s601i60 11605 chr6ptel1M 586501 TGGACTTGAAAAGTAAAAGACTTAAGTTCAAGTCCAGATTCTATTGTTTG 586550 - ii vviiii i ii ? ? v ii iiiii ? MIR1_Amn#SINE 34 TGGACT-GGGACTCGGGAGACCTGGGTTCNANTCCCGGCTCTGCCACTNG 82 chr6ptel1M 586551 GTAGCCATGCTCCTGTGAGCCAGCCTCTGAGCTTCTGATTCCTTCAGAAA 586600 vi? ii? ivv iv i v i v v?i i -------------- MIR1_Amn#SINE 83 CCNGCTGNGTGACCTTGGGCAAGTCACTTNACCTCT-------------- 118 chr6ptel1M 586601 TCACTTCTGAGCTTCAGTTTCTTCTTGGGAAACATTGTGACAATAAG--T 586648 ------ ? i i v vv v v v v i i v-- MIR1_Amn#SINE 119 ------CTGNGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATGATACT 162 chr6ptel1M 586649 AATACTCGTAGT-AGGT-CTTTCATAT-GACTGTTGTAAAATGCTACACA 586695 i ivii v v - i - v v -v v v i i MIR1_Amn#SINE 163 GACCTCCTTTGTAAAGTGCTTTGAGATCTACTGATGAAAAGTGCTACATA 212 chr6ptel1M 586696 ACTACCAGCTGTGTTATGAT 586715 vvi i -- i v MIR1_Amn#SINE 213 AGAGCTAG--GTATTATTAT 230 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 51.32 CpG sites = 39, Kimura (unadjusted) = 52.59 Transitions / transversions = 1.34 (39/29) Gap_init rate = 0.13 (27 / 214), avg. gap size = 1.04 (28 / 27) 264 39.00 0.00 15.00 chr6ptel1M 586501 586684 (413316) MIRc#SINE/MIR 31 190 (78) m_b286s601i59 11605 chr6ptel1M 586501 TGGACTTGAAAAGTAAAAGACTTAAGTTCAAGTCCAGATTCTATTGTTTG 586550 i ivvvii i ii i v ii iiiii i MIRc#SINE/MIR 31 TGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTA 80 chr6ptel1M 586551 GTAGCCATGCTCCTGTGAGCCAGCCTCTGAGCTTCTGATTCCTTCAGAAA 586600 v ii ivv iv i v i v v i i --------------- MIRc#SINE/MIR 81 CTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC--------------- 115 chr6ptel1M 586601 TCACTTCTGAGCTTCAGTTTCTTCTTGGGAAACATTGTGACAATAAGTAA 586650 ----- i i v vv v v v v i ---- MIRc#SINE/MIR 116 -----TCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAA----TAA 156 chr6ptel1M 586651 TACTCGTAGTAGGTCTTTCATATGACTGTTGTAA 586684 ii ivv ivv vii i v ii i MIRc#SINE/MIR 157 TACCTGCCCTGCCTACCTCACAGGGTTGTTGTGA 190 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 54.89 CpG sites = 37, Kimura (unadjusted) = 56.32 Transitions / transversions = 1.54 (37/24) Gap_init rate = 0.13 (24 / 183), avg. gap size = 1.00 (24 / 24) 642 24.69 13.20 9.27 chr6ptel1M 586944 587193 (412807) C MIRc#SINE/MIR (0) 268 10 m_b286s601i61 11606 chr6ptel1M 586944 AACAACAACAGTAGCTCACATTTAGATAGTGCTTTAAAACTTTCCTAGCA 586993 i i i ii?v i iv ii v ii v vv i C MIRc#SINE/MIR 268 AATAATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCG 219 chr6ptel1M 586994 CTTTC--------------------TCC--ACAACAGCTCTGTGATA-AG 587020 -------------------- -- i i vi- C MIRc#SINE/MIR 218 CTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAG 169 chr6ptel1M 587021 GCAGCAAGAGTATTATGATTTTCATTTTATTTTTTATTTTTTTGTTGTTG 587070 vivii v iii i----- ------------- C MIRc#SINE/MIR 168 GCAGGGCAGGTATTATTATCCCCATTTTAC-----A-------------G 137 chr6ptel1M 587071 TTGAGGAAATTGGGG-------A---TAAGTGACTTGCCCAGGGTCACAC 587110 v i i ------- --- i C MIRc#SINE/MIR 136 ATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACAC 87 chr6ptel1M 587111 AGCTAGGAAGTATAAGTGTCTAAGATTAGATTTGAACTCAGGTCCTCCTG 587160 ------ v vi vivi i i i i C MIRc#SINE/MIR 86 AGCTAG------TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTG 43 chr6ptel1M 587161 ACTTCAGGGCTGGTGCTTTATCTACTGCATCAC 587193 i i v ii i v i i C MIRc#SINE/MIR 42 ACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.49 CpG sites = 39, Kimura (unadjusted) = 31.52 Transitions / transversions = 2.29 (39/17) Gap_init rate = 0.12 (29 / 249), avg. gap size = 1.97 (57 / 29) 192 25.57 0.00 5.88 chr6ptel1M 587195 587248 (412752) C MIR#SINE/MIR (101) 161 111 m_b286s601i62 11607 chr6ptel1M 587195 TAGCTGCCCTCATGATTTTCATTTTAATGATGAGGAAAAAAATGAGACAC 587244 v i iv i v iii vv --- v i C MIR#SINE/MIR 161 TAGGTACTATTATTATCCCCATTTTACAGATGAGG---AAACTGAGGCAC 115 chr6ptel1M 587245 AGAG 587248 C MIR#SINE/MIR 114 AGAG 111 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 31.60 CpG sites = 7, Kimura (unadjusted) = 31.60 Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.06 (3 / 53), avg. gap size = 1.00 (3 / 3) 298 29.20 16.11 1.17 chr6ptel1M 587438 587586 (412414) C MIR3#SINE/MIR (8) 200 30 m_b286s601i63 11608 chr6ptel1M 587438 GAATCAT-TCATGTGTGAG-TGGAGGAGGAAT--GAGATCATCTTAGTC- 587482 -vv vv - i i ivv -- - - C MIR3#SINE/MIR 200 GAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCT-AGTCC 152 chr6ptel1M 587483 AACCTTTT-GTTTTATAAGCAAGG-----------CAAAG-------GTA 587513 iii -i i iiii ----------- i ------- i C MIR3#SINE/MIR 151 AACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTG 102 chr6ptel1M 587514 ACTCACTTAAAGCTGTAGAGCATAGTTTTTGGCAGAACCAGCACCAGAAG 587563 ii ii i iiii v ?- vv i i v i v C MIR3#SINE/MIR 101 ACTTGCCCAAGGTCACACAGCN-AGTTAGTGGCAGAGCCGGGACTAGAAC 53 chr6ptel1M 587564 TCACATCTCCTGCTTCCCAGACC 587586 i vi vi v C MIR3#SINE/MIR 52 CCAGGTCTCCTGACTCCCAGTCC 30 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 38.10 CpG sites = 29, Kimura (unadjusted) = 39.30 Transitions / transversions = 2.07 (29/14) Gap_init rate = 0.06 (9 / 148), avg. gap size = 2.89 (26 / 9) 260 34.21 1.72 1.72 chr6ptel1M 587499 587614 (412386) C MIR1_Amn#SINE/MIR (110) 120 5 m_b286s601i64 11608 chr6ptel1M 587499 AGCAAGGCAAAGGTAACTCACTTAAAGCTGTAGAGCATAGTTTTTGGCAG 587548 vi i? - i ii ii i iiii?v ?-i i?vv C MIR1_Amn#SINE 120 AGAGAGGTNAAG-TGACTTGCCCAAGGTCACNCAGCN-GGCNAGTGGCAG 73 chr6ptel1M 587549 AACCAGCACCAGAAGTCACATCTCCTGCTTCCCAGACCAAT--TCTACTC 587596 i i v ?i? vi vi i vv v i -- ii C MIR1_Amn#SINE 72 AGCCGGGANTNGAACCCAGGTCTCCCGAGTCCCAGTCCAGTGCTCTATCC 23 chr6ptel1M 587597 AATATACTGCATGGCCTC 587614 v v ii iv C MIR1_Amn#SINE 22 ACTAGACCACACTGCCTC 5 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 48.91 CpG sites = 26, Kimura (unadjusted) = 52.93 Transitions / transversions = 2.00 (26/13) Gap_init rate = 0.03 (3 / 115), avg. gap size = 1.33 (4 / 3) 244 25.96 7.41 5.84 chr6ptel1M 588559 588693 (411307) C L2d2_3end#LINE/L2 (1) 554 418 m_b286s601i65 11609 chr6ptel1M 588559 CAATTGAAATGAATAAAAACC-ATTAATGCCTTGCTTGTCCTATG-ATAG 588606 v v v i v ii- i - --- i iiiv i - vi C L2d2_3end#LIN 554 CAAATCAAATCAACAAATATTTATTGA-GC---GCCTACTGTGTGCAAGG 509 chr6ptel1M 588607 CACTGTGCTAAGTGCT---GGGGCTACAAATACAAGCTTCCAGACA--GT 588651 i i --- v -- v - viv -- C L2d2_3end#LIN 508 CACTGTGCTAGGCGCTGTGGGGGATACAA--AGAAG-TATAAGACATGGT 462 chr6ptel1M 588652 CCCTGCCTTTTA-GAGCT--CATTCTCACAGGAGAAGACAAGATA 588693 i iv - -- v viiv - i i C L2d2_3end#LIN 461 CCCTGCCCTCAAGGAGCTTACAATCTAGTTGG-GGAGACAAGACA 418 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 31.38 CpG sites = 19, Kimura (unadjusted) = 32.56 Transitions / transversions = 1.36 (19/14) Gap_init rate = 0.10 (14 / 134), avg. gap size = 1.29 (18 / 14) 248 30.57 4.92 0.79 chr6ptel1M 588605 588726 (411274) C L2d_3end#LINE/L2 (47) 469 343 m_b286s601i66 11609 chr6ptel1M 588605 AGCACTGTGCTAAGTGCTG-GGGCTACAAATACAAGCTTCCAGACA--GT 588651 i i - vv i ?v v ?iv viv -- C L2d_3end#LINE 469 AGCACTGTGCTAGGCGCTGTGGGGAACGANAAAANAGTATAAGACATGGT 420 chr6ptel1M 588652 CCCTGCCTTTTA-GAGCT--CATTCTCACAGGAGAAGACAAGATAAATTG 588698 i iv - -- v viiv - i iv ivv C L2d_3end#LINE 419 CCCTGCCCTCAAGGAGCTTACAATCTAGTTGG-GGAGACAAGACTAACAC 371 chr6ptel1M 588699 GAGTGCAAGATTTAGAAAGCAGGGCAAG 588726 ivi v v v i i ivi C L2d_3end#LINE 370 ACATGAAACAATTAGAGAACAATACAAG 343 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 37.89 CpG sites = 18, Kimura (unadjusted) = 40.63 Transitions / transversions = 0.95 (18/19) Gap_init rate = 0.04 (5 / 121), avg. gap size = 1.40 (7 / 5) 292 19.94 11.24 4.21 chr6ptel1M 588606 588694 (411306) C L2a_3end#LINE/L2 (46) 471 377 m_b286s601i67 11609 chr6ptel1M 588606 GCACTGTGCTAAGTGCTGGGGCTACA--AAT--ACAAGCTTCCAGAC--- 588648 v i i v -- i -- i---v --- C L2a_3end#LINE 471 GCACTGTTCTAGGCGCTGGGGATACAGCAGTGAACAAA---ACAGACAAA 425 chr6ptel1M 588649 AGTCCCTGCCTTT-TAGAGCT--CATTCTCACAGGAGAAGACAAGATAA 588694 i i- i -- viii i i - i C L2a_3end#LINE 424 AGTCCCTGCCCTCATGGAGCTTACATTCTAGTGGGGGGAGAC-AGACAA 377 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 22.63 CpG sites = 13, Kimura (unadjusted) = 24.24 Transitions / transversions = 3.25 (13/4) Gap_init rate = 0.10 (9 / 88), avg. gap size = 1.56 (14 / 9) 30 5.95 0.00 0.00 chr6ptel1M 589485 589519 (410481) (AC)n#Simple_repeat 1 35 (0) c_b286s251i1 11610 chr6ptel1M 589485 ACACACACACACACACACTCGCACACACACACACA 589519 v i (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACA 35 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 18 34.39 1.32 0.00 chr6ptel1M 589583 589658 (410342) (TATA)n#Simple_repeat 1 77 (0) m_b286s252i13 11611 chr6ptel1M 589583 TATGTATA-ATATATATACATATATATGTGTACATACATACACAGACATA 589631 i - i i i i i i i v i (TATA)n#Simpl 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr6ptel1M 589632 AGCAGACATGTAGGTATTTATACATAT 589658 vii v i i vi v i (TATA)n#Simpl 51 TATATATATATATATATATATATATAT 77 Matrix = Unknown Transitions / transversions = 3.00 (15/5) Gap_init rate = 0.01 (1 / 75), avg. gap size = 1.00 (1 / 1) 569 35.04 8.60 5.02 chr6ptel1M 589668 590283 (409717) C L2#LINE/L2 (24) 3058 2422 m_b286s601i68 11612 chr6ptel1M 589668 GAAACAATTAGAG-AAAAACCAAGAGTTGGGCCATGTAGCATGCCTTGAG 589716 i iiv v - ii vv vi ------ i v v C L2#LINE/L2 3058 GGAACAGCAAGTGCAAAGGCCCTGAGGCGGG------AGCGTGCCTGGCG 3015 chr6ptel1M 589717 AG--AGAGGAGCAGCAAGAAGGCCAATGTCACTCGATCACACACTTCTTG 589764 v --v i i i vi v v iv v------ C L2#LINE/L2 3014 TGTTCGAGGAACAGCAAGGAGGCCAGTGTGGCTGGAGCGGAG------TG 2971 chr6ptel1M 589765 GGGGGGGGGGGGAAGAATATAAAATGTAAACACTAGAAAT--TTGGGGA- 589811 i v i i ivii vi i viiv v- ii --iv - C L2#LINE/L2 2970 AGCGAGGGGGAGAGTGGTAGGAGATGAGGTCAG-AGAGGTAACGGGGGAC 2922 chr6ptel1M 589812 --GGTTATGATGGGTTTTGGGTAG--CAGAGTA-----------TTTTAT 589846 -- i i vv ii -- -- vv ----------- i C L2#LINE/L2 2921 CAGATCATGTAGGGCCTTG--TAGGCCATTGTAAGGACTTTGGCTTTTAC 2874 chr6ptel1M 589847 TTT---TGAGATAATCAGGAGTTTGTTGAGTGTGTATATTTA--TATGTG 589891 i --- ii--- i iivv v v ----- i--i viv C L2#LINE/L2 2873 TCTGAGTGAGATGG---GAAGCCATTGGAGGGT-----TTTGAGCAGAGG 2832 chr6ptel1M 589892 GGTGACATGGTCAGACCTGGGCTTCGGGAGGATCATTTTGACAGATGAAT 589941 i i v i iv i iiii i i i v v vi C L2#LINE/L2 2831 AGTGACATGATCTGACTTACGTTTTAAAAGGATCACTCTGGCTGCTGTGT 2782 chr6ptel1M 589942 GGAGGACTGACTGGAGTAGAG-AGAGATTTAAGCAG------CAG----- 589979 v i iv ? vi i - ii i vv ------ ----- C L2#LINE/L2 2781 TGAGAATAGACTGNAGGGGGGCAAGGGTGGAAGCAGGGAGACCAGTTAGG 2732 chr6ptel1M 589980 --GCTATCACAAAAATCCAGATGTGATGTGATAAGGACCTGGACCAGGGA 590027 -- ii iv ii v vi iiv i i v C L2#LINE/L2 2731 AGGCTATTGCAGTAATCCAGGCGAGAGATGATGGTGGCTTGGACCAGGGT 2682 chr6ptel1M 590028 GGTGACCATAAAAAAGGGAGAGAATGGGCCATATGCAAGAGATGTTATGA 590077 i vi ii iiv v- vv i iv v vi v i v C L2#LINE/L2 2681 GGTGGCAGTGGAGGTGGT-GAGAAGTGGTCGGATTCTGGATATATTTTGA 2633 chr6ptel1M 590078 A----------ATAGACTTTGGCTACAGATCACACATGAGGGGTAAGAGG 590117 ---------- i iv viv ii iiv ii i v i i C L2#LINE/L2 2632 AGGTAGAGCCGACAGGATTTGCTGATGGATTGGATGTGGGGTGTGAGAGA 2583 chr6ptel1M 590118 AAGTGGGGAGTTGAAGATGATGCGTAGGTTAGGAGTTTGGGTGACTGAAA 590167 v i ii i iv vv vvvi ii i ii i C L2#LINE/L2 2582 AAGAGAGGAGTCAAGGATGACTCCAAGGTTTTTGGCCTGAGCAACTGGAA 2533 chr6ptel1M 590168 GGATCTTGGTGTCCTTGGCAATGACAGGGAA-AT--CAGGAAGATAGAAT 590214 vvv v i v ?i viv ii - i-- i i -- v v C L2#LINE/L2 2532 GGATGGAGTTGCCATTNACTGAGATGGGGAAGACTGCGGGAGG--AGCAG 2485 chr6ptel1M 590215 GTTTGGGGAGAAAAAAACAAGTCCTGAGTTCGGTTTGGGGTGTGTAGAGT 590264 i i i i ------ vv i v iii vi C L2#LINE/L2 2484 GTTTGAGGGGGAAGA------TCAGGAGTTCAGTTTTGGACATGTTAAGT 2441 chr6ptel1M 590265 TTAAGATGTTTATAAGACA 590283 i ii v C L2#LINE/L2 2440 TTGAGATGCCTATTAGACA 2422 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 47.31 CpG sites = 123, Kimura (unadjusted) = 49.73 Transitions / transversions = 1.50 (123/82) Gap_init rate = 0.08 (48 / 615), avg. gap size = 1.77 (85 / 48) 326 23.61 1.39 0.00 chr6ptel1M 590356 590427 (409573) MIR3#SINE/MIR 75 147 (61) m_b286s601i69 11613 chr6ptel1M 590356 TGACTGTGTGTGTGACTTTGGGCAAGTTGCTTAATCCACATGTGCTTCAA 590405 i ?vv i ii v i iviv v i i MIR3#SINE/MIR 75 TAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAG 124 chr6ptel1M 590406 CTTCCTCATTTGTAAAA-GAGGG 590427 i i - MIR3#SINE/MIR 125 TTTCCTCATCTGTAAAATGAGGG 147 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.70 CpG sites = 11, Kimura (unadjusted) = 29.70 Transitions / transversions = 1.83 (11/6) Gap_init rate = 0.01 (1 / 71), avg. gap size = 1.00 (1 / 1) 646 22.29 5.06 0.61 chr6ptel1M 590364 590521 (409479) MIRc#SINE/MIR 86 250 (18) m_b286s601i70 11613 chr6ptel1M 590364 TGTGTGACTTTGGGCAAGTTGCTTAATCCACATGTGCTTCAACTTCCTCA 590413 i ii i iviv v i ii MIRc#SINE/MIR 86 TGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCA 135 chr6ptel1M 590414 TTTGTAAAAGAGGGAAAATAATG---GCATCTG---ATTTC-CAGGGTTG 590456 i vi v i--- -i --- ii - MIRc#SINE/MIR 136 TCTGTAAAATGGGGATAATAATACCTGC-CCTGCCTACCTCACAGGGTTG 184 chr6ptel1M 590457 TTGTGAGGATAAAATAAGATTATATTTGT-AAAGGATTTTGTAGACTTTC 590505 v i v i v - vii i v v MIRc#SINE/MIR 185 TTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTTTGTAAACTGTA 234 chr6ptel1M 590506 AAGCCCTATTTAAATG 590521 iv vi MIRc#SINE/MIR 235 AAGTGCTATACAAATG 250 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 26.19 CpG sites = 22, Kimura (unadjusted) = 27.08 Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.03 (5 / 157), avg. gap size = 1.80 (9 / 5) 312 26.49 0.00 2.94 chr6ptel1M 590656 590725 (409275) L2b_3end#LINE/L2 388 455 (11) m_b286s601i71 11614 chr6ptel1M 590656 TCCTTGCTGAATACTTAGTATACTTAGCACAGTGCCTGACACACAGTAGG 590705 vii v v ii ii-- i ? i L2b_3end#LINE 388 TCACCGCTGTATCCCCAGCG--CCTAGCACAGNGCCTGGCACACAGTAGG 435 chr6ptel1M 590706 CCTTTAACAAATGTTTGCTG 590725 vi i ii i i L2b_3end#LINE 436 CGCTCAGTAAATATTTGTTG 455 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.49 CpG sites = 14, Kimura (unadjusted) = 35.65 Transitions / transversions = 3.50 (14/4) Gap_init rate = 0.03 (2 / 69), avg. gap size = 1.00 (2 / 2) 423 30.51 3.83 4.33 chr6ptel1M 591153 591361 (408639) C L2#LINE/L2 (482) 2600 2393 m_b286s601i72 11615 chr6ptel1M 591153 GGTGTGGGAACTGAGGGAAAGGAAAGATTCAGCAA--AATCCAAGGTTGT 591200 i ivv i ii i v ivi -- v v C L2#LINE/L2 2600 GATGTGGGGTGTGAGAGAAAGAGAGGAGTCAAGGATGACTCCAAGGTTTT 2551 chr6ptel1M 591201 GAACTTGGGGGACCCAAACGATGAA-TGACTAAATTCTCTGCTGAAATAA 591249 vii i i vi ivi v i - vi i ----- i?i i ii C L2#LINE/L2 2550 TGGCCTGAGCAACTGGAAGGATGGAGTTGCCA-----TTNACTGAGATGG 2506 chr6ptel1M 591250 AGGAG--TGAGGAAAAAGGACAAGTTTTAGGGGGTAGA-CAGTGAATTCA 591296 i i -- v i ii -- i v v - - i C L2#LINE/L2 2505 GGAAGACTGCGGGAGGAG--CAGGTTTGAGGGGGAAGATCAG-GAGTTCA 2459 chr6ptel1M 591297 GTTT-GGATACAACAAATTTCAGATGT-TAGTGGAAATTTCAGGCAGAGA 591344 - i iivi i v i- v i v i- i ii C L2#LINE/L2 2458 GTTTTGGACATGTTAAGTTTGAGATGCCTATTAGACATC-CAAGTGGAGA 2410 chr6ptel1M 591345 TGTCCAGGAGGCAGTTG 591361 v v C L2#LINE/L2 2409 TGTCGAGTAGGCAGTTG 2393 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 41.54 CpG sites = 41, Kimura (unadjusted) = 41.54 Transitions / transversions = 2.05 (41/20) Gap_init rate = 0.07 (15 / 208), avg. gap size = 1.13 (17 / 15) 451 12.18 0.98 0.42 chr6ptel1M 591643 592354 (407646) (TTCC)n#Simple_repeat 1 716 (0) m_b286s252i14 11616 chr6ptel1M 591643 TTTCTTTC-TCCCTCCCTCTCTCCCTCCTTCTTTCCTCCCTCCCTTCCTT 591691 i i - i i ii i i i i (TTCC)n#Simpl 1 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 50 chr6ptel1M 591692 CCTCCCTCCCTCCCTCCCTGCCTCCCTTCCTTCCTTCCTTCTTTCCTTCC 591741 i i i i v i i (TTCC)n#Simpl 51 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 100 chr6ptel1M 591742 TCCCTCCCTTCCATCCTCCCTTCCCTCCTTCCTCCCTTCCTTCCTTCCTC 591791 i i v i i i i (TTCC)n#Simpl 101 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 150 chr6ptel1M 591792 CCTTCCTTCCTCCTTTCCCTCCTTCCTCCCTTCCCTCCTTCCTCCCTTCC 591841 i i i i i i (TTCC)n#Simpl 151 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 200 chr6ptel1M 591842 TTCCTTCCTTCCACCCTTCCCTCCTTCCTTCCTCCCTCCTTTCCTTCCTT 591891 vi i i i i (TTCC)n#Simpl 201 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 250 chr6ptel1M 591892 CCTTCCACCCTTCCCTCCTTCCTCCCTCCCTCCCTTCCTTTCTTCCCTCC 591941 vi i i i i i i (TTCC)n#Simpl 251 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 300 chr6ptel1M 591942 TTCCTTCC-TCCTTCCCTCCTTCCTCCCTCTCTCCCTTCTTTCCTTCCTT 591990 - i i ii i i (TTCC)n#Simpl 301 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 350 chr6ptel1M 591991 CTTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTCCCTCCC 592040 i i i (TTCC)n#Simpl 351 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 400 chr6ptel1M 592041 TTCCTTCTTTCTTTCCTTCCTTCCTTCCTTCTTTGCTTCCTTCCTTCCTT 592090 i i i v (TTCC)n#Simpl 401 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 450 chr6ptel1M 592091 CCTTCCCTTCTCCCTCCCTTCCTTCCTTCTTTCCTTCCTTCCTTCTTTCC 592140 i i i i i i (TTCC)n#Simpl 451 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 500 chr6ptel1M 592141 TTCCCTCC-TCCCTCCGTCCCTCCTTCCTTCCTTCTTTCCTTCCTTCCTT 592189 i - i v i i (TTCC)n#Simpl 501 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 550 chr6ptel1M 592190 CTTTCCTTCTTTCCTTCCTTCTTTCCTTCTTTCCTTCCTTCCTTCCTTCC 592239 i i i i (TTCC)n#Simpl 551 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 600 chr6ptel1M 592240 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 592289 (TTCC)n#Simpl 601 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 650 chr6ptel1M 592290 CCTTCCTTCCTTCCTTCCTTCC-TCCCTCCCTCCTCTCTCTT-TTTCTCT 592337 - i i - - -i - (TTCC)n#Simpl 651 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT-TC-CTTCCTTC-CT 697 chr6ptel1M 592338 T-CTTTCTT-TTTCCTTCC 592354 - i -i (TTCC)n#Simpl 698 TCCTTCCTTCCTTCCTTCC 716 Matrix = Unknown Transitions / transversions = 11.83 (71/6) Gap_init rate = 0.01 (10 / 711), avg. gap size = 1.00 (10 / 10) 214 30.58 5.94 2.88 chr6ptel1M 594417 594517 (405483) L2a_3end#LINE/L2 357 460 (57) m_b287s601i0 11617 chr6ptel1M 594417 TTTACCTATGTAAGTATTTACCATTCCTTTCCCCTCCCCCATGGAATATA 594466 i v vv i iii -- v i i v - i i L2a_3end#LINE 357 TTTACTTATTTATTTGTTTATTGT--CTGTCTCCCCCCAC-TAGAATGTA 403 chr6ptel1M 594467 AGCTTTTGGAGGGGAGGGTCTATTA---ATT---TTTATTTCTTTATCCT 594510 iivv v v v i---i --- i i v v i L2a_3end#LINE 404 AGCTCCATGAGGGCAGGGACTTTTGTCTGTTTTGTTCACTGCTGTATCCC 453 chr6ptel1M 594511 TAGCACC 594517 i i L2a_3end#LINE 454 CAGCGCC 460 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.90 CpG sites = 18, Kimura (unadjusted) = 40.67 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.05 (5 / 100), avg. gap size = 1.80 (9 / 5) 931 29.76 3.49 3.99 chr6ptel1M 595425 596054 (403946) C L1MC1_3end#LINE/L1 (447) 633 7 m_b287s551i0 11618 chr6ptel1M 595425 GCTCATTTCACTCAGTATCAGTTCGTGTAGGTCTC-TCCAGGCCTTTCTG 595473 iv i vi - v i v i i - v i --- C L1MC1_3end#LI 633 GCTTCTTTCACTTAGTAATA-TGCATTTAAGTTTCCTCCATGTCTTT--- 588 chr6ptel1M 595474 AAATCAT--CCTGTTGG-TCATTTCTTAC-AGAAC--AATAATATTCTAT 595517 --- -- i v i - vi- vi -- i C L1MC1_3end#LI 587 ---TCATGGCTTGATAGCTCATTTCTTTTTAGCGCTGAATAATATTCCAT 541 chr6ptel1M 595518 AATATTCATATACCACAATTTATTCAGCCATTCTCCAACTGATGGGCATC 595567 vi v vv i i i v v v v i C L1MC1_3end#LI 540 TGTCTGGATGTACCACAGTTTATTTATCCATTCACCTACTGAAGGACATC 491 chr6ptel1M 595568 C--ATTCAGTTTCCAGTTTCTAGCTATTACAAAAAGGGCTGCCACAAACA 595615 i--i -- i iv i i v ii v ii i i C L1MC1_3end#LI 490 TTGGTT--GCTTCCAAGTTTTGGCAATTATGAATAAAGCTGCTATAAACA 443 chr6ptel1M 595616 TTCGTGCACATACAGGTCCCTTTCCCTTC-----TTTATAATCTCTTTGG 595660 i ---- i iii v vivvv ----- vi iii C L1MC1_3end#LI 442 TCCGTG----TGCAGGTTTTTGTGTGGACATAAGTTTTCAACTCCTTTGG 397 chr6ptel1M 595661 GATATAATCCCA-GTAGTAACACTGCTAGATCAAAGGGTATGCACAGTTT 595709 - - v - v iivv i i iv v --- v v C L1MC1_3end#LI 396 G-TA-AATACCAAGGAGCGCGATTGCTGGATCGTATGGTA---AGAGTAT 352 chr6ptel1M 595710 GATAACTTTT-TGAGCATAGTTCCAAACTACTCTCCAGAATGGTTGGATT 595758 v v v - i v - v v iiii i i i v ii C L1MC1_3end#LI 351 GTTTAGTTTTGTAAGAA-ACTGCCAAACTGTCTTCCAAAGTGGCTGTACC 303 chr6ptel1M 595759 CGTTCACAACTCCACCAACAATGCATCAATGTCCCAGTTTTCCCGCATCC 595808 vv ii vii i v v iv i v vii i C L1MC1_3end#LI 302 ATTTTGCATTCCCACCAGCAATGAATGAGAGTTCCTGTTGCTCCACATCC 253 chr6ptel1M 595809 CCTCCAACAATCATCATTATT--TTTTCCTGTCATCTTAGCCACTCTGAC 595856 i v i v iivii i i-- v iv -- i i i i i C L1MC1_3end#LI 252 TCGCCAGCATTTGGTGTTGTCAGTGTTCTGG--ATTTTGGCCATTCTAAT 205 chr6ptel1M 595857 AAGTGTATAGTGGTATCTTAGAGTTGTCTTAATTTGCATTTCTCTGATTA 595906 i i i vv i i v C L1MC1_3end#LI 204 AGGTGTGTAGTGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGATGA 155 chr6ptel1M 595907 -ATAATGACTTGGAGCATCTTTTCATATGACTAGAAATAGTTTCAATTTC 595955 - - iv vi vvviivi i vv v C L1MC1_3end#LI 154 CATA-TGATGTGGAGCATCTTTTCATATGCTTATTTGCCATCTGTATATC 106 chr6ptel1M 595956 TTCATCTGAGAATTGTCTGTTCATATCCTTTGACCATTTTTCAATTGGAG 596005 v iv v iv ? vi i v v ? i -- C L1MC1_3end#LI 105 TTCTTTGGTGAGGTGTCTGTTNAGGTCTTTGGCCCATTTTTNAATCGG-- 58 chr6ptel1M 596006 AATGGCTTGATTTTTTATAAATTAGAGTTAA---TTCTCTATATATTTTG 596052 -i v i i v i viv v vv --- i i C L1MC1_3end#LI 57 -GTTGTTCGTTTTCTTATTGTTGAGTTTTAAGAGTTCTTTGTATATTTTG 9 chr6ptel1M 596053 GA 596054 C L1MC1_3end#LI 8 GA 7 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.56 CpG sites = 101, Kimura (unadjusted) = 38.96 Transitions / transversions = 1.28 (101/79) Gap_init rate = 0.06 (37 / 629), avg. gap size = 1.27 (47 / 37) 1451 27.78 0.36 1.66 chr6ptel1M 595506 596054 (403946) C L1ME3G_3end#LINE/L1 (376) 548 7 m_b287s551i1 11618 chr6ptel1M 595506 ATAATATTCTATAATATTCATATACCACAATTTATTCAGCCATTCTCCAA 595555 i i i vv i i i i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr6ptel1M 595556 CTGATGGGCATCCATTCAGTTTCCAGTTTCTAGCTATTACAAAAAGGGCT 595605 i i ii vviv i i v v iv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr6ptel1M 595606 GCCACAAACATTCGTGCACATACAGGTCCCTTTCC-CTTCTTT-ATAATC 595653 v ii i v i i ?-- i v v - v v vi- vv i C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATT 401 chr6ptel1M 595654 TCTTTGGGATATAATCCCAGTAGTAACACTGCTAGATCAAAGGGTATGCA 595703 ? i v v? ? v iiv i i i i C L1ME3G_3end#L 400 TCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCG 351 chr6ptel1M 595704 CAGTTTGATAACTTTTTGAGCATAGTTCCAAACTACTCTCCAGAATGGTT 595753 v i -- i vvv - v v i i i i ? i C L1ME3G_3end#L 350 CATTTTAA--ATTTTAATAG-ATACTGCCAAATTGCCCTCCAAAANGGCT 304 chr6ptel1M 595754 GGATTCGTTCACAACTCCACCAACAATGCATCAATGTCCCAGTTTTCCCG 595803 v iivi i vii i i i v iv v v i i C L1ME3G_3end#L 303 GTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCA 254 chr6ptel1M 595804 CATCCCCTCCAACAATCATCATTATTTTTTCCTGTCATCTTAGCCACTCT 595853 i i v v ?ivi ivv?iii vvv i v v C L1ME3G_3end#L 253 CACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATCT 204 chr6ptel1M 595854 GACAAGTGTATAGTGGTATCTTAGAGTTGTCTTAATTTGCATTTCTCTGA 595903 iii v v i i vv i i C L1ME3G_3end#L 203 GATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGA 154 chr6ptel1M 595904 TTAATAATGACTTGGAGCATCTTTTCATATGACTAGAAATAGTTTCAATT 595953 v i vv v vi vviiivi vv C L1ME3G_3end#L 153 TTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGTATT 104 chr6ptel1M 595954 TCTTCATCTGAGAATTGTCTGTTCATATCCTTTGACCATTTTTCAATTGG 596003 i v v i v v C L1ME3G_3end#L 103 TCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGG 54 chr6ptel1M 596004 AGAATGGCTTGATTTTTTATAAATTAGAGTTAATTCTCTATATATTTTGG 596053 iv-- v -- i vi v vivv i i i C L1ME3G_3end#L 53 GT--TGTCTT--TTTCTTATTGATTTGTAGGAGTTCTTTATATATTCTGG 8 chr6ptel1M 596054 A 596054 C L1ME3G_3end#L 7 A 7 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.27 CpG sites = 80, Kimura (unadjusted) = 35.86 Transitions / transversions = 1.14 (80/70) Gap_init rate = 0.02 (11 / 548), avg. gap size = 1.00 (11 / 11) 444 27.97 2.97 2.97 chr6ptel1M 595918 596186 (403814) C L1M3_orf2#LINE/L1 (7) 3281 3013 m_b287s551i2 11618 chr6ptel1M 595918 GAGCATCTTTTCATATGACTAGAAATAGTTTCAATTTCTTCATCTGAGAA 595967 iv ivviiivi vv v v iv C L1M3_orf2#LIN 3281 GAGCATCTTTTCATATACCTGTTGGCCATTTGTATGTCTTCTTTGGAGAA 3232 chr6ptel1M 595968 TTGTCTGTTCATATCCTTTGACCATTTTTCAATTGGAGAATGGCTTGATT 596017 v i vi v ? i ivv --- v C L1M3_orf2#LIN 3231 ATGTCTATTCAGGTCCTTTGCCCATTTTTNAATCGGGTTAT---TTGTTT 3185 chr6ptel1M 596018 TTTTATAAATTAGAGTT-----AATTCTCTATATATTTTGGAAATGAGGC 596062 ii-v - ----- i ii v v iv C L1M3_orf2#LIN 3184 TTTTGC-TATT-GAGTTGTANGAGTTCCTTATATATTTTGGATATTAACC 3137 chr6ptel1M 596063 CTTTATCAGAACCTTTGACTGTAAAAATATTTTCCCAGTTGATTGCTTCC 596112 i vviv v vi i v v i v ivi v v v C L1M3_orf2#LIN 3136 CCTTATCAGATATATGGTTTGCAAATATTTTCTCCCATTCCGTAGGTTGC 3087 chr6ptel1M 596113 CTTCTGATCTTGTCTGCATTAGTTTTGTT---TGTACAAAAACTTTTCAG 596159 i v iii - - - iv --- i i i i C L1M3_orf2#LIN 3086 CTTTTCACTCTGT-TG-ATT-GTTTCCTTTGCTGTGCAGAAGCTTTTTAG 3040 chr6ptel1M 596160 TTTGGTATAATCGAAATTTTCTATTTT 596186 i i i vv v v C L1M3_orf2#LIN 3039 TTTGATGTAGTCCCACTTGTCTATTTT 3013 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.37 CpG sites = 36, Kimura (unadjusted) = 35.54 Transitions / transversions = 0.97 (36/37) Gap_init rate = 0.04 (10 / 268), avg. gap size = 1.60 (16 / 10) 328 26.64 4.46 4.46 chr6ptel1M 596317 596540 (403460) C L1M5_orf2#LINE/L1 (456) 2838 2615 m_b287s551i3 11618 chr6ptel1M 596317 TTTCTGCCATATTAGTTTCCAATTTTCCCAGCAATTTTTATCAAACAGTA 596366 i v vii v v i viv i ii v vv C L1M5_orf2#LIN 2838 TTTTTTCCATATGGATATCCAATTGTTCCAGCACCATTTGTTGAAAAGAC 2789 chr6ptel1M 596367 AGTTCTTATCCCAAAAGCTGGGGT-CTTTGGG---TTTGTCAAAGACTAG 596412 vi i vi ---- iiv - ? v--- i ii i C L1M5_orf2#LIN 2788 TATCCTTTCCCCA----CTGAATTGCNTTGGCACCTTTGTCAAAAATCAA 2743 chr6ptel1M 596413 GTTGCTATATTTGT-TGACTGTTTTATCCCTTGAAC---CTAACCTATTC 596458 ? v? i v - --- v i ii - i --- vi i C L1M5_orf2#LIN 2742 NTGNCCATATATGTGTG---GGTCTATTTCT-GGACTCTCTATTCTGTTC 2697 chr6ptel1M 596459 CACTGATCAACTAATCTATTCCTTA-GCCAATACCAAATGGTTTTGGTAA 596507 i v i vi - - v iv i i v C L1M5_orf2#LIN 2696 CATTGATCTATTTGTCTAT-CCTTACGCCAATACCACACTGTCTTGATTA 2648 chr6ptel1M 596508 CTGCTGCTCTATAATATAATTTT-AGATCTGGTA 596540 iv i - i i - ? ? C L1M5_orf2#LIN 2647 CTGTAGCTTTATAATA-AGTCTTGANATCNGGTA 2615 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.80 CpG sites = 34, Kimura (unadjusted) = 34.80 Transitions / transversions = 1.48 (34/23) Gap_init rate = 0.07 (16 / 223), avg. gap size = 1.25 (20 / 16) 247 30.69 4.14 7.86 chr6ptel1M 596654 596798 (403202) L3#LINE/CR1 3547 3686 (413) m_b287s601i1 11619 chr6ptel1M 596654 GATAATAAACTCCCCATTTTTTTCTCTTAGTGAGGTCACATCTTGAGTAT 596703 i iv i v ii vi i v v -i v ii v L3#LINE/CR1 3547 GGTAATAGTCCCGCTGTACTCTGCGCT-GGTCAGACCACATCTGGAGTAT 3595 chr6ptel1M 596704 TG------ATTCTGGGTGTTGCCTTTAAGGAAGGACATTCATTGATAAGT 596747 ------i i iii v v i i ---- i ii L3#LINE/CR1 3596 TGCGTTCAGTTCTGGGCGCCACATTTTAAGAGGGA----CATTGACAAAC 3641 chr6ptel1M 596748 CAGAGCTTGCCACTAGCAGGATGATGGAGCAGGGAGTGTGGTAGGGTTTG 596797 ii -- vv i - - vv v iv - i- i L3#LINE/CR1 3642 TGGAGC--GCGTCCAG-AGGA-GAGCGACCAGGATG-GTGA-AGGGTCTG 3685 chr6ptel1M 596798 G 596798 L3#LINE/CR1 3686 G 3686 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.67 CpG sites = 26, Kimura (unadjusted) = 40.99 Transitions / transversions = 1.73 (26/15) Gap_init rate = 0.08 (12 / 144), avg. gap size = 1.42 (17 / 12) 289 36.46 9.85 1.36 chr6ptel1M 596784 596986 (403014) L3#LINE/CR1 3796 4015 (84) m_b287s601i2 11619 chr6ptel1M 596784 TGTGG--TAGGGTTTGGGTGCTTCTTTCATGTGATTACAGAAAGCAGAAT 596831 --v v i i-- v iii ii v ii i L3#LINE/CR1 3796 TGTGGAAGAGGGATTAGA--CTTATTCTGTGTGGCTCCAGAGGGCAGAAC 3843 chr6ptel1M 596832 TAAAATGAGTGGATAAATATTATGGGGAGATCATTTTTCATTTACTTTTA 596881 ii iv i i ii vi ii iiviv ivii i v v v L3#LINE/CR1 3844 TAGGACCAATGGGTGGAAGTTACAGGGAGGCAGATTTCGGCTCAATATAA 3893 chr6ptel1M 596882 --AAGAACATT---GGAAACA-AACTGCCCCCAAAATGAAAATGGCTTCC 596925 -- v ---iv v - i -i v i vv v L3#LINE/CR1 3894 GGAAGAACTTTCTAACAATCAGAGCTG-TCCAAAAATGGAATGGGCTGCC 3942 chr6ptel1M 596926 CTAGGAAG----GATTTTTCCATTTCTGGGAATATTC------ATGCTCC 596965 iii? i ---- vi ii i iv iii i ------ v vv L3#LINE/CR1 3943 TCGNGAGGTAGTGAGCTCCCCGTCACTGGAGGTGTTCAAGCAGAGGCTGG 3992 chr6ptel1M 596966 A--ACCACATGTTGGAGATGATG 596986 -- v ii i v L3#LINE/CR1 3993 ATGACCACTTGTCAGGGATGTTG 4015 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 50.34 CpG sites = 47, Kimura (unadjusted) = 53.76 Transitions / transversions = 1.81 (47/26) Gap_init rate = 0.05 (10 / 202), avg. gap size = 2.30 (23 / 10) 296 17.90 17.76 0.80 chr6ptel1M 597258 597304 (402696) MIRc#SINE/MIR 129 187 (81) m_b287s601i3 11620 chr6ptel1M 597258 TCCCTCATCTGTCAAAAGGGGATAAT-----CAGCTTT--CTGCCTCACA 597300 i v v ----- v ii -- i MIRc#SINE/MIR 129 TTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACA 178 chr6ptel1M 597301 GGAT----- 597304 i ----- MIRc#SINE/MIR 179 GGGTTGTTG 187 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 19.77 CpG sites = 11, Kimura (unadjusted) = 20.96 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.07 (3 / 46), avg. gap size = 4.00 (12 / 3) 26 0.00 8.33 0.00 chr6ptel1M 597305 597340 (402660) (TTTTG)n#Simple_repeat 1 39 (0) c_b287s251i0 11621 chr6ptel1M 597305 TTTTG-TTTG-TTTG-TTTGTTTTGTTTTGTTTTGTTTT 597340 - - - (TTTTG)n#Simp 1 TTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTT 39 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.09 (3 / 35), avg. gap size = 1.00 (3 / 3) 296 17.90 17.76 0.80 chr6ptel1M 597341 597399 (402601) MIRc#SINE/MIR 188 252 (16) m_b287s601i3 11620 chr6ptel1M 597341 AAGGATCAAAT--GATCCT-TA-ATGAAAGTGTCTTCCT--ACT-TCAAA 597383 i -- vv - -i i - iv -- - v i MIRc#SINE/MIR 188 GAGGATCAAATGAGATAATGTATGTGAAAGCG-CTTTGTAAACTGTAAAG 236 chr6ptel1M 597384 TGGTATATAAATGTAA 597399 v i MIRc#SINE/MIR 237 TGCTATACAAATGTAA 252 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 19.77 CpG sites = 11, Kimura (unadjusted) = 20.96 Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.10 (6 / 58), avg. gap size = 1.33 (8 / 6) 283 28.56 8.66 0.73 chr6ptel1M 597404 597530 (402470) L2d_3end#LINE/L2 372 508 (8) m_b287s601i4 11622 chr6ptel1M 597404 TGCTACTACTGTCCCCCTCATGGGGAATCTAACCCTCTTGTGGAGAGGGA 597453 i v vi i iv ivi - v v v ii v iv L2d_3end#LINE 372 TGTTAGTCTTGTCTCCCCAACTAG-ATTGTAAGCTCCTTGAGGGCAGGGA 420 chr6ptel1M 597454 ATGGGTCTTGTTCTTGTTTTTCAT--CCCATTGC------CACTGAGCTG 597495 viiv i v ?v ? i -- iv ------ v v L2d_3end#LINE 421 CCATGTCTTATACTNTTTTNTCGTTCCCCACAGCGCCTAGCACAGTGCTG 470 chr6ptel1M 597496 AGCAC--AGAAAGCACTCAA-AAATATTTGCTGAGTGA 597530 -- v i i - i i v L2d_3end#LINE 471 AGCACATAGTAGGCGCTCAATAAATACTTGTTGATTGA 508 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.66 CpG sites = 18, Kimura (unadjusted) = 37.16 Transitions / transversions = 1.00 (18/18) Gap_init rate = 0.04 (5 / 126), avg. gap size = 2.40 (12 / 5) 228 22.60 4.55 6.15 chr6ptel1M 598579 598644 (401356) MIRc#SINE/MIR 42 106 (162) m_b287s601i5 11623 chr6ptel1M 598579 TCAGGAAGACAT---TTCAGGCCCTGCCTCCTACCCTTAATTGCTAACTA 598625 v --- ii i i v - i --- v i i i MIRc#SINE/MIR 42 TCAGGAAGACCTGGGTTCGAGTCCCGGCTC-TGCC---ACTTACTAGCTG 87 chr6ptel1M 598626 TGTGACTTTGTGCAATTCA 598644 i v v MIRc#SINE/MIR 88 TGTGACCTTGGGCAAGTCA 106 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 23.16 CpG sites = 9, Kimura (unadjusted) = 27.58 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.08 (5 / 65), avg. gap size = 1.40 (7 / 5) 38 4.77 0.00 0.00 chr6ptel1M 598645 598688 (401312) (T)n#Simple_repeat 1 44 (0) c_b287s251i1 11624 chr6ptel1M 598645 TTTTCTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 598688 i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 44 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 22 17.52 0.00 0.00 chr6ptel1M 598704 598742 (401258) (T)n#Simple_repeat 1 39 (0) m_b287s252i1 11624 chr6ptel1M 598704 TTTTTTTTTCATTCCTTTCTTTTTTTTTTTTTTTTATTT 598742 iv ii i v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 39 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 345 25.52 21.38 0.00 chr6ptel1M 598749 598893 (401107) MIRc#SINE/MIR 93 268 (0) m_b287s601i6 11623 chr6ptel1M 598749 CTTTGTGCAATTCATTT--------TAAATCTCAATTCCTTTATCTG--- 598787 i v v i -------- i ii i i i i --- MIRc#SINE/MIR 93 CCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAA 142 chr6ptel1M 598788 ---GTAAACAACAA-----G---TGCCCAATTCAAAAGGTTGTTGTGAGT 598826 --- vii i i ----- --- i vi v i v MIRc#SINE/MIR 143 AATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGG 192 chr6ptel1M 598827 CTCAAAT------ATGTATAAGGAAGC---TTATAAACTTTAAAATGCTT 598867 v ------ iv i --- i v i v MIRc#SINE/MIR 193 ATCAAATGAGATAATGTATGTGAAAGCGCTTTGTAAACTGTAAAGTGCTA 242 chr6ptel1M 598868 TATAAATGCAAAATCTTATTGGTATT 598893 i i ii?v iv MIRc#SINE/MIR 243 TACAAATGTAAGGNGTTATTATTATT 268 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.71 CpG sites = 25, Kimura (unadjusted) = 32.71 Transitions / transversions = 2.08 (25/12) Gap_init rate = 0.05 (7 / 144), avg. gap size = 4.43 (31 / 7) 13 20.32 6.67 0.00 chr6ptel1M 598947 598991 (401009) (AAT)n#Simple_repeat 1 48 (0) m_b287s252i2 11625 chr6ptel1M 598947 AATAAGAAGAATTAT-GTGCTAATAATAAAAAT-ATAAT-ATTATAAT 598991 v v v -i iv v - - v (AAT)n#Simple 1 AATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAAT 48 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.07 (3 / 44), avg. gap size = 1.00 (3 / 3) 288 20.95 1.41 5.88 chr6ptel1M 599001 599071 (400929) C MIRb#SINE/MIR (11) 257 190 m_b287s601i7 11626 chr6ptel1M 599001 TATCATTAGTT-AGCACTTATATATGATGTGCCAGGTACTATGCTAAGTG 599049 i vi - i i----v i i i C MIRb#SINE/MIR 257 TACCATTTATTGAGCGCTTAC----TATGTGCCAGGCACTGTGCTAAGCG 212 chr6ptel1M 599050 CTTTACAGATATTATTTCTTTT 599071 vii i v C MIRb#SINE/MIR 211 CTTTACATGCATTATCTCATTT 190 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 21.33 CpG sites = 10, Kimura (unadjusted) = 25.35 Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.07 (5 / 70), avg. gap size = 1.00 (5 / 5) 12 3.81 11.11 0.00 chr6ptel1M 599176 599202 (400798) (TTCCC)n#Simple_repeat 1 30 (0) m_b287s252i3 11627 chr6ptel1M 599176 TTCCC-TCCCTTCCC--CCCATCCCTTCCC 599202 - -- v (TTCCC)n#Simp 1 TTCCCTTCCCTTCCCTTCCCTTCCCTTCCC 30 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.08 (2 / 26), avg. gap size = 1.50 (3 / 2) 15 29.72 0.00 0.00 chr6ptel1M 599289 599337 (400663) (AAA)n#Simple_repeat 1 49 (0) m_b287s252i5 11628 chr6ptel1M 599289 AAAAAAAAAAAACGAAAGAAAACAAAATGCAATCAAACAACAACAAAAA 599337 vi i v viv vv v v v (AAA)n#Simple 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 49 Matrix = Unknown Transitions / transversions = 0.33 (3/9) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 275 30.14 0.00 4.07 chr6ptel1M 599598 599725 (400275) C L1ME3E_3end#LINE/L1 (438) 551 429 m_b287s551i4 11629 chr6ptel1M 599598 ATAGTATTCCCTAACATTTATATCCCATAACTTAATTCAGCCATTCTCCA 599647 v vii vv v i i - i v v C L1ME3E_3end#L 551 ATAGTATTCCATTGTATGAATATACCACAATTTA-TTTATCCATTCTCCT 503 chr6ptel1M 599648 GCTGATGGGCATCCACTCCGTTTCCAGTTCCTTGCCACAACAAAAAGGGC 599697 ii i iiivvii ii i iv v iv C L1ME3E_3end#L 502 GTCGATGGACATTTGGGTTGTTTCCAGTTTTTTGCTATTACAAACAATGC 453 chr6ptel1M 599698 TGCCACATGTGAGGCTTTTTGCATATGT 599725 ---- i ivv i i i C L1ME3E_3end#L 452 TGC----TATGAACATTCTTGTACATGT 429 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.50 CpG sites = 23, Kimura (unadjusted) = 39.91 Transitions / transversions = 1.64 (23/14) Gap_init rate = 0.04 (5 / 127), avg. gap size = 1.00 (5 / 5) 880 22.22 2.36 2.36 chr6ptel1M 599760 599971 (400029) C MIRc#SINE/MIR (53) 215 4 m_b287s601i8 11630 chr6ptel1M 599760 TTACAAATATTATTTCATTTGATCCTCACAGCAGCCCAAGGAGTGAGG-- 599807 i v i i i i viv vv -- C MIRc#SINE/MIR 215 TCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCA 166 chr6ptel1M 599808 -GGCTATTATTATCATCCCCATTTTACAGAAGAGGAAACCAAAG--CAGA 599854 - viv i v ii i -- - C MIRc#SINE/MIR 165 GGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAG- 117 chr6ptel1M 599855 AGAGAGTTAAGTGACTTACCCAAGATCACAGAGCTAGTATGTGTGTGGGA 599904 - i i v v vvv i v C MIRc#SINE/MIR 116 AGAG-GTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGC 68 chr6ptel1M 599905 CTGGATTTGTACTCAGGTCCTCCTGACTCTGGGCCTGGTGCTCTTAAACA 599954 v i i v i i iii i ii -vv C MIRc#SINE/MIR 67 CGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTT-TCCA 19 chr6ptel1M 599955 CTTTGCCACCCCGTGCC 599971 vii v -- C MIRc#SINE/MIR 18 CTGCACCACAC--TGCC 4 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.08 CpG sites = 26, Kimura (unadjusted) = 26.74 Transitions / transversions = 1.30 (26/20) Gap_init rate = 0.04 (8 / 211), avg. gap size = 1.25 (10 / 8) 28 10.48 0.00 0.00 chr6ptel1M 600072 600112 (399888) (A)n#Simple_repeat 1 41 (0) m_b287s252i6 11631 chr6ptel1M 600072 AACAAGACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAA 600112 v i v i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 41 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 19 0.00 0.00 0.00 chr6ptel1M 600190 600210 (399790) (A)n#Simple_repeat 1 21 (0) m_b287s252i7 11632 chr6ptel1M 600190 AAAAAAAAAAAAAAAAAAAAA 600210 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAA 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 236 26.44 6.99 4.79 chr6ptel1M 601350 601492 (398508) C MIR#SINE/MIR (96) 166 21 m_b287s601i9 11626 chr6ptel1M 601350 TGGAGTGGCTCCTATTTTCTTCTCCCGCTCGTTGTACAGGCGAGGAAACT 601399 ii i v v --v v --- i v ii C MIR#SINE/MIR 166 TGAGGTAGGTACTATT--ATTATCCC---CATTTTACAGATGAGGAAACT 122 chr6ptel1M 601400 GAGGCACACAGA-GCTAAGTGACTTAGCC----TC-CG-AGATGGCAAGT 601442 v - i i iv ---- - i- v i i C MIR#SINE/MIR 121 GAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGT 72 chr6ptel1M 601443 GTCTGAAGCCGG--CTCG-TCCTAGATCTCCTTGGCTCTAGGACCGGGGC 601489 v v - --i -v i iivvi - i ii v v C MIR#SINE/MIR 71 GGCAG-AGCCGGGATTCGAACCCAGGCAGTC-TGGCTCCAGAGCCCGTGC 24 chr6ptel1M 601490 TTT 601492 i C MIR#SINE/MIR 23 TCT 21 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.39 CpG sites = 21, Kimura (unadjusted) = 33.39 Transitions / transversions = 1.40 (21/15) Gap_init rate = 0.09 (13 / 142), avg. gap size = 1.31 (17 / 13) 225 25.70 10.14 4.11 chr6ptel1M 601373 601510 (398490) C MIR3#SINE/MIR (59) 149 4 m_b287s601i10 11626 chr6ptel1M 601373 CCCGCTCGTTGTACAGGCGAGGAAACTGAGGCACACAGAGCT-AAGTGAC 601421 v i v ii v v v - C MIR3#SINE/MIR 149 CCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGAC 100 chr6ptel1M 601422 TTAGCCTCCGAGATGGCA---------AGTGTCTGAAGCCGG--CTCG-T 601459 - -- i i vi --------- v v - -- v -v C MIR3#SINE/MIR 99 TT-GC--CCAAGGTCACACAGCNAGTTAGTGGCAG-AGCCGGGACTAGAA 54 chr6ptel1M 601460 CCTAGATCTCCTTGGCTCTAGGACCGGGGCTTTCCCCATTT-GCTTCCTT 601508 i i - i ivi v - v i i iii i- iv ii C MIR3#SINE/MIR 53 CCCAGGTCTCC-TGACTCCCAGTCC-GTGCTCTCTCTGCTCAGCCACTCT 6 chr6ptel1M 601509 GC 601510 C MIR3#SINE/MIR 5 GC 4 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.26 CpG sites = 20, Kimura (unadjusted) = 32.26 Transitions / transversions = 1.43 (20/14) Gap_init rate = 0.08 (11 / 137), avg. gap size = 1.82 (20 / 11) 328 25.39 8.13 0.76 chr6ptel1M 601377 601499 (398501) C MIRc#SINE/MIR (120) 148 17 m_b287s601i11 11626 chr6ptel1M 601377 CTCGTTGTACAGGCGAGGAAACTGAGGCACACAGA-GCTAAGTGACTTAG 601425 i i v ii v v - i iv C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr6ptel1M 601426 CC----TC-CG-AGATGGCAAGTGTCTGAAGCCGG--CTCG-TCCTAGAT 601466 ---- - i- v i i v v - -- -v i i C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAG-AGCCGGGACTCGAACCCAGGT 50 chr6ptel1M 601467 CTCCTTGGCTCTAGGACCGGGGCTTTCCCCATT 601499 i i i i i v i v i ii i C MIRc#SINE/MIR 49 CTTCCTGACTCCAAGTCCAGTGCTCTTTCCACT 17 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.25 CpG sites = 21, Kimura (unadjusted) = 32.25 Transitions / transversions = 2.10 (21/10) Gap_init rate = 0.06 (7 / 122), avg. gap size = 1.57 (11 / 7) 829 5.22 1.03 2.08 chr6ptel1M 601869 602939 (397061) (CCTT)n#Simple_repeat 1 1060 (0) c_b287s251i2 11633 chr6ptel1M 601869 CCTTCCTTCCCTCCCTTCCTTCCTTCCCTCCCTCTCTCCCTCTCCCTTCC 601918 - i i i - i - - (CCTT)n#Simpl 1 CCTTCCTT-CCTTCCTTCCTTCCTTCCTTCCTTC-CTTCCT-T-CCTTCC 46 chr6ptel1M 601919 TTCCTTCCTTCCTTCCTTCCTTCCTCCCTCCCTTCTTTCCTTCCTTCCTT 601968 i i i (CCTT)n#Simpl 47 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 96 chr6ptel1M 601969 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 602018 (CCTT)n#Simpl 97 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 146 chr6ptel1M 602019 TTCCTTCCTTCCTTCCTTCCTCCCTCCCTCCCTTCCTTCCTTCC-TCCTT 602067 i i i - (CCTT)n#Simpl 147 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 196 chr6ptel1M 602068 CTCTCCCTTCTTTCCTTCCTTCCTTCTCTCCCTTCCTTCCTTCCTTCCTT 602117 - i i - i (CCTT)n#Simpl 197 C-CTTCCTTCCTTCCTTCCTTCCTTC-CTTCCTTCCTTCCTTCCTTCCTT 244 chr6ptel1M 602118 -CTCTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT-C-TCCTTC 602164 - - - - (CCTT)n#Simpl 245 CCT-TCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC 293 chr6ptel1M 602165 CTTCCTTCCTTCCTTCCTTCCCTCCCTCCCTTCCTTCCTTCTTTCCTTCC 602214 - i i i (CCTT)n#Simpl 294 CTTCCTTCCTTCCTTCCTT-CCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 342 chr6ptel1M 602215 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 602264 (CCTT)n#Simpl 343 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 392 chr6ptel1M 602265 CCTTCCTTCCCTTCCTCCCTCCCTTCCTTCCTTCCTCCCTTCTCTCCCTT 602314 - i i i - i (CCTT)n#Simpl 393 CCTTCCTT-CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC-CTTCCTT 440 chr6ptel1M 602315 CTTTCCTTCCTTCCTTCTCTCCCTTCCTTCCTTCCTTCCTTCTCTCCCCT 602364 i - i - -i (CCTT)n#Simpl 441 CCTTCCTTCCTTCCTTC-CTTCCTTCCTTCCTTCCTTCCTTC-CT-TCCT 487 chr6ptel1M 602365 TCCTTCCTTCCTTCCCTTCCCTTCCTTCCTTCTCTCCCTTCCTTCCTTCC 602414 - - - i (CCTT)n#Simpl 488 TCCTTCCTTCCTT-CCTT-CCTTCCTTCCTTC-CTTCCTTCCTTCCTTCC 534 chr6ptel1M 602415 TTCCTTCTCTCCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT 602464 - i (CCTT)n#Simpl 535 TTCCTTC-CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT 583 chr6ptel1M 602465 TCCTTCCTTCCTTCTCTCCCTTCCTTCCTTCCTTCCTTCCCTTCCCTCCC 602514 - i - - i (CCTT)n#Simpl 584 TCCTTCCTTCCTTC-CTTCCTTCCTTCCTTCCTTCCTT-CCTT-CCTTCC 630 chr6ptel1M 602515 TCCCTTCCTTCCTTCTTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 602564 i i (CCTT)n#Simpl 631 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 680 chr6ptel1M 602565 CCTTCCTTCCTTCCCTCCTCCCTCCCTCCCTTCC-TCCCTCCTTCCTTCC 602613 i i i i - i (CCTT)n#Simpl 681 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 730 chr6ptel1M 602614 TTCCTTCTTTCCTTCCTTCCTTCTTTCCTTTCCTTCCTTCCTTCCTTCTT 602663 i i - i (CCTT)n#Simpl 731 TTCCTTCCTTCCTTCCTTCCTTCCTTCC-TTCCTTCCTTCCTTCCTTCCT 779 chr6ptel1M 602664 TCCTT--TTCCTTCCTTCCTTCTTTCCTTCCTTCCTTCCTTCCTTCTTTC 602711 -- i i (CCTT)n#Simpl 780 TCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC 829 chr6ptel1M 602712 CTTCCTTCCTTCTTTCTTTCTTTCCTTCCTTCCTTCCTTCCTTCTTTCCT 602761 i i i i (CCTT)n#Simpl 830 CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT 879 chr6ptel1M 602762 TCCTTCCTT-CTT-CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC 602809 - - (CCTT)n#Simpl 880 TCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC 929 chr6ptel1M 602810 CTTCCTTCCTTCCTTCCTTCCTTCCTTCTTTCCTTCCTTCCTTCCTTCCT 602859 i (CCTT)n#Simpl 930 CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT 979 chr6ptel1M 602860 TCCTTCCTTCCTTCCTTCCTTCCTCCCTCCCTCCCTCCCTTCCTTCCTT- 602908 i i i i - (CCTT)n#Simpl 980 TCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC 1029 chr6ptel1M 602909 -TTCCCTCCCTCCCTCCCTTCCTTCCTTCCTT 602939 - - i i i (CCTT)n#Simpl 1030 CTT-CCTTCCTTCCTTCCTTCCTTCCTTCCTT 1060 Matrix = Unknown Transitions / transversions = 1.00 (51/0) Gap_init rate = 0.03 (32 / 1070), avg. gap size = 1.03 (33 / 32) 191 31.98 0.30 1.38 chr6ptel1M 602942 603600 (396400) (TC)n#Simple_repeat 1 652 (0) m_b287s252i8 11634 chr6ptel1M 602942 TCTCTCTCTCTCTGTTTCTCTGTGTGTCTCTGTTTCTGTTAATCTCTGTC 602991 v i v v v v i v ivv v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr6ptel1M 602992 TATCTTTCTGTCTGTCTCTTTCTGTCTGTCAGTCTCTGTCTCTCTCACAC 603041 v i v v i v v vv v v v (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chr6ptel1M 603042 TTTCTCTGTGTATCTGTCTCTGTCTCTATCGCACTGTTTCTCTGTGTGTC 603091 i v v v v v v v v v i v v v (TC)n#Simple_ 101 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 150 chr6ptel1M 603092 TGTCTCTGTCAATCTCTGTGTGTCTGTTTCTGTCTCTCTCTCACACACAC 603141 v v vv v v v v i v v v v v (TC)n#Simple_ 151 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 200 chr6ptel1M 603142 TTTCTCTCTGTGTATCTCTCCGTCTCTGTCAATCTCTCTCTATCTCTTTG 603191 i v v v iv v vv v i v (TC)n#Simple_ 201 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 250 chr6ptel1M 603192 TCTCTGTCTCTCTGCCTCTCACACACATACTTTGTGTGTGTCTCTCTGGC 603241 v vi v v v - - i v v v v vv (TC)n#Simple_ 251 TCTCTCTCTCTCTCTCTCTCTCTCTC-T-CTCTCTCTCTCTCTCTCTCTC 298 chr6ptel1M 603242 TCTGTCTTTCTCTCTCACACACTCTCTGTGTATGTGTCTCTTTTTCTATC 603291 v i v v v v v v v v i i v (TC)n#Simple_ 299 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 348 chr6ptel1M 603292 TCACTGTTTCTCGGTGTATCTGTCTCTGTCTCTATATCTCTCTTTCTCTG 603341 v v i vv v v v v v v i v (TC)n#Simple_ 349 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 398 chr6ptel1M 603342 TGTCTCTCTGTCTCTGTCTGTCTGTCTCTCTCTCAAATACACATGCTTTC 603391 v v v v v -vv - v - - i (TC)n#Simple_ 399 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TCT-CTC-T-CTCTC 444 chr6ptel1M 603392 TCATTCTGTGTGTCTCTCTGTCTCTGTCGAACTCTCTATCTCTCTGTCTG 603441 vi v v v v v vvv v v v (TC)n#Simple_ 445 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 494 chr6ptel1M 603442 TCTCTGTCTCTTTCTCACATACACACTTTGTGTGTGTCTGTCTGTCTCTG 603491 v i v - - v v i v v v v v v v (TC)n#Simple_ 495 TCTCTCTCTCTCTCTCTC-T-CTCTCTCTCTCTCTCTCTCTCTCTCTCTC 542 chr6ptel1M 603492 TCAATTTTTGTCTCTCTCTCAGTCTCTGTGTGTCTCTGTCTCTCTCTGTG 603541 vv i i v vv v v v v v v (TC)n#Simple_ 543 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 592 chr6ptel1M 603542 TGGTC-CTCTGGCTC-CTCTCTGACTCTATGTCTCTGTCCCGGTCTCCCT 603589 -v - vv - vv v v v i vv i (TC)n#Simple_ 593 T-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 641 chr6ptel1M 603590 CCCTGTCCCTC 603600 i v i (TC)n#Simple_ 642 CTCTCTCTCTC 652 Matrix = Unknown Transitions / transversions = 0.20 (28/138) Gap_init rate = 0.02 (11 / 658), avg. gap size = 1.00 (11 / 11) 199 32.32 6.54 4.59 chr6ptel1M 603710 603816 (396184) C L2d2_3end#LINE/L2 (33) 522 414 m_b287s601i12 11635 chr6ptel1M 603710 TATCATGTAGCAGACATCTTGCTA--TACTGCGAGGT-TACAGGGAA--- 603753 iii ivv i iiv --ii i i v- ii --- C L2d2_3end#LIN 522 TACTGTGTGCAAGGCACTGTGCTAGGCGCTGTGGGGGATACAAAGAAGTA 473 chr6ptel1M 603754 -AAGCCAAAGCAGCCCCTGACCTCAAGGAACTAACTTTCTAATGGGGTAA 603802 - v ---ii i v i v vv i v v i C L2d2_3end#LIN 472 TAAGACA---TGGTCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGGAG 426 chr6ptel1M 603803 ATAACAGACACAGA 603816 i -- i i C L2d2_3end#LIN 425 ACA--AGACATAAA 414 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.73 CpG sites = 22, Kimura (unadjusted) = 44.81 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.08 (9 / 106), avg. gap size = 1.33 (12 / 9) 225 31.32 1.19 1.19 chr6ptel1M 603827 603910 (396090) L2d2_3end#LINE/L2 203 286 (269) m_b287s601i13 11636 chr6ptel1M 603827 CCTTCAAGGCTCTGCTCATGCACCGTCTGCTGGGAAAAGCCTTTTCTG-C 603875 i v vii? ii v vv vi ii - L2d2_3end#LIN 203 CCTTCAAGGCCCAGCTCAAATNCCACCTCCTCCGTGAAGCCTTCCCTGAC 252 chr6ptel1M 603876 TGCCTCAGCAAGGAGTGCTCCCTGCCTTTTTCTAA 603910 ii ii vv ? v i - i ii i L2d2_3end#LIN 253 CACTCCAGCCCGNAGTGATCTCT-CCCTCCTCTGA 286 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.13 CpG sites = 17, Kimura (unadjusted) = 44.13 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.02 (2 / 83), avg. gap size = 1.00 (2 / 2) 216 25.73 7.35 2.82 chr6ptel1M 604361 604428 (395572) MIRc#SINE/MIR 2 72 (196) m_b287s601i14 11637 chr6ptel1M 604361 GAGGCAAGATGTGGCACAATGGAAAGAACGCTGGATCTGGAT---GGTGG 604407 i-- ii i i i ii v--- vi MIRc#SINE/MIR 2 GAGGCAG--TGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAG 49 chr6ptel1M 604408 --CTGGGCTCATTTCCTGACTCT 604428 -- i ivv i i MIRc#SINE/MIR 50 ACCTGGGTTCGAGTCCCGGCTCT 72 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.77 CpG sites = 13, Kimura (unadjusted) = 33.54 Transitions / transversions = 3.25 (13/4) Gap_init rate = 0.06 (4 / 67), avg. gap size = 1.75 (7 / 4) 210 31.48 8.33 0.00 chr6ptel1M 604865 604972 (395028) L2d_3end#LINE/L2 203 319 (197) m_b287s601i16 11638 chr6ptel1M 604865 CCTTCAAGGCTCTGCTCATGCACCATCTGCTGGGAAAAGCCTTTCCTTCT 604914 i v v iv i v vvivi i vvi L2d_3end#LINE 203 CCTTCAAGGCCCAGCTCAAGTCCCACCTCCTCCACGAAGCCTTCCCTGAC 252 chr6ptel1M 604915 CCCT-CAGCAAGGAGTGCTCTCTACC-TCTTGGAAT-------GCCCTTA 604955 v - vviv v v v - iv i------- v L2d_3end#LINE 253 CACTCCAGCCCACACTGATCTCTCCCTTCTCTGAACTCCTATAGCACTTA 302 chr6ptel1M 604956 TAGCCCATAGAATGCAA 604972 i ii vv i L2d_3end#LINE 303 TAGTCTGTACCACGCAA 319 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.04 CpG sites = 14, Kimura (unadjusted) = 40.95 Transitions / transversions = 0.70 (14/20) Gap_init rate = 0.03 (3 / 107), avg. gap size = 3.00 (9 / 3) 257 25.80 2.11 2.11 chr6ptel1M 604865 604959 (395041) L2d2_3end#LINE/L2 203 297 (258) m_b287s601i15 11638 chr6ptel1M 604865 CCTTCAAGGCTCTGCTCATGCACCATCTGCTGGGAAAAGCCTTTCCTTCT 604914 i v vii? i v vv vi i vvi L2d2_3end#LIN 203 CCTTCAAGGCCCAGCTCAAATNCCACCTCCTCCGTGAAGCCTTCCCTGAC 252 chr6ptel1M 604915 CCCT-CAGCAAGGAGTGCTCTCTACCTCTTG-GAATGCCCTTATAGC 604959 v - vv ? v v i v- -- i i L2d2_3end#LIN 253 CACTCCAGCCCGNAGTGATCTCTCCCTCCTCTGAA--CTCCTATAGC 297 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.58 CpG sites = 10, Kimura (unadjusted) = 32.58 Transitions / transversions = 0.71 (10/14) Gap_init rate = 0.04 (4 / 94), avg. gap size = 1.00 (4 / 4) 358 30.70 4.39 0.00 chr6ptel1M 604959 605072 (394928) L2a_3end#LINE/L2 390 508 (9) m_b287s601i17 11639 chr6ptel1M 604959 CCCA-TAGAATGCAAGCTCCTGGAAGGCAGGAAACTTTCTCAATTTTGTT 605007 - i vv i i vi v vi L2a_3end#LINE 390 CCCACTAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTCTGTTTTGTT 439 chr6ptel1M 605008 T----TTGCATCCCTGGGATACAGAATTGTTTCTTGCACGCGGTAGGAGC 605053 i----i i ii viivi iv vi v iii v L2a_3end#LINE 440 CACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGGCGC 489 chr6ptel1M 605054 TTCACAACTCCTTGTTGAA 605072 iv i v vi L2a_3end#LINE 490 TCAATAAATATTTGTTGAA 508 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.31 CpG sites = 21, Kimura (unadjusted) = 40.83 Transitions / transversions = 1.50 (21/14) Gap_init rate = 0.02 (2 / 113), avg. gap size = 2.50 (5 / 2) 304 33.75 2.22 7.81 chr6ptel1M 605120 605254 (394746) C MIRc#SINE/MIR (139) 129 2 m_b287s601i18 11640 chr6ptel1M 605120 AACAAAAGCTCAGAGAGGATAAAAAGACTTGAA-GAGGACATGTAACTGA 605168 vi i v iv- vv-i v iii i ii C MIRc#SINE/MIR 129 AACTGAGGCTCAGAGAGGTTAAGT-GACTTGCCCAAGGTCACACAGCTAG 81 chr6ptel1M 605169 TAGGTTAGGGCTCCTAGGGAGCCAAGATTCAGAATGGGGTCTTTGTGACT 605218 i --- ------i ii i ii vivi iv C MIRc#SINE/MIR 80 TAAGT---GGC------AGAGCCGGGACTCGAACCCAGGTCTTCCTGACT 40 chr6ptel1M 605219 C--AGTCTGAGGTTCCTTCTATAACACCATACTATCTC 605254 -- iiiv i i i ivi i ii C MIRc#SINE/MIR 39 CCAAGTCCAGTGCTCTTTCCACTGCACCACACTGCCTC 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.35 CpG sites = 31, Kimura (unadjusted) = 48.69 Transitions / transversions = 2.82 (31/11) Gap_init rate = 0.09 (12 / 134), avg. gap size = 1.08 (13 / 12) 489 29.69 3.61 0.58 chr6ptel1M 605260 605425 (394575) C MIR3#SINE/MIR (11) 197 27 m_b287s601i19 11641 chr6ptel1M 605260 TCGTAGGAT-TAAGAGCTGAAAGGGACTGTTGAAATAATTTAGTTCAACC 605308 i i - v i iv v i v i i C MIR3#SINE/MIR 197 TCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACC 148 chr6ptel1M 605309 CATTCTTTTTCTTGTTGAGGAAGCTGAAGCCCAG-GAGTT---GTCTTTT 605354 vi v viv v i i - v --- vvi C MIR3#SINE/MIR 147 CCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTT 98 chr6ptel1M 605355 GTCTGGTTTTACCAAGGTGGTAAGTAGCAGAGCCCGAATTCAAGCCCCTG 605404 i iiivv i vv v?i v i v i i vi i vv C MIR3#SINE/MIR 97 GCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGG 48 chr6ptel1M 605405 CCT-CTGATTCCAAATCCAGTG 605425 i - i v i - C MIR3#SINE/MIR 47 TCTCCTGACTCCCAGTCC-GTG 27 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.79 CpG sites = 26, Kimura (unadjusted) = 38.79 Transitions / transversions = 1.13 (26/23) Gap_init rate = 0.03 (5 / 165), avg. gap size = 1.40 (7 / 5) 331 28.87 14.88 1.05 chr6ptel1M 605423 605590 (394410) MIRc#SINE/MIR 10 200 (68) m_b287s601i20 11642 chr6ptel1M 605423 GTGGTGC--TGGGAAAAGCCCCTGA---GGAGTC---------TTGGTTT 605458 -- i i v iv --- --------- v i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr6ptel1M 605459 GCGTTGGAGTTCTGCCAC---------GAGTGACTTTGACCAAAATCACT 605499 v ivvi i --------- v i iv i- MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAG-TCACT 108 chr6ptel1M 605500 TT-CTTCTCTGA-CCTCGGTTCCCTACTGGGTGGGATGACCATGACAATC 605547 v- i - i i vv vv iii ivv i i v MIRc#SINE/MIR 109 TAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATA 158 chr6ptel1M 605548 CTTGCTCGATCTATCCCACAAGGTTGTTGGTGGGAAGAAAGTG 605590 i i vii i i i - i i vv i MIRc#SINE/MIR 159 CCTGCCCTGCCTACCTCACAGGGTTGTT-GTGAGGATCAAATG 200 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.68 CpG sites = 29, Kimura (unadjusted) = 37.67 Transitions / transversions = 1.53 (29/19) Gap_init rate = 0.05 (8 / 167), avg. gap size = 3.38 (27 / 8) 23 11.27 1.85 5.77 chr6ptel1M 606127 606180 (393820) (TAAAAA)n#Simple_repeat 1 52 (0) m_b287s252i9 11643 chr6ptel1M 606127 TAAAAATAAATATAACATAAGTACAAATAAAAATAATAATCACAA-AAAA 606175 v - - - v v v v - (TAAAAA)n#Sim 1 TAAAAATAAAAATAA-A-AA-TAAAAATAAAAATAAAAATAAAAATAAAA 47 chr6ptel1M 606176 ATAAA 606180 (TAAAAA)n#Sim 48 ATAAA 52 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.08 (4 / 53), avg. gap size = 1.00 (4 / 4) 286 34.90 5.10 3.52 chr6ptel1M 606527 606722 (393278) L2#LINE/L2 2817 3015 (67) m_b287s601i21 11644 chr6ptel1M 606527 TCTGACCATGTTACCCC-CTACTCAATAAACCC---AGCAGCTCCCAGTT 606572 v i i i - i -- --- iii i vi i L2#LINE/L2 2817 TCAGATCATGTCACTCCTCTGCTCAA--AACCCTCCAATGGCTTCCCATC 2864 chr6ptel1M 606573 GCTTCCAGAATTAAACCTAAAACCCTCTACTGGGGTTTTTAAAGGCCTTC 606622 v vii i v v i ii - viv ii vi i v v L2#LINE/L2 2865 TCACTCAGAGTAAAAGCCAAAGTCCT-TACAATGGCCTACAAGGCCCTAC 2913 chr6ptel1M 606623 ACAACTCAGGTTCTTCCTC-TCTTTCTAGTCTTCTTACATGTTAGTACTT 606671 ii - v i ii v i-i i iii iv i--- vi vi i L2#LINE/L2 2914 ATGA-TCTGGTCCCCCGTTACCTCTCTGACCTCATC---TCCTACCACTC 2959 chr6ptel1M 606672 TCCGTGT-ACTC-TTATAATTCAGCAACTCTGGCCTCCTTGTTGTTCC-- 606717 viv -i -i viiv i v v i -- L2#LINE/L2 2960 TCCCCCTCGCTCACTCCGCTCCAGCCACACTGGCCTCCTTGCTGTTCCTC 3009 chr6ptel1M 606718 -AACAC 606722 - L2#LINE/L2 3010 GAACAC 3015 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 47.89 CpG sites = 44, Kimura (unadjusted) = 50.24 Transitions / transversions = 2.00 (44/22) Gap_init rate = 0.07 (14 / 195), avg. gap size = 1.21 (17 / 14) 230 30.57 10.58 4.07 chr6ptel1M 606639 606846 (393154) L2b_3end#LINE/L2 19 239 (227) m_b287s601i22 11644 chr6ptel1M 606639 CTCTCTTTCTAGTCTTCTTACATGTTAGTACTTTCCGTGTACTC-TTATA 606687 vi i ii i iv i--- vi vi i viv i -i v i L2b_3end#LINE 19 CTACCTCTCCGGCCTCATC---TCCTACCACTCTCCCCTTGCTCACTCTG 65 chr6ptel1M 606688 ATTCAGCAACTCTGGCCTCCTTGTTGTTCC---AACACA--ACTCTGTCT 606732 v i v v i --- i-- ?v v? L2b_3end#LINE 66 CTCCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACACGCCANGCTCNCT 115 chr6ptel1M 606733 GTTGCCT--GTGCC----------CTCTCCCATC--CCAGAAACAC--TT 606766 vii -- v ---------- v i v -- v i i -- L2b_3end#LINE 116 CCCGCCTCAGGGCCTTTGCACNTGCTGTTCCCTCTGCCTGGAACGCCCTT 165 chr6ptel1M 606767 CTCCTCCTCTGCCACTTGTTCTCTTGACTTCTCTTCTTTCCTTCAAGACT 606816 i v -i i i vi ----i i vi v - i v L2b_3end#LINE 166 CCCCACCTCT-TCGCCTGGCC----AACTCCTACTCAT-CCTTCAGGTCT 209 chr6ptel1M 606817 CAGTTCAAATCCCACCTACTGCCAGAAGTC 606846 i vi v v vi i L2b_3end#LINE 210 CAGCTCAAATGTCACCTCCTCCGGGAAGCC 239 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.71 CpG sites = 35, Kimura (unadjusted) = 41.07 Transitions / transversions = 1.35 (35/26) Gap_init rate = 0.08 (16 / 207), avg. gap size = 1.94 (31 / 16) 26 17.36 0.00 3.70 chr6ptel1M 606907 606962 (393038) (TA)n#Simple_repeat 1 54 (0) m_b287s252i10 11645 chr6ptel1M 606907 TATACATATATGTGTAAAGTGAGATATATATTTGTGTATATATATATATA 606956 i i i v - - v v i i (TA)n#Simple_ 1 TATATATATATATATATA-T-ATATATATATATATATATATATATATATA 48 chr6ptel1M 606957 TATATA 606962 (TA)n#Simple_ 49 TATATA 54 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.04 (2 / 55), avg. gap size = 1.00 (2 / 2) 40 0.00 0.00 0.00 chr6ptel1M 606964 606997 (393003) (AG)n#Simple_repeat 1 34 (0) c_b287s251i3 11646 chr6ptel1M 606964 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 606997 (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 34 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 409 27.82 6.90 0.81 chr6ptel1M 607024 607139 (392861) L2d2_3end#LINE/L2 425 547 (8) m_b287s601i23 11638 chr6ptel1M 607024 TCTCCCCTATTAGAATGGAAGCTCTTTAAGAACAGACACCATG------- 607066 v i v v i i ii iv ------- L2d2_3end#LIN 425 TCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATA 474 chr6ptel1M 607067 CTTTTTTGCCTTTCTT-CAACCCTTAGCCCAGCTCCTGGCATATATTAAG 607115 i iv ii ii- i v i v iv v i i v i L2d2_3end#LIN 475 CTTCTTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAGTAGG 524 chr6ptel1M 607116 TGCTTAATAAATGTTTCATTGATT 607139 i i i -i L2d2_3end#LIN 525 CGCTCAATAAATATTT-GTTGATT 547 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.03 CpG sites = 22, Kimura (unadjusted) = 36.48 Transitions / transversions = 2.20 (22/10) Gap_init rate = 0.03 (3 / 115), avg. gap size = 3.00 (9 / 3) 264 30.00 1.43 0.00 chr6ptel1M 607202 607271 (392729) MIRc#SINE/MIR 3 73 (195) m_b287s601i24 11647 chr6ptel1M 607202 AAGCAGTGTGGGAAACTCTGAAGAACATGGAAATTGGAATCAAGAA-ACC 607250 i viv v vvi i iv i v i i - MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chr6ptel1M 607251 TGGGTTCAAATCCCAAATTTG 607271 i i iiv i MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTG 73 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.97 CpG sites = 13, Kimura (unadjusted) = 39.74 Transitions / transversions = 1.62 (13/8) Gap_init rate = 0.01 (1 / 69), avg. gap size = 1.00 (1 / 1) 309 28.08 1.79 4.59 chr6ptel1M 607267 607378 (392622) MIRc#SINE/MIR 34 142 (126) m_b287s601i25 11648 chr6ptel1M 607267 ATTTGGATACAG-AGGACCTGGGTTCAAATTTCTGCTTTGGCAGTTATGA 607315 i vv - i i i ii v i v v iv MIRc#SINE/MIR 34 ACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTA 83 chr6ptel1M 607316 CCTTTATGTAAACTTTAGCAAATCAGTTCTTTTGCTGTATGTATCTTAGT 607365 v -- i i v vi i --- vvv v v vii i MIRc#SINE/MIR 84 GC--TGTGTGACCTTGGGCAAGTCA---CTTAACCTCTCTGAGCCTCAGT 128 chr6ptel1M 607366 TT-CTCATCTGTAA 607378 - MIRc#SINE/MIR 129 TTCCTCATCTGTAA 142 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.08 CpG sites = 15, Kimura (unadjusted) = 35.51 Transitions / transversions = 1.00 (15/15) Gap_init rate = 0.06 (7 / 111), avg. gap size = 1.00 (7 / 7) 313 27.34 2.42 8.55 chr6ptel1M 607376 607499 (392501) MIR1_Amn#SINE/MIR 111 227 (3) m_b287s601i27 11649 chr6ptel1M 607376 TAACCTCTGTGAACCTCAGTTTCCCTATGTGTAAAATGGAAACAACAATA 607425 ? v ?i ii v ii i ii MIR1_Amn#SINE 111 TNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATGATA 160 chr6ptel1M 607426 -TCATCAACCTTACAGAACTATTGTGAGAATAAAATAAAATATTTAT--A 607472 - v i vv i ii - v ii v vi--------- i v -- MIR1_Amn#SINE 161 CTGACCTCCTTTGTA-AAGTGCTTTGAGATC---------TACTGATGAA 200 chr6ptel1M 607473 AAGTACTGTATAAAAGCTAGCTGTTAT 607499 i ii i v i MIR1_Amn#SINE 201 AAGTGCTACATAAGAGCTAGGTATTAT 227 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.13 CpG sites = 21, Kimura (unadjusted) = 36.13 Transitions / transversions = 2.10 (21/10) Gap_init rate = 0.10 (12 / 123), avg. gap size = 1.08 (13 / 12) 425 23.76 2.88 2.88 chr6ptel1M 607376 607479 (392521) MIRb#SINE/MIR 112 215 (53) m_b287s601i26 11649 chr6ptel1M 607376 TAACCTCTGTGAACCTCAGTTTCCCTATGTGTAAAATGGAAACAACAATA 607425 v i ii v ii i i MIRb#SINE/MIR 112 TAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATA 161 chr6ptel1M 607426 TCATCAACCTTACAGAACTATTGTGAGAATAAAATAAAATATT---TATA 607472 i - -- ii iii i i v i i v --- i MIRb#SINE/MIR 162 CC-T--ACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTA 208 chr6ptel1M 607473 AAGTACT 607479 ii MIRb#SINE/MIR 209 AAGCGCT 215 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.28 CpG sites = 20, Kimura (unadjusted) = 30.67 Transitions / transversions = 5.00 (20/4) Gap_init rate = 0.04 (4 / 103), avg. gap size = 1.50 (6 / 4) 196 33.78 2.70 0.00 chr6ptel1M 607956 608029 (391971) MIRb#SINE/MIR 37 112 (156) m_b287s601i28 11650 chr6ptel1M 607956 CCTTAGAGCCAG-CAGGCCCCGATCTGAATCCAAGCTCTAATCCTTGCTA 608004 i i i - i iv i ii vi iviv i MIRb#SINE/MIR 37 CTTTGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTA 86 chr6ptel1M 608005 TCTCTAGGATTCTGGG-AAGCTCCTT 608029 v v iv iii - i v MIRb#SINE/MIR 87 GCTGTGTGACCTTGGGCAAGTTACTT 112 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.68 CpG sites = 17, Kimura (unadjusted) = 48.01 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.03 (2 / 73), avg. gap size = 1.00 (2 / 2) 306 32.91 8.23 0.00 chr6ptel1M 608033 608190 (391810) MIR3#SINE/MIR 35 205 (3) m_b287s601i29 11651 chr6ptel1M 608033 GAGAGGCAAGATGGCTGGATTCATTTCCTGACT--GCCACTTCATCACTG 608080 i v i viv i vvv i i -- vvv ?i MIR3#SINE/MIR 35 GGGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTG 84 chr6ptel1M 608081 TGTGACTTGGGTCAAATCAGTT--------TGGGAATTAGTAT-TTCATG 608121 i v v i v -------- vv i v -i v MIR3#SINE/MIR 85 TGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATC 134 chr6ptel1M 608122 GAGAAAATGCTGGCAGTGGGCTAGATGATGTTTGCATTTCCCCCAAGCAC 608171 viv vv viv i v i iviv i ii v v MIR3#SINE/MIR 135 TGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTC 184 chr6ptel1M 608172 C-ACG-TCCATAATCCTATGA 608190 i- i- i i i MIR3#SINE/MIR 185 TGACATTCTATGATTCTATGA 205 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.14 CpG sites = 25, Kimura (unadjusted) = 44.25 Transitions / transversions = 0.93 (25/27) Gap_init rate = 0.03 (5 / 157), avg. gap size = 2.60 (13 / 5) 487 30.40 8.51 2.00 chr6ptel1M 609001 609188 (390812) C MIR3#SINE/MIR (6) 202 3 m_b287s601i30 11652 chr6ptel1M 609001 TAGGATCATAGA--TTTAGTGATGGAAGGGCCTGTGAAAGCTATCAGGTT 609048 i --v i v v v iv ii iiii vi i C MIR3#SINE/MIR 202 TAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTC 153 chr6ptel1M 609049 CAATGTCCTCATTTTATAGAAGAGGAAATGGATCCCCAAAGAGAAGAA-- 609096 ivi i v iv vv i iv -- C MIR3#SINE/MIR 152 CAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGT 103 chr6ptel1M 609097 ---------AAG--CATACAGTTAGTGACTAGGAGAGCTGAGATTGGAAA 609135 --------- -- i i? v v i v i i i i v C MIR3#SINE/MIR 102 GACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAAC 53 chr6ptel1M 609136 TCGGGTCCTCTTCTAACTCCAAAATCAGTAGTCTCTCC-CTGTGTCATGT 609184 i i --- i i -v i v iv i- vv i ivi C MIR3#SINE/MIR 52 CCAGG---TCTCCTGACTCC-CAGTCCGTGCTCTCTCTGCTCAGCCACTC 7 chr6ptel1M 609185 TGCC 609188 C MIR3#SINE/MIR 6 TGCC 3 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.76 CpG sites = 34, Kimura (unadjusted) = 40.72 Transitions / transversions = 1.55 (34/22) Gap_init rate = 0.05 (9 / 187), avg. gap size = 2.22 (20 / 9) 709 27.29 2.75 4.19 chr6ptel1M 609430 609647 (390353) MIRb#SINE/MIR 2 216 (52) m_b287s601i31 11653 chr6ptel1M 609430 AGTGAGGCAGCTCAATGATAAAAGGGGTAAGAGTGCGGATGCTGAAGTCA 609479 v i ---i i iv - v v ii iivi i MIRb#SINE/MIR 2 AGAGGGGCAGC---GTGGTGCA-GTGGAAAGAGCACGGGCTTTGGAGTCA 47 chr6ptel1M 609480 GGAAGACCTGAG-----ACCTGGATTCAGATCCTCACTGGTTAGTATGAC 609524 iv i ----- i iv ii v viv i i i - i MIRb#SINE/MIR 48 GACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCT-GTGTGAC 96 chr6ptel1M 609525 TTTGGGCAAGTGATTAAACCTTCCTGTTCTTCAGTTTCCTCATCTGGAAA 609574 i v i v ii vv i v MIRb#SINE/MIR 97 CTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAA 146 chr6ptel1M 609575 GTGAGGATAATAATAGCATCTA-TTAGCTAGAGTTGTTGTGAGAAGAAAA 609623 i i --- i -i v - i i vv MIRb#SINE/MIR 147 ATGGGGATAATAAT---ACCTACCTCGC-AGGGTTGTTGTGAGGATTAAA 192 chr6ptel1M 609624 TGAGGTAATATTTGTAAGGCACCT 609647 i iiv i i i MIRb#SINE/MIR 193 TGAGATAATGCATGTAAAGCGCTT 216 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.77 CpG sites = 38, Kimura (unadjusted) = 35.32 Transitions / transversions = 2.00 (38/19) Gap_init rate = 0.05 (11 / 217), avg. gap size = 1.36 (15 / 11) 748 27.60 2.58 1.02 chr6ptel1M 609454 609647 (390353) MIR#SINE/MIR 16 212 (50) m_b287s601i32 11653 chr6ptel1M 609454 GGGTAAGAGTGCGGATGCTGAAGTCAGGAAGACCTGAG-----ACCTGGA 609498 v ii iiv i i - vvi i ----- i iv i MIR#SINE/MIR 16 GGTTAAGAGCACGGGCTCTGGAGCCAG-ACTGCCTGGGTTCGAATCCCGG 64 chr6ptel1M 609499 TTCAGATCCTCACTGGTTAGTATGACTTTGGGCAAGTGATTAAACCTTCC 609548 i v viv i i i - i i v i v ii MIR#SINE/MIR 65 CTCTGCCACTTACTAGCT-GTGTGACCTTGGGCAAGTTACTTAACCTCTC 113 chr6ptel1M 609549 TGTTCTTCAGTTTCCTCATCTGGAAAGTGAGGATAATAATAGCATCTATT 609598 v i v i i i i ii MIR#SINE/MIR 114 TGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTACC 163 chr6ptel1M 609599 AGCTAGAGTTGTTGTGAGAAGAAAATGAGGTAATATTTGTAAGGCACCT 609647 vvv i i vv v iv i i i MIR#SINE/MIR 164 TCATAGGGTTGTTGTGAGGATTAAATGAGTTAATACATGTAAAGCGCTT 212 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.84 CpG sites = 34, Kimura (unadjusted) = 35.69 Transitions / transversions = 1.79 (34/19) Gap_init rate = 0.02 (3 / 193), avg. gap size = 2.33 (7 / 3) 231 20.51 0.00 0.00 chr6ptel1M 610324 610362 (389638) C L2c_3end#LINE/L2 (13) 465 427 m_b287s601i33 11654 chr6ptel1M 610324 ACAAACATTTAAGAAGCACTTGCTATGTGCCAGGCATTG 610362 vvi i i i ii C L2c_3end#LINE 465 ACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTG 427 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 18.21 CpG sites = 6, Kimura (unadjusted) = 24.94 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 672 26.22 6.47 4.66 chr6ptel1M 610329 610560 (389440) C MIRb#SINE/MIR (14) 254 19 m_b287s601i34 11655 chr6ptel1M 610329 CATTTAAGAAGCACTTGCTATGTGCCAGGCATTGTGCTAAATGTTTTACA 610378 vvi i i i ii i C MIRb#SINE/MIR 254 CATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACA 205 chr6ptel1M 610379 AGTGTTACCTCATTTGGTCTTCACAA-AGT------AGGTGCTTGTTATT 610421 v ii i ii i - ii------ ivv i C MIRb#SINE/MIR 204 TGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATT 155 chr6ptel1M 610422 ATCCA------ACAGTTGAGGAAACTGAGAGAGACAAAAGATGGAATCTG 610465 v------ v --- viv i - ---- v C MIRb#SINE/MIR 154 ATCCCCATTTTACAGATGAGGAAACTGAG---GCTCAGAGA-GG----TT 113 chr6ptel1M 610466 AGACAGATTTACCCAGGATTACCTAGCTAGTAAACGTTTGAGGCTAAATT 610515 iii - i i i i i vi ii viv v vii C MIRb#SINE/MIR 112 AAGTA-ACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATT 64 chr6ptel1M 610516 TGAATACAAGTCT-TCTAGACTGCAGGAACATG-GCTCTATCCACTG 610560 i iv i - - v -i i vi - v C MIRb#SINE/MIR 63 CGAACCCAGGTCTGTCT-GACTCCA-AAGCCCGTGCTCTTTCCACTG 19 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.79 CpG sites = 39, Kimura (unadjusted) = 33.61 Transitions / transversions = 2.05 (39/19) Gap_init rate = 0.07 (16 / 231), avg. gap size = 1.62 (26 / 16) 329 29.79 5.32 0.00 chr6ptel1M 610683 610776 (389224) C L3#LINE/CR1 (382) 3717 3619 m_b287s601i35 11656 chr6ptel1M 610683 TCCTTTTATGGGATCTCATATAGCATAATTTCCA-----TTTATCATCCT 610727 iv iv vvi ii ii ----- i i C L3#LINE/CR1 3717 TCCTTCAACCGTTCCTCATATGACATGGTTTCCAGACCCTTCACCATCCT 3668 chr6ptel1M 610728 GGTCACTATCCTTTGGTTTTGTTCCAGTTTATTAATATCCTGTCTAAAA 610776 i v i vivi i i i i ivii C L3#LINE/CR1 3667 GGTCGCTCTCCTCTGGACGCGCTCCAGTTTGTCAATGTCCCTCTTAAAA 3619 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.85 CpG sites = 20, Kimura (unadjusted) = 40.40 Transitions / transversions = 2.50 (20/8) Gap_init rate = 0.01 (1 / 93), avg. gap size = 5.00 (5 / 1) 17 6.54 6.25 0.00 chr6ptel1M 611352 611383 (388617) (AAAACA)n#Simple_repeat 1 34 (0) m_b287s252i11 11657 chr6ptel1M 611352 AAAAC-AAAAC-AAAACAAAAACAAAACCAGAAA 611383 - - v i (AAAACA)n#Sim 1 AAAACAAAAACAAAAACAAAAACAAAAACAAAAA 34 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.06 (2 / 31), avg. gap size = 1.00 (2 / 2) 242 30.96 3.48 1.71 chr6ptel1M 611631 611745 (388255) L3#LINE/CR1 3970 4086 (13) m_b287s601i36 11658 chr6ptel1M 611631 GGGCGTATGTAAGCAGAGCCTAAATGCCCATTAGTCAGGGA-GGTGTTGA 611679 iv i vi v ii v i v - v v L3#LINE/CR1 3970 GGAGGTGTTCAAGCAGAGGCTGGATGACCACTTGTCAGGGATGTTGTAGA 4019 chr6ptel1M 611680 AGGAGAGTCC--CATTAACTTATTGCTTTGGATTTCATTA-GTCTAAGGC 611726 - v -- iiv vivv -v i vv v -v i L3#LINE/CR1 4020 AGG-GATTCCTGCATTGGATGGGAG-GTTGGACTAGATGACCTCTAAGGT 4067 chr6ptel1M 611727 CCTATCCACTTCTAGGGTT 611745 iv vi ii i L3#LINE/CR1 4068 CCCTTCCAACTCTGAGATT 4086 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.26 CpG sites = 16, Kimura (unadjusted) = 40.26 Transitions / transversions = 0.84 (16/19) Gap_init rate = 0.04 (5 / 114), avg. gap size = 1.20 (6 / 5) 800 31.69 13.80 1.39 chr6ptel1M 611749 612132 (387868) L3#LINE/CR1 3666 4096 (3) m_b287s601i37 11659 chr6ptel1M 611749 CCAAGATAACAAGAAAACTAGAAGTCAAACCACAGCAGGATTAATTTAAG 611798 i iiii iiiiv i ii vii i vv viii v L3#LINE/CR1 3666 CCAGGATGGTGAAGGGTCTGGAAACCATGTCATATGAGGAACGGTTGAAG 3715 chr6ptel1M 611799 GAATTGAAGCTATTTAGCCCAGAGAAGATAAGACTTAAAGCTAGATGTAA 611848 i ii v i ii v i v- ii i L3#LINE/CR1 3716 GAACTGGGGATGTTTAGCCTGGAGAAGAGAAGACTTAGAGG-AGACATGA 3764 chr6ptel1M 611849 TAAAGGATGCC--CAAGCACTTGAAGAGATGCCATTAGGAATAAAGACTC 611896 --- v i -- ii i i v i vv v ii i v L3#LINE/CR1 3765 TA---GCTGTCTTCAAATATTTGAAGGGCTGTCATGTGGAAGAGGGATTA 3811 chr6ptel1M 611897 AGCTT----------GTTCCCGAAAGCAG---------C----------- 611916 ii ---------- i v ii --------- ----------- L3#LINE/CR1 3812 GACTTATTCTGTGTGGCTCCAGAGGGCAGAACTAGGACCAATGGGTGGAA 3861 chr6ptel1M 611917 GTTAT-GGAAGGCA---TCCAGGTTTATGTAAGGAAAGCTTTCCTAACAA 611962 i- i --- i i v iv i iivi i L3#LINE/CR1 3862 GTTACAGGGAGGCAGATTTCGGCTCAATATAAGGAAGAACTTTCTAACAA 3911 chr6ptel1M 611963 TTAGAGCTCTCCAAAAGTGAAAGGTGATA-CTCATTTGGGATGCTATGCG 612011 i v i i v v v i- i--? i i iv iv v L3#LINE/CR1 3912 TCAGAGCTGTCCAAAAATGGAATGGGCTGCCTCG--NGAGGTAGTGAGCT 3959 chr6ptel1M 612012 TCTCATAAATGGAGGTCTTCAAATGGAAGATACATGTTTATTTGTTGAGG 612061 i i i v v v iii i v iv vii i iii L3#LINE/CR1 3960 CCCCGTCACTGGAGGTGTTCAAGCAGAGGCTGGATGACCACTTGTCAGGG 4009 chr6ptel1M 612062 --TTTGTAGGGGAGATTCCTG-ATTAG-TGACAA--TGGATT-------- 612097 --v ii i - i - iv i-- i -------- L3#LINE/CR1 4010 ATGTTGTAGAAGGGATTCCTGCATTGGATGGGAGGTTGGACTAGATGACC 4059 chr6ptel1M 612098 TTT-AGGTTCC-TCCAAGTCTGAGCTTCTGTGATTCT 612132 i - i - v v L3#LINE/CR1 4060 TCTAAGGTCCCTTCCAACTCTGAGATTCTGTGATTCT 4096 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.15 CpG sites = 84, Kimura (unadjusted) = 44.25 Transitions / transversions = 2.33 (84/36) Gap_init rate = 0.05 (19 / 383), avg. gap size = 3.11 (59 / 19) 287 31.19 1.82 0.90 chr6ptel1M 612162 612271 (387729) MIR1_Amn#SINE/MIR 3 113 (117) m_b287s601i38 11660 chr6ptel1M 612162 GAGAGGTAGGATGGCATGGTAGATAGAGAACTCTTCCTGAAACCAGGCAG 612211 i i vi iv i i v vv-v ii iv v MIR1_Amn#SINE 3 GGGAGGCAGTGTGGTCTAGTGGATAGAGCACTGG-ACTGGGACTCGGGAG 51 chr6ptel1M 612212 ACCTGGATGCAAACCTTGCCTCTGTCACTGAACTTCTCAATG-CTCTGTG 612260 i v ? ?i ii v i ?iv ?v v?i - ii v MIR1_Amn#SINE 52 ACCTGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGG 101 chr6ptel1M 612261 -AAGTAATTTAA 612271 - v i ? MIR1_Amn#SINE 102 CAAGTCACTTNA 113 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.97 CpG sites = 19, Kimura (unadjusted) = 44.74 Transitions / transversions = 1.27 (19/15) Gap_init rate = 0.03 (3 / 109), avg. gap size = 1.00 (3 / 3) 13 15.24 0.00 7.69 chr6ptel1M 612597 612638 (387362) (AAGGAAA)n#Simple_repeat 1 39 (0) m_b287s252i12 11661 chr6ptel1M 612597 AAGGAAAGAGTGATAAATGATAAAGGAAAAAGTGATGAAAGG 612638 i - v v v - -i (AAGGAAA)n#Si 1 AAGGAAAAAG-GAAAAAGGAAAAAGGAAAAAG-GA-AAAAGG 39 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.07 (3 / 41), avg. gap size = 1.00 (3 / 3) 284 30.66 8.03 0.00 chr6ptel1M 613221 613357 (386643) MIR1_Amn#SINE/MIR 3 150 (80) m_b287s601i39 11662 chr6ptel1M 613221 GAGCAGCTGGGCGATACAGCGAGTAGAGTGCCTG-CTGGAGATGGGAAGA 613269 i vi v v i i vi i ii ii iv - iiv v i MIR1_Amn#SINE 3 GGGAGGCAGTGTGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGAGA 52 chr6ptel1M 613270 ACTGAATTCAAATCCAG--TCTG--ATTCAGCGTCTTTGTGATCCAGGGC 613315 v ii ? ? v -- -- i ?iv ?v v? i iv MIR1_Amn#SINE 53 CCTGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGC 102 chr6ptel1M 613316 ----CGGTTTGCCCGTTTG--CCTCCGTTTCCTCATCAGTAAAATGAG 613357 ---- iv ?i iv i -- v v i MIR1_Amn#SINE 103 AAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGG 150 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.33 CpG sites = 25, Kimura (unadjusted) = 43.33 Transitions / transversions = 1.47 (25/17) Gap_init rate = 0.04 (5 / 136), avg. gap size = 2.20 (11 / 5) 287 33.48 13.14 2.99 chr6ptel1M 614451 614724 (385276) L3#LINE/CR1 3795 4095 (4) m_b287s601i40 11663 chr6ptel1M 614451 ATGGGAAAACAAGGGATTGGATTCGTTTGCTTTGGCCCCAG-GCTCATAA 614499 v i i-- i i ii ivv v i - vv v L3#LINE/CR1 3795 ATGTGGAAG--AGGGATTAGACTTATTCTGTGTGGCTCCAGAGGGCAGAA 3842 chr6ptel1M 614500 TGGAGAGCAGGGATTAGACG-TGCAAAGAAGCATAATTAGATTGGACATC 614548 ivii v iv iv i v - i ii i v v v ii vi i v L3#LINE/CR1 3843 CTAGGACCAATGGGTGGAAGTTACAGGGAGGCAGATTTCGGCTCAATATA 3892 chr6ptel1M 614549 ATGAGAAGAACGT-----CAATTGGAAC--TCC--AAGTGGCCGGGACTG 614589 --i v ----- ii i -- -- i vvv i L3#LINE/CR1 3893 A--GGAAGAACTTTCTAACAATCAGAGCTGTCCAAAAATGGAATGGGCTG 3940 chr6ptel1M 614590 CTTCAAGAGGGAGCCAGTTCCCTTTCTTTGGCGAGTTTCAGTTCGACGGC 614639 i i? v iv i iv vi v ivv iviv - L3#LINE/CR1 3941 CCTCGNGAGGTAGTGAGCTCCCCGTCACTGGAGGTGTTCAAGCAGA-GGC 3989 chr6ptel1M 614640 TTGCTGGGCATGTGACAATGATG-----------------GCATGGTCTG 614672 v v iv iv v iv ----------------- v vv L3#LINE/CR1 3990 TGGATGACCACTTGTCAGGGATGTTGTAGAAGGGATTCCTGCATTGGATG 4039 chr6ptel1M 614673 ---GGCTGGGCCAGATGCCAGGCTTTTAAGG-----TCCAACTCTCAAAT 614714 --- i i i ---- i i i ----- v i L3#LINE/CR1 4040 GGAGGTTGGACTAGAT----GACCTCTAAGGTCCCTTCCAACTCTGAGAT 4085 chr6ptel1M 614715 TTGGTGATTC 614724 iv L3#LINE/CR1 4086 TCTGTGATTC 4095 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.49 CpG sites = 48, Kimura (unadjusted) = 45.89 Transitions / transversions = 1.17 (48/41) Gap_init rate = 0.06 (17 / 273), avg. gap size = 2.65 (45 / 17) 180 23.08 2.56 0.00 chr6ptel1M 614736 614774 (385226) MIR3#SINE/MIR 163 202 (6) m_b287s601i41 11664 chr6ptel1M 614736 TCTCTGAGGTTCTTTCCAGCTCCAA-ATTCTGTGACCTTA 614774 i i i ii - i iii MIR3#SINE/MIR 163 TCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTA 202 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.95 CpG sites = 9, Kimura (unadjusted) = 30.95 Transitions / transversions = 1.00 (9/0) Gap_init rate = 0.03 (1 / 38), avg. gap size = 1.00 (1 / 1) 231 28.11 0.00 3.51 chr6ptel1M 614770 614828 (385172) C MIR3#SINE/MIR (61) 147 91 m_b287s601i42 11665 chr6ptel1M 614770 CCTTAATTTCATAGATGAGAACACTGAGTGGCCCAGAAGATTGAAATGAG 614819 i v i i i v -- iiiv i v C MIR3#SINE/MIR 147 CCCTCATTTTACAGATGAGGAAACTGA--GGCCCAGAGAGGTGAAGTGAC 100 chr6ptel1M 614820 TTCTCTGAG 614828 vi ii C MIR3#SINE/MIR 99 TTGCCCAAG 91 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.92 CpG sites = 11, Kimura (unadjusted) = 36.92 Transitions / transversions = 2.20 (11/5) Gap_init rate = 0.03 (2 / 58), avg. gap size = 1.00 (2 / 2) 196 25.53 0.00 0.00 chr6ptel1M 614906 614952 (385048) C L2d2_3end#LINE/L2 (499) 56 10 m_b287s601i43 11666 chr6ptel1M 614906 GTACGAGTACAGTGAAAAATAAGGCTAGAAAGGTGCATTGGAGCCAG 614952 ? v i v i ii i i ?ivi i C L2d2_3end#LIN 56 GNAGGGGAATAGTGGGAGATAAGGCTGGAAAGGNAGGTTGGGGCCAG 10 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.01 CpG sites = 9, Kimura (unadjusted) = 35.01 Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 58 0.00 1.89 0.00 chr6ptel1M 616738 616790 (383210) (AT)n#Simple_repeat 1 54 (0) c_b287s251i4 11667 chr6ptel1M 616738 ATATATATATATATATATATATATATATATATATATATATATATATA-AT 616786 - (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr6ptel1M 616787 ATAT 616790 (AT)n#Simple_ 51 ATAT 54 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.02 (1 / 52), avg. gap size = 1.00 (1 / 1) 263 32.21 4.84 2.36 chr6ptel1M 617365 617488 (382512) MIRb#SINE/MIR 4 130 (138) m_b287s601i44 11668 chr6ptel1M 617365 AGGAGGAACCTGCAGCA-TGGTAAAAGCA--ACCCATAGAGACTC---CA 617408 i v i v vv - v i --iv iv i -- --- MIRb#SINE/MIR 4 AGGGGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAG--TCAGACA 51 chr6ptel1M 617409 GTGCTGAGTTTAAATCCAGGCACTGCTACTTACTAACTTGCATCAGCCTG 617458 vv i ii v v i i - ii v v i MIRb#SINE/MIR 52 GACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGC-TGTGTGACCTTG 100 chr6ptel1M 617459 AGTAGATGCCTTCACTCCTCTGCTTCTCAG 617488 i i ii vv v ii vvi MIRb#SINE/MIR 101 GGCAAGTTACTTAACCTCTCTGAGCCTCAG 130 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.46 CpG sites = 21, Kimura (unadjusted) = 43.07 Transitions / transversions = 1.17 (21/18) Gap_init rate = 0.05 (6 / 123), avg. gap size = 1.50 (9 / 6) 228 8.16 12.24 0.00 chr6ptel1M 617538 617586 (382414) C Plat_L3#LINE/CR1 (0) 3573 3519 m_b287s551i5 11669 chr6ptel1M 617538 CGTAGA-TCATAGAATGTCAGAGCTGGAAGGGACCTT-AGA----ATCTG 617581 - v?i i- ---- C Plat_L3#LINE/ 3573 CGTAGAATCATAGAATCNTAGAGCTGGAAGGGACCTCGAGAGGTCATCTG 3524 chr6ptel1M 617582 GTGCA 617586 v C Plat_L3#LINE/ 3523 GTCCA 3519 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 6.75 CpG sites = 2, Kimura (unadjusted) = 8.85 Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.06 (3 / 48), avg. gap size = 2.00 (6 / 3) 284 26.62 3.03 5.15 chr6ptel1M 617681 617779 (382221) L2c_3end#LINE/L2 366 462 (16) m_b287s601i46 11670 chr6ptel1M 617681 CCTCAGCAGTAAAATGTAAGCTCCTTGGGGGCAGCCACCATTTC--ACCT 617728 -- v i v i i vv i v -- iii L2c_3end#LINE 366 CCTC--CACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTC 413 chr6ptel1M 617729 GTCTTTGTATGTCCACAGCACTCTGTTGT-TTGCAGATGCTTAATAAAGG 617777 i -- v i - viii- v i ii i v L2c_3end#LINE 414 ATCTTTGTA--TCCCCAGCGC-CTGGCACATAGTAGGCGCTCAATAAATG 460 chr6ptel1M 617778 TT 617779 L2c_3end#LINE 461 TT 462 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.11 CpG sites = 16, Kimura (unadjusted) = 33.96 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.07 (7 / 98), avg. gap size = 1.14 (8 / 7) 29 5.64 0.00 0.00 chr6ptel1M 618897 618933 (381067) (AAAAC)n#Simple_repeat 1 37 (0) c_b287s251i5 11671 chr6ptel1M 618897 AAAACAAAACAAAACAAAACAAAAAAAAAAAAAACAA 618933 v v (AAAAC)n#Simp 1 AAAACAAAACAAAACAAAACAAAACAAAACAAAACAA 37 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 301 23.84 2.91 10.42 chr6ptel1M 619368 619470 (380530) C MIR3#SINE/MIR (21) 187 92 m_b287s601i47 11672 chr6ptel1M 619368 TTAAAGTTGAAAGGAACCTTAGAGAGTGTCTGGTCCTTCTCCTTGGATGG 619417 i i i i i vii i vv i -------- C MIR3#SINE/MIR 187 TCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCC-------- 146 chr6ptel1M 619418 TTCTTATATTACAGAGGAGAAATATGAGGACTA-AGA-GTG-AGTGACTT 619464 -- i v v i vv v i - - - C MIR3#SINE/MIR 145 --CTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTT 98 chr6ptel1M 619465 GTCAAA 619470 i v C MIR3#SINE/MIR 97 GCCCAA 92 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.99 CpG sites = 13, Kimura (unadjusted) = 28.99 Transitions / transversions = 1.44 (13/9) Gap_init rate = 0.13 (13 / 102), avg. gap size = 1.00 (13 / 13) 205 29.51 3.28 0.00 chr6ptel1M 619522 619582 (380418) C MIRb#SINE/MIR (189) 79 17 m_b287s601i48 11673 chr6ptel1M 619522 TGGCAGAGCGGGGATGCTATTCCCACTCT-TCTGACTCCAAATTTTATAC 619570 v v v vi viv - viiii i C MIRb#SINE/MIR 79 TGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGC 30 chr6ptel1M 619571 TTTTTTT-CTACA 619582 i ii- i C MIRb#SINE/MIR 29 TCTTTCCACTGCA 17 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.74 CpG sites = 11, Kimura (unadjusted) = 38.78 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.03 (2 / 60), avg. gap size = 1.00 (2 / 2) 452 26.26 2.34 4.80 chr6ptel1M 620128 620255 (379745) MIRc#SINE/MIR 3 127 (141) m_b287s601i49 11674 chr6ptel1M 620128 AGCTAGTG-GGTGTAGTGGATAGAGTACTAGTCCTGAAATCAGGGGGATC 620176 vi - i v i i v i i i ii i MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chr6ptel1M 620177 TAAATTCAAAT-GTGACTTTAGATACAATACTTCCTAGCTGGGTGACCTT 620225 iii i i -vi i i---- i --i v v MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTC----TGC--CACTTACTAGCTGTGTGACCTT 96 chr6ptel1M 620226 AGGCAAGTCACTTCACCCCAATT-GCCTCAG 620255 i v i vv v- MIRc#SINE/MIR 97 GGGCAAGTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.12 CpG sites = 22, Kimura (unadjusted) = 33.70 Transitions / transversions = 2.20 (22/10) Gap_init rate = 0.07 (9 / 127), avg. gap size = 1.00 (9 / 9) 18 8.72 0.00 0.00 chr6ptel1M 620257 620281 (379719) (A)n#Simple_repeat 1 25 (0) m_b287s252i13 11675 chr6ptel1M 620257 AAAAAAAGAAAAAAAAAAAGAAAAA 620281 i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAA 25 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 257 38.94 6.08 1.95 chr6ptel1M 620491 620786 (379214) L2d_3end#LINE/L2 124 431 (85) m_b287s601i51 11676 chr6ptel1M 620491 CTCTATGCCTTTAC-CACTATTATTTCCCATACCTGAGTTTCCTACTCTT 620539 ii i - -iiii i vii iiv v -- iii L2d_3end#LINE 124 CTCTGCGCCTTTGCTCAC-GCCGTTCCCCCCGCCTGGAATGCC--CTTCC 170 chr6ptel1M 620540 CCTTCCATTTCATCTACTAAAATCCTATCCCACTTTTAAGACCTATTCTT 620589 vi iiv iiv i vv i i i i -v i L2d_3end#LINE 171 CCTTCCTCTCTCTCTATCCAAATCCTACCCATCCTTCAAGGCCCA-GCTC 219 chr6ptel1M 620590 ATGT--CATCACCACCATGAAG-ATTCCCTGAT--TTCTGACCAATGGTA 620634 v -- i v v i -v i--i iii v iiv i L2d_3end#LINE 220 AAGTCCCACCTCCTCCACGAAGCCTTCCCTGACCACTCCAGCCCACACTG 269 chr6ptel1M 620635 CTCTTTTCTTACTGCAAATTCTAATGTGTCTCTGTGCTTTTT-TTTTTTT 620683 v i i i v vii i iv i- ivii i iv i v -iiviviv L2d_3end#LINE 270 ATCTCTCCCTTCTCTGAACTCCTATA-GCACTTATAGTCTGTACCACGCA 318 chr6ptel1M 620684 TTTTTGCAC-AAACTGCAAAGTAGTTTGAAAGTGGTTTTTAA----TCTA 620728 v v -v i ii v v - i viv v v i i ---- ii L2d_3end#LINE 319 ATTTAGCACTTAATTATATACT-GTCTTGTATTGTTCTCTAATTGTTTCA 367 chr6ptel1M 620729 TATATCTTA-TCTT-----CCCTACTAGAGTGTAAGCTTTGTAAGAGTAG 620772 i i v - ----- v v iiv i i i L2d_3end#LINE 368 TGTGTGTTAGTCTTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAG 417 chr6ptel1M 620773 GGACTCCTTCTTGT 620786 iviv i L2d_3end#LINE 418 GGACCATGTCTTAT 431 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 54.23 CpG sites = 73, Kimura (unadjusted) = 59.34 Transitions / transversions = 1.82 (73/40) Gap_init rate = 0.05 (15 / 295), avg. gap size = 1.60 (24 / 15) 285 36.42 3.03 1.80 chr6ptel1M 620491 620655 (379345) L2d2_3end#LINE/L2 124 290 (265) m_b287s601i50 11676 chr6ptel1M 620491 CTCTATGCCTTTAC-CACTATTATTTCCCATACCTGAGTTTCCTACTCTT 620539 ii i - -iiii i vii iiv v -- iii L2d2_3end#LIN 124 CTCTGCGCCTTTGCTCAC-GCCGTTCCCCCCGCCTGGAATGCC--CTTCC 170 chr6ptel1M 620540 CCTTCCATTTCATCTACTAAAATCCTATCCCACTTTTAAGACCTA-TTCT 620588 vi i i iiv i vv i i i i -i v L2d2_3end#LIN 171 CCTTCCTCTCCACCTATCCAAATCCTACCCATCCTTCAAGGCCCAGCTCA 220 chr6ptel1M 620589 TATGTCATCACCACCATGAAG-ATTCCCTGAT--TTCTGACCAATGGTAC 620635 v ?i i v v i -v i--i iii vi?i iv L2d2_3end#LIN 221 AATNCCACCTCCTCCGTGAAGCCTTCCCTGACCACTCCAGCCCGNAGTGA 270 chr6ptel1M 620636 TCTTTTCTTACTGCAAATTC 620655 i i i v vii i L2d2_3end#LIN 271 TCTCTCCCTCCTCTGAACTC 290 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 47.49 CpG sites = 43, Kimura (unadjusted) = 56.32 Transitions / transversions = 2.69 (43/16) Gap_init rate = 0.04 (7 / 164), avg. gap size = 1.14 (8 / 7) 320 26.02 5.41 1.30 chr6ptel1M 620727 620800 (379200) L2b_3end#LINE/L2 325 401 (65) m_b287s601i52 11676 chr6ptel1M 620727 TATATATCTTATCTTCCCTACTAGAGTGTAAGCTTTGTAAGAGTAGGGAC 620776 i i -i i i v i ii i i i L2b_3end#LINE 325 TACATGTCT-GTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGAC 373 chr6ptel1M 620777 ----TCCTTCTTGTTTGCTGCTAGATCC 620800 ---- iv ii i iv L2b_3end#LINE 374 CGNGTCTGTCTTGTTCACCGCTGTATCC 401 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.26 CpG sites = 16, Kimura (unadjusted) = 34.79 Transitions / transversions = 5.33 (16/3) Gap_init rate = 0.03 (2 / 73), avg. gap size = 2.50 (5 / 2) 268 30.13 1.18 2.38 chr6ptel1M 620729 620813 (379187) L2d2_3end#LINE/L2 416 499 (56) m_b287s601i53 11676 chr6ptel1M 620729 TATATCTTATCTTCCCTACTAGAGTGTAAGCTTTGTAAGAGTAGGGACTC 620778 i i i v v iiv i i i iv L2d2_3end#LIN 416 TATGTCTTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCA 465 chr6ptel1M 620779 CTTCTTGT-TTGCTGCTAGATCCACTCACAGAACTT 620813 iv i -i v -i iv - i vi i L2d2_3end#LIN 466 TGTCTTATACTTCT-TTGTATCC-CCCACAGCGCCT 499 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.47 CpG sites = 17, Kimura (unadjusted) = 40.62 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.04 (3 / 84), avg. gap size = 1.00 (3 / 3) 326 14.04 1.75 0.00 chr6ptel1M 621419 621475 (378525) Plat_L3#LINE/CR1 3513 3570 (3) m_b287s551i6 11677 chr6ptel1M 621419 GGGAGTTGGACCAGATGATCTCTCT-GGTATCTTCCAGCTCTAAATTTCT 621467 i i i v- vi ?iv Plat_L3#LINE/ 3513 GGGGGCTGGACCAGATGACCTCTCGAGGTCCCTTCCAGCTCTANGATTCT 3562 chr6ptel1M 621468 ATGATTCT 621475 Plat_L3#LINE/ 3563 ATGATTCT 3570 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 16.04 CpG sites = 5, Kimura (unadjusted) = 16.04 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.02 (1 / 56), avg. gap size = 1.00 (1 / 1) 20 11.26 0.00 0.00 chr6ptel1M 621554 621582 (378418) (T)n#Simple_repeat 1 29 (0) m_b287s252i14 11678 chr6ptel1M 621554 TTTTTTTTTATTTTTTATTTTTTTTATTT 621582 v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 11 14.09 10.26 0.00 chr6ptel1M 622757 622795 (377205) (TATATATA)n#Simple_repeat 1 43 (0) m_b287s252i15 11679 chr6ptel1M 622757 TATAATTATATATATAT-TAT-TATGT-TATTTATTTAT-TAT 622795 vv - - i - v v - (TATATATA)n#S 1 TATATATATATATATATATATATATATATATATATATATATAT 43 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.11 (4 / 38), avg. gap size = 1.00 (4 / 4) 20 8.97 5.66 5.66 chr6ptel1M 622759 622811 (377189) (TATT)n#Simple_repeat 1 53 (0) m_b287s252i16 11679 chr6ptel1M 622759 TAATTATATATATA-TTA-TTATGTTATTTATTTA-TTATGTTACTTATT 622805 v v v - - - - - i - (TATT)n#Simpl 1 TATTTATTTATTTATTTATTTAT-TTATTTATTTATTTAT-TTATTTA-T 47 chr6ptel1M 622806 TTATTT 622811 (TATT)n#Simpl 48 TTATTT 53 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.12 (6 / 52), avg. gap size = 1.00 (6 / 6) 17 16.87 0.00 8.00 chr6ptel1M 622894 622947 (377053) (TCTTTT)n#Simple_repeat 1 50 (0) m_b287s252i17 11680 chr6ptel1M 622894 TCTTATTCTTTCTTTTATTTCTTTTTCCTTTTCCTTTATTCATTCACTTT 622943 v - i v - i - v iv (TCTTTT)n#Sim 1 TCTTTTTCTTT-TTCTTTTTCTTTTT-CTTTTTCTTT-TTCTTTTTCTTT 47 chr6ptel1M 622944 ATTC 622947 - (TCTTTT)n#Sim 48 -TTC 50 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.08 (4 / 53), avg. gap size = 1.00 (4 / 4) 24 21.07 0.00 0.00 chr6ptel1M 624129 624177 (375823) (T)n#Simple_repeat 1 49 (0) m_b287s252i18 11681 chr6ptel1M 624129 TTTTTTTGTTATTGTTGCTGTTCTTTGTCTTTTTTTTTTTTTTTTTTTT 624177 v v v vi v i v i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 49 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 399 30.81 4.85 3.59 chr6ptel1M 625851 626015 (373985) C MIR1_Amn#SINE/MIR (60) 170 4 m_b287s601i54 11682 chr6ptel1M 625851 AGGAGATTGAGTG-CATCCTCCCTCATTTGAGAGATAAGGAATATCAGAC 625899 i i- i- iv - v v i vv v i C MIR1_Amn#SINE 170 AGGAGGTC-AGTATCATTATCCC-CATTTTACAGATGAGGAAACTGAGGC 123 chr6ptel1M 625900 CTAGAATGAGTATGTAACTTGTCTGAAGTCACAAGGGAAGTAAGGAAGTA 625949 ?i iv iv? v i i ii i ?v---- i?i v? i C MIR1_Amn#SINE 122 NCAGAGAGGTNAAGTGACTTGCCCAAGGTCACNC----AGCNGGCNAGTG 77 chr6ptel1M 625950 ACAAAGCCATCAAGTGAACCCAAATCTTCTGA-------TCTATTGCTCT 625992 i i ivv ?v? ii i i ------- i v C MIR1_Amn#SINE 76 GCAGAGCCGGGANTNGAACCCAGGTCTCCCGAGTCCCAGTCCAGTGCTCT 27 chr6ptel1M 625993 TTTCCTTACATCATGCTTCCTCC 626015 v i vi v i ii v C MIR1_Amn#SINE 26 ATCCACTAGACCACACTGCCTCC 4 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.46 CpG sites = 30, Kimura (unadjusted) = 43.86 Transitions / transversions = 1.58 (30/19) Gap_init rate = 0.05 (8 / 164), avg. gap size = 1.75 (14 / 8) 404 32.12 5.56 2.70 chr6ptel1M 625871 626014 (373986) C MIRc#SINE/MIR (119) 149 2 m_b287s601i55 11682 chr6ptel1M 625871 CCTCATTTGAGAGATAAGGAATATCAGACCTAGAATGAGTATGTAACTTG 625920 i v v i vv v i ii iv iv v i C MIRc#SINE/MIR 149 CCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTG 100 chr6ptel1M 625921 TCTGAAGTCACAAGGGAAGTAAGGAAGTAACAAAGCCATCAAGTGAACCC 625970 i ii i vi vv ---- ii i ivv vvi C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGT----AAGTGGCAGAGCCGGGACTCGAACCC 54 chr6ptel1M 625971 AAATCTT-CTGA-------TCTATTGCTCTTTTCCTTACATCATGCTTCC 626012 ii - ------- i v i vi i i ii v C MIRc#SINE/MIR 53 AGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTGCC 4 chr6ptel1M 626013 TC 626014 C MIRc#SINE/MIR 3 TC 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.96 CpG sites = 27, Kimura (unadjusted) = 43.54 Transitions / transversions = 1.50 (27/18) Gap_init rate = 0.04 (6 / 143), avg. gap size = 2.00 (12 / 6) 297 22.03 0.00 0.00 chr6ptel1M 626250 626308 (373692) C MIR3#SINE/MIR (24) 184 126 m_b287s601i56 11683 chr6ptel1M 626250 GAGCTAGCTGGAACATTAGAAATCATCTGGCCAGACCCCGTCATTTTAGA 626299 i vv i v i i i vi v v C MIR3#SINE/MIR 184 GAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACA 135 chr6ptel1M 626300 GATGAAGAA 626308 i C MIR3#SINE/MIR 134 GATGAGGAA 126 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.38 CpG sites = 7, Kimura (unadjusted) = 26.38 Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.0 (0 / 0) 228 22.83 11.27 1.28 chr6ptel1M 626695 626765 (373235) C MIR3#SINE/MIR (6) 202 125 m_b287s601i57 11684 chr6ptel1M 626695 TGGGATGATGGGAT-TTAGAACTAGAAGGGAATCTTAAAGTT--TCTAGT 626741 i i v i i - i i i -i i v -- C MIR3#SINE/MIR 202 TAGAATCATAGAATGTCAGAGCTGGAAGGGA-CCTTAGAGATCATCTAGT 154 chr6ptel1M 626742 CCAATTCTC-----TTATAGAAGAGGAAA 626765 ii i ----- i v C MIR3#SINE/MIR 153 CCAACCCCCTCATTTTACAGATGAGGAAA 125 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.99 CpG sites = 13, Kimura (unadjusted) = 28.99 Transitions / transversions = 4.33 (13/3) Gap_init rate = 0.06 (4 / 70), avg. gap size = 2.25 (9 / 4) 12 16.31 2.78 2.78 chr6ptel1M 626796 626831 (373169) (ATAAATC)n#Simple_repeat 1 36 (0) m_b287s252i19 11685 chr6ptel1M 626796 ATAATTTTTAAGATCATAAATCAGAAACCA-AAATCA 626831 v iv - v i - (ATAAATC)n#Si 1 ATAAATCATAA-ATCATAAATCATAAATCATAAATCA 36 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 17 12.69 0.00 0.00 chr6ptel1M 626930 626955 (373045) (G)n#Simple_repeat 1 26 (0) m_b287s252i20 11686 chr6ptel1M 626930 GGGTGGGGGGGGGCCGGGGGGGGGGG 626955 v vv (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGG 26 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 18 22.00 3.77 0.00 chr6ptel1M 627572 627624 (372376) (ATG)n#Simple_repeat 1 55 (0) m_b287s252i21 11687 chr6ptel1M 627572 ATGATGATGATGTAGATGGTTAAGATGATGATGAAGAAG-GGAGGAAGA- 627619 vv i v v v v -v v v - (ATG)n#Simple 1 ATGATGATGATGATGATGATGATGATGATGATGATGATGATGATGATGAT 50 chr6ptel1M 627620 GATGA 627624 (ATG)n#Simple 51 GATGA 55 Matrix = Unknown Transitions / transversions = 0.11 (1/9) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.00 (2 / 2) 18 17.57 0.00 0.00 chr6ptel1M 627851 627882 (372118) (A)n#Simple_repeat 1 32 (0) m_b287s252i22 11688 chr6ptel1M 627851 AAAAAAAAAAAAAAAAGACAAATTAAAAACAA 627882 i v vv v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 32 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 40 0.00 0.00 0.00 chr6ptel1M 628990 629023 (370977) (AC)n#Simple_repeat 1 34 (0) c_b287s251i6 11689 chr6ptel1M 628990 ACACACACACACACACACACACACACACACACAC 629023 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACAC 34 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 12 28.69 0.00 0.00 chr6ptel1M 629178 629219 (370781) (ACATAA)n#Simple_repeat 1 42 (0) m_b287s252i23 11690 chr6ptel1M 629178 ACATAAACATACTTATGTATATAATCAGACACATAAATATAA 629219 vvi iv i v v v i (ACATAA)n#Sim 1 ACATAAACATAAACATAAACATAAACATAAACATAAACATAA 42 Matrix = Unknown Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 278 22.87 4.05 5.48 chr6ptel1M 629393 629466 (370534) C UCON73#DNA/hAT (5) 164 92 m_b288s502i0 11691 chr6ptel1M 629393 TTGTAAAGAGCTACTTGCCT---GCAAGTAAGCCACAATTTATGTCGAGA 629439 i v i i i--- i ---- i i i v C UCON73#DNA/hA 164 TTGCAAATAGCCACTCGCCCAGGGCGAGTAA----CGATTTATGCCGGGC 119 chr6ptel1M 629440 GCATAAAAGAGAATGATGGTTTCATTT 629466 vi i? i v i C UCON73#DNA/hA 118 GAGTAGNAAAGAATGCTGATTTCATTT 92 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 22.92 CpG sites = 12, Kimura (unadjusted) = 29.11 Transitions / transversions = 3.00 (12/4) Gap_init rate = 0.07 (5 / 73), avg. gap size = 1.40 (7 / 5) 424 33.86 8.97 2.82 chr6ptel1M 629857 630090 (369910) C MIRc#SINE/MIR (11) 257 10 m_b288s601i0 11692 chr6ptel1M 629857 CATCTCATATTGATAGACCGCTTT-CATATATGCAAAGTGTTTT-ACATA 629904 ?i i i vi v v i - -i v i i i - C MIRc#SINE/MIR 257 CNCCTTACATTTGTATAGCACTTTACA-GTTTACAAAGCGCTTTCACATA 209 chr6ptel1M 629905 AGCTCTCTTCTTAGATCCTCAGGACAACC-------GTA--CAAGTCAAG 629945 vii v iv v vi ------- -- i v i C MIRc#SINE/MIR 208 CATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGG 159 chr6ptel1M 629946 TCCTATCATTATTCTTATTTTACAGATGGGGGGAAACTGTGGCTGAAGGA 629995 --- i i ii -- i v v ii C MIRc#SINE/MIR 158 T---ATTATTATCCCCATTTTACAGAT--GAGGAAACTGAGGCTCAGAGA 114 chr6ptel1M 629996 AGGGAAGGCAATCTGTTGAGTGT----------GCAAGTGTAGGAAGCAG 630035 i vv - ii ii iiv iv ---------- i vvi iv i C MIRc#SINE/MIR 113 GGTTAA-GTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGG 65 chr6ptel1M 630036 AATTCAAACTCAAGCCTTCTGAAGACTAAATCCAACATACCATCCAATCT 630085 i i i i i i ivi vv i i iiiiv iv v vi C MIRc#SINE/MIR 64 GACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGC 15 chr6ptel1M 630086 GCCAC 630090 i C MIRc#SINE/MIR 14 ACCAC 10 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 45.63 CpG sites = 51, Kimura (unadjusted) = 48.32 Transitions / transversions = 1.96 (51/26) Gap_init rate = 0.05 (12 / 233), avg. gap size = 2.33 (28 / 12) 433 31.71 6.36 3.37 chr6ptel1M 629885 630057 (369943) C MIRb#SINE/MIR (46) 222 45 m_b288s601i1 11692 chr6ptel1M 629885 TATGCAAAGTGTTTTACATAAGCTCTCTTCTTAGATCCTCAGGACAACCG 629934 i v i i ivii v iv vi vi v C MIRb#SINE/MIR 222 TGTGCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCC 173 chr6ptel1M 629935 TACAAGTCAAGTCCTATCATTATTCTTATTTTACAGATGGGGGGAAACTG 629984 i i vi i --- i i ii -- i C MIRb#SINE/MIR 172 TGCGAGGTAGG---TATTATTATCCCCATTTTACAGAT--GAGGAAACTG 128 chr6ptel1M 629985 TGGCTGAAGGAAGGGAAGGCAATCTGTTGAGTGT----------GCAAGT 630024 v v ii i vv - i ii iiv iv ---------- i C MIRb#SINE/MIR 127 AGGCTCAGAGAGGTTAA-GTAACTTGCCCAAGGTCACACAGCTAGTAAGT 79 chr6ptel1M 630025 GTAGGAAGCAGAATTCAAACTCAAGCCT-TCTGA 630057 vvi iv i i i i i i - C MIRb#SINE/MIR 78 GGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGA 45 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.34 CpG sites = 36, Kimura (unadjusted) = 43.76 Transitions / transversions = 2.12 (36/17) Gap_init rate = 0.05 (8 / 172), avg. gap size = 2.12 (17 / 8) 263 28.65 21.55 0.71 chr6ptel1M 630481 630596 (369404) C MIR3#SINE/MIR (33) 175 36 m_b288s601i2 11693 chr6ptel1M 630481 GAGACCCCAGAAGCTGTCTAGTCCAGC---------TTG-----GGGGAA 630516 i ii iiiii i --------- i----- i C MIR3#SINE/MIR 175 GGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGAA 126 chr6ptel1M 630517 ATTGAGGCCCCAGGAAGTTATATGACTTGCCTAGAGGTAACACAGTAATT 630566 i vii i v vi i - v i? v C MIR3#SINE/MIR 125 ACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCA-AGGTCACACAGCNAGT 77 chr6ptel1M 630567 CA--GGC---------ATTTGCATTCTGATCTTCTGATTCC 630596 i -- --------- i v v ii v i i i C MIR3#SINE/MIR 76 TAGTGGCAGAGCCGGGACTAGAACCCAGGTCTCCTGACTCC 36 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.32 CpG sites = 25, Kimura (unadjusted) = 39.32 Transitions / transversions = 3.12 (25/8) Gap_init rate = 0.04 (5 / 115), avg. gap size = 5.20 (26 / 5) 265 23.23 13.79 1.02 chr6ptel1M 630511 630597 (369403) C MIRc#SINE/MIR (134) 134 37 m_b288s601i3 11693 chr6ptel1M 630511 GGGGAAATTGAGGCCCCAGGAAGTTATATGACTTGCCTAGAGGTAACAC- 630559 i i i vii i vi i - v - C MIRc#SINE/MIR 134 GAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCA-AGGTCACACA 86 chr6ptel1M 630560 ---AGTAATT--CAG-GC----ATTTGCATTCTGATCTT-CTGATTCCA 630597 --- v -- - ---- i i v ii v i - i C MIRc#SINE/MIR 85 GCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCA 37 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.21 CpG sites = 14, Kimura (unadjusted) = 28.91 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.08 (7 / 86), avg. gap size = 1.86 (13 / 7) 359 29.08 9.94 3.11 chr6ptel1M 631578 631758 (368242) C MIR1_Amn#SINE/MIR (18) 212 20 m_b288s601i4 11694 chr6ptel1M 631578 TATGGAGCATCTCTTCAT-----GATCT-AAATCACATAAC--------C 631613 v - i ----- - v v v --------i C MIR1_Amn#SINE 212 TATGTAGCA-CTTTTCATCAGTAGATCTCAAAGCACTTTACAAAGGAGGT 164 chr6ptel1M 631614 TAGT-CCAATGTCCTCATTATA-AGATGAAGAAATTGGGCCCCCCAAAAG 631661 i -i v i i v - i i i v ? vv i i C MIR1_Amn#SINE 163 CAGTATCATTATCCCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGG 114 chr6ptel1M 631662 AGAAATGATTTATCCAAGAGCAAATACAGGAGTAGTTAAGTGGCAGATTG 631711 v? i i ii iv -- i? --- i? vi? viv C MIR1_Amn#SINE 113 TNAAGTGACTTGCCCAAGGTC--ACNC---AGCNGGCNAGTGGCAGAGCC 69 chr6ptel1M 631712 AAGACTCAAATTTAGATCTTTTGA--CTAAGTCCTATGTTCTTTCCATT 631758 ii ? ?i iii i iii -- iv vi i v i C MIR1_Amn#SINE 68 GGGANTNGAACCCAGGTCTCCCGAGTCCCAGTCCAGTGCTCTATCCACT 20 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.79 CpG sites = 34, Kimura (unadjusted) = 40.91 Transitions / transversions = 2.00 (34/17) Gap_init rate = 0.07 (12 / 180), avg. gap size = 2.00 (24 / 12) 471 29.48 1.97 4.03 chr6ptel1M 631608 631759 (368241) C MIR3#SINE/MIR (45) 163 15 m_b288s601i5 11694 chr6ptel1M 631608 ATAACCTAGTCCAATGTCCTCATTATA-AGATGAAGAAATTGGGCCCCCC 631656 v i ivi v - i i i v vv C MIR3#SINE/MIR 163 ATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAG 114 chr6ptel1M 631657 AAAAGAGAAATGATTTATCCAAGAGCAAATACAGGAGTAGTTAAGTGGCA 631706 i i v i i ii iv -- i --v? - C MIR3#SINE/MIR 113 AGAGGTGAAGTGACTTGCCCAAGGTC--ACACAG--CNAGTT-AGTGGCA 69 chr6ptel1M 631707 GATTGAAGACTCAAATTTAGATCTTTTGACT--AAGTCCTATGTTCTTTC 631754 vivii vi iii i ii --v -i i i C MIR3#SINE/MIR 68 GAGCCGGGACTAGAACCCAGGTCTCCTGACTCCCAGTCC-GTGCTCTCTC 20 chr6ptel1M 631755 CATTC 631759 iii C MIR3#SINE/MIR 19 TGCTC 15 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.50 CpG sites = 30, Kimura (unadjusted) = 39.94 Transitions / transversions = 2.31 (30/13) Gap_init rate = 0.05 (8 / 151), avg. gap size = 1.12 (9 / 8) 564 34.59 5.70 8.07 chr6ptel1M 631750 632205 (367795) C L3#LINE/CR1 (55) 4044 3599 m_b288s601i6 11695 chr6ptel1M 631750 CTTTCCATTCTTGAAT--AGAAATTTCATTCCCAATATTACATCCCCTAT 631797 i i i --- -- i ii - ---- iv iv i C L3#LINE/CR1 4044 CCTCCCATCC---AATGCAGGAATCCC-TTC----TACAACATCCCTGAC 4003 chr6ptel1M 631798 AAGTGGCCTTTTGGCTTTCCATTGAAGA-TTTGAGTTTAAAATGGGGAAC 631846 i v iii i iivv v -i iv ----i i i C L3#LINE/CR1 4002 AAGTGGTCATCCAGCCTCTGCTTGAACACCTCCAGT----GACGGGGAGC 3957 chr6ptel1M 631847 TC---------TGAGACAGCCCCATCTAGTTTTGAATAACTC-AATTTTG 631886 ---------i i vv i v i i i -i v v C L3#LINE/CR1 3956 TCACTACCTCNCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGATTGTT 3907 chr6ptel1M 631887 TAAGAGATTTTCC--ATGTT------AAATCTGTCTTTTTG--ACTTTTG 631926 vi i v i -- i ------ i iii -- iii C L3#LINE/CR1 3906 AGAAAGTTCTTCCTTATATTGAGCCGAAATCTGCCTCCCTGTAACTTCCA 3857 chr6ptel1M 631927 CCAACAGCTCCAAGTTCTGATTTACAGGGTCAAGAAGGTCAAGTCTAATG 631976 v iv v v vii vii i i viv ivi v C L3#LINE/CR1 3856 CCCATTGGTCCTAGTTCTGCCCTCTGGAGCCACACAGAATAAGTCTAATC 3807 chr6ptel1M 631977 ACTCTTCCATGTAGTAGTACCCCTTCAAATTCTTAAAGTTTGAATTTTTT 632026 v ii iii --- vi i vi-- ii v iv C L3#LINE/CR1 3806 CCTCTTCCACATGACAG---CCCTTCAAATATTTGAAGAC--AGCTATCA 3762 chr6ptel1M 632027 TTTTTAATTTTTCCTAAAACTTGTCTTCTCCAGGCTAACTGTGCTCA-TT 632075 -----i i iii iv v vii v i - C L3#LINE/CR1 3761 T-----GTCTCCTCTAAGTCTTCTCTTCTCCAGGCTAAACATCCCCAGTT 3717 chr6ptel1M 632076 CTTTCAATTGATTCTTGTCGTTTTAACATGGCTTTGAATTATCTCTTCCC 632125 i ii v i ii v---- i i iv i-- - i v C L3#LINE/CR1 3716 CCTTCAACCGTTCCTCATA----TGACATGGTTTCCAG--A-CCCTTCAC 3674 chr6ptel1M 632126 ACTGGTCATCTTTGGTTTTTTTTTTTTTAATGTCCTGTTCTTTTTCCATA 632175 ------ -i ivi i ii i vi i iv vivv v v i C L3#LINE/CR1 3673 ------CATC-CTGGTCGCTCTCCTCTGGACGCGCTCCAGTTTGTCAATG 3631 chr6ptel1M 632176 --CTTTTAAAAATATGATACCCAGAAATGAAC 632205 -- i i v i iii v C L3#LINE/CR1 3630 TCCCTCTTAAAATGTGGCGCCCAGAACTGAAC 3599 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 46.05 CpG sites = 98, Kimura (unadjusted) = 49.54 Transitions / transversions = 2.09 (98/47) Gap_init rate = 0.10 (45 / 455), avg. gap size = 1.38 (62 / 45) 387 33.12 1.95 1.95 chr6ptel1M 632272 632425 (367575) MIR3#SINE/MIR 21 174 (34) m_b288s601i7 11696 chr6ptel1M 632272 AGTGAAAAGGGACTGAGAGGCAGAGGAGCTGGATC--AGTTT-AGCTACA 632318 v iv v i v ii v i i-- ii-i vii MIR3#SINE/MIR 21 AGAGAGCACGGACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTG 70 chr6ptel1M 632319 ACATTTATTGCCTCTGTGACCTTGGCTAATCCAATTAAATTTGGGGGGTC 632368 v i v i ?v v vi vi v v vi ivvv i MIR3#SINE/MIR 71 CCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCC 120 chr6ptel1M 632369 TCAGTTTCCTCTTCTGTTAAAAATGAAGAGGATTGTATTCACCAACTTCC 632418 v -- - i i v i vivii ii i MIR3#SINE/MIR 121 TCAGTTTCCTCATCTGT--AAAATG-AGGGGGTTGGACTAGATGATCTCT 167 chr6ptel1M 632419 AAGGCCC 632425 i MIR3#SINE/MIR 168 AAGGTCC 174 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 44.14 CpG sites = 28, Kimura (unadjusted) = 45.38 Transitions / transversions = 1.27 (28/22) Gap_init rate = 0.03 (5 / 153), avg. gap size = 1.20 (6 / 5) 349 31.84 6.62 0.69 chr6ptel1M 632495 632630 (367370) MIRc#SINE/MIR 5 148 (120) m_b288s601i8 11697 chr6ptel1M 632495 GCCATGTGGTACAAAGAAAAGAGGCTTGAATTAGGAGTTCAAG--GACCT 632542 vi i iv i vvi i i v - i -- MIRc#SINE/MIR 5 GCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGT-CAGGAAGACCT 53 chr6ptel1M 632543 GGTTTTGAATCTCAGCTCTCTGACTGACCACCTATGTAAACT----CA-- 632586 v i i i i viv v i v i i v ---- -- MIRc#SINE/MIR 54 GGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAG 103 chr6ptel1M 632587 -CAATTAATACCTGTGGGACTAAGAATCCCTGTCTCTAAAATAAG 632630 - v ivi v i v v vv iii v ii MIRc#SINE/MIR 104 TCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.97 CpG sites = 24, Kimura (unadjusted) = 42.55 Transitions / transversions = 1.26 (24/19) Gap_init rate = 0.04 (5 / 135), avg. gap size = 2.00 (10 / 5) 336 30.57 8.43 3.45 chr6ptel1M 632509 632674 (367326) MIR3#SINE/MIR 16 189 (19) m_b288s601i9 11697 chr6ptel1M 632509 AGAAAAGAG-GCTTGAATTAGGAGTTCAAGGACCTGGTTTTGAATCTCAG 632557 v i - vi i i i iviii v iv i i i MIR3#SINE/MIR 16 AGCAGAGAGAGCACGGACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCGG 65 chr6ptel1M 632558 CTCTCTGACTGACCACCTATGTAAACT----CA---CAATTAATACCTGT 632600 viv i i?v i i v ---- --- v v ivi v MIR3#SINE/MIR 66 CTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCT 115 chr6ptel1M 632601 GGGACTAAGAATCCCTGTCTCTAAAATAAGAGGGCTCCTGAAGACT-GAT 632649 v v vv iii v i i i -----i - MIR3#SINE/MIR 116 GGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTT-----GGACTAGAT 160 chr6ptel1M 632650 GAAGTCT---GCTCCT--CAGCTCCTGACA 632674 vv --- ii -- - MIR3#SINE/MIR 161 GATCTCTAAGGTCCCTTCCAGCT-CTGACA 189 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.79 CpG sites = 29, Kimura (unadjusted) = 40.97 Transitions / transversions = 1.45 (29/20) Gap_init rate = 0.07 (12 / 165), avg. gap size = 1.67 (20 / 12) 15 5.56 0.00 0.00 chr6ptel1M 632741 632759 (367241) (T)n#Simple_repeat 1 19 (0) m_b288s252i1 11698 chr6ptel1M 632741 TTTTTTTTTTTTTCTTTTT 632759 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 254 34.07 6.22 6.22 chr6ptel1M 632876 633116 (366884) C L3b_3end#LINE/CR1 (555) 651 411 m_b288s601i10 11699 chr6ptel1M 632876 ATCTCCCTTATTCTTTATTTATTGGGCAGTTGGCTCCTCTCAATAAAGTC 632925 i i? ------i i - ii ?-- i v i iv i C L3b_3end#LINE 651 ACCTCCCTTGNTCT------GTCGG-CGATN--CTTCTGTTAATGCAGCC 611 chr6ptel1M 632926 CAAGGGAAAACTAACATTTT--GCTGCCATGTCACAG-GTTAGATTCATC 632972 ivviv i i v -- v ii i v- i - i v C L3b_3end#LINE 610 CAAGATCGCATTAGCTTTTTTGGCAGCCGCGTCGCACTGCT-GACTCATA 562 chr6ptel1M 632973 TGACACTGATTATCCACCCCAATTTCCAGAACTTTTTTTAATATAAGGTT 633022 vivi viivi v ivv iii iv i-- i i? v v C L3b_3end#LINE 561 TTGAGCTTGCGGTCAACTAAAACCCCCAGGTCTTTTTC--ACATGNGCTG 514 chr6ptel1M 633023 TTTTTATGC----TCTTTCCTGCTCCATGTTCTTAAAGGATGGATTTTTT 633068 i vi v ---- ii ii- - v iiviv v ? C L3b_3end#LINE 513 CTGCTAAGCCGCGTCTCCCCCA-TCC-TGTACTCGCGCGATTGNTTTTTT 466 chr6ptel1M 633069 AAAACCCAAG--------TTTGCATTTTCCCCTATGAGATTTGATCTTAT 633110 i - -------- i i vi i vii v i C L3b_3end#LINE 465 GAA-CCCAAGTGCAGGACTTTACGTTTATCCCTGTTGAATTTCATCTTGT 417 chr6ptel1M 633111 TGGATT 633116 ? C L3b_3end#LINE 416 TGGNTT 411 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 40.76 CpG sites = 49, Kimura (unadjusted) = 49.52 Transitions / transversions = 1.75 (49/28) Gap_init rate = 0.08 (19 / 240), avg. gap size = 1.58 (30 / 19) 272 25.39 10.57 0.74 chr6ptel1M 633413 633535 (366465) MIRb#SINE/MIR 19 153 (115) m_b288s601i11 11700 chr6ptel1M 633413 CAGCACAAAGAACGTGGCATTTGCCCTCAGAT-GAC-TGGGTTTG---CC 633457 iiv i ii vv vvv i- - i --- MIRb#SINE/MIR 19 CAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCGAATCC 68 chr6ptel1M 633458 C----CTGA-ACTTACTGCTCTGGGTGACCTTGGGCAAATGGCTCAA--T 633500 ---- v- iv- v i vi i -- MIRb#SINE/MIR 69 CGGCTCTGCCACTTACTAG-CTGTGTGACCTTGGGCAAGTTACTTAACCT 117 chr6ptel1M 633501 GACTGGGCCTGA-TTTCTTGGTCTGTAAAGGGGAGA 633535 vv i v - i vi iv i MIRb#SINE/MIR 118 CTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGA 153 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.04 CpG sites = 16, Kimura (unadjusted) = 31.38 Transitions / transversions = 1.07 (16/15) Gap_init rate = 0.07 (8 / 122), avg. gap size = 1.75 (14 / 8) 187 30.32 3.15 6.50 chr6ptel1M 633447 633573 (366427) MIR3#SINE/MIR 62 184 (24) m_b288s601i12 11700 chr6ptel1M 633447 CTGGGTTTGCCCCTGAACTTACTGCTCTGGGTGACCTTGGGCAAATGGCT 633496 i v i v - ?i i----- i vi MIR3#SINE/MIR 62 CCGGCTCTGCCACT-AACTNGCTGT-----GTGACCTTGGGCAAGTCACT 105 chr6ptel1M 633497 CAA--TGACTGGGCCTGA-TTTCTTGGTCTGTAAAGGGGAGAGGAATCGC 633543 iv -- vv v - i vi iv ii i -- i v MIR3#SINE/MIR 106 TCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGG--TTGG 153 chr6ptel1M 633544 CCTGCGGGTCCTCCGGGGT-CCTTTCAGTTC 633573 v iviv vi iii - i i MIR3#SINE/MIR 154 ACTAGATGATCTCTAAGGTCCCTTCCAGCTC 184 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.11 CpG sites = 22, Kimura (unadjusted) = 40.59 Transitions / transversions = 1.57 (22/14) Gap_init rate = 0.09 (11 / 126), avg. gap size = 1.09 (12 / 11) 15 9.12 4.17 0.00 chr6ptel1M 633665 633688 (366312) (CT)n#Simple_repeat 1 25 (0) m_b288s252i2 11701 chr6ptel1M 633665 CTCTCTCTCCCTCCCTCTC-CTCTC 633688 i i - (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTC 25 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 12 13.67 0.00 0.00 chr6ptel1M 634459 634482 (365518) (GGC)n#Simple_repeat 1 24 (0) m_b288s252i3 11702 chr6ptel1M 634459 GGTGGCGGGGGCGGCGGCGGGGGC 634482 i v v (GGC)n#Simple 1 GGCGGCGGCGGCGGCGGCGGCGGC 24 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 45 0.00 0.00 0.00 chr6ptel1M 634875 634915 (365085) (G)n#Simple_repeat 1 41 (0) c_b288s251i1 11703 chr6ptel1M 634875 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 634915 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 41 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 18 11.35 5.26 0.00 chr6ptel1M 635066 635103 (364897) (AAAAC)n#Simple_repeat 1 40 (0) m_b288s252i4 11704 chr6ptel1M 635066 AAAACAAAACAAAACAAAA-GAAAC-AAACAACCCCAAAC 635103 -i - vv v (AAAAC)n#Simp 1 AAAACAAAACAAAACAAAACAAAACAAAACAAAACAAAAC 40 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 215 23.38 14.29 0.00 chr6ptel1M 635189 635265 (364735) C MIRb#SINE/MIR (117) 151 64 m_b288s601i13 11705 chr6ptel1M 635189 CCCATTTCATAAACTAGGAAACCGAGG----GAGAGA--AAATCCCATGT 635232 i i i iv i ---- i-- i vv v i C MIRb#SINE/MIR 151 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGC 102 chr6ptel1M 635233 GCAAGGTCACACA-CT----GGTGTCAGGGGCGTGATT 635265 v - ----i v i v v C MIRb#SINE/MIR 101 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATT 64 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.42 CpG sites = 10, Kimura (unadjusted) = 28.42 Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.05 (4 / 76), avg. gap size = 2.75 (11 / 4) 225 24.35 6.06 12.90 chr6ptel1M 635279 635377 (364623) C L2c_3end#LINE/L2 (6) 472 380 m_b288s601i14 11706 chr6ptel1M 635279 TCATTCTCCAACCGTTTATTTAGCATCTACAAGGGACTTTGCTGAGTGCT 635328 vv v i v ii v v ----- iii i C L2c_3end#LINE 472 TCATTCAACAAACATTTATTGAGCGCCTACTATG-----TGCCAGGCGCT 428 chr6ptel1M 635329 GGGGCTACTAGCTCAAAGAGTGTGT------CGATCCCTGCTCTCCGGGA 635372 v ------ - vi ------ i i vi C L2c_3end#LINE 427 GGGGATAC------AAAGA-TGAATAAGACACGGTCCCTGCCCTCAAGGA 385 chr6ptel1M 635373 GCTTA 635377 i C L2c_3end#LINE 384 GCTCA 380 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 26.41 CpG sites = 12, Kimura (unadjusted) = 29.64 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.13 (13 / 98), avg. gap size = 1.38 (18 / 13) 41 0.00 0.00 0.00 chr6ptel1M 635665 635699 (364301) (AC)n#Simple_repeat 1 35 (0) c_b288s251i2 11707 chr6ptel1M 635665 ACACACACACACACACACACACACACACACACACA 635699 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACA 35 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 457 30.41 5.42 2.94 chr6ptel1M 635859 636024 (363976) MIR3#SINE/MIR 13 182 (26) m_b288s601i15 11708 chr6ptel1M 635859 CTGAAGTATAGAGAGCAGACACGATTTGAAGTAAAACAATCTGAATACCA 635908 - i v -- i- i v i v iivi i ii v i MIR3#SINE/MIR 13 CTGA-GCAGAGAGAGCA--CG-GACTGGGAGTCAGGAGACCTGGGTTCTA 58 chr6ptel1M 635909 ATTTTGCCTTTGTTACTTACTACACTG----AC--TGAGCAAGACACTTG 635952 i iii v i ii v ?-i ---- -- i v v MIR3#SINE/MIR 59 GTCCCGGCTCTGCCACTAACTN-GCTGTGTGACCTTGGGCAAGTCACTTC 107 chr6ptel1M 635953 ACTTTGCTGGGACCTGGTTTCTCTAGCTGTAAAATATAGGGATTGGATCA 636002 i iv v iii iii v ivi i ii MIR3#SINE/MIR 108 ACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTA 157 chr6ptel1M 636003 GAC--TC-CTAAAGTCCATTCCAGC 636024 i-- - i v MIR3#SINE/MIR 158 GATGATCTCTAAGGTCCCTTCCAGC 182 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.72 CpG sites = 35, Kimura (unadjusted) = 42.03 Transitions / transversions = 2.50 (35/14) Gap_init rate = 0.05 (9 / 165), avg. gap size = 1.56 (14 / 9) 241 14.29 0.00 2.38 chr6ptel1M 636096 636138 (363862) EutTc1-N1#DNA/TcMar-Tc1 546 587 (1) m_b288s502i1 11709 chr6ptel1M 636096 TTATTAAAAGCTTAAAACTTTAGCAAGATTTTTGGGATACTCT 636138 - vi v i i i EutTc1-N1#DNA 546 TTATTAAA-GCTTAAAACTGCACCAAGACTTTTGGGACACCCT 587 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 16.10 CpG sites = 4, Kimura (unadjusted) = 16.10 Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.02 (1 / 42), avg. gap size = 1.00 (1 / 1) 17 19.74 1.96 4.00 chr6ptel1M 636480 636530 (363470) (ATC)n#Simple_repeat 1 50 (0) m_b288s252i5 11710 chr6ptel1M 636480 ATC-TCAACATTACCATCACTATCATTATAATCAATCAATTATCATCATC 636528 - v i i ii i v - - i (ATC)n#Simple 1 ATCATCATCATCATCATCATCATCATCATCATC-ATC-ATCATCATCATC 48 chr6ptel1M 636529 AT 636530 (ATC)n#Simple 49 AT 50 Matrix = Unknown Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.06 (3 / 50), avg. gap size = 1.00 (3 / 3) 279 30.04 6.63 10.00 chr6ptel1M 636568 636763 (363237) MIRb#SINE/MIR 36 225 (43) m_b288s601i16 11711 chr6ptel1M 636568 GTTTTGGAAAGAGCACAGCTCT---TTCCAAAAGGTTTCAGCTTTGACAT 636614 i ivv - vi --- v ---- ii i i v i MIRb#SINE/MIR 36 GCTTTGGAGTCAG-ACAGACCTGGGTTCGAA----TCCCGGCTCTGCCAC 80 chr6ptel1M 636615 TATCTAGCTGTGTAATCATGTGTGTATCACTTCCTCTCTCTGGGT----- 636659 vv i i v v iivi i vvi i i----- MIRb#SINE/MIR 81 TTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAG 130 chr6ptel1M 636660 TTTTCTCCTTTCTTCCATGGAGAGAATACTACTTGCACTGATTACCTTAC 636709 i v i v vvv i v v ---------i ii MIRb#SINE/MIR 131 TTTCCTCATCTGTAAAATGGGGATAATAATAC---------CTACCTCGC 171 chr6ptel1M 636710 AGA---GTTGTAAGCAGTCAATAAAGTATAATGTCCTATGTAA--CTATT 636754 i--- i v v v i i-- ---i -- vv MIRb#SINE/MIR 172 AGGGTTGTTGTGAGGATTAAATGAG--ATAATG---CATGTAAAGCGCTT 216 chr6ptel1M 636755 ATCACAGTG 636763 v MIRb#SINE/MIR 217 AGCACAGTG 225 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.95 CpG sites = 28, Kimura (unadjusted) = 38.89 Transitions / transversions = 1.12 (28/25) Gap_init rate = 0.12 (23 / 195), avg. gap size = 1.39 (32 / 23) 359 31.09 4.20 0.00 chr6ptel1M 636599 636717 (363283) MIRc#SINE/MIR 62 185 (83) m_b288s601i17 11711 chr6ptel1M 636599 GTTTCAGCTTTGACATTATCTAGCTGTGTAATCATGTGTGTATCACTTCC 636648 ii i i v i vv i i v v iivi vv MIRc#SINE/MIR 62 GTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAA 111 chr6ptel1M 636649 TCTCTCTGGGT-----TTTTCTCCTTTCTTCCATGGAGAGAATACTACTT 636693 i i i----- i v i v vvv i v v i MIRc#SINE/MIR 112 CCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCT 161 chr6ptel1M 636694 GCACTGATTACCTTACAGAGTTGT 636717 v vi i i MIRc#SINE/MIR 162 GCCCTGCCTACCTCACAGGGTTGT 185 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.58 CpG sites = 20, Kimura (unadjusted) = 41.01 Transitions / transversions = 1.18 (20/17) Gap_init rate = 0.01 (1 / 118), avg. gap size = 5.00 (5 / 1) 13 9.26 0.00 0.00 chr6ptel1M 636820 636842 (363158) (AAAC)n#Simple_repeat 1 23 (0) m_b288s252i6 11712 chr6ptel1M 636820 AAACAAACAAACAGACAAAAAAA 636842 i v (AAAC)n#Simpl 1 AAACAAACAAACAAACAAACAAA 23 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 317 20.45 8.24 2.22 chr6ptel1M 637003 637087 (362913) MIR3#SINE/MIR 115 204 (4) m_b288s601i18 11713 chr6ptel1M 637003 TGGTCCTCCATTTTTTCACCTGTATAATTAGGAGGCTGGACTAGA----C 637048 v vi ii i v v i i ---- MIR3#SINE/MIR 115 TGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATC 164 chr6ptel1M 637049 TGTTAGGGTCCTTTCCAGCTCTAGA---TGTATGATCTCATG 637087 -i i i - --- v iii MIR3#SINE/MIR 165 T-CTAAGGTCCCTTCCAGCTCT-GACATTCTATGATTCTATG 204 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 24.70 CpG sites = 12, Kimura (unadjusted) = 24.70 Transitions / transversions = 2.40 (12/5) Gap_init rate = 0.05 (4 / 84), avg. gap size = 2.25 (9 / 4) 218 20.79 4.88 6.17 chr6ptel1M 637066 637147 (362853) C MIRb#SINE/MIR (56) 212 132 m_b288s601i19 11714 chr6ptel1M 637066 GCTCTAGATGTATGATCTCATGTAAATCTCAACAA-AGCC---CAAAGTT 637111 i v i v v vi - - i --- i i v C MIRb#SINE/MIR 212 GCTTTACATGCATTATCTCATTTAATCCTC-ACAACAACCCTGCGAGGTA 164 chr6ptel1M 637112 CATACGTTATTATCCCTATTCTGACAGAGGGAGGAA 637147 vi -- i i - -v C MIRb#SINE/MIR 163 GGTA--TTATTATCCCCATTTT-ACAGA-TGAGGAA 132 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 22.94 CpG sites = 9, Kimura (unadjusted) = 24.64 Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.09 (7 / 81), avg. gap size = 1.29 (9 / 7) 206 17.95 0.00 0.00 chr6ptel1M 637385 637423 (362577) C MIRb#SINE/MIR (156) 112 74 m_b288s601i20 11714 chr6ptel1M 637385 AAATAACTAGTCCAAGGTCACAGATCTCCTAAGTGGCAG 637423 i v i v v vv C MIRb#SINE/MIR 112 AAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAG 74 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 20.52 CpG sites = 2, Kimura (unadjusted) = 20.52 Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 386 30.78 8.72 1.89 chr6ptel1M 637448 637596 (362404) MIRc#SINE/MIR 4 162 (106) m_b288s601i21 11715 chr6ptel1M 637448 GGCAGCATGGTGTAATGAATAGGGGATCAGGCCAGGAGTCAAGAAG---- 637493 ii i i i v i v iii i iv i ---- MIRc#SINE/MIR 4 GGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCT 53 chr6ptel1M 637494 ----CAAAATCTCTACTCTGTTGCTCACCAATTGTTTGATCTT-TGCCAG 637538 ----ivi i i vi iii i i ii v i -v v MIRc#SINE/MIR 54 GGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAG 103 chr6ptel1M 637539 TTATGTCACC---CTGACCCTT-GTTTTCTCTGTCTGGAAAATGGGAATA 637584 i iv v --- v i- i -i v i MIRc#SINE/MIR 104 TCACTTAACCTCTCTGAGCCTCAGTTTCCTC-ATCTGTAAAATGGGGATA 152 chr6ptel1M 637585 CTATTATTCCTG 637596 v -- v MIRc#SINE/MIR 153 ATA--ATACCTG 162 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 40.81 CpG sites = 31, Kimura (unadjusted) = 42.08 Transitions / transversions = 2.21 (31/14) Gap_init rate = 0.05 (8 / 148), avg. gap size = 2.00 (16 / 8) 294 17.24 3.45 0.00 chr6ptel1M 638036 638093 (361907) C MIR#SINE/MIR (116) 146 87 m_b288s601i22 11716 chr6ptel1M 638036 TCTCCATTTTGCAGATGAGGAAACTAAGGCAAACAGA-GTTGACTAAGTT 638084 i i i v v - i v v C MIR#SINE/MIR 146 TCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTT 97 chr6ptel1M 638085 ACTC-AGGTC 638093 i i - C MIR#SINE/MIR 96 GCCCAAGGTC 87 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 19.85 CpG sites = 6, Kimura (unadjusted) = 19.85 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.04 (2 / 57), avg. gap size = 1.00 (2 / 2) 14 15.26 0.00 0.00 chr6ptel1M 638235 638263 (361737) (TTTA)n#Simple_repeat 1 29 (0) m_b288s252i8 11717 chr6ptel1M 638235 TTTATTTATGTATTTATTTGTTATTTTAT 638263 v i vv (TTTA)n#Simpl 1 TTTATTTATTTATTTATTTATTTATTTAT 29 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 204 32.38 2.83 0.93 chr6ptel1M 638320 638425 (361575) MIRc#SINE/MIR 155 262 (6) m_b288s601i23 11715 chr6ptel1M 638320 AATATTTGAGATTCCTAC-TGGCAAGGTCGTCATAAGTGTCAAA-GACAA 638367 ii vvv v - vi i i ii i vi - v v MIRc#SINE/MIR 155 AATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGAT 204 chr6ptel1M 638368 AACTAAATGTCAAA-CTCCTCAGAAGCTGTAAAGTGCCACAAAAATATGA 638416 - iv v - v i iiv i i i v i i MIRc#SINE/MIR 205 AA-TGTATGTGAAAGCGCTTTGTAAACTGTAAAGTGCTATACAAATGTAA 253 chr6ptel1M 638417 GCTATCATT 638425 v?i i MIRc#SINE/MIR 254 GGNGTTATT 262 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 44.46 CpG sites = 20, Kimura (unadjusted) = 44.46 Transitions / transversions = 1.43 (20/14) Gap_init rate = 0.04 (4 / 105), avg. gap size = 1.00 (4 / 4) 254 31.65 1.27 0.00 chr6ptel1M 638429 638507 (361493) C MIR1_Amn#SINE/MIR (150) 80 1 m_b288s601i24 11718 chr6ptel1M 638429 AATGAGAGAGTTGGCACTGGAGCCCAGGGCTTCTGGCTTCCAGAGCAATG 638478 i iv ii v ? ? i v i i iv i vv i C MIR1_Amn#SINE 80 AGTGGCAGAGCCGGGANTNGAACCCAGGTCTCCCGAGTCCCAGTCCAGTG 31 chr6ptel1M 638479 CACT-TTCTCTGGATTAGGCTGCCTCTCTA 638507 v - i v i ii vi i C MIR1_Amn#SINE 30 CTCTATCCACTAGACCACACTGCCTCCCTA 1 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.91 CpG sites = 16, Kimura (unadjusted) = 44.67 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.01 (1 / 78), avg. gap size = 1.00 (1 / 1) 221 30.56 9.30 1.08 chr6ptel1M 638803 638888 (361112) MIRc#SINE/MIR 53 145 (123) m_b288s601i25 11719 chr6ptel1M 638803 TGGGTTCAAGTTCTA-TTTTGTATATTTATTAGATGTAAAAGCATGGCAA 638851 i i ii-i i i-i i i v ivi v v vv MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGC-CACTTACTAGCTGTGTGACCTTGGGCA 101 chr6ptel1M 638852 AGTAATTT-------CTAAGCCTCGGTTTCCCTAATTGTAAAAT 638888 v i ------- i i ii vi MIRc#SINE/MIR 102 AGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAAT 145 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.24 CpG sites = 18, Kimura (unadjusted) = 41.67 Transitions / transversions = 2.25 (18/8) Gap_init rate = 0.04 (3 / 85), avg. gap size = 3.00 (9 / 3) 513 21.94 2.92 6.82 chr6ptel1M 638934 639070 (360930) MIRc#SINE/MIR 17 148 (120) m_b288s601i26 11720 chr6ptel1M 638934 AGTGGCTAGTGTGCCAGGCTTGGAGTTACAGAAGTTCATCACCCTGAGTT 638983 vv v ii ii i i -i -------v i MIRc#SINE/MIR 17 AGTGGAAAGAGCACTGGACTTGGAGTCA-GGAAG-------ACCTGGGTT 58 chr6ptel1M 638984 CCAAT---GGTCTCAGATACTCACTAGCTATTCAACACTGGGCAAGTCAC 639030 v i --- - v vi i i vii vi MIRc#SINE/MIR 59 CGAGTCCCGG-CTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCAC 107 chr6ptel1M 639031 TTAACCTTATTGA-CCTCAGTTTCCTCATCTGTAAAATGAG 639070 ivi - i MIRc#SINE/MIR 108 TTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 26.51 CpG sites = 18, Kimura (unadjusted) = 26.51 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.08 (11 / 136), avg. gap size = 1.18 (13 / 11) 270 30.00 1.96 1.96 chr6ptel1M 639177 639278 (360722) MIR1_Amn#SINE/MIR 2 103 (127) m_b288s601i27 11721 chr6ptel1M 639177 AGAAAGATAAAGCTGGTATAGTGGATAGATCACTAGATTTAGAATCAAGA 639226 ii ii iv - v v i i vi v -i i MIR1_Amn#SINE 2 AGGGAGGCAGTG-TGGTCTAGTGGATAGAGCACTGGACTGGGACTC-GGG 49 chr6ptel1M 639227 AGTCCTGGCTCTTAATCCT-GCCCAG-CAGACACTGGCTAGGTGATCTCC 639274 v v ii? ? i- i v - vv?i i? i? i iv MIR1_Amn#SINE 50 AGACCTGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTG 99 chr6ptel1M 639275 GGCA 639278 MIR1_Amn#SINE 100 GGCA 103 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.08 CpG sites = 19, Kimura (unadjusted) = 42.85 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.04 (4 / 101), avg. gap size = 1.00 (4 / 4) 310 30.34 2.25 0.00 chr6ptel1M 639190 639278 (360722) MIRc#SINE/MIR 11 101 (167) m_b288s601i28 11721 chr6ptel1M 639190 TGGTATAGTGGATAGATCACTAGATTTAGAATCAAGAAGTCCTGGCTCTT 639239 ii v v i i i i i v v iiv MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr6ptel1M 639240 AATCCT-GCCCAG-CAGACACTGGCTAGGTGATCTCCGGCA 639278 i i- i v - vvi i iv i iv MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 101 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.61 CpG sites = 17, Kimura (unadjusted) = 40.46 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.02 (2 / 88), avg. gap size = 1.00 (2 / 2) 285 25.71 0.67 17.05 chr6ptel1M 639785 639934 (360066) MER63D#DNA/hAT-Tip100 340 468 (593) m_b288s502i2 11722 chr6ptel1M 639785 GAGCATTTATATCTTGGATATCGGCCAACA-TACCAAACAGAGCTTATTT 639833 i i i vi v v i- v v i iv MER63D#DNA/hA 340 GAGTATTTACACCACGGAAATCGGCAAACGCTACAAATCAGGGCTTGATT 389 chr6ptel1M 639834 TTTTTTTTTGTTGTTGTTGTTGTTGTTGCTTGTGCAGGATTTTTTCTAGA 639883 v v --i -------- ------i i ------i MER63D#DNA/hA 390 TATTGTTTTGTTG--ATTGT--------CT------AGACTT------AA 417 chr6ptel1M 639884 AAAGGTGGTGAAGGAAATGTTTCTTATTTAGACTAAACTTCAAAATGTGT 639933 i i i i i vv v vi i v i MER63D#DNA/hA 418 GAAAGTGATGGAGAAAATGTTAATAATGCAGATTAAACTTAAAAGTGTGT 467 chr6ptel1M 639934 C 639934 MER63D#DNA/hA 468 C 468 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 28.80 CpG sites = 19, Kimura (unadjusted) = 31.09 Transitions / transversions = 1.46 (19/13) Gap_init rate = 0.15 (23 / 149), avg. gap size = 1.00 (23 / 23) 274 28.24 2.35 0.00 chr6ptel1M 639909 639993 (360007) MER63C#DNA/hAT-Tip100 844 930 (0) m_b288s502i3 11723 chr6ptel1M 639909 ATTTAGACTAAACTTCAAAATGTGT-CACATGCCCAT-TTTTTTTTCTTG 639956 v v vv v i -i i vi i- i iii MER63C#DNA/hA 844 ATTTATAATAAACTTATATATGTATATACATACATACATTTTTTTCCCCA 893 chr6ptel1M 639957 GAGAGTCGGTCATCAAACATTTACTACCATATCCCTG 639993 i ii i i v i i v MER63C#DNA/hA 894 GAGAGCCGGTTGTTAAACATTTACCAGCACACCACTG 930 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.01 CpG sites = 16, Kimura (unadjusted) = 37.01 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.02 (2 / 84), avg. gap size = 1.00 (2 / 2) 23 15.68 2.33 0.00 chr6ptel1M 640797 640839 (359161) (AT)n#Simple_repeat 1 44 (0) m_b288s252i9 11724 chr6ptel1M 640797 ATATAT-TATATATGTATATATACATATATAAATATGTTCATAT 640839 - i i v i vi (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATAT 44 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.02 (1 / 42), avg. gap size = 1.00 (1 / 1) 206 29.14 0.00 2.53 chr6ptel1M 641129 641209 (358791) MIR3#SINE/MIR 114 192 (16) m_b288s601i29 11725 chr6ptel1M 641129 CTGAGCCTCAGTTTCCCTCGCTTTTACGAGGAAAGGGTTGCCCCAGATCA 641178 i - iii v vi v ii vv i v MIR3#SINE/MIR 114 CTGGGCCTCAGTTT-CCTCATCTGTAAAATGAGGGGGTTGGACTAGATGA 162 chr6ptel1M 641179 TTCCCTGAAGTCCCTCGCGCCTCTCCCATTC 641209 - i i i iv iv vv MIR3#SINE/MIR 163 -TCTCTAAGGTCCCTTCCAGCTCTGACATTC 192 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.71 CpG sites = 13, Kimura (unadjusted) = 37.71 Transitions / transversions = 1.30 (13/10) Gap_init rate = 0.03 (2 / 80), avg. gap size = 1.00 (2 / 2) 12 18.86 2.63 2.63 chr6ptel1M 641723 641760 (358240) (GGGC)n#Simple_repeat 1 38 (0) m_b288s252i10 11726 chr6ptel1M 641723 GGGC-GACGGGCAGGCCGGCGGGCCAGCGGAGCCGGCGG 641760 - i i v vi - v (GGGC)n#Simpl 1 GGGCGGGCGGGCGGGCGGGCGGGCGGGCGG-GCGGGCGG 38 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 12 24.71 1.72 5.36 chr6ptel1M 641980 642037 (357963) (GGGAGCC)n#Simple_repeat 1 56 (0) m_b288s252i11 11727 chr6ptel1M 641980 GGGACGCGCGGGAGGCAGGATGC-TGAGGCGGGATGCGGGCGCCGAGATG 642028 - - v i vv -v v vv v i - (GGGAGCC)n#Si 1 GGGA-GC-CGGGAGCCGGGAGCCGGGAGCCGGGAGCCGGGAGCCGGGA-G 47 chr6ptel1M 642029 CCCGGAGCC 642037 v (GGGAGCC)n#Si 48 CCGGGAGCC 56 Matrix = Unknown Transitions / transversions = 0.22 (2/9) Gap_init rate = 0.07 (4 / 57), avg. gap size = 1.00 (4 / 4) 15 21.41 2.33 0.00 chr6ptel1M 641987 642029 (357971) (GCGGGAG)n#Simple_repeat 1 44 (0) m_b288s252i12 11727 chr6ptel1M 641987 GCGGGAGGCAGGATGC-TGAGGCGGGATGCGGGCGCCGAGATGC 642029 i v -v v v v i v (GCGGGAG)n#Si 1 GCGGGAGGCGGGAGGCGGGAGGCGGGAGGCGGGAGGCGGGAGGC 44 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.02 (1 / 42), avg. gap size = 1.00 (1 / 1) 337 23.73 3.39 0.00 chr6ptel1M 642193 642310 (357690) MIR1_Amn#SINE/MIR 30 151 (79) m_b288s601i30 11728 chr6ptel1M 642193 GCGCTGTGGTGCGGCGCGGAGGAGCTGGGTTCGAATCCCTCCTC--CCGC 642240 i viv v i v ii v ? ? vv -- i MIR1_Amn#SINE 30 GCACTGGACTGGGACTCGGGAGACCTGGGTTCNANTCCCGGCTCTGCCAC 79 chr6ptel1M 642241 TGCCTCGCCAGCTGACCTTGGACAA-TCA-TTTACCTCGCGGAGCCTCAA 642288 ?v i? ii?v i - - ? v v ? i MIR1_Amn#SINE 80 TNGCCNGCTGNGTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAG 129 chr6ptel1M 642289 TTTCCCCTTCTGTAGATCGAGG 642310 i v i vi i MIR1_Amn#SINE 130 TTTCCTCATCTGTAAAATGGGG 151 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.17 CpG sites = 15, Kimura (unadjusted) = 31.17 Transitions / transversions = 1.15 (15/13) Gap_init rate = 0.03 (3 / 117), avg. gap size = 1.33 (4 / 3) 363 23.72 4.43 9.27 chr6ptel1M 642212 642369 (357631) MIR3#SINE/MIR 42 192 (16) m_b288s601i31 11728 chr6ptel1M 642212 AGGAG--CTGGGTTCGAATCCCTCCTC--CCGCTGCCTCGCCAGCTGACC 642257 -- v i vv -- i iv ? iivv MIR3#SINE/MIR 42 AGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACC 91 chr6ptel1M 642258 TTGGACAA-TCATTT-ACCTCGCGGAGCCTCAATTTCCCCTTCTGTAGAT 642305 i - i - v v i i i v i v MIR3#SINE/MIR 92 TTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAA 141 chr6ptel1M 642306 CGAGGTGGGGTGGGGGAGGGGAGAGGACGCGACAATTGCGAAGGTCTCTC 642355 i - v ------------- vv ii iv v i i MIR3#SINE/MIR 142 TGAGG-GGGTT-------------GGACTAGATGATCTCTAAGGTCCCTT 177 chr6ptel1M 642356 CCAGATCTGG-ATTC 642369 v i- MIR3#SINE/MIR 178 CCAGCTCTGACATTC 192 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.93 CpG sites = 18, Kimura (unadjusted) = 28.93 Transitions / transversions = 1.12 (18/16) Gap_init rate = 0.12 (19 / 157), avg. gap size = 1.11 (21 / 19) 428 21.65 6.35 4.69 chr6ptel1M 642814 642939 (357061) MIR3#SINE/MIR 61 188 (20) m_b288s601i32 11729 chr6ptel1M 642814 CCCGGCTTCTGCTATTGACTCCTGGGGTGACCTTGGGCAAGACGCT---- 642859 - i i i ?viv v v i ---- MIR3#SINE/MIR 61 CCCGGCT-CTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCAC 109 chr6ptel1M 642860 ---TCTGAGACTCAGTTTCCTCTTATGT-AAGTGCGATGATTGGACTAAG 642905 --- i v v v - i v iv i ii MIR3#SINE/MIR 110 CTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGA 159 chr6ptel1M 642906 TGATGTCCACGGCACCTGCCCTTCCAAATCTGAC 642939 v i v i----- iv MIR3#SINE/MIR 160 TGATCTCTAAGGT-----CCCTTCCAGCTCTGAC 188 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 26.11 CpG sites = 14, Kimura (unadjusted) = 26.11 Transitions / transversions = 1.17 (14/12) Gap_init rate = 0.07 (9 / 125), avg. gap size = 1.56 (14 / 9) 484 23.35 6.85 6.12 chr6ptel1M 643681 643826 (356174) C MIRc#SINE/MIR (120) 148 2 m_b288s601i33 11730 chr6ptel1M 643681 CTCATTTTTCAGGTGAGGAAACCGAGG--CAGACAAGATAAAGTGACTTG 643728 i v i i -- -i i v C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGA-GAGGTTAAGTGACTTG 100 chr6ptel1M 643729 GCCA--GTCACAAAGTTAGTATATATCTGAGGCCAGAATTGAACTCAGGA 643776 v -- v i vi iv v v vi v i i -- C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAG-- 52 chr6ptel1M 643777 TGATGAGTTCTCCTGACTCCAGGTCAAGCACTCCATTCACT------TAC 643820 ------ ii i v ii iv i ------i C MIRc#SINE/MIR 51 ------GTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACAC 8 chr6ptel1M 643821 TGCCCC 643826 i C MIRc#SINE/MIR 7 TGCCTC 2 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.63 CpG sites = 20, Kimura (unadjusted) = 28.68 Transitions / transversions = 1.67 (20/12) Gap_init rate = 0.08 (12 / 145), avg. gap size = 1.58 (19 / 12) 13 18.80 0.00 5.26 chr6ptel1M 643902 643941 (356059) (ACTTGTG)n#Simple_repeat 1 38 (0) m_b288s252i13 11731 chr6ptel1M 643902 ACTTGTGACTTGTGACTACTTGACTGCCTGCTTTGTGACT 643941 -iv -iv vi (ACTTGTG)n#Si 1 ACTTGTGACTTGTGACT-TGTGACT-TGTGACTTGTGACT 38 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 15 13.79 7.50 0.00 chr6ptel1M 644006 644045 (355955) (TATAAA)n#Simple_repeat 1 43 (0) m_b288s252i14 11732 chr6ptel1M 644006 TATAAA-GTGAATATACATATAAATA-AAATAGAAA-ATGAAT 644045 -i i v - v - i (TATAAA)n#Sim 1 TATAAATATAAATATAAATATAAATATAAATATAAATATAAAT 43 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.08 (3 / 39), avg. gap size = 1.00 (3 / 3) 18 0.00 0.00 0.00 chr6ptel1M 644334 644353 (355647) (GA)n#Simple_repeat 1 20 (0) m_b288s252i15 11733 chr6ptel1M 644334 GAGAGAGAGAGAGAGAGAGA 644353 (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGA 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 259 32.71 5.61 0.00 chr6ptel1M 644618 644724 (355276) C MIR3#SINE/MIR (11) 197 85 m_b288s601i34 11734 chr6ptel1M 644618 TCATAGC-TTTTAAAGCTGAAATAAGCCATAGAGATCAACTAAACCAGCT 644666 v- v i i i viii v v iv i i C MIR3#SINE/MIR 197 TCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACC 148 chr6ptel1M 644667 TACTTATTTT---GTTGAAGCG--TTATGATCAAGGAAGAGAAATTACTT 644711 iv i --- v i vi-- v v vi ii i v i v C MIR3#SINE/MIR 147 CCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTT 98 chr6ptel1M 644712 GTGCAAAGTCACA 644724 iv i C MIR3#SINE/MIR 97 GCCCAAGGTCACA 85 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 44.30 CpG sites = 20, Kimura (unadjusted) = 44.30 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.03 (3 / 106), avg. gap size = 2.00 (6 / 3) 274 35.42 1.04 0.00 chr6ptel1M 644932 645027 (354973) C MIRb#SINE/MIR (168) 100 4 m_b288s601i35 11735 chr6ptel1M 644932 CAGGATCACACAGTCAATAAGAATAAGAGACTGAACTTGAAACCAGATCT 644981 i i ii i vivv v v i i i v i C MIRb#SINE/MIR 100 CAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCT 51 chr6ptel1M 644982 TCTTAGATTCAATGCTTATTCTCTAGCCAA-GTACCAAGCTGCTCCT 645027 vii iiv i v iii v vv v- i v i C MIRb#SINE/MIR 50 GTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCACCACGCTGCCCCT 4 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 45.62 CpG sites = 20, Kimura (unadjusted) = 49.95 Transitions / transversions = 1.43 (20/14) Gap_init rate = 0.01 (1 / 95), avg. gap size = 1.00 (1 / 1) 32 0.00 0.00 7.32 chr6ptel1M 645037 645080 (354920) (TATC)n#Simple_repeat 1 41 (0) c_b288s251i3 11736 chr6ptel1M 645037 TATCTATCTATCTTATCTTATCTTATCTATCTATCTATCTATCT 645080 - - - (TATC)n#Simpl 1 TATCTATCTATC-TATC-TATC-TATCTATCTATCTATCTATCT 41 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.07 (3 / 43), avg. gap size = 1.00 (3 / 3) 24 36.66 1.92 0.00 chr6ptel1M 645596 645699 (354301) (GGA)n#Simple_repeat 1 106 (0) m_b288s252i16 11737 chr6ptel1M 645596 GGA-GAGGAGAAGGAGGAGAAACAAGGGGAAAAGGAGGAGGAAGAAGAGG 645644 - i i iv i i ii i i (GGA)n#Simple 1 GGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGG 50 chr6ptel1M 645645 AGGAAATGGA-GAATAAAAAGAAGAGAAGGAGAAGGAAAAAGTGAAAGAA 645693 iiv - iv ii i i i i ii i v i i i (GGA)n#Simple 51 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG 100 chr6ptel1M 645694 GAGGAG 645699 (GGA)n#Simple 101 GAGGAG 106 Matrix = Unknown Transitions / transversions = 6.00 (24/4) Gap_init rate = 0.02 (2 / 103), avg. gap size = 1.00 (2 / 2) 186 27.42 3.23 0.00 chr6ptel1M 645900 645961 (354039) C AmnL2-1#LINE/L2 (353) 2260 2197 m_b288s601i36 11738 chr6ptel1M 645900 GAGG-AGGCTGGAACCAGTTGGTGAAGGGCTTTAAATACCAAACAGG-AG 645947 - i v ivi i i v v iiv - i C AmnL2-1#LINE/ 2260 GAGGTAGGCTGGAGCAAGTCCATGGAGGGTTTTAAAAACAAGGAAGGCAA 2211 chr6ptel1M 645948 TTTTATAGTTGATC 645961 iv v v C AmnL2-1#LINE/ 2210 TTTTGAACTGGATC 2197 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.64 CpG sites = 9, Kimura (unadjusted) = 34.64 Transitions / transversions = 1.12 (9/8) Gap_init rate = 0.03 (2 / 61), avg. gap size = 1.00 (2 / 2) 300 34.06 9.33 0.82 chr6ptel1M 645987 646211 (353789) C L2#LINE/L2 (285) 2797 2554 m_b288s601i37 11739 chr6ptel1M 645987 ACTTTAGCAGCTTTGTAAAGGGTAGATGGGAGAGGGGGAAAGGCCATAAG 646036 i i v v vi ii iv ? - v viiv C L2#LINE/L2 2797 ACTCTGGCTGCTGTGTTGAGAATAGACTGNAG-GGGGGCAAGGGTGGAAG 2749 chr6ptel1M 646037 AAAGCAAAGCAATCAGA---CT-TTACAATAATATAGATGAGAGGTGATA 646082 v i v i v i i i--- - i i vi ii i i C L2#LINE/L2 2748 CAGGGAGACCAGTTAGGAGGCTATTGCAGTAATCCAGGCGAGAGATGATG 2699 chr6ptel1M 646083 CTGGTTTGGACTTGGGTGATAG-AGAAAAGG-GGACAGATGTG---AGAG 646127 v i iv i i - vii - vv v ---i v C L2#LINE/L2 2698 GTGGCTTGGACCAGGGTGGTGGCAGTGGAGGTGGTGAGAAGTGGTCGGAT 2649 chr6ptel1M 646128 TGGGGA------------ATAGCACTGATGAGACTTAGCAAATGGAGTGG 646165 vv ------------i vi i iii i - vi v C L2#LINE/L2 2648 TCTGGATATATTTTGAAGGTAGAGCCGACAGGATTT-GCTGATGGATTGG 2600 chr6ptel1M 646166 AGAGGGTAGATGAGGGAGAGAAAGCAATTCAGGATGACCCTGAGAT 646211 viv vivi i i i v i iv i ii i C L2#LINE/L2 2599 ATGTGGGGTGTGAGAGAAAGAGAGGAGTCAAGGATGACTCCAAGGT 2554 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 45.29 CpG sites = 47, Kimura (unadjusted) = 47.95 Transitions / transversions = 1.62 (47/29) Gap_init rate = 0.04 (8 / 224), avg. gap size = 2.88 (23 / 8) 349 26.99 0.91 5.71 chr6ptel1M 646385 646494 (353506) L3#LINE/CR1 3897 4001 (98) m_b288s601i38 11740 chr6ptel1M 646385 AAAACTTTCTGCTCATTTGAGTTATTCCAAAGTGGAATGGCCTTCCTTGA 646434 i iviv iv i i i v i v v i ? L3#LINE/CR1 3897 AGAACTTTCTAACAATCAGAGCTGTCCAAAAATGGAATGGGCTGCCTCGN 3946 chr6ptel1M 646435 GAGAGGAGGAAATTGCTTTCCCCAGCACTGGAGGTCTTTAAGT-GAAGTT 646483 - v vi --- -- iv v i i- i i L3#LINE/CR1 3947 GAG-GTAGTGA---GC--TCCCCGTCACTGGAGGTGTTCAAGCAGAGGCT 3990 chr6ptel1M 646484 GGATAAGTACT 646494 i vi L3#LINE/CR1 3991 GGATGACCACT 4001 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.71 CpG sites = 17, Kimura (unadjusted) = 34.72 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.06 (7 / 109), avg. gap size = 1.00 (7 / 7) 29 0.00 3.23 0.00 chr6ptel1M 646705 646735 (353265) (CAAA)n#Simple_repeat 1 32 (0) c_b288s251i4 11741 chr6ptel1M 646705 CAAA-AAACAAACAAACAAACAAACAAACAAA 646735 - (CAAA)n#Simpl 1 CAAACAAACAAACAAACAAACAAACAAACAAA 32 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.03 (1 / 30), avg. gap size = 1.00 (1 / 1) 300 25.00 1.39 0.00 chr6ptel1M 646943 647014 (352986) C MIR#SINE/MIR (141) 121 49 m_b288s601i39 11742 chr6ptel1M 646943 GAGGCA-ATTGGGTTTAAGGGACTTTCCCAGGGTCACACAGCTAATAAGT 646991 - vv i v vi v i i C MIR#SINE/MIR 121 GAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGT 72 chr6ptel1M 646992 GTCTGAAGTCAGATTTGAACTCA 647014 v v ivivi i i C MIR#SINE/MIR 71 GGCAGAGCCGGGATTCGAACCCA 49 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 26.84 CpG sites = 9, Kimura (unadjusted) = 30.69 Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.01 (1 / 71), avg. gap size = 1.00 (1 / 1) 363 27.85 0.00 0.00 chr6ptel1M 646952 647030 (352970) C MIRc#SINE/MIR (153) 115 37 m_b288s601i40 11742 chr6ptel1M 646952 GGGTTTAAGGGACTTTCCCAGGGTCACACAGCTAATAAGTGTCTGAAGTC 647001 i v v v i i v v iviv C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 66 chr6ptel1M 647002 AGATTTGAACTCATATTCTTCTGATTCCA 647030 i i i i vi ii i i C MIRc#SINE/MIR 65 GGACTCGAACCCAGGTCTTCCTGACTCCA 37 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.05 CpG sites = 14, Kimura (unadjusted) = 36.07 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.00 (0 / 78), avg. gap size = 0.0 (0 / 0) 507 36.01 1.41 0.93 chr6ptel1M 647680 647892 (352108) C 7SLRNA#SINE/Alu (106) 214 1 m_b288s502i4 11743 chr6ptel1M 647680 TTGACTTGTTCTGTTTCTGCCCTGGGCTGGTTTGCCCCAAGTT-GGCAGA 647728 i i i i v i ii vvv - - C 7SLRNA#SINE/A 214 TTGACCTGCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTAGGCA-A 166 chr6ptel1M 647729 CTAAGCACTCCTCTTACTCTGGAGAGCTCATTATATTGCAGCTAGACTTG 647778 ivi iiv i i-i iv i v ii vv iii i C 7SLRNA#SINE/A 165 CCTGGTGGTCCCCC-GCTCCCGGGAGGTCACCATATTGATGCCGAACTTA 117 chr6ptel1M 647779 GTATAGGCAACCAATCGGTTTATCCCTCTGCAACTTAGAACTCCTCAGGT 647828 iii i v i iv v v v i i ii vi v C 7SLRNA#SINE/A 116 GTGCGGACACCCGATCGGCATAGCGCACTACAGCCCAGAACTCCTGGGCT 67 chr6ptel1M 647829 CAAGTAATCCATGGGCCTCAACCTCC--AATGGCAGGGCTTGCTAACATG 647876 ii vivv i -- i i v vi i vii ii C 7SLRNA#SINE/A 66 CAAGCGATCCTCCCGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCG 17 chr6ptel1M 647877 TGTCCTCCCATCTGGC 647892 i i vi v ii i C 7SLRNA#SINE/A 16 CGCCACCGCGCCCGGC 1 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.16 CpG sites = 51, Kimura (unadjusted) = 52.81 Transitions / transversions = 2.04 (51/25) Gap_init rate = 0.02 (4 / 212), avg. gap size = 1.25 (5 / 4) 516 32.30 0.62 0.00 chr6ptel1M 647943 648103 (351897) C L3#LINE/CR1 (30) 4069 3908 m_b288s601i41 11744 chr6ptel1M 647943 GGAC-TTAGAGACCCCCTAGCTCAGACTCTCACCTAGTTGAGGGGTCTTT 647991 - ii vi ii iv i i i i vv ii ii C L3#LINE/CR1 4069 GGACCTTAGAGGTCATCTAGTCCAACCTCCCATCCAATGCAGGAATCCCT 4020 chr6ptel1M 647992 TTTACAACATCCCTCCTAAACAGTCACTCAGCCTTTGCTTGTAGCTTTCC 648041 i vvi iii ii i v vvii C L3#LINE/CR1 4019 TCTACAACATCCCTGACAAGTGGTCATCCAGCCTCTGCTTGAACACCTCC 3970 chr6ptel1M 648042 CACAACGGGGCTCTCATTGTCTCCCAAGGCAGCACCTTCCATTAGTTGAC 648091 viii vv i ii ? i v v vv v C L3#LINE/CR1 3969 AGTGACGGGGAGCTCACTACCTCNCGAGGCAGCCCATTCCATTTTTGGAC 3920 chr6ptel1M 648092 ACAGCTGACTGT 648103 vvv i C L3#LINE/CR1 3919 AGCTCTGATTGT 3908 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 43.24 CpG sites = 32, Kimura (unadjusted) = 44.41 Transitions / transversions = 1.60 (32/20) Gap_init rate = 0.01 (1 / 160), avg. gap size = 1.00 (1 / 1) 510 29.95 2.89 3.49 chr6ptel1M 648359 648531 (351469) MIR3#SINE/MIR 16 187 (21) m_b288s601i42 11745 chr6ptel1M 648359 AGTGGAAAGATTATGA--TTGGAGTTAAAGGATATGGGTTCAAATTCTGC 648406 ii i vi i i-- v i iii iv v i i i v MIR3#SINE/MIR 16 AGCAGAGAGAGCACGGACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCGG 65 chr6ptel1M 648407 TCTTGCTGTTTACT--CTGAATAGGACTTTGGGCAAGTCACTTACACC-C 648453 iii iii v -- -- iv i - - MIR3#SINE/MIR 66 CTCTGCCACTAACTNGCTG--TGTGACCTTGGGCAAGTCACTT-CACCTC 112 chr6ptel1M 648454 TCAATGGGGACCCAGTTTCCTTGGCTTTAAAATGAGAGGGTTTGACTAGC 648503 ---v v i iiv v i v v MIR3#SINE/MIR 113 TC---TGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGA 159 chr6ptel1M 648504 CAGTGTCTGAATTCCCTTATACTTCTGA 648531 iii v i iv vi vi MIR3#SINE/MIR 160 TGATCTCTAAGGTCCCTTCCAGCTCTGA 187 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.95 CpG sites = 33, Kimura (unadjusted) = 40.05 Transitions / transversions = 1.94 (33/17) Gap_init rate = 0.05 (9 / 172), avg. gap size = 1.22 (11 / 9) 215 32.93 1.19 2.41 chr6ptel1M 648548 648631 (351369) MIR3#SINE/MIR 97 179 (29) m_b288s601i43 11746 chr6ptel1M 648548 CAATTCAATCTCACC-ATTTGGGCCTTAGTTTTGTCAATAGTAAAATAAA 648596 v v - -v i i iv viv i i MIR3#SINE/MIR 97 CAAGTCACT-TCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAG 145 chr6ptel1M 648597 AATAGTGGGTTAAAATAAACTCTAAGATTTCCCCC 648631 iiviv ii - i i v i ii ii MIR3#SINE/MIR 146 GGGGTTGGACT-AGATGATCTCTAAGGTCCCTTCC 179 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 45.99 CpG sites = 18, Kimura (unadjusted) = 45.99 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.04 (3 / 83), avg. gap size = 1.00 (3 / 3) 267 25.24 17.48 0.00 chr6ptel1M 649705 649807 (350193) MIR3#SINE/MIR 85 205 (3) m_b288s601i44 11747 chr6ptel1M 649705 TGGGACCCTGAACAAGTCACTTA-----TCAAGG-----GT-----CATC 649739 v i ii v----- vi ----- ----- MIR3#SINE/MIR 85 TGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATC 134 chr6ptel1M 649740 TGTTACATAAGTCA-TTGGGCTCAGTGATCTTTAAGATCTCTTCCAGGTC 649788 v v i vvi- i vii i i i v MIR3#SINE/MIR 135 TGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTC 184 chr6ptel1M 649789 TGAAAT--TATGGGTCTGTAA 649807 v -- iv i i MIR3#SINE/MIR 185 TGACATTCTATGATTCTATGA 205 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.39 CpG sites = 15, Kimura (unadjusted) = 31.39 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.05 (5 / 102), avg. gap size = 3.60 (18 / 5) 466 20.38 2.52 5.17 chr6ptel1M 649813 649931 (350069) MIRb#SINE/MIR 107 222 (46) m_b288s601i45 11748 chr6ptel1M 649813 TTACTTGCTCTCTCTGTCAGTCTCAGTTTCTTTATCTGTACAATGTGAGT 649862 ivi -- i i i v v --- MIRb#SINE/MIR 107 TTACTTAACCTCTCTG--AGCCTCAGTTTCCTCATCTGTAAAATGGG--- 151 chr6ptel1M 649863 GATAATTGTATCTATATTGCAGGGCTGTGGTGAGGACCAAATGAAATA-- 649910 vi i iv i i v ii i -- MIRb#SINE/MIR 152 GATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAAT 201 chr6ptel1M 649911 GCAT-TGAAGTGTCATAGTACA 649931 - i i - v i MIRb#SINE/MIR 202 GCATGTAAAGCG-CTTAGCACA 222 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 22.10 CpG sites = 16, Kimura (unadjusted) = 24.47 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.07 (8 / 118), avg. gap size = 1.12 (9 / 8) 537 23.15 1.44 3.68 chr6ptel1M 649919 650057 (349943) MIRc#SINE/MIR 10 145 (123) m_b288s601i46 11749 chr6ptel1M 649919 GTGTCATAGTACATAGATTGCTGGCCCTGGAGTCAGAAAG-CCTGGGTTC 649967 viii iv v vii v i i - MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr6ptel1M 649968 AAATCCAGTCTCAGTCACTTACTAGCTGTGTGACCCTGGGTAAGGCAC-T 650016 i i v v v i i i v - MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTT 109 chr6ptel1M 650017 AAACACTGTGTGCCTGGATGTGTAACCTTGATCTGTAAAAT 650057 v v v v vii v ---- i- MIRc#SINE/MIR 110 AACCTCTCTGAGCCTCAGTTT----CCTC-ATCTGTAAAAT 145 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 26.91 CpG sites = 16, Kimura (unadjusted) = 27.93 Transitions / transversions = 1.07 (16/15) Gap_init rate = 0.05 (7 / 138), avg. gap size = 1.00 (7 / 7) 226 24.44 0.00 0.00 chr6ptel1M 650956 651000 (349000) C MIR3#SINE/MIR (34) 174 130 m_b288s601i47 11750 chr6ptel1M 650956 GGTCCTTGGAGATCATCTGGTTGAACCTCTTTATTTCATGGATGA 651000 v i i iv i i i i ii C MIR3#SINE/MIR 174 GGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGA 130 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.72 CpG sites = 9, Kimura (unadjusted) = 31.72 Transitions / transversions = 4.50 (9/2) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 296 18.62 2.94 2.94 chr6ptel1M 651113 651350 (348650) C HERVIP10FH#LTR/ERV1 (4083) 1019 782 m_b288s701i0 11751 chr6ptel1M 651113 CACCTTTTCTCCTCCACACCTTTTCTTTCTCTCTCTCTCTCTCTCTCT-- 651160 iv i i ii vv i v i i i i -- C HERVIP10FH#LT 1019 CACTGTTTTTTCTTTACTACTTCTATCTCTCTCTTTCTTTCTCTCTTTGA 970 chr6ptel1M 651161 CTCTCTCTCTCTCTCTCTCTCTCT--CTCTCTCTCTCTCTCTCTGTCTCT 651208 i v -- i i v C HERVIP10FH#LT 969 CTTTCTGTCTCTCTCTCTCTCTCTGACTCCCTCTTTGTCTCTCTGTCTCT 920 chr6ptel1M 651209 CTCTCTCTCTGTCTCTCTCTCTCTCTGTCTGTCTCTCTCTCTGTCTCTCT 651258 ii i i v ---- i i C HERVIP10FH#LT 919 TCCTCTCTCTGCCTCTCTCTCTCTTTGACT----CCCTCTTTGTCTCTCT 874 chr6ptel1M 651259 ATCTTTCTCTCTGTCTCTCTGTCTCTGTCTCTCTTTCTCTCTCTCTCTGT 651308 v ii v i v v i v C HERVIP10FH#LT 873 CTCTCCCTCTCTCTCTCTTTCTCTCTCTCTCTCTTCCTCTCTCTCTCTCT 824 chr6ptel1M 651309 CTGTC-TCTCTATCT-CTCTCTGTCTCT-ATCTCTTTCTGTCTCT 651350 v - v i - --- -i i ii i C HERVIP10FH#LT 823 CTCTCTTCTCTCTTTCCTCTCTG---CTGGTCTTTCCCTGCCTCT 782 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 21.91 CpG sites = 29, Kimura (unadjusted) = 21.91 Transitions / transversions = 2.07 (29/14) Gap_init rate = 0.05 (12 / 237), avg. gap size = 1.17 (14 / 12) 303 18.60 2.27 2.27 chr6ptel1M 651166 651385 (348615) C HERVIP10FH#LTR/ERV1 (4104) 998 779 m_b288s701i1 11751 chr6ptel1M 651166 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTCTCTCTCTCTC 651215 v i i i vv i v v C HERVIP10FH#LT 998 TCTATCTCTCTCTTTCTTTCTCTCTTTGACTTTCTGTCTCTCTCTCTCTC 949 chr6ptel1M 651216 TCTGTCTCTCTCTCTCTCTGTCTGTCTCTCTCTCTGTCTCTCTATCTTTC 651265 v i i v v ii v vi v i C HERVIP10FH#LT 948 TCTGACTCCCTCTTTGTCTCTCTGTCTCTTCCTCTCTCTGCCTCTCTCTC 899 chr6ptel1M 651266 TCTCTGTCTCTCTGTCTCTGTCTCTCTTTCTCTCTCTCTCTGTCTGTCTC 651315 i v i -- i i i v v C HERVIP10FH#LT 898 TCTTTGACTCCC--TCTTTGTCTCTCTCTCTCCCTCTCTCTCTCTTTCTC 851 chr6ptel1M 651316 TCTATCTCTCTCTGTCTCTATCTCTTTCTGTCTCTCTCTCTCTGT-GTCT 651364 -- vi v i v - v -v C HERVIP10FH#LT 850 TC--TCTCTCTCTTCCTCTCTCTCTCTCTCTCTCT-TCTCTCTTTCCTCT 804 chr6ptel1M 651365 CT----GTCTATCTCTGTCTCTGTC 651385 ---- v i i i C HERVIP10FH#LT 803 CTGCTGGTCTTTCCCTGCCTCTGCC 779 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 21.51 CpG sites = 20, Kimura (unadjusted) = 21.51 Transitions / transversions = 1.00 (20/20) Gap_init rate = 0.03 (7 / 219), avg. gap size = 1.43 (10 / 7) 394 16.30 3.21 1.58 chr6ptel1M 651206 651392 (348608) C HERVIP10FH#LTR/ERV1 (4104) 998 809 m_b288s701i2 11751 chr6ptel1M 651206 TCTCTCTCTCTCTGTCTCTCTCTCTCT--CTGTCTGTCTCTCTCTCTGTC 651253 v v i i -- v -- C HERVIP10FH#LT 998 TCTATCTCTCTCTTTCTTTCTCTCTTTGACTTTCTGTCTCTCTCTCT--C 951 chr6ptel1M 651254 TCTCTATCTTTCTCTCTGTCTCTCTGTCTCTGTCTCTCT----TTCTCTC 651299 iv ii i vi ----i C HERVIP10FH#LT 950 TCTCTGACTCCCTCTTTGTCTCTCTGTCTCTTCCTCTCTCTGCCTCTCTC 901 chr6ptel1M 651300 TCTCTCTGTCTGTCTCTCTATCTCTCTCTGTCTCTATCTCTTTCTGTCTC 651349 i v vi i i v i v i v C HERVIP10FH#LT 900 TCTCTTTGACTCCCTCTTTGTCTCTCTCTCTCCCTCTCTCTCTCTTTCTC 851 chr6ptel1M 651350 TCTCTCTCTGTGTCTCTGTCTATCTCTGTCTCTGTCTCTCTTT 651392 v vi v v v - C HERVIP10FH#LT 850 TCTCTCTCTCTTCCTCTCTCTCTCTCTCTCTCT-TCTCTCTTT 809 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 18.47 CpG sites = 15, Kimura (unadjusted) = 18.47 Transitions / transversions = 1.00 (15/15) Gap_init rate = 0.03 (5 / 186), avg. gap size = 1.80 (9 / 5) 220 32.89 7.89 0.00 chr6ptel1M 651487 651562 (348438) C MIR3#SINE/MIR (26) 182 101 m_b288s601i48 11752 chr6ptel1M 651487 GTTGGAAGAGACCGGACAAACCATCAAGTGAAACTCCTCCATCTTACAAA 651536 i i vv v i i v vv i ii i i C MIR3#SINE/MIR 182 GCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGA 133 chr6ptel1M 651537 TG------CTGAGATCTAGGAAAACTCAGTGA 651562 ------ ii i ii iiivv C MIR3#SINE/MIR 132 TGAGGAAACTGAGGCCCAGAGAGGTGAAGTGA 101 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 46.13 CpG sites = 17, Kimura (unadjusted) = 46.13 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.01 (1 / 75), avg. gap size = 6.00 (6 / 1) 326 16.18 4.41 0.00 chr6ptel1M 651615 651682 (348318) C MER63C#DNA/hAT-Tip100 (8) 922 852 m_b288s502i5 11753 chr6ptel1M 651615 TGCTGGTAAATGTTTAACAGCTGGCTCCCTGAAAATAAAAGTGTATGTGT 651664 i i i iii v i i C MER63C#DNA/hA 922 TGCTGGTAAATGTTTAACAACCGGCTCTCTGGGGAAAAAAATGTATGTAT 873 chr6ptel1M 651665 G-AAATAC-T-TTTAAGTTTA 651682 - v - - v C MER63C#DNA/hA 872 GTATATACATATATAAGTTTA 852 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 16.89 CpG sites = 8, Kimura (unadjusted) = 18.69 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.04 (3 / 67), avg. gap size = 1.00 (3 / 3) 521 11.49 0.00 1.15 chr6ptel1M 651665 651752 (348248) C MER63D#DNA/hAT-Tip100 (593) 468 382 m_b288s502i6 11753 chr6ptel1M 651665 GAAATACTTTTAAGTTTAATTTGCAGGATTAACATTTTCTCCATCACTTT 651714 v i i vv C MER63D#DNA/hA 468 GACACACTTTTAAGTTTAATCTGCATTATTAACATTTTCTCCATCACTTT 419 chr6ptel1M 651715 ATTAATTTTTAGACAATCAATAAAATAATAAATCAAGC 651752 v -v i i i C MER63D#DNA/hA 418 CTTAA-GTCTAGACAATCAACAAAACAATAAATCAAGC 382 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 12.51 CpG sites = 5, Kimura (unadjusted) = 12.51 Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.01 (1 / 87), avg. gap size = 1.00 (1 / 1) 437 27.57 0.63 8.16 chr6ptel1M 651864 652021 (347979) MIRb#SINE/MIR 5 151 (117) m_b288s601i49 11754 chr6ptel1M 651864 GGGGCAGCTAGAGGGCACAGTGGGTAGAATGCAGGGCCTGAGAGTCTGAA 651913 ---iv ii iv iii - i vi v v MIRb#SINE/MIR 5 GGGGCAGC---GTGGTGCAGTGGAAAGAGCAC-GGGCTTTGGAGTCAGAC 50 chr6ptel1M 651914 AGACTCATCTTCCTGAGTTCACATCTGGTCTTAGATAATTTCTGTCATTG 651963 -------- i iv iv v iv vi v v iv vv MIRb#SINE/MIR 51 AGAC--------CTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTG 92 chr6ptel1M 651964 TGGCTCTGGGCAAGTCACTTTACCT-TGTGTGTCTCAGTTTCCTCATCAG 652012 i ii i v - v v i v MIRb#SINE/MIR 93 TGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTG 142 chr6ptel1M 652013 TAAAATGAG 652021 i MIRb#SINE/MIR 143 TAAAATGGG 151 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.51 CpG sites = 21, Kimura (unadjusted) = 34.58 Transitions / transversions = 1.11 (21/19) Gap_init rate = 0.08 (13 / 157), avg. gap size = 1.00 (13 / 13) 225 23.96 0.00 7.94 chr6ptel1M 653296 653363 (346637) C DNM1r#Unknown (2113) 2549 2487 m_b288s502i7 11755 chr6ptel1M 653296 TTGTATATATGCATGACAGTGTATATACATACATACACACAATACACACA 653345 v ? i i i---- i i i - C DNM1r#Unknown 2549 TTCTATANATACGTA----TATATACACATATATACACACA-TACACACA 2505 chr6ptel1M 653346 TGTATGTGTATGTCTACA 653363 i iiiii i v C DNM1r#Unknown 2504 TATACACACATATATACA 2487 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 29.13 CpG sites = 13, Kimura (unadjusted) = 31.71 Transitions / transversions = 6.50 (13/2) Gap_init rate = 0.07 (5 / 67), avg. gap size = 1.00 (5 / 5) 234 6.47 1.89 12.50 chr6ptel1M 653298 653350 (346650) C DNM1r#Unknown (2125) 2537 2490 m_b288s502i8 11755 chr6ptel1M 653298 GTATATATGCATGACAGTGTATATACATACATACACACA-ATACACACAT 653346 i --- --- i - C DNM1r#Unknown 2537 GTATATATACA---CA---TATATACACACATACACACATATACACACAT 2494 chr6ptel1M 653347 GTAT 653350 i C DNM1r#Unknown 2493 ATAT 2490 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 6.83 CpG sites = 3, Kimura (unadjusted) = 6.83 Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.13 (7 / 52), avg. gap size = 1.00 (7 / 7) 225 31.97 0.00 4.26 chr6ptel1M 653390 653487 (346513) MIR1_Amn#SINE/MIR 1 94 (136) m_b288s601i50 11756 chr6ptel1M 653390 TATGGAGACAAATAAGTGGCTCAGTGGATAAAGCAATGGGGCTACAGTCA 653439 v i i- -- iii i v i- iviiiiv MIR1_Amn#SINE 1 TAGGGAGGCAG-T--GTGGTCTAGTGGATAGAGCACTGGA-CTGGGACTC 46 chr6ptel1M 653440 GGAAGACCCGAGTTCAAATACAGCCACAGACATTTACTAGTTGTTTGA 653487 i i i ? ? v v v v v v i ?i i? i ?v MIR1_Amn#SINE 47 GGGAGACCTGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGA 94 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 47.09 CpG sites = 19, Kimura (unadjusted) = 47.09 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.04 (4 / 97), avg. gap size = 1.00 (4 / 4) 331 27.71 0.00 0.00 chr6ptel1M 653405 653487 (346513) MIRc#SINE/MIR 10 92 (176) m_b288s601i51 11756 chr6ptel1M 653405 GTGGCTCAGTGGATAAAGCAATGGGGCTACAGTCAGGAAGACCCGAGTTC 653454 iv v i v ivi iv i i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr6ptel1M 653455 AAATACAGCCACAGACATTTACTAGTTGTTTGA 653487 i i v v v v v v i i v MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGA 92 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.08 CpG sites = 11, Kimura (unadjusted) = 34.88 Transitions / transversions = 0.92 (11/12) Gap_init rate = 0.00 (0 / 82), avg. gap size = 0.0 (0 / 0) 357 28.44 6.42 0.00 chr6ptel1M 653900 654008 (345992) C MIRc#SINE/MIR (53) 215 100 m_b288s601i52 11757 chr6ptel1M 653900 TTATATAAATTATTCCATTTAATCCTCACAATTATGCTGTGAAATTTGTA 653949 i i v ii i iv iv ii vv i C MIRc#SINE/MIR 215 TCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCA 166 chr6ptel1M 653950 GTGCA---ACCATTATTCCCATTTTAAGGATGAGGAAATTGAAAT----A 653992 v --- ii i vi i iii---- C MIRc#SINE/MIR 165 GGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGA 116 chr6ptel1M 653993 TAAATGAAATGATTTG 654008 v ii v i i C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTG 100 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.81 CpG sites = 22, Kimura (unadjusted) = 37.81 Transitions / transversions = 2.44 (22/9) Gap_init rate = 0.02 (2 / 108), avg. gap size = 3.50 (7 / 2) 186 27.13 0.00 4.17 chr6ptel1M 654075 654124 (345876) C L2d_3end#LINE/L2 (0) 516 469 m_b288s601i53 11758 chr6ptel1M 654075 TTAGTCAATTTATTTCAACAAACATTTGTTAAACACCTACCATGTGTTTA 654124 i i iv -- ii i i i i i i i C L2d_3end#LINE 516 TCAATCAATCAAT--CAACAAGTATTTATTGAGCGCCTACTATGTGCTCA 469 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.08 CpG sites = 12, Kimura (unadjusted) = 37.85 Transitions / transversions = 12.00 (12/1) Gap_init rate = 0.04 (2 / 49), avg. gap size = 1.00 (2 / 2) 215 28.15 2.14 16.26 chr6ptel1M 654082 654221 (345779) C L2a_3end#LINE/L2 (4) 513 391 m_b288s601i54 11758 chr6ptel1M 654082 ATTTATTTCAACAAACATTTGTTAAACACCTACCATGTGTTTACTTACAC 654131 i - i i i i i i i--- vvi C L2a_3end#LINE 513 ATTCATT-CAACAAATATTTATTGAGCGCCTACTATGTGC---CAGGCAC 468 chr6ptel1M 654132 CATTAGAAAAGGGAGTGGGCTCCTCCTTCCTGGATGATGGATTAAA-AAA 654180 ii vv ---- v iv ------------ ivv v v i - C L2a_3end#LINE 467 TGTTCTA----GGCGCTGG------------GGATACAGCAGTGAACAAA 434 chr6ptel1M 654181 AAAGAC-ACAGTCCTTGCCCTTG-GGATCTAATATTCTACTGG 654221 v - v i ii- v v i v C L2a_3end#LINE 433 ACAGACAAAAGTCCCTGCCCTCATGGAGCTTACATTCTAGTGG 391 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.57 CpG sites = 18, Kimura (unadjusted) = 34.86 Transitions / transversions = 1.20 (18/15) Gap_init rate = 0.17 (23 / 139), avg. gap size = 1.00 (23 / 23) 12 11.59 6.90 0.00 chr6ptel1M 655480 655508 (344492) (CTTTC)n#Simple_repeat 1 31 (0) m_b288s252i17 11759 chr6ptel1M 655480 CTCTCCTTTCC-TT-CTTTCCTTCTCTTTCC 655508 i - - ii (CTTTC)n#Simp 1 CTTTCCTTTCCTTTCCTTTCCTTTCCTTTCC 31 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.07 (2 / 28), avg. gap size = 1.00 (2 / 2) 198 25.00 0.00 0.00 chr6ptel1M 655556 655595 (344405) MIR3#SINE/MIR 64 103 (105) m_b288s601i55 11760 chr6ptel1M 655556 GGCCTTGCTACCAACTTCCTATGTAGCCTTTGACAAGTCA 655595 ii i i ?v i ii v i MIR3#SINE/MIR 64 GGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCA 103 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.66 CpG sites = 8, Kimura (unadjusted) = 33.66 Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 210 34.20 0.00 2.53 chr6ptel1M 655768 655848 (344152) L3#LINE/CR1 2882 2960 (1139) m_b288s601i56 11761 chr6ptel1M 655768 ACTTACTTTCTCTTCTTTTTGTTTTCAAGATTACTAAATTAGTAGATAAA 655817 v i iv i i -- vvi i i i i i v i L3#LINE/CR1 2882 ACTAACCTCATTTCCTTTTT--TGATAGGGTTACTAGACTGGTAGATCAG 2929 chr6ptel1M 655818 GGGAACGTTGTGGGTATAATTTAGCTAAATT 655848 i ii i ii ? i v v ii L3#LINE/CR1 2930 GGGAATGCCGTAGACANAGTGTATCTGGATT 2960 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 48.26 CpG sites = 20, Kimura (unadjusted) = 51.08 Transitions / transversions = 2.86 (20/7) Gap_init rate = 0.03 (2 / 80), avg. gap size = 1.00 (2 / 2) 724 24.86 7.35 1.39 chr6ptel1M 655875 656078 (343922) C MIRb#SINE/MIR (15) 253 38 m_b288s601i57 11762 chr6ptel1M 655875 ATTTATTAAGTGTCTGATATGTGCTGGGCA--GTGTTAAGCACTTTATA- 655921 i i ii iv ii -- i i i - C MIRb#SINE/MIR 253 ATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACAT 204 chr6ptel1M 655922 -CATTAT----TTTGATCCTCACAACTTTCCTGGCAGGTAGGTGCTAGCT 655966 - ---- i vvi vv ii --- C MIRb#SINE/MIR 203 GCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTA--- 157 chr6ptel1M 655967 TTATCCCCATTT-ACAATTGAGGAAATGAAGGCAGATAGAGATTAACTGA 656015 - iv ivi vv v i v i C MIRb#SINE/MIR 156 TTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAA 107 chr6ptel1M 656016 TTTTCCTGGGAGTATGCTGCTAGTAAG-----AAGCC-AGATTTGAATTC 656059 i v iii ivi ii v -----i -i i ii C MIRb#SINE/MIR 106 CTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCC 57 chr6ptel1M 656060 AGGTCTTTCTGATTGCAGA 656078 v i v i C MIRb#SINE/MIR 56 AGGTCTGTCTGACTCCAAA 38 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.14 CpG sites = 34, Kimura (unadjusted) = 31.39 Transitions / transversions = 2.12 (34/16) Gap_init rate = 0.05 (10 / 203), avg. gap size = 1.80 (18 / 10) 263 32.75 5.69 3.17 chr6ptel1M 655971 656093 (343907) C MIR3#SINE/MIR (62) 146 21 m_b288s601i58 11762 chr6ptel1M 655971 CCCCATTT-ACAATTGAGGAAATGAAGGCAGATAGAGATTAACTGATTTT 656019 i - iv ivi vv v i v v i v C MIR3#SINE/MIR 146 CCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTG 97 chr6ptel1M 656020 CCTGGGAGTATGCTGCTAGTAAG-----AAGCC-AGATTTGAATTCAGGT 656063 iii ivi ii v ? v -----i -i i v ii C MIR3#SINE/MIR 96 CCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGT 47 chr6ptel1M 656064 CTTTCTGATTGCAGATAGGCTGGACTCCCT 656093 - i i v ---i v i vi i C MIR3#SINE/MIR 46 C-TCCTGACTCC---CAGTCCGTGCTCTCT 21 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 43.89 CpG sites = 24, Kimura (unadjusted) = 45.50 Transitions / transversions = 1.60 (24/15) Gap_init rate = 0.06 (7 / 122), avg. gap size = 1.57 (11 / 7) 791 35.98 4.73 1.37 chr6ptel1M 656125 656758 (343242) CR1-3_Croc#LINE/CR1 1948 2602 (1003) m_b288s551i0 11763 chr6ptel1M 656125 GCAAAGCTTTTGATAAAGTTCCATATATCATTGCTGTGAAGAAGATGGAG 656174 i i i i ii iv v viii i v iv CR1-3_Croc#LI 1948 GCAAGGCTTTTGACAAGGTCCCGCATGACCTTCTCATAAACAAATTGGAG 1997 chr6ptel1M 656175 AGATTGTGGACTG--CAAAGCCA------GGTGGATTCAGAAGCGGTTGG 656216 i - i -- i i ------ vv v vi i vi CR1-3_Croc#LI 1998 AAAT-GTGGGCTGGACAAAACTACTACAAGGTGGATAGATAACTGGCTCA 2046 chr6ptel1M 656217 ATGA--GCAGACACCATACGTAGTGAACAACGGCTCCATGGAAGCGTGGC 656264 ii-- ii -- viv i v vi v vv vi CR1-3_Croc#LI 2047 ATAGCCGCAAGCA--AAGGGTAATTATTAACGGGTCCATGTCAGAATGGC 2094 chr6ptel1M 656265 AGG--TCTTCG-GCCGAGTCTCTCCGGGATCTGTGCTTGGCCCTTTGCTG 656311 --vi - iv i v v i v v vv CR1-3_Croc#LI 2095 AGGAGGTTTCGAGTGGAGTCCCACAGGGGTCTGTCCTGGGCCCGGTGCTG 2144 chr6ptel1M 656312 TTCAGCATTCTATATTGGTGACTTGGATAGAAGCACACATGGCCTGCTCA 656361 i i vi - ii i ivvi i v vi i vi v CR1-3_Croc#LI 2145 TTCAACGTGTT-TATTAATGATTTGGATGCTGGCATAGAAAGCTTCTTGA 2193 chr6ptel1M 656362 TCAAAGTTTCAGATGGCACGGAGCTGAGAAGGCGAGCTAATATAGCAGCT 656411 v iv v i i i i i vvv v i iivii vv CR1-3_Croc#LI 2194 GCAAGTTTGCAGACGACACGAAACTGGGAAGGATTGCGAACACGTTGGAG 2243 chr6ptel1M 656412 GATGGAATCGGGAGCCAAAGGGATCTTGGCAGGCTAGAGTGTTAGGCTGA 656461 i ?i v vi vi i i i i ii i iv i i ii CR1-3_Croc#LI 2244 GACGNGAGCGCAATTCAGAAGGATCTCGACAGATTGGAAAGCTGGGCTAG 2293 chr6ptel1M 656462 ATCTAATAAGCTGAAATCCAATAGGGATAAATGGAAAGCCTTGC-CCTTG 656510 v i i v i i iv i v i ivi i - i CR1-3_Croc#LI 2294 AGCTAACAGGATGAAGTTCAATGCGGACAAATGCAAGGTGCTACACCTCG 2343 chr6ptel1M 656511 GATACGGAAT--TCAATCTCGTGAGTAGGGAA--GCTG-----TGGGTAG 656551 --iv -- vvv iii i vii -- v ----- v i CR1-3_Croc#LI 2344 G--GAGGAATAATCAAAAACACAAATACAAAATGGGTGACACCTGGCTGG 2391 chr6ptel1M 656552 ACAGCAGTTGTCTTGAAAAAGATCTGGGGGCTTTAGTGAGCTACCAGCTC 656601 ii ivv v v i i i ii i iiiii vii CR1-3_Croc#LI 2392 ATGGCAGCACTATGGAAAAGGACCTGGGAGTCTTGGTAGATCACAGACTC 2441 chr6ptel1M 656602 AATATATGTCTCCAGAGTGATGTCAGT----CAAAAGCGCTAATATAATC 656647 iv v v - i---- - v iiii i CR1-3_Croc#LI 2442 AATATGAGTCTGCAGTGTGATG-CAGCCGCACAAAAG-GCGAATGCGGTT 2489 chr6ptel1M 656648 TCGAGCCACAAGGAGAGGGGCA-GAGCCTCCAGTAACGGGGAGTTGAT-C 656695 i i vii vvi v ii -v viv v vv - v -v CR1-3_Croc#LI 2490 TTGGGATGCATCAATAGAAGCATTAGGTGCAAGACAC-GGGAGGTGATAG 2538 chr6ptel1M 656696 TCCCACCGTACTCTG-GCTTCTCAAACCTCCTCGGGAATATTGCATCTGC 656744 v v iv v -i vv i ii v v i i ii viiv CR1-3_Croc#LI 2539 TGCCTCTCTACTCGGCACTGGTTAGGCCTCATCTGGAGTACTGTGTGCAG 2588 chr6ptel1M 656745 CTCTGAGTGCCACA 656758 i i iv CR1-3_Croc#LI 2589 TTCTGGGCTCCACA 2602 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 48.72 CpG sites = 134, Kimura (unadjusted) = 51.44 Transitions / transversions = 1.47 (134/91) Gap_init rate = 0.03 (22 / 633), avg. gap size = 1.77 (39 / 22) 683 29.69 9.71 2.73 chr6ptel1M 656759 657170 (342830) L3#LINE/CR1 3655 4094 (5) m_b288s601i59 11761 chr6ptel1M 656759 GAGGAGGGCGGCGGGAACGGTGAAGGGCTTTCTGTG---TATGTGGTTAT 656805 i i vi i i --- vi---i vi - L3#LINE/CR1 3655 GAGGAGAGCGACCAGGATGGTGAAGGG---TCTGGAAACCATGTCAT-AT 3700 chr6ptel1M 656806 G-GGAGCATTAATGAAAGAGCTGGCCACGTTCAGCCTGGAGAGTAGAAGG 656854 - i iv -- i i vv i i iv i L3#LINE/CR1 3701 GAGGAACGGT--TGAAGGAACTGGGGATGTTTAGCCTGGAGAAGAGAAGA 3748 chr6ptel1M 656855 CCT-------------TGGCTGGGTTCAAGTATTTGAAGGCTTTTCACAG 656891 i ------------- i vv i vi v iiv L3#LINE/CR1 3749 CTTAGAGGAGACATGATAGCTGTCTTCAAATATTTGAAGGGCTGTCATGT 3798 chr6ptel1M 656892 AGAGGAGGAGACAAGGGGCTTATTTAGTTTGGCCTGGGAAGGCAGAACTA 656941 i i - iv i-- iv v iivi i L3#LINE/CR1 3799 GGAAGAGG-GATTAGA--CTTATTCTGTGTGGCTCCAGAGGGCAGAACTA 3845 chr6ptel1M 656942 GGCGCAAGTGGGT-AAAGTTGCA-AGAGACCGGGTTAAGCTTGATATTAG 656989 vv - -i i -i i v iv vi ii v L3#LINE/CR1 3846 GGACCAA-TGGGTGGAAGTTACAGGGAGGCAGATTTCGGCTCAATATAAG 3894 chr6ptel1M 656990 G-GGAAATCTCTTCCAGTCAGAGCTGTCCCA---------GGGCTTTCTA 657029 -i v i vv i v --------- vi v L3#LINE/CR1 3895 GAAGAACTTTCTAACAATCAGAGCTGTCCAAAAATGGAATGGGCTGCCTC 3944 chr6ptel1M 657030 GGCAGGACTTGGTTTCCCCTTC-CTACGATGTCTTCAAGCAGGAGCAGGA 657078 ?v vvv ivi v - i- v v ii v L3#LINE/CR1 3945 GNGAGGTAGTGAGCTCCCCGTCACTG-GAGGTGTTCAAGCAGAGGCTGGA 3993 chr6ptel1M 657079 TCATTGCT------GGATGTATTATGGGG----CCTGTGTTATATGTTAT 657118 v iii ------ vv vii ---- ii iv vv v L3#LINE/CR1 3994 TGACCACTTGTCAGGGATGTTGTAGAAGGGATTCCTGCATTGGATGGGAG 4043 chr6ptel1M 657119 AGTGGCCCGGTGTTTCCTCTGAGTACTCTTCCAGCTAATAGATCCTGTGA 657168 iv v ii -i vv i vv i i vvv i L3#LINE/CR1 4044 GTTGGACTAG-ATGACCTCTAAGGTCCCTTCCAACTCTGAGATTCTGTGA 4092 chr6ptel1M 657169 CT 657170 i L3#LINE/CR1 4093 TT 4094 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.98 CpG sites = 65, Kimura (unadjusted) = 38.81 Transitions / transversions = 1.20 (65/54) Gap_init rate = 0.05 (22 / 411), avg. gap size = 2.36 (52 / 22) 229 26.00 0.00 0.00 chr6ptel1M 657843 657892 (342108) C L3#LINE/CR1 (5) 4094 4045 m_b288s601i60 11764 chr6ptel1M 657843 AGTCACAGACTTTGGAAATTGGAAGGGTTCTCAGAGGCAGTCTAGTCCAA 657892 i v i vii i vi i ivi C L3#LINE/CR1 4094 AATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCAA 4045 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.35 CpG sites = 9, Kimura (unadjusted) = 33.35 Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 347 28.73 18.41 3.03 chr6ptel1M 658001 658201 (341799) MIRc#SINE/MIR 29 259 (9) m_b288s601i61 11765 chr6ptel1M 658001 ACTGGAGTTGGAATGAGAAAG-CCCGAGTTTGGGCCTTGGCTCTATTAC- 658048 v i v i - i i i i i ii iii - MIRc#SINE/MIR 29 ACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACT 78 chr6ptel1M 658049 --CTAAATGTGTGCTTCTGAGGAAG-CAGTCAACCATGTTCTTT----TT 658091 -- iv viii i v - v i ---- i ----i MIRc#SINE/MIR 79 TACTAGCTGTGTGACCTTGGGCAAGTCACTTAACC----TCTCTGAGCCT 124 chr6ptel1M 658092 TTG-TTCCT--TCTGGAAA---GGAACGGAATCGGTATTTGCTCCATTTA 658135 iv - -- v --- i i-- -ii ii i iiii MIRc#SINE/MIR 125 CAGTTTCCTCATCTGTAAAATGGGGAT--AAT-AATACCTGCCCTGCCTA 171 chr6ptel1M 658136 CTTCACTGGGCTTTTGGGAAG-------GAG-----------GAA----C 658163 i v i v v i ------- ----------- ---- MIRc#SINE/MIR 172 CCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGC 221 chr6ptel1M 658164 TTTGTAAACCTTAAAGCACCACATAAATATGAGCTGTT 658201 iv ii i i i i i v? MIRc#SINE/MIR 222 TTTGTAAACTGTAAAGTGCTATACAAATGTAAGGNGTT 259 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.71 CpG sites = 43, Kimura (unadjusted) = 39.59 Transitions / transversions = 3.31 (43/13) Gap_init rate = 0.09 (18 / 200), avg. gap size = 2.44 (44 / 18) 12 17.55 9.43 1.75 chr6ptel1M 658306 658358 (341642) (CATTT)n#Simple_repeat 1 57 (0) m_b288s252i18 11766 chr6ptel1M 658306 CATTTCATTTGATGGACATTTC-TTTC-TTTC-TTT-TTTTTTTTTTTTT 658351 v -vv - - - -v iv iv (CATTT)n#Simp 1 CATTTCATTTCAT-TTCATTTCATTTCATTTCATTTCATTTCATTTCATT 49 chr6ptel1M 658352 TC-TTTCA 658358 - (CATTT)n#Simp 50 TCATTTCA 57 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.12 (6 / 52), avg. gap size = 1.00 (6 / 6) 21 13.88 0.00 0.00 chr6ptel1M 658324 658356 (341644) (T)n#Simple_repeat 1 33 (0) m_b288s252i19 11767 chr6ptel1M 658324 TTTCTTTCTTTCTTTTTTTTTTTTTTTTTCTTT 658356 i i i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 33 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 520 28.05 10.31 2.50 chr6ptel1M 658434 658656 (341344) MIRc#SINE/MIR 3 242 (26) m_b288s601i62 11768 chr6ptel1M 658434 AGGCAGCTAGGTGGAATAATGGGTAAAGC-CAGGACTTGAATTAGCATTA 658482 i--- vii i iv i - v i v -- vv MIRc#SINE/MIR 3 AGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGT--CAGGA 47 chr6ptel1M 658483 AAATCTG----------CC--CTCCAACCCTTATCAGCAGTATAATTATC 658520 i i ---------- -- iiv v ii v i i iiv v MIRc#SINE/MIR 48 AGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTG 97 chr6ptel1M 658521 AGCAAGATTA-TTAACTTCTGTCTGCCTCAGTTTCCTATTCTGTTCAAAG 658569 i - i - i v vv vv vv v MIRc#SINE/MIR 98 GGCAAG-TCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATG 146 chr6ptel1M 658570 GAGATAATAATA--------ACCTCCCTCCAAATGTTGATATGAGGATCA 658611 i --------i v vv iv v i MIRc#SINE/MIR 147 GGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCA 196 chr6ptel1M 658612 AATGAAAGAATATTTATGAAA-TGTTTTATAAACCTTAAGGGACTA 658656 i v i v i -i i i iv i vi MIRc#SINE/MIR 197 AATGAGATAATGTATGTGAAAGCGCTTTGTAAACTGTAAAGTGCTA 242 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.12 CpG sites = 33, Kimura (unadjusted) = 35.85 Transitions / transversions = 1.18 (33/28) Gap_init rate = 0.05 (12 / 222), avg. gap size = 2.42 (29 / 12) 17 31.23 0.00 0.00 chr6ptel1M 658665 658719 (341281) (CCATTA)n#Simple_repeat 1 55 (0) m_b288s252i20 11769 chr6ptel1M 658665 CCATCATCATTATCATTGCTATTACTGTCACCATTACGATTATTATTACT 658714 i i i i i ii i v ii i (CCATTA)n#Sim 1 CCATTACCATTACCATTACCATTACCATTACCATTACCATTACCATTACC 50 chr6ptel1M 658715 ATCAC 658719 i (CCATTA)n#Sim 51 ATTAC 55 Matrix = Unknown Transitions / transversions = 12.00 (12/1) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 chr6ptel1M 658813 658829 (341171) (T)n#Simple_repeat 1 17 (0) m_b288s252i21 11770 chr6ptel1M 658813 TTTTTTTTTTTTTTTTT 658829 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTT 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 249 28.73 1.65 10.81 chr6ptel1M 659216 659336 (340664) C MIR3#SINE/MIR (24) 184 74 m_b288s601i63 11771 chr6ptel1M 659216 GAGTCGGCAGCACCCTCAGAAATCATACAGTCCAGTTCACAT-TTTTACA 659264 ii v viv i i vi iii v vi- C MIR3#SINE/MIR 184 GAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACA 135 chr6ptel1M 659265 GCTCAGCAAACTGAGGTCCACA-AAGTGCAAATTACTTCCGTCAAATTGC 659313 v v v i v - i - i v -- --------- C MIR3#SINE/MIR 134 GATGAGGAAACTGAGGCCCAGAGAGGTG-AAGTGACTT--G--------- 97 chr6ptel1M 659314 CCCAAAGCCCCATAACTAGCTGG 659336 i i v i i ? i i C MIR3#SINE/MIR 96 CCCAAGGTCACACAGCNAGTTAG 74 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.37 CpG sites = 19, Kimura (unadjusted) = 37.37 Transitions / transversions = 1.58 (19/12) Gap_init rate = 0.12 (14 / 120), avg. gap size = 1.00 (14 / 14) 565 21.09 1.35 10.29 chr6ptel1M 659535 659682 (340318) MIRc#SINE/MIR 13 148 (120) m_b288s601i64 11772 chr6ptel1M 659535 GTGCAATGACTAGAGCACAGGACTGGGAGCCTGGCAGACTCATTTATCTT 659584 i ivv v v i v v ----------- MIRc#SINE/MIR 13 GTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC----------- 51 chr6ptel1M 659585 CCTGGGTTTAAATGT-GACTTTAAGACATTTACTGGCTGTGTGATTCTGG 659633 - ii i vi- i i -- v i i iii MIRc#SINE/MIR 52 -CTGGGTTCGAGTCCCGGCTCT--GCCACTTACTAGCTGTGTGACCTTGG 98 chr6ptel1M 659634 GCAAGTCACTTAACCCTGCT-CGCCTCAGTTTCCTCATCTGTAAAGTGAG 659682 iiv -v i i MIRc#SINE/MIR 99 GCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 23.94 CpG sites = 18, Kimura (unadjusted) = 25.07 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.11 (16 / 147), avg. gap size = 1.00 (16 / 16) 241 35.26 12.25 7.96 chr6ptel1M 660457 660758 (339242) L2b_3end#LINE/L2 140 453 (13) m_b288s601i65 11773 chr6ptel1M 660457 CTGTTCTCCC-------AACCCCTCTCTCCACTTCCCAGCTTGTCCCCTT 660499 i i ------- v ii i i iiv i v ---- L2b_3end#LINE 140 CTGTTCCCTCTGCCTGGAACGCCCTTCCCCACCTCTTCGCCTGGCC---- 185 chr6ptel1M 660500 AAAATCCCACATTTCTTTCCAAGCTCAGGCCAAATGTTGCCTTCTACATG 660549 - v i viv i viiv vi ii i v iv L2b_3end#LINE 186 -AACTCCTACTCATCCTTCAGGTCTCAGCTCAAATGTCACCTCCTCCGGG 234 chr6ptel1M 660550 AAGCATTTCCTGGTCCCTCTGG-----------------CTTT---CCCC 660579 vi i ii i v ----------------- i --- L2b_3end#LINE 235 AAGCCCTCCCTGACCCCCCAGGCCGGGTCAGGCGCCCTCCTCTGGGCCCC 284 chr6ptel1M 660580 TCAAGTAC--CTTTGATTGCTTTG---TAT--TTGTTCAGGTATTTATTT 660622 i v v -- ii -iii i --- -- iii?v iv i- i L2b_3end#LINE 285 CCCAGTCCTACCCTG-CCACTCTGGGTTATNATTGTCTGNTTACATG-TC 332 chr6ptel1M 660623 TTTCTCCCTCAATAGAGTATAAGCTCTTCAGGAATAGGGACTATTTATAT 660672 v i v v i i iviii iii ii?v v i L2b_3end#LINE 333 TGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGT 382 chr6ptel1M 660673 AATTTTAATGTAAGTTTGAACTTTAATTCTGAACCCTCAGTGCCT---AC 660719 --------------i --- i viv v i i i --- L2b_3end#LINE 383 --------------CTTG---TTCACCGCTGTATCCCCAGCGCCTAGCAC 415 chr6ptel1M 660720 TGTTCATTGGAGTATAGTAAATGCTTAAATAATATTTAT 660758 v ?v -i vii i iii i ivv i L2b_3end#LINE 416 AGNGC-CTGGCACACAGTAGGCGCTCAGTAAATATTTGT 453 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 47.70 CpG sites = 67, Kimura (unadjusted) = 52.50 Transitions / transversions = 2.16 (67/31) Gap_init rate = 0.11 (32 / 301), avg. gap size = 1.94 (62 / 32) 12 4.93 0.00 4.55 chr6ptel1M 660904 660926 (339074) (TATT)n#Simple_repeat 1 22 (0) m_b288s252i22 11774 chr6ptel1M 660904 TATCTTATTTATTTATTTTTTTA 660926 - v (TATT)n#Simpl 1 TAT-TTATTTATTTATTTATTTA 22 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.05 (1 / 22), avg. gap size = 1.00 (1 / 1) 19 11.56 0.00 0.00 chr6ptel1M 661262 661289 (338711) (A)n#Simple_repeat 1 28 (0) m_b288s252i23 11775 chr6ptel1M 661262 AAAAACAAAATGAAAAAAAAAAAAAAAA 661289 v vi (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA 28 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 15 27.03 0.00 5.00 chr6ptel1M 661982 662044 (337956) (TACA)n#Simple_repeat 1 60 (0) m_b288s252i24 11776 chr6ptel1M 661982 TAGATACATAGATACATATGTATAAATGCATACATATTTTACACAAATTT 662031 v v --i v i -iv i v vi (TACA)n#Simpl 1 TACATACATACATACATA--CATACATACATACATA-CATACATACATAC 47 chr6ptel1M 662032 ATATATAAATACA 662044 i v (TACA)n#Simpl 48 ATACATACATACA 60 Matrix = Unknown Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.05 (3 / 62), avg. gap size = 1.00 (3 / 3) 557 18.56 0.00 1.03 chr6ptel1M 662490 662587 (337413) C Charlie4#DNA/hAT-Charlie (3276) 102 6 m_b288s502i9 11777 chr6ptel1M 662490 TGAAAATAAAGGGGTATTTTTTTTCCAGCCAAGTTCACAGACCATCTTGA 662539 iv v i v i -i i C Charlie4#DNA/ 102 TGAAAATAAAGATGTAATTTTTTCCCATCCAAGTTCACGGACC-CCCTGA 54 chr6ptel1M 662540 AATCTATCCATGGTCTGCTTGGGGATCCCTGGATCTTAGGTTAAGAAC 662587 v i v iv i v i ii C Charlie4#DNA/ 53 ATTCTATCCACGGACCCCTTGGGGGTCCGTGGACCCCAGGTTAAGAAC 6 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 19.08 CpG sites = 11, Kimura (unadjusted) = 21.66 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.01 (1 / 97), avg. gap size = 1.00 (1 / 1) 13 21.41 5.17 3.39 chr6ptel1M 663007 663064 (336936) (ATATAT)n#Simple_repeat 1 59 (0) m_b288s252i25 11778 chr6ptel1M 663007 ATATATGT-TAAATATGTCAAAGTATATGT-TAAATACA-ATATATGTAT 663053 i - v i - v - i - v i - i (ATATAT)n#Sim 1 ATATATATATATATATAT-ATA-TATATATATATATATATATATATATAT 48 chr6ptel1M 663054 ACATATTTATA 663064 i v (ATATAT)n#Sim 49 ATATATATATA 59 Matrix = Unknown Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.09 (5 / 57), avg. gap size = 1.00 (5 / 5) 427 33.97 2.95 3.33 chr6ptel1M 663319 663589 (336411) C L1ME5_3end#LINE/L1 (316) 625 356 m_b288s551i1 11779 chr6ptel1M 663319 CACTCAGCATGA-GTTCATGTAA-ATCTCTCCAGGCCTCTTTGTATTCAT 663366 iv - -- v - iv v iiv v i v C L1ME5_3end#LI 625 CACTCAGCACTATGTT--TTTAAGATCCATCCATGTTGCTATGTGTACAT 578 chr6ptel1M 663367 CCTGCTGGTCATTTCTTATAGAACAATAATATTCCATAACATTCATATTC 663416 iv iiv iii v iv vvvv i i iiii v viv C L1ME5_3end#LI 577 CTAGTCCGTTGCTTCTAACTGCTGCATAGTACTCCATGGTGTGCATCCAC 528 chr6ptel1M 663417 CACAATTTACCCAACCATTCTTCAATTTAAGGGTATCCA--TTCATTTTC 663464 v i v i i v v v v ii i -- v--ii C L1ME5_3end#LI 527 CACATTTTACCTATCCACTCTCCCAGTGATGGACACCCAGGTTG--CCTC 480 chr6ptel1M 663465 CAGCTTCTAGCTACTACAAACAGTGCTGCCACAAACATTTTGGCACATAC 663514 i i iv i i ii v ii ii ---- i C L1ME5_3end#LI 479 CAACTCCCCGCCACCACAAACAACGCTGCAATGAACATCCT----CGTAC 434 chr6ptel1M 663515 AGGTCTCTTT----CCCTTCTTTAAAATCTCTTTTGGGATATAAGCTGTG 663560 v i i ----v viv v i i - vi ivv C L1ME5_3end#LI 433 ATGTCCCCTTATGGACCTGTGTGAGAATTTC-TTTGGGATATATACCCAG 385 chr6ptel1M 663561 TAACAGCACTGCTGGATCAAAGGGTATAC 663589 v i i v i i v i C L1ME5_3end#LI 384 GAGCGGAATTGCTGGGTCATAGGGTATGC 356 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 44.62 CpG sites = 51, Kimura (unadjusted) = 46.78 Transitions / transversions = 1.34 (51/38) Gap_init rate = 0.05 (13 / 270), avg. gap size = 1.31 (17 / 13) 461 33.04 1.72 2.16 chr6ptel1M 663375 663606 (336394) C L1ME4c_3end#LINE/L1 (258) 572 342 m_b288s551i2 11779 chr6ptel1M 663375 TCATTTCTTATAGAACAATAATATTCCATAACATTCATATTCCACAATTT 663424 i v i vvvv vivi ?v i v i C L1ME4c_3end#L 572 TCATTTTTAATGGCTGCATAATATTCCATCGAGTNGATGTACCATAATTT 523 chr6ptel1M 663425 ACCCAACCATTCTTCAATTTAAGGGTATCCA--TTCATTTTCCAGCTTCT 663472 ii ii v vvv ii ii -- v-- ii i C L1ME4c_3end#L 522 ACTTAACCATTCCCCTATTGTTGGACATTTAGGTTG--TTTCCAATTTTT 475 chr6ptel1M 663473 AGCTACTACAAACAGTGCTGCCACAAACATTTTGGCACATACAGGTCTCT 663522 v i i i ii v ii i v ii i -- i C L1ME4c_3end#L 474 CGCTATTATAAATAACGCTGCAATGAACATCTTCGTGCATATAG--CTTT 427 chr6ptel1M 663523 TTCCCTTCTTTAAA--ATCTCTTTTGGGATATAAGCTGTGTAACAGCACT 663570 i ii i -- i -i i v vv ivv v iii v i C L1ME4c_3end#L 426 TTCCTTCTTTTGAATTATTTC-CTTAGGATAAATTCCCAGAAGTGGAATT 378 chr6ptel1M 663571 GCTGGATCAAAGGGTATACACAGTTTGATAACCTTT 663606 i i iv v v ii ii C L1ME4c_3end#L 377 ACTGGGTCAAAGGGTATGAACATTTTTATGGCTCTT 342 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 44.40 CpG sites = 48, Kimura (unadjusted) = 46.12 Transitions / transversions = 1.78 (48/27) Gap_init rate = 0.03 (7 / 231), avg. gap size = 1.29 (9 / 7) 469 30.20 1.93 2.43 chr6ptel1M 663392 663598 (336402) C L1ME3G_3end#LINE/L1 (376) 548 343 m_b288s551i3 11779 chr6ptel1M 663392 ATAATATTCCATAACATTCATATTCCACAATTTACCCAACCATTCTTCAA 663441 i ii vv v i iii ii v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr6ptel1M 663442 TTTAAGGGTATCCA--TTCATTTTCCAGCTTCTAGCTACTACAAACAGTG 663489 v v ii ii -- v-- ii i v i i C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTG--TTTCCAATTTTTCGCTATTACAAACAATG 451 chr6ptel1M 663490 CTGCCACAAACATTTTGGCACATACAGGTCTCTTTCC-CTTCTTTAAA-A 663537 v ii ii v i i --? ii v v - v v vii i- C L1ME3G_3end#L 450 CTGCAATGAACATCCTTGTACATGC--NTCCTTGTGCACATGTGCGAGTA 403 chr6ptel1M 663538 TCTCTTTTGGGATATAAGCTGTGTAACAGCACTGCTGGATCAAAGGGTAT 663587 i - ? i v v? i?v v iii v i i C L1ME3G_3end#L 402 TTTC-TNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTAT 354 chr6ptel1M 663588 ACACAGTTTGA 663598 i i v i C L1ME3G_3end#L 353 GCGCATTTTAA 343 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.72 CpG sites = 40, Kimura (unadjusted) = 41.64 Transitions / transversions = 1.90 (40/21) Gap_init rate = 0.04 (8 / 206), avg. gap size = 1.12 (9 / 8) 306 23.99 5.94 0.94 chr6ptel1M 664092 664192 (335808) EuthAT-N1#DNA/hAT-Tip100 113 218 (117) m_b288s502i10 11780 chr6ptel1M 664092 TTAGATATCCATGGTAGCATCCGCATGTAGTCCATCAGAAGTCTAAAAAC 664141 v v v v ii -v i i v v v iv i EuthAT-N1#DNA 113 TTACATTTACATGTTGACA-GCACATGCACTCCTTCAGCAGCGTAGAAAC 161 chr6ptel1M 664142 AAT--AGCTTTTCCCCTTCTTTGCAAGAATA----GTTAAAAGAGGAAGT 664185 i-- vv v vv v ---- v i EuthAT-N1#DNA 162 AACTGAGCTTAGCACCTAGTTAGCAAGAATAATTAGTTAAAATAGGAAGC 211 chr6ptel1M 664186 TACCAGA 664192 EuthAT-N1#DNA 212 TACCAGA 218 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 27.62 CpG sites = 8, Kimura (unadjusted) = 28.92 Transitions / transversions = 0.50 (8/16) Gap_init rate = 0.03 (3 / 100), avg. gap size = 2.33 (7 / 3) 458 26.67 1.90 0.00 chr6ptel1M 664228 664332 (335668) MIRc#SINE/MIR 10 116 (152) m_b288s601i66 11781 chr6ptel1M 664228 GTGGCTCAGTGGA--TAGCAAAGGACCCAGAATCAGGAAAACCCGAGTTC 664275 iv --v vv iii i i i i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr6ptel1M 664276 ATATCCAGCCTTAGGCACTTATTAGCTATATGATAGTGGACAAGTCACTT 664325 ivi v v iv v i i i ivv i MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTT 109 chr6ptel1M 664326 AATCTCT 664332 i MIRc#SINE/MIR 110 AACCTCT 116 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.38 CpG sites = 17, Kimura (unadjusted) = 33.86 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.01 (1 / 104), avg. gap size = 2.00 (2 / 1) 442 28.59 3.03 4.62 chr6ptel1M 664338 664469 (335531) MIRc#SINE/MIR 4 133 (135) m_b288s601i67 11782 chr6ptel1M 664338 GGCAGCAGTGATGCATCTCTGTGGATAGAACCCTGAATCTGGAATTGGGA 664387 i- i ----- v i v i ii i ii MIRc#SINE/MIR 4 GGCAGT-GTGGTGCA-----GTGGAAAGAGCACTGGACTTGGAGTCAGGA 47 chr6ptel1M 664388 AGACCCGAGGTCAAATATGACCTGAAACATTGACTAGCTGTGTGACCCTA 664437 i i v i i viviv vviv i v i i MIRc#SINE/MIR 48 AGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTG 97 chr6ptel1M 664438 GATAAGTCACTTATACTCT----GCCTTAATTTACT 664469 ii vv ---- i i v MIRc#SINE/MIR 98 GGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCT 133 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.74 CpG sites = 23, Kimura (unadjusted) = 37.36 Transitions / transversions = 1.77 (23/13) Gap_init rate = 0.05 (7 / 131), avg. gap size = 1.43 (10 / 7) 21 0.00 0.00 0.00 chr6ptel1M 664675 664697 (335303) (T)n#Simple_repeat 1 23 (0) m_b288s252i26 11783 chr6ptel1M 664675 TTTTTTTTTTTTTTTTTTTTTTT 664697 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTT 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 595 26.44 5.03 2.45 chr6ptel1M 665384 665542 (334458) MIR3#SINE/MIR 15 177 (31) m_b288s601i68 11784 chr6ptel1M 665384 GAGTAGATAAAGAGCATCAGCTGTGGGGTCAGGAGATAAAGGTTCAAATG 665433 i --i ivii - i ivvi v i v MIR3#SINE/MIR 15 GAGCAGA--GAGAGCACGGACTG-GGAGTCAGGAGACCTGGGTTCTAGTC 61 chr6ptel1M 665434 TCACTTTT----TTTACTCATTGTGAGATCTTGGACAAATCACTTTTCAT 665479 i ivi i ----i v ?ii v i i i iv -i MIR3#SINE/MIR 62 CCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCAC-C 110 chr6ptel1M 665480 TCTTTGAGCCTCAGTTTCCTCATCTGTAAAATGAGGCAATTGGACAAG-- 665527 i i vii v -- MIR3#SINE/MIR 111 TCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGAT 160 chr6ptel1M 665528 --TTTCCGAAGTCTCTT 665542 -- i ii i i MIR3#SINE/MIR 161 GATCTCTAAGGTCCCTT 177 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.64 CpG sites = 30, Kimura (unadjusted) = 34.76 Transitions / transversions = 2.73 (30/11) Gap_init rate = 0.04 (7 / 158), avg. gap size = 1.71 (12 / 7) 181 33.62 3.09 6.37 chr6ptel1M 666202 666363 (333637) C L2d2_3end#LINE/L2 (307) 248 92 m_b288s601i69 11785 chr6ptel1M 666202 GGGAAGGCTTCATGGAGGAAATGCTATCACAATGGAGGCCTGCAGGA-AA 666250 i ii v? ivv iiv i v i v -ii C L2d2_3end#LIN 248 GGGAAGGCTTCACGGAGGAGGTGGNATTTGAGCTGGGCCTTGAAGGATGG 199 chr6ptel1M 666251 GAAGGATCTCCAAAAGTTTAGATGGCAGGGAA-TTCATTCCAAGCAGTGG 666299 v i vv v i vv v ivi -vv i i v C L2d2_3end#LIN 198 GTAGGATTTGGATAGGTGGAGAGGAAGGGGAAGGGCATTCCAGGCGGGGG 149 chr6ptel1M 666300 --ATGGCATAGTTGTGGCAATGATGGTGGAGGAGGTAGGGT-TAAGACAG 666346 -- i i i-----i v ii- ii v v i? i-i i - C L2d2_3end#LIN 148 GAACGGCGTG-----AGCAAAGGC-GCAGAGGCGGGAANGCGCAAGGC-G 106 chr6ptel1M 666347 TGTGATCAAAGAGACAG 666363 -- -ii i C L2d2_3end#LIN 105 TGT--TC-GGGGGACAG 92 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.81 CpG sites = 31, Kimura (unadjusted) = 47.31 Transitions / transversions = 1.55 (31/20) Gap_init rate = 0.09 (14 / 161), avg. gap size = 1.07 (15 / 14) 193 32.68 4.76 0.92 chr6ptel1M 666202 666306 (333694) C L2c_3end#LINE/L2 (231) 247 139 m_b288s601i70 11785 chr6ptel1M 666202 GGGAAGGCTTCATGGAGGAAATGCTATCACAATGGAGGCCTGCAGGA-AA 666250 vi ii vi vv iiv ? i v -i C L2c_3end#LINE 247 GGGAAGGCTTCCCGGAGGAGGTGACATCTGAGCTGAGNCTTGAAGGATGA 198 chr6ptel1M 666251 GAAGGATCT--CCAAAAGTTTAGATGGCAGGGAATTCATTCCAAGCAGTG 666298 v vi -- iiv -vv iv vi i ivv i v C L2c_3end#LINE 197 GTAGGAGTTAGCCAGGTG-GAAGGAGGGGGGAAGAGCATTCCAGGCAGAG 149 chr6ptel1M 666299 G--ATGGCAT 666306 -- ii C L2c_3end#LINE 148 GGAACAGCAT 139 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 42.71 CpG sites = 18, Kimura (unadjusted) = 44.45 Transitions / transversions = 1.12 (18/16) Gap_init rate = 0.04 (4 / 104), avg. gap size = 1.50 (6 / 4) 197 4.00 0.00 0.00 chr6ptel1M 666548 666572 (333428) C MIR3#SINE/MIR (64) 144 120 m_b289s601i2 11786 chr6ptel1M 666548 TCATTTTACAGATGAGGAGACTGAG 666572 i C MIR3#SINE/MIR 144 TCATTTTACAGATGAGGAAACTGAG 120 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 4.17 CpG sites = 1, Kimura (unadjusted) = 4.17 Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 194 27.13 5.63 1.35 chr6ptel1M 666571 666641 (333359) C MIR#SINE/MIR (180) 82 9 m_b289s601i3 11786 chr6ptel1M 666571 AGCTAGTAAGTATCTGAGGCTGGATTTGACCTTAGAAAGATGAGTCTCCT 666620 iv v v v i v ii iv - vv v v C MIR#SINE/MIR 82 AGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGCAG-TCTGGCTCCA 34 chr6ptel1M 666621 GA-CCTAGGCCC---ACCACTATGC 666641 - iiv i --- C MIR#SINE/MIR 33 GAGCCCGTGCTCTTAACCACTATGC 9 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.56 CpG sites = 8, Kimura (unadjusted) = 33.80 Transitions / transversions = 0.73 (8/11) Gap_init rate = 0.04 (3 / 70), avg. gap size = 1.67 (5 / 3) 433 21.16 7.32 3.94 chr6ptel1M 667545 667667 (332333) C L2d2_3end#LINE/L2 (15) 540 414 m_b289s601i4 11787 chr6ptel1M 667545 AAAAACTTATTAAGCGCCCACTATGTGC----CATTGTGCTAAGTGC--- 667587 v i i i i ---- i i i --- C L2d2_3end#LIN 540 AAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGT 491 chr6ptel1M 667588 AAGGGGTACAATTGGAAAAAGCAAGACA--GTCTCTGCTCTCAAGGGACT 667635 ii i --i iv -i -- i i ii C L2d2_3end#LIN 490 GGGGGATACAA--AGAAGTA-TAAGACATGGTCCCTGCCCTCAAGGAGCT 444 chr6ptel1M 667636 AACACATTTAATTGGGAGAGAAAACATATAAA 667667 v - i i - v v i C L2d2_3end#LIN 443 TACA-ATCTAGTTGGG-GAGACAAGACATAAA 414 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 25.01 CpG sites = 20, Kimura (unadjusted) = 26.23 Transitions / transversions = 4.00 (20/5) Gap_init rate = 0.07 (8 / 122), avg. gap size = 1.75 (14 / 8) 190 36.25 5.03 2.96 chr6ptel1M 668164 668362 (331638) L2d2_3end#LINE/L2 9 211 (344) m_b289s601i5 11788 chr6ptel1M 668164 TCTAGCC--AGTCTCTCTTTCCAGACTGCCTTCAGATTACTGCCCTTCAC 668211 i -- ii ?i v vvii vv i i v ? L2d2_3end#LIN 9 TCTGGCCCCAACCTNCCTTTCCAGCCTTATCTCCCACTATTCCCCTNCAC 58 chr6ptel1M 668212 T--CCCTTAACCCTCCTACCAAACGAGCCTACGAGCTGTTCTGCCACAGA 668259 v-- i-- v vi vi i vvi ---- v v L2d2_3end#LIN 59 GAACCCTC--CGCTCCAGCCAAACTGGTCTACTCACTGT----CCCCCGA 102 chr6ptel1M 668260 GAATATTCTGC---CTCCCACCTTTGCA--TTTGCACAAGCAGTCTCCCA 668304 iv iiiii ---i i i i-- v v v ii v L2d2_3end#LIN 103 ACACGCCTTGCGCNTTCCCGCCTCTGCGCCTTTGCTCACGCCGTTCCCCC 152 chr6ptel1M 668305 TACCTGGGACACTCTCCTTCCTCATTTCTGTCCCTCAGAA-CCACTCTGT 668353 ii i ii i i ii i v i iii iv vi - vvi ii L2d2_3end#LIN 153 CGCCTGGAATGCCCTTCCCCTTCCTCTCCACCTATCCAAATCCTACCCAT 202 chr6ptel1M 668354 CCCTCCAGG 668362 i v L2d2_3end#LIN 203 CCTTCAAGG 211 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 48.90 CpG sites = 45, Kimura (unadjusted) = 53.66 Transitions / transversions = 1.80 (45/25) Gap_init rate = 0.06 (11 / 198), avg. gap size = 1.45 (16 / 11) 12 33.47 0.00 0.00 chr6ptel1M 668368 668419 (331581) (GTAT)n#Simple_repeat 1 52 (0) m_b289s252i0 11789 chr6ptel1M 668368 GTATGTATGTATGTGTGTGAATCAATATCTATCCATTTATATCTGTATCT 668417 i ivi vvi v vi v i v v (GTAT)n#Simpl 1 GTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGT 50 chr6ptel1M 668418 AT 668419 (GTAT)n#Simpl 51 AT 52 Matrix = Unknown Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 784 32.77 5.08 0.94 chr6ptel1M 669584 670193 (329807) C L1MD_orf2#LINE/L1 (894) 2400 1766 m_b289s551i0 11790 chr6ptel1M 669584 TCTCTAATTGTTTAGAT-----TTG--TATTTTTATGAAAATTTTCTTGT 669626 i v i ----- -- vi i v ivi v v C L1MD_orf2#LIN 2400 TCTCCATTTATTTAGATCTTCTTTGATTTCTTTCATCAGCGTTTTGTAGT 2351 chr6ptel1M 669627 AATTATCATAAAATTTCTGTGTTTGTCTTAGGAAGTTTA--CTTAAAATA 669674 vv i v v v i iiv i ivv ii -- i i- C L1MD_orf2#LIN 2350 TTTCAGCATACAAGTCCTGTACATGTTTTGTTAGATTTATACCTAAG-TA 2302 chr6ptel1M 669675 GTTTATGTTATATACAGCTATTTTAAAAGAAATTTTTCTTTCTACCTC-- 669722 v i v v v vv v v v iv v vi iv ii -- C L1MD_orf2#LIN 2301 TTTCATTTTTTTTTGAGCGATTGTAAATGGTATTGTATTTTTAATTTCGG 2252 chr6ptel1M 669723 TTCCTGCTGGGGTTTGTTGGTAGTATACAGAAAGGC---TGACTTCCATG 669769 i ii -- v ii v i vi --- i iii i C L1MD_orf2#LIN 2251 TTTCCAC--GTGTTCATTGCTAGTATATAGAAATACAATTGATTTTTGTA 2204 chr6ptel1M 669770 GGTTTATTT---ATCCTGCAACTTTGTTAAAATTCTTAATTCTTTCAATT 669816 v ? i --- i i i i v ivi v vv v vv C L1MD_orf2#LIN 2203 TGTTNATCTTGTATCCTGCGACCTTGCTGAACTCACTTATTAGTTCTAGG 2154 chr6ptel1M 669817 AGTTTTTTAGTTGATTCTTTAGGGTTCTCTAAGTATA---TCATGTCATT 669863 v v i i i i v v --- i C L1MD_orf2#LIN 2153 AGTTTTTTTGTAGATTCCTTGGGATTTTCTACGTAGACAATCATGTCATC 2104 chr6ptel1M 669864 TGCAGAGAATAATAGTTAAACTTTTTTCATTTCTTA-GTGTAATTTCTCC 669912 i v ivi i vv - i v iv -v - vi ii C L1MD_orf2#LIN 2103 TGCAAATAGGGACAGTTTTA-TTTCTTCCTTTCCAATCTGTA-TGCCTTT 2056 chr6ptel1M 669913 AACTTCTTTTTCTTTTTTT---------GCTAAAGCTTGTAGTATAATAT 669953 v i i vii --------- i i vi iv i C L1MD_orf2#LIN 2055 TATTTCCTTTTCTTGCCTTATTGCACTGGCTAGAACTTCCAGTACTATGT 2006 chr6ptel1M 669954 TGAATAATAATGGTGATAATGGGTATCCCTGCTTCACCCCTCATAGTATT 670003 v i v ii ii i i iiii iv vv vv C L1MD_orf2#LIN 2005 TGAATAAGAGTGGTGAGAGCGGACATCCTTGCCTTGTTCCCGATCTTAGG 1956 chr6ptel1M 670004 GGGAAGGCTTCTAGCTTATTCTCATTGCAAACAATGCTTGCTGATGGTTT 670053 i v ii ii v ivi iviv ii i v vv C L1MD_orf2#LIN 1955 GGGAAAGCATTCAGTCTTTCACCATTAAGTATGATGTTAGCTGTAGGTTT 1906 chr6ptel1M 670054 TAGATAAATGTTAATTATCATTTTAAGAGAGACCCCATTGATTCCTATGT 670103 vvi i i vv vv i ii vi v iv - C L1MD_orf2#LIN 1905 TTTGTAGATGCTCTTTATCAAGTTGAGGAAGTTCCCCTCTATTCCTA-GT 1857 chr6ptel1M 670104 TTCCT-AGTGTTTTTAATAGGAGTGGATGTTATATTTTGTTAAAGGCCTT 670152 ? - v vi v i i iv i v i C L1MD_orf2#LIN 1856 TTNCTGAGAGTTTTTATCATGAATGGGTGTTGAATTTTGTCAAATGCTTT 1807 chr6ptel1M 670153 TTCTGCATATATTAATACAATCGTTTATTTTTTTTTTGTTA 670193 vv i ii i v iv i iv C L1MD_orf2#LIN 1806 TTCTGCATCAATTGATATGATCATGTGATTTTTCTTCTTTA 1766 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.22 CpG sites = 109, Kimura (unadjusted) = 44.43 Transitions / transversions = 1.22 (109/89) Gap_init rate = 0.03 (16 / 609), avg. gap size = 2.31 (37 / 16) 882 31.36 4.14 0.91 chr6ptel1M 669670 670200 (329800) C L1M5_orf2#LINE/L1 (988) 2306 1759 m_b289s551i1 11790 chr6ptel1M 669670 AAATAGTTTATGTTATATACAGCTATTTTAAAAGAAATTTTTCTTTCTAC 669719 i v ? v v ivv v v iv v i ?vv i C L1M5_orf2#LIN 2306 AAGTATTTNATGTTTTTTGATGCTATTGTAAATGGTATTGTTTTTNAAAT 2257 chr6ptel1M 669720 CTC---TTCCTGCTGGGGTTTGTTGGTAGTATACAGAAAGGC---TGACT 669763 i --- vii --- v i vi --- i C L1M5_orf2#LIN 2256 TTCATTTTCCAATTG---TTTGTTGCTAGTATATAGAAATACAATTGATT 2210 chr6ptel1M 669764 TCCATGGGTTTA---TTTATCCTGCAACTTTGTTAAAATTCTTAATTCTT 669810 iii ivi v --- v ? i i i v ivi v vv C L1M5_orf2#LIN 2209 TTTGTATATTGACCTTGTATCCNGCGACCTTGCTAAATTCACTTATTAGT 2160 chr6ptel1M 669811 TCAATTAGTTTTTTAGTTGATTCTTTAGGGTTCTCTAAGTATA---TCAT 669857 v v ? v v ? i i v ? --- C L1M5_orf2#LIN 2159 TCTAGTAGTTTNTTTGTAGATTCTTTNGGATTTTCTACGTANACAATCAT 2110 chr6ptel1M 669858 GTCATTTGCAGAGAATAATAGTTAAACTTTTTTCATTTCTTAGTGTAATT 669907 i ii v ?i i vv - i v iv viv v v C L1M5_orf2#LIN 2109 GTCATCTGCGAATAANGACAGTTTTA-TTTCTTCCTTTCCAATCTTTATG 2061 chr6ptel1M 669908 TCTCCAACTTCTTTTTCTTTTTTT---------GCTAAAGCTTGTAGTAT 669948 i iiv i vii --------- iii i vi i C L1M5_orf2#LIN 2060 CCTTTTATTTCTTTTTCTTGCCTTATTGCACTGGCTAGGACCTCCAGTAC 2011 chr6ptel1M 669949 AATATTGAATAATAATGGTGATAATGGGTATCCCTGCTTCACCCCTCATA 669998 i iv i ? ii ii i ii iiii iv v C L1M5_orf2#LIN 2010 AATGTTGAATAGAAGTGGTGANAGCGGACATCCTTGTCTTGTTCCCGATC 1961 chr6ptel1M 669999 GTATTGGGAAGGCTTCTAGCTTATTCTCATTGCAAACAATGCTTGCTGAT 670048 v vv i ? ii i? v ivi iviv ii i ? vv C L1M5_orf2#LIN 1960 TTAGGGGGAAAGCNTTCAGTNTTTCACCATTAAGTATGATGTTNGCTGTA 1911 chr6ptel1M 670049 GGTTTTAGATAAATGTTAATTATCATTTTAAGAGAGACCCCATTGATTCC 670098 vvi i iivv vv i ii vi v iv C L1M5_orf2#LIN 1910 GGTTTTTCGTAGATGCCCTTTATCAGGTTGAGGAAGTTCCCTTCTATTCC 1861 chr6ptel1M 670099 TATGTTTCCT-AGTGTTTTTAATAGGAGTGGATGTTATATTTTGTTAAAG 670147 - v - v vi v i i iv i v C L1M5_orf2#LIN 1860 TA-GTTTGCTGAGAGTTTTTATCATGAATGGGTGTTGAATTTTGTCAAAT 1812 chr6ptel1M 670148 GCCTTTTCTGCATATATTAATACAATCGTTTATTTTTTTTTTGTTATTTT 670197 i v i v ii i v iv i iiv i C L1M5_orf2#LIN 1811 GCTTTTTCTGCATCTATTGAGATGATCATATGATTTTTCTCCTTTATTCT 1762 chr6ptel1M 670198 TTT 670200 v C L1M5_orf2#LIN 1761 GTT 1759 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.23 CpG sites = 93, Kimura (unadjusted) = 42.95 Transitions / transversions = 1.29 (93/72) Gap_init rate = 0.02 (11 / 530), avg. gap size = 2.45 (27 / 11) 933 31.50 4.35 0.63 chr6ptel1M 669734 670193 (329807) C L1MC_orf2#LINE/L1 (1052) 2242 1766 m_b289s551i2 11790 chr6ptel1M 669734 GTTTGTTGGTAGTATACAGAAAGGC---TGACTTCCATGGGTTTA---TT 669777 ii v i i i i --- iii ivi v --- v C L1MC_orf2#LIN 2242 GTTCATTGCTGGTATATAGGAAAGCGATTGACTTTTGTATATTAACCTTG 2193 chr6ptel1M 669778 TATCCTGCAACTTTGTTAAAATTCTTAATTCTTTCAATTAGTTTTTTAGT 669827 i i v ivi v vv v vv v C L1MC_orf2#LIN 2192 TATCCTGCAACCTTGCTATAATCGCTTATTAGTTCCAGGAGTTTTTTTGT 2143 chr6ptel1M 669828 TGATTCTTTAGGGTTCTCTAAGTATA---TCATGTCATTTGCAGAGAATA 669874 i v i i vi v --- i ii v vi C L1MC_orf2#LIN 2142 CGATTCTTTCGGATTTTCTACATAGACAATCATGTCATCTGCGAACAAAG 2093 chr6ptel1M 669875 ATAGTTAAACTTTTTTCATTTCTTAGTGTA-ATTTCTCCAACTTCTTTTT 669923 i vv i i i -- ii i v i- vi iiv i i C L1MC_orf2#LIN 2092 ACAGTTTTATTTCTTCC--TTCCCAATCTGTATACCTTTTATTTCCTTTT 2045 chr6ptel1M 669924 CTTTTTTT---------GCTAAAGCTTGTAGTATAATATTGAATAATAAT 669964 v i --------- iii vi ii i v iv i C L1MC_orf2#LIN 2044 CTTGTCTTATTGCATTAGCTAGGACTTCCAGTACGATGTTGAAAAGGAGT 1995 chr6ptel1M 669965 GGTGATAATGGGTATCCCTGCTTCACCCCTCATAGTATTGGGAAGGCTTC 670014 v iv ii i i iiii v vv vi i C L1MC_orf2#LIN 1994 GGTGAGAGGGGACATCCTTGCCTTGTTCCTGATCTTAGCGGGAAAGCTTC 1945 chr6ptel1M 670015 TAGCTTATTCTCATTGCAAACAATGCTTGCTGATGGTTTTAGATAAATGT 670064 ? i v ivi iviv ii i v vv vvi i C L1MC_orf2#LIN 1944 NAGTTTCTCACCATTAAGTATGATGTTAGCTGTAGGTTTTTTGTAGATGT 1895 chr6ptel1M 670065 TAATTATCATTTTAAGAGAGACCCCATTGATTCCTATGTTTCCT-AGTGT 670113 vv vv i ii vi v iv - v - v C L1MC_orf2#LIN 1894 TCTTTATCAAGTTGAGGAAGTTCCCCTCTATTCCTA-GTTTGCTGAGAGT 1846 chr6ptel1M 670114 TTTTAATAGGAGTGGATGTTATATTTTGTTAAAGGCCTTTTCTGCATATA 670163 vi v i i iv i v i v C L1MC_orf2#LIN 1845 TTTTATCATGAATGGGTGTTGGATTTTGTCAAATGCTTTTTCTGCATCTA 1796 chr6ptel1M 670164 TTAATACAATCGTTTATTTTTTTTTTGTTA 670193 i ii i v iv i iv C L1MC_orf2#LIN 1795 TTGATATGATCATGTGATTTTTCTTCTTTA 1766 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.38 CpG sites = 85, Kimura (unadjusted) = 42.36 Transitions / transversions = 1.44 (85/59) Gap_init rate = 0.02 (9 / 459), avg. gap size = 2.56 (23 / 9) 263 20.78 3.85 2.86 chr6ptel1M 670373 670476 (329524) C L1P4_orf2#LINE/L1 (2389) 905 801 m_b289s551i3 11790 chr6ptel1M 670373 AGGGATATACAATTTCCCC--AATGTACTAATTTGGCTACATCTCATATA 670420 v v v v i -- i-- iv ? i i v v C L1P4_orf2#LIN 905 AGCGCTATAAACTTTCCTCTTAAC--ACTGCTTTNGCTGCATCCCAGAGA 858 chr6ptel1M 670421 TTTTGGTATGTTGTCTCATTGTTTTCATTCTATTTAATCCAATTATT--A 670468 v vi -? v vvv v -- C L1P4_orf2#LIN 857 TTTTGGTATGTTGTGTCTCTGTTTTCATT-NATTTCAAAGAATTTTTTGA 809 chr6ptel1M 670469 TTTCTGTC 670476 i C L1P4_orf2#LIN 808 TTTCTGCC 801 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 24.93 CpG sites = 7, Kimura (unadjusted) = 24.93 Transitions / transversions = 0.50 (7/14) Gap_init rate = 0.05 (5 / 103), avg. gap size = 1.40 (7 / 5) 252 27.65 6.64 3.88 chr6ptel1M 670378 670678 (329322) C L1M4_orf2#LINE/L1 (2394) 900 592 m_b289s551i4 11790 chr6ptel1M 670378 TATACAATTTCCC-CAATGTACTAATTTGGCTACATCTCATATATTTTGG 670426 - - v v i iv ? i i vi C L1M4_orf2#LIN 900 TATA-AATTTCCCTCTAAGCACTGCTTTNGCTGCATCCCATAAGTTTTGG 852 chr6ptel1M 670427 TATGTTGTCTCATTGTTTTCATTCTATTTAATCCAATTATT-----ATTT 670471 v iv i - i--- v v ----- C L1M4_orf2#LIN 851 TATGTTGTGTTTTCGTTTTCATTC-ATC---TCAAAGTATTTTCTAATTT 806 chr6ptel1M 670472 C---TGTCATTTGTTCTTCAACTCATTC----TTTGGGGTTAGATTATTT 670514 --- v v ii i v---- i iv ivi i C L1M4_orf2#LIN 805 CCCTTGTGATTTCTTCTTTGACCCATTGGTTATTTAGGAGTGTGTTGTTT 756 chr6ptel1M 670515 TGTTTCTAATTAGTTTTTTAAT---CCATATTT-CTACTGCCCTTTATTG 670560 vi i vv - v v --- v - v iiv v - C L1M4_orf2#LIN 755 AATTTCCACATA-TTTGTGAATTTCCCAAATTTCCTTCTGTTATTGATT- 708 chr6ptel1M 670561 GATGTAATTATTGTTTTATTGCAGCTTAAAGAAGGTA-TGTGTAATATTA 670609 -- v - ii ii ii - iii vi - v vv v C L1M4_orf2#LIN 707 --TCTAATT-TCATTCCATTGTGG-TCGGAGAACATACTTTGTATGATTT 662 chr6ptel1M 670610 CTATCTTTTTACATTTTGTTGAAAGTTTTTATACACTCTTACATA--GTC 670657 v i v - i i v v v iivi v -- C L1M4_orf2#LIN 661 CAATCCTTTTAAA-TTTATTGAGACTTGTTTTATGGCCTAACATATGGTC 613 chr6ptel1M 670658 AGTTTTTATGAAGGTGCCATG 670678 vi ii viv v v C L1M4_orf2#LIN 612 TATCCTGGAGAATGTTCCATG 592 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.97 CpG sites = 40, Kimura (unadjusted) = 35.09 Transitions / transversions = 1.00 (40/40) Gap_init rate = 0.07 (20 / 300), avg. gap size = 1.60 (32 / 20) 323 30.98 8.89 3.16 chr6ptel1M 670833 671012 (328988) MIRc#SINE/MIR 27 216 (52) m_b289s601i6 11791 chr6ptel1M 670833 GCACTGAA----AAGTCAGCA-TATCTCATTTGTAGTCCTGGT------A 670871 i ----i v -v i viv vv i i------ MIRc#SINE/MIR 27 GCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCA 76 chr6ptel1M 670872 TTAAATATCTCTGTGACCCTGGGCAAATCACAT--CATATATAAGTCTTA 670919 i v v v v i i v -- v v v i i i MIRc#SINE/MIR 77 CTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCA 126 chr6ptel1M 670920 TTGTATCTACTCAGCCAAGAAATGGAGATAATCATCCTTGTCCTATCTAG 670969 -- v -- v iivi i v v i i ii v MIRc#SINE/MIR 127 --GTTTC--CTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTAC 172 chr6ptel1M 670970 ATCGCA---TAGTAGTGAGGGGAAATTAAAAATTAATATAAATAAA 671012 v i --- v v ivv v i i -- i vi i MIRc#SINE/MIR 173 CTCACAGGGTTGTTGTGAGGATCAAATGAGA--TAATGTATGTGAA 216 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.65 CpG sites = 27, Kimura (unadjusted) = 40.61 Transitions / transversions = 1.00 (27/27) Gap_init rate = 0.06 (11 / 179), avg. gap size = 2.00 (22 / 11) 15 22.55 2.38 0.00 chr6ptel1M 672131 672172 (327828) (AATT)n#Simple_repeat 1 43 (0) m_b289s252i1 11792 chr6ptel1M 672131 AATTAAATATTGATTTAAAATATTAATTTATTAATTAA-TAAT 672172 v v v v vvv v - (AATT)n#Simpl 1 AATTAATTAATTAATTAATTAATTAATTAATTAATTAATTAAT 43 Matrix = Unknown Transitions / transversions = 0.00 (0/8) Gap_init rate = 0.02 (1 / 41), avg. gap size = 1.00 (1 / 1) 393 37.77 4.52 0.54 chr6ptel1M 672549 672902 (327098) C CR1-3_Croc#LINE/CR1 (658) 2947 2580 m_b289s551i5 11793 chr6ptel1M 672549 GGAAATCCCAGCACTTCTTGAGGCAGCCTATTCCACCTTTGGATTATTCT 672598 i vi vv iiv i iviivv i i C CR1-3_Croc#LI 2947 GGAGAGTCCACAACTTCCCTAGGCAGTCTATTCCACTGCCTCACTGTTCT 2898 chr6ptel1M 672599 AAT-GTTGGGAAATTTCCCTAAATGCCATGCTTAAATCAGAATTTTG--G 672645 i- vii i ii iii ii vviii i --v i -- C CR1-3_Croc#LI 2897 AACAGTGAAGAAGTTTTTCCGGATATCCAATCTAAACC--TACTTTGCTG 2850 chr6ptel1M 672646 CAACTTCCA-CC-TTGTTTCTGGT-----TCTCTGGGACAAATG-GAAGC 672687 v - - v i vv ----- vii iv - iv C CR1-3_Croc#LI 2849 CAACTTCAAGCCATTGGTCCGCGTCCTCCTCTCTGCAGCAAGAGAGAAAA 2800 chr6ptel1M 672688 AGTCCAATTCCCCTTTGACACAGCTGCCCTTTAAATACTTAGAGGTGGCT 672737 i v vv i i ivvi ii v i i i ii iiv C CR1-3_Croc#LI 2799 GGTGCTTTCCCTCTTCTTTATGGCAGCCCTTCAAGTATTTGAAGACTGCT 2750 chr6ptel1M 672738 ACCATGAACTATGTTTGACTTCTCTTCTCCAGGTCAAACATTCCTA---- 672783 i vv iv v vii vi i iv i iii v ---- C CR1-3_Croc#LI 2749 ATCATGTCCCCTCTTAAGCGCCTTTTCCGCAAGCTGAACATGCCTAGCTC 2700 chr6ptel1M 672784 CTTCAATGAATCCTTATATGAGATGGATTCGAGATCATTCA-CAACCTGG 672832 iivvv ii vv vv v iii v i - v i v C CR1-3_Croc#LI 2699 CTTCAGCCTCTCCTCGTATGACTTGCCTTCCAAGCCCTTTATCATCTTTG 2650 chr6ptel1M 672833 TGGCACTTCTCTGGATGCTTAATAATTTATAAATCTTCCTTCTAAAATCT 672882 v v vi iv ivv i v vv iv i i i v C CR1-3_Croc#LI 2649 TTGCCCGCCTCTGGACCCTCTCTAACTTCTCCACGTCCTTTTTAAAATGT 2600 chr6ptel1M 672883 GGTTCTCAGAACTAAACACA 672902 vv i iv C CR1-3_Croc#LI 2599 GGAGCCCAGAACTGCACACA 2580 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 52.11 CpG sites = 75, Kimura (unadjusted) = 54.69 Transitions / transversions = 1.29 (75/58) Gap_init rate = 0.03 (10 / 353), avg. gap size = 1.80 (18 / 10) 474 30.72 1.29 1.29 chr6ptel1M 672963 673117 (326883) MIR1_Amn#SINE/MIR 2 156 (74) m_b289s601i7 11794 chr6ptel1M 672963 AAGAAAATAGTAGAGACAAATAGATGGTTCAATGG-CTAGAACTCTGG-G 673010 i i iii ivi v v i i i vv v - i i v - MIR1_Amn#SINE 2 AGGGAGGCAGTGTGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGAG 51 chr6ptel1M 673011 ACTGGAGTCAACAAGTCCAACCTCAGATACCTATTACCTTTATGATCTAT 673060 iv i i-- ? ? viv v vi i?iii?v v?i i vv MIR1_Amn#SINE 52 ACCTGGGTT--CNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTG 99 chr6ptel1M 673061 CACAAGTCACTTAATCTCTTTCTGCCTCATTTTTCTCATCTATAAAATGG 673110 vi ? i i v? v i i MIR1_Amn#SINE 100 GGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGG 149 chr6ptel1M 673111 GGATAAT 673117 MIR1_Amn#SINE 150 GGATAAT 156 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.33 CpG sites = 28, Kimura (unadjusted) = 43.58 Transitions / transversions = 1.47 (28/19) Gap_init rate = 0.03 (4 / 154), avg. gap size = 1.00 (4 / 4) 626 28.37 14.42 0.00 chr6ptel1M 672987 673194 (326806) MIRc#SINE/MIR 11 248 (20) m_b289s601i8 11794 chr6ptel1M 672987 TGGTTCAATGGCTAGAACTCTGGGACTGGAGTCAA-------------CA 673023 v i vv i v ivi i------------- i MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr6ptel1M 673024 AGTCCAACCTCAGATACCTATTACCTTTATGATCTATCACAAGTCACTTA 673073 viv v vi i i v v i i vvvi MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTA 110 chr6ptel1M 673074 ATCTCTTTCTGCCTCATTTTTCTCATCTATAAAATGGGGATAATAGCATC 673123 i i vv v i i ii i MIRc#SINE/MIR 111 ACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACC 160 chr6ptel1M 673124 T-----------------AGGTAATTGTGAGATTCAAAGCAAATAATATT 673156 -----------------i vi iv vv i i v MIRc#SINE/MIR 161 TGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTA 210 chr6ptel1M 673157 TGAAAAAAAGTGTTGTAAAATTTAAAATGTTGTATAAA 673194 vi iv iv v v i i i i MIRc#SINE/MIR 211 TGTGAAAGCGCTTTGTAAACTGTAAAGTGCTATACAAA 248 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.77 CpG sites = 32, Kimura (unadjusted) = 36.28 Transitions / transversions = 1.19 (32/27) Gap_init rate = 0.01 (2 / 207), avg. gap size = 15.00 (30 / 2) 279 31.82 1.79 1.79 chr6ptel1M 673501 673612 (326388) C L3#LINE/CR1 (790) 3309 3198 m_b289s601i9 11795 chr6ptel1M 673501 TTGGACTATACTTACTAAACTGACTAGATCTTTTCAGATCCTGATT--GT 673548 i v i vv - i iv v v ? iii i -- C L3#LINE/CR1 3309 TCGGCCCATCGTT-CCAGCCTGTCGAGATCNTTTTGAATCTTGATTCTGT 3261 chr6ptel1M 673549 CATCGAGTACATTGGTAATGCTATTTAGATTTGGGTAAATCACAAATTTG 673598 v ?iii i iv v iviii v v v viii C L3#LINE/CR1 3260 CATCCANCGTATTAGCTATCCCTCCCAGCTTTGTGTCATCTGCAAATTTG 3211 chr6ptel1M 673599 ATAAGCAGTTCCTT 673612 - v C L3#LINE/CR1 3210 ATAAGCA-TGCCTT 3198 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.27 CpG sites = 20, Kimura (unadjusted) = 43.73 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.03 (3 / 111), avg. gap size = 1.33 (4 / 3) 18 16.82 0.00 0.00 chr6ptel1M 673615 673649 (326351) (CAG)n#Simple_repeat 1 35 (0) m_b289s252i3 11796 chr6ptel1M 673615 CAACAGCAGTAACAGCAGCAGCAGCAGCAACAACA 673649 i i i i i (CAG)n#Simple 1 CAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA 35 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 15 30.31 0.00 0.00 chr6ptel1M 673613 673656 (326344) (AAC)n#Simple_repeat 1 44 (0) m_b289s252i2 11797 chr6ptel1M 673613 AACAACAGCAGTAACAGCAGCAGCAGCAGCAACAACAATAATAA 673656 i ii i i i i i i i (AAC)n#Simple 1 AACAACAACAACAACAACAACAACAACAACAACAACAACAACAA 44 Matrix = Unknown Transitions / transversions = 1.00 (10/0) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 585 27.22 13.62 1.52 chr6ptel1M 673766 674000 (326000) C MIRc#SINE/MIR (2) 266 4 m_b289s601i10 11798 chr6ptel1M 673766 TAATAATGATAGCTAATATTTGCATAG------------TGCAAAATACT 673803 i i?v v i i ------------ i iii C MIRc#SINE/MIR 266 TAATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCGCT 217 chr6ptel1M 673804 T---CAAATATCATATCATTTGATTCTCACAACATTCTTCAGAGATAAAC 673850 --- v i i v i vi i vv i ii C MIRc#SINE/MIR 216 TTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGC 167 chr6ptel1M 673851 A---C---TATTATCACCTCTGACTTTCAGATGAGAAAACTGAGG--CAG 673892 --- --- i i i iivi v i -- C MIRc#SINE/MIR 166 AGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAG 117 chr6ptel1M 673893 CTAGAGGCTAACT---TTGCTGAGGTTCACACAGTTTACTAAGTAGCTAA 673939 -- i v --- iv i v -i v i - i C MIRc#SINE/MIR 116 --AGAGGTTAAGTGACTTGCCCAAGGTCACACAG-CTAGTAAGTGGC-AG 71 chr6ptel1M 673940 AGCC-AGACTTGGACTTAGGATTTATTGAGTTTCAGT----TGATTCCAC 673984 -i i i ii vi vi v iiv ---- v iiiv C MIRc#SINE/MIR 70 AGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTC 21 chr6ptel1M 673985 CACTG-ACTATCCTGCC 674000 - i iv C MIRc#SINE/MIR 20 CACTGCACCACACTGCC 4 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.16 CpG sites = 43, Kimura (unadjusted) = 35.67 Transitions / transversions = 2.15 (43/20) Gap_init rate = 0.06 (13 / 234), avg. gap size = 2.77 (36 / 13) 12 39.77 0.00 3.33 chr6ptel1M 674772 674864 (325136) (TATGTA)n#Simple_repeat 1 90 (0) m_b289s252i4 11799 chr6ptel1M 674772 TATTTATATCTAGAAATGTATGAATATGTACATACACGTGTGTTTATACA 674821 v v v vi i v i ii ii i v i i (TATGTA)n#Sim 1 TATGTATATGTATATGTATATGTATATGTATATGTATATGTATATGTATA 50 chr6ptel1M 674822 CAGAACACGTGTGTATGTATATACATGTATATACATATATGTA 674864 -v v i -- i ii i i ii (TATGTA)n#Sim 51 -TGTATA--TGTATATGTATATGTATATGTATATGTATATGTA 90 Matrix = Unknown Transitions / transversions = 2.25 (18/8) Gap_init rate = 0.03 (3 / 92), avg. gap size = 1.00 (3 / 3) 409 27.55 4.79 5.52 chr6ptel1M 675512 675657 (324343) MIRc#SINE/MIR 2 146 (122) m_b289s601i11 11800 chr6ptel1M 675512 GGGGCAGCTAGGTGGTGTGGCAGATGGAGTACTGGACTTGGAATCTGGAA 675561 i i--- ii ii vi i i v MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr6ptel1M 675562 GATTCA---TC--TTCCTGACTTTGAAGCTGGCTTCTTAGCTATGTGACG 675606 iiii--- --v i i i --- i-i vi i v MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCT---GCC-ACTTACTAGCTGTGTGACC 94 chr6ptel1M 675607 CTGGGCAAGACATTTCAGCCCATTT--GCTTTAATTTCCTTATCTGCCAA 675654 i v i - i iv i -- i i i i iv MIRc#SINE/MIR 95 TTGGGCAAGTCACTT-AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAA 143 chr6ptel1M 675655 ATG 675657 MIRc#SINE/MIR 144 ATG 146 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.75 CpG sites = 30, Kimura (unadjusted) = 37.02 Transitions / transversions = 3.75 (30/8) Gap_init rate = 0.08 (11 / 145), avg. gap size = 1.36 (15 / 11) 14 28.03 0.00 0.00 chr6ptel1M 675926 675966 (324034) (TGTA)n#Simple_repeat 1 41 (0) m_b289s252i5 11801 chr6ptel1M 675926 TGTATGTACATACATACATACGTAAATATGTATGTATGTAT 675966 ii ii ii i vi (TGTA)n#Simpl 1 TGTATGTATGTATGTATGTATGTATGTATGTATGTATGTAT 41 Matrix = Unknown Transitions / transversions = 8.00 (8/1) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 268 33.63 3.23 4.07 chr6ptel1M 677124 677247 (322753) MIRc#SINE/MIR 11 133 (135) m_b289s601i12 11802 chr6ptel1M 677124 TGGTG--GCGGAGCAGAATGTTAGGCTTGGAGTTGCGAAGACCCACATTC 677171 -- i i- iiii i i iiv iivi MIRc#SINE/MIR 11 TGGTGCAGTGGAA-AGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr6ptel1M 677172 TGTTCTTTCCTCAGACACTGACTAGCAAGCACTGTGACTCTGGGTGATTA 677221 viv iivv v v v vi---- ii ii v v MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTG----TGTGACCTTGGGCAAGTC 105 chr6ptel1M 677222 ACTTAACCTTGCTCATCTTT--TTTTCT 677247 iv v v i i-- i MIRc#SINE/MIR 106 ACTTAACCTCTCTGAGCCTCAGTTTCCT 133 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 45.13 CpG sites = 25, Kimura (unadjusted) = 46.77 Transitions / transversions = 1.67 (25/15) Gap_init rate = 0.06 (7 / 123), avg. gap size = 1.29 (9 / 7) 221 28.21 6.41 0.00 chr6ptel1M 677270 677347 (322653) MIRc#SINE/MIR 186 268 (0) m_b289s601i13 11802 chr6ptel1M 677270 TATAAAAATCAAATGAGACAATGTATAT-AGATCTCCTTACCAACTTTTA 677318 i i ii i i - i v v i iiv v v MIRc#SINE/MIR 186 TGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTTTGTAAACTGTAA 235 chr6ptel1M 677319 AGTGCGACATACATGT----TACTATTACTATT 677347 v i i v ----?ii i MIRc#SINE/MIR 236 AGTGCTATACAAATGTAAGGNGTTATTATTATT 268 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.76 CpG sites = 15, Kimura (unadjusted) = 37.76 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.03 (2 / 77), avg. gap size = 2.50 (5 / 2) 342 25.20 3.31 10.64 chr6ptel1M 677341 677491 (322509) C MIR#SINE/MIR (105) 157 17 m_b289s601i14 11803 chr6ptel1M 677341 TACTATTACTATTCAAAATTGCTCATTT--GAGATGAGGAAAGT-AGGGA 677387 i i --------i --v v - v C MIR#SINE/MIR 157 TACTATTATTATCC--------CCATTTTACAGATGAGGAAACTGAGGCA 116 chr6ptel1M 677388 C-CAGGGTTTCAATTACTTGCCCACAGTCTCTACAGCCACATAGTGAGGT 677436 -v i v v i v vi v - ---- i vv C MIR#SINE/MIR 115 CAGAGAGGTTAAGTAACTTGCCCAAGGTCAC-ACAGC----TAGTAAGTG 71 chr6ptel1M 677437 GCAAGGCTAGGATGTGAAAGCAAGCCTTCTGACTCCAAATTGACTGTG-T 677485 ii ii vi vv i vv i i -- v i - C MIR#SINE/MIR 70 GCAGAGCCGGGATTCGAACCCAGGCAGTCTGGCTCCAGA--GCCCGTGCT 23 chr6ptel1M 677486 TTTAAC 677491 i C MIR#SINE/MIR 22 CTTAAC 17 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 27.50 CpG sites = 17, Kimura (unadjusted) = 30.69 Transitions / transversions = 1.00 (17/17) Gap_init rate = 0.13 (19 / 150), avg. gap size = 1.05 (20 / 19) 343 29.07 11.54 2.11 chr6ptel1M 677708 677837 (322163) C MIR3#SINE/MIR (21) 187 46 m_b289s601i15 11804 chr6ptel1M 677708 TCAGAATTTGAAGGAATCTTACAGATCATGTAGCTCAACTCACTCCCCCT 677757 ii v i i v v ii i --- i v C MIR3#SINE/MIR 187 TCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCC---CCTCAT 141 chr6ptel1M 677758 TTT-CAGATGAGAAAAT--AGATTTATAGAGG----------TGTCCAA- 677793 - i i-- iiii v ---------- i - C MIR3#SINE/MIR 140 TTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAG 91 chr6ptel1M 677794 -TAATACGGATAGGAAATGTTTGAGGTGAGATTTGAACCTAGATC 677837 - v i i v? vv i viv vi i i v i i C MIR3#SINE/MIR 90 GTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGTC 46 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.51 CpG sites = 24, Kimura (unadjusted) = 38.87 Transitions / transversions = 1.85 (24/13) Gap_init rate = 0.06 (8 / 129), avg. gap size = 2.25 (18 / 8) 392 25.16 8.76 1.36 chr6ptel1M 677835 677971 (322029) C MIR3#SINE/MIR (2) 206 60 m_b289s601i16 11805 chr6ptel1M 677835 ATCATAGACTCATAGA---TCAATAACTATA-GGGATCCGAGAGAACATC 677880 v --- i- i iv - i iv v C MIR3#SINE/MIR 206 ATCATAGAATCATAGAATGTCAG-AGCTGGAAGGGACCTTAGAGATCATC 158 chr6ptel1M 677881 TAG-CTTACACCGGTATTTTATAGATGGGAAAG--GAGACATAGAGAGGT 677927 - iv v vvi i i i i-- i vi C MIR3#SINE/MIR 157 TAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGT 108 chr6ptel1M 677928 GGAAATGACTTATACAATATTATATAG--AG---GGGGCAGAGCCAAGA 677971 - i iiv vi i i i -- --- v ii C MIR3#SINE/MIR 107 -GAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGA 60 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 30.56 CpG sites = 22, Kimura (unadjusted) = 31.68 Transitions / transversions = 1.83 (22/12) Gap_init rate = 0.06 (8 / 136), avg. gap size = 1.75 (14 / 8) 18 30.95 1.92 0.00 chr6ptel1M 678858 678909 (321091) (AG)n#Simple_repeat 1 53 (0) m_b289s252i6 11806 chr6ptel1M 678858 AGGGAGAAGGAGA-AAAGAGAAAAGGAGAGAGAGGGGAAGAGGGGGAGAG 678906 i ii - i i ii i ii i i (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr6ptel1M 678907 AGA 678909 (AG)n#Simple_ 51 AGA 53 Matrix = Unknown Transitions / transversions = 1.00 (12/0) Gap_init rate = 0.02 (1 / 51), avg. gap size = 1.00 (1 / 1) 13 29.62 0.00 0.00 chr6ptel1M 679051 679095 (320905) (AAAAC)n#Simple_repeat 1 45 (0) m_b289s252i7 11807 chr6ptel1M 679051 AAATCAAGAAACAATAAAACAAAACCAAAAGAATGAAAAAAAAAC 679095 v i v v i v vi vv v (AAAAC)n#Simp 1 AAAACAAAACAAAACAAAACAAAACAAAACAAAACAAAACAAAAC 45 Matrix = Unknown Transitions / transversions = 0.38 (3/8) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 chr6ptel1M 679341 679357 (320643) (T)n#Simple_repeat 1 17 (0) m_b289s252i8 11808 chr6ptel1M 679341 TTTTTTTTTTTTTTTTT 679357 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTT 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 12 9.24 0.00 4.17 chr6ptel1M 679397 679421 (320579) (TCCC)n#Simple_repeat 1 24 (0) m_b289s252i9 11809 chr6ptel1M 679397 TCCCTCCCACCCTCCACCCCCTCCC 679421 v - i (TCCC)n#Simpl 1 TCCCTCCCTCCCTCC-CTCCCTCCC 24 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 251 28.57 0.00 0.00 chr6ptel1M 679655 679731 (320269) L1MEj_5end#LINE/L1 1063 1139 (1021) m_b289s551i6 11810 chr6ptel1M 679655 CCAGGAATATTATGATCAAATTCTAGGGCTCTCAGGTCAAGGAGAAAATA 679704 i v iv i v iv ii iv vi i v L1MEj_5end#LI 1063 CTAGGCATATCCTGGTAAAATTCCTGAACTCCAAGGATAAAGAGAAAATC 1112 chr6ptel1M 679705 TTTCAAGCTTCCAGAAAGGGAAAAAAA 679731 v v ii i v L1MEj_5end#LI 1113 TTACAAGCTTCCAGACAGAAAGAACAA 1139 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.65 CpG sites = 12, Kimura (unadjusted) = 36.65 Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.00 (0 / 76), avg. gap size = 0.0 (0 / 0) 551 30.17 4.60 5.57 chr6ptel1M 680524 681067 (318933) L1ME4c_3end#LINE/L1 40 578 (252) m_b289s551i7 11811 chr6ptel1M 680524 AAAAAAAACAATAAGAACTATTCCCAAATTCATGAATAATCAAAGGATAT 680573 i ? vi ------ v vv i iiv i L1ME4c_3end#L 40 AAGAAAAANATCAAGA------CCCCAATAGATAAATGGGCAAAGGACAT 83 chr6ptel1M 680574 GAACAG----TTT---TTAGATGAAATAATCAAGTTATTCATAATCATAT 680616 ---- i---?v v -- ? vi vv i v i L1ME4c_3end#L 84 GAACAGACAATTCACANAAGAGGAAATA--CAANTAGTAAACAAACACAT 131 chr6ptel1M 680617 GAAAAAAAATTC----TCGCTATTGATTGGAGAAATGCAAATTCAAATTT 680662 i vi ---- v i iii - viv L1ME4c_3end#L 132 GGAAAAATGTTCAACCTCGCTAGTAATCAAAGAAATGCAAATT-AAAGCA 180 chr6ptel1M 680663 GCATTCCGAGGTAGC---TCATATCTATTAGATTGGCTAATAGGACAGAA 680709 i v -- i v --- i iii i i v v vvvv i L1ME4c_3end#L 181 ACAAT--GAGATACCATTTTACGCCTATTAAATTAGCAAAAATTTAAAAA 228 chr6ptel1M 680710 AAGGAAAATGACAAATGTTGGAGGCAATGTTGCCTAAATGAGATATTAAT 680759 vv v iv v i v ivi? iv ivv v iv i?i v L1ME4c_3end#L 229 ATTGATAATACCCAATGCTGGCGAGGNTGCGGTGAAACTGGTACNCTCAT 278 chr6ptel1M 680760 GCAGTGTTGGTGGAATTTTGAACTGATTCAACCGTTCTGTAGAGCTATTT 680809 i v i v ? v i i i v v i v i v L1ME4c_3end#L 279 ACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTT 328 chr6ptel1M 680810 GGAATTATACTCA--AAGAGCTATAAAATCCTTTGCCTACTTTGCCTACC 680857 v -- vi -- i viv -- v -------- L1ME4c_3end#L 329 GGCA--ATACGTATCAAGAGCCATAAAAATGTT--CATAC--------CC 366 chr6ptel1M 680858 TTTGATCTACTAATATTACTTCTAAGCTTGTATTTCAAAAAAA-GATTAA 680906 i i v vii ii vv v iii ii -i v L1ME4c_3end#L 367 TTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCA 416 chr6ptel1M 680907 AAAGC-GTAAAATGCCTATATAAAC-AAGA-GT--ATAGTAGACTT-TTT 680950 v- v v - iv - - -- v i vv - L1ME4c_3end#L 417 AAAGAAGGAAAAAGC-TATATGCACGAAGATGTTCATTGCAGCGTTATTT 465 chr6ptel1M 680951 CTTAGGGCAAAGAATTGAAAATTGAGGGACTGTTCATTAACTGGGGAATG 681000 v v vi i i i ivivvvi v i vi iv L1ME4c_3end#L 466 ATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAATG 515 chr6ptel1M 681001 GCTGAACAAATTGTGGTATGT-GATTATGATGGGATACTAACTATTGTA- 681048 i i ii i ii -? i -i i i ----- i - L1ME4c_3end#L 516 GTTAAGTAAATTATGGTACATCNACT-CGATGGAATATTA-----TGCAG 559 chr6ptel1M 681049 CCATTAAAAAAAATGATTA 681067 vi i L1ME4c_3end#L 560 CCATTAAAAATGATAATTA 578 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.69 CpG sites = 83, Kimura (unadjusted) = 40.04 Transitions / transversions = 1.15 (83/72) Gap_init rate = 0.08 (43 / 543), avg. gap size = 1.28 (55 / 43) 456 31.38 4.35 0.70 chr6ptel1M 681701 681838 (318162) MIRc#SINE/MIR 8 150 (118) m_b289s601i17 11812 chr6ptel1M 681701 GTGTGATAC--TG---AGGGCCCTGGGCTTCCAGTTGGGAAAACTTGGGC 681745 i i -- --- i v i vv ii i i i MIRc#SINE/MIR 8 GTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGT 57 chr6ptel1M 681746 TTACATACCACCTCAAGACATTCATTAGC-ATATGAATTTGGGTAAAGCA 681794 iivi v iv v- v i i i -i i vi i iv MIRc#SINE/MIR 58 TCGAGTCCCGGCTCT-GCCACTTACTAGCTGTGTGACCTTGGGCAAGTCA 106 chr6ptel1M 681795 TTTAATCATTCAGGAACTTAGTTTCCTTATCTGTAAAATGAGAA 681838 i i vi v iiv i i i i MIRc#SINE/MIR 107 CTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGA 150 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.43 CpG sites = 30, Kimura (unadjusted) = 43.32 Transitions / transversions = 2.31 (30/13) Gap_init rate = 0.03 (4 / 137), avg. gap size = 1.75 (7 / 4) 16 0.00 0.00 0.00 chr6ptel1M 681858 681874 (318126) (T)n#Simple_repeat 1 17 (0) m_b289s252i10 11813 chr6ptel1M 681858 TTTTTTTTTTTTTTTTT 681874 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTT 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 355 24.49 7.77 0.91 chr6ptel1M 682560 682662 (317338) C Charlie4#DNA/hAT-Charlie (30) 3348 3239 m_b289s502i0 11814 chr6ptel1M 682560 ACCCCTTATGATGGACTGGTGAAAGTTATGGGTCCTTTATTAAAATCATG 682609 - iii v ivi ii i v i i v C Charlie4#DNA/ 3348 ACCCCTT-TGGCAGTCTGGTGAAGCCTATGGACCCCTTCTCAGAATAATG 3300 chr6ptel1M 682610 TTGTTGAATCCATGGATT--------TAGGATTGCCAAGGAAATCAATTA 682651 v i v ii v -------- i v i C Charlie4#DNA/ 3299 TTTTTAAATGCATAAAATAAAATACATAGGATTACAAAGGAAACCAATTA 3250 chr6ptel1M 682652 TATTACAATAT 682662 iv C Charlie4#DNA/ 3249 TATTGAAATAT 3239 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 30.56 CpG sites = 16, Kimura (unadjusted) = 30.56 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.02 (2 / 102), avg. gap size = 4.50 (9 / 2) 529 34.98 8.63 5.22 chr6ptel1M 683304 683674 (316326) L3#LINE/CR1 3713 4095 (4) m_b289s601i18 11815 chr6ptel1M 683304 AAAAAACTTGAGATATTCATCTTAAAGCAAGGGAGATTGAGGAGAGGTGA 683353 ii v i i i v i ii v ii i i v ii ---- L3#LINE/CR1 3713 AAGGAACTGGGGATGTTTAGCCTGGAGAAGAGAAGACTTAGAGGAG---- 3758 chr6ptel1M 683354 GGGAAGGCATATGAATGGTGTGT--AAGTTTCTTAAGGGCTATTA---AA 683398 -------- i vv v v -- i v i v i i ---ii L3#LINE/CR1 3759 --------ACATGATAGCTGTCTTCAAATATTTGAAGGGCTGTCATGTGG 3800 chr6ptel1M 683399 GAGAATGATT-CATTT-TTCTGC-TAGCTGTAATAAGAATATAGATAGAG 683445 i iv -v i - i- i vi i-- iii v iv - L3#LINE/CR1 3801 AAGAGGGATTAGACTTATTCTGTGTGGCTCCAG--AGGGCAGAACTAG-G 3847 chr6ptel1M 683446 ACCCA---GTGG------CAGAGAAATAGATTTTGATCTCCTATAAGACA 683486 v --- ------ i iii i iiiivv iv L3#LINE/CR1 3848 ACCAATGGGTGGAAGTTACAGGGAGGCAGATTTCGGCTCAATATAAGGAA 3897 chr6ptel1M 683487 AAACTTGGTGGGGATATATCAG---TATCCCACAGTAGAATAAGCGGCTT 683533 i vv i--- i - --- i v v i i ii v i L3#LINE/CR1 3898 GAACTTTCTA---ACA-ATCAGAGCTGTCCAAAAATGGAATGGGCTGCCT 3943 chr6ptel1M 683534 TAGTAACTAGGGAATTTTCTGTCATTGGAGGCATTTAAGAATACATTGAA 683583 ii?v iv v ii ii i i ii i v v vii i L3#LINE/CR1 3944 CGNGAGGTAGTGAGCTCCCCGTCACTGGAGGTGTTCAAGCAGAGGCTGGA 3993 chr6ptel1M 683584 CAGCTATTTGTCA-GAATATTGTAAGAATGTATTCTTACATTG---AGGA 683629 iii i i - i i - v v i i ---i L3#LINE/CR1 3994 TGACCACTTGTCAGGGATGTTGT-AGAAGGGATTCCTGCATTGGATGGGA 4042 chr6ptel1M 683630 --TTAAAATAGGT--CTTCTCAG----CTCTGAGTTCTAGGATTCTATGA 683671 -- ii v i -- i v ---- iiv ii ii i L3#LINE/CR1 4043 GGTTGGACTAGATGACCTCTAAGGTCCCTTCCAACTCTGAGATTCTGTGA 4092 chr6ptel1M 683672 CTC 683674 i L3#LINE/CR1 4093 TTC 4095 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 49.78 CpG sites = 88, Kimura (unadjusted) = 51.75 Transitions / transversions = 2.51 (88/35) Gap_init rate = 0.09 (33 / 370), avg. gap size = 1.58 (52 / 33) 355 29.06 7.02 7.96 chr6ptel1M 683731 683958 (316042) C MamGypsy2-I#LTR/Gypsy (2910) 1256 1031 m_b289s551i8 11816 chr6ptel1M 683731 AAGGAGACTTACTGGGCATGCACAATTTGGCTTGTAGTGATA--AA---- 683774 v vii vi v ivii vi ii i -- ---- C MamGypsy2-I#L 1256 AAGGAGCCACGCTGCACATTCACAACACAGCTTCCAGCAACATCAACTGT 1207 chr6ptel1M 683775 -TGATTAG-GTAACATTAAA---TGCATGACAAT----ATAACTTTG-CA 683814 - i v- iv i --- iiiii---- i - C MamGypsy2-I#L 1206 GTGATCATTGTAATCTTGAAGAATGCATGGTGGCCTCAACAACTTTGGCA 1157 chr6ptel1M 683815 ATAGGTCTCCTGAGAAGAGATTGTGTTTTAATTTTCATGGATTTTATCAA 683864 vi i iv i v v--- ------- ---- -- C MamGypsy2-I#L 1156 AAGGGCCTTGTGAGAAAATATTGTGG---AA-------GG----TATC-- 1123 chr6ptel1M 683865 TTTTAATCAATTATTGATAGCCCACAATGAGGTTAGACCTTCATCTTGTA 683914 - -i i vv ivi iv v i i i C MamGypsy2-I#L 1122 -TTTA-CCGATTATTGATATACCACAACCGGAGTCGACTTCCATCTTGCA 1075 chr6ptel1M 683915 TTCATGGCTATCTTTAAATATGGTTGCTGACACTGAAGTGTCCT 683958 i i i v i i iv vi i v i C MamGypsy2-I#L 1074 CTCATGGCCATTTATGAGTACTGTTGCAAATACTGCAGTATCCT 1031 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.86 CpG sites = 40, Kimura (unadjusted) = 38.37 Transitions / transversions = 1.90 (40/21) Gap_init rate = 0.11 (25 / 227), avg. gap size = 1.36 (34 / 25) 253 27.87 9.84 0.00 chr6ptel1M 684013 684134 (315866) C L2d_3end#LINE/L2 (6) 510 377 m_b289s601i19 11817 chr6ptel1M 684013 AATGAATAAAAAAGATTTTATTAAGC-TCTGTTATATGTTGTACATTGTG 684061 v v v vv i -i ii i i vvi i C L2d_3end#LINE 510 AATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTGTG 461 chr6ptel1M 684062 GTA--CATTTTGGG--AC--TCAAATGGAA-AAAAGATAATCCCTGTCAT 684104 v -- ii v -- --?v ?i v - i v ii i v C L2d_3end#LINE 460 CTAGGCGCTGTGGGGAACGANAAAANAGTATAAGACATGGTCCCTGCCCT 411 chr6ptel1M 684105 CAAGGACCTTTCATTCCCAT--GGGAG--AAGAC 684134 v v v ivi -- -- C L2d_3end#LINE 410 CAAGGAGCTTACAATCTAGTTGGGGAGACAAGAC 377 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.71 CpG sites = 17, Kimura (unadjusted) = 36.00 Transitions / transversions = 1.00 (17/17) Gap_init rate = 0.06 (7 / 121), avg. gap size = 1.71 (12 / 7) 261 32.08 8.49 0.00 chr6ptel1M 684029 684134 (315866) C L2a_3end#LINE/L2 (20) 497 383 m_b289s601i20 11817 chr6ptel1M 684029 TTTATTAAGC-TCTGTTATATGTTGTACATTGTGGTACATTTTGGGACT- 684076 i -i ii i iiivi i vv viivi iv - C L2a_3end#LINE 497 TTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGCGCTGGGGATA 448 chr6ptel1M 684077 CA--AATGGAAAAAA--GATAA---TCCCTGTCATCAAGGACCTTTCATT 684119 -- i i v -- i --- i v v v v C L2a_3end#LINE 447 CAGCAGTGAACAAAACAGACAAAAGTCCCTGCCCTCATGGAGCTTACATT 398 chr6ptel1M 684120 CCCATGGGAGAAGAC 684134 ivi i i C L2a_3end#LINE 397 CTAGTGGGGGGAGAC 383 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.22 CpG sites = 22, Kimura (unadjusted) = 43.99 Transitions / transversions = 1.83 (22/12) Gap_init rate = 0.05 (5 / 105), avg. gap size = 1.80 (9 / 5) 473 31.96 1.72 2.91 chr6ptel1M 684980 685153 (314847) C L3#LINE/CR1 (1157) 2942 2771 m_b289s601i21 11818 chr6ptel1M 684980 CTAAAGCTTGCCCTTTGTTCACAAACTTAGCCATCCTGATAAATGACGAA 685029 vi v v i vi ii v iii iv i ivi vi v C L3#LINE/CR1 2942 CTACGGCATTCCCCTGATCTACCAGTCTAGTAACCCTATCAAAAAAGGAA 2893 chr6ptel1M 685030 ACCAATTTAATGTGGCGTGACTTGTTCTTTGTGGACCCCATATTGGTTTC 685079 iv iv i v i v i - ii i i C L3#LINE/CR1 2892 ATGAGGTTAGTTTGGCATGACTTGTTCTTAGTGAA-CCCATGCTGGCTCC 2844 chr6ptel1M 685080 TGAGGATCACTGCTCCTCCCTTTTAGAAGTTGCT-ATAAA--ATTCTTTT 685126 iiv i --- i vv - - i -- iiv C L3#LINE/CR1 2843 TAGTGATCACCG---CTTCCTTTTCTAAG-TGCTCACAAACCATCTGTTT 2798 chr6ptel1M 685127 AGAAATCCATGTTAAAATTTTACCAGG 685153 iv i vi i i i C L3#LINE/CR1 2797 AATAATCCGTTCTAGAATTTTGCCGGG 2771 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.45 CpG sites = 35, Kimura (unadjusted) = 43.76 Transitions / transversions = 1.84 (35/19) Gap_init rate = 0.04 (7 / 173), avg. gap size = 1.14 (8 / 7) 258 32.00 0.00 0.00 chr6ptel1M 685161 685235 (314765) C MamGypsy2-I#LTR/Gypsy (3719) 447 373 m_b289s551i9 11816 chr6ptel1M 685161 ACCAAGTTGTCAGTGCCAACTGTGAAATGTAGGTCTTTGAACAATGGCGT 685210 i i iii v vi v ii i i vv C MamGypsy2-I#L 447 ACCAGGCTGTTGATTCCATTTGTGAAATTTAAATCTCTGAACAATGACTG 398 chr6ptel1M 685211 ATAATTCTGATAAGAAACCCTCCTT 685235 ii v i i iiv v C MamGypsy2-I#L 397 ATGGTGCTGGTGAGAAGTGCGCCTT 373 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 44.11 CpG sites = 16, Kimura (unadjusted) = 44.11 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.00 (0 / 74), avg. gap size = 0.0 (0 / 0) 190 37.35 8.95 8.28 chr6ptel1M 685342 685665 (314335) C L2b_3end#LINE/L2 (26) 440 115 m_b289s601i22 11819 chr6ptel1M 685342 GAGCATTAATTATATTCCAGGCCCTCCATAAAGTTCTGGTGAAAAAAAAA 685391 iiiv i i i v ? viiiv i iv v v v ivii C L2b_3end#LINE 440 GAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGGGATACAGCGG 391 chr6ptel1M 685392 AAAAAAAAAAGGCAAAGGCTCTTCCTGCTCTCAACAAACTCAT--TCTCA 685439 vi v i --- i v? vv i i vvi i i-- vi C L2b_3end#LINE 390 TGAACAAGA---CAGACNCGGTCCCTGCCCTCACGGAGCTCACAGTCTAG 344 chr6ptel1M 685440 TGAAGG-----GAAATGT----------TAATAACTGGGGACATGCCAGG 685474 ii ----- v ---------- ? ivi ii-- v C L2b_3end#LINE 343 TGGGGGAGACAGACATGTAANCAGACAATNATAACCCAGAG--TGGCAGG 296 chr6ptel1M 685475 TATATATAGAAGAGGGAGAATATAATCTCAGGAAAGTACACACTAGCT-- 685522 -----i i vv i ii------ i iii vi i - ii i-- C L2b_3end#LINE 295 -----GTAGGACTGGGGGGG------CCCAGAGGAGGGCGC-CTGACCCG 258 chr6ptel1M 685523 GCTGGGAGAAATGAGAAATACCTCCTGCAGGAGATGGGCATTGGAGCTGA 685572 iv i iiviii i ivi i i v i i- v C L2b_3end#LINE 257 GCCTGGGGGGTCAGGGAGGGCTTCCCGGAGGAGGTGA-CATTTGAGCTGA 209 chr6ptel1M 685573 GTTTTGAAGAA---GCCAA----GGCC--GTTAAGAGGTGTGAGTGAGAA 685613 vii i --- ivii---- -- iv ----- i C L2b_3end#LINE 208 GACCTGAAGGATGAGTAGGAGTTGGCCAGGCGAAGAGGTG-----GGGAA 164 chr6ptel1M 685614 GAGAGCATTCTAGATATGGAGGCAA-GGCTGGGGCAAAGACTTGGAGAAG 685662 i -- i i ii -- v -i v? v i iiv iv C L2b_3end#LINE 163 GGG--CGTTCCAGGCA--GAGGGAACAGCANGTGCAAAGGCCCTGAGGCG 118 chr6ptel1M 685663 GGA 685665 C L2b_3end#LINE 117 GGA 115 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 51.85 CpG sites = 75, Kimura (unadjusted) = 57.42 Transitions / transversions = 2.08 (75/36) Gap_init rate = 0.11 (34 / 323), avg. gap size = 1.65 (56 / 34) 223 29.93 4.88 4.24 chr6ptel1M 685504 685667 (314333) C L2c_3end#LINE/L2 (199) 279 115 m_b289s601i23 11819 chr6ptel1M 685504 AGGAAAGTAC--ACACTAGCTGCTGGGAGAAATGAGAAATACCTCCTGCA 685551 ii i -- v ?-- v i iiviii i vi i i v C L2c_3end#LINE 279 AGGAGGGCACCTAGACTAGN--CTTGGGGGGTCAGGGAAGGCTTCCCGGA 232 chr6ptel1M 685552 GGAGATGGGCATTGGAGCTGAGTTTTGAAGAA-GCCAAGGCCGTTAA-GA 685599 i i- iv ?i i - vvv -v i-v C L2c_3end#LINE 231 GGAGGTGA-CATCTGAGCTGAGNCTTGAAGGATGAGTAGG-AGTTAGCCA 184 chr6ptel1M 685600 GGTGTGAGTGAGAAG---AGAGCATTCTAGATATGGAGGCAA-GGCTGGG 685645 - iv ii --- i ii -- v -i vv v C L2c_3end#LINE 183 GGTG-GAAGGAGGGGGGAAGAGCATTCCAGGCA--GAGGGAACAGCATGT 137 chr6ptel1M 685646 GCAAAGACTTGGAGAAGGGAAA 685667 i ?i ivi C L2c_3end#LINE 136 GCAAAGGCNCGGAGGCAGGAAA 115 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.61 CpG sites = 30, Kimura (unadjusted) = 40.89 Transitions / transversions = 1.76 (30/17) Gap_init rate = 0.07 (12 / 163), avg. gap size = 1.25 (15 / 12) 248 21.82 1.82 0.00 chr6ptel1M 685732 685786 (314214) C MamGypsy2-LTR#LTR/Gypsy (124) 59 4 m_b289s601i24 11820 chr6ptel1M 685732 AACTCAAAGGGAATAAACAGACTAAGATTGAA-CACTGTGCCCCTTGGTG 685780 i i v v v - v i i ii C MamGypsy2-LTR 59 AACTCAAAAGGAACAAAAACACTAACATTGAACCACAGCGCCCCCTGGCA 10 chr6ptel1M 685781 AATATA 685786 v i C MamGypsy2-LTR 9 TACATA 4 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 23.77 CpG sites = 7, Kimura (unadjusted) = 26.21 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1) 211 30.13 0.00 6.67 chr6ptel1M 685794 685889 (314111) L2d2_3end#LINE/L2 198 287 (268) m_b289s601i25 11821 chr6ptel1M 685794 CCCATCCAAAATTTGAAAACCTGGTCAAAATCTTAACTTCCCTCTGCAGC 685843 ----- v ii ii iiv ?ii v i i iv v L2d2_3end#LIN 198 CCCATCC-----TTCAAGGCCCAGCTCAAATNCCACCTCCTCCGTGAAGC 242 chr6ptel1M 685844 CTTTCCTGTCCATTCCAGCTGCTCAGTTCTGCCTTCCTTCTCTGAA 685889 i v i i- v? vv vi i i L2d2_3end#LIN 243 CTTCCCTGACCACTCCAGCC-CGNAGTGATCTCTCCCTCCTCTGAA 287 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.10 CpG sites = 17, Kimura (unadjusted) = 41.10 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.06 (6 / 95), avg. gap size = 1.00 (6 / 6) 224 27.15 4.11 4.11 chr6ptel1M 686166 686238 (313762) MIR3#SINE/MIR 105 177 (31) m_b289s601i26 11822 chr6ptel1M 686166 TTTATTTCCCTGAATGTTCTTAGTTGCTATAT---TAATATTAGGGGATT 686212 i ii i --- vi i v ivi --- v v i MIR3#SINE/MIR 105 TTCACCTCTCTG---GGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTT 151 chr6ptel1M 686213 GGAATAGGTAATCTCTAAATTCCCTT 686238 v i i iv MIR3#SINE/MIR 152 GGACTAGATGATCTCTAAGGTCCCTT 177 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.83 CpG sites = 12, Kimura (unadjusted) = 34.83 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.06 (4 / 72), avg. gap size = 1.50 (6 / 4) 446 17.99 8.77 2.48 chr6ptel1M 686287 686400 (313600) MIR3#SINE/MIR 85 205 (3) m_b289s601i27 11823 chr6ptel1M 686287 TGTGACCTTGAGGAA----CTTT-CCTCTATGGACCTCAGTTTCCCCATT 686331 i v ---- i- v i i i MIR3#SINE/MIR 85 TGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATC 134 chr6ptel1M 686332 TGCAAAAATGAAGAGGTTGGACTCAAAT-ATCTCCCAAAT-CCTTCCAGT 686379 i- i i - i - iv ii - i MIR3#SINE/MIR 135 TGT-AAAATGAGGGGGTTGGACT-AGATGATCTCTAAGGTCCCTTCCAGC 182 chr6ptel1M 686380 TCTAGA---TCTGTGATCCGATAA 686400 - --- i i v i MIR3#SINE/MIR 183 TCT-GACATTCTATGATTCTATGA 205 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 21.47 CpG sites = 16, Kimura (unadjusted) = 21.47 Transitions / transversions = 4.00 (16/4) Gap_init rate = 0.07 (8 / 113), avg. gap size = 1.62 (13 / 8) 251 27.12 0.00 0.00 chr6ptel1M 686414 686472 (313528) MIR#SINE/MIR 36 94 (168) m_b289s601i28 11824 chr6ptel1M 686414 GAGGCAGACAGCCTGGGTTCAAATTCTAGTTTTTCTTCATACTTGCTTTT 686463 v v i i ii i i v iv v v v v MIR#SINE/MIR 36 GAGCCAGACTGCCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTG 85 chr6ptel1M 686464 TGACCTTAG 686472 i MIR#SINE/MIR 86 TGACCTTGG 94 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.86 CpG sites = 8, Kimura (unadjusted) = 34.02 Transitions / transversions = 1.00 (8/8) Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.0 (0 / 0) 226 21.16 0.00 1.92 chr6ptel1M 687812 687864 (312136) L2d_3end#LINE/L2 436 487 (29) m_b289s601i29 11821 chr6ptel1M 687812 TTTTCTCCTTCCCCCATTGTTCCTAGTACAGTCCTGAGCACATAATAGTT 687861 ? v - iv iv i v i vi L2d_3end#LINE 436 TTTTNTCGTTCCCC-ACAGCGCCTAGCACAGTGCTGAGCACATAGTAGGC 484 chr6ptel1M 687862 GTT 687864 i L2d_3end#LINE 485 GCT 487 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 20.70 CpG sites = 6, Kimura (unadjusted) = 25.73 Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.02 (1 / 52), avg. gap size = 1.00 (1 / 1) 249 36.93 13.51 1.20 chr6ptel1M 688093 688240 (311760) MIR3#SINE/MIR 12 177 (31) m_b289s601i31 11825 chr6ptel1M 688093 GTTCAGTGGAAGGAGCATTTGGATTCAGAGCTAGAAGGCCTGAGTTTGGA 688142 i v ii ii i-- i vi ii i i i ivii MIR3#SINE/MIR 12 GCTGAGCAGAGAGAGCAC--GGACTGGGAGTCAGGAGACCTGGGTTCTAG 59 chr6ptel1M 688143 TTTATTCCTTCCTGTTTGTTATTTGAAAAATCCTGAGCTACCCAGTTTGC 688192 iivvv ii v iii vii ?vi vivi i i i v vi v ii MIR3#SINE/MIR 60 TCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCAC 109 chr6ptel1M 688193 -TCTTT-----CCAGTTTCCTCCTCTGTAAAATGAGAGG----------- 688225 - i -----i v i ----------- MIR3#SINE/MIR 110 CTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGA 159 chr6ptel1M 688226 ---TCTCCAAAGTCCCTT 688240 --- i i MIR3#SINE/MIR 160 TGATCTCTAAGGTCCCTT 177 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 55.37 CpG sites = 39, Kimura (unadjusted) = 57.07 Transitions / transversions = 2.60 (39/15) Gap_init rate = 0.03 (5 / 147), avg. gap size = 4.40 (22 / 5) 313 34.88 5.38 0.74 chr6ptel1M 688093 688222 (311778) MIRc#SINE/MIR 13 148 (120) m_b289s601i30 11825 chr6ptel1M 688093 GTTCAGTGGAAGGAGCATTTGGATTCAGAGCTA-GAAGGCCTGAGTTTGG 688141 v i -i i ii ii - i i i i MIRc#SINE/MIR 13 GTGCAGTGGAAAGAGCA-CTGGACTTGGAGTCAGGAAGACCTGGGTTCGA 61 chr6ptel1M 688142 ATTTATTCCTTCCTGTTTGTTATTTGAAAAATCCTGAGCTACCCAGTTTG 688191 i iivvv ii v iii ii vi vivi i i i v vi v vi MIRc#SINE/MIR 62 GTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAA 111 chr6ptel1M 688192 -CTCTTT-----CCAGTTTCCTCCTCTGTAAAATGAG 688222 - i -----i v i MIRc#SINE/MIR 112 CCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 49.35 CpG sites = 32, Kimura (unadjusted) = 51.06 Transitions / transversions = 2.46 (32/13) Gap_init rate = 0.03 (4 / 129), avg. gap size = 2.00 (8 / 4) 298 27.78 11.11 0.00 chr6ptel1M 688928 689035 (310965) MIRc#SINE/MIR 2 121 (147) m_b289s601i32 11826 chr6ptel1M 688928 GAGACTGTGTGGT----CGGAGA---C-CTTGCCTTAGAGTCAAGAAGAT 688969 i v ----i i --- - v v i i i MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr6ptel1M 688970 GTGAGATCAAGTTTCTCCTTTGATACATACTAAC--AATGATCATGGACA 689017 v i v i ii vv i vi v i --vi i v i MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 101 chr6ptel1M 689018 AGTCA-TTAA-TTCTCTAGG 689035 - -i ii MIRc#SINE/MIR 102 AGTCACTTAACCTCTCTGAG 121 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.42 CpG sites = 19, Kimura (unadjusted) = 35.92 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.06 (6 / 107), avg. gap size = 2.00 (12 / 6) 223 37.61 3.67 0.00 chr6ptel1M 689133 689241 (310759) L2d2_3end#LINE/L2 436 548 (7) m_b289s601i33 11827 chr6ptel1M 689133 AAACTCTAAGGTTCTTGAGCATAAGGAATGTGTTTTACTCATTTCTGAAT 689182 i i v v i vii i vii i iv v i i v L2d2_3end#LIN 436 AGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACTTCTTTGTAT 485 chr6ptel1M 689183 -ACAGACGCCTCCTGACTCTTTATCTTGTACAAGGCAGACACT---TAAA 689228 -v vv iv v ii v vv ii i vi i i i --- L2d2_3end#LIN 486 CCCCCACAGCGCCTAGCACAGTGCCTTGCACACAGTAGGCGCTCAATAAA 535 chr6ptel1M 689229 TGTCTGTTGATCT 689241 i i i L2d2_3end#LIN 536 TATTTGTTGATTT 548 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 53.15 CpG sites = 25, Kimura (unadjusted) = 55.20 Transitions / transversions = 1.56 (25/16) Gap_init rate = 0.02 (2 / 108), avg. gap size = 2.00 (4 / 2) 555 33.03 3.91 2.76 chr6ptel1M 689244 689601 (310399) L1ME3A_3end#LINE/L1 188 549 (371) m_b289s551i10 11828 chr6ptel1M 689244 GGTACCACTTCATCCCTCGTAGGTTATTTAAGATGACAGGGAAAGATAA- 689292 i v iv ivvi iv ivi i v ii v i - L1ME3A_3end#L 188 GATACCACTACACACCCACCAGAATGGCTAAAATGAAAAAGACAGACAAT 237 chr6ptel1M 689293 -----ATGTTGAAGGGTATGTGGGGAAAACAGGGACACTAATACCTTCTT 689337 -----i iv i v i v v - i v v vi vi L1ME3A_3end#L 238 ACCAAGTGTTGGCGAGGATGTGGAGCAACC-GGAACTCTCATACACTGCT 286 chr6ptel1M 689338 GGCGGAGTTGGGAACTGCTCCAACCATTCTGAAGAGCAATTTGGAACTAT 689387 i iiv vi i v v i i i i i vi v v L1ME3A_3end#L 287 GGTGGGAGTGTAAATTGGTACAACCACTTTGGAAAACTGTTTGGCAGTAT 336 chr6ptel1M 689388 GCCTA--AGAGGCTACCAAAC-TGTGCATACCCACTGATCCAGCAATGTC 689434 -- -- i ---- ii - i vv i vi L1ME3A_3end#L 337 --CTACTAAAG----CTGAACATATGCATACCCTATGACCCAGCAATTCC 380 chr6ptel1M 689435 TTTCCTAGGCCTGTATCCCAAAGAGA-GCATAAAAGAG----GGAAAAGT 689479 vi iv i i v v i - i v viv ----vv - L1ME3A_3end#L 381 ACTCCTAGGTATATACCCAACAGAAATGCGTACATATGTTCACCAAAAG- 429 chr6ptel1M 689480 GAAAATGTGAAAAAATGTTTGTAGGAGCCTTTTTTGTAGTGGCAAGAAAC 689529 -- v iv i ii v vi v i i i v?? L1ME3A_3end#L 430 --ACATGTACAAGAATGTTCATAGCAGCACTATTCGTAATAGCCNNAAAC 477 chr6ptel1M 689530 TGGAAACTGAGTGAATACCCATCAATTGGGGAATGATTGAATGAGTTATG 689579 ?ivvii ii iv vi iv i i i i L1ME3A_3end#L 478 TGGAAACNACCCAAATGTCCATCAACAGTAGAATGGATAAATAAATTGTG 527 chr6ptel1M 689580 ATGTATGAATATAAAGGAATAC 689601 i i vv i i v L1ME3A_3end#L 528 GTATATTCACACAATGGAATAC 549 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 44.45 CpG sites = 66, Kimura (unadjusted) = 45.54 Transitions / transversions = 1.35 (66/49) Gap_init rate = 0.04 (16 / 357), avg. gap size = 1.50 (24 / 16) 701 31.82 0.65 0.32 chr6ptel1M 689292 689600 (310400) L1ME4a_3end#LINE/L1 242 551 (320) m_b289s551i11 11828 chr6ptel1M 689292 AATGTTGAAGGGTATGTGGGGAAAACAGGGACACTAATACCTTCTTGGCG 689341 i iv i vi ? - i v v v vi vi i L1ME4a_3end#L 242 AGTGTTGGCGAGGGTGTGGNGAAA-CGGGCACTCTCATACACTGCTGGTG 290 chr6ptel1M 689342 GAGTTGGGAACTGCTCCAACCATTCTGAAGAGCAATTTGGAACTATGCCT 689391 iiv vi i v v v i i v v iv L1ME4a_3end#L 291 GGAGTGTAAATTGGTACAACCTTTCTGGAGGGCAATTTGGCAATATGTAT 340 chr6ptel1M 689392 AAGAGGCTACCAAACTGTGCATACCCACTGATCCAGCAATGTCTTTCCTA 689441 v i i iviv v ? vi i i vi vi i L1ME4a_3end#L 341 CAAAAGCCTTAAAAATGTNCATACCCTTTGACCCAGTAATTCCACTTCTA 390 chr6ptel1M 689442 GGCCTGTATCCCAAAGAGAGCATAAAAGA-GGGAAAAGTGA-AAATGTGA 689489 vv v i i i vv v i - v ? v iv -vv iv L1ME4a_3end#L 391 GGAATTTATCCTAAGGAAATAATCAGAGATGTGNACAAAGATTTATGTAC 440 chr6ptel1M 689490 AAAAATGTTTGTAGGAGCCTTTTTTGTAGTGGCAAGAAACTGGAAACTGA 689539 ii ii v v v v i i i i i i viv L1ME4a_3end#L 441 AAGGATGTTCATCGCAGCATTATTTATAATAGCGAAAAATTGGAAACAAC 490 chr6ptel1M 689540 GTGAATACCCATCAATTGGGGAATGATTGAATGAGTTATGATGTATGAAT 689589 v i ii v v ? i i i i i ii vv L1ME4a_3end#L 491 CTAAATGTCCAACAATAGGGGANTGGTTAAATAAATTATGGTACATCCAT 540 chr6ptel1M 689590 ATAAAGGAATA 689600 ? v L1ME4a_3end#L 541 ANAATGGAATA 551 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 42.05 CpG sites = 52, Kimura (unadjusted) = 43.21 Transitions / transversions = 1.13 (52/46) Gap_init rate = 0.01 (3 / 308), avg. gap size = 1.00 (3 / 3) 26 32.26 0.00 0.00 chr6ptel1M 690139 690217 (309783) (AT)n#Simple_repeat 1 79 (0) m_b289s252i11 11829 chr6ptel1M 690139 ATTTACATATACATATGTAAATATGTACATATACACATGTGCTTATATAC 690188 v i i i v i i i i i iiv i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr6ptel1M 690189 ATATATATAGCAACACATATATGTATATA 690217 vvv i i i (AT)n#Simple_ 51 ATATATATATATATATATATATATATATA 79 Matrix = Unknown Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.00 (0 / 78), avg. gap size = 0.0 (0 / 0) 12 17.22 4.88 2.38 chr6ptel1M 690232 690272 (309728) (ATATTT)n#Simple_repeat 1 42 (0) m_b289s252i12 11830 chr6ptel1M 690232 ATAATTATTGTTTTATTTATATTTA-ATAGTAT-TTTATGTTT 690272 v vv v - -v - i (ATATTT)n#Sim 1 ATATTTATATTTATATTTATATTTATAT-TTATATTTATATTT 42 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.07 (3 / 40), avg. gap size = 1.00 (3 / 3) 241 32.35 11.82 1.65 chr6ptel1M 690411 690520 (309480) C MIRc#SINE/MIR (120) 148 28 m_b289s601i34 11831 chr6ptel1M 690411 CTCATTTTACATGTGCAAGAGACCAATGC------AAGTTATAT------ 690448 i vi - i i ii v ------ i vi ------ C MIRc#SINE/MIR 148 CCCATTTTACAGATG-AGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTG 100 chr6ptel1M 690449 TCCAAGGAAATATAACTAGTAAGTAGAAAATCCAGGATTTGAACTGGAGA 690498 i vv i i i i v i v i i i i-v i C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACC-CAGG 51 chr6ptel1M 690499 TCCT-CTGATCTTAAGAGCAATG 690520 i - iiii vv i C MIRc#SINE/MIR 50 TCTTCCTGACTCCAAGTCCAGTG 28 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.05 CpG sites = 25, Kimura (unadjusted) = 45.67 Transitions / transversions = 2.50 (25/10) Gap_init rate = 0.05 (5 / 109), avg. gap size = 3.00 (15 / 5) 729 20.09 6.74 2.15 chr6ptel1M 690511 690688 (309312) MIRc#SINE/MIR 23 208 (60) m_b289s601i35 11832 chr6ptel1M 690511 AAGAGCAATGAGGTAGTGGAGTGTCAGGA-GCCCTGAGTTCAAATCTTG- 690558 v iiv -- -- - v i i i ii - MIRc#SINE/MIR 23 AAGAGCACTGGACT--TGGAGT--CAGGAAGACCTGGGTTCGAGTCCCGG 68 chr6ptel1M 690559 TTCAGACACTTATTAACCTTGTGACCT-GGGCAAGGAACTTGTCCTGTTT 690607 i v v i i iv - vv iv v i MIRc#SINE/MIR 69 CTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCT 118 chr6ptel1M 690608 G--CCTCAGTTTCTACATCTGTAAAATGAGG-TGATAATATC------AC 690648 -- iv i - i i ------i MIRc#SINE/MIR 119 GAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGC 168 chr6ptel1M 690649 CTACCTCCTAGGACTGTTATGAGGATCTAATGAGATAATG 690688 vi ii i v MIRc#SINE/MIR 169 CTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATG 208 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 22.37 CpG sites = 22, Kimura (unadjusted) = 23.89 Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.06 (10 / 177), avg. gap size = 1.60 (16 / 10) 183 37.12 4.63 2.73 chr6ptel1M 690928 691035 (308965) L2d2_3end#LINE/L2 440 549 (6) m_b289s601i36 11833 chr6ptel1M 690928 TGTAAGCTTCATCTTCACAAGAACTTTGCCTT-TATGTAAACTTTTCAAT 690976 i v vvvvi i i iv i - iv --- vi vi L2d2_3end#LIN 440 TGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACTT---CTTTGTATC 486 chr6ptel1M 690977 CTTTGTAGATTTTCATACAGTGCTCTGTACACAGTAGATACTTAATCA-- 691024 iiiii vvii vii ii i iii i v -- L2d2_3end#LIN 487 CCCCACAGCGCCTAGCACAGTGCCTTGCACACAGTAGGCGCTCAATAAAT 536 chr6ptel1M 691025 --TTGTTGTTTTG 691035 -- v L2d2_3end#LIN 537 ATTTGTTGATTTG 549 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 52.39 CpG sites = 25, Kimura (unadjusted) = 54.77 Transitions / transversions = 1.79 (25/14) Gap_init rate = 0.06 (6 / 107), avg. gap size = 1.33 (8 / 6) 506 22.99 0.00 8.77 chr6ptel1M 691116 691239 (308761) C MIRc#SINE/MIR (153) 115 2 m_b289s601i37 11834 chr6ptel1M 691116 GGGATTAAGTGACTTGCCAAGGGTCACATGGCTAGGAAGTGTTAAGTGTC 691165 i i v i ii ------- v C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGC 73 chr6ptel1M 691166 TGAGATGAAATTTGAACTCGGGTCCTTCTGACTTCAGGGCTGGTGCTCTA 691215 v vi ii i i i i i i i i v ii v C MIRc#SINE/MIR 72 AGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTT 23 chr6ptel1M 691216 TCCATTGCACCACCTAGCTGCCTC 691239 i ---i C MIRc#SINE/MIR 22 TCCACTGCACCAC---ACTGCCTC 2 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.04 CpG sites = 20, Kimura (unadjusted) = 28.62 Transitions / transversions = 3.33 (20/6) Gap_init rate = 0.08 (10 / 123), avg. gap size = 1.00 (10 / 10) 18 24.54 0.00 0.00 chr6ptel1M 691303 691345 (308655) (TT)n#Simple_repeat 1 43 (0) m_b289s252i14 11835 chr6ptel1M 691303 TTTTTTACTTTTTTCTTTTTTTATTATTATAGCTTTTTTTTTT 691345 vi i v v v vvi (TT)n#Simple_ 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 43 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 816 30.00 4.75 5.42 chr6ptel1M 691767 692397 (307603) C L1MC1_3end#LINE/L1 (447) 633 7 m_b289s551i12 11836 chr6ptel1M 691767 GCTCATTTCACTCAGCATCAGTTCATGTAAGTATC-TCCAGGCCTTTCTG 691815 iv i i vi - v v v - v i --- C L1MC1_3end#LI 633 GCTTCTTTCACTTAGTAATA-TGCATTTAAGTTTCCTCCATGTCTTT--- 588 chr6ptel1M 691816 AAATCAT--CCCGCTGG-TCATTTCTTAC-AGAAC--AATAATATTCCAT 691859 --- -- ii v i - vi- vi -- C L1MC1_3end#LI 587 ---TCATGGCTTGATAGCTCATTTCTTTTTAGCGCTGAATAATATTCCAT 541 chr6ptel1M 691860 AACATGCATATACCACAACTTATTCAGCCATTCTCCAGTTGATGGGCATC 691909 viiv v i ii i v v vii v i C L1MC1_3end#LI 540 TGTCTGGATGTACCACAGTTTATTTATCCATTCACCTACTGAAGGACATC 491 chr6ptel1M 691910 C--ATTCAATTTCCAGTTTCTAACCACTACAAAAAGGGCTGCCACAAATA 691957 i--i --ii iv i ii v i ii v ii i i i C L1MC1_3end#LI 490 TTGGTT--GCTTCCAAGTTTTGGCAATTATGAATAAAGCTGCTATAAACA 443 chr6ptel1M 691958 TTTTTTGCACATACAGGTCCCTTTCC---CTT---CTTTAAAATCTCTTT 692001 i----- iii i iii v vi--- v ---i v v - C L1MC1_3end#LI 442 TC-----CGTGTGCAGGTTTTTGTGTGGACATAAGTTTTCAACTC-CTTT 399 chr6ptel1M 692002 GGG-ACATAAGCCCAATAGTAACACTGCTGGATCAAAGGGTATGCACAGT 692050 - v -- v iv iivv i iv v v --- C L1MC1_3end#LI 398 GGGTAAATA--CCAAGGAGCGCGATTGCTGGATCGTATGGTAAG---AGT 354 chr6ptel1M 692051 TTGATAACTTTT-TGAGCATAGTTCCAAATCACTTTCTAGAATGGCTGGA 692099 v v v v - i v - v v iiiii i i i v C L1MC1_3end#LI 353 ATGTTTAGTTTTGTAAGAA-ACTGCCAAACTGTCTTCCAAAGTGGCTGTA 305 chr6ptel1M 692100 T-ATATTCATAGTTCCACCAACAATGTATCAGTGTCCCAGTTTTCCCACA 692148 i- - iii v i i v v v i v vii C L1MC1_3end#LI 304 CCAT-TTTGCATTCCCACCAGCAATGAATGAGAGTTCCTGTTGCTCCACA 256 chr6ptel1M 692149 TCCCCTCCAACATTCACCATTATC--TTTTCCTGTCATCCTAGCTAACCT 692196 i v i iivii i -- v iv -- ii i i vi C L1MC1_3end#LI 255 TCCTCGCCAGCATTTGGTGTTGTCAGTGTTCTGG--ATTTTGGCCATTCT 208 chr6ptel1M 692197 GAGAGGTGTGTAGTAGTATCTCAGAGTTGTCTTAATTTGCATTTATCTGA 692246 i v i vv i vi C L1MC1_3end#LI 207 AATAGGTGTGTAGTGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGA 158 chr6ptel1M 692247 TTA-ATAATGACTTGAAGCATTTTTTCATTTGGCTAGAAATAGTTTCAAT 692295 v - - iv i i v - ----- v v v C L1MC1_3end#LI 157 TGACAT-ATGATGTGGAGCATCTTTTCATAT-GCT-----TATTTGCCAT 115 chr6ptel1M 692296 TTCTTTATCT------GAAAATCATCTGTTTGTATCTTTTGACCATTTAT 692339 i v v ------ vi ivii ?ivi v v v C L1MC1_3end#LI 114 CTGTATATCTTCTTTGGTGAGGTGTCTGTTNAGGTCTTTGGCCCATTTTT 65 chr6ptel1M 692340 CAATTGAAGAATGGCTTGATTTCTTATAAATTAGGGTCAA---TTCTTTA 692386 ? i--- ii v i i v viv v vv i --- i C L1MC1_3end#LI 64 NAATC---GGGTTGTTCGTTTTCTTATTGTTGAGTTTTAAGAGTTCTTTG 18 chr6ptel1M 692387 TATATTTTGGA 692397 C L1MC1_3end#LI 17 TATATTTTGGA 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.77 CpG sites = 103, Kimura (unadjusted) = 39.49 Transitions / transversions = 1.36 (103/76) Gap_init rate = 0.08 (49 / 630), avg. gap size = 1.31 (64 / 49) 1379 29.62 0.91 2.40 chr6ptel1M 691848 692397 (307603) C L1ME3G_3end#LINE/L1 (376) 548 7 m_b289s551i13 11836 chr6ptel1M 691848 ATAATATTCCATAACATGCATATACCACAACTTATTCAGCCATTCTCCAG 691897 i ii v i i i i i vi C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr6ptel1M 691898 TTGATGGGCATCCATTCAATTTCCAGTTTCTAACCACTACAAAAAGGGCT 691947 i ii vvivi i i vi i i v iv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr6ptel1M 691948 GCCACAAATATTTTTTGCACATACAGGTCCCTTTCC-CTTCTTTAAA-AT 691995 v ii i ii - i i ?-- i v v - v v vii i- C L1ME3G_3end#L 448 GCAATGAACATCCTT-GTACATGCN--TCCTTGTGCACATGTGCGAGTAT 402 chr6ptel1M 691996 CTCTTTGGGACATAAGCCCAATAGTAACACTGCTGGATCAAAGGGTATGC 692045 i ? i i v v? ? iv iiv i i C L1ME3G_3end#L 401 TTCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGC 352 chr6ptel1M 692046 ACAGTTTGATAACTTTTTGAGCATAGTTCCAAATCACTTTCTAGAATGGC 692095 i v i -- i vvv - v v ii ii i i ? C L1ME3G_3end#L 351 GCATTTTAA--ATTTTAATAG-ATACTGCCAAATTGCCCTCCAAAANGGC 305 chr6ptel1M 692096 TGGATATATTCATAGTTCCACCAACAATGTATCAGTGTCCCAGTTTTCCC 692145 v ivv i i v i i i v v v v i C L1ME3G_3end#L 304 TGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCC 255 chr6ptel1M 692146 ACATCCCCTCCAACATTCACCATTATCTTTTCCTGTCATCCTAGCTAACC 692195 i i v i ?ivi vv?iii vvv ii v i i C L1ME3G_3end#L 254 ACACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATC 205 chr6ptel1M 692196 TGAGAGGTGTGTAGTAGTATCTCAGAGTTGTCTTAATTTGCATTTATCTG 692245 vi viv i i vv i vi C L1ME3G_3end#L 204 TGATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTG 155 chr6ptel1M 692246 ATTAATAATGACTTGAAGCATTTTTTCATTTGGCTAGAAATAGTTTCAAT 692295 v i vv vi i v vi vviiivi vv C L1ME3G_3end#L 154 ATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGTAT 105 chr6ptel1M 692296 TTCTTTATCTGAAAATCATCTGTTTGTATCTTTTGACCATTTATCAATTG 692345 i iv vi iii ii i v v v C L1ME3G_3end#L 104 TTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTG 55 chr6ptel1M 692346 AAGAATGGCTTGATTTCTTATAAAT---TAGGGTCAATTCTTTATATATT 692392 -- iv v -- vi --- --- i C L1ME3G_3end#L 54 --GGTTGTCTT--TTTCTTATTGATTTGTAGG---AGTTCTTTATATATT 12 chr6ptel1M 692393 TTGGA 692397 i C L1ME3G_3end#L 11 CTGGA 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.48 CpG sites = 94, Kimura (unadjusted) = 39.48 Transitions / transversions = 1.45 (94/65) Gap_init rate = 0.03 (16 / 549), avg. gap size = 1.12 (18 / 16) 3598 30.20 3.90 2.45 chr6ptel1M 692254 694588 (305412) C L1M5_orf2#LINE/L1 (0) 3294 927 m_b289s551i14 11836 chr6ptel1M 692254 TGACTTGAAGCATTTTTTCATTTGGCTAGAAATAGTTTCAATTTCTTTAT 692303 ?v vi i v vi vviiivi v? v iv C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr6ptel1M 692304 CTGAAAATCATCTGTTTGTATCTTTTGACCATTTATCAATTGAA--GAAT 692351 i vi vii iivi v v ?v ii-- vv C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTT 3195 chr6ptel1M 692352 GGCTTGATTTCTTAT-AAATT--AGGGTCAATTCTTTATATATTTTGGAA 692398 v -- ? -i ? -- --- i i v C L1M5_orf2#LIN 3194 GTCTT--TTTNTTATTGANTTGTAGG---AGTTCTTTATATATTCTGGAT 3150 chr6ptel1M 692399 ATGAGGCCTTTAATAGAACCTTTGACTGTACAAATGTTTTT--CCAGTTT 692446 i v ivi -iv v v? - i i i-- ? i C L1M5_orf2#LIN 3149 ACGAGTCCTTTGTCAGA-TATATGTNT-TGCAAATATTTTCTCCCANTCT 3102 chr6ptel1M 692447 ATTGTATCCCTTTTAAT---CTTATCTGCATTAGTTTTGTTTGTAAAAAA 692493 i v iv v v --- v v ii i-- v?- viv i C L1M5_orf2#LIN 3101 GTGGCTTGCCTTTTCATTTTCTTAACGGTGTC--TTTTGAN-GAGCAGAA 3055 chr6ptel1M 692494 GCTTTTTAATTTGATATAATCAAA-------ATTTTCTATTTTGTGATCA 692536 i v v i? i v ------- i v i i -- C L1M5_orf2#LIN 3054 GTTTTTAATTTTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGGT-- 3007 chr6ptel1M 692537 ATAATGCTCTCTAGTTCTTCTTTGGTCACAAATTCCTGCCTCCTCCACAA 692586 - ?i i i ivv i v i--- v iii v?i - i C L1M5_orf2#LIN 3006 -TNGTGCTTTTTGTGTCCTGTTTA---AGAAATCTTTGCCTANCCCA-AG 2962 chr6ptel1M 692587 GTCTGAGAGGTAAACTATCCTATGTTATTCTAATTTA-----TTTCTAAT 692631 vvii i --i v - -- i ----- v i C L1M5_orf2#LIN 2961 GTCACGAAGATA--TTCTCCTATGTT-TTCT--TCTAGAAGTTTTATAGT 2917 chr6ptel1M 692632 CTTATTTTTTATGCCTAGGTC-ATGAACCCATTTTGACCTTATCTTGGTA 692680 i ?i iiii - -i i ? vi v i v i C L1M5_orf2#LIN 2916 TTTANCTTTTACATTTAGGTCTATGA-TCCATCTNGAATTAATTTTTGTG 2868 chr6ptel1M 692681 TATGGTGTTAAGTGTGGGTCAATGCCTAATTTCATCCATACTAATTTCCA 692730 v i iv i v?iii v iv ivi v C L1M5_orf2#LIN 2867 TATGGTGTGAGGTAGGGGTCGAGNTTCATTTTTTTCCATATGGATATCCA 2818 chr6ptel1M 692731 ATTTTCCTAGCAGTTTTTGTCAAGTAGTGAATTCTTGTCCCAAAACCTGG 692780 v i i viv ii iv vvv i vi ---- i C L1M5_orf2#LIN 2817 ATTGTTCCAGCACCATTTGTTGAAAAGACTATCCTTTCCCCA----CTGA 2772 chr6ptel1M 692781 GGT-CTTTG---TGTTTGTCAAATACCAGATTATTAAAGTTAT-TGA--C 692823 iv - ? ---iv v i i? v?ii v vv i - i-- C L1M5_orf2#LIN 2771 ATTGCNTTGGCACCTTTGTCAAAAATCAANTGNCCATATATGTGTGGGTC 2722 chr6ptel1M 692824 TATTTTAACCTGGGAAGGTTAC-CTATTCCACTGATCAACTAGTCTATTT 692872 ---- ivvvvi i- i i v i v i- C L1M5_orf2#LIN 2721 TATTT----CTGGACTCTCTATTCTGTTCCATTGATCTATTTGTCTATC- 2677 chr6ptel1M 692873 CTTA-GCCAATACCAAATGGTTTTGGTAACTGGTGCTTTATAATATAGTT 692921 - v iv i i v vv - i C L1M5_orf2#LIN 2676 CTTACGCCAATACCACACTGTCTTGATTACTGTAGCTTTATAATA-AGTC 2628 chr6ptel1M 692922 TT-ACATCTGGTACAGCTAGGACACCTTC--CTTAGATTTTTCTTTCATT 692968 - ? ? vv iv v--- i -- v - i iviv C L1M5_orf2#LIN 2627 TTGANATCNGGTAGTGTAAGT---CCTCCAACTTTG-TTCTTCTTTTTCA 2582 chr6ptel1M 692969 AG-TTCCCTTGAA-AGTCTTGACCTTTTGGTCTTCCAGATGAATTTTG-- 693014 - vii iv- v ? ii i vvi v i i-- C L1M5_orf2#LIN 2581 AGATTGTTTTGGCTATTCTNGGTCCTTTGCATTTCCATATAAATTTTAGA 2532 chr6ptel1M 693015 -TTATTTTTTCTAGGTCATTAAAAGAGTTTTTTGGGTGTTTGATTGGTAT 693063 - i vi v v vv vvi i iii vi vv v C L1M5_orf2#LIN 2531 ATCAGCTTGTCAATTTCTACAAAAAAACCTGCTGGGATTTTGATTGGGAT 2482 chr6ptel1M 693064 AGCACTAAATAAATAGATTAGTTTAAGTAGTATTGTCATCTTTATTATAT 693113 v i i vv i i ii v v v ? iv C L1M5_orf2#LIN 2481 TGCATTGAATCTATAGATCAATTTGGGGAGAATTGACATCTTNACAATAT 2432 chr6ptel1M 693114 TTGCTCGACTTATCCAAGAGCACTTAATATTTTTCCAATTGGTTAGATCT 693163 viv vv iv v i ivvv i i v iv i C L1M5_orf2#LIN 2431 TGAGTCTTCCAATCCATGAACATGGTATATCTCTCCATTTATTTAGGTCT 2382 chr6ptel1M 693164 GGCTTTACTTGTGTGGGAAGTGTTTTATAATTTTGCTCATATAGTTCCTG 693213 vvi v i v v vi v i i i vvvii ? v i C L1M5_orf2#LIN 2381 TCTTTAATTTCTCTCAGCAATGTTTTGTAGTTTTCAGTGTANAGGTCTTG 2332 chr6ptel1M 693214 ACTTTCCCTTGGCAGATACATTCCCAAATATTTTATACTATAGGCAGTTA 693263 vviv ?ii vi vi i i ? ii v vv vv i C L1M5_orf2#LIN 2331 CACATNTTTTGTTAGATTTATTCCTAAGTATTTNATGTTTTTTGATGCTA 2282 chr6ptel1M 693264 CTTTAAATGGAATTTCTCTTTATATCTCTAACTGTTGGAT--TTTGTTAG 693311 i v v vi i ? v i -- i v ivi -- iv C L1M5_orf2#LIN 2281 TTGTAAATGGTATTGTTTTTNAAATTTC--ATTTTCCAATTGTTTGTTGC 2234 chr6ptel1M 693312 TGATATATAAGAATGCTGATGATTTATGTAGGTTTATTTTGTGTCCTTCA 693361 ii ii i viv v vi v ii i ?v i C L1M5_orf2#LIN 2233 TAGTATATAGAAATACAATTGATTTTTGTATATTGACCTTGTATCCNGCG 2184 chr6ptel1M 693362 ACTTTGCTAAAGGTGTGGATTATTTCTAATAGCTTTTTAGTAGAATCTCT 693411 i vviiivv v i i ? v v i C L1M5_orf2#LIN 2183 ACCTTGCTAAATTCACTTATTAGTTCTAGTAGTTTNTTTGTAGATTCTTT 2134 chr6ptel1M 693412 AGGGTTCTCTAAGTATAACATCATATCATCAGCAAAGAGTGATAATTTGG 693461 ? i i v ? vv i v i v i? i i vi C L1M5_orf2#LIN 2133 NGGATTTTCTACGTANACAATCATGTCATCTGCGAATAANGACAGTTTTA 2084 chr6ptel1M 693462 TTTCCTTATTACCTACTATAATTCCTTTAATCTCTTTCTCAACTCTTATT 693511 i iv v v iiv v v v i i vvvi C L1M5_orf2#LIN 2083 TTTCTTCCTTTCCAATCTTTATGCCTTTTATTTCTTTTTCTTGCCTTATT 2034 chr6ptel1M 693512 GCCAAAGCAAGCATTTCTAATACAATATTGAATAGTGATTGTGATAGTGG 693561 vvvi v v ii i i i vii v ? i C L1M5_orf2#LIN 2033 GCACTGGCTAGGACCTCCAGTACAATGTTGAATAGAAGTGGTGANAGCGG 1984 chr6ptel1M 693562 GCAACTTTGTTTCACTCCTGATCTTATTGGGAATGGTTCCAGTTTATCCC 693611 i v i i iii i vv v v? i ? v v C L1M5_orf2#LIN 1983 ACATCCTTGTCTTGTTCCCGATCTTAGGGGGAAAGCNTTCAGTNTTTCAC 1934 chr6ptel1M 693612 CATTACATATGATGATTATTGATGGTTTTAAATAGATGCTACTGACTATT 693661 vi v ?ii vv vvi ivi v ii vv C L1M5_orf2#LIN 1933 CATTAAGTATGATGTTNGCTGTAGGTTTTTCGTAGATGCCCTTTATCAGG 1884 chr6ptel1M 693662 TTAAGGAAAAGTCCATTTATTCTTATGCTTTC--AATGTTTTTTTTTTAA 693709 i ivvi v i i - i v -- iv ----- v C L1M5_orf2#LIN 1883 TTGAGGAAGTTCCCTTCTATTCCTA-GTTTGCTGAGAG-----TTTTTAT 1840 chr6ptel1M 693710 TAGGAATGGATGTTGGATTTTATCAAATGCTTTTTCTGCTTCTATTTAGA 693759 i v i i i v v C L1M5_orf2#LIN 1839 CATGAATGGGTGTTGAATTTTGTCAAATGCTTTTTCTGCATCTATTGAGA 1790 chr6ptel1M 693760 TGATCATATGGTTTTT---GTTAATTTGGTTATTGATATAGTCAGTTATA 693806 i ---v v iv --- i v i i C L1M5_orf2#LIN 1789 TGATCATATGATTTTTCTCCTTTATTCTGTTA---ATATGGTGAATTACA 1743 chr6ptel1M 693807 CTAATAGTTTTCCTAATATTGAACCAGCCCTGCATTCCTGGTATAAATTC 693856 i i v v i v i i i i v ii C L1M5_orf2#LIN 1742 TTGATTGATTTTCGAATGTTAAACCAACCTTGCATTCCTGGGATAAACCC 1693 chr6ptel1M 693857 TACTTGGTCATAGTGTATTATCCTGGGGATGATTTTCTATAATCTTTTTG 693906 i ii vvvv ivv v iv v vv C L1M5_orf2#LIN 1692 CACTTGGTCATGATGTATTATCCTTTTTATATATTGCTGGATTCGATTTG 1643 chr6ptel1M 693907 CTAATGATTTATTTAAGATTTTTGCATCAATATTCATTTAAGGAGATTGG 693956 iv i ? i v i - v i v C L1M5_orf2#LIN 1642 CTAATATTTTGTTNAGGATTTTTGCATCTATGTTCA-TGAGGGATATTGG 1594 chr6ptel1M 693957 TCTACAATTTGCTTTCTCTGT--TTTCAACCTAACTGGTTTATCTATCAG 694004 ii v iii -- v --ii iv ? vvv C L1M5_orf2#LIN 1593 TCTGTAATTTTCTTTTCTTGTAATGTC--TTTGTCNGGTTTTGGTATCAG 1546 chr6ptel1M 694005 TATCATGTCTG-----------TG---TAGGAG----TCCTTCAATCCCT 694036 vi ? - ----------- --- i i---- i vv ii C L1M5_orf2#LIN 1545 GGTNATG-CTGGCCTCATAAAATGAGTTGGGAAGTGTTCCCTCTTTTTCT 1497 chr6ptel1M 694037 ATTTTTTCAAATAGTTCATATAACATTGGAGTTAATTGTTCTTTAAATGT 694086 i vi v ii i v vi v v i C L1M5_orf2#LIN 1496 ATTTTCTGGAAGAGTTTGTGTAAGATTGGTATTATTTCTTCCTTAAATGT 1447 chr6ptel1M 694087 TTGGTAGAATTCATATGTAAATCCATCTGGTCCTGGGGATTTTTTTTCTT 694136 ivv i v v i -- i iv C L1M5_orf2#LIN 1446 TTGGTAGAATTCACCAGTGAAGCCATCTGGGCCTGGAG--TTTTCTTTGT 1399 chr6ptel1M 694137 AGGAAGTTGATTAATAGCTTGTTTTATTTCTTTTTCTAAAATGGGACTAT 694186 i v vv vi vvi iv vvivi v i i C L1M5_orf2#LIN 1398 GGGAAGGTTTTTAATTACAAATTCAATTTCTTTAATAGATATAGGGCTAT 1349 chr6ptel1M 694187 TTAAGCAATTTATTTCCTCCTCTGTTAATCTGGGAAGCCTATATTTTTGA 694236 i iiivv i i i v? i i i v v i?i i i v C L1M5_orf2#LIN 1348 TCAGATTTTCTATTTCTTCTTGNGTCAGTTTTGGTAANTTGTGTTTTTCA 1299 chr6ptel1M 694237 AAGTAGCCATCCATTTCACTTAGGTTTTCAAATTTATTGGCATAAAGTTG 694286 i v viii ii i ? C L1M5_orf2#LIN 1298 AGGAATTTGTCCATTTCATCTAAGTTNTCAAATTTATTGGCATAAAGTTG 1249 chr6ptel1M 694287 GACAAAGTA-ACTCCTATTTATTGCTCTAATTTCCTCTTCATTGGTGGAA 694335 vv v i -v i - ivi i v ivivvv iv i vi C L1M5_orf2#LIN 1248 TTCATAATATTCTCTTA-TTATCCTTTTAATGTCTGTAGGATCTGTAGTG 1200 chr6ptel1M 694336 AGTTGTCCCTTTTCATTTTTAAGACTAACAATTTGATTTTCCTCTTTCCT 694385 vv v i ii i v i iii vv i i i ii C L1M5_orf2#LIN 1199 ATGTCTCCTTTTTCATTCCTGATATTGGTAATTTGTGTCTTCTCTCTTTT 1150 chr6ptel1M 694386 TTTTCTAACCAAT-TTACCAAAGGTTTATCTATTTTGTTGTTTTTTTTCA 694434 ii i i i - ?i i i v i v i iv C L1M5_orf2#LIN 1149 TTTCTTGATCAGTCTNGCTAGAGGTTTATCAATTTTATTGATCTTTTCAA 1100 chr6ptel1M 694435 TAAACCAGCTCTTAGTTTTATTTATTAATTCAATAGCTTTTTTAACTTTC 694484 vi i i i ii v vvi v v i? ? -ii C L1M5_orf2#LIN 1099 AGAACCAGCTTTTGGCTTCGTTGATTTTCTCTATTGTNTNTTT-GTTTTC 1051 chr6ptel1M 694485 AATTTTATTAATTTCTCCTTTTAATTTTAGAATTTCA------------- 694521 v i i v i vi vv v------------- C L1M5_orf2#LIN 1050 TATTTCATTGATTTCTGCTCTTATCTTTATTATTTCCTTCCTTCTACTTN 1001 chr6ptel1M 694522 ----AGGTTTTAAATTTGC---TCTTTTTCTAGCTTTTTAAGTTGCAGGG 694564 ----i -- --- i v v i v C L1M5_orf2#LIN 1000 CTTTGGGTTT--AATTTGCTCTTCTTTTTCTAGCTTCTTAAGGTGGAAGC 953 chr6ptel1M 694565 CCAATTCATTGATCTT--CCCTTTCT 694588 ii iv i --v C L1M5_orf2#LIN 952 TTAGATCATTGATTTTAAGCCTTTCT 927 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.80 CpG sites = 373, Kimura (unadjusted) = 40.49 Transitions / transversions = 1.18 (373/315) Gap_init rate = 0.04 (91 / 2334), avg. gap size = 1.64 (149 / 91) 18 12.03 2.63 2.63 chr6ptel1M 694832 694869 (305131) (TTA)n#Simple_repeat 1 38 (0) m_b289s252i15 11837 chr6ptel1M 694832 TTATT-TAATTCATTATTATTATTGTTATTGTTATTTTT 694869 - v - i i v (TTA)n#Simple 1 TTATTATTATT-ATTATTATTATTATTATTATTATTATT 38 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 267 28.74 10.85 2.88 chr6ptel1M 694920 695048 (304952) C MIRb#SINE/MIR (76) 192 54 m_b289s601i38 11838 chr6ptel1M 694920 TTTGATTTTTACAACAGAGCTCTGGGATGTA------ATGA-----ATTT 694958 i ii i i-- i v v ------ v ----- C MIRb#SINE/MIR 192 TTTAATCCTCACAACAA--CCCTGCGAGGTAGGTATTATTATCCCCATTT 145 chr6ptel1M 694959 GACAGATGAATAAATTGAGAC--AGAAAA-TTAAGTGAATTAACCAAGAT 695005 v iv i i -- i i- i v iv i C MIRb#SINE/MIR 144 TACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGT 95 chr6ptel1M 695006 CACACAAATATAAAGTAAGAGAATTGAGATGTATAAAACCAGG 695048 iv vv iiv iii i v--ii v C MIRb#SINE/MIR 94 CACACAGCTAGTAAGTGGCAGAGCCGGGATT--CGAACCCAGG 54 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.96 CpG sites = 23, Kimura (unadjusted) = 37.76 Transitions / transversions = 1.77 (23/13) Gap_init rate = 0.06 (8 / 128), avg. gap size = 2.25 (18 / 8) 276 28.58 2.94 3.96 chr6ptel1M 694955 695056 (304944) C MIRc#SINE/MIR (123) 145 45 m_b289s601i39 11838 chr6ptel1M 694955 ATTTGACAGATGAATAAATTGAGAC--AGAAAA-TTAAGTGAATTAACCA 695001 v iv i i -- i i- v iv C MIRc#SINE/MIR 145 ATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCA 96 chr6ptel1M 695002 AGATCACACAAATATAAAGTAAGAGAATTGAGATGTATAAAACCAGGGTT 695051 i iv vv iiv iii i iv--ii v -- C MIRc#SINE/MIR 95 AGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACT--CGAACCCAGG--T 50 chr6ptel1M 695052 CTTTC 695056 i C MIRc#SINE/MIR 49 CTTCC 45 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.87 CpG sites = 18, Kimura (unadjusted) = 37.39 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.06 (6 / 101), avg. gap size = 1.17 (7 / 6) 255 32.61 1.08 1.08 chr6ptel1M 695099 695191 (304809) C MIR3#SINE/MIR (52) 156 64 m_b289s601i40 11839 chr6ptel1M 695099 AGTCCAATTTCCTAGTTGTATTGAGGAAGAAACCAAGG-CCACTTAACTA 695147 iii vi v iv v i ii - vvv iv i C MIR3#SINE/MIR 156 AGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTG 107 chr6ptel1M 695148 AAATGACTAATGCTAGGTCACACAGGGAATTTAGTGTTGGATCC 695191 i viiv v v? i- vii v C MIR3#SINE/MIR 106 AAGTGACTTGCCCAAGGTCACACAGCNAG-TTAGTGGCAGAGCC 64 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 44.40 CpG sites = 16, Kimura (unadjusted) = 44.40 Transitions / transversions = 1.14 (16/14) Gap_init rate = 0.02 (2 / 92), avg. gap size = 1.00 (2 / 2) 508 30.19 8.06 1.72 chr6ptel1M 695636 695908 (304092) C L1ME4c_3end#LINE/L1 (255) 575 286 m_b289s551i15 11840 chr6ptel1M 695636 TTATCATTTCTTATAGCACAATAATATTCTATTACATTCATATACTATAA 695685 i v i vvv i iivi ?v i i C L1ME4c_3end#L 575 TTATCATTTTTAATGGCTGCATAATATTCCATCGAGTNGATGTACCATAA 526 chr6ptel1M 695686 CAGATTCAACAAAAAATTCTCCAATTCTC------TCAA----TCTCCAA 695725 ivv i i v ---- i v v i------ i i---- i C L1ME4c_3end#L 525 TTTACTTAACCA----TTCCCCTATTGTTGGACATTTAGGTTGTTTCCAA 480 chr6ptel1M 695726 TTTTTTGCTACTACAAA-AGTGCTGATATAAATATTTTTGCATATATAGT 695774 i i i - ii vv i i i i iii i C L1ME4c_3end#L 479 TTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTCGTGCATATAGC 430 chr6ptel1M 695775 TTTTTTTCTTTTTTCATTTGATCTCCTTGGG-----------GAAGTGGC 695813 iii i v v - i i ----------- v C L1ME4c_3end#L 429 TTTTTCCTTCTTTTGAATT-ATTTCCTTAGGATAAATTCCCAGAAGTGGA 381 chr6ptel1M 695814 ATTTTTGGATTACAGCATATGCACAGTTTTATAGTACTTTGGGCAGAGTT 695863 vi i i v vi v v i iv vivi iv v v C L1ME4c_3end#L 380 ATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTCTTGATACGTATTG 331 chr6ptel1M 695864 CCAAATTGCTTTTCACAATGGTTGGGCTAGTTTAAACTTCTACCA 695908 i v v vi i i v ? v i C L1ME4c_3end#L 330 CCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACANTGCCACCA 286 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.15 CpG sites = 49, Kimura (unadjusted) = 40.42 Transitions / transversions = 1.53 (49/32) Gap_init rate = 0.03 (9 / 272), avg. gap size = 3.00 (27 / 9) 380 26.67 14.48 4.98 chr6ptel1M 695721 695941 (304059) C L1ME3F_3end#LINE/L1 (509) 481 241 m_b289s551i16 11840 chr6ptel1M 695721 TCCAATTTTTTGCTACTACAAA-AGTGCTGATATAAATATTTTTGCATAT 695769 i i i - v i i i i i C L1ME3F_3end#L 481 TCCAGTTTTTTGCTATTACGAACAGTGCTGCTATGAACATTCTTGTACAT 432 chr6ptel1M 695770 ATAGTTTTTTTTCTTTTTTCATTTG-------ATCTC-CTTGGG------ 695805 i --------i i vv v iv -------i i - ------ C L1ME3F_3end#L 431 GT--------CTCCTGGTGCACATGTGCAAGAGTTTCTCTTGGGTATATA 390 chr6ptel1M 695806 ----GAAGTGGCATTTTTGGATTACAGCATATGCACAGTTTTATAGTACT 695851 ---- i v vi i iii vi iv vv i ---- C L1ME3F_3end#L 389 CCTAGGAGTGGAATTGCTGGGTCGTAGGGTATGCGAATGTTCA----ACT 344 chr6ptel1M 695852 TTG-GGCAGAGTTCCAAATTGCTTTTCACAATGGTTGGGCTAGTTTAAAC 695900 i- iv v i v i i v i vi i i v C L1ME3F_3end#L 343 TTACGAGATAATGCCAAATTGTTTTCCAAAGTGGTTGTACCAATTTACAC 294 chr6ptel1M 695901 TTCTACCA-C-GTG-----GA-----CATTAATGCACATCCTTTCCAACA 695938 i i - - ----- ----- i i v i C L1ME3F_3end#L 293 TCCCACCAGCAGTGTATAAGAGTTCCCGTTGATCCACATCCTCTCCAACA 244 chr6ptel1M 695939 TTT 695941 i C L1ME3F_3end#L 243 CTT 241 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 31.48 CpG sites = 38, Kimura (unadjusted) = 34.60 Transitions / transversions = 2.11 (38/18) Gap_init rate = 0.10 (22 / 220), avg. gap size = 2.00 (44 / 22) 37 4.44 2.04 2.04 chr6ptel1M 696605 696653 (303347) (TA)n#Simple_repeat 1 49 (0) c_b289s251i0 11841 chr6ptel1M 696605 TATATATAT-TATATATGTGTATATCATATATATATATATATATATATAT 696653 - i i - (TA)n#Simple_ 1 TATATATATATATATATATATATAT-ATATATATATATATATATATATAT 49 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.04 (2 / 48), avg. gap size = 1.00 (2 / 2) 29 0.00 0.00 0.00 chr6ptel1M 696757 696788 (303212) (TC)n#Simple_repeat 1 32 (0) m_b289s252i16 11842 chr6ptel1M 696757 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 696788 (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 32 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 50 5.29 0.00 0.00 chr6ptel1M 696789 696847 (303153) (TATAGA)n#Simple_repeat 1 59 (0) c_b289s251i1 11843 chr6ptel1M 696789 TATATATATATATATATATATAGATATAGATATAGATATAGATATAGATA 696838 v v v (TATAGA)n#Sim 1 TATAGATATAGATATAGATATAGATATAGATATAGATATAGATATAGATA 50 chr6ptel1M 696839 TAGATATAG 696847 (TATAGA)n#Sim 51 TAGATATAG 59 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.0 (0 / 0) 223 28.47 0.00 4.94 chr6ptel1M 697683 697767 (302233) C L2d_3end#LINE/L2 (9) 507 427 m_b289s601i41 11844 chr6ptel1M 697683 CAAGTGACAAGAATTCATTAAGCACCACCCATGTATCAGGCACTGTGCTA 697732 vii v i i i vv i iiivi C L2d_3end#LINE 507 CAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTGTGCTA 458 chr6ptel1M 697733 GGCACGGTATTTGGGATACAAATATAAAGGATTAG 697767 i v i--- - i ?v v ? v v C L2d_3end#LINE 457 GGCGCTGTG---GGGA-ACGANAAAANAGTATAAG 427 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.80 CpG sites = 13, Kimura (unadjusted) = 37.71 Transitions / transversions = 1.30 (13/10) Gap_init rate = 0.05 (4 / 84), avg. gap size = 1.00 (4 / 4) 267 25.02 0.00 3.12 chr6ptel1M 697689 697754 (302246) C L2d2_3end#LINE/L2 (13) 542 479 m_b289s601i42 11844 chr6ptel1M 697689 ACAAGAATTCATTAAGCACCACCCATGTATCAGGCACTGTGCTAGGCACG 697738 iv i i i vv ii iiv i v C L2d2_3end#LIN 542 ACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCT 493 chr6ptel1M 697739 GTATTTGGGATACAAA 697754 i--v C L2d2_3end#LIN 492 GTG--GGGGATACAAA 479 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.73 CpG sites = 10, Kimura (unadjusted) = 31.26 Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.03 (2 / 65), avg. gap size = 1.00 (2 / 2) 323 38.91 6.90 0.89 chr6ptel1M 698156 698474 (301526) C L2#LINE/L2 (271) 2811 2474 m_b289s601i43 11845 chr6ptel1M 698156 GCTTAAAGAAAATACCTTTGACCACAGTGTGCAGTCCTAGAGTGGAGAGA 698205 i v i ii vv i i ii v vv -vv v ? i i C L2#LINE/L2 2811 GTTTTAAAAGGATCACTCTGGCTGCTGTGTTGAG-AATAGACTGNAGGGG 2763 chr6ptel1M 698206 AAC-----TTGAAACAGGGAAACAAATTTGAAGACTCATATGACAATTTA 698250 ii ----- v i i v i v i i vv iiiii ii C L2#LINE/L2 2762 GGCAAGGGTGGAAGCAGGGAGACCAGTTAGGAGGCTATTGCAGTAATCCA 2713 chr6ptel1M 698251 GACAAGAGGTAACATGGGATTGAATTTAGGTGGTAACTATATGAGTGGAG 698300 i i i i iivv v i iivi ii vi ivii v C L2#LINE/L2 2712 GGCGAGAGATGATGGTGGCTTGGACCAGGGTGGTGGCAGTGGAGGTGGTG 2663 chr6ptel1M 698301 ATAAAGAGAGAAGATGCAAGATATATTATGAAGGCTAAAATGGCAAGCTT 698350 -i v ivvi v vi v ivi ivi i i v C L2#LINE/L2 2662 A-GAAGTGGTCGGATTCTGGATATATTTTGAAGGTAGAGCCGACAGGATT 2614 chr6ptel1M 698351 TGACAATTGAT--GATTGAAAATATAAGATGAAAG---GGAATTATGGGG 698395 vii v -- vviiii i i - --- i i v iv C L2#LINE/L2 2613 TGCTGATGGATTGGATGTGGGGTGTGAGA-GAAAGAGAGGAGTCAAGGAT 2565 chr6ptel1M 698396 GATTGTGAAG--------CTGAGAGACCAGGAGAATAGTGGTACCTTTGA 698437 i vii i -------- vi ii i i i v v i v ? C L2#LINE/L2 2564 GACTCCAAGGTTTTTGGCCTGAGCAACTGGAAGGATGGAGTTGCCATTNA 2515 chr6ptel1M 698438 TAGAAATAGGGAAG-CT--GGGAAGAGGGGG-CTAAGGTGG 698474 iv i i - -- i vi -i i v C L2#LINE/L2 2514 CTGAGATGGGGAAGACTGCGGGAGGAGCAGGTTTGAGGGGG 2474 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 57.41 CpG sites = 79, Kimura (unadjusted) = 59.77 Transitions / transversions = 1.80 (79/44) Gap_init rate = 0.03 (10 / 318), avg. gap size = 2.50 (25 / 10) 246 20.59 5.88 0.00 chr6ptel1M 698574 698641 (301359) C DNM1r#Unknown (2106) 2556 2485 m_b289s502i1 11846 chr6ptel1M 698574 TACTCTCTTTTATAGA--AGTTTATATATACATACATACATACA--CACA 698619 i i v i ? --v v i i i -- C DNM1r#Unknown 2556 TGCCCTGTTCTATANATACGTATATATACACATATATACACACATACACA 2507 chr6ptel1M 698620 CATATACATATATATATGTGCA 698641 i i iii C DNM1r#Unknown 2506 CATATACACACATATATACACA 2485 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 25.70 CpG sites = 11, Kimura (unadjusted) = 25.70 Transitions / transversions = 3.67 (11/3) Gap_init rate = 0.03 (2 / 67), avg. gap size = 2.00 (4 / 2) 509 22.77 3.96 0.00 chr6ptel1M 698788 698888 (301112) C L2c_3end#LINE/L2 (8) 470 366 m_b289s601i44 11844 chr6ptel1M 698788 ATTCAATAAACATCTCTTGAGTACCTACTATGTGCCAAGGGCTAGAGATA 698837 i i v ii i v i i C L2c_3end#LINE 470 ATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGATA 421 chr6ptel1M 698838 CAGAAAGG--CAAGACA--GTCCTTGCTTTCAGGGAACTTATAGTCCAGT 698883 i i v --i -- i ii i i i i i C L2c_3end#LINE 420 CAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAGT 371 chr6ptel1M 698884 AGTGG 698888 i v C L2c_3end#LINE 370 GGAGG 366 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 27.28 CpG sites = 19, Kimura (unadjusted) = 28.94 Transitions / transversions = 4.75 (19/4) Gap_init rate = 0.02 (2 / 100), avg. gap size = 2.00 (4 / 2) 251 30.38 8.90 9.36 chr6ptel1M 699016 699251 (300749) C L2c_3end#LINE/L2 (17) 461 227 m_b289s601i45 11847 chr6ptel1M 699016 ACAGTTATTCACTGTCTACTATGTGCCCAGCATTGGGCTAAGTGTTGGAA 699065 v v vi i ------------ i i i ii C L2c_3end#LINE 461 ACATTTATTGAGCGCCTACTATGTGCC------------AGGCGCTGGGG 424 chr6ptel1M 699066 ATATAAAAAGGGGAAAAAGATATTCCTTGCCCTAAAGGAGTTCACAGTGC 699115 i i v iiv i v iiv i v i vi C L2c_3end#LINE 423 ATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCT 374 chr6ptel1M 699116 AATGCAGAGTAAAAAAAAAAAAAAAAAAACAG--AAGA-AAAAGCTACAT 699162 i -- v i v i v ?iv v i i-- vi - v i - C L2c_3end#LINE 373 AGTG--GAGGAGACAGACANGTAAACAGACAATTACAATACAAGTTA-AT 327 chr6ptel1M 699163 -ATA---GCTAT--TTAGAGGATGAATAG-------TAATAATTAACAGA 699199 - --- -- vi v ii i ------- iiv ii-- C L2c_3end#LINE 326 GATAAGTGCTATAATGGGAGTATAGACAGGGTGCTATGGGAGC--ACAGA 279 chr6ptel1M 699200 TGGAAGGT-TTTATAACTAAC----AGCGGTTAGGAAAGGCTCTCTAGCG 699244 - i i-ii -i i?----i v i i ii --- C L2c_3end#LINE 278 -GGAGGGCACCTA-GACTAGNCTTGGGGGGTCAGGGAAGGCTTCC---CG 234 chr6ptel1M 699245 AAGGAGG 699251 i C L2c_3end#LINE 233 GAGGAGG 227 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.14 CpG sites = 45, Kimura (unadjusted) = 41.81 Transitions / transversions = 2.25 (45/20) Gap_init rate = 0.13 (30 / 235), avg. gap size = 1.43 (43 / 30) 303 32.48 3.70 3.07 chr6ptel1M 699020 699181 (300819) C L2a_3end#LINE/L2 (21) 496 334 m_b289s601i47 11847 chr6ptel1M 699020 TTATTCACTGTCTACTATGTGCCCAGCATTGGGCTAAGTGTTGGAAATAT 699069 v vi i vi i vv i i i ii i C L2a_3end#LINE 496 TTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGCGCTGGGGATAC 447 chr6ptel1M 699070 AAAAAGGG--GAAAAAGAT---ATTCCTTGCCCTAAAGGAGTTCACAGTG 699114 iv iv i--i v i--- v i v v i i v v C L2a_3end#LINE 446 AGCAGTGAACAAAACAGACAAAAGTCCCTGCCCTCATGGAGCTTACATTC 397 chr6ptel1M 699115 CAATGCAGAGTAAAAAAAAAAAAAAAAAAACAGAAGAAAAAGCTACATAT 699164 i i vi i vi v i v v v v v v v ---- i C L2a_3end#LINE 396 TAGTGGGGGGAGACAGACAATAAACAAATAAATAAGTAAA----ATATAT 351 chr6ptel1M 699165 AGCTAT-TTAGAGGATGA 699181 - - i v i C L2a_3end#LINE 350 AG-TATGTCAGATGGTGA 334 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.23 CpG sites = 27, Kimura (unadjusted) = 43.46 Transitions / transversions = 1.12 (27/24) Gap_init rate = 0.05 (8 / 161), avg. gap size = 1.38 (11 / 8) 367 25.53 4.26 0.00 chr6ptel1M 699020 699113 (300887) C L2d_3end#LINE/L2 (23) 493 396 m_b289s601i46 11847 chr6ptel1M 699020 TTATTCACTGTCTACTATGTGCCCAGCATTGGGCTAAG---TGTTGGAAA 699066 v vi i i i v i --- v i C L2d_3end#LINE 493 TTATTGAGCGCCTACTATGTGCTCAGCACTGTGCTAGGCGCTGTGGGGAA 444 chr6ptel1M 699067 TATAAAAAGGGGA-AAAAGATATTCCTTGCCCTAAAGGAGTTCACAGT 699113 iiv? ?i v - i v iv i v i i i C L2d_3end#LINE 443 CGANAAAANAGTATAAGACATGGTCCCTGCCCTCAAGGAGCTTACAAT 396 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.56 CpG sites = 15, Kimura (unadjusted) = 33.02 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.02 (2 / 93), avg. gap size = 2.00 (4 / 2) 11 24.08 0.00 0.00 chr6ptel1M 699533 699566 (300434) (ATCTCT)n#Simple_repeat 1 34 (0) m_b289s252i17 11848 chr6ptel1M 699533 ATCTCTAGCTCTATCTCTTTAACTTTCTTTGTCT 699566 v v vv v i i (ATCTCT)n#Sim 1 ATCTCTATCTCTATCTCTATCTCTATCTCTATCT 34 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 283 32.46 4.13 3.28 chr6ptel1M 700000 700120 (299880) C MIR3#SINE/MIR (10) 198 77 m_b289s601i48 11849 chr6ptel1M 700000 ATCATAGA--GTCAGATCTAAAAAGCAACTTGGAAGTCTTTT-GCCTTAG 700046 -- v ii i v v i ii v i - i i--- C MIR3#SINE/MIR 198 ATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCC--- 152 chr6ptel1M 700047 AACCATTCTTAGATCATAG--CAGCAAAATGAGAGCTAGAGAAAGGAGAT 700094 -ii i vv i i --v v v iv i iiv ii C MIR3#SINE/MIR 151 AACC-CCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGT 103 chr6ptel1M 700095 GGTTTGTCAGAGGTCACATAACTAGT 700120 ii i vi i i ? C MIR3#SINE/MIR 102 GACTTGCCCAAGGTCACACAGCNAGT 77 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 45.91 CpG sites = 26, Kimura (unadjusted) = 45.91 Transitions / transversions = 2.17 (26/12) Gap_init rate = 0.06 (7 / 120), avg. gap size = 1.29 (9 / 7) 251 27.25 6.52 4.26 chr6ptel1M 700272 700363 (299637) MIR3#SINE/MIR 108 201 (7) m_b289s601i49 11850 chr6ptel1M 700272 ACTTCTTTTGTCTCACTCAAATTTCCTCATTTGTAAAATAAAGGGACTGC 700321 i i v v --- i- i i i ii v MIR3#SINE/MIR 108 ACCTCTCTGGGC---CTCAG-TTTCCTCATCTGTAAAATGAGGGGGTTGG 153 chr6ptel1M 700322 CCTGAAAGATTTCTGAGATG----TCAGTCCTAA-ATT-TATGATTTT 700363 v ii v i i i v----i ii i - - i MIR3#SINE/MIR 154 ACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCT 201 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.10 CpG sites = 18, Kimura (unadjusted) = 36.10 Transitions / transversions = 3.00 (18/6) Gap_init rate = 0.08 (7 / 91), avg. gap size = 1.43 (10 / 7) 16 20.34 2.86 0.00 chr6ptel1M 700656 700690 (299310) (GT)n#Simple_repeat 1 36 (0) m_b289s252i18 11851 chr6ptel1M 700656 GTGT-TGTGCTTGTATGTATGTGTGTGTGTATATGT 700690 - iv i i i i (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 36 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 495 33.62 3.03 6.25 chr6ptel1M 700808 701137 (298863) 7SLRNA#SINE/Alu 1 320 (0) c_b289s355i0 11852 chr6ptel1M 700808 GCCAGGAGTGGTGGAGTATGTCCAGAGTTCCTGATGCTAGAAAGGCTGAG 700857 i v i v iii i iiv i v v i v ii 7SLRNA#SINE/A 1 GCCGGGCGCGGTGGCGCGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAG 50 chr6ptel1M 700858 TCA--ATGATGTCTCAACTTTGGGAATTTTGAGGTAAAGTAGG-TATAAA 700904 v i-- v vv ii viiii i i i v iv iv - --- 7SLRNA#SINE/A 51 GCGGGAGGATCGCTTGAGCCCAGGAGTTCTGGGCTGTAGTGCGCTAT--- 97 chr6ptel1M 700905 GTCTATTGGATGGCAGCATATAG------ATCAATATAGTTAATCTCCTT 700948 i v i i v v ivv ------ i -i i iv 7SLRNA#SINE/A 98 GCCGATCGGGTGTCCGCACTAAGTTCGGCATCAATATGGT-GACCTCCCG 146 chr6ptel1M 700949 A-AGTACATGACAACTGGACTATCTGAAGAGGGGTGAACTGGCTCATGTT 700997 i- iiviv v ii ii ii i i i i v i 7SLRNA#SINE/A 147 GGAGCGGGGGACCACCAGGTTGCCTAAGGAGGGGTGAACCGGCCCAGGTC 196 chr6ptel1M 700998 AAGAAAAAGCAGCTGGTTAAAGCATTCATGATGATTTGCATTAGGATCAG 701047 -- i v v v i i vii i v iv i v i iv 7SLRNA#SINE/A 197 --GGAAACGGAGCAGGTCAAAACTCCCGTGCTGATCAGTAGTGGGATCGC 244 chr6ptel1M 701048 GCTTGTGAGTGGCCACAGCACTTCCAGTGTGGACAAAACAAAATTCAATG 701097 i i i v - iv i v i i---- i - 7SLRNA#SINE/A 245 GCCTGTGAATAGCCACTGCAC-TCCAGCCTGGGCAACATAG----CGA-G 288 chr6ptel1M 701098 ATCCTCCTCTCTTTTTTTATAAAAACAAAAAACAAAAAAA 701137 - i v ------- v v 7SLRNA#SINE/A 289 A-CCCCGTCTCT-------TAAAAAAAAAAAAAAAAAAAA 320 Matrix = 18p37g.matrix Kimura (with divCpGMod) = 38.93 CpG sites = 66, Kimura (unadjusted) = 46.78 Transitions / transversions = 1.74 (66/38) Gap_init rate = 0.07 (24 / 329), avg. gap size = 1.25 (30 / 24) 192 30.61 0.00 0.00 chr6ptel1M 701622 701670 (298330) L3#LINE/CR1 4048 4096 (3) m_b289s601i50 11853 chr6ptel1M 701622 GATTCAGTGGCTACTGAGGTTCCTTCCAACTCTCAGAACCTATAATCCT 701670 i vii i iv i i v vi i i i L3#LINE/CR1 4048 GACTAGATGACCTCTAAGGTCCCTTCCAACTCTGAGATTCTGTGATTCT 4096 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.27 CpG sites = 11, Kimura (unadjusted) = 42.27 Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 278 31.52 5.88 4.35 chr6ptel1M 702102 702237 (297763) L2c_3end#LINE/L2 339 476 (2) m_b289s601i51 11854 chr6ptel1M 702102 TGTAACTGTATTTTGACATGT-TGTCCCTACTATTAAA-TCTAAGTTCAG 702149 i v v v ? - i iv i i i - v i i vv L2c_3end#LINE 339 TGTAATTGTCTGTTTACNTGTCTGTCTCCTCCACTAGACTGTGAGCTCCT 388 chr6ptel1M 702150 TGAGTGCAAAGACTACTGTTT--TTCCTTTTCCTGCACCTTCAGTGCTTA 702197 v ii ii- i -- v i -- i i ii i i i L2c_3end#LINE 389 TGAGGGCAGGGACCG-TGTCTTATTCATCTT--TGTATCCCCAGCGCCTG 435 chr6ptel1M 702198 GCAC----TAAGTGCTTAAGAATTCATATTTACTAACTTACTGA 702237 ---- i i i v --- i ii i v v v L2c_3end#LINE 436 GCACATAGTAGGCGCTCAATAA---ATGTTTGTTGAATGAATGA 476 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.44 CpG sites = 28, Kimura (unadjusted) = 43.90 Transitions / transversions = 2.15 (28/13) Gap_init rate = 0.07 (10 / 135), avg. gap size = 1.40 (14 / 10) 40 0.00 0.00 0.00 chr6ptel1M 702849 702882 (297118) (GT)n#Simple_repeat 1 34 (0) c_b289s251i2 11855 chr6ptel1M 702849 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 702882 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 34 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 345 27.63 0.00 0.00 chr6ptel1M 703065 703140 (296860) MIR3#SINE/MIR 105 180 (28) m_b289s601i52 11856 chr6ptel1M 703065 TTTACCTTTCTGATCCTGAGCCTCCTCATTTTTGAAACAAAGGACTTGGA 703114 i i iv v ii i v i ii i iv MIR3#SINE/MIR 105 TTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGA 154 chr6ptel1M 703115 CTAGAGGATTTCAAAGGACCTTTTCA 703140 v i v v i i MIR3#SINE/MIR 155 CTAGATGATCTCTAAGGTCCCTTCCA 180 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.95 CpG sites = 14, Kimura (unadjusted) = 35.95 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.00 (0 / 75), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 chr6ptel1M 703956 703972 (296028) (T)n#Simple_repeat 1 17 (0) m_b290s252i0 11857 chr6ptel1M 703956 TTTTTTTTTTTTTTTTT 703972 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTT 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 20 26.05 0.00 0.00 chr6ptel1M 704092 704141 (295859) (TT)n#Simple_repeat 1 50 (0) m_b290s252i1 11858 chr6ptel1M 704092 TTTTGTTTTTTTTTTTTTTAGTATTTTATTGATTTTTCCTTCTCTTTTTT 704141 v vv v v vv ii i i (TT)n#Simple_ 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 17 18.17 6.90 1.64 chr6ptel1M 704430 704487 (295513) (TATA)n#Simple_repeat 1 61 (0) m_b290s252i2 11859 chr6ptel1M 704430 TATAAATATGTATACATATAT-TATATTTA-ACATATACTTTA-ACATAT 704476 v i i - v - i - v - i (TATA)n#Simpl 1 TATATATATATATATATATATATATATATATATATATA-TATATATATAT 49 chr6ptel1M 704477 TTA-ATATGTAT 704487 v - i (TATA)n#Simpl 50 ATATATATATAT 61 Matrix = Unknown Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.09 (5 / 57), avg. gap size = 1.00 (5 / 5) 250 37.50 3.12 0.00 chr6ptel1M 704641 704736 (295264) MIRc#SINE/MIR 2 100 (168) m_b290s601i1 11860 chr6ptel1M 704641 GAGACAGCATGGCACAAAGGATAGAAAATGATACCAGAGATCAGGATGGC 704690 i ii ii iv v iv iviv iv iii v i MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr6ptel1M 704691 CTGGATTCAAGTCCTAA--CTGCTACATATTGACTAAATGA-CTCAGGC 704736 i i iii-- i v i ii ivi - ii MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGC 100 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 53.13 CpG sites = 27, Kimura (unadjusted) = 58.58 Transitions / transversions = 3.00 (27/9) Gap_init rate = 0.02 (2 / 95), avg. gap size = 1.50 (3 / 2) 27 0.00 2.94 2.94 chr6ptel1M 705545 705578 (294422) (TTTAATAA)n#Simple_repeat 1 34 (0) c_b290s251i1 11861 chr6ptel1M 705545 TTTAATAATTTAATAATTTAAATAATTTAA-AATT 705578 - - (TTTAATAA)n#S 1 TTTAATAATTTAATAATTT-AATAATTTAATAATT 34 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2) 16 19.38 2.44 0.00 chr6ptel1M 706841 706881 (293119) (CCTCTT)n#Simple_repeat 1 42 (0) m_b290s252i3 11862 chr6ptel1M 706841 CCTATTCCTCATCCTCTT-AACTTTCTCTTCCCATTCCTCTT 706881 v v -vv i iv (CCTCTT)n#Sim 1 CCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTT 42 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 251 21.98 9.52 6.15 chr6ptel1M 707202 707327 (292673) L1ME5_3end#LINE/L1 341 470 (471) m_b290s551i0 11863 chr6ptel1M 707202 TCAAAGTAAGCAAACTGCACACACCCTATGACCCAGGAATAACAATCCTA 707251 v i --- i i i v vv iv i L1ME5_3end#LI 341 TCAAATTAAGTA---TACGCATACCCTATGACCCAGCAATTCCGCTCCTG 387 chr6ptel1M 707252 GAAATTTACCACAAAGAAA---TCAAAGAGG-----AAAAGGACCCATAT 707293 iv v i v --- v v ----- ii ---- L1ME5_3end#LI 388 GGTATATATCCCAAAGAAATTCTCACACAGGTCCATAAGGGGAC----AT 433 chr6ptel1M 707294 GTACAAAAA-GTGCA--GCAGCTGTT-TTTGTGGCAGC 707327 i ii - v -- - - ii L1ME5_3end#LI 434 GTACGAGGATGTTCATTGCAGC-GTTGTTTGTGGTGGC 470 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 23.11 CpG sites = 15, Kimura (unadjusted) = 26.50 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.10 (13 / 125), avg. gap size = 1.54 (20 / 13) 237 24.17 9.92 2.13 chr6ptel1M 707213 707343 (292657) L1ME4c_3end#LINE/L1 352 492 (338) m_b290s551i1 11863 chr6ptel1M 707213 AAACTGCACACACCCTATGACCCAGGAATAACAATCCTAGAAATTTACCA 707262 v iv i v v vv v i i i i v L1ME4c_3end#L 352 AAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCC 401 chr6ptel1M 707263 CAAAGAAA----TCAAA--GAGGAAAAGGACCCATATGTACAAAAA-GTG 707305 i i ---- --i i -- i i i i - v L1ME4c_3end#L 402 TAAGGAAATAATTCAAAAGAAGGAAAAAG--CTATATGCACGAAGATGTT 449 chr6ptel1M 707306 CA--GCAGCTGTT-TTTGTGGCAGCAAAA---TGCGAACAAACT 707343 -- - - i iii i --- vi v L1ME4c_3end#L 450 CATTGCAGC-GTTATTTATAATAGCGAAAAATTGGAAACAACCT 492 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 27.84 CpG sites = 20, Kimura (unadjusted) = 30.13 Transitions / transversions = 1.82 (20/11) Gap_init rate = 0.07 (9 / 130), avg. gap size = 1.78 (16 / 9) 56 0.00 0.00 0.00 chr6ptel1M 707743 707790 (292210) (TA)n#Simple_repeat 1 48 (0) c_b290s251i2 11864 chr6ptel1M 707743 TATATATATATATATATATATATATATATATATATATATATATATATA 707790 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATA 48 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 555 31.19 10.55 0.00 chr6ptel1M 707951 708168 (291832) C MIRc#SINE/MIR (18) 250 10 m_b290s601i2 11865 chr6ptel1M 707951 CATTTATGTGCCATTTTGAGGTTTGCAAA---CTT----ATTTAATATTT 707993 i i iv i ivi i --- ---- vi v i C MIRc#SINE/MIR 250 CATTTGTATAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATCT 201 chr6ptel1M 707994 CATT--------ACAGTAACTCTGC-ACCCAG--AAGGC--TCATTATTT 708030 -------- ii i i- vvi -- i --vi v C MIRc#SINE/MIR 200 CATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTA 151 chr6ptel1M 708031 TCTTCATTTTACAGGTGAGGAAACTGAGACTTAGAGAAAGTAAGTGAATT 708080 ii i i i iiv v C MIRc#SINE/MIR 150 TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTT 101 chr6ptel1M 708081 CCCCAAGCTTACACAGTTAGATAAT--CTGAGGTAAATTTTGAACTTGAA 708128 v v i i vv i -- v viiiivi i iiiii C MIRc#SINE/MIR 100 GCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGG 51 chr6ptel1M 708129 TTCTTTTGACTTCAAGTCCCCTG-TTTAACTTCTGTGCCAC 708168 ii ii i vv - i vv iv ii C MIRc#SINE/MIR 50 TCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.85 CpG sites = 46, Kimura (unadjusted) = 42.64 Transitions / transversions = 2.09 (46/22) Gap_init rate = 0.04 (8 / 217), avg. gap size = 2.88 (23 / 8) 565 30.77 1.99 6.22 chr6ptel1M 707980 708180 (291820) C MIRb#SINE/MIR (72) 196 4 m_b290s601i3 11865 chr6ptel1M 707980 CTTATTTAATATTTCATTACAGTAACTCTGCACCCAGA-AGGCTCATTAT 708028 i ---- v i ii i i--- i- i-- C MIRb#SINE/MIR 196 CTCATTTAAT----CCTCACAACAACCCTGCG---AGGTAGGT--ATTAT 156 chr6ptel1M 708029 TTTCTTCATTTTACAGGTGAGGAAACTGAGACTTAGAGAAAGTAAGTGAA 708078 v ii i i i iiv i v C MIRb#SINE/MIR 155 TATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAAC 106 chr6ptel1M 708079 TTCCCCAAGCTTACACAGTTAGATAAT--CTGAGGTAAATTTTGAACTTG 708126 v v i i vv i -- v viiiiv i iii C MIRb#SINE/MIR 105 TTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCA 56 chr6ptel1M 708127 AATTCTTTTGACTTCAAGTCCCCTG-TTTAACTTCTGTGCCACTTAGCTA 708175 ii iiv i i iv v - i vv iv ii --- i C MIRb#SINE/MIR 55 GGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCACCAC---GCTG 9 chr6ptel1M 708176 CTTCT 708180 ii C MIRb#SINE/MIR 8 CCCCT 4 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.04 CpG sites = 41, Kimura (unadjusted) = 42.05 Transitions / transversions = 2.41 (41/17) Gap_init rate = 0.07 (15 / 200), avg. gap size = 1.07 (16 / 15) 248 31.33 11.20 2.96 chr6ptel1M 708584 708708 (291292) L3#LINE/CR1 3948 4082 (17) m_b290s601i4 11866 chr6ptel1M 708584 AGGGAGTGATGGATTTCAACTTCACTTAAGGTCTTTAAGCAG-------- 708625 v -- v ii -- v vi v i -------- L3#LINE/CR1 3948 AGGTAGTGA--GCTCCC--CGTCACTGGAGGTGTTCAAGCAGAGGCTGGA 3993 chr6ptel1M 708626 ---TCATTTGTCAAGGATATTGTAAATGAAATTCCTGC-CTAGGTACT-T 708670 ---i i i i i v ii -i i i ivv-v L3#LINE/CR1 3994 TGACCACTTGTCAGGGATGTTGTAGAAGGGATTCCTGCATTGGATGGGAG 4043 chr6ptel1M 708671 ATTGGATTATTCAGATTTTAAGAT-TCTACCAAGTCTGA 708708 i i vviiivi i i -i v v L3#LINE/CR1 4044 GTTGGACTAGATGACCTCTAAGGTCCCTTCCAACTCTGA 4082 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.49 CpG sites = 24, Kimura (unadjusted) = 42.49 Transitions / transversions = 1.71 (24/14) Gap_init rate = 0.07 (9 / 124), avg. gap size = 2.00 (18 / 9) 247 17.07 0.00 0.00 chr6ptel1M 708708 708748 (291252) L3#LINE/CR1 3731 3771 (328) m_b290s601i5 11867 chr6ptel1M 708708 AACCTGAAGAAGAGAAGATTTAAGGGAGACATGACAGTTGT 708748 i i i ii i i L3#LINE/CR1 3731 AGCCTGGAGAAGAGAAGACTTAGAGGAGACATGATAGCTGT 3771 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 20.89 CpG sites = 7, Kimura (unadjusted) = 20.89 Transitions / transversions = 1.00 (7/0) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 274 31.24 0.88 4.55 chr6ptel1M 708815 708928 (291072) MIRc#SINE/MIR 9 118 (150) m_b290s601i6 11868 chr6ptel1M 708815 TGTGGAATAATCGATTGTGTGCTTGACCTGGAATAAAGTACATATATCTG 708864 vii i v vv v ii v i i v i --- - v i MIRc#SINE/MIR 9 TGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGG---A-AGACCTG 54 chr6ptel1M 708865 GGTTC-AGATCTGACTTGGGAAATCTATTATCTGTGCTACTATGGGCAAG 708913 - vi i i iv vv v - i v iv iv MIRc#SINE/MIR 55 GGTTCGAGTCCCGGCTCTGCCACT-TACTAGCTGTGTGACCTTGGGCAAG 103 chr6ptel1M 708914 TTACTTGACCTCTCT 708928 i i MIRc#SINE/MIR 104 TCACTTAACCTCTCT 118 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.55 CpG sites = 18, Kimura (unadjusted) = 41.10 Transitions / transversions = 1.12 (18/16) Gap_init rate = 0.05 (6 / 113), avg. gap size = 1.00 (6 / 6) 223 31.94 4.17 0.00 chr6ptel1M 709048 709119 (290881) C MIRc#SINE/MIR (172) 96 22 m_b290s601i7 11869 chr6ptel1M 709048 AGGATCAGAGAG--AGTAAGTGAACAAATCAGCATTCTAGTCCAACTCTT 709095 i i v v -- ivvi ii i v i v ii iv C MIRc#SINE/MIR 96 AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTT 47 chr6ptel1M 709096 AC-GACTCCAAATGCAATGTTCTTT 709119 v - i v i i C MIRc#SINE/MIR 46 CCTGACTCCAAGTCCAGTGCTCTTT 22 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.75 CpG sites = 14, Kimura (unadjusted) = 43.26 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.03 (2 / 71), avg. gap size = 1.50 (3 / 2) 263 10.81 0.00 0.00 chr6ptel1M 709199 709235 (290765) EutTc1-N2#DNA/TcMar-Tc1 1 37 (341) m_b290s502i0 11870 chr6ptel1M 709199 CAGGGTGTCTCAAAAGTTTTAGTGTAGTTTTAAGTTT 709235 i i i i EutTc1-N2#DNA 1 CAGGGTGTCCCAAAAGTCTTAGTGCAGTTTTAAGCTT 37 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 12.18 CpG sites = 4, Kimura (unadjusted) = 12.18 Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 307 15.09 1.89 0.00 chr6ptel1M 709223 709275 (290725) EutTc1-N1#DNA/TcMar-Tc1 535 588 (0) m_b290s502i1 11871 chr6ptel1M 709223 TAGTTTTAAGTTTATTAAAGCTTAAA-CTGCTCTAAGACCTTTGGGACAC 709271 v i i v - v i i EutTc1-N1#DNA 535 TACTTCTGAGGTTATTAAAGCTTAAAACTGCACCAAGACTTTTGGGACAC 584 chr6ptel1M 709272 TCTG 709275 i EutTc1-N1#DNA 585 CCTG 588 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 17.07 CpG sites = 5, Kimura (unadjusted) = 17.07 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.02 (1 / 52), avg. gap size = 1.00 (1 / 1) 13 8.18 3.85 0.00 chr6ptel1M 709392 709417 (290583) (CTTCC)n#Simple_repeat 1 27 (0) m_b290s252i4 11872 chr6ptel1M 709392 CTT-CCTTGCCTTCCCATCCCTTCCCT 709417 - v v (CTTCC)n#Simp 1 CTTCCCTTCCCTTCCCTTCCCTTCCCT 27 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.04 (1 / 25), avg. gap size = 1.00 (1 / 1) 12 22.63 4.17 2.04 chr6ptel1M 709552 709599 (290401) (TTCTA)n#Simple_repeat 1 49 (0) m_b290s252i5 11873 chr6ptel1M 709552 TTCTATTTTGTTTATATTGCA-TCTATTCTATACAAGTCTCTTCT-TTCT 709599 i -v v vi - v v v v - (TTCTA)n#Simp 1 TTCTATTCT-ATTCTATTCTATTCTATTCTATTCTATTCTATTCTATTCT 49 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.06 (3 / 47), avg. gap size = 1.00 (3 / 3) 275 40.60 0.75 0.00 chr6ptel1M 709737 709869 (290131) C L2d_3end#LINE/L2 (0) 516 383 m_b290s601i8 11874 chr6ptel1M 709737 TTACTTAATGAATCAACAAATGCTTACCAAATACCGA-TCTCTGTCTGGT 709785 i v i v i ii iii iii v - v v iiii i C L2d_3end#LINE 516 TCAATCAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGC 467 chr6ptel1M 709786 ACCTTCCTCAGTATACTGGGACATGCAAGAAAAACATGCATTCTTTCCCT 709835 iv v vi iiivv iv i v? i ? ii iviviv vvi i C L2d_3end#LINE 466 ACTGTGCTAGGCGCTGTGGGGAACGANAAAANAGTATAAGACATGGTCCC 417 chr6ptel1M 709836 TGTCCTCAAAGAACTTACAATGTGGTTTGGGAGA 709869 i i i v i v C L2d_3end#LINE 416 TGCCCTCAAGGAGCTTACAATCTAGTTGGGGAGA 383 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 58.97 CpG sites = 35, Kimura (unadjusted) = 65.44 Transitions / transversions = 1.84 (35/19) Gap_init rate = 0.01 (1 / 132), avg. gap size = 1.00 (1 / 1) 390 26.56 18.87 0.53 chr6ptel1M 710867 711025 (288975) MIR3#SINE/MIR 20 207 (1) m_b290s601i9 11875 chr6ptel1M 710867 GAAAGAATACCATACTGGCCTTTAAAAGACCTGGCTTCTAG---CAGA-- 710911 i ii vi- vvv i ii v --- i v-- MIR3#SINE/MIR 20 GAGAGAGCACGG-ACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTC 68 chr6ptel1M 710912 -GCCACTGA--TGCT--------TTGGACAAGCCACTTTACCTCTCTGGG 710950 - i --? -------- i i i MIR3#SINE/MIR 69 TGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGG 118 chr6ptel1M 710951 ATTCAGGTTCATGATCTATAA--------------ACAAGAGGATTTCCA 710986 vi v v v i -------------- v v i i MIR3#SINE/MIR 119 CCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTA 168 chr6ptel1M 710987 AGGCCCCCTTTGACTCTTAGAATTCATGAGACTATGCTT 711025 i i iiii v v v ii vv v MIR3#SINE/MIR 169 AGGTCCCTTCCAGCTCTGACATTCTATGATTCTATGATT 207 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.80 CpG sites = 24, Kimura (unadjusted) = 33.78 Transitions / transversions = 1.33 (24/18) Gap_init rate = 0.04 (7 / 158), avg. gap size = 4.43 (31 / 7) 378 23.77 3.42 2.03 chr6ptel1M 711168 711313 (288687) Charlie4#DNA/hAT-Charlie 3218 3365 (13) m_b290s502i2 11876 chr6ptel1M 711168 TTTTTAAAT---TTG-TACATATATTTTAGTATAATTGGCTTCCCTTCTA 711213 --- - vv i i i i v Charlie4#DNA/ 3218 TTTTTAAATATTTTGATAACTATATTTCAATATAATTGGTTTCCTTTGTA 3267 chr6ptel1M 711214 ATCCAATGTATGTTATTTTATGAATTTAAAGTGTTTTTTATGA-AAGGAG 711262 v v v ivvv v v - i Charlie4#DNA/ 3268 ATCCTATGTATTTTATTTTATGCATTTAAAAACATTATTCTGAGAAGGGG 3317 chr6ptel1M 711263 TGTCATATGTTGTACTAGATAGTCAAGGTGTGATCAACATCCCAGAAAAG 711312 -i v i vi i iv i i - - i v iiv v i Charlie4#DNA/ 3318 T-CCATAGGCTTCACCAGACTGCCAAAG-G-GGTCCATGGCACAAAAAAG 3364 chr6ptel1M 711313 G 711313 Charlie4#DNA/ 3365 G 3365 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 28.84 CpG sites = 17, Kimura (unadjusted) = 28.84 Transitions / transversions = 1.00 (17/17) Gap_init rate = 0.04 (6 / 145), avg. gap size = 1.33 (8 / 6) 23 15.33 6.74 5.56 chr6ptel1M 711314 711402 (288598) (GGAAGAG)n#Simple_repeat 1 90 (0) m_b290s252i6 11877 chr6ptel1M 711314 GGAGAGAGGGCA-AGGGAA-AGGG-AGACGG--CAGGGAAGAAGGAAG-G 711357 - v - - - v --v i - (GGAAGAG)n#Si 1 GGA-AGAGGGAAGAGGGAAGAGGGAAGAGGGAAGAGGGAAGAGGGAAGAG 49 chr6ptel1M 711358 TGAGAGGGGGTAACAAGTGAAGGGGGAAGAGGGGAAGGAGGAAGA 711402 v - i - -i v i - ii (GGAAGAG)n#Si 50 GGA-AGAGGG-AA-GAGGGAAGAGGGAAGA-GGGAAGAGGGAAGA 90 Matrix = Unknown Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.11 (10 / 88), avg. gap size = 1.10 (11 / 10) 17 14.79 4.08 4.08 chr6ptel1M 711317 711365 (288635) (GAGAGG)n#Simple_repeat 1 49 (0) m_b290s252i7 11877 chr6ptel1M 711317 GAGAGGGCAAGGGAAAGGGAGACGGCAG-GGAAGAAGGA-AGGTGAGAGG 711364 vi i - v - i i - - (GAGAGG)n#Sim 1 GAGAGGGAGAGGGAGAGGGAGA-GGGAGAGGGAGAGGGAGAGG-GAGAGG 48 chr6ptel1M 711365 G 711365 (GAGAGG)n#Sim 49 G 49 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.08 (4 / 48), avg. gap size = 1.00 (4 / 4) 13 10.36 0.00 11.43 chr6ptel1M 712079 712117 (287883) (ATAC)n#Simple_repeat 1 35 (0) m_b290s252i8 11878 chr6ptel1M 712079 ATACATATGCATACATATCCACACATACAGACATATATA 712117 -- -- i v i (ATAC)n#Simpl 1 ATACATA--CATACATA--CATACATACATACATACATA 35 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.11 (4 / 38), avg. gap size = 1.00 (4 / 4) 349 35.51 5.85 2.84 chr6ptel1M 712244 712414 (287586) C MIRc#SINE/MIR (78) 190 15 m_b290s601i10 11879 chr6ptel1M 712244 TTATAACATCATTGCAAGGTAGATGGGACCAGG----GTCAGCTTTCTTT 712289 i i v vi ii iii i - ----i i v iiiv C MIRc#SINE/MIR 190 TCACAACAACCCTGTGAGGTAGGCAGGGC-AGGTATTATTATCCCCATTT 142 chr6ptel1M 712290 CACATTTGAGGAAATTGAGGTCCTGAAGAATTATCTGACTT---TAATGC 712336 i vv i ii v iiii vv ---i v - C MIRc#SINE/MIR 141 TACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGG- 93 chr6ptel1M 712337 ATTCATTCAGCTAAGAAATTAACAGAGCTAAAATTTGAATCTTGATCTTA 712386 -- iv - v v ii iiii i i i iv i v C MIRc#SINE/MIR 92 --TCACACAGCT-AGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTC 46 chr6ptel1M 712387 TTTTCCCCAA-TTTGGTGCTTTTT--ATTGC 712414 i vv i - iii i -- i C MIRc#SINE/MIR 45 CTGACTCCAAGTCCAGTGCTCTTTCCACTGC 15 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 49.77 CpG sites = 42, Kimura (unadjusted) = 52.61 Transitions / transversions = 2.47 (42/17) Gap_init rate = 0.05 (9 / 170), avg. gap size = 1.67 (15 / 9) 252 23.14 18.11 1.35 chr6ptel1M 713026 713152 (286848) C MIRc#SINE/MIR (0) 268 121 m_b290s601i11 11880 chr6ptel1M 713026 AATAATAAGAATAGTTTACGTCTGTATAATGATTTGACA-TTTACAAAGT 713074 v i?vi i i ii- i v - i C MIRc#SINE/MIR 268 AATAATAATAACNCCTTACATTTGTATAGC-ACTTTACAGTTTACAAAGC 220 chr6ptel1M 713075 GATTTC-CTTACACACTACCATTTTGTCGT----ATATACTATG-GTGGT 713118 v - v ivv vi vi v ---- i - iv - v C MIRc#SINE/MIR 219 GCTTTCACATACATTATCTCATTTGATCCTCACAACA-ACCCTGTGAGGT 171 chr6ptel1M 713119 A--CTGGG--------------CCCATTTTAGAGATGAGGAAAGTGAAGC 713152 -- v -------------- v v i C MIRc#SINE/MIR 170 AGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGC 121 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 27.12 CpG sites = 14, Kimura (unadjusted) = 28.22 Transitions / transversions = 0.93 (14/15) Gap_init rate = 0.06 (8 / 126), avg. gap size = 3.12 (25 / 8) 226 25.16 2.63 9.35 chr6ptel1M 713059 713172 (286828) C MIR#SINE/MIR (56) 206 100 m_b290s601i12 11880 chr6ptel1M 713059 TTGACATTTACAAAGTGATTT---CCTTACACACTACCATTTTGTCGTAT 713105 v v iv v v --- i - v -i v vv v C MIR#SINE/MIR 206 TTTACATGTATTAACTCATTTAATCCTCACA-ACAACC-CTATGAGGTAG 159 chr6ptel1M 713106 ATACTATGGTGGTACTGGGCCCATTTTAGAGATGAGGAAAGTGAAGCATG 713155 i ----- i ivv v v i -- C MIR#SINE/MIR 158 GTACTAT-----TATTATCCCCATTTTACAGATGAGGAAACTGAGGCA-- 116 chr6ptel1M 713156 TAGGAAGAATTTAGTAA 713172 i ii -i v C MIR#SINE/MIR 115 CAGAGAG-GTTAAGTAA 100 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 30.49 CpG sites = 11, Kimura (unadjusted) = 30.49 Transitions / transversions = 0.73 (11/15) Gap_init rate = 0.10 (11 / 113), avg. gap size = 1.18 (13 / 11) 192 28.71 2.14 27.33 chr6ptel1M 713125 713311 (286689) C MIRb#SINE/MIR (117) 151 2 m_b290s601i13 11880 chr6ptel1M 713125 CCCATTTTAGAGATGAGGAAAGTGAAGCATGTAGGAAGAATTTAGTAAAT 713174 v v i --- vi iiii v -- C MIRb#SINE/MIR 151 CCCATTTTACAGATGAGGAAACTGAGGC---TCAGAGAGGTTAAGTAA-- 107 chr6ptel1M 713175 GCTTTTTGATTAGTTGAGTCTCAGAGTCTTAG--AATGACATGTCCAATT 713222 ----i vii ---ii v v --i -- i i - --- iii C MIRb#SINE/MIR 106 ----CTTGCCCA---AGGTCACACAG--CTAGTAAGTGGCA-G---AGCC 70 chr6ptel1M 713223 GGGATGCCACACCTAGCCAGGATATGGGTTCAAGTCT-TCTGACTTCAAG 713271 v v - i ----------------- - i - C MIRb#SINE/MIR 69 GGGATTCGA-ACCCAG-----------------GTCTGTCTGACTCCAA- 39 chr6ptel1M 713272 TCTAGATCAGTGCTC-TTCTTTTGTACCACACTGTTTCCCT 713311 --- -i v - ivi i i iii i C MIRb#SINE/MIR 38 ---AG-CCCGTGCTCTTTCCACTGCACCACGCTGCCCCTCT 2 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.56 CpG sites = 28, Kimura (unadjusted) = 34.79 Transitions / transversions = 2.55 (28/11) Gap_init rate = 0.24 (44 / 186), avg. gap size = 1.02 (45 / 44) 283 26.05 11.67 7.20 chr6ptel1M 713189 713308 (286692) C MIRc#SINE/MIR (142) 126 2 m_b290s601i14 11880 chr6ptel1M 713189 TGAGTCTCAGAGTCTTAGAATGACATGTCCAATTGGGATGCCACACCTAG 713238 v vvv vi i v i ---- i vv v C MIRc#SINE/MIR 126 TGAGGCTCAGAGAGGTTAAGTGACTTGCCCAA----GGTCACACAGCTAG 81 chr6ptel1M 713239 ------------CCAGGATATGGGTTCAAGTCTTC-TGACTTCAAGTCTA 713275 ------------ i ivi iiii i - i -- C MIRc#SINE/MIR 80 TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTC-- 33 chr6ptel1M 713276 GATCAGTGCTC-TTCTTTTGTACCACACTGTTTC 713308 --- - ivi i ii C MIRc#SINE/MIR 32 ---CAGTGCTCTTTCCACTGCACCACACTGCCTC 2 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 30.32 CpG sites = 18, Kimura (unadjusted) = 33.05 Transitions / transversions = 1.64 (18/11) Gap_init rate = 0.10 (12 / 119), avg. gap size = 1.92 (23 / 12) 12 17.55 9.43 1.75 chr6ptel1M 713673 713725 (286275) (AATATTT)n#Simple_repeat 1 57 (0) m_b290s252i9 11881 chr6ptel1M 713673 AATATTGAAT-TCTCAAATAATCATCTTTAATA-TT--TACTTAATATTT 713718 v - i v v -v v v - -- i (AATATTT)n#Si 1 AATATTTAATATTTAATAT-TTAATATTTAATATTTAATATTTAATATTT 49 chr6ptel1M 713719 AAT-TTTA 713725 - (AATATTT)n#Si 50 AATATTTA 57 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.10 (5 / 52), avg. gap size = 1.20 (6 / 5) 728 24.94 9.79 4.45 chr6ptel1M 713818 714052 (285948) C MIRb#SINE/MIR (7) 261 15 m_b290s601i15 11882 chr6ptel1M 713818 GAACAGCTATTTATTAAGCACTTACTATGTGCCAGAAATTATGCTGCACA 713867 i vi i i i iv i i ivi i C MIRb#SINE/MIR 261 GAGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCG 212 chr6ptel1M 713868 TTTTACA---AATATCTCATTTAATT----------------GATGTAGG 713898 i --- v i---------------- v C MIRb#SINE/MIR 211 CTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGG 162 chr6ptel1M 713899 TGCTATAATTATCCCCATTTTTCAATTGAGGAAACTGAAGC----AGAGA 713944 --- v v iv i ---- i C MIRb#SINE/MIR 161 T---ATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGG 115 chr6ptel1M 713945 TTACCCAATTTGCTCATGGTCTAGAAAAATCACAGCTAGAAAATTTCTGA 713994 vvi i i v ------- - v i vv v C MIRb#SINE/MIR 114 TTAAGTAACTTGCCCAAGGTC-------A-CACAGCTAGTAAGTGGCAGA 73 chr6ptel1M 713995 GGCCATATTTAAATTCAGGTCTTTATTACTCCAAGTCTAACATTCCATCC 714044 v viv ii ii v v v iv iviiii iv C MIRb#SINE/MIR 72 GCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCC 23 chr6ptel1M 714045 ACTGCACC 714052 C MIRb#SINE/MIR 22 ACTGCACC 15 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.33 CpG sites = 32, Kimura (unadjusted) = 30.98 Transitions / transversions = 1.33 (32/24) Gap_init rate = 0.06 (14 / 234), avg. gap size = 2.43 (34 / 14) 303 33.87 5.14 7.92 chr6ptel1M 714055 714365 (285635) C L2d_3end#LINE/L2 (82) 434 132 m_b290s601i16 11883 chr6ptel1M 714055 AGAATAAGATATAGTCTCTGCCTTCCAGAAACTTA--GTCCACCAAGAGA 714102 v i i i i v i i --i i vivi i C L2d_3end#LINE 434 AGTATAAGACATGGTCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGGA 385 chr6ptel1M 714103 GATAAAAAGATTGATAGAGTACTTATAAAATTCTTATGATATTAAATGCC 714152 i --- i i i ---i -- i i------- - i viv C L2d_3end#LINE 384 GACAA---GACTAACA---CAC--ATGAAAC-------A-ATTAGAGAAC 351 chr6ptel1M 714153 CACAAAAGCAACAATACA-AATTAGAATGTGATATGTACACAAGATA--- 714198 v i v -- i i - - i iv v - i iiiiv i --- C L2d_3end#LINE 350 AATACAAG--ACAGTATATAATTA-AGTGCTAAAT-TGCGTGGTACAGAC 305 chr6ptel1M 714199 TATACATGATTCTACGAGTGCTCACATGGGAAA-ATTAGT-TATCCAAGA 714246 vi -i v v v vv v v i - i - ivv vi C L2d_3end#LINE 304 TATAAGTG-CTATAGGAGTTCAGAGAAGGGAGAGATCAGTGTGGGCTGGA 256 chr6ptel1M 714247 ------AAATAAGTCTCCATGATTGAGATGGCATTTGAGCTGGGTCTTGA 714290 ------ iiv v i i ivv i v i i C L2d_3end#LINE 255 GTGGTCAGGGAAGGCTTCGTGGAGGAGGTGGGACTTGAGCTGGGCCTTGA 206 chr6ptel1M 714291 A-GATAAGTAATATTT-GATAGGTGGTAATGGATCTGGAGCGTACATTCC 714338 - ii iv - i- iv iv vvv i- vi C L2d_3end#LINE 205 AGGATGGGTAGGATTTGGATAGA-GAGAGAGGAAGGGGAA-GGGCATTCC 158 chr6ptel1M 714339 AGTTATTGGAAAATGGCCTGACTAAAG 714365 vii-v ii i v vi C L2d_3end#LINE 157 AGGCG-GGGGGAACGGCGTGAGCAAAG 132 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 44.16 CpG sites = 59, Kimura (unadjusted) = 46.90 Transitions / transversions = 1.55 (59/38) Gap_init rate = 0.10 (32 / 310), avg. gap size = 1.25 (40 / 32) 235 35.46 9.67 4.11 chr6ptel1M 714163 714462 (285538) C L2c_3end#LINE/L2 (137) 341 26 m_b290s601i17 11883 chr6ptel1M 714163 ACAATACAAATTAGAATGTGATATGTAC----ACAAGA-TATATACATGA 714207 i i---- v i ---- iii - v v i C L2c_3end#LINE 341 ACAATACAAGTTAA----TGATAAGTGCTATAATGGGAGTATAGACAGGG 296 chr6ptel1M 714208 TTCTACGAGTGCTCACATGGGA------AAATTAGTTATCCAAGA--AAA 714249 v i i v v v v i i------ i i ?iv vvii i-- ii C L2c_3end#LINE 295 TGCTATGGGAGCACAGAGGAGGGCACCTAGACTAGNCTTGGGGGGTCAGG 246 chr6ptel1M 714250 TAAGTCTCCATGATTGAGATGGCATTTGAGCTGGGTCTTGAAG-ATAAGT 714298 v v i vi ivv i i i i ? - i C L2c_3end#LINE 245 GAAGGCTTCCCGGAGGAGGTGACATCTGAGCTGAGNCTTGAAGGATGAGT 196 chr6ptel1M 714299 AATATTT-GATAGGTGGTAATGGATCTGGAGCGTACATTCCAGTTATTGG 714347 iv v - vi - - vvv iiv vi vi vv C L2c_3end#LINE 195 AGGAGTTAGCCAGGTGG-AA-GGAGGGGGGAAGAGCATTCCAGGCAGAGG 148 chr6ptel1M 714348 AAA----AT-------GGCCTGACTAAAGAAATCAACT--AATTAATTAA 714384 i ---- ------- ?i ivviv i vv --iiivvi vi C L2c_3end#LINE 147 GAACAGCATGTGCAAAGGCNCGGAGGCAGGAAAGAACTGCGGCGTGTTTG 98 chr6ptel1M 714385 AGAAATGACAAGTAGTCCAGTTTGACCAG-GTTTTACAGGCTTGATAGGG 714433 i i - ? i v i ii - iv viii vv i- C L2c_3end#LINE 97 GGGAATG-CAAGNAGTTCAGTGTGGCTGGAGCATAGTGGGCGAGG-AGGG 50 chr6ptel1M 714434 AAATAAAGCTAGAAATGTCAGGTGGAAGA 714462 i i ii --- i -- iv i C L2c_3end#LINE 49 GAGTGGAG---GAGATG--AGGCTGGAGA 26 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 48.54 CpG sites = 61, Kimura (unadjusted) = 51.45 Transitions / transversions = 1.49 (61/41) Gap_init rate = 0.08 (23 / 299), avg. gap size = 1.83 (42 / 23) 347 26.79 1.74 2.63 chr6ptel1M 714251 714365 (285635) C L2d2_3end#LINE/L2 (310) 245 132 m_b290s601i18 11883 chr6ptel1M 714251 AAGTCTCCATGATTGAGATGGCATTTGAGCTGGGTCTTGAA-GATAAGTA 714299 v i i ivv i ? i - ii C L2d2_3end#LIN 245 AAGGCTTCACGGAGGAGGTGGNATTTGAGCTGGGCCTTGAAGGATGGGTA 196 chr6ptel1M 714300 ATATTT-GATAGGTGGTAATGGATCTGGAGCGTACATTCCAGTTATTGGA 714348 iv - - iv vvv i- vi vii-v i C L2d2_3end#LIN 195 GGATTTGGATAGGTGG-AGAGGAAGGGGAA-GGGCATTCCAGGCG-GGGG 149 chr6ptel1M 714349 AAATGGCCTGACTAAAG 714365 i i v vi C L2d2_3end#LIN 148 GAACGGCGTGAGCAAAG 132 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 30.01 CpG sites = 17, Kimura (unadjusted) = 34.20 Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.04 (5 / 114), avg. gap size = 1.00 (5 / 5) 511 36.82 11.66 1.70 chr6ptel1M 714503 715411 (284589) C L2#LINE/L2 (229) 2853 1856 m_b290s601i19 11883 chr6ptel1M 714503 ATTGGAGGCATTTGAG--GAGAAACACTGTGTTCAAAGCTTTGATTTAGA 714550 vv -- i iiivii v vi vi vi v i C L2#LINE/L2 2853 ATTGGAGGGTTTTGAGCAGAGGAGTGACATGATCTGACTTACGTTTTAAA 2804 chr6ptel1M 714551 AAGATTAAGCTTTCAGTTTTGTCTAAGGGAGATTGAAGAGAGGAGCAACT 714600 i i vv vv v i v iv iiiv i ? i i viviiv C L2#LINE/L2 2803 AGGATCACTCTGGCTGCTGTGTTGAGAATAGACTGNAGGGGGGCAAGGGT 2754 chr6ptel1M 714601 GTAAGTGGAGAGACCAGATAGGAAGAAGTAATAAGAATCCAAAT------ 714644 v ii i v i vvi vii iv iii------ C L2#LINE/L2 2753 GGAAGCAGGGAGACCAGTTAGGAGGCTATTGCAGTAATCCAGGCGAGAGA 2704 chr6ptel1M 714645 TGAAGGT--CT-------GGATAGTCATAGTGGGAAGGGGGAGGAGAGAA 714685 v -- ------- i i vii iiiv v i v iv C L2#LINE/L2 2703 TGATGGTGGCTTGGACCAGGGTGGTGGCAGTGGAGGTGGTGAGAAGTGGT 2654 chr6ptel1M 714686 TAGATGTGAGAT-TAT---GGAAGCAGAAT-GA-AGAGTTTATTGAC--- 714726 ii vivi - --- i i i ii- - ii ii i--- C L2#LINE/L2 2653 CGGATTCTGGATATATTTTGAAGGTAGAGCCGACAGGATTTGCTGATGGA 2604 chr6ptel1M 714727 -TGGATGT------TGAGA-----ACGGCAGTCAAAGTTCACATTAGCAT 714764 - ------ ----- vi v i v v vii ivi C L2#LINE/L2 2603 TTGGATGTGGGGTGTGAGAGAAAGAGAGGAGTCAAGGATGACTCCAAGGT 2554 chr6ptel1M 714765 TTTTTGGTTTGGGTGGCTAG--GAATTCAGTTAACGGCAATTAGGTATCA 714812 - ii i iii i -- i vv ---- v ?iv i-- C L2#LINE/L2 2553 TTTT-GGCCTGAGCAACTGGAAGGATGGAGTT----GCCATTNACTG--A 2511 chr6ptel1M 714813 GGTAGAGGA-ACAAGTGGAGGAGTGGGCATTGGGGTAAAGATGATGAGTT 714861 i i i i - vivv ii iv vi vi v v C L2#LINE/L2 2510 GATGGGGAAGACTGCGGGAGGAGCAGGTTTGAGGGGGAAGATCAGGAGTT 2461 chr6ptel1M 714862 CAGTTTTAAACATGTTGACATTGAGGTGCTGCTGAAGTATCTAGGTAAAG 714911 ii i vv i ivv v iii i i ii C L2#LINE/L2 2460 CAGTTTTGGACATGTTAAGTTTGAGATGCCTATTAGACATCCAAGTGGAG 2411 chr6ptel1M 714912 ATTTTATGCTGGCAATTAGCAAAATG-GACTGGGATCAAAGAGAAAGTTT 714960 v iiv iv i i vv v i - v ii iv i i i v i C L2#LINE/L2 2410 ATGTCGAGTAGGCAGTTGGATATACGAGTCTGGAGTTCAGGGGAGAGGTC 2361 chr6ptel1M 714961 CAGACAAGAGCTATAAATTTGGGGCTTACCTGT---TATGTGG------A 715001 i i vi v iv i i v i--- vi ------ C L2#LINE/L2 2360 CGGGCTGGAGATATAAATTTGGGAGTCATCAGCATATAGATGGTATTTAA 2311 chr6ptel1M 715002 AGCTAGGAGA-TGAAT---ATTTCTCAGAA---GCATCAAGAGAGAAAAG 715044 i v - i --- iv i? ii--- vi vv v i C L2#LINE/L2 2310 AGCCATGAGACTGGATGAGATCACCNAGGGAGTGAGTGTAGATAGAGAAG 2261 chr6ptel1M 715045 TGTTGAGG---AAGGAGTGCTTCCCAAGGAAATT--ATG----------G 715079 v vv --- v vvi iii v v i-- i ---------- C L2#LINE/L2 2260 AGAAGAGGTCCAAGGACTGAGCCCTGGGGCACTCCAACGTTNAGAGGTCG 2211 chr6ptel1M 715080 GGGA----AAGGGGAATAGGCAA---AAACT-ACAAATAGTA--CAGAGA 715119 ---- i i ivi --- i - v iv ii-- v C L2#LINE/L2 2210 GGGAGATGAGGAGGAACCAGCAAAGGAGACTGAGAAGGAGCGGCCAGTGA 2161 chr6ptel1M 715120 ATCAGGAAGAAGTTCGTTCAGGTGAGT-TTGCCTACTAGAAGTAGAAGTA 715168 ivi i ----ivi v - v iv v i i-v i C L2#LINE/L2 2160 GGTAGGAGGAA----AACCAGGAGAGTGTGGTGTCCTGGAAGC-CAAGTG 2116 chr6ptel1M 715169 GAAAAAATA--CCAAAAGGAATGGGGTAGTCAAAAGGGACAAATACTGC- 715215 i i i i--i i i i v i ii vv v v i - C L2#LINE/L2 2115 AAGAAAGTGTTTCAAGAAGGAGGGAGTGATCAACTGTGTCAAATGCTGCT 2066 chr6ptel1M 715216 AAAAGATCA------CTGAGGATGGAAAAAAGGCTACAAGAGTTGGTGAT 715259 i ? i ------v iv i vv i i ivi v i ii i C L2#LINE/L2 2065 GANAGGTCAAGTAAGATGAGGACTGAGAATTGACCATTGGATTTAGCAAC 2016 chr6ptel1M 715260 ATGGAGGTCTTTGATGCCATTGGAGAAAGAAGTTTTCTTAG---GGTGGG 715306 i v i v v ivi i v ivv i --- C L2#LINE/L2 2015 GTGGAGGTCATTGGTGACCTTGACAAGAGCAGTTTCGGTGGAGTGGTGGG 1966 chr6ptel1M 715307 --TGGAAGCTAGATCACAA------CATGAGAAAACAGGTGATGCAAAAT 715348 --i i iv iiv i------ v i ii v iv vii C L2#LINE/L2 1965 GACGAAAGCCTGATTGGAGTGGGTTCAAGAGAGAATGGGAGGAGAGGAAT 1916 chr6ptel1M 715349 TAAGG--GACGAGTGAAAAATGGCTTTTTCTAAAAGGTTAGAGTTTAAAG 715396 iii --ii - v i iii i v ii v v -v v C L2#LINE/L2 1915 TGGAGACAGCGAGT-ATAGACAACTCTTTCGAGGAGTTTTG-CTGTAAAG 1868 chr6ptel1M 715397 AAAGGTAGGAGAGAA 715411 --- v v C L2#LINE/L2 1867 ---GGGAGCAGAGAA 1856 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 51.18 CpG sites = 202, Kimura (unadjusted) = 53.98 Transitions / transversions = 1.59 (202/127) Gap_init rate = 0.06 (52 / 908), avg. gap size = 2.37 (123 / 52) 551 24.35 1.74 0.00 chr6ptel1M 715492 715606 (284394) C MIR3#SINE/MIR (6) 202 86 m_b290s601i20 11884 chr6ptel1M 715492 TAAGATCAT-GAACTTTTTAGCTGGAAAGGACCTTAAGAATCATTTAGTC 715540 ii - iv ivv i iii i C MIR3#SINE/MIR 202 TAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTC 153 chr6ptel1M 715541 CAGCCTCAT-ATTTTACCGGTAGGGAAATTGAGACCAGGAGCGGTGAAGT 715589 i i v - v i ii i i vi v C MIR3#SINE/MIR 152 CAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGT 103 chr6ptel1M 715590 GACTTATCTAAGATCAC 715606 ii i i C MIR3#SINE/MIR 102 GACTTGCCCAAGGTCAC 86 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.01 CpG sites = 21, Kimura (unadjusted) = 31.01 Transitions / transversions = 3.00 (21/7) Gap_init rate = 0.02 (2 / 114), avg. gap size = 1.00 (2 / 2) 369 34.07 2.22 0.00 chr6ptel1M 715550 715684 (284316) C MIRc#SINE/MIR (123) 145 8 m_b290s601i21 11884 chr6ptel1M 715550 ATTTTACCGGTAGGGAAATTGAGACCAGGAGCGGTGAAGTGACTTATCTA 715599 v i ii i i ivi v v ii i C MIRc#SINE/MIR 145 ATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCA 96 chr6ptel1M 715600 AGATCACTGAAATTGAAAATATGAGTACTAGGAGCTGAACTGAGGTAGGT 715649 i vv iv v v i ivv vi ii vii iv vvvi C MIRc#SINE/MIR 95 AGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTC 46 chr6ptel1M 715650 C--AC-CCAACTGCAGCACTCATTTCACTGCCCCATAC 715684 -- - v v ii v i v i C MIRc#SINE/MIR 45 CTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACAC 8 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.75 CpG sites = 25, Kimura (unadjusted) = 46.64 Transitions / transversions = 1.19 (25/21) Gap_init rate = 0.01 (2 / 134), avg. gap size = 1.50 (3 / 2) 353 32.28 10.13 0.00 chr6ptel1M 715711 715868 (284132) C L3#LINE/CR1 (69) 4030 3857 m_b290s601i22 11885 chr6ptel1M 715711 CAGGATTTCCTTCCACAAA--CTTTTATGAAC--TCATCCAGCCACTATT 715756 v i i v-- ii v ii ii-- v ii C L3#LINE/CR1 4030 CAGGAATCCCTTCTACAACATCCCTGACAAGTGGTCATCCAGCCTCTGCT 3981 chr6ptel1M 715757 TAAAAATCTCCAGGGACAGGGAACTCATTACTTCTCTTTTTAGTCCATTG 715806 i v i v i i i i ? vvvvi i v C L3#LINE/CR1 3980 TGAACACCTCCAGTGACGGGGAGCTCACTACCTCNCGAGGCAGCCCATTC 3931 chr6ptel1M 715807 C--TCTGGGATTGATCTCATT-TCAGGCAA--------CA-ACTTAGCTA 715844 -- i v iv v v - i iv i--------i - i v ii C L3#LINE/CR1 3930 CATTTTTGGACAGCTCTGATTGTTAGAAAGTTCTTCCTTATATTGAGCCG 3881 chr6ptel1M 715845 AAATCTGTCTCTGTAGAACTTTTA 715868 i iv iv ii C L3#LINE/CR1 3880 AAATCTGCCTCCCTGTAACTTCCA 3857 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.03 CpG sites = 32, Kimura (unadjusted) = 44.54 Transitions / transversions = 1.68 (32/19) Gap_init rate = 0.04 (6 / 157), avg. gap size = 2.67 (16 / 6) 14 9.66 5.71 2.78 chr6ptel1M 716903 716937 (283063) (TAAATAA)n#Simple_repeat 1 36 (0) m_b290s252i10 11886 chr6ptel1M 716903 TAAATAATTAAAT-ATAAATAAGATATAA-AGATAAT 716937 - - v v - i (TAAATAA)n#Si 1 TAAATAA-TAAATAATAAATAATAAATAATAAATAAT 36 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.09 (3 / 34), avg. gap size = 1.00 (3 / 3) 376 23.47 4.27 1.67 chr6ptel1M 717457 717573 (282427) MIR#SINE/MIR 23 142 (120) m_b290s601i23 11887 chr6ptel1M 717457 AGCTGGGGCAGTGGA--TGGAGTGC-TGGGTCTTCAGAACTTGTCTCAGA 717503 vv vv --ii v - -- ii v ii v v v MIR#SINE/MIR 23 AGCACGGGCTCTGGAGCCAGACTGCCTGGGT--TCGAATCCCGGCTCTGC 70 chr6ptel1M 717504 CACTGCCTTG-TATGTGACTCTGGGCAAGTCACTAAACC-CTGTTTGTCT 717551 vv v - i ii i v - v v i MIR#SINE/MIR 71 CACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCT 120 chr6ptel1M 717552 CAATTTCCTCATCTGTAAAATG 717573 i MIR#SINE/MIR 121 CAGTTTCCTCATCTGTAAAATG 142 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 25.95 CpG sites = 12, Kimura (unadjusted) = 28.27 Transitions / transversions = 0.80 (12/15) Gap_init rate = 0.05 (6 / 116), avg. gap size = 1.17 (7 / 6) 391 19.19 1.98 1.98 chr6ptel1M 717473 717573 (282427) MIR1_Amn#SINE/MIR 48 148 (82) m_b290s601i24 11887 chr6ptel1M 717473 GGAGTGCTGGGTCTTCAGAACTTGTCTCAGACACT-GCCTTGTATGTGAC 717521 vv -- ?i?v ii v v v - ?vv i? MIR1_Amn#SINE 48 GGAGACCTGGGT--TCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGAC 95 chr6ptel1M 717522 TCTGGGCAAGTCACTAAACC-CTGTTTGTCTCAATTTCCTCATCTGTAAA 717570 ii v? - v v? i i MIR1_Amn#SINE 96 CTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAA 145 chr6ptel1M 717571 ATG 717573 MIR1_Amn#SINE 146 ATG 148 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 22.55 CpG sites = 8, Kimura (unadjusted) = 23.90 Transitions / transversions = 0.73 (8/11) Gap_init rate = 0.04 (4 / 100), avg. gap size = 1.00 (4 / 4) 21 7.18 6.52 2.08 chr6ptel1M 717739 717784 (282216) (ATAAAAT)n#Simple_repeat 1 48 (0) m_b290s252i11 11888 chr6ptel1M 717739 ATAAAAAATAAAATAT--AATA-AAAATAATAAAAAATACAATATAAAA 717784 v -- - - v v (ATAAAAT)n#Si 1 ATAAAATATAAAATATAAAATATAAAAT-ATAAAATATAAAATATAAAA 48 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.07 (3 / 45), avg. gap size = 1.33 (4 / 3) 468 27.15 0.61 12.93 chr6ptel1M 719682 719846 (280154) MIR3#SINE/MIR 17 163 (45) m_b290s601i25 11889 chr6ptel1M 719682 GTAGAAAGAGTCCTAGATCTGGAGTTGGAGGACTTGGGTTCTAATCCTAT 719731 i i iv -i iiv ii ii i i iiv MIR3#SINE/MIR 17 GCAGAGAGAGCAC-GGACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCGG 65 chr6ptel1M 719732 CTCTGGGGTTCACGCCATATACATCCACTAATTGGGTGACCTTGGACTCT 719781 --------- i- ----- ?ii v i --- MIR3#SINE/MIR 66 CTCTG---------CCAC-TA-----ACTNGCTGTGTGACCTTGGGC--- 97 chr6ptel1M 719782 GGGTGACTTAATCTCCCCAAGG-TCAGTCTCCTCACTGGCAAAATGAGGG 719830 ii v v i i iii v- i iiv i MIR3#SINE/MIR 98 AAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGG 147 chr6ptel1M 719831 GATTGGACTAGACGAT 719846 i i MIR3#SINE/MIR 148 GGTTGGACTAGATGAT 163 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.41 CpG sites = 31, Kimura (unadjusted) = 35.89 Transitions / transversions = 3.88 (31/8) Gap_init rate = 0.12 (20 / 164), avg. gap size = 1.00 (20 / 20) 192 35.45 12.80 0.71 chr6ptel1M 719996 720120 (279880) C MIRc#SINE/MIR (71) 197 58 m_b290s601i26 11890 chr6ptel1M 719996 TTGAACCTCACAGTAACTATGTTAGGGAGGAGAAATAAATGTTAT----- 720040 v ii iv v v viiiii ii i ----- C MIRc#SINE/MIR 197 TTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCC 148 chr6ptel1M 720041 -----------ATAAGGCAATTTGGGGGTCAGGGAGATAAAGTGACTTCT 720079 ----------- i v i - i v i i v vi C MIRc#SINE/MIR 147 CCATTTTACAGATGAGGAAACT-GAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr6ptel1M 720080 TCAGGGCCGCATTGAAAGCAGAAGCCAGACCAAGGAGTAGA 720120 i i i i iv vv i iiv v v vi v v C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGA 58 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 48.50 CpG sites = 26, Kimura (unadjusted) = 50.14 Transitions / transversions = 1.44 (26/18) Gap_init rate = 0.02 (3 / 124), avg. gap size = 5.67 (17 / 3) 25 9.10 0.00 0.00 chr6ptel1M 720323 720357 (279643) (A)n#Simple_repeat 1 35 (0) m_b290s252i12 11891 chr6ptel1M 720323 AAAAACCAAAAAAAAAAAAAAAAAAAAAAAAAGAA 720357 vv i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 35 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 22 3.85 0.00 0.00 chr6ptel1M 720940 720966 (279034) (GT)n#Simple_repeat 1 27 (0) m_b290s252i13 11892 chr6ptel1M 720940 GTGTGTGTGTGTGCGTGTGTGTGTGTG 720966 i (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTG 27 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 258 34.14 12.57 3.22 chr6ptel1M 721005 721346 (278654) C L2b_3end#LINE/L2 (18) 448 76 m_b290s601i27 11893 chr6ptel1M 721005 TGTTTATTAAGTATCTCTTTTGCGCCAGG---TATGTTAGA-------GA 721044 i i i iii vi v i --- i i i------- C L2b_3end#LINE 448 TATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGGGA 399 chr6ptel1M 721045 TACA---------AAGACTAAAAGGACCCTTGCCCTCCACGCAGTTACAT 721085 --------- vi v?v ii i - v i - i C L2b_3end#LINE 398 TACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTC-ACGGAGCT-CAC 351 chr6ptel1M 721086 TGTCTCAGAGAACACACATACACGTTAAGTG-----TATA---CAAAATG 721127 v vivi iiv v v i v ?vv -----? --- i i C L2b_3end#LINE 350 AGTCTAGTGGGGGAGACAGACATGTAANCAGACAATNATAACCCAGAGTG 301 chr6ptel1M 721128 AATCGATTCGAATTTGGGGGG------AGAAAGCATTAGGATTTGGGGAT 721171 i-iv iv v i i v ------i ii iii-v iii vv- C L2b_3end#LINE 300 G-CAGGGTAGGACTGGGGGGGCCCAGAGGAGGGCGCC-TGACCCGGCC-T 254 chr6ptel1M 721172 GGGGAGGGCAGGGTAATGTTTCAAAGAGCATGTGGCTTTTGGACTGAGCT 721221 - v - iv i vvi v v i v ii vi C L2b_3end#LINE 253 GGGG-GGTCAGGG-AGGGCTTCCCGGAGGAGGTGACATTTGAGCTGAGAC 206 chr6ptel1M 721222 GTGAAGCA-AAGTAAGGATTCTAGG--AGGGAAAGAGG-GCGGCAGGTAG 721267 v v -i i ii --- -- vi - v v -- C L2b_3end#LINE 205 CTGAAGGATGAGTAGGAGTT---GGCCAGGCGAAGAGGTGGGGAAGG--G 161 chr6ptel1M 721268 AGTT-CAGCCATGGGGACCTGCTTATATAGAAATCCAGAG--GAGAAAGA 721314 v - v vi v v v?i ii i iii v -- i i? C L2b_3end#LINE 160 CGTTCCAGGCAGAGGGAACAGCANGTGCAAAGGCCCTGAGGCGGGAGNGA 111 chr6ptel1M 721315 GTGTTGTATAT--GAAG-ATAGCAAGAAAGCTTGT 721346 i? v ii i -- i - i i i iv C L2b_3end#LINE 110 GCNTGGCGTGTTCGAGGAACAGCAAGGAGGCCAGT 76 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 45.37 CpG sites = 69, Kimura (unadjusted) = 49.17 Transitions / transversions = 1.57 (69/44) Gap_init rate = 0.07 (25 / 341), avg. gap size = 2.20 (55 / 25) 261 31.06 4.67 3.70 chr6ptel1M 721007 721113 (278887) C L2c_3end#LINE/L2 (20) 458 351 m_b290s601i28 11893 chr6ptel1M 721007 TTTATTAAGTATCTCTTTTGCGCCAGGTATGTTAGAGATACAAAGACTAA 721056 i iii vi v i --i i i i iv C L2c_3end#LINE 458 TTTATTGAGCGCCTACTATGTGCCAGG--CGCTGGGGATACAAAGATGAA 411 chr6ptel1M 721057 AAGGAC-----CCTTGCCCTCCACGCAGTTACATTGTCTCAGAGAACACA 721101 v i ----- i v v viv i -- vivi iv v C L2c_3end#LINE 410 TAAGACACGGTCCCTGCCCTCAAGGAGCTCACA--GTCTAGTGGAGGAGA 363 chr6ptel1M 721102 CATACACGTTAA 721113 v ? v C L2c_3end#LINE 362 CAGACANGTAAA 351 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.18 CpG sites = 18, Kimura (unadjusted) = 41.71 Transitions / transversions = 1.29 (18/14) Gap_init rate = 0.05 (5 / 106), avg. gap size = 1.80 (9 / 5) 355 28.00 17.60 0.00 chr6ptel1M 721678 721802 (278198) MIRc#SINE/MIR 2 148 (120) m_b290s601i29 11894 chr6ptel1M 721678 GGAGCTGGGTGGCTAAGTGGGTAGACTATCAGATCTGGAGTCAGGAAGAT 721727 ii v v ivv iv vi iii ii i MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr6ptel1M 721728 CTCAGTTTAAATC---------------------TGTGTGACCCTGGTTA 721756 vi ii i --------------------- i vi MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 101 chr6ptel1M 721757 AGTCATTTAA-CTCTTTTTGCATCATTTTACTCCTATGTAAAATGAG 721802 i - i vv v v v v v i MIRc#SINE/MIR 102 AGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.44 CpG sites = 20, Kimura (unadjusted) = 35.85 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.02 (2 / 124), avg. gap size = 11.00 (22 / 2) 306 25.47 3.82 7.09 chr6ptel1M 721740 721870 (278130) MIR#SINE/MIR 81 207 (55) m_b290s601i30 11894 chr6ptel1M 721740 CTGTGTGACCCTGGTTAAGTCATTTAA-CTCTTTTTGCATCATTTTACTC 721788 i vi i i - i v v v v MIR#SINE/MIR 81 CTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTC 130 chr6ptel1M 721789 CTATGTAAAATGAGCTGGAGAAGGAAATGGTAAACCTCTCTAGTATTTTT 721838 v v i--- v v-- i -- vi vi vvv MIR#SINE/MIR 131 ATCTGTAAAATGG---GGATAAT--AATAGT--ACCTACCTCATAGGGTT 173 chr6ptel1M 721839 GCTAAGAGAATCCCAAATGGGGT----CATGAAAAG 721870 i iv i --i i v ---- v MIR#SINE/MIR 174 GTTGTGAGGAT--TAAATGAGTTAATACATGTAAAG 207 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.18 CpG sites = 14, Kimura (unadjusted) = 31.18 Transitions / transversions = 0.82 (14/17) Gap_init rate = 0.08 (11 / 130), avg. gap size = 1.27 (14 / 11) 326 29.56 5.41 4.00 chr6ptel1M 721938 722085 (277915) L3#LINE/CR1 3335 3484 (615) m_b290s601i31 11895 chr6ptel1M 721938 GATAAATGTAAATTATTATAGTTAAGCTGAAATAAAAGCAACTCTATAAG 721987 v vi ii v i i v -- v vi i L3#LINE/CR1 3335 GATAAATGTAAAGTCCTGCATTTAGGTTCAAA--AAATCAACTGCACAAG 3382 chr6ptel1M 721988 TAAAAGACTGGGAAAGTATTT---TTAG-AGAAGT----GTGAAAAATAA 722029 v i i-- i v i --- - v ---- v v L3#LINE/CR1 3383 TACAGGAT--GGAGAGGATCTGGCTTAGCAGCAGTTCACGTGAAAAAGAC 3430 chr6ptel1M 722030 CTAGGGACTTCAATGAATTGTGAACTCATAATGGGTTAGCAGACTGTGGT 722079 ii i i vi ii ii i vv i ii i -- i L3#LINE/CR1 3431 CTAGGGGTTTTAGTTGACCGCAAGCTCAATATGAGCCAACAG--TGTGAT 3478 chr6ptel1M 722080 ATGACT 722085 i i L3#LINE/CR1 3479 GTGGCT 3484 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.21 CpG sites = 28, Kimura (unadjusted) = 39.45 Transitions / transversions = 2.00 (28/14) Gap_init rate = 0.06 (9 / 147), avg. gap size = 1.56 (14 / 9) 341 24.29 0.00 0.00 chr6ptel1M 722119 722188 (277812) L3#LINE/CR1 3576 3645 (454) m_b290s601i32 11895 chr6ptel1M 722119 TCAGATTAGATCTGGAATATTGAGTTTGATTTAGGGTGACACATTTTAGG 722168 ii v i v iii iv i v i L3#LINE/CR1 3576 TCAGACCACATCTGGAGTATTGCGTTCAGTTCTGGGCGCCACATTTTAAG 3625 chr6ptel1M 722169 AAAGACATTGATAAACGGGA 722188 ii i v L3#LINE/CR1 3626 AGGGACATTGACAAACTGGA 3645 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.45 CpG sites = 12, Kimura (unadjusted) = 30.60 Transitions / transversions = 2.40 (12/5) Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0) 226 24.07 0.00 0.00 chr6ptel1M 722212 722265 (277735) Plat_L3#LINE/CR1 3173 3226 (347) m_b290s551i2 11896 chr6ptel1M 722212 TGAAGAGAAGTTAAAGAAACTGGAAATGTTTCAGCTGGAAAAGAGAAGAC 722261 i i i i i iiv viv i i Plat_L3#LINE/ 3173 TGAGGAAAGGTTAAAGGAATTGGGGTTGTTTAGCCTGGAGAAGAGAAGGC 3222 chr6ptel1M 722262 TAAG 722265 Plat_L3#LINE/ 3223 TAAG 3226 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 30.69 CpG sites = 10, Kimura (unadjusted) = 30.69 Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 575 26.09 7.97 8.40 chr6ptel1M 722282 722532 (277468) L3#LINE/CR1 3780 4029 (70) m_b290s601i33 11895 chr6ptel1M 722282 ATTTAAAGTTCTTGACTGTCATG-AAAAAAATGAT-AGATTTGCTTTGTA 722329 i ----- i -ii i iv - i ii i i L3#LINE/CR1 3780 ATTTGAAG-----GGCTGTCATGTGGAAGAGGGATTAGACTTATTCTGTG 3824 chr6ptel1M 722330 AGG-TCCAGAGGGCAGAAGTAGGAA--------GGAAG---AAGGGA--- 722364 v - v v-------- ---v --- L3#LINE/CR1 3825 TGGCTCCAGAGGGCAGAACTAGGACCAATGGGTGGAAGTTACAGGGAGGC 3874 chr6ptel1M 722365 AAATTTGGGTTTGATGTTAGGAAAATCTTTCCTAACAACT--AGTTACCC 722412 i v i ii i v i v - ii-- i ii L3#LINE/CR1 3875 AGATTTCGGCTCAATATAAGGAAGAACTTT-CTAACAATCAGAGCTGTCC 3923 chr6ptel1M 722413 AAAAGTGTAAAGTGCTTCCTCTGGAAGTAATGAATTCCCCTATAATGAAT 722462 i v v v v v? i i ii vvi v i v L3#LINE/CR1 3924 AAAAATGGAATGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGTCACTGGAG 3973 chr6ptel1M 722463 GTCTGCAAGCAAAGACATGCTGTCTATTT-TCAGAGTAATATGGGACTAT 722511 v v i i vv v v i i - i -------------- L3#LINE/CR1 3974 GTGTTCAAGCAGAGGCTGGATGACCACTTGTCAGGG-------------- 4009 chr6ptel1M 722512 CATGCTGTAGAAGAGATTCTT 722532 - i i i L3#LINE/CR1 4010 -ATGTTGTAGAAGGGATTCCT 4029 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.15 CpG sites = 37, Kimura (unadjusted) = 33.15 Transitions / transversions = 1.61 (37/23) Gap_init rate = 0.12 (29 / 250), avg. gap size = 1.41 (41 / 29) 16 10.71 0.00 3.23 chr6ptel1M 722533 722564 (277436) (ATTTTT)n#Simple_repeat 1 31 (0) m_b290s252i14 11897 chr6ptel1M 722533 ATTTTTATTTCTATTAATTTTTTTTATTTTTA 722564 i -v v (ATTTTT)n#Sim 1 ATTTTTATTTTTATT-TTTATTTTTATTTTTA 31 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 14 18.24 0.00 5.13 chr6ptel1M 722769 722809 (277191) (GAAAA)n#Simple_repeat 1 39 (0) m_b290s252i15 11898 chr6ptel1M 722769 GAAAATGAGAAAGAAAACAAAAGGCAAGTAAACAACAGAAA 722809 - - v iv v v v (GAAAA)n#Simp 1 GAAAA-GA-AAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAA 39 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 767 33.01 3.65 3.18 chr6ptel1M 722990 723427 (276573) C L1ME5_3end#LINE/L1 (313) 628 189 m_b290s551i3 11899 chr6ptel1M 722990 TTTCACTCAGCATCA-ATTCATGTAA-ATCTCTCCAAGCCTCTCTGAAAT 723037 ii -i -- v - iv v iiv v vivv C L1ME5_3end#LI 628 TTTCACTCAGCACTATGTT--TTTAAGATCCATCCATGTTGCTATGTGTA 581 chr6ptel1M 723038 TATCCTGTTGGTTGTTTCTTACAGAACAGTAATAATATTCCATAACATTC 723087 i iv iv i v v -- v i - i i iiii v C L1ME5_3end#LI 580 CATCTAGTCCGTTGCTTCTAACTG--CTGCA-TAGTACTCCATGGTGTGC 534 chr6ptel1M 723088 ATATACCATAATTTACT----CATTCTCCCACTGATGGGCATCCATTCAT 723133 vi i v i---- i v i i vvivv C L1ME5_3end#LI 533 ATCCACCACATTTTACCTATCCACTCTCCCAGTGATGGACACCCAGGTTG 484 chr6ptel1M 723134 TTTCCAGTTTCTAGCCACTATAAGGAGGGTTGCCACAATCATTTTTGCAC 723183 ii ii i iv i i iv iv i v ii v ii i i C L1ME5_3end#LI 483 CCTCCAACTCCCCGCCACCACAAACAACGCTGCAATGAACATCCTCGTAC 434 chr6ptel1M 723184 ATATGGGTCCCTTTCC---CTTCTTTAAGA-TCTCTTTGGGATATAAGCC 723229 ---- i vi--- i v v i - i vi C L1ME5_3end#LI 433 AT----GTCCCCTTATGGACCTGTGTGAGAATTTCTTTGGGATATATACC 388 chr6ptel1M 723230 CAGTAGAAACACTGCTGAATCAAAGAGTATGCACAGTTTGATAACCCTTT 723279 v viiv i ii v i ii vvi -- --- C L1ME5_3end#LI 387 CAGGAGCGGAATTGCTGGGTCATAGGGTATGCGTATACT--TAA---TTT 343 chr6ptel1M 723280 GGGCA--TAGTTCCAAATTGTTCTACAGAATGGTTGGATCTATTCACAGT 723327 ivi -- v v i i v i v i vi ii v C L1ME5_3end#LI 342 GACTAAGTACTGCCAGATTGCTCTCCAGAATGGCTGCACCAGTCTACACT 293 chr6ptel1M 723328 TCCACTAACAATGTATCAGTGTCCCAGTTTTCTTACTTCCT--CCAACAT 723375 i i i i i v v i vi ? i ii v -- i C L1ME5_3end#LI 292 CCCACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATCCTCGCCAACAC 243 chr6ptel1M 723376 TCATCATTATCT--TTTCCTGTCATTAGCCAGTCTGAGAGGTGTACAGTG 723423 iiv i--i i iviv v i v v C L1ME5_3end#LI 242 TTGGCATTATCCAGCTTTCTAATTTTTGCCAGTCTAATAGGTGTAAAGTG 193 chr6ptel1M 723424 GCAT 723427 ii C L1ME5_3end#LI 192 ATAT 189 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 44.32 CpG sites = 87, Kimura (unadjusted) = 45.67 Transitions / transversions = 1.64 (87/53) Gap_init rate = 0.05 (22 / 437), avg. gap size = 1.36 (30 / 22) 816 29.84 2.83 0.93 chr6ptel1M 723069 723386 (276614) C L1ME4c_3end#LINE/L1 (275) 555 232 m_b290s551i4 11899 chr6ptel1M 723069 ATAATATTCCATAACATTCATATACCATAATTTACT----CATTCTCCCA 723114 vivi ?v i ---- i i C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chr6ptel1M 723115 CTGATGGGCATCCATTCATTTTCCAGTTTCTAGCCACTATAAGGAGGGTT 723164 i v i ii vvivv i i v i i iv iv i C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCT 456 chr6ptel1M 723165 GCCACAATCATTTTTGCACATATGGGTCCCTTTCCCTTCTTT--AAG-AT 723211 v ii v i i ii i --- i i -- v- C L1ME4c_3end#L 455 GCAATGAACATCTTCGTGCATATAG---CTTTTTCCTTCTTTTGAATTAT 409 chr6ptel1M 723212 CTCTTTGGGATATAAGCCCAGTAGAAACACTGCTGAATCAAAGAGTATGC 723261 i i i v vv v viiv i i ii i v C L1ME4c_3end#L 408 TTCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGA 359 chr6ptel1M 723262 ACAGTTTGATAACCCTTTGGGCATAGTTCCAAATTGTTCTACAGAATGGT 723311 v v ii i vivi i v v i i v i v C L1ME4c_3end#L 358 ACATTTTTATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGT 309 chr6ptel1M 723312 TGGATCTATTCACAGTTCCACTAACAATGTATCAGTGTCCCAGTTTTCTT 723361 v i v i ? v i i v ? v ivii C L1ME4c_3end#L 308 TGTACCAATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCACC 259 chr6ptel1M 723362 ACTTCCT--CCAACATTCATCATTATC 723386 i v? -- i vivi C L1ME4c_3end#L 258 GCANCCTCGCCAGCATTGGGTATTATC 232 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.68 CpG sites = 56, Kimura (unadjusted) = 39.92 Transitions / transversions = 1.47 (56/38) Gap_init rate = 0.02 (7 / 317), avg. gap size = 1.71 (12 / 7) 269 34.59 9.52 0.88 chr6ptel1M 723504 723608 (276392) MIR3#SINE/MIR 60 173 (35) m_b290s601i34 11900 chr6ptel1M 723504 TCTTAGTTCTATTTCTAAATAATTATATGACTTTAAATGAGTTGCTTTGT 723553 iii i iiiv v ?ii i i i iiiii ii iii MIR3#SINE/MIR 60 TCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCAC 109 chr6ptel1M 723554 TTCTCTGA-----AACTTC----TCTGTAAATTGAAGGGGCTAGACTAGG 723594 i i----- ii ---- v i i i i MIR3#SINE/MIR 110 CTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGA 159 chr6ptel1M 723595 -AAGCTATAAAGGTC 723608 -i v v - MIR3#SINE/MIR 160 TGATCTCT-AAGGTC 173 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 52.41 CpG sites = 31, Kimura (unadjusted) = 55.11 Transitions / transversions = 6.20 (31/5) Gap_init rate = 0.04 (4 / 104), avg. gap size = 2.75 (11 / 4) 228 30.38 5.06 0.00 chr6ptel1M 723633 723711 (276289) C MIR3#SINE/MIR (39) 169 87 m_b290s601i35 11901 chr6ptel1M 723633 TTCAAGGTCATTTAACCTGGCTACCTCATTTTAAAGA-GAGGGAAAAGTG 723681 vi i i ii iii iv v - i vv v C MIR3#SINE/MIR 169 TTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAG 120 chr6ptel1M 723682 TCCAAGAGAAGTTAATTATCTT---CAAAGTCA 723711 v v i v v iv --- i C MIR3#SINE/MIR 119 GCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCA 87 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.75 CpG sites = 13, Kimura (unadjusted) = 39.75 Transitions / transversions = 1.18 (13/11) Gap_init rate = 0.03 (2 / 78), avg. gap size = 2.00 (4 / 2) 22 23.67 4.29 0.00 chr6ptel1M 723881 723950 (276050) (AGAC)n#Simple_repeat 1 73 (0) m_b290s252i16 11902 chr6ptel1M 723881 AGAAAGACACACACACACACACACAGACAGAGAGTGACATAGAGAGACAG 723930 v v v v v v vv v i v (AGAC)n#Simpl 1 AGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAG 50 chr6ptel1M 723931 --AGACAGAGAGCCA-ACACACA 723950 -- v v - v (AGAC)n#Simpl 51 ACAGACAGACAGACAGACAGACA 73 Matrix = Unknown Transitions / transversions = 0.08 (1/13) Gap_init rate = 0.03 (2 / 69), avg. gap size = 1.50 (3 / 2) 201 36.37 4.01 9.58 chr6ptel1M 724101 724474 (275526) L2c_3end#LINE/L2 106 460 (18) m_b290s601i36 11903 chr6ptel1M 724101 CTGAAATTCTTTACATGTAGCCATGTCTTCATCAGTTCCTGT-GCCTCTA 724149 i v i v - ivv i? i ii- vv v -v i L2c_3end#LINE 106 CCGCAGTTCTTTCC-TGCCTCCGNGCCTTTG-CACATGCTGTTCCCTCTG 153 chr6ptel1M 724150 CC----ATACTCCTTCCTTTTC--TCTGCCTGGGAAAAACCATCTCTTCT 724193 ---- i i i iii -- ii vv vv vv v i L2c_3end#LINE 154 CCTGGAATGCTCTTCCCCCCTCCTTCCACCTGGCTAACTCCTACTCATCC 203 chr6ptel1M 724194 CTTAAGTGTTAGTTC-GCTAACTGCTGCTCCATCAAGCCTAGCCTGATCC 724242 i i ?v i i - v iv vv v ivv vv i L2c_3end#LINE 204 TTCAAGNCTCAGCTCAGATGTCACCTCCTCCGGGAAGCCTTCCCTGACCC 253 chr6ptel1M 724243 ACCCTTTCCCCAAATGAAAATGATATTTCCCTCTCTCAGATGTTTCAGAA 724292 -------- i?vv iviv vi vi ii ---i i i viv L2c_3end#LINE 254 --------CCCAAGNCTAGTCTAGGTGCCCTCCTCT---GTGCTCCCATA 292 chr6ptel1M 724293 GAATTTTCTCCGATTCTTCCTTT---GTGCTTATTGCATT--TTTCTCCT 724337 v iii v i- v i v --- ii -- --i v --- L2c_3end#LINE 293 GCACCCTGTCT-ATACTCCCATTATAGCACTTAT--CATTAACTTGT--- 336 chr6ptel1M 724338 CATCATGCTTTTTGGGGTATATGTGATCTATGATTCTTATTAGACTAGAA 724387 - ii iv v iv vv i? --- i vviiiii i ivi L2c_3end#LINE 337 -ATTGTAATTGTCTGTTTACNTGT---CTGTCTCCTCCACTAGACTGTGA 382 chr6ptel1M 724388 CCTTCTTGGGGGGAGGAAC--TATCATTTTTCATCTCTATATCCAGCAGA 724435 v i i v i -- i - v i i -v v L2c_3end#LINE 383 GCTCCTTGAGGGCAGGGACCGTGTC-TTATTCATCTTTGTATCC-CCAGC 430 chr6ptel1M 724436 GAATTTGGAACCTTTCACTTAAAAGGTACTTAATACATG 724474 --------- vv v iv ii i v L2c_3end#LINE 431 G---------CCTGGCACATAGTAGGCGCTCAATAAATG 460 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 49.34 CpG sites = 67, Kimura (unadjusted) = 51.81 Transitions / transversions = 1.20 (67/56) Gap_init rate = 0.11 (41 / 373), avg. gap size = 1.20 (49 / 41) 21 23.85 2.53 3.85 chr6ptel1M 724665 724743 (275257) (TTTC)n#Simple_repeat 1 78 (0) m_b290s252i18 11904 chr6ptel1M 724665 TTTCTTTGCTTTCTTGTAAAT-TTTCTTTTGTTCTCTATTGTGTTTTTTT 724713 - - vvv - iv i v - v i (TTTC)n#Simpl 1 TTTCTTT-CTTTCTT-TCTTTCTTTCTTTCTTTCTTTCTT-TCTTTCTTT 47 chr6ptel1M 724714 TTTAGTTTATTCCTTTTTTTC-TTCTTTCTT 724743 i vv v i i - (TTTC)n#Simpl 48 CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 78 Matrix = Unknown Transitions / transversions = 0.67 (6/9) Gap_init rate = 0.06 (5 / 78), avg. gap size = 1.00 (5 / 5) 575 29.54 1.05 3.78 chr6ptel1M 725313 725502 (274498) MIR3#SINE/MIR 17 201 (7) m_b290s601i37 11905 chr6ptel1M 725313 GTGGAAAGAATCATAGACTTGGGGTTTTAGG-GAAATGAGCTC-AGTTTC 725360 ii i i- ii v i i-- - vv i i - -- MIR3#SINE/MIR 17 GCAGAGAGAG-CACGGACTGGGAGTC--AGGAGACCTGGGTTCTAGT--C 61 chr6ptel1M 725361 CTGGCTCTGTCACTCATTGGCTCTGTGACATGGGACAATTTACCTTACTT 725410 i i v i ? v v v i v i i i i MIR3#SINE/MIR 62 CCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCT 111 chr6ptel1M 725411 CTCTGTGCTTCAGTGTGTGCACATCTGCAAAATGTTGCAATTAGAAGAGC 725460 v i -- v v v i vv vii i vv v MIR3#SINE/MIR 112 CTCTGGGCCTCA--GTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGA 159 chr6ptel1M 725461 TGATTTCTAAGATCTCTTTTAGCTTTAATGTGAAATGAGTCT 725502 i i i ii i i ii vvv v MIR3#SINE/MIR 160 TGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCT 201 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.96 CpG sites = 32, Kimura (unadjusted) = 38.90 Transitions / transversions = 1.45 (32/22) Gap_init rate = 0.05 (9 / 189), avg. gap size = 1.00 (9 / 9) 13 28.07 0.00 3.77 chr6ptel1M 725584 725638 (274362) (TTTCCT)n#Simple_repeat 1 53 (0) m_b290s252i19 11906 chr6ptel1M 725584 TTTGCTTTTTCTCTTTCTTTCTGCTGAACATTTTTTTTTTACCTTTTCAT 725633 v i - i i v vvv v ii - v (TTTCCT)n#Sim 1 TTTCCTTTTCCT-TTTCCTTTTCCTTTTCCTTTTCCTTTT-CCTTTTCCT 48 chr6ptel1M 725634 TTTCC 725638 (TTTCCT)n#Sim 49 TTTCC 53 Matrix = Unknown Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.04 (2 / 54), avg. gap size = 1.00 (2 / 2) 339 22.92 5.88 5.88 chr6ptel1M 725763 725864 (274136) C MIR3#SINE/MIR (28) 180 79 m_b290s601i38 11907 chr6ptel1M 725763 TGGAAGAGATATTGGAATGGTTGATCATTT-CTCTAGC----TCATTTTA 725807 i iv i ------ i -v i i ---- C MIR3#SINE/MIR 180 TGGAAGGGACCTTAGA------GATCATCTAGTCCAACCCCCTCATTTTA 137 chr6ptel1M 725808 CACATGAGAAAATTGGGGCAAACAGGGGT-AAGTGATTTGCTAAGAGTCA 725856 v i i i vv v i - i iv ii C MIR3#SINE/MIR 136 CAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCA 87 chr6ptel1M 725857 CACAACTA 725864 i ? C MIR3#SINE/MIR 86 CACAGCNA 79 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.66 CpG sites = 15, Kimura (unadjusted) = 28.66 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.09 (9 / 101), avg. gap size = 1.33 (12 / 9) 371 29.72 10.45 2.07 chr6ptel1M 725799 725932 (274068) C MIRc#SINE/MIR (120) 148 4 m_b290s601i39 11907 chr6ptel1M 725799 CTCATTTTACACATGAGAAAATTGGGGCAAACAGGGG-TAAGTGATTTGC 725847 i v i i i vv v i - i C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr6ptel1M 725848 TAAGAGTCACACAACTATT----------GTCTTGA---GGAAGTAAGCC 725884 iv ii i v ---------- i vv --- i vvi i i C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTC 49 chr6ptel1M 725885 TTCCTGGCTCTAGGTCTAGCATCCTAACCACTGTGCAACCTAACTGTC 725932 i i i i iiii vv ii v --- i C MIRc#SINE/MIR 48 TTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC---ACTGCC 4 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.81 CpG sites = 26, Kimura (unadjusted) = 39.81 Transitions / transversions = 2.00 (26/13) Gap_init rate = 0.05 (6 / 133), avg. gap size = 2.83 (17 / 6) 340 9.43 3.77 0.00 chr6ptel1M 725974 726026 (273974) MIR#SINE/MIR 90 144 (118) m_b290s601i40 11908 chr6ptel1M 725974 CTTGAGCAAGTTACTTAACCTTGCT-TGCCT-AGTTTCTTCATCTGTAAA 726021 i iv - - i MIR#SINE/MIR 90 CTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAA 139 chr6ptel1M 726022 ATGAG 726026 i MIR#SINE/MIR 140 ATGGG 144 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 10.27 CpG sites = 4, Kimura (unadjusted) = 10.27 Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.00 (2 / 2) 256 36.27 5.88 0.00 chr6ptel1M 726328 726429 (273571) C L2b_3end#LINE/L2 (179) 287 180 m_b290s601i41 11909 chr6ptel1M 726328 GGGGGGGTTCAG--GAGGGT-TTTGATATA---TAAAAGTTCAGTAGACA 726371 ii -- i-ii ivii--- iiii v viiivi C L2b_3end#LINE 287 GGGGGGGCCCAGAGGAGGGCGCCTGACCCGGCCTGGGGGGTCAGGGAGGG 238 chr6ptel1M 726372 CTTCCTGAAGGAAGTGATATTTAAGCTGGACCTTCAAGGATAGAGAGGAT 726421 i i i i i iiv i v iiiv v C L2b_3end#LINE 237 CTTCCCGGAGGAGGTGACATTTGAGCTGAGACCTGAAGGATGAGTAGGAG 188 chr6ptel1M 726422 TTTGACAG 726429 v v C L2b_3end#LINE 187 TTGGCCAG 180 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 47.95 CpG sites = 27, Kimura (unadjusted) = 54.83 Transitions / transversions = 2.70 (27/10) Gap_init rate = 0.03 (3 / 101), avg. gap size = 2.00 (6 / 3) 320 27.28 2.22 2.22 chr6ptel1M 726362 726451 (273549) C L2d2_3end#LINE/L2 (304) 251 162 m_b290s601i42 11909 chr6ptel1M 726362 TCAGTAGACACTTCCTGAAGGAAGTGATATTTAAGCTGGACCTTCAAGGA 726411 vii vi vi i i i? i i v C L2d2_3end#LIN 251 TCAGGGAAGGCTTCACGGAGGAGGTGGNATTTGAGCTGGGCCTTGAAGGA 202 chr6ptel1M 726412 TAGAGAGGATTTTGACAGTTAGATATGAGAATAGGA--GGCA 726451 i iv v i v i v --i vi -- C L2d2_3end#LIN 201 TGGGTAGGATTTGGATAGGTGGAGA--GGAAGGGGAAGGGCA 162 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.69 CpG sites = 15, Kimura (unadjusted) = 35.53 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.03 (3 / 89), avg. gap size = 1.33 (4 / 3) 282 25.86 1.72 0.00 chr6ptel1M 727321 727378 (272622) MIR3#SINE/MIR 129 187 (21) m_b290s601i43 11910 chr6ptel1M 727321 CTTATCTATAAAATGAAAGAATTAGATCAGAAAATCTCTAA-GCCCCTTC 727369 i i ii ii i ii vi - i MIR3#SINE/MIR 129 CTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTC 178 chr6ptel1M 727370 TAGCTTTAA 727378 i i i MIR3#SINE/MIR 179 CAGCTCTGA 187 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.53 CpG sites = 14, Kimura (unadjusted) = 35.53 Transitions / transversions = 14.00 (14/1) Gap_init rate = 0.02 (1 / 57), avg. gap size = 1.00 (1 / 1) 357 25.49 16.58 1.40 chr6ptel1M 727392 727578 (272422) C Tigger15a#DNA/TcMar-Tigger (86) 629 415 m_b290s502i3 11911 chr6ptel1M 727392 AAGCATCAACGCTTC----ATTTTAATC-TTTTGGAGCTGGGAATCTTCA 727436 i vi i---- i - -- i iv C Tigger15a#DNA 629 AAGCACCAAAACTTTTNTAATTTTAACCATTTTGGA--TGGAAATCTTTC 582 chr6ptel1M 727437 TAAAATGTG---CATCATGTTTCAGAATTCGAAAGCAGAATAT--CAAAC 727481 i--- - iv ii v vv vv i i --ii C Tigger15a#DNA 581 TAAAATGTATTACA-CACTTCCCTGCCTTCTTAAACAGAGTATACTGAAC 533 chr6ptel1M 727482 ATGATTTATCCTATTTTTGATGACTTAAG----TCATTG-------CAGT 727520 i v v i i i ---- i------- C Tigger15a#DNA 532 ATAATTTAACCTTTTCTTGATGACTCAGGGTCATCATTATGAACATCAGT 483 chr6ptel1M 727521 T------CTGAATTGTAATGTACTTATACCTTCAAAGTC-ATCAAGG--- 727560 ------ vii ii v v i i ii v - ii --- C Tigger15a#DNA 482 TATTGTACTGTGCTGTAATACAGTGATGCCCTCAGGGGCTATTGAGGTGT 433 chr6ptel1M 727561 GCAGGGCTGGTTTTCCCT 727578 i v vi C Tigger15a#DNA 432 GTAGGGCTGTTTGCCCCT 415 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.35 CpG sites = 31, Kimura (unadjusted) = 32.35 Transitions / transversions = 1.94 (31/16) Gap_init rate = 0.06 (12 / 186), avg. gap size = 2.83 (34 / 12) 50 9.49 1.22 1.22 chr6ptel1M 727761 727842 (272158) (TA)n#Simple_repeat 1 82 (0) c_b290s251i3 11912 chr6ptel1M 727761 TATATATATATATATATATGTATGTATGTATATATATATGTAGT-TTTAT 727809 i i i i - - v (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATA-TATATAT 49 chr6ptel1M 727810 ATATACATATATATATATATATATACATATATA 727842 i i (TA)n#Simple_ 50 ATATATATATATATATATATATATATATATATA 82 Matrix = Unknown Transitions / transversions = 6.00 (6/1) Gap_init rate = 0.02 (2 / 81), avg. gap size = 1.00 (2 / 2) 373 32.56 1.53 1.53 chr6ptel1M 727843 727971 (272029) C MIRc#SINE/MIR (116) 152 24 m_b290s601i44 11913 chr6ptel1M 727843 ATCCTTTTTTTTAAGATTAGGAAGCTAATACT-ATAAAAACTAAATGGCT 727891 iiv vv v i i vi - v i iii i i C MIRc#SINE/MIR 152 ATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACT 103 chr6ptel1M 727892 TGCTAAAGTTCATGCAGTTAGTAATTGTTACATTGAAGCCTCAAACCCAC 727941 iv v ii i v vi v vivii v i v C MIRc#SINE/MIR 102 TGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAG 53 chr6ptel1M 727942 GTCTTCA-GATTCTGAAAACCAAGTACTCTT 727971 v- i i-- ii v i C MIRc#SINE/MIR 52 GTCTTCCTGACTCC--AAGTCCAGTGCTCTT 24 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.91 CpG sites = 25, Kimura (unadjusted) = 44.78 Transitions / transversions = 1.47 (25/17) Gap_init rate = 0.03 (4 / 128), avg. gap size = 1.00 (4 / 4) 204 29.85 0.00 1.49 chr6ptel1M 728001 728068 (271932) C MIR3#SINE/MIR (84) 124 58 m_b290s601i45 11914 chr6ptel1M 728001 CTGAGGCTTGCAGAGAAGAAAGGACTTGCCAAAGGTCACAGAGGATATTC 728050 iiiv iv iv v v v?vi v C MIR3#SINE/MIR 124 CTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTA 75 chr6ptel1M 728051 ATGAGAAATTCTGGGACT 728068 i iv i -v i C MIR3#SINE/MIR 74 GTGGCAGA-GCCGGGACT 58 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.89 CpG sites = 10, Kimura (unadjusted) = 39.33 Transitions / transversions = 1.00 (10/10) Gap_init rate = 0.01 (1 / 67), avg. gap size = 1.00 (1 / 1) 288 35.05 12.21 4.76 chr6ptel1M 728104 728750 (271250) L2#LINE/L2 2152 2844 (238) m_b290s601i46 11915 chr6ptel1M 728104 CTTCCTTGCTCTTTCGCCAACCCTCCTTAGATTTCCTTTGCCA---CCTC 728150 i vv vi v ivi i i - i ii--- L2#LINE/L2 2152 CCTCCTACCTCACTGGCCGCTCCTTCTCAG-TCTCCTTTGCTGGTTCCTC 2200 chr6ptel1M 728151 ATGATCCATCTTCTGCCT----ACAT--AAATGCTTCCAAAGC-CA---- 728189 v v -- ii vi ---- i --i i i- ii - ---- L2#LINE/L2 2201 CTCATC--TCCCCGACCTCTNAACGTTGGAGTGCC-CCAGGGCTCAGTCC 2247 chr6ptel1M 728190 ------------TCTTCTCTCTCTCCATTCCTTCACT-GGTGATCACCTA 728226 ------------ v v i vi v - v v v L2#LINE/L2 2248 TTGGACCTCTTCTCTTCTCTATCTACACTCACTCCCTNGGTGATCTCATC 2297 chr6ptel1M 728227 TATTCAGACAGGTTCAATTATTGGA-GTA-GCCAA-GACTCCCGCATTTA 728273 i v vv ii v i v iiivv-i - ii - iv L2#LINE/L2 2298 CAGTCTCATGGCTTTAAATACCATCTATATGCTGATGACTCCCAAATTTA 2347 chr6ptel1M 728274 TCTAACAAGTTCTAATCCTTCTCTTGAATTTTTGTCCTGAAGCTCT--CT 728321 v vv v ii vi i ii i i i iiv v ii v vv i-- L2#LINE/L2 2348 TATCTCCAGCCCGGACCTCTCCCCTGAACTCCAGACTCGTATATCCAACT 2397 chr6ptel1M 728322 TTC--CTGGATTTTTCTAAGCAAATGTCTTGAT-GGTATCTAAAAATGAA 728368 vi -- v iv i i vviii - i - i v v v L2#LINE/L2 2398 GCCTACTCGACATCTCCACTTGGATGTC-TAATAGGCATCTCAAACTTAA 2446 chr6ptel1M 728369 CATTTCTAAGACTAAAGTGATCTCCAGCCCTCCTCCCACATCCCCAATCT 728418 v i i i ----- v vi i i v vv ii-- L2#LINE/L2 2447 CATGTCCAAAACTGAA-----CTCCTGATCTTCCCCCTCAAACCTG--CT 2489 chr6ptel1M 728419 CTCTCTTTCCATCCTCCCTGTTTCTGTTGAGGGCAGCACCATTCCCACCA 728468 - iiv vi i ii i v ?i v i v --------- L2#LINE/L2 2490 C-CTCCCGCAGTCTTCCCCATCTCAGTNAATGGCAACTCCA--------- 2529 chr6ptel1M 728469 TCCCCTCCTCCTTCTACTTACCTCAGTTC-AACACATT--AATCAT-TTT 728514 -------- i v i- vi - v v -- i -i L2#LINE/L2 2530 --------TCCTTCCAGTTG-CTCAGGCCAAAAACCTTGGAGTCATCCTT 2570 chr6ptel1M 728515 GACTCTTCTGTATCCTTCACACTCC-CATC----TCGTCAGC----CTTG 728555 i v v ii i - ----i i ---- i L2#LINE/L2 2571 GACTCCTCTCTTTCTCTCACACCCCACATCCAATCCATCAGCAAATCCTG 2620 chr6ptel1M 728556 TTGATTATAGCTCTGAACCATCGCTGGCAGCCATCTATCTTCT------T 728599 i ii v v iii vi vv ii v v iv i - ------i L2#LINE/L2 2621 TCGGCTCTACCTTCAAAATATATCCAGAATCCGACCA-CTTCTCACCACC 2669 chr6ptel1M 728600 TTCTCTACAATCACTCT-ATTTAAGTCACCCCTCCTCTATTCTCTGGACA 728648 i v i v i i -i ii i - v v v ivi iv L2#LINE/L2 2670 TCCACTGCCACCACCCTGGTCCAAGCCA-CCATCATCTCTCGCCTGGATT 2718 chr6ptel1M 728649 ATT--AAGAGTCT-----CTGGTTTG---GTTT---------CTTCCTTA 728679 i -- v i ----- i v--- i --------- ii i ? L2#LINE/L2 2719 ACTGCAATAGCCTCCTAACTGGTCTCCCTGCTTCCACCCTTGCCCCCCTN 2768 chr6ptel1M 728680 CAA---ATCCTAAGCACAGTTGCTTAGATGATTTTTCTAAGGCACAGGCT 728726 i--- i v i iv iviii ii i ii ii i ii L2#LINE/L2 2769 CAGTCTATTCTCAACACAGCAGCCAGAGTGATCCTTTTAAAACGTAAGTC 2818 chr6ptel1M 728727 TGACTACGCC-TTTCTCTG-TCAAAA 728750 v ii i i -i i - L2#LINE/L2 2819 AGATCATGTCACTCCTCTGCTCAAAA 2844 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 47.76 CpG sites = 137, Kimura (unadjusted) = 50.46 Transitions / transversions = 1.73 (137/79) Gap_init rate = 0.09 (61 / 646), avg. gap size = 1.84 (112 / 61) 227 28.16 3.37 8.24 chr6ptel1M 729247 729335 (270665) MIRb#SINE/MIR 65 149 (119) m_b290s601i47 11916 chr6ptel1M 729247 ATCCTGATTCTGGAGTCACACATTTATTATCTGTATGACCTTAAAAAAAT 729296 i ii ------ - i i v i iiiv i MIRb#SINE/MIR 65 ATCCCGGCTCTG------C-CACTTACTAGCTGTGTGACCTTGGGCAAGT 107 chr6ptel1M 729297 CAC--AAAATCCCTGGGTCTCAGTTTCA-CATTTAAAACATG 729335 i -- vv i i i v- i iv v MIRb#SINE/MIR 108 TACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATG 149 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.91 CpG sites = 16, Kimura (unadjusted) = 36.96 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.10 (9 / 88), avg. gap size = 1.11 (10 / 9) 394 30.89 3.25 0.00 chr6ptel1M 729267 729389 (270611) MIR3#SINE/MIR 72 198 (10) m_b290s601i48 11916 chr6ptel1M 729267 CATTTATTATCTGTATGACCTTAAAAAAATCAC--AAAATCCCTGGGTCT 729314 i v i ?v i iiiv i --v vv i i MIR3#SINE/MIR 72 CACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCT 121 chr6ptel1M 729315 CAGTTTCA-CATTTAAAACATGAATGAGTTGGACCAAGTGGCTTCTGAAT 729363 v- i iv v iv i i ii iii i iv MIR3#SINE/MIR 122 CAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGG 171 chr6ptel1M 729364 TCCTTTCCAGCTTT-ATCTCCTATCAT 729389 i i - iv i v MIR3#SINE/MIR 172 TCCCTTCCAGCTCTGACATTCTATGAT 198 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.32 CpG sites = 25, Kimura (unadjusted) = 42.32 Transitions / transversions = 1.92 (25/13) Gap_init rate = 0.02 (3 / 122), avg. gap size = 1.33 (4 / 3) 11 20.52 5.13 0.00 chr6ptel1M 730048 730086 (269914) (AATATAA)n#Simple_repeat 1 41 (0) m_b290s252i20 11917 chr6ptel1M 730048 AACATAAAA-AGAAATGAGGAAAAATAAAATAT-AAATATA 730086 i - v vv vi v - (AATATAA)n#Si 1 AATATAAAATATAAAATATAAAATATAAAATATAAAATATA 41 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2) 371 35.13 2.67 1.32 chr6ptel1M 730170 730319 (269681) C MIRc#SINE/MIR (115) 153 2 m_b290s601i49 11918 chr6ptel1M 730170 TTCTCTTCAATTTATAGA---GAAAGTTGCAAGAGTCTAAGAGGTGAAGT 730216 v ii v i --- i ii -- iv vi v C MIRc#SINE/MIR 153 TTATCCCCATTTTACAGATGAGGAAACTG--AGGCTCAGAGAGGTTAAGT 106 chr6ptel1M 730217 TATTTGTTCATGGTCACAGAACCAGAGTTTACCAGAGAAAGAACTTGAAC 730266 v i ii v v i i vivv iv vvi i i C MIRc#SINE/MIR 105 GACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAAC 56 chr6ptel1M 730267 CCAGTGCTTCTGGACTTTAAGGCTGACTCTCTAGTCACTATGCC-CAGTC 730315 vv iv ii v iiiiv vvi iii - v v C MIRc#SINE/MIR 55 CCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTG 6 chr6ptel1M 730316 CCTC 730319 C MIRc#SINE/MIR 5 CCTC 2 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 46.32 CpG sites = 29, Kimura (unadjusted) = 48.93 Transitions / transversions = 1.26 (29/23) Gap_init rate = 0.03 (4 / 149), avg. gap size = 1.50 (6 / 4) 16 18.22 6.52 2.08 chr6ptel1M 730627 730672 (269328) (AT)n#Simple_repeat 1 48 (0) m_b290s252i22 11919 chr6ptel1M 730627 ATTTATATAT-TAAATATAGCACAT-TATACATACATATATGT-TATAT 730672 v - v -i i - i i i - (AT)n#Simple_ 1 ATATATATATATATATATA-TATATATATATATATATATATATATATAT 48 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.09 (4 / 45), avg. gap size = 1.00 (4 / 4) 192 10.88 0.00 8.11 chr6ptel1M 730843 730882 (269118) Tigger19a#DNA/TcMar-Tigger 221 257 (66) m_b290s601i50 11920 chr6ptel1M 730843 TGCACTCCAAAGCTATAAAATAGTAAAGATTTTTGGATTA 730882 i i --- ?v v Tigger19a#DNA 221 TGCATTCCAAAGCCA---AATANAAATGATTTTTGGATTA 257 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 12.06 CpG sites = 2, Kimura (unadjusted) = 12.06 Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.08 (3 / 39), avg. gap size = 1.00 (3 / 3) 561 34.89 5.96 0.00 chr6ptel1M 731010 731244 (268756) MIRc#SINE/MIR 2 250 (18) m_b290s601i51 11921 chr6ptel1M 731010 GAAGTAGTGTCGCATAATGTGTAGTGCACGAGATTTGAATTCAGGAAGCT 731059 i i v iii i viv v vi i i v vi MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr6ptel1M 731060 TTGGTTTTTACTTTGGACTCAGAAGCTCA------GTGT----TTGAAAA 731099 i v iv v iiv i v vvi i ------ ---- iiv MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 101 chr6ptel1M 731100 AGTCACTTTTCCTCTCTGACCCTCACCTTCCTGTTCTGTAAAATGGGGAG 731149 vv v vi vv v MIRc#SINE/MIR 102 AGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGAT 151 chr6ptel1M 731150 AACAAT---TATCATATCTATCTTGCTACACTGATGTTAGATACAAAGAA 731196 i --- ii v ii i ii vivii v v ivv vi MIRc#SINE/MIR 152 AATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGA 201 chr6ptel1M 731197 CATGGAATATGT-AAAATATTTTGCAAAACTTAAATCACTGCACAAATG 731244 v iivi - iiii i viv vii ii MIRc#SINE/MIR 202 GATAATGTATGTGAAAGCGCTTTGTAAACTGTAAAGTGCTATACAAATG 250 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 46.89 CpG sites = 47, Kimura (unadjusted) = 48.65 Transitions / transversions = 1.34 (47/35) Gap_init rate = 0.02 (4 / 234), avg. gap size = 3.50 (14 / 4) 34 28.40 3.23 3.23 chr6ptel1M 731914 732068 (267932) (TCTC)n#Simple_repeat 1 155 (0) m_b290s252i23 11922 chr6ptel1M 731914 TCTCATCTTTCAACTGTATCTGT-TCTCT-TCGTCT-TCTCCCTCTTTCC 731960 - i -v v v v - - - - i i i (TCTC)n#Simpl 1 TCTC-TCTCTC-TCTCTCTCTCTCTCTCTCTC-TCTCTCTCTCTCTCTCT 47 chr6ptel1M 731961 CT-TAACCTTCTCTCCCTTCCTTCCTCACTCCCT-TCTTTTATTCTCTCT 732008 - vv ii i ii ii v i - i ivi (TCTC)n#Simpl 48 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 97 chr6ptel1M 732009 GCTGTTTGTCTCTCTTTTTCTCTGTCTGTCTCTTTCTCTGTTTCTCTCTC 732058 - v i v i i v v i v i (TCTC)n#Simpl 98 -CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 146 chr6ptel1M 732059 TCATCACTCT 732068 - v (TCTC)n#Simpl 147 TC-TCTCTCT 155 Matrix = Unknown Transitions / transversions = 1.43 (20/14) Gap_init rate = 0.06 (10 / 154), avg. gap size = 1.00 (10 / 10) 27 18.14 6.67 6.67 chr6ptel1M 731932 732066 (267934) (TCTCT)n#Simple_repeat 1 135 (0) m_b290s252i24 11923 chr6ptel1M 731932 TCTGTTCTCTTCGTCTTCTC-CCTCTTTCCCTTAACCTTCTC-TCCCTTC 731979 v - -i - i -vi - i (TCTCT)n#Simp 1 TCTCTTCTCTTC-TCTTCTCTTCTC-TTCTCTT-CTCTTCTCTTCTCTTC 47 chr6ptel1M 731980 -CTTCCTCACTCCCTTCTTTTATTCTCTCTGCTGTT-TGTCTCTCTT-T- 732025 - - -i i i v ii v v - v - - - (TCTCT)n#Simp 48 TCTT-CTC-TTCTCTTCTCTTCTCTTCTCTTCTCTTCTCT-TCTCTTCTC 94 chr6ptel1M 732026 TTCTCTGTCT-GTCTCTT-TC-TCTGTTTCTCTCTCTCATCACT 732066 - -v - - -i - v v (TCTCT)n#Simp 95 TTCTCT-TCTCTTCTCTTCTCTTCT-CTTCTCT-TCTCTTCTCT 135 Matrix = Unknown Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.13 (17 / 134), avg. gap size = 1.06 (18 / 17) 205 19.51 0.00 0.00 chr6ptel1M 732362 732402 (267598) MIR3#SINE/MIR 167 207 (1) m_b290s601i52 11924 chr6ptel1M 732362 TAAGGTCTCTTTCAACTTTGACGTTCTATTATTTTATTATT 732402 i i i i i v i v MIR3#SINE/MIR 167 TAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTATGATT 207 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 23.45 CpG sites = 6, Kimura (unadjusted) = 23.45 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 626 22.62 5.07 0.69 chr6ptel1M 733155 733292 (266708) MIRc#SINE/MIR 1 144 (124) m_b290s601i53 11925 chr6ptel1M 733155 CAAGTTAGTGTAGTACA-TGGAA----TCCTGGGATTGGAGTCAGGAGCA 733199 i vi i i - ----iv iv iv MIRc#SINE/MIR 1 CGAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA 50 chr6ptel1M 733200 CCTGAATTTAAATGCAGTTTCAGATACTTACTAGCTGTGTGACTCTGGAC 733249 ii ii i v v vi v vi ii i MIRc#SINE/MIR 51 CCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGC 100 chr6ptel1M 733250 AAGTCATATAACCTTGTTT--GCCTCAGTTTCCTCATTTGTAAAA 733292 iv i- i -- i MIRc#SINE/MIR 101 AAGTCACTTAACCTC-TCTGAGCCTCAGTTTCCTCATCTGTAAAA 144 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 25.62 CpG sites = 21, Kimura (unadjusted) = 27.81 Transitions / transversions = 2.10 (21/10) Gap_init rate = 0.03 (4 / 137), avg. gap size = 2.00 (8 / 4) 16 27.62 4.55 0.00 chr6ptel1M 733422 733487 (266513) (ATAT)n#Simple_repeat 1 69 (0) m_b290s252i25 11926 chr6ptel1M 733422 ATACATAAAT-TACATA-AAATACCTAAATACATATGTATTTATACAGGT 733469 i v - i - v iv v i i v i vi (ATAT)n#Simpl 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr6ptel1M 733470 ATATATACATA-ATACATA 733487 i - i (ATAT)n#Simpl 51 ATATATATATATATATATA 69 Matrix = Unknown Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.05 (3 / 65), avg. gap size = 1.00 (3 / 3) 288 25.74 11.63 3.60 chr6ptel1M 733666 733794 (266206) MIRc#SINE/MIR 11 149 (119) m_b290s601i54 11927 chr6ptel1M 733666 TGGTGTGGGGGAAGGACCACCGGTGTTGGAGCC---AAAATCTCGGAGCT 733712 ii v i v i vv i --- i i -- i i MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCT--GGGTT 58 chr6ptel1M 733713 GAAGTCCTG----TGTCATTTTCTAGCTATGGAACCATTGGCAAA----- 733753 vi i ---- i i v i vi v v i----- MIRc#SINE/MIR 59 CGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACT 108 chr6ptel1M 733754 TAGCCTCTTTG-GCTGGGTCTGTCTCCTCATGTGTGAA--GGGG 733794 i i - i--- v i v i -- MIRc#SINE/MIR 109 TAACCTCTCTGAGCC---TCAGTTTCCTCATCTGTAAAATGGGG 149 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 30.29 CpG sites = 21, Kimura (unadjusted) = 32.76 Transitions / transversions = 1.91 (21/11) Gap_init rate = 0.08 (10 / 128), avg. gap size = 2.00 (20 / 10) 229 35.95 7.83 1.13 chr6ptel1M 733676 733841 (266159) MIR3#SINE/MIR 20 196 (12) m_b290s601i55 11927 chr6ptel1M 733676 GAAGGACCACCGGTGTTGGAGCCAAAATCTCGGAGCTGAAGTCCTG---- 733721 ii v - vv v i ii vvi v i i vv i ---- MIR3#SINE/MIR 20 GAGAGAGCAC-GGACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTC 68 chr6ptel1M 733722 TGTCATTTTCTAGCTATGGAACCATTGGCAAATAGCCTC-TTTGGCTGGG 733770 i i vv ? i vi v v i vi i -ii vv MIR3#SINE/MIR 69 TGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGG 118 chr6ptel1M 733771 TCT--GTCTCCTCATGTG-----TGAAGGGG-TGAACTTAACAGTGAAAA 733812 i -- i v ----- i - i vi iii vvvv MIR3#SINE/MIR 119 CCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTA 168 chr6ptel1M 733813 AAGTACTTTGTAAACATTAACATGCTATG 733841 i v i -iv i vi i v MIR3#SINE/MIR 169 AGGTCCCTT-CCAGCTCTGACATTCTATG 196 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 49.68 CpG sites = 32, Kimura (unadjusted) = 50.91 Transitions / transversions = 1.19 (32/27) Gap_init rate = 0.04 (7 / 165), avg. gap size = 2.14 (15 / 7) 187 22.00 6.00 0.00 chr6ptel1M 733812 733861 (266139) MIRc#SINE/MIR 215 267 (1) m_b290s601i56 11927 chr6ptel1M 733812 AAAGTACTTTGTAAACATTAACATGCTATGGAAAT---AGGAATTGTTAT 733858 ii vv vi iv --- ?i i MIRc#SINE/MIR 215 AAAGCGCTTTGTAAACTGTAAAGTGCTATACAAATGTAAGGNGTTATTAT 264 chr6ptel1M 733859 CAT 733861 i MIRc#SINE/MIR 265 TAT 267 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 24.22 CpG sites = 7, Kimura (unadjusted) = 27.35 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.02 (1 / 49), avg. gap size = 3.00 (3 / 1) 725 25.78 7.14 1.27 chr6ptel1M 733916 734139 (265861) MIRc#SINE/MIR 17 253 (15) m_b290s601i57 11928 chr6ptel1M 733916 AATGGATAGAGT-TAGGGCTTG-AGTCGGAAAGACTCAGGTTCAAGTTCC 733963 i v i-iv i - i i iii i - MIRc#SINE/MIR 17 AGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGT-CC 65 chr6ptel1M 733964 CCTCTCAGACTCTTACTTTCTCTATGAGTCTGGACAAGCCACTCAATGAT 734013 vv v v v vv v i vii i i i ivvi MIRc#SINE/MIR 66 CGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 chr6ptel1M 734014 TGCCAGACTCAACTTCCTCATCTATAAAAT-GGAATAATAGTA---G--- 734056 viv v ii i - i i --- --- MIRc#SINE/MIR 116 TCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCC 165 chr6ptel1M 734057 TGCCTACCTCACAAGGTTGTTGTAAGGACTCAATAAGACATTCTA---GA 734103 i i iiv i i v v --- MIRc#SINE/MIR 166 TGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGA 215 chr6ptel1M 734104 AG----TTTGCAAAAACTTTAAAAGGCTATGTAAATGCAA 734139 i---- i-- v iv ii i MIRc#SINE/MIR 216 AAGCGCTTTGT--AAACTGTAAAGTGCTATACAAATGTAA 253 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.88 CpG sites = 36, Kimura (unadjusted) = 32.58 Transitions / transversions = 1.71 (36/21) Gap_init rate = 0.04 (10 / 223), avg. gap size = 1.90 (19 / 10) 200 30.61 2.63 5.41 chr6ptel1M 734185 734298 (265702) X7B_LINE#LINE/CR1 101 211 (39) m_b290s601i58 11929 chr6ptel1M 734185 AAACTTATAGAATT-GTTGCCCTTTCCCAACAAATATTGCTATAGGTTGA 734233 i i -i i ---- - i vi v - i i X7B_LINE#LINE 101 AAACTTATGGAACTCATTAC----TCCCAA-AGAGGTAG-TACAGGCTGA 144 chr6ptel1M 734234 AAACAGAATT--CTTCTATGAAAATTGAAACAAGTTCAAGAATTACAAAT 734281 i v v --v v vi ii v i i i v i v i i X7B_LINE#LINE 145 AAATATAAATAGGTTCAAAAAAGGTTTAGATAAATTCATGGATGATAGAT 194 chr6ptel1M 734282 CTCTAATAGTCTATTAA 734298 iv i vi X7B_LINE#LINE 195 CCATAATGGGTTATTAA 211 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.94 CpG sites = 21, Kimura (unadjusted) = 40.94 Transitions / transversions = 1.75 (21/12) Gap_init rate = 0.07 (8 / 113), avg. gap size = 1.12 (9 / 8) 14 31.32 0.00 6.33 chr6ptel1M 734436 734519 (265481) (AAGGA)n#Simple_repeat 1 79 (0) m_b290s252i26 11930 chr6ptel1M 734436 AAGGATTAGAAAGTCAAAAACAGGAAGGTGAAAGTTGAGAAGAAAAGGAA 734485 vvi vv ii v i - -- - i (AAGGA)n#Simp 1 AAGGAAAGGAAAGGAAAGGAAAGGAAAG-GAAAG--GA-AAGGAAAGGAA 46 chr6ptel1M 734486 AGGACAAGAAAATAAAATAAGAAGATATGAAAGG 734519 - i vi vi i i v v (AAGGA)n#Simp 47 AGGA-AAGGAAAGGAAAGGAAAGGAAAGGAAAGG 79 Matrix = Unknown Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.06 (5 / 83), avg. gap size = 1.00 (5 / 5) 297 28.75 2.50 0.00 chr6ptel1M 734746 734825 (265175) MIR3#SINE/MIR 118 199 (9) m_b290s601i59 11931 chr6ptel1M 734746 GCCTTAATGACCTCCTTTGTAAAGTCAAGAGAT-AGACTAGATGTTTTCT 734794 i i vv v i i v i i i -i v i MIR3#SINE/MIR 118 GCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCT 167 chr6ptel1M 734795 AGATTCTCTTCTAGTTCAGA-ATCTTATGATT 734825 iiv i i i v - ii MIR3#SINE/MIR 168 AAGGTCCCTTCCAGCTCTGACATTCTATGATT 199 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.23 CpG sites = 16, Kimura (unadjusted) = 38.23 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.03 (2 / 79), avg. gap size = 1.00 (2 / 2) 44 0.00 0.00 0.00 chr6ptel1M 735051 735088 (264912) (GT)n#Simple_repeat 1 38 (0) c_b290s251i4 11932 chr6ptel1M 735051 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 735088 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 38 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 30 14.55 1.89 0.00 chr6ptel1M 735095 735147 (264853) (GA)n#Simple_repeat 1 54 (0) m_b290s252i27 11933 chr6ptel1M 735095 GAGGGAGAGAGAGA-AGAGAGAGACAGACAGAGACACAGAGGAAGAGAGA 735143 i - v v v v ii (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chr6ptel1M 735144 GAGA 735147 (GA)n#Simple_ 51 GAGA 54 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.02 (1 / 52), avg. gap size = 1.00 (1 / 1) 301 27.38 0.00 0.00 chr6ptel1M 735148 735231 (264769) C Tigger15a#DNA/TcMar-Tigger (474) 241 158 m_b290s502i4 11911 chr6ptel1M 735148 GAGCTAACAAACCAGACAACCAATCTTAGCAGAATCCTATATAAAGTAAC 735197 i iiv i v ivi iv i ? i v C Tigger15a#DNA 241 GGGCTGGGAAACCAGATAACCAAGCTTGTTAGAATTGTGTNTAAAATAAG 192 chr6ptel1M 735198 AATCCTAAGGCTCTGAGTGAGGTCCCAATGGGCT 735231 i vvvv v ii v C Tigger15a#DNA 191 AGTAAATAGGCTCTGAGTGAGGGCCTGAGGGGCT 158 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.08 CpG sites = 12, Kimura (unadjusted) = 35.08 Transitions / transversions = 1.09 (12/11) Gap_init rate = 0.00 (0 / 83), avg. gap size = 0.0 (0 / 0) 16 9.32 0.00 0.00 chr6ptel1M 735251 735273 (264727) (T)n#Simple_repeat 1 23 (0) m_b290s252i28 11934 chr6ptel1M 735251 TTTTTTTTTTTATTTTTTTATTT 735273 v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTT 23 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 361 38.64 2.44 0.60 chr6ptel1M 736308 736471 (263529) C MIR3#SINE/MIR (21) 187 21 m_b290s601i60 11935 chr6ptel1M 736308 TTAGAATGGGATTAGCCCTCTGACATCATCTCATCTAATTTCTTTACTTT 736357 i iiv vvi v iv v vi i iii i i - C MIR3#SINE/MIR 187 TCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCA-TTT 139 chr6ptel1M 736358 TTTGGAGGAGGAAAAT--GGTCTAGCTACATTAAGTAAGTTATCAAAAGC 736405 vii v v -- i i vv vi v i v ii v i i C MIR3#SINE/MIR 138 TACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGT 89 chr6ptel1M 736406 CATACTGCTTATAAGTGATAGAGATGGGATTGGAATCCAGATTCTTT--C 736453 i v ?vi v ii vi i i i i iiii -- C MIR3#SINE/MIR 88 CACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGTCTCCTGAC 39 chr6ptel1M 736454 TCTTATACTGTCTTATCT 736471 ii vv i vi v C MIR3#SINE/MIR 38 TCCCAGTCCGTGCTCTCT 21 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 55.53 CpG sites = 39, Kimura (unadjusted) = 58.45 Transitions / transversions = 1.62 (39/24) Gap_init rate = 0.02 (3 / 163), avg. gap size = 1.67 (5 / 3) 278 35.83 9.09 4.56 chr6ptel1M 736675 736905 (263095) L3b_3end#LINE/CR1 330 570 (636) m_b290s601i61 11936 chr6ptel1M 736675 CAGAAGCCCAGAGTTATCACTGACATCATGGTGGATG-AGGGTCAAGATC 736723 ivi iv ivi i i i--- v - iii i L3b_3end#LINE 330 CAGAAGCTGGGAGCGACGGCTAATAC---GTTGGATGCAAAATCAGGATC 376 chr6ptel1M 736724 CA----------GACAAGTTGGCATGTTTGTCCAAATCTGAGAAGAAGAA 736763 ---------- iii i v i ?iv v i ? ii v v L3b_3end#LINE 377 CAAAACGATCTCGACAGACTAGAACGNCGGGCCGAANCCAACAAGATGAA 426 chr6ptel1M 736764 AGTGAATGAGAATAAATGTAAGGAGCCATACTATACTGAGTCTAA----- 736808 v v iii i i i vv iii ---- i ii ----- L3b_3end#LINE 427 ATTCAACAGGGATAAACGTAAAGTCCTGCACT----TGGGTTCAAAAAAN 472 chr6ptel1M 736809 TTATAAAGGGAATACGTAACCCTAAGGGAGACATAGCTAGATAGTGGTTT 736858 iv viv v i ivi --- ii iii viii ii i?i L3b_3end#LINE 473 CAATCGCGCGAGTACAGGA---TGGGGGAGACGCGGCTTAGCAGCAGCNC 519 chr6ptel1M 736859 GTGTGAGGAAAA----AGGGTTTTAATGGCACC-CAAAATCAAAATGAGT 736903 i ii i ----i i v - - iv v L3b_3end#LINE 520 ATGTGAAAAAGACCTGGGGGTTTTAGTTG-ACCGCAAGCTCAATATGAGT 568 chr6ptel1M 736904 CA 736905 L3b_3end#LINE 569 CA 570 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 44.80 CpG sites = 57, Kimura (unadjusted) = 54.94 Transitions / transversions = 2.59 (57/22) Gap_init rate = 0.07 (16 / 230), avg. gap size = 2.00 (32 / 16) 458 23.40 5.30 6.11 chr6ptel1M 737076 737207 (262793) C MIRc#SINE/MIR (122) 146 16 m_b290s601i62 11937 chr6ptel1M 737076 CATTTTACAAATAATGAAACTGAGGCAAACAGA-GTAAAATTATGTCCCC 737124 i i v vv v - v i v iv v C MIRc#SINE/MIR 146 CATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCC 97 chr6ptel1M 737125 TGGGTCACATAGCTAGTAAAT----GAGGTTGGATTTGAACCCACAAAGA 737170 vi i i ---- viv i i ------ C MIRc#SINE/MIR 96 AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCA------ 53 chr6ptel1M 737171 TGAGTCTTGATGACTCCAGATTCAGT--TCTTTCTATTG 737207 --i vv ii i -- i i C MIRc#SINE/MIR 52 --GGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTG 16 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.20 CpG sites = 16, Kimura (unadjusted) = 28.42 Transitions / transversions = 1.23 (16/13) Gap_init rate = 0.08 (11 / 131), avg. gap size = 1.36 (15 / 11) 187 28.38 3.90 3.90 chr6ptel1M 737200 737276 (262724) L2d_3end#LINE/L2 436 512 (4) m_b290s601i63 11938 chr6ptel1M 737200 TTCTATTGTTTCCTAAACTATCCCCTAGT-CTGTAC--ATAACATAATAA 737246 i ? i i i ---i v v i- v i -- vv i i L2d_3end#LINE 436 TTTTNTCGTTCCCCA---CAGCGCCTAGCACAGTGCTGAGCACATAGTAG 482 chr6ptel1M 737247 GCACTTAATAAATTTTTGTTAAATGAATGA 737276 i i vi i v v L2d_3end#LINE 483 GCGCTCAATAAATACTTGTTGATTGATTGA 512 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.12 CpG sites = 13, Kimura (unadjusted) = 37.53 Transitions / transversions = 1.62 (13/8) Gap_init rate = 0.07 (5 / 76), avg. gap size = 1.20 (6 / 5) 231 15.00 0.00 0.00 chr6ptel1M 737238 737277 (262723) L2c_3end#LINE/L2 438 477 (1) m_b290s601i64 11938 chr6ptel1M 737238 ACATAATAAGCACTTAATAAATTTTTGTTAAATGAATGAA 737277 i i i i v i L2c_3end#LINE 438 ACATAGTAGGCGCTCAATAAATGTTTGTTGAATGAATGAA 477 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 14.35 CpG sites = 5, Kimura (unadjusted) = 17.36 Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 317 31.19 2.38 0.78 chr6ptel1M 737494 737619 (262381) MIRc#SINE/MIR 110 237 (31) m_b290s601i65 11939 chr6ptel1M 737494 AAACTCACTG-GTCTCAATTTCTTCCTCTTCAAAAGGGGAGATAATAATG 737542 v v - i i i v vi v - i MIRc#SINE/MIR 110 AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG-GATAATAATA 158 chr6ptel1M 737543 TCTATGTCTCTTACATCTCCGAGTTTTTGTGATGTTTAAATGAAATCCTG 737592 i iiviiv i v v v i v v v i i vv MIRc#SINE/MIR 159 CCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATG 208 chr6ptel1M 737593 TGCAT-ATTGAGTTCTGCAACCT-TAAAG 737619 iii - vv v i i i v - MIRc#SINE/MIR 209 TATGTGAAAGCGCTTTGTAAACTGTAAAG 237 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.99 CpG sites = 20, Kimura (unadjusted) = 40.99 Transitions / transversions = 1.05 (20/19) Gap_init rate = 0.03 (4 / 125), avg. gap size = 1.00 (4 / 4) 276 30.39 3.92 0.00 chr6ptel1M 737669 737770 (262230) L3#LINE/CR1 3766 3871 (228) m_b290s601i66 11940 chr6ptel1M 737669 AGCTGTCGATAAATATTTGAAGTGCCACCATGTGGTAGAGGGGAAGGATG 737718 vvi v iii v ivvi iv L3#LINE/CR1 3766 AGCTGTCTTCAAATATTTGAAGGGCTGTCATGTGGAAGAGGGATTAGACT 3815 chr6ptel1M 737719 GAGTCTGTG----TTTACAGGGTTAAGCTAGGACCGACATGTTGAAATGC 737764 v v ---- ii v ivi i i iiv v i vv L3#LINE/CR1 3816 TATTCTGTGTGGCTCCAGAGGGCAGAACTAGGACCAATGGGTGGAAGTTA 3865 chr6ptel1M 737765 CAGGGA 737770 L3#LINE/CR1 3866 CAGGGA 3871 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.59 CpG sites = 16, Kimura (unadjusted) = 39.59 Transitions / transversions = 1.07 (16/15) Gap_init rate = 0.01 (1 / 101), avg. gap size = 4.00 (4 / 1) 454 24.53 2.83 0.00 chr6ptel1M 738048 738153 (261847) MIR3#SINE/MIR 97 205 (3) m_b290s601i67 11941 chr6ptel1M 738048 CAAATCAATGCCCTTTTCTGG-CCTCAGTTTTCCCATCAGTAAAATAAAG 738096 i v v v i i - i i v i i MIR3#SINE/MIR 97 CAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGG 146 chr6ptel1M 738097 GATCTGAACTTGATGGACTCTAAGGTCCTGTCCAGCTATGAC--TTTGTG 738144 ivi i v iv iv v -- i i MIR3#SINE/MIR 147 GGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATG 196 chr6ptel1M 738145 ATCTTCTGA 738153 ii v MIR3#SINE/MIR 197 ATTCTATGA 205 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 30.46 CpG sites = 16, Kimura (unadjusted) = 30.46 Transitions / transversions = 1.60 (16/10) Gap_init rate = 0.02 (2 / 105), avg. gap size = 1.50 (3 / 2) 228 37.54 8.75 1.75 chr6ptel1M 738536 738695 (261305) C MIR3#SINE/MIR (0) 208 38 m_b290s601i68 11942 chr6ptel1M 738536 GAATCA--GGGTAAAAGAATCTTAATACTGGA-GAGAACTTAGAAAGCAC 738582 -- ii v v v i ivi - i v i v i C MIR3#SINE/MIR 208 GAATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCAT 159 chr6ptel1M 738583 TGAATACA----------TTTACCACTAAGGAC-CTGGAGCCCATAAAAA 738621 iv i v ---------- viv i v- ii ---i i C MIR3#SINE/MIR 158 CTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCA---GAG 112 chr6ptel1M 738622 AAATGAAGCAAGATATTCAGGGCCACTTGAAGAGTAAGCAGCAAACCTTG 738671 ii ii vv iii i i viiiv? v ii i v iv C MIR3#SINE/MIR 111 AGGTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGG 62 chr6ptel1M 738672 GTCTTCAGTTCGGGTCTCTTAACT 738695 v vv iii i i i C MIR3#SINE/MIR 61 GACTAGAACCCAGGTCTCCTGACT 38 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 54.95 CpG sites = 38, Kimura (unadjusted) = 56.46 Transitions / transversions = 1.81 (38/21) Gap_init rate = 0.04 (7 / 159), avg. gap size = 2.43 (17 / 7) 191 32.63 5.26 0.00 chr6ptel1M 738920 739014 (260986) L2d2_3end#LINE/L2 452 551 (4) m_b290s601i69 11943 chr6ptel1M 738920 GAGTTCATGGACTCCATTTTC--CTTCTTTGTTTCCTC---AACTCCCTG 738964 vv v ivii i v-- v i --- i v iv L2d2_3end#LIN 452 GAGGGCAGGGACCATGTCTTATACTTCTTTGTATCCCCCACAGCGCCTAG 501 chr6ptel1M 738965 TGCAGTGCCTTCAACCCAGGATGTGCTAAACCAGCATTTGCTGGTTGGAT 739014 ii vv v v v i v iv ii i i v L2d2_3end#LIN 502 CACAGTGCCTTGCACACAGTAGGCGCTCAATAAATATTTGTTGATTTGAT 551 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.57 CpG sites = 15, Kimura (unadjusted) = 43.37 Transitions / transversions = 0.94 (15/16) Gap_init rate = 0.02 (2 / 94), avg. gap size = 2.50 (5 / 2) 544 26.17 0.68 5.76 chr6ptel1M 739789 739934 (260066) C MIRc#SINE/MIR (120) 148 10 m_b290s601i70 11944 chr6ptel1M 739789 CTCATTTTATAGAAGAGGAAACTGAGTTAACCAACAGGGTTAAGTGACTT 739838 i i v vi--i ivii C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGC--TCAGAGAGGTTAAGTGACTT 101 chr6ptel1M 739839 GCTCAGGGTTACATAGCTAGTAAGAGTCTGAGGCCATGCTGGAACTTAAA 739888 i i i i v v v ------ i i ii C MIRc#SINE/MIR 100 GCCCAAGGTCACACAGCTAGTAAGTGGCAGA------GCCGGGACTCGAA 57 chr6ptel1M 739889 GATGCATCTTCCTGACTCC-AGTGGGGCACTGTATCCACTGCATTAC 739934 vviivi - vvi ii v v ii C MIRc#SINE/MIR 56 CCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 30.76 CpG sites = 23, Kimura (unadjusted) = 33.11 Transitions / transversions = 1.77 (23/13) Gap_init rate = 0.06 (9 / 145), avg. gap size = 1.00 (9 / 9) 316 30.93 3.09 0.00 chr6ptel1M 739946 740042 (259958) C MIR3#SINE/MIR (35) 173 74 m_b290s601i71 11945 chr6ptel1M 739946 GACCTTAAAAGCCATAAAATCCAGCTCTCTCAT---ATCGATGAGAAAAC 739992 i iii vv i i i i --- iv i C MIR3#SINE/MIR 173 GACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAAC 124 chr6ptel1M 739993 TGAGGCAGAGAAAATAGAAATGATATATTCAGAGTCACACAAAGAGTAAG 740042 vv i ivv i iv iii ii iv? v C MIR3#SINE/MIR 123 TGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAG 74 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.63 CpG sites = 20, Kimura (unadjusted) = 42.63 Transitions / transversions = 2.00 (20/10) Gap_init rate = 0.01 (1 / 96), avg. gap size = 3.00 (3 / 1) 220 35.96 0.00 0.00 chr6ptel1M 739978 740066 (259934) C MIR#SINE/MIR (125) 137 49 m_b290s601i72 11945 chr6ptel1M 739978 TATCGATGAGAAAACTGAGGCAGAGAAAATAGAAATGATATATTCAGAGT 740027 iv i v i ivvv i i iv iii ii C MIR#SINE/MIR 137 TACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGT 88 chr6ptel1M 740028 CACACAAAGAGTAAGAGTCTGAAGCTCAATATGAACTCA 740066 ivv v v v iv vvi vi i C MIR#SINE/MIR 87 CACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCA 49 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 48.06 CpG sites = 17, Kimura (unadjusted) = 50.27 Transitions / transversions = 1.13 (17/15) Gap_init rate = 0.00 (0 / 88), avg. gap size = 0.0 (0 / 0) 33 0.00 0.00 0.00 chr6ptel1M 740150 740177 (259823) (GT)n#Simple_repeat 1 28 (0) c_b290s251i5 11946 chr6ptel1M 740150 GTGTGTGTGTGTGTGTGTGTGTGTGTGT 740177 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGT 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 305 31.11 2.20 1.09 chr6ptel1M 741072 741162 (258838) C MIR3#SINE/MIR (26) 182 91 m_b291s601i3 11947 chr6ptel1M 741072 GCTTGATAGAATCTCAGGAGCTGTCCATGTC--ACACCATCATTACACAG 741119 v vi i i i iiiiii i - -- v v vi C MIR3#SINE/MIR 182 GCTGGAAGGGACCTTAGAGATCATCTA-GTCCAACCCCCTCATTTTACAG 134 chr6ptel1M 741120 AAGAGGAAACTGAGGCTCAAGGAAGTTAAATAATTTTTCCAAG 741162 v i ii i v i i i vi C MIR3#SINE/MIR 133 ATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAG 91 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.00 CpG sites = 20, Kimura (unadjusted) = 43.00 Transitions / transversions = 2.50 (20/8) Gap_init rate = 0.02 (2 / 90), avg. gap size = 1.50 (3 / 2) 20 17.36 0.00 0.00 chr6ptel1M 741499 741538 (258462) (CATT)n#Simple_repeat 1 40 (0) m_b291s252i0 11948 chr6ptel1M 741499 CATTCATTCATTCATTCATTCACTCACTTATTTCTTTATT 741538 i i i iv i (CATT)n#Simpl 1 CATTCATTCATTCATTCATTCATTCATTCATTCATTCATT 40 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 188 29.10 1.02 5.32 chr6ptel1M 742405 742502 (257498) L2a_3end#LINE/L2 424 517 (0) m_b291s601i4 11949 chr6ptel1M 742405 TTCTGTTTTTTTTTTTTTTTTTTTTAATTCTTAGTTCCTAGTACAGTGCC 742454 i i v v ivi vi v - i ii iv v L2a_3end#LINE 424 TTTTGTCTGTTTTGTTCACTGCTGTA-TCCCCAGCGCCTAGAACAGTGCC 472 chr6ptel1M 742455 TGATGTAC-CTAGGGGCTTAATAAATGTTTGTGCATTGATTGATTGAAT 742502 iiii i-v v i i ---- v v L2a_3end#LINE 473 TGGCACATAGTAGGCGCTCAATAAATATTTG----TTGAATGAATGAAT 517 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.01 CpG sites = 16, Kimura (unadjusted) = 37.78 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.06 (6 / 97), avg. gap size = 1.00 (6 / 6) 260 18.16 7.59 2.41 chr6ptel1M 742422 742500 (257500) L2d_3end#LINE/L2 434 516 (0) m_b291s601i5 11949 chr6ptel1M 742422 TTTTTTTTAATTCTT---AGTTCCTAGTACAGTGCCTGATGTACCTAG-- 742466 ? ? vi ii--- iv i - - i v -- L2d_3end#LINE 434 TNTTTTNTCGTTCCCCACAGCGCCTAGCACAGTGC-TGA-GCACATAGTA 481 chr6ptel1M 742467 GG-GCTTAATAAATGTTTGTGCATTGATTGATTGA 742500 - i ii vv L2d_3end#LINE 482 GGCGCTCAATAAATACTTGTTGATTGATTGATTGA 516 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 18.54 CpG sites = 9, Kimura (unadjusted) = 21.89 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.06 (5 / 78), avg. gap size = 1.60 (8 / 5) 277 34.77 0.00 3.16 chr6ptel1M 742568 742665 (257335) C L2c_3end#LINE/L2 (7) 471 377 m_b291s601i6 11950 chr6ptel1M 742568 CAATTAATTAATTTTTATTAAGTGCCTACTATATTCCAAGTATCATGAGG 742617 v i iv iv i i i v i iiiii- i i C L2c_3end#LINE 471 CATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTG-GGGA 423 chr6ptel1M 742618 TACACAGAGGATTATGTGACATAGGCCCTTTACTCTGAAAGCTTACAG 742665 v v -- iv ii v viv viii i C L2c_3end#LINE 422 TACAAAGATGA--ATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAG 377 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.07 CpG sites = 22, Kimura (unadjusted) = 49.84 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.03 (3 / 97), avg. gap size = 1.00 (3 / 3) 766 29.35 3.64 0.88 chr6ptel1M 742668 742887 (257113) MIRc#SINE/MIR 3 228 (40) m_b291s601i7 11951 chr6ptel1M 742668 AGGTAGCATGGCACTGCAGATGGAG---TGGACTTGGAGCCAGGAAGACC 742714 i ii ii v ii vi --- i MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chr6ptel1M 742715 TGAATTCAAATTCTGCCTTTGACACTTAGGTAGCTCTATGATTCTGGGTA 742764 ii i i i i v i v v- v i iii i MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCACTTAC-TAGCTGTGTGACCTTGGGCA 101 chr6ptel1M 742765 ACTCATTTAAATACTCTGAGCCTTAATTTCTACATTTGTGAAAAAGGTAT 742814 v i viv i i iv i i vi v MIRc#SINE/MIR 102 AGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGAT 151 chr6ptel1M 742815 GATAAAAACTCTGCTTCCAACCT--GAGGGTTATTTCAAAGCTTAAATGA 742862 i v v viv v v --v i vii i v i MIRc#SINE/MIR 152 AATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGA 201 chr6ptel1M 742863 GATTAAAAAATATG---GTACTTTGCAA 742887 - viv i --- ii i MIRc#SINE/MIR 202 GA-TAATGTATGTGAAAGCGCTTTGTAA 228 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.36 CpG sites = 41, Kimura (unadjusted) = 38.78 Transitions / transversions = 1.78 (41/23) Gap_init rate = 0.02 (5 / 219), avg. gap size = 2.00 (10 / 5) 289 30.49 4.92 3.23 chr6ptel1M 743241 743362 (256638) MIR3#SINE/MIR 84 207 (1) m_b291s601i8 11952 chr6ptel1M 743241 GTGCGATTCTGAAGAAACAGCTTGAATTGCTCTGTGCCTCAGTTTCCCCA 743290 i iii iiv iivi v vi - v i MIR3#SINE/MIR 84 GTGTGACCTTGGGCAAGTCACTTCACCT-CTCTGGGCCTCAGTTTCCTCA 132 chr6ptel1M 743291 AATGTAAAATGCAGAGATTAGACTGTCTGATTTTGTAGTTCCAATTCCA- 743339 vv vi i i i ivv i ivv v -v - MIR3#SINE/MIR 133 TCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCC-CTTCCAG 181 chr6ptel1M 743340 -TTTG----TCTATGAGACTTTATGGTT 743362 - i ---- -- i i i MIR3#SINE/MIR 182 CTCTGACATTCTAT--GATTCTATGATT 207 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.59 CpG sites = 22, Kimura (unadjusted) = 40.59 Transitions / transversions = 1.57 (22/14) Gap_init rate = 0.06 (7 / 121), avg. gap size = 1.43 (10 / 7) 236 32.02 2.40 7.56 chr6ptel1M 743781 743905 (256095) MIRb#SINE/MIR 94 212 (56) m_b291s601i9 11953 chr6ptel1M 743781 GACTCCAGACAAGTAATTTAATATATATCGAGCCTCATTCTCATGGTTTG 743830 iiii i v i iv v v - v i v vi i MIRb#SINE/MIR 94 GACCTTGGGCAAGTTACTTAACCTCTCT-GAGCCTCAGTTTCCTCATCTG 142 chr6ptel1M 743831 TTAAATGGGAATGACAGTGTTTTCAGAATGCTCCTGCAGGATT-TTCTGG 743879 v i i i i iii v ------ -- i - v i MIRb#SINE/MIR 143 TAAAATGGGGATAATAATACCTAC------CTC--GCAGGGTTGTTGTGA 184 chr6ptel1M 743880 GGAAAGGATTGGACAA--CATGTAAAAC 743905 vvii vi i -- i MIRb#SINE/MIR 185 GGATTAAATGAGATAATGCATGTAAAGC 212 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.66 CpG sites = 24, Kimura (unadjusted) = 43.66 Transitions / transversions = 1.85 (24/13) Gap_init rate = 0.09 (11 / 124), avg. gap size = 1.09 (12 / 11) 189 35.88 4.17 2.46 chr6ptel1M 743921 744040 (255960) L2#LINE/L2 2790 2911 (171) m_b291s601i10 11954 chr6ptel1M 743921 GCCAAAATACTCTTCGTGAAACACGGGACTAATCTTGTCACTCTCCTGTA 743970 i i iv i iv i iiii v vi v ii iv L2#LINE/L2 2790 GCCAGAGTGATCCTTTTAAAACGTAAGTCAGATCATGTCACTCCTCTGCT 2839 chr6ptel1M 743971 CAGAAGTGTTTATTA--TCCCCAGTGTC-CACT--GGTTAAAATACATAC 744015 i viv ii v i-- i --- - -- iv vv v v L2#LINE/L2 2840 CAAAACCCTCCAATGGCTTCCCA---TCTCACTCAGAGTAAAAGCCAAAG 2886 chr6ptel1M 744016 TCCTTAGCATGACATTCAAGGTCTT 744040 vv i v v i i L2#LINE/L2 2887 TCCTTACAATGGCCTACAAGGCCCT 2911 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 48.98 CpG sites = 24, Kimura (unadjusted) = 50.71 Transitions / transversions = 1.33 (24/18) Gap_init rate = 0.05 (6 / 119), avg. gap size = 1.33 (8 / 6) 688 26.21 2.41 8.05 chr6ptel1M 744782 745030 (254970) MIRb#SINE/MIR 19 254 (14) m_b291s601i11 11955 chr6ptel1M 744782 CAGTGGTTAGAACACTGGGCCTGGAGTATAGA-AGACCGAAGTTCAAATC 744830 vv i v vii -i - vii i MIRb#SINE/MIR 19 CAGTGGAAAGAGCACGGGCTTTGGAGT-CAGACAGACCTGGGTTCGAATC 67 chr6ptel1M 744831 CAGCTTCAG--ACT--CTAGCTCTGTGACCCTGG-CAAGTCACTTAATCT 744875 v vi v -- -- v i - i i MIRb#SINE/MIR 68 CCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCT 117 chr6ptel1M 744876 CTGTGTTCCTCAGTTTCCTCCAATGCAAAATGGGGGTAATAAAACCAGTG 744925 v vv vvv i i v ---- MIRb#SINE/MIR 118 CTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACC---- 163 chr6ptel1M 744926 TTACTAATACTAATGTCCAGTATTCTTGCACAGATCAAATTAAATCACAT 744975 - ----- --i -- vi v iivi i v i v iii MIRb#SINE/MIR 164 -TAC-----CT--CG--CAGGGTTGTTGTGAGGATTAAATGAGATAATGC 203 chr6ptel1M 744976 TTATAAAGGATTTACCTAACATAATAGCTGGAACATAGTCAGTGCTTAAT 745025 v i ----ii i i i i iv v v i i MIRb#SINE/MIR 204 ATGTAAAG----CGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAAT 249 chr6ptel1M 745026 AGACG 745030 i i MIRb#SINE/MIR 250 AAATG 254 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 30.10 CpG sites = 35, Kimura (unadjusted) = 32.77 Transitions / transversions = 1.40 (35/25) Gap_init rate = 0.09 (23 / 248), avg. gap size = 1.09 (25 / 23) 12 20.12 0.00 5.41 chr6ptel1M 745655 745693 (254307) (TTTCTCC)n#Simple_repeat 1 37 (0) m_b291s252i1 11956 chr6ptel1M 745655 TTTGTTCCTTCTCTTTTCTCCCTATTCTTCTTTCCCCTT 745693 v i i i - - i i (TTTCTCC)n#Si 1 TTTCTCCTTTCTCCTTTCT-CCT-TTCTCCTTTCTCCTT 37 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2) 261 32.63 5.26 0.00 chr6ptel1M 745756 745850 (254150) C MIR3#SINE/MIR (27) 181 82 m_b291s601i12 11957 chr6ptel1M 745756 CTAGA--GAATTCTAGAGTCTATTTCACCCCAGCCCTTCATTTTG--GA- 745800 i -- i iii vii i vii v v i i-- - C MIR3#SINE/MIR 181 CTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGAT 132 chr6ptel1M 745801 GAAGAAACTGAGGTCCATAGAGACAAAGGGAATTCCCCCTGGTTTCGTAG 745850 i i v iii v v v vv iv ii C MIR3#SINE/MIR 131 GAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAG 82 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 45.07 CpG sites = 20, Kimura (unadjusted) = 45.07 Transitions / transversions = 1.82 (20/11) Gap_init rate = 0.03 (3 / 94), avg. gap size = 1.67 (5 / 3) 351 32.08 0.65 6.90 chr6ptel1M 745882 746035 (253965) MIR1_Amn#SINE/MIR 28 172 (58) m_b291s601i14 11958 chr6ptel1M 745882 GGGCAATAGACCTGGGAGTCAGAGAATCAGGGTTCAAATCTCAGTCCCAT 745931 i v i - v i iii i v ? ? i i ii iii MIR1_Amn#SINE 28 GAGCACTGGAC-TGGGACTCGGGAGACCTGGGTTCNANTCCCGGCTCTGC 76 chr6ptel1M 745932 CACTTATCA-CCAGATGGTTTGAGATAAATCATTTAACCTCTTTGGGCCT 745980 ?ii ?- ii?i iii vi ii i i ? i ? MIR1_Amn#SINE 77 CACTNGCCNGCTGNGTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCT 126 chr6ptel1M 745981 TTGTTACTGGGCCTCTACTTGTAAATTTGTAACTCATGATTTTGAGCAAT 746030 iv -----v - ii v v vi - v vi v -- MIR1_Amn#SINE 127 CAGTT-----TCCTC-ATCTGTAAAATGGGGA-TAATGATACTGACC--T 167 chr6ptel1M 746031 CTTTT 746035 i MIR1_Amn#SINE 168 CCTTT 172 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 45.60 CpG sites = 34, Kimura (unadjusted) = 48.66 Transitions / transversions = 2.83 (34/12) Gap_init rate = 0.07 (11 / 153), avg. gap size = 1.00 (11 / 11) 353 33.97 1.92 0.95 chr6ptel1M 745882 745985 (254015) MIRc#SINE/MIR 25 129 (139) m_b291s601i13 11958 chr6ptel1M 745882 GGGCAATAGACCTGGGAGTCAGAGA-ATCAGGGTTCAAATCTCAGTCCCA 745930 i v i i - ii - i v i i i i ii ii MIRc#SINE/MIR 25 GAGCACTGGACTTGG-AGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTG 73 chr6ptel1M 745931 TCACTTATCACCAG-ATGGTTTGAGATAAATCATTTAACCTCTTTGGGCC 745979 i ii v v -i iii vi ii i i i i MIRc#SINE/MIR 74 CCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCC 123 chr6ptel1M 745980 TTTGTT 745985 iv MIRc#SINE/MIR 124 TCAGTT 129 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 47.24 CpG sites = 29, Kimura (unadjusted) = 51.66 Transitions / transversions = 4.83 (29/6) Gap_init rate = 0.03 (3 / 103), avg. gap size = 1.00 (3 / 3) 59 4.92 0.00 0.00 chr6ptel1M 746725 746788 (253212) (AT)n#Simple_repeat 1 64 (0) c_b291s251i1 11959 chr6ptel1M 746725 ATATATGTATGTATGTATATATATATATATATATATATATATATATATAT 746774 i i i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr6ptel1M 746775 ATATATATATATAT 746788 (AT)n#Simple_ 51 ATATATATATATAT 64 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0) 185 32.18 15.38 0.96 chr6ptel1M 747357 747538 (252462) C MIRb#SINE/MIR (58) 210 3 m_b291s601i15 11960 chr6ptel1M 747357 TTTACATACATTTTCTTATTTAGCCTTC-C-ACAAATATGGGGAGTGGGT 747404 i v i ii i - - viv v ii i C MIRb#SINE/MIR 210 TTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGT 161 chr6ptel1M 747405 ACTACAGATACCATCTTCC---------AAC--AGGCTTAGAGAATGGAA 747443 i iviviv i v --------- -- i ivvv C MIRb#SINE/MIR 160 ATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAA 111 chr6ptel1M 747444 GTCCTGTGCTGCCA--GCTGCATTGCTCCTAAG-GGCA-AGTTTGGATTA 747489 vviv -- -- iii iv vv - - iiv v C MIRb#SINE/MIR 110 GTAACTTGC--CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTC 63 chr6ptel1M 747490 GAGC-----TCCGCTTG----CAAGTGCAGGGTGCTGTCCACTG--CCAC 747528 i ----- i ii ---- ivv v v iv v -- C MIRb#SINE/MIR 62 GAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCACCAC 13 chr6ptel1M 747529 ATTCCCTCTC 747538 ii v i C MIRb#SINE/MIR 12 GCTGCCCCTC 3 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.22 CpG sites = 32, Kimura (unadjusted) = 43.18 Transitions / transversions = 1.23 (32/26) Gap_init rate = 0.07 (12 / 181), avg. gap size = 2.50 (30 / 12) 56 19.71 3.64 3.01 chr6ptel1M 747583 747747 (252253) (AGAGAC)n#Simple_repeat 1 166 (0) m_b291s252i2 11961 chr6ptel1M 747583 AGATGAAAGAGACAGAGACAGAGGCAGACACAGCGACAGAAAGACAGAGA 747632 - v i v v -- (AGAGAC)n#Sim 1 AGA-GACAGAGACAGAGACAGAGACAGAGACAGAGACAG--AGACAGAGA 47 chr6ptel1M 747633 CATAGACAAAAGGAGAGAGCAG-GAAGGAGAAAGAGA-A-ACAGATAGAC 747679 v i iiv - - vi v - - v v v (AGAGAC)n#Sim 48 CAGAGACAGAGACAGAGA-CAGAGACAGAGACAGAGACAGAGACAGAGAC 96 chr6ptel1M 747680 AGAGTCAGAGACAGAGATAGAAAGACAGACAGAAAAAGTAGGC-CAGCCA 747728 v i i v v i v - i -v v (AGAGAC)n#Sim 97 AGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAG-AGACAGAGACA 145 chr6ptel1M 747729 GAG-C-GAGACACAGATAGAG 747747 - - v i (AGAGAC)n#Sim 146 GAGACAGAGACAGAGACAGAG 166 Matrix = Unknown Transitions / transversions = 0.59 (10/17) Gap_init rate = 0.07 (11 / 164), avg. gap size = 1.00 (11 / 11) 477 24.81 6.98 0.00 chr6ptel1M 749325 749453 (250547) Charlie4#DNA/hAT-Charlie 3 140 (3238) m_b291s502i0 11962 chr6ptel1M 749325 GAGATTCTTAATTTGGGATCTATG-ATTCCT-----GT--ATGGATAAAT 749366 i i ii i i i - ii i----- --i i v Charlie4#DNA/ 3 GGGGTTCTTAACCTGGGGTCCACGGACCCCCAAGGGGTCCGTGGATAGAA 52 chr6ptel1M 749367 TTCAAAGGGTCAATGAATTTGCATAGGGAAAAAATGCATCTTTATTATCA 749416 ii vi i v i i v i v Charlie4#DNA/ 53 TTCAGGGGGTCCGTGAACTTGGATGGGAAAAAATTACATCTTTATTTTCA 102 chr6ptel1M 749417 TTAATCTTTAATGGAAGTTTA-CATTCCCTTCCATTAT 749453 i i i iv i - i v Charlie4#DNA/ 103 CTAACCTCTAACTGAAATTTAGCATTTCCTTCAATTAT 140 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 28.41 CpG sites = 25, Kimura (unadjusted) = 32.03 Transitions / transversions = 3.57 (25/7) Gap_init rate = 0.03 (4 / 128), avg. gap size = 2.25 (9 / 4) 53 0.00 1.89 1.89 chr6ptel1M 749487 749539 (250461) (AC)n#Simple_repeat 1 53 (0) c_b291s251i2 11963 chr6ptel1M 749487 ACACACACTA-ACACACACACACACACACACACACACACACACACACACA 749535 - - (AC)n#Simple_ 1 ACACACAC-ACACACACACACACACACACACACACACACACACACACACA 49 chr6ptel1M 749536 CACA 749539 (AC)n#Simple_ 50 CACA 53 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.00 (2 / 2) 34 5.27 0.00 0.00 chr6ptel1M 750726 750765 (249235) (ACC)n#Simple_repeat 1 40 (0) c_b291s251i3 11964 chr6ptel1M 750726 ACCACCACCACCACCACCACCACCATCACCACCATCACCA 750765 i i (ACC)n#Simple 1 ACCACCACCACCACCACCACCACCACCACCACCACCACCA 40 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 16 24.11 4.62 1.49 chr6ptel1M 751045 751109 (248891) (TTTTC)n#Simple_repeat 1 67 (0) m_b291s252i3 11965 chr6ptel1M 751045 TTTTGTTGTTGTTTGCTTGCATTTTATTTTC-TTTCTTTT-TTTCTTTTT 751092 v - v v viv v - - ii (TTTTC)n#Simp 1 TTTTCTT-TTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTT 49 chr6ptel1M 751093 GATTTGATTT-TTTTCTT 751109 vv vv - (TTTTC)n#Simp 50 CTTTTCTTTTCTTTTCTT 67 Matrix = Unknown Transitions / transversions = 0.30 (3/10) Gap_init rate = 0.06 (4 / 64), avg. gap size = 1.00 (4 / 4) 13 19.41 4.88 0.00 chr6ptel1M 751132 751172 (248828) (ATATTT)n#Simple_repeat 1 43 (0) m_b291s252i4 11966 chr6ptel1M 751132 ATATTTATACATATA-TTAGATTTA-ATATAAATTCATGTTTA 751172 iv - v - v v i i (ATATTT)n#Sim 1 ATATTTATATTTATATTTATATTTATATTTATATTTATATTTA 43 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 487 30.96 4.26 2.58 chr6ptel1M 751322 751626 (248374) C L1ME4c_3end#LINE/L1 (179) 651 342 m_b291s551i0 11967 chr6ptel1M 751322 TACAATGTTCTTTTTGTTCTACTTATTTCACTCAGCATCAGTTCATGGAA 751371 ---- v i i v i i i vv ii v C L1ME4c_3end#L 651 TACAAT----TTTGTATTCTGCTTTTTTCACTTAACATTATATCATAAAC 606 chr6ptel1M 751372 GTCTTTCCAGGCTTTTCCGAAATCAGCCTGCTGATCATTTCTTATAA--A 751419 i - v i vi v iv i vv v iv v i v ii--i C L1ME4c_3end#L 605 AT-TTTCCATGTTGCTACATAGTCTTCATAATTATCATTTTTAATGGCTG 557 chr6ptel1M 751420 CAGTAATATTCCATTATCTTCATATGTCATAATTTATTCATCCATTCCCC 751469 - iivv ?v i ii i i v C L1ME4c_3end#L 556 CA-TAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCC 508 chr6ptel1M 751470 AACTGACGGGCATCCACTCAGTTTT-AATTCCTTGCTGCTACAAAAAGAG 751518 v i vi i ii vviv i- ii i ii i v iv C L1ME4c_3end#L 507 TATTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACG 458 chr6ptel1M 751519 ACTGCTATAAATATGTGGGTTC--------TTTCCCCTCTGTT--ATGAT 751558 - v i i v vv v -------- i i v -- v C L1ME4c_3end#L 457 -CTGCAATGAACATCTTCGTGCATATAGCTTTTTCCTTCTTTTGAATTAT 409 chr6ptel1M 751559 TTCTTTGGGATACAGATCCAGTCGTGAGACTGCTGGATCAAAGGGTATGC 751608 i i v vvi vv ii i i i - C L1ME4c_3end#L 408 TTCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATG- 360 chr6ptel1M 751609 CACAATTTTATAGCCCTT 751626 v v i i C L1ME4c_3end#L 359 AACATTTTTATGGCTCTT 342 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.97 CpG sites = 52, Kimura (unadjusted) = 41.20 Transitions / transversions = 1.30 (52/40) Gap_init rate = 0.04 (12 / 304), avg. gap size = 1.75 (21 / 12) 345 22.62 12.14 5.43 chr6ptel1M 751686 751858 (248142) L2d_3end#LINE/L2 328 511 (5) m_b291s601i16 11968 chr6ptel1M 751686 TTAATTATTTCCTATTTATTCAGTATATAGCT-TCT--TTGTATCG-ATT 751731 v v i i ------ i v i - -- v i-i v L2d_3end#LINE 328 TTAATTATATACTGTCT------TGTATTGTTCTCTAATTGTTTCATGTG 371 chr6ptel1M 751732 TGTTAGTGTGCTATGTCCACCATTAGATTGTAAACTCCTTGAGAGTAGGA 751781 v -- i v v v i i i i i L2d_3end#LINE 372 TGTTAGTCT--TGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGG 419 chr6ptel1M 751782 ACTAT---TTA-ATTTTTATTTTTGT-------ATCGC------CAGTAC 751814 i --- - i ? - ? i ------- v ------ i L2d_3end#LINE 420 ACCATGTCTTATACTNTT-TTNTCGTTCCCCACAGCGCCTAGCACAGTGC 468 chr6ptel1M 751815 CTATAATATAGTAGACAACTTAATAAATGATTGTTGATTGACTG 751858 iv vv i i -i i iv i L2d_3end#LINE 469 TGAGCACATAGTAGGC-GCTCAATAAATACTTGTTGATTGATTG 511 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.34 CpG sites = 23, Kimura (unadjusted) = 28.09 Transitions / transversions = 1.64 (23/14) Gap_init rate = 0.10 (17 / 172), avg. gap size = 1.82 (31 / 17) 509 28.27 1.37 0.68 chr6ptel1M 751713 751858 (248142) L2c_3end#LINE/L2 329 475 (3) m_b291s601i17 11968 chr6ptel1M 751713 TAGCTTCT-TTGTATCGATTTGTTAGTGTG-CTATGTCCACCATTAGATT 751760 i v - vivi i vii? - i v v i i L2c_3end#LINE 329 TAACTTGTATTGTAATTGTCTGTTTACNTGTCTGTCTCCTCCACTAGACT 378 chr6ptel1M 751761 GTAAACTCCTTGAGAGTAGGAACTATTTAATTTTTATTTTTGTATCGCCA 751810 i i i i i ii v vv v i i v L2c_3end#LINE 379 GTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTATCCCCA 428 chr6ptel1M 751811 GTACCTATAATATAGTAGACAACTTAATAAATGATTGTTGATTGACTG 751858 ii ivv i i -i i v v v L2c_3end#LINE 429 GCGCCTGGCACATAGTAGGC-GCTCAATAAATGTTTGTTGAATGAATG 475 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.35 CpG sites = 25, Kimura (unadjusted) = 36.94 Transitions / transversions = 1.56 (25/16) Gap_init rate = 0.02 (3 / 145), avg. gap size = 1.00 (3 / 3) 191 38.20 9.38 0.48 chr6ptel1M 752867 753058 (246942) L2a_3end#LINE/L2 6 214 (303) m_b291s601i18 11969 chr6ptel1M 752867 TAACCTGACTCCTTCTGACTTTTTTTATTTTATTAAATCTTACTTTCCAT 752916 i i i i iiv v i i i v ii i ivvv vii i vi L2a_3end#LINE 6 TGATCTGGCCCCCCGTTACCTCTCTGACCTCATCTCCTACCACTCTCCCC 55 chr6ptel1M 752917 TTGATTTAC-------CAGTCA-----GCCAGCTT--TGTTCTTTGAACA 752952 i vii i ------- i ----- vv -- i i L2a_3end#LINE 56 CTCGCTCACTCCGCTCCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACA 105 chr6ptel1M 752953 AGACAGGCCTTATCCCAGCTCCTGACATTTTCCCTAGTTGTTCCTTATTC 753002 v v vivv iv vv i v v v v i i v v L2a_3end#LINE 106 CGCCAGGCACGCTCCCGCCTCAGGGCCTTTGCACTTGCTGTTCCCTCTGC 155 chr6ptel1M 753003 C-AGAATCTACTTCCTT---ATATTTGACTTCCTTGCTTCCCTCACATCC 753048 -i iviv ii--- ii vv vv i - v L2a_3end#LINE 156 CTGGAACGCTCTTCCCCCAGATATCCGCATGGCTCGC-TCCCTCACCTCC 204 chr6ptel1M 753049 TCCAAATCCT 753058 i ii i L2a_3end#LINE 205 TTCAGGTCTT 214 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 47.05 CpG sites = 41, Kimura (unadjusted) = 55.63 Transitions / transversions = 1.28 (41/32) Gap_init rate = 0.03 (6 / 191), avg. gap size = 3.17 (19 / 6) 16 8.13 0.00 0.00 chr6ptel1M 754144 754169 (245831) (TAAAA)n#Simple_repeat 1 26 (0) m_b291s252i5 11970 chr6ptel1M 754144 TAAAAAAAAATGAAATAAAATAAAAT 754169 v i (TAAAA)n#Simp 1 TAAAATAAAATAAAATAAAATAAAAT 26 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 11 23.17 0.00 8.16 chr6ptel1M 755120 755172 (244828) (ATCTAT)n#Simple_repeat 1 49 (0) m_b291s252i6 11971 chr6ptel1M 755120 ATCTATATCTTTATATCATATGTCTGTATTTACATATAGACATATGATAT 755169 -- - i i i i v v iv - v (ATCTAT)n#Sim 1 ATCTATATC--TATATC-TATATCTATATCTATATCTATATCTAT-ATCT 46 chr6ptel1M 755170 ATA 755172 (ATCTAT)n#Sim 47 ATA 49 Matrix = Unknown Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.08 (4 / 52), avg. gap size = 1.00 (4 / 4) 11 22.47 0.00 6.82 chr6ptel1M 755131 755177 (244823) (TATAACA)n#Simple_repeat 1 44 (0) m_b291s252i7 11971 chr6ptel1M 755131 TATATCATATGTCTGTATTTACATATAGACATATGATATATACCATA 755177 v iv -i - v - i i v (TATAACA)n#Si 1 TATAACATATAAC-ATA-TAACATATA-ACATATAACATATAACATA 44 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.07 (3 / 46), avg. gap size = 1.00 (3 / 3) 303 25.35 0.00 0.00 chr6ptel1M 755198 755268 (244732) C MER63D#DNA/hAT-Tip100 (626) 435 365 m_b291s502i1 11972 chr6ptel1M 755198 ATTTTCTCCATTGTTTTCTTAAAACTAGGTAATTGACAAATCAATAAATT 755247 iii iv ii ii v i C MER63D#DNA/hA 435 ATTTTCTCCATCACTTTCTTAAGTCTAGACAATCAACAAAACAATAAATC 386 chr6ptel1M 755248 GTGACTTGACTTGTAGTATTT 755268 iv v i i ii C MER63D#DNA/hA 385 AAGCCCTGATTTGTAGCGTTT 365 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 30.44 CpG sites = 14, Kimura (unadjusted) = 32.94 Transitions / transversions = 3.50 (14/4) Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0) 18 13.29 5.66 3.70 chr6ptel1M 755382 755434 (244566) (ATTATTT)n#Simple_repeat 1 54 (0) m_b291s252i8 11973 chr6ptel1M 755382 ATCATTTGTTA-TTATTAAATTA-AATTTATTATTTATTATATTA-TATG 755428 i i - - v -v - - v (ATTATTT)n#Si 1 ATTATTTATTATTTATT-ATTTATTATTTATTATTTATTAT-TTATTATT 48 chr6ptel1M 755429 TAATAT 755434 v (ATTATTT)n#Si 49 TATTAT 54 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.10 (5 / 52), avg. gap size = 1.00 (5 / 5) 284 24.31 19.01 1.41 chr6ptel1M 755435 755555 (244445) C L2c_3end#LINE/L2 (4) 474 333 m_b291s601i19 11974 chr6ptel1M 755435 ATTCTATTATAATAAATATT-ATTAAATACTGACTTTG-----GGCACCA 755478 - -i i i - i iii iv v ----- i ii C L2c_3end#LINE 474 ATTC-ATT-CAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTG 427 chr6ptel1M 755479 GGGATGCAAAAA--AAAAAG---TAG-----------AGGGAACTCACAG 755512 i i -- v ---ii ----------- i i C L2c_3end#LINE 426 GGGATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAG 377 chr6ptel1M 755513 TCTAATGGGAGGGACAG-CATGCAAACAAACAACTATTATACAA 755555 i ii i - ? i i i iv C L2c_3end#LINE 376 TCTAGTGGAGGAGACAGACANGTAAACAGACAATTACAATACAA 333 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.01 CpG sites = 25, Kimura (unadjusted) = 32.35 Transitions / transversions = 6.25 (25/4) Gap_init rate = 0.07 (8 / 120), avg. gap size = 3.12 (25 / 8) 17 13.26 0.00 0.00 chr6ptel1M 755560 755586 (244414) (TATC)n#Simple_repeat 1 27 (7) m_b291s252i10 11975 chr6ptel1M 755560 TATCTACCTATCTGTCTATCTATATAT 755586 i i v (TATC)n#Simpl 1 TATCTATCTATCTATCTATCTATCTAT 27 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 31 0.00 0.00 0.00 chr6ptel1M 755587 755613 (244387) (AC)n#Simple_repeat 1 27 (0) c_b291s251i4 11976 chr6ptel1M 755587 ACACACACACACACACACACACACACA 755613 (AC)n#Simple_ 1 ACACACACACACACACACACACACACA 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 274 32.00 1.33 0.00 chr6ptel1M 756009 756083 (243917) C L2d2_3end#LINE/L2 (9) 546 471 m_b291s601i20 11977 chr6ptel1M 756009 ATGAGTAAACATTTATTAAATGTTGACTATCTGTCAAACATTGTGTTAAG 756058 v ii i i ii iiv i v iv ii i i i C L2d2_3end#LIN 546 ATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGG 497 chr6ptel1M 756059 TGCTG-GGGAGATGCAATGAAGTCTA 756083 i - i i v v C L2d2_3end#LIN 496 CGCTGTGGGGGATACAAAGAAGTATA 471 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.23 CpG sites = 18, Kimura (unadjusted) = 45.41 Transitions / transversions = 3.00 (18/6) Gap_init rate = 0.01 (1 / 74), avg. gap size = 1.00 (1 / 1) 324 27.10 4.03 8.39 chr6ptel1M 756489 756637 (243363) MIRc#SINE/MIR 2 144 (124) m_b291s601i21 11978 chr6ptel1M 756489 GAGGT--TGTGGTGCAGTCCGGATAGTGAAAGGAACTTGTAAGCAGGAGT 756536 i-- -- v v v vv i ------- MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGT--GGAAAGAGCACTGGACTTG-------GAGT 42 chr6ptel1M 756537 CA-CAAGCTCTAGAATCTTAGTCCCAATTCTGCTCTTAACT--CTGATGT 756583 -v vi i iv -v iii ivi v -- - MIRc#SINE/MIR 43 CAGGAAGACCTGGGTTC-GAGTCCCGGCTCTGCCACTTACTAGCTG-TGT 90 chr6ptel1M 756584 CTACTCTGGACAAGTCATTGGATTTTTCTGAGCTTTAGTTTTTGCTTCT- 756632 -v ii i i vi ii i i i iiv v - MIRc#SINE/MIR 91 -GACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTG 139 chr6ptel1M 756633 TAAAA 756637 MIRc#SINE/MIR 140 TAAAA 144 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.20 CpG sites = 22, Kimura (unadjusted) = 34.34 Transitions / transversions = 1.47 (22/15) Gap_init rate = 0.10 (15 / 148), avg. gap size = 1.20 (18 / 15) 447 29.99 3.52 1.38 chr6ptel1M 756532 756673 (243327) MIR3#SINE/MIR 36 180 (28) m_b291s601i22 11978 chr6ptel1M 756532 GGAGTCACAAGCTCTAGAATCTTAGTCCCAATTCTGCTCTTAACTCTGAT 756581 vi vi i iv - iii ivi -? v MIR3#SINE/MIR 36 GGAGTCAGGAGACCTGGGTTCT-AGTCCCGGCTCTGCCACTAACT-NGCT 83 chr6ptel1M 756582 GTCT-ACTCTGGACAAGTCATTGGATTTTTCTGAGCTTTAGTTTTTGCTT 756630 v - ii i i vv ii i i i i iiv v MIR3#SINE/MIR 84 GTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCAT 133 chr6ptel1M 756631 CTTAAAAGTTAAGGAGTTGGACAAGTTGATTTGTA----CCTTTCCA 756673 vv i v i i v v i v ---- i MIR3#SINE/MIR 134 CTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCA 180 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.88 CpG sites = 26, Kimura (unadjusted) = 40.13 Transitions / transversions = 1.62 (26/16) Gap_init rate = 0.03 (4 / 141), avg. gap size = 1.75 (7 / 4) 708 27.49 6.16 0.00 chr6ptel1M 757095 757305 (242695) MIRc#SINE/MIR 42 265 (3) m_b291s601i23 11979 chr6ptel1M 757095 TCAGGAGTACTGGGATTCCAATCCAGCCTC--ATATTTCCTAGCTATGTG 757142 iv iv i v i v v --vi i v i MIRc#SINE/MIR 42 TCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTG 91 chr6ptel1M 757143 ACTCTGAGCAAGACACTTAACCTGTGTCTGCTTCAGTTGCCTTATTTGTA 757192 ii i v v v vv i v i i MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTA 141 chr6ptel1M 757193 AAATGGGGATAACAATA------CTGTCTTTCACACAAGGTTGTATTAAA 757236 i ------ i vi v i vv i i MIRc#SINE/MIR 142 AAATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAG 191 chr6ptel1M 757237 GATCAAATGGGCTA----CTTTTAAAGTGCTTTGGGATCCTTAAAGT-TT 757281 i v ----v v v i vi v iv -i MIRc#SINE/MIR 192 GATCAAATGAGATAATGTATGTGAAAGCGCTTTGTAAACTGTAAAGTGCT 241 chr6ptel1M 757282 CCAAGAATACCAGATGTTGCTATT 757305 vi vi iiv i? ii MIRc#SINE/MIR 242 ATACAAATGTAAGGNGTTATTATT 265 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.26 CpG sites = 31, Kimura (unadjusted) = 35.00 Transitions / transversions = 1.15 (31/27) Gap_init rate = 0.02 (4 / 210), avg. gap size = 3.25 (13 / 4) 515 30.58 4.07 1.13 chr6ptel1M 758081 758252 (241748) C MIR3#SINE/MIR (9) 199 23 m_b291s601i24 11980 chr6ptel1M 758081 AATCACAGA--TTTGGAGCTGAAAGGGAAGTTAGAGGCCATTGTGATCAA 758128 i --v ii i vv ii ivv vi C MIR3#SINE/MIR 199 AATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAA 150 chr6ptel1M 758129 CTTTCTAATTTTATAGATGATGGAAGTAGGACCTAGAGAGGTTAGATGAA 758178 iii v i v i v ii i i v ii v C MIR3#SINE/MIR 149 CCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGAC 100 chr6ptel1M 758179 TTGGCCAGCATCACTTAACTCGT--GTG---AATTTGGGATTTGAGTTCA 758223 v ivi vi i ?v -- ---i vii i v iii C MIR3#SINE/MIR 99 TTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCA 50 chr6ptel1M 758224 TATTTTCCTGACTCCAGGTCCAGTGCTCT 758252 -iv i vi - C MIR3#SINE/MIR 49 -GGTCTCCTGACTCCCAGTCC-GTGCTCT 23 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.26 CpG sites = 33, Kimura (unadjusted) = 41.32 Transitions / transversions = 1.74 (33/19) Gap_init rate = 0.03 (5 / 171), avg. gap size = 1.80 (9 / 5) 474 29.54 3.68 2.42 chr6ptel1M 758112 758274 (241726) C MIR1_Amn#SINE/MIR (62) 168 4 m_b291s601i25 11980 chr6ptel1M 758112 GAGGCCATTGTGATCAACTTTCTAATTTTATAGATGATGGAAGTAGGACC 758161 i v i v i --- i iv i v i v ii i ? C MIR1_Amn#SINE 168 GAGGTCAGTATCATTA---TCCCCATTTTACAGATGAGGAAACTGAGGCN 122 chr6ptel1M 758162 TAGAGAGGTTAGATGAATTGGCCAGCATCACTTAACTCGT--GTG---AA 758206 i ? ii v v ivi ?i i ?v i-- ---i C MIR1_Amn#SINE 121 CAGAGAGGTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNAGTGGCAGA 72 chr6ptel1M 758207 TTTGGGATTTGAGTTCATATTTTCCTGACTCCAGGTCCAGTGCTCTACCC 758256 vii ? ? iii -iv i i v vi i C MIR1_Amn#SINE 71 GCCGGGANTNGAACCCA-GGTCTCCCGAGTCCCAGTCCAGTGCTCTATCC 23 chr6ptel1M 758257 ATT-GACTGAACTGCATCC 758274 i - iiv v C MIR1_Amn#SINE 22 ACTAGACCACACTGCCTCC 4 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.40 CpG sites = 32, Kimura (unadjusted) = 41.77 Transitions / transversions = 2.13 (32/15) Gap_init rate = 0.04 (7 / 162), avg. gap size = 1.43 (10 / 7) 523 30.07 4.20 0.00 chr6ptel1M 758131 758273 (241727) C MIRc#SINE/MIR (118) 150 2 m_b291s601i26 11980 chr6ptel1M 758131 TTCTAATTTTATAGATGATGGAAGTAGGACCTAGAGAGGTTAGATGAATT 758180 i iv i v i v ii i ii ii v C MIRc#SINE/MIR 150 TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTT 101 chr6ptel1M 758181 GGCCAGCATCACTTAACTCGT--GTGA---ATTTGGGATTTGAGTTCATA 758225 v ivi vi i v -- i--- vii i i iii vi C MIRc#SINE/MIR 100 GCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGG 51 chr6ptel1M 758226 TTTTCCTGACTCCAGGTCCAGTGCTCTACCCATTG-ACTGAACTGCATC 758273 i i vi i - iiv v C MIRc#SINE/MIR 50 TCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTGCCTC 2 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.23 CpG sites = 30, Kimura (unadjusted) = 40.73 Transitions / transversions = 2.31 (30/13) Gap_init rate = 0.02 (3 / 142), avg. gap size = 2.00 (6 / 3) 259 31.12 5.56 1.79 chr6ptel1M 758294 758401 (241599) L2d_3end#LINE/L2 398 509 (7) m_b291s601i27 11981 chr6ptel1M 758294 TGGAAGCTCCTTGAGAATAAGGCTTATAACTTACACTTCCTTTAT--TTC 758341 v iii i vii iv i - ?i ? -- L2d_3end#LINE 398 TGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATAC-TNTTTTNTCGTTC 446 chr6ptel1M 758342 TTCAAAGTATTGAACCACAGTTGTAGGCATTTAGTAGAT-TTCAATAGAT 758390 ii v iiiiv i- vv ii iv ii-i i L2d_3end#LINE 447 CCCACAGCGCCTAG-CACAGTGCTGAGCACATAGTAGGCGCTCAATAAAT 495 chr6ptel1M 758391 -CT--CTAATTGAT 758401 - --i i L2d_3end#LINE 496 ACTTGTTGATTGAT 509 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.00 CpG sites = 25, Kimura (unadjusted) = 44.96 Transitions / transversions = 3.12 (25/8) Gap_init rate = 0.06 (6 / 107), avg. gap size = 1.33 (8 / 6) 411 27.78 12.42 1.18 chr6ptel1M 758475 758627 (241373) MIR3#SINE/MIR 12 181 (27) m_b291s601i28 11982 chr6ptel1M 758475 GTTGA--AGAGAAGGTGTGGATTTGAATCCAGA------GGGTTCTAGTG 758516 i -- ii iii i v i vi i------ v MIR3#SINE/MIR 12 GCTGAGCAGAGAGAGCACGGACTGGGAGTCAGGAGACCTGGGTTCTAGTC 61 chr6ptel1M 758517 TAAGCCATACTCATTACCAATC-------CCTTTGGTAAGTC--TTTAAT 758557 ivi iv i - i v v?v ------- v i -- i vi MIR3#SINE/MIR 62 CCGGCTCTGC-CACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACC 110 chr6ptel1M 758558 TCTGCTAAACCTCAATTTCTTC-TCTGTAAAGTGATAGGGTTGGACTAGA 758606 - iii i i - i vi MIR3#SINE/MIR 111 TCT-CTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGA 159 chr6ptel1M 758607 TGTTCTC-AAGAACCTATCTAG 758627 v - iv iv i MIR3#SINE/MIR 160 TGATCTCTAAGGTCCCTTCCAG 181 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.39 CpG sites = 28, Kimura (unadjusted) = 36.60 Transitions / transversions = 2.00 (28/14) Gap_init rate = 0.05 (8 / 152), avg. gap size = 2.62 (21 / 8) 14 11.71 8.11 0.00 chr6ptel1M 758662 758698 (241302) (ATTTGG)n#Simple_repeat 1 40 (0) m_b291s252i11 11983 chr6ptel1M 758662 ATTTGGATTT-AATTTGGATTTAGAGTTGG--TTGGCTTT 758698 -i i v -- v (ATTTGG)n#Sim 1 ATTTGGATTTGGATTTGGATTTGGATTTGGATTTGGATTT 40 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.50 (3 / 2) 204 25.32 15.19 0.00 chr6ptel1M 759857 759935 (240065) MIR3#SINE/MIR 77 167 (41) m_b291s601i29 11984 chr6ptel1M 759857 ATTGTCTGTGTAACCTTTGGTAAGTTA----ACCTGTCT----CTGAGTT 759898 i ?v i v i i ---- v ---- v MIR3#SINE/MIR 77 ACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTT 126 chr6ptel1M 759899 ---TTAGCTAGAAAGC-AAGAGGTTGTACTAGATTACTTCT 759935 --- i v iv ii- i i v v ii MIR3#SINE/MIR 127 TCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCT 167 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.14 CpG sites = 12, Kimura (unadjusted) = 32.14 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.05 (4 / 78), avg. gap size = 3.00 (12 / 4) 196 32.79 12.84 3.94 chr6ptel1M 760156 760482 (239518) L2#LINE/L2 2698 3052 (30) m_b291s601i30 11985 chr6ptel1M 760156 CCATCACCTCTTGCTTGGACTATTTCAATGGCTTC----------TC--- 760192 i i i i i v i i ---------- --- L2#LINE/L2 2698 CCATCATCTCTCGCCTGGATTACTGCAATAGCCTCCTAACTGGTCTCCCT 2747 chr6ptel1M 760193 GCTTTCAA--TTGTCCCTCTTC--TCTGCTCAGTCCTTCAAAA-AGCTGC 760237 i v-- i i ? -- ii ------ v - v L2#LINE/L2 2748 GCTTCCACCCTTGCCCCCCTNCAGTCTATTC------TCAACACAGCAGC 2791 chr6ptel1M 760238 CCAAATAATCCATCTCAAACACA--TCTGGCCACGTTAATC-TCTGCCAA 760284 vi i i v i v ii -- v ii i i v - iv L2#LINE/L2 2792 CAGAGTGATCCTTTTAAAACGTAAGTCAGATCATGTCACTCCTCTGCTCA 2841 chr6ptel1M 760285 GCAATCTTGAGCGACTTGTTGCTACATTCAGCACAAAAACC-AATTCCT- 760332 iv vi iv ii i viiiiiv i vii i - v - L2#LINE/L2 2842 AAACCCTCCAATGGCTTCCCATCTCACTCAGAGTAAAAGCCAAAGTCCTT 2891 chr6ptel1M 760333 -CTGTCGGGCTTTTAAAG-CTTCTATGATTT-TTCTCCAGCTTTCCTTTT 760379 - vi -- i vi i - i vi i -v i -- v v i i L2#LINE/L2 2892 ACAAT--GGCCTACAAGGCCCTACATGATCTGGTCCCC--CGTTACCTCT 2937 chr6ptel1M 760380 CTGGGCTCCTCAGATTTGATTCCTTTCTCCACATGGTGATTCC-CT---- 760424 i--- vv iiv iiv i i - vi v v i - ---- L2#LINE/L2 2938 CTGA---CCTCATCTCCTACCACTCTCCCC-CTCGCTCACTCCGCTCCAG 2983 chr6ptel1M 760425 TTACATTGTCCTAC-TGCCCTTTCCCGAAC---TCA-GCA---TCCTGTC 760466 ii i v v - iv i i ---i - --- i i L2#LINE/L2 2984 CCACACTGGCCTCCTTGCTGTTCCTCGAACACGCCAGGCACGCTCCCGCC 3033 chr6ptel1M 760467 TT---CCCTGTGCATTTGC 760482 i---v v i L2#LINE/L2 3034 TCAGGGCCTTTGCACTTGC 3052 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.57 CpG sites = 68, Kimura (unadjusted) = 46.06 Transitions / transversions = 1.94 (68/35) Gap_init rate = 0.10 (33 / 326), avg. gap size = 1.70 (56 / 33) 16 34.40 2.88 3.88 chr6ptel1M 760619 760722 (239278) (TA)n#Simple_repeat 1 103 (0) m_b291s252i12 11986 chr6ptel1M 760619 TATGTATCCATGCATACATATATATTCATACATCCATGCTAACAAAATGT 760668 i vi ii i vi i vi -v vvv v i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATAT-ATATATATATAT 49 chr6ptel1M 760669 ACACTA-ATAT-TATGTGCATATATAGTTTA-ATATATGTGTAGTACATA 760715 i - - - i ii - v - i i - i (TA)n#Simple_ 50 ATA-TATATATATATATATATATATA-TATATATATATATATA-TATATA 96 chr6ptel1M 760716 TACATAT 760722 i (TA)n#Simple_ 97 TATATAT 103 Matrix = Unknown Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.07 (7 / 103), avg. gap size = 1.00 (7 / 7) 256 30.25 1.12 3.45 chr6ptel1M 760723 760811 (239189) MIRb#SINE/MIR 2 88 (180) m_b291s601i31 11987 chr6ptel1M 760723 AGAGGCACGTCATTGGCACAATGGATCAAGTACTGGGTTTGGAATCAGAC 760772 vi iv i - ii i vvi i v v i MIRb#SINE/MIR 2 AGAGGGGCAGCGT-GGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGAC 50 chr6ptel1M 760773 TCTTCATGAGTTCAAAT-CTGGCTTTAGATACTTATTAGC 760811 vvvi - i i - i i - vi i MIRb#SINE/MIR 51 AGACC-TGGGTTCGAATCCCGGCTCT-GCCACTTACTAGC 88 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.34 CpG sites = 16, Kimura (unadjusted) = 40.13 Transitions / transversions = 1.60 (16/10) Gap_init rate = 0.05 (4 / 88), avg. gap size = 1.00 (4 / 4) 371 29.52 5.38 7.10 chr6ptel1M 762188 762373 (237627) C L2b_3end#LINE/L2 (13) 453 271 m_b291s601i32 11988 chr6ptel1M 762188 ACAAGAGCTTACTAACCATTTACAGTGTGCCAGGCACTGTGCCAAGCCCC 762237 ivii i v iii v ? i i v i C L2b_3end#LINE 453 ACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCT 404 chr6ptel1M 762238 GGGGGTTCA------AACAAAGGCAAAAACACAATCTCTGCCCTCAAGAA 762281 i v ------ i--- v i ? ii i v i C L2b_3end#LINE 403 GGGGATACAGCGGTGAACAAG---ACAGACNCGGTCCCTGCCCTCACGGA 357 chr6ptel1M 762282 GCACATGTTCTAATGATGGTAAT-GACATACAAG-ATATATCGCACCATA 762329 v iiv i iv vi i- ii ?- v i ---- i? C L2b_3end#LINE 356 GCTCACAGTCTAGTGGGGGAGACAGACATGTAANCAGACA----ATNATA 311 chr6ptel1M 762330 ATCCCAGGGGGTCATTAAGGAGTAAGA--GAGAAGGCACAAATAAG 762373 - i v v ----- i i -- i ii v i vi C L2b_3end#LINE 310 A-CCCAGAGTGGCA-----GGGTAGGACTGGGGGGGCCCAGAGGAG 271 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.68 CpG sites = 35, Kimura (unadjusted) = 40.80 Transitions / transversions = 2.19 (35/16) Gap_init rate = 0.09 (17 / 185), avg. gap size = 1.35 (23 / 17) 231 36.82 4.19 2.75 chr6ptel1M 762201 762415 (237585) C L2c_3end#LINE/L2 (15) 463 246 m_b291s601i33 11988 chr6ptel1M 762201 AACCATTTACAGTGTGCCAGGCACTGTGCCAAGCCCCGGGGGTTCAAACA 762250 v iv v i vivi - i v i i v -i C L2c_3end#LINE 463 AAACATTTATTGAGCGCCTACTA-TGTGCCAGGCGCTGGGGATACAAA-G 416 chr6ptel1M 762251 AAGGCAAAAACACAATCTCTGCCCTCAAGAAGCACATGTTCTAATGATGG 762300 v ivv i ii i i v iiv i iv C L2c_3end#LINE 415 ATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAGTGGAGG 366 chr6ptel1M 762301 TAAT-GACATACA---AGATATATCGCACCATAATCCCAGG----GGGTC 762342 vi i- ?ii --- i - ii vi i viiv v ---- v ii C L2c_3end#LINE 365 AGACAGACANGTAAACAGACA-ATTACAATACAAGTTAATGATAAGTGCT 317 chr6ptel1M 762343 ATTA-AGGAGTAAGAGAGAAGGCACAAATAAGATCCACAGAAAATGGAGT 762391 v -i - v v i ii -v ii -v ii v vii C L2c_3end#LINE 316 ATAATGGGAGT-ATAGACAGGGTGC-TATGGGA-GCACAGAGGAGGGCAC 270 chr6ptel1M 762392 TTGAACTAGAAGCAAGGAATCAGG 762415 i ii ?vviii ii C L2c_3end#LINE 269 CTAGACTAGNCTTGGGGGGTCAGG 246 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 52.63 CpG sites = 49, Kimura (unadjusted) = 54.80 Transitions / transversions = 1.75 (49/28) Gap_init rate = 0.05 (10 / 214), avg. gap size = 1.50 (15 / 10) 16 24.62 0.00 0.00 chr6ptel1M 762650 762692 (237308) (TTTT)n#Simple_repeat 1 43 (0) m_b291s252i13 11989 chr6ptel1M 762650 TTTTCTTTCTTTCTTTTTTTTTTTTTATTATAGCTTTTTATTT 762692 i i i v v vvi v (TTTT)n#Simpl 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 43 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 326 28.62 2.55 8.78 chr6ptel1M 763144 763300 (236700) C MIRb#SINE/MIR (117) 151 4 m_b291s601i35 11990 chr6ptel1M 763144 CTCATTTTATAGTTGAT-AAAGTGAAAC--AAATGGGATGCAGTGACTTG 763190 i i v v- v ii -- i - i i vv i C MIRb#SINE/MIR 151 CCCATTTTACAGATGAGGAAACTGAGGCTCAGA-GAGGTTAAGTAACTTG 103 chr6ptel1M 763191 TCCAGAGTCATACAGCTAGTAAATCCCTGAGGCCAGAATAGAACTCATGA 763240 i ii i i vv v v vi v v i ---- C MIRb#SINE/MIR 102 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCC---- 57 chr6ptel1M 763241 TGAGAAGCCTTCCTGACTCCAAGTCCAGTTGTCTAAGTCTTGTGCTAGCC 763290 ---- i i vi iv v vv --v ivv --i C MIRb#SINE/MIR 56 ----AGGTCTGTCTGACTCCAAAGCCCGTGCTCT--TTCCACTGC--ACC 15 chr6ptel1M 763291 A-GCTGCCCCT 763300 - C MIRb#SINE/MIR 14 ACGCTGCCCCT 4 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.29 CpG sites = 21, Kimura (unadjusted) = 36.29 Transitions / transversions = 1.05 (21/20) Gap_init rate = 0.10 (16 / 156), avg. gap size = 1.06 (17 / 16) 433 24.68 2.29 7.20 chr6ptel1M 763144 763274 (236726) C MIRc#SINE/MIR (120) 148 24 m_b291s601i34 11990 chr6ptel1M 763144 CTCATTTTATAGTTGAT-AAAGTGAAAC--AAATGGGATGCAGTGACTTG 763190 i i v v- v ii -- i - i i vv C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGA-GAGGTTAAGTGACTTG 100 chr6ptel1M 763191 TCCAGAGTCATACAGCTAGTAAATCCCTGAGGCCAGAATAGAACTCATGA 763240 i ii i i vv v v vi v v i ---- C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCC---- 54 chr6ptel1M 763241 TGAGAAGCCTTCCTGACTCCAAGTCCAGTTGTCT 763274 ---- i i vv C MIRc#SINE/MIR 53 ----AGGTCTTCCTGACTCCAAGTCCAGTGCTCT 24 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 30.18 CpG sites = 16, Kimura (unadjusted) = 30.18 Transitions / transversions = 1.14 (16/14) Gap_init rate = 0.08 (11 / 130), avg. gap size = 1.09 (12 / 11) 186 30.13 5.74 7.50 chr6ptel1M 763401 763522 (236478) C L2c_3end#LINE/L2 (20) 458 339 m_b291s601i36 11991 chr6ptel1M 763401 TTTCCTAATTGCTTGCTATGTGCTGAGGCTGCCTTGTGTGGAGACACAAA 763450 vi i vi i i i- - ------ i i C L2c_3end#LINE 458 TTTATTGAGCGCCTACTATGTGCC-AGGC-GC------TGGGGATACAAA 417 chr6ptel1M 763451 GA--AAGGAGAAAAGAAACCCTGCCTGCAAGGGGATGGTGATCCAATGGG 763498 -- vi v v iv- iv i v viiii i i i C L2c_3end#LINE 416 GATGAATAAGACACGGT-CCCTGCCCTCAAGGAGCTCACAGTCTAGTGGA 368 chr6ptel1M 763499 GCAGAGAGA---GT--GCAAACGATTATA 763522 v v --- --i i i i C L2c_3end#LINE 367 GGAGACAGACANGTAAACAGACAATTACA 339 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.93 CpG sites = 23, Kimura (unadjusted) = 40.52 Transitions / transversions = 2.09 (23/11) Gap_init rate = 0.10 (12 / 121), avg. gap size = 1.33 (16 / 12) 27 8.01 7.55 0.00 chr6ptel1M 765195 765247 (234753) (TTAAAA)n#Simple_repeat 1 57 (0) m_b291s252i14 11992 chr6ptel1M 765195 TTAAAATT--ATTTAAAATTAAAATAAAAAATAAAA-T-ATATTAAAATT 765240 -- v v v - - v (TTAAAA)n#Sim 1 TTAAAATTAAAATTAAAATTAAAATTAAAATTAAAATTAAAATTAAAATT 50 chr6ptel1M 765241 AAAATTA 765247 (TTAAAA)n#Sim 51 AAAATTA 57 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.06 (3 / 52), avg. gap size = 1.33 (4 / 3) 316 35.99 3.15 1.55 chr6ptel1M 765297 765423 (234577) MIRc#SINE/MIR 18 146 (122) m_b291s601i37 11993 chr6ptel1M 765297 GTAGAAAGAGAACTAGATTTTGGGCCAA-AAGACTCAAATT-GAATTCTG 765344 i v i i v i i i- iiiii - i i i MIRc#SINE/MIR 18 GTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCG 67 chr6ptel1M 765345 CTTTTAGATCATCTGAT--CTGAGTGACCACAGCCAAGTCATTTGGTCTT 765392 vi i i--i ii iv -- v vii v i iii i MIRc#SINE/MIR 68 GCTCTG--CCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 chr6ptel1M 765393 TCATAACTGGAATTTCCTTTTCTGTTAAATG 765423 vv i ivv i iv v MIRc#SINE/MIR 116 TCTGAGCCTCAGTTTCCTCATCTGTAAAATG 146 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 51.84 CpG sites = 32, Kimura (unadjusted) = 53.69 Transitions / transversions = 2.46 (32/13) Gap_init rate = 0.04 (5 / 126), avg. gap size = 1.20 (6 / 5) 520 32.85 8.21 2.43 chr6ptel1M 765611 766000 (234000) C L1MD1_3end#LINE/L1 (356) 633 222 m_b291s551i1 11994 chr6ptel1M 765611 GCTTATTTCACTCAGCATCAGTTTCTGTAAGTCTCTCCAGGCCTTTCTG- 765659 v v v i v ii iiv iiv vi - C L1MD1_3end#LI 633 GCTTTTTTCACTCAGCATAATTCTCTGGAGATTCATCCAGGTTGTTGCGT 584 chr6ptel1M 765660 --ATCA---------TCCTGTTGGTATTTCTTA-TAATGAAATATAACAT 765697 -- --------- v -- v v - i ivvvi iii C L1MD1_3end#LI 583 GTATCAATAGTTCGTTCCTTTT--TATTGCTGAGTAGTATTCCATGGTAT 536 chr6ptel1M 765698 TCATATATCATAACTTATTCAGCCATTCTCCTATTGATGGGCATCCACTC 765747 vv i i i ii i i i v ii v i iivvi C L1MD1_3end#LI 535 GGATGTACCACAGTTTGTTTAACCATTCACCCGTTGAAGGACATCTGGGT 486 chr6ptel1M 765748 AGTTTCCAGCTTCTTGCCACTCCAAAAAAGGGCTGCCACAAACATTTGTG 765797 v i i v i i v i v -i i i i C L1MD1_3end#LI 485 TGTTTCCAGTTTTTGGCTATTACGAATAA-AGCTGCTATAAACATTCGTG 437 chr6ptel1M 765798 ----GGTCTTTTTCCTGCCTTTAAG-----ATCTCTTTGGGATATAAGCC 765838 ---- - viv vviv ----- i i v v C L1MD1_3end#LI 436 TACAGGT-TTTTGTGTGAACATAAGTTTTCATTTCTCTGGGATAAATGCC 388 chr6ptel1M 765839 CAGTAAAAACACTGCTAGATCAAAGGGT--CTGCACAGTTAATAGCCCTT 765886 v ivivv i i i iv v --i i- -- iii C L1MD1_3end#LI 387 CAGGAGTGCAATTGCTGGGTCGTATGGTAGTTGCAT-GTT--TAGTTTTT 341 chr6ptel1M 765887 TGGGCATAGAT--CCAAATTGCTCTCTAGAATAGTTGGATCACTCCATGA 765934 ii --- i i-- i i i i i i i v i i ii iiv C L1MD1_3end#LI 340 TAAG---AAACTGCCAAACTGTTTTCCAGAGTGGCTGTACCATTTTACAT 294 chr6ptel1M 765935 CCACATCAACAATGCCTTAGTGTCCCAGTTTTCCCATATCCCCTCCAACA 765984 i v i i iv v vi ii ii i v i C L1MD1_3end#LI 293 TCCCACCAGCAATGTATGAGTGATCCAGTTTCTCCGCATCCTCGCCAGCA 244 chr6ptel1M 765985 T------TTATCACTATCTTTT 766000 ------ i i C L1MD1_3end#LI 243 TTTGGTGTTGTCACTATTTTTT 222 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 42.68 CpG sites = 82, Kimura (unadjusted) = 45.76 Transitions / transversions = 1.91 (82/43) Gap_init rate = 0.05 (19 / 389), avg. gap size = 2.21 (42 / 19) 616 31.81 4.70 2.97 chr6ptel1M 765699 765996 (234004) C L1ME5_3end#LINE/L1 (407) 534 232 m_b291s551i2 11994 chr6ptel1M 765699 CATATATCATAACTTATTCAGCCATTCTCCTATTGATGGGCATCCACTCA 765748 vi i i vi iii v i i v i i vviv C L1ME5_3end#LI 534 CATCCACCACATTTTACCTATCCACTCTCCCAGTGATGGACACCCAGGTT 485 chr6ptel1M 765749 GTTTCCAGCTTCTTGCCACTCCAAAAAAGGGCTGCCACAAACAT--TTGT 765796 ii i i ii iv v v - v ii -- i C L1ME5_3end#LI 484 GCCTCCAACTCCCCGCCACCACAAACAACG-CTGCAATGAACATCCTCGT 436 chr6ptel1M 765797 GG--GTCTTTTT-----CCTGCCTTTAAGA-TCTCTTTGGGATATAAGCC 765838 iv-- iii ----- -- v i - i vi C L1ME5_3end#LI 435 ACATGTCCCCTTATGGACCTG--TGTGAGAATTTCTTTGGGATATATACC 388 chr6ptel1M 765839 CAGTAAAAACACTGCTAGATCAAAGGGTCTGC--ACAGTTAATAGCCCTT 765886 v iviiv i i i v v -- i v ------ C L1ME5_3end#LI 387 CAGGAGCGGAATTGCTGGGTCATAGGGTATGCGTATACTTAAT------T 344 chr6ptel1M 765887 TGGGCA--TAGATCCAAATTGCTCTCTAGAATAGTTGGATCACTCCATGA 765934 ivi -- vvv i i i i v i v i iiv C L1ME5_3end#LI 343 TGACTAAGTACTGCCAGATTGCTCTCCAGAATGGCTGCACCAGTCTACAC 294 chr6ptel1M 765935 CCACATCAACAATGCCTTAGTGTCCCAGTTTTCCCATATCCCCTCCAACA 765984 i v i i i v v v i vi ? i i i v C L1ME5_3end#LI 293 TCCCACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATCCTCGCCAACA 244 chr6ptel1M 765985 TTTATCACTATC 765996 i iv i C L1ME5_3end#LI 243 CTTGGCATTATC 232 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.60 CpG sites = 58, Kimura (unadjusted) = 43.52 Transitions / transversions = 1.71 (58/34) Gap_init rate = 0.05 (15 / 297), avg. gap size = 1.53 (23 / 15) 298 33.87 2.33 5.26 chr6ptel1M 765813 766027 (233973) C L1PA4_3end#LINE/L1 (491) 411 203 m_b291s551i3 11994 chr6ptel1M 765813 TTTAAGATCTCTTTGGGATATAAGCCCAGTAAAAACACTGCTAGATCAAA 765862 vi - - vi viiv iv i i C L1PA4_3end#LI 411 TTTATAATC-CTTTGGG-TATATACCCAGTAATGGGATGGCTGGGTCAAA 364 chr6ptel1M 765863 GGGTCTGCACAGTTAATAGCCCTTTG-GGCATAGATCCAAATTGCTCTCT 765911 v v vivi -v vi ii - v v -- v i vii i C L1PA4_3end#LI 363 TGGTATTTCTAGTT-CTAGATCCCTGAGGAATCG--CCACACTGACTTCC 317 chr6ptel1M 765912 AGAATAGTTGGATCACTCCATGACCACATCAACAATGCCTTAGTGTCCCA 765961 v i i ii v ii iiii v i i ivvv i v C L1PA4_3end#LI 316 ACAATGGTTGAACTAGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCT 267 chr6ptel1M 765962 GTTTTCCCATATCCCCTCCAACATTTATCACTATCTTTTCCTG---TTCT 766008 i ii i i i i------ i iv --- i C L1PA4_3end#LI 266 ATTTCTCCACATCCTCTCCAGCAC------CTGTTGTTTCCTGACTTTTT 223 chr6ptel1M 766009 GATGACCAATA-TCTAATTG 766027 i i ivi - i C L1PA4_3end#LI 222 AATGATCGCCATTCTAACTG 203 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 46.63 CpG sites = 45, Kimura (unadjusted) = 47.62 Transitions / transversions = 1.88 (45/24) Gap_init rate = 0.07 (14 / 214), avg. gap size = 1.14 (16 / 14) 22 10.76 0.00 0.00 chr6ptel1M 766490 766520 (233480) (A)n#Simple_repeat 1 31 (0) m_b291s252i15 11995 chr6ptel1M 766490 AAAAAAAAAAAAAGAAAGAAAAAAAAGAAAA 766520 i i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 31 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 237 34.92 6.35 0.00 chr6ptel1M 767050 767175 (232825) MIRb#SINE/MIR 2 135 (133) m_b291s601i38 11996 chr6ptel1M 767050 AAAGGAGC--CGTAATG-AGTAGCAATACCCCTGGTTTGGGAGATGGG-G 767095 i i -- ii - i v v v v v i v vii i-i MIRb#SINE/MIR 2 AGAGGGGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACA 51 chr6ptel1M 767096 GATTCGCGTTCACGTTCCCTTCCTAACA-TTACT--TCAT-TGATGTCGG 767141 iii v ivi i vvii iv - --iii - iv i MIRb#SINE/MIR 52 GACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 101 chr6ptel1M 767142 TCAAGTTATTCAATCTCTGTGAGCCTCACCTTCC 767175 v i i i v vi MIRb#SINE/MIR 102 GCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCC 135 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 48.05 CpG sites = 28, Kimura (unadjusted) = 49.69 Transitions / transversions = 1.75 (28/16) Gap_init rate = 0.05 (6 / 125), avg. gap size = 1.33 (8 / 6) 575 27.48 9.38 2.51 chr6ptel1M 767285 767508 (232492) MIRb#SINE/MIR 7 245 (23) m_b291s601i39 11997 chr6ptel1M 767285 GGCAGCACGA------GGAATAGAGCACTGAGCCT--GAGTCAAGAACAC 767326 ii i------ - - i i -- iiv v MIRb#SINE/MIR 7 GGCAGCGTGGTGCAGTGGAA-AGAGCAC-GGGCTTTGGAGTCAGACAGAC 54 chr6ptel1M 767327 CTGAGTTCAAATTA-GGCTTTAG-----AGTAGCTGTTTGATTCTTT--T 767368 i i iv- i iv----- v v i- v--i MIRb#SINE/MIR 55 CTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGAC-CTTGGGC 103 chr6ptel1M 767369 AAGTCACTTCACTTCTATCTGTCTCAGTTTTACCAATTGTAAAATGGGAA 767418 i v i v vv i ivi vi i MIRb#SINE/MIR 104 AAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGA 153 chr6ptel1M 767419 TAACAACAGAATCTATATCCCAGGAC--TTGTTTGGTTCAATTGAGATAT 767466 i i--- i iv v ii-- vv v i v v MIRb#SINE/MIR 154 TAATAAT---ACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAA 200 chr6ptel1M 767467 T---TGCAGAACATTTATCACAGAACCTGAAACATAGTATGTGCT 767508 --- i i i ii v vi iv v i MIRb#SINE/MIR 201 TGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCT 245 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.37 CpG sites = 36, Kimura (unadjusted) = 35.24 Transitions / transversions = 1.50 (36/24) Gap_init rate = 0.06 (13 / 223), avg. gap size = 2.08 (27 / 13) 119 21.37 0.00 0.00 chr6ptel1M 767729 767970 (232030) (TG)n#Simple_repeat 1 242 (0) m_b291s252i16 11998 chr6ptel1M 767729 TGAGTGTGAATATATGTGAGTGAGTGTGAGTGTGTGTATAAGTGTGAGAG 767778 v vi i i v v v i iv v v (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr6ptel1M 767779 TATATGTGTGTGTGAGTATGAATATGTGTGTGAGTGTGTGTTTGTGAGTG 767828 i i v i vi i v v v (TG)n#Simple_ 51 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 100 chr6ptel1M 767829 TGTGAAAGTATGTGTGTGTGTGAGAGTGTGTGTGTGTGAGAGTGTGTGTG 767878 viv i v v v v (TG)n#Simple_ 101 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 150 chr6ptel1M 767879 TGTGAAAGAGTGTGTGTGTGAGAGAGTGTGTGTGTGAGTGTGTGTGTGTG 767928 viv v v v v v (TG)n#Simple_ 151 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 200 chr6ptel1M 767929 TGAGTGTGTGTGTATGTGTGTGAGTACGTGTGTGAGTGTGTG 767970 v i v ii v (TG)n#Simple_ 201 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 242 Matrix = Unknown Transitions / transversions = 0.55 (16/29) Gap_init rate = 0.00 (0 / 241), avg. gap size = 0.0 (0 / 0) 288 34.48 2.28 17.89 chr6ptel1M 768460 768678 (231322) C MIRc#SINE/MIR (52) 216 27 m_b291s601i40 11999 chr6ptel1M 768460 TTCACTTATATGTAGCT--TTTCAGGTTTCTCACAACAGCCGAGTAAAGT 768507 v i - v -- v --- i i vv i i C MIRc#SINE/MIR 216 TTCACATACAT-TATCTCATTTGA---TCCTCACAACAACCCTGTGAGGT 171 chr6ptel1M 768508 ATGAGGTGAAAGTGGTGTCACCTCCACTTTGTAGATAAGAAAACTCAAGC 768557 v vi v v i iv i i i i i ii i i v i C MIRc#SINE/MIR 170 AGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGC 121 chr6ptel1M 768558 ATAGTGATAGTTACATTGTCATCTGTTTCACTTGCCCTTGTAGCTGCAAC 768607 vi v -i - v ----------- ------------- C MIRc#SINE/MIR 120 TCAGAGA-GGTTA-AGTG-----------ACTTGCCC------------- 97 chr6ptel1M 768608 TATGGAAGTTAGTCGACTATCGTGTAGTGAAGTTGAGATTTGAATTCACG 768657 ----i i i vv ii viiv i iii ii i i i ii v C MIRc#SINE/MIR 96 ----AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGG 51 chr6ptel1M 768658 TCT---TGATTCCAAGCCTAACGC 768678 --- i i i ii C MIRc#SINE/MIR 50 TCTTCCTGACTCCAAGTCCAGTGC 27 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 45.46 CpG sites = 43, Kimura (unadjusted) = 47.66 Transitions / transversions = 2.26 (43/19) Gap_init rate = 0.17 (36 / 218), avg. gap size = 1.08 (39 / 36) 293 26.01 3.60 6.48 chr6ptel1M 768753 768863 (231137) C MIRb#SINE/MIR (144) 124 17 m_b291s601i41 12000 chr6ptel1M 768753 CTCAGACAAGGTGATGTTCTTTTCCCAAGGTCACATATGTGCTAAGTAAG 768802 -i v v vvi v i vv iv iiv C MIRb#SINE/MIR 124 CTCAGA-GAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGC 76 chr6ptel1M 768803 AGAGT--GTATACAAGCCTCCGGTCT--TTGACTCCAAAGCCAGAATTCT 768848 i-- v v i i - v --i v vii C MIRb#SINE/MIR 75 AGAGCCGGGATTCGAACC-CAGGTCTGTCTGACTCCAAAGCCCGTGCTCT 27 chr6ptel1M 768849 TTCTTGAACACTACA 768863 ----- i C MIRb#SINE/MIR 26 TTC-----CACTGCA 17 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 30.73 CpG sites = 13, Kimura (unadjusted) = 32.12 Transitions / transversions = 0.93 (13/14) Gap_init rate = 0.08 (9 / 110), avg. gap size = 1.22 (11 / 9) 702 28.17 7.69 0.42 chr6ptel1M 769413 769633 (230367) MIRc#SINE/MIR 32 268 (0) m_b291s601i42 12001 chr6ptel1M 769413 GGATCTGTAGTCAGGAAAACCTAAATTCAAATCT-GGCCTTGGA---TAC 769458 ii v i iii i i i- ii vv--- MIRc#SINE/MIR 32 GGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTAC 81 chr6ptel1M 769459 TAGCTGTGTGATCCTGGAGAAGTCACTTAATCTTTGTCTGTCTCAGTTTA 769508 i i iv i i v vv i v MIRc#SINE/MIR 82 TAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTC 131 chr6ptel1M 769509 CGCACTTGAAAAATGAAAATAAAAATAGCAGCTACTTCCTA------AGG 769552 v ii v iii v v v i- v ------ MIRc#SINE/MIR 132 CTCATCTGTAAAATGGGGATAATAATACCTGCC-CTGCCTACCTCACAGG 180 chr6ptel1M 769553 GGTATTTTAAGGATAAAACAAGATATTTTAT---AAAGTACTTTGGAGAT 769599 v i v i v ii v v --- ii v i i MIRc#SINE/MIR 181 GTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTTTGTAAAC 230 chr6ptel1M 769600 CTTCAAACACTTTATAAATGC----TATTATTGTTATT 769633 iv v iii v i i----?i i MIRc#SINE/MIR 231 TGTAAAGTGCTATACAAATGTAAGGNGTTATTATTATT 268 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.23 CpG sites = 39, Kimura (unadjusted) = 36.81 Transitions / transversions = 1.70 (39/23) Gap_init rate = 0.03 (6 / 220), avg. gap size = 3.00 (18 / 6) 12 0.00 5.26 0.00 chr6ptel1M 769642 769660 (230340) (CAT)n#Simple_repeat 1 20 (0) m_b291s252i17 12002 chr6ptel1M 769642 CATCATCATCATCATC-TCA 769660 - (CAT)n#Simple 1 CATCATCATCATCATCATCA 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.06 (1 / 18), avg. gap size = 1.00 (1 / 1) 212 18.92 0.00 0.00 chr6ptel1M 770366 770402 (229598) C L2c_3end#LINE/L2 (15) 463 427 m_b291s601i43 12003 chr6ptel1M 770366 AAGCATTTATATAGTACCTCCTATGTGCCAGGTGCTG 770402 i vv ii v i C L2c_3end#LINE 463 AAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTG 427 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 15.24 CpG sites = 4, Kimura (unadjusted) = 22.06 Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 257 30.60 5.99 4.12 chr6ptel1M 770450 770616 (229384) C L2c_3end#LINE/L2 (4) 474 305 m_b291s601i44 12004 chr6ptel1M 770450 ATTCACCCAACAAACATTT-CTGAGGGCCT------TACAAGATGCTGGA 770492 ii -i v ------ i v ii i C L2c_3end#LINE 474 ATTCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGG 425 chr6ptel1M 770493 GAAGACACAAAATGGAGAAGGGATGGCCCCTGCCCCCCTTCACAAGCATC 770542 -v - i i v iv i i --- iv vi - C L2c_3end#LINE 424 GA-TACA-AAGATGAATAAGACACGGTCCCTG---CCCTCAAGGAGC-TC 381 chr6ptel1M 770543 CCTTTCT--TTGGGGAAATAAGGCAGGTATAAGAAGAACTCCAGAACAGG 770590 v vv -- v i i i- i ? v vii v i v iv i C L2c_3end#LINE 380 ACAGTCTAGTGGAGGAGAC-AGACANGTAAACAGACAATTACAATACAAG 332 chr6ptel1M 770591 CTAGGAAT-TGTGTGGTAGTGGTAGTA 770616 i ivi -v ivi i v C L2c_3end#LINE 331 TTAATGATAAGTGCTATAATGGGAGTA 305 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.79 CpG sites = 29, Kimura (unadjusted) = 40.97 Transitions / transversions = 1.45 (29/20) Gap_init rate = 0.07 (11 / 166), avg. gap size = 1.55 (17 / 11) 584 32.00 5.13 2.50 chr6ptel1M 770769 771002 (228998) C MIRb#SINE/MIR (16) 252 13 m_b291s601i45 12005 chr6ptel1M 770769 TTAATTAAGAGCCTCCTGTGGGCCAAGCATTGGATTAATTGCTTTAC--- 770815 v i v i v i v i i vii vi --- C MIRb#SINE/MIR 252 TTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACATG 203 chr6ptel1M 770816 CAGTACTTCCTTTGATCCTCATAACAGTCCCTGGATGGAGT-GCTATCAT 770864 v ii v i i i- --i ii - v i C MIRb#SINE/MIR 202 CATTATCTCATTTAATCCTCACAACAA-CCCTG--CGAGGTAGGTATTAT 156 chr6ptel1M 770865 TACCCCCATTTTATGACTGAGGAGAT--AGGCAGTTAAAT-GGTAGATCA 770911 i iiiv i i-- -- i i v- vi vi C MIRb#SINE/MIR 155 TATCCCCATTTTACAGATGAGGAAACTGAGGC--TCAGAGAGGTTAAGTA 108 chr6ptel1M 770912 ATTTGCCCAGGGCAATATAATGAGCAAATATC----TCAGGATTTGAACT 770957 i i iv i i iiv i i iv ----i i i i C MIRb#SINE/MIR 107 ACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACC 58 chr6ptel1M 770958 TGGGCCT-TCTGGATTTCATGTCTAATACTCTATACATTGCCCCAC 771002 ii i - - i i viv ivi i v v i v C MIRb#SINE/MIR 57 CAGGTCTGTCT-GACTCCAAAGCCCGTGCTCTTTCCACTGCACCAC 13 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.46 CpG sites = 51, Kimura (unadjusted) = 44.61 Transitions / transversions = 2.32 (51/22) Gap_init rate = 0.05 (12 / 233), avg. gap size = 1.50 (18 / 12) 295 32.29 6.11 0.72 chr6ptel1M 771025 771062 (228938) MIR#SINE/MIR 45 86 (176) m_b291s601i46 12006 chr6ptel1M 771025 TACTTGTGTTTAAAACCTTTCTCAGACATTTATTAG----GG 771062 i i v ii v ivv v v i i ---- v MIR#SINE/MIR 45 TGCCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGT 86 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.56 CpG sites = 21, Kimura (unadjusted) = 43.36 Transitions / transversions = 1.00 (7/7) Gap_init rate = 0.03 (1 / 37), avg. gap size = 4.00 (4 / 1) 34 0.00 0.00 0.00 chr6ptel1M 771063 771091 (228909) (GT)n#Simple_repeat 1 29 (0) c_b291s251i5 12007 chr6ptel1M 771063 GTGTGTGTGTGTGTGTGTGTGTGTGTGTG 771091 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTG 29 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 295 32.29 6.11 0.72 chr6ptel1M 771092 771183 (228817) MIR#SINE/MIR 87 181 (81) m_b291s601i46 12006 chr6ptel1M 771092 ACACCCAGAAAGTCTCAGAATCTCTTTCAGCCTTAGTTTATCTCTTCCT- 771140 viivi v iv vv i i vv i -i v iv- MIR#SINE/MIR 87 ACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTT-CCTCATCTGT 135 chr6ptel1M 771141 ---ATGGCACTAATAATAGCACCTTCCTTATAAGGTTCTTATGAGG 771183 --- viv i v i i v i MIR#SINE/MIR 136 AAAATGGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGG 181 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.56 CpG sites = 21, Kimura (unadjusted) = 43.36 Transitions / transversions = 1.00 (14/14) Gap_init rate = 0.03 (3 / 91), avg. gap size = 1.67 (5 / 3) 37 24.50 3.67 0.89 chr6ptel1M 771206 771314 (228686) (TA)n#Simple_repeat 1 112 (0) m_b291s252i18 12008 chr6ptel1M 771206 TATTTAAATGTATATACACATACATATATGT-TTTATATACACACATATG 771254 v v i i i i i - v i i i i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr6ptel1M 771255 TACCTATGTAATTATATGTATA-ATATATATATATACATCAT-TATAGAT 771302 iv i vv i - i - - v (TA)n#Simple_ 51 TATATATATATATATATATATATATATATATATATATAT-ATATATATAT 99 chr6ptel1M 771303 -TATAAACATATA 771314 - v i (TA)n#Simple_ 100 ATATATATATATA 112 Matrix = Unknown Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.05 (5 / 108), avg. gap size = 1.00 (5 / 5) 19 13.73 3.80 10.81 chr6ptel1M 771265 771343 (228657) (ATT)n#Simple_repeat 1 74 (0) m_b291s252i19 12009 chr6ptel1M 771265 ATTA-TATGTA-TAATATATATATATACATCATTATAGATTATAAACATA 771312 - - - v - - -i i -v v vi - (ATT)n#Simple 1 ATTATTAT-TATTATTAT-TAT-TAT-TATTATTAT-TATTATTATTAT- 44 chr6ptel1M 771313 TACTTGTTATTATTAATTATT-TTATTATTAT 771343 - i - - (ATT)n#Simple 45 TA-TTATTATTATT-ATTATTATTATTATTAT 74 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.14 (11 / 78), avg. gap size = 1.00 (11 / 11) 295 33.00 0.99 0.99 chr6ptel1M 771346 771446 (228554) C MIRc#SINE/MIR (107) 161 61 m_b291s601i47 12010 chr6ptel1M 771346 AGGAATTATTAGTAGTGTTTCACAGATGAGG-AACCAAGACTTTAGTGAA 771394 v vivvii i - ii i - i v i C MIRc#SINE/MIR 161 AGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGC-TCAGAGAG 113 chr6ptel1M 771395 AGAAAGTGGCTTGTCCAAGGCCACAAAATGAATTAATGGTGGAATCAGGT 771444 ivv i i i v iiv i v i ii ii i v C MIRc#SINE/MIR 112 GTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGA 63 chr6ptel1M 771445 CT 771446 C MIRc#SINE/MIR 62 CT 61 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 44.18 CpG sites = 22, Kimura (unadjusted) = 46.14 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.02 (2 / 100), avg. gap size = 1.00 (2 / 2) 325 29.76 1.18 1.18 chr6ptel1M 771363 771447 (228553) C MIR3#SINE/MIR (67) 141 57 m_b291s601i48 12010 chr6ptel1M 771363 TTTCACAGATGAGG-AACCAAGACTTTAGTGAAAGAAAGTGGCTTGTCCA 771411 i - ii i -ii v iivi i i C MIR3#SINE/MIR 141 TTTTACAGATGAGGAAACTGAGGC-CCAGAGAGGTGAAGTGACTTGCCCA 93 chr6ptel1M 771412 AGGCCACAAAATGAATTAATGGTGGAATCAGGTCTA 771447 i v ii? i i ii ii i v C MIR3#SINE/MIR 92 AGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTA 57 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.55 CpG sites = 21, Kimura (unadjusted) = 42.93 Transitions / transversions = 5.25 (21/4) Gap_init rate = 0.02 (2 / 84), avg. gap size = 1.00 (2 / 2) 197 8.83 0.00 2.94 chr6ptel1M 771688 771722 (228278) C L2d2_3end#LINE/L2 (520) 35 2 m_b291s601i49 12011 chr6ptel1M 771688 AGGCTGGAAAGGCAAGTATGGAGCCAGATTGTGGA 771722 ? i - i i C L2d2_3end#LIN 35 AGGCTGGAAAGGNAGGT-TGGGGCCAGATCGTGGA 2 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 6.81 CpG sites = 3, Kimura (unadjusted) = 10.03 Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 23 17.53 0.00 3.77 chr6ptel1M 771936 771990 (228010) (TAT)n#Simple_repeat 1 53 (0) m_b291s252i20 12012 chr6ptel1M 771936 TATTCTTTCTTTTTTTATTTGTTATTATTATTATTTATTATTATTATTTT 771985 v vi v v - i - v (TAT)n#Simple 1 TATTATTATTATTATTA-TTATTATTATTATTA-TTATTATTATTATTAT 48 chr6ptel1M 771986 TTTTA 771990 v (TAT)n#Simple 49 TATTA 53 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.04 (2 / 54), avg. gap size = 1.00 (2 / 2) 410 28.12 15.62 0.00 chr6ptel1M 773243 773370 (226630) MIRc#SINE/MIR 3 150 (118) m_b291s601i50 12013 chr6ptel1M 773243 AGACATTGTGATGCAGTAGAGATGACCTTGGATATGAAGTC-CAAGGACT 773291 i v i i i vii vi iv i -vi i i MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chr6ptel1M 773292 CTGGCTCAAATTTAG--TTTGATACTTA-------TGTGATCTTGGCCAA 773332 iv i i i iiv -- i vi ------- i v MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 102 chr6ptel1M 773333 GTCACC----------AAACTTCAGTTTCCTTATCTGTAAAATGCGGA 773370 i----------i i i i v MIRc#SINE/MIR 103 GTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGA 150 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.02 CpG sites = 26, Kimura (unadjusted) = 37.37 Transitions / transversions = 2.60 (26/10) Gap_init rate = 0.03 (4 / 127), avg. gap size = 5.00 (20 / 4) 360 31.90 12.18 3.55 chr6ptel1M 773257 773412 (226588) MIR3#SINE/MIR 16 184 (24) m_b291s601i51 12013 chr6ptel1M 773257 AGTAGAGATGACCTTGGATATGAAGTCCAAGGACTCTGGCTCAAATTTAG 773306 i - v vi ivv i viii iiv i v i iiv MIR3#SINE/MIR 16 AGCAGAGA-GAGCACGGACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCG 64 chr6ptel1M 773307 --TTTGATACT-------TATGTGATCTTGGCCAAGTCAC--CA------ 773339 -- i vi ------- i i v -- ------ MIR3#SINE/MIR 65 GCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTC 114 chr6ptel1M 773340 --AACTTCAGTTTCCTTATCTGTAAAATGCGGAAGTGAAACTAGTATAGA 773387 --ii i i v ii vii ----- MIR3#SINE/MIR 115 TGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGAC-----TAGA 159 chr6ptel1M 773388 TGACATCTAAATTTCTTTTTGACCC 773412 iv iv i i iiii i MIR3#SINE/MIR 160 TGATCTCTAAGGTCCCTTCCAGCTC 184 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.42 CpG sites = 34, Kimura (unadjusted) = 44.72 Transitions / transversions = 2.43 (34/14) Gap_init rate = 0.06 (10 / 155), avg. gap size = 2.50 (25 / 10) 48 24.75 4.91 1.79 chr6ptel1M 773906 774068 (225932) (TC)n#Simple_repeat 1 168 (0) m_b291s252i21 12014 chr6ptel1M 773906 TCCCTCTGTGCTCTCTCTCTC-CTTCCCCTC-CTCT-TTTCTCTCTCT-T 773951 i v - - ii i - - i - (TC)n#Simple_ 1 TCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 49 chr6ptel1M 773952 CTCTTTCTCTATCTCTCTTTTTGTTTTTCTCCCCCT-TTTATCTTCCTCC 774000 i v i i v i i i i - i v ii i (TC)n#Simple_ 50 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 99 chr6ptel1M 774001 TTTTTTCTCCCTCTCTCTC-CTCAC-CTCTCTCCCTTTCTCTC-CTTTCT 774047 i i i i - v - i i - i (TC)n#Simple_ 100 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 149 chr6ptel1M 774048 CTTTCACATTTATCATCTCTC 774068 i v - i v - (TC)n#Simple_ 150 CTCTCTC-TCTCTC-TCTCTC 168 Matrix = Unknown Transitions / transversions = 3.57 (25/7) Gap_init rate = 0.07 (11 / 162), avg. gap size = 1.00 (11 / 11) 17 16.55 7.32 0.00 chr6ptel1M 774435 774475 (225525) (CA)n#Simple_repeat 1 44 (0) m_b291s252i22 12015 chr6ptel1M 774435 CATACACACACACAC-CCCAC-CAC-CACCCACACATATGCACA 774475 i - v - - v i ii (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACA 44 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.07 (3 / 40), avg. gap size = 1.00 (3 / 3) 505 19.86 3.12 5.60 chr6ptel1M 774502 774629 (225371) MIRc#SINE/MIR 3 127 (141) m_b291s601i52 12016 chr6ptel1M 774502 AGCTAGT-TGGTGTAGTGGATAAAGCACCAGCCCTCAAGTCAGGAAGACA 774550 vi - i v i ii v i vi v MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chr6ptel1M 774551 TGAGTTCAAATCTGGCTTCAGACACAACACTTCCTGGCTGTGTGACCCTG 774600 i i i iv vi v - ---- v i i MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTG-C----CACTTACTAGCTGTGTGACCTTG 97 chr6ptel1M 774601 GGCAAGTCACTTAACC---CTAATTGCCTCAG 774629 --- i -- MIRc#SINE/MIR 98 GGCAAGTCACTTAACCTCTCTGA--GCCTCAG 127 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 22.39 CpG sites = 15, Kimura (unadjusted) = 23.48 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.07 (9 / 127), avg. gap size = 1.22 (11 / 9) 33 25.07 3.92 0.95 chr6ptel1M 774715 774816 (225184) (AG)n#Simple_repeat 1 105 (0) m_b291s252i23 12017 chr6ptel1M 774715 AGAGAGAAAAAGACAGAGAGATGGAGAGAGAGGAACAGAGAAAGAGGGAC 774764 i i v vi ii v i i v (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr6ptel1M 774765 ACAGAG-GAATGCAGAGACAGGAAGA-ATGGAGAGGGAGAG-GGGAG-GA 774810 v - iv - v ii - vi i - i - (AG)n#Simple_ 51 AGAGAGAGAGAG-AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 99 chr6ptel1M 774811 GAGAGA 774816 (AG)n#Simple_ 100 GAGAGA 105 Matrix = Unknown Transitions / transversions = 1.62 (13/8) Gap_init rate = 0.05 (5 / 101), avg. gap size = 1.00 (5 / 5) 243 37.19 0.00 1.28 chr6ptel1M 774895 774973 (225027) MamSINE1#SINE/tRNA-RTE 2 79 (211) m_b291s601i53 12018 chr6ptel1M 774895 TTTTTGCTTGGTTTGCTCAGATGTCTAGAATATGGTGCTAATGGAACCCA 774944 i v vi v v vi ii i iii v MamSINE1#SINE 2 TCTGTGGCTGGTTAGCTCAGTTGGTTAGAGCACGGTGCTAATGAGGCCAA 51 chr6ptel1M 774945 AATCATAGATTCAGTTTATTGTTTAGGTC 774973 ii ii i ii ii-ii v i i MamSINE1#SINE 52 GGTCACGGGTTCGATCC-CCGTGTGGGCC 79 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 45.88 CpG sites = 22, Kimura (unadjusted) = 57.99 Transitions / transversions = 3.14 (22/7) Gap_init rate = 0.01 (1 / 78), avg. gap size = 1.00 (1 / 1) 240 30.86 7.41 0.00 chr6ptel1M 774998 775078 (224922) MIR3#SINE/MIR 77 163 (45) m_b291s601i54 12019 chr6ptel1M 774998 ACTAGCTGAATGA--TTATACAAGTCACT----GTTTCTGGGCCTTGATG 775041 ? vi -- ivi ----v i iii v MIR3#SINE/MIR 77 ACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTT 126 chr6ptel1M 775042 TCATTCCTTATAAAATGAGTATGTAGAGCTAGACAAT 775078 v ivii i viv v ii ii MIR3#SINE/MIR 127 TCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGAT 163 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.30 CpG sites = 16, Kimura (unadjusted) = 42.30 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.03 (2 / 80), avg. gap size = 3.00 (6 / 2) 219 33.33 1.15 0.00 chr6ptel1M 775425 775511 (224489) MIRb#SINE/MIR 43 130 (138) m_b291s601i55 12020 chr6ptel1M 775425 AGTCTTAAATACATGATTTCAAATCCCATCCCAACC-CTTCCTATTTGTA 775473 vv v v v iv i iv i vi - v vi i MIRb#SINE/MIR 43 AGTCAGACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTG 92 chr6ptel1M 775474 TAACTATGGGAAATTTACTATGCTTGTCTGATCTTCAG 775511 i iv v v vvi i v v i MIRb#SINE/MIR 93 TGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAG 130 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.49 CpG sites = 12, Kimura (unadjusted) = 44.25 Transitions / transversions = 0.71 (12/17) Gap_init rate = 0.01 (1 / 86), avg. gap size = 1.00 (1 / 1) 529 19.49 0.00 9.24 chr6ptel1M 776062 776191 (223809) C Charlie1b#DNA/hAT-Charlie (2) 521 403 m_b291s502i2 12021 chr6ptel1M 776062 GTGGTTCTTAAACTTCTTTTTTGGTCTCAAGATCTTTTTATGTTCTTAAA 776111 i i ---- i i ii iii C Charlie1b#DNA 521 GCGGTTCTCAAACTT----TTTGGTCTCAGGACCCCTTTACACTCTTAAA 476 chr6ptel1M 776112 AATTATTAATGACCTTCCCCTTACAAGAGCTTTCATTTAAGTGGGTTATA 776161 i v ---- ---v ii v C Charlie1b#DNA 475 AATTATTGAGGACC----CC---AAAGAGCTTTTGTTTATGTGGGTTATA 433 chr6ptel1M 776162 GCTGTTGACATTTACTGCATTAGGAAATAA 776191 v i i i i i i v C Charlie1b#DNA 432 TCTATCGATATTTACCGTATTAGAAATTAA 403 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 19.97 CpG sites = 18, Kimura (unadjusted) = 23.32 Transitions / transversions = 3.60 (18/5) Gap_init rate = 0.09 (11 / 129), avg. gap size = 1.00 (11 / 11) 419 28.16 2.91 0.00 chr6ptel1M 776186 776288 (223712) C Charlie1b#DNA/hAT-Charlie (417) 106 1 m_b291s502i3 12021 chr6ptel1M 776186 AAATAACCTTTTA---TTGTCATAAAGGTAGTTTTGACCTTGTGGATTTC 776232 v i --- i i i ii i i iii C Charlie1b#DNA 106 AAATAACGTCTTAGTATTATTATGAAAATAGTTTTGACCTCGCGGACCCC 57 chr6ptel1M 776233 TTAAAAGGTCCTTGAGGACATCCTGGGGTCCCTGATCCCCAGCTTGAGAA 776282 i i vi i i vi v i iv v vi C Charlie1b#DNA 56 CTGAAAGGGTCTCGGGGACCCCCAGGGGTCCCCGGACCACACTTTGAGAA 7 chr6ptel1M 776283 CAGTTG 776288 v i C Charlie1b#DNA 6 CCGCTG 1 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 31.07 CpG sites = 21, Kimura (unadjusted) = 37.44 Transitions / transversions = 2.62 (21/8) Gap_init rate = 0.01 (1 / 102), avg. gap size = 3.00 (3 / 1) 785 27.34 4.15 2.87 chr6ptel1M 776591 776831 (223169) MIRc#SINE/MIR 3 246 (22) m_b291s601i56 12022 chr6ptel1M 776591 AGGTAGTTT--TGCA-TAGAAGGCTAGCAAACTGAACTCAGAGTTAGGAA 776637 i v -- - i i -- -- i ii i MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAG--AGCA--CTGGACTTGGAGTCAGGAA 48 chr6ptel1M 776638 GAACCGAGTTCAAATCCTTTCTCAGAAACTTGCTGAGCTATATGATCCTG 776687 v i i i i ivv v vv i - i i i i MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCCACTTACT-AGCTGTGTGACCTTG 97 chr6ptel1M 776688 GGCAAATTACTCAGCTTCTCCTAGTTTCAGTTT-TTCACCTGTAAAATGG 776736 i i i i i iv ii -i i MIRc#SINE/MIR 98 GGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGG 147 chr6ptel1M 776737 GGATAATAATA---AGACAATC--CCTTGTAGGCTTGCTGTGATGATAAA 776781 ---ivv vii -- iii v i v v MIRc#SINE/MIR 148 GGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAA 197 chr6ptel1M 776782 AAGAAGTAATGCATAT-AAATTTCTTTTCAAGTCTTATAAAGTGTTAGAT 776830 v ii i i - viv vi i--i i i v i MIRc#SINE/MIR 198 ATGAGATAATGTATGTGAAAGCGCTTTGTAAA--CTGTAAAGTGCTATAC 245 chr6ptel1M 776831 A 776831 MIRc#SINE/MIR 246 A 246 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.67 CpG sites = 45, Kimura (unadjusted) = 35.78 Transitions / transversions = 2.37 (45/19) Gap_init rate = 0.05 (13 / 240), avg. gap size = 1.31 (17 / 13) 16 7.28 3.45 0.00 chr6ptel1M 777649 777677 (222323) (ATTTT)n#Simple_repeat 1 30 (0) m_b292s252i0 12023 chr6ptel1M 777649 ATTTTATTTTATTTTATTTT-TTTACTTTT 777677 - vv (ATTTT)n#Simp 1 ATTTTATTTTATTTTATTTTATTTTATTTT 30 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1) 465 21.04 0.00 6.67 chr6ptel1M 777699 777810 (222190) C MIRc#SINE/MIR (153) 115 11 m_b292s601i1 12024 chr6ptel1M 777699 GGGGTTAAGTGACTTGCCTAGGATCACACAGCTAGTAAGTGTTAAGCATC 777748 i i i i ---- -- C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTG----GCA-- 72 chr6ptel1M 777749 TGAGGCCAGGTTTGAGCTCAAGTCCTCCTGACTCCAGGGCCAGTCATCCA 777798 - v vi ii i i i i i i v vv iv C MIRc#SINE/MIR 71 -GAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTT 23 chr6ptel1M 777799 TCCACTGAATCA 777810 v i C MIRc#SINE/MIR 22 TCCACTGCACCA 11 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 23.99 CpG sites = 15, Kimura (unadjusted) = 25.30 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.06 (7 / 111), avg. gap size = 1.00 (7 / 7) 525 23.15 0.00 0.00 chr6ptel1M 779561 779668 (220332) C Charlie4a#DNA/hAT-Charlie (32) 476 369 m_b292s502i1 12025 chr6ptel1M 779561 CCCTCTGGTAGTTTGGTGAAACCCATAGACCTTTTCACAGTATAACATTT 779610 i i i i i i ii v v ii C Charlie4a#DNA 476 CCCTTTGGCAGTCTGGTGAAGCCTATGGACCCCTTCTCAGAATAATGTTT 427 chr6ptel1M 779611 TGAAATGTATAAAATAAAATGCATAATATTACGGTGTAAGCCAATCATAT 779660 v i i iv iiv v i i C Charlie4a#DNA 426 TTAAATGCATAAAATAAAATACATAGGATTACAAAGGAAACCAATTATAT 377 chr6ptel1M 779661 GAAAATAC 779668 vi C Charlie4a#DNA 376 TGAAATAC 369 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 28.86 CpG sites = 18, Kimura (unadjusted) = 28.86 Transitions / transversions = 2.57 (18/7) Gap_init rate = 0.00 (0 / 107), avg. gap size = 0.0 (0 / 0) 494 27.88 1.82 4.35 chr6ptel1M 779986 780150 (219850) C MIR3#SINE/MIR (28) 180 20 m_b292s601i2 12026 chr6ptel1M 779986 TGGAAA--ACCTTAGAATGGTTTGCTATTTTCTTCTCCAGTTCATTTGAC 780033 i-- -- i ivv v iivvi i --- v C MIR3#SINE/MIR 180 TGGAAGGGACCTTAGA--GATCATCTAGTCCAACCCCC---TCATTTTAC 136 chr6ptel1M 780034 AGATGAGAAAATTGAGACAAATAGGGAT-AAGCGATTTATCTAGGGTGAC 780082 i i i vv v i i - i i ii i i v C MIR3#SINE/MIR 135 AGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCAC 86 chr6ptel1M 780083 ACAGCTAGCAAGTGTCCACGACTGGATTCGAATTCAGGTCTTCCTGACTT 780132 ? iv v viv v v i v ii - i C MIR3#SINE/MIR 85 ACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGTC-TCCTGACTC 37 chr6ptel1M 780133 CCTGTCTGGTGCTCTATC 780150 v i- v C MIR3#SINE/MIR 36 CCAGTCC-GTGCTCTCTC 20 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 34.86 CpG sites = 25, Kimura (unadjusted) = 35.87 Transitions / transversions = 1.32 (25/19) Gap_init rate = 0.05 (9 / 164), avg. gap size = 1.11 (10 / 9) 630 23.70 0.74 0.00 chr6ptel1M 780026 780160 (219840) C MIRc#SINE/MIR (122) 146 11 m_b292s601i3 12026 chr6ptel1M 780026 CATTTGACAGATGAGAAAATTGAGACAAATAG-GGATAAGCGATTTATCT 780074 v i i i vv v - v i i ii i C MIRc#SINE/MIR 146 CATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCC 97 chr6ptel1M 780075 AGGGTGACACAGCTAGCAAGTGTCCACGACTGGATTCGAATTCAGGTCTT 780124 i v i v viv v v i ii C MIRc#SINE/MIR 96 AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTT 47 chr6ptel1M 780125 CCTGACTTCCTGTCTGGTGCTCTATCCAGTGCACCA 780160 i vv ii v v C MIRc#SINE/MIR 46 CCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCA 11 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 28.83 CpG sites = 17, Kimura (unadjusted) = 28.83 Transitions / transversions = 1.13 (17/15) Gap_init rate = 0.01 (1 / 134), avg. gap size = 1.00 (1 / 1) 22 7.25 0.00 0.00 chr6ptel1M 780302 780330 (219670) (T)n#Simple_repeat 1 29 (0) m_b292s252i1 12027 chr6ptel1M 780302 TTTTCTTTTTTTTTTTTTTTTTTTTATTT 780330 i v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 1379 28.69 3.63 2.92 chr6ptel1M 780780 781357 (218643) C L1ME5_3end#LINE/L1 (304) 637 56 m_b292s551i0 12028 chr6ptel1M 780780 TCCTGCTCATTTCACTTAGCATCA-GTTCGTGTAAG-TCTCTCCAGGC-- 780825 i i iv i ii - -- v - iv v i-- C L1ME5_3end#LI 637 TCTTACTTTTTTCACTCAGCACTATGTT--TTTAAGATCCATCCATGTTG 590 chr6ptel1M 780826 CTTTCTGAAATCATCCTGTTGGTCATTTCTTACAGA-ACAGTAATATTCC 780874 v v v -- iv iv iii v v v-i - i i C L1ME5_3end#LI 589 CTATGTGTA--CATCTAGTCCGTTGCTTCTAACTGCTGCA-TAGTACTCC 543 chr6ptel1M 780875 ATAATTTTCATATACCACAATTTATTCAGCCATTCTCA-ACTGATGGACA 780923 ii v v vi v iii v i v- v C L1ME5_3end#LI 542 ATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCAGTGATGGACA 493 chr6ptel1M 780924 TCCAT-TCAGTTTCAGTTTCTAGCCACTACAAA-AGGGCTGCA-CAAACA 780970 i v- iivi i ii i iv i - iv -ii C L1ME5_3end#LI 492 CCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCTGCAATGAACA 443 chr6ptel1M 780971 TTCGTGCACATACAGGTCCCTTTC----CCTTCTTTATAATCTCTTTGGG 781016 i vi i ---- i v---- viv v v i C L1ME5_3end#LI 442 TCCTCGTACAT----GTCCCCTTATGGACCTGTGTGAGAATTTCTTTGGG 397 chr6ptel1M 781017 ATATAATCCCAGTAGTAACACTACTGGATCAAAGGGTATGC--ACAGTTG 781064 vv v iiiv i i i v -- i v i C L1ME5_3end#LI 396 ATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATGCGTATACTTA 347 chr6ptel1M 781065 ATAACTTTTGAGCA--TAGTTCCAAACTACTCTC-AAAATGGTTGGATTC 781111 ----- vi -- v v i i i - i i v iiv C L1ME5_3end#LI 346 AT-----TTGACTAAGTACTGCCAGATTGCTCTCCAGAATGGCTGCACCA 302 chr6ptel1M 781112 GTTCACAACTCCACCAACAATGAATCAATGTCCCAGTTTTCCCACATCCC 781161 ii vii i i v v iv i vi ? i i C L1ME5_3end#LI 301 GTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATCCT 252 chr6ptel1M 781162 CTCCAACAATCATCATTATTT--TTTCCTGTCATCTTAGCCAATCTGACA 781209 v v iiv ii--i i i-- i v i i i C L1ME5_3end#LI 251 CGCCAACACTTGGCATTATCCAGCTTTCTA--ATTTTTGCCAGTCTAATA 204 chr6ptel1M 781210 GGTGTGTAGTAGTATCTTAGAGGTTGTCTTAATTTGCATTTCTCTGATTA 781259 iv ii i v-v i C L1ME5_3end#LI 203 GGTGTAAAGTGATATCTCAT-TGTTGTTTTAATTTGCATTTCTCTGATTA 155 chr6ptel1M 781260 ATAATGACTTGGAGCATCTTTTCATATGACTAGAAATATTTTCAATTTCT 781309 v v v i vi ivv iiv ivii i C L1ME5_3end#LI 154 CTAATGAGTTTGAGCATCTCTTCATATGCTTGTTAGCCTTTCGGGTTTCC 105 chr6ptel1M 781310 TCATCTGAGAATTGTCTGTTCATATCCTTTGACCA-TTTTCAATTGGAG 781357 v vi i v - v i C L1ME5_3end#LI 104 TCTTCTGTAAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGGGG 56 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.44 CpG sites = 97, Kimura (unadjusted) = 37.36 Transitions / transversions = 1.52 (97/64) Gap_init rate = 0.05 (31 / 577), avg. gap size = 1.23 (38 / 31) 1403 27.63 1.67 1.48 chr6ptel1M 780866 781405 (218595) C L1ME3G_3end#LINE/L1 (377) 547 7 m_b292s551i1 12028 chr6ptel1M 780866 TAATATTCCATAATTTTCATATACCACAATTTATTCAGCCATTCTCA-AC 780914 i i v vv i i i i v- i C L1ME3G_3end#L 547 TAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTAT 498 chr6ptel1M 780915 TGATGGACATCCATTCAGTTTC-AGTTTCTAGCCACTACAAA-AGGGCTG 780962 ii vviv - i i v i i - iv C L1ME3G_3end#L 497 TGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCTG 448 chr6ptel1M 780963 CA-CAAACATTCGTGCACATACAGGTCCCTTTCC-CTTCTTT-ATAATCT 781009 -ii i v i i ?-- i v v - v v vi- vv i C L1ME3G_3end#L 447 CAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATTT 400 chr6ptel1M 781010 CTTTGGGATATAATCCCAGTAGTAACACTACTGGATCAAAGGGTATGCAC 781059 ? i v v? ? v iiv i i i i C L1ME3G_3end#L 399 CTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGC 350 chr6ptel1M 781060 AGTTGATAACTTTTGA-GCATAGTTCCAAACTACTCTC-AAAATGGTTGG 781107 v -- v i -iv v v i i i - ? i v C L1ME3G_3end#L 349 ATTT--TAAATTTTAATAGATACTGCCAAATTGCCCTCCAAAANGGCTGT 302 chr6ptel1M 781108 ATTCGTTCACAACTCCACCAACAATGAATCAATGTCCCAGTTTTCCCACA 781157 iivi i vii i i v v iv v v i C L1ME3G_3end#L 301 ACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCACA 252 chr6ptel1M 781158 TCCCCTCCAACAATCATCATTATTTTTTCCTGTCATCTTAGCCAATCTGA 781207 i i v v ?ivi ivv?iii vvv i v C L1ME3G_3end#L 251 CCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATCTGA 202 chr6ptel1M 781208 CAGGTGTGTAGTAGTATCTTAGAGGTTGTCTTAATTTGCATTTCTCTGAT 781257 ii viv i i i v-v i i C L1ME3G_3end#L 201 TGGGTGAAAAATGGTATCTCAT-TGTTGTTTTAATTTGCATTTCCCTGAT 153 chr6ptel1M 781258 TAATAATGACTTGGAGCATCTTTTCATATGACTAGAAATATTTTCAATTT 781307 v i vv v vi vviiivv vv C L1ME3G_3end#L 152 TACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGTATTT 103 chr6ptel1M 781308 CTTCATCTGAGAATTGTCTGTTCATATCCTTTGACCA-TTTTCAATTGGA 781356 i v v i v - v i C L1ME3G_3end#L 102 CCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGGG 53 chr6ptel1M 781357 GAATGGCTTGATTTTTATAAATTAGAGTTAATTCTCTATATATTTTGGA 781405 v-- v v- i vi v vivv i i i C L1ME3G_3end#L 52 T--TGTCTTT-TTCTTATTGATTTGTAGGAGTTCTTTATATATTCTGGA 7 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 34.97 CpG sites = 77, Kimura (unadjusted) = 35.57 Transitions / transversions = 1.10 (77/70) Gap_init rate = 0.03 (17 / 539), avg. gap size = 1.00 (17 / 17) 1084 29.58 4.38 3.42 chr6ptel1M 781264 782131 (217869) C L1M5_orf2#LINE/L1 (0) 3294 2419 m_b292s551i2 12028 chr6ptel1M 781264 TGACTTGGAGCATCTTTTCATATGACTAGAAATATTTTCAATTTCTTCAT 781313 ?v v i vi vviiivv v? v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr6ptel1M 781314 CTGAGAATTGTCTGTTCATATCCTTTGACCATTTTCA-ATTGGA--GAAT 781360 i v v vi i v i?- i-- vv C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTT 3195 chr6ptel1M 781361 GGCTTGATTTTTA-TAAATTAGAGTTAATTCTCTATATATTTTGGAAATG 781409 v v- ? - i ? iv -v i i i v i C L1M5_orf2#LIN 3194 GTCTTT-TTNTTATTGANTTGTAG-GAGTTCTTTATATATTCTGGATACG 3147 chr6ptel1M 781410 AGGCCTTTATCAGA-ACCTTTGACTGTAAAAATATTTTCCCAGTTTATTG 781458 v i - iv v -?i i v v i ? i i v C L1M5_orf2#LIN 3146 AGTCCTTTGTCAGATATATGT-NTTGCAAATATTTTCTCCCANTCTGTGG 3098 chr6ptel1M 781459 CTT-CCTTCTAATCTTGTCTGCATTAGTTTTGTTTGTACAAAAACTTTTC 781507 - i v i v ivi iv ivi vvv? vi i ii v C L1M5_orf2#LIN 3097 CTTGCCTTTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTTTA 3048 chr6ptel1M 781508 AGTTTAGTATAATC--------AAATTTTCTATTTTGTGATCAGTAATGA 781549 v ii i? i --------v i v i i --- ?i v C L1M5_orf2#LIN 3047 ATTTTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGGT---TNGTGC 3001 chr6ptel1M 781550 TCTCTA-GTTCTGCTTTAGTCATAAAACCTTCCCCT-TCCACAGGTC-TG 781596 i i i- i i v ----- i iv -? vv -i C L1M5_orf2#LIN 3000 TTTTTGTGTCCTGTTTAAG-----AAATCTTTGCCTANCCCAAGGTCACG 2956 chr6ptel1M 781597 AAG-TAAACTATCTATG--TTCCTCTAATTTATTAATAATTTCATTCTTT 781643 - vv -i -- i ivvvv v i i ?ii C L1M5_orf2#LIN 2955 AAGATATTCT-CCTATGTTTTCTTCTAGAAGTTTTATAGTTTTANCTTTT 2907 chr6ptel1M 781644 ATGCCTAGGTC-ATGAACCCATTTTGACCTTATCTTGGTGTACGGCGTTA 781692 iiii - - i i ? vi v i v i i v C L1M5_orf2#LIN 2906 ACATTTAGGTCTATG-ATCCATCTNGAATTAATTTTTGTGTATGGTGTGA 2858 chr6ptel1M 781693 AGTATGGATCAATGCCTAGTTTCTGCCATATTAGT-TTCAATTTTCCCAG 781741 i v i i v?iii v i v vii - i v i C L1M5_orf2#LIN 2857 GGTAGGGGTCGAGNTTCATTTTTTTCCATATGGATATCCAATTGTTCCAG 2808 chr6ptel1M 781742 CAAT-TTTATCAAACAGTAAGTTCTTATCCCAAAAGCTGGGAT-CTTTGG 781789 vi- i ii v vvvi i vi ---- iiv - ? C L1M5_orf2#LIN 2807 CACCATTTGTTGAAAAGACTATCCTTTCCCCA----CTGAATTGCNTTGG 2762 chr6ptel1M 781790 ---GTTTGTCAAAGACTAGGTTGCTATATTTGT-TGACTGTTTTATCCCT 781835 ---v i ii i? v? i v - --- v i ii - C L1M5_orf2#LIN 2761 CACCTTTGTCAAAAATCAANTGNCCATATATGTGTG---GGTCTATTTC- 2716 chr6ptel1M 781836 TGAAC---CTAATCTATTCCACTGATCAACTAATCTATTCCTTA-GCCAA 781881 i --- v i i v i vi - - C L1M5_orf2#LIN 2715 TGGACTCTCTATTCTGTTCCATTGATCTATTTGTCTA-TCCTTACGCCAA 2667 chr6ptel1M 781882 TACCAAATAGTTTTGGTAACTGCTGCTCTATAGTATAGTTTT-AGATCTG 781930 v iv i i v iv i i - i - ? ? C L1M5_orf2#LIN 2666 TACCACACTGTCTTGATTACTGTAGCTTTATAATA-AGTCTTGANATCNG 2618 chr6ptel1M 781931 GTACAGCTAAG-CCACCATCATTTGAT-TTTTTTTTCATTAATTCCTTAA 781978 vv - - v v - v - i vv v vii ii C L1M5_orf2#LIN 2617 GTAGTG-TAAGTCCTCCAAC-TTTGTTCTTCTTTTTCAAGATTGTTTTGG 2570 chr6ptel1M 781979 --ATTCTTGACCTTTTGT-TTTCCATATGAACTTTGTTGTTATTTTTTCT 782025 -- ? ii i i- i i ivvi i vi v v C L1M5_orf2#LIN 2569 CTATTCTNGGTCCTTTGCATTTCCATATAAATTTTAGAATCAGCTTGTCA 2520 chr6ptel1M 782026 AGGTCATTAAAATAGTTTTTTGGGAGTCTGATTGGTATAGCGCTAAATAA 782075 vv vvi v iii vi v i v v ii i vv C L1M5_orf2#LIN 2519 ATTTCTACAAAAAAACCTGCTGGGATTTTGATTGGGATTGCATTGAATCT 2470 chr6ptel1M 782076 ATAGATTAGTTTAGGTAATATTGTCATCTTTATTATATTTGCTCGAGCCT 782125 i i i v iv v ? iv ----- i C L1M5_orf2#LIN 2469 ATAGATCAATTTGGGGAGAATTGACATCTTNACAATATT-----GAGTCT 2425 chr6ptel1M 782126 TCTAGT 782131 i i C L1M5_orf2#LIN 2424 TCCAAT 2419 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 39.02 CpG sites = 139, Kimura (unadjusted) = 39.85 Transitions / transversions = 1.28 (139/109) Gap_init rate = 0.06 (54 / 867), avg. gap size = 1.26 (68 / 54) 524 24.52 2.08 6.52 chr6ptel1M 783008 783151 (216849) C MIRc#SINE/MIR (120) 148 11 m_b292s601i4 12029 chr6ptel1M 783008 CTCATTTGACAAATAACTAT-TTGAGGC--AGACAGTGTTAAGTGACTTA 783054 i v i i vv v-i -- v - i C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAG-GTTAAGTGACTTG 100 chr6ptel1M 783055 CCAAGGATCACACAGCTAGTGAGTGTCTGAGGCTGGATTTGAACTTGGGA 783104 v i i i v v v v i i iii -- C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAG-- 52 chr6ptel1M 783105 AGATGAGTCTTCCTGGTTCTAAGTCCAATGGTCCCTCCATTGTGCCA 783151 ------ ii i i v ii i ii C MIRc#SINE/MIR 51 ------GTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCA 11 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 29.50 CpG sites = 22, Kimura (unadjusted) = 30.61 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.08 (11 / 143), avg. gap size = 1.09 (12 / 11) 12 28.43 2.13 0.00 chr6ptel1M 783676 783722 (216278) (TTTA)n#Simple_repeat 1 48 (0) m_b292s252i2 12030 chr6ptel1M 783676 TTTATTTGTTT-CCAAATCATTTGTTTATATATTCATATATATATTTA 783722 i -iiv v i i v i v v (TTTA)n#Simpl 1 TTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTA 48 Matrix = Unknown Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.02 (1 / 46), avg. gap size = 1.00 (1 / 1) 242 28.57 0.00 0.00 chr6ptel1M 783855 783910 (216090) C L2d2_3end#LINE/L2 (3) 552 497 m_b292s601i5 12031 chr6ptel1M 783855 AATCAGTTCAACAAGCATTTCTTAAGTACATACTTTATGCCAGACACTAT 783904 iv ii v i ii v v i v i i C L2d2_3end#LIN 552 AATCAAATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGT 503 chr6ptel1M 783905 ATTAGG 783910 ii C L2d2_3end#LIN 502 GCTAGG 497 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 34.49 CpG sites = 11, Kimura (unadjusted) = 37.82 Transitions / transversions = 2.20 (11/5) Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0) 204 27.78 1.82 1.82 chr6ptel1M 784329 784383 (215617) C MIR3#SINE/MIR (23) 185 131 m_b292s601i6 12032 chr6ptel1M 784329 AGATTTAGA-GGAAACTTGAAGGTCAGCTAGTCCAATTCTCTTATTTTGA 784377 vi i - i v ii i v ii i i - C MIR3#SINE/MIR 185 AGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTT-A 137 chr6ptel1M 784378 AAAATG 784383 v i C MIR3#SINE/MIR 136 CAGATG 131 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 36.85 CpG sites = 11, Kimura (unadjusted) = 36.85 Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.04 (2 / 54), avg. gap size = 1.00 (2 / 2) 305 28.57 4.27 4.27 chr6ptel1M 784663 784779 (215221) C MIR3#SINE/MIR (52) 156 40 m_b292s601i7 12032 chr6ptel1M 784663 AATCAAATCCCCTTATTTTGGGGATAAGCAACCTGAGGTCCAGAGAGGAA 784712 i v i i ivi i v v i vi C MIR3#SINE/MIR 156 AGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTG 107 chr6ptel1M 784713 AACTCATGTGCTCATTGTCAGAATGACAGTGAGTAG--GAACCTAGGACC 784760 v v iv i vv v vv v? v i -- i -i i C MIR3#SINE/MIR 106 AAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCC-GGGACT 58 chr6ptel1M 784761 ---ACTCAGTGAAATTTCCTGA 784779 --- i ----i i C MIR3#SINE/MIR 57 AGAACCCAG----GTCTCCTGA 40 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 35.57 CpG sites = 17, Kimura (unadjusted) = 37.00 Transitions / transversions = 1.13 (17/15) Gap_init rate = 0.06 (7 / 116), avg. gap size = 1.43 (10 / 7) 360 35.25 3.98 1.67 chr6ptel1M 784739 784914 (215086) L3#LINE/CR1 3831 4010 (89) m_b292s601i8 12033 chr6ptel1M 784739 CAGTGAGTAGGAACCTAGGACCACTCAGTGAAATTTCCTGAGAGAAAAAT 784788 v i i i -- v vi i v v v i iv i L3#LINE/CR1 3831 CAGAGGGCAGAA--CTAGGACCAATGGGTGGAAGTTACAGGGAGGCAGAT 3878 chr6ptel1M 784789 G-CAACTCCAACGAGGGAAGGACTTGCCT-----TCAGAGTTGACCCAGA 784832 v- ii v vvv i i -i ----- i v v i L3#LINE/CR1 3879 TTCGGCTCAATATAAGGAAGAACTT-TCTAACAATCAGAGCTGTCCAAAA 3927 chr6ptel1M 784833 ATGAGATTAACTGTTTCAAGAAATAGTTCATTGCCTTTAACTAGATGAGT 784882 ii vii ii i? ii vvii v iv v i v v L3#LINE/CR1 3928 ATGGAATGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGTCACTGGAGGTGT 3977 chr6ptel1M 784883 TCAAGCCCATACTAAA-AACCACCCCTTAGGGA 784914 vv vi ii -i iiv i L3#LINE/CR1 3978 TCAAGCAGAGGCTGGATGACCACTTGTCAGGGA 4010 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 46.41 CpG sites = 35, Kimura (unadjusted) = 49.84 Transitions / transversions = 1.35 (35/26) Gap_init rate = 0.03 (6 / 175), avg. gap size = 1.67 (10 / 6) 325 29.49 4.83 4.11 chr6ptel1M 784923 785067 (214933) MIR3#SINE/MIR 36 181 (27) m_b292s601i9 12034 chr6ptel1M 784923 GGAGTCTAAAGATCTGGAATGAAATCCTAG-TCTGCCAATTGGTAGCTGG 784971 vii i iv vv i ii - v viv ? v MIR3#SINE/MIR 36 GGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGT 85 chr6ptel1M 784972 ATGAGCTTGGACAGTTCATTTTTTTTTCTCTACATGTCAGTATCCT---- 785017 i v i iv -i ivii iviiv v ---- MIR3#SINE/MIR 86 GTGACCTTGGGCAAGTCA-CTTCACCTCTCTGGGCCTCAGTTTCCTCATC 134 chr6ptel1M 785018 TCTAATATCTGGAGAGTGTGGGACTACATGGTCACT--GGTCTCTTTTCC 785065 v v --- i v v v i v -- i -- MIR3#SINE/MIR 135 TGTAAAAT---GAGGGGGTTGGACTAGATGATCTCTAAGGTCCC--TTCC 179 chr6ptel1M 785066 AG 785067 MIR3#SINE/MIR 180 AG 181 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 37.08 CpG sites = 21, Kimura (unadjusted) = 38.38 Transitions / transversions = 1.05 (21/20) Gap_init rate = 0.06 (9 / 144), avg. gap size = 1.44 (13 / 9) 268 32.78 3.20 2.38 chr6ptel1M 785270 785394 (214606) C MIRc#SINE/MIR (141) 127 2 m_b292s601i10 12035 chr6ptel1M 785270 CTGGGTCCCTGAGGGGCT--GTGACTTGGTTAAGGTAACACATAGC-AGA 785316 i v i v i i -- vii -- i - v C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGT--CACACAGCTAGT 80 chr6ptel1M 785317 ATGTGTCAAAGATGGTCCTTGTACTCAGATAATCATGACTACAAAGTCA- 785365 v v i vi vv i v i i vv v v ivi - C MIRc#SINE/MIR 79 AAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAG 30 chr6ptel1M 785366 TATCCTTATTCATTACCCCTCAGTGATTC 785394 iii - i i i v v v vi C MIRc#SINE/MIR 29 TGCTCTT-TCCACTGCACCACACTGCCTC 2 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 41.12 CpG sites = 21, Kimura (unadjusted) = 43.99 Transitions / transversions = 1.11 (21/19) Gap_init rate = 0.05 (6 / 124), avg. gap size = 1.17 (7 / 6) 383 33.30 7.60 1.66 chr6ptel1M 786985 787155 (212845) MIR3#SINE/MIR 17 197 (11) m_b292s601i12 12036 chr6ptel1M 786985 GTAAGAAGAACACTGAAATCTGGG--TCATAGAGTTTGATTTCAAGTCCT 787032 i iii i v --- -- viiiiii iv v i MIR3#SINE/MIR 17 GCAGAGAGAGCACGGA---CTGGGAGTCAGGAGACCTGGGTTCTAGTCCC 63 chr6ptel1M 787033 GGCTCTGCTGCTTAATGCCTGTATGACCTTATATAAATTCCCCAGACTCT 787082 ii v v ?v i ivii i iv iiviv MIR3#SINE/MIR 64 GGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCT 113 chr6ptel1M 787083 CTGATTCCCATTGTCCACATCTGTATAA--------TTGGACTAACTGGG 787124 ivi i v v v v -------- iv iv MIR3#SINE/MIR 114 CTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGAT 163 chr6ptel1M 787125 CCTT--GGTCCCTTTAAGATGCAA-ATTCCATGA 787155 ii -- iv v vii - i MIR3#SINE/MIR 164 CTCTAAGGTCCCTTCCAGCTCTGACATTCTATGA 197 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 45.43 CpG sites = 35, Kimura (unadjusted) = 46.61 Transitions / transversions = 1.67 (35/21) Gap_init rate = 0.04 (7 / 170), avg. gap size = 2.29 (16 / 7) 464 33.33 0.74 0.00 chr6ptel1M 786985 787119 (212881) MIRc#SINE/MIR 18 153 (115) m_b292s601i11 12036 chr6ptel1M 786985 GTAAGAAGAACACTGAAATCTGGGTCATAGAG-TTTGATTTCAAGTCCTG 787033 iii i i v iv i vii -ii iv i i MIRc#SINE/MIR 18 GTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCG 67 chr6ptel1M 787034 GCTCTGCTGCTTAATGCCTGTATGACCTTATATAAATTCCCCAGACTCTC 787083 ii v iv i ivii i iv ii iv MIRc#SINE/MIR 68 GCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTC 117 chr6ptel1M 787084 TGATTCCCATTGTCCACATCTGTATAATTGGACTAA 787119 vi i v v v v v iv MIRc#SINE/MIR 118 TGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAA 153 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 43.62 CpG sites = 29, Kimura (unadjusted) = 46.48 Transitions / transversions = 1.81 (29/16) Gap_init rate = 0.01 (1 / 134), avg. gap size = 1.00 (1 / 1) 18 11.99 5.26 2.56 chr6ptel1M 787361 787398 (212602) (TA)n#Simple_repeat 1 39 (0) m_b292s252i3 12037 chr6ptel1M 787361 TATATATATATGGATAT-TATATATTTATTTCATAT-TAT 787398 iv - v v - - (TA)n#Simple_ 1 TATATATATATATATATATATATATATATAT-ATATATAT 39 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.08 (3 / 37), avg. gap size = 1.00 (3 / 3) 30 37.70 2.14 0.00 chr6ptel1M 787521 787660 (212340) (TA)n#Simple_repeat 1 143 (0) m_b292s252i4 12038 chr6ptel1M 787521 TATTTATAGTTATATATGTATAAATA-ATATACACACAGAAACACA-ATA 787568 v vv i v - i i i v v i i - (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr6ptel1M 787569 TACATGTATTTGTGTGTGTGCATATATATACAAACATGTATCTATACATA 787618 i i v i i i i ii i v i i v i (TA)n#Simple_ 51 TATATATATATATATATATATATATATATATATATATATATATATATATA 100 chr6ptel1M 787619 TGTATGT-TTTGTCTACATGCATATACATATACACATTTAAAT 787660 i i - v i v i ii i i i v v (TA)n#Simple_ 101 TATATATATATATATATATATATATATATATATATATATATAT 143 Matrix = Unknown Transitions / transversions = 2.08 (27/13) Gap_init rate = 0.02 (3 / 139), avg. gap size = 1.00 (3 / 3) 253 27.66 2.42 15.45 chr6ptel1M 788789 788912 (211088) MIRb#SINE/MIR 2 111 (157) m_b292s601i13 12039 chr6ptel1M 788789 AGAGGGGCA-CATGGTATAATGTAGAAGATCTTTGACAT-GGAATCAGGA 788836 - i ii i v - v viv i v - i iv MIRb#SINE/MIR 2 AGAGGGGCAGCGTGGTGCAGTGGA-AAGAGCACGGGCTTTGGAGTCAGAC 50 chr6ptel1M 788837 ATACCTGCATTCAAATTATGCTTGAAAATAAATAGGTATTTGT-ACTTAC 788885 v vi i i--- i------------ i- i i- MIRb#SINE/MIR 51 AGACCTGGGTTCGAATC---CC------------GGC-TCTGCCACTTAC 84 chr6ptel1M 788886 TGGCTGTGTGACCCTGAAGAAGTTATT 788912 i i iiv i MIRb#SINE/MIR 85 TAGCTGTGTGACCTTGGGCAAGTTACT 111 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 29.37 CpG sites = 20, Kimura (unadjusted) = 35.22 Transitions / transversions = 2.22 (20/9) Gap_init rate = 0.16 (20 / 123), avg. gap size = 1.00 (20 / 20) 268 19.76 5.56 4.40 chr6ptel1M 788918 789007 (210993) CR1-L3B_Croc#LINE/CR1 3184 3274 (3) m_b292s551i3 12040 chr6ptel1M 788918 TAACTGGGC----TTTAATTGCCTCATCTATAAAATGAGATGATTGGACT 788963 i---- v vvv? v i- i v --- CR1-L3B_Croc# 3184 TAACTGGGTGAAATTTAATGGCCTGTGNTATACAG-GAGGTCA---GACT 3229 chr6ptel1M 788964 TGATGGTCTACTGGTCCCTTCTGGCTTTACA-TCTGTGATCCTAT 789007 v i v i v - i vi CR1-L3B_Croc# 3230 AGATGATCTAATGGTCCCTTCTGGCCTTAAANTCTATGAATCTAT 3274 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 23.30 CpG sites = 7, Kimura (unadjusted) = 23.30 Transitions / transversions = 0.70 (7/10) Gap_init rate = 0.07 (6 / 89), avg. gap size = 1.50 (9 / 6) 285 31.58 0.00 0.00 chr6ptel1M 789010 789085 (210915) C L2a_3end#LINE/L2 (47) 470 395 m_b292s601i14 12041 chr6ptel1M 789010 CATTGTGCTGAGTGCTGAGAATACAAAGGGTGATAAAAATGAAAAAAAAC 789059 i v ii i i i ivi vvi i vv v iv C L2a_3end#LINE 470 CACTGTTCTAGGCGCTGGGGATACAGCAGTGAACAAAACAGACAAAAGTC 421 chr6ptel1M 789060 TCTACCCTCAAGGAATTTACATTCTA 789085 i i v ii C L2a_3end#LINE 420 CCTGCCCTCATGGAGCTTACATTCTA 395 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 40.37 CpG sites = 15, Kimura (unadjusted) = 42.75 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.00 (0 / 75), avg. gap size = 0.0 (0 / 0) 442 33.88 3.89 1.63 chr6ptel1M 789491 789670 (210330) C MIR3#SINE/MIR (6) 202 19 m_b292s601i15 12042 chr6ptel1M 789491 TGGAAACATGGA--GTCATAGTTTTGGAAGAACCATTAGACATTATCTGA 789538 i v i -- v i -- iiv v v i ii C MIR3#SINE/MIR 202 TAGAATCATAGAATGTCAGAGCT--GGAAGGGACCTTAGAGATCATCTAG 155 chr6ptel1M 789539 TTTGAAACCTCCATTTTACACATGAGTAAGATGAGGCTCAGAG-GAAAAA 789587 iii vv ii v v iv i - ivi C MIR3#SINE/MIR 154 TCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAA 105 chr6ptel1M 789588 GCA--TTGACTAAGATATTGTAGCAAAATAGTAATCTATCTGGAGTGGAA 789635 ii-- v i i vviii ? iv iiivv v i iiivii C MIR3#SINE/MIR 104 GTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGA 55 chr6ptel1M 789636 ACCCAGGCCT--TGACTCCAGAGTCGGTGTTTTTTTT 789670 i -- -v v i i i i C MIR3#SINE/MIR 54 ACCCAGGTCTCCTGACTCC-CAGTCCGTGCTCTCTCT 19 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 46.99 CpG sites = 39, Kimura (unadjusted) = 48.15 Transitions / transversions = 1.86 (39/21) Gap_init rate = 0.04 (7 / 179), avg. gap size = 1.43 (10 / 7) 16 22.13 0.00 0.00 chr6ptel1M 789671 789702 (210298) (T)n#Simple_repeat 1 32 (0) m_b292s252i5 12043 chr6ptel1M 789671 TTTTGTTTGTTTGTTTGTTTGGTTTTTTTTTT 789702 v v v v vv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 32 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 18 10.47 0.00 0.00 chr6ptel1M 789672 789702 (210298) (TTTG)n#Simple_repeat 1 31 (0) m_b292s252i6 12043 chr6ptel1M 789672 TTTGTTTGTTTGTTTGTTTGGTTTTTTTTTT 789702 v v v (TTTG)n#Simpl 1 TTTGTTTGTTTGTTTGTTTGTTTGTTTGTTT 31 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 267 30.14 4.39 2.88 chr6ptel1M 790107 790311 (209689) C L1MEh_5end#LINE/L1 (759) 1476 1269 m_b292s551i4 12044 chr6ptel1M 790107 TATTTCATGATCTCTATTCCTGCAGTGTTGCAGCTGCTAAGTCCTGTATA 790156 i i vi iiv v v v v i vv ivi i v C L1MEh_5end#LI 1476 TACTCCATTGTCTTCTTGCATCCAGTGTTGCTGTTGAGAAGTCTGATGTC 1427 chr6ptel1M 790157 ATCCTGATTGTGGTTCCCTGATATTTGAATTG---TTTCTTTCTGGCTAC 790203 vi v v i vi vv vi --- i vvi C L1MEh_5end#LI 1426 AATCTGATTCTTGTTCCTTTGTAGGTGATCTGTCTTTTCTCTCTGGAAGC 1377 chr6ptel1M 790204 TTGCAGTATTTTTTTCTTGAC-CTGATAGCTCTAAAATTTGATTATAATG 790252 vi v i ii v -i - i v v i C L1MEh_5end#LI 1376 TTTTAGAATTTTCTCTTTGTCTTTGAT-GTTCTTAAATTTCACTATAATG 1328 chr6ptel1M 790253 -ATCT--TTGGAGTTTTTATTTTAGGAACTCTTTCCTG--AGGTCATTGA 790297 -i --v vi v v ----- ? --v ivv iv C L1MEh_5end#LI 1327 TGTCTAGGTGTGGGTTTTCTTTTA-----TCTNTCCTGTTTGGCACTCTA 1283 chr6ptel1M 790298 TGGACCCTTTCAAT 790311 ii C L1MEh_5end#LI 1282 TGAGCCCTTTCAAT 1269 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 39.15 CpG sites = 28, Kimura (unadjusted) = 39.15 Transitions / transversions = 0.88 (28/32) Gap_init rate = 0.05 (11 / 204), avg. gap size = 1.36 (15 / 11) 238 33.31 6.75 1.20 chr6ptel1M 790129 790365 (209635) C HAL1#LINE/L1 (985) 1522 1273 m_b292s551i5 12044 chr6ptel1M 790129 CAGTGTTGCAGCTGCTAAGTCCTGTATAATCCTGATTGTGGTTCCCTGAT 790178 v i vv vi iiv i viv v i vi C HAL1#LINE/L1 1522 CAGTGTTGCTGTTGAGAAGTCCGATGCCATTCTGATTCCTGATCCTTTGT 1473 chr6ptel1M 790179 ATTTGAATTG---TTTCTTTCTGGCTACTTGCAGTATTTTTTTCTTG-AC 790224 v vi --- i vvi vi v i i ii i-v C HAL1#LINE/L1 1472 ATGTGACCTGTTTTTTCTCTCTGGAAGCTTTTAGGATCTTCTCTTTATCC 1423 chr6ptel1M 790225 CTGATAGCTCTAAAATTTGATTATAATGATCTTTGGAGT--TTTTATTTT 790272 i i - i i v iv i vv i v --v i C HAL1#LINE/L1 1422 CCGGT-GTTCTGAAATTTCACGATGATGTGCCTTGGTGTGGGTCTATTTT 1374 chr6ptel1M 790273 AGGAACTC--TTTCCTGAGGTCA-TTGATGGACCCTTTCAATGTCTA--- 790316 vvvv i -- v v i -- - i i i v vv --- C HAL1#LINE/L1 1373 TTTCATTCATTGTGCTGGG--CACTCGGTGGGCCCTTTCAATCTGGAAAC 1326 chr6ptel1M 790317 TTTTGCTCTCTGGTCCTAGGACAT----CAGGACATTTTCCTTAATAATT 790362 iv ii iii i i v ----iv ? ivv i i C HAL1#LINE/L1 1325 TCATGTCCTTCAGTTCTGGGAAATTTTCTTGNATTATTTCTTTGATAATT 1276 chr6ptel1M 790363 TCT 790365 C HAL1#LINE/L1 1275 TCT 1273 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 43.09 CpG sites = 42, Kimura (unadjusted) = 45.42 Transitions / transversions = 1.17 (42/36) Gap_init rate = 0.04 (10 / 236), avg. gap size = 1.90 (19 / 10) 430 26.25 15.00 0.00 chr6ptel1M 791543 791702 (208298) C MIRc#SINE/MIR (0) 268 85 m_b292s601i16 12045 chr6ptel1M 791543 AATGATAATAGTGGCCAACATTTATATAGTGCTTTAAATTTTATCAAGTG 791592 i ii?v iv i ii v v iv i C MIRc#SINE/MIR 268 AATAATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCG 219 chr6ptel1M 791593 CTTT---ATATGCTATCTTACTAAATCTTT------------TGATGT-- 791625 --- iii i i vi i i------------ v -- C MIRc#SINE/MIR 218 CTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAG 169 chr6ptel1M 791626 -CATTGC---TATTATTATCTTCATTTTACTACTGAGGAAACTGAGACT- 791670 - vv --- ii viv i - C MIRc#SINE/MIR 168 GCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC 119 chr6ptel1M 791671 -GAGATATGAAGTGACTCTCTT-AGCTAACATAG 791702 - vi v iv ii- v v i C MIRc#SINE/MIR 118 AGAGAGGTTAAGTGACTTGCCCAAGGTCACACAG 85 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 32.54 CpG sites = 26, Kimura (unadjusted) = 33.52 Transitions / transversions = 1.62 (26/16) Gap_init rate = 0.04 (7 / 159), avg. gap size = 3.43 (24 / 7) 325 28.71 0.99 0.00 chr6ptel1M 792059 792159 (207841) C MIR1_Amn#SINE/MIR (80) 150 49 m_b292s601i18 12046 chr6ptel1M 792059 CTCATTGTACATGTGAGCAAACTGAAGCAAATA-AGCTTAAGTGACTTGC 792107 i v vi v i ?v v - v ? C MIR1_Amn#SINE 150 CCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGC 101 chr6ptel1M 792108 CCAGAGTCACAAAGCTAAGAAGTGAGAAAGATCTGAGTTAAAATCAAACT 792157 ii ?v ?iiv? iv i vivv ? ?i vi iiii C MIR1_Amn#SINE 100 CCAAGGTCACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAACCCAGGTC 51 chr6ptel1M 792158 TC 792159 C MIR1_Amn#SINE 50 TC 49 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 38.86 CpG sites = 16, Kimura (unadjusted) = 40.67 Transitions / transversions = 1.23 (16/13) Gap_init rate = 0.01 (1 / 100), avg. gap size = 1.00 (1 / 1) 346 22.78 1.27 0.00 chr6ptel1M 792059 792137 (207863) C MIR#SINE/MIR (118) 144 65 m_b292s601i17 12046 chr6ptel1M 792059 CTCATTGTACATGTGAGCAAACTGAAGCAAATA-AGCTTAAGTGACTTGC 792107 i v vi v i v v - v i C MIR#SINE/MIR 144 CCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGC 95 chr6ptel1M 792108 CCAGAGTCACAAAGCTAAGAAGTGAGAAAG 792137 ii v iv iv i C MIR#SINE/MIR 94 CCAAGGTCACACAGCTAGTAAGTGGCAGAG 65 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 27.37 CpG sites = 9, Kimura (unadjusted) = 27.37 Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.01 (1 / 78), avg. gap size = 1.00 (1 / 1) 595 25.28 3.26 3.26 chr6ptel1M 792110 792293 (207707) MIRb#SINE/MIR 27 210 (58) m_b292s601i19 12047 chr6ptel1M 792110 AGAGTCACAAAGCTAAGAAGTGAGAAAGATCTGAGTTAAAATCAAACTTC 792159 - ii- vv i v v i i vi vvivi MIRb#SINE/MIR 27 AGAG-CACGG-GCTTTGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTC 74 chr6ptel1M 792160 TATCATATACTACTTGTTTTATGTTAGG-AAGTCACTTAACTGTGTCTG- 792207 ii iv vi v v iv i - i i- v - MIRb#SINE/MIR 75 TGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACC-TCTCTGA 123 chr6ptel1M 792208 -CCTTAGTTTCTTCATTTGTAAAATATGGATGATAGTTATAGC-ACCTCT 792255 - i i i iv i --- v - v MIRb#SINE/MIR 124 GCCTCAGTTTCCTCATCTGTAAAATGGGGATAATA---ATACCTACCTCG 170 chr6ptel1M 792256 TA-GCTTGTTGTGAGGATCAAGTAAGACAATG-ATGCAAA 792293 i - v i i i i - i MIRb#SINE/MIR 171 CAGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAA 210 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 29.08 CpG sites = 27, Kimura (unadjusted) = 31.57 Transitions / transversions = 1.50 (27/18) Gap_init rate = 0.07 (12 / 183), avg. gap size = 1.00 (12 / 12) 40 17.92 9.56 1.36 chr6ptel1M 792368 792503 (207497) (AT)n#Simple_repeat 1 147 (0) m_b292s252i7 12048 chr6ptel1M 792368 ATATA-ATAAATA-ACATGTA-ATATTTTTATA-ATATATGTGTGTGACA 792413 - v - i i - v v - i i i - i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATAT-ATA 49 chr6ptel1M 792414 TATATATATATATA-AAATATATATAT-TGTATATAGCATATGTA-AAAT 792460 - v - i -i i - v (AT)n#Simple_ 50 TATATATATATATATATATATATATATATATATATA-TATATATATATAT 98 chr6ptel1M 792461 ATACAT-TACATTAATAAATAAAT-TAT-TATTTAT-TATA-ATA-ATA 792503 i - i vv v v - - v - - - (AT)n#Simple_ 99 ATATATATATATATATATATATATATATATATATATATATATATATATA 147 Matrix = Unknown Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.11 (15 / 135), avg. gap size = 1.00 (15 / 15) 187 31.58 7.91 2.04 chr6ptel1M 792565 792703 (207297) C MIR1_Amn#SINE/MIR (60) 170 24 m_b292s601i20 12049 chr6ptel1M 792565 AGAAAGTCAGTGCC-TTCTCTGCAGTTTTTA-ATCTTAGAGAATTG---T 792609 i i ii - v iv -- - vv v ii i ---i C MIR1_Amn#SINE 170 AGGAGGTCAGTATCATTATCCCCA--TTTTACAGATGAGGAAACTGAGGC 123 chr6ptel1M 792610 GTGGA-AGTTCAGGTGAGTTGTCTG-GATCACAC--CCTGCAGATGTCAG 792655 ?ii - v ? i v i ii- i ? -- ?v ?ii v C MIR1_Amn#SINE 122 NCAGAGAGGTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNAGTGGCAG 73 chr6ptel1M 792656 GGGTGAGTCTTGAACACAGATCTTTTGGGCCTCAAGGCCA--ACTCTGTC 792703 i vi i v? ? v i iii i i i - v --i i C MIR1_Amn#SINE 72 AGCCGGGANTNGAACCCAGGTCTCCCGAGTCCC-AGTCCAGTGCTCTATC 24 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 44.23 CpG sites = 30, Kimura (unadjusted) = 47.35 Transitions / transversions = 2.31 (30/13) Gap_init rate = 0.07 (10 / 138), avg. gap size = 1.40 (14 / 10) 309 36.39 1.75 3.57 chr6ptel1M 792758 792928 (207072) C MIR#SINE/MIR (79) 183 16 m_b292s601i21 12050 chr6ptel1M 792758 TCGTTGCAACACACTTATGAGGTAAATAACCTCCACATTCTTATCCATAT 792807 v ii vv i ii -- ---- v vi C MIR#SINE/MIR 183 TCCTCACAACAACCCTATGAGGTAGGTA--CT----ATTATTATCCCCAT 140 chr6ptel1M 792808 TTTGCAGAAGTACAGACTAATGCACCTAGAAATTCAACTATTTGCCCACA 792857 i v viv i i v vv ii v iiv i vi C MIR#SINE/MIR 139 TTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAG 90 chr6ptel1M 792858 ATCCTTCAGCTTATCTGTGTCTGAG--GGGACTTTCTTTCCTGTGG-CCG 792904 i viv vi vv v v -- i ivvvii vv ii - i C MIR#SINE/MIR 89 GTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGCAGTCTG 40 chr6ptel1M 792905 GTCCTAAGGCCAGTGCTCCTAATC 792928 ii i ii v i i C MIR#SINE/MIR 39 GCTCCAGAGCCCGTGCTCTTAACC 16 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 50.14 CpG sites = 33, Kimura (unadjusted) = 51.37 Transitions / transversions = 1.22 (33/27) Gap_init rate = 0.05 (8 / 170), avg. gap size = 1.12 (9 / 8) 22 0.00 0.00 0.00 chr6ptel1M 793125 793148 (206852) (GT)n#Simple_repeat 1 24 (0) m_b292s252i8 12051 chr6ptel1M 793125 GTGTGTGTGTGTGTGTGTGTGTGT 793148 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGT 24 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 485 34.78 0.52 2.66 chr6ptel1M 793465 793656 (206344) 7SLRNA#SINE/Alu 109 296 (24) m_b292s502i2 12052 chr6ptel1M 793465 GTCCACAATAAGGCCAGGGTTAATTTATGGAGAGC-CCTGGAAGTGGAAG 793513 i v vi i vi i -- v v - i i i ii 7SLRNA#SINE/A 109 GTCCGCACTAAGTTCGGCATCAAT--ATGGTGACCTCCCGGGAGCGGGGG 156 chr6ptel1M 793514 GCCATCAGATTGCCTAAGGTGGCACAAAGCAGTTCAGGTCAAAAAACAAA 793563 i i i v viii v i ii -ii ii 7SLRNA#SINE/A 157 ACCACCAGGTTGCCTAAGGAGGGGTGAACCGGCCCAGGTC-GGAAACGGA 205 chr6ptel1M 793564 ACAGGTTAAAGCTTCCAATCTGATCAGCAGCAGGATTGAACCCCATCAGT 793613 i i i i ivv i ii i vi- ii v i 7SLRNA#SINE/A 206 GCAGGTCAAAACTCCCGTGCTGATCAGTAGTGGGATCGCG-CCTGTGAAT 254 chr6ptel1M 793614 GACTGCTTTATTTCCAACCTGAGTGAGATAGGGAGTCTCAATC 793656 ii ii vi -i i i ii v v v i vi 7SLRNA#SINE/A 255 AGCCACTGCA-CTCCAGCCTGGGCAACATAGCGAGACCCCGTC 296 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 39.51 CpG sites = 48, Kimura (unadjusted) = 51.37 Transitions / transversions = 2.82 (48/17) Gap_init rate = 0.03 (6 / 191), avg. gap size = 1.00 (6 / 6) 70 30.39 3.09 2.39 chr6ptel1M 793661 793951 (206049) (TCT)n#Simple_repeat 1 293 (0) m_b292s252i9 12053 chr6ptel1M 793661 TCGTCGTCGTCATCATCAT-TTCTTCCTCCTTTTCATCCTTCTT-TTCCT 793708 v v v v v v - i i i - i - i (TCT)n#Simple 1 TCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTC-TTCTTCTTCTTCTT 49 chr6ptel1M 793709 ATTTTTTCTCTTCTTTCTCTTCTTCTCTCTTCTTTCTTCCTCCTCCTCTT 793758 v i ii ii - - i i i (TCT)n#Simple 50 CTTCTTCTTCTTCTTCTTCTTCTTCT-TCTTC-TTCTTCTTCTTCTTCTT 97 chr6ptel1M 793759 CTTCCTTTTCCTGCTCTGCTTTTTCCTTCTT-TTCCTCTTCCTCCTTTTC 793807 i i i vi v i - - i i i i (TCT)n#Simple 98 CTTCTTCTTCTTCTTCTTCTTCTT-CTTCTTCTTCTTCTTCTTCTTCTTC 146 chr6ptel1M 793808 CTCCCTTTCCTTTTCTTCCTTTTCTTCCCTTTCCTCCTCCTCCTCCTCTC 793857 i iii i i i i iii i i i i i i (TCT)n#Simple 147 TTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTT 196 chr6ptel1M 793858 CCTC-CCAT-TTCTT-TT-TTATTTATCTTTCTCCTT-TTCCTCCTCCTC 793902 i -i v - - - v iv - i - i i i (TCT)n#Simple 197 CTTCTTCTTCTTCTTCTTCTTCTTCTTC-TTCTTCTTCTTCTTCTTCTTC 245 chr6ptel1M 793903 TTCTTTCTT-TTCTTCTTCCTCTTGCTCCTTTTCCTCCTCCTCCTCCTTC 793951 - - i - i i i i i i i (TCT)n#Simple 246 TTC-TTCTTCTTCTTCTTCTTCTT-CTTCTTCTTCTTCTTCTTCTTCTTC 293 Matrix = Unknown Transitions / transversions = 4.50 (54/12) Gap_init rate = 0.06 (16 / 290), avg. gap size = 1.00 (16 / 16) 286 25.09 27.12 2.04 chr6ptel1M 794264 794381 (205619) C MIRc#SINE/MIR (120) 148 2 m_b292s601i22 12054 chr6ptel1M 794264 CCCATTTTACAGATGAAG-AACTGAGGCAAATAGTGGTCA------TTAT 794306 i - vv v v i ------ ii C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr6ptel1M 794307 CTGAGG------------------------CTGG-ATTTGAACTCAGATC 794331 ii ------------------------ i - i i i i C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTC 49 chr6ptel1M 794332 TTCCCAACTCTATGCCCAATGCTCTATTCACTATGTCACCTAGCTGTCTC 794381 ii i v i i v i iiii ---i i C MIRc#SINE/MIR 48 TTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC---ACTGCCTC 2 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 30.07 CpG sites = 23, Kimura (unadjusted) = 32.84 Transitions / transversions = 3.83 (23/6) Gap_init rate = 0.06 (7 / 117), avg. gap size = 5.00 (35 / 7) 315 24.70 3.49 1.14 chr6ptel1M 794450 794535 (205465) C MIR#SINE/MIR (105) 157 70 m_b292s601i23 12055 chr6ptel1M 794450 TACCATTATTATCTACATCTTACA-ATAAGG-AACTGAGGAAAATGGGGA 794497 i iv i - i - v v vi i i C MIR#SINE/MIR 157 TACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGG 108 chr6ptel1M 794498 TTAAAT-ATTTGCTCAGGGTTGTACAGATGGTGAAATGG 794535 i - i i i iii v i - i C MIR#SINE/MIR 107 TTAAGTAACTTGCCCAAGGTCACACAGCTAGT-AAGTGG 70 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 31.70 CpG sites = 16, Kimura (unadjusted) = 31.70 Transitions / transversions = 3.20 (16/5) Gap_init rate = 0.05 (4 / 85), avg. gap size = 1.00 (4 / 4) 270 23.23 5.93 7.52 chr6ptel1M 794454 794588 (205412) C MIR1_Amn#SINE/MIR (71) 159 27 m_b292s601i25 12055 chr6ptel1M 794454 ATTATTATCTACATCTTACA-ATAAGG-AACTGAGGAAAATGGGGATTAA 794501 i iv i - i - v?v vi i i ? C MIR1_Amn#SINE 159 ATCATTATCCCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAA 110 chr6ptel1M 794502 AT-ATTTGCTCAGGGTTGTACAGATGGTGAAATGGTGAACATTGAGTCCA 794550 i - i i i iii? v? i? ---- -i -- - i C MIR1_Amn#SINE 109 GTGACTTGCCCAAGGTCACNCAGCNGGCNA----GTG-GCA--GAG-CCG 68 chr6ptel1M 794551 ACATTCCCAACCATAGG--TCCCGATTCTCAGT---GGGCTCT 794588 iv ? -?v -i -- v i --- v C MIR1_Amn#SINE 67 GGANT-NGAACC-CAGGTCTCCCGAGTCCCAGTCCAGTGCTCT 27 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 29.68 CpG sites = 20, Kimura (unadjusted) = 30.97 Transitions / transversions = 2.22 (20/9) Gap_init rate = 0.11 (15 / 134), avg. gap size = 1.20 (18 / 15) 272 28.56 4.04 0.98 chr6ptel1M 794454 794552 (205448) C MIRc#SINE/MIR (111) 157 56 m_b292s601i24 12055 chr6ptel1M 794454 ATTATTATCTACATCTTACA-ATAAGG-AACTGAGGAAAATGGGGATTAA 794501 iv i - i - vvv vi i i C MIRc#SINE/MIR 157 ATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAA 108 chr6ptel1M 794502 AT-ATTTGCTCAGGGTTGTACAGATGGTGAAATGGT-GAACATTGAGTCC 794549 i - i i i iii v i - i i- i vvv v v C MIRc#SINE/MIR 107 GTGACTTGCCCAAGGTCACACAGCTAGT-AAGTGGCAGAGCCGGGACTCG 59 chr6ptel1M 794550 AAC 794552 C MIRc#SINE/MIR 58 AAC 56 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 37.09 CpG sites = 17, Kimura (unadjusted) = 37.09 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.05 (5 / 98), avg. gap size = 1.00 (5 / 5) 263 37.96 0.96 8.81 chr6ptel1M 794575 794782 (205218) C MIRc#SINE/MIR (65) 203 11 m_b292s601i26 12056 chr6ptel1M 794575 TCTCAGTGGGCTCTCAGAGTTATTCTGTGAAGAATATAGCACGTGTAGCA 794624 v v iii v iiv ii i v vii vi iv vi C MIRc#SINE/MIR 203 TCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTA 154 chr6ptel1M 794625 GCACCTTCGTTTCACTTTAATGGAGGATGGGGAGGAGCAGAGAAATGAAG 794674 vi i ii i i v--i - vivv vv ii v C MIRc#SINE/MIR 153 TTATCCCCATTTTACA--GATG-AGGAAACTGAGGCTCAGAGAGGTTAAG 107 chr6ptel1M 794675 CACATTGCTCAACATTGCACAGCTCCTAGAGGTCAGGGGTTATATGTTAG 794724 iivv i vi ii vv iiv v i-------- iii C MIRc#SINE/MIR 106 TGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGA--------GCCGG 65 chr6ptel1M 794725 AATTCACACCCAGAT-TTTCTGA-TCCAAAAGTACAATAAATACTGTCTC 794772 i i iv i - i - -- v ---- i i v i C MIRc#SINE/MIR 64 GACTCGAACCCAGGTCTTCCTGACTCC--AAGTCC----AGTGCTCTTTC 21 chr6ptel1M 794773 CATCGCACCA 794782 ii C MIRc#SINE/MIR 20 CACTGCACCA 11 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 53.21 CpG sites = 45, Kimura (unadjusted) = 55.72 Transitions / transversions = 1.67 (45/27) Gap_init rate = 0.09 (19 / 207), avg. gap size = 1.00 (19 / 19) 258 28.56 5.26 4.17 chr6ptel1M 795154 795248 (204752) C MIR3#SINE/MIR (5) 203 108 m_b292s601i27 12057 chr6ptel1M 795154 ACAGAGACATAGAAT--TAGAAATGAAAAGGATCTCGGG--TCCTCCAGA 795199 i iv --i iv i i i ii i-- v i - C MIR3#SINE/MIR 203 ATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAG- 155 chr6ptel1M 795200 ATAACCAACATTC-CATTTTATAGATGAGAAAACTAAGACTCATGGAAAT 795248 - -- vii - i i i i i vi ii C MIR3#SINE/MIR 154 -T--CCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGT 108 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 39.24 CpG sites = 21, Kimura (unadjusted) = 39.24 Transitions / transversions = 4.20 (21/5) Gap_init rate = 0.07 (7 / 94), avg. gap size = 1.29 (9 / 7) 205 28.73 20.41 2.91 chr6ptel1M 795715 795861 (204139) C MIR3#SINE/MIR (20) 188 17 m_b292s601i28 12058 chr6ptel1M 795715 GTTAAAGCTGC--GGTGCATTA-AGATCATCTGGT-------------TT 795748 i i v-- vi v - i ------------- C MIR3#SINE/MIR 188 GTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTT 139 chr6ptel1M 795749 CCCAGATGGGGAAACTGAGATCCACAGA---AAATTGATTT----AAGAT 795791 iv i ii v ---i v i ---- i C MIR3#SINE/MIR 138 TACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGT 89 chr6ptel1M 795792 TGCAGAACT------TGGC-TAGCTTTGACCAGAAGATTCATATCGCAAG 795834 ii v i ?------ -v ivv i -- ii vi v vv C MIR3#SINE/MIR 88 CACACAGCNAGTTAGTGGCAGAGCCGGGACTAGA--ACCCAGGTCTCCTG 41 chr6ptel1M 795835 ATTTCCTTTAATCTGTAATATGTCTGC 795861 i i --- i i iv v v C MIR3#SINE/MIR 40 ACTCCC---AGTCCGTGCTCTCTCTGC 17 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 35.49 CpG sites = 24, Kimura (unadjusted) = 37.80 Transitions / transversions = 1.41 (24/17) Gap_init rate = 0.08 (12 / 146), avg. gap size = 2.92 (35 / 12) 256 33.72 1.16 0.00 chr6ptel1M 796136 796221 (203779) C L3#LINE/CR1 (9) 4090 4004 m_b292s601i29 12059 chr6ptel1M 796136 ACAAAATCTTAGCAC-AGAACAGACATTATTTCATATCTAGTTCAAATTC 796184 i i vii-i vi v vvvvvi i vi C L3#LINE/CR1 4090 ACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCAACCTC 4041 chr6ptel1M 796185 TTATCCAGTTTAGAAATGTTTTCTACAACATTCATGA 796221 ii i vi i vii i v C L3#LINE/CR1 4040 CCATCCAATGCAGGAATCCCTTCTACAACATCCCTGA 4004 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 46.45 CpG sites = 17, Kimura (unadjusted) = 46.45 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.01 (1 / 85), avg. gap size = 1.00 (1 / 1) 464 31.16 12.59 1.26 chr6ptel1M 796354 796639 (203361) C L3#LINE/CR1 (174) 3925 3608 m_b292s601i30 12059 chr6ptel1M 796354 TTGAATAGC----ATTGCT-GAAAGTTCTTGATT---TTGATGCCCACTT 796395 i i ---- i - vv --- - v vv C L3#LINE/CR1 3925 TTGGACAGCTCTGATTGTTAGAAAGTTCTTCCTTATATTGA-GCCGAAAT 3877 chr6ptel1M 796396 C-ACTTCCGTGTAACTTCTATCCGATGATTCTAGGTCTACTGTCAAGAGC 796444 -i i v i i iv i i v i iv vi C L3#LINE/CR1 3876 CTGCCTCCCTGTAACTTCCACCCATTGGTCCTAGTTCTGCCCTCTGGAGC 3827 chr6ptel1M 796445 AAC-CAAAATCAAATCT---CCTTCCTCTAT----TAGTTCTTCATATAT 796486 v - i - i --- i i i i----i ii v C L3#LINE/CR1 3826 CACACAGAAT-AAGTCTAATCCCTCTTCCACATGACAGCCCTTCAAATAT 3778 chr6ptel1M 796487 CCT----TTCCCATTATTTGTC-TCTGGATGCTTTTTTTCTTGTAGG--- 796528 iiv----ivv i i v v - iii - i i i-i --- C L3#LINE/CR1 3777 TTGAAGACAGCTATCATGTCTCCTCTAAGT-CTTCTCTTCTC-CAGGCTA 3730 chr6ptel1M 796529 -ACA-----AATTGTCTCAA---TTCTTTATATGCCTTGTTTTTCATATT 796569 - ----- i vii --- i i v v v i v ii C L3#LINE/CR1 3729 AACATCCCCAGTTCCTTCAACCGTTCCTCATATGACATGGTTTCCAGACC 3680 chr6ptel1M 796570 CCTCACCATCCCTGTATCCCTTACCTGGACATATTCCAATTTATCAACAG 796619 i iv vv i ivi iiii i i iiv C L3#LINE/CR1 3679 CTTCACCATCCTGGTCGCTCTCCTCTGGACGCGCTCCAGTTTGTCAATGT 3630 chr6ptel1M 796620 CCTTTT--GAATTTGGGGTCCA 796639 i i --i v v i C L3#LINE/CR1 3629 CCCTCTTAAAATGTGGCGCCCA 3608 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 41.20 CpG sites = 59, Kimura (unadjusted) = 42.59 Transitions / transversions = 2.03 (59/29) Gap_init rate = 0.06 (18 / 285), avg. gap size = 2.22 (40 / 18) 29 4.69 4.55 0.00 chr6ptel1M 796688 796731 (203269) (AGATCAACCC)n#Simple_repeat 1 46 (0) c_b292s251i0 12060 chr6ptel1M 796688 AGATCAA-CCAGATCAACCCAGATC-ACTCAGATCAAGCCAGATCA 796731 - - i v (AGATCAACCC)n 1 AGATCAACCCAGATCAACCCAGATCAACCCAGATCAACCCAGATCA 46 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2) 406 20.93 0.00 1.16 chr6ptel1M 796732 796818 (203182) C Charlie4#DNA/hAT-Charlie (2) 3376 3291 m_b292s502i3 12061 chr6ptel1M 796732 GGGGTTCTTCAGATTCTGATGTGTCATAGACCCTTTTGACTATCTCGTGA 796781 v vv i v- i i i i vi v C Charlie4#DNA/ 3376 GGGGTTCTTAACCTTTTT-TGTGCCATGGACCCCTTTGGCAGTCTGGTGA 3328 chr6ptel1M 796782 AACTTATGGAGCCCTTCTCAGAAAAGTGTTTTGAAAT 796818 i i v v i v C Charlie4#DNA/ 3327 AGCCTATGGACCCCTTCTCAGAATAATGTTTTTAAAT 3291 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 24.71 CpG sites = 9, Kimura (unadjusted) = 24.71 Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.01 (1 / 86), avg. gap size = 1.00 (1 / 1) 356 19.51 3.61 1.18 chr6ptel1M 796817 796899 (203101) C Charlie4a#DNA/hAT-Charlie (385) 123 39 m_b292s502i4 12061 chr6ptel1M 796817 ATAATTTAAGAAAATGCTGAATTTCAGTTTGAGGTTAATGAAAATATCAA 796866 v i i v i vvi C Charlie4a#DNA 123 ATAATTGAAGGAAATGCTAAATTTCAGTTAGAGGTTAGTGAAAATAAAGA 74 chr6ptel1M 796867 TGTA---TTTTTCCCTAACCTAACCTTATTGATCCC 796899 --- i v - vi i iv i C Charlie4a#DNA 73 TGTAATTTTTTTCCCCATCC-AAGTTCACGGACCCC 39 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 21.31 CpG sites = 9, Kimura (unadjusted) = 22.86 Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.02 (2 / 82), avg. gap size = 2.00 (4 / 2) 830 28.26 6.30 0.40 chr6ptel1M 796900 797137 (202863) MIR#SINE/MIR 11 262 (0) m_b292s601i31 12062 chr6ptel1M 796900 ATAGTGG---ACAGAATGCATCCTGAGGCTAGAAAGATCTAAGTTCAAAT 796946 --- v v i viii ii i vv -i ii i MIR#SINE/MIR 11 ATAGTGGTTAAGAGCACGGGCTCTGGAGCCAGACTG-CCTGGGTTCGAAT 59 chr6ptel1M 796947 CCTGCCTTAGATGCTTACTAGTTATGTGACTTCAGA-AAGTCATTTAACC 796995 i v iv vii i i i ii i- i i MIR#SINE/MIR 60 CCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACC 109 chr6ptel1M 796996 TCAGTTTGAATCCGTTTTCTCAGCTGTAAAATGGGAATAATAACAGAACC 797045 vv v vv v i v i i v MIR#SINE/MIR 110 TCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACC 159 chr6ptel1M 797046 CATCTCCTAGATTTGTTGTAAGTTTTAAATGTGATGACATCTGTAAGACA 797095 i i v iv i vv v v i i iv ii i MIR#SINE/MIR 160 TACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATACATGTAAAGCG 209 chr6ptel1M 797096 CTTAGCACAGTGTGTAG-----AGCAGAC------TAAATGTTAGTTATT 797134 v iv i ----- i ii ------ i MIR#SINE/MIR 210 CTTAGAACAGTGCCTGGCACATAGTAAGCGCTCAATAAATGTTAGCTATT 259 chr6ptel1M 797135 ATT 797137 MIR#SINE/MIR 260 ATT 262 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 33.99 CpG sites = 42, Kimura (unadjusted) = 36.73 Transitions / transversions = 1.68 (42/25) Gap_init rate = 0.02 (5 / 237), avg. gap size = 3.20 (16 / 5) 272 24.69 4.94 0.00 chr6ptel1M 797199 797279 (202721) C MIRc#SINE/MIR (0) 268 184 m_b292s601i32 12063 chr6ptel1M 797199 AATAATGATAATATCTGGCATTT-TATAATGCTTTAAGGTTTGGAAATCA 797247 i i?i vi - iii vi iv v i C MIRc#SINE/MIR 268 AATAATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCG 219 chr6ptel1M 797248 CACT-ACATATATTATCCCATTTGA--CATACAAC 797279 vi - i i -- vi C MIRc#SINE/MIR 218 CTTTCACATACATTATCTCATTTGATCCTCACAAC 184 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 29.81 CpG sites = 14, Kimura (unadjusted) = 31.73 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.04 (3 / 80), avg. gap size = 1.33 (4 / 3) 38 8.22 2.99 1.47 chr6ptel1M 797298 797364 (202636) (AT)n#Simple_repeat 1 68 (0) c_b292s251i1 12064 chr6ptel1M 797298 ATATATATATATATATATATATAT-TCACATAGATGTATGTATATATATA 797346 - - i v i i (AT)n#Simple_ 1 ATATATATATATATATATATATATAT-ATATATATATATATATATATATA 49 chr6ptel1M 797347 TATATATATGTA-ATATAT 797364 i - (AT)n#Simple_ 50 TATATATATATATATATAT 68 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.05 (3 / 66), avg. gap size = 1.00 (3 / 3) 13 12.12 0.00 3.57 chr6ptel1M 797415 797443 (202557) (TGTA)n#Simple_repeat 1 28 (0) m_b292s252i10 12065 chr6ptel1M 797415 TGTATGTGTGTATGTGTGTATGATATCTA 797443 i i - v (TGTA)n#Simpl 1 TGTATGTATGTATGTATGTATG-TATGTA 28 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1) 212 31.34 1.47 1.47 chr6ptel1M 797499 797566 (202434) C MIRc#SINE/MIR (175) 93 26 m_b292s601i33 12063 chr6ptel1M 797499 GTCACATGATCTCATAACCTGCA-AGTTGTATTTTGAACCTAGGTCTTCC 797547 i- v vi viv - ii vivi i i C MIRc#SINE/MIR 93 GTCACAC-AGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCC 45 chr6ptel1M 797548 TAACTCCAATTTGAGCGTT 797566 i v iv i i C MIRc#SINE/MIR 44 TGACTCCAAGTCCAGTGCT 26 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 37.05 CpG sites = 13, Kimura (unadjusted) = 42.23 Transitions / transversions = 1.62 (13/8) Gap_init rate = 0.03 (2 / 67), avg. gap size = 1.00 (2 / 2) 348 34.32 7.88 2.89 chr6ptel1M 797681 797845 (202155) C MIRc#SINE/MIR (88) 180 8 m_b292s601i34 12066 chr6ptel1M 797681 CCTGTTATATAAATATTGCAAGTTTCAT----CTCATTTTCTAGGTGAAC 797726 v vi iii vv i v i ---- i vi i -- C MIRc#SINE/MIR 180 CCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGA-- 133 chr6ptel1M 797727 TTGGA----GAAGCTTAGAGAATTTG---CACTGTGCTCAAGATCATGTA 797769 -- ---- i i iv i---v - i i iii C MIRc#SINE/MIR 132 --GGAAACTGAGGCTCAGAGAGGTTAAGTGACT-TGCCCAAGGTCACACA 86 chr6ptel1M 797770 GCTAATAAGCCACAGAGGCAAGATTGAAAATGAGATC-TCTTGACTCTTA 797818 i ivi v ii i vi viv i - i iv C MIRc#SINE/MIR 85 GCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAA 36 chr6ptel1M 797819 ACCCCATTTTCATTTCTCTATA-TACAC 797845 ii vi vi v i v ii -i C MIRc#SINE/MIR 35 GTCCAGTGCTCTTTCCACTGCACCACAC 8 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 46.58 CpG sites = 37, Kimura (unadjusted) = 49.16 Transitions / transversions = 2.06 (37/18) Gap_init rate = 0.06 (10 / 164), avg. gap size = 1.80 (18 / 10) 352 32.79 5.30 2.96 chr6ptel1M 797709 797840 (202160) C MIRb#SINE/MIR (117) 151 17 m_b292s601i35 12066 chr6ptel1M 797709 CTCATTTTCTAGGTGAACTTGGA----GAAGCTTAGAGAATTT--GCACT 797752 i vi i ---- ---- i i iv -- i vi C MIRb#SINE/MIR 151 CCCATTTTACAGATGA----GGAAACTGAGGCTCAGAGAGGTTAAGTAAC 106 chr6ptel1M 797753 GTGCTCAAGATCATGTAGCTAATAAGCCACAGAGGCAAGATTGAAAATGA 797802 v i i iii i ivi v ii vi viv C MIRb#SINE/MIR 105 TTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCA 56 chr6ptel1M 797803 GATCTCT-TGACTCTTAACCCCATTTTCATTTCTCTATA 797840 i v - iv v i vi v i v ii C MIRb#SINE/MIR 55 GGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCA 17 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 41.02 CpG sites = 27, Kimura (unadjusted) = 45.40 Transitions / transversions = 1.80 (27/15) Gap_init rate = 0.05 (7 / 131), avg. gap size = 1.57 (11 / 7) 16 31.83 0.00 0.00 chr6ptel1M 798474 798529 (201471) (ATAG)n#Simple_repeat 1 56 (0) m_b292s252i11 12067 chr6ptel1M 798474 ATAAATGGATGGATGAATAGAGAGTTATTCAGACAGATAGACAAACAGAT 798523 i i i ii v v vvi i i i i (ATAG)n#Simpl 1 ATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGAT 50 chr6ptel1M 798524 AGATAG 798529 (ATAG)n#Simpl 51 AGATAG 56 Matrix = Unknown Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0) 200 37.68 2.31 8.13 chr6ptel1M 798531 798660 (201340) C L2a_3end#LINE/L2 (17) 500 378 m_b292s601i36 12068 chr6ptel1M 798531 ATATTTATTAAGTGATTACCATATGTCACAACTCTGACCCCATGCTATGT 798580 i i vi i i i ------- i v ii v v i C L2a_3end#LINE 500 ATATTTATTGAGCGCCTACTATGTGCCA-------GGCACTGTTCTAGGC 458 chr6ptel1M 798581 CCCGGGGAGGTA--AGTAAGTTCAAGCAAGCAAGCTCATCCCTGCACTTG 798628 v i vii -- i i-iv i ii i--vi v ii C L2a_3end#LINE 457 GCTGGGGATACAGCAGTGAA-CAAAACAGACAAA--AGTCCCTGCCCTCA 411 chr6ptel1M 798629 AAGTGTTTATGTTCCATCAGGAGAAGA-AAACA 798660 vi v i ii i vii i i - i C L2a_3end#LINE 410 TGGAGCTTACATTCTAGTGGGGGGAGACAGACA 378 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 53.96 CpG sites = 33, Kimura (unadjusted) = 58.07 Transitions / transversions = 2.75 (33/12) Gap_init rate = 0.09 (12 / 129), avg. gap size = 1.08 (13 / 12) 595 34.89 0.00 1.40 chr6ptel1M 799540 799757 (200243) C L3#LINE/CR1 (109) 3990 3776 m_b292s601i37 12069 chr6ptel1M 799540 AGTCTCTCCTCAAAGAACCACATGGACAAGGAAGCCATGATCGCTCAAGG 799589 i v ii v v iv vv ii ivi iv i v ? i C L3#LINE/CR1 3990 AGCCTCTGCTTGAACACCTCCAGTGACGGGGAGCTCACTACCTCNCGAGG 3941 chr6ptel1M 799590 CTTCCCATTCTACTTTTGGACAGCTTTAATGTTTAGGAATGTTTTTCAAG 799639 vv i i i i vv i - i vvv C L3#LINE/CR1 3940 CAGCCCATTCCATTTTTGGACAGCTCTGATTGTTAGAAA-GTTCTTCCTT 3892 chr6ptel1M 799640 GAATCAAGCCCCAAATTGGCCTTTTTATGATTGTTACCCATTACCCTTCC 799689 iv ii v- iv iii i i i vii ivi i vv C L3#LINE/CR1 3891 ATATTGAGCCG-AAATCTGCCTCCCTGTAACTTCCACCCATTGGTCCTAG 3843 chr6ptel1M 799690 TTTTGCCCTTTGAGGCAAAACAGAATTAACTAAATCCTTCCTATGTGTGA 799739 i i ii v v v iiiv i i viiii C L3#LINE/CR1 3842 TTCTGCCCTCTGGAGCCACACAGAATAAGTCTAATCCCTCTTCCACATGA 3793 chr6ptel1M 799740 CAGCCCCTTCAAGTCTTT 799757 - i v C L3#LINE/CR1 3792 CAG-CCCTTCAAATATTT 3776 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 47.67 CpG sites = 46, Kimura (unadjusted) = 49.57 Transitions / transversions = 1.59 (46/29) Gap_init rate = 0.01 (3 / 217), avg. gap size = 1.00 (3 / 3) 239 31.86 12.39 0.00 chr6ptel1M 799991 800103 (199897) C L2c_3end#LINE/L2 (235) 243 117 m_b292s601i38 12068 chr6ptel1M 799991 AGGCTTCCATGAGAAAGTGAGATTGGATCTGCGTCTTGAAGGATCAATAG 800040 vv i i v iv v v ? v i C L2c_3end#LINE 243 AGGCTTCCCGGAGGAGGTGACATCTGAGCTGAGNCTTGAAGGATGAGTAG 194 chr6ptel1M 800041 GATT--------TGAATGGAGTTCCA------ATTTTAGGTAGAAGTTAT 800076 v -------- i v vvvvi------ ii i i vv i C L2c_3end#LINE 193 GAGTTAGCCAGGTGGAAGGAGGGGGGAAGAGCATTCCAGGCAGAGGGAAC 144 chr6ptel1M 800077 AACATGAACATAGACTTGGGAGTATGA 800103 i vi v i ?i ii i v C L2c_3end#LINE 143 AGCATGTGCAAAGGCNCGGAGGCAGGA 117 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 41.57 CpG sites = 18, Kimura (unadjusted) = 43.12 Transitions / transversions = 1.00 (18/18) Gap_init rate = 0.02 (2 / 112), avg. gap size = 7.00 (14 / 2) 279 25.40 0.00 0.00 chr6ptel1M 799991 800053 (199947) C L2d_3end#LINE/L2 (272) 244 182 m_b292s601i39 12068 chr6ptel1M 799991 AGGCTTCCATGAGAAAGTGAGATTGGATCTGCGTCTTGAAGGATCAATAG 800040 vvv i i i i v v v i vii C L2d_3end#LINE 244 AGGCTTCGTGGAGGAGGTGGGACTTGAGCTGGGCCTTGAAGGATGGGTAG 195 chr6ptel1M 800041 GATTTGAATGGAG 800053 i i C L2d_3end#LINE 194 GATTTGGATAGAG 182 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 31.56 CpG sites = 9, Kimura (unadjusted) = 31.56 Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0) 540 30.70 5.92 1.70 chr6ptel1M 800283 800451 (199549) MIRc#SINE/MIR 18 193 (75) m_b292s601i40 12070 chr6ptel1M 800283 GTAGAAAGGGCCCTGAGTTAGACGT--GAAGGAATTGGATTTGAATTCGA 800330 i i v iii v iv -- i i vi i i i i vi MIRc#SINE/MIR 18 GTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCG 67 chr6ptel1M 800331 GCTTTGGCACTTTTTAGCTCTGTGACTTTGGGG----CAATTA----CAC 800372 i v vi v i v---- v ---- v MIRc#SINE/MIR 68 GCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTC 117 chr6ptel1M 800373 TGAGTTTCAGTTTTCTCATCAGTAAGGTAAGAATAATCATAATATTTATT 800422 ii i v ii ii i --- ii iii MIRc#SINE/MIR 118 TGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATA---ATAATACCTGCC 164 chr6ptel1M 800423 CTACCAACTTCTAAGAATTGTTTTGAGAA 800451 i v i vv ii v i MIRc#SINE/MIR 165 CTGCCTACCTCACAGGGTTGTTGTGAGGA 193 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 39.65 CpG sites = 35, Kimura (unadjusted) = 41.85 Transitions / transversions = 2.19 (35/16) Gap_init rate = 0.04 (6 / 168), avg. gap size = 2.17 (13 / 6) 336 27.40 3.94 4.71 chr6ptel1M 802653 803058 (196942) L3#LINE/CR1 3631 4033 (66) m_b292s601i41 12071 chr6ptel1M 802653 CACTGATGAGCTAGAATAGTTCCAAAGGAGTGGGACCAGCCAGATGAGGG 802702 i ii i i iiivv i v v --- - v L3#LINE/CR1 3631 CATTGACAAACTGGAGCGCGTCCAGAGGAGAGCGACCAG---GATG-GTG 3676 chr6ptel1M 802703 AAGGGGAGCCCTGACAACTGCAAAT-ATGTCAGTCANNNNNNNNNNNNNN 802751 ----i iv -- vi - i v vv ?????????????? L3#LINE/CR1 3677 AAGGG----TCTGGAAAC--CATGTCATATGAGGAACGGTTGAAGGAACT 3720 chr6ptel1M 802752 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 802801 ?????????????????????????????????????????????????? L3#LINE/CR1 3721 GGGGATGTTTAGCCTGGAGAAGAGAAGACTTAGAGGAGACATGATAGCTG 3770 chr6ptel1M 802802 NNNNNNNNNCTTTGAAGAACAGCTGTGCAGAAGAAAGTTTGAGTTTGTTC 802851 ?????????v ii v iii ii ii v iiii i L3#LINE/CR1 3771 TCTTCAAATATTTGAAGGGCTGTCATGTGGAAGAGGGATTAGACTTATTC 3820 chr6ptel1M 802852 TGGTTGGCTCCAGACAACAGAAATAGATGCTGTGAGTGAAAGTTGTAGGA 802901 vv vii v ivv vi i i ii i L3#LINE/CR1 3821 TGTGTGGCTCCAGAGGGCAGAACTAGGACCAATGGGTGGAAGTTACAGGG 3870 chr6ptel1M 802902 GGAAATATTAAGG---AA---AGAGGAAAATTTCCTAAC--TTGGTGGTA 802943 i iv v vv --- --- ii i i i i -- ii v v i L3#LINE/CR1 3871 AGGCAGATTTCGGCTCAATATAAGGAAGAACTTTCTAACAATCAGAGCTG 3920 chr6ptel1M 802944 TCCGAGACAGGAAACCATTGGCTTGGAAG--AGT-AGCTCCTGATGACT- 802989 i i vv vvvii v i ?i -- - ivi v - L3#LINE/CR1 3921 TCCAAAAATGGAATGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGTCACTG 3970 chr6ptel1M 802990 GAAGTCTTCAGTGATCGATAGTCAATGATTTAAGGTGATCAAAGATCATT 803039 i v ivv -- viv vi ii-- vv - ii -i L3#LINE/CR1 3971 GAGGTGTTCAAGCA--GAGGCTGGATGACC--ACTTG-TCAGGGAT-GTT 4014 chr6ptel1M 803040 GTAGACTGAGGGA---CTGCAT 803058 --- --- L3#LINE/CR1 4015 GTAGA---AGGGATTCCTGCAT 4033 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 45.06 CpG sites = 64, Kimura (unadjusted) = 46.98 Transitions / transversions = 1.52 (64/42) Gap_init rate = 0.07 (27 / 405), avg. gap size = 1.30 (35 / 27) 256 22.90 0.00 4.29 chr6ptel1M 802738 802810 (197190) Plat_L3#LINE/CR1 3182 3251 (322) m_b292s551i6 12071 chr6ptel1M 802738 GTTGAAAGAACATGGAAATGTTTAGCCTGGAGAAGAGAAGACCCAGGAGG 802787 i i i- iiv i iv i v Plat_L3#LINE/ 3182 GTTAAAGGAAT-TGGGGTTGTTTAGCCTGGAGAAGAGAAGGCTAAGGGGT 3230 chr6ptel1M 802788 AACATGATAGCTCAGTCTTAAAG 802810 i v i i -- v Plat_L3#LINE/ 3231 GACTTAATAACT--GTCTTCAAG 3251 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 28.22 CpG sites = 11, Kimura (unadjusted) = 28.22 Transitions / transversions = 2.20 (11/5) Gap_init rate = 0.04 (3 / 72), avg. gap size = 1.00 (3 / 3) 262 29.95 12.71 4.08 chr6ptel1M 803168 803348 (196652) C MIR3#SINE/MIR (2) 206 11 m_b292s601i42 12072 chr6ptel1M 803168 ATCA-AGAA--ATAGGAT-TTAGAGATAGATGTGAATTGCCTT-CATATC 803212 - -- i - i v i v v ---- -v v C MIR3#SINE/MIR 206 ATCATAGAATCATAGAATGTCAGAGCTGGAAGGGA----CCTTAGAGATC 161 chr6ptel1M 803213 -TCAAGTCTGG-----TCATTCTTCACATGAGAAAACTGAGA-CTAGAAA 803255 - v iii----- i v v i i- i i C MIR3#SINE/MIR 160 ATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGA 111 chr6ptel1M 803256 CGATCAA------TGGTCAGGGTTATATA--TAG---GTGAATGATCTGG 803294 - i v ------ vi i i i i --? --- ivv v i C MIR3#SINE/MIR 110 -GGTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGG 62 chr6ptel1M 803295 GGTTGAAACCAGAATCCTCTGAGTTCAAATCCAATGTGCTTTTACTGTAC 803344 ii ii viii ii v i v i --- i iv iv C MIR3#SINE/MIR 61 GACTAGAACCCAGGTCTCCTGACTCCCAGTCC---GTGCTCTCTCTGCTC 15 chr6ptel1M 803345 AACC 803348 i C MIR3#SINE/MIR 14 AGCC 11 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 39.49 CpG sites = 34, Kimura (unadjusted) = 40.53 Transitions / transversions = 1.89 (34/18) Gap_init rate = 0.10 (18 / 180), avg. gap size = 1.72 (31 / 18) 315 31.47 10.94 0.71 chr6ptel1M 803224 803351 (196649) C MIRc#SINE/MIR (122) 146 6 m_b292s601i43 12072 chr6ptel1M 803224 CATTCTTCACATGAGAAAACTGAGACT-AGAAACGATCAA------TGGT 803266 i v v i i - i - i i ------ vi C MIRc#SINE/MIR 146 CATTTTACAGATGAGGAAACTGAGGCTCAGAGA-GGTTAAGTGACTTGCC 98 chr6ptel1M 803267 CAGGGTTATATA-----TAGGTGAATGATCTGGGGTTGAAACCAGAATCC 803311 i i i i ----- i ivv v i ii vi viii i C MIRc#SINE/MIR 97 CAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCT 48 chr6ptel1M 803312 T-CTGAGTTCAAATCCAATGTGCTTT-TACTGTACAACCTTG 803351 - v i i i iv -i i v vi C MIRc#SINE/MIR 47 TCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTG 6 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 40.61 CpG sites = 28, Kimura (unadjusted) = 43.57 Transitions / transversions = 2.33 (28/12) Gap_init rate = 0.05 (6 / 127), avg. gap size = 2.50 (15 / 6) 240 24.69 14.56 1.72 chr6ptel1M 804542 804644 (195356) MIR3#SINE/MIR 57 172 (36) m_b292s601i44 12073 chr6ptel1M 804542 TAGTCTCTAGCGCT----CTTACTAGCTACATGACTTTGAACAAATACAT 804587 i -i v ---- v ? iii i ii i - i MIR3#SINE/MIR 57 TAGTCCC-GGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGT-CAC 104 chr6ptel1M 804588 TCTCCATCT----GCCTCAGTTTCATCAT-TGCAAAAT--GGTGAT---A 804627 iiv v ---- v - i -- v i --- MIR3#SINE/MIR 105 TTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGA 154 chr6ptel1M 804628 CT-GATAGTTCCCAAGGT 804644 - ii ii i MIR3#SINE/MIR 155 CTAGATGATCTCTAAGGT 172 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 30.60 CpG sites = 19, Kimura (unadjusted) = 32.19 Transitions / transversions = 3.17 (19/6) Gap_init rate = 0.08 (8 / 102), avg. gap size = 2.12 (17 / 8) 628 21.32 7.28 0.62 chr6ptel1M 804556 804706 (195294) MIR#SINE/MIR 73 233 (29) m_b292s601i45 12073 chr6ptel1M 804556 CTTACTAGCTACATGACTTTGAACAAAT-ACAT--TCTCCATCTGCCTCA 804602 iii i ii i - v --i iv v MIR#SINE/MIR 73 CTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCA 122 chr6ptel1M 804603 GTTTCATCAT-TGCAAAATGGTGATACTGATAGTTCCCA-------AGGT 804644 v - i v v i v i -------i MIR#SINE/MIR 123 GTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTCATAGGGT 172 chr6ptel1M 804645 TGTTGTGAGGATCAAAAGAGATATTATGTATCCAGTGCTTAGAACAATGC 804694 i v v v ii i vv i i MIR#SINE/MIR 173 TGTTGTGAGGATTAAATGAGTTAATACATGTAAAGCGCTTAGAACAGTGC 222 chr6ptel1M 804695 CTGAGCATATAG 804706 - i MIR#SINE/MIR 223 CTG-GCACATAG 233 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 24.73 CpG sites = 20, Kimura (unadjusted) = 25.64 Transitions / transversions = 1.67 (20/12) Gap_init rate = 0.03 (5 / 150), avg. gap size = 2.40 (12 / 5) 237 30.31 10.07 2.68 chr6ptel1M 804783 804819 (195181) C MIRb#SINE/MIR (101) 167 133 m_b292s601i46 12074 chr6ptel1M 804783 GGAAGGTCATATTCAAACGTCATTTCCCAAATGAGGA 804819 v vv -- v vi iv i C MIRb#SINE/MIR 167 GGTAGGTATTATT--ATCCCCATTTTACAGATGAGGA 133 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 38.38 CpG sites = 26, Kimura (unadjusted) = 40.99 Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 27 0.00 0.00 0.00 chr6ptel1M 804820 804845 (195155) (AACCCT)n#Simple_repeat 1 26 (0) c_b292s251i2 12075 chr6ptel1M 804820 AACCCTAACCCTAACCCTAACCCTAA 804845 (AACCCT)n#Sim 1 AACCCTAACCCTAACCCTAACCCTAA 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 237 30.31 10.07 2.68 chr6ptel1M 804846 804946 (195054) C MIRb#SINE/MIR (136) 132 20 m_b292s601i46 12074 chr6ptel1M 804846 TC-------CAAATGAGG---A--AACTCCACACAAACCCACACAGCTAA 804883 v ------- i - --- -- i-i v ivi i C MIRb#SINE/MIR 132 ACTGAGGCTCAGA-GAGGTTAAGTAACTT-GCCCAAGGTCACACAGCTAG 85 chr6ptel1M 804884 CAA-TAGGAAAACTGAGCTTTGAAGCCAAGTC-ACCAAATTCTAGAACCA 804931 i - i v i i i i v i v i -ii vi i i i i v C MIRb#SINE/MIR 84 TAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCC 35 chr6ptel1M 804932 GTATTCTTTGCACTG 804946 ii v C MIRb#SINE/MIR 34 GTGCTCTTTCCACTG 20 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 38.38 CpG sites = 26, Kimura (unadjusted) = 40.99 Transitions / transversions = 2.56 (23/9) Gap_init rate = 0.07 (7 / 100), avg. gap size = 2.29 (16 / 7) 450 18.38 0.87 14.85 chr6ptel1M 807662 807776 (192224) C L2c_3end#LINE/L2 (0) 478 378 m_b292s601i47 12076 chr6ptel1M 807662 ATCCATTCAT-CATCAACCATTTATTAAGCACCTACTATGTACTAAGCAA 807710 i - v v i i i ------- C L2c_3end#LINE 478 ATTCATTCATTCAACAAACATTTATTGAGCGCCTACTATGTGC------- 436 chr6ptel1M 807711 TGAACCAGGCACTGGTTAAGGTACAAAGATAAATAAGACAGAGTCCCTGA 807760 ----- i ---i i i vi v C L2c_3end#LINE 435 -----CAGGCGCTGG---GGATACAAAGATGAATAAGACACGGTCCCTGC 394 chr6ptel1M 807761 TTATAAGGAGCTTACA 807776 iivi i C L2c_3end#LINE 393 CCTCAAGGAGCTCACA 378 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 17.42 CpG sites = 13, Kimura (unadjusted) = 21.19 Transitions / transversions = 2.60 (13/5) Gap_init rate = 0.14 (16 / 114), avg. gap size = 1.00 (16 / 16) 245 33.33 1.80 0.00 chr6ptel1M 808353 808463 (191537) MIR1_Amn#SINE/MIR 42 154 (76) m_b292s601i48 12077 chr6ptel1M 808353 GACTCAGTGGTATTAGATTCAAATCTCACCTGGCTCAGTTTCCC-CAGTG 808401 i vi vvi i i ? ? i iv vvvi v ?v ?- v ? MIR1_Amn#SINE 42 GACTCGGGAGACCTGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNG 91 chr6ptel1M 808402 TGATCACAATTAATTCATTTTCTCTCTCTG-GCCTCAGTTTCTTCCTTTG 808450 i viiivi v i ?vi - i v i MIR1_Amn#SINE 92 TGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTG 141 chr6ptel1M 808451 TAACACTAGGGTA 808463 v ivi i MIR1_Amn#SINE 142 TAAAATGGGGATA 154 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 45.30 CpG sites = 20, Kimura (unadjusted) = 48.92 Transitions / transversions = 1.18 (20/17) Gap_init rate = 0.02 (2 / 110), avg. gap size = 1.00 (2 / 2) 366 25.88 1.18 0.00 chr6ptel1M 808399 808483 (191517) MIR3#SINE/MIR 84 169 (39) m_b292s601i49 12077 chr6ptel1M 808399 GTGTGATCACAATTAATTCATTTTCTCTCTCTGG-CCTCAGTTTCTTCCT 808447 i viiivi v i ivi - i v MIR3#SINE/MIR 84 GTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCAT 133 chr6ptel1M 808448 TTGTAACACTAGGGTATTAGGCTAGATGATCTCTAA 808483 i v iv vi i i MIR3#SINE/MIR 134 CTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAA 169 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 32.76 CpG sites = 14, Kimura (unadjusted) = 32.76 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.01 (1 / 84), avg. gap size = 1.00 (1 / 1) 335 31.27 2.41 5.59 chr6ptel1M 808723 808888 (191112) MIRc#SINE/MIR 39 199 (69) m_b292s601i50 12078 chr6ptel1M 808723 GAGTC-GGAAAACTTCAGATTCG-TTCACAACTTTTGGTTTTAACAGCTA 808770 - i i -i i -v v ii i vvvvi vi i MIRc#SINE/MIR 39 GAGTCAGGAAGACCT-GGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTG 87 chr6ptel1M 808771 TGTGAGCTTGCCTAGCTGGGTCACTTGACCTGCTTTGTCTACCTTGATTA 808820 v ---- viii i - i v--i iii v MIRc#SINE/MIR 88 TGTGACCTTG----GGCAAGTCACTTAACCT-CTCTGA--GCCTCAGTTT 130 chr6ptel1M 808821 AGCTATCTGTAAAATGATTTGAATAATATTGATACTTCCTACTTCACTGG 808870 vvii ivvvv iiviiv v i v MIRc#SINE/MIR 131 CCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAGG 180 chr6ptel1M 808871 GTTTTCTGTGAGG--CAAAT 808888 v - -- MIRc#SINE/MIR 181 GTTGT-TGTGAGGATCAAAT 199 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 40.21 CpG sites = 27, Kimura (unadjusted) = 41.31 Transitions / transversions = 1.23 (27/22) Gap_init rate = 0.07 (12 / 165), avg. gap size = 1.08 (13 / 12) 687 27.23 12.95 0.00 chr6ptel1M 809059 809282 (190718) MIRc#SINE/MIR 12 264 (4) m_b292s601i51 12079 chr6ptel1M 809059 GGCATAGTGGAT-GAGCTTAGGAGTTAGATTCAGAAAC-CCTGAGTTCAA 809106 iii v- viv v i v i v- i i MIRc#SINE/MIR 12 GGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGA 61 chr6ptel1M 809107 ATTTTGGCTA-GATACTTACT----GTATGACCCACGGTAAGCCATTTAA 809151 i iii v- vi ---- i ivv i i i MIRc#SINE/MIR 62 GTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAA 111 chr6ptel1M 809152 TCTCCCCC--TCTCAATTTTCTCATCTG---------AATAATAGTACCT 809190 i i iv--i i i ---------i i MIRc#SINE/MIR 112 CCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCT 161 chr6ptel1M 809191 CCC---------TCATAGAGTTATTATGAAGATCAAATGAGGTAACAAAT 809231 v --------- i i i i i i iiv MIRc#SINE/MIR 162 GCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTAT 211 chr6ptel1M 809232 AT-AAAGTACTTTGCTATCCTTAAAGTGCTATGT-AATGCTAGCTATTAT 809279 i - ii iv v iv ii- iv v?i MIRc#SINE/MIR 212 GTGAAAGCGCTTTGTAAACTGTAAAGTGCTATACAAATGTAAGGNGTTAT 261 chr6ptel1M 809280 TAT 809282 MIRc#SINE/MIR 262 TAT 264 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 33.50 CpG sites = 43, Kimura (unadjusted) = 35.80 Transitions / transversions = 2.39 (43/18) Gap_init rate = 0.04 (9 / 223), avg. gap size = 3.22 (29 / 9) 12 15.85 0.00 3.45 chr6ptel1M 809285 809314 (190686) (TTA)n#Simple_repeat 1 29 (0) m_b292s252i12 12080 chr6ptel1M 809285 TTATTATCAGTATCAATTATTATCATTATT 809314 i v -v i (TTA)n#Simple 1 TTATTATTATTAT-TATTATTATTATTATT 29 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 421 28.94 9.50 1.55 chr6ptel1M 809533 809711 (190289) MIR3#SINE/MIR 15 207 (1) m_b292s601i52 12081 chr6ptel1M 809533 GAATAGAAAGAGCAGCAAATTTGGACTT-GGAGAAC------------CT 809569 ii i - ii i v v i- v ------------ i MIR3#SINE/MIR 15 GAGCAGAGAGAGCA-CGGACTGGGAGTCAGGAGACCTGGGTTCTAGTCCC 63 chr6ptel1M 809570 GTCTCTACTACTTCCCACCTGGGTTTGCTTCGGCAAGT--CTTAGGCTCT 809617 v i i vv i?v v vvv v -- viv MIR3#SINE/MIR 64 GGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCT 113 chr6ptel1M 809618 CAGGGTTTCAGCTGTCTTATTTGTGTAAAGGGAGGGATAAGGATTAGATG 809667 v ii i vi i i iv v i i v -- i MIR3#SINE/MIR 114 CTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTT--GGACTAGATG 161 chr6ptel1M 809668 GTGGCTAA-GTCCTTTCCAGTTCTAA-ATCCTATGACTCTCTTATT 809711 i vv - i i i - i i v v MIR3#SINE/MIR 162 ATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTATGATT 207 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 35.81 CpG sites = 28, Kimura (unadjusted) = 37.65 Transitions / transversions = 1.22 (28/23) Gap_init rate = 0.04 (8 / 178), avg. gap size = 2.50 (20 / 8) 357 33.33 6.35 0.00 chr6ptel1M 810032 810157 (189843) MIRc#SINE/MIR 2 135 (133) m_b292s601i53 12082 chr6ptel1M 810032 GAGGTAGCATGGTGCAGTGAATAGAGAGCTAGCCTCAGAATCTGGACAAC 810081 i ii i v vi i v ii i v vi MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr6ptel1M 810082 CCGGGTTTAAATTCTCCCATTGACATGCAATTGCTGTTTTACTCTGAGCA 810131 i ii i i ivv vi v ivi v v v v ii i MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 101 chr6ptel1M 810132 AAGC-CTTAACTTTT-------TCAGTGTCCCCA 810157 iv - i i ------- v i MIRc#SINE/MIR 102 AGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCA 135 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 42.94 CpG sites = 26, Kimura (unadjusted) = 46.12 Transitions / transversions = 1.62 (26/16) Gap_init rate = 0.02 (2 / 125), avg. gap size = 4.00 (8 / 2) 239 22.00 0.00 0.00 chr6ptel1M 811693 811742 (188258) L2d2_3end#LINE/L2 505 554 (1) m_b292s601i54 12083 chr6ptel1M 811693 AGTACTTTGCACATAGTCGTTGCTAAATAAATAGTTGCTGAATTGAATTG 811742 i i i v vi v v i v v L2d2_3end#LIN 505 AGTGCCTTGCACACAGTAGGCGCTCAATAAATATTTGTTGATTTGATTTG 554 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 23.56 CpG sites = 5, Kimura (unadjusted) = 26.14 Transitions / transversions = 0.83 (5/6) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 185 33.33 13.98 0.00 chr6ptel1M 812255 812347 (187653) L2d_3end#LINE/L2 406 511 (5) m_b292s601i55 12084 chr6ptel1M 812255 CTCTGAGGGAAGG--------CTTAT----TTCCTTCCTCTTCCATATT- 812291 ii v -------- ---- ii? v iii i vi- L2d_3end#LINE 406 CCTTGAGGGCAGGGACCATGTCTTATACTNTTTTNTCGTTCCCCACAGCG 455 chr6ptel1M 812292 TCTAACACAGAACCTAGTGCATAATAAGGGCTTAATACATGACTCTAGAT 812341 i i vi iv ii i i v i v ivi v v L2d_3end#LINE 456 CCTAGCACAGTGCTGAGCACATAGTAGGCGCTCAATAAATACTTGTTGAT 505 chr6ptel1M 812342 TGACTG 812347 i L2d_3end#LINE 506 TGATTG 511 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 45.57 CpG sites = 21, Kimura (unadjusted) = 47.77 Transitions / transversions = 2.10 (21/10) Gap_init rate = 0.03 (3 / 92), avg. gap size = 4.33 (13 / 3) 429 31.42 5.67 0.68 chr6ptel1M 812797 812937 (187063) MIRc#SINE/MIR 3 150 (118) m_b292s601i56 12085 chr6ptel1M 812797 AGATAGTAAGGTATTTTGAAAAAAAAAATG-ATTTGGAGACAGAGA-ACC 812844 ii iv iivv i i iv v - i v ii - MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chr6ptel1M 812845 CGAGTTCAAATTCTAACTCTGCCACTTACTGGCTATATGAATTTCAACAT 812894 i i i i i iii i i i vi vii v MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 102 chr6ptel1M 812895 CCCATTT---CTCTCTGGCTCTCAAATTTTCT--TCTG-AAAAAGAGGA 812937 vi i --- ivi - i i -- - v i MIRc#SINE/MIR 103 GTCACTTAACCTCTCTGAGCCTC-AGTTTCCTCATCTGTAAAATGGGGA 150 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 40.96 CpG sites = 32, Kimura (unadjusted) = 43.84 Transitions / transversions = 2.67 (32/12) Gap_init rate = 0.04 (6 / 140), avg. gap size = 1.50 (9 / 6) 544 27.49 4.97 0.60 chr6ptel1M 812826 812986 (187014) MIR3#SINE/MIR 31 198 (10) m_b292s601i57 12085 chr6ptel1M 812826 GATTTGGAGACAGAGAACCCGAGTTCAAATTCTAACTCTGCCACTTACTG 812875 i v v iii i i v i i iii v ? MIR3#SINE/MIR 31 GACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTN 80 chr6ptel1M 812876 GCTATATGAATTTCAACATCCCATTT---CTCTCTGGCTCTCAAATTTTC 812922 i i vi vii vvi i --- vi - i i MIR3#SINE/MIR 81 GCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTC-AGTTTCC 129 chr6ptel1M 812923 T--TCTG-AAAAAGAGGAGGTTGGACAAGATGATGAC-ATGGTTCTCTTC 812968 -- - v i v vv - v i ii i MIR3#SINE/MIR 130 TCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCC 179 chr6ptel1M 812969 AAATCT-ACTTCCTATGAT 812986 iv - v i MIR3#SINE/MIR 180 AGCTCTGACATTCTATGAT 198 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 34.63 CpG sites = 28, Kimura (unadjusted) = 35.77 Transitions / transversions = 1.75 (28/16) Gap_init rate = 0.04 (6 / 160), avg. gap size = 1.50 (9 / 6) 244 21.96 0.00 6.25 chr6ptel1M 813078 813145 (186855) C Charlie4z#DNA/hAT-Charlie (0) 167 104 m_b292s502i5 12086 chr6ptel1M 813078 CAGTGGTTTATAATTTTGTGTGTGTGTGTCATGGACTCCTTTGGCAGTTG 813127 iv ii v --- v - i i iv i iv C Charlie4z#DNA 167 CAGTGGTTCTTAACCTTTT---TGGG-GTCACGGACCCCTTTGAGAATCT 122 chr6ptel1M 813128 GATGAAACCTATGGACCC 813145 v C Charlie4z#DNA 121 GATGAAAGCTATGGACCC 104 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 24.15 CpG sites = 8, Kimura (unadjusted) = 26.25 Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.06 (4 / 67), avg. gap size = 1.00 (4 / 4) 568 19.71 3.47 1.36 chr6ptel1M 813102 813245 (186755) C Charlie4#DNA/hAT-Charlie (20) 3358 3212 m_b292s502i6 12086 chr6ptel1M 813102 TGTGTCATGGACTCCTTTGGCAGTTGGATGAAACCTATGGACCCCTTTGC 813151 i i iv i i iv C Charlie4#DNA/ 3358 TGTGCCATGGACCCCTTTGGCAGTCTGGTGAAGCCTATGGACCCCTTCTC 3309 chr6ptel1M 813152 ATAATGA-GTTTTTTAATGTAAAGAACCAAAATAAATTGTATTA-AAATG 813199 v i - v i v i -i v v v - v C Charlie4#DNA/ 3308 AGAATAATGTTTTTAAATGCATAAAA-TAAAATACATAGGATTACAAAGG 3260 chr6ptel1M 813200 AAATCAATTGCACTAAAATAATTATCATCAAAATAT---AAAATAAATT 813245 i ii i i - vi i --- i C Charlie4#DNA/ 3259 AAACCAATTATATTGAAAT-ATAGTTATCAAAATATTTAAAAACAAATT 3212 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 23.37 CpG sites = 18, Kimura (unadjusted) = 23.37 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.03 (5 / 143), avg. gap size = 1.40 (7 / 5) 215 26.42 0.00 0.00 chr6ptel1M 813680 813732 (186268) C MIRc#SINE/MIR (1) 267 215 m_b292s601i58 12087 chr6ptel1M 813680 ATAATGATGACAGTCGGCATTTACATAGTATTTTACATTTTACAAAGACC 813729 i i ?viivi ii i i v vv C MIRc#SINE/MIR 267 ATAATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCGC 218 chr6ptel1M 813730 TTT 813732 C MIRc#SINE/MIR 217 TTT 215 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 34.54 CpG sites = 9, Kimura (unadjusted) = 34.54 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 394 33.50 6.45 0.51 chr6ptel1M 813821 814006 (185994) MIRc#SINE/MIR 71 267 (1) m_b292s601i59 12088 chr6ptel1M 813821 CTTTCATTTACCAACTGAATGCCATTGGACAAGTCACTTTACTGCTTAGC 813870 vi i i i vi v v i v iv iv v MIRc#SINE/MIR 71 CTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGA 120 chr6ptel1M 813871 TCTTTAGCTTCCTTGCCTACACAATGGAAAC-ATTATCTTTTCCCTAGCT 813919 v i i i iii ii v ii i- v vii v iv MIRc#SINE/MIR 121 GCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCT 170 chr6ptel1M 813920 A-TTTAC----CTGTTATGATGA--GAATG---TAATTTACA-GGAATTG 813958 -i i ----i i v --i --- v ii- i vi MIRc#SINE/MIR 171 ACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCG 220 chr6ptel1M 813959 CTTTGCAAACATTAAAATGCTATTTAAAATATCAAATATTACTGTCAT 814006 i vv i vi- i v ii?i i i i MIRc#SINE/MIR 221 CTTTGTAAACTGTAAAGTGCTATAC-AAATGTAAGGNGTTATTATTAT 267 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 46.40 CpG sites = 41, Kimura (unadjusted) = 47.50 Transitions / transversions = 1.95 (41/21) Gap_init rate = 0.04 (7 / 185), avg. gap size = 1.86 (13 / 7) 598 29.67 10.53 0.00 chr6ptel1M 814741 814949 (185051) MIRc#SINE/MIR 14 244 (24) m_b293s601i2 12089 chr6ptel1M 814741 TGCAGTGGAGAGAGTATCCAAC----AATCAGGAAAAC--GAATTCAAAT 814784 i i iivi ---- i i -- ii i i MIRc#SINE/MIR 14 TGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGT 63 chr6ptel1M 814785 GCAGACTCAGATACTTAACAGGTTTGTGATACTGGGACAGTCATTTCACC 814834 v v i v vi vi v v ivi vv i v MIRc#SINE/MIR 64 CCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACC 113 chr6ptel1M 814835 TCTTTCTGCCTCAGTTTCCTTGTCTACAAACTGAAGATAATAGCATCTT- 814883 i vv ii ii v ii ii i v- MIRc#SINE/MIR 114 TCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGC 163 chr6ptel1M 814884 --------CCTC-CAAA--TATTATGAAGATAAAATGGGAT-ATTTAT-- 814919 -------- - ii-- i i i v i - v -- MIRc#SINE/MIR 164 CCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGT 213 chr6ptel1M 814920 -AATGTGCCTTGCAAAACTTTAAGCATTATA 814949 - v i i i viv v iii MIRc#SINE/MIR 214 GAAAGCGCTTTGTAAACTGTAAAGTGCTATA 244 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 37.73 CpG sites = 40, Kimura (unadjusted) = 39.38 Transitions / transversions = 1.82 (40/22) Gap_init rate = 0.04 (8 / 208), avg. gap size = 2.75 (22 / 8) 24 10.88 0.00 2.44 chr6ptel1M 814951 814992 (185008) (ATC)n#Simple_repeat 1 41 (0) m_b293s252i0 12090 chr6ptel1M 814951 ATCACCATCACCATCATCATCGTCATTCATCATCATCCTCAT 814992 i i i - v (ATC)n#Simple 1 ATCATCATCATCATCATCATCATCA-TCATCATCATCATCAT 41 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.02 (1 / 41), avg. gap size = 1.00 (1 / 1) 205 28.50 3.79 9.60 chr6ptel1M 815074 815205 (184795) L2d_3end#LINE/L2 345 469 (47) m_b293s601i3 12091 chr6ptel1M 815074 TGTATTCTCCTTTCTGAAATTATATTTATTTGTCTGTTTGCATGTTATAT 815123 v i i ---- i - i -- v v -- v i v L2d_3end#LINE 345 TGTATTGTTCTCT----AATTGT-TTCAT--GTGTGTTAG--TCTTGTCT 385 chr6ptel1M 815124 TCTCCATTAGGGTATAAGTTCCTTCAGTACAGGGAT--TGTT---TGCCA 815168 i i v i iv i i v vi i-- i--- i i? L2d_3end#LINE 386 CCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACTN 435 chr6ptel1M 815169 TTTCTGCCTTTAAACTTTCAGCAACTAGCACAGTGCT 815205 i?v v i--- iiv iv L2d_3end#LINE 436 TTTTNTCGTTC---CCCACAGCGCCTAGCACAGTGCT 469 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 36.19 CpG sites = 21, Kimura (unadjusted) = 37.60 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.11 (14 / 131), avg. gap size = 1.21 (17 / 14) 339 30.45 4.62 1.49 chr6ptel1M 815090 815219 (184781) L2c_3end#LINE/L2 330 463 (15) m_b293s601i4 12091 chr6ptel1M 815090 AAATTATATT-TATTTGTCTGTTTGCATGT-TATATTCTCCATTAGGGTA 815137 v i - v i ? - i v i i iv i L2c_3end#LINE 330 AACTTGTATTGTAATTGTCTGTTTACNTGTCTGTCTCCTCCACTAGACTG 379 chr6ptel1M 815138 TAAGTTCCTTCAGTACAGGGATTGTTTGCCATTTCTGCCTTTAAACTTTC 815187 i i v vi ii v vii iv -- iv iiii L2c_3end#LINE 380 TGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCAT--CTTTGTATCCCC 427 chr6ptel1M 815188 AGCAACTAGCAC--AGT--GCTCTTATTAGATACTT 815219 iv i -- -- v i v i ii L2c_3end#LINE 428 AGCGCCTGGCACATAGTAGGCGCTCAATAAATGTTT 463 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 38.76 CpG sites = 26, Kimura (unadjusted) = 41.58 Transitions / transversions = 2.00 (26/13) Gap_init rate = 0.05 (6 / 129), avg. gap size = 1.33 (8 / 6) 276 23.88 5.97 0.00 chr6ptel1M 815228 815294 (184706) C L3#LINE/CR1 (1647) 2452 2382 m_b293s601i5 12092 chr6ptel1M 815228 CTTGACTGAAGAAACAGAAA-AAAGTAGG---TACATATTTTTGCCTTCT 815273 iv ii i i i- i --- ivi v i i C L3#LINE/CR1 2452 CTTGATAGAGAAGACGGAAGCAAAATAGGAGTTGAGTAGTTCTGCTTTCT 2403 chr6ptel1M 815274 CTCTATCATCTGTTATCATTA 815294 i v C L3#LINE/CR1 2402 CTCTGTCATCTGTTAACATTA 2382 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 27.98 CpG sites = 12, Kimura (unadjusted) = 30.24 Transitions / transversions = 3.00 (12/4) Gap_init rate = 0.03 (2 / 66), avg. gap size = 2.00 (4 / 2) 206 31.47 11.89 2.01 chr6ptel1M 815339 815565 (184435) C L3#LINE/CR1 (1822) 2277 2029 m_b293s601i6 12092 chr6ptel1M 815339 AATTTTAGCTCATTTGGGACTCAAG--------ACATTATTCTGATGGGA 815380 iii i iv i iv -------- i v ii v C L3#LINE/CR1 2277 AGCCTCAGCTCATTCTGGGCTTTAGCCTTCCTGACACTATTCTTACAGGC 2228 chr6ptel1M 815381 TCCCACTATTTT-TCTATATTTTTATTCAT---TTTTATTTCC-TTTTCT 815425 ivii? i i - v i ii iv i --- ii v - i C L3#LINE/CR1 2227 TTGTGNTACTCTCTCTTTGTCCTTGGTTATATGTCCTCTTTCCATCTTCT 2178 chr6ptel1M 815426 --TCCATCTC----TAACAT-----ATCCGAGTTGGTCCT-TGTCCAGCC 815463 -- v v ---- v ----- v --ii ? - i v? C L3#LINE/CR1 2177 GATACATGTCCTTTTAAAATCTGACATCAGAG--AATNCTCTATGNAGCC 2130 chr6ptel1M 815464 ACGTTAATTTGCTTCA--GCCATCTACTCTATTTCTTCTTATTAGAATAA 815511 ii - v -- v i- v ii i i i - v C L3#LINE/CR1 2129 ACGTTGGTTT-CTTAAATGCCCTCC-CTCTTTTCTTCCTCATTGGA-TCA 2083 chr6ptel1M 815512 TTTGTCTATATTATTAGATTTTCATTTGTGATATCAATCCATCCCTCTCA 815561 vvv i vi i v v i v v vvi ? ii C L3#LINE/CR1 2082 TTTGTAATTGTAGTCAGAATTTCATTTTTAAGAGCTTCCCANCCCTCTTG 2033 chr6ptel1M 815562 AATC 815565 ii C L3#LINE/CR1 2032 AGCC 2029 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 43.64 CpG sites = 43, Kimura (unadjusted) = 43.64 Transitions / transversions = 1.59 (43/27) Gap_init rate = 0.06 (14 / 226), avg. gap size = 2.29 (32 / 14) 327 26.45 2.88 7.52 chr6ptel1M 815610 815748 (184252) C L3#LINE/CR1 (2178) 1921 1789 m_b293s601i7 12092 chr6ptel1M 815610 TCCTTCCTTAGCTCTT-TGAAATCTAAGCTAACAAATTCGAAGATGACTT 815658 i i v -i v v i --- v -----v C L3#LINE/CR1 1921 TCCTTTCTTGGCTATTACGAACTCTAAGATGACA---TGG-----CACTT 1880 chr6ptel1M 815659 TTTTCAAAGGTTCCCATC-ATTTTTA--TCTCCAATTTCTATTCCTCCCT 815705 i i v i - i ii -- v --i vi i i C L3#LINE/CR1 1879 TCTCCCAAGGTTCCTATCGACTTCCACTTCACCAA--CCAGTTCTTCCTT 1832 chr6ptel1M 815706 ATTGATCAGAGTCATGCCCAGAATAGCTGTCACCCTCATTCCT 815748 i i i i v i i v iv i v C L3#LINE/CR1 1831 GTTGGTCAGAATTAAGTCCAGAGTAGCAGTTCCCCTCGTTGCT 1789 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 31.21 CpG sites = 22, Kimura (unadjusted) = 33.61 Transitions / transversions = 1.83 (22/12) Gap_init rate = 0.09 (13 / 138), avg. gap size = 1.08 (14 / 13) 406 35.99 2.82 1.11 chr6ptel1M 816249 816425 (183575) C L3#LINE/CR1 (12) 4087 3908 m_b293s601i8 12093 chr6ptel1M 816249 GAATGGCAGAGCTTAGAATGCCATCAGAAAGCATCTAGGACAACTT---A 816295 vv i vii iv v v i iiv vv i --- C L3#LINE/CR1 4087 GAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCAACCTCCCA 4038 chr6ptel1M 816296 TGCCTGAAAAAAAATTCCT-CTATAACAGTTCCTGACAAGTTATCATCCA 816344 - viviv ii i - i - i vi C L3#LINE/CR1 4037 T-CCAATGCAGGAATCCCTTCTACAACA-TCCCTGACAAGTGGTCATCCA 3990 chr6ptel1M 816345 TTTTTCATTTTAAGATAGCTAGTGATGGGAATC-CGCCATAATGTGAGGT 816393 vii iiii v v ivv i i i v - i i ivvi?i i C L3#LINE/CR1 3989 GCCTCTGCTTGAACACCTCCAGTGACGGGGAGCTCACTACCTCNCGAGGC 3940 chr6ptel1M 816394 AACCTATCCTACTTTTGGGCATCTCAAAATGT 816425 i i i i i i v vi v C L3#LINE/CR1 3939 AGCCCATTCCATTTTTGGACAGCTCTGATTGT 3908 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 49.75 CpG sites = 39, Kimura (unadjusted) = 52.19 Transitions / transversions = 1.62 (39/24) Gap_init rate = 0.03 (5 / 176), avg. gap size = 1.40 (7 / 5) 522 23.58 0.81 0.00 chr6ptel1M 816516 816638 (183362) MER63D#DNA/hAT-Tip100 344 467 (594) m_b293s502i0 12094 chr6ptel1M 816516 ATTTATACCTTTAAAACTGGAAAGTTCTACACATCAGAGCTTGATTTACT 816565 i vivi ii v iiv v i i MER63D#DNA/hA 344 ATTTACACCACGGAAATCGGCAAACGCTACAAATCAGGGCTTGATTTATT 393 chr6ptel1M 816566 ATTTTGTTGATT-TCTAGACTTAGGAAAGTGGTGGAGTCAATGTTTATCA 816614 i - i i vv v v MER63D#DNA/hA 394 GTTTTGTTGATTGTCTAGACTTAAGAAAGTGATGGAGAAAATGTTAATAA 443 chr6ptel1M 816615 CATACATTCAGCTTGCAAGTGTGT 816638 iii v v i iv MER63D#DNA/hA 444 TGCAGATTAAACTTAAAAGTGTGT 467 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 25.46 CpG sites = 17, Kimura (unadjusted) = 28.85 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.01 (1 / 122), avg. gap size = 1.00 (1 / 1) 191 23.08 0.00 0.00 chr6ptel1M 816697 816735 (183265) C L3#LINE/CR1 (70) 4029 3991 m_b293s601i9 12095 chr6ptel1M 816697 AGAAAGCCCCTCCACAATTTTCCTTACAAGTGGTTATCC 816735 i v i i iv i v i C L3#LINE/CR1 4029 AGGAATCCCTTCTACAACATCCCTGACAAGTGGTCATCC 3991 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 28.45 CpG sites = 6, Kimura (unadjusted) = 28.45 Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 765 28.68 10.95 2.01 chr6ptel1M 816733 817006 (182994) C L3#LINE/CR1 (203) 3896 3599 m_b293s601i10 12095 chr6ptel1M 816733 TCCTTACATTGTCCCCAAATTTACCTATGTCTGCAACATGTATATATACA 816782 i vv v i i --vi i --- - vi iv C L3#LINE/CR1 3896 TCCTTATATTGAGCCGAAATCTGCCT--CCCTGTAAC---T-TCCACCCA 3853 chr6ptel1M 816783 TTGTTCCTAATTCTACATTATGGGGTTGAAAATAACAAGTTTA------- 816825 v i i vi v i iiiv v v i i ------- C L3#LINE/CR1 3852 TTGGTCCTAGTTCTGCCCTCTGGAGCCACACAGAATAAGTCTAATCCCTC 3803 chr6ptel1M 816826 ---TACAT-ACAGCCATTTAAATATTTGGAAAGAGCTGTCATGTTTCCTG 816871 ---i - v i i i v i i v C L3#LINE/CR1 3802 TTCCACATGACAGCCCTTCAAATATTTGAAGACAGCTATCATGTCTCCTC 3753 chr6ptel1M 816872 TAAATCTTCTATCTTTCAGGTAAAATAGCCTCGGTTTGTTCAATTATTCT 816921 i v ii i iv i v i i iv iii i C L3#LINE/CR1 3752 TAAGTCTTCTCTTCTCCAGGCTAAACATCCCCAGTTCCTTCAACCGTTCC 3703 chr6ptel1M 816922 ACATATGACAAGGTATTCAG-----TCTCCA------------TTCTCTG 816954 v v v i ----- v ------------ i C L3#LINE/CR1 3702 TCATATGACATGGTTTCCAGACCCTTCACCATCCTGGTCGCTCTCCTCTG 3653 chr6ptel1M 816955 CACATACTCCAGTTTG-AAATATCTTCTCTAAAACGTGGTA-CCAGAAGT 817002 v iii -v i iiiii i ii- v C L3#LINE/CR1 3652 GACGCGCTCCAGTTTGTCAATGTCCCTCTTAAAATGTGGCGCCCAGAACT 3603 chr6ptel1M 817003 AAGC 817006 i i C L3#LINE/CR1 3602 GAAC 3599 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 35.15 CpG sites = 51, Kimura (unadjusted) = 37.86 Transitions / transversions = 1.96 (51/26) Gap_init rate = 0.05 (13 / 273), avg. gap size = 2.77 (36 / 13) 14 31.50 1.47 1.47 chr6ptel1M 817176 817243 (182757) (TTTTCT)n#Simple_repeat 1 68 (0) m_b293s252i1 12096 chr6ptel1M 817176 TTTTCATTTTCTTTTTGTTGCTGTTTGTC-CTTTCTCTTGGCTTTCCCCT 817224 v v vi v v -i - vv ii i (TTTTCT)n#Sim 1 TTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCT-TTTTCTTTTTCTT 49 chr6ptel1M 817225 TTTGTTCTGATTCTTCTTT 817243 v i vv i (TTTTCT)n#Sim 50 TTTCTTTTTCTTTTTCTTT 68 Matrix = Unknown Transitions / transversions = 0.70 (7/10) Gap_init rate = 0.03 (2 / 67), avg. gap size = 1.00 (2 / 2) 467 21.62 2.70 0.00 chr6ptel1M 817573 817683 (182317) C Charlie1a#DNA/hAT-Charlie (10) 1445 1332 m_b293s502i1 12097 chr6ptel1M 817573 CAAAGCTTGTGGTTTCAAAACTCCATTATGCTTTTAAA--TTATTGAGC- 817619 vi v i ii i v ii i -- v- C Charlie1a#DNA 1445 CAAACTTTTTGGTCTCAGGACCCCTTTACACTCTTAAAAATTATTGAGGA 1396 chr6ptel1M 817620 CCCCAAAGAACCTTTATTTCTATGGGTTATATATATCAATATTTATCATA 817669 i i i v i v i i C Charlie1a#DNA 1395 CCCCAAAGAGCTTTTGTTTATGTGGGTTATATCTATCGATATTTACCATA 1346 chr6ptel1M 817670 TTAACTATTTAAAC 817683 ivv v C Charlie1a#DNA 1345 TTAGAAATTAAAAC 1332 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 24.83 CpG sites = 15, Kimura (unadjusted) = 26.07 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.02 (2 / 110), avg. gap size = 1.50 (3 / 2) 284 18.55 0.00 3.70 chr6ptel1M 817690 817745 (182255) C Charlie1a#DNA/hAT-Charlie (1364) 91 38 m_b293s502i2 12097 chr6ptel1M 817690 ATGATTAAGAAAATAGTTTTGACTTTTCAGACCCCATGGAAAAAGGTCTT 817739 v v i iv i v -- i i C Charlie1a#DNA 91 ATTATTATGAAAATAGTTTTGACCTCGCGGACCCCCTG--AAAGGGTCTC 44 chr6ptel1M 817740 GGAGAC 817745 i C Charlie1a#DNA 43 GGGGAC 38 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 14.93 CpG sites = 6, Kimura (unadjusted) = 21.58 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.04 (2 / 55), avg. gap size = 1.00 (2 / 2) 385 32.21 0.48 3.45 chr6ptel1M 817758 817966 (182034) L2#LINE/L2 2288 2490 (592) m_b293s601i11 12098 chr6ptel1M 817758 TGAACTCATC-AGTTCTTTGTGAATTCCATTTTTATATCTGTGCTGATGA 817806 v - i-- ii iv iv v vii v v i L2#LINE/L2 2288 TGATCTCATCCAGTC--TCATGGCTTTAAATACCATCTATATGCTGATGA 2335 chr6ptel1M 817807 TTTTCACATTGACCTTATCTAGCCCTAACCTGTCTCCTGACCTCCACTTT 817856 i ii v v iv i- i vi v i v vvi L2#LINE/L2 2336 CTCCCAAATTTATATC-TCCAGCCCGGACCTCTCCCCTGAACTCCAGACT 2384 chr6ptel1M 817857 CTTATTTTAAATGGCCTGTTGGACAACTAAAACTAGATTTCTCATCTGCA 817906 v v iv iv ii v v vv vi i v v vv L2#LINE/L2 2385 CGTATATCCAACTGCCTACTCGACATCTCCACTTGGATGTCTAATAGGCA 2434 chr6ptel1M 817907 TCTCAAACTCAACATGTTCATAATTTTTCCCTGCTCATCTTTCCCTCTTC 817956 i i v i vvv i -- v -- i i L2#LINE/L2 2435 TCTCAAACTTAACATGTCCAAAACTGAACTC--CTGATCTT--CCCCCTC 2480 chr6ptel1M 817957 ATAACTTCTC 817966 v v v L2#LINE/L2 2481 AAACCTGCTC 2490 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 42.33 CpG sites = 29, Kimura (unadjusted) = 42.33 Transitions / transversions = 0.81 (29/36) Gap_init rate = 0.04 (8 / 208), avg. gap size = 1.00 (8 / 8) 229 30.30 0.00 0.00 chr6ptel1M 818086 818151 (181849) C CR1-3_Croc#LINE/CR1 (1118) 2487 2422 m_b293s551i0 12099 chr6ptel1M 818086 CCACCTTAGCTTATTTTGCTACTACATCATAGTGTTGCCCCATATTGAGT 818135 i v v i v v vi i i v iv v i C CR1-3_Croc#LI 2487 CCGCATTCGCCTTTTGTGCGGCTGCATCACACTGCAGACTCATATTGAGT 2438 chr6ptel1M 818136 TTGCAATCCAGCAAGA 818151 i ii i v C CR1-3_Croc#LI 2437 CTGTGATCTACCAAGA 2422 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 37.17 CpG sites = 11, Kimura (unadjusted) = 39.68 Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0) 234 32.69 11.76 2.31 chr6ptel1M 818205 818323 (181677) MIR3#SINE/MIR 67 196 (12) m_b293s601i12 12100 chr6ptel1M 818205 TCTGCTATTAACT---TATGTGACCTTGGACATGTCATATGATATTAATT 818251 i i --- i i v iv v iv ivv v MIR3#SINE/MIR 67 TCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTG 116 chr6ptel1M 818252 GGCCCCA----------TTAAAAAATAAAAGTTCTGATTTCTAAAATGAT 818291 i ----------i iv i ii vvi ivi --- i MIR3#SINE/MIR 117 GGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACT---AGATGAT 163 chr6ptel1M 818292 -TTTAAATTACTTTCTAGCACTAATGTTCTATG 818323 - i iv v i i v i ii MIR3#SINE/MIR 164 CTCTAAGGTCCCTTCCAGCTCTGACATTCTATG 196 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 45.14 CpG sites = 24, Kimura (unadjusted) = 45.14 Transitions / transversions = 1.71 (24/14) Gap_init rate = 0.05 (6 / 118), avg. gap size = 2.83 (17 / 6) 368 29.26 2.23 10.24 chr6ptel1M 818924 819102 (180898) C MIRb#SINE/MIR (67) 201 36 m_b293s601i13 12101 chr6ptel1M 818924 ATTATCTCTAGTACTTTATATTTTAAAAACCAATGCTGTGAAGCAGGTAG 818973 -----v - ii v v - iv i i i - C MIRb#SINE/MIR 201 ATTATCTC-----ATTTA-ATCCTCACAAC-AACCCTGCGAGGTAGGTA- 160 chr6ptel1M 818974 TGACCAAATTATTATCCCGATTCTATAAAAGAAAAATCTGAGCCTGAGAG 819023 -------- v i i i v ii v v v C MIRb#SINE/MIR 159 --------TTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAG 118 chr6ptel1M 819024 AGAAAAGGTGATTTACCCAACATAAAAAATTTAGCAAA-GGGAAAGCTAA 819072 ivv i i i i vi v v v vi i i- v i i-i C MIRb#SINE/MIR 117 AGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCC-G 69 chr6ptel1M 819073 GGA--CAATCTCAGGTTT-TCTGAATTCAATGC 819102 -- i v i i - v i v C MIRb#SINE/MIR 68 GGATTCGAACCCAGGTCTGTCTGACTCCAAAGC 36 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 34.52 CpG sites = 27, Kimura (unadjusted) = 37.60 Transitions / transversions = 1.35 (27/20) Gap_init rate = 0.11 (20 / 178), avg. gap size = 1.05 (21 / 20) 405 29.36 4.11 2.01 chr6ptel1M 818954 819099 (180901) C MIRc#SINE/MIR (84) 184 36 m_b293s601i14 12101 chr6ptel1M 818954 CAATGCTGTGAAGCAGGTAGTGACCAA--ATTATTATCCCGATTCTATAA 819001 iv i i i v -- i-- v i i i C MIRc#SINE/MIR 184 CAACCCTGTGAGGTAGGCAGGG--CAGGTATTATTATCCCCATTTTACAG 137 chr6ptel1M 819002 AAGAAAAATCTGAGCCTGAGAGAGAAAAGGTGATTTACCCAACATAAAAA 819051 v ii v v v ivv i i i vi v v v C MIRc#SINE/MIR 136 ATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACAC 87 chr6ptel1M 819052 ATTTAGCAAA-GGGAAAGCTAAGGA--CAATCTCAGGT-TTTCTGAATTC 819097 vi i i- v i i-i -- i v i - i v i C MIRc#SINE/MIR 86 AGCTAGTAAGTGGCAGAGCC-GGGACTCGAACCCAGGTCTTCCTGACTCC 38 chr6ptel1M 819098 AA 819099 C MIRc#SINE/MIR 37 AA 36 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 35.95 CpG sites = 25, Kimura (unadjusted) = 38.39 Transitions / transversions = 1.47 (25/17) Gap_init rate = 0.05 (7 / 145), avg. gap size = 1.29 (9 / 7) 237 34.98 2.34 3.97 chr6ptel1M 819202 819329 (180671) MIR1_Amn#SINE/MIR 34 159 (71) m_b293s601i15 12102 chr6ptel1M 819202 TGTACTGACAACTAAGGTGATCTTTGTCAAGATCCTACCTGAACTGTTAG 819251 v i-i vi v i vv iv?i? iiv vvi iii ? MIR1_Amn#SINE 34 TGGACTGG-GACTCGGGAGACCTGGGTTCNANTCCCGGCTCTGCCACTNG 82 chr6ptel1M 819252 CT---TATGTGATGTTGGACAGATTATTTTCCCTACTTAGGTTTTATTTT 819298 i--- i? iv i ii i i ?v vii i? ii i v MIR1_Amn#SINE 83 CCNGCTGNGTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTT 132 chr6ptel1M 819299 CCTGGTCTATAAAATAAGGGCATTAAATGAT 819329 vi i -- v -- MIR1_Amn#SINE 133 CCTCATCTGTAAAAT--GGGGAT--AATGAT 159 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 50.11 CpG sites = 28, Kimura (unadjusted) = 54.08 Transitions / transversions = 1.87 (28/15) Gap_init rate = 0.05 (6 / 127), avg. gap size = 1.33 (8 / 6) 375 31.82 4.55 0.00 chr6ptel1M 819254 819363 (180637) MIR3#SINE/MIR 83 197 (11) m_b293s601i16 12102 chr6ptel1M 819254 TATGTGATGTTGGACAGATTATTTTCCCTACTTAGGTTTTATTTTCCTGG 819303 i iv i ii i i iv vii i ii i v vi MIR3#SINE/MIR 83 TGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCA 132 chr6ptel1M 819304 TCTATAAAATAAGG-----GCATTAAATGATCTCTAAGGATATTTCCAGT 819348 i i ----- v i i vivi i MIR3#SINE/MIR 133 TCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGC 182 chr6ptel1M 819349 TCTGTGATTTAGTGA 819363 vv ivi MIR3#SINE/MIR 183 TCTGACATTCTATGA 197 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 44.01 CpG sites = 24, Kimura (unadjusted) = 44.01 Transitions / transversions = 2.18 (24/11) Gap_init rate = 0.01 (1 / 109), avg. gap size = 5.00 (5 / 1) 230 23.18 19.47 0.75 chr6ptel1M 819651 819763 (180237) C MIR3#SINE/MIR (3) 205 72 m_b293s601i17 12103 chr6ptel1M 819651 TCATAGCAACACAGA--TTTAGAGCTGGAATGAACCTGAGAGATAATCTG 819698 v v i --v i v i v v i C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTA 156 chr6ptel1M 819699 GT--AAC---------------ATGAGGAAAC--AGGCTTGGAGA-ATGT 819728 -- --------------- -- iii -i - C MIR3#SINE/MIR 155 GTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTG- 107 chr6ptel1M 819729 AAGGGATTTCATCAAGTTCAATGAGACACTTAATG 819763 v i vvi v vvv v? v i C MIR3#SINE/MIR 106 AAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTG 72 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 28.15 CpG sites = 11, Kimura (unadjusted) = 28.15 Transitions / transversions = 0.73 (11/15) Gap_init rate = 0.05 (6 / 112), avg. gap size = 3.83 (23 / 6) 233 28.51 14.00 1.79 chr6ptel1M 820035 820134 (179866) L2d2_3end#LINE/L2 440 551 (4) m_b293s601i18 12104 chr6ptel1M 820035 TGTATACTCTTTGAGGGCCAGGATCGT-TCTGCTATAC------ATATCT 820077 vi i vi i i - -- ------i i L2d2_3end#LIN 440 TGTAAGCTCCTTGAGGGCAGGGACCATGTCT--TATACTTCTTTGTATCC 487 chr6ptel1M 820078 C---TAGCA-TTAGCATAGTCCATTGTATATGACAGATACT---TAAATT 820120 ---i i-i i v v i i iiii iii --- v L2d2_3end#LIN 488 CCCACAGCGCCTAGCACAGTGCCTTGCACACAGTAGGCGCTCAATAAATA 537 chr6ptel1M 820121 ATTATTGATTAGAT 820134 v i v L2d2_3end#LIN 538 TTTGTTGATTTGAT 551 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 34.78 CpG sites = 21, Kimura (unadjusted) = 38.51 Transitions / transversions = 3.00 (21/7) Gap_init rate = 0.07 (7 / 99), avg. gap size = 2.29 (16 / 7) 227 34.21 0.00 0.00 chr6ptel1M 820135 820210 (179790) MIRc#SINE/MIR 126 201 (67) m_b293s601i19 12105 chr6ptel1M 820135 AATTCCCATATATGTAAAAATCAGATAATAATACTTGCATCAGTTACCTC 820184 i i vi v vvvi i viiivi MIRc#SINE/MIR 126 AGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTC 175 chr6ptel1M 820185 ACTCAGATGGTATGAGGACTATATAA 820210 vvi v v i ii v i MIRc#SINE/MIR 176 ACAGGGTTGTTGTGAGGATCAAATGA 201 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 46.85 CpG sites = 14, Kimura (unadjusted) = 46.85 Transitions / transversions = 1.17 (14/12) Gap_init rate = 0.00 (0 / 75), avg. gap size = 0.0 (0 / 0) 295 28.97 10.16 2.92 chr6ptel1M 820571 820698 (179302) L2d_3end#LINE/L2 374 510 (6) m_b293s601i20 12106 chr6ptel1M 820571 TTAGTATTAACTTCCCTCATTACATCAAAAGCTTCTTAGAGGCAATGG-- 820618 v iv i -v i v iiv i iii iv i-- L2d_3end#LINE 374 TTAGTCTTGTCTCCCC-AACTAGATTGTAAGCTCCTTGAGGGCAGGGACC 422 chr6ptel1M 820619 ATGTTATTACACTTCTTTAATAAATTT------GTGCTGATCACAATGT- 820661 i- i ?i ?vii-- i------ i iv v i i- L2d_3end#LINE 423 ATGTC-TTATACTNTTTTNTCG--TTCCCCACAGCGCCTAGCACAGTGCT 469 chr6ptel1M 820662 ----ACATAGCACGTGCTTAATAAATACTTATTAATTGATT 820698 ---- i v i i i i L2d_3end#LINE 470 GAGCACATAGTAGGCGCTCAATAAATACTTGTTGATTGATT 510 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 35.50 CpG sites = 26, Kimura (unadjusted) = 39.96 Transitions / transversions = 2.60 (26/10) Gap_init rate = 0.06 (8 / 127), avg. gap size = 2.12 (17 / 8) 14 21.33 1.82 5.66 chr6ptel1M 821224 821278 (178722) (ATTTTAA)n#Simple_repeat 1 53 (0) m_b293s252i2 12107 chr6ptel1M 821224 ATTTTAAATCTTCTACCTATT-ATTTTTAATTTTTTAAATTTTAATAAAT 821272 - - vv v - v -v vvvv (ATTTTAA)n#Si 1 ATTTTAAAT-TT-TAAATTTTAAATTTTAA-ATTTTAAATTTTAAATTTT 47 chr6ptel1M 821273 AAATTT 821278 (ATTTTAA)n#Si 48 AAATTT 53 Matrix = Unknown Transitions / transversions = 0.00 (0/9) Gap_init rate = 0.07 (4 / 54), avg. gap size = 1.00 (4 / 4) 244 26.00 0.00 0.00 chr6ptel1M 821790 821839 (178161) MIRb#SINE/MIR 64 113 (155) m_b293s601i21 12108 chr6ptel1M 821790 AATTCCGACTCTGACACATGCTGAAAGTATGACTCTGGGCAAGTTATTTA 821839 i i v v i iivv i ii i MIRb#SINE/MIR 64 AATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTA 113 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 33.35 CpG sites = 9, Kimura (unadjusted) = 33.35 Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 289 31.01 13.01 0.61 chr6ptel1M 822316 822461 (177539) MIR1_Amn#SINE/MIR 1 164 (66) m_b293s601i22 12109 chr6ptel1M 822316 TATGAGAGCAGGGTACTCCAA-----AGAACACGGAATTTTAGAGTCAGT 822360 v iii v iv i i----- i v i i v-i v i v MIR1_Amn#SINE 1 TAGGGAGGCAGTGTGGTCTAGTGGATAGAGCACTGGACTG-GGACTCGGG 49 chr6ptel1M 822361 -GATTTGGACTCAAATCCTGGTTTTAG-ATTTCTTAGCTGTGTGACCTTG 822408 - ii ii ? ? i i i iv- i ?vii? ? MIR1_Amn#SINE 50 AGACCTGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTG 99 chr6ptel1M 822409 GAATAATCACT-----TCTCTCAATCTTAG-----TCAGTTGTAAAATGT 822448 ivv i ----- v?ii i ----- vi v MIR1_Amn#SINE 100 GGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGG 149 chr6ptel1M 822449 GGGTGCTG--ACTGA 822461 i iv -- MIR1_Amn#SINE 150 GGATAATGATACTGA 164 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 42.12 CpG sites = 30, Kimura (unadjusted) = 44.86 Transitions / transversions = 2.00 (30/15) Gap_init rate = 0.05 (7 / 145), avg. gap size = 2.86 (20 / 7) 441 27.12 9.04 2.26 chr6ptel1M 822335 822500 (177500) MIR3#SINE/MIR 21 197 (11) m_b293s601i23 12109 chr6ptel1M 822335 AAAGAACACGGAATTTTAGAGTCAGT-GATTTGGACTCAAATCCTGGTTT 822383 i i --i vi v- ii ii v i i i i MIR3#SINE/MIR 21 AGAGAGCACGGA--CTGGGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTC 68 chr6ptel1M 822384 TAG-ATTTCTTAGCTGTGTGACCTTGG---AATAA--TCACTTCTCTCAA 822427 iv- i vvi ? --- i v -- i vii MIR3#SINE/MIR 69 TGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGG 118 chr6ptel1M 822428 TCTTAG-----TCAGTTGTAAAATGTGGGTGCT-GACTGAAGACGATCT- 822470 i i ----- vi v v i - -- i - MIR3#SINE/MIR 119 CCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACT--AGATGATCTC 166 chr6ptel1M 822471 TAAGAACATTTACAGCTTTAA-ATCCTAGGA 822500 iv vi v i i - i v MIR3#SINE/MIR 167 TAAGGTCCCTTCCAGCTCTGACATTCTATGA 197 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 34.35 CpG sites = 29, Kimura (unadjusted) = 35.36 Transitions / transversions = 1.93 (29/15) Gap_init rate = 0.07 (12 / 165), avg. gap size = 1.58 (19 / 12) 202 31.42 1.12 3.45 chr6ptel1M 824387 824475 (175525) C L2d2_3end#LINE/L2 (9) 546 460 m_b293s601i24 12110 chr6ptel1M 824387 ATCCAGAAGCACTTATCAAGTGCCTACCTATGTGCTGGGCCATGTGCCTG 824436 v v ii i ii i - i vi vv i-- C L2d2_3end#LIN 546 ATCAACAAATATTTATTGAGCGCCTA-CTGTGTGCAAGGCACTGTGCT-- 500 chr6ptel1M 824437 AGGAGATAAAGAGGAAATAAAGAAAAGCAA-ACATAGTCC 824475 v v ivi i v i ivii - i C L2d2_3end#LIN 499 AGGCGCTGTGGGGGATACAAAGAAGTATAAGACATGGTCC 460 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 40.35 CpG sites = 17, Kimura (unadjusted) = 42.45 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.05 (4 / 88), avg. gap size = 1.00 (4 / 4) 13 5.20 0.00 0.00 chr6ptel1M 825364 825383 (174617) (GAG)n#Simple_repeat 1 20 (0) m_b293s252i3 12111 chr6ptel1M 825364 GAGGAGGAGGAGGAGGATGA 825383 v (GAG)n#Simple 1 GAGGAGGAGGAGGAGGAGGA 20 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 211 30.22 0.00 8.57 chr6ptel1M 825967 826042 (173958) C MIR3#SINE/MIR (18) 190 121 m_b293s601i25 12112 chr6ptel1M 825967 ATGTCAGGATTGTAATGGCTGTTAGTGATTCTCCTCTAAGCCAACTCCTC 826016 iii v v viv v --- v iv i -- C MIR3#SINE/MIR 190 ATGTCAGAGCTGGAAGGGACCTTAGAGAT---CATCTAGTCCAACCCC-- 146 chr6ptel1M 826017 CCTCATTTTATAGGTAAAACAGCTAA 826042 - i i i iiv i i C MIR3#SINE/MIR 145 -CTCATTTTACAGATGAGGAAACTGA 121 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 39.74 CpG sites = 13, Kimura (unadjusted) = 39.74 Transitions / transversions = 1.62 (13/8) Gap_init rate = 0.08 (6 / 75), avg. gap size = 1.00 (6 / 6) 235 35.83 7.41 2.84 chr6ptel1M 826855 826989 (173011) C MIRc#SINE/MIR (125) 143 3 m_b293s601i26 12113 chr6ptel1M 826855 TTTACAGTTTACAGACTTGGAATCTAAAGAGGTTACAAATGACTT-TCCA 826903 v v vii vi iiiiii i -- i -i C MIRc#SINE/MIR 143 TTTACAGATGAGGAAACTGAGGCTCAGAGAGGTT--AAGTGACTTGCCCA 96 chr6ptel1M 826904 CTACTCTACAACTACT--GTGTCAGATGCAGGACTTGAACCTGGTTTTCT 826951 vviiivi i v -- v vv i i ii v i ii C MIRc#SINE/MIR 95 AGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTC 46 chr6ptel1M 826952 CTGGTTT----TGCAGTAAACTCTTTAAA---CACTATGCTGACT 826989 ii i---- v --i vv --- i ii v C MIRc#SINE/MIR 45 CTGACTCCAAGTCCAGT--GCTCTTTCCACTGCACCACACTGCCT 3 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 48.96 CpG sites = 31, Kimura (unadjusted) = 52.25 Transitions / transversions = 1.94 (31/16) Gap_init rate = 0.06 (8 / 134), avg. gap size = 1.75 (14 / 8) 711 31.81 10.51 4.87 chr6ptel1M 827255 827644 (172356) C L3#LINE/CR1 (1923) 2176 1766 m_b293s601i27 12114 chr6ptel1M 827255 ATACATGTTTTCTAAAAATATGAGTTGATTGAAGAGTTCCCTATGCATTC 827304 ii i v v v--- iii i ? i ? vi C L3#LINE/CR1 2176 ATACATGTCCTTTTAAAATCTGAC---ATCAGAGAATNCTCTATGNAGCC 2130 chr6ptel1M 827305 ACATCAATTGTTCAGGTGTCTCCTCTTTTTGCGTCTTCA----------- 827343 i iii vi i ii i ii i i v v i ----------- C L3#LINE/CR1 2129 ACGTTGGTTTCTTAAATGCCCTCCCTCTTTTCTTCCTCATTGGATCATTT 2080 chr6ptel1M 827344 -------------GAATTTCCTTCTTGACAGCTTCT------TCCTGAAC 827374 ------------- v i i v i------ i i C L3#LINE/CR1 2079 GTAATTGTAGTCAGAATTTCATTTTTAAGAGCTTCCCANCCCTCTTGAGC 2030 chr6ptel1M 827375 TGACTTATTCTATGACATTTTAGCCCATGGGAGTCTACTTATCTTTTATT 827424 iiv vi i v -i i i? v i viv i --------i C L3#LINE/CR1 2029 CATCTTTCTTTTTGA-GTCTCNGGCCATGGAATCATACCT--------CT 1989 chr6ptel1M 827425 TTTCTCTGAATCTTTTGAATTTTGCTTTTCC----AAAATCTAGGGCTCA 827470 i v i ---- i i ii vi C L3#LINE/CR1 1988 TTTCTCTGAATTTTTTGAAATCTGCTTTTCCTCGTAAAGTCTGGAACATA 1939 chr6ptel1M 827471 TGTCACACTGGGTCTGGTTTTTCCTTTCTTATCTATCAT--ACCGGGAAA 827518 vi- --- i iii iv i i-- ivvi i C L3#LINE/CR1 1938 TGTGG-ACT---TTTAACTTTTCCTTTCTTGGCTATTACGAACTCTAAGA 1893 chr6ptel1M 827519 TAGTGTAAGCAGTTCTCTTCAAAGTTCCCATTG----TCATTATCCCAGA 827564 iiii i- v iiiii i i i ----i i viv -- C L3#LINE/CR1 1892 TGACATG-GCACTTTCTCCCAAGGTTCCTATCGACTTCCACTTCACCA-- 1846 chr6ptel1M 827565 TACTAGTTCTTCTATGTTGCCAACGATTAGGTTAAAAATAGCAGTTCTCC 827614 - i iv viv vi i iv i i i C L3#LINE/CR1 1845 -ACCAGTTCTTCCTTGTTGGTCAGAATTAAGTCCAGAGTAGCAGTTCCCC 1797 chr6ptel1M 827615 TC-TTGGTTTCTATAAGTTTTGAAAGATGAA 827644 - v i v vv i i C L3#LINE/CR1 1796 TCGTTGCTTCCTCTACCTTCTGAGAGATGAA 1766 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 43.61 CpG sites = 85, Kimura (unadjusted) = 45.23 Transitions / transversions = 2.58 (85/33) Gap_init rate = 0.07 (27 / 389), avg. gap size = 2.26 (61 / 27) 377 33.63 1.77 0.00 chr6ptel1M 828128 828240 (171760) MIRc#SINE/MIR 2 116 (152) m_b293s601i28 12115 chr6ptel1M 828128 GAGTCAGTCTGGCATAATAGGGAAAG-GCTGGGCTTGGAGCCAAGAAAAT 828176 v v iii i i ii i -i i i i i i MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr6ptel1M 828177 CTAAGTTAAAGTGCTGCCCCTGATAGAGACT-GTTATGTGATCCTGGACA 828225 ii vi v i v i vi vvv - i i i i i MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 101 chr6ptel1M 828226 AGTCCTCTAACTTCT 828240 vii i MIRc#SINE/MIR 102 AGTCACTTAACCTCT 116 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 45.04 CpG sites = 28, Kimura (unadjusted) = 48.73 Transitions / transversions = 2.80 (28/10) Gap_init rate = 0.02 (2 / 112), avg. gap size = 1.00 (2 / 2) 641 33.26 10.19 3.90 chr6ptel1M 828769 829494 (170506) C L2#LINE/L2 (162) 2920 2151 m_b293s601i29 12116 chr6ptel1M 828769 AGGTCATGAAGGGCTTTGGAAGTTAACTAGAAAAAATTCTATTTTGTACT 828818 i v i v i ii -- v v ii i i ivi v C L2#LINE/L2 2920 AGATCATGTAGGGCCTTGTAGGCCA--TTGTAAGGACTTTGGCTTTTACT 2873 chr6ptel1M 828819 TAGAA-GAAATGGGA---TATTTCTGGACTTGACTGAGTAGGAGAGAGGA 828864 iv i- i ---i vvv ii --- i ii v iv C L2#LINE/L2 2872 CTGAGTGAGATGGGAAGCCATTGGAGGGTTT---TGAGCAGAGGAGTGAC 2826 chr6ptel1M 828865 ATGTTCAGATATGCTCTTAAGGAAAACCACTCTGACAGAACT-TG--GAG 828911 v v iv i vi v ii ii i i v -- - -- C L2#LINE/L2 2825 ATGATCTGACTTACGTTTTAAAAGGATCACTCTGGCTG--CTGTGTTGAG 2778 chr6ptel1M 828912 GACAGGCTGGAGCAGGGAGCAAT--TTGAGG---GAAGAACAATTGTAAG 828956 i i i ? -- i v-- v i --- i v i ivi C L2#LINE/L2 2777 AATAGACTGNAG--GGGGGCAAGGGTGGAAGCAGGGAGACCAGTTAGGAG 2730 chr6ptel1M 828957 GCTGCTGCAATAATCCAGGCAAGAGACTGTGAAGATCTGAACAAAGATGT 829006 ii i i ivi iv iii i v i i v C L2#LINE/L2 2729 GCTATTGCAGTAATCCAGGCGAGAGATGATGGTGGCTTGGACCAGGGTGG 2680 chr6ptel1M 829007 TGGC--TG--GGTGAGTGTGAGGTG----------AGATGT--------G 829034 -- -- - v i ----------i i -------- C L2#LINE/L2 2679 TGGCAGTGGAGGTG-GTGAGAAGTGGTCGGATTCTGGATATATTTTGAAG 2631 chr6ptel1M 829035 AGAGAAATAGCAAGATTTGTAACTTGATGGGATATACAGGAT-------- 829076 iv iviii i iviv v v i ivi vi -------- C L2#LINE/L2 2630 GTAGAGCCGACAGGATTTGCTGATGGATTGGATGTGGGGTGTGAGAGAAA 2581 chr6ptel1M 829077 --GGTGAGTCAAGAACAATGTCAAGATTATGAATCTGGGAGACTGCAAGG 829124 -- iv i ii ivi i v viii i vi v C L2#LINE/L2 2580 GAGAGGAGTCAAGGATGACTCCAAGGTTTTTGGCCTGAGCAACTGGAAGG 2531 chr6ptel1M 829125 ATAGGAGTTGCT-TTGATGGGAAATAAGGAGGG-TAAGGAAGAGGGTAAG 829172 - i- ? i-v i ii i i- iv -- ivv C L2#LINE/L2 2530 AT-GGAGTTGCCATTNAC-TGAGATGGGGAAGACTGCGG--GAGGAGCAG 2485 chr6ptel1M 829173 GTTT---GGGGAAAAT-ATTAGTTCTGATTT---TTTATCCAGTTTCAAA 829215 --- i - vv v v ---iv i iv v i C L2#LINE/L2 2484 GTTTGAGGGGGAAGATCAGGAGTTCAGTTTTGGACATGTTAAGTTTGAGA 2435 chr6ptel1M 829216 TGTCTCCAGAATATCTAAGT-TAAATGTTCAA-AGGCACTT---TGTAAG 829260 i vivii i i -v i iv i- v --- i v C L2#LINE/L2 2434 TGCCTATTAGACATCCAAGTGGAGATGTCGAGTAGGCAGTTGGATATACG 2385 chr6ptel1M 829261 A--CTAATGCTCAATGGA-AAGTTCAGACTGAATAATGTAGATCCAAGAG 829307 -- iiv i iv - i i i i i -i i i iiii C L2#LINE/L2 2384 AGTCTGGAGTTCAGGGGAGAGGTCCGGGCTGGA-GATATAAATTTGGGAG 2336 chr6ptel1M 829308 TTAAAGGC-TATAGTAATAATAATTGAACTCATG-GA-TGATGATGATGA 829354 i vvi - -- ii v i vi - - -- - C L2#LINE/L2 2335 TCATCAGCATATAG--ATGGTATTTAAAGCCATGAGACTG--GATGA-GA 2291 chr6ptel1M 829355 TGATGACGAGAATGATGACGTCAAT-GATGAGTGAGTAAAT-AGAGTATT 829402 v iv?v i i --ii vi - vi v iv ii -vi v i C L2#LINE/L2 2290 TCACCNAGGGAGTGA--GTGTAGATAGAGAAGAGAAGAGGTCCAAGGACT 2243 chr6ptel1M 829403 -AATCCTGGGCAAGAAAACAATC--ACATTTAGAGGGC-ATGAGATGGAT 829448 - ii -------i v -- i ? v -iv - v C L2#LINE/L2 2242 GAGCCCTGGG-------GCACTCCAACGTTNAGAGGTCGGGGAGAT-GAG 2201 chr6ptel1M 829449 AAGGAATCAGAAAAAGAGGTGGAAAAGGAACT----ATTAGGTAGGAAGA 829494 i i v i iiv i i v----i v i C L2#LINE/L2 2200 GAGGAACCAGCAAAGGAGACTGAGAAGGAGCGGCCAGTGAGGTAGGAGGA 2151 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 45.51 CpG sites = 151, Kimura (unadjusted) = 46.98 Transitions / transversions = 1.86 (151/81) Gap_init rate = 0.08 (61 / 725), avg. gap size = 1.70 (104 / 61) 696 28.81 7.17 0.40 chr6ptel1M 829727 829963 (170037) C MIRc#SINE/MIR (0) 268 16 m_b293s601i30 12117 chr6ptel1M 829727 AACAATAACAAATAGCTAGCTTTTACATAGCACTT-AAGGTTTGAAAAGA 829775 i i -i?v vi v ii - vi iv v C MIRc#SINE/MIR 268 AATAATAATAA-CNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGC 220 chr6ptel1M 829776 ATTTT-AGAAACATT---TTATTTGAT----ATAATAACTCTTTGAGATA 829817 ii - v v --- i ---- i i i v i C MIRc#SINE/MIR 219 GCTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTA 170 chr6ptel1M 829818 GCTAC------TGTTATTATCTCTACTTTGCACACAAGTATA-TGAGGCA 829860 vi v------ i i i i i v ii v v - v C MIRc#SINE/MIR 169 GGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCT 120 chr6ptel1M 829861 CACAG-TTTTAAGTGACCTGGCTAGAGTCACACAAGTACCAAATATTTGA 829909 v -vv i v i ii iv vi i iviv C MIRc#SINE/MIR 119 CAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGA 70 chr6ptel1M 829910 GGCAGGATTTGAACTCAGGTTTTTATAACTCCAAATCCACTGCTCTATTC 829959 v i i i i i iv i i v v i C MIRc#SINE/MIR 69 GCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCC 20 chr6ptel1M 829960 ACTG 829963 C MIRc#SINE/MIR 19 ACTG 16 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 35.59 CpG sites = 41, Kimura (unadjusted) = 37.69 Transitions / transversions = 1.52 (41/27) Gap_init rate = 0.03 (8 / 236), avg. gap size = 2.25 (18 / 8) 369 29.90 2.06 0.00 chr6ptel1M 830330 830426 (169574) C UCON58#DNA (25) 460 362 m_b293s502i3 12118 chr6ptel1M 830330 TACAAAAATACACCTATTTGCACCTGGACCAGCCCACTTGCAAATTAACA 830379 i i ivvi i vv i i ii ii C UCON58#DNA 460 TGCAGAAACCGGCCCATTTGCAAATGGGCCGGCCCATCTGCAAATTGGCA 411 chr6ptel1M 830380 GGCAGAGGCTTTTCAGGTGTAAAGAAA--TTTGACTTAGGCCATAAAAA 830426 i i v vii i i i --i i i v v C UCON58#DNA 410 GACGGAGCCTGCCCAAGTGCAGAGAAAAGCTTGATTCAGGGCTTAAAAA 362 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 37.04 CpG sites = 21, Kimura (unadjusted) = 40.73 Transitions / transversions = 2.62 (21/8) Gap_init rate = 0.01 (1 / 96), avg. gap size = 2.00 (2 / 1) 14 15.60 0.00 0.00 chr6ptel1M 830884 830912 (169088) (TATG)n#Simple_repeat 1 29 (0) m_b293s252i4 12119 chr6ptel1M 830884 TATATATGTATGTATATATGTATATTTGT 830912 i i i v (TATG)n#Simpl 1 TATGTATGTATGTATGTATGTATGTATGT 29 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 395 34.48 5.52 0.00 chr6ptel1M 830956 831100 (168900) MIRc#SINE/MIR 15 167 (101) m_b293s601i31 12120 chr6ptel1M 830956 GCAGTCAAAAGAACATTGA-----TAATCAG-AAGATCAGATATTAAGCT 830999 vi i i i-----v i - i v ivv ii ii MIRc#SINE/MIR 15 GCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTC 64 chr6ptel1M 831000 CTAG-TCTTCTATGCCTTAGGCATGAGACCATGGCTGATTCATTCCAACT 831048 ii - v i ivivi vii v v vii v i iv v MIRc#SINE/MIR 65 CCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCT 114 chr6ptel1M 831049 CTCTGAGCCTCAGTTTCTTTATCTTTAAAACTAGAATGATAA-ATTTGTC 831097 i i v ivi i i - ii i MIRc#SINE/MIR 115 CTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCC 164 chr6ptel1M 831098 TTG 831100 i MIRc#SINE/MIR 165 CTG 167 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 46.03 CpG sites = 33, Kimura (unadjusted) = 49.16 Transitions / transversions = 1.94 (33/17) Gap_init rate = 0.03 (4 / 144), avg. gap size = 2.00 (8 / 4) 13 16.62 5.88 3.85 chr6ptel1M 831299 831349 (168651) (TAAAATTA)n#Simple_repeat 1 52 (0) m_b293s252i5 12121 chr6ptel1M 831299 TATAATTATGAAAACT-CCAAA-TGCAAAATTATAAAATTAATACAA-TA 831345 v - i -iv - ii - v - (TAAAATTA)n#S 1 TAAAATTAT-AAAATTATAAAATTATAAAATTATAAAATT-ATAAAATTA 48 chr6ptel1M 831346 TAAA 831349 (TAAAATTA)n#S 49 TAAA 52 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.10 (5 / 50), avg. gap size = 1.00 (5 / 5) 811 30.95 3.33 0.40 chr6ptel1M 831374 831613 (168387) C MIRb#SINE/MIR (18) 250 4 m_b293s601i32 12122 chr6ptel1M 831374 TATTAACCACCTATTATATCACAGACACTGTGCTAAGTGCTTTACAAAAA 831423 i v i i i i vv i i viv C MIRb#SINE/MIR 250 TATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACATGCA 201 chr6ptel1M 831424 TGATCTAATTTAACCCCTGCAA-AACCATGGGGAGTAAGCACTATTATTC 831472 v v i iii - v v ii i i i i C MIRb#SINE/MIR 200 TTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATTATCC 151 chr6ptel1M 831473 CTGTTTTACAGTTATGGAAACTGAGACAAAGAGAAGTTATGTTACTTG-- 831520 ii v iv i vv i v v -- C MIRb#SINE/MIR 150 CCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCC 101 chr6ptel1M 831521 -AGAGTCATATAGC----AAGTGTCTGAGGTTAGGTTTGGACTTGGGTCT 831565 - ii i i ---- v v vivi i i i iii C MIRb#SINE/MIR 100 CAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCT 51 chr6ptel1M 831566 TTCTGATTGCAGCACCAACACTCTGTCCCCAAGTGCCACCCTATTCTT 831613 v i v ivi viii v v -v ii v iii i C MIRb#SINE/MIR 50 GTCTGACTCCAAAGCCCGTGCTCTTTCCAC-TGCACCACGCTGCCCCT 4 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 38.02 CpG sites = 47, Kimura (unadjusted) = 41.69 Transitions / transversions = 1.74 (47/27) Gap_init rate = 0.02 (5 / 239), avg. gap size = 1.80 (9 / 5) 343 25.31 11.35 7.53 chr6ptel1M 831803 831943 (168057) MIRb#SINE/MIR 4 149 (119) m_b293s601i33 12123 chr6ptel1M 831803 AAGGGCACCTAGATGGCATATGGATAGAGCCCAGGACTAGGAATTAGGAA 831852 i v vv i - -i v v i vi v i i iv MIRb#SINE/MIR 4 AGGGGCAGCGTGGTG-CA-GTGGAAAGAGCACGGGCTTTGGAGTCAGACA 51 chr6ptel1M 831853 GCCTCATCCTTCCAAGTTCAAATCTGGACTCAGATACTTATTAG------ 831896 v -------- iii i iv i v vi i ------ MIRb#SINE/MIR 52 GAC--------CTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGT 93 chr6ptel1M 831897 --------GCAAGTCACTTAACCCTTTTTGA--CTCAGTTTGCTTATCTG 831936 -------- i - i i -- v i MIRb#SINE/MIR 94 GACCTTGGGCAAGTTACTTAACC-TCTCTGAGCCTCAGTTTCCTCATCTG 142 chr6ptel1M 831937 TAAAATG 831943 MIRb#SINE/MIR 143 TAAAATG 149 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 29.48 CpG sites = 20, Kimura (unadjusted) = 31.77 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.10 (14 / 140), avg. gap size = 1.93 (27 / 14) 401 20.45 13.22 7.03 chr6ptel1M 831823 831943 (168057) MIRc#SINE/MIR 19 146 (122) m_b293s601i34 12123 chr6ptel1M 831823 TGGATAGAGCCCAGGACTAGGAATTAGGAAGCCTCATCCTTCCAAGTTCA 831872 v v v v i i v -------- iii i MIRc#SINE/MIR 19 TGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC--------CTGGGTTCG 60 chr6ptel1M 831873 AATCTGGACTCAGATACTTATTAG--------------GCAAGTCACTTA 831908 i iv i v vi i -------------- MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTA 110 chr6ptel1M 831909 ACCCTTTTTGA--CTCAGTTTGCTTATCTGTAAAATG 831943 - i i -- v i MIRc#SINE/MIR 111 ACC-TCTCTGAGCCTCAGTTTCCTCATCTGTAAAATG 146 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 23.24 CpG sites = 14, Kimura (unadjusted) = 24.43 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.09 (11 / 120), avg. gap size = 2.27 (25 / 11) 46 3.85 1.79 1.79 chr6ptel1M 833257 833312 (166688) (TA)n#Simple_repeat 1 56 (0) c_b293s251i0 12124 chr6ptel1M 833257 TATATATATATATATATATATATATATATATATATA-ATGATACATATAC 833305 - - i i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATAT-ATATATATAT 49 chr6ptel1M 833306 ATATATA 833312 (TA)n#Simple_ 50 ATATATA 56 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.04 (2 / 55), avg. gap size = 1.00 (2 / 2) 16 19.90 7.50 3.61 chr6ptel1M 833319 833398 (166602) (GTATATTA)n#Simple_repeat 1 83 (0) m_b293s252i6 12125 chr6ptel1M 833319 GTATATAGGTACA-TAGTAT-TTATTACA-T-GTGTCAT-GTATATT-GT 833362 vi i - - v i - - i vv - - (GTATATTA)n#S 1 GTATATTAGTATATTAGTATATTAGTATATTAGTATATTAGTATATTAGT 50 chr6ptel1M 833363 ATAATTACATATATTATAATAATAATACTATTAGTA 833398 - -i vv v i - (GTATATTA)n#S 51 AT-ATTA-GTATATTAGTATATTAGTA-TATTAGTA 83 Matrix = Unknown Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.11 (9 / 79), avg. gap size = 1.00 (9 / 9) 403 24.03 6.62 8.21 chr6ptel1M 833597 833732 (166268) MIRc#SINE/MIR 15 148 (120) m_b293s601i35 12126 chr6ptel1M 833597 GCAATGTAAATAGAGCACTGGGTTTAAAATCAGAAAAAGTCATCTTTATG 833646 i v -- ii ii i i i vi-------- MIRc#SINE/MIR 15 GCAGTGGAAA--GAGCACTGGACTTGGAGTCAGGAAGACC--------TG 54 chr6ptel1M 833647 CATTCAAGTCCAGTCTCAAAAACTTACTAGCTAT-------TGGACAAAA 833689 vi i v v vivv i ------- i i- MIRc#SINE/MIR 55 GGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAG- 103 chr6ptel1M 833690 TCATTTAACC-CAGTTTGTCTTAGTTTC-TCATCTGTAAAATGGG 833732 i - vv vv i i - MIRc#SINE/MIR 104 TCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 28.40 CpG sites = 18, Kimura (unadjusted) = 29.56 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.10 (14 / 135), avg. gap size = 1.43 (20 / 14) 16 0.00 0.00 0.00 chr6ptel1M 833762 833779 (166221) (T)n#Simple_repeat 1 18 (0) m_b293s252i7 12127 chr6ptel1M 833762 TTTTTTTTTTTTTTTTTT 833779 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTT 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 13 11.63 0.00 6.67 chr6ptel1M 834408 834439 (165561) (ATTTT)n#Simple_repeat 1 30 (0) m_b293s252i8 12128 chr6ptel1M 834408 ATTTTATTATATTTTCAGTAATATTTTATTTT 834439 v - - vv (ATTTT)n#Simp 1 ATTTTATTTTATTTT-A-TTTTATTTTATTTT 30 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.06 (2 / 31), avg. gap size = 1.00 (2 / 2) 510 34.01 5.49 1.77 chr6ptel1M 834880 835316 (164684) C L1ME4a_3end#LINE/L1 (316) 555 103 m_b293s551i1 12129 chr6ptel1M 834880 ATAATATTCCATTACATTCATATATCCTAACTTATTCAGCTATTCCCTAA 834929 ?i vv i i v i i i i ? iv C L1ME4a_3end#L 555 ATAATATTCCATTNTATGGATGTACCATAATTTATTTAACCANTCCCCTA 506 chr6ptel1M 834930 CTGTTGAGCTCCCACTCAATTTTTAGTTCCTTTCCAGTATGAAAAGGGCT 834979 i ii viii vvivi ii i ii iv i v i v iv C L1ME4a_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAATGCT 456 chr6ptel1M 834980 GATACAAATATTTTTGCACATGTGAGTTCTTTTCCC---TCTTTGATGAT 835026 vv ii i ii i --- iv vi? --- i v C L1ME4a_3end#L 455 GCGATGAACATCCTTGTACAT---AAATCTTTGTNCACATCTCTGATTAT 409 chr6ptel1M 835027 CTCTTTGGTATATAGATCCAGTAGTGAGACTGCTAGATTAAACGATATAT 835076 i i i v v vvi i v ii i i i i i v i i? C L1ME4a_3end#L 408 TTCCTTAGGATAAATTCCTAGAAGTGGAATTACTGGGTCAAAGGGTATGN 359 chr6ptel1M 835077 ACAATTGATTAATTCTTTGG--GCAAAGCTCCAAATTGCTCTCCTGAACT 835124 v -- vv v --i v viv i v vv C L1ME4a_3end#L 358 ACATTT--TTAAGGCTTTTGATACATATTGCCAAATTGCCCTCCAGAAAG 311 chr6ptel1M 835125 ATTGGGTCATTTCACAATTCCACCAATAATGCATTAGCAT--CCAT---- 835168 i vii v i v i ii i i v vi -- i ---- C L1ME4a_3end#L 310 GTTGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTGCCCGTTTCN 261 chr6ptel1M 835169 -CATTCCCT--TCAACATT---TATCATTATTTTTTCCTGTAATTTTAGC 835212 - iv --i i --- i i v i iv--- i v C L1ME4a_3end#L 260 CCACACCCTCGCCAACACTGGGTATTATCAATCTTTTA---AATCTTTGC 214 chr6ptel1M 835213 CAGTCTGAGAGATATAAAGTGGT---TTGCTGTTATTTTCTTCAGTATTT 835259 i i v i iv i --- iii i vv iv i C L1ME4a_3end#L 213 CAATTTGATAGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTT 164 chr6ptel1M 835260 TTCTGTCTCCT--TCAAGCTGTTGACATTTTCATGATTTTATTGA--ATT 835305 i i vi v -- v i i vvv i? ivv i-- C L1ME4a_3end#L 163 CTTTGATTACTAGTGAGGTTGAACATNTTTTCATATGTTTATTGGCCATT 114 chr6ptel1M 835306 TGTTTATCTTC 835316 v v C L1ME4a_3end#L 113 TGTATTTCTTC 103 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 47.28 CpG sites = 89, Kimura (unadjusted) = 48.23 Transitions / transversions = 1.56 (89/57) Gap_init rate = 0.04 (18 / 436), avg. gap size = 1.78 (32 / 18) 407 35.38 4.64 6.01 chr6ptel1M 836986 837373 (162627) C L2#LINE/L2 (219) 2863 2481 m_b293s601i36 12130 chr6ptel1M 836986 ATAGGGAACCATTGGAAATGGTTGAGAATAGGAGTCACATGGTTAGACAT 837035 i i i iivvv v v v i iv v C L2#LINE/L2 2863 ATGGGAAGCCATTGGAGGGTTTTGAGCAGAGGAGTGACATGATCTGACTT 2814 chr6ptel1M 837036 GTTTTTTAAGGAAAATCACTTTGGCAGT-------AGGATGGATTGAAGT 837078 iiv i- ii i v i------- i i i ? v C L2#LINE/L2 2813 ACGTTTTAAA-AGGATCACTCTGGCTGCTGTGTTGAGAATAGACTGNAGG 2765 chr6ptel1M 837079 GGAGAGAAATTTAGGGC-TGAACTCCAGTGAGAAAACTGTTGTAATCGTC 837127 i vi iiv viii -v i vv v i ii i i i vi C L2#LINE/L2 2764 GGGGCAAGGGTGGAAGCAGGGAGACCAGTTAGGAGGCTATTGCAGTAATC 2715 chr6ptel1M 837128 TGGATGAGAAGCAATG------TGGATC--TGTGGTAA-AGTGGAGTTGA 837168 ii ii iiii ------ i --v ii- ---- C L2#LINE/L2 2714 CAGGCGAGAGATGATGGTGGCTTGGACCAGGGTGGTGGCAGTGGAG---- 2669 chr6ptel1M 837169 GTGTGTGAGCAGACATAAAGGTCTGAAGTGAGAGTTGTTGTGCAGGTAAA 837218 - v --- --- v vvivi vv i v v i C L2#LINE/L2 2668 GTG-GTGAGAAG---T---GGTCGGATTCTGGATATATTTTGAAGGTAGA 2626 chr6ptel1M 837219 AGTAACAAGATCTGGCAACTGATTGGATGTGTAGGGTGAAGCAAAGTAAG 837268 ivii i i vii iv vi v iiv vi C L2#LINE/L2 2625 GCCGACAGGATTTGCTGATGGATTGGATGTGGGGTGTGAGAGAAAGAGAG 2576 chr6ptel1M 837269 AATTTGAGGATTATAGCAA-GTTTATGGACTTAGAAGACCATAAAGATGG 837317 i v ii v ivv - v v v v - iiv i C L2#LINE/L2 2575 GAGTCAAGGATGACTCCAAGGTTTTTGGCCTGAGCA-ACTGGAAGGATGG 2527 chr6ptel1M 837318 TCTTCTCAAAGAAGCCTTTGACAGAAAAAGGAAACATAGGTAATAGAAGT 837367 vv --------- v ? v i vi i v i-v iiiv i i C L2#LINE/L2 2526 AGTT---------GCCATTNACTGAGATGGGGAAGAC-TGCGGGAGGAGC 2487 chr6ptel1M 837368 GGGTTT 837373 i C L2#LINE/L2 2486 AGGTTT 2481 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 47.87 CpG sites = 76, Kimura (unadjusted) = 50.22 Transitions / transversions = 1.43 (76/53) Gap_init rate = 0.07 (29 / 387), avg. gap size = 1.41 (41 / 29) 317 35.25 5.76 0.00 chr6ptel1M 837397 837535 (162465) C L2#LINE/L2 (596) 2486 2340 m_b293s601i37 12130 chr6ptel1M 837397 AGGATTAAGTAGAAAGAAAATTAGTCCTGTTTTGTGCATATTGAATTTCA 837446 v i vi i vv vv i v vi i i i v C L2#LINE/L2 2486 AGGTTTGAGGGGGAAGATCAGGAGTTCAGTTTTGGACATGTTAAGTTTGA 2437 chr6ptel1M 837447 TGTGCCTCTAAAATTTCTAGTTTGAGATATTCAATAAGTAATT-GACAT- 837494 vi v v i iv i iv v i iv i i i i - i - C L2#LINE/L2 2436 GATGCCTATTAGACATCCAAGTGGAGATGTCGAGTAGGCAGTTGGATATA 2387 chr6ptel1M 837495 ------TGAAGTTCAGAGGAGAGACTGAGGCTTTACATGTAGATCTG 837535 ------ i i iiivi vv v i i i C L2#LINE/L2 2386 CGAGTCTGGAGTTCAGGGGAGAGGTCCGGGCTGGAGATATAAATTTG 2340 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 46.80 CpG sites = 29, Kimura (unadjusted) = 49.66 Transitions / transversions = 1.45 (29/20) Gap_init rate = 0.02 (3 / 138), avg. gap size = 2.67 (8 / 3) 259 27.95 6.40 5.56 chr6ptel1M 837914 838038 (161962) L2a_3end#LINE/L2 387 512 (5) m_b293s601i38 12131 chr6ptel1M 837914 CCTTCCAAGGGAATATAAGCTCTTTGAGGTCAGGGACAGTTTTGT---TT 837960 ii vvi i iv v -- --- L2a_3end#LINE 387 CCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGAC--TTTTGTCTGTT 434 chr6ptel1M 837961 TTA-TCTCT-TTGTAT--CCATGACTTAGCAT-GTATTGCACACATAGAA 838005 i- v -i -- vvi i v i- iiivvi v L2a_3end#LINE 435 TTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACATAGTA 484 chr6ptel1M 838006 TGTGTTTATTTTGTAAATATTTAATTAACTGAA 838038 v i i i ----i -i i v L2a_3end#LINE 485 GGCGCTCA----ATAAATATTT-GTTGAATGAA 512 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 33.34 CpG sites = 20, Kimura (unadjusted) = 36.04 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.10 (12 / 124), avg. gap size = 1.25 (15 / 12) 259 20.21 9.62 9.62 chr6ptel1M 837924 838027 (161973) L2d2_3end#LINE/L2 437 540 (15) m_b293s601i39 12131 chr6ptel1M 837924 GAATATAAGCTCTTTGAGGTCAGGGACAGTTTTGTTTT-TATCTCTTTGT 837972 v i i v ---iv i - ii L2d2_3end#LIN 437 GATTGTAAGCTCCTTGAGGGCAGGGAC---CATGTCTTATACTTCTTTGT 483 chr6ptel1M 837973 ATCCATGAC-----TTAGCA---TGTATTGCACACA-TAGAATGTGTTTA 838013 viv -----i --- iv - --- i i i L2d2_3end#LIN 484 ATCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAGTAG---GCGCTCA 530 chr6ptel1M 838014 TTTTGTAAATATTT 838027 ----i L2d2_3end#LIN 531 ----ATAAATATTT 540 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 22.79 CpG sites = 13, Kimura (unadjusted) = 24.22 Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.14 (14 / 103), avg. gap size = 1.43 (20 / 14) 241 27.42 0.00 1.61 chr6ptel1M 838201 838263 (161737) L2b_3end#LINE/L2 405 466 (0) m_b293s601i40 12132 chr6ptel1M 838201 GTGCTCATTCCAGTGTTCTTGCACACAGTAGTGACTTCATAAGTATTTGT 838250 i ii viv ? i- v vvi ivi i L2b_3end#LINE 405 GCGCCTAGCACAGNGC-CTGGCACACAGTAGGCGCTCAGTAAATATTTGT 453 chr6ptel1M 838251 TGAAAGAATAAAT 838263 v i L2b_3end#LINE 454 TGAATGAATGAAT 466 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 30.71 CpG sites = 10, Kimura (unadjusted) = 35.74 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.02 (1 / 62), avg. gap size = 1.00 (1 / 1) 242 21.16 0.00 1.92 chr6ptel1M 838211 838263 (161737) L2a_3end#LINE/L2 466 517 (0) m_b293s601i41 12132 chr6ptel1M 838211 CAGTGTTCTTGCACACAGTAGTGACTTCATAAGTATTTGTTGAAAGAATA 838260 i- v i vvi iv i v i L2a_3end#LINE 466 CAGTGC-CTGGCACATAGTAGGCGCTCAATAAATATTTGTTGAATGAATG 514 chr6ptel1M 838261 AAT 838263 L2a_3end#LINE 515 AAT 517 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 22.63 CpG sites = 6, Kimura (unadjusted) = 25.13 Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.02 (1 / 52), avg. gap size = 1.00 (1 / 1) 557 24.06 11.28 0.00 chr6ptel1M 838290 838422 (161578) MIRc#SINE/MIR 11 158 (110) m_b293s601i42 12133 chr6ptel1M 838290 TGGTATGGTGGATAGAGTGCAGAACC-AGAGTCAGGAAGAACCAAGTACA 838338 iii v ii v i i-i v iii v i MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr6ptel1M 838339 AATCCAGCCTCTGACACTTACTAACTGTGTGATTCTGGACAAATCATTTA 838388 i v v v i iii i i i MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTA 110 chr6ptel1M 838389 ACCT-------------TTTCC-CTTCTGTAAAATGAAAATAATAGTA 838422 ------------- - v iii i MIRc#SINE/MIR 111 ACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATA 158 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 29.38 CpG sites = 24, Kimura (unadjusted) = 30.53 Transitions / transversions = 3.00 (24/8) Gap_init rate = 0.02 (3 / 132), avg. gap size = 5.00 (15 / 3) 344 25.95 10.08 1.43 chr6ptel1M 838458 838584 (161416) L3#LINE/CR1 3815 3952 (147) m_b293s601i43 12134 chr6ptel1M 838458 TTATTCTTTGTCACTGTTCAGGGAG-AGAAC-AGTAACAA---GTGGAAG 838502 v vi --i i i - - v v --- L3#LINE/CR1 3815 TTATTCTGTGTGGCT--CCAGAGGGCAGAACTAGGACCAATGGGTGGAAG 3862 chr6ptel1M 838503 TTACAAGGATG--GATTTCCACTCAATGTGAGAAAAAATATCCTTATACT 838550 i v -- vi i i i i iv i v i v L3#LINE/CR1 3863 TTACAGGGAGGCAGATTTCGGCTCAATATAAGGAAGAACTTTCTAACAAT 3912 chr6ptel1M 838551 ------TATTCACTAGTGAAATGGGTTGCCTACTTAGGTG 838584 ------ i i vv i i i vv?v i L3#LINE/CR1 3913 CAGAGCTGTCCAAAAATGGAATGGGCTGCCTCGNGAGGTA 3952 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 33.23 CpG sites = 19, Kimura (unadjusted) = 33.23 Transitions / transversions = 1.36 (19/14) Gap_init rate = 0.06 (7 / 126), avg. gap size = 2.14 (15 / 7) 67 3.13 0.00 0.00 chr6ptel1M 838585 838650 (161350) (AT)n#Simple_repeat 1 66 (0) c_b293s251i1 12135 chr6ptel1M 838585 ATATATATATATATATATATGTATATATATACATATATATATATATATAT 838634 i i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr6ptel1M 838635 ATATATATATATATAT 838650 (AT)n#Simple_ 51 ATATATATATATATAT 66 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0) 575 22.12 7.36 2.94 chr6ptel1M 838762 838924 (161076) MIRc#SINE/MIR 69 238 (30) m_b293s601i44 12136 chr6ptel1M 838762 CTCTGACACTTAATAGCTG------GTTAATCATGTCACATAATCTCTTG 838805 v v ------v iiv v v i iv MIRc#SINE/MIR 69 CTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCT 118 chr6ptel1M 838806 TAGCCTCAGTTTCTTTATCTATAAAATGGGAATTATAATCCCTATTGGCA 838855 v i i i i v v ---- v MIRc#SINE/MIR 119 GAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCT----GCC 164 chr6ptel1M 838856 TTGACCAT----CAAGGTAGTTG-GAGGATTAATTAGAGAAAATACATGT 838900 i v i i---- i v - i v - v ii MIRc#SINE/MIR 165 CTGCCTACCTCACAGGGTTGTTGTGAGGATCAAAT-GAGATAATGTATGT 213 chr6ptel1M 838901 -AAAGTGCTTTGTACTCCATAAAGT 838924 - i vv ii MIRc#SINE/MIR 214 GAAAGCGCTTTGTAAACTGTAAAGT 238 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 25.64 CpG sites = 18, Kimura (unadjusted) = 26.49 Transitions / transversions = 1.06 (18/17) Gap_init rate = 0.06 (9 / 162), avg. gap size = 1.89 (17 / 9) 242 27.75 3.41 5.81 chr6ptel1M 839141 839228 (160772) C MIRc#SINE/MIR (61) 207 122 m_b293s601i45 12137 chr6ptel1M 839141 ACTATTTCACTGGATCCTTCCAAACCA--CTTGTGAGGTTGGCAGGACAA 839188 i i i v iv -- -- i v i i C MIRc#SINE/MIR 207 ATTATCTCATTTGATCCTCACAA--CAACCCTGTGAGGTAGGCAGGGCAG 160 chr6ptel1M 839189 G-ATAAGGTTTGCTTCTGTTTTATAGAAGAGAAAATGTAGG 839228 - v --- iiii ii i v i ivv C MIRc#SINE/MIR 159 GTATTA---TTATCCCCATTTTACAGATGAGGAAACTGAGG 122 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 36.35 CpG sites = 16, Kimura (unadjusted) = 36.35 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.08 (7 / 87), avg. gap size = 1.14 (8 / 7) 689 29.68 6.49 0.82 chr6ptel1M 839228 839458 (160542) MIRc#SINE/MIR 10 253 (15) m_b293s601i46 12138 chr6ptel1M 839228 GTGTTACAACTAATAGAACATGGGGCCCAGAGTCAGGAAAACCCGAGTTC 839277 v i iivi v i iv i iii i i i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr6ptel1M 839278 AAATATATATGCAGACACTAGTTAGCTGTGTGATCATTGGCAAGTCATTT 839327 i i vivviiv v v vii i v v i MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTT 109 chr6ptel1M 839328 AATCTCT----GTCTGA-----CCCAT--ATAAAATGGGGGCAATAACAG 839366 i ---- i v ----- i --i ii i - MIRc#SINE/MIR 110 AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATA- 158 chr6ptel1M 839367 CCAGCCC---CTACCTCCCAAGATTATTATGAGAATAAAATGAAATACTG 839413 v --- v i i i i i v i v MIRc#SINE/MIR 159 CCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATG 208 chr6ptel1M 839414 TTAGT-AATGTTCTTTGCAAATCTTCAGGCAGTATATAAATAGTAA 839458 vv - v iv i iiv v i iiv i - MIRc#SINE/MIR 209 TATGTGAAAGCGCTTTGTAAACTGTAAAGTGCTATACAAAT-GTAA 253 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 37.81 CpG sites = 43, Kimura (unadjusted) = 39.31 Transitions / transversions = 1.72 (43/25) Gap_init rate = 0.03 (7 / 230), avg. gap size = 2.43 (17 / 7) 13 28.69 0.00 0.00 chr6ptel1M 840662 840703 (159297) (AAA)n#Simple_repeat 1 42 (0) m_b293s252i9 12139 chr6ptel1M 840662 AAAGAAAAAAAAAAAACAAGCAAGCAAACAGCAACAAAAAAA 840703 i v iv iv v iv v (AAA)n#Simple 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 42 Matrix = Unknown Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 12 15.89 5.71 0.00 chr6ptel1M 840980 841014 (158986) (TACTTA)n#Simple_repeat 1 37 (0) m_b293s252i11 12140 chr6ptel1M 840980 TACATATA-TTATATTTA-ACTTATACTTTAACATAT 841014 v - i - vv v (TACTTA)n#Sim 1 TACTTATACTTATACTTATACTTATACTTATACTTAT 37 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 263 32.76 6.32 5.21 chr6ptel1M 841233 841422 (158578) C L1MD2_3end#LINE/L1 (474) 632 441 m_b293s551i2 12141 chr6ptel1M 841233 CTTTTTGCTTCACTCAGCATCAGTTCCTGTGTCTCCAGACCCCTCTGAAA 841282 --- - i iv ----- i v i- i C L1MD2_3end#LI 632 CTTTTT---TCACTCAGCAT-AATTCCCTTG-----AGATCCATCC-AAG 593 chr6ptel1M 841283 TCATCCTGTG-ATCA-----------TTTTTTACAGAACAATAATATTCT 841320 ii ivi - -----------i iv vvv i i i C L1MD2_3end#LI 592 TTGTTGCGTGTATCAATAGTTCGTTCCTTTTTATTGCTGAGTAGTATTCC 543 chr6ptel1M 841321 ACAACATTCATGTTCCATAATTTATTCAGCCACTCCCCAGCTGATGGGCA 841370 iiii vv v i i i i i i v v i v i C L1MD2_3end#LI 542 ATGGTATGGATGTACCACAGTTTGTTTAACCATTCACCCGTTGAAGGACA 493 chr6ptel1M 841371 TCCATTCAGTTTCCAGTTACTTGCCATTGCAAAAAGGGCTGCCACAAATA 841420 iiivviv vi v i i i v ii i ii i C L1MD2_3end#LI 492 TTTGGGTTGTTTCCAGTTTTTGGCTATTACGAATAAAGCTGCTATGAACA 443 chr6ptel1M 841421 TT 841422 C L1MD2_3end#LI 442 TT 441 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 43.68 CpG sites = 40, Kimura (unadjusted) = 45.85 Transitions / transversions = 2.11 (40/19) Gap_init rate = 0.06 (12 / 189), avg. gap size = 1.83 (22 / 12) 365 30.52 0.64 1.29 chr6ptel1M 841279 841434 (158566) C L1MC4a_3end#LINE/L1 (2049) 580 426 m_b293s551i3 12141 chr6ptel1M 841279 GAAATCATCCTGTGATCATTTTTTACAGAACAATAATATTCTACAACATT 841328 i v v-- iv vvvv i i i iviii v C L1MC4a_3end#L 580 GAGATCTTCCTC--ATTCTTTTTTACAGCTGCATAGTACTCCATTGTGTG 533 chr6ptel1M 841329 CATGTTCCATAATTTATTCAGCCACTCCCCAGCTGATGGGCATCCATTCA 841378 v v i i ? i vii?? ii vviv C L1MC4a_3end#L 532 GATGTACCATAGTTTATTCAACCANTCTCCTATNNATGGGCATTTAGGTT 483 chr6ptel1M 841379 GTTTCCAGTTACTTGCCATTGCAAAAAGGGCTGCCACAAAT-ATTTTTTG 841427 i vvi v i v iv v ii - ii v C L1MC4a_3end#L 482 GTTTCCAATATTTTGCAATTACAAACAATGCTGCAATGAATAACCTTGTG 433 chr6ptel1M 841428 CATATGT 841434 C L1MC4a_3end#L 432 CATATGT 426 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 41.00 CpG sites = 25, Kimura (unadjusted) = 41.00 Transitions / transversions = 1.14 (25/22) Gap_init rate = 0.02 (3 / 155), avg. gap size = 1.00 (3 / 3) 438 28.32 7.77 2.30 chr6ptel1M 841298 841503 (158497) C L1MC5_3end#LINE/L1 (2129) 565 349 m_b293s551i4 12141 chr6ptel1M 841298 TTTTTACAGAACAATAATATTCTACAACATTCATGTTCCATAATTTATTC 841347 vvvv i i i iviii vv v i C L1MC5_3end#LI 565 TTTTTACAGCTGCATAGTACTCCATTGTGTGGATGTACCATAGTTTATTC 516 chr6ptel1M 841348 AGCCACTCCCCAGCTGATGGGCATCCATTCAGTTTCCAGTTACTTGCCAT 841397 i v vii i iiivviv ivi i C L1MC5_3end#LI 515 AACCAGTCCCCTATTGATGGACATTTGGGTTGTTTCCAGTCTTTTGCTAT 466 chr6ptel1M 841398 TGCAAAAAGGGCTGCCACAAATA-TTTTTTGCATATGTGGGTTCTTAACC 841446 i v v v ii -ii v i vvv v --- C L1MC5_3end#LI 465 TACAAATAGTGCTGCAATGAATAGCCTTGTGCATACGTCTTTTCGTA--- 419 chr6ptel1M 841447 CTTTTTTG---GTATTTCTTTGGGA------CCCAGTA--GAGAT--CTC 841483 -- --- i v ------ i v -- i -- v C L1MC5_3end#LI 418 --TTTTTGCCAGTGTATCTTTGGGATAGATTCCTAGAAGTGGGATTGCTG 371 chr6ptel1M 841484 CATCAAAGGAT--ATGCATGTG 841503 vi i -- i C L1MC5_3end#LI 370 GGTCAAAGGGTAAATGCATATG 349 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 35.49 CpG sites = 31, Kimura (unadjusted) = 36.28 Transitions / transversions = 1.19 (31/26) Gap_init rate = 0.05 (11 / 205), avg. gap size = 1.91 (21 / 11) 747 21.43 1.30 0.00 chr6ptel1M 841507 841660 (158340) Charlie4#DNA/hAT-Charlie 3221 3376 (2) m_b293s502i4 12142 chr6ptel1M 841507 TTAAACATTTTAAT--CTGTATTTCAATATAATCAGTTTCCTTTGTAATT 841554 i i -- i ii i Charlie4#DNA/ 3221 TTAAATATTTTGATAACTATATTTCAATATAATTGGTTTCCTTTGTAATC 3270 chr6ptel1M 841555 CTCTGAAATTTAGTTCATGCATTTATAAGCCTTATTCTGAGAAGAGCTCC 841604 v v v v i v i v i v Charlie4#DNA/ 3271 CTATGTATTTTATTTTATGCATTTAAAAACATTATTCTGAGAAGGGGTCC 3320 chr6ptel1M 841605 ACAGGTTTCACCAGACTTCCAGAGTGATCCACAGTGCACAGCAGATCAAG 841654 i i v i v i ii ii v iv i i Charlie4#DNA/ 3321 ATAGGCTTCACCAGACTGCCAAAGGGGTCCATGGCACAAAAAAGGTTAAG 3370 chr6ptel1M 841655 AACTTC 841660 ii Charlie4#DNA/ 3371 AACCCC 3376 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 25.95 CpG sites = 22, Kimura (unadjusted) = 25.95 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.01 (1 / 153), avg. gap size = 2.00 (2 / 1) 520 28.67 2.69 4.37 chr6ptel1M 841746 841931 (158069) C MIRb#SINE/MIR (26) 242 60 m_b293s601i47 12143 chr6ptel1M 841746 GCTTATTATGTGCCAGGATCTGTACTGATCACTTTATCAT-TATTGTCTT 841794 i vv i i v i - -i i i C MIRb#SINE/MIR 242 GCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTA-CATGCATTATCTC 194 chr6ptel1M 841795 CTTTGATCATCATCATATCAGCTCTGGAAAGTGAATGCTGTTATTGTCCC 841844 v i v iv --- i i vi i i--- v i i C MIRb#SINE/MIR 193 ATTTAATCCTCACAA---CAACCCTGCGAGGTA---GGTATTATTATCCC 150 chr6ptel1M 841845 CA-CTCATAATTAAGGAAGTCAAG--TGAAAGAGTTTATATAACTTGGGT 841891 -i i i iv i iiii -- v i v vi - vi C MIRb#SINE/MIR 149 CATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTT-GCC 101 chr6ptel1M 841892 CAGAGTCACACAG-TAGGAAGTATCTGAGACTAGATTTGAA 841931 ii - v iv v v vi i C MIRb#SINE/MIR 100 CAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAA 60 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 34.78 CpG sites = 33, Kimura (unadjusted) = 37.57 Transitions / transversions = 1.83 (33/18) Gap_init rate = 0.06 (12 / 185), avg. gap size = 1.08 (13 / 12) 588 20.16 2.07 4.23 chr6ptel1M 841946 842090 (157910) MIRc#SINE/MIR 5 146 (122) m_b293s601i48 12144 chr6ptel1M 841946 GCTGGGTGACTCAGTGCATACAGTGCTAGACCTGGAGTTAG-AAGAGCTC 841994 v v iiv v v v ii i i i - ---- MIRc#SINE/MIR 5 GCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA---- 50 chr6ptel1M 841995 TTCCCGAGTTCAAATCTGGCCTCAGGCACTTGCTAGCTGTGTGACC-TGG 842043 -- i i i i iv v v v i - MIRc#SINE/MIR 51 --CCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 98 chr6ptel1M 842044 GCAAATCACTTAA-CTCTGTTTGCCTCAGTTACCTCATCTGTAAAATG 842090 i - v vv v MIRc#SINE/MIR 99 GCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATG 146 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 22.69 CpG sites = 14, Kimura (unadjusted) = 23.61 Transitions / transversions = 1.00 (14/14) Gap_init rate = 0.06 (9 / 144), avg. gap size = 1.00 (9 / 9) 436 35.70 2.69 6.64 chr6ptel1M 842292 842588 (157412) 7SLRNA#SINE/Alu 12 297 (23) m_b293s502i5 12145 chr6ptel1M 842292 TGGTGCATGTTTCTGATTCCAACTA-TGAGGAGACTGAACCCGCTGGAGC 842340 i ii ii v ii i i - vi i iv v vv v 7SLRNA#SINE/A 12 TGGCGCGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCGGGAGGATC 61 chr6ptel1M 842341 TCCTGGGCTCCAGAATTCCAAATTACAATGGACTATGCTGCTGGGATGTT 842390 v i i i vi i iiiii ii i vi i v v i i 7SLRNA#SINE/A 62 GCTTGAGCCCAGGAGTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGTC 111 chr6ptel1M 842391 GGTACCTAAATGAAGAATTGATATGGTGAGGTCTCAAGAGATAGTCATGG 842440 v i - i vvi v ii vv i ------------- 7SLRNA#SINE/A 112 CGCAC-TAAGTTCGGCATCAATATGGTGACCTCCC-------------GG 147 chr6ptel1M 842441 TAGCAGTGGTCCCTCCTGTTTGCCCAAGGAGGGACAAATTTGCTTAAGTT 842490 v i v v v- v v i iii iiv ii i i 7SLRNA#SINE/A 148 GAGCGGGGGACCA-CCAGGTTGCCTAAGGAGGGGTGAACCGGCCCAGGTC 196 chr6ptel1M 842491 GGAAA--GAGCATATT--GGCTCTCATGGCAATCTCAGTGGCTTTGGATT 842536 -- vi i--ii i i vii -- i -- v i 7SLRNA#SINE/A 197 GGAAACGGAGCAGGTCAAAACTCCCGTGCTGA--TCAGTAG--TGGGATC 242 chr6ptel1M 842537 CAGGATTTG--TAGCCACTGCATTTTAGCCTGGTCAA-ATTGGGAGACTT 842583 vv vv v -- i ii v - v v ii 7SLRNA#SINE/A 243 GCGCCTGTGAATAGCCACTGCACTCCAGCCTGGGCAACATAGCGAGACCC 292 chr6ptel1M 842584 AATCT 842588 vi 7SLRNA#SINE/A 293 CGTCT 297 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 41.89 CpG sites = 62, Kimura (unadjusted) = 51.01 Transitions / transversions = 1.68 (62/37) Gap_init rate = 0.08 (24 / 296), avg. gap size = 1.12 (27 / 24) 201 31.82 0.00 0.00 chr6ptel1M 842662 842705 (157295) C L2#LINE/L2 (505) 2577 2534 m_b293s601i49 12146 chr6ptel1M 842662 AAGAGTCAGAAATGACCCTGAGATTTTTAATCTGAAAGACTGGA 842705 i iii i ii i iii ivi C L2#LINE/L2 2577 AGGAGTCAAGGATGACTCCAAGGTTTTTGGCCTGAGCAACTGGA 2534 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 48.71 CpG sites = 13, Kimura (unadjusted) = 48.71 Transitions / transversions = 13.00 (13/1) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 217 33.55 5.63 3.45 chr6ptel1M 843134 843275 (156725) C L2#LINE/L2 (2262) 820 676 m_b293s601i50 12146 chr6ptel1M 843134 TTGAAAGGA-CATTAGTGTAAATACTGAATTACCCAATGATGAGGTCAGG 843182 i - ivii ii i v vv vi v v v C L2#LINE/L2 820 TTGGAAGGATCATCTACGTGGATATTGAAATCACCAAGAATTATGACAGG 771 chr6ptel1M 843183 GTTTGAGGTAAAGAG---GA-AGTTTGGAGTCAGATAATAACCTCTTTTT 843228 iv v v v ii --- - --- i iviv vv i-- C L2#LINE/L2 770 AGTAGTGTTGGAGAGAGTGACAGT---GAGCCAGGAGCTAAAATCTTC-- 726 chr6ptel1M 843229 AAACAATG---GGGACTGGTCTAGAAGCTAGTAGATGTCTGCAGTAAGAA 843275 iv --- v ii ii i iii v ii i C L2#LINE/L2 725 AAGGAATGAGGGGGAGTGACCCGGAGGTCGGTAGATGACTGCAACAAGGA 676 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 41.84 CpG sites = 27, Kimura (unadjusted) = 46.18 Transitions / transversions = 1.42 (27/19) Gap_init rate = 0.06 (9 / 141), avg. gap size = 1.44 (13 / 9) 195 25.35 5.63 0.00 chr6ptel1M 843599 843669 (156331) L2#LINE/L2 2887 2961 (121) m_b293s601i51 12147 chr6ptel1M 843599 TCCTTATCTTGGCATTCAAGCCCCTTTGTAATATGGCCCCACATTACCTT 843648 ivv v v v vii i v i v i i L2#LINE/L2 2887 TCCTTACAATGGCCTACAAGGCCCTACATGATCTGGTCCCCCGTTACCTC 2936 chr6ptel1M 843649 TCT---CTTATCTCATACTAC-CTC 843669 --- i v i - L2#LINE/L2 2937 TCTGACCTCATCTCCTACCACTCTC 2961 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 29.23 CpG sites = 9, Kimura (unadjusted) = 31.23 Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.03 (2 / 70), avg. gap size = 2.00 (4 / 2) 24 20.88 2.94 1.45 chr6ptel1M 844005 844072 (155928) (TAA)n#Simple_repeat 1 69 (0) m_b293s252i12 12148 chr6ptel1M 844005 TAATAACAACAATAATAATAAATATCATTAT-TTACT-ATAATAAACAAC 844052 i i vv v v -v v - - i i (TAA)n#Simple 1 TAATAATAATAATAATAATAATAATAATAATAATAATAATAAT-AATAAT 49 chr6ptel1M 844053 AACAATAATAATAATAACAA 844072 i i (TAA)n#Simple 50 AATAATAATAATAATAATAA 69 Matrix = Unknown Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.04 (3 / 67), avg. gap size = 1.00 (3 / 3) 676 26.58 1.26 0.62 chr6ptel1M 844092 844250 (155750) C MIRc#SINE/MIR (89) 179 20 m_b293s601i52 12149 chr6ptel1M 844092 CTGTGAGATAATTAGTGTGAATATTTTTTATTCCCATATTACAAAGGAGG 844141 i ivi v iiii - v i v i v C MIRc#SINE/MIR 179 CTGTGAGGTAGGCAGGGCAGGTA-TTATTATCCCCATTTTACAGATGAGG 131 chr6ptel1M 844142 AAACTGAGGCAT-GAAAGATGAAGTAACTTGTCCAAAGTCACATAGCTAT 844190 vi- i i v i i i i v C MIRc#SINE/MIR 130 AAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG 81 chr6ptel1M 844191 TAAGTCAAAGATGCGTGACTTGAATTCAAATCCT-TTGACTCAAAGTCCA 844239 viv vv v i ii ii i -i v C MIRc#SINE/MIR 80 TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCA 31 chr6ptel1M 844240 TTGCATTCTCC 844250 v vi i C MIRc#SINE/MIR 30 GTGCTCTTTCC 20 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 32.81 CpG sites = 26, Kimura (unadjusted) = 33.80 Transitions / transversions = 1.62 (26/16) Gap_init rate = 0.02 (3 / 158), avg. gap size = 1.00 (3 / 3) 394 33.31 6.35 3.08 chr6ptel1M 844308 844496 (155504) MIRb#SINE/MIR 4 198 (70) m_b293s601i53 12150 chr6ptel1M 844308 AGAGGTACCTGGATCAAGTGGACAGTGTGTTGGTCTCAAAGATAATCAGA 844357 i i v vv i vv v v iiiv ii iii vi iv MIRb#SINE/MIR 4 AGGGGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGA 53 chr6ptel1M 844358 CTTGACTTCAAATCCCAAC----------ACTAGTTGTGTGGCCATGAGC 844397 i iv i ii ---------- i i v i MIRb#SINE/MIR 54 CCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGC 103 chr6ptel1M 844398 AAAAGACTCCACCTCTATGAACCTCTGTTTTCTCATTTGGCAGGAATGAG 844447 ivv iv v i v i i vv -- i MIRb#SINE/MIR 104 AAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAA--AATGGG 151 chr6ptel1M 844448 AGCTATCATGGCTTAAGTGGGTAGAGTAATGTTGTCA-GATTAAA-GAAA 844495 iiiv v iv -- vivv i i -- v - - i MIRb#SINE/MIR 152 GATAATAATACCT--ACCTCGCAGGGT--TGTTGTGAGGATTAAATGAGA 197 chr6ptel1M 844496 T 844496 MIRb#SINE/MIR 198 T 198 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 42.53 CpG sites = 35, Kimura (unadjusted) = 45.54 Transitions / transversions = 1.35 (35/26) Gap_init rate = 0.05 (9 / 188), avg. gap size = 2.00 (18 / 9) 523 27.77 4.88 1.18 chr6ptel1M 844494 844657 (155343) MIRc#SINE/MIR 61 230 (38) m_b293s601i54 12151 chr6ptel1M 844494 AATCCTGACCCTGGAACTTACTAGCCATATATGATCATGGGCAAATAAAT 844543 i i i i vv -- i i i v i v v MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTACTAGC--TGTGTGACCTTGGGCAAGTCACT 108 chr6ptel1M 844544 CCATCCCTCTGATCCCCAAATTACTCATTTGTAAAATGGGTATAATCATA 844593 iv i i v i iv v i v v MIRc#SINE/MIR 109 TAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATA 158 chr6ptel1M 844594 GCT-CCCT-----TCTC-CAGAATTGTTGGGATATTCAAATGACAGCACA 844636 v - -----i - ii v viv v vv ii MIRc#SINE/MIR 159 CCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATG 208 chr6ptel1M 844637 TTTGT-AAAATATTTGATAAAC 844657 v - iiii vi MIRc#SINE/MIR 209 TATGTGAAAGCGCTTTGTAAAC 230 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 33.36 CpG sites = 25, Kimura (unadjusted) = 35.38 Transitions / transversions = 1.25 (25/20) Gap_init rate = 0.04 (6 / 163), avg. gap size = 1.67 (10 / 6) 430 25.94 9.24 3.61 chr6ptel1M 845190 845373 (154627) MIRb#SINE/MIR 23 216 (52) m_b293s601i55 12152 chr6ptel1M 845190 GGCAAGAAGATGGGCCT--GAATCTGTAAAGAGAAAACCTTGATTTCTAT 845237 v iv i i -- i ----- v i - v i ivv MIRb#SINE/MIR 23 GGAAAGAGCACGGGCTTTGGAGTC-----AGACAGA-CCTGGGTTCGAAT 66 chr6ptel1M 845238 TCCCACTCCAAACTCTTCTTAACTATGTGAGCT-GGGCAAGT--CTTA-- 845282 i vi iiv- v vi i i v - -- -- MIRb#SINE/MIR 67 CCCGGCTCTGC-CACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAAC 115 chr6ptel1M 845283 --CTCTCGGCCTCATTTTCCTTATGTGTAAAATATTGATCATAATG-GTA 845329 -- vi v i v ivv v i-v MIRb#SINE/MIR 116 CTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTA 165 chr6ptel1M 845330 -TTTGCAAG---GTTGTGATTATCAAATGAAATTA---ATGTCAAGTGCT 845372 -i i i --- vv i i v --- v i MIRb#SINE/MIR 166 CCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCGCT 215 chr6ptel1M 845373 T 845373 MIRb#SINE/MIR 216 T 216 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 29.05 CpG sites = 24, Kimura (unadjusted) = 32.31 Transitions / transversions = 1.09 (24/22) Gap_init rate = 0.09 (16 / 183), avg. gap size = 1.50 (24 / 16) 404 26.65 14.95 1.36 chr6ptel1M 845205 845398 (154602) MIRc#SINE/MIR 30 249 (19) m_b293s601i56 12152 chr6ptel1M 845205 CTGAATCTGTAAAGAGAAAACCTTGATTTCTATTCCCACTCCAAACTCTT 845254 i ii v ivv i iv i iv v v ivii viv v MIRc#SINE/MIR 30 CTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTT 79 chr6ptel1M 845255 CTTAACTATGTGAGCT-GGGCAAGTC--TTA----CTCTCGGCCTCATTT 845297 vi i i v - -- ---- vi v MIRc#SINE/MIR 80 ACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTT 129 chr6ptel1M 845298 TCCTTATGTGTAAAATATTGATCATAATG--------GTAT---TTGCAA 845336 i v ivv v i-------- iv --- ii i MIRc#SINE/MIR 130 TCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAG 179 chr6ptel1M 845337 G---GTTGTGATTATCAAATGAAATTAATGT-----CAAGTGCTTTGATA 845378 --- vv i - -----v i - MIRc#SINE/MIR 180 GGTTGTTGTGAGGATCAAATGAGA-TAATGTATGTGAAAGCGCTTTG-TA 227 chr6ptel1M 845379 A--TGTGAAAGT-TTACATAAAT 845398 -- - -i i i MIRc#SINE/MIR 228 AACTGT-AAAGTGCTATACAAAT 249 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 32.00 CpG sites = 28, Kimura (unadjusted) = 33.58 Transitions / transversions = 1.22 (28/23) Gap_init rate = 0.06 (12 / 193), avg. gap size = 2.67 (32 / 12) 377 28.87 6.67 3.78 chr6ptel1M 845885 846064 (153936) C MIR3#SINE/MIR (6) 202 18 m_b293s601i57 12153 chr6ptel1M 845885 TAGGATCATTAGTAT---AGAGGCAGAAGGGACCTCGCAGGCCACCTTGG 845931 i - v --- vii iiv ii i v v C MIR3#SINE/MIR 202 TAGAATCAT-AGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGT 154 chr6ptel1M 845932 CCAACTTGCTCTTCATTTTATAGATGATAGGATAT-----CCTAG-GAGG 845975 --- i i i -- v i----- i - C MIR3#SINE/MIR 153 CCAAC---CCCCTCATTTTACAGATGA--GGAAACTGAGGCCCAGAGAGG 109 chr6ptel1M 845976 TTCAGTGACTTGGCCAACATGACCCAGGTAATGAACATCAAAGTAAGGGT 846025 vv v vi v v v? i v iiiv i ivi ii C MIR3#SINE/MIR 108 TGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGAC 59 chr6ptel1M 846026 TTGAATCCAGA--GACTGACTTAAAAGTCATTGTTCT-TCTG 846064 v i i--vv i-vv vv i - C MIR3#SINE/MIR 58 TAGAACCCAGGTCTCCTGACTC-CCAGTCCGTGCTCTCTCTG 18 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 36.52 CpG sites = 27, Kimura (unadjusted) = 37.46 Transitions / transversions = 1.17 (27/23) Gap_init rate = 0.07 (12 / 179), avg. gap size = 1.58 (19 / 12) 279 39.33 3.33 0.00 chr6ptel1M 846591 846740 (153260) L2a_3end#LINE/L2 362 516 (1) m_b293s601i58 12154 chr6ptel1M 846591 TTATCTGTGTGTTCGTACTCAATCTGCTCATCCTAGACGATAAATCTCAT 846640 i i v ii vv vi v i viv vvi iiii L2a_3end#LINE 362 TTATTTATTTGTTTATTGTCTGTCTCCCCCCACTAGAATGTAAGCTCCAT 411 chr6ptel1M 846641 GAGAATACACATTCTTATCTTACCTTTTTATTCCTCCAT-----GCACCT 846685 iii viv i i i vvii v i i v vi ----- i L2a_3end#LINE 412 GAGGGCAGGGACTTTTGTCTGTTTTGTTCACTGCTGTATCCCCAGCGCCT 461 chr6ptel1M 846686 AATACAGTGCTCTGCTCACAGTAGGTGCAAAATGAGTGTAAGTTGACAAA 846735 iv iiv v i i vv i i i vv vvi L2a_3end#LINE 462 AGAACAGTGCCTGGCACATAGTAGGCGCTCAATAAATATTTGTTGAATGA 511 chr6ptel1M 846736 ATGAA 846740 L2a_3end#LINE 512 ATGAA 516 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 55.45 CpG sites = 34, Kimura (unadjusted) = 58.52 Transitions / transversions = 1.36 (34/25) Gap_init rate = 0.01 (1 / 149), avg. gap size = 5.00 (5 / 1) 304 33.32 4.51 2.96 chr6ptel1M 846599 846731 (153269) L2d2_3end#LINE/L2 411 545 (10) m_b293s601i59 12154 chr6ptel1M 846599 GTGTTCGTACTCAATCTGCTCATCCTAGACGATAAATCTCATGAGAATAC 846648 ii iiiivi v i -v ivi iiii v iii v L2d2_3end#LIN 411 GTGTTTATGTCTTGTCTCCCCA-ACTAGATTGTAAGCTCCTTGAGGGCAG 459 chr6ptel1M 846649 A---CAT-TCTTATCTTACCTTTTTAT-TCCTCCAT-GCACCTAATACAG 846692 i--- - --- i i i - i i- i ii L2d2_3end#LIN 460 GGACCATGTCTTAT---ACTTCTTTGTATCCCCCACAGCGCCTAGCACAG 506 chr6ptel1M 846693 TGCTCTGCTCACAGTAGGTGCAAAATGAGTGTAAGTTGA 846731 ii v i vv i i i vv L2d2_3end#LIN 507 TGCCTTGCACACAGTAGGCGCTCAATAAATATTTGTTGA 545 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 44.99 CpG sites = 32, Kimura (unadjusted) = 48.22 Transitions / transversions = 2.91 (32/11) Gap_init rate = 0.06 (8 / 132), avg. gap size = 1.25 (10 / 8) 22 22.47 1.37 4.23 chr6ptel1M 847611 847683 (152317) (TTTTC)n#Simple_repeat 1 71 (0) m_b293s252i13 12155 chr6ptel1M 847611 TTTTCTTTTCTTTT-TTTTCTCTCATTTTCTTTTGATCTTATTTTATAGT 847659 - i iv -v i v v -- (TTTTC)n#Simp 1 TTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTT-CTTTTCTTTTCT--T 47 chr6ptel1M 847660 TTTTGTTCCTTTTTTTGTTTTTCT 847683 i v i i vi (TTTTC)n#Simp 48 TTCTTTTCTTTTCTTTTCTTTTCT 71 Matrix = Unknown Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.06 (4 / 72), avg. gap size = 1.00 (4 / 4) 284 22.22 8.33 0.00 chr6ptel1M 848108 848179 (151821) MIR#SINE/MIR 74 151 (111) m_b293s601i60 12156 chr6ptel1M 848108 TTCTTAGCTGTATGACCTGAAACAAGTC-CTT---CTTT-TGTGTCTTAA 848152 vi i viii i- --- i - i i i MIR#SINE/MIR 74 TTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAG 123 chr6ptel1M 848153 TTTTCTCATCTGC-AAATAGGCATAATA 848179 i i- i v MIR#SINE/MIR 124 TTTCCTCATCTGTAAAATGGGGATAATA 151 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 27.95 CpG sites = 13, Kimura (unadjusted) = 27.95 Transitions / transversions = 4.33 (13/3) Gap_init rate = 0.06 (4 / 71), avg. gap size = 1.50 (6 / 4) 270 20.53 7.69 6.33 chr6ptel1M 848114 848191 (151809) MIR1_Amn#SINE/MIR 86 164 (66) m_b293s601i61 12156 chr6ptel1M 848114 GCTGTATGACCTGAAACAAGTC-CTTC----TTTTGTGTCTTAATTTTCT 848158 ?i viii - ?----i i ? i i i i MIR1_Amn#SINE 86 GCTGNGTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCT 135 chr6ptel1M 848159 CATCTGC-AAATAGGCATAATAGCACGATATTGA 848191 i- i v ----- i MIR1_Amn#SINE 136 CATCTGTAAAATGGGGATAAT-----GATACTGA 164 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 27.01 CpG sites = 13, Kimura (unadjusted) = 27.01 Transitions / transversions = 6.50 (13/2) Gap_init rate = 0.10 (8 / 77), avg. gap size = 1.38 (11 / 8) 304 30.54 0.00 2.11 chr6ptel1M 849694 849790 (150210) C L2c_3end#LINE/L2 (35) 443 349 m_b293s601i62 12157 chr6ptel1M 849694 CTATTAATCAAGCAATGGATATTCAAGCATGAAAAATGAAACCATCCCTG 849743 vvii i iv iv v iv v - v vi C L2c_3end#LINE 443 CTATGTGCCAGGCGCTGGGGATACAAAGATGAATAA-GACACGGTCCCTG 395 chr6ptel1M 849744 TCCTCAAGGAACTTACAATCCAGTAGTGTGGATATGATATATATACA 849790 i i i i i i v vi i - i ?i v C L2c_3end#LINE 394 CCCTCAAGGAGCTCACAGTCTAGTGGAGGAGACA-GACANGTAAACA 349 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 39.13 CpG sites = 17, Kimura (unadjusted) = 40.97 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.02 (2 / 96), avg. gap size = 1.00 (2 / 2) 292 27.20 11.40 3.25 chr6ptel1M 850172 850285 (149715) MIR#SINE/MIR 18 140 (122) m_b293s601i63 12158 chr6ptel1M 850172 TTCAGGGAACAGTCTCTGATGATCATCAG-CCACTT---TTTGAACCTTG 850217 v i v i v -- v -- - ii i --- i i ii MIR#SINE/MIR 18 TTAAGAGCACGGGCTCTG--GAGC--CAGACTGCCTGGGTTCGAATCCCG 63 chr6ptel1M 850218 ACTCTGTT---------TTGTGTGATATTGGGCACATCACTTCACCTTTC 850258 i ii---------i iv vi i v i MIR#SINE/MIR 64 GCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTC 113 chr6ptel1M 850259 TGGGCTTCAGCTTTCTCTTCTATAAAA 850285 v i i i v i MIR#SINE/MIR 114 TGTGCCTCAGTTTCCTCATCTGTAAAA 140 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 31.24 CpG sites = 21, Kimura (unadjusted) = 35.61 Transitions / transversions = 2.33 (21/9) Gap_init rate = 0.06 (7 / 113), avg. gap size = 2.43 (17 / 7) 308 26.58 11.39 0.00 chr6ptel1M 850207 850285 (149715) MIRc#SINE/MIR 57 144 (124) m_b293s601i64 12158 chr6ptel1M 850207 TTTGAACCTTGACTCTGTT---------TTGTGTGATATTGGGCACATCA 850247 i ii ii i ii---------i iv vi MIRc#SINE/MIR 57 TTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCA 106 chr6ptel1M 850248 CTTCACCTTTCTGGGCTTCAGCTTTCTCTTCTATAAAA 850285 v i i i i i v i MIRc#SINE/MIR 107 CTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAA 144 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 31.25 CpG sites = 17, Kimura (unadjusted) = 35.46 Transitions / transversions = 4.25 (17/4) Gap_init rate = 0.01 (1 / 78), avg. gap size = 9.00 (9 / 1) 367 19.72 1.41 0.00 chr6ptel1M 850227 850297 (149703) MIR3#SINE/MIR 83 154 (54) m_b293s601i65 12158 chr6ptel1M 850227 TGTGTGATATTGGGCACATCACTTCACCTTTCTGGGCTTCAGCTTTCTCT 850276 iv vi i i i i v MIR3#SINE/MIR 83 TGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCA 132 chr6ptel1M 850277 TCTATAAAA-GATGATGGTGGA 850297 i - v iv v MIR3#SINE/MIR 133 TCTGTAAAATGAGGGGGTTGGA 154 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 23.17 CpG sites = 8, Kimura (unadjusted) = 23.17 Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.01 (1 / 70), avg. gap size = 1.00 (1 / 1) 22 25.55 0.00 1.75 chr6ptel1M 851361 851418 (148582) (AT)n#Simple_repeat 1 57 (0) m_b294s252i0 12159 chr6ptel1M 851361 ATACATACATATATACACATACACTATATATTTAAATATACATAGAGAGA 851410 i i i i i - v v i v v v (AT)n#Simple_ 1 ATATATATATATATATATATATA-TATATATATATATATATATATATATA 49 chr6ptel1M 851411 CATATATA 851418 i (AT)n#Simple_ 50 TATATATA 57 Matrix = Unknown Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.02 (1 / 57), avg. gap size = 1.00 (1 / 1) 233 31.15 0.00 0.00 chr6ptel1M 851419 851479 (148521) DNM1r#Unknown 2480 2540 (2122) m_b294s502i0 12160 chr6ptel1M 851419 GTGTATGTGTATATATGTGTATGCAGGCACACATACACACATATATGTGT 851468 i i i ii v iiiii iiiiii DNM1r#Unknown 2480 GTATGTGTGTATATATGTGTGTATATGTGTGTATGTGTGTATATATGTGT 2529 chr6ptel1M 851469 ATATGTATGTA 851479 i i DNM1r#Unknown 2530 ATATATACGTA 2540 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.86 CpG sites = 18, Kimura (unadjusted) = 47.47 Transitions / transversions = 18.00 (18/1) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 210 37.00 0.00 0.00 chr6ptel1M 851538 851637 (148363) C L2#LINE/L2 (112) 2970 2871 m_b294s601i3 12157 chr6ptel1M 851538 AGCAAAGGAGAGGGGGAGAGGTTGTCAGGTTGCAGAGACAAACTAGGGCC 851587 i i i i v iv vvi v iiv ii vvvi i C L2#LINE/L2 2970 AGCGAGGGGGAGAGTGGTAGGAGATGAGGTCAGAGAGGTAACGGGGGACC 2921 chr6ptel1M 851588 AGGTTAGGGAGAGCCTTACAGGCCCTGCTAAGCAATCTGTACTTTACTCT 851637 i i v v i ii v vv v v i vvi C L2#LINE/L2 2920 AGATCATGTAGGGCCTTGTAGGCCATTGTAAGGACTTTGGCTTTTACTCT 2871 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 50.20 CpG sites = 19, Kimura (unadjusted) = 52.21 Transitions / transversions = 1.06 (19/18) Gap_init rate = 0.00 (0 / 99), avg. gap size = 0.0 (0 / 0) 459 30.37 6.01 1.04 chr6ptel1M 852268 852450 (147550) MIR3#SINE/MIR 4 195 (13) m_b294s601i4 12161 chr6ptel1M 852268 GTACAGTGGT---GCAGAAAAAACAATGGACTAGAAG--GAGAGATCTGG 852312 i v i--- i i i -i i i --ii i MIR3#SINE/MIR 4 GCAGAGTGGCTGAGCAGAGAGAGCA-CGGACTGGGAGTCAGGAGACCTGG 52 chr6ptel1M 852313 GATGTAATGGTCATTGTGGTGCTAA-TAACTG-GTGAATTTGGGGCACCT 852360 v v i vvivii v vii - ?i - vi - vv MIR3#SINE/MIR 53 GTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGG-CAAGT 101 chr6ptel1M 852361 GAATTCCCTCCTTTGGGTTAGACTTTCCTCCCCTGAAAAATCAGGGTTTT 852410 v v v ii i iivv v vi v v vv MIR3#SINE/MIR 102 CACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTT 151 chr6ptel1M 852411 ----TAATTGAACTCTAAGGTCTCTTTCAGATCTGAGATTCCAT 852450 ---- iv v i i v v i MIR3#SINE/MIR 152 GGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTAT 195 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.11 CpG sites = 29, Kimura (unadjusted) = 39.95 Transitions / transversions = 1.12 (29/26) Gap_init rate = 0.04 (7 / 182), avg. gap size = 1.86 (13 / 7) 14 0.00 4.76 0.00 chr6ptel1M 852902 852922 (147078) (ACAA)n#Simple_repeat 1 22 (0) m_b294s252i1 12162 chr6ptel1M 852902 ACAAACAAACAAACAAA-AAAC 852922 - (ACAA)n#Simpl 1 ACAAACAAACAAACAAACAAAC 22 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.05 (1 / 20), avg. gap size = 1.00 (1 / 1) 613 33.36 0.00 2.94 chr6ptel1M 853008 853217 (146783) C L3#LINE/CR1 (531) 3568 3365 m_b294s601i5 12163 chr6ptel1M 853008 AGAATACAATGGGATCATCAATTTCTTTTTTCTAGATATTATACTTTTCT 853057 i ii ii i vi i i v? i i i i v C L3#LINE/CR1 3568 AGAGTACAGCGGGACTATTACCTCCCTTGNTCTGGACACTATACTTCTAT 3519 chr6ptel1M 853058 TAAAGAAGCCTGAGGTTGCCTAGGTCTGGTTCTGACTGCTATTTTTCACT 853107 v v i i v vi ii -- i i v i iv iv C L3#LINE/CR1 3518 TAATGCAGCCTAAGATTGCATTAGCTT--TTTTGGCAGCCACATCACACT 3471 chr6ptel1M 853108 GATGGCTCACATTGAGTTTACAGTAAGTGAAGATCTCTGAGATTCGTTTT 853157 v i i i i v iiv i i i - i ---i C L3#LINE/CR1 3470 GTTGGCTCATATTGAGCTTGCGGTCAACTAAAACCCCT-AGGT---CTTT 3425 chr6ptel1M 853158 TGCATATGTACTGCTATCCAGCCACATCTGTCATATCTTAAACTTGTGAA 853207 v ii v iiiv v iviivi i iv v C L3#LINE/CR1 3424 TTCACGTGAACTGCTGCTAAGCCAGATCCTCTCCATCCTGTACTTGTGCA 3375 chr6ptel1M 853208 GTTCACTTTT 853217 v i C L3#LINE/CR1 3374 GTTGATTTTT 3365 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 44.28 CpG sites = 46, Kimura (unadjusted) = 47.34 Transitions / transversions = 2.09 (46/22) Gap_init rate = 0.03 (6 / 209), avg. gap size = 1.00 (6 / 6) 418 33.77 7.69 3.00 chr6ptel1M 853134 853484 (146516) C L3b_3end#LINE/CR1 (815) 391 25 m_b294s601i6 12163 chr6ptel1M 853134 GTGAAGATC-TCTGAGATTC-GTTTTTGCAT---ATGTACT-GCTATC-C 853176 vi - i vi i - v --- i i - ii - C L3b_3end#LINE 391 GTCGAGATCGTTTTGGATCCTGATTTTGCATCCAACGTATTAGCCGTCGC 342 chr6ptel1M 853177 AGCCA-CATCTGTCATATCTTAAACTTGTGAAGTTCACTTTTAAAAAGTC 853225 vv - v i i- ?vi i vv i vvi iiiv vvv C L3b_3end#LINE 341 TCCCAGCTTCTGCCAC-TNGCAAATTTGATAAGCTGCTTTCCGTATCTTC 293 chr6ptel1M 853226 ATCTAGGT--TTTATCCAAGTCACATTAAGCCTTATAAATCCAGAGGTAG 853273 i i -- v v i ---- i ii vvv i iv ii ii C L3b_3end#LINE 292 ATCCAAGTCATTGATACAAAT----TCAGACAGGACAAGGCCAAGGACAG 247 chr6ptel1M 853274 ATCCATGAATCTTGGTACTAAAGCTTTTCTAATAAGTTTTCATCGAACCA 853323 v v viv vi vi i vi ii v-i i vv ? C L3b_3end#LINE 246 AGCCCTGCGGCACGCCACTAGAGACTCCCTC-CAGGTTGACATCGANCCA 198 chr6ptel1M 853324 TTAA-CAATTTCTCTATGATTATGGCTATTTAATGTGTTCCAAA-GTCAT 853371 ? - iv - v iv ?i i i i ivv i v?i - -- C L3b_3end#LINE 197 TTNATCAACGTC-CTTTGGGTNCGGTTGTTCAACCAGCTANGAATGTC-- 151 chr6ptel1M 853372 ACAAATATACTGTCTTCTTCCCCATGTCTCTCCA-CTT-----------T 853409 -i v i- ii i? ivv ii i i- ----------- C L3b_3end#LINE 150 -TAACTG-ACCATTNTCCAGCCCACATTTCTCCGTCTTGTCCACGAGGAT 103 chr6ptel1M 853410 AGTACGAGAGACTTTATAACATGCTTTGCTAAA--C-AGATAAACTAGAA 853456 vi i v v i i -- - v viv C L3b_3end#LINE 102 ATCACGAGAGACTTTGTCAAATGCCTTGCTGAAATCAAGATACACTATGT 53 chr6ptel1M 853457 TTATAGAATTTCCCTAACTTGCTACTCT 853484 i i ? i i ii v ? C L3b_3end#LINE 52 CTATGGNATTCCCCTGATCTGCTAGTNT 25 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.10 CpG sites = 68, Kimura (unadjusted) = 48.38 Transitions / transversions = 1.45 (68/47) Gap_init rate = 0.07 (24 / 350), avg. gap size = 1.58 (38 / 24) 436 36.98 9.85 0.33 chr6ptel1M 853223 853496 (146504) C L3#LINE/CR1 (897) 3202 2903 m_b294s601i7 12163 chr6ptel1M 853223 GTCATCTAGGTTTT-ATCCAAGTCAC----------ATTAAGCCTTATAA 853261 i v v i - i----------i i i vvv i i C L3#LINE/CR1 3202 GCCTTCTATGTCTTCATCCAAGTCATTGATAAAAATGTTGAACAGGACAG 3153 chr6ptel1M 853262 ATCCAGAGGTAGATCCATGAATCTTGGTACTAAAGCTTTTCTAATAAGTT 853311 iv ii ii v v viv vi vi i vii i ivvi i C L3#LINE/CR1 3152 GGCCAAGGACAGAGCCCTGTGGCACGCCACTAGAGACCTCCCTCCAGGTT 3103 chr6ptel1M 853312 TTCATCGAACCATTAA-CAATTTCTCTATGATTATGGCTATTTAATGTGT 853360 vv v - ivi i - iv i iii i ivv i C L3#LINE/CR1 3102 GACATCGATCCATTAATCAACACCTTT-TGGGTATAGTCGTTCAACCAGC 3054 chr6ptel1M 853361 TCCAAAGTCATACAAATATACTGTCTTCTTCCCCATGTCTCTCCA-CTT- 853408 v i vi ivi v i i v ivv i i - - C L3#LINE/CR1 3053 TACGAATCCACCTAACTGTACTATCATCCAGCCCATATTTCTCCATCTTG 3004 chr6ptel1M 853409 ----------TAGTACGAGAGACTTTATAACATGCTTTGCTAAA---CAG 853445 ---------- vi i i v v i i --- C L3#LINE/CR1 3003 TCCACAAGGATATCATGAGAGACTTTGTCAAATGCCTTGCTGAAATCCAG 2954 chr6ptel1M 853446 ATAAACTAGAATTATAGAATTTCCCTAACTTGCTACTCTTAGAATTCTTT 853495 v ?vivi ii v i i ii i i v viv ii v C L3#LINE/CR1 2953 ATACACTNTGTCTACGGCATTCCCCTGATCTACCAGTCTAGTAACCCTAT 2904 chr6ptel1M 853496 C 853496 C L3#LINE/CR1 2903 C 2903 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 50.63 CpG sites = 61, Kimura (unadjusted) = 53.97 Transitions / transversions = 1.52 (61/40) Gap_init rate = 0.03 (8 / 273), avg. gap size = 3.50 (28 / 8) 191 25.46 0.00 1.82 chr6ptel1M 853597 853652 (146348) L3#LINE/CR1 3716 3770 (329) m_b294s601i8 12164 chr6ptel1M 853597 GAATTGGGGATGTTCAGCCTGAGGAATAGAATGTTCAGGGGATATTTGAA 853646 i i ii v vii i i v iv - L3#LINE/CR1 3716 GAACTGGGGATGTTTAGCCTGGAGAAGAGAAGACTTAGAGGAGACATG-A 3764 chr6ptel1M 853647 GAGCTG 853652 v L3#LINE/CR1 3765 TAGCTG 3770 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.10 CpG sites = 9, Kimura (unadjusted) = 32.10 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.02 (1 / 55), avg. gap size = 1.00 (1 / 1) 446 25.64 2.56 0.00 chr6ptel1M 854690 854806 (145194) C MIR3#SINE/MIR (23) 185 66 m_b294s601i9 12165 chr6ptel1M 854690 AGAGCTGGAAAAGACCTCAGATATAATTGGGTCTAATCTC-TCATTTTTA 854738 ii i v v ivi i i i - vv C MIR3#SINE/MIR 185 AGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTAC 136 chr6ptel1M 854739 ACATTAGAAAATTGAGCCCCAGAGAGGTCA--TCACTTGGCCAGGGTCAC 854786 v v i i v v -- v v i C MIR3#SINE/MIR 135 AGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCAC 86 chr6ptel1M 854787 CCATGTAGTAAACATCAGAG 854806 v vv? v iiiv C MIR3#SINE/MIR 85 ACAGCNAGTTAGTGGCAGAG 66 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.92 CpG sites = 14, Kimura (unadjusted) = 31.92 Transitions / transversions = 0.88 (14/16) Gap_init rate = 0.02 (2 / 116), avg. gap size = 1.50 (3 / 2) 224 33.73 0.81 5.98 chr6ptel1M 855171 855293 (144707) C L2d2_3end#LINE/L2 (13) 542 426 m_b294s601i10 12166 chr6ptel1M 855171 ACAAACATTGTAT-AAACCCTTTCTGTTTGCAATTCATTGTATGCCAAGT 855219 i - -i i v i v v vv i -- i i i C L2d2_3end#LIN 542 ACAAATATT-TATTGAGCGCCTACTGTGTGCAAGGCACTGT--GCTAGGC 496 chr6ptel1M 855220 TCCAAGGGAGAGAAAAAAGATAAATAAAAGAGAGGGCTTCTGGATTTATG 855269 v iiv i v v i--- i v v v iii vvi i v C L2d2_3end#LIN 495 GCTGTGGGGGATACAAAG---AAGTATAAGACATGGTCCCTGCCCTCAAG 449 chr6ptel1M 855270 TAGCTTACAACCTCAGCAGGAAAG 855293 v i - iv ii C L2d2_3end#LIN 448 GAGCTTACAATCT-AGTTGGGGAG 426 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 44.37 CpG sites = 22, Kimura (unadjusted) = 45.98 Transitions / transversions = 1.29 (22/17) Gap_init rate = 0.07 (8 / 122), avg. gap size = 1.00 (8 / 8) 195 25.29 14.47 1.16 chr6ptel1M 855303 855378 (144622) C L3#LINE/CR1 (3) 4096 4011 m_b294s601i11 12167 chr6ptel1M 855303 AGAATCACAAAACTTGAGAATCGGAAATGACC-------TCACTTAGTCC 855345 i ii v i i iv ------- ii C L3#LINE/CR1 4096 AGAATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCC 4047 chr6ptel1M 855346 AAATCGTACAT-GAAT---GGAATCCTTACTTTAACA 855378 - i viv -v --- i v vi C L3#LINE/CR1 4046 -AACCTCCCATCCAATGCAGGAATCCCTTCTACAACA 4011 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.83 CpG sites = 12, Kimura (unadjusted) = 31.83 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.05 (4 / 75), avg. gap size = 3.00 (12 / 4) 221 32.79 17.48 0.83 chr6ptel1M 855397 855602 (144398) C L2d2_3end#LINE/L2 (255) 300 61 m_b294s601i12 12166 chr6ptel1M 855397 AATGTAATAGAAAGACA-AGAAGAGAAATTGATCTTTTCTGGTTGTAATT 855445 ? iv i ivv - i i i -- vi ? v i v i v C L2d2_3end#LIN 300 ANTGCTATAGGAGTTCAGAGGAGGGAGA--GATCACTNCGGGCTGGAGTG 253 chr6ptel1M 855446 G----GGAAGA-TTCATGAGGGAAATGCTATTAGAGCTGGGTTTTGAAAG 855490 ---- i- i ii ii v? v ii i C L2d2_3end#LIN 252 GTCAGGGAAGGCTTCACGGAGGAGGTGGNATTTGAGCTGGGCCTTGAAGG 203 chr6ptel1M 855491 CTGGGTGGGAT-------GCTGGA---GAATGG------------ATGTG 855518 v i ------- v --- v ------------ v i C L2d2_3end#LIN 202 ATGGGTAGGATTTGGATAGGTGGAGAGGAAGGGGAAGGGCATTCCAGGCG 153 chr6ptel1M 855519 GGTG-------GTGACCACAGGTGAGAAGGCAGAAGTATTCAGGACCCAT 855561 v ------- v v i vii i i i?iiv i i vii C L2d2_3end#LIN 152 GGGGGAACGGCGTGAGCAAAGGCGCAGAGGCGGGAANGCGCAAGGCGTGT 103 chr6ptel1M 855562 TT-GAGGACAGCAAGCAATGTGGTTTGGGTGCAGTGAAGAAT 855602 i- i ii i ivvii v v i i ii C L2d2_3end#LIN 102 TCGGGGGACAGTGAGTAGACCAGTTTGGCTGGAGCGGAGGGT 61 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.40 CpG sites = 44, Kimura (unadjusted) = 47.02 Transitions / transversions = 1.91 (44/23) Gap_init rate = 0.05 (10 / 205), avg. gap size = 3.80 (38 / 10) 214 20.93 27.91 0.00 chr6ptel1M 855933 856018 (143982) MIRc#SINE/MIR 28 137 (131) m_b294s601i13 12168 chr6ptel1M 855933 CACTCCATGTGGAATCAGG--GACCCAGGTTCTAAATTTGGCTCTG---- 855976 vv iv i -- ii v iviii ---- MIRc#SINE/MIR 28 CACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCAC 77 chr6ptel1M 855977 ------------TGACTTTGGGCAACTCGCT-----TCTCTG-GCCTCAT 856008 ------------ i v i ----- - v MIRc#SINE/MIR 78 TTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAG 127 chr6ptel1M 856009 TTGCCTCATC 856018 v MIRc#SINE/MIR 128 TTTCCTCATC 137 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 23.31 CpG sites = 10, Kimura (unadjusted) = 24.84 Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.06 (5 / 85), avg. gap size = 4.80 (24 / 5) 267 23.38 22.30 4.62 chr6ptel1M 855943 856090 (143910) MIR3#SINE/MIR 36 208 (0) m_b294s601i14 12168 chr6ptel1M 855943 GGAATCAGG-GACCCAGGTTCTAAATTTGGCTCTG--------------- 855976 i - ii iviii --------------- MIR3#SINE/MIR 36 GGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGT 85 chr6ptel1M 855977 -TGACTTTGGGCAACTCGCTT---CTCT---GGCCTCATTTGCCTCATC- 856018 - i v i --- --- v v - MIR3#SINE/MIR 86 GTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCT 135 chr6ptel1M 856019 ------CAAGGCTCTTTCTCAGTCTAGAAATTTATATTTGACATTTTCTT 856062 ------ii vvv ----i v --- v v i i -iv ii MIR3#SINE/MIR 136 GTAAAATGAGGGGGTT----GGACTAGA---TGATCTCTAA-GGTCCCTT 177 chr6ptel1M 856063 CTAGATCTAACATTCTATGGTC---TGATTC 856090 i v i i i--- MIR3#SINE/MIR 178 CCAGCTCTGACATTCTATGATTCTATGATTC 208 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.03 CpG sites = 21, Kimura (unadjusted) = 29.07 Transitions / transversions = 1.75 (21/12) Gap_init rate = 0.10 (15 / 147), avg. gap size = 2.73 (41 / 15) 294 31.91 3.19 0.00 chr6ptel1M 856899 856992 (143008) MIR3#SINE/MIR 110 206 (2) m_b294s601i15 12169 chr6ptel1M 856899 CTCTGTGGATCCCATTTTTCTCACCTATAAAACCCAGGGGTTAAACTA-A 856947 v ii i v i i i ivvi ii - MIR3#SINE/MIR 110 CTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGA 159 chr6ptel1M 856948 GAGCCACTAGGATTCCTTCTTGCTCTAAA--TCTCTAACTCTGTGAT 856992 viii v i i i iv i v-- v i i i MIR3#SINE/MIR 160 TGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTATGAT 206 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 44.42 CpG sites = 21, Kimura (unadjusted) = 44.42 Transitions / transversions = 2.33 (21/9) Gap_init rate = 0.02 (2 / 93), avg. gap size = 1.50 (3 / 2) 261 29.49 3.85 0.00 chr6ptel1M 857239 857316 (142684) MIRc#SINE/MIR 100 180 (88) m_b294s601i16 12170 chr6ptel1M 857239 CAAGTCACTGAACCACATGGACACTCAACTTCTCTGCCTATAAAATGGGG 857288 v v viv vv ii iiiii i MIRc#SINE/MIR 100 CAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGG 149 chr6ptel1M 857289 ATAATAAT---TACACTAACAGCCTCATGGG 857316 --- i v iv vi ii MIRc#SINE/MIR 150 ATAATAATACCTGCCCTGCCTACCTCACAGG 180 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.72 CpG sites = 14, Kimura (unadjusted) = 38.72 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.01 (1 / 77), avg. gap size = 3.00 (3 / 1) 208 27.91 0.00 0.00 chr6ptel1M 857546 857588 (142412) C L2c_3end#LINE/L2 (19) 459 417 m_b294s601i17 12171 chr6ptel1M 857546 ATTCATTAGACATTCACAATGTGCCAGAAGCTGGGAATACAAA 857588 i iii iiii v iv i C L2c_3end#LINE 459 ATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGATACAAA 417 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.16 CpG sites = 10, Kimura (unadjusted) = 38.27 Transitions / transversions = 5.00 (10/2) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 186 22.74 0.00 2.27 chr6ptel1M 857703 857747 (142253) MIRc#SINE/MIR 2 45 (223) m_b294s601i18 12172 chr6ptel1M 857703 GAGGCATTGTGGTATATTGGAAAGTGCACATGATTTTGCAATCAG 857747 v ii v v - ivi v i MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCAC-TGGACTTGGAGTCAG 45 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 27.29 CpG sites = 5, Kimura (unadjusted) = 27.29 Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 396 18.17 7.87 1.05 chr6ptel1M 857733 857821 (142179) MIRb#SINE/MIR 93 187 (81) m_b294s601i19 12173 chr6ptel1M 857733 TGATTTTGCAATCAGTCACTT--CCTGTC--AGTCTCAGTTTCTTCATCT 857778 ii -iiiv i -- v -- i i MIRb#SINE/MIR 93 TGACCTTG-GGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCT 141 chr6ptel1M 857779 ATAAAATGGGACTAAT-ATACCTACCTCAAAGGGC--TTGTGAGGA 857821 i iv - iv i-- MIRb#SINE/MIR 142 GTAAAATGGGGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGA 187 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 20.05 CpG sites = 12, Kimura (unadjusted) = 21.53 Transitions / transversions = 3.00 (12/4) Gap_init rate = 0.06 (5 / 88), avg. gap size = 1.60 (8 / 5) 361 33.89 12.12 1.65 chr6ptel1M 859056 859220 (140780) C MIR3#SINE/MIR (6) 202 21 m_b294s601i20 12174 chr6ptel1M 859056 TAGAA-CATAG--TGTTAGAATGAAAATCAATGTTAGAGATCCTCTAATT 859102 - -- i iivii vvi iv v i i C MIR3#SINE/MIR 202 TAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTC 153 chr6ptel1M 859103 TTA-----TCATTGTGCAGAGAAGGGGATTGAGATCCAAA---------T 859138 iv ----- v i vi ii i ii i --------- C MIR3#SINE/MIR 152 CAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGT 103 chr6ptel1M 859139 TCCTTACTCACAGTCATGCAATGAGTTCACGGCAGAACTGAGACTCTAAG 859188 vv i i vi ii ii? vii i i i --- C MIR3#SINE/MIR 102 GACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACT---AG 56 chr6ptel1M 859189 AA---AGGCCATGTGATTCTTATCCTGTGTCCTTT 859220 --- i viv i ii vi i ii i C MIR3#SINE/MIR 55 AACCCAGGTCTCCTGACTCCCAGTCCGTGCTCTCT 21 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 47.09 CpG sites = 40, Kimura (unadjusted) = 49.74 Transitions / transversions = 2.67 (40/15) Gap_init rate = 0.05 (8 / 164), avg. gap size = 2.88 (23 / 8) 264 37.23 8.76 0.00 chr6ptel1M 859107 859243 (140757) C MIRb#SINE/MIR (119) 149 1 m_b294s601i21 12174 chr6ptel1M 859107 CATTGTGCAGAGAAGGGGATTGAGATCCAAA----TTC-----CTTACTC 859147 v i vi ii i iii i ---- v----- i i C MIRb#SINE/MIR 149 CATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCC 100 chr6ptel1M 859148 ACAGTCATGCAATGAGTTCACGGCAGAACTGAGACTCTAAGAAAGG-CCA 859196 vi ii iiv vvii i i i i v vvv - ii C MIRb#SINE/MIR 99 AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTG 50 chr6ptel1M 859197 TGTGATTCT-TATCCTGTGTCCTTTGTAATATACCATGATGTCCC-CTG 859243 v i i-v v i ii vi v ii i v i - C MIRb#SINE/MIR 49 TCTGACTCCAAAGCCCGTGCTCTTTCCACTGCACCACGCTGCCCCTCTG 1 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 50.63 CpG sites = 34, Kimura (unadjusted) = 55.57 Transitions / transversions = 2.00 (34/17) Gap_init rate = 0.04 (5 / 136), avg. gap size = 2.40 (12 / 5) 393 29.82 3.03 5.15 chr6ptel1M 859311 859508 (140492) C MIRb#SINE/MIR (23) 245 52 m_b294s601i22 12175 chr6ptel1M 859311 AGTGCTTGCTGTGGGCCAAGAA-TGGGCTGAAAAATTTGCAAACAAATAG 859359 i i i v i v - v i iviv ---- vii v C MIRb#SINE/MIR 245 AGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTT----ACATGCAT 200 chr6ptel1M 859360 CATCTCATGTGATCCTCACAACTAACACGTGAGGTACGTGCAGC--TCAC 859407 i v i v v vi i v iivii-- v C MIRb#SINE/MIR 199 TATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATTATCCC 150 chr6ptel1M 859408 CATTTTACAATGGAGGAAAGTATGTATTGC-CAGAGCTGG--AAGTTATT 859454 ivv v iv ---- - v- -- v i C MIRb#SINE/MIR 149 CATTTTACAGATGAGGAAACTGAG----GCTCAGAGA-GGTTAAGTAACT 105 chr6ptel1M 859455 TGGCCAGGGTCAGGCAAACTGGGAAGTGTCAGCATCTGGACTGGAACTCA 859504 v i vi - i i v v vii v i v i C MIRb#SINE/MIR 104 TGCCCAAGGTCACAC-AGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCA 56 chr6ptel1M 859505 GTTC 859508 v C MIRb#SINE/MIR 55 GGTC 52 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.91 CpG sites = 28, Kimura (unadjusted) = 38.44 Transitions / transversions = 1.00 (28/28) Gap_init rate = 0.07 (14 / 197), avg. gap size = 1.14 (16 / 14) 372 25.76 14.13 2.94 chr6ptel1M 859352 859535 (140465) C MIRc#SINE/MIR (55) 213 10 m_b294s601i23 12175 chr6ptel1M 859352 ACAAATAGCATCTCATGTGATCCTCACAACTAACACGTGAGGTACGT--- 859398 v i vi v v v vi v i--- C MIRc#SINE/MIR 213 ACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGG 164 chr6ptel1M 859399 GCAGC--------TCACCATTTTACAATGGAGGAAAGTATGTATTGC-CA 859439 v-------- v ivv v iv ---- - C MIRc#SINE/MIR 163 GCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAG----GCTCA 118 chr6ptel1M 859440 GAGCTGG--AAGTTATTTGGCCAGGGTCAGGCAAACTGGGAAGTGTCAGC 859487 v- -- v i v i vi - i i v v v C MIRc#SINE/MIR 117 GAGA-GGTTAAGTGACTTGCCCAAGGTCACAC-AGCTAGTAAGTGGCAGA 70 chr6ptel1M 859488 ATCTGGACTGGAACTCAGTTC------------AGATGAGGACTCTATCC 859525 ii v v i v ------------ viv vi v C MIRc#SINE/MIR 69 GCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCC 20 chr6ptel1M 859526 GTTGTACCAC 859535 ii i C MIRc#SINE/MIR 19 ACTGCACCAC 10 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.76 CpG sites = 19, Kimura (unadjusted) = 31.76 Transitions / transversions = 0.70 (19/27) Gap_init rate = 0.06 (11 / 183), avg. gap size = 2.91 (32 / 11) 357 36.66 3.30 1.08 chr6ptel1M 860497 860678 (139322) C MIR3#SINE/MIR (5) 203 18 m_b294s601i24 12176 chr6ptel1M 860497 ATAAAATTA-GGGAT-TTAGAATTGGGAGGAATC--AAGGGCTATTTGGT 860542 i i -i i - i ii i i i -- ii iii i i C MIR3#SINE/MIR 203 ATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGT 154 chr6ptel1M 860543 CTAACTCACCTCAAGTTACAGATGGAGAAACTGAGGATCGCATTAGAGAA 860592 i i - vv ii vi iv vvi v C MIR3#SINE/MIR 153 CCAACCC-CCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAA 105 chr6ptel1M 860593 CCGACTC-CTCAGGATTATGAAGGTTGTATATGCAAGAGCAAAGGTTTCA 860641 vi i- i i i i iiv v?v vvi vv vii ii vv C MIR3#SINE/MIR 104 GTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGA 55 chr6ptel1M 860642 ACCCAAGTTATCTGATGCCAAATTCAGTG-TCCCTATG 860678 i ivi iv v i i - - i v C MIR3#SINE/MIR 54 ACCCAGGTCTCCTGACTCCCAGTCC-GTGCTCTCTCTG 18 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 53.43 CpG sites = 44, Kimura (unadjusted) = 54.72 Transitions / transversions = 2.00 (44/22) Gap_init rate = 0.04 (7 / 181), avg. gap size = 1.14 (8 / 7) 293 34.72 2.76 0.68 chr6ptel1M 860551 860695 (139305) C MIR1_Amn#SINE/MIR (79) 151 4 m_b294s601i25 12176 chr6ptel1M 860551 CCTCAAGTTACAGATGGAGAAACTGAGGATCGCATTAGAGAACCGACTC- 860599 i vv ii v? iv vvi v? vi i- C MIR1_Amn#SINE 151 CCCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTG 102 chr6ptel1M 860600 CTCAGGATTATGAAGGTTGTATATGCAAGAGCAAAGGTTTCAACCCAAGT 860649 i i i i i?v v?v i?vi vv vii i? ?v i C MIR1_Amn#SINE 101 CCCAAGGTCACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAACCCAGGT 52 chr6ptel1M 860650 TATCTGATGCCAAATTCAGTGTCCCTAT---GTAGGTCACAATTCCTTC 860695 ivi i vv v i i - i ---v ii v v i C MIR1_Amn#SINE 51 CTCCCGAGTCCCAGTCCAGTG-CTCTATCCACTAGACCACACTGCCTCC 4 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 48.60 CpG sites = 27, Kimura (unadjusted) = 51.51 Transitions / transversions = 1.17 (27/23) Gap_init rate = 0.02 (3 / 144), avg. gap size = 1.67 (5 / 3) 13 22.47 2.82 7.35 chr6ptel1M 860700 860770 (139230) (ATAGA)n#Simple_repeat 1 68 (0) m_b294s252i2 12177 chr6ptel1M 860700 ATAAAATGAAAATTAGAATAGAATACTATTATACTAGATATTATCCTGGA 860749 i - i - -v v v v - - vvv i (ATAGA)n#Simp 1 ATAGAAT-AGAA-TAGAATAGAATA-GAATAGAATAGA-A-TAGAATAGA 45 chr6ptel1M 860750 ATAAAATAGAA-AG-TTAGAATA 860770 i - -v (ATAGA)n#Simp 46 ATAGAATAGAATAGAATAGAATA 68 Matrix = Unknown Transitions / transversions = 0.50 (4/8) Gap_init rate = 0.10 (7 / 70), avg. gap size = 1.00 (7 / 7) 12 22.69 6.90 1.64 chr6ptel1M 860909 860966 (139034) (ATTCTAA)n#Simple_repeat 1 61 (0) m_b294s252i3 12178 chr6ptel1M 860909 ATTCTATACTCT--GTTCTACATTCT--CTTCTAAATTGGATATTATGAG 860954 v i --i v --v vv v v i i (ATTCTAA)n#Si 1 ATTCTAAATTCTAAATTCTAAATTCTAAATTCTAAATTCTAAATTCTAAA 50 chr6ptel1M 860955 TTCTAAGATTCT 860966 - (ATTCTAA)n#Si 51 TTCTAA-ATTCT 61 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.05 (3 / 57), avg. gap size = 1.67 (5 / 3) 221 21.79 13.48 2.02 chr6ptel1M 861302 861390 (138610) C L2a_3end#LINE/L2 (37) 480 382 m_b294s601i26 12179 chr6ptel1M 861302 ATGTTCCAGGGACCCTTCTAG---CTATGGCATTC--CATGTCAA--AAA 861344 v v iv --- iv - v -- - v -- C L2a_3end#LINE 480 ATGTGCCAGGCACTGTTCTAGGCGCTGGGG-ATACAGCA-GTGAACAAAA 433 chr6ptel1M 861345 GAAGCAAAATTTTCTGA----ATG-AGCTTACATTCTAATAGGGGAGGAC 861389 v ii v ii v---- - i i ii C L2a_3end#LINE 432 CAGACAAAAGTCCCTGCCCTCATGGAGCTTACATTCTAGTGGGGGGAGAC 383 chr6ptel1M 861390 A 861390 C L2a_3end#LINE 382 A 382 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.07 CpG sites = 10, Kimura (unadjusted) = 26.07 Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.08 (7 / 88), avg. gap size = 2.00 (14 / 7) 385 28.32 11.95 2.30 chr6ptel1M 862062 862220 (137780) L3#LINE/CR1 3857 4030 (69) m_b294s601i27 12180 chr6ptel1M 862062 TAGAAGTTTCAGAGAGTCTGATTTCTGTTCAATCTAAAGGAAAAAATACC 862111 i v i v v v i v - i --- i L3#LINE/CR1 3857 TGGAAGTTACAGGGAGGCAGATTTCGGCTCAATAT-AAGGAAGA---ACT 3902 chr6ptel1M 862112 TTTTAACAATTAGAAGCCTCCTCAAGTGGGA--AACTG------------ 862147 i i iviv vv i i --ii ------------ L3#LINE/CR1 3903 TTCTAACAATCAGAGCTGTCCAAAAATGGAATGGGCTGCCTCGNGAGGTA 3952 chr6ptel1M 862148 ATGATTTCTCAG-CACTGGTGATTTTAAA----AAGTCAGAAGACCACTT 862192 i vi i v - v i v v ---- i iii v L3#LINE/CR1 3953 GTGAGCTCCCCGTCACTGGAGGTGTTCAAGCAGAGGCTGGATGACCACTT 4002 chr6ptel1M 862193 GATAGTGATGTTTCAGAAGGAATTATTG 862220 vi v vi i vi L3#LINE/CR1 4003 GTCAGGGATGTTGTAGAAGGGATTCCTG 4030 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.49 CpG sites = 25, Kimura (unadjusted) = 36.49 Transitions / transversions = 1.32 (25/19) Gap_init rate = 0.05 (8 / 158), avg. gap size = 2.88 (23 / 8) 516 23.47 11.28 0.68 chr6ptel1M 862255 862387 (137613) MIRc#SINE/MIR 2 148 (120) m_b294s601i28 12181 chr6ptel1M 862255 GAGCTAG-ATGGCACAGTGGCTAGAGCGTTAGGTCTAGAGTCAATAAGAC 862303 vi -i ii vv ii i iii i iv MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr6ptel1M 862304 CTGG-------TCTCAGA-----CACTTACTAGCTCTGGGACCCTGGGCA 862341 ------- i i v----- v v i MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 101 chr6ptel1M 862342 AATTATTTAATCCTGTTT--GCCTCAGTTTCTTCATCTATAAGATGAG 862387 i i i - v i -- i i i i MIRc#SINE/MIR 102 AGTCACTTAA-CCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.39 CpG sites = 23, Kimura (unadjusted) = 29.53 Transitions / transversions = 2.88 (23/8) Gap_init rate = 0.04 (5 / 132), avg. gap size = 3.20 (16 / 5) 632 30.42 5.19 0.41 chr6ptel1M 863446 863676 (136324) C MIR#SINE/MIR (10) 252 11 m_b294s601i29 12182 chr6ptel1M 863446 AACATTT-TAAAGTAACTATTATGTGACAGTGATTGTGCTAAGAACTTT- 863493 - vi iivi i v vv i v vi - C MIR#SINE/MIR 252 AACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGCGCTTTA 203 chr6ptel1M 863494 TATA-ATT--TTTATTTGATCCTTAA------TTTGGAAGATAGGTGCTC 863534 i i- --i i i i v------ii ivi i i v C MIR#SINE/MIR 202 CATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGGTAGGTACTA 153 chr6ptel1M 863535 TTACTATTCCCATTTTCCAGTTTAGGTAACTGAGACAGGCAGAGTTTAAG 863584 i i v v v v i viv v C MIR#SINE/MIR 152 TTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAG 103 chr6ptel1M 863585 TAACATTTCCAGAGTCATATAGCAAATAAATGTCTGAAAGTAGATTTGAA 863634 v vi ii i i v i i v v ivvvi i C MIR#SINE/MIR 102 TAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAA 53 chr6ptel1M 863635 -GCAGGTCTTCTGGACTCCAGGCCCAGAAATTTTATCCACTAT 863676 -v ivv - iv v viv i v C MIR#SINE/MIR 52 CCCAGGCAGTCTGG-CTCCAGAGCCCGTGCTCTTAACCACTAT 11 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.52 CpG sites = 37, Kimura (unadjusted) = 39.75 Transitions / transversions = 1.12 (37/33) Gap_init rate = 0.03 (7 / 230), avg. gap size = 1.86 (13 / 7) 204 31.32 12.02 4.06 chr6ptel1M 863785 863967 (136033) C MIR#SINE/MIR (56) 206 10 m_b294s601i30 12183 chr6ptel1M 863785 TTTACATAATAATTAAGGCTTATAATGAGCTTTATAACAATCCCATGAGG 863834 i- - vv v v --- i i i i i C MIR#SINE/MIR 206 TTTACATG-TA-TTAACTCATTTAAT---CCTCACAACAACCCTATGAGG 162 chr6ptel1M 863835 CAGGTACTGTAATACGTCCTA--------------AAACTCATGCATCAT 863870 i i v vvvi i -------------- v v - - C MIR#SINE/MIR 161 TAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCA-CA- 114 chr6ptel1M 863871 AAGACG----GTAGCTTATCCA--GTCACATAGCTGTTAAATATCTCCAG 863914 i v ---- i ii -- i iv i iv vvviv C MIR#SINE/MIR 113 GAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGC 64 chr6ptel1M 863915 TGGGCCTCTGACCCAGATCTTCCTTGCTCCA-AGTGCA-ACCCTCTATCC 863962 i vi vi iivv - v - iv i-i i iv i v C MIR#SINE/MIR 63 CGGGATTCGAACCCAGGCAGT-CTGGCTCCAGAGCCCGTGCTCTTAACCA 15 chr6ptel1M 863963 CTATG 863967 C MIR#SINE/MIR 14 CTATG 10 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.70 CpG sites = 30, Kimura (unadjusted) = 41.66 Transitions / transversions = 1.20 (30/25) Gap_init rate = 0.07 (13 / 182), avg. gap size = 2.31 (30 / 13) 268 29.75 16.99 1.13 chr6ptel1M 863810 863962 (136038) C MIRc#SINE/MIR (72) 196 20 m_b294s601i31 12183 chr6ptel1M 863810 TGAGCTTTATAACAATCCCATGAGG---------CAGGTACTGTAATAC- 863849 v i i i i ii --------- i i v v - C MIRc#SINE/MIR 196 TGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCC 147 chr6ptel1M 863850 -GTCCTA---------AAACTCATGCATCATAAGACG----GTAGCTTAT 863885 -i ii --------- v v - -i v ---- ii ii C MIRc#SINE/MIR 146 CATTTTACAGATGAGGAAACTGAGGC-TCA-GAGAGGTTAAGTGACTTGC 99 chr6ptel1M 863886 CCA--GTCACATAGCTGTTAAATATCTCCAGTGGGCCTCTGACCCAGATC 863933 -- i iv i iv vvvivi v vi i C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTC 49 chr6ptel1M 863934 TTCCTTGCTCCAAGTGCAACCCTCTATCC 863962 vi v iiv v C MIRc#SINE/MIR 48 TTCCTGACTCCAAGTCCAGTGCTCTTTCC 20 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.07 CpG sites = 27, Kimura (unadjusted) = 39.20 Transitions / transversions = 1.50 (27/18) Gap_init rate = 0.05 (8 / 152), avg. gap size = 3.50 (28 / 8) 198 34.78 7.78 4.92 chr6ptel1M 863982 864238 (135762) C L2d_3end#LINE/L2 (146) 370 107 m_b294s601i32 12184 chr6ptel1M 863982 ACATGAAGCAA--AGAACACAAT----GTCA-TATCAAAGTTCCTGCCCC 864024 i -- iv ---- v - vv v vvv ivv C L2d_3end#LINE 370 ACATGAAACAATTAGAGAACAATACAAGACAGTATATAATTAAGTGCTAA 321 chr6ptel1M 864025 ACTGCATGTTGCAAACTGTGAGTTCTCTTAAGAAGCCAAAAGAAAGG-GT 864073 i i v i i i i v v -- i iiv i i - v C L2d_3end#LINE 320 ATTGCGTGGTACAGACTATAAGTGCTAT--AGGAGTTCAGAGAAGGGAGA 273 chr6ptel1M 864074 GTTTAATG------AGAGTG-TCAGGGGACTCTTCCCAAAAGAGGAAATG 864116 v i i ------i - i vv ---ivi ii C L2d_3end#LINE 272 GATCAGTGTGGGCTGGAGTGGTCAGGGAAGGCTTC---GTGGAGGAGGTG 226 chr6ptel1M 864117 GTGCTTGAGCAGGACCTTGGACAGCGCACAGCATTTTAAAAAATTG-GAG 864165 vi v i i viii vii v vi v i vv - C L2d_3end#LINE 225 GGACTTGAGCTGGGCCTTGAAGGATGGGTAGGATTTGGATAGAGAGAGAG 176 chr6ptel1M 864166 GAATTTAAGGAACAGCAACTGAGAGAAAGGGAA----ATAACCAAAGTGG 864211 ---ii vi viiv iviii ----i i v - - C L2d_3end#LINE 175 GAA---GGGGAAGGGCATTCCAGGCGGGGGGAACGGCGTGAGCAAAG-G- 131 chr6ptel1M 864212 TCATAAATGTTGGGAACTGTGTAGAGC 864238 - ii i - vi - i i ii C L2d_3end#LINE 130 -CGCAGA-GGCGGGAA-TGCGCAAGGC 107 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.40 CpG sites = 51, Kimura (unadjusted) = 48.92 Transitions / transversions = 1.50 (51/34) Gap_init rate = 0.08 (21 / 256), avg. gap size = 1.57 (33 / 21) 259 26.60 18.09 0.00 chr6ptel1M 864712 864805 (135195) C MIRc#SINE/MIR (145) 123 13 m_b294s601i33 12185 chr6ptel1M 864712 GGCTTGAAGAAGCTGAATGACTTGCCAAAGATCACACATCT--TAGTCAT 864759 iii i i i i v i v -- iviiv C MIRc#SINE/MIR 123 GGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGG 74 chr6ptel1M 864760 CAGAG--GAGA----AACTTGGGTCTTCC-----CCA--TCT--TGTTCT 864794 -- i ---- iii ----- -- i-- i C MIRc#SINE/MIR 73 CAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCT 24 chr6ptel1M 864795 ATCCATTATAC 864805 v i ii C MIRc#SINE/MIR 23 TTCCACTGCAC 13 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.39 CpG sites = 20, Kimura (unadjusted) = 35.39 Transitions / transversions = 4.00 (20/5) Gap_init rate = 0.06 (6 / 93), avg. gap size = 2.83 (17 / 6) 235 30.39 3.88 0.94 chr6ptel1M 865325 865427 (134573) C CR1-3_Croc#LINE/CR1 (592) 3013 2908 m_b294s551i0 12186 chr6ptel1M 865325 CATAACTCCAACTAGAACATACCCAGCCAGTGGGCA-CCAGTCT-TTCTT 865372 i v iv v v ii vii- ii - C CR1-3_Croc#LI 3013 CATAGCTACGCCTAGATCATCCCCGACCAGTGGCTGTCCAACCTCTTCTT 2964 chr6ptel1M 865373 GAAGATGGTCAGTGAAGGGGAGCTCATGA--TCGTTAGAGGAGCTCATTC 865420 v ivvi v i ii ii -- vi - v iii C CR1-3_Croc#LI 2963 GAACACCTCCAGTGATGGAGAGTCCACAACTTCCCTAG-GCAGTCTATTC 2915 chr6ptel1M 865421 CACTCCC 865427 v C CR1-3_Croc#LI 2914 CACTGCC 2908 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.05 CpG sites = 19, Kimura (unadjusted) = 40.39 Transitions / transversions = 1.58 (19/12) Gap_init rate = 0.04 (4 / 102), avg. gap size = 1.25 (5 / 4) 371 29.36 2.68 10.87 chr6ptel1M 865967 866115 (133885) C MIRc#SINE/MIR (120) 148 11 m_b294s601i34 12187 chr6ptel1M 865967 CTCATTCTACAGATTAGGAGACTGAGGCAAACAGGGAG---AAGTGCCTT 866013 i i v i v-- i --- v C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCT--CAGAGAGGTTAAGTGACTT 101 chr6ptel1M 866014 GTGTGTGGGGTCATACAGCTGGTAAATGTTTGAGGCCAGATTTGAATTCA 866063 ivii--i i i i viv v vi i i ii C MIRc#SINE/MIR 100 GCCCA--AGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCA 53 chr6ptel1M 866064 GAAAAATGACCTTTCTTAACTTCAGACCTTGTAGGACTC-TACTACTGCA 866112 i--------ii i i i iii ---i vi - v i C MIRc#SINE/MIR 52 GG--------TCTTCCTGACTCCAAGTC---CAGTGCTCTTTCCACTGCA 14 chr6ptel1M 866113 CCA 866115 C MIRc#SINE/MIR 13 CCA 11 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.10 CpG sites = 29, Kimura (unadjusted) = 39.45 Transitions / transversions = 2.90 (29/10) Gap_init rate = 0.11 (17 / 148), avg. gap size = 1.12 (19 / 17) 257 28.97 0.00 2.63 chr6ptel1M 866337 866414 (133586) MIR1_Amn#SINE/MIR 83 158 (72) m_b294s601i35 12188 chr6ptel1M 866337 CCCACTGCTCATAGCCTGGAACAAACCACTTCCTCATTGTGGACTTCAGG 866386 ?i ?--i ii v ii ii ?vi vi v ?i i v MIR1_Amn#SINE 83 CCNGCTGN--GTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGT 130 chr6ptel1M 866387 TTCCTCATCTATAAAATGAGAAAACTGA 866414 i i i v v MIR1_Amn#SINE 131 TTCCTCATCTGTAAAATGGGGATAATGA 158 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.47 CpG sites = 15, Kimura (unadjusted) = 41.47 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.03 (2 / 77), avg. gap size = 1.00 (2 / 2) 437 26.72 2.54 1.68 chr6ptel1M 866351 866468 (133532) MIR3#SINE/MIR 90 208 (0) m_b294s601i36 12188 chr6ptel1M 866351 CCTGGAACAAACCACTTCCTCATTGTGGACTTCAGGTTCCTCATCTATAA 866400 v ii ii vi vi v i i v i MIR3#SINE/MIR 90 CCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAA 139 chr6ptel1M 866401 AATGAGAAAACTGAACTAGGTGAACCTTT--GATCCACTTTCAGCTCCAA 866448 iiiii i i - i i -- i - i ii MIR3#SINE/MIR 140 AATGAGGGGGTTGGACTAGATG-ATCTCTAAGGTCC-CTTCCAGCTCTGA 187 chr6ptel1M 866449 CTTTCCATG-TTCTAAGCTTC 866468 v i - v v MIR3#SINE/MIR 188 CATTCTATGATTCTATGATTC 208 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.03 CpG sites = 23, Kimura (unadjusted) = 35.03 Transitions / transversions = 2.88 (23/8) Gap_init rate = 0.03 (4 / 117), avg. gap size = 1.25 (5 / 4) 229 25.37 1.49 0.00 chr6ptel1M 867131 867197 (132803) C DNM1r#Unknown (2119) 2543 2476 m_b294s502i1 12189 chr6ptel1M 867131 ACATATGTA-GTATGTATGTATGTATAATTATATACATATATACACATAT 867179 ? i -i ii ii i i vvi i i i C DNM1r#Unknown 2543 ANATACGTATATATACACATATATACACACATACACACATATACACACAT 2494 chr6ptel1M 867180 ATAAACACACATATATGT 867197 v i i C DNM1r#Unknown 2493 ATATACACACATACACGT 2476 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 29.20 CpG sites = 14, Kimura (unadjusted) = 34.10 Transitions / transversions = 4.67 (14/3) Gap_init rate = 0.02 (1 / 66), avg. gap size = 1.00 (1 / 1) 245 26.41 0.00 2.78 chr6ptel1M 867143 867216 (132784) C DNM1r#Unknown (2116) 2546 2475 m_b294s502i2 12189 chr6ptel1M 867143 TGTATGTATGTATAATTATATACATATATACACATATATAAACACACATA 867192 i ?i i -- i i i v i i i C DNM1r#Unknown 2546 TATANATACGTATA--TATACACATATATACACACATACACACATATACA 2499 chr6ptel1M 867193 TATGTATATATATATATATGTGTG 867216 i ii i i i iii C DNM1r#Unknown 2498 CACATATATACACACATACACGTG 2475 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.50 CpG sites = 18, Kimura (unadjusted) = 37.53 Transitions / transversions = 18.00 (18/1) Gap_init rate = 0.03 (2 / 73), avg. gap size = 1.00 (2 / 2) 249 29.23 0.00 0.00 chr6ptel1M 867190 867254 (132746) DNM1r#Unknown 2482 2546 (2116) m_b294s502i3 12189 chr6ptel1M 867190 ATATATGTATATATATATATATGTGTGTGTCTGTGCATACACATACACAC 867239 i i i i i i v ii i i iiii i DNM1r#Unknown 2482 ATGTGTGTATATATGTGTGTATATGTGTGTATGTGTGTATATATGTGTAT 2531 chr6ptel1M 867240 ACACACATATATATA 867254 i i i ? DNM1r#Unknown 2532 ATATACGTATNTATA 2546 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.72 CpG sites = 18, Kimura (unadjusted) = 43.95 Transitions / transversions = 18.00 (18/1) Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0) 48 4.17 0.00 0.00 chr6ptel1M 867270 867319 (132681) (AT)n#Simple_repeat 1 50 (0) c_b294s251i0 12190 chr6ptel1M 867270 ATATGTATATATATATATATATATATGTATATATATATATATATATATAT 867319 i i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 581 28.36 0.00 0.00 chr6ptel1M 867457 867590 (132410) MIRc#SINE/MIR 22 155 (113) m_b294s601i37 12191 chr6ptel1M 867457 AGAAAGCCCTGACCCCATAATCAGGAAAACTTGAGTTCAAATTCAGCCTC 867506 i i v iv iiiv i i i i i i i v v MIRc#SINE/MIR 22 AAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTC 71 chr6ptel1M 867507 GAATATTTACTAGCTAAGTGACCCCGGGCAAATCAATTAATTGCTTTTTG 867556 vivi i iv ii i v iiv i vv MIRc#SINE/MIR 72 TGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAG 121 chr6ptel1M 867557 CCTCAGTATCCTCATCTGTATAATGGGCATAATA 867590 v v v MIRc#SINE/MIR 122 CCTCAGTTTCCTCATCTGTAAAATGGGGATAATA 155 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.49 CpG sites = 23, Kimura (unadjusted) = 36.71 Transitions / transversions = 1.53 (23/15) Gap_init rate = 0.00 (0 / 133), avg. gap size = 0.0 (0 / 0) 24 27.40 0.00 0.00 chr6ptel1M 867626 867686 (132314) (TT)n#Simple_repeat 1 61 (0) m_b294s252i4 12192 chr6ptel1M 867626 TTTTTTTTCTATTTTTTTTCCTTTTTCCTTTTTAAAAAAGGTTTTTTTTT 867675 i v ii ii vvvvvvvv (TT)n#Simple_ 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr6ptel1M 867676 TTTTTTTTTTT 867686 (TT)n#Simple_ 51 TTTTTTTTTTT 61 Matrix = Unknown Transitions / transversions = 0.56 (5/9) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 815 21.56 9.38 0.96 chr6ptel1M 867765 867956 (132044) C MIRc#SINE/MIR (45) 223 16 m_b294s601i38 12193 chr6ptel1M 867765 AAGTGCTTT-AGAAATGTTATCTTATTTGATTCTCATAACAACCC----- 867808 i - v v ii i i i ----- C MIRc#SINE/MIR 223 AAGCGCTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGA 174 chr6ptel1M 867809 ------CAGAAT--CTATTCTTATCCCCATTTTCCAGATAAGGAAACTGA 867850 ------ iii--v v v i C MIRc#SINE/MIR 173 GGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGA 124 chr6ptel1M 867851 GGC--AGACAGATTTAGTGACTTGCTCAGGGTCACACAGCTAGTGAGTAT 867898 -- v i v i i i iv C MIRc#SINE/MIR 123 GGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGG 74 chr6ptel1M 867899 C--AATTGGTAGATTTGATTTTAGGTCTTTTTTACTCCAGGTTTATTGCT 867946 -- iii -- i i viii ii v i ii v C MIRc#SINE/MIR 73 CAGAGCCGG--GACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCT 26 chr6ptel1M 867947 CTATCCCCTG 867956 v v C MIRc#SINE/MIR 25 CTTTCCACTG 16 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 24.06 CpG sites = 28, Kimura (unadjusted) = 26.24 Transitions / transversions = 2.15 (28/13) Gap_init rate = 0.04 (8 / 191), avg. gap size = 2.50 (20 / 8) 12 26.40 0.00 5.77 chr6ptel1M 867961 868015 (131985) (TAAAAA)n#Simple_repeat 1 52 (0) m_b294s252i5 12194 chr6ptel1M 867961 TAAAAACAAAAATTACCAATAAATTTATTTTAAAGAAAATAAAAGTAACA 868010 i - vv --v vvv vi i v (TAAAAA)n#Sim 1 TAAAAATAAAAA-TAAAAATAAA--AATAAAAATAAAAATAAAAATAAAA 47 chr6ptel1M 868011 ATAAA 868015 (TAAAAA)n#Sim 48 ATAAA 52 Matrix = Unknown Transitions / transversions = 0.38 (3/8) Gap_init rate = 0.06 (3 / 54), avg. gap size = 1.00 (3 / 3) 14 24.98 1.61 5.00 chr6ptel1M 868164 868225 (131775) (ATTTT)n#Simple_repeat 1 60 (0) m_b294s252i6 12195 chr6ptel1M 868164 ATTTTATTGCATTGTA-TTGAATCTATTTGAATCTATGTTGTATTTTTAT 868212 vi v - v v i v v i - - - (ATTTT)n#Simp 1 ATTTTATTTTATTTTATTTTATTTTATTTTATTTTAT-TT-TA-TTTTAT 47 chr6ptel1M 868213 TTTGTTAAATTTT 868225 i vv (ATTTT)n#Simp 48 TTTATTTTATTTT 60 Matrix = Unknown Transitions / transversions = 0.50 (4/8) Gap_init rate = 0.07 (4 / 61), avg. gap size = 1.00 (4 / 4) 445 27.19 1.75 0.00 chr6ptel1M 868796 868909 (131091) MIRc#SINE/MIR 12 127 (141) m_b294s601i39 12196 chr6ptel1M 868796 GGCGCAGTGGATAGAGCACCAGCCCTGAAGTCAGAAGGACCTGAGATCAA 868845 i v ii v i i i i i v i MIRc#SINE/MIR 12 GGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGA 61 chr6ptel1M 868846 AT-CAATATTTAACACTTCCTAGGTGTGTAACCCTAGGCAATTCATTTAA 868894 i - vivv i iv v v i i i v i MIRc#SINE/MIR 62 GTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAA 111 chr6ptel1M 868895 CCCCAGTT-GCCTCAG 868909 i vv v- MIRc#SINE/MIR 112 CCTCTCTGAGCCTCAG 127 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.87 CpG sites = 18, Kimura (unadjusted) = 34.56 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.02 (2 / 113), avg. gap size = 1.00 (2 / 2) 16 12.57 0.00 0.00 chr6ptel1M 868910 868925 (131075) (A)n#Simple_repeat 1 16 (12) m_b294s252i7 12197 chr6ptel1M 868910 AAAAAAAAAAAAAGAA 868925 i (A)n#Simple_r 1 AAAAAAAAAAAAAAAA 16 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 15), avg. gap size = 0.0 (0 / 0) 28 0.00 3.33 0.00 chr6ptel1M 868926 868955 (131045) (AAAG)n#Simple_repeat 1 31 (0) c_b294s251i1 12198 chr6ptel1M 868926 AAAGAAA-AAAGAAAGAAAGAAAGAAAGAAA 868955 - (AAAG)n#Simpl 1 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 16 12.57 0.00 0.00 chr6ptel1M 868956 868966 (131034) (A)n#Simple_repeat 17 27 (1) m_b294s252i7 12199 chr6ptel1M 868956 AAGAAAAGAAA 868966 i i (A)n#Simple_r 17 AAAAAAAAAAA 27 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 10), avg. gap size = 0.0 (0 / 0) 452 31.60 4.04 4.69 chr6ptel1M 869231 869361 (130639) C L1ME3F_3end#LINE/L1 (439) 551 416 m_b294s551i1 12200 chr6ptel1M 869231 TAATATTCCATCAT---AATTCCATACTAGAATTTATTCAGGCATTTTGC 869277 ii --- --- i v i vv i v C L1ME3F_3end#L 551 TAATATTCCATTGTGTGAAT---ATACCACAATTTATTTATCCATTCTCC 505 chr6ptel1M 869278 AATTGATATGTATCCCCTAAATTTCCTGTTCTTTTCCCTGA-GAAAAGAG 869326 vi i ivii iivvvvvi v i v iv v - v v C L1ME3F_3end#L 504 TGTCGATGGACATTTGGGTTGTTTCCAGTTTTTTGCTATTACGAACAGTG 455 chr6ptel1M 869327 CTGATGGAAATATTGTTGTACATATA----GGTCCAATT 869361 v ivi i v i v---- v vv C L1ME3F_3end#L 454 CTGCTATGAACATTCTTGTACATGTCTCCTGGTGCACAT 416 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.07 CpG sites = 55, Kimura (unadjusted) = 42.35 Transitions / transversions = 0.79 (19/24) Gap_init rate = 0.05 (6 / 130), avg. gap size = 1.83 (11 / 6) 38 0.00 0.00 0.00 chr6ptel1M 869362 869394 (130606) (TC)n#Simple_repeat 1 33 (0) c_b294s251i2 12201 chr6ptel1M 869362 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 869394 (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 33 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 452 31.60 4.04 4.69 chr6ptel1M 869395 869584 (130416) C L1ME3F_3end#LINE/L1 (575) 415 233 m_b294s551i1 12200 chr6ptel1M 869395 T---AAACTCTCTTTTGGAATACATGCCTAGTAGTGAGTGGTATTACTAG 869441 --- i v i i -i i i ---- v i i C L1ME3F_3end#L 415 TGCAAGAGTTTCTCTTGG-GTATATACCTAG----GAGTGGAATTGCTGG 371 chr6ptel1M 869442 GTCAAAGGGTGTACATAATTTTATACCACTTAGGGCATAGTTTCAAATTG 869491 iv i i i- v vv --i v iv i vi C L1ME3F_3end#L 370 GTCGTAGGGTATGCG-AATGTTCAAC--TTTACGAGATAATGCCAAATTG 324 chr6ptel1M 869492 CTCTACAGAATGGTTGACTCAGTTCACAACTCCACAAACAATGCATTAAT 869541 i i v i i vvi i i vii v i i i - v C L1ME3F_3end#L 323 TTTTCCAAAGTGGTTGTACCAATTTACACTCCCACCAGCAGTGTA-TAAG 275 chr6ptel1M 869542 A--TCTCATTTTTTCCCCACATCTCCTTCAATATTTGATATTTTC 869584 -- i i vv --- ii i i i i v C L1ME3F_3end#L 274 AGTTCCCGTTGAT---CCACATCCTCTCCAACACTTGGTATTGTC 233 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.07 CpG sites = 55, Kimura (unadjusted) = 42.35 Transitions / transversions = 2.00 (36/18) Gap_init rate = 0.07 (14 / 189), avg. gap size = 1.21 (17 / 14) 481 29.45 1.60 5.56 chr6ptel1M 869405 869591 (130409) C L1ME5_3end#LINE/L1 (539) 402 223 m_b294s551i2 12200 chr6ptel1M 869405 TTTGGAATACATGCCTAGTAGTGAGTGGTATTACTAGGTCAAAGGGTGTA 869454 i i i i ---- i v i i v i i C L1ME5_3end#LI 402 TTTGGGATATATACCCAG----GAGCGGAATTGCTGGGTCATAGGGTATG 357 chr6ptel1M 869455 CATA-ATTTTATACCACTTAGGGCATAGTTTCAAATTGCTCTACAGAATG 869503 i - i v viv v ---- v vi i v C L1ME5_3end#LI 356 CGTATACTTAATTTGACTAAG----TACTGCCAGATTGCTCTCCAGAATG 311 chr6ptel1M 869504 GTTGACTCAGTTCACAACTCCACAAACAATGCATTAATATCTCATTTTTT 869553 i vvi ii vii v i i v ivi ii -- v ? C L1ME5_3end#LI 310 GCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCC--TATNT 263 chr6ptel1M 869554 CCCCACATCTCCTTCAATATTTGATATTTTCC--TTTTCT 869591 ii vi i i ii v --i C L1ME5_3end#LI 262 CCCCACATCCTCGCCAACACTTGGCATTATCCAGCTTTCT 223 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.29 CpG sites = 34, Kimura (unadjusted) = 39.25 Transitions / transversions = 1.89 (34/18) Gap_init rate = 0.06 (12 / 186), avg. gap size = 1.08 (13 / 12) 436 30.55 1.90 4.90 chr6ptel1M 869406 869615 (130385) C L1ME4a_3end#LINE/L1 (467) 404 201 m_b294s551i3 12200 chr6ptel1M 869406 TTGGAATACATGCCTAGTAGTGAGTGGTATTACTAGGTCAAAGGGTGTAC 869455 i i v v ----i v i i i? C L1ME4a_3end#L 404 TTAGGATAAATTCCTAG----AAGTGGAATTACTGGGTCAAAGGGTATGN 359 chr6ptel1M 869456 ATAATTTTATACCACTTAGGGCATAGTTTCAAATTGCTCTACAGAATGGT 869505 i v viv vi iivi v vi i v v C L1ME4a_3end#L 358 ACATTTTTAAGGCTTTTGATACATATTGCCAAATTGCCCTCCAGAAAGGT 309 chr6ptel1M 869506 TGACTCAGTTCACAACTCCACAAACAATGCATTAATAT-CTCATTTTTTC 869554 vvi i i vii v i i i v ivi - i i--- C L1ME4a_3end#L 308 TGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTGCCCG---TTTC 262 chr6ptel1M 869555 CCCACATCTCCTTCAATATTTGATATTTTC---CTTTTCTGTCCAATTAG 869601 ? i ii vi i i v i v --- vvi --- v C L1ME4a_3end#L 261 NCCACACCCTCGCCAACACTGGGTATTATCAATCTTTTAAATC---TTTG 215 chr6ptel1M 869602 CCTATCTGATATGT 869615 v i v C L1ME4a_3end#L 214 CCAATTTGATAGGT 201 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.91 CpG sites = 35, Kimura (unadjusted) = 40.78 Transitions / transversions = 1.35 (35/26) Gap_init rate = 0.06 (12 / 209), avg. gap size = 1.17 (14 / 12) 388 32.51 1.09 7.56 chr6ptel1M 870016 870198 (129802) MIR3#SINE/MIR 11 182 (26) m_b294s601i40 12202 chr6ptel1M 870016 GGATTAGAGGAAAGGGCACAGGGTTGTGATTT--GATATCTGACTGTTGG 870063 v v vi i i - ii v v i-- v i iv vi i MIR3#SINE/MIR 11 GGCTGAGCAGAGAGAGCAC-GGACTGGGAGTCAGGAGACCTGGGTTCTAG 59 chr6ptel1M 870064 TCTTGGCTTAGTTGAATCACATGGCTGTGTGACTTTTAATGAGTCACTTT 870113 ii iv ii- v v - ? i viiii i MIR3#SINE/MIR 60 TCCCGGCTCTGCC-ACTAAC-TNGCTGTGTGACCTTGGGCAAGTCACTTC 107 chr6ptel1M 870114 TCCTCTTTGTTCTTCAGTTTCTACATTTACACAATGAAGGAGATGGAAGT 870163 v i vv i iv i ii v i i v --- MIR3#SINE/MIR 108 ACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGA--- 154 chr6ptel1M 870164 CCACTTGTCTGATGATATCTGGGGTCTCATGTAGC 870198 i ------- v ii i v vi MIR3#SINE/MIR 155 CTA-------GATGATCTCTAAGGTCCCTTCCAGC 182 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.42 CpG sites = 34, Kimura (unadjusted) = 44.54 Transitions / transversions = 1.62 (34/21) Gap_init rate = 0.08 (14 / 182), avg. gap size = 1.07 (15 / 14) 19 19.18 3.57 1.75 chr6ptel1M 870489 870544 (129456) (AATATG)n#Simple_repeat 1 57 (0) m_b294s252i8 12203 chr6ptel1M 870489 AATAT-TATATGACTATGAATCAT-AATAATAATAATAATAAGAAGAAGA 870536 -v v - - vv vv v v v (AATATG)n#Sim 1 AATATGAATATGAATATGAAT-ATGAATATGAATATGAATATGAATATGA 49 chr6ptel1M 870537 ATATGAAT 870544 (AATATG)n#Sim 50 ATATGAAT 57 Matrix = Unknown Transitions / transversions = 0.00 (0/9) Gap_init rate = 0.05 (3 / 55), avg. gap size = 1.00 (3 / 3) 19 12.96 0.00 0.00 chr6ptel1M 870506 870539 (129461) (AAT)n#Simple_repeat 1 34 (0) m_b294s252i9 12204 chr6ptel1M 870506 AATCATAATAATAATAATAATAAGAAGAAGAATA 870539 v v v v (AAT)n#Simple 1 AATAATAATAATAATAATAATAATAATAATAATA 34 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 229 34.94 4.72 3.10 chr6ptel1M 871150 871276 (128724) L2a_3end#LINE/L2 385 513 (4) m_b294s601i41 12205 chr6ptel1M 871150 CTCCTCCTCATTGGAATATGAAATCCTTAAGGGCAGGAACTATTTTTTTA 871199 i - i i i i iv v i i - v i i L2a_3end#LINE 385 CTCCCCC-CACTAGAATGTAAGCTCCATGAGGGCAGGGACT-TTTGTCTG 432 chr6ptel1M 871200 TTATTATTAAA------AAACAAAAAATCCAACATGGTACCTATTATAGA 871243 - i v v------ vv vv ivii i iv ii i ivi i v L2a_3end#LINE 433 TT-TTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACATA 481 chr6ptel1M 871244 GTAAGTGATTAATAATTTCTTGCTGAATTGAAT 871276 i i v i v vi i - L2a_3end#LINE 482 GTAGGCGCTCAATAAATATTTGTTGAA-TGAAT 513 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 46.34 CpG sites = 27, Kimura (unadjusted) = 49.63 Transitions / transversions = 1.69 (27/16) Gap_init rate = 0.04 (5 / 126), avg. gap size = 2.00 (10 / 5) 426 28.45 3.42 0.83 chr6ptel1M 871292 871408 (128592) C MIRc#SINE/MIR (40) 228 109 m_b294s601i42 12206 chr6ptel1M 871292 TTATGAAGTAATGTCAAATATATTATTTCATCTAATCCTCACCATCAACC 871341 ii iiv v v i i i i v - C MIRc#SINE/MIR 228 TTACAAAGCGCTTTCACATACATTATCTCATTTGATCCTCACAA-CAACC 180 chr6ptel1M 871342 GAGTGAGGTAA-TAATGTG---ATTGCCATCTTTATTTTACAGATAAGGG 871387 vv i-i iv ii--- iii iii i i C MIRc#SINE/MIR 179 CTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGA 130 chr6ptel1M 871388 TACTGAGTCTCAAAGAGATCA 871408 v v i i i C MIRc#SINE/MIR 129 AACTGAGGCTCAGAGAGGTTA 109 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.35 CpG sites = 24, Kimura (unadjusted) = 38.02 Transitions / transversions = 2.67 (24/9) Gap_init rate = 0.03 (3 / 116), avg. gap size = 1.67 (5 / 3) 247 18.88 1.82 3.70 chr6ptel1M 871791 871845 (128155) C L2d_3end#LINE/L2 (0) 516 463 m_b294s601i43 12207 chr6ptel1M 871791 TCAGTCAGTCAGTCAACAAGTATTT-TTGAAAATGCCTATGGTGTTCTAA 871839 i i i - -- ii ivi v v C L2d_3end#LINE 516 TCAATCAATCAATCAACAAGTATTTATTG--AGCGCCTACTATGTGCTCA 469 chr6ptel1M 871840 GCACTG 871845 C L2d_3end#LINE 468 GCACTG 463 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 19.90 CpG sites = 7, Kimura (unadjusted) = 22.34 Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.06 (3 / 54), avg. gap size = 1.00 (3 / 3) 230 30.02 1.39 2.82 chr6ptel1M 871795 871866 (128134) C L2c_3end#LINE/L2 (2) 476 406 m_b294s601i44 12207 chr6ptel1M 871795 TCAGTCAGTCAACAAGTATTT-TTGAAAATGCCTATGGTGTTCTAAGCAC 871843 v v ii - -- ii ivi v i i i C L2c_3end#LINE 476 TCATTCATTCAACAAACATTTATTG--AGCGCCTACTATGTGCCAGGCGC 429 chr6ptel1M 871844 TGGAGAAATAAAAGGAAATAAAA 871866 i v i iivi i C L2c_3end#LINE 428 TGGGGATACAAAGATGAATAAGA 406 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.78 CpG sites = 15, Kimura (unadjusted) = 40.81 Transitions / transversions = 2.50 (15/6) Gap_init rate = 0.04 (3 / 71), avg. gap size = 1.00 (3 / 3) 809 27.36 5.67 2.35 chr6ptel1M 872211 872457 (127543) MIRb#SINE/MIR 4 258 (10) m_b294s601i45 12208 chr6ptel1M 872211 AGAGGCAGCTGAGTGGCCCAGCGATTCAAATATTGGGCCTGGAGGCAAAA 872260 i --- iv i ivvvi ii iv vii v i v MIRb#SINE/MIR 4 AGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGAC 50 chr6ptel1M 872261 AGACCTGAATTCAAATCTGACCTCAGACACT----AGCTGTGTGACCCTA 872306 ii i iviv v v ---- i i MIRb#SINE/MIR 51 AGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTG 100 chr6ptel1M 872307 GGCAAGTTACTTCAC-TCTGTTTGCCTCAAATTCCTCATCTACAAAA-AA 872354 v - v vv iv ii -ii MIRb#SINE/MIR 101 GGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGG 150 chr6ptel1M 872355 GAATAATAATGGCATTTGCCTCCCCAGATTGTTGTGAGGATCAAATGAGA 872404 i --- ii i v vi i i MIRb#SINE/MIR 151 GGATAATAAT---ACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGA 197 chr6ptel1M 872405 TAATAATTGGAAAGTACTT--CACA-----TAATACATAACAAGTACAT- 872446 ivv v ii -- ----- iii ii ii vi- MIRb#SINE/MIR 198 TAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCA 247 chr6ptel1M 872447 ATAAATATTAG 872457 iv MIRb#SINE/MIR 248 ATAAATGGTAG 258 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.86 CpG sites = 42, Kimura (unadjusted) = 35.28 Transitions / transversions = 1.75 (42/24) Gap_init rate = 0.05 (12 / 246), avg. gap size = 1.67 (20 / 12) 13 28.80 0.00 1.96 chr6ptel1M 872595 872646 (127354) (AAAACAA)n#Simple_repeat 1 51 (0) m_b294s252i10 12209 chr6ptel1M 872595 AAAACATACAAACAAAAAGGATAAAGAACAAGACAACAAACAAATAGCAT 872644 - v iv v iv v i v v i v (AAAACAA)n#Si 1 AAAACA-AAAAACAAAAAACAAAAAACAAAAAACAAAAAACAAAAAACAA 49 chr6ptel1M 872645 AA 872646 (AAAACAA)n#Si 50 AA 51 Matrix = Unknown Transitions / transversions = 0.50 (4/8) Gap_init rate = 0.02 (1 / 51), avg. gap size = 1.00 (1 / 1) 14 13.97 4.65 4.65 chr6ptel1M 872596 872638 (127362) (AAAC)n#Simple_repeat 1 43 (0) m_b294s252i11 12209 chr6ptel1M 872596 AAACATACAAACAAA-AAGGATAAAGAACAAGAC-AACAAACAAA 872638 v - iv - vi - - (AAAC)n#Simpl 1 AAACAAACAAACAAACAAACA-AACAAACAA-ACAAACAAACAAA 43 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.10 (4 / 42), avg. gap size = 1.00 (4 / 4) 512 35.45 7.54 1.50 chr6ptel1M 872662 872913 (127087) L3#LINE/CR1 3829 4095 (4) m_b294s601i46 12210 chr6ptel1M 872662 TCTGGAGGACAGACTTCAGGAC-ACTGGATTAAACTTTCAGGAAAGCAGA 872710 ii i vi - - v i vi v v i i L3#LINE/CR1 3829 TCCAGAGGGCAGAACT-AGGACCAATGGGTGGAAGTTACAGGGAGGCAGA 3877 chr6ptel1M 872711 CTTCAATTCTGCATAAGGAATATGGTCCAAACA--CAGTGTGATATAGAA 872758 i iii vii v vvv i v -- v i-- i vv L3#LINE/CR1 3878 TTTCGGCTCAATATAAGGAAGAACTTTCTAACAATCAGAGC--TGTCCAA 3925 chr6ptel1M 872759 AAGGAGAATGAACCATCTCATAAAATAGTGATTTTTCTGACCATGG---- 872804 ivi ii iii i?i ii vi ii i v vv ---- L3#LINE/CR1 3926 AAATGGAATGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGTCACTGGAGGT 3975 chr6ptel1M 872805 ----AAACAGTAGATAGGATA-----TTCTAAAAGTTGTCA-AGACAATA 872844 ---- i - iiv i----- v v ii v ii- viiv L3#LINE/CR1 3976 GTTCAAGCAG-AGGCTGGATGACCACTTGTCAGGGATGTTGTAGAAGGGA 4024 chr6ptel1M 872845 TATCTGTGTTAATTGAAAGATTAGATTAGATCACCTTTGAGATTCCTTCT 872894 vi ii iiv ii i i i v i i i i i L3#LINE/CR1 4025 TTCCTGCATTGGATGGGAGGTTGGACTAGATGACCTCTAAGGTCCCTTCC 4074 chr6ptel1M 872895 AACTC--AGGTTTTCTGATTC 872913 -- i i v L3#LINE/CR1 4075 AACTCTGAGATTCTGTGATTC 4095 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 49.27 CpG sites = 59, Kimura (unadjusted) = 51.90 Transitions / transversions = 2.03 (59/29) Gap_init rate = 0.04 (11 / 251), avg. gap size = 2.09 (23 / 11) 317 32.25 4.69 5.51 chr6ptel1M 873746 873873 (126127) C L2a_3end#LINE/L2 (16) 501 375 m_b294s601i47 12211 chr6ptel1M 873746 AGTATTTCTTAAATGCTCACTGCGTGTCAGGTGCTATGCTAA-TGCTAGA 873794 i v i ii ii ii i ii i v i-i i i C L2a_3end#LINE 501 AATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGCGCTGGG 452 chr6ptel1M 873795 GAAATG--AATGGGCAAAA---ACAAGACGGTCTCTTCTCTAAAAGATCT 873839 v ii-- i ii --- i -- i v i v vi v C L2a_3end#LINE 451 GATACAGCAGTGAACAAAACAGACAAAA--GTCCCTGCCCTCATGGAGCT 404 chr6ptel1M 873840 TACATTCCAGTGTAGAAGGAAAAGAGAGGTAATA 873873 i ----- iii v ii C L2a_3end#LINE 403 TACATTCTAGTG-----GGGGGAGACAGACAATA 375 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.33 CpG sites = 31, Kimura (unadjusted) = 46.74 Transitions / transversions = 3.88 (31/8) Gap_init rate = 0.08 (10 / 127), avg. gap size = 1.30 (13 / 10) 411 26.97 8.57 2.01 chr6ptel1M 874071 874210 (125790) MIRc#SINE/MIR 81 229 (39) m_b294s601i48 12212 chr6ptel1M 874071 CTTGTCATGTGACCTGGAACAAATCCCATAACCTCTCTGAGCCT--GTTT 874118 v iii v ii i v v -- MIRc#SINE/MIR 81 CTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTT 130 chr6ptel1M 874119 TATCATATGTGAAAATTAAGGTAATAATATTTATATTCTGTGCCTTATAG 874168 iv v - vii i ii iivi viv i i i MIRc#SINE/MIR 131 CCTCATCTGT-AAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAG 179 chr6ptel1M 874169 G---ATTGTGGGGTT----TGAGATGCAAGGTAT---AAAATGCTTTAGA 874208 ---i i v ---- -- v --- ii iv MIRc#SINE/MIR 180 GGTTGTTGTGAGGATCAAATGAGAT--AATGTATGTGAAAGCGCTTTGTA 227 chr6ptel1M 874209 AA 874210 MIRc#SINE/MIR 228 AA 229 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.55 CpG sites = 24, Kimura (unadjusted) = 34.72 Transitions / transversions = 1.85 (24/13) Gap_init rate = 0.05 (7 / 139), avg. gap size = 2.14 (15 / 7) 14 5.00 0.00 0.00 chr6ptel1M 875507 875527 (124473) (TAA)n#Simple_repeat 1 21 (0) m_b294s252i12 12213 chr6ptel1M 875507 TAATAACAATAATAATAATAA 875527 i (TAA)n#Simple 1 TAATAATAATAATAATAATAA 21 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 484 32.46 7.26 3.10 chr6ptel1M 875540 875787 (124213) C MIRc#SINE/MIR (4) 264 7 m_b294s601i49 12214 chr6ptel1M 875540 ACAATAATAACTAACATTTGTATAGTATATTAAAGCTT-CAAAATATTTT 875588 i i?v v i iv v i - iiii C MIRc#SINE/MIR 264 ATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCGCTTT 215 chr6ptel1M 875589 T---TAT-TTCTTTTATTTGAACCTCATAGAA--TCTGTGAATTAGAT-- 875630 i--- i- v i i v i iv --i iv ii-- C MIRc#SINE/MIR 214 CACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAG 165 chr6ptel1M 875631 -GC------CATTATCCGCATTTTCCAGAGAAGAAACCCGAGGTTCAGAA 875673 - ------i v v vi i v i i i C MIRc#SINE/MIR 164 GGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAG 115 chr6ptel1M 875674 GAGTTAAGTGCTTTTCCTAGAGCTAGCCAACAAATAATCAAACATTTGAC 875723 ii vi v i ii ii vv i v i vi-ii --- v C MIRc#SINE/MIR 114 AGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGT-GGCA---GAG 69 chr6ptel1M 875724 TCTGATCT-GAATTTAGCTCCTTCT-ACTCCAAATAGATACCTATTTGTA 875771 i v iv - iii v i i - i vv vvv v ---- C MIRc#SINE/MIR 68 CCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTT---- 23 chr6ptel1M 875772 TCTGTTGCATCACACT 875787 iii i C MIRc#SINE/MIR 22 TCCACTGCACCACACT 7 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 44.13 CpG sites = 50, Kimura (unadjusted) = 45.02 Transitions / transversions = 1.79 (50/28) Gap_init rate = 0.07 (17 / 247), avg. gap size = 1.53 (26 / 17) 400 33.32 6.49 0.61 chr6ptel1M 875950 876103 (123897) C MIR3#SINE/MIR (10) 198 36 m_b294s601i50 12215 chr6ptel1M 875950 ATCTTAGAATTATAGAACTGGAAAGAACGTTAGAAATCTTGTAAT----- 875994 v vvi i i i v i v v i ----- C MIR3#SINE/MIR 198 ATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAAC 149 chr6ptel1M 875995 -CTTTCATTTTGAAAATGAAGAAAGTAGAGTCCAGAGA---GAGCTTATT 876040 - ii iv i i v iii i --- iv v i C MIR3#SINE/MIR 148 CCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACT 99 chr6ptel1M 876041 TATTGCAGAACAGCAAACTTATTTA-TTGCAACACTGGAACTAGGGCTCG 876089 iiivv iv - v vi? v - v ivi i i ii i i C MIR3#SINE/MIR 98 TGCCCAAGGTCA-CACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCA 50 chr6ptel1M 876090 AGTCTCTTGCCTCC 876103 i i v C MIR3#SINE/MIR 49 GGTCTCCTGACTCC 36 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 45.39 CpG sites = 32, Kimura (unadjusted) = 46.68 Transitions / transversions = 1.68 (32/19) Gap_init rate = 0.03 (5 / 153), avg. gap size = 2.20 (11 / 5) 357 27.03 4.05 0.00 chr6ptel1M 876183 876256 (123744) C MIRc#SINE/MIR (77) 191 115 m_b294s601i51 12216 chr6ptel1M 876183 CTCACAATAATTCTGTGGGACAGGTAGGTCAAGTACTATGATTTCTGTTT 876232 i ii i ii i v i i v ii ii C MIRc#SINE/MIR 191 CTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTT 142 chr6ptel1M 876233 TACAGATGAAG---CTAAAATTCAGAG 876256 i --- i iii C MIRc#SINE/MIR 141 TACAGATGAGGAAACTGAGGCTCAGAG 115 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.42 CpG sites = 18, Kimura (unadjusted) = 37.42 Transitions / transversions = 9.00 (18/2) Gap_init rate = 0.01 (1 / 73), avg. gap size = 3.00 (3 / 1) 283 33.96 5.73 2.47 chr6ptel1M 876750 876906 (123094) C L3#LINE/CR1 (22) 4077 3916 m_b294s601i52 12217 chr6ptel1M 876750 GCTAGAAAGGGTTTCAGAGGACATCTGATCCAACCTAGAGGTGTCCTA-- 876797 i i i iii i v ii vv---ii v -- C L3#LINE/CR1 4077 GTTGGAAGGGACCTTAGAGGTCATCTAGTCCAACCTCC---CATCCAATG 4031 chr6ptel1M 876798 ---GAATCCCTTTTGCAGCACCACCCCACACACCACCATCCTGCCTTTAG 876844 --- i i i i - iv viivii v i iv C L3#LINE/CR1 4030 CAGGAATCCCTTCTACAACATC-CCTGACAAGTGGTCATCCAGCCTCTGC 3982 chr6ptel1M 876845 GTAAAGAGCTCCAGGGAGAGAGAGCCCATCCCTTCCTGA-GCACTCTGTG 876893 v i v v v vi i i iiv i ?i - vi ii v C L3#LINE/CR1 3981 TTGAACACCTCCAGTGACGGGGAGCTCACTACCTCNCGAGGCAGCCCATT 3932 chr6ptel1M 876894 TC-TTTTT--ACAACT 876906 i - -- i C L3#LINE/CR1 3931 CCATTTTTGGACAGCT 3916 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 46.11 CpG sites = 35, Kimura (unadjusted) = 48.80 Transitions / transversions = 2.06 (35/17) Gap_init rate = 0.06 (9 / 156), avg. gap size = 1.44 (13 / 9) 302 31.77 0.77 3.15 chr6ptel1M 877144 877273 (122727) C L3#LINE/CR1 (3125) 974 848 m_b294s601i53 12218 chr6ptel1M 877144 AATACCAAATTGCCTTCTTAGACACC-TCTTCCCAATCAGCCATTCACTT 877192 v iviv v - v vi ii ii C L3#LINE/CR1 974 AAAACCAAATCCTGTTCTTCGACACCATCTACGTAGCCAGCTGTTCACTT 925 chr6ptel1M 877193 CTTCCAAACTCTCACTTTTCTTTGGAATTCTTTATTTTCATTAGTGACAA 877242 -- v ii vi i ivi v viv ii -- v iv i C L3#LINE/CR1 924 C--CCATATCCTCCTTTCTCTTCCAAAGTCACGACCTTCA--ACTGGAAG 879 chr6ptel1M 877243 CAGTGATAAACATTCTACCTGTGCTCCCAAG 877273 v v i v iv i i C L3#LINE/CR1 878 AAGAGATGAAAACACCACCTGTGCCCCCAAG 848 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.89 CpG sites = 22, Kimura (unadjusted) = 42.28 Transitions / transversions = 1.22 (22/18) Gap_init rate = 0.04 (5 / 129), avg. gap size = 1.00 (5 / 5) 379 27.58 3.10 7.26 chr6ptel1M 877966 878094 (121906) MIRb#SINE/MIR 4 127 (141) m_b294s601i54 12219 chr6ptel1M 877966 AGGGACATCATGTAGGACAGTGGAAACAGCACTAACTTTAGAGCCAGAGA 878015 i v i -- vi v vii i i v MIRb#SINE/MIR 4 AGGGGCAGCGTG--GTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACA 51 chr6ptel1M 878016 GTTC-AAGTTCAGATCTCACATCTTTGGTGCTTATTACCT---TGAGCTT 878061 vi -ii ii i-- iv i vii i v --- v MIRb#SINE/MIR 52 GACCTGGGTTCGAATCC--CGGCTCTGCCACTTACTAGCTGTGTGACCTT 99 chr6ptel1M 878062 GGGCAATTAAAGTCACTTAACCTCCACAAGCCT 878094 ----- i ivii MIRb#SINE/MIR 100 GGGC-----AAGTTACTTAACCTCTCTGAGCCT 127 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.73 CpG sites = 22, Kimura (unadjusted) = 35.72 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.09 (11 / 128), avg. gap size = 1.18 (13 / 11) 264 26.80 8.93 3.39 chr6ptel1M 878134 878245 (121755) C L2d_3end#LINE/L2 (14) 502 385 m_b294s601i55 12220 chr6ptel1M 878134 AACAAGCATCTATTAAGCATTTGCTATATGAAAGGTACTGCAATG-TAGG 878182 i i i iii i i vvvi i --- - C L2d_3end#LINE 502 AACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTG---TGCTAGG 456 chr6ptel1M 878183 TGCTGAAAAAAAGGAAAAAA----AT--GACATAGGCCCTTCACCTC--T 878224 i viiii v ? ---- -- i v v - --v C L2d_3end#LINE 455 CGCTGTGGGGAACGANAAAANAGTATAAGACATGGTCCCTGC-CCTCAAG 407 chr6ptel1M 878225 GAACTTAGAGTCTA-CTGGAGA 878245 i v i -i i C L2d_3end#LINE 406 GAGCTTACAATCTAGTTGGGGA 385 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.21 CpG sites = 20, Kimura (unadjusted) = 35.22 Transitions / transversions = 2.22 (20/9) Gap_init rate = 0.08 (9 / 111), avg. gap size = 1.56 (14 / 9) 22 0.00 0.00 0.00 chr6ptel1M 878788 878811 (121189) (AC)n#Simple_repeat 1 24 (0) m_b294s252i13 12221 chr6ptel1M 878788 ACACACACACACACACACACACAC 878811 (AC)n#Simple_ 1 ACACACACACACACACACACACAC 24 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 274 28.07 5.41 6.12 chr6ptel1M 878836 878983 (121017) L2d2_3end#LINE/L2 399 545 (10) m_b294s601i56 12222 chr6ptel1M 878836 TTAACTTTTGG-GTGTTTTAATGCCTATGCAGTTTTTGCCCAGGAAAATT 878884 vi- -- i - ----- i v ivv i L2d2_3end#LIN 399 TTAACTTTTCACGTGTTT--ATGTCT-TG-----TCTCCCCAACTAGATT 440 chr6ptel1M 878885 -CAATCTCCTTGAAGACAGGGA--ATGTTTTGTTTCGTTTTTGT---CTT 878928 -i v i i -- i i- v v i --- ii L2d2_3end#LIN 441 GTAAGCTCCTTGAGGGCAGGGACCATGTCTTA-TACTTCTTTGTATCCCC 489 chr6ptel1M 878929 TGCATC-CCCAGAACTCTGCCTAGCACATATCAGGCTCCTAATGAATGCT 878977 ii v - i v vv v i vi v ii i ii L2d2_3end#LIN 490 CACAGCGCCTAGCACAGTGCCTTGCACACAGTAGGCGCTCAATAAATATT 539 chr6ptel1M 878978 AGTTAA 878983 v i L2d2_3end#LIN 540 TGTTGA 545 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.27 CpG sites = 24, Kimura (unadjusted) = 36.27 Transitions / transversions = 1.60 (24/15) Gap_init rate = 0.10 (14 / 147), avg. gap size = 1.21 (17 / 14) 339 30.57 6.56 0.78 chr6ptel1M 878866 878987 (121013) L2a_3end#LINE/L2 383 511 (6) m_b294s601i57 12222 chr6ptel1M 878866 GTTTTTGCCCAGGAAAATTCAATCTCCTTGAAGACAGGGAAT-------G 878908 i iiv vv i vi v v i i v ------- L2a_3end#LINE 383 GTCTCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTCTG 432 chr6ptel1M 878909 TTTTGTTTCGTTTTTGTCTTTGCATC-CCCAGAACTCTGCCTAGCACATA 878957 - ii vi v iiv v - i vv i L2a_3end#LINE 433 TTTTG-TTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACATA 481 chr6ptel1M 878958 TCAGGCTCCTAATGAATGCTAGTTAAATGA 878987 vi v ii i ii v i L2a_3end#LINE 482 GTAGGCGCTCAATAAATATTTGTTGAATGA 511 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.31 CpG sites = 21, Kimura (unadjusted) = 40.31 Transitions / transversions = 1.31 (21/16) Gap_init rate = 0.02 (3 / 121), avg. gap size = 3.00 (9 / 3) 363 22.76 0.00 11.24 chr6ptel1M 878889 878987 (121013) L2c_3end#LINE/L2 384 472 (6) m_b294s601i58 12222 chr6ptel1M 878889 CTCCTTGAAGACAGGGAATGTTTTGTTTCGTTTTTGTCTTTGCATCCCCA 878938 i i vi --- i -- v ii i L2c_3end#LINE 384 CTCCTTGAGGGCAGGGACCGT---GTCT--TATTCATCTTTGTATCCCCA 428 chr6ptel1M 878939 GAACTCTGCCTAGCACATATCAGGCTCCTAATGAATGCTAGTTAAATGA 878987 -----i i vi v ii i i v i L2c_3end#LINE 429 G-----CGCCTGGCACATAGTAGGCGCTCAATAAATGTTTGTTGAATGA 472 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 24.74 CpG sites = 15, Kimura (unadjusted) = 27.96 Transitions / transversions = 3.00 (15/5) Gap_init rate = 0.10 (10 / 98), avg. gap size = 1.00 (10 / 10) 309 38.10 7.72 3.42 chr6ptel1M 879075 879411 (120589) C L3#LINE/CR1 (3573) 526 176 m_b294s601i59 12218 chr6ptel1M 879075 TTCCTTGGCACACATGAAGATGCTACCTATCTCCTGATATGGACCAGAGT 879124 v vi -- i - i i v - i v v v v i v C L3#LINE/CR1 526 TTCCGTGGAGCA--TGGA-ATGCTGCTTCT-TCTTCAGAAGGTCCGGATT 481 chr6ptel1M 879125 C-TCTTCTCTGAAAAAATAAAATGCTT--TACCTATCATTTAGATCTCAT 879171 -i i iv ii i ------ i -- i ii ? v ivi C L3#LINE/CR1 480 CACCCTCCGTGGGAAGA------GCCTCATACCTGTTGTNTAGCTCCAGT 437 chr6ptel1M 879172 TGTTTAAAGGT-CTTC-------------CTTCTATGTCACACACTTCCA 879207 v viii v - ------------- i i iv C L3#LINE/CR1 436 GGTGCGGAGTTTCTTCTCTTTCTCCTTTTCCTCTGTGTCACATTCTTCCA 387 chr6ptel1M 879208 CTTGC--ATCTCCTCATG--AGTTAGGATGCCTTTGTATCCATTCACCTC 879253 i -- i i v i --i vv v i viii ivi vvvi C L3#LINE/CR1 386 CTCGCCAACCTCTTGACGCTGGTTTTGATTCCCTTCCGCCTCCTCAGAAT 337 chr6ptel1M 879254 CCTTTATCCCTTACATTTCTTTTTAGAAGTACTTGTTTTATTCTTCCAAG 879303 i - ii ivv? i iiv i v i v ii i ?i v C L3#LINE/CR1 336 CTTTT-TCTTTCTGNTTTCCTTCCTGGATTATTTCTTCCATCCTNTCTAG 288 chr6ptel1M 879304 AAATACAGGAATGACATTGATAAGCTGGAAAAT--AGAACTATTTTTATA 879351 i iv vvv vivv vi i i ivi -- ivii ii vv C L3#LINE/CR1 287 GAACCCTTCATCCTCTCTAATAAGCCGGAGCGTAGAGAGGCGTTCCTCAA 238 chr6ptel1M 879352 GTCTTTTTATTTTTTTCTGAAATA--GAGATCAACTAACATTT-TATGCA 879398 i i i ii i i vv ii -- i i vi - - C L3#LINE/CR1 237 GCCCTTTCACCTTCTCCTCTAGCAGGGAGACCAGCTTGCATTTATA-GCA 189 chr6ptel1M 879399 TATATAGTTATTG 879411 i i i iv C L3#LINE/CR1 188 CACATAATTGGTG 176 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 51.21 CpG sites = 78, Kimura (unadjusted) = 57.76 Transitions / transversions = 1.70 (78/46) Gap_init rate = 0.06 (21 / 336), avg. gap size = 1.81 (38 / 21) 388 36.23 4.53 1.20 chr6ptel1M 879505 879747 (120253) C MIRc#SINE/MIR (0) 268 18 m_b294s601i60 12223 chr6ptel1M 879505 AATTATCATTATAATTTGCCTTTATGTAGTACTTTAAAATCTATAAAAGT 879554 v v v i?vi i v i i i v i i i - i C MIRc#SINE/MIR 268 AATAATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAA-GC 220 chr6ptel1M 879555 G-TTTCAGATTTGTTCATTCACTTAAACTTTATAAAAATGCCATCAGGTA 879603 - v vii vvi i i v i i i v iv ii v C MIRc#SINE/MIR 219 GCTTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTA 170 chr6ptel1M 879604 CTTA---C---TATTGATTAACTCCATTTTAGAATTCAGGAAACTAGGAA 879647 vvi --- --- - v i v iv v ii iv C MIRc#SINE/MIR 169 GGCAGGGCAGGTATT-ATTATCCCCATTTTACAGATGAGGAAACTGAGGC 121 chr6ptel1M 879648 TGCAAAAGGGTCAGTGGCTTATTTATGATTACATAGCTGTT--GTGTCAA 879695 vvi i v v i iiii v i i i iv -- v i C MIRc#SINE/MIR 120 TCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAG 71 chr6ptel1M 879696 ATGCC-CTATTGCAACATGAAT-TTCCTGACTTTCAATTTAGAACTCTAT 879743 - -vv i vv viiii - iiv i ii vi v C MIRc#SINE/MIR 70 A-GCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTT 22 chr6ptel1M 879744 TCAC 879747 i C MIRc#SINE/MIR 21 CCAC 18 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 51.15 CpG sites = 51, Kimura (unadjusted) = 52.03 Transitions / transversions = 1.42 (51/36) Gap_init rate = 0.04 (9 / 242), avg. gap size = 1.56 (14 / 9) 236 34.52 8.22 6.76 chr6ptel1M 880029 880174 (119826) L3#LINE/CR1 3951 4098 (1) m_b294s601i61 12224 chr6ptel1M 880029 TAGTAGATTTCTTTTCAGTAGAAGT----AGGTAGAGCCTGGAAAACCAT 880074 iiii i iiv v i i ---- i i v vi i L3#LINE/CR1 3951 TAGTGAGCTCCCCGTCACTGGAGGTGTTCAAGCAGAGGCTGGATGACCAC 4000 chr6ptel1M 880075 CCATCC----CATTGGAAAACAAGTGGGAATTATTG-ATCAGGTATGAC- 880118 iii v----ii v i ------ i vi - ii i iv v- L3#LINE/CR1 4001 TTGTCAGGGATGTTGTAGAA------GGGATTCCTGCATTGGATGGGAGG 4044 chr6ptel1M 880119 TTGCACTAAGTAGCTGACCTCTGAGGTCCTTTCCGGTTCAAAAGTTCTAT 880168 v ---- v i i iii vi ii i L3#LINE/CR1 4045 TTGGACTA----GATGACCTCTAAGGTCCCTTCCAACTCTGAGATTCTGT 4090 chr6ptel1M 880169 A--TCTAT 880174 i-- L3#LINE/CR1 4091 GATTCTAT 4098 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 49.40 CpG sites = 35, Kimura (unadjusted) = 51.04 Transitions / transversions = 2.92 (35/12) Gap_init rate = 0.10 (15 / 145), avg. gap size = 1.47 (22 / 15) 290 34.31 1.95 5.37 chr6ptel1M 880590 880743 (119257) C L2d2_3end#LINE/L2 (9) 546 398 m_b294s601i62 12225 chr6ptel1M 880590 ATTAATAAATAAGTTTATTTGGCAGAATCTTCTACCTACAAAGCACAATT 880639 i i -- vi i---i v iiv i i vi v C L2d2_3end#LIN 546 ATCAACAAATA--TTTATTGAGCG---CCTACTGTGTGCAAGGCACTGTG 502 chr6ptel1M 880640 CCAGG-GCATGTGAAAATTATAA-GAAGCATTTGGCAGGATCCCTATCCT 880687 i - - iiiiv i - i vv i v i ii C L2d2_3end#LIN 501 CTAGGCGC-TGTGGGGGATACAAAGAAGTATAAGACATGGTCCCTGCCCT 453 chr6ptel1M 880688 TGCAGTGTTTATAGTTTGTCTGGAGAGA-AAAATCTAAGATATGTAAATA 880736 iivi v i i i i ivi i - i iv - i i i - C L2d2_3end#LIN 452 CAAGGAGCTTACAATCTAGTTGGGGAGACAAGACATAA-ACACGTGAA-A 405 chr6ptel1M 880737 ATTTAAA 880743 v C L2d2_3end#LIN 404 AGTTAAA 398 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 46.87 CpG sites = 36, Kimura (unadjusted) = 49.79 Transitions / transversions = 2.57 (36/14) Gap_init rate = 0.07 (11 / 153), avg. gap size = 1.00 (11 / 11) 531 30.03 4.98 3.57 chr6ptel1M 880752 880972 (119028) C MIRc#SINE/MIR (20) 248 25 m_b294s601i63 12226 chr6ptel1M 880752 TTTATATAATTCTATGCAGTTTGCAAAAGAACTT--ATATGTGCTAT-TC 880798 i iiv v i i - vi -- i iiii - C MIRc#SINE/MIR 248 TTTGTATAGCACTTTACAGTTTACAAA-GCGCTTTCACATACATTATCTC 200 chr6ptel1M 880799 ATTTGAACCTCACAATTATCCAGGGAGGTATAT------GTTATTATTAA 880842 v iv i v v vii------ v v C MIRc#SINE/MIR 199 ATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTAT 150 chr6ptel1M 880843 TCCCATTTTACAAATGAGGAAAAGGAGACAGAGAGGGATT--CTGACTTG 880890 i i vv i vv i i --v C MIRc#SINE/MIR 149 CCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTG 100 chr6ptel1M 880891 TCCACCATTACAAAGGTTATAAGTGTTTGAATCAGGTTTCAGAAATTCTC 880940 i vvi i v v vi viv ii i vi --i ii vv C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTC--GAACCCAG 52 chr6ptel1M 880941 TTTTTACTTGCCTATTCAAAGCTCAGTGTCTC 880972 v i - i --- i v ii - C MIRc#SINE/MIR 51 GTCTT-CCTG---ACTCCAAGTCCAGTG-CTC 25 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.09 CpG sites = 37, Kimura (unadjusted) = 39.45 Transitions / transversions = 1.37 (37/27) Gap_init rate = 0.05 (12 / 220), avg. gap size = 1.58 (19 / 12) 345 24.89 3.74 9.90 chr6ptel1M 881563 881669 (118331) L2b_3end#LINE/L2 173 273 (193) m_b294s601i64 12227 chr6ptel1M 881563 TTTTCACCTGTGGAAAGCCATTGGATTTTTACCCATCCTTAAAGCC-CAA 881611 i i ------ ---- i ii i v i i - i L2b_3end#LINE 173 TCTTCGCCTG------GCCA----ACTCCTACTCATCCTTCAGGTCTCAG 212 chr6ptel1M 881612 ATCAAATGTCATTTCCTCTGGGAAGTCTTCCATGATCCTCCAAGCCA--- 881658 v ii i i i v i i i i--- L2b_3end#LINE 213 CTCAAATGTCACCTCCTCCGGGAAGCCCTCCCTGACCCCCCAGGCCGGGT 262 chr6ptel1M 881659 CTGGAGCTCTC 881669 v v i L2b_3end#LINE 263 CAGGCGCCCTC 273 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 27.24 CpG sites = 19, Kimura (unadjusted) = 32.01 Transitions / transversions = 3.80 (19/5) Gap_init rate = 0.11 (12 / 106), avg. gap size = 1.17 (14 / 12) 361 21.13 1.41 0.00 chr6ptel1M 881587 881657 (118343) L2c_3end#LINE/L2 190 261 (217) m_b294s601i65 12227 chr6ptel1M 881587 ATTTTTACCCATCCTTAAAGCC-CAAATCAAATGTCATTTCCTCTGGGAA 881635 i ii i v ? - iv i ii i L2c_3end#LINE 190 ACTCCTACTCATCCTTCAAGNCTCAGCTCAGATGTCACCTCCTCCGGGAA 239 chr6ptel1M 881636 GTCTTCCATGATCCTCCAAGCC 881657 i v i i ? L2c_3end#LINE 240 GCCTTCCCTGACCCCCCAAGNC 261 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 25.00 CpG sites = 12, Kimura (unadjusted) = 27.10 Transitions / transversions = 4.00 (12/3) Gap_init rate = 0.01 (1 / 70), avg. gap size = 1.00 (1 / 1) 17 0.00 5.88 5.88 chr6ptel1M 882229 882262 (117738) (ATTTTT)n#Simple_repeat 1 34 (0) m_b294s252i14 12228 chr6ptel1M 882229 ATTTTTAGTCTTTTATTTTTA-TTTT-TTTTTATTT 882262 - - - - (ATTTTT)n#Sim 1 ATTTTTA-T-TTTTATTTTTATTTTTATTTTTATTT 34 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.12 (4 / 33), avg. gap size = 1.00 (4 / 4) 1477 27.31 3.08 3.61 chr6ptel1M 882722 883306 (116694) C L1ME5_3end#LINE/L1 (304) 637 56 m_b294s551i4 12229 chr6ptel1M 882722 TCCTGCTCATTTCACTCAGCATCA-GTTCGTGTAAG-TCTCTCCA-GTC- 882767 i i iv ii - -- v - iv - i- C L1ME5_3end#LI 637 TCTTACTTTTTTCACTCAGCACTATGTT--TTTAAGATCCATCCATGTTG 590 chr6ptel1M 882768 CTTTCTGAAATCATCCTGTTGGTCATTTCTTACAGAACAATAATATTCCA 882817 v v v -- iv iv iii v v vvvv i i C L1ME5_3end#LI 589 CTATGTGTA--CATCTAGTCCGTTGCTTCTAACTGCTGCATAGTACTCCA 542 chr6ptel1M 882818 TAATATTCATATACCACAATTTATTCAGCCATTCTCCAGCTGATGGTCAT 882867 ii i v vi v iii v i viv v i C L1ME5_3end#LI 541 TGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCAGTGATGGACAC 492 chr6ptel1M 882868 CCATTCAGTTTCCAGTTTCTAGCCACTACAAAAAGGGCTGCCACAAACAT 882917 vviv ii ii i iv i v iv v ii C L1ME5_3end#LI 491 CCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCTGCAATGAACAT 442 chr6ptel1M 882918 TCGTGCACATACAGGTCCCTTTC----CCTTCTTTATAATCTCTTTGGGA 882963 i vi i ---- i v---- viv v v i C L1ME5_3end#LI 441 CCTCGTACAT----GTCCCCTTATGGACCTGTGTGAGAATTTCTTTGGGA 396 chr6ptel1M 882964 TAGAATCCCAGTAGTAACACTGCTGGATCAAAGGGTGTGCACAGTTTGAT 883013 v vv v iiiv i i v i --- --- C L1ME5_3end#LI 395 TATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATGC---GT---AT 352 chr6ptel1M 883014 AACTT--TTTGAGCA--TAGCTCCAAACTACTCTCCAAAATGGTTGGATT 883059 - -- vi -- viv i i i i i v ii C L1ME5_3end#LI 351 A-CTTAATTTGACTAAGTACTGCCAGATTGCTCTCCAGAATGGCTGCACC 303 chr6ptel1M 883060 CGTTCACAACTCCACCAACAATGCATCAATGTCCCAGTTTTCCCACATCC 883109 v ii vii i i v iv i vi ? i C L1ME5_3end#LI 302 AGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATCC 253 chr6ptel1M 883110 CCTCCAACAATCATCATTATTT---TTTCCTGTCATCTTAGCCAATCTGA 883156 i v v iiv ii--- --- v i v i i C L1ME5_3end#LI 252 TCGCCAACACTTGGCATTATCCAGCTTTC---TAATTTTTGCCAGTCTAA 206 chr6ptel1M 883157 CAGGTGTGTAGTGGTATCTTAGAGTTGTCTTAATTTGCATTTCTCTGATG 883206 i iv i i vv i v C L1ME5_3end#LI 205 TAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATTTCTCTGATT 156 chr6ptel1M 883207 AATAATGACTTGGAGCATCTTTCCATATGACTAGAAATAG--TTTCAA-T 883253 v v v i i - v v-- -- ii- C L1ME5_3end#LI 155 ACTAATGAGTTTGAGCATCTCTTCATATG-CTTGT--TAGCCTTTCGGGT 109 chr6ptel1M 883254 TTCTTCATCTGAGAATTGTCTGTTCATATCCTTTGACCATTTTTCAATTG 883303 i v vi i v v C L1ME5_3end#LI 108 TTCCTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTG 59 chr6ptel1M 883304 GAG 883306 i C L1ME5_3end#LI 58 GGG 56 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.87 CpG sites = 87, Kimura (unadjusted) = 34.73 Transitions / transversions = 1.30 (87/67) Gap_init rate = 0.05 (31 / 584), avg. gap size = 1.26 (39 / 31) 1517 27.79 0.40 1.01 chr6ptel1M 882807 883304 (116696) C L1ME3G_3end#LINE/L1 (376) 548 54 m_b294s551i5 12229 chr6ptel1M 882807 ATAATATTCCATAATATTCATATACCACAATTTATTCAGCCATTCTCCAG 882856 i i vv i i i i vi C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr6ptel1M 882857 CTGATGGTCATCCATTCAGTTTCCAGTTTCTAGCCACTACAAAAAGGGCT 882906 i v ii vviv i i v i i v iv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr6ptel1M 882907 GCCACAAACATTCGTGCACATACAGGTCCCTTTCC-CTTCTTT-ATAATC 882954 v ii i v i i ?-- i v v - v v vi- vv i C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATT 401 chr6ptel1M 882955 TCTTTGGGATAGAATCCCAGTAGTAACACTGCTGGATCAAAGGGTGTGCA 883004 ? i v? ? v iiv i i i i C L1ME3G_3end#L 400 TCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCG 351 chr6ptel1M 883005 CAGTTTGATAACTTTTTGAGCATAGCTCCAAACTACTCTCCAAAATGGTT 883054 v i -- i vvv - viv i i i ? i C L1ME3G_3end#L 350 CATTTTAA--ATTTTAATAG-ATACTGCCAAATTGCCCTCCAAAANGGCT 304 chr6ptel1M 883055 GGATTCGTTCACAACTCCACCAACAATGCATCAATGTCCCAGTTTTCCCA 883104 v iivi i vii i i i v iv v v i C L1ME3G_3end#L 303 GTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCA 254 chr6ptel1M 883105 CATCCCCTCCAACAATCATCATTATTTTTTCCTGTCATCTTAGCCAATCT 883154 i i v v ?ivi ivv?iii vvv i v C L1ME3G_3end#L 253 CACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATCT 204 chr6ptel1M 883155 GACAGGTGTGTAGTGGTATCTTAGAGTTGTCTTAATTTGCATTTCTCTGA 883204 ii viv i i vv i i C L1ME3G_3end#L 203 GATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGA 154 chr6ptel1M 883205 TGAATAATGACTTGGAGCATCTTTCCATATGACTAGAAATAGTTTCAATT 883254 v v i vv v i vi vviiivi vv C L1ME3G_3end#L 153 TTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGTATT 104 chr6ptel1M 883255 TCTTCATCTGAGAATTGTCTGTTCATATCCTTTGACCATTTTTCAATTGG 883304 i v v i v v C L1ME3G_3end#L 103 TCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGG 54 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.32 CpG sites = 74, Kimura (unadjusted) = 35.97 Transitions / transversions = 1.17 (74/63) Gap_init rate = 0.01 (7 / 497), avg. gap size = 1.00 (7 / 7) 245 31.85 16.96 3.07 chr6ptel1M 883851 884080 (115920) C L2c_3end#LINE/L2 (172) 306 46 m_b294s601i66 12225 chr6ptel1M 883851 TATACACAGAGTAATTTCAGGGATTAT---GAAAAGCACC---ATTAA-- 883892 v i iv v -- vi i--- i ii --- i i-- C L2c_3end#LINE 306 TATAGACAGGGTGCTAT--GGGAGCACAGAGGAGGGCACCTAGACTAGNC 259 chr6ptel1M 883893 TTGAGAGAATTAGAAAAGATCTTGTTAGAAAAG-TGGCCCCTTAGGTGAA 883941 i i i- i ii i- viii ii - i vi v v i C L2c_3end#LINE 258 TTGGGGGG-TCAGGGAAGG-CTTCCCGGAGGAGGTGACATCTGAGCTGAG 211 chr6ptel1M 883942 CCTTTAAGGAATTGAGT-------------------GGAAGGGTGAAGAG 883972 ? v -- ------------------- i v C L2c_3end#LINE 210 NCTTGAAGGA--TGAGTAGGAGTTAGCCAGGTGGAAGGAGGGGGGAAGAG 163 chr6ptel1M 883973 CATTGTAGGCATGAGAAGCTGCTTGTATAAAGGAATGGAAAT-GGAAA-- 884019 vi vii i i v v ii v?i iii- -- C L2c_3end#LINE 162 CATTCCAGGCAGAGGGAACAGCATGTGCAAAGGCNCGGAGGCAGGAAAGA 113 chr6ptel1M 884020 ---GTGGAATATTAGGAGTAC-CAAG----TCAGTTTGACTAGAAAGCAG 884061 --- i vi i v i v i- ---- v i i -- v C L2c_3end#LINE 112 ACTGCGGCGTGTTTGGGGAATGCAAGNAGTTCAGTGTGGCTGG--AGCAT 65 chr6ptel1M 884062 AATACTCCAGCAGGGAAAT 884080 i ivv v v i i C L2c_3end#LINE 64 AGTGGGCGAGGAGGGGAGT 46 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.08 CpG sites = 47, Kimura (unadjusted) = 44.59 Transitions / transversions = 1.96 (47/24) Gap_init rate = 0.08 (18 / 229), avg. gap size = 2.61 (47 / 18) 229 34.09 7.60 2.22 chr6ptel1M 883955 884125 (115875) C L2d2_3end#LINE/L2 (375) 180 1 m_b294s601i67 12225 chr6ptel1M 883955 GAGTGGAAGGGTGAAGAGCATTGTAGGCATGAGAAGCTGCTTGTATAAAG 884004 v - i vi iv i i i v v vii C L2d2_3end#LIN 180 GAGAGGAAGGG-GAAGGGCATTCCAGGCGGGGGGAACGGCGTGAGCAAAG 132 chr6ptel1M 884005 GAATGGAAATGG-AAAGTGGAA----TATTAGGAGTAC--CAAGT----C 884043 viii iii - ? i v ---- i v i v --ii ---- C L2d2_3end#LIN 131 GCGCAGAGGCGGGAANGCGCAAGGCGTGTTCGGGGGACAGTGAGTAGACC 82 chr6ptel1M 884044 AGTTTGACTAGAAAGCAGAATACTCCAGCAGGGAAATCATGTGAAGTA-- 884091 i i -- i ivii vv ? i vi v ii -- C L2d2_3end#LIN 81 AGTTTGGCTGGA--GCGGAGGGTTCGTGNAGGGGAATAGTGGGAGATAAG 34 chr6ptel1M 884092 TTTGCTACGAGAGCTTGGAACCCAGGTGGTAAAG 884125 vi vv v i? v ii- i v ii C L2d2_3end#LIN 33 GCTGGAAAGGNAGGTTGGGG-CCAGATCGTGGAG 1 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.29 CpG sites = 36, Kimura (unadjusted) = 49.26 Transitions / transversions = 1.71 (36/21) Gap_init rate = 0.05 (9 / 170), avg. gap size = 1.89 (17 / 9) 21 26.63 1.47 2.99 chr6ptel1M 885327 885394 (114606) (TA)n#Simple_repeat 1 67 (0) m_b294s252i16 12230 chr6ptel1M 885327 TATATATACATATGTATATGAT-TATGCTTATGTCCATATGTTTTTATAC 885375 i i - - iiv i vi i v v i (TA)n#Simple_ 1 TATATATATATATATATAT-ATATATATATATATATATATATATATATAT 49 chr6ptel1M 885376 ACTACATATATGTATATAT 885394 - i i (TA)n#Simple_ 50 A-TATATATATATATATAT 67 Matrix = Unknown Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.04 (3 / 67), avg. gap size = 1.00 (3 / 3) 574 20.50 3.70 6.06 chr6ptel1M 885410 885544 (114456) MIRc#SINE/MIR 17 148 (120) m_b294s601i68 12231 chr6ptel1M 885410 AGTAGATAGAGCACTAGGCTTGGAATCAGGAAGACTTAATCTTTGAGTTC 885459 i v i i i -------i i MIRc#SINE/MIR 17 AGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC-------CTGGGTTC 59 chr6ptel1M 885460 GAATCTGATCTCAGATACT---TGGTTATGTGAGCTTAGGCAAGTCACTT 885506 i iviv v vi --- i i i v i - MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCAC-T 108 chr6ptel1M 885507 TACCCTCTCT--GCCTCAGTTTCCTCATTAATACAATGAG 885544 v -- ivi v i MIRc#SINE/MIR 109 TAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 23.43 CpG sites = 17, Kimura (unadjusted) = 24.49 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.07 (10 / 134), avg. gap size = 1.30 (13 / 10) 32 17.19 0.00 0.00 chr6ptel1M 885670 885699 (114301) (AT)n#Simple_repeat 1 30 (30) m_b294s252i17 12232 chr6ptel1M 885670 ATACACACATGTATATATAATTATTTGTAT 885699 i i i i vv v i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATAT 30 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 34 0.00 0.00 0.00 chr6ptel1M 885700 885728 (114272) (AC)n#Simple_repeat 1 29 (0) c_b294s251i3 12233 chr6ptel1M 885700 ACACACACACACACACACACACACACACA 885728 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACA 29 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 32 17.19 0.00 0.00 chr6ptel1M 885729 885757 (114243) (AT)n#Simple_repeat 31 59 (1) m_b294s252i17 12234 chr6ptel1M 885729 TATATATATATATATATATATATATAAAT 885757 v (AT)n#Simple_ 31 TATATATATATATATATATATATATATAT 59 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 221 24.51 2.11 14.12 chr6ptel1M 885920 886014 (113986) C L2d_3end#LINE/L2 (24) 492 408 m_b294s601i69 12235 chr6ptel1M 885920 TATTAAGTGCTTATTATGTGCCCAACTCTTTGC-AAGCATT-TATAGAAC 885967 i i i i i i v v - i ii - ivi C L2d_3end#LINE 492 TATTGAGCGCCTACTATGTGCTCAGCACTGTGCTAGGCGCTGTGGGGAAC 443 chr6ptel1M 885968 AGACAAACAGAATATGAAAATGAAACCAAAATAATCCCTGACCTCAA 886014 - ? - ? i - i i--------- ii v C L2d_3end#LINE 442 -GANAAA-ANAGTAT-AAGAC---------ATGGTCCCTGCCCTCAA 408 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.14 CpG sites = 16, Kimura (unadjusted) = 31.99 Transitions / transversions = 4.00 (16/4) Gap_init rate = 0.15 (14 / 94), avg. gap size = 1.00 (14 / 14) 231 35.29 3.92 0.00 chr6ptel1M 888766 888867 (111133) C L3#LINE/CR1 (1) 4098 3993 m_b295s601i0 12236 chr6ptel1M 888766 ATTGAATCAGAGAACTTTATTGCTCCTTGGGACCTCAAAGG---TCTATT 888812 v v ii i vv i vvvv i i --- v C L3#LINE/CR1 4098 ATAGAATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGT 4049 chr6ptel1M 888813 CTAACTTCTC-TTTAAAGCCTGAATTTCTTTCTTATCATCCTTGAAGGGT 888861 i i i - ii v vv ii iivi v i vii C L3#LINE/CR1 4048 CCAACCTCCCATCCAATGCAGGAATCCCTTCTACAACATCCCTGACAAGT 3999 chr6ptel1M 888862 AGCCAT 888867 i i C L3#LINE/CR1 3998 GGTCAT 3993 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 49.62 CpG sites = 21, Kimura (unadjusted) = 49.62 Transitions / transversions = 1.40 (21/15) Gap_init rate = 0.02 (2 / 101), avg. gap size = 2.00 (4 / 2) 364 25.48 6.93 2.86 chr6ptel1M 888880 888980 (111020) MIRc#SINE/MIR 11 115 (153) m_b295s601i1 12237 chr6ptel1M 888880 TGGCACAGTGAATACAGCACCTGCTCAGGAGTCAGGAGGACCTGAGTTCA 888929 ii i v v iv viiv i i i MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr6ptel1M 888930 AA-------TCTGTCCCTTGACACTATTTGTGTGGCCCCAGTCAAGTCAC 888972 i------- i v --- vi i iii v MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTT---ACTAGCTGTGTGACCTTGGGCAAGTCAC 107 chr6ptel1M 888973 TTAACCCC 888980 i MIRc#SINE/MIR 108 TTAACCTC 115 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.86 CpG sites = 17, Kimura (unadjusted) = 32.44 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.04 (4 / 100), avg. gap size = 2.50 (10 / 4) 546 32.76 2.51 5.93 chr6ptel1M 888990 889268 (110732) C L3#LINE/CR1 (90) 4009 3740 m_b295s601i2 12236 chr6ptel1M 888990 CCCAAAAAAGTAACCAGGCAGCCACTACATAAAGGGC-CCAA-GATGGGG 889037 vi v iii vv v i v i viv - i- i C L3#LINE/CR1 4009 CCCTGACAAGTGGTCATCCAGCCTCTGCTTGAACACCTCCAGTGACGGGG 3960 chr6ptel1M 889038 AAGTTACTCCTTTTCAGGGCAGCCCATCTCACTGCTGGACAACAACCCTA 889087 iv i v i i? ii ii i vi i ---i i C L3#LINE/CR1 3959 AGCTCACTACCTCNCGAGGCAGCCCATTCCATTTTTGGACAGC---TCTG 3913 chr6ptel1M 889088 AATGCTAGGAACTACTTCTTTATTTTGGGCCAAAGTCTTTCTTTATGAAA 889137 v i i v v i v i i i vi iiv v C L3#LINE/CR1 3912 ATTGTTAGAAAGTTCTTCCTTATATTGAGCCGAAATCTGCCTCCCTGTAA 3863 chr6ptel1M 889138 CCTGCACACATGGTTCCTAGTTCTTCTCCCTGATAACATAAGCACAACAA 889187 i v v v v v i i i- i ----- - - C L3#LINE/CR1 3862 CTTCCACCCATTGGTCCTAGTTCTGCCCTCTGG-AGC-----CAC-ACA- 3821 chr6ptel1M 889188 TGATAACATAACCATAATTAATATT-TACAT---AGTGCTTT-AATGTTT 889232 - ---- viv ivv v -i --- iv i- i C L3#LINE/CR1 3820 -GA----ATAAGTCTAATCCCTCTTCCACATGACAGCCCTTCAAATATTT 3776 chr6ptel1M 889233 GCAAATGGTTATTAGTTCTTTGAAAAATCTTCCCTT 889268 v i ii i i vv iivvv i i C L3#LINE/CR1 3775 GAAGACAGCTATCATGTCTCCTCTAAGTCTTCTCTT 3740 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.66 CpG sites = 51, Kimura (unadjusted) = 44.77 Transitions / transversions = 1.46 (51/35) Gap_init rate = 0.08 (21 / 278), avg. gap size = 1.10 (23 / 21) 297 36.14 4.40 2.70 chr6ptel1M 889272 889453 (110547) MIR3#SINE/MIR 14 198 (10) m_b295s601i3 12238 chr6ptel1M 889272 TGTGTAAAGAAGAGGAGGGAGCTAGGAAATAAAAGACTTG--TTCTTATG 889319 v i i - v v - i ivi ii i -- vi - MIR3#SINE/MIR 14 TGAGCAGAGA-GAGCACGGA-CTGGGAGTCAGGAGACCTGGGTTCTAGT- 60 chr6ptel1M 889320 CTCCAACTTTTCCATTTTCCAGCTGTATGAC-TTGGGTGAGGTGT----- 889363 -i ii i v i vv i? i - ii viii----- MIR3#SINE/MIR 61 -CCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCAC 109 chr6ptel1M 889364 CTGTTTAAGTCATGATTTCCTTGGATATTAAATGAAGGATTTGGGTTACA 889413 v i ii i viii iivv i v i iv ii v MIR3#SINE/MIR 110 CTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGA 159 chr6ptel1M 889414 GGATGTCTGATGTCTATTTTAGGATGTAACTTTCTATGGT 889453 v v i v iv ii - v v i v i MIR3#SINE/MIR 160 TGATCTCTAAGGTCCCTTCCA-GCTCTGACATTCTATGAT 198 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 51.71 CpG sites = 41, Kimura (unadjusted) = 52.96 Transitions / transversions = 1.78 (41/23) Gap_init rate = 0.04 (7 / 181), avg. gap size = 1.86 (13 / 7) 208 20.51 0.00 0.00 chr6ptel1M 890694 890732 (109268) L2d_3end#LINE/L2 469 507 (9) m_b295s601i4 12239 chr6ptel1M 890694 TGGGCACATGGTAAGTGCTCAATTAATGCATGTTGACTG 890732 i i i i v i v i L2d_3end#LINE 469 TGAGCACATAGTAGGCGCTCAATAAATACTTGTTGATTG 507 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 21.46 CpG sites = 6, Kimura (unadjusted) = 24.94 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 13 21.71 4.69 4.69 chr6ptel1M 890881 890944 (109056) (TCATATT)n#Simple_repeat 1 64 (0) m_b295s252i0 12240 chr6ptel1M 890881 TCACATAGCAT-TTTGAT-TTTCATATTTCGAATATGTCTCATTTAATAT 890928 i vv - v - -- v vi v (TCATATT)n#Si 1 TCATATTTCATATTTCATATTTCATATTTC--ATATTTCATATTTCATAT 48 chr6ptel1M 890929 TCTATGTTTGCA-ATTT 890944 ii i - - (TCATATT)n#Si 49 TTCATATTT-CATATTT 64 Matrix = Unknown Transitions / transversions = 0.83 (5/6) Gap_init rate = 0.10 (6 / 63), avg. gap size = 1.00 (6 / 6) 261 34.21 1.32 0.00 chr6ptel1M 891773 891848 (108152) C MIRc#SINE/MIR (186) 82 6 m_b295s601i5 12241 chr6ptel1M 891773 AATAAGCAGTGGAATCAAGTTCTGAACTCTGGTCCTC-TGACCCCAAGTT 891821 i ii ii ii ii viii i v i - i i C MIRc#SINE/MIR 82 AGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTC 33 chr6ptel1M 891822 CAGGGATCCTTCCATTTGACTACTCTG 891848 v v i i vv i v C MIRc#SINE/MIR 32 CAGTGCTCTTTCCACTGCACCACACTG 6 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.43 CpG sites = 19, Kimura (unadjusted) = 49.93 Transitions / transversions = 2.71 (19/7) Gap_init rate = 0.01 (1 / 75), avg. gap size = 1.00 (1 / 1) 325 25.47 7.55 0.00 chr6ptel1M 891950 892055 (107945) MIR#SINE/MIR 31 144 (118) m_b295s601i6 12242 chr6ptel1M 891950 CTTTGGACCTA--CTTTCTAAGGTC-AATCCATCCCCAGACACTTACTA- 891995 i v i -- vi ii v - vvv i v v - MIR#SINE/MIR 31 CTCTGGAGCCAGACTGCCTGGGTTCGAATCCCGGCTCTGCCACTTACTAG 80 chr6ptel1M 891996 ---TTTGACCCTGGGCAAGCCACTTAGCC-CTGTTTGCCTCAGTTTCTTC 892041 --- v i ii i - v v i MIR#SINE/MIR 81 CTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTC 130 chr6ptel1M 892042 ATATTGAAAGTGAG 892055 v vv i i MIR#SINE/MIR 131 ATCTGTAAAATGGG 144 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.36 CpG sites = 13, Kimura (unadjusted) = 31.36 Transitions / transversions = 0.93 (13/14) Gap_init rate = 0.05 (5 / 105), avg. gap size = 1.60 (8 / 5) 233 21.52 0.00 9.84 chr6ptel1M 892337 892403 (107597) MIR#SINE/MIR 124 184 (78) m_b295s601i7 12242 chr6ptel1M 892337 TTTCCTTATCTGTAAAGTTGGAATAACAGTTTCAGTCCCTCTCTCATTGG 892386 i i v i i i --- v vi v MIR#SINE/MIR 124 TTTCCTCATCTGTAAAATGGGGATAATAAT---AGTACCTACCTCATAGG 170 chr6ptel1M 892387 ATTATTTTTAAGAGGAT 892403 i i v --- MIR#SINE/MIR 171 GTTGTTGT---GAGGAT 184 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.58 CpG sites = 8, Kimura (unadjusted) = 25.58 Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.09 (6 / 66), avg. gap size = 1.00 (6 / 6) 32 7.78 5.36 1.72 chr6ptel1M 892500 892555 (107445) (TA)n#Simple_repeat 1 58 (0) m_b295s252i1 12243 chr6ptel1M 892500 TATATAAACATATATATATATATATA-ATATTTATA-ATATATAT-TAAA 892546 v i - v - - v (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr6ptel1M 892547 CTATATATA 892555 - (TA)n#Simple_ 51 -TATATATA 58 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.07 (4 / 55), avg. gap size = 1.00 (4 / 4) 307 29.59 5.10 0.00 chr6ptel1M 892659 892756 (107244) MIR3#SINE/MIR 103 205 (3) m_b295s601i8 12244 chr6ptel1M 892659 ACCTAACCTTCCTAGGCATC--TTTTCTTATCTACACAATGAGGGTCTTG 892706 i v ii i v -- i i ii v vv MIR3#SINE/MIR 103 ACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTG 152 chr6ptel1M 892707 AACATGATGACCTCTGAGCCTCCTTCTATTTCAAA---TCTGTGATTCAG 892753 i vv i i vii i vi vi --- i vi MIR3#SINE/MIR 153 GACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTA 202 chr6ptel1M 892754 TGA 892756 MIR3#SINE/MIR 203 TGA 205 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.01 CpG sites = 18, Kimura (unadjusted) = 39.01 Transitions / transversions = 1.64 (18/11) Gap_init rate = 0.02 (2 / 97), avg. gap size = 2.50 (5 / 2) 261 24.99 4.29 2.82 chr6ptel1M 892758 892827 (107173) L3#LINE/CR1 4017 4087 (12) m_b295s601i9 12245 chr6ptel1M 892758 AGAAGGGATATTTGTGCAC---AAGTGAGGTTGGACCATACAGCCCTTCA 892804 -- iv i--- v v i v iii ii v L3#LINE/CR1 4017 AGAAGGGAT--TCCTGCATTGGATGGGAGGTTGGACTAGATGACCTCTAA 4064 chr6ptel1M 892805 AGTCCCTTCCAACTCCAAAATTC 892827 i ii i L3#LINE/CR1 4065 GGTCCCTTCCAACTCTGAGATTC 4087 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.77 CpG sites = 12, Kimura (unadjusted) = 31.77 Transitions / transversions = 2.40 (12/5) Gap_init rate = 0.04 (3 / 69), avg. gap size = 1.67 (5 / 3) 244 30.36 0.00 0.00 chr6ptel1M 893884 893939 (106061) C MIR3#SINE/MIR (12) 196 141 m_b295s601i10 12246 chr6ptel1M 893884 CATGGAATGTTGGAGTCAGACTGGACCTTGAAGATCATTCAATCCAGCCT 893933 i ii iii vv ii ii i i i C MIR3#SINE/MIR 196 CATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCC 147 chr6ptel1M 893934 GATCAT 893939 vv C MIR3#SINE/MIR 146 CCTCAT 141 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.22 CpG sites = 13, Kimura (unadjusted) = 42.22 Transitions / transversions = 3.25 (13/4) Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0) 16 16.57 0.00 0.00 chr6ptel1M 894319 894345 (105655) (A)n#Simple_repeat 1 27 (0) m_b295s252i2 12247 chr6ptel1M 894319 AAAAAAGAAAGAAAAAAAAAATATAAA 894345 i i v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAA 27 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 225 31.51 9.24 4.00 chr6ptel1M 894730 894848 (105152) MIR3#SINE/MIR 24 148 (60) m_b295s601i11 12248 chr6ptel1M 894730 GAGCACACGTTGGAGAGTAATTGAGGACACCTGTGTATTATTCTCATCTC 894779 ivii - v ---- v v vi v i iv MIR3#SINE/MIR 24 GAGCACGGACTGG-GAGTCA----GGAGACCTGGGTTCTAGTCCCGGCTC 68 chr6ptel1M 894780 TCCTACTAATTCGGTCTTACACCTTTG--------TTTTAGCTCCTTCAG 894821 v i i ? v v vvv v --------i i v ii vi MIR3#SINE/MIR 69 TGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGG 118 chr6ptel1M 894822 CTTCA---TCCTTCTCTGTAAGATAAGAAG 894848 i --- iv i i ii MIR3#SINE/MIR 119 CCTCAGTTTCCTCATCTGTAAAATGAGGGG 148 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.28 CpG sites = 19, Kimura (unadjusted) = 42.30 Transitions / transversions = 1.12 (19/17) Gap_init rate = 0.06 (7 / 118), avg. gap size = 2.29 (16 / 7) 381 34.11 4.23 0.91 chr6ptel1M 894894 895106 (104894) C L3#LINE/CR1 (66) 4033 3814 m_b295s601i12 12249 chr6ptel1M 894894 ATGCAGAATGTTTCTTCTCTGGCATATAGAACAGATGTTCATCAAACTTC 894943 i -i ii viii vivvi ii v v i i C L3#LINE/CR1 4033 ATGCAGGA-ATCCCTTCTACAACATCCCTGACAAGTGGTCATCCAGCCTC 3985 chr6ptel1M 894944 TGGGCGAAGATTTCCAGTGACAGAGAGCTCACCGCCTCCAGAGGCAGCCC 894993 vvi v ii i i ii ?v C L3#LINE/CR1 3984 TGCTTGAACACCTCCAGTGACGGGGAGCTCACTACCTCNCGAGGCAGCCC 3935 chr6ptel1M 894994 -CCACATTTTGGGTCACCTTT-ATTCTTTACAATTGCTTTCATCTGTTGT 895041 -iiv v v v i - v viv v v i v v i v C L3#LINE/CR1 3934 ATTCCATTTTTGGACAGCTCTGATTGTTAGAAAGTTCTTCCTTATATTGA 3885 chr6ptel1M 895042 ATTTCGCTCTGTTGCCCTCGTGCTCTTTACCT-CTCTTCCT-TTTCT-CC 895088 iiivviv iiv - ivii ii i-i vv -v - C L3#LINE/CR1 3884 GCCGAAATCTGCCTCCCT-GTAACTTCCACCCATTGGTCCTAGTTCTGCC 3836 chr6ptel1M 895089 ATCC----CCACTCAGAATAAG 895106 v i---- v C L3#LINE/CR1 3835 CTCTGGAGCCACACAGAATAAG 3814 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.39 CpG sites = 40, Kimura (unadjusted) = 47.19 Transitions / transversions = 1.25 (40/32) Gap_init rate = 0.04 (8 / 212), avg. gap size = 1.38 (11 / 8) 246 28.38 11.76 6.74 chr6ptel1M 896160 896329 (103671) MIR1_Amn#SINE/MIR 3 180 (50) m_b295s601i13 12250 chr6ptel1M 896160 GGAAGGGAGTATG--CTATTTGATA-AGGAATGATCTGTGAACTTGGAAA 896206 i v i -- v v - v v iv - i i i - MIR1_Amn#SINE 3 GGGAGGCAGTGTGGTCTAGTGGATAGAGCACTGGACTG-GGACTCGGGA- 50 chr6ptel1M 896207 TTAGACAGGGGTTC-----CCAGCTAGAATACTGACTGGCTAGGAGCAAA 896251 --- vv ----- i vvivi ?i i? i? ------ MIR1_Amn#SINE 51 ---GACCTGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNG------ 91 chr6ptel1M 896252 TGATTGTGCACAACTGATTTAACAT---TATG-------TTCCTCATTTG 896291 iiv vi v v i ? v --- i? ------- i MIR1_Amn#SINE 92 TGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTG 141 chr6ptel1M 896292 TAAAACAGAGATCATAACAC--ACTGTCTACTGCAAAGTG 896329 ii i v i i -- ivi -i i MIR1_Amn#SINE 142 TAAAATGGGGATAATGATACTGACCTCCT-TTGTAAAGTG 180 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.33 CpG sites = 27, Kimura (unadjusted) = 38.51 Transitions / transversions = 1.50 (27/18) Gap_init rate = 0.11 (18 / 169), avg. gap size = 1.78 (32 / 18) 241 13.16 0.00 0.00 chr6ptel1M 896335 896372 (103628) EutTc1-N1#DNA/TcMar-Tc1 1 38 (550) m_b295s502i0 12251 chr6ptel1M 896335 CAGGGTGTTCCAAAAGTCATAATGCCATTTTAAGTTTT 896372 i v i v i EutTc1-N1#DNA 1 CAGGGTGTCCCAAAAGTCTTAGTGCAATTTTAAGCTTT 38 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 14.60 CpG sites = 3, Kimura (unadjusted) = 14.60 Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 491 27.82 0.69 5.80 chr6ptel1M 896473 896617 (103383) C MIRc#SINE/MIR (120) 148 11 m_b295s601i14 12252 chr6ptel1M 896473 CTCCTTTTACAGAAAAGGAAACTGAGGCATACAG-TGTGAAGTGACTTGC 896521 i v vi vi v -v v C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr6ptel1M 896522 CCAGAGACACACTTTTATTAAGTGTTTGGGGCCAGATTCGAACTCAGGAA 896571 ii v vvi v viv i v vi i i --- C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAG--- 52 chr6ptel1M 896572 TATAAGTCTTCCTGGTTCTAGGCTCTGCATTCTATCCACTGCCCTA 896617 ----- ii i i ii v iii v v i C MIRc#SINE/MIR 51 -----GTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCA 11 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.29 CpG sites = 21, Kimura (unadjusted) = 35.29 Transitions / transversions = 1.24 (21/17) Gap_init rate = 0.06 (9 / 144), avg. gap size = 1.00 (9 / 9) 307 21.13 18.31 0.00 chr6ptel1M 897000 897070 (102930) C MER58C#DNA/hAT-Charlie (125) 90 7 m_b295s502i1 12253 chr6ptel1M 897000 AAGATATAAAAACCATTCTTAGCTCCCAGACCATATA------------- 897036 i i v i i i i ------------- C MER58C#DNA/hA 90 AAAATGTAAAAACCATTCTTAGCTCGCGGGCCGTACAAAAACAGGCCGCG 41 chr6ptel1M 897037 GGCTGGACTGGGCTCATGGGCCATAGTTTGCCAA 897070 i i v i ii i i C MER58C#DNA/hA 40 GGCCGGATTTGGCCCGCGGGCCGTAGTTTGCCGA 7 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 13.67 CpG sites = 13, Kimura (unadjusted) = 26.52 Transitions / transversions = 6.50 (13/2) Gap_init rate = 0.01 (1 / 70), avg. gap size = 13.00 (13 / 1) 16 20.57 7.89 2.50 chr6ptel1M 897128 897203 (102797) (TGATATT)n#Simple_repeat 1 80 (0) m_b295s252i3 12254 chr6ptel1M 897128 TGAT-TTTGATGTTTGAT-TTT-AAAGTTGATAAATG-T-TTTCATTATC 897172 - i - - v v vv - - v - - (TGATATT)n#Si 1 TGATATTTGATATTTGATATTTGATATTTGATATTTGATATTTGA-TAT- 48 chr6ptel1M 897173 TTATTATTATAAATTAG-CATTTGATATTTGA 897203 iv vv v v -i (TGATATT)n#Si 49 TTGATATTTGATATTTGATATTTGATATTTGA 80 Matrix = Unknown Transitions / transversions = 0.30 (3/10) Gap_init rate = 0.11 (8 / 75), avg. gap size = 1.00 (8 / 8) 695 25.77 1.81 1.81 chr6ptel1M 897257 897422 (102578) MIRb#SINE/MIR 88 253 (15) m_b295s601i15 12255 chr6ptel1M 897257 CTATGTGATTCTGAATAGGTCACT-AACCTCTGTCTGCCTCAGTTTCCTC 897305 i iii iii i i - v vv MIRb#SINE/MIR 88 CTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTC 137 chr6ptel1M 897306 AGCTGCAAAATGGAGATGTTAATAATACTTATCTCCCTGGGTTGT--TGA 897353 v i i --- i i v v -- MIRb#SINE/MIR 138 ATCTGTAAAATGGGGA---TAATAATACCTACCTCGCAGGGTTGTTGTGA 184 chr6ptel1M 897354 GGATCGGATGAGATAATATTGATAAAGTTCTTGCCACAGTGTCTAGAATA 897403 iii iivvi iv iv i i v i MIRb#SINE/MIR 185 GGATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACA 234 chr6ptel1M 897404 TAATAGGCTTTTAGTAAGT 897422 i i vi i i i MIRb#SINE/MIR 235 TAGTAAGCGCTCAATAAAT 253 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.15 CpG sites = 30, Kimura (unadjusted) = 33.13 Transitions / transversions = 2.50 (30/12) Gap_init rate = 0.03 (5 / 165), avg. gap size = 1.20 (6 / 5) 247 30.21 6.25 0.00 chr6ptel1M 897774 897869 (102131) C MIR3#SINE/MIR (6) 202 101 m_b295s601i16 12256 chr6ptel1M 897774 TAGAATAA-AGAATGACAGAAC---GACATATTTTGGAAATCACTCAATC 897819 v - v i ---i viv ii i i iii i C MIR3#SINE/MIR 202 TAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTC 153 chr6ptel1M 897820 TAAAAGTCTCATTTCATAGTTTAGAAAA-TAAGACTCAGAGAGG-GAAAT 897867 i vvvi i i v v i - i i i - i C MIR3#SINE/MIR 152 CAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGT 103 chr6ptel1M 897868 GA 897869 C MIR3#SINE/MIR 102 GA 101 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.90 CpG sites = 20, Kimura (unadjusted) = 40.90 Transitions / transversions = 2.22 (20/9) Gap_init rate = 0.04 (4 / 95), avg. gap size = 1.50 (6 / 4) 190 29.57 0.00 14.47 chr6ptel1M 898923 899009 (100991) L2a_3end#LINE/L2 440 515 (2) m_b295s601i17 12257 chr6ptel1M 898923 CACCGTTGTGTTCTTGGGGCCTGTCACAGTGACACAGTACATGCTGCCAC 898972 i i i i iii v i------- - i --- v L2a_3end#LINE 440 CACTGCTGTATCCCCAGCGCCTA-------GA-ACAGTGC---CTGGCAC 478 chr6ptel1M 898973 CTTGTAAATGCTCAATAAATGCTTGTGGACTGGGTGA 899009 v v iii ii v v ii L2a_3end#LINE 479 ATAGTAGGCGCTCAATAAATATTTGTTGAATGAATGA 515 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.64 CpG sites = 16, Kimura (unadjusted) = 38.95 Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.13 (11 / 86), avg. gap size = 1.00 (11 / 11) 245 24.24 2.99 1.47 chr6ptel1M 898947 899013 (100987) L2d_3end#LINE/L2 449 516 (0) m_b295s601i18 12257 chr6ptel1M 898947 CACAGTGACACAGTACA-TGCTG-CCACCTTGTAAATGCTCAATAAATGC 898994 i v -i i - -v v v iii i L2d_3end#LINE 449 CACAGCGCC-TAGCACAGTGCTGAGCACATAGTAGGCGCTCAATAAATAC 497 chr6ptel1M 898995 TTGTGGACTGGGTGATTAA 899013 v i iv i L2d_3end#LINE 498 TTGTTGATTGATTGATTGA 516 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.75 CpG sites = 10, Kimura (unadjusted) = 30.06 Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.05 (3 / 66), avg. gap size = 1.00 (3 / 3) 260 31.22 6.18 11.83 chr6ptel1M 899089 899266 (100734) MIR3#SINE/MIR 30 198 (10) m_b295s601i19 12258 chr6ptel1M 899089 GGATTGAGGGGCAGAGGATCTGGATTCAAATCCT--CCCGTGATAC--AA 899134 i i i v ii i i v i i-- i - vi -- v MIR3#SINE/MIR 30 GGACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTC-TGCCACTAAC 78 chr6ptel1M 899135 TACCTACATCATTTT---CA--TAACTTAAACCTTTGTGAAACTTAATAT 899179 ?v iii v ii --- -- v v - i v iiv i i v MIR3#SINE/MIR 79 TNGCTGTGTGACCTTGGGCAAGTCACTTCA-CCTCTCTGGGCCTCAGTTT 127 chr6ptel1M 899180 CCTCATCAAAAAAAAAAAAAAGAAAAGAAAAATGAGGAGCTTGGAATAGA 899229 v------------------ v i v v MIR3#SINE/MIR 128 CCTCATCT------------------GTAAAATGAGGGGGTTGGACTAGA 159 chr6ptel1M 899230 GAGCTTTTAAGATCACTTGCAGCTCT--CAGCCTCTGAT 899266 viiii i i v v -- vi v MIR3#SINE/MIR 160 TGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGAT 198 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.57 CpG sites = 29, Kimura (unadjusted) = 41.69 Transitions / transversions = 1.45 (29/20) Gap_init rate = 0.14 (25 / 177), avg. gap size = 1.24 (31 / 25) 269 32.15 5.13 1.65 chr6ptel1M 899256 899372 (100628) MIR#SINE/MIR 27 147 (115) m_b295s601i20 12259 chr6ptel1M 899256 CAGCCTCTGA--TCACATTTTCTAATTCCAAATGCTGGCTCC----TTCA 899299 i v i--i v i vi iiv i i v i i----i i MIR#SINE/MIR 27 CGGGCTCTGGAGCCAGACTGCCTGGGTTCGAATCCCGGCTCTGCCACTTA 76 chr6ptel1M 899300 CTATCTGTTTGTCCTTGATTGAGACACAAAACATTTCTGAGGGCTCAGTT 899349 v v v ivii vi vv v i -v v MIR#SINE/MIR 77 CTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTG-TGCCTCAGTT 125 chr6ptel1M 899350 TCTTAATCTGGAAAGTGAGGGAT 899372 i v v i - MIR#SINE/MIR 126 TCCTCATCTGTAAAATG-GGGAT 147 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.54 CpG sites = 20, Kimura (unadjusted) = 42.99 Transitions / transversions = 1.18 (20/17) Gap_init rate = 0.03 (4 / 116), avg. gap size = 2.00 (8 / 4) 327 26.83 8.70 2.74 chr6ptel1M 899273 899410 (100590) MIR3#SINE/MIR 54 199 (9) m_b295s601i21 12259 chr6ptel1M 899273 TTCTAATTCCAAATGCTGGCTCCTTCACTATCTGTTTGTCCTTGATTGAG 899322 i i iiv - v v -- v ?v v v ivii MIR3#SINE/MIR 54 TTCTAGTCCCGGCT-CTGCCAC--TAACTNGCTGTGTGACCTTGGGCAAG 100 chr6ptel1M 899323 ACACAAAACATTTCTGAGGGCTCAGTTTCTTAATCTGGAAAGTGAGGGAT 899372 v vvv v i - v i v v i iv MIR3#SINE/MIR 101 TCACTTCACCTCTCTG-GGCCTCAGTTTCCTCATCTGTAAAATGAGGGGG 149 chr6ptel1M 899373 ----------TGATCCCTAAAGTCACTGCCAGGTCTAA-ATTTCA-GATT 899410 ---------- i i v v v i - ii - MIR3#SINE/MIR 150 TTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATT 199 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.64 CpG sites = 16, Kimura (unadjusted) = 33.74 Transitions / transversions = 0.80 (16/20) Gap_init rate = 0.05 (7 / 137), avg. gap size = 2.29 (16 / 7) 214 36.93 3.57 0.87 chr6ptel1M 899442 899553 (100447) C MIRc#SINE/MIR (17) 251 137 m_b295s601i22 12260 chr6ptel1M 899442 ATATTTATATAACAATTGATGATTTATAAAGTTTTTTTTTAATGTCTGTT 899491 i i i v v iii i ivi ivi - iiv vv C MIRc#SINE/MIR 251 ACATTTGTATAGCACTTTACAGTTTACAAAGCGCTTTCACA-TACATTAT 203 chr6ptel1M 899492 CTCATTTGCTCCATGTAACAAGGCTGTAAGGTAGATAATGTAAA----AA 899537 v viii vv i ii iv i ii---- v C MIRc#SINE/MIR 202 CTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTAT 153 chr6ptel1M 899538 TAACCTTATTGTGCAG 899553 v ii v i C MIRc#SINE/MIR 152 TATCCCCATTTTACAG 137 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 52.14 CpG sites = 26, Kimura (unadjusted) = 54.14 Transitions / transversions = 1.73 (26/15) Gap_init rate = 0.02 (2 / 111), avg. gap size = 2.50 (5 / 2) 415 27.88 1.90 0.94 chr6ptel1M 899609 899713 (100287) C MIRc#SINE/MIR (133) 135 30 m_b295s601i23 12260 chr6ptel1M 899609 TGAGGAAACTGAGG--CAAAGAGGATTAAGCGACTGGCTCAAGTTGATAC 899656 -- i - i v i v v i C MIRc#SINE/MIR 135 TGAGGAAACTGAGGCTCAGAGAGG-TTAAGTGACTTGCCCAAGGTCACAC 87 chr6ptel1M 899657 AATTAATAAATGTTTGAGTCTGAATTTGAAGTCAGACATTTGTGACCCCA 899706 ii i i viv i v i i i vi iiv iv i C MIRc#SINE/MIR 86 AGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCA 37 chr6ptel1M 899707 AGGCTAG 899713 v i C MIRc#SINE/MIR 36 AGTCCAG 30 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.71 CpG sites = 19, Kimura (unadjusted) = 36.29 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.02 (2 / 104), avg. gap size = 1.50 (3 / 2) 242 28.67 10.42 1.92 chr6ptel1M 899756 899851 (100149) C MIRb#SINE/MIR (115) 153 50 m_b295s601i24 12261 chr6ptel1M 899756 TCCCTTTTTTATAGAAGAGGC--CTGAAATTCAGGGCAGGTTAAATGA-T 899802 iv i v v-- iii i - i i - C MIRb#SINE/MIR 153 TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAG-AGGTTAAGTAACT 105 chr6ptel1M 899803 GGACCAA-------CAGTTGGCAAATTGCAGAGCTATGACTTCCAATCAA 899845 v v ------- i i i i v iiv - v i v C MIRb#SINE/MIR 104 TGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGA-TTCGAACCCA 56 chr6ptel1M 899846 AGCTTG 899851 i ii C MIRb#SINE/MIR 55 GGTCTG 50 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.89 CpG sites = 18, Kimura (unadjusted) = 37.89 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.05 (5 / 95), avg. gap size = 2.40 (12 / 5) 249 24.97 12.35 1.11 chr6ptel1M 899756 899836 (100164) C MIRc#SINE/MIR (118) 150 61 m_b295s601i25 12261 chr6ptel1M 899756 TCCCTTTTTTATAGAAGAGGC--CTGAAATTCAGGGCAGGTTAAATGA-T 899802 iv i v v-- iii i - i - C MIRc#SINE/MIR 150 TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAG-AGGTTAAGTGACT 102 chr6ptel1M 899803 GGACCAA-------CAGTTGGCAAATTGCAGAGCTATGACT 899836 v v ------- i i i i v iiv C MIRc#SINE/MIR 101 TGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACT 61 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.32 CpG sites = 13, Kimura (unadjusted) = 31.40 Transitions / transversions = 1.86 (13/7) Gap_init rate = 0.05 (4 / 80), avg. gap size = 2.75 (11 / 4) 450 30.69 7.58 2.90 chr6ptel1M 899875 900072 (99928) MIRc#SINE/MIR 48 254 (14) m_b295s601i26 12262 chr6ptel1M 899875 AGATTTGGGTTTTAGTCTTTCCTTTTCTGGCTACTGGCCATGTGTTTTCA 899924 ii iv iivv i v iivi i ii vii ii MIRc#SINE/MIR 48 AGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTG 97 chr6ptel1M 899925 AGGAATTCATTTGACTTTTCAGAGTCTCTATTTTCTCATCTGTAAAATGG 899974 i v v i i i i v i vi i MIRc#SINE/MIR 98 GGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGG 147 chr6ptel1M 899975 GAATAAATAAAA-------TGGCCACCT-----GATTGTTTTTAAGAATG 900012 i - v ------- v i ----- i - v i i v MIRc#SINE/MIR 148 GGAT-AATAATACCTGCCCTGCCTACCTCACAGGGTTG-TTGTGAGGATC 195 chr6ptel1M 900013 AAATGATATAAAGTAT-TTAAAGTA--TTACAGTTTACAAAGTATTACAT 900059 v v - v ii-- ii ivi ii ii i i MIRc#SINE/MIR 196 AAATGAGATAATGTATGTGAAAGCGCTTTGTAAACTGTAAAGTGCTATAC 245 chr6ptel1M 900060 ATTAATTTGTAAG 900072 -- -- MIRc#SINE/MIR 246 A--AA--TGTAAG 254 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.02 CpG sites = 41, Kimura (unadjusted) = 41.98 Transitions / transversions = 2.28 (41/18) Gap_init rate = 0.05 (10 / 197), avg. gap size = 2.10 (21 / 10) 239 39.12 0.00 3.91 chr6ptel1M 900271 900403 (99597) C MIR3#SINE/MIR (79) 129 2 m_b295s601i27 12256 chr6ptel1M 900271 GAAAACTGGGTTTCCAAGCAGTCAAATCTCTTGACCAAAGACAAACAGCT 900320 i i vii vi vi v i vv v i v v ? C MIR3#SINE/MIR 129 GGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGCN 80 chr6ptel1M 900321 AAATAATAGTGGACCAAGAGTTGGGACCATGATCCCTTGCTTCCTATTCC 900370 iv i i ii v vi iii i i vv i i i vi i v C MIR3#SINE/MIR 79 AGTTAGTGGCAGAGCCGGGACTAGAACCCAGGTCTCCTGACTCCCAGTCC 30 chr6ptel1M 900371 AATGAGTTTTTCTCCCCCTCACCTCTCCTGCCA 900403 -i ---i i - iv v ivii C MIR3#SINE/MIR 29 -GTG---CTCTCT-CTGCTCAGCCACTCTGCCA 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 55.90 CpG sites = 31, Kimura (unadjusted) = 59.67 Transitions / transversions = 1.63 (31/19) Gap_init rate = 0.04 (5 / 132), avg. gap size = 1.00 (5 / 5) 242 34.96 0.96 0.96 chr6ptel1M 900271 900374 (99626) C MIR1_Amn#SINE/MIR (96) 134 31 m_b295s601i28 12256 chr6ptel1M 900271 GAAAACTGGGTTTCCAAGCAGTCAAATCTCTTGACCAAAGACAAACAGCT 900320 i i vi? vi vi ? i vv v i v v? ? C MIR1_Amn#SINE 134 GGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGCCCAAGGTCACNCAGCN 85 chr6ptel1M 900321 AAATAATAGTGGA-CCAAGAGTTGGGACCATGATCCCTTGCTTCCTATTC 900369 iiv? i i ii - ii ? ? iiv - i i ii vv i v C MIR1_Amn#SINE 84 GGCNAGTGGCAGAGCCGGGANTNGAACCCA-GGTCTCCCGAGTCCCAGTC 36 chr6ptel1M 900370 CAATG 900374 i C MIR1_Amn#SINE 35 CAGTG 31 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 50.93 CpG sites = 23, Kimura (unadjusted) = 55.57 Transitions / transversions = 1.77 (23/13) Gap_init rate = 0.02 (2 / 103), avg. gap size = 1.00 (2 / 2) 226 28.99 11.67 2.29 chr6ptel1M 900865 900984 (99016) C L2d2_3end#LINE/L2 (33) 522 392 m_b295s601i29 12263 chr6ptel1M 900865 TACTGGGTACCAAGCACTGTGCTA---ACTGTTGGGGATACAA------- 900904 v i v i ---i v ------- C L2d2_3end#LIN 522 TACTGTGTGCAAGGCACTGTGCTAGGCGCTGTGGGGGATACAAAGAAGTA 473 chr6ptel1M 900905 -AAACCA--GTCTCTTCCTTCAAGGGATCCTCCATCTCAATAAGACGTAC 900951 - iv -- i v i iiiiiv v viv ii iv - C L2d2_3end#LIN 472 TAAGACATGGTCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGGAG-AC 424 chr6ptel1M 900952 AAAA-ATGAATAAGCAATAGCGTGTCAATAACAA 900984 i - i i v ii - iv - v C L2d2_3end#LIN 423 AAGACATAAACACGTGA-AAAGT-TAAATAACAA 392 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.60 CpG sites = 21, Kimura (unadjusted) = 38.03 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.07 (8 / 119), avg. gap size = 2.12 (17 / 8) 197 35.35 2.00 0.99 chr6ptel1M 901927 902026 (97974) C MIRc#SINE/MIR (75) 193 93 m_b295s601i30 12264 chr6ptel1M 901927 TCTTCATAATTAACTTATTAAA-AATCAGCACCAGTAAAGTTATATTCAT 901975 i i iv v i i v ii- iv vi vi vvi vii C MIRc#SINE/MIR 193 TCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCAT 144 chr6ptel1M 901976 TTTTACAGAGAAGGAAACTGAGGCTACATGATTTTATGTGA-TCACCTTA 902024 - vi vviv vv v - ii iv C MIRc#SINE/MIR 143 TTT-ACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAA 95 chr6ptel1M 902025 GG 902026 C MIRc#SINE/MIR 94 GG 93 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 48.84 CpG sites = 18, Kimura (unadjusted) = 48.84 Transitions / transversions = 1.06 (18/17) Gap_init rate = 0.03 (3 / 99), avg. gap size = 1.00 (3 / 3) 332 27.55 0.72 13.82 chr6ptel1M 903163 903301 (96699) L2d_3end#LINE/L2 386 508 (8) m_b295s601i31 12265 chr6ptel1M 903163 CTCTAATTAGATTGCAAGCTCCATAAAAGCAAGCTTTGTACCATCTCTGT 903212 i i i i v i ii i ---- - ---- L2d_3end#LINE 386 CCCCAACTAGATTGTAAGCTCCTTGAGGGCAGG----G-ACCAT----GT 426 chr6ptel1M 903213 TTCATTTCCATGTGTCATATATCTTTTCCCTAGTGCTTAGCACATGTCCT 903262 i i vii?v v ? i ------ ii vi i i - v L2d_3end#LINE 427 CTTATACTNTTTTNTCGT------TCCCCACAGCGCCTAGCACA-GTGCT 469 chr6ptel1M 903263 AAGCAC-TTGTAGGTGCTTAATAAATGTTTACTGGGTTGA 903301 i - v i i ii ii - i L2d_3end#LINE 470 GAGCACATAGTAGGCGCTCAATAAATACTTGTT-GATTGA 508 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.69 CpG sites = 26, Kimura (unadjusted) = 36.93 Transitions / transversions = 3.71 (26/7) Gap_init rate = 0.13 (18 / 138), avg. gap size = 1.00 (18 / 18) 34 7.37 0.00 0.00 chr6ptel1M 903713 903755 (96245) (TC)n#Simple_repeat 1 43 (0) c_b295s251i0 12266 chr6ptel1M 903713 TCTCTGTCTCTCTCTGTCTCTGTCTCTCTCTCTCTCTCTCTCT 903755 v v v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 43 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 403 28.23 5.30 0.72 chr6ptel1M 903865 903996 (96004) C MIRc#SINE/MIR (120) 148 11 m_b295s601i32 12267 chr6ptel1M 903865 CTCATTTTACAAATGAGGAAACGGAAGCAAACAG-GGTTTAGTGACTTCT 903913 i i v i vv v - v vi C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr6ptel1M 903914 TTGGGGGTCACTCAGCTCGGAAGTGTCTGAGGCCGGATTACAGC---AGT 903960 ii-ii v v v v v v v i vv i ---i C MIRc#SINE/MIR 98 CC-AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGT 50 chr6ptel1M 903961 CTT-CTGACTCCGAGCCTGACACTTTTT--ATTGTGCCA 903996 - i i iiiii i -- i ii C MIRc#SINE/MIR 49 CTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCA 11 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.43 CpG sites = 22, Kimura (unadjusted) = 36.43 Transitions / transversions = 1.47 (22/15) Gap_init rate = 0.04 (5 / 131), avg. gap size = 1.60 (8 / 5) 242 27.58 0.00 18.99 chr6ptel1M 904570 904663 (95337) C L2c_3end#LINE/L2 (4) 474 396 m_b295s601i33 12268 chr6ptel1M 904570 ATTCTCTGAGTGAGCATTTATTCAAAGACTATTATATGTAGGTTACAGAG 904619 vi v iii i v iv v i i ------------ C L2c_3end#LINE 474 ATTCATTCAACAAACATTTATTGAGCGCCTACTATGTG------------ 437 chr6ptel1M 904620 CCTGGTGCTGTGGGAGATACAGAAATAAATGAGATACGGTCCCT 904663 v i --- i i i i i i C L2c_3end#LINE 436 CCAGGCGCTG---GGGATACAAAGATGAATAAGACACGGTCCCT 396 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.48 CpG sites = 15, Kimura (unadjusted) = 34.53 Transitions / transversions = 2.50 (15/6) Gap_init rate = 0.16 (15 / 93), avg. gap size = 1.00 (15 / 15) 296 31.65 0.00 0.00 chr6ptel1M 904585 904663 (95337) C L2d2_3end#LINE/L2 (19) 536 458 m_b295s601i34 12268 chr6ptel1M 904585 ATTTATTCAAAGACTATTATATGTAGGTTACAGAGCCTGGTGCTGTGGGA 904634 v iv v i i i i i vi v v iv i i C L2d2_3end#LIN 536 ATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGTGGGG 487 chr6ptel1M 904635 GATACAGAAATAAATGAGATACGGTCCCT 904663 i i viv i i i C L2d2_3end#LIN 486 GATACAAAGAAGTATAAGACATGGTCCCT 458 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.74 CpG sites = 16, Kimura (unadjusted) = 43.06 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.00 (0 / 78), avg. gap size = 0.0 (0 / 0) 62 25.46 2.52 5.17 chr6ptel1M 904805 905042 (94958) (CTTT)n#Simple_repeat 1 232 (0) m_b295s252i4 12269 chr6ptel1M 904805 CTTCCCTTTTTTCTTCCTTCTTTTCTTCCTCTCTCCCTTTTTTTC-CTCT 904853 i i i i ii i i ii i -i (CTTT)n#Simpl 1 CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 50 chr6ptel1M 904854 CTTCCTTCTTTCTTTCCTTTCCTTCTTTCCTCCCCTTTCATGCCCTTCCT 904903 - i - i - -ii - vi i i (CTTT)n#Simpl 51 -TTCTTTCTTTCTTT-CTTTCTTTCTTT-CT-TTCTTTC-TTTCTTTCTT 95 chr6ptel1M 904904 TCATCCCTTCTCTTTCCTTCTCTCCCTTCTTATC-CCCTTTACTCTC-TT 904951 - ii - i - i i - -ii - i - (CTTT)n#Simpl 96 TC-TTTCTT-TCTTTCTTTCT-TTCTTTCTT-TCTTTCTTT-CTTTCTTT 140 chr6ptel1M 904952 CTTCCCTTTTTCCTTTATCCCTTCCTTTC-TTCCTTCTTTGCTTCCATTT 905000 i i i i v ii i - i - i v i (CTTT)n#Simpl 141 CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT-CTTTCTTTC 189 chr6ptel1M 905001 ATTCCTTCTTTCCTTCCTT-TTTCTTTCCTTTCTTT-TTTCTTT 905042 v i i i - - - (CTTT)n#Simpl 190 TTTCTTTCTTTCTTTCTTTCTTTCTTT-CTTTCTTTCTTTCTTT 232 Matrix = Unknown Transitions / transversions = 10.00 (40/4) Gap_init rate = 0.08 (18 / 237), avg. gap size = 1.00 (18 / 18) 47 0.00 0.00 0.00 chr6ptel1M 905043 905082 (94918) (CA)n#Simple_repeat 1 40 (0) c_b295s251i1 12270 chr6ptel1M 905043 CACACACACACACACACACACACACACACACACACACACA 905082 (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACA 40 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 13 21.15 0.00 0.00 chr6ptel1M 905083 905106 (94894) (TTTATAT)n#Simple_repeat 15 38 (1) m_b295s252i5 12271 chr6ptel1M 905083 TAATGTTTTATATTTTATATTCTA 905106 v i i (TTTATAT)n#Si 15 TTATATTTTATATTTTATATTTTA 38 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 311 25.32 2.53 0.00 chr6ptel1M 905599 905677 (94323) MIRc#SINE/MIR 113 193 (75) m_b295s601i35 12272 chr6ptel1M 905599 CTCTCTG-GATGCAGTTTTTGCATCTGTAAAATGGG-ACAGTAATAGCTG 905646 - viv iiv - i i v MIRc#SINE/MIR 113 CTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTG 162 chr6ptel1M 905647 GATCACCTTCCCCACAGGATGGTTCTGAAGA 905677 vviii v i i v v i MIRc#SINE/MIR 163 CCCTGCCTACCTCACAGGGTTGTTGTGAGGA 193 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.38 CpG sites = 11, Kimura (unadjusted) = 31.38 Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.03 (2 / 78), avg. gap size = 1.00 (2 / 2) 239 33.72 3.57 1.16 chr6ptel1M 906273 906356 (93644) C L2c_3end#LINE/L2 (18) 460 375 m_b295s601i36 12268 chr6ptel1M 906273 CATTT-TGAAGTGTCTACTATATGCAATAGTGCCAGAGATGTAAATA-GC 906320 - vi i i i v -i i ii i ii v - v C L2c_3end#LINE 460 CATTTATTGAGCGCCTACTATGTGCCA-GGCGCTGGGGATACAAAGATGA 412 chr6ptel1M 906321 A-GAGAGACAGCTCTTGCTTTCAGAGAGCCCATATTC 906356 -i v i ii i ii ii i i v C L2c_3end#LINE 411 ATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTC 375 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.44 CpG sites = 22, Kimura (unadjusted) = 50.02 Transitions / transversions = 3.67 (22/6) Gap_init rate = 0.05 (4 / 83), avg. gap size = 1.00 (4 / 4) 13 15.91 0.00 0.00 chr6ptel1M 907215 907242 (92758) (TCCC)n#Simple_repeat 1 28 (0) m_b295s252i6 12273 chr6ptel1M 907215 TCCCTCCCTCCCCACCTCCCCACCTCCC 907242 iv iv (TCCC)n#Simpl 1 TCCCTCCCTCCCTCCCTCCCTCCCTCCC 28 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 18 23.30 0.00 0.00 chr6ptel1M 907566 907605 (92395) (T)n#Simple_repeat 1 40 (0) m_b295s252i7 12274 chr6ptel1M 907566 TTTTTTTTTTTTAGCTTTTTAATATTTTATTTCTTTTTTT 907605 vvi vv v v i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 40 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 303 28.08 23.66 0.44 chr6ptel1M 908105 908290 (91710) MIRc#SINE/MIR 2 230 (38) m_b295s601i37 12275 chr6ptel1M 908105 GAGGCAGCTTTGGTGTATTTGAAAGTATATTCCACTTGGCTTCTAAAAG- 908153 - v i v v vii i vv vv vii - MIRc#SINE/MIR 2 GAGGCAG-TGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA 50 chr6ptel1M 908154 CTTAGGTCCGAATCTCGTCCCCACC---------TTGTAGGACCACG--- 908191 i i i i i v i ii ---------i iv vi --- MIRc#SINE/MIR 51 CCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGC 100 chr6ptel1M 908192 ----CACTTGGTCTTTCTGCGT-----TTTTATTA-----AAAATAAGCA 908227 ---- iii i v i----- iv i ----- ii v MIRc#SINE/MIR 101 AAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGA 150 chr6ptel1M 908228 TAGTAAAAGCT-CCCAGATT--------GGTTTG----GAGGATCAAATG 908264 i v v - v vi -------- v ---- MIRc#SINE/MIR 151 TAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATG 200 chr6ptel1M 908265 AG--AACG--TGTGCAAGTCCTTTGTAAAC 908290 -- i -- v iv MIRc#SINE/MIR 201 AGATAATGTATGTGAAAGCGCTTTGTAAAC 230 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.21 CpG sites = 30, Kimura (unadjusted) = 36.07 Transitions / transversions = 1.36 (30/22) Gap_init rate = 0.06 (12 / 185), avg. gap size = 3.75 (45 / 12) 324 31.37 0.72 5.30 chr6ptel1M 908409 908546 (91454) C MIRc#SINE/MIR (46) 222 91 m_b295s601i38 12276 chr6ptel1M 908409 AGTGATTCCATAGCCATTATTTCATGTGAATTTTTACAGCATCCCTGTGA 908458 i v i i vv i v - ii i i v C MIRc#SINE/MIR 222 AGCGCTTTCACATACATTATCTCATTTGA-TCCTCACAACAACCCTGTGA 174 chr6ptel1M 908459 GGAAGGCAATGAAAATATTCTTACTTTTATCTT-CAGATAATTAGAGCTG 908507 v iv v ii v iiiii i - i vv - i - C MIRc#SINE/MIR 173 GGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGA-AACT- 126 chr6ptel1M 908508 GGAGAGTCCTAGGAGTTAATTTAGTCTTAGCCTAGGATC 908546 - iv vv ii v v -- - i i i C MIRc#SINE/MIR 125 -GAGGCTCAGAGAGGTTAAGTGA--CTT-GCCCAAGGTC 91 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.68 CpG sites = 25, Kimura (unadjusted) = 42.04 Transitions / transversions = 1.56 (25/16) Gap_init rate = 0.06 (8 / 137), avg. gap size = 1.00 (8 / 8) 262 33.33 6.90 6.90 chr6ptel1M 908541 908714 (91286) C MIR3#SINE/MIR (32) 176 3 m_b295s601i39 12277 chr6ptel1M 908541 AGGATCCTTAAACCTTGTTTAAAC--ACTTCTTTTTTTCTTTGCTGAGGC 908588 iv i vv ii i iv -- ii i iv iviv v v C MIR3#SINE/MIR 176 AGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGA 127 chr6ptel1M 908589 AATTG-GGTTTAAAGGG---------CTTGCCCAGGGTCTCACAGCCAGG 908628 i - iii i i --------- i v ? - C MIR3#SINE/MIR 126 AACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGCNAG- 78 chr6ptel1M 908629 AAGTGTTGAGTGTCTGAGTTCAGATTTGAACTGAAGCCCTCTTGACTTCA 908678 ------ v v v iivi i v iv i -i i i v C MIR3#SINE/MIR 77 ------TTAGTGGCAGAGCCGGGACTAGAACCCAGG-TCTCCTGACTCCC 35 chr6ptel1M 908679 GGACTGGTGCTCTATCCACTGCGCCACCTAGCTGCC 908714 i v i- v ii vv i--- C MIR3#SINE/MIR 34 AGTCC-GTGCTCTCTCTGCTCAGCCACT---CTGCC 3 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.05 CpG sites = 33, Kimura (unadjusted) = 46.42 Transitions / transversions = 1.57 (33/21) Gap_init rate = 0.09 (15 / 173), avg. gap size = 1.60 (24 / 15) 386 28.17 0.74 7.94 chr6ptel1M 908582 908716 (91284) C MIRc#SINE/MIR (141) 127 2 m_b295s601i40 12277 chr6ptel1M 908582 CTGAGGC-AATTGGGTTTAAAGGGCTTGCCCAGGGTCTCACAGCCAGGAA 908630 -v vv i v iv i i v i --- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG--- 81 chr6ptel1M 908631 GTGTTGAGTGTCTGAGTTCAGATTTGAACTGAAGCCCTCTTGACTTCAGG 908680 ---- i v v iivi i i iv i i i i i i C MIRc#SINE/MIR 80 ----TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr6ptel1M 908681 ACTGGTGCTCTATCCACTGCGCCACCTAGCTGCCCC 908716 v ii v i ---i i C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTGCACCAC---ACTGCCTC 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.89 CpG sites = 23, Kimura (unadjusted) = 36.51 Transitions / transversions = 1.92 (23/12) Gap_init rate = 0.08 (11 / 134), avg. gap size = 1.00 (11 / 11) 281 23.86 11.36 0.00 chr6ptel1M 908778 908865 (91135) Charlie4a#DNA/hAT-Charlie 409 506 (2) m_b295s502i2 12278 chr6ptel1M 908778 TTTATTTGATGCATTTAACAACCTT---CTCGGTAGAAGCTTACAG-CTT 908823 v v v --- vi v ii iii i - Charlie4a#DNA 409 TTTATTTTATGCATTTAAAAACATTATTCTGAGAAGGGGTCCATAGGCTT 458 chr6ptel1M 908824 TACCAGATGACTAAAGGGGTCTAT------AAGAAAATTAAGAACCCC 908865 i ivi i i ------ i ii Charlie4a#DNA 459 CACCAGACTGCCAAAGGGGTCCATGGCACAAAAAAGGTTAAGAACCCC 506 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 29.97 CpG sites = 15, Kimura (unadjusted) = 29.97 Transitions / transversions = 2.50 (15/6) Gap_init rate = 0.03 (3 / 87), avg. gap size = 3.33 (10 / 3) 189 22.50 2.41 8.97 chr6ptel1M 908878 908960 (91040) C MIR1_Amn#SINE/MIR (80) 150 73 m_b295s601i41 12279 chr6ptel1M 908878 CTCATTTTCCTAATGAG-AAACTGAGGCTTTGCTCAGCAGGAGGAGCGAC 908926 i v vi - ?iv --- - v?i i C MIR1_Amn#SINE 150 CCCATTTTACAGATGAGGAAACTGAGGCNCAG---AG-AGGTNAAGTGAC 105 chr6ptel1M 908927 AACTTGTTCTAAGTCACTCGG-GAGCCAGTGGTGG 908960 --- ii v i ? i -?i ? ii C MIR1_Amn#SINE 104 ---TTGCCCAAGGTCACNCAGCNGGCNAGTGGCAG 73 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.05 CpG sites = 12, Kimura (unadjusted) = 30.05 Transitions / transversions = 2.40 (12/5) Gap_init rate = 0.11 (9 / 82), avg. gap size = 1.00 (9 / 9) 499 24.99 6.90 0.65 chr6ptel1M 909240 909384 (90616) C MIR3#SINE/MIR (3) 205 52 m_b295s601i42 12280 chr6ptel1M 909240 TCCTAGGATCAGAGACTTAGAGAGGCTGG--GGAA--TTAGAAGTTATCT 909285 v i v v vvv - -- i -- ii i C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAG-CTGGAAGGGACCTTAGAGATCATCT 157 chr6ptel1M 909286 AGTCTAACCCACTCATTTTACAGATAAGGAAACTGAGGCACAGGAAGCTA 909335 i v i v ii v i C MIR3#SINE/MIR 156 AGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTG 107 chr6ptel1M 909336 AATGGACTAATCT---GTC---CAGATTGTCAGTAACAGAGCCAGACTTC 909379 vv vii i--- --- v?v i ii i ivi v C MIR3#SINE/MIR 106 AAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTA 57 chr6ptel1M 909380 GGACC 909384 i C MIR3#SINE/MIR 56 GAACC 52 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.16 CpG sites = 20, Kimura (unadjusted) = 31.18 Transitions / transversions = 1.25 (20/16) Gap_init rate = 0.03 (5 / 144), avg. gap size = 2.20 (11 / 5) 231 27.62 2.80 11.36 chr6ptel1M 909382 909524 (90476) C L2d_3end#LINE/L2 (3) 513 382 m_b295s601i43 12281 chr6ptel1M 909382 ACCAGTCAGTTAATAAGCATTTGTTAAGTGTCCTCCTGTGTTGTTGTGTC 909431 i i i i i i i i i - v i - i vv iv C L2d_3end#LINE 513 ATCAATCAATCAACAAGTATTTATTGAGCG-CCTACTATGT-GCTCAGCA 466 chr6ptel1M 909432 CTTCTGGGCGTGAGCACTAG-CGCCGAGGATTCCGAGACAAACA--ACAG 909478 ------- ---- - i v ivvv ? - ? -- i i C L2d_3end#LINE 465 CT-------GTG----CTAGGCGCTGTGGGGAACGANA-AAANAGTATAA 428 chr6ptel1M 909479 GCCATCAGCCCCTACTCTTGAGGCGCTTGCTACCTA-TTGGGGAGAC 909524 v -i i i i ii v i v i - C L2d_3end#LINE 427 GACAT-GGTCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGGAGAC 382 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.05 CpG sites = 24, Kimura (unadjusted) = 36.38 Transitions / transversions = 2.18 (24/11) Gap_init rate = 0.13 (18 / 142), avg. gap size = 1.06 (19 / 18) 357 29.41 0.88 4.55 chr6ptel1M 909878 909991 (90009) C MIR#SINE/MIR (89) 173 64 m_b295s601i44 12282 chr6ptel1M 909878 AACCTCTTGAGGTTAGAGGTACAATTTTATTCTTCCCATTTCAGACTCGG 909927 iiv --- v -- v i i v vvi i C MIR#SINE/MIR 173 AACCCTATGAGGT---AGGTACTATT--ATTATCCCCATTTTACAGATGA 129 chr6ptel1M 909928 GGAAATCGAAATGTAGAGAAAGGAAATGATTTACT-AGGGTCACGCAGCT 909976 ii iiiii iivv i i i i i- i i C MIR#SINE/MIR 128 GGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCT 79 chr6ptel1M 909977 AGTAAGTGTCTGAGC 909991 v v C MIR#SINE/MIR 78 AGTAAGTGGCAGAGC 64 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.27 CpG sites = 22, Kimura (unadjusted) = 39.27 Transitions / transversions = 2.20 (22/10) Gap_init rate = 0.05 (6 / 113), avg. gap size = 1.00 (6 / 6) 234 33.97 3.28 5.88 chr6ptel1M 910020 910141 (89859) C MIRc#SINE/MIR (75) 193 75 m_b295s601i45 12283 chr6ptel1M 910020 TCTTCACAATGACTCCCTAAGGCAGCTACTAGAAGTGTTACT---CCCAT 910066 i ii i iv i i vi vviv i i i --- C MIRc#SINE/MIR 193 TCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCAT 144 chr6ptel1M 910067 TTTATAGGGGAGGGGGGGAGAACTGCAGCTCATAAGCATACAATGACTCC 910116 i iv ------i vi v iivi vv i -i C MIRc#SINE/MIR 143 TTTACAGATGAGG------AAACTGAGGCTCAGAGAGGTTAAGTGACT-T 101 chr6ptel1M 910117 ACCAAAGGGCACACCA-TATTAAATG 910141 i v v vi- v i C MIRc#SINE/MIR 100 GCCCAAGGTCACACAGCTAGTAAGTG 75 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 47.24 CpG sites = 24, Kimura (unadjusted) = 47.24 Transitions / transversions = 1.60 (24/15) Gap_init rate = 0.07 (9 / 121), avg. gap size = 1.22 (11 / 9) 17 24.56 4.23 2.78 chr6ptel1M 910145 910215 (89785) (TTAA)n#Simple_repeat 1 72 (0) m_b295s252i8 12284 chr6ptel1M 910145 TTAGTTATTTAATTAA-ACTTTAAATAAATAAAT-TTTATTTAAATGTAC 910192 i v -vvv v v v -v v - - v (TTAA)n#Simpl 1 TTAATTAATTAATTAATTAATTAATTAATTAATTAATTAATT-AAT-TAA 48 chr6ptel1M 910193 TTCATTATTTAATTAACT-ATTAA 910215 v v i - (TTAA)n#Simpl 49 TTAATTAATTAATTAATTAATTAA 72 Matrix = Unknown Transitions / transversions = 0.17 (2/12) Gap_init rate = 0.07 (5 / 70), avg. gap size = 1.00 (5 / 5) 339 22.22 2.74 1.35 chr6ptel1M 910309 910381 (89619) C MIR3#SINE/MIR (27) 181 108 m_b295s601i46 12285 chr6ptel1M 910309 CTGGAAAGTGTGTTAGAAATCATCTAAGCTTAATCCCCTCATTGTATAGA 910358 i viiv i - iii i v i C MIR3#SINE/MIR 181 CTGGAAGGGACCTTAGAGATCATCTA-GTCCAACCCCCTCATTTTACAGA 133 chr6ptel1M 910359 GGAGGAAAC--AGGTTCAGAGGGGT 910381 v -- ii i C MIR3#SINE/MIR 132 TGAGGAAACTGAGGCCCAGAGAGGT 108 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.57 CpG sites = 12, Kimura (unadjusted) = 27.57 Transitions / transversions = 3.00 (12/4) Gap_init rate = 0.03 (2 / 72), avg. gap size = 1.50 (3 / 2) 203 20.45 4.55 0.00 chr6ptel1M 910345 910388 (89612) C MIRb#SINE/MIR (116) 152 107 m_b295s601i47 12285 chr6ptel1M 910345 CCTCATTGTATAGAGGAGGAAAC--AGGTTCAGAGGGGTTGAACAA 910388 i v i v -- i i i ii C MIRb#SINE/MIR 152 CCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAA 107 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.98 CpG sites = 7, Kimura (unadjusted) = 24.98 Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.02 (1 / 43), avg. gap size = 2.00 (2 / 1) 224 32.75 22.06 1.22 chr6ptel1M 910432 910567 (89433) MIRc#SINE/MIR 78 241 (27) m_b295s601i48 12286 chr6ptel1M 910432 TTGTTGGCTATATTAGTGTGCACAAACCATTTATCCTCCCTGAATTCTAA 910481 ii i i i v viv vi ii i v i iiiii i MIRc#SINE/MIR 78 TTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAG 127 chr6ptel1M 910482 TGT-------TATAAAATGCATGTAA-AA-ACCTTCACTGTACCCATTTC 910522 v ------- i vivi - - v v -- i ii MIRc#SINE/MIR 128 TTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTG--CCTACCTC 175 chr6ptel1M 910523 GCAGGGCTGTCATTAAG---------------------GAAAATGCTTTG 910551 i i ii v i --------------------- ii MIRc#SINE/MIR 176 ACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTTTG 225 chr6ptel1M 910552 CAAACTTTAAAATGCT 910567 i v i MIRc#SINE/MIR 226 TAAACTGTAAAGTGCT 241 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.28 CpG sites = 32, Kimura (unadjusted) = 46.80 Transitions / transversions = 2.67 (32/12) Gap_init rate = 0.04 (6 / 135), avg. gap size = 5.33 (32 / 6) 540 23.72 14.21 2.36 chr6ptel1M 910885 911074 (88926) MIRb#SINE/MIR 51 262 (6) m_b295s601i49 12287 chr6ptel1M 910885 AGACCTGGAATTCAAATCTAGCCTC--CAAA--ACTAATTGTGTGACCTC 910930 i- i iv v -- v v-- ii i MIRb#SINE/MIR 51 AGACCTGGG-TTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTT 99 chr6ptel1M 910931 CAGAAAGTCACTTAACTTGTTTG-----------TCTCATCTGCAAAATG 910969 vi v i i v i -----------i i MIRb#SINE/MIR 100 GGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATG 149 chr6ptel1M 910970 GGGATAATTATAGCTGTGACCTC-TGAGGTTATTGTGAG--TCAAATGGA 911016 v v --- -iii i -- i ii MIRb#SINE/MIR 150 GGGATAATAATACCT---ACCTCGCAGGGTTGTTGTGAGGATTAAATGAG 196 chr6ptel1M 911017 AAAACAATTGTAAAGGG-------CAATGCTTGGTGCATAGTAATTGGCT 911059 v iivv v ------- i i ii vi- MIRb#SINE/MIR 197 ATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGC-GCT 245 chr6ptel1M 911060 --ATAAATGCTGACGCT 911074 -- v ii v MIRb#SINE/MIR 246 CAATAAATGGTAGCTCT 262 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.83 CpG sites = 28, Kimura (unadjusted) = 29.40 Transitions / transversions = 1.75 (28/16) Gap_init rate = 0.06 (12 / 189), avg. gap size = 2.67 (32 / 12) 342 38.95 2.34 2.82 chr6ptel1M 911193 911406 (88594) C L2b_3end#LINE/L2 (6) 460 248 m_b295s601i51 12288 chr6ptel1M 911193 TCAGTAAACACATATTAATTAAGCACTGACTGTATACCAGGTACTCTCTT 911242 v v v v i i i iv i i i? v vi C L2b_3end#LINE 460 TCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCT 411 chr6ptel1M 911243 AACTCCTGGGGATAAAAATATAAGCAGAAATAAAGACAACGCCTGACTTC 911292 iviv v ivvi i i - i i i v? iiiv v i C L2b_3end#LINE 410 AGGCGCTGGGGATACAGCGGTGAACA-AGACAGACNCGGTCCCTGCCCTC 362 chr6ptel1M 911293 AAGGAGTTTATACTCTAACGAGAGATGAGGAAAATACACACATATGA--- 911339 v i i i v ii i i - vii v ii v? v ii --- C L2b_3end#LINE 361 ACGGAGCTCACAGTCTAGTGGGGGA-GACAGACATGTAANCAGACAATNA 313 chr6ptel1M 911340 -AATTGAAAGGAGGAGGA-AGAACGAGGCAAGGGGCATGATGGAGGAGTC 911387 - iiv i vi v i- i vi --- viiiv ivv C L2b_3end#LINE 312 TAACCCAGAGTGGCAGGGTAGGACTGGG---GGGGCCCAGAGGAGGGCGC 266 chr6ptel1M 911388 CAGATTTCAGTCTGTGGAG 911406 v -ii i i v i C L2b_3end#LINE 265 CTGA-CCCGGCCTGGGGGG 248 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 55.31 CpG sites = 50, Kimura (unadjusted) = 59.95 Transitions / transversions = 1.61 (50/31) Gap_init rate = 0.04 (9 / 213), avg. gap size = 1.22 (11 / 9) 368 33.56 1.39 0.69 chr6ptel1M 911193 911336 (88664) C L2a_3end#LINE/L2 (6) 511 367 m_b295s601i50 12288 chr6ptel1M 911193 TCAGTAAACACATATTAATTAAGCACTGACTGTATACCAGGTACTCTCTT 911242 v v v v i i iv i i i i v ii C L2a_3end#LINE 511 TCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCT 462 chr6ptel1M 911243 AACTCCTGGGGATAAAAATATAAGCAGAAATAAAGACAA-CGCCTGACTT 911291 iviv v ivvi i i - i i v v -iv v i C L2a_3end#LINE 461 AGGCGCTGGGGATACAGCAGTGAACA-AAACAGACAAAAGTCCCTGCCCT 413 chr6ptel1M 911292 CAAGGAGTTTATACTCTAACGAGAGATGA-GGAAAATACACACATA 911336 v i i i ii i i iv -i v v v C L2a_3end#LINE 412 CATGGAGCTTACATTCTAGTGGGGGGAGACAGACAATAAACAAATA 367 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.49 CpG sites = 28, Kimura (unadjusted) = 46.11 Transitions / transversions = 1.40 (28/20) Gap_init rate = 0.02 (3 / 143), avg. gap size = 1.00 (3 / 3) 12 5.48 0.00 0.00 chr6ptel1M 911816 911834 (88166) (TTA)n#Simple_repeat 1 19 (0) m_b295s252i9 12289 chr6ptel1M 911816 TTTTTATTATTATTATTAT 911834 v (TTA)n#Simple 1 TTATTATTATTATTATTAT 19 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 12 7.51 0.00 12.50 chr6ptel1M 912068 912103 (87897) (AACAAA)n#Simple_repeat 1 32 (0) m_b295s252i10 12290 chr6ptel1M 912068 AAGAAAAACAAAAATGCAAGCAAACAACAACAAAAA 912103 v -- -- v (AACAAA)n#Sim 1 AACAAAAACAAAAA--CAA--AAACAAAAACAAAAA 32 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.11 (4 / 35), avg. gap size = 1.00 (4 / 4) 18 8.88 5.26 2.56 chr6ptel1M 912186 912223 (87777) (ATT)n#Simple_repeat 1 39 (0) m_b295s252i11 12291 chr6ptel1M 912186 ATGATT-TAATTATTATTCTTATTATTAATTATT-TTATT 912223 v - v v - - (ATT)n#Simple 1 ATTATTATTATTATTATTATTATTATT-ATTATTATTATT 39 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.08 (3 / 37), avg. gap size = 1.00 (3 / 3) 285 34.85 9.16 3.62 chr6ptel1M 912464 912594 (87406) C MIRc#SINE/MIR (120) 148 11 m_b295s601i52 12292 chr6ptel1M 912464 CTCATTTTATGGATAAAGGAACTGAGGC-----------AAATGACTTGC 912502 i ii i i i ----------- i C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr6ptel1M 912503 CTGGAGTCACAAAGCTGTTGTCTGGGAACAGATTTAAG-CTCAAGAAGAT 912551 iiii v iv ivv --- viiii - -- vvi C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGG---CAGAGCCGGGACTC--GAACCC 54 chr6ptel1M 912552 GAGTTTTCTTGACTTTTGGCTTTGCACTCTATCAACTGTGCTA 912594 ii i i iivi iiiv ii v v ii i C MIRc#SINE/MIR 53 AGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCA 11 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 50.02 CpG sites = 33, Kimura (unadjusted) = 52.02 Transitions / transversions = 3.00 (33/11) Gap_init rate = 0.05 (7 / 130), avg. gap size = 2.43 (17 / 7) 196 26.56 6.25 0.00 chr6ptel1M 912717 912780 (87220) MIR3#SINE/MIR 135 202 (6) m_b295s601i53 12293 chr6ptel1M 912717 TATGAAATGAAATTATTGAACTAGAT---CTCTAATTTCTCTTCTATTTT 912763 i i iivvi i --- vv i i vi i MIR3#SINE/MIR 135 TGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTC 184 chr6ptel1M 912764 TGAAATCCTATG-TTCTA 912780 v i - MIR3#SINE/MIR 185 TGACATTCTATGATTCTA 202 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.96 CpG sites = 11, Kimura (unadjusted) = 33.96 Transitions / transversions = 1.83 (11/6) Gap_init rate = 0.03 (2 / 63), avg. gap size = 2.00 (4 / 2) 183 11.90 4.76 0.00 chr6ptel1M 912819 912860 (87140) MIR3#SINE/MIR 165 208 (0) m_b295s601i54 12294 chr6ptel1M 912819 TCTAAGG-ACCTTCCATCTCTGACATTCTAC-ATTCTAACATTC 912860 -v v i- vv MIR3#SINE/MIR 165 TCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTATGATTC 208 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 12.99 CpG sites = 1, Kimura (unadjusted) = 12.99 Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.05 (2 / 41), avg. gap size = 1.00 (2 / 2) 271 37.93 1.72 0.00 chr6ptel1M 913914 914029 (85971) C MIRb#SINE/MIR (148) 120 3 m_b295s601i55 12295 chr6ptel1M 913914 GAGAGATGAAGTGATTTGTCCA--TTTACCCTGCCAGTGTATGTCAGAGA 913961 i v i i i --v i v v i ivi v v C MIRb#SINE/MIR 120 GAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGC 71 chr6ptel1M 913962 CAAAACTGAAATGCAGGGCTTCTTGCTTTGGAATTCAGCTTTCTATCCAC 914011 iii i vi iv v vii vi ivi vi v ivi v C MIRb#SINE/MIR 70 CGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCAC 21 chr6ptel1M 914012 TGCACTGGGATGCCCGTC 914029 iiv v v C MIRb#SINE/MIR 20 TGCACCACGCTGCCCCTC 3 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 51.07 CpG sites = 24, Kimura (unadjusted) = 54.69 Transitions / transversions = 1.20 (24/20) Gap_init rate = 0.01 (1 / 115), avg. gap size = 2.00 (2 / 1) 345 33.01 1.94 0.00 chr6ptel1M 913914 914016 (85984) C MIRc#SINE/MIR (151) 117 13 m_b295s601i56 12295 chr6ptel1M 913914 GAGAGATGAAGTGATTTGTCCA--TTTACCCTGCCAGTGTATGTCAGAGA 913961 i v i i --v i v v i ivi v v C MIRc#SINE/MIR 117 GAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGC 68 chr6ptel1M 913962 CAAAACTGAAATGCAGGGCTTCTTGCTTTGGAATTCAGCTTTCTATCCAC 914011 iii vi iv v i vi ivi i i ivi v C MIRc#SINE/MIR 67 CGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCAC 18 chr6ptel1M 914012 TGCAC 914016 C MIRc#SINE/MIR 17 TGCAC 13 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.53 CpG sites = 20, Kimura (unadjusted) = 45.08 Transitions / transversions = 1.43 (20/14) Gap_init rate = 0.01 (1 / 102), avg. gap size = 2.00 (2 / 1) 12 7.49 6.67 3.23 chr6ptel1M 914164 914193 (85807) (TCTT)n#Simple_repeat 1 31 (0) m_b295s252i12 12296 chr6ptel1M 914164 TCTTTCCTACTTTCTTTC--TCTTTCTTCTCT 914193 i v -- - (TCTT)n#Simpl 1 TCTTTCTTTCTTTCTTTCTTTCTTTCTT-TCT 31 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.07 (2 / 29), avg. gap size = 1.50 (3 / 2) 12 11.65 3.33 3.33 chr6ptel1M 914458 914487 (85513) (ATTTT)n#Simple_repeat 1 30 (0) m_b295s252i13 12297 chr6ptel1M 914458 ATTTT-TTTTATTTCAATAGTATTTTATTTT 914487 - -v vv (ATTTT)n#Simp 1 ATTTTATTTTATTT-TATTTTATTTTATTTT 30 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.07 (2 / 29), avg. gap size = 1.00 (2 / 2) 244 32.15 9.80 0.90 chr6ptel1M 914944 915147 (84853) C L1ME4a_3end#LINE/L1 (297) 574 353 m_b295s551i0 12298 chr6ptel1M 914944 CATTATTTCTTAAAGACCAT-TAATATTCTATTACATTCAAATGTCATAA 914992 ? - v i iii- i ?i vv vi ii C L1ME4a_3end#L 574 CATNATTT-TTAATGGCTGCATAATATTCCATTNTATGGATGTACCATAA 526 chr6ptel1M 914993 CTTATTCAGTCGTTCCTCAATT-------------------TCCAGTCCC 915023 i i ii i? i v ------------------- i iii C L1ME4a_3end#L 525 TTTATTTAACCANTCCCCTATTGTTGGACATTTAGGTTGTTTCCAATTTT 476 chr6ptel1M 915024 TTGCTACTACATAAAGGGCTGCTGCAAACATTTTTGTACATGTGTGTTCC 915073 i i i v v iv viii ii ivi v iv C L1ME4a_3end#L 475 TCGCTATTATAAATAATGCTGCGATGAACATCCTTGTACATAAATCTTTG 426 chr6ptel1M 915074 TAACCCTTTTTTTATTATCTCTTTGGGATACAGACCTGGTTTTGAGACTG 915123 -? v v i i v i i i v vv i vvv ii i i C L1ME4a_3end#L 425 T-NCACATCTCTGATTATTTCCTTAGGATAAATTCCTAGAAGTGGAATTA 377 chr6ptel1M 915124 CTGGCTCAAAGGATATGGACAGTT 915147 v i ? v C L1ME4a_3end#L 376 CTGGGTCAAAGGGTATGNACATTT 353 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 44.83 CpG sites = 42, Kimura (unadjusted) = 45.82 Transitions / transversions = 1.83 (42/23) Gap_init rate = 0.02 (4 / 203), avg. gap size = 5.50 (22 / 4) 280 29.27 1.59 2.40 chr6ptel1M 915013 915138 (84862) C L1MC5_3end#LINE/L1 (2211) 483 359 m_b295s551i1 12298 chr6ptel1M 915013 TTTCCAGTCCCTTGCTACTACATAAAGGGCTGCTGCAAACATTTTTGTAC 915062 ii i v v v viii i vii i C L1MC5_3end#LI 483 TTTCCAGTCTTTTGCTATTACAAATAGTGCTGCAATGAATAGCCTTGTGC 434 chr6ptel1M 915063 AT--GTGTGTTCCTAACCCTTTTTTTATTATCTCTTTGGGATACAGACCT 915110 -- v v v ---i vii v i v v vv C L1MC5_3end#LI 433 ATACGTCTTTTCGTA---TTTTTGCCAGTGTATCTTTGGGATAGATTCCT 387 chr6ptel1M 915111 GGTTTTGAGACTGCTGGCTCAAAGGATA 915138 i vvv i i v i C L1MC5_3end#LI 386 AGAAGTGGGATTGCTGGGTCAAAGGGTA 359 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.56 CpG sites = 18, Kimura (unadjusted) = 37.56 Transitions / transversions = 1.00 (18/18) Gap_init rate = 0.03 (4 / 125), avg. gap size = 1.25 (5 / 4) 523 30.87 12.57 3.52 chr6ptel1M 915404 915769 (84231) L2c_3end#LINE/L2 1 398 (80) m_b295s601i57 12299 chr6ptel1M 915404 CTCCAAAATGTGGTACTAGCTTGCCTTTCTAGTCTTA---------CTCC 915444 ? vi v iv iv i i i i i i --------- L2c_3end#LINE 1 CTNCACGATCTGGCCCCTGCCTACCTCTCCAGCCTCATCTCCTCCACTCC 50 chr6ptel1M 915445 CTTCTACTTCCTCTGTGATTCAGCCAAACTGGCCACT-CTTTC-TTCCCC 915492 i iv vi v i v i v i-- - v - L2c_3end#LINE 51 CCTCCTCGCCCACTATGCTCCAGCCACACTGA--ACTNCTTGCATTCCCC 98 chr6ptel1M 915493 AAACATA--GTA----TTTCC--CCTTTGGGC--TTG---ATGCCTTTGT 915529 ii-- i ---- -- ii ? -- --- --- L2c_3end#LINE 99 AAACACGCCGCAGTTCTTTCCTGCCTCCGNGCCTTTGCACATGC---TGT 145 chr6ptel1M 915530 CCCCTCTGCTTAGAATAGAATCCTTCTCCATCTTTGTCAGCTG---AATT 915576 i i i --iv i i i v i -i v --- i L2c_3end#LINE 146 TCCCTCTGCCTGGAAT--GCTCTTCCCCCCTCCTT-CCACCTGGCTAACT 192 chr6ptel1M 915577 TCTATCTCCTCTTTAAAACCCAACTTGAATGTTCTTTCCATCAGGAAGTC 915626 i iiivii i i? i i iii ivii vi i i L2c_3end#LINE 193 CCTACTCATCCTTCAAGNCTCAGCTCAGATGTCACCTCCTCCGGGAAGCC 242 chr6ptel1M 915627 TTTCCTAATTTCTAAAGTT--ATCT------CCACC-CTGGAATTCAGTG 915667 i i iii iv ?i--i ------ v - viv i vi - L2c_3end#LINE 243 TTCCCTGACCCCCCAAGNCTAGTCTAGGTGCCCTCCTCTGTGCTCCCAT- 291 chr6ptel1M 915668 AGCACTCTG----TACTTCC-TAAT-GTACTTACCACTTAATGATGTGCA 915711 i ---- i - v - i i i v v vi i -ii L2c_3end#LINE 292 AGCACCCTGTCTATACTCCCATTATAGCACTTATCATTAACTTGTAT-TG 340 chr6ptel1M 915712 TAGTTACTTGATGGATATGTAGCCTATTCCCT--ACTAGAC--TGATCCT 915757 i iii v --- i? - i i ii -- -- v ii L2c_3end#LINE 341 TAATTGTCTGTT---TACNT-GTCTGTCTCCTCCACTAGACTGTGAGCTC 386 chr6ptel1M 915758 CTTGAGAGCAAG 915769 i i L2c_3end#LINE 387 CTTGAGGGCAGG 398 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.88 CpG sites = 82, Kimura (unadjusted) = 44.20 Transitions / transversions = 3.04 (82/27) Gap_init rate = 0.08 (31 / 365), avg. gap size = 1.94 (60 / 31) 240 30.53 7.02 5.17 chr6ptel1M 916007 916120 (83880) MIRb#SINE/MIR 21 136 (132) m_b295s601i58 12300 chr6ptel1M 916007 GTAGTAAGAGCACAAAAGAGCTC----ATCAGA-AGACCTAGATTCATAT 916051 i v ---- i i----i - i i iv MIRb#SINE/MIR 21 GTGGAAAGAGCAC----GGGCTTTGGAGTCAGACAGACCTGGGTTCGAAT 66 chr6ptel1M 916052 TCTCGATCAACCATTCAATATCTGTGCATGATGGTAAGTGGATT-CTAAA 916100 i iv v vi i i v v -- ivv ii iiii - v MIRb#SINE/MIR 67 CCCGGCTCTGCCACTTACTAGCTGTG--TGACCTTGGGCAAGTTACTTAA 114 chr6ptel1M 916101 --TTTTTGAGGCTCATTTTCCT 916120 -- i i v v MIRb#SINE/MIR 115 CCTCTCTGAGCCTCAGTTTCCT 136 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.71 CpG sites = 21, Kimura (unadjusted) = 40.94 Transitions / transversions = 1.75 (21/12) Gap_init rate = 0.09 (10 / 113), avg. gap size = 1.40 (14 / 10) 468 33.76 3.82 0.00 chr6ptel1M 916137 916293 (83707) L3#LINE/CR1 2423 2585 (1514) m_b295s601i59 12301 chr6ptel1M 916137 TCTTATTTTACTTCTTTTTTTCCTTTCAAGAAGAGTGATCTGTAGGTTGG 916186 i i iv i ii v i i vi ii L3#LINE/CR1 2423 TCCTATTTTGCTTCCGTCTTCTCTATCAAGGAGAATGATCTTCAGACTGG 2472 chr6ptel1M 916187 AA-----AAAATAAAAATAGCTCCGAGGGAACTGACACTCAAGATAAATA 916231 ----- i i v v i vv i vi i ii i L3#LINE/CR1 2473 AAAGGGTAGAACAAACATCGTTAAGAGGGAATTGAAGCCCAAGATAGGTG 2522 chr6ptel1M 916232 AGAAAAAATTAAAATAATATCTAGTTTCCTT-GATGAACTGATGTTTCCT 916280 i i v v i v ii i iiv i -i ii v v i v L3#LINE/CR1 2523 AGGAGATAGTAAGAGAGCACCTAGCCGCTTTAAATGAGTTCAAGTCTCCA 2572 chr6ptel1M 916281 ACTCCATATGAAT 916293 ivi v i L3#LINE/CR1 2573 GGCCCAGACGAAT 2585 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.12 CpG sites = 36, Kimura (unadjusted) = 47.94 Transitions / transversions = 2.12 (36/17) Gap_init rate = 0.01 (2 / 156), avg. gap size = 3.00 (6 / 2) 272 32.74 2.26 4.63 chr6ptel1M 916296 916516 (83484) Plat_L3#LINE/CR1 2061 2276 (1297) m_b295s551i2 12302 chr6ptel1M 916296 CATCCTTGGGTACTAAAGGAATCTGCAGATCTAATTCCTTAATCACTA-T 916344 v v iv i v v v vv ii -i Plat_L3#LINE/ 2061 CATCCTAGGGTACTTAAGGAATTGGCGGATGTTATTGCAGAGCCACTAGC 2110 chr6ptel1M 916345 AATTAGATTTGAAAGCTCCCTCAGAATCAAAGAGATGATATAGAATTAGA 916394 v vv i i v vv i ivii ii vvivv i i Plat_L3#LINE/ 2111 TATTATTTTTGAGAACTCGCGGAGGACGGGAGAAGTCCCTGAGGATTGGA 2160 chr6ptel1M 916395 AAAGGCCA---GCTATCCTGATTTATAAAAAAAAGGGAAAAAAATAGACG 916441 v --- i i v iv i v -- ---i Plat_L3#LINE/ 2161 AAAGGGCAAACGTTGTGCCCATCTTTAAAA--AAGGGAAAAA---GGACG 2205 chr6ptel1M 916442 AGAATCTTCA-AAATGTAGGCTGGTGAGTTTGACTTTGTTTCCTAAGGGA 916490 --- i i vi- v ii i i v i i v i v v -- Plat_L3#LINE/ 2206 ---ACCCTGGTAATTACAGACCGGTCAGCTTAACATCGATACCT--GGGA 2250 chr6ptel1M 916491 GGAAATTAGAATGTATTATTAAAAAA 916516 i v i iiv i i v Plat_L3#LINE/ 2251 AGATACTAGAACAAATCATCAAACAA 2276 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.61 CpG sites = 37, Kimura (unadjusted) = 43.93 Transitions / transversions = 1.16 (37/32) Gap_init rate = 0.06 (13 / 220), avg. gap size = 1.15 (15 / 13) 1069 27.12 10.51 1.86 chr6ptel1M 916534 916980 (83020) L3#LINE/CR1 2820 3304 (795) m_b295s601i60 12301 chr6ptel1M 916534 TAGAAATCACAGTGATGATCAC--AGAGTCAGCATGGCAACATCAAGAAG 916581 vviv i i --i i vvv ii v L3#LINE/CR1 2820 TAGAAAAGGAAGCGGTGATCACTAGGAGCCAGCATGGGTTCACTAAGAAC 2869 chr6ptel1M 916582 ATGTTCTGCCAAACTAATATTGTCTTTCCTTTTTGACAAGATTTTTAC-C 916630 v iv iv ii - i i i i i vi v- L3#LINE/CR1 2870 AAGTCATGCCAAACTAACCTCAT-TTCCTTTTTTGATAGGGTTACTAGAC 2918 chr6ptel1M 916631 TGTCAGATCAGGGGAATGAATACTGTAGCTATAATTTATTTATATT-AAG 916679 vi ---- i vi ? i v i iv -v L3#LINE/CR1 2919 TGGTAGATCAGGGGAATG----CCGTAGACANAGTGTATCTGGATTTCAG 2964 chr6ptel1M 916680 CCATG--TTTGATAAAGTCTCTTATGG---------GGA--ATATGGATG 916716 v v -- i i i--------- -- v vi L3#LINE/CR1 2965 CAAGGCATTTGACAAAGTCTCTCATGATATCCTTGTGGACAAGATGGAGA 3014 chr6ptel1M 916717 GATA-GGGATTGATAATAGTAAAATGAGATGGATTGAGAACTAGATGAAT 916765 i - v v i v i v i viv i i v i L3#LINE/CR1 3015 AATATGGGCTGGATGATAGTACAGTTAGGTGGATTCGTAGCTGGTTGAAC 3064 chr6ptel1M 916766 GACT-TGCCCTAAAAGGTAGTTATT------CC--TACTAACATGGATCA 916806 - i - iv v ------i -- iii v vvi L3#LINE/CR1 3065 GACTATACCC-AAAAGGTGTTGATTAATGGATCGATGTCAACCTGGAGGG 3113 chr6ptel1M 916807 ATGCCTTTAGGTGAACGTTCT-CAGGA-TCTGTGCT-GGTCGGGTGTAGC 916853 v i i - i- v i- i- v - i vv viv i L3#LINE/CR1 3114 AGGTCTCTAG-TGG-CGTGCCACAGGGCTCTGTCCTTGGCCCTGTCCTGT 3161 chr6ptel1M 916854 TTAATCATATTTACCAGTGACCTGGATAAAGACA--GATGGTTTGCTTAT 916901 i - v i i i i -- v iv L3#LINE/CR1 3162 TCAA-CATTTTTATCAATGACTTGGATGAAGACATAGAAGGCATGCTTAT 3210 chr6ptel1M 916902 AATATTTGCTGATGACCCATCACTGAGAGAGATAGTTAATG-GCTGTGTG 916950 v v v v vvi i i i i- ? vi L3#LINE/CR1 3211 CAAATTTGCAGATGACACAAAGCTGGGAGGGATAGCTAATACGNTGGATG 3260 chr6ptel1M 916951 TCAGAA--------------GATTTTGACAAGCTAGAATGGTGG 916980 v -------------- i i i i i i L3#LINE/CR1 3261 ACAGAATCAAGATTCAAAANGATCTCGACAGGCTGGAACGATGG 3304 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.55 CpG sites = 68, Kimura (unadjusted) = 34.67 Transitions / transversions = 1.33 (68/51) Gap_init rate = 0.06 (25 / 446), avg. gap size = 2.24 (56 / 25) 337 32.41 0.91 1.83 chr6ptel1M 917478 917587 (82413) C MIRc#SINE/MIR (75) 193 85 m_b295s601i61 12303 chr6ptel1M 917478 TCCTTGGCAAGAACCTTATAAAATAATCAGAGCAAGTGTTGTTACTATCA 917527 ii- v i i i ii iv i i i i iivi C MIRc#SINE/MIR 193 TCCTCA-CAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCA 145 chr6ptel1M 917528 TTTTATTGAT-AAGAAACTGGAGTCTCAGAAAACTGATGCTTCTTACCCA 917576 iv - i - v i iv v v ivv i C MIRc#SINE/MIR 144 TTTTACAGATGAGGAAACT-GAGGCTCAGAGAGGTTAAGTGACTTGCCCA 96 chr6ptel1M 917577 GAGTCTTACAG 917587 ii vi C MIRc#SINE/MIR 95 AGGTCACACAG 85 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.21 CpG sites = 24, Kimura (unadjusted) = 45.21 Transitions / transversions = 2.18 (24/11) Gap_init rate = 0.03 (3 / 109), avg. gap size = 1.00 (3 / 3) 198 22.81 4.17 8.70 chr6ptel1M 918216 918311 (81689) C MIR#SINE/MIR (46) 216 125 m_b295s601i62 12304 chr6ptel1M 918216 TTCTAGGCTGCTTTA-AGGTAT--AC-AATATATTTCTCAACAACAGCCC 918261 i - - v -- -v v v i - i C MIR#SINE/MIR 216 TTCTAAGC-GCTTTACATGTATTAACTCATTTAATCCTCA-CAACAACCC 169 chr6ptel1M 918262 CCTGAGGCAGGTAGATCAGGCACTAGCCTCCCTGTCTTTCAGATGAGAAA 918311 iv i --- ---i i viv ii i v i C MIR#SINE/MIR 168 TATGAGGTAGGTA---C---TATTATTATCCCCATTTTACAGATGAGGAA 125 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.62 CpG sites = 12, Kimura (unadjusted) = 27.62 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.12 (11 / 95), avg. gap size = 1.09 (12 / 11) 248 27.70 0.00 1.54 chr6ptel1M 918246 918311 (81689) C MIRc#SINE/MIR (75) 193 129 m_b295s601i63 12304 chr6ptel1M 918246 TTCTCAACAACAGCCCCCTGAGGCAGGTAGATCAGGCACTAGCCTCCCTG 918295 i - i iv i i iv i i viv ii C MIRc#SINE/MIR 193 TCCTCA-CAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCA 145 chr6ptel1M 918296 TCTTTCAGATGAGAAA 918311 i v i C MIRc#SINE/MIR 144 TTTTACAGATGAGGAA 129 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.58 CpG sites = 13, Kimura (unadjusted) = 36.58 Transitions / transversions = 2.60 (13/5) Gap_init rate = 0.02 (1 / 65), avg. gap size = 1.00 (1 / 1) 391 25.78 0.00 10.20 chr6ptel1M 921321 921428 (78572) C MIR3#SINE/MIR (3) 205 108 m_b295s601i64 12305 chr6ptel1M 921321 TCAAAGAATCATAAAATGTCAGTGTCGGAAAGGACCTCGGAGAGCGCCTG 921370 v i v ii i ii v ii i C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTA 156 chr6ptel1M 921371 GTTCAGCATTTACATCCCTTGCTATTTTACAAGGGAGGAACTTAAAGCCT 921420 i -------- i i --i iiv vi i i i C MIR3#SINE/MIR 155 GTCCA--------ACCCCCT--CATTTTACAGATGAGGAAACTGAGGCCC 116 chr6ptel1M 921421 GGAGAGGT 921428 i C MIR3#SINE/MIR 115 AGAGAGGT 108 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.42 CpG sites = 20, Kimura (unadjusted) = 33.42 Transitions / transversions = 4.00 (20/5) Gap_init rate = 0.09 (10 / 107), avg. gap size = 1.00 (10 / 10) 187 34.56 4.59 1.79 chr6ptel1M 921392 921500 (78500) C MIRb#SINE/MIR (118) 150 39 m_b295s601i65 12305 chr6ptel1M 921392 CTATTTTACAAGGGAGGAACTTAAAGCCTGGAGAGGTC-AGTATAGTGG- 921439 i iiv vi i i iii i- - v v - C MIRb#SINE/MIR 150 CCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTA-ACTTGC 102 chr6ptel1M 921440 -AAAGATCATTGGGCTGAGAGATAG-AGAACCTGGCTTTCAGCTCAGCAT 921487 -v i ivvi iiv ii i - i v v iv i i -i C MIRb#SINE/MIR 101 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAG-GT 53 chr6ptel1M 921488 CTG-CTGCTTACAA 921500 - vi v C MIRb#SINE/MIR 52 CTGTCTGACTCCAA 39 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 47.25 CpG sites = 24, Kimura (unadjusted) = 49.17 Transitions / transversions = 1.85 (24/13) Gap_init rate = 0.06 (7 / 108), avg. gap size = 1.00 (7 / 7) 487 27.31 6.30 6.30 chr6ptel1M 921430 921683 (78317) MIR#SINE/MIR 8 261 (1) m_b295s601i66 12306 chr6ptel1M 921430 AGTATAGTGGA-AAGATCATTGGGCTG-AGAGATAGAGAACCTGGCTTTC 921477 i v- v i- v-i vi vvi v iv MIR#SINE/MIR 8 AGCATAGTGGTTAAGAGCAC-GGGCTCTGGAGCCAGACTGCCTGGGTTCG 56 chr6ptel1M 921478 AG-CTCAGCATCTGCTGCTTACAAGCTGTATGACCTCAGGAGAATCCTTT 921526 i- i i - ii v i ii vi i ivi MIR#SINE/MIR 57 AATCCCGGC-TCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTT 105 chr6ptel1M 921527 CTCCTCTCATTTCCTCTCATTTTCCTCATTTGTAAAATACAGTTACTCCT 921576 vv - v v - v i ivi v v vv MIR#SINE/MIR 106 AACCTCTC-TGTGC-CTCAGTTTCCTCATCTGTAAAATGGGGATAATAAT 153 chr6ptel1M 921577 GGCCCTACTTACTTCGTGGGGTTGTT----GAATCAACTGA---AATATC 921619 i --- i i i i ---- i i v --- - MIR#SINE/MIR 154 AG---TACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATA-C 199 chr6ptel1M 921620 AGGTGAAGATTCTCGGTGAAAATAAAGCTACTATTACATGAGTA-----T 921664 v i ----- v v i i iv -- ivi - ----- MIR#SINE/MIR 200 ATGTAAAG-----CGCTTAGAACAGTGC--CTGGCACAT-AGTAAGCGCT 241 chr6ptel1M 921665 AAACAATTGTAAGC-ATTAT 921683 v i v v - MIR#SINE/MIR 242 CAATAAATGTTAGCTATTAT 261 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.59 CpG sites = 35, Kimura (unadjusted) = 34.51 Transitions / transversions = 1.17 (35/30) Gap_init rate = 0.09 (23 / 253), avg. gap size = 1.39 (32 / 23) 640 28.41 5.83 2.16 chr6ptel1M 921431 921653 (78347) MIRc#SINE/MIR 13 243 (25) m_b295s601i67 12306 chr6ptel1M 921431 GTATAGTGGAAAGATCATTGGGCTGAGAGATAGAGA-ACCTGGCTTTCAG 921479 ii v i i vi vi ii - v iv MIRc#SINE/MIR 13 GTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAG 62 chr6ptel1M 921480 -CTCAGCATCTGCTGCTTACAAGCTGTATGACCTCAGGAGAATCCTTTCT 921528 - i i - ii v i ii vi i vi vv MIRc#SINE/MIR 63 TCCCGGC-TCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAA 111 chr6ptel1M 921529 CCTCTCATTTCCTCTCATTTTCCTCATTTGTAAAATACAGTTACT----C 921574 -- vvvi v i ivi v v ---- MIRc#SINE/MIR 112 CCTCTC--TGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAC 159 chr6ptel1M 921575 CTGGCCCTACTTACTTCGTGGGGTTGTT----GAATCAACTGAAATA--T 921618 - i i i iii ---- i v i --v MIRc#SINE/MIR 160 CT-GCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATG 208 chr6ptel1M 921619 CAGGTGAAGATTCTCGGTGAAA-ATAAAGCTACTAT 921653 i v iiiv iv i v-i - i MIRc#SINE/MIR 209 TATGTGAAAGCGCTTTGTAAACTGTAAAG-TGCTAT 243 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.79 CpG sites = 39, Kimura (unadjusted) = 37.04 Transitions / transversions = 1.70 (39/23) Gap_init rate = 0.05 (11 / 222), avg. gap size = 1.64 (18 / 11) 217 28.58 13.23 1.90 chr6ptel1M 921676 921864 (78136) L2d_3end#LINE/L2 295 504 (12) m_b295s601i68 12307 chr6ptel1M 921676 AGCA-TTATAG---GAAACACG-AATTT-GTTTTTA-TTATATAATATAT 921718 - --- v v - - ivi - v i v L2d_3end#LINE 295 AGCACTTATAGTCTGTACCACGCAATTTAGCACTTAATTATATACTGTCT 344 chr6ptel1M 921719 TATAT-ATAATATA--TATTTTATTATATAATAAT----TATTAACAA-T 921760 i -i vv v -- i i -i i iv i ---- v ivv - L2d_3end#LINE 345 TGTATTGTTCTCTAATTGTTTCAT-GTGTGTTAGTCTTGTCTCCCCAACT 393 chr6ptel1M 921761 AGAATATAGACTTCTTGAGAGCAGAGACTATTTC--ATTTTGTCCATATT 921808 v i ii i i i i v -- vi ? ii- ? i L2d_3end#LINE 394 AGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACTNTTT-TNTC 442 chr6ptel1M 921809 GCTTCCTCCTGCATTCCCACCACAA---TGGGCA-AT----GGTGCTTAA 921850 i i iv v i-- i v i--- i - ---- i i L2d_3end#LINE 443 GTTCCCCACAGCG--CCTAGCACAGTGCTGAGCACATAGTAGGCGCTCAA 490 chr6ptel1M 921851 TAAATGTCTGTTGA 921864 iii L2d_3end#LINE 491 TAAATACTTGTTGA 504 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.49 CpG sites = 35, Kimura (unadjusted) = 38.26 Transitions / transversions = 1.94 (35/18) Gap_init rate = 0.09 (17 / 188), avg. gap size = 1.71 (29 / 17) 298 28.66 11.38 3.91 chr6ptel1M 921700 921866 (78134) L2a_3end#LINE/L2 331 509 (8) m_b295s601i69 12307 chr6ptel1M 921700 TTTTTATTATATAATATATTATATATAATATATATTTTATTATATAATAA 921749 v i ii v i i i vv iv vv i v v iv L2a_3end#LINE 331 TTATCACCATCTGACATACTATATATTTTACTTATTTATTTGTTTATTGT 380 chr6ptel1M 921750 TTATT----AACAATAGAATATAGACTTCTTGAGAGCAGAGACTATTTCA 921795 i i i----vv v i ii i v i i ------- L2a_3end#LINE 381 CTGTCTCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGAC------- 423 chr6ptel1M 921796 TTTTGTCCATATTGCTTCCTCCTGCATTCCCA---CC----ACAATG--- 921835 ii v i iv v i i --- ---- i --- L2a_3end#LINE 424 TTTTGTCTGTTTTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCT 473 chr6ptel1M 921836 GGCA-AT----GGTGCTTAATAAATGTCTGTTGAAT 921866 - ---- i i i i L2a_3end#LINE 474 GGCACATAGTAGGCGCTCAATAAATATTTGTTGAAT 509 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.55 CpG sites = 29, Kimura (unadjusted) = 37.60 Transitions / transversions = 1.71 (29/17) Gap_init rate = 0.08 (13 / 166), avg. gap size = 2.00 (26 / 13) 216 32.35 2.94 0.00 chr6ptel1M 923024 923091 (76909) C MIRc#SINE/MIR (68) 200 131 m_b295s601i70 12308 chr6ptel1M 923024 CATTT--TCCTTATGATAACCCTGGGAAGGAAGAAGAGCAAGGGGTATAA 923071 -- i ii i v i v i v i i viv v C MIRc#SINE/MIR 200 CATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTA 151 chr6ptel1M 923072 TCACCACTCCATAGACAAGG 923091 v i ii i ii C MIRc#SINE/MIR 150 TCCCCATTTTACAGATGAGG 131 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.04 CpG sites = 15, Kimura (unadjusted) = 45.04 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.01 (1 / 67), avg. gap size = 2.00 (2 / 1) 12 30.20 0.00 0.00 chr6ptel1M 924779 924823 (75177) (AATTTAA)n#Simple_repeat 1 45 (0) m_b295s252i14 12309 chr6ptel1M 924779 AAGTTAAAATAAAGAATTATCAAGTTAAAATAAAAATTTTAAAAT 924823 v vv i vvv v vv v (AATTTAA)n#Si 1 AATTTAAAATTTAAAATTTAAAATTTAAAATTTAAAATTTAAAAT 45 Matrix = Unknown Transitions / transversions = 0.10 (1/10) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 26 0.00 0.00 0.00 chr6ptel1M 924972 924996 (75004) (TTGTTT)n#Simple_repeat 1 25 (0) c_b295s251i2 12310 chr6ptel1M 924972 TTGTTTTTGTTTTTGTTTTTGTTTT 924996 (TTGTTT)n#Sim 1 TTGTTTTTGTTTTTGTTTTTGTTTT 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 474 25.91 5.76 2.80 chr6ptel1M 925173 925311 (74689) MIRc#SINE/MIR 9 151 (117) m_b296s601i0 12311 chr6ptel1M 925173 TGTGGTGGAGCATGGAAGGTGC--TGAACCTCTAGGGTCAAGAAAACCCG 925220 v -- i v -- i i --i i i i i MIRc#SINE/MIR 9 TGTGGTGCAG--TGGAAAGAGCACTGGACTT--GGAGTCAGGAAGACCTG 54 chr6ptel1M 925221 AGTTCAAGTTT-GGATCAGATGCTTAATGTTTGTGTGATTTTAG-TAAAT 925268 i i ii- v v vii v ivi ii i -i i MIRc#SINE/MIR 55 GGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGT 104 chr6ptel1M 925269 CACCTA--TTATCTG--CCTCAGTTTCCTCATCTGTAAAACAAGAAT 925311 i --i v -- iii i MIRc#SINE/MIR 105 CACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGAT 151 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.68 CpG sites = 27, Kimura (unadjusted) = 33.89 Transitions / transversions = 3.38 (27/8) Gap_init rate = 0.07 (9 / 138), avg. gap size = 1.33 (12 / 9) 244 26.25 1.59 3.23 chr6ptel1M 926405 926467 (73533) MIR3#SINE/MIR 115 176 (32) m_b296s601i1 12312 chr6ptel1M 926405 TGAACTTCAGTTTCTTCATTTG-AACATTTTAAGGGGTTGGAATAGATGG 926453 ii i i i - v v-- i v i MIR3#SINE/MIR 115 TGGGCCTCAGTTTCCTCATCTGTAAAATG--AGGGGGTTGGACTAGATGA 162 chr6ptel1M 926454 CTTCTGGAGTCCTT 926467 ii iii i MIR3#SINE/MIR 163 TCTCTAAGGTCCCT 176 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.85 CpG sites = 13, Kimura (unadjusted) = 34.85 Transitions / transversions = 4.33 (13/3) Gap_init rate = 0.05 (3 / 62), avg. gap size = 1.00 (3 / 3) 245 28.35 11.22 2.83 chr6ptel1M 926648 926745 (73255) L2c_3end#LINE/L2 363 468 (10) m_b296s601i2 12313 chr6ptel1M 926648 TCTCTTACA--AAACAG-AAGCTTCTCGAAGTC--------TGTTTCATT 926686 i v -- i v -i i i i v -------- i i L2c_3end#LINE 363 TCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATT 412 chr6ptel1M 926687 CATATTTTTGCACCCCTGATTCCCTGACACATAATAGTTACTTAGTAAAT 926736 --i i i i- viv i i vii i i L2c_3end#LINE 413 CAT--CTTTGTATCCCC-AGCGCCTGGCACATAGTAGGCGCTCAATAAAT 459 chr6ptel1M 926737 GCCTGTTGA 926745 ii L2c_3end#LINE 460 GTTTGTTGA 468 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.67 CpG sites = 21, Kimura (unadjusted) = 38.56 Transitions / transversions = 3.50 (21/6) Gap_init rate = 0.06 (6 / 97), avg. gap size = 2.33 (14 / 6) 212 21.74 2.17 0.00 chr6ptel1M 926710 926755 (73245) L2d_3end#LINE/L2 468 514 (2) m_b296s601i3 12313 chr6ptel1M 926710 CTGA-CACATAATAGTTACTTAGTAAATGCCTGTTGATTTATTAATT 926755 - i vii i i i i v i L2d_3end#LINE 468 CTGAGCACATAGTAGGCGCTCAATAAATACTTGTTGATTGATTGATT 514 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 23.65 CpG sites = 8, Kimura (unadjusted) = 27.10 Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1) 578 25.68 0.64 3.27 chr6ptel1M 927664 927820 (72180) MIR1_Amn#SINE/MIR 6 158 (72) m_b296s601i4 12314 chr6ptel1M 927664 AGGCAGATGGATAGCTTGTTGGATAGAACACTAGACCAGAAGTTGGGTAA 927713 - -- i ii iv i i ii i v i - i MIR1_Amn#SINE 6 AGGCAG-TG--TGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGG-AG 51 chr6ptel1M 927714 ATCAGAGTTCAAATCCTGCCTCAGATACTTATTAACTGCGTGATCCTGGG 927763 i v i ? ? i v v vi ?iii?i ? i i MIR1_Amn#SINE 52 ACCTGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGG 101 chr6ptel1M 927764 AAAGTCA-TTTACCCTTGTGCAGCCTCGATTTGCCCATCCATAAAAAGGG 927812 v - ? ii v ?- ii v i ii v MIR1_Amn#SINE 102 CAAGTCACTTNACCTCTCTGN-GCCTCAGTTTCCTCATCTGTAAAATGGG 150 chr6ptel1M 927813 GATAATAA 927820 i MIR1_Amn#SINE 151 GATAATGA 158 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.07 CpG sites = 29, Kimura (unadjusted) = 35.36 Transitions / transversions = 2.90 (29/10) Gap_init rate = 0.04 (6 / 156), avg. gap size = 1.00 (6 / 6) 623 24.39 13.61 0.52 chr6ptel1M 927683 927851 (72149) MIRc#SINE/MIR 19 209 (59) m_b296s601i5 12314 chr6ptel1M 927683 TGGATAGAACACTAGACCAGAAGTTGGGTAAATCAGAGTTCAAATCCTGC 927732 v i i iv i ii v i i v i i i i v MIRc#SINE/MIR 19 TGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGG 68 chr6ptel1M 927733 CTCAGATACTTATTAACTGCGTGATCCTGGGAAAGTCATTTACCCT-TGT 927781 v vi i i i i i v i v - v MIRc#SINE/MIR 69 CTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCT 118 chr6ptel1M 927782 GCAGCCTCGATTTGCCCATCCATAAAAAGGGGATAATA------------ 927819 - ii v i ii v ------------ MIRc#SINE/MIR 119 G-AGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTG 167 chr6ptel1M 927820 ----------AGGGTAGTTGTGAGGACAAAATGAGATCATAT 927851 ---------- v iv v i MIRc#SINE/MIR 168 CCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGT 209 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.61 CpG sites = 26, Kimura (unadjusted) = 30.36 Transitions / transversions = 1.73 (26/15) Gap_init rate = 0.02 (4 / 168), avg. gap size = 6.00 (24 / 4) 202 32.04 0.00 5.56 chr6ptel1M 927980 928055 (71945) L3#LINE/CR1 3925 3996 (103) m_b296s601i6 12315 chr6ptel1M 927980 AAAATGGAGTGAGTTGCTTGGGAAGGTAGGAAGTAAGGATTTCATCCCTG 928029 i i i i v ?i ---- i vviii i v L3#LINE/CR1 3925 AAAATGGAATGGGCTGCCTCGNGAGGT----AGTGAGCTCCCCGTCACTG 3970 chr6ptel1M 928030 GAGACCTTCTTGTGGAAGCTGGTTGA 928055 iiv vv ii i v L3#LINE/CR1 3971 GAGGTGTTCAAGCAGAGGCTGGATGA 3996 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.04 CpG sites = 15, Kimura (unadjusted) = 44.69 Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.05 (4 / 75), avg. gap size = 1.00 (4 / 4) 208 30.42 4.29 1.39 chr6ptel1M 928204 928273 (71727) MIR#SINE/MIR 35 106 (156) m_b296s601i7 12316 chr6ptel1M 928204 GAAGCTAGA--GCTTAGCCTGGAGTTCCAACTCTGCCCAGTT-CTAGCTT 928250 i i -- i i vi v i i ii - v - v MIR#SINE/MIR 35 GGAGCCAGACTGCCTGGGTTCGAATCCCGGCTCTG-CCACTTACTAGCTG 83 chr6ptel1M 928251 AGTTATTTTGGGCACATCATTTA 928273 v v ii vi i i MIR#SINE/MIR 84 TGTGACCTTGGGCAAGTTACTTA 106 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.48 CpG sites = 14, Kimura (unadjusted) = 41.06 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.04 (3 / 69), avg. gap size = 1.33 (4 / 3) 83 34.24 4.89 0.82 chr6ptel1M 928810 929248 (70752) (AGAG)n#Simple_repeat 1 458 (31) m_b296s252i1 12317 chr6ptel1M 928810 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA-AGAGA-AGAGA-AGAGA- 928855 - - - - (AGAG)n#Simpl 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr6ptel1M 928856 AGAGA-AGAGA-AGAGA-AGAGA-AGAGA-AGAGA-AGAGA-AGAGA-AG 928897 - - - - - - - - (AGAG)n#Simpl 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 100 chr6ptel1M 928898 GGA-AGAGA-AGAGAGACCCAGAGAGACA-AGAGAGTGAGGGAGAGATGG 928944 i - - vvv v - v i vi (AGAG)n#Simpl 101 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 150 chr6ptel1M 928945 AGGGA-AGA-AGGAAGAAAGGGAGGGAAGGAGAGAGGGATAAATGAAAGA 928992 i - - ii i i i ii i v i - i (AGAG)n#Simpl 151 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA-GAGAGA 199 chr6ptel1M 928993 AAGGAAGGAAGA-AGGGAGGAAGGAAGGAAGCAAAG-GAGGGATAAAAAA 929040 i ii ii - i ii ii ii - i - i v i i i (AGAG)n#Simpl 200 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG-AGAGAGAGAGAGAGAGAG 248 chr6ptel1M 929041 AGGGAAGGAAAGAGGGAG-GAAGGAAGGAAAAAGGAAGCAAGGAAGGAAG 929089 i ii i i - ii ii i i ii vi ii ii (AGAG)n#Simpl 249 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 298 chr6ptel1M 929090 GGAAAAAGGAAGCAAGGAAGGAAGGAAAAAAGGAAGGGAGGGAGGGAGAA 929139 i i i ii vi ii ii ii i i ii i i i i (AGAG)n#Simpl 299 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 348 chr6ptel1M 929140 AGAGGAAGGGAGGGAGGAAGGAAGAAAG-GATGGA-AGGAAGGAAAAGAG 929187 ii i i ii ii i - vi - ii ii i (AGAG)n#Simpl 349 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 398 chr6ptel1M 929188 -GATGGGAGGAAGACAGACACAGACATATACAGAGAGAGAGATAAAGATA 929236 - - i ii v v v v v v v v i v (AGAG)n#Simpl 399 AGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 447 chr6ptel1M 929237 GCTAGAGATGAT 929248 vv - v (AGAG)n#Simpl 448 GAGAGAGA-GAG 458 Matrix = Unknown Transitions / transversions = 3.83 (88/23) Gap_init rate = 0.06 (27 / 438), avg. gap size = 1.00 (27 / 27) 31 4.93 2.38 0.00 chr6ptel1M 929249 929290 (70710) (AGAGACAG)n#Simple_repeat 1 43 (0) c_b296s251i1 12318 chr6ptel1M 929249 AGAGATAGAGAGACAGAGAGACACAGAGA-AGAGAGACAGAGA 929290 i v - (AGAGACAG)n#S 1 AGAGACAGAGAGACAGAGAGACAGAGAGACAGAGAGACAGAGA 43 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.02 (1 / 41), avg. gap size = 1.00 (1 / 1) 83 34.24 4.89 0.82 chr6ptel1M 929291 929320 (70680) (AGAG)n#Simple_repeat 459 488 (1) m_b296s252i1 12319 chr6ptel1M 929291 CAGAGGCAGACAGATGGACAAAGGTAGAGA 929320 v iv v vi v i iv (AGAG)n#Simpl 459 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 488 Matrix = Unknown Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 485 32.60 9.69 1.42 chr6ptel1M 929734 929929 (70071) C MIR#SINE/MIR (0) 262 51 m_b296s601i8 12320 chr6ptel1M 929734 AATGAGAGCGAGCATTGATGGAGCACGCTAATATTTGCCAAGCACCTT-- 929781 i v v i v v i -i v v i iv -- C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGC-TTACTATGTGCCAGGCACTGTTC 214 chr6ptel1M 929782 ---GCACCTTGCAT------------TCAATCCTCATAATAACTCT-TGG 929815 --- i i i ------------ i i i i - i C MIR#SINE/MIR 213 TAAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGA 164 chr6ptel1M 929816 GGGAGGGGTTCTGCTATCATTCTCGTATCATGGATGATGAAATTGAGACA 929865 v -- v ii i i i i v i ii v i i C MIR#SINE/MIR 163 GGTA--GGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCA 116 chr6ptel1M 929866 TAGA-AGGTCAAATGGCTTGCTTTGATTTGTGAAGTTCATAAACATCAGA 929914 i - i i ii iiviiv iiiiv i vi iiiv C MIR#SINE/MIR 115 CAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGA 66 chr6ptel1M 929915 GTCTGGATTTGAATC 929929 i v i i C MIR#SINE/MIR 65 GCCGGGATTCGAACC 51 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.32 CpG sites = 46, Kimura (unadjusted) = 46.44 Transitions / transversions = 2.71 (46/17) Gap_init rate = 0.04 (8 / 195), avg. gap size = 2.75 (22 / 8) 198 13.16 5.00 5.00 chr6ptel1M 930333 930372 (69628) L2c_3end#LINE/L2 380 419 (59) m_b296s601i9 12321 chr6ptel1M 930333 TAAGCTCCTTGAAGGCAGGAAC--TGTCTTGCTTTCATATTT 930372 i i i -- i-- v L2c_3end#LINE 380 TGAGCTCCTTGAGGGCAGGGACCGTGTCTTA--TTCATCTTT 419 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 14.87 CpG sites = 4, Kimura (unadjusted) = 14.87 Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.08 (3 / 39), avg. gap size = 1.33 (4 / 3) 305 27.33 2.00 8.51 chr6ptel1M 930468 930567 (69433) C L2c_3end#LINE/L2 (18) 460 367 m_b296s601i10 12322 chr6ptel1M 930468 CATTT-TAAAATATCAACTATGTGTCAAGCGTTGTGCTGGAAGTACAAAT 930516 - vi iiii v i i ----- iii - C L2c_3end#LINE 460 CATTTATTGAGCGCCTACTATGTGCCAGGCG-----CTGGGGATACAAA- 417 chr6ptel1M 930517 GATAAA-AAGCAGTACAGTGCCTGCCTTCAAGAAACTTACAGCCTACCAG 930565 i - --ii i v i i i i i vii C L2c_3end#LINE 416 GATGAATAAG--ACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAGTGG 369 chr6ptel1M 930566 AG 930567 C L2c_3end#LINE 368 AG 367 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.96 CpG sites = 21, Kimura (unadjusted) = 36.93 Transitions / transversions = 5.25 (21/4) Gap_init rate = 0.10 (10 / 99), avg. gap size = 1.00 (10 / 10) 221 29.24 6.33 9.09 chr6ptel1M 930483 930640 (69360) C L2d2_3end#LINE/L2 (34) 521 368 m_b296s601i12 12322 chr6ptel1M 930483 ACTATGTGTCAAGCGTTGTGCTGGAAG-TACAAATGATAAAAAGCAGTAC 930531 i iv i ii i iv - iiiiiv v v i C L2d2_3end#LIN 521 ACTGTGTGCAAGGCACTGTGCTAGGCGCTGTGGGGGATACAAAGAAGTAT 472 chr6ptel1M 930532 A-------GTGCCTGCCTTCAAGAAACTTACAGCCTACCAGAGTACTGAA 930574 ------- v i i i ii ----- -- ii C L2d2_3end#LIN 471 AAGACATGGTCCCTGCCCTCAAGGAGCTTACAATCT-----AGT--TGGG 429 chr6ptel1M 930575 G-GATAAGACTATATACAAGCACAGAAAGTAGGAAAGAA-AGTAGAAGGT 930622 - i - v -- iiii --v v - i v i C L2d2_3end#LIN 428 GAGACAAGAC-ATAAACA--CGTGAAAAGT--TAAATAACAATACAAGAT 384 chr6ptel1M 930623 TATTGGATAAAGGATCAA 930640 -- ii vi v C L2d2_3end#LIN 383 --TTAAATAACAGTTCAA 368 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.98 CpG sites = 30, Kimura (unadjusted) = 39.22 Transitions / transversions = 2.50 (30/12) Gap_init rate = 0.11 (18 / 157), avg. gap size = 1.33 (24 / 18) 239 27.69 9.17 7.21 chr6ptel1M 930483 930591 (69409) C L2d_3end#LINE/L2 (36) 480 370 m_b296s601i11 12322 chr6ptel1M 930483 ACTATGTGTCAAGCGTTGTGCTGGAAGT----ACAAATGATAAAA-AGCA 930527 iiv ii i iv i----ivi i ? - i C L2d_3end#LINE 480 ACTATGTGCTCAGCACTGTGCTAGGCGCTGTGGGGAACGANAAAANAGTA 431 chr6ptel1M 930528 ----GTACAGTGCCTGCCTTCAAGAAACTTACAGCCTACCAGAGTACTGA 930573 ----ii ii v i i i ii ----- -- i C L2d_3end#LINE 430 TAAGACATGGTCCCTGCCCTCAAGGAGCTTACAATCT-----AGT--TGG 388 chr6ptel1M 930574 AG-GATAAGACTATATACA 930591 i - i - i C L2d_3end#LINE 387 GGAGACAAGACTA-ACACA 370 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.94 CpG sites = 24, Kimura (unadjusted) = 38.78 Transitions / transversions = 6.00 (24/4) Gap_init rate = 0.11 (12 / 108), avg. gap size = 1.50 (18 / 12) 53 17.86 2.50 1.65 chr6ptel1M 930742 930861 (69139) (AGGA)n#Simple_repeat 1 121 (0) m_b296s252i2 12323 chr6ptel1M 930742 AGGGAGGGAGTGATGAGGGAA-GAGGGGA-GAGGGAAGG-AGGAAGGGAG 930788 i i vi v i - i i - i - i (AGGA)n#Simpl 1 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG 50 chr6ptel1M 930789 GAAGAGAGGAAGAAAGGAAAGGAAGGAAGGAAGGAAAGAAAGAAGAAAGG 930838 ii i - i i i (AGGA)n#Simpl 51 GAAGGAAGGAAGGAAGG-AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG 99 chr6ptel1M 930839 AAGGAAGGAAGAGAATGAATGAA 930861 - v v (AGGA)n#Simpl 100 AAGGAAGGAAG-GAAGGAAGGAA 121 Matrix = Unknown Transitions / transversions = 3.50 (14/4) Gap_init rate = 0.04 (5 / 119), avg. gap size = 1.00 (5 / 5) 201 20.78 20.78 0.00 chr6ptel1M 930871 930947 (69053) C X7B_LINE#LINE/CR1 (26) 224 132 m_b296s601i13 12324 chr6ptel1M 930871 ATCCTGGCTTCTTTGAATAACTCATTGT-------TAATCCATGACTTGA 930913 iii i v i i ------- v v v C X7B_LINE#LINE 224 ATCCTAATTTCCTTTAATAACCCATTATGGATCTATCATCCATGAATTTA 175 chr6ptel1M 930914 ---AGATCTTTCTTAAACC-A-----ATTTTCAGCCTTTACCA 930947 --- i i i i - ----- v i C X7B_LINE#LINE 174 TCTAAACCTTTTTTGAACCTATTTATATTTTCAGCCTGTACTA 132 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.07 CpG sites = 11, Kimura (unadjusted) = 25.07 Transitions / transversions = 2.20 (11/5) Gap_init rate = 0.05 (4 / 76), avg. gap size = 4.00 (16 / 4) 19 15.40 2.78 0.00 chr6ptel1M 931006 931041 (68959) (TA)n#Simple_repeat 1 37 (0) m_b296s252i3 12325 chr6ptel1M 931006 TAAATATATATCTGTA-ATATATTTATTTATATATAT 931041 v v i - v v (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATAT 37 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) 196 19.57 0.00 2.17 chr6ptel1M 931182 931228 (68772) C L2c_3end#LINE/L2 (86) 392 347 m_b296s601i15 12322 chr6ptel1M 931182 CTTAAGGAGATTACATTCTAATGGAGGAAGACAGCCCAGAAAGCAGA 931228 i v i v i - v v? v i C L2c_3end#LINE 392 CTCAAGGAGCTCACAGTCTAGTGGAGG-AGACAGACANGTAAACAGA 347 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 23.33 CpG sites = 4, Kimura (unadjusted) = 23.33 Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.02 (1 / 46), avg. gap size = 1.00 (1 / 1) 203 21.43 0.00 0.00 chr6ptel1M 931182 931223 (68777) C L2a_3end#LINE/L2 (103) 414 373 m_b296s601i14 12322 chr6ptel1M 931182 CTTAAGGAGATTACATTCTAATGGAGGAAGACAGCCCAGAAA 931223 i v v i i i v v v C L2a_3end#LINE 414 CTCATGGAGCTTACATTCTAGTGGGGGGAGACAGACAATAAA 373 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.32 CpG sites = 4, Kimura (unadjusted) = 25.32 Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 14 15.60 0.00 0.00 chr6ptel1M 932229 932257 (67743) (AGGGA)n#Simple_repeat 1 29 (0) m_b296s252i4 12326 chr6ptel1M 932229 AGAGAAGGGCGGGGAAAGGAAGGGAAGGG 932257 i vi i (AGGGA)n#Simp 1 AGGGAAGGGAAGGGAAGGGAAGGGAAGGG 29 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 181 21.95 4.88 0.00 chr6ptel1M 932479 932519 (67481) C MIRb#SINE/MIR (34) 234 192 m_b296s601i16 12327 chr6ptel1M 932479 TGTCCCAGGCACTGTGCTAGGGACCTTGCAAATAT--TCTCAT 932519 v i vi i i vii -- C MIRb#SINE/MIR 234 TGTGCCAGGCACTGTGCTAAGCGCTTTACATGCATTATCTCAT 192 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 23.38 CpG sites = 6, Kimura (unadjusted) = 26.73 Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.03 (1 / 40), avg. gap size = 2.00 (2 / 1) 209 32.12 7.50 4.03 chr6ptel1M 932784 932903 (67097) C MIR3#SINE/MIR (20) 188 65 m_b296s601i17 12328 chr6ptel1M 932784 GCCAGAAGCTGTCAAAGGCCTTGTAGGTCATTTTGTCTGCTGTCTCTCCT 932833 i - vv ii i iv i i v iivi-i i v C MIR3#SINE/MIR 188 GTCAGA-GCTGGAAGGGACCTTAGAGATCATCTAGTCCAAC-CCCCTCAT 141 chr6ptel1M 932834 GGTACAGA---GGAAAT------CCAGAGGGAAACACTAACTTGCCTGAG 932874 vv --- i------ i iviv v i ii C MIR3#SINE/MIR 140 TTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAG 91 chr6ptel1M 932875 GTCATGCGGTAAAGTTCAGGAGGCAGAAC 932903 ii i i-? --i v i C MIR3#SINE/MIR 90 GTCACACAGC-NAGTT--AGTGGCAGAGC 65 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.16 CpG sites = 25, Kimura (unadjusted) = 45.16 Transitions / transversions = 2.08 (25/12) Gap_init rate = 0.06 (7 / 119), avg. gap size = 2.00 (14 / 7) 552 22.58 2.65 6.16 chr6ptel1M 933081 933231 (66769) C MIRc#SINE/MIR (122) 146 1 m_b296s601i18 12329 chr6ptel1M 933081 CATTTTACAGATGAGGAAACTGAGGC--AAACTAGCTGAAGTGACTTGCC 933128 -- i v- v v C MIRc#SINE/MIR 146 CATTTTACAGATGAGGAAACTGAGGCTCAGAG-AGGTTAAGTGACTTGCC 98 chr6ptel1M 933129 CAGAATCACACCTCTAGGAA-TGTCTGAGATCAGATTTGAACTCATGAAG 933177 iii vv v - v v vivi i i i ----- C MIRc#SINE/MIR 97 CAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCA----- 53 chr6ptel1M 933178 GTGAGTCTTCCTGAGTCCAGGCCCTAGGCTCTGTCCACTGTACTAC-CTG 933226 ---i v i i viv v i i - C MIRc#SINE/MIR 52 ---GGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTG 6 chr6ptel1M 933227 GTTTG 933231 vi i C MIRc#SINE/MIR 5 CCTCG 1 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.27 CpG sites = 17, Kimura (unadjusted) = 27.09 Transitions / transversions = 1.13 (17/15) Gap_init rate = 0.08 (12 / 150), avg. gap size = 1.08 (13 / 12) 183 29.01 2.78 4.23 chr6ptel1M 934338 934409 (65591) C L2d2_3end#LINE/L2 (56) 499 429 m_b296s601i19 12330 chr6ptel1M 934338 AAACATTGTGGGGG-TAGCCAGAGAAGT-TCAGATCATGCTTCTTGCCCC 934385 ii ii - -- i - v - v i i i C L2d2_3end#LIN 499 AGGCGCTGTGGGGGATA--CAAAGAAGTATAAGA-CATGGTCCCTGCCCT 453 chr6ptel1M 934386 CAGAGTACTTGCGGTCCATGTGGG 934409 ii vi i ii i vv C L2d2_3end#LIN 452 CAAGGAGCTTACAATCTAGTTGGG 429 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.72 CpG sites = 15, Kimura (unadjusted) = 39.30 Transitions / transversions = 3.00 (15/5) Gap_init rate = 0.07 (5 / 71), avg. gap size = 1.00 (5 / 5) 307 29.34 2.15 1.06 chr6ptel1M 934945 935037 (64963) L2c_3end#LINE/L2 329 422 (56) m_b296s601i20 12331 chr6ptel1M 934945 TATCTTGCAT-GTAACTATGTGTTTACAGGTC-ATGTTCTCCATCAGAAC 934992 v i - i i v ?v -i v i ii vi L2c_3end#LINE 329 TAACTTGTATTGTAATTGTCTGTTTACNTGTCTGTCTCCTCCACTAGACT 378 chr6ptel1M 934993 ATAAGCTCCCCAAAGGTAGGGAATGTGTTTTTGTCTCTCTTTGTA 935037 i i iii i i vi - i i iiv L2c_3end#LINE 379 GTGAGCTCCTTGAGGGCAGGGACCGTG-TCTTATTCATCTTTGTA 422 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.51 CpG sites = 20, Kimura (unadjusted) = 40.51 Transitions / transversions = 2.86 (20/7) Gap_init rate = 0.03 (3 / 92), avg. gap size = 1.00 (3 / 3) 255 23.62 3.26 7.95 chr6ptel1M 935243 935334 (64666) C L2d2_3end#LINE/L2 (211) 344 257 m_b296s601i21 12330 chr6ptel1M 935243 AAAATAGTTACATGATTCATCCTCGAGTGAATGGTATATATAGTACAACA 935292 iii - v ivi i i i v i i ----- C L2d2_3end#LIN 344 AAGGCAGT-ACATGATTAATTGCCAAATGAATGGTACAGACAATA----- 301 chr6ptel1M 935293 GATGGCTCTA--AGTTCAAAGG-GGGAAAGATGATTGTGGGCTGG 935334 - ?v v -- i - i v i ?i C L2d2_3end#LIN 300 -ANTGCTATAGGAGTTCAGAGGAGGGAGAGATCACTNCGGGCTGG 257 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.45 CpG sites = 14, Kimura (unadjusted) = 30.26 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.10 (9 / 91), avg. gap size = 1.11 (10 / 9) 382 22.99 0.00 1.15 chr6ptel1M 935344 935431 (64569) MER58B#DNA/hAT-Charlie 9 95 (246) m_b296s502i0 12332 chr6ptel1M 935344 GACCAACTACAGATAGCAGACCAAATCCAGCCTGCCTGCCTCTTTTTCTA 935393 i v i viv i i i i - v v MER58B#DNA/hA 9 GGCAAACTACGGCCCGCGGGCCAAATCCGGCCCGCC-GCCTGTTTTTGTA 57 chr6ptel1M 935394 CAGCCTCTGAGCCAAGAATGCTTTTTGCATTGTTAAAT 935431 i ivi i v i v MER58B#DNA/hA 58 CGGCCCGCGAGCTAAGAATGGTTTTTACATTTTTAAAT 95 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 17.70 CpG sites = 12, Kimura (unadjusted) = 28.01 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.01 (1 / 87), avg. gap size = 1.00 (1 / 1) 449 29.62 7.98 0.57 chr6ptel1M 935670 935832 (64168) MIR3#SINE/MIR 7 181 (27) m_b296s601i22 12333 chr6ptel1M 935670 GGGTGGCTCAGTACATACTGTGCTAGTTGG-AGTCAGGAAGAACTGGATT 935718 i v i v v vv ii viii - - v i MIR3#SINE/MIR 7 GAGTGGCTGAGCAGAGAGAGCACGGACTGGGAGTCAGGA-GACCTGGGTT 55 chr6ptel1M 935719 CAGATCCTGCCTC-------AGAGGGTCGTGTGACCCTCAGCTAGTCATG 935761 vii i v ------- ivv? ii i vi v iv MIR3#SINE/MIR 56 CTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACT 105 chr6ptel1M 935762 TAATCTC----AGCCTCCATTTGCTCATCTATAAAGCAAGGTGCTTGGAT 935807 v i ----i vi v i iii v v i MIR3#SINE/MIR 106 TCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGAC 155 chr6ptel1M 935808 CAGATGACCTCCAA-GTCCCTTTCAG 935832 i i i - i MIR3#SINE/MIR 156 TAGATGATCTCTAAGGTCCCTTCCAG 181 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.20 CpG sites = 29, Kimura (unadjusted) = 39.26 Transitions / transversions = 1.53 (29/19) Gap_init rate = 0.03 (5 / 162), avg. gap size = 2.80 (14 / 5) 204 30.86 8.05 10.59 chr6ptel1M 936068 936241 (63759) C MIRb#SINE/MIR (64) 204 35 m_b296s601i23 12334 chr6ptel1M 936068 TGCGTCCTTTCATTTGATCCTTACAACATCTCTGCTCTGGGGAGCTTACC 936117 i iv i i i v i ------ v ---- C MIRb#SINE/MIR 204 TGCATTATCTCATTTAATCCTCACAACAACCCTGC------GAGGT---- 165 chr6ptel1M 936118 CAAGTGCT-TTAAATTATAATTGCCCCAAAGAGGAAGCTGGAAACCTGTT 936166 - i ii - -- iviv viv vi v i - ii --- i C MIRb#SINE/MIR 164 -AGGTATTATT--ATCCCCATTTTACAGATGAGGAAACT-GAGGC---TC 122 chr6ptel1M 936167 AGCAAGGTCAAGTCATTTTCCCAAGG-----CAGTTGGTGA-----AGAA 936206 vi i v i v ----- i i i ----- i C MIRb#SINE/MIR 121 AGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAG 72 chr6ptel1M 936207 CTGGAAGGTGCATTTGGGCCT-TCT--CTCACTAAGCC 936241 i i vvi v iiii i - -- - v C MIRb#SINE/MIR 71 CCGGGATTCGAACCCAGGTCTGTCTGACTC-CAAAGCC 35 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.38 CpG sites = 32, Kimura (unadjusted) = 41.70 Transitions / transversions = 2.00 (32/16) Gap_init rate = 0.13 (23 / 173), avg. gap size = 1.39 (32 / 23) 204 22.03 1.43 9.23 chr6ptel1M 936789 936858 (63142) L2d_3end#LINE/L2 385 449 (67) m_b296s601i24 12335 chr6ptel1M 936789 TCCCCCATTAGAATGTAAGATCATTGAAAG-AAGGACTGGGTTTTTTCTT 936837 v i v v v ii - i iiv ----- L2d_3end#LINE 385 TCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATG-----TCTT 429 chr6ptel1M 936838 AAACCATTTTTTAGTGTCCCC 936858 v i? ? v - L2d_3end#LINE 430 ATACTNTTTTNTCGT-TCCCC 449 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.08 CpG sites = 7, Kimura (unadjusted) = 27.08 Transitions / transversions = 1.00 (7/7) Gap_init rate = 0.10 (7 / 69), avg. gap size = 1.00 (7 / 7) 241 34.81 4.42 0.85 chr6ptel1M 937265 937377 (62623) MIR1_Amn#SINE/MIR 34 150 (80) m_b296s601i25 12336 chr6ptel1M 937265 TGGATGAAAGCTCAG-ACACCTTGATTTTCTTTTTGGCTTCATT-CCAGC 937312 iviiii i - v v i i?v? iii iiiii- i? MIR1_Amn#SINE 34 TGGACTGGGACTCGGGAGACCTGGGTTCNANTCCCGGCTCTGCCACTNGC 83 chr6ptel1M 937313 TTAGATGGGTGAGCTTTAACAAATCACTTT---TCTGTGTATTTTAGTTT 937359 i?- v ? v vii i ?--- v ?iii i MIR1_Amn#SINE 84 CN-GCTGNGTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTT 132 chr6ptel1M 937360 TCTCACTTGCAAATTGAG 937377 i ii i v i MIR1_Amn#SINE 133 CCTCATCTGTAAAATGGG 150 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 53.46 CpG sites = 30, Kimura (unadjusted) = 58.22 Transitions / transversions = 3.33 (30/9) Gap_init rate = 0.04 (4 / 112), avg. gap size = 1.50 (6 / 4) 219 30.95 12.73 9.54 chr6ptel1M 937803 938077 (61923) L2c_3end#LINE/L2 191 473 (5) m_b296s601i26 12337 chr6ptel1M 937803 CTCCTCCTCGAGTCCTTCAAAGTGCAGATCAGATGTC---TCTTCCATGA 937849 v i-- i?iv v --- i iv L2c_3end#LINE 191 CTCCTACTCA--TCCTTCAAGNCTCAGCTCAGATGTCACCTCCTCCGGGA 238 chr6ptel1M 937850 GGTTTATTTGGATTTTCCCAGTT--G-CT-GGAGC--TCCTC----CTCC 937889 i ii viiiv iiii v ?i-- - - v -- ---- L2c_3end#LINE 239 AGCCTTCCCTGACCCCCCAAGNCTAGTCTAGGTGCCCTCCTCTGTGCTCC 288 chr6ptel1M 937890 ------------TTTGTACTTATATTAT-----TTAT----AGTTTGTAT 937918 ------------ i i ivi ----- ---- ii L2c_3end#LINE 289 CATAGCACCCTGTCTATACTCCCATTATAGCACTTATCATTAACTTGTAT 338 chr6ptel1M 937919 T-TACTTGTCAGTGTCCAAATTTCATCATCCCAAAATGAAAGAAGATACT 937967 - v v v v ?vi i -i - ivv v ------ i--- L2c_3end#LINE 339 TGTAATTGTCTGTTTACNTGTCT-GTC-TCCTCCACT------AGAC--- 377 chr6ptel1M 937968 TATGTAAGGTCCTTAAAAGCGGGAGCTATTTCATTTTTGTTGTTGTGGCC 938017 -- i v i ii i ii ii v v v ii iv ---- L2c_3end#LINE 378 --TGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGT---- 421 chr6ptel1M 938018 CCAGAATCCAGCTCAGTGTGTAGCATATAGTAAATGCTTAGGAAATAATT 938067 ----- ---i i iv i i iii i iv iv L2c_3end#LINE 422 -----ATCC---CCAGCGCCTGGCACATAGTAGGCGCTCAATAAATGTTT 463 chr6ptel1M 938068 TTTGAATGGA 938077 v i L2c_3end#LINE 464 GTTGAATGAA 473 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.85 CpG sites = 51, Kimura (unadjusted) = 42.92 Transitions / transversions = 1.96 (51/26) Gap_init rate = 0.14 (37 / 274), avg. gap size = 1.68 (62 / 37) 226 30.83 9.45 2.96 chr6ptel1M 937804 937930 (62070) L2d2_3end#LINE/L2 193 327 (228) m_b296s601i27 12337 chr6ptel1M 937804 TCCTCCTCGAGTCCTTCAAAGTGCAGATCAGATG---TCTCTTCCATGAG 937850 v i i-- i iv v i ?---i i i i L2d2_3end#LIN 193 TCCTACCCA--TCCTTCAAGGCCCAGCTCAAATNCCACCTCCTCCGTGAA 240 chr6ptel1M 937851 GTTTATTTGGATTTTCCCAGTTGCTGGAG----CTCCTCCTCCTTTGTAC 937896 ii viiiv iivii i-- i ? ---- ii i v L2d2_3end#LIN 241 GCCTTCCCTGACCACTCCAGC--CCGNAGTGATCTCTCCCTCCTCTGAAC 288 chr6ptel1M 937897 T--TATATTATTTATAGTTTGT---ATTTACTTGTCAGT 937930 -- vi ? v i --- i i v i L2d2_3end#LIN 289 TCCTATAGCANTTATTGTCTGTACCATTCATTTGGCAAT 327 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.26 CpG sites = 28, Kimura (unadjusted) = 44.48 Transitions / transversions = 2.80 (28/10) Gap_init rate = 0.06 (8 / 126), avg. gap size = 2.00 (16 / 8) 302 26.73 8.06 7.49 chr6ptel1M 937890 938075 (61925) L2d_3end#LINE/L2 321 507 (9) m_b296s601i28 12337 chr6ptel1M 937890 TTTGTACTTATATTATTTATAGT-TTGTATT------TACTTGT--CA-G 937929 v i - v iv - ------ v -- - L2d_3end#LINE 321 TTAGCACTTA-ATTATATACTGTCTTGTATTGTTCTCTAATTGTTTCATG 369 chr6ptel1M 937930 TGTCCAAATTTCATCATCCCAAAATGAAAGAAGATACTTATGTAAGGTCC 937979 viv i i ii - v v ------ ----- v L2d_3end#LINE 370 TGTGTTAGTCTTGTC-TCCCCAACT------AGAT-----TGTAAGCTCC 407 chr6ptel1M 937980 TTAAAAGCGGGAGCTATTTC----ATTTTTGTTGTTGTGGCCC-CAGAAT 938024 i ii i ii i v ---- i ? - ? i vv - vii L2d_3end#LINE 408 TTGAGGGCAGGGACCATGTCTTATACTNTT-TTNTCGTTCCCCACAGCGC 456 chr6ptel1M 938025 CCAGCTCAGTGTGTAGCATATAGTAAATGCTTAGGAAATAATTTTTGAAT 938074 i v ivv i iii i iv v v v L2d_3end#LINE 457 CTAGCACAGTGCTGAGCACATAGTAGGCGCTCAATAAATACTTGTTGATT 506 chr6ptel1M 938075 G 938075 L2d_3end#LINE 507 G 507 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.57 CpG sites = 26, Kimura (unadjusted) = 34.25 Transitions / transversions = 1.30 (26/20) Gap_init rate = 0.11 (20 / 185), avg. gap size = 1.45 (29 / 20) 344 30.28 4.59 0.00 chr6ptel1M 937969 938077 (61923) L2a_3end#LINE/L2 399 512 (5) m_b296s601i29 12337 chr6ptel1M 937969 ATGTAAGGTCCTTAAAAGCGGGAGCTATT-TCATTTTTGTT----GTTGT 938013 v v i ii i ii v - vv ---- i L2a_3end#LINE 399 ATGTAAGCTCCATGAGGGCAGGGACTTTTGTCTGTTTTGTTCACTGCTGT 448 chr6ptel1M 938014 GGCCCCAGAATCCAGCTCAGTGTGTAGCATATAGTAAATGCTTAGGAAAT 938063 iv vii i vv iv i i iii i iv L2a_3end#LINE 449 ATCCCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGGCGCTCAATAAAT 498 chr6ptel1M 938064 AATTTTTGAATGGA 938077 v v i L2a_3end#LINE 499 ATTTGTTGAATGAA 512 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.00 CpG sites = 20, Kimura (unadjusted) = 40.11 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.02 (2 / 108), avg. gap size = 2.50 (5 / 2) 236 26.51 19.28 0.00 chr6ptel1M 938105 938187 (61813) C MIR3#SINE/MIR (47) 161 63 m_b296s601i30 12338 chr6ptel1M 938105 CATCAAATTAAACACACCCATTTTCTAGATGAGAAAACTGAG---CA--- 938148 v i iv v v i vi i --- --- C MIR3#SINE/MIR 161 CATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAG 112 chr6ptel1M 938149 ----------ATTTGCCTAAGATTACACAGATAGTAAATACTAGAGTTG 938187 ---------- i i i i v? v i ivi ii C MIR3#SINE/MIR 111 AGGTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCG 63 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.41 CpG sites = 14, Kimura (unadjusted) = 34.33 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.04 (3 / 82), avg. gap size = 5.33 (16 / 3) 268 22.39 23.88 0.00 chr6ptel1M 938121 938187 (61813) C MIRb#SINE/MIR (117) 151 69 m_b296s601i31 12338 chr6ptel1M 938121 CCCATTTTCTAGATGAGAAAACTGAG----------------CAATTTGC 938154 vi i ----------------i i C MIRb#SINE/MIR 151 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGC 102 chr6ptel1M 938155 CTAAGATTACACAGATAGTAAATACTAGAGTTG 938187 i i i v i ivi ii C MIRb#SINE/MIR 101 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 69 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.94 CpG sites = 12, Kimura (unadjusted) = 28.14 Transitions / transversions = 4.00 (12/3) Gap_init rate = 0.02 (1 / 66), avg. gap size = 16.00 (16 / 1) 244 34.37 12.70 0.71 chr6ptel1M 938486 938611 (61389) C MIR3#SINE/MIR (1) 207 67 m_b296s601i32 12339 chr6ptel1M 938486 AATCATATGAGTATATGAATATTAAGGCTGGAAAATACCTTAGATATTCT 938535 vi vi - i i ii iiv v iv C MIR3#SINE/MIR 207 AATCATAGAATCATA-GAATGTCAGAGCTGGAAGGGACCTTAGAGATCAT 159 chr6ptel1M 938536 CTAGTGTGGGTCCC-----TTACGG---------CAGAAACTTAGAGAGA 938571 viiivi ----- i --------- v ii ii i C MIR3#SINE/MIR 158 CTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGG 109 chr6ptel1M 938572 CCAGATGAGTTATCCCAAATGATAAAACTAG--AGCTGCAGA 938611 iv ii v ii v ii v i v i ? -- iv C MIR3#SINE/MIR 108 TGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGA 67 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 49.85 CpG sites = 29, Kimura (unadjusted) = 49.85 Transitions / transversions = 2.07 (29/14) Gap_init rate = 0.03 (4 / 125), avg. gap size = 4.25 (17 / 4) 237 28.46 0.00 5.41 chr6ptel1M 938687 938764 (61236) C L2b_3end#LINE/L2 (15) 451 378 m_b296s601i33 12340 chr6ptel1M 938687 AATTAATTATTAAGCACATACGGTTTGCCAATCAATCTGCTGAATTCTGG 938736 v v i i i v v v iv ?v v iiiiv C L2b_3end#LINE 451 AAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGG 402 chr6ptel1M 938737 GAATACAAATACAGGCAAACAAGACAGA 938764 i i--- - ii C L2b_3end#LINE 401 GGATACAG---C-GGTGAACAAGACAGA 378 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.85 CpG sites = 12, Kimura (unadjusted) = 37.16 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.05 (4 / 77), avg. gap size = 1.00 (4 / 4) 270 29.20 0.00 7.53 chr6ptel1M 939130 939229 (60771) C MIR3#SINE/MIR (94) 114 22 m_b296s601i35 12341 chr6ptel1M 939130 GAGAAATTAAGTGATTTGCTCACAGTCCCATAGTTAGTATGCATCAGAGA 939179 ii v i i vi v i i? vv iiv v C MIR3#SINE/MIR 114 GAGAGGTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGC 65 chr6ptel1M 939180 CAGGATTTCAACCCAGTTCTTCCTACCTTAGAGACCATCTCCATGCCCTC 939229 i i vv v - iv i----- -v i i C MIR3#SINE/MIR 64 CGGGACTAGAACCCAGGTC-TCCTGACTC-----CCA-GTCCGTGCTCTC 22 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.57 CpG sites = 15, Kimura (unadjusted) = 38.05 Transitions / transversions = 1.25 (15/12) Gap_init rate = 0.07 (7 / 99), avg. gap size = 1.00 (7 / 7) 386 28.74 0.00 0.00 chr6ptel1M 939130 939216 (60784) C MIRc#SINE/MIR (151) 117 31 m_b296s601i34 12341 chr6ptel1M 939130 GAGAAATTAAGTGATTTGCTCACAGTCCCATAGTTAGTATGCATCAGAGA 939179 ii i i vi v i i v iiv v C MIRc#SINE/MIR 117 GAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGC 68 chr6ptel1M 939180 CAGGATTTCAACCCAGTTCTTCCTACCTTAGAGACCA 939216 i i iv v iv ivi v C MIRc#SINE/MIR 67 CGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCA 31 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.63 CpG sites = 15, Kimura (unadjusted) = 37.32 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.00 (0 / 86), avg. gap size = 0.0 (0 / 0) 260 28.18 5.79 3.23 chr6ptel1M 939287 939407 (60593) C MIRc#SINE/MIR (19) 249 126 m_b296s601i36 12342 chr6ptel1M 939287 ATTTATAGAGACTTTTAAAGTTTACACATTATTTTATCA-ACATGATCTC 939335 i v vvi v v viii vv - v C MIRc#SINE/MIR 249 ATTTGTATAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATCTC 200 chr6ptel1M 939336 CCATTTGGCTTCATAATAACAATCTCATGAGGCTTGC---GC---TATTT 939379 -- i-- v v i i iii ivv --- --- v C MIRc#SINE/MIR 199 --ATTTGA--TCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTA 154 chr6ptel1M 939380 TGACTTCTATTTTACAGATGAGAATACT 939407 v iii i i v C MIRc#SINE/MIR 153 TTATCCCCATTTTACAGATGAGGAAACT 126 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.39 CpG sites = 17, Kimura (unadjusted) = 35.86 Transitions / transversions = 1.06 (17/16) Gap_init rate = 0.06 (7 / 120), avg. gap size = 1.57 (11 / 7) 15 20.59 2.94 0.00 chr6ptel1M 940850 940883 (59117) (AT)n#Simple_repeat 1 35 (0) m_b296s252i5 12343 chr6ptel1M 940850 ATATATATATATATTTATTTTTCT-TTTATTTATA 940883 v v v v - v v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATA 35 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 283 19.06 0.00 3.17 chr6ptel1M 940932 940996 (59004) Charlie4#DNA/hAT-Charlie 53 115 (3263) m_b296s502i1 12344 chr6ptel1M 940932 TTTAGGGAGTCCAATGAACTTGGATGAGAAAAAAGGTACATCTTAATGTT 940981 i i i- i -v v v Charlie4#DNA/ 53 TTCAGGGGGTCCG-TGAACTTGGATGGGAAAAAA-TTACATCTTTATTTT 100 chr6ptel1M 940982 TACTAACTTTTGGCT 940996 i i i ii Charlie4#DNA/ 101 CACTAACCTCTAACT 115 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 20.68 CpG sites = 9, Kimura (unadjusted) = 22.78 Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.03 (2 / 64), avg. gap size = 1.00 (2 / 2) 257 26.58 0.00 3.54 chr6ptel1M 941716 941832 (58168) L1M3_orf2#LINE/L1 1718 1830 (1458) m_b296s551i0 12345 chr6ptel1M 941716 ACATATATGCATCAAATGGCATAATTTACCATATCAATAGCAGAAACAAC 941765 ii?iv v?iiii i vi i i i v vi vi i L1M3_orf2#LIN 1718 ACATACGNAAATCAATNAATGTGATACACCACATTAACAGAATGAAGGAT 1767 chr6ptel1M 941766 AAAAATCAAATGATTATCTCAATAATTGCAGAAAAAGCATTGTTTGAGAA 941815 v i iv --- v L1M3_orf2#LIN 1768 AAAAATCACATGATCATCTCAATAGATGCAGAAAAAGCA---TTTGACAA 1814 chr6ptel1M 941816 TAATAAAACATTCATTC 941832 - vv i v L1M3_orf2#LIN 1815 -AATTCAACATCCTTTC 1830 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 32.85 CpG sites = 18, Kimura (unadjusted) = 34.41 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.03 (4 / 116), avg. gap size = 1.00 (4 / 4) 319 18.52 0.00 4.35 chr6ptel1M 941737 941832 (58168) L1M5_orf2#LINE/L1 1745 1836 (1458) m_b296s551i1 12345 chr6ptel1M 941737 TAATTTACCATATCAATAGCAGAAACAACAAAAATCAAATGATTATCTCA 941786 i i i v v vi v v i L1M5_orf2#LIN 1745 TAATTCACCATATTAACAGAATAAAGGAGAAAAATCATATGATCATCTCA 1794 chr6ptel1M 941787 ATAATTGCAGAAAAAGCATTGTTTGAGAATAATAAAACATTCATTC 941832 iv --- v - vv ii L1M5_orf2#LIN 1795 ATAGATGCAGAAAAAGCA---TTTGACAA-AATTCAACACCCATTC 1836 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 21.30 CpG sites = 8, Kimura (unadjusted) = 21.30 Transitions / transversions = 0.89 (8/9) Gap_init rate = 0.04 (4 / 95), avg. gap size = 1.00 (4 / 4) 225 31.13 6.25 9.68 chr6ptel1M 941878 941973 (58027) MIRc#SINE/MIR 3 95 (173) m_b296s601i37 12346 chr6ptel1M 941878 AGGTAACATGGTGCA-----AAGTGTACTGAGCTTGGAATCAGGAATATT 941922 i iii ----- v i ii i v -- MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA-- 50 chr6ptel1M 941923 CATCTTCATAAATTCAAAT-CTGACCATAGACATTTATTCACTGTGTGAT 941971 ------ v iii i i - i i iv - v i i vi i MIRc#SINE/MIR 51 ------CCTGGGTTCGAGTCCCGGCTCT-GCCACTTACTAGCTGTGTGAC 93 chr6ptel1M 941972 TT 941973 i MIRc#SINE/MIR 94 CT 95 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.41 CpG sites = 21, Kimura (unadjusted) = 43.83 Transitions / transversions = 3.50 (21/6) Gap_init rate = 0.12 (11 / 95), avg. gap size = 1.36 (15 / 11) 11 18.44 6.67 2.13 chr6ptel1M 942209 942253 (57747) (AGAAAGA)n#Simple_repeat 1 47 (0) m_b296s252i6 12347 chr6ptel1M 942209 AGAAAGAAGAAAG--GGAAGAAGAGGGTTGAGAAGTAGGAAG-AGAAA 942253 -- i ii vv - v i - (AGAAAGA)n#Si 1 AGAAAGAAGAAAGAAGAAAGAAGAAAGAAGA-AAGAAGAAAGAAGAAA 47 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.07 (3 / 44), avg. gap size = 1.33 (4 / 3) 395 27.26 5.74 0.78 chr6ptel1M 942992 943113 (56887) MIRb#SINE/MIR 118 245 (23) m_b296s601i38 12348 chr6ptel1M 942992 CTCTGTGTCT--GGTTCCTCAAATGAAAAATAAGCTTAA----ACC-AAT 943034 v i -- v vv v ii vv ---- - vi MIRb#SINE/MIR 118 CTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTACC 167 chr6ptel1M 943035 TCACAGGGTTGTCATGAGGATCCAATGAGATGATATGTGGAAAAGTATTT 943084 i ii iv i iii v- iii MIRb#SINE/MIR 168 TCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCATGT-AAAGCGCTT 216 chr6ptel1M 943085 GGCTCAGTCCTTGGCACCTAGTAGGAACT 943113 i v v i v i vi MIRb#SINE/MIR 217 AGCACAGTGCCTGGCACATAGTAAGCGCT 245 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.76 CpG sites = 19, Kimura (unadjusted) = 34.66 Transitions / transversions = 1.36 (19/14) Gap_init rate = 0.03 (4 / 121), avg. gap size = 2.00 (8 / 4) 284 24.15 3.55 8.96 chr6ptel1M 943584 943724 (56276) MIR1_Amn#SINE/MIR 7 140 (90) m_b296s601i39 12349 chr6ptel1M 943584 GATAATGAGCTATAGAAGGTGGAGTGACAGGTCTGGAA-TCAGAAGACCT 943632 ii i v v v vi i i i- v v i - i i MIR1_Amn#SINE 7 GGCAGTGTGGTCTAGTGGATAGAGC-ACTGGACTGGGACTCGGGAGACCT 55 chr6ptel1M 943633 GGGTTCAAATCACAGCTCTGAATTCCACCTTCTTTCAGCTTCTATGAACC 943682 ? ? v i ---- i?v --- ? - v?i - MIR1_Amn#SINE 56 GGGTTCNANTCCCGGCTCTG----CCACTNGC---CNGC-TGNGTG-ACC 96 chr6ptel1M 943683 TTCTGGGC-ACTCACT--GCTTTTCT-TCCCTCAGCTTCTGCATTT 943724 -- - v --i i i -?v i iv i MIR1_Amn#SINE 97 T--TGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCT 140 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.11 CpG sites = 19, Kimura (unadjusted) = 31.51 Transitions / transversions = 1.58 (19/12) Gap_init rate = 0.11 (16 / 140), avg. gap size = 1.06 (17 / 16) 245 33.72 8.14 0.00 chr6ptel1M 943887 943972 (56028) C L3#LINE/CR1 (426) 3673 3581 m_b296s601i40 12350 chr6ptel1M 943887 CATTCTGGCCACTC--CTCTGGACTTACTCCATGGTGTCAATGTC----- 943929 i i i -- vii vvv ----- C L3#LINE/CR1 3673 CATCCTGGTCGCTCTCCTCTGGACGCGCTCCAGTTTGTCAATGTCCCTCT 3624 chr6ptel1M 943930 TAAAATATAATATATAAAATAGAATGAAGTTCCTCACATATAG 943972 i iiiiivi i iv i v i v ii v i i C L3#LINE/CR1 3623 TAAAATGTGGCGCCCAGAACTGAACGCAATACTCCAGATGTGG 3581 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.70 CpG sites = 20, Kimura (unadjusted) = 48.04 Transitions / transversions = 2.22 (20/9) Gap_init rate = 0.02 (2 / 85), avg. gap size = 3.50 (7 / 2) 220 34.39 6.38 1.01 chr6ptel1M 944015 944108 (55892) C L2a_3end#LINE/L2 (17) 500 402 m_b296s601i41 12351 chr6ptel1M 944015 ATATTATAGTCAACAAATATTAAATGCCAGACACCATTCTAAGCATTAAA 944064 - v v i ivv i vi i ii i ii iii C L2a_3end#LINE 500 ATATT-TATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGCGCTGGG 452 chr6ptel1M 944065 GGTCCAAAAAGAAGCAAA--AGACAG----CCCTGCCCTTAAGGGGTTCA 944108 i v iv ivi i -- i---- i v i i i C L2a_3end#LINE 451 GATACAGCAGTGAACAAAACAGACAAAAGTCCCTGCCCTCATGGAGCTTA 402 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.60 CpG sites = 23, Kimura (unadjusted) = 50.13 Transitions / transversions = 2.56 (23/9) Gap_init rate = 0.03 (3 / 93), avg. gap size = 2.33 (7 / 3) 347 30.54 5.48 1.32 chr6ptel1M 944186 944331 (55669) C L3b_3end#LINE/CR1 (577) 629 478 m_b296s601i42 12352 chr6ptel1M 944186 TGCTTTTATTAATGGAGATAAAGATTTCAGTGCCTTTTTAAGCTGCCTTT 944235 ? i i v viv iv v iv vi v viv C L3b_3end#LINE 629 TNCTTCTGTTAATGCAGCCCAAGATCGCATTAGCTTTTTTGGCAGCCGCG 580 chr6ptel1M 944236 TC--ACT-TTAACTTGTATTGAACTTGCATTCTACTTATTCCCTCAAACC 944282 -- -i i ii i iv v v vv i iii C L3b_3end#LINE 579 TCGCACTGCTGACTCATATTGAGCTTGCGGTCAACTAAAACCCCCAGGTC 530 chr6ptel1M 944283 TTTTTTTTACATGAACTGTTGTCTAGC--CATCTTTC---TCCTGTATTG 944327 -- i ?i i iiv -- i ii --- i v C L3b_3end#LINE 529 T--TTTTCACATGNGCTGCTGCTAAGCCGCGTCTCCCCCATCCTGTACTC 482 chr6ptel1M 944328 GCAC 944331 i C L3b_3end#LINE 481 GCGC 478 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.53 CpG sites = 27, Kimura (unadjusted) = 41.50 Transitions / transversions = 1.59 (27/17) Gap_init rate = 0.04 (6 / 145), avg. gap size = 1.67 (10 / 6) 800 29.48 3.91 1.92 chr6ptel1M 945485 945740 (54260) MIRb#SINE/MIR 7 267 (1) m_b296s601i43 12353 chr6ptel1M 945485 GGCAGCA--GTGAAGTGGCTCAGTGAACAGAGTTCCTGGAATCAGGAAGA 945532 i-- v --- iv i vi viii i iv MIRb#SINE/MIR 7 GGCAGCGTGGTGCAGTGG---AAAGAGCACGGGCTTTGGAGTCAGACAGA 53 chr6ptel1M 945533 CC------AAAATCTAGGCTCAAACATTTATTATCTGTGTGACTCAAGAC 945576 ------vi iv viv i i v iivi i MIRb#SINE/MIR 54 CCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGC 103 chr6ptel1M 945577 AAAGCA-TTAATCTTTGTTTGCCTGAAAGTTTTTAT-TATAAAATGTGAA 945624 ivi - i i v vv v ivv ii i - i v i MIRb#SINE/MIR 104 AAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGA 153 chr6ptel1M 945625 GAATGAGTATCCTCCTCCCAGGGTTGCTGTAAGGATCAAATGAAATCATA 945674 v i - i iv v i i i i v i MIRb#SINE/MIR 154 TAATAA-TACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATG 202 chr6ptel1M 945675 ATTGTAAAGCACTTAGCACAACACCTGGCATACAGTGAGTGCTATGTAAA 945724 vv i iii i i i i vvi MIRb#SINE/MIR 203 CATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAAA 252 chr6ptel1M 945725 TGTTAGCTATTATTAT 945740 v -i MIRb#SINE/MIR 253 TGGTAGCT-CTATTAT 267 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.50 CpG sites = 46, Kimura (unadjusted) = 38.82 Transitions / transversions = 1.64 (46/28) Gap_init rate = 0.04 (9 / 255), avg. gap size = 1.67 (15 / 9) 455 33.68 6.56 1.04 chr6ptel1M 946717 946899 (53101) MIRc#SINE/MIR 1 193 (75) m_b296s601i44 12354 chr6ptel1M 946717 CAAGGCAGCAAGATAAAGTGCCAAGGGT-TTGG-CCTGGAATTAGAAAAC 946764 i iiv i iv vv i i-i - i i i i iv MIRc#SINE/MIR 1 CGAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA 50 chr6ptel1M 946765 TCCTGGGTTGGCAGCCCAGCTTTATTACTTGTCAGGTTCAT-ACC----- 946808 - v viv i i iii iii v vii - ----- MIRc#SINE/MIR 51 -CCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGG 99 chr6ptel1M 946809 --AGTCACTTTGATCAATCAAAGTGTCAGTTTCCCTACCAGTAAAATGGG 946856 -- -i i vv vi iv ii i v MIRc#SINE/MIR 100 CAAGTCACTT-AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 chr6ptel1M 946857 --TAATGGCACTTTCATTACTTACCTCATGGGGCTGCTCTAAGGA 946899 -- iii i v vi i i ii i i v i MIRc#SINE/MIR 149 GATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGA 193 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.99 CpG sites = 43, Kimura (unadjusted) = 48.28 Transitions / transversions = 2.39 (43/18) Gap_init rate = 0.04 (7 / 182), avg. gap size = 2.00 (14 / 7) 335 29.55 7.30 4.95 chr6ptel1M 946747 946924 (53076) MIR#SINE/MIR 29 210 (52) m_b296s601i45 12354 chr6ptel1M 946747 GGC-CTGGAATTAGAAAACT-CCTGGGTTGGCAGCCCAGCTTTATTACTT 946794 - iii --- - v v v i i iii MIR#SINE/MIR 29 GGCTCTGGAGCCAGA---CTGCCTGGGTTCGAATCCCGGCTCTGCCACTT 75 chr6ptel1M 946795 GTCAGGTTCAT-ACC-------AGTCACTTTGATCAATCAAAGTGTCAGT 946836 iii v vii - ------- i -i i vv viv iv MIR#SINE/MIR 76 ACTAGCTGTGTGACCTTGGGCAAGTTACTT-AACCTCTCTGTGCCTCAGT 124 chr6ptel1M 946837 TTCCCTACCAGTAAAATGGGTAATGGCACTTTCATTACTTACCTCATGGG 946886 ii i v -i iii v --- v i i MIR#SINE/MIR 125 TTCCTCATCTGTAAAATGGG-GATAATAAT---AGTACCTACCTCATAGG 170 chr6ptel1M 946887 GCTGCTCTAAGGA--AAAT-ACTTAGGACACTGTGAAAGGC 946924 i i v i -- - v iv - i iv MIR#SINE/MIR 171 GTTGTTGTGAGGATTAAATGAGTTAATACA-TGTAAAGCGC 210 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.36 CpG sites = 33, Kimura (unadjusted) = 39.39 Transitions / transversions = 1.94 (33/17) Gap_init rate = 0.08 (15 / 177), avg. gap size = 1.47 (22 / 15) 470 26.35 0.80 5.88 chr6ptel1M 947851 947975 (52025) MIRc#SINE/MIR 9 127 (141) m_b296s601i46 12355 chr6ptel1M 947851 TATAACACAGTGGATAGAGCACCAGCCCTGAAGTCGGGAGAACCTGAGTT 947900 i iiii v ii v i i i ii i MIRc#SINE/MIR 9 TGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTT 58 chr6ptel1M 947901 CAAATATGACCTCAGACACTTAAGACTTCCTAGCTGTGTGACCTTGGGCA 947950 i i viviv v v ------- MIRc#SINE/MIR 59 CGAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTGACCTTGGGCA 101 chr6ptel1M 947951 CATCATTTAACCCCAATT-GCCTCAG 947975 vi i i vv v- MIRc#SINE/MIR 102 AGTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.84 CpG sites = 20, Kimura (unadjusted) = 33.46 Transitions / transversions = 1.82 (20/11) Gap_init rate = 0.06 (8 / 124), avg. gap size = 1.00 (8 / 8) 348 33.49 5.39 4.88 chr6ptel1M 948029 948232 (51768) C MIRc#SINE/MIR (38) 230 26 m_b296s601i47 12356 chr6ptel1M 948029 GTTGGTAAAGCA---TCATATAGTTTATTAAACACTT--TCTTTACAACA 948073 vii i--- i vv iv-- i -- i i C MIRc#SINE/MIR 230 GTTTACAAAGCGCTTTCACATACATTATCT--CATTTGATCCTCACAACA 183 chr6ptel1M 948074 CTTCAGTGAGACAAATAAATCAGGTACTGT---CTCTATTTTACAGATAA 948120 vii v ii iii iiv i i --- i i i C MIRc#SINE/MIR 182 ACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGA 133 chr6ptel1M 948121 GGCAGCT-AAACTCAAAGATGTTAAACAACTTAAATGACCAGGAAAGCAC 948169 v i - ii i v iii ---- v -- iiv C MIRc#SINE/MIR 132 GGAAACTGAGGCTCAGAGAGGTTAAGTGACT----TGCCCA--AGGTCAC 89 chr6ptel1M 948170 TACGAATACCAAGGGGC-CAGCT-GGACTCAGAACTTCTATGTTCCTTTT 948217 - iiv vi v -v i- - iivvi v vvi C MIRc#SINE/MIR 88 -ACAGCTAGTAAGTGGCAGAGCCGGGACTC-GAACCCAGGTCTTCCTGAC 41 chr6ptel1M 948218 ACCAGAAGCAGTGTT 948232 v iivv i C MIRc#SINE/MIR 40 TCCAAGTCCAGTGCT 26 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.84 CpG sites = 42, Kimura (unadjusted) = 46.86 Transitions / transversions = 1.83 (42/23) Gap_init rate = 0.08 (16 / 203), avg. gap size = 1.31 (21 / 16) 442 27.14 2.92 7.32 chr6ptel1M 948387 948557 (51443) C MIR3#SINE/MIR (43) 165 2 m_b296s601i48 12357 chr6ptel1M 948387 AGGTCAATTCAGTCTAATTTCCTCATTTTACAGATGAGAAAACTTGAGTC 948436 i - ii i iii i - v C MIR3#SINE/MIR 165 AGATCA-TCTAGTCCAACCCCCTCATTTTACAGATGAGGAAAC-TGAGGC 118 chr6ptel1M 948437 TTCCAGAGAG--GAGGTAACATGTCCAAAGTCTGTCAGGTCACAGGTGCC 948484 -- -- i i v i i vvv v?viivi v C MIR3#SINE/MIR 117 --CCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGC 70 chr6ptel1M 948485 AGAGCTAGGATGGGAGCCCAGAAACTCTT---TCTCAGGATCCTGTGATT 948531 ii ivi i -iv i --- i -- - v i C MIR3#SINE/MIR 69 AGAGCCGGGACTAGAACCCAG-GTCTCCTGACTCCCAG--TCC-GTGCTC 24 chr6ptel1M 948532 TTTTTTTTTACTGCATCAGTCTGCTA 948557 i i vi i -- -- v i C MIR3#SINE/MIR 23 TCTCTGCTCA--GC--CACTCTGCCA 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.14 CpG sites = 29, Kimura (unadjusted) = 35.29 Transitions / transversions = 2.07 (29/14) Gap_init rate = 0.08 (14 / 170), avg. gap size = 1.21 (17 / 14) 459 26.10 2.67 5.48 chr6ptel1M 948406 948555 (51445) C MIRb#SINE/MIR (115) 153 8 m_b296s601i49 12357 chr6ptel1M 948406 TCCTCATTTTACAGATGAGAAAACTTGAGTCTTCCAGAGAGG--AGGTAA 948453 i i - v -- -- i C MIRb#SINE/MIR 153 TCCCCATTTTACAGATGAGGAAACT-GAGGCT--CAGAGAGGTTAAGTAA 107 chr6ptel1M 948454 CATGTCCAAAGTCTGTCAGGTCACAGGTGCCAGAGCTAGGATGGGAGCCC 948503 v i i vvv v vii i v ii vv i C MIRb#SINE/MIR 106 CTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCC 57 chr6ptel1M 948504 AGAAACTCTTT--CTCAGGATCCTGTGATTTTTTTTTTTACTGCATCAGT 948551 -iv v i -- vii v i ----i i ii i vv C MIRb#SINE/MIR 56 AG-GTCTGTCTGACTCCAAAGCCCGTG----CTCTTTCCACTGCACCACG 12 chr6ptel1M 948552 CTGC 948555 C MIRb#SINE/MIR 11 CTGC 8 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.42 CpG sites = 21, Kimura (unadjusted) = 32.63 Transitions / transversions = 1.31 (21/16) Gap_init rate = 0.07 (10 / 149), avg. gap size = 1.20 (12 / 10) 194 35.05 0.78 20.37 chr6ptel1M 948662 948790 (51210) MIRb#SINE/MIR 2 109 (159) m_b296s601i50 12358 chr6ptel1M 948662 AGAAAGGTGTTATAGTGCTATGGAAAGATTGGGGAACTTGGAGACTCTCC 948711 ii iivii i vi viiv ivi ------- MIRb#SINE/MIR 2 AGAGGGGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAG------- 44 chr6ptel1M 948712 AACTTCAGACAAAT-TGGCTACATGTAACATTCACATTTTGTATCTGCTC 948760 ---- i i- -----------i iv iii vv iv MIRb#SINE/MIR 45 ----TCAGACAGACCTGG-----------GTTCGAATCCCGGCTCTGCCA 79 chr6ptel1M 948761 CTTGCAACCTGTGTGATCTTGGTCGAGTCA 948790 i v v i v i i MIRb#SINE/MIR 80 CTTACTAGCTGTGTGACCTTGGGCAAGTTA 109 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.86 CpG sites = 24, Kimura (unadjusted) = 47.48 Transitions / transversions = 2.00 (24/12) Gap_init rate = 0.18 (23 / 128), avg. gap size = 1.00 (23 / 23) 256 24.73 18.28 0.00 chr6ptel1M 948754 948846 (51154) MIR3#SINE/MIR 67 176 (32) m_b296s601i51 12358 chr6ptel1M 948754 TCTGCTCCTTGCAACCTGTGTGATCTTGGTCGAGTCAT---AC------A 948794 iv vi v?v i v i i--- ------i MIR3#SINE/MIR 67 TCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTG 116 chr6ptel1M 948795 GGT---AGCAT-----TCTGCAAATTGAGGAGATTTGACTAGATGATCTT 948836 i--- iv ----- i v i i v i MIR3#SINE/MIR 117 GGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTC 166 chr6ptel1M 948837 AAAAGTTCCT 948846 v i i MIR3#SINE/MIR 167 TAAGGTCCCT 176 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.17 CpG sites = 14, Kimura (unadjusted) = 31.17 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.04 (4 / 92), avg. gap size = 4.25 (17 / 4) 247 34.72 8.92 2.65 chr6ptel1M 950032 950244 (49756) C MIRc#SINE/MIR (26) 242 17 m_b296s601i52 12359 chr6ptel1M 950032 TATCACTTGAGAGCT-ACAGACTCCTTTCATGTCCTTCATTT-ATTTGTC 950079 v v v i - i viv ii v v i i - vi C MIRc#SINE/MIR 242 TAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATCTCATTTGAT 193 chr6ptel1M 950080 TCTCATGACAACCTCGAAGGGTCAGCGGGGCAA-----ACTTGGCTGGTA 950124 i ii ii vii vi i i----- i vvv ivi v C MIRc#SINE/MIR 192 CCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATT 143 chr6ptel1M 950125 TAATAGATGCGGGCCCTGGGACTCGGAGGAATATTA--TGACAAGCCCAA 950172 v i v ivv i i i -- vi -- vv C MIRc#SINE/MIR 142 TTACAGATGAGGAAACTGAGGCTCAGAG--AGGTTAAGTGACTTGCCCAA 95 chr6ptel1M 950173 -GTCA-----CTAATAGTTTACAGAGAACTGAGA---GAAGACCTAGA-C 950212 - ----- i iv vi -- i i --- -- i i- C MIRc#SINE/MIR 94 GGTCACACAGCTAGTAAGTGGCAGAG--CCGGGACTCGA--ACCCAGGTC 49 chr6ptel1M 950213 TTGATAGTTCCTCCTCCAGTAAATTTTCTGCT 950244 vv iii vvv ivvi ii C MIRc#SINE/MIR 48 TTCCTGACTCCAAGTCCAGTGCTCTTTCCACT 17 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 46.49 CpG sites = 41, Kimura (unadjusted) = 48.37 Transitions / transversions = 1.32 (41/31) Gap_init rate = 0.07 (14 / 212), avg. gap size = 1.79 (25 / 14) 401 29.47 2.92 4.76 chr6ptel1M 950354 950524 (49476) MIRb#SINE/MIR 12 179 (89) m_b296s601i53 12360 chr6ptel1M 950354 CGTGGAATGG-GGAAATAGGGCTAATGCTGGAGCAAGA--GACCTGGGTT 950400 viii - v vi viiivi iv -- MIRb#SINE/MIR 12 CGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTT 61 chr6ptel1M 950401 AAAGCTTTCCTCTCCCCCATCTTCTACCACCTGGGTGACCTTGAAAAAAA 950450 vi i- ii vv iv - -- i v v iiv i- MIRb#SINE/MIR 62 CGAA-TCCCGGCTCTGCCA-CTT--ACTAGCTGTGTGACCTTGGGCAAG- 106 chr6ptel1M 950451 TTGTTCAATTTCTC-GGGTCTCAGTTTCCTCATCTGTAAAATGAAAGGGT 950499 ii i ii - i i --i i MIRb#SINE/MIR 107 TTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATG--GGGAT 154 chr6ptel1M 950500 TGGAATAAATGACCTC-CAAAGCTGT 950524 viv vv - - ii i MIRb#SINE/MIR 155 AATAATACCT-ACCTCGCAGGGTTGT 179 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.94 CpG sites = 31, Kimura (unadjusted) = 39.00 Transitions / transversions = 1.82 (31/17) Gap_init rate = 0.07 (12 / 170), avg. gap size = 1.08 (13 / 12) 412 25.83 2.33 3.94 chr6ptel1M 950364 950492 (49508) MIRc#SINE/MIR 20 146 (122) m_b296s601i54 12360 chr6ptel1M 950364 GGAAATAGGGCTAATGCTGGAG-CAAGA-GACCTGGGTTAAAGCTTTCCT 950411 v vi iivvi - i - vi - ii vv MIRc#SINE/MIR 20 GGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAG-TCCCGG 68 chr6ptel1M 950412 CTCCCCCATCTTCTACCACCTGGGTGACCTTGAAAAAAATTGTTCAATTT 950461 iv - -- i v v iiv i- iii i ii MIRc#SINE/MIR 69 CTCTGCCA-CTT--ACTAGCTGTGTGACCTTGGGCAAG-TCACTTAACCT 114 chr6ptel1M 950462 CTC-GGGTCTCAGTTTCCTCATCTGTAAAATG 950492 - i i MIRc#SINE/MIR 115 CTCTGAGCCTCAGTTTCCTCATCTGTAAAATG 146 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.51 CpG sites = 21, Kimura (unadjusted) = 32.76 Transitions / transversions = 1.91 (21/11) Gap_init rate = 0.06 (8 / 128), avg. gap size = 1.00 (8 / 8) 566 22.74 3.11 4.40 chr6ptel1M 950382 950542 (49458) MIR3#SINE/MIR 36 194 (14) m_b296s601i55 12360 chr6ptel1M 950382 GGAG-CAAGAGACCTGGGTTAAAGCTTTCCTCTCCCCCATCTTCTA-CCA 950429 - i vv - ii vv iv ---- - i? MIR3#SINE/MIR 36 GGAGTCAGGAGACCTGGGTTCTAG-TCCCGGCTCTGCCA----CTAACTN 80 chr6ptel1M 950430 CCTGGGTGACCTTGAAAAAAATTGTTCAATTTCTC-GGGTCTCAGTTTCC 950478 v v iiv i- iii iv ii - i MIR3#SINE/MIR 81 GCTGTGTGACCTTGGGCAAG-TCACTTCACCTCTCTGGGCCTCAGTTTCC 129 chr6ptel1M 950479 TCATCTGTAAAATGAAAGGGTTGGAATAAATGACCTCCAAAGCTGTCTTC 950528 ii v i i i i - vi MIR3#SINE/MIR 130 TCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGG-TCCCTTC 178 chr6ptel1M 950529 TAG-TCTCA-ATTCTA 950542 i - v - MIR3#SINE/MIR 179 CAGCTCTGACATTCTA 194 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.09 CpG sites = 23, Kimura (unadjusted) = 28.09 Transitions / transversions = 1.92 (23/12) Gap_init rate = 0.07 (12 / 160), avg. gap size = 1.00 (12 / 12) 188 17.14 0.00 0.00 chr6ptel1M 950719 950753 (49247) C L3#LINE/CR1 (4) 4095 4061 m_b296s601i56 12361 chr6ptel1M 950719 GAAATGTAGAATCTAAGGGTTGGAAGGGACCTTAG 950753 viii v i C L3#LINE/CR1 4095 GAATCACAGAATCTCAGAGTTGGAAGGGACCTTAG 4061 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 19.86 CpG sites = 4, Kimura (unadjusted) = 19.86 Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 409 31.70 2.65 4.86 chr6ptel1M 950921 951109 (48891) MIR3#SINE/MIR 17 201 (7) m_b296s601i57 12362 chr6ptel1M 950921 GCAGAGAAATCCACAGA--GGGAA--AATTGGCCTGGTTTCTAGTCCAAA 950966 i v - i -- i-- ivv i v vii MIR3#SINE/MIR 17 GCAGAGAGAGC-ACGGACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCGG 65 chr6ptel1M 950967 GTCCCACGCTCACTCCCTTAATGTTCAAGCTCAGGTAAGGCAATTGTTAT 951016 v i--- - vv ?iv vii v ii i v v --i i MIR3#SINE/MIR 66 CTCT---GC-CACTAACTNGCTGTGTGACCTTGGGCAAGTCACTT--CAC 109 chr6ptel1M 951017 CTGTGTGGGCCTTAGTGTTAAGATCTATAAAAGCAAGAGATTAGAAGCTA 951066 v v i v ivvv i vv i i i i -- MIR3#SINE/MIR 110 CTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGA--CTA 157 chr6ptel1M 951067 C-TAGTTTCTAAGGCTACTCCAAGTTCTGACATAATGTGATTCT 951109 v- ii i iiv i v i vv i MIR3#SINE/MIR 158 GATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCT 201 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.47 CpG sites = 31, Kimura (unadjusted) = 42.41 Transitions / transversions = 1.19 (31/26) Gap_init rate = 0.06 (12 / 188), avg. gap size = 1.17 (14 / 12) 448 26.09 6.13 3.59 chr6ptel1M 951127 951289 (48711) C MIRc#SINE/MIR (70) 198 32 m_b296s601i58 12363 chr6ptel1M 951127 TTGGAGCTTCACAGCTTCTCTGTCAGGCAGGTAGCAAACATAGTAATTAT 951176 v v i i vv i v i i --ii -i - C MIRc#SINE/MIR 198 TTTGATCCTCACAACAACCCTGTGAGGTAGGCAG--GGCA-GGTA-TTAT 153 chr6ptel1M 951177 TATTCAAATTTTACAGCTGAGGAAACTGAGGCACAGAGCTGC--AGTCAT 951224 i vv v v vv i-- v i C MIRc#SINE/MIR 152 TATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGAC 103 chr6ptel1M 951225 TT----AAGGTCATGGAGC---CAACTGGCAGATGGTAGGGATTAGAATT 951267 ---- iiv ---i v -- iv i v ii C MIRc#SINE/MIR 102 TTGCCCAAGGTCACACAGCTAGTAAGTGGCAGA--GCCGGGACTCGAACC 55 chr6ptel1M 951268 GAAG-CTTTCTGACTGTAAAGCC 951289 v i - i vi iv C MIRc#SINE/MIR 54 CAGGTCTTCCTGACTCCAAGTCC 32 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.58 CpG sites = 22, Kimura (unadjusted) = 32.58 Transitions / transversions = 1.16 (22/19) Gap_init rate = 0.06 (10 / 162), avg. gap size = 1.60 (16 / 10) 256 25.68 0.00 3.85 chr6ptel1M 951332 951412 (48588) C Charlie4#DNA/hAT-Charlie (0) 3378 3301 m_b296s502i2 12364 chr6ptel1M 951332 CAAGGATTCTTGACAATTTTTTGCATGTTATAGATGACTTTGGAAGTGTG 951381 i i i v- -- ii i ivv v v C Charlie4#DNA/ 3378 CAGGGGTTCTTAACC-TTTTTTG--TGCCATGGACCCCTTTGGCAGTCTG 3332 chr6ptel1M 951382 CTGAAGCCTTTAGATCCTTTTTCAAAATCAT 951412 v v i i i i i v C Charlie4#DNA/ 3331 GTGAAGCCTATGGACCCCTTCTCAGAATAAT 3301 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 32.14 CpG sites = 12, Kimura (unadjusted) = 32.14 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.04 (3 / 80), avg. gap size = 1.00 (3 / 3) 24 24.63 0.00 0.00 chr6ptel1M 951506 951559 (48441) (TA)n#Simple_repeat 1 54 (0) m_b296s252i7 12365 chr6ptel1M 951506 TATATACATAACTATATATATGTATGCATATATTTGTGTATATACATATA 951555 i vv i ii v i i i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr6ptel1M 951556 CATA 951559 i (TA)n#Simple_ 51 TATA 54 Matrix = Unknown Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 187 32.27 18.52 0.52 chr6ptel1M 951610 951771 (48229) C MIRc#SINE/MIR (76) 192 2 m_b296s601i59 12366 chr6ptel1M 951610 CCTCCTAACAATCCC---AGG--AACACTGTACATATTATTAGCCCTATT 951654 vi i i--- --ii vv i vi v i C MIRc#SINE/MIR 192 CCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATT 143 chr6ptel1M 951655 CTACAAATAA------TAAAG-TCAAGGGGGTTAA-CCACCTCCCCCAGA 951696 i i i ------ i i - ii i -iv i v v i C MIRc#SINE/MIR 142 TTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGG 93 chr6ptel1M 951697 TGACATTG---------GACAGAACCCAG-CATAAAGCC------TCC-A 951729 v iv --------- i i vi - vii v ------ -i C MIRc#SINE/MIR 92 TCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTG 43 chr6ptel1M 951730 ACTCCTAAATCCAATTTTCCTTCTGTTACAACCCACCGTCTC 951771 - i i vi i iii i v v i i C MIRc#SINE/MIR 42 ACTCC-AAGTCCAGTGCTCTTTCCACTGCACCACACTGCCTC 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.74 CpG sites = 36, Kimura (unadjusted) = 45.09 Transitions / transversions = 2.25 (36/16) Gap_init rate = 0.06 (10 / 161), avg. gap size = 3.10 (31 / 10) 212 24.53 0.00 1.89 chr6ptel1M 951758 951811 (48189) MIR3#SINE/MIR 97 149 (59) m_b296s601i60 12367 chr6ptel1M 951758 CAACCCACCGTCTCTTCTCTGCACCTCAGTTTTCTCACCTGGTAAATGAG 951807 vi i- v i vi i i vv MIR3#SINE/MIR 97 CAAGTCACT-TCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAG 145 chr6ptel1M 951808 AAGG 951811 ii MIR3#SINE/MIR 146 GGGG 149 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.46 CpG sites = 8, Kimura (unadjusted) = 30.46 Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.02 (1 / 53), avg. gap size = 1.00 (1 / 1) 213 20.51 0.00 0.00 chr6ptel1M 951771 951809 (48191) MIR1_Amn#SINE/MIR 114 152 (78) m_b296s601i61 12367 chr6ptel1M 951771 CTTCTCTGCACCTCAGTTTTCTCACCTGGTAAATGAGAA 951809 i ?i i i vv i i MIR1_Amn#SINE 114 CCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGGA 152 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.76 CpG sites = 6, Kimura (unadjusted) = 25.76 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 243 29.36 22.33 0.80 chr6ptel1M 952322 952424 (47576) MIRc#SINE/MIR 14 138 (130) m_b296s601i62 12368 chr6ptel1M 952322 TGTAATGAAAAGA-CATCTGAC----AATGCGAGAAGGTCTAAGTTTGAA 952366 i i i - iiv ---- i - ii ii ii i i MIRc#SINE/MIR 14 TGCAGTGGAAAGAGCACTGGACTTGGAGT-CAGGAAGACCTGGGTTCGAG 62 chr6ptel1M 952367 CCCTGTCTTTGC-----------------ACATGGGACA-GTCACTGAAT 952398 i i v i ----------------- v v i - v i MIRc#SINE/MIR 63 TCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAAC 112 chr6ptel1M 952399 ATTTCTGAGCCTTCATTTTCTCATCT 952424 v i ivi i MIRc#SINE/MIR 113 CTCTCTGAGCCTCAGTTTCCTCATCT 138 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.80 CpG sites = 23, Kimura (unadjusted) = 40.35 Transitions / transversions = 3.29 (23/7) Gap_init rate = 0.05 (5 / 102), avg. gap size = 4.80 (24 / 5) 219 23.81 29.76 0.00 chr6ptel1M 952382 952465 (47535) MIRb#SINE/MIR 99 207 (61) m_b296s601i63 12368 chr6ptel1M 952382 TGGGACAGTCACTGAATATTTCTGAGCCTTCATTTTCTCATCT------- 952424 vv i v iv i ivi i ------- MIRb#SINE/MIR 99 TGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAAT 148 chr6ptel1M 952425 ----------------ACCTCCCAAGGTTGCAG--AAGATAAAATGAGAT 952456 ---------------- v i iv -- i v MIRb#SINE/MIR 149 GGGGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGAT 198 chr6ptel1M 952457 AGTGGATAT 952465 i v i MIRb#SINE/MIR 199 AATGCATGT 207 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.06 CpG sites = 11, Kimura (unadjusted) = 29.06 Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.04 (3 / 83), avg. gap size = 8.33 (25 / 3) 235 24.24 2.99 1.47 chr6ptel1M 952423 952489 (47511) MIRc#SINE/MIR 169 236 (32) m_b296s601i64 12368 chr6ptel1M 952423 CTACCTCCCAAGGTTGCAG--AAGATAAAATGAGATAGTGGATATGGATT 952470 v i iv -- i v i v i i -v MIRc#SINE/MIR 169 CTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAA-A 217 chr6ptel1M 952471 TTACTTTGTAAAATATAAA 952489 vii v i MIRc#SINE/MIR 218 GCGCTTTGTAAACTGTAAA 236 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.38 CpG sites = 9, Kimura (unadjusted) = 29.76 Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.03 (2 / 66), avg. gap size = 1.50 (3 / 2) 465 18.09 0.65 17.42 chr6ptel1M 953052 953205 (46795) MER63D#DNA/hAT-Tip100 336 467 (594) m_b296s502i3 12369 chr6ptel1M 953052 GTGTGAGCATTTGCACCTCAGAGATTAGGGAATGCTGCAAATCAGGGCTT 953101 v i i v i i ii vi i i MER63D#DNA/hA 336 GTGGGAGTATTTACACCACGGAAATCGGCAAACGCTACAAATCAGGGCTT 385 chr6ptel1M 953102 GATTTTTTTTTGTTGTTGTTTACTTTCCTTTTATTGATTGTCTCTAGACT 953151 ---------i ---------- i -- MER63D#DNA/hA 386 GATTT---------ATTGTTT----------TGTTGATTGTCT--AGACT 414 chr6ptel1M 953152 TTTAAAAAAGTGACTGAGAAAATATTAACAATGCACACT-GACTTAAGAG 953200 -- i iv i i v i -i i MER63D#DNA/hA 415 T--AAGAAAGTGATGGAGAAAATGTTAATAATGCAGATTAAACTTAAAAG 462 chr6ptel1M 953201 TGTGT 953205 MER63D#DNA/hA 463 TGTGT 467 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 17.74 CpG sites = 18, Kimura (unadjusted) = 20.75 Transitions / transversions = 3.60 (18/5) Gap_init rate = 0.16 (24 / 153), avg. gap size = 1.00 (24 / 24) 257 28.41 20.83 1.50 chr6ptel1M 953675 953738 (46262) MIR3#SINE/MIR 9 74 (134) m_b296s601i65 12370 chr6ptel1M 953675 GTGGTCCAGCAGAGAAAGTGCT--TTGAGA--CAATTGGGCATCTGGGTT 953720 iiv i ii v--i i -- --- iv i MIR3#SINE/MIR 9 GTGGCTGAGCAGAGAGAGCACGGACTGGGAGTCA---GGAGACCTGGGTT 55 chr6ptel1M 953721 GAAATCAGAGCTCTGCT-C 953738 vv i vvi i- MIR3#SINE/MIR 56 CTAGTCCCGGCTCTGCCAC 74 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.31 CpG sites = 29, Kimura (unadjusted) = 37.32 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.10 (6 / 63), avg. gap size = 1.33 (8 / 6) 39 0.00 0.00 0.00 chr6ptel1M 953739 953774 (46226) (T)n#Simple_repeat 1 36 (0) c_b296s251i2 12371 chr6ptel1M 953739 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 953774 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 36 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 257 28.41 20.83 1.50 chr6ptel1M 953775 953877 (46123) MIR3#SINE/MIR 75 207 (1) m_b296s601i65 12370 chr6ptel1M 953775 AAC--AATGTGTGAGCCT----------CTTC-----------CATAAAT 953801 --iv v i ---------- ----------- v v i MIR3#SINE/MIR 75 AACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGT 124 chr6ptel1M 953802 --CCTCAATTACAAATTGGGAAGACTGGACTAGATGGTCTCAAAGGGCCA 953849 -- vi ii v i ii ii i v v v MIR3#SINE/MIR 125 TTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCC 174 chr6ptel1M 953850 TCTC----CTGACAATCCATG-TTCTACCATCC 953877 ii ---- v i - iv i MIR3#SINE/MIR 175 TTCCAGCTCTGACATTCTATGATTCTATGATTC 207 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.31 CpG sites = 29, Kimura (unadjusted) = 37.32 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.06 (6 / 102), avg. gap size = 5.00 (30 / 6) 552 29.02 4.40 2.47 chr6ptel1M 954093 954251 (45749) C MIRc#SINE/MIR (104) 164 3 m_b296s601i66 12372 chr6ptel1M 954093 GGTAGGTGTTATAACCATTCTCCTTTGACAGACTGGGAAGCTGAAACT-A 954141 i i ---i i i v v ivi i ii - C MIRc#SINE/MIR 164 GGCAGGTATTAT---TATCCCCATTTTACAGATGAGGAAACTGAGGCTCA 118 chr6ptel1M 954142 GATGAAATGAAATGACTTACTCAGGATCACTCAGACAAGAAGTGCCTGAA 954191 - ii v i i i i i v vi iv v v i C MIRc#SINE/MIR 117 GA-GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAG 69 chr6ptel1M 954192 GTTGGATTTGAACTCAGGGCTTCCTGATTCTAAGGCCAGTGCTCTCCCT- 954240 viv i i i v i i v ii i- C MIRc#SINE/MIR 68 CCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCA 19 chr6ptel1M 954241 -----CCATGTTGCCT 954251 ----- iii C MIRc#SINE/MIR 18 CTGCACCACACTGCCT 3 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.67 CpG sites = 32, Kimura (unadjusted) = 38.93 Transitions / transversions = 2.46 (32/13) Gap_init rate = 0.04 (7 / 158), avg. gap size = 1.57 (11 / 7) 252 14.59 0.00 2.08 chr6ptel1M 954271 954319 (45681) EutTc1-N2#DNA/TcMar-Tc1 8 55 (323) m_b296s502i4 12373 chr6ptel1M 954271 TCCCGAAATTCTTAGTGCAGTTTTAAACTTTAATAGCTCAAAACAGTAT 954319 i v i i iv i - EutTc1-N2#DNA 8 TCCCAAAAGTCTTAGTGCAGTTTTAAGCTTTAATAACTTCAGA-AGTAT 55 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 16.56 CpG sites = 5, Kimura (unadjusted) = 16.56 Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.02 (1 / 48), avg. gap size = 1.00 (1 / 1) 17 16.00 4.76 6.45 chr6ptel1M 956255 956317 (43683) (TTC)n#Simple_repeat 1 62 (0) m_b296s252i8 12374 chr6ptel1M 956255 TTCTCTCTGTTTTC-ACTTCTT-TTCTTCCTTCTTGGGCAACTCCTTTCT 956302 - - i -v - - vvv vv i - (TTC)n#Simple 1 TTCT-TCT-TCTTCTTCTTCTTCTTCTT-CTTCTTCTTCTTCTTC-TTCT 46 chr6ptel1M 956303 TCTTCTT-TTCTTCTT 956317 - (TTC)n#Simple 47 TCTTCTTCTTCTTCTT 62 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.11 (7 / 62), avg. gap size = 1.00 (7 / 7) 250 27.17 13.04 0.00 chr6ptel1M 957082 957173 (42827) C MIR3#SINE/MIR (10) 198 95 m_b296s601i67 12375 chr6ptel1M 957082 ATCCTAGACTTTGAGAATTTAAGTAAATCTCAGAGATTTTCTAGTCCAA- 957130 v v v v ii vi ivii i i iv - C MIR3#SINE/MIR 198 ATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAAC 149 chr6ptel1M 957131 AGTTTGAATTTAGAGATGAGGAAACTG-----------TGTGAAGTGTCT 957169 vvii v v v -----------v v C MIR3#SINE/MIR 148 CCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACT 99 chr6ptel1M 957170 TGCC 957173 C MIR3#SINE/MIR 98 TGCC 95 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.89 CpG sites = 11, Kimura (unadjusted) = 33.89 Transitions / transversions = 0.79 (11/14) Gap_init rate = 0.02 (2 / 91), avg. gap size = 6.00 (12 / 2) 477 30.23 13.95 0.00 chr6ptel1M 957577 957791 (42209) MIRc#SINE/MIR 16 260 (8) m_b296s601i68 12376 chr6ptel1M 957577 CAGTGTAAAGAAAACTGAACA-AGATTTAG--AG----GGGT--GAGTT- 957616 v iv i v-i v i -- ---- -- i- MIRc#SINE/MIR 16 CAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCC 65 chr6ptel1M 957617 ----TCTGCCACC----AGCT-------CTTAGAGAAGTTATTAAATCTC 957651 ---- i---- ------- i iv i i v i MIRc#SINE/MIR 66 CGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 chr6ptel1M 957652 TCTAAGCCTCAACTTTC-AAACTTTGAAATGGAGATGATGATAATTATAG 957700 i ii i -v v v i i i i vi iivv MIRc#SINE/MIR 116 TCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCC 165 chr6ptel1M 957701 CATCTTTTTCATGAG---ATAGTGAGGATTGTATGAGATATTAGATGTGA 957747 iii vii iii ---i v iiv v iv MIRc#SINE/MIR 166 TGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGA 215 chr6ptel1M 957748 AAATGTTTTGC-AACCATGAATTGCTGAACAGATATAAACTGTTA 957791 ii i i- ii i v iv i i iv? MIRc#SINE/MIR 216 AAGCGCTTTGTAAACTGTAAAGTGCTATACAAATGTAAGGNGTTA 260 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.39 CpG sites = 45, Kimura (unadjusted) = 41.25 Transitions / transversions = 2.25 (45/20) Gap_init rate = 0.05 (11 / 214), avg. gap size = 2.73 (30 / 11) 370 31.49 3.23 9.27 chr6ptel1M 958227 958443 (41557) C MIR3#SINE/MIR (3) 205 1 m_b296s601i69 12377 chr6ptel1M 958227 TCATAGGCTCATTGGATGT-AAACCTTGAAGGGAATTTACAAATAATATA 958275 iv v i - i v v vi v i v v C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTA 156 chr6ptel1M 958276 ATAAATAATGCCAAAATGCCTCATTGTTTATAAA--AAGAAGCCAAGCCC 958323 i -------- vvi- -- i i -- i i ii v C MIR3#SINE/MIR 155 GT--------CCAACCC-CCTCATT--TTACAGATGAGGAAACTGAGGCC 117 chr6ptel1M 958324 CACGAGAGA--AAATGATTTTTTCCCATAATCACATGGGCAGT-AGTAAA 958370 - i-- i i v-- vii ii v? - i-- C MIR3#SINE/MIR 116 CA-GAGAGGTGAAGTGACTTG--CCCAAGGTCACACAGCNAGTTAGTG-- 72 chr6ptel1M 958371 GAGCAGAGCTGGGATTGAAACCTTGCTCATCAGATTGCAGATCCA-ATTC 958419 -- i i ii iv v vi v i v vii i-ii C MIR3#SINE/MIR 71 --GCAGAGCCGGGACTAGAACCCAGGTCTCCTGACTCCCAGTCCGTGCTC 24 chr6ptel1M 958420 TCTTGGTGGAGATCAGTCTACTAG 958443 iv ivv -i v i i C MIR3#SINE/MIR 23 TCTCTGCTCAG-CCACTCTGCCAG 1 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.58 CpG sites = 38, Kimura (unadjusted) = 42.41 Transitions / transversions = 1.58 (38/24) Gap_init rate = 0.11 (24 / 216), avg. gap size = 1.08 (26 / 24) 180 28.53 7.94 5.43 chr6ptel1M 958780 958905 (41095) C L2d2_3end#LINE/L2 (24) 531 403 m_b296s601i71 12378 chr6ptel1M 958780 TTGTACACCTACGATGTAACATGCACTGGACTAAGCACTGGGGAGCCCAG 958829 vi i vi ivv v vi i i v i ---ii C L2d2_3end#LIN 531 TTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGTGGGG---GA 485 chr6ptel1M 958830 TACCAGAAAG---AAG-CA--GTTCCTGCCCTT---GAGCATAGGATC-A 958869 v ii --- - -- i i--- v vi - C L2d2_3end#LIN 484 TACAAAGAAGTATAAGACATGGTCCCTGCCCTCAAGGAGCTTACAATCTA 435 chr6ptel1M 958870 ATGGGAGAAGACAGTGTCCACAAAGAAGCTGAAAAG 958905 i v - i ivi-- i v v - C L2d2_3end#LIN 434 GTTGG-GGAGACAAGA--CATAAACACG-TGAAAAG 403 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.25 CpG sites = 20, Kimura (unadjusted) = 36.94 Transitions / transversions = 1.43 (20/14) Gap_init rate = 0.10 (12 / 125), avg. gap size = 1.42 (17 / 12) 279 25.96 8.65 0.00 chr6ptel1M 958780 958883 (41117) C L2a_3end#LINE/L2 (24) 493 381 m_b296s601i70 12378 chr6ptel1M 958780 TTGTACACCTACGATGTAACATGCACTGGACTAAGCACTGGGGAGCC--C 958827 vi i v iv v vv i i vv -- C L2a_3end#LINE 493 TTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGCGCTGGGGATACAGC 444 chr6ptel1M 958828 AGT--ACCAGAAAGA-AGCAGTTCCTGCCCTT---GAGCATAGGATC-AA 958870 -- v i v - iv i i--- v viv - i C L2a_3end#LINE 443 AGTGAACAAAACAGACAAAAGTCCCTGCCCTCATGGAGCTTACATTCTAG 394 chr6ptel1M 958871 TGGGAGAAGACAG 958883 i i C L2a_3end#LINE 393 TGGGGGGAGACAG 381 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.38 CpG sites = 13, Kimura (unadjusted) = 32.12 Transitions / transversions = 0.93 (13/14) Gap_init rate = 0.05 (5 / 103), avg. gap size = 1.80 (9 / 5) 253 32.99 4.12 0.00 chr6ptel1M 960128 960224 (39776) MIRc#SINE/MIR 61 161 (107) m_b296s601i72 12379 chr6ptel1M 960128 AATCTTTGCTTCAACATTTTCTAGCACTAAGATCATGGACAAGCCAGTTA 960177 i iiv iiiv i v vv iv i v i i v MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTA 110 chr6ptel1M 960178 CCCTACCTGAGCTTCCATTTAC---TATGTAAAAGTAGGATAA-AATATT 960223 v vi i vi v --- v vvi - ii MIRc#SINE/MIR 111 ACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACC 160 chr6ptel1M 960224 T 960224 MIRc#SINE/MIR 161 T 161 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.59 CpG sites = 17, Kimura (unadjusted) = 44.43 Transitions / transversions = 1.13 (17/15) Gap_init rate = 0.02 (2 / 96), avg. gap size = 2.00 (4 / 2) 337 24.97 7.32 2.33 chr6ptel1M 960440 960562 (39438) L4_C_Mam#LINE/RTE-X 3677 3805 (1333) m_b296s551i2 12380 chr6ptel1M 960440 AGCTGCCCTGATTTTTAGCTTG-ATTTTAAAAATAACTTGCTGTAGCTTC 960488 iv vv i i- i --- v ii i L4_C_Mam#LINE 3677 AGCCCCCCTCCTTTTTAACTTATATCT---AAATAACTTGATACAGCTTT 3723 chr6ptel1M 960489 TAGATAAAATGGATG--TG------TGCGACAGCAAACTGTGAGACGAAC 960530 i v -- ------ v i v vi i i L4_C_Mam#LINE 3724 TAGATGAACTGGATGCATGCCCTCCTGCCATAGCAAACAGGAAGACAAGC 3773 chr6ptel1M 960531 ACCCTCCCCTGTGACAATGGTACTGTTTTATT 960562 i i i vii ii iv L4_C_Mam#LINE 3774 ATCCTCCTCTATGCTGATGACATGGTTTTATT 3805 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 31.51 CpG sites = 20, Kimura (unadjusted) = 31.51 Transitions / transversions = 2.00 (20/10) Gap_init rate = 0.05 (6 / 122), avg. gap size = 2.00 (12 / 6) 437 32.35 1.46 2.96 chr6ptel1M 960774 960910 (39090) MIRc#SINE/MIR 19 153 (115) m_b296s601i73 12381 chr6ptel1M 960774 TGAGAAGACTTCTGTTTCTAGAATCAC-AGGGTCTGGGT-CAAATCCCCT 960821 ii viv vvii i i v- i ii - i i vv MIRc#SINE/MIR 19 TGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGG 68 chr6ptel1M 960822 CTCTGATGCTTGCTAGTCAAATGGTCTTCAGCAAGTCACTTCATCCCTCC 960871 vii i iiivi ii vi v i i i MIRc#SINE/MIR 69 CTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCT 118 chr6ptel1M 960872 AAACTTCAGTTTCTTCATCCATAAAGTGAGAAGGGATAA 960910 i i i i ii i ---- MIRc#SINE/MIR 119 GAGCCTCAGTTTCCTCATCTGTAAAATG----GGGATAA 153 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.49 CpG sites = 32, Kimura (unadjusted) = 46.02 Transitions / transversions = 2.91 (32/11) Gap_init rate = 0.04 (6 / 136), avg. gap size = 1.00 (6 / 6) 469 31.46 4.17 0.67 chr6ptel1M 960794 960937 (39063) MIR3#SINE/MIR 37 185 (23) m_b296s601i74 12381 chr6ptel1M 960794 GAATCACAGGGTCTGGGT-CAAATCCCCTCTCTGATGCTTGCTAGTCAAA 960842 i vii ii - v i vv vii vi ? iiivi MIR3#SINE/MIR 37 GAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTG 86 chr6ptel1M 960843 TGGTCTTCAGCAAGTCACTTCATCCCTCCAAACTTCAGTTTCTTCATCCA 960892 ii vi i i iiii i i ii MIR3#SINE/MIR 87 TGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTG 136 chr6ptel1M 960893 TAAAGTGAGAAGGGATAAACTAAAT--TCCCTA---TCATTTCTAGATCT 960937 i -i v ii i -- i --- vi i v MIR3#SINE/MIR 137 TAAAATGAG-GGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCT 185 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.84 CpG sites = 34, Kimura (unadjusted) = 44.84 Transitions / transversions = 3.09 (34/11) Gap_init rate = 0.03 (4 / 143), avg. gap size = 1.75 (7 / 4) 24 17.60 1.85 0.00 chr6ptel1M 961195 961242 (38758) (TCA)n#Simple_repeat 1 49 (6) m_b296s252i9 12382 chr6ptel1M 961195 TCATCATCATCATCATCATCATCA-CATTATTATTATTATTATTATTAT 961242 - i i i i i i i (TCA)n#Simple 1 TCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCAT 49 Matrix = Unknown Transitions / transversions = 1.00 (7/0) Gap_init rate = 0.02 (1 / 47), avg. gap size = 1.00 (1 / 1) 79 1.37 0.00 0.00 chr6ptel1M 961243 961316 (38684) (TAG)n#Simple_repeat 1 74 (0) c_b296s251i3 12383 chr6ptel1M 961243 TAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGCAGTA 961292 i (TAG)n#Simple 1 TAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTA 50 chr6ptel1M 961293 GTAGTAGTAGTAGTAGTAGTAGTA 961316 (TAG)n#Simple 51 GTAGTAGTAGTAGTAGTAGTAGTA 74 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 73), avg. gap size = 0.0 (0 / 0) 339 20.95 14.71 1.74 chr6ptel1M 961398 961499 (38501) C MIRc#SINE/MIR (94) 174 60 m_b296s601i75 12384 chr6ptel1M 961398 AGGTAAGCAGCCCAATTATAATTATCCTCTCTTGACAGATGAGGAGACTG 961447 i vv iv v i vi v i C MIRc#SINE/MIR 174 AGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTG 125 chr6ptel1M 961448 AAGCCCAAAGAGG---AGCTTTCCTTGTTCA--TTCACA--------AAG 961484 i i i --- -- vv ii --v -------- C MIRc#SINE/MIR 124 AGGCTCAGAGAGGTTAAG--TGACTTGCCCAAGGTCACACAGCTAGTAAG 77 chr6ptel1M 961485 T--CAGAGCTAGGACTC 961499 -- ii C MIRc#SINE/MIR 76 TGGCAGAGCCGGGACTC 60 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 23.51 CpG sites = 12, Kimura (unadjusted) = 24.99 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.06 (6 / 101), avg. gap size = 2.83 (17 / 6) 271 24.68 15.15 1.79 chr6ptel1M 961414 961512 (38488) C MIRb#SINE/MIR (107) 161 50 m_b296s601i76 12384 chr6ptel1M 961414 TATAATTATCCTCTCTTGACAGATGAGGAGACTGAAGCCCAAAGAGG--- 961460 v i vi v i i i i --- C MIRb#SINE/MIR 161 TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTA 112 chr6ptel1M 961461 AGCTTTCCTTGTTCA--TTCACA--------AAGT--CAGAGCTAGGACT 961498 -- vv ii --v -------- -- ii i C MIRb#SINE/MIR 111 AG--TAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATT 64 chr6ptel1M 961499 CTGCATTAGGTTTG 961512 vivvii i C MIRb#SINE/MIR 63 CGAACCCAGGTCTG 50 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.15 CpG sites = 15, Kimura (unadjusted) = 30.84 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.06 (6 / 98), avg. gap size = 2.83 (17 / 6) 219 36.65 1.16 4.82 chr6ptel1M 961501 961586 (38414) MIRc#SINE/MIR 27 109 (159) m_b296s601i77 12385 chr6ptel1M 961501 GCATTAGGTTTGGGGTTAGAGAG-CTTGTGTCACAATCCTAGCTCCATCA 961549 i i ii i i ii - i v ivv i ii iii MIRc#SINE/MIR 27 GCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCA 76 chr6ptel1M 961550 TTTCTTTATTATTCCTGTAATCTTGGGCTCATCACTT 961586 i ---- i viiv i i vvi MIRc#SINE/MIR 77 CTT----ACTAGCTGTGTGACCTTGGGCAAGTCACTT 109 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 53.32 CpG sites = 23, Kimura (unadjusted) = 56.65 Transitions / transversions = 3.29 (23/7) Gap_init rate = 0.06 (5 / 85), avg. gap size = 1.00 (5 / 5) 222 27.27 1.82 0.00 chr6ptel1M 961585 961639 (38361) MIR3#SINE/MIR 150 205 (3) m_b296s601i78 12386 chr6ptel1M 961585 TTGGATCAAACAGTCTCTATGGTCCCTTCCAGCCCTGA-GCTTAATTATC 961633 ii i iii v i -ii iv v i MIR3#SINE/MIR 150 TTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATT 199 chr6ptel1M 961634 TTATGA 961639 i MIR3#SINE/MIR 200 CTATGA 205 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.64 CpG sites = 12, Kimura (unadjusted) = 36.64 Transitions / transversions = 4.00 (12/3) Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1) 224 30.10 11.41 2.50 chr6ptel1M 961679 961862 (38138) L3#LINE/CR1 3790 3989 (110) m_b296s601i79 12387 chr6ptel1M 961679 CTTTCATGTGGAAGAGAGAAGAGACTCATCTAGTGTG---CTAGTGGTC- 961724 v i vv i iiv --- i v v - L3#LINE/CR1 3790 CTGTCATGTGGAAGAGGGATTAGACTTATTCTGTGTGGCTCCAGAGGGCA 3839 chr6ptel1M 961725 --TCCAAGACCAGATCTAGGAGAAT--CAGGGAA--ATATTACAAC---A 961765 --v i i - vviv ii i -- i-- v v ii --- L3#LINE/CR1 3840 GAACTAGGACCA-ATGGGTGGAAGTTACAGGGAGGCAGATTTCGGCTCAA 3888 chr6ptel1M 961766 TGGAAGGAGATACTTCCTAGCATTC--TTCTAGGCATTAGATTAGACAT- 961812 iv iiv i i v --vv ivv -- i v i - - L3#LINE/CR1 3889 TATAAGGAAGAACTTTCTAACAATCAGAGCTGTCCA--AAAATGGA-ATG 3935 chr6ptel1M 961813 GGCCCCTTCCTGAGG----GAGATCTTGGATTA-TGAAGGTGTTCAAAGA 961857 iv i v? ---- v iiv - i - i iv L3#LINE/CR1 3936 GGCTGCCTCGNGAGGTAGTGAGCTCCCCG-TCACTGGAGGTGTTCAAGCA 3984 chr6ptel1M 961858 GAGGC 961862 L3#LINE/CR1 3985 GAGGC 3989 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.70 CpG sites = 29, Kimura (unadjusted) = 39.64 Transitions / transversions = 1.16 (29/25) Gap_init rate = 0.08 (15 / 183), avg. gap size = 1.73 (26 / 15) 191 22.64 16.98 0.00 chr6ptel1M 962105 962157 (37843) L2d_3end#LINE/L2 449 510 (6) m_b297s601i5 12388 chr6ptel1M 962105 CAAAGGGCCCAGCATAG----AAGCACA-----AACACTCAATAGATATT 962145 v v i i ----i -----ii i i i L2d_3end#LINE 449 CACAGCGCCTAGCACAGTGCTGAGCACATAGTAGGCGCTCAATAAATACT 498 chr6ptel1M 962146 TTCTGATTGATT 962157 vi L2d_3end#LINE 499 TGTTGATTGATT 510 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 25.50 CpG sites = 9, Kimura (unadjusted) = 28.23 Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.04 (2 / 52), avg. gap size = 4.50 (9 / 2) 367 30.56 5.23 8.05 chr6ptel1M 962273 962425 (37575) C L3#LINE/CR1 (147) 3952 3804 m_b297s601i6 12389 chr6ptel1M 962273 TACCTCATGAGGC--CCAA--GGATTTTTAAATGACCTTTATTATTAGGA 962318 ?i -- v --vv ii iii ii v i i C L3#LINE/CR1 3952 TACCTCNCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGATTGTTAGAA 3903 chr6ptel1M 962319 AGTTTTTCTTTATATTTTCGTTATATTAAACTAAAACCC-CCTTCTTACA 962367 i i -----------i i ii i i- i i ii C L3#LINE/CR1 3902 AGTTCTTCCTTATATT-----------GAGCCGAAATCTGCCTCCCTGTA 3864 chr6ptel1M 962368 AACTTTCATCCATTGCTCTTAGTTCTCTCTGTCAAGGTCA---AGAACAA 962414 - i i v i vi iviiiii i --- i C L3#LINE/CR1 3863 A-CTTCCACCCATTGGTCCTAGTTCTGCCCTCTGGAGCCACACAGAATAA 3815 chr6ptel1M 962415 ATCTAATCCTT 962425 i i C L3#LINE/CR1 3814 GTCTAATCCCT 3804 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.15 CpG sites = 36, Kimura (unadjusted) = 44.17 Transitions / transversions = 5.14 (36/7) Gap_init rate = 0.11 (16 / 152), avg. gap size = 1.25 (20 / 16) 342 36.90 13.46 1.37 chr6ptel1M 962437 962763 (37237) L3#LINE/CR1 3314 3679 (420) m_b297s601i7 12390 chr6ptel1M 962437 AACAA-AT-AAATGTAATAAGTATAAAGGGAAA------CATTTCGGTTT 962478 - - v i i v v v ------ v i L3#LINE/CR1 3314 AACAAGATGAAATTTAACAGGGATAAATGTAAAGTCCTGCATTTAGGTTC 3363 chr6ptel1M 962479 AAAAACTCAACTTCCTAA-TAT----TCGCAAGG-----------TAGAA 962512 v v vi - i---- v vi -----------i v L3#LINE/CR1 3364 AAAAAATCAACTGCACAAGTACAGGATGGAGAGGATCTGGCTTAGCAGCA 3413 chr6ptel1M 962513 TTTTATCTGAAAAAAATGTGAGGGTTTTTGTAAATTTTGAGGTCAAGATG 962562 v i iv i iv ii v vi iivii v v L3#LINE/CR1 3414 GTTCACGTGAAAAAGACCTAGGGGTTTTAGTTGACCGCAAGCTCAATATG 3463 chr6ptel1M 962563 AGTTA----------------TCCCAAGAATTGGATATGAGCTTAGATAA 962596 ii ----------------v v i vivi iii v iivi L3#LINE/CR1 3464 AGCCAACAGTGTGATGTGGCTGCCAAAAAAGCTAATGCAATCTTAGGCTG 3513 chr6ptel1M 962597 TGTTAAGTAAAGTATGGTACTGCAATCACACCGAAGTGAGTAATCATCCC 962646 ii vvi i iii----- v ? i i vii vi L3#LINE/CR1 3514 CATTAATAGAAGTATAGTGTC-----CAGANCAAGGGAGGTAATAGTCCC 3558 chr6ptel1M 962647 ATTGAAGATGGCTTTGGTCAGATCAA--CTGAAGGACCGTGTTCACTTTT 962694 ii v vviv vi i v-- i v ii i v i L3#LINE/CR1 3559 GCTGTACTCTGCGCTGGTCAGACCACATCTGGAGTATTGCGTTCAGTTCT 3608 chr6ptel1M 962695 AAAAACTACGAT--AGAAAAGTCAGTGATATTTTGAGGAGCATAAATAGG 962742 iiivi i iv -- ii ii v v i vvi ii v i vv v L3#LINE/CR1 3609 GGGCGCCACATTTTAAGAGGGACATTGACAAACTGGAGCGCGTCCAGAGG 3658 chr6ptel1M 962743 AAGGTGATAAGGATGGTGAAG 962763 ii i iv L3#LINE/CR1 3659 AGAGCGACCAGGATGGTGAAG 3679 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 48.98 CpG sites = 70, Kimura (unadjusted) = 53.54 Transitions / transversions = 1.43 (70/49) Gap_init rate = 0.04 (14 / 326), avg. gap size = 3.50 (49 / 14) 458 32.67 0.66 1.32 chr6ptel1M 962933 963084 (36916) L3#LINE/CR1 3683 3833 (266) m_b297s601i8 12390 chr6ptel1M 962933 CTCAAAACTATGCTGACTGAAGAGTGAAAGAAGGAACTAGGAATATTTAT 962982 vi i iiivv i ii ivv i i i v L3#LINE/CR1 3683 CTGGAAACCATGTCATATGAGGAACGGTTGAAGGAACTGGGGATGTTTAG 3732 chr6ptel1M 962983 CTTGGGGAAGAAAAGGCTT-GAAGCCACATAGATGGTGATTTTCAAGGGT 963031 i i i i - i vv - i ivi i ivi L3#LINE/CR1 3733 CCTGGAGAAGAGAAGACTTAGAGGAGACAT-GATAGCTGTCTTCAAATAT 3781 chr6ptel1M 963032 GTAAAAGGGCCGTCTTGTGAAAGAAGGATTAAATGTGTTCTGCTCGGTCC 963081 v -i i v i i i iv i ivi ii L3#LINE/CR1 3782 TT-GAAGGGCTGTCATGTGGAAGAGGGATTAGACTTATTCTGTGTGGCTC 3830 chr6ptel1M 963082 TAG 963084 i L3#LINE/CR1 3831 CAG 3833 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 44.87 CpG sites = 35, Kimura (unadjusted) = 46.21 Transitions / transversions = 2.50 (35/14) Gap_init rate = 0.02 (3 / 151), avg. gap size = 1.00 (3 / 3) 549 30.43 3.09 0.60 chr6ptel1M 963558 963719 (36281) C MIR3#SINE/MIR (1) 207 42 m_b297s601i9 12391 chr6ptel1M 963558 AATCACAGGATAACAGA--CTTAGAACAAAATGTGAACTTTGAATTCATC 963605 i i v i --v i i vii v v v v iv C MIR3#SINE/MIR 207 AATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATC 158 chr6ptel1M 963606 TAGTCCAGTCCCCTCATTTTACAAATAAGGAAAC--GGGTCCAGAGAGAG 963653 ii i i --i i iv C MIR3#SINE/MIR 157 TAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGT 108 chr6ptel1M 963654 TAAGTAAGTTGCTTAAAACTAAATGAACGAA-CAATGGCTGAACCAGAAT 963702 v i v ii iiii v i- i ? i-i i v i i i i C MIR3#SINE/MIR 107 GAAGTGACTTGCCCAAGGTCACAC-AGCNAGTTAGTGGCAGAGCCGGGAC 59 chr6ptel1M 963703 TTGAACCCTGGTTTTTT 963719 v v i ii C MIR3#SINE/MIR 58 TAGAACCCAGGTCTCCT 42 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.60 CpG sites = 34, Kimura (unadjusted) = 41.76 Transitions / transversions = 2.27 (34/15) Gap_init rate = 0.02 (4 / 161), avg. gap size = 1.50 (6 / 4) 392 24.36 0.00 0.00 chr6ptel1M 964105 964182 (35818) C MIR3#SINE/MIR (23) 185 108 m_b297s601i10 12392 chr6ptel1M 964105 AGATCTGGAAGAGCCCTCAGAGATCATTTAATTCAATCTTGGCTTGTTCC 964154 v i v i i i i i iivv v v v C MIR3#SINE/MIR 185 AGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTAC 136 chr6ptel1M 964155 AGATGGAGAAACTGAAGCCCAGAGAGAT 964182 ii i i C MIR3#SINE/MIR 135 AGATGAGGAAACTGAGGCCCAGAGAGGT 108 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 30.27 CpG sites = 12, Kimura (unadjusted) = 30.27 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.00 (0 / 77), avg. gap size = 0.0 (0 / 0) 478 27.33 11.33 0.00 chr6ptel1M 964345 964494 (35506) C L3#LINE/CR1 (1) 4098 3932 m_b297s601i11 12393 chr6ptel1M 964345 ACAGAA-CACATGATCTCAG--TTAGA-----CCTCAGAAGCAGTCTTTT 964386 i - vi -- i ----- i i ivi vv C L3#LINE/CR1 4098 ATAGAATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGT 4049 chr6ptel1M 964387 TCAATCTTT-ACACAA-ACAAGAATG-----TGCAAAATATCTGACAAAT 964429 i i ii- iv -i i v----- i v vi i C L3#LINE/CR1 4048 CCAACCTCCCATCCAATGCAGGAATCCCTTCTACAACATCCCTGACAAGT 3999 chr6ptel1M 964430 G--CATTCGGCTCTTGCTTGAAGCCCTCCAGTGATAGGAAACTCATTACC 964477 -- i i iii vv ii i i i C L3#LINE/CR1 3998 GGTCATCCAGCCTCTGCTTGAACACCTCCAGTGACGGGGAGCTCACTACC 3949 chr6ptel1M 964478 TTTTGAGGTAGCTCATT 964494 i?i i i C L3#LINE/CR1 3948 TCNCGAGGCAGCCCATT 3932 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.20 CpG sites = 31, Kimura (unadjusted) = 36.61 Transitions / transversions = 3.10 (31/10) Gap_init rate = 0.05 (7 / 149), avg. gap size = 2.43 (17 / 7) 21 11.44 8.16 1.92 chr6ptel1M 965395 965443 (34557) (TA)n#Simple_repeat 1 52 (0) m_b297s252i1 12394 chr6ptel1M 965395 TAT-TATATAT-TATATTTATTAATATAT-TATGTATATGTGAT-TATAT 965440 - - v vv - i i - - (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATAT-ATATATAT 49 chr6ptel1M 965441 ATA 965443 (TA)n#Simple_ 50 ATA 52 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.10 (5 / 48), avg. gap size = 1.00 (5 / 5) 12 21.71 0.00 0.00 chr6ptel1M 965488 965519 (34481) (ATAAAG)n#Simple_repeat 1 32 (0) m_b297s252i2 12395 chr6ptel1M 965488 ATAAAGTGAAAGAAAATTATAAAGATAAAAAT 965519 vv v vv i (ATAAAG)n#Sim 1 ATAAAGATAAAGATAAAGATAAAGATAAAGAT 32 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 450 36.05 1.73 0.57 chr6ptel1M 965547 965719 (34281) MIR3#SINE/MIR 19 193 (15) m_b297s601i12 12396 chr6ptel1M 965547 AAAGAAATC-TGAATTTGGAACCAGATGATATCAGTTTGGATTCTGGTTC 965595 i i v -i i i v ii iv iv vi ivii i i i MIR3#SINE/MIR 19 AGAGAGAGCACGGACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTC 68 chr6ptel1M 965596 GGCTGCTTAAGACCCGTGTGAT-TTGAACAAATCTCTTAATTTCTCTGAC 965644 v ii v vv?v i i- ii i v v ii iv MIR3#SINE/MIR 69 TGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGG 118 chr6ptel1M 965645 CTTCGGCATCTACCTCTATAAAATGGAAGAGGTTGATCAAGAAAATGTTT 965694 i i iv iv v i - i i iv v vi v i MIR3#SINE/MIR 119 CCTCAGTTTCCTCATCTGTAAAAT-GAGGGGGTTGGACTAGATGATCTCT 167 chr6ptel1M 965695 AAGATCCCTTAAAGCTTTAA-ATTCT 965719 i vv i i - MIR3#SINE/MIR 168 AAGGTCCCTTCCAGCTCTGACATTCT 193 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 49.98 CpG sites = 39, Kimura (unadjusted) = 52.49 Transitions / transversions = 1.70 (39/23) Gap_init rate = 0.02 (4 / 172), avg. gap size = 1.00 (4 / 4) 368 35.09 2.27 2.86 chr6ptel1M 966210 966385 (33615) MIR3#SINE/MIR 2 176 (32) m_b297s601i13 12397 chr6ptel1M 966210 TGTTAGGGCAGTGCAGTGGAAAGGATGATGAACTGGTTATCAGGAAAGAT 966259 vi i ii ivv ii i iii- i i vvi -- i MIR3#SINE/MIR 2 TGGCAGAGTGGCTGAGCAGAGAGAGC-ACGGACTGGGAGTCAGGA--GAC 48 chr6ptel1M 966260 CAGGGGGCATATTGTGGTTCT-TCGCTAAGCTAG--AGGTCACTAGCAGA 966306 v vv vvi ivi i -i i - ? --iv v i-vii i MIR3#SINE/MIR 49 CTGGGTTCTAGTCCCGGCTCTGCCACTAA-CTNGCTGTGTGACC-TTGGG 96 chr6ptel1M 966307 CTGGTCATTTC-TTTATCTGGACCTCAGTTTCCTCATTTGTAAAGTGACA 966355 vi i -ii v i i i vi MIR3#SINE/MIR 97 CAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGG 146 chr6ptel1M 966356 AGATTGGGCTATGTGATCTCCACAGTACCT 966385 i i i vi i vi v MIR3#SINE/MIR 147 GGGTTGGACTAGATGATCTCTAAGGTCCCT 176 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 48.56 CpG sites = 40, Kimura (unadjusted) = 51.07 Transitions / transversions = 2.00 (40/20) Gap_init rate = 0.05 (8 / 175), avg. gap size = 1.12 (9 / 8) 264 21.65 6.56 1.56 chr6ptel1M 966639 966699 (33301) MIRb#SINE/MIR 88 151 (117) m_b297s601i14 12398 chr6ptel1M 966639 CTGTGTGAAGTTAGAGAAATTAC----CCTCTCTGAGCCTTAGTTTTTTT 966684 vv i iv i ---- i ii i MIRb#SINE/MIR 88 CTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTC 137 chr6ptel1M 966685 AGTCTTTAAAATAAG 966699 - v ii MIRb#SINE/MIR 138 A-TCTGTAAAATGGG 151 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.42 CpG sites = 9, Kimura (unadjusted) = 26.42 Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.03 (2 / 60), avg. gap size = 2.50 (5 / 2) 206 34.28 1.41 1.41 chr6ptel1M 967791 967861 (32139) C L2d_3end#LINE/L2 (5) 511 441 m_b297s601i15 12399 chr6ptel1M 967791 CAATGAATGAGTGAGGCATTTATTAAACATCTACTATGTGCTGCACATTG 967840 v v iii -i i i ii vvi i C L2d_3end#LINE 511 CAATCAATCAACAAG-TATTTATTGAGCGCCTACTATGTGCTCAGCACTG 463 chr6ptel1M 967841 TAGTGAACTCTA-GGGATACAA 967861 iv iii v i- iv i C L2d_3end#LINE 462 TGCTAGGCGCTGTGGGGAACGA 441 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.79 CpG sites = 17, Kimura (unadjusted) = 49.64 Transitions / transversions = 2.43 (17/7) Gap_init rate = 0.03 (2 / 70), avg. gap size = 1.00 (2 / 2) 241 30.19 0.00 0.00 chr6ptel1M 967808 967860 (32140) C L2a_3end#LINE/L2 (19) 498 446 m_b297s601i16 12399 chr6ptel1M 967808 ATTTATTAAACATCTACTATGTGCTGCACATTGTAGTGAACTCTAGGGAT 967857 i i ii iivi i vv iii v i C L2a_3end#LINE 498 ATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGCGCTGGGGAT 449 chr6ptel1M 967858 ACA 967860 C L2a_3end#LINE 448 ACA 446 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.19 CpG sites = 12, Kimura (unadjusted) = 41.66 Transitions / transversions = 3.00 (12/4) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 510 22.35 0.65 7.59 chr6ptel1M 967909 968063 (31937) MIRc#SINE/MIR 2 146 (122) m_b297s601i17 12400 chr6ptel1M 967909 GGGGTAGTTAGGTGGTGCAGTGCTCAGAGAGCTGAGCCTGCCATCAGGAA 967958 i i --- vvv vi ii i vvi MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr6ptel1M 967959 GACCCATCTTCATGAGTTTCAATGTGGCCTCAGACATCTGCTAGCTGTGT 968008 iivv -- ii ----- - v v ii i MIRc#SINE/MIR 49 GACCTGGGTTC--GAGTCCC-----GGC-TCTGCCACTTACTAGCTGTGT 90 chr6ptel1M 968009 GACCCTGGCCAAGTCACTTCACC-CTATTTGCTTCAGTCTCCTCATCTGT 968057 i v v - v vv i i MIRc#SINE/MIR 91 GACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGT 140 chr6ptel1M 968058 AAAATG 968063 MIRc#SINE/MIR 141 AAAATG 146 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.64 CpG sites = 17, Kimura (unadjusted) = 26.64 Transitions / transversions = 1.13 (17/15) Gap_init rate = 0.08 (12 / 154), avg. gap size = 1.00 (12 / 12) 376 23.84 3.57 2.65 chr6ptel1M 968601 968712 (31288) C MIRc#SINE/MIR (52) 216 104 m_b297s601i18 12401 chr6ptel1M 968601 TTTACATCCATGATCTTATTTGAGTCTAAAAAGAGCCCTGTGACATAGAA 968650 i v v i vi v v v i vi iv C MIRc#SINE/MIR 216 TTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGC 167 chr6ptel1M 968651 ACAACAAATATTTGTGATCTCATTTTACAGATGAGGAAA-TG-GGCTAAC 968698 vii ii vv ivi i - - -- C MIRc#SINE/MIR 166 AGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCT--C 119 chr6ptel1M 968699 AGAAGGGGTT--GTGA 968712 - i -- C MIRc#SINE/MIR 118 AG-AGAGGTTAAGTGA 104 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.08 CpG sites = 14, Kimura (unadjusted) = 29.08 Transitions / transversions = 1.17 (14/12) Gap_init rate = 0.05 (6 / 111), avg. gap size = 1.17 (7 / 6) 587 26.44 2.55 1.26 chr6ptel1M 968699 968855 (31145) MIR3#SINE/MIR 25 183 (25) m_b297s601i19 12402 chr6ptel1M 968699 AGAAGGGGTTGTGAGT-AAGAGCTCTC--TTTTAGTCCTGAATCTTGACA 968745 v v ii v - i vi v-- i i iv - v MIR3#SINE/MIR 25 AGCACGGACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCT-GCCA 73 chr6ptel1M 968746 CTAATTTTCTGTTTGATCTCAAATAAGTCACTTCCTTTTTCTGTGTCAGC 968795 i ?v v i iiiii vii i v i -v MIR3#SINE/MIR 74 CTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCC-TC 122 chr6ptel1M 968796 AATTTT-TCATCTGTTAAATAATAGAGCTGGACTAGAGGATCACTAAGAT 968844 i i- v i vi i i v v i MIR3#SINE/MIR 123 AGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGT 172 chr6ptel1M 968845 CCCTTCCAGCT 968855 MIR3#SINE/MIR 173 CCCTTCCAGCT 183 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.79 CpG sites = 25, Kimura (unadjusted) = 33.80 Transitions / transversions = 1.56 (25/16) Gap_init rate = 0.03 (5 / 156), avg. gap size = 1.20 (6 / 5) 26 15.36 0.00 6.45 chr6ptel1M 969700 969765 (30235) (CTGTCT)n#Simple_repeat 1 62 (0) m_b297s252i3 12403 chr6ptel1M 969700 CTCTCTCTGTCTTTCTGTCGCTGTCTCTGTCTCTTTTTCTCTGTCTGTCT 969749 v -- v -- v v v (CTGTCT)n#Sim 1 CTGTCTCTGTC--TCTGTCTCTGTCTCTGTCTC--TGTCTCTGTCTCTGT 46 chr6ptel1M 969750 GTCTGACTCTTTCTCT 969765 v v v (CTGTCT)n#Sim 47 CTCTGTCTCTGTCTCT 62 Matrix = Unknown Transitions / transversions = 0.00 (0/8) Gap_init rate = 0.06 (4 / 65), avg. gap size = 1.00 (4 / 4) 274 26.98 0.00 0.00 chr6ptel1M 969946 970008 (29992) C MIRb#SINE/MIR (107) 161 99 m_b297s601i20 12404 chr6ptel1M 969946 TGTTTTTCTCCCAATTTTATAGATGAAGAAACTAAAACTGAGAGAATTGA 969995 i v v v i i i ii v iv v C MIRb#SINE/MIR 161 TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTA 112 chr6ptel1M 969996 AGCAATTGGTCCA 970008 i i v i C MIRb#SINE/MIR 111 AGTAACTTGCCCA 99 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.26 CpG sites = 10, Kimura (unadjusted) = 34.26 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0) 203 21.44 1.72 3.51 chr6ptel1M 970030 970042 (29958) MIR#SINE/MIR 74 85 (177) m_b297s601i21 12405 chr6ptel1M 970030 TTACAAGCATAAG 970042 v - iv MIR#SINE/MIR 74 TTACTAGC-TGTG 85 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.21 CpG sites = 7, Kimura (unadjusted) = 26.21 Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.08 (1 / 12), avg. gap size = 1.00 (1 / 1) 63 1.75 0.00 0.00 chr6ptel1M 970043 970100 (29900) (AT)n#Simple_repeat 1 58 (0) c_b297s251i1 12406 chr6ptel1M 970043 ATATATATATATATATATATATATATATATATATATATATATATATACAT 970092 i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr6ptel1M 970093 ATATATAT 970100 (AT)n#Simple_ 51 ATATATAT 58 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0) 203 21.44 1.72 3.51 chr6ptel1M 970101 970144 (29856) MIR#SINE/MIR 86 129 (133) m_b297s601i21 12405 chr6ptel1M 970101 GATCTTGAGCAAGTAATTTAACCTTTTAGTG-CTCACTCTCGCTC 970144 i i v i i iv - v i - MIR#SINE/MIR 86 GACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTC-CTC 129 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.21 CpG sites = 7, Kimura (unadjusted) = 26.21 Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2) 12 8.91 4.17 0.00 chr6ptel1M 970714 970737 (29263) (AAAT)n#Simple_repeat 1 25 (0) m_b297s252i5 12407 chr6ptel1M 970714 AAATAAATAAAAAAATTAA-AAATA 970737 v v - (AAAT)n#Simpl 1 AAATAAATAAATAAATAAATAAATA 25 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 211 31.03 11.49 0.00 chr6ptel1M 971269 971355 (28645) MIR3#SINE/MIR 40 136 (72) m_b297s601i22 12408 chr6ptel1M 971269 TCAGAGAACATGGGTT--AATTCATG-TCTGACA-----TTGCCTTATGA 971310 iii v -- i i vv - v ----- ? iv i MIR3#SINE/MIR 40 TCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGA 89 chr6ptel1M 971311 TCTTGGACAAGTCACTTAACTTCCCCAGTTTTT--TTTTTTAATTTG 971355 i i v i i ii vii i-- ii v i MIR3#SINE/MIR 90 CCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTG 136 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.42 CpG sites = 19, Kimura (unadjusted) = 43.42 Transitions / transversions = 2.38 (19/8) Gap_init rate = 0.05 (4 / 86), avg. gap size = 2.50 (10 / 4) 228 19.40 11.94 0.00 chr6ptel1M 971269 971335 (28665) MIR1_Amn#SINE/MIR 45 119 (111) m_b297s601i23 12408 chr6ptel1M 971269 TCAGAGAACATGGGTT-AATTCATG--TCTGACA-TTGCCT----TATGA 971310 i iii v -? ? vi -- v - ? ?----?i MIR1_Amn#SINE 45 TCGGGAGACCTGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGA 94 chr6ptel1M 971311 TCTTGGACAAGTCACTTAACTTCCC 971335 i i ? i i MIR1_Amn#SINE 95 CCTTGGGCAAGTCACTTNACCTCTC 119 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 21.73 CpG sites = 10, Kimura (unadjusted) = 26.25 Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.06 (4 / 66), avg. gap size = 2.00 (8 / 4) 183 22.50 0.00 0.00 chr6ptel1M 971546 971585 (28415) C L2d2_3end#LINE/L2 (508) 47 8 m_b297s601i24 12409 chr6ptel1M 971546 TAGTGGGATATAAAGCAGAAGAGCTAAGTTGAAGCCAGAT 971585 v i v i i v? i ii C L2d2_3end#LIN 47 TAGTGGGAGATAAGGCTGGAAAGGNAGGTTGGGGCCAGAT 8 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.45 CpG sites = 6, Kimura (unadjusted) = 28.45 Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 283 36.10 3.67 0.89 chr6ptel1M 972049 972266 (27734) CR1-3_Croc#LINE/CR1 2407 2630 (975) m_b297s551i0 12410 chr6ptel1M 972049 AAAAGTTGATCTGACAGTTTTAGTGGACCTCAAGCTTGATATGA-TCAGC 972097 -- i iv i i i i v ii ii - v CR1-3_Croc#LI 2407 AAAAG--GACCTGGGAGTCTTGGTAGATCACAGACTCAATATGAGTCTGC 2454 chr6ptel1M 972098 AGTGAGA-GAAGATCCAGAAAACTC--ATGCTAATTCAGGCTTCTTTGA- 972143 v - v viv v vv -- viv ii v v v ii - CR1-3_Croc#LI 2455 AGTGTGATGCAGCCGCACAAAAGGCGAATGCGGTTTTGGGATGCATCAAT 2504 chr6ptel1M 972144 -GAAGCACAGCATTCAGAACACAGGAACTTAGACTCCCATTGTCTTCTGT 972192 - ivivi v ii i iv v v v v vi v vi v i CR1-3_Croc#LI 2505 AGAAGCATTAGGTGCAAGACACGGGAGGTGATAGTGCCTCTCTACTCGGC 2554 chr6ptel1M 972193 -CTCATC-TTCCACATTTAGAGCCCTGTATACAGTCCCAGGACTCACATT 972240 - vi i-vv v i i iv i i i ii vii CR1-3_Croc#LI 2555 ACTGGTTAGGCCTCATCTGGAGTACTGTGTGCAGTTCTGGGCTCCACATT 2604 chr6ptel1M 972241 TTAGGAAGGATGTTGATATGCTAGAG 972266 ii i v v v i CR1-3_Croc#LI 2605 TTAAAAAGGACGTGGAGAAGTTAGAG 2630 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 47.95 CpG sites = 42, Kimura (unadjusted) = 50.68 Transitions / transversions = 1.17 (42/36) Gap_init rate = 0.04 (9 / 217), avg. gap size = 1.11 (10 / 9) 236 33.03 6.30 2.27 chr6ptel1M 972587 972713 (27287) MIRb#SINE/MIR 22 153 (115) m_b297s601i25 12411 chr6ptel1M 972587 TAGAAAGA--ACGAGATTTGGACTCAAA-AGACTTTTGCT----TTCATG 972629 i -- i v v i - i vv i ---- i vv MIRb#SINE/MIR 22 TGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCGAATCCCGG 71 chr6ptel1M 972630 TTTTCCTAATTATTATACT-TGTAATTACAGGGAGGCAATTTAGCTACTA 972678 i i v i v i -i - i iivii v i iv i i iv v MIRb#SINE/MIR 72 CTCTGCCACTTACTA-GCTGTGTGACCTTGGGCAAGTTACTTAACCTCTC 120 chr6ptel1M 972679 AGAGCCTCAGTTTGCTCAGCTAGAATATCTGAGGA 972713 v v v iv v -- i MIRb#SINE/MIR 121 TGAGCCTCAGTTTCCTCATCTGTAAAA--TGGGGA 153 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 44.87 CpG sites = 23, Kimura (unadjusted) = 44.87 Transitions / transversions = 1.28 (23/18) Gap_init rate = 0.06 (7 / 126), avg. gap size = 1.57 (11 / 7) 444 31.43 3.97 7.82 chr6ptel1M 972744 972995 (27005) MIRc#SINE/MIR 5 247 (21) m_b297s601i26 12412 chr6ptel1M 972744 GCAGTCTGGGTGGTACGGTTGGGTTGGGAG-GTTGTACTT--AATCAGGA 972790 ---- i i - i--ii -ii v -- i MIRc#SINE/MIR 5 GCAGT----GTGGTGCAGT-GGA--AAGAGCACTGGACTTGGAGTCAGGA 47 chr6ptel1M 972791 GGACTTGCGTTTGAAGTCTACTTCAGACTTTATTATTAACTATGTGGTTT 972840 i i v i ivi iivi v v vi -- i i i iii MIRc#SINE/MIR 48 AGACCTGGGTTCGAGTCCCGGCTCTGCCACT--TACTAGCTGTGTGACCT 95 chr6ptel1M 972841 GAGAGCAAGATGCATAACCTTTTTTTTCCTCCCAAATTCAGTATCTTCAC 972890 vi - vii v -------- iv ivi v i i MIRc#SINE/MIR 96 TGG-GCAAGTCACTTAACCT--------CTCTGAGCCTCAGTTTCCTCAT 136 chr6ptel1M 972891 CTGTAAGATAGGGATGATATTAG--G----ATCTACCTCCCAGAGTTATT 972934 i i i v v-- ----ii v i i MIRc#SINE/MIR 137 CTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTT 186 chr6ptel1M 972935 GTGGGACTCTAATGAGTTAATTGATAT-AACCTGATTTGGTGAAAATTAA 972983 i iv v v vv i - vvi v - i vvv MIRc#SINE/MIR 187 GTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTTT-GTAAACTGTAA 235 chr6ptel1M 972984 AGTAATATATAA 972995 iv i MIRc#SINE/MIR 236 AGTGCTATACAA 247 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.80 CpG sites = 45, Kimura (unadjusted) = 42.18 Transitions / transversions = 1.61 (45/28) Gap_init rate = 0.10 (24 / 251), avg. gap size = 1.21 (29 / 24) 469 30.96 0.00 6.92 chr6ptel1M 972794 972963 (27037) MIR#SINE/MIR 47 205 (57) m_b297s601i27 12412 chr6ptel1M 972794 CTTGCGTTTGAAGTCTACTTCAGACTTTATTATTAACTATGTGGTTTGAG 972843 i v i vi iivi v v vi -- i i i iii vi MIR#SINE/MIR 47 CCTGGGTTCGAATCCCGGCTCTGCCACT--TACTAGCTGTGTGACCTTGG 94 chr6ptel1M 972844 AGCAAGATGCATAACCTTTTTTTTCCTCCCAAATTCAGTATCTTCACCTG 972893 - v i v i i v v -------- v i i MIR#SINE/MIR 95 -GCAAGTTACTTAACCTCTCTGTGCCTC--------AGTTTCCTCATCTG 135 chr6ptel1M 972894 TAAGATAGGGATGATATTAGGATCTACCTCCCAGAGTTATTGTGGGACTC 972943 i i i v v i vi i i i iv i MIR#SINE/MIR 136 TAAAATGGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGGATT 185 chr6ptel1M 972944 TAATGAGTTAATTGATATAA 972963 v vv i MIR#SINE/MIR 186 AAATGAGTTAATACATGTAA 205 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.85 CpG sites = 30, Kimura (unadjusted) = 41.17 Transitions / transversions = 1.58 (30/19) Gap_init rate = 0.07 (11 / 169), avg. gap size = 1.00 (11 / 11) 47 5.67 0.00 0.00 chr6ptel1M 973050 973105 (26895) (CTACTG)n#Simple_repeat 1 56 (0) c_b297s251i2 12413 chr6ptel1M 973050 CTACTACTACTACTACTGCTACTGCTACTGCTACTGCTACTGCTACTGCT 973099 i i (CTACTG)n#Sim 1 CTACTGCTACTGCTACTGCTACTGCTACTGCTACTGCTACTGCTACTGCT 50 chr6ptel1M 973100 GCTGCT 973105 i (CTACTG)n#Sim 51 ACTGCT 56 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0) 12 5.00 0.00 4.55 chr6ptel1M 973259 973281 (26719) (CCTC)n#Simple_repeat 1 22 (0) m_b297s252i6 12414 chr6ptel1M 973259 CCTCCCTCCCTCCACCCCCTCCC 973281 - i (CCTC)n#Simpl 1 CCTCCCTCCCTCC-CTCCCTCCC 22 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.05 (1 / 22), avg. gap size = 1.00 (1 / 1) 299 26.52 6.22 6.22 chr6ptel1M 973600 973792 (26208) C L1MC2_3end#LINE/L1 (458) 633 441 m_b297s551i1 12415 chr6ptel1M 973600 GCTCATTTCACTTAGCATCAGTTCATGTAA--TTCTCTCCAAAAATCTCT 973647 iv vi - v v -- - -------- C L1MC2_3end#LI 633 GCTTCTTTCACTTAGCAATA-TGCATTTAAGGTTC-CTCCA--------T 594 chr6ptel1M 973648 GTGTTTATGCTGCT-----GGTCATTTCTT---ACAGAACAATAATATTC 973689 v vi iv ----- v --- iv vvv C L1MC2_3end#LI 593 GTCTTTTCGTGGCTTGATAGCTCATTTCTTTTTATCGCTGAATAATATTC 544 chr6ptel1M 973690 CATAACATTCATATACCACAGTTTATCCAACCATTCTCCAATGGATGGGC 973739 vii vv i i ii v v v v v i C L1MC2_3end#LI 543 CATTGTATGGATGTACCACAGTTTGTTTATCCATTCACCTATTGAAGGAC 494 chr6ptel1M 973740 ATCCATTCATT--TTGCAGTTTCTAGCCACTACAAACAGGGCTGCCACAA 973787 -- vi -- v iv i i v i ii i ii i i C L1MC2_3end#LI 493 ATC--TTGGTTGCTTCCAAGTTTTGGCAATTATGAATAAAGCTGCTATAA 446 chr6ptel1M 973788 ACATT 973792 C L1MC2_3end#LI 445 ACATT 441 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.24 CpG sites = 24, Kimura (unadjusted) = 33.06 Transitions / transversions = 1.00 (24/24) Gap_init rate = 0.08 (16 / 192), avg. gap size = 1.50 (24 / 16) 328 28.45 0.00 0.00 chr6ptel1M 973667 973782 (26218) C L1MC4a_3end#LINE/L1 (2065) 564 449 m_b297s551i2 12415 chr6ptel1M 973667 TTTCTTACAGAACAATAATATTCCATAACATTCATATACCACAGTTTATC 973716 i vvvv i i viii vv i i i C L1MC4a_3end#L 564 TTTTTTACAGCTGCATAGTACTCCATTGTGTGGATGTACCATAGTTTATT 515 chr6ptel1M 973717 CAACCATTCTCCAATGGATGGGCATCCATTCATTTTGCAGTTTCTAGCCA 973766 ? v ?? ii vvivv v i v i v v C L1MC4a_3end#L 514 CAACCANTCTCCTATNNATGGGCATTTAGGTTGTTTCCAATATTTTGCAA 465 chr6ptel1M 973767 CTACAAACAGGGCTGC 973782 i iv C L1MC4a_3end#L 464 TTACAAACAATGCTGC 449 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.37 CpG sites = 16, Kimura (unadjusted) = 37.37 Transitions / transversions = 0.94 (16/17) Gap_init rate = 0.00 (0 / 115), avg. gap size = 0.0 (0 / 0) 349 30.95 0.00 2.16 chr6ptel1M 973681 973822 (26178) C L1ME4c_3end#LINE/L1 (275) 555 417 m_b297s551i4 12415 chr6ptel1M 973681 ATAATATTCCATAACATTCATATACCACAGTTTATCCAACCATTCTCCAA 973730 vivi ?v i i i iii i v C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chr6ptel1M 973731 TGGATGGGCATCCATTCATTTTGCAGTTTCTAGCCACTACAAACAGGGCT 973780 v v i ii vvivv v i i v i i i i iv C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCT 456 chr6ptel1M 973781 GCCACAAACATTTTGGCACATACAGGTCCCTTTCCCTTCTTT 973822 v ii i v ii i --- i i C L1ME4c_3end#L 455 GCAATGAACATCTTCGTGCATATAG---CTTTTTCCTTCTTT 417 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.93 CpG sites = 28, Kimura (unadjusted) = 42.26 Transitions / transversions = 1.87 (28/15) Gap_init rate = 0.02 (3 / 141), avg. gap size = 1.00 (3 / 3) 401 29.27 0.00 0.00 chr6ptel1M 973681 973803 (26197) C L1ME3G_3end#LINE/L1 (376) 548 426 m_b297s551i3 12415 chr6ptel1M 973681 ATAATATTCCATAACATTCATATACCACAGTTTATCCAACCATTCTCCAA 973730 i ii vv i i ii i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr6ptel1M 973731 TGGATGGGCATCCATTCATTTTGCAGTTTCTAGCCACTACAAACAGGGCT 973780 v i ii vvivv v i i v i i iv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr6ptel1M 973781 GCCACAAACATTTTGGCACATAC 973803 v ii ii v i i C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACATGC 426 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.60 CpG sites = 23, Kimura (unadjusted) = 38.60 Transitions / transversions = 1.77 (23/13) Gap_init rate = 0.00 (0 / 122), avg. gap size = 0.0 (0 / 0) 451 21.78 2.97 0.00 chr6ptel1M 973844 973944 (26056) C Charlie4#DNA/hAT-Charlie (3249) 129 26 m_b297s502i0 12416 chr6ptel1M 973844 AAATAATAAATTTTAATTAGTAGTTGGTAAAAATAAATATGTAGTTTTT- 973892 iv i i vi i i v i - C Charlie4#DNA/ 129 AAATGCTAAATTTCAGTTAGAGGTTAGTGAAAATAAAGATGTAATTTTTT 80 chr6ptel1M 973893 CACATCCAAGTTCCTAGATTCCCTGAAATCCATGCACAGA--CATTGGAG 973940 v vii ii v i v i -- v i C Charlie4#DNA/ 79 CCCATCCAAGTTCACGGACCCCCTGAATTCTATCCACGGACCCCTTGGGG 30 chr6ptel1M 973941 GTCC 973944 C Charlie4#DNA/ 29 GTCC 26 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 23.51 CpG sites = 14, Kimura (unadjusted) = 26.35 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.02 (2 / 100), avg. gap size = 1.50 (3 / 2) 331 29.18 5.00 2.08 chr6ptel1M 974320 974459 (25541) MIR3#SINE/MIR 60 203 (5) m_b297s601i28 12417 chr6ptel1M 974320 TCCCATCTCTACATAAAATCAGCTGAG-AATCTTAC-CATGGTCATTTAA 974367 iv i vvvv ii? v -i i iv- -i i v MIR3#SINE/MIR 60 TCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCA-AGTCACTTCA 108 chr6ptel1M 974368 TCACTTTG--TCTCAGTT-CCTTATCTCTAAAACTGGAGAAACTAGGAAA 974414 i v i --i - i v - ii iiii i ivv MIR3#SINE/MIR 109 CCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAA-TGAGGGGGTTGGACTA 157 chr6ptel1M 974415 AATGATCTATAAGGTCCCTTCTATCTCCAATCA--CCATGATTCTAT 974459 i v i v ii - -- i MIR3#SINE/MIR 158 GATGATCTCTAAGGTCCCTTCCAGCTCTGA-CATTCTATGATTCTAT 203 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.70 CpG sites = 26, Kimura (unadjusted) = 38.97 Transitions / transversions = 1.86 (26/14) Gap_init rate = 0.06 (8 / 139), avg. gap size = 1.25 (10 / 8) 429 20.92 3.45 1.12 chr6ptel1M 974534 974620 (25380) C MIR3#SINE/MIR (23) 185 97 m_b297s601i29 12418 chr6ptel1M 974534 AGACCTAGAAGAAACTTTAGAGATCATCTTGTCTAATTTCCTTATTTATA 974583 v i ii i v i iii i - C MIR3#SINE/MIR 185 AGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTT-TA 137 chr6ptel1M 974584 -AGATGAG--AATCAAGACCCAGAGAGGGAAAGTGACCTG 974620 - -- iii i vi i C MIR3#SINE/MIR 136 CAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTG 97 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.01 CpG sites = 15, Kimura (unadjusted) = 26.01 Transitions / transversions = 5.00 (15/3) Gap_init rate = 0.03 (3 / 86), avg. gap size = 1.33 (4 / 3) 445 15.79 1.32 0.00 chr6ptel1M 975156 975231 (24769) C Charlie4#DNA/hAT-Charlie (0) 3378 3302 m_b297s502i1 12419 chr6ptel1M 975156 CAGGGGTCCTTAAA-TTTTTTGTTTCATAGACTCCTTTGACAATCTGGTG 975204 i v- vi i i i i C Charlie4#DNA/ 3378 CAGGGGTTCTTAACCTTTTTTGTGCCATGGACCCCTTTGGCAGTCTGGTG 3329 chr6ptel1M 975205 AAGCATCTGTACCCCTTCTCAGAAGAA 975231 v v v v C Charlie4#DNA/ 3328 AAGCCTATGGACCCCTTCTCAGAATAA 3302 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 17.81 CpG sites = 6, Kimura (unadjusted) = 17.81 Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.01 (1 / 75), avg. gap size = 1.00 (1 / 1) 306 16.36 0.00 0.00 chr6ptel1M 975236 975290 (24710) C Charlie4#DNA/hAT-Charlie (3224) 154 100 m_b297s502i2 12419 chr6ptel1M 975236 TGTTGCCTATACTCATAAATGGAGGTCATGGTGAATTTCAGTTAAAGGTT 975285 i i v i vv v i i C Charlie4#DNA/ 154 TGTTGCCTACATTCATAATTGAAGGAAATGCTAAATTTCAGTTAGAGGTT 105 chr6ptel1M 975286 AGTGA 975290 C Charlie4#DNA/ 104 AGTGA 100 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 18.62 CpG sites = 5, Kimura (unadjusted) = 18.62 Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 667 37.23 10.23 0.92 chr6ptel1M 975307 976000 (24000) C L3#LINE/CR1 (2672) 1427 670 m_b297s601i30 12420 chr6ptel1M 975307 TTCTTTTATAAATAAGGTATACTCTTCTGGAACCATACTTTCACCATAAT 975356 i-- i ? i iivvi i i iivii i v C L3#LINE/CR1 1427 TTCTTTTG--AACAAGGTNTACCCTTCCATCGCCGTATTCCAGTCATGAG 1380 chr6ptel1M 975357 TTCCACTCCA----GTTTTAGCGTTAGCT------TC-CA---ACTTGCT 975392 i ii ---- i ii i v v ------ -i --- i v C L3#LINE/CR1 1379 TCCCATCCCACCAAGTCTCGGTGATACCTATGAGATCGTATTTACCTCCT 1330 chr6ptel1M 975393 TGCTTTAA----TCAAACT--CTTAAACTAGAACAAAGTCTCTGT---TT 975433 iv ---- ii -- v?vi vv vv vv --- C L3#LINE/CR1 1329 TGTGTTAAAATTTCAAGTTNACTTTNTTTATTACCCATACTCTGTGCATT 1280 chr6ptel1M 975434 GTT-TATAGGCATTTTTGAGGGTATGGGT--TGAT-CT-GTTGAATTTCC 975478 v - i i -- vi ii -- v - - i vvv C L3#LINE/CR1 1279 GGTATATAGACATCT--GAGGCCATAAGTATTGTTTCTAGCTTCTTTTCC 1232 chr6ptel1M 975479 --------TCTTCAATGAATTTCTGG-----TTCTGCTCTTTTCTTCTCC 975515 -------- i vi? v ----- i v v v v i C L3#LINE/CR1 1231 NGTTATTTTCTCCTGNGAATTACTGGGCACCTCCTCCACTGTTGTTCTTC 1182 chr6ptel1M 975516 TTTCTATGGTATATTGGCTACTTTCTGGGGTCCCAGACTTGTCAAGTTAA 975565 vi iiv ? iii iivi vi v ii vv iv v C L3#LINE/CR1 1181 TTTCTATGTCATACCTGNTATCCTCCATAGTATCCGGTTTTACAGTTTTA 1132 chr6ptel1M 975566 TGTAGGAAGTTTCCTTCTTCTTTCTTA----TTAATCAAAAGTCCTCTGC 975611 v i v v ii i i ii i ---- i i iv vv C L3#LINE/CR1 1131 TCTGGGCATTTTTTTTCCTTTCCCTCAAATTTCAGTTTAAAGTCCTCTTG 1082 chr6ptel1M 975612 ATGGGCTTTCCAGGATTCTAGGCATCTGTTATTATTATTGGCCCTTATTA 975661 vi v ivv ii vi i? ? vviii-i v vii i i ii v C L3#LINE/CR1 1081 ATCAGGTCGGCGAGTCTCCNGNCAAACAC-GTTCTTCCCGGTCTTCGTGA 1033 chr6ptel1M 975662 G-TGC---------CTTGACAAGGTCTCATTATTCCTAAATTCTAAACTG 975701 - --------- ? v i iv i ii iviv i? i ii C L3#LINE/CR1 1032 GATGCACTCCGTCCCTNGCCAGGAGCCCATCGTTCTGGTATCNTAAGCCA 983 chr6ptel1M 975702 -GGTTCAGAAATCTTAAATCTCATTGTTAGTGACTATCT---TAGCCATG 975747 - i v i- iii v v vv i --- vv C L3#LINE/CR1 982 TGGTCCAGAAAACC-AAATCCTGTTCTTCGACACCATCTACGTAGCCAGC 934 chr6ptel1M 975748 TGTTCATTTCTCAATTCCACTTTTTTCTTCTGATTCCCCCACCTATAATC 975797 i i vv v i i ii vvi v v vi ii C L3#LINE/CR1 933 TGTTCACTTCCCATATCCTCCTTTCTCTTCCAAAGTCACGACCTTCAACT 884 chr6ptel1M 975798 AGCACTAATAATG-AAATATCACCTGTGCCCCCA---CCTTC----CTCT 975839 i v vv ivi - i i --- ----ii C L3#LINE/CR1 883 GGAAGAAGAGATGAAAACACCACCTGTGCCCCCAAGTCCTTCAGTTTCCT 834 chr6ptel1M 975840 TTCCAACATTCTCTGAGCC-TTAGCAATGCCATATATATTCTTCCTGGGG 975888 vi iv i - vi i -i vi vv vi vi ii i ivv C L3#LINE/CR1 833 GCCCAGGACT-TCAAAGTCACTAGAGATGCATTCCAGGTTTCTTCTGACT 785 chr6ptel1M 975889 GTGTTGGTTGTCCCC-CATGAATCATCAGAAATAAGGAGTGGT--ATTTG 975935 iiv i i - i v i i ii v i --iivv C L3#LINE/CR1 784 GTGTCATTCGTTCCCACGTGAATCAGCAGGAGTGGGTAGCGGTCGGCGGG 735 chr6ptel1M 975936 TTCAGCAATTCTCAGGTGACTCTCCACTGTTACCCACATATATGCCCTTG 975985 iiiii v ii vv i iiiiivv i iv i i i iv C L3#LINE/CR1 734 TTTGATGAGTCTTGGCAGGCTCTCCGTCACGTCTCGGATACACGCTCCAG 685 chr6ptel1M 975986 AAATACAGCTGACCT 976000 i v vv C L3#LINE/CR1 684 GAAGACAGCACACCT 670 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 49.77 CpG sites = 155, Kimura (unadjusted) = 55.31 Transitions / transversions = 1.53 (155/101) Gap_init rate = 0.04 (31 / 693), avg. gap size = 2.52 (78 / 31) 295 23.48 8.99 4.30 chr6ptel1M 976290 976378 (23622) C L2c_3end#LINE/L2 (6) 472 380 m_b297s601i32 12421 chr6ptel1M 976290 TCATTCAGTAAACATTTATTGAGTGACTACTGTGTGCTGGACACTGCTCT 976339 ii i v i ii i i ---v C L2c_3end#LINE 472 TCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTG---G 426 chr6ptel1M 976340 AAACACTAAAGAT--AT----CAAGTTTCCT--CCTTAAAGAACTTA 976378 ii i - -- ---- v v i -- i i i i C L2c_3end#LINE 425 GGATAC-AAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCA 380 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.47 CpG sites = 16, Kimura (unadjusted) = 30.01 Transitions / transversions = 4.00 (16/4) Gap_init rate = 0.08 (7 / 88), avg. gap size = 1.71 (12 / 7) 358 25.00 0.00 0.00 chr6ptel1M 976290 976353 (23647) C L2a_3end#LINE/L2 (6) 511 448 m_b297s601i31 12421 chr6ptel1M 976290 TCATTCAGTAAACATTTATTGAGTGACTACTGTGTGCTGGACACTGCTCT 976339 ii i i v i ii i i C L2a_3end#LINE 511 TCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCT 462 chr6ptel1M 976340 AAACACTAAAGATA 976353 ii i iii C L2a_3end#LINE 461 AGGCGCTGGGGATA 448 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.74 CpG sites = 15, Kimura (unadjusted) = 33.91 Transitions / transversions = 15.00 (15/1) Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0) 389 34.30 8.86 1.57 chr6ptel1M 976359 976595 (23405) C L3#LINE/CR1 (3777) 322 69 m_b297s601i33 12420 chr6ptel1M 976359 TTTCCTCCTTAAAGAACTTAACTGATTCTTTCATGGATGAATTCTTCATC 976408 i i ii vv i vviiv i ? - i -- ii C L3#LINE/CR1 322 TTTCCTTCCTGGATTATTTCTTCCATCCTNTC-TAG--GAACCCTTCATC 276 chr6ptel1M 976409 CTCTC--ATAGCCTGGAGAGTAGAAAGGTGTTTCCCTAATGCTTTCATTT 976456 -- iv i v i i i i v iiv ii C L3#LINE/CR1 275 CTCTCTAATAAGCCGGAGCGTAGAGAGGCGTTCCTCAAGCCCTTTCACCT 226 chr6ptel1M 976457 CCTCTTCTAGACCAGATATTAACTTTTACTTTGT-GTGTGTGCTACTGG- 976504 i i vvvi v ii i vi - i - iiiiiiiv i - C L3#LINE/CR1 225 TCTCCTCTAGCAGGGAGACCAGCTTGCA-TTTATAGCACACATAATTGGT 177 chr6ptel1M 976505 ---CATC---GGCAGAAACACAAAGATA----ATCCTCTATTGCTCATT- 976543 --- ii --- i v v ---- v i iiv v i - C L3#LINE/CR1 176 GANCGCCTCAGGCAGGAAGACAAACATAGCACATACCCTGCAGGTCACTG 127 chr6ptel1M 976544 -AAGGGCCTTCTTGCT-TCCATACTTTCTTGA-ATCAAGGT---TTACAG 976587 - vi iiii i v - i v i-? i ---i C L3#LINE/CR1 126 GAACAGTTCCCTCGGTGTCCATACTTCCTGGGTNTCAAGATGAACTACAG 77 chr6ptel1M 976588 TTATATGT 976595 iv v C L3#LINE/CR1 76 TCCTTTGT 69 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 46.39 CpG sites = 55, Kimura (unadjusted) = 50.00 Transitions / transversions = 2.20 (55/25) Gap_init rate = 0.06 (14 / 236), avg. gap size = 1.79 (25 / 14) 227 23.30 7.53 3.09 chr6ptel1M 976904 976996 (23004) C Plat_L3#LINE/CR1 (302) 3271 3175 m_b297s551i5 12422 chr6ptel1M 976904 CCATATGGATCTTTTAAATACTTGAAAACAGCTATTAAG-CTTCCTCAAG 976952 vii i i i v i i - vi iiv C Plat_L3#LINE/ 3271 CCATAAAAACCCTTCATATACTTGAAGACAGTTATTAAGTCACCCCTTAG 3222 chr6ptel1M 976953 CCTTTTTTCAT-----CTAAAC-ATCCCAATTTCTTTCAACCAGTTTTCT 976996 i i iv ----- - i i - -- i C Plat_L3#LINE/ 3221 CCTTCTCTTCTCCAGGCTAAACAACCCCAATTCCTTT-AACC--TTTCCT 3175 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 29.42 CpG sites = 16, Kimura (unadjusted) = 29.42 Transitions / transversions = 3.20 (16/5) Gap_init rate = 0.07 (6 / 92), avg. gap size = 1.67 (10 / 6) 212 32.38 0.00 2.94 chr6ptel1M 977260 977329 (22671) C L3b_3end#LINE/CR1 (607) 599 532 m_b297s601i34 12423 chr6ptel1M 977260 TACCTTCTATGGTTGCCATAGAACATGGCTGATTACTGTTGAGCTTAAGG 977309 v i v iv iiivvi iv i vv i iv C L3b_3end#LINE 599 TAGCTTTTTTGGCAGCCGCGTCGCACTGCTGACTCATATTGAGCTTGCGG 550 chr6ptel1M 977310 TCCACTAAAATTGCCCCAAG 977329 v i-- i C L3b_3end#LINE 549 TCAACTAAAAC--CCCCAGG 532 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.74 CpG sites = 12, Kimura (unadjusted) = 43.37 Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.03 (2 / 69), avg. gap size = 1.00 (2 / 2) 360 38.05 6.84 2.18 chr6ptel1M 977372 977766 (22234) C L3b_3end#LINE/CR1 (774) 432 20 m_b297s601i35 12423 chr6ptel1M 977372 TTAAATGTAATGTGATTAGATTCACCCAGAAGTTCTTTTTTATTGCTCTA 977421 i v v v vi i ? iv v ?v vv i i i vvv v C L3b_3end#LINE 432 TTGAATTTCATCTTGTTGGNTTCGGCCCGNCGTTCTAGTCTGTCGAGATC 383 chr6ptel1M 977422 TCTTTGGATCCTGACTGGGCAGTCTATTGTATTAACCATATATATTA-TT 977470 vi i vv - i vi i i vvv vii -i C L3b_3end#LINE 382 GTTTTGGATCCTGATTTTGCA-TCCAACGTATTAGCCGTCGCTCCCAGCT 334 chr6ptel1M 977471 TATTTCACCTCCAAATTTAACA---TCCTATATATTTTTTTAT-CAAGTT 977516 v vi i?v i i --- v v vii v i i - i C L3b_3end#LINE 333 TCTGCCACTNGCAAATTTGATAAGCTGCTTTCCGTATCTTCATCCAAGTC 284 chr6ptel1M 977517 ATTGACAAAAATTATTAAATTTTTGGGTTTGGGTCTTTGCCAAAGGACCA 977566 i v -- i i ----ii vivi i vvv v i vv ii C L3b_3end#LINE 283 ATTGATACAAAT--TCAGA----CAGGACAAGGCCAAGGACAGAGCCCTG 240 chr6ptel1M 977567 -GGTCTTCTACTAAAGACGTATCCTAAAACAGACATCAATTCACTGATGA 977615 - iviv i i - vi iiv iiiv i ?i i ? v C L3b_3end#LINE 239 CGGCACGCCACTAGAGAC-TCCCTCCAGGTTGACATCGANCCATTNATCA 191 chr6ptel1M 977616 --GCTCTTGGGGTCTAGTTAGCTATTC--CCAAGTCTACCTATATGTGCC 977661 -- ii v ?ii ivii vi -- i ? vv ii vv -i C L3b_3end#LINE 190 ACGTCCTTTGGGTNCGGTTGTTCAACCAGCTANGAATGTCTAACTG-ACC 142 chr6ptel1M 977662 ATTGTCTATACTGTCTTGCTCCCTCTTTTTCATGA------CATAA---- 977701 ? i vv iiiv v v v i i ------ ii ---- C L3b_3end#LINE 141 ATTNTCCAGCCCACATTTCTCCGTCTTGTCCACGAGGATATCACGAGAGA 92 chr6ptel1M 977702 -TGTGGCAGATGTTTTACTGAAAT----ATATGCCG-ATC-ATTACATTC 977744 - v v i ii i ---- ii ii-i - vi? C L3b_3end#LINE 91 CTTTGTCAAATGCCTTGCTGAAATCAAGATACACTATGTCTATGGNATTC 42 chr6ptel1M 977745 TTCTGATTTACCAGCCTAATAG 977766 ii i i i i? iii C L3b_3end#LINE 41 CCCTGATCTGCTAGTNTAGCGG 20 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 51.64 CpG sites = 88, Kimura (unadjusted) = 58.46 Transitions / transversions = 1.49 (88/59) Gap_init rate = 0.05 (21 / 394), avg. gap size = 1.71 (36 / 21) 577 35.09 9.78 1.29 chr6ptel1M 977424 977781 (22219) C L3#LINE/CR1 (821) 3278 2891 m_b297s601i36 12423 chr6ptel1M 977424 TTTGGATCCTGACTGGGCAGTCTATTGTATTAACCATATATATTA--TTT 977471 i i i vv ivi i ?i i i viv vii -- C L3#LINE/CR1 3278 TTTGAATCTTGATTCTGTCATCCANCGTATTAGCTATCCCTCCCAGCTTT 3229 chr6ptel1M 977472 ATTTCACCTCCAAATTTAA----CATCCTATATATTTTTTTATC-AAGTT 977516 i v i v i ---- v iv v v i i - i C L3#LINE/CR1 3228 GTGTCATCTGCAAATTTGATAAGCATGCCTTCTATGTCTTCATCCAAGTC 3179 chr6ptel1M 977517 ATTGACAAAAATTATTAAATTTTTGGGTTTGGGTCTTTGCCAAAGGACCA 977566 i -i i i----i viv i vvv v i vv ii C L3#LINE/CR1 3178 ATTGATAAAAAT-GTTGAAC----AGGACAGGGCCAAGGACAGAGCCCTG 3134 chr6ptel1M 977567 -GGTCTTCTACTAAAGACGTATCCTAAAACAGACATCAATTCACTGATGA 977615 - iviv i i v vi iiv iiiv i i i i v C L3#LINE/CR1 3133 TGGCACGCCACTAGAGACCTCCCTCCAGGTTGACATCGATCCATTAATCA 3084 chr6ptel1M 977616 GCTC--TTGGGGTCTAG----TTAGCTATTCCCAAGTCTACCTATATGTG 977659 i v -- v v ---- i i i viiv i i i vv i C L3#LINE/CR1 3083 ACACCTTTTGGGTATAGTCGTTCAACCAGCTACGAATCCACCTAACTGTA 3034 chr6ptel1M 977660 CCATTGTCTATACTGTCTTGCTCCCTCTTTTTCAT---GACATAATG--- 977703 i ii i vv ii v v v v i i--- i v --- C L3#LINE/CR1 3033 CTATCATCCAGCCCATATTTCTCCATCTTGTCCACAAGGATATCATGAGA 2984 chr6ptel1M 977704 -----TGGCAGATGTTTTACTGAAAT----ATATGCCG-ATC-ATTACAT 977742 ----- v i ii i ---- ii i?-i - ivi C L3#LINE/CR1 2983 GACTTTGTCAAATGCCTTGCTGAAATCCAGATACACTNTGTCTACGGCAT 2934 chr6ptel1M 977743 TCTTCTGATTTACCAGCCTAATAG----ATCAGAAAAGAAAGT 977781 ii i i i i---- i i i C L3#LINE/CR1 2933 TCCCCTGATCTACCAGTCTAGTAACCCTATCAAAAAAGGAAAT 2891 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 47.89 CpG sites = 81, Kimura (unadjusted) = 50.89 Transitions / transversions = 1.88 (81/43) Gap_init rate = 0.05 (18 / 357), avg. gap size = 2.22 (40 / 18) 354 21.83 5.68 1.09 chr6ptel1M 978783 978870 (21130) C Charlie4#DNA/hAT-Charlie (0) 3378 3287 m_b297s502i3 12424 chr6ptel1M 978783 CAAGAGTTCGTAACCTTTTGTTGTGTCATGGTCTCTTTTGGTAATCTGAT 978832 i i v - i v i i i i i C Charlie4#DNA/ 3378 CAGGGGTTCTTAACCTTTT-TTGTGCCATGGACCCCTTTGGCAGTCTGGT 3330 chr6ptel1M 978833 GAAATGTAAGGGTACTTTCTC---ATAATATTTT--AATGCAT 978870 iiv v iiv i --- i -- C Charlie4#DNA/ 3329 GAAGCCTATGGACCCCTTCTCAGAATAATGTTTTTAAATGCAT 3287 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 26.90 CpG sites = 14, Kimura (unadjusted) = 26.90 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.03 (3 / 87), avg. gap size = 2.00 (6 / 3) 25 22.78 1.59 0.00 chr6ptel1M 978872 978934 (21066) (TATA)n#Simple_repeat 1 64 (0) m_b297s252i7 12425 chr6ptel1M 978872 TAT-TATACTTATGTATATACATATATATATGTATGTACATTTTTATGCA 978920 - iv i i i i i v v ii (TATA)n#Simpl 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr6ptel1M 978921 TATATATACATATA 978934 i (TATA)n#Simpl 51 TATATATATATATA 64 Matrix = Unknown Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.02 (1 / 62), avg. gap size = 1.00 (1 / 1) 564 32.47 8.63 2.03 chr6ptel1M 979501 979871 (20129) C L2#LINE/L2 (601) 2481 2087 m_b297s601i37 12426 chr6ptel1M 979501 TGAGGGGAAAGAT----AATTATGCTTTGAA---------TTTGAGATGT 979537 i ---- i vv i i --------- i C L2#LINE/L2 2481 TGAGGGGGAAGATCAGGAGTTCAGTTTTGGACATGTTAAGTTTGAGATGC 2432 chr6ptel1M 979538 CTGT-GGACATGCAGTTTGAGGTGTCC-GTAGATACCTGGTGATGTGAGA 979585 i -i v iv v i v- ii vi vv ii v C L2#LINE/L2 2431 CTATTAGACATCCAAGTGGAGATGTCGAGTAGGCAGTTGGATATACGAGT 2382 chr6ptel1M 979586 CTGCGATGCAAGAGAGAGATTAGGGCTAGAAATACAAATGTGGGTTTCTT 979635 vii v i i i iv i i i v vv v C L2#LINE/L2 2381 CTGGAGTTCAGGGGAGAGGTCCGGGCTGGAGATATAAATTTGGGAGTCAT 2332 chr6ptel1M 979636 CA-----TAGATCTAACAGTTAAACCCATGGAACTTGAAAGAATTGCCAA 979680 ----- --iii v v ii v viii ii ? C L2#LINE/L2 2331 CAGCATATAGAT--GGTATTTAAAGCCATGAGACTGGATGAGATCACCNA 2284 chr6ptel1M 979681 GTAAGAGAATGTAGAATGAAAATAGA---CATCCTCTTACAAAGCTTTGA 979727 vi v i vv i v ---vi vvvv vi ii - C L2#LINE/L2 2283 GGGAGTGAGTGTAGATAGAGAAGAGAAGAGGTCCAAGGACTGAGCCCTG- 2235 chr6ptel1M 979728 GAGGGAACCACA--GGTAAGTGGGCACGGA-ATGGGTAAAGAACCAGCAG 979774 -- v iv -- v ? v v iv - i -i i i C L2#LINE/L2 2234 --GGGCACTCCAACGTTNAGAGGTCGGGGAGATGAG-GAGGAACCAGCAA 2188 chr6ptel1M 979775 AGGAGATCG---ATGAGTAGTCAGGTAGATAGAAGAAAAGAAGCAGGAAA 979821 ii --- v ii i vv i i i -- v i C L2#LINE/L2 2187 AGGAGACTGAGAAGGAGCGGCCAGTGAGGTAGGAGGAA--AACCAGGAGA 2140 chr6ptel1M 979822 AATCAGCATCATAAAAACCTATAGAAAAGAGACT---ATGTAGAAGGGAG 979868 ivvii ii v ii i v vv i i vv --- v v i C L2#LINE/L2 2139 GTGTGGTGTCCTGGAAGCCAAGTGAAGAAAGTGTTTCAAGAAGGAGGGAG 2090 chr6ptel1M 979869 TGA 979871 C L2#LINE/L2 2089 TGA 2087 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.57 CpG sites = 66, Kimura (unadjusted) = 44.13 Transitions / transversions = 1.27 (66/52) Gap_init rate = 0.05 (18 / 370), avg. gap size = 2.22 (40 / 18) 14 10.69 3.12 3.12 chr6ptel1M 980270 980301 (19699) (ATA)n#Simple_repeat 1 32 (0) m_b297s252i9 12427 chr6ptel1M 980270 ATAATAAAGATCTATAAT-ATAATAATAATAAT 980301 vi -v - (ATA)n#Simple 1 ATAATAATAAT-AATAATAATAATAATAATAAT 32 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.06 (2 / 31), avg. gap size = 1.00 (2 / 2) 13 24.88 0.00 0.00 chr6ptel1M 980772 980809 (19191) (TATGTA)n#Simple_repeat 1 38 (0) m_b297s252i10 12428 chr6ptel1M 980772 TATGAATACATATCTGTATATCTATATGTGTAAATATA 980809 v ii v v i vi (TATGTA)n#Sim 1 TATGTATATGTATATGTATATGTATATGTATATGTATA 38 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 11 32.20 3.39 0.00 chr6ptel1M 980777 980835 (19165) (ATACAT)n#Simple_repeat 1 61 (0) m_b297s252i11 12428 chr6ptel1M 980777 ATACATATCTGTATATCTATATGTGTAAATATA-ATAGACACATATACAT 980825 vii iv ii i v - v i i i (ATACAT)n#Sim 1 ATACATATACATATACATATACATATACATATACATATACATATACATAT 50 chr6ptel1M 980826 GCTTAT-CATA 980835 i v - (ATACAT)n#Sim 51 ACATATACATA 61 Matrix = Unknown Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.03 (2 / 58), avg. gap size = 1.00 (2 / 2) 27 22.93 0.00 0.00 chr6ptel1M 981516 981577 (18423) (TCC)n#Simple_repeat 1 62 (0) m_b297s252i12 12429 chr6ptel1M 981516 TCCTTCTCCTCCTCCTCCGTCTCCATTTTCTCTTCCTCCTCCTCCACTTT 981565 i vi vii i i v i i (TCC)n#Simple 1 TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC 50 chr6ptel1M 981566 CTCCTCCTCATC 981577 v (TCC)n#Simple 51 CTCCTCCTCCTC 62 Matrix = Unknown Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0) 292 36.63 0.00 0.00 chr6ptel1M 981694 981794 (18206) MIR3#SINE/MIR 105 205 (3) m_b297s601i38 12430 chr6ptel1M 981694 TTTCCCCCTTTGAGTTTCAATTTTGCCTTCTATAAAATGTGAGAACCACA 981743 iv i i i ii i ivi v i v i iiiiiv MIR3#SINE/MIR 105 TTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGA 154 chr6ptel1M 981744 CAATACAGGCTCTAAGGGCCCTCCCAGCTTGAACATTCATTTATTTTATA 981793 v v iiiv v i ivi vv v i i MIR3#SINE/MIR 155 CTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTATG 204 chr6ptel1M 981794 A 981794 MIR3#SINE/MIR 205 A 205 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 53.75 CpG sites = 24, Kimura (unadjusted) = 53.75 Transitions / transversions = 1.85 (24/13) Gap_init rate = 0.00 (0 / 100), avg. gap size = 0.0 (0 / 0) 308 23.19 2.90 0.00 chr6ptel1M 981797 981865 (18135) C MIRc#SINE/MIR (57) 211 141 m_b297s601i39 12431 chr6ptel1M 981797 ATCCATTATCTTATTGGAAGCTTACAATAAGCCTGAAAA--AAGTAGGGC 981844 v i v vv i i v vi i-- i i C MIRc#SINE/MIR 211 ATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGC 162 chr6ptel1M 981845 AGAAATTATTGTCCCCATTTT 981865 iv i C MIRc#SINE/MIR 161 AGGTATTATTATCCCCATTTT 141 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.17 CpG sites = 9, Kimura (unadjusted) = 28.17 Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.01 (1 / 68), avg. gap size = 2.00 (2 / 1) 217 30.72 4.48 5.26 chr6ptel1M 982078 982211 (17789) C L2d_3end#LINE/L2 (0) 516 384 m_b297s601i40 12432 chr6ptel1M 982078 TTAATGAATGAATGAA-AAGTA---AT-GAGTATTTACTACACACAAAAC 982122 i v v v - --- - iiii iiii vv i C L2d_3end#LINE 516 TCAATCAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGC 467 chr6ptel1M 982123 TATGTGCTAGACACTAAAATTGTAAAT-ACAAATAAATACAAAAGCATGA 982171 vv i i ---i v vi i- ? v? i i i - - C L2d_3end#LINE 466 ACTGTGCTAGGCGCT---GTGGGGAACGANAAAANAGTATAAGA-CATG- 422 chr6ptel1M 982172 TAGTACCTGCTCTGAAGAAGCTCACATACTAATGGGACAG 982211 -- v i v i i vv i v iv C L2d_3end#LINE 421 --GTCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGGAG 384 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.39 CpG sites = 23, Kimura (unadjusted) = 41.65 Transitions / transversions = 1.44 (23/16) Gap_init rate = 0.08 (11 / 133), avg. gap size = 1.18 (13 / 11) 285 33.47 0.00 6.48 chr6ptel1M 982097 982211 (17789) C L2d2_3end#LINE/L2 (22) 533 426 m_b297s601i41 12432 chr6ptel1M 982097 TAATGAGTATTTACTACACACAAAACTATGTGCTAGACACTAAAATTGTA 982146 v iiii iiiii ii vv i i ---i v vi C L2d2_3end#LIN 533 TATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCT---GTGGGG 487 chr6ptel1M 982147 AATACAAATAAATACAAAAGCATGATAGTACCTGCTCTGAAGAAGCTCAC 982196 i v i i i - --- v i v i i C L2d2_3end#LIN 486 GATACAAAGAAGTATAAGA-CATG---GTCCCTGCCCTCAAGGAGCTTAC 441 chr6ptel1M 982197 ATACTAATGGGACAG 982211 vv i v iv C L2d2_3end#LIN 440 AATCTAGTTGGGGAG 426 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.02 CpG sites = 24, Kimura (unadjusted) = 46.83 Transitions / transversions = 2.00 (24/12) Gap_init rate = 0.06 (7 / 114), avg. gap size = 1.00 (7 / 7) 477 16.84 1.05 0.00 chr6ptel1M 982245 982339 (17661) Charlie4#DNA/hAT-Charlie 3223 3318 (60) m_b297s502i4 12433 chr6ptel1M 982245 AAACATTTTGATAACTACATTTCAGTATACTTGGTTTCCTTTGAAATTCT 982294 i i i v v i Charlie4#DNA/ 3223 AAATATTTTGATAACTATATTTCAATATAATTGGTTTCCTTTGTAATCCT 3272 chr6ptel1M 982295 CCAGATTTTGTTTTATTCATTC-AAAATATGATTCTGAGAAGGGAT 982339 viiv i v i- i v i Charlie4#DNA/ 3273 ATGTATTTTATTTTATGCATTTAAAAACATTATTCTGAGAAGGGGT 3318 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 19.36 CpG sites = 10, Kimura (unadjusted) = 19.36 Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.01 (1 / 94), avg. gap size = 1.00 (1 / 1) 728 25.28 5.62 0.00 chr6ptel1M 982825 983002 (16998) MIRc#SINE/MIR 30 217 (51) m_b297s601i42 12434 chr6ptel1M 982825 CTGGATCTGGAGTCAAGAAGATCTGAATTCAGATCTTATCTCAGTTACTT 982874 ii i i ii iii iiiv v ii MIRc#SINE/MIR 30 CTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTT 79 chr6ptel1M 982875 ACCAGCTGTGTGACCCC-TGC-ATTCACTTACCAACTCT--GTCTCAGTT 982920 i ii-v - v v vv -- i MIRc#SINE/MIR 80 ACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTT 129 chr6ptel1M 982921 TCCTCAACTGTTAAATGAAGACAATAATA---GC---ACCTATATGCCAA 982964 v v ii i --- ---i iv vv i MIRc#SINE/MIR 130 TCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAG 179 chr6ptel1M 982965 AGTTGTTATGAGAATCAAATGAAACAATAGTTATGAAA 983002 i i i i i ivv i MIRc#SINE/MIR 180 GGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAA 217 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 30.29 CpG sites = 31, Kimura (unadjusted) = 32.12 Transitions / transversions = 2.21 (31/14) Gap_init rate = 0.03 (5 / 177), avg. gap size = 2.00 (10 / 5) 715 27.84 4.04 1.75 chr6ptel1M 982827 983049 (16951) MIRb#SINE/MIR 35 262 (6) m_b297s601i43 12434 chr6ptel1M 982827 GGATCTGGAGTCAAGAAGATCTGAATTCAGATCTTATCTCAGTTACTTAC 982876 v i iiv i ii ii iiiv v ii MIRb#SINE/MIR 35 GGCTTTGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTAC 84 chr6ptel1M 982877 CAGCTGTGTGACCCC-TGC-ATTCACTTACCAACTCT--GTCTCAGTTTC 982922 i ii-v - v i v vv -- i MIRb#SINE/MIR 85 TAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTC 134 chr6ptel1M 982923 CTCAACTGTTAAATGAAGACAATAATAGCACCTATATGCCAAAGTTGTTA 982972 v v ii i --- iv vv ii i MIRb#SINE/MIR 135 CTCATCTGTAAAATGGGGATAATAAT---ACCTACCTCGCAGGGTTGTTG 181 chr6ptel1M 982973 TGAGAATCAAATGAAACAATAGTTATGAAACACATATCCAAGTACCTGTT 983022 i i i i ivv i i i i v v vv i vi MIRb#SINE/MIR 182 TGAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGC 231 chr6ptel1M 983023 TGATAGTACAGC-CTGTATAAA----AGCTCT 983049 vv - - vv ---- MIRb#SINE/MIR 232 ACATAGTA-AGCGCTCAATAAATGGTAGCTCT 262 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.49 CpG sites = 36, Kimura (unadjusted) = 35.73 Transitions / transversions = 1.44 (36/25) Gap_init rate = 0.04 (9 / 222), avg. gap size = 1.44 (13 / 9) 17 11.04 7.69 0.00 chr6ptel1M 983061 983099 (16901) (TCTA)n#Simple_repeat 1 42 (0) m_b297s252i13 12435 chr6ptel1M 983061 TCTATCTTTCTCTCTATGTATCTATTTATC-ATC-ATC-ATC 983099 v v v i - - - (TCTA)n#Simpl 1 TCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATC 42 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.08 (3 / 38), avg. gap size = 1.00 (3 / 3) 26 20.12 0.00 0.00 chr6ptel1M 983264 983314 (16686) (GT)n#Simple_repeat 1 51 (0) m_b297s252i14 12436 chr6ptel1M 983264 GTGTGTGTGAGCGTGTGTGTTTGTGTGTATGTGTGTGTCTAAGATTGTGT 983313 v i v i v iv vv (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50 chr6ptel1M 983314 G 983314 (GT)n#Simple_ 51 G 51 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 17 18.53 0.00 0.00 chr6ptel1M 983650 983680 (16320) (A)n#Simple_repeat 1 31 (0) m_b297s252i15 12437 chr6ptel1M 983650 AAAAAAAAATTTAAAAAATTAAAAAAAAAAA 983680 vvv vv (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 31 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 263 29.31 8.51 2.00 chr6ptel1M 983903 983996 (16004) MIRc#SINE/MIR 83 182 (86) m_b297s601i44 12438 chr6ptel1M 983903 AGCTGTGTAACCTTG---AAACAAC---AATTTTCTGAGTATCCCAAT-- 983944 i --- iiv --- vi i i-- i i -- MIRc#SINE/MIR 83 AGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGC--CTCAGTTT 130 chr6ptel1M 983945 CCTCTTCTGTAAATTGAAAATAAAGTTACTTGTATTATCTGCCTCAAAAG 983994 v v iii viv i ivi ii i v i MIRc#SINE/MIR 131 CCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAGG 180 chr6ptel1M 983995 GT 983996 MIRc#SINE/MIR 181 GT 182 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.43 CpG sites = 19, Kimura (unadjusted) = 39.43 Transitions / transversions = 2.38 (19/8) Gap_init rate = 0.05 (5 / 93), avg. gap size = 2.00 (10 / 5) 15 8.00 0.00 3.57 chr6ptel1M 984185 984213 (15787) (AAAAG)n#Simple_repeat 1 28 (0) m_b297s252i16 12439 chr6ptel1M 984185 AAAAGAAAAAAAAATGAAAAGAAAGGAAA 984213 i - i (AAAAG)n#Simp 1 AAAAGAAAAGAAAA-GAAAAGAAAAGAAA 28 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1) 12 24.94 1.56 6.56 chr6ptel1M 984414 984477 (15523) (TCTTAT)n#Simple_repeat 1 61 (0) m_b297s252i17 12440 chr6ptel1M 984414 TCTTATTCTTAATTATATTATTATT-TTATGAATTGTCCTGGTTCTGATT 984462 v iv v - -vv i i vi v (TCTTAT)n#Sim 1 TCTTATTCTTATTCTTATTCTTATTCTTAT-TCTTATTCTTATTCTTATT 49 chr6ptel1M 984463 ATTTCATTCTATATT 984477 -i - - (TCTTAT)n#Sim 50 -CTT-ATTCT-TATT 61 Matrix = Unknown Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.08 (5 / 63), avg. gap size = 1.00 (5 / 5) 506 29.58 5.83 2.35 chr6ptel1M 984517 984928 (15072) C L1ME4a_3end#LINE/L1 (316) 555 130 m_b297s551i6 12441 chr6ptel1M 984517 ATAATATTTCATTATATTCAAATATCATAATTTATTCAGTC--TCCATAA 984564 i ? vv vi i i ii -- viv C L1ME4a_3end#L 555 ATAATATTCCATTNTATGGATGTACCATAATTTATTTAACCANTCCCCTA 506 chr6ptel1M 984565 GGGATGGTACCTCCAG--TACTAC--ATTTTTTAATATT-TAAA-AA-GC 984607 vv v - v ii -- ii v -- iiv - - - C L1ME4a_3end#L 505 TTGTTGG-ACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAATGC 457 chr6ptel1M 984608 TGCTAT--AT-TTCTTACACATAGGAATCATTTTCC---TCTTTGAC-AC 984650 v -- i- i ii -- v v ? --- i i- i C L1ME4a_3end#L 456 TGCGATGAACATCCTTGTACATA--AATCTTTGTNCACATCTCTGATTAT 409 chr6ptel1M 984651 --CTTTAGTGATATAGGTCTAAAAGAAATATCACTGGATCAAAGGATATG 984698 -- i - v vvi i viiv i i i C L1ME4a_3end#L 408 TTCCTTAG-GATAAATTCCTAGAAGTGGAATTACTGGGTCAAAGGGTATG 360 chr6ptel1M 984699 GAGAGTTTTGTGAACTGGGGAACATCATT-TCAAATTGCTGTCCAGAATA 984747 ? v v iv ivi vv iv - -i iv vi C L1ME4a_3end#L 359 NACATTTTTAAGGCTTTTGATACAT-ATTGCCAAATTGCCCTCCAGAAAG 311 chr6ptel1M 984748 --TCTAGCAATTCAGAGCTCCC-CCAATGGCAGATTGGTGGGCCTGTGTT 984794 -- v v i v - - iii iiv vi v v i v i C L1ME4a_3end#L 310 GTTGTACCAATTTACA-CTCCCACCAGCAGTGTATGAGAGTGCCCGTTTC 262 chr6ptel1M 984795 CTCACTGCCCCTCCAGCATTTGTCATTTTCT-TTTTTTGGTCATTTTTGC 984843 ?i vv i v i i v vi v v- i ii-- i C L1ME4a_3end#L 261 NCCACACCCTCGCCAACACTGGGTATTATCAATCTTTTAA--ATCTTTGC 214 chr6ptel1M 984844 CAATCTGACAGATGTGAGGTGAAATTTCAGAACTGCTTTAATTGGCATTT 984893 i i i vi ii iv i vvii i v C L1ME4a_3end#L 213 CAATTTGATAGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTT 164 chr6ptel1M 984894 ATTTAATTATGAGGGA-TTTGAAGAGCTTTTTTCAT 984928 v i iv v -v v -- ? C L1ME4a_3end#L 163 CTTTGATTACTAGTGAGGTTGAACA--TNTTTTCAT 130 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.24 CpG sites = 66, Kimura (unadjusted) = 39.13 Transitions / transversions = 1.25 (66/53) Gap_init rate = 0.06 (26 / 411), avg. gap size = 1.31 (34 / 26) 49 0.00 0.00 2.22 chr6ptel1M 985419 985464 (14536) (CA)n#Simple_repeat 1 45 (0) c_b297s251i3 12442 chr6ptel1M 985419 CACACACACACACACACACACACACACACACACACACACACTACAC 985464 - (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACAC-ACAC 45 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1) 297 27.76 0.95 3.92 chr6ptel1M 985584 985688 (14312) C L1ME3D_3end#LINE/L1 (585) 404 303 m_b297s551i7 12443 chr6ptel1M 985584 TTCTTTGGGGTATAGACCCAGTAGTGATATCTCTTGATCAAAGGCTTTGC 985633 i i v i v iv iv v i iv v v C L1ME3D_3end#L 404 TTCTCTAGGGTATATACCTAGGAGTGGAATTGCTGGGTCGTAGGGTATGC 355 chr6ptel1M 985634 ACA-GTTTAATAACATTTTGTGTGTAATTCCAAATTGTTTCCCACAATAG 985682 i - i i---- vv iv v i v i i C L1ME3D_3end#L 354 GCATGTTCAAC----TTTACTAGGTAATGCCAAATTGTTTTCCAAAGTGG 309 chr6ptel1M 985683 TTATAC 985688 i C L1ME3D_3end#L 308 TTGTAC 303 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.16 CpG sites = 15, Kimura (unadjusted) = 35.17 Transitions / transversions = 1.15 (15/13) Gap_init rate = 0.05 (5 / 104), avg. gap size = 1.00 (5 / 5) 188 29.34 2.30 5.95 chr6ptel1M 986543 986629 (13371) C MIRc#SINE/MIR (0) 268 185 m_b297s601i45 12444 chr6ptel1M 986543 AATAATAAAGACATCTCTCATTTATAAAGGGCTTTAAAACTTGCAGAGAG 986592 vi ?i iv i v vi v ii i i v C MIRc#SINE/MIR 268 AATAATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCG 219 chr6ptel1M 986593 TTTTGA-ATATGTCATTTAGTCT-ATCCCTGCCTCACAA 986629 i v - ii i i vi i - ----- C MIRc#SINE/MIR 218 CTTTCACATACATTATCTCATTTGAT-----CCTCACAA 185 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.55 CpG sites = 16, Kimura (unadjusted) = 39.55 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.08 (7 / 86), avg. gap size = 1.00 (7 / 7) 384 31.64 4.32 6.04 chr6ptel1M 986576 986760 (13240) C MIR3#SINE/MIR (21) 187 6 m_b297s601i46 12444 chr6ptel1M 986576 TTAAAACTTGCAGAGAGTTTTGAATATGTCATTTAGTCTATCCCTGCCTC 986625 i i i v v i vi v i---i i i v -- C MIR3#SINE/MIR 187 TCAGAGCTGGAAGGGACCTTAGAG---ATCATCTAGTCCAACCC--CCTC 143 chr6ptel1M 986626 A-----CAATTGAAAAAACTGAGGCTGCAAGAGGCTGCTAATAACTTGTT 986670 ----- iv ii ivvi - v- i i ii C MIR3#SINE/MIR 142 ATTTTACAGATGAGGAAACTGAGGCCCAGAGAGG-TGA-AGTGACTTGCC 95 chr6ptel1M 986671 CATGAT--AACGGTTGGCAAATGTCAAAGGTGGGATTCCAACCCAGATCT 986718 v i --v i i?i iv i v i vi i vv i - C MIR3#SINE/MIR 94 CAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGTC- 46 chr6ptel1M 986719 GTCCTAAGT-CAAATCTGCCTGCTCTTTCCAATGAGCCACACT 986760 - i v - v i i -- i iiv v v C MIR3#SINE/MIR 45 -TCCTGACTCCCAGTCCG--TGCTCTCTCTGCTCAGCCACTCT 6 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.98 CpG sites = 34, Kimura (unadjusted) = 43.08 Transitions / transversions = 1.62 (34/21) Gap_init rate = 0.08 (14 / 184), avg. gap size = 1.36 (19 / 14) 502 29.86 1.36 2.05 chr6ptel1M 986614 986760 (13240) C MIRb#SINE/MIR (113) 155 10 m_b297s601i47 12444 chr6ptel1M 986614 TATCCCTGCCTCACAATTGAAAAAACTGAGGCTGCAAGAGGCTGCTAATA 986663 iiii i iv ii vvi i i-- i C MIRb#SINE/MIR 155 TATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTA--AGTA 108 chr6ptel1M 986664 ACTTGTTCATGAT--AACGGTTGGCAAATGTCAAAGGTGGGATTCCAACC 986711 ii v i --v i i i i i v i vi v C MIRb#SINE/MIR 107 ACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACC 58 chr6ptel1M 986712 CAGATCTGTCCTAAGTCAAATCTGCCTGCTCTTTCCAATGAGCCACACT 986760 i iv vvi v i- v v vi i C MIRb#SINE/MIR 57 CAGGTCTGTCTGACTCCAAAGCC-CGTGCTCTTTCCACTGCACCACGCT 10 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.40 CpG sites = 28, Kimura (unadjusted) = 39.81 Transitions / transversions = 1.87 (28/15) Gap_init rate = 0.03 (4 / 146), avg. gap size = 1.25 (5 / 4) 689 27.04 5.80 2.60 chr6ptel1M 987204 987427 (12573) MIRb#SINE/MIR 7 237 (31) m_b297s601i48 12445 chr6ptel1M 987204 GGCAGTCAGGTGGCACAGTAGATACAGAGCTCTCAGCAATG-AGGCAGGA 987252 i--- ii i --v v v-i vv - v iv MIRb#SINE/MIR 7 GGCAGC---GTGGTGCAGTGGA--AAGAGCACG-GGCTTTGGAGTCAGAC 50 chr6ptel1M 987253 AGAATTGAGTACAAATCCAGCCTCAGAAACTTACTAGCTATGTGATTCCA 987302 vi i v i v v v vv i iiiii MIRb#SINE/MIR 51 AGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTG 100 chr6ptel1M 987303 CGTAAGTCACTTAATCTCT----GCCTCCGATTTCTCA----AGAGATGG 987344 v i i i ---- v v i ----vi i MIRb#SINE/MIR 101 GGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGG 150 chr6ptel1M 987345 GGATAATAATAGCT---TC-CAGGACTGTTGTGAGAATCAAATCAGATAA 987390 v --- - ii i i v MIRb#SINE/MIR 151 GGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAA 200 chr6ptel1M 987391 TATTTATAAAGCATTTGGCAAAATTCTTGATACAGAG 987427 iiv i ii i v i v i ii v MIRb#SINE/MIR 201 TGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAG 237 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.30 CpG sites = 35, Kimura (unadjusted) = 34.43 Transitions / transversions = 1.46 (35/24) Gap_init rate = 0.05 (11 / 223), avg. gap size = 1.73 (19 / 11) 430 29.73 4.56 3.70 chr6ptel1M 987466 987706 (12294) L1ME4c_3end#LINE/L1 313 555 (275) m_b297s551i8 12446 chr6ptel1M 987466 TTTTGGAGAGCGATTTGGAGCCATACCCATTCAATGGCTATAAAACTGTG 987515 i i -- v vi - vi i v v L1ME4c_3end#L 313 TTTTGGAAAGCAATTTGG--CAATACGTAT-CAAGAGCCATAAAAATGTT 359 chr6ptel1M 987516 CATAACCTTTGATCCATCAGGGTCACTACTGAATCTGTGTCCCAGAGAGA 987565 v i vi ivvi v iivv v i i ii i L1ME4c_3end#L 360 CATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAA 409 chr6ptel1M 987566 CCA--CAAAAGAGGGGGGAATGTCCCATATACA------TATTTGTAGCA 987607 iv -- i iii - -- i i ------ i ii v L1ME4c_3end#L 410 TAATTCAAAAGAAGGAAAAA-G--CTATATGCACGAAGATGTTCATTGCA 456 chr6ptel1M 987608 GCCCTTTTTGTGGTGGCAAAGAATTGGAAATTGAATGTA--TGCCTGTCG 987655 vi v i ii i i i i-- iv -- i iiv i L1ME4c_3end#L 457 GCGTTATTTATAATAGCGAAAAATTGGAAAC--AACCTAAATGTCCAACA 504 chr6ptel1M 987656 AGTGGGGAATGACTGAATAAATTAGGGAATAT-GACTGTAATGGAATATT 987704 vv ii i i v v i -? -ii L1ME4c_3end#L 505 ATAGGGGAATGGTTAAGTAAATTATGGTACATCNACT-CGATGGAATATT 553 chr6ptel1M 987705 AT 987706 L1ME4c_3end#L 554 AT 555 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.38 CpG sites = 46, Kimura (unadjusted) = 39.99 Transitions / transversions = 2.00 (46/23) Gap_init rate = 0.05 (13 / 240), avg. gap size = 1.54 (20 / 13) 41 0.00 0.00 0.00 chr6ptel1M 987912 987946 (12054) (AG)n#Simple_repeat 1 35 (0) c_b297s251i4 12447 chr6ptel1M 987912 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 987946 (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 35 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 714 32.44 1.87 3.03 chr6ptel1M 988328 988594 (11406) C MIRb#SINE/MIR (2) 266 3 m_b297s601i49 12448 chr6ptel1M 988328 TAATAATACTAGTATTTATATAGGAATCCATGTGTACTAGATACTATACT 988377 ivi vi vv viv ivv i i i ii i i C MIRb#SINE/MIR 266 TAATAGAGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCT 217 chr6ptel1M 988378 AAATACTAAACAAATATATTCTCATTATAATCTTCACAACAGCACTGGAA 988427 iii vv vii vv - i i v vi C MIRb#SINE/MIR 216 AAGCGCTTTACATGCATTATCTCATT-TAATCCTCACAACAACCCTGCGA 168 chr6ptel1M 988428 GTTAGATATTATTATTATTGTTTCCATTTTACAGATGACAAAACTGAGTT 988477 v i i------i vi vi C MIRb#SINE/MIR 167 GGTAGGTATTATTATC------CCCATTTTACAGATGAGGAAACTGAGGC 124 chr6ptel1M 988478 AGAAAGAGAATAAAAAATTTCCCCTGGGTCACACAATGAGTAA-TTATAA 988526 vv i iv iv i v vi iiv - vii i C MIRb#SINE/MIR 123 TCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAG 74 chr6ptel1M 988527 GGCT--GATTTATATTCAGATCT-TCTAAGTTCCAGGCCCAATGTTCTAT 988573 i i-- iiv ii i - i v i v i -i i v C MIRb#SINE/MIR 73 AGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCC-GTGCTCTTT 25 chr6ptel1M 988574 GTACTGTACTAC-CTCTCTCTC 988594 vi i i - vi i C MIRb#SINE/MIR 24 CCACTGCACCACGCTGCCCCTC 3 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.97 CpG sites = 52, Kimura (unadjusted) = 44.33 Transitions / transversions = 1.62 (52/32) Gap_init rate = 0.05 (12 / 266), avg. gap size = 1.08 (13 / 12) 1589 28.28 2.54 3.63 chr6ptel1M 989042 989709 (10291) C L1ME5_3end#LINE/L1 (274) 667 7 m_b297s551i9 12449 chr6ptel1M 989042 ATAGTATTGTTGTTG-AAATATAATGATCTCTTCACCCTGCTCGTTTCAC 989090 i - i- ? v v -- v i-- i i iv C L1ME5_3end#LI 667 ATGGTATTGT-GTTATANATCTCAT--TCTGTTT--CTTACTTTTTTCAC 623 chr6ptel1M 989091 TCAGCATCA-GTTCATGTAAG-TCTCTCCAGGC--CTTTCTGAAATCATC 989136 ii - -- v - iv v i-- v v v -- C L1ME5_3end#LI 622 TCAGCACTATGTT--TTTAAGATCCATCCATGTTGCTATGTGTA--CATC 577 chr6ptel1M 989137 CTGTTGGTCATTTCTTACAGA-GCAATAATATTCCATAATATTCATGTAC 989185 iv iv iii v v v- - i i ii i v vi C L1ME5_3end#LI 576 TAGTCCGTTGCTTCTAACTGCTGCA-TAGTACTCCATGGTGTGCATCCAC 528 chr6ptel1M 989186 CACAATTTATTCAGTCATTCCCCAATTGATGAGCATCCACTCAGTTTCCA 989235 v iii vi i i v v ii i vviv ii C L1ME5_3end#LI 527 CACATTTTACCTATCCACTCTCCCAGTGATGGACACCCAGGTTGCCTCCA 478 chr6ptel1M 989236 GTTTCTGGCCACTACAAAGAGGGCCGCCACAAACATTCGTGCACATACAG 989285 ii i iv i v iv i v ii i vi i --- C L1ME5_3end#LI 477 ACTCCCCGCCACCACAAACAACGCTGCAATGAACATCCTCGTACAT---G 431 chr6ptel1M 989286 CTCCCTTTCCCTTCTTTGTGA---TCTCTTTGGAATATAAGCCCAGTAGT 989332 ii vivvvi v --- i i vi v i C L1ME5_3end#LI 430 TCCCCTTATGGACCTGTGTGAGAATTTCTTTGGGATATATACCCAGGAGC 381 chr6ptel1M 989333 AACACTGCTGGATCAAAGGGTATGTCCA-ATTTGATAACTTTTTGAGCA- 989380 iiv i i v ivi - i i ------ vi - C L1ME5_3end#LI 380 GGAATTGCTGGGTCATAGGGTATGCGTATACTTAAT------TTGACTAA 337 chr6ptel1M 989381 -TAGTTCCAAATTGCTCTCCAGAATGGTTGGATGTATTCACAGTTCCACC 989429 - v v i i v ivvi ii v i C L1ME5_3end#LI 336 GTACTGCCAGATTGCTCTCCAGAATGGCTGCACCAGTCTACACTCCCACC 287 chr6ptel1M 989430 AACAATGTATTAGTGTCCCTGTTTTCCCACATCCCCTCCAACATTCTGCA 989479 i i i v v i i ? i i v i iv C L1ME5_3end#LI 286 AGCAGTGCATGAGGGTTCCTATNTCCCCACATCCTCGCCAACACTTGGCA 237 chr6ptel1M 989480 TTATCTTTCCCTGTCATTCTAGCCAATCTGACAGGTGTGTAGAGATATCT 989529 ivv ii v v i v i i i iv v C L1ME5_3end#LI 236 TTATCCAGCTTTCTAATTTTTGCCAGTCTAATAGGTGTAAAGTGATATCT 187 chr6ptel1M 989530 CAGAGTTGTCTTAATTTGCATTTCTCTGATTAATAATGACTTGGAGCATC 989579 vv i v v v C L1ME5_3end#LI 186 CATTGTTGTTTTAATTTGCATTTCTCTGATTACTAATGAGTTTGAGCATC 137 chr6ptel1M 989580 TTTTCATATGGCTAGAAATAG--TTTCAA-TTTCTTCATCTGAGAATTAT 989626 i - v v-- -- ii- i v vi ii C L1ME5_3end#LI 136 TCTTCATATG-CTTGT--TAGCCTTTCGGGTTTCCTCTTCTGTAAATTGC 90 chr6ptel1M 989627 CTGTTCATATCCTTTGACCATTTATCAATTGGAG--AATGGTTTGATTTC 989674 v v v i --?vi vi -- C L1ME5_3end#LI 89 CTGTTCATATCCTTTGCCCATTTTTCTATTGGGGTTNCCGTCTT--TTTC 42 chr6ptel1M 989675 TTGTAAATTAGAGTCAATTCTCTATACATTTTGGA 989709 vi v vivv i ii i i i i C L1ME5_3end#LI 41 TTGTTGATTTGCAGGAGTTCCTTGTATATTCTAGA 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.31 CpG sites = 106, Kimura (unadjusted) = 36.59 Transitions / transversions = 1.39 (106/76) Gap_init rate = 0.05 (36 / 667), avg. gap size = 1.14 (41 / 36) 1641 27.47 0.55 1.85 chr6ptel1M 989161 989709 (10291) C L1ME3G_3end#LINE/L1 (376) 548 7 m_b297s551i10 12449 chr6ptel1M 989161 ATAATATTCCATAATATTCATGTACCACAATTTATTCAGTCATTCCCCAA 989210 i i vv i i i ii v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr6ptel1M 989211 TTGATGAGCATCCACTCAGTTTCCAGTTTCTGGCCACTACAAAGAGGGCC 989260 ii ii vviv i i v i i v iv i C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr6ptel1M 989261 GCCACAAACATTCGTGCACATACAGCTCCCTTTCCCTTCTTTGTGA---T 989307 v ii i v i --- ?i viv viv v i --- C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACAT---GCNTCCTTGTGCACATGTGCGAGTAT 402 chr6ptel1M 989308 CTCTTTGGAATATAAGCCCAGTAGTAACACTGCTGGATCAAAGGGTATGT 989357 i ? i i v v? ? v iiv i i i C L1ME3G_3end#L 401 TTCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGC 352 chr6ptel1M 989358 CCAATTTGATAACTTTTTGAGCATAGTTCCAAATTGCTCTCCAGAATGGT 989407 v - -- v viviv v v i i ? i C L1ME3G_3end#L 351 GCA-TTT--TAAATTTTAATAGATACTGCCAAATTGCCCTCCAAAANGGC 305 chr6ptel1M 989408 TGGATGTATTCACAGTTCCACCAACAATGTATTAGTGTCCCTGTTTTCCC 989457 v ivv i v i i i v v v i i C L1ME3G_3end#L 304 TGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCC 255 chr6ptel1M 989458 ACATCCCCTCCAACATTCTGCATTATCTTTCCCTGTCATTCTAGCCAATC 989507 i i v i ?vii vv? ii vvv i v C L1ME3G_3end#L 254 ACACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATC 205 chr6ptel1M 989508 TGACAGGTGTGTAGAGATATCTCAGAGTTGTCTTAATTTGCATTTCTCTG 989557 ii viv iv i vv i i C L1ME3G_3end#L 204 TGATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTG 155 chr6ptel1M 989558 ATTAATAATGACTTGGAGCATCTTTTCATATGGCTAGAAATAGTTTCAAT 989607 v i vv v vi vviiivi vv C L1ME3G_3end#L 154 ATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGTAT 105 chr6ptel1M 989608 TTCTTCATCTGAGAATTATCTGTTCATATCCTTTGACCATTTATCAATTG 989657 i v v ii v v v C L1ME3G_3end#L 104 TTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTG 55 chr6ptel1M 989658 GAGAATGGTTTGATTTCTTGTAAATTAGAGTCAATTCTCTATACATTTTG 989707 iv-- vi -- i vi v vivv i i i i C L1ME3G_3end#L 54 GGT--TGTCTT--TTTCTTATTGATTTGTAGGAGTTCTTTATATATTCTG 9 chr6ptel1M 989708 GA 989709 C L1ME3G_3end#L 8 GA 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.45 CpG sites = 79, Kimura (unadjusted) = 35.32 Transitions / transversions = 1.14 (79/69) Gap_init rate = 0.02 (11 / 548), avg. gap size = 1.18 (13 / 11) 442 29.70 1.90 2.68 chr6ptel1M 989566 989828 (10172) C L1M5_orf2#LINE/L1 (0) 3294 3034 m_b297s551i11 12449 chr6ptel1M 989566 TGACTTGGAGCATCTTTTCATATGGCTAGAAATAGTTTCAATTTCTTCAT 989615 ?v v i vi vviiivi v? v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chr6ptel1M 989616 CTGAGAATTATCTGTTCATATCCTTTGACCATTTATCAATTGGAGAATGG 989665 i v v i vi i v v ?v ---i v C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGG---GTTG 3198 chr6ptel1M 989666 TTTGATTTCTTG----TAAATTAGAGTCAATTCTCTATACATTTTGGAAA 989711 vi i ?---- i ? iv -v i i i i v C L1M5_orf2#LIN 3197 TTTGTCTTTTTNTTATTGANTTGTAG-GAGTTCTTTATATATTCTGGATA 3149 chr6ptel1M 989712 TGAGGCCTTTATCAGA-ACCTTTGACTGTAAAAATATTTTCCCAGTTTAT 989760 i v i - iv v -?i i v v i ? i i C L1M5_orf2#LIN 3148 CGAGTCCTTTGTCAGATATATGT-NTTGCAAATATTTTCTCCCANTCTGT 3100 chr6ptel1M 989761 TGCTTCCCTTCTAATCTTGTCTGCATTAGTTTTGTTTGTAAAAAAAAACT 989810 v v i v i v ivi iv - i - vi?i iv i ii C L1M5_orf2#LIN 3099 GGCTTGCCTTTTCATTTTCTTAACGGT-GTCTT-TTGANGAGCAGAAGTT 3052 chr6ptel1M 989811 TTTCACTTTGGTATAGTC 989828 v i i i? C L1M5_orf2#LIN 3051 TTTAATTTTGATGNAGTC 3034 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.15 CpG sites = 42, Kimura (unadjusted) = 40.53 Transitions / transversions = 1.24 (42/34) Gap_init rate = 0.03 (9 / 262), avg. gap size = 1.33 (12 / 9) 459 29.38 1.52 1.52 chr6ptel1M 989573 989769 (10231) C L1P3_orf2#LINE/L1 (7) 3287 3091 m_b297s551i12 12449 chr6ptel1M 989573 GAGCATCTTTTCATATGGCTAGAAATAGTTTCAATTTCTTCATCTGAGAA 989622 v i vi ivviiiv iv v v v i C L1P3_orf2#LIN 3287 GAGCTTTTTTTCATATGTTTGTTGGCCGCATAAATGTCTTCTTTTGAGAA 3238 chr6ptel1M 989623 TTATCTGTTCATATCCTTTGACCATTTATCAATTGGAGAATGGTTTGATT 989672 v i i v i v ii - i -- v v C L1P3_orf2#LIN 3237 GTGTCTGTTCATATCCTTCGCCCACTTTTTGAT-GGGG--TTGTTTGTTT 3191 chr6ptel1M 989673 T---CTTGTAAATTAGAGTCAATTCTCTATACATTTTGGAAATGAGGCCT 989719 --- v vv v i ii i v i v v v C L1P3_orf2#LIN 3190 TTTTCTTGTAAATTTGTTTAAGTTCCTTGTAGATTCTGGATATTAGCCCT 3141 chr6ptel1M 989720 TTATCAGAACCTTTGACTGTAAAAATATTTTCCCAGTTTATTGCTTCCCT 989769 i vvvv v i i v i v i i v v v C L1P3_orf2#LIN 3140 TTGTCAGATGGATAGATTGCAAAAATTTTCTCCCATTCTGTAGGTTGCCT 3091 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.68 CpG sites = 25, Kimura (unadjusted) = 37.48 Transitions / transversions = 0.78 (25/32) Gap_init rate = 0.02 (4 / 196), avg. gap size = 1.50 (6 / 4) 216 35.73 0.00 1.79 chr6ptel1M 990044 990157 (9843) AmnL2-1#LINE/L2 2162 2273 (340) m_b297s601i50 12450 chr6ptel1M 990044 CTAAAACAAATCTTCTGTTGATCTCAATTTCCTAAAGAACCAAGTTTACA 990093 v v iv -- v i v ivi vv i i v i v AmnL2-1#LINE/ 2162 CTCAAACAACTCCACTG--GCTCCCCATTCATTTCAGGATCCAGTTCAAA 2209 chr6ptel1M 990094 AATGTCTGCCTGGCATTGAAAGCCCTTCACAATCTAGCTCTATGCTGACT 990143 v i v v iv v i i iiiv v i vv iv AmnL2-1#LINE/ 2210 ATTGCCTTCCTTGTTTTTAAAACCCTCCATGGACTTGCTCCAGCCTACCT 2259 chr6ptel1M 990144 CTCCCACTTTGTCT 990157 v vv i AmnL2-1#LINE/ 2260 CACGGACCTTGTCT 2273 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 48.78 CpG sites = 17, Kimura (unadjusted) = 48.78 Transitions / transversions = 0.74 (17/23) Gap_init rate = 0.02 (2 / 113), avg. gap size = 1.00 (2 / 2) 191 31.75 0.00 1.59 chr6ptel1M 990285 990348 (9652) L2b_3end#LINE/L2 189 251 (215) m_b297s601i51 12451 chr6ptel1M 990285 TCCTAACCATCCTTTAAGTCACTACTCAAAGGCTGCCTTCTCCAGGATAT 990334 vi i i v vi v iii i i - v L2b_3end#LINE 189 TCCTACTCATCCTTCAGGTCTCAGCTCAAATGTCACCTCCTCCGGGA-AG 237 chr6ptel1M 990335 TATTCCTTGTTCCC 990348 ivi i vi L2b_3end#LINE 238 CCCTCCCTGACCCC 251 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.47 CpG sites = 13, Kimura (unadjusted) = 43.38 Transitions / transversions = 1.86 (13/7) Gap_init rate = 0.02 (1 / 63), avg. gap size = 1.00 (1 / 1) 15 0.00 4.55 0.00 chr6ptel1M 991112 991133 (8867) (TTCC)n#Simple_repeat 1 23 (0) m_b297s252i18 12452 chr6ptel1M 991112 TTCCTTCCTTCCTTCCTT-CTTC 991133 - (TTCC)n#Simpl 1 TTCCTTCCTTCCTTCCTTCCTTC 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.05 (1 / 21), avg. gap size = 1.00 (1 / 1) 565 28.77 1.90 3.21 chr6ptel1M 991217 991374 (8626) MIR3#SINE/MIR 35 190 (18) m_b297s601i52 12453 chr6ptel1M 991217 GGGAGCTACTTGGAAGATCTAGATTGGAATCGTGAATCTATCATTAATTA 991266 ii ---- i i i i vv i vi iv ii i i ? MIR3#SINE/MIR 35 GGGAGTCA----GGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTN 80 chr6ptel1M 991267 GCC-TGCTGAC--TGGGCAAATCATTTCATCTCTCTGGGACTCAGTTTCC 991313 i- - -- i i i v MIR3#SINE/MIR 81 GCTGTG-TGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCC 129 chr6ptel1M 991314 TTATGTTTAAAATATGATAAATGGACTAGATGACTTCTAAAGACCTTTTG 991363 i v v iv iviiv ii i v i iv MIR3#SINE/MIR 130 TCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCC 179 chr6ptel1M 991364 AAGCCTCATAT 991374 ivi v i MIR3#SINE/MIR 180 AGCTCTGACAT 190 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.31 CpG sites = 30, Kimura (unadjusted) = 38.45 Transitions / transversions = 2.14 (30/14) Gap_init rate = 0.04 (7 / 157), avg. gap size = 1.14 (8 / 7) 300 41.00 4.89 3.72 chr6ptel1M 991432 991697 (8303) C L2b_3end#LINE/L2 (0) 466 198 m_b297s601i54 12454 chr6ptel1M 991432 ATTCAGTCAGCCAGTGAGCATTTATTAAGGGCCTAATGTTTACCAGGCAT 991481 v vi iii ii i i v v v i ?i C L2b_3end#LINE 466 ATTCATTCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNC 417 chr6ptel1M 991482 TATGCTACACTCAAGAGACACAAAGAAAAGCAAAAC-----TGTTCCCTG 991526 i vi v vi i i iv ivi i i -----i v C L2b_3end#LINE 416 TGTGCTAGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTG 367 chr6ptel1M 991527 TCCTCCAAAAACATACG---TAATGGGGAATGGAAGGGAGACATTAAGTA 991573 i vvii i vi i--- i ----- i iv --- C L2b_3end#LINE 366 CCCTCACGGAGCTCACAGTCTAGTGG-----GGGAGACAGACAT---GTA 325 chr6ptel1M 991574 AATAGGCACATATAATATATATTAAAAGAAGATGA--AAGGAAAAAAAAA 991621 ?i i vv? ivi v v iiv iiv v --ii iiivvv i C L2b_3end#LINE 324 ANCAGACAATNATAACCCAGAGTGGCAGGGTAGGACTGGGGGGGCCCAGA 275 chr6ptel1M 991622 GGAAGGCATTTG---CAAGTTGGTGAACTGGCAAAAATTTCTTTCAGAAA 991668 i iii --- iivi v iiiii vi iiii --i i ii C L2b_3end#LINE 274 GGAGGGCGCCTGACCCGGCCTGGGGGGTCAGGGAGGGCTTC--CCGGAGG 227 chr6ptel1M 991669 GGGGGACATATGGAAGGAAAATGGAAGGA 991697 i v v iivv i viv C L2b_3end#LINE 226 AGGTGACATTTGAGCTGAGACCTGAAGGA 198 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 61.47 CpG sites = 70, Kimura (unadjusted) = 66.93 Transitions / transversions = 2.00 (70/35) Gap_init rate = 0.05 (14 / 265), avg. gap size = 1.64 (23 / 14) 321 32.42 10.61 1.86 chr6ptel1M 991432 991629 (8371) C L2a_3end#LINE/L2 (0) 517 303 m_b297s601i53 12454 chr6ptel1M 991432 ATTCAGTCAGCCAGTGAGCATTTATTAAGGGCCTAATGTTTACCAGGCAT 991481 v vi iii ii i v v i v i i C L2a_3end#LINE 517 ATTCATTCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCAC 468 chr6ptel1M 991482 TATGCTACACTCAAGAGACACAAAGAAAAGCAAAACTG------TTCCCT 991525 i v vi v vi i i iviivi i v ------v C L2a_3end#LINE 467 TGTTCTAGGCGCTGGGGATACAGCAGTGAACAAAACAGACAAAAGTCCCT 418 chr6ptel1M 991526 GTCCTCCAAAAACATACG---TAATGGGGAATGGAAGGGAGACATTAAGT 991572 i vvii i v i--- i ---- i iv v ii C L2a_3end#LINE 417 GCCCTCATGGAGCTTACATTCTAGTGGG----GGGAGACAGACAATAAAC 372 chr6ptel1M 991573 AAATAGGCACATATAATATATATTAAA--AGAAGATGA-AAG-------- 991611 iii vi v v vi-- v i - -------- C L2a_3end#LINE 371 AAATAAATAAGTAAAATATATAGTATGTCAGATGGTGATAAGTGCTATGG 322 chr6ptel1M 991612 -GAAAAAAAAAGGAAGGCA 991629 - v v i i C L2a_3end#LINE 321 AGAAAAATAAAGCAGGGTA 303 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 44.21 CpG sites = 38, Kimura (unadjusted) = 44.21 Transitions / transversions = 1.52 (38/25) Gap_init rate = 0.05 (10 / 197), avg. gap size = 2.50 (25 / 10) 326 29.92 1.20 11.92 chr6ptel1M 991432 991598 (8402) C L2c_3end#LINE/L2 (0) 478 328 m_b297s601i55 12454 chr6ptel1M 991432 ATTCAGTCAGCCAGTGAGCATTTATTAAGGGCCTAATGTTTACCAGGCAT 991481 v vi iii i i v v i v i -- C L2c_3end#LINE 478 ATTCATTCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGC-- 431 chr6ptel1M 991482 TATGCTACACTCAAGAGACACAAAGAAAAGCAAAAC-TGTTCCCTGTCCT 991530 --- i------- i i vi ii i -i v i C L2c_3end#LINE 430 ---GCTG-------GGGATACAAAGATGAATAAGACACGGTCCCTGCCCT 391 chr6ptel1M 991531 CCAAAAACATACGTAATGGGGAATGGAAGGGAGACAT-TAAGTAAATAGG 991579 v ii i vi -- i --vv i -- v-i ? i i C L2c_3end#LINE 390 CAAGGAGCTCAC--AGT--CTAGTGGA--GGAGACAGACANGTAAACAGA 347 chr6ptel1M 991580 CACATATAATATATATTAA 991598 vv i i vi C L2c_3end#LINE 346 CAATTACAATACAAGTTAA 328 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.46 CpG sites = 29, Kimura (unadjusted) = 39.65 Transitions / transversions = 1.93 (29/15) Gap_init rate = 0.12 (20 / 166), avg. gap size = 1.00 (20 / 20) 54 0.00 0.00 0.00 chr6ptel1M 991983 992028 (7972) (TC)n#Simple_repeat 1 46 (0) c_b297s251i5 12455 chr6ptel1M 991983 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 992028 (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 46 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 17 10.69 1.96 10.64 chr6ptel1M 992034 992084 (7916) (TCC)n#Simple_repeat 1 47 (0) m_b297s252i20 12456 chr6ptel1M 992034 TCCTCCCTCCCTCCCTCCTCCTCTTCTTCTTCCT-CTCCCCCTCTCTCTC 992082 - - - i i i - i - - (TCC)n#Simple 1 TCCT-CCT-CCT-CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC-CTC-C 45 chr6ptel1M 992083 TC 992084 (TCC)n#Simple 46 TC 47 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.12 (6 / 50), avg. gap size = 1.00 (6 / 6) 21 23.73 1.67 1.67 chr6ptel1M 992029 992088 (7912) (CCTCTT)n#Simple_repeat 1 60 (0) m_b297s252i19 12457 chr6ptel1M 992029 CCCCTTCCTCCCTCC-CTCCCTCCTCCTCTTCTTCTTCCTCTCCCCCTCT 992077 i - i - i i i i i ii (CCTCTT)n#Sim 1 CCTCTTCCT-CTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTCTTC 49 chr6ptel1M 992078 CTCTCTCTCTT 992088 ii (CCTCTT)n#Sim 50 CTCTTCCTCTT 60 Matrix = Unknown Transitions / transversions = 1.00 (11/0) Gap_init rate = 0.03 (2 / 59), avg. gap size = 1.00 (2 / 2) 20 17.19 7.27 0.00 chr6ptel1M 992036 992090 (7910) (CTCT)n#Simple_repeat 1 59 (0) m_b297s252i21 12457 chr6ptel1M 992036 CTCCCTCCCTCCCTC-CTC-CTCT-TCT-TCTTCCTCTCCCCCTCTCTCT 992081 i i i - - - - ii i i (CTCT)n#Simpl 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chr6ptel1M 992082 CTCTCTTTC 992090 i (CTCT)n#Simpl 51 CTCTCTCTC 59 Matrix = Unknown Transitions / transversions = 1.00 (8/0) Gap_init rate = 0.07 (4 / 54), avg. gap size = 1.00 (4 / 4) 22 0.00 0.00 0.00 chr6ptel1M 992725 992748 (7252) (AC)n#Simple_repeat 1 24 (0) m_b297s252i22 12458 chr6ptel1M 992725 ACACACACACACACACACACACAC 992748 (AC)n#Simple_ 1 ACACACACACACACACACACACAC 24 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 17 0.00 0.00 0.00 chr6ptel1M 992750 992768 (7232) (TG)n#Simple_repeat 1 19 (0) m_b297s252i23 12459 chr6ptel1M 992750 TGTGTGTGTGTGTGTGTGT 992768 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGT 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 235 27.47 3.30 0.00 chr6ptel1M 992798 992888 (7112) MIRc#SINE/MIR 174 267 (1) m_b297s601i56 12460 chr6ptel1M 992798 TCAAAAAGTT-TTATGAAGCTCAAATGGGATAATATAT-TTAAAATGTTC 992845 v ii - i i v i i - v ii i i MIRc#SINE/MIR 174 TCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTT 223 chr6ptel1M 992846 TGCAAAACTTAAATTGTTTTATAAATATTAGTCATTA-TATTAT 992888 i viv v i v i i v v?i - MIRc#SINE/MIR 224 TGTAAACTGTAAAGTGCTATACAAATGTAAGGNGTTATTATTAT 267 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.17 CpG sites = 16, Kimura (unadjusted) = 35.98 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.03 (3 / 90), avg. gap size = 1.00 (3 / 3) 246 22.57 3.17 1.56 chr6ptel1M 992953 993015 (6985) X6b_DNA#DNA/TcMar-Tigger 2 65 (174) m_b297s502i5 12461 chr6ptel1M 992953 AGATGTGCTCTACTTTGAGAAAAC--AATGTACAGAAATCTTAATTTACA 993000 i i ii i --i i ii iv i X6b_DNA#DNA/T 2 AGGTGTGCCCCGCTTTAAGAAAACCCGATATACGAAAATCCGAACTTACA 51 chr6ptel1M 993001 AAAATAGATACATTA 993015 - i v X6b_DNA#DNA/T 52 -AAACAGATAAATTA 65 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 19.50 CpG sites = 12, Kimura (unadjusted) = 28.85 Transitions / transversions = 6.00 (12/2) Gap_init rate = 0.03 (2 / 62), avg. gap size = 1.50 (3 / 2) 239 29.23 4.62 0.00 chr6ptel1M 993518 993582 (6418) C MIRc#SINE/MIR (148) 120 53 m_b297s601i57 12462 chr6ptel1M 993518 TCAAAGA---TAAATGACTTGCCTAGGGTCGCATAGCTTGCAGTTATCTG 993564 i --- i i i i i v i iv iv v C MIRc#SINE/MIR 120 TCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAG 71 chr6ptel1M 993565 AGGCTTGATTTGAACTCA 993582 v vv i i i C MIRc#SINE/MIR 70 AGCCGGGACTCGAACCCA 53 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.89 CpG sites = 12, Kimura (unadjusted) = 38.47 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.02 (1 / 64), avg. gap size = 3.00 (3 / 1) 548 29.88 5.11 1.09 chr6ptel1M 994823 994998 (5002) MIR3#SINE/MIR 16 198 (10) m_b297s601i58 12463 chr6ptel1M 994823 AATAGAGAAAACACTGAGCCTGGAAA-GAGGAGCCTTGGGTGCTAATCCT 994871 ii i i v -- i i-v v i v i i MIR3#SINE/MIR 16 AGCAGAGAGAGCACGGA--CTGGGAGTCAGGAGACCTGGGTTCTAGTCCC 63 chr6ptel1M 994872 CATTCTGCTTCTAACTTGCTGGGTAGCCTTGGGTAAGTGATTTCAGCTTT 994921 vii iv ? v ii i v i v i MIR3#SINE/MIR 64 GGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCT 113 chr6ptel1M 994922 GTGCGCCTCAATGTCCACATCT-TAA----AGAAAGTTACACT---CCAT 994963 v v i v v - ---- iii iv ---iv MIR3#SINE/MIR 114 CTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGAT 163 chr6ptel1M 994964 TTCAAAAGGATCTTCTACCCTTAACTTTCTGGGAT 994998 i v i vvi i v ii i v iv MIR3#SINE/MIR 164 CTCTAAGGTCCCTTCCAGCTCTGACATTCTATGAT 198 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.64 CpG sites = 31, Kimura (unadjusted) = 39.63 Transitions / transversions = 1.48 (31/21) Gap_init rate = 0.03 (6 / 175), avg. gap size = 1.83 (11 / 6) 49 0.00 2.22 0.00 chr6ptel1M 995080 995124 (4876) (TA)n#Simple_repeat 1 46 (0) c_b297s251i6 12464 chr6ptel1M 995080 TATA-ATATATATATATATATATATATATATATATATATATATATA 995124 - (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATA 46 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 389 32.46 4.39 0.00 chr6ptel1M 995681 995794 (4206) MIRc#SINE/MIR 4 122 (146) m_b297s601i59 12465 chr6ptel1M 995681 GGTGATGTA-TACAATGGAAGTAGTTCTAGATTTGA--T--GAAATACTT 995725 iii i- i i iv iv i i i-- -- i v i MIRc#SINE/MIR 4 GGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCT 53 chr6ptel1M 995726 GGGTGCAAATCCTGGTTTGACAGCTTATTACTTATGTGACCTTAGAAAAA 995775 v i i i i ivi vi i vi i i iv i MIRc#SINE/MIR 54 GGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAG 103 chr6ptel1M 995776 TCAAGTAACCTCTCTGGGC 995794 vv i MIRc#SINE/MIR 104 TCACTTAACCTCTCTGAGC 122 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.56 CpG sites = 27, Kimura (unadjusted) = 46.03 Transitions / transversions = 2.70 (27/10) Gap_init rate = 0.03 (3 / 113), avg. gap size = 1.67 (5 / 3) 186 19.35 0.00 0.00 chr6ptel1M 995790 995820 (4180) L3#LINE/CR1 4046 4076 (23) m_b297s601i60 12466 chr6ptel1M 995790 TGGGCTAGATGATCTTTAATGTCTCTTTCAA 995820 i i i v i i L3#LINE/CR1 4046 TGGACTAGATGACCTCTAAGGTCCCTTCCAA 4076 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 23.58 CpG sites = 5, Kimura (unadjusted) = 23.58 Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 623 27.71 3.61 0.00 chr6ptel1M 996245 996410 (3590) C MIR3#SINE/MIR (2) 206 35 m_b297s601i61 12467 chr6ptel1M 996245 ATTATGAAACTATAGAACGTCAGAGTTGGAAAGCATCTTAGAGATCATTC 996294 i ii ii i i i v i ii C MIR3#SINE/MIR 206 ATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCT 157 chr6ptel1M 996295 ACT-CAATGACCTCATTGTACAGCAGAGGAATCTGACAATCAGCGAAATG 996343 v - ivv v vv v vivi v ii C MIR3#SINE/MIR 156 AGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTG 107 chr6ptel1M 996344 AAGGAACTTGTTCGAGATCACATGGCCAA-TAATG---GAGCCAGAACTG 996389 vi ii i i ii ? i- i --- i i i C MIR3#SINE/MIR 106 AAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTA 57 chr6ptel1M 996390 GAACGAATG-CTTCTGCCTCTC 996410 vv v - i v i C MIR3#SINE/MIR 56 GAACCCAGGTCTCCTGACTCCC 35 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.25 CpG sites = 30, Kimura (unadjusted) = 36.26 Transitions / transversions = 1.88 (30/16) Gap_init rate = 0.02 (4 / 165), avg. gap size = 1.50 (6 / 4) 462 32.04 2.39 5.94 chr6ptel1M 996599 996807 (3193) C L3#LINE/CR1 (8) 4091 3890 m_b297s601i62 12468 chr6ptel1M 996599 CACACAATTTCTGAACTGAAAAGGACCTCCAAGGCTACCTAATCCCACC- 996647 v i v ii i i ivi ii i i v - C L3#LINE/CR1 4091 CACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCAACCT 4042 chr6ptel1M 996648 CACGTGTGA-GTAGGAACCCCTTTCACATCACCATTCCTCCCAAAATCAC 996696 v i vii - i i ii ---v i vv ivvvv C L3#LINE/CR1 4041 CCCATCCAATGCAGGAATCCCTTCTACA---ACATCCCTGACAAGTGGTC 3995 chr6ptel1M 996697 ATGTAATCACTTTATTTGAAGACTTCTAGTAATGTGGTGCTTTCT--CTA 996744 vi ii -- i ii v i i i i v v iv -- v C L3#LINE/CR1 3994 ATCCAGCC--TCTGCTTGAACACCTCCAGTGACGGGGAGCTCACTACCTC 3947 chr6ptel1M 996745 TC-AGACAGCCAATGGTCTGTTCTATTGTTGAACACATTTTATTGTTAGA 996793 ? - i v ------- i v i vv i v C L3#LINE/CR1 3946 NCGAGGCAGCCCAT-------TCCATTTTTGGACAGCTCTGATTGTTAGA 3904 chr6ptel1M 996794 AAATTCTCTGTTAT 996807 i iiv C L3#LINE/CR1 3903 AAGTTCTTCCTTAT 3890 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.64 CpG sites = 38, Kimura (unadjusted) = 43.57 Transitions / transversions = 1.52 (38/25) Gap_init rate = 0.08 (16 / 208), avg. gap size = 1.06 (17 / 16) 305 28.59 9.14 9.73 chr6ptel1M 996834 997019 (2981) C MIR1_Amn#SINE/MIR (45) 185 1 m_b297s601i63 12469 chr6ptel1M 996834 CAAAACACTTTTCCCCACAGAGGAAGTGAAAAATAGTGAATGTATTATTA 996883 i ----- i i v ------------ i C MIR1_Amn#SINE 185 CAAAGCACTTT-----ACAAAGGAGGTCA------------GTATCATTA 153 chr6ptel1M 996884 TCTACATTTTATAGAAGAG-----------ACAGAGAGCTTAATGAATTT 996922 iv i v -----------? v ? vvi i C MIR1_Amn#SINE 152 TCCCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTT 103 chr6ptel1M 996923 GTCCATGGTTAAGCAGTACACATGTGGAATA-----AATCTGAACAGAAG 996967 i v i v? i?vi ?v v v -----i ?i? vv i C MIR1_Amn#SINE 102 GCCCAAGGTCACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAACCCAGG 53 chr6ptel1M 996968 ACTCTCCCCTTCCGATCCTGGGCTC-ACTCATTTGTACTACAGTGTTTCT 997016 v i vvv i ii v v - ii i v - i v ii i C MIR1_Amn#SINE 52 TCTCCCGAGTCCCAGTCCAGTGCTCTATCCACTAG-ACCACACTGCCTCC 4 chr6ptel1M 997017 CTA 997019 C MIR1_Amn#SINE 3 CTA 1 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.76 CpG sites = 26, Kimura (unadjusted) = 38.76 Transitions / transversions = 1.18 (26/22) Gap_init rate = 0.11 (21 / 185), avg. gap size = 1.67 (35 / 21) 618 32.29 4.76 0.98 chr6ptel1M 997015 997308 (2692) C L3#LINE/CR1 (142) 3957 3653 m_b297s601i64 12470 chr6ptel1M 997015 CTCTACTATCTCTAGAGCTTGCTCAGCCC-TTGCTGGCCAACTCTTGTTT 997063 - i ?v viv i vi - vi v i vi v C L3#LINE/CR1 3957 CTC-ACTACCTCNCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGATTG 3909 chr6ptel1M 997064 TTAGGAAGATTTTCCAGGTGTTAAACCCAAAGGTTCCTTTCTGTTACTTC 997113 i v i vvi i i i v vv v ii v C L3#LINE/CR1 3908 TTAGAAAGTTCTTCCTTATATTGAGCCGAAATCTGCCTCCCTGTAACTTC 3859 chr6ptel1M 997114 TACTTATTGGTCTTAGTTCT------TTAAATCAAGTGTAGCAATTCTGA 997157 i ii i ------ vi ii viiiv ii v i C L3#LINE/CR1 3858 CACCCATTGGTCCTAGTTCTGCCCTCTGGAGCCACACAGAATAAGTCTAA 3809 chr6ptel1M 997158 CATCTCTGCCATATGTTAACTCTTAATATATTTAGACACAA--ATTCTA- 997204 ivi v i vi i i v v ii v i-- iv i- C L3#LINE/CR1 3808 TCCCTCTTCCACATGACAGCCCTTCAAATATTTGAAGACAGCTATCATGT 3759 chr6ptel1M 997205 ATCC-CTAAGTTATCTCTTCTCTTGGCTTAATTTTCCAGGTTCCTTCTAT 997253 v - iv iv v iv i vi v i C L3#LINE/CR1 3758 CTCCTCTAAGTCTTCTCTTCTCCAGGCTAAACATCCCCAGTTCCTTCAAC 3709 chr6ptel1M 997254 ATGTCCTTAT-TTTCATGGCTTT--AACCTACCCCACCATCCTGTTCATT 997300 vvv i - vv i i--i -- ii v ii C L3#LINE/CR1 3708 CGTTCCTCATATGACATGGTTTCCAGACC--CTTCACCATCCTGGTCGCT 3661 chr6ptel1M 997301 CTCCTTTG 997308 i C L3#LINE/CR1 3660 CTCCTCTG 3653 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.14 CpG sites = 54, Kimura (unadjusted) = 43.77 Transitions / transversions = 1.35 (54/40) Gap_init rate = 0.03 (10 / 293), avg. gap size = 1.70 (17 / 10) 194 37.78 1.11 0.00 chr6ptel1M 997294 997383 (2617) MIRc#SINE/MIR 56 146 (122) m_b297s601i65 12471 chr6ptel1M 997294 GTTC-ATTCTCCTTTGTATTACTTATGAAAAGTATCATCTTTAGCAAGTC 997342 - v i vvi v iii iv ivv i v i vi MIRc#SINE/MIR 56 GTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTC 105 chr6ptel1M 997343 TCTTAACCTTCATATATTCTAGTTTCTTTCTCTATAAAATG 997383 v iiv iviiiii i iv i MIRc#SINE/MIR 106 ACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATG 146 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 55.75 CpG sites = 21, Kimura (unadjusted) = 55.75 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.01 (1 / 89), avg. gap size = 1.00 (1 / 1) 209 37.33 0.00 0.00 chr6ptel1M 997309 997383 (2617) MIR#SINE/MIR 68 142 (120) m_b297s601i66 12471 chr6ptel1M 997309 TATTACTTATGAAAAGTATCATCTTTAGCAAGTCTCTTAACCTTCATATA 997358 iii iv ivv i v i vi iv iiv i i MIR#SINE/MIR 68 TGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTG 117 chr6ptel1M 997359 TTCTAGTTTCTTTCTCTATAAAATG 997383 iiii i iv i MIR#SINE/MIR 118 CCTCAGTTTCCTCATCTGTAAAATG 142 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 57.08 CpG sites = 20, Kimura (unadjusted) = 57.08 Transitions / transversions = 2.50 (20/8) Gap_init rate = 0.00 (0 / 74), avg. gap size = 0.0 (0 / 0) 298 35.00 0.00 0.00 chr6ptel1M 997324 997423 (2577) MIR3#SINE/MIR 84 183 (25) m_b297s601i67 12471 chr6ptel1M 997324 GTATCATCTTTAGCAAGTCTCTTAACCTTCATATATTCTAGTTTCTTTCT 997373 i v i vi v v iiv iviiiii i iv MIR3#SINE/MIR 84 GTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCAT 133 chr6ptel1M 997374 CTATAAAATGAATGCACTGACCTAGAGGATCTCTTAACTCCCATGGAGCT 997423 i iv vii iv v v iv v vv MIR3#SINE/MIR 134 CTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCT 183 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 48.47 CpG sites = 19, Kimura (unadjusted) = 48.47 Transitions / transversions = 1.19 (19/16) Gap_init rate = 0.00 (0 / 99), avg. gap size = 0.0 (0 / 0) 275 27.37 4.60 3.41 chr6ptel1M 998157 998243 (1757) MIR3#SINE/MIR 98 185 (23) m_b297s601i68 12472 chr6ptel1M 998157 AAGTCATTTTAAGTCTTTGGGTTTCGGGCTTTTCCTTGT---TAAAATTC 998203 i i vv i ii i --- ii --- vv MIR3#SINE/MIR 98 AAGTCACTTCACCTCTCTGGGCCTCAG---TTTCCTCATCTGTAAAATGA 144 chr6ptel1M 998204 AGAGGATGGATTAGATTATCTCAGAAGT-TCTTCCAATTCT 998243 i i v i v vi i -i ii MIR3#SINE/MIR 145 GGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCT 185 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.77 CpG sites = 16, Kimura (unadjusted) = 35.77 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.06 (5 / 86), avg. gap size = 1.40 (7 / 5) 581 30.46 2.86 0.56 chr6ptel1M 998374 998548 (1452) MIR3#SINE/MIR 9 187 (21) m_b297s601i69 12473 chr6ptel1M 998374 GTAGCATAGTGAATAGAGTACTACACTTGGAAT--GAAGA--TGAGCTTA 998419 i vv iii v i vi- v i -- i -- i i iv MIR3#SINE/MIR 9 GTGGCTGAGCAGAGAGAGCACGG-ACTGGGAGTCAGGAGACCTGGGTTCT 57 chr6ptel1M 998420 AATTCTGCTTCAGAAACTTAATAGCTATGTGCATCTAGGCAAGTCACATA 998469 i i i vi v vv v v ? i vvii i v v MIR3#SINE/MIR 58 AGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTC 107 chr6ptel1M 998470 ACCTCTCTGTGCC-CAATTTCCTAATCTGTAAAATGAAGCAATTGGACTT 998518 v - i v i vii v MIR3#SINE/MIR 108 ACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTA 157 chr6ptel1M 998519 GATGGTTTTAGAAGTCCCTTTCACCTTTAA 998548 i i ivi i i v i i MIR3#SINE/MIR 158 GATGATCTCTAAGGTCCCTTCCAGCTCTGA 187 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.57 CpG sites = 31, Kimura (unadjusted) = 40.57 Transitions / transversions = 1.41 (31/22) Gap_init rate = 0.02 (4 / 174), avg. gap size = 1.50 (6 / 4) 226 27.69 15.70 4.48 chr6ptel1M 998557 998677 (1323) L3#LINE/CR1 3965 4098 (1) m_b297s601i70 12474 chr6ptel1M 998557 TCATTGGAAA-GCTCTGAAGCAGAATTTGGATA---------CAGGG--- 998593 i ii- i -- ivi i--------- --- L3#LINE/CR1 3965 TCACTGGAGGTGTTC--AAGCAGAGGCTGGATGACCACTTGTCAGGGATG 4012 chr6ptel1M 998594 ---TAATAAGAATCACCT---TTGGGTAAGTAAGGATGAGACCAGATGCT 998637 --- iv i i i- --- i ii -- v - i vi L3#LINE/CR1 4013 TTGTAGAAGGGATT-CCTGCATTGGATGGG--AGGTTG-GACTAGATGAC 4058 chr6ptel1M 998638 TTTTGAGCTTCCATCTAACTCTGAGAATCTAGGACTCTGT 998677 i i i v i v i v iv i i L3#LINE/CR1 4059 CTCTAAGGTCCCTTCCAACTCTGAGATTCTGTGATTCTAT 4098 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.12 CpG sites = 24, Kimura (unadjusted) = 37.12 Transitions / transversions = 3.00 (24/8) Gap_init rate = 0.09 (11 / 120), avg. gap size = 2.27 (25 / 11) 285 26.15 10.28 3.51 chr6ptel1M 999635 999741 (259) C MIRc#SINE/MIR (152) 116 3 m_b297s601i71 12475 chr6ptel1M 999635 AGAGGTTCAGCAAATTGC--AAAGTGATTCA-CAAATA-GTGATAAGGTT 999680 v ii v -- i v iv - v i - ii ii ii C MIRc#SINE/MIR 116 AGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCC 67 chr6ptel1M 999681 GGGATTCCAAACCAG-------TGACTCCAAGACCTTTCAGGGATCATTC 999723 i v v ------- ---- i v v v C MIRc#SINE/MIR 66 GGGACTCGAACCCAGGTCTTCCTGACTCCAAG----TCCAGTGCTCTTTC 21 chr6ptel1M 999724 CACTGAACCACTTTGCTT 999741 v vi i C MIRc#SINE/MIR 20 CACTGCACCACACTGCCT 3 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.37 CpG sites = 15, Kimura (unadjusted) = 32.82 Transitions / transversions = 1.25 (15/12) Gap_init rate = 0.08 (8 / 106), avg. gap size = 1.88 (15 / 8) 69 1.61 0.00 0.00 chr6qtel1M 949 1011 (998989) (TC)n#Simple_repeat 1 63 (0) c_b298s251i0 12476 chr6qtel1M 949 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 998 (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr6qtel1M 999 TTTCTCTCTCTCT 1011 i (TC)n#Simple_ 51 TCTCTCTCTCTCT 63 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0) 418 27.03 0.00 5.22 chr6qtel1M 1595 1715 (998285) MIRb#SINE/MIR 4 118 (150) m_b298s601i0 12477 chr6qtel1M 1595 AGGGGCAGTTACAGGGCATAATGAATAGAAGAATGCAGCTCCGAAAGTCA 1644 --- iv iii i i v - v i -i ii i - MIRb#SINE/MIR 4 AGGGGCAG---CGTGGTGCAGTGGAAAGA-GCACG-GGCTTTGGA-GTCA 47 chr6qtel1M 1645 GGAGAACCTGAATTCAAATACAGCCTCAGACACTTACTAGTTGTGTAACC 1694 ivii ii i v v v v v i i MIRb#SINE/MIR 48 GACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACC 97 chr6qtel1M 1695 TTGGGCAGGTTATTTAACCCC 1715 i i i MIRb#SINE/MIR 98 TTGGGCAAGTTACTTAACCTC 118 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 30.97 CpG sites = 22, Kimura (unadjusted) = 35.15 Transitions / transversions = 2.44 (22/9) Gap_init rate = 0.05 (6 / 120), avg. gap size = 1.00 (6 / 6) 440 26.56 0.86 2.63 chr6qtel1M 1610 1725 (998275) MIR#SINE/MIR 9 122 (140) m_b298s601i1 12477 chr6qtel1M 1610 GCATAATGAATAGAAGAATGCAGCTCCGAAAGTCAGGAGAACCTGAATTC 1659 i iv ii v i -i i i - i - vvi ii MIR#SINE/MIR 9 GCATAGTGGTTAAGAGCACG-GGCTCTGGA-GCCAG-ACTGCCTGGGTTC 55 chr6qtel1M 1660 AAATACAGCCTCAGACACTTACTAGTTGTGTAACCTTGGGCAGGTTATTT 1709 i v v v v v i i i i MIR#SINE/MIR 56 GAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTT 105 chr6qtel1M 1710 AACCCCATT-TGCCTTA 1725 i vi - i MIR#SINE/MIR 106 AACCTCTCTGTGCCTCA 122 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 31.30 CpG sites = 20, Kimura (unadjusted) = 34.08 Transitions / transversions = 2.00 (20/10) Gap_init rate = 0.03 (4 / 115), avg. gap size = 1.00 (4 / 4) 13 26.86 2.22 0.00 chr6qtel1M 2107 2151 (997849) (CTTT)n#Simple_repeat 1 46 (0) m_b298s252i0 12478 chr6qtel1M 2107 CTTTTTTTTAATCTTTCTTACCTT-TTTCCTTCCTCCATTCTTTCT 2151 i ivv v i - i i i v (CTTT)n#Simpl 1 CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 46 Matrix = Unknown Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 245 28.67 15.97 3.09 chr6qtel1M 2153 2296 (997704) C MIR1_Amn#SINE/MIR (56) 174 13 m_b298s601i2 12479 chr6qtel1M 2153 ACAAAGTAGATCAG-AGTAGTATTTTT-TTTT---GATAAGGCAATTG-- 2195 v i - vi v iiii- --- i v i -- C MIR1_Amn#SINE 174 ACAAAGGAGGTCAGTATCATTATCCCCATTTTACAGATGAGGAAACTGAG 125 chr6qtel1M 2196 -------GAGTT---GTGACTTGTCCAGGGTCACATAGATAG-AAGTATT 2234 ------- v --- i i ?i v?i -? ivi C MIR1_Amn#SINE 124 GCNCAGAGAGGTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNAGTGGC 75 chr6qtel1M 2235 AAA-----TATTTGAGACCAGATTTGAACTCCTGACTTTAGGGCTAGTGC 2279 i -----v ? ? iv i ----- i v iivi v i C MIR1_Amn#SINE 74 AGAGCCGGGANTNGAACCCAGGT-----CTCCCGAGTCCCAGTCCAGTGC 30 chr6qtel1M 2280 TCTATTCCTTAAGCAAC 2296 i vi ii v C MIR1_Amn#SINE 29 TCTATCCACTAGACCAC 13 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 38.47 CpG sites = 26, Kimura (unadjusted) = 39.78 Transitions / transversions = 1.86 (26/14) Gap_init rate = 0.09 (13 / 143), avg. gap size = 2.15 (28 / 13) 247 28.19 10.20 5.88 chr6qtel1M 2185 2282 (997718) C MIR#SINE/MIR (140) 122 21 m_b298s601i3 12479 chr6qtel1M 2185 TAAGGCA-ATTGGAGTT--GTGACTTGTCCAGGGTCACATAGATAGAAGT 2231 i - vv ii -- i i i i v ---- C MIR#SINE/MIR 122 TGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAG---- 77 chr6qtel1M 2232 ATTAAATATTTGAGACCAGATTTGAACTC-------CTGACTTTAGGGCT 2274 -- i iviv v vi i i ------- i ii i i C MIR#SINE/MIR 76 --TAAGTGGCAGAGCCGGGATTCGAACCCAGGCAGTCTGGCTCCAGAGCC 29 chr6qtel1M 2275 AGTGCTCT 2282 v C MIR#SINE/MIR 28 CGTGCTCT 21 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 35.47 CpG sites = 18, Kimura (unadjusted) = 37.31 Transitions / transversions = 2.25 (18/8) Gap_init rate = 0.09 (9 / 97), avg. gap size = 1.78 (16 / 9) 292 24.37 6.90 5.68 chr6qtel1M 2201 2287 (997713) C MIRc#SINE/MIR (161) 107 20 m_b298s601i4 12479 chr6qtel1M 2201 GTGACTTGTCCAGGGTCACATAGATAG-AAGTATTAAA-----TATTTGA 2244 i i i v - ivi i -----v i i C MIRc#SINE/MIR 107 GTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGA 58 chr6qtel1M 2245 GACCAGATTTGAACTCCTGACTTTAGGGCTAGTGCTCTATTCC 2287 iv i i ---- ii i v i - C MIRc#SINE/MIR 57 ACCCAGGTCT----TCCTGACTCCAAGTCCAGTGCTCT-TTCC 20 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 29.20 CpG sites = 15, Kimura (unadjusted) = 31.08 Transitions / transversions = 3.00 (15/5) Gap_init rate = 0.08 (7 / 86), avg. gap size = 1.57 (11 / 7) 13 5.27 0.00 0.00 chr6qtel1M 2442 2461 (997539) (ATG)n#Simple_repeat 1 20 (0) m_b298s252i1 12480 chr6qtel1M 2442 ATGATGATGATGATAATGAT 2461 i (ATG)n#Simple 1 ATGATGATGATGATGATGAT 20 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 556 32.76 2.94 1.24 chr6qtel1M 2465 2702 (997298) C MIR#SINE/MIR (0) 262 21 m_b298s601i5 12481 chr6qtel1M 2465 AATAACA-CTAATATATATGATTTATGTTCTATGCTCTAGCTATTGTGCT 2513 i - i v vivviiiv v iv i vi i v C MIR#SINE/MIR 262 AATAATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCT 213 chr6qtel1M 2514 AAGTACAATTA-ATCTA--ACCTCATTTAATGAACCCAACAATTGTGGGA 2560 ii v- - v -- v vvv v iiv iv C MIR#SINE/MIR 212 AAGCGCT-TTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGA 164 chr6qtel1M 2561 ATTAAGTGTTATTATTTTCTCCATTCTACAGTTGGAGAA-CTGAAAATAG 2609 iv i ii v i i v ii - ii-i v C MIR#SINE/MIR 163 GGTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGG-CAC 115 chr6qtel1M 2610 ATAGAAATTAAGTGACTTGCTCAGGGTCACACAG-TAA-AAGTGTTTAAA 2657 v ii i i i - i- vivi i C MIR#SINE/MIR 114 AGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAG 65 chr6qtel1M 2658 CTTAGATTTGAATTGAGTCCTTCCTGAATCGAGTACCAGTCCTCT 2702 ivi i iiv v vv - iv v vi v v C MIR#SINE/MIR 64 CCGGGATTCGAACCCAGGCAGT-CTGGCTCCAGAGCCCGTGCTCT 21 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 40.97 CpG sites = 42, Kimura (unadjusted) = 44.14 Transitions / transversions = 1.20 (42/35) Gap_init rate = 0.04 (9 / 237), avg. gap size = 1.11 (10 / 9) 621 31.05 2.68 2.22 chr6qtel1M 2493 2716 (997284) C MIRb#SINE/MIR (31) 237 13 m_b298s601i6 12481 chr6qtel1M 2493 CTATGCTCTAGCTATTGTGCTAAGTACAATTA-ATCTA--ACCTCATTTA 2539 iv i vi i ii v- - vi -- i C MIRb#SINE/MIR 237 CTATGTGCCAGGCACTGTGCTAAGCGCT-TTACATGCATTATCTCATTTA 189 chr6qtel1M 2540 ATGAACCCAACAATTGTGGGAATTAAGTGTTATTATTTTCTCCATTCTAC 2589 vvv v iiv v iv i i --- i i C MIRb#SINE/MIR 188 ATCCTCACAACAACCCTGCGAGGTAGGTATTATTAT---CCCCATTTTAC 142 chr6qtel1M 2590 AGTTGGAGAA-CTGAAAATAGATAGAAATTAAGTGACTTGCTCAGGGTCA 2638 v ii - iiv -v v ii i i i C MIRb#SINE/MIR 141 AGATGAGGAAACTGAGGCT-CAGAGAGGTTAAGTAACTTGCCCAAGGTCA 93 chr6qtel1M 2639 CACAG-TAA-AAGTGTTTAAACTTAGATTTGAATTGAGTCCTTCCTGAAT 2686 - i- vivi i ivi i iiv vi vi v C MIRb#SINE/MIR 92 CACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACT 43 chr6qtel1M 2687 CGAGTACCAGTCCTCTGTCTTCTATACCAC 2716 v ivi v v v iv ii C MIRb#SINE/MIR 42 CCAAAGCCCGTGCTCTTTCCACTGCACCAC 13 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 38.90 CpG sites = 40, Kimura (unadjusted) = 41.36 Transitions / transversions = 1.43 (40/28) Gap_init rate = 0.04 (10 / 223), avg. gap size = 1.10 (11 / 10) 13 16.12 0.00 0.00 chr6qtel1M 3992 4019 (995981) (AATTT)n#Simple_repeat 1 28 (0) m_b298s252i2 12482 chr6qtel1M 3992 AAATTAATTTCATTAAATTTTATTTAAT 4019 v v v v (AATTT)n#Simp 1 AATTTAATTTAATTTAATTTAATTTAAT 28 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 430 28.57 2.36 0.78 chr6qtel1M 4598 4724 (995276) C MIRb#SINE/MIR (48) 220 92 m_b298s601i7 12483 chr6qtel1M 4598 TGCTAGAATCTTTACAAACTATTATCTCATTTTATACTCACAAAA---TT 4644 iivv vi - v v v ---i C MIRb#SINE/MIR 220 TGCTAAGCGCTTTACATGC-ATTATCTCATTTAATCCTCACAACAACCCT 172 chr6qtel1M 4645 GAAAGATGGGTGACATTACCCCCATTATACATCTGGGAAAACTGAAGCAG 4694 vi i i ivi i v vv i i i vv C MIRb#SINE/MIR 171 GCGAGGTAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC 122 chr6qtel1M 4695 GCAGAAGTTAATTGACCTGTTCAGGGTAAC 4724 iv i v i i ii i v C MIRb#SINE/MIR 121 AGAGAGGTTAAGTAACTTGCCCAAGGTCAC 92 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 35.44 CpG sites = 20, Kimura (unadjusted) = 36.71 Transitions / transversions = 1.25 (20/16) Gap_init rate = 0.02 (2 / 126), avg. gap size = 2.00 (4 / 2) 15 12.44 5.71 0.00 chr6qtel1M 5012 5046 (994954) (TTTGT)n#Simple_repeat 1 37 (0) m_b298s252i3 12484 chr6qtel1M 5012 TTTCTGTTGTTTTATCTTG--TTGTTTTGTTTTGTTT 5046 v v i i -- (TTTGT)n#Simp 1 TTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTT 37 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.03 (1 / 34), avg. gap size = 2.00 (2 / 1) 200 37.16 2.61 1.72 chr6qtel1M 5198 5312 (994688) C L2a_3end#LINE/L2 (259) 258 143 m_b298s601i8 12485 chr6qtel1M 5198 AGAGTGATTGGAAAAGGTTTCTTTTAAAAACAGG-ATTTTAATTGAGACT 5246 i i ii ii ii ?i v i ivv i- v iivi i C L2a_3end#LINE 258 AGGGTGGTCAGGGAAGGCCTCNCTGAGAAGGTGACATTTGAGCAAAGACC 209 chr6qtel1M 5247 TAAAGAAAGTCAGGGAA--AACAATAGGCAGAGAAAAGGAGTAATAGCTT 5294 i i i v i-- i v -- i v vvv i v v v C L2a_3end#LINE 208 TGAAGGAGGTGAGGGAGCGAGCCAT--GCGGATATCTGGGGGAAGAGCGT 161 chr6qtel1M 5295 TTCAGATATGGGGAACAG 5312 i ii vi C L2a_3end#LINE 160 TCCAGGCAGAGGGAACAG 143 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 53.61 CpG sites = 27, Kimura (unadjusted) = 55.66 Transitions / transversions = 1.80 (27/15) Gap_init rate = 0.04 (4 / 114), avg. gap size = 1.25 (5 / 4) 197 33.79 0.00 4.65 chr6qtel1M 5986 6075 (993925) C AmnL2-1#LINE/L2 (397) 2216 2131 m_b298s601i9 12486 chr6qtel1M 5986 AGAGAATTTTCTATTTGAACCTGGAAGTAATAGTGAGTCAATGAATTTCA 6035 iv vv i v v i vv i v i i i v vv C AmnL2-1#LINE/ 2216 AGGCAATTTTGAACTGGATCCTGAAATGAATGGGGAGCCAGTGGAGTTGT 2167 chr6qtel1M 6036 TTGGAAGTGAGAGTTTTGATGTGGTCACCACTTTGTTTTA 6075 iiii i i --- i- i iv v C AmnL2-1#LINE/ 2166 TTGAGGATGGGGG---TGATGTGGTCG-CGCTTCTTTGTA 2131 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 41.83 CpG sites = 16, Kimura (unadjusted) = 46.04 Transitions / transversions = 1.23 (16/13) Gap_init rate = 0.04 (4 / 89), avg. gap size = 1.00 (4 / 4) 11 14.81 4.88 4.88 chr6qtel1M 6702 6742 (993258) (GAATGAG)n#Simple_repeat 1 41 (0) m_b298s252i4 12487 chr6qtel1M 6702 GAA-GAGAAAACAGGAAATAGAGGAAAGA-GAATGAGGACTGA 6742 - i vv - - v - v (GAATGAG)n#Si 1 GAATGAGGAATGAGG-AAT-GAGGAATGAGGAATGAGGAATGA 41 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.10 (4 / 40), avg. gap size = 1.00 (4 / 4) 183 14.25 11.36 4.26 chr6qtel1M 7312 7355 (992645) C MIRc#SINE/MIR (141) 127 81 m_b298s601i10 12488 chr6qtel1M 7312 CTGAGGCAATTAG---GGTTAAGTGATTTGTCTAGGGT--CACAACTAG 7355 -- i --- i i i i -- i C MIRc#SINE/MIR 127 CTGAGGC--TCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG 81 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 16.82 CpG sites = 6, Kimura (unadjusted) = 16.82 Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.09 (4 / 43), avg. gap size = 1.75 (7 / 4) 278 28.09 9.69 1.22 chr6qtel1M 7826 8052 (991948) L1M5_orf2#LINE/L1 1564 1809 (1485) m_b298s551i0 12489 chr6qtel1M 7826 AAAATCATTTCATGTAAAAGAAAAATCATAGACCAA-ATCCCTTAATGAA 7874 iv v v - - i i - i - L1M5_orf2#LIN 1564 AAAGACATTACAAG-AAAAGAAAA-TTACAGACCAATATCCCTCA-TGAA 1610 chr6qtel1M 7875 TATCAAAGCACAAATTG-AAATAAAATGATGGCAAAAAGATTATAATATT 7923 i vi v v iv-? i iv i vv v vi ii v L1M5_orf2#LIN 1611 CATAGATGCAAAAATCCTNAACAAAATATTAGCAAATCGAATCCAGCAAT 1660 chr6qtel1M 7924 GTATCAAGACAATATTAAA--------AGGTGGAATTTATAT----AATA 7961 i v i vi v v -------- i ii vi---- i L1M5_orf2#LIN 1661 ATATAAAAAGGATAATACATCATGACCAAGTGGGGTTTATCCCAGGAATG 1710 chr6qtel1M 7962 CATAACTAGTTTAATATGAAGAAAACAATCAGCATAATTAGCCATATTAA 8011 viii i i vvii v iii vi L1M5_orf2#LIN 1711 CAAGGTTGGTTTAACATTCGAAAATCAATCAATGTAATTCACCATATTAA 1760 chr6qtel1M 8012 TAAAAT-------ATAAAT-ATATAATTATTTTAATAGATGCAAAAAAA 8052 i i ------- v - i i i i i L1M5_orf2#LIN 1761 CAGAATAAAGGAGAAAAATCATATGATCATCTCAATAGATGCAGAAAAA 1809 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 35.89 CpG sites = 39, Kimura (unadjusted) = 36.63 Transitions / transversions = 1.62 (39/24) Gap_init rate = 0.04 (9 / 226), avg. gap size = 2.78 (25 / 9) 228 15.69 7.84 0.00 chr6qtel1M 8071 8121 (991879) DNM1r#Unknown 2490 2544 (2118) m_b298s502i0 12490 chr6qtel1M 8071 ATATATGTATGTATAAGTATGTATATGT----ACATGTGTATACATCCAT 8116 i v i i ---- i i v i DNM1r#Unknown 2490 ATATATGTGTGTATATGTGTGTATGTGTGTATATATGTGTATATATACGT 2539 chr6qtel1M 8117 ATATA 8121 ? DNM1r#Unknown 2540 ATNTA 2544 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 16.07 CpG sites = 6, Kimura (unadjusted) = 18.51 Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.02 (1 / 50), avg. gap size = 4.00 (4 / 1) 16 21.31 0.00 2.27 chr6qtel1M 8847 8891 (991109) (AATAA)n#Simple_repeat 1 44 (0) m_b298s252i5 12491 chr6qtel1M 8847 AATAAAATAAAATCAAAGAATTAAAAAATGGAAGAAAACAAAATA 8891 v v -v v ii v i (AATAA)n#Simp 1 AATAAAATAAAATAAAATAA-AATAAAATAAAATAAAATAAAATA 44 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 13 30.24 2.78 2.78 chr6qtel1M 8999 9070 (990930) (TAT)n#Simple_repeat 1 72 (0) m_b298s252i6 12492 chr6qtel1M 8999 TATTATTGTTGATATTGTAATT-TTATTAATATTGGCATCATTA-TACAA 9046 i iv i v - v ivi i - iv (TAT)n#Simple 1 TATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTA 50 chr6qtel1M 9047 TTATATAAAATAATAAATTATAAT 9070 - vv v -v v (TAT)n#Simple 51 TTAT-TATTATTAT-TATTATTAT 72 Matrix = Unknown Transitions / transversions = 0.70 (7/10) Gap_init rate = 0.06 (4 / 71), avg. gap size = 1.00 (4 / 4) 258 32.84 5.56 4.83 chr6qtel1M 9551 9694 (990306) MIRc#SINE/MIR 5 149 (119) m_b298s601i11 12493 chr6qtel1M 9551 GCAGAAGAGCACAGTGAAAGGGGC----TACGTAGCAGTCAGAGAACAAA 9596 vivi ii i i i ----v v i - - v vv MIRc#SINE/MIR 5 GCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGG-AGTCAG-GAAGACC 52 chr6qtel1M 9597 TGCATTGAAAGACAGTCTCAG-TATACCA-TAACTTGCTTTA--ACTTTA 9642 vi vi ----- i i - v i - v v v i-- i i MIRc#SINE/MIR 53 TGGGTTCGA-----GTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTG 97 chr6qtel1M 9643 AAAAATTCCCTAAGTCTCTCTGGATCTTAGTTCCCTCACCTGTAAAAGGA 9692 iiv v v v ii iii i i i v i MIRc#SINE/MIR 98 GGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGG 147 chr6qtel1M 9693 GG 9694 MIRc#SINE/MIR 148 GG 149 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 42.21 CpG sites = 27, Kimura (unadjusted) = 44.90 Transitions / transversions = 1.50 (27/18) Gap_init rate = 0.08 (11 / 143), avg. gap size = 1.36 (15 / 11) 325 28.89 6.67 0.00 chr6qtel1M 9610 9744 (990256) MIR3#SINE/MIR 58 201 (7) m_b298s601i12 12493 chr6qtel1M 9610 AGTCTCAG-TATACCA-TAACTTGCTTTA--ACTTTAAAAAATTCCCTAA 9655 i i - v i - ? v i-- i iiiv v v vv MIR3#SINE/MIR 58 AGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTC 107 chr6qtel1M 9656 GTCTCTCTGGATCTTAGTTCCCTCACCTGTAAAAGGAGGGCTTTGA--TA 9703 ii ii i i i v vv i-- MIR3#SINE/MIR 108 ACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTA 157 chr6qtel1M 9704 ATTTTTTTCTAACTTCTTTTCT-GTTCT-ACA-TCTCTGAGTCT 9744 iv vv i vv ii i- i - - v v MIR3#SINE/MIR 158 GATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCT 201 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 36.47 CpG sites = 22, Kimura (unadjusted) = 37.69 Transitions / transversions = 1.29 (22/17) Gap_init rate = 0.05 (7 / 134), avg. gap size = 1.29 (9 / 7) 42 0.00 0.00 0.00 chr6qtel1M 10459 10494 (989506) (TG)n#Simple_repeat 1 36 (0) c_b298s251i1 12494 chr6qtel1M 10459 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 10494 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 36 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 22 25.44 6.67 1.05 chr6qtel1M 11130 11219 (988781) (TA)n#Simple_repeat 1 95 (0) m_b298s252i7 12495 chr6qtel1M 11130 TATATATGTACATATATATA-AAATCTATGTGTATA-ACAT-TTTGTTTA 11176 i i - v v i i - i - v i v (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr6qtel1M 11177 TATCATATATTCATAATTATTTA-ATACAT-TAGAT-TTTAGATAT 11219 - vi vv v - i - v - v v (TA)n#Simple_ 51 TAT-ATATATATATATATATATATATATATATATATATATATATAT 95 Matrix = Unknown Transitions / transversions = 0.73 (8/11) Gap_init rate = 0.08 (7 / 89), avg. gap size = 1.00 (7 / 7) 226 23.21 1.79 0.00 chr6qtel1M 12317 12372 (987628) MIRc#SINE/MIR 190 246 (22) m_b298s601i13 12493 chr6qtel1M 12317 AAAATCAAATAAAATAATATGTGTAAAA-CACTTTGCAAACAATCAAGTA 12365 ii i i i i i - i i vi v i MIRc#SINE/MIR 190 AGGATCAAATGAGATAATGTATGTGAAAGCGCTTTGTAAACTGTAAAGTG 239 chr6qtel1M 12366 CTATACA 12372 MIRc#SINE/MIR 240 CTATACA 246 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 27.10 CpG sites = 11, Kimura (unadjusted) = 29.83 Transitions / transversions = 5.50 (11/2) Gap_init rate = 0.02 (1 / 55), avg. gap size = 1.00 (1 / 1) 19 20.80 3.45 1.69 chr6qtel1M 12455 12512 (987488) (ATAG)n#Simple_repeat 1 59 (0) m_b298s252i8 12496 chr6qtel1M 12455 ATAGA-ATATATATAGAGATATAGATATAGATATCCTATAGA-ATATAGA 12502 - v v v v v v v -vv - v (ATAG)n#Simpl 1 ATAGATAGATAGATAGATAGATAGATAGATAGAT-AGATAGATAGATAGA 49 chr6qtel1M 12503 TAGATAGATA 12512 (ATAG)n#Simpl 50 TAGATAGATA 59 Matrix = Unknown Transitions / transversions = 0.00 (0/10) Gap_init rate = 0.05 (3 / 57), avg. gap size = 1.00 (3 / 3) 311 24.40 3.50 4.31 chr6qtel1M 17486 17742 (982258) C HERVIP10FH#LTR/ERV1 (4069) 1033 779 m_b298s701i0 12497 chr6qtel1M 17486 AAATGAA-AAGCCACACTTTTTCTTCTACCAATACTTTTCAAAGCATTTT 17534 v - i vi v i -ii v i - vvv vi i C HERVIP10FH#LT 1033 AAAGGAATAGGGTACACTGTTTTTTCT-TTACTACTTCT-ATCTCTCTCT 986 chr6qtel1M 17535 TTCTGCCTGTCTCTGTCTTTCTGTATCCATAAATCTGTCTGTCTGTCTGT 17584 vi v i v --- ----- v v v v C HERVIP10FH#LT 985 TTCTTTCTCTCTTTGACTTTCTGT---C-----TCTCTCTCTCTCTCTGA 944 chr6qtel1M 17585 CTCTCTCTCTG-CTCTCTGTCTCTGTGTCTTTCTGTCTCTCTCTGTCTCT 17633 i i - viv i i v i C HERVIP10FH#LT 943 CTCCCTCTTTGTCTCTCTGTCTCTTCCTCTCTCTGCCTCTCTCTCTCTTT 894 chr6qtel1M 17634 GTCTCTTTCTGTTTCTCTGTCTCTATCTCTGTCTCTCTTCCCCCCCCATC 17683 v ii v v v vi v i i i i - C HERVIP10FH#LT 893 GACTCCCTCTTTGTCTCTCTCTCTCCCTCTCTCTCTCTTTCTCTCTC-TC 845 chr6qtel1M 17684 TGTCTGTCTCTGTCTATCTGTCTCTCTCTGCTCT---CTCTCTGT--GTC 17728 v vi v v v iiv --- i-- C HERVIP10FH#LT 844 TCTCTTCCTCTCTCTCTCTCTCTCTCTTCTCTCTTTCCTCTCTGCTGGTC 795 chr6qtel1M 17729 --TCTCTGTCTCTGTC 17742 -- i i i C HERVIP10FH#LT 794 TTTCCCTGCCTCTGCC 779 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 29.76 CpG sites = 30, Kimura (unadjusted) = 29.76 Transitions / transversions = 1.00 (30/30) Gap_init rate = 0.06 (16 / 256), avg. gap size = 1.25 (20 / 16) 52 28.27 0.00 0.00 chr6qtel1M 17745 17881 (982119) (TC)n#Simple_repeat 1 137 (0) m_b298s252i10 12498 chr6qtel1M 17745 TCTGTCTCTCTCTCTCTCTCTCTCTGTGTGTGTGTGTGTGTGTGTGTATG 17794 v v v v v v v v v v v v v v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr6qtel1M 17795 TGTGTCTCTCTCTCTGTCTCTCTCTGTCTGCCTCTCTGTTTCTCTGTGTC 17844 v v v v vi v i v v (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chr6qtel1M 17845 TCCGTGTCTCTGTGTCTCTGTCTCCCTCTCTCTTTCT 17881 iv v v v v i i (TC)n#Simple_ 101 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 137 Matrix = Unknown Transitions / transversions = 0.19 (5/27) Gap_init rate = 0.00 (0 / 136), avg. gap size = 0.0 (0 / 0) 18 34.15 0.00 0.00 chr6qtel1M 19437 19498 (980502) (TT)n#Simple_repeat 1 62 (0) m_b298s252i11 12499 chr6qtel1M 19437 TTTTCTATTTTTTTTTTTTTTTACTTTCTTGATACAAGTATTCTTTTTTG 19486 i v vi i vv vivvv v i v (TT)n#Simple_ 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr6qtel1M 19487 GGTTTTTTTTTT 19498 vv (TT)n#Simple_ 51 TTTTTTTTTTTT 62 Matrix = Unknown Transitions / transversions = 0.42 (5/12) Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0) 15 14.98 2.56 2.56 chr6qtel1M 19516 19554 (980446) (TTATATT)n#Simple_repeat 1 39 (0) m_b298s252i12 12500 chr6qtel1M 19516 TTATATTTTATGTCTTATATGTTTATGTATT-TATTTGAT 19554 i i - i v - v (TTATATT)n#Si 1 TTATATTTTATATTTTATAT-TTTATATTTTATATTTTAT 39 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2) 42 33.34 1.18 1.79 chr6qtel1M 19938 20106 (979894) (AT)n#Simple_repeat 1 168 (0) m_b298s252i13 12501 chr6qtel1M 19938 ATATATATATATATTAATA-ATGACATAT-TGTGTGAGTATATATATATA 19985 vv - - i - i i - - (AT)n#Simple_ 1 ATATATATATATATATATATAT-ATATATATATAT-A-TATATATATATA 47 chr6qtel1M 19986 TATATATATAAACAGACACACATATACAAATGAACTTATACACAAATATA 20035 v i v i i i i v iv iv i i v (AT)n#Simple_ 48 TATATATATATATATATATATATATATATATATATATATATATATATATA 97 chr6qtel1M 20036 AATATATTCAAGCATATACATAGGTATCTATATCCACACTTACATATACA 20085 v vi vii i vi v vi i iv i i (AT)n#Simple_ 98 TATATATATATATATATATATATATATATATATATATATATATATATATA 147 chr6qtel1M 20086 TGCATATGTATATGCATCTAT 20106 ii i ii v (AT)n#Simple_ 148 TATATATATATATATATATAT 168 Matrix = Unknown Transitions / transversions = 1.69 (27/16) Gap_init rate = 0.03 (5 / 168), avg. gap size = 1.00 (5 / 5) 355 26.20 0.75 8.87 chr6qtel1M 22575 22708 (977292) MIRb#SINE/MIR 6 129 (139) m_b298s601i14 12502 chr6qtel1M 22575 GGCCAGCTAGATGACTCATTGGGATAGAGAACTGGCCGTGGAGTCAGGAG 22624 v vv i --- v i - v v iv ivi MIRb#SINE/MIR 6 GGGCAGCGTGGTG---CAGTGGAA-AGAGCACGGGCTTTGGAGTCAGACA 51 chr6qtel1M 22625 GCCCTGAGTTTAAATCCAGCCACAGACATTTAATAGTTACTAGCTTTTTG 22674 v i ii v v ------- i ivi v v v MIRb#SINE/MIR 52 GACCTGGGTTCGAATCCCGGC-------TCTGCCACTTACTAGCTGTGTG 94 chr6qtel1M 22675 ACCCTGGGCAAGTCATTTAACAGCTCTT-GCCTCA 22708 i i i vv v- MIRb#SINE/MIR 95 ACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCA 129 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 30.79 CpG sites = 14, Kimura (unadjusted) = 32.08 Transitions / transversions = 0.78 (14/18) Gap_init rate = 0.09 (12 / 133), avg. gap size = 1.00 (12 / 12) 420 22.73 0.88 6.54 chr6qtel1M 22596 22708 (977292) MIRc#SINE/MIR 20 126 (142) m_b298s601i15 12502 chr6qtel1M 22596 GGATAGAGAACTGGCCGTGGAGTCAGGAGGCCCTGAGTTTAAATCCAGCC 22645 v v v v i v i ii i v v MIRc#SINE/MIR 20 GGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGC 69 chr6qtel1M 22646 ACAGACATTTAATAGTTACTAGCTTTTTGACCCTGGGCAAGTCATTTAAC 22695 ------- i ivi v v v i i MIRc#SINE/MIR 70 -------TCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAAC 112 chr6qtel1M 22696 AGCTCTT-GCCTCA 22708 vv v- MIRc#SINE/MIR 113 CTCTCTGAGCCTCA 126 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 25.64 CpG sites = 10, Kimura (unadjusted) = 27.01 Transitions / transversions = 0.71 (10/14) Gap_init rate = 0.07 (8 / 112), avg. gap size = 1.00 (8 / 8) 240 30.48 3.28 5.88 chr6qtel1M 22748 22869 (977131) MIR3#SINE/MIR 71 189 (19) m_b298s601i16 12503 chr6qtel1M 22748 CCAATAACTTCCTTTG--ATTGTGAAAAAAACACT-CAGTTCCCTTGGTC 22794 v ?v v -- iiv iiv iv - vi i v i MIR3#SINE/MIR 71 CCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCC 120 chr6qtel1M 22795 TCAGTTACCTCAACTATACAATGGGTGTTTTGGTCAAATTGTCTGACTTT 22844 v v i v i v ---- iii i ivv --- MIR3#SINE/MIR 121 TCAGTTTCCTCATCTGTAAAATGAGGG----GGTTGGACTAGATGA---T 163 chr6qtel1M 22845 CTTT-AGGTTCCATAATGCTCTGACA 22869 i - i v vvv MIR3#SINE/MIR 164 CTCTAAGGTCCCTTCCAGCTCTGACA 189 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 39.94 CpG sites = 17, Kimura (unadjusted) = 39.94 Transitions / transversions = 0.94 (17/18) Gap_init rate = 0.08 (10 / 121), avg. gap size = 1.10 (11 / 10) 45 23.75 0.00 0.96 chr6qtel1M 23564 23668 (976332) (TG)n#Simple_repeat 1 104 (0) m_b298s252i14 12504 chr6qtel1M 23564 TGTGAGTGTGGGCGAGTGTGTGTGACTGTGCTTGTGTGTGTGTGTGTGTG 23613 v v i v vv iv (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr6qtel1M 23614 TGTGTTTCTGTGAGTGTCAGTGTGTGCTTGTGCAAGTGTGCATGTGTGAT 23663 v v v vv iv iiv ii - (TG)n#Simple_ 51 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG-T 99 chr6qtel1M 23664 CTGTG 23668 v (TG)n#Simple_ 100 GTGTG 104 Matrix = Unknown Transitions / transversions = 0.50 (7/14) Gap_init rate = 0.01 (1 / 104), avg. gap size = 1.00 (1 / 1) 12 11.25 6.90 0.00 chr6qtel1M 27227 27255 (972745) (AATAA)n#Simple_repeat 1 31 (0) m_b298s252i15 12505 chr6qtel1M 27227 AAT-AAAT-AAGTAAAATTAAACAAAATAAA 27255 - - i v i (AATAA)n#Simp 1 AATAAAATAAAATAAAATAAAATAAAATAAA 31 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.07 (2 / 28), avg. gap size = 1.00 (2 / 2) 31 25.98 1.94 0.96 chr6qtel1M 27739 27780 (972220) (TCTG)n#Simple_repeat 1 44 (60) m_b298s252i16 12506 chr6qtel1M 27739 TCTTTATCTCTGTCCGTC--TCTGTCTATTTGTCTGTCTGTCTG 27780 v v v i -- i i (TCTG)n#Simpl 1 TCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTG 44 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.02 (1 / 41), avg. gap size = 2.00 (2 / 1) 39 6.67 0.00 0.00 chr6qtel1M 27781 27827 (972173) (TC)n#Simple_repeat 1 47 (0) c_b298s251i2 12507 chr6qtel1M 27781 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTCTCACTCTTTCTCT 27827 v v i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 47 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 31 25.98 1.94 0.96 chr6qtel1M 27828 27887 (972113) (TCTG)n#Simple_repeat 45 103 (1) m_b298s252i16 12508 chr6qtel1M 27828 GTGTGTGTAGGGTCTGCCTCTCTGCCTCTCTGTGTCTTTGTCTCCCTCTC 27877 v v -vv i v i v v v i vi v (TCTG)n#Simpl 45 CTGTCTGT-CTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTC 93 chr6qtel1M 27878 TCTCTGTGTG 27887 v v (TCTG)n#Simpl 94 TGTCTGTCTG 103 Matrix = Unknown Transitions / transversions = 0.33 (4/12) Gap_init rate = 0.02 (1 / 59), avg. gap size = 1.00 (1 / 1) 65 0.00 0.00 0.00 chr6qtel1M 29564 29618 (970382) (TA)n#Simple_repeat 1 55 (0) c_b298s251i3 12509 chr6qtel1M 29564 TATATATATATATATATATATATATATATATATATATATATATATATATA 29613 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr6qtel1M 29614 TATAT 29618 (TA)n#Simple_ 51 TATAT 55 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 44 0.00 0.00 0.00 chr6qtel1M 30114 30151 (969849) (AT)n#Simple_repeat 1 38 (0) c_b298s251i4 12510 chr6qtel1M 30114 ATATATATATATATATATATATATATATATATATATAT 30151 (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATAT 38 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 27 0.00 0.00 0.00 chr6qtel1M 30152 30181 (969819) (GT)n#Simple_repeat 1 30 (0) m_b298s252i17 12511 chr6qtel1M 30152 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 30181 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 30 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 46 0.00 0.00 0.00 chr6qtel1M 30437 30475 (969525) (TA)n#Simple_repeat 1 39 (0) c_b298s251i5 12512 chr6qtel1M 30437 TATATATATATATATATATATATATATATATATATATAT 30475 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATAT 39 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 33 33.62 2.47 1.84 chr6qtel1M 33128 33289 (966711) (TA)n#Simple_repeat 1 163 (0) m_b298s252i18 12513 chr6qtel1M 33128 TATATAT-TAT-TAAAGACATAT-TGTGTGAGTATATATATATTTATATA 33174 - - v v i - i i - - v (TA)n#Simple_ 1 TATATATATATATATATATATATATATAT-A-TATATATATATATATATA 48 chr6qtel1M 33175 TATAGAAACAGACACACATATACAAATGAACTTATACACAAATATAATTG 33224 v v i v i i i i v iv iv i i v vv i (TA)n#Simple_ 49 TATATATATATATATATATATATATATATATATATATATATATATATATA 98 chr6qtel1M 33225 TAT-TCAATCATATACATAGATATCTATAACCACACTTACATATACATAC 33273 - vv - i v v vvi i iv i i i (TA)n#Simple_ 99 TATATATAT-ATATATATATATATATATATATATATATATATATATATAT 147 chr6qtel1M 33274 ATATATATGCATCTAT 33289 ii v (TA)n#Simple_ 148 ATATATATATATATAT 163 Matrix = Unknown Transitions / transversions = 1.10 (22/20) Gap_init rate = 0.04 (7 / 161), avg. gap size = 1.00 (7 / 7) 63 0.00 0.00 0.00 chr6qtel1M 33878 33931 (966069) (AT)n#Simple_repeat 1 54 (0) c_b298s251i6 12514 chr6qtel1M 33878 ATATATATATATATATATATATATATATATATATATATATATATATATAT 33927 (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr6qtel1M 33928 ATAT 33931 (AT)n#Simple_ 51 ATAT 54 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 449 25.35 0.75 8.06 chr6qtel1M 35772 35904 (964096) MIRc#SINE/MIR 4 127 (141) m_b298s601i17 12515 chr6qtel1M 35772 GGCAGCTAGATGGCTCAGTGGATAGAGAACTGACCCTTAAGTCAGGAGGA 35821 i---i iv v v iv i vi i MIRc#SINE/MIR 4 GGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA 50 chr6qtel1M 35822 CCTGAGTTTAAATGCAGCCTCAGACATTTAATAGGTACTAGTTTTGTGAC 35871 i ii i v v v v v i ------- i v MIRc#SINE/MIR 51 CCTGGGTTCGAGTCCCGGCTCTGCCACT-------TACTAGCTGTGTGAC 93 chr6qtel1M 35872 CCTGGGCAAGTCATTTAATTCCACTT-GCCTCAG 35904 i i iii v v- MIRc#SINE/MIR 94 CTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 30.01 CpG sites = 18, Kimura (unadjusted) = 31.34 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.08 (11 / 132), avg. gap size = 1.00 (11 / 11) 17 12.17 0.00 5.26 chr6qtel1M 35980 36019 (963981) (AAAAGAA)n#Simple_repeat 1 38 (0) m_b298s252i19 12516 chr6qtel1M 35980 AAAAGAATAAAGAAAAAGGAAAGACAGGAAGAAAGAAAAA 36019 v i - - i i (AAAAGAA)n#Si 1 AAAAGAAAAAAGAAAAAAGAAA-A-AAGAAAAAAGAAAAA 38 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 183 33.03 5.50 0.00 chr6qtel1M 36520 36628 (963372) MIR3#SINE/MIR 71 185 (23) m_b298s601i18 12517 chr6qtel1M 36520 CCAATAACTTCCTTTC--ACTGTGAAAAAATCACT-CAGTTCCCTTGTCC 36566 v ?v v v-- iv iiv i - vi i v v MIR3#SINE/MIR 71 CCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCC 120 chr6qtel1M 36567 TCAGTTACCTCACCTATAAAATAGATGCTTTTGGTCAACT--TCTCTGAC 36614 v i i iiiv vv v iii iv -- i v MIR3#SINE/MIR 121 TCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAG 170 chr6qtel1M 36615 TTCCTTTAT-GCTCT 36628 v i vi- MIR3#SINE/MIR 171 GTCCCTTCCAGCTCT 185 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 44.79 CpG sites = 18, Kimura (unadjusted) = 44.79 Transitions / transversions = 1.00 (18/18) Gap_init rate = 0.04 (4 / 108), avg. gap size = 1.50 (6 / 4) 186 27.27 1.82 0.00 chr6qtel1M 36536 36590 (963410) MIR1_Amn#SINE/MIR 94 149 (81) m_b298s601i19 12517 chr6qtel1M 36536 ACTGTGAAAAAATCACT-CAGTTCCCTTGTCCTCAGTTACCTCACCTATA 36584 iv iiv i -? vi i v?v v i i MIR1_Amn#SINE 94 ACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTA 143 chr6qtel1M 36585 AAATAG 36590 i MIR1_Amn#SINE 144 AAATGG 149 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 36.57 CpG sites = 9, Kimura (unadjusted) = 36.57 Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1) 29 0.00 0.00 0.00 chr6qtel1M 37367 37391 (962609) (TG)n#Simple_repeat 1 25 (0) c_b298s251i7 12518 chr6qtel1M 37367 TGTGTGTGTGTGTGTGTGTGTGTGT 37391 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGT 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 35 5.07 0.00 0.00 chr6qtel1M 39752 39792 (960208) (TATATC)n#Simple_repeat 1 41 (0) c_b299s251i1 12519 chr6qtel1M 39752 TATATCTATATCTATATCTATATCTATATATATATATATAT 39792 v v (TATATC)n#Sim 1 TATATCTATATCTATATCTATATCTATATCTATATCTATAT 41 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 13 9.26 0.00 0.00 chr6qtel1M 39802 39824 (960176) (ATAC)n#Simple_repeat 1 23 (0) m_b299s252i0 12520 chr6qtel1M 39802 ATATATACTTACATACATACATA 39824 i v (ATAC)n#Simpl 1 ATACATACATACATACATACATA 23 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 12 6.83 2.56 11.11 chr6qtel1M 42395 42433 (957567) (GAAAAG)n#Simple_repeat 1 36 (0) m_b299s252i1 12521 chr6qtel1M 42395 GAAAAGTGAGAAGGGAAAAGTGAAAAGG-GAAGGAATAAG 42433 - - i - -i - (GAAAAG)n#Sim 1 GAAAAG-GA-AAAGGAAAAG-GAAAAGGAAAAGGAA-AAG 36 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.13 (5 / 38), avg. gap size = 1.00 (5 / 5) 354 27.47 7.39 1.40 chr6qtel1M 42529 42731 (957269) L1MEi_5end#LINE/L1 1993 2207 (5) m_b299s551i0 12522 chr6qtel1M 42529 GAAGGGGGGGAAGGGGAGAAAAGGGGA-GAAAA----CCATAAACAG--- 42570 vi i i i ?i - ----iv --- L1MEi_5end#LI 1993 GAAGGCAGGAAAGGAGAGAAAAAGNAAAGAAAAAGNATGATAAACAGAAA 2042 chr6qtel1M 42571 -CGGTTAACAAGATGG--GAAGTAA-TACAAA---ATTGGTAATTTTAAC 42613 - ivvv i -- i - v --- ii i--- L1MEi_5end#LI 2043 ACACAAAATAAGATGGTAGAAATAAGTCCAAATATATCAGTAATC---AC 2089 chr6qtel1M 42614 CATAAATATGAATGAGGCAAACTCCCCCATAAAGAGGAAGCGGTTAGCAA 42663 v i i iivi v i v i iv v i v i L1MEi_5end#LI 2090 AATAAATGTAAATGGATTAAACTCACCTATTAAAAGACAGAGATTATCAG 2139 chr6qtel1M 42664 AATGGATTAAAATGCAGAATCATACAATATGTTGTTTACAGGAAACATAC 42713 v viv i vvi v i i i i L1MEi_5end#LI 2140 ATTGGATTAAAAAAAAAAATCCAGCTATATGCTGTTTACAAGAGACACAC 2189 chr6qtel1M 42714 CTGAAGCAGGGAGATACA 42731 i i iiiv i L1MEi_5end#LI 2190 CTAAAACAAAACGACACA 2207 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 35.71 CpG sites = 35, Kimura (unadjusted) = 35.71 Transitions / transversions = 1.75 (35/20) Gap_init rate = 0.05 (10 / 202), avg. gap size = 1.80 (18 / 10) 2440 29.63 4.43 2.83 chr6qtel1M 42616 44286 (955714) L1M5_orf2#LINE/L1 38 1734 (1560) m_b299s551i1 12522 chr6qtel1M 42616 TAAATATGAATGAGGCAAACTCCCCCATAAAGAGGAAGCGGTTAGCAAAA 42665 i i i?vi v i v v i v v i iv i v L1M5_orf2#LIN 38 TAAATGTAAATGGNCTAAACACTCCAATTAAAAGGCAGAGATTGTCAGAC 87 chr6qtel1M 42666 TGGATTAAAATGCAGAATCATACAATATGTTGTTTACAGGAAACATACCT 42715 v vi ii i vv v i i i i ii i L1M5_orf2#LIN 88 TGGATAAAAAAACAAGACCCAACTATATGCTGTCTACAAGAGACGCACTT 137 chr6qtel1M 42716 GAAGCAGGGAGATACATTCAGAGTAAAGGTAAAAGGTTGGAGCAAAATCT 42765 v ii vii i vv? iv i i v iv i v L1M5_orf2#LIN 138 TAAATATAAAGACACAGANAGGTTGAAAGTAAAAGGATGGAAAAAGATAT 187 chr6qtel1M 42766 -TCAGGTGAA-----GTCAAAA--AAGCAGTGATAGCCATCCTAATCTTA 42807 -i v ii -----i? -- v v?i i i vi v i L1M5_orf2#LIN 188 ACCATGCAAACACTAANCAAAAGAAAGCTGGNGTGGCTATATTAATATCA 237 chr6qtel1M 42808 GATCAAGCA------AAAGCAA-AAATCGAT--CTA---ATTAAAAGAGG 42845 iv i ------ i - -- -- i --- v i i i L1M5_orf2#LIN 238 GACAAAGTAGACTTCAAGGCAAGAAAT--ATTACCAGAGATAAAGAGGGA 285 chr6qtel1M 42846 CACTATATCTTGCTAAA-CGGTAACATAGATTATGAAGCAATATCAATAT 42894 i vi vv v -v v - vv i v vv v vi L1M5_orf2#LIN 286 CATTTCATAATGATAAAAGGGTCA-ATTCATCAAGAAGACATAACAATCC 334 chr6qtel1M 42895 TAAACACATATGCACCAAGTGTTGTAGCATCTAAATTCTTAAAAGAGAAA 42944 iiii v i iviiv v v v v i iv i L1M5_orf2#LIN 335 TAAATGTGTATGCACCTAATAACAGAGCTTCAAAATACATGAAGCAAAAA 384 chr6qtel1M 42945 TTAAGAGAGCTGCAAGAAGAAATAGACAG---CAAAATTATAATAGTGGG 42991 i i v i iv i i--- v --- ? L1M5_orf2#LIN 385 CTGACAGAACTAAAAGGAGAAATAGACAAATCCACAATTATA---GTNGG 431 chr6qtel1M 42992 AGATCTCAACCTTGGACTCTCAG-AATTAGATAAATCAAAC---CACAAA 43037 i i vi?vvv - - i v ii--- v L1M5_orf2#LIN 432 AGATTTTAACACNCCTCTCTCAGTAATT-GATAGAACAAGTAGACAAAAA 480 chr6qtel1M 43038 ATAAATAAGAAAGAAGTCAAAGATGTAAATAGAATACTAGAAA--AGTTA 43085 v i --- vi vi v i i -- i vv -- ii v L1M5_orf2#LIN 481 ATCAGTAAG---GATATAGAAGATTTGAACA--ACACTATCAACCAACTT 525 chr6qtel1M 43086 GATCTGATAGATCTCTGGAGATAACTAAATGGAG--ACAGAAAGGATTAC 43133 i i v iv i iv vv ?v ivv i-- ? v -- v L1M5_orf2#LIN 526 GACCTAATTGACATTTATAGAACACTNCACCCAACAACNGCA--GAATAC 573 chr6qtel1M 43134 ACTTTCTTTTCAGCAGTTCATGGAACCTATACAAAAATAGACCATATATT 43183 v ivv iv v v v i ?i L1M5_orf2#LIN 574 ACATTCTTTTCAAGTGCACATGGAACATTTACCAAGATAGACCATATNCT 623 chr6qtel1M 43184 AGGACATTAAAAC----CTCAAACTCAAATGCAGTAAGGCAGAAATAATA 43229 i v - ---- ---i vi?iv i iiv v L1M5_orf2#LIN 624 GGGCCAT-AAAACAAGTCTCAA---TAAATTTNAAAGGATTGAAATCATA 669 chr6qtel1M 43230 -AATGCATCCTTTTCAGACCACGACCCAATAAAAATTACATTCAA---CA 43275 - iv i v- i v i ivv v v viv v --- L1M5_orf2#LIN 670 CAGAGTATG-TTCTCTGACCACAATGGAATTAAATTAGAAATCAATAACA 718 chr6qtel1M 43276 AAAAGCCGGGGGAAAGTAGACCAAA-----AAATAATTGGAAACTAAATG 43320 vi------ ?v -- ----- v i ii L1M5_orf2#LIN 719 AAAAGAT------ANCTAGA--AAATCCCCAAATATTTGGAAATTAAACA 760 chr6qtel1M 43321 ATCTCA-TACTAAAGAAT--AAAGGTAAAACAGCAAATCATAGACATGAT 43367 - v - v v i-- vi v v iv i i?vivi L1M5_orf2#LIN 761 A-CACACTTCTAAATAACCCATGGGTCAAAGAAGAAATCACAANGGAAAT 809 chr6qtel1M 43368 TAATAACCTCACCCAAGAAAACAACAATAATGAAACGTCATACCAAAATG 43417 iv viviviiv vvi ii ? i vi v iv i v L1M5_orf2#LIN 810 TAGAAAATATTTTGAACTGAATGANAATGAAAATACAACATATCAAAATT 859 chr6qtel1M 43418 TGTGGGATGCAGGCAAAGCAGTAAT-AAAGGGAAATTTCATATCTCTAAA 43466 vi iv - i - v ?i L1M5_orf2#LIN 860 TGTGGGATGCAGCTAAAGCAGTGCTTAGAGGGAAATTT-ATAGCNTTAAA 908 chr6qtel1M 43467 GGCCTACTTGCATAAAATAGA-GAAAGAA--AAGGTCAATGAATTGGGCT 43513 v ? iv --- i v - iv-- ii vi ii L1M5_orf2#LIN 909 TGCNTATAT---TAGAAAAGAAGAAAGGCTTAAAATCAATGATCTAAGCT 955 chr6qtel1M 43514 TGCAACTAAAAATGCTAGAAAAGGAA---CAAATTAAAAATCCCCAATCA 43560 v v v i v i --- --- v v? L1M5_orf2#LIN 956 TCCACCTTAAGAAGCTAGAAAAAGAAGAGCAAATTAAA---CCCAAAGNA 1002 chr6qtel1M 43561 AACACTAAACTTGAAATTCTAAAAATAAAATGAGAGATCAATAAAATTGA 43610 ii vv iivvv vv i i vv i i v L1M5_orf2#LIN 1003 AGTAGAAGGAAGGAAATAATAAAGATAAGAGCAGAAATCAATGAAATAGA 1052 chr6qtel1M 43611 AAGTAAAAAAACTATTGA----ATTAATAAAACTAAGAGTTGGTTCTATG 43656 ii ? ? v v ---- i ii i i i i v L1M5_orf2#LIN 1053 AAACAAANANACAATAGAGAAAATCAACGAAGCCAAAAGCTGGTTCTTTG 1102 chr6qtel1M 43657 AAAAAACCAACAAAATAGACAAACCCTTAGTAAATCTGATTTTAAAAAGG 43706 i i i v i ii i? iv i-- i ii L1M5_orf2#LIN 1103 AAAAGATCAATAAAATTGATAAACCTCTAGCNAGACTGATC--AAGAAAA 1150 chr6qtel1M 43707 AAAGAG-GAAAAT-CAAATTGTTAGTCTTAAAAATGAAAAGGGAGAACTC 43754 - i i- iii i v i ii i vv L1M5_orf2#LIN 1151 AAAGAGAGAAGACACAAATTACCAATATCAGGAATGAAAAAGGAGACATC 1200 chr6qtel1M 43755 GCCACTAATGAAGAGGAAATTA---GGGCAATAATTAAGAATTACTTTGC 43801 i i vi vvvivi v --- ii --i - i v v L1M5_orf2#LIN 1201 ACTACAGATCCTACAGACATTAAAAGGATAATAA--GAGAAT-ATTATGA 1247 chr6qtel1M 43802 CCAACTTTATGCCAATAAATTCGACAAGTTAAATGAAATGGAAGAATACC 43851 v i ? v i vi v L1M5_orf2#LIN 1248 ACAACTTTATGCCAATAAATTTGANAACTTAGATGAAATGGACAAATTCC 1297 chr6qtel1M 43852 TTCAAAAATATAGATTGCCCATATTAA---GAGAAGAAGTAAATATCCTA 43898 v i i i? i v v i i ---i i i v vi i L1M5_orf2#LIN 1298 TTGAAAAACACAANTTACCAAAACTGACNCAAGAAGAAATAGAAAATCTG 1347 chr6qtel1M 43899 AACAGTTCCATATTAGAAAAATAAATAGAACAGACTATTAACCAACTTCC 43948 i ii i ivivv v v ivviiv vv v L1M5_orf2#LIN 1348 AATAGCCCTATATCTATTAAAGAAATTGAATTTGTAATTAAAAACCTTCC 1397 chr6qtel1M 43949 TAAGAAAAAATCCCCAAGTCCAGATGGGATTTACATGTGAATTCTACCAA 43998 i vi i v i i i v- i vv L1M5_orf2#LIN 1398 CACAAAGAAAACTCCAGGCCCAGATGGC-TTCACTGGTGAATTCTACCAA 1446 chr6qtel1M 43999 ACATTCAAG-AGCAATTAACTCCTATGCTATATAAACTATTTGAAAAAAT 44047 i - iv v iv v vi i i v iv i L1M5_orf2#LIN 1447 ACATTTAAGGAAGAAATAATACCAATCTTACACAAACTCTTCCAGAAAAT 1496 chr6qtel1M 44048 AGGGAATGAAGGA----TTCCTAACAAATTCCTATTATGACACAGACATG 44093 ii v i ---- i ---- v v vi vii ? L1M5_orf2#LIN 1497 AGAAAAAGAGGGAACACTTCCCAAC----TCATTTTATGAGGCCAGCATN 1542 chr6qtel1M 44094 GTACTGATTCCTAAACCAAGTAGGTTGAAA--ACAGAGAAAGAAAATTAT 44141 iiv v v ?iii ii-- v -- iii i L1M5_orf2#LIN 1543 ACCCTGATACCAAAACCNGACAAA--GACATTACAAGAAAAGAAAATTAC 1590 chr6qtel1M 44142 AGACCATTCTCCCTAATGAATATCAATGCTAAAATCTTAAATAAAATATT 44191 v v v i vi v i ? i L1M5_orf2#LIN 1591 AGACCAATATCCCTCATGAACATAGATGCAAAAATCCTNAACAAAATATT 1640 chr6qtel1M 44192 AGCAAAAAGATTACAGAAAATCATCCCCAGGATAATACACTATGACCAAG 44241 vv v v v vvi vvvv ii L1M5_orf2#LIN 1641 AGCAAATCGAATCCAGCAATATATAAAAAGGATAATACATCATGACCAAG 1690 chr6qtel1M 44242 TAAGCTTTATACCAAGAATGCAGCGCTGATTCAATATTACGAAAA 44286 ii v v i iv i i i i - L1M5_orf2#LIN 1691 TGGGGTTTATCCCAGGAATGCAAGGTTGGTTTAACATT-CGAAAA 1734 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 39.01 CpG sites = 261, Kimura (unadjusted) = 39.23 Transitions / transversions = 1.19 (261/220) Gap_init rate = 0.05 (79 / 1670), avg. gap size = 1.54 (122 / 79) 51 0.00 0.00 0.00 chr6qtel1M 46125 46168 (953832) (TA)n#Simple_repeat 1 44 (0) c_b299s251i2 12523 chr6qtel1M 46125 TATATATATATATATATATATATATATATATATATATATATATA 46168 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATA 44 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 15 21.31 4.44 2.17 chr6qtel1M 46186 46230 (953770) (AT)n#Simple_repeat 1 46 (0) m_b299s252i2 12524 chr6qtel1M 46186 ATATATA-ATATATATAAATAT-TTTACATGTAGTCAATATTTTTAT 46230 - v - v i i - vv v v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATA-TATATATATATAT 46 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.07 (3 / 44), avg. gap size = 1.00 (3 / 3) 13 23.10 1.79 5.56 chr6qtel1M 49537 49592 (950408) (TTTA)n#Simple_repeat 1 54 (0) m_b299s252i3 12525 chr6qtel1M 49537 TTTATGTATTTATTTCAATATCTA-TTAATTATTAACTATTATTTTTGTT 49585 v vvv i - v v - - v - (TTTA)n#Simpl 1 TTTATTTATTTATTTATTTATTTATTTATTTATTTA-T-TTATTTAT-TT 47 chr6qtel1M 49586 GATTATT 49592 iv (TTTA)n#Simpl 48 ATTTATT 54 Matrix = Unknown Transitions / transversions = 0.25 (2/8) Gap_init rate = 0.07 (4 / 55), avg. gap size = 1.00 (4 / 4) 271 37.11 4.41 2.90 chr6qtel1M 49778 49913 (950087) C MIRc#SINE/MIR (112) 156 19 m_b299s601i0 12526 chr6qtel1M 49778 TTATTATCTATATTTAACACTTGAGAAAACTGACAGACAGAACTTGAGGT 49827 ivi v vv i vivv ---- C MIRc#SINE/MIR 156 TTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGA----GAGGT 111 chr6qtel1M 49828 TA------TTGAGCATGTTTATGTAGATAATAAATCTCTGAAGTAAAGTT 49871 ------ vv v v i iii v i i vv v iviiiiii C MIRc#SINE/MIR 110 TAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACT 61 chr6qtel1M 49872 TGAAATCATGCCTTTCTAACTCCAGACACAAAGTACTCTCCA 49913 i vi v i i i iiiv iv iv i C MIRc#SINE/MIR 60 CGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCA 19 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 50.01 CpG sites = 28, Kimura (unadjusted) = 53.35 Transitions / transversions = 1.33 (28/21) Gap_init rate = 0.04 (5 / 135), avg. gap size = 2.00 (10 / 5) 34 28.00 5.84 0.00 chr6qtel1M 50020 50156 (949844) (TA)n#Simple_repeat 1 145 (0) m_b299s252i4 12527 chr6qtel1M 50020 TATATTTATAT-TATA-ATATACATTTATAT-TGCATGTCT-TATATACA 50065 v - - i v - ii i v - i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr6qtel1M 50066 TAGGTATTGAT-TATATATATTTATGAATATTTA-ATTCATAAAGGTAAA 50113 vi vv - v iv v - vi v vi v (TA)n#Simple_ 51 TATATATATATATATATATATATATATATATATATATATATATATATATA 100 chr6qtel1M 50114 TAT-TCAATATATATTTCTACATGTGTATAGATATTGAT-TATAT 50156 - vv v v i i i v vv - (TA)n#Simple_ 101 TATATATATATATATATATATATATATATATATATATATATATAT 145 Matrix = Unknown Transitions / transversions = 0.60 (12/20) Gap_init rate = 0.06 (8 / 136), avg. gap size = 1.00 (8 / 8) 14 24.52 4.17 0.00 chr6qtel1M 51768 51815 (948185) (ATT)n#Simple_repeat 1 50 (0) m_b299s252i5 12528 chr6qtel1M 51768 ATTATTGTTGTTTTTAATATTATTAATAATAGTA-AATTA-TAAAATTAT 51815 i i v v v v v -v - vv (ATT)n#Simple 1 ATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTAT 50 Matrix = Unknown Transitions / transversions = 0.25 (2/8) Gap_init rate = 0.04 (2 / 47), avg. gap size = 1.00 (2 / 2) 16 16.24 6.00 1.92 chr6qtel1M 51782 51831 (948169) (TAATAA)n#Simple_repeat 1 52 (0) m_b299s252i6 12528 chr6qtel1M 51782 TAATATTATTAATAATAGTAAATTATAA-AATTAT-CTAA-AATAATAAA 51828 v v i - v - v -v - v (TAATAA)n#Sim 1 TAATAATAATAATAATAAT-AATAATAATAATAATAATAATAATAATAAT 49 chr6qtel1M 51829 AAT 51831 (TAATAA)n#Sim 50 AAT 52 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.08 (4 / 49), avg. gap size = 1.00 (4 / 4) 181 23.73 4.84 4.84 chr6qtel1M 52706 52767 (947233) X17_LINE#LINE/CR1 223 284 (12) m_b299s601i1 12529 chr6qtel1M 52706 AGGGAATAATCCCTACAGTGGCTAAAAAA-GGA--AAATCATCTGCAAGG 52752 i - i ? ii ii - -- i v i ivv X17_LINE#LINE 223 AGGGAACAATCC-TGCANTGGCTGGAGGATGGACNAGATGACCTAATAGG 271 chr6qtel1M 52753 TCTCTTCTGCATCCC 52767 i -- i X17_LINE#LINE 272 TCTTTTC--CATCTC 284 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 30.93 CpG sites = 11, Kimura (unadjusted) = 30.93 Transitions / transversions = 3.67 (11/3) Gap_init rate = 0.08 (5 / 61), avg. gap size = 1.20 (6 / 5) 20 19.47 4.26 0.00 chr6qtel1M 52886 52932 (947068) (GT)n#Simple_repeat 1 49 (0) m_b299s252i7 12530 chr6qtel1M 52886 GTGT-TGTTTGGGT-TTTGAGTGTGTGAGTGTGTGTTTGTGTGCTTGTG 52932 - v v - v v v v iv (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 49 Matrix = Unknown Transitions / transversions = 0.14 (1/7) Gap_init rate = 0.04 (2 / 46), avg. gap size = 1.00 (2 / 2) 39 31.53 1.27 1.91 chr6qtel1M 57067 57129 (942871) (TC)n#Simple_repeat 1 61 (96) m_b299s252i8 12531 chr6qtel1M 57067 TCTTTCTCTCTGTCAGTCTCTGTCTCTCTGTGTGTGTTTCTCTGTGTCTC 57116 i v vv v v v v v i v v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr6qtel1M 57117 TCTGCGGCCCCCC 57129 - -v i i i (TC)n#Simple_ 51 TCT-C-TCTCTCT 61 Matrix = Unknown Transitions / transversions = 0.45 (5/11) Gap_init rate = 0.03 (2 / 62), avg. gap size = 1.00 (2 / 2) 30 9.71 0.00 0.00 chr6qtel1M 57130 57173 (942827) (CT)n#Simple_repeat 1 44 (0) c_b299s251i3 12532 chr6qtel1M 57130 CTCTCTCCCTCTCTCTCTCTCTGTCTCTCTCTTTGTCTCTCTCT 57173 i v i v (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 44 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 39 31.53 1.27 1.91 chr6qtel1M 57174 57267 (942733) (TC)n#Simple_repeat 62 156 (1) m_b299s252i8 12533 chr6qtel1M 57174 TGT-TTTCTGACTTTCTTTGTCTCTGTCTCTCTGTCTCACTCTTTCTGTG 57222 v - i vv i i v v v v i v v (TC)n#Simple_ 62 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 111 chr6qtel1M 57223 TGTCTGTCTGCCTGTCTGCCTCTCTGTGTCTCTGTCT-TCATCTCT 57267 v v vi v vi v v v - - (TC)n#Simple_ 112 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TCTCT 156 Matrix = Unknown Transitions / transversions = 0.35 (6/17) Gap_init rate = 0.03 (3 / 93), avg. gap size = 1.00 (3 / 3) 15 11.66 5.13 2.50 chr6qtel1M 59045 59083 (940917) (TTTTG)n#Simple_repeat 1 40 (0) m_b299s252i9 12534 chr6qtel1M 59045 TTTTTTTTTGTTTTGTTTTG--TTGTTTTACTTTCTTGTTG 59083 v -- ii v - (TTTTG)n#Simp 1 TTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTT-TTG 40 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.50 (3 / 2) 358 30.01 0.75 8.00 chr6qtel1M 59358 59491 (940509) MIRb#SINE/MIR 6 130 (138) m_b299s601i2 12535 chr6qtel1M 59358 GGGCAGCTAGATGGCTAAGTGGCTAGAGAAGTTACCCTGAAGTCAGGAGG 59407 ---i ivv vv v vvvi ii i ivi MIRb#SINE/MIR 6 GGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAG 52 chr6qtel1M 59408 ACCTGAGTTTAAATTCAGCCTCAGACATTTAATAGGTACTAATTTTGTGA 59457 i ii i v v v v i ------- ii v MIRb#SINE/MIR 53 ACCTGGGTTCGAATCCCGGCTCTGCCACT-------TACTAGCTGTGTGA 95 chr6qtel1M 59458 CCCTGGGCAAGTCATTTAATTCCACTT-GCCTCAG 59491 i i i iii v v- MIRb#SINE/MIR 96 CCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAG 130 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 36.19 CpG sites = 21, Kimura (unadjusted) = 38.99 Transitions / transversions = 1.31 (21/16) Gap_init rate = 0.08 (11 / 133), avg. gap size = 1.00 (11 / 11) 401 27.37 0.85 6.31 chr6qtel1M 59375 59491 (940509) MIRc#SINE/MIR 17 127 (141) m_b299s601i3 12535 chr6qtel1M 59375 AGTGGCTAGAGAAGTTACCCTGAAGTCAGGAGGACCTGAGTTTAAATTCA 59424 vv v v viv i i i i ii i i v MIRc#SINE/MIR 17 AGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCC 66 chr6qtel1M 59425 GCCTCAGACATTTAATAGGTACTAATTTTGTGACCCTGGGCAAGTCATTT 59474 v v v i ------- ii v i i MIRc#SINE/MIR 67 GGCTCTGCCACT-------TACTAGCTGTGTGACCTTGGGCAAGTCACTT 109 chr6qtel1M 59475 AATTCCACTT-GCCTCAG 59491 iii v v- MIRc#SINE/MIR 110 AACCTCTCTGAGCCTCAG 127 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 33.05 CpG sites = 17, Kimura (unadjusted) = 34.61 Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.07 (8 / 116), avg. gap size = 1.00 (8 / 8) 17 12.17 0.00 5.26 chr6qtel1M 59567 59606 (940394) (AAAAGAA)n#Simple_repeat 1 38 (0) m_b299s252i10 12536 chr6qtel1M 59567 AAAAGAATAAAGAAAAAGGAAAGACAGGAAGAAAGAAAAA 59606 v i - - i i (AAAAGAA)n#Si 1 AAAAGAAAAAAGAAAAAAGAAA-A-AAGAAAAAAGAAAAA 38 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 26 18.94 0.00 0.00 chr6qtel1M 60439 60486 (939514) (A)n#Simple_repeat 1 48 (0) m_b299s252i11 12537 chr6qtel1M 60439 AAAACAAAAAAAAAAAAAAACAAAAAAAAGGAGAATTGAAAAAAAAAA 60486 v v ii i vvi (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 48 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 17 12.53 0.00 0.00 chr6qtel1M 60645 60670 (939330) (A)n#Simple_repeat 1 26 (0) m_b299s252i12 12538 chr6qtel1M 60645 AAAAAAAAGAAAAATAATAAAAAAAA 60670 i v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAA 26 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 13 16.94 3.03 0.00 chr6qtel1M 60842 60874 (939126) (AACAG)n#Simple_repeat 1 34 (0) m_b299s252i13 12539 chr6qtel1M 60842 AATAGAACAGAAAAAAAGCGAA-AGAACAGAACA 60874 i v i vv - (AACAG)n#Simp 1 AACAGAACAGAACAGAACAGAACAGAACAGAACA 34 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 19 13.92 2.33 2.33 chr6qtel1M 61371 61413 (938587) (GGAAA)n#Simple_repeat 1 43 (0) m_b299s252i14 12540 chr6qtel1M 61371 GGAGAGGAAAGGAAA-AAAAGGAAAGGGAAGGAAGGGGAAAAGA 61413 i -i i -i i (GGAAA)n#Simp 1 GGAAAGGAAAGGAAAGGAAAGGAAAGGAAAGGAA-AGGAAAGGA 43 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.00 (2 / 2) 12 18.14 0.00 3.12 chr6qtel1M 61694 61726 (938274) (CAAAA)n#Simple_repeat 1 32 (0) m_b299s252i15 12541 chr6qtel1M 61694 CAACACAAAACAACAACAAATCAAATTTAAACA 61726 v - v viv (CAAAA)n#Simp 1 CAAAACAAAACAA-AACAAAACAAAACAAAACA 32 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 416 24.33 21.17 0.59 chr6qtel1M 62179 63170 (936830) L1M5_orf2#LINE/L1 971 2165 (1129) m_b299s551i2 12542 chr6qtel1M 62179 TAAAAACAAAAAACCAAATTAAAAACCAATCAAATTAAATT---GAAATT 62225 i v i i v vv v v? i vi vv--- v L1M5_orf2#LIN 971 TAGAAAAAGAAGAGCAAATTAAACCCAAAGNAAGTAGAAGGAAGGAAATA 1020 chr6qtel1M 62226 -TAAAATTAAAAGGACAAATAAA--ATATTGAAAGTAAA---ACCATTGA 62269 - iv i v v v -- v v ii --- v v L1M5_orf2#LIN 1021 ATAAAGATAAGAGCAGAAATCAATGAAATAGAAAACAAANANACAATAGA 1070 chr6qtel1M 62270 -ATAATTAATAAACC---AAGTTGGTTCAT---AAAAACCAATAAAA--A 62310 - v i ii v --- i v --- i i --i L1M5_orf2#LIN 1071 GAAAATCAACGAAGCCAAAAGCTGGTTCTTTGAAAAGATCAATAAAATTG 1120 chr6qtel1M 62311 ATAA-CCTTT---TAAATTGATTA-GAAAAAAGGGGAGGGAAAAGAAATT 62355 - i ---? i i i - i i iii v v L1M5_orf2#LIN 1121 ATAAACCTCTAGCNAGACTGATCAAGAAAAAAAGAGAGAAGACACAAATT 1170 chr6qtel1M 62356 A---GTATTTAAAAAGAAAAGGGAGA----ACCACCGA------AGA-GT 62391 ---i ivii v i ---- i v ------ -i L1M5_orf2#LIN 1171 ACCAATATCAGGAATGAAAAAGGAGACATCACTACAGATCCTACAGACAT 1220 chr6qtel1M 62392 ---GAGAAAAATAAGGG----TTACT--CAACTTTA-GCCAATAAATTTG 62431 ---i i v i ---- iv-- - L1M5_orf2#LIN 1221 TAAAAGGATAATAAGAGAATATTATGAACAACTTTATGCCAATAAATTTG 1270 chr6qtel1M 62432 ATAACCCA--TGAAA-GGATCA----CCCAAAAAATA-GACTTCCCA--- 62470 ? ii -- - iv ---- iii i -i ? v --- L1M5_orf2#LIN 1271 ANAACTTAGATGAAATGGACAAATTCCTTGAAAAACACAANTTACCAAAA 1320 chr6qtel1M 62471 --GACTAAAAGGGAGGAAGAAATTTTTGAAAGTCCCATTTCCAGAAAAAA 62518 -- ?v iii iiv v i vi v i i v i vv i L1M5_orf2#LIN 1321 CTGACNCAAGAAGAAATAGAAAATCTGAATAGCCCTATATCTATTAAAGA 1370 chr6qtel1M 62519 AA--GAA------AC-AAAAACAACCCCT---AGAAAAC-CCAGGACCAG 62555 -- ------ i- vvi v--- - v L1M5_orf2#LIN 1371 AATTGAATTTGTAATTAAAAACCTTCCCACAAAGAAAACTCCAGGCCCAG 1420 chr6qtel1M 62556 ATGGTT--AT--GTGAATTTT-CCAAA-ATTTAAAAAAAA-------CCA 62592 i -- i-- i - - ii i ------- L1M5_orf2#LIN 1421 ATGGCTTCACTGGTGAATTCTACCAAACATTTAAGGAAGAAATAATACCA 1470 chr6qtel1M 62593 ATC--ATATAAATTTTT----AAAATAGGAAGAAAGGAGTCCCT--CCAA 62634 -- i i i i ---- i i i iiv v -- L1M5_orf2#LIN 1471 ATCTTACACAAACTCTTCCAGAAAATAGAAAAAGAGGGAACACTTCCCAA 1520 chr6qtel1M 62635 ATCCTTCT----GACACAG-ACAATCCTAA-ACCAGGTACTGA---AAAC 62675 v v i ---- i - - i? i i - iivv ? --- i L1M5_orf2#LIN 1521 CTCATTTTATGAGGC-CAGCATNACCCTGATACCAAAACCNGACAAAGAC 1569 chr6qtel1M 62676 A----GAGAAAAGAAAAATTTAGACCAA----CCCAATGAA-ATTGAT-T 62715 ----i v vi ---- iv - v -i L1M5_orf2#LIN 1570 ATTACAAGAAAAGAAAATTACAGACCAATATCCCTCATGAACATAGATGC 1619 chr6qtel1M 62716 AAAA--CTTAAATAAGATATTAGCAAA--AAAGACACGAAAATCAT-CCC 62760 -- i ? i i --i vv vv v - -vvv L1M5_orf2#LIN 1620 AAAAATCCTNAACAAAATATTAGCAAATCGAATCCAGCAATAT-ATAAAA 1668 chr6qtel1M 62761 AGGATAA-ACACTAAGATCAAG-GGGATTTATTTGAAGA---------TG 62799 - ii v i - i iiv i --------- L1M5_orf2#LIN 1669 AGGATAATACATCATGACCAAGTGGGGTTTATCCCAGGAATGCAAGGTTG 1718 chr6qtel1M 62800 ATTCA--ATTAGGAA---AACCAATATAATT--CCTTATTAAAACCAAAT 62842 i i -- v i --- i i -- v -- vi L1M5_orf2#LIN 1719 GTTTAACATTCGAAAATCAATCAATGTAATTCACCATATT--AACAGAAT 1766 chr6qtel1M 62843 ------TAAAAACC--ATGATCATTTCAA-AGATGCAGAAAA--CATTTG 62881 ------v i -- i - -- L1M5_orf2#LIN 1767 AAAGGAGAAAAATCATATGATCATCTCAATAGATGCAGAAAAAGCATTTG 1816 chr6qtel1M 62882 ACAAAATCCAACATCCAGTCCAT--TAAAACACTTGAACCA---TGGGAA 62926 i i - i -- - ivv v --- i L1M5_orf2#LIN 1817 ACAAAATTCAACACCCA-TTCATGATAAAA-ACTCTCAGCAAACTAGGAA 1864 chr6qtel1M 62927 T--AAATGATTTTCCAAAAC------AATCACATC-ATTTAAAACC---- 62963 -- iv vi vv ------ vvi - ivv ---- L1M5_orf2#LIN 1865 TAGAAGGGAACTTCCTCAACCTGATAAAGGGCATCTACGAAAAACCTACA 1914 chr6qtel1M 62964 ACATACATCATATGTAATGG-GAAA-ACCAAAC-CTT---CCCTAAG--C 63005 i ?v iv - - ii ?- --- -- L1M5_orf2#LIN 1915 GCNAACATCATACTTAATGGTGAAANACTGAANGCTTTCCCCCTAAGATC 1964 chr6qtel1M 63006 GGGAA----------ACTTCCCCCATCACCGTTTAAATTTAAAATTA--- 63042 ---------- iv v i? ii vv i v i--- L1M5_orf2#LIN 1965 GGGAACAAGACAAGGATGTCCGCTNTCACCACTTCTATTCAACATTGTAC 2014 chr6qtel1M 63043 -GAAAG---TAGC---TTTGGTAAGATTAG--AAAGAGATTAAAGGAA-A 63082 - i i --- --- viii iiv -- i v v - L1M5_orf2#LIN 2015 TGGAGGTCCTAGCCAGTGCAATAAGGCAAGAAAAAGAAATAAAAGGCATA 2064 chr6qtel1M 63083 AGAATAGGCAATGAGGAAACTAAA-TACCTTT-----CCGACAACATGAT 63126 ii v v v i iv - ii ? ----- v ii L1M5_orf2#LIN 2065 AAGATTGGAAAGGAAGAAATAAAACTGTCNTTATTCGCAGATGACATGAT 2114 chr6qtel1M 63127 GGATTT---TAGAGAACCCG--AGATTCT---TAAAAGTTATTAGAAATA 63168 v - ? --- i i ?-- v ---v ? ii i v L1M5_orf2#LIN 2115 TG-TNTACGTAGAAAATCCNAAAGAATCTACAAANAAACTACTAGAACTA 2163 chr6qtel1M 63169 AT 63170 L1M5_orf2#LIN 2164 AT 2165 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 30.22 CpG sites = 143, Kimura (unadjusted) = 30.69 Transitions / transversions = 1.47 (143/97) Gap_init rate = 0.09 (89 / 991), avg. gap size = 2.44 (217 / 89) 496 25.71 14.44 1.92 chr6qtel1M 64026 64489 (935511) L1ME3G_3end#LINE/L1 7 527 (397) m_b299s551i3 12542 chr6qtel1M 64026 TCCAAAATATA--GAGAATTAACCTA---ATTTATAAAAAATCTATTCTC 64070 i --i i -- --- iv i vvv ivvi L1ME3G_3end#L 7 TCCAGAATATATAAAGAACT--CCTACAAATCAATAAGAAAAAGACAACC 54 chr6qtel1M 64071 CAATTGAAAA--TGGTAAAGGGAATGAAC-GACAATTT-CAGATGAAGAA 64116 v --v i iv - i i- v i L1ME3G_3end#L 55 CAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGGAA 104 chr6qtel1M 64117 ATTGAAACTATT--TCATCATATGAAAAGATGCCCG---TCATTATTAAT 64161 vv iviii-- v v i i--- i v L1ME3G_3end#L 105 ATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTAAT 154 chr6qtel1M 64162 CAGAGAAATGCAAATTAAGACAAC-CTAAGATACCCAAA-----CACCCG 64205 i i -v i --- ----- i L1ME3G_3end#L 155 CAGGGAAATGCAAATTAAAACAACAATGAGATACC---ATTTTTCACCCA 201 chr6qtel1M 64206 CC-GATT--CTAAGA--TGACAGGAAAAAAATA------ATT----AGGG 64240 i - -- v i -- i v ?vvi v ------i ---- L1ME3G_3end#L 202 TCAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGG 251 chr6qtel1M 64241 GATGGGGAAAACTGGGGA----AAGATATTGTTGGT-GGAGTTTGAACGA 64285 vi --i v ----v v i i i - v i ivi L1ME3G_3end#L 252 TGTGGGGAAA--CGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTG 299 chr6qtel1M 64286 ATCC--CCATTTT--AAGGTAGTTTG--AACATGC-TCAAAAGTTATCAA 64328 i v -- ? -- i i i -- ii vi- i v -- L1ME3G_3end#L 300 GTACAGCCNTTTTGGAGGGCAATTTGGCAGTATCTATTAAAATTTA--AA 347 chr6qtel1M 64329 A----CCTACCCTTTGATCCAGC-ATGTTACTACTTTAA---TATCCCAA 64370 ---- v i - vii v ?vi?--- i ? L1ME3G_3end#L 348 ATGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTAN 397 chr6qtel1M 64371 AAAGATA-TTATAAAGAAGGA-AAGGACCTGTTGTGCACGAATGT---TT 64415 i i - iii v viv v - ?vii- i v i --- L1ME3G_3end#L 398 AGAAATACTCGCACATGTGCACAAGGANGCA-TGTACAAGGATGTTCATT 446 chr6qtel1M 64416 GTGGCCCTTTTTG---TAGTTAAAAACTGGAAACTGAATAGATGTCCATC 64462 ii vi v --- iv i vivv i L1ME3G_3end#L 447 GCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATC 496 chr6qtel1M 64463 -ATTGGAGAA-GG-TGAATAAATTG-GGTAT 64489 - v i - - i i- L1ME3G_3end#L 497 AATAGGGGAATGGTTAAATAAATTATGGTAT 527 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 31.79 CpG sites = 69, Kimura (unadjusted) = 32.85 Transitions / transversions = 1.44 (69/48) Gap_init rate = 0.09 (41 / 463), avg. gap size = 1.88 (77 / 41) 1199 30.31 8.16 1.32 chr6qtel1M 64990 65982 (934018) L1PREC2_orf2#LINE/L1 1761 2820 (474) m_b299s551i4 12543 chr6qtel1M 64990 CAAAACCAAACTAAAAAACC-CATGATCATCTCAATAGATGCAGAAAAAG 65038 i i vvv - i i L1PREC2_orf2# 1761 CAGAACTAAAGACAAAAACCACATGATTATCTCAATAGATGCAGAAAAGG 1810 chr6qtel1M 65039 CATTT--TAAAATCCAA-ATCCATTCCTAATAAAAACACT---TAAA-TA 65081 v i-- i - v v iv v --- - L1PREC2_orf2# 1811 CTTTCGATAAAATTCAACATCCCTTCATGTTAAAAACTCTCAATAAACTA 1860 chr6qtel1M 65082 GGAAT-AAATGGACTTTTTTAAAAAGAGTCAGA---ATATATTTAAAATG 65127 v -i v i v vii v v i v --- v vvv iv L1PREC2_orf2# 1861 GGTATTGAAGGAACATACCTCAAAATAATAAGAGCCATCTATGACAAACC 1910 chr6qtel1M 65128 CAAAGC----ATTATATAAAATGGGGAAAAACTGGAACCTTTCCC--TGT 65171 v ---- i ivi v i v v -- v L1PREC2_orf2# 1911 CACAGCCAACATCATACTGAATGGGCAAAAGCTGGAAGCATTCCCCTTGA 1960 chr6qtel1M 65172 AATATGTCGAGGAACAAGGTTGCCC------ATAATTATTATTCAATATT 65215 vvi v iviii v ------ iv i vi i v L1PREC2_orf2# 1961 AAACCGGCACAAGACAAGGATGCCCTCTCTCACCACTCCTATTCAACATA 2010 chr6qtel1M 65216 GTATTAAAA-TGCTAACTTGGAAAA--AGTC--GAGAAAAGATTAAAAGG 65260 ii - v ii iv iiv -- v -- ii v i L1PREC2_orf2# 2011 GTATTGGAAGTCCTGGCCAGAGCAATCAGGCAAGAGAAAGAAATAAAGGG 2060 chr6qtel1M 65261 AATTAGCGTAGGCAATGAGGAAACCAAACTATCCCT--TTGCAGAAGATA 65308 v ivivi v iv ii -- v i L1PREC2_orf2# 2061 CATCCAAATAGGAAGAGAGGAAGTCAAACTATCCCTGTTTGCAGACGACA 2110 chr6qtel1M 65309 -GATGGTAT---T-GAGAACCCCA-------GACCCATACAAAGCTA-TT 65345 - vv --- - i ------- i --- v- L1PREC2_orf2# 2111 TGATTCTATATCTAGAAAACCCCATAGTCTCGGCCCA---AAAGCTCCTT 2157 chr6qtel1M 65346 AAAATAATTC-TAACTTTA--AAAGTT--GGGAT-TAAAATAAATCTCCA 65389 ? iv i vv-i i -- --i -i v v v L1PREC2_orf2# 2158 NAGCTGATAAACAACTTCAGCAAAGTTTCAGGATACAAAATCAATGTACA 2207 chr6qtel1M 65390 TAAATCCTCAGCATTTTTATCAACCAAAAA-ACCCAACAGCAAGAGATAC 65438 v vii ii vv v - v -iv i vi v L1PREC2_orf2# 2208 AAAATCACTAGCATTCCTATACACCAACAACAGCCAA-GCCGAGAGCCAA 2256 chr6qtel1M 65439 A--AAGAA----ATTCCATTCAAAAATAACTGTGACAAATA----AAAAT 65478 -- i ---- i ----i i iv v ---- L1PREC2_orf2# 2257 ATCAGGAACGCAATCCCATTCA----CAATTGCCACAAAAAGAATAAAAT 2302 chr6qtel1M 65479 ---TGGGAAT-CATCTATCAAAGGAAAGTCAGGAAT-TATATGAGCAAAA 65523 --- i - v v v i i- v iii - v ii vv i L1PREC2_orf2# 2303 ACCTAGGAATACAGCTAACCAGGGAG-GTGAAAGATCTCTACAATGAGAA 2351 chr6qtel1M 65524 TTACAAAAAACTTTCCACATAAATAAGGTCAGACTTAAATAATTCGAAAA 65573 v vii v v v ivvv vi i v v L1PREC2_orf2# 2352 TTACAAAACACTGCTCAAAGAAATCAGAGATGACACAAACAAATGGAAAA 2401 chr6qtel1M 65574 ATATTAAGTGCTCTTGGATAGGCCGAGCGAATATAATGAAGATGACAATA 65623 i vvi v vv iiv vi v i i v L1PREC2_orf2# 2402 ACATTCCATGCTCATGGATAGGAAGAATCAATATCGTTAAAATGGCCATA 2451 chr6qtel1M 65624 CTCCCTAAACTAATCTATTTATTTAGTGCTATACCAATCAGACTTCCAAG 65673 v i vi i ivv i i v v i v v L1PREC2_orf2# 2452 CTGCCCAAAGCAATTTACAGATTCAATGCTATTCCTATCAAACTACCAAT 2501 chr6qtel1M 65674 AAAATATTTTAATGATCTAG-AAAAATAACAGCAAAATTCATATGGAA-T 65721 i v vi i vv v - iv ivvi -i L1PREC2_orf2# 2502 GACATTCTTCACAGAACTAGAAAAAACTATTTTAAAATTCATATGGAACC 2551 chr6qtel1M 65722 AATAAAAAGGTCGAGAATCTCAAGGGAAT--TAATGAAAAAAAATCAAA- 65768 v i vi iv v - v -- vv i - - L1PREC2_orf2# 2552 AAAAAAGAGCCCGAATAGC-CAAGGCAATCCTAAGCAAAAAGAA-CAAAG 2599 chr6qtel1M 65769 -TGAAGG---TGGGCTTGGAAAGCTAAAACTATATTATAAAGCAGCAGTC 65814 - i ---iiv vvvvi vi v i i ii vi v L1PREC2_orf2# 2600 CTGGAGGCATCACGCTACCCGACTTCAAACTATACTACAGGGCTACAGTA 2649 chr6qtel1M 65815 ACCAAAATCATTTGGTATTGACTAAGAAATAGATTAGTTGATAAGTGGAA 65864 iviiv i iivv i i ivvi v iv i L1PREC2_orf2# 2650 ACCAAAACAGCATGGTACTGGTACAAAAACAGACACATAGACCAATGGAA 2699 chr6qtel1M 65865 CAGGTTA---AGTTCACAAGACAGAATAGTCAACTATAGCAATCTAGTGT 65911 iv --- ii v ivv iviivv v i i v ii v L1PREC2_orf2# 2700 CAGAATAGAGAGCCCAGAAATAAGGCCGCACACCTACAACCATCTGATCT 2749 chr6qtel1M 65912 TCAACAAAAC---CAAAGATCCTAACTTTTGTGATAAGAATTCATTATTT 65958 i i --- i -- v i vv v v - i i vi i L1PREC2_orf2# 2750 TCGACAAAGCTGACAAAAA--CAAGCAATGGGGA-AAGGACTCCCTATTC 2796 chr6qtel1M 65959 GACAAAAACTGCTGGGATAGCTGG 65982 i i viv i L1PREC2_orf2# 2797 AATAAATGGTGCTGGGATAACTGG 2820 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 38.23 CpG sites = 147, Kimura (unadjusted) = 39.41 Transitions / transversions = 0.98 (147/150) Gap_init rate = 0.05 (52 / 992), avg. gap size = 1.83 (95 / 52) 67 31.08 0.00 0.00 chr6qtel1M 66548 66756 (933244) (TCTC)n#Simple_repeat 1 209 (0) m_b299s252i16 12544 chr6qtel1M 66548 TCTTTCTCTCTGTCAGTCTGTCTAGCTGTCTCTCTGTCTCTCCCTATCTC 66597 i v vv v vv v v i v (TCTC)n#Simpl 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr6qtel1M 66598 TCTCTCTGTATGTGTGTGTGTGTGTCTGTCTGTCTCTGTCTCTCTCTTAG 66647 v v v v v v v v v v v v ivv (TCTC)n#Simpl 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chr6qtel1M 66648 TCTCTTTCTCTGTCTCTCTCTGTCTGTCTTTCTGTCTCTCTGTTTCTGTC 66697 i v v v i v v i v (TCTC)n#Simpl 101 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 150 chr6qtel1M 66698 TTTGTGTGTGAGTTTCTGTCTTTCTGTCTGCCTCTCTGTGCCTCTGTCTC 66747 i v v v vvv i v i v vi v vi v (TCTC)n#Simpl 151 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 200 chr6qtel1M 66748 CCTCTCTCT 66756 i (TCTC)n#Simpl 201 TCTCTCTCT 209 Matrix = Unknown Transitions / transversions = 0.29 (12/41) Gap_init rate = 0.00 (0 / 208), avg. gap size = 0.0 (0 / 0) 18 4.77 0.00 0.00 chr6qtel1M 67811 67832 (932168) (CA)n#Simple_repeat 1 22 (0) m_b299s252i17 12545 chr6qtel1M 67811 CACACACACACACACATACACA 67832 i (CA)n#Simple_ 1 CACACACACACACACACACACA 22 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 332 26.26 6.90 4.33 chr6qtel1M 69439 69641 (930359) L1MEi_5end#LINE/L1 2000 2207 (5) m_b299s551i5 12546 chr6qtel1M 69439 GGGAAGGGGATAAGGAGGAAAGAAGGGAGAAAAGTATAAACAGGGGTTAC 69488 i i v ii ? --- i i? vv iiivi L1MEi_5end#LI 2000 GGAAAGGAGAGAAAAAGNAAAGAA---AAAGNATGATAAACAGAAAACAC 2046 chr6qtel1M 69489 ----CAAGATGGCAAGTAATAG---CGAAC----TGGTAATTTTAACCAT 69527 ----i i - v i--- i i----ii i--- v L1MEi_5end#LI 2047 AAAATAAGATGGTA-GAAATAAGTCCAAATATATCAGTAATC---ACAAT 2092 chr6qtel1M 69528 AAATGTGAATGGGGTAAACTCTCCCAT--ATAGACAAAGTGGTTA-GAGA 69574 i iv v i -- v i --i -v L1MEi_5end#LI 2093 AAATGTAAATGGATTAAACTCACCTATTAAAAGACAGAG--ATTATCAGA 2140 chr6qtel1M 69575 ATGGAATTAAAGCCAAAATCCTACAATATGTTGTTTACAGGAAACACATC 69624 v v v ivv vi v i i i i L1MEi_5end#LI 2141 TTGGATTAAAAAAAAAAATCCAGCTATATGCTGTTTACAAGAGACACACC 2190 chr6qtel1M 69625 TGAAGCAAAGTGATACA 69641 i i ii i L1MEi_5end#LI 2191 TAAAACAAAACGACACA 2207 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 33.27 CpG sites = 34, Kimura (unadjusted) = 34.11 Transitions / transversions = 2.00 (34/17) Gap_init rate = 0.07 (14 / 202), avg. gap size = 1.64 (23 / 14) 401 25.69 3.45 0.67 chr6qtel1M 69490 69634 (930366) L1M6_5end#LINE/L1 2363 2511 (4) m_b299s551i6 12546 chr6qtel1M 69490 AAGATGGCAAG--TAATAGCGAAC-TGGTAATTTTAACCATAAATGTGAA 69536 i i-- v v i - ivi i v i v i L1M6_5end#LIN 2363 AAGATGACAAANATAAGACCAAACATATCAGTTATGACAATAAATGTAAA 2412 chr6qtel1M 69537 TGGGGTAAACTCTCCCAT--ATAGACAAAGTGGTTAGAGAATGGAATTAA 69584 v i i -- v -iv ivv v iv v L1M6_5end#LIN 2413 TGGGTTAAACTCCCCTATTAAAAGACAAAG-ACTCTCAGATTGGGTTAAA 2461 chr6qtel1M 69585 AGCCAAAATCCTACAATATGTTGTTTACAGGAAACACATCTGAAGCAAAG 69634 iv v v i i i i i vv L1M6_5end#LIN 2462 AAACAAAATCCAACTATATGCTGTTTACAAGAGACACACCTAAATAAAAG 2511 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 31.82 CpG sites = 19, Kimura (unadjusted) = 31.82 Transitions / transversions = 1.06 (19/18) Gap_init rate = 0.03 (4 / 144), avg. gap size = 1.50 (6 / 4) 694 30.23 6.53 2.82 chr6qtel1M 69521 70102 (929898) L1M2_orf2#LINE/L1 32 634 (2657) m_b299s551i7 12546 chr6qtel1M 69521 TAACCATAAATGTGAATGGGGTAAACTCTCCCAT--ATAGACA--AAGTG 69566 v i i iv i v -- v --i ? L1M2_orf2#LIN 32 TAACCTTGAATGTAAATGGATTAAATTCTCCAATTAAAAGACATAGANTG 81 chr6qtel1M 69567 GTTAGAGAATGGAATTAAAGCCAAAATCCTACAATATGTTGTTTACAGGA 69616 i --- vvv iv i i v v i ii i L1M2_orf2#LIN 82 GCT---GAATGGATAAAAAAACAAGACCCAACTATATGCTGCCTACAAGA 128 chr6qtel1M 69617 AACACATCTGAA--GCAAAGTGATACACACAGAATAAAGGTAAAAGATTG 69664 v ii v v-- i -- i i v i i i i iv L1M2_orf2#LIN 129 AACTCACTTCACCTGTAAAG--ACACACATAGACTGAAAGTGAAGGGATG 176 chr6qtel1M 69665 TAGCTGAATCTACCATGCTCCAGGTGAATTCAAAAA--AGCAGAGACAGC 69712 v ivvii v v --v ivv vi i-- iiii L1M2_orf2#LIN 177 GAAAAAGATATTCCATGC--AAACGGAAACCAAAAGNGAGCAGGAGTAGC 224 chr6qtel1M 69713 CATCCTGATCTCAGATCAAGCAAA-----AG-CAAAAATTGATCTATTTA 69756 i v v v v ii i ----- - i --- --- L1M2_orf2#LIN 225 TATACTTATATCAGATAAAATAGACTTTAAGTCAAAAACTG---TA---A 268 chr6qtel1M 69757 AAAGAGATAAGGAAGGGCACTATATCTTGCTAAAGGG-------TAGCAT 69799 i i v i vv v -------i v L1M2_orf2#LIN 269 AAAGAGACAAAGAAGGTCATTATATAATGATAAAGGGGTCAATTCAGCAA 318 chr6qtel1M 69800 AGCAATAT--CAATGTTAAACATATATGCACCAAGTAGTGTAGCATTTAA 69847 iivi -- v? i v ii vi v iii i L1M2_orf2#LIN 319 GAGGATATAACAATTNTAAATATATATGCACCCAACACCGGAGCACCCAG 368 chr6qtel1M 69848 ATTCTTAAAAGAGAAATTAAGAGAGCTGCGAGAAGAAATAGTCAGCAAAA 69897 viv iv i v ?v v ivii i i v v? v L1M2_orf2#LIN 369 ATATATAAAGCAAATATTANTAGATCTAAAGGGAGAGATAGACTNCAATA 418 chr6qtel1M 69898 CTATAATAGTGGGAGATCTCAA-ACTTGCACCCTGAGAATTAGATAAATC 69946 v ? i ii - ii- i v v ? i i i L1M2_orf2#LIN 419 CAATAATAGTNGGGGACTTCAACACCC-CACTCTCAGCANTGGACAGATC 467 chr6qtel1M 69947 A---AACCATAAAATAAAT-AAGAAA----GAA--TAAATAGAATACTAG 69986 --- iv v v i- ---- i -- iv v iv? L1M2_orf2#LIN 468 ATCCAGACAGAAAATCAACAAAGAAACATCGGACTTAAACTGCACTNTAG 517 chr6qtel1M 69987 ---AAATTTATATATGATAGATCTTTGGAAAAAACGAAATGGAGACAGA- 70032 --- vv iv -- i iv iv i v ivvv vv - v- L1M2_orf2#LIN 518 ACCAAATGGACCTA--ACAGACATTTACAGAACATTTCATCCA-ACAGCT 564 chr6qtel1M 70033 AAGGAGTACACTTTCTTCGCAGCAGCTCATGGAACTTATACAAAAATTGA 70082 ivi i v v v v v viv v ii v L1M2_orf2#LIN 565 GCAGAATACACATTCTTCTCATCAGCACATGGAACATTCTCCAGGATAGA 614 chr6qtel1M 70083 CCTCATATTAGGACATAAAA 70102 vi i v i L1M2_orf2#LIN 615 CCATATGTTAGGCCACAAAA 634 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 39.80 CpG sites = 90, Kimura (unadjusted) = 40.10 Transitions / transversions = 1.11 (90/81) Gap_init rate = 0.05 (31 / 581), avg. gap size = 1.77 (55 / 31) 740 30.53 5.20 2.20 chr6qtel1M 69527 69968 (930032) L1M3_orf2#LINE/L1 38 492 (2796) m_b299s551i8 12546 chr6qtel1M 69527 TAAATGTGAATGGGGTAAACTCTCCCAT--ATAGACA--AAGTGGTTAGA 69572 i iv v -- v --i i --- L1M3_orf2#LIN 38 TAAATGTAAATGGATTAAACTCTCCAATCAAAAGACATAGAGTGGCT--- 84 chr6qtel1M 69573 GAATGGAATTAAAGCCAAAATCCTACAATATGTTGTTTACAGGAAACACA 69622 vvv iv i v v i ii i i v L1M3_orf2#LIN 85 GAATGGATAAAAAAACAAGATCCAACTATATGCTGCCTACAAGAGACTCA 134 chr6qtel1M 69623 TCTGAAGCAAAGTGATACACACAGAATAAAGGTAAAAGATTGTAGCTGAA 69672 ii v i?ivv iv i i iv i i i i iv v ivvii L1M3_orf2#LIN 135 CTTTAGNTTTAAGGACACACATAGGCTGAAAGTGAAGGGATGGAAAAAGA 184 chr6qtel1M 69673 TCTACCATGCTCCAGGTGAATTCAAAAAAGCAGAGACAGCCATCCTGATC 69722 v v vvvv i vivv i i i iii i v v v L1M3_orf2#LIN 185 TATTCCATGCAAATGGTAACCAAAAGAGAGCAGGGGTGGCTATACTTATA 234 chr6qtel1M 69723 TCAGATCAAGCAAA-----AG-CAAAAATTGATCTATTTAAAAGAGATAA 69766 iv ii i ----- - i ------ i v i L1M3_orf2#LIN 235 TCAGACAAAATAGACTTTAAGTCAAAAACTG------TCACAAGAGACAA 278 chr6qtel1M 69767 GGAAGGGCACTATATCTTGCTAAA-GGGT------AGCATAGCAATAT-- 69807 i ? i vv v - ------ ? viivi -- L1M3_orf2#LIN 279 AGAAGGNCATTATATAATGATAAAAGGGTCAATTCANCAAGAAGATATAA 328 chr6qtel1M 69808 CAATGTTAAACATATATGCACCAAGTAGTGTAGCATTTAAATTCTTAAAA 69857 vv i v ii vi v ii viv i L1M3_orf2#LIN 329 CAATTATAAATATATATGCACCCAACATCGGAGCACCTAAATATATAAAG 378 chr6qtel1M 69858 GAGAAATTAAGAGAGCTGCGAGAAGAAATAGTCAGCAAAACTATAATAGT 69907 v i v i v i vii i v v v L1M3_orf2#LIN 379 CAAATATTGACAGAACTGAAGGGAGAAATAGACAGCAATACAATAATAGT 428 chr6qtel1M 69908 GGGAGATCTCAA-ACTTGCACCCTGAGAATTAGATAAATCA---AACCAT 69953 i ii - ii- ii v iv v i i ? --- iv v L1M3_orf2#LIN 429 AGGAGACTTCAATACCC-CACTTTCAACAATGGATAGANCATCCAGACAG 477 chr6qtel1M 69954 AAAATAAATAAGAAA 69968 v i L1M3_orf2#LIN 478 AAAATCAATAAGGAA 492 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 40.32 CpG sites = 74, Kimura (unadjusted) = 40.73 Transitions / transversions = 1.28 (74/58) Gap_init rate = 0.04 (19 / 441), avg. gap size = 1.74 (33 / 19) 661 28.94 5.28 4.99 chr6qtel1M 72392 72751 (927249) L1ME5_3end#LINE/L1 277 637 (304) m_b299s551i9 12546 chr6qtel1M 72392 ATGCACATGC-----GGAGTTGTGAACGAATCCAACCATTTTGGAGAGTA 72436 - ----- - ii vii v i i i L1ME5_3end#LI 277 ATGCAC-TGCTGGTGGGAGT-GTAGACTGGTGCAGCCATTCTGGAGAGCA 324 chr6qtel1M 72437 GTTTGGAACTA--TGCTCAAA--AAGTTATCAAACTGTGCATACCCTTTG 72482 i i v v -- iv -- - --- --- v L1ME5_3end#LI 325 ATCTGGCAGTACTTAGTCAAATTAAGT-AT---AC---GCATACCCTATG 367 chr6qtel1M 72483 ATTCAGCAGTGTTACTACTGGGATTGTATCCCAAAGAGATTATAAAGAAG 72532 ii i viii v vv i i v v viv L1ME5_3end#LI 368 ACCCAGCAATTCCGCTCCTGGGTATATATCCCAAAGAAATTCTCACACAG 417 chr6qtel1M 72533 G-----AAAGGGACCTGTATGTGCACGAATGTTTGTGGCAGCCCTTTTTG 72577 ----- i ---- i iv i ii v vi v L1ME5_3end#LI 418 GTCCATAAGGGGAC----ATGTACGAGGATGTTCATTGCAGCGTTGTTTG 463 chr6qtel1M 72578 TAGTGGCTAAAAACTGGAAACTGAATGGATGTCCATCAGTTGGAGAATGG 72627 i viii ii ii vivv i v v i L1ME5_3end#LI 464 TGGTGGCGGGGAGTTGGAGGCAACCTGGGTGTCCATCACTGGGAGAGTGG 513 chr6qtel1M 72628 CTGAATAAATTGTGGTATATGAATATTATGGAATATTACTGT-TCTGTAA 72676 v iii v iv v i ii i i - i-v v v L1ME5_3end#LI 514 ATAGGTAAAATGTGGTGGATGCACACCATGGAGTACTA-TGCAGCAGTTA 562 chr6qtel1M 72677 GAAATGACCAACAGGATGATTTCAGAAAG--GCCTGGAGAGA-CTTACAC 72723 iii vi vi -- v v v --i v vi - v - L1ME5_3end#LI 563 GAAGCAACGGACTAGATG--TACACATAGCAACATGGATGGATCTTAAA- 609 chr6qtel1M 72724 GAAC-TGATGCTGAGTGAAATGAGCAGGA 72751 - - ii vi i i L1ME5_3end#LI 610 -AACATAGTGCTGAGTGAAAAAAGTAAGA 637 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.63 CpG sites = 59, Kimura (unadjusted) = 37.66 Transitions / transversions = 1.48 (59/40) Gap_init rate = 0.07 (26 / 359), avg. gap size = 1.42 (37 / 26) 783 28.63 1.88 1.50 chr6qtel1M 72400 72665 (927335) L1ME4c_3end#LINE/L1 288 554 (276) m_b299s551i10 12546 chr6qtel1M 72400 GCGGAGTTGTGAACGAATCCAACCATTTTGGAGAGTAGTTTGGAACTATG 72449 i vi? i ivii v v i i i v v i L1ME4c_3end#L 288 GTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACG 337 chr6qtel1M 72450 CTCAAAAAGTTATCAAACTGTGCATACCCTTTGATTCAGCAGTGTTACTA 72499 iviv i ii v v v ii i i vii v L1ME4c_3end#L 338 TATCAAGAGCCATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTT 387 chr6qtel1M 72500 CTGGGATTGTATCCCAAAGAGATTAT---AAAGAAGGAAAGGGACCTGTA 72546 v v i i i v --- ii ----v L1ME4c_3end#L 388 CTGGGAATTTATCCTAAGGAAATAATTCAAAAGAAGGAAAAAG----CTA 433 chr6qtel1M 72547 TGTGCACGAA--TGTTTGTGGCAGCCCTTTTTGTAGTGGCTAAAAACTGG 72594 i -- ii v vi v i i i v i L1ME4c_3end#L 434 TATGCACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGG 483 chr6qtel1M 72595 AAACTGAATGGATGTCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTA 72644 vivv ii v i v i i i i i L1ME4c_3end#L 484 AAACAACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTA 533 chr6qtel1M 72645 TATGAATATTATGGAATATTA 72665 i v? iviv L1ME4c_3end#L 534 CATCNACTCGATGGAATATTA 554 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.34 CpG sites = 46, Kimura (unadjusted) = 37.62 Transitions / transversions = 1.59 (46/29) Gap_init rate = 0.02 (6 / 265), avg. gap size = 1.50 (9 / 6) 24 30.75 5.93 0.00 chr6qtel1M 74031 74165 (925835) (TATA)n#Simple_repeat 1 143 (0) m_b299s252i18 12547 chr6qtel1M 74031 TATTTTTATAT-TATA-ATATACATTTAT-TTTGCATGTAT-TTTATATA 74076 v v - - i v - v ii i - v (TATA)n#Simpl 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr6qtel1M 74077 TAGGTATTGAT-TATTTACATAAATATTTATTTACGTGTAGA-AGCTAAA 74124 vi vv - v i v v v ii i v - vv v (TATA)n#Simpl 51 TATATATATATATATATATATATATATATATATATATATATATATATATA 100 chr6qtel1M 74125 TATTTA-ATATATATTTGTGCATGTGTATAGAT-TATATCTAT 74165 v - v i ii i i v - v (TATA)n#Simpl 101 TATATATATATATATATATATATATATATATATATATATATAT 143 Matrix = Unknown Transitions / transversions = 0.70 (14/20) Gap_init rate = 0.06 (8 / 134), avg. gap size = 1.00 (8 / 8) 34 1.92 7.27 1.72 chr6qtel1M 75651 75705 (924295) (TATACAAT)n#Simple_repeat 1 58 (0) c_b300s251i0 12548 chr6qtel1M 75651 TATACAATTATAC-ATTATACAATGTATAC---TATACAATTATACGATT 75696 - - --- i (TATACAAT)n#S 1 TATACAATTATACAATTATACAAT-TATACAATTATACAATTATACAATT 49 chr6qtel1M 75697 ATACAATTA 75705 (TATACAAT)n#S 50 ATACAATTA 58 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.06 (3 / 54), avg. gap size = 1.67 (5 / 3) 16 29.72 2.60 2.60 chr6qtel1M 75921 75997 (924003) (ATT)n#Simple_repeat 1 77 (0) m_b300s252i1 12549 chr6qtel1M 75921 ATTATTGTTAATATTATTGGCATT-TTATTAATAATAGTACAATTATGA- 75968 i v ivi - v v v iv v - (ATT)n#Simple 1 ATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTAT 50 chr6qtel1M 75969 AATTATGTAAAATAATAAATAATTATCAT 75997 v - vv v -v v i (ATT)n#Simple 51 TATTAT-TATTATTAT-TATTATTATTAT 77 Matrix = Unknown Transitions / transversions = 0.38 (5/13) Gap_init rate = 0.05 (4 / 76), avg. gap size = 1.00 (4 / 4) 238 36.84 2.94 2.19 chr6qtel1M 76478 76613 (923387) MIRc#SINE/MIR 13 149 (119) m_b300s601i0 12550 chr6qtel1M 76478 GCACAGTAGAAGGAACTACCTAAC----AGTCAGAGAACAAGTGCATTGA 76523 ii i i i - ivi ---- - v vv vi vi MIRc#SINE/MIR 13 GTGCAGTGGAAAGAGC-ACTGGACTTGGAGTCAG-GAAGACCTGGGTTCG 60 chr6qtel1M 76524 AATACAGCCTCAGTAAAACATAAGTTGTTTTAACTTTGAAAAATTCCCAA 76573 i v v v v iv vvi iv i v -i i iiv v v vv MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTACTAGCTGTGT-GACCTTGGGCAAGTCACTT 109 chr6qtel1M 76574 AGTGTCTTTGGATCTCAGTTCCCACACCTATAAAATGGGG 76613 iiv i iii i v i i MIRc#SINE/MIR 110 AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGG 149 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 50.85 CpG sites = 27, Kimura (unadjusted) = 52.41 Transitions / transversions = 1.23 (27/22) Gap_init rate = 0.03 (4 / 135), avg. gap size = 1.75 (7 / 4) 244 32.26 5.38 0.00 chr6qtel1M 76578 76670 (923330) MIR3#SINE/MIR 111 208 (0) m_b300s601i1 12550 chr6qtel1M 76578 TCTTTGGATCTCAGTTCCCACACCTATAAAATGGGGGCTTTAGATCAATT 76627 i ii i v i i i vv i ii iv MIR3#SINE/MIR 111 TCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGAT 160 chr6qtel1M 76628 --TCTCTGAAATATTTTCT-GCTCC--TAATCGCTGAGTCTGAGATTC 76670 -- i ii vii i- i--i v vv v iv MIR3#SINE/MIR 161 GATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTATGATTC 208 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 44.62 CpG sites = 20, Kimura (unadjusted) = 44.62 Transitions / transversions = 2.00 (20/10) Gap_init rate = 0.03 (3 / 92), avg. gap size = 1.67 (5 / 3) 69 3.00 0.00 0.00 chr6qtel1M 76675 76742 (923258) (AG)n#Simple_repeat 1 68 (0) c_b300s251i1 12551 chr6qtel1M 76675 AGAGAGAGAGAGACAGAGAGAGAGAAAGAGAGAGAGAGAGAGAGAGAGAG 76724 v i (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr6qtel1M 76725 AGAGAGAGAGAGAGAGAG 76742 (AG)n#Simple_ 51 AGAGAGAGAGAGAGAGAG 68 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0) 159 0.00 0.00 0.00 chr6qtel1M 76747 76883 (923117) (AGA)n#Simple_repeat 1 137 (0) c_b300s251i2 12552 chr6qtel1M 76747 AGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAG 76796 (AGA)n#Simple 1 AGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAG 50 chr6qtel1M 76797 AAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAA 76846 (AGA)n#Simple 51 AAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAA 100 chr6qtel1M 76847 GAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAG 76883 (AGA)n#Simple 101 GAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAG 137 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 136), avg. gap size = 0.0 (0 / 0) 107 8.05 1.17 2.98 chr6qtel1M 76884 77054 (922946) (GAG)n#Simple_repeat 1 168 (0) m_b300s252i2 12553 chr6qtel1M 76884 GAGGAGGAGGAGGAGGAGGAGGAAGAGGGAGGAGGAGGAGGAGGAGGAGG 76933 i - (GAG)n#Simple 1 GAGGAGGAGGAGGAGGAGGAGGAGGA-GGAGGAGGAGGAGGAGGAGGAGG 49 chr6qtel1M 76934 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAAAAGGAGGAG 76983 ii (GAG)n#Simple 50 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG 99 chr6qtel1M 76984 GAAGAGGAAGAAGAGGAGGAGGAGGAAAAGGA-GAGAGAGAAAGAGAAGG 77032 i i i ii - - i i i (GAG)n#Simple 100 GAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG-GAGGAGGAGGAGG 148 chr6qtel1M 77033 A-GAAGAGGAGGGAGTGAGAGAG 77054 - i - - - (GAG)n#Simple 149 AGGAGGAGGA-GGAG-GAG-GAG 168 Matrix = Unknown Transitions / transversions = 1.00 (12/0) Gap_init rate = 0.04 (7 / 170), avg. gap size = 1.00 (7 / 7) 16 31.69 1.82 0.00 chr6qtel1M 77604 77658 (922342) (TG)n#Simple_repeat 1 56 (0) m_b300s252i3 12554 chr6qtel1M 77604 TGTGTATATGTGAGAGAATGTGTGCTTGTGTAAGTGTGTATATATGTGT- 77652 i i v v vi iv iv i i i - (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr6qtel1M 77653 TCTGTG 77658 v (TG)n#Simple_ 51 TGTGTG 56 Matrix = Unknown Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1) 230 29.49 0.00 0.00 chr6qtel1M 79750 79827 (920173) L1ME3G_3end#LINE/L1 471 548 (376) m_b300s551i0 12555 chr6qtel1M 79750 AACTGGAAACTGAGTAGATGTTGATCTATTGGGAAATGGATGAATAAGTT 79799 i vivv i iv v v i v i i L1ME3G_3end#L 471 AATTGGAAACAACCTAAATGTCCATCAATAGGGGAATGGTTAAATAAATT 520 chr6qtel1M 79800 ATGACACACGAATGTTATGGAATATTAT 79827 ii i ivv ii i L1ME3G_3end#L 521 ATGGTATATCCATACTATGGAATACTAT 548 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 38.72 CpG sites = 14, Kimura (unadjusted) = 38.72 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.00 (0 / 77), avg. gap size = 0.0 (0 / 0) 16 14.88 2.56 2.56 chr6qtel1M 81926 81964 (918036) (AATA)n#Simple_repeat 1 39 (0) m_b300s252i4 12556 chr6qtel1M 81926 AATAAA-AAGTTATTATAATAAAAAAATTAATAAATAAAT 81964 - i v v - v v (AATA)n#Simpl 1 AATAAATAAATAAATA-AATAAATAAATAAATAAATAAAT 39 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2) 12 11.68 10.81 0.00 chr6qtel1M 82142 82178 (917822) (TACAATT)n#Simple_repeat 1 41 (0) m_b300s252i5 12557 chr6qtel1M 82142 TAC-ATTT-CACTTTA-TATTTATTATTTACAATTTA-AAT 82178 - - v -v iv - (TACAATT)n#Si 1 TACAATTTACAATTTACAATTTACAATTTACAATTTACAAT 41 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.11 (4 / 36), avg. gap size = 1.00 (4 / 4) 29 38.52 1.26 1.26 chr6qtel1M 82420 82578 (917422) (AT)n#Simple_repeat 1 159 (0) m_b300s252i6 12558 chr6qtel1M 82420 ATATATATGTATAT-TGTTTGTCAAATGCATATGCATGCATGTGAATATA 82468 i - i v i - v ii ii ii i iv (AT)n#Simple_ 1 ATATATATATATATATATATAT-ATATATATATATATATATATATATATA 49 chr6qtel1M 82469 TGTGCAAACACACACACATATATCAATATAAATATACATATACATGCATA 82518 i ii v i i i i i vv v i i ii (AT)n#Simple_ 50 TATATATATATATATATATATATATATATATATATATATATATATATATA 99 chr6qtel1M 82519 TATATAGACATCTCTA-ATCATATACCAATAGATAGATAGATAAATAGAT 82567 v i v v - - ivv v v v v v (AT)n#Simple_ 100 TATATATATATATATATAT-ATATATATATATATATATATATATATATAT 148 chr6qtel1M 82568 GAATCGATATA 82578 iv vv (AT)n#Simple_ 149 ATATATATATA 159 Matrix = Unknown Transitions / transversions = 1.30 (26/20) Gap_init rate = 0.03 (4 / 158), avg. gap size = 1.00 (4 / 4) 14 8.85 0.00 0.00 chr6qtel1M 82704 82727 (917273) (TCCC)n#Simple_repeat 1 24 (0) m_b300s252i7 12559 chr6qtel1M 82704 TCCCTCCCTCCCTCCACCCCTCCC 82727 vi (TCCC)n#Simpl 1 TCCCTCCCTCCCTCCCTCCCTCCC 24 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 874 31.84 1.04 1.04 chr6qtel1M 83038 83421 (916579) C L1ME4c_3end#LINE/L1 (191) 639 256 m_b300s551i1 12560 chr6qtel1M 83038 TTCTGTTCATTTCACGTAGCATTACTTCATGTAAGTCTCTCCAAGCCTCT 83087 i iv v i iv i- vvi i v iiv C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATA-AACATTTTCCATGTTGCT 591 chr6qtel1M 83088 CTGTATTCATCCTACTGGTCATTTCTTACAGAAAAATAATATTGCATAAC 83137 vii v v v v vi i v ii vviv v viv C L1ME4c_3end#L 590 ACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCGA 541 chr6qtel1M 83138 ATTTATATACCACAATTTACCCAACCATTCTCCAATTGATGGGCATCCAT 83187 i ?v i i ii i v v i ii v C L1ME4c_3end#L 540 GTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAG 491 chr6qtel1M 83188 TCATTTTCCAGCTTCTAGCCACTACAAACAGGGCTGCCACAAACATTTTG 83237 vivv ii i v i i i i iv v ii i v C L1ME4c_3end#L 490 GTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTC 441 chr6qtel1M 83238 GCACAAAGAGGTCCCTTTTCGTTCTTTAG---TATCTCTTTGGGGTATAA 83284 ii v v --- i v v --- i i i i v v C L1ME4c_3end#L 440 GTGCATATAG---CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAAT 394 chr6qtel1M 83285 GCCTAGTAGAAACACTGCTGGATCAAAGGCTATGCACGGTTTGATAACTT 83334 v i v viiv i i i v v iv v ii i C L1ME4c_3end#L 393 TCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTC 344 chr6qtel1M 83335 TTGA-GCATAGTTCCAAATTGCTCTCCAGAATGGTTGGATGTATTCACAA 83383 -i i v v i i v v ivv i ? C L1ME4c_3end#L 343 TTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACAN 294 chr6qtel1M 83384 TTCCACCAACAATGTATTAAAGTCCCTGTTTTCCCACA 83421 v i v i? v v iv i C L1ME4c_3end#L 293 TGCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCA 256 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 41.42 CpG sites = 65, Kimura (unadjusted) = 42.81 Transitions / transversions = 1.16 (65/56) Gap_init rate = 0.02 (6 / 383), avg. gap size = 1.33 (8 / 6) 228 16.34 6.67 11.63 chr6qtel1M 83404 83493 (916507) C L1MEj_5end#LINE/L1 (70) 2090 2005 m_b300s551i2 12561 chr6qtel1M 83404 AGTCCCTGTTTTCCCACACTTTATGGGAGAGTTCATCCCATTCACATTTA 83453 i i ------- v i vi C L1MEj_5end#LI 2090 AGTCTCTGTCTT-------TTAATGGGAGAATTCAGTCCATTCACATTTA 2048 chr6qtel1M 83454 TGGTTAAAATGACTAAT-T-CTTTAT----TTCCTGCCATCTTATT 83493 vv --- i i - - v ---- v i C L1MEj_5end#LI 2047 GTGT---AACGACTGATATACTTGATTTTATTCCTTCCATCTTACT 2005 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 16.97 CpG sites = 7, Kimura (unadjusted) = 18.45 Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.15 (13 / 89), avg. gap size = 1.23 (16 / 13) 16 26.43 0.00 5.08 chr6qtel1M 83613 83674 (916326) (TCCCTT)n#Simple_repeat 1 59 (0) m_b300s252i8 12562 chr6qtel1M 83613 TCTCTTCCCCTTTCTTGTACCCTTCCCTTATTACTCTTTTCCTTTTCCCT 83662 i i iiv v i i - - - i i (TCCCTT)n#Sim 1 TCCCTTTCCCTTTCCCTTTCCCTTTCCCT-TT-C-CCTTTCCCTTTCCCT 47 chr6qtel1M 83663 TTTCCTCTCCCT 83674 i i (TCCCTT)n#Sim 48 TTCCCTTTCCCT 59 Matrix = Unknown Transitions / transversions = 5.00 (10/2) Gap_init rate = 0.05 (3 / 61), avg. gap size = 1.00 (3 / 3) 3556 30.45 4.81 3.54 chr6qtel1M 83787 86966 (913034) L1M5_orf2#LINE/L1 69 3287 (7) m_b300s551i3 12563 chr6qtel1M 83787 AAAGCAGA---TAGCAGACTGGATCCAAAGTCAGAACTCTACAATATGTT 83833 i --- iv vv iv ii i v v i L1M5_orf2#LIN 69 AAGGCAGAGATTGTCAGACTGGATAAAAAAACAAGACCCAACTATATGCT 118 chr6qtel1M 83834 GTTTACAGGCAACACATTTAAAGCAAGGAGATATATACAGAGTAAAGGTA 83883 i i vi i i v ii vii i i v ? iv i i L1M5_orf2#LIN 119 GTCTACAAGAGACGCACTTTAAATATAAAGACACAGANAGGTTGAAAGTA 168 chr6qtel1M 83884 AA-GGCTGGAGCAGAATCTATATCCTTCAGGTG--AAGTAAAA-AAAGC- 83928 - v -- i vv i v v iiii-- ?i - - L1M5_orf2#LIN 169 AAAGGATGGA--AAAAGATATACCATGCAAACACTAANCAAAAGAAAGCT 216 chr6qtel1M 83929 AGGGTAGCCATCCTTATCTCATATCAAGCA------AAAGCAAAATTGAC 83972 i ? i i vi v v v iv i ------ i i --i i L1M5_orf2#LIN 217 GGNGTGGCTATATTAATATCAGACAAAGTAGACTTCAAGGCAAGA--AAT 264 chr6qtel1M 83973 CTAATCAAAGAGATAAGGTAAGAAACTCTATCTTACTAAA-GGGTAG--- 84018 v v i -- i vii v i ii vv iv - vi--- L1M5_orf2#LIN 265 ATTACCA--GAGATAAAGAGGGACATTTCATAATGATAAAAGGGTCAATT 312 chr6qtel1M 84019 CATAGACAACAAAGTAATGTCAATACTAAACATATATGCATCAAGTGGTA 84068 --- -i vv iv v ii i i v i iii L1M5_orf2#LIN 313 CAT---CAA-GAAGACATAACAATCCTAAATGTGTATGCACCTAATAACA 358 chr6qtel1M 84069 TAACATCTAACTTCCTAAAGGAGAAGTTAA--GAGTTGCAAGAAGAGACA 84116 v i v v v v v i v i ii i -- ii iv i i i L1M5_orf2#LIN 359 GAGCTTCAAAATACATGAAGCAAAAACTGACAGAACTAAAAGGAGAAATA 408 chr6qtel1M 84117 GCTAAA-CTGTAAT---AGTGGGAGAATCTCAATATTGCACTC--AG-AA 84159 vi - iii --- ? - i i i i?v v -- - L1M5_orf2#LIN 409 GACAAATCCACAATTATAGTNGGAGA-TTTTAACACNCCTCTCTCAGTAA 457 chr6qtel1M 84160 TTAGACAAATCAAAC-CACAAAACAAATAAGAAAGAA-ATCAAAGAGGTA 84207 - i i v ii-v -- v v i - vi vv i L1M5_orf2#LIN 458 TT-GATAGAACAAGTAGACAAAA--AATCAGTAAGGATATAGAAGATTTG 504 chr6qtel1M 84208 AATAG-ACTATTAGAAAATTAGGTATGATAGATCTCTGGAGAAAACTGAA 84256 i i- i ivv i v iiv i v iv i iv v ?v L1M5_orf2#LIN 505 AACAACACTATCAACCAACTTGACCTAATTGACATTTATAGAACACTNCA 554 chr6qtel1M 84257 GGGAGAAAGAAAGGAATATA-----TTTTTAGCAGTTCATGGAACCTAT- 84300 vvv iv v?ivi i ----- i ivv iv v v - L1M5_orf2#LIN 555 CCCAACAACNGCAGAATACACATTCTTTTCAAGTGCACATGGAACATTTA 604 chr6qtel1M 84301 TCAAAATTGACCATATATTAGGACATAAAA--ACTTCCAAATTAAATGCA 84348 i i v ?i i v -- v ii -- vi? L1M5_orf2#LIN 605 CCAAGATAGACCATATNCTGGGCCATAAAACAAGTCTCAA--TAAATTTN 652 chr6qtel1M 84349 GGAAGACAGCAATAGTA---AATGCTTTCTTTCAGATCACCATTCAATAG 84395 ii i iv v vi --- i iiv i -- i v vv v- L1M5_orf2#LIN 653 AAAGGATTGAAATCATACAGAGTATGTTCTCT--GACCACAATGGAATT- 699 chr6qtel1M 84396 AAAACTACAT-TCAACAAAAGTTAGAGGTAAATAGA----TCAAAAGTAA 84440 - i v v- i v i-- i i ?v ----i vv i v L1M5_orf2#LIN 700 -AAATTAGAAATCAATAACAA--AAAGATANCTAGAAAATCCCCAAATAT 746 chr6qtel1M 84441 TTGCAAACTAAATAATCTCATCT-TAAAGAATGAATGGGTGAAACAGCAA 84489 v i i - v ii - v ivv v v iv L1M5_orf2#LIN 747 TTGGAAATTAAACAA-CACACTTCTAAATAACCCATGGGTCAAAGAAGAA 795 chr6qtel1M 84490 ATTATA-GAAAAATTA----ATAATTTACCAAGATAATGACAAATGATGA 84534 i i -?ii ---- v i-- vvv ? - vi L1M5_orf2#LIN 796 ATCACAANGGAAATTAGAAAATATTTTG--AACTGAATGANAA-TGAAAA 842 chr6qtel1M 84535 GACACCATACCAAAATTTGTGGAATGT--CCAAAGCACTAATAAGAGGAA 84582 v v i i i-- i v iv v i L1M5_orf2#LIN 843 TACAACATATCAAAATTTGTGGGATGCAGCTAAAGCAGTGCTTAGAGGGA 892 chr6qtel1M 84583 ATTTTATATCCTTAGAGGCTTACTGAATAAAATAGA-GAAAG--TGAAGA 84629 v v ? i v ? i-- v i v - -- v i L1M5_orf2#LIN 893 AATTTATAGCNTTAAATGCNTAT--ATTAGAAAAGAAGAAAGGCTTAAAA 940 chr6qtel1M 84630 TCAATGAATTAGGCTTGCAACTAAAAACGCTAGAAAA----GACCAAATT 84675 vi i v v v i v ---- v L1M5_orf2#LIN 941 TCAATGATCTAAGCTTCCACCTTAAGAAGCTAGAAAAAGAAGAGCAAATT 990 chr6qtel1M 84676 AAAAACCCCAATCAAATATTAAATTTGAAATT-TAAAATTAAAAGAAGAA 84724 -- v v? i vv iivvv v- iv i v L1M5_orf2#LIN 991 AAA--CCCAAAGNAAGTAGAAGGAAGGAAATAATAAAGATAAGAGCAGAA 1038 chr6qtel1M 84725 AGTAATAATATTGAAAGTAAAAAAAAACTATTGAACTAATAAAAAAAGT- 84773 vi i v v ii ? ? v v vv -- v vi i- L1M5_orf2#LIN 1039 ATCAATGAAATAGAAAACAAANANACAATAGAGAA--AATCAACGAAGCC 1086 chr6qtel1M 84774 AAGAGTTGGTTGTAAGAAAA-ACCAATAAAATAGATG--TCTTTGGTAAA 84820 i i v vv - i v i--i i i i? i L1M5_orf2#LIN 1087 AAAAGCTGGTTCTTTGAAAAGATCAATAAAATTGATAAACCTCTAGCNAG 1136 chr6qtel1M 84821 TCTGATTA-GAAAAGGAGGGAGGAAAATGAAATTAGTAGTCTTAA-AATG 84868 v i - ii i i i vvv vi i v i i- L1M5_orf2#LIN 1137 ACTGATCAAGAAAAAAAGAGAGAAGACACAAATTACCAATATCAGGAATG 1186 chr6qtel1M 84869 AAAAGGGAGAACTTTCCACCAATGAAGAGGAAATTAGAGAAATAATAAGG 84918 i vv iv i vi vvvivi v i iii i L1M5_orf2#LIN 1187 AAAAAGGAGACATCACTACAGATCCTACAGACATTAAAAGGATAATAAGA 1236 chr6qtel1M 84919 AGTTATTTTGC-TAACTTTATGCCAATAAATTTGATAACCTA-AGGAAAT 84966 iiv v v-i ? i - v L1M5_orf2#LIN 1237 GAATATTATGAACAACTTTATGCCAATAAATTTGANAACTTAGATGAAAT 1286 chr6qtel1M 84967 GGATGACTACCTCCAAAAATATAGACTTCCCAGACTAATAGAGGAGGAAG 85016 ii v v iv i i i?i v v i i i?v i i i L1M5_orf2#LIN 1287 GGACAAATTCCTTGAAAAACACAANTTACCAAAACTGACNCAAGAAGAAA 1336 chr6qtel1M 85017 TAAATTGTTTGAATAGTCCCAT-TC-AGAAAAAAAATAGAACAAAGTATT 85064 i vvi i i i - - vv i v i---- vv L1M5_orf2#LIN 1337 TAGAAAATCTGAATAGCCCTATATCTATTAAAGAAATTGAAT----TTGT 1382 chr6qtel1M 85065 AATCAA-----TTCCCTAAGAAAAATCCCTAAGACCAGATAGATTTAATG 85109 i ----- vv i i v i i i v i v i v L1M5_orf2#LIN 1383 AATTAAAAACCTTCCCACAAAGAAAACTCCAGGCCCAGATGGCTTCACTG 1432 chr6qtel1M 85110 -TGAATT-TACCAAACATTTAAAGAACAATTGC--CCAATGCTATATAAA 85155 - - i v v iv-- vi i i L1M5_orf2#LIN 1433 GTGAATTCTACCAAACATTTAAGGAAGAAATAATACCAATCTTACACAAA 1482 chr6qtel1M 85156 TTATTCGATAAAATAGAGAATGAAGGAGTTCTATCAAATTCCTTTTATGA 85205 i v v v i v i iiv vi v i v L1M5_orf2#LIN 1483 CTCTTCCAGAAAATAGAAAAAGAGGGAACACTTCCCAACTCATTTTATGA 1532 chr6qtel1M 85206 CACAGACATGGTACTGATACCTAAAGCAGGTAGGTTGAAA--ACAGAGAA 85253 vi vii ?iiv v v ? ii ii-- v -- iii L1M5_orf2#LIN 1533 GGCCAGCATNACCCTGATACCAAAACCNGACAAA--GACATTACAAGAAA 1580 chr6qtel1M 85254 AGCAAATTATAGACCAAT-TCCCTAATGAATATTGATGCTAAAATCTTAA 85302 v i - v i v v i ? L1M5_orf2#LIN 1581 AGAAAATTACAGACCAATATCCCTCATGAACATAGATGCAAAAATCCTNA 1630 chr6qtel1M 85303 ATAAGATATTAGTTGATGCTAAAATCTTAAATAAGATATTAGCAAAAAGA 85352 i i i-------- --i ------ii ----- L1M5_orf2#LIN 1631 ACAAAATATTAGC--------AAATC--GAAT------CCAGCAA----- 1659 chr6qtel1M 85353 CTACAGAAAATTATCCCCAGGATAATCCACTATGATCAAGTAGGATTTAT 85402 - i v -------- v ii i i i L1M5_orf2#LIN 1660 -TATATAAAA--------AGGATAATACATCATGACCAAGTGGGGTTTAT 1700 chr6qtel1M 85403 ACCAGGAATGCAGGGCTGCTTCAATATTAGAAA--CAGTATCAGTATAAT 85450 v i i v i i v -- -- i i L1M5_orf2#LIN 1701 CCCAGGAATGCAAGGTTGGTTTAACATTCGAAAATCA--ATCAATGTAAT 1748 chr6qtel1M 85451 TGACCATATTAACAACCACAAATTAATAAAAACCATATGAATATCCCAAT 85500 v i-v i -vi v i vi i L1M5_orf2#LIN 1749 TCACCATATTAACAG-AATAAA-GGAGAAAAATCATATGATCATCTCAAT 1796 chr6qtel1M 85501 AGATGCA-AAAAAGCATTTGATAAAATCCAAACATCTATTCCTATTAAAA 85549 - i i - i i v iv L1M5_orf2#LIN 1797 AGATGCAGAAAAAGCATTTGACAAAATTC-AACACCCATTCATGATAAAA 1845 chr6qtel1M 85550 GCACTTGAGAATAAAGGAATAAATGGACTGTTCCTTAAAATAATAAGTAG 85599 i v iiiv vvv i v ivvv i vv i ivi L1M5_orf2#LIN 1846 ACTCTCAGCAAACTAGGAATAGAAGGGAACTTCCTCAACCTGATAAAGGG 1895 chr6qtel1M 85600 CATCTATTTAAAACCATCAG-TAAGACCATTTATAATAGAGAAAACTTGC 85648 ivv vv -? v i viv i v ?vi v L1M5_orf2#LIN 1896 CATCTACGAAAAACCTACAGCNAACATCATACTTAATGGTGAAANACTGA 1945 chr6qtel1M 85649 AAGCATTCCTAGTAAGATCAGGAATCAAACAAGATTGCCC-CTATCACCA 85697 ? v ivv i iv i iv i - ? L1M5_orf2#LIN 1946 ANGCTTTCCCCCTAAGATCGGGAACAAGACAAGGATGTCCGCTNTCACCA 1995 chr6qtel1M 85698 TTACTATTCAA-ATTGTCTTAGAAATGCTAGCTTTGGCAATAAGAGTTGA 85746 i v - vi i ii v ivvv ivvv L1M5_orf2#LIN 1996 CTTCTATTCAACATTGTACTGGAGGTCCTAGCCAGTGCAATAAGGCAAGA 2045 chr6qtel1M 85747 GAAAGAGATAAA--GAATTAGAATAGGCAATGAGGAAATCAAATTATACC 85794 i i -- v v ii v v v i v i i v?i L1M5_orf2#LIN 2046 AAAAGAAATAAAAGGCATAAAGATTGGAAAGGAAGAAATAAAACTGTCNT 2095 chr6qtel1M 85795 --TTTGCTGATGATATGATGGTATACTTGGAGAACCCTAGAGATTCTACT 85842 -- i v i v ? v i i i ? i v v L1M5_orf2#LIN 2096 TATTCGCAGATGACATGATTGTNTACGTAGAAAATCCNAAAGAATCTACA 2145 chr6qtel1M 85843 AAAAAGTTATTTTGAAATAATCCACACCTTTAGCAAAATTG-AGGATACA 85891 ? ii -i v v vviiivv ii i -? L1M5_orf2#LIN 2146 AANAAACTA-CTAGAACTAATAAGTGAATTTAGCAAGGTCGCNGGATACA 2194 chr6qtel1M 85892 AAATAAACCTACATAACTCATCAGCATTCTTAAATATCACTA--AAAAAA 85939 ii v iv v v viv i ii v ii vi -- v L1M5_orf2#LIN 2195 AGGTCAATATACAAAAATCAATTGTATTTCTATATACTAGCAACAAACAA 2244 chr6qtel1M 85940 TCCAGCAGTC-AGTTACAAGAGAAAT-TCTTTTAAAGTAACTACTGATAG 85987 iviiv i v- i v? i iv -i v v i i vv vi v i L1M5_orf2#LIN 2245 TTGGAAAATGAAATTTNAAAAACAATACCATTTACAATAGCATCAAAAAA 2294 chr6qtel1M 85988 TATAAAATACTTA-GAATCTATCT-GCAAGGAAAAT---CAGAAACTTTA 86032 i ? - vv -i -- ? --- ii v ? L1M5_orf2#LIN 2295 CATNAAATACTTAGGAATAAATCTAACAA--AANATGTGCAAGACCTNTA 2342 chr6qtel1M 86033 TGGGCAAAACTACAAAGCACTTTCCACATAAATTAAGTCTGATCTAACCA 86082 iivvv i i viiv v v ivvv i vi L1M5_orf2#LIN 2343 CACTGAAAACTACAAAACATTGCTGAGAGAAATTAAAGAAGACCTAAATA 2392 chr6qtel1M 86083 ATTGAAA----ATATTAAATGCCTGGATAGG-CGAGCAAATACAATAAAG 86127 v i i---- ii vi v v v -v viv ivi ? L1M5_orf2#LIN 2393 AATGGAGAGATATACCATGTTCATGGATTGGAAGACTCAATATTGTNAAG 2442 chr6qtel1M 86128 ATGGCAATACTACCTAAACTAATCTATTTGTTTAGTGCTATACCAATCAG 86177 v v v i i i vvi i i v v i L1M5_orf2#LIN 2443 ATGTCAATTCTCCCCAAATTGATCTATAGATTCAATGCAATCCCAATCAA 2492 chr6qtel1M 86178 ACTCTAAAAAACTATTTTAATGACCTAAAAAAATAACAA--------CAA 86219 v iv iv iv v vi ------ i v i --------i L1M5_orf2#LIN 2493 AATCCCAGCAGGTTTTTTTGT------AGAAATTGACAAGCTGATTCTAA 2536 chr6qtel1M 86220 AGTTCATATGGAAA-ACAAAAGGTCAATAAT-TTCAAGGGAATTAATTAA 86267 i i -i i ii ? v -vi iiv i-- i L1M5_orf2#LIN 2537 AATTTATATGGAAATGCAAAGGACCNAGAATAGCCAAAACAATC--TTGA 2584 chr6qtel1M 86268 AAAAATCAAATGAAAGTTG-----CCTA-GCTGAACCAGATCT-AAAATT 86310 ivvi i- ----- i -i -- ? ? - i i L1M5_orf2#LIN 2585 AAAAGAAGAAC-AAAGTTGGAGGACTTACACT--ACCNGATNTCAAGACT 2631 chr6qtel1M 86311 ATATTATAAAGCAGCGGGTACCAAAATCATTTGGTATTGGC-TAAGGAAT 86359 - vi i vv i i ivi v - - L1M5_orf2#LIN 2632 -TATTATAAAGCTACAGTAATCAAGACAGTGTGGTATTGGCGTAAGG-AT 2679 chr6qtel1M 86360 AGATTAGTTGATCGATAGAATAGGTTAG---GTTCAAAGGACAAAACAGT 86406 iv i v i i i iv --- i i -i i i v vii L1M5_orf2#LIN 2680 AGACAAATAGATCAATGGAACAGAATAGAGAGTCCAGA-AATAGACCCAC 2728 chr6qtel1M 86407 CAATAACTATAGCAATCTAGTGTTTGACAAA----CCCAGACATCTCCAA 86452 vv -- i ?v ?i ii v ---- v ?i -v i i L1M5_orf2#LIN 2729 ACATA--TATGGNCANTTGATTTTTGACAAAGGTGCCAANGCA-ATTCAG 2775 chr6qtel1M 86453 TTTGGGGATAAGAACCTACTGTTTGACAAAAATTGCTGGGAAAATTGGAA 86502 -- - i ivvv v ii viv i v v L1M5_orf2#LIN 2776 --TGGGGA-AAGGATAGTCTTTTCAACAAATGGTGCTGGAACAATTGGAT 2822 chr6qtel1M 86503 ACTAGTATGG-CAGAAACAAGTCATCGACTGACAATTAACACCATACACC 86551 iivi -v i ii i? - ivvi vi v v L1M5_orf2#LIN 2823 ATCCATATGGAAAAAAATGAANC-TCGACCCCTACCTCACACCATACACA 2871 chr6qtel1M 86552 ACAA-TAACGTCAAATGGGTTCAT-GACCTAGGCATAAAGAATGAGATTA 86599 v - ivi? i i- - iiii ii? i i i L1M5_orf2#LIN 2872 AAAATTAATTCNAGATGGA-TCATAGACCTAAATGTAAAAGNTAAAACTA 2920 chr6qtel1M 86600 TAAATAAATTAGAGG--AACATAGGATAGTTTACCTCTCAGACCTGTGGA 86647 vvvvi i -- v i-- i iivv vv ? L1M5_orf2#LIN 2921 TAAAACTTCTAGAAGAAAACATAGGAGAA--TATCTTCGTGACCTTGGGN 2968 chr6qtel1M 86648 -AGACGAAGGAATTTATGACCAAAAAAGAAC-TAAAGAGAAGACCTGATC 86695 - i i -- ---- iv v i -i i v --- ?i i L1M5_orf2#LIN 2969 TAGGCAAAG--ATTT----CTTAAACAGGACACAAAAAGCA---CNAACC 3009 chr6qtel1M 86696 ACAAAATCAAAAAT-------TTTGATTTTATCAAATTGAAAAGTTTTTG 86738 i vv ------- v i ?i v v ii i L1M5_orf2#LIN 3010 ATAAAAGAAAAAATTGATAAATTGGACTNCATCAAAATTAAAAACTTCTG 3059 chr6qtel1M 86739 TACAAACAAAACTAATGCAGACAAGATTAGAAGGGAAGCAATAAACTGGG 86788 iv ?vvv ivi vi ivi v i v i v v i i ? L1M5_orf2#LIN 3060 CTCNTCAAAAGACACCGTTAAGAAAATGAAAAGGCAAGCCACAGANTGGG 3109 chr6qtel1M 86789 AAAACATTTTTACAGT-CAAAGGTTATAATAAAGACCTCATTTCCAAAAT 86837 i v v i i?- v vi i- i i iv i v i L1M5_orf2#LIN 3110 AGAAAATATTTGCAANACATATATC-TGACAAAGGACTCGTATCCAGAAT 3158 chr6qtel1M 86838 ATATAGAGAATTGACTCTAATTT-ATAAGAAA---TCAAGCCATTTTCCA 86883 i i v- vi ? i- ? ---v i v ---i L1M5_orf2#LIN 3159 ATATAAAGAACTC-CTACAANTCAATAANAAAAAGACAAACAA---CCCA 3204 chr6qtel1M 86884 GTTGATGAATGGTCAAAGCATATGAACAGATAATTCTCAAAAGAAGAAAT 86933 i v? vi v iv iv i v v v L1M5_orf2#LIN 3205 ATANAAAAATGGGCAAAAGACTTGAACAGACACTTCACAAAAGAAGATAT 3254 chr6qtel1M 86934 TGAAACTATTTCTAGCCATATGAAAAGATGCTC 86966 ?v iviiivv iv i L1M5_orf2#LIN 3255 NCAAATGGCCAATAAGCACATGAAAAGATGCTC 3287 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 40.46 CpG sites = 518, Kimura (unadjusted) = 41.03 Transitions / transversions = 1.25 (518/416) Gap_init rate = 0.06 (194 / 3179), avg. gap size = 1.38 (267 / 194) 1451 28.09 1.47 1.85 chr6qtel1M 86830 87373 (912627) L1ME3G_3end#LINE/L1 7 548 (376) m_b300s551i4 12563 chr6qtel1M 86830 TCCAAAATATATAGAGAATTGACTCTAATTTATAAGAAATCAAGCCATTT 86879 i i i vviv v iv -- v vi- L1ME3G_3end#L 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAA--AAGACAAC- 53 chr6qtel1M 86880 TCCAGTTGATGAATGGTCAAAGCATATGAACAGATAATTCTCAAAAGAAG 86929 - i v vi v v ii v i i L1ME3G_3end#L 54 -CCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chr6qtel1M 86930 AAATTGAAACTATTTCTAGCCATATGAAAAGATGCTCCAAAGCATTATTA 86979 vv iviiivv iv v vvv i v L1ME3G_3end#L 103 AAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTA 152 chr6qtel1M 86980 ATCAGAGAAATGCAAACTAAGACAACTCTAAGATGTCATTACACACCTGT 87029 i i i vv i ii viv ii L1ME3G_3end#L 153 ATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCAT 202 chr6qtel1M 87030 CAGACTGGCTAGAATGACAAGGAAAGAGAATGCAGAATGTTGA-GGGGAT 87078 i v i vvv i ?vv v iiv? i i- i i L1ME3G_3end#L 203 CAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGT 252 chr6qtel1M 87079 GTGGGAAAACAGAGACACTAACACATT-TTGGTGGAATTGTGAATACATC 87127 i i iv v v i i -i i v i vvi v L1ME3G_3end#L 253 GTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTA 302 chr6qtel1M 87128 CAGCCATTCT-GAGAGCAATTTGGAGCTATGC-TCAAAATGTTATCAAAC 87175 ? i - i viv vi- i ---- i v L1ME3G_3end#L 303 CAGCCNTTTTGGAGGGCAATTTGGCAGTATCTATTAAAAT----TTAAAA 348 chr6qtel1M 87176 TGTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGCTTACATCCCAAA 87225 i i i vii v ? ?v vi i ? L1ME3G_3end#L 349 TGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANA 398 chr6qtel1M 87226 GAGAT-CTTAAAGAAG-GGAAAGGGGCCTGTATGTACAAGACTGTTTGTG 87273 i - iiv v v - v v i i--? i iv ii v L1ME3G_3end#L 399 GAAATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTCATT 446 chr6qtel1M 87274 GCAAC-CTCTTTGTAGTGGCTAGAAACT-GAAACTGAGTAGATGCCCATC 87321 i -i v i i v i i - vivv i i L1ME3G_3end#L 447 GCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATC 496 chr6qtel1M 87322 AATTATAGAAGGGCTGAATAAATTGTGGTATATGAATATTATGGAATATT 87371 vivi v i i i vv i i L1ME3G_3end#L 497 AATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACT 546 chr6qtel1M 87372 AT 87373 L1ME3G_3end#L 547 AT 548 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 35.57 CpG sites = 83, Kimura (unadjusted) = 36.52 Transitions / transversions = 1.24 (83/67) Gap_init rate = 0.03 (18 / 543), avg. gap size = 1.00 (18 / 18) 15 12.73 9.30 0.00 chr6qtel1M 87706 87748 (912252) (ATTTAT)n#Simple_repeat 1 47 (0) m_b300s252i9 12564 chr6qtel1M 87706 ATGTATACTTAT-TTTGTATTTA-ATTTATACTT-TA-ATATATTTA 87748 v i - i - i - -v (ATTTAT)n#Sim 1 ATTTATATTTATATTTATATTTATATTTATATTTATATTTATATTTA 47 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.10 (4 / 42), avg. gap size = 1.00 (4 / 4) 113 19.77 1.58 0.78 chr6qtel1M 89325 89574 (910426) (TCTGTC)n#Simple_repeat 1 252 (3) m_b300s252i10 12565 chr6qtel1M 89325 TCTTTCTTTCTCTCTGTCTCTGTCTTTGTCTATCTATAAGTCTGTCTGTC 89374 v i v i v v v vv v v v (TCTGTC)n#Sim 1 TCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTC 50 chr6qtel1M 89375 TGTCTGGCTGTCTCTATCTCTCTCT-ACTCTCTGTCTCTGTGTCTTTCTA 89423 -- i v -vv v v v (TCTGTC)n#Sim 51 TGTCT--CTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTC 98 chr6qtel1M 89424 TCTGTCTATCTCTTTCTCTGTCCCTGTCTCTATGTCTGTCTCTGTCTCTC 89473 v v i v i i v v (TCTGTC)n#Sim 99 TGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTG 148 chr6qtel1M 89474 TCTGTGTCTCTCTCTCTTTCTCTGTCTCTCTCTCAATCTCTGTCTCTGAC 89523 v v v v vi v (TCTGTC)n#Sim 149 TCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTC 198 chr6qtel1M 89524 TC--TCTGTCTCTCTGTCT-TTTCTCTTTCTCTCTCTCTGCCTCTCTGTC 89570 -- v v - v v v i v v (TCTGTC)n#Sim 199 TCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTC 248 chr6qtel1M 89571 TTTC 89574 v (TCTGTC)n#Sim 249 TGTC 252 Matrix = Unknown Transitions / transversions = 0.23 (8/35) Gap_init rate = 0.02 (5 / 249), avg. gap size = 1.20 (6 / 5) 44 0.00 0.00 0.00 chr6qtel1M 89575 89612 (910388) (TG)n#Simple_repeat 1 38 (0) c_b300s251i3 12566 chr6qtel1M 89575 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 89612 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 38 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 19 23.83 4.88 2.38 chr6qtel1M 92060 92141 (907859) (TCTTT)n#Simple_repeat 1 84 (0) m_b300s252i11 12567 chr6qtel1M 92060 TCTTTTCTTTACTCTTGTAGT-TTTTCATTCCTTTTCTGTTGTGTACTTT 92108 v i v vv - v i v v v v (TCTTT)n#Simp 1 TCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTT 50 chr6qtel1M 92109 GTAATTTTGTTTTC--CCCTTTTC-TTCCTTTTCTT 92141 - -v v --ii - i (TCTTT)n#Simp 51 -T-CTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTT 84 Matrix = Unknown Transitions / transversions = 0.45 (5/11) Gap_init rate = 0.06 (5 / 81), avg. gap size = 1.20 (6 / 5) 31 39.07 0.61 1.23 chr6qtel1M 92167 92330 (907670) (AT)n#Simple_repeat 1 163 (0) m_b300s252i12 12568 chr6qtel1M 92167 ATTTAAATATATATATATATATAAAGACAT-TGTGTGAGTACATATATAT 92215 v v v v i - i i - - i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATAT-A-TATATATATAT 48 chr6qtel1M 92216 AAGCAGACACACATATACAGATTAACTTATACACAAATATAAATACATTC 92265 vii v i i i i v vv iv i i v v i vi (AT)n#Simple_ 49 ATATATATATATATATATATATATATATATATATATATATATATATATAT 98 chr6qtel1M 92266 ATGCATATACATAGATATCTATAACCCTACTTACATATCCATACATATGT 92315 ii i v v vviv iv i vi i i (AT)n#Simple_ 99 ATATATATATATATATATATATATATATATATATATATATATATATATAT 148 chr6qtel1M 92316 ATATGCATCTGTATA 92330 ii v i (AT)n#Simple_ 149 ATATATATATATATA 163 Matrix = Unknown Transitions / transversions = 1.29 (27/21) Gap_init rate = 0.02 (3 / 163), avg. gap size = 1.00 (3 / 3) 428 22.90 3.57 6.42 chr6qtel1M 94439 94550 (905450) MIRc#SINE/MIR 19 127 (141) m_b300s601i2 12569 chr6qtel1M 94439 TGGATAGAGAAGTGGACCTGAAGTCAGGAGGACCTGAGTTCAAATCCAAC 94488 v v v i i i i i i viv MIRc#SINE/MIR 19 TGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGG 68 chr6qtel1M 94489 TTCAGACATTTAATAGTTACTAATTTTGTGACC-TAGGCAAGTCCTTTAA 94537 i v v i------- ii v - i vi MIRc#SINE/MIR 69 CTCTGCCAC-------TTACTAGCTGTGTGACCTTGGGCAAGTCACTTAA 111 chr6qtel1M 94538 CCCCTT---GCCTCAG 94550 i i--- MIRc#SINE/MIR 112 CCTCTCTGAGCCTCAG 127 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 25.26 CpG sites = 15, Kimura (unadjusted) = 27.92 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.08 (9 / 111), avg. gap size = 1.22 (11 / 9) 223 33.64 3.74 0.00 chr6qtel1M 94825 94931 (905069) MIR3#SINE/MIR 87 197 (11) m_b300s601i3 12570 chr6qtel1M 94825 TGACTGTGAAAATATC-CCTCAGTTCCATTGGTCTCAGTTACCTCACCTG 94873 iv iiv vi - i vi iv v i v i MIR3#SINE/MIR 87 TGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTG 136 chr6qtel1M 94874 TAAAATGGGTGCTTTTGGTCAACT--TCTCTGA-CTTCCTTTAAGCTCTA 94920 i v vv v iii iv -- i -v i iv i MIR3#SINE/MIR 137 TAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTG 186 chr6qtel1M 94921 TAATGCTCTGA 94931 vv v v MIR3#SINE/MIR 187 ACATTCTATGA 197 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 45.38 CpG sites = 18, Kimura (unadjusted) = 45.38 Transitions / transversions = 1.00 (18/18) Gap_init rate = 0.03 (3 / 106), avg. gap size = 1.33 (4 / 3) 22 18.88 0.00 0.00 chr6qtel1M 95598 95639 (904361) (GT)n#Simple_repeat 1 42 (0) m_b300s252i13 12571 chr6qtel1M 95598 GTGTGTGTGAGTGTGTGTTTGGGTAAGTGTGCATGTGTGTGT 95639 v v v iv ii (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 42 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 12 11.71 10.81 0.00 chr6qtel1M 96637 96673 (903327) (ATTCAAA)n#Simple_repeat 1 41 (0) m_b300s252i14 12572 chr6qtel1M 96637 ATTCAAAAGTCAAAATT-GAAA-T-AAAGTTC-AACTTCAA 96673 v -i - - i - v (ATTCAAA)n#Si 1 ATTCAAAATTCAAAATTCAAAATTCAAAATTCAAAATTCAA 41 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.11 (4 / 36), avg. gap size = 1.00 (4 / 4) 112 25.07 3.31 1.36 chr6qtel1M 99552 99580 (900420) (TCTG)n#Simple_repeat 1 28 (341) m_b300s252i15 12573 chr6qtel1M 99552 TCTTTCCCTCTGTCAGTCTGTACTGTCTG 99580 v iv v - (TCTG)n#Simpl 1 TCTGTCTGTCTGTCTGTCTGT-CTGTCTG 28 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1) 183 9.46 0.74 0.00 chr6qtel1M 99581 99850 (900150) (TC)n#Simple_repeat 1 272 (0) c_b300s251i4 12574 chr6qtel1M 99581 TCTCTCTCTGTCTCTGTCTCTGTCTCTCTTTCTTTCTCTGTCTCTCTCTC 99630 v v v i i v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr6qtel1M 99631 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTTTCTCAGTCTCTGTCTCTCTC 99680 i vv v (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chr6qtel1M 99681 TCTCTGTCTCTGTTTCTCTCTCTGTCTCTCTGTC-CTCTCTCTCTCTCTC 99729 v v i v v - (TC)n#Simple_ 101 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 150 chr6qtel1M 99730 TGTCTCTCTCTCTCTTTCTCTCTCTCTCTCTCTCTCTCTGTCTCTCTCTC 99779 v i v (TC)n#Simple_ 151 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 200 chr6qtel1M 99780 TCTCTGTCTCTCTCTCTGTCTCTCTCTCCCTTTCTCTCTCTCTCTGTCTC 99829 v v i i v (TC)n#Simple_ 201 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 250 chr6qtel1M 99830 TCTGTCTCTCTCTC-CTCTCTC 99850 v - (TC)n#Simple_ 251 TCTCTCTCTCTCTCTCTCTCTC 272 Matrix = Unknown Transitions / transversions = 0.41 (7/17) Gap_init rate = 0.01 (2 / 269), avg. gap size = 1.00 (2 / 2) 112 25.07 3.31 1.36 chr6qtel1M 99851 100021 (899979) (TCTG)n#Simple_repeat 29 204 (165) m_b300s252i15 12575 chr6qtel1M 99851 CCTCCCTCCCCCCCCTCTCCCTCTGTCTCACTTTCTCTGTATGTGTGTGT 99900 i vi -vi ivi v iv vv v v v i v v (TCTG)n#Simpl 29 TCTGTCT-GTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGT 77 chr6qtel1M 99901 GTGTCTGTCTGCCTGATTGCCTGTCTTCCTGTCTGTTTCTCTGTCAGTC- 99949 v i vi i vi i v v - (TCTG)n#Simpl 78 CTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCT 127 chr6qtel1M 99950 -TCTGTCTTTCTCTCTCTCTCTCTGTC--TCTGTCTCTCT-TTTG-GTCT 99994 - v v v v -- v - i -v v (TCTG)n#Simpl 128 GTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGT 177 chr6qtel1M 99995 CTGCCTCTCTGTCTCTCTGTCTCTCTC 100021 i v v v v (TCTG)n#Simpl 178 CTGTCTGTCTGTCTGTCTGTCTGTCTG 204 Matrix = Unknown Transitions / transversions = 0.50 (14/28) Gap_init rate = 0.04 (6 / 170), avg. gap size = 1.17 (7 / 6) 43 0.00 0.00 0.00 chr6qtel1M 100022 100058 (899942) (TG)n#Simple_repeat 1 37 (0) c_b300s251i5 12576 chr6qtel1M 100022 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 100058 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 37 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 112 25.07 3.31 1.36 chr6qtel1M 100059 100165 (899835) (TCTG)n#Simple_repeat 205 316 (53) m_b300s252i15 12577 chr6qtel1M 100059 CTGCCTGTCTTCCTGTCTGTTTCTCTGTCAGTC--TCTGTCTTTCTCTCT 100106 i vi i v v -- v v (TCTG)n#Simpl 205 CTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCT 254 chr6qtel1M 100107 CTCTCTCTGTC--TCTGTCTCTCT-TTTG-GTCTCTGCCCCTCTGTCTCT 100152 v v -- v - i -v v i iv v (TCTG)n#Simpl 255 GTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGT 304 chr6qtel1M 100153 CTGTCTCTCTGTC 100165 v - (TCTG)n#Simpl 305 CTGTCTGTCTGT- 316 Matrix = Unknown Transitions / transversions = 0.46 (6/13) Gap_init rate = 0.05 (5 / 106), avg. gap size = 1.40 (7 / 5) 46 0.00 0.00 0.00 chr6qtel1M 100166 100204 (899796) (TG)n#Simple_repeat 1 39 (0) c_b300s251i6 12578 chr6qtel1M 100166 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 100204 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 39 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 112 25.07 3.31 1.36 chr6qtel1M 100205 100256 (899744) (TCTG)n#Simple_repeat 317 368 (1) m_b300s252i15 12579 chr6qtel1M 100205 CTGTCTGTCTGCCTGTCTGCCTCCCTGTGTCTCTGTCTCCCTCTCTGTGT 100254 i i vi v v vi v v (TCTG)n#Simpl 317 CTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCT 366 chr6qtel1M 100255 GT 100256 (TCTG)n#Simpl 367 GT 368 Matrix = Unknown Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 67 6.28 1.20 0.00 chr6qtel1M 100890 100972 (899028) (TC)n#Simple_repeat 1 84 (0) c_b300s251i7 12580 chr6qtel1M 100890 TCTCTGTCTCTGTCTCTCTTTCTCTCTCTGTCTCTCTCTCTCTCTCTCTC 100939 v v i v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr6qtel1M 100940 TCTCTCTCTCT-TTTCTCTCTCTCTCTCTCTCTC 100972 - i (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 84 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.01 (1 / 82), avg. gap size = 1.00 (1 / 1) 18 25.89 0.00 1.79 chr6qtel1M 100973 101020 (898980) (TCTG)n#Simple_repeat 9 56 (0) m_b300s252i16 12581 chr6qtel1M 100973 GCTGTCTGCCTGTCTGTCTGTGACTCTGTCTCCCTCTCTCTGTGTGTG 101020 v i vvv vi v v v v (TCTG)n#Simpl 9 TCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTG 56 Matrix = Unknown Transitions / transversions = 0.22 (2/9) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 256 23.53 1.33 1.79 chr6qtel1M 102022 102246 (897754) C HERVIP10FH#LTR/ERV1 (4097) 1005 782 m_b300s701i0 12582 chr6qtel1M 102022 TACTGGTTTTTTCTCTGTCCGTCTCTGTATATCTGTCTCTCTGTATCTCT 102071 iv i v v iv i v v v i v i v C HERVIP10FH#LT 1005 TACTACTTCTATCTCTCTCTTTCTTTCTCTCTTTGACTTTCTGTCTCTCT 956 chr6qtel1M 102072 CTGCTTTCTCTGTTTCTCTCTGTGTCTCTCTGTCTCTCCCTATCTCTTTC 102121 - i vi i v i v vi C HERVIP10FH#LT 955 CT-CTCTCTCTGACTCCCTCTTTGTCTCTCTGTCTCTTCCTCTCTCTGCC 907 chr6qtel1M 102122 TCTCTCTCTCTGTCTCTGTCTCTCTTTCCCTCTGTCTCTCTCTCTCTCTC 102171 v vv vi i v i v i C HERVIP10FH#LT 906 TCTCTCTCTCTTTGACTCCCTCTTTGTCTCTCTCTCTCCCTCTCTCTCTC 857 chr6qtel1M 102172 TAACTCTCTCTCTCACTCTTTCTCTCTATGTATCAGTCTACCTCTGCCT- 102220 --i v i v v v vv - i vi - C HERVIP10FH#LT 856 T--TTCTCTCTCTCTCTCTTCCTCTCTCTCTCTCTCTCT-CTTCTCTCTT 810 chr6qtel1M 102221 --CTCTCTGTCTTTGTTTCCCTCTCTCT 102246 -- iivv v vi C HERVIP10FH#LT 809 TCCTCTCTGCTGGTCTTTCCCTGCCTCT 782 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 28.31 CpG sites = 22, Kimura (unadjusted) = 28.31 Transitions / transversions = 0.73 (22/30) Gap_init rate = 0.03 (6 / 224), avg. gap size = 1.17 (7 / 6) 282 18.79 3.16 4.81 chr6qtel1M 102033 102222 (897778) C HERVIP10FH#LTR/ERV1 (4134) 968 782 m_b300s701i1 12582 chr6qtel1M 102033 TCTCTGTCCGTCTCTGTATATCTG--TCTCTCTGTATCTCTCTGCTTTCT 102080 i iv v v v -- i v i --- C HERVIP10FH#LT 968 TTTCTGTCTCTCTCTCTCTCTCTGACTCCCTCTTTGTCTCTCTG---TCT 922 chr6qtel1M 102081 CTGTTTCTCTCTGTGTCTCTCTGTCTCTCCCTATCTCTTTCTCTCTCTCT 102130 vii iv v i vv vi v C HERVIP10FH#LT 921 CTTCCTCTCTCTGCCTCTCTCTCTCTTTGACTCCCTCTTTGTCTCTCTCT 872 chr6qtel1M 102131 CTGTCTCTGTCTCTCTTTCCCTCTGTCTCTCT----CTCTCTCTCTAACT 102176 vi v i v ---- -- C HERVIP10FH#LT 871 CTCCCTCTCTCTCTCTTTCTCTCTCTCTCTCTTCCTCTCTCTCTCT--CT 824 chr6qtel1M 102177 CTCTCTCTCACTCTTTCTCTCTATGTATCAGTCTACCTCTGCCTCT 102222 - v - v --iii vi i C HERVIP10FH#LT 823 CTCTCT-TCTCTCTTTC-CTCTCTG--CTGGTCTTTCCCTGCCTCT 782 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 21.71 CpG sites = 16, Kimura (unadjusted) = 21.71 Transitions / transversions = 0.89 (16/18) Gap_init rate = 0.06 (11 / 189), avg. gap size = 1.36 (15 / 11) 288 22.36 0.00 2.79 chr6qtel1M 102065 102248 (897752) C HERVIP10FH#LTR/ERV1 (4106) 996 818 m_b300s701i2 12582 chr6qtel1M 102065 TATCTCTCTGCTTTCTCTGTTTCTCTCTGTGTCTCTCTGTCTCTCCCTAT 102114 - ---- v v i i v C HERVIP10FH#LT 996 TATCTCTCT-CTTTCT----TTCTCTCTTTGACTTTCTGTCTCTCTCTCT 952 chr6qtel1M 102115 CTCTTTCTCTCTCTCTCTGTCTCTGTCTCTCTTTCCCTCTGTCTCTCTCT 102164 i vv i i v v i i v vi C HERVIP10FH#LT 951 CTCTCTGACTCCCTCTTTGTCTCTCTGTCTCTTCCTCTCTCTGCCTCTCT 902 chr6qtel1M 102165 CTCTCTCTAACTCTCTCTCTCACTCTTTCTCTCTATGTATCAGTCTACCT 102214 i i i i vv i iv v v vv vi C HERVIP10FH#LT 901 CTCTCTTTGACTCCCTCTTTGTCTCTCTCTCTCCCTCTCTCTCTCTTTCT 852 chr6qtel1M 102215 CTGCCTCTCTCTGTCTTTGTTTCCCTCTCTCTCT 102248 vi vi i v i i C HERVIP10FH#LT 851 CTCTCTCTCTCTTCCTCTCTCTCTCTCTCTCTCT 818 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 26.74 CpG sites = 20, Kimura (unadjusted) = 26.74 Transitions / transversions = 1.00 (20/20) Gap_init rate = 0.03 (5 / 183), avg. gap size = 1.00 (5 / 5) 15 19.85 0.00 0.00 chr6qtel1M 103924 103952 (896048) (T)n#Simple_repeat 1 29 (0) m_b300s252i17 12583 chr6qtel1M 103924 TTTTCTATTTTTTTTTTTTTTACTTTCTT 103952 i v vi i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 15 30.59 1.67 0.00 chr6qtel1M 104346 104405 (895595) (TTTCT)n#Simple_repeat 1 61 (0) m_b300s252i18 12584 chr6qtel1M 104346 TTTATTTTGTTTTCTGCTGTGTACTTTTTATTTTATTTCTCTCCTTTTC- 104394 v v vi v v v iv iv i i - (TTTCT)n#Simp 1 TTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCT 50 chr6qtel1M 104395 TTCCCTTTCTT 104405 i i (TTTCT)n#Simp 51 TTTCTTTTCTT 61 Matrix = Unknown Transitions / transversions = 0.88 (7/8) Gap_init rate = 0.02 (1 / 59), avg. gap size = 1.00 (1 / 1) 67 2.67 2.56 1.27 chr6qtel1M 104429 104506 (895494) (TA)n#Simple_repeat 1 79 (0) c_b300s251i8 12585 chr6qtel1M 104429 TATATATATATATATATATATATATATATA-ATGTATGA-ATATATATAT 104476 - i - - (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATAT-ATATATATATAT 49 chr6qtel1M 104477 ATATAAATATATATATATATATATATATAT 104506 v (TA)n#Simple_ 50 ATATATATATATATATATATATATATATAT 79 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (3 / 77), avg. gap size = 1.00 (3 / 3) 25 20.46 5.83 3.81 chr6qtel1M 104938 104999 (895001) (TCTGTC)n#Simple_repeat 1 64 (41) m_b300s252i19 12586 chr6qtel1M 104938 TCTTTCTTTCTCTCTGT-T-GGTCTCTGTCAATTTGTCTG--TCTGTCTC 104983 v i v - -v vv v v -- (TCTGTC)n#Sim 1 TCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTC 50 chr6qtel1M 104984 TGTCTCTGTATCTCGG 104999 -- v (TCTGTC)n#Sim 51 TGTCTCTG--TCTCTG 64 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.08 (5 / 61), avg. gap size = 1.20 (6 / 5) 93 3.20 1.04 0.00 chr6qtel1M 105000 105095 (894905) (TC)n#Simple_repeat 1 97 (0) c_b300s251i9 12587 chr6qtel1M 105000 TCTCTCTCTGTCTCTCTCTCTCTCT-TCTCTCTCTCTCTCTCTCTCTCTC 105048 v - (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr6qtel1M 105049 TCTCTCTTTCTCTCTCTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 105095 i i (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 97 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.01 (1 / 95), avg. gap size = 1.00 (1 / 1) 25 20.46 5.83 3.81 chr6qtel1M 105096 105135 (894865) (TCTGTC)n#Simple_repeat 65 105 (0) m_b300s252i19 12588 chr6qtel1M 105096 TTCTATGTGTGTGTGTCTGCCTCT-T-TGTGTCTGTTTCTCT 105135 - v v v v i - - v v v (TCTGTC)n#Sim 65 -TCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCT 105 Matrix = Unknown Transitions / transversions = 0.14 (1/7) Gap_init rate = 0.08 (3 / 39), avg. gap size = 1.00 (3 / 3) 21 27.44 4.31 3.42 chr6qtel1M 108559 108674 (891326) (TTTATA)n#Simple_repeat 1 117 (0) m_b300s252i20 12589 chr6qtel1M 108559 TTTCTATTCTTATCTTAT-TAAATATTT-TCTCTAAATTCAAATTCAAAA 108606 v iv - - vv - v i v i v i v v (TTTATA)n#Sim 1 TTTATATTTATAT-TTATATTTATATTTATATTTATATTTATATTTATAT 49 chr6qtel1M 108607 AATTACTTATATTTATAATTATACATTTATATTGCAT-CTTATATACATA 108655 vvv i - - i -i -i vi (TTTATA)n#Sim 50 TTATATTTATATTTAT-ATT-TATATTTATATT-TATATTTATATTTATA 96 chr6qtel1M 108656 GGTATATTT-TA-ATATATTT 108674 vv - -v (TTTATA)n#Sim 97 TTTATATTTATATTTATATTT 117 Matrix = Unknown Transitions / transversions = 0.56 (9/16) Gap_init rate = 0.08 (9 / 115), avg. gap size = 1.00 (9 / 9) 12 11.95 0.00 6.90 chr6qtel1M 108779 108809 (891191) (AAATT)n#Simple_repeat 1 29 (0) m_b300s252i21 12590 chr6qtel1M 108779 AATTTAAGTTAAAGATATAATTAAATTAAAT 108809 v i -v - (AAATT)n#Simp 1 AAATTAAATTAAA-TTA-AATTAAATTAAAT 29 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2) 14 0.00 0.00 0.00 chr6qtel1M 109191 109208 (890792) (AAT)n#Simple_repeat 1 18 (0) m_b300s252i22 12591 chr6qtel1M 109191 AATAATAATAATAATAAT 109208 (AAT)n#Simple 1 AATAATAATAATAATAAT 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 15 5.48 0.00 0.00 chr6qtel1M 113284 113302 (886698) (T)n#Simple_repeat 1 19 (0) m_b301s252i0 12592 chr6qtel1M 113284 TTTTTTTTTTTATTTTTTT 113302 v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 14 22.42 0.00 9.68 chr6qtel1M 114212 114279 (885721) (TTTTTAA)n#Simple_repeat 1 62 (0) m_b301s252i1 12593 chr6qtel1M 114212 TTTTTAATTTTAAAATTTTTTATTCAACCCAATTTTTTCTGTTTGAATTT 114261 -v v ---iii vv - v (TTTTTAA)n#Si 1 TTTTTAATTTT-TAATTTTTAATT---TTTAATTTTTAAT-TTTTAATTT 45 chr6qtel1M 114262 TAGAATGCTTAATTTTTA 114279 -v vi (TTTTTAA)n#Si 46 T-TAATTTTTAATTTTTA 62 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.09 (6 / 67), avg. gap size = 1.00 (6 / 6) 17 12.69 0.00 0.00 chr6qtel1M 115123 115148 (884852) (A)n#Simple_repeat 1 26 (0) m_b301s252i3 12594 chr6qtel1M 115123 AAATAAAACAAAACAAAAAAAAAAAA 115148 v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAA 26 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 47 19.66 5.62 3.05 chr6qtel1M 115730 115889 (884111) (TCTGTC)n#Simple_repeat 1 164 (0) m_b301s252i4 12595 chr6qtel1M 115730 TCTCTCTCAATCTCTGTCTATGTTCTCTGTGT-T-TCTCTG-CCCCCCCT 115776 v vi v - v - - - i ivi (TCTGTC)n#Sim 1 TCTGTCTCTGTCTCTGTCTCTG-TCTCTGTCTCTGTCTCTGTCTCTGTCT 49 chr6qtel1M 115777 CTCTCTCTCTCTCT-TTTGTGTGTGTGTGTGTGTCTTCTGTCTCTGTCT- 115824 v v - i v v v v v - - (TCTGTC)n#Sim 50 CTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTC-TCTGTCTCTGTCTC 98 chr6qtel1M 115825 TTTCTCTGTGTCTCACTCT-T-TCTCTCTGTGTGTCTGTCTGCCTGTC-G 115871 v v vv - - v v v -- -v (TCTGTC)n#Sim 99 TGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCT--CTGTCTC 146 chr6qtel1M 115872 TTTCTCTTGTCTCT-TCTC 115889 v - - (TCTGTC)n#Sim 147 TGTCTC-TGTCTCTGTCTC 164 Matrix = Unknown Transitions / transversions = 0.24 (5/21) Gap_init rate = 0.09 (14 / 159), avg. gap size = 1.00 (14 / 14) 45 27.19 4.22 1.17 chr6qtel1M 115730 115895 (884105) (TC)n#Simple_repeat 1 171 (0) m_b301s252i5 12596 chr6qtel1M 115730 TCTCTCTCAATCTCTGTCTATGT-TCTCTGTGTTTCTCTGCCCCCCCTCT 115778 vv v v v - v v i - i i i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT-CTCTCTCTCT 49 chr6qtel1M 115779 CTCTCTCTCTCT-TTTGTGTGTGTGTGTGTGTCT-TCTGTCTCTGTCT-T 115825 - i v v v v v v v v - v v - (TC)n#Simple_ 50 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 99 chr6qtel1M 115826 TTCTCTGTGTCTCACTCTTTCTCTCTGTGTGTCTGTCTGCCTGTCGTTTC 115875 i v v v i v v v v vi v - i (TC)n#Simple_ 100 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TCTC 148 chr6qtel1M 115876 TCT-TGTCTCT-TCTC-CCCTCT 115895 - v - - i (TC)n#Simple_ 149 TCTCTCTCTCTCTCTCTCTCTCT 171 Matrix = Unknown Transitions / transversions = 0.37 (10/27) Gap_init rate = 0.05 (9 / 165), avg. gap size = 1.00 (9 / 9) 17 23.74 0.00 2.00 chr6qtel1M 116422 116472 (883528) (ACCC)n#Simple_repeat 1 50 (0) m_b301s252i6 12597 chr6qtel1M 116422 ACCCATCCACCCACCCCCCCACCCCCTTCACACACACAGACATCCACACA 116471 i v v -i v v vv i v (ACCC)n#Simpl 1 ACCCACCCACCCACCCACCCACCCAC-CCACCCACCCACCCACCCACCCA 49 chr6qtel1M 116472 C 116472 (ACCC)n#Simpl 50 C 50 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.02 (1 / 50), avg. gap size = 1.00 (1 / 1) 15 13.67 0.00 0.00 chr6qtel1M 116450 116473 (883527) (CA)n#Simple_repeat 1 24 (0) m_b301s252i7 12598 chr6qtel1M 116450 CACACACACAGACATCCACACACA 116473 v iv (CA)n#Simple_ 1 CACACACACACACACACACACACA 24 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 18 4.77 0.00 0.00 chr6qtel1M 116773 116794 (883206) (A)n#Simple_repeat 1 22 (0) m_b301s252i8 12599 chr6qtel1M 116773 AAAGAAAAAAAAAAAAAAAAAA 116794 i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAA 22 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 21 21.39 0.00 0.00 chr6qtel1M 116982 117024 (882976) (A)n#Simple_repeat 1 43 (0) m_b301s252i9 12600 chr6qtel1M 116982 AAAACAAAAAAAAAAAAAATGAAACAATGAAGAAAAAAAACAA 117024 v vi v vi i v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 43 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 13 22.82 0.00 4.65 chr6qtel1M 117779 117823 (882177) (AAAGG)n#Simple_repeat 1 43 (0) m_b301s252i10 12601 chr6qtel1M 117779 AATGGAAGGAAAAGTGAAAAGGGAAGGAATAGCAAGGGAAGGAAA 117823 v i i - - i vi v i (AAAGG)n#Simp 1 AAAGGAAAGGAAAG-G-AAAGGAAAGGAAAGGAAAGGAAAGGAAA 43 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.05 (2 / 44), avg. gap size = 1.00 (2 / 2) 1336 29.71 5.42 3.48 chr6qtel1M 118235 119618 (880382) L1M5_orf2#LINE/L1 325 1734 (1560) m_b301s551i0 12602 chr6qtel1M 118235 ATATCAATATTAAAAATATATGCACCAAGTGTGAAAGG---GAAATT--T 118279 v vi vi i v i ivv i v---i v-- L1M5_orf2#LIN 325 ATAACAATCCTAAATGTGTATGCACCTAATAACAGAGCTTCAAAATACAT 374 chr6qtel1M 118280 TAAAAAGAAATTAAGAGAACTGCAAGAAGATATAGACTGCAAA-CCACAA 118328 v iv i i i v iv i v --- - L1M5_orf2#LIN 375 GAAGCAAAAACTGACAGAACTAAAAGGAGAAATAGAC---AAATCCACAA 421 chr6qtel1M 118329 T---AGTGGGAGATCTCAACCTTGCAC-CTCAGCATTAGATAAATCAAAC 118374 --- ? i i vi?v v - i v v i v i- L1M5_orf2#LIN 422 TTATAGTNGGAGATTTTAACACNCCTCTCTCAGTAATTGATAGAACAAG- 470 chr6qtel1M 118375 TACAAAATAAATAAGAAAGAA-GTCAAAGAGATAAATAGAATACTAGAAA 118423 v v v v v i -i vi vv i i -- i vv L1M5_orf2#LIN 471 TAGACAAAAAATCAGTAAGGATATAGAAGATTTGAACA--ACACTATCAA 518 chr6qtel1M 118424 --AGTTAGATAGGATACATCTTTGGAGAAAACTAAAT--AGAGACAGACA 118469 -- ii v ivvi vv iv iv v ?v i-- ivi ? - L1M5_orf2#LIN 519 CCAACTTGACCTAATTGACATTTATAGAACACTNCACCCAACAACNG-CA 567 chr6qtel1M 118470 GAGTACATGTTCTTCT--AGCAGTTCATGGAACCTATAC-AAAATTGACC 118516 i ii i -- i- iv v v - i v L1M5_orf2#LIN 568 GAATACACATTCTTTTCAAGT-GCACATGGAACATTTACCAAGATAGACC 616 chr6qtel1M 118517 ATAT--TAGGACATAAAA---ACCTCAA---ACTCAAA-----TGCAGTA 118553 -- i v ---ii --- i i? ----- v i v L1M5_orf2#LIN 617 ATATNCTGGGCCATAAAACAAGTCTCAATAAATTTNAAAGGATTGAAATC 666 chr6qtel1M 118554 ATGCAGAAATAGTAAATGCATCCTTTTCAGACCACGATGCAATGAAAATT 118603 i ---- -- ----- i v i v v v v L1M5_orf2#LIN 667 ATACAGA----GTA--TG-----TTCTCTGACCACAATGGAATTAAATTA 705 chr6qtel1M 118604 ACAGTCAATAA-------ATAGCTCAGGAAAATAAACCAAAAAATAATTG 118646 iv i ------- ? --i vv- --- v L1M5_orf2#LIN 706 GAAATCAATAACAAAAAGATANCT--AGAAAATCC-CCAAA---TATTTG 749 chr6qtel1M 118647 -AAACTAAATAATTCA-TACTAAAGAATGTGTGGG-GAAACAGCAAATTG 118693 - i i iv - v v ivii -v v iv ii L1M5_orf2#LIN 750 GAAATTAAACAACACACTTCTAAATAACCCATGGGTCAAAGAAGAAATCA 799 chr6qtel1M 118694 TTGACATAATTAATAACTTCACCCAAGAAAATGACAATAATGAGACATCA 118743 ivi?viv iv v viviiv vvi ? i vi v v L1M5_orf2#LIN 800 CAANGGAAATTAGAAAATATTTTGAACTGAATGANAATGAAAATACAACA 849 chr6qtel1M 118744 TACCAAAATGTGTGG-ATTTAGCAAAAGCAGTAAT--AAGGGAAATTTTA 118790 i v - vi v iv --i - L1M5_orf2#LIN 850 TATCAAAATTTGTGGGATGCAGCTAAAGCAGTGCTTAGAGGGAAATTT-A 898 chr6qtel1M 118791 TATCTCTAGAGGTCTACTTGTATAAAATAGAGAAAGAG--AGAGTCAAAG 118838 v ?i i v i? iv - v v - iv-- i i v L1M5_orf2#LIN 899 TAGCNTTAAATGCNTATAT-TAGAAAAGA-AGAAAGGCTTAAAATCAATG 946 chr6qtel1M 118839 AATTAGGGTTACAGATTAA-AAGCTATAAAAAGAA---CAAATTAAA--- 118881 vi i v v vv - v --- --- L1M5_orf2#LIN 947 ATCTAAGCTTCCACCTTAAGAAGCTAGAAAAAGAAGAGCAAATTAAACCC 996 chr6qtel1M 118882 -AAACACCAGTCAAACATTAACTTGAAATTTTAAAAATAAAAGAAGAGAT 118930 - i? -- vi vi-- v-- vv i i v i L1M5_orf2#LIN 997 AAAGNA--AGTAGAAGG--AAG--GAAATAATAAAGATAAGAGCAGAAAT 1040 chr6qtel1M 118931 TAATAAAATTGAAAGTAAAAAAAACTATTGAATTAAT-AATAAACTTAAA 118979 i i v ii ? ? - v v ivv - ii vii L1M5_orf2#LIN 1041 CAATGAAATAGAAAACAAANANA-CAATAGAGAAAATCAACGAAGCCAAA 1089 chr6qtel1M 118980 AGTTGGTTTTGTGAAAACCAACAACAAAATATATATATATATACCTTCAG 119029 i i v v- v i ----- i- v ii L1M5_orf2#LIN 1090 AGCTGGTTCTTTGAAAAG-ATCAATAAAAT-----TG-ATAAACCTCTAG 1132 chr6qtel1M 119030 TAAATGTGATTTAAAAGGAAAGAG-GAAAAT-TAAATTGTTAGTCTTAAA 119077 i? ivv iv i ii - i i-i iii i v i ii L1M5_orf2#LIN 1133 CNAGACTGATCAAGAAAAAAAGAGAGAAGACACAAATTACCAATATCAGG 1182 chr6qtel1M 119078 AATGAGAAAGGAGAGGTCGCCACTAATGAAAAAGAAAATTAGAGCAATAA 119127 i vi i i vi vvv v v - i ivi L1M5_orf2#LIN 1183 AATGAAAAAGGAGACATCACTACAGATCCTACAGACA-TTAAAAGGATAA 1231 chr6qtel1M 119128 TTAGGAGTTACTTTGTCCAGCTTTATGCAAATAAATCAGATAA-----AT 119172 v iiiv i v vv i v iv ? ----- L1M5_orf2#LIN 1232 TAAGAGAATATTATGAACAACTTTATGCCAATAAATTTGANAACTTAGAT 1281 chr6qtel1M 119173 GAAATGGAAGAATATCTTCAAAAATATAGCTTACCCAAATTAACAGAGGA 119222 vi vi v i i i? v i i ?v i L1M5_orf2#LIN 1282 GAAATGGACAAATTCCTTGAAAAACACAANTTACCAAAACTGACNCAAGA 1331 chr6qtel1M 119223 AGAGGTAAATGGT-TAAACAATACCATTTTAGAAAAAGAAACAGAACAAG 119271 ii i vii - i i iiv i v ivivv iv ivv L1M5_orf2#LIN 1332 AGAAATAGAAAATCTGAATAGCCCTATATCTATTAAAGAAATTGAATTTG 1381 chr6qtel1M 119272 CTATTACTCAACTCTCT----AAGAAAAATCCATAGAACCAGATGGAGTT 119317 iv v-v ii i---- v -- iv vv i L1M5_orf2#LIN 1382 TAATTAA-AAACCTTCCCACAAAGAAAACTCCA--GGCCCAGATGGCTTC 1428 chr6qtel1M 119318 GC-AGTGAATTCTACCAAATATTTAAAGAA----TTACCTCAGTGCTTAT 119362 i -i i i ---- v ivi i - i L1M5_orf2#LIN 1429 ACTGGTGAATTCTACCAAACATTTAAGGAAGAAATAATACCAAT-CTTAC 1477 chr6qtel1M 119363 ATAAACTATTTTTAAAAAATAGGGATTTAAGGAGTCCTATCAAATTCCTT 119412 i -i ii i ii vvv i iiv vi v i v L1M5_orf2#LIN 1478 ACAAACT-CTTCCAGAAAATAGAAAAAGAGGGAACACTTCCCAACTCATT 1526 chr6qtel1M 119413 TCATGAC-CCAGACATGGTA-TGATACCTAAACCAGGTAGGGTGAA-ACA 119459 i v- - ?iiv- v ? ii ii vv v- L1M5_orf2#LIN 1527 TTATGAGGCCAG-CATNACCCTGATACCAAAACCNGACAAAGACATTACA 1575 chr6qtel1M 119460 GAGAAAGAAAATTATAGACCAATCTTCCTAATAAATATTGATTCTAAAAT 119509 iii i v i v i i v v v L1M5_orf2#LIN 1576 AGAAAAGAAAATTACAGACCAATATCCCTCATGAACATAGATGCAAAAAT 1625 chr6qtel1M 119510 CATAAATACAATATTAGCAAAAAGATTAGAGAAAATCATCACCAGGATAA 119559 v ? i v vv v vv v vvi v vv L1M5_orf2#LIN 1626 CCTNAACAAAATATTAGCAAATCGAATCCAGCAATATATAAAAAGGATAA 1675 chr6qtel1M 119560 TACACTATGACCAAGTAAATTTTATACCAAGAATGTAGGGCTGATTCAAT 119609 ii iiiv v i i i i i i i L1M5_orf2#LIN 1676 TACATCATGACCAAGTGGGGTTTATCCCAGGAATGCAAGGTTGGTTTAAC 1725 chr6qtel1M 119610 ATTAGGAAA 119618 v i L1M5_orf2#LIN 1726 ATTCGAAAA 1734 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 39.24 CpG sites = 213, Kimura (unadjusted) = 39.38 Transitions / transversions = 1.16 (213/184) Gap_init rate = 0.06 (85 / 1383), avg. gap size = 1.46 (124 / 85) 12 8.12 0.00 10.34 chr6qtel1M 119665 119696 (880304) (TTTTG)n#Simple_repeat 1 29 (0) m_b301s252i11 12603 chr6qtel1M 119665 TTTTGTTTCTCTTCCGTGTTTTGTTTTGTTTT 119696 - v --v (TTTTG)n#Simp 1 TTTTGTTT-TGTT--TTGTTTTGTTTTGTTTT 29 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.10 (3 / 31), avg. gap size = 1.00 (3 / 3) 18 18.13 0.00 0.00 chr6qtel1M 121111 121142 (878858) (T)n#Simple_repeat 1 32 (0) m_b301s252i12 12604 chr6qtel1M 121111 TTTTCTTTTTTTTTTTTTCTTTTTACTTTCTT 121142 i i vi i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 32 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 453 23.77 3.17 3.17 chr6qtel1M 122291 122416 (877584) MIRc#SINE/MIR 2 127 (141) m_b301s601i0 12605 chr6qtel1M 122291 GAGCTAG-ATGGCTCAGTGGAGAGA--AGTGCCCCTGAAGTCAGGAGGAT 122337 vi -i iv i -- v vv i i i i MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr6qtel1M 122338 CTAAGTTCAAATCCAGCCTCATTTAATAGTTACTAGATTTGTGACCCTGG 122387 ii i i v v --- ivi v v v i MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTC---TGCCACTTACTAGCTGTGTGACCTTGG 98 chr6qtel1M 122388 GCAAAGTCATTTAACTTCACTG-GCCTCAG 122416 - i i v - MIRc#SINE/MIR 99 GC-AAGTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 27.97 CpG sites = 17, Kimura (unadjusted) = 29.14 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.06 (7 / 125), avg. gap size = 1.14 (8 / 7) 253 30.73 6.83 2.99 chr6qtel1M 122632 122792 (877208) MIR3#SINE/MIR 19 185 (23) m_b301s601i1 12606 chr6qtel1M 122632 AGAGAGGGAGTTAAATAGCTGGCAGG-GACCAGAGTTATTGAAACTCAGC 122680 i viivi v i vv v - v i v -- iv i i MIR3#SINE/MIR 19 AGAGAGAGCACGGACTGGGAGTCAGGAGACCTGGGTTCT--AGTCCCGGC 66 chr6qtel1M 122681 CC---CAATAACTT--TGTTTGCCTGTGAAAAAATCACA-CAGTTCCCTT 122724 i --- v ?-- v v iv iiv i v- vi i v MIR3#SINE/MIR 67 TCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTG 116 chr6qtel1M 122725 GGCCTCACCTGTTACCTCACCTGTAAAATGGGTGTTTTGGTC-AACT--T 122771 --- v i i v vv v - iv -- MIR3#SINE/MIR 117 GGCCTCA---GTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGAT 163 chr6qtel1M 122772 CTCTGACTTCCTTTATA-CTCT 122792 i vv i vi - MIR3#SINE/MIR 164 CTCTAAGGTCCCTTCCAGCTCT 185 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 38.18 CpG sites = 22, Kimura (unadjusted) = 40.26 Transitions / transversions = 0.85 (22/26) Gap_init rate = 0.07 (12 / 160), avg. gap size = 1.33 (16 / 12) 29 14.20 0.00 0.00 chr6qtel1M 123491 123537 (876463) (GT)n#Simple_repeat 1 47 (0) m_b301s252i13 12607 chr6qtel1M 123491 GTGTGTGTGAGTGTGTGTGAGTTTGTGTGTGTTTGAGGGTGTGTGTG 123537 v v v v v v (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 47 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 15 16.57 4.88 0.00 chr6qtel1M 124266 124306 (875694) (ATTCAGA)n#Simple_repeat 1 43 (0) m_b301s252i14 12608 chr6qtel1M 124266 ATTCAGAAGTCAGTATTCAGTA-TGAG-ATTCACAAGTCAGAA 124306 v v v - v - v v (ATTCAGA)n#Si 1 ATTCAGAATTCAGAATTCAGAATTCAGAATTCAGAATTCAGAA 43 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 13 20.58 0.00 8.33 chr6qtel1M 127174 127225 (872775) (TTTTTAC)n#Simple_repeat 1 48 (0) m_b301s252i15 12609 chr6qtel1M 127174 TTTGTTCTTTTATACTTTTTACTAATTTCCTTTTCTGATTTTTTGATTGT 127223 v v - -v v - - i iv v (TTTTTAC)n#Si 1 TTTTTACTTTT-TACTTTTTACT-TTTTACTTTT-T-ACTTTTTACTTTT 46 chr6qtel1M 127224 TA 127225 (TTTTTAC)n#Si 47 TA 48 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.08 (4 / 51), avg. gap size = 1.00 (4 / 4) 69 22.93 1.78 0.58 chr6qtel1M 128059 128227 (871773) (TC)n#Simple_repeat 1 171 (0) m_b301s252i16 12610 chr6qtel1M 128059 TCTTTCTCTCTGTCAGTTTCTGTCTATGTCTCTCTGTGTTTCTCTGTGTC 128108 i v vv i v v v v v i v v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr6qtel1M 128109 TCTGTCTC-CTCTACTCTCTATCTC-CTTCCTCTCTCTCTCTCTCTGTCT 128156 v - - v - ii v (TC)n#Simple_ 51 TCTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 99 chr6qtel1M 128157 CACTCTTTCTCTCTATGTGTCTGTCTGCCTCTCTGCCTCTCTGTTTCTCT 128206 v i v v v v vi vi v i (TC)n#Simple_ 100 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 149 chr6qtel1M 128207 GTGTCTCTGTCTCTCTC-CTCT 128227 v v v - (TC)n#Simple_ 150 CTCTCTCTCTCTCTCTCTCTCT 171 Matrix = Unknown Transitions / transversions = 0.38 (9/24) Gap_init rate = 0.02 (4 / 168), avg. gap size = 1.00 (4 / 4) 22 0.00 0.00 0.00 chr6qtel1M 128833 128856 (871144) (CA)n#Simple_repeat 1 24 (0) m_b301s252i17 12611 chr6qtel1M 128833 CACACACACACACACACACACACA 128856 (CA)n#Simple_ 1 CACACACACACACACACACACACA 24 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 23 7.03 0.00 0.00 chr6qtel1M 129413 129442 (870558) (A)n#Simple_repeat 1 30 (0) m_b301s252i18 12612 chr6qtel1M 129413 AAAACCAAAAAAAAAAAAAAAAAAAAAAAA 129442 vv (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 30 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 12 18.36 5.41 0.00 chr6qtel1M 130296 130332 (869668) (AAAGGAG)n#Simple_repeat 1 39 (0) m_b301s252i19 12613 chr6qtel1M 130296 AAAGCAG-AAGGGGAAAAGTGAAAAG-GAAAGGAGTAAG 130332 v - i i v i - v (AAAGGAG)n#Si 1 AAAGGAGAAAGGAGAAAGGAGAAAGGAGAAAGGAGAAAG 39 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 285 27.49 6.77 1.49 chr6qtel1M 130462 130653 (869347) L1MEh_5end#LINE/L1 2033 2234 (1) m_b301s551i1 12614 chr6qtel1M 130462 AAGGGATAAGGAGGAAGGAAGAGAGAAAGTATAAATAGGGGT----TATC 130507 i v i? i i i v vi v i iiiv---- vi L1MEh_5end#LI 2033 AAGGAAAAAANAGAAAGAAAAACAGATGGGACAAATAGAAAACAAATAAT 2082 chr6qtel1M 130508 AAGTTGGCA--AGTAA----TAGCAAACTGGTAATTTTAACCATAAATGT 130551 v -- i ----? ii v ?ii --- v L1MEh_5end#LI 2083 AAGATGGCAGAAATAAGTCCNAATATANCAGTAATT---ACAATAAATGT 2129 chr6qtel1M 130552 GAATGGGGTAAACTGCCCCATAGAGAGGAAGTGGTTA-GAGAATGGATTA 130600 i v vv v vi i iv v i ?-v v ? L1MEh_5end#LI 2130 AAATGGGTTAAACTCACCAATTAAAAGACAGAGATTNTCAGATTGGATTN 2179 chr6qtel1M 130601 AAAGCCAGAATCCTGCAATATGTTGTTGACAGGAAACACACCTGAAGC-- 130648 iv i vi i iv i i i i i -- L1MEh_5end#LI 2180 AAAAACAAAATCCAACAATATGCTGTCTACAAGAGACACACTTAAAACAN 2229 chr6qtel1M 130649 AAGGA 130653 L1MEh_5end#LI 2230 AAGGA 2234 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.47 CpG sites = 31, Kimura (unadjusted) = 36.47 Transitions / transversions = 1.48 (31/21) Gap_init rate = 0.04 (8 / 191), avg. gap size = 2.00 (16 / 8) 349 26.35 3.31 1.96 chr6qtel1M 130508 130658 (869342) L1M6_5end#LINE/L1 2363 2515 (0) m_b301s551i2 12614 chr6qtel1M 130508 AAGTTGGCAAG--TAATAGCAAAC-TGGTAATTTTAACCATAAATGTGAA 130554 v i i-- v v - ivi i v i v i L1M6_5end#LIN 2363 AAGATGACAAANATAAGACCAAACATATCAGTTATGACAATAAATGTAAA 2412 chr6qtel1M 130555 TGGGGTAAACTGCCCCAT--AGAGAGGAAGTGGTTAGAGAATGGATTAAA 130602 v v i -- i vi -iv ivv v i L1M6_5end#LIN 2413 TGGGTTAAACTCCCCTATTAAAAGACAAAG-ACTCTCAGATTGGGTTAAA 2461 chr6qtel1M 130603 AGCCAGAATCCTGCAATATGTTGTTGACAGGAAACACACCTGAAGCAAGG 130652 iv i vi v i v i i i vv -- L1M6_5end#LIN 2462 AAACAAAATCCAACTATATGCTGTTTACAAGAGACACACCTAAATAAA-- 2509 chr6qtel1M 130653 AGATAC 130658 L1M6_5end#LIN 2510 AGATAC 2515 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 32.85 CpG sites = 20, Kimura (unadjusted) = 32.85 Transitions / transversions = 1.05 (20/19) Gap_init rate = 0.04 (6 / 150), avg. gap size = 1.33 (8 / 6) 952 29.57 5.60 4.52 chr6qtel1M 130539 131413 (868587) L1M2_orf2#LINE/L1 32 915 (2376) m_b301s551i3 12614 chr6qtel1M 130539 TAACCATAAATGTGAATGGGGTAAACTGCCCCAT----AGAGAGGAAGTG 130584 v i i iv i vi v ---- v vii ? L1M2_orf2#LIN 32 TAACCTTGAATGTAAATGGATTAAATTCTCCAATTAAAAGACATAGANTG 81 chr6qtel1M 130585 GTTAGAGAATGGATTAAAAGCCAGAATCCTGCAATATGTTGTTGACAGGA 130634 i --- v iv ii i vi v i iiv i L1M2_orf2#LIN 82 GCT---GAATGGATAAAAAAACAAGACCCAACTATATGCTGCCTACAAGA 128 chr6qtel1M 130635 AACACACCTGAA--GCAAGGAGATACATGCAGAATAAAGGTAAAAGGTTG 130682 v i v v-- i i v i -- v i i i i v L1M2_orf2#LIN 129 AACTCACTTCACCTGTAAAGACACACAT--AGACTGAAAGTGAAGGGATG 176 chr6qtel1M 130683 AAGCAGAATCTACCATGCTCAGGTGAAGTCAAAA---AGCAGG-GTAGC- 130727 i iv ii v v vv v - ii --- - - L1M2_orf2#LIN 177 GAAAAAGATATTCCATGCAAACG-GAAACCAAAAGNGAGCAGGAGTAGCT 225 chr6qtel1M 130728 ATCCTGATCTCAGATCAAGCAAA-----AGC--AAAATTGATCTAATTAA 130770 v v v v ii i ----- i-- i --- --- L1M2_orf2#LIN 226 ATACTTATATCAGATAAAATAGACTTTAAGTCAAAAACTG---TAA---A 269 chr6qtel1M 130771 AAGAGATAAGGAAGGGCACTATATCTTGCTAAAGGG-------TAGCATA 130813 i i v i vv v -------i - L1M2_orf2#LIN 270 AAGAGACAAAGAAGGTCATTATATAATGATAAAGGGGTCAATTCAGCA-A 318 chr6qtel1M 130814 GATAATCAAGCAATATCAATATTAAACATATATGCACCAAGTAGTGTGGC 130863 vi ------ v v? i v ii vi vi L1M2_orf2#LIN 319 GAGGAT------ATAACAATTNTAAATATATATGCACCCAACACCGGAGC 362 chr6qtel1M 130864 AAGTAAATTCTTAAAAGAGAAATTAAGAGAGCTGCAAGAAGATATAGACT 130913 vvi i viv iv i v ?v v iv i i v L1M2_orf2#LIN 363 ACCCAGATATATAAAGCAAATATTANTAGATCTAAAGGGAGAGATAGACT 412 chr6qtel1M 130914 GCAAAACCATAATAGTGGGAGAAGATCTCAACCTTGCACTCTCAGCATTA 130963 ? v v ? ---i ii viiv ? i L1M2_orf2#LIN 413 NCAATACAATAATAGTNGG---GGACTTCAACACCCCACTCTCAGCANTG 459 chr6qtel1M 130964 GATAAATCA---AACTACAAAATAAATAAGAAAAAGTCAAAGAGATAAAT 131010 i i --- ivi v v i ii vi --i vv i L1M2_orf2#LIN 460 GACAGATCATCCAGACAGAAAATCAACAAAGAAACATC--GGACTTAAAC 507 chr6qtel1M 131011 AGAATACTAGAAAAGTTAGATATGATACATCTTTG-AGAAAACT-----A 131054 v v iv? vv iv i iv i i v iv i- v i -----v L1M2_orf2#LIN 508 TGCACTNTAGACCAAATGGACCTAACAGACATTTACAGAACATTTCATCC 557 chr6qtel1M 131055 AATAGAGACAGAAAGGAGTACACTTTTTCTTCTCAGCAGTTCATGGAAC- 131103 i vvi ----- --v v iv - L1M2_orf2#LIN 558 AACAGCTGCAGAA-----TACAC--ATTCTTCTCATCAGCACATGGAACA 600 chr6qtel1M 131104 CTATACAAAATTGACCATATATTAGGACATAA---AAACCTCAAACTCAA 131150 i v v ii v i v i --- ii --- L1M2_orf2#LIN 601 TTCTCCAGGATAGACCATATGTTAGGCCACAAAACAAGTCTCAA---CAA 647 chr6qtel1M 131151 ATGCAGTAATGCAGAAATAGTA--AATGCATCCTTTTCAGACCACGATGC 131198 vi?iv viiv vi -- - i - ? i v L1M2_orf2#LIN 648 ATTTNAAAAAATCGAAATCATATCAA-GTAT-CTTTTCNGACCACAATGG 695 chr6qtel1M 131199 AATGAAAATTACAGTCAATAAATAGCCAGGGAAAAAT---AAACCA-AAA 131244 - i v --- v i v i i vv --- i?- v L1M2_orf2#LIN 696 AAT-AAAACTAGA---AATCAATAACAAGAGGAACTTTGGAAACTNTACA 741 chr6qtel1M 131245 AATA-ATTGAAACTAAATAATCTA-TACTAAAGAATGTGTGGG--AAACA 131290 - v i i iv i- v i vi ivvi -- vv L1M2_orf2#LIN 742 AATACATGGAAATTAAACAACATGCTCCTGAACGACCAATGGGTCAATGA 791 chr6qtel1M 131291 GCAAATTGTTGACATAATTAATAACTTCACCCAAGAAAATGACAATAATG 131340 iv ivvi viv ? v v iviiv iv v iivi L1M2_orf2#LIN 792 AGAAATTAAGAAGGAAATTNAAAAATTTCTTGAAACAAATGAAAATGGAA 841 chr6qtel1M 131341 AGACATCATA-CAAAATGTGTGGGATTTAGCCAAAGCAGTAATAAGGGGA 131389 v v - iv i vi v ?v i i L1M2_orf2#LIN 842 ACACAACATACCAAAACCTATGGGATACAGCAAAAGCAGTNCTAAGAGGG 891 chr6qtel1M 131390 AATTTTATATCTCTAGAGGTCTAC 131413 v v vv i v i L1M2_orf2#LIN 892 AAGTTTATAGCAATAAACGCCTAC 915 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 38.32 CpG sites = 127, Kimura (unadjusted) = 38.92 Transitions / transversions = 1.06 (127/120) Gap_init rate = 0.07 (60 / 874), avg. gap size = 1.48 (89 / 60) 1578 28.86 3.31 3.08 chr6qtel1M 131515 132390 (867610) L1M5_orf2#LINE/L1 857 1734 (1560) m_b301s551i4 12614 chr6qtel1M 131515 ATGTGTGGGATTTAGCCAAAGCAGTAATAAGGGGAAATTTTATATCTCTA 131564 v vi i iv v i i v v ?i L1M5_orf2#LIN 857 ATTTGTGGGATGCAGCTAAAGCAGTGCTTAGAGGGAAATTTATAGCNTTA 906 chr6qtel1M 131565 GAGGTCTACTTGCATAAAATAGAGAA--AGAGAGGGTCAAA------GAA 131606 i -------- ? v v i -- i v i ------ v L1M5_orf2#LIN 907 AA--------TGCNTATATTAGAAAAGAAGAAAGGCTTAAAATCAATGAT 948 chr6qtel1M 131607 TTAGGCTTACAGATTAAAAAGCTAGAAAAAAAAAA-CAAATTAAAAACA- 131654 i i v vv i i i - vv - L1M5_orf2#LIN 949 CTAAGCTTCCACCTTAAGAAGCTAGAAAAAGAAGAGCAAATTAAACCCAA 998 chr6qtel1M 131655 -CCCAGTCAAACATTAACTTGAAATTTTAAAAATAAAAGAAGAGATTAAT 131703 -v?v vi vi-- v-- vv i i v i i L1M5_orf2#LIN 999 AGNAAGTAGAAGG--AAG--GAAATAATAAAGATAAGAGCAGAAATCAAT 1044 chr6qtel1M 131704 AAAACTGAAAGTAACAAAAAAACTATTGAATTAATAAATAAAACTAAAAG 131753 i iv --- ? ? v v ivv v ii i i L1M5_orf2#LIN 1045 GAAATAGAAA---ACAAANANACAATAGAGAAAATCAACGAAGCCAAAAG 1091 chr6qtel1M 131754 TTGGTTTTGTGAAAAGAAAAACAACAAAATATATATAAATCTTCAGTAAA 131803 i i v v--- i - i- i ii i? i L1M5_orf2#LIN 1092 CTGGTTCTTTGAAAAGAT---CAATAAAAT-TG-ATAAACCTCTAGCNAG 1136 chr6qtel1M 131804 TGTGATTTAAAAGAAAAGAG-GAAAAT-TAAATTGTTAGTCATAAAAATG 131851 vv iv i i - i i-i iii i vvi ii L1M5_orf2#LIN 1137 ACTGATCAAGAAAAAAAGAGAGAAGACACAAATTACCAATATCAGGAATG 1186 chr6qtel1M 131852 AGAAGGGAGAGGTTGCCACTAATGAAAAGAAAATTAGAGCAATAATTAGG 131901 i i vi ii i vi vvv vii v i ivi v i L1M5_orf2#LIN 1187 AAAAAGGAGACATCACTACAGATCCTACAGACATTAAAAGGATAATAAGA 1236 chr6qtel1M 131902 AGTTACTTTGTCCAACTTTATGCCAATAAATCAGATAA-----ATGAAAT 131946 iiv i v vv iv ? ----- L1M5_orf2#LIN 1237 GAATATTATGAACAACTTTATGCCAATAAATTTGANAACTTAGATGAAAT 1286 chr6qtel1M 131947 GGAAGAATATCTTCAAAAATATAGCTTACCCAAATTAACAGAGGAAGAAG 131996 vi vi v i i i? v i i ?v i i L1M5_orf2#LIN 1287 GGACAAATTCCTTGAAAAACACAANTTACCAAAACTGACNCAAGAAGAAA 1336 chr6qtel1M 131997 TAAAATGGTTAAGCCATCCCATTTTAGAAAAAGAAATAGAATAAGCTATT 132046 i vivi i iivii i v ivivv v vv iv L1M5_orf2#LIN 1337 TAGAAAATCTGAATAGCCCTATATCTATTAAAGAAATTGAATTTGTAATT 1386 chr6qtel1M 132047 ACTCAACACTCT-----AAGAAAAATCCCAGGACCAAATGGATTTACATG 132091 --- v ii ----- ii ii v i v i vv L1M5_orf2#LIN 1387 A---AAAACCTTCCCACAAAGAAAACTCCAGGCCCAGATGGCTTCACTGG 1433 chr6qtel1M 132092 TAAATTCTACCAAATATTTAA---AGAATTAACTCCAATGATATATAAAC 132138 i i --- v iv vv i i L1M5_orf2#LIN 1434 TGAATTCTACCAAACATTTAAGGAAGAAATAATACCAATCTTACACAAAC 1483 chr6qtel1M 132139 TATTTGAAAAAAATAGGGATTGAAGGAGTCCTATCAAATTCCTTTCATGA 132188 v iv i - ii vv i iiv vi v i v i L1M5_orf2#LIN 1484 TCTTCCAGAAAA-TAGAAAAAGAGGGAACACTTCCCAACTCATTTTATGA 1532 chr6qtel1M 132189 C-CCAGACATGATACTGATACCTAAACCAGGTAGGTTGAAA--ACAGAGA 132235 v- - ? iv v ? ii ii-- v -- iii L1M5_orf2#LIN 1533 GGCCAG-CATNACCCTGATACCAAAACCNGACAAA--GACATTACAAGAA 1579 chr6qtel1M 132236 AAGAAAATTATAGACCAATCTTCCTAATGAATATTGATGCTAAAATCATA 132285 i v i v i v v v ? L1M5_orf2#LIN 1580 AAGAAAATTACAGACCAATATCCCTCATGAACATAGATGCAAAAATCCTN 1629 chr6qtel1M 132286 AATACAATATTAGCAAAAAGATTAGAGAAAATCATCACCAGGATAATACA 132335 i v vv v vv v vvi v vv L1M5_orf2#LIN 1630 AACAAAATATTAGCAAATCGAATCCAGCAATATATAAAAAGGATAATACA 1679 chr6qtel1M 132336 CTATGAGCAAGTAAATTTTATACCAAGAATGTAGGGCTGATTCAATATTA 132385 ii v iiiv v i i i i i i i v L1M5_orf2#LIN 1680 TCATGACCAAGTGGGGTTTATCCCAGGAATGCAAGGTTGGTTTAACATTC 1729 chr6qtel1M 132386 GGAAA 132390 i L1M5_orf2#LIN 1730 GAAAA 1734 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 37.72 CpG sites = 137, Kimura (unadjusted) = 37.94 Transitions / transversions = 1.27 (137/108) Gap_init rate = 0.04 (39 / 875), avg. gap size = 1.44 (56 / 39) 12 26.18 4.48 2.94 chr6qtel1M 134639 134705 (865295) (ATAATT)n#Simple_repeat 1 68 (0) m_b301s252i20 12615 chr6qtel1M 134639 ATAATTATAAGTTATTGTTGAT-ATTGCTATAGTAATTTTACTAAT-ATT 134686 - vi - - iiv vi v v v - (ATAATT)n#Sim 1 ATAATTATAA-TTATAATT-ATAATTATAATTATAATTATAATTATAATT 48 chr6qtel1M 134687 TGCATTATAA-TAAAATTAT 134705 vvv - v (ATAATT)n#Sim 49 ATAATTATAATTATAATTAT 68 Matrix = Unknown Transitions / transversions = 0.40 (4/10) Gap_init rate = 0.08 (5 / 66), avg. gap size = 1.00 (5 / 5) 441 22.15 3.33 5.98 chr6qtel1M 135050 135169 (864831) MIRc#SINE/MIR 11 127 (141) m_b301s601i2 12616 chr6qtel1M 135050 TGGCTCAGTGGAGAGA--AGTATCCCTGAAGTCAGGAGGACCTAAGTTCA 135097 iv i -- v ivv i i i ii i MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr6qtel1M 135098 AATCCAGCCTCACACATTTAGTAGTTACTAGTTTTGTGACCCTGGGCAAG 135147 i v v ------- ivi v i v i MIRc#SINE/MIR 61 AGTCCCGGCTC-------TGCCACTTACTAGCTGTGTGACCTTGGGCAAG 103 chr6qtel1M 135148 TCATTTAACC-CCCTG-GCCTCAG 135169 i - i - MIRc#SINE/MIR 104 TCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 25.64 CpG sites = 16, Kimura (unadjusted) = 26.87 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.08 (10 / 119), avg. gap size = 1.10 (11 / 10) 297 33.92 5.92 0.56 chr6qtel1M 135380 135548 (864452) MIR3#SINE/MIR 19 196 (12) m_b301s601i3 12617 chr6qtel1M 135380 AGAGAGGGAACTAAATAGCAGGCAGAGAGCCTAGGCACTGAAATGCAGCC 135429 i v vi v i v v iiii i iv - iviv i i MIR3#SINE/MIR 19 AGAGAGAGCACGGACTGGGAGTCAGGAGACCTGGGTTCT-AGTCCCGGCT 67 chr6qtel1M 135430 C---CAATAACTTCCTTTG---ACTTGAAAAACTCACA-CAGTTCCCTTG 135472 --- v ?v v ---v iiv v v- vi i v MIR3#SINE/MIR 68 CTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGG 117 chr6qtel1M 135473 GCCTCAGTTACCTCACCTATAAAATGATTGCTTTTGGTCAACT--TCTCT 135520 v i i vv vv v iii iv -- MIR3#SINE/MIR 118 GCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCT 167 chr6qtel1M 135521 GA-CTTCCTTTAAGCTCTATAATCCTCTG 135548 i -v i iv ivv i v MIR3#SINE/MIR 168 AAGGTCCCTTCCAGCTCTGACATTCTATG 196 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 45.14 CpG sites = 28, Kimura (unadjusted) = 46.23 Transitions / transversions = 0.97 (28/29) Gap_init rate = 0.04 (6 / 168), avg. gap size = 1.83 (11 / 6) 17 0.00 0.00 0.00 chr6qtel1M 136864 136882 (863118) (T)n#Simple_repeat 1 19 (0) m_b301s252i21 12618 chr6qtel1M 136864 TTTTTTTTTTTTTTTTTTT 136882 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 15 16.57 4.88 0.00 chr6qtel1M 137034 137074 (862926) (ATTCAGA)n#Simple_repeat 1 43 (0) m_b301s252i22 12619 chr6qtel1M 137034 ATTCAGAAGTCAGTATTCAGTA-TGAG-ATTCACAAGTCAGAA 137074 v v v - v - v v (ATTCAGA)n#Si 1 ATTCAGAATTCAGAATTCAGAATTCAGAATTCAGAATTCAGAA 43 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 78 28.11 0.85 0.85 chr6qtel1M 140832 141066 (858934) (TCTC)n#Simple_repeat 1 235 (0) m_b301s252i23 12620 chr6qtel1M 140832 TCTCTCTGTCAGTCTCTGTGTAGCTGTCTC-CTTGCTCTCTCTGTGTCTC 140880 v vv v v vv v - iv v v (TCTC)n#Simpl 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr6qtel1M 140881 TCTGTCTCTCCCTATCTCTGCGTGTGTGTCTGTCTGTTTGTCTCTTTCGC 140930 v i v - - v v v v v i v i v (TCTC)n#Simpl 51 TCTCTCTCTCTCTCTCTCT-C-TCTCTCTCTCTCTCTCTCTCTCTCTCTC 98 chr6qtel1M 140931 TCTCTTAGTCTCT-TTTCTCTCTGTCTCTGTCTCTGTCTCTCTGTCTCAC 140979 ivv - i v v v v v (TCTC)n#Simpl 99 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 148 chr6qtel1M 140980 TCTGTCTTTCTTTCTGTCTCTCTGTCTGTCTCTGTGTGTGTGTCTGTCTT 141029 v i i v v v v v v v v v i (TCTC)n#Simpl 149 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 198 chr6qtel1M 141030 TCTGTCTGCCTCTCTGTGTCTCTGTCTCCCTATCTCT 141066 v vi v v v i v (TCTC)n#Simpl 199 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 235 Matrix = Unknown Transitions / transversions = 0.26 (11/43) Gap_init rate = 0.02 (4 / 234), avg. gap size = 1.00 (4 / 4) 15 21.12 1.61 6.78 chr6qtel1M 143568 143629 (856371) (GAAAAG)n#Simple_repeat 1 59 (0) m_b301s252i24 12621 chr6qtel1M 143568 GAAAAGGGAGAAGGGAAAATTGAAAAGG-GAAGGAATAAGCTAAGTGGAA 143616 - - i -v -i - vv iv i (GAAAAG)n#Sim 1 GAAAA-GGA-AAAGGAAAA-GGAAAAGGAAAAGGAA-AAGGAAAAGGAAA 46 chr6qtel1M 143617 GGGAATAGGAAAA 143629 i v (GAAAAG)n#Sim 47 AGGAAAAGGAAAA 59 Matrix = Unknown Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.08 (5 / 61), avg. gap size = 1.00 (5 / 5) 252 27.76 10.83 3.91 chr6qtel1M 143735 143974 (856026) L1MEc_5end#LINE/L1 2223 2478 (49) m_b301s551i5 12622 chr6qtel1M 143735 GAAGGGATAAGGAGGAAGGAAGGGAGAAAAGTATAAACAG--GGGTTAAC 143782 v v ii i -- i i ---- -- vi v L1MEc_5end#LI 2223 GAAGGCAGAAAAAGAAA--AAAGGAAAAAAG----AACAGATGGGACAAA 2266 chr6qtel1M 143783 AAGATGGCATGTAATAGCAAACTGGTAGTTTTAA-CCC------------ 143819 v vii --- iv v - ------------ L1MEc_5end#LI 2267 TAGAAAACA---AATAGCAAGATGGTAGATTTAAACCCAACCATATCAAT 2313 chr6qtel1M 143820 --------TAAATGTGAATGAGGGTAAACTGCCCCATAGAGAGGAAGTGG 143861 -------- i - vv vv v vi i v v i L1MEc_5end#LI 2314 AATCACATTAAATGTAAATG-GTCTAAACACCCCAATTAAAAGGCAGAGA 2362 chr6qtel1M 143862 TTA-GAGAATGAATTAAAAGCCTTAATCCTACAATATGTTGTTTACAGGA 143910 i-v v i v iv vvi i v v i ii i L1MEc_5end#LI 2363 TTGTCAGATTGGATAAAAAAGCAAGACCCAACTATATGCTGCCTACAAGA 2412 chr6qtel1M 143911 AACACAGCTGAAGCAGGAAGATACACACAG--TAAAGGTAAAAGGTTGTA 143958 ? vi v ii vi i v i -- i v v L1MEc_5end#LI 2413 AACNCACTTTAAATATAAAGACACAAATAGGTTAAAAGTAAAAGGATGGA 2462 chr6qtel1M 143959 GCAGAATCTACCATGC 143974 iv ii v L1MEc_5end#LI 2463 AAAAGATATACCATGC 2478 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 35.36 CpG sites = 32, Kimura (unadjusted) = 35.36 Transitions / transversions = 1.00 (32/32) Gap_init rate = 0.07 (16 / 239), avg. gap size = 2.25 (36 / 16) 308 26.49 3.23 2.56 chr6qtel1M 143780 143934 (856066) L1M6_5end#LINE/L1 2360 2515 (0) m_b301s551i6 12622 chr6qtel1M 143780 AACAAGATGGCA--TGTAATAGCAAAC-TGGTAGTTTTAACCCTAAATGT 143826 i? i --?i v v - ivi v i vv L1M6_5end#LIN 2360 AGNAAGATGACAAANATAAGACCAAACATATCAGTTATGACAATAAATGT 2409 chr6qtel1M 143827 GAATGAGGGTAAACTGCCCCAT--AGAGAGGAAGTGGTTAGAGAATGAAT 143874 i - v v i -- i vi -iv ivv v ii L1M6_5end#LIN 2410 AAATG-GGTTAAACTCCCCTATTAAAAGACAAAG-ACTCTCAGATTGGGT 2457 chr6qtel1M 143875 TAAAAGCCTTAATCCTACAATATGTTGTTTACAGGAAACACAGCTGAAGC 143924 iv vv v v i i i v i vv L1M6_5end#LIN 2458 TAAAAAACAAAATCCAACTATATGCTGTTTACAAGAGACACACCTAAATA 2507 chr6qtel1M 143925 AGGAAGATAC 143934 -- L1M6_5end#LIN 2508 A--AAGATAC 2515 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 33.48 CpG sites = 19, Kimura (unadjusted) = 33.48 Transitions / transversions = 0.90 (19/21) Gap_init rate = 0.05 (7 / 154), avg. gap size = 1.29 (9 / 7) 2314 30.10 4.65 3.05 chr6qtel1M 143820 145498 (854502) L1M5_orf2#LINE/L1 38 1742 (1552) m_b301s551i7 12622 chr6qtel1M 143820 TAAATGTGAATGAGGGTAAACTGCCCCATAGAGAGGAAGTGGTTA-GAGA 143868 i - ?v vvi v vi i v v i i-v L1M5_orf2#LIN 38 TAAATGTAAATG-GNCTAAACACTCCAATTAAAAGGCAGAGATTGTCAGA 86 chr6qtel1M 143869 ATGAATTAAAAGCCTTAATCCTACAATATGTTGTTTACAGGAAACACAGC 143918 v i v iv vvi i v v i i i i i vi L1M5_orf2#LIN 87 CTGGATAAAAAAACAAGACCCAACTATATGCTGTCTACAAGAGACGCACT 136 chr6qtel1M 143919 TGAAGCAGGAAGATACACACAG--TAAAGGTAAAAGGTTGTAGCAGAATC 143966 v ii vi i v ? -- i i v v iv ii v L1M5_orf2#LIN 137 TTAAATATAAAGACACAGANAGGTTGAAAGTAAAAGGATGGAAAAAGATA 186 chr6qtel1M 143967 TACCATGCT----TCAGGTGAAGTAAAAAGC-AGGGTAGCTATCCTGATC 144011 v----ii i?ii -- i -i ? i vi i v L1M5_orf2#LIN 187 TACCATGCAAACACTAANCAAA--AGAAAGCTGGNGTGGCTATATTAATA 234 chr6qtel1M 144012 TCAGATCAAGCA------AAAGCAAAAATTGATCTAATTAAAAGAGATAT 144055 iv i ------ i i --- --- vv v L1M5_orf2#LIN 235 TCAGACAAAGTAGACTTCAAGGCAAGAA---AT---ATTACCAGAGATAA 278 chr6qtel1M 144056 GAAGGG-CACTATATCTTGCTAAA-GGGTAGCATAGATAATCAAGCA--- 144100 ii - i vi vv v - ----i iv v v --- L1M5_orf2#LIN 279 AGAGGGACATTTCATAATGATAAAAGGGT----CAATTCATCAAGAAGAC 324 chr6qtel1M 144101 ATATCAATATTAAACATATATGCACCAAGTAGTGTAGCATTTAAATTCTT 144150 v vi ii i v i iiiv v iv v v L1M5_orf2#LIN 325 ATAACAATCCTAAATGTGTATGCACCTAATAACAGAGCTTCAAAATACAT 374 chr6qtel1M 144151 AAAAGAGAAATTAAGAGAGCTGCAAGAAGAAATAGACAG---CAAAAGTA 144197 i iv i i i v i iv i i--- v v L1M5_orf2#LIN 375 GAAGCAAAAACTGACAGAACTAAAAGGAGAAATAGACAAATCCACAATTA 424 chr6qtel1M 144198 TAATATTGGGTGATCTCAACCTTGCATCCTGAG-AATTAGATAAATCAAA 144246 i--- ? v i i vi?v vii v - - i v i L1M5_orf2#LIN 425 TAG---TNGGAGATTTTAACACNCCTCTCTCAGTAATT-GATAGAACAAG 470 chr6qtel1M 144247 C---CATAAAATAAATAAGAA---AGAA---TTAATAGAATACTAGAAA- 144286 i--- v v i i --- --- i - v i vv - L1M5_orf2#LIN 471 TAGACAAAAAATCAGTAAGGATATAGAAGATTTGA-ACAACACTATCAAC 519 chr6qtel1M 144287 -AGTTAGATATGATAGATCTTTGGAGAA-AATGAAATGGAC-ACAGAAAG 144333 - ii v iv i v iv iv - v ?v vivi - ? v -- L1M5_orf2#LIN 520 CAACTTGACCTAATTGACATTTATAGAACACTNCACCCAACAACNGCA-- 567 chr6qtel1M 144334 GAATACACTTTCTTCTCAGCAGCTCATGGAACCTATACAAAAATAGACCA 144383 v i ivv v v v v i L1M5_orf2#LIN 568 GAATACACATTCTTTTCAAGTGCACATGGAACATTTACCAAGATAGACCA 617 chr6qtel1M 144384 TATATTAGGACATAAAAACATCAAA-CTC---AAATGCAGGAAGGCAGAA 144429 ?i i v ---- i- --- vi?ii i iiv L1M5_orf2#LIN 618 TATNCTGGGCCATAAAA----CAAGTCTCAATAAATTTNAAAGGATTGAA 663 chr6qtel1M 144430 ATAGTA-AATGCATCTTTTTCAGACCATGATGCAGTGAAAATTACACTCA 144478 vi - iv i v- i v ii v i v v viv v L1M5_orf2#LIN 664 ATCATACAGAGTATG-TTCTCTGACCACAATGGAATTAAATTAGAAATCA 712 chr6qtel1M 144479 ACAGAAAACAAG------GGGAAATGGACCAAAAATTAATTGAAACTAAA 144522 i iv - ------i i vv- v -- v i L1M5_orf2#LIN 713 ATAACAAA-AAGATANCTAGAAAATCC-CCAAATATT--TGGAAATTAAA 758 chr6qtel1M 144523 TAATCTCA-TACTAAAGAATGATTGGGTAAAACAGTAAATTGTACACATA 144571 i - v - v v ivvv v v iv iii v?viv L1M5_orf2#LIN 759 CAA-CACACTTCTAAATAACCCATGGGTCAAAGAAGAAATCACAANGGAA 807 chr6qtel1M 144572 ATT---AATCACTTCACCCAAGAAAATGACAATAATGAGACATCATACCA 144618 --- vi i ii--- vvi ? i vi v v i L1M5_orf2#LIN 808 ATTAGAAAATATTTTG---AACTGAATGANAATGAAAATACAACATATCA 854 chr6qtel1M 144619 AAATGTGTAGGATACAGCCAAAGCGGTAA-TAAAGGGAAATTTTATATCA 144667 v i i i i iv- i - v ? L1M5_orf2#LIN 855 AAATTTGTGGGATGCAGCTAAAGCAGTGCTTAGAGGGAAA-TTTATAGCN 903 chr6qtel1M 144668 CTAGAGGCCTACTTGCATAAAATATAAAAAGAG---AAGGTCAATGAATT 144714 i i v ? iv --- i v v i ii --- ii vi L1M5_orf2#LIN 904 TTAAATGCNTATAT---TAGAAAAGAAGAAAGGCTTAAAATCAATGATCT 950 chr6qtel1M 144715 GGGTTTGCAAC-TAAAATGCTAGAAAAGGAA---CAAATTAAAAATCCCC 144760 ii i v v - i v i --- --- v L1M5_orf2#LIN 951 AAGCTTCCACCTTAAGAAGCTAGAAAAAGAAGAGCAAATTAAA---CCCA 997 chr6qtel1M 144761 AGTCAAACACTAAACTTGAAATTCTAAAAATGAAATGAGAGATTGATAAC 144810 iv? ii vv iivvv vv i i i vv i ii i v L1M5_orf2#LIN 998 AAGNAAGTAGAAGGAAGGAAATAATAAAGATAAGAGCAGAAATCAATGAA 1047 chr6qtel1M 144811 ATTGAAAGTAAAAAAGCTATTGAATTAATTAATAAAACTAAGAGTTGGTT 144860 v ii ? ?i v v ivv i ii i i i i L1M5_orf2#LIN 1048 ATAGAAAACAAANANACAATAGAGAAAATCAACGAAGCCAAAAGCTGGTT 1097 chr6qtel1M 144861 CTATGAAAA---CAACAAAATAGATAAACCCTTAGCAAATCTGATTTA-A 144906 v --- i v ii ? iv iv - L1M5_orf2#LIN 1098 CTTTGAAAAGATCAATAAAATTGATAAACCTCTAGCNAGACTGATCAAGA 1147 chr6qtel1M 144907 AAAGGAGAGAGGAAAATCAAATTGTTAGTCTTA-AAATGAAAAGGGAGAA 144955 ii i i vv iii i v i -i i v L1M5_orf2#LIN 1148 AAAAAAGAGAGAAGACACAAATTACCAATATCAGGAATGAAAAAGGAGAC 1197 chr6qtel1M 144956 CTCTGCCACTAATGAAGAGGAAATTAGAGCAATAATTAGAAGTTACTTTG 145005 v -i i vi vvvivi v i ivi v iiv i v L1M5_orf2#LIN 1198 ATC-ACTACAGATCCTACAGACATTAAAAGGATAATAAGAGAATATTATG 1246 chr6qtel1M 145006 ACCAACTTTATGCCAATCAATTCAACAAGTTAAATGAAATGGAAGAATAC 145055 v v ii ? v i vi v L1M5_orf2#LIN 1247 AACAACTTTATGCCAATAAATTTGANAACTTAGATGAAATGGACAAATTC 1296 chr6qtel1M 145056 CTTCAAAAATATAGCTTGCCCAGATTAACAGAGGAAGAAGTAAATATCCT 145105 v i i i? i v i i i ?v i i i v vi L1M5_orf2#LIN 1297 CTTGAAAAACACAANTTACCAAAACTGACNCAAGAAGAAATAGAAAATCT 1346 chr6qtel1M 145106 AAACAGTCCCATCTTAGAAAAAGAAATAGAACAGGCTATTAGCCAACTCC 145155 i i i i v ivivv v ivv iv ivv v i L1M5_orf2#LIN 1347 GAATAGCCCTATATCTATTAAAGAAATTGAATTTGTAATTAAAAACCTTC 1396 chr6qtel1M 145156 C--TGAGAAAAATCCCTGGACCAGATGGATTTACATGTGAATTCGACCAA 145203 --ii ii ii v v v i vv v L1M5_orf2#LIN 1397 CCACAAAGAAAACTCCAGGCCCAGATGGCTTCACTGGTGAATTCTACCAA 1446 chr6qtel1M 145204 ACATTCAAAGAACAATTAACTCCAATGTTATATAGACTATTTGAAAAAAT 145253 i i v v iv v i i i v iv i L1M5_orf2#LIN 1447 ACATTTAAGGAAGAAATAATACCAATCTTACACAAACTCTTCCAGAAAAT 1496 chr6qtel1M 145254 AGGGAATGAAGG-TCTCCTACCAATTTCCTTTTATGACACAGATATGGTA 145302 ii v i -v v i v -i v vi viii ?iiv L1M5_orf2#LIN 1497 AGAAAAAGAGGGAACACTTCCCAA-CTCATTTTATGAGGCCAGCATNACC 1545 chr6qtel1M 145303 CTGATACCTAAACTAGGTAGGTTGAAA--ACAGAGAAAGAAAATTATCGA 145350 v i? ii ii-- v -- iii iv L1M5_orf2#LIN 1546 CTGATACCAAAACCNGACAAA--GACATTACAAGAAAAGAAAATTACAGA 1593 chr6qtel1M 145351 CCAATCTCCCTAATGAATATTGATGCTAAAATCTTAAATAAAATGTTAGC 145400 v v i v v i ? i i L1M5_orf2#LIN 1594 CCAATATCCCTCATGAACATAGATGCAAAAATCCTNAACAAAATATTAGC 1643 chr6qtel1M 145401 AAA--------AACATTACAGAAAACCATCCCCAGGATAATACATTATGA 145442 -------- i v i v -------- i L1M5_orf2#LIN 1644 AAATCGAATCCAGCAATATATAAAA--------AGGATAATACATCATGA 1685 chr6qtel1M 145443 -CAAGTAATTTTTATACCCAGAATGCAGGGCTGGTTCAATAGTAGGAAAA 145491 - iivv v vi i i i i v v i v L1M5_orf2#LIN 1686 CCAAGTGGGGTTTATCCCAGGAATGCAAGGTTGGTTTAACATTCGAAAAT 1735 chr6qtel1M 145492 CTATTAA 145498 v i L1M5_orf2#LIN 1736 CAATCAA 1742 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 39.95 CpG sites = 271, Kimura (unadjusted) = 40.17 Transitions / transversions = 1.24 (271/219) Gap_init rate = 0.05 (87 / 1678), avg. gap size = 1.49 (130 / 87) 16 9.98 0.00 5.88 chr6qtel1M 145538 145573 (854427) (TTTTG)n#Simple_repeat 1 34 (0) m_b301s252i25 12623 chr6qtel1M 145538 TTTTGTTTCTCTTACTGTTTTGTTTTGTTTTTTTTT 145573 - v -i v (TTTTG)n#Simp 1 TTTTGTTT-TGTT-TTGTTTTGTTTTGTTTTGTTTT 34 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 13 9.26 0.00 0.00 chr6qtel1M 145692 145714 (854286) (GGGA)n#Simple_repeat 1 23 (0) m_b301s252i26 12624 chr6qtel1M 145692 GGGAGGGGTGGAGGGAGGGAGGG 145714 iv (GGGA)n#Simpl 1 GGGAGGGAGGGAGGGAGGGAGGG 23 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 12 27.09 3.28 3.28 chr6qtel1M 147064 147124 (852876) (ATTT)n#Simple_repeat 1 61 (0) m_b301s252i27 12625 chr6qtel1M 147064 ATTT-TTAATTCTATTT-TCTGTCTCATGTGTTTATGTATTTCTTTGATT 147111 - v - - i i - i v i v v iv (ATTT)n#Simpl 1 ATTTATTTATT-TATTTATTTAT-TTATTTATTTATTTATTTATTTATTT 48 chr6qtel1M 147112 GTATATTTATGTA 147124 i v v (ATTT)n#Simpl 49 ATTTATTTATTTA 61 Matrix = Unknown Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.07 (4 / 60), avg. gap size = 1.00 (4 / 4) 83 9.31 0.00 0.00 chr6qtel1M 147537 147652 (852348) (TA)n#Simple_repeat 1 116 (0) c_b301s251i0 12626 chr6qtel1M 147537 TATATATATATATATATATATATATATATGTATATATATAAAGGCATATG 147586 i v vii i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr6qtel1M 147587 TATGTGTGTATATATATATATATATATATATATATATATATATATATATA 147636 i i i (TA)n#Simple_ 51 TATATATATATATATATATATATATATATATATATATATATATATATATA 100 chr6qtel1M 147637 TATACATATATATATA 147652 i (TA)n#Simple_ 101 TATATATATATATATA 116 Matrix = Unknown Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.00 (0 / 115), avg. gap size = 0.0 (0 / 0) 36 28.14 0.00 3.91 chr6qtel1M 148104 148236 (851764) (TCTG)n#Simple_repeat 1 128 (0) m_b301s252i28 12627 chr6qtel1M 148104 TCTTTCTTTCTCTCTGTTGGTCTCCACCTTTCTAATCTGTCTGTCTGTCT 148153 v v v iv --ii v -i (TCTG)n#Simpl 1 TCTGTCTGTCTGTCTGTCTGTCT--GTCTGTCT-GTCTGTCTGTCTGTCT 47 chr6qtel1M 148154 CTGTCTCTGTCTGTCTCTCTCTGCATCTCTCATTCTCTTTGTGTATGTCT 148203 v v v v v - - v vvi v v v v (TCTG)n#Simpl 48 GTCTGTCTGTCTGTCTGTCTGT-C-TGTCTGTCTGTCTGTCTGTCTGTCT 95 chr6qtel1M 148204 GTCTGCCTCTCAGTCTCTCTGTTTCTCTGTGTG 148236 i v v v i v v (TCTG)n#Simpl 96 GTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTG 128 Matrix = Unknown Transitions / transversions = 0.32 (7/22) Gap_init rate = 0.04 (5 / 132), avg. gap size = 1.00 (5 / 5) 293 36.44 1.67 1.67 chr6qtel1M 151812 151931 (848069) C MIRc#SINE/MIR (112) 156 37 m_b302s601i0 12628 chr6qtel1M 151812 TTATTATCTATATTTAACACTTGAGAAAACTGAGA--CAGACAGAACTGA 151859 ivi v vv i i-- v -ii i C MIRc#SINE/MIR 156 TTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAG-GTTAA 108 chr6qtel1M 151860 ATGATATTGAGTATGGTTATGTAGATAATAAATCTCTGAAGTAAAGTTTG 151909 i i- vvi v i iii v i i vv v iviiiiii i C MIRc#SINE/MIR 107 GTGAC-TTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCG 59 chr6qtel1M 151910 AAATCATGCCTTTCTAACTCCA 151931 vi v i i i C MIRc#SINE/MIR 58 AACCCAGGTCTTCCTGACTCCA 37 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 49.47 CpG sites = 28, Kimura (unadjusted) = 53.36 Transitions / transversions = 1.87 (28/15) Gap_init rate = 0.03 (3 / 119), avg. gap size = 1.33 (4 / 3) 34 26.15 6.90 0.00 chr6qtel1M 152053 152197 (847803) (TATA)n#Simple_repeat 1 155 (0) m_b302s252i1 12629 chr6qtel1M 152053 TATAT-TAT-TATATACATTTATAT-TGTATGTAT-TTTATATATA-AGG 152097 - - i v - i i - v - vi (TATA)n#Simpl 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr6qtel1M 152098 TATTGAT-TAATTATATAAATATGTATTTATGTGTAGA-AGATAAATATT 152145 vv - vv v i v i i v - v v v (TATA)n#Simpl 51 TATATATATATATATATATATATATATATATATATATATATATATATATA 100 chr6qtel1M 152146 TA-ATATATATTTGTGCAT-TGTATAGATATTGAT-TATATCTATTCATA 152192 - v i ii - i v vv - v vi (TATA)n#Simpl 101 TATATATATATATATATATATATATATATATATATATATATATATATATA 150 chr6qtel1M 152193 TTTAT 152197 v (TATA)n#Simpl 151 TATAT 155 Matrix = Unknown Transitions / transversions = 0.60 (12/20) Gap_init rate = 0.07 (10 / 144), avg. gap size = 1.00 (10 / 10) 17 28.03 1.67 0.00 chr6qtel1M 153457 153516 (846484) (GGAA)n#Simple_repeat 1 61 (0) m_b302s252i2 12630 chr6qtel1M 153457 GGAAGAAAAGAAGGCAGTAAAGACTAAATGAAGTAAAGAAGGAAATTA-G 153505 i i v v i vvi v v i ivv - (GGAA)n#Simpl 1 GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG 50 chr6qtel1M 153506 AAGGAAGGAAG 153516 (GGAA)n#Simpl 51 AAGGAAGGAAG 61 Matrix = Unknown Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.02 (1 / 59), avg. gap size = 1.00 (1 / 1) 17 20.56 3.85 1.89 chr6qtel1M 153935 153986 (846014) (ATT)n#Simple_repeat 1 53 (0) m_b302s252i3 12631 chr6qtel1M 153935 ATTATTGTCTA-TATTATTGATATTATTAATAATAGTATAATTA-TAAAA 153982 i - - iv v v v v - vv (ATT)n#Simple 1 ATTATTAT-TATTATTATTATTATTATTATTATTATTATTATTATTATTA 49 chr6qtel1M 153983 TTAT 153986 (ATT)n#Simple 50 TTAT 53 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.00 (3 / 3) 287 34.67 1.26 3.87 chr6qtel1M 154486 154644 (845356) MIRb#SINE/MIR 26 180 (88) m_b302s601i1 12632 chr6qtel1M 154486 AAAAGCACAGTAGCTACCTAGCAGTCAGAGAACAAGTGCATTGAAATACA 154535 i i -- --- v v v i- vv vi vi v v MIRb#SINE/MIR 26 AAGAGCACGG--GCT---TTGGAGTCAGACAG-ACCTGGGTTCGAATCCC 69 chr6qtel1M 154536 TCCTCAGTAAAACATAAGCTGTTTTAACTTTGAAAAATTCCTAAGTGTCT 154585 vv v iv vvi iv v v v v iv i v v iiv MIRb#SINE/MIR 70 GGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCT 119 chr6qtel1M 154586 CTGGATCTCAGTTCCCACACCTATAAAATGGGGCT--TTAGATCAACTTC 154633 iii i v i i v -- v v i v i MIRb#SINE/MIR 120 CTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTACCTC 169 chr6qtel1M 154634 TCTGAATTGTT 154644 v v ii MIRb#SINE/MIR 170 GCAGGGTTGTT 180 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 44.42 CpG sites = 22, Kimura (unadjusted) = 46.68 Transitions / transversions = 0.71 (22/31) Gap_init rate = 0.04 (7 / 158), avg. gap size = 1.14 (8 / 7) 247 34.71 5.79 0.00 chr6qtel1M 154553 154673 (845327) MIR3#SINE/MIR 81 208 (0) m_b302s601i2 12632 chr6qtel1M 154553 GCTGTTTTAACTTTGAAAAATTCCTAAGTGTCTCTGGATCTCAGTTCCCA 154602 v v v v iv i iv vviiv ii i v MIR3#SINE/MIR 81 GCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCT 130 chr6qtel1M 154603 CACCTATAAAATG-GGGCTTTAGATCAACT--TCTCTGAATTGTTTTCT- 154648 i i - vv i ii iv -- i iv vii i- MIR3#SINE/MIR 131 CATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCA 180 chr6qtel1M 154649 GTTCTAA---TCTCTAAGTCTGAGATCC 154673 i i --- v i v iv i MIR3#SINE/MIR 181 GCTCTGACATTCTATGATTCTATGATTC 208 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 48.25 CpG sites = 24, Kimura (unadjusted) = 48.25 Transitions / transversions = 1.33 (24/18) Gap_init rate = 0.03 (4 / 120), avg. gap size = 1.75 (7 / 4) 112 11.95 1.64 0.54 chr6qtel1M 154678 154860 (845140) (AG)n#Simple_repeat 1 185 (0) m_b302s252i4 12633 chr6qtel1M 154678 AGAGAGAGAGACAGAGAGACAGAGAGAGACACGTGAGCGAGAGAAACAGA 154727 v v v - v v i v (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA-GAGAGAGAGAGAGAGAGA 49 chr6qtel1M 154728 TAGACAGAGATAGAGACAGATAAACAGAGACAGAGACAGAGAGAGAG-GA 154776 v v v v v i v v v - (AG)n#Simple_ 50 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 99 chr6qtel1M 154777 GA-AAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 154825 - i (AG)n#Simple_ 100 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 149 chr6qtel1M 154826 GAGAGAGAGAG-GAGAGGGAGAGGGATAGAGAGAGA 154860 - i i v (AG)n#Simple_ 150 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 185 Matrix = Unknown Transitions / transversions = 0.33 (5/15) Gap_init rate = 0.02 (4 / 182), avg. gap size = 1.00 (4 / 4) 648 30.93 5.58 2.94 chr6qtel1M 155348 156010 (843990) L1M5_orf2#LINE/L1 2615 3294 (0) m_b302s551i0 12634 chr6qtel1M 155348 TACCAGATCT-AAAATTATATTATAGAGCAGCAGTTACCAAAACCATTTG 155396 ? ? - i i - i vi v i i vi v L1M5_orf2#LIN 2615 TACCNGATNTCAAGACT-TATTATAAAGCTACAGTAATCAAGACAGTGTG 2663 chr6qtel1M 155397 GTATTGGC-TAAGGAATAGATTAGTCGATCAGTGGAGTAGGTTAG---GT 155442 - - iv i v i ii iv --- L1M5_orf2#LIN 2664 GTATTGGCGTAAGG-ATAGACAAATAGATCAATGGAACAGAATAGAGAGT 2712 chr6qtel1M 155443 TCAAGGACAAAACAGTCA-ACAACTATAGCAACCTAGTCTTTGACAAA-- 155489 i iii i i v --- - vv i ?v ?i ii i -- L1M5_orf2#LIN 2713 CCAGAAATAGACC---CACACATATATGGNCANTTGATTTTTGACAAAGG 2759 chr6qtel1M 155490 -CCCAAAG-ACCCCAGCTTTTGGGATAAGAACTTACTGTTTGACAAAAAT 155537 -v ? - vii ---- iv i ivvv v ii viv L1M5_orf2#LIN 2760 TGCCAANGCAATTCAG----TGGGGAAAGGATAGTCTTTTCAACAAATGG 2805 chr6qtel1M 155538 TGCTGGGAAAATTGGAAACTAATATGGCAGAAACTAGGCATTGATCCACA 155587 i v v iiv v i v iii?v i i vi L1M5_orf2#LIN 2806 TGCTGGAACAATTGGATATCCATATGGAAAAAAATGAANCTCGACCCCTA 2855 chr6qtel1M 155588 CTTAACA-CGTACACCAACCGTTA-------------CAT-GACCTAGGC 155622 i v - i - vvi ------------- - iii L1M5_orf2#LIN 2856 CCTCACACCATACA-CAAAAATTAATTCNAGATGGATCATAGACCTAAAT 2904 chr6qtel1M 155623 ATAAAGAATGAAATTATTAATAAATTAGAGG--AACACAGGATAGTTTAC 155670 i ii? i i v vvvvi i -- i v i-- i L1M5_orf2#LIN 2905 GTAAAAGNTAAAACTATAAAACTTCTAGAAGAAAACATAGGAGAA--TAT 2952 chr6qtel1M 155671 CTCTCAGAACTGTGGAA-GGGGAAGGACTTTATGACCAA---AGAAAAAC 155716 - ivi iv i?-i v i i iv i v i--- v v L1M5_orf2#LIN 2953 CT-TCGTGACCTTGGGNTAGGCAAAGATTTCTTAAACAGGACACAAAAAG 3001 chr6qtel1M 155717 TAGAGATCATTACTGATCACAAAATAGAAAATTTTGACTATA-CTAAACT 155765 i v?i i v vv --- v v v v v ?i - v i L1M5_orf2#LIN 3002 CACNAACCATAAAAG---AAAAAATTGATAAATTGGACTNCATCAAAATT 3048 chr6qtel1M 155766 GAAAGTTTTTGCACAAACAAAACTAATGCAGACAAGATTAGAAGG-AAGC 155814 i ii i v ?vvv ivi vi ivi v i v i - L1M5_orf2#LIN 3049 AAAAACTTCTGCTCNTCAAAAGACACCGTTAAGAAAATGAAAAGGCAAGC 3098 chr6qtel1M 155815 AATAAACTTGGAAAATATTTTTACAGT-CAAAGGTTCTGCATAAAGGCCT 155863 v i i ? v i v v i i?- v vi- - i v L1M5_orf2#LIN 3099 CACAGANTGGGAGAAAATATTTGCAANACATATA-TCTG-ACAAAGGACT 3146 chr6qtel1M 155864 CATTTCCAAAATATATAGAGAATTATCTCTAATTT-ATAAAAATCAAGCC 155912 i v i i i -i vi ? i- ? -v v L1M5_orf2#LIN 3147 CGTATCCAGAATATATAAAGAACT-CCTACAANTCAATAANAA-AAAGAC 3194 chr6qtel1M 155913 ATTC--TCCAATTGAAATATGGTCAAAGGATATGAACAGACAATTCTCAG 155960 vv --i v? v v i iv v v i L1M5_orf2#LIN 3195 AAACAACCCAATANAAAAATGGGCAAAAGACTTGAACAGACACTTCACAA 3244 chr6qtel1M 155961 ATGAAGAAATTGAAACTATTTCTAGTCATATGGAAAGATGCTCCAAGTCA 156010 v v ?v iviiivv iv i i v v? L1M5_orf2#LIN 3245 AAGAAGATATNCAAATGGCCAATAAGCACATGAAAAGATGCTCAACNTCA 3294 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 41.31 CpG sites = 109, Kimura (unadjusted) = 42.43 Transitions / transversions = 1.21 (109/90) Gap_init rate = 0.06 (38 / 662), avg. gap size = 1.50 (57 / 38) 1487 27.12 1.86 1.48 chr6qtel1M 155868 156406 (843594) L1ME3G_3end#LINE/L1 7 547 (377) m_b302s551i1 12634 chr6qtel1M 155868 TCCAAAATATATAGAGAATTATCTCTAATTTATAAAAATCAAGCCATTCT 155917 i i i viiv v iv i -v v --vi L1ME3G_3end#L 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAA-AAAGACA--AC 53 chr6qtel1M 155918 CCAATTGAAATATGGTCAAAGGATATGAACAGACAATTCTCAGATGAAGA 155967 v v v i v v i L1ME3G_3end#L 54 CCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGGA 103 chr6qtel1M 155968 AATTGAAACTATTTCTAGTCATATGGAAAGATGCTCCAAGTCATTATTAA 156017 vv iviiivv iv i v vv i v L1ME3G_3end#L 104 AATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTAA 153 chr6qtel1M 156018 TCAGAGAAATGCAAATTAAGACAATTCTAAGATACCACTACACACCTGTC 156067 i i ivv i i viv ii L1ME3G_3end#L 154 TCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCATC 203 chr6qtel1M 156068 AGATTGGCTAAGA-TGACAGGAAAAATAATGACGATTGTT---GAGGGGA 156113 v i - v v i ?vvi iv ? v --- vi L1ME3G_3end#L 204 AGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGTG 253 chr6qtel1M 156114 TCGGAAAACTGGGACATTGATGCATTGTTGGTGGAGTTGTGAACGAATCC 156163 v i v v vi v i i i iiv i ivii v L1ME3G_3end#L 254 TGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTAC 303 chr6qtel1M 156164 AACCATTTTGGAGAGTAGTTTGA-ACTATGCTCAAAAAGTTATCAAACTG 156212 i ? i i i i- v - vvv i -- i v L1ME3G_3end#L 304 AGCCNTTTTGGAGGGCAATTTGGCAGTAT-CTATTAAAAT--TTAAAATG 350 chr6qtel1M 156213 TGCATACCCTTTGATCCAGCAGTGTTACTACTGGGCTTATATCCCAAAGA 156262 i i i vii v ? ?v v i ? L1ME3G_3end#L 351 CGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAGA 400 chr6qtel1M 156263 GATTAT-AAAGAAG-GGAAAGGGACCTGTATGTGCATGAATGTTTGTGGC 156310 i vv -iv v v - v v i --? i i v i ii v L1ME3G_3end#L 401 AATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTCATTGC 448 chr6qtel1M 156311 AGCCCT-TTTGTAGTGGCTAAAACT--GAAACTGAATGGATGTCCATCAG 156357 vi - i i v v -- vivv ii i L1ME3G_3end#L 449 AGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCAA 498 chr6qtel1M 156358 TTGGAGAATGGTTGAATAAATTGTGGTATATGAAAATTATGGAATATTA 156406 v i i i vv v i i L1ME3G_3end#L 499 TAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACTA 547 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 34.08 CpG sites = 74, Kimura (unadjusted) = 34.67 Transitions / transversions = 1.06 (74/70) Gap_init rate = 0.03 (15 / 538), avg. gap size = 1.20 (18 / 15) 12 9.71 0.00 0.00 chr6qtel1M 157069 157090 (842910) (AAGA)n#Simple_repeat 1 22 (0) m_b302s252i5 12635 chr6qtel1M 157069 AAAAAAGAAAGAAAGAAATAAA 157090 i v (AAGA)n#Simpl 1 AAGAAAGAAAGAAAGAAAGAAA 22 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 18 26.02 0.00 2.13 chr6qtel1M 157200 157247 (842753) (TG)n#Simple_repeat 1 47 (0) m_b302s252i6 12636 chr6qtel1M 157200 TGTGTATGTGATGAGAGTGTGTGCTTGTGTAAGTGTGTATATATGTGT 157247 i - v v iv iv i i i (TG)n#Simple_ 1 TGTGTGTGTG-TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 47 Matrix = Unknown Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.02 (1 / 47), avg. gap size = 1.00 (1 / 1) 252 25.00 0.00 0.00 chr6qtel1M 163630 163697 (836303) C DNM1r#Unknown (2116) 2546 2479 m_b302s502i0 12637 chr6qtel1M 163630 TATACATGCATATGAATATATATGCAAACACACATACACATATAAATATA 163679 ? i i iv i i ii v i v i i C DNM1r#Unknown 2546 TATANATACGTATATATACACATATATACACACATACACACATATACACA 2497 chr6qtel1M 163680 CATATACATGCATATACA 163697 i ii i C DNM1r#Unknown 2496 CATATATACACACATACA 2479 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 30.96 CpG sites = 14, Kimura (unadjusted) = 33.40 Transitions / transversions = 4.67 (14/3) Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0) 22 6.68 0.00 0.00 chr6qtel1M 163719 163750 (836250) (AGAT)n#Simple_repeat 1 32 (0) m_b302s252i7 12638 chr6qtel1M 163719 AGATAGATAGATAGACAGACAGATAGATAGAT 163750 i i (AGAT)n#Simpl 1 AGATAGATAGATAGATAGATAGATAGATAGAT 32 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 269 31.36 12.00 2.75 chr6qtel1M 164836 165035 (834965) MIRc#SINE/MIR 6 223 (45) m_b302s601i3 12639 chr6qtel1M 164836 CAGTAAGGTGTGGGGCAGAGAGCTTTGAA-TTGGGGTACAAGAAATAAAT 164884 iv ii v v i vi i - i - i i- vv MIRc#SINE/MIR 6 CAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGT-CAGGAAG-ACCT 53 chr6qtel1M 164885 GGATTTAACAACTCTTTGCT--GCC-CCTAATAGCATGAGTA--CT--AA 164927 i --- i v iiv -- - i v - v i-- --ii MIRc#SINE/MIR 54 GGGTT---CGAGTCCCGGCTCTGCCACTTACTAGC-TGTGTGACCTTGGG 99 chr6qtel1M 164928 CATATCACTTAATCTCTATATGTTTCAA-TCCCACATCAGTAACATGAGC 164976 vi i v iv ii i- i v v v i v MIRc#SINE/MIR 100 CAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGG 149 chr6qtel1M 164977 ATCATA----CAG------TTAGCTTATATATTTTCTGTAAGGAT--AAT 165014 v ---- v ------i v i i viv vi i -- MIRc#SINE/MIR 150 ATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAAT 199 chr6qtel1M 165015 ---ATGGTATATTTAAAAGGACTT 165035 --- ii i v i vi MIRc#SINE/MIR 200 GAGATAATGTATGTGAAAGCGCTT 223 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 39.40 CpG sites = 36, Kimura (unadjusted) = 42.11 Transitions / transversions = 1.44 (36/25) Gap_init rate = 0.08 (16 / 199), avg. gap size = 1.88 (30 / 16) 426 25.87 0.84 2.56 chr6qtel1M 166251 166369 (833631) MIRc#SINE/MIR 11 127 (141) m_b302s601i4 12640 chr6qtel1M 166251 TGGCTCATTGGATAGAGAAGTGGCCCTGAAGTCCTGAGGCCCTGAGTTTA 166300 iv v v v v v i i vv i v i ii MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr6qtel1M 166301 AATCCAACCTCAGACATTTAATACTAGCTTTGTGACCCTGGGCAAGTCAT 166350 i viv v v i --- v i i MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTA---CTAGCTGTGTGACCTTGGGCAAGTCAC 107 chr6qtel1M 166351 TTAACCCCACTT-GCTTCAG 166369 i v v- i MIRc#SINE/MIR 108 TTAACCTCTCTGAGCCTCAG 127 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 29.34 CpG sites = 14, Kimura (unadjusted) = 31.92 Transitions / transversions = 0.88 (14/16) Gap_init rate = 0.03 (4 / 118), avg. gap size = 1.00 (4 / 4) 16 11.98 2.50 5.13 chr6qtel1M 166444 166483 (833517) (AAAG)n#Simple_repeat 1 39 (0) m_b302s252i8 12641 chr6qtel1M 166444 AAAG-AATAAAGAAAAGGAAAGACAGGAAGAAAGGAAGAAA 166483 - v - - v i i (AAAG)n#Simpl 1 AAAGAAAGAAAG-AAA-GAAAGAAAGAAAGAAAGAAAGAAA 39 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.08 (3 / 39), avg. gap size = 1.00 (3 / 3) 12 7.25 10.34 0.00 chr6qtel1M 166451 166479 (833521) (AAAGG)n#Simple_repeat 1 32 (0) m_b302s252i9 12641 chr6qtel1M 166451 AAAGAAAAGGAAA-GACAGG-AA-GAAAGGAA 166479 i - v - - (AAAGG)n#Simp 1 AAAGGAAAGGAAAGGAAAGGAAAGGAAAGGAA 32 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.11 (3 / 28), avg. gap size = 1.00 (3 / 3) 250 25.00 4.17 0.00 chr6qtel1M 166601 166672 (833328) MIR3#SINE/MIR 71 145 (63) m_b302s601i5 12642 chr6qtel1M 166601 CCAATAACTTCCTTTC--ACTGTGAAAAAATCACT-CAGTTCCCTTGGTC 166647 v ?v v v-- iv iiv i - vi i v i MIR3#SINE/MIR 71 CCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCC 120 chr6qtel1M 166648 TCAGTTACCTCACCTGTAAAATGGG 166672 v i i MIR3#SINE/MIR 121 TCAGTTTCCTCATCTGTAAAATGAG 145 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 31.23 CpG sites = 9, Kimura (unadjusted) = 31.23 Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.03 (2 / 71), avg. gap size = 1.50 (3 / 2) 26 10.48 2.44 0.00 chr6qtel1M 167387 167427 (832573) (TG)n#Simple_repeat 1 42 (0) m_b302s252i11 12643 chr6qtel1M 167387 TGTGAGTGTGTGTG-GTGTGTGTGTGTGTGTATGTGCCTGTG 167427 v - i iv (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 42 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 12 27.89 0.00 5.77 chr6qtel1M 167387 167441 (832559) (TGTGCA)n#Simple_repeat 1 52 (0) m_b302s252i10 12644 chr6qtel1M 167387 TGTGAGTGTGTGTGGTGTGTGTGTGTGTGTATGTGCCTGTGCAACTGTAC 167436 vi ii - ii ii i v - - i (TGTGCA)n#Sim 1 TGTGCATGTGCAT-GTGCATGTGCATGTGCATGTGCATGTGC-A-TGTGC 47 chr6qtel1M 167437 ATGTG 167441 (TGTGCA)n#Sim 48 ATGTG 52 Matrix = Unknown Transitions / transversions = 4.50 (9/2) Gap_init rate = 0.06 (3 / 54), avg. gap size = 1.00 (3 / 3) 12 8.58 13.51 0.00 chr6qtel1M 169266 169302 (830698) (ATACTCT)n#Simple_repeat 1 42 (0) m_b302s252i12 12645 chr6qtel1M 169266 ATACT-TAT-C-CTATACTCTATA--CAATTCTCTATATTCT 169302 - - - -- v v i (ATACTCT)n#Si 1 ATACTCTATACTCTATACTCTATACTCTATACTCTATACTCT 42 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.11 (4 / 36), avg. gap size = 1.25 (5 / 4) 18 10.01 6.25 0.00 chr6qtel1M 169688 169719 (830281) (AT)n#Simple_repeat 1 34 (0) m_b302s252i13 12646 chr6qtel1M 169688 ATAAATATATAT-TACATATATAT-TATATTTAT 169719 v - i - v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATAT 34 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.06 (2 / 31), avg. gap size = 1.00 (2 / 2) 181 25.50 0.45 0.45 chr6qtel1M 170128 170576 (829424) (TC)n#Simple_repeat 1 449 (0) m_b302s252i14 12647 chr6qtel1M 170128 TCTTTCTCTCTGTTGGTCTCTTTCTCTCTCTCTCTCTCTCTCTCTCTCTC 170177 i v ivv i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr6qtel1M 170178 TCTCTCTCTCTCT-TCTCTCACTCTCTTTCTATGTGTGTGTCTCTCTTGG 170226 - v i v v v v v ivv (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chr6qtel1M 170227 TTTCTGTCTCTCTGTCTCTGTCTCTGTCTCTCTCTCTTTCTATGTGTGTG 170276 i v v v v i v v v v - (TC)n#Simple_ 101 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT- 149 chr6qtel1M 170277 CTCTCTTGGTTTCTGTCTCTCTGTCTCTGTCTCTCTGTCTCTCTTTCTCT 170326 ivv i v v v v i (TC)n#Simple_ 150 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 199 chr6qtel1M 170327 CTCTCTCTCTTGCTCTTTGCCTCTGTCTCTCTGTCTCTGTCTGTGTGTGT 170376 iv i vi v v v v v v v (TC)n#Simple_ 200 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 249 chr6qtel1M 170377 GTGTGTGTGTGTGGTCTCTATCTCTGTCTCTCTCTGTCTCATTTTCTGTG 170426 v v v v v v -v v v v vi i v v (TC)n#Simple_ 250 CTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 298 chr6qtel1M 170427 TGTGTGTGTGTGTGTGTCTGTCTGCCTCTCTGTCTCTCTGTCAGTCTCTG 170476 v v v v v v v v v vi v v vv v (TC)n#Simple_ 299 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 348 chr6qtel1M 170477 TCTCTTTCTCTCTGTCTCT-TCTCTCTCTTGGTTTCTGTCTCTCTCTTTG 170525 i v - ivv i v i v (TC)n#Simple_ 349 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 398 chr6qtel1M 170526 TCTCTGTCTCTCTGTCTCTGTCTCTGTGTGTCTCTCTGTCTCTGTTTCTC 170575 v v v v v v v v i (TC)n#Simple_ 399 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 448 chr6qtel1M 170576 T 170576 (TC)n#Simple_ 449 T 449 Matrix = Unknown Transitions / transversions = 0.28 (21/75) Gap_init rate = 0.01 (4 / 448), avg. gap size = 1.00 (4 / 4) 121 26.59 2.72 4.14 chr6qtel1M 171221 171481 (828519) (TGTCTC)n#Simple_repeat 1 257 (250) m_b302s252i15 12648 chr6qtel1M 171221 TGTTTCTTTCTCT-TGTCAGTCTCTG--TCTGTTTCTGTCTCTCTCTTCT 171267 i v - v v -- i v - (TGTCTC)n#Sim 1 TGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTC-TCT 49 chr6qtel1M 171268 GTCTGTCTCTCTATCTATCCTATCTATCTCCTTCTCTCTATGTGCATCTC 171317 v v i v -v v i iv v v v -- (TGTCTC)n#Sim 50 GTCTCTGTCTCTGTCTCT-GTCTCTGTCTCTGTCTCTGTCTCTG--TCTC 96 chr6qtel1M 171318 TTGTCTCTGTCTCTATCTCTCTCATTCTGTGTGTGTGTGTGT-TCTGGCT 171366 - i v -- v v v v - v (TGTCTC)n#Sim 97 -TGTCTCTGTCTCTGTCTCTGTC--TCTGTCTCTGTCTCTGTCTCTGTCT 143 chr6qtel1M 171367 ACTG-C-CTGTCTGTTCTCTCTTGTCTCTGTCTCCCTCTCT-TGTGTG-C 171412 - - - -i v - iv - v v - (TGTCTC)n#Sim 144 -CTGTCTCTGTCT-CTGTCTC-TGTCTCTGTCTCTGTCTCTGTCTCTGTC 190 chr6qtel1M 171413 TTAAACTCCATTTCTCGTTTCCCTGTCTATCTATGTTTCTCTCTGCTCTC 171462 iviv ii i - i iv v i v i v - v (TGTCTC)n#Sim 191 TCTGTCTCTGTCTCT-GTCTCTGTCTCTGTCTCTGTCTCTGTCT-CTGTC 238 chr6qtel1M 171463 TCT-TGTGGGTATCTGTGGG 171481 - v vv v -vv (TGTCTC)n#Sim 239 TCTGTCTCTGTCTCTGT-CT 257 Matrix = Unknown Transitions / transversions = 0.47 (17/36) Gap_init rate = 0.08 (21 / 260), avg. gap size = 1.05 (22 / 21) 64 6.21 2.38 0.00 chr6qtel1M 171482 171565 (828435) (CT)n#Simple_repeat 1 86 (0) c_b302s251i0 12649 chr6qtel1M 171482 CTCTCTCTGTCTCTGTCTCT-TTTCTCTCTCTCTCTCTCTCTCTCTCTCT 171530 v v - i (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chr6qtel1M 171531 CTCTCTCTC-CTCTGTCTCTCTGTCTCTCTCTCTCT 171565 - v v (CT)n#Simple_ 51 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 86 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.02 (2 / 83), avg. gap size = 1.00 (2 / 2) 121 26.59 2.72 4.14 chr6qtel1M 171566 171757 (828243) (TGTCTC)n#Simple_repeat 258 446 (61) m_b302s252i15 12650 chr6qtel1M 171566 TCTATCAATCTGTGTCTGTGTGTGTGT-TATGTCTGTGTGTCTGTGTGTC 171614 v v vi v v v v - v v v v v v (TGTCTC)n#Sim 258 TGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTG 307 chr6qtel1M 171615 TCT-TGTCTGTGTGTGTGTGTTCTCGTCTCTGTCTCTCATCTCTGTTTCC 171663 - v v v -i - -i i - (TGTCTC)n#Sim 308 TCTCTGTCTCTGTCTCTGT-CTCT-GTCTCTGTCTCT-GTCTCTGTCT-C 353 chr6qtel1M 171664 ATTTCTCT-TCTCTGACTCTATCTCTGTCTCTCTCCGTCTCACTTTCTCT 171712 - v - v i v iv v v v (TGTCTC)n#Sim 354 -TGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCT 402 chr6qtel1M 171713 GTGTGTGTGTGTGGTTTCTGTCTCCCTCTCCTGTCTCTCTGTCAG- 171757 v v v v - i iv - v v v - (TGTCTC)n#Sim 403 GTCTCTGTCTCT-GTCTCTGTCTCTGTCT-CTGTCTCTGTCTCTGT 446 Matrix = Unknown Transitions / transversions = 0.26 (8/31) Gap_init rate = 0.06 (11 / 191), avg. gap size = 1.00 (11 / 11) 30 8.73 4.76 1.54 chr6qtel1M 171758 171820 (828180) (TC)n#Simple_repeat 1 65 (0) c_b302s251i1 12651 chr6qtel1M 171758 TCTCTATCTGTCTCTGTCTCTGTCTCT-TGTCTCTCT-TCTCTCTCTCTC 171805 v v v v - v - (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr6qtel1M 171806 GT-TCTCTCTCTCTCT 171820 - - (TC)n#Simple_ 51 -TCTCTCTCTCTCTCT 65 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.06 (4 / 62), avg. gap size = 1.00 (4 / 4) 121 26.59 2.72 4.14 chr6qtel1M 171821 171879 (828121) (TGTCTC)n#Simple_repeat 447 505 (2) m_b302s252i15 12652 chr6qtel1M 171821 TGTGTCTGTCTGCCTGTCTGCCTGTCT-TCTCTGTTCTCTGTCTCCCTCT 171869 v v v vi viv v - - iv (TGTCTC)n#Sim 447 TCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTG-TCTCTGTCTCTGTCT 495 chr6qtel1M 171870 CTCTGTGTGT 171879 v v v (TGTCTC)n#Sim 496 CTGTCTCTGT 505 Matrix = Unknown Transitions / transversions = 0.27 (3/11) Gap_init rate = 0.03 (2 / 58), avg. gap size = 1.00 (2 / 2) 14 21.98 2.38 0.00 chr6qtel1M 173550 173591 (826409) (TTTTATG)n#Simple_repeat 1 43 (0) m_b302s252i16 12653 chr6qtel1M 173550 TTTTCTGTCTCATGTTTTATGTTTT-TATTTGATTGTATATGT 173591 v i i - i v vv v (TTTTATG)n#Si 1 TTTTATGTTTTATGTTTTATGTTTTATGTTTTATGTTTTATGT 43 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.02 (1 / 41), avg. gap size = 1.00 (1 / 1) 13 29.20 3.85 2.53 chr6qtel1M 173850 173927 (826073) (TCTTT)n#Simple_repeat 1 79 (0) m_b302s252i17 12654 chr6qtel1M 173850 TCTTTTCTTTAC--CTCTTGTAGTTTATTTTGTTTTCTGTGTTGCTTTTT 173897 v --i v vv v v v vi vi i (TCTTT)n#Simp 1 TCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTT 50 chr6qtel1M 173898 AATTTTATTTCTCCTTTTC-TTCCCTTTCTT 173927 vv v - - - i i (TCTTT)n#Simp 51 TCTTTTCTTT-T-CTTTTCTTTTCTTTTCTT 79 Matrix = Unknown Transitions / transversions = 0.50 (6/12) Gap_init rate = 0.05 (4 / 77), avg. gap size = 1.25 (5 / 4) 37 2.86 0.00 0.00 chr6qtel1M 173981 174016 (825984) (TA)n#Simple_repeat 1 36 (0) c_b302s251i2 12655 chr6qtel1M 173981 TATATATATATATATATATATATATACATATATATA 174016 i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATA 36 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 49 6.22 2.99 0.00 chr6qtel1M 174471 174537 (825463) (TC)n#Simple_repeat 1 69 (0) c_b302s251i3 12656 chr6qtel1M 174471 TCTCTGTCT-TCTCTCTGTTTC-CTCTCTCTCTCTCTCTCTCTCTCTCTC 174518 v - v i - (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr6qtel1M 174519 TCTCTCTCTCTCTGTCTCT 174537 v (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCT 69 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.03 (2 / 66), avg. gap size = 1.00 (2 / 2) 193 30.75 7.62 0.89 chr6qtel1M 176028 176132 (823868) MIR#SINE/MIR 95 206 (56) m_b302s601i6 12657 chr6qtel1M 176028 GCATTTCACTTAATTTCTATATGTTTCAG--ACCTCTATCAGCAACATGA 176075 vv i ii v i ii --v - v i v i MIR#SINE/MIR 95 GCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTC-ATCTGTAAAATGG 143 chr6qtel1M 176076 GCATCAT-ACCGT---TAGCTTATAACTTTTCTAAAAGGATCAAATGA-- 176119 v v - iv --- v i ivv vi ivi i -- MIR#SINE/MIR 144 GGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGT 193 chr6qtel1M 176120 TATCATATGTAAA 176132 vi i MIR#SINE/MIR 194 TAATACATGTAAA 206 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 40.36 CpG sites = 17, Kimura (unadjusted) = 40.36 Transitions / transversions = 1.13 (17/15) Gap_init rate = 0.05 (5 / 104), avg. gap size = 1.80 (9 / 5) 219 31.75 8.40 1.43 chr6qtel1M 177042 177172 (822828) MIRb#SINE/MIR 2 141 (127) m_b302s601i7 12658 chr6qtel1M 177042 AGTGAGTTAGCTAGTAGTTCAGTAGATTATGTATTAGCCTTGCAGTCAAA 177091 v i vi -- i v i vviv i ivi i v i MIRb#SINE/MIR 2 AGAGGGGCAGC--GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGA 49 chr6qtel1M 177092 GTTAT-TGAGTTCAAATCT-AGCCTTG--ATTTACTACTTCTGTGTCACT 177137 vvv i- i i i-i ii -- i vi v v vi MIRb#SINE/MIR 50 CAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTT 99 chr6qtel1M 177138 GGG---ATT--TTAACC-CTGTTTGCCTTAG-TTCCTCATTT 177172 ---i -- - v vv i - i MIRb#SINE/MIR 100 GGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCT 141 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 38.46 CpG sites = 23, Kimura (unadjusted) = 42.45 Transitions / transversions = 1.28 (23/18) Gap_init rate = 0.07 (9 / 130), avg. gap size = 1.44 (13 / 9) 13 21.75 0.00 6.67 chr6qtel1M 177815 177862 (822138) (TTA)n#Simple_repeat 1 45 (0) m_b302s252i18 12659 chr6qtel1M 177815 TTATTTCAATAACTATGACTTATTAATTATTATTTTTATTGATCATTA 177862 viv v i v - - v - i (TTA)n#Simple 1 TTATTATTATTATTATTA-TTATT-ATTATTATTATTATT-ATTATTA 45 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.06 (3 / 47), avg. gap size = 1.00 (3 / 3) 229 22.81 1.75 0.00 chr6qtel1M 179165 179221 (820779) C DNM1r#Unknown (2126) 2536 2479 m_b302s502i1 12660 chr6qtel1M 179165 TATATGTACACATACATATACAAACGCATGCATACACATGCAT-CATACA 179213 i i i v ii ii i ii -i C DNM1r#Unknown 2536 TATATATACACATATATACACACATACACACATATACACACATATATACA 2487 chr6qtel1M 179214 CATATACA 179221 i C DNM1r#Unknown 2486 CACATACA 2479 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 29.76 CpG sites = 12, Kimura (unadjusted) = 29.76 Transitions / transversions = 12.00 (12/1) Gap_init rate = 0.02 (1 / 56), avg. gap size = 1.00 (1 / 1) 15 14.13 0.00 3.12 chr6qtel1M 180462 180494 (819506) (TAT)n#Simple_repeat 1 32 (0) m_b302s252i19 12661 chr6qtel1M 180462 TATTATTTATATTATTACTATTATTGATGATTA 180494 vv i - v (TAT)n#Simple 1 TATTATTATTATTATTATTATTATT-ATTATTA 32 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 214 26.84 4.81 6.86 chr6qtel1M 180623 180726 (819274) C MIRb#SINE/MIR (44) 224 123 m_b302s601i8 12662 chr6qtel1M 180623 ACTGTGATAATCACTTCACA---ATTATTTAACAACTTTTAAAC--TATG 180667 v v i i --- i -- --- v --i ii C MIRb#SINE/MIR 224 ACTGTGCTAAGCGCTTTACATGCATTATCT--CA---TTTAATCCTCACA 180 chr6qtel1M 180668 AAAAACCTTAGACTTTTAAGTGTTATTGTCTATATTTGACATTTGAAGAA 180717 v v vv v--v i i i ivi v vv i C MIRb#SINE/MIR 179 ACAACCCTGCGAG--GTAGGTATTATTATCCCCATTTTACAGATGAGGAA 132 chr6qtel1M 180718 ACTAAGGCT 180726 i C MIRb#SINE/MIR 131 ACTGAGGCT 123 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 31.99 CpG sites = 13, Kimura (unadjusted) = 33.51 Transitions / transversions = 1.00 (13/13) Gap_init rate = 0.09 (9 / 103), avg. gap size = 1.33 (12 / 9) 276 32.63 1.69 9.09 chr6qtel1M 181142 181259 (818741) MIRc#SINE/MIR 6 115 (153) m_b302s601i9 12663 chr6qtel1M 181142 CAGTTTGATGAAACCATGGATAGAGGACTAGCCTGAGTGTCAGTAGGATC 181191 v i --- vi v v i v vi v v i i MIRc#SINE/MIR 6 CAGTGTGGTG---CAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chr6qtel1M 181192 TGAGTTCAAAAGCAGCCCCAGAAATTTAACAC--ATTAACCATATAATCC 181239 i i ----- i i v-- i iv -- i i ii i i i i MIRc#SINE/MIR 53 TGGGTTCGA-----GTCCCGGC--TCTGCCACTTACTAGCTGTGTGACCT 95 chr6qtel1M 181240 TGAACAAATCACTTAAACCC 181259 ii i v i MIRc#SINE/MIR 96 TGGGCAAGTCACTTAACCTC 115 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 41.67 CpG sites = 24, Kimura (unadjusted) = 45.21 Transitions / transversions = 2.18 (24/11) Gap_init rate = 0.09 (11 / 117), avg. gap size = 1.09 (12 / 11) 1331 28.19 4.60 2.94 chr6qtel1M 181653 182456 (817544) L1M5_orf2#LINE/L1 918 1734 (1560) m_b302s551i2 12664 chr6qtel1M 181653 TAAAATAGAGAAAAG----AGGGTCAAAGAATTAGGCTTACAGATTAAAA 181698 i v ii ---- iii v vi i v vv i L1M5_orf2#LIN 918 TAGAAAAGAAGAAAGGCTTAAAATCAATGATCTAAGCTTCCACCTTAAGA 967 chr6qtel1M 181699 AGCTAGAAAAAAA----CAAATTAAAAC---ACCCAGTCAAACATTAACT 181741 i ---- v --- v?v vi vi-- v- L1M5_orf2#LIN 968 AGCTAGAAAAAGAAGAGCAAATTAAACCCAAAGNAAGTAGAAGG--AAG- 1014 chr6qtel1M 181742 TGAAATTTTAAAAATAA-AGAAGAGATTAATAAAACTGAAAGTAACAAAA 181790 - vv i - v i i i iv ii -- ? L1M5_orf2#LIN 1015 -GAAATAATAAAGATAAGAGCAGAAATCAATGAAATAGAAAACAA--ANA 1061 chr6qtel1M 181791 AACTATTGAATTAATAAATAAAACTAAAAGTTGGTTTTGTGAAAAGAAAA 181840 ? v v ivv v ii i i i i v v-- L1M5_orf2#LIN 1062 NACAATAGAGAAAATCAACGAAGCCAAAAGCTGGTTCTTTGAAAAGAT-- 1109 chr6qtel1M 181841 CAACAAAATATATATAAATCTTCAGTAAATGTGATTTAAAAGAAAAGAG- 181889 i - i- i ii i? ivv iv i i - L1M5_orf2#LIN 1110 CAATAAAAT-TG-ATAAACCTCTAGCNAGACTGATCAAGAAAAAAAGAGA 1157 chr6qtel1M 181890 GAAAAT-TAAATTGTTAGT--CATAAAATGAGAAGGGAGAGGTTGCCACT 181936 i i-i iii i -- -ii i i vi ii i v L1M5_orf2#LIN 1158 GAAGACACAAATTACCAATATCA-GGAATGAAAAAGGAGACATCACTACA 1206 chr6qtel1M 181937 AATGAAAAGAAAATTAGAGCAATAATTAGAGT-TACTTTTGTCCAACTTT 181985 i vvv vii v i ivi v v- - v vv L1M5_orf2#LIN 1207 GATCCTACAGACATTAAAAGGATAATAAGAGAATA-TTATGAACAACTTT 1255 chr6qtel1M 181986 ATGCCAATAAATCAGATAA-----ATGAAATGGAAGAATATCTTCAAAAA 182030 iv ? ----- vi - i ii L1M5_orf2#LIN 1256 ATGCCAATAAATTTGANAACTTAGATGAAATGGACAAAT-TCCTTGAAAA 1304 chr6qtel1M 182031 ATATAGCTTACCCAAATTAACAGAGGAAGAAGTAAAATGGTTAAGCCATC 182080 i i i? v i i ?v i i i vivi i iivii L1M5_orf2#LIN 1305 ACACAANTTACCAAAACTGACNCAAGAAGAAATAGAAAATCTGAATAGCC 1354 chr6qtel1M 182081 CCATTTTAGAAAAAGAAATAGAATAAGCTATTACTCAACACTCT------ 182124 i v ivivv v vv iv --- v ii ------ L1M5_orf2#LIN 1355 CTATATCTATTAAAGAAATTGAATTTGTAATTA---AAAACCTTCCCACA 1401 chr6qtel1M 182125 AAGAAAAATCCCCAGGACCAAATGGATTTACATGTAAATTCTACCAAATA 182174 -- i v i v i vv i i L1M5_orf2#LIN 1402 AAGAAAA--CTCCAGGCCCAGATGGCTTCACTGGTGAATTCTACCAAACA 1449 chr6qtel1M 182175 TTTAA---AGAATTAACTCCAATGATATATAAACTATTTGAAAAAATAGG 182221 --- v iv vv i i v iv i i L1M5_orf2#LIN 1450 TTTAAGGAAGAAATAATACCAATCTTACACAAACTCTTCCAGAAAATAGA 1499 chr6qtel1M 182222 GATTGAAGGAGTCCTATCAAATTCTTTTCATGAC-CCAGACATGATACTG 182270 i vv i iiv vi v i v i v- - ? iv L1M5_orf2#LIN 1500 AAAAGAGGGAACACTTCCCAACTCATTTTATGAGGCCAG-CATNACCCTG 1548 chr6qtel1M 182271 ATACCTAAACCAGGTAGGTTGAAAACA----GAGAAAGAAAAATTATAGA 182316 v ? ii ----- i ----i ii i L1M5_orf2#LIN 1549 ATACCAAAACCNGACA-----AAGACATTACAAGAAAAGAAAATTACAGA 1593 chr6qtel1M 182317 CCAATCTTCCTAATGAATATTGATGCTAAAATCATAAATACAATATTAGC 182366 v i v i v v v ? i v L1M5_orf2#LIN 1594 CCAATATCCCTCATGAACATAGATGCAAAAATCCTNAACAAAATATTAGC 1643 chr6qtel1M 182367 AAA-AGATTAGAGAAAATCATCACCAGGATAATACACTATGAGCAAGTAA 182415 -v v vv v vvi v vv ii v ii L1M5_orf2#LIN 1644 AAATCGAATCCAGCAATATATAAAAAGGATAATACATCATGACCAAGTGG 1693 chr6qtel1M 182416 ATTTTATACCAAGAATGTAGGGCTGATTCAATATTAGGAAA 182456 iv v i i i i i i i v i L1M5_orf2#LIN 1694 GGTTTATCCCAGGAATGCAAGGTTGGTTTAACATTCGAAAA 1734 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.60 CpG sites = 126, Kimura (unadjusted) = 36.83 Transitions / transversions = 1.34 (126/94) Gap_init rate = 0.05 (38 / 803), avg. gap size = 1.61 (61 / 38) 441 22.15 3.33 5.98 chr6qtel1M 185111 185230 (814770) MIRc#SINE/MIR 11 127 (141) m_b302s601i10 12665 chr6qtel1M 185111 TGGCTCAGTGGAGAGA--AGTATCCCTGAAGTCAGGAGGACCTAAGTTCA 185158 iv i -- v ivv i i i ii i MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr6qtel1M 185159 AATCCAGCCTCACACATTTAGTAGTTACTAGTTTTGTGACCCTGGGCAAG 185208 i v v ------- ivi v i v i MIRc#SINE/MIR 61 AGTCCCGGCTC-------TGCCACTTACTAGCTGTGTGACCTTGGGCAAG 103 chr6qtel1M 185209 TCATTTAACC-CCCTG-GCCTCAG 185230 i - i - MIRc#SINE/MIR 104 TCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 25.64 CpG sites = 16, Kimura (unadjusted) = 26.87 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.08 (10 / 119), avg. gap size = 1.10 (11 / 10) 300 34.31 5.29 0.56 chr6qtel1M 185441 185610 (814390) MIR3#SINE/MIR 19 196 (12) m_b302s601i11 12666 chr6qtel1M 185441 AGAGAGGGAACTAAATAGCAGGCAGAGAGCCTAGGCACTGAAATGCAGCC 185490 i v vi v i v v iiii i iv - iviv i i MIR3#SINE/MIR 19 AGAGAGAGCACGGACTGGGAGTCAGGAGACCTGGGTTCT-AGTCCCGGCT 67 chr6qtel1M 185491 C---CAATAACTTCCTTTG--ACTGTGAAAAACTCACA-CAGTTCCCTTG 185534 --- v ?v v -- iv iiv v v- vi i v MIR3#SINE/MIR 68 CTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGG 117 chr6qtel1M 185535 GCCTCAGTTACCTCACCTATAAAATGATTGCTTTTGGTCAACT--TCTCT 185582 v i i vv vv v iii iv -- MIR3#SINE/MIR 118 GCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCT 167 chr6qtel1M 185583 GA-CTTCCTTTAAGCTCTATAATCCTCTG 185610 i -v i iv ivv i v MIR3#SINE/MIR 168 AAGGTCCCTTCCAGCTCTGACATTCTATG 196 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 45.96 CpG sites = 29, Kimura (unadjusted) = 47.06 Transitions / transversions = 1.00 (29/29) Gap_init rate = 0.04 (6 / 169), avg. gap size = 1.67 (10 / 6) 17 0.00 0.00 0.00 chr6qtel1M 186924 186942 (813058) (T)n#Simple_repeat 1 19 (0) m_b303s252i0 12667 chr6qtel1M 186924 TTTTTTTTTTTTTTTTTTT 186942 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 15 16.57 4.88 0.00 chr6qtel1M 187094 187134 (812866) (ATTCAGA)n#Simple_repeat 1 43 (0) m_b303s252i1 12668 chr6qtel1M 187094 ATTCAGAAGTCAGTATTCAGTA-TGAG-ATTCACAAGTCAGAA 187134 v v v - v - v v (ATTCAGA)n#Si 1 ATTCAGAATTCAGAATTCAGAATTCAGAATTCAGAATTCAGAA 43 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 83 27.97 0.42 0.84 chr6qtel1M 190890 191129 (808871) (TCTC)n#Simple_repeat 1 239 (0) m_b303s252i2 12669 chr6qtel1M 190890 TCTTTCTCTCTGTCAGTCTCTGTGTAGCTGTCTC-CTTGCTCTCTCTGTG 190938 i v vv v v vv v - iv v v (TCTC)n#Simpl 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr6qtel1M 190939 TCTCTCTGTCTCTCCCTATCTCTGCGTGTGTGTCTGTCTGTTTGTCTCTT 190988 v i v - - v v v v v i v i (TCTC)n#Simpl 51 TCTCTCTCTCTCTCTCTCTCTCT-C-TCTCTCTCTCTCTCTCTCTCTCTC 98 chr6qtel1M 190989 TCGCTCTCTTAGTCTCTTTCTCTCTCTGTCTCTGTCTCTGTCTCTCTGTC 191038 v ivv i v v v v (TCTC)n#Simpl 99 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 148 chr6qtel1M 191039 TCACTCTGTCTTTCTTTCTGTCTCTCTGTCTGTCTCTGTGTGTGTGTCTG 191088 v v i i v v v v v v v v v (TCTC)n#Simpl 149 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 198 chr6qtel1M 191089 TCTTTCTGTCTGCCTCTCTGTGTCTCTGTCTCCCTATCTCT 191129 i v vi v v v i v (TCTC)n#Simpl 199 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 239 Matrix = Unknown Transitions / transversions = 0.28 (12/43) Gap_init rate = 0.01 (3 / 239), avg. gap size = 1.00 (3 / 3) 15 21.12 1.61 6.78 chr6qtel1M 193648 193709 (806291) (GAAAAG)n#Simple_repeat 1 59 (0) m_b303s252i3 12670 chr6qtel1M 193648 GAAAAGGGAGAAGGGAAAATTGAAAAGG-GAAGGAATAAGCTAAGTGGAA 193696 - - i -v -i - vv iv i (GAAAAG)n#Sim 1 GAAAA-GGA-AAAGGAAAA-GGAAAAGGAAAAGGAA-AAGGAAAAGGAAA 46 chr6qtel1M 193697 GGGAATAGGAAAA 193709 i v (GAAAAG)n#Sim 47 AGGAAAAGGAAAA 59 Matrix = Unknown Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.08 (5 / 61), avg. gap size = 1.00 (5 / 5) 256 28.46 12.93 1.55 chr6qtel1M 193824 194055 (805945) L1MEc_5end#LINE/L1 2221 2478 (49) m_b303s551i0 12671 chr6qtel1M 193824 AAGGAGGAAGGAAGGGAGAAAAGTATAAA----CAG--GGGTTAACAAGA 193867 i v i ii i v v ---- -- vi vv L1MEc_5end#LI 2221 AAGAAGGCAGAAAAAGAAAAAAGGAAAAAAGAACAGATGGGACAAATAGA 2270 chr6qtel1M 193868 TGGCATGTAATAGCAAACTGGTAGTTTTAA-CCC---------------- 193900 vii --- iv v - ---------------- L1MEc_5end#LI 2271 AAACA---AATAGCAAGATGGTAGATTTAAACCCAACCATATCAATAATC 2317 chr6qtel1M 193901 ----TAAATGTGAATGAGGGTAAACTGCCCCATAGAGAGGAAGTGGTTA- 193945 ---- i - vv vv v vi i v v i i- L1MEc_5end#LI 2318 ACATTAAATGTAAATG-GTCTAAACACCCCAATTAAAAGGCAGAGATTGT 2366 chr6qtel1M 193946 GAGAATGAATTAAAAGCCTTAATCCTACAATATGTTGTTTACAGGAAACA 193995 v v i v iv vvi i v v i ii i ? L1MEc_5end#LI 2367 CAGATTGGATAAAAAAGCAAGACCCAACTATATGCTGCCTACAAGAAACN 2416 chr6qtel1M 193996 CAGCTGAAGCAGGAAGATACACACAG--TAAAGGTAAAAGGTTGTAGCAG 194043 vi v ii vi i v i -- i v v iv i L1MEc_5end#LI 2417 CACTTTAAATATAAAGACACAAATAGGTTAAAAGTAAAAGGATGGAAAAA 2466 chr6qtel1M 194044 AATCTACCATGC 194055 i v L1MEc_5end#LI 2467 GATATACCATGC 2478 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.46 CpG sites = 32, Kimura (unadjusted) = 36.46 Transitions / transversions = 0.97 (32/33) Gap_init rate = 0.04 (10 / 231), avg. gap size = 3.40 (34 / 10) 308 26.49 3.23 2.56 chr6qtel1M 193861 194015 (805985) L1M6_5end#LINE/L1 2360 2515 (0) m_b303s551i1 12671 chr6qtel1M 193861 AACAAGATGGCA--TGTAATAGCAAAC-TGGTAGTTTTAACCCTAAATGT 193907 i? i --?i v v - ivi v i vv L1M6_5end#LIN 2360 AGNAAGATGACAAANATAAGACCAAACATATCAGTTATGACAATAAATGT 2409 chr6qtel1M 193908 GAATGAGGGTAAACTGCCCCAT--AGAGAGGAAGTGGTTAGAGAATGAAT 193955 i - v v i -- i vi -iv ivv v ii L1M6_5end#LIN 2410 AAATG-GGTTAAACTCCCCTATTAAAAGACAAAG-ACTCTCAGATTGGGT 2457 chr6qtel1M 193956 TAAAAGCCTTAATCCTACAATATGTTGTTTACAGGAAACACAGCTGAAGC 194005 iv vv v v i i i v i vv L1M6_5end#LIN 2458 TAAAAAACAAAATCCAACTATATGCTGTTTACAAGAGACACACCTAAATA 2507 chr6qtel1M 194006 AGGAAGATAC 194015 -- L1M6_5end#LIN 2508 A--AAGATAC 2515 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 33.48 CpG sites = 19, Kimura (unadjusted) = 33.48 Transitions / transversions = 0.90 (19/21) Gap_init rate = 0.05 (7 / 154), avg. gap size = 1.29 (9 / 7) 2309 29.95 4.52 2.99 chr6qtel1M 193901 195580 (804420) L1M5_orf2#LINE/L1 38 1742 (1552) m_b303s551i2 12671 chr6qtel1M 193901 TAAATGTGAATGAGGGTAAACTGCCCCATAGAGAGGAAGTGGTTA-GAGA 193949 i - ?v vvi v vi i v v i i-v L1M5_orf2#LIN 38 TAAATGTAAATG-GNCTAAACACTCCAATTAAAAGGCAGAGATTGTCAGA 86 chr6qtel1M 193950 ATGAATTAAAAGCCTTAATCCTACAATATGTTGTTTACAGGAAACACAGC 193999 v i v iv vvi i v v i i i i i vi L1M5_orf2#LIN 87 CTGGATAAAAAAACAAGACCCAACTATATGCTGTCTACAAGAGACGCACT 136 chr6qtel1M 194000 TGAAGCAGGAAGATACACACAG--TAAAGGTAAAAGGTTGTAGCAGAATC 194047 v ii vi i v ? -- i i v v iv ii v L1M5_orf2#LIN 137 TTAAATATAAAGACACAGANAGGTTGAAAGTAAAAGGATGGAAAAAGATA 186 chr6qtel1M 194048 TACCATGCTTCAGGTGAAGTAAAA-AAAGCAGGGGTAGCCATCCTGATCT 194096 v-v viiv ?i - v ? i i vi i v L1M5_orf2#LIN 187 TACCATGCA-AACACTAANCAAAAGAAAGCTGGNGTGGCTATATTAATAT 235 chr6qtel1M 194097 CAGATCAAGCA------AAAGCAAAAATTGATCTAATTAAAAGAGATAAG 194140 iv i ------ i i --- --- vv i L1M5_orf2#LIN 236 CAGACAAAGTAGACTTCAAGGCAAGAA---AT---ATTACCAGAGATAAA 279 chr6qtel1M 194141 GAAGGGCACTATATCTTGCTAAA-GGGTAGCATAGATAATCAAGCA---A 194186 i i i vi vv v - ----i iv v v --- L1M5_orf2#LIN 280 GAGGGACATTTCATAATGATAAAAGGGT----CAATTCATCAAGAAGACA 325 chr6qtel1M 194187 TATCAATATTAAACATATATGCACCAAGTAGTGTAGCATTTAAATTCTTA 194236 v vi ii i v i iiiv v iv v v i L1M5_orf2#LIN 326 TAACAATCCTAAATGTGTATGCACCTAATAACAGAGCTTCAAAATACATG 375 chr6qtel1M 194237 AAAGAGAAATTAAGAGAGCTGCAAGAAGAAATAGACAG---CAAAAGTAT 194283 iv i i i v i iv i i--- v v L1M5_orf2#LIN 376 AAGCAAAAACTGACAGAACTAAAAGGAGAAATAGACAAATCCACAATTAT 425 chr6qtel1M 194284 AATATTGGGTGATCTCAACCTTGCATCCTGAG-AATTAGATAAATCAAAC 194332 i--- ? v i i vi?v vii v - - i v ii L1M5_orf2#LIN 426 AG---TNGGAGATTTTAACACNCCTCTCTCAGTAATT-GATAGAACAAGT 471 chr6qtel1M 194333 ---CATAAAATAAATAAGAA---AGAA---TTAATAGAATACTAGAAA-- 194371 --- v v i i --- --- i - v i vv -- L1M5_orf2#LIN 472 AGACAAAAAATCAGTAAGGATATAGAAGATTTGA-ACAACACTATCAACC 520 chr6qtel1M 194372 AGTTAGATATGATAGATCTTTGGAGAA-AATGAAATGGAC-ACAGAAAGG 194419 ii v iv i v iv iv - v ?v vivi - ? v -- L1M5_orf2#LIN 521 AACTTGACCTAATTGACATTTATAGAACACTNCACCCAACAACNGCA--G 568 chr6qtel1M 194420 AATACACTTTCTTCTCAGCAGCTCATGGAACCTATA-CAAAATAGACCAT 194468 v i ivv v v v - i L1M5_orf2#LIN 569 AATACACATTCTTTTCAAGTGCACATGGAACATTTACCAAGATAGACCAT 618 chr6qtel1M 194469 ATATTAGGACATAAAAACATCAAA-CTC---AAATGCAGGAAGGCAGAAA 194514 ?i i v ---- i- --- vi?ii i iiv L1M5_orf2#LIN 619 ATNCTGGGCCATAAAA----CAAGTCTCAATAAATTTNAAAGGATTGAAA 664 chr6qtel1M 194515 TAGTA-AATGCATCTTTTCAGACCATGATGCAGTGAAAATTACACTCAAC 194563 vi - iv i v i v ii v i v v viv v i L1M5_orf2#LIN 665 TCATACAGAGTATGTTCTCTGACCACAATGGAATTAAATTAGAAATCAAT 714 chr6qtel1M 194564 AGAAAACAAG------GGGAAATGGACCAAAAATTAATTGAAACTAAATA 194607 iv - ------i i vv- v -- v i i L1M5_orf2#LIN 715 AACAAA-AAGATANCTAGAAAATCC-CCAAATATT--TGGAAATTAAACA 760 chr6qtel1M 194608 ATCTCA-TACTAAAGAATGATTGGGTAAAACAGTAAATTGTACACATAAT 194656 - v - v v ivvv v v iv iii v?viv L1M5_orf2#LIN 761 A-CACACTTCTAAATAACCCATGGGTCAAAGAAGAAATCACAANGGAAAT 809 chr6qtel1M 194657 T---AATCACTTCACCCAAGAAAATGACAATAATGAGACATCATACCAAA 194703 --- vi i ii--- vvi ? i vi v v i L1M5_orf2#LIN 810 TAGAAAATATTTTG---AACTGAATGANAATGAAAATACAACATATCAAA 856 chr6qtel1M 194704 ATGTGTAGGATACAGCCAAAGCGGTAA-TAAAGGGAAATTTTATATCACT 194752 v i i i i iv- i - v ?i L1M5_orf2#LIN 857 ATTTGTGGGATGCAGCTAAAGCAGTGCTTAGAGGGAAA-TTTATAGCNTT 905 chr6qtel1M 194753 AGAGGCCTACTTGCATAAAATATAAAAAGAG---AAGGTCAATGAATTGG 194799 i v ? iv --- i v v i ii --- ii vi ii L1M5_orf2#LIN 906 AAATGCNTATAT---TAGAAAAGAAGAAAGGCTTAAAATCAATGATCTAA 952 chr6qtel1M 194800 GTTTGCAAC-TAAAATGCTAGAAAAGGAA---CAAATTAAAATCCCCAGT 194845 i v v - i v i --- -- v iv L1M5_orf2#LIN 953 GCTTCCACCTTAAGAAGCTAGAAAAAGAAGAGCAAATTAAA--CCCAAAG 1000 chr6qtel1M 194846 CAAACACTAAACTTGAAATTCTAAA-ATGAAATGAGAGATTGATAACATT 194894 ? ii vv iivvv vv - i i vv i ii i v v L1M5_orf2#LIN 1001 NAAGTAGAAGGAAGGAAATAATAAAGATAAGAGCAGAAATCAATGAAATA 1050 chr6qtel1M 194895 GAAAGTAAAAAAGCTATTGAATTAATTAATAAAACTAAGAGTTGGTTCTA 194944 ii ? ?i v v ivv i ii i i i i v L1M5_orf2#LIN 1051 GAAAACAAANANACAATAGAGAAAATCAACGAAGCCAAAAGCTGGTTCTT 1100 chr6qtel1M 194945 TGAAAA---CAACAAAATAGATAAACCCTTAGCAAATCTGATTTA-AAAA 194990 --- i v ii ? iv iv - L1M5_orf2#LIN 1101 TGAAAAGATCAATAAAATTGATAAACCTCTAGCNAGACTGATCAAGAAAA 1150 chr6qtel1M 194991 GGAGAGAGGAAAATCAAATTGTTAGTCTTA-AAATGAAAAGGGAGAACTC 195039 ii i i vv iii i v i -i i vv L1M5_orf2#LIN 1151 AAAGAGAGAAGACACAAATTACCAATATCAGGAATGAAAAAGGAGACATC 1200 chr6qtel1M 195040 TGCCACTAATGAAGAGGAAATTAGAGCAATAATTAGAAGTTACTTTGACC 195089 -i i vi vvvivi v i ivi v iiv i v v L1M5_orf2#LIN 1201 -ACTACAGATCCTACAGACATTAAAAGGATAATAAGAGAATATTATGAAC 1249 chr6qtel1M 195090 AACTTTATGCCAATCAATTCAACAAGTTAAATGAAATGGAAGAATACCTT 195139 v ii ? v i vi v L1M5_orf2#LIN 1250 AACTTTATGCCAATAAATTTGANAACTTAGATGAAATGGACAAATTCCTT 1299 chr6qtel1M 195140 CAAAAATATAGCTTGCCCAGATTAACAGAGGAAGAAGTAAATATCCTAAA 195189 v i i i? i v i i i ?v i i i v vi i L1M5_orf2#LIN 1300 GAAAAACACAANTTACCAAAACTGACNCAAGAAGAAATAGAAAATCTGAA 1349 chr6qtel1M 195190 CAGTCCCATCTTAGAAAAAGAAATAGAACAGGCTATTAGCCAACTCCC-- 195237 i i i v ivivv v ivv iv ivv v i -- L1M5_orf2#LIN 1350 TAGCCCTATATCTATTAAAGAAATTGAATTTGTAATTAAAAACCTTCCCA 1399 chr6qtel1M 195238 TGAGAAAAATCCCTGGACCAGATGGATTTACATGTGAATTCTACCAAACA 195287 ii ii ii v v v i vv L1M5_orf2#LIN 1400 CAAAGAAAACTCCAGGCCCAGATGGCTTCACTGGTGAATTCTACCAAACA 1449 chr6qtel1M 195288 TTCAAAGAACAATTAACTCCAATGTTATATAGACTATTTGAAAAAAATAG 195337 i i v v iv v i i i -i vv i L1M5_orf2#LIN 1450 TTTAAGGAAGAAATAATACCAATCTTACACAAACT-CTTCCAGAAAATAG 1498 chr6qtel1M 195338 GGAATGAAGG-TCTCCTACCAATTTCCTTTTATGACACAGATATGGTACT 195386 ii v i -v v i v -i v vi viii ?iiv L1M5_orf2#LIN 1499 AAAAAGAGGGAACACTTCCCAA-CTCATTTTATGAGGCCAGCATNACCCT 1547 chr6qtel1M 195387 GATACCTAAACTAGGTAGGTTGAAA--ACAGAGAAAGAAAATTATCGACT 195434 v i? ii ii-- v -- iii iv - L1M5_orf2#LIN 1548 GATACCAAAACCNGACAAA--GACATTACAAGAAAAGAAAATTACAGAC- 1594 chr6qtel1M 195435 CAATCT-CCTAATGAATATTGATGCTAAAATCTTAAATAAAATGTTAGCA 195483 v - v i v v i ? i i L1M5_orf2#LIN 1595 CAATATCCCTCATGAACATAGATGCAAAAATCCTNAACAAAATATTAGCA 1644 chr6qtel1M 195484 AA--------AACATTACAGAAAACCATCCCCAGGATAATACATTATGA- 195524 -------- i v i v -------- i - L1M5_orf2#LIN 1645 AATCGAATCCAGCAATATATAAAA--------AGGATAATACATCATGAC 1686 chr6qtel1M 195525 CAAGTAATTTTTATACCCAGAATGCAGGGCTGGTTCAATAGTAGGAAAAC 195574 iivv v vi i i i i v v i v L1M5_orf2#LIN 1687 CAAGTGGGGTTTATCCCAGGAATGCAAGGTTGGTTTAACATTCGAAAATC 1736 chr6qtel1M 195575 TATTAA 195580 v i L1M5_orf2#LIN 1737 AATCAA 1742 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 39.63 CpG sites = 268, Kimura (unadjusted) = 39.85 Transitions / transversions = 1.22 (268/220) Gap_init rate = 0.05 (85 / 1679), avg. gap size = 1.49 (127 / 85) 16 9.98 0.00 5.88 chr6qtel1M 195620 195655 (804345) (TTTTG)n#Simple_repeat 1 34 (0) m_b303s252i4 12672 chr6qtel1M 195620 TTTTGTTTCTCTTACTGTTTTGTTTTGTTTTTTTTT 195655 - v -i v (TTTTG)n#Simp 1 TTTTGTTT-TGTT-TTGTTTTGTTTTGTTTTGTTTT 34 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 13 9.26 0.00 0.00 chr6qtel1M 195774 195796 (804204) (GGGA)n#Simple_repeat 1 23 (0) m_b303s252i5 12673 chr6qtel1M 195774 GGGAGGGGTGGAGGGAGGGAGGG 195796 iv (GGGA)n#Simpl 1 GGGAGGGAGGGAGGGAGGGAGGG 23 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 12 27.09 3.28 3.28 chr6qtel1M 197143 197203 (802797) (ATTT)n#Simple_repeat 1 61 (0) m_b303s252i6 12674 chr6qtel1M 197143 ATTT-TTAATTCTATTT-TCTGTCTCATGTGTTTATGTATTTCTTTGATT 197190 - v - - i i - i v i v v iv (ATTT)n#Simpl 1 ATTTATTTATT-TATTTATTTAT-TTATTTATTTATTTATTTATTTATTT 48 chr6qtel1M 197191 GTATATTTATGTA 197203 i v v (ATTT)n#Simpl 49 ATTTATTTATTTA 61 Matrix = Unknown Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.07 (4 / 60), avg. gap size = 1.00 (4 / 4) 83 9.31 0.00 0.00 chr6qtel1M 197615 197730 (802270) (TA)n#Simple_repeat 1 116 (0) c_b303s251i0 12675 chr6qtel1M 197615 TATATATATATATATATATATATATATATGTATATATATAAAGGCATATG 197664 i v vii i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr6qtel1M 197665 TATGTGTGTATATATATATATATATATATATATATATATATATATATATA 197714 i i i (TA)n#Simple_ 51 TATATATATATATATATATATATATATATATATATATATATATATATATA 100 chr6qtel1M 197715 TATACATATATATATA 197730 i (TA)n#Simple_ 101 TATATATATATATATA 116 Matrix = Unknown Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.00 (0 / 115), avg. gap size = 0.0 (0 / 0) 293 36.44 1.67 1.67 chr6qtel1M 201887 202006 (797994) C MIRc#SINE/MIR (112) 156 37 m_b303s601i2 12676 chr6qtel1M 201887 TTATTATCTATATTTAACACTTGAGAAAACTGAGA--CAGACAGAACTGA 201934 ivi v vv i i-- v -ii i C MIRc#SINE/MIR 156 TTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAG-GTTAA 108 chr6qtel1M 201935 ATGATATTGAGTATGGTTATGTAGATAATAAATCTCTGAAGTAAAGTTTG 201984 i i- vvi v i iii v i i vv v iviiiiii i C MIRc#SINE/MIR 107 GTGAC-TTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCG 59 chr6qtel1M 201985 AAATCATGCCTTTCTAACTCCA 202006 vi v i i i C MIRc#SINE/MIR 58 AACCCAGGTCTTCCTGACTCCA 37 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 49.47 CpG sites = 28, Kimura (unadjusted) = 53.36 Transitions / transversions = 1.87 (28/15) Gap_init rate = 0.03 (3 / 119), avg. gap size = 1.33 (4 / 3) 34 26.15 6.90 0.00 chr6qtel1M 202128 202272 (797728) (TATA)n#Simple_repeat 1 155 (0) m_b303s252i7 12677 chr6qtel1M 202128 TATAT-TAT-TATATACATTTATAT-TGTATGTAT-TTTATATATA-AGG 202172 - - i v - i i - v - vi (TATA)n#Simpl 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr6qtel1M 202173 TATTGAT-TAATTATATAAATATGTATTTATGTGTAGA-AGATAAATATT 202220 vv - vv v i v i i v - v v v (TATA)n#Simpl 51 TATATATATATATATATATATATATATATATATATATATATATATATATA 100 chr6qtel1M 202221 TA-ATATATATTTGTGCAT-TGTATAGATATTGAT-TATATCTATTCATA 202267 - v i ii - i v vv - v vi (TATA)n#Simpl 101 TATATATATATATATATATATATATATATATATATATATATATATATATA 150 chr6qtel1M 202268 TTTAT 202272 v (TATA)n#Simpl 151 TATAT 155 Matrix = Unknown Transitions / transversions = 0.60 (12/20) Gap_init rate = 0.07 (10 / 144), avg. gap size = 1.00 (10 / 10) 17 20.56 3.85 1.89 chr6qtel1M 204014 204065 (795935) (ATT)n#Simple_repeat 1 53 (0) m_b303s252i8 12678 chr6qtel1M 204014 ATTATTGTCTA-TATTATTGATATTATTAATAATAGTATAATTA-TAAAA 204061 i - - iv v v v v - vv (ATT)n#Simple 1 ATTATTAT-TATTATTATTATTATTATTATTATTATTATTATTATTATTA 49 chr6qtel1M 204062 TTAT 204065 (ATT)n#Simple 50 TTAT 53 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.00 (3 / 3) 287 34.67 1.26 3.87 chr6qtel1M 204565 204723 (795277) MIRb#SINE/MIR 26 180 (88) m_b303s601i3 12679 chr6qtel1M 204565 AAAAGCACAGTAGCTACCTAGCAGTCAGAGAACAAGTGCATTGAAATACA 204614 i i -- --- v v v i- vv vi vi v v MIRb#SINE/MIR 26 AAGAGCACGG--GCT---TTGGAGTCAGACAG-ACCTGGGTTCGAATCCC 69 chr6qtel1M 204615 TCCTCAGTAAAACATAAGCTGTTTTAACTTTGAAAAATTCCTAAGTGTCT 204664 vv v iv vvi iv v v v v iv i v v iiv MIRb#SINE/MIR 70 GGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCT 119 chr6qtel1M 204665 CTGGATCTCAGTTCCCACACCTATAAAATGGGGCT--TTAGATCAACTTC 204712 iii i v i i v -- v v i v i MIRb#SINE/MIR 120 CTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTACCTC 169 chr6qtel1M 204713 TCTGAATTGTT 204723 v v ii MIRb#SINE/MIR 170 GCAGGGTTGTT 180 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 44.42 CpG sites = 22, Kimura (unadjusted) = 46.68 Transitions / transversions = 0.71 (22/31) Gap_init rate = 0.04 (7 / 158), avg. gap size = 1.14 (8 / 7) 247 34.71 5.79 0.00 chr6qtel1M 204632 204752 (795248) MIR3#SINE/MIR 81 208 (0) m_b303s601i4 12679 chr6qtel1M 204632 GCTGTTTTAACTTTGAAAAATTCCTAAGTGTCTCTGGATCTCAGTTCCCA 204681 v v v v iv i iv vviiv ii i v MIR3#SINE/MIR 81 GCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCT 130 chr6qtel1M 204682 CACCTATAAAATG-GGGCTTTAGATCAACT--TCTCTGAATTGTTTTCT- 204727 i i - vv i ii iv -- i iv vii i- MIR3#SINE/MIR 131 CATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCA 180 chr6qtel1M 204728 GTTCTAA---TCTCTAAGTCTGAGATCC 204752 i i --- v i v iv i MIR3#SINE/MIR 181 GCTCTGACATTCTATGATTCTATGATTC 208 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 48.25 CpG sites = 24, Kimura (unadjusted) = 48.25 Transitions / transversions = 1.33 (24/18) Gap_init rate = 0.03 (4 / 120), avg. gap size = 1.75 (7 / 4) 112 11.95 1.64 0.54 chr6qtel1M 204757 204939 (795061) (AG)n#Simple_repeat 1 185 (0) m_b303s252i9 12680 chr6qtel1M 204757 AGAGAGAGAGACAGAGAGACAGAGAGAGACACGTGAGCGAGAGAAACAGA 204806 v v v - v v i v (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA-GAGAGAGAGAGAGAGAGA 49 chr6qtel1M 204807 TAGACAGAGATAGAGACAGATAAACAGAGACAGAGACAGAGAGAGAG-GA 204855 v v v v v i v v v - (AG)n#Simple_ 50 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 99 chr6qtel1M 204856 GA-AAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 204904 - i (AG)n#Simple_ 100 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 149 chr6qtel1M 204905 GAGAGAGAGAG-GAGAGGGAGAGGGATAGAGAGAGA 204939 - i i v (AG)n#Simple_ 150 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 185 Matrix = Unknown Transitions / transversions = 0.33 (5/15) Gap_init rate = 0.02 (4 / 182), avg. gap size = 1.00 (4 / 4) 648 30.93 5.58 2.94 chr6qtel1M 205427 206089 (793911) L1M5_orf2#LINE/L1 2615 3294 (0) m_b303s551i3 12681 chr6qtel1M 205427 TACCAGATCT-AAAATTATATTATAGAGCAGCAGTTACCAAAACCATTTG 205475 ? ? - i i - i vi v i i vi v L1M5_orf2#LIN 2615 TACCNGATNTCAAGACT-TATTATAAAGCTACAGTAATCAAGACAGTGTG 2663 chr6qtel1M 205476 GTATTGGC-TAAGGAATAGATTAGTCGATCAGTGGAGTAGGTTAG---GT 205521 - - iv i v i ii iv --- L1M5_orf2#LIN 2664 GTATTGGCGTAAGG-ATAGACAAATAGATCAATGGAACAGAATAGAGAGT 2712 chr6qtel1M 205522 TCAAGGACAAAACAGTCA-ACAACTATAGCAACCTAGTCTTTGACAAA-- 205568 i iii i i v --- - vv i ?v ?i ii i -- L1M5_orf2#LIN 2713 CCAGAAATAGACC---CACACATATATGGNCANTTGATTTTTGACAAAGG 2759 chr6qtel1M 205569 -CCCAAAG-ACCCCAGCTTTTGGGATAAGAACTTACTGTTTGACAAAAAT 205616 -v ? - vii ---- iv i ivvv v ii viv L1M5_orf2#LIN 2760 TGCCAANGCAATTCAG----TGGGGAAAGGATAGTCTTTTCAACAAATGG 2805 chr6qtel1M 205617 TGCTGGGAAAATTGGAAACTAATATGGCAGAAACTAGGCATTGATCCACA 205666 i v v iiv v i v iii?v i i vi L1M5_orf2#LIN 2806 TGCTGGAACAATTGGATATCCATATGGAAAAAAATGAANCTCGACCCCTA 2855 chr6qtel1M 205667 CTTAACA-CGTACACCAACCGTTA-------------CAT-GACCTAGGC 205701 i v - i - vvi ------------- - iii L1M5_orf2#LIN 2856 CCTCACACCATACA-CAAAAATTAATTCNAGATGGATCATAGACCTAAAT 2904 chr6qtel1M 205702 ATAAAGAATGAAATTATTAATAAATTAGAGG--AACACAGGATAGTTTAC 205749 i ii? i i v vvvvi i -- i v i-- i L1M5_orf2#LIN 2905 GTAAAAGNTAAAACTATAAAACTTCTAGAAGAAAACATAGGAGAA--TAT 2952 chr6qtel1M 205750 CTCTCAGAACTGTGGAA-GGGGAAGGACTTTATGACCAA---AGAAAAAC 205795 - ivi iv i?-i v i i iv i v i--- v v L1M5_orf2#LIN 2953 CT-TCGTGACCTTGGGNTAGGCAAAGATTTCTTAAACAGGACACAAAAAG 3001 chr6qtel1M 205796 TAGAGATCATTACTGATCACAAAATAGAAAATTTTGACTATA-CTAAACT 205844 i v?i i v vv --- v v v v v ?i - v i L1M5_orf2#LIN 3002 CACNAACCATAAAAG---AAAAAATTGATAAATTGGACTNCATCAAAATT 3048 chr6qtel1M 205845 GAAAGTTTTTGCACAAACAAAACTAATGCAGACAAGATTAGAAGG-AAGC 205893 i ii i v ?vvv ivi vi ivi v i v i - L1M5_orf2#LIN 3049 AAAAACTTCTGCTCNTCAAAAGACACCGTTAAGAAAATGAAAAGGCAAGC 3098 chr6qtel1M 205894 AATAAACTTGGAAAATATTTTTACAGT-CAAAGGTTCTGCATAAAGGCCT 205942 v i i ? v i v v i i?- v vi- - i v L1M5_orf2#LIN 3099 CACAGANTGGGAGAAAATATTTGCAANACATATA-TCTG-ACAAAGGACT 3146 chr6qtel1M 205943 CATTTCCAAAATATATAGAGAATTATCTCTAATTT-ATAAAAATCAAGCC 205991 i v i i i -i vi ? i- ? -v v L1M5_orf2#LIN 3147 CGTATCCAGAATATATAAAGAACT-CCTACAANTCAATAANAA-AAAGAC 3194 chr6qtel1M 205992 ATTC--TCCAATTGAAATATGGTCAAAGGATATGAACAGACAATTCTCAG 206039 vv --i v? v v i iv v v i L1M5_orf2#LIN 3195 AAACAACCCAATANAAAAATGGGCAAAAGACTTGAACAGACACTTCACAA 3244 chr6qtel1M 206040 ATGAAGAAATTGAAACTATTTCTAGTCATATGGAAAGATGCTCCAAGTCA 206089 v v ?v iviiivv iv i i v v? L1M5_orf2#LIN 3245 AAGAAGATATNCAAATGGCCAATAAGCACATGAAAAGATGCTCAACNTCA 3294 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 41.31 CpG sites = 109, Kimura (unadjusted) = 42.43 Transitions / transversions = 1.21 (109/90) Gap_init rate = 0.06 (38 / 662), avg. gap size = 1.50 (57 / 38) 1487 27.12 1.86 1.48 chr6qtel1M 205947 206485 (793515) L1ME3G_3end#LINE/L1 7 547 (377) m_b303s551i4 12681 chr6qtel1M 205947 TCCAAAATATATAGAGAATTATCTCTAATTTATAAAAATCAAGCCATTCT 205996 i i i viiv v iv i -v v --vi L1ME3G_3end#L 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAA-AAAGACA--AC 53 chr6qtel1M 205997 CCAATTGAAATATGGTCAAAGGATATGAACAGACAATTCTCAGATGAAGA 206046 v v v i v v i L1ME3G_3end#L 54 CCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGGA 103 chr6qtel1M 206047 AATTGAAACTATTTCTAGTCATATGGAAAGATGCTCCAAGTCATTATTAA 206096 vv iviiivv iv i v vv i v L1ME3G_3end#L 104 AATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTAA 153 chr6qtel1M 206097 TCAGAGAAATGCAAATTAAGACAATTCTAAGATACCACTACACACCTGTC 206146 i i ivv i i viv ii L1ME3G_3end#L 154 TCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCATC 203 chr6qtel1M 206147 AGATTGGCTAAGA-TGACAGGAAAAATAATGACGATTGTT---GAGGGGA 206192 v i - v v i ?vvi iv ? v --- vi L1ME3G_3end#L 204 AGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGTG 253 chr6qtel1M 206193 TCGGAAAACTGGGACATTGATGCATTGTTGGTGGAGTTGTGAACGAATCC 206242 v i v v vi v i i i iiv i ivii v L1ME3G_3end#L 254 TGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTAC 303 chr6qtel1M 206243 AACCATTTTGGAGAGTAGTTTGA-ACTATGCTCAAAAAGTTATCAAACTG 206291 i ? i i i i- v - vvv i -- i v L1ME3G_3end#L 304 AGCCNTTTTGGAGGGCAATTTGGCAGTAT-CTATTAAAAT--TTAAAATG 350 chr6qtel1M 206292 TGCATACCCTTTGATCCAGCAGTGTTACTACTGGGCTTATATCCCAAAGA 206341 i i i vii v ? ?v v i ? L1ME3G_3end#L 351 CGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAGA 400 chr6qtel1M 206342 GATTAT-AAAGAAG-GGAAAGGGACCTGTATGTGCATGAATGTTTGTGGC 206389 i vv -iv v v - v v i --? i i v i ii v L1ME3G_3end#L 401 AATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTCATTGC 448 chr6qtel1M 206390 AGCCCT-TTTGTAGTGGCTAAAACT--GAAACTGAATGGATGTCCATCAG 206436 vi - i i v v -- vivv ii i L1ME3G_3end#L 449 AGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCAA 498 chr6qtel1M 206437 TTGGAGAATGGTTGAATAAATTGTGGTATATGAAAATTATGGAATATTA 206485 v i i i vv v i i L1ME3G_3end#L 499 TAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACTA 547 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 34.08 CpG sites = 74, Kimura (unadjusted) = 34.67 Transitions / transversions = 1.06 (74/70) Gap_init rate = 0.03 (15 / 538), avg. gap size = 1.20 (18 / 15) 12 9.71 0.00 0.00 chr6qtel1M 207148 207169 (792831) (AAGA)n#Simple_repeat 1 22 (0) m_b303s252i10 12682 chr6qtel1M 207148 AAAAAAGAAAGAAAGAAATAAA 207169 i v (AAGA)n#Simpl 1 AAGAAAGAAAGAAAGAAAGAAA 22 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 18 26.02 0.00 2.13 chr6qtel1M 207279 207326 (792674) (TG)n#Simple_repeat 1 47 (0) m_b303s252i11 12683 chr6qtel1M 207279 TGTGTATGTGATGAGAGTGTGTGCTTGTGTAAGTGTGTATATATGTGT 207326 i - v v iv iv i i i (TG)n#Simple_ 1 TGTGTGTGTG-TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 47 Matrix = Unknown Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.02 (1 / 47), avg. gap size = 1.00 (1 / 1) 230 35.29 0.98 0.00 chr6qtel1M 211246 211347 (788653) L1ME3F_3end#LINE/L1 433 535 (455) m_b303s551i5 12684 chr6qtel1M 211246 TGTACAAAAATGCTTGTAACAGCCCTTTTTGTCGTGGCAAGGAGCTGGAA 211295 i i ii i v v i vi i ii i L1ME3F_3end#L 433 TGTACAAGAATGTTCATAGCAGCACTGTTCGTAATAGCAAAAAACTGGAA 482 chr6qtel1M 211296 ACTGAGTGGAAGCTGATCTGTTGGGAAATGGATAACTAAGTTATGA-ATG 211344 vivviii v iiv viiv ii v i i i- i L1ME3F_3end#L 483 ACAACCCAAATGTCCATCGACAGGAGAATGGATAAATAAATTGTGGTATA 532 chr6qtel1M 211345 TTC 211347 L1ME3F_3end#L 533 TTC 535 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 49.50 CpG sites = 25, Kimura (unadjusted) = 51.64 Transitions / transversions = 2.27 (25/11) Gap_init rate = 0.01 (1 / 101), avg. gap size = 1.00 (1 / 1) 13 21.20 0.00 8.51 chr6qtel1M 211913 211963 (788037) (ATT)n#Simple_repeat 1 47 (0) m_b303s252i12 12685 chr6qtel1M 211913 ATAATTTTTATTATACATAATTATATATCATGTAGTATTATTGTATACTA 211962 v v -i v - i - v i - i (ATT)n#Simple 1 ATTATTATTATTAT-TATTATTAT-TATTAT-TATTATTATTAT-TATTA 46 chr6qtel1M 211963 T 211963 (ATT)n#Simple 47 T 47 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.08 (4 / 50), avg. gap size = 1.00 (4 / 4) 252 25.00 0.00 0.00 chr6qtel1M 213708 213775 (786225) C DNM1r#Unknown (2116) 2546 2479 m_b303s502i0 12686 chr6qtel1M 213708 TATACATGCATATGAATATATATGCAAACACACATACACATATAAATATA 213757 ? i i iv i i ii v i v i i C DNM1r#Unknown 2546 TATANATACGTATATATACACATATATACACACATACACACATATACACA 2497 chr6qtel1M 213758 CATATACATGCATATACA 213775 i ii i C DNM1r#Unknown 2496 CATATATACACACATACA 2479 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 30.96 CpG sites = 14, Kimura (unadjusted) = 33.40 Transitions / transversions = 4.67 (14/3) Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0) 22 6.68 0.00 0.00 chr6qtel1M 213797 213828 (786172) (AGAT)n#Simple_repeat 1 32 (0) m_b303s252i13 12687 chr6qtel1M 213797 AGATAGATAGATAGACAGACAGATAGATAGAT 213828 i i (AGAT)n#Simpl 1 AGATAGATAGATAGATAGATAGATAGATAGAT 32 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 269 31.36 12.00 2.75 chr6qtel1M 214912 215111 (784889) MIRc#SINE/MIR 6 223 (45) m_b303s601i5 12688 chr6qtel1M 214912 CAGTAAGGTGTGGGGCAGAGAGCTTTGAA-TTGGGGTACAAGAAATAAAT 214960 iv ii v v i vi i - i - i i- vv MIRc#SINE/MIR 6 CAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGT-CAGGAAG-ACCT 53 chr6qtel1M 214961 GGATTTAACAACTCTTTGCT--GCC-CCTAATAGCATGAGTA--CT--AA 215003 i --- i v iiv -- - i v - v i-- --ii MIRc#SINE/MIR 54 GGGTT---CGAGTCCCGGCTCTGCCACTTACTAGC-TGTGTGACCTTGGG 99 chr6qtel1M 215004 CATATCACTTAATCTCTATATGTTTCAA-TCCCACATCAGTAACATGAGC 215052 vi i v iv ii i- i v v v i v MIRc#SINE/MIR 100 CAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGG 149 chr6qtel1M 215053 ATCATA----CAG------TTAGCTTATATATTTTCTGTAAGGAT--AAT 215090 v ---- v ------i v i i viv vi i -- MIRc#SINE/MIR 150 ATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAAT 199 chr6qtel1M 215091 ---ATGGTATATTTAAAAGGACTT 215111 --- ii i v i vi MIRc#SINE/MIR 200 GAGATAATGTATGTGAAAGCGCTT 223 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 39.40 CpG sites = 36, Kimura (unadjusted) = 42.11 Transitions / transversions = 1.44 (36/25) Gap_init rate = 0.08 (16 / 199), avg. gap size = 1.88 (30 / 16) 426 25.87 0.84 2.56 chr6qtel1M 216326 216444 (783556) MIRc#SINE/MIR 11 127 (141) m_b303s601i6 12689 chr6qtel1M 216326 TGGCTCATTGGATAGAGAAGTGGCCCTGAAGTCCTGAGGCCCTGAGTTTA 216375 iv v v v v v i i vv i v i ii MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr6qtel1M 216376 AATCCAACCTCAGACATTTAATACTAGCTTTGTGACCCTGGGCAAGTCAT 216425 i viv v v i --- v i i MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTA---CTAGCTGTGTGACCTTGGGCAAGTCAC 107 chr6qtel1M 216426 TTAACCCCACTT-GCTTCAG 216444 i v v- i MIRc#SINE/MIR 108 TTAACCTCTCTGAGCCTCAG 127 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 29.34 CpG sites = 14, Kimura (unadjusted) = 31.92 Transitions / transversions = 0.88 (14/16) Gap_init rate = 0.03 (4 / 118), avg. gap size = 1.00 (4 / 4) 16 11.98 2.50 5.13 chr6qtel1M 216519 216558 (783442) (AAAG)n#Simple_repeat 1 39 (0) m_b303s252i14 12690 chr6qtel1M 216519 AAAG-AATAAAGAAAAGGAAAGACAGGAAGAAAGGAAGAAA 216558 - v - - v i i (AAAG)n#Simpl 1 AAAGAAAGAAAG-AAA-GAAAGAAAGAAAGAAAGAAAGAAA 39 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.08 (3 / 39), avg. gap size = 1.00 (3 / 3) 12 7.25 10.34 0.00 chr6qtel1M 216526 216554 (783446) (AAAGG)n#Simple_repeat 1 32 (0) m_b303s252i15 12690 chr6qtel1M 216526 AAAGAAAAGGAAA-GACAGG-AA-GAAAGGAA 216554 i - v - - (AAAGG)n#Simp 1 AAAGGAAAGGAAAGGAAAGGAAAGGAAAGGAA 32 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.11 (3 / 28), avg. gap size = 1.00 (3 / 3) 250 25.00 4.17 0.00 chr6qtel1M 216676 216747 (783253) MIR3#SINE/MIR 71 145 (63) m_b303s601i7 12691 chr6qtel1M 216676 CCAATAACTTCCTTTC--ACTGTGAAAAAATCACT-CAGTTCCCTTGGTC 216722 v ?v v v-- iv iiv i - vi i v i MIR3#SINE/MIR 71 CCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCC 120 chr6qtel1M 216723 TCAGTTACCTCACCTGTAAAATGGG 216747 v i i MIR3#SINE/MIR 121 TCAGTTTCCTCATCTGTAAAATGAG 145 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 31.23 CpG sites = 9, Kimura (unadjusted) = 31.23 Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.03 (2 / 71), avg. gap size = 1.50 (3 / 2) 26 10.48 2.44 0.00 chr6qtel1M 217462 217502 (782498) (TG)n#Simple_repeat 1 42 (0) m_b303s252i17 12692 chr6qtel1M 217462 TGTGAGTGTGTGTG-GTGTGTGTGTGTGTGTATGTGCCTGTG 217502 v - i iv (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 42 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 12 27.89 0.00 5.77 chr6qtel1M 217462 217516 (782484) (TGTGCA)n#Simple_repeat 1 52 (0) m_b303s252i16 12693 chr6qtel1M 217462 TGTGAGTGTGTGTGGTGTGTGTGTGTGTGTATGTGCCTGTGCAACTGTAC 217511 vi ii - ii ii i v - - i (TGTGCA)n#Sim 1 TGTGCATGTGCAT-GTGCATGTGCATGTGCATGTGCATGTGC-A-TGTGC 47 chr6qtel1M 217512 ATGTG 217516 (TGTGCA)n#Sim 48 ATGTG 52 Matrix = Unknown Transitions / transversions = 4.50 (9/2) Gap_init rate = 0.06 (3 / 54), avg. gap size = 1.00 (3 / 3) 12 8.58 13.51 0.00 chr6qtel1M 219339 219375 (780625) (ATACTCT)n#Simple_repeat 1 42 (0) m_b303s252i18 12694 chr6qtel1M 219339 ATACT-TAT-C-CTATACTCTATA--CAATTCTCTATATTCT 219375 - - - -- v v i (ATACTCT)n#Si 1 ATACTCTATACTCTATACTCTATACTCTATACTCTATACTCT 42 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.11 (4 / 36), avg. gap size = 1.25 (5 / 4) 18 10.01 6.25 0.00 chr6qtel1M 219761 219792 (780208) (AT)n#Simple_repeat 1 34 (0) m_b303s252i19 12695 chr6qtel1M 219761 ATAAATATATAT-TACATATATAT-TATATTTAT 219792 v - i - v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATAT 34 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.06 (2 / 31), avg. gap size = 1.00 (2 / 2) 181 25.50 0.45 0.45 chr6qtel1M 220201 220649 (779351) (TC)n#Simple_repeat 1 449 (0) m_b303s252i20 12696 chr6qtel1M 220201 TCTTTCTCTCTGTTGGTCTCTTTCTCTCTCTCTCTCTCTCTCTCTCTCTC 220250 i v ivv i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr6qtel1M 220251 TCTCTCTCTCTCT-TCTCTCACTCTCTTTCTATGTGTGTGTCTCTCTTGG 220299 - v i v v v v v ivv (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chr6qtel1M 220300 TTTCTGTCTCTCTGTCTCTGTCTCTGTCTCTCTCTCTTTCTATGTGTGTG 220349 i v v v v i v v v v - (TC)n#Simple_ 101 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT- 149 chr6qtel1M 220350 CTCTCTTGGTTTCTGTCTCTCTGTCTCTGTCTCTCTGTCTCTCTTTCTCT 220399 ivv i v v v v i (TC)n#Simple_ 150 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 199 chr6qtel1M 220400 CTCTCTCTCTTGCTCTTTGCCTCTGTCTCTCTGTCTCTGTCTGTGTGTGT 220449 iv i vi v v v v v v v (TC)n#Simple_ 200 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 249 chr6qtel1M 220450 GTGTGTGTGTGTGGTCTCTATCTCTGTCTCTCTCTGTCTCATTTTCTGTG 220499 v v v v v v -v v v v vi i v v (TC)n#Simple_ 250 CTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 298 chr6qtel1M 220500 TGTGTGTGTGTGTGTGTCTGTCTGCCTCTCTGTCTCTCTGTCAGTCTCTG 220549 v v v v v v v v v vi v v vv v (TC)n#Simple_ 299 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 348 chr6qtel1M 220550 TCTCTTTCTCTCTGTCTCT-TCTCTCTCTTGGTTTCTGTCTCTCTCTTTG 220598 i v - ivv i v i v (TC)n#Simple_ 349 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 398 chr6qtel1M 220599 TCTCTGTCTCTCTGTCTCTGTCTCTGTGTGTCTCTCTGTCTCTGTTTCTC 220648 v v v v v v v v i (TC)n#Simple_ 399 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 448 chr6qtel1M 220649 T 220649 (TC)n#Simple_ 449 T 449 Matrix = Unknown Transitions / transversions = 0.28 (21/75) Gap_init rate = 0.01 (4 / 448), avg. gap size = 1.00 (4 / 4) 121 26.59 2.72 4.14 chr6qtel1M 221294 221554 (778446) (TGTCTC)n#Simple_repeat 1 257 (250) m_b303s252i21 12697 chr6qtel1M 221294 TGTTTCTTTCTCT-TGTCAGTCTCTG--TCTGTTTCTGTCTCTCTCTTCT 221340 i v - v v -- i v - (TGTCTC)n#Sim 1 TGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTC-TCT 49 chr6qtel1M 221341 GTCTGTCTCTCTATCTATCCTATCTATCTCCTTCTCTCTATGTGCATCTC 221390 v v i v -v v i iv v v v -- (TGTCTC)n#Sim 50 GTCTCTGTCTCTGTCTCT-GTCTCTGTCTCTGTCTCTGTCTCTG--TCTC 96 chr6qtel1M 221391 TTGTCTCTGTCTCTATCTCTCTCATTCTGTGTGTGTGTGTGT-TCTGGCT 221439 - i v -- v v v v - v (TGTCTC)n#Sim 97 -TGTCTCTGTCTCTGTCTCTGTC--TCTGTCTCTGTCTCTGTCTCTGTCT 143 chr6qtel1M 221440 ACTG-C-CTGTCTGTTCTCTCTTGTCTCTGTCTCCCTCTCT-TGTGTG-C 221485 - - - -i v - iv - v v - (TGTCTC)n#Sim 144 -CTGTCTCTGTCT-CTGTCTC-TGTCTCTGTCTCTGTCTCTGTCTCTGTC 190 chr6qtel1M 221486 TTAAACTCCATTTCTCGTTTCCCTGTCTATCTATGTTTCTCTCTGCTCTC 221535 iviv ii i - i iv v i v i v - v (TGTCTC)n#Sim 191 TCTGTCTCTGTCTCT-GTCTCTGTCTCTGTCTCTGTCTCTGTCT-CTGTC 238 chr6qtel1M 221536 TCT-TGTGGGTATCTGTGGG 221554 - v vv v -vv (TGTCTC)n#Sim 239 TCTGTCTCTGTCTCTGT-CT 257 Matrix = Unknown Transitions / transversions = 0.47 (17/36) Gap_init rate = 0.08 (21 / 260), avg. gap size = 1.05 (22 / 21) 64 6.21 2.38 0.00 chr6qtel1M 221555 221638 (778362) (CT)n#Simple_repeat 1 86 (0) c_b303s251i1 12698 chr6qtel1M 221555 CTCTCTCTGTCTCTGTCTCT-TTTCTCTCTCTCTCTCTCTCTCTCTCTCT 221603 v v - i (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chr6qtel1M 221604 CTCTCTCTC-CTCTGTCTCTCTGTCTCTCTCTCTCT 221638 - v v (CT)n#Simple_ 51 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 86 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.02 (2 / 83), avg. gap size = 1.00 (2 / 2) 121 26.59 2.72 4.14 chr6qtel1M 221639 221830 (778170) (TGTCTC)n#Simple_repeat 258 446 (61) m_b303s252i21 12699 chr6qtel1M 221639 TCTATCAATCTGTGTCTGTGTGTGTGT-TATGTCTGTGTGTCTGTGTGTC 221687 v v vi v v v v - v v v v v v (TGTCTC)n#Sim 258 TGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTG 307 chr6qtel1M 221688 TCT-TGTCTGTGTGTGTGTGTTCTCGTCTCTGTCTCTCATCTCTGTTTCC 221736 - v v v -i - -i i - (TGTCTC)n#Sim 308 TCTCTGTCTCTGTCTCTGT-CTCT-GTCTCTGTCTCT-GTCTCTGTCT-C 353 chr6qtel1M 221737 ATTTCTCT-TCTCTGACTCTATCTCTGTCTCTCTCCGTCTCACTTTCTCT 221785 - v - v i v iv v v v (TGTCTC)n#Sim 354 -TGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCT 402 chr6qtel1M 221786 GTGTGTGTGTGTGGTTTCTGTCTCCCTCTCCTGTCTCTCTGTCAG- 221830 v v v v - i iv - v v v - (TGTCTC)n#Sim 403 GTCTCTGTCTCT-GTCTCTGTCTCTGTCT-CTGTCTCTGTCTCTGT 446 Matrix = Unknown Transitions / transversions = 0.26 (8/31) Gap_init rate = 0.06 (11 / 191), avg. gap size = 1.00 (11 / 11) 30 8.73 4.76 1.54 chr6qtel1M 221831 221893 (778107) (TC)n#Simple_repeat 1 65 (0) c_b303s251i2 12700 chr6qtel1M 221831 TCTCTATCTGTCTCTGTCTCTGTCTCT-TGTCTCTCT-TCTCTCTCTCTC 221878 v v v v - v - (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr6qtel1M 221879 GT-TCTCTCTCTCTCT 221893 - - (TC)n#Simple_ 51 -TCTCTCTCTCTCTCT 65 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.06 (4 / 62), avg. gap size = 1.00 (4 / 4) 121 26.59 2.72 4.14 chr6qtel1M 221894 221952 (778048) (TGTCTC)n#Simple_repeat 447 505 (2) m_b303s252i21 12701 chr6qtel1M 221894 TGTGTCTGTCTGCCTGTCTGCCTGTCT-TCTCTGTTCTCTGTCTCCCTCT 221942 v v v vi viv v - - iv (TGTCTC)n#Sim 447 TCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTG-TCTCTGTCTCTGTCT 495 chr6qtel1M 221943 CTCTGTGTGT 221952 v v v (TGTCTC)n#Sim 496 CTGTCTCTGT 505 Matrix = Unknown Transitions / transversions = 0.27 (3/11) Gap_init rate = 0.03 (2 / 58), avg. gap size = 1.00 (2 / 2) 14 21.98 2.38 0.00 chr6qtel1M 223623 223664 (776336) (TTTTATG)n#Simple_repeat 1 43 (0) m_b304s252i1 12702 chr6qtel1M 223623 TTTTCTGTCTCATGTTTTATGTTTT-TATTTGATTGTATATGT 223664 v i i - i v vv v (TTTTATG)n#Si 1 TTTTATGTTTTATGTTTTATGTTTTATGTTTTATGTTTTATGT 43 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.02 (1 / 41), avg. gap size = 1.00 (1 / 1) 13 29.20 3.85 2.53 chr6qtel1M 223923 224000 (776000) (TCTTT)n#Simple_repeat 1 79 (0) m_b304s252i2 12703 chr6qtel1M 223923 TCTTTTCTTTAC--CTCTTGTAGTTTATTTTGTTTTCTGTGTTGCTTTTT 223970 v --i v vv v v v vi vi i (TCTTT)n#Simp 1 TCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTT 50 chr6qtel1M 223971 AATTTTATTTCTCCTTTTC-TTCCCTTTCTT 224000 vv v - - - i i (TCTTT)n#Simp 51 TCTTTTCTTT-T-CTTTTCTTTTCTTTTCTT 79 Matrix = Unknown Transitions / transversions = 0.50 (6/12) Gap_init rate = 0.05 (4 / 77), avg. gap size = 1.25 (5 / 4) 37 2.86 0.00 0.00 chr6qtel1M 224054 224089 (775911) (TA)n#Simple_repeat 1 36 (0) c_b304s251i1 12704 chr6qtel1M 224054 TATATATATATATATATATATATATACATATATATA 224089 i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATA 36 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 21 29.99 0.00 1.27 chr6qtel1M 224532 224561 (775439) (TCTCTG)n#Simple_repeat 1 30 (49) m_b304s252i3 12705 chr6qtel1M 224532 TCTCTTTCTCTCTGTTGGTCTCTGTCTTTG 224561 v v v iv i (TCTCTG)n#Sim 1 TCTCTGTCTCTGTCTCTGTCTCTGTCTCTG 30 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 53 6.64 0.00 0.00 chr6qtel1M 224562 224624 (775376) (TC)n#Simple_repeat 1 63 (0) c_b304s251i2 12706 chr6qtel1M 224562 TCTCTGTCTATCTCTCTGTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 224611 v v v i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr6qtel1M 224612 TCTCTCTCTCTCT 224624 (TC)n#Simple_ 51 TCTCTCTCTCTCT 63 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0) 21 29.99 0.00 1.27 chr6qtel1M 224625 224673 (775327) (TCTCTG)n#Simple_repeat 31 78 (1) m_b304s252i3 12707 chr6qtel1M 224625 GTCCTGTGTGTGTGTGTGTGTCTGCCTCTCTGCCTCTCTGTTTCTCTGT 224673 v - v v v v v i v vi v v v (TCTCTG)n#Sim 31 CT-CTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGT 78 Matrix = Unknown Transitions / transversions = 0.18 (2/11) Gap_init rate = 0.02 (1 / 48), avg. gap size = 1.00 (1 / 1) 193 30.75 7.62 0.89 chr6qtel1M 226124 226228 (773772) MIR#SINE/MIR 95 206 (56) m_b304s601i0 12708 chr6qtel1M 226124 GCATTTCACTTAATTTCTATATGTTTCAG--ACCTCTATCAGCAACATGA 226171 vv i ii v i ii --v - v i v i MIR#SINE/MIR 95 GCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTC-ATCTGTAAAATGG 143 chr6qtel1M 226172 GCATCAT-ACCGT---TAGCTTATAACTTTTCTAAAAGGATCAAATGA-- 226215 v v - iv --- v i ivv vi ivi i -- MIR#SINE/MIR 144 GGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGT 193 chr6qtel1M 226216 TATCATATGTAAA 226228 vi i MIR#SINE/MIR 194 TAATACATGTAAA 206 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 40.36 CpG sites = 17, Kimura (unadjusted) = 40.36 Transitions / transversions = 1.13 (17/15) Gap_init rate = 0.05 (5 / 104), avg. gap size = 1.80 (9 / 5) 221 32.04 6.77 1.43 chr6qtel1M 227139 227271 (772729) MIRb#SINE/MIR 2 141 (127) m_b304s601i1 12709 chr6qtel1M 227139 AGTGAGTTAGCTAGTAGTTCAGTAGATTATGTATTAGCCTTGCAGTCAAA 227188 v i vi -- i v i vviv i ivi i v i MIRb#SINE/MIR 2 AGAGGGGCAGC--GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGA 49 chr6qtel1M 227189 GTTAT-TGAGTTCAAATCTAGCCTTGG--ATTTACTACTTCTGTGTCACT 227235 vvv i- i i iv v iv -- i vi v v vi MIRb#SINE/MIR 50 CAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTT 99 chr6qtel1M 227236 GGGGA--TT--TTAACC-CTGTTTGCCTTAG-TTCCTCATTT 227271 v -- -- - v vv i - i MIRb#SINE/MIR 100 GGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCT 141 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 39.74 CpG sites = 20, Kimura (unadjusted) = 42.29 Transitions / transversions = 0.91 (20/22) Gap_init rate = 0.06 (8 / 132), avg. gap size = 1.38 (11 / 8) 13 21.75 0.00 6.67 chr6qtel1M 227915 227962 (772038) (TTA)n#Simple_repeat 1 45 (0) m_b304s252i4 12710 chr6qtel1M 227915 TTATTTCAATAACTATGACTTATTAATTATTATTTTTATTGATCATTA 227962 viv v i v - - v - i (TTA)n#Simple 1 TTATTATTATTATTATTA-TTATT-ATTATTATTATTATT-ATTATTA 45 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.06 (3 / 47), avg. gap size = 1.00 (3 / 3) 229 22.81 1.75 0.00 chr6qtel1M 229267 229323 (770677) C DNM1r#Unknown (2126) 2536 2479 m_b304s502i0 12711 chr6qtel1M 229267 TATATGTACACATACATATACAAACGCATGCATACACATGCAT-CATACA 229315 i i i v ii ii i ii -i C DNM1r#Unknown 2536 TATATATACACATATATACACACATACACACATATACACACATATATACA 2487 chr6qtel1M 229316 CATATACA 229323 i C DNM1r#Unknown 2486 CACATACA 2479 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 29.76 CpG sites = 12, Kimura (unadjusted) = 29.76 Transitions / transversions = 12.00 (12/1) Gap_init rate = 0.02 (1 / 56), avg. gap size = 1.00 (1 / 1) 15 14.13 0.00 3.12 chr6qtel1M 230566 230598 (769402) (TAT)n#Simple_repeat 1 32 (0) m_b304s252i5 12712 chr6qtel1M 230566 TATTATTTATATTATTACTATTATTGATGATTA 230598 vv i - v (TAT)n#Simple 1 TATTATTATTATTATTATTATTATT-ATTATTA 32 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 214 26.84 4.81 6.86 chr6qtel1M 230727 230830 (769170) C MIRb#SINE/MIR (44) 224 123 m_b304s601i3 12713 chr6qtel1M 230727 ACTGTGATAATCACTTCACA---ATTATTTAACAACTTTTAAAC--TATG 230771 v v i i --- i -- --- v --i ii C MIRb#SINE/MIR 224 ACTGTGCTAAGCGCTTTACATGCATTATCT--CA---TTTAATCCTCACA 180 chr6qtel1M 230772 AAAAACCTTAGACTTTTAAGTGTTATTGTCTATATTTGACATTTGAAGAA 230821 v v vv v--v i i i ivi v vv i C MIRb#SINE/MIR 179 ACAACCCTGCGAG--GTAGGTATTATTATCCCCATTTTACAGATGAGGAA 132 chr6qtel1M 230822 ACTAAGGCT 230830 i C MIRb#SINE/MIR 131 ACTGAGGCT 123 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 31.99 CpG sites = 13, Kimura (unadjusted) = 33.51 Transitions / transversions = 1.00 (13/13) Gap_init rate = 0.09 (9 / 103), avg. gap size = 1.33 (12 / 9) 278 33.25 1.64 8.77 chr6qtel1M 231246 231367 (768633) MIRc#SINE/MIR 2 115 (153) m_b304s601i4 12714 chr6qtel1M 231246 GGGTCAGTTTGATGAAACCATGGATAGAGGACTAGCCTGAGTGTCAGTAG 231295 i v v i --- vi v v i v vi v v i MIRc#SINE/MIR 2 GAGGCAGTGTGGTG---CAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr6qtel1M 231296 GATCTGAGTTCAAAAGCAGCCCCAGAAATTTAACAC--ATTAACCATATA 231343 i i i ----- i i v-- i iv -- i i ii i i MIRc#SINE/MIR 49 GACCTGGGTTCGA-----GTCCCGGC--TCTGCCACTTACTAGCTGTGTG 91 chr6qtel1M 231344 ATCCTGAACAAATCACTTAAACCC 231367 i i ii i v i MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 42.88 CpG sites = 25, Kimura (unadjusted) = 46.35 Transitions / transversions = 2.08 (25/12) Gap_init rate = 0.09 (11 / 121), avg. gap size = 1.09 (12 / 11) 655 32.65 4.49 3.73 chr6qtel1M 231758 232581 (767419) C L1PREC2_orf2#LINE/L1 (2438) 856 27 m_b304s551i0 12715 chr6qtel1M 231758 TTTGGTATGATGTCTCATTATTGTCATTTTCTTGGGTGAAGTTATTAATT 231807 i v v v i v vvi viiv v v i C L1PREC2_orf2# 856 TCTGGTATGTTGTATCTTTGTTCTCATTAGTTTCAAAGAACTTCTTGATT 807 chr6qtel1M 231808 -ATGTCAACAATTT-GCTGTTTCCCCACACATTCTTTAGTATGAGATTAT 231855 -v i v-i -ii i v v vi iv i v vv i i C L1PREC2_orf2# 806 TCTGCCT-TAATTTCATTATTTACCCAAAAGTCATTCAGGAGCAGGTTGT 758 chr6qtel1M 231856 TTAGTTTCCA-ATTATTTTTTGGTTT------ATTTTTCCCTGGCTATTT 231898 i -i v v v ------ -- i i ----- C L1PREC2_orf2# 757 TTAATTTCCATGTAATTGTATGGTTTTGAGCGATTTT--CTTAG-----T 715 chr6qtel1M 231899 ATTGACTGTAATTTTCATTGCATCGTGGTCTGAAAAGGATGCATT--TAC 231946 v i viv i iii i i i? - i- -- i C L1PREC2_orf2# 714 CTTGATTTCTATTTTTATTGCGCTGTGGTCCGAGAGNG-TGT-TTGGTAT 667 chr6qtel1M 231947 TATTTCTGCATTACTGCATTTGAGTTTGAGG---TTTTTATGTCCTAATA 231993 v v ivi vi ---i ---v v v C L1PREC2_orf2# 666 GATTTCGGTTCTTTTGCATTTG---CTGAGGATTGTTTTATGTCCGATTA 620 chr6qtel1M 231994 TATGGTCAATTTTTGTATAGGTTCCATGAACTGCTGAGAAGAAAGTGTAC 232043 i i v vi v v vivi v v i i C L1PREC2_orf2# 619 TGTGGTCGATTTTAGAGTATGTGCCATGTGGCGATGAGAAGAATGTATAT 570 chr6qtel1M 232044 TCCTTTCTGTCTCTATTTAGTTTTCTCCAAAGATGTATCCTATCTAACTT 232093 iv v v i?vvi vv vv vi i vi v vvi i vi v C L1PREC2_orf2# 569 TCTGTTGTTTTNGGGTGGAGAGTTCTGTAGATGTCTATCAGGTCCATTTG 520 chr6qtel1M 232094 TTCTAGTATTCTATTTATCTCTTTGACTTTTTCTTATTTATTTTGTAGTT 232143 v i i vvi i vv i - v v i - i v v ivi C L1PREC2_orf2# 519 GTCCAGTGTTGAGTTCAGGTCCT-GAATATCT-TTGTTAATTTTCTGCCT 472 chr6qtel1M 232144 ---TGATTTATCTAATGCTG-AGGTGCAAGGTTGAGATCTTCTCCCACTA 232189 --- i i i -vi viiv ii --- C L1PREC2_orf2# 471 CGATGATCTGTCTAATACTGTCAGTGGGGTGTTGAAGTCT---CCCACTA 425 chr6qtel1M 232190 TTATGGTTTTGCAGTCTATATCTTCTTGCA-GCCTCT--TAATTTCTCTT 232236 v v v v vi ii ? - i --v i vii C L1PREC2_orf2# 424 TTATTGTGTGGGAGTCTAAGTCTCTTTGNAGGTCTCTAAGAACTTGCTTT 375 chr6qtel1M 232237 TTAAATTTACTTGCCACACTACTTGGTGCATATATGTTTAATATTGATA- 232285 v i i ivv iv vv ii v i iv v v - C L1PREC2_orf2# 374 ATGAATCTGGGTGCTCCTGTGTTGGGTGCATATATATTTAGGATAGTTAG 325 chr6qtel1M 232286 --TTGCTTGATTATCTATGCTACCTTTAGTAAGATATAAGTGCCCTTCCT 232333 --i v v v vi ivi -- vi vv i - i C L1PREC2_orf2# 324 GTCTTCTTGTTGAATTGAAC--CCTTTACCATTATGTAA-TGCCCTTCTT 278 chr6qtel1M 232334 TATCTCTTTTAAT-TAGATCAATTTTGCTTTTGCTTGATCTGAGATCAGG 232382 i i i - vvi iii vivv i i vi i i C L1PREC2_orf2# 277 TGTCTTTTTTGATCTTTGTTGGTTTAAAGTCTGTTTTGTCTGAAATTAGG 228 chr6qtel1M 232383 ATGAGCTA-CCCTGCTTTT---TGACTT-CACCTGAAGCATGGTAGATTC 232427 v- v - --- vi - ii --- v i C L1PREC2_orf2# 227 ATT-GCAACCCCTGCTTTTTTCTGTTTTCCATTT---GCTTGGTAGATTT 182 chr6qtel1M 232428 TGCTTCAACCTTTTACCTTTATTCTGCATGTATCTCCTTGC--TTCAGGT 232475 v i v i ii v vi -- vi v v --v v i C L1PREC2_orf2# 181 TTCTCCATCCCTTTATTTTGAGCCT--ATGGGTGTCATTGCATGTGAGAT 134 chr6qtel1M 232476 GTGTTTCCTGTCAACAACATATTGCAGGATTCTGGCTTTTAATCCATTCT 232525 v i i vvi i iiiiv i ii vi i v ---v C L1PREC2_orf2# 133 GGGTCTCTTGAAGACAGCATACCATTGGGTCTTGCTTCTTTATCCA---G 87 chr6qtel1M 232526 CTAACCACT---TCCTCTCTA--TGGGGCAGTTTACCCCATTCACATTTA 232570 vi --- v ii i -- - v i i C L1PREC2_orf2# 86 CTTGCCACTCTGTGCCTTTTAATTGGGGCA-TTTAGCCCATTTACATTCA 38 chr6qtel1M 232571 TGGTTAAAATT 232581 v iv C L1PREC2_orf2# 37 AGGTTAGTATT 27 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 43.02 CpG sites = 134, Kimura (unadjusted) = 43.92 Transitions / transversions = 1.07 (134/125) Gap_init rate = 0.06 (50 / 823), avg. gap size = 1.36 (68 / 50) 723 28.60 6.21 5.48 chr6qtel1M 231852 232576 (767424) C L1M2_orf2#LINE/L1 (2530) 761 32 m_b304s551i1 12715 chr6qtel1M 231852 TTATTTAGTTTCCAATTATTTTT-TGGTTT---ATTTTTCCCTGGCTATT 231897 i i vv v -?i --- vv i i v i C L1M2_orf2#LIN 761 TTGTTTAATTTCCATGTATTTGTANAGTTTCCAAAGTTCCTCTTGTTATT 712 chr6qtel1M 231898 TATTGACTGTAATTTTCATTGCATCGTGGTCTGAAAAGGATGCATT--TA 231945 v --- v i - v i ? - i - -- C L1M2_orf2#LIN 711 GATT---TCTAGTTTT-ATTCCATTGTGGTCNGAAAAG-ATAC-TTGATA 668 chr6qtel1M 231946 CTATTTCTGCATTACTGCATTTGAGTTTGAGGTTT---TTATGTCCTAAT 231992 iv viiv vi?iv --- ii --- i v i C L1M2_orf2#LIN 667 TGATTTCGATTTTTTNAAATTTG---TTGAGACTTGTTTTGTGGCCTAAC 621 chr6qtel1M 231993 ATATGGTCAATTTTTGTATAGGTTCCATGAACTGCTGAGAAGAAAGTGTA 232042 v ii v viv v vi v v C L1M2_orf2#LIN 620 ATATGGTCTATCCTGGAGAATGTTCCATGTGCTGATGAGAAGAATGTGTA 571 chr6qtel1M 232043 CTCCTTTCTGTCTCTATTT-----AGTTTTCTCCAAAGATGTATCCTATC 232087 ----- ivv i v----- i v vi vi v i ivvi C L1M2_orf2#LIN 570 -----TTCTGCAGCTGTTGGATGAAATGTTCTGTAAATGTCTGTTAGGTC 526 chr6qtel1M 232088 TAACTTTTCTAGTATTCTATTTATCTCTTTGACTTTTTCTTATTTATTTT 232137 i vi vv ?vi v vi vv i-- iv ii i v C L1M2_orf2#LIN 525 CATTTGGTCTANAGTGCAGTTTAAGTCC--GATGTTTCTTTGTTGATTTT 478 chr6qtel1M 232138 GTAGTT---TGATTTATCTAATGCTGAG-GTGCAAGGTTGAGATCTTCTC 232183 v ivi --- i i i ? - viiv ii i--- C L1M2_orf2#LIN 477 CTGTCTGGATGATCTGTCCANTGCTGAGAGTGGGGTGTTGAAGTCC---C 431 chr6qtel1M 232184 CCACTATTATGGTTTTGCAGTCTATATCTTCTTGCAG-CCTCTTAAT-TT 232231 ? v v ? v i i vi -i v? - C L1M2_orf2#LIN 430 CNACTATTATTGTATTGNAGTCTATCTCTCCCTTTAGATCTANTAATATT 381 chr6qtel1M 232232 CTCTTT-TAAATTTACTTGCCACACTACTTGGTGCATATATGTTTAATAT 232280 iv - v i ivv iv iv ii v i ?v C L1M2_orf2#LIN 380 TGCTTTATATATCTGGGTGCTCCGGTGTTGGGTGCATATATATTTANAAT 331 chr6qtel1M 232281 TG--ATAT-----TGCTTGATTATCTATGCTACCTTTAGTAAGATATAAG 232323 -- ----- vi iv i------ vi vv - C L1M2_orf2#LIN 330 TGTTATATCCTCTTGCTGAATTGACC------CCTTTATCATTATATAA- 288 chr6qtel1M 232324 TGCCCTTCCTTATCTCTTTTAATTAGATCAATTTT--GCTT-----TTGC 232366 v i i --- --- i --i -----i ii C L1M2_orf2#LIN 287 TGACCTTCTTTGTCTCTTTT---TA---CAGTTTTTGACTTAAAGTCTAT 244 chr6qtel1M 232367 TTGATCTGAGATCAGGATGAGCTAC-CCTGCT---TTTTGACTTCACCTG 232412 v v v v - - --- ii vvi v C L1M2_orf2#LIN 243 TTTATCTGATATAAGTAT-AGCTACTCCTGCTCNCTTTTGGTTTCCGTTT 195 chr6qtel1M 232413 AAGCATGGTAGATTCTGCTTCAACCTTTTACCTTTATTCTGCATGTATCT 232462 -- v v ii vi i v i i i i v -- i v C L1M2_orf2#LIN 194 --GCATGGAATATCTTTTTCCATCCCTTCACTTTCAGTCT--ATGTGTGT 149 chr6qtel1M 232463 CCTTGC--TTCAGGTGTGTTTCCTGTCAACAACATATTGCAGGATTCTGG 232510 i i --v v i v i vii i v iv i ii v C L1M2_orf2#LIN 148 CTTTACAGGTGAAGTGAGTTTCTTGTAGGCAGCATATAGTTGGGTCTTGT 99 chr6qtel1M 232511 CTTTTAATCCATTCTCTAACCACTTCCTCTCT----ATGGGGCAGTTTAC 232556 i v --- i ? iiv v ---- v iv i v C L1M2_orf2#LIN 98 TTTTTTATCCATTC---AGCCANTCTATGTCTTTTAATTGGAGAATTTAA 52 chr6qtel1M 232557 CCCATTCACATTTATGGTTA 232576 i i i v C L1M2_orf2#LIN 51 TCCATTTACATTCAAGGTTA 32 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.87 CpG sites = 104, Kimura (unadjusted) = 37.35 Transitions / transversions = 1.13 (104/92) Gap_init rate = 0.08 (58 / 724), avg. gap size = 1.47 (85 / 58) 283 30.46 9.34 2.93 chr6qtel1M 232415 232671 (767329) C L1MEc_5end#LINE/L1 (49) 2478 2206 m_b304s551i2 12715 chr6qtel1M 232415 GCATGGTAGATTCTGCTTCAACCTTTTACCTTTATTCTGCATGTATCTCC 232464 v ii vi i v i vi iiv i ii C L1MEc_5end#LI 2478 GCATGGTATATCTTTTTCCATCCTTTTACTTTTAACCTATTTGTGTCTTT 2429 chr6qtel1M 232465 TTGCTTCAGGTGTGTTTCCTGTCAACAACATATTGCAGGATTCTGGCTTT 232514 v ii v i ? i vii i v iv i ii vi C L1MEc_5end#LI 2428 ATATTTAAAGTGNGTTTCTTGTAGGCAGCATATAGTTGGGTCTTGCTTTT 2379 chr6qtel1M 232515 TAATCCATTCTC-TAACCACTTCCTCTCTATGGGGCAGTTTACCCCATTC 232563 v v v-i i v v i iv v vv vv i C L1MEc_5end#LI 2378 TTATCCAATCTGACAATCTCTGCCTTTTAATTGGGGTGTTTAGACCATTT 2329 chr6qtel1M 232564 ACATT---------------TATGGTTA-----AAAT-TACCAGTTTGCT 232592 --------------- i----- - vi C L1MEc_5end#LI 2328 ACATTTAATGTGATTATTGATATGGTTGGGTTTAAATCTACCATCTTGCT 2279 chr6qtel1M 232593 ATTACTTGCCAACTTGATAACCCCTATTTATACTTTTCTCTTCCTTCCTC 232642 vv vi v i -----i i i i v --- ii i C L1MEc_5end#LI 2278 ATTTGTTTTCTATTTG-----TCCCATCTGTTCTTTT---TTCCTTTTTT 2237 chr6qtel1M 232643 CTTATCC--CCTTCCCCAGTATTAAATGTGT 232671 v i -- iiiv v v v C L1MEc_5end#LI 2236 CTTTTTCTGCCTTCTTTTGGATTAATTGAGT 2206 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 40.42 CpG sites = 43, Kimura (unadjusted) = 40.42 Transitions / transversions = 1.30 (43/33) Gap_init rate = 0.05 (13 / 256), avg. gap size = 2.46 (32 / 13) 349 26.35 3.31 1.96 chr6qtel1M 232457 232607 (767393) C L1M6_5end#LINE/L1 (0) 2515 2363 m_b304s551i3 12715 chr6qtel1M 232457 GTATCTCCTTGCTTCAGGTGTGTTTCCTGTCAACAACATATTGCAGGATT 232506 -- vv i i i v i v iv C L1M6_5end#LIN 2515 GTATCT--TTTATTTAGGTGTGTCTCTTGTAAACAGCATATAGTTGGATT 2468 chr6qtel1M 232507 CTGGCTTTTAATCCATTCTCTAACCACTTCCTCTCT--ATGGGGCAGTTT 232554 i vi i v vvi vi- iv i -- i v C L1M6_5end#LIN 2467 TTGTTTTTTAACCCAATCTGAGAGT-CTTTGTCTTTTAATAGGGGAGTTT 2419 chr6qtel1M 232555 ACCCCATTCACATTTATGGTTAAAATTACCA-GTTTGCTATTA--CTTGC 232601 v i v i v i ivi - v v --i i C L1M6_5end#LIN 2418 AACCCATTTACATTTATTGTCATAACTGATATGTTTGGTCTTATNTTTGT 2369 chr6qtel1M 232602 CAACTT 232607 v C L1M6_5end#LIN 2368 CATCTT 2363 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 32.85 CpG sites = 20, Kimura (unadjusted) = 32.85 Transitions / transversions = 1.05 (20/19) Gap_init rate = 0.04 (6 / 150), avg. gap size = 1.33 (8 / 6) 23 7.03 0.00 0.00 chr6qtel1M 233680 233709 (766291) (T)n#Simple_repeat 1 30 (0) m_b304s252i6 12716 chr6qtel1M 233680 TTTTTTTTTTTTTTTTTTTTTTTTGGTTTT 233709 vv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 30 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 22 0.00 0.00 0.00 chr6qtel1M 234266 234289 (765711) (TG)n#Simple_repeat 1 24 (0) m_b304s252i7 12717 chr6qtel1M 234266 TGTGTGTGTGTGTGTGTGTGTGTG 234289 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTG 24 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 69 22.93 1.78 0.58 chr6qtel1M 234895 235063 (764937) (AG)n#Simple_repeat 1 171 (0) m_b304s252i8 12718 chr6qtel1M 234895 AGAG-GAGAGAGACAGAGACACAGAGAAACAGAGAGGCAGAGAGGCAGAC 234943 - v v v i v iv iv v (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr6qtel1M 234944 AGACACATAGAGAGAAAGAGTGAGACAGAGAGAGAGAGAGAG-GAAGGAG 234992 v v v i v v - ii (AG)n#Simple_ 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 100 chr6qtel1M 234993 ATAGAGAGTAGAG-GAGACAGAGACACAGAGAAACACAGAGAGACATAGA 235041 v - - v v v i v v v v (AG)n#Simple_ 101 AGAGAGAG-AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 149 chr6qtel1M 235042 CAGAAACTGACAGAGAGAAAGA 235063 v i vv v i (AG)n#Simple_ 150 GAGAGAGAGAGAGAGAGAGAGA 171 Matrix = Unknown Transitions / transversions = 0.38 (9/24) Gap_init rate = 0.02 (4 / 168), avg. gap size = 1.00 (4 / 4) 13 17.55 5.13 0.00 chr6qtel1M 238781 238819 (761181) (CTGAATA)n#Simple_repeat 1 41 (0) m_b304s252i9 12719 chr6qtel1M 238781 CTGACTTGTGAAT-CT-CATACTGAATACTGACTTCTGAAT 238819 v vv - -v v v (CTGAATA)n#Si 1 CTGAATACTGAATACTGAATACTGAATACTGAATACTGAAT 41 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2) 21 15.69 4.65 0.00 chr6qtel1M 239534 239576 (760424) (CA)n#Simple_repeat 1 45 (0) m_b304s252i10 12720 chr6qtel1M 239534 CACACACAC-CTCAAACACACACAACCACACTC-CACACACTCAC 239576 - v v vv v - v (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACAC 45 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.00 (2 / 2) 454 23.00 2.33 5.60 chr6qtel1M 240637 240765 (759235) C MIRc#SINE/MIR (141) 127 3 m_b304s601i5 12721 chr6qtel1M 240637 CTGAGGC-CAGTGAAGTTAAATGACTTTGCCCAGGGTCACAAATCTAGTA 240685 - v i i - i v v C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTT-GCCCAAGGTCACACAGCTAGTA 79 chr6qtel1M 240686 ACTATTAAATGAGGCTGGATTTGAACTTAGATCCTCCTGACTTCAGGGGC 240735 v ivi --- v v i i ii i i i i vv C MIRc#SINE/MIR 78 AGTGGCA---GAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCC 32 chr6qtel1M 240736 ACT--TCTCTCCACTGAGCCATCTAGCTGCCT 240765 v -- i vi i---i C MIRc#SINE/MIR 31 AGTGCTCTTTCCACTGCACCAC---ACTGCCT 3 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 26.83 CpG sites = 17, Kimura (unadjusted) = 27.98 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.07 (9 / 128), avg. gap size = 1.11 (10 / 9) 18 18.13 0.00 0.00 chr6qtel1M 241911 241942 (758058) (A)n#Simple_repeat 1 32 (0) m_b304s252i11 12722 chr6qtel1M 241911 AAGAAAGTAAAAAGAAAAAAAAAAAAAGAAAA 241942 i iv i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 32 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 13 17.11 3.03 0.00 chr6qtel1M 243362 243394 (756606) (AAAAC)n#Simple_repeat 1 34 (0) m_b304s252i12 12723 chr6qtel1M 243362 AAAACAAAACAAAACACAGGAAGA-GAAACAAAA 243394 v iv i -i (AAAAC)n#Simp 1 AAAACAAAACAAAACAAAACAAAACAAAACAAAA 34 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 1555 31.57 4.70 3.65 chr6qtel1M 243441 245120 (754880) C L1M5_orf2#LINE/L1 (1560) 1734 38 m_b304s551i4 12724 chr6qtel1M 243441 TTTCCTAATATTGAATCAGCCCTACATTCTTGGTATAAAATTTACTTGGT 243490 i v i i i i i i i v viii C L1M5_orf2#LIN 1734 TTTTCGAATGTTAAACCAACCTTGCATTCCTGGGATAAACCCCACTTGGT 1685 chr6qtel1M 243491 CATAGTGTATTATCCTGGTGATGATTTTTCTCTAATCTTTTTTGCTAATA 243540 ii vv v - v v v-i iivv C L1M5_orf2#LIN 1684 CATGATGTATTATCCTTTTTAT-ATATTGCTG-GATTCGATTTGCTAATA 1637 chr6qtel1M 243541 TTGTATTTATGATTTTAGAATCAATATTTATTAGGAAGATTGGTCTATAA 243590 v i ? v v v v i i v i v i C L1M5_orf2#LIN 1636 TTTTGTTNAGGATTTTTGCATCTATGTTCATGAGGGATATTGGTCTGTAA 1587 chr6qtel1M 243591 TTTTCTTTCTCTGTT-TCACCCTACCTGGTTTAGGTATCAGTACCATGTC 243639 iii v- vv ii ii ? v vii? - C L1M5_orf2#LIN 1586 TTTTCTTTTCTTGTAATGTCTTTGTCNGGTTTTGGTATCAGGGTNATG-C 1538 chr6qtel1M 243640 TGGG-TCATGAAAGGAATTTGATAGGACTCCTTAAATCCCTATTTTTTTA 243688 v- i v i v iv vii i vvv ii i vi C L1M5_orf2#LIN 1537 TGGCCTCATAAAATGAGTTGGGAAGTGTTCCCTCTTTTTCTATTTTCTGG 1488 chr6qtel1M 243689 AAAATAGTTTATATA-CACTGAGGTAATT----CTTTAAATATTTGGTAG 243733 i -- i i -v i ivi v ---- i i C L1M5_orf2#LIN 1487 AAGA--GTTTGTGTAAGATTGGTATTATTTCTTCCTTAAATGTTTGGTAG 1440 chr6qtel1M 243734 AATTCACATGCAACTCCATCTGGTTCTATGGATTTTTTCTTAGAGAGTTG 243783 vv ii vv vi ivi v i iv i ii v v C L1M5_orf2#LIN 1439 AATTCACCAGTGAAGCCATCTGGGCCTGGAGTTTTCTTTGTGGGAAGGTT 1390 chr6qtel1M 243784 AGTAATAGCTTGTTCTGTTTCTTTTTCTAAAATGGTATTGTTTAACCATT 243833 vv vi vvi vi vvivi v i vii i i iviv C L1M5_orf2#LIN 1389 TTTAATTACAAATTCAATTTCTTTAATAGATATAGGGCTATTCAGATTTT 1340 chr6qtel1M 243834 TTACCTCTTCCTCTATTAATTTGGGTAAGCTATATTTTTGAAGATATTCT 243883 i ii i v?i i i v ?i i i v iv iv C L1M5_orf2#LIN 1339 CTATTTCTTCTTGNGTCAGTTTTGGTAANTTGTGTTTTTCAAGGAATTTG 1290 chr6qtel1M 243884 TCCATTTCAT-----TTATCTGATTTATTTGCATAAAGCTGGACAAAGTA 243928 ----- ? vi v i vv v i C L1M5_orf2#LIN 1289 TCCATTTCATCTAAGTTNTCAAATTTATTGGCATAAAGTTGTTCATAATA 1240 chr6qtel1M 243929 -ACTCTAATTATTGCTCTAATTTTCTTTTCATTAGTGGCGACCTCTCCTT 243977 -v v ivi i v iiv vvv iv i i iv C L1M5_orf2#LIN 1239 TTCTCTTATTATCCTTTTAATGTCTGTAGGATCTGTAGTGATGTCTCCTT 1190 chr6qtel1M 243978 TCTCATTTTTAAGACTAACAATTTA-ATTTTC-CTCTTTCCTTTTAAATC 244025 i ii i v i iii i-i i - ii i vi C L1M5_orf2#LIN 1189 TTTCATTCCTGATATTGGTAATTTGTGTCTTCTCTCTTTTTTTCTTGATC 1140 chr6qtel1M 244026 ACATTTACTGAAGGTATTATATATATATTTTTGTTGTTGGTTTTCACAAA 244075 vvi ?i ii - -----i v i v -v v i C L1M5_orf2#LIN 1139 AGTCTNGCTAGAGGT-TTAT-----CAATTTTATTGAT-CTTTTCAAAGA 1097 chr6qtel1M 244076 ACCAACTTTTAG-TTTATTTATTAATTCAATAGTTTTTATGTTACTTTCA 244124 i i - ii v vvi v v ? ? v --- v C L1M5_orf2#LIN 1096 ACCAGCTTTTGGCTTCGTTGATTTTCTCTATTGTNTNTTTGT---TTTCT 1050 chr6qtel1M 244125 ATTTTATTAATCTCTTCTTTTATTTTTAAAATTTCAAGTTAATGTTTGAC 244174 i i i v i i vv --v --iv iv C L1M5_orf2#LIN 1049 ATTTCATTGATTTCTGCTCTTATCTTTATTATTTC--CTT--CCTTCTAC 1004 chr6qtel1M 244175 TGGT----GTTTTAATTTGTTC----TTTTATAGCTTTTTAATCTGTAAC 244216 v?i---- v i ---- v i vv v v C L1M5_orf2#LIN 1003 TTNCTTTGGGTTTAATTTGCTCTTCTTTTTCTAGCTTCTTAAGGTGGAAG 954 chr6qtel1M 244217 CCTAATTCTTTGACTCT--CTCTTTCTCTATTTTATCAAGTAGACCTCTA 244264 i iv v i i --vi - v v v vi ?i v i C L1M5_orf2#LIN 953 CTTAGATCATTGATTTTAAGCCTTTCT-TCTTTTCTAATATANGCATTTA 905 chr6qtel1M 244265 GAGATATAAAATTTCCCCTTATTACTGCTTTTGCTAAATCCCAC--ATTT 244312 i? v v i i v vi v iv -- C L1M5_orf2#LIN 904 ANGCTATAAATTTCCCTCTAAGCACTGCTTTAGCTGCATCCCACAAATTT 855 chr6qtel1M 244313 TGGTATGATGTCTCATTATTGTCATTTTCTTGGGTGAAGTTATTAATTAT 244362 i v v iv i ? ivv viiviv v vi vi C L1M5_orf2#LIN 854 TGATATGTTGTATTTTCATTNTCATTCAGTTCAAAATATTTTCTAATTTC 805 chr6qtel1M 244363 GTCAACAATTTGCTGTTTC-CCCACACATTCTTTAGTA-TGAGATTATTT 244410 v?iviii vi v v- iivi v v - v - i C L1M5_orf2#LIN 804 CNTTGTGATTTCTTCTTTGACCCATGGGTTATTTAGAAGTGTG-TTGTTT 756 chr6qtel1M 244411 AGTTT-CAATTATTTTTTGGTTTATTTTTCCCTAGCTAT-------TTAT 244452 i - v --- -vv --- ? ------- C L1M5_orf2#LIN 755 AATTTCCAAATA---TTTGG-GGATTTT---CTAGNTATCTTTTTGTTAT 713 chr6qtel1M 244453 TGACTGTAATTTTCATTGCATCGTGGTCTGAAAAGGATGCATTTACTATT 244502 i viv v v v i v i ----- -- ---- C L1M5_orf2#LIN 712 TGATTTCTAATTTAATTCCATTGTGGTCAGAGAA-----CA--TAC---- 674 chr6qtel1M 244503 TCTGCATTACTGCA-----TTTGAGT---TTGAGGT---TTTTATGTCCT 244541 i v i v ----- ?i i --- ii--- v i C L1M5_orf2#LIN 673 TCTGTATGATTTCAATCCTTTNAAATTTATTGAGACTTGTTTTATGGCCC 624 chr6qtel1M 244542 A--ATATGGTCAATTTTTGTATAGGTTCCATGAACTGCTGAGAAGAAAAT 244589 -- v i v v v vi vvi i vi C L1M5_orf2#LIN 623 AGNATATGGTCTATCTTGGTAAATGTTCCATGTGCACTTGAAAAGAATGT 574 chr6qtel1M 244590 GTACTCCTTTCTGTCTCT--ATTTAGTTTTCTCCAAAGATGTATCCTATC 244637 i -- v ? ivi --i v? v vi vi vv ivvi C L1M5_orf2#LIN 573 GTATTC--TGCNGTTGTTGGGTGNAGTGTTCTATAAATGTCAATTAGGTC 526 chr6qtel1M 244638 TAACT--TTTCTAGTATTCTATTTATCTCTTTGACTTTTTCTTATTTATT 244685 v ii -- vv i -- i i vv iv -- v i i v C L1M5_orf2#LIN 525 AAGTTGGTTGATAGTGT--TGTTCAAATCTTCTA--TATCCTTACTGATT 480 chr6qtel1M 244686 TTGTA---GTTTGATTTATCTAATGCTGAG-GTGCAAGGTTGAGATCTTC 244731 v i---ii v i v v i - v v?iv i i i C L1M5_orf2#LIN 479 TTTTGTCTACTTGTTCTATCAATTACTGAGAGAGGNGTGTTAAAATCTCC 430 chr6qtel1M 244732 TCCCACTATTATGGTTTTGCAGTCTATATCTTCTTGCAG-CCTCTTAATT 244780 ?v i iv i v --- v i vi -i v i i C L1M5_orf2#LIN 429 NACTATAATTGTGGATTT---GTCTATTTCTCCTTTTAGTTCTGTCAGTT 383 chr6qtel1M 244781 TCTCTTTTAAATTTACTT----GCCACACTACTTGGTGCATATATGTTTA 244826 i vi i-- v i ---- iviii i v i ii C L1M5_orf2#LIN 382 TTTGCTTC--ATGTATTTTGAAGCTCTGTTATTAGGTGCATACACATTTA 335 chr6qtel1M 244827 ATATTGATAT---TGCTTGATTATCTATGCTACCTTTAGTAAGATATAAG 244873 iv v --- v v vi-- viv i vi vv i- i C L1M5_orf2#LIN 334 GGATTGTTATGTCTTCTTGATGAAT--TGACCCTTTTATCATTATG-AAA 288 chr6qtel1M 244874 TGCCCTTCCTTATCTCTTTTAATTAGATCAATTTTGCTTT------TGCT 244917 i i i vv --- i-- i i ------ i C L1M5_orf2#LIN 287 TGTCCCTCTTTATCTCTGGTAAT---ATT--TCTTGCCTTGAAGTCTACT 243 chr6qtel1M 244918 TGATCTGAGATCAGGATGAGCTACCCT-GCTTTTTGACTTCACCTGA--- 244963 vi v i iv - i ? i- i --- ii?i ii--- C L1M5_orf2#LIN 242 TTGTCTGATATTAATAT-AGCCACNCCAGCTTTCT---TTTGNTTAGTGT 197 chr6qtel1M 244964 -AGCATGGTAGATTCTGCTTCAACCTTTTACCTTTATTCTGCATGTATCT 245012 -v v ii vi i v i i vi ?iv i C L1M5_orf2#LIN 196 TTGCATGGTATATCTTTTTCCATCCTTTTACTTTCAACCTNTCTGTGTCT 147 chr6qtel1M 245013 CCTTGCTTCAGGTGTGTTTCCTGTCAACAACATATTGCAGGATTCTGGCT 245062 iiv ii v i i i i vi i v iv i ii vi C L1M5_orf2#LIN 146 TTATATTTAAAGTGCGTCTCTTGTAGACAGCATATAGTTGGGTCTTGTTT 97 chr6qtel1M 245063 TTTAATCCATTCTC-TAACCACTTCCTCTCTATGGGGCAGTTTACCCCAT 245111 v v v-i i v v i iv v ivv v? C L1M5_orf2#LIN 96 TTTTATCCAGTCTGACAATCTCTGCCTTTTAATTGGAGTGTTTAGNCCAT 47 chr6qtel1M 245112 TCACATTTA 245120 i C L1M5_orf2#LIN 46 TTACATTTA 38 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 42.47 CpG sites = 279, Kimura (unadjusted) = 42.82 Transitions / transversions = 1.20 (279/232) Gap_init rate = 0.06 (95 / 1679), avg. gap size = 1.48 (141 / 95) 306 31.83 8.59 1.83 chr6qtel1M 244965 245220 (754780) C L1MEc_5end#LINE/L1 (49) 2478 2206 m_b304s551i5 12724 chr6qtel1M 244965 GCATGGTAGATTCTGCTTCAACCTTTTACCTTTATTCTGCATGTATCTCC 245014 v ii vi i v i vi iiv i ii C L1MEc_5end#LI 2478 GCATGGTATATCTTTTTCCATCCTTTTACTTTTAACCTATTTGTGTCTTT 2429 chr6qtel1M 245015 TTGCTTCAGGTGTGTTTCCTGTCAACAACATATTGCAGGATTCTGGCTTT 245064 v ii v i ? i vii i v iv i ii vi C L1MEc_5end#LI 2428 ATATTTAAAGTGNGTTTCTTGTAGGCAGCATATAGTTGGGTCTTGCTTTT 2379 chr6qtel1M 245065 TAATCCATTCTC-TAACCACTTCCTCTCTATGGGGCAGTTTACCCCATTC 245113 v v v-i i v v i iv v vv vv i C L1MEc_5end#LI 2378 TTATCCAATCTGACAATCTCTGCCTTTTAATTGGGGTGTTTAGACCATTT 2329 chr6qtel1M 245114 ACATT---------------TATGGTTA-----AAAT-TACCAGTTTGCT 245142 --------------- i----- - vi C L1MEc_5end#LI 2328 ACATTTAATGTGATTATTGATATGGTTGGGTTTAAATCTACCATCTTGCT 2279 chr6qtel1M 245143 ATTACTTGCCAACTTGATAACCCCTATTTATACTTTTCTCTTCCTTCCTC 245192 vv vi v i -----i i i i v i i ii i i C L1MEc_5end#LI 2278 ATTTGTTTTCTATTTG-----TCCCATCTGTTCTTTTTTCCTTTTTTCTT 2234 chr6qtel1M 245193 CTTATCCCTTCCCCAGTATTAAATGTGT 245220 i v v iiiv v v v C L1MEc_5end#LI 2233 TTTCTGCCTTCTTTTGGATTAATTGAGT 2206 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 43.00 CpG sites = 46, Kimura (unadjusted) = 43.00 Transitions / transversions = 1.35 (46/34) Gap_init rate = 0.04 (9 / 255), avg. gap size = 3.00 (27 / 9) 349 26.35 3.31 1.96 chr6qtel1M 245007 245157 (754843) C L1M6_5end#LINE/L1 (0) 2515 2363 m_b304s551i6 12724 chr6qtel1M 245007 GTATCTCCTTGCTTCAGGTGTGTTTCCTGTCAACAACATATTGCAGGATT 245056 -- vv i i i v i v iv C L1M6_5end#LIN 2515 GTATCT--TTTATTTAGGTGTGTCTCTTGTAAACAGCATATAGTTGGATT 2468 chr6qtel1M 245057 CTGGCTTTTAATCCATTCTCTAACCACTTCCTCTCT--ATGGGGCAGTTT 245104 i vi i v vvi vi- iv i -- i v C L1M6_5end#LIN 2467 TTGTTTTTTAACCCAATCTGAGAGT-CTTTGTCTTTTAATAGGGGAGTTT 2419 chr6qtel1M 245105 ACCCCATTCACATTTATGGTTAAAATTACCA-GTTTGCTATTA--CTTGC 245151 v i v i v i ivi - v v --i i C L1M6_5end#LIN 2418 AACCCATTTACATTTATTGTCATAACTGATATGTTTGGTCTTATNTTTGT 2369 chr6qtel1M 245152 CAACTT 245157 v C L1M6_5end#LIN 2368 CATCTT 2363 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 32.85 CpG sites = 20, Kimura (unadjusted) = 32.85 Transitions / transversions = 1.05 (20/19) Gap_init rate = 0.04 (6 / 150), avg. gap size = 1.33 (8 / 6) 350 23.53 2.46 2.46 chr6qtel1M 245012 245133 (754867) C L1MEh_5end#LINE/L1 (1) 2234 2113 m_b304s551i7 12724 chr6qtel1M 245012 TCCTT--GCTTCAGGTGTGTTTCCTGTCAACAACATATTGCAGGATTCTG 245059 -- i i i i i vi i iv i C L1MEh_5end#LI 2234 TCCTTNTGTTTTAAGTGTGTCTCTTGTAGACAGCATATTGTTGGATTTTG 2185 chr6qtel1M 245060 GCTTTTAATCCATTCTC-TAACCACTTCCTCTCTATGGGGCAGTTTACCC 245108 vi ? v v-? i v vi i iv v vv v C L1MEh_5end#LI 2184 TTTTTNAATCCAATCTGANAATCTCTGTCTTTTAATTGGTGAGTTTAACC 2135 chr6qtel1M 245109 CATTCACATTTATGGTTAAAATTAC 245133 i v --- C L1MEh_5end#LI 2134 CATTTACATTTATTGT---AATTAC 2113 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 29.19 CpG sites = 15, Kimura (unadjusted) = 29.19 Transitions / transversions = 1.15 (15/13) Gap_init rate = 0.04 (5 / 121), avg. gap size = 1.20 (6 / 5) 23 7.03 0.00 0.00 chr6qtel1M 246229 246258 (753742) (T)n#Simple_repeat 1 30 (0) m_b304s252i13 12725 chr6qtel1M 246229 TTTTTTTTTTTTTTTTTTTTTTTTGGTTTT 246258 vv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 30 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 22 0.00 0.00 0.00 chr6qtel1M 246815 246838 (753162) (TG)n#Simple_repeat 1 24 (0) m_b304s252i14 12726 chr6qtel1M 246815 TGTGTGTGTGTGTGTGTGTGTGTG 246838 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTG 24 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 69 22.93 1.78 0.58 chr6qtel1M 247444 247612 (752388) (AG)n#Simple_repeat 1 171 (0) m_b304s252i15 12727 chr6qtel1M 247444 AGAG-GAGAGAGACAGAGACACAGAGAAACAGAGAGGCAGAGAGGCAGAC 247492 - v v v i v iv iv v (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr6qtel1M 247493 AGACACATAGAGAGAAAGAGTGAGACAGAGAGAGAGAGAGAG-GAAGGAG 247541 v v v i v v - ii (AG)n#Simple_ 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 100 chr6qtel1M 247542 ATAGAGAGTAGAG-GAGACAGAGACACAGAGAAACACAGAGAGACATAGA 247590 v - - v v v i v v v v (AG)n#Simple_ 101 AGAGAGAG-AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 149 chr6qtel1M 247591 CAGAAACTGACAGAGAGAAAGA 247612 v i vv v i (AG)n#Simple_ 150 GAGAGAGAGAGAGAGAGAGAGA 171 Matrix = Unknown Transitions / transversions = 0.38 (9/24) Gap_init rate = 0.02 (4 / 168), avg. gap size = 1.00 (4 / 4) 13 17.55 5.13 0.00 chr6qtel1M 251333 251371 (748629) (CTGAATA)n#Simple_repeat 1 41 (0) m_b304s252i16 12728 chr6qtel1M 251333 CTGACTTGTGAAT-CT-CATACTGAATACTGACTTCTGAAT 251371 v vv - -v v v (CTGAATA)n#Si 1 CTGAATACTGAATACTGAATACTGAATACTGAATACTGAAT 41 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2) 21 15.69 4.65 0.00 chr6qtel1M 252086 252128 (747872) (CA)n#Simple_repeat 1 45 (0) m_b304s252i17 12729 chr6qtel1M 252086 CACACACAC-CTCAAACACACACAACCACACTC-CACACACTCAC 252128 - v v vv v - v (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACAC 45 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.00 (2 / 2) 454 23.00 2.33 5.60 chr6qtel1M 253189 253317 (746683) C MIRc#SINE/MIR (141) 127 3 m_b304s601i6 12730 chr6qtel1M 253189 CTGAGGC-CAGTGAAGTTAAATGACTTTGCCCAGGGTCACAAATCTAGTA 253237 - v i i - i v v C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTT-GCCCAAGGTCACACAGCTAGTA 79 chr6qtel1M 253238 ACTATTAAATGAGGCTGGATTTGAACTTAGATCCTCCTGACTTCAGGGGC 253287 v ivi --- v v i i ii i i i i vv C MIRc#SINE/MIR 78 AGTGGCA---GAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCC 32 chr6qtel1M 253288 ACT--TCTCTCCACTGAGCCATCTAGCTGCCT 253317 v -- i vi i---i C MIRc#SINE/MIR 31 AGTGCTCTTTCCACTGCACCAC---ACTGCCT 3 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 26.83 CpG sites = 17, Kimura (unadjusted) = 27.98 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.07 (9 / 128), avg. gap size = 1.11 (10 / 9) 21 16.33 0.00 0.00 chr6qtel1M 254470 254504 (745496) (A)n#Simple_repeat 1 35 (0) m_b304s252i18 12731 chr6qtel1M 254470 AAGAAAGTAAAAAAGAAAAAAAAAAAAAAAGAAAA 254504 i iv i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 35 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 12 13.86 0.00 0.00 chr6qtel1M 255777 255800 (744200) (TCC)n#Simple_repeat 1 24 (0) m_b304s252i19 12732 chr6qtel1M 255777 TCCCCTTCCTCCTCCACCTCCTCC 255800 i i v (TCC)n#Simple 1 TCCTCCTCCTCCTCCTCCTCCTCC 24 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 14 3.95 0.00 10.34 chr6qtel1M 255919 255950 (744050) (AAAAC)n#Simple_repeat 1 29 (0) m_b304s252i21 12733 chr6qtel1M 255919 AAAACAAAACAAAACACAGGAAGAAAACAAAA 255950 - -- v (AAAAC)n#Simp 1 AAAACAAAACAAAACA-A--AACAAAACAAAA 29 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.10 (3 / 31), avg. gap size = 1.00 (3 / 3) 1206 29.47 6.75 4.48 chr6qtel1M 255995 257653 (742347) C L1M5_orf2#LINE/L1 (1560) 1734 40 m_b304s551i8 12734 chr6qtel1M 255995 TTTTCTAATATTAGATCAA--TACCATTCTTGGTATAAAATTTACTTGGT 256042 v i i i -- vv i v viii C L1M5_orf2#LIN 1734 TTTTCGAATGTTAAACCAACCTTGCATTCCTGGGATAAACCCCACTTGGT 1685 chr6qtel1M 256043 CATAGTGTATTATC-TGGTGATGATTTTTCTCTAATCTTTTTGCTAATAT 256091 ii - vv v - v v vv v vv C L1M5_orf2#LIN 1684 CATGATGTATTATCCTTTTTAT-ATATTGCTGGATTCGATTTGCTAATAT 1636 chr6qtel1M 256092 TGTATTTATGATTTTTG-ATCAATATTTATTAGGAGAGGAATTGGTCTAT 256140 v i ? v - v i i --- i iv i C L1M5_orf2#LIN 1635 TTTGTTNAGGATTTTTGCATCTATGTTCAT---GAGGGATATTGGTCTGT 1589 chr6qtel1M 256141 AATTTTTCTTTCTCTGTT-TCACCCTACCTGGTTTAGGTATCAGTACCAT 256189 ii - v- vv ii ii ? v vii? C L1M5_orf2#LIN 1588 AATTTTCTTTTCT-TGTAATGTCTTTGTCNGGTTTTGGTATCAGGGTNAT 1540 chr6qtel1M 256190 GTCTAGG-TCATAGAAAGGAATTTG-ATGGACTCCTTAAATCCCTATTTT 256237 - i v- - v i v - v vii i vvv ii C L1M5_orf2#LIN 1539 G-CTGGCCTCATA-AAATGAGTTGGGAAGTGTTCCCTCTTTTTCTATTTT 1492 chr6qtel1M 256238 TTAAAATAGTTTATATAGCACTGGAGGTAATTCTT---TAAATATTTGGT 256284 i ii v i i iv i viv v --- i C L1M5_orf2#LIN 1491 CTGGAAGAGTTTGTGTAAGATTGGTATTATTTCTTCCTTAAATGTTTGGT 1442 chr6qtel1M 256285 AGAGATTCAT--ACAACTCCATCTGGTTCTATGGATTTTCTTAGAGAG-- 256330 - i--iii vv vi i- ii v v i -- C L1M5_orf2#LIN 1441 AGA-ATTCACCAGTGAAGCCATCTGGGCCTG-GAGTTTTCTTTGTGGGAA 1394 chr6qtel1M 256331 ----TTGAGTAATAAGCTTGTTCTGTTTTCTTTTCTAAA-ATGGTATTGT 256375 ---- v i v i i---- vi - vv i - i vii i C L1M5_orf2#LIN 1393 GGTTTTTAATTACAAA----TTCAATTT-CTTTAATAGATATAGGGCTAT 1349 chr6qtel1M 256376 TTAACCATTTTACACCTCTTCCTCTATTAATTTGGGTAGCT-ATATTTTT 256424 i i-- vi ii i v?i i i v i? -i i C L1M5_orf2#LIN 1348 TCAG--ATTTTCTATTTCTTCTTGNGTCAGTTTTGGTAANTTGTGTTTTT 1301 chr6qtel1M 256425 GAAGATATTC-TTCATTTCAT------TATCTGATTTATTTGCATAAAGC 256467 v iv i- i ------ ? vi v i C L1M5_orf2#LIN 1300 CAAGGAATTTGTCCATTTCATCTAAGTTNTCAAATTTATTGGCATAAAGT 1251 chr6qtel1M 256468 TGGACA-AGTAACTCCTAATTATTACTCTATTTTCTTT-TCATTAGTAGC 256515 vv - i viii v ivi i v v v -vv iv i C L1M5_orf2#LIN 1250 TGTTCATAATATTCTCTTATTATCCTTTTAATGTCTGTAGGATCTGTAGT 1201 chr6qtel1M 256516 GACCTCTCCTTTCTCATTT-TAAGACTAACAATTTAATTTTCCTCTTTCC 256564 iv i i- i v i iii ivv i i i ii C L1M5_orf2#LIN 1200 GATGTCTCCTTTTTCATTCCTGATATTGGTAATTTGTGTCTTCTCTCTTT 1151 chr6qtel1M 256565 TTTTTTAAATCACATTTTACTGAAGGTATATATATATATTTTGTTGTTGG 256614 i vi -i i ?i ii v ---i - i v vv C L1M5_orf2#LIN 1150 TTTTCTTGATCA-GTCTNGCTAGAGGTTTAT---CA-ATTTTATTGATCT 1106 chr6qtel1M 256615 TTTCACA-AACCAACTTTTAGTTATTATTAATT----CAATAGTTTTTGT 256659 v - i i i - ii i ---- v v ? ? - C L1M5_orf2#LIN 1105 TTTCAAAGAACCAGCTTTTGGCT-TCGTTGATTTTCTCTATTGTNTNT-T 1058 chr6qtel1M 256660 TACTTTCAATTTTTATTAATCTCTTCTTTTAT-TTTAAAATTTCAAGTTA 256708 ii v i- i i v i - vv --v - C L1M5_orf2#LIN 1057 TGTTTTCTATTTC-ATTGATTTCTGCTCTTATCTTTATTATTTC--CTT- 1012 chr6qtel1M 256709 ATGTTTGACTGGGT--GTTTTTAATTTGTTCTT----TTATAGCTTTTTA 256752 -iv iv v?v -- vv i ---- v i C L1M5_orf2#LIN 1011 -CCTTCTACTTNCTTTGGGTTTAATTTGCTCTTCTTTTTCTAGCTTCTTA 963 chr6qtel1M 256753 ATCACAACAACCCTAATTCTTTGA--------CTCTCTCTTTCTCTATTT 256794 --ivviv v i iv v -------- i ii i v v C L1M5_orf2#LIN 962 A--GGTGGAAGCTTAGATCATTGATTTTAAGCCTTTCTTCTTTTCTAATA 915 chr6qtel1M 256795 TATGCAAGTAGACCTCTAGAATAATTTCCCCTTA----TTACTTTTGCTA 256840 ? vv i?v v ---- ii ----i i v i C L1M5_orf2#LIN 914 TANGCATTTAANGCTATA----AATTTCCCTCTAAGCACTGCTTTAGCTG 869 chr6qtel1M 256841 AATCC-ACACATTTTGGTATGATGTCTCATTATTGTCATTTCTTGGGTGA 256889 v - v i v v iv i ? i---i v v C L1M5_orf2#LIN 868 CATCCCACAAATTTTGATATGTTGTATTTTCATTNTCATTC---AGTTCA 822 chr6qtel1M 256890 AGTTATT----AATTATGTCAACAATTTGCTGTTTCCCCACACACATTCT 256935 iv ---- viv?iviii vi v vv - iivi v C L1M5_orf2#LIN 821 AAATATTTTCTAATTTCCNTTGTGATTTCTTCTTTGACC-CATGGGTTAT 773 chr6qtel1M 256936 TTAGTA-TGAGATTATTTAGTTTCCAA----TT----ATTTTTTGGTTTA 256976 v - v - i i ---- ---- i i ? - C L1M5_orf2#LIN 772 TTAGAAGTGTG-TTGTTTAATTTCCAAATATTTGGGGATTTTCTAGNT-A 725 chr6qtel1M 256977 TTTTTCCCTGGCTATTTATTG--ACTTTCATTACATCGTGGTCTAGAAAA 257024 i --- v i v v-- v v v i - i C L1M5_orf2#LIN 724 TCTTT---TTGTTATTGATTTCTAATTTAATTCCATTGTGGTC-AGAGAA 679 chr6qtel1M 257025 GGATGCATTTATTTCTGCATTACTGCA----TTTGG----T-TTGAG--- 257062 v- i ------- i v i v ---- ?i---- - --- C L1M5_orf2#LIN 678 C-ATAC-------TCTGTATGATTTCAATCCTTTNAAATTTATTGAGACT 637 chr6qtel1M 257063 -GTTTTATGTCCTA--ATATGGTCAGTTTTTGTATAGGTTCCATGAACTG 257109 - v i -- vi i v v v vi -i C L1M5_orf2#LIN 636 TGTTTTATGGCCCAGNATATGGTCTATCTTGGTAAATGTTCCATGTGC-A 588 chr6qtel1M 257110 CTGGGAAAAGAACGTGTACTCTGTCTGTCTCTATTTAGT----TTTTCTC 257155 v - i i - ? --- i vi ---- v - C L1M5_orf2#LIN 587 CTTG-AAAAGAATGTGTATTCTG-CNGT---TGTTGGGTGNAGTGTTCT- 544 chr6qtel1M 257156 AAAGATGT--ATCCTATCTAACT--TTTCTAGTATTCTTTATCTCTTTGA 257201 v i -- ivvi v ii -- vv i v i vv iv C L1M5_orf2#LIN 543 ATAAATGTCAATTAGGTCAAGTTGGTTGATAGTGTTGTTCAAATCTTCTA 494 chr6qtel1M 257202 CTTCTTT-CTTATTTATTTTGTAGTTTGATTTATCTAATGCTGAG-GTGC 257249 iv i - v v v v -i v i v v i - v v C L1M5_orf2#LIN 493 TATCCTTACTGATTTTTTGTCTA-CTTGTTCTATCAATTACTGAGAGAGG 445 chr6qtel1M 257250 AAGGTTGAGATCTCC-ACTAT---TGTGGTTTTGCAGTCTATATCTTCTT 257295 ?iv i i - --- v --- v i C L1M5_orf2#LIN 444 NGTGTTAAAATCTCCNACTATAATTGTGGATTTG---TCTATTTCTCCTT 398 chr6qtel1M 257296 GCAGTTCTCATAATTTCT-CTTTGAGAATTTACTTGCTACACTACTTGGT 257344 vi vvi i i - iiv v vvvv viii i v C L1M5_orf2#LIN 397 TTAGTTCTGTCAGTTTTTGCTTCATGTATTTTGAAGCTCTGTTATTAGGT 348 chr6qtel1M 257345 GCATATATGTTTAATATTGATAT---TGCTTGATTATCTATGCTACCCTT 257391 i ii iv v --- v v vi i---- C L1M5_orf2#LIN 347 GCATACACATTTAGGATTGTTATGTCTTCTTGATGAATTG----ACCCTT 302 chr6qtel1M 257392 T-AGCAAGATATAGTGCCCTTCCTTATCTCTTTTAATTAGATCAATTTTT 257440 - v vv iv i i i i vv --- --- i C L1M5_orf2#LIN 301 TTATCATTATGAAATGTCCCTCTTTATCTCTGGTAAT---AT---TTCTT 258 chr6qtel1M 257441 GCTTT------TGCTTGATCTGAGATCAGGATGGCTACCCCTGCTTT-TT 257483 i ------ i vi v i iv i i ? v - C L1M5_orf2#LIN 257 GCCTTGAAGTCTACTTTGTCTGATATTAATATAGCCACNCCAGCTTTCTT 208 chr6qtel1M 257484 TGACTTCACCTGAAGCATGGTAGATTCTGCTTCAACCTTTTACCTTTACT 257533 vi? viiv vv- v ii vi i v i i vi C L1M5_orf2#LIN 207 TTGNTTAGTGTTT-GCATGGTATATCTTTTTCCATCCTTTTACTTTCAAC 159 chr6qtel1M 257534 GTGCATGTATCCTTCCCTGCTTCAGGTGTGTTTCCTATCAACAATATATT 257583 v ?iv i i --v ii v i i i i i vi ii v C L1M5_orf2#LIN 158 CTNTCTGTGTCTTT--ATATTTAAAGTGCGTCTCTTGTAGACAGCATATA 111 chr6qtel1M 257584 GTAGGATTCTGGCTTTTAATCCATTCTC-TAACCACTTCCTCTCTATGGG 257632 v i ii vi v v v-i i v v i iv v C L1M5_orf2#LIN 110 GTTGGGTCTTGTTTTTTTATCCAGTCTGACAATCTCTGCCTTTTAATTGG 61 chr6qtel1M 257633 GAAGTTTACCCCATTCACATT 257653 iiv v? i C L1M5_orf2#LIN 60 AGTGTTTAGNCCATTTACATT 40 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 38.70 CpG sites = 252, Kimura (unadjusted) = 38.92 Transitions / transversions = 1.17 (252/215) Gap_init rate = 0.08 (125 / 1658), avg. gap size = 1.50 (188 / 125) 237 28.42 5.26 0.00 chr6qtel1M 258613 258707 (741293) C L1PA13_5end#LINE/L1 (670) 2211 2112 m_b304s551i9 12735 chr6qtel1M 258613 GGGCAGTTTTCTTTGATAATTTCCTGGAAAATAGTATCCAGG---CTCTT 258659 v i v v ii v i v iv v i --- i?i C L1PA13_5end#L 2211 GGGAAGTTCTCATGGACGATATCCTGAAATATGTTTTCCAAGTTGCTTNC 2162 chr6qtel1M 258660 TTTTTCATCATATTTTTCAGGGAGTCTAATAATTCTCAGATT--GTCTCT 258707 ? i vi v i vv i i v vi -- C L1PA13_5end#L 2161 NTTCTCCCCATCTCTTTCAGGGACGCCAATGAGTCGTAGATTTGGTCTCT 2112 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 35.38 CpG sites = 14, Kimura (unadjusted) = 37.27 Transitions / transversions = 1.08 (14/13) Gap_init rate = 0.02 (2 / 94), avg. gap size = 2.50 (5 / 2) 21 21.39 0.00 0.00 chr6qtel1M 258756 258798 (741202) (T)n#Simple_repeat 1 43 (0) m_b304s252i22 12736 chr6qtel1M 258756 TTTTTTCTTCATTGTTTCATTTTTTTTTTTTTTTTTTGGTTTT 258798 i iv v iv vv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 43 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 chr6qtel1M 259004 259021 (740979) (T)n#Simple_repeat 1 18 (0) m_b304s252i23 12737 chr6qtel1M 259004 TTTTTTTTTTTTTTTTTT 259021 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTT 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 15 13.67 0.00 0.00 chr6qtel1M 259348 259371 (740629) (TG)n#Simple_repeat 1 24 (0) m_b304s252i24 12738 chr6qtel1M 259348 TGTGTGTGGATGTCTGTGTGTGTG 259371 vi v (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTG 24 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 12 23.07 2.04 4.17 chr6qtel1M 259349 259397 (740603) (GTGG)n#Simple_repeat 1 48 (0) m_b304s252i25 12738 chr6qtel1M 259349 GTGTGTGGATGTCTGTGTGTGTGAAGGGGGTGGG-GGGTGGGCTGGATGG 259397 v i vv v v -i v - - i (GTGG)n#Simpl 1 GTGGGTGGGTGGGTGGGTGGGTG-GGTGGGTGGGTGGGTGGG-TGGGTGG 48 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.06 (3 / 48), avg. gap size = 1.00 (3 / 3) 54 27.05 1.27 0.00 chr6qtel1M 260004 260119 (739881) (AGAC)n#Simple_repeat 1 118 (41) m_b305s252i4 12739 chr6qtel1M 260004 AGAGAGGGAGACAGAGACACAGAGAAACAGACAGGCAGACAGACACACAG 260053 v iv v v v i i v (AGAC)n#Simpl 1 AGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAG 50 chr6qtel1M 260054 AGAGAAAGAGTGAGACACAGAGACAGAGACAGACAG--AGACAGACAGAC 260101 v v vv v v v v v -- (AGAC)n#Simpl 51 ACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGAC 100 chr6qtel1M 260102 ACACACACACACACACAC 260119 v v v v v (AGAC)n#Simpl 101 AGACAGACAGACAGACAG 118 Matrix = Unknown Transitions / transversions = 0.15 (3/20) Gap_init rate = 0.01 (1 / 115), avg. gap size = 2.00 (2 / 1) 47 2.26 0.00 0.00 chr6qtel1M 260120 260164 (739836) (AG)n#Simple_repeat 1 45 (0) c_b305s251i0 12740 chr6qtel1M 260120 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGACAGAGA 260164 v (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 45 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 54 27.05 1.27 0.00 chr6qtel1M 260165 260204 (739796) (AGAC)n#Simple_repeat 119 158 (1) m_b305s252i4 12741 chr6qtel1M 260165 AACACAGAGAGACATAGACAGAGATTGAGAGAGAGAAAGA 260204 v v v v v v v iv v v v (AGAC)n#Simpl 119 CAGACAGACAGACAGACAGACAGACAGACAGACAGACAGA 158 Matrix = Unknown Transitions / transversions = 0.09 (1/11) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 16 19.25 0.00 0.00 chr6qtel1M 260851 260880 (739120) (T)n#Simple_repeat 1 30 (0) m_b305s252i6 12742 chr6qtel1M 260851 TTTTTTGTTTTGTTTTGTTTTGTTTTATTT 260880 v v v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 30 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 20 3.71 0.00 0.00 chr6qtel1M 260853 260880 (739120) (TTTTG)n#Simple_repeat 1 28 (0) m_b305s252i7 12742 chr6qtel1M 260853 TTTTGTTTTGTTTTGTTTTGTTTTATTT 260880 i (TTTTG)n#Simp 1 TTTTGTTTTGTTTTGTTTTGTTTTGTTT 28 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 26 8.12 0.00 0.00 chr6qtel1M 265082 265120 (734880) (CACACACT)n#Simple_repeat 1 39 (0) c_b305s251i1 12743 chr6qtel1M 265082 CACACACTCACGCACTCAAACAGTCACACACTCACACAC 265120 i v v (CACACACT)n#S 1 CACACACTCACACACTCACACACTCACACACTCACACAC 39 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 198 30.20 6.19 0.98 chr6qtel1M 265818 265914 (734086) C MIR1_Amn#SINE/MIR (37) 193 92 m_b305s601i0 12744 chr6qtel1M 265818 GTAGAGCATAAAGGAAATCAGAGAAGGTGACCAAAAGCAT-----CCATT 265862 v vi v vv i v - v ii iv v ----- C MIR1_Amn#SINE 193 GTAGATCTCAAAGCACTTTACA-AAGGAGGTCAGTATCATTATCCCCATT 145 chr6qtel1M 265863 TTATAGGTGAAGTAACTGAGGCCAAGGGAACTG-AGTGTTTTTTTCACAG 265911 i i i v ?v i iv ?- vi vii vi C MIR1_Amn#SINE 144 TTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGCCCAAGG 95 chr6qtel1M 265912 TCA 265914 C MIR1_Amn#SINE 94 TCA 92 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 40.18 CpG sites = 14, Kimura (unadjusted) = 40.18 Transitions / transversions = 0.93 (14/15) Gap_init rate = 0.03 (3 / 96), avg. gap size = 2.33 (7 / 3) 225 26.09 4.35 0.00 chr6qtel1M 265859 265927 (734073) C MIR3#SINE/MIR (65) 143 72 m_b305s601i1 12744 chr6qtel1M 265859 CATTTTATAGGTGAAGTAACTGAGGCCAAGGGAACTG-AGTGTTTTTTTC 265907 i i i v v i iv - vi vii C MIR3#SINE/MIR 143 CATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCC 94 chr6qtel1M 265908 ACAGT--CAAAGGAAGTTATTG 265927 vi -- v v? v C MIR3#SINE/MIR 93 AAGGTCACACAGCNAGTTAGTG 72 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 32.98 CpG sites = 9, Kimura (unadjusted) = 32.98 Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.03 (2 / 68), avg. gap size = 1.50 (3 / 2) 18 25.01 1.92 0.00 chr6qtel1M 266256 266307 (733693) (ATA)n#Simple_repeat 1 53 (0) m_b305s252i8 12745 chr6qtel1M 266256 ATAAT-TTTATAATTGTACTATTATTAATAATATTAAAAATATTAACAAT 266304 -v v vi v v v v v v i (ATA)n#Simple 1 ATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAAT 50 chr6qtel1M 266305 AAT 266307 (ATA)n#Simple 51 AAT 53 Matrix = Unknown Transitions / transversions = 0.22 (2/9) Gap_init rate = 0.02 (1 / 51), avg. gap size = 1.00 (1 / 1) 242 36.54 0.95 0.95 chr6qtel1M 266393 266497 (733503) MIRc#SINE/MIR 11 115 (153) m_b305s601i2 12746 chr6qtel1M 266393 TGAAGCAATAGATAGAATACTAGATCTGTGAGTCAGGAA-ACATGAACAC 266441 iv i i v ii i ii - - v iiiv MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTG-GAGTCAGGAAGACCTGGGTTC 59 chr6qtel1M 266442 TTATTCAGTTTCAAACACCTAATAGTTGTGGTAGCCTGGCCTAGTCATTG 266491 vvi i v vi viv i v i vv v i v v i v MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTT 109 chr6qtel1M 266492 ATTCTC 266497 vi MIRc#SINE/MIR 110 AACCTC 115 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 51.41 CpG sites = 20, Kimura (unadjusted) = 51.41 Transitions / transversions = 1.11 (20/18) Gap_init rate = 0.02 (2 / 104), avg. gap size = 1.00 (2 / 2) 25 2.69 2.38 4.88 chr6qtel1M 266584 266625 (733375) (AATTGTAT)n#Simple_repeat 1 41 (0) c_b305s251i2 12747 chr6qtel1M 266584 AATTGCATAATTGTATAA-TGTATAATATGTATATATTGTATA 266625 i - - - (AATTGTAT)n#S 1 AATTGTATAATTGTATAATTGTATAAT-TGTATA-ATTGTATA 41 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.07 (3 / 41), avg. gap size = 1.00 (3 / 3) 12 30.86 0.00 0.00 chr6qtel1M 266733 266776 (733224) (TTCC)n#Simple_repeat 1 44 (0) m_b305s252i9 12748 chr6qtel1M 266733 TTCCTTCTTTCCTTCATTTAGTCTTTACTGCCTTTTTTTCTTCC 266776 i v ivv i v v ii i (TTCC)n#Simpl 1 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 44 Matrix = Unknown Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 14 0.00 0.00 0.00 chr6qtel1M 267524 267541 (732459) (ATT)n#Simple_repeat 1 18 (0) m_b305s252i10 12749 chr6qtel1M 267524 ATTATTATTATTATTATT 267541 (ATT)n#Simple 1 ATTATTATTATTATTATT 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 31 23.56 6.06 0.00 chr6qtel1M 268078 268176 (731824) (AT)n#Simple_repeat 1 105 (0) m_b305s252i11 12750 chr6qtel1M 268078 ATAGATA-AAATCAATATCTATACACATGTAGAAATATATAT-TAAATAT 268125 v - v vv v i i i v v - v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr6qtel1M 268126 ATACCTATGTATATA-AGATGCA-ATATAAATGTATATA-ATA-ATATAA 268171 iv i - v ii - v i - - v (AT)n#Simple_ 51 ATATATATATATATATATATATATATATATATATATATATATATATATAT 100 chr6qtel1M 268172 ATATA 268176 (AT)n#Simple_ 101 ATATA 105 Matrix = Unknown Transitions / transversions = 0.67 (8/12) Gap_init rate = 0.06 (6 / 98), avg. gap size = 1.00 (6 / 6) 249 39.89 1.29 4.91 chr6qtel1M 268299 268530 (731470) MIRb#SINE/MIR 38 261 (7) m_b305s601i3 12751 chr6qtel1M 268299 TCTGGAGTTAGAAAGGCATGATTTCAACCTTTACTTCAGAGTTTTATTAT 268348 i i v i v iv i viiiiivi v vvvi i v MIRb#SINE/MIR 38 TTTGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAG 87 chr6qtel1M 268349 CTACATAAGCATGCTCAATATCCTCAAGTTCTATCTGGTTCAGGTTTTTC 268398 iii i v v vv vv v i vi v vv vi v ii MIRb#SINE/MIR 88 CTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTC 137 chr6qtel1M 268399 AAGTGTTAAATATAGATAACAAAAGC-ACTCCCTGGTGT--TTTTCAGGT 268445 vv v ivi i v v - ii vii v -- v v v MIRb#SINE/MIR 138 ATCTGTAAAATGGGGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGA 187 chr6qtel1M 268446 TCAAAACTGGTTATGTATTTGTATAGTGATTGCCGTATTGCTTGACGTAA 268495 i vvv i v i -- v i v iv ii v i i --- MIRb#SINE/MIR 188 TTAAATGAGATAATGCA--TGTAAAGCGCTTAGCACAGTGCCTGGC---A 232 chr6qtel1M 268496 AATAGTCTTTAAAAACACTTGATACATTGTAGTTC 268530 v ------ i i ii v v i MIRb#SINE/MIR 233 CATAGT------AAGCGCTCAATAAATGGTAGCTC 261 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 54.04 CpG sites = 43, Kimura (unadjusted) = 57.99 Transitions / transversions = 0.96 (43/45) Gap_init rate = 0.06 (13 / 231), avg. gap size = 1.08 (14 / 13) 12 16.52 2.08 8.89 chr6qtel1M 268608 268655 (731345) (TAA)n#Simple_repeat 1 45 (0) m_b305s252i12 12752 chr6qtel1M 268608 TAATAATCAACAAAAATAATAGTTAATAATTCATACATATTGA-AATAA 268655 - i v -v - v - v i - (TAA)n#Simple 1 TAATAAT-AATAATAATAATA-ATAATAA-TAATA-ATAATAATAATAA 45 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.11 (5 / 47), avg. gap size = 1.00 (5 / 5) 26 28.92 1.94 0.96 chr6qtel1M 271884 271923 (728077) (CAGA)n#Simple_repeat 1 39 (65) m_b305s252i13 12753 chr6qtel1M 271884 CACACACGAGAAACAGAGAGGCAGACACACACACATAGAA 271923 v - v i v i v v v v i (CAGA)n#Simpl 1 CAGACA-GACAGACAGACAGACAGACAGACAGACAGACAG 39 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1) 91 3.27 1.06 0.00 chr6qtel1M 271924 272017 (727983) (AG)n#Simple_repeat 1 95 (0) c_b305s251i3 12754 chr6qtel1M 271924 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAAAGAGAGAGAAAGAGAGAGAG 271973 i i (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr6qtel1M 271974 AGAGAGAGAGAGAGAGAGAGA-AGAGAGAGAGAGAGACAGAGAGA 272017 - v (AG)n#Simple_ 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 95 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.01 (1 / 93), avg. gap size = 1.00 (1 / 1) 26 28.92 1.94 0.96 chr6qtel1M 272018 272079 (727921) (CAGA)n#Simple_repeat 40 103 (1) m_b305s252i13 12755 chr6qtel1M 272018 CCGAGATACAGAGACAGAGACAGACAGACAAATTGACAG--AGACCAACA 272065 v v v v v v i iv -- vi (CAGA)n#Simpl 40 CAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACA 89 chr6qtel1M 272066 GAGAGAAAGAAAGA 272079 v v v (CAGA)n#Simpl 90 GACAGACAGACAGA 103 Matrix = Unknown Transitions / transversions = 0.27 (3/11) Gap_init rate = 0.02 (1 / 61), avg. gap size = 2.00 (2 / 1) 65 2.76 2.63 1.30 chr6qtel1M 272510 272585 (727415) (AT)n#Simple_repeat 1 77 (0) c_b305s251i4 12756 chr6qtel1M 272510 ATATATATATATATATATATATTTATATATATATATAT-TCATACAT-TA 272557 v - - i - (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATAT-ATATATATA 49 chr6qtel1M 272558 TATATATATATATATATATATATATATA 272585 (AT)n#Simple_ 50 TATATATATATATATATATATATATATA 77 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (3 / 75), avg. gap size = 1.00 (3 / 3) 15 30.59 1.67 0.00 chr6qtel1M 272609 272668 (727332) (AAGAA)n#Simple_repeat 1 61 (0) m_b305s252i15 12757 chr6qtel1M 272609 AAG-AAAGGGAAGAAAAGGAGAGAAATAAAATAAAAAGTACACAGCAGAA 272657 - ii i i vi vi v v v iv (AAGAA)n#Simp 1 AAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAA 50 chr6qtel1M 272658 AACAAAATAAA 272668 v v (AAGAA)n#Simp 51 AAGAAAAGAAA 61 Matrix = Unknown Transitions / transversions = 0.88 (7/8) Gap_init rate = 0.02 (1 / 59), avg. gap size = 1.00 (1 / 1) 15 19.85 0.00 0.00 chr6qtel1M 273063 273091 (726909) (A)n#Simple_repeat 1 29 (0) m_b305s252i16 12758 chr6qtel1M 273063 AAGAAAGTAAAAAAAAAAAAAATAGAAAA 273091 i iv v i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA 29 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 279 22.92 0.00 2.79 chr6qtel1M 274764 274947 (725053) HERVIP10FH#LTR/ERV1 818 996 (4106) m_b305s701i0 12759 chr6qtel1M 274764 AGAGAGAGAGGGAAACAAAGACAGAGAGAGGCAGAGGTAGACTGATACAT 274813 i i v i iv iv iv vv v v v HERVIP10FH#LT 818 AGAGAGAGAGAGAGAGAGAGGAAGAGAGAGAGAGAGAAAGAGAGAGAGAG 867 chr6qtel1M 274814 AGAGAGAAAGAGTGAGACAGAGAGTTAGAGAGAGAGAGAGAGACAGAGGG 274863 i i vv i v i i i iv v i HERVIP10FH#LT 868 GGAGAGAGAGAGACAAAGAGGGAGTCAAAGAGAGAGAGAGGCAGAGAGAG 917 chr6qtel1M 274864 AAAGAGAGACAGAGACAGAGAGAGAGAGAAAGAGATAGGGAGAGACAGAG 274913 i v v i i vv i v i i HERVIP10FH#LT 918 GAAGAGACAGAGAGACAAAGAGGGAGTCAGAGAGAGAGAGAGAGACAGAA 967 chr6qtel1M 274914 AGACACAGAGAGAAACAGAGAAAGCAGAGAGATA 274947 v v ---- - HERVIP10FH#LT 968 AGTCAAAGAGAGAA----AGAAAG-AGAGAGATA 996 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 27.52 CpG sites = 20, Kimura (unadjusted) = 27.52 Transitions / transversions = 0.95 (20/21) Gap_init rate = 0.03 (5 / 183), avg. gap size = 1.00 (5 / 5) 75 15.06 0.76 0.00 chr6qtel1M 276002 276133 (723867) (AGAG)n#Simple_repeat 1 133 (0) m_b305s252i17 12760 chr6qtel1M 276002 AGAGAGAGGGAGACAGAGTCACAGACAGACAGGCAGACAGCGAGAGAGAG 276051 i v vv v v v iv v v (AGAG)n#Simpl 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr6qtel1M 276052 AGAGAGAGAGA-AAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGACAGAG 276100 - i v (AGAG)n#Simpl 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 100 chr6qtel1M 276101 AGAGAAAGAGAGACAGAGACAGAGACAGAAAGA 276133 i v v v i (AGAG)n#Simpl 101 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 133 Matrix = Unknown Transitions / transversions = 0.38 (5/13) Gap_init rate = 0.01 (1 / 131), avg. gap size = 1.00 (1 / 1) 294 20.63 0.48 0.48 chr6qtel1M 276769 276814 (723186) (AGAG)n#Simple_repeat 1 46 (577) m_b305s252i19 12761 chr6qtel1M 276769 AGAGAGGGAGACAGAGACACAGGGAGGCAGACAGGCAGACAGACAG 276814 i v v v i iv v iv v v (AGAG)n#Simpl 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 46 Matrix = Unknown Transitions / transversions = 0.50 (4/8) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 43 0.00 0.00 0.00 chr6qtel1M 276815 276851 (723149) (AC)n#Simple_repeat 1 37 (0) c_b305s251i5 12762 chr6qtel1M 276815 ACACACACACACACACACACACACACACACACACACA 276851 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACA 37 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 294 20.63 0.48 0.48 chr6qtel1M 276852 276958 (723042) (AGAG)n#Simple_repeat 47 153 (470) m_b305s252i19 12763 chr6qtel1M 276852 GACAGAGAGACAGAGAGACAGAGGGGCAGAGACCAAAAGAGAGACAGAGA 276901 v v v i iv vvi i v (AGAG)n#Simpl 47 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 96 chr6qtel1M 276902 CAGAGAGAGAGAGAGAAAGACAGAGACTGACAGAGAAACAGACAGGAAGA 276951 v i v vv v i v v ii (AGAG)n#Simpl 97 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 146 chr6qtel1M 276952 CAGGCAG 276958 v iv (AGAG)n#Simpl 147 GAGAGAG 153 Matrix = Unknown Transitions / transversions = 0.56 (9/16) Gap_init rate = 0.00 (0 / 106), avg. gap size = 0.0 (0 / 0) 43 0.00 0.00 0.00 chr6qtel1M 276959 276995 (723005) (AC)n#Simple_repeat 1 37 (0) c_b305s251i6 12764 chr6qtel1M 276959 ACACACACACACACACACACACACACACACACACACA 276995 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACA 37 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 294 20.63 0.48 0.48 chr6qtel1M 276996 277463 (722537) (AGAG)n#Simple_repeat 154 621 (2) m_b305s252i19 12765 chr6qtel1M 276996 GAGAGAGACAGAGAGACAGAGAGGCAGAGACCAAAAGAGAGACAGAGACA 277045 v v iv vvi i v v (AGAG)n#Simpl 154 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 203 chr6qtel1M 277046 GAGAGAGAGAGAGAAAGACAGAGACTGACAGAGAAACAGACAGGAAGACA 277095 i v vv v i v v ii v (AGAG)n#Simpl 204 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 253 chr6qtel1M 277096 GGCAATCAGGCAGACAGACACACACACACATACAGAGAAAGTGAGACAGA 277145 iv ivv iv v v v v v v v v v i v v (AGAG)n#Simpl 254 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 303 chr6qtel1M 277146 GGGAGAG-GGGGGGGAGGGAGGGAGAGAG-GAGAGAGACAGAGAGACAGA 277193 i - i i i i i - v v (AGAG)n#Simpl 304 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 353 chr6qtel1M 277194 GAGAGAGAGAAAG-GAGAGAGAGACAGAGAGAGAGAGAGAGAGAGAGAGA 277242 i - v (AGAG)n#Simpl 354 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 403 chr6qtel1M 277243 GCAGAGAGAGAGAGAGAGAGAGAGCAGAGAGAGAGAGAGACAGAGAGAGA 277292 - - v (AGAG)n#Simpl 404 G-AGAGAGAGAGAGAGAGAGAGAG-AGAGAGAGAGAGAGAGAGAGAGAGA 451 chr6qtel1M 277293 GAGAGAGAGACAGAGAGACAGAGAGAGAAACAGAGACAGAGAGAGAGAGA 277342 v v i v v (AGAG)n#Simpl 452 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 501 chr6qtel1M 277343 CAGAGACTGAGAAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 277392 v vv i (AGAG)n#Simpl 502 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 551 chr6qtel1M 277393 GACAGAGAAAGAAAGAGAGACAGAGACAGAGACAGAGAGAGACAGACAGT 277442 v i i v v v v v - (AGAG)n#Simpl 552 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG- 600 chr6qtel1M 277443 ACAGACTGACAGAGGGAAAGA 277463 v vv v i i (AGAG)n#Simpl 601 AGAGAGAGAGAGAGAGAGAGA 621 Matrix = Unknown Transitions / transversions = 0.48 (24/50) Gap_init rate = 0.01 (6 / 467), avg. gap size = 1.00 (6 / 6) 12 11.68 10.81 0.00 chr6qtel1M 280346 280382 (719618) (TTGAATT)n#Simple_repeat 1 41 (0) m_b305s252i21 12766 chr6qtel1M 280346 TTGAA-GTTGAACTTT--A-TTTCAATTTTGACTTTTGAAT 280382 -v i -- - v v (TTGAATT)n#Si 1 TTGAATTTTGAATTTTGAATTTTGAATTTTGAATTTTGAAT 41 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.08 (3 / 36), avg. gap size = 1.33 (4 / 3) 24 19.31 0.00 0.00 chr6qtel1M 281380 281426 (718574) (AC)n#Simple_repeat 1 47 (0) m_b305s252i22 12767 chr6qtel1M 281380 ACACACACATGCACACTTACCCAAACACACACTCACACACACTCACA 281426 ii vi v v v v (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACA 47 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 223 33.64 3.74 0.00 chr6qtel1M 282088 282194 (717806) C MIR3#SINE/MIR (11) 197 87 m_b305s601i4 12768 chr6qtel1M 282088 TCAGAGCATTATAGAGCTTAAAGGAAG-TCAGAGA--AGTTGACCAAAAG 282134 v v vvi vi i v- i -- vi iii v vv C MIR3#SINE/MIR 197 TCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACC 148 chr6qtel1M 282135 CACCCATTTTACAGGTGAGGTAACTGAGACCAATGGAACTGAGG-GATAT 282183 v i i v i v vi iv i - iv C MIR3#SINE/MIR 147 CCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTT 98 chr6qtel1M 282184 TTTCACAGTCA 282194 vii vi C MIR3#SINE/MIR 97 GCCCAAGGTCA 87 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 45.38 CpG sites = 18, Kimura (unadjusted) = 45.38 Transitions / transversions = 1.00 (18/18) Gap_init rate = 0.03 (3 / 106), avg. gap size = 1.33 (4 / 3) 428 22.90 3.57 6.42 chr6qtel1M 282469 282580 (717420) C MIRc#SINE/MIR (141) 127 19 m_b305s601i5 12769 chr6qtel1M 282469 CTGAGGC---AAGGGGTTAAAGGACTTGCCTA-GGTCACAAAATTAGTAA 282514 ---i i iv i - v ii C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAA 78 chr6qtel1M 282515 CTATTAAATGTCTGAAGTTGGATTTGAACTCAGGTCCTCCTGACTTCAGG 282564 -------i v v iviv i i i i i i C MIRc#SINE/MIR 77 -------GTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr6qtel1M 282565 TCCACTTCTCTATCCA 282580 v v v C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCA 19 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 25.26 CpG sites = 15, Kimura (unadjusted) = 27.92 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.08 (9 / 111), avg. gap size = 1.22 (11 / 9) 31 39.07 0.61 1.23 chr6qtel1M 284690 284853 (715147) (TA)n#Simple_repeat 1 163 (0) m_b305s252i23 12770 chr6qtel1M 284690 TATACAGATGCATATACATATGTATGGATATGTAAGTAGGGTTATAGATA 284739 i v ii i i iv i vi vivv v (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr6qtel1M 284740 TCTATGTATATGCATGAATGTATTTATATTTGTGTATAAGTTAATCTGTA 284789 v i ii iv i v v i i vi vv v i (TA)n#Simple_ 51 TATATATATATATATATATATATATATATATATATATATATATATATATA 100 chr6qtel1M 284790 TATGTGTGTCTGCTTATATATATGTACTCACACA-ATGTCTTTATATATA 284838 i i i v iiv i - - i i - i v v (TA)n#Simple_ 101 TATATATATATATATATATATATATA-T-ATATATATATATATATATATA 148 chr6qtel1M 284839 TATATATATTTAAAT 284853 v v (TA)n#Simple_ 149 TATATATATATATAT 163 Matrix = Unknown Transitions / transversions = 1.29 (27/21) Gap_init rate = 0.02 (3 / 163), avg. gap size = 1.00 (3 / 3) 19 23.83 4.88 2.38 chr6qtel1M 284879 284960 (715040) (AAGAA)n#Simple_repeat 1 84 (0) m_b305s252i24 12771 chr6qtel1M 284879 AAGAAAAG-GAAGAAAAG--GGGAAAACAAAATTACAAAGTACACAACAG 284925 -i --ii v -v - v v v v (AAGAA)n#Simp 1 AAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAA-GA-AAAGAAAAGAAAAG 48 chr6qtel1M 284926 AAAAGGAATGAAAA-ACTACAAGAGTAAAGAAAAGA 284960 i v - vv v i v (AAGAA)n#Simp 49 AAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGA 84 Matrix = Unknown Transitions / transversions = 0.45 (5/11) Gap_init rate = 0.06 (5 / 81), avg. gap size = 1.20 (6 / 5) 35 6.87 0.00 0.00 chr6qtel1M 287406 287451 (712549) (CA)n#Simple_repeat 1 46 (0) m_b305s252i25 12772 chr6qtel1M 287406 CACACACACACACACACACACACACACACACACACACAGAAAGACA 287451 v v v (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACA 46 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 304 19.86 0.96 6.03 chr6qtel1M 287457 287665 (712335) HERVIP10FH#LTR/ERV1 800 998 (4104) m_b305s701i1 12773 chr6qtel1M 287457 GCAGAGAGAGAGAAAGAGAAAAGACAGAGAGACAGAGAGTCAGAGACAGA 287506 - i i i v v vv v HERVIP10FH#LT 800 GCAGAGAG-GAAAGAGAGAAGAGAGAGAGAGAGAGAGAGGAAGAGAGAGA 848 chr6qtel1M 287507 GATTGAGAGAGAGACAGAGAAAGAGAGAGAGACACAGAGAGAGACAGAGA 287556 vv i v ii v i v i HERVIP10FH#LT 849 GAGAGAAAGAGAGAGAGAGGGAGAGAGAGAGACAAAGAGGGAGTCAAAGA 898 chr6qtel1M 287557 CAGACATAGAGACAGGGACAGAGAAAGAGATAGACAGATAGAAAGACACA 287606 v v-- i i -- i i v i i i ----i HERVIP10FH#LT 899 GAGAG--AGAGGCAGAG--AGAGGAAGAGACAGAGAGACAAAGAG----G 940 chr6qtel1M 287607 GAGACAGAGAGTAGAGAGAGATAGAGACAGCC--AGACAGACAGACAGAC 287654 v - v v v i -- v v v v HERVIP10FH#LT 941 GAGTCAGAGAG-AGAGAGAGAGACAGAAAGTCAAAGAGAGAAAGAAAGAG 989 chr6qtel1M 287655 TTATAGATAGA 287665 -- v HERVIP10FH#LT 990 --AGAGATAGA 998 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 23.04 CpG sites = 17, Kimura (unadjusted) = 23.04 Transitions / transversions = 0.77 (17/22) Gap_init rate = 0.06 (13 / 208), avg. gap size = 1.08 (14 / 13) 1467 28.74 1.10 1.48 chr6qtel1M 289643 290186 (709814) C L1ME3G_3end#LINE/L1 (376) 548 7 m_b305s551i0 12774 chr6qtel1M 289643 ATAATATTCCATAATATTCATATACCACAATTTATTCAGCCCTTCTATAA 289692 i i vv i i i v iviv C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr6qtel1M 289693 TTGATGGGCATCTACTCAGTTTC-AGTTTCTGGCCACTACAAAGAGGGTT 289741 i i vviv - i i v i i v iv i C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chr6qtel1M 289742 GCCACAAACAGTCTTGTACATACAGGCCCCTTTCCTTCTTTAAG-ATCTC 289790 v ii vi i ?vv iiv viv v v vii - i C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACATGCNTCCTTGTGCACATGTGCGAGTATTTC 399 chr6qtel1M 289791 TTTGGGATGTAAGCCCAGTAGTAACACTGCTGGATCAAAGGGTATGCACA 289840 ? i iv v? ? v iiv i i i C L1ME3G_3end#L 398 TNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGCA 349 chr6qtel1M 289841 GTTTGATAACATTTTGA-GCATAGCTCCAAATTGCTCTC-AGAATGGCTG 289888 v i ---- i -iv viv i - i ? C L1ME3G_3end#L 348 TTTTAA----ATTTTAATAGATACTGCCAAATTGCCCTCCAAAANGGCTG 303 chr6qtel1M 289889 GATGTATTCACAATTCCACCAA-AATGTGTTAGTGTCTCTGTTTTCCCAC 289937 v ivv i v i i- i i v v vi i i C L1ME3G_3end#L 302 TACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCAC 253 chr6qtel1M 289938 ATCC-CTCCAACATTCTGCATTCTCTTTCCTTGTCATTCTAGCCAGTCTG 289986 i - v i ?vii v vv? i vvv i v i C L1ME3G_3end#L 252 ACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATCTG 203 chr6qtel1M 289987 ACAGGTGTGTAATGACATCTTAGAGTTGTCTTAGTTTGCATTTCTCTGAT 290036 ii viv ii i vv i i i C L1ME3G_3end#L 202 ATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGAT 153 chr6qtel1M 290037 TAATAATGCTTTGGAGCATCTTTTCATATGGCTAGAAATAGTTTCAATTT 290086 v i vvv v vi vviiivi vv C L1ME3G_3end#L 152 TACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGTATTT 103 chr6qtel1M 290087 CTTCTTTTGAGAATTATCTGTTCATATGCTTTGACCATTCATCAACTGGA 290136 i i v ii v v iv v i - C L1ME3G_3end#L 102 CCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGG- 54 chr6qtel1M 290137 AAATGGCTTGATTTCTTATAAATTAGAGTCAATTCTCTATATATTTTGGA 290186 -iv v -- vi v vivv i i i C L1ME3G_3end#L 53 -GTTGTCTT--TTTCTTATTGATTTGTAGGAGTTCTTTATATATTCTGGA 7 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.54 CpG sites = 82, Kimura (unadjusted) = 37.48 Transitions / transversions = 1.14 (82/72) Gap_init rate = 0.03 (14 / 543), avg. gap size = 1.00 (14 / 14) 4700 31.07 3.01 3.20 chr6qtel1M 290050 293274 (706726) C L1M5_orf2#LINE/L1 (7) 3287 69 m_b305s551i1 12774 chr6qtel1M 290050 GAGCATCTTTTCATATGGCTAGAAATAGTTTCAATTTCTTCTTTTGAGAA 290099 i vi vviiivi v? v v C L1M5_orf2#LIN 3287 GAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTTTTGTGAA 3238 chr6qtel1M 290100 TTATCTGTTCATATGCTTTGACCATTCATCAACTGGAAAATGGCTTG--- 290146 v i vi vi v iv ?v i ---i v i --- C L1M5_orf2#LIN 3237 GTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGG---GTTGTTTGTCT 3191 chr6qtel1M 290147 ATTTCTTA-TAAATTAGAGTCAATTCTCTATATATTTTGGAAATGAGGTC 290195 v ? - i ? iv -v i i i v i vi C L1M5_orf2#LIN 3190 TTTTNTTATTGANTTGTAG-GAGTTCTTTATATATTCTGGATACGAGTCC 3142 chr6qtel1M 290196 TTTATTATAACCTTTG-ACTGTAAAAATGTTTTCCCAGTTTATTGCTTCC 290244 i i -i iv v -?i i v v i ? i i v v C L1M5_orf2#LIN 3141 TTTGTCA-GATATATGTNTTGCAAATATTTTCTCCCANTCTGTGGCTTGC 3093 chr6qtel1M 290245 CTTCTAATCTTGTCTGCATTAGTTTTGTTTGTACAAAAACTTTTCAATTT 290294 i v i v ivi iv ivi vvv? vi i ii v v C L1M5_orf2#LIN 3092 CTTTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTTTAATTTT 3043 chr6qtel1M 290295 GATAAAATCAA-------AATTTTTGATTTTGTGATCAGGTCTTCTCTTT 290337 i? i v ------- vv i i i? --- v i C L1M5_orf2#LIN 3042 GATGNAGTCCAATTTATCAATTTTTTCTTTTATGGTTNG---TGCTTTTT 2996 chr6qtel1M 290338 A-GTTCTTTTTTGGTCATAAATTCCTTCGTCT-TCCACAGGTCTGAGAGG 290385 i- i v vi ---- -- i i -? vv vvii i C L1M5_orf2#LIN 2995 GTGTCCTGTTTAAG----AAAT--CTTTGCCTANCCCAAGGTCACGAAGA 2952 chr6qtel1M 290386 TAAACTATCCTATG--TTCCTCTAATTTATTTATAATCTCATTCTTTATG 290433 -- i v -- i ivvvv i i i ?ii ii C L1M5_orf2#LIN 2951 T--ATTCTCCTATGTTTTCTTCTAGAAGTTTTATAGTTTTANCTTTTACA 2904 chr6qtel1M 290434 CCTAGGTC-ATGAACCCATTTGACGTT-ATTGTGGTGTATGGTGTTAATT 290481 ii - - i i ?ivi - v v v iv C L1M5_orf2#LIN 2903 TTTAGGTCTATG-ATCCATCTNGAATTAATTTTTGTGTATGGTGTGAGGT 2855 chr6qtel1M 290482 GTCAGTCGATGACTTG-TTTCTGCCATACTAGTTTCCAATTTTCCCAGCA 290530 ivvi - ?i ii- i v ivii v v i C L1M5_orf2#LIN 2854 AGGGGTCGA-GNTTCATTTTTTTCCATATGGATATCCAATTGTTCCAGCA 2806 chr6qtel1M 290531 ATTTTTGTCAAACAGTAGGTTCTTATCCCCAAATTGGAGATGTCTGGG-- 290578 viv ii v vvvi i - -- i i v- i? v -- C L1M5_orf2#LIN 2805 CCATTTGTTGAAAAGACTATCCTT-TCCCC--ACTGAAT-TGCNTTGGCA 2760 chr6qtel1M 290579 --TTTGTCAAACACTAGATTGCTATAGTTATTGACTGTTTTGTCCTTTGA 290626 -- v ii i? v? i -- vviiv v i i -i i i C L1M5_orf2#LIN 2759 CCTTTGTCAAAAATCAANTGNCCATA--TATGTGTGGGTCTAT-TTCTGG 2713 chr6qtel1M 290627 AC---CTAACCTATTCTATCGATCAACTAATCTATTCCTTA-GCCAATAC 290672 --- vi i i i v i vi - - C L1M5_orf2#LIN 2712 ACTCTCTATTCTGTTCCATTGATCTATTTGTCTA-TCCTTACGCCAATAC 2664 chr6qtel1M 290673 CAAATGATTTTGGTAACCGCTGCTTTATAATATAATTTT-AGATCTGGTA 290721 v ivi i i v i iv - i i - ? ? C L1M5_orf2#LIN 2663 CACACTGTCTTGATTACTGTAGCTTTATAATA-AGTCTTGANATCNGGTA 2615 chr6qtel1M 290722 CAGCTAGGCCACCTTCA--TTTGATTTTTTTTTATTAA---TGCCCTTGA 290766 vv - i i-- i -- - i i v i --- iii v v C L1M5_orf2#LIN 2614 GTG-TAAGT--CCTCCAACTTTG-TTCTTCTTTTTCAAGATTGTTTTGGC 2569 chr6qtel1M 290767 AATTCTTGACCTTTTGTTTTTCCATATGAACTTTG--------TTGTTAT 290808 v ? ii i iv i i i-------- i v C L1M5_orf2#LIN 2568 TATTCTNGGTCCTTTGCATTTCCATATAAATTTTAGAATCAGCTTGTCAA 2519 chr6qtel1M 290809 TTTTTAGGTCATTAAAATAGTTTTTTGGGGAGTCTGATTGGTATAGCACT 290858 i ------i v iii vi - v i v v i C L1M5_orf2#LIN 2518 TTTCTA------CAAAAAAACCTGCT-GGGATTTTGATTGGGATTGCATT 2476 chr6qtel1M 290859 AAACAAATAGATTAGTTTAGGTAGTATTGCCATCTTTATTGTATTTGCTC 290908 i ivv i i i v v v ? ivi viv C L1M5_orf2#LIN 2475 GAATCTATAGATCAATTTGGGGAGAATTGACATCTTNACAATATTGAGTC 2426 chr6qtel1M 290909 GCCCTATCCAAGAGCATTTAATATTTTTCCAATTGGTTAGATCAGACTTA 290958 vi v v i vvv i i v iv i vvvi C L1M5_orf2#LIN 2425 TTCCAATCCATGAACATGGTATATCTCTCCATTTATTTAGGTCTTCTTTA 2376 chr6qtel1M 290959 ATTTATGTGGAAAGTGCTTTGTAGTTTTGCCCATAAAGTTTCTG---ATT 291005 v v viiv i i vvvii ? v ii --- ? C L1M5_orf2#LIN 2375 ATTTCTCTCAGCAATGTTTTGTAGTTTTCAGTGTANAGGTCTTGCACATN 2326 chr6qtel1M 291006 TTCCCTTGGCAGATAGATTCCTAAGTATTTTATACTATCAGTAGTTACTT 291055 --- vi vv ? ii v iv vv i i v C L1M5_orf2#LIN 2325 TT---TTGTTAGATTTATTCCTAAGTATTTNATGTTTTTTGATGCTATTG 2279 chr6qtel1M 291056 TAAAAGGAATTTCTCTTTGTAACTGACTGCTGGAT--TTTGTTAGTGATA 291103 v v vi i ?iv vi v i viivi -- iv ii C L1M5_orf2#LIN 2278 TAAATGGTATTGTTTTTNAAATTTCATTTTCCAATTGTTTGTTGCTAGTA 2229 chr6qtel1M 291104 TTTAAGAATGCTGATGAGTTATGTGGGTTTATTTTGTATCCTGCAATTTT 291153 v ii i viv v v ivi v ii ? i ii C L1M5_orf2#LIN 2228 TATAGAAATACAATTGATTTTTGTATATTGACCTTGTATCCNGCGACCTT 2179 chr6qtel1M 291154 GCTAAAGGTGTGGATTATTTCAAATAACTTTTTAGTAGAATCTCTAGGGT 291203 vviiivv v v i ii ? v v i ? i C L1M5_orf2#LIN 2178 GCTAAATTCACTTATTAGTTCTAGTAGTTTNTTTGTAGATTCTTTNGGAT 2129 chr6qtel1M 291204 TCTCCAAGTATACCATCATATCATCAGCAAAGAGTGATAATTTGATTTCC 291253 i i v ? v i v i v i? i i v i C L1M5_orf2#LIN 2128 TTTCTACGTANACAATCATGTCATCTGCGAATAANGACAGTTTTATTTCT 2079 chr6qtel1M 291254 TCATTGCCTATTCTAATTCCTTTAATCTCTTTCTCAACTCTTATTGCCAA 291303 v v v ii v v v i i vvvi vvv C L1M5_orf2#LIN 2078 TCCTTTCCAATCTTTATGCCTTTTATTTCTTTTTCTTGCCTTATTGCACT 2029 chr6qtel1M 291304 AGCTAGCATTTCTAAGACAATATTGAATAGTAATGGTGATAGGGGGCAAT 291353 i v ii i iv i v i ? v i vi C L1M5_orf2#LIN 2028 GGCTAGGACCTCCAGTACAATGTTGAATAGAAGTGGTGANAGCGGACATC 1979 chr6qtel1M 291354 CTTGTTTGATTCCTGATCTTACTAGGAATGCTTGCAGTTTTTCTCTATTA 291403 i vi i vvi v ? v ? v i C L1M5_orf2#LIN 1978 CTTGTCTTGTTCCCGATCTTAGGGGGAAAGCNTTCAGTNTTTCACCATTA 1929 chr6qtel1M 291404 TAAATGATGCTTACTGATGGTTTTAAATAGATGCTACTTATTATTTTAAG 291453 viv i ?i vv vvi ivi i vv i C L1M5_orf2#LIN 1928 AGTATGATGTTNGCTGTAGGTTTTTCGTAGATGCCCTTTATCAGGTTGAG 1879 chr6qtel1M 291454 GAACAGTCCATTTATTCCTTTATTCTCAAGTGCTTTTAATAGGAATGAAT 291503 vvvi v i vvv viii v i vi v ii C L1M5_orf2#LIN 1878 GAAGTTCCCTTCTATTCCTAGTTTGCTGAGAGTTTTTATCATGAATGGGT 1829 chr6qtel1M 291504 GTTGGATTTTATCAAATGCTTTTTTTGCATCTATTGAGATATTCATATGG 291553 i i i iv i C L1M5_orf2#LIN 1828 GTTGAATTTTGTCAAATGCTTTTTCTGCATCTATTGAGATGATCATATGA 1779 chr6qtel1M 291554 TTTTTGTTAATTTGGT-TGTTAATATGGTCAATTATACTGATACTG-TTT 291601 v i-v iv - v i i -- - C L1M5_orf2#LIN 1778 TTTTTCTC-CTTTATTCTGTTAATATGGTGAATTACATTGAT--TGATTT 1732 chr6qtel1M 291602 CCTAATATTGAAGCAGCCCTGCATTCCTGGTATAAATCCTACTTGATCAT 291651 i v i i v i i v i i i C L1M5_orf2#LIN 1731 TCGAATGTTAAACCAACCTTGCATTCCTGGGATAAACCCCACTTGGTCAT 1682 chr6qtel1M 291652 AGTGGATTATCCTGGGGATAATTTTCTGTAGTCTTTTTGCTAATATCTTA 291701 ii v vvvv vv v v v vv i i C L1M5_orf2#LIN 1681 GATGTATTATCCTTTTTATATATTGCTGGATTCGATTTGCTAATATTTTG 1632 chr6qtel1M 291702 TTTAAGATTTTAGCATCAACTAATATCTTATTTAAGATTTTAGCATCAAT 291751 ? i v --- --------------------------- C L1M5_orf2#LIN 1631 TTNAGGATTTTTGCAT---CT---------------------------AT 1612 chr6qtel1M 291752 ATTCATTAGGGAGATTGGTCTATAATTTGCTTTCTCTGT--TTTCAACCT 291799 i v v i v iii -- v --ii C L1M5_orf2#LIN 1611 GTTCATGAGGGATATTGGTCTGTAATTTTCTTTTCTTGTAATGTC--TTT 1564 chr6qtel1M 291800 ACCTGCTTTAGGTATCAGTACCATGTCTGTGTCATAAAAGGAATTTGATA 291849 ii ? v v vii? iiv iv v i v iv C L1M5_orf2#LIN 1563 GTCNGGTTTTGGTATCAGGGTNATGCTGGCCTCATAAAATGAGTTGGGAA 1514 chr6qtel1M 291850 GAACTCCTTCATTCTCTATTTTATCGAATAATTTATATAGCATTGG-GGC 291898 vii i v i v v v i i i iv -ivi C L1M5_orf2#LIN 1513 GTGTTCCCTCTTTTTCTATTTTCTGGAAGAGTTTGTGTAAGATTGGTATT 1464 chr6qtel1M 291899 AATTGTTCTTTAAATGTTTGGTAGAATTCACATGTAAATCTATCTGGTCT 291948 v v i vv i v i v i C L1M5_orf2#LIN 1463 ATTTCTTCCTTAAATGTTTGGTAGAATTCACCAGTGAAGCCATCTGGGCC 1414 chr6qtel1M 291949 TAGGGATTTTTTCTTAGGGAATTGATTAATACTTTGTTCTATTTCTTTTT 291998 i i v i iv i i iv vv vvivvi v vv C L1M5_orf2#LIN 1413 TGGAGTTTTCTTTGTGGGAAGGTTTTTAATTACAAATTCAATTTCTTTAA 1364 chr6qtel1M 291999 CTGAAATGGGACTATTCAAGCAATTTACTTCCTCCTCTGTTAGTCTGGGA 292048 iv v i i iiivv i i i i v? i i v v C L1M5_orf2#LIN 1363 TAGATATAGGGCTATTCAGATTTTCTATTTCTTCTTGNGTCAGTTTTGGT 1314 chr6qtel1M 292049 AGTCTATATTTTTGGAGGTAGTCATCCATTTCACTTAGGTTATCAAATTT 292098 i?i i i vi v v ii ii i ? C L1M5_orf2#LIN 1313 AANTTGTGTTTTTCAAGGAATTTGTCCATTTCATCTAAGTTNTCAAATTT 1264 chr6qtel1M 292099 ATTGGCATAAAGTTGAGCAAAATAACTCCTTATTATTTCTCTAATTTCCT 292148 vv v viii iii i v iv C L1M5_orf2#LIN 1263 ATTGGCATAAAGTTGTTCATAATATTCTCTTATTATCCTTTTAATGTCTG 1214 chr6qtel1M 292149 CTTCATTGGTGGAAAGTTCTCCCTTTTCATTTTTAAGACTACTAATTTCA 292198 ivvv iv i vi vv i ii i v i iv vv C L1M5_orf2#LIN 1213 TAGGATCTGTAGTGATGTCTCCTTTTTCATTCCTGATATTGGTAATTTGT 1164 chr6qtel1M 292199 TTTTCCTCCCTCCTTTTC-TAATCAGATTTACCAAAGA--CATCTATTTT 292245 v i i i ii - i vi ?i i i i--i v C L1M5_orf2#LIN 1163 GTCTTCTCTCTTTTTTTCTTGATCAGTCTNGCTAGAGGTTTATCAATTTT 1114 chr6qtel1M 292246 ATTGGT-TTTTCATACAACCAACTCTTACTTTTATTTATTAGTTCAATAG 292294 i - v v i i ivi ii v vvi v v C L1M5_orf2#LIN 1113 ATTGATCTTTTCAAAGAACCAGCTTTTGGCTTCGTTGATTTTCTCTATTG 1064 chr6qtel1M 292295 TTTTTTTACTTTCAATATTATTACTTTCTTCTTTTAATTTTA-AATTTCA 292343 ? ? ii v v i iv v i vi -v v C L1M5_orf2#LIN 1063 TNTNTTTGTTTTCTATTTCATTGATTTCTGCTCTTATCTTTATTATTTCC 1014 chr6qtel1M 292344 AATTTAATATTTGATTGGGGGGTTTTAATTTGGTC----TTTTCTAGCGT 292389 vvii vv i ?v v --- v ---- v C L1M5_orf2#LIN 1013 TTCCTTCTACTTNCTTTGGG---TTTAATTTGCTCTTCTTTTTCTAGCTT 967 chr6qtel1M 292390 TTTTAGTTGCAAGCCTAATTCATTGATCTTCACTTTCTCTATTTTATTCA 292439 i v v v i iv i v vii i vi vi v C L1M5_orf2#LIN 966 CTTAAGGTGGAAGCTTAGATCATTGATTTTAAGCCTTTCTTCTTTTCTAA 917 chr6qtel1M 292440 AGTAAGCCTCTAAGGATATAAAATTTCCTCTTATTAGTGCTTTGGCCACA 292489 vi ? v i ? v v i v vi v i ii C L1M5_orf2#LIN 916 TATANGCATTTAANGCTATAAATTTCCCTCTAAGCACTGCTTTAGCTGCA 867 chr6qtel1M 292490 TTCCACAAATTTTGGTATGGTGTCTCATCATTGTCATTATCTTGAGTGAA 292539 i i v v iv ? vvv v iviv C L1M5_orf2#LIN 866 TCCCACAAATTTTGATATGTTGTATTTTCATTNTCATTCAGTTCAAAATA 817 chr6qtel1M 292540 ATTATTAATTGTTTCTATAATTTGCTGTTTCACCCATTCATTCTTTA-AG 292588 v vi vii?i i i vi v v vvi v - i C L1M5_orf2#LIN 816 TTTTCTAATTTCCNTTGTGATTTCTTCTTTGACCCATGGGTTATTTAGAA 767 chr6qtel1M 292589 ATGAGATTATTTAGTTTGCAATTACTTTTTGATCTATTTACCTCTAACTT 292638 i v - i i v v i vvv i - i v? v -- C L1M5_orf2#LIN 766 GTGTG-TTGTTTAATTTCCAAATATTTGGGGATTT-TCTAGNTAT--CTT 721 chr6qtel1M 292639 TTTGTTGAATGTAGTTTCTA--TTGA----ATGGTGATCTGAAAAGAAAG 292682 -- - ii -- i ---- v i v i v v v C L1M5_orf2#LIN 720 TTTGTT--AT-TGATTTCTAATTTAATTCCATTGTGGTCAGAGAACATAC 674 chr6qtel1M 292683 CATTTACTATTGCTGTCTTCCTGCATTTAATTTGGAGGT-TTTTATGTCC 292731 iv v iv v vi i ii?iv - vi vv - v C L1M5_orf2#LIN 673 TCTGTATGATTTCAATCCTTTNAAATTT-ATTGAGACTTGTTTTATGGCC 625 chr6qtel1M 292732 TAATATATGGTCAATTTTTGAATAGGTTCCATGAAC---TGCTAAGAAAA 292778 i i? v i v v v v vi --- vv vi C L1M5_orf2#LIN 624 CAGNATATGGTCTATCTTGGTAAATGTTCCATGTGCACTTGAAAAGAATG 575 chr6qtel1M 292779 TATATTCCTTTCTTTCTCCCTTCAGTTTTCTCCAGAGATCTATCATACCT 292828 i ivi?v vi vvv v? v vi i vi v i vii - C L1M5_orf2#LIN 574 TGTATTCTGCNGTTGTTGGGTGNAGTGTTCTATAAATGTCAATTAGGTC- 526 chr6qtel1M 292829 AATTTTTCTAATAGT-CTATTTACCTCTTTGAT-TTCTTTCTTATTTGTT 292876 v vvi i -i i i vv iv - i v v -- C L1M5_orf2#LIN 525 AAGTTGGTTGATAGTGTTGTTCAAATCTTCTATATCCTTACTGATT--TT 478 chr6qtel1M 292877 TTGTG-GTTTGATTTGTCTAATT-CTGAGAGTGCAATATTGAGATCTCCC 292924 v-ii v i i - - v v?i i i i ? C L1M5_orf2#LIN 477 TTGTCTACTTGTTCTATC-AATTACTGAGAGAGGNGTGTTAAAATCTCCN 429 chr6qtel1M 292925 ACT---ATTACAG-TTTAGCTGTCTCTTCTTGCAACTC--TTAACTTCTC 292968 --- iii - iv i i i vi ii -- i ii i v C L1M5_orf2#LIN 428 ACTATAATTGTGGATTTGTCTATTTCTCCTTTTAGTTCTGTCAGTTTTTG 379 chr6qtel1M 292969 CTTTAGGAAGTTAGATGTTATACCACTTGATGCATATATGTTTAGTATTG 293018 i v v v v v i v iii i v i i ii v C L1M5_orf2#LIN 378 CTTCATGTATTTTGAAGCTCTGTTATTAGGTGCATACACATTTAGGATTG 329 chr6qtel1M 293019 ACATTACTTTGTTGTCTATG---CTACCC-TTTAGCAAGATAGAGTTTCT 293064 vi vv i- --- ---iv - v vv ii i v i C L1M5_orf2#LIN 328 TTATGTCTTC-TTG---ATGAATTGACCCTTTTATCATTATGAAATGTCC 283 chr6qtel1M 293065 TACCTTATCTCTTTTGATTAGGTCAATTTTTGCTTT------TGCTTGAT 293108 iv i vv i ------ v i i ------ i vi C L1M5_orf2#LIN 282 CTCTTTATCTCTGGTAAT------ATTTCTTGCCTTGAAGTCTACTTTGT 239 chr6qtel1M 293109 ATGAGATAAGGATGGCTACCCCTGCTTTTTTTTACTT--CACCTGAAGGA 293156 v v v iv i i ? v i i? --iiii v v i C L1M5_orf2#LIN 238 CTGATATTAATATAGCCACNCCAGCTTTCTTTTGNTTAGTGTTTGCATGG 189 chr6qtel1M 293157 TATAGATTCTGCTCCAGCC-TTTACCTTTACTCTGTATATATCTCCTTGC 293205 vv i -- v - i i vi ? v i i iiv ii C L1M5_orf2#LIN 188 TATATCTTTT--TCCATCCTTTTACTTTCAACCTNTCTGTGTCTTTATAT 141 chr6qtel1M 293206 TTTAAATGTGTTGCCTGTAAACAACATATTGTAGAGTTCTGACTTTGGAT 293255 v i i iv i i i v v i ii vi vv C L1M5_orf2#LIN 140 TTAAAGTGCGTCTCTTGTAGACAGCATATAGTTGGGTCTTGTTTTTTTAT 91 chr6qtel1M 293256 CCAGTCTGCTA---TCTGCTTT 293274 vi --- i C L1M5_orf2#LIN 90 CCAGTCTGACAATCTCTGCCTT 69 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 41.47 CpG sites = 521, Kimura (unadjusted) = 41.99 Transitions / transversions = 1.16 (521/449) Gap_init rate = 0.05 (150 / 3224), avg. gap size = 1.33 (200 / 150) 19 21.94 0.00 5.26 chr6qtel1M 293382 293441 (706559) (AAAAGG)n#Simple_repeat 1 57 (0) m_b305s252i26 12775 chr6qtel1M 293382 AAGAGGGAGAGGAAAAGGAAAAGGAAAAGAGTAATAAGGGAAGGGTACAA 293431 i i i - - - i i v v i (AAAAGG)n#Sim 1 AAAAGGAAAAGGAAAAGGAAAAGGAAAAG-G-AA-AAGGAAAAGGAAAAG 47 chr6qtel1M 293432 GAAAGGGGAA 293441 i i (AAAAGG)n#Sim 48 GAAAAGGAAA 57 Matrix = Unknown Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.05 (3 / 59), avg. gap size = 1.00 (3 / 3) 228 16.34 6.67 11.63 chr6qtel1M 293563 293652 (706348) L1MEj_5end#LINE/L1 2005 2090 (70) m_b305s551i2 12776 chr6qtel1M 293563 AATAAGATGGCAGGAA----ATAAAG-A-ATTAGTCATTTTAACCATAAA 293606 i v ---- v - - i i --- vv L1MEj_5end#LI 2005 AGTAAGATGGAAGGAATAAAATCAAGTATATCAGTCGTT---ACACTAAA 2051 chr6qtel1M 293607 TGTGAATGGGATGAACTCTCCCATAAAGTGTGGGAAAACAGGGACT 293652 iv i v ------- i i L1MEj_5end#LI 2052 TGTGAATGGACTGAATTCTCCCATTAA-------AAGACAGAGACT 2090 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 16.97 CpG sites = 7, Kimura (unadjusted) = 18.45 Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.15 (13 / 89), avg. gap size = 1.23 (16 / 13) 874 31.84 1.04 1.04 chr6qtel1M 293635 294018 (705982) L1ME4c_3end#LINE/L1 256 639 (191) m_b305s551i3 12777 chr6qtel1M 293635 TGTGGGAAAACAGGGACTTTAATACATTGTTGGTGGAATTGTGAATACAT 293684 i vi v v ?i v i v ? i vvi L1ME4c_3end#L 256 TGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGT 305 chr6qtel1M 293685 CCAACCATTCTGGAGAGCAATTTGGAACTATGC-TCAAAAGTTATCAAAC 293733 v v i i v v i i- i ii v v L1ME4c_3end#L 306 ACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAAAA 355 chr6qtel1M 293734 CGTGCATAGCCTTTGATCCAGCAGTGTTTCTACTAGGCTTATACCCCAAA 293783 i v v i i i viiv v i vv v i i i L1ME4c_3end#L 356 TGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAG 405 chr6qtel1M 293784 GAGATA---CTAAAGAACGAAAAGGGACCTCTTTGTGCCAAAATGTTTGT 293830 i --- v v i --- v v ii v i ii L1ME4c_3end#L 406 GAAATAATTCAAAAGAAGGAAAAAG---CTATATGCACGAAGATGTTCAT 452 chr6qtel1M 293831 GGCAGCCCTGTTTGTAGTGGCTAGAAGCTGGAAAATGAATGGATGCCCAT 293880 v vi i i i i v i ii vvivv ii i v L1ME4c_3end#L 453 TGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAA 502 chr6qtel1M 293881 CAATTGGAGAATGGTTGGGTAAATTGTGGTATATAAATGTTATGCAATAT 293930 v i ii i i v? iviv v L1ME4c_3end#L 503 CAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATAT 552 chr6qtel1M 293931 TATTTTTCTGTAAGAAATGACCAGTAGGATGAATACAGAGAGGCTTGGAG 293980 vivv ii v i iv v v v v iiv vii v i L1ME4c_3end#L 553 TATGCAGCCATTAAAAATGATAATTATGAAGACTATGTAGCAACATGGAA 602 chr6qtel1M 293981 AGACTTACATGAAGTAATGCTACGTGAAATGAACAGAA 294018 ivv -i vi i v vi i L1ME4c_3end#L 603 AATGTT-TATGATATAATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 41.42 CpG sites = 65, Kimura (unadjusted) = 42.81 Transitions / transversions = 1.16 (65/56) Gap_init rate = 0.02 (6 / 383), avg. gap size = 1.33 (8 / 6) 14 8.85 0.00 0.00 chr6qtel1M 294331 294354 (705646) (GGGA)n#Simple_repeat 1 24 (0) m_b305s252i27 12778 chr6qtel1M 294331 GGGAGGGGTGGAGGGAGGGAGGGA 294354 iv (GGGA)n#Simpl 1 GGGAGGGAGGGAGGGAGGGAGGGA 24 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 16 14.46 0.00 0.00 chr6qtel1M 294480 294510 (705490) (TATC)n#Simple_repeat 1 31 (0) m_b305s252i28 12779 chr6qtel1M 294480 TATCGATTCATCTATTTATCTATCTATCTAT 294510 v ii i (TATC)n#Simpl 1 TATCTATCTATCTATCTATCTATCTATCTAT 31 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 227 29.18 0.00 1.39 chr6qtel1M 294531 294603 (705397) DNM1r#Unknown 2474 2545 (2117) m_b305s502i0 12780 chr6qtel1M 294531 CTATATATATGCATGTATATGTATATTTATATGTGATATATGTGTGTGTG 294580 i ii i ii i i i v - i i i DNM1r#Unknown 2474 CCACGTGTATGTGTGTATATATGTGTGTATATGTG-TGTATGTGTGTATA 2522 chr6qtel1M 294581 TTTGCACATATATTCACATGCAT 294603 v iii v ii ?i DNM1r#Unknown 2523 TATGTGTATATATACGTATNTAT 2545 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.44 CpG sites = 18, Kimura (unadjusted) = 42.05 Transitions / transversions = 6.00 (18/3) Gap_init rate = 0.01 (1 / 72), avg. gap size = 1.00 (1 / 1) 246 25.38 0.00 1.49 chr6qtel1M 294542 294609 (705391) DNM1r#Unknown 2477 2543 (2119) m_b305s502i1 12780 chr6qtel1M 294542 CATGTATATGTATATTTATATGTGATATATGTGTGTGTGTTTGCACATAT 294591 i i i v i - i v i i DNM1r#Unknown 2477 CGTGTATGTGTGTATATATGTGTG-TATATGTGTGTATGTGTGTATATAT 2525 chr6qtel1M 294592 ATTCACATGCATGCATAT 294609 i vi i ii i i ? DNM1r#Unknown 2526 GTGTATATATACGTATNT 2543 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 29.20 CpG sites = 14, Kimura (unadjusted) = 34.10 Transitions / transversions = 4.67 (14/3) Gap_init rate = 0.01 (1 / 67), avg. gap size = 1.00 (1 / 1) 14 15.99 4.35 4.35 chr6qtel1M 294881 294926 (705074) (ATTTAA)n#Simple_repeat 1 46 (0) m_b305s252i29 12781 chr6qtel1M 294881 ATTTAAATTGTAAATAATAAATATAAAGTGAAATGT--ATTTAACTTT 294926 - -v v v v v -- v (ATTTAA)n#Sim 1 ATTTAAATT-TAAAT-TTAAATTTAAATTTAAATTTAAATTTAAATTT 46 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.07 (3 / 45), avg. gap size = 1.33 (4 / 3) 12 4.71 4.55 0.00 chr6qtel1M 295097 295118 (704882) (ATTT)n#Simple_repeat 1 23 (0) m_b305s252i30 12782 chr6qtel1M 295097 ATTTATTTATTAATTT-TTTATT 295118 v - (ATTT)n#Simpl 1 ATTTATTTATTTATTTATTTATT 23 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.05 (1 / 21), avg. gap size = 1.00 (1 / 1) 230 29.49 0.00 0.00 chr6qtel1M 297214 297291 (702709) C L1ME3G_3end#LINE/L1 (376) 548 471 m_b306s551i0 12783 chr6qtel1M 297214 ATAATATTCCATAACATTCGTGTGTCATAACTTATTCATCCATTTCCCAA 297263 i ii vvi i ii i i v i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr6qtel1M 297264 TAGATCAACATCTACTCAGTTTCCAGTT 297291 v vi i vviv i C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATT 471 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 38.72 CpG sites = 14, Kimura (unadjusted) = 38.72 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.00 (0 / 77), avg. gap size = 0.0 (0 / 0) 230 29.49 0.00 0.00 chr6qtel1M 297608 297685 (702315) L1ME3G_3end#LINE/L1 471 548 (376) m_b306s551i1 12784 chr6qtel1M 297608 AACTGGAAACTGAGTAGATGTTGATCTATTGGGAAATGGATGAATAAGTT 297657 i vivv i iv v v i v i i L1ME3G_3end#L 471 AATTGGAAACAACCTAAATGTCCATCAATAGGGGAATGGTTAAATAAATT 520 chr6qtel1M 297658 ATGACACACGAATGTTATGGAATATTAT 297685 ii i ivv ii i L1ME3G_3end#L 521 ATGGTATATCCATACTATGGAATACTAT 548 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 38.72 CpG sites = 14, Kimura (unadjusted) = 38.72 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.00 (0 / 77), avg. gap size = 0.0 (0 / 0) 16 14.88 2.56 2.56 chr6qtel1M 299781 299819 (700181) (AATA)n#Simple_repeat 1 39 (0) m_b306s252i0 12785 chr6qtel1M 299781 AATAAA-AAGTTATTATAATAAAAAAATTAATAAATAAAT 299819 - i v v - v v (AATA)n#Simpl 1 AATAAATAAATAAATA-AATAAATAAATAAATAAATAAAT 39 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2) 12 11.68 10.81 0.00 chr6qtel1M 300001 300037 (699963) (TACAATT)n#Simple_repeat 1 41 (0) m_b306s252i1 12786 chr6qtel1M 300001 TAC-ATTT-CACTTTA-TATTTATTATTTACAATTTA-AAT 300037 - - v -v iv - (TACAATT)n#Si 1 TACAATTTACAATTTACAATTTACAATTTACAATTTACAAT 41 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.11 (4 / 36), avg. gap size = 1.00 (4 / 4) 246 25.38 0.00 1.49 chr6qtel1M 300311 300378 (699622) C DNM1r#Unknown (2119) 2543 2477 m_b306s502i0 12787 chr6qtel1M 300311 ATATGCATGCATGTGAATATATGTGCAAACACACACACATATATCACATA 300360 ? i i ii i iv i i i v i - i C DNM1r#Unknown 2543 ANATACGTATATATACACATATATACACACATACACACATATA-CACACA 2495 chr6qtel1M 300361 TAAATATACATATACATG 300378 v i i i C DNM1r#Unknown 2494 TATATACACACATACACG 2477 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 29.20 CpG sites = 14, Kimura (unadjusted) = 34.10 Transitions / transversions = 4.67 (14/3) Gap_init rate = 0.01 (1 / 67), avg. gap size = 1.00 (1 / 1) 227 29.18 0.00 1.39 chr6qtel1M 300317 300389 (699611) C DNM1r#Unknown (2117) 2545 2474 m_b306s502i1 12787 chr6qtel1M 300317 ATGCATGTGAATATATGTGCAAACACACACACATATATCACATATAAATA 300366 i? ii v iii v i i i - v i C DNM1r#Unknown 2545 ATANATACGTATATATACACATATATACACACATACA-CACATATACACA 2497 chr6qtel1M 300367 TACATATACATGCATATATATAG 300389 i i ii i ii i C DNM1r#Unknown 2496 CATATATACACACATACACGTGG 2474 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.44 CpG sites = 18, Kimura (unadjusted) = 42.05 Transitions / transversions = 6.00 (18/3) Gap_init rate = 0.01 (1 / 72), avg. gap size = 1.00 (1 / 1) 16 14.46 0.00 0.00 chr6qtel1M 300410 300440 (699560) (ATAG)n#Simple_repeat 1 31 (0) m_b306s252i2 12788 chr6qtel1M 300410 ATAGATAGATAGATAAATAGATGAATCGATA 300440 i ii v (ATAG)n#Simpl 1 ATAGATAGATAGATAGATAGATAGATAGATA 31 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 13 4.76 0.00 4.35 chr6qtel1M 300571 300594 (699406) (CCCT)n#Simple_repeat 1 23 (0) m_b306s252i3 12789 chr6qtel1M 300571 CCCTCCCTCCCTCCACCCCCTCCC 300594 - i (CCCT)n#Simpl 1 CCCTCCCTCCCTCC-CTCCCTCCC 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 847 32.55 0.78 1.04 chr6qtel1M 300907 301291 (698709) C L1ME4c_3end#LINE/L1 (191) 639 256 m_b306s551i2 12790 chr6qtel1M 300907 TTCTGTTCATTTCACGTAGCATTACTTCATGTAAGTCTCTCCAAGCCTCT 300956 i iv v i iv i- vvi i v iiv C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATA-AACATTTTCCATGTTGCT 591 chr6qtel1M 300957 CTGTATTCATCCTACTGGTCATTTCTTACAGAAAAATAATATTGCATAAC 301006 vii v v v v vi i v ii vviv v viv C L1ME4c_3end#L 590 ACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCGA 541 chr6qtel1M 301007 ATTTATATACCACAATTTACCCAACCATTCTCCAATTGATGGGCATCCAT 301056 i ?v i i ii i v v i ii v C L1ME4c_3end#L 540 GTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAG 491 chr6qtel1M 301057 TCATTTTCCAGCTTCTAGCCACTACAAACAGGGCTGCCACAAACATTTTG 301106 vivv ii i v i i i i iv v ii i v C L1ME4c_3end#L 490 GTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTC 441 chr6qtel1M 301107 GCACAAAGAGGTCCCTTTTCGTTCTTTAG---TATCTCTTTGGGGTATAA 301153 ii v v --- i v v --- i i i i v v C L1ME4c_3end#L 440 GTGCATATAG---CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAAT 394 chr6qtel1M 301154 GCCTAGTAGAAACACTGCTGGATCAAAGGCTATGCACGGTTTGATAACTT 301203 v i v viiv i i i v v iv v ii i C L1ME4c_3end#L 393 TCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTC 344 chr6qtel1M 301204 TTTGAGCATAGTTCCAAATTGCTCTCCAGAATGGTTGGATGTATTCACAA 301253 vivi i v v i i v v ivv i ? C L1ME4c_3end#L 343 TTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACAN 294 chr6qtel1M 301254 TTCCACCAACAATGTATTAAAGTCCCTGTTTTCCCACA 301291 v i v i? v v iv i C L1ME4c_3end#L 293 TGCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCA 256 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 42.67 CpG sites = 66, Kimura (unadjusted) = 44.09 Transitions / transversions = 1.14 (66/58) Gap_init rate = 0.01 (5 / 384), avg. gap size = 1.40 (7 / 5) 228 16.34 6.67 11.63 chr6qtel1M 301274 301363 (698637) C L1MEj_5end#LINE/L1 (70) 2090 2005 m_b306s551i3 12791 chr6qtel1M 301274 AGTCCCTGTTTTCCCACACTTTATGGGAGAGTTCATCCCATTCACATTTA 301323 i i ------- v i vi C L1MEj_5end#LI 2090 AGTCTCTGTCTT-------TTAATGGGAGAATTCAGTCCATTCACATTTA 2048 chr6qtel1M 301324 TGGTTAAAATGACTAAT-T-CTTTAT----TTCCTGCCATCTTATT 301363 vv --- i i - - v ---- v i C L1MEj_5end#LI 2047 GTGT---AACGACTGATATACTTGATTTTATTCCTTCCATCTTACT 2005 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 16.97 CpG sites = 7, Kimura (unadjusted) = 18.45 Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.15 (13 / 89), avg. gap size = 1.23 (16 / 13) 4672 31.37 2.63 3.17 chr6qtel1M 301660 304895 (695105) L1M5_orf2#LINE/L1 69 3287 (7) m_b306s551i4 12792 chr6qtel1M 301660 AAAGCAGA---TAGCAGACTGGATCCAAAGTCAGAACTCTACAATATGTT 301706 i --- iv vv iv ii i v v i L1M5_orf2#LIN 69 AAGGCAGAGATTGTCAGACTGGATAAAAAAACAAGACCCAACTATATGCT 118 chr6qtel1M 301707 GTTTACAGGCAACACATTTAAAGCAAGGAGATATATACAGAGTAAAGGTA 301756 i i vi i i v ii vii i i v ? iv i i L1M5_orf2#LIN 119 GTCTACAAGAGACGCACTTTAAATATAAAGACACAGANAGGTTGAAAGTA 168 chr6qtel1M 301757 AA-GGCTGGAGCAGAATCTATATCCTTCAGGTG--AAGTAAAAAAAAGCA 301803 - v -- i vv i v v iiii-- ?i i v L1M5_orf2#LIN 169 AAAGGATGGA--AAAAGATATACCATGCAAACACTAANCAAAAGAAAGCT 216 chr6qtel1M 301804 GGGGTAGCCATCCTTATCTCATATCAAGCA------AAAGCAAAAATTGA 301847 ? i i vi v v v iv i ------ i i v -- L1M5_orf2#LIN 217 GGNGTGGCTATATTAATATCAGACAAAGTAGACTTCAAGGCAAGAAAT-- 264 chr6qtel1M 301848 CCTAATCAAAAGAGATAAGGTAAGAAACTCTATCTTGCTAAA-GGGTAG- 301895 ---- i vv i vii v i ii vv v - vi- L1M5_orf2#LIN 265 ----ATTACCAGAGATAAAGAGGGACATTTCATAATGATAAAAGGGTCAA 310 chr6qtel1M 301896 --CATAGACAACAAAGTAATGTCAATACTAAACATATATGCATCAAGTGG 301943 -- --- -i vv iv v ii i i v i ii L1M5_orf2#LIN 311 TTCAT---CAA-GAAGACATAACAATCCTAAATGTGTATGCACCTAATAA 356 chr6qtel1M 301944 TATAACATCTAACTTCCTAAAGGAGAAGTTAA--GAGTTGCAAGAAGAGA 301991 i v i v v v v v i v i ii i -- ii iv i i L1M5_orf2#LIN 357 CAGAGCTTCAAAATACATGAAGCAAAAACTGACAGAACTAAAAGGAGAAA 406 chr6qtel1M 301992 CAGCTAAA-CTGTAAT---AGTGGGAGATCTCAATATTGCACTCTCAG-A 302036 i vi - iii --- ? i i i i?v v - L1M5_orf2#LIN 407 TAGACAAATCCACAATTATAGTNGGAGATTTTAACACNCCTCTCTCAGTA 456 chr6qtel1M 302037 ATTAGACAAATCAAAC-CACAAAACAAATAAGAAAGAA-ATCAAAGAGGT 302084 - i i v ii-v -- v v i - vi vv L1M5_orf2#LIN 457 ATT-GATAGAACAAGTAGACAAAA--AATCAGTAAGGATATAGAAGATTT 503 chr6qtel1M 302085 AAATAG-ACTATTAGAAAAATTAGGTATGATAGATCTCTGGAGAAAACTG 302133 i i i- i ivv v - iiv i v iv i iv v ? L1M5_orf2#LIN 504 GAACAACACTATCAACCAACTT-GACCTAATTGACATTTATAGAACACTN 552 chr6qtel1M 302134 AAGGGAGAAAGAAAGGAATATATTTTCTTAGCA---GTTCATGGAACCTA 302180 v vvv iv v?ivi i iv vv --- iv v v L1M5_orf2#LIN 553 CACCCAACAACNGCAGAATACACATTCTTTTCAAGTGCACATGGAACATT 602 chr6qtel1M 302181 TTCAAAAATTGACCATATATTAGGACATAAAA-ACCTCCAAATTAAATGC 302229 v v i v ?i i v - vv iv - vi L1M5_orf2#LIN 603 TACCAAGATAGACCATATNCTGGGCCATAAAACAAGTCTCAAT-AAATTT 651 chr6qtel1M 302230 AGGAAGACAGCAATAGTAAATGCTTTCTTTTCAGATCACCAT----TCAA 302275 ?ii i iv v vi v viv v v i v i v ---- i L1M5_orf2#LIN 652 NAAAGGATTGAAATCATACAGAGTATGTTCTCTGACCACAATGGAATTAA 701 chr6qtel1M 302276 --TAGAAACTACATTCAACAAAAAGTTAGAGGTAAATAGATCAAAAAGTA 302323 -- ii - -- -- v ?v i - i vvv i L1M5_orf2#LIN 702 ATTAGAAATCA-AT--AACAAAAAG--ATANCTAGA-AAATCCCCAAATA 745 chr6qtel1M 302324 ATTGCAAACTAAATAATCTCATCT-TAAAGAATGAATGGGTGAAACAGCA 302372 v v i i - v ii - v ivv v v iv L1M5_orf2#LIN 746 TTTGGAAATTAAACAA-CACACTTCTAAATAACCCATGGGTCAAAGAAGA 794 chr6qtel1M 302373 AATTATAGAAACAATTAATAATTTCACTCAAGATAATGACAATGATGAGA 302422 i i i?iiv iv v vivi v vvv ? vi v L1M5_orf2#LIN 795 AATCACAANGGAAATTAGAAAATATTTTGAACTGAATGANAATGAAAATA 844 chr6qtel1M 302423 CACCATACCAAAATTTGTGGAATGTGGCCAAAGCACTAATAAGAGGAAAT 302472 v i i ii i v iv v i v L1M5_orf2#LIN 845 CAACATATCAAAATTTGTGGGATGCAGCTAAAGCAGTGCTTAGAGGGAAA 894 chr6qtel1M 302473 TTTATATCCTTAGAGGCTTACTTGAATAAAATAGAGAAAGTGAAGATCAA 302522 v ? i v ? iv v iv iv i iiv v i L1M5_orf2#LIN 895 TTTATAGCNTTAAATGCNTATATTAGAAAAGAAGAAAGGCTTAAAATCAA 944 chr6qtel1M 302523 TGAATTAGGCTTGCAACTAAAAACGCTAGAAAAAGA---CCAAATTAAAA 302569 vi i v v v i v ---v - L1M5_orf2#LIN 945 TGATCTAAGCTTCCACCTTAAGAAGCTAGAAAAAGAAGAGCAAATTAAA- 993 chr6qtel1M 302570 ACCCCCAATCAAATATTAAATTTGAAATTCTAAAATTAAAAGAAGAAAGT 302619 -- v v? i vv iivvv vv iv i v vi L1M5_orf2#LIN 994 --CCCAAAGNAAGTAGAAGGAAGGAAATAATAAAGATAAGAGCAGAAATC 1041 chr6qtel1M 302620 AATAATATTGAAAGTAAAAAAAAACTATTGAACTAATAAATAAAAGTAAG 302669 i v v ii ? ? v v vv -- v ii ivi i L1M5_orf2#LIN 1042 AATGAAATAGAAAACAAANANACAATAGAGAA--AATCAACGAAGCCAAA 1089 chr6qtel1M 302670 AGTTGGTTGTATGAAAAAACCAATAAAATAGATG--TCTTTGGTAAATCT 302717 i v v i i v i--i i i i? iv L1M5_orf2#LIN 1090 AGCTGGTTCTTTGAAAAGATCAATAAAATTGATAAACCTCTAGCNAGACT 1139 chr6qtel1M 302718 GATTAGAAAAAGGAGGGAGGAAAATGAAATTAGTAGTCTTAAAAATGAAA 302767 i ii ii i i i vvv vi i v i ii L1M5_orf2#LIN 1140 GATCAAGAAAAAAAGAGAGAAGACACAAATTACCAATATCAGGAATGAAA 1189 chr6qtel1M 302768 AGGGAGAACTTTCCACCAATGAAGAGGAAATTAGAGAAATAATAAGGAGT 302817 i vv iv i vi vvvivi v i iii iiiv L1M5_orf2#LIN 1190 AAGGAGACATCACTACAGATCCTACAGACATTAAAAGGATAATAAGAGAA 1239 chr6qtel1M 302818 TATTTTGCTCAACTTTATGCCAATAAATTTGATAACCTAAGTGAAATGGA 302867 v vv ? i ii L1M5_orf2#LIN 1240 TATTATGAACAACTTTATGCCAATAAATTTGANAACTTAGATGAAATGGA 1289 chr6qtel1M 302868 TGACTACCTCCAAAAATATAGACTTCCCAGACTAACAGAGGAGGAAGTAA 302917 ii v v iv i i i?i v v i i ?v i i i i L1M5_orf2#LIN 1290 CAAATTCCTTGAAAAACACAANTTACCAAAACTGACNCAAGAAGAAATAG 1339 chr6qtel1M 302918 ATTGCTTGAATAGTCCCATTTCAGAAAAAGAAATAGAACAAAGTATTAAT 302967 vviii i i v vivv v ivvivv v L1M5_orf2#LIN 1340 AAAATCTGAATAGCCCTATATCTATTAAAGAAATTGAATTTGTAATTAAA 1389 chr6qtel1M 302968 CAATTCCCTAAGAAAAAATCCCTAAGACCAGATAGATTTACATGTGAATT 303017 v vi i i vi i v i i i v i v i vv L1M5_orf2#LIN 1390 AACCTTCCCACAAAGAAAACTCCAGGCCCAGATGGCTTCACTGGTGAATT 1439 chr6qtel1M 303018 CTACCAAACATTTAAAGAACAATTGCC-CCAATGCTATATAAATTATTCG 303066 i v v ivi- vi i i i v v L1M5_orf2#LIN 1440 CTACCAAACATTTAAGGAAGAAATAATACCAATCTTACACAAACTCTTCC 1489 chr6qtel1M 303067 ATAAAATAGAGAATGAAGGAGTTCTATCAAATTCCTTTTATGACACAGAC 303116 v i v i iiv vi v i v vi vii L1M5_orf2#LIN 1490 AGAAAATAGAAAAAGAGGGAACACTTCCCAACTCATTTTATGAGGCCAGC 1539 chr6qtel1M 303117 ATGGTACTGATACCTAAAGCAGGTAGGTTGAAA--ACAGAGAAAGCAAAT 303164 ?iiv v v ? ii ii-- v -- iii v L1M5_orf2#LIN 1540 ATNACCCTGATACCAAAACCNGACAAA--GACATTACAAGAAAAGAAAAT 1587 chr6qtel1M 303165 TATAGACCAATCTCCCTAATGAATATTGATGCTAAAATCTTAAATAAGAT 303214 i v v i ------------------------ L1M5_orf2#LIN 1588 TACAGACCAATATCCCTCATGAACAT------------------------ 1613 chr6qtel1M 303215 ATTAGTTGATGCTAAAATCTTAAATAAGATATTAGCAAAAAGACTACAGA 303264 --- --- v i ? i i vv v v v L1M5_orf2#LIN 1614 ---AG---ATGCAAAAATCCTNAACAAAATATTAGCAAATCGAATCCAGC 1657 chr6qtel1M 303265 AAATTATCCCCAGGATAATCCACTATGATCAAGTAGGATTTATACCAGGA 303314 vv vvvv v ii i i i v L1M5_orf2#LIN 1658 AATATATAAAAAGGATAATACATCATGACCAAGTGGGGTTTATCCCAGGA 1707 chr6qtel1M 303315 ATGCAGGGCTGCTTCAATATTAGGAAA-CAGTATCAGTATAATTGACCAT 303363 i i v i i v i - -- i i v L1M5_orf2#LIN 1708 ATGCAAGGTTGGTTTAACATTCGAAAATCA--ATCAATGTAATTCACCAT 1755 chr6qtel1M 303364 ATTAACA-ACCAAATTAACAAAAACCATATGAATATCTCAATAGATGCAA 303412 - vi -vi v i vi i L1M5_orf2#LIN 1756 ATTAACAGAATAAA-GGAGAAAAATCATATGATCATCTCAATAGATGCAG 1804 chr6qtel1M 303413 AAAAAGCATTTGATAAAATCCAACATTCATTCCTATTAAAAGCACTTGAG 303462 i i ii v iv i v iiiv L1M5_orf2#LIN 1805 AAAAAGCATTTGACAAAATTCAACACCCATTCATGATAAAAACTCTCAGC 1854 chr6qtel1M 303463 AATAAAGGAATAAATGGACTGTTCCTTAAAATAATAAGTAGCATCTATTT 303512 vvv i v ivvv i vv i ivi ivv L1M5_orf2#LIN 1855 AAACTAGGAATAGAAGGGAACTTCCTCAACCTGATAAAGGGCATCTACGA 1904 chr6qtel1M 303513 AAAACCATCAGTAAGCATCATTTATAATAGAGAAAAACTGCAAGCATTCC 303562 vv i? i viv i v ? v ? v L1M5_orf2#LIN 1905 AAAACCTACAGCNAACATCATACTTAATGGTGAAANACTGAANGCTTTCC 1954 chr6qtel1M 303563 TAGTAAGATCAGGAATCAAACAAGATTGCCCCCTATCACCATTACTATTC 303612 ivv i iv i iv i v ? i v L1M5_orf2#LIN 1955 CCCTAAGATCGGGAACAAGACAAGGATGTCCGCTNTCACCACTTCTATTC 2004 chr6qtel1M 303613 AATATTGTCTTAGAAATGCTAGCTTTGGCAATAAGAGTTGAGAAAGAGAT 303662 i vi i ii v ivvv ivvv i i L1M5_orf2#LIN 2005 AACATTGTACTGGAGGTCCTAGCCAGTGCAATAAGGCAAGAAAAAGAAAT 2054 chr6qtel1M 303663 TAAAGGAATTAGAATAGGCAATGAGGAAATCAAATTATCACTCTTTGCTG 303712 v v v ii v v v i v i i ?i v i v L1M5_orf2#LIN 2055 AAAAGGCATAAAGATTGGAAAGGAAGAAATAAAACTGTCNTTATTCGCAG 2104 chr6qtel1M 303713 ATGATATGATGGTATACTTGGAGAACCCTAGAGATTCTACTAAAAAGTTA 303762 i v ? v i i i ? i v v ? ii L1M5_orf2#LIN 2105 ATGACATGATTGTNTACGTAGAAAATCCNAAAGAATCTACAAANAAACTA 2154 chr6qtel1M 303763 TTTGAAATAATCCACACCTTTAGCAAAATTGCAGGATACAAAATAAACCC 303812 i v v vviiivv ii i ? ii v ivi L1M5_orf2#LIN 2155 CTAGAACTAATAAGTGAATTTAGCAAGGTCGCNGGATACAAGGTCAATAT 2204 chr6qtel1M 303813 ACATAACTCATCAGCATTCTTAAATATCACTAACAA--AATCCAGCAGTC 303860 v v viv i ii v ii vi -- iviiv i v L1M5_orf2#LIN 2205 ACAAAAATCAATTGTATTTCTATATACTAGCAACAAACAATTGGAAAATG 2254 chr6qtel1M 303861 AGTTACAAAGAGAAATTCCTTTTAAAGTAACTACTGATAGTATAAAATAC 303910 iv vi? i iv v v v i i vv vi v ii ? L1M5_orf2#LIN 2255 AAATTTNAAAAACAATACCATTTACAATAGCATCAAAAAACATNAAATAC 2304 chr6qtel1M 303911 TTAGGAATCTATCTGCCAAGGGAAAAT---CAGAAACTTTATGGGCAAAA 303957 vv iv --- ? --- ii v ? iivvv L1M5_orf2#LIN 2305 TTAGGAATAAATCTAACAA---AANATGTGCAAGACCTNTACACTGAAAA 2351 chr6qtel1M 303958 CTACAAAGCACTTTCCACATAAATTAAGTCTGATCTAACCAATTGGAAAA 304007 i i viiv v v ivvv i vi v i i L1M5_orf2#LIN 2352 CTACAAAACATTGCTGAGAGAAATTAAAGAAGACCTAAATAAATGGAGAG 2401 chr6qtel1M 304008 A-ATATTAAATGCTCTTGGATAGGGCGAGCAAATACAATAAAGATGGCAA 304056 - ii-- i v v iv viv ivi ? v L1M5_orf2#LIN 2402 ATATACC--ATGTTCATGGATTGGAAGACTCAATATTGTNAAGATGTCAA 2449 chr6qtel1M 304057 TACTACCTAAACTAATCTATTTGTTTAGTGCTATACCAATCAGACTCCCC 304106 v v i i i vvi i i v v i v - L1M5_orf2#LIN 2450 TTCTCCCCAAATTGATCTATAGATTCAATGCAATCCCAATCAAAATCCC- 2498 chr6qtel1M 304107 AAAAAAACTATTTTA-ATGACCTAAAAAAATAACAACAAAGTTCATATGG 304155 - iv iii v i- vi vi i v iv i ivvi i i L1M5_orf2#LIN 2499 -AGCAGGTTTTTTTGTAGAAATTGACAAGCTGATTCTAAAATTTATATGG 2547 chr6qtel1M 304156 AAAAACAAAAGGTCAAGAATTTCAAGGGCATTAAT-AAAAAAAAAATCAA 304204 vi i ii ? vv v iii v vv - i i v L1M5_orf2#LIN 2548 AAATGCAAAGGACCNAGAATAGCCAAAACAATCTTGAAAAAGAAGAACAA 2597 chr6qtel1M 304205 A--TGAAGGTGGCCTAGCTGTACCAGATCT-AAAATTATATTATAAAGCA 304251 -- i -- i i - vv ? ? - i i - v L1M5_orf2#LIN 2598 AGTTGGAG--GACTTA-CACTACCNGATNTCAAGACT-TATTATAAAGCT 2643 chr6qtel1M 304252 GCGGTTACCAAAATCATTTGGTATTGGC-TAAGGAATAGATTAGTTGATC 304300 i i v i i ivi v - - iv i v L1M5_orf2#LIN 2644 ACAGTAATCAAGACAGTGTGGTATTGGCGTAAGG-ATAGACAAATAGATC 2692 chr6qtel1M 304301 GATAGAATAGGTTAG---GTTCAAAGGACAAAACAGTCAATAACTATAGC 304347 i i i iv --- i i -i i i v viivv -- i ? L1M5_orf2#LIN 2693 AATGGAACAGAATAGAGAGTCCAGA-AATAGACCCACACATA--TATGGN 2739 chr6qtel1M 304348 AATCTAGTGTTTGACAAA----CCCAGACATCTCCAATTTGGGGGATAAG 304393 v ?i ii v ---- v ?i -v i i --- - L1M5_orf2#LIN 2740 CANTTGATTTTTGACAAAGGTGCCAANGCA-ATTCAGT---GGGGA-AAG 2784 chr6qtel1M 304394 AACCTACTGTTTGACAAAAATTGCTGGGAAAATTGGAAACTAGTATGG-C 304442 i ivvv v ii viv i v v iivi -v L1M5_orf2#LIN 2785 GATAGTCTTTTCAACAAATGGTGCTGGAACAATTGGATATCCATATGGAA 2834 chr6qtel1M 304443 AGAAACAAGTCATCGACTGACAATTAACACCATACACCACAA-TAACGTC 304491 i ii i? - ivvi vi v v v - ivi? L1M5_orf2#LIN 2835 AAAAATGAANC-TCGACCCCTACCTCACACCATACACAAAAATTAATTCN 2883 chr6qtel1M 304492 AAATGGGTTCAT-GACCTAGGCATAAAGAATGAGATTATAAATAAATTAG 304540 i i- - iiii ii? i i i vvvvi L1M5_orf2#LIN 2884 AGATGGA-TCATAGACCTAAATGTAAAAGNTAAAACTATAAAACTTCTAG 2932 chr6qtel1M 304541 AGG--AACATAGGATAGTTTACCTCTCAGACCTGTGGA-AGACGAAGGAA 304587 i -- v i-- i iivv vv ?- i i -- L1M5_orf2#LIN 2933 AAGAAAACATAGGAGAA--TATCTTCGTGACCTTGGGNTAGGCAAAG--A 2978 chr6qtel1M 304588 TTTATGACCAAAAAAGAAC-TAAAGAGAAGACCTGATCACAAAATCAAAA 304636 ---- iv v i -i i v --- ?i i i vv L1M5_orf2#LIN 2979 TTT----CTTAAACAGGACACAAAAAGCA---CNAACCATAAAAGAAAAA 3021 chr6qtel1M 304637 AT-------TTTGATTTTATCAAATTGAAAAGTTTTTGTACAAACAAAAC 304679 ------- v i ?i v v ii i iv ?vvv iv L1M5_orf2#LIN 3022 ATTGATAAATTGGACTNCATCAAAATTAAAAACTTCTGCTCNTCAAAAGA 3071 chr6qtel1M 304680 TAATGCAGACAAGATTAGAAGGGAAGCAATAAACTGGGAAAACATTTTTA 304729 i vi ivi v i v i v v i i ? i v v i L1M5_orf2#LIN 3072 CACCGTTAAGAAAATGAAAAGGCAAGCCACAGANTGGGAGAAAATATTTG 3121 chr6qtel1M 304730 CAGT-CAAAGGTTATAATAAAGACCTCATTTCCAAAATATATAGAGAATT 304778 i?- v vi i- i i iv i v i i i L1M5_orf2#LIN 3122 CAANACATATATC-TGACAAAGGACTCGTATCCAGAATATATAAAGAACT 3170 chr6qtel1M 304779 GACTCTAATTT-ATAAGAAA---TCAAGCCATTTTCCAGTTGATGAATGG 304824 v- vi ? i- ? ---v i v ---i i v? vi L1M5_orf2#LIN 3171 C-CTACAANTCAATAANAAAAAGACAAACAA---CCCAATANAAAAATGG 3216 chr6qtel1M 304825 TCAAAGCATATGAACAGATAATTCTCAAAAGAAGAAATTGAAACTATTTC 304874 v iv iv i v v v ?v iviiivv L1M5_orf2#LIN 3217 GCAAAAGACTTGAACAGACACTTCACAAAAGAAGATATNCAAATGGCCAA 3266 chr6qtel1M 304875 TAGCCATATGAAAAGATGCTC 304895 iv i L1M5_orf2#LIN 3267 TAAGCACATGAAAAGATGCTC 3287 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 42.02 CpG sites = 528, Kimura (unadjusted) = 42.54 Transitions / transversions = 1.16 (528/455) Gap_init rate = 0.05 (146 / 3235), avg. gap size = 1.28 (187 / 146) 1575 28.07 0.73 1.85 chr6qtel1M 304759 305306 (694694) L1ME3G_3end#LINE/L1 7 548 (376) m_b306s551i5 12792 chr6qtel1M 304759 TCCAAAATATATAGAGAATTGACTCTAATTTATAAGAAATCAAGCCATTT 304808 i i i vviv v iv -- v vi- L1ME3G_3end#L 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAA--AAGACAAC- 53 chr6qtel1M 304809 TCCAGTTGATGAATGGTCAAAGCATATGAACAGATAATTCTCAAAAGAAG 304858 - i v vi v v ii v i i L1ME3G_3end#L 54 -CCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chr6qtel1M 304859 AAATTGAAACTATTTCTAGCCATATGAAAAGATGCTCCAAAGCATTATTA 304908 vv iviiivv iv v vvv i v L1ME3G_3end#L 103 AAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTA 152 chr6qtel1M 304909 ATCAGAGAAATGCAAACTAAGACAACTCTAAGATGTCATTACACACCTGT 304958 i i i vv i ii viv ii L1ME3G_3end#L 153 ATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCAT 202 chr6qtel1M 304959 CAGACTGGCTAGAATGACAAGGAAAGAGAATGCAGAATGTTGGAGGGGAT 305008 i v i vvv i ?vv v iiv? i v i i L1ME3G_3end#L 203 CAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGT 252 chr6qtel1M 305009 GTGGGAAAACAGAGACACTAACACATT-TTGGTGGAATTGTGAATACATC 305057 i i iv v v i i -i i v i vvi v L1ME3G_3end#L 253 GTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTA 302 chr6qtel1M 305058 CAGCCATTCTGGAGAGCAATTTGGAGCTATGC-TCAAAATGTTATCAAAC 305106 ? i i viv vi- i ---- i v L1ME3G_3end#L 303 CAGCCNTTTTGGAGGGCAATTTGGCAGTATCTATTAAAAT----TTAAAA 348 chr6qtel1M 305107 TGTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGCTTACATCCCAAA 305156 i i i vii v ? ?v vi i ? L1ME3G_3end#L 349 TGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANA 398 chr6qtel1M 305157 GAGAT-CTTAAAGAAG-GGAAAGGGGCCTGTATGTACAAGACTGTTTGTG 305204 i - iiv v v - v v i i--? i iv ii v L1ME3G_3end#L 399 GAAATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTCATT 446 chr6qtel1M 305205 GCAACCCTCTTTGTAGTGGCCAGAAACTGGAAACTGAGTAGATGCCCATC 305254 i vi v i i v i i vivv i i L1ME3G_3end#L 447 GCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATC 496 chr6qtel1M 305255 AATTATAGAAGGGCTGAATAAATTGTGGTATATGAATATTATGGAATATT 305304 vivi v i i i vv i i L1ME3G_3end#L 497 AATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACT 546 chr6qtel1M 305305 AT 305306 L1ME3G_3end#L 547 AT 548 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 35.48 CpG sites = 82, Kimura (unadjusted) = 36.41 Transitions / transversions = 1.19 (82/69) Gap_init rate = 0.03 (14 / 547), avg. gap size = 1.00 (14 / 14) 15 12.73 9.30 0.00 chr6qtel1M 305641 305683 (694317) (ATTTAT)n#Simple_repeat 1 47 (0) m_b306s252i4 12793 chr6qtel1M 305641 ATGTATACTTAT-TTTGTATTTA-ATTTATACTT-TA-ATATATTTA 305683 v i - i - i - -v (ATTTAT)n#Sim 1 ATTTATATTTATATTTATATTTATATTTATATTTATATTTATATTTA 47 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.10 (4 / 42), avg. gap size = 1.00 (4 / 4) 111 19.82 1.17 1.57 chr6qtel1M 307262 307514 (692486) (TCTGTC)n#Simple_repeat 1 252 (3) m_b306s252i5 12794 chr6qtel1M 307262 TCTTTCTTTCTCTCTGTCTCTGTCTTTGTCTATCTATAAGTCTGTCTGTC 307311 v i v i v v v vv v v v (TCTGTC)n#Sim 1 TCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTC 50 chr6qtel1M 307312 TGTCTGGCTGTCTCTATCTCTCTCT-ACTCTCTGTCTCTGTGTCTTTCTA 307360 -- i v -vv v v v (TCTGTC)n#Sim 51 TGTCT--CTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTC 98 chr6qtel1M 307361 TCTGTCTATCTCTTTCTCTGTCCCTGTCTCTATGTCTGTCTCTGTCTCTC 307410 v v i v i i v v (TCTGTC)n#Sim 99 TGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTG 148 chr6qtel1M 307411 TCTGTGTCTCTCTCTCTTTCTCTGTCTCTCTCTCAATCTCTGTCTCTGAC 307460 v v v v vi -- (TCTGTC)n#Sim 149 TCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTG-- 196 chr6qtel1M 307461 TCTCTGTCTCTCTGTCT-T-TTTCTCTCTTTCTCTCTCTCTGCCTCTCTG 307508 v v - - i v v v i v v (TCTGTC)n#Sim 197 TCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTC 246 chr6qtel1M 307509 TCTTTC 307514 v (TCTGTC)n#Sim 247 TCTGTC 252 Matrix = Unknown Transitions / transversions = 0.26 (9/34) Gap_init rate = 0.03 (7 / 252), avg. gap size = 1.00 (7 / 7) 44 0.00 0.00 0.00 chr6qtel1M 307515 307552 (692448) (TG)n#Simple_repeat 1 38 (0) c_b306s251i0 12795 chr6qtel1M 307515 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 307552 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 38 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 111 25.43 0.00 0.71 chr6qtel1M 307553 307581 (692419) (TCTC)n#Simple_repeat 253 280 (1) m_b306s252i6 12796 chr6qtel1M 307553 CTTAAACTCCATTTCTCATTTCCCTCTCT 307581 ivvv iv i - i i (TCTC)n#Simpl 253 CTCTCTCTCTCTCTCTC-TCTCTCTCTCT 280 Matrix = Unknown Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1) 33 38.42 0.60 1.21 chr6qtel1M 310125 310290 (689710) (AT)n#Simple_repeat 1 165 (0) m_b306s252i7 12797 chr6qtel1M 310125 ATTTAAATATATATATATATATATAAAGACAT-TGTGTGAGTACATATAT 310173 v v v v i - i i - - i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATAT-A-TATATATAT 48 chr6qtel1M 310174 ATAAGCAGACACACATATACAGATTAACTTATACACAAATATAAATACAT 310223 vii v i i i i v vv iv i i v v i (AT)n#Simple_ 49 ATATATATATATATATATATATATATATATATATATATATATATATATAT 98 chr6qtel1M 310224 TCATGCATATACATAGATATCTATAACCCTACTTACATATCCATACATAT 310273 vi ii i v v vviv iv i vi i (AT)n#Simple_ 99 ATATATATATATATATATATATATATATATATATATATATATATATATAT 148 chr6qtel1M 310274 GTATATGCATCTGTATA 310290 i ii v i (AT)n#Simple_ 149 ATATATATATATATATA 165 Matrix = Unknown Transitions / transversions = 1.29 (27/21) Gap_init rate = 0.02 (3 / 165), avg. gap size = 1.00 (3 / 3) 452 23.23 0.87 6.42 chr6qtel1M 312411 312525 (687475) MIRc#SINE/MIR 19 127 (141) m_b306s601i0 12798 chr6qtel1M 312411 TGGATAGAGAAGTGGACCTGAAGTCAGGAGGACCTGAGTTCAAATCCAAC 312460 v v v i i i i i i viv MIRc#SINE/MIR 19 TGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGG 68 chr6qtel1M 312461 TTCAGACATTTAATAGTTACTAATTTTGTGACCCTGGGCAAGTCCTTTAA 312510 i v v i------- ii v i vi MIRc#SINE/MIR 69 CTCTGCCAC-------TTACTAGCTGTGTGACCTTGGGCAAGTCACTTAA 111 chr6qtel1M 312511 CCCCACTT-GCCTCAG 312525 i v v- MIRc#SINE/MIR 112 CCTCTCTGAGCCTCAG 127 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 25.55 CpG sites = 14, Kimura (unadjusted) = 28.10 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.07 (8 / 114), avg. gap size = 1.00 (8 / 8) 223 33.64 3.74 0.00 chr6qtel1M 312801 312907 (687093) MIR3#SINE/MIR 87 197 (11) m_b306s601i1 12799 chr6qtel1M 312801 TGACTGTGAAAATATC-CCTCAGTTCCATTGGTCTCAGTTACCTCACCTG 312849 iv iiv vi - i vi iv v i v i MIR3#SINE/MIR 87 TGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTG 136 chr6qtel1M 312850 TAAAATGGGTGCTTTTGGTCAACT--TCTCTGA-CTTCCTTTAAGCTCTA 312896 i v vv v iii iv -- i -v i iv i MIR3#SINE/MIR 137 TAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTG 186 chr6qtel1M 312897 TAATGCTCTGA 312907 vv v v MIR3#SINE/MIR 187 ACATTCTATGA 197 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 45.38 CpG sites = 18, Kimura (unadjusted) = 45.38 Transitions / transversions = 1.00 (18/18) Gap_init rate = 0.03 (3 / 106), avg. gap size = 1.33 (4 / 3) 24 19.31 0.00 0.00 chr6qtel1M 313578 313624 (686376) (TG)n#Simple_repeat 1 47 (0) m_b306s252i8 12800 chr6qtel1M 313578 TGTGAGTGTGTGTGAGTGTGTGTTTGGGTAAGTGTGCATGTGTGTGT 313624 v v v v iv ii (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 47 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 94 26.64 2.52 1.25 chr6qtel1M 317563 317591 (682409) (TCTG)n#Simple_repeat 1 28 (293) m_b306s252i9 12801 chr6qtel1M 317563 TCTTTCCCTCTGTCAGTCTGTACTGTCTG 317591 v iv v - (TCTG)n#Simpl 1 TCTGTCTGTCTGTCTGTCTGT-CTGTCTG 28 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1) 186 8.74 1.12 0.00 chr6qtel1M 317592 317858 (682142) (TC)n#Simple_repeat 1 270 (0) c_b306s251i1 12802 chr6qtel1M 317592 TCTCTCTCTGTCTCTGTCTCTGTCTCTCTTTCTTTCTCTGTCTCTCTCTC 317641 v v v i i v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr6qtel1M 317642 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTTTCTCTGTCTCTGTCTCTCTC 317691 i v v (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chr6qtel1M 317692 TCTCTGTCTCTGTTTCTCTCTCTGTCTCTCTGTC-CTCTCTCTCTCTCTC 317740 v v i v v - (TC)n#Simple_ 101 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 150 chr6qtel1M 317741 TGTCTCTCTCTCTCTCTGTCTCTCTCTCTCTCTCTCTCTGTCTCTCTCTC 317790 v v v (TC)n#Simple_ 151 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 200 chr6qtel1M 317791 TCTCTGTCTCTCTCTCTGTCTCTCTCTC-CTTTCTCTCTCTCTCTGTCTC 317839 v v - i v (TC)n#Simple_ 201 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 250 chr6qtel1M 317840 TCTGTCTCTCTCTC-CTCTC 317858 v - (TC)n#Simple_ 251 TCTCTCTCTCTCTCTCTCTC 270 Matrix = Unknown Transitions / transversions = 0.29 (5/17) Gap_init rate = 0.01 (3 / 266), avg. gap size = 1.00 (3 / 3) 94 26.64 2.52 1.25 chr6qtel1M 317859 318026 (681974) (TCTG)n#Simple_repeat 29 203 (118) m_b306s252i9 12803 chr6qtel1M 317859 C-CTCCCCCCCCCTCTCCCTCTGTCTCACTTTCTCTGTATGTGTGTGTGT 317907 -v ivi ivi v iv vv v v v i v v v (TCTG)n#Simpl 29 CTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCT 78 chr6qtel1M 317908 GTCTGTCTGCCTGATTGCCTGTCTTCCTGTCTGTTTCTCTGTCAGTC--T 317955 i vi i vi i v v -- (TCTG)n#Simpl 79 GTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGT 128 chr6qtel1M 317956 CTGTCTTTCTCTCTCTCTCTCTGTC--TCTGTCTCTCT-TTTG-GTCTCT 318001 v v v v -- v - i -v v (TCTG)n#Simpl 129 CTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCT 178 chr6qtel1M 318002 GCCTCTCTGTCTCTCTGTCTCTCTC 318026 i v v v v (TCTG)n#Simpl 179 GTCTGTCTGTCTGTCTGTCTGTCTG 203 Matrix = Unknown Transitions / transversions = 0.46 (13/28) Gap_init rate = 0.03 (5 / 167), avg. gap size = 1.40 (7 / 5) 43 0.00 0.00 0.00 chr6qtel1M 318027 318063 (681937) (TG)n#Simple_repeat 1 37 (0) c_b306s251i2 12804 chr6qtel1M 318027 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 318063 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 37 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 94 26.64 2.52 1.25 chr6qtel1M 318064 318094 (681906) (TCTG)n#Simple_repeat 204 234 (87) m_b306s252i9 12805 chr6qtel1M 318064 CTGCCTGTCTTCCTGTCTGTTTCTCTGTCAG 318094 i vi i v v (TCTG)n#Simpl 204 CTGTCTGTCTGTCTGTCTGTCTGTCTGTCTG 234 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 30 8.18 0.00 0.00 chr6qtel1M 318095 318133 (681867) (TC)n#Simple_repeat 1 39 (0) c_b306s251i3 12806 chr6qtel1M 318095 TCTCTGTCTCTCTCTCTCTCTCTCTGTCTCTGTCTCTCT 318133 v v v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 39 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 94 26.64 2.52 1.25 chr6qtel1M 318134 318170 (681830) (TCTG)n#Simple_repeat 235 271 (50) m_b306s252i9 12807 chr6qtel1M 318134 TTTG-GTCTCTGCCCCTCTGTCTCTCTGTCTCTCTGTC 318170 i -v v i iv v v - (TCTG)n#Simpl 235 TCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGT- 271 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 46 0.00 0.00 0.00 chr6qtel1M 318171 318209 (681791) (TG)n#Simple_repeat 1 39 (0) c_b306s251i4 12808 chr6qtel1M 318171 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 318209 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 39 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 94 26.64 2.52 1.25 chr6qtel1M 318210 318257 (681743) (TCTG)n#Simple_repeat 272 319 (2) m_b306s252i9 12809 chr6qtel1M 318210 CTGTCTGCCTGTCTGCCTCCCTGTGTCTCTGTCTCCCTCTCTGTGTGT 318257 i i vi v v vi v v (TCTG)n#Simpl 272 CTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGT 319 Matrix = Unknown Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 69 7.34 0.00 0.00 chr6qtel1M 318896 318981 (681019) (TC)n#Simple_repeat 1 86 (0) c_b306s251i5 12810 chr6qtel1M 318896 TCTCTGTCTCTGTCTCTCTTTCTCTCTCTGTCTCTCTCTCTCTCTCTCTC 318945 v v i v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr6qtel1M 318946 TCTCTCTCTCTCTTTTTCTCTCTCTCTCTCTCTCTC 318981 i i (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 86 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.00 (0 / 85), avg. gap size = 0.0 (0 / 0) 18 25.89 0.00 1.79 chr6qtel1M 318982 319029 (680971) (TCTG)n#Simple_repeat 9 56 (0) m_b306s252i10 12811 chr6qtel1M 318982 GCTGTCTGCCTGTCTGTCTGTGACTCTGTCTCCCTCTCTCTGTGTGTG 319029 v i vvv vi v v v v (TCTG)n#Simpl 9 TCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTG 56 Matrix = Unknown Transitions / transversions = 0.22 (2/9) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 279 22.92 0.00 2.79 chr6qtel1M 320081 320264 (679736) C HERVIP10FH#LTR/ERV1 (4106) 996 818 m_b306s701i0 12812 chr6qtel1M 320081 TATCTCTCTGCTTTCTCTGTTTCTCTCTGTGTCTCTCTGTCTCTCCCTAT 320130 - ---- v v i i v C HERVIP10FH#LT 996 TATCTCTCT-CTTTCT----TTCTCTCTTTGACTTTCTGTCTCTCTCTCT 952 chr6qtel1M 320131 CTCTTTCTCTCTCTCTCTGTCTCTGTCTCTCTTTCCCTCTGTCTCTCTCT 320180 i vv i i v v i i v vi C HERVIP10FH#LT 951 CTCTCTGACTCCCTCTTTGTCTCTCTGTCTCTTCCTCTCTCTGCCTCTCT 902 chr6qtel1M 320181 CTCTCTCTAACTCTCTGTCTCACTCTTTCTCTCTATGTATCAGTCTACCT 320230 i i i v i vv i iv v v vv vi C HERVIP10FH#LT 901 CTCTCTTTGACTCCCTCTTTGTCTCTCTCTCTCCCTCTCTCTCTCTTTCT 852 chr6qtel1M 320231 CTGCCTCTCTCTGTCTTTGTTTCCCTCTCTCTCT 320264 vi vi i v i i C HERVIP10FH#LT 851 CTCTCTCTCTCTTCCTCTCTCTCTCTCTCTCTCT 818 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 27.52 CpG sites = 20, Kimura (unadjusted) = 27.52 Transitions / transversions = 0.95 (20/21) Gap_init rate = 0.03 (5 / 183), avg. gap size = 1.00 (5 / 5) 15 19.85 0.00 0.00 chr6qtel1M 321950 321978 (678022) (T)n#Simple_repeat 1 29 (0) m_b306s252i11 12813 chr6qtel1M 321950 TTTTCTATTTTTTTTTTTTTTACTTTCTT 321978 i v vi i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 15 28.65 1.64 1.64 chr6qtel1M 322377 322437 (677563) (TTTCT)n#Simple_repeat 1 61 (0) m_b306s252i12 12814 chr6qtel1M 322377 TTTATTTTGTTTTCTGCTGTGTACTTTTTTATTTTATTTCTCTCCTTTTC 322426 v v vi v v v i - iv i i (TTTCT)n#Simp 1 TTTCTTTTCTTTTCTTTTCTTTTCTTTTCT-TTTCTTTTCTTTTCTTTTC 49 chr6qtel1M 322427 -TTCCCTTTCTT 322437 - i i (TTTCT)n#Simp 50 TTTTCTTTTCTT 61 Matrix = Unknown Transitions / transversions = 1.00 (7/7) Gap_init rate = 0.03 (2 / 60), avg. gap size = 1.00 (2 / 2) 70 1.58 0.00 0.00 chr6qtel1M 322461 322524 (677476) (TA)n#Simple_repeat 1 64 (0) c_b306s251i6 12815 chr6qtel1M 322461 TATATATATATATATATATATATATATATATATATATATATATAAATATA 322510 v (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr6qtel1M 322511 TATATATATATATA 322524 (TA)n#Simple_ 51 TATATATATATATA 64 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0) 25 25.99 2.41 0.00 chr6qtel1M 322958 322999 (677001) (TCTG)n#Simple_repeat 1 44 (41) m_b306s252i13 12816 chr6qtel1M 322958 TCTTTCTTTCTCTCTGT-TG-GTCTCTGTCAATTTGTCTGTCTG 322999 v v v - -v v vi i (TCTG)n#Simpl 1 TCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTG 44 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.05 (2 / 41), avg. gap size = 1.00 (2 / 2) 86 4.74 2.70 0.88 chr6qtel1M 323000 323110 (676890) (TC)n#Simple_repeat 1 113 (0) c_b306s251i7 12817 chr6qtel1M 323000 TCTCTGTCTCTGTCTCGTCTCT-TTTCTCTCTCTCTCT-TCTCTCTCTCT 323047 v v - - i - (TC)n#Simple_ 1 TCTCTCTCTCTCTCTC-TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 49 chr6qtel1M 323048 CTCTCTCTCTCTCTCTCTCTTTCTCTCTCTTTCTCTCTCTCTCTCTC-CT 323096 i i - (TC)n#Simple_ 50 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 99 chr6qtel1M 323097 CTCTCTCTCTCTCT 323110 (TC)n#Simple_ 100 CTCTCTCTCTCTCT 113 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.04 (4 / 110), avg. gap size = 1.00 (4 / 4) 25 25.99 2.41 0.00 chr6qtel1M 323111 323150 (676850) (TCTG)n#Simple_repeat 45 84 (1) m_b306s252i13 12818 chr6qtel1M 323111 TTCTATGTGTGTGTGTCTGCCTCTCTGTTTCTCTGTGTGT 323150 i v v v v i v i v v (TCTG)n#Simpl 45 CTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGT 84 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 12 16.58 2.08 8.89 chr6qtel1M 326371 326418 (673582) (TTA)n#Simple_repeat 1 45 (0) m_b306s252i15 12819 chr6qtel1M 326371 TTATT-TCAATATGTATGAATTATTAACTATTATTTTTGTTGATTATTA 326418 - i v - -v - i v i - (TTA)n#Simple 1 TTATTATTATTAT-TAT-TATTATT-ATTATTATTATTATT-ATTATTA 45 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.11 (5 / 47), avg. gap size = 1.00 (5 / 5) 31 23.56 6.06 0.00 chr6qtel1M 326847 326945 (673055) (TA)n#Simple_repeat 1 105 (0) m_b306s252i16 12820 chr6qtel1M 326847 TATATTTATAT-TAT-TATATACATTTATAT-TGCATCT-TATATACATA 326892 v - - i v - ii v - i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr6qtel1M 326893 GGTATATATTTA-ATATATATTTCTACATGTGTATAGATATTGAT-TTTA 326940 vi v - v v i i i v vv - v (TA)n#Simple_ 51 TATATATATATATATATATATATATATATATATATATATATATATATATA 100 chr6qtel1M 326941 TCTAT 326945 v (TA)n#Simple_ 101 TATAT 105 Matrix = Unknown Transitions / transversions = 0.67 (8/12) Gap_init rate = 0.06 (6 / 98), avg. gap size = 1.00 (6 / 6) 17 0.00 0.00 0.00 chr6qtel1M 327469 327489 (672511) (AAT)n#Simple_repeat 1 21 (0) m_b306s252i17 12821 chr6qtel1M 327469 AATAATAATAATAATAATAAT 327489 (AAT)n#Simple 1 AATAATAATAATAATAATAAT 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 12 25.94 0.00 2.38 chr6qtel1M 328244 328286 (671714) (AAGA)n#Simple_repeat 1 42 (0) m_b306s252i18 12822 chr6qtel1M 328244 AAGAAAAAAAGGCAGTAAAGACTAAATGAAGGAAAGAACGAAA 328286 i iv - vvi v i v (AAGA)n#Simpl 1 AAGAAAGAAAGAAAG-AAAGAAAGAAAGAAAGAAAGAAAGAAA 42 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.02 (1 / 42), avg. gap size = 1.00 (1 / 1) 15 21.79 6.67 1.59 chr6qtel1M 328712 328771 (671229) (TAA)n#Simple_repeat 1 63 (0) m_b306s252i19 12823 chr6qtel1M 328712 TAATATTTTTAACATTATTAATAATAGT-ACAATTATAA-AATTAT-GTA 328758 v vv i v v i - i v - v -i (TAA)n#Simple 1 TAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATA 50 chr6qtel1M 328759 A-AATAATAAATAA 328771 - - (TAA)n#Simple 51 ATAATAAT-AATAA 63 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.08 (5 / 59), avg. gap size = 1.00 (5 / 5) 235 28.80 8.41 2.65 chr6qtel1M 329025 329131 (670869) MIR3#SINE/MIR 31 143 (65) m_b306s601i2 12824 chr6qtel1M 329025 GACTAAGA--CAGAGAAATAATTGGATTTT---CCCAATGCAGCAA-TAA 329068 ii -- - i i--i i i --- iiiv v v - MIR3#SINE/MIR 31 GACTGGGAGTCAG-GAGAC--CTGGGTTCTAGTCCCGGCTCTGCCACTAA 77 chr6qtel1M 329069 CTTCCTTTG--ACTGTGAAAAAAACACT-CAGTTCCCTTGGCCTCAGTTA 329115 ?v v -- iv iiv iv - vi i v v MIR3#SINE/MIR 78 CTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTT 127 chr6qtel1M 329116 CTTCACCTATAAAATG 329131 i i i MIR3#SINE/MIR 128 CCTCATCTGTAAAATG 143 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 36.65 CpG sites = 19, Kimura (unadjusted) = 38.29 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.08 (8 / 106), avg. gap size = 1.50 (12 / 8) 198 30.20 6.19 0.98 chr6qtel1M 329076 329172 (670828) MIR1_Amn#SINE/MIR 92 193 (37) m_b306s601i3 12824 chr6qtel1M 329076 TGACTGTGAAAAAAACACT-CAGTTCCCTTGGCCTCAGTTACTTCACCTA 329124 iv iiv iv -? vi i v? v i i i MIR1_Amn#SINE 92 TGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTG 141 chr6qtel1M 329125 TAAAATGG-----ATGCTTTTGGTCACCTTCTCTGATTTCCTTTATGCTC 329169 ----- v vi ii v - v i vv v iv v MIR1_Amn#SINE 142 TAAAATGGGGATAATGATACTGACCTCCTT-TGTAAAGTGCTTTGAGATC 190 chr6qtel1M 329170 TAC 329172 MIR1_Amn#SINE 191 TAC 193 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 40.18 CpG sites = 14, Kimura (unadjusted) = 40.18 Transitions / transversions = 0.93 (14/15) Gap_init rate = 0.03 (3 / 96), avg. gap size = 2.33 (7 / 3) 26 8.12 0.00 0.00 chr6qtel1M 329865 329903 (670097) (GTGTGTGA)n#Simple_repeat 1 39 (0) c_b306s251i8 12825 chr6qtel1M 329865 GTGTGTGAGTGTGTGACTGTTTGAGTGCGTGAGTGTGTG 329903 v v i (GTGTGTGA)n#S 1 GTGTGTGAGTGTGTGAGTGTGTGAGTGTGTGAGTGTGTG 39 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 20 3.71 0.00 0.00 chr6qtel1M 334026 334053 (665947) (AAACA)n#Simple_repeat 1 28 (0) m_b307s252i0 12826 chr6qtel1M 334026 AAATAAAACAAAACAAAACAAAACAAAA 334053 i (AAACA)n#Simp 1 AAACAAAACAAAACAAAACAAAACAAAA 28 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 36 22.69 3.42 1.68 chr6qtel1M 334730 334739 (665261) (TCTG)n#Simple_repeat 1 11 (108) m_b307s252i2 12827 chr6qtel1M 334730 TCTCTTTGT-T 334739 v i - (TCTG)n#Simpl 1 TCTGTCTGTCT 11 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.11 (1 / 9), avg. gap size = 1.00 (1 / 1) 33 0.00 3.12 0.00 chr6qtel1M 334740 334771 (665229) (TC)n#Simple_repeat 1 33 (0) c_b307s251i0 12828 chr6qtel1M 334740 TCTCT-TCTCTCTCTCTCTCTCTCTCTCTCTCT 334771 - (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 33 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 36 22.69 3.42 1.68 chr6qtel1M 334772 334877 (665123) (TCTG)n#Simple_repeat 12 118 (1) m_b307s252i2 12829 chr6qtel1M 334772 TTTGTGTGTGTGTGTGTCTGTCTGTC--TCTGTCTGTCTCTTCTTGTTTG 334819 i v v v -- -v - i (TCTG)n#Simpl 12 TCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCT-GTC-TGTCTG 59 chr6qtel1M 334820 TGTCTCACCTTTTCTCTCT-TGTGTCTGTCTGCCTGTCTGTTTCTCTGTG 334868 v v vvii v v - v i i v v (TCTG)n#Simpl 60 TCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTC 109 chr6qtel1M 334869 TCTCTGTCT 334877 v (TCTG)n#Simpl 110 TGTCTGTCT 118 Matrix = Unknown Transitions / transversions = 0.43 (6/14) Gap_init rate = 0.04 (4 / 105), avg. gap size = 1.25 (5 / 4) 16 23.27 0.00 0.00 chr6qtel1M 336049 336083 (663917) (A)n#Simple_repeat 1 35 (0) m_b307s252i3 12830 chr6qtel1M 336049 AAAGAATCAAATAAGAAAACCAAAAAAAAAAAAAA 336083 i vv v i vv (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 35 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 374 24.36 0.85 2.59 chr6qtel1M 337162 337279 (662721) L1MEh_5end#LINE/L1 2113 2228 (7) m_b307s551i0 12831 chr6qtel1M 337162 GTAATTTTAACCATAAATGTGAATGGGGTAAACTTCCCCATAGAGAGGAA 337211 --- v i v iv v vi i iv L1MEh_5end#LI 2113 GTAATT---ACAATAAATGTAAATGGGTTAAACTCACCAATTAAAAGACA 2159 chr6qtel1M 337212 GTGGTTA-GAGAATGGATTAAAAGCCAGAATCCTACAATATATTGTTGAC 337260 v i ?-v v ? iv i v ii iv L1MEh_5end#LI 2160 GAGATTNTCAGATTGGATTNAAAAACAAAATCCAACAATATGCTGTCTAC 2209 chr6qtel1M 337261 AGGAAACACACCTGAAGCA 337279 i i i i i L1MEh_5end#LI 2210 AAGAGACACACTTAAAACA 2228 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 30.63 CpG sites = 16, Kimura (unadjusted) = 30.63 Transitions / transversions = 1.33 (16/12) Gap_init rate = 0.03 (4 / 117), avg. gap size = 1.00 (4 / 4) 2074 31.20 3.48 3.48 chr6qtel1M 337175 338871 (661129) L1M5_orf2#LINE/L1 38 1734 (1560) m_b307s551i1 12831 chr6qtel1M 337175 TAAATGTGAATGGGGTAAACTTCCCCATAGAGAGGAAGTGGTTA-GAGAA 337223 i ?v vii v vi i v v i i-v v L1M5_orf2#LIN 38 TAAATGTAAATGGNCTAAACACTCCAATTAAAAGGCAGAGATTGTCAGAC 87 chr6qtel1M 337224 TGGATTAAAAGCCAGAATCCTACAATATATTGTTGACAGGAAACACACCT 337273 v iv ii i v v ii iv i i i i L1M5_orf2#LIN 88 TGGATAAAAAAACAAGACCCAACTATATGCTGTCTACAAGAGACGCACTT 137 chr6qtel1M 337274 GAAGCAGGGAGATACATGCACAGTAAAGGTAAAAGGTTGAAGCAGAATCT 337323 v ii vii i vi? viv i i v i iv ii v L1M5_orf2#LIN 138 TAAATATAAAGACACAGANAGGTTGAAAGTAAAAGGATGGAAAAAGATAT 187 chr6qtel1M 337324 ACCATGCTTCAGGTGAAGTCAAA-AAAGCAGGGGTAGCCATCCTGATCTC 337372 v-v viiv ?iv - v ? i i vi i v L1M5_orf2#LIN 188 ACCATGCA-AACACTAANCAAAAGAAAGCTGGNGTGGCTATATTAATATC 236 chr6qtel1M 337373 AGATCAAGCA------AAAGCAAAAATTGATCTAATTAAAAGAGATAAGG 337416 iv i ------ i i --- --- vv i L1M5_orf2#LIN 237 AGACAAAGTAGACTTCAAGGCAAGAA---AT---ATTACCAGAGATAAAG 280 chr6qtel1M 337417 AAGGGCACTATATCTTGCTAAA-GGGTAGCATAGATAATCAAGCA---AT 337462 i i i vi vv v - ----i iv v v --- L1M5_orf2#LIN 281 AGGGACATTTCATAATGATAAAAGGGT----CAATTCATCAAGAAGACAT 326 chr6qtel1M 337463 ATCAATATTAAACATATATGCACCAAGTAGTGTAGCAAGTAAATTCTTAA 337512 v vi ii i v i iiiv vvvv v v i L1M5_orf2#LIN 327 AACAATCCTAAATGTGTATGCACCTAATAACAGAGCTTCAAAATACATGA 376 chr6qtel1M 337513 AAGAGAAATTAAGAGAACTGCAAGAAGATATAGACTGCAAAACCACAAT- 337561 iv i i i v iv i v --- v - L1M5_orf2#LIN 377 AGCAAAAACTGACAGAACTAAAAGGAGAAATAGAC---AAATCCACAATT 423 chr6qtel1M 337562 --AGTGGGAGATCTCAACCTTGCACTCTCAGCATTAGATAAATCAAACTA 337609 -- ? i i vi?v v i v v i v i- L1M5_orf2#LIN 424 ATAGTNGGAGATTTTAACACNCCTCTCTCAGTAATTGATAGAACAAG-TA 472 chr6qtel1M 337610 CAAAATAAATAAGAAAGAA-GTCAAAGAGATAAATAGAATACTAGAAA-- 337656 v v v v v i -i vi vv i i -- i vv -- L1M5_orf2#LIN 473 GACAAAAAATCAGTAAGGATATAGAAGATTTGAACA--ACACTATCAACC 520 chr6qtel1M 337657 AGTTAGATAGGATACATCTTTGGAGAAAACTAAATAGAGACAGACAG--G 337704 ii v ivvi vv iv iv v ?v ivv - - ? -- L1M5_orf2#LIN 521 AACTTGACCTAATTGACATTTATAGAACACTNCACCCA-ACA-ACNGCAG 568 chr6qtel1M 337705 AGTACACGTTCTTCTCAGCAGTTCATGGAACCTATACAAAAATTGACCAT 337754 i i i ivv iv v v v i v L1M5_orf2#LIN 569 AATACACATTCTTTTCAAGTGCACATGGAACATTTACCAAGATAGACCAT 618 chr6qtel1M 337755 ATATTAGGACATAAAA---ACCTCAA---ACTCAAA-----TGCAGTAAT 337793 ?i i v ---ii --- i i? ----- v i v L1M5_orf2#LIN 619 ATNCTGGGCCATAAAACAAGTCTCAATAAATTTNAAAGGATTGAAATCAT 668 chr6qtel1M 337794 GCAGAAATAGTAAATGCATCCTTTTCAGACCACGATGCAATGAAAATTAC 337843 i ---- -- ----- i v i v v v viv L1M5_orf2#LIN 669 ACAGA----GTA--TG-----TTCTCTGACCACAATGGAATTAAATTAGA 707 chr6qtel1M 337844 AGTCAATAA-------ATAGCCAGGGAAAAATAAACCAAAAAATAATTGG 337886 i ------- ? i --- vv- --- v L1M5_orf2#LIN 708 AATCAATAACAAAAAGATANCTAG---AAAATCC-CCAAA---TATTTGG 750 chr6qtel1M 337887 AAACTAAATAATCTCA-TACTAAAGAATGTGTGGG-GAAACAGCAAATTG 337934 i i - v - v v ivii -v v iv ii L1M5_orf2#LIN 751 AAATTAAACAA-CACACTTCTAAATAACCCATGGGTCAAAGAAGAAATCA 799 chr6qtel1M 337935 TTGACATAATTAATAACTTCACCCAAGAAAATGACAATAATGAGACATCA 337984 ivi?viv iv v viviiv vvi ? i vi v v L1M5_orf2#LIN 800 CAANGGAAATTAGAAAATATTTTGAACTGAATGANAATGAAAATACAACA 849 chr6qtel1M 337985 TACCAAAATGTGTGGGATTTAGCAAAAGCAGTAATAAGGGGAAATTTTAT 338034 i v vi v iv v i i v L1M5_orf2#LIN 850 TATCAAAATTTGTGGGATGCAGCTAAAGCAGTGCTTAGAGGGAAATTTAT 899 chr6qtel1M 338035 ATCTCTAGAGGTCTACTTGCATAAAATAGAGAAAGAG---AGAGTCAAAG 338081 v ?i i v i? iv --- i v ii ii --- i i v L1M5_orf2#LIN 900 AGCNTTAAATGCNTATAT---TAGAAAAGAAGAAAGGCTTAAAATCAATG 946 chr6qtel1M 338082 AATTAGGGTTACAGATTAAAAAGCTATAAAAAGAA---CAAATTAAAAAC 338128 vi i v v vv i v --- vv L1M5_orf2#LIN 947 ATCTAAGCTTCCACCTTAAGAAGCTAGAAAAAGAAGAGCAAATTAAACCC 996 chr6qtel1M 338129 A--CCCAGTCAAACATTAACTTGAAATTTTAAAAATAAAAGAAGAGATTA 338176 --v?v vi vi-- v-- vv i i v i i L1M5_orf2#LIN 997 AAAGNAAGTAGAAGG--AAG--GAAATAATAAAGATAAGAGCAGAAATCA 1042 chr6qtel1M 338177 ATAAAATTGAAAGTAACAAAAAAACTATTGAATTAATAAATAAAACTAAA 338226 i v --- ? ? v v ivv v ii i i L1M5_orf2#LIN 1043 ATGAAATAGAAA---ACAAANANACAATAGAGAAAATCAACGAAGCCAAA 1089 chr6qtel1M 338227 AGTTGGTTTTGTGAAAAACCAACAACAAAATATATATATATATACCTTCA 338276 i i v i-- v i ----- i- v ii L1M5_orf2#LIN 1090 AGCTGGTTCTTTGAAAAG--ATCAATAAAAT-----TG-ATAAACCTCTA 1131 chr6qtel1M 338277 GTAAATGTGATTTAAAAGGAAAGAG-GAAAAT-TAAATTGTTAGTCTTAA 338324 i? ivv iv i ii - i i-i iii i v i i L1M5_orf2#LIN 1132 GCNAGACTGATCAAGAAAAAAAGAGAGAAGACACAAATTACCAATATCAG 1181 chr6qtel1M 338325 AAATGAGAAAGGAGAGGTCGCCACTAATGAAAAGAAAATTAGAGCAATAA 338374 i i vi i i vi vvv vii v i ivi L1M5_orf2#LIN 1182 GAATGAAAAAGGAGACATCACTACAGATCCTACAGACATTAAAAGGATAA 1231 chr6qtel1M 338375 TTAGGAGTTACTTTGTCCAGCTTTATGCAAATAAATCAGATAA-----AT 338419 v iiiv i v vv i v iv ? ----- L1M5_orf2#LIN 1232 TAAGAGAATATTATGAACAACTTTATGCCAATAAATTTGANAACTTAGAT 1281 chr6qtel1M 338420 GAAATGGAAGAATATCTTCAAAAATATAGCTTACCCAAATTAACAGAGGA 338469 vi vi v i i i? v i i ?v i L1M5_orf2#LIN 1282 GAAATGGACAAATTCCTTGAAAAACACAANTTACCAAAACTGACNCAAGA 1331 chr6qtel1M 338470 AGAGGTAAAATGGTTAAACAATACCATTTTAGAAAAAGAAACAGAACAAG 338519 ii i vivi i i iiv i v ivivv iv ivv L1M5_orf2#LIN 1332 AGAAATAGAAAATCTGAATAGCCCTATATCTATTAAAGAAATTGAATTTG 1381 chr6qtel1M 338520 CTATTACTCAACTCTCTAAGAAAAAATCCATAGAACCAGATGGAGTTGCA 338569 iv vvv v ii i vi i v ivi iv vv ii v L1M5_orf2#LIN 1382 TAATTAAAAACCTTCCCACAAAGAAAACTCCAGGCCCAGATGGCTTCACT 1431 chr6qtel1M 338570 TGTGAATTCTACCAAATATTTA---AAGAATTACCTCCAGTGCTATATAA 338616 v i --- v viv i vi i i L1M5_orf2#LIN 1432 GGTGAATTCTACCAAACATTTAAGGAAGAAATAATACCAATCTTACACAA 1481 chr6qtel1M 338617 ACTATTTTTAAAAAAATAGGGATTTAAGGAGTCCTATCAAATTCCTTTCA 338666 -- i iv i ii vvv i iiv vi v i v i L1M5_orf2#LIN 1482 AC--TCTTCCAGAAAATAGAAAAAGAGGGAACACTTCCCAACTCATTTTA 1529 chr6qtel1M 338667 TGA-CCCAGACATGGTACTGATACCTAAACCAGGTAGGGTGAAAACAGAG 338715 -v - ?iiv v ? ii ii vv vv iii L1M5_orf2#LIN 1530 TGAGGCCAG-CATNACCCTGATACCAAAACCNGACAAAGACATTACAAGA 1578 chr6qtel1M 338716 AAAGAAAATTATAGACCAATCTTCCTAATAAATATTGATTCTAAAATCAT 338765 i v i v i i v v v v L1M5_orf2#LIN 1579 AAAGAAAATTACAGACCAATATCCCTCATGAACATAGATGCAAAAATCCT 1628 chr6qtel1M 338766 AAATACAATATTAGCAAAAAGATTAGAGAAAATCATCACCAGGATAATAC 338815 ? i v vv v vv v vvi v vv L1M5_orf2#LIN 1629 NAACAAAATATTAGCAAATCGAATCCAGCAATATATAAAAAGGATAATAC 1678 chr6qtel1M 338816 ACTATGACCAAGTAAATTTTATACCAAGAATGTAGGGCTGATTCAATATT 338865 ii iiiv v i i i i i i i L1M5_orf2#LIN 1679 ATCATGACCAAGTGGGGTTTATCCCAGGAATGCAAGGTTGGTTTAACATT 1728 chr6qtel1M 338866 AGGAAA 338871 v i L1M5_orf2#LIN 1729 CGAAAA 1734 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 41.72 CpG sites = 268, Kimura (unadjusted) = 41.94 Transitions / transversions = 1.10 (268/243) Gap_init rate = 0.05 (83 / 1696), avg. gap size = 1.42 (118 / 83) 22 15.81 0.00 0.00 chr6qtel1M 340379 340414 (659586) (T)n#Simple_repeat 1 36 (0) m_b307s252i4 12832 chr6qtel1M 340379 TTTTCTTTTTTTTTTTTTTCTTTTTTTTACTTTCTT 340414 i i vi i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 36 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 471 23.17 2.36 4.84 chr6qtel1M 341571 341697 (658303) MIRc#SINE/MIR 4 127 (141) m_b307s601i0 12833 chr6qtel1M 341571 GGCAGCTAGATGGCTCAGTGGAGAGA--AGTGCCCCTGAAGTCAGGAGGA 341618 i---i iv i -- v vv i i i MIRc#SINE/MIR 4 GGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA 50 chr6qtel1M 341619 TCTAAGTTCAAATCCAGCCTCATTTAATAGTTACTAGATTTGTGACCCTG 341668 i ii i i v v --- ivi v v v i MIRc#SINE/MIR 51 CCTGGGTTCGAGTCCCGGCTC---TGCCACTTACTAGCTGTGTGACCTTG 97 chr6qtel1M 341669 GGCAAGTCATTTAACTTCACTG-GCCTCAG 341697 i i v - MIRc#SINE/MIR 98 GGCAAGTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 27.10 CpG sites = 17, Kimura (unadjusted) = 28.27 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.06 (8 / 126), avg. gap size = 1.12 (9 / 8) 12 18.17 0.00 7.50 chr6qtel1M 341773 341815 (658185) (AAAAGA)n#Simple_repeat 1 40 (0) m_b307s252i5 12834 chr6qtel1M 341773 AAAAGAATAAAGAAAAAGGAAAGTCAGAAAGAAAGGAGCAAAA 341815 - - ivv i -i v (AAAAGA)n#Sim 1 AAAAGAA-AAAGAAAAA-GAAAAAGAAAAAGAAA-AAGAAAAA 40 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.07 (3 / 42), avg. gap size = 1.00 (3 / 3) 14 12.81 5.88 0.00 chr6qtel1M 341774 341807 (658193) (AAAG)n#Simple_repeat 1 36 (0) m_b307s252i6 12834 chr6qtel1M 341774 AAAG-AATAAAGAAA-AAGGAAAGTCAGAAAGAAAG 341807 - v - i vv (AAAG)n#Simpl 1 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG 36 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2) 223 32.46 6.13 3.59 chr6qtel1M 341915 342077 (657923) MIR3#SINE/MIR 19 185 (23) m_b307s601i1 12835 chr6qtel1M 341915 AGAGAGGGAGTTAAATAGCTGGCAGG-GACCAGAGTTATTGAAACTCAGC 341963 i viivi v i vv v - v i v -- iv i i MIR3#SINE/MIR 19 AGAGAGAGCACGGACTGGGAGTCAGGAGACCTGGGTTCT--AGTCCCGGC 66 chr6qtel1M 341964 CC---CAATAACTT--TGTTTGCCTGTGAAAAAAATCACA-CAGTTCCCT 342007 i --- v ?-- v v iv iiv i- v- vi i MIR3#SINE/MIR 67 TCTGCCACTAACTNGCTGTGTGACCTTGGGCAAG-TCACTTCACCTCTCT 115 chr6qtel1M 342008 TGGCCTCACCTGTTACCTCACCTGTAAAATGGGTGTTTTTGGTCAACT-- 342055 v --- v i i v vv v iii iv -- MIR3#SINE/MIR 116 GGGCCTCA---GTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGA 162 chr6qtel1M 342056 TCTCTGACTTCCTTTATA-CTCT 342077 i vv i vi - MIR3#SINE/MIR 163 TCTCTAAGGTCCCTTCCAGCTCT 185 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 41.33 CpG sites = 25, Kimura (unadjusted) = 43.53 Transitions / transversions = 0.96 (25/26) Gap_init rate = 0.07 (12 / 162), avg. gap size = 1.33 (16 / 12) 29 14.20 0.00 0.00 chr6qtel1M 342777 342823 (657177) (GT)n#Simple_repeat 1 47 (0) m_b307s252i7 12836 chr6qtel1M 342777 GTGTGTGTGAGTGTGTGTGAGTTTGTGTGTGTTTGAGGGTGTGTGTG 342823 v v v v v v (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 47 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 15 16.57 4.88 0.00 chr6qtel1M 343558 343598 (656402) (ATTCAGA)n#Simple_repeat 1 43 (0) m_b307s252i8 12837 chr6qtel1M 343558 ATTCAGAAGTCAGTATTCAGTA-TGAG-ATTCACAAGTCAGAA 343598 v v v - v - v v (ATTCAGA)n#Si 1 ATTCAGAATTCAGAATTCAGAATTCAGAATTCAGAATTCAGAA 43 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 287 20.26 1.14 4.12 chr6qtel1M 347366 347540 (652460) C HERVIP10FH#LTR/ERV1 (4116) 986 817 m_b307s701i0 12838 chr6qtel1M 347366 TTTCTTTCTCTCTGTCAGTTTCTGTCTATGTCTCTCTGTGTTTCTCTG-- 347413 v v v v v ------ -- C HERVIP10FH#LT 986 TTTCTTTCTCTCTTTGACTTTCTGTCTCTCTCTCTCT------CTCTGAC 943 chr6qtel1M 347414 TGTCTCTCTGTCTCCTCTATCTCTCTATCTCCTTCCCTCTCTCTCTCTCT 347463 vi i - i iiv ii v i C HERVIP10FH#LT 942 TCCCTCTTTGTCTC-TCTGTCTCTTCCTCTCTCTGCCTCTCTCTCTCTTT 894 chr6qtel1M 347464 GTCTCACTCTTTCTCTCTATGTGTCTGTCTGCCTCTCTGCCTCTCTGTTT 347513 v v v v v v iv vi vi v i C HERVIP10FH#LT 893 GACTCCCTCTTTGTCTCTCTCTCTCCCTCTCTCTCTCTTTCTCTCTCTCT 844 chr6qtel1M 347514 CTCTGTGTCTCTGTCTCTCTCTCTCTT 347540 viv v C HERVIP10FH#LT 843 CTCTTCCTCTCTCTCTCTCTCTCTCTT 817 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 23.60 CpG sites = 13, Kimura (unadjusted) = 23.60 Transitions / transversions = 0.62 (13/21) Gap_init rate = 0.05 (8 / 174), avg. gap size = 1.12 (9 / 8) 22 0.00 0.00 0.00 chr6qtel1M 348150 348173 (651827) (CA)n#Simple_repeat 1 24 (0) m_b307s252i9 12839 chr6qtel1M 348150 CACACACACACACACACACACACA 348173 (CA)n#Simple_ 1 CACACACACACACACACACACACA 24 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 24 6.79 0.00 0.00 chr6qtel1M 348743 348773 (651227) (A)n#Simple_repeat 1 31 (0) m_b307s252i10 12840 chr6qtel1M 348743 AAAACCAAAAAAAAAAAAAAAAAAAAAAAAA 348773 vv (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 31 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 349 26.35 3.31 1.96 chr6qtel1M 349855 350005 (649995) L1M6_5end#LINE/L1 2363 2515 (0) m_b307s551i2 12841 chr6qtel1M 349855 AAGTTGGCAAG--TAATAGCAAAC-TGGTAATTTTAACCATAAATGTGAA 349901 v i i-- v v - ivi i v i v i L1M6_5end#LIN 2363 AAGATGACAAANATAAGACCAAACATATCAGTTATGACAATAAATGTAAA 2412 chr6qtel1M 349902 TGGGGTAAACTGCCCCAT--AGAGAGGAAGTGGTTAGAGAATGGATTAAA 349949 v v i -- i vi -iv ivv v i L1M6_5end#LIN 2413 TGGGTTAAACTCCCCTATTAAAAGACAAAG-ACTCTCAGATTGGGTTAAA 2461 chr6qtel1M 349950 AGCCAGAATCCTGCAATATGTTGTTGACAGGAAACACACCTGAAGCAAGG 349999 iv i vi v i v i i i vv -- L1M6_5end#LIN 2462 AAACAAAATCCAACTATATGCTGTTTACAAGAGACACACCTAAATAAA-- 2509 chr6qtel1M 350000 AGATAC 350005 L1M6_5end#LIN 2510 AGATAC 2515 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 32.85 CpG sites = 20, Kimura (unadjusted) = 32.85 Transitions / transversions = 1.05 (20/19) Gap_init rate = 0.04 (6 / 150), avg. gap size = 1.33 (8 / 6) 350 23.53 2.46 2.46 chr6qtel1M 349879 350000 (650000) L1MEh_5end#LINE/L1 2113 2234 (1) m_b307s551i3 12841 chr6qtel1M 349879 GTAATTTTAACCATAAATGTGAATGGGGTAAACTGCCCCATAGAGAGGAA 349928 --- v i v vv v vi i iv L1MEh_5end#LI 2113 GTAATT---ACAATAAATGTAAATGGGTTAAACTCACCAATTAAAAGACA 2159 chr6qtel1M 349929 GTGGTTA-GAGAATGGATTAAAAGCCAGAATCCTGCAATATGTTGTTGAC 349977 v i ?-v v ? iv i vi i iv L1MEh_5end#LI 2160 GAGATTNTCAGATTGGATTNAAAAACAAAATCCAACAATATGCTGTCTAC 2209 chr6qtel1M 349978 AGGAAACACACCTGAAGC--AAGGA 350000 i i i i i -- L1MEh_5end#LI 2210 AAGAGACACACTTAAAACANAAGGA 2234 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 29.19 CpG sites = 15, Kimura (unadjusted) = 29.19 Transitions / transversions = 1.15 (15/13) Gap_init rate = 0.04 (5 / 121), avg. gap size = 1.20 (6 / 5) 2176 30.29 3.89 3.95 chr6qtel1M 349892 351589 (648411) L1M5_orf2#LINE/L1 38 1734 (1560) m_b307s551i4 12841 chr6qtel1M 349892 TAAATGTGAATGGGGTAAACTGCCCCATAGAGAGGAAGTGGTTA-GAGAA 349940 i ?v vvi v vi i v v i i-v v L1M5_orf2#LIN 38 TAAATGTAAATGGNCTAAACACTCCAATTAAAAGGCAGAGATTGTCAGAC 87 chr6qtel1M 349941 TGGATTAAAAGCCAGAATCCTGCAATATGTTGTTGACAGGAAACACACCT 349990 v iv ii i vi v i iv i i i i L1M5_orf2#LIN 88 TGGATAAAAAAACAAGACCCAACTATATGCTGTCTACAAGAGACGCACTT 137 chr6qtel1M 349991 GAAGCAAGGAGATACATGCAGAATAAAGGTAAAAGGTTGAAGCAGAATCT 350040 v ii vii i vi? iv i i v i iv ii v L1M5_orf2#LIN 138 TAAATATAAAGACACAGANAGGTTGAAAGTAAAAGGATGGAAAAAGATAT 187 chr6qtel1M 350041 ACCATGCTTCAGGTGAAGTCAAA-AAAGCAGGGGTAGCCATCCTGATCTC 350089 v-v viiv ?iv - v ? i i vi i v L1M5_orf2#LIN 188 ACCATGCA-AACACTAANCAAAAGAAAGCTGGNGTGGCTATATTAATATC 236 chr6qtel1M 350090 AGATCAAGCA------AAAGCAAAAATTGATCTAATTAAAAGAGATAAGG 350133 iv i ------ i i --- --- vv i L1M5_orf2#LIN 237 AGACAAAGTAGACTTCAAGGCAAGAA---AT---ATTACCAGAGATAAAG 280 chr6qtel1M 350134 AAGGGCACTATATCTTGCTAAA-GGGTAGCATAGATAATCAAGCA---AT 350179 i i i vi vv v - ----i iv v v --- L1M5_orf2#LIN 281 AGGGACATTTCATAATGATAAAAGGGT----CAATTCATCAAGAAGACAT 326 chr6qtel1M 350180 ATCAATATTAAACATATATGCACCAAGTAGTGTGGCAAGTAAATTCTTAA 350229 v vi ii i v i iiivi vvvv v v i L1M5_orf2#LIN 327 AACAATCCTAAATGTGTATGCACCTAATAACAGAGCTTCAAAATACATGA 376 chr6qtel1M 350230 AAGAGAAATTAAGAGAGCTGCAAGAAGATATAGACTGCAAAACCATAATA 350279 iv i i i v i iv i v --- v i v L1M5_orf2#LIN 377 AGCAAAAACTGACAGAACTAAAAGGAGAAATAGAC---AAATCCACAATT 423 chr6qtel1M 350280 GTGGGAGAAGATCTCAACCTTGCACTCTCAGCATTAGATAAATCAAAC-- 350327 i i v? i i i vi?v v i v v i v ii-- L1M5_orf2#LIN 424 ATAGTNGGAGATTTTAACACNCCTCTCTCAGTAATTGATAGAACAAGTAG 473 chr6qtel1M 350328 -TACAAAATAAATAAGAAAAAAGTCAAAGAGATAAATAGAATACTAGAAA 350376 -i v v i i v v --- vv i i -- i vv L1M5_orf2#LIN 474 ACAAAAAATCAGTAAGGATATAG---AAGATTTGAACA--ACACTATCAA 518 chr6qtel1M 350377 --AGTTAGATATGATACATCTTTGGAGAAAACTAAAT--AGAGACAGAAA 350422 -- ii v iv i vv iv iv v ?v i-- ivi ? v - L1M5_orf2#LIN 519 CCAACTTGACCTAATTGACATTTATAGAACACTNCACCCAACAACNGCA- 567 chr6qtel1M 350423 GGAGTACACTTTCTTCTCAGCAGTTCATGGAACCTATACAAAAATTGACC 350472 - i v i ivv iv v v v i v L1M5_orf2#LIN 568 -GAATACACATTCTTTTCAAGTGCACATGGAACATTTACCAAGATAGACC 616 chr6qtel1M 350473 ATATATTAGGACATAAAA---ACCTCAA---ACTCAAA-----TGCAGTA 350511 ?i i v ---ii --- i i? ----- v i v L1M5_orf2#LIN 617 ATATNCTGGGCCATAAAACAAGTCTCAATAAATTTNAAAGGATTGAAATC 666 chr6qtel1M 350512 ATGCAGAAATAGTAAATGCATCCTTTTCAGACCACGATGCAATGAAAATT 350561 i ---- -- ----- i v i v v v v L1M5_orf2#LIN 667 ATACAGA----GTA--TG-----TTCTCTGACCACAATGGAATTAAATTA 705 chr6qtel1M 350562 ACAGTCAATAA-------ATAGCCAGGGAAAAATAAACCAAAAAATAATT 350604 iv i ------- ? i --- vv- --- v L1M5_orf2#LIN 706 GAAATCAATAACAAAAAGATANCTAG---AAAATCC-CCAAA---TATTT 748 chr6qtel1M 350605 GGAAACTAAATAATCTCA-TACTAAAGAATGTGTGGG-GAAACAGCAAAT 350652 i i - v - v v ivii -v v iv L1M5_orf2#LIN 749 GGAAATTAAACAA-CACACTTCTAAATAACCCATGGGTCAAAGAAGAAAT 797 chr6qtel1M 350653 TGTTGACATAATTAATAACTTCACCCAAGAAAATGACAATAATGAGACAT 350702 iiivi?viv iv v viviiv vvi ? i vi v v L1M5_orf2#LIN 798 CACAANGGAAATTAGAAAATATTTTGAACTGAATGANAATGAAAATACAA 847 chr6qtel1M 350703 CATACCAAAATGTGTGGGATTTAGCCAAAGCAGTAATAAGGGGAAATTTT 350752 i v vi i iv v i i v L1M5_orf2#LIN 848 CATATCAAAATTTGTGGGATGCAGCTAAAGCAGTGCTTAGAGGGAAATTT 897 chr6qtel1M 350753 ATATCTCTAGAGGTCTACTTGCATAAAATAGAGAA--AGAGAGGGTCAAA 350800 v ?i i -------- ? v v i -- i v i L1M5_orf2#LIN 898 ATAGCNTTAAA--------TGCNTATATTAGAAAAGAAGAAAGGCTTAAA 939 chr6qtel1M 350801 ------GAATTAGGCTTACAGATTAAAAAGCTAGAAAAAAAAAA-CAAAT 350843 ------ vi i v vv i i i - L1M5_orf2#LIN 940 ATCAATGATCTAAGCTTCCACCTTAAGAAGCTAGAAAAAGAAGAGCAAAT 989 chr6qtel1M 350844 TAAAAACA--CCCAGTCAAACATTAACTTGAAATTTTAAAAATAAAAGAA 350891 vv --v?v vi vi-- v-- vv i i v L1M5_orf2#LIN 990 TAAACCCAAAGNAAGTAGAAGG--AAG--GAAATAATAAAGATAAGAGCA 1035 chr6qtel1M 350892 GAGATTAATAAAACTGAAAGTAACAAAAAAACTATTGAATTAATAAATAA 350941 i i i iv --- ? ? v v ivv v ii L1M5_orf2#LIN 1036 GAAATCAATGAAATAGAAA---ACAAANANACAATAGAGAAAATCAACGA 1082 chr6qtel1M 350942 AACTAAAAGTTGGTTTTGTGAAAAGAAAAACAACAAAATATATATAAATC 350991 i i i i v v--- i - i- i L1M5_orf2#LIN 1083 AGCCAAAAGCTGGTTCTTTGAAAAGAT---CAATAAAAT-TG-ATAAACC 1127 chr6qtel1M 350992 TTCAGTAAATGTGATTTAAAAGAAAAGAG-GAAAAT-TAAATTGTTAGTC 351039 ii i? ivv iv i i - i i-i iii i v L1M5_orf2#LIN 1128 TCTAGCNAGACTGATCAAGAAAAAAAGAGAGAAGACACAAATTACCAATA 1177 chr6qtel1M 351040 ATAAAAATGAGAAGGGAGAGGTTGCCACTAATGAAAAGAAAATTAGAGCA 351089 vi ii i i vi ii i vi vvv vii v i ivi L1M5_orf2#LIN 1178 TCAGGAATGAAAAAGGAGACATCACTACAGATCCTACAGACATTAAAAGG 1227 chr6qtel1M 351090 ATAATTAGGAGTTACTTTGTCCAACTTTATGCCAATAAATCAGATAA--- 351136 v iiiv i v vv iv ? --- L1M5_orf2#LIN 1228 ATAATAAGAGAATATTATGAACAACTTTATGCCAATAAATTTGANAACTT 1277 chr6qtel1M 351137 --ATGAAATGGAAGAATATCTTCAAAAATATAGCTTACCCAAATTAACAG 351184 -- vi vi v i i i? v i i ?v L1M5_orf2#LIN 1278 AGATGAAATGGACAAATTCCTTGAAAAACACAANTTACCAAAACTGACNC 1327 chr6qtel1M 351185 AGGAAGAAGTAAAATGGTTAAGCCATCCCATTTTAGAAAAAGAAATAGAA 351234 i i i vivi i iivii i v ivivv v L1M5_orf2#LIN 1328 AAGAAGAAATAGAAAATCTGAATAGCCCTATATCTATTAAAGAAATTGAA 1377 chr6qtel1M 351235 TAAGCTATTACTCAACACT---CTAAGAAAAAATCCCCAGGACCAAATGG 351281 vv iv --- v i--- i vi i v i v i L1M5_orf2#LIN 1378 TTTGTAATTA---AAAACCTTCCCACAAAGAAAACTCCAGGCCCAGATGG 1424 chr6qtel1M 351282 ATTTACATGTAAATTCTACCAAATATTTAA---AGAATTAACTCCAATGA 351328 v i vv i i --- v iv vv L1M5_orf2#LIN 1425 CTTCACTGGTGAATTCTACCAAACATTTAAGGAAGAAATAATACCAATCT 1474 chr6qtel1M 351329 TATATAAACTATTTGAAAAAAATAGGGATTGAAGGAGTCCTATCAAATTC 351378 i i v iv i - ii vv i iiv vi v i L1M5_orf2#LIN 1475 TACACAAACTCTTCCAGAAAA-TAGAAAAAGAGGGAACACTTCCCAACTC 1523 chr6qtel1M 351379 CTTTCATGAC-CCAGACATGATACTGATACCTAAACCAGGTAGGTTGAAA 351427 v i v- - ? iv v ? ii ii-- v L1M5_orf2#LIN 1524 ATTTTATGAGGCCAG-CATNACCCTGATACCAAAACCNGACAAA--GACA 1570 chr6qtel1M 351428 --ACAGAGAAAGAAAATTATAGACCAATCTTCCTAATGAATATTGATGCT 351475 -- iii i v i v i v v L1M5_orf2#LIN 1571 TTACAAGAAAAGAAAATTACAGACCAATATCCCTCATGAACATAGATGCA 1620 chr6qtel1M 351476 AAAATCATAAATACAATATTAGCAAAAAGATTAGAGAAAATCATCACCAG 351525 v ? i v vv v vv v vvi v vv L1M5_orf2#LIN 1621 AAAATCCTNAACAAAATATTAGCAAATCGAATCCAGCAATATATAAAAAG 1670 chr6qtel1M 351526 GATAATACACTATGAGCAAGTAAATTTTATACCAAGAATGTAGGGCTGAT 351575 ii v iiiv v i i i i i L1M5_orf2#LIN 1671 GATAATACATCATGACCAAGTGGGGTTTATCCCAGGAATGCAAGGTTGGT 1720 chr6qtel1M 351576 TCAATATTAGGAAA 351589 i i v i L1M5_orf2#LIN 1721 TTAACATTCGAAAA 1734 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 40.14 CpG sites = 264, Kimura (unadjusted) = 40.37 Transitions / transversions = 1.15 (264/230) Gap_init rate = 0.06 (94 / 1697), avg. gap size = 1.41 (133 / 94) 12 26.18 4.48 2.94 chr6qtel1M 353844 353910 (646090) (ATAATT)n#Simple_repeat 1 68 (0) m_b307s252i11 12842 chr6qtel1M 353844 ATAATTATAAGTTATTGTTGAT-ATTGCTATAGTAATTTTACTAAT-ATT 353891 - vi - - iiv vi v v v - (ATAATT)n#Sim 1 ATAATTATAA-TTATAATT-ATAATTATAATTATAATTATAATTATAATT 48 chr6qtel1M 353892 TGCATTATAA-TAAAATTAT 353910 vvv - v (ATAATT)n#Sim 49 ATAATTATAATTATAATTAT 68 Matrix = Unknown Transitions / transversions = 0.40 (4/10) Gap_init rate = 0.08 (5 / 66), avg. gap size = 1.00 (5 / 5) 441 22.15 3.33 5.98 chr6qtel1M 354256 354375 (645625) MIRc#SINE/MIR 11 127 (141) m_b307s601i2 12843 chr6qtel1M 354256 TGGCTCAGTGGAGAGA--AGTATCCCTGAAGTCAGGAGGACCTAAGTTCA 354303 iv i -- v ivv i i i ii i MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr6qtel1M 354304 AATCCAGCCTCACACATTTAGTAGTTACTAGTTTTGTGACCCTGGGCAAG 354353 i v v ------- ivi v i v i MIRc#SINE/MIR 61 AGTCCCGGCTC-------TGCCACTTACTAGCTGTGTGACCTTGGGCAAG 103 chr6qtel1M 354354 TCATTTAACC-CCCTG-GCCTCAG 354375 i - i - MIRc#SINE/MIR 104 TCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 25.64 CpG sites = 16, Kimura (unadjusted) = 26.87 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.08 (10 / 119), avg. gap size = 1.10 (11 / 10) 300 34.31 5.29 0.56 chr6qtel1M 354587 354756 (645244) MIR3#SINE/MIR 19 196 (12) m_b307s601i3 12844 chr6qtel1M 354587 AGAGAGGGAACTAAATAGCAGGCAGAGAGCCTAGGCACTGAAATGCAGCC 354636 i v vi v i v v iiii i iv - iviv i i MIR3#SINE/MIR 19 AGAGAGAGCACGGACTGGGAGTCAGGAGACCTGGGTTCT-AGTCCCGGCT 67 chr6qtel1M 354637 C---CAATAACTTCCTTTG--ACTGTGAAAAACTCACA-CAGTTCCCTTG 354680 --- v ?v v -- iv iiv v v- vi i v MIR3#SINE/MIR 68 CTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGG 117 chr6qtel1M 354681 GCCTCAGTTACCTCACCTATAAAATGATTGCTTTTGGTCAACT--TCTCT 354728 v i i vv vv v iii iv -- MIR3#SINE/MIR 118 GCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCT 167 chr6qtel1M 354729 GA-CTTCCTTTAAGCTCTATAATCCTCTG 354756 i -v i iv ivv i v MIR3#SINE/MIR 168 AAGGTCCCTTCCAGCTCTGACATTCTATG 196 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 45.96 CpG sites = 29, Kimura (unadjusted) = 47.06 Transitions / transversions = 1.00 (29/29) Gap_init rate = 0.04 (6 / 169), avg. gap size = 1.67 (10 / 6) 18 4.71 0.00 0.00 chr6qtel1M 356080 356101 (643899) (T)n#Simple_repeat 1 22 (0) m_b307s252i12 12845 chr6qtel1M 356080 TTTTTTGTTTTTTTTTTTTTTT 356101 v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTT 22 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 15 16.57 4.88 0.00 chr6qtel1M 356253 356293 (643707) (ATTCAGA)n#Simple_repeat 1 43 (0) m_b307s252i13 12846 chr6qtel1M 356253 ATTCAGAAGTCAGTATTCAGTA-TGAG-ATTCACAAGTCAGAA 356293 v v v - v - v v (ATTCAGA)n#Si 1 ATTCAGAATTCAGAATTCAGAATTCAGAATTCAGAATTCAGAA 43 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 83 27.97 0.42 0.84 chr6qtel1M 360064 360303 (639697) (TCTC)n#Simple_repeat 1 239 (0) m_b307s252i14 12847 chr6qtel1M 360064 TCTTTCTCTCTGTCAGTCTCTGTGTAGCTGTCTC-CTTGCTCTCTCTGTG 360112 i v vv v v vv v - iv v v (TCTC)n#Simpl 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr6qtel1M 360113 TCTCTCTGTCTCTCCCTATCTCTGCGTGTGTGTCTGTCTGTTTGTCTCTT 360162 v i v - - v v v v v i v i (TCTC)n#Simpl 51 TCTCTCTCTCTCTCTCTCTCTCT-C-TCTCTCTCTCTCTCTCTCTCTCTC 98 chr6qtel1M 360163 TCGCTCTCTTAGTCTCTTTCTCTCTCTGTCTCTGTCTCTGTCTCTCTGTC 360212 v ivv i v v v v (TCTC)n#Simpl 99 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 148 chr6qtel1M 360213 TCACTCTGTCTTTCTTTCTGTCTCTCTGTCTGTCTCTGTGTGTGTGTCTG 360262 v v i i v v v v v v v v v (TCTC)n#Simpl 149 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 198 chr6qtel1M 360263 TCTTTCTGTCTGCCTCTCTGTGTCTCTGTCTCCCTATCTCT 360303 i v vi v v v i v (TCTC)n#Simpl 199 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 239 Matrix = Unknown Transitions / transversions = 0.28 (12/43) Gap_init rate = 0.01 (3 / 239), avg. gap size = 1.00 (3 / 3) 61 3.19 0.00 0.00 chr6qtel1M 361331 361394 (638606) (C)n#Simple_repeat 1 64 (0) c_b307s251i1 12848 chr6qtel1M 361331 CCCCCCCCCCCCCCCCCCCCCCCCTCCCCCCCACCCCCCCCCCCCCCCCC 361380 i v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 50 chr6qtel1M 361381 CCCCCCCCCCCCCC 361394 (C)n#Simple_r 51 CCCCCCCCCCCCCC 64 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0) 15 21.12 1.61 6.78 chr6qtel1M 362903 362964 (637036) (GAAAAG)n#Simple_repeat 1 59 (0) m_b307s252i15 12849 chr6qtel1M 362903 GAAAAGGGAGAAGGGAAAATTGAAAAGG-GAAGGAATAAGCTAAGTGGAA 362951 - - i -v -i - vv iv i (GAAAAG)n#Sim 1 GAAAA-GGA-AAAGGAAAA-GGAAAAGGAAAAGGAA-AAGGAAAAGGAAA 46 chr6qtel1M 362952 GGGAATAGGAAAA 362964 i v (GAAAAG)n#Sim 47 AGGAAAAGGAAAA 59 Matrix = Unknown Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.08 (5 / 61), avg. gap size = 1.00 (5 / 5) 256 28.46 12.93 1.55 chr6qtel1M 363081 363312 (636688) L1MEc_5end#LINE/L1 2221 2478 (49) m_b307s551i5 12850 chr6qtel1M 363081 AAGGAGGAAGGAAGGGAGAAAAGTATAAA----CAG--GGGTTAACAAGA 363124 i v i ii i v v ---- -- vi vv L1MEc_5end#LI 2221 AAGAAGGCAGAAAAAGAAAAAAGGAAAAAAGAACAGATGGGACAAATAGA 2270 chr6qtel1M 363125 TGGCATGTAATAGCAAACTGGTAGTTTTAA-CCC---------------- 363157 vii --- iv v - ---------------- L1MEc_5end#LI 2271 AAACA---AATAGCAAGATGGTAGATTTAAACCCAACCATATCAATAATC 2317 chr6qtel1M 363158 ----TAAATGTGAATGAGGGTAAACTGCCCCATAGAGAGGAAGTGGTTA- 363202 ---- i - vv vv v vi i v v i i- L1MEc_5end#LI 2318 ACATTAAATGTAAATG-GTCTAAACACCCCAATTAAAAGGCAGAGATTGT 2366 chr6qtel1M 363203 GAGAATGAATTAAAAGCCTTAATCCTACAATATGTTGTTTACAGGAAACA 363252 v v i v iv vvi i v v i ii i ? L1MEc_5end#LI 2367 CAGATTGGATAAAAAAGCAAGACCCAACTATATGCTGCCTACAAGAAACN 2416 chr6qtel1M 363253 CAGCTGAAGCAGGAAGATACACACAG--TAAAGGTAAAAGGTTGTAGCAG 363300 vi v ii vi i v i -- i v v iv i L1MEc_5end#LI 2417 CACTTTAAATATAAAGACACAAATAGGTTAAAAGTAAAAGGATGGAAAAA 2466 chr6qtel1M 363301 AATCTACCATGC 363312 i v L1MEc_5end#LI 2467 GATATACCATGC 2478 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.46 CpG sites = 32, Kimura (unadjusted) = 36.46 Transitions / transversions = 0.97 (32/33) Gap_init rate = 0.04 (10 / 231), avg. gap size = 3.40 (34 / 10) 308 26.49 3.23 2.56 chr6qtel1M 363118 363272 (636728) L1M6_5end#LINE/L1 2360 2515 (0) m_b307s551i6 12850 chr6qtel1M 363118 AACAAGATGGCA--TGTAATAGCAAAC-TGGTAGTTTTAACCCTAAATGT 363164 i? i --?i v v - ivi v i vv L1M6_5end#LIN 2360 AGNAAGATGACAAANATAAGACCAAACATATCAGTTATGACAATAAATGT 2409 chr6qtel1M 363165 GAATGAGGGTAAACTGCCCCAT--AGAGAGGAAGTGGTTAGAGAATGAAT 363212 i - v v i -- i vi -iv ivv v ii L1M6_5end#LIN 2410 AAATG-GGTTAAACTCCCCTATTAAAAGACAAAG-ACTCTCAGATTGGGT 2457 chr6qtel1M 363213 TAAAAGCCTTAATCCTACAATATGTTGTTTACAGGAAACACAGCTGAAGC 363262 iv vv v v i i i v i vv L1M6_5end#LIN 2458 TAAAAAACAAAATCCAACTATATGCTGTTTACAAGAGACACACCTAAATA 2507 chr6qtel1M 363263 AGGAAGATAC 363272 -- L1M6_5end#LIN 2508 A--AAGATAC 2515 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 33.48 CpG sites = 19, Kimura (unadjusted) = 33.48 Transitions / transversions = 0.90 (19/21) Gap_init rate = 0.05 (7 / 154), avg. gap size = 1.29 (9 / 7) 2486 30.26 3.72 2.99 chr6qtel1M 363158 364850 (635150) L1M5_orf2#LINE/L1 38 1742 (1552) m_b307s551i7 12850 chr6qtel1M 363158 TAAATGTGAATGAGGGTAAACTGCCCCATAGAGAGGAAGTGGTTA-GAGA 363206 i - ?v vvi v vi i v v i i-v L1M5_orf2#LIN 38 TAAATGTAAATG-GNCTAAACACTCCAATTAAAAGGCAGAGATTGTCAGA 86 chr6qtel1M 363207 ATGAATTAAAAGCCTTAATCCTACAATATGTTGTTTACAGGAAACACAGC 363256 v i v iv vvi i v v i i i i i vi L1M5_orf2#LIN 87 CTGGATAAAAAAACAAGACCCAACTATATGCTGTCTACAAGAGACGCACT 136 chr6qtel1M 363257 TGAAGCAGGAAGATACACACAG--TAAAGGTAAAAGGTTGTAGCAGAATC 363304 v ii vi i v ? -- i i v v iv ii v L1M5_orf2#LIN 137 TTAAATATAAAGACACAGANAGGTTGAAAGTAAAAGGATGGAAAAAGATA 186 chr6qtel1M 363305 TACCATGCTTCAGGTGAAGTAAAA-AAAGCAGGGGTAGCCATCCTGATCT 363353 v-v viiv ?i - v ? i i vi i v L1M5_orf2#LIN 187 TACCATGCA-AACACTAANCAAAAGAAAGCTGGNGTGGCTATATTAATAT 235 chr6qtel1M 363354 CAGATCAAGCA------AAAGCAAAAATTGATCTAATTAAAAGAGATAAG 363397 iv i ------ i i --- --- vv i L1M5_orf2#LIN 236 CAGACAAAGTAGACTTCAAGGCAAGAA---AT---ATTACCAGAGATAAA 279 chr6qtel1M 363398 GAAGGGCACTATATCTTGCTAAA-GGGTAGCATAGATAATCAAGCA---A 363443 i i i vi vv v - ----i iv v v --- L1M5_orf2#LIN 280 GAGGGACATTTCATAATGATAAAAGGGT----CAATTCATCAAGAAGACA 325 chr6qtel1M 363444 TATCAATATTAAACATATATGCACCAAGTAGTGTAGCATTTAAATTCTTA 363493 v vi ii i v i iiiv v iv v v i L1M5_orf2#LIN 326 TAACAATCCTAAATGTGTATGCACCTAATAACAGAGCTTCAAAATACATG 375 chr6qtel1M 363494 AAAGAGAAATTAAGAGAGCTGCAAGAAGAAATAGACAG---CAAAAGTAT 363540 iv i i i v i iv i i--- v v L1M5_orf2#LIN 376 AAGCAAAAACTGACAGAACTAAAAGGAGAAATAGACAAATCCACAATTAT 425 chr6qtel1M 363541 AATATTGGGTGATCTCAACCTTGCATCCTGAG-AATTAGATAAATCAAAC 363589 i--- ? v i i vi?v vii v - - i v ii L1M5_orf2#LIN 426 AG---TNGGAGATTTTAACACNCCTCTCTCAGTAATT-GATAGAACAAGT 471 chr6qtel1M 363590 ---CATAAAATAAATAAGAA---AGAA---TTAATAGAATACTAGAAA-- 363628 --- v v i i --- --- i - v i vv -- L1M5_orf2#LIN 472 AGACAAAAAATCAGTAAGGATATAGAAGATTTGA-ACAACACTATCAACC 520 chr6qtel1M 363629 AGTTAGATATGATAGATCTTTGGAGAA-AATGAAATGGAC-ACAGAAAGG 363676 ii v iv i v iv iv - v ?v vivi - ? v -- L1M5_orf2#LIN 521 AACTTGACCTAATTGACATTTATAGAACACTNCACCCAACAACNGCA--G 568 chr6qtel1M 363677 AATACACTTTCTTCTCAGCAGCTCATGGAACCTATACAAAAATAGACCAT 363726 v i ivv v v v v i L1M5_orf2#LIN 569 AATACACATTCTTTTCAAGTGCACATGGAACATTTACCAAGATAGACCAT 618 chr6qtel1M 363727 ATATTAGGACATAAAAACATCAAA-CTC---AAATGCAGGAAGGCAGAAA 363772 ?i i v ---- i- --- vi?ii i iiv L1M5_orf2#LIN 619 ATNCTGGGCCATAAAA----CAAGTCTCAATAAATTTNAAAGGATTGAAA 664 chr6qtel1M 363773 TAGTA-AATGCATCTTTTTCAGACCATGATGCAGTGAAAATTACACTC-- 363819 vi - iv i v- i v ii v i v v viv v -- L1M5_orf2#LIN 665 TCATACAGAGTATG-TTCTCTGACCACAATGGAATTAAATTAGAAATCAA 713 chr6qtel1M 363820 -AACAGAAA-ACAAGGGGGAAATGGACCAAAAATTAATTGGAAACTAAAT 363867 - i - i ?vvi i vv- --- v i i L1M5_orf2#LIN 714 TAACAAAAAGATANCTAGAAAATCC-CCAAA---TATTTGGAAATTAAAC 759 chr6qtel1M 363868 AATCTCA-TACTAAAGAATGATTGGGTAAAACAGTAAATTGTACACATAA 363916 - v - v v ivvv v v iv iii v?viv L1M5_orf2#LIN 760 AA-CACACTTCTAAATAACCCATGGGTCAAAGAAGAAATCACAANGGAAA 808 chr6qtel1M 363917 TT---AATCACTTCACCCAAGAAAATGACAATAATGAGACATCATACCAA 363963 --- vi i ii--- vvi ? i vi v v i L1M5_orf2#LIN 809 TTAGAAAATATTTTG---AACTGAATGANAATGAAAATACAACATATCAA 855 chr6qtel1M 363964 AATGTGTAGGATACAGCCAAAGCGGTAA-TAAAGGGAAATTTTATATCAC 364012 v i i i i iv- i - v ?i L1M5_orf2#LIN 856 AATTTGTGGGATGCAGCTAAAGCAGTGCTTAGAGGGAAA-TTTATAGCNT 904 chr6qtel1M 364013 TAGAGGCCTACTTGCATAAAATATAAAAAGAG---AAGGTCAATGAATTG 364059 i v ? iv --- i v v i ii --- ii vi i L1M5_orf2#LIN 905 TAAATGCNTATAT---TAGAAAAGAAGAAAGGCTTAAAATCAATGATCTA 951 chr6qtel1M 364060 GGTTTGCAACTAAAAATGCTAGAAAAGGAA---CAAATTAAAAATCCCCA 364106 i i v v v i v i --- --- v L1M5_orf2#LIN 952 AGCTTCCACCTTAAGAAGCTAGAAAAAGAAGAGCAAATTAAA---CCCAA 998 chr6qtel1M 364107 GTCAAACACTAAACTTGAAATTCTAAAAATGAAATGAGAGATTGATAACA 364156 iv? ii vv iivvv vv i i i vv i ii i v L1M5_orf2#LIN 999 AGNAAGTAGAAGGAAGGAAATAATAAAGATAAGAGCAGAAATCAATGAAA 1048 chr6qtel1M 364157 TTGAAAGTAAAAAAAGCTATTGAATTAATTAATAAAACTAAGAGTTGGTT 364206 v ii ? ? - v v ivv i ii i i i i L1M5_orf2#LIN 1049 TAGAAAACAAANANA-CAATAGAGAAAATCAACGAAGCCAAAAGCTGGTT 1097 chr6qtel1M 364207 CTATGAAAAAA-CAACAAAATAGATAAACCCTTAGCAAATCTGATTTAAA 364255 v i - i v ii ? iv iv i L1M5_orf2#LIN 1098 CTTTGAAAAGATCAATAAAATTGATAAACCTCTAGCNAGACTGATCAAGA 1147 chr6qtel1M 364256 AAAGGAGAGAGGAAAATCAAATTGTTAGTCTTAAAAATGAAAAGGGAGAA 364305 ii i i vv iii i v i ii i v L1M5_orf2#LIN 1148 AAAAAAGAGAGAAGACACAAATTACCAATATCAGGAATGAAAAAGGAGAC 1197 chr6qtel1M 364306 CTCGCCACTAATGAAGAGGAAATTAGAGCAATAATTAGAAGTTACTTTGA 364355 v i i vi vvvivi v i ivi v iiv i v L1M5_orf2#LIN 1198 ATCACTACAGATCCTACAGACATTAAAAGGATAATAAGAGAATATTATGA 1247 chr6qtel1M 364356 CCAACTTTATGCCAATCAATTCAACAAGTTAAATGAAATGGAAGAATACC 364405 v v ii ? v i vi v L1M5_orf2#LIN 1248 ACAACTTTATGCCAATAAATTTGANAACTTAGATGAAATGGACAAATTCC 1297 chr6qtel1M 364406 TTCAAAAATATAGCTTGCCCAGATTAACAGAGGAAGAAGTAAATATCCTA 364455 v i i i? i v i i i ?v i i i v vi i L1M5_orf2#LIN 1298 TTGAAAAACACAANTTACCAAAACTGACNCAAGAAGAAATAGAAAATCTG 1347 chr6qtel1M 364456 AACAGTCCCATCTTAGAAAAAGAAATAGAACAGGCTATTAGCCAACTCCC 364505 i i i v ivivv v ivv iv ivv v i L1M5_orf2#LIN 1348 AATAGCCCTATATCTATTAAAGAAATTGAATTTGTAATTAAAAACCTTCC 1397 chr6qtel1M 364506 TGAGAAAAAATCCCCGGGACCAGATGGATTTACATGTGAATTCGACCAAA 364555 iivi i v i i v v i vv v L1M5_orf2#LIN 1398 CACAAAGAAAACTCCAGGCCCAGATGGCTTCACTGGTGAATTCTACCAAA 1447 chr6qtel1M 364556 CATTCAAAGAACAATTAACTCCAATGCTATATAAACTATTTGAAAACATA 364605 i i v v iv vi i i v iv i v L1M5_orf2#LIN 1448 CATTTAAGGAAGAAATAATACCAATCTTACACAAACTCTTCCAGAAAATA 1497 chr6qtel1M 364606 GGGAATGAAGGATTCCTACCAAATTCCCTTTATGACACAGAGATGGTACT 364655 ii v i viv v v i vi vi viiv ?iiv L1M5_orf2#LIN 1498 GAAAAAGAGGGAACACTTCCCAACTCATTTTATGAGGCCAGCATNACCCT 1547 chr6qtel1M 364656 GATACCTAAACCAGGTAGGTTGAAA--ACAGAGAAAGAAAATTATCGACC 364703 v ? ii ii-- v -- iii iv L1M5_orf2#LIN 1548 GATACCAAAACCNGACAAA--GACATTACAAGAAAAGAAAATTACAGACC 1595 chr6qtel1M 364704 AATCTCCCTAATGAATATTGATGCTAAAATCTTAAATAAAATGTTAGCAA 364753 v v i v v i ? i i L1M5_orf2#LIN 1596 AATATCCCTCATGAACATAGATGCAAAAATCCTNAACAAAATATTAGCAA 1645 chr6qtel1M 364754 A--------AACATTACAGAAAACCATCCCCAGGATAATACATTATGA-C 364794 -------- i v i v -------- i - L1M5_orf2#LIN 1646 ATCGAATCCAGCAATATATAAAA--------AGGATAATACATCATGACC 1687 chr6qtel1M 364795 AAGTAATTTTTTATACCCAGAATGCAGGGCTGGTTCAATAGTAGGAAAAC 364844 ii-vv v vi i i i i v v i v L1M5_orf2#LIN 1688 AAGTGG-GGTTTATCCCAGGAATGCAAGGTTGGTTTAACATTCGAAAATC 1736 chr6qtel1M 364845 TATTAA 364850 v i L1M5_orf2#LIN 1737 AATCAA 1742 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 40.17 CpG sites = 270, Kimura (unadjusted) = 40.39 Transitions / transversions = 1.19 (270/227) Gap_init rate = 0.05 (79 / 1692), avg. gap size = 1.44 (114 / 79) 16 9.98 0.00 5.88 chr6qtel1M 364890 364925 (635075) (TTTTG)n#Simple_repeat 1 34 (0) m_b307s252i16 12851 chr6qtel1M 364890 TTTTGTTTCTCTTACTGTTTTGTTTTGTTTTTTTTT 364925 - v -i v (TTTTG)n#Simp 1 TTTTGTTT-TGTT-TTGTTTTGTTTTGTTTTGTTTT 34 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 13 4.76 0.00 4.35 chr6qtel1M 365045 365068 (634932) (GGGA)n#Simple_repeat 1 23 (0) m_b307s252i17 12852 chr6qtel1M 365045 GGGAGGGGGTGGAGGGAGGGAGGG 365068 i - (GGGA)n#Simpl 1 GGGAGGGAG-GGAGGGAGGGAGGG 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 12 27.09 3.28 3.28 chr6qtel1M 366429 366489 (633511) (ATTT)n#Simple_repeat 1 61 (0) m_b307s252i18 12853 chr6qtel1M 366429 ATTT-TTAATTCTATTT-TCTGTCTCATGTGTTTATGTATTTCTTTGATT 366476 - v - - i i - i v i v v iv (ATTT)n#Simpl 1 ATTTATTTATT-TATTTATTTAT-TTATTTATTTATTTATTTATTTATTT 48 chr6qtel1M 366477 GTATATTTATGTA 366489 i v v (ATTT)n#Simpl 49 ATTTATTTATTTA 61 Matrix = Unknown Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.07 (4 / 60), avg. gap size = 1.00 (4 / 4) 85 9.79 0.00 0.00 chr6qtel1M 366903 367024 (632976) (TA)n#Simple_repeat 1 122 (0) c_b307s251i2 12854 chr6qtel1M 366903 TATATATATATATATATATATATATATATATATGTATATATATAAAGGCA 366952 i v vii (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr6qtel1M 366953 TATGTGTATGTGTGTATATATATATATATATATATATATATATATATATA 367002 i i i i i (TA)n#Simple_ 51 TATATATATATATATATATATATATATATATATATATATATATATATATA 100 chr6qtel1M 367003 TATATATATACATATATATATA 367024 i (TA)n#Simple_ 101 TATATATATATATATATATATA 122 Matrix = Unknown Transitions / transversions = 4.50 (9/2) Gap_init rate = 0.00 (0 / 121), avg. gap size = 0.0 (0 / 0) 36 28.14 0.00 3.91 chr6qtel1M 367475 367607 (632393) (TCTG)n#Simple_repeat 1 128 (0) m_b307s252i19 12855 chr6qtel1M 367475 TCTTTCTTTCTCTCTGTTGGTCTCCACCTTTCTAATCTGTCTGTCTGTCT 367524 v v v iv --ii v -i (TCTG)n#Simpl 1 TCTGTCTGTCTGTCTGTCTGTCT--GTCTGTCT-GTCTGTCTGTCTGTCT 47 chr6qtel1M 367525 CTGTCTCTGTCTGTCTCTCTCTGCATCTCTCATTCTCTTTGTGTATGTCT 367574 v v v v v - - v vvi v v v v (TCTG)n#Simpl 48 GTCTGTCTGTCTGTCTGTCTGT-C-TGTCTGTCTGTCTGTCTGTCTGTCT 95 chr6qtel1M 367575 GTCTGCCTCTCAGTCTCTCTGTTTCTCTGTGTG 367607 i v v v i v v (TCTG)n#Simpl 96 GTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTG 128 Matrix = Unknown Transitions / transversions = 0.32 (7/22) Gap_init rate = 0.04 (5 / 132), avg. gap size = 1.00 (5 / 5) 312 34.60 3.79 1.48 chr6qtel1M 371179 371310 (628690) C MIRc#SINE/MIR (97) 171 37 m_b308s601i0 12856 chr6qtel1M 371179 TAGGGAGTGC---TTTTATTATCTATATTTAACACTTGAGAAAACTGAGA 371225 v v --- v ivi v vv i i C MIRc#SINE/MIR 171 TAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGG 122 chr6qtel1M 371226 --CAGACAGAACTGAATGATATTGAGCATGGTTATGTAGATAATAAATCT 371273 -- v -ii i i i- vv v i iii v i i vv C MIRc#SINE/MIR 121 CTCAGAGAG-GTTAAGTGAC-TTGCCCAAGGTCACACAGCTAGTAAGTGG 74 chr6qtel1M 371274 CTGAAGTAAAGTTTGAAATCATGCCTTTCTAACTCCA 371310 v iviiiiii i vi v i i i C MIRc#SINE/MIR 73 CAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCA 37 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 45.29 CpG sites = 27, Kimura (unadjusted) = 48.46 Transitions / transversions = 1.50 (27/18) Gap_init rate = 0.03 (4 / 131), avg. gap size = 1.75 (7 / 4) 32 27.94 6.16 0.00 chr6qtel1M 371435 371580 (628420) (TATA)n#Simple_repeat 1 155 (0) m_b308s252i0 12857 chr6qtel1M 371435 TATAT-TAT-TATATACATTTATAT-TGCATGTAT-TTTATATATA-AGG 371479 - - i v - ii i - v - vi (TATA)n#Simpl 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr6qtel1M 371480 TATTGAT-TAATTATATAAATATGTATTTATGTGTAGA-AGATAAATATT 371527 vv - vv v i v i i v - v v v (TATA)n#Simpl 51 TATATATATATATATATATATATATATATATATATATATATATATATATA 100 chr6qtel1M 371528 TA-ATATATATTTGTGCATGTGTATAGATATTGAT-TATATCTATTCATA 371575 - v i ii i i v vv - v vi (TATA)n#Simpl 101 TATATATATATATATATATATATATATATATATATATATATATATATATA 150 chr6qtel1M 371576 TTTAT 371580 v (TATA)n#Simpl 151 TATAT 155 Matrix = Unknown Transitions / transversions = 0.70 (14/20) Gap_init rate = 0.06 (9 / 145), avg. gap size = 1.00 (9 / 9) 257 37.50 0.95 0.95 chr6qtel1M 373135 373239 (626761) C MIRc#SINE/MIR (153) 115 11 m_b308s601i1 12858 chr6qtel1M 373135 GAGAATCAATGACTAGGCTAGGGTAACACAACTATCAGGTGTTTGAAACT 373184 iv v i v v i i v i vi i viv iv v C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 66 chr6qtel1M 373185 GAATCAGTGTTCAAGT-TTCCTGACTCACAGATCTAGAATTCTATCTATT 373233 i iiv viii i - - ii i vii v i i C MIRc#SINE/MIR 65 GGACTCGAACCCAGGTCTTCCTGACTC-CAAGTCCAGTGCTCTTTCCACT 17 chr6qtel1M 373234 GAATCA 373239 v i C MIRc#SINE/MIR 16 GCACCA 11 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 55.05 CpG sites = 24, Kimura (unadjusted) = 55.05 Transitions / transversions = 1.60 (24/15) Gap_init rate = 0.02 (2 / 104), avg. gap size = 1.00 (2 / 2) 13 30.44 1.92 0.00 chr6qtel1M 373336 373387 (626613) (ATT)n#Simple_repeat 1 53 (0) m_b308s252i1 12859 chr6qtel1M 373336 ATTATTGTCGATATTATTGACATTATTAATAATAGTATAATTA-TAAAAT 373384 i iiv ivi v v v v - vv (ATT)n#Simple 1 ATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTAT 50 chr6qtel1M 373385 TAT 373387 (ATT)n#Simple 51 TAT 53 Matrix = Unknown Transitions / transversions = 0.62 (5/8) Gap_init rate = 0.02 (1 / 51), avg. gap size = 1.00 (1 / 1) 273 35.13 0.62 4.52 chr6qtel1M 373892 374052 (625948) MIRb#SINE/MIR 26 180 (88) m_b308s601i2 12860 chr6qtel1M 373892 AAAAGCACAGTAGCTACCTAGCAGTCAGAGAACAAGTGCATTGAAATACA 373941 i i -- --- v v v i- vv vi vi v v MIRb#SINE/MIR 26 AAGAGCACGG--GCT---TTGGAGTCAGACAG-ACCTGGGTTCGAATCCC 69 chr6qtel1M 373942 TCCTCAGTAAAACATAAGCTGTTTTAACTTTGAAAAATTCCCTAAGTGTC 373991 vv v iv vvi iv v v v v iv i v i vi- MIRb#SINE/MIR 70 GGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACC-TC 118 chr6qtel1M 373992 TCTGGATCTCAGTTCCCACACCTATAAAATGGGGGCTTTAG-ATCAACTT 374040 iii i v i i iivv i- i v i MIRb#SINE/MIR 119 TCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTACCT 168 chr6qtel1M 374041 CTCTGAATTGTT 374052 v v ii MIRb#SINE/MIR 169 CGCAGGGTTGTT 180 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 45.44 CpG sites = 25, Kimura (unadjusted) = 47.79 Transitions / transversions = 0.86 (25/29) Gap_init rate = 0.05 (8 / 160), avg. gap size = 1.00 (8 / 8) 274 34.14 4.03 0.78 chr6qtel1M 373959 374082 (625918) MIR3#SINE/MIR 81 208 (0) m_b308s601i3 12860 chr6qtel1M 373959 GCTGTTTTAACTTTGAAAAATTCCCTAAGTGTCTCTGGATCTCAGTTCCC 374008 v -i i iiv v v vviiv ii i MIR3#SINE/MIR 81 GCTGTGT-GACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCC 129 chr6qtel1M 374009 ACACCTATAAAATGGGGGCTTTAGATCAACT--TCTCTGAATTGTTTTCT 374056 v i i i vv i ii iv -- i iv vii i MIR3#SINE/MIR 130 TCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCC 179 chr6qtel1M 374057 -GCTCCGAA--TCTCTAAGTCTGAGATCC 374082 - i v-- v i v iv i MIR3#SINE/MIR 180 AGCTCTGACATTCTATGATTCTATGATTC 208 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 47.43 CpG sites = 25, Kimura (unadjusted) = 47.43 Transitions / transversions = 1.47 (25/17) Gap_init rate = 0.03 (4 / 123), avg. gap size = 1.50 (6 / 4) 124 12.43 0.52 0.00 chr6qtel1M 374087 374278 (625722) (AG)n#Simple_repeat 1 193 (0) m_b308s252i2 12861 chr6qtel1M 374087 AGAGAGAGAGAGACAGAGAGACAGAGAGAGACACGGAGCGAGAGAGAAAC 374136 v v v vi v i v (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr6qtel1M 374137 AGATAGACAGAGATAGAGACAGATAAACAGAGACAGAGACAGAGAGAGAG 374186 v v v v v i v v v (AG)n#Simple_ 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 100 chr6qtel1M 374187 -GAGAAAAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 374235 - i i (AG)n#Simple_ 101 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 150 chr6qtel1M 374236 AGAGAGAGAGAGAGAGAGAGAGGGAGAGGGAGATAGAGAGAGA 374278 i i v (AG)n#Simple_ 151 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 193 Matrix = Unknown Transitions / transversions = 0.47 (7/15) Gap_init rate = 0.01 (1 / 191), avg. gap size = 1.00 (1 / 1) 733 30.94 5.11 2.94 chr6qtel1M 374767 375432 (624568) L1M5_orf2#LINE/L1 2615 3294 (0) m_b308s551i0 12862 chr6qtel1M 374767 TACCAGATCT-AAAATTATATTATAGAGCAGCAGTTACCAAAACCATTTG 374815 ? ? - i i - i vi v i i vi v L1M5_orf2#LIN 2615 TACCNGATNTCAAGACT-TATTATAAAGCTACAGTAATCAAGACAGTGTG 2663 chr6qtel1M 374816 GTATTGGC-TAAGGAATAGATTAGTCGATCAGTGGAGTAGGTTAG---GT 374861 - - iv i v i ii iv --- L1M5_orf2#LIN 2664 GTATTGGCGTAAGGA-TAGACAAATAGATCAATGGAACAGAATAGAGAGT 2712 chr6qtel1M 374862 TCAAGGGACAAAACAGTCA-ACAACTATAGCAACCTAGTCTTTGACAAAC 374910 i - ii i i v --- - vv i ?v ?i ii i v L1M5_orf2#LIN 2713 CCA-GAAATAGACC---CACACATATATGGNCANTTGATTTTTGACAAAG 2758 chr6qtel1M 374911 ---CCAAAG-ACCCCAGCTTTTGGGATAAGAACTTACTGTTTGACAAAAA 374956 --- ? - vii ---- iv i ivvv v ii vi L1M5_orf2#LIN 2759 GTGCCAANGCAATTCAG----TGGGGAAAGGATAGTCTTTTCAACAAATG 2804 chr6qtel1M 374957 TTGCTGGGAAAATTGGAAACTAATATGGCAGAAACTAGGCATTGATCCAC 375006 v i v v iiv v i v iii?v i i vi L1M5_orf2#LIN 2805 GTGCTGGAACAATTGGATATCCATATGGAAAAAAATGAANCTCGACCCCT 2854 chr6qtel1M 375007 ACTTAACACCGTACACCAA--------CCGTA-----CAT-GACCTAGGC 375042 i v i v -------- ?iv ----- - iii L1M5_orf2#LIN 2855 ACCTCACACCATACACAAAAATTAATTCNAGATGGATCATAGACCTAAAT 2904 chr6qtel1M 375043 ATAAAGAATGAAATTATTAATAAATTAGAGGAA--CACAGGATAGTTTAC 375090 i ii? i i v vvvvi i -- i v i -- i L1M5_orf2#LIN 2905 GTAAAAGNTAAAACTATAAAACTTCTAGAAGAAAACATAGGAGAAT--AT 2952 chr6qtel1M 375091 CTCTCAGAACTGTGGAA-GGGGAAGGACTTTATGACCAA---AGAAAAAC 375136 - ivi iv i?-i v i i iv i v i--- v v L1M5_orf2#LIN 2953 CT-TCGTGACCTTGGGNTAGGCAAAGATTTCTTAAACAGGACACAAAAAG 3001 chr6qtel1M 375137 TAGAGATCATTACTGATCACAAAATAGAAAATTTTGACTATACCAAACTG 375186 i v?i i v vv ---v v v v v ?i i v v L1M5_orf2#LIN 3002 CACNAACCATAAAAGA---AAAAATTGATAAATTGGACTNCATCAAAATT 3048 chr6qtel1M 375187 AAAAGTTTTTGTACAAACAAAACTAATGCAGACAAGATTAGAAGGGAAGC 375236 ii i iv ?vvv ivi vi ivi v i v i v L1M5_orf2#LIN 3049 AAAAACTTCTGCTCNTCAAAAGACACCGTTAAGAAAATGAAAAGGCAAGC 3098 chr6qtel1M 375237 AATAAACTTGGAAAATATTTTTACAGTCAAAGGT-TCTGCTAAAGGCCTC 375285 v i i ? v i v v i i?- v vi - vi v L1M5_orf2#LIN 3099 CACAGANTGGGAGAAAATATTTGCAAN-ACATATATCTGACAAAGGACTC 3147 chr6qtel1M 375286 ATTTCCAAAATATATAGAGAATTATCTCTAATTTA-TAAAAAATCAAGCC 375334 i v i i i -i vi ? i - ? -- v L1M5_orf2#LIN 3148 GTATCCAGAATATATAAAGAACT-CCTACAANTCAATAANAAA--AAGAC 3194 chr6qtel1M 375335 ATTC--TCCAATTGAAATATGGTCAAAGGATATGAACAGACAATTCTCAG 375382 vv --i v? v v i iv v v i L1M5_orf2#LIN 3195 AAACAACCCAATANAAAAATGGGCAAAAGACTTGAACAGACACTTCACAA 3244 chr6qtel1M 375383 ATGAAGAAATTGAAACTATTTCTAGTCATATGGAAAGATGCTCCAAGTCA 375432 v v ?v iviiivv iv i i v v? L1M5_orf2#LIN 3245 AAGAAGATATNCAAATGGCCAATAAGCACATGAAAAGATGCTCAACNTCA 3294 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 41.36 CpG sites = 108, Kimura (unadjusted) = 42.47 Transitions / transversions = 1.17 (108/92) Gap_init rate = 0.05 (35 / 665), avg. gap size = 1.54 (54 / 35) 1604 27.47 2.99 4.24 chr6qtel1M 375289 375957 (624043) L1ME5_3end#LINE/L1 7 667 (274) m_b308s551i2 12862 chr6qtel1M 375289 TCCAAAATATATAGAGAATTATCTCTAATTTATAAAAAATCAAGCCATT- 375337 i i i ii i viiv v iv i i -- v iv?- L1ME5_3end#LI 7 TCTAGAATATACAAGGAACTCCTGCAAATCAACAAGAAA--AAGACGGNA 54 chr6qtel1M 375338 -CTCCAATTGAAATATGGTCAAAGGATATGAACAGACAATTCTCAGATGA 375386 - i v v v i iv v L1ME5_3end#LI 55 ACCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGA 104 chr6qtel1M 375387 AGAAA-TTGAAA--CTATTTCTAGTCATATGGAAAGATGCTCCAAGTCAT 375433 i -ii -- --v v - i i v v L1ME5_3end#LI 105 GGAAACCCGAAAGGCTA--ACAAG-CATATGAAGAGATGCTCAAACTCAT 151 chr6qtel1M 375434 TATTAATCAGAGAAATGCAAATTAAGACAATTCTAAGATACCACTACACA 375483 v i ivv i i vi L1ME5_3end#LI 152 TAGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACA 201 chr6qtel1M 375484 CCTGTCAGATTGGCTAAGATGACAGGAAA--AAATAATGACGATTGTTGG 375531 i i i v i --i i i--ii v i v L1ME5_3end#LI 202 CCTATTAGACTGGCAAAAAT--TAGAAAGCTGGATAATGCCAAGTGTTGG 249 chr6qtel1M 375532 AGGGGATGCGGGAAAACTGGGACATTGATGCATTGTTGGTGGAGTTGTGA 375581 v i i i ? iv i vi v i i iiv ii L1ME5_3end#LI 250 CGAGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAG 299 chr6qtel1M 375582 ACGAATCCAACCATTTTGGAGAGTAGTTTGGAACTA--TGCTCAAA--AA 375627 vii v i i i i i v v -- iv -- L1ME5_3end#LI 300 ACTGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTAA 349 chr6qtel1M 375628 GTTATCAAACTGTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGCTT 375677 - --- --- v i i viii v iv L1ME5_3end#LI 350 G-TAT---AC---GCATACCCTATGACCCAGCAATTCCGCTCCTGGGTAT 392 chr6qtel1M 375678 ATATCCCAAAGAGATTATAAAGAAGG----GAAAGGGACCTGTATGTGCA 375723 i v v viv ----v i ---- i i L1ME5_3end#LI 393 ATATCCCAAAGAAATTCTCACACAGGTCCATAAGGGGAC----ATGTACG 438 chr6qtel1M 375724 CGAATGTTTGTGGCAGCCCTTTTTGTAGTGGCTAGAAACTGGAAACTGAA 375773 v i ii v vi v i vi i ii ii vivv L1ME5_3end#LI 439 AGGATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACC 488 chr6qtel1M 375774 TGGATGTCCATCAGTTGGAGAATGGTTGAATAAATTGTGGTATATGAAAA 375823 i v v i v iii v iv v v L1ME5_3end#LI 489 TGGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACA 538 chr6qtel1M 375824 TTATGGAATATTACTGT-TCTGTAAGAAATGACCAACAGGATAATTTCAG 375872 ii i i - i-v v v iii vi vi i-- v v L1ME5_3end#LI 539 CCATGGAGTACTA-TGCAGCAGTTAGAAGCAACGGACTAGATG--TACAC 585 chr6qtel1M 375873 AAAG--GCCTGGAGAGA-CTTACACGAAC-TGATGCTGAGTGAAATGAGC 375918 v --i v vi - v -- - ii vi i L1ME5_3end#LI 586 ATAGCAACATGGATGGATCTTAAA--AACATAGTGCTGAGTGAAAAAAGT 633 chr6qtel1M 375919 AGGACCACAGATCATTAAATACTTCAACAACAATACTAT 375957 i -v -- v i -? vi - i L1ME5_3end#LI 634 AAGA-AACAGA--ATGAGAT-NTATAAC-ACAATACCAT 667 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 34.30 CpG sites = 105, Kimura (unadjusted) = 35.32 Transitions / transversions = 1.48 (105/71) Gap_init rate = 0.06 (40 / 668), avg. gap size = 1.20 (48 / 40) 1639 27.65 0.36 1.66 chr6qtel1M 375289 375836 (624164) L1ME3G_3end#LINE/L1 7 547 (377) m_b308s551i1 12862 chr6qtel1M 375289 TCCAAAATATATAGAGAATTATCTCTAATTTATAAAAAATCAAGCCATTC 375338 i i i viiv v iv i -- v --v L1ME3G_3end#L 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAA--AAGACA--A 52 chr6qtel1M 375339 TCCAATTGAAATATGGTCAAAGGATATGAACAGACAATTCTCAGATGAAG 375388 i v v v i v v i L1ME3G_3end#L 53 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chr6qtel1M 375389 AAATTGAAACTATTTCTAGTCATATGGAAAGATGCTCCAAGTCATTATTA 375438 vv iviiivv iv i v vv i v L1ME3G_3end#L 103 AAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTA 152 chr6qtel1M 375439 ATCAGAGAAATGCAAATTAAGACAATTCTAAGATACCACTACACACCTGT 375488 i i ivv i i viv ii L1ME3G_3end#L 153 ATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCAT 202 chr6qtel1M 375489 CAGATTGGCTAAGATGACAGGAAAAAATAATGACGATTGTTGGAGGGGAT 375538 v i vvv iii?vvi iv ? v v i i L1ME3G_3end#L 203 CAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGT 252 chr6qtel1M 375539 GCGGGAAAACTGGGACATTGATGCATTGTTGGTGGAGTTGTGAACGAATC 375588 i i v v vi v i i i iiv i ivii v L1ME3G_3end#L 253 GTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTA 302 chr6qtel1M 375589 CAACCATTTTGGAGAGTAGTTTGGAACTATGCTCAAAAAGTTATCAAACT 375638 i ? i i i v v - vvv i -- i v L1ME3G_3end#L 303 CAGCCNTTTTGGAGGGCAATTTGGCAGTAT-CTATTAAAAT--TTAAAAT 349 chr6qtel1M 375639 GTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGCTTATATCCCAAAG 375688 i i i vii v ? ?v v i ? L1ME3G_3end#L 350 GCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAG 399 chr6qtel1M 375689 AGATTAT-AAAGAAG-GGAAAGGGACCTGTATGTGCACGAATGTTTGTGG 375736 i vv -iv v v - v v i --? i i v i ii v L1ME3G_3end#L 400 AAATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTCATTG 447 chr6qtel1M 375737 CAGCCCTTTTTGTAGTGGCTAGAAACTGGAAACTGAATGGATGTCCATCA 375786 vi v i i v i i vivv ii L1ME3G_3end#L 448 CAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCA 497 chr6qtel1M 375787 GTTGGAGAATGGTTGAATAAATTGTGGTATATGAAAATTATGGAATATTA 375836 i v i i i vv v i i L1ME3G_3end#L 498 ATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACTA 547 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 35.03 CpG sites = 79, Kimura (unadjusted) = 35.62 Transitions / transversions = 1.13 (79/70) Gap_init rate = 0.02 (11 / 547), avg. gap size = 1.00 (11 / 11) 13 9.26 0.00 0.00 chr6qtel1M 376508 376530 (623470) (AAAG)n#Simple_repeat 1 23 (0) m_b308s252i3 12863 chr6qtel1M 376508 AAAAAAAGAAAGAAAGAAATAAA 376530 i v (AAAG)n#Simpl 1 AAAGAAAGAAAGAAAGAAAGAAA 23 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 19 27.01 0.00 0.00 chr6qtel1M 376640 376688 (623312) (TG)n#Simple_repeat 1 49 (0) m_b308s252i4 12864 chr6qtel1M 376640 TGTGTATGTGTGAGAGAGTGTGTGCTTGTGTAAGTGTGTATATATGTGT 376688 i v v v iv iv i i i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 49 Matrix = Unknown Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 230 35.29 0.98 0.00 chr6qtel1M 380630 380731 (619269) L1ME3F_3end#LINE/L1 433 535 (455) m_b308s551i3 12865 chr6qtel1M 380630 TGTACAAAAATGCTTGTAACAGCCCTTTTTGTCGTGGCAAGGAGCTGGAA 380679 i i ii i v v i vi i ii i L1ME3F_3end#L 433 TGTACAAGAATGTTCATAGCAGCACTGTTCGTAATAGCAAAAAACTGGAA 482 chr6qtel1M 380680 ACTGAGTGGAAGCTGATCTGTTGGGAAATGGATAACTAAGTTATGA-ATG 380728 vivviii v iiv viiv ii v i i i- i L1ME3F_3end#L 483 ACAACCCAAATGTCCATCGACAGGAGAATGGATAAATAAATTGTGGTATA 532 chr6qtel1M 380729 TTC 380731 L1ME3F_3end#L 533 TTC 535 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 49.50 CpG sites = 25, Kimura (unadjusted) = 51.64 Transitions / transversions = 2.27 (25/11) Gap_init rate = 0.01 (1 / 101), avg. gap size = 1.00 (1 / 1) 13 21.20 0.00 8.51 chr6qtel1M 381297 381347 (618653) (ATT)n#Simple_repeat 1 47 (0) m_b308s252i5 12866 chr6qtel1M 381297 ATAATTTTTATTATACATAATTATATATCATGTAGTATTATTGTATACTA 381346 v v -i v - i - v i - i (ATT)n#Simple 1 ATTATTATTATTAT-TATTATTAT-TATTAT-TATTATTATTAT-TATTA 46 chr6qtel1M 381347 T 381347 (ATT)n#Simple 47 T 47 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.08 (4 / 50), avg. gap size = 1.00 (4 / 4) 252 25.00 0.00 0.00 chr6qtel1M 383101 383168 (616832) C DNM1r#Unknown (2116) 2546 2479 m_b308s502i0 12867 chr6qtel1M 383101 TATACATGCATATGAATATATATGCAAACACACATACACATATAAATATA 383150 ? i i iv i i ii v i v i i C DNM1r#Unknown 2546 TATANATACGTATATATACACATATATACACACATACACACATATACACA 2497 chr6qtel1M 383151 CATATACATGCATATACA 383168 i ii i C DNM1r#Unknown 2496 CATATATACACACATACA 2479 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 30.96 CpG sites = 14, Kimura (unadjusted) = 33.40 Transitions / transversions = 4.67 (14/3) Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0) 22 6.68 0.00 0.00 chr6qtel1M 383190 383221 (616779) (AGAT)n#Simple_repeat 1 32 (0) m_b308s252i6 12868 chr6qtel1M 383190 AGATAGATAGATAGACAGACAGATAGATAGAT 383221 i i (AGAT)n#Simpl 1 AGATAGATAGATAGATAGATAGATAGATAGAT 32 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 250 28.68 6.90 0.81 chr6qtel1M 384400 384515 (615485) MIR#SINE/MIR 96 218 (44) m_b308s601i4 12869 chr6qtel1M 384400 CATATCACTTAATCTCTATATGTTTCAA-TCCCACATCAGTAACATGAGC 384448 vi i i v i ii i- i v v v i v MIR#SINE/MIR 96 CAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGG 145 chr6qtel1M 384449 ATCAT-ACAGT---TAGCTTATATATTTTCTGTAAGGATAATATG-GT-- 384491 v - i --- v i viv vi i v v - -- MIR#SINE/MIR 146 ATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTA 195 chr6qtel1M 384492 ATATTTAAAAAGGACTTCAGAACA 384515 iv iv vi - MIR#SINE/MIR 196 ATACATGTAAAGCGCTT-AGAACA 218 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 35.31 CpG sites = 17, Kimura (unadjusted) = 36.68 Transitions / transversions = 1.06 (17/16) Gap_init rate = 0.05 (6 / 115), avg. gap size = 1.50 (9 / 6) 422 25.87 0.84 2.56 chr6qtel1M 385731 385849 (614151) MIRc#SINE/MIR 11 127 (141) m_b308s601i5 12870 chr6qtel1M 385731 TGGCTCATTGGATAGAGAAGTGGCCCTGAAGTCCCGAGGCCCTGAGTTTA 385780 iv v v v v v i i vv i v i ii MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr6qtel1M 385781 AATCCAACCTCAGACATTTAATACTAGCTTTGTGACCCTGGGCAAGTCAT 385830 i viv v v i --- v i i MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTA---CTAGCTGTGTGACCTTGGGCAAGTCAC 107 chr6qtel1M 385831 TTAACCCCACTT-GCTTCAG 385849 i v v- i MIRc#SINE/MIR 108 TTAACCTCTCTGAGCCTCAG 127 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 29.34 CpG sites = 14, Kimura (unadjusted) = 31.92 Transitions / transversions = 0.88 (14/16) Gap_init rate = 0.03 (4 / 118), avg. gap size = 1.00 (4 / 4) 13 12.49 0.00 10.26 chr6qtel1M 385923 385965 (614035) (AAAAGA)n#Simple_repeat 1 39 (0) m_b308s252i7 12871 chr6qtel1M 385923 AAAAGAATAAAGAAAAAGGAAAGACAGGAAGAAAGGAAGAAAA 385965 - - i v ii -- (AAAAGA)n#Sim 1 AAAAGAA-AAAGAAAAA-GAAAAAGAAAAAGAAA--AAGAAAA 39 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.10 (4 / 42), avg. gap size = 1.00 (4 / 4) 250 25.00 4.17 0.00 chr6qtel1M 386082 386153 (613847) MIR3#SINE/MIR 71 145 (63) m_b308s601i6 12872 chr6qtel1M 386082 CCAATAACTTCCTTTC--ACTGTGAAAAAATCACT-CAGTTCCCTTGGTC 386128 v ?v v v-- iv iiv i - vi i v i MIR3#SINE/MIR 71 CCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCC 120 chr6qtel1M 386129 TCAGTTACCTCACCTGTAAAATGGG 386153 v i i MIR3#SINE/MIR 121 TCAGTTTCCTCATCTGTAAAATGAG 145 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 31.23 CpG sites = 9, Kimura (unadjusted) = 31.23 Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.03 (2 / 71), avg. gap size = 1.50 (3 / 2) 29 22.21 0.00 1.56 chr6qtel1M 386877 386941 (613059) (TG)n#Simple_repeat 1 64 (0) m_b308s252i8 12873 chr6qtel1M 386877 TGTGAGTGTGTGTGAGTGTGTGTGTGTGTGTATGTGCCTGTGCAACTGTA 386926 v v i iv iivv i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr6qtel1M 386927 CATGTGTGTGCTGTG 386941 ii - (TG)n#Simple_ 51 TGTGTGTGTG-TGTG 64 Matrix = Unknown Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.02 (1 / 64), avg. gap size = 1.00 (1 / 1) 13 25.68 2.17 0.00 chr6qtel1M 388650 388695 (611305) (TTATTTT)n#Simple_repeat 1 47 (0) m_b308s252i9 12874 chr6qtel1M 388650 TTATGTGTT-TTTCTGAATGTATGTTTTTTATTCTTTATTTTTTTTT 388695 v v - i v v v v i i v (TTATTTT)n#Si 1 TTATTTTTTATTTTTTATTTTTTATTTTTTATTTTTTATTTTTTATT 47 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1) 12 10.76 12.50 0.00 chr6qtel1M 388773 388812 (611188) (ATACTCT)n#Simple_repeat 1 45 (0) m_b308s252i10 12875 chr6qtel1M 388773 ATACT-TAT-C-CTATACTCTATA--CAATTCTCTATATTCTGTA 388812 - - - -- v v i i (ATACTCT)n#Si 1 ATACTCTATACTCTATACTCTATACTCTATACTCTATACTCTATA 45 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.10 (4 / 39), avg. gap size = 1.25 (5 / 4) 18 10.01 6.25 0.00 chr6qtel1M 389201 389232 (610768) (AT)n#Simple_repeat 1 34 (0) m_b308s252i11 12876 chr6qtel1M 389201 ATAAATATATAT-TACATATATAT-TATATTTAT 389232 v - i - v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATAT 34 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.06 (2 / 31), avg. gap size = 1.00 (2 / 2) 188 26.05 0.00 0.00 chr6qtel1M 389647 390100 (609900) (TC)n#Simple_repeat 1 454 (3) m_b308s252i12 12877 chr6qtel1M 389647 TCTTTCTCTCTGTTGGTCTCTTTCTCTCTCTCTCTCTCTCTCTCTCTCTC 389696 i v ivv i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr6qtel1M 389697 TCTCTCTCTCTCTCTCTCTCACTCTCTTTCTATGTGTGTGTCTCTCTTGG 389746 v i v v v v v ivv (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chr6qtel1M 389747 TTTCTGTCTCTCTGTCTCTGTCTCTGTCTCTCTCTCTTTCTATGTGTGTG 389796 i v v v v i v v v v v (TC)n#Simple_ 101 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 150 chr6qtel1M 389797 TCTCTCTTGGTTTCTGTCTCTCTGTCTCTGTCTCTCTGTCTCTCTTTCTC 389846 ivv i v v v v i (TC)n#Simple_ 151 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 200 chr6qtel1M 389847 TCTCTCTCTCTTGCTCTTTGCCTCTGTCTCTCTGTCTCTGTCTGTGTGTG 389896 iv i vi v v v v v v v (TC)n#Simple_ 201 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 250 chr6qtel1M 389897 TGTGTGTATGTGTGGGTCTCTATCTCTGTCTCTCTCTGTCTCATTTTCTG 389946 v v v v v v vvv v v v vi i v (TC)n#Simple_ 251 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 300 chr6qtel1M 389947 TGTGTGTGTGTGTGTGTGTCTGTCTGCCTCTCTGTCTCTCTGTCAGTCTC 389996 v v v v v v v v v v vi v v vv (TC)n#Simple_ 301 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 350 chr6qtel1M 389997 TGTCTCTTTCTCTCTCTGTCTCTGTCTCTCTCTTGGTTTCTGTCTCTCTC 390046 v i v v ivv i v (TC)n#Simple_ 351 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 400 chr6qtel1M 390047 TTTGTCTCTGTCTCTCTGTCTCTGTCTCTGTGTGTCTCTCTGTCTCTGTT 390096 i v v v v v v v v v i (TC)n#Simple_ 401 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 450 chr6qtel1M 390097 TCTC 390100 (TC)n#Simple_ 451 TCTC 454 Matrix = Unknown Transitions / transversions = 0.27 (21/79) Gap_init rate = 0.00 (0 / 453), avg. gap size = 0.0 (0 / 0) 35 0.00 0.00 0.00 chr6qtel1M 390101 390130 (609870) (TG)n#Simple_repeat 1 30 (0) c_b308s251i0 12878 chr6qtel1M 390101 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 390130 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 30 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 144 25.03 1.62 3.73 chr6qtel1M 390747 390756 (609244) (TGTCTC)n#Simple_repeat 1 10 (473) m_b308s252i13 12879 chr6qtel1M 390747 TGTTTCTTTC 390756 i v (TGTCTC)n#Sim 1 TGTCTCTGTC 10 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 9), avg. gap size = 0.0 (0 / 0) 30 7.32 0.00 0.00 chr6qtel1M 390757 390799 (609201) (TCTCTGTCTG)n#Simple_repeat 1 43 (0) c_b308s251i1 12880 chr6qtel1M 390757 TCTCTGTCAGTCTCTGTCTGTTTCTGTCTCTCTCTGTCTGTCT 390799 v i v (TCTCTGTCTG)n 1 TCTCTGTCTGTCTCTGTCTGTCTCTGTCTGTCTCTGTCTGTCT 43 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 144 25.03 1.62 3.73 chr6qtel1M 390800 391018 (608982) (TGTCTC)n#Simple_repeat 11 220 (263) m_b308s252i13 12881 chr6qtel1M 390800 GTCTCTCTATCTATCTATCTATCTCCTTCTCTCTATGTGCATCTCTGTCT 390849 v v i v v v i iv v v v -- (TGTCTC)n#Sim 11 CTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTG--TCTCTGTCT 58 chr6qtel1M 390850 CTGTCTCTATCTCTGTCTCATTCTGTGTGTGTGTGTGTGTCTCTGGCTAT 390899 i vv v v v v v - - v (TGTCTC)n#Sim 59 CTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCT-G-TCT 106 chr6qtel1M 390900 CTGCCTGTCTGTCTCTCTGTGTCTCTGTCTCCCTCTCTCTGTGTGTGCTT 390949 i v v v v v -- v v v - i (TGTCTC)n#Sim 107 CTGTCTCTGTCTCTGTCTCTGTCTCTGTCT--CTGTCTCTGTCTCTG-TC 153 chr6qtel1M 390950 ACAAACTCCATTTCTCGTTTCCCTGTCTATCTATGTTTCTCTCTGCTCTC 390999 v viv ii i - i iv v i v i v - v (TGTCTC)n#Sim 154 TCTGTCTCTGTCTCT-GTCTCTGTCTCTGTCTCTGTCTCTGTCT-CTGTC 201 chr6qtel1M 391000 TCTGTGGGTATCTGTGAGG 391018 vvv i v vvv (TGTCTC)n#Sim 202 TCTGTCTCTGTCTCTGTCT 220 Matrix = Unknown Transitions / transversions = 0.38 (15/40) Gap_init rate = 0.04 (9 / 218), avg. gap size = 1.00 (9 / 9) 54 6.53 0.00 0.00 chr6qtel1M 391019 391082 (608918) (CT)n#Simple_repeat 1 64 (0) c_b308s251i2 12882 chr6qtel1M 391019 CTCTCTCTGTCTCTGTCTCTGTTTCTCTCTCTCTCTCTCTCTCTCTCTCT 391068 v v v i (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chr6qtel1M 391069 CTCTCTCTCTCTCT 391082 (CT)n#Simple_ 51 CTCTCTCTCTCTCT 64 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0) 54 6.22 0.00 0.00 chr6qtel1M 391092 391158 (608842) (TCTGTGTG)n#Simple_repeat 1 67 (0) c_b308s251i3 12883 chr6qtel1M 391092 TCTGTGTGTCTGTGTGTGTGTATGTCTGTGTGTCTGTGTGTCTCTGTGTC 391141 v i v (TCTGTGTG)n#S 1 TCTGTGTGTCTGTGTGTCTGTGTGTCTGTGTGTCTGTGTGTCTGTGTGTC 50 chr6qtel1M 391142 TGTGTGTGTGTGTGTCT 391158 v (TCTGTGTG)n#S 51 TGTGTGTCTGTGTGTCT 67 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.0 (0 / 0) 144 25.03 1.62 3.73 chr6qtel1M 391159 391410 (608590) (TGTCTC)n#Simple_repeat 231 480 (3) m_b308s252i13 12884 chr6qtel1M 391159 CGGTCTCTGTCTCTCGGTCTCTGTTTCCATTTCTCTGTCTCTGACTCTAT 391208 v -- i - - v v i (TGTCTC)n#Sim 231 CTGTCTCTGTCTCT--GTCTCTGTCT-C-TGTCTCTGTCTCTGTCTCTGT 276 chr6qtel1M 391209 CTCTGTCTCTCTCTGTCTCACTTTCTCTGTGTGTGTGTGTGTCGTTCTGT 391258 v v v v v v v v v -- (TGTCTC)n#Sim 277 CTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTC--TCTGT 324 chr6qtel1M 391259 CTCCCTCTCTGTCTCTCTGTCAGTCTC--TATCTGTCTCTGTCTCTGTCT 391306 iv v v v -- v (TGTCTC)n#Sim 325 CTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCT 374 chr6qtel1M 391307 C--TCTGTCTCTCTGTCTCTCTCTCTCGT-TCTCTCTCTCTCTCTGTGTC 391353 -- v v v - - v v v (TGTCTC)n#Sim 375 CTGTCTCTGTCTCTGTCTCTGTCTCT-GTCTCTGTCTCTGTCTCTGTCTC 423 chr6qtel1M 391354 TGTCTGCCTGTCTGCCTGTCTGTCTC--TCTGTGTCTCTGTCTCCCTCTC 391401 -- viv v -- v iv (TGTCTC)n#Sim 424 TGTCT--CTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTC 471 chr6qtel1M 391402 TCTGTGTGT 391410 v v v (TGTCTC)n#Sim 472 TGTCTCTGT 480 Matrix = Unknown Transitions / transversions = 0.16 (5/31) Gap_init rate = 0.05 (13 / 251), avg. gap size = 1.23 (16 / 13) 13 35.73 1.18 2.38 chr6qtel1M 393486 393570 (606430) (TCTTT)n#Simple_repeat 1 84 (0) m_b308s252i15 12885 chr6qtel1M 393486 TCTTTTCTTTACCTCTTGTAGTTTATTTTTTTGTTTTCTGCTGTGTACTT 393535 -i i v vv i v i v vi v v v - (TCTTT)n#Simp 1 TCTTTTCTTT-TCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTC-T 48 chr6qtel1M 393536 TTTAATTTTATTTCTCCCCTTTTC-TTCCCTTTCTT 393570 vv iv iii - i i (TCTTT)n#Simp 49 TTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTT 84 Matrix = Unknown Transitions / transversions = 0.92 (11/12) Gap_init rate = 0.04 (3 / 84), avg. gap size = 1.00 (3 / 3) 12 22.42 0.00 2.70 chr6qtel1M 393507 393544 (606456) (TTTACTT)n#Simple_repeat 1 37 (0) m_b308s252i16 12886 chr6qtel1M 393507 TTTATTTTTTTGTTTTCTGCTGTGTACTTTTTAATTTT 393544 i vv - i v v v (TTTACTT)n#Si 1 TTTACTTTTTACTTTT-TACTTTTTACTTTTTACTTTT 37 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 13 35.73 1.18 2.38 chr6qtel1M 393486 393570 (606430) (TCTTT)n#Simple_repeat 1 84 (0) m_b308s252i15 12885 chr6qtel1M 393486 TCTTTTCTTTACCTCTTGTAGTTTATTTTTTTGTTTTCTGCTGTGTACTT 393535 -i i v vv i v i v vi v v v - (TCTTT)n#Simp 1 TCTTTTCTTT-TCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTC-T 48 chr6qtel1M 393536 TTTAATTTTATTTCTCCCCTTTTC-TTCCCTTTCTT 393570 vv iv iii - i i (TCTTT)n#Simp 49 TTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTT 84 Matrix = Unknown Transitions / transversions = 0.92 (11/12) Gap_init rate = 0.04 (3 / 84), avg. gap size = 1.00 (3 / 3) 36 2.94 0.00 0.00 chr6qtel1M 393626 393660 (606340) (TA)n#Simple_repeat 1 35 (0) c_b308s251i4 12887 chr6qtel1M 393626 TATATATATATATATATATATATATACATATATAT 393660 i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATAT 35 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 71 22.01 0.00 0.00 chr6qtel1M 394097 394243 (605757) (TC)n#Simple_repeat 1 147 (0) m_b308s252i17 12888 chr6qtel1M 394097 TCTCTCTTTCTCTCTGTTGGTCTCTGTCTTTGTCTCTGTCTATCTCTCTG 394146 i v ivv v i v v v v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr6qtel1M 394147 TTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTC 394196 i v (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chr6qtel1M 394197 TCTGTGTGTGTGTGTGTGTGTCTGCCTCTCTGCCTCTCTGTTTCTCT 394243 v v v v v v v v v vi vi v i (TC)n#Simple_ 101 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 147 Matrix = Unknown Transitions / transversions = 0.33 (7/21) Gap_init rate = 0.00 (0 / 146), avg. gap size = 0.0 (0 / 0) 193 30.75 7.62 0.89 chr6qtel1M 395701 395805 (604195) MIR#SINE/MIR 95 206 (56) m_b308s601i7 12889 chr6qtel1M 395701 GCATTTCACTTAATTTCTATATGTTTCAG--ACCTCTATCAGCAACATGA 395748 vv i ii v i ii --v - v i v i MIR#SINE/MIR 95 GCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTC-ATCTGTAAAATGG 143 chr6qtel1M 395749 GCATCAT-ACCGT---TAGCTTATAACTTTTCTAAAAGGATCAAATGA-- 395792 v v - iv --- v i ivv vi ivi i -- MIR#SINE/MIR 144 GGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGT 193 chr6qtel1M 395793 TATCATATGTAAA 395805 vi i MIR#SINE/MIR 194 TAATACATGTAAA 206 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 40.36 CpG sites = 17, Kimura (unadjusted) = 40.36 Transitions / transversions = 1.13 (17/15) Gap_init rate = 0.05 (5 / 104), avg. gap size = 1.80 (9 / 5) 221 32.04 6.77 1.43 chr6qtel1M 396720 396852 (603148) MIRb#SINE/MIR 2 141 (127) m_b308s601i8 12890 chr6qtel1M 396720 AGTGAGTTAGCTAGTAGTTCAGTAGATTATGTATTAGCCTTGCAGTCAAA 396769 v i vi -- i v i vviv i ivi i v i MIRb#SINE/MIR 2 AGAGGGGCAGC--GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGA 49 chr6qtel1M 396770 GTTAT-TGAGTTCAAATCTAGCCTTGG--ATTTACTACTTCTGTGTCACT 396816 vvv i- i i iv v iv -- i vi v v vi MIRb#SINE/MIR 50 CAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTT 99 chr6qtel1M 396817 GGGGA--TT--TTAACC-CTGTTTGCCTTAG-TTCCTCATTT 396852 v -- -- - v vv i - i MIRb#SINE/MIR 100 GGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCT 141 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 39.74 CpG sites = 20, Kimura (unadjusted) = 42.29 Transitions / transversions = 0.91 (20/22) Gap_init rate = 0.06 (8 / 132), avg. gap size = 1.38 (11 / 8) 13 21.75 0.00 6.67 chr6qtel1M 397496 397543 (602457) (TTA)n#Simple_repeat 1 45 (0) m_b308s252i18 12891 chr6qtel1M 397496 TTATTTCAATAACTATGACTTATTAATTATTATTTTTATTGATCATTA 397543 viv v i v - - v - i (TTA)n#Simple 1 TTATTATTATTATTATTA-TTATT-ATTATTATTATTATT-ATTATTA 45 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.06 (3 / 47), avg. gap size = 1.00 (3 / 3) 229 22.81 1.75 0.00 chr6qtel1M 398848 398904 (601096) C DNM1r#Unknown (2126) 2536 2479 m_b308s502i1 12892 chr6qtel1M 398848 TATATGTACACATACATATACAAACGCATGCATACACATGCAT-CATACA 398896 i i i v ii ii i ii -i C DNM1r#Unknown 2536 TATATATACACATATATACACACATACACACATATACACACATATATACA 2487 chr6qtel1M 398897 CATATACA 398904 i C DNM1r#Unknown 2486 CACATACA 2479 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 29.76 CpG sites = 12, Kimura (unadjusted) = 29.76 Transitions / transversions = 12.00 (12/1) Gap_init rate = 0.02 (1 / 56), avg. gap size = 1.00 (1 / 1) 15 14.13 0.00 3.12 chr6qtel1M 400147 400179 (599821) (TAT)n#Simple_repeat 1 32 (0) m_b308s252i19 12893 chr6qtel1M 400147 TATTATTTATATTATTACTATTATTGATGATTA 400179 vv i - v (TAT)n#Simple 1 TATTATTATTATTATTATTATTATT-ATTATTA 32 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 214 26.84 4.81 6.86 chr6qtel1M 400308 400411 (599589) C MIRb#SINE/MIR (44) 224 123 m_b308s601i10 12894 chr6qtel1M 400308 ACTGTGATAATCACTTCACA---ATTATTTAACAACTTTTAAAC--TATG 400352 v v i i --- i -- --- v --i ii C MIRb#SINE/MIR 224 ACTGTGCTAAGCGCTTTACATGCATTATCT--CA---TTTAATCCTCACA 180 chr6qtel1M 400353 AAAAACCTTAGACTTTTAAGTGTTATTGTCTATATTTGACATTTGAAGAA 400402 v v vv v--v i i i ivi v vv i C MIRb#SINE/MIR 179 ACAACCCTGCGAG--GTAGGTATTATTATCCCCATTTTACAGATGAGGAA 132 chr6qtel1M 400403 ACTAAGGCT 400411 i C MIRb#SINE/MIR 131 ACTGAGGCT 123 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 31.99 CpG sites = 13, Kimura (unadjusted) = 33.51 Transitions / transversions = 1.00 (13/13) Gap_init rate = 0.09 (9 / 103), avg. gap size = 1.33 (12 / 9) 259 34.14 1.64 8.77 chr6qtel1M 400827 400948 (599052) MIRc#SINE/MIR 2 115 (153) m_b308s601i11 12895 chr6qtel1M 400827 GGGTCAGTTTGATGAAACCATGGATAGAGGACTAGCCCGAGTGTCAGTAG 400876 i v v i --- vi v v i v ivi v v i MIRc#SINE/MIR 2 GAGGCAGTGTGGTG---CAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr6qtel1M 400877 GATCTGAGTTCAAAAGCAGCCCCAGAAATTTAACAC--ATTAACCATATA 400924 i i i ----- i i v-- i iv -- i i ii i i MIRc#SINE/MIR 49 GACCTGGGTTCGA-----GTCCCGGC--TCTGCCACTTACTAGCTGTGTG 91 chr6qtel1M 400925 ATCCTGAACAAATCACTTAAACCC 400948 i i ii i v i MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 44.78 CpG sites = 26, Kimura (unadjusted) = 48.39 Transitions / transversions = 2.17 (26/12) Gap_init rate = 0.09 (11 / 121), avg. gap size = 1.09 (12 / 11) 51 24.30 3.80 1.23 chr6qtel1M 401720 401877 (598123) (AT)n#Simple_repeat 1 162 (0) m_b308s252i20 12896 chr6qtel1M 401720 ATTTATATATATACATATATTAATA-ATATGGGCA-AGAAGAATTTCATT 401767 v i vv - ivii - v viv v - v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATAT-ATA 49 chr6qtel1M 401768 TA-AAAGATTTATATATATATATATATCAAT-TGTATATAT-TATA-ATA 401813 - v v v vv - i - - (AT)n#Simple_ 50 TATATATATATATATATATATATATATATATATATATATATATATATATA 99 chr6qtel1M 401814 TAGATATGATCTATATAGACACATTTATGTAAATACATGCATGTATATAT 401863 v - v v i i v i v i ii i (AT)n#Simple_ 100 TATATAT-ATATATATATATATATATATATATATATATATATATATATAT 148 chr6qtel1M 401864 ATATATATATATAT 401877 (AT)n#Simple_ 149 ATATATATATATAT 162 Matrix = Unknown Transitions / transversions = 0.68 (13/19) Gap_init rate = 0.05 (8 / 157), avg. gap size = 1.00 (8 / 8) 288 36.93 2.29 4.07 chr6qtel1M 402320 402494 (597506) C MIRb#SINE/MIR (86) 182 11 m_b308s601i12 12897 chr6qtel1M 402320 ACAA-AACTCTGAGAAATATATGAATTGTTATTTTTAGGATATAATTAGG 402368 - i v ii vi -- i iiii vvv i iv ii C MIRb#SINE/MIR 182 ACAACAACCCTGCGAGGTAGGT--ATTATTATCCCCATTTTACAGATGAG 135 chr6qtel1M 402369 GAAACTGAAGG--AGATGAGAATCACTGACCCCTCCAGGGTCACCCCACT 402416 i v-- - iv v v i iivi i v v--- C MIRb#SINE/MIR 134 GAAACTGAGGCTCAGA-GAGGTTAAGTAACTTGCCCAAGGTCACACA--- 89 chr6qtel1M 402417 CGCTATTAAGTATTTGAAACCGGAAAAAAATTCATATTTCT-TGACTCCA 402465 - v iviv iv v vvvi ii vi i v - C MIRb#SINE/MIR 88 -GCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCA 40 chr6qtel1M 402466 AATTCAGTATTCTACCTACTGCTTCACAC 402494 vi v ii vi i vi i C MIRb#SINE/MIR 39 AAGCCCGTGCTCTTTCCACTGCACCACGC 11 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 50.29 CpG sites = 35, Kimura (unadjusted) = 52.76 Transitions / transversions = 1.30 (35/27) Gap_init rate = 0.06 (10 / 174), avg. gap size = 1.10 (11 / 10) 332 35.39 1.97 3.33 chr6qtel1M 402343 402494 (597506) C MIRc#SINE/MIR (111) 157 8 m_b308s601i13 12897 chr6qtel1M 402343 ATTGTTATTTTTAGGATATAATTAGGGAAACTGAAGG--AGATGAGAATC 402390 i iiii vvv i iv ii i v-- - iv v C MIRc#SINE/MIR 157 ATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGA-GAGGTTA 109 chr6qtel1M 402391 ACTGACCCCTCCAGGGTCACCCCACTCGCTATTAAGTATTTGAAACCGGA 402440 v iivi i v v---- v iviv iv v C MIRc#SINE/MIR 108 AGTGACTTGCCCAAGGTCACACA----GCTAGTAAGTGGCAGAGCCGGGA 63 chr6qtel1M 402441 AAAAAATTCATAT-TTCTTGACTCCAAATTCAGTATTCTACCTACTGCTT 402489 vvvi ii vi - i i i ii vi i vi C MIRc#SINE/MIR 62 CTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCAC 13 chr6qtel1M 402490 CACAC 402494 C MIRc#SINE/MIR 12 CACAC 8 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 48.33 CpG sites = 30, Kimura (unadjusted) = 49.69 Transitions / transversions = 1.36 (30/22) Gap_init rate = 0.05 (7 / 151), avg. gap size = 1.14 (8 / 7) 18 9.69 3.03 0.00 chr6qtel1M 402590 402622 (597378) (ATT)n#Simple_repeat 1 34 (0) m_b308s252i21 12898 chr6qtel1M 402590 ATTATTATTTATATTATTATTGTTATT-TTATTA 402622 vv i - (ATT)n#Simple 1 ATTATTATTATTATTATTATTATTATTATTATTA 34 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 280 34.50 3.42 2.72 chr6qtel1M 403101 403246 (596754) MIRb#SINE/MIR 6 152 (116) m_b308s601i14 12899 chr6qtel1M 403101 GAGCAAAACAACACAATGGAAGGAGC---TATTTAGGAGTCAGAGAGCAG 403147 i iviiiiii i i ---vii v v - v MIRb#SINE/MIR 6 GGGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAG-AC 54 chr6qtel1M 403148 GTGCATTGAAATACAGCCCCAATAAAACATAACTTGCTTTG--ACTTTTA 403195 v vi vi v v v i -- ivv v - v v -- i vi MIRb#SINE/MIR 55 CTGGGTTCGAATCCCGGCTC--TGCCACTTA-CTAGCTGTGTGACCTTGG 101 chr6qtel1M 403196 AAAATCCCCTAAATCTCTCTGGATCTCCGATCCCTCATCTGTAAAATGGG 403245 iv viiv v i iii v v i MIRb#SINE/MIR 102 GCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 151 chr6qtel1M 403246 G 403246 MIRb#SINE/MIR 152 G 152 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 44.73 CpG sites = 26, Kimura (unadjusted) = 47.34 Transitions / transversions = 1.13 (26/23) Gap_init rate = 0.04 (6 / 145), avg. gap size = 1.50 (9 / 6) 316 27.18 4.31 1.68 chr6qtel1M 403177 403292 (596708) MIR3#SINE/MIR 75 193 (15) m_b308s601i15 12899 chr6qtel1M 403177 TAACTTGCTTTG--ACTTTTAAAAATCCCCTAAATCTCTCTGGATCTCCG 403224 ? v -- i viiv vi v vv i ii v MIR3#SINE/MIR 75 TAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAG 124 chr6qtel1M 403225 ATCCCTCATCTGTAAAATGGGGGCTTTAGATCAACT--TCTCTGACTTCC 403272 v i i vv i ii iv -- i vv MIR3#SINE/MIR 125 TTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCC 174 chr6qtel1M 403273 TTTCT-GCTCTGTAACACTCT 403292 i i- -- i MIR3#SINE/MIR 175 CTTCCAGCTCTG--ACATTCT 193 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 34.77 CpG sites = 17, Kimura (unadjusted) = 34.77 Transitions / transversions = 1.21 (17/14) Gap_init rate = 0.04 (5 / 115), avg. gap size = 1.40 (7 / 5) 16 31.01 0.00 0.00 chr6qtel1M 403982 404026 (595974) (TG)n#Simple_repeat 1 45 (0) m_b308s252i22 12900 chr6qtel1M 403982 TGTGAATGTGTGAGTGTGTGCTTGTGCATATGTATATGTATGTGT 404026 vi v iv ii i i i i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 45 Matrix = Unknown Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 283 29.57 10.02 6.01 chr6qtel1M 404466 404994 (595006) L1ME4b_3end#LINE/L1 31 579 (313) m_b308s551i4 12901 chr6qtel1M 404466 CAAATTTATAAGAATAAAAGTCACTCCTCAATTGATCAATGGTCAAAGGA 404515 iv v i viv vv i v vv v L1ME4b_3end#L 31 CAAATCAATAAGAAAAAGACCAACAACCCAATAGAAAAATGGGCAAAGGA 80 chr6qtel1M 404516 TATGAACAGATAATTTTCAGGTGATGAAAT--TAATGTCATCTATACTCA 404563 i i iv ivi v --v v - - vv L1ME4b_3end#L 81 TATGAACAGACAGTTCACAGAAAAGGAAATACAAATGGC-TCT-TAAACA 128 chr6qtel1M 404564 TATGAAAAAAGGCTCTAAATTA-TGATGGATAACACAAATGATTATTTTT 404612 i v v vv i - v -i v v vvv --- L1ME4b_3end#L 129 TATGAAAAGATGCTCAACCTCACTCAT-AATAAGAGAAATGCAAATT--- 174 chr6qtel1M 404613 AAAAATT----TGAAATATCACCTCAAAATGCTCAGA-TGGCATATAATG 404657 - i ---- i i ii ivv vivv - --- - L1ME4b_3end#L 175 -AAAACTACACTGAGATACCATTTTTCACCTATCAGATTGGCA---AA-G 219 chr6qtel1M 404658 ATGACTGGAAAAGATAATGATAA------ATGTTGGAGGAGACGTGGGAA 404701 v ---- v -- ------i v ii ii i L1ME4b_3end#L 220 ATCA----AAAAGTT--TGATAACACACTGTGTTGGCGAGGGTGTGGGGA 263 chr6qtel1M 404702 AACTGGGAAACTAATGCATGGTTGGTGAAGTTGTGAAATTTTATAACC-- 404749 v v vv v i v i iiiv i v vv i -- L1ME4b_3end#L 264 AACAGGCACTCTCATACATTGCTGGTGGGAGTGTAAATTGGTACAACCTC 313 chr6qtel1M 404750 ----AAGGGA-------------CTGTCAAATTT-----TGCAAAT--CC 404775 ----i v------------- i v ----- v -- L1ME4b_3end#L 314 TATGGAGGGCAATTTGGCAATATCTATCAAAATTACAAATGCACATACCC 363 chr6qtel1M 404776 TTTGACCTGGTATATCCCAATGACTCTA------TATCCCA-AGA-A-AC 404816 ii i - i v --- ------ i - - - L1ME4b_3end#L 364 TTTGACCCAGCA-ATTCCACT---TCTAGGAATTTATCCTACAGATATAC 409 chr6qtel1M 404817 TCACAAAAGAGGGAAGAGAAAACCACATAAGCAAAAAAAAATGATATGCA 404866 i v v v v ------ iv i v i v i----- v v L1ME4b_3end#L 410 TCGCACATGTGCG------AAATGACGTATGTACAAG-----GTTATTCA 448 chr6qtel1M 404867 --GGGGTTCTTTTTGTAGTAGGAAAGTATTGGAAAGTGAGTAGATGCCCA 404914 -- vi ivi v i v iv vvivv i i L1ME4b_3end#L 449 TTGCAGCATTGTTTGTAATAGCAAAAGATTGGAAACAACCTAAATGTCCA 498 chr6qtel1M 404915 TCAGATAGGTAAA-GGTTGAGGAAGTTGTGACATATAAACGTAATAGAAT 404963 - vi v- i iv i i ii i vv iii i L1ME4b_3end#L 499 TCA-ATAGGGGACTGGTTAAATAAATTATGGTACATCCATACAATGGAAT 547 chr6qtel1M 404964 ATTATTGTTCTATGAAAATG-ATGAACAAGCT 404994 i vvvv ii i v - iv L1ME4b_3end#L 548 ACTATGCAGCCGTAAAAAAGAATGAGGAAGCT 579 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 37.04 CpG sites = 69, Kimura (unadjusted) = 38.03 Transitions / transversions = 0.88 (69/78) Gap_init rate = 0.09 (50 / 528), avg. gap size = 1.72 (86 / 50) 350 30.94 3.62 5.15 chr6qtel1M 404466 404741 (595259) L1PA13_3end#LINE/L1 31 302 (608) m_b308s551i5 12901 chr6qtel1M 404466 CAAATTTATAAGAATAAAAGTCACTCCTCAATTGATCAATGGTCAAAGGA 404515 i v vvv vv i v i vv i v L1PA13_3end#L 31 CAAATTTACAAGAAAAAAACAAACAACCCCATTAAAAAGTGGGCAAAGGA 80 chr6qtel1M 404516 TATGAACAGATAATTTTCAGGTGATGAAATTAATGTCATCTATACTCATA 404565 i i v iiv v v vv ivii v i v L1PA13_3end#L 81 CATGAACAGACACTTTTCAAAAGAAGACATACATGCGGCCAACAATCATA 130 chr6qtel1M 404566 TGAAAAAAGGCTCTAAATTA-TGATGGATAACACAAATGATTATTTTTAA 404614 i v v i - -v v v v vvv i---- L1PA13_3end#L 131 TGAAAAAAAGCTCAACATCACTGAT-CATTAGAGAAATGCAAATC----A 175 chr6qtel1M 404615 AAATT----TGAAATATCACCTCAAAATGCTCAG-ATGGCATATAATGAT 404659 ii---- i i i v viiv - - v v - L1PA13_3end#L 176 AAACCACAATGAGATACCATCTCACACCAGTCAGAATGGC-TATTATTA- 223 chr6qtel1M 404660 GACTGGAAAAG----ATAATGATAAATGTTGGAGGAGACGTGGGAAAACT 404705 ------ ---- v i i i i v ii vi i ii vv L1PA13_3end#L 224 ------AAAAGTCAAAAAATAACAGATGCTGGCGAGGTTGCGGAGAAAAA 267 chr6qtel1M 404706 GGGAAACTAATGCATGGTTGGTGAAGTTGTGAAATT 404741 i vi v i iv iiiv - L1PA13_3end#L 268 GGAACGCTTATACACTGTTGGTGGGAGTGT-AAATT 302 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 38.42 CpG sites = 39, Kimura (unadjusted) = 40.29 Transitions / transversions = 0.93 (39/42) Gap_init rate = 0.07 (18 / 275), avg. gap size = 1.33 (24 / 18) 683 32.52 3.45 2.71 chr6qtel1M 405501 406050 (593950) L1P3_orf2#LINE/L1 2734 3287 (7) m_b308s551i6 12902 chr6qtel1M 405501 TATAGCAACCTAGTCGTTGACAAACC---CAAAGACCCCAGCTTTTGGGA 405547 i i v i ii v --- i v-- vv v L1P3_orf2#LIN 2734 TACAACCATCTGATCTTTGACAAACCTGACAAAAACA--AGCAATGGGGA 2781 chr6qtel1M 405548 TAAGAACTTACTGTTTGATAAAAATTGGGGGGAAAATTGGAAACTAATAT 405597 - i i iv i i viv vv i vv viv L1P3_orf2#LIN 2782 -AAGGATTCCCTATTTAATAAATGGTGTTGGGAAAACTGGCTAGCCATAT 2830 chr6qtel1M 405598 GGCAGAAA-CTAGGCATTGATCCACACTTAACACCGTACACCAAGATAAG 405646 - - iiivv v i viv i v v i v i v i L1P3_orf2#LIN 2831 G-CAGAAAACTGAAACTGGACCCCTTCCTTACACCTTATACAAAAATTAA 2879 chr6qtel1M 405647 GTCAAAATGGGTTCATGACCTAGGCATAGAA--TGAAATTATTAATAAAT 405694 v i i v v i ii i ii -- i ii v v vvi L1P3_orf2#LIN 2880 CTCAAGATGGATTAAAGACTTAAACGTAAGACCTAAAACCATAAAAACCC 2929 chr6qtel1M 405695 TAGAGGAACAC--AGGATAGTTTACCTCTCAG-ACCTGTGGAAGGGGAAG 405741 i v -- vv --- vi - v iv v v v i L1P3_orf2#LIN 2930 TAGAAGAAAACCTAGGCAA---TACCATTCAGGACATAGGCATGGGCAAA 2976 chr6qtel1M 405742 GACTTTATGACCAAAGCAGAACTAGGGATCATTACTGATCACAAAATAGA 405791 i i i vv vv vi viiv vi vvv v L1P3_orf2#LIN 2977 GACTTCATGACTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGA 3026 chr6qtel1M 405792 AAATTTCGATTATACCAAACTGAAAAGTTTTTGTACA---AACAAAACTA 405838 v v vv ivv ii i i i i i --- vi L1P3_orf2#LIN 3027 CAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTA 3076 chr6qtel1M 405839 --ATGCAGACAAGATTAGAAGGGAAGCAATAAACTGGGAAAATATTTTTA 405886 -- - ----i v iv v v v i i v i v i L1P3_orf2#LIN 3077 TCAT-CAGA----GTGAACAGGCAACCTACAGAATGGGAGAAAATTTTTG 3121 chr6qtel1M 405887 CAGTCAAAGGTTCTGATAAAGGTC--ATTTCCAAAATATATAGAGAATTA 405934 i v vvvv i v -- v i v i ii i v L1P3_orf2#LIN 3122 CAATCTATCCATCTGACAAAGGGCTAATATCCAGAATCTACAAGGAACTT 3171 chr6qtel1M 405935 ACTCTAATTTATAA---AAAATCAAGCCATTCTCCAATTGAAAAATGGTC 405981 vv v i --- v i v -- i - ii i v L1P3_orf2#LIN 3172 AAACAAATTTACAAGAAAAAAACAAACAA--CCCCA-TCAAAAAGTGGGC 3218 chr6qtel1M 405982 AAAGGATATGAACAGACAATTCTCAGATGAAGAAATTGAAACTATTTCTA 406031 i v i v v v vi viiivvi L1P3_orf2#LIN 3219 GAAGGATATGAACAGACACTTCTCAAAAGAAGACATTTATGCGGCCAACA 3268 chr6qtel1M 406032 GTCATATGAAAAGATGCTC 406050 iv i v L1P3_orf2#LIN 3269 AACATATGAAAAAAAGCTC 3287 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 42.48 CpG sites = 83, Kimura (unadjusted) = 43.13 Transitions / transversions = 0.91 (83/91) Gap_init rate = 0.04 (24 / 549), avg. gap size = 1.42 (34 / 24) 1484 25.41 3.83 5.18 chr6qtel1M 405914 406461 (593539) L1ME3G_3end#LINE/L1 7 547 (377) m_b308s551i7 12902 chr6qtel1M 405914 TCCAAAATATATAGAGAATTAACTCTAATTTATAAAAAATCAAGCCATTC 405963 i i i vviv v iv i -- v --v L1ME3G_3end#L 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAA--AAGACA--A 52 chr6qtel1M 405964 TCCAATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGAAG 406013 i v v i v v i L1ME3G_3end#L 53 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chr6qtel1M 406014 AAATTGAAACTATTTCTAGTCATATGAAAAGATGCTCCAAGTCATTATTA 406063 vv iviiivv iv v vv i v L1ME3G_3end#L 103 AAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTA 152 chr6qtel1M 406064 ATCCGAGAAATGCGAATTAAGACAACTCTGAGATACCACTACACACCTGT 406113 v i i i vv i viv ii L1ME3G_3end#L 153 ATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCAT 202 chr6qtel1M 406114 CAGATTGGC-------TAAGA---TGAT---------TGTTGGAGGGGAT 406144 ------- i --- --------- v i i L1ME3G_3end#L 203 CAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGT 252 chr6qtel1M 406145 GTGGGAAAACTGGGACATTGATGCATTGTTGGTGGAGTGATGCATTGTTG 406194 i v v vi v i i i ---------------- L1ME3G_3end#L 253 GTGGGGAAACGGGTACTCTCATACACTGCTGGTG---------------- 286 chr6qtel1M 406195 GTGGAGTTGTGAACGAATCCAACCATTTTGGAGAGTAGTTTGGAACTATG 406244 -- - i ivii v i ? i i i v v - L1ME3G_3end#L 287 --GGAG-TGTAAATTGGTACAGCCNTTTTGGAGGGCAATTTGGCAGTAT- 332 chr6qtel1M 406245 CTCAAAAAGTTATCAAACTGTGCATACCCTTTGATCCAGCAGTGTTACTA 406294 vvv i -- i v i i i vii v L1ME3G_3end#L 333 CTATTAAAAT--TTAAAATGCGCATACCCTTTGACCCAGCAATTCCACTT 380 chr6qtel1M 406295 CTGGGATTATATCCCAAAGAGATTAT-AAAGAAG-GGAAAGGGACCTGTA 406342 ? ?v v i ? i vv -iv v v - v v i --? i L1ME3G_3end#L 381 CTNGGNATCTATCCTANAGAAATACTCGCACATGTGCACAAGGA--NGCA 428 chr6qtel1M 406343 TGTGCACGAATGTTTGTGGCAGCCCTTTTAGTAGCGGCTAGAAACTGGAA 406392 i v i ii v vi v v iii v i i L1ME3G_3end#L 429 TGTACAAGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAA 478 chr6qtel1M 406393 ACTGAATGGATGTCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATA 406442 vivv ii i v i i i i L1ME3G_3end#L 479 ACAACCTAAATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGTATA 528 chr6qtel1M 406443 TGAATATTATGGAATATTA 406461 vv i i L1ME3G_3end#L 529 TCCATACTATGGAATACTA 547 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 31.21 CpG sites = 70, Kimura (unadjusted) = 31.78 Transitions / transversions = 1.13 (70/62) Gap_init rate = 0.06 (33 / 547), avg. gap size = 1.48 (49 / 33) 1370 26.97 4.94 4.94 chr6qtel1M 405919 406546 (593454) L1ME4a_3end#LINE/L1 12 639 (232) m_b308s551i8 12902 chr6qtel1M 405919 AATATATAGAGAATTAACT--CTAATTTATAAAAAATCAAGCC--ATTCT 405964 i ii -- -- v iv i -- v -- iv i L1ME4a_3end#L 12 AATATATAAAGAGCT--CTTACAAATCAATAAGAAA--AAGACGAACACC 57 chr6qtel1M 405965 CCAATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGAAGA 406014 v v i v i v L1ME4a_3end#L 58 CCAATAGAAAAATGGGCAAAGGACATGAACAGACAATTCACAAAAGAAGA 107 chr6qtel1M 406015 AATTGAAACTATTTCTAGTCATATGAAAAGATGCTCCAAGTCATTATTAA 406064 vv iviiivv iv ? i v vv i v L1ME4a_3end#L 108 AATACAAATGGCCAATAAACATATGAAAANATGTTCAACCTCACTAGTAA 157 chr6qtel1M 406065 TCCGAGAAATGCGAATTAAGACAACTCTGAGATACCACTACACACCTGTC 406114 vi i i vv i viv i L1ME4a_3end#L 158 TCAAAGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCTATC 207 chr6qtel1M 406115 AGATTGGCTAAGAT------GAT-------------TGTTGGAGGGGATG 406145 i v ------ ------------- v i i L1ME4a_3end#L 208 AAATTGGCAAAGATTTAAAAGATTGATAATACCCAGTGTTGGCGAGGGTG 257 chr6qtel1M 406146 TGGGAAAACTGGGACATTGATGCATTGTTGGTGGAGTGATGCATTGTTGG 406195 ?i v v vi v i i i ----------------- L1ME4a_3end#L 258 TGGNGAAACGGGCACTCTCATACACTGCTGGTG----------------- 290 chr6qtel1M 406196 TGGAGTTGTGAACGAATCCAACCATTTTGGAGAGTAGTTTGGAACTATGC 406245 - - i ivii v v i i i i v v i L1ME4a_3end#L 291 -GGAG-TGTAAATTGGTACAACCTTTCTGGAGGGCAATTTGGCAATATGT 338 chr6qtel1M 406246 TCAAAAAGTTATCAAACTGTGCATACCCTTTGATCCAGCAGTGTTACTAC 406295 viv iiv v v ? i i i vii v L1ME4a_3end#L 339 ATCAAAAGCCTTAAAAATGTNCATACCCTTTGACCCAGTAATTCCACTTC 388 chr6qtel1M 406296 TGGGATTATATCCCAAAGAGATTAT-AAAGAAG-GGAAAGGGACCTGTAT 406343 i v v i i i v - i v - ? v ii -- v L1ME4a_3end#L 389 TAGGAATTTATCCTAAGGAAATAATCAGAGATGTGNACAAAGA--TTTAT 436 chr6qtel1M 406344 GTGCACGAATGTTTGTGGCAGCCCTTTTAGTAGCGGCTAGAAACTGGAAA 406393 i v i ii v vi v vi iii v i i L1ME4a_3end#L 437 GTACAAGGATGTTCATCGCAGCATTATTTATAATAGCGAAAAATTGGAAA 486 chr6qtel1M 406394 CTGAATGGATGTCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATAT 406443 vivv ii v i v i ? i i i i L1ME4a_3end#L 487 CAACCTAAATGTCCAACAATAGGGGANTGGTTAAATAAATTATGGTACAT 536 chr6qtel1M 406444 GAATATTATGGAATATTACTGT-TCTATAAGAAATGA-----CCAACAGG 406487 vv ?v - i-v i v i ? -----i i - i L1ME4a_3end#L 537 CCATANAATGGAATATTA-TGCAGCCATTAAAAATNATGTTTTCGA-AGA 584 chr6qtel1M 406488 ATGATTTCAGAAAGGCCTGGAGAGACTTACACGAACTGATGCTGAGTGAA 406537 - --- v i v ii i iviv i vv i i i L1ME4a_3end#L 585 AT-ATTT---AATGACATGGGAAAATGCTCATGATATAATGTTAAGTGAA 630 chr6qtel1M 406538 ATGAGCAGG 406546 vi L1ME4a_3end#L 631 AAAAGCAGG 639 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 34.36 CpG sites = 91, Kimura (unadjusted) = 34.63 Transitions / transversions = 1.30 (91/70) Gap_init rate = 0.06 (39 / 627), avg. gap size = 1.59 (62 / 39) 14 18.38 0.00 0.00 chr6qtel1M 407081 407111 (592889) (TTTG)n#Simple_repeat 1 31 (0) m_b308s252i24 12903 chr6qtel1M 407081 TTTGTTTGTTTATTTGTTTTCTTTCTTGTTT 407111 i vi vi (TTTG)n#Simpl 1 TTTGTTTGTTTGTTTGTTTGTTTGTTTGTTT 31 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 229 19.41 1.45 2.94 chr6qtel1M 407805 407873 (592127) C DNM1r#Unknown (2116) 2546 2479 m_b309s502i0 12904 chr6qtel1M 407805 TATGCATATATATATATACACATATGTATATATAATATGCCTATATATA- 407853 i? ii i i i i- ii vi i - C DNM1r#Unknown 2546 TATANATACGTATATATACACATATATACACAC-ATACACACATATACAC 2498 chr6qtel1M 407854 ATATATATACACACAATACA 407873 i - C DNM1r#Unknown 2497 ACATATATACACAC-ATACA 2479 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 22.19 CpG sites = 12, Kimura (unadjusted) = 24.57 Transitions / transversions = 12.00 (12/1) Gap_init rate = 0.04 (3 / 68), avg. gap size = 1.00 (3 / 3) 230 30.00 2.86 0.00 chr6qtel1M 407900 407969 (592031) DNM1r#Unknown 2475 2546 (2116) m_b309s502i1 12904 chr6qtel1M 407900 CACATATATATGCACATGCATATATACATATATGTGT--GTGTACACAAA 407947 i i i iii ii i i ii i -- ii i v DNM1r#Unknown 2475 CACGTGTATGTGTGTATATATGTGTGTATATGTGTGTATGTGTGTATATA 2524 chr6qtel1M 407948 TGTGTATAAGTACATATATACA 407969 vi i ? i DNM1r#Unknown 2525 TGTGTATATATACGTATNTATA 2546 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 38.98 CpG sites = 19, Kimura (unadjusted) = 44.83 Transitions / transversions = 9.50 (19/2) Gap_init rate = 0.01 (1 / 69), avg. gap size = 2.00 (2 / 1) 247 24.24 3.03 0.00 chr6qtel1M 407924 407989 (592011) C DNM1r#Unknown (2116) 2546 2479 m_b309s502i2 12904 chr6qtel1M 407924 TACATATATGTGTGTGTACACAAATGTGTATAAGTACATA--TATACACA 407971 i ? i i i i v i ii i vi i -- C DNM1r#Unknown 2546 TATANATACGTATATATACACATATATACACACATACACACATATACACA 2497 chr6qtel1M 407972 CAAACATACACACATGCA 407989 v i i C DNM1r#Unknown 2496 CATATATACACACATACA 2479 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 29.53 CpG sites = 13, Kimura (unadjusted) = 31.96 Transitions / transversions = 4.33 (13/3) Gap_init rate = 0.02 (1 / 65), avg. gap size = 2.00 (2 / 1) 12 28.32 0.00 0.00 chr6qtel1M 409465 409501 (590499) (ACAT)n#Simple_repeat 1 37 (0) m_b309s252i1 12905 chr6qtel1M 409465 ACACACATACACACATACATATATGTATATGTATATA 409501 i i i ii ii i (ACAT)n#Simpl 1 ACATACATACATACATACATACATACATACATACATA 37 Matrix = Unknown Transitions / transversions = 1.00 (8/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 12 27.38 0.00 0.00 chr6qtel1M 409469 409505 (590495) (ACATAT)n#Simple_repeat 1 37 (0) m_b309s252i2 12905 chr6qtel1M 409469 ACATACACACATACATATATGTATATGTATATATTTA 409505 i i ii ii i v (ACATAT)n#Sim 1 ACATATACATATACATATACATATACATATACATATA 37 Matrix = Unknown Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 13 24.69 0.00 0.00 chr6qtel1M 409471 409505 (590495) (ATAT)n#Simple_repeat 1 35 (0) m_b309s252i3 12905 chr6qtel1M 409471 ATACACACATACATATATGTATATGTATATATTTA 409505 i i i i i i v (ATAT)n#Simpl 1 ATATATATATATATATATATATATATATATATATA 35 Matrix = Unknown Transitions / transversions = 6.00 (6/1) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 261 34.38 1.04 0.00 chr6qtel1M 409714 409809 (590191) MIRc#SINE/MIR 2 98 (170) m_b309s601i0 12906 chr6qtel1M 409714 GAGGAAGT-TAGGACAGTACATAAAGCACCAGCACTGGAGTCAGAATATC 409762 v - i vi iv v i ii vvi i viv MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr6qtel1M 409763 CTGAGTTTAAGTCCAGTCTTAGATACTTACCACCGGAATGTCCCTGG 409809 i ii v v iv vi i v v vi v i MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 98 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 44.79 CpG sites = 17, Kimura (unadjusted) = 46.92 Transitions / transversions = 1.06 (17/16) Gap_init rate = 0.01 (1 / 95), avg. gap size = 1.00 (1 / 1) 44 23.90 2.22 2.22 chr6qtel1M 411441 411575 (588425) (AAGAAG)n#Simple_repeat 1 135 (0) m_b309s252i4 12907 chr6qtel1M 411441 AAGAAGAAGAAAAAG-TGAAGGAGAAGGATACAG-AGGAGAATGAGGAAG 411488 i -v i i v - - i - i (AAGAAG)n#Sim 1 AAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA-AGAAGAAGAA-GAAGAAG 48 chr6qtel1M 411489 AGAAAAAAGAA-AAGAAAAACAAGGGGAAGGGAAAGAATAAGAAAAAGGA 411537 ii i - i v ii iii v i - (AAGAAG)n#Sim 49 AAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAA-GA 97 chr6qtel1M 411538 AGAAGAAAAATAAAAACAAGAAGAACAAGAAGCATAAG 411575 i v i v v v v (AAGAAG)n#Sim 98 AGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAG 135 Matrix = Unknown Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.04 (6 / 134), avg. gap size = 1.00 (6 / 6) 21 0.00 3.85 0.00 chr6qtel1M 413143 413168 (586832) (CT)n#Simple_repeat 1 27 (0) m_b309s252i5 12908 chr6qtel1M 413143 CTCTCTCTCTCT-TCTCTCTCTCTCTC 413168 - (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTC 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.04 (1 / 25), avg. gap size = 1.00 (1 / 1) 597 33.21 2.81 4.28 chr6qtel1M 415454 416164 (583836) L1M3_orf2#LINE/L1 2434 3134 (154) m_b309s551i0 12909 chr6qtel1M 415454 AAAATGACAATTCTATCTAAAGTGATCTACTTGTTCAGTGCCATACCAAT 415503 v v v i i i vvi i v v v L1M3_orf2#LIN 2434 AAAATGTCCATACTACCCAAAGCGATCTACAGATTCAATGCAATCCCTAT 2483 chr6qtel1M 415504 CAAACTGCCAAAAACATTATTTTATACAACTAGAAAAAA--ATAACAAAA 415551 v v vii - i v v -- vvi L1M3_orf2#LIN 2484 CAAAATCCCAATGGCATT-TTTTACAGAAATAGAAAAAACAATCCTAAAA 2532 chr6qtel1M 415552 TTCATCTGGAGA-ATAAAAGGTGAAGAATATCAAGGGCATTAATGAAAAA 415600 v iv- i iivvv v v ii v vv i L1M3_orf2#LIN 2533 TTCATATGGAACCACAAAAGACCCCGAATAGCCAAAGCAATCTTGAGAAA 2582 chr6qtel1M 415601 TAAATAGAAAGGATGGTGACTTAGCAGGACCAAACCTAAAACTGCATTAT 415650 v iv v v- v i v vi vvv vi ii v v ii i L1M3_orf2#LIN 2583 GAAGAACAAAGC-TGGAGGCATCACACTTCCTGATTTCAAAATATATTAC 2631 chr6qtel1M 415651 AAGGCAGCAGTCATTAAAACCATTTGGTACTGGCTAAGAAATAG---TGG 415697 i vi v i vi v vv i i --- -i L1M3_orf2#LIN 2632 AAAGCTACAGTAATCAAAACAGTATGGTACTGGCATAAAAACAGACAT-A 2680 chr6qtel1M 415698 TGGATCAGGAGAATAAATTAAATATACAAGACACAATAATCATGGCCTAT 415747 i i ivi i i v i v vv v v i - vi i- v L1M3_orf2#LIN 2681 TAGACCAATGGAACAGAATAGAGAGCCCAGAAATAA-ACCCAC-GCATAT 2728 chr6qtel1M 415748 AGCAATTAAAAG---TTTGATAA--ATGCTCAAGCTCCAGTCTCTGCAAT 415792 - ii i vv --- i i --i iv iiv v -- vv viiv L1M3_orf2#LIN 2729 A-CGGTCAACTGATCTTCGACAAGGGTGCCAAGAATACA--CAATGGGGA 2775 chr6qtel1M 415793 AAGAATTCACTATTTAACAAAAATTGCTGGGAAAACTGGAAAATAATATA 415842 i vvv v i viv i v viv i i L1M3_orf2#LIN 2776 AAGGATAGTCTCTTCAACAAATGGTGTTGGGAAAACTGGATATCCACATG 2825 chr6qtel1M 415843 TCACAAACTCAACATAGACCTACATCTCATACCCTGTAATAAAATCAAAT 415892 iv v i v v vv i ivi i i v ii vv v L1M3_orf2#LIN 2826 CAAAAGAATGAAATTGGACCCTTATCTTACACCATACACAAAAATCAACT 2875 chr6qtel1M 415893 CAAAATGGGTACATGATTTGGACATCAAGGATGATACCATAAACCAATTA 415942 i vv v i ii i v iivv v i v vvi L1M3_orf2#LIN 2876 CAAAATGGATTAAAGACTTAAACGTAAGACCTGAAACTATAAAACTCCTA 2925 chr6qtel1M 415943 GAAG--AACA-AGGGGAAAATCTACCTATCA--GATCTTTGAAGAAGGGA 415987 -- - v v ? iv -- i v v ------ L1M3_orf2#LIN 2926 GAAGAAAACATAGGGGAAAAGCTTCNTGACATTGGTCTTGGCA------A 2969 chr6qtel1M 415988 GGAATTTATGATCAAAGAAGAACTATTTTATTCTGAAAGAAC-TTTAAGA 416036 v v iv i------------- v v iv ii v -vvi v L1M3_orf2#LIN 2970 TGATTTCTTGG-------------ATATGACACCAAAAGCACAGGCAACA 3006 chr6qtel1M 416037 AAGGC-AAAATGGACAACTTTGATCACATTAAATTAAAAAGGTTTTGCAC 416085 i - i v vv ii i i v i L1M3_orf2#LIN 3007 AAAGCAAAAATAGACAAGTGGGACTACATCAAACTAAAAAGCTTCTGCAC 3056 chr6qtel1M 416086 AAACAAAATCAACAG-AAACAAGATTAAAAGGGAA-GTACATAACTGGGA 416133 - i ivv i-v iii v v -v iv - - L1M3_orf2#LIN 3057 -AGCAAAGGAAACAATCAACAGAGTGAAAAGGCAACCTACGGAA-TGGG- 3103 chr6qtel1M 416134 AAAAAATCTTTACAACCAGTATTTCTAATAA 416164 i v i v vi v i L1M3_orf2#LIN 3104 AGAAAATATTTGCAAACCATATATCTGATAA 3134 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 42.80 CpG sites = 104, Kimura (unadjusted) = 44.32 Transitions / transversions = 0.85 (104/122) Gap_init rate = 0.06 (42 / 710), avg. gap size = 1.19 (50 / 42) 361 31.25 2.08 0.00 chr6qtel1M 416864 416959 (583041) C MIRc#SINE/MIR (163) 105 8 m_b309s601i1 12910 chr6qtel1M 416864 GACTTATTGAAGGTCATACAACTATTAAGTATCTGA-CTTAAATTCAAAT 416912 iiiv i i v iv v - ivii i i i C MIRc#SINE/MIR 105 GACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAAC 56 chr6qtel1M 416913 TCAAGTCT-CCTGACTGTAGATCCAATTTTCTGTCCACTGCTTTACAC 416959 i i - vi ii i vi v vii C MIRc#SINE/MIR 55 CCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACAC 8 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 39.23 CpG sites = 21, Kimura (unadjusted) = 43.08 Transitions / transversions = 2.33 (21/9) Gap_init rate = 0.02 (2 / 95), avg. gap size = 1.00 (2 / 2) 12 31.98 1.45 2.94 chr6qtel1M 416965 417033 (582967) (AAAG)n#Simple_repeat 1 68 (0) m_b309s252i6 12911 chr6qtel1M 416965 AATGAGAGAGGGAGAGAAAGAAAGTGTGGAGCAGAAGAAAGAAAG-CTGA 417013 v i ii i viv i iv - -vv (AAAG)n#Simpl 1 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA-AAGAAAGAAAGAAAGA 49 chr6qtel1M 417014 AGAGTAACATACAAAGAAAG 417033 - v v v v (AAAG)n#Simpl 50 A-AGAAAGAAAGAAAGAAAG 68 Matrix = Unknown Transitions / transversions = 0.70 (7/10) Gap_init rate = 0.04 (3 / 68), avg. gap size = 1.00 (3 / 3) 16 29.73 0.00 1.61 chr6qtel1M 417082 417144 (582856) (TAAATAA)n#Simple_repeat 1 62 (0) m_b309s252i7 12911 chr6qtel1M 417082 TAAATGATAAATAATAAAAAGTAATCACTTACAAAATGAATCATATTTAA 417131 i v i vi -v v v i v vv (TAAATAA)n#Si 1 TAAATAATAAATAATAAATAATAAATA-ATAAATAATAAATAATAAATAA 49 chr6qtel1M 417132 TATAAAATTAATA 417144 v v v (TAAATAA)n#Si 50 TAAATAATAAATA 62 Matrix = Unknown Transitions / transversions = 0.36 (4/11) Gap_init rate = 0.02 (1 / 62), avg. gap size = 1.00 (1 / 1) 19 11.56 0.00 0.00 chr6qtel1M 417190 417217 (582783) (A)n#Simple_repeat 1 28 (0) m_b309s252i8 12912 chr6qtel1M 417190 AAAAAAAAAAAAAAAACAAATAAGAAAA 417217 v v i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA 28 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 411 28.24 0.00 1.18 chr6qtel1M 418578 418663 (581337) Charlie1b#DNA/hAT-Charlie 1 85 (438) m_b309s502i3 12913 chr6qtel1M 418578 CAGTGGTTCTCAAAGTATGGTCTAGAGAATCCTGAGGATCTCTGAAACCC 418627 i i ii i vi i i i i i Charlie1b#DNA 1 CAGCGGTTCTCAAAGTGTGGTCCGGGGACCCCTGGGGGTCCCCGAGACCC 50 chr6qtel1M 418628 TTTTAAAAGATCTACAAATTCAAAAATAGTTTTTAT 418663 i iii i ii i iv v - i Charlie1b#DNA 51 TTTCAGGGGGTCCGCGAGGTCAAAACTA-TTTTCAT 85 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 28.97 CpG sites = 21, Kimura (unadjusted) = 39.52 Transitions / transversions = 7.00 (21/3) Gap_init rate = 0.01 (1 / 85), avg. gap size = 1.00 (1 / 1) 584 16.02 5.97 2.16 chr6qtel1M 418646 418779 (581221) Charlie1a#DNA/hAT-Charlie 1317 1455 (0) m_b309s502i4 12914 chr6qtel1M 418646 TTCAAAAAT-----AGTTTTTATTTCCAATATGGTAAATGTCTATAAATA 418690 i ----- v i i v i Charlie1a#DNA 1317 TTTAAAAATTTCTCAGTTTTAATTTCTAATATGGTAAATATCGATAGATA 1366 chr6qtel1M 418691 TAACCCAGATAAACAAAAATGCTTTGGAGAGATCTTCAATCATTTTTAAT 418740 v iiv --- i i v v Charlie1a#DNA 1367 TAACCCACATAAACAAAAGCTCTTTGG---GGTCCTCAATAATTTTTAAG 1413 chr6qtel1M 418741 AGGATAAA--GATACTGAAAAC-AAAAGTTTGAGAACCACTG 418779 vi -- i v i v - i Charlie1a#DNA 1414 AGTGTAAAGGGGTCCTGAGACCAAAAAGTTTGAGAACCGCTG 1455 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 17.30 CpG sites = 12, Kimura (unadjusted) = 18.21 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.05 (6 / 133), avg. gap size = 1.83 (11 / 6) 18 12.17 0.00 0.00 chr6qtel1M 419560 419586 (580414) (T)n#Simple_repeat 1 27 (0) m_b309s252i9 12915 chr6qtel1M 419560 TTTTTGTTTTTTGTTTTTGTTTTTTTT 419586 v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTT 27 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 413 24.17 0.74 8.73 chr6qtel1M 420011 420146 (579854) C MIRc#SINE/MIR (141) 127 2 m_b309s601i2 12916 chr6qtel1M 420011 CTGAGGC-AATTGGGATTAAATGACTTGCCCAGGGTCACACAGCTAGAAA 420059 -v vv i i i i --- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG--- 81 chr6qtel1M 420060 ATGTTAAGTGTCTGAGGGCAGTTTTGAAACTCAGGTCCTCCTGACTTCAG 420109 ---- v v vvvi vi i - i i i i C MIRc#SINE/MIR 80 ----TAAGTGGCAGAGCCGGGACTCG-AACCCAGGTCTTCCTGACTCCAA 36 chr6qtel1M 420110 GGCTGGTGCTCTACCTACTGTGCCACCTAGCTGCCCC 420146 v ii vi i ii ---i i C MIRc#SINE/MIR 35 GTCCAGTGCTCTTTCCACTGCACCAC---ACTGCCTC 2 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 28.55 CpG sites = 19, Kimura (unadjusted) = 29.72 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.09 (12 / 135), avg. gap size = 1.00 (12 / 12) 363 25.71 3.89 2.75 chr6qtel1M 421010 421189 (578811) C L1M3_orf2#LINE/L1 (2084) 1204 1023 m_b309s551i1 12917 chr6qtel1M 421010 CATTAGTGATATTGTCACCCTTTTCATTTTTGATGCGGATGATTTGGAGT 421059 i vi v v ii i viviv v iivi C L1M3_orf2#LIN 1204 CATCAGTTGTAATGTCTCCTCTTTCATTTCTGATTTTATTTATTTGAGTC 1155 chr6qtel1M 421060 TTTTCTGTCTTT--TAATCAAATTAAACAATGGTTTATCTATTTAATTTA 421107 i v i -- i v ii ---- i v vi C L1M3_orf2#LIN 1154 TTCTCTTTTTTTCTTAGTCTAGCTAAA----GGTTTGTCAATTTTGTTTA 1109 chr6qtel1M 421108 T---TTCACAAAACCAACTCTTAGTTTTATTTATTAATTCAATGGCTTTT 421154 --- v ii v vv v v i C L1M3_orf2#LIN 1108 TCTTTTCAAAAAACCAACTCTTAGTTTCGTTGATTTTTTCTATTGTTTTT 1059 chr6qtel1M 421155 -TACTCTCAATTTTATCAATCTC-ACTACTAATTTTT 421189 - ? v i iv i -i - i C L1M3_orf2#LIN 1058 CTANTCTCTATTTCATTTATTTCTGCT-CTAATCTTT 1023 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 31.31 CpG sites = 25, Kimura (unadjusted) = 32.26 Transitions / transversions = 1.25 (25/20) Gap_init rate = 0.05 (9 / 179), avg. gap size = 1.33 (12 / 9) 471 22.36 0.79 8.47 chr6qtel1M 421444 421570 (578430) C MIRc#SINE/MIR (141) 127 10 m_b309s601i3 12918 chr6qtel1M 421444 CTGAGGC-AATTGGGGTTAAGTGACTTGCCCAGGGTTACATATAACTAGG 421492 -v vv i i i i --i - C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACA--GCTAG- 81 chr6qtel1M 421493 AATTAATAAATGTCTGAGGTGAGATTTGAACTCATGTCCTTCCCGACTTC 421542 ------ i v v vi i i i i v - i i C MIRc#SINE/MIR 80 ------TAAGTGGCAGAGCCGGGACTCGAACCCAGGTC-TTCCTGACTCC 38 chr6qtel1M 421543 AGGGCTAGTGCTCTATCCACTAAACCAC 421570 i v i v iv C MIRc#SINE/MIR 37 AAGTCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 24.58 CpG sites = 16, Kimura (unadjusted) = 26.92 Transitions / transversions = 1.60 (16/10) Gap_init rate = 0.09 (11 / 126), avg. gap size = 1.00 (11 / 11) 46 29.01 2.99 1.18 chr6qtel1M 422123 422289 (577711) (TA)n#Simple_repeat 1 170 (0) m_b309s252i10 12919 chr6qtel1M 422123 TATATATGGAAATACATCTATATATCTATTGACTTGTATATGTATGTATA 422172 iv v i v v vv iv i i i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr6qtel1M 422173 GGT-TTTCTCATATATCTGTATCTATATATCTTTGTATATACAGTTTATA 422221 vi - v v - v i v v v i i - v (TA)n#Simple_ 51 TATATATAT-ATATATATATATATATATATATATATATATATA-TATATA 98 chr6qtel1M 422222 TGTTGATGTGTGCAT-TATATATATATATA-ATCAAT-TATGTAT-TGTA 422267 i vv i i ii - - vv - i - i (TA)n#Simple_ 99 TATATATATATATATATATATATATATATATATATATATATATATATATA 148 chr6qtel1M 422268 TATACATATACATATACATATA 422289 i i i (TA)n#Simple_ 149 TATATATATATATATATATATA 170 Matrix = Unknown Transitions / transversions = 1.05 (20/19) Gap_init rate = 0.04 (7 / 166), avg. gap size = 1.00 (7 / 7) 236 35.39 5.11 5.11 chr6qtel1M 425989 426125 (573875) L3#LINE/CR1 3615 3751 (348) m_b309s601i4 12920 chr6qtel1M 425989 CAAATTTAAAGAAGGACATTTATATTTTAATAATTATCTAGATACGGATG 426038 v v i v i vvi iivivvii i viv iii L3#LINE/CR1 3615 CACATTTTAAGAGGGACATTGACAAACTGGAGCGCGTCCAGAGGAGAGCG 3664 chr6qtel1M 426039 ACCAAAAATCACGAAGGACTTAGTGAAA-------ATATGCAGAATTCAT 426081 ii - vii iii i -- ------- vi i---- L3#LINE/CR1 3665 ACCAGGA-TGGTGAAGGGTCTGG--AAACCATGTCATATGAGGAAC---- 3707 chr6qtel1M 426082 GGTTCAAGAAAACTGAGATGTTTTTCCTGAGGAAGAAAAGACTT 426125 v i viv i vv ii i L3#LINE/CR1 3708 GGTTGAAGGAACTGGGGATGTTTAGCCTGGAGAAGAGAAGACTT 3751 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 45.74 CpG sites = 29, Kimura (unadjusted) = 50.59 Transitions / transversions = 1.71 (29/17) Gap_init rate = 0.06 (8 / 136), avg. gap size = 1.75 (14 / 8) 15 18.27 5.41 0.00 chr6qtel1M 426629 426665 (573335) (AT)n#Simple_repeat 1 39 (0) m_b309s252i11 12921 chr6qtel1M 426629 ATATATAT-TAAAT-TCAATATATGTATACATATTTATA 426665 - v - vv i i v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATA 39 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 17 25.18 1.72 1.72 chr6qtel1M 426698 426755 (573245) (AAGA)n#Simple_repeat 1 58 (0) m_b309s252i13 12922 chr6qtel1M 426698 AAAAAAGAAAGAAAG-AAGAAAGAAAACAAAATTCAAATAAACAACAAAA 426746 i - iv i vvv v v - i (AAGA)n#Simpl 1 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAA-AGAA 49 chr6qtel1M 426747 AGAGTGAAA 426755 iv (AAGA)n#Simpl 50 AGAAAGAAA 58 Matrix = Unknown Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.04 (2 / 57), avg. gap size = 1.00 (2 / 2) 385 22.50 10.71 0.81 chr6qtel1M 427331 427442 (572558) C MIR#SINE/MIR (43) 219 97 m_b309s601i5 12923 chr6qtel1M 427331 CTGTGCTAAGTACCTTACA--------ATCATGTAATCCTCACAACAACC 427372 v ii i --------v v C MIR#SINE/MIR 219 CTGTTCTAAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACC 170 chr6qtel1M 427373 CTGGAGGGCAGATTCTATTATTATTTTC-TTT--CAGAATAGTAAACTGA 427419 ivii i i v iii - -- vv v C MIR#SINE/MIR 169 CTATGAGGTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGA 120 chr6qtel1M 427420 GGTA-AAATAGCATGAGGTAACTT 427442 i - i v -i v i C MIR#SINE/MIR 119 GGCACAGAGAG-GTTAAGTAACTT 97 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 25.92 CpG sites = 15, Kimura (unadjusted) = 27.31 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.05 (5 / 111), avg. gap size = 2.60 (13 / 5) 12 17.86 6.25 6.25 chr6qtel1M 429936 429999 (570001) (TATTTA)n#Simple_repeat 1 64 (0) m_b309s252i14 12924 chr6qtel1M 429936 TATTGTATATTT-TATCTTCAAGTTATA--TGTATTTATAATTATTCTAT 429982 - - - vv v -- i v - v v (TATTTA)n#Sim 1 TATT-TATATTTATAT-TTATATTTATATTTATATTTATATTTA-TATTT 47 chr6qtel1M 429983 ACATTGCATATTTA-ATT 429999 i -i - (TATTTA)n#Sim 48 ATATT-TATATTTATATT 64 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.11 (7 / 63), avg. gap size = 1.14 (8 / 7) 13 14.21 3.23 0.00 chr6qtel1M 430378 430408 (569592) (TTGGA)n#Simple_repeat 1 32 (0) m_b309s252i15 12925 chr6qtel1M 430378 TTGGAAT-TATTAAATTGGATTGGATTGGATT 430408 v -v ii (TTGGA)n#Simp 1 TTGGATTGGATTGGATTGGATTGGATTGGATT 32 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.03 (1 / 30), avg. gap size = 1.00 (1 / 1) 17 17.48 0.00 2.50 chr6qtel1M 431305 431345 (568655) (AGCTGAA)n#Simple_repeat 1 40 (0) m_b309s252i16 12926 chr6qtel1M 431305 AGCTCAAAGCTGAATGCTGAATGCTGAAACAGGAAAGACTG 431345 v v v vvv - (AGCTGAA)n#Si 1 AGCTGAAAGCTGAAAGCTGAAAGCTGAAAGCTGAAAG-CTG 40 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 42 31.00 0.75 0.00 chr6qtel1M 431984 432117 (567883) (CT)n#Simple_repeat 1 135 (0) m_b309s252i17 12927 chr6qtel1M 431984 CTCTCTGTGTCTTTGTCTCTTGGTCTCCCTCCCCCTGTATCTCTCTCTGT 432033 v v i v ivv i i i v v v (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chr6qtel1M 432034 CTGTCTTTCTCTGTCTCTGTCTCTGTCTTTCTGTCTGTCTCTCTATATAT 432083 v i v v v i v v v v v (CT)n#Simple_ 51 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 100 chr6qtel1M 432084 ATAT-TTTTTCTTTCTCTCTTTCATTTTCTCTGTC 432117 v v - i i i i vi i v (CT)n#Simple_ 101 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 135 Matrix = Unknown Transitions / transversions = 0.62 (13/21) Gap_init rate = 0.01 (1 / 133), avg. gap size = 1.00 (1 / 1) 235 35.19 4.42 4.42 chr6qtel1M 432280 432505 (567495) L3#LINE/CR1 3133 3358 (741) m_b309s601i6 12928 chr6qtel1M 432280 ATAGGAATCTATC-TTGAATCTAGACTAATTAGCATTTT-AGCAATGATA 432327 i iv i - ivi ivv iv i i - v iv L3#LINE/CR1 3133 ACAGGGCTCTGTCCTTGGCCCTGTCCTGTTCAACATTTTTATCAATGACT 3182 chr6qtel1M 432328 TAGATAAGCAGGTAG--TTTATGC--ATTAAATTTAAATA-GTCAATAAA 432372 i i iv vi --vvi -- i iv v - v vv i L3#LINE/CR1 3183 TGGATGAAGACATAGAAGGCATGCTTATCAAATTTGCAGATGACACAAAG 3232 chr6qtel1M 432373 CTGGGAGTAACATTTAAAATGTTGGATGGCCAAGTTAAGATTAAACTAAA 432422 vi i vi v i ? i vi i i --- ---- L3#LINE/CR1 3233 CTGGGAGGGATAGCTAATACGNTGGATGACAGAATCAAGATT---C---- 3275 chr6qtel1M 432423 AAAAAAAGTTCCTGAAATGTCAGAAC-ATGCATACTAATTAAAGAAAATT 432471 -- ? v ii v v iii - vii- v viv v i v L3#LINE/CR1 3276 --AAAANGATCTCGACAGGCTGGAACGATGGGC-CGAAACCAACAAGATG 3322 chr6qtel1M 432472 AAAATTTTTAGAAACAAATATCA--TCTTAAATTTA 432505 v vvi ii i i v -- i iv L3#LINE/CR1 3323 AAATTTAACAGGGATAAATGTAAAGTCCTGCATTTA 3358 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 47.80 CpG sites = 42, Kimura (unadjusted) = 49.64 Transitions / transversions = 1.24 (42/34) Gap_init rate = 0.08 (17 / 225), avg. gap size = 1.18 (20 / 17) 15 7.67 6.67 3.23 chr6qtel1M 432611 432640 (567360) (TC)n#Simple_repeat 1 31 (0) m_b309s252i18 12929 chr6qtel1M 432611 TCTCTCTCTC-CTTTCTTTCTCTCATCT-TCT 432640 - i i - - (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTC-TCTCTCT 31 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.10 (3 / 29), avg. gap size = 1.00 (3 / 3) 285 30.84 16.17 2.92 chr6qtel1M 433192 433525 (566475) L2c_3end#LINE/L2 24 400 (78) m_b309s601i7 12930 chr6qtel1M 433192 CCTTTCCCAAGCTTC--CTCATTCACCATCACTTACTCTTCTA------T 433233 i -- i -- v i -- v i v vi i ------ L2c_3end#LINE 24 CCTCTCC--AGCCTCATCTCCTCCAC--TCCCCTCCTCGCCCACTATGCT 69 chr6qtel1M 433234 CCAGTAACATCAGCCTTCTGATTATTCCACAAACAAG----AGAGCT--- 433276 iv iiiiv ? vii- v v ---- vv --- L2c_3end#LINE 70 CCAGCCACACTGAACTNCTTGC-ATTCCCCAAACACGCCGCAGTTCTTTC 118 chr6qtel1M 433277 CTGGGTATAT-TCTTTG-----ACTAGTTACCCATGAATAAAATACTCT- 433319 vv vii?-i -----i - v iv vv ii i - L2c_3end#LINE 119 CTGCCTCCGNGCCTTTGCACATGCT-GTTCCCTCTGCCTGGAATGCTCTT 167 chr6qtel1M 433320 CCCTTCTCCTCTCCAGT--ACTAACTTCCCTGGGCTTA-CTTTTAAAAGT 433366 ii - vi--i -- i-- i - i i i?v L2c_3end#LINE 168 CCCCCCTCCT-TCCACCTGGCTAACT--CCTA--CTCATCCTTCAAGNCT 212 chr6qtel1M 433367 TAACTAAATTCTCATCTT-TCCAGAAAGCCTTTCC-AACTC---ATGTTA 433411 i i v iv v i i- i i i -i i --- v ?iv L2c_3end#LINE 213 CAGCTCAGATGTCACCTCCTCCGGGAAGCCTTCCCTGACCCCCCAAGNCT 262 chr6qtel1M 433412 ATTCTAGCTCCTTTCCTCTGT-------TAATCACTTATTTAATCTG--- 433451 v v v ii ------- iivv i i i vv v--- L2c_3end#LINE 263 AGTCTAGGTGCCCTCCTCTGTGCTCCCATAGCACCCTGTCTATACTCCCA 312 chr6qtel1M 433452 -TATATGACTTGCTTTCAA----TATT-------TGTATTTACTTGT--A 433487 - vv iiiv i ---- ------- v i ? --i L2c_3end#LINE 313 TTATAGCACTTATCATTAACTTGTATTGTAATTGTCTGTTTACNTGTCTG 362 chr6qtel1M 433488 GCTCCCCCATTAGATTACAAGCTCTTTGAAGGCAGGGA 433525 v i i i iii i i L2c_3end#LINE 363 TCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGA 400 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 41.23 CpG sites = 62, Kimura (unadjusted) = 42.44 Transitions / transversions = 1.63 (62/38) Gap_init rate = 0.09 (29 / 333), avg. gap size = 2.24 (65 / 29) 33 9.55 0.00 0.00 chr6qtel1M 433789 433834 (566166) (AT)n#Simple_repeat 1 46 (0) c_b309s251i0 12931 chr6qtel1M 433789 ATATATATATATATATATACATATATATATGTATGTATACATATAT 433834 i i i i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATAT 46 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 36 27.78 1.89 0.93 chr6qtel1M 433841 433946 (566054) (AT)n#Simple_repeat 1 107 (0) m_b309s252i19 12931 chr6qtel1M 433841 ATATATATCTATACATATGCACACATACATACATATATATGT-TGTATCT 433889 v i ii i i i i i - i v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr6qtel1M 433890 GTATAAATATATATA-ATATGTGTATATATACACACATACACATGCATAA 433938 i v - i i i i i i i ii v (AT)n#Simple_ 51 ATATATATATATATATATATATATATATATATATATATATATATATATAT 100 chr6qtel1M 433939 ATACTATA 433946 - (AT)n#Simple_ 101 ATA-TATA 107 Matrix = Unknown Transitions / transversions = 4.75 (19/4) Gap_init rate = 0.03 (3 / 105), avg. gap size = 1.00 (3 / 3) 282 27.95 7.69 3.70 chr6qtel1M 434079 434208 (565792) MIRb#SINE/MIR 91 225 (43) m_b309s601i8 12932 chr6qtel1M 434079 TATGAAATTGGGCAAATCATTTAACTTATTTATGCCACAGTCTTCTTCTC 434128 i vv i i i i v i iv v - -- MIRb#SINE/MIR 91 TGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGT-TTC--CTC 137 chr6qtel1M 434129 ATTTGAAAAATTGGCATAAAATAGTACCTAACTT-CAAG------TTGAA 434171 i v v v -- i v i- i ------v i MIRb#SINE/MIR 138 ATCTGTAAAATGGGGAT--AATAATACCTACCTCGCAGGGTTGTTGTGAG 185 chr6qtel1M 434172 GACAAAGTTAAATATT---TGTAAACTACTTTACAAAATG 434208 iv i v i v --- vii vi v i MIRb#SINE/MIR 186 GATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAGTG 225 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 33.07 CpG sites = 19, Kimura (unadjusted) = 35.67 Transitions / transversions = 1.19 (19/16) Gap_init rate = 0.06 (8 / 129), avg. gap size = 1.88 (15 / 8) 340 19.54 1.16 4.82 chr6qtel1M 434079 434164 (565836) MIR#SINE/MIR 84 166 (96) m_b309s601i9 12932 chr6qtel1M 434079 TATGAAATTGGGCAAATCATTTAACTTATTTATGCCACAGTCTTCTTCTC 434128 i vv i i i i v i i v - -- MIR#SINE/MIR 84 TGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGT-TTC--CTC 130 chr6qtel1M 434129 ATTTGAAAAATTGGCATAA-AATAGTACCTAACTTCA 434164 i v v v - - i MIR#SINE/MIR 131 ATCTGTAAAATGGGGATAATAATAGTACCT-ACCTCA 166 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 22.86 CpG sites = 9, Kimura (unadjusted) = 22.86 Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.06 (5 / 85), avg. gap size = 1.00 (5 / 5) 16 11.88 10.87 0.00 chr6qtel1M 434223 434268 (565732) (TTAAAT)n#Simple_repeat 1 51 (0) m_b309s252i20 12933 chr6qtel1M 434223 TTATATTTAAATTT--ATATACATTTATATTT-AATTT--ATTTAAATAT 434267 v -- v v v - -- v (TTAAAT)n#Sim 1 TTAAATTTAAATTTAAATTTAAATTTAAATTTAAATTTAAATTTAAATTT 50 chr6qtel1M 434268 A 434268 (TTAAAT)n#Sim 51 A 51 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.07 (3 / 45), avg. gap size = 1.67 (5 / 3) 319 28.86 16.67 1.61 chr6qtel1M 434285 434446 (565554) C MIRb#SINE/MIR (68) 200 15 m_b309s601i10 12934 chr6qtel1M 434285 TTATTTTATTT--TTCTGGCAAATACACTG-----TATTTAGCATTATC- 434326 i i -- i vi vv v ----- vv vi - C MIRb#SINE/MIR 200 TTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATTATCC 151 chr6qtel1M 434327 ---TTCTATAGATAAGGAAACTGAGG---AAAACCAGATTTAGTGATTTG 434370 --- i i i --- i i-- i v i i C MIRb#SINE/MIR 150 CCATTTTACAGATGAGGAAACTGAGGCTCAGAG--AGGTTAAGTAACTTG 103 chr6qtel1M 434371 TCCAAC------------GTAAGTGTTTGAAGCTGGATTTGAACTCTGGT 434408 i v------------ viv iv v i i v C MIRb#SINE/MIR 102 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGT 53 chr6qtel1M 434409 TTTTATGAAT-CAAAGTCCAGCATCCCATCCACTATATC 434446 i v v v - i - iiii iv ii i C MIRb#SINE/MIR 52 CTGTCTGACTCCAAAGCCC-GTGCTCTTTCCACTGCACC 15 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 36.68 CpG sites = 28, Kimura (unadjusted) = 37.73 Transitions / transversions = 1.56 (28/18) Gap_init rate = 0.06 (10 / 161), avg. gap size = 3.00 (30 / 10) 380 27.36 15.08 1.40 chr6qtel1M 434321 434446 (565554) C MIRc#SINE/MIR (114) 154 12 m_b309s601i11 12934 chr6qtel1M 434321 ATTATC----TTCTATAGATAAGGAAACTGAGG---AAAACCAGATTTAG 434363 ---- i i i --- i i-- i v C MIRc#SINE/MIR 154 ATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAG--AGGTTAAG 107 chr6qtel1M 434364 TGATTTGTCCAACGT------------AAGTGTTTGAAGCTGGATTTGAA 434401 i i v ------------ viv iv v i i C MIRc#SINE/MIR 106 TGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAA 57 chr6qtel1M 434402 CTCTGGTTTTTATGAATCAAAGTCCAGCATCCCATCCACTATATC 434446 i v i iv v v iiii iv ii i C MIRc#SINE/MIR 56 CCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACC 12 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 34.34 CpG sites = 23, Kimura (unadjusted) = 35.66 Transitions / transversions = 2.09 (23/11) Gap_init rate = 0.04 (5 / 125), avg. gap size = 4.20 (21 / 5) 1353 30.58 2.96 2.96 chr6qtel1M 434555 435501 (564499) L1M5_orf2#LINE/L1 2348 3294 (0) m_b309s551i2 12935 chr6qtel1M 434555 AAAATTACAGACCACTTTTCACACAAATTAAGTCTGATCTAACCAATTGG 434604 i i v i vi v v v ivvv i vi v L1M5_orf2#LIN 2348 AAAACTACAAAACATTGCTGAGAGAAATTAAAGAAGACCTAAATAAATGG 2397 chr6qtel1M 434605 AAAAATATTAAATGCTCTTGGATAGGGCGAGCAAATATAATAAAGATGAC 434654 i i vvv i v v iv viv vi ? v L1M5_orf2#LIN 2398 AGAGATATACCATGTTCATGGATTGGAAGACTCAATATTGTNAAGATGTC 2447 chr6qtel1M 434655 AATATTACCTAAACTAATCTATTTATTTAGCGCTATACCAATCAGACTCC 434704 vi v i i i vv i ii v v i v L1M5_orf2#LIN 2448 AATTCTCCCCAAATTGATCTATAGATTCAATGCAATCCCAATCAAAATCC 2497 chr6qtel1M 434705 CAAAAAACTATTTTAATGACCTAGAAAAAATAACAACAAAGTTCATATGG 434754 iv iii v ivv vv v v iv i ivvi i i L1M5_orf2#LIN 2498 CAGCAGGTTTTTTTGTAGAAATTGACAAGCTGATTCTAAAATTTATATGG 2547 chr6qtel1M 434755 AAAAACAAAAGGTCAAGAAT-TTCAAGGGAATTAATGAAAAAAAA-ATCA 434802 vi i ii ? -vi iiv iv- i - v L1M5_orf2#LIN 2548 AAATGCAAAGGACCNAGAATAGCCAAAACAATCT-TGAAAAAGAAGAACA 2596 chr6qtel1M 434803 AATGATGGTGG-CTTAGCTGTACCAGATCT-AAAATTATATTATAGAGCA 434850 - v v - - vv ? ? - i i - i v L1M5_orf2#LIN 2597 AA-GTTGGAGGACTTA-CACTACCNGATNTCAAGACT-TATTATAAAGCT 2643 chr6qtel1M 434851 GCAGTTACCAAAACTATTTGGTATTGGC-TAAGGAATAGATTAGTTGATC 434899 i v i i vi v - - iv i v L1M5_orf2#LIN 2644 ACAGTAATCAAGACAGTGTGGTATTGGCGTAAGGA-TAGACAAATAGATC 2692 chr6qtel1M 434900 AGTGGAATAGATTAG---GTTCAAGGGATAAAACAGTCA-ACAAATATAG 434945 i i v --- i - ii i v --- - v i L1M5_orf2#LIN 2693 AATGGAACAGAATAGAGAGTCCA-GAAATAGACC---CACACATATATGG 2738 chr6qtel1M 434946 CAACCTAGTCTTTGACAAAC---CCAAAG-ATCCCAGCTTTTGGGATAAG 434991 ?v ?i ii i v--- ? - vii ---- iv L1M5_orf2#LIN 2739 NCANTTGATTTTTGACAAAGGTGCCAANGCAATTCAG----TGGGGAAAG 2784 chr6qtel1M 434992 AACTTACTGTTTGATAAAAATTGCTGGGAAAATTGGAAACTAATATGGCA 435041 i ivvv v ii i viv i v v iiv v L1M5_orf2#LIN 2785 GATAGTCTTTTCAACAAATGGTGCTGGAACAATTGGATATCCATATGGAA 2834 chr6qtel1M 435042 GAAACTAGGCATTGATCCATACTTAACGCCGTACACCAAGATAAGGTCAA 435091 i v iii?v i i v i v i i v i v iv ? L1M5_orf2#LIN 2835 AAAAATGAANCTCGACCCCTACCTCACACCATACACAAAAATTAATTCNA 2884 chr6qtel1M 435092 AATGGGTTCAT-GACCTAGGCATAAAGAATGAAATTATTAATAAATTAGA 435140 i i - - iiii ii? i i v vvvvi L1M5_orf2#LIN 2885 GATGGAT-CATAGACCTAAATGTAAAAGNTAAAACTATAAAACTTCTAGA 2933 chr6qtel1M 435141 GGAA--CATAGGATAGTTTACCTCTCAGACCTGTGGA-AGGGGAAGGTCT 435187 i -- v i -- i iivv vv ?- vi i i L1M5_orf2#LIN 2934 AGAAAACATAGGAGAAT--ATCTTCGTGACCTTGGGNTAGGCAAAGATTT 2981 chr6qtel1M 435188 TTATGACCAAAGCAGAACTAGAGATCATTACTGATCACAAAATAGAAAAT 435237 i - i v iii v -- i -----i ?i i i v i L1M5_orf2#LIN 2982 CT-TAAACAGGACACAA--AAAG-----CACNAACCATAAAAGAAAAAAT 3023 chr6qtel1M 435238 T-------TCGATTATACCAAACTGAAAAGTTTTTGTACAAACAAAACTA 435280 ------- v i ?i i v v ii i iv ?vvv ivi L1M5_orf2#LIN 3024 TGATAAATTGGACTNCATCAAAATTAAAAACTTCTGCTCNTCAAAAGACA 3073 chr6qtel1M 435281 ATGCAGACAAGATTAGAAGGGAAGCAATAAACTGGGAAAATATTTTTACA 435330 vi ivi v i v i v v i i ? i v v i L1M5_orf2#LIN 3074 CCGTTAAGAAAATGAAAAGGCAAGCCACAGANTGGGAGAAAATATTTGCA 3123 chr6qtel1M 435331 GTCAAAGGT-TCTGATAAAGGCCTCATTTCCAAAATATATAGAGAATTAA 435379 i?- v vi - i v i v i i i v- L1M5_orf2#LIN 3124 AN-ACATATATCTGACAAAGGACTCGTATCCAGAATATATAAAGAACTC- 3171 chr6qtel1M 435380 CTCTAATTTA-TAAAAAATCAAGCCATTC--TCCAATTGAAAAATGGTCA 435426 vi ? i - ? -- v vv --i v? v L1M5_orf2#LIN 3172 CTACAANTCAATAANAAA--AAGACAAACAACCCAATANAAAAATGGGCA 3219 chr6qtel1M 435427 AAGGATATGAACAGACAATTCTCAGATGAAGAAATTGAAACTATTTCTAG 435476 i iv v v i v v ?v iviiivv i L1M5_orf2#LIN 3220 AAAGACTTGAACAGACACTTCACAAAAGAAGATATNCAAATGGCCAATAA 3269 chr6qtel1M 435477 TCATATGAAAAGATGCTCCAAGTCA 435501 v i v v? L1M5_orf2#LIN 3270 GCACATGAAAAGATGCTCAACNTCA 3294 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 40.58 CpG sites = 151, Kimura (unadjusted) = 41.35 Transitions / transversions = 1.16 (151/130) Gap_init rate = 0.05 (44 / 946), avg. gap size = 1.27 (56 / 44) 1614 27.34 3.15 3.65 chr6qtel1M 435358 435991 (564009) L1ME5_3end#LINE/L1 7 637 (304) m_b309s551i4 12935 chr6qtel1M 435358 TCCAAAATATATAGAGAATTAACTCTAATTTATAAAAAATCAAGCCATT- 435406 i i i ii i vviv v iv i i -- v iv?- L1ME5_3end#LI 7 TCTAGAATATACAAGGAACTCCTGCAAATCAACAAGAAA--AAGACGGNA 54 chr6qtel1M 435407 -CTCCAATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGA 435455 - i v v i iv v L1ME5_3end#LI 55 ACCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGA 104 chr6qtel1M 435456 AGAAA-TTGAAA--CTATTTCTAGTCATATGAAAAGATGCTCCAAGTCAT 435502 i -ii -- --v v - i v v L1ME5_3end#LI 105 GGAAACCCGAAAGGCTA--ACAAG-CATATGAAGAGATGCTCAAACTCAT 151 chr6qtel1M 435503 TATTAATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACA 435552 v i vv i i vi L1ME5_3end#LI 152 TAGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACA 201 chr6qtel1M 435553 CCTGTCAGATTGGCTAAGATGACAGGAAA--AAATAATGATGATTGTTGG 435600 i i i v i --i i i--ii vii v L1ME5_3end#LI 202 CCTATTAGACTGGCAAAAAT--TAGAAAGCTGGATAATGCCAAGTGTTGG 249 chr6qtel1M 435601 AGGGGATGCGGGAAAACTGGGACATTGATGCATTGTTGGTGGAGTTGTGA 435650 v i i i ? iv i vi v i i iiv ii L1ME5_3end#LI 250 CGAGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAG 299 chr6qtel1M 435651 ACGAATCCAACCATTTTGGAGAGTAGTTTGGAACTA--TGCTCAAA--AA 435696 vii v i i i i i v v -- iv -- L1ME5_3end#LI 300 ACTGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTAA 349 chr6qtel1M 435697 GTTATCAAACTGTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGATT 435746 - --- --- v i i viii v vv L1ME5_3end#LI 350 G-TAT---AC---GCATACCCTATGACCCAGCAATTCCGCTCCTGGGTAT 392 chr6qtel1M 435747 ATATCCCAAAGAGATTATAAAGAAGG----GAAAGGGACCTGTATGTGCA 435792 i v v viv ----v i ---- i i L1ME5_3end#LI 393 ATATCCCAAAGAAATTCTCACACAGGTCCATAAGGGGAC----ATGTACG 438 chr6qtel1M 435793 CGAATGTTTGTGGCAGCCCTTTTTGTAGTGGCTAGAAACTGGAAACTGAA 435842 v i ii v vi v i vi i ii ii vivv L1ME5_3end#LI 439 AGGATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACC 488 chr6qtel1M 435843 TGGATGTCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATATGAAAA 435892 i v v i v iii v iv v v L1ME5_3end#LI 489 TGGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACA 538 chr6qtel1M 435893 TTATGGAATATTACTGT-TCTGTAAGAAATGACCAACAGGATGATTTCAG 435941 ii i i - i-v v v iii vi vi -- v v L1ME5_3end#LI 539 CCATGGAGTACTA-TGCAGCAGTTAGAAGCAACGGACTAGATG--TACAC 585 chr6qtel1M 435942 AAAG--GCCTGGAGAGA-CTTACACGAAC-TGATGCTGAGTGAAATGAGC 435987 v --i v vi - v -- - ii vi i L1ME5_3end#LI 586 ATAGCAACATGGATGGATCTTAAA--AACATAGTGCTGAGTGAAAAAAGT 633 chr6qtel1M 435988 AGGA 435991 i L1ME5_3end#LI 634 AAGA 637 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 33.92 CpG sites = 98, Kimura (unadjusted) = 34.98 Transitions / transversions = 1.42 (98/69) Gap_init rate = 0.06 (35 / 633), avg. gap size = 1.23 (43 / 35) 1648 27.47 0.36 1.66 chr6qtel1M 435358 435905 (564095) L1ME3G_3end#LINE/L1 7 547 (377) m_b309s551i3 12935 chr6qtel1M 435358 TCCAAAATATATAGAGAATTAACTCTAATTTATAAAAAATCAAGCCATTC 435407 i i i vviv v iv i -- v --v L1ME3G_3end#L 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAA--AAGACA--A 52 chr6qtel1M 435408 TCCAATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGAAG 435457 i v v i v v i L1ME3G_3end#L 53 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chr6qtel1M 435458 AAATTGAAACTATTTCTAGTCATATGAAAAGATGCTCCAAGTCATTATTA 435507 vv iviiivv iv v vv i v L1ME3G_3end#L 103 AAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTA 152 chr6qtel1M 435508 ATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACACCTGT 435557 i i vv i i viv ii L1ME3G_3end#L 153 ATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCAT 202 chr6qtel1M 435558 CAGATTGGCTAAGATGACAGGAAAAAATAATGATGATTGTTGGAGGGGAT 435607 v i vvv iii?vvi ivi? v v i i L1ME3G_3end#L 203 CAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGT 252 chr6qtel1M 435608 GCGGGAAAACTGGGACATTGATGCATTGTTGGTGGAGTTGTGAACGAATC 435657 i i v v vi v i i i iiv i ivii v L1ME3G_3end#L 253 GTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTA 302 chr6qtel1M 435658 CAACCATTTTGGAGAGTAGTTTGGAACTATGCTCAAAAAGTTATCAAACT 435707 i ? i i i v v - vvv i -- i v L1ME3G_3end#L 303 CAGCCNTTTTGGAGGGCAATTTGGCAGTAT-CTATTAAAAT--TTAAAAT 349 chr6qtel1M 435708 GTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGATTATATCCCAAAG 435757 i i i vii v ? ?v v i ? L1ME3G_3end#L 350 GCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAG 399 chr6qtel1M 435758 AGATTAT-AAAGAAG-GGAAAGGGACCTGTATGTGCACGAATGTTTGTGG 435805 i vv -iv v v - v v i --? i i v i ii v L1ME3G_3end#L 400 AAATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTCATTG 447 chr6qtel1M 435806 CAGCCCTTTTTGTAGTGGCTAGAAACTGGAAACTGAATGGATGTCCATCA 435855 vi v i i v i i vivv ii L1ME3G_3end#L 448 CAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCA 497 chr6qtel1M 435856 GTTGGAGAATGGCTGAATAAATTGTGGTATATGAAAATTATGGAATATTA 435905 i v i i i i vv v i i L1ME3G_3end#L 498 ATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACTA 547 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 34.70 CpG sites = 78, Kimura (unadjusted) = 35.29 Transitions / transversions = 1.11 (78/70) Gap_init rate = 0.02 (11 / 547), avg. gap size = 1.00 (11 / 11) 30 16.08 0.00 0.00 chr6qtel1M 436452 436501 (563499) (A)n#Simple_repeat 1 50 (0) m_b309s252i21 12936 chr6qtel1M 436452 AAAAAAAAAAAAAAGAGAGGAAAAAAAAATAAAAAAAAAAGAAAGAAAAA 436501 i i ii v i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 Matrix = Unknown Transitions / transversions = 6.00 (6/1) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 20 7.86 0.00 0.00 chr6qtel1M 437748 437774 (562226) (TA)n#Simple_repeat 1 27 (0) m_b309s252i22 12937 chr6qtel1M 437748 TAAATTTATATATATATATATATATAT 437774 v v (TA)n#Simple_ 1 TATATATATATATATATATATATATAT 27 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 33 0.00 0.00 0.00 chr6qtel1M 437776 437803 (562197) (GA)n#Simple_repeat 1 28 (0) c_b309s251i1 12938 chr6qtel1M 437776 GAGAGAGAGAGAGAGAGAGAGAGAGAGA 437803 (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGA 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 24 26.73 2.90 0.00 chr6qtel1M 438026 438094 (561906) (AT)n#Simple_repeat 1 71 (0) m_b309s252i23 12939 chr6qtel1M 438026 ATACACATACACACATATATATGTAAATGTGTATGTGTATATTTATACAT 438075 i i i i i i v i i i i v i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr6qtel1M 438076 ATATAT-TAGCT-TATATATA 438094 - vv - (AT)n#Simple_ 51 ATATATATATATATATATATA 71 Matrix = Unknown Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.03 (2 / 68), avg. gap size = 1.00 (2 / 2) 17 13.99 0.00 7.14 chr6qtel1M 438814 438858 (561142) (AATA)n#Simple_repeat 1 42 (0) m_b309s252i24 12940 chr6qtel1M 438814 AATCAATTAGTAAGATAAATAAGATAAATTAATAAGATATATAAA 438858 v v i - - v - v (AATA)n#Simpl 1 AATAAATAAATAA-ATAAATAA-ATAAATAAATAA-ATAAATAAA 42 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.07 (3 / 44), avg. gap size = 1.00 (3 / 3) 24 36.33 1.89 0.00 chr6qtel1M 440124 440229 (559771) (AT)n#Simple_repeat 1 108 (0) m_b309s252i25 12941 chr6qtel1M 440124 ATACATATATTCCTAGA-AAATATATTCAAAGAGATATAAATACAGATAT 440172 i viv v - v vi v v v v i v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr6qtel1M 440173 ATACACATATGTGTATGTATACAAAAATATACATAGATGCATATGTGTGC 440222 i i i i i i v v i v ii i i ii (AT)n#Simple_ 51 ATATATATATATATATATATATATATATATATATATATATATATATATAT 100 chr6qtel1M 440223 AT-TATAT 440229 - (AT)n#Simple_ 101 ATATATAT 108 Matrix = Unknown Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.02 (2 / 105), avg. gap size = 1.00 (2 / 2) 19 26.14 2.74 1.35 chr6qtel1M 440565 440618 (559382) (ATGTGT)n#Simple_repeat 1 55 (19) m_b309s252i26 12942 chr6qtel1M 440565 ATGTGTCTGTGCTTTGTGTATGTGTGTATACATGTATAT-TATATGTAGA 440613 v - v i i ii i - i iv (ATGTGT)n#Sim 1 ATGTGTATGTG-TATGTGTATGTGTATGTGTATGTGTATGTGTATGTGTA 49 chr6qtel1M 440614 TGTG-G 440618 -i (ATGTGT)n#Sim 50 TGTGTA 55 Matrix = Unknown Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.06 (3 / 53), avg. gap size = 1.00 (3 / 3) 29 6.13 0.00 0.00 chr6qtel1M 440619 440652 (559348) (AT)n#Simple_repeat 1 34 (0) c_b309s251i2 12943 chr6qtel1M 440619 ATATATGTATATCTATATATATATATATATATAT 440652 i v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATAT 34 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 19 26.14 2.74 1.35 chr6qtel1M 440653 440670 (559330) (ATGTGT)n#Simple_repeat 56 73 (1) m_b309s252i26 12944 chr6qtel1M 440653 GTATTTGTGTGTGTGCAT 440670 i v i i (ATGTGT)n#Sim 56 GTGTATGTGTATGTGTAT 73 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 56 3.64 0.00 0.00 chr6qtel1M 440676 440732 (559268) (TG)n#Simple_repeat 1 57 (0) c_b309s251i3 12945 chr6qtel1M 440676 TGTGTGTGTGTATGTGTGTGTGTGTATGTGTGTGTGTGTGTGTGTGTGTG 440725 i i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chr6qtel1M 440726 TGTGTGT 440732 (TG)n#Simple_ 51 TGTGTGT 57 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0) 258 18.14 2.84 3.33 chr6qtel1M 441346 441556 (558444) C HERVIP10FH#LTR/ERV1 (4104) 998 789 m_b309s701i0 12946 chr6qtel1M 441346 TCTGTCTTTCTCTAGCTCTCTCTGTCTCAGTATCAGTGTCTCTCGGTCTC 441395 i i vv i v i v v v -- -- C HERVIP10FH#LT 998 TCTATCTCTCTCTTTCTTTCTCTCTTTGACTTTC--TGTCTCTC--TCTC 953 chr6qtel1M 441396 CATCTCTTTTTCTCTCTTTGTCT----GTCTCTGTCTGTCTCTGTCTCTC 441441 iv vvi i ---- vi v i C HERVIP10FH#LT 952 TCTCTCTGACTCCCTCTTTGTCTCTCTGTCTCTTCCTCTCTCTGCCTCTC 903 chr6qtel1M 441442 TGTTTGTTT--CTCCATCTGTTTGTCTCTGTCTCTCCCTTCCTCCTTCTC 441489 v i v -- -- v v ii ii i C HERVIP10FH#LT 902 TCTCTCTTTGACTCC--CTCTTTGTCTCTCTCTCTCCCTCTCTCTCTCTT 855 chr6qtel1M 441490 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTCTCTCTTTCTCT 441539 ii - C HERVIP10FH#LT 854 TCTCTCTCTCTCTCTTCCTCTCTCTCTCTCTCTCTCTTCTCTCTTTC-CT 806 chr6qtel1M 441540 CTCTCCCTCTCTCTCCC 441556 v ivv i C HERVIP10FH#LT 805 CTCTGCTGGTCTTTCCC 789 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 20.90 CpG sites = 19, Kimura (unadjusted) = 20.90 Transitions / transversions = 1.06 (19/18) Gap_init rate = 0.04 (9 / 210), avg. gap size = 1.44 (13 / 9) 207 31.54 7.19 4.20 chr6qtel1M 441683 441821 (558179) C MIR3#SINE/MIR (51) 157 15 m_b309s601i12 12947 chr6qtel1M 441683 TAATCAAAAATCCTCACTATACACATGAGG-AACTGAGG--CAAAAATAT 441729 i v vvi i v v - -- i i vi C MIR3#SINE/MIR 157 TAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGT 108 chr6qtel1M 441730 TCAATGACTCATCCAAAAACACAGAAGCAGC-----ACAGACCTGAGAGT 441774 vv i iii iiv v iv? i-----i v i i v C MIR3#SINE/MIR 107 GAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACT 58 chr6qtel1M 441775 ATATTTGAACCTACATCTCA-GTTTCCTCATTCAATACTTTC-CTCCTC 441821 ----- i vi v- vi - v vi i i - v C MIR3#SINE/MIR 57 A-----GAACCCAGGTCTCCTGACTCC-CAGTCCGTGCTCTCTCTGCTC 15 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 39.78 CpG sites = 23, Kimura (unadjusted) = 42.39 Transitions / transversions = 1.21 (23/19) Gap_init rate = 0.08 (11 / 138), avg. gap size = 1.45 (16 / 11) 233 33.00 8.13 3.91 chr6qtel1M 441692 441814 (558186) C MIRc#SINE/MIR (117) 151 24 m_b309s601i13 12947 chr6qtel1M 441692 ATCCTCACTATACACATGAGG-AACTGAGG--CAAAAATATTCAATGACT 441738 i i v v - -- i i vi v i C MIRc#SINE/MIR 151 ATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACT 102 chr6qtel1M 441739 CATCCAAAAACACAGAAGCAGCA-----CAGACCTGAGAGTATATTTGAA 441783 iii iiv v ivi i ----- v i i ----- i i C MIRc#SINE/MIR 101 TGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGG-----ACTCGAA 57 chr6qtel1M 441784 CCTACATCT--CAGTTTCCTCATTCAATACTTT 441814 i vi -- v vi vvi i i i i C MIRc#SINE/MIR 56 CCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCT 24 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 42.96 CpG sites = 26, Kimura (unadjusted) = 46.24 Transitions / transversions = 2.00 (26/13) Gap_init rate = 0.07 (9 / 122), avg. gap size = 1.67 (15 / 9) 14 12.84 5.88 0.00 chr6qtel1M 442409 442442 (557558) (ATGT)n#Simple_repeat 1 36 (0) m_b309s252i29 12948 chr6qtel1M 442409 ATGTCTGTGTGT-T-TGTGTATGTATGTATTTATGT 442442 v i - - i v (ATGT)n#Simpl 1 ATGTATGTATGTATGTATGTATGTATGTATGTATGT 36 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2) 34 0.00 0.00 0.00 chr6qtel1M 442907 442935 (557065) (TA)n#Simple_repeat 1 29 (0) c_b309s251i4 12949 chr6qtel1M 442907 TATATATATATATATATATATATATATAT 442935 (TA)n#Simple_ 1 TATATATATATATATATATATATATATAT 29 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 287 29.38 8.54 5.21 chr6qtel1M 444638 444953 (555047) C L1PB_orf2#LINE/L1 (2357) 937 612 m_b310s551i0 12950 chr6qtel1M 444638 GTGCTTTTTCTCTGTCTTATTGATGTAA----TTAGAAATATACAATTTC 444683 i v-- v v i---- iiv iv v C L1PB_orf2#LIN 937 GTGCTCTTTCA--GACTTTTTGATGTAGGCATTTAGGGCTATGAACTTTC 890 chr6qtel1M 444684 CTCTAAGAATCACTATGACTGAAGGCCAGAAATTCTGA---GTTTTGTCT 444730 v v i i iv vi v vv ii i --- v v C L1PB_orf2#LIN 889 CTCTTAGCACCGCCTTTGCTGTATCCCAGAGGTTTTGATAGGTTGTGTCA 840 chr6qtel1M 444731 C-ATTAT--TTC---TTGAATGAAATTGTTGATTGTTTCTAT---GATTT 444771 - i -- --- i --i v ? --i i --- C L1PB_orf2#LIN 839 CTATTGTCGTTCAGTTCGAA--GAATTTTTNA--ATTTCCATCTTGATTT 794 chr6qtel1M 444772 GTTCCTTGACCCAATTGCCTTTTAGGATTGAATTATGTAATTTC------ 444815 vv i? vii v i viiii v ------ C L1PB_orf2#LIN 793 CATTNTTGACCCAATGATCATTCAGGAGCAGGTTATTTAATTTCCATGTA 744 chr6qtel1M 444816 --TGCTTAACTTTTAGGGTTTCTTTCCATTGCCCATTATTGGATGCAATT 444863 -- v iii v i ---- vv----i iv v v v C L1PB_orf2#LIN 743 TTTGCATGGTTTTGAGGGTTCCTT----TTGGA----GTTGATTTCCAGT 702 chr6qtel1M 444864 TTTATTATGTTATAAACTGAAAAGGATGTGTTCATTAT--TTCTGATTTT 444911 viii i iiv i -- - i iiv -- ii C L1PB_orf2#LIN 701 TTTATTCCACTGTGGTCTGAGA--GA-GTGCTTGATATAATTTCGATTTT 655 chr6qtel1M 444912 CTTCATTTTGTTGAGGGTT-TTTTAGGCCCTAATACATAGTCT 444953 v v i v i- iv v vi i i C L1PB_orf2#LIN 654 CTTAAATTTATTGAGGCTCGTTTTGTGGCCTATCATATGGTCT 612 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.34 CpG sites = 49, Kimura (unadjusted) = 38.54 Transitions / transversions = 1.26 (49/39) Gap_init rate = 0.09 (27 / 315), avg. gap size = 1.63 (44 / 27) 36 0.00 0.00 0.00 chr6qtel1M 444955 444985 (555015) (TG)n#Simple_repeat 1 31 (0) c_b310s251i0 12951 chr6qtel1M 444955 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 444985 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 250 17.74 6.45 0.00 chr6qtel1M 448441 448502 (551498) Charlie4a#DNA/hAT-Charlie 40 105 (403) m_b310s502i0 12952 chr6qtel1M 448441 GAGTCCATAAACTTGGAAGGGG-AAGAAATGAAA---TTATTTTTACAAA 448486 i i i v - i v v --- i v Charlie4a#DNA 40 GGGTCCGTGAACTTGGATGGGGAAAAAAATTACATCTTTATTTTCACTAA 89 chr6qtel1M 448487 CATCTAAGTGAAATTT 448502 v v Charlie4a#DNA 90 CCTCTAACTGAAATTT 105 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 18.38 CpG sites = 5, Kimura (unadjusted) = 20.30 Transitions / transversions = 0.83 (5/6) Gap_init rate = 0.03 (2 / 61), avg. gap size = 2.00 (4 / 2) 554 34.05 2.51 2.94 chr6qtel1M 448736 448974 (551026) C MIRb#SINE/MIR (27) 241 4 m_b310s601i0 12953 chr6qtel1M 448736 CCTACTATGTGCCAGGAATTCTACCAATTGCTTTTTATAAAGTATATCAC 448785 i v i v i i vi vi iv v v i C MIRb#SINE/MIR 241 CTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACATGCATTATCTCAT 192 chr6qtel1M 448786 AATTGATCCTCACATCAACTCTGTAAGACAAAAGCAATTACTATATTTAT 448835 -- i v i ii ii--- vv i viii C MIRb#SINE/MIR 191 --TTAATCCTCACAACAACCCTGCGAGGT---AGGTATTATTATCCCCAT 147 chr6qtel1M 448836 TTTATCATTGATGAAATTTTGGC----AGAAGTTAAATTTCTGTCCCAAT 448881 iviv v i vv ---- i i vv vv v C MIRb#SINE/MIR 146 TTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAG 97 chr6qtel1M 448882 ATTACATACATTGTAAGCTTCA-AGCT-GGATTTGAACAGAGATCTTCTT 448929 i i i vv v ivv - i- i vv i vii C MIRb#SINE/MIR 96 GTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCT 47 chr6qtel1M 448930 GATTCTGGGACCAACATTCTATCAACTGTTCCACAAACTGCCTTT 448974 i iiiii viiii v v iv --i ii C MIRb#SINE/MIR 46 GACTCCAAAGCCCGTGCTCTTTCCACTGCACCAC--GCTGCCCCT 4 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 42.17 CpG sites = 46, Kimura (unadjusted) = 47.06 Transitions / transversions = 1.39 (46/33) Gap_init rate = 0.04 (10 / 238), avg. gap size = 1.30 (13 / 10) 248 33.89 0.00 9.38 chr6qtel1M 449032 449171 (550829) C MIR#SINE/MIR (38) 224 97 m_b310s601i1 12954 chr6qtel1M 449032 AAGCCTTGTGATAAATGCTTTATAAATGTAATCTTACTAGATCCTTACTT 449081 i vi vv ii i vi i v v i i vi i vv C MIR#SINE/MIR 224 AGGCACTGTTCTAAGCGCTTTACATGTATTAACTCATTTAATCCTCACAA 175 chr6qtel1M 449082 CAACCCTAAAAGGCAGGTCATTTTATGTTATCTGATTAACCCTTACACAG 449131 vi i vv v -- i------ v vi C MIR#SINE/MIR 174 CAACCCTATGAGGTAGGTACTATTA--TTATCC------CCATTTTACAG 133 chr6qtel1M 449132 AAGATGAAGATGTGGAAGGTATGGAAAAAATCAGTAATTT 449171 v v iv ---- i ii i iiv v i C MIR#SINE/MIR 132 ATGAGGAAACTG----AGGCACAGAGAGGTTAAGTAACTT 97 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 44.18 CpG sites = 23, Kimura (unadjusted) = 45.61 Transitions / transversions = 1.15 (23/20) Gap_init rate = 0.09 (12 / 139), avg. gap size = 1.00 (12 / 12) 86 8.65 4.05 0.00 chr6qtel1M 449847 449994 (550006) (TC)n#Simple_repeat 1 154 (0) c_b310s251i1 12955 chr6qtel1M 449847 TCTCTCTCTCTC-CT-TCTCTCCCTCTTTCTCTCTCTCTCTCCCT-TCTC 449893 - - i i i - (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr6qtel1M 449894 -CTCTCTCTCTCTCTC-CTCTCTCTCTTTCTC-CTCTCTCTCTCTCTTTC 449940 - - i - i (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chr6qtel1M 449941 TCTTTCTCTTTCTCTCTCTCTTTCTCTCTCTGTCTCAGTCTCTCTGTCTC 449990 i i i v vv v (TC)n#Simple_ 101 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 150 chr6qtel1M 449991 TCTC 449994 (TC)n#Simple_ 151 TCTC 154 Matrix = Unknown Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.04 (6 / 147), avg. gap size = 1.00 (6 / 6) 12 23.33 4.44 0.00 chr6qtel1M 450723 450767 (549233) (ACAAAT)n#Simple_repeat 1 47 (0) m_b310s252i0 12956 chr6qtel1M 450723 ACAAAAACATGTAAATGTATAAATACAACCACAAA-A-AAATACAAA 450767 v vi v vi i vi - - (ACAAAT)n#Sim 1 ACAAATACAAATACAAATACAAATACAAATACAAATACAAATACAAA 47 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.05 (2 / 44), avg. gap size = 1.00 (2 / 2) 19 6.98 3.12 3.12 chr6qtel1M 451010 451041 (548959) (AT)n#Simple_repeat 1 32 (0) m_b310s252i1 12957 chr6qtel1M 451010 ATA-ATATACATATATATATATATATGAAATAT 451041 - i - v (AT)n#Simple_ 1 ATATATATATATATATATATATATAT-ATATAT 32 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.06 (2 / 31), avg. gap size = 1.00 (2 / 2) 260 38.30 3.19 0.00 chr6qtel1M 451530 451623 (548377) MIRc#SINE/MIR 10 106 (162) m_b310s601i2 12958 chr6qtel1M 451530 GTGGTGTAGTGAAGAAAGTGATAG-TTCCAAGTCA--AAAACTTAAACTT 451576 i i i i iiv i -i ivi -- i i iiii i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr6qtel1M 451577 GTATCCTAATTCAGTCACTTTCCATTTGTGAGATCCTGGGGAACTCA 451623 vi iiii v i v i vi v i i v v MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCA 106 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 55.00 CpG sites = 27, Kimura (unadjusted) = 60.78 Transitions / transversions = 3.00 (27/9) Gap_init rate = 0.02 (2 / 93), avg. gap size = 1.50 (3 / 2) 16 9.55 0.00 0.00 chr6qtel1M 451640 451662 (548338) (TA)n#Simple_repeat 1 23 (0) m_b310s252i2 12959 chr6qtel1M 451640 TATATATATGTATACATATATAT 451662 i i (TA)n#Simple_ 1 TATATATATATATATATATATAT 23 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 19 8.27 11.32 1.72 chr6qtel1M 451786 451838 (548162) (AATT)n#Simple_repeat 1 58 (0) m_b310s252i3 12960 chr6qtel1M 451786 AATT-ATT-ATTCATT-GTTAATTAATTAA-CAATTAATTAA-AAATTAA 451830 - - v -i -i -v (AATT)n#Simpl 1 AATTAATTAATTAATTAATTAATTAATTAATTAATTAATTAATTAATTAA 50 chr6qtel1M 451831 -TAATATAA 451838 - - (AATT)n#Simpl 51 TTAAT-TAA 58 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.13 (7 / 52), avg. gap size = 1.00 (7 / 7) 25 17.44 0.00 0.00 chr6qtel1M 452261 452305 (547695) (AC)n#Simple_repeat 1 45 (0) m_b310s252i4 12961 chr6qtel1M 452261 ACATACACACACAGAGAGAGAGACACACACACACATACACACACA 452305 i v v v v v i (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACA 45 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 13 21.64 6.25 0.00 chr6qtel1M 452339 452386 (547614) (AGAT)n#Simple_repeat 1 51 (0) m_b310s252i5 12962 chr6qtel1M 452339 AGATACATATATTTCTAGA-AAATAAATTTATAGAT--ATAGATAGATAG 452385 v v vvv - i i vv -- (AGAT)n#Simpl 1 AGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAG 50 chr6qtel1M 452386 A 452386 (AGAT)n#Simpl 51 A 51 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.04 (2 / 47), avg. gap size = 1.50 (3 / 2) 281 23.94 0.00 0.00 chr6qtel1M 452388 452458 (547542) C DNM1r#Unknown (2117) 2545 2475 m_b310s502i1 12963 chr6qtel1M 452388 ATACATACATGTATATACACAGAGAAATAAACACACACACACACATATAT 452437 ? i i v v v i v i i i i i i C DNM1r#Unknown 2545 ATANATACGTATATATACACATATATACACACATACACACATATACACAC 2496 chr6qtel1M 452438 ATATTTACACACATATGTGTG 452458 v iii C DNM1r#Unknown 2495 ATATATACACACATACACGTG 2475 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 26.39 CpG sites = 12, Kimura (unadjusted) = 30.60 Transitions / transversions = 2.40 (12/5) Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0) 244 16.71 0.00 5.00 chr6qtel1M 452648 452710 (547290) DNM1r#Unknown 2489 2548 (2114) m_b310s502i2 12964 chr6qtel1M 452648 TATATATCTCTGTGTGTATGTGTATATGTGTATACATGTATATTATATGC 452697 v v i i i i i i - i DNM1r#Unknown 2489 TATATATGTGTGTATATGTGTGTATGTGTGTATATATGTGTA-TATATAC 2537 chr6qtel1M 452698 AAATATTTATAGA 452710 --i ? DNM1r#Unknown 2538 --GTATNTATAGA 2548 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 17.81 CpG sites = 8, Kimura (unadjusted) = 19.95 Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.05 (3 / 62), avg. gap size = 1.00 (3 / 3) 13 19.47 0.00 0.00 chr6qtel1M 452711 452741 (547259) (TGTATG)n#Simple_repeat 1 31 (0) m_b310s252i6 12965 chr6qtel1M 452711 TGTATGTGTATATATATATGTGTGTGTGTGT 452741 i i i i i (TGTATG)n#Sim 1 TGTATGTGTATGTGTATGTGTATGTGTATGT 31 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 36 0.00 0.00 0.00 chr6qtel1M 452754 452784 (547216) (GT)n#Simple_repeat 1 31 (0) c_b310s251i2 12966 chr6qtel1M 452754 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 452784 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 30 23.37 3.36 4.24 chr6qtel1M 453032 453150 (546850) (CTCTGT)n#Simple_repeat 1 118 (0) m_b310s252i7 12967 chr6qtel1M 453032 CTCTATATCTATCT-TTTGT-TTTCCCTTTCTCCTGTATTCTGTCTCTAG 453079 i v i - v v - v i v - -i - (CTCTGT)n#Sim 1 CTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCT-CTGT-CTCTGTCTCT-G 47 chr6qtel1M 453080 CACTCTTTTATGTGTCCCTATCTTTATCTATGTCTCTG--TCTGTCTCTG 453127 -v - v v v i i i i v -- (CTCTGT)n#Sim 48 -TCTC-TGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTG 95 chr6qtel1M 453128 TTTCTTTCTGTGTCTCTATCTCT 453150 i v v i (CTCTGT)n#Sim 96 TCTCTGTCTCTGTCTCTGTCTCT 118 Matrix = Unknown Transitions / transversions = 0.83 (10/12) Gap_init rate = 0.07 (8 / 118), avg. gap size = 1.12 (9 / 8) 127 8.17 0.59 0.00 chr6qtel1M 453155 453324 (546676) (CT)n#Simple_repeat 1 171 (0) c_b310s251i3 12968 chr6qtel1M 453155 CTCTCTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 453204 i (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chr6qtel1M 453205 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCCCCTCTC-CTCTTT 453253 i i - i (CT)n#Simple_ 51 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 100 chr6qtel1M 453254 CCCTCTCTCTCTCTCCCTCTCTCTCTGTTTCTGTCTCTCTCTGTCTCTTT 453303 i i v i v v i (CT)n#Simple_ 101 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 150 chr6qtel1M 453304 CTCTCCCTCTCTCCCTCTCTC 453324 i i (CT)n#Simple_ 151 CTCTCTCTCTCTCTCTCTCTC 171 Matrix = Unknown Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.01 (1 / 169), avg. gap size = 1.00 (1 / 1) 32 0.00 0.00 0.00 chr6qtel1M 453646 453675 (546325) (GGTTAG)n#Simple_repeat 1 30 (0) c_b310s251i4 12969 chr6qtel1M 453646 GGTTAGGGTTAGGGTTAGGGTTAGGGTTAG 453675 (GGTTAG)n#Sim 1 GGTTAGGGTTAGGGTTAGGGTTAGGGTTAG 30 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 288 30.02 5.09 5.09 chr6qtel1M 455539 456068 (543932) C L1MC_orf2#LINE/L1 (2167) 1127 598 m_b310s551i1 12970 chr6qtel1M 455539 GGTTTACCTATTTTATTAATTTGTTTTTTTTCCTTAAAACCTCCTTCTGT 455588 i i v i i ------- i vv i vv i v C L1MC_orf2#LIN 1127 GGCTTATCAATTTTATTGATCT-------TTTCAAAGAACCAGCTTTTGG 1085 chr6qtel1M 455589 TTT---TTATTTACTA-ATTCAAAGATTTTCT----TTAATTTTACTCAT 455630 --- v v v- ---- i ---- i i i v C L1MC_orf2#LIN 1084 TTTCGTTGATTTTCTCTATT----GATTTCCTGTTTTCAATTTCATTGAT 1039 chr6qtel1M 455631 CTATGCTTTGATTTTCAAGATTTCCAATCTGGTATTTAATTGGAAAATTT 455680 i v i i i vv ivv vv ii v v i -- C L1MC_orf2#LIN 1038 TTCTGCTCTAATTTTTATTATTTCTTTTCTTCTGCTTACTTTGGA--TTT 991 chr6qtel1M 455681 AAATTTGTTCTT-TTTTTCTAGTTATTTTTTTAGTTGCATGCCCAATTCA 455729 - i - --- ii v v v v ii iv i C L1MC_orf2#LIN 990 AA-TTTGCTCTTCTTTTTCTAGTT---TCCTAAGGTGGAAGCTTAGATTA 945 chr6qtel1M 455730 TTGACCT--GCTTTTTCT-CTATTTTAATAATGTAAGCAATTAGAAATAT 455776 ii -- v i - v i --- v v i iviv C L1MC_orf2#LIN 944 TTGATTTTAGATCTTTCTTCTTTTCTAATA---TATGCATTCAATGCTAT 898 chr6qtel1M 455777 ATAATTTCCC-CTAAGAATTACTATGTCTGTAGCTCGTAAATTTTGAT-T 455824 - - v i i v vv i v i ii -v C L1MC_orf2#LIN 897 A-AATTTCCCTCTAAGCACTGCTTTCGCTGCATCCCACAAATTTTGATAA 849 chr6qtel1M 455825 TTTGTCTCATTATTTTC-TTGAA--CGAAATGATTT---ATTGTTTGTAT 455868 v v iv i - v i-- i iv --- vi iv iv C L1MC_orf2#LIN 848 GTTGTATTTTCATTTTCATTTAGTTCAAAATATTTTTAAATTTCTCTTGA 799 chr6qtel1M 455869 GATTTGTTCCTTAATACTCTTGTT-TTTAGGATTAGGTTATTTAATTTCC 455917 v i i iv viv - i v iv i i C L1MC_orf2#LIN 798 GATTTCTTCTTTGACCCATGTGTTATTTAGAAGTGTGTTGTTTAATCTCC 749 chr6qtel1M 455918 AATTAACTTTTAAGATTTT---GTTCATTGTCCATTATTGGATGTAAATT 455964 v -- ii --- i vvi v ii iv viv i C L1MC_orf2#LIN 748 AAGTA--TTTTGGGATTTTCCAGCTATCTTTCTGTTATTGATTTCTAGTT 701 chr6qtel1M 455965 TTGTTGCATCATGATCTGAAAG-GGATG-TGTTTGATATTTCTGCTTTTC 456012 vi v ii i i -i? i?- v -- i- i i C L1MC_orf2#LIN 700 TAATTCCATTGTGGTCTGAGAGCANACNTTGTATG--ATTTCTA-TTCTT 654 chr6qtel1M 456013 TTCAACTGTCTGAGGAGT-TTTTATGTCCTAATAAATGGTCTTTTGTGTG 456061 v i vvi i v - v i iv vi v iv - C L1MC_orf2#LIN 653 TTAAATTTGTTAAGGTGTGTTTTATGGCCCAGAATGTGGTCTATCTTG-G 605 chr6qtel1M 456062 TGTATGT 456068 v C L1MC_orf2#LIN 604 TGAATGT 598 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 39.29 CpG sites = 81, Kimura (unadjusted) = 39.29 Transitions / transversions = 1.16 (81/70) Gap_init rate = 0.08 (43 / 529), avg. gap size = 1.26 (54 / 43) 341 27.99 3.99 4.63 chr6qtel1M 455611 455936 (544064) C L1M5_orf2#LINE/L1 (2239) 1055 732 m_b310s551i2 12970 chr6qtel1M 455611 TTTTCTTTAATTTTACTCATCTATGCTTTGATTTTCAAGATTTCCAATCT 455660 --- i i v i v i v i i vv vvi C L1M5_orf2#LIN 1055 TTTTCT---ATTTCATTGATTTCTGCTCTTATCTTTATTATTTCCTTCCT 1009 chr6qtel1M 455661 GGTATTTAATTGGAAAATTTAAATTTGTTCTT-TTTTTCTAGTTATTTTT 455709 vv i ?v v ii-- - i - i --- i C L1M5_orf2#LIN 1008 TCTACTTNCTTTGGG--TTTAA-TTTGCTCTTCTTTTTCTAGCT---TCT 965 chr6qtel1M 455710 TTAGTTGCATGCCCAATTCATTGACCT---GCTTTTTCTCTATTTTAATA 455756 v v v v ii iv ii --- i ii v i C L1M5_orf2#LIN 964 TAAGGTGGAAGCTTAGATCATTGATTTTAAGCCTTTCTTCTTTTCTAATA 915 chr6qtel1M 455757 ATGTAAGCAATTAGAAATATATAATTTCCC-CTAAGAATTACTATGTCTG 455805 --- ? v i?iv - - v i i v iv C L1M5_orf2#LIN 914 ---TANGCATTTAANGCTATA-AATTTCCCTCTAAGCACTGCTTTAGCTG 869 chr6qtel1M 455806 TAGCTCGTAAATTTTGAT-TTTTGTCTCATTATTTTC-TTGAA--CGAAA 455851 i v i ii - v v iv i ? - v i-- i C L1M5_orf2#LIN 868 CATCCCACAAATTTTGATATGTTGTATTTTCATTNTCATTCAGTTCAAAA 819 chr6qtel1M 455852 TGATTT---ATTGTTTGTATGATTTGTTCCTTAATACTCTTGTT-TTTAG 455897 iv --- vii?v i v i i iv vivv - C L1M5_orf2#LIN 818 TATTTTCTAATTTCCNTTGTGATTTCTTCTTTGACCCATGGGTTATTTAG 769 chr6qtel1M 455898 GATTAGGTTATTTAATTTCCAATTAACTTTTAAGATTTT 455936 i v iv i v -- vii C L1M5_orf2#LIN 768 AAGTGTGTTGTTTAATTTCCAAATA--TTTGGGGATTTT 732 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.45 CpG sites = 48, Kimura (unadjusted) = 36.45 Transitions / transversions = 1.23 (48/39) Gap_init rate = 0.07 (23 / 325), avg. gap size = 1.22 (28 / 23) 498 30.48 3.77 4.02 chr6qtel1M 456502 456925 (543075) C L1M4_orf2#LINE/L1 (2105) 1189 767 m_b310s551i3 12971 chr6qtel1M 456502 TTTCAGTTTTGAGTCTGGTTATTTGATTTTTCTTCTTTCCTTTTTCTAAT 456551 v ii v i i v v i - i ii ii ii C L1M4_orf2#LIN 1189 TTTCATTCCTGATTTTAGTAATTTGAGTCTTCT-CTCTTTTTTTCTTGGT 1141 chr6qtel1M 456552 CAAATTAACTAAAGGTTTAACTACTTTATT----TGTTCATAAAACCAAA 456597 ivi i iv v i i ---- v v i v C L1M4_orf2#LIN 1140 CAGTCTAGCTAAAGGTTTGTCAATTTTGTTGATCTTTTCAAAGAACCAAC 1091 chr6qtel1M 456598 TCTTAATTT----AATTTTTAGTTCAATAGTTTTCTTACTTTCAATTTTA 456643 i ii ----i i--- v v ii i i v i C L1M4_orf2#LIN 1090 TTTTGGTTTCGTTGATTTTC---TCTATTGTTTTTCTATTCTCTATTTCA 1044 chr6qtel1M 456644 TTACTTTCTCCTTTTATTTTCAGAATTTCAAATTTGGTATATAATTGGGG 456693 vv iv i v i i vv ---i vv - v iv vvv C L1M4_orf2#LIN 1043 TTTATTTCCGCTCTAATCTTTATTATTTC---CTTCCT-TCTGCTTGCTT 998 chr6qtel1M 456694 GGGGGGGTTAATTTG---TTTTTGTTCTAGCTTTTTA--GTTGCATGTCC 456738 v v-- i --- i v i i -- v v v iv C L1M4_orf2#LIN 997 TGGGT--TTAGTTTGCTCTTCTTTTTCTAGTTTCTTAAGGTGGAAGGTTA 950 chr6qtel1M 456739 AATGCACTGATCTTC--TCTTTAGCTATTTTTTTTTTAATGTAAGCATCT 456786 ii -i i i vv-- -----i i i i i C L1M4_orf2#LIN 949 GGT-TATTGATTTGAGATCTTT-----CTTCTTTTTTAATATAGGCATTT 906 chr6qtel1M 456787 AAAGATATAAAATTAGCTCTAAAAACTACTTTGGCTGCATCCCATACATT 456836 v v v vv iv i ? vi C L1M4_orf2#LIN 905 ACAGCTATAAATTTCCCTCTAAGCACTGCTTTNGCTGCATCCCATAAGTT 856 chr6qtel1M 456837 TTGGTTTGTTGTCTCATTATTTTCATTC-TCTAGGATGAACTTATCAATT 456885 v v iv ii - vii - v i vii C L1M4_orf2#LIN 855 TTGGTATGTTGTGTTTTCGTTTTCATTCATCTCAAA-GTATTTTCTAATT 807 chr6qtel1M 456886 GTTTCTATGATCTGTTATTTCTCCCTTTCATTCTTTAGGA 456925 viiii i i v v vv v vi v C L1M4_orf2#LIN 806 TCCCTTGTGATTTCTTCTTTGACCCATTGGTTATTTAGGA 767 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 39.21 CpG sites = 68, Kimura (unadjusted) = 40.09 Transitions / transversions = 1.21 (68/56) Gap_init rate = 0.05 (23 / 423), avg. gap size = 1.43 (33 / 23) 555 27.46 4.41 4.70 chr6qtel1M 456502 456864 (543136) C L1M5_orf2#LINE/L1 (2105) 1189 828 m_b310s551i4 12971 chr6qtel1M 456502 TTTCAGTTTTGAGTCTGGTTATTTGATTTTTCTTCTTTCCTTTTTC--TA 456549 v ii vvi v --- v i i i-- i C L1M5_orf2#LIN 1189 TTTCATTCCTGATATTGGTAATTTG---TGTCTTCTCTCTTTTTTTCTTG 1143 chr6qtel1M 456550 ATCAAATTAACTAAAGGTTTAACTACTTTATT----TGTTCATAAAACCA 456595 ivi ?i i v v i ---- v v i C L1M5_orf2#LIN 1142 ATCAGTCTNGCTAGAGGTTTATCAATTTTATTGATCTTTTCAAAGAACCA 1093 chr6qtel1M 456596 AATCTTAATTT----AATTTTTAGTTCAATAGTTTTCTTACTTTCAATTT 456641 iv i iii ----i i--- v v ? ?i ii v C L1M5_orf2#LIN 1092 GCTTTTGGCTTCGTTGATTTTC---TCTATTGTNTNTTTGTTTTCTATTT 1046 chr6qtel1M 456642 TATTACTTTCTCCTTTTATTTTCAGAATTTCAAATTTGGTATATAATTGG 456691 i iv v i i i vv vvvii vv iv ?v v C L1M5_orf2#LIN 1045 CATTGATTTCTGCTCTTATCTTTATTATTTCCTTCCTTCTACTTNCTTTG 996 chr6qtel1M 456692 GGGGGGGGGTTAATTTG---TTTTTGTTCTAGCTTTTTA-GTTGCATGTC 456737 v------ --- i v i - v v v ii C L1M5_orf2#LIN 995 GGT------TTAATTTGCTCTTCTTTTTCTAGCTTCTTAAGGTGGAAGCT 952 chr6qtel1M 456738 CAATGCACTGATCTT--CTCTTTAGCTATTTTTTTTTTAATGTAAGCATC 456785 i ivv i i --vi -----i i i i ? i C L1M5_orf2#LIN 951 TAGATCATTGATTTTAAGCCTTT-----CTTCTTTTCTAATATANGCATT 907 chr6qtel1M 456786 TAAAGATATAAAATTAGCTCTAAAAACTACTTTGGCTGCATCCCATACAT 456835 ? v v vv iv i i i v C L1M5_orf2#LIN 906 TAANGCTATAAATTTCCCTCTAAGCACTGCTTTAGCTGCATCCCACAAAT 857 chr6qtel1M 456836 TTTGGTTTGTTGTCTCATTATTTTCATTC 456864 i v v iv i ? C L1M5_orf2#LIN 856 TTTGATATGTTGTATTTTCATTNTCATTC 828 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 35.74 CpG sites = 52, Kimura (unadjusted) = 35.74 Transitions / transversions = 1.21 (52/43) Gap_init rate = 0.06 (23 / 362), avg. gap size = 1.43 (33 / 23) 18 28.68 5.56 0.00 chr6qtel1M 458978 459049 (540951) (TA)n#Simple_repeat 1 76 (0) m_b310s252i8 12972 chr6qtel1M 458978 TATATTTATATGTGGCCAT-TATATTTATGTATGTA-ATATATAAACA-A 459024 v i ivvi - v i i - v i - (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr6qtel1M 459025 TATAT-TGCTTATATATAGGAATATA 459049 - iiv viv (TA)n#Simple_ 51 TATATATATATATATATATATATATA 76 Matrix = Unknown Transitions / transversions = 1.12 (9/8) Gap_init rate = 0.06 (4 / 71), avg. gap size = 1.00 (4 / 4) 379 33.90 5.34 1.17 chr6qtel1M 459050 459461 (540539) L1M1_orf2#LINE/L1 1859 2287 (1007) m_b310s551i6 12973 chr6qtel1M 459050 TAGGAATAAATGGAGTTTTCTTTAATATAATAAATAGTATCTATCTCAAA 459099 i v i v iiv v i i i vivi v ivv i L1M1_orf2#LIN 1859 TGGGTATAGAAGGAACATACCTCAACATAATAAAAGCCATATACGACAGA 1908 chr6qtel1M 459100 ACATCAACAAGCATTAC-CTGTAATAGGTATAATCTAGAAATCAATTCAA 459148 v vv i v i i i- - i v v v ii ii vv i vv L1M1_orf2#LIN 1909 CCCACAGCTAGTATCATACTG-AATGGGGAAAAACTGAAAGCCTTTCCTC 1957 chr6qtel1M 459149 TAACATCAAGGGTAAGGCAAGTGTGTTAATTGTCAGCACTGTTATTCAAT 459198 v vi iii v i vi iiv i v v i L1M1_orf2#LIN 1958 TAAGATCTGGAACACGACAAGGATGCCCACTTTCACCACTGTTATTCAAC 2007 chr6qtel1M 459199 ATTGTATT---------------AGCAATAAGAAAAGA-AAATATTTTAG 459232 v i --------------- v v - v vv v i L1M1_orf2#LIN 2008 ATAGTACTGGAAGTCCTAGCTAGAGCAATCAGACAAGAGAAAGAAATAAA 2057 chr6qtel1M 459233 AGGAATACAAATAGACAATGAAAAAATAAAACTTTCCTT--CTACAGACC 459280 i v v v iv v i i v i v --i i iv L1M1_orf2#LIN 2058 GGGCATCCAAATTGGAAAGGAAGAAGTCAAATTATCCTTGTTTGCAGATG 2107 chr6qtel1M 459281 ACATGATAAGCTACTTAGACAATCCTGAAGAATCAAATAAACAATTAAAT 459330 i vvvv i i v v i v v v? v i vvv L1M1_orf2#LIN 2108 ATATGATCTTATATTTGGAAAAACCTAAAGACTCCACNAAAAAACTATTA 2157 chr6qtel1M 459331 GAAACAATTAATGACTTAAATAAATCTACAGAATATAAAATAAA-ATA-A 459378 vii v ii v v i vi i i i v - - L1M1_orf2#LIN 2158 GAACTGATAAACAAATTCAGTAAAGTTGCAGGATACAAAATCAACATACA 2207 chr6qtel1M 459379 AAAATCATCATCATTTTTACATGCTACCAATGAA-ACCCAGCAAGAAGAG 459427 vi v i i i v i - vi v - i i L1M1_orf2#LIN 2208 AAAATCAGTAGCATTTCTATATGCCAACAGTGAACAATCTG-AAAAAGAA 2256 chr6qtel1M 459428 GTAGAAAAAGAAATTACACTTAAAGTAATGGCCA 459461 i vi v iv i ---i i L1M1_orf2#LIN 2257 ATCAAAAAAGTAATCCCATTTA---CAATAGCCA 2287 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 45.59 CpG sites = 69, Kimura (unadjusted) = 46.04 Transitions / transversions = 1.00 (69/69) Gap_init rate = 0.03 (12 / 411), avg. gap size = 2.25 (27 / 12) 485 30.63 8.54 2.87 chr6qtel1M 459050 459412 (540588) L1MD_orf2#LINE/L1 1859 2241 (1053) m_b310s551i5 12973 chr6qtel1M 459050 TAGGAATAAATGGAGTTTTCTTTAATATAATAAATAGTATCTATCTCAAA 459099 i v iivi i i iv i v i --- L1MD_orf2#LIN 1859 TAGGAATAGAGGGGAACTTCCTCAACTTGATAAAGAGCATCTA---CAAA 1905 chr6qtel1M 459100 ACATCAACA---AGCATTACCTGTAATAGGTATAATCTAGAAATCAATTC 459146 v i v --- i i iviv i vv v iv ii viiivvii L1MD_orf2#LIN 1906 AAACCTACAGCTAACATCATACTTAATGGTGAAAGACTGAATGCTTTCCC 1955 chr6qtel1M 459147 AATAACATCAAGGGTAAGGCAAGTGTGTTAATTGTCAGCACTGTTATTCA 459196 vv v ii iii vi ivii v v v L1MD_orf2#LIN 1956 CCTAAGATCGGGAACAAGGCAAGGATGTCCGCTCTCACCACTCTTATTCA 2005 chr6qtel1M 459197 ATATTGTATTAG---------------CAATAAG-----AAAAGAAAATA 459226 i v i i --------------- ----- i L1MD_orf2#LIN 2006 ACATAGTACTGGAAGTTCTAGCCAGTGCAATAAGGCAAGAAAAGGAAATA 2055 chr6qtel1M 459227 TTTTAGAGGAATACAAATAGACAATGAAAAAATAAAACTTTCCT--TCTA 459274 ---- i v i v iv v i v i-- i i L1MD_orf2#LIN 2056 ----AAAGGCATACAGATTGGAAAGGAAGAAATAAAACTGTCCCTATTTG 2101 chr6qtel1M 459275 CAGACCACATGATAAGCTACTTAGACAATCCTGAAGAAT---CAAATAAA 459321 iv viv v v ii i --- v L1MD_orf2#LIN 2102 CAGATGACATGATTGTCTACGTAGAAAATCCCAAGGAATCTACAAAAAAA 2151 chr6qtel1M 459322 CAATTAAATGAAACAATTAATGACTTAAATAAATCTACAGAATATAAAAT 459371 vvi --- vi v i v v ii iviii i i i L1MD_orf2#LIN 2152 CTCCTA---GAACTAATAAGTGAGTTCAGCAAGGTCGCAGGATACAAGAT 2198 chr6qtel1M 459372 AAA-ATA-AAAAATC-ATCATCATTTTTACATGCTACCAATGAA 459412 ? - - - ii - i i i v L1MD_orf2#LIN 2199 NAACATACAAAAATCAATTGT-ATTTCTATATACTAGCAATGAA 2241 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 39.43 CpG sites = 65, Kimura (unadjusted) = 40.98 Transitions / transversions = 1.51 (65/43) Gap_init rate = 0.05 (19 / 362), avg. gap size = 2.21 (42 / 19) 20 19.79 2.13 0.00 chr6qtel1M 459480 459493 (540507) (AT)n#Simple_repeat 1 15 (33) m_b310s252i9 12974 chr6qtel1M 459480 ATTTATATAT-TGTT 459493 v - i v (AT)n#Simple_ 1 ATATATATATATATA 15 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.08 (1 / 13), avg. gap size = 1.00 (1 / 1) 27 3.03 2.94 0.00 chr6qtel1M 459494 459527 (540473) (TATGTAAA)n#Simple_repeat 1 35 (0) c_b310s251i5 12975 chr6qtel1M 459494 TATGTAAATATGTAAA-ATATAAATATGTAAATAT 459527 - i (TATGTAAA)n#S 1 TATGTAAATATGTAAATATGTAAATATGTAAATAT 35 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 20 19.79 2.13 0.00 chr6qtel1M 459528 459559 (540441) (AT)n#Simple_repeat 16 47 (1) m_b310s252i9 12976 chr6qtel1M 459528 TTATATTTATATATATATAAATGTGTATATAT 459559 v v v i i (AT)n#Simple_ 16 ATATATATATATATATATATATATATATATAT 47 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 17 0.00 0.00 0.00 chr6qtel1M 461042 461060 (538940) (A)n#Simple_repeat 1 19 (0) m_b310s252i10 12977 chr6qtel1M 461042 AAAAAAAAAAAAAAAAAAA 461060 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAA 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 16 16.35 4.88 0.00 chr6qtel1M 461311 461351 (538649) (TATC)n#Simple_repeat 1 43 (0) m_b310s252i11 12978 chr6qtel1M 461311 TATCTATCTTTCTATCTATCT-T-TATGTATGTATGCATGTAT 461351 v - - v v vi v (TATC)n#Simpl 1 TATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTAT 43 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 914 32.25 6.09 3.32 chr6qtel1M 461458 462278 (537722) L1MD_orf2#LINE/L1 1399 2241 (1053) m_b310s551i7 12979 chr6qtel1M 461458 AAAGAAAAATGCCTAGAATCAGAAGGATTTACAAGTGAATTATAGCAAAG 461507 i i vi i ivi v v i vi v v v v L1MD_orf2#LIN 1399 AAAAAGAAATCTCCAGGCCCAGATGGTTTCACTGGAGAATTCTACCAAAC 1448 chr6qtel1M 461508 ATTTGAGGAAAAATTAATTCCAATACTACATG--TTATTTAAGGGGGAAA 461555 i i i i iv v ii--i v iv ---- L1MD_orf2#LIN 1449 GTTTAAAGAAGAATTAACACCAATTCTACACAATCTCTTCCAG----AAA 1494 chr6qtel1M 461556 ATAGGTAAAGAAGGAGTCCCACCAAATTTATTTTATATGATAAATGTT-- 461603 ivi i i iiv iv v i i iv iiv i i -- L1MD_orf2#LIN 1495 ATAGAAGAGGAGGGAACACTTCCCAACTCATTTTATGAGGCCAGTATTAC 1544 chr6qtel1M 461604 -TTAATACCTTAACCAGG--GAGATCAAAACTAAGAAAAAAAACTACAAA 461650 -i i vv i--i - iv v i i i L1MD_orf2#LIN 1545 CCTGATACCAAAACCAGACAAAGA-CAGTACAAAAAAAGAAAACTACAGA 1593 chr6qtel1M 461651 ATAATTTTCTTAATGAATATTGACCCCTTCAAAA--CTTAAATAAAACAC 461698 vi v i i v i v v ---- -- i v i i i L1MD_orf2#LIN 1594 CCAATATCCCTCATGAACATAGACGC----AAAAATCCTCAACAAAATAT 1639 chr6qtel1M 461699 TTATAAA-GAAATTATAGCAATAGGCCACAAATATTATGTACTCTGACCA 461747 vii -?i -i viiv v iv ii iv L1MD_orf2#LIN 1640 TAGCAAATNGAATT-CAGCAATATATAAAAAGAATTATACACCATGACCA 1688 chr6qtel1M 461748 GG--GAGTTTCAAGATT--AGGAGGGCAAAATGGGTTCCATAGTAGGAAA 461793 i -- i ---- -- ?iv iiiv v v -v L1MD_orf2#LIN 1689 AGTGGGGTTT----ATTCCAGGNATGCAAGGCTGGTTCAATATT-CGAAA 1733 chr6qtel1M 461794 ATT--TTAAGCTTAATTGACCATAAAAATAAA--AAAGAACAAAAATCAT 461839 i-- i -iv iv vv i ii-- v i L1MD_orf2#LIN 1734 ATCAATCAA-TGTAATCCACCATATTAACAGGCTAAAGAAGAAAAATCAC 1782 chr6qtel1M 461840 ATGATTATACTTGTCAATGCAGAAAATACTTTT--CAAAATACAACACCC 461887 i iivi ii vi v -- v L1MD_orf2#LIN 1783 ATGATCATATCAATTGATGCAGAAAAAGCATTTGACAAAATTCAACACCC 1832 chr6qtel1M 461888 ATTTCTATTAAAAAACACTACAAATCATATGAATAAATGGAGTTTTCTTT 461937 iv iv vivii v? v - v i v iivi i i L1MD_orf2#LIN 1833 ATTCATGATAAAAACTCTCAGNAAAC-TAGGAATAGAGGGGAACTTCCTC 1881 chr6qtel1M 461938 AATATAATGAATAGTATCTATCTCAAAACATCAACA---AGCATTACCTG 461984 iv i i v i --- v i v --- i i iviv L1MD_orf2#LIN 1882 AACTTGATAAAGAGCATCTA---CAAAAAACCTACAGCTAACATCATACT 1928 chr6qtel1M 461985 TAATAGGTATAATCTAAAAATCAATTCAATATCACCAAGGGTAAGGCAAG 462034 i vv v iv i viiivvii vv vv i ii iii L1MD_orf2#LIN 1929 TAATGGTGAAAGACTGAATGCTTTCCCCCTAAGATCGGGAACAAGGCAAG 1978 chr6qtel1M 462035 TGTGTTCATTGTCAGCATTGTTATTCAATATTGTATTA------------ 462072 vi i ii v v i v i v i i------------ L1MD_orf2#LIN 1979 GATGTCCGCTCTCACCACTCTTATTCAACATAGTACTGGAAGTTCTAGCC 2028 chr6qtel1M 462073 ---GCAAT-----AAGAAAAGAAAATATTTTGGAGGAATACAAATAGACA 462114 --- ----- i ----ii v i v iv L1MD_orf2#LIN 2029 AGTGCAATAAGGCAAGAAAAGGAAATA----AAAGGCATACAGATTGGAA 2074 chr6qtel1M 462115 ATGGAAAAATAAAACTTTCCT--TCTACAGACCATATG-TAAGCTACTTA 462161 v i i v i-- i i iv i - viv v L1MD_orf2#LIN 2075 AGGAAGAAATAAAACTGTCCCTATTTGCAGATGACATGATTGTCTACGTA 2124 chr6qtel1M 462162 GACAATCCTGAAGAGT---CAAATAAACAATTAAATGAAACAATTAATGA 462208 v ii i i --- v vvi --- vi v i L1MD_orf2#LIN 2125 GAAAATCCCAAGGAATCTACAAAAAAACTCCTA---GAACTAATAAGTGA 2171 chr6qtel1M 462209 CTTAAACAAATCTACAGAATATAAAATAAAATTTAAAAAATC-ATCATCA 462257 v v i iviii i i i ? vv vv - ii - L1MD_orf2#LIN 2172 GTTCAGCAAGGTCGCAGGATACAAGATNAACATACAAAAATCAATTGT-A 2220 chr6qtel1M 462258 TTTTTACATGCTACCAATGAA 462278 i i i v L1MD_orf2#LIN 2221 TTTCTATATACTAGCAATGAA 2241 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 43.13 CpG sites = 153, Kimura (unadjusted) = 44.09 Transitions / transversions = 1.49 (153/103) Gap_init rate = 0.06 (47 / 820), avg. gap size = 1.66 (78 / 47) 365 28.97 3.65 6.77 chr6qtel1M 464103 464239 (535761) MIRc#SINE/MIR 10 142 (126) m_b310s601i3 12980 chr6qtel1M 464103 GTGGCACAATAGATAGAGCATGAAGATTGAAATTAGGAAAATTCATCTTC 464152 ii i i v iviiiv i i i i -------- MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA--------C 51 chr6qtel1M 464153 CCGAGTTCAAATATAGTCTGAGACGCT-ACTAACTGTGTGACCCTGGGCA 464201 i i i i viv v vv v i - i i MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 101 chr6qtel1M 464202 AGTGACTT-ATCTCTGCTTATCTTT-GTTTTCACA--TGTAA 464239 v - i - v v i i- i v -- MIRc#SINE/MIR 102 AGTCACTTAACCTCT-CTGAGCCTCAGTTTCCTCATCTGTAA 142 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 36.72 CpG sites = 24, Kimura (unadjusted) = 38.04 Transitions / transversions = 1.85 (24/13) Gap_init rate = 0.10 (13 / 136), avg. gap size = 1.08 (14 / 13) 443 34.63 1.48 1.48 chr6qtel1M 464243 464579 (535421) C L1M5_orf2#LINE/L1 (1871) 1423 1087 m_b310s551i8 12981 chr6qtel1M 464243 CATTTGGCCTTGGAGATTTTTTTTTTAGGGAGTTAATTAATAGCTTGTTA 464292 i v i - i v i i v vv vi vvi v C L1M5_orf2#LIN 1423 CATCTGGGCCTGGAG-TTTTCTTTGTGGGAAGGTTTTTAATTACAAATTC 1375 chr6qtel1M 464293 AATTTCTTTTTTCTAAA-ATAGAACTTTCGAAGTAATTTAATTCCTCT-- 464339 v--v i - ii v iv ii vv i v i -- C L1M5_orf2#LIN 1374 AATTTCTTTA--ATAGATATAGGGCTATTCAGATTTTCTATTTCTTCTTG 1327 chr6qtel1M 464340 -GCTAATTGGGGCAATCTATATTTTTTGTAAATGTTCAACCATTTCACTT 464388 - ii i vv i ?i i i iivii -i iiv ii C L1M5_orf2#LIN 1326 NGTCAGTTTTGGTAANTTGTGTTTTTCAAGGA-ATTTGTCCATTTCATCT 1278 chr6qtel1M 464389 AGATTATCAGATTTATTGGCATATAGTTGGGCAAAGTAGCTCCTAATTAT 464438 ii ? i v vv v i viii v C L1M5_orf2#LIN 1277 AAGTTNTCAAATTTATTGGCATAAAGTTGTTCATAATATTCTCTTATTAT 1228 chr6qtel1M 464439 TGCTCTAATTTCCTCTTCATTGGTAGAAAGTTGACACTTTTCATTTTTGA 464488 ivi i v ivivvv iv vi vv vv vi ii C L1M5_orf2#LIN 1227 CCTTTTAATGTCTGTAGGATCTGTAGTGATGTCTCCTTTTTCATTCCTGA 1178 chr6qtel1M 464489 AACTAACAAATTG-GTTTTCTTTTTTATTTATTCTAATCAATTTAACTAA 464537 v i iii v - i i i - v ii i i i ?i i C L1M5_orf2#LIN 1177 TATTGGTAATTTGTGTCTTCTCTCTT-TTTTTCTTGATCAGTCTNGCTAG 1129 chr6qtel1M 464538 AAGTTTATCTATGTTGTTATTTTTTTTATAAAACCAGCTCTT 464579 i v v i iv i i v i i C L1M5_orf2#LIN 1128 AGGTTTATCAATTTTATTGATCTTTTCAAAGAACCAGCTTTT 1087 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 49.17 CpG sites = 69, Kimura (unadjusted) = 49.17 Transitions / transversions = 1.50 (69/46) Gap_init rate = 0.03 (9 / 336), avg. gap size = 1.11 (10 / 9) 656 34.47 2.90 4.42 chr6qtel1M 464624 465312 (534688) C L1PREC2_orf2#LINE/L1 (2589) 705 27 m_b310s551i9 12981 chr6qtel1M 464624 TATTTTTATTGCATCATGATCTGAAAAAAGATGCATTTACTAT---TTCT 464670 iiii i i i i?---- ii iv --- v C L1PREC2_orf2# 705 TATTTTTATTGCGCTGTGGTCCGAGAGN----GTGTTTGGTATGATTTCG 660 chr6qtel1M 464671 GCCTTTCTGCACTTGATTGTGAAAT-TTTTATGCCCTAAAACATGGGCAA 464719 iii i i -i v i v - i v vv ii v i C L1PREC2_orf2# 659 GTTCTTTTGCATTTG-CTGAGGATTGTTTTATGTCCGATTATGTGGTCGA 611 chr6qtel1M 464720 TTTTTA--TAGGTTCCATTTAGCACCAGGGGTAGGGTGGAAGTATATTCC 464767 vi-- v v v i ------ i ii iv i v i C L1PREC2_orf2# 610 TTTTAGAGTATGTGCCATGTGGC------GATGAGAAGAATGTATATTCT 567 chr6qtel1M 464768 TTTCTGTCTCCATTCAATTTTCTCCAAAAGTCTATCATATATAATTTTTC 464817 v v v i?vvi vv ivv vi i v vi vi v vv C L1PREC2_orf2# 566 GTTGTTTTNGGGTGGAGAGTTCTGTAGATGTCTATCAGGTCCATTTGGTC 517 chr6qtel1M 464818 TAAAATTCCATTTACCTCCTTAACTTCTTTCTCATTCATTTTGTGGTT-- 464865 i ivi vvi i vv v iv ---i v v vi -- C L1PREC2_orf2# 516 CAGTGTTGAGTTCAGGTCCTGAATATCTTT---GTTAATTTTCTGCCTCG 470 chr6qtel1M 464866 -TGATTTATCAAGTTCTGATAGAGCGAGGT-TTGAGATCCCCCAGTAGTT 464913 - i i v i v vi --i i - ii i v v v C L1PREC2_orf2# 469 ATGATCTGTCTAATACTGTCAG--TGGGGTGTTGAAGTCTCCCACTATTA 422 chr6qtel1M 464914 TAGTTTTGCTGTCTAATTTTTCTTGCAGCTCTCTTAACTTTTCCTTTAGG 464963 v v v vv v i ii ? v v ivvi v v C L1PREC2_orf2# 421 TTGTGTGGGAGTCTAAGTCTCTTTGNAGGTCTCTAAGAACTTGCTTTATG 372 chr6qtel1M 464964 AATATGGATGTT---ATGTCACATGACACATATATGTTTAGTATTGATAT 465010 v i i ---i iivi --- i v v v v C L1PREC2_orf2# 371 AATCTGGGTGCTCCTGTGTTGGGTG---CATATATATTTAGGATAGTTAG 325 chr6qtel1M 465011 TACTTCATTATCTA-TGGTACCTTTTAGCAAAATGTAATTTCCTTCCTTA 465059 vv - i iv - v v i v vv vi i i C L1PREC2_orf2# 324 GTCTTC-TTGTTGAATTGAACCCTTTACCATTATGTAATGCCCTTCTTTG 276 chr6qtel1M 465060 TCTCTTTTAATTACCTCTATTTTTGTTT-----TTGCTTAATGTGAGATC 465104 i i ----- v v v -----i i vi v i i C L1PREC2_orf2# 275 TCTTTTTTGAT-----CTTTGTTGGTTTAAAGTCTGTTTTGTCTGAAATT 231 chr6qtel1M 465105 AGGATTGCTACCACTGATTTTTTTT-TTTTACTTTAGCTGAGTATAATAA 465153 v v v i - v v v ----- ii i C L1PREC2_orf2# 230 AGGATTGCAACCCCTGCTTTTTTCTGTTTTCCATTTGCT-----TGGTAG 186 chr6qtel1M 465154 ATTCTGCTCCAGCCTTTTACCTTAACTCTGTGTGTATCACTCTGATTTAA 465203 i v v i ii i vi i v i i viivv v i C L1PREC2_orf2# 185 ATTTTTCTCCATCCCTTTATTTTGAGCCTATGGGTGTCATTGCATGTGAG 136 chr6qtel1M 465204 ATGTGTTTCTTGTAAACAACATATTGTAAGATTCTGGCTTTTAATCTAGT 465253 v i v i i iii vi i ii vi i v i i C L1PREC2_orf2# 135 ATGGGTCTCTTGAAGACAGCATACCATTGGGTCTTGCTTCTTTATCCAGC 86 chr6qtel1M 465254 TTGCTATCCACTTCCATGTTATAGGAGAGTTCATCCCATTCACATTAACA 465303 i ii vv v v v v v i vi i v i v vi C L1PREC2_orf2# 85 TTGCCACTCTGTGCCTTTTAATTGGGGCATTTAGCCCATTTACATTCAAG 36 chr6qtel1M 465304 GTTAAAATT 465312 iv C L1PREC2_orf2# 35 GTTAGTATT 27 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 46.56 CpG sites = 118, Kimura (unadjusted) = 47.42 Transitions / transversions = 1.08 (118/109) Gap_init rate = 0.06 (40 / 688), avg. gap size = 1.25 (50 / 40) 254 32.17 6.81 0.80 chr6qtel1M 465145 465379 (534621) C L1MEc_5end#LINE/L1 (49) 2478 2230 m_b310s551i10 12981 chr6qtel1M 465145 GTATAATAAATTCTGCTCCAGCCTTTTACCTTAACTCTGTGTGTATCACT 465194 i ii v ii vi v i v vi i v i vi C L1MEc_5end#LI 2478 GCATGGTATATCTTTTTCCATCCTTTTACTTTTAACCTATTTGTGTCTTT 2429 chr6qtel1M 465195 CTGATTTAAA-TGTGTTTCTTGTAAACAACATATTGTAAGATTCTGGCTT 465243 v - - ? ii i v vi i ii vi C L1MEc_5end#LI 2428 AT-ATTTAAAGTGNGTTTCTTGTAGGCAGCATATAGTTGGGTCTTGCTTT 2380 chr6qtel1M 465244 TTAATCTAGTTTGCTATCCACTTCCATGTTATAGGAGAGTTCATCCCATT 465293 v i i i vi vi v v v v v v i v i vv C L1MEc_5end#LI 2379 TTTATCCAATCTGACAATCTCTGCCTTTTAATTGGGGTGTTTAGACCATT 2330 chr6qtel1M 465294 CACATTAACAGTTAAAATTA------------TTAACTCTATT-TCTTAC 465330 i v vv v vv i------------ v ii- i C L1MEc_5end#LI 2329 TACATTTAATGTGATTATTGATATGGTTGGGTTTAAATCTACCATCTTGC 2280 chr6qtel1M 465331 CATCTTATTTTCTCTAAGT--TATATTTTGCTTTTTCCTTTCCCCCTTTT 465378 i - i v vv --i v v vi iii i C L1MEc_5end#LI 2279 TAT-TTGTTTTCTATTTGTCCCATCTGTTCTTTTTTCCTTTTTTCTTTTT 2231 chr6qtel1M 465379 C 465379 C L1MEc_5end#LI 2230 C 2230 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 43.09 CpG sites = 39, Kimura (unadjusted) = 43.09 Transitions / transversions = 1.08 (39/36) Gap_init rate = 0.03 (6 / 234), avg. gap size = 3.00 (18 / 6) 439 26.30 5.15 2.00 chr6qtel1M 465189 465382 (534618) C L1MEj_5end#LINE/L1 (0) 2160 1961 m_b310s551i11 12981 chr6qtel1M 465189 ATCACTCTGATTTAAATGTGTTTCTTGTAAACAACATATTGTAAGATTCT 465238 i v i i v ivi i i C L1MEj_5end#LI 2160 ATCACTTTGTTTTAAGTGTGTTTCTTGTAAACAGCATATAGCTGGGTTTT 2111 chr6qtel1M 465239 GGCTTTTAATCTAGTTTGCTATCCACTTCCATGTTATAGGAGAGTTCATC 465288 vi i i i i vi vi v vi v v v i i vi C L1MEj_5end#LI 2110 GTTTTTTAACCCAATCTGACAGTCTCTGTCTTTTAATGGGAGAATTCAGT 2061 chr6qtel1M 465289 CCATTCACAT------TAACAGTTAAAATTATTAACTCTATTTCTTACCA 465332 ------ iii i v vv i i i i - C L1MEj_5end#LI 2060 CCATTCACATTTAGTGTAACGACTGATATACTTGATTTTATTCCTT-CCA 2012 chr6qtel1M 465333 TCTTATT---TTCTCTAAGTTATATTTTG-CTTTTTCCTTTCCCCCTTTT 465378 i --- ? i -- - -i ?i iiii C L1MEj_5end#LI 2011 TCTTACTTTATTNTTTA--TT-TATTTTGTTTTTTTNTTTTTTTTCTTTT 1965 chr6qtel1M 465379 CCCT 465382 i C L1MEj_5end#LI 1964 TCCT 1961 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 33.57 CpG sites = 35, Kimura (unadjusted) = 34.43 Transitions / transversions = 2.33 (35/15) Gap_init rate = 0.04 (7 / 193), avg. gap size = 2.00 (14 / 7) 381 26.15 1.50 8.00 chr6qtel1M 465744 465876 (534124) C MIRb#SINE/MIR (138) 130 6 m_b310s601i4 12982 chr6qtel1M 465744 CTGAGGC-AATTGCAGTTAAATAACTTGCCCA-GGTCACCCAGCTAGGAA 465791 -v vv vi i - v --- C MIRb#SINE/MIR 130 CTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAG--- 84 chr6qtel1M 465792 ATGTTAAGTGTCTGAGGTCATATTTGAATTCAGTTCCTGCTGACTTCATG 465841 ---- v v viviv i ii v ivv i vi C MIRb#SINE/MIR 83 ----TAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAA 38 chr6qtel1M 465842 GCTGGTATTCTATCTACTGTGCCACCTAGCTGCCC 465876 iv ii v i ii --- C MIRb#SINE/MIR 37 GCCCGTGCTCTTTCCACTGCACCAC---GCTGCCC 6 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 29.92 CpG sites = 16, Kimura (unadjusted) = 32.27 Transitions / transversions = 1.00 (16/16) Gap_init rate = 0.09 (12 / 132), avg. gap size = 1.00 (12 / 12) 48 24.00 0.89 0.00 chr6qtel1M 467288 467399 (532601) (AG)n#Simple_repeat 1 113 (0) m_b310s252i12 12983 chr6qtel1M 467288 AGAGAGAGAGAGATAGACAGACAGACATACAAACAGACAGAAACAAAGAA 467337 v v v v v v i v v i v i i (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr6qtel1M 467338 AGAGAGAGAGAGAGAGAAACAAAGACAGAG-GAGAGAGACACACAGAGAA 467386 i v i v - v v v i (AG)n#Simple_ 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 100 chr6qtel1M 467387 ACAGAGACAGAGA 467399 v v (AG)n#Simple_ 101 AGAGAGAGAGAGA 113 Matrix = Unknown Transitions / transversions = 0.44 (7/16) Gap_init rate = 0.01 (1 / 111), avg. gap size = 1.00 (1 / 1) 84 14.80 1.69 3.43 chr6qtel1M 467486 467663 (532337) (TTTC)n#Simple_repeat 1 175 (0) m_b310s252i13 12984 chr6qtel1M 467486 TTTGTTTGTTTC-TTCCTTCCTTCCTTCTTTCCTTTC-TTCCTTCTTTCT 467533 v v - i i i - - i (TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT-CTTTCTTTCTTTCTTTCT 49 chr6qtel1M 467534 TTCCTTCCTTTC-TTCTTTCCTTCCTTCCTTTCTTACTTTCTTTGTTTCC 467582 - i - - i i v v - (TTTC)n#Simpl 50 TT-CTTTCTTTCTTTCTTT-CTTTCTTTCTTTCTTTCTTTCTTTCTTT-C 96 chr6qtel1M 467583 TTTCTTTCTTACTTTCTTTCTTTGTTTCCTTCCTTTTTCCCTTCCTTCCT 467632 v v - i i ii i i (TTTC)n#Simpl 97 TTTCTTTCTTTCTTTCTTTCTTTCTTT-CTTTCTTTCTTTCTTTCTTTCT 145 chr6qtel1M 467633 TTCTTTCTTTCCTTCCTTCCTTTCCTTCTTT 467663 - i i i (TTTC)n#Simpl 146 TTCTTTCTTT-CTTTCTTTCTTTCTTTCTTT 175 Matrix = Unknown Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.05 (9 / 177), avg. gap size = 1.00 (9 / 9) 17 22.61 2.44 0.00 chr6qtel1M 468605 468645 (531355) (TA)n#Simple_repeat 1 42 (0) m_b310s252i14 12985 chr6qtel1M 468605 TATATATA-AGATATAAATCTTTGCATATATGTTTATATATA 468645 - v v v v ii i v (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATA 42 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 346 30.36 5.15 0.70 chr6qtel1M 468651 468786 (531214) C MIRc#SINE/MIR (123) 145 4 m_b310s601i5 12986 chr6qtel1M 468651 ACTTTACACATAAGAAAACTGAG----AAAGTAGTTTAATTGACTTGGAC 468696 i v i i ---- i - v v vv C MIRc#SINE/MIR 145 ATTTTACAGATGAGGAAACTGAGGCTCAGAG-AGGTTAAGTGACTTGCCC 97 chr6qtel1M 468697 --CGTCACAGAGTTAATTAGTATCTGTGC-AGGATTTCAACTCTGGTCTT 468743 --v v i i v iv v v -i i iv i v C MIRc#SINE/MIR 96 AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTT 47 chr6qtel1M 468744 CATTACTAGAAGTTTTGAGTACTGTCCATTAAAGCACTCTCCC 468786 v v vv iiv v iv v i iv v v v C MIRc#SINE/MIR 46 CCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTGCC 4 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 36.74 CpG sites = 16, Kimura (unadjusted) = 38.99 Transitions / transversions = 0.64 (16/25) Gap_init rate = 0.03 (4 / 135), avg. gap size = 2.00 (8 / 4) 226 37.87 0.00 0.97 chr6qtel1M 468944 469047 (530953) C L2#LINE/L2 (586) 2496 2394 m_b310s601i6 12987 chr6qtel1M 468944 CAGAAGAAGAATGGTTTAATAGAAATGATATAGAGTTCTGTTTTGAACAC 468993 i i i v - i vi ii v vvi v i i C L2#LINE/L2 2496 CGGGAGGAGCA-GGTTTGAGGGGGAAGATCAGGAGTTCAGTTTTGGACAT 2448 chr6qtel1M 468994 AATGAACTTGAAATATTGATGGGATGTTCATTGGGAGATGTCCAATATGA 469043 iv i ii i iiiv vi ii i vvv v i v v C L2#LINE/L2 2447 GTTAAGTTTGAGATGCCTATTAGACATCCAAGTGGAGATGTCGAGTAGGC 2398 chr6qtel1M 469044 AATT 469047 i C L2#LINE/L2 2397 AGTT 2394 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 53.70 CpG sites = 24, Kimura (unadjusted) = 55.90 Transitions / transversions = 1.60 (24/15) Gap_init rate = 0.01 (1 / 103), avg. gap size = 1.00 (1 / 1) 393 27.78 0.79 0.00 chr6qtel1M 469185 469310 (530690) C Charlie4a#DNA/hAT-Charlie (11) 497 371 m_b310s502i3 12988 chr6qtel1M 469185 AACCTTCTTGGAGTCATGGACTGTTCTGTAATTGTGGTGAGGTCTATGGA 469234 i v v i ivi i vv v v i i C Charlie4a#DNA 497 AACCTTTTTTGTGCCATGGACCCCTTTGGCAGTCTGGTGAAGCCTATGGA 448 chr6qtel1M 469235 CCCATTCT-AAAATACTTTCTGGAAATGCGTAATATCAGATACATGGGAT 469283 v - i v v i vv i v v i i C Charlie4a#DNA 447 CCCCTTCTCAGAATAATGTTTTTAAATGCATAAAATAAAATACATAGGAT 398 chr6qtel1M 469284 TAGTAAAAAATCCTATTAAACTTAAAT 469310 vv ii v v v i v C Charlie4a#DNA 397 TACAAAGGAAACCAATTATATTGAAAT 371 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 34.83 CpG sites = 15, Kimura (unadjusted) = 34.83 Transitions / transversions = 0.75 (15/20) Gap_init rate = 0.01 (1 / 125), avg. gap size = 1.00 (1 / 1) 65 3.03 1.47 0.00 chr6qtel1M 470194 470261 (529739) (CA)n#Simple_repeat 1 69 (0) c_b310s251i6 12989 chr6qtel1M 470194 CACA-ACACACACACACACACACACACACACACACACACACACATACACA 470242 - i (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 chr6qtel1M 470243 CACACATACACACACACAC 470261 i (CA)n#Simple_ 51 CACACACACACACACACAC 69 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.01 (1 / 67), avg. gap size = 1.00 (1 / 1) 54 1.89 1.85 0.00 chr6qtel1M 472318 472371 (527629) (AT)n#Simple_repeat 1 55 (0) c_b310s251i7 12990 chr6qtel1M 472318 ATATAT-TATATATATATATATATATATATATATATATATATATGTATAT 472366 - i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr6qtel1M 472367 ATATA 472371 (AT)n#Simple_ 51 ATATA 55 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.02 (1 / 53), avg. gap size = 1.00 (1 / 1) 12 24.50 2.22 2.22 chr6qtel1M 472382 472426 (527574) (TATAT)n#Simple_repeat 1 45 (0) m_b310s252i15 12991 chr6qtel1M 472382 TATATT-TGTAATAATATATAGTAATGTAATCATATTATATTAGAT 472426 - i v v vi v i - i v (TATAT)n#Simp 1 TATATTATATTATATTATATTATATTAT-ATTATATTATATTATAT 45 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.05 (2 / 44), avg. gap size = 1.00 (2 / 2) 250 29.35 5.45 0.87 chr6qtel1M 473265 473374 (526626) L3#LINE/CR1 3169 3283 (816) m_b310s601i7 12992 chr6qtel1M 473265 TTTTATCAATGACTTGAATAAAAAGATAGATATC-TGATATGTGAAATTT 473313 i i i v viv - v - i v L3#LINE/CR1 3169 TTTTATCAATGACTTGGATGAAGACATAGAAGGCATGCT-TATCAAATTT 3217 chr6qtel1M 473314 TAAGTAAACATTCTGCTAAAAGGGACAACTAACA-----GATGATGGAAT 473358 vv vvi ivvv iii i i i ----- ii L3#LINE/CR1 3218 GCAGATGACACAAAGCTGGGAGGGATAGCTAATACGNTGGATGACAGAAT 3267 chr6qtel1M 473359 TAGGATGGAAAAATAT 473374 i i vv ?v L3#LINE/CR1 3268 CAAGATTCAAAANGAT 3283 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 38.37 CpG sites = 17, Kimura (unadjusted) = 38.37 Transitions / transversions = 1.13 (17/15) Gap_init rate = 0.03 (3 / 109), avg. gap size = 2.33 (7 / 3) 13 17.50 0.00 3.03 chr6qtel1M 474034 474067 (525933) (AAAAAT)n#Simple_repeat 1 33 (0) m_b310s252i16 12993 chr6qtel1M 474034 AACAATGTAAATAAAAAGAAAAAATCAAAATAAA 474067 v iv -v v (AAAAAT)n#Sim 1 AAAAATAAAAATAAAAA-TAAAAATAAAAATAAA 33 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 20 4.13 0.00 0.00 chr6qtel1M 474204 474228 (525772) (TG)n#Simple_repeat 1 25 (0) m_b310s252i17 12994 chr6qtel1M 474204 TGTTTGTGTGTGTGTGTGTGTGTGT 474228 v (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGT 25 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 12 19.11 2.63 2.63 chr6qtel1M 475817 475854 (524146) (AAAGAG)n#Simple_repeat 1 38 (0) m_b310s252i18 12995 chr6qtel1M 475817 AAAGAGAACTAG-AAGAAAAACGGGAAAAGGAAAGAGAA 475854 vv - i - i ii (AAAGAG)n#Sim 1 AAAGAGAAAGAGAAAGAGAAA-GAGAAAGAGAAAGAGAA 38 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 16 15.91 0.00 0.00 chr6qtel1M 476039 476066 (523934) (A)n#Simple_repeat 1 28 (0) m_b310s252i19 12996 chr6qtel1M 476039 AAAAAGAAGTTAAAAAAAAAAAAAAAAA 476066 i ivv (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA 28 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 30 2.25 4.08 4.08 chr6qtel1M 476147 476195 (523805) (CAAA)n#Simple_repeat 1 49 (0) c_b310s251i8 12997 chr6qtel1M 476147 CAAACAAA-ACAACAACAAAAACAAACAAACAAACAAACAAACAAA-AAA 476194 - - - v - (CAAA)n#Simpl 1 CAAACAAACA-AACAA-ACAAACAAACAAACAAACAAACAAACAAACAAA 48 chr6qtel1M 476195 C 476195 (CAAA)n#Simpl 49 C 49 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.08 (4 / 48), avg. gap size = 1.00 (4 / 4) 227 30.43 3.26 0.00 chr6qtel1M 476437 476528 (523472) HAL1#LINE/L1 1385 1479 (1028) m_b310s551i12 12998 chr6qtel1M 476437 ACTCCAAGGAATATTGTGGCCAAATTTCAGAATTTTCAGACTAAAGAAAA 476486 v v i ii v iv iviivi iv i HAL1#LINE/L1 1385 ACACCAAGGCACATCATCGTGAAATTTCAGAACACCGGGGATAAAGAGAA 1434 chr6qtel1M 476487 AATATTACAAGCAGCCAG---GAAAAAACAATTCAAATACTGAGG 476528 i vi v vv --- iv v vi HAL1#LINE/L1 1435 GATCCTAAAAGCTTCCAGAGAGAAAAAACAGGTCACATACAAAGG 1479 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 37.79 CpG sites = 14, Kimura (unadjusted) = 39.56 Transitions / transversions = 1.00 (14/14) Gap_init rate = 0.01 (1 / 91), avg. gap size = 3.00 (3 / 1) 276 17.91 4.48 0.00 chr6qtel1M 476447 476513 (523487) L1M6_5end#LINE/L1 1521 1590 (925) m_b310s551i13 12998 chr6qtel1M 476447 ATATTGTGGCCAAATTTCAGAATTTTCAGACTAAAGAAAAAATATTACAA 476496 iv v iv ?iv iv vi L1M6_5end#LIN 1521 ATATCCTGGCAAAATTTTTGAATTNCAAGGATAAAGAAAAAATCCTACAA 1570 chr6qtel1M 476497 GCAGCCAG---GAAAAAACA 476513 v --- L1M6_5end#LIN 1571 GCATCCAGGCAGAAAAAACA 1590 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 20.85 CpG sites = 5, Kimura (unadjusted) = 20.85 Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.02 (1 / 66), avg. gap size = 3.00 (3 / 1) 15 27.89 0.00 4.76 chr6qtel1M 476873 476938 (523062) (AAAGGG)n#Simple_repeat 1 63 (0) m_b310s252i20 12999 chr6qtel1M 476873 AAAGGGAAGTAGAAATGGAAAGGGGATAGTGTCAGAAAAAGGGAAAAGGG 476922 ivi v - v v vv ii - - (AAAGGG)n#Sim 1 AAAGGGAAAGGGAAAGGGAAA-GGGAAAGGGAAAGGGAAAGGG-AAA-GG 47 chr6qtel1M 476923 GAGATAAAAAGGGAAA 476938 i vii (AAAGGG)n#Sim 48 GAAAGGGAAAGGGAAA 63 Matrix = Unknown Transitions / transversions = 1.00 (7/7) Gap_init rate = 0.05 (3 / 65), avg. gap size = 1.00 (3 / 3) 20 23.82 2.74 2.74 chr6qtel1M 477105 477177 (522823) (GGAAAAG)n#Simple_repeat 1 73 (0) m_b310s252i21 13000 chr6qtel1M 477105 GGAAAAGGGAAAAGGAAAAAGAGTAAAAAGG-GAAGGGTACA-AGAAAGG 477152 i - v i -i v v -i i (GGAAAAG)n#Si 1 GGAAAAGGGAAAAGGGAAAAG-GGAAAAGGGAAAAGGGAAAAGGGAAAAG 49 chr6qtel1M 477153 GGAAAGGATTCAAAGGGAGGAGGGA 477177 i -vvv ii (GGAAAAG)n#Si 50 GGAAAAG-GGAAAAGGGAAAAGGGA 73 Matrix = Unknown Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.06 (4 / 72), avg. gap size = 1.00 (4 / 4) 334 22.92 12.31 3.79 chr6qtel1M 477234 477428 (522572) L1MEh_5end#LINE/L1 2018 2228 (7) m_b310s551i14 13001 chr6qtel1M 477234 AGGGAAG--GGGAGAAGGGAGACAAGAAAAAGGAAAACATAATCTGGGG- 477280 i -- i i i i v ? i i v --- i- L1MEh_5end#LI 2018 AGGAAAGCAGGAAAAAAGGAAAAAANAGAAAGAAAAACAGA---TGGGAC 2064 chr6qtel1M 477281 -------------ATATTAGGATGGCAGGAAATA---CAGAAT----TAG 477310 ------------- v i - --- v? ----i L1MEh_5end#LI 2065 AAATAGAAAACAAATAATAAGATGGCAG-AAATAAGTCCNAATATANCAG 2113 chr6qtel1M 477311 TAATTCTAACCGTAAACGTGAATGGGATGAACTCCCCCATAAAGAGGAGG 477360 vi --- i i v i v v v i ivi L1MEh_5end#LI 2114 TAATTACAA---TAAATGTAAATGGGTTAAACTCACCAATTAAAAGACAG 2160 chr6qtel1M 477361 CAGAT-AGCAGGCTGGATCAAAAGCCAGAACCCTATAATATGTTGCTTAC 477409 - -?v ii i? iv i i v i i ii L1MEh_5end#LI 2161 -AGATTNTCAGATTGGATTNAAAAACAAAATCCAACAATATGCTGTCTAC 2209 chr6qtel1M 477410 AGGAAACACATTTAAAACA 477428 i i i L1MEh_5end#LI 2210 AAGAGACACACTTAAAACA 2228 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 29.28 CpG sites = 30, Kimura (unadjusted) = 29.28 Transitions / transversions = 2.31 (30/13) Gap_init rate = 0.07 (14 / 194), avg. gap size = 2.29 (32 / 14) 569 30.85 3.76 2.57 chr6qtel1M 477289 477634 (522366) L1PREC2_orf2#LINE/L1 1 350 (2944) m_b310s551i15 13001 chr6qtel1M 477289 ATGGCAGGA---AATACAGAATTAGTAATTCTAACCGTAAACGTGAATGG 477335 i --- v v vv vi v v i i i L1PREC2_orf2# 1 ATGACAGGATCAAATCCACACATATCAATACTAACCTTGAATGTAAATGG 50 chr6qtel1M 477336 GATGAACTCCCCCATAAAGAGGAGGCAGA-TAGCAGGCTGGATCAAAAGC 477384 v i iv v v i -vi - i i v i iv L1PREC2_orf2# 51 GCTAAATGCCCCAATTAAAAGG-CACAGAGTGGCAAGCTGGATAAAGAAG 99 chr6qtel1M 477385 CAGAACCCTATAATATGTTGCTTACAGGAAACACATTTAAAACAGGGAGA 477434 ii v ii i ii v i i v i v v iiviiv L1PREC2_orf2# 100 CAAGACCCAATGGTATGCTGTCTTCAAGAGACCCATCTCACATGCAATGA 149 chr6qtel1M 477435 TACATACAGAGTAGAGGTAAAAGGCTGGAGCAGAATCTATTATGCTTCAG 477484 i vi i iv vi ii i v v i ii v --- i L1PREC2_orf2# 150 CACCCATAGGCTCAAAATAAAGGGATGGAGAAAAATCTACCAAGC---AA 196 chr6qtel1M 477485 GTG-AAGTCA--AGAAAGCAGGGGTAGCCATCCTTATCTCAGATCAAGCA 477531 i - iv -- i v v v i iv i L1PREC2_orf2# 197 ATGGAAAACAGAAAAAAGCAGGGGTTGCAATCCTAATTTCAGACAAAACA 246 chr6qtel1M 477532 A-----AAGCCAAAACTGATCTAATCAAAAAGATAAGGAAGGAAACTAAA 477576 i----- i v vv ----v i i iv i v L1PREC2_orf2# 247 GACTTTAAACCAACAAAGATC----AAAAAAGACAAAGAAGGGCATTACA 292 chr6qtel1M 477577 TCTTGCTAAAGGGTACTA-TAGACAACGAAGCTATATCAATATTAAACAT 477625 vv v v v - vi - viv v v vi i L1PREC2_orf2# 293 TAATGGTAAAGGGTTCAATTCAACAA-GAAGACCTAACTATCCTAAATAT 341 chr6qtel1M 477626 ATATGCACC 477634 L1PREC2_orf2# 342 ATATGCACC 350 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 40.51 CpG sites = 55, Kimura (unadjusted) = 40.51 Transitions / transversions = 1.12 (55/49) Gap_init rate = 0.04 (15 / 345), avg. gap size = 1.47 (22 / 15) 262 25.58 2.30 1.14 chr6qtel1M 478050 478136 (521864) L1M4_orf2#LINE/L1 1682 1769 (1525) m_b310s551i16 13002 chr6qtel1M 478050 ATGACCAATTTGGATTTATATTCA--AATGCTAAGATGGTTCCACATTAG 478097 v v -ii -- v i v v ?v L1M4_orf2#LIN 1682 ATGACCAAGTGGGATTTAT-CCCAGGAATGCAAGGTTGGTTCAACATNCG 1730 chr6qtel1M 478098 AGAAACAATCAACATAATGAATTGTACCAATATAATGAA 478136 i v ii iv iii ii v i L1M4_orf2#LIN 1731 AAAATCAATCAATGTAATACACCATATTAATAGAATAAA 1769 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 32.48 CpG sites = 13, Kimura (unadjusted) = 32.48 Transitions / transversions = 1.44 (13/9) Gap_init rate = 0.02 (2 / 86), avg. gap size = 1.50 (3 / 2) 12 19.70 4.65 2.27 chr6qtel1M 479767 479809 (520191) (TATGTT)n#Simple_repeat 1 44 (0) m_b310s252i22 13003 chr6qtel1M 479767 TATGTTTATGTTTTATGTTAAT-TTAAT-AAAATGTTTAATTTTA 479809 - v - v -vvv vv (TATGTT)n#Sim 1 TATGTTTATG-TTTATGTTTATGTTTATGTTTATGTTTATGTTTA 44 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.07 (3 / 42), avg. gap size = 1.00 (3 / 3) 297 32.10 2.44 1.20 chr6qtel1M 479924 480005 (519995) L2b_3end#LINE/L2 361 443 (23) m_b310s601i8 13004 chr6qtel1M 479924 TGAGAACAGGTGCTATCTTTTGTCTTTTTTATTGTT--ATTCTTAGTACT 479971 ii vi ii?v i - v i ii i -- i ii ii i L2b_3end#LINE 361 TGAGGGCAGGGACCGNGTCT-GTCTTGTTCACCGCTGTATCCCCAGCGCC 409 chr6qtel1M 479972 TAGCACAGGGTCTGGCAAAGAGTAGACACTTAAT 480005 ? i v v i i i i L2b_3end#LINE 410 TAGCACAGNGCCTGGCACACAGTAGGCGCTCAGT 443 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 37.91 CpG sites = 21, Kimura (unadjusted) = 48.57 Transitions / transversions = 4.20 (21/5) Gap_init rate = 0.02 (2 / 81), avg. gap size = 1.50 (3 / 2) 65 4.48 0.00 0.00 chr6qtel1M 480037 480105 (519895) (AT)n#Simple_repeat 1 69 (0) c_b310s251i9 13005 chr6qtel1M 480037 ATATATGTATATATATAGAAATATATATATATATATATATATATATATAT 480086 i v v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr6qtel1M 480087 ATATATATATATATATATA 480105 (AT)n#Simple_ 51 ATATATATATATATATATA 69 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 68), avg. gap size = 0.0 (0 / 0) 13 17.83 5.36 5.36 chr6qtel1M 480713 480768 (519232) (GGCAAGAG)n#Simple_repeat 1 56 (0) m_b310s252i23 13006 chr6qtel1M 480713 GGAAAGAGGG-AAG-CCCCAAGA-TGAAGGAGGGCAAGAGGGTTAAGAGG 480759 v - -vvv -v v i -i (GGCAAGAG)n#S 1 GGCAAGAGGGCAAGAGGGCAAGAGGGCAAGAGGGCAAGAGGG-CAAGAGG 49 chr6qtel1M 480760 AGCACAGAG 480768 - - (GGCAAGAG)n#S 50 -GCA-AGAG 56 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.11 (6 / 55), avg. gap size = 1.00 (6 / 6) 14 13.68 7.50 0.00 chr6qtel1M 480860 480899 (519101) (AAAAGGA)n#Simple_repeat 1 43 (0) m_b310s252i24 13007 chr6qtel1M 480860 AAGAGGAAGAAGGAAAAAGGTCTAAGG--AAA-GAAAAAGGAA 480899 i i vvv -- - (AAAAGGA)n#Si 1 AAAAGGAAAAAGGAAAAAGGAAAAAGGAAAAAGGAAAAAGGAA 43 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.50 (3 / 2) 43 19.12 1.10 1.10 chr6qtel1M 481629 481656 (518344) (AG)n#Simple_repeat 1 29 (62) m_b311s252i2 13008 chr6qtel1M 481629 AGTGAGAGAAAGTGGGA-AGAGAGAAACA 481656 v i v i - i v (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGA 29 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 31 0.00 0.00 0.00 chr6qtel1M 481657 481683 (518317) (AC)n#Simple_repeat 1 27 (0) c_b311s251i0 13009 chr6qtel1M 481657 ACACACACACACACACACACACACACA 481683 (AC)n#Simple_ 1 ACACACACACACACACACACACACACA 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 43 19.12 1.10 1.10 chr6qtel1M 481684 481745 (518255) (AG)n#Simple_repeat 30 91 (0) m_b311s252i2 13010 chr6qtel1M 481684 GAGAAAGAGAGACAGGGACAGAGAGAGAGAGACAGAGAGAAAAAGAGACA 481733 i v i v v i i v (AG)n#Simple_ 30 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 79 chr6qtel1M 481734 GAGACAGAGAGA 481745 v (AG)n#Simple_ 80 GAGAGAGAGAGA 91 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0) 17 24.17 0.00 0.00 chr6qtel1M 485054 485097 (514903) (ATTT)n#Simple_repeat 1 44 (0) m_b311s252i3 13011 chr6qtel1M 485054 ATTTAGTGATTTATGTATTTATTTATTGGCTTGTTTGTTTGTTT 485097 v v v vii i i i (ATTT)n#Simpl 1 ATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTT 44 Matrix = Unknown Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 522 22.29 0.81 5.93 chr6qtel1M 485100 485223 (514777) C MIRc#SINE/MIR (141) 127 10 m_b311s601i0 13012 chr6qtel1M 485100 CTGAGGC-AATTGGGGTTAAGTGACTTGCCCAGGGTCACACAGCTAGAAA 485148 -v vv i i --- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG--- 81 chr6qtel1M 485149 GTATTAAGTGTCTGAGATCAGATTTGAACTCAGATCCTCCTGACTTCAGG 485198 ---- v v vivi i i i i i i i C MIRc#SINE/MIR 80 ----TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr6qtel1M 485199 ACTGGTGCTTTATCCACTATGCCAC 485223 v ii i v iii C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 24.71 CpG sites = 17, Kimura (unadjusted) = 27.08 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.07 (8 / 123), avg. gap size = 1.00 (8 / 8) 344 37.87 11.59 1.20 chr6qtel1M 485324 485625 (514375) C L3#LINE/CR1 (0) 4099 3767 m_b311s601i1 13013 chr6qtel1M 485324 GACATAATCATAGAATTTGAGAGTCAAAAGGGACCTTGATGACCATCTG- 485372 i v i i v iii iiv ii i- C L3#LINE/CR1 4099 GATAGAATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAG 4050 chr6qtel1M 485373 --CA-----TCATCTACAAAAGGAGTCCCAAGTACAAT------------ 485403 -- -----i i vviv i vvv i------------ C L3#LINE/CR1 4049 TCCAACCTCCCATCCAATGCAGGAATCCCTTCTACAACATCCCTGACAAG 4000 chr6qtel1M 485404 ---TTATC--ACCT-----TGACAATGTTCAAAAAAAGAATTCTC-CTAT 485442 --- i --i ----- vv iv i ivi vi iivv - i C L3#LINE/CR1 3999 TGGTCATCCAGCCTCTGCTTGAACACCTCCAGTGACGGGGAGCTCACTAC 3950 chr6qtel1M 485443 ATGTCCAGGTATTCTATCACACCCT-GTACAACTTTAATTTTTAGGAATA 485491 v v? v i vi i iv iii - v i i i v i -i C L3#LINE/CR1 3949 CTCNCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGATTGTTAGAAA-G 3901 chr6qtel1M 485492 TTTTCTCTTGGCGTTG--TCTAAACTTCTTTTTTTCATAAATGTCATCTA 485539 i ii i-ii --i v ii vii iii -i v vi i i C L3#LINE/CR1 3900 TTCTTCCTTA-TATTGAGCCGAAATCTGCCTCCCT-GTAACTTCCACCCA 3853 chr6qtel1M 485540 CTGCTTCTGGTTCTAGCTTCTTGGAAACATTT-GAATAAACTTAATCTCC 485588 i v i i iv i - iv ivi- iii i i C L3#LINE/CR1 3852 TTGGTCCTAGTTCTGCCCTCT-GGAGCCACACAGAATAAGTCTAATCCCT 3804 chr6qtel1M 485589 CTTATGCTTGAAATCCATTTAAATACTAAATGCCAGC 485625 vii v v v v i i vi v v C L3#LINE/CR1 3803 CTTCCACATGACAGCCCTTCAAATATTTGAAGACAGC 3767 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 56.47 CpG sites = 74, Kimura (unadjusted) = 57.28 Transitions / transversions = 1.90 (74/39) Gap_init rate = 0.05 (14 / 301), avg. gap size = 2.79 (39 / 14) 349 30.00 4.04 4.04 chr6qtel1M 485626 485823 (514177) C Plat_L3#LINE/CR1 (339) 3234 3037 m_b311s551i0 13014 chr6qtel1M 485626 AATCAACCCTTAGTCTTCTCTTTTCCAGGTTAAAGATCCCCTTTTCCTTC 485675 i v i i i v v vv i C Plat_L3#LINE/ 3234 AGTCACCCCTTAGCCTTCTCTTCTCCAGGCTAAACAACCCCAATTCCTTT 3185 chr6qtel1M 485676 ACACAAATCTGATATAAAAAATTATCTTAAAGCCCTTCAG-CAAACTGAT 485724 vv vvvi v --- ii vi i vv v i i- vvi vi C Plat_L3#LINE/ 3184 AACCTTTCCTCAT---AGGACCTATTTTCCATCCCTTTAATCATTTTTGT 3138 chr6qtel1M 485725 TACTTTTTTCTGGACA--TTCCAGCTTATCCATGTCCTGCTTAAACTATT 485772 ii i i v--i i v ii vi v iiv C Plat_L3#LINE/ 3137 CGCTCTTCTCTGGACCCTCTCCAGTTTCTCCACATCCTTTTTAAAGTGCG 3088 chr6qtel1M 485773 TTGTGCCAAAAA-GAACAAAGAACTCT--TAAAG--CTGATTAGTGAGGA 485817 v -i v- i v v -- i -- ii ---- C Plat_L3#LINE/ 3087 GTG-ACCAAAACTGGACACAGTACTCTAATAAGGGTCTGACCAGTG---- 3043 chr6qtel1M 485818 CAGAGT 485823 C Plat_L3#LINE/ 3042 CAGAGT 3037 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 37.16 CpG sites = 30, Kimura (unadjusted) = 38.97 Transitions / transversions = 1.11 (30/27) Gap_init rate = 0.07 (13 / 197), avg. gap size = 1.23 (16 / 13) 202 36.37 0.00 2.02 chr6qtel1M 485864 485964 (514036) C L3b_3end#LINE/CR1 (583) 623 525 m_b311s601i2 13015 chr6qtel1M 485864 TGTAAAAACAAGCCAAAATACCAATGAAATTTTTGGCTCCTACATCACAC 485913 v vi iv i vv v iivv vv ii i i C L3b_3end#LINE 623 TGTTAATGCAGCCCAAGATCGCATTAGCTTTTTTGGCAGCCGCGTCGCAC 574 chr6qtel1M 485914 AATGCTAAACCAAATTGAAATCATTATCCACTAAAAACTTCAGAACTTTT 485963 -- i vi v iv iiivi v v ii iv C L3b_3end#LINE 573 --TGCTGACTCATATTGAGCTTGCGGTCAACTAAAACCCCCAGGTCTTTT 526 chr6qtel1M 485964 T 485964 C L3b_3end#LINE 525 T 525 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 43.29 CpG sites = 19, Kimura (unadjusted) = 51.06 Transitions / transversions = 1.12 (19/17) Gap_init rate = 0.02 (2 / 100), avg. gap size = 1.00 (2 / 2) 277 37.04 15.16 0.93 chr6qtel1M 485981 486356 (513644) C L3b_3end#LINE/CR1 (744) 462 34 m_b311s601i3 13015 chr6qtel1M 485981 CCCCAGTGAAAAAATTCACCCTTATCCTTAATGAATTTCAACTTATAAGA 486030 v v ii v i vi i iv v i vi ? C L3b_3end#LINE 462 CCCAAGTGCAGGACTTTACGTTTATCCCTGTTGAATTTCATCTTGTTGGN 413 chr6qtel1M 486031 TTCAGTCCATTTTTTCTTATCTGTGAAGA--------AAT-CTGAC---- 486067 i i i-?iv vi vi --------i - i---- C L3b_3end#LINE 412 TTCGGCCCG-NCGTTCTAGTCTGTCGAGATCGTTTTGGATCCTGATTTTG 364 chr6qtel1M 486068 CATAAAACTTTGTCAGCCATAATTCATA-CTTAAATCCCCGAAAAATATG 486116 vv -v i i i vii vi - vvii v i?iv v C L3b_3end#LINE 363 CATCCAAC-GTATTAGCCGTCGCTCCCAGCTTCTGCCACTNGCAAATTTG 315 chr6qtel1M 486117 ATGAAC-ACATTTCATGCATATAGTTAAGTCTTCAAGAAAAAAATTCA-A 486164 i i -i v i i iiv vi vii v i-- v v - C L3b_3end#LINE 314 ATAAGCTGCTTTCCGTATCTTCATCCAAGTCATT--GATACAAATTCAGA 267 chr6qtel1M 486165 TAGTGTAGGATTCAGCACAGTTTTCTGAGATCCTTCATTGTAAAT----- 486209 i vii i iiiv v vvii v iiv vi i iv i i----- C L3b_3end#LINE 266 CAGGACAAGGCCAAGGACAGAGCCCTGCGGCACGCCACTAGAGACTCCCT 217 chr6qtel1M 486210 --------ATGTTGAATCATTAACCAAAA-CCTTTAAGTCC----ACACA 486246 -------- ii i ?i ? i vi- ii ? ----iiv C L3b_3end#LINE 216 CCAGGTTGACATCGANCCATTNATCAACGTCCTTTGGGTNCGGTTGTTCA 167 chr6qtel1M 486247 ATCAGCTCTAAAT-TC-ATCTG-----------------ATTTCTTTAT- 486276 i v?i - - v ----------------- iii - C L3b_3end#LINE 166 ACCAGCTANGAATGTCTAACTGACCATTNTCCAGCCCACATTTCTCCGTC 117 chr6qtel1M 486277 ---TTAACAAGAATAGTATAAAATAACTTGCTAAAAGTTTTGCTAAAATC 486323 --- iv i i vi ii i v vi ii v ii i C L3b_3end#LINE 116 TTGTCCACGAGGATATCACGAGAGACTTTGTCAAATGCCTTGCTGAAATC 67 chr6qtel1M 486324 TAGACAAAGTAAATCTATAATATCCTGCTCATC 486356 v i v v vi ii? i iv v C L3b_3end#LINE 66 AAGATACACTATGTCTATGGNATTCCCCTGATC 34 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 49.01 CpG sites = 87, Kimura (unadjusted) = 56.35 Transitions / transversions = 1.71 (87/51) Gap_init rate = 0.05 (19 / 375), avg. gap size = 3.21 (61 / 19) 356 38.20 8.04 5.91 chr6qtel1M 486402 486735 (513265) C L3#LINE/CR1 (1307) 2792 2443 m_b311s601i4 13013 chr6qtel1M 486402 TCTGTTCATGAGAATTTTCCCAGGAGCTAAAATGAAGCTAAATGGCTTAT 486451 i --v v i iiiii vi v v vi ii i C L3#LINE/CR1 2792 TCCGTTC--TAGAATTTTGCCGGGGATCGACGTCAAGCTTACCGGTCTGT 2745 chr6qtel1M 486452 AATTTGCAGCATTCATTATTTGCTTTCTTTTTTCTTTCTTGTTGAAAATT 486501 i ? v i ---------- --i v i ? v C L3#LINE/CR1 2744 AGTTTNCAGAATCCA----------TCTTTTTTC--CCTTTTTAAAANTA 2707 chr6qtel1M 486502 GAGAAGATATTAATTTA-CATCAATCT--TGTCA-TTCTATCATTTTTC- 486546 i? v? i viiiii- vi i -- v -i vi i i i - C L3#LINE/CR1 2706 GGNACNACATTTGCCCGTCTCCAGTCTTCTGGCACCTCTTCCGTTCTCCG 2657 chr6qtel1M 486547 TGA--TCTTGAA-ATTATTGCTAATTTCTCAGTAATTGTATTTAACAGGT 486593 -- ii - ii vi iivvi v ii iii i ivv v C L3#LINE/CR1 2656 TGATTTCTCAAAGATTACCGACAGCGGTTCCGCGATCACATCTGCAAGTT 2607 chr6qtel1M 486594 CTTTCAAGA-CCTCAGAT--------------------GACTTGAATTTA 486622 iv - vi -------------------- i i C L3#LINE/CR1 2606 CTTTCAGTACCCTGGGATGTAATTCGTCTGGGCCTGGAGACTTGAACTCA 2557 chr6qtel1M 486623 TCAAAGGCACTTA------TTTTTAAAAATTATCTCCTTACTTATTTGAG 486666 iv i ivi ------i i ---- i i i i vi C L3#LINE/CR1 2556 TTTAAAGCGGCTAGGTGCTCTCTT----ACTATCTCCTCACCTATCTTGG 2511 chr6qtel1M 486667 GTGTCATCTTCATTCCAGTCATTTTGGGCTTGTCATTTTCAGAGTAAACA 486716 iv vi i v iii iiv v v vii ii v i vv i v C L3#LINE/CR1 2510 GCTTCAATTCCCTCTTAACGATGTTTGTTCTACCCTTTCCAGTCTGAAGA 2461 chr6qtel1M 486717 TTATCTTTATTTCAGAGAA 486735 i - i vi v v i C L3#LINE/CR1 2460 TCAT-TCTCCTTGATAGAG 2443 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 50.52 CpG sites = 100, Kimura (unadjusted) = 58.27 Transitions / transversions = 1.95 (78/40) Gap_init rate = 0.08 (28 / 333), avg. gap size = 1.93 (54 / 28) 65 0.00 1.69 0.00 chr6qtel1M 486736 486794 (513206) (AT)n#Simple_repeat 1 60 (0) c_b311s251i1 13016 chr6qtel1M 486736 ATATATATATATATATATATATATATAT-TATATATATATATATATATAT 486784 - (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr6qtel1M 486785 ATATATATAT 486794 (AT)n#Simple_ 51 ATATATATAT 60 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1) 356 38.20 8.04 5.91 chr6qtel1M 486795 486907 (513093) C L3#LINE/CR1 (1657) 2442 2337 m_b311s601i4 13013 chr6qtel1M 486795 TAACAGCAACAACAACAACAAAAAGGAAATGAACAGAGACAA-TCCTCTC 486843 vi i v i -------- v iv ii vvviiv- i C L3#LINE/CR1 2442 AGACGGAAGCA--------AAATAGGAGTTGAGTAGTTCTGCTTTCTCTC 2401 chr6qtel1M 486844 TGTTTTCATTCACTGTAATTCTATCTACCACAAGCAAAGGTTGTGTCCTA 486893 iv vv i vii v iv i i v iv viv ?iv C L3#LINE/CR1 2400 TGTCATCTGTTAACATTACGCCATCTGCCCCAAGCAGCGGGCCTGTCNCT 2351 chr6qtel1M 486894 GTTTTGTTTCTTTT 486907 v i v i i C L3#LINE/CR1 2350 TTCTTTTTCCTTCT 2337 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 50.52 CpG sites = 100, Kimura (unadjusted) = 58.27 Transitions / transversions = 1.05 (22/21) Gap_init rate = 0.08 (9 / 112), avg. gap size = 1.00 (9 / 9) 658 23.88 3.73 0.00 chr6qtel1M 487460 487593 (512407) MIRc#SINE/MIR 10 148 (120) m_b311s601i5 13017 chr6qtel1M 487460 GTATTGCAATGGAGAGAGAACCAGACATAGAATCAAGAAGACCTTGACTC 487509 iv i i v ii v i i i v ii MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr6qtel1M 487510 AAAATCAGGCTGAAACACTTAATAACTGTGTGATCCTGGGCAAATCACTT 487559 i ivi v vviv v i i i i MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTT 109 chr6qtel1M 487560 AACTTC-----ACCTCAGTTTCCTTATCTGTAAAATGAG 487593 i -----i i i MIRc#SINE/MIR 110 AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 28.72 CpG sites = 22, Kimura (unadjusted) = 29.83 Transitions / transversions = 2.20 (22/10) Gap_init rate = 0.01 (1 / 133), avg. gap size = 5.00 (5 / 1) 40 0.00 0.00 0.00 chr6qtel1M 487836 487869 (512131) (TA)n#Simple_repeat 1 34 (0) c_b311s251i2 13018 chr6qtel1M 487836 TATATATATATATATATATATATATATATATATA 487869 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATA 34 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 243 11.63 1.97 0.98 chr6qtel1M 488548 488953 (511047) (CTTT)n#Simple_repeat 1 410 (0) m_b311s252i4 13019 chr6qtel1M 488548 CTGTCTTT-TGACTGTTTTTCTTTCCTTCTTTCCTGCCTGCCTTCCTTCC 488596 v - vv v i i i v i v i i i (CTTT)n#Simpl 1 CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 50 chr6qtel1M 488597 TTTTTCCTTTCCTTCCTT-TTTCTTTCTTTCTTTCTTTCTTTTTTCTCTT 488645 i i i i - i - (CTTT)n#Simpl 51 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT-TCTT 99 chr6qtel1M 488646 TCTTCCTTTCTTTCTGT-TTT-TTTCTTTC-TTCTCTTCTTT-TTTCTTT 488691 i v - - - - - (CTTT)n#Simpl 100 TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT-TTCTTTCTTTCTTT 148 chr6qtel1M 488692 CTTTTCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCTTTCC 488741 ii i i i i i i i i i i (CTTT)n#Simpl 149 CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 198 chr6qtel1M 488742 TTCCTTCCTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT 488791 i i (CTTT)n#Simpl 199 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT 248 chr6qtel1M 488792 CTTTCTTTCTGTTTTTTCTTTC-TTCTCTTCTTT-TTTCTTTCTTTTCTT 488839 - i - - - ii (CTTT)n#Simpl 249 CTTTCTTTCT-TTCTTTCTTTCTTTCT-TTCTTTCTTTCTTTCTTTCTTT 296 chr6qtel1M 488840 CCTTCCTTCCTTCCTTCCTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 488889 i i i i i (CTTT)n#Simpl 297 CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 346 chr6qtel1M 488890 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT 488939 (CTTT)n#Simpl 347 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT 396 chr6qtel1M 488940 CTTTCTTTCTTTCT 488953 (CTTT)n#Simpl 397 CTTTCTTTCTTTCT 410 Matrix = Unknown Transitions / transversions = 5.00 (35/7) Gap_init rate = 0.03 (12 / 405), avg. gap size = 1.00 (12 / 12) 224 28.99 4.35 0.00 chr6qtel1M 488954 489022 (510978) L2d2_3end#LINE/L2 476 547 (8) m_b311s601i6 13020 chr6qtel1M 488954 TTCTTTCTTTCTCC---AGAACTGTGCACAATGCCTGAAACAAAGTAGAA 489000 v v i --- vi ivv i viv v iv L2d2_3end#LIN 476 TTCTTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAGTAGGC 525 chr6qtel1M 489001 GGTTAAGAAATGTTTGTTGACT 489022 v i v i i L2d2_3end#LIN 526 GCTCAATAAATATTTGTTGATT 547 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 34.66 CpG sites = 9, Kimura (unadjusted) = 36.86 Transitions / transversions = 0.82 (9/11) Gap_init rate = 0.01 (1 / 68), avg. gap size = 3.00 (3 / 1) 227 30.65 0.00 0.00 chr6qtel1M 488963 489024 (510976) L2b_3end#LINE/L2 399 460 (6) m_b311s601i7 13020 chr6qtel1M 488963 TCTCCAGAACTGTGCACAATGCCTGAAACAAAGTAGAAGGTTAAGAAATG 489012 i vi ivv i? iv v iv v i iv i L2b_3end#LINE 399 TCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATA 448 chr6qtel1M 489013 TTTGTTGACTAA 489024 v i L2b_3end#LINE 449 TTTGTTGAATGA 460 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 38.26 CpG sites = 10, Kimura (unadjusted) = 41.00 Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0) 26 0.00 0.00 0.00 chr6qtel1M 489775 489799 (510201) (CTAACC)n#Simple_repeat 1 25 (0) c_b311s251i3 13021 chr6qtel1M 489775 CTAACCCTAACCCTAACCCTAACCC 489799 (CTAACC)n#Sim 1 CTAACCCTAACCCTAACCCTAACCC 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 216 20.07 0.00 6.00 chr6qtel1M 490592 490644 (509356) C MIR3#SINE/MIR (39) 169 120 m_b311s601i8 13022 chr6qtel1M 490592 TTAGGGATGTCATTTAGTCCAATTCTCATAGTTTTACATATGAGGATCCT 490641 i -- i ii i vi - v vv C MIR3#SINE/MIR 169 TTAGAGAT--CATCTAGTCCAACCCCCTCA-TTTTACAGATGAGGAAACT 123 chr6qtel1M 490642 GAG 490644 C MIR3#SINE/MIR 122 GAG 120 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 23.64 CpG sites = 6, Kimura (unadjusted) = 23.64 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.06 (3 / 52), avg. gap size = 1.00 (3 / 3) 12 16.57 0.00 0.00 chr6qtel1M 490662 490688 (509312) (AATG)n#Simple_repeat 1 27 (0) m_b311s252i5 13023 chr6qtel1M 490662 AATGAGTGACTGAAAGAATGAATAAAT 490688 i v v i (AATG)n#Simpl 1 AATGAATGAATGAATGAATGAATGAAT 27 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 303 22.34 3.12 2.06 chr6qtel1M 490830 490925 (509075) C L1ME5_3end#LINE/L1 (759) 182 86 m_b311s551i1 13024 chr6qtel1M 490830 GTTGTCTTAATTTGCATTTCTCTGATCAGAAGTGATTTGGAACAT-TTTA 490878 i i vv i v v i - i v C L1ME5_3end#LI 182 GTTGTTTTAATTTGCATTTCTCTGATTACTAATGAGTTTGAGCATCTCTT 133 chr6qtel1M 490879 CATGTGATTATTAATACCTTT--GATTTATTCTTCTGAAAATAGATTGT 490925 i v i --i -- i vi v v vi C L1ME5_3end#LI 132 CATATGCTTGTTA--GCCTTTCGGGTTTCCTCTTCTGTAAATTGCCTGT 86 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 26.79 CpG sites = 11, Kimura (unadjusted) = 26.79 Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.04 (4 / 95), avg. gap size = 1.25 (5 / 4) 264 28.98 13.29 4.26 chr6qtel1M 490955 491127 (508873) C L2c_3end#LINE/L2 (0) 478 291 m_b311s601i9 13025 chr6qtel1M 490955 ACTCACTCATTCATAATATTTTTATTAAACACCAGCTATATGCATAGCAT 491004 i i vv v iv i i i vi i vvi ii C L2c_3end#LINE 478 ATTCATTCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGC 429 chr6qtel1M 491005 TTTCAGAAGTACTAAG------AAGACA--GTCTCTATC--CAAAAATAC 491044 ---i iii v ------ -- i ii -- ii -i C L2c_3end#LINE 428 T---GGGGATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGA-GC 383 chr6qtel1M 491045 TCACAGTCTCAATGTGGAAG-GATGGAAGAAGCAAACTGATCA-TGCAAC 491092 v--- i - ii - v ? i v iv - i i C L2c_3end#LINE 382 TCACAGTCTA---GTGGAGGAGACAG-ACANGTAAACAGACAATTACAAT 337 chr6qtel1M 491093 -TAAATCAGT--TGGGTGGCATA--------ATAGACAGGGTGCTA 491127 -i i i i -- ii vi -------- C L2c_3end#LINE 336 ACAAGTTAATGATAAGTGCTATAATGGGAGTATAGACAGGGTGCTA 291 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 37.41 CpG sites = 35, Kimura (unadjusted) = 39.59 Transitions / transversions = 2.69 (35/13) Gap_init rate = 0.09 (16 / 172), avg. gap size = 1.94 (31 / 16) 22 10.25 6.67 2.13 chr6qtel1M 491237 491281 (508719) (AT)n#Simple_repeat 1 47 (0) m_b311s252i6 13026 chr6qtel1M 491237 ATATAT-TATATATATATATGCATGTGTATATATATA-ATCATA-ATA 491281 - ii i i - - - (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATAT-ATATATA 47 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4) 23 18.18 2.22 0.00 chr6qtel1M 491335 491379 (508621) (TC)n#Simple_repeat 1 46 (0) m_b311s252i7 13027 chr6qtel1M 491335 TCTCTCTTTCTCTATCTCCTTTTCT-TCTCTCTTTTTCTCTCTCTC 491379 i v ii i - i i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 46 Matrix = Unknown Transitions / transversions = 6.00 (6/1) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 246 35.42 4.94 2.41 chr6qtel1M 491678 491808 (508192) AmnL2-1#LINE/L2 2167 2299 (314) m_b311s601i10 13028 chr6qtel1M 491678 ACAATTTTATTAGCTCCCTATTGGCTCCAGAATGAAATTTGAAAT--CCT 491725 i ii i i i vii i i vv i ii -- AmnL2-1#LINE/ 2167 ACAACTCCACTGGCTCCCCATTCATTTCAGGATCCAGTTCAAAATTGCCT 2216 chr6qtel1M 491726 ATTTGGTTTTTAAAATTCTTAGTAACCTGGTATTCTCAGTCT-TATTA-- 491772 vii v ii ivi iiv -- ii - i -iv i -- AmnL2-1#LINE/ 2217 TCCTTGTTTTTAAAACCCTCCATGGACT--TGCTC-CAGCCTACCTCACG 2263 chr6qtel1M 491773 GTCCTCCTCCTCCTCC-TTCTCCTCCTCCTCTTCTTC 491808 v iv iii i-i i - v i i AmnL2-1#LINE/ 2264 GACCTTGTCTCTCTCTACTCCCCTCC-CCGCTCCCTC 2299 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 51.84 CpG sites = 43, Kimura (unadjusted) = 54.90 Transitions / transversions = 3.18 (35/11) Gap_init rate = 0.06 (8 / 130), avg. gap size = 1.25 (10 / 8) 47 0.00 0.00 0.00 chr6qtel1M 491809 491848 (508152) (CA)n#Simple_repeat 1 40 (0) c_b311s251i4 13029 chr6qtel1M 491809 CACACACACACACACACACACACACACACACACACACACA 491848 (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACA 40 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 45 2.38 0.00 0.00 chr6qtel1M 491852 491894 (508106) (AG)n#Simple_repeat 1 43 (0) c_b311s251i5 13030 chr6qtel1M 491852 AGAGAGAGAGAGAGAAAGAGAGAGAGAGAGAGAGAGAGAGAGA 491894 i (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 43 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 246 35.42 4.94 2.41 chr6qtel1M 491895 491920 (508080) AmnL2-1#LINE/L2 2305 2330 (283) m_b311s601i10 13028 chr6qtel1M 491895 ATGACATCAGCCTCCTTCCTGTTCCT 491920 v ii i i ii i AmnL2-1#LINE/ 2305 CTAGCACCGGCCTCCTCTCTGTCCCT 2330 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 51.84 CpG sites = 43, Kimura (unadjusted) = 54.90 Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 943 30.91 4.81 1.38 chr6qtel1M 492095 492655 (507345) C L1M5_orf2#LINE/L1 (1054) 2240 1661 m_b311s551i2 13024 chr6qtel1M 492095 TTTTTAGTAATATGTAGAAATATAGATAATATATGTGTTTTTTTTTTAAT 492144 v iv i i i iv i v v i v vvii i- C L1M5_orf2#LIN 2240 TTGTTGCTAGTATATAGAAATACAATTGATTTTTGTATATTGACCTTG-T 2192 chr6qtel1M 492145 ATTTTACAACTTTGCTAAAGTTGTTAACTATTTCAAAGAGATT-TTAGTT 492193 ii?i i i v iii v i v v iv v - v v C L1M5_orf2#LIN 2191 ATCCNGCGACCTTGCTAAATTCACTTATTAGTTCTAGTAGTTTNTTTGTA 2142 chr6qtel1M 492194 GATTTTCTAGGATTTTCTAACTATACCATTGTATCGTCTG---------A 492234 i i ? vv ? v ii i i --------- C L1M5_orf2#LIN 2141 GATTCTTTNGGATTTTCTACGTANACAATCATGTCATCTGCGAATAANGA 2092 chr6qtel1M 492235 TACTTTT---TCCCACTATTCAA-----ATTCTTTCAATTTTTTTATTCT 492276 i v --- iiv v i ----- v i iv i - C L1M5_orf2#LIN 2091 CAGTTTTATTTCTTCCTTTCCAATCTTTATGCCTTTTATTTCTTT-TTCT 2043 chr6qtel1M 492277 TCTCCTATAGCTAAAGATAATATATCTAGTAAAATATTGAACAATAGTGG 492326 vi i v vvvi v iv iv i v i i iv C L1M5_orf2#LIN 2042 TGCCTTATTGCACTGGCTAGGACCTCCAGTACAATGTTGAATAGAAGTGG 1993 chr6qtel1M 492327 TGATAAGGAGCATCCTTGTTTCACCCCTGATTTTACTGAAATCACTTCTA 492376 ? iv ii i iiii i i vv ii vvi ? ii C L1M5_orf2#LIN 1992 TGANAGCGGACATCCTTGTCTTGTTCCCGATCTTAGGGGGAAAGCNTTCA 1943 chr6qtel1M 492377 GCTTATTCAA-ATTAAATATAAAACTTGCTGGTGATTT--AGTAGATGCT 492423 i? - v- i i vii ? vv i --v i C L1M5_orf2#LIN 1942 GTNT-TTCACCATTAAGTATGATGTTNGCTGTAGGTTTTTCGTAGATGCC 1894 chr6qtel1M 492424 GCTTATCATTTTATATAAAACTCCGTATATTACTATTCTTTCTAGTGCTT 492473 vi vv iviv ivii v v v v i viiv v -- C L1M5_orf2#LIN 1893 CTTTATCAGGTTGAGGAAGTTCCCTTCTATTCCTAGTTTGCTGAGAG--T 1846 chr6qtel1M 492474 TTTTATAA-AAATGGCTGCAACATTTTGTCAAAGTCCTTTTCTATGTCTA 492522 v -i v iviv vv i iii C L1M5_orf2#LIN 1845 TTTTATCATGAATGGGTGTTGAATTTTGTCAAATGCTTTTTCTGCATCTA 1796 chr6qtel1M 492523 TTGAGGTTATCAAATGATTGCTTATTAGCTTTGTT--ATTGATAGGGTCA 492570 i v v -i v i-- i --i i v v C L1M5_orf2#LIN 1795 TTGAGATGATCATATGATT-TTTCTC--CTTTATTCTGTTAATATGGTGA 1749 chr6qtel1M 492571 ATTATGTTGATAGTTTTCCTAATACTGAATCAACCTTGCATTCCTGGTAT 492620 ii v v i v ii i i v C L1M5_orf2#LIN 1748 ATTACATTGATTGATTTTCGAATGTTAAACCAACCTTGCATTCCTGGGAT 1699 chr6qtel1M 492621 AAACCCCTCTTCATCATAATGTATT---TTTTTTACAT 492655 v vi i ---i i C L1M5_orf2#LIN 1698 AAACCCCACTTGGTCATGATGTATTATCCTTTTTATAT 1661 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 41.01 CpG sites = 97, Kimura (unadjusted) = 41.65 Transitions / transversions = 1.31 (97/74) Gap_init rate = 0.03 (17 / 560), avg. gap size = 2.06 (35 / 17) 774 30.65 5.53 3.58 chr6qtel1M 492647 493387 (506613) C L1M5_orf2#LINE/L1 (1670) 1624 870 m_b311s551i3 13024 chr6qtel1M 492647 TTTTTACATTGATATTTATTAGGGAAATGGATCTACAATTTTTTTCTCTC 492696 i iv i i v v v i ii i i i C L1M5_orf2#LIN 1624 TTTTTGCATCTATGTTCATGAGGGATATTGGTCTGTAATTTTCTTTTCTT 1575 chr6qtel1M 492697 TTT-TGGCTCATTCTGTTTTAGGTATCAGCACCATATTTATGTCATAGAA 492745 v v- v ivv ? v v vii? ii viiv i C L1M5_orf2#LIN 1574 GTAATGTCTTTGTCNGGTTTTGGTATCAGGGTNATGCTGGCCTCATAAAA 1525 chr6qtel1M 492746 GGAATTTGGCAGGACTCCTTCTTTACCAATTTTTCCAAATAATTTCGATA 492795 v i v v vii i vi v iivi v i vvi C L1M5_orf2#LIN 1524 TGAGTTGGGAAGTGTTCCCTCTTTTTCTATTTTCTGGAAGAGTTTGTGTA 1475 chr6qtel1M 492796 GTATTAGAATTAATTGATCTTTATATGTTTGATAGAATTTACTTATAAAT 492845 iv i v v vv i v i i ivi i v C L1M5_orf2#LIN 1474 AGATTGGTATTATTTCTTCCTTAAATGTTTGGTAGAATTCACCAGTGAAG 1425 chr6qtel1M 492846 CCATCAGACTCTGCATATTTTTTCCTTAGGGTCTTCACTGATGGTTTGTT 492895 v ivi v v--- i iv -------- v v v C L1M5_orf2#LIN 1424 CCATCTGGGCCTGGAG---TTTTCTTTGTGG--------GAAGGTTTTTA 1386 chr6qtel1M 492896 CTT-----TT---TTTTTTTTCTAAA-ATGGGCTTCTGTAG----TTTAT 492932 v ----- --- i vv i - i vi v vi ---- i C L1M5_orf2#LIN 1385 ATTACAAATTCAATTTCTTTAATAGATATAGGGCTATTCAGATTTTCTAT 1336 chr6qtel1M 492933 TTCTTCTTCTTTTATTCTGGGCAAC--ATACTTTTCATAAGTATTCCTCC 492980 v?v i v i v i ?--i ii - i v iv C L1M5_orf2#LIN 1335 TTCTTCTTGNGTCAGTTTTGGTAANTTGTGTTTTTCA-AGGAATTTGTCC 1287 chr6qtel1M 492981 ATTTCACTCACATGGTCAAATTTATTAGCATATAGTTGGGCAAAATAGCT 493030 iii vi v? i v vv v vii C L1M5_orf2#LIN 1286 ATTTCATCTAAGTTNTCAAATTTATTGGCATAAAGTTGTTCATAATATTC 1237 chr6qtel1M 493031 TTGCATTATTGCTTTAATTTCCTTTGCATTGATGGTGA-ATTCACTTTTT 493079 ivi ivi v iv v v ivi i -i iiv C L1M5_orf2#LIN 1236 TCTTATTATCCTTTTAATGTCTGTAGGATCTGTAGTGATGTCTCCTTTTT 1187 chr6qtel1M 493080 CATTTTTGATAATGGTAATCTGGTTTTCTTCTTTCTTTTTTTTTTTTAAT 493129 ii v i -- v i i --i C L1M5_orf2#LIN 1186 CATTCCTGATATTGGTAATTTG--TGTCTTCTCTCTTTTTTTCTT--GAT 1141 chr6qtel1M 493130 AAAATTAAGAACAAGTTTATC----TTATTGTATTTTTTCTCATAAAAGC 493175 v ivi ?ivv v i ---- - i -- v i v C L1M5_orf2#LIN 1140 CAGTCTNGCTAGAGGTTTATCAATTTTATTG-ATCTTTTC--AAAGAACC 1094 chr6qtel1M 493176 AACTTTTAGATTTATTTGTTATTTCAATGATCTTCTTGCTTTCAATTT-- 493223 i i v ii vi v i v vi ? ?i i v -- C L1M5_orf2#LIN 1093 AGCTTTTGGCTTCGTTGATTTTCTCTATTGTNTNTTTGTTTTCTATTTCA 1044 chr6qtel1M 493224 --------TCCTTTGATTTTCAACATTTCTAATTTGGTACTTAATTGGGG 493265 -------- v i v i i vi ivvii vv ?v v C L1M5_orf2#LIN 1043 TTGATTTCTGCTCTTATCTTTATTATTTCCTTCCTTCTACTTNCTTTGGG 994 chr6qtel1M 493266 ATTTTTAAATT--TTTTCTTTTAATTTTTTTTTAAGCTTCATGCCCAATT 493313 --- v -- i vv vvi i v vv v ii iv C L1M5_orf2#LIN 993 ---TTTAATTTGCTCTTCTTTTTCTAGCTTCTTAAGGTGGAAGCTTAGAT 947 chr6qtel1M 493314 CATTGATCT-----CTTTCT-CTATTTTATTTGTATAACCATTTA--GGT 493355 i ----- - v i ---i ?v -- v C L1M5_orf2#LIN 946 CATTGATTTTAAGCCTTTCTTCTTTTCTA---ATATANGCATTTAANGCT 900 chr6qtel1M 493356 ATGAAAAATTTCTTCTAAGAACTGCTTTGACT 493387 -- v i i v ii C L1M5_orf2#LIN 899 AT--AAATTTCCCTCTAAGCACTGCTTTAGCT 870 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 40.58 CpG sites = 113, Kimura (unadjusted) = 40.85 Transitions / transversions = 1.07 (113/106) Gap_init rate = 0.06 (41 / 740), avg. gap size = 1.66 (68 / 41) 300 37.07 0.85 0.85 chr6qtel1M 494325 494441 (505559) MIRc#SINE/MIR 17 133 (135) m_b311s601i11 13031 chr6qtel1M 494325 AGAAGAAAGGGGACCTAAGGTTGGATTTCTGAGGATTCATTTTC-ACTTC 494373 vi i v - iiiv v ivv i iiiivv - v i MIRc#SINE/MIR 17 AGTGGAAAGAGCAC-TGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCC 65 chr6qtel1M 494374 TGTCTCCAATATTTAATAGCTATATGAAACTGGGAAAGTCATTTAGCATT 494423 i v iivi i v i i vvi v i i v i MIRc#SINE/MIR 66 CGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 chr6qtel1M 494424 TCTAAACCTTACTTTCCT 494441 i i i v MIRc#SINE/MIR 116 TCTGAGCCTCAGTTTCCT 133 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 51.96 CpG sites = 26, Kimura (unadjusted) = 53.84 Transitions / transversions = 1.53 (26/17) Gap_init rate = 0.02 (2 / 116), avg. gap size = 1.00 (2 / 2) 447 24.75 0.00 9.09 chr6qtel1M 495097 495216 (504784) MIRc#SINE/MIR 4 113 (155) m_b311s601i12 13032 chr6qtel1M 495097 GGCAGCTTGTTGGTGCAATAGATAAAGCACCAACCTTGAAGTCAGAAGAA 495146 -- - i i v i iiiv i i ii MIRc#SINE/MIR 4 GGCAG--TGT-GGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA 50 chr6qtel1M 495147 CCTGAATTCAAATCTGGCCTCAGAAACTTAATACTTTCCAGCTTTGTGAC 495196 ii i i iv v v vv ------- i v MIRc#SINE/MIR 51 CCTGGGTTCGAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTGAC 93 chr6qtel1M 495197 TCTGGGTAAGTCACTTAACC 495216 ii i MIRc#SINE/MIR 94 CTTGGGCAAGTCACTTAACC 113 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 29.62 CpG sites = 19, Kimura (unadjusted) = 31.01 Transitions / transversions = 2.38 (19/8) Gap_init rate = 0.08 (10 / 119), avg. gap size = 1.00 (10 / 10) 289 29.86 0.92 7.84 chr6qtel1M 495120 495228 (504772) MIR#SINE/MIR 21 122 (140) m_b311s601i13 13032 chr6qtel1M 495120 AAAGCACCAACCTTGAAGTCAGAAGAACCTGAATTCAAATCTGGCCTCAG 495169 i vii ii i i vvi- ii i iv v v MIR#SINE/MIR 21 AGAGCACGGGCTCTGGAGCCAGACTG-CCTGGGTTCGAATCCCGGCTCTG 69 chr6qtel1M 495170 AAACTTAATACTTTCCAGCTTTGTGACTCTGGGTAAGTCACTTAACCACA 495219 vv ------- i v ii i i v v MIR#SINE/MIR 70 CCACTTA-------CTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCT 112 chr6qtel1M 495220 AT-TACCTCA 495228 v - i MIR#SINE/MIR 113 CTGTGCCTCA 122 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 37.35 CpG sites = 18, Kimura (unadjusted) = 39.02 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.08 (9 / 108), avg. gap size = 1.00 (9 / 9) 448 31.50 7.49 2.09 chr6qtel1M 495558 495784 (504216) C L3#LINE/CR1 (167) 3932 3694 m_b311s601i14 13033 chr6qtel1M 495558 TCTACTTTTGGACAGATTTAATTGTTAGGAAGTTGCTTTCTAA----AAA 495603 i i v i i i - i v ----i i C L3#LINE/CR1 3932 TCCATTTTTGGACAGCTCTGATTGTTAGAAAGTT-CTTCCTTATATTGAG 3884 chr6qtel1M 495604 CTGAGGTTTTCCCCTTTGCAATTCTCATTCACTTATCCTAAGTTGT-TCC 495652 i ii i v i ii i i ii ii i vi - v -i C L3#LINE/CR1 3883 CCGAAATCTGCCTCCCTGTAACTTCCACCCATTGGTCCT-AGTTCTGCCC 3835 chr6qtel1M 495653 TATGGTTCTACCCAAAA-AAGCATCATCTTTTCTCCACATAATTG-TTTT 495700 v vv i v i - iv v ii ii i iv -ii C L3#LINE/CR1 3834 TCTGGAGCCACACAGAATAAGTCTAATCCCTCTTCCACATGACAGCCCTT 3785 chr6qtel1M 495701 TAAATATCTAACAAACAT---TCATGAGCTCCTGCTAAA-----TTTTGT 495742 i i i - i v--- -v - i----- i v C L3#LINE/CR1 3784 CAAATATTTGA-AGACAGCTATCATG-TCTCCT-CTAAGTCTTCTCTTCT 3738 chr6qtel1M 495743 TAAGAATAAATATCTTCATTTGCTTT-ACTCTGTCTCAT-TGAC 495784 iv iv i ii v v i- iv vi - C L3#LINE/CR1 3737 CCAGGCTAAACATCCCCAGTTCCTTCAACCGTTCCTCATATGAC 3694 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 41.92 CpG sites = 49, Kimura (unadjusted) = 43.64 Transitions / transversions = 2.33 (49/21) Gap_init rate = 0.06 (13 / 226), avg. gap size = 1.69 (22 / 13) 426 29.35 3.94 0.76 chr6qtel1M 495893 496019 (503981) MIRc#SINE/MIR 15 145 (123) m_b311s601i15 13034 chr6qtel1M 495893 GCAGTTAAATGAGACAATGGATACAGAGGGAGCAAGATTTTAATTACAGT 495942 vi v - v ivii vv v ii vii vv MIRc#SINE/MIR 15 GCAGTGGAAAGAG-CACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGT 63 chr6qtel1M 495943 CACAAT-----CACTAACTAGCTGTGTAATCTTGGGCAAGTCACTTAACT 495987 v iii----- v i i i MIRc#SINE/MIR 64 CCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACC 113 chr6qtel1M 495988 CTGCTTGTCCCCTATGTCCTCATATGTAAAAT 496019 iiv viv i vi v v MIRc#SINE/MIR 114 TCTCTGAGCCTCAGTTTCCTCATCTGTAAAAT 145 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 36.53 CpG sites = 19, Kimura (unadjusted) = 37.80 Transitions / transversions = 1.06 (19/18) Gap_init rate = 0.02 (2 / 126), avg. gap size = 3.00 (6 / 2) 31 7.75 0.00 0.00 chr6qtel1M 496061 496101 (503899) (A)n#Simple_repeat 1 41 (0) m_b311s252i8 13035 chr6qtel1M 496061 AAAAAAAAAAAAAAAAAAAAAAAAAACAAAACAAAACAAAA 496101 v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 41 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 16 12.74 0.00 5.56 chr6qtel1M 496358 496395 (503605) (AAAAAT)n#Simple_repeat 1 36 (0) m_b311s252i10 13036 chr6qtel1M 496358 AAAAATAATAATAATAATAATAAACAAACAAAAAAAAT 496395 v v - i - v (AAAAAT)n#Sim 1 AAAAATAAAAATAAAAATAA-AAATAAA-AATAAAAAT 36 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 13 4.76 0.00 4.35 chr6qtel1M 497781 497804 (502196) (TTTG)n#Simple_repeat 1 23 (0) m_b311s252i12 13037 chr6qtel1M 497781 TTTGTTTGTTTTGTCTGTTTGTTT 497804 - i (TTTG)n#Simpl 1 TTTGTTTG-TTTGTTTGTTTGTTT 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 939 30.37 3.27 0.74 chr6qtel1M 499279 499676 (500324) L1ME4a_3end#LINE/L1 148 555 (316) m_b311s551i4 13038 chr6qtel1M 499279 TCACTAGCATTCATACAACAGCAAAT--AAATAATCAGTG---------T 499317 i v v v vv -- i - i --------- L1ME4a_3end#L 148 TCACTAGTAATCAAAGAAATGCAAATTAAAACAA-CAATGAGATACCATT 196 chr6qtel1M 499318 CCTCACCTGTCAGATTGGCTAAGATGAGAGGAAAAAATAATGATGATTGT 499367 ii i i v vvi iii vvi iviv v L1ME4a_3end#L 197 TTTCACCTATCAAATTGGCAAAGATTTAAAAGATTGATAATACCCAGTGT 246 chr6qtel1M 499368 TGGAGGGGATGCGGGAAAACTGGGACATTGATGCATTGTTGGTGGAGTTG 499417 v i i i ?i v v vi v i i i iiv L1ME4a_3end#L 247 TGGCGAGGGTGTGGNGAAACGGGCACTCTCATACACTGCTGGTGGGAGTG 296 chr6qtel1M 499418 TGAATGAATCCAATCATTCTGGAGAGTAGTTTGGAACTATGCTCAAAAAG 499467 i vii v i v i i i v v iviv L1ME4a_3end#L 297 TAAATTGGTACAACCTTTCTGGAGGGCAATTTGGCAATATGTATCAAAAG 346 chr6qtel1M 499468 TTATCAAACTGTGCATACCCTTTGATCCAGCACTGTTACTACTGGGCTTA 499517 iiv v v ? i i v vii v i vv v L1ME4a_3end#L 347 CCTTAAAAATGTNCATACCCTTTGACCCAGTAATTCCACTTCTAGGAATT 396 chr6qtel1M 499518 TATCCCAAAGAGATTAT-AAAGAAG-GGAAAGGGACCTGTATGTGCACGA 499565 i i i v - i v - ? v ii -- v i v i L1ME4a_3end#L 397 TATCCTAAGGAAATAATCAGAGATGTGNACAAAGA--TTTATGTACAAGG 444 chr6qtel1M 499566 ATGTTTGTGGCAACCCTTTTTGTAGTGGCTAGAAACTGGAAACTGAATGG 499615 ii v i vi v i i i v i i vivv ii L1ME4a_3end#L 445 ATGTTCATCGCAGCATTATTTATAATAGCGAAAAATTGGAAACAACCTAA 494 chr6qtel1M 499616 ATGCCCATCAGTGGGAGAATGGCTGAATAAATTGTGGTATATGAATGTTA 499665 i v i i i ? i i i i vv i?v L1ME4a_3end#L 495 ATGTCCAACAATAGGGGANTGGTTAAATAAATTATGGTACATCCATANAA 544 chr6qtel1M 499666 TGGAATATTAT 499676 L1ME4a_3end#L 545 TGGAATATTAT 555 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 40.72 CpG sites = 69, Kimura (unadjusted) = 40.72 Transitions / transversions = 1.35 (69/51) Gap_init rate = 0.02 (7 / 397), avg. gap size = 2.29 (16 / 7) 899 32.10 1.59 1.82 chr6qtel1M 499321 499761 (500239) L1ME4c_3end#LINE/L1 200 639 (191) m_b311s551i5 13038 chr6qtel1M 499321 CACCTGTCAGATTGGCTAAGATGAGAGGAAAAAATAATGATGATTGTTGG 499370 i i i i i v i vvi ii vvi iviv v i L1ME4c_3end#L 200 CGCCTATTAAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGCTGG 249 chr6qtel1M 499371 AGGGGATGCGGGAAAACTGGGACATTGATGCATTGTTGGTGGAGTTGTGA 499420 v i ? vi v ?i v i i vi? i L1ME4c_3end#L 250 CGAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAA 299 chr6qtel1M 499421 ATGAATCCAATCATTCTGGAGAGTAGTTTGGAACTATGCTCAAAAAGTTA 499470 vii v i v i i i i v v i iviv i ii L1ME4c_3end#L 300 ATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCA 349 chr6qtel1M 499471 TCAAACTGTGCATACCCTTTGATCCAGCACTGTTACTACTGGGCTTATAT 499520 v v v i i v vii v vv v L1ME4c_3end#L 350 TAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTAT 399 chr6qtel1M 499521 CCCAAAGAGATTAT---AAAGAAGGGAAAGGGACCTGTATGTGCACGA-- 499565 i i i v --- i i -----v i -- L1ME4c_3end#L 400 CCTAAGGAAATAATTCAAAAGAAGGAAAAAG-----CTATATGCACGAAG 444 chr6qtel1M 499566 ATGTTTGTGGCAACCCTTTTTGTAGTGGCTAGAAACTGGAAACTGAATGG 499615 ii v i vi v i i i v i i vivv ii L1ME4c_3end#L 445 ATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAA 494 chr6qtel1M 499616 ATGCCCATCAGTGGGAGAATGGCTGAATAAATTGTGGTATATGAATGTTA 499665 i v i i i i i i i i v? iviv L1ME4c_3end#L 495 ATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGA 544 chr6qtel1M 499666 TGGAATATTATTGTTCTGTAAGAAATGACCAACAGGAAGAT--TTCAGAA 499713 vvvv ii v i iv vi v i-- vi v L1ME4c_3end#L 545 TGGAATATTATGCAGCCATTAAAAATGATAATTATGAAGACTATGTAGCA 594 chr6qtel1M 499714 AGTCCTGGAGAGACTTACATGAACTGATGCTGAGTGAAATGAGCAGGA 499761 -- v i ivv -i vv i i i vi i L1ME4c_3end#L 595 A--CATGGAAAATGTT-TATGATATAATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 42.56 CpG sites = 81, Kimura (unadjusted) = 43.84 Transitions / transversions = 1.40 (81/58) Gap_init rate = 0.03 (11 / 440), avg. gap size = 1.36 (15 / 11) 418 27.81 3.35 5.37 chr6qtel1M 500930 501138 (498862) L1MC2_3end#LINE/L1 429 633 (458) m_b311s551i6 13039 chr6qtel1M 500930 AACCTGTATATTCACGAATGTTTGTGGCAGCCCTCTTTGTAGTGGCTAGA 500979 i ---- i i ii v ii i v i i L1MC2_3end#LI 429 AACCTGCA----CACGAATGTTTATAGCAGCTTTATTCATAATTGCCAAA 474 chr6qtel1M 500980 AATTGGAA--AATGAGTGAATGCCCATCAGTTGGAGAATGGCTGAATAAA 501027 v -- iv --ii i v i v v v i i L1MC2_3end#LI 475 ACTTGGAAGCAACCA--AGATGTCCTTCAATAGGTGAATGGATAAACAAA 522 chr6qtel1M 501028 TTGTGGTATATGAATATTATGGAATATTATTGTTCTGT---AAGAAATGA 501074 i i vv iv vvv vi --- L1MC2_3end#LI 523 CTGTGGTACATCCATACAATGGAATATTATTCAGCGATAAAAAGAAATGA 572 chr6qtel1M 501075 -CCAACAGGAAGATTTCAGAAAGTCCTGGAGAGA-CTTACATGAACTGAT 501122 - i v i ----iiv ii v v ii - v v - iv L1MC2_3end#LI 573 GCTATCAAG----CCACGAAAAGACATGGAGGAACCTTAAATGCA-TATT 617 chr6qtel1M 501123 GCTGAGTGAAATGAGC 501138 i vi L1MC2_3end#LI 618 GCTAAGTGAAAGAAGC 633 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 34.74 CpG sites = 32, Kimura (unadjusted) = 35.55 Transitions / transversions = 1.39 (32/23) Gap_init rate = 0.07 (15 / 208), avg. gap size = 1.20 (18 / 15) 472 26.02 0.00 0.00 chr6qtel1M 500935 501057 (498943) L1ME3G_3end#LINE/L1 426 548 (376) m_b311s551i7 13039 chr6qtel1M 500935 GTATATTCACGAATGTTTGTGGCAGCCCTCTTTGTAGTGGCTAGAAATTG 500984 i i v v i ii v vi v i i v i L1ME3G_3end#L 426 GCATGTACAAGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTG 475 chr6qtel1M 500985 GAAAATGAGTGAATGCCCATCAGTTGGAGAATGGCTGAATAAATTGTGGT 501034 vvivv i i i v i i i i L1ME3G_3end#L 476 GAAACAACCTAAATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGT 525 chr6qtel1M 501035 ATATGAATATTATGGAATATTAT 501057 vv i i L1ME3G_3end#L 526 ATATCCATACTATGGAATACTAT 548 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 32.71 CpG sites = 19, Kimura (unadjusted) = 32.71 Transitions / transversions = 1.46 (19/13) Gap_init rate = 0.00 (0 / 122), avg. gap size = 0.0 (0 / 0) 65 0.00 0.00 0.00 chr6qtel1M 501600 501654 (498346) (AT)n#Simple_repeat 1 55 (0) c_b311s251i6 13040 chr6qtel1M 501600 ATATATATATATATATATATATATATATATATATATATATATATATATAT 501649 (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr6qtel1M 501650 ATATA 501654 (AT)n#Simple_ 51 ATATA 55 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 457 32.18 4.97 3.26 chr6qtel1M 502584 502885 (497115) L1ME5_3end#LINE/L1 75 381 (560) m_b311s551i8 13041 chr6qtel1M 502584 AAAGGCTAAAAAGAGTTAGTTTTCAGAAGAAGAAATC--AAAGA-----A 502626 v vi v vi i v i i -- i----- L1ME5_3end#LI 75 AAAGGATATGAACAGGCAATTTACAGAAGAGGAAACCCGAAAGGCTAACA 124 chr6qtel1M 502627 ATCACATGTAAA-ATGTCCCAAATCACTTTTGAATAGAGAAATACAAATT 502675 v i v i - ii v v i vv i vi i L1ME5_3end#LI 125 AGCATATGAAGAGATGCTCAAACTCATTAGTAATCAGAGAAATGCAAATT 174 chr6qtel1M 502676 AAAACAACTCTGAAGTATTACTACCCACCTATCAGA-TGG-AATAATATG 502723 vv ii i viv i - - v --- L1ME5_3end#LI 175 AAAACAACAATGAGATATCACTTTACACCTATTAGACTGGCAAAAAT--- 221 chr6qtel1M 502724 ACAGAAAA--GGAAAAGAATCAATGCTGGAAGGCTTATGGAAAAATACAA 502771 -i i-- v viviv i i vii vv i ii ? vi L1ME5_3end#LI 222 -TAGAAAGCTGGATAATGCCAAGTGTTGGCGAGGATGTGGGGANATAGGA 270 chr6qtel1M 502772 ACAGCAATGTGTTATTGGTGGAGTTCTGAACTGATCCAACCATTCTCAGG 502821 vviv iii ii iiv v ii i v i vii L1ME5_3end#LI 271 ACCCTCATGCACTGCTGGTGGGAGTGTAGACTGGTGCAGCCATTCTGGAG 320 chr6qtel1M 502822 GAAAATTTGGAACTATACCAAG--AGATTTGTAAAAT-TGTGCATACTCT 502868 iiv i -- vi iv -- i ---- i - ii i L1ME5_3end#LI 321 AGCAATCTGG--CAGTACTTAGTCAAATT----AAGTATACGCATACCCT 364 chr6qtel1M 502869 TTGACCAAGCAATCCTG 502885 v v i i L1ME5_3end#LI 365 ATGACCCAGCAATTCCG 381 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 42.03 CpG sites = 57, Kimura (unadjusted) = 43.92 Transitions / transversions = 1.54 (57/37) Gap_init rate = 0.06 (18 / 301), avg. gap size = 1.39 (25 / 18) 20 19.83 1.59 4.92 chr6qtel1M 503010 503072 (496928) (ATCT)n#Simple_repeat 1 61 (0) m_b311s252i13 13042 chr6qtel1M 503010 ATCTCT-TATCTATTGCTCCTTATTTTTCTATCTATCTATGTCATCGATC 503058 v - - - vii i v v - v (ATCT)n#Simpl 1 ATCTATCTATCTA-T-CTATCTATCTATCTATCTATCTATCT-ATCTATC 47 chr6qtel1M 503059 TATCAATCTATATA 503072 v v (ATCT)n#Simpl 48 TATCTATCTATCTA 61 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.06 (4 / 62), avg. gap size = 1.00 (4 / 4) 48 4.43 4.17 1.35 chr6qtel1M 504737 504808 (495192) (ATAG)n#Simple_repeat 1 74 (0) c_b311s251i7 13043 chr6qtel1M 504737 ATAGATTGATAGATCGATGATATAGATAGATAGATAGATAGATAGATAGA 504786 v v - v (ATAG)n#Simpl 1 ATAGATAGATAGATAGAT-AGATAGATAGATAGATAGATAGATAGATAGA 49 chr6qtel1M 504787 T-GATAGATAGATA-A-AGATAGAT 504808 - - - (ATAG)n#Simpl 50 TAGATAGATAGATAGATAGATAGAT 74 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.06 (4 / 71), avg. gap size = 1.00 (4 / 4) 439 23.17 0.81 8.77 chr6qtel1M 505011 505133 (494867) C MIRc#SINE/MIR (153) 115 2 m_b311s601i16 13044 chr6qtel1M 505011 GGGGTTAAGTGACATGTCCAGAGTCACACAGCTAGGAAGTGTTAAGTGTC 505060 i v i ii ------- v C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGC 73 chr6qtel1M 505061 TGAAGCTAGATTTGAACTCAGGTCCTCCTGACTTTTGGGCTGGTACTCTA 505110 v iv vi i i i i iivi v ii i v C MIRc#SINE/MIR 72 AGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTT 23 chr6qtel1M 505111 T-CACTGCACCACCTAGCTGCCCC 505133 - ---i i C MIRc#SINE/MIR 22 TCCACTGCACCAC---ACTGCCTC 2 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 27.19 CpG sites = 18, Kimura (unadjusted) = 28.48 Transitions / transversions = 2.25 (18/8) Gap_init rate = 0.09 (11 / 122), avg. gap size = 1.00 (11 / 11) 212 32.20 0.00 0.00 chr6qtel1M 505186 505244 (494756) MIR#SINE/MIR 66 124 (138) m_b311s601i17 13045 chr6qtel1M 505186 TCTGACATATCCTAGACATAGGACCTTGAGCAAATCACTTAAGCTCTTCG 505235 v iv v vii iv i i i v ii MIR#SINE/MIR 66 TCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTG 115 chr6qtel1M 505236 TTCCCTAAT 505244 v ii i MIR#SINE/MIR 116 TGCCTCAGT 124 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 44.04 CpG sites = 12, Kimura (unadjusted) = 44.04 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.0 (0 / 0) 270 32.30 0.90 9.76 chr6qtel1M 505242 505464 (494536) C L2d_3end#LINE/L2 (2) 514 310 m_b311s601i18 13046 chr6qtel1M 505242 AATAAGTCAATCAACAAACGTGTATTAAGGGCTTACCAGTTGCTCAAAGA 505291 v i iii v i v i i vv - iv C L2d_3end#LINE 514 AATCAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTC-AGCA 466 chr6qtel1M 505292 TATGTGCTAAGCACTAGCGTTAAACT-CAAAAAAGCACAAAACTCAAGGC 505340 i- i i - i vvi v-? ? i i i viiivv C L2d_3end#LINE 465 C-TGTGCTAGGCGCT-GTGGGGAACGANAAAANAGTATAAGACATGGTCC 418 chr6qtel1M 505341 CTTTCCTTAAGGTGATGACATGCTAGTGGTGGGGAAAATATGCAAAAA-A 505389 vi i v v v vv -- i ----- i v- C L2d_3end#LINE 417 CTGCCCTCAAGGAGCTTACAATCTAGT--TGGGGAGA-----CAAGACTA 375 chr6qtel1M 505390 GAAAAAAAAAAACAACTATGTATGGGGAACATATATAAAACAAGATCCAA 505439 iv v v vi i ------ i - i i iv vi C L2d_3end#LINE 374 ACACACATGAAACAATTA------GAGAACA-ATACAAGACAGTATATAA 332 chr6qtel1M 505440 TATATAAGATATAAACTATATAATA 505464 --- vvv i iii ii C L2d_3end#LINE 331 T---TAAGTGCTAAATTGCGTGGTA 310 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 41.69 CpG sites = 37, Kimura (unadjusted) = 43.57 Transitions / transversions = 1.32 (37/28) Gap_init rate = 0.10 (22 / 222), avg. gap size = 1.00 (22 / 22) 278 29.56 3.18 5.19 chr6qtel1M 505248 505404 (494596) C L2a_3end#LINE/L2 (6) 511 358 m_b311s601i20 13046 chr6qtel1M 505248 TCAATCAACAAACGTGTATTAAGGGCTTACCAGTTGCTCAAAGATATGTG 505297 v ii v i v i i vv - iiv i- v C L2a_3end#LINE 511 TCATTCAACAAATATTTATTGAGCGCCTACTATGTGC-CAGGCAC-TGTT 464 chr6qtel1M 505298 CTAAGCACTAGCGTTA-AAC--TCAAAAAAGC--ACAAAACTCAAGGCCT 505342 i i i v v - i -- v v i -- v ---- C L2a_3end#LINE 463 CTAGGCGCTGGGGATACAGCAGTGAACAAAACAGACAAAAGTC----CCT 418 chr6qtel1M 505343 TTCCTTAAGGTGATGACATGCTAGTGGTGGGGAAAATATGCAAAAAAGAA 505392 vi i v v v v v -- i i i vi v v C L2a_3end#LINE 417 GCCCTCATGGAGCTTACATTCTAGTG--GGGGGAGACAGACAATAAACAA 370 chr6qtel1M 505393 AAAAAAAAACAA 505404 v v ii C L2a_3end#LINE 369 ATAAATAAGTAA 358 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 36.83 CpG sites = 21, Kimura (unadjusted) = 37.89 Transitions / transversions = 0.91 (21/23) Gap_init rate = 0.07 (11 / 156), avg. gap size = 1.18 (13 / 11) 281 29.54 0.72 14.75 chr6qtel1M 505248 505386 (494614) C L2c_3end#LINE/L2 (6) 472 351 m_b311s601i19 13046 chr6qtel1M 505248 TCAATCAACAAACGTGTATTAAGGGCTTACCAGTTGCTCAAAGATATGTG 505297 v i v i v i -------------- C L2c_3end#LINE 472 TCATTCAACAAACATTTATTGAGCGCCTAC--------------TATGTG 437 chr6qtel1M 505298 CTAAGCACTAGCGTTAAACTCAAAAAAGCACAAAACTCAAGGCCTTTCCT 505347 i i i i v v ---- i v v i i v iivv vi C L2c_3end#LINE 436 CCAGGCGCTGGGGATA----CAAAGATGAATAAGACACGGTCCCTGCCCT 391 chr6qtel1M 505348 TAAGGTGATGACATGCTAGTGGTGGGGA-AAATATGCAAA 505386 i v v v vv v i - i i ? i C L2c_3end#LINE 390 CAAGGAGCTCACAGTCTAGTGGAGGAGACAGACANGTAAA 351 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 34.85 CpG sites = 18, Kimura (unadjusted) = 37.47 Transitions / transversions = 1.06 (18/17) Gap_init rate = 0.14 (19 / 138), avg. gap size = 1.00 (19 / 19) 20 30.63 0.00 0.00 chr6qtel1M 506333 506394 (493606) (ATG)n#Simple_repeat 1 62 (0) m_b311s252i14 13047 chr6qtel1M 506333 ATGATGATGATGGTAGTGGTGGTGATGGTAGGGATGAGGATGGGGATGAG 506382 i ii i i i iiv v iv v (ATG)n#Simple 1 ATGATGATGATGATGATGATGATGATGATGATGATGATGATGATGATGAT 50 chr6qtel1M 506383 GATGATAATAAT 506394 i i (ATG)n#Simple 51 GATGATGATGAT 62 Matrix = Unknown Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0) 265 28.14 1.01 3.09 chr6qtel1M 507297 507395 (492605) L1ME3E_3end#LINE/L1 307 403 (586) m_b311s551i9 13048 chr6qtel1M 507297 AACCACGGTGGGAAGCAATTTGGAATTATTCAATAAAATGGATAAATGTT 507346 vv i i v ii i i v - i iv L1ME3E_3end#L 307 AACCACTTTGGAAAACAATTTGGCATTATCTAGTAAAGTTGA-AGATGCG 355 chr6qtel1M 507347 T-TACCTTTTTGACTCAGAGATTCCAATACCAAGAGATATATCCTAAGGA 507395 i- -i vi i vi v - v iv i ii L1ME3E_3end#L 356 CATACC-CTACGACCCAGCAATTCCACT-CCTAGGTATATACCCTAGAGA 403 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 33.15 CpG sites = 17, Kimura (unadjusted) = 36.50 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.04 (4 / 98), avg. gap size = 1.00 (4 / 4) 48 0.00 0.00 0.00 chr6qtel1M 507500 507540 (492460) (AC)n#Simple_repeat 1 41 (0) c_b311s251i8 13049 chr6qtel1M 507500 ACACACACACACACACACACACACACACACACACACACACA 507540 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACA 41 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 443 27.33 2.04 7.91 chr6qtel1M 508658 508804 (491196) MIRc#SINE/MIR 10 148 (120) m_b311s601i21 13050 chr6qtel1M 508658 GTGACACAGTGGAT-GAGTTCTGGACTTGGAGTCAGGAAGACTCATTTGT 508706 iii v- iv -------- MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC-------- 51 chr6qtel1M 508707 CCAAATTCAGATCTAGCCTCAGACACTTCCTAGCTGGGTCATCCTGGGCA 508756 iiii iii iv v v v v v v i i MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 101 chr6qtel1M 508757 AGTTACT--GTTTGAAGAAATTTTACAGATTTCTTCATCTGTAAAATGAG 508804 i --iii vvvvi iii -- - i i MIRc#SINE/MIR 102 AGTCACTTAACCTCTCTGAGCCT--CAG-TTTCCTCATCTGTAAAATGGG 148 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 33.88 CpG sites = 24, Kimura (unadjusted) = 35.06 Transitions / transversions = 1.85 (24/13) Gap_init rate = 0.09 (13 / 146), avg. gap size = 1.08 (14 / 13) 232 31.94 6.40 2.31 chr6qtel1M 508986 509110 (490890) L2d2_3end#LINE/L2 386 515 (40) m_b311s601i22 13051 chr6qtel1M 508986 CTCATCTCATTCTTTAGCTTCCATTCATGTG---GTATCTT-TGTGTCCA 509031 ii v ii v i --- i ---i i - v vi L2d2_3end#LIN 386 CTTGTATTGTTATTTAACTT---TTCACGTGTTTATGTCTTGTCTCCCCA 432 chr6qtel1M 509032 GC-AAATTGTTAGCTTCTGGAGGTGAGGGACTGCCTCTTCTTCCTATTTG 509080 i - i v i v vv iiiv v v i v L2d2_3end#LIN 433 ACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACTTCTTTG 482 chr6qtel1M 509081 CATGCC---TAGAACCCAGCAGAATATCTGGCA 509110 i v ---i vi i v i ii v L2d2_3end#LIN 483 TATCCCCCACAGCGCCTAGCACAGTGCCTTGCA 515 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 40.18 CpG sites = 23, Kimura (unadjusted) = 43.09 Transitions / transversions = 1.44 (23/16) Gap_init rate = 0.06 (7 / 124), avg. gap size = 1.57 (11 / 7) 241 30.99 0.00 0.00 chr6qtel1M 509028 509098 (490902) L2c_3end#LINE/L2 368 438 (40) m_b311s601i23 13051 chr6qtel1M 509028 TCCAGCAAATTGTTAGCTTCTGGAGGTGAGGGACTGCCTCTTCTTCCTAT 509077 vi i i v i v vv i iv v v v L2c_3end#LINE 368 TCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCT 417 chr6qtel1M 509078 TTGCATGCCTAGAACCCAGCA 509098 i v i vi ii L2c_3end#LINE 418 TTGTATCCCCAGCGCCTGGCA 438 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 36.00 CpG sites = 11, Kimura (unadjusted) = 40.53 Transitions / transversions = 1.00 (11/11) Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0) 12 21.71 0.00 0.00 chr6qtel1M 509266 509297 (490703) (AATTG)n#Simple_repeat 1 32 (0) m_b311s252i15 13052 chr6qtel1M 509266 AATTGTATTGATTTCAAGGAAATTGAATTGAA 509297 v v v vvi (AATTG)n#Simp 1 AATTGAATTGAATTGAATTGAATTGAATTGAA 32 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 234 20.85 0.00 8.62 chr6qtel1M 510438 510500 (489500) C MIR3#SINE/MIR (31) 177 120 m_b311s601i24 13053 chr6qtel1M 510438 AAAGGCCCTTTTTAGGGATGGCATTTAGTTCAACTCCCATAGTTTACAGA 510487 i v --- i -- i i i vi v C MIR3#SINE/MIR 177 AAGGGACCTT---AGAGAT--CATCTAGTCCAACCCCCTCATTTTACAGA 133 chr6qtel1M 510488 TGAGTACCCTGAG 510500 v vv C MIR3#SINE/MIR 132 TGAGGAAACTGAG 120 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 24.37 CpG sites = 6, Kimura (unadjusted) = 24.37 Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.08 (5 / 62), avg. gap size = 1.00 (5 / 5) 307 27.35 12.87 3.76 chr6qtel1M 510984 511154 (488846) C L2c_3end#LINE/L2 (2) 476 291 m_b311s601i25 13054 chr6qtel1M 510984 TCACTCATTCATAATATTTCTATTGAGCACCAACTATATGCATAGCATTC 511033 i vv v iv i i v i vvi ii - C L2c_3end#LINE 476 TCATTCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCT- 428 chr6qtel1M 511034 TCAGGAGTATGAAGA-AAATA-------GTCTCTATC--CAAAGATGCTC 511073 --i ii ii -i ------- i ii -- i - C L2c_3end#LINE 427 --GGGGATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGA-GCTC 381 chr6qtel1M 511074 ACAGTCTCAATGTGGAAAGATGGAAGAAGCAAACTGATCA-TGTAAT-TA 511121 - i - iii ii - v ? i v iv - ii -i C L2c_3end#LINE 380 ACAGTCT-AGTG-GAGGAGACAG-ACANGTAAACAGACAATTACAATACA 334 chr6qtel1M 511122 AATCAAT--TGAGTGGCATAA-GG-------GACAGAGTGCTA 511154 i i -- i vi - ------- i C L2c_3end#LINE 333 AGTTAATGATAAGTGCTATAATGGGAGTATAGACAGGGTGCTA 291 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 34.67 CpG sites = 34, Kimura (unadjusted) = 36.77 Transitions / transversions = 3.09 (34/11) Gap_init rate = 0.09 (15 / 170), avg. gap size = 1.93 (29 / 15) 242 36.75 4.27 0.00 chr6qtel1M 511132 511248 (488752) MIRc#SINE/MIR 10 131 (137) m_b311s601i26 13055 chr6qtel1M 511132 GTGGCATAAGGGACAGAGTGCTAGTATTACATGCAGGAAGAATTGAGTTA 511181 iii iv v ii i vv iv vv vi i v MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr6qtel1M 511182 GAA-ACTATTTCATACAATTACTAGCTCTGTAATATTAGGTA--TCAC-- 511226 i-v iivi vvv v v i iv i i -- -- MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTT 109 chr6qtel1M 511227 AGCCTCCTTCAAACTAAGGTTC 511248 i ii v iv v v MIRc#SINE/MIR 110 AACCTCTCTGAGCCTCAGTTTC 131 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 49.78 CpG sites = 22, Kimura (unadjusted) = 51.66 Transitions / transversions = 1.05 (22/21) Gap_init rate = 0.03 (3 / 116), avg. gap size = 1.67 (5 / 3) 25 33.02 2.54 1.68 chr6qtel1M 511253 511370 (488630) (TCTT)n#Simple_repeat 1 119 (0) m_b311s252i16 13056 chr6qtel1M 511253 TCTTTCTTTCTTTCCCTCCCTGCTTCCTTCTGTCTCTTC-CTCCCTCCCT 511301 ii ii vi i v - -i ii ii (TCTT)n#Simpl 1 TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT-TTCTTTCTTTCTTT 49 chr6qtel1M 511302 CCTTCCCTCCCTCCCTCTCTCTCTTTTTCTTATTTTCTTTTCTCTCTGTC 511351 i ii ii ii i i i vi - i v (TCTT)n#Simpl 50 CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC-TTTCTTTCTTTC 98 chr6qtel1M 511352 TTTC--TCTTTCTGTCTGTCT 511370 -- v v (TCTT)n#Simpl 99 TTTCTTTCTTTCTTTCTTTCT 119 Matrix = Unknown Transitions / transversions = 3.83 (23/6) Gap_init rate = 0.03 (4 / 117), avg. gap size = 1.25 (5 / 4) 46 1.75 6.90 0.00 chr6qtel1M 511381 511438 (488562) (TC)n#Simple_repeat 1 62 (0) c_b311s251i9 13057 chr6qtel1M 511381 TCTCT-TCTCT-TCTCT-TCTCT-TCTCTCTCTCTCTCTCTCTCTTTCTC 511426 - - - - i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chr6qtel1M 511427 TCTCTCTCTCTC 511438 (TC)n#Simple_ 51 TCTCTCTCTCTC 62 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.07 (4 / 57), avg. gap size = 1.00 (4 / 4) 44 4.39 0.00 0.00 chr6qtel1M 511799 511845 (488155) (AC)n#Simple_repeat 1 47 (0) c_b311s251i10 13058 chr6qtel1M 511799 ACACACACACACACACACACACACACACACACATACACACTCACACA 511845 i v (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACA 47 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 905 32.15 3.29 0.46 chr6qtel1M 512052 512476 (487524) C L1P3_orf2#LINE/L1 (1057) 2237 1801 m_b311s551i10 13059 chr6qtel1M 512052 TTAGTAATATGTAGAAATACTGATGATTTATGTAGATTTATTTTATATCC 512101 v ii i i i i vi v i v v i C L1P3_orf2#LIN 2237 TTATTGGTGTATAGGAATGCTTGTGATTTTTGCACATTGATTTTGTATCC 2188 chr6qtel1M 512102 TGCAACTTTGCTAAAGTT-CTTAACTATTTAAAGGAGTTTTTAGTTGATT 512150 vi i - v vii i ii? vi i vv C L1P3_orf2#LIN 2187 TGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGGAGNTTTTGGGCTGAGA 2138 chr6qtel1M 512151 ATCTAGGATTTTCTAAGTCTACCATCTTATCGTCTG---ATAG------- 512190 vvv i i i v v v i i --- i ------- C L1P3_orf2#LIN 2137 CGATGGGGTTTTCTAAATATACAATCATGTCATCTGCAAACAGAGACAAT 2088 chr6qtel1M 512191 TTGGTTCCCTCACTGGGTATTCTAATATTTTCCATTTATTATTCTTCTCT 512240 ii i v vvv iv iii ii v vi vi C L1P3_orf2#LIN 2087 TTGACTTCCTCTCTTCCTATTTGAATACCCTTTATTTCTTTCTCTTGCCT 2038 chr6qtel1M 512241 TATTGCTGAAGCTAATATTTCTGGTAAAATATTGAATAATAGTGGTGATA 512290 v ivvi i iv i iii vv i iv v C L1P3_orf2#LIN 2037 GATTGCCCTGGCCAGAACTTCCAATACTATGTTGAATAGGAGTGGTGAGA 1988 chr6qtel1M 512291 AGGGGCATCCTTATTTCGTCCCTGATTTTATTGAGAATGCTTCTAGATTA 512340 ii i i i v v v i vv i i v v C L1P3_orf2#LIN 1987 GAGGGCATCCTTGTCTTGTGCCGGTTTTCAAAGGGAATGCTTCCAGCTTT 1938 chr6qtel1M 512341 TTCTCATTACATATAAAACTTGCTGGTAGTTTA--ATAGAT-GCTACTTA 512387 v i vvi i v i v vvi i-- i - - C L1P3_orf2#LIN 1937 TGCCCATTCAGTATGATATTGGCTGTGGGTTTGTCATAAATAGCT-CTTA 1889 chr6qtel1M 512388 TCATTTTAACAAAAACTCCATTTATTACTATTCTGTCTAGTGTTTTTAAT 512437 i i v v vii iv vv v i i iv v ii C L1P3_orf2#LIN 1888 TTATTTTGAGATACGTTCCATCAATACCTAGTTTATTGAGAGTTTTTAGC 1839 chr6qtel1M 512438 AGAAATGGGTACAAATATTTTCTCAAAGTCCTTTTCTGC 512476 vi v iivi - v i v C L1P3_orf2#LIN 1838 ATGAAGGGGTGTTGA-ATTTTATCGAAGGCCTTTTCTGC 1801 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 42.34 CpG sites = 75, Kimura (unadjusted) = 43.19 Transitions / transversions = 1.23 (75/61) Gap_init rate = 0.02 (7 / 424), avg. gap size = 2.29 (16 / 7) 306 31.65 8.60 2.78 chr6qtel1M 512550 512991 (487009) C L1M5_orf2#LINE/L1 (1953) 1341 875 m_b311s551i11 13060 chr6qtel1M 512550 TTCTGCTTCCTCTACTATTAATTTGGGAAACTTACATTTTCATAAGCATT 512599 ii i vv?i i i v v ? iii ivv i v C L1M5_orf2#LIN 1341 TTCTATTTCTTCTTGNGTCAGTTTTGGTAANTTGTGTTTTTCAAGGAATT 1292 chr6qtel1M 512600 ----AATTTCACTCACATGATCAAATTTATTGACATATAATTGGGCAAGA 512645 ----v iii vi v? i v i vv vi C L1M5_orf2#LIN 1291 TGTCCATTTCATCTAAGTTNTCAAATTTATTGGCATAAAGTTGTTCATAA 1242 chr6qtel1M 512646 TAATTTTGCATTGTTGCTTTAATTTGCTTTGCATTGATGGTGAATTTACC 512695 v i ivi i ivi v viv v v ivi i vv iv C L1M5_orf2#LIN 1241 TATTCTCTTATTATCCTTTTAATGTCTGTAGGATCTGTAGTGATGTCTCC 1192 chr6qtel1M 512696 TTTTTT-----TGATAATGGTAAATTGTTTTTTCTTTCTTTTTTTA--AA 512738 i----- v v v i i v--i C L1M5_orf2#LIN 1191 TTTTTCATTCCTGATATTGGTAATTTGTGTCTTCTCTCTTTTTTTCTTGA 1142 chr6qtel1M 512739 TCAAATTAATTAAATTTTTAATCTCTCTTATAGTTTTCCCCATAAAACCA 512788 ivi ?ii i vv - vv i v v i iii v i C L1M5_orf2#LIN 1141 TCAGTCTNGCTAGAGGTTTA-TCAATTTTATTGATCTTTTCAAAGAACCA 1093 chr6qtel1M 512789 GCTTTATTATTTCAATGATTTTCTTAA-------------TTCAATTTTA 512825 - vii iv iv ------------- v i C L1M5_orf2#LIN 1092 GCTTT-TGGCTTCGTTGATTTTCTCTATTGTNTNTTTGTTTTCTATTTCA 1044 chr6qtel1M 512826 TTAATCTTTCCTTTGATTTTCAGCTTTTCTAATTTAGTATTTAATTGAAG 512875 i i i v i v i i viv ivvii vv i ?v vii C L1M5_orf2#LIN 1043 TTGATTTCTGCTCTTATCTTTATTATTTCCTTCCTTCTACTTNCTTTGGG 994 chr6qtel1M 512876 ATTTTTAAGTTTGTTTTTTTTAAATGTTTTTAGCTTC---------ATGC 512916 --- - i i i ----- i --------- v C L1M5_orf2#LIN 993 ---TTTAA-TTTGCTCTTCTT-----TTTCTAGCTTCTTAAGGTGGAAGC 953 chr6qtel1M 512917 ACAATTTATTGATCT-----CTTTCTCTATTTCACTGATATAAGCATTTA 512961 vi iv i i ----- iiv -- i ? C L1M5_orf2#LIN 952 TTAGATCATTGATTTTAAGCCTTTCTTCTTTT--CTAATATANGCATTTA 905 chr6qtel1M 512962 AAGATATAAAATTTCTTCTAAGAACTATTT 512991 ? v v i i v ii C L1M5_orf2#LIN 904 ANGCTATAAATTTCCCTCTAAGCACTGCTT 875 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 42.90 CpG sites = 77, Kimura (unadjusted) = 43.33 Transitions / transversions = 1.31 (77/59) Gap_init rate = 0.04 (19 / 441), avg. gap size = 2.68 (51 / 19) 31 19.00 0.00 0.00 chr6qtel1M 513160 513215 (486785) (T)n#Simple_repeat 1 56 (0) m_b311s252i17 13061 chr6qtel1M 513160 TTCTTTCCTTTTTCTTTCTTTCTTTTCTTTTCTATTTTTTTTTTTTTTTT 513209 i ii i i i i i v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chr6qtel1M 513210 TTTTTT 513215 (T)n#Simple_r 51 TTTTTT 56 Matrix = Unknown Transitions / transversions = 8.00 (8/1) Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0) 414 26.02 0.87 6.42 chr6qtel1M 513220 513334 (486666) C MIRc#SINE/MIR (157) 111 3 m_b311s601i27 13062 chr6qtel1M 513220 TTAAATGACTTGCCCAAAGTGACACAGCTAGAAAGTGTTAAGTGTCTGAG 513269 i i v ------- v v C MIRc#SINE/MIR 111 TTAAGTGACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGCAGAG 69 chr6qtel1M 513270 ATCAGATTTGAATGTAGGTTCTCCTGACTTCAGGGTTGGGGCTCTACCCA 513319 vivi i i ivi ii i i viii v vi C MIRc#SINE/MIR 68 CCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCA 19 chr6qtel1M 513320 CTGCCCCA-ACTAGCT 513334 v - iv C MIRc#SINE/MIR 18 CTGCACCACACTGCCT 3 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 29.87 CpG sites = 17, Kimura (unadjusted) = 32.64 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.07 (8 / 114), avg. gap size = 1.00 (8 / 8) 266 37.93 1.69 1.69 chr6qtel1M 516224 516341 (483659) MIRc#SINE/MIR 16 133 (135) m_b311s601i28 13063 chr6qtel1M 516224 CAGAAGAAAG-GCAAACTAAGGTTGG-GTTCTAAGGATTCATTTTTCACT 516271 vi - -- iiiv - ivvi i iiiivv iv v MIRc#SINE/MIR 16 CAGTGGAAAGAGCA--CTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGT 63 chr6qtel1M 516272 TCTGTCTCCAATATTTAATAGCTATATGAAACTGGAAAAGTCATTTAGCA 516321 i i v iivi i v i i vvi iv i i v MIRc#SINE/MIR 64 CCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACC 113 chr6qtel1M 516322 TTCCTGAACCTCATCTTCCT 516341 ii i vi MIRc#SINE/MIR 114 TCTCTGAGCCTCAGTTTCCT 133 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 52.61 CpG sites = 28, Kimura (unadjusted) = 56.54 Transitions / transversions = 1.75 (28/16) Gap_init rate = 0.03 (4 / 117), avg. gap size = 1.00 (4 / 4) 25 14.69 0.00 4.17 chr6qtel1M 516440 516489 (483511) (TA)n#Simple_repeat 1 48 (0) m_b311s252i18 13064 chr6qtel1M 516440 TATAGTTTACATATACATATATGGCATATATACATATATATATATATATA 516489 - v i i -ii i (TA)n#Simple_ 1 TATA-TATATATATATATATAT-ATATATATATATATATATATATATATA 48 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.04 (2 / 49), avg. gap size = 1.00 (2 / 2) 15 5.48 0.00 0.00 chr6qtel1M 518086 518104 (481896) (T)n#Simple_repeat 1 19 (0) m_b311s252i19 13065 chr6qtel1M 518086 TTGTTTTTTTTTTTTTTTT 518104 v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 17 21.03 7.35 1.39 chr6qtel1M 518305 518372 (481628) (TATAAT)n#Simple_repeat 1 72 (0) m_b311s252i20 13066 chr6qtel1M 518305 TATAATATTAATTAT--TT-TATGTATACAAATATTTATATTTTATAATT 518351 vv -- - vv vvv v -v (TATAAT)n#Sim 1 TATAATTATAATTATAATTATAATTATAATTATAATTATA-ATTATAATT 49 chr6qtel1M 518352 AT-A-TAAAATTATAATGACAAT 518372 - - v v i (TATAAT)n#Sim 50 ATAATTATAATTATAATTATAAT 72 Matrix = Unknown Transitions / transversions = 0.09 (1/11) Gap_init rate = 0.07 (5 / 67), avg. gap size = 1.20 (6 / 5) 262 38.79 5.36 4.05 chr6qtel1M 518708 519024 (480976) C L3#LINE/CR1 (127) 3972 3652 m_b312s601i0 13067 chr6qtel1M 518708 TTCATTTATGAGTAATCAACAACTTCTTAACATGAGCAAATCTACTTTTG 518757 i v v i i v iiiv v i ?ii viiiiv v v i i C L3#LINE/CR1 3972 TCCAGTGACGGGGAGCTCACTACCTCNCGAGGCAGCCCATTCCATTTTTG 3923 chr6qtel1M 518758 TATAGATTCAATTGTTTGGATGTTGCTT--TTAAA--AAACTGATTAAGA 518803 v i v iii v i v - -- v --i i i -- -- C L3#LINE/CR1 3922 GACAGCTCTGATTGTTAGAAAGTT-CTTCCTTATATTGAGCCGA--AA-- 3878 chr6qtel1M 518804 TTTTTGCCT--CTACAATTCTCGTCCATTTATTCTAAGTTGT-TCCTATA 518850 -- i -- ii i ii ii vi i - v -i v i C L3#LINE/CR1 3877 --TCTGCCTCCCTGTAACTTCCACCCATTGGTCCT-AGTTCTGCCCTCTG 3831 chr6qtel1M 518851 TACCTACACATAAAAAAGCATCATCTTCTCTCCACATAATTG-TTTTTAA 518899 v v i -i v iv v iiiii i iv -ii i C L3#LINE/CR1 3830 GAGCCACACA-GAATAAGTCTAATCCCTCTTCCACATGACAGCCCTTCAA 3782 chr6qtel1M 518900 ATACCTGATAAACAT---TCCTGAGCTCCTACTAAG-----TTTTGTTAA 518941 ii - i v--- v -v - ----- i v iv C L3#LINE/CR1 3781 ATATTTGA-AGACAGCTATCATG-TCTCCT-CTAAGTCTTCTCTTCTCCA 3735 chr6qtel1M 518942 GAATAAATATCTTCATTTGCTTTAAAACTCTGTCTTATGG-ACTGTTGTC 518990 iv i ii v v i vvv iiv v i- iv vi C L3#LINE/CR1 3734 GGCTAAACATCCCCAGTTCCTTCAACCGTTCCTCATATGACATGGTTTCC 3685 chr6qtel1M 518991 AAATATCCTCATTGCTCAAGTTACTTTCTTTAGG 519024 i i-i i iiiii vi ii i i iv C L3#LINE/CR1 3684 AGAC-CCTTCACCATCCTGGTCGCTCTCCTCTGG 3652 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 56.28 CpG sites = 78, Kimura (unadjusted) = 59.71 Transitions / transversions = 1.95 (78/40) Gap_init rate = 0.07 (21 / 316), avg. gap size = 1.43 (30 / 21) 344 17.14 1.41 1.41 chr6qtel1M 519114 519184 (480816) MIR#SINE/MIR 71 141 (121) m_b312s601i1 13068 chr6qtel1M 519114 CACTAACTAGCTGTGTGATCCTGGGCAAGTAACTTAACTCTGTTTGCCCC 519163 v i i v - v i iv MIR#SINE/MIR 71 CACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAAC-CTCTCTGTGCC 119 chr6qtel1M 519164 TTA-TGTCCTCATATGTGAAAT 519184 i - v v i MIR#SINE/MIR 120 TCAGTTTCCTCATCTGTAAAAT 141 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 19.56 CpG sites = 6, Kimura (unadjusted) = 19.56 Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.03 (2 / 70), avg. gap size = 1.00 (2 / 2) 231 28.63 4.23 2.07 chr6qtel1M 520251 520439 (479561) L1MCa_5end#LINE/L1 2242 2434 (0) m_b312s551i0 13069 chr6qtel1M 520251 AGGGACAAAG--CTACAGTAACAGGAATAGGATAAAAAAAGAAAT-TGAT 520297 i -- v vi i -- i v v iv v - i L1MCa_5end#LI 2242 AGGAACAAAGAACAAGGGCAACA--AATAGAAAACAGTAACAAATATGGT 2289 chr6qtel1M 520298 AAATAGTGAGTAAAATTTGT-AATAATAACTATGAATGTAAATGGTATGA 520346 i v i viv v v i - v v i i v v i L1MCa_5end#LI 2290 AGATATTAATCCAACTATATCAATAATCACTTTAAACGTCAATGGTCTAA 2339 chr6qtel1M 520347 ACTCACCCAT-AAAACTGAAATAGACAG-CAGAATCTATTAAAAACCAAA 520394 iv v - -- v v iv - i vv i v i L1MCa_5end#LI 2340 ATACACCAATTAAAA--GACAGAGATTGTCAGAGTGGATCAAAAAACAAG 2387 chr6qtel1M 520395 ATCCAATCTTATGTTGTTTAGAAGAAGTACATTT--AAGAAAAAGAC 520439 i iiv i v iiv i -- v v L1MCa_5end#LI 2388 ACCCAACTATATGTTGTCTACAAGAAACCCACTTTAAATATAAAGAC 2434 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 35.56 CpG sites = 25, Kimura (unadjusted) = 36.39 Transitions / transversions = 0.89 (25/28) Gap_init rate = 0.05 (10 / 188), avg. gap size = 1.20 (12 / 10) 265 31.32 5.30 3.63 chr6qtel1M 520318 520751 (479249) L1M2_orf2#LINE/L1 27 467 (2824) m_b312s551i3 13069 chr6qtel1M 520318 AATAATAACTATGAATGTAAATGGTATGAACTCACCCA-TAAAACTGAAA 520366 iv vv i i v v - -- v L1M2_orf2#LIN 27 AATAATAACCTTGAATGTAAATGGATTAAATTCTCCAATTAAAA--GACA 74 chr6qtel1M 520367 TAGAC-AGCAGAATCTATTAAAAACCAAAATCCAATCTTATGTTGTTTAG 520415 ?-i v vv v v i i iiv i ii v L1M2_orf2#LIN 75 TAGANTGGCTGAATGGATAAAAAAACAAGACCCAACTATATGCTGCCTAC 124 chr6qtel1M 520416 AAGAAGTACATTTAAG--AAAAAGACATACATAAGAGTTAAAATAGATAG 520463 iiv i v v--iv i - v v i - vi L1M2_orf2#LIN 125 AAGAAACTCACTTCACCTGTAAAGACACACAT-AGACTGAAAGT-GAAGG 172 chr6qtel1M 520464 AGTAGAAATAATTATGCCTCATTTCATGGGGAAA--AAAAGTAAAAGGGC 520511 ii i v iv v -- - v viv -- ?i ivi - L1M2_orf2#LIN 173 GATGGAAAAAGATATTC--CA-TGCAAACGGAAACCAAAAGNGAGCAGG- 218 chr6qtel1M 520512 AGCAACTATG---ATCTCAGATAAAG------TTGAGGCTAAAA---TAG 520549 i i i--- v i------ i v v --- i L1M2_orf2#LIN 219 AGTAGCTATACTTATATCAGATAAAATAGACTTTAAGTCAAAAACTGTAA 268 chr6qtel1M 520550 ATTTAATTAAGGAAAATCAACAGATTATCTTCTGATAAAATGTACTATAG 520599 vvv ivi i ii ----- v vv iv vv v vv L1M2_orf2#LIN 269 AAAGAGACAAAGAAGGTC-----ATTATATAATGATAAAGGGGTCAATTC 313 chr6qtel1M 520600 ATAATGAAGTAATATCAATATTTAACCTATATATACCAAATACTATAGAA 520649 vv v i vv v v? v iv ii v i iiv v L1M2_orf2#LIN 314 AGCAAGAGGATATAACAATTNTAAATATATATGCACCCAACACCGGAGCA 363 chr6qtel1M 520650 CCAAATTA-AAAAAAAAAAT-TCACTGTATTTCAAGTGA-AGATAGATAG 520696 v iv - v iv - i ? iv i v v - iv? L1M2_orf2#LIN 364 CCCAGATATATAAAGCAAATATTANTAGATCTAAAGGGAGAGATAGACTN 413 chr6qtel1M 520697 TAATCGTATTATAGTGGGGTTGGGCTT--ATCTTTTACTCTCAATATTAG 520744 i vvv v ? --- i -- iviiii ii ? i L1M2_orf2#LIN 414 CAATACAATAATAGTNGG---GGACTTCAACACCCCACTCTCAGCANTGG 460 chr6qtel1M 520745 ATAAATC 520751 i i L1M2_orf2#LIN 461 ACAGATC 467 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 41.52 CpG sites = 63, Kimura (unadjusted) = 41.98 Transitions / transversions = 0.93 (63/68) Gap_init rate = 0.06 (27 / 433), avg. gap size = 1.44 (39 / 27) 288 29.45 2.29 1.99 chr6qtel1M 520318 520667 (479333) L1MC4_5end#LINE/L1 2204 2554 (1) m_b312s551i2 13069 chr6qtel1M 520318 AATAATAACTATGAATGTAAATGGTATGAACTCACCCA-TAAAACTGAAA 520366 i ? ? v i vv ? ? - -- ? L1MC4_5end#LI 2204 AGTNATANCAATAAATGTAAATGGGCTNAACTCACCNATTAAAA--GANA 2251 chr6qtel1M 520367 TAGA-CAGCAGAATCTATTAAAAACCAAAATCCAATCTTATGTTGTTTAG 520415 v -ivv i?v vv? ? ? v i i iiv i ? v L1MC4_5end#LI 2252 AAGATTTTCAANTTGGNTNANAAAGCAAGACCCAACTATATGCTGTNTAC 2301 chr6qtel1M 520416 AAGAAGTACATTTAAGAAAAAGACATACATAAGAGTT-AAAATAGATAGA 520464 iii ii - vv v v ii i - i vi L1MC4_5end#LI 2302 AAGAGACACACCTAA-AAAAAGTGATTCAGAAAGGCTGAAAATAAAGGGA 2350 chr6qtel1M 520465 GTAGAAATAATTATGCCTCATTTCATGGGGAAAAAAAGTAAAAGGGCAGC 520514 - i ? v iv i vvi--- viv v iv i iv L1MC4_5end#LI 2351 -TGGANAAAGATATACCAGG---CAAATGGAAACAAAAAAGAAGGGTTGC 2396 chr6qtel1M 520515 AACTATGATCTCAGATAAAGTTGAGGCTAAAATAGATTTAATTAAGGAAA 520564 i?v ? v i v ?vii i?i i vvvv i?i i L1MC4_5end#LI 2397 AATNTTNATATCAGACAAAGTAGANTTCAAGNCAAAAAGCATTAAANGAG 2446 chr6qtel1M 520565 ATCAAC-AGATTATCTT---CTGATAAAATGTACTATAGATAATGAAGTA 520610 iv v- i?i i ---v ? iv??? v vv i vv L1MC4_5end#LI 2447 ACAAAGAAGGNCATTTTATAATGNTAAAGGNNNCAATTCACAATGAAGAT 2496 chr6qtel1M 520611 ATATCAATATTTAACCTATATATACCAAATACTATAG-AACCAAATTAAA 520659 v vv v iv ? ii vi ? - ? v? v v L1MC4_5end#LI 2497 ATAACAATTATAAATATNTATGCACCAAATAACANAGCANCCACNTTTAT 2546 chr6qtel1M 520660 AAAAAAAA 520667 iv L1MC4_5end#LI 2547 AAAGCAAA 2554 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 41.74 CpG sites = 48, Kimura (unadjusted) = 41.74 Transitions / transversions = 0.91 (48/53) Gap_init rate = 0.04 (13 / 349), avg. gap size = 1.15 (15 / 13) 327 24.99 4.52 4.05 chr6qtel1M 520318 520538 (479462) L1M1_orf2#LINE/L1 27 248 (3046) m_b312s551i1 13069 chr6qtel1M 520318 AATAATAACTATGAATGTAAATGGTATGAACTCACCCAT-AAAACTGAAA 520366 vv vv i v v - -- v L1M1_orf2#LIN 27 AATAATAACATTGAATGTAAATGGACTAAACTCTCCAATCAAAA--GACA 74 chr6qtel1M 520367 TAGA-CAGCAGAATCTATTAAAAACCAAAATCCAATCTTATGTTGTTTAG 520415 -ii v vv v v i i ? vv v ii v L1M1_orf2#LIN 75 TAGAGTGGCTGAATGGATGAAAAAACAAGACCCANTGATCTGTTGCCTAC 124 chr6qtel1M 520416 AAGAAGTACATTTAAG--AAAAAGACATACATAAGAGTTAAAATAGATAG 520463 ii i v v-- v i - v v i vi L1M1_orf2#LIN 125 AAGAAACACACTTCACCTATAAAGACACACAT-AGACTGAAAATAAAGGG 173 chr6qtel1M 520464 AGTAGAAATAATTATGCCTCATTTC-ATGGGGA--AAAAAAGTAAAAGGG 520510 - i v iv v -- vi - ii -- - iv - L1M1_orf2#LIN 174 A-TGGAAAAAGATATTC--CATGCCAATGGAAACCAAAAAAG-AGCAGG- 218 chr6qtel1M 520511 CAGCAACTATG---ATCTCAGATAAAGTTGA 520538 - i i i--- v i i v L1M1_orf2#LIN 219 -AGTAGCTATACTTATATCAGACAAAATAGA 248 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 30.74 CpG sites = 24, Kimura (unadjusted) = 30.74 Transitions / transversions = 0.83 (24/29) Gap_init rate = 0.07 (15 / 220), avg. gap size = 1.27 (19 / 15) 413 28.70 0.00 6.67 chr6qtel1M 521116 521227 (478773) MIRc#SINE/MIR 9 113 (155) m_b312s601i2 13070 chr6qtel1M 521116 TATAGGGCAGTAGATAGAGTACCAATTTTGGAGTTTGGAGAATCTGAGTT 521165 i i v i v i iiivi iv ii i i MIRc#SINE/MIR 9 TGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTT 58 chr6qtel1M 521166 TAAATGTGGCCTAAGGCACTTAATACTTATTAGTTGTGTGACCCTGAGCA 521215 ii i ---- i-- v -ivi i i i i MIRc#SINE/MIR 59 CGAGT----CCC--GGCTCT-GCCACTTACTAGCTGTGTGACCTTGGGCA 101 chr6qtel1M 521216 AGTCACTTAATC 521227 i MIRc#SINE/MIR 102 AGTCACTTAACC 113 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 35.55 CpG sites = 24, Kimura (unadjusted) = 39.14 Transitions / transversions = 4.00 (24/6) Gap_init rate = 0.06 (7 / 111), avg. gap size = 1.00 (7 / 7) 291 32.17 7.49 2.80 chr6qtel1M 521761 522067 (477933) L1PB_orf2#LINE/L1 2388 2708 (586) m_b312s551i4 13071 chr6qtel1M 521761 AAACAATTGGAGAAATATTAATTGTTTATTGGTAGGTA------ATATAA 521804 v i v i ivvv i i v i i ------ vi L1PB_orf2#LIN 2388 AAACAAATGGAAACACATCCCATGCTCATGGATGGGTAGAATCAATATTG 2437 chr6qtel1M 521805 TGAAAATGGTCATTTCACTGAAATTAATTTATATATTCAATG-ATTTCCC 521853 ii viii ii vi i i v - v L1PB_orf2#LIN 2438 TGAAAATGACCATACTGCCAAAAGCAATCTACAAATTCAATGCAATTCCC 2487 chr6qtel1M 521854 ACTTAAATTAC-------ATTTT--ACAGAATTAAGAAAATAATAATAAC 521894 - i v ------- i -- i - - i vvi L1PB_orf2#LIN 2488 A-TCAAAATACCACCATCATTCTTCACAGAACTA-GAAAA-AACAATCCT 2534 chr6qtel1M 521895 AAAATTAATTTGTAA--GAACAAGAACTCA-ATAATAACAAAG-AAAACC 521940 v v v --i v i i i- ii-- - i i L1PB_orf2#LIN 2535 AAAATTCATATGGAACCAAAAAAGAGCCCGCATAGC--CAAAGCAAGACT 2582 chr6qtel1M 521941 ATTTTATTAAAAAAAAGGAA---AGAGGTTTTGCATCACCATAACTAAAA 521987 ---- vi i vi ---i iv ii i vv vi v L1PB_orf2#LIN 2583 A----AGCAAAAAGAACAAATCTGGAGGCATCACATTACCCGACTTCAAA 2628 chr6qtel1M 521988 CTATATTTTATGGTCGTAATTATCCAAACTATCTCACCCTTGTTAAGAAA 522037 i v v i i i i i v viiv viiv v vv i L1PB_orf2#LIN 2629 CTATACTATAAGGCCATAGTCACCAAAACAGCATGGTACTGGTATAAAAA 2678 chr6qtel1M 522038 TAGAAAAGTGGATCAACAGAACAGAGTAAA 522067 iv vi i i ii i i L1PB_orf2#LIN 2679 TAGGCACATAGACCAATGGAACAGAATAGA 2708 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 43.22 CpG sites = 59, Kimura (unadjusted) = 43.85 Transitions / transversions = 1.59 (59/37) Gap_init rate = 0.06 (17 / 306), avg. gap size = 1.88 (32 / 17) 394 29.27 4.52 3.27 chr6qtel1M 522467 522798 (477202) L1ME4c_3end#LINE/L1 3 338 (492) m_b312s551i6 13069 chr6qtel1M 522467 AATACCTCAAATACATAAAAATCTTTATAAAATATATTAGAAAACAAGTC 522516 i ?v ? i i v ivv v vv v - ?i L1ME4c_3end#L 3 AATATCTNTANTATATAAAGAGCTCATTCAAATTGATAAGAAAA-ANATC 51 chr6qtel1M 522517 ATTTTCATTCCCTATTTGAAAAATGTTCAAAGCATATGAAGAGGCAGTTT 522566 ----- vv i v v v vv v i v i i i L1ME4c_3end#L 52 A-----AGACCCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTC 96 chr6qtel1M 522567 TCAGGTGAAGAAATCAAAACTATT---TATATTCATTTGAAAAATATTCT 522613 v ?iv i - v ? v ---i v iv v- i v L1ME4c_3end#L 97 ACANAAGAGGAAAT-ACAANTAGTAAACAAACACATG-GAAAAATGTTCA 144 chr6qtel1M 522614 AAATAATTATTGATTAAAATGTTGCAAATTAAAACAACCTTGAGATAACA 522663 vv vii v i i iviv i vv v L1ME4c_3end#L 145 ACCTCGCTAGTAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCA 194 chr6qtel1M 522664 TTTTATGCCTAGCAGATTGACTAAAATGATT---AAATGGAAAAGCAACA 522710 i vi i ii v -- --- v v -i v v L1ME4c_3end#L 195 TTTTACGCCTATTAAATTAGCAAAAAT--TTAAAAAATTGATAA-TACCC 241 chr6qtel1M 522711 AATGTTGGTGAGGATGTGGAAAAATTGGGAAAATAAT---TTG-----GA 522752 i i ? i vi i v v?v v --- ----- i L1ME4c_3end#L 242 AATGCTGGCGAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGG 291 chr6qtel1M 522753 AATTGTGGACTGATCCAACAG-GTTGGAGAACAATCTGGAACTATGT 522798 v ? ii i i v vv-v i i i v v i L1ME4c_3end#L 292 CANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGT 338 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.12 CpG sites = 42, Kimura (unadjusted) = 38.60 Transitions / transversions = 0.81 (42/52) Gap_init rate = 0.05 (16 / 331), avg. gap size = 1.62 (26 / 16) 596 28.89 4.53 0.73 chr6qtel1M 522526 522790 (477210) L1ME5_3end#LINE/L1 56 330 (611) m_b312s551i7 13069 chr6qtel1M 522526 CCCTATTTGAAAAATGTTCAAAGCATATGAAGAGGCAGTTTTCAGGTGAA 522575 i v v vv v v i v iv i L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chr6qtel1M 522576 GAAATCAAAACTATTTATATTCATTTGAAAA-ATATTCTAAATAATTATT 522624 i vi vvii v i vv v i - ii v v v v L1ME5_3end#LI 106 GAAACCCGAAAGGCTAACAAGCATATGAAGAGATGCTCAAACTCATTAGT 155 chr6qtel1M 522625 GATTAAAATGTTGCAAATTAAAACAACCTTGAGATAACATTTTATGCCTA 522674 i i i iviv vv v i ii L1ME5_3end#LI 156 AATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCTA 205 chr6qtel1M 522675 GCAGATTGACTAAAATGATTAAA-TGGA-AAAGCAACAAATGTTGGTGAG 522722 vi i i v v vv i- - v -- i i L1ME5_3end#LI 206 TTAGACTGGCAAAAATTAGAAAGCTGGATAATGC--CAAGTGTTGGCGAG 253 chr6qtel1M 522723 GATGTGGAAAAATTGGGAAAATAAT---TTG-----GAAATTGTGGACTG 522764 ii ? v i vvv v ---i ----- ii v i L1ME5_3end#LI 254 GATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACTG 303 chr6qtel1M 522765 ATCCAA-CAGGTTGGAGAACAATCTGG 522790 i v i- vvi i L1ME5_3end#LI 304 GTGCAGCCATTCTGGAGAGCAATCTGG 330 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 35.86 CpG sites = 37, Kimura (unadjusted) = 37.06 Transitions / transversions = 0.95 (37/39) Gap_init rate = 0.03 (8 / 264), avg. gap size = 1.75 (14 / 8) 27 6.07 0.00 0.00 chr6qtel1M 523466 523500 (476500) (TTCTCC)n#Simple_repeat 1 35 (0) c_b312s251i0 13072 chr6qtel1M 523466 TTCTCCTCCTCCTTCTCCTTCTCCTTCTCCCTCTC 523500 i i (TTCTCC)n#Sim 1 TTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTC 35 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 55 23.21 1.40 2.11 chr6qtel1M 524255 524397 (475603) (AT)n#Simple_repeat 1 142 (0) m_b312s252i2 13073 chr6qtel1M 524255 ATATCTCATGTATATGTATATATATATATATATATCTTTATATATGTATA 524304 v - i i v v i (AT)n#Simple_ 1 ATATAT-ATATATATATATATATATATATATATATATATATATATATATA 49 chr6qtel1M 524305 TTTGTCTGCTTTATACA-ATATATATATATGTATATATGAATGCATACAT 524353 v i v -v v i - i iv ii i (AT)n#Simple_ 50 TATATAT-ATATATATATATATATATATATATATATATATATATATATAT 98 chr6qtel1M 524354 ATTCATATATGTA-ATATATGCACATATGAAATATATGCATATAT 524397 vi i - ii i - v ii (AT)n#Simple_ 99 ATATATATATATATATATATATATATAT-ATATATATATATATAT 142 Matrix = Unknown Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.04 (5 / 142), avg. gap size = 1.00 (5 / 5) 29 15.54 0.00 3.39 chr6qtel1M 527971 528031 (471969) (ATG)n#Simple_repeat 1 59 (0) m_b312s252i3 13074 chr6qtel1M 527971 ATGATGATGGTGATGATGATGATGGGGGGGCAGTGATGATGACGATGAAG 528020 i iv iv - - i v (ATG)n#Simple 1 ATGATGATGATGATGATGATGATGATGATG-A-TGATGATGATGATGATG 48 chr6qtel1M 528021 AGGATGATGAT 528031 v (ATG)n#Simple 49 ATGATGATGAT 59 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.03 (2 / 60), avg. gap size = 1.00 (2 / 2) 37 0.00 0.00 0.00 chr6qtel1M 528380 528411 (471589) (AC)n#Simple_repeat 1 32 (0) c_b312s251i1 13075 chr6qtel1M 528380 ACACACACACACACACACACACACACACACAC 528411 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACAC 32 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 395 25.75 7.43 8.16 chr6qtel1M 529461 529608 (470392) MIRc#SINE/MIR 2 148 (120) m_b312s601i3 13076 chr6qtel1M 529461 GAAGCAAGGTGACATAGTAGAT-GAGTTCTGGACTTGGATGGAGTTAGGA 529509 i iv iiii i v- iv ---- i MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGA----GTCAGGA 47 chr6qtel1M 529510 TCACTCAATTACTAAAGTTCAGAACTGACCTCAGATACTTCCTAGCTGTG 529559 vv ------- ii- iiiv iviv v vi v MIRc#SINE/MIR 48 AGAC-------CTGG-GTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTG 89 chr6qtel1M 529560 TAAC--TGGACAAGTTACT------GTTTG--CCTCAGTTTTCTCATCTG 529599 i -- i i ------v i -- i MIRc#SINE/MIR 90 TGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTG 139 chr6qtel1M 529600 TAAAATGAG 529608 i MIRc#SINE/MIR 140 TAAAATGGG 148 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 30.40 CpG sites = 23, Kimura (unadjusted) = 32.65 Transitions / transversions = 1.92 (23/12) Gap_init rate = 0.11 (16 / 147), avg. gap size = 1.44 (23 / 16) 217 36.96 0.00 1.09 chr6qtel1M 529808 529900 (470100) L2c_3end#LINE/L2 347 438 (40) m_b312s601i4 13077 chr6qtel1M 529808 TCTATTCATGTGACTCTTTGTGTGCAGCAAATTATTAACTCCTAGAAATG 529857 i i i? v v i vi- v vi i i i v i v iivv L2c_3end#LINE 347 TCTGTTTACNTGTCTGTCTCC-TCCACTAGACTGTGAGCTCCTTGAGGGC 395 chr6qtel1M 529858 AGGGATTGCCTCTTCTCCTTATTTGCATGCCCAGCACCCAGCA 529900 ii iv v i v v i v i ii L2c_3end#LINE 396 AGGGACCGTGTCTTATTCATCTTTGTATCCCCAGCGCCTGGCA 438 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 49.55 CpG sites = 20, Kimura (unadjusted) = 54.19 Transitions / transversions = 1.43 (20/14) Gap_init rate = 0.01 (1 / 92), avg. gap size = 1.00 (1 / 1) 28 22.03 4.30 2.11 chr6qtel1M 530682 530774 (469226) (TCTC)n#Simple_repeat 1 95 (0) m_b312s252i4 13078 chr6qtel1M 530682 TCT-TCCCTCTCTTTATCTGTCTGTCTCTCGCTGTTTTTAATTTCTGGGT 530730 - i i v v v v v i i -v i vvv (TCTC)n#Simpl 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT-CTCTCTCTCT 49 chr6qtel1M 530731 CTCTCTCTCTCTCTCTCTCTCCTTCTC-CTC-CTC-CTCCCTACTCT 530774 ii - - - i - (TCTC)n#Simpl 50 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT-CTCT 95 Matrix = Unknown Transitions / transversions = 0.89 (8/9) Gap_init rate = 0.07 (6 / 92), avg. gap size = 1.00 (6 / 6) 22 20.94 1.82 0.00 chr6qtel1M 533737 533791 (466209) (AGAAA)n#Simple_repeat 1 56 (0) m_b312s252i6 13079 chr6qtel1M 533737 AGAAAAAAAAAGGAAAGAAAAGAAAACAAGA-TCATGAAAAGTAAAAAAA 533785 i i v i -vv v v i (AGAAA)n#Simp 1 AGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAA 50 chr6qtel1M 533786 AAAAAA 533791 i (AGAAA)n#Simp 51 AGAAAA 56 Matrix = Unknown Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1) 297 33.15 8.13 4.21 chr6qtel1M 534736 535239 (464761) L1ME3G_3end#LINE/L1 53 575 (349) m_b312s551i9 13080 chr6qtel1M 534736 CCCAGTTTATAAATGGGCAAAAGATATAAACAAGAAGTTTTCAGAAGAAG 534785 i vv v i i i v i iv i L1ME3G_3end#L 53 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chr6qtel1M 534786 AAAC-CAAA-AATTAATAATCACATGAAAA-----TC-ACTTC-TGAACA 534826 i- -iiii v i ----- - i -iv ii L1ME3G_3end#L 103 AAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTA 152 chr6qtel1M 534827 A-CAGATATATGTTAAAAAAAAAAGCTTTGAGATACTACTTACACACCTT 534875 - iv v iv vv v i vv i i -iv iv L1ME3G_3end#L 153 ATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTT-TTCACCCA 201 chr6qtel1M 534876 TCAG--------------AAAAG---GAAAATGATCAATGCTGGAAGACA 534908 -------------- --- v ivi? i i viiivi L1ME3G_3end#L 202 TCAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGG 251 chr6qtel1M 534909 CATGGAAAAATGCAAACAGTTATGTATTATTGGTAGAGTTGTGACCTGAT 534958 ii ii i viv vv i ii i ii i iiv i vi i L1ME3G_3end#L 252 TGTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGT 301 chr6qtel1M 534959 CTAACCATTCCAGGGGACAATTTGAAACTATACCAAATGAGATATAAAAC 535008 vi i ? iii i i iv v -- v v i i v - L1ME3G_3end#L 302 ACAGCCNTTTTGGAGGGCAATTTGGCAGTAT--CTATTAAAATTTAAAA- 348 chr6qtel1M 535009 TGTGCATACTACTCATTGAACTACTCAACAATACAAGTACTAGGTCCCTG 535058 i i- -- ---- i i v v v v ? ?vi i L1ME3G_3end#L 349 TGCGCATACC-CT--TTG----ACCCAGCAATTCCACTTCTNGGNATCTA 391 chr6qtel1M 535059 ---TATCAAAATGATCAAAGAAAATGAGATTGTGTATATTTCTATAAAAA 535105 --- ?vi iv --- v v v vviiv v ?iiv v i ii L1ME3G_3end#L 392 TCCTANAGAAATACTC---GCACATGTGCACAAGGANGCATGTACAAGGA 438 chr6qtel1M 535106 TAT---TTGTAACATTTCTTTTTTGCTTGCAAATAATTAGAAAATGAGC- 535151 i --- i i --v v iv v i v - i ii v - L1ME3G_3end#L 439 TGTTCATTGCAGCATT--GTTTGTAATAGCGAAAAATT-GGAAACAACCT 485 chr6qtel1M 535152 AGATGCTCCTTAATTGGAAAATGACAGAACAACTTATGTTAT---CAGAT 535198 i ii v i v ii iivi i v v --- v i L1ME3G_3end#L 486 AAATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCATAC 535 chr6qtel1M 535199 TGTAATGGAATAATTTG----TGTTATAAGAAATGAGGAGTAGAT 535239 --- v v ----? v ii -- L1ME3G_3end#L 536 T---ATGGAATACTATGCAGCNGTTAAAAAGAATGAG--GTAGAT 575 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 44.94 CpG sites = 96, Kimura (unadjusted) = 46.56 Transitions / transversions = 1.50 (96/64) Gap_init rate = 0.07 (35 / 503), avg. gap size = 1.80 (63 / 35) 387 31.97 8.81 3.59 chr6qtel1M 534736 535053 (464947) L1ME3Cz_3end#LINE/L1 53 386 (611) m_b312s551i8 13080 chr6qtel1M 534736 CCCAGTTTATAAATGGGCAAAAGATATAAACAAGAAGTTTTCAGAAGAAG 534785 i vv v i i i v i iv i L1ME3Cz_3end# 53 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chr6qtel1M 534786 AAACCAAAA--ATTAATAATCACATGAAAA-----TC-ACTTC-TGAACA 534826 vi --iii v i ----- - i -iv ii L1ME3Cz_3end# 103 AAACCCGAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTA 152 chr6qtel1M 534827 A-CAGATATATGTTAAAAAAAAAAGCTTTGAGATACTACTTACACACCTT 534875 - iv v iv vv v?i vv i i - iv L1ME3Cz_3end# 153 ATCAGGGAAATGCAAATTAAAACNACAATGAGATACCATTT-CACACCCA 201 chr6qtel1M 534876 TCAG--------------AAAAG---GAAAATGATCAA-TGCTGGAAGAC 534907 -------------- --- v - i - i viiiv L1ME3Cz_3end# 202 TCAGATTGGCAAAAATTTAAAAGTCTGACAAT-ACCAAGTGTTGGCGAGG 250 chr6qtel1M 534908 ACATGGAAAAATGCAAACAGTTATGTATTATTGGTAGAGTTGTGACCTGA 534957 ii i i vi vv i ii i ii i iiv i vi i L1ME3Cz_3end# 251 ATGTGGAGAAACGGGAACTCTCATACACTGCTGGTGGGAGTGTAAATTGG 300 chr6qtel1M 534958 TCTAACCATTCCAGGGGACAATTTGAAACTATACCAAATGAGATATAAAA 535007 vi i iii i ii --i v i v i i ii - i i L1ME3Cz_3end# 301 TACAACCACTTTGGAGAGCAATTTG--GCAATATCTAGTAAAGT-TGAAG 347 chr6qtel1M 535008 CTGTGCATACTACTCATTGAACTACTCAACAATACAAGTACTAGGT 535053 v i i- ------ v i i v v v v L1ME3Cz_3end# 348 ATGCGCATACC-CT------ACGACCCAGCAATTCCACTTCTAGGT 386 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 41.72 CpG sites = 64, Kimura (unadjusted) = 44.18 Transitions / transversions = 1.88 (64/34) Gap_init rate = 0.06 (20 / 317), avg. gap size = 2.00 (40 / 20) 407 32.51 10.93 0.37 chr6qtel1M 534736 534982 (465018) L1ME5_3end#LINE/L1 57 329 (612) m_b312s551i10 13080 chr6qtel1M 534736 CCCAGTTTATAAATGGGCAAAAGATATAAACAAGAAGTTTTCAGAAGAAG 534785 i vv v i i i v i v i L1ME5_3end#LI 57 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAGG 106 chr6qtel1M 534786 AAACC--AAAAATTAATAATCACATGAAAA-----TC--ACTTCTGAACA 534826 -- iii i v i i ----- -- iv v ii L1ME5_3end#LI 107 AAACCCGAAAGGCTAACAAGCATATGAAGAGATGCTCAAACTCATTAGTA 156 chr6qtel1M 534827 A-CAGATATATGTTAAAAAAAAAAGCTTTGAGATACTACTTACACACCTT 534875 - v v iv vv v i vv ii -i v L1ME5_3end#LI 157 ATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTT-TACACCTA 205 chr6qtel1M 534876 TCAGA-----AAA------------GGAAAATGATCAATGCTGGAAGACA 534908 i ----- ------------ v viv i i viiiv L1ME5_3end#LI 206 TTAGACTGGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTGGCGAGGA 255 chr6qtel1M 534909 CATGGAAAAATGCAAACAGTTATGTATTATTGGTAGAGTTGTGACCTGAT 534958 ii ii ? ivi vv i i i ii i iiv iiv i L1ME5_3end#LI 256 TGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACTGGT 305 chr6qtel1M 534959 CTAACCATTCCAGGGGACAATTTG 534982 vi i ii i ii i L1ME5_3end#LI 306 GCAGCCATTCTGGAGAGCAATCTG 329 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 44.39 CpG sites = 52, Kimura (unadjusted) = 45.18 Transitions / transversions = 1.86 (52/28) Gap_init rate = 0.03 (7 / 246), avg. gap size = 4.00 (28 / 7) 12 28.18 0.00 2.27 chr6qtel1M 535613 535657 (464343) (TAAA)n#Simple_repeat 1 44 (0) m_b312s252i7 13081 chr6qtel1M 535613 TAAATACATAATTTAATCAATAAAGTATGTTAAAATATAACTAAA 535657 v v v v - vi v v v v (TAAA)n#Simpl 1 TAAATAAATAAATAAATAAATAAA-TAAATAAATAAATAAATAAA 44 Matrix = Unknown Transitions / transversions = 0.11 (1/9) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 43 0.00 0.00 0.00 chr6qtel1M 536184 536220 (463780) (AT)n#Simple_repeat 1 37 (0) c_b312s251i2 13082 chr6qtel1M 536184 ATATATATATATATATATATATATATATATATATATA 536220 (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATA 37 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 313 36.35 6.43 7.12 chr6qtel1M 536469 536779 (463221) C L2b_3end#LINE/L2 (6) 460 152 m_b312s601i6 13083 chr6qtel1M 536469 TTATTCAACAAACATTTATTAAAGGCTTACCAATTGCTAAAAGGCATCAT 536518 i i i i iv i iivv i--- ?iii C L2b_3end#LINE 460 TCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCC---AGGCNCTGT 414 chr6qtel1M 536519 GATAAGCACTGGGGATA-ACC--TCAA-AAGACACAAAATTTGAGTCCTT 536564 v i i - v -- v - --- i i?i ivi v C L2b_3end#LINE 413 GCTAGGCGCTGGGGATACAGCGGTGAACAAGAC---AGACNCGGTCCCTG 367 chr6qtel1M 536565 TCTTTAAGAAGCTGACATTCTACTACTGGAGA-AAACATGCAAG-AAAGA 536612 i i i v i v v v ivv - i i ?- i v C L2b_3end#LINE 366 CCCTCACGGAGCTCACAGTCTAGTGGGGGAGACAGACATGTAANCAGACA 317 chr6qtel1M 536613 A--AAAACCCAACTATATATTGGTAAGGTAAATACGATATAATTCAGATG 536660 -- v i------ v i i iivvi iviviiii v C L2b_3end#LINE 316 ATNATAACCCAG------AGTGGCAGGGTAGGACTGGGGGGGCCCAGAGG 273 chr6qtel1M 536661 A-----TTTTATACCAATGTGGAAGGCAGAATAAGGGAAGTGATATTACA 536705 -----ii v i- iiiv ii ----- v i vvv viiiv C L2b_3end#LINE 272 AGGGCGCCTGAC-CCGGCCTGGGGGG-----TCAGGGAGGGCTTCCCGGA 229 chr6qtel1M 536706 AAAAGTAATATTTGGGGTCAGTAGTGAAG--CCA--AGGAAT---CCAGA 536748 ii i i i i v v vvv --iv -- i --- - C L2b_3end#LINE 228 GGAGGTGACATTTGAGCTGAGACCTGAAGGATGAGTAGGAGTTGGCCAG- 180 chr6qtel1M 536749 AGGGAAAGGTCATGAGAGAGAACATTCCAGG 536779 - v ii --i i ii ii i C L2b_3end#LINE 179 -GCGAAGAG--GTGGGGAAGGGCGTTCCAGG 152 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 50.00 CpG sites = 68, Kimura (unadjusted) = 53.92 Transitions / transversions = 1.84 (68/37) Gap_init rate = 0.10 (32 / 310), avg. gap size = 1.31 (42 / 32) 357 26.66 4.70 6.85 chr6qtel1M 536469 536617 (463383) C L2a_3end#LINE/L2 (6) 511 366 m_b312s601i5 13083 chr6qtel1M 536469 TTATTCAACAAACATTTATTAAAGGCTTACCAATTGCTAAAAGGCATCAT 536518 i i i iv i i vv i--- iii C L2a_3end#LINE 511 TCATTCAACAAATATTTATTGAGCGCCTACTATGTGCC---AGGCACTGT 465 chr6qtel1M 536519 GATAAGCACTGGGGATA-ACC--T---CAAAAGACACAAAATTTGAGTCC 536562 vv i i - v -- --- v v ----- C L2a_3end#LINE 464 TCTAGGCGCTGGGGATACAGCAGTGAACAAAACAGACAAA-----AGTCC 420 chr6qtel1M 536563 TT-TCTTTAAGAAGCTGACATTCTACTACTGGAGAAAACATGCAAGAAAG 536611 i -i i i v i v v i-- i i i vi v v C L2a_3end#LINE 419 CTGCCCTCATGGAGCTTACATTCTAGTG--GGGGGAGACAGACAATAAAC 372 chr6qtel1M 536612 AAAAAA 536617 v C L2a_3end#LINE 371 AAATAA 366 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 32.59 CpG sites = 22, Kimura (unadjusted) = 33.70 Transitions / transversions = 1.47 (22/15) Gap_init rate = 0.09 (14 / 148), avg. gap size = 1.21 (17 / 14) 880 32.01 5.32 1.41 chr6qtel1M 537492 538036 (461964) C L1ME4c_3end#LINE/L1 (257) 573 8 m_b312s551i11 13084 chr6qtel1M 537492 ATCATTTCTTATAGA-ACATAATATTCCATTGCATTCATATACCATAATT 537540 i v i v-i i vi ?v i C L1ME4c_3end#L 573 ATCATTTTTAATGGCTGCATAATATTCCATCGAGTNGATGTACCATAATT 524 chr6qtel1M 537541 TACTCAACCCTTCTCCAATGGAGGGGCATCCA-------TTCAGTTTGCT 537583 i v i v v vv i ii ------- i i -i C L1ME4c_3end#L 523 TACTTAACCATTCCCCTATTGTTGGACATTTAGGTTGTTTCCAATTT-TT 475 chr6qtel1M 537584 GGCCACAACAAAAAGGACCACTATAAATATGTTTGCATATGTGGGTCCGT 537633 v i iv i v ivi ii v i i v i iii i i -- iv C L1ME4c_3end#L 474 CGCTATTATAAATAACGCTGCAATGAACATCTTCGTGCATATAG--CTTT 427 chr6qtel1M 537634 TTCCTTTTTTTA---TGTTCTCTGTGGGTA------CAGAAAC---ATTG 537671 i i--- i ii vv i ------ ii--- i C L1ME4c_3end#L 426 TTCCTTCTTTTGAATTATTTCCTTAGGATAAATTCCCAGAAGTGGAATTA 377 chr6qtel1M 537672 TTGAACGAAAGGGTCTGAACAGTTTCGTAGCCTATGGGGCATAGTTCCAA 537721 i iiiv v v ii i iiv ivi i v v C L1ME4c_3end#L 376 CTGGGTCAAAGGGTATGAACATTTTTATGGCTCTTGATACGTATTGCCAA 327 chr6qtel1M 537722 ATTCCTCTCTAGAATGATCTGATCAGCTCACAGTTCCACCAAAAATGTAT 537771 v i i i v i ivv i ii i ? v iv C L1ME4c_3end#L 326 ATTGCTTTCCAAAAGGGTTGTACCAATTTACANTGCCACCAGCAATGTAT 277 chr6qtel1M 537772 TATTATCCTAGATTTTA-CACATCTCCTTTGGAATTTACCTTTATC--TT 537818 v v?i v i - i - i ? ii viii v viviv -- C L1ME4c_3end#L 276 GAGNGTACCAG-TTTCACCGCANCCTCGCCAGCATTGGGTATTATCAATT 228 chr6qtel1M 537819 TCCCTGTAAA-CTTAGCCAATCTGAGAAATGTGAAGTGGTACCTTAGAGT 537867 --- v -i v i i i v iii i i i i vv C L1ME4c_3end#L 227 T---TTTAAATTTTTGCTAATTTAATAGGCGTAAAATGGTATCTCATTGT 181 chr6qtel1M 537868 TGCCTTAATTTTCATTTCTCTAATCCATAGGGA--TTTAGCATTTTT-CA 537914 i v i i ivv v -- v i - C L1ME4c_3end#L 180 TGCTTTAATTTGCATTTCTTTGATTACTAGCGAGGTTGAACATTTTTCCA 131 chr6qtel1M 537915 TATGATTGAAAATCAGTTTAATTTCTTCATCTGAAAATTATCTATTCATA 537964 i v vvv ii ? vv i v ? vi i i i C L1ME4c_3end#L 130 TGTGTTTGTTTACTANTTGTATTTCCTCTTNTGTGAATTGTCTGTTCATG 81 chr6qtel1M 537965 TCCTTTA-ATATTTGTCAATTGGAAAATGGCATG-TATTCTTATTAATTT 538012 i-vi i v iivv v - ?- v i C L1ME4c_3end#L 80 TCCTTTGCCCATTTATCTATTGGGGTCTTG-ATNTTTTTCTTATCAATTT 32 chr6qtel1M 538013 GAGTCAATGCTCTATATATTTTAG 538036 i v iiv i ? v? C L1ME4c_3end#L 31 GAATGAGCTCTTTATATANTANAG 8 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 42.46 CpG sites = 106, Kimura (unadjusted) = 44.57 Transitions / transversions = 1.61 (106/66) Gap_init rate = 0.04 (20 / 544), avg. gap size = 1.85 (37 / 20) 230 31.01 4.33 3.52 chr6qtel1M 537901 538154 (461846) C L1M3_orf2#LINE/L1 (5) 3283 3028 m_b312s551i13 13084 chr6qtel1M 537901 TTTAGCAT-TTTTCATATGATTGAAAATCAGTTTAATTTCTTCATCTGAA 537949 v - ivi vviii v vv v v iv i C L1M3_orf2#LIN 3283 TTGAGCATCTTTTCATATACCTGTTGGCCATTTGTATGTCTTCTTTGGAG 3234 chr6qtel1M 537950 AATTATCTATTCATATCCTTTA-ATATTTGTCAATTGGAAAATGGCATGT 537998 v i vi i-vi v ? i ivv v--- C L1M3_orf2#LIN 3233 AAATGTCTATTCAGGTCCTTTGCCCATTTTTNAATCGGGTTATT---TGT 3187 chr6qtel1M 537999 ATTCTTATTAATTTGAGTC-----AATGCTCTATATATTTTAGGAATGAG 538043 v i ii -- i----- i v ii i iv v i C L1M3_orf2#LIN 3186 TTTTTTGCTA--TTGAGTTGTANGAGTTCCTTATATATTTTGGATATTAA 3139 chr6qtel1M 538044 GCCTTTATCCAAATCTTTTG-ATGCAAATTTTTTTCCCAATTTCCT-GCT 538091 v i - i v v v -v v ii v i v - v C L1M3_orf2#LIN 3138 CCCCTTAT-CAGATATATGGTTTGCAAATATTTTCTCCCATTCCGTAGGT 3090 chr6qtel1M 538092 TCCCTTCTAATTTGG--GATGTATTGGTTTTGTTGGGACAAAACCTTTTT 538139 v i v i iv -- - i vvi i v - i v - C L1M3_orf2#LIN 3089 TGCCTTTTCACTCTGTTGAT-TGTTTCCTTTGCTGTG-CAGAAGC-TTTT 3043 chr6qtel1M 538140 TAATTTAATATAATC 538154 i i i i C L1M3_orf2#LIN 3042 TAGTTTGATGTAGTC 3028 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 40.21 CpG sites = 39, Kimura (unadjusted) = 40.90 Transitions / transversions = 1.05 (39/37) Gap_init rate = 0.06 (15 / 253), avg. gap size = 1.33 (20 / 15) 264 28.27 4.41 2.90 chr6qtel1M 537901 538104 (461896) C L1M5_orf2#LINE/L1 (5) 3289 3083 m_b312s551i12 13084 chr6qtel1M 537901 TTTAGCAT-TTTTCATATGATTGAAAATCAGTTTAATTTCTTCATCTGAA 537949 v - i v ivviii v v? v v i vi C L1M5_orf2#LIN 3289 TTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTTTTGTG 3240 chr6qtel1M 537950 AATTATCTATTCATATCCTTTAAT-ATTTGTCAATTGGAAAATGGCATGT 537998 v i i vi i ivi- v ?v i--- v iv C L1M5_orf2#LIN 3239 AAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGG---TTGTTTGT 3193 chr6qtel1M 537999 ATTCTTATTAATTTGAGTC-----AATGCTCTATATATTTTAGGAATGAG 538043 v i ? -- ? i----- i v i i i iv i C L1M5_orf2#LIN 3192 CTTTTTNTTA--TTGANTTGTAGGAGTTCTTTATATATTCTGGATACGAG 3145 chr6qtel1M 538044 GCCTTTATCCAAATCT-TTTGATGCAAAT-TTTTTTCCCAATTTCCTGCT 538091 v i - i v - v ?v - i ? i viv C L1M5_orf2#LIN 3144 TCCTTTGT-CAGATATATGTNTTGCAAATATTTTCTCCCANTCTGTGGCT 3096 chr6qtel1M 538092 TCCCTTCTAATTT 538104 v i v C L1M5_orf2#LIN 3095 TGCCTTTTCATTT 3083 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.66 CpG sites = 29, Kimura (unadjusted) = 37.49 Transitions / transversions = 1.07 (29/27) Gap_init rate = 0.05 (11 / 203), avg. gap size = 1.36 (15 / 11) 591 27.92 8.11 1.82 chr6qtel1M 538886 539144 (460856) L1ME3G_3end#LINE/L1 274 548 (376) m_b312s551i14 13085 chr6qtel1M 538886 TAAATTGTTTATGGAATTGTGAACTGATCCCAC-ATTCTGAAGAGTAATT 538934 v i i vi i v i i i v vi -? i i i i L1ME3G_3end#L 274 TACACTGCTGGTGGGAGTGTAAATTGGTACAGCCNTTTTGGAGGGCAATT 323 chr6qtel1M 538935 TGGAACTATAACCA--AAGAGTTATCAAACTGCGCATACCCTTAGATCCA 538982 v v -- i -- i v --- v v i L1ME3G_3end#L 324 TGGCAGTAT--CTATTAAAATTTA---AAATGCGCATACCCTTTGACCCA 368 chr6qtel1M 538983 ACAGT---------GGGCTTAGATCCCAAAGAGAT-CT--------TAAA 539014 i i ---------? ?v vv i ? i - -------- iv L1ME3G_3end#L 369 GCAATTCCACTTCTNGGNATCTATCCTANAGAAATACTCGCACATGTGCA 418 chr6qtel1M 539015 GGAGGGAAAATGTGCAAAAATGTTTGTTACAGCCCTTTTTGTAGTGGCTA 539064 vi i?iv i ii ii i vi v i i v L1ME3G_3end#L 419 CAAGGANGCATGTACAAGGATGTTCATTGCAGCATTGTTTGTAATAGCGA 468 chr6qtel1M 539065 GAAACTGGAAACTTGATGAATGCCCATCAATTGGGGAATGGCTGAATACG 539114 i i vvvv i i v i i vi L1ME3G_3end#L 469 AAAATTGGAAACAACCTAAATGTCCATCAATAGGGGAATGGTTAAATAAA 518 chr6qtel1M 539115 TTATGGTAAATGAATGTTATGGAATATCAT 539144 v vv ii ii L1ME3G_3end#L 519 TTATGGTATATCCATACTATGGAATACTAT 548 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.98 CpG sites = 43, Kimura (unadjusted) = 36.98 Transitions / transversions = 1.54 (43/28) Gap_init rate = 0.04 (10 / 258), avg. gap size = 2.60 (26 / 10) 319 33.78 0.00 0.00 chr6qtel1M 539024 539171 (460829) L1MC4a_3end#LINE/L1 430 577 (2052) m_b312s551i15 13085 chr6qtel1M 539024 ATGTGCAAAAATGTTTGTTACAGCCCTTTTTGTAGTGGCTAGAAACTGGA 539073 ii iiv i ii i vi v i v v i v i L1MC4a_3end#L 430 ATGCACAAGGTTATTCATTGCAGCATTGTTTGTAATTGCAAAATATTGGA 479 chr6qtel1M 539074 AACTTGATGAATGCCCATCAATTGGGGAATGGCTGAATACGTTATGGTAA 539123 vvvv i ?? v i ? i vii v L1MC4a_3end#L 480 AACAACCTAAATGCCCATNNATAGGAGANTGGTTGAATAAACTATGGTAC 529 chr6qtel1M 539124 ATGAATGTTATGGAATATCATTGTTCTATAAGAAATGATGACCAGGAT 539171 vv iiiv i ii vvvv i i vi vv i L1MC4a_3end#L 530 ATCCACACAATGGAGTACTATGCAGCTGTAAAAAAGAATGAGGAAGAT 577 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 47.40 CpG sites = 27, Kimura (unadjusted) = 47.40 Transitions / transversions = 1.17 (27/23) Gap_init rate = 0.00 (0 / 147), avg. gap size = 0.0 (0 / 0) 20 18.19 1.92 1.92 chr6qtel1M 539963 540014 (459986) (ATAATG)n#Simple_repeat 1 52 (0) m_b312s252i8 13086 chr6qtel1M 539963 ATACATGA-AATGAGGATGATAATGATGAAGATGATGATGCTAATAATGA 540011 - - vi i v i iv i (ATAATG)n#Sim 1 ATA-ATGATAATGATAATGATAATGATAATGATAATGATAATGATAATGA 49 chr6qtel1M 540012 TAA 540014 (ATAATG)n#Sim 50 TAA 52 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.00 (2 / 2) 21 16.35 0.00 0.00 chr6qtel1M 539972 540012 (459988) (ATG)n#Simple_repeat 1 41 (0) m_b312s252i9 13087 chr6qtel1M 539972 ATGAGGATGATAATGATGAAGATGATGATGCTAATAATGAT 540012 v i v v i i (ATG)n#Simple 1 ATGATGATGATGATGATGATGATGATGATGATGATGATGAT 41 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 43 0.00 0.00 0.00 chr6qtel1M 540349 540385 (459615) (CA)n#Simple_repeat 1 37 (0) c_b312s251i3 13088 chr6qtel1M 540349 CACACACACACACACACACACACACACACACACACAC 540385 (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACAC 37 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 247 13.95 2.33 0.00 chr6qtel1M 540855 540897 (459103) C EutTc1-N2#DNA/TcMar-Tc1 (333) 45 2 m_b312s502i0 13089 chr6qtel1M 540855 AGTTGTTAAAAATTAAGACTTCACTAAGA-TTTTGGGACACCTT 540897 i iv i v - i C EutTc1-N2#DNA 45 AGTTATTAAAGCTTAAAACTGCACTAAGACTTTTGGGACACCCT 2 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 15.68 CpG sites = 4, Kimura (unadjusted) = 15.68 Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.02 (1 / 42), avg. gap size = 1.00 (1 / 1) 14 19.31 8.16 0.00 chr6qtel1M 540927 540975 (459025) (AAGA)n#Simple_repeat 1 53 (0) m_b312s252i10 13090 chr6qtel1M 540927 AAGAAAGAGGGAGA-AAAAATAGGAAGAGAG-AAGGAAG-AAGAAAG-AA 540972 ii i - i v i i - i - - (AAGA)n#Simpl 1 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 50 chr6qtel1M 540973 GAA 540975 (AAGA)n#Simpl 51 GAA 53 Matrix = Unknown Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.08 (4 / 48), avg. gap size = 1.00 (4 / 4) 542 21.88 6.90 5.44 chr6qtel1M 541481 541625 (458375) MIRc#SINE/MIR 2 148 (120) m_b312s601i7 13091 chr6qtel1M 541481 GAAGCTAGGTGACACAGTG--ATGAGTTCTGGACTTGGATTCAGGAAGAC 541528 i viv iii -- v iv v MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr6qtel1M 541529 TCATGTCCCCAAATTCAGATCTGGCCTCAGACACTTCCTAGTTGTGTGAT 541578 -------- iiii iii iv v v v v i i MIRc#SINE/MIR 52 --------CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGAC 93 chr6qtel1M 541579 CCTGGGCAAGTC------CCTGTTTGA--CTCAGTTTCCTCATCTGTAAA 541620 i ------ v i -- MIRc#SINE/MIR 94 CTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAA 143 chr6qtel1M 541621 ATGAG 541625 i MIRc#SINE/MIR 144 ATGGG 148 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 25.50 CpG sites = 19, Kimura (unadjusted) = 26.51 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.08 (11 / 144), avg. gap size = 1.64 (18 / 11) 241 28.57 3.90 0.00 chr6qtel1M 541856 541932 (458068) L2d2_3end#LINE/L2 436 515 (40) m_b312s601i8 13092 chr6qtel1M 541856 AAATTGTTAGCTCCTGGAGGTGAGGGACTGCCTCTTCTTCCTATTTGCAT 541905 i v v vv iiiv v v i v i L2d2_3end#LIN 436 AGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACTTCTTTGTAT 485 chr6qtel1M 541906 GCC---CAGCACCCAGCAGAATATCTGGCA 541932 v --- i i v i ii v L2d2_3end#LIN 486 CCCCCACAGCGCCTAGCACAGTGCCTTGCA 515 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 34.39 CpG sites = 11, Kimura (unadjusted) = 36.39 Transitions / transversions = 1.00 (11/11) Gap_init rate = 0.01 (1 / 76), avg. gap size = 3.00 (3 / 1) 259 26.15 0.00 0.00 chr6qtel1M 541856 541920 (458080) L2c_3end#LINE/L2 374 438 (40) m_b312s601i9 13092 chr6qtel1M 541856 AAATTGTTAGCTCCTGGAGGTGAGGGACTGCCTCTTCTTCCTATTTGCAT 541905 i i v v vv i iv v v v i L2c_3end#LINE 374 AGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTAT 423 chr6qtel1M 541906 GCCCAGCACCCAGCA 541920 v i ii L2c_3end#LINE 424 CCCCAGCGCCTGGCA 438 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 28.07 CpG sites = 8, Kimura (unadjusted) = 32.38 Transitions / transversions = 0.89 (8/9) Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0) 135 23.20 2.23 1.10 chr6qtel1M 542716 543074 (456926) (TCTCTC)n#Simple_repeat 1 363 (0) m_b312s252i11 13093 chr6qtel1M 542716 TCT-TCCCTGTCTTTCTATGTCTGTCTGTCTCTCACTGT-TTTTTGTACT 542763 - i v i v v v v v v - i i v - (TCTCTC)n#Sim 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT-CT 49 chr6qtel1M 542764 GGGTGTCTCTGTCTCTCTCTATCTCTCTGT-TCTCTCTCCCTCTATGATT 542812 vvv v v v v - i v vvi (TCTCTC)n#Sim 50 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 99 chr6qtel1M 542813 CTGTGTGTGTGTCTATGCCTCTCTTTTTCTTTTTCTACCCTCTCTCTCTC 542862 v v v v v v vi i i i i - i (TCTCTC)n#Sim 100 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT-CTCTCTCTCTCTC 148 chr6qtel1M 542863 TCCCTCCCTCTCTCCCTCTCCCTGTTCCTTTCTCCCTCTTTCTCTTACTC 542912 i i i i v ii i i i iv (TCTCTC)n#Sim 149 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 198 chr6qtel1M 542913 TCTTCCTATCTTTCTCTCTCTCTCTCTTTATTTCTCTCTCAAAC-CTCTC 542961 ii v i i v i vvv - (TCTCTC)n#Sim 199 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 248 chr6qtel1M 542962 TCTC-CTCTCTCTGTCTCTCTCTCTGTGTCTCTCTC-CTCTCTCTGTCTC 543009 - v v v - v (TCTCTC)n#Sim 249 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 298 chr6qtel1M 543010 TCTCTGTCTCTCTGTCTCTCTCTTTGTCTCTCTCTCTCTCCCTCTGCCCT 543059 v v i v i - i (TCTCTC)n#Sim 299 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT-CTCT 347 chr6qtel1M 543060 -TCTC-CTCCCTACTCT 543074 - - i - (TCTCTC)n#Sim 348 CTCTCTCTCTCT-CTCT 363 Matrix = Unknown Transitions / transversions = 0.79 (31/39) Gap_init rate = 0.03 (12 / 358), avg. gap size = 1.00 (12 / 12) 717 31.92 2.22 1.93 chr6qtel1M 547078 547438 (452562) L1ME4c_3end#LINE/L1 278 639 (191) m_b312s551i16 13094 chr6qtel1M 547078 TAAATTGTTGGTGGGATTGTGAACTGATCCAACA-TTCTGGAGAGCAATT 547126 v i v ? i i i v v- i i L1ME4c_3end#L 278 TACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGCAATT 327 chr6qtel1M 547127 TG--AA-ACTTGCCCAAAGAGTTATCAAACTGCCCATCCCCTTTGATACA 547173 -- - v ii -- ii v v ii v iv L1ME4c_3end#L 328 TGGCAATACGTATC--AAGAGCCATAAAAATGTTCATACCCTTTGACCCA 375 chr6qtel1M 547174 GCAGTGTTTCTACTGGGTCTATATTCCAAAGAGAT--CTTAAAGGAGGGA 547221 i i viiv v vv v i i i i --i i i i L1ME4c_3end#L 376 GTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAAGAAGGA 425 chr6qtel1M 547222 AAGGGACCCACATGTGCAAAAATGTTTGTGACAGTCCTTTTTGTAGTGGC 547271 ii -- i i ii i i ii vi ivi v i i i L1ME4c_3end#L 426 AAAAG--CTATATGCACGAAGATGTTCATTGCAGCGTTATTTATAATAGC 473 chr6qtel1M 547272 AAGAAACTGGAAACTGAATTAATGCCCATCAGTTGGGGAATGGCTGAATA 547321 i i i vivv v i v i v i i i L1ME4c_3end#L 474 GAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAATGGTTAAGTA 523 chr6qtel1M 547322 AGTTATGGTAAATAAATGTTATGGAATATTACTGT-TCTATAAGAAATGA 547370 i v v? iviv - i-v i v i L1ME4c_3end#L 524 AATTATGGTACATCNACTCGATGGAATATTA-TGCAGCCATTAAAAATGA 572 chr6qtel1M 547371 TGACCAGGATGAATTCAGAGAGGCCTGGAGAG-ACTTACAAGAACTGATG 547419 i ii v v v viiv vii v i i-ii ii v -- i L1ME4c_3end#L 573 TAATTATGAAGACTATGTAGCAACATGGAAAATGTTTATGATA--TAATG 620 chr6qtel1M 547420 TTAAGTGAAGTGAATAGAA 547438 ivi ii L1ME4c_3end#L 621 TTAAGTGAAAAAAGCAGAA 639 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 42.01 CpG sites = 74, Kimura (unadjusted) = 44.15 Transitions / transversions = 1.90 (74/39) Gap_init rate = 0.04 (13 / 360), avg. gap size = 1.15 (15 / 13) 23 15.58 1.92 1.92 chr6qtel1M 547753 547804 (452196) (ATAATG)n#Simple_repeat 1 52 (0) m_b312s252i14 13095 chr6qtel1M 547753 ATACATGA-AATGAGAATGATAATGATGAAGATGATGGTGCTGATAATGA 547801 - - v i v i i iv (ATAATG)n#Sim 1 ATA-ATGATAATGATAATGATAATGATAATGATAATGATAATGATAATGA 49 chr6qtel1M 547802 TAA 547804 (ATAATG)n#Sim 50 TAA 52 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.00 (2 / 2) 17 0.00 0.00 0.00 chr6qtel1M 547944 547962 (452038) (A)n#Simple_repeat 1 19 (0) m_b312s252i15 13096 chr6qtel1M 547944 AAAAAAAAAAAAAAAAAAA 547962 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAA 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 29 0.00 0.00 0.00 chr6qtel1M 548149 548173 (451827) (CA)n#Simple_repeat 1 25 (0) c_b312s251i4 13097 chr6qtel1M 548149 CACACACACACACACACACACACAC 548173 (CA)n#Simple_ 1 CACACACACACACACACACACACAC 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 97 26.29 4.20 3.97 chr6qtel1M 548804 549255 (450745) (TCTGTC)n#Simple_repeat 1 453 (0) m_b312s252i16 13098 chr6qtel1M 548804 TCT-TCTCTGTCTCTCTCTGGGTCTATCTGTCTATATCTGTCTCTGTCTC 548852 - v vv v v v i v (TCTGTC)n#Sim 1 TCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTC 50 chr6qtel1M 548853 AGTCT-T-TCTCTGTCTCTCTCTTTGTGTCCGTCTCTATGTCTATGTGTC 548900 v - - v i v i -- v v (TCTGTC)n#Sim 51 TGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTC--TGTCTCTGTCTC 98 chr6qtel1M 548901 TGTCTATCTTTCTGTCTC--TCTAAATCTCTGGATGTCTGTCTCTATCTC 548948 v v i -- vvi - - v i (TCTGTC)n#Sim 99 TGTCTCTGTCTCTGTCTCTGTCTCTGTCTCT-G-TCTCTGTCTCTGTCTC 146 chr6qtel1M 548949 TATTTCTGTATGTGTACCTTTTTGTGTGTCACTGTTTGTGTTTCTCTGTA 548998 i i v v -- i v v v v i v -- v (TCTGTC)n#Sim 147 TGTCTCTGTCTCTGT--CTCTGTCTCTGTCTCTGTCTCTG--TCTCTGTC 192 chr6qtel1M 548999 TCTCTGCCTATGTGTGTCTCTGTCTCTGTATCTCTATCTGTGCT-TATCT 549047 v vi i v v v v v - - i (TCTGTC)n#Sim 193 TCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGT-CTCTGTCT 241 chr6qtel1M 549048 ACTTTTTCT-CCTCCTCCTC-CTCATCT-TCTTCATC-CTCCTCATCT-T 549092 - v i -i ivi -v - - iii - -v - - (TCTGTC)n#Sim 242 -CTGTCTCTGTCTCTGTCTCTGTC-TCTGTCTCTGTCTCT-GTC-TCTGT 287 chr6qtel1M 549093 CATCATCCTCT-TCTTCCTCCTCCTTCTCTACATC-CTC-CT-CCTCCTT 549138 - vvi - - ivi iv iiv -v - -i iv (TCTGTC)n#Sim 288 C-TCTGTCTCTGTC-TCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGT 335 chr6qtel1M 549139 ATCCTTCTTGTTTTTCCCTCTGTGTCTCTGTGTGTGTCTCT-T-ACTTTC 549186 v iv - v v i iv v v v - -v v (TCTGTC)n#Sim 336 CTCTGTC-TCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTC 384 chr6qtel1M 549187 TGTATCTTTGTCTCTGTCTCTGTCT-T-TTTCTGTCTCTTTCTTTGTGTG 549234 v i i - - i v i v v (TCTGTC)n#Sim 385 TCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTC 434 chr6qtel1M 549235 TGTCTCTTTGTTTCTGTCTCT 549255 -- i (TCTGTC)n#Sim 435 TGTCTC--TGTCTCTGTCTCT 453 Matrix = Unknown Transitions / transversions = 0.63 (36/57) Gap_init rate = 0.08 (36 / 451), avg. gap size = 1.03 (37 / 36) 43 21.38 0.00 0.00 chr6qtel1M 549055 549146 (450854) (CTC)n#Simple_repeat 1 92 (0) m_b312s252i17 13099 chr6qtel1M 549055 CTCCTCCTCCTCCTCATCTTCTTCATCCTCCTCATCTTCATCATCCTCTT 549104 v i i v v i v v i (CTC)n#Simple 1 CTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT 50 chr6qtel1M 549105 CTTCCTCCTCCTTCTCTACATCCTCCTCCTCCTTATCCTTCT 549146 i i iv v iv i (CTC)n#Simple 51 CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT 92 Matrix = Unknown Transitions / transversions = 1.12 (9/8) Gap_init rate = 0.00 (0 / 91), avg. gap size = 0.0 (0 / 0) 97 26.29 4.20 3.97 chr6qtel1M 548804 549255 (450745) (TCTGTC)n#Simple_repeat 1 453 (0) m_b312s252i16 13098 chr6qtel1M 548804 TCT-TCTCTGTCTCTCTCTGGGTCTATCTGTCTATATCTGTCTCTGTCTC 548852 - v vv v v v i v (TCTGTC)n#Sim 1 TCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTC 50 chr6qtel1M 548853 AGTCT-T-TCTCTGTCTCTCTCTTTGTGTCCGTCTCTATGTCTATGTGTC 548900 v - - v i v i -- v v (TCTGTC)n#Sim 51 TGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTC--TGTCTCTGTCTC 98 chr6qtel1M 548901 TGTCTATCTTTCTGTCTC--TCTAAATCTCTGGATGTCTGTCTCTATCTC 548948 v v i -- vvi - - v i (TCTGTC)n#Sim 99 TGTCTCTGTCTCTGTCTCTGTCTCTGTCTCT-G-TCTCTGTCTCTGTCTC 146 chr6qtel1M 548949 TATTTCTGTATGTGTACCTTTTTGTGTGTCACTGTTTGTGTTTCTCTGTA 548998 i i v v -- i v v v v i v -- v (TCTGTC)n#Sim 147 TGTCTCTGTCTCTGT--CTCTGTCTCTGTCTCTGTCTCTG--TCTCTGTC 192 chr6qtel1M 548999 TCTCTGCCTATGTGTGTCTCTGTCTCTGTATCTCTATCTGTGCT-TATCT 549047 v vi i v v v v v - - i (TCTGTC)n#Sim 193 TCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGT-CTCTGTCT 241 chr6qtel1M 549048 ACTTTTTCT-CCTCCTCCTC-CTCATCT-TCTTCATC-CTCCTCATCT-T 549092 - v i -i ivi -v - - iii - -v - - (TCTGTC)n#Sim 242 -CTGTCTCTGTCTCTGTCTCTGTC-TCTGTCTCTGTCTCT-GTC-TCTGT 287 chr6qtel1M 549093 CATCATCCTCT-TCTTCCTCCTCCTTCTCTACATC-CTC-CT-CCTCCTT 549138 - vvi - - ivi iv iiv -v - -i iv (TCTGTC)n#Sim 288 C-TCTGTCTCTGTC-TCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGT 335 chr6qtel1M 549139 ATCCTTCTTGTTTTTCCCTCTGTGTCTCTGTGTGTGTCTCT-T-ACTTTC 549186 v iv - v v i iv v v v - -v v (TCTGTC)n#Sim 336 CTCTGTC-TCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTC 384 chr6qtel1M 549187 TGTATCTTTGTCTCTGTCTCTGTCT-T-TTTCTGTCTCTTTCTTTGTGTG 549234 v i i - - i v i v v (TCTGTC)n#Sim 385 TCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTC 434 chr6qtel1M 549235 TGTCTCTTTGTTTCTGTCTCT 549255 -- i (TCTGTC)n#Sim 435 TGTCTC--TGTCTCTGTCTCT 453 Matrix = Unknown Transitions / transversions = 0.63 (36/57) Gap_init rate = 0.08 (36 / 451), avg. gap size = 1.03 (37 / 36) 254 29.39 13.33 0.74 chr6qtel1M 549339 549458 (450542) MIR1_Amn#SINE/MIR 14 148 (82) m_b312s601i10 13100 chr6qtel1M 549339 TGGCACAATCGATAGACAACTGGTCCTGAAATCAGGTAGATGTGAGTTCA 549388 ivi i v vv v iv i v i - iv i ? MIR1_Amn#SINE 14 TGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGG-AGACCTGGGTTCN 62 chr6qtel1M 549389 AATGCAGTCTCAGACACT---------------CCTGGTCAAGCGACTTA 549423 ? v v v v v --------------- i v iv ? MIR1_Amn#SINE 63 ANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGTCACTTN 112 chr6qtel1M 549424 A-CTCTATTTACCCTTGTTTCTTTATCTATAAAGTG 549458 - v v?i iiv i i i i MIR1_Amn#SINE 113 ACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATG 148 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 38.07 CpG sites = 17, Kimura (unadjusted) = 39.48 Transitions / transversions = 0.94 (17/18) Gap_init rate = 0.03 (3 / 119), avg. gap size = 5.67 (17 / 3) 358 29.91 1.83 1.83 chr6qtel1M 549942 550050 (449950) MIRc#SINE/MIR 10 118 (150) m_b312s601i11 13101 chr6qtel1M 549942 GTGGTACGATGGACAGAGAAGTAG-CCTGGAGTCAGGAAAACCTAAATTC 549990 i ii v v v i - i i iii MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr6qtel1M 549991 AAATTTGATATCAGACTCTTACTAGTTGTGTGACCCTACTC-AGTCTTTC 550039 i i iivivv v v v i i ivv - --v MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTC--AC 107 chr6qtel1M 550040 TCTATCTCTCT 550050 iv i MIRc#SINE/MIR 108 TTAACCTCTCT 118 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 36.22 CpG sites = 19, Kimura (unadjusted) = 39.33 Transitions / transversions = 1.46 (19/13) Gap_init rate = 0.04 (4 / 108), avg. gap size = 1.00 (4 / 4) 16 17.81 2.63 0.00 chr6qtel1M 550241 550278 (449722) (TTA)n#Simple_repeat 1 39 (0) m_b312s252i18 13102 chr6qtel1M 550241 TTATTATTATTAAGGCTAATATTACTATT-TTATTATTA 550278 vvii v i - (TTA)n#Simple 1 TTATTATTATTATTATTATTATTATTATTATTATTATTA 39 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 365 30.32 7.56 2.21 chr6qtel1M 551529 551700 (448300) C L3#LINE/CR1 (430) 3669 3489 m_b312s601i12 13103 chr6qtel1M 551529 CTATTTACCCTCTTGTAGGTGCTCTCAAGATTATCAAAGTCATTCTAACA 551578 iv ii i i v i ii v v v i v vi v v C L3#LINE/CR1 3669 CTGGTCGCTCTCCTCTGGACGCGCTCCAGTTTGTCAATGTCCCTCTTAAA 3620 chr6qtel1M 551579 A---GGGGCACAGGAATTAATACAATACTTAAG-------CTGACCAGAG 551618 --- v v i v v ii iv ------- v C L3#LINE/CR1 3619 ATGTGGCGCCCAGAACTGAACGCAATACTCCAGATGTGGTCTGACCAGCG 3570 chr6qtel1M 551619 AAGACTATATTTGCTTGCCT-TTAA-TCTTTGGTCCTGGATGCTATTCCT 551666 v v i --- vv v - v- ii v ?i ii v i C L3#LINE/CR1 3569 CAGAGTACA---GCGGGACTATTACCTCCCTTGNTCTGGACACTATACTT 3523 chr6qtel1M 551667 C-ATTGAATATAGCCTAAGATCTCAGTAGTTGTTT 551700 - - ii iv v i v C L3#LINE/CR1 3522 CTATT-AATGCAGCCTAAGATTGCATTAGCTTTTT 3489 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 36.59 CpG sites = 25, Kimura (unadjusted) = 39.68 Transitions / transversions = 0.96 (25/26) Gap_init rate = 0.05 (9 / 171), avg. gap size = 1.89 (17 / 9) 30 35.89 1.59 0.00 chr6qtel1M 551735 551860 (448140) (TA)n#Simple_repeat 1 128 (0) m_b312s252i19 13104 chr6qtel1M 551735 TAAATATATAGATATAGATATATAGATGTCCACAAAT-TATATTCAGA-A 551782 v v v v i vi i v - vi v - (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr6qtel1M 551783 TGTGTATGTACATATATTTATACATTTATCTATATATGTGTGTGTGTGTG 551832 i i i i v i v v i i i i i i i (TA)n#Simple_ 51 TATATATATATATATATATATATATATATATATATATATATATATATATA 100 chr6qtel1M 551833 TGTGTGTACATATTTATAAACACATATA 551860 i i i i v v i i (TA)n#Simple_ 101 TATATATATATATATATATATATATATA 128 Matrix = Unknown Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.02 (2 / 125), avg. gap size = 1.00 (2 / 2) 506 20.57 0.81 5.93 chr6qtel1M 553492 553615 (446385) C MIRc#SINE/MIR (141) 127 10 m_b312s601i13 13105 chr6qtel1M 553492 CTGAGGC-AATTGGGGTTAAGTGACTTGCCCAGAGTCATACAGCTAGGAA 553540 -v vv i ii i v C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAA 78 chr6qtel1M 553541 GTGTTAAGTATCTGAGGCCAGATTTGAACTCGGGTCCTCCTGACTTCAGG 553590 ---- i --- v vi i i i i i i i C MIRc#SINE/MIR 77 GTG----GCA---GAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chr6qtel1M 553591 ACGAGTACTCTATCCACTTCACCAC 553615 v v i v v C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 23.20 CpG sites = 14, Kimura (unadjusted) = 24.32 Transitions / transversions = 1.40 (14/10) Gap_init rate = 0.07 (8 / 123), avg. gap size = 1.00 (8 / 8) 212 37.53 4.37 5.75 chr6qtel1M 556205 556433 (443567) C L2c_3end#LINE/L2 (9) 469 244 m_b313s601i0 13106 chr6qtel1M 556205 TTCAACAAACAATTATTCAACACTCAAGAACTTTGCTAACAACCAGGGAT 556254 v v i i ii vv -- v i ivvi ii C L2c_3end#LINE 469 TTCAACAAACATTTATTGAGCGCCTACTA--TGTGCCAGGCGCTGGGGAT 422 chr6qtel1M 556255 CAAAAGAAAGACAAAAGACATTATTGGCTCTTGACAACCACACAGTATAG 556304 vv vii i i v iv viiv i ii vi v v v C L2c_3end#LINE 421 ACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAG 372 chr6qtel1M 556305 TGCACAGTAAACA---ATGTGGAACAAAAGAGTTATTTACAGGATAAATT 556351 --v v i --- ? ------ v vi v iv i i C L2c_3end#LINE 371 TG--GAGGAGACAGACANGT------AAACAGACAATTACAATACAAGTT 330 chr6qtel1M 556352 GGTAATAGGTA--ATTAGGTAAATATTGAGA-AATGCTTC----TTATAG 556394 ii i i i-- v v vi i v v -ii vi----vi i C L2c_3end#LINE 329 AATGATAAGTGCTATAATGGGAGTATAGACAGGGTGCTATGGGAGCACAG 280 chr6qtel1M 556395 AAGATAGGATTTTAGCTGAGACTTGCAGGAAGTCAGAAA 556433 i vi v ii vii - ? -- ii ii C L2c_3end#LINE 279 AGGAGGGCACCTAGACT-AGNCTTG--GGGGGTCAGGGA 244 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 52.10 CpG sites = 47, Kimura (unadjusted) = 55.14 Transitions / transversions = 1.38 (47/34) Gap_init rate = 0.07 (17 / 228), avg. gap size = 1.35 (23 / 17) 219 31.88 10.14 2.52 chr6qtel1M 556379 556526 (443474) C L2a_3end#LINE/L2 (270) 247 89 m_b313s601i1 13106 chr6qtel1M 556379 GAAATGCTTCTTATAGAAGATAGGATTTTAGCTGAGACTTGCAGGAAGTC 556428 i v i ?ivv i iiv v vi i v i v C L2a_3end#LINE 247 GGAAGGCCTCNCTGAGAAGGTGACATTTGAGCAAAGACCTGAAGGAGGTG 198 chr6qtel1M 556429 AGAAAGC-AG--ATTTGGAGATT-----GAAAA-CATTCCAGTGATAGGG 556469 ii - -- vi v i----- i - i vv v C L2a_3end#LINE 197 AGGGAGCGAGCCATGCGGATATCTGGGGGAAGAGCGTTCCAGGCAGAGGG 148 chr6qtel1M 556470 GATAGCCAGT--AAAATCTATGGATTCTAGAGATCAGTGTCT----TGCT 556513 i i v -- iv iv iivi--- i v - i ---- i C L2a_3end#LINE 147 AACAGCAAGTGCAAAGGCCCTGAGGC---GGGAGC-GTGCCTGGCGTGTT 102 chr6qtel1M 556514 CATGGAAGAGCAA 556526 iv v C L2a_3end#LINE 101 CGAGGAACAGCAA 89 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 38.38 CpG sites = 26, Kimura (unadjusted) = 43.21 Transitions / transversions = 1.30 (26/20) Gap_init rate = 0.07 (10 / 147), avg. gap size = 1.90 (19 / 10) 446 24.20 0.73 9.52 chr6qtel1M 556576 556712 (443288) MIRb#SINE/MIR 5 130 (138) m_b313s601i2 13107 chr6qtel1M 556576 GGGGCAGCTAGATGATGCAGTAGATAGAGCACCAGCCCTGAAGTCAGGAA 556625 ---i i i v vi ii i iv MIRb#SINE/MIR 5 GGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACA 51 chr6qtel1M 556626 AGGACCTGAATTCAAATCTGGTTTCAGACACTTAACACTTCCTAGATGTG 556675 -- ii i iv vi v v ------- v MIRb#SINE/MIR 52 --GACCTGGGTTCGAATCCCGGCTCTGCCACTTA-------CTAGCTGTG 92 chr6qtel1M 556676 TAACCTTGGTCAAATGACTTGACCCCAATT-GCCTCAG 556712 i v i v i i vv v- MIRb#SINE/MIR 93 TGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAG 130 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 27.15 CpG sites = 17, Kimura (unadjusted) = 29.41 Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.10 (13 / 136), avg. gap size = 1.00 (13 / 13) 33 26.25 1.56 5.69 chr6qtel1M 556713 556840 (443160) (GAA)n#Simple_repeat 1 123 (0) m_b313s252i0 13108 chr6qtel1M 556713 GAAGAATAAGAA-AAAAAGGAGAGGAGGAGGGAGGAGGAAGAGAAAGGAG 556761 v - i i i i -i i i ii i (GAA)n#Simple 1 GAAGAAGAAGAAGAAGAAGAAGAAGAAGA-AGAAGAAGAAGAAGAAGAAG 49 chr6qtel1M 556762 AAGGAAGGGAGAAGATGGGAGGAGAGAGTAGGAGGAAGGAGGAGGAAG-A 556810 - - i -i i i - - i i - i i - (GAA)n#Simple 50 AA-GAA-GAAGAAGA-AGAAGAAGA-AG-AAGAAGAA-GAAGAAGAAGAA 93 chr6qtel1M 556811 GGAGGAGGAGAACAAGGAGAAGAAGAAGAA 556840 i i i v i (GAA)n#Simple 94 GAAGAAGAAGAAGAAGAAGAAGAAGAAGAA 123 Matrix = Unknown Transitions / transversions = 11.00 (22/2) Gap_init rate = 0.07 (9 / 127), avg. gap size = 1.00 (9 / 9) 44 15.47 3.64 3.64 chr6qtel1M 556729 556838 (443162) (AGG)n#Simple_repeat 1 110 (0) m_b313s252i1 13108 chr6qtel1M 556729 AGGA-GAGGAGGAGGGAGGAGGAAGAGAAAGGAGAAGGAAG-GGA-GAAG 556775 - - i -i i i - - i (AGG)n#Simple 1 AGGAGGAGGAGGA-GGAGGAGGAGGAG-GAGGAGGAGGAGGAGGAGGAGG 48 chr6qtel1M 556776 ATG-GGAGGAGAGAGTAGGAGGAAGGAGGAGGAAGAGGAGGAGGAGAACA 556824 v - - v - i i vi (AGG)n#Simple 49 AGGAGGAGGAG-GAGGAGGAGG-AGGAGGAGGAGGAGGAGGAGGAGGAGG 96 chr6qtel1M 556825 AGGAGAAGAAGAAG 556838 i i i (AGG)n#Simple 97 AGGAGGAGGAGGAG 110 Matrix = Unknown Transitions / transversions = 3.67 (11/3) Gap_init rate = 0.07 (8 / 109), avg. gap size = 1.00 (8 / 8) 12 29.26 0.00 0.00 chr6qtel1M 557539 557580 (442420) (TTTT)n#Simple_repeat 1 42 (0) m_b313s252i2 13109 chr6qtel1M 557539 TTGTTTGTTTGCTTTTTTCTCTCTATTTTTTTTTTCCTTTTT 557580 v v vi i i i v ii (TTTT)n#Simpl 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 42 Matrix = Unknown Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 381 27.45 2.94 0.00 chr6qtel1M 558440 558541 (441459) C MIRc#SINE/MIR (153) 115 11 m_b313s601i3 13110 chr6qtel1M 558440 GGGGTTAAGTGATTTGCCCCAATTAATA-AGTT-TTAAGAGTCTAGGCCA 558487 i i v iv v i - i -v v v vii i C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 66 chr6qtel1M 558488 G-ATTTGAACTTAGATCCTCCTGACTCCAAGACCACTGATCTATCTACTG 558536 - i i ii i i v v v v i C MIRc#SINE/MIR 65 GGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTG 16 chr6qtel1M 558537 CGCTA 558541 i i C MIRc#SINE/MIR 15 CACCA 11 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 32.11 CpG sites = 17, Kimura (unadjusted) = 35.17 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.03 (3 / 101), avg. gap size = 1.00 (3 / 3) 507 33.51 5.22 1.99 chr6qtel1M 559665 560200 (439800) C L1PB_orf2#LINE/L1 (1237) 2057 1505 m_b313s551i1 13111 chr6qtel1M 559665 TTTATTTTTTT-TCTTTTCTTATTGATATAGCCAAGATTTGTGATAAAAT 559713 i - v v v v i i i i viii vv C L1PB_orf2#LIN 2057 TTTATTTCTTTCTCTTGTCTGATTGCTCTGGCTAGGACTTCCAGTACTAT 2008 chr6qtel1M 559714 GTTGAGTAAAAGTGATTATAATAGGGTTCCTTGCTTCACCACAGATCTTA 559763 i? i i v v i i vv ii iiiiv v i C L1PB_orf2#LIN 2007 GTTGAANAGAAGTGGTGAGAGTGGGCATCCTTGTCTTGTTCCAGTTCTCA 1958 chr6qtel1M 559764 TTAAAAAGATTTCTAGCTTATTCCTATTATAGAA-AATGCTTGCTGATGG 559812 vviii vii ii i v i i -i v -? i v vv C L1PB_orf2#LIN 1957 GGGGGAATGCTTTCAACTTTTCCCCATT-CAGTATNATGTTGGCTGTGGG 1909 chr6qtel1M 559813 TTCCAAATATAAAATATTTATCTTTTGAAAGAAAGCTTAATTTATGCTTA 559862 ivvv v viiiv ivi? v i v v iiivv ? iv C L1PB_orf2#LIN 1908 TTTGTCATAGATGGCTTTTATTACNTTAAGGTATGTCCCTTNTATGCCGA 1859 chr6qtel1M 559863 TGTTTTCCTATGTTTTTAA----AATGCAAT--TGTATTTTATTTTAAAA 559906 - v iv v v ---- v vi -- v i i--- C L1PB_orf2#LIN 1858 T-TTTGCTGAGGGTTTTAATCATAAAGGGATGCTGGATTTTGTC---AAA 1813 chr6qtel1M 559907 AG--------GCATTTATTGAGATAATAACAACATTGTTGGTTTTG---T 559945 v -------- i i v iivv v v i---i C L1PB_orf2#LIN 1812 TGCTTTTTCTGCATCTATTGAGATGATCATGTGATTTTTGTTTTTAATTC 1763 chr6qtel1M 559946 TATTTATATGTTA-ATTATATTCATAG-TTTTTTTA-GTTTGAAACCAGC 559992 i i v i- i i i v -i viv - -- v C L1PB_orf2#LIN 1762 TGTTTATGTGGTGTATCACATTTATTGACTTGCGTATGTT--AAACCATC 1715 chr6qtel1M 559993 CCTACATTCCTGGTATAAACCACACTTTGTCATAATATATGATCCTTGTG 560042 i i i v v vi ii iv v i v C L1PB_orf2#LIN 1714 CCTGCATCCCTGGTATGAAACCCACTTGATCATGGTGGATTATCTTTTTG 1665 chr6qtel1M 560043 ATATACTGCTGTAATC--TTAA-TAGAATTTTATTTAAATTTTTTGTTAT 560089 i i v v -- i- v i v iiv ? -i C L1PB_orf2#LIN 1664 ATATGCTGTTGGATTCGGTTAGCTAGTATTTTGTTGAGGATTTTNG-CAT 1616 chr6qtel1M 560090 CAACATGAATTAGAGAAATTGGTCTGTAGTTTTTTTCCCCCCTTTTTGCC 560139 v ii vv i i v i iiii?v v vv C L1PB_orf2#LIN 1615 CTATGTTCATCAGGGATATTGGTCTGTAGTTTTCTTTTTTNGTTATGTCC 1566 chr6qtel1M 560140 TCTTCT--TTTTAAAGTATCAGCTCTGTATTAGTATTATAAAGGTAATTT 560187 i i -- --i i vvivi i i iv i i -i i C L1PB_orf2#LIN 1565 TTTCCTGGTTTT--GGTATTAGGGTGATACTGGCTTCATAGA-ATGATTT 1519 chr6qtel1M 560188 -GGTAGGACTCCTT 560200 - v i i C L1PB_orf2#LIN 1518 AGGGAGGATTCCCT 1505 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 45.87 CpG sites = 100, Kimura (unadjusted) = 46.61 Transitions / transversions = 1.32 (100/76) Gap_init rate = 0.04 (24 / 535), avg. gap size = 1.62 (39 / 24) 585 31.11 5.42 1.67 chr6qtel1M 559665 560125 (439875) C L1M5_orf2#LINE/L1 (1237) 2057 1580 m_b313s551i0 13111 chr6qtel1M 559665 TTTATTT-TTTTTCTTTTCTTATTGATATAGCCAAGATTTGTGATAAAAT 559713 - vi vvv i i i ii viii v C L1M5_orf2#LIN 2057 TTTATTTCTTTTTCTTGCCTTATTGCACTGGCTAGGACCTCCAGTACAAT 2008 chr6qtel1M 559714 GTTGAGTAAAAGTGATTATAATAGGGTTCCTTGCTTCACCACAGATCTTA 559763 i i i v ? iii ivv ii iiiiv v C L1M5_orf2#LIN 2007 GTTGAATAGAAGTGGTGANAGCGGACATCCTTGTCTTGTTCCCGATCTTA 1958 chr6qtel1M 559764 TTAAAAAGATTTCTAGCTTATTCCTATTATAGAAAATGCTTGCTGATGGT 559813 vviii iii? ii i? v iv i viv vi i ? vv C L1M5_orf2#LIN 1957 GGGGGAAAGCNTTCAGTNTTTCACCATTAAGTATGATGTTNGCTGTAGGT 1908 chr6qtel1M 559814 TCCAAATATAAAATATTTATC-TTTTGAAAGAAAGCTTAATT-TATGCTT 559861 iivvi v viviv -vv -- i i ivv - v i C L1M5_orf2#LIN 1907 TTTTCGTAGATGCCCTTTATCAGGTTGA--GGAAGTTCCCTTCTATTCCT 1860 chr6qtel1M 559862 ATGTTTTCCTAT-GTTTTTAAAATGCAATTG-TATTTTATTTTA--AAAA 559907 - v iv v- vv - v - i vv i-- v C L1M5_orf2#LIN 1859 A-GTTTGCTGAGAGTTTTTATCATG-AATGGGTGTTGAATTTTGTCAAAT 1812 chr6qtel1M 559908 G--------GCATTTATTGAGATAATAACAACATTGTTG------GTTTT 559943 -------- i i v i vv v v------i i C L1M5_orf2#LIN 1811 GCTTTTTCTGCATCTATTGAGATGATCATATGATTTTTCTCCTTTATTCT 1762 chr6qtel1M 559944 GTTATTTATATGTT-AATTATATTCATAGTTTTTTTAGTTTGAAACCAGC 559992 --- v - i v v v iv i v v i C L1M5_orf2#LIN 1761 GTTA---ATATGGTGAATTACATTGATTGATTTTCGAATGTTAAACCAAC 1715 chr6qtel1M 559993 CCTACATTCCTGGTATAAACCACACTTTGTCATAATATATGATCCTTGTG 560042 i i v v v i i v v v C L1M5_orf2#LIN 1714 CTTGCATTCCTGGGATAAACCCCACTTGGTCATGATGTATTATCCTTTTT 1665 chr6qtel1M 560043 ATATACTGCTGTAATC---TTAATAGAATTTTATTTAAATTTTTTGTTAT 560089 i v v --- iv iv i ? iiv -i C L1M5_orf2#LIN 1664 ATATATTGCTGGATTCGATTTGCTAATATTTTGTTNAGGATTTTTG-CAT 1616 chr6qtel1M 560090 CAACATGAATTAGAGAAATTGGTCTGTAGTTTTTTT 560125 v ii vv v i v i i C L1M5_orf2#LIN 1615 CTATGTTCATGAGGGATATTGGTCTGTAATTTTCTT 1580 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 40.34 CpG sites = 73, Kimura (unadjusted) = 41.52 Transitions / transversions = 1.07 (73/68) Gap_init rate = 0.04 (18 / 460), avg. gap size = 1.83 (33 / 18) 322 27.83 4.31 7.08 chr6qtel1M 562666 562781 (437219) C MIRc#SINE/MIR (153) 115 3 m_b313s601i4 13112 chr6qtel1M 562666 GAAGTTAAGTGATTTGCCCAA---CTGGGAAATGTTATGTGTCTAAAACT 562712 i i --- vviv iv iv v v vi iv v C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 66 chr6qtel1M 562713 GGATTTGAACTCAGGTTCTCCTGAG-CTAGATAGATAGAGCTAGTGCTCT 562761 i i i ii v- i ii -------- i C MIRc#SINE/MIR 65 GGACTCGAACCCAGGTCTTCCTGACTCCAAGT--------CCAGTGCTCT 24 chr6qtel1M 562762 ATCCACTGCACCAT-CTACCT 562781 v i- i C MIRc#SINE/MIR 23 TTCCACTGCACCACACTGCCT 3 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 34.19 CpG sites = 18, Kimura (unadjusted) = 35.67 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.10 (11 / 115), avg. gap size = 1.18 (13 / 11) 12 19.80 2.27 4.65 chr6qtel1M 562886 562929 (437071) (AATAA)n#Simple_repeat 1 43 (0) m_b313s252i3 13113 chr6qtel1M 562886 AATACATATAGAGTAGAAGAAAAGAGTAATAAAA-AAAATAAAAT 562929 - v i i i v v -v - (AATAA)n#Simp 1 AATA-AAATAAAATAAAATAAAATA-AAATAAAATAAAATAAAAT 43 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.07 (3 / 43), avg. gap size = 1.00 (3 / 3) 547 24.37 2.10 8.15 chr6qtel1M 562985 563127 (436873) MIRc#SINE/MIR 10 144 (124) m_b313s601i5 13114 chr6qtel1M 562985 GTGATATAGTGGATAAATTGTCAGGCCTGGAGTCTGAAAAACTCATCTTC 563034 i ii v i viiiii i i v i i -------- MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC-------- 51 chr6qtel1M 563035 CTGAGTTCAAATCCAGTGTCAAATATTTATTAGCTGTGTGAACCTTGGGC 563084 i i i v vv vivi i i - MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTG-ACCTTGGGC 100 chr6qtel1M 563085 AAGTCACTCAATC---CTAATTGCCTCAGTTTCCTTATCTGTAAAA 563127 i i --- i -- i MIRc#SINE/MIR 101 AAGTCACTTAACCTCTCTGA--GCCTCAGTTTCCTCATCTGTAAAA 144 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 29.66 CpG sites = 24, Kimura (unadjusted) = 30.83 Transitions / transversions = 3.00 (24/8) Gap_init rate = 0.08 (12 / 142), avg. gap size = 1.17 (14 / 12) 26 42.36 0.76 0.00 chr6qtel1M 564060 564190 (435810) (AT)n#Simple_repeat 1 132 (0) m_b313s252i4 13115 chr6qtel1M 564060 ATATATGTGTGTAGGTGTGTATGTATATATACATAAACACACACCCACAC 564109 i i i vi i i i i v i i i ivi i i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr6qtel1M 564110 ATATATAGGTAAGCATATGGATTTGCATATACATATATGTGTGTGCATAT 564159 vi vii iv v ii i i i i ii (AT)n#Simple_ 51 ATATATATATATATATATATATATATATATATATATATATATATATATAT 100 chr6qtel1M 564160 CTATATACATATATATGT-TGTATTTATAAAT 564190 v i i - i v v (AT)n#Simple_ 101 ATATATATATATATATATATATATATATATAT 132 Matrix = Unknown Transitions / transversions = 3.00 (30/10) Gap_init rate = 0.01 (1 / 130), avg. gap size = 1.00 (1 / 1) 402 32.45 6.87 3.66 chr6qtel1M 564417 564867 (435133) L1ME4c_3end#LINE/L1 3 467 (363) m_b313s551i2 13116 chr6qtel1M 564417 AATTTCTTTCAAATATATAGAGAACTGAGTCAAATTTAGAAGAAACAAGT 564466 v ? -- ? i i v v v v v ?i L1ME4c_3end#L 3 AATATCTNT--ANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANAT 50 chr6qtel1M 564467 CATT-CTCCACATA-----ATAGTCAATGCTTATGAAGAAGTACTTTTCA 564510 vv- i - ----- i v v vvi v iii v iv L1ME4c_3end#L 51 CAAGACCCCA-ATAGATAAATGGGCAAAGGACATGAACAGACAATTCACA 99 chr6qtel1M 564511 TACAAAGAAAT-CAA---------AGGTTTATGAAAAACTCTCCAAA-TC 564549 ? vi i - --------- iiivi i v v i v- L1ME4c_3end#L 100 NAAGAGGAAATACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTC 149 chr6qtel1M 564550 ACTATTGATCAGATTAATGAAAATTAAAAGAACTCTAAAGTATTATGTCA 564599 i v i i vv v iv vv i ii ii v i L1ME4c_3end#L 150 GCTAGTAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTA 199 chr6qtel1M 564600 TACATATCATATGGGCCAATACAAAAAAA---AAAAAAAAGAAAAGAATA 564646 ii v i v vi -------- --- vv v v viv L1ME4c_3end#L 200 CGCCTATTAAATTAGC--------AAAAATTTAAAAAATTGATAATACCC 241 chr6qtel1M 564647 AAAGTTGGTGGGAATGTAGGAAAACTGGGACACTAATGTACTGTCGGTAG 564696 v i i i i? ii vi v ? v ii i ii i L1ME4c_3end#L 242 AATGCTGGCGAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGG 291 chr6qtel1M 564697 AGTTGCTATCTGACCTAATCATTACAGAGAGCAATTTGAAATTATAC--- 564743 vi? iv vi iivi i v vii i iv -- --- L1ME4c_3end#L 292 CANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGGCA--ATACGTA 339 chr6qtel1M 564744 TCAAAATGCAACTAAATTTTGCATACTCTTTGATCCAGCAATACTATCGC 564793 i - v iv v v v i i i v i iiv L1ME4c_3end#L 340 TCAAGA-GCCATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTC 388 chr6qtel1M 564794 TAAGTCTATATCTCA---AAATAATTTTAAAAGGGGGAATTAGATCCATT 564840 ii vv v ii --- - i ii -- i v i v L1ME4c_3end#L 389 TGGGAATTTATCCTAAGGAAATAA-TTCAAAAGAAGGAA--AAAGCTATA 435 chr6qtel1M 564841 TGT-----GATATTTATAGCAGCTCTTTTTAT 564867 i----- i i v vi v L1ME4c_3end#L 436 TGCACGAAGATGTTCATTGCAGCGTTATTTAT 467 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 42.91 CpG sites = 78, Kimura (unadjusted) = 44.70 Transitions / transversions = 1.24 (78/63) Gap_init rate = 0.06 (26 / 450), avg. gap size = 1.85 (48 / 26) 497 32.86 5.63 3.51 chr6qtel1M 564428 564818 (435182) L1ME5_3end#LINE/L1 12 410 (531) m_b313s551i3 13116 chr6qtel1M 564428 AATATATAGAGAACTGAGTCAAATTTAGAAGAAACAAGTCATT--CTCCA 564475 i ii vvvv iv v - v iv?-- i L1ME5_3end#LI 12 AATATACAAGGAACTCCTGCAAATCAACAAGAAA-AAGACGGNAACCCCA 60 chr6qtel1M 564476 CATA-----ATAGTCAATGCTTATGAAGAAGTACTTTTCATACAAAGAAA 564520 - ----- i v v vv v i i v v v vi i L1ME5_3end#LI 61 -ATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAGGAAA 109 chr6qtel1M 564521 TC--AAAGGTT--------TATGAAAAACT-CTCCAAATCACTATTGATC 564559 i -- i -------- i iv - v v i v i L1ME5_3end#LI 110 CCCGAAAGGCTAACAAGCATATGAAGAGATGCTCAAACTCATTAGTAATC 159 chr6qtel1M 564560 AGATTAATGAAAATTAAAAGAACTCTAAAGTATTATGTCATACATATCAT 564609 vv v v vv i ii i iv i i v i v L1ME5_3end#LI 160 AGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCTATTAG 209 chr6qtel1M 564610 ATGGGCCAATACAAAAAA--AAAAAAAAAGAAAAGAATAAAAGTTGGTGG 564657 iv ------- -- i ivvi v vivi iv i i L1ME5_3end#LI 210 ACTGGC-------AAAAATTAGAAAGCTGGATAATGCCAAGTGTTGGCGA 252 chr6qtel1M 564658 GAATGTAGGAAAACTGGGACACTAATGTACTGTCGGTAGAGTTGCTATCT 564707 i i i ? iv i v v i ii i iiv iviv L1ME5_3end#LI 253 GGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACT 302 chr6qtel1M 564708 GACCTAATCATTACAGAGAGCAATTTGAAATTA--TACTCAAAATGCAAC 564755 iivi ii vii i iv v -- v v -- v L1ME5_3end#LI 303 GGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATT--AAG 350 chr6qtel1M 564756 TAAATTTTGCATACTCTTTGATCCAGCAATACTATCGCTAAGTCTATATC 564805 --- vi i v i v iiiiv ii v L1ME5_3end#LI 351 TA---TACGCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATATC 397 chr6qtel1M 564806 TCAAAATAATTTT 564818 i iv i L1ME5_3end#LI 398 CCAAAGAAATTCT 410 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 42.76 CpG sites = 68, Kimura (unadjusted) = 44.74 Transitions / transversions = 1.21 (68/56) Gap_init rate = 0.05 (21 / 390), avg. gap size = 1.71 (36 / 21) 435 34.39 3.04 3.67 chr6qtel1M 564530 564858 (435142) L1MB2_3end#LINE/L1 129 455 (463) m_b313s551i4 13116 chr6qtel1M 564530 TATGAAAAACT-CTCCAAATCACTATTGATCAGATTAATGAAAATTAAAA 564578 iv - v v v v i ivv v i L1MB2_3end#LI 129 TATGAAAAGATGCTCAACATCACTAATCATTAGGGAAATGCAAATCAAAA 178 chr6qtel1M 564579 GAACTCTAAAGTATTATGTCATACATATCATATGGGCCAATACAAAAAAA 564628 vv vv i ii i iv i vi i vivv i v iv L1MB2_3end#LI 179 CCACAATGAGATATCACCTCACACCCATTAGGATGGCTACTATCAAAAAA 228 chr6qtel1M 564629 AAAAAAAAGAAAAGAATAAAAGTTGGTGGGAATGTAGGAAAACTGGGACA 564678 v ----- v i iv i i i i ii i i v L1MB2_3end#LI 229 ACA-----GAAAATAACAAGTGTTGGCGAGGATGTGGAGAAATTGGAACC 273 chr6qtel1M 564679 CTAATGTACTGTCGGTAGAGTTGCTATCTGACCTAATCATTACAGAGAGC 564728 vi i i i iiv iv vv iivi ii ii ii i i L1MB2_3end#LI 274 CTTGTGCACTGTTGGTGGGAATGTAAAATGGTGCAGCCGCTATGGAAAAC 323 chr6qtel1M 564729 AATTTGAAATTATACTCAAAATGCAACTAAATTTTGCAT-ACTCTTTGAT 564777 i v iviv - v --- i vv v v - iv v L1MB2_3end#LI 324 AGTATGGCGGT-TCCTCAAAA---AATTAAAAATAGAATTACCATATGAT 369 chr6qtel1M 564778 CCAGCAATACTATCGCTAAGTCTATATCTCAAAATAATTTTAAAAGGGGG 564827 v i iiv ii v - v -- i vi L1MB2_3end#LI 370 CCAGCAATCCCACTTCTGGGTATATATC-CAAAAGAA--TTGAAAGCAGG 416 chr6qtel1M 564828 AATT---AGATCCATTTGTG-----ATATTTATAGCAGC 564858 ivi --- vvi ii----- i i L1MB2_3end#LI 417 GTCTCGAAGAGATATTTGCACACCCATGTTCATAGCAGC 455 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 45.74 CpG sites = 62, Kimura (unadjusted) = 47.56 Transitions / transversions = 1.32 (62/47) Gap_init rate = 0.05 (16 / 328), avg. gap size = 1.38 (22 / 16) 269 34.43 4.74 4.46 chr6qtel1M 565204 565583 (434417) L1P1_orf2#LINE/L1 2438 2818 (476) m_b313s551i5 13117 chr6qtel1M 565204 TAAAAATGACAATTCTACCTAAGTTAATTTGCTTATTCAATGTCATACCA 565253 i i v v i i v iivv i v v L1P1_orf2#LIN 2438 TGAAAATGGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCC 2487 chr6qtel1M 565254 ATCAAATTACCAATAACAT--TTTATAGAACTAGAAATTA-TAAAGAAAA 565300 ii i v -- i i i i vv - vvvv L1P1_orf2#LIN 2488 ATCAAGCTACCAATGACTTTCTTCACAGAATTGGAAAAAACTACTTTAAA 2537 chr6qtel1M 565301 ATTCATCTGGAAGAATTAAAAAATCAAGAATATCAAGGTAATTAATTTTT 565350 i v vv vv i ii viv viii vi ------- i L1P1_orf2#LIN 2538 GTTCATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAA-------TC 2580 chr6qtel1M 565351 TTAAATTGCAAAGA--AAAGT----GGCTTAGTAATATCAAAGCTCAAAC 565394 i iiii- -- i---- v viiiv i vi vi L1P1_orf2#LIN 2581 CTAAGCCA-AAAGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAAC 2629 chr6qtel1M 565395 TACATTATAAAG---AAGTAATCATCTAAACTATCTGATTCTAGTTTTAA 565441 i i i i ---v i --- viiv i v i vii L1P1_orf2#LIN 2630 TATACTACAAGGCTACAGTAACCA---AAACAGCATGGTACTGGTACCAA 2676 chr6qtel1M 565442 AATGGATTAGTTGATCAGTGGACTAGATTAGATACACAAGACATA--GTA 565489 ii vvvi v i vi vi vv viv v -- iv L1P1_orf2#LIN 2677 AACAGAGATATAGATCAATGGAACAGAACAGAGCCCTCAGAAATAACGCC 2726 chr6qtel1M 565490 GTATTTCTGGTCATAGTAACCTACTATTTTATAAA--TGCAAAGACCTAG 565537 i v ---- i iiv i iv v v i -- vi i v v L1P1_orf2#LIN 2727 GCATATCT----ACAACTATCTGATCTTTGACAAACCTGAGAAAAACAAG 2772 chr6qtel1M 565538 CTTTGGGGACAAGAATT--CTATTTAACAAAAAACTGCTGTGAAAACT 565583 vv - i -- i vii- v L1P1_orf2#LIN 2773 CAATGGGGA-AAGGATTCCCTATTTAATAAATGG-TGCTGGGAAAACT 2818 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 45.68 CpG sites = 68, Kimura (unadjusted) = 47.35 Transitions / transversions = 1.19 (68/57) Gap_init rate = 0.07 (25 / 379), avg. gap size = 1.40 (35 / 25) 313 24.44 3.65 1.43 chr6qtel1M 565206 565342 (434658) L1PREC2_orf2#LINE/L1 2440 2579 (715) m_b313s551i6 13117 chr6qtel1M 565206 AAAATGACAATTCTACCTAAGTTAATTTGCTTATTCAATGTCATACCAAT 565255 i v v i i ivi i vv ii v v L1PREC2_orf2# 2440 AAAATGGCCATACTGCCCAAAGCAATTTACAGATTCAATGCTATTCCTAT 2489 chr6qtel1M 565256 CAAATTACCAATAACAT--TTTATAGAACTAGAAATTA-TAAAGAAAAAT 565302 i i -- i i vv - vvvv L1PREC2_orf2# 2490 CAAACTACCAATGACATTCTTCACAGAACTAGAAAAAACTATTTTAAAAT 2539 chr6qtel1M 565303 TCATCTGGAA-GAATTAAAAAATCAAGAATA-TCAAGGTAAT 565342 v -v -- i v vv -i i L1PREC2_orf2# 2540 TCATATGGAACCAA--AAAAGAGCCCGAATAGCCAAGGCAAT 2579 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 29.72 CpG sites = 15, Kimura (unadjusted) = 29.72 Transitions / transversions = 0.83 (15/18) Gap_init rate = 0.04 (6 / 136), avg. gap size = 1.17 (7 / 6) 185 21.61 4.29 14.06 chr6qtel1M 565813 565882 (434118) C MIR#SINE/MIR (108) 154 91 m_b313s601i6 13118 chr6qtel1M 565813 TATTGTTATCCTCATCATTATTTTTTACAAGAGAGGAAACTGAGGGAGAC 565862 i i -------- iiv v v v C MIR#SINE/MIR 154 TATTATTATCCCCAT--------TTTACAGATGAGGAAACTGAGGCACAG 113 chr6qtel1M 565863 AAAATTTTAAGTG---TGCCTAA 565882 i i-v i--- i C MIR#SINE/MIR 112 AGAG-GTTAAGTAACTTGCCCAA 91 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 25.58 CpG sites = 8, Kimura (unadjusted) = 25.58 Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.14 (10 / 69), avg. gap size = 1.20 (12 / 10) 16 16.97 0.00 0.00 chr6qtel1M 566642 566674 (433326) (ATTT)n#Simple_repeat 1 33 (0) m_b313s252i5 13119 chr6qtel1M 566642 ATTTATTTTTTTAACTATTTTGTTATTTATTTA 566674 v vi vv (ATTT)n#Simpl 1 ATTTATTTATTTATTTATTTATTTATTTATTTA 33 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 1299 30.11 1.79 1.79 chr6qtel1M 567134 567691 (432309) C L1ME4a_3end#LINE/L1 (232) 639 82 m_b313s551i7 13120 chr6qtel1M 567134 CCTGCTCATTTCACTCAGCATCAGTTCATGTAAGTCTCTCCAGGCCTTTC 567183 iv i i i vv vivi i ii v i v - C L1ME4a_3end#L 639 CCTGCTTTTTTCACTTAACATTATATCATGAGCATTTTCCCATGTCATT- 591 chr6qtel1M 567184 TGAACCTTTCT--GAAATCA-CATTTCTTACAGA-ACAGTAATATTCCAT 567229 -- viv -- v -? i v ii v-i - C L1ME4a_3end#L 590 --AAATATTCTTCGAAAACATNATTTTTAATGGCTGCA-TAATATTCCAT 544 chr6qtel1M 567230 AATATTCATATACCACAATTTATTCAGCCATTCTCCAACTGATGGGCATC 567279 v? vv i i i i ? i v i v i i C L1ME4a_3end#L 543 TNTATGGATGTACCATAATTTATTTAACCANTCCCCTATTGTTGGACATT 494 chr6qtel1M 567280 CATTCAGTTTCCAGTTTCTAGCCACTACAAAGAGGCCTGCCACAAACATT 567329 i vviv i i v i i i v ivv v ii i C L1ME4a_3end#L 493 TAGGTTGTTTCCAATTTTTCGCTATTATAAATAATGCTGCGATGAACATC 444 chr6qtel1M 567330 TGTGCACATACAGGTCCCTTTCCCTTTTTTATAATCTCTTTGGGATATAA 567379 iv i v vv iiv ?iv v i i v v i i i v v C L1ME4a_3end#L 443 CTTGTACATAAATCTTTGTNCACATCTCTGATTATTTCCTTAGGATAAAT 394 chr6qtel1M 567380 GCCCAGTAGTAACACTGCTGGATCAAAGGATATGCACGGTTTGATAACTT 567429 v i v iiv i i i i ? iv v vii C L1ME4a_3end#L 393 TCCTAGAAGTGGAATTACTGGGTCAAAGGGTATGNACATTTTTAAGGCTT 344 chr6qtel1M 567430 TTTGAGCATAGTTCCAAACTACTCTCCAAAATGGTTGGATTTGTTCACAA 567479 vivi v v i i i i v v iivi i v C L1ME4a_3end#L 343 TTGATACATATTGCCAAATTGCCCTCCAGAAAGGTTGTACCAATTTACAC 294 chr6qtel1M 567480 CTCCACCAACAATGCATCAATGTCCCAGTTTTCCCACATCCCCTCCAACA 567529 ii i i i v iv v v i? i i v C L1ME4a_3end#L 293 TCCCACCAGCAGTGTATGAGAGTGCCCGTTTCNCCACACCCTCGCCAACA 244 chr6qtel1M 567530 ------ATCATCATTATTTTTTCCTGTCATCTTAGCCAATCTGACAGGTG 567573 ------ i -- i vv---- v i i C L1ME4a_3end#L 243 CTGGGTATTATCA--ATCTTTTAA----ATCTTTGCCAATTTGATAGGTG 200 chr6qtel1M 567574 TGTAGTGGTATCTTAGAGTTGTCTTAATTTGCATTTCTCTGATTAATAAT 567623 viv i i vv i i v i C L1ME4a_3end#L 199 AAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCTTTGATTACTAGT 150 chr6qtel1M 567624 GACTTGGAGCATCTTTTCGTATGACTAGAAATAGTTTCAATTTCTTCATC 567673 vv v i ? i vi vviiivi vv v i C L1ME4a_3end#L 149 GAGGTTGAACATNTTTTCATATGTTTATTGGCCATTTGTATTTCTTCTTT 100 chr6qtel1M 567674 TGAGAATTGTCTGTTCAT 567691 v C L1ME4a_3end#L 99 TGTGAATTGTCTGTTCAT 82 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 40.04 CpG sites = 91, Kimura (unadjusted) = 40.04 Transitions / transversions = 1.23 (91/74) Gap_init rate = 0.03 (14 / 557), avg. gap size = 1.43 (20 / 14) 1414 26.86 2.74 3.40 chr6qtel1M 567219 567692 (432308) C L1ME5_3end#LINE/L1 (390) 551 81 m_b313s551i8 13120 chr6qtel1M 567219 TAATATTCCATAATATTCATATACCACAATTTATTCAGCCATTCTCCAAC 567268 i i ii i v vi v iii v i v v C L1ME5_3end#LI 551 TAGTACTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCAG 502 chr6qtel1M 567269 TGATGGGCATCCATTCAGTTTCCAGTTTCTAGCCACTACAAAGAGGCCTG 567318 i i vviv ii ii i iv i v ivv C L1ME5_3end#LI 501 TGATGGACACCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCTG 452 chr6qtel1M 567319 CCACAAACATTTGTGCACATACAGGTCCCTTTC----CCTTTTTTATAAT 567364 v ii i---- v i v i v---- v v v v C L1ME5_3end#LI 451 CAATGAACATC----CTCGTACATGTCCCCTTATGGACCTGTGTGAGAAT 406 chr6qtel1M 567365 CTCTTTGGGATATAAGCCCAGTAGTAACACTGCTGGATCAAAGGATATGC 567414 i vi v iiiv i i v i C L1ME5_3end#LI 405 TTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATGC 356 chr6qtel1M 567415 ACGGTTTGATAACTT--TTTGAGCA--TAGTTCCAAACTACTCTCCAAAA 567460 --- --- - -- vi -- v v i i i i C L1ME5_3end#LI 355 ---GT---ATA-CTTAATTTGACTAAGTACTGCCAGATTGCTCTCCAGAA 313 chr6qtel1M 567461 TGGTTGGATTTGTTCACAACTCCACCAACAATGCATCAATGTCCCAGTTT 567510 i v iiv ii vii i i v iv i vi ? C L1ME5_3end#LI 312 TGGCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATNT 263 chr6qtel1M 567511 TCCCACATCCCCTCCAACAATCATCATTATTT--TTTCCTGTCATCTTAG 567558 i i v v iiv ii--i i i-- i v C L1ME5_3end#LI 262 CCCCACATCCTCGCCAACACTTGGCATTATCCAGCTTTCTA--ATTTTTG 215 chr6qtel1M 567559 CCAATCTGACAGGTGTGTAGTGGTATCTTAGAGTTGTCTTAATTTGCATT 567608 i i i iv i i vv i C L1ME5_3end#LI 214 CCAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATT 165 chr6qtel1M 567609 TCTCTGATTAATAATGACTTGGAGCATCTTTTCGTATGACTAGAAATAG- 567657 v v v i i - v --v - C L1ME5_3end#LI 164 TCTCTGATTACTAATGAGTTTGAGCATCTCTTCATATG-CTTG--TTAGC 118 chr6qtel1M 567658 -TTTC-AATTTCTTCATCTGAGAATTGTCTGTTCATA 567692 - -ii i v vi i C L1ME5_3end#LI 117 CTTTCGGGTTTCCTCTTCTGTAAATTGCCTGTTCATA 81 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 33.56 CpG sites = 75, Kimura (unadjusted) = 34.29 Transitions / transversions = 1.56 (75/48) Gap_init rate = 0.05 (23 / 473), avg. gap size = 1.26 (29 / 23) 450 22.40 7.27 2.61 chr6qtel1M 568384 568493 (431507) MIRc#SINE/MIR 1 115 (153) m_b313s601i7 13121 chr6qtel1M 568384 CAAGGCAGCTAGGTGGTACAGTGGATAAAGCACCAGCCCTGAAGTCAGAA 568433 i i--- i v i ii v i i i MIRc#SINE/MIR 1 CGAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGA 47 chr6qtel1M 568434 GGACCTGAGTTCAAAT-CTAGC-------CTAGCTAGATGTATGATCCTG 568475 i i i i - ii ------- vi v i i i MIRc#SINE/MIR 48 AGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTG 97 chr6qtel1M 568476 GGCAAGTCACTTAACCCC 568493 i MIRc#SINE/MIR 98 GGCAAGTCACTTAACCTC 115 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 24.17 CpG sites = 20, Kimura (unadjusted) = 28.43 Transitions / transversions = 5.00 (20/4) Gap_init rate = 0.05 (5 / 109), avg. gap size = 2.20 (11 / 5) 27 16.61 0.00 0.00 chr6qtel1M 568506 568552 (431448) (A)n#Simple_repeat 1 47 (0) m_b313s252i6 13122 chr6qtel1M 568506 AAAAATTAAAAAAAATGAACAAAAAAAAAAAAAAAAAAAAAGCAAAA 568552 vv vi v iv (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 47 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 15 15.28 0.00 5.26 chr6qtel1M 569051 569090 (430910) (AAACAA)n#Simple_repeat 1 38 (0) m_b313s252i8 13123 chr6qtel1M 569051 AAACAAAAACAAAAAGAAAAAAACAGAAGAAAATGCAAAA 569090 v v - i v -i (AAACAA)n#Sim 1 AAACAAAAACAAAAACAAAAACA-AAAACAAAA-ACAAAA 38 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 16 20.94 0.00 0.00 chr6qtel1M 569051 569083 (430917) (A)n#Simple_repeat 1 33 (0) m_b313s252i7 13123 chr6qtel1M 569051 AAACAAAAACAAAAAGAAAAAAACAGAAGAAAA 569083 v v i v i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 33 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 314 34.17 2.34 3.97 chr6qtel1M 569756 569883 (430117) MIRb#SINE/MIR 22 147 (121) m_b313s601i8 13124 chr6qtel1M 569756 TGGAAAGAAGAGTTATTTTGGAGTTAGAAAAAAAAAAAGGTTCAGATTCT 569805 iv vvvii i -- v i vvvi ii i i MIRb#SINE/MIR 22 TGGAAAGAGCACGGGCTTTGGAGTCAG--ACAGACCTGGGTTCGAATCCC 69 chr6qtel1M 569806 GGCTTTCCTCATTACTGTCCATATTATTTTAGGCAA---ATTTAATCTCT 569852 i v ivv iv ii i v ii i --- i i MIRb#SINE/MIR 70 GGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCT 119 chr6qtel1M 569853 CATTTAATCTTCACTTTCATCACCTAAAAAA 569883 --- i v i v v i iv MIRb#SINE/MIR 120 C---TGAGCCTCAGTTTCCTCATCTGTAAAA 147 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 44.32 CpG sites = 25, Kimura (unadjusted) = 47.43 Transitions / transversions = 1.47 (25/17) Gap_init rate = 0.05 (6 / 127), avg. gap size = 1.33 (8 / 6) 19 36.95 2.16 2.90 chr6qtel1M 571266 571404 (428596) (GAAAA)n#Simple_repeat 1 138 (0) m_b313s252i9 13125 chr6qtel1M 571266 GAAAGGAAAGAGAAAATAAGAGAAGGGGGAGAAAAAGAAAAG-GAAGAAC 571314 i - v i ii ii ii -i v (GAAAA)n#Simp 1 GAAAAGAAA-AGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAA 49 chr6qtel1M 571315 AGAGGCAGAGAACAGGGGAAAAGAGGAGGGAAGGGGAAAG-AGATCAGAG 571363 -iv i v iii -- ii ii i - i vv i (GAAAA)n#Simp 50 AGA-AAAGAAAAGAAAAGAAAAGA--AAAGAAAAGAAAAGAAAAGAAAAG 96 chr6qtel1M 571364 AAATTAACTGAAAA-AGGAAAAGAGAAAAGGAAAGAAAATAA 571404 vv vv - ii i i i v (GAAAA)n#Simp 97 AAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAA 138 Matrix = Unknown Transitions / transversions = 2.36 (26/11) Gap_init rate = 0.05 (7 / 138), avg. gap size = 1.00 (7 / 7) 268 34.21 1.65 3.36 chr6qtel1M 573083 573203 (426797) C L2b_3end#LINE/L2 (28) 438 320 m_b313s601i9 13126 chr6qtel1M 573083 GCACTTATTGGTGTAACAGTCACTTTGCTAAATG-TGGTGAGACAAAAAA 573131 i i i - iv v ? v iii - v v ivi-- C L2b_3end#LINE 438 GCGCCTACTG-TGTGCCAGGCNCTGTGCTAGGCGCTGGGGATACAGCG-- 392 chr6qtel1M 573132 AGCAAAAAACAAAAACCCAAAGCCTGTTATCAAGAAACTTTCAGTCTAAT 573181 - ii v v v i ? iivv iiv v i i iv i C L2b_3end#LINE 391 -GTGAACAAGACAGACNCGGTCCCTGCCCTCACGGAGCTCACAGTCTAGT 343 chr6qtel1M 573182 GGGATAGGCA-ACATGCAAATGG 573203 iv i - i ?ii C L2b_3end#LINE 342 GGGGGAGACAGACATGTAANCAG 320 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 43.00 CpG sites = 25, Kimura (unadjusted) = 49.85 Transitions / transversions = 1.67 (25/15) Gap_init rate = 0.05 (6 / 120), avg. gap size = 1.00 (6 / 6) 275 37.13 6.79 5.99 chr6qtel1M 573958 574487 (425513) C L2#LINE/L2 (124) 2958 2425 m_b313s601i10 13126 chr6qtel1M 573958 AATGGTGGGGAATGGGGTTTAGGAAGATGGAAATGTGGCAAGAGAGTTAA 574007 i i ii i i- ii i --- i v v vv -- v C L2#LINE/L2 2958 AGTGGTAGGAGATGAGGTC-AGAGAGGT---AACGGGGGACCAGA--TCA 2915 chr6qtel1M 574008 TGAAGGACTTTG-AATCCA--GACAGTACATCATATATTTGATTTTCAAT 574054 v i i - iv -- vv v v -- ivv v i i v i C L2#LINE/L2 2914 TGTAGGGCCTTGTAGGCCATTGTAAGGACTT--TGGCTTTTACTCTGAGT 2867 chr6qtel1M 574055 GTAATAGGGAGTAATTGTAG---TTTAAATAAAAGGGTTGTTCATAAGAT 574101 vi i i iv v --- i ii i i i ----v i v C L2#LINE/L2 2866 GAGATGGGAAGCCATTGGAGGGTTTTGAGCAGAGGAGT----GACATGAT 2821 chr6qtel1M 574102 CAGACC--------AGGACCATCAGTTTAACAGATGAGTGGAGAATGGAT 574143 v i-------- ii vv v i ii v v v v i i C L2#LINE/L2 2820 CTGACTTACGTTTTAAAAGGATCACTCTGGCTGCTGTGTTGAGAATAGAC 2771 chr6qtel1M 574144 TAGAATGGGGAGAGATTTAAATCAGGTAAACTAGCTAGCAGTCTATGACA 574193 i? iv vi iv vi v v i i i v v vi C L2#LINE/L2 2770 TGNAGGGGGGCAAGGGTGGAAGCAGGGAGACCAGTTAGGAGGCTATTGCA 2721 chr6qtel1M 574194 TTTGTCTGGGCATGAGATAATCATGACCTGGACGAATGTGTTAGAAATGT 574243 v vi ii iv i vi i i v iv v i v i - C L2#LINE/L2 2720 GTAATCCAGGCGAGAGATGATGGTGGCTTGGACCAGGGTGGTGGCAGTG- 2672 chr6qtel1M 574244 CAAAATA--GAGAAGAGGGAATATGTAAGACATGATACAGAGGAAAAATT 574291 -i ii i-- v vviv vivi i iv viii v i iii C L2#LINE/L2 2671 -GAGGTGGTGAGAAGTGGTCGGATTCTGGATATATTTTGAAGGTAGAGCC 2623 chr6qtel1M 574292 AGAAGGATTTGGCAATG--------ATGGTG-GTCAGAAAAAGTGTGAAG 574332 iiv vii --------i v - v i v v i C L2#LINE/L2 2622 GACAGGATTTGCTGATGGATTGGATGTGGGGTGTGAGAGAAAGAGAGGAG 2573 chr6qtel1M 574333 TCAA----AACTTGA--GTTTTAATCTTGAGTGACAAGGAAGATGTTTGC 574376 ----i iv -- viv i ii vi i i ----- C L2#LINE/L2 2572 TCAAGGATGACTCCAAGGTTTTTGGCCTGAGCAACTGGAAGGATG----- 2528 chr6qtel1M 574377 AGTGTTAACAATAAC-AAAAGGGCAGCTAGGTGGAGCAAGGGATTGAGTA 574425 - v iv v ? -i i v ------ vi viiv ---- v C L2#LINE/L2 2527 -GAGTTGCCATTNACTGAGATGG------GGAAGACTGCGG----GAGGA 2489 chr6qtel1M 574426 GCAGTCCTGAAGTCAGGAGGACC-TGAGTTCAACTCCAGGCTTA-GAAAT 574473 vii i --i i i -v ii iii i v i-v i C L2#LINE/L2 2488 GCAGGTTTGAGG--GGGAAGATCAGGAGTTCAGTTTTGGACATGTTAAGT 2441 chr6qtel1M 574474 TTGACATG--TATTAG 574487 v -- C L2#LINE/L2 2440 TTGAGATGCCTATTAG 2425 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 52.17 CpG sites = 108, Kimura (unadjusted) = 53.96 Transitions / transversions = 1.40 (108/77) Gap_init rate = 0.09 (45 / 529), avg. gap size = 1.51 (68 / 45) 412 23.50 2.27 9.76 chr6qtel1M 574397 574528 (425472) MIRc#SINE/MIR 4 126 (142) m_b313s601i11 13127 chr6qtel1M 574397 GGCAGCTAGGTGGAGCAAGGGATTGAGTAGCAGTCCTGAAGTCAGGAGGA 574446 i--- v iv vv i vii v i i i MIRc#SINE/MIR 4 GGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA 50 chr6qtel1M 574447 CCTGAGTTCAACTCCAGGCTTAGAAATTTGACATGTATTAGCTGTGTGAC 574496 i i v v ------- i v iv i MIRc#SINE/MIR 51 CCTGGGTTCGAGTCCCGGC-------TCTGCCACTTACTAGCTGTGTGAC 93 chr6qtel1M 574497 CCTGAGCAAGTCATTCAACC---CTGACTGCCTTA 574528 i i i i --- -- i MIRc#SINE/MIR 94 CTTGGGCAAGTCACTTAACCTCTCTGA--GCCTCA 126 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 27.53 CpG sites = 18, Kimura (unadjusted) = 28.73 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.10 (13 / 131), avg. gap size = 1.15 (15 / 13) 12 16.04 0.00 3.45 chr6qtel1M 574798 574827 (425173) (AAGAA)n#Simple_repeat 1 29 (0) m_b313s252i10 13128 chr6qtel1M 574798 AAGCAAAGAAAATAATATAAAAGGAAAAGA 574827 v v v v - (AAGAA)n#Simp 1 AAGAAAAGAAAAGAAAAGAAAA-GAAAAGA 29 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 15 14.69 5.26 0.00 chr6qtel1M 578440 578477 (421523) (TTAAT)n#Simple_repeat 1 40 (0) m_b313s252i12 13129 chr6qtel1M 578440 TTAATTGTTTTTTTTTTAATTT-ATTT-ATTTAATTTAAT 578477 vvv vv - - (TTAAT)n#Simp 1 TTAATTTAATTTAATTTAATTTAATTTAATTTAATTTAAT 40 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 49 10.68 0.00 0.00 chr6qtel1M 578620 578690 (421310) (A)n#Simple_repeat 1 71 (0) m_b313s252i13 13130 chr6qtel1M 578620 AAATAAAAAAATAAAATAAAATAAAAAATAAAAAAAATAAAAAAAAAAAA 578669 v v v v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chr6qtel1M 578670 AAAAAAAAAAAAAAAAACAAA 578690 v (A)n#Simple_r 51 AAAAAAAAAAAAAAAAAAAAA 71 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0) 304 30.86 8.24 2.07 chr6qtel1M 579012 579193 (420807) C L1ME4c_3end#LINE/L1 (255) 575 383 m_b313s551i9 13131 chr6qtel1M 579012 TCATCATTGTTTATAGA-GCAATAATATTCCATTACCTACATATATCATA 579060 i v v i v- - iivv ?v i i C L1ME4c_3end#L 575 TTATCATTTTTAATGGCTGCA-TAATATTCCATCGAGTNGATGTACCATA 527 chr6qtel1M 579061 ACTTGCTCAGACACTTCCCAATTGACAGATATCTACTCAGTTTTTGATTC 579110 i i i iv i i v vii i i vviv iii i C L1ME4c_3end#L 526 ATTTACTTAACCATTCCCCTATTGTTGGACATTTAGGTTGTTTCCAATTT 477 chr6qtel1M 579111 TTTGTTAC-----------CTGCAACAAACATTTGTGCACATATGGGTTC 579149 i i i----------- ii i vi ii i --- C L1ME4c_3end#L 476 TTCGCTATTATAAATAACGCTGCAATGAACATCTTCGTGCATATAG---C 430 chr6qtel1M 579150 TTTTCCCTCCTTT---ATGTTTTCCTTGGTATACAAACCCAGTAATG 579193 i i --- vv i v v vv v i C L1ME4c_3end#L 429 TTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAATTCCCAGAAGTG 383 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 38.80 CpG sites = 35, Kimura (unadjusted) = 41.92 Transitions / transversions = 1.75 (35/20) Gap_init rate = 0.04 (7 / 181), avg. gap size = 2.71 (19 / 7) 961 33.44 4.60 2.71 chr6qtel1M 579260 580129 (419871) C L1PREC2_orf2#LINE/L1 (584) 2710 1825 m_b313s551i10 13132 chr6qtel1M 579260 TTTCTAATCTATTCTACTGATCTACCATCCTATTTCTTAGCCTGTTCTAA 579309 i v i i i i ivvvi i i vvi v v i v C L1PREC2_orf2# 2710 TCTCTATTCTGTTCCATTGGTCTATGTGTCTGTTTTTGTACCAGTACCAT 2661 chr6qtel1M 579310 ATGGTTCTGATGGCTAATGCTTTATAATAGAGTTTTAGGTCTGGTACTAC 579359 iiv i i vi ivv ii i i v v i v viii C L1PREC2_orf2# 2660 GCTGTTTTGGTTACTGTAGCCCTGTAGTATAGTTTGAAGTCGGGTAGCGT 2611 chr6qtel1M 579360 TAGACCACGATCCTTTGTAAAAATTTTTTTTGTT--AAAT--CCCTGGAA 579405 v vi v v -v ------ i i --ii -- i vv C L1PREC2_orf2# 2610 GATGCCTCCA-GCTTTGT------TCTTTTTGCTTAGGATTGCCTTGGCT 2568 chr6qtel1M 579406 ATTCTTGACCCTTTCTAGGT-------GAATTTTA---TTGTTATTTTTC 579445 v- i i i v ------- --- v -- C L1PREC2_orf2# 2567 ATTCG-GGCTCTTTTTTGGTTCCATATGAATTTTAAAATAGTT--TTTTC 2521 chr6qtel1M 579446 TGGCTCTATAAGAAAAAATTTTTGGCAGTTTGATTGTTTTGGTATTGAAT 579495 i i i i - i vi iv i v vvv i i C L1PREC2_orf2# 2520 TAGTTCTGTGA-AGAATGTCATTGGTAGTTTGATAGGAATAGCATTGAAT 2472 chr6qtel1M 579496 AAGTAGACCAATTTAGTCAGATTTGTCACTTTTATTATATATATTAGGTT 579545 vv i iiiv i v vv v i i v iv vv --v C L1PREC2_orf2# 2471 CTGTAAATTGCTTTGGGCAGTATGGCCATTTTAACGATATTGATT--CTT 2424 chr6qtel1M 579546 GGCCTACCCAGGAGCAATTGATATTTTTCTAATTGTTTAGATGGGAACTC 579595 -- i v vvvi i i v i-- vv v C L1PREC2_orf2# 2423 --CCTATCCATGAGCATGGAATGTTTTTCCATTTGTTTG--TGTCATCTC 2378 chr6qtel1M 579596 --ATTTGTGTAAGAAGTGGTCTATAATTTTGTTCAAATAGTTCTTGGGTT 579643 -- v v i v v i i i vv iiv v v vviii C L1PREC2_orf2# 2377 TGATTTCTTTGAGCAGTGTTTTGTAATTCTCATTGTAGAGATCTTTCACC 2328 chr6qtel1M 579644 TGGCTTGTCAGGTAGACAACTATATATTTTATTTTATCTATAATTATTTA 579693 vv v i v iv ivv vi i v i i iiiv vv C L1PREC2_orf2# 2327 TCCCTGGTTAGCTGTATTCCTAGGTATTTTATTCTTTTTGTGGCAATTGT 2278 chr6qtel1M 579694 AAATGGAATT---TCCCTT-TTTATCTCTTGCTGATGGGCT-TTGTTAGT 579738 i i --- i v- iv i -- v v - i C L1PREC2_orf2# 2277 GAATGGGATTGCGTTCCTGATTTGGCTCTCG--GCTTGGCTGTTGTTGGT 2230 chr6qtel1M 579739 AATATTTAGAAATGCTGAAGATTTGTGTGTGTTTATTTTATATCCTGTAA 579788 i- -- i iiv v iii v i v C L1PREC2_orf2# 2229 G-TAT--AGGAATGCTAGTGATTTTTGTACATTGATTTTGTATCCTGAAA 2183 chr6qtel1M 579789 CTTTGCTAAAGTTGATTGT-ATCCAATGGGTTTTTTGA--TGATTTTCTA 579835 i v i - v i? v ivi i--i vvi v i C L1PREC2_orf2# 2182 CTTTGCTGAAGTTGTTTATCAGCTNAAGGAGCTTTTGGGCCGAGACTATG 2133 chr6qtel1M 579836 GGATGCTCTATAT-T---ATCATATCATCTACAAAGAGTGATAGTTTTAT 579881 i vi v - --- i i i v v v i C L1PREC2_orf2# 2132 GGGTTTTCTAGATATAGAATCATGTCGTCTGCAAACAGGGATAGTTTGAC 2083 chr6qtel1M 579882 CTCCATATTACTTATT---------CTAATTTCTTTTTCTTTTCTTTTTG 579922 i vivi v i ---------i v i vi vv C L1PREC2_orf2# 2082 TTCCTCTCTTCCTATTTGGATGCCCTTTATTTCTTTCTCTTGCCTGATTG 2033 chr6qtel1M 579923 CCAAAGCCAACATTTCTAGTACAATATTGTATAATAGTGGTGATGATGGG 579972 ivvi iv i i i v i v iv viiv C L1PREC2_orf2# 2032 CTCTGGCCAGGACTTCCAATACTATGTTGAATAGGAGTGGTGAGAGAGGG 1983 chr6qtel1M 579973 CATTCTTATTTCATCCCTGTTCTT-ATAAGAATACATCCATCTTCTCTCC 580021 i i i ii v v i i- vii i v v i vi C L1PREC2_orf2# 1982 CATCCTTGTCTTGTGCCGGTTTTCAAGGGGAATGCTTCCAGCTTTTGCCC 1933 chr6qtel1M 580022 ATTACAA-ATAGTGTTGGTTGTTTGTTTTAGATAGATACTGCTTATTATT 580070 - i- ii i vv vvv iviv C L1PREC2_orf2# 1932 ATT-CAGTATGATGTTGGCTGTGGGTTTGTCATAGATGGCTCTTATTATT 1884 chr6qtel1M 580071 TCAAGAAAAGCTCCCTTGATCCCTATGCTT-TCTAGTGTTTTTAATAAGA 580119 ii iv v i i ii v - i - iv v i v C L1PREC2_orf2# 1883 TTGAGGTATGTTCCTTCAATACCTA-GTTTATTGAGAGTTTTTAACATGA 1835 chr6qtel1M 580120 ATGGGTGCTG 580129 v i i C L1PREC2_orf2# 1834 AGGGATGTTG 1825 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 44.33 CpG sites = 152, Kimura (unadjusted) = 45.44 Transitions / transversions = 1.16 (152/131) Gap_init rate = 0.05 (40 / 869), avg. gap size = 1.60 (64 / 40) 501 29.84 2.75 2.75 chr6qtel1M 580120 580374 (419626) L1ME4b_3end#LINE/L1 315 569 (323) m_b313s551i11 13133 chr6qtel1M 580120 ATGG-GTGCTGTTTGGAAGTATG-ATCAAAAAGTTTTCAAACTGTGCATA 580167 - v vi v i v- --- v - ii L1ME4b_3end#L 315 ATGGAGGGCAATTTGGCAATATCTATCAAAA---TTACAAA-TGCACATA 360 chr6qtel1M 580168 CCCTTTGATCCAGCAGTGTTTCTACTGGGATTATATCACAAAGAGAT--- 580214 i i viiv v i v v vi v v --- L1ME4b_3end#L 361 CCCTTTGACCCAGCAATTCCACTTCTAGGAATTTATCCTACAGATATACT 410 chr6qtel1M 580215 CTTAAAGGAGGGAAGGGGACCCAAATGTGCAAA--TGTCTGTAGCAGCCC 580262 vi v v v v iv i--- iv i i-- i iii v vi L1ME4b_3end#L 411 CGCACATGTGCGAAATGA---CGTATGTACAAGGTTATTCATTGCAGCAT 457 chr6qtel1M 580263 TCTTTGTAGTAGCAAGAAACTAGAAACTGAGTGGATGCCCATCAATTGGG 580312 v i i i i i vivv ii i v L1ME4b_3end#L 458 TGTTTGTAATAGCAAAAGATTGGAAACAACCTAAATGTCCATCAATAGGG 507 chr6qtel1M 580313 CAATGGCTGAATCAATTATGGTATATGAATGCTATGGAATACTATTGTTC 580362 v v i i v i vv i v vvvv L1ME4b_3end#L 508 GACTGGTTAAATAAATTATGGTACATCCATACAATGGAATACTATGCAGC 557 chr6qtel1M 580363 TGTAAGAAACAA 580374 i i v L1ME4b_3end#L 558 CGTAAAAAAGAA 569 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 37.17 CpG sites = 36, Kimura (unadjusted) = 38.46 Transitions / transversions = 0.95 (36/38) Gap_init rate = 0.04 (11 / 254), avg. gap size = 1.27 (14 / 11) 643 25.00 3.07 3.52 chr6qtel1M 580130 580357 (419643) L1ME3G_3end#LINE/L1 322 548 (376) m_b313s551i12 13133 chr6qtel1M 580130 TTTGGAAGTATG-ATCAAAAAGTTTTCAAACTGTGCATACCCTTTGATCC 580178 v v- i ---- i v i i L1ME3G_3end#L 322 TTTGGCAGTATCTATTAAAA----TTTAAAATGCGCATACCCTTTGACCC 367 chr6qtel1M 580179 AGCAGTGTTTCTACTGGGATTATATCACAAAGAGAT-CTTAAAGGAGGG- 580226 i viiv v ? ?v v vi ? i - iiv viv v - L1ME3G_3end#L 368 AGCAATTCCACTTCTNGGNATCTATCCTANAGAAATACTCGCACATGTGC 417 chr6qtel1M 580227 --AAGGGGACCCAAATGTGCAA--ATGTCTGTAGCAGCCCTCTTTGTAGT 580272 -- i?i ---- i -- iii v vi v i L1ME3G_3end#L 418 ACAAGGANGC----ATGTACAAGGATGTTCATTGCAGCATTGTTTGTAAT 463 chr6qtel1M 580273 AGCAAGAAACTAGAAACTGAGTGGATGCCCATCAATTGGGCAATGGCTGA 580322 i i i i vivv ii i v v i i L1ME3G_3end#L 464 AGCGAAAAATTGGAAACAACCTAAATGTCCATCAATAGGGGAATGGTTAA 513 chr6qtel1M 580323 ATCAATTATGGTATATGAATGCTATGGAATACTAT 580357 v vv i L1ME3G_3end#L 514 ATAAATTATGGTATATCCATACTATGGAATACTAT 548 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 29.56 CpG sites = 31, Kimura (unadjusted) = 31.67 Transitions / transversions = 1.29 (31/24) Gap_init rate = 0.06 (13 / 227), avg. gap size = 1.15 (15 / 13) 496 32.94 3.32 2.56 chr6qtel1M 580163 580433 (419567) L1ME5_3end#LINE/L1 356 628 (313) m_b313s551i13 13133 chr6qtel1M 580163 GCATACCCTTTGATCCAGCAGTGTTTCTACTGGGATTATATCACAAAGAG 580212 v i i viiv v vv v i L1ME5_3end#LI 356 GCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATATCCCAAAGAA 405 chr6qtel1M 580213 ATCTTAAAGGAGG----GAAGGGGACCCAAATGTGCAA--ATGTCTGTAG 580256 ii v viv ----v ---- i i -- iii v L1ME5_3end#LI 406 ATTCTCACACAGGTCCATAAGGGGAC----ATGTACGAGGATGTTCATTG 451 chr6qtel1M 580257 CAGCCCTCTTTGTAGTAGCAAGAAACTAGAAACTGAGTGGATGCCCATCA 580306 vi v i i ii i ii i ii vivv i i L1ME5_3end#LI 452 CAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGGGTGTCCATCA 501 chr6qtel1M 580307 ATTGGGCAATGGCTGAATCAATTATGGTATATGAATGCTATGGAATACTA 580356 v v iv i v iii v v i iv v ii i i L1ME5_3end#LI 502 CTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACACCATGGAGTACTA 551 chr6qtel1M 580357 TTGTTCTGTAAGAAACAACCAGCAGGATGAAAACAAAGAGGCTTGAA--G 580404 vvvv v v i vii vi v v v vii v i -- L1ME5_3end#LI 552 TGCAGCAGTTAGAAGCAACGGACTAGATGTACACATAGCAACATGGATGG 601 chr6qtel1M 580405 ATACTTACATGAAC-TGATGCTTAGTGAAA 580433 - v -- - ii v L1ME5_3end#LI 602 AT-CTTAAA--AACATAGTGCTGAGTGAAA 628 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 42.41 CpG sites = 47, Kimura (unadjusted) = 44.45 Transitions / transversions = 1.18 (47/40) Gap_init rate = 0.04 (11 / 270), avg. gap size = 1.45 (16 / 11) 1244 29.79 1.50 1.12 chr6qtel1M 580897 581429 (418571) C L1M5_orf2#LINE/L1 (1459) 1835 1301 m_b313s551i14 13134 chr6qtel1M 580897 AATGAGTGCTGTATTTTGTCAAAAGCTTTTTCTGCATCTATTGAGATTAT 580946 i i v v v C L1M5_orf2#LIN 1835 AATGGGTGTTGAATTTTGTCAAATGCTTTTTCTGCATCTATTGAGATGAT 1786 chr6qtel1M 580947 CAT--GATTTCTGTTGGATTTTTTATTGATGCTGTTGATTATTATGATAG 580994 -- i v ivvv v i i i iiv vi ivv v C L1M5_orf2#LIN 1785 CATATGATTTTTCTCCTTTATTCTGTTAATATGGTGAATTACATTGATTG 1736 chr6qtel1M 580995 TTTTCCTGAAATTGAATTAGTCCTGGATGCCTGATATAAATCCCACTTAG 581044 v i vi vi i ii ii i v v iv i i C L1M5_orf2#LIN 1735 ATTTTCGAATGTTAAACCAACCTTGCATTCCTGGGATAAACCCCACTTGG 1686 chr6qtel1M 581045 TCATAGTATATTATCCTGCTGATA-AGTGCTTGTAATATC--TTTGATAA 581091 ii i vi v - v v -- - -- v C L1M5_orf2#LIN 1685 TCATGATGTATTATCCTTTTTATATATTGCTGG--AT-TCGATTTGCTAA 1639 chr6qtel1M 581092 TATTTTATTTAAAACTTATACATCAAAATTCATTAAGGATATTGGTCTGT 581141 i ? ii i v i v vi v i C L1M5_orf2#LIN 1638 TATTTTGTTNAGGATTTTTGCATCTATGTTCATGAGGGATATTGGTCTGT 1589 chr6qtel1M 581142 AATGTTCTTTCTCTGTTTTGGCTCTTCCTGGTTTAGATATCAATACCATA 581191 v iii vv v i vi ? v i ivii? i C L1M5_orf2#LIN 1588 AATTTTCTTTTCTTGTAATGTCTTTGTCNGGTTTTGGTATCAGGGTNATG 1539 chr6qtel1M 581192 TTTGTGTCATAGAAGGAATTTGGCAGGA--CTCTTCTTTACCATTTTTAC 581239 i v iv i v i v v vi-- i ii v i ivv C L1M5_orf2#LIN 1538 CTGGCCTCATAAAATGAGTTGGGAAGTGTTCCCTCTTTTTCTATTTTCTG 1489 chr6qtel1M 581240 AAATAGTTTACATAGCACTGGAATTAATTGTTCTTTAAATGTTTGGTAGA 581289 i v iii iv i v v v i C L1M5_orf2#LIN 1488 GAAGAGTTTGTGTAAGATTGGTATTATTTCTTCCTTAAATGTTTGGTAGA 1439 chr6qtel1M 581290 ATTCACTTGTAAATCCATCAGGTCCTGGAGATTTTTTTCTTAAGGAATTC 581339 iv i v v v - i iv ii i iv i C L1M5_orf2#LIN 1438 ATTCACCAGTGAAGCCATCTGGGCCTGGAG-TTTTCTTTGTGGGAAGGTT 1390 chr6qtel1M 581340 ATTGATGACTTATTAAATTTCATTTTTCTAAA-ATAGTATTGTTTAAATA 581388 v i v vv v -- vv i - vii i i i v C L1M5_orf2#LIN 1389 TTTAATTACAAATTCAATTTC--TTTAATAGATATAGGGCTATTCAGATT 1342 chr6qtel1M 581389 GTTCGTTTTCTTTTCTGTTAATATAGGCAATTGATATTTTT 581429 v iii ii i v? i i v v i ? vi i C L1M5_orf2#LIN 1341 TTCTATTTCTTCTTGNGTCAGTTTTGGTAANTTGTGTTTTT 1301 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 39.36 CpG sites = 88, Kimura (unadjusted) = 39.36 Transitions / transversions = 1.28 (88/69) Gap_init rate = 0.02 (11 / 532), avg. gap size = 1.27 (14 / 11) 1348 28.69 0.87 0.22 chr6qtel1M 580900 581360 (418640) C L1M4_orf2#LINE/L1 (1462) 1832 1369 m_b313s551i15 13134 chr6qtel1M 580900 GAGTGCTGTATTTTGTCAAAAGCTTTTTCTGCATCTATTGAGATTATCAT 580949 i i v v i v C L1M4_orf2#LIN 1832 GGGTGTTGGATTTTGTCAAATGCTTTTTCTGCGTCTATTGAGATGATCAT 1783 chr6qtel1M 580950 G--ATTTCTGTTGGATTTTTTATTGATGCTGTTGATTATTATGATAGTTT 580997 --i i ivvv v i i iiv vv ivv v v C L1M4_orf2#LIN 1782 GTGGTTTTTGTCCTTTATTCTATTAATATGGTGTATTACATTGATTGATT 1733 chr6qtel1M 580998 TCCTGAAATTGAATTAGTCCTGGATGCCTGATATAAATCCCACTTAGTCA 581047 i v? vi ii ii i v v iv i C L1M4_orf2#LIN 1732 TTCGNATGTTGAACCAACCTTGCATTCCTGGGATAAATCCCACTTGGTCA 1683 chr6qtel1M 581048 TAGTATATTATCCTGCTGATAAGTGCTTGTAATATCTTTGATAATATTTT 581097 i i v vi v v vvi v v vvv v i C L1M4_orf2#LIN 1682 TGGTGTATAATCCTTTTTATATGTTGCTGGATTCGGTTTGCTAGTATTTT 1633 chr6qtel1M 581098 ATTTAAAACTTATACATCAAAATTCATTAAGGATATTGGTCTGTAATGTT 581147 i v ii i v i v v v i i v C L1M4_orf2#LIN 1632 GTTGAGGATTTTTGCATCTATATTCATAAGGGATATTGGTCTGTAGTTTT 1583 chr6qtel1M 581148 CTTTCTCTGTTTTGGCTCTTCCTGGTTTAGATATCAATACCATATTTGTG 581197 iii vv v i vi v i iviiv i v iv C L1M4_orf2#LIN 1582 CTTTTCTTGTGATGTCTTTGTCTGGTTTTGGTATCAGGGTAATACTGGCC 1533 chr6qtel1M 581198 TCATAGAAGGAATTTGGCAGGA--CTCTTCTTTACCATTTTTACAAATAG 581245 v i v v vi-- i i i v i vvi v C L1M4_orf2#LIN 1532 TCATAGAATGAGTTGGGAAGTGTTCCCTCCTCTTCTATTTTTTGGAAGAG 1483 chr6qtel1M 581246 TTTACATAGCACTGGAATTAATTGTTCTTTAAATGTTTGGTAGAATTCAC 581295 iiiv v i vi v C L1M4_orf2#LIN 1482 TTTGTGAAGGATTGGTGTTAATTCTTCTTTAAATGTTTGGTAGAATTCAC 1433 chr6qtel1M 581296 TTGTAAATCCATCAGGTCCTGGAGATTTTTTTCTTAAGGAATTCATTGAT 581345 iv i v v ? - v i iv ii i i iv C L1M4_orf2#LIN 1432 CAGTGAAGCCATCTGGNCCTGG-GCTTTTCTTTGTGGGAAGTTTTTTGAT 1384 chr6qtel1M 581346 GACTTATTAAATTTC 581360 v v v i C L1M4_orf2#LIN 1383 TACTAATTCAATCTC 1369 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.43 CpG sites = 65, Kimura (unadjusted) = 36.77 Transitions / transversions = 0.97 (65/67) Gap_init rate = 0.01 (3 / 460), avg. gap size = 1.67 (5 / 3) 712 24.22 13.65 1.41 chr6qtel1M 582186 582566 (417434) C L1ME1_3end#LINE/L1 (373) 553 127 m_b313s551i16 13135 chr6qtel1M 582186 AGTAATATTCCAT-ATATTCATATACCA------ATTTATTCAGT-ACCA 582227 i -i vv ------i i v - ? C L1ME1_3end#LI 553 AGTAGTATTCCATTGTATGGATATACCACAATTTGTTTATCCATTCACCN 504 chr6qtel1M 582228 ACTGATGGGCATCCAT-TCGT---CAGTTT--AGCCACTACAAA--AAGG 582269 ii i iiiv- i --- --i i i i -- v C L1ME1_3end#LI 503 GTTGATGGACATTTGGGTTGTTTCCAGTTTTTGGCTATTACGAATAAAGC 454 chr6qtel1M 582270 TGCCA--AACATTCA-ATACAGTCCTTT-------CCTTCTTTATAATCT 582309 i -- i-i ivi ------- v viv v v i C L1ME1_3end#LI 453 TGCTATGAACATTCGTGTACAAGTCTTTGTGTGGACATATGTTTTCATTT 404 chr6qtel1M 582310 CTTTGGGATAAGTTC--AGTAGTAACACTGTTGGATCAAAGGGTA--TGC 582355 i v i i v -- v iiv i i i v v -- i C L1ME1_3end#LI 403 CTCTTGGGTAAATACCTAGGAGTGGAATTGCTGGGTCATATGGTAAGTGT 354 chr6qtel1M 582356 CAGTTGAAACTTTG--AGATGTT-CCAAACTACTT-CCAAAATGGTTG-- 582399 vv v - ?-- vii - ii - i i -- C L1ME1_3end#LI 353 ATGTTTAA-CTTTNTAAGAAACTGCCAAACTGTTTTCCAAAGTGGCTGTA 305 chr6qtel1M 582400 --ATTGTTCACAACCCACCAACAATGCATCAATGT-CCAGTT-TTCCACA 582445 -- v v iv- i i v iv - -i C L1ME1_3end#LI 304 CCATTTTGCATT-CCCACCAGCAATGTATGAGAGTTCCAGTTGCTCCACA 256 chr6qtel1M 582446 TCCTC--CAACA------ATCATTTGTTTTTTCCTGTCATCTTAGCCAA- 582486 -- ------ ii iv i ---- v i v- C L1ME1_3end#LI 255 TCCTCGCCAACACTTGGTATTGTCAGTCTTTT----TAATTTTAGCCATT 210 chr6qtel1M 582487 CTGACAGGTGTGTAG-GGTATCCGA--GTTGTCTTAATTTGTATTTCTCT 582533 i i - iv -- v i i i C L1ME1_3end#LI 209 CTAATAGGTGTGTAGTGGTATCTCATTGTGGTTTTAATTTGCATTTCCCT 160 chr6qtel1M 582534 GATTAATAATGACTTGGAGCATCTTTTCATATG 582566 i v v iv v i C L1ME1_3end#LI 159 AATGACTAATGATGTTGAGCATCTTTTCATGTG 127 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 29.46 CpG sites = 56, Kimura (unadjusted) = 30.25 Transitions / transversions = 1.60 (56/35) Gap_init rate = 0.08 (30 / 380), avg. gap size = 1.93 (58 / 30) 700 22.96 14.05 2.10 chr6qtel1M 582188 582614 (417386) C L1ME3G_3end#LINE/L1 (377) 547 71 m_b313s551i17 13135 chr6qtel1M 582188 TAATATTCCATA-TATTCATATACCA--ATTTATTCAGTACCA------- 582227 i - vv -- i -- ------- C L1ME3G_3end#L 547 TAGTATTCCATAGTATGGATATACCATAATTTATTTA--ACCATTCCCCT 500 chr6qtel1M 582228 ACTGATGGGCATCCAT-TCGT---CAGTTT--AGCCACTACAAAAA--GG 582269 i i ii v- i --- i --v i i v -- v C L1ME3G_3end#L 499 ATTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGC 450 chr6qtel1M 582270 TGCCA--AACATTCA-ATACAGTCCTTTCCTTCTTTATA---------AT 582307 v -- i v-i vv ? -- v vi i --------- C L1ME3G_3end#L 449 TGCAATGAACATCCTTGTACATGCNT--CCTTGTGCACATGTGCGAGTAT 402 chr6qtel1M 582308 CTCTTTGGGATAAGTTC--AGTAGTAACACTGTTGGATCAAAGGGTATGC 582355 i ? i ii ? -- v iiv i i i C L1ME3G_3end#L 401 TTCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGC 352 chr6qtel1M 582356 -CAGTTGAAACTTTGA--GATGTT-CCAAACTACT-TCCAAAATGGTTG- 582399 - v v i i -- ii - i i i- ? i - C L1ME3G_3end#L 351 GCATTTTAAATTTTAATAGATACTGCCAAATTGCCCTCCAAAANGGCTGT 302 chr6qtel1M 582400 ATTG-TTCACAA-CCCACCAACAATGCATCAATGT-CCAGTTTTCC-ACA 582445 iii- i v- i i i v iv - v i - C L1ME3G_3end#L 301 ACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCACA 252 chr6qtel1M 582446 TCCTC--CAACA------ATCATTTGTTTTTTCCTGTCATCTTAGCCAA- 582486 i -- ------ i ivi?i vv---- i v - C L1ME3G_3end#L 251 CCCTCGCCAACACTNGATATTATCAANCTTTTAA----ATTTTTGCCAAT 206 chr6qtel1M 582487 CTGACAGGTGTGTAG-GGTATCCGA--GTTGTCTTAATTTGTATTTCTCT 582533 ii viv i- iv -- i i i C L1ME3G_3end#L 205 CTGATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCT 156 chr6qtel1M 582534 GATTAATAATGACTTGGAGCATCTTTTCATATG---ATAGAAATAGTTCA 582580 v i vv v --- v -ivi v vv C L1ME3G_3end#L 155 GATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTG-GCCATTTGT 107 chr6qtel1M 582581 ATTTCTTC-TCTGAGAATTG-TTGTTCA-ATCGCTTT 582614 i - v -i - - C L1ME3G_3end#L 106 ATTTCCTCTTCTGTGAATTGCCTGTTCATATC-CTTT 71 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 28.55 CpG sites = 59, Kimura (unadjusted) = 28.55 Transitions / transversions = 1.59 (59/37) Gap_init rate = 0.09 (38 / 426), avg. gap size = 1.84 (70 / 38) 1897 27.32 12.15 2.20 chr6qtel1M 582896 585504 (414496) C L1M5_orf2#LINE/L1 (394) 2900 38 m_b313s551i18 13135 chr6qtel1M 582896 AGGTC-ATGAACCATTTTGACCTTTATCTTGGTGTACGGTGTTAG-TGTG 582943 - v i ? v- v i v i v - iv C L1M5_orf2#LIN 2900 AGGTCTATGATCCATCTNGAA-TTAATTTTTGTGTATGGTGTGAGGTAGG 2852 chr6qtel1M 582944 GATCAAG-----TGTTTCGCCATATTAGTTTCCA--TTTCCCAGCAAT-T 582985 i i ----- v iv vii v -- v i vi- C L1M5_orf2#LIN 2851 GGTCGAGNTTCATTTTTTTCCATATGGATATCCAATTGTTCCAGCACCAT 2802 chr6qtel1M 582986 TTATCAAACAG--TGTTTTATCCCAA--AAGTTGGGTCTTTGGG----TT 583027 i ii v -- i ii v v --i i --- ? v---- C L1M5_orf2#LIN 2801 TTGTTGAAAAGACTATCCTTTCCCCACTGAATTG---CNTTGGCACCTTT 2755 chr6qtel1M 583028 GC--AAGACTAGGTTGCTATATTTGT-TGATGTTTTATCCTGAA---TCT 583071 i-- i ii i? v? i v - i- i vv i i --- C L1M5_orf2#LIN 2754 GTCAAAAATCAANTGNCCATATATGTGTGG-GTCTATTTCTGGACTCTCT 2706 chr6qtel1M 583072 AA-CTATTCCACTGATCAACTAATTT--CCTTTAATCAA----ATGCT-T 583113 v- i i v i vi i -- vvii ---- ii - C L1M5_orf2#LIN 2705 ATTCTGTTCCATTGATCTATTTGTCTATCCTTACGCCAATACCACACTGT 2656 chr6qtel1M 583114 TTTGGTAAC----GCTCCATAATATAGTTT---GATCTGGTACAGCTAAG 583156 i i v ---- ii - i ---? ? vv - C L1M5_orf2#LIN 2655 CTTGATTACTGTAGCTTTATAATA-AGTCTTGANATCNGGTAGTG-TAAG 2608 chr6qtel1M 583157 TCAATTTCA--TTTGATTTT-TTTTTCA---TTAATTTTGA--ATTCTGG 583198 --i i -- v i - --- i- i-- ? C L1M5_orf2#LIN 2607 TC--CTCCAACTTTGTTCTTCTTTTTCAAGATTG-TTTTGGCTATTCTNG 2561 chr6qtel1M 583199 A-CCTTTGTTTTTCCA----------AGAATT---TTGTTGATTTTTCTA 583234 i- iv ---------- i--- ii -- C L1M5_orf2#LIN 2560 GTCCTTTGCATTTCCATATAAATTTTAGAATCAGCTTGTCAATTT--CTA 2513 chr6qtel1M 583235 GTCATTAAA---TAGTGG-AGTCTGATTGGTATAACAATAAAT----AGG 583276 -- vv --- iv - v i v vi v i ---- i C L1M5_orf2#LIN 2512 --CAAAAAAACCTGCTGGGATTTTGATTGGGATTGCATTGAATCTATAGA 2465 chr6qtel1M 583277 TTAGTTTAGGTAATATTGTCATCTTTATTATATTTGCTCACCCTATCCAA 583326 i i i v iv v ? iv viv vi v v C L1M5_orf2#LIN 2464 TCAATTTGGGGAGAATTGACATCTTNACAATATTGAGTCTTCCAATCCAT 2415 chr6qtel1M 583327 GAGCA--ATTTATTTTTCCAATTGTT--GATCA-----GACTTCATTTGG 583367 i --i v i i v i -- i v-----i i vi ii C L1M5_orf2#LIN 2414 GAACATGGTATATCTCTCCATTTATTTAGGTCTTCTTTAATTTCTCTCAG 2365 chr6qtel1M 583368 GAAAAGTGGTCTGTAATTT-----G-AAAAGTTTTG---ATTTTCCCTTG 583408 v --- v i i ----- - ? i i --- ? iiv - C L1M5_orf2#LIN 2364 CAA---TGTTTTGTAGTTTTCAGTGTANAGGTCTTGCACATNTTTTGTT- 2319 chr6qtel1M 583409 CAGAAAGATTCCTAA---TTTTATATTATCAGA-GTTACTTTAAATGGAA 583454 - vvv --- ? i v iv - i i v v C L1M5_orf2#LIN 2318 -AGATTTATTCCTAAGTATTTNATGTTTTTTGATGCTATTGTAAATGGTA 2270 chr6qtel1M 583455 TT-TCTTTGTAACTTGACTGTG-GATT-----TTGTCAGTGATATAAGAA 583497 - i ?v i v i v v-i ----- ii - ii C L1M5_orf2#LIN 2269 TTGTTTTTNAAATTTCATTTTCCAATTGTTTGTTGCTAGT-ATATAGAAA 2221 chr6qtel1M 583498 TGCTGATGACTTATGGG-GTTTATTTTATAACCAGCAAC-TTGCTAAAGT 583545 i viv i v vi-i v ii i v ? i - v C L1M5_orf2#LIN 2220 TACAATTGATTTTTGTATATTGACCTTGTATCCNGCGACCTTGCTAAATT 2171 chr6qtel1M 583546 TG-TGATTATTTCTAATAACTTTTTAGTAGA--ACTTGGGGTTCCCAA-- 583590 ii- v v i ii ? v --vi ? i ii v -- C L1M5_orf2#LIN 2170 CACTTATTAGTTCTAGTAGTTTNTTTGTAGATTCTTTNGGATTTTCTACG 2121 chr6qtel1M 583591 TATACCATC-TGTCATTGGC-AAGAGTGATAATTTGGTTTC---ATTGCC 583635 ? v - iv - v i? i i vi ---v v C L1M5_orf2#LIN 2120 TANACAATCATGTCATCTGCGAATAANGACAGTTTTATTTCTTCCTTTCC 2071 chr6qtel1M 583636 TATTTCT-TACCTTTAATCT----TTCCTGCCTGATCAAA---GCTAG-A 583676 v i i - i v i ---- i v iiv --- - C L1M5_orf2#LIN 2070 AATCTTTATGCCTTTTATTTCTTTTTCTTGCCTTATTGCACTGGCTAGGA 2021 chr6qtel1M 583677 TTTCTACTACAATATTAAATAGTAACGGTGATAGTGGGCAACCTTGTTTC 583726 ii i v i i v ii ? i i v i i C L1M5_orf2#LIN 2020 CCTCCAGTACAATGTTGAATAGAAGTGGTGANAGCGGACATCCTTGTCTT 1971 chr6qtel1M 583727 AC-CTAGATCTTATTTTGGGAATGGTT---GT-TTGCTCCATTAA---TG 583768 ii- iv vv-- v v? --- - v v --- C L1M5_orf2#LIN 1970 GTTCCCGATCTTAGG--GGGAAAGCNTTCAGTNTTTCACCATTAAGTATG 1923 chr6qtel1M 583769 ATACTTACTGATGGTTTTAAATAGATGTTGATTATTTTTATGAG-AAGTC 583817 ii ?i vv vvi iivv ivvvv - i C L1M5_orf2#LIN 1922 ATGTTNGCTGTAGGTTTTTCGTAGATGCCCTTTATCAGGTTGAGGAAGTT 1873 chr6qtel1M 583818 CATTTTCTATACCTCAAT---------GTTTTAAT-AGGAAGTGATGTTG 583857 -ii v - i --------- v - v vv i C L1M5_orf2#LIN 1872 C-CCTTCTATTCCT-AGTTTGCTGAGAGTTTTTATCATGAATGGGTGTTG 1825 chr6qtel1M 583858 GATTT-GTCAAATG-TTTTTCTGCATCTGTTCAGATAATCAT-TGGTTTT 583904 i - - i v i - i C L1M5_orf2#LIN 1824 AATTTTGTCAAATGCTTTTTCTGCATCTATTGAGATGATCATATGATTTT 1775 chr6qtel1M 583905 TGT----TAATTTGTTTAATATGGC-AATTATATTGGATAGTTTTCTA-T 583948 v ---- v i - i- i iv ii v - C L1M5_orf2#LIN 1774 TCTCCTTTATTCTGTT-AATATGGTGAATTACATTGATTGATTTTCGAAT 1726 chr6qtel1M 583949 ATTGAACCAGCCCTGCATTC-TGGTATAAACT--ACTTGATCATAGTGTA 583995 i i i i - v i-- i ii C L1M5_orf2#LIN 1725 GTTAAACCAACCTTGCATTCCTGGGATAAACCCCACTTGGTCATGATGTA 1676 chr6qtel1M 583996 TTATCCTG---AGATGATT------TTCGTTTTTC-AATATTT-ATTTAA 584034 v--- v - ------ v v - -i ? i C L1M5_orf2#LIN 1675 TTATCCTTTTTATAT-ATTGCTGGATTCGATTTGCTAATATTTTGTTNAG 1627 chr6qtel1M 584035 GATTTT-GCATCAATATTCATTAGG-AGATTGGTCTATAATTGTTTCTCT 584082 - v i v - v i -- i C L1M5_orf2#LIN 1626 GATTTTTGCATCTATGTTCATGAGGGATATTGGTCTGTAATT--TTCTTT 1579 chr6qtel1M 584083 GTTTTCAAC----CTACCTGGTTTAGGTATCAGTA-CATGTCTGTGTTAT 584127 vi vi i----i ii ? v vi-? iiv iv i C L1M5_orf2#LIN 1578 TCTTGTAATGTCTTTGTCNGGTTTTGGTATCAGGGTNATGCTGGCCTCAT 1529 chr6qtel1M 584128 GAAGGAATTTGGTAGGACTTTCAT----TCCTATTTTATCAAATAATTTA 584173 i ivi v v i vv i v ---- i v vi v i i C L1M5_orf2#LIN 1528 AAAATGAGTTGGGAAGTGTTCCCTCTTTTTCTATTTTCTGGAAGAGTTTG 1479 chr6qtel1M 584174 TATAGCATGGGGCAATTGTT-----CTTAAATGTTTGGTAAAATT-ACAT 584217 i iv v v-- i ----- i - vv C L1M5_orf2#LIN 1478 TGTAAGATTGGT--ATTATTTCTTCCTTAAATGTTTGGTAGAATTCACCA 1431 chr6qtel1M 584218 GTAAATCCATCTGGTCCTGGGGATTTTTTTCTTAGGGAGTTGTTTAATTG 584267 i v v i - i iv i i v v i C L1M5_orf2#LIN 1430 GTGAAGCCATCTGGGCCTGGAG-TTTTCTTTGTGGGAAGGTTTTTAATTA 1382 chr6qtel1M 584268 ----TTCTATTTCTTTTTTCTGAAAT--GATTATTCA-ACAATATACTTC 584310 ---- v vv v- v -- ii - ivv v i C L1M5_orf2#LIN 1381 CAAATTCAATTTCTTTAATA-GATATAGGGCTATTCAGATTTTCTATTTC 1333 chr6qtel1M 584311 TTCCC-TGTTAGTTTGGG-AAGTC-TATTTTTGGAGGTAGTCATCCATTT 584357 ii-? i v - ? i- i vi v v ii C L1M5_orf2#LIN 1332 TTCTTGNGTCAGTTTTGGTAANTTGTGTTTTTCAAGGAATTTGTCCATTT 1283 chr6qtel1M 584358 CACTTAGGGTTATCAAATTTATTG-CATAAAGTTGAGCAAAATAACC-CT 584405 ii i - ? - vv v vi - C L1M5_orf2#LIN 1282 CATCTAAG-TTNTCAAATTTATTGGCATAAAGTTGTTCATAATATTCTCT 1234 chr6qtel1M 584406 TATTAT---TTTAATTTCTTT-----CATTGGGAAAGTTTC--TTTTCAT 584445 --- v v ----- vv i vi v i -- C L1M5_orf2#LIN 1233 TATTATCCTTTTAATGTCTGTAGGATCTGTAGTGATGTCTCCTTTTTCAT 1184 chr6qtel1M 584446 TTTTAAGACTACTAATTT-CATTTTCTCCTTCTTTTTC--AATCAGATTT 584492 ii i v i iv -ii i ii i --i vi ? C L1M5_orf2#LIN 1183 TCCTGATATTGGTAATTTGTGTCTTCTCTCTTTTTTTCTTGATCAGTCTN 1134 chr6qtel1M 584493 ACTAAAGGCTTATCTATTTTATTGG-CTTTTCACAGAACCAACTCTT-GT 584540 i i i v i- v i i - i C L1M5_orf2#LIN 1133 GCTAGAGGTTTATCAATTTTATTGATCTTTTCAAAGAACCAGCTTTTGGC 1084 chr6qtel1M 584541 TTTATTAATTAGTTCAATAGTTTTTTAATGTTCAATATTTTTAATTTCT- 584589 ii i vvi v v ? ? vi v v v iv i - C L1M5_orf2#LIN 1083 TTCGTTGATTTTCTCTATTGTNTNTTTGTTTTCTATTTCATTGATTTCTG 1034 chr6qtel1M 584590 CT-TTAATTTTAGAATTTCCAATTTAGTATTTGATTGGGGGTTTTAATTT 584638 - vi vv vvii vv i ?v v -- C L1M5_orf2#LIN 1033 CTCTTATCTTTATTATTTCCTTCCTTCTACTTNCTTTGGG--TTTAATTT 986 chr6qtel1M 584639 GC------TTTTTTAGTTTTTT-AGTTGCAACC----ATTATTAATCTT- 584676 ------ i i i - v v v ---- i i i - C L1M5_orf2#LIN 985 GCTCTTCTTTTTCTAGCTTCTTAAGGTGGAAGCTTAGATCATTGATTTTA 936 chr6qtel1M 584677 -TTCTTTCTGTTTTATTTAA-GTAAGCCTCTGATA----AAATTTCTT-- 584718 -vi vi - i -i ? v i i ?i---- ii-- C L1M5_orf2#LIN 935 AGCCTTTCTTCTTT-TCTAATATANGCATTTAANGCTATAAATTTCCCTC 887 chr6qtel1M 584719 --ATTACCGCTTTCGATCCAT------AATTTTGGTATGACGT-TCATCA 584759 -- vi i v v v ------ i vi - iv C L1M5_orf2#LIN 886 TAAGCACTGCTTTAGCTGCATCCCACAAATTTTGATATGTTGTATTTTCA 837 chr6qtel1M 584760 TTGTCATTATTGGGTGAAATTA------AATTGTATCTATAATTTGCTGC 584803 ? -- ii v v v ------ viv?i i i vi vi C L1M5_orf2#LIN 836 TTNTCAT--TCAGTTCAAAATATTTTCTAATTTCCNTTGTGATTTCTTCT 789 chr6qtel1M 584804 TTCACCCAATCATTCTTTA-AGATGGATTGTTTGTTTT---AATAACTTT 584849 v vvvi v - ii vi iv --- --- C L1M5_orf2#LIN 788 TTGACCCATGGGTTATTTAGAAGTGTGTTGTTTAATTTCCAAATA---TT 742 chr6qtel1M 584850 TGG------TCTATTTCAACTTTTGTTG--AATGT---GTTTTATTGCAT 584888 ------ v? vvvi i--i v ---i v v C L1M5_orf2#LIN 741 TGGGGATTTTCTAGNTATCTTTTTGTTATTGATTTCTAATTTAATTCCAT 692 chr6qtel1M 584889 CATGATCTGAAAGAAAGCATT---TACTATTTC--TGCTTTTTGATTTAA 584933 ii i -- i vii i --- iv -- v ?vi - C L1M5_orf2#LIN 691 TGTGGTC--AGAGAACATACTCTGTATGATTTCAATCCTTTNAAATTTA- 645 chr6qtel1M 584934 TTTTGAG----GTTTTATATCCTAAA--ATGGTCAATTTTG---AATAGG 584974 -- ---- iv i i?-- v i --- - v C L1M5_orf2#LIN 644 --TTGAGACTTGTTTTATGGCCCAGNATATGGTCTATCTTGGTAAAT-GT 598 chr6qtel1M 584975 TTCATGAACTGCTGAGAAGAAAG-GT-TTCTTTC--TATTCATTCAATTG 585020 i vi vvi i v - - vi?-- i viv v? v C L1M5_orf2#LIN 597 TCCATGTGCACTTGAAAAGAATGTGTATTCTGCNGTTGTTGGGTGNAGTG 548 chr6qtel1M 585021 TTCCAAAGATCTTAA-TATACCTAATTTATTC-TAATATTTATTTATTCT 585068 i v i v i - vii v i vi v- i i vv iv v C L1M5_orf2#LIN 547 TTCTATAAATGTCAATTAGGTCAAGTTGGTTGATAGTGTTGTTCAAATCT 498 chr6qtel1M 585069 TTAATTTCTTTATTTG-TTTTGGTTTGATTTGTT-TAC------CTGAGA 585110 iv v i i vi- v i - i - i------ C L1M5_orf2#LIN 497 TCTATATCCTTACTGATTTTTTGTCT-ACTTGTTCTATCAATTACTGAGA 449 chr6qtel1M 585111 GTGCAAGGTTGAGATCTCCAACTATTACAGTTTTG---TTGTTCTATTTC 585157 v v?iv i i ? --- i v --- - C L1M5_orf2#LIN 448 GAGGNGTGTTAAAATCTCCNACTAT---AATTGTGGATTTG-TCTATTTC 403 chr6qtel1M 585158 TTCTTTGCAATCTCTTAACTTTC-CTTTAGGAAGTTGGATGCCATACCAC 585206 i vviv v i ii i- i v v v v v iv iii i C L1M5_orf2#LIN 402 TCCTTTTAGTTCTGTCAGTTTTTGCTTCATGTATTTTGAAGCTCTGTTAT 353 chr6qtel1M 585207 TTGGTG-ATATATGTTTAATATTGATATTGCTTCGTTGTTTATGTTACC- 585254 v - i ii iv v vv - v v vv v - C L1M5_orf2#LIN 352 TAGGTGCATACACATTTAGGATTGTTATGTCTTC-TTGATGAATTGACCC 304 chr6qtel1M 585255 -TTTAGCAGGATGTAGTTACTGTCCTTATTCTTTAATTAGATAATT-TTG 585302 - v vv v i vv iv i - i ii --i v - C L1M5_orf2#LIN 303 TTTTATCATTATGAAATGTCCCTCTTTA-TCTCTGGT--AATATTTCTTG 257 chr6qtel1M 585303 CTTT------TGCTTGATCTGAGA-TAATGGATGGCTACC----CTGTTT 585341 i ------ i vi v - -- i i ?---- v i C L1M5_orf2#LIN 256 CCTTGAAGTCTACTTTGTCTGATATTAAT--ATAGCCACNCCAGCTTTCT 209 chr6qtel1M 585342 TTTGATTCAACTGAAGATAATAGATTTTGCTCCAGCCACCTTTTACT--- 585388 ? vivv vviv ii v i vi v--- --- C L1M5_orf2#LIN 208 TTTGNTTAGTGTTTGCATGGTATATCTTTTTCCAT---CCTTTTACTTTC 162 chr6qtel1M 585389 ---CTATATGTAT-TCCCTGCTTTAAATGTG--TTTTGTAAACAACATAT 585432 --- ? v i - iiv ii v i i -- i i i C L1M5_orf2#LIN 161 AACCTNTCTGTGTCTTTATATTTAAAGTGCGTCTCTTGTAGACAGCATAT 112 chr6qtel1M 585433 TGTAGGGTTCTG-ACTTTGATCCAGTCTG-CTATCTGCCTCCTCTTTA-- 585478 v v ii -vi v - v -- v ii -- C L1M5_orf2#LIN 111 AGTTGGGTCTTGTTTTTTTATCCAGTCTGACAATCT--CTGCCTTTTAAT 64 chr6qtel1M 585479 TGGGGAGTTCATCCCATTCACATTTA 585504 i v i v? i C L1M5_orf2#LIN 63 TGGAGTGTTTAGNCCATTTACATTTA 38 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 35.06 CpG sites = 385, Kimura (unadjusted) = 35.51 Transitions / transversions = 1.23 (385/312) Gap_init rate = 0.08 (201 / 2608), avg. gap size = 1.89 (380 / 201) 1997 28.44 10.75 1.69 chr6qtel1M 583273 585504 (414496) C L1M4_orf2#LINE/L1 (826) 2468 38 m_b313s551i19 13135 chr6qtel1M 583273 TAGGTTAGTTTAGGTAATATTGTCATCTTTATTATATTTGCTCACCCTAT 583322 i i i i v i i v iv viv vi v C L1M4_orf2#LIN 2468 TAGATCAATTTGGGGAGTATTGCCATCTTAACAATATTAAGTCTTCCAAT 2419 chr6qtel1M 583323 CCAAGAGCA--ATTTATTTTTCCAATTGTT--GATCAGACTTCATTTGG- 583367 v i --ivv i i v i -- i vvvi v vv- C L1M4_orf2#LIN 2418 CCATGAACATGGGATGTCTTTCCATTTATTTAGGTCTTCTTTAATTTCTT 2369 chr6qtel1M 583368 -GAAAAGTGGTCTGTAATTT-----G-AAAAGTTTTGATTTTCCCTTGCA 583410 -v v i v i i ----- - v i vvi ii iv C L1M4_orf2#LIN 2368 TCAACAATGTTTTGTAGTTTTCAGTGTACAAGTCTTGCACTTCTTTTGTT 2319 chr6qtel1M 583411 GAAAG-ATTCCTAA---TTTTATATTATCAGA-GTTACTTTAAATGGAAT 583455 i vv- --- vi v iv - i i v C L1M4_orf2#LIN 2318 AAATTTATTCCTAAGTATTTTATTCTTTTTGATGCTATTGTAAATGGAAT 2269 chr6qtel1M 583456 T-TCTTTGTAACTTGACTGT-GGATT-----TTGTCAGTGATATAAGAAT 583498 - i iv i v i v - ----- ii - ii C L1M4_orf2#LIN 2268 TGTTTTCTTAATTTCATTTTCGGATTGTTCATTGCTAGTG-TATAGAAAT 2220 chr6qtel1M 583499 GCTGATGACTTATGGG-GTTTATTTTATAACCAGCAAC-TTGCTAAAGTT 583546 i viv i v vi-i v i i v v - i v i C L1M4_orf2#LIN 2219 ACAATTGATTTTTGTATATTGATCTTGTATCCTGCAACCTTGCTGAACTC 2170 chr6qtel1M 583547 GTG-ATTATTTCTAATAACTTTTTAGTAGA--ACTTGGGGTTCCCAATAT 583593 v- v ii ? i --v i i ii v C L1M4_orf2#LIN 2169 GTTTATTAGTTCTAATAGTTTTTTNGTGGATTCCTTAGGATTTTCTATAT 2120 chr6qtel1M 583594 AC--CATC-TGTCATTGGC-AAGAGTGATAATTTGGTTTCATTGCCTATT 583639 --v - iv - v v i vii -- v v i C L1M4_orf2#LIN 2119 ACAAGATCATGTCATCTGCGAATAGAGATAGTTTTACTTC--TTCCTTTC 2072 chr6qtel1M 583640 ---TCT---TACCTTTAATCT----TTCCTGCCTGAT---CAAAGCTAGA 583676 --- --- i v i ---- i i --- vvi C L1M4_orf2#LIN 2071 CAATCTGGATGCCTTTTATTTCTTTTTCTTGCCTAATTGCCCTGGCTAGA 2022 chr6qtel1M 583677 -TTTCTACTACAATATTAAATAGTAACGGTGATAGTGGGCAACCTTGTTT 583725 -ii i v i i v ii i v i i v i C L1M4_orf2#LIN 2021 ACCTCCAGTACAATGTTGAATAGAAGTGGCGAGAGCGGACATCCTTGTCT 1972 chr6qtel1M 583726 CA--CCTAGATCTTATTTTGGGAATGGTT---GT-TTGCTCCATTAA--- 583766 ii-- - vv-- v v? --- - v v --- C L1M4_orf2#LIN 1971 TGTTCCT-GATCTTAGG--GGGAAAGCNTTCAGTCTTTCACCATTAAGTA 1925 chr6qtel1M 583767 TGATACTTACTGATGGTTTTAAATAGATGTTGATTATTTTTATGAG-AAG 583815 ii vi vv vvi iivv ivvvv - C L1M4_orf2#LIN 1924 TGATGTTAGCTGTGGGTTTTTCGTAGATGCCCTTTATCAGGTTGAGGAAG 1875 chr6qtel1M 583816 TCCATTTTCTATACCT--------CAATGTTTTAAT-AGGAAGTGATGTT 583856 i -ii v --------v i v - v iv i C L1M4_orf2#LIN 1874 TTC-CCTTCTATTCCTAGTTTGTTGAGTGTTTTTATCATGAAAGGGTGTT 1826 chr6qtel1M 583857 GGATTT-GTCAAATG-TTTTTCTGCATCTGTTCAGATAATCAT-TGGTTT 583903 - - i i v i - C L1M4_orf2#LIN 1825 GGATTTTGTCAAATGCTTTTTCTGCGTCTATTGAGATGATCATGTGGTTT 1776 chr6qtel1M 583904 TTGT---TAATTTGTTTAATATGGCA-ATTATATTGGATAGTTTTC-TAT 583948 --- v ivv ii- i iv ii -? C L1M4_orf2#LIN 1775 TTGTCCTTTATTCTATTAATATGGTGTATTACATTGATTGATTTTCGNAT 1726 chr6qtel1M 583949 ATTGAACCAGCCCTGCATTC-TGGTATAAA--CTACTTGATCATAGTGTA 583995 i i i - v -- i i i C L1M4_orf2#LIN 1725 GTTGAACCAACCTTGCATTCCTGGGATAAATCCCACTTGGTCATGGTGTA 1676 chr6qtel1M 583996 TTATCCTG---AGATGATT------TTCGTTTTTC-AATATTT-ATTTAA 584034 v v--- v - ------ v v - i -i v i C L1M4_orf2#LIN 1675 TAATCCTTTTTATATG-TTGCTGGATTCGGTTTGCTAGTATTTTGTTGAG 1627 chr6qtel1M 584035 GATTTT-GCATCAATATTCATTAGG-AGATTGGTCTATAATTGTTTCTCT 584082 - v v - v i i -- i C L1M4_orf2#LIN 1626 GATTTTTGCATCTATATTCATAAGGGATATTGGTCTGTAGTT--TTCTTT 1579 chr6qtel1M 584083 GTTTTCAAC----CTACCTGGTTTAGGTATCAG--TACATGTCTGTGTTA 584126 vi vii i----i ii v -- - iiiv iv i C L1M4_orf2#LIN 1578 TCTTGTGATGTCTTTGTCTGGTTTTGGTATCAGGGTA-ATACTGGCCTCA 1530 chr6qtel1M 584127 T-GAAGGAATTTGGTAGGA---CTTTCATTCCTATTTTATCAAATAATTT 584172 - v i v v vi--- i i vi i v vi v i C L1M4_orf2#LIN 1529 TAGAATGAGTTGGGAAGTGTTCCCTCCTCTTCTATTTTTTGGAAGAGTTT 1480 chr6qtel1M 584173 ATATAGCATGGG-GC-AATTGTTCTT-AAATGTTTGGTAAAATT-ACATG 584218 i iv v v - i- v - i - vv C L1M4_orf2#LIN 1479 GTGAAGGATTGGTGTTAATTCTTCTTTAAATGTTTGGTAGAATTCACCAG 1430 chr6qtel1M 584219 TAAATCCATCTGGTCCTGGGGATTTTTTTCTTAGGGAGTTGTTTAATT-- 584266 i v ? v- i iv i i v i -- C L1M4_orf2#LIN 1429 TGAAGCCATCTGGNCCTGGGC-TTTTCTTTGTGGGAAGTTTTTTGATTAC 1381 chr6qtel1M 584267 --GTTCTATTTCTTT-TTTCTGAAATGATTATTCA-ACAATATACTTCTT 584312 --i v i -i v v v v vi - ivv v i C L1M4_orf2#LIN 1380 TAATTCAATCTCTTTACTTGTTATAGGTCTATTCAGATTTTCTATTTCTT 1331 chr6qtel1M 584313 CCCT-GTTAGTTTGGGAAGTC--TATTTTTGGAGGTAGTCATCCATTTCA 584359 iiv- i v v i-- i i vv v v ii C L1M4_orf2#LIN 1330 CTTGAGTCAGTTTCGGTAGTTTGTGTCTTTCTAGGAATTTGTCCATTTCA 1281 chr6qtel1M 584360 CTTAGGGTTATCAAATTTATT-GCATAAAGTTGAGCAAAATA-ACCCTTA 584407 ii - v i - v i vv v i -v C L1M4_orf2#LIN 1280 TCTA-GGTTATCTAATTTGTTGGCATACAATTGTTCATAGTATTCCCTTA 1232 chr6qtel1M 584408 TTA---TTTTAATTTCT-----TTCATTGGGAAAGTTTC--TTTTCATTT 584447 v --- v -----v iv i v v ii --i i C L1M4_orf2#LIN 1231 TAATCCTTTTTATTTCTGTAAGGTCGGTAGTAATGTCCCCTCTTTCATTC 1182 chr6qtel1M 584448 TTAAGACTACTAATTTCA---TTTTCTCCTTCTTTTTCAATCAGATTTAC 584494 i i vvi v v --- i i i i iii vi vi C L1M4_orf2#LIN 1181 CTGATTTTAGTAATTTGAGTCTTCTCTCTTTTTTTCTTGGTCAGTCTAGC 1132 chr6qtel1M 584495 TAAAGGCTTATCTATTTTATTGG-CTTTTCACAGAACCAACTCTT-GTTT 584542 i i v i i- v i - C L1M4_orf2#LIN 1131 TAAAGGTTTGTCAATTTTGTTGATCTTTTCAAAGAACCAACTTTTGGTTT 1082 chr6qtel1M 584543 TATTAATTAGTTCAATAGTTTTTTAATGTTCAATATT-TTTAATTTCTCT 584591 ii i vvi v v iv vi v v i- v i v C L1M4_orf2#LIN 1081 CGTTGATTTTCTCTATTGTTTTTCTATTCTCTATTTCATTTATTTCCGCT 1032 chr6qtel1M 584592 TTAAT-TTTAGAATTTCCAATTTAGTATTTGATTGGGGGTTTTAATTTGC 584640 i - vv vvii vv ii v v -- i C L1M4_orf2#LIN 1031 CTAATCTTTATTATTTCCTTCCTTCTGCTTGCTTTGGG--TTTAGTTTGC 984 chr6qtel1M 584641 ------TTTTTTAGTTTTTT-AGTTGCAAC----CATTATTAATCT--TT 584677 ------ i i - v v v----vi i i --vv C L1M4_orf2#LIN 983 TCTTCTTTTTCTAGTTTCTTAAGGTGGAAGGTTAGGTTATTGATTTGAGA 934 chr6qtel1M 584678 TCTTTCTGTTTTATTTAA-GTAAGCCTCTG-----ATAAAATTTCTT--- 584718 vi - -i i v i i----- v i i --- C L1M4_orf2#LIN 933 TCTTTCTTCTTT-TTTAATATAGGCATTTACAGCTATAAATTTCCCTCTA 885 chr6qtel1M 584719 ATTACCGCTTTCGAT-----CCATAA-TTTTGGTATGACGT-TCATCATT 584761 vi i ? v ----- - vi - iv i C L1M4_orf2#LIN 884 AGCACTGCTTTNGCTGCATCCCATAAGTTTTGGTATGTTGTGTTTTCGTT 835 chr6qtel1M 584762 GTCATT-ATTGGGTGAAATTA------AATTGTATCTATAATTTGCTGCT 584804 v - i--- v v ------ vivii i i vi vi C L1M4_orf2#LIN 834 TTCATTCATC---TCAAAGTATTTTCTAATTTCCCTTGTGATTTCTTCTT 788 chr6qtel1M 584805 TCACCCAATCATTCTTTAAGA-TGGATTGTTT-GTTTTAATA-ACTTTTG 584851 v v vi v i - vi -i iv i - i v C L1M4_orf2#LIN 787 TGACCCATTGGTTATTTAGGAGTGTGTTGTTTAATTTCCACATATTTGTG 738 chr6qtel1M 584852 G---TCT---ATTTCAACTTTTGTTG--AATGT---GTTTTATTGCATCA 584890 i--- i--- -- i i--i v ---i i v ii C L1M4_orf2#LIN 737 AATTTCCCAAATTTC--CTTCTGTTATTGATTTCTAATTTCATTCCATTG 690 chr6qtel1M 584891 TGATCTGAAAGAAAGCATT-TACTATTTC--TGCTTTTTGATTTAATTTT 584937 i v i iv vi v - iv -- v vi --- C L1M4_orf2#LIN 689 TGGTCGGAGAACATACTTTGTATGATTTCAATCCTTTTAAATTTA---TT 643 chr6qtel1M 584938 GAG----GTTTTATATCCTAAA--ATGGTCAATTTTGAATA--GGTTCAT 584979 ---- iv v-- v ii i v -- v i C L1M4_orf2#LIN 642 GAGACTTGTTTTATGGCCTAACATATGGTCTATCCTGGAGAATGTTCCAT 593 chr6qtel1M 584980 GAACTGCTGAGAAGAAAG-GT-TTCT--TTCTATTCATTCAATTGTTCCA 585025 vi vvi v - - -- vi i viv vi v i C L1M4_orf2#LIN 592 GTGCACTTGAGAAGAATGTGTATTCTGCTGTTGTTGGGTGGAGTGTTCTA 543 chr6qtel1M 585026 AAGATCT-TAATATACCTAATTTATTC-TAATATTTATTTATTCTTTAAT 585073 v v - iv vii i vi i- i i vv iv v iv C L1M4_orf2#LIN 542 TAGATGTCTGTTAGGTCTAGTTGGTTTATAGTGTTGTTCAAGTCTTCTAT 493 chr6qtel1M 585074 TTCTTTATTTGTTTTG-GTTTGATTTGTTTACC------TGAGAGTGCAA 585116 i i vi i v- i ii vv i i ------ i vii C L1M4_orf2#LIN 492 TTCCTTGTTGATCTTCTGTCTAGTTGTTCTATCCATTATTGAAAGTGGGG 443 chr6qtel1M 585117 GGTTGAGATCTCCAACTATTACAGTTTTGTTGTTCTATTTCTTCTTTGCA 585166 vi ii iv vvi - i i - C L1M4_orf2#LIN 442 TATTGAAGTCTCCAACTATTATTGTTGAATTG-TCTATTTCTCCCTT-CA 395 chr6qtel1M 585167 A-TCTCTTAACTTTC-CTTTAGGAAGTTGGATGCCATACCACTTGGTG-A 585213 - v i ii i- i v v v v iv iv iiiii v - C L1M4_orf2#LIN 394 ATTCTGTCAGTTTTTGCTTCATGTATTTTGGGGCTCTGTTGTTAGGTGCA 345 chr6qtel1M 585214 TATATGTTTAATATTGATATTGCTTCGTTGTTTATGTTACC--TTTAGCA 585261 vv v vv v vi vv - v -- v C L1M4_orf2#LIN 344 TATATGTTTATAATTGTTATATCTTCCTGATGGAT-TGACCCTTTTATCA 296 chr6qtel1M 585262 GGATGTAGTTACTGTCCTTAT---TCTTTAATTAGATAATTTTGCTTT-- 585306 v-- i i-- v v --- i i v v -?v ii -- C L1M4_orf2#LIN 295 T--TATAA--AATGTCCTTCTTTGTCTCTAGTAACA-NTTTTTGTCTTAA 251 chr6qtel1M 585307 ----TGCTTGATCTGAGATAATGGATGGCTACC----CTGTTTTTTGATT 585348 ---- ii vi v v - v i i i---- v i i C L1M4_orf2#LIN 250 AGTCTATTTTGTCTGATATTA-GTATAGCCACTCCAGCTCTCTTTTGGTT 202 chr6qtel1M 585349 CAACTG--AAGATAATAGATTTTGCTCCAGCCACCTTTTACT------CT 585390 -- --viv ii v i vi v--- ------ C L1M4_orf2#LIN 201 --ACTGTTTGCATGGTATATCTTTTTCCAT---CCTTTTACTTTCAACCT 157 chr6qtel1M 585391 ATATGTATTCCCTG-CTTTAAA---TGTGTTTTGTAAACAACATATTGTA 585436 v i- ii -v i --- v i i i v v C L1M4_orf2#LIN 156 ATTTGTG-TCTTTGAATCTAAAGTGTGTCTCTTGTAGACAGCATATAGTT 108 chr6qtel1M 585437 GGGTTCTG-ACTTTGATCCAGTCTGCTA---TCTGCCTCCTCTTTATGGG 585482 i iv -vi v v i --- ii vv -- i C L1M4_orf2#LIN 107 GGATCATGTTTTTTTATCCATTCTGCCAATCTCTGCCTTTTGAT--TGGA 60 chr6qtel1M 585483 GAGTTCATCCCATTCACATTTA 585504 v i vi i C L1M4_orf2#LIN 59 GTGTTTAATCCATTTACATTTA 38 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 35.97 CpG sites = 334, Kimura (unadjusted) = 36.56 Transitions / transversions = 1.15 (334/290) Gap_init rate = 0.07 (155 / 2231), avg. gap size = 1.81 (281 / 155) 348 17.58 6.96 6.03 chr6qtel1M 585403 585517 (414483) C L1MEh_5end#LINE/L1 (7) 2228 2113 m_b313s551i20 13135 chr6qtel1M 585403 TGCTTTAAATGTGTTT--TGTAAACAACATATTGTAGGGTTCTGACTTTG 585450 i i i -- i i v i i vi ? C L1MEh_5end#LI 2228 TGTTTTAAGTGTGTCTCTTGTAGACAGCATATTGTTGGATTTTGTTTTTN 2179 chr6qtel1M 585451 -ATCCAGTCTGCTA---TCTGCCTCCTCTTTA--TGGGGAGTTCATCCCA 585494 - i v? --- i ---- -- v i v C L1MEh_5end#LI 2178 AATCCAATCTGANAATCTCTGTCT----TTTAATTGGTGAGTTTAACCCA 2133 chr6qtel1M 585495 TTCACATTTACGGTTAGAATTAC 585517 i --- iv C L1MEh_5end#LI 2132 TTTACATTTA---TTGTAATTAC 2113 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 20.97 CpG sites = 13, Kimura (unadjusted) = 20.97 Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.10 (11 / 114), avg. gap size = 1.36 (15 / 11) 257 31.26 7.18 1.63 chr6qtel1M 588167 588514 (411486) C L1M5_orf2#LINE/L1 (2033) 1261 895 m_b313s551i21 13136 chr6qtel1M 588167 TGACATAGAATAGGGCAAAATAACTCCTAATTATTCTTT-AATTTCTTTT 588215 i i i v vv v viii v i - v v v C L1M5_orf2#LIN 1261 TGGCATAAAGTTGTTCATAATATTCTCTTATTATCCTTTTAATGTCTGTA 1212 chr6qtel1M 588216 TCATTGGTGGTAAATTAACCCTTTTCATTTTGAATACTGGTGATTTTTAT 588265 vv iv i i vv vv i iivi i i v i C L1M5_orf2#LIN 1211 GGATCTGTAGTGATGTCTCCTTTTTCATTCCTGATATTGGTAATTTGTGT 1162 chr6qtel1M 588266 C-TCTTTCCTTTTT--CTAATCA--------AAAGTTTTATCTATGTT-- 588302 - i i --i i -------- i v v v -- C L1M5_orf2#LIN 1161 CTTCTCTCTTTTTTTCTTGATCAGTCTNGCTAGAGGTTTATCAATTTTAT 1112 chr6qtel1M 588303 ---TTTTTTTAAATAAAACCAACTCTTACTTTTATTAATTGT-TCAATAA 588348 --- i i -- i i i ivi ii i v - v vi C L1M5_orf2#LIN 1111 TGATCTTTTCAA--AGAACCAGCTTTTGGCTTCGTTGATTTTCTCTATTG 1064 chr6qtel1M 588349 TTTTCCTAATTTCAATTTTATTATTCTCTCTTCTGAATTCCAGAATTTC- 588397 ? ?ii iv v i iv i vi v vi ii vv - C L1M5_orf2#LIN 1063 TNTNTTTGTTTTCTATTTCATTGATTTCTGCTCTTATCTTTATTATTTCC 1014 chr6qtel1M 588398 -TGATTAGACATTTAATTGGGGGTTATTTTG---TTCTTTTTTCAGCTTT 588443 - vv vv -- ?v v v v --- ii i C L1M5_orf2#LIN 1013 TTCCTTCTAC--TTNCTTTGGGTTTAATTTGCTCTTCTTTTTCTAGCTTC 966 chr6qtel1M 588444 TTTAGTTGCATGTCCAATTCATTGATCTC--CTCTTTCCTTATTTCATTC 588491 v v v v iii iv i i--vi i iv -- v C L1M5_orf2#LIN 965 TTAAGGTGGAAGCTTAGATCATTGATTTTAAGCCTTTCTTCTTTTC--TA 918 chr6qtel1M 588492 ATATAGCTATTTAAAGATATAAA 588514 ?vi ? v C L1M5_orf2#LIN 917 ATATANGCATTTAANGCTATAAA 895 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 41.49 CpG sites = 56, Kimura (unadjusted) = 42.06 Transitions / transversions = 1.10 (56/51) Gap_init rate = 0.05 (17 / 347), avg. gap size = 1.82 (31 / 17) 195 32.08 4.35 2.86 chr6qtel1M 588628 588765 (411235) L3#LINE/CR1 1213 1352 (2747) m_b313s601i12 13137 chr6qtel1M 588628 TTCATAGGAGACAAGTTCCTTGAAAACAA--TAAAATATAAAATTTATTA 588675 ?i - i vv ?v v -- i - i v i vi L3#LINE/CR1 1213 TTCNCAGGAGA-AAATAACNGGAAAAGAAGCTAGAA-ACAATACTTATGG 1260 chr6qtel1M 588676 CCTCAAATATTCATACAAATTAACTCACAG-GT-TAAGCACCCAACAAG- 588722 i i ii i --ii iv - - ii i viv ? i- L3#LINE/CR1 1261 CCTCAGATGTCTATATA--CCAATGCACAGAGTATGGGTAATAAANAAAG 1308 chr6qtel1M 588723 -AAGTTCTAAATTCTAAATCAAGGAGAGAAACTTGACTTCACAG 588765 -? ii iv i vv iv ivi ii i L3#LINE/CR1 1309 TNAACTTGAAATTTTAACACAAGGAGGTAAATACGATCTCATAG 1352 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 44.89 CpG sites = 29, Kimura (unadjusted) = 46.42 Transitions / transversions = 2.07 (29/14) Gap_init rate = 0.07 (9 / 137), avg. gap size = 1.11 (10 / 9) 488 34.45 8.07 3.25 chr6qtel1M 588788 589258 (410742) L2#LINE/L2 1909 2401 (681) m_b313s601i13 13138 chr6qtel1M 588788 GCCTATAGTTTCTCTCTTCCTATGTTCTTCTT--ATCTACAACATT--GT 588833 i vi i i i i vi - -- i i vv v -- v L2#LINE/L2 1909 GTCTCCAATTCCTCTCCTCCCATTCTCT-CTTGAACCCACTCCAATCAGG 1957 chr6qtel1M 588834 CTTCTGATCTTGTTATTCCATCAAAACTGCTTTCTCCAAAGTCAAGAATG 588883 ii vi iiiii i i i i ivi i vv L2#LINE/L2 1958 CTTTCGTCCCCACCACTCCACCGAAACTGCTCTTGTCAAGGTCACCAATG 2007 chr6qtel1M 588884 GTTTTTTAAGAT-CCAAATCAAATGG--GGTTTTTTAAAATAGTAATTCT 588930 iii ii- v v - i v --ii i i--- i vv v ii L2#LINE/L2 2008 ACCTCC-ACGTTGCTAAATCCAATGGTCAATTCTC---AGTCCTCATCTT 2053 chr6qtel1M 588931 CTTTGAGCTCAAGGCAGTCTTTAACACTGTTGATTCCTCTCTCCTTCTGG 588980 vi v ?vvi iv i v iv i v L2#LINE/L2 2054 ACTTGACCTNTCAGCAGCATTTGACACAGTTGATCACTCCCTCCTTCTTG 2103 chr6qtel1M 588981 --ATGCTCTCTTCTTTCAGGATT----GATTCTACCCTCTCTTCATTTTC 589024 -- ii i vi i- v ---- iv i v i vi L2#LINE/L2 2104 AAACACTTTCTTCACTT-GGCTTCCAGGACACCACACTCTCCTGGTTTTC 2152 chr6qtel1M 589025 TTGCTACATATTTCTT-TTGGTCTTTGTCTCTCAGT----TTTGATGGAT 589069 i v ------ i-i i vi vii ---- v - L2#LINE/L2 2153 CTCCTAC------CTCACTGGCCGCTCCTTCTCAGTCTCCTTTGCTGG-T 2195 chr6qtel1M 589070 TCTTCTCCAGATCAT--ACC-ATCAATATAGCAATTCCTCA--GCT---- 589110 i ii vv vi-- -v ? ii v v i v i -- ---- L2#LINE/L2 2196 TCCTCCTCATCTCCCCGACCTCTNAACGTTGGAGTGCCCCAGGGCTCAGT 2245 chr6qtel1M 589111 --------CTTTTCTCTTCTCTCTCTATACAATTTCACTTGCTGATTTTA 589152 -------- i v i vvvi v ? v i i L2#LINE/L2 2246 CCTTGGACCTCTTCTCTTCTCTATCTACACTCACTCCCTNGGTGATCTCA 2295 chr6qtel1M 589153 TTAGCTCACATGAACGTACTTATCTTCGCCAGGCTAATGATTCTCAAATC 589202 iviv v iviv vv i v vvi v i i i i L2#LINE/L2 2296 TCCAGTCTCATGGCTTTAAATACCATCTATATGCTGATGACTCCCAAATT 2345 chr6qtel1M 589203 TACCTATCCTGATTCC--ATCTCTCTAACTCACCTCTAATCTTGCAT-TT 589249 -- iiv vi -- i i-v v v i iv i i - i L2#LINE/L2 2346 TA--TATCTCCAGCCCGGACCTCTCC-CCTGAACTCCAGACTCGTATATC 2392 chr6qtel1M 589250 TAACTGCTT 589258 i i L2#LINE/L2 2393 CAACTGCCT 2401 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 46.88 CpG sites = 94, Kimura (unadjusted) = 48.69 Transitions / transversions = 1.49 (94/63) Gap_init rate = 0.07 (31 / 470), avg. gap size = 1.74 (54 / 31) 15 27.58 0.00 0.00 chr6qtel1M 589728 589766 (410234) (AA)n#Simple_repeat 1 39 (0) m_b313s252i15 13139 chr6qtel1M 589728 AAAAAAAAAAAAAAAAGACATAATTAAGAAGTCAAAAAA 589766 i v v vv i ivv (AA)n#Simple_ 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 39 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 411 39.44 4.02 5.03 chr6qtel1M 590363 590984 (409016) L3#LINE/CR1 2229 2844 (1255) m_b313s601i14 13137 chr6qtel1M 590363 CCTATAA-AATACTCTCTGGAGGACTG--GCTCAAAATGAACAAAGACTA 590409 i - v v v i i i-- i i i vi i v L3#LINE/CR1 2229 CCTGTAAGAATAGTGTCAGGAAGGCTAAAGCCCAGAATGAGCTGAGGCTT 2278 chr6qtel1M 590410 CTCAATGGAAAT---AAAGAAAAAATTTAAAAGGTTTTTCAAA-TTATGT 590455 viv vii --- i v v vvv ? i -i L3#LINE/CR1 2279 GCAAAAAAAAATGCTAAGGACAACAAAAANAAGGCTTTTCAAAGCTATGT 2328 chr6qtel1M 590456 T----GTAGAGGGAAACAGTATATAAAAGTAACAAAATTATCTTTGTTCA 590501 ---- i i v ------ ?i ii---vi vi i ii L3#LINE/CR1 2329 TCGGAGCAGAAGGAAAAAG------AAAGNGACAGG---CCCGCTGCTTG 2369 chr6qtel1M 590502 GTTTGGATGATTCAATGATGACTGATATCCT-GAGAATACCTGGCTGAGC 590550 vvii iivi v i v iv vv- vi vvii ivv L3#LINE/CR1 2370 GGGCAGATGGCGTAATGTTAACAGATGACAGAGAGAAAGCAGAACTACTC 2419 chr6qtel1M 590551 TAGTTTTGCTTTCCTTATTTGTTTTTCCTGCCAAATTGAATAACCTCTGC 590600 v v ii ii v -- ii i ii ii ivv i i iiiv L3#LINE/CR1 2420 AACTCCTATTTTGCT--TCCGTCTTCTCTATCAAGGAGAATGATCTTCAG 2467 chr6qtel1M 590601 ATCAGGAATGAGAGAACAAAATTTAATGACTGAAAATAATAAGTACA--A 590648 iii i v iv vv iiv i vv ii vi- iv -- L3#LINE/CR1 2468 ACTGGAAAGGGTAGAACAAACATCGTTAAGAGGGAATTG-AAGCCCAAGA 2516 chr6qtel1M 590649 TGAGTAATATTGCATATTATTCGAGTA---AGTTGCTTTTGATGAAATCA 590695 ii i vi--iv v vvv i --- ii vi iv L3#LINE/CR1 2517 TAGGTGAGG--AGATAGTAAGAGAGCACCTAGCCGCTTTAAATGAGTTCA 2564 chr6qtel1M 590696 TAGGACTTATACAAGACCAAATG---TATATTCTTAGACACTGAAGAATG 590742 - ---- v v i v i i --- i i ivi ii ii -- L3#LINE/CR1 2565 -AG----TCTCCAGGCCCAGACGAATTACATCCCAGGGTACTGAAAGA-- 2607 chr6qtel1M 590743 TGTTTGAACAAACTGTCTCATTGCTGAGCTACTGTGAGTAACATTTGAAA 590792 -ii -- i --- v v i v i ii vi iv i L3#LINE/CR1 2608 -ACTTG--CAGA---TGTGATCGCGGAACCGCTGTCGGTAATCTTTGAGA 2651 chr6qtel1M 590793 TTGCAAGGAGCATGGGAGAATTATGCAAAGA-TAAAGTAAGAAAAATTCT 590841 vvv v v i i iv iivvi - ii vvi iv vi? L3#LINE/CR1 2652 AATCACGGAGAACGGAAGAGGTGCCAGAAGACTGGAGACGGGCAAATGTN 2701 chr6qtel1M 590842 ACCCTGAATTTCATAAATGGGGGAAAGTAT-GATTTTCCCA--TATATAC 590888 ii? iv ? i - v ii iv - i v?v -- i v L3#LINE/CR1 2702 GTNCCTANTTTTA-AAAAGGGAAAAAAGATGGATTCTGNAAACTACAGAC 2750 chr6qtel1M 590889 TAGTAAAATTGAT-TTGATTTCTTAGGGAAATTCTGAAAAAAAATACATT 590937 ii iv i- i - i iii vi - i vii -i L3#LINE/CR1 2751 CGGTAAGCTTGACGTCGA-TCCCCGGCAAAATTCT-AGAACGGAT-TATT 2797 chr6qtel1M 590938 AAAGTGATAATAGGTTAATATTTGTAAATGAATATGATGAATACAAG 590984 vv ii vv v ii i iv v i vii i vi v L3#LINE/CR1 2798 AAACAGATGGTTTGTGAGCACTTAGAAAAGGAAGCGGTGATCACTAG 2844 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 53.87 CpG sites = 141, Kimura (unadjusted) = 60.43 Transitions / transversions = 1.53 (141/92) Gap_init rate = 0.07 (44 / 621), avg. gap size = 1.27 (56 / 44) 332 27.13 0.83 1.68 chr6qtel1M 590988 591107 (408893) X20_LINE#LINE/CR1 8 126 (127) m_b313s551i22 13140 chr6qtel1M 590988 AGCATGGAATTATGGAGGTTACATCATGCCAGAATAAACTT-ATTTCCTT 591036 iv ii ivi v - i - v i X20_LINE#LINE 8 AGCATGGGTTTATAAAGAACAAATCATGCCAG-ACAAACTTGATTGCTTT 56 chr6qtel1M 591037 TTGGCATAGGATTACTAAACTGGTCAATGAGAGGAATGATGAAGATGTAC 591086 vvv i v i i i vi - i i vv v v X20_LINE#LINE 57 TTTTGATAGAATTACAAGATTAGTGGAT-AAAGGGATGCAGTAGATGTAA 105 chr6qtel1M 591087 TTTACCTAGATTTTAACAAAG 591107 v i v ii X20_LINE#LINE 106 TATATCTTGATTTTAGTAAAG 126 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 34.16 CpG sites = 17, Kimura (unadjusted) = 34.16 Transitions / transversions = 1.13 (17/15) Gap_init rate = 0.03 (3 / 119), avg. gap size = 1.00 (3 / 3) 41 0.00 0.00 0.00 chr6qtel1M 591374 591408 (408592) (AC)n#Simple_repeat 1 35 (0) c_b313s251i0 13141 chr6qtel1M 591374 ACACACACACACACACACACACACACACACACACA 591408 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACA 35 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 36 0.00 0.00 0.00 chr6qtel1M 592309 592339 (407661) (AT)n#Simple_repeat 1 31 (0) c_b313s251i1 13142 chr6qtel1M 592309 ATATATATATATATATATATATATATATATA 592339 (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATA 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 488 31.86 7.98 1.50 chr6qtel1M 592913 593100 (406900) C MIRc#SINE/MIR (59) 209 10 m_b314s601i0 13143 chr6qtel1M 592913 ATATTATTTCCTTTTATTTTCCTAATGATATTGGGAGGTAAGT------G 592956 i i v v ii vi ii ivi v i i------ C MIRc#SINE/MIR 209 ACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAG 160 chr6qtel1M 592957 CTATGAATATCCTTATTTTACGATTTAACGAACTGAGATT---AAACATT 593003 v v v ii iiv v ivi ii --- i vi C MIRc#SINE/MIR 159 GTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTT 110 chr6qtel1M 593004 ----CACTTGACTATGGTCACAAAGCTAGTAAGGATTAGCA-AGT-AGAA 593047 ----v v i v v --- i - i-i i C MIRc#SINE/MIR 109 AAGTGACTTGCCCAAGGTCACACAGCTAGTAAG---TGGCAGAGCCGGGA 63 chr6qtel1M 593048 TTTGAACTCTGTTCTTCCTAATTCTAATTCTAGAGCTCTCTCCATTATTT 593097 i i i v v i i i v i v i i iivi C MIRc#SINE/MIR 62 CTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCAC 13 chr6qtel1M 593098 CAC 593100 C MIRc#SINE/MIR 12 CAC 10 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 41.58 CpG sites = 38, Kimura (unadjusted) = 43.59 Transitions / transversions = 1.81 (38/21) Gap_init rate = 0.04 (8 / 187), avg. gap size = 2.25 (18 / 8) 185 23.71 13.59 1.74 chr6qtel1M 593782 593884 (406116) C MIR3#SINE/MIR (1) 207 93 m_b314s601i1 13144 chr6qtel1M 593782 AATTGTAGAATCAAAGAATG---GACTTTG-GGGGAC---AG---TCATT 593821 ii v --- vi v -i --- --- - C MIR3#SINE/MIR 207 AATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCA-T 159 chr6qtel1M 593822 CTAGTCAAAAAC---AATTTTATATAAGAGGGAAGTTAGGTCCAGATTTG 593868 v vv ---v i v v i v v i -vv C MIR3#SINE/MIR 158 CTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGA-GAG 110 chr6qtel1M 593869 GT-AAGTGATTTATTCA 593884 - i iii C MIR3#SINE/MIR 109 GTGAAGTGACTTGCCCA 93 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 28.71 CpG sites = 11, Kimura (unadjusted) = 28.71 Transitions / transversions = 0.85 (11/13) Gap_init rate = 0.08 (8 / 102), avg. gap size = 2.00 (16 / 8) 21 10.85 0.00 0.00 chr6qtel1M 594923 594952 (405048) (A)n#Simple_repeat 1 30 (0) m_b314s252i0 13145 chr6qtel1M 594923 AAAACAAAAACAAAAACAAAAAAAAAAAAA 594952 v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 30 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 16 9.71 0.00 0.00 chr6qtel1M 595502 595523 (404477) (T)n#Simple_repeat 1 22 (0) m_b314s252i1 13146 chr6qtel1M 595502 TTTTTTTTTGTTTTCTTTTTTT 595523 v i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTT 22 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 14 18.15 4.17 4.17 chr6qtel1M 595755 595802 (404198) (GGA)n#Simple_repeat 1 48 (0) m_b314s252i2 13147 chr6qtel1M 595755 GGGGGAGG-GGGGGTGGAGGGAGTGGGGGGAAGGAGGAGGA-GTGGAGGA 595802 i - i v - - i i i - v (GGA)n#Simple 1 GGAGGAGGAGGAGGAGGA-GGAG-GAGGAGGAGGAGGAGGAGGAGGAGGA 48 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.09 (4 / 47), avg. gap size = 1.00 (4 / 4) 833 32.01 5.59 3.42 chr6qtel1M 597045 598189 (401811) L1M5_orf2#LINE/L1 2071 3239 (55) m_b314s551i0 13148 chr6qtel1M 597045 GGAATTAGAAGAAAATAAAATTATTACTACTTACACATGATATGATGATA 597094 -- i ii i i i?i i ii v i vi ? L1M5_orf2#LIN 2071 GGAA--AGGAAGAAATAAAACTGTCNTTATTCGCAGATGACATGATTGTN 2118 chr6qtel1M 597095 TTCTTAGAGAATTCTACAAAAATCATACAAA-AATGTACTAGAAACAATT 597143 v v i i ? - i - - vv vi v L1M5_orf2#LIN 2119 TACGTAGAAAATCCNA-AAGAATC-TACAAANAAACTACTAGAACTAATA 2166 chr6qtel1M 597144 CATAGCTTTAGCAAAGTTGCAAGATATAAAATAAACCCACAGAAATTATC 597193 vi iiv i i ?i i ii v ivi i i vi L1M5_orf2#LIN 2167 AGTGAATTTAGCAAGGTCGCNGGATACAAGGTCAATATACAAAAATCAAT 2216 chr6qtel1M 597194 AGCATTTCTATATATTACTGATAAAGACCACCAGCAAGAAAAAGAAA--- 597240 v i i vii i ------ iivi v --- L1M5_orf2#LIN 2217 TGTATTTCTATATACTAGCAACAAA------CAATTGGAAAATGAAATTT 2260 chr6qtel1M 597241 GAGA---AATTCCATTTAGAATTATTAT-AGACAAAATAAAATACCTGGG 597286 ? i --- v v - vi - i v v ? i i L1M5_orf2#LIN 2261 NAAAAACAATACCATTTACAA-TAGCATCAAAAAACATNAAATACTTAGG 2309 chr6qtel1M 597287 GGTCTATCTGTAAAGATAAACCCAAGAACTATA---TGAACACAATTACA 597333 ii vv ivv i ? viiv v ? --- --- i L1M5_orf2#LIN 2310 AATAAATCTAACAAAANATGTGCAAGACCTNTACACTGAA---AACTACA 2356 chr6qtel1M 597334 AAACACTTCTCACACAAATAAAGTCAGATATAAACAATTAGAAGAATATT 597383 i v v v v v ivv iv i v i iii v L1M5_orf2#LIN 2357 AAACATTGCTGAGAGAAATTAAAGAAGACCTAAATAAATGGAGAGATATA 2406 chr6qtel1M 597384 GATTGTTCCTGGATACAACAAGCTAATGTAATGAAAATGATAATTCTGCT 597433 vvv v vvi vi vii i vi ? i vi v i L1M5_orf2#LIN 2407 CCATGTTCATGGATTGGAAGACTCAATATTGTNAAGATGTCAATTCTCCC 2456 chr6qtel1M 597434 TAAATTGACCTACTTGCTCAGTGCCCTATCAATTAAACTGTCAAAAAATT 597483 i i ivvii i vv vi i v vi iv ii L1M5_orf2#LIN 2457 CAAATTGATCTATAGATTCAATGCAATCCCAATCAAAATCCCAGCAGGTT 2506 chr6qtel1M 597484 ATTTTACAGAACTAGAAAAAATAA---TAAAATTCATGTGGAAGAACAAA 597530 v ii v v v iv i --- i i ivi L1M5_orf2#LIN 2507 TTTTTGTAGAAATTGACAAGCTGATTCTAAAATTTATATGGAAATGCAAA 2556 chr6qtel1M 597531 AAGTCAAGAATA-TCAAGAGAATTAATGAGAA--AAGTACAAAGGAGGGT 597577 iiii ? -i i v i-v i -- v vv iv L1M5_orf2#LIN 2557 GGACCNAGAATAGCCAAAACAATC-TTGAAAAAGAAGAACAAAGTTGGAG 2605 chr6qtel1M 597578 AGCTTAGCAACACCCAATTT-AAAACTATATTATAAAACAATAGTCATCA 597626 ii - vi ?i ? - i - i v i v L1M5_orf2#LIN 2606 GACTTA-CACTACCNGATNTCAAGACT-TATTATAAAGCTACAGTAATCA 2653 chr6qtel1M 597627 AAGTCATTTAGTATTGGC-TAAAAA-AGAGTGTTGGATCAGTGGAAGAGA 597674 iiivi v i - ii - vviv i i v L1M5_orf2#LIN 2654 AGACAGTGTGGTATTGGCGTAAGGATAGACAAATAGATCAATGGAACAGA 2703 chr6qtel1M 597675 TTAGATACATACAACACAATA-ATAAAAACCTATAT--TAATCTAGTGTT 597721 v v -i v --iv - ivv v v --?v ?i ii v L1M5_orf2#LIN 2704 ATAGAGA-GTCCA--GAAATAGACCCACACATATATGGNCANTTGATTTT 2750 chr6qtel1M 597722 TGATAAACCCCCAAATTCCAGTTTCTAGAATAAGAACTCACTATTTGACA 597771 i vviv v ?v v v ivv i iiv i ivvv v ii L1M5_orf2#LIN 2751 TGACAAAGGTGCCAANGCAATTCAGTGGGGAAAGGATAGTCTTTTCAACA 2800 chr6qtel1M 597772 AAAATTGCTGGGAAAAT------------TAGAAAATAATATGTCAGGAC 597809 viv i v ------------ i v ivi? vv L1M5_orf2#LIN 2801 AATGGTGCTGGAACAATTGGATATCCATATGGAAAAAAATGAANCTCGAC 2850 chr6qtel1M 597810 CTACATTTCATACCACATACCAAAATAGGGTCAAAATGGGTACAT-GATT 597858 ivi ii i i i v viiv ? i i - - ii L1M5_orf2#LIN 2851 CCCTACCTCACACCATACACAAAAATTAATTCNAGATGGAT-CATAGACC 2899 chr6qtel1M 597859 TGTGTATAAAGAATGATACCATAAGCAAATT----AGGAGAACAAGGGAT 597904 ivi i ii? i v i -- v ---- i i vi v L1M5_orf2#LIN 2900 TAAATGTAAAAGNTAAAACTATAA--AACTTCTAGAAGAAAACATAGGAG 2947 chr6qtel1M 597905 AATTTATCTATCA-GATCTTTGA--AG--AAGGA------AGACAAAAC- 597942 -- - i- i v i-- -- i ------ i ii - L1M5_orf2#LIN 2948 AA--TATCT-TCGTGACCTTGGGNTAGGCAAAGATTTCTTAAACAGGACA 2994 chr6qtel1M 597943 TAGAAAATATT----ATGAAAATAAAAACAAACAACTTTGATTACATGAA 597988 i i ii i?---- i iv ivi i v v i ? v L1M5_orf2#LIN 2995 CAAAAAGCACNAACCATAAAAGAAAAAATTGATAAATTGGACTNCATCAA 3044 chr6qtel1M 597989 ATTGAAAAACAAATTGCAC-CAACAAAACTAACA-----AACAAGATTAA 598032 v v --- vii - ?v --i ----- v i v L1M5_orf2#LIN 3045 AATTAAAAAC---TTCTGCTCNTCAAAA--GACACCGTTAAGAAAATGAA 3089 chr6qtel1M 598033 AAGGGAAGTTCAAAGCTGGGTGGGGGGGGGAAGTCTTTACAAATAAGGTT 598082 v -i v ------i?v i i i v i ?vv vi v L1M5_orf2#LIN 3090 AAGGCAAG-CCACAG------ANTGGGAGAAAATATTTGCAANACATATA 3132 chr6qtel1M 598083 TCTGATTAAGGTCTCATTTCTAAAACATGTAAAGAAATATGTCAAATTTA 598132 iv v i v i i i i v vivv ? iv L1M5_orf2#LIN 3133 TCTGACAAAGGACTCGTATCCAGAATATATAAAGAACTCCTACAANTCAA 3182 chr6qtel1M 598133 TAAAAATAAAAGTCATTC--CCCGATAGATAAACGATCAGAGGATATGAA 598180 ? -- v vv -- i ? v i iv i i iv L1M5_orf2#LIN 3183 TAANA--AAAAGACAAACAACCCAATANAAAAATGGGCAAAAGACTTGAA 3230 chr6qtel1M 598181 CAGACAATT 598189 v L1M5_orf2#LIN 3231 CAGACACTT 3239 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 43.72 CpG sites = 200, Kimura (unadjusted) = 44.42 Transitions / transversions = 1.30 (200/154) Gap_init rate = 0.06 (65 / 1144), avg. gap size = 1.60 (104 / 65) 850 34.56 4.89 2.70 chr6qtel1M 597054 597850 (402150) L1PREC2_orf2#LINE/L1 2078 2891 (403) m_b314s551i1 13148 chr6qtel1M 597054 AGAAAATAAAATTATTACTACTTACACATGATATGATGATATTCTTAGAG 597103 i i v i iv ii i v i i vv vii i L1PREC2_orf2# 2078 AGGAAGTCAAACTATCCCTGTTTGCAGACGACATGATTCTATATCTAGAA 2127 chr6qtel1M 597104 AATTCTACAAAAATCATACAAAAATGTACTAGAAACAATTCATAGCTTTA 597153 ii i i ivv- ivv v vv v v? ivii vv i i i L1PREC2_orf2# 2128 AACCCCATAGTC-TCGGCCCAAAAGCTCCTTNAGCTGATAAACAACTTCA 2176 chr6qtel1M 597154 GCAAAGTTGCAAGATATAAAATAAACCCACAGAAATTATCAGCATTTCTA 597203 v i i v ivi i i ii i L1PREC2_orf2# 2177 GCAAAGTTTCAGGATACAAAATCAATGTACAAAAATCACTAGCATTCCTA 2226 chr6qtel1M 597204 TATATTACTGATAAAGACCACCAGC-AAGAA--AAAGAAAGA--GAAATT 597248 i ii --- i vii -- -i i-- vv i -- v i L1PREC2_orf2# 2227 TACACCA---ACAACAGCCA--AGCCGAGAGCCAAATCAGGAACGCAATC 2271 chr6qtel1M 597249 CCATTTAGAATTATTATAGACAAAATAAAATACCTGGGGGT----CTATC 597294 i v iii i i v i i ii ---- v L1PREC2_orf2# 2272 CCATTCACAATTGCCACAAAAAGAATAAAATACCTAGGAATACAGCTAAC 2321 chr6qtel1M 597295 TGTAAAGATAAACCCAAGAACTATATGAACACAATTACAAAACACTTCTC 597344 iivii i i ---- v v ii vv v v L1PREC2_orf2# 2322 CAGGGAGGTGAA----AGATCTCTACAATGAGAATTACAAAACACTGCTC 2367 chr6qtel1M 597345 ACACAAAT-AAAGTCAGATATAAACAATTAGAAGAATATTGATTGTTCCT 597393 v v - i vi- i i v i i i vvv i v L1PREC2_orf2# 2368 AAAGAAATCAGAGAT-GACACAAACAAATGGAAAAACATTCCATGCTCAT 2416 chr6qtel1M 597394 GGATACAACAAGCTAATGTAATGAAAATGATAATTCTGCTTAAATTGACC 597443 vi vi iii i vi v iiv v ii vii ii L1PREC2_orf2# 2417 GGATAGGAAGAATCAATATCGTTAAAATGGCCATACTGCCCAAAGCAATT 2466 chr6qtel1M 597444 TACTTGCTCAGTGCCCTATCAATTAAACTGTCAA-AAAATTATTTTACAG 597492 vvii i iv vi v i ii -i v -i i L1PREC2_orf2# 2467 TACAGATTCAATGCTATTCCTATCAAACTACCAATGACATT-CTTCACAG 2515 chr6qtel1M 597493 AACTAGAAAAAATAA---TAAAATTCATGTGGAA-GAACAAAAAGTCAAG 597538 iv --- i -v v i i -v L1PREC2_orf2# 2516 AACTAGAAAAAACTATTTTAAAATTCATATGGAACCAAAAAAGAGCC-CG 2564 chr6qtel1M 597539 AATA-TCAAGAGAAT--TAATGAGAAAAGTACAAAGGAGGGTAGCTTAGC 597585 -i iv -- - vi v vv i-i v vi L1PREC2_orf2# 2565 AATAGCCAAGGCAATCCTAA-GCAAAAAGAACAAAGCTGGA-GGCATCAC 2612 chr6qtel1M 597586 AACACCCAATTTAAAACTATATTATAAAACAATAGTCATCAAAGTCATTT 597635 ivi i i v i i iii v i v i iiviiv L1PREC2_orf2# 2613 GCTACCCGACTTCAAACTATACTACAGGGCTACAGTAACCAAAACAGCAT 2662 chr6qtel1M 597636 AGTATTGG--CTAAAAAAGAGTGTTGGATCAGTGGAAGAGATTAGATACA 597683 i i -- v v vvvv i i i v v ----- L1PREC2_orf2# 2663 GGTACTGGTACAAAAACAGACACATAGACCAATGGAACAGAATAG----- 2707 chr6qtel1M 597684 TACAACACAATAATAA------AAACCTATATTAATCTAGTGTTTGATAA 597727 - v i v iv ------ v i viv ii v i i L1PREC2_orf2# 2708 -AGAGCCCAGAAATAAGGCCGCACACCTACAACCATCTGATCTTCGACAA 2756 chr6qtel1M 597728 ACCCC-CAAATTCCAGTTTCTAGAATAAGAACTCACTATTTGACAAAAAT 597776 v iv- vv v -ivv i iiv i v ii i viv L1PREC2_orf2# 2757 AGCTGACAAAAACAAG-CAATGGGGAAAGGACTCCCTATTCAATAAATGG 2805 chr6qtel1M 597777 TGCTGGGAAAATTAGAAAATAATATGT------------CAGGACCTACA 597814 v i i vv iiv i------------ v iviv L1PREC2_orf2# 2806 TGCTGGGATAACTGGCTAGCCATATGCAGAAGATTGAAACTGGACCCCTT 2855 chr6qtel1M 597815 TTTCATACCACATACCAAAATAGGGTCAAAATGGGT 597850 ii i i i v viiv i i L1PREC2_orf2# 2856 CCTTACACCATATACAAAAATCAACTCAAGATGGAT 2891 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 46.60 CpG sites = 159, Kimura (unadjusted) = 48.38 Transitions / transversions = 1.46 (159/109) Gap_init rate = 0.05 (36 / 796), avg. gap size = 1.69 (61 / 36) 928 29.99 3.86 6.32 chr6qtel1M 598101 598748 (401252) L1ME4c_3end#LINE/L1 7 639 (191) m_b314s551i2 13148 chr6qtel1M 598101 TCTAAAACATGTAAAGAAAT-ATGTCAAATTTATAAAAATAAAAGTCATT 598149 ?v ?i i iv - - v i - ?i vv L1ME4c_3end#L 7 TCTNTANTATATAAAGAGCTCAT-TCAAATTGATAAGAA-AAANATCAAG 54 chr6qtel1M 598150 -CCCCGATAGATAAACGATCAGAGGATATGAACAGACAATTTTTAGATGA 598198 - i i iv i i ivi ? v L1ME4c_3end#L 55 ACCCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGA 104 chr6qtel1M 598199 CAAAATTAAAGCTATCTATACTTATAGGGATGTCCTATACTTACAAGGAA 598248 vi - v i? -v v --------------- v -- v L1ME4c_3end#L 105 GGAAA-TACAANTA-GTAAAC---------------AAAC--ACATGGAA 135 chr6qtel1M 598249 AAGTGCTCTGAATCACTA-TAAATTTATTACATTTCTCTAAAATGCAAAT 598297 i i vivv i - ----- i v -------i L1ME4c_3end#L 136 AAATGTTCAACCTCGCTAGTAA-----TCAAA-------GAAATGCAAAT 173 chr6qtel1M 598298 TAAAACAACTCTGAGGTACCACCTCATACCTGTCAGATTTACTAAGATGA 598347 i vv i ii i ii i i i vi v i v- L1ME4c_3end#L 174 TAAAGCAACAATGAGATACCATTTTACGCCTATTAAATTAGCAAAAATT- 222 chr6qtel1M 598348 CAGGAAAAAATAATGATA---AATGTTGGAGGAGATGTGGGAAAACTGGG 598394 --vi v i i --- i v ii ? i vi v L1ME4c_3end#L 223 --TAAAAAATTGATAATACCCAATGCTGGCGAGGNTGCGGTGAAACTGGT 270 chr6qtel1M 598395 ACACTAATGCATTGTTGGTAGAGTTATGAAATGATTCAA-----TTGGGA 598439 ? v i i i vi? i i v i v ----- i L1ME4c_3end#L 271 ACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAA 320 chr6qtel1M 598440 A---------CTATGCCCA--AAGGGTTTTAAAACTATGCATATCTTTTC 598478 --------- v i vi -- i iiv v i v i i v L1ME4c_3end#L 321 AGCAATTTGGCAATACGTATCAAGAGCCATAAAAATGTTCATACCCTTTG 370 chr6qtel1M 598479 ATTTAGCAGTCCCATTACAGGGTCTATATCCCAAGGAAATCAT--AAAGG 598526 iii i i i i v v vv v i v -- i L1ME4c_3end#L 371 ACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAAG 420 chr6qtel1M 598527 AGGGAAAAGGAACCACATGTACAAAAATGCTTGTAGCAGCTCTTTTTGTG 598576 i -- i i i i i i i ii v vi v i i L1ME4c_3end#L 421 AAGGAAAA--AGCTATATGCACGAAGATGTTCATTGCAGCGTTATTTATA 468 chr6qtel1M 598577 GTAGCAAAGAATTGGAAAAGGAGTAAAAACCCATCCATTAGGGAATGGCT 598626 i i i viivv vii v v vi i L1ME4c_3end#L 469 ATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAATGGTT 518 chr6qtel1M 598627 GAACAAGTTGTGGTATATGGAAATAATGGAATATTTTTATTCTATAAAAA 598676 i ii i i i v? vvii v vvvv i v L1ME4c_3end#L 519 AAGTAAATTATGGTACATCNACTCGATGGAATATTATGCAGCCATTAAAA 568 chr6qtel1M 598677 GTGATAAATAAGCTGATTTTAGAAAGGCCT-GAAAAGATTTACACATAGT 598725 i v v vv i v iv ivii v - vi ii- - L1ME4c_3end#L 569 ATGATAATTATGAAGACTATGTAGCAACATGGAAAATGTTTATG-ATA-T 616 chr6qtel1M 598726 GATGTTGAATGAAACAAACAGAA 598748 i i i v i L1ME4c_3end#L 617 AATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 38.46 CpG sites = 109, Kimura (unadjusted) = 40.24 Transitions / transversions = 1.49 (109/73) Gap_init rate = 0.08 (49 / 647), avg. gap size = 1.33 (65 / 49) 20 4.13 0.00 0.00 chr6qtel1M 598832 598856 (401144) (TA)n#Simple_repeat 1 25 (0) m_b314s252i3 13149 chr6qtel1M 598832 TATATATATATATATATATATAAAT 598856 v (TA)n#Simple_ 1 TATATATATATATATATATATATAT 25 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 18 16.01 2.86 0.00 chr6qtel1M 600193 600227 (399773) (AG)n#Simple_repeat 1 36 (0) m_b314s252i4 13150 chr6qtel1M 600193 AGAGAGAAAAAAAGAGAGACAGAGACAGAGA-AGAG 600227 i i i v v - (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 36 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 216 34.36 4.12 1.00 chr6qtel1M 601464 601560 (398440) MIR#SINE/MIR 41 140 (122) m_b314s601i2 13151 chr6qtel1M 601464 AGACTGAAAGGGTTCAAATTCTGACTCTCCTTCCTGCTACCCATATGTCT 601513 vvv i i i i v iv i i v ii i v i MIR#SINE/MIR 41 AGACTGCCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACC 90 chr6qtel1M 601514 TTGGGTAATTCCCATCACTTTTC---AACTTGGTTTTCATTAT-TGAAAA 601559 i v iv v v i i ---iv ii i - i - v MIR#SINE/MIR 91 TTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCC-TCATCTGTAAA 139 chr6qtel1M 601560 A 601560 MIR#SINE/MIR 140 A 140 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 44.03 CpG sites = 20, Kimura (unadjusted) = 48.05 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.03 (3 / 96), avg. gap size = 1.67 (5 / 3) 15 8.11 0.00 3.70 chr6qtel1M 602663 602690 (397310) (GGGA)n#Simple_repeat 1 27 (0) m_b314s252i5 13152 chr6qtel1M 602663 GGGAGGAGGTGGAGGGAGGGAGGGAGGG 602690 - iv (GGGA)n#Simpl 1 GGGAGG-GAGGGAGGGAGGGAGGGAGGG 27 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 185 31.96 2.02 2.02 chr6qtel1M 602780 602878 (397122) C L2d2_3end#LINE/L2 (455) 100 2 m_b314s601i3 13153 chr6qtel1M 602780 GAAAGAAAGAAAGAAAGCCAGTTTTCCTGCATTGCAGGCTTTGTGGTAAG 602829 iii v vi v ii vv v vi v v i ?- i C L2d2_3end#LIN 100 GGGGGACAGTGAGTAGACCAGTTTGGCTGGAGCGGAGGGTTCGTGN-AGG 52 chr6qtel1M 602830 GGATATGGTTTAAGA--AAACTGGAAATGGTGGGAGGGGCCAGATTATGA 602877 - i vvi -- ii v ?v vv ii i C L2d2_3end#LIN 51 GGA-ATAGTGGGAGATAAGGCTGGAAAGGNAGGTTGGGGCCAGATCGTGG 3 chr6qtel1M 602878 A 602878 C L2d2_3end#LIN 2 A 2 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 38.10 CpG sites = 16, Kimura (unadjusted) = 43.62 Transitions / transversions = 1.07 (16/15) Gap_init rate = 0.03 (3 / 98), avg. gap size = 1.33 (4 / 3) 467 37.89 5.61 6.62 chr6qtel1M 602822 603980 (396020) C L2#LINE/L2 (125) 2957 1810 m_b314s601i4 13153 chr6qtel1M 602822 GTGGTAAGGGATATGGTTTAAGAAAACTGGAAATGGTGGGAGGGGCCAGA 602871 i i iv i-- i --- v i ----- i C L2#LINE/L2 2957 GTGGTAGGAGATGAGGTC--AGAGA---GGTAACGG-----GGGACCAGA 2918 chr6qtel1M 602872 TTATGAAAGGATTTGAATAAAAAAA-GT--GAATTTCATATTTGAGTCTG 602918 i v i vi -- iivv v- -- i i iivv v v C L2#LINE/L2 2917 TCATGTAGGGCCTTG--TAGGCCATTGTAAGGACTTTGGCTTTTACTCTG 2870 chr6qtel1M 602919 AATGTAATAAAATGTAATTGTAGTTTACTGAAAAGGTGAGTTGATAACAT 602968 i vi iii v iv v vv vi iv iv - i vv C L2#LINE/L2 2869 AGTGAGATGGGAAGCCATTGGAGGGTTTTGAGCAGAGGAGT-GACATGAT 2821 chr6qtel1M 602969 TAGATCAACACTGCAGGAAGATCAGTTTGACAGGTGAGTAGAAGATGAAC 603018 iv iiv ii vi ii i v i i v v v v ii ii C L2#LINE/L2 2820 CTGACTTACGTTTTAAAAGGATCACTCTGGCTGCTGTGTTGAGAATAGAC 2771 chr6qtel1M 603019 TAAAGTAGAGAGAGATTTAATTCAGAGATGATC---TATCAGTCTATGAC 603065 i? vi i vi iv vi vv i - i --- vv v vi C L2#LINE/L2 2770 TGNAGGGGGGCAAGGGTGGAAGCAGGGA-GACCAGTTAGGAGGCTATTGC 2722 chr6qtel1M 603066 ATTTATTTGGGTGTGAGATAATGAAAACATGCAACAGGGTCATTATAATG 603115 v v iii i v i ivii v v v vi vii i C L2#LINE/L2 2721 AGTAATCCAGGCGAGAGATGATGGTGGCTTGGACCAGGGTGGTGGCAGTG 2672 chr6qtel1M 603116 TCAGAGG-GAAAAGTGCC---ATGTAAGACATGATATAAATATAAAATTA 603161 vvi v - i vi--- vivi i iv v i vi i iiii C L2#LINE/L2 2671 GAGGTGGTGAGAAGTGGTCGGATTCTGGATATATTTTGAAGGTAGAGCCG 2622 chr6qtel1M 603162 ACAGGATTTGGCAACAAAACGATCAT-GGGTGTAAGAGTGGGAAAAGAAC 603210 vii iii vi ivii - i vii i i i- C L2#LINE/L2 2621 ACAGGATTTGCTGATGGATTGGATGTGGGGTGTGAGAGAAAGAGAGGAG- 2573 chr6qtel1M 603211 TCATGAAAAAATGATATGTTTCAAGCCAAAGG----GGAAAAAAAGATGT 603256 v i vi v vvv v ivi vi v---- ii vi - C L2#LINE/L2 2572 TCAAGGATGACTCCAAGGTTTTTGGCCTGAGCAACTGGAAGGATGGA-GT 2524 chr6qtel1M 603257 TGGCAGTATTAACAGGAATAAGGAAATATG-AAAAAGAAAAGTTTTTGAG 603305 v --- ? v ii ii ivv -iii i iv v vii C L2#LINE/L2 2523 TGCC---ATTNACTGAGATGGGGAAGACTGCGGGAGGAGCAGGTTTGAGG 2477 chr6qtel1M 603306 AGAAAGATAATAAATTAAGCCTTTTAGATATTAATTTTAAGACAGCTATG 603355 i i v vi i v ii vv v i v i iiv v C L2#LINE/L2 2476 GGGAAGATCAGGAGTTCAGTTTTGGACATGTTAAGTTTGAGATGCCTATT 2427 chr6qtel1M 603356 GAACATTCATTATGAGATATAGGAAATTCAGTTATGGATGTAAGAA--TG 603403 ii i vvvv i v iiv vv -- i v i-- C L2#LINE/L2 2426 AGACATCCAAGTGGAGATGTCGAGTAGGCAGT--TGGATATACGAGTCTG 2379 chr6qtel1M 603404 GAGGTCAGGAAAGAGGATAGCTCCAGGTT---AATA-GGATTT----ATA 603445 v ii ----- i i ---i -ii ----i v C L2#LINE/L2 2378 GAGTTCAGGGGAGAGG-----TCCGGGCTGGAGATATAAATTTGGGAGTC 2334 chr6qtel1M 603446 ATCAATATAGAGATAATTCTTCTATTCATGGAATAATAATGATTTCAATA 603495 ii v ii vi vv vi ii ivi-i vv --- C L2#LINE/L2 2333 ATCAGCATATAGATGGTATTTAAAGCCATGAGACTG-GATGAGATC---A 2288 chr6qtel1M 603496 CTATATGAAATATAGTATATACAATAGTATATAAGAAATATTATAGAGAA 603545 i-? v i i i- i ---i ------ -------- C L2#LINE/L2 2287 CC-NAGGGAGTG-AGTGTA---GATAG------AGA--------AGAGAA 2257 chr6qtel1M 603546 AAAG--AAAAGACCTAGCACAGGAATTGGAAAGCATACATCAACCACCCA 603593 i i --v i iv v ------ --i -- vi vvi?vi C L2#LINE/L2 2256 GAGGTCCAAGGACTGAGCCC------TGG--GGC--ACTCCAACGTTNAG 2217 chr6qtel1M 603594 AGGTGGAATGTGAGATAAATTAAGATACACCAAAGGAGACTATGAAGTAG 603643 v --- v i i-v i vv v iv v C L2#LINE/L2 2216 AGGTCG---GGGAGATGAG-GAGGAACCAGCAAAGGAGACTGAGAAGGAG 2171 chr6qtel1M 603644 CAGTCAAAGTAGCAGGAAGGGAACCA--AGAATATA--GCCATGAAAATC 603689 i i iv vi i i ii -- i i i-- i v i ii C L2#LINE/L2 2170 CGGCCAGTGAGGTAGGAGGAAAACCAGGAGAGTGTGGTGTCCTGGAAGCC 2121 chr6qtel1M 603690 GAGAAAGTAAAGACAA----TCAACTCAATG-----GTAAGCAACAGGTC 603730 ---- i v i---- --v v ----- i v v vvi C L2#LINE/L2 2120 ----AAGTGAAGAAAGTGTTTCAA--GAAGGAGGGAGTGATCAACTGTGT 2077 chr6qtel1M 603731 CAAAAGAAGCAGGTAAATACCAATGA-ATAAG--CTGAGAAGAGGCCATA 603777 v vv v i? ii - v i i - i -- vv i v C L2#LINE/L2 2076 CAAATGCTGCTGANAGGT-CAAGTAAGATGAGGACTGAGAATTGACCATT 2028 chr6qtel1M 603778 AGAGTGACCATTTAAGAGACCATTAGTAAATTTGTAGAGAAAAGTTCTGG 603827 i v v v vivvi ii i i vi vvi iv ii C L2#LINE/L2 2027 GGATTTAGCAACGTGGAGGTCATTGGTGACCTTGACAAGAGCAGTTTCGG 1978 chr6qtel1M 603828 TTGAATAG-AAACCCAGAAATCAGATTTTTCAGT--GTT---AAGAAAAT 603871 v i i -iiivv ii ii v -- vv -- ---i i C L2#LINE/L2 1977 TGGAGTGGTGGGGACGAAAGCCTGA--TTGGAGTGGGTTCAAGAGAGAAT 1930 chr6qtel1M 603872 AAGAAGAAATAAAGGAAAGGCAACATTGTGTA-AGATA---TTCTCAAGG 603917 ii i i vi vvii i i --- v - i ---i i i C L2#LINE/L2 1929 GGGAGGAGAGGAATTGGAGACAGC---GAGTATAGACAACTCTTTCGAGG 1883 chr6qtel1M 603918 AATTTAGCCACAAAAAGAAGAGGAGATAT-------TTTCT----GAGGA 603956 i v iii ii i vi v ------- vv ---- i C L2#LINE/L2 1882 AGTTTTGCTGTAAAGGGGAGCAGAGAAATGGGGCGGTAGCTGGAGGGGGA 1833 chr6qtel1M 603957 TATGGGCTATAAAGGAAAATTTCT 603980 ?i v -i i i i C L2#LINE/L2 1832 NGTGGGGT-CAAGGGAGAATTTTT 1810 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 53.54 CpG sites = 242, Kimura (unadjusted) = 55.84 Transitions / transversions = 1.44 (242/168) Gap_init rate = 0.09 (102 / 1158), avg. gap size = 1.38 (141 / 102) 280 31.43 0.00 0.00 chr6qtel1M 605143 605212 (394788) C MIRc#SINE/MIR (162) 106 37 m_b314s601i5 13154 chr6qtel1M 605143 TGACTAAACAAGGATCACACAACTAGTAAATGTGAGAGACTGCATTTGAA 605192 viv v i i i i vv v v v i i C MIRc#SINE/MIR 106 TGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAA 57 chr6qtel1M 605193 TTTGGGTCTTCTTGACACTA 605212 iiii i v i C MIRc#SINE/MIR 56 CCCAGGTCTTCCTGACTCCA 37 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 39.58 CpG sites = 13, Kimura (unadjusted) = 42.09 Transitions / transversions = 1.44 (13/9) Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0) 13 19.90 2.86 0.00 chr6qtel1M 605981 606015 (393985) (ATA)n#Simple_repeat 1 36 (0) m_b314s252i6 13155 chr6qtel1M 605981 ATAATAATAATAAT-ATAAAATTTAAAATCTTAATA 606015 - v v v v vv (ATA)n#Simple 1 ATAATAATAATAATAATAATAATAATAATAATAATA 36 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 15 23.67 0.00 2.70 chr6qtel1M 607859 607896 (392104) (TA)n#Simple_repeat 1 37 (0) m_b314s252i8 13156 chr6qtel1M 607859 TATTTGTGTATATATACATGTATGTCATATACATATAT 607896 v i i i i i - i (TA)n#Simple_ 1 TATATATATATATATATATATATAT-ATATATATATAT 37 Matrix = Unknown Transitions / transversions = 6.00 (6/1) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 13 33.20 0.00 1.82 chr6qtel1M 607859 607914 (392086) (TATG)n#Simple_repeat 1 55 (0) m_b314s252i7 13157 chr6qtel1M 607859 TATTTGTGTATATATACATGTATGTCATATACATATATGTCTCTGTGTGT 607908 v i i ii - i ii i i v v i (TATG)n#Simpl 1 TATGTATGTATGTATGTATGTATGT-ATGTATGTATGTATGTATGTATGT 49 chr6qtel1M 607909 ATGAAT 607914 v (TATG)n#Simpl 50 ATGTAT 55 Matrix = Unknown Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.02 (1 / 55), avg. gap size = 1.00 (1 / 1) 347 31.74 4.77 4.77 chr6qtel1M 608743 609182 (390818) L1M2_orf2#LINE/L1 27 466 (2825) m_b314s551i3 13158 chr6qtel1M 608743 AATCACAACTGTGAATATGATTGGGATGAACTTTCTCATAAAACTGAAGC 608792 v i iv i i v iv i i i iv v --- ii L1M2_orf2#LIN 27 AATAATAACCTTGAATGTAAATGGATTAAATTCTCCAATTAAA---AGAC 73 chr6qtel1M 608793 A---AATAGCAAAGTGGATTAAAAAAGAGAATGCTAGAACATGTT---TA 608836 --- ? i vi i v v ii iv v vv i i --- L1M2_orf2#LIN 74 ATAGANTGGCTGAATGGATAAAAAAACAAGACCCAACTATATGCTGCCTA 123 chr6qtel1M 608837 CAAGAAACACATTTCAC----AGAGAGATAAATTACAGAGTAAAGGTAAA 608882 v i ---- i v i v --- v i i i L1M2_orf2#LIN 124 CAAGAAACTCACTTCACCTGTAAAGACACACAT---AGACTGAAAGTGAA 170 chr6qtel1M 608883 AGGCT-GAAATCGAGTTTATTATTCTACTTCAACAGAAGTTTAAAAAAAA 608931 i v - vv ------ i iviv i i-ii i?i L1M2_orf2#LIN 171 GGGATGGAAAAAGA------TATTCCATGCAAACGGAAA-CCAAAAGNGA 213 chr6qtel1M 608932 GCAGCATGAGGAACT---CTGATCTCAGATAAAGAAAAAATAAAAATAGA 608978 --- v i --- v v iv i vv v ivi i L1M2_orf2#LIN 214 GCAG---GAGTAGCTATACTTATATCAGATAAAATAGACTTTAAGTCAAA 260 chr6qtel1M 608979 TATAACT---AAAAGAGATAAGAAAAGAAAGTACATCTTGATAAA-GGAT 609024 --- --- i ii i vv v i vv - i L1M2_orf2#LIN 261 ---AACTGTAAAAAGAGACAAAGAAGGTCATTATATAATGATAAAGGGGT 307 chr6qtel1M 609025 AGATTAAACAATGAAG-TATTAATGATATTAAATGTATATACACCAAGTA 609073 vi v i - i - - ii v? i i v ii L1M2_orf2#LIN 308 CAATTCAGCAA-GAGGATA-TAACAATTNTAAATATATATGCACCCAACA 355 chr6qtel1M 609074 GTAGAGCACTCATATCTAGACAG--GATATTAAGGCAGTTACAGGGAAAA 609121 vii i v v v v --i ?viv vi v i i L1M2_orf2#LIN 356 CCGGAGCACCCAGATATATAAAGCAAATATTANTAGATCTAAAGGGAGAG 405 chr6qtel1M 609122 ATATATAGCAACATTCTATCACTGGGGGACCTCAAACTTCCCCTCTCAGA 609171 v iv? i ivv vi v ? i vvii v v L1M2_orf2#LIN 406 ATAGACTNCAATACAATAATAGTNGGGGACTTCAACACCCCACTCTCAGC 455 chr6qtel1M 609172 ATCATACAAAT 609182 ?iiv i L1M2_orf2#LIN 456 ANTGGACAGAT 466 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 42.42 CpG sites = 74, Kimura (unadjusted) = 43.34 Transitions / transversions = 1.25 (74/59) Gap_init rate = 0.07 (30 / 439), avg. gap size = 1.40 (42 / 30) 363 31.96 3.00 3.00 chr6qtel1M 609939 610238 (389762) L1M1_orf2#LINE/L1 829 1128 (2166) m_b314s551i4 13158 chr6qtel1M 609939 AATGACAATAATTAGGCAACATACTGAAAACTATGGGATGAAGCCAAAAC 609988 i iivv vi ii v iv v i L1M1_orf2#LIN 829 AATGATAATGGAAACACAACATACCAAAACCTATGGGATACAGCAAAAGC 878 chr6qtel1M 609989 AGTTTTTAGGGGAAATTTTATATCGATAAATAGCTACCTGAATAAAACAG 610038 vi v i i v v v i iv v v v iv L1M1_orf2#LIN 879 AGTACTAAGAGGGAAGTTTATAGCTATAAGTGCCTACATCAAAAAAGAAG 928 chr6qtel1M 610039 ACAAAGAGAAGATAGATGTATTGGGCATGTAACTAAAAACTCTAGGAA-- 610086 v vvvv i i iivvi iivv i v v ivv i -- L1M1_orf2#LIN 929 AAAAACTTCAAATAAACAACCTAACGATGCATCTTAAAGAACTAGAAAAG 978 chr6qtel1M 610087 -AAGAACAAATTAAAAATCCCCAATTAAATACAAAATTAAAAATTATGAA 610135 - i ii --- v v v i v i vv i v i L1M1_orf2#LIN 979 CAAGAGCAAACCAAA---CCCAAAATTAGTAGAAGAAAAGAAATAATAAA 1025 chr6qtel1M 610136 ACTCCAAGGCTAGATTAGTAAAATTGAAACTAAGAAAACTATTGA----A 610181 iv vi vvv i v i i iv v vv ---- L1M1_orf2#LIN 1026 GATCAGAGCAGAAATAAATGAAATTGAAATGAAGAAAACAATACAAAAGA 1075 chr6qtel1M 610182 CTAATAAAACTAAAAGTTGGTTTTATTTTTTTTAAAA--TCAACACAATA 610229 ii i v ------ v -- v v v L1M1_orf2#LIN 1076 TCAATGAAACAAAAAGTTGG------TTTTTTGAAAAGNTAAACAAAATT 1119 chr6qtel1M 610230 GGCAAACTT 610238 i i L1M1_orf2#LIN 1120 GACAAACCT 1128 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 41.96 CpG sites = 42, Kimura (unadjusted) = 41.96 Transitions / transversions = 0.82 (42/51) Gap_init rate = 0.04 (13 / 299), avg. gap size = 1.38 (18 / 13) 510 34.32 4.92 3.28 chr6qtel1M 610246 611384 (388616) L1M2_orf2#LINE/L1 2123 3279 (12) m_b314s551i5 13158 chr6qtel1M 610246 AGAATCCTATAAAATCATCCAAAAATCTAATGGAAACAATTCACAGCTTT 610295 i ? v i v vv v ?v i vii vv iiv i L1M2_orf2#LIN 2123 AAAANCCTAAAGACTCCACCAAAAAACTNTTAGAACTGATAAACGAATTC 2172 chr6qtel1M 610296 AGCAGAGTTGCAAGATATAAAACAAACTCCCATGAATCATCAACATTTAT 610345 i i i i iv viv vi vi i v L1M2_orf2#LIN 2173 AGTAAAGTTGCAGGATACAAAATCAACATACAAAAATCAGTAGCATTTCT 2222 chr6qtel1M 610346 ATATATTACTGACAAAGCCTAGCAGCTAGAGAAA-GAAGAGA--AATTCC 610392 iiii vii i -- v v vv i -v i -- i L1M2_orf2#LIN 2223 ATACGCCAACAACGAA--CTATCTGAAAAAGAAATCAAGAAAGCAATCCC 2270 chr6qtel1M 610393 ATTTAAAATTACTGTTGACAAAATAAGATATGTGAGTGTCTATCTG-TCA 610441 v vi iivi v i iv ii vi vv i i-i L1M2_orf2#LIN 2271 ATTTACAATAGCTACAAAAAAAATAAAATACCTAGGAATAAATTTAACCA 2320 chr6qtel1M 610442 AGAACAAACCTAAGAACTATGTGAACATAATTAGAAAATTTTTTTCATAC 610491 i --iiivv v v iii ?v v i v ivi vv v v v L1M2_orf2#LIN 2321 AGGA--GGTGAAAGATCTCTACAANGAAAACTATAAAACACTGATGAAAG 2368 chr6qtel1M 610492 AAATAAAGTCAGATCTACACAACTGGAAAAATATAAATTGTTCCTTGATA 610541 vi ivvi ivi v ? v i vvvv i v v v L1M2_orf2#LIN 2369 AAATTGAAGAGGACACAAANAAATGGAAAGATATCCCATGCTCATGGATT 2418 chr6qtel1M 610542 CCCTGAGCTAATATGATACAAAT-------CTACCTAAATCACTTTATTC 610584 vvvv ii vi vv ------- i v iv i ivv L1M2_orf2#LIN 2419 GGAAGAATTAATATTGTTAAAATGNCCATACTACCCAAAGCGATCTACAG 2468 chr6qtel1M 610585 ATTTAGTGCAATATCCATCAAACTGCCAA-AATATTATTTTATAGA--TA 610631 i i vi i v i -i i -i i i -- L1M2_orf2#LIN 2469 ATTCAATGCAATCCCTATCAAAATACCAATGACATT-CTTCACAGAAATA 2517 chr6qtel1M 610632 GAAAAAATAATAACAAAATTCTTCCAGAAGAACAAAAAGTCACGCATA-T 610680 ? vvi v vii vv iii v v -i L1M2_orf2#LIN 2518 GAAAAAANAATCCTAAAATTCGTATGGAACCACAAAAGACCCCGAATAGC 2567 chr6qtel1M 610681 TAAAGAAATTAATGAAAAAATATATAAAGGATGGTGGGTTAGCAGTACCA 610730 i v iv- iv v v vv i v v vv vi v v L1M2_orf2#LIN 2568 CAAAGCAATCC-TGAGCAAAAAGAACAAAGCTGGAGGCATCACACTACCT 2616 chr6qtel1M 610731 AACCTAAAACCATATTATACAAC---AGCACCATCAAAACCTTTTGGTAC 610777 i i v vi i i v i --- i -- i vviv L1M2_orf2#LIN 2617 GACTTCAAAATATACTACAAAGCTATAGTA--ACCAAAACAGCATGGTAC 2664 chr6qtel1M 610778 TGGTTAAGAAATATAGTGCTGGATCATTGGGATAAATTAGATA---CAAA 610824 ivv i i v vvvv i i v i i i v v --- i L1M2_orf2#LIN 2665 TGGCATAAAAACAGACACATAGACCAATGGAACAGAATAGAGAACCCAGA 2714 chr6qtel1M 610825 CAATACATTGATAAAAGCCTATAGCAATCTAGTGTTTGATAAACCCTCAA 610874 - v iv iiv --ii i v v ii v i i vv v v L1M2_orf2#LIN 2715 -AATAAATCCACGCA--TTTACAGCCAACTGATTTTCGACAAAGGCGCCA 2761 chr6qtel1M 610875 ATTCCAGCTTCTATACTG-----AGAACTCACTCTTTGACAAA-ATTTCT 610918 vvv ----- i ? ----- i vvv ii i -iv v L1M2_orf2#LIN 2762 AGAACA-----TACANTGGGGAAAGGACAGTCTCTTCAATAAATGGTGCT 2806 chr6qtel1M 610919 GGGAAAACTGGAAAATAATATGTCAG--GAACTCAGCATAGACCCACACT 610966 v viv - -- ivv i - vi ii L1M2_orf2#LIN 2807 GGGAAAACTGGATATCCATATG-CAGAAGAATGAAAC-TAGACCCCTATC 2854 chr6qtel1M 610967 GCACATCTCACACCAATATAAGGTCAAAATGAGTACATGACTTGGGTGTA 611016 v v i vi i v v v iv ii vv v iii L1M2_orf2#LIN 2855 TCTCACCATATACAAAAATCAACTCAAAATGGATTAAAGACTTAAATGTA 2904 chr6qtel1M 611017 AAGGATGATACCTTAAACAAATTAG--GAAAACA-AGGGATAACTTACCT 611063 iivvi v iv vvv i -- - iv ---v L1M2_orf2#LIN 2905 AGACCCGAAACTATAAAACTACTAGAAGAAAACATAGGGGAAAC---GCT 2951 chr6qtel1M 611064 ATTAGATCTTTGAAGAAGGGAGAAATTTAT-GAACAA----TTAAGAA-A 611107 - i iv v ivvvi v i i v - i?i ---- i i i- L1M2_orf2#LIN 2952 -TCAGGACATTGGTCTGGGCAAAGATTTTTTGGNTAAGACCTCAAAAGCA 3000 chr6qtel1M 611108 TAGAGAACATTTTGAAAGACAAAATAGACAACTCTGATTACATTAAATTA 611157 i iv ----- vv v vv i i L1M2_orf2#LIN 3001 CAGGCAACA-----AAAGCAAAAATAGACAAATGGGATTACATCAAACTA 3045 chr6qtel1M 611158 AAAAA----TGCACAAACAAATCTGAACAG-AAACAAAATTAAAAGGTAA 611202 i---- - i -vvi i-v i i v i ii L1M2_orf2#LIN 3046 AAAAGCTTCTGCAC-AGCAAA-GGAAACAATCAACAGAGTGAAGAGACAA 3093 chr6qtel1M 611203 -GTAAAGAGCTGGGGAAAATACTTAACAGCTAGTGTTTCTGA-AAAGGCC 611250 -v v iiv i i ivv i - ?iv - i vi L1M2_orf2#LIN 3094 CCTACAGAATGGGAGAAAATATTTGCAAACTA-TNCATCTGACAAGGGAT 3142 chr6qtel1M 611251 TCATTTCTAAAATATATAAAGAACT-----GGCTCAAATTTGTCAGAATA 611295 v v i i i -----ii ---iiv i v L1M2_orf2#LIN 3143 TAATATCCAGAATATATAAGGAACTCAAACAACTCAA---CAGCAAAAAA 3189 chr6qtel1M 611296 A-AAATCATTCCACAATTGACAAATGGTCAGAGGATATGA--AGACAATT 611342 - v i--- i ? v v i iv -- v L1M2_orf2#LIN 3190 ACAAATAATC---CGATTNAAAAATGGGCAAAGGACCTGAATAGACATTT 3236 chr6qtel1M 611343 TTCAAATGATAAGAT-TAAA--GCCACTGTACTTATATGAAAAAA 611384 i v vi v -i -- --ii vv L1M2_orf2#LIN 3237 CTCAAAAGAAGACATACAAATGGCCA--ACAGGTATATGAAAAAA 3279 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 45.87 CpG sites = 190, Kimura (unadjusted) = 47.27 Transitions / transversions = 1.01 (190/188) Gap_init rate = 0.06 (64 / 1138), avg. gap size = 1.47 (94 / 64) 774 31.42 2.59 8.20 chr6qtel1M 611256 611834 (388166) L1ME4c_3end#LINE/L1 7 555 (275) m_b314s551i6 13158 chr6qtel1M 611256 TCTAAAATATATAAAGAACTGGCTCAAATTTGTCAGAATAAAAATCATT- 611304 ?v ? i vii vi v - ? vv- L1ME4c_3end#L 7 TCTNTANTATATAAAGAGCTCATTCAAATTGATAAGAA-AAANATCAAGA 55 chr6qtel1M 611305 CCACAATTGACAAATGGTCAGAGGATATGAA--GACAATTTTCAAATGAT 611352 v v i v i i -- iv ? v v L1ME4c_3end#L 56 CCCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAG 105 chr6qtel1M 611353 AAGATTAAAGCCACTGTACT--TATATGAAAAAAAATTGTCTAAGC-CAG 611399 i i - v i?i v iv v--i i i --- ii v - iv L1ME4c_3end#L 106 GAAAT-ACAANTAGTAAACAAACACATGGAAAAA---TGTTCAACCTCGC 151 chr6qtel1M 611400 TATTAATTTATTGCATTTCTCTAAAATGCAAAGGAAAACAACTCCAAAGT 611449 v iv ---- -------i vv i vvii ii L1ME4c_3end#L 152 TAGTAATCAA----A-------GAAATGCAAATTAAAGCAACAATGAGAT 190 chr6qtel1M 611450 ATCTCCTCATACCTCTCAGGTTGATTACGATAATAGAAAAAGATAATGAT 611499 i vii i ii v i ii ii--- i v vv iv i i L1ME4c_3end#L 191 ACCATTTTACGCCTATTAAATTAG---CAAAAATTTAAAAAATTGATAAT 237 chr6qtel1M 611500 A---AGTGTTGGAGGGGATATGGGAAAACTGGTTCACTAATGCATTGTTG 611546 --- i i v i ? ii vi v ? v i i L1ME4c_3end#L 238 ACCCAATGCTGGCGAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTG 287 chr6qtel1M 611547 GTAGAGTAGTGAAGTGATTCAACCATTTTGGAGAGCAATTTGGAACTGTG 611596 i vi?v i v i v v i v v ii L1ME4c_3end#L 288 GTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACG 337 chr6qtel1M 611597 CCCAAAGGGCTATAACAATGTGCATACCCTTTCACTTAGCAGTTGCATTA 611646 iviv i i v v v ii i i v i v L1ME4c_3end#L 338 TATCAAGAGCCATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTT 387 chr6qtel1M 611647 CTGGATAAGTACTCCAAAGAAATCAT--AAAGGAAGGGAACGGACCCACA 611694 iv vv ii i i v -- i i vi -- i i L1ME4c_3end#L 388 CTGGGAATTTATCCTAAGGAAATAATTCAAAAGAAGGAAAAAG--CTATA 435 chr6qtel1M 611695 CATGCAAACATGTTTGTAGCAGTTTTTTTGTTGTTGTTGTTGTTGTTTTT 611744 iiii i v ii v ------i i-------------- L1ME4c_3end#L 436 TGCACGAAGATGTTCATTGCAG------CGTTA--------------TTT 465 chr6qtel1M 611745 TTGGTAGCAAAGAATGGGAAA----ATGAATGGAAACTCATCCATTGGGG 611790 v ii i i v ----v i ----ii v v v L1ME4c_3end#L 466 ATAATAGCGAAAAATTGGAAACAACCTAAATG----TCCAACAATAGGGG 511 chr6qtel1M 611791 AATGGCTGGACAACTTGTGATACGTGTAAGTAATGGGATATTAT 611834 i iiii v i i i v? vvii i L1ME4c_3end#L 512 AATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATATTAT 555 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 40.21 CpG sites = 102, Kimura (unadjusted) = 43.02 Transitions / transversions = 1.57 (102/65) Gap_init rate = 0.09 (52 / 578), avg. gap size = 1.15 (60 / 52) 25 22.06 0.00 0.00 chr6qtel1M 612196 612248 (387752) (TA)n#Simple_repeat 1 53 (0) m_b314s252i9 13159 chr6qtel1M 612196 TATATATACATAAATACACACAAATATAAATACATATATATACATATATA 612245 i v i i i v v i i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr6qtel1M 612246 AAT 612248 v (TA)n#Simple_ 51 TAT 53 Matrix = Unknown Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 197 28.77 9.40 4.92 chr6qtel1M 612265 612381 (387619) L2a_3end#LINE/L2 396 517 (0) m_b314s601i6 13160 chr6qtel1M 612265 AAAATGGAAAATGTTTGAGATCAGAAATTTAATTTTC-ATTTTGGTCATT 612313 i v iv viv iv ii i -- v -i v i L2a_3end#LINE 396 AGAATGTAAGCTCCATGAGGGCAGGGACTT--TTGTCTGTTTTGTTCACT 443 chr6qtel1M 612314 -----ATCACCATATGT---GAACCCAATGTCTATTGCATGGTAGGAGCT 612355 ----- v -ii i--- -- i i ivii i v L2a_3end#LINE 444 GCTGTATCCCCA-GCGCCTAGAAC--AGTGCCTGGCACATAGTAGGCGCT 490 chr6qtel1M 612356 TAATAAATGTTTGACTGA--GAAGGAAT 612381 i i -i -- v L2a_3end#LINE 491 CAATAAATATTTG-TTGAATGAATGAAT 517 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 36.45 CpG sites = 21, Kimura (unadjusted) = 37.98 Transitions / transversions = 1.91 (21/11) Gap_init rate = 0.09 (10 / 116), avg. gap size = 1.70 (17 / 10) 217 23.07 3.77 1.85 chr6qtel1M 612329 612381 (387619) L2c_3end#LINE/L2 425 478 (0) m_b314s601i7 13160 chr6qtel1M 612329 CCCAATGTCTATTGCATGGTAGGAGCTTAATAAATGTTTGACTGA--GAA 612376 ii i ivii i v i -i -- L2c_3end#LINE 425 CCCAGCGCCTGGCACATAGTAGGCGCTCAATAAATGTTTG-TTGAATGAA 473 chr6qtel1M 612377 GGAAT 612381 v L2c_3end#LINE 474 TGAAT 478 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 26.11 CpG sites = 9, Kimura (unadjusted) = 28.93 Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.50 (3 / 2) 477 38.32 2.95 8.59 chr6qtel1M 615226 616207 (383793) C L2#LINE/L2 (68) 3014 2084 m_b314s601i8 13161 chr6qtel1M 615226 TGTTCAAGGAA-ATCAAGAAAGCCAGTTTCCCTGCATGGCAG---GCTAT 615271 i - v i i v vv v vv v --- v v C L2#LINE/L2 3014 TGTTCGAGGAACAGCAAGGAGGCCAGTGTGGCTGGAGCGGAGTGAGCGAG 2965 chr6qtel1M 615272 ATGGTAA-----AGGATATGATTTAAGAAAACTGGAAATGGTGGGAGGGG 615316 iv vi ----- v vv v i --- v i ----- i C L2#LINE/L2 2964 GGGGAGAGTGGTAGGAGATGAGGTCAGAGA---GGTAACGG-----GGGA 2923 chr6qtel1M 615317 CCAGATTATGAAAGGATTTGAATAAAAAAA-GT--GAATTTCATATTTGA 615363 i v i vi -- iivv v- -- i i iivv v C L2#LINE/L2 2922 CCAGATCATGTAGGGCCTTG--TAGGCCATTGTAAGGACTTTGGCTTTTA 2875 chr6qtel1M 615364 GTCTGAATG-TATAAAATGTAATTGTAGTTTACTGAAAAGGTGAGTTGAT 615412 v i -v iii v iv v vv vi iv iv - i C L2#LINE/L2 2874 CTCTGAGTGAGATGGGAAGCCATTGGAGGGTTTTGAGCAGAGGAGT-GAC 2826 chr6qtel1M 615413 AAGATTAGACCAACACTGCAGGAAGATCAGTTTGACAGGTGAGTGCAAGA 615462 v iv iv ii vi ii i v i i v v v vv ii C L2#LINE/L2 2825 ATGATCTGACTTACGTTTTAAAAGGATCACTCTGGCTGCTGTGTTGAGAA 2776 chr6qtel1M 615463 TGAACTAAAGTAGAGAGAGATTTAATTCAGAGAGACGATCTAGCAGTCTA 615512 ii i? vi i vi iv vi vv i v vi v v C L2#LINE/L2 2775 TAGACTGNAGGGGGGCAAGGGTGGAAGCAGGGAGACCAGTTAGGAGGCTA 2726 chr6qtel1M 615513 CT-CATTTATTTGGGCATGAGATAATGAAAACGCGCAACAGGGTCATTGT 615561 i - v v iii iv i ivii vi v v vi v i C L2#LINE/L2 2725 TTGCAGTAATCCAGGCGAGAGATGATGGTGGCTTGGACCAGGGTGGTGGC 2676 chr6qtel1M 615562 AA---AGTCAGAGAGAAA-AGTGCCATGTAAGACATGATATAAATATAAA 615607 i--- vii v i-i vvv vivi i iv v i vi i C L2#LINE/L2 2675 AGTGGAGGTGGTGAGAAGTGGTCGGATTCTGGATATATTTTGAAGGTAGA 2626 chr6qtel1M 615608 ATTAACAGGATTTGGCAAAAAAAAAAAAAAATGATCATGGGTGTAAGAGT 615657 iiii vii vii vvi------- vvv i v C L2#LINE/L2 2625 GCCGACAGGATTTGCTGATGGATTG-------GATGTGGGGTGTGAGAGA 2583 chr6qtel1M 615658 GGGAAGAGAACTCATGAATAAATGACATGTTTCAAGTCAAAGTGACAAAA 615707 ii - i v v i i v vvv v ivi i vi ii vii C L2#LINE/L2 2582 AAGA-GAGGAGTCAAGGATGACTCCAAGGTTTTTGGCCTGAGCAACTGGA 2534 chr6qtel1M 615708 AAGATGTTGGCAATATTAACAGGAATAAGGAAATATGAAAGAGGAA-AGT 615756 i vv viivi ? v ii ii ivv vii i- v C L2#LINE/L2 2533 AGGATGGAGTTGCCATTNACTGAGATGGGGAAGACTGCGGGAGGAGCAGG 2484 chr6qtel1M 615757 TTTGGAGAAAAAGATAATAAATTAAGCCTTTTAAATATTAATTTTAAGAC 615806 ii iii v vi i v ii vv v i v i i C L2#LINE/L2 2483 TTTGAGGGGGAAGATCAGGAGTTCAGTTTTGGACATGTTAAGTTTGAGAT 2434 chr6qtel1M 615807 TGTTATGGAACATTCATAATG-AGATGTAGGAAATTCAGTTATGCATGTA 615855 vvi vii i - i - v iiv vv ivii iii C L2#LINE/L2 2433 GCCTATTAGACATCCA-AGTGGAGATGTCGAGTAGGCAGTTGGATATACG 2385 chr6qtel1M 615856 AGAATGAAGGTCAGGAAAAAGGATAGCTCCAGGTAAATAGATTTT---AT 615902 vv i v ii i viv vv ii iv v i v---i C L2#LINE/L2 2384 AGTCTGGAGTTCAGGGGAGAGGTCCGGGCTGGAGATATAAATTTGGGAGT 2335 chr6qtel1M 615903 AATCAATATAGAGATAATTCTTCTATTCATGGAATGATATTGATTTCAAG 615952 v ii v ii vi vv vi ----------------- C L2#LINE/L2 2334 CATCAGCATATAGATGGTATTTAAAGCCATG-----------------AG 2302 chr6qtel1M 615953 ACTACATGAAGTATAGCATATGCAAT-AGTATATAT-GAAATACTATAGA 616000 iv i-- vi v? v v i - i v - i ------ C L2#LINE/L2 2301 ACTGGATGAG--ATCACCNAGGGAGTGAGTGTAGATAGAGA------AGA 2260 chr6qtel1M 616001 AAAAAAG-GAAAAGACCTAGCACAGGAATTGGAAAGCATACATCAACCAC 616049 i i i -vv i iv v ------ --i -- vi vvi C L2#LINE/L2 2259 GAAGAGGTCCAAGGACTGAGCCC------TGG--GGC--ACTCCAACGTT 2220 chr6qtel1M 616050 CCAAGGTGGAATGTGAGATAAATTAAGATACACCAAAGGAGACTAGGAAG 616099 ?vi v --- v i i-v i vv v ii C L2#LINE/L2 2219 NAGAGGTCG---GGGAGATGAG-GAGGAACCAGCAAAGGAGACTGAGAAG 2174 chr6qtel1M 616100 TAACAGTCAAAGTAGCAGGAAGGGAACCA--AGAATATGGTAATCAACAG 616147 v i i i iv vi i i ii -- i i --------- C L2#LINE/L2 2173 GAGCGGCCAGTGAGGTAGGAGGAAAACCAGGAGAGTGTGGT--------- 2133 chr6qtel1M 616148 GTCC-AAAAGCAACAAGTAAAAACCAGTGAATAAGCTGAGAAGAGGCCAT 616196 -ii -- i i -v vv v ---- ii ---- C L2#LINE/L2 2132 GTCCTGGAAGC--CAAGTGAAGA-AAGTGTTTCA----AGAAGGAG---- 2094 chr6qtel1M 616197 AGGAGTGATCA 616207 - C L2#LINE/L2 2093 -GGAGTGATCA 2084 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 53.43 CpG sites = 185, Kimura (unadjusted) = 55.40 Transitions / transversions = 1.16 (185/159) Gap_init rate = 0.10 (97 / 981), avg. gap size = 1.12 (109 / 97) 13 32.07 0.00 1.89 chr6qtel1M 620495 620548 (379452) (GAGG)n#Simple_repeat 1 53 (0) m_b314s252i10 13162 chr6qtel1M 620495 GAGGGAAGGAAAGAGTGAGGGAAAGAGGAAAAGAAGTGATAGGGGGAGGG 620544 i ii v ii -i i i v vi i (GAGG)n#Simpl 1 GAGGGAGGGAGGGAGGGAGGGAGGGAGG-GAGGGAGGGAGGGAGGGAGGG 49 chr6qtel1M 620545 AGGG 620548 (GAGG)n#Simpl 50 AGGG 53 Matrix = Unknown Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.02 (1 / 53), avg. gap size = 1.00 (1 / 1) 291 35.74 3.37 3.57 chr6qtel1M 621731 622235 (377765) L1PREC2_orf2#LINE/L1 118 621 (2673) m_b314s551i9 13163 chr6qtel1M 621731 TGTTTACAAGAAGCACATTTCGTATAGA--GATAAATACAGAGTAAAGAT 621778 i v ii v i ii iv -- i vvi i iv v i L1PREC2_orf2# 118 TGTCTTCAAGAGACCCATCTCACATGCAATGACACCCATAGGCTCAAAAT 167 chr6qtel1M 621779 AAAGGGCTGAACTAGAATTTATTATTGTACTTCAACAGAAGTTAAAAAAA 621828 v i vv i i ii v- i ---- ii ivi i L1PREC2_orf2# 168 AAAGGGATGGAGAAAAATCTACCAA-GCA----AATGGAAAACAGAAAAA 212 chr6qtel1M 621829 AGCAACACTAGGAATTCTGATCTCAGATAAAGAAAAAATAAAAATAGATA 621878 iviv v v i i i i iv i vv v vi ivv L1PREC2_orf2# 213 AGCAGGGGTTGCAATCCTAATTTCAGACAAAACAGACTTTAAACCAACAA 262 chr6qtel1M 621879 TAACTAAAAGAGATAAGAAAGGAAAATACATCTTGATAAAGGATAC-ATT 621927 vi ii i i ii iv v vv i i v - L1PREC2_orf2# 263 AGATCAAAAAAGACAAAGAAGGGCATTACATAATGGTAAAGGGTTCAATT 312 chr6qtel1M 621928 AAACAATGAAGTATTAATGATATTAAATGTATATACTCCAAGTAGTAGAG 621977 v - vvi iv vi i i v v ii vvi L1PREC2_orf2# 313 CAACAA-GAAGACCTAACTATCCTAAATATATATGCACCCAACACAGGAG 361 chr6qtel1M 621978 CACTCATATCTAGA---CAAGATATT-GAGGCAGTTACAGGGAGAAATAG 622023 i v ii v --- v v - i --i ? ii vv L1PREC2_orf2# 362 CACCCAGATTCATAAAGCAAGTTCTTAGAGAC--CTNCAAAGAGACTTAG 409 chr6qtel1M 622024 ACAGCAACATTCTATTACTGGGGGACCTCAAACTTCCCCTCTCAGAAACA 622073 vv v ivv v v i i vvii v vv v vi L1PREC2_orf2# 410 ACTCCCACACAATAATAGTGGGAGACTTCAACACCCCACTGACAGTATTA 459 chr6qtel1M 622074 TACAAATGTAACTTAAAAATAAACAA-TAAAAAAGAAATTAGGGACTTTA 622122 v i ---- v vi iii i v - v v vi i v L1PREC2_orf2# 460 GACAGAT----CATCGAGGCAGAAAATTAACAAAGATATTCAGGACCTGA 505 chr6qtel1M 622123 AGAGAGTCCTAGA--AAACCTGGATATGATAGATGTATAGAGAA------ 622164 vvv iiv i -- -- iv ii v v ------ L1PREC2_orf2# 506 ACTCAACACTGGACCAAA--TGGACCTGATAGACATCTACAGAACTCTCC 553 chr6qtel1M 622165 AACTAAATACATAAAAGGAATTCCCGGTTTTTCTTGACACTATATGGTAT 622214 v i? v --- vi viv -i i iiv i i i i i L1PREC2_orf2# 554 ACCCNAAAAC---AACAGAATATAC-ATTCTTCTCATCGCCACATGGCAC 599 chr6qtel1M 622215 CTAC-AAAAAATGGACCACGTA 622235 v -vv v i L1PREC2_orf2# 600 ATACTCTAAAATCGACCACATA 621 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 49.19 CpG sites = 91, Kimura (unadjusted) = 50.00 Transitions / transversions = 1.10 (91/83) Gap_init rate = 0.05 (26 / 504), avg. gap size = 1.35 (35 / 26) 334 35.00 2.51 3.46 chr6qtel1M 621731 622168 (377832) L1P4_orf2#LINE/L1 118 551 (2743) m_b314s551i8 13163 chr6qtel1M 621731 TGTTTACAAGAAGCACATTTCGTATAGA--GATAAATACAGAGTAAAGAT 621778 i v ii v i ii iv -- i vvi i iv v ii L1P4_orf2#LIN 118 TGTCTTCAAGAGACCCATCTCACATGTAACGACACCCATAGGCTCAAAGT 167 chr6qtel1M 621779 AAAGGGCTGAACTAGAATTTATTATTGTACTTCAACAGAAGTTAAAAAAA 621828 ? i vv ii i i i- i ---- i ivi i L1P4_orf2#LIN 168 AAAGGGNTGGAGAAAGATCTATCAC-GCA----AACGGAAAACAAAAAAG 212 chr6qtel1M 621829 AGCAACACTAGGAATTCTGATCTCAGATAAAGAAAAAATAAAAATAGATA 621878 iviv v vv v v iv i vv v vi ivv L1P4_orf2#LIN 213 AGCAGGGGTCGCTATTCTTATATCAGATAAAACAGACTTTAAACCAACAA 262 chr6qtel1M 621879 TAACTAAAAGAGATAAGAAAGGAAAATACATCTTGATAAAGGATAC-ATT 621927 i iiv ii i ii iv v vv i v - L1P4_orf2#LIN 263 CAGTAAAAAAGGACAAAGAAGGGCATTACATAATGATAAAGGGTTCAATT 312 chr6qtel1M 621928 AAACAATGAAGTATTAATGATATTAAATGTATATACTCCAAGTAGTAGAG 621977 v - vv iv vi i ii v v ii v i L1P4_orf2#LIN 313 CAACAA-GAAGACTTAACTATCCTAAATATATACGCACCCAACATTGGAG 361 chr6qtel1M 621978 CACTCATATCT---AGACAAGATATTG-AGGCAGTTACAGGGAGAAATAG 622023 i v ii--- i v?v v- i --i iiii vv L1P4_orf2#LIN 362 CACCCAGATTCATAAAACAAGTNCTTCTAGAC--CTACGAAAAGACTTAG 409 chr6qtel1M 622024 ACAGCAACATTCTATTACTGGGGGACCTCAAACTTCCCCTCTCAGAAACA 622073 v ivv v v i vvii v vv vivi L1P4_orf2#LIN 410 ACAGCCACACAATAATAGTGGGGGACTTCAACACCCCACTGACAGCGTTA 459 chr6qtel1M 622074 TACAAATGTAACTTAAAAATAAACAA-TAAAAAAGAAATTAGGGACTTTA 622122 v i ---- v vi iii i v - v vv v L1P4_orf2#LIN 460 GACAGAT----CATCGAGGCAGAAAACTAACAAAGAAATTCTGGACTTAA 505 chr6qtel1M 622123 A---GAGAGTCCTAGAAAACCTGGATATGATAGATGTATAGAGAAAACT 622168 --- v --- v vv vi iv i ii v v v L1P4_orf2#LIN 506 ACTCGACA---CTTGACCAATTGGACCTAATAGACATCTACAGAATACT 551 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 45.66 CpG sites = 75, Kimura (unadjusted) = 48.36 Transitions / transversions = 1.03 (75/73) Gap_init rate = 0.05 (21 / 437), avg. gap size = 1.24 (26 / 21) 434 34.31 1.79 2.85 chr6qtel1M 621731 622120 (377880) L1M1_orf2#LINE/L1 118 503 (2791) m_b314s551i7 13163 chr6qtel1M 621731 TGTTTACAAGAAGCACATTTCG--TATAGAGATAAATACAGAGTAAAGAT 621778 ii i i i-- i i v i i v i i L1M1_orf2#LIN 118 TGCCTACAAGAAACACACTTCACCTATAAAGACACACATAGACTGAAAAT 167 chr6qtel1M 621779 AAAGGGCTGAACTAGAATTTATTATTGTACTTCAACAGAAGTTAAAAAAA 621828 v i vv ii ----- vi ivi ii iii i L1M1_orf2#LIN 168 AAAGGGATGGAAAAAGAT-----ATTCCATGCCAATGGAAACCAAAAAAG 212 chr6qtel1M 621829 AGCAACACTAGGAATTCTGATCTCAGATAAAGAAAAAATAAAAATAGATA 621878 iv v vv v v v i iv i vv v i i i v L1M1_orf2#LIN 213 AGCAGGAGTAGCTATACTTATATCAGACAAAATAGATTTCAAGACAAAAA 262 chr6qtel1M 621879 TAACTAAAAGAGATAAGAAAGGAAAATACATCTTGATAAAGGATAC-ATT 621927 iv iv i i ii vv v i vv ivv - L1M1_orf2#LIN 263 CTATAAGAAGAGACAAAGAAGGTCACTATATAATGATAAAGGGGTCAATT 312 chr6qtel1M 621928 AAACAATGAAG-TATTAATGATATTAAATGTATATACTCCAAGTAGTAGA 621976 v i - i - - ii v? i i v v ii v i L1M1_orf2#LIN 313 CAGCAA-GAGGATA-TAACAATTNTAAATATATATGCACCCAACACTGGA 360 chr6qtel1M 621977 GCACTC--ATATCTAGACAAGATATTGAGGCAGTTACAGGGAGAAATAGA 622024 i -- v i vv i ivviv i v i i L1M1_orf2#LIN 361 GCACCCAGATATATAAAGCAAATATTATTAGAGCTAAAGAGAGAGATAGA 410 chr6qtel1M 622025 CAGCAACATTCTATTACTGGGGGACCTCAAACTTCCCCTCTCAGAAACAT 622074 vv i ivv v viv i i vvii v i v viiv L1M1_orf2#LIN 411 CCCCAATACAATAATAGCTGGAGACTTCAACACCCCACTTTCAGCATTGG 460 chr6qtel1M 622075 ACAAATGTAACTTAAAAATAAACAAT-AAAAAAGAAATTAGGGACTT 622120 i ---- vv i i i v - v ivvv L1M1_orf2#LIN 461 ACAGAT----CTTCCAGACAGAAAATCAACAAAGAAACATCGGACTT 503 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 47.20 CpG sites = 70, Kimura (unadjusted) = 47.20 Transitions / transversions = 1.17 (70/60) Gap_init rate = 0.04 (16 / 389), avg. gap size = 1.12 (18 / 16) 447 33.42 2.58 2.84 chr6qtel1M 622787 623174 (376826) L1M4_orf2#LINE/L1 748 1134 (2160) m_b314s551i10 13164 chr6qtel1M 622787 TGGAAATTAAATAATCTAATTCTAAATAAT-GATGGGTCATGCAACAAAT 622835 i ivi v i i-i viv v L1M4_orf2#LIN 748 TGGAAATTAAACAACACACTCCTAAATAACCAATGGGTCAAAGAAGAAAT 797 chr6qtel1M 622836 GGCAGAAACAATCCTCAATTTCATCCAAGAC-AATGACAATAATGAGAAA 622884 vi iiiiv ivvv v v - iii i- v ii vi v v L1M4_orf2#LIN 798 CACAAGGGAAATTAGAAAATAC-TTTGAGATGAATGAAAACGAAAACACA 846 chr6qtel1M 622885 CCATACCCAAAACTT-TGGGATGCAGCCAAAGCAGTTTTTAGGAGAAGTT 622933 v - - ? vi ii i iv L1M4_orf2#LIN 847 ACATACC-AAAACTTATGGGATGCAGCNAAAGCAGTGCTTAGAGGGAAAT 895 chr6qtel1M 622934 TTAAATCAATAAATATCTAACTGAATAAAACAGACAAAGAAAAGATCAAT 622983 v v vi ii vv v v iv v i vvvv i L1M4_orf2#LIN 896 TTATAGCTGTAAATGCCTATATTAAAAAAGAAGAAAGATCTCAAATCAAT 945 chr6qtel1M 622984 GAATTGGGCATGCAACTAAAAACTCTAGAAAAAGAA---CAAAATAAAAC 623030 i vi iiv v v v v i vv --- v -- L1M4_orf2#LIN 946 AACCTAACCTTCCACCTTAAGAAACTAGAAAAAGAAGAGCAAACTAAA-- 993 chr6qtel1M 623031 CCCCAATTAAATACAAAATTGGAAATTATGAAACTCCAAGGCTAGGTTAA 623080 v vi ii v iivv v i iv ivi vvv ii v L1M4_orf2#LIN 994 CCCAAAGCAAGCAGAAGGAAGGAAATAATAAAGATTAGAGCGGAAATAAA 1043 chr6qtel1M 623081 TAAAATTGAAAGTAATAAAATTATTGAC----CTAATAAAACTAAGAATT 623126 i v i i iv iv v v----ii ii i i i L1M4_orf2#LIN 1044 TGAAATAGAGAATAGAAAAACAATAGAGAAAATCAACGAAACCAAAAGTT 1093 chr6qtel1M 623127 AGTTTTATTTTTTTTAAAAAAATCAACAACATTGGCAAACTTTTGGTT 623174 i ------- i i i v i i i i L1M4_orf2#LIN 1094 GG-------TTCTTTGAAAAGATCAACAAAATTGACAAACCTTTAGCT 1134 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 44.34 CpG sites = 67, Kimura (unadjusted) = 45.42 Transitions / transversions = 1.14 (67/59) Gap_init rate = 0.04 (16 / 387), avg. gap size = 1.31 (21 / 16) 1812 27.81 0.35 0.53 chr6qtel1M 623342 623905 (376095) L1M4_orf2#LINE/L1 1413 1975 (1319) m_b314s551i11 13164 chr6qtel1M 623342 AAGACAAGATGTATTTACATGTGAATTCTACCAAACATTTAAAGAACAAT 623391 i ? v vv i vv v L1M4_orf2#LIN 1413 AGGNCCAGATGGCTTCACTGGTGAATTCTACCAAACATTTAAAGAAGAAT 1462 chr6qtel1M 623392 CAACTCCAATGCTATATACACTATTTGAAAAAAATAGGAAGTGAAGGAGG 623441 i v v vi i v v iv - i iiv i iv L1M4_orf2#LIN 1463 TAACACCAATCCTTCACAAACTCTTCCAAAAAA-TAGAAGAGGAGGGAAC 1511 chr6qtel1M 623442 CCTACCAAATTCCTTTTATGACACAGACATGGTACTGATACACAGATCAG 623491 v v v i v i vi viii viiv vv i i L1M4_orf2#LIN 1512 ACTTCCCAACTCATTCTATGAGGCCAGTATTACCCTGATACCAAAACCAG 1561 chr6qtel1M 623492 GTAGGTTGAAA--ACAGAGAAAGAAAATTATAGACCAATCTCCCTGATGA 623539 ii ii-- v -- iii i i v v L1M4_orf2#LIN 1562 ACAAA--GACATCACAAGAAAAGAAAACTACAGACCAATATCCCTTATGA 1609 chr6qtel1M 623540 ATATTGATGCTAAAATCTTAAATAAAATATTAGCAAAAAGATTACAGAAA 623589 v v i v i i vv v v v L1M4_orf2#LIN 1610 ATATAGATGCAAAAATCCTCAACAAAATACTAGCAAACCGAATCCAGCAA 1659 chr6qtel1M 623590 ATCATCCCCAGAATAATACACTATGAGCAAGTAGGATTTATACCAGGAAT 623639 vvi vvvv i v i v i v L1M4_orf2#LIN 1660 CATATAAAAAGGATTATACACCATGACCAAGTGGGATTTATCCCAGGAAT 1709 chr6qtel1M 623640 GCAAGGCTGGTTCAATATTAGGAAAACTATTAGCATAATTGACTATATCA 623689 i i ?v i v v i iii vv i i L1M4_orf2#LIN 1710 GCAAGGTTGGTTCAACATNCGAAAATCAATCAATGTAATACACCATATTA 1759 chr6qtel1M 623690 ATAACGAAATTAACAAAAACCATATGATCATCTCCATAAATGGAGAAAAA 623739 iviv vvi i v i i v L1M4_orf2#LIN 1760 ATAGAATAAAGGACAAAAACCACATGATCATCTCAATAGACGCAGAAAAA 1809 chr6qtel1M 623740 GCATTTGATAAAATCCAACATCCATTCCTAATAAAAACACTTGAGAGGAT 623789 i i v v i ii v iiv L1M4_orf2#LIN 1810 GCATTTGACAAAATCCAACACCCTTTCATGATAAAAACACTCAACAAACT 1859 chr6qtel1M 623790 AGGAATAAACGGAATTTTCTTTAAAATAGTCAGGAGTATATATTTAAAAC 623839 i v i vi i i vv ii v i i i v ivv L1M4_orf2#LIN 1860 AGGAATAGAAGGGAACTTCCTCAACCTGATAAAGGGCATCTACGAAAAAC 1909 chr6qtel1M 623840 CATCAGTAAGCATCATATGCAATGGGGAAAAACTAGAACCTTTCCCAGTA 623889 vv iv i ivi v i ii ?v vv L1M4_orf2#LIN 1910 CCACAGCTAACATCATACTTAATGGTGAAAGACTGAANGCTTTCCCCCTA 1959 chr6qtel1M 623890 AGATCAGGAGTGAAAC 623905 iii i L1M4_orf2#LIN 1960 AGATCAGGAACAAGAC 1975 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 34.92 CpG sites = 81, Kimura (unadjusted) = 35.47 Transitions / transversions = 1.08 (81/75) Gap_init rate = 0.01 (4 / 563), avg. gap size = 1.25 (5 / 4) 267 30.78 3.80 4.66 chr6qtel1M 623906 624273 (375727) L1M5_orf2#LINE/L1 2806 3170 (124) m_b314s551i13 13164 chr6qtel1M 623906 TGGTGGCATAACTGGAAATTTAGTATGGCAGAAATTAGGCATGGACCCAC 623955 v v i i v ii - v i v iii?v v vi L1M5_orf2#LIN 2806 TGCTGGAACAATTGGATATCCA-TATGGAAAAAAATGAANCTCGACCCCT 2854 chr6qtel1M 623956 ACTTAACACCATCTACCAAGATAAGATCAAAATGGGTCTAT-GATTTAGG 624004 i v vi v i v iv ? i i - - ii ii L1M5_orf2#LIN 2855 ACCTCACACCATACACAAAAATTAATTCNAGATGGATC-ATAGACCTAAA 2903 chr6qtel1M 624005 CATAAAAAACAAGATTATAAATAAATTAGAAG--AACATAGTCTAGTTTA 624052 ii i?i i i vvvvi -- --v vv L1M5_orf2#LIN 2904 TGTAAAAGNTAAAACTATAAAACTTCTAGAAGAAAACATAG--GAGAATA 2951 chr6qtel1M 624053 TCTCTCAGACCTGTAGAGGAG--AAAGA------AAACTGTGAC-CAAAG 624093 iivv - i i?v -- ------ v - - - L1M5_orf2#LIN 2952 TCTTCGTGACCT-TGGGNTAGGCAAAGATTTCTTAAACAG-GACACAAA- 2998 chr6qtel1M 624094 ATGAACTACAGATTATTATTGATCACAAAATAGA-AAATGTTGATTACAT 624142 --- vi ?i ii v --- vv v v - - v i ? L1M5_orf2#LIN 2999 ---AAGCACNAACCATAA---AAGAAAAAATTGATAAAT-TGGACTNCAT 3041 chr6qtel1M 624143 CAAATTAAAAAGCCTTTGTACAAACAAAACTAATGCAGACAAGATTAGAA 624192 v v i i i iv ?vvv ivi vi ivi v i v i L1M5_orf2#LIN 3042 CAAAATTAAAAACTTCTGCTCNTCAAAAGACACCGTTAAGAAAATGAAAA 3091 chr6qtel1M 624193 GGGAAGCAATAAACTGGGAAAATATTTTTACAGT-CAAAGGTTCTGATAA 624241 v v i i ? i v v i i?- v vi- i L1M5_orf2#LIN 3092 GGCAAGCCACAGANTGGGAGAAAATATTTGCAANACATATA-TCTGACAA 3140 chr6qtel1M 624242 AGGCCCTTATTTCCAAAAATATATAGAGAATT 624273 -v ii v - i i i L1M5_orf2#LIN 3141 AGG-ACTCGTATCC-AGAATATATAAAGAACT 3170 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 40.30 CpG sites = 58, Kimura (unadjusted) = 41.86 Transitions / transversions = 1.16 (58/50) Gap_init rate = 0.07 (24 / 367), avg. gap size = 1.29 (31 / 24) 495 30.23 7.64 2.64 chr6qtel1M 624259 624873 (375127) L1ME4c_3end#LINE/L1 12 656 (174) m_b314s551i14 13164 chr6qtel1M 624259 AATATATAGAGAATTGACTTAA-TTTATAAGAAA----TCGCCATTTCCA 624303 ? i ii v i i - v ---- ivv ii- L1ME4c_3end#L 12 ANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAAGACC-CCA 60 chr6qtel1M 624304 AATGATAAAATGGTC---GGATAAGAACAGACAAC---CAGATGATGAAA 624347 vv - v --- i v i--- ? v v L1ME4c_3end#L 61 ATAGATAAA-TGGGCAAAGGACATGAACAGACAATTCACANAAGAGGAAA 109 chr6qtel1M 624348 TTAAAACTATTT------CCAATGAAAGA--GTTCCAAATCAC-ATTGAC 624388 - v ? v v------ vv i i -- v vv i - v i i L1ME4c_3end#L 110 T-ACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTAGTAAT 158 chr6qtel1M 624389 CGGAGAAATGCAAATTAAA----CAATTTGGAGAT--TACTACATACCT- 624431 ii ---- --- --i i vi ii - L1ME4c_3end#L 159 CAAAGAAATGCAAATTAAAGCAACAAT---GAGATACCATTTTACGCCTA 205 chr6qtel1M 624432 TTCGATTGGCCAAGATGACAGGGAA--AATAATGATGAAT-TTGG--AGG 624476 vi i v i v-i iii --i iviv -i -- L1ME4c_3end#L 206 TTAAATTAGCAAAAATT-TAAAAAATTGATAATACCCAATGCTGGCGAGG 254 chr6qtel1M 624477 ATGGGA--AAACTGGGAAAATTAATTACGTT--TGGTGG-GTTG-GAACG 624520 ? v i-- v v?v i -- i -- -i? -i iv L1ME4c_3end#L 255 NTGCGGTGAAACTGGTACNCTCA--TACATTGCTGGTGGCANTGTAAATT 302 chr6qtel1M 624521 GGAACCAACCATTCTGGAGGAGCAATTAAATTATGC-TCCCAAAAGTTAT 624569 v - v i i- viiiv i - vi i ii L1ME4c_3end#L 303 GGTAC-AACCCTTTTGGAA-AGCAATTTGGCAATACGTATCAAGAGCCAT 350 chr6qtel1M 624570 CAAACTGTGCATACCCTTTCATCCAGAACTACCAC----GGGCTTATACC 624615 v v v v i v v v ---- vv v i L1ME4c_3end#L 351 AAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATC 400 chr6qtel1M 624616 CCAAAGAGA-AACTTTAAAGAAGGAAAAGGACCATGTA-GCCAAAATGTT 624663 i i i - i iv i - i i i-i v i L1ME4c_3end#L 401 CTAAGGAAATAATTCAAAAGAAGGAAAAAG-CTATATGCACGAAGATGTT 449 chr6qtel1M 624664 TTGGTTAAAGTCCTGTTTATAGTGGCTAGAAACCGAAAATGA-ATGGATG 624712 i--i iv ivi i i i v i ii i ii -v ii L1ME4c_3end#L 450 C--ATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATG 497 chr6qtel1M 624713 CCCACCAATTGGAGAATGGTTGGGGAAA-AGTGGTATATGAATGTTATGG 624761 i v v i ii v -vi i v? iviv L1ME4c_3end#L 498 TCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGG 547 chr6qtel1M 624762 AATATTATTGTTCTGTAAGAAATGATCAGCAGAATGAATACAGAGAGTCT 624811 vvvv ii v i v vi vi v v iiv viv v L1ME4c_3end#L 548 AATATTATGCAGCCATTAAAAATGATAATTATGAAGACTATGTAGCAACA 597 chr6qtel1M 624812 TGGAGAGACTTACATGAAGTGATGCTAAGTGAAATGAGCAGAACCAGAAG 624861 i ivv -i vi i i vi -i v i L1ME4c_3end#L 598 TGGAAAATGTT-TATGATATAATGTTAAGTGAAAAAAGCAGAA-TACAAA 645 chr6qtel1M 624862 ATCAGTATATAC 624873 i- ? L1ME4c_3end#L 646 ATT-GTATNTAC 656 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 39.35 CpG sites = 104, Kimura (unadjusted) = 40.55 Transitions / transversions = 1.35 (104/77) Gap_init rate = 0.07 (40 / 614), avg. gap size = 1.60 (64 / 40) 12 24.76 0.00 2.56 chr6qtel1M 625811 625850 (374150) (TTCTT)n#Simple_repeat 1 39 (0) m_b314s252i11 13165 chr6qtel1M 625811 TTCGTTTTGTTTTCTTTCCATACTTTTTCTCTTCTGTTCT 625850 - v i v vii i v (TTCTT)n#Simp 1 TTC-TTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCT 39 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1) 13 21.92 0.00 10.94 chr6qtel1M 625944 626014 (373986) (AAAATTG)n#Simple_repeat 1 64 (0) m_b314s252i12 13166 chr6qtel1M 625944 AAAATTTTAATTCCAAATCTTGTAAAAATGAATATATTTGGAAAATTGAA 625993 vv v iv -v - v - - - - (AAAATTG)n#Si 1 AAAATTGAAAATTGAAA-ATTG-AAAATTGAA-A-A-TT-GAAAATTGAA 44 chr6qtel1M 625994 AACCAAAAATTGTAAAAATGA 626014 iii - v (AAAATTG)n#Si 45 AATTGAAAATTG-AAAATTGA 64 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.10 (7 / 70), avg. gap size = 1.00 (7 / 7) 46 0.00 0.00 0.00 chr6qtel1M 626158 626196 (373804) (AT)n#Simple_repeat 1 39 (0) c_b314s251i1 13167 chr6qtel1M 626158 ATATATATATATATATATATATATATATATATATATATA 626196 (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATA 39 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 390 21.82 1.82 0.00 chr6qtel1M 627504 627613 (372387) L1M3_orf2#LINE/L1 822 933 (2355) m_b314s551i15 13168 chr6qtel1M 627504 TAAGACAA-TGACAATAATGAGACAACATACTAAAAATTATGGGATGCAG 627552 i - v i vi v i v L1M3_orf2#LIN 822 TGAGACAAATGAAAATGAAAACACAACATACCAAAACTTATGGGATGCAG 871 chr6qtel1M 627553 CTAATTCAGTTTTTAGGGGAAATTTTATATCAATAAA-GCCAACCTTAAA 627601 v vv ?i v i i v v i - v v L1M3_orf2#LIN 872 CAAAAGCAGTNCTAAGAGGGAAGTTTATAGCGATAAACGCCTACATTAAA 921 chr6qtel1M 627602 TAAAAACAGAGA 627613 v i v i L1M3_orf2#LIN 922 AAAGAAGAAAGA 933 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 24.93 CpG sites = 10, Kimura (unadjusted) = 26.12 Transitions / transversions = 0.71 (10/14) Gap_init rate = 0.02 (2 / 109), avg. gap size = 1.00 (2 / 2) 232 29.91 4.92 3.56 chr6qtel1M 627510 627814 (372186) L1M2_orf2#LINE/L1 829 1137 (2154) m_b314s551i16 13168 chr6qtel1M 627510 AATGACAATAATGAGACAACATACTAAAAATTATGGGATGCAGCTAATTC 627559 v iivi v i vi i v vv L1M2_orf2#LIN 829 AATGAAAATGGAAACACAACATACCAAAACCTATGGGATACAGCAAAAGC 878 chr6qtel1M 627560 AGTTTTTAGGGGAAATTTTATATCAATAAA-GCCAACCTTAAATAAAAAC 627608 ?i v i i v v - v v i v iv v L1M2_orf2#LIN 879 AGTNCTAAGAGGGAAGTTTATAGCAATAAACGCCTACATCAAAAAAGTAG 928 chr6qtel1M 627609 AGAGA----AAGAAGAAGATCAAATGAATTGGG---CAGGGAACTA-AAA 627650 i ---- iv i vi i v i -- vi--- i - L1M2_orf2#LIN 929 AAAGATTTCAAATAAACAACCTAACGA--TGCACCTCAAGGAACTAGAAA 976 chr6qtel1M 627651 ACTTAGAA-AACTTAAAACGAAAATTAA-ACACCGGGGTTAGAAATTAAG 627698 viv - vii v v i- v ---i vv -- i L1M2_orf2#LIN 977 AGCAAGAACAAACCAAACCCAAAATTAGTAGA---AGGAAAGAAAT--AA 1021 chr6qtel1M 627699 GAAAACCCAACGCTAGAATTAATAAAACTGAAGCCAAAGAAAGATTTTGA 627748 v ivi iv vii v i iv ii i i v v vii L1M2_orf2#LIN 1022 TAAAGATCAGAGCAGAAATAAATGAAATAGAGACTAAAAAAACAATACAA 1071 chr6qtel1M 627749 A----CTAAAAAACTAGGAGATGGTTGTATTAAAAACAATCAACAAAATG 627794 ---- v vi v ii v v - i -i v v L1M2_orf2#LIN 1072 AAGATCAACGAAACGAAAAGTTGGTTTT-TTGAAAA-GATAAACAAAATC 1119 chr6qtel1M 627795 GAACAAACTTTTGGTCTAGA 627814 - i? i - L1M2_orf2#LIN 1120 G-ACAAACCNTTAG-CTAGA 1137 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 37.99 CpG sites = 45, Kimura (unadjusted) = 39.11 Transitions / transversions = 1.05 (45/43) Gap_init rate = 0.06 (18 / 304), avg. gap size = 1.44 (26 / 18) 252 26.67 7.64 4.59 chr6qtel1M 628652 628926 (371074) L1M2_orf2#LINE/L1 3009 3291 (0) m_b314s551i17 13168 chr6qtel1M 628652 AAAAGCAAAA-TGGACAATTCTGATTACATTAAATTTTAAAAAA----TG 628696 - i v vv i i -- i---- L1M2_orf2#LIN 3009 AAAAGCAAAAATAGACAAATGGGATTACATCAAACT--AAAAAGCTTCTG 3056 chr6qtel1M 628697 CA-ACCAAAAAAATAAAATAACAG--TAACAAGATTAAAAGGTGAAAGCT 628743 - v ii vv vi -- i vi i--- vv iv iiv L1M2_orf2#LIN 3057 CACAGCAAAGGAAACAATCAACAGAGTGAAGAGAC---AACCTACAGAAT 3103 chr6qtel1M 628744 GGG-GAAAATACTTAACAACTAGTGTTTCTGA-AATGGTCTCATTTCTAA 628791 - i ivv - ?iv - v vi v v i i L1M2_orf2#LIN 3104 GGGAGAAAATATTTGCAAACTA-TNCATCTGACAAGGGATTAATATCCAG 3152 chr6qtel1M 628792 AATATATAAAAAACAATGTCAAAT---TTATCA----AAATATAAGTCAT 628834 ii ---- i--- i v ---- v i i v L1M2_orf2#LIN 3153 AATATATAAGGAAC----TCAAACAACTCAACAGCAAAAAAACAAATAAT 3198 chr6qtel1M 628835 TCTGTAATTGATAAATGGTCAGAGGATCTGAA---AAATTT-TCAAATGA 628880 i ---i ? v v i i --- v - v L1M2_orf2#LIN 3199 CC---GATTNAAAAATGGGCAAAGGACCTGAATAGACATTTCTCAAAAGA 3245 chr6qtel1M 628881 TAAAATTAAAGCCACCTATACTTATATGAAAAAATGCTCTAAATCA 628926 vi v vv iivi v i vv v v L1M2_orf2#LIN 3246 AGACATACAAATGGCCAACAGGTATATGAAAAAATGCTCAACATCA 3291 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 33.07 CpG sites = 34, Kimura (unadjusted) = 33.65 Transitions / transversions = 0.94 (34/36) Gap_init rate = 0.08 (23 / 274), avg. gap size = 1.48 (34 / 23) 431 29.47 3.08 8.65 chr6qtel1M 628787 629176 (370824) L1ME3G_3end#LINE/L1 7 376 (548) m_b314s551i18 13168 chr6qtel1M 628787 TCTAAAATATATAAAAAACAATGTCAAATTTATCAAAATATAAGTCATTC 628836 i i i vvivv iv v i - - v vi L1ME3G_3end#L 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAA-A-AAGACAACC 54 chr6qtel1M 628837 TGTAATTGATAAATGGTCAGAGGATCTGAAAA----ATTTTCAAATGATA 628882 i-- v v v i v v ---- iv i v vi L1ME3G_3end#L 55 C--AATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chr6qtel1M 628883 AAATTAAAGCCACCTATACTTATATGAAAAAATGCTCTAAATCAGTATTA 628932 vv iivi v vvi i v vv v v L1ME3G_3end#L 103 AAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTA 152 chr6qtel1M 628933 TTTCATTGCATTTCTCTAAAATGCAAAGTAAA-CAACTCTAAAGTACCAC 628981 v - vv ---------- v - vv i ii i L1ME3G_3end#L 153 AT-CAGGG----------AAATGCAAATTAAAACAACAATGAGATACCAT 191 chr6qtel1M 628982 CTCACACTTCCCAAATGGAC-----TTTAAGTAAGATAATAGAAAAAGAT 629026 i iv iivi i v i ----- -- ? -- ------- L1ME3G_3end#L 192 TTTTCACCCATCAGATTGGCAAAAATTTAA--AAGNT--T-------GAT 230 chr6qtel1M 629027 AAAAATCAAG-GTGGGAGAAGGTTATGGGAAAACTGGGACACTAATGCAT 629075 v - ? - v v i -i i v v v v i i L1ME3G_3end#L 231 AATA-TCNAGTGTTGGCGAGGGT-GTGGGGAAACGGGTACTCTCATACAC 278 chr6qtel1M 629076 TGTTGG-GGGAGTTATGAAGTGATTCAACCATTCTGGAAAATAATTTGAA 629124 i - -i i v i v i ? i iiii iv L1ME3G_3end#L 279 TGCTGGTGGGAGT-GTAAATTGGTACAGCCNTTTTGGAGGGCAATTTGGC 327 chr6qtel1M 629125 ACTATGCCCAAAAAGGTTATAAACTGTATACCCCTTTTCACCCAGCAGTT 629174 v -- i vv ii - v iii iv i v i L1ME3G_3end#L 328 AGTAT--CTATTAAAATT-TAAAATGCGCATACCCTTTGACCCAGCAATT 374 chr6qtel1M 629175 CC 629176 L1ME3G_3end#L 375 CC 376 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 37.61 CpG sites = 53, Kimura (unadjusted) = 38.11 Transitions / transversions = 1.02 (53/52) Gap_init rate = 0.10 (37 / 389), avg. gap size = 1.19 (44 / 37) 431 29.02 3.21 8.59 chr6qtel1M 628841 629183 (370817) L1PREC2_3end#LINE/L1 61 386 (521) m_b314s551i19 13168 chr6qtel1M 628841 ATTGATAAATGGTCAGAGGATCTGAAAAA----TTTTCAAATGATAAAAT 628886 i v i v i iv v i---- v vi v L1PREC2_3end# 61 ATTAAAAAGTGGGCAAAGGACATGAACAGACACTTTTCAAAAGAAGACAT 110 chr6qtel1M 628887 TAAAGCCACCTATACTTATATGAAAAAATGCTCTAAATCAGTATTATT-- 628934 vv v vi v i vvi v ------ i i i -- L1PREC2_3end# 111 ACATGCGGCCAACAAGCATATGAAAAAAAGCTC------AATATCACTGA 154 chr6qtel1M 628935 TCATTGCATTTCTCTAAAATGCAAAGTAAA-CAACTCTAAAGTACCACCT 628983 iv -------i vi - v vv i ii i L1PREC2_3end# 155 TCATTAGA-------GAAATGCAAATCAAAACCACAATGAGATACCATCT 197 chr6qtel1M 628984 CACACTTCCCA-AATGGACTTTAAGTAAGATAATAGAAAAAGATAA-AAA 629031 ivvi - - v v v i - i vi -- - i L1PREC2_3end# 198 CACACCAGTCAGAATGG-CTATTATTAAAA-AGTCAAAAAA--TAACAGA 243 chr6qtel1M 629032 TCAAGGTGGGAGAAGGTTATGGGAAAACTGGGACACTAATGCATTGTTGG 629081 ---- iv v - ii ii vv i i v i i L1PREC2_3end# 244 T----GCTGGCGA-GGTTGCGGAGAAAAGGGAACGCTTATACACTGTTGG 288 chr6qtel1M 629082 -GGGAGTTATGAAGTGATTCAACCATTCTGGAAAATAATTTGAAACTATG 629130 - -i i v ii v ii i v --i v v L1PREC2_3end# 289 TGGGAGT-GTAAATTAGTTCAACCATTGTGGAAAGCAGTGTG--GCGATT 335 chr6qtel1M 629131 CCCAAAAAGGTTATAAACTGTA-TACCCCTTTTCACCCAGCAGTTCCCAT 629179 iv ii i v v v - v-- iv i- L1PREC2_3end# 336 CCTCAAAGAGCTAAAAACAGAACTACCA--TTCGACCCAGCAA-TCCCAT 382 chr6qtel1M 629180 TATT 629183 i L1PREC2_3end# 383 TACT 386 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 35.62 CpG sites = 49, Kimura (unadjusted) = 37.14 Transitions / transversions = 1.17 (49/42) Gap_init rate = 0.10 (35 / 342), avg. gap size = 1.11 (39 / 35) 28 23.30 1.30 1.30 chr6qtel1M 629705 629781 (370219) (ATAA)n#Simple_repeat 1 77 (0) m_b315s252i0 13169 chr6qtel1M 629705 ATAGATATATACATATATAAATGTATATTATACAAACATAAATAAATATA 629754 i v v v iv -v v v v v (ATAA)n#Simpl 1 ATAAATAAATAAATAAATAAATAAATA-AATAAATAAATAAATAAATAAA 49 chr6qtel1M 629755 TTTTTAAA-AAATAAATAAACAAATAAA 629781 vvv - i (ATAA)n#Simpl 50 TAAATAAATAAATAAATAAATAAATAAA 77 Matrix = Unknown Transitions / transversions = 0.25 (3/12) Gap_init rate = 0.03 (2 / 76), avg. gap size = 1.00 (2 / 2) 211 26.25 7.55 6.54 chr6qtel1M 629796 629901 (370099) L2a_3end#LINE/L2 411 517 (0) m_b315s601i0 13170 chr6qtel1M 629796 TGAGGTCAGAAATTTCTTTTTTTTTTTTTT-----TG-GTCACAAACACC 629839 v ii i i v i v v i----- -i v v i i L2a_3end#LINE 411 TGAGGGCAGGGACTTTTGTCTGTTTTGTTCACTGCTGTATCCCCAGCGCC 460 chr6qtel1M 629840 ATAGCTGAACCCAATGTGTGGCACATGGTAAGGGCTTAATAAAGGTTTAA 629889 - --- -- i iv i i v i vi -i L2a_3end#LINE 461 -TAG---AAC--AGTGCCTGGCACATAGTAGGCGCTCAATAAATATTT-G 503 chr6qtel1M 629890 TTGAA--AAGGAAT 629901 -- v L2a_3end#LINE 504 TTGAATGAATGAAT 517 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 31.69 CpG sites = 16, Kimura (unadjusted) = 33.25 Transitions / transversions = 1.60 (16/10) Gap_init rate = 0.10 (10 / 105), avg. gap size = 1.50 (15 / 10) 216 21.14 3.77 1.85 chr6qtel1M 629849 629901 (370099) L2c_3end#LINE/L2 425 478 (0) m_b315s601i1 13170 chr6qtel1M 629849 CCCAATGTGTGGCACATGGTAAGGGCTTAATAAAGGTTTAATTGAA--AA 629896 ii iv i i v i v -i -- L2c_3end#LINE 425 CCCAGCGCCTGGCACATAGTAGGCGCTCAATAAATGTTT-GTTGAATGAA 473 chr6qtel1M 629897 GGAAT 629901 v L2c_3end#LINE 474 TGAAT 478 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 22.84 CpG sites = 7, Kimura (unadjusted) = 25.42 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.50 (3 / 2) 18 17.29 0.00 10.17 chr6qtel1M 631063 631127 (368873) (GAAAGG)n#Simple_repeat 1 59 (0) m_b315s252i1 13171 chr6qtel1M 631063 GAAAGGGAAAGGGAGAAGGAGGAGGAGAAAGGAAAATAGGAAAGGAAAAT 631112 - - i i i i -i i - (GAAAGG)n#Sim 1 GAAAGGGAAAGGGA-AAGG-GAAAGGGAAAGGGAAA-GGGAAAGGGAAA- 46 chr6qtel1M 631113 ATGAAAGAGAGAAAG 631127 iv - - (GAAAGG)n#Sim 47 GGGAAAG-G-GAAAG 59 Matrix = Unknown Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.09 (6 / 64), avg. gap size = 1.00 (6 / 6) 251 39.49 6.74 3.70 chr6qtel1M 633186 634313 (365687) C L2#LINE/L2 (68) 3014 1854 m_b315s601i2 13172 chr6qtel1M 633186 TGTTCAAGGAACATCAAGAAAGCCAATTTTCCTTCCTTGCAGGCTATATG 633235 i v i i i v vv vvv-- i iv ivii C L2#LINE/L2 3014 TGTTCGAGGAACAGCAAGGAGGCCAGTGTGGCTGGA--GCGGAGTGAGCG 2967 chr6qtel1M 633236 GTGACGGATATGGTTTAAGA--AAACTGGAAGTGTTAGGAGGGGCCAGAT 633283 iv iv iivi vvi -- iiiii iiv v v i i C L2#LINE/L2 2966 AGGGGGAGAGTGGTAGGAGATGAGGTCAGAGAGGTAACGGGGGACCAGAT 2917 chr6qtel1M 633284 TTTGAAGGGATTTG-AATTAAAAATATGAATTTTGTATTTT--CCTGAAT 633330 iv v vi - iviv vvi v i i vv --i i C L2#LINE/L2 2916 CATGTAGGGCCTTGTAGGCCATTGTAAGGACTTTGGCTTTTACTCTGAGT 2867 chr6qtel1M 633331 GGAATAAAATGTAATTGTACCTTACTGAAAAGGAGAGTTGATAACATTAG 633380 ii iii v iv v vvv vi iv ii - i vv iv C L2#LINE/L2 2866 GAGATGGGAAGCCATTGGAGGGTTTTGAGCAGAGGAGT-GACATGATCTG 2818 chr6qtel1M 633381 ATCATCACTGTAGAAAGGTCAGTTTGACAGGTGAGTGGAAGAAGAACTAA 633430 iivv ii v i i i v i i v v v v ii vii i? C L2#LINE/L2 2817 ACTTACGTTTTAAAAGGATCACTCTGGCTGCTGTGTTGAGAATAGACTGN 2768 chr6qtel1M 633431 AGTATAG-AGAGATGTAATTCAGAGAGACGATCTTGCAGTCTGCAACATT 633479 vivi - ii i v v- i v vi v v v iivi v C L2#LINE/L2 2767 AGGGGGGCAAGGGTGGAAG-CAGGGAGACCAGTTAGGAGGCTATTGCAGT 2719 chr6qtel1M 633480 TATTTGGGCATGAGATAATGAAATCCCTGCACCAGGGTCGTCATAATGTC 633529 v iii iv i ivi-v i v v vii i vv C L2#LINE/L2 2718 AATCCAGGCGAGAGATGATGGTG-GCTTGGACCAGGGTGGTGGCAGTGGA 2670 chr6qtel1M 633530 AGAGAGGA-AAGTGCCATGTAAGACATGATATAAATATAAATT-AAGA-A 633576 i v iv - ---- vi i---- v ii vv - i- C L2#LINE/L2 2669 GGTGGTGAGAAGTG----GTCGGAT----TCTGGATATATTTTGAAGGTA 2628 chr6qtel1M 633577 GGGC-AACAAAAAT-GATCATGGG--------GGGGT-----AGGAAGAG 633611 i -i ii v - v v i-------- ----- i C L2#LINE/L2 2627 GAGCCGACAGGATTTGCTGATGGATTGGATGTGGGGTGTGAGAGAAAGAG 2578 chr6qtel1M 633612 AACCTTGTTTAA-ATGGC----ATGTTTCCGGCCAAAGTTAGAAAAAAAG 633656 ivv-- iv i- i ---- v ii vi i- ivvii i C L2#LINE/L2 2577 AGGA--GTCAAGGATGACTCCAAGGTTTTTGGCCTGAGC-AACTGGAAGG 2531 chr6qtel1M 633657 ATAGGGGCAATATTAACAGGGAATAAGGAAAAA-GAAAGAGGAA-AGTTT 633704 i i viivi ? v i - ii i v- vii i- v C L2#LINE/L2 2530 ATGGAGTTGCCATTNACTGAGA-TGGGGAAGACTGCGGGAGGAGCAGGTT 2482 chr6qtel1M 633705 TTGAGAGAAAGAT-AAAAATTGCCTTTTA---AT-TTAATTTTTAAGACA 633749 vii i i - ii i vvv i--- - v -i ii C L2#LINE/L2 2481 TGAGGGGGAAGATCAGGAGTTCAGTTTTGGACATGTTAAGTTT-GAGATG 2433 chr6qtel1M 633750 GCTATGGAACATT--ATTATGAGAAG--GAAAATTCAGTTATGGATGTAA 633795 v vii i-- v i- v -- iv vv -- i v C L2#LINE/L2 2432 CCTATTAGACATCCAAGTG-GAGATGTCGAGTAGGCAGTT--GGATATAC 2386 chr6qtel1M 633796 GAAT--GGCAGTCAGAAAGAGGGATAGCCCAGGTTA-----ATAGATTT- 633837 i -- viv ii- i i --- i i i----- i - C L2#LINE/L2 2385 GAGTCTGGAGTTCAGGG-GAGAGGT---CCGGGCTGGAGATATAAATTTG 2340 chr6qtel1M 633838 -----TAT-AACTTATAGAGAATTCCTTGTATTCATGGAATGAGA-ATGA 633880 -----i - i v vii -vi iv vi ii ivi -iv C L2#LINE/L2 2339 GGAGTCATCAGCATATAGATGGT-ATTTAAAGCCATGAGACTGGATGAGA 2291 chr6qtel1M 633881 TT-TCAAAGCAAAGAAAACAAA---AGAAAAGAAAAGACCTAGGAAAAGA 633926 i-i ? i v iv ivii i --- i i ii i i i vv C L2#LINE/L2 2290 TCACCNAGGGAGTGAGTGTAGATAGAGAAGAGAAGAGGTCCAAGGACTGA 2241 chr6qtel1M 633927 AGAAGTGGAAGGGATATATCAACAAATCCAAGGGTAGATTGTGAGATAAA 633976 - vvv ---- ii ivi i-- i? ii v --- v i i C L2#LINE/L2 2240 -GCCCTGG----GGCACTCCAACG--TTNAGAGGTCG---GGGAGATGAG 2201 chr6qtel1M 633977 TTAAGATCCAGCAAAGGAAGATTAAGGAA-AGCAGTCAAAAAGAGAGGAA 634025 v- i v - i i i i- i i ivi iv i C L2#LINE/L2 2200 G-AGGAACCAGCAAAGGA-GACTGAGAAGGAGCGGCCAGTGAGGTAGGAG 2153 chr6qtel1M 634026 AAGAACCA--AGACTATAGC--CATGAAAAACCAGAAAGTAAAGATGAT- 634070 i i -- v i i i-- v i iv v vi iv - v - C L2#LINE/L2 2152 GAAAACCAGGAGAGTGTGGTGTCCTGGAAGCCAAGTGAAGAAAG-TGTTT 2104 chr6qtel1M 634071 ---AAACTAAATGGTAATCAACAATTCCAGAAGCAACAGATAAATACCAA 634117 ---i vv iivi i vi vi i v vi v ? ii - v i C L2#LINE/L2 2103 CAAGAAGGAGGGAGTGATCAACTGTGTCAAATGCTGCTGANAGGT-CAAG 2055 chr6qtel1M 634118 TGA-ATGAGGGCTGAGAAGAGGCCATAAGAGTGAGCATTTAAGAGCCCAT 634166 i - i vv i vi v v vivvi vi C L2#LINE/L2 2054 TAAGATGAGGACTGAGAATTGACCATTGGATTTAGCAACGTGGAGGTCAT 2005 chr6qtel1M 634167 TAGTAAATTTGTACACCAA-AGTTCTGGTTGAATA-CAAATTCAGAAATC 634214 i i vi - vv i- ii v i i-iiiivv ii ii C L2#LINE/L2 2004 TGGTGACCTTG-ACAAGAGCAGTTTCGGTGGAGTGGTGGGGACGAAAGCC 1956 chr6qtel1M 634215 AGATTGTTGAGTG---TTAAGAAA--ATAAGAAGAAATAAAGGGAAGGCA 634259 v -- --- i i -- ii i i vi vv i i C L2#LINE/L2 1955 TGATTG--GAGTGGGTTCAAGAGAGAATGGGAGGAGAGGAATTGGAGACA 1908 chr6qtel1M 634260 CCAATTGTATAAGATATTCTCGAGGAATTGAGACACAAAAAGAAGAGGAG 634309 v i v i v vi ivi i i vv viii ii i vi C L2#LINE/L2 1907 GCGAGTATAGACAACTCTTTCGAGGAGTTTTGCTGTAAAGGGGAGCAGAG 1858 chr6qtel1M 634310 AAAT 634313 C L2#LINE/L2 1857 AAAT 1854 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 56.79 CpG sites = 259, Kimura (unadjusted) = 60.12 Transitions / transversions = 1.52 (259/170) Gap_init rate = 0.07 (81 / 1127), avg. gap size = 1.47 (119 / 81) 13 17.81 5.26 0.00 chr6qtel1M 634404 634441 (365559) (TATTTTT)n#Simple_repeat 1 40 (0) m_b315s252i2 13173 chr6qtel1M 634404 TATTTTTT-CTTTTTATTATTTA-TTATAGCTTTTTATTT 634441 -i v - v vii (TATTTTT)n#Si 1 TATTTTTTATTTTTTATTTTTTATTTTTTATTTTTTATTT 40 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 254 32.50 1.23 1.23 chr6qtel1M 635702 635782 (364218) C MIRc#SINE/MIR (162) 106 26 m_b315s601i3 13174 chr6qtel1M 635702 TGACTAATCAAGGATTGCAAAACTAGTAAATGTGAGAGACTGCATTAGAA 635751 vii v i i ii v i i vv v v v i v C MIRc#SINE/MIR 106 TGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAA 57 chr6qtel1M 635752 CTCAGATCTTCTTGGCACTATAGT-CAATACT 635782 i i i i v i - - i i C MIRc#SINE/MIR 56 CCCAGGTCTTCCTGACTCCA-AGTCCAGTGCT 26 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 44.41 CpG sites = 16, Kimura (unadjusted) = 44.41 Transitions / transversions = 1.60 (16/10) Gap_init rate = 0.03 (2 / 80), avg. gap size = 1.00 (2 / 2) 12 0.00 8.00 3.85 chr6qtel1M 636536 636560 (363440) (ATA)n#Simple_repeat 1 26 (0) m_b315s252i3 13175 chr6qtel1M 636536 ATATATAATAATAATAAT-ATAA-AAT 636560 - - - (ATA)n#Simple 1 ATA-ATAATAATAATAATAATAATAAT 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.12 (3 / 24), avg. gap size = 1.00 (3 / 3) 57 0.00 0.00 0.00 chr6qtel1M 637589 637637 (362363) (AT)n#Simple_repeat 1 49 (0) c_b315s251i0 13176 chr6qtel1M 637589 ATATATATATATATATATATATATATATATATATATATATATATATATA 637637 (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATA 49 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 1082 27.45 5.53 6.19 chr6qtel1M 637908 638703 (361297) C HERVK14C#LTR/ERVK (3799) 3635 2845 m_b315s701i0 13177 chr6qtel1M 637908 ATATCTCATATCAATTTCTGAAAATCATTTAAGGTGTTGAG-----CTTC 637952 i v vi i i v v ----- i C HERVK14C#LTR/ 3635 ATATCCCCTAATAATTTTTGAAAATCATTTAAAGTTTTCAGAGAGTCTTT 3586 chr6qtel1M 637953 TCTGGTTCTTAAAGACAGTTTTGGTACTATAA--GCACCTTAGGGTACAC 638000 vii i----- vvv ?vi - -- v i vvv v - C HERVK14C#LTR/ 3585 TCGAATTT-----GAACCTTTTGNGGCT-TAATTGCCCTTTCCTGAAC-C 3543 chr6qtel1M 638001 TTCATGTCCTAAATATTGAAAAGGAGCATGTCCTTGAATTTTTTCTGGAG 638050 v - i i i v?ivi v ? ? C HERVK14C#LTR/ 3542 TGCAT-TCCCAAATATTGGAAAGGAGTAGNCGTTTGAATTTTATCNGGNG 3494 chr6qtel1M 638051 CTATGTACAGTTTGTAGTTCCTTAGTGTTTTTTTTTTGGTCTTTTGTAAA 638100 v? i -------- -- i ivvi?vii-- i i C HERVK14C#LTR/ 3493 CTATGANCAAT--------CC--AGCGTCGGCNACC--GCCTTCTGTAAA 3456 chr6qtel1M 638101 CATGCTTCTAACATTTG-----TT--CCTCATGT-------GCACATCCC 638136 ii v--v i v ----- --i iv ------- ?--- C HERVK14C#LTR/ 3455 TGTGA--ATAACACTGGATAAGTTGGTCTCGAGTTTCGGCCGCACAN--- 3411 chr6qtel1M 638137 AATATATCATCCATGTAATGTAATAACAT-TACTTTTGGAAA-TGCTTGT 638184 i i - i i -?ivv i - v i- C HERVK14C#LTR/ 3410 AATATGTCATCCATATAATG-AATGATATANGAATCTGGAAACTGATC-T 3363 chr6qtel1M 638185 CTTAC---TTGAGTAAGAGCAGCAGCAGCATACATTTGACACATAGTAGG 638231 ? --- i iv-- v? vv - ? vi v ? ? C HERVK14C#LTR/ 3362 CTNACAGGTTGAATAGC--CTNCCCCA-CANAAGTTTGACAAATNGTNGG 3316 chr6qtel1M 638232 GCTGTTTCTCATTCCCTGTGGCAAAACTGTCCATTCATATCTTTTATAAG 638281 i i ivv v i ? v v v ? vvivvv? C HERVK14C#LTR/ 3315 ACTATTCAACATGCCCTGCGGCAANACTTTCCAATGATANCTGGCTGCNG 3266 chr6qtel1M 638282 GCTCA--GCTAAGTTAATGCTGGGCACGGAAAAGGCAAATCTTTTTGTAT 638329 i v-- i -- v ivii v ii v i i iviv C HERVK14C#LTR/ 3265 GTTCCTTGTT--GTTCATAGCAGGAATAGTAAAAGCAAATTTTTCAAAAT 3218 chr6qtel1M 638330 CCC-CTTTATCTGGTAGGATAGAATAGAAACAATCCTTAATGTCTATAAC 638378 ?v- i i- i vi i v v i i v vi C HERVK14C#LTR/ 3217 CNGGCTCTG-CTAGAGGAATAGTAAAGAAGCAGTCCTTCAAATCTATAAC 3169 chr6qtel1M 638379 -ACAAAGAGGCCATTCTCTAGGCAATT-CAGTAGGAGATGGAAGTCCAGG 638426 - iv ?- v - i-ii ii i ? v i v C HERVK14C#LTR/ 3168 TATTAAN-GGCCAGTCTCTAGG-AATCATGGCGGGGGANGGCAGCCCTGG 3121 chr6qtel1M 638427 CTGAAGAGTTCCCATAATTTCCAT--CTGTTCT-----TTCTTAAATCAG 638469 v ? ii ?iv v? -- ivi -----i v i i C HERVK14C#LTR/ 3120 CTGCAGNGCCCCCATNGGTTGNATGACTGCATTGACGGCTCGTAAGTCGG 3071 chr6qtel1M 638470 TCAACATCCTCCTTTTTCTAGATTTCTTTTTTACAACAAATACTGGGGAA 638519 i i ? v v i v ii i i ? iv i ? C HERVK14C#LTR/ 3070 TTAGCATNCGCCATCTGCCGGATTTTTTCTTNATTACAAACACTGGNGAA 3021 chr6qtel1M 638520 TTCCAAGGACTTAGAGAA----GGTTGTAGGTGTCCTTGGTCAAGTTGCT 638565 ? ---- i ---- i v? v v? v i i C HERVK14C#LTR/ 3020 TTCCANGGA----GAAAATGTGGGCTCNATGTGTCCTTTNTCTAATTGTT 2975 chr6qtel1M 638566 CCTGTAATATATT--TTTAAGGCCTGAATTTTATCGCTACCTAAGGGCCA 638613 i vv v - -- v ivv v v viv v?? iv C HERVK14C#LTR/ 2974 CTTTGACTA-ATTCCTGTAAGGCCCCCAGTTTTTCCTGAGNNAGCGGCCA 2926 chr6qtel1M 638614 CTGTTCTATCCATACTGGTATATCAGTTTTCCATTGGATAGGAACGGGTA 638663 ? ? i v ? ?v v vi i? vv vi ii -- C HERVK14C#LTR/ 2925 CTGNTCNACCCAAACNGGNTTTTGGGTCNTCCATTTTAAGGGAATAGG-- 2878 chr6qtel1M 638664 AAAGTGTTGGCAGGCCTTCAACAACAGCCCTGCCTAAAAA 638703 -----? iv v -- iii viv C HERVK14C#LTR/ 2877 -----NTCTGGAGGC--TCAACAGTGGCCGCCCCTAAAAA 2845 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 34.89 CpG sites = 106, Kimura (unadjusted) = 36.92 Transitions / transversions = 1.07 (106/99) Gap_init rate = 0.08 (65 / 795), avg. gap size = 1.43 (93 / 65) 13 18.61 0.00 3.03 chr6qtel1M 640720 640753 (359247) (GGGTGG)n#Simple_repeat 1 33 (0) m_b315s252i4 13178 chr6qtel1M 640720 GGGTGAGGGTGGGGGTTGGGGGTAAGGATGGAGG 640753 i - ii i i (GGGTGG)n#Sim 1 GGGTGGGGGTGGGGG-TGGGGGTGGGGGTGGGGG 33 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 468 30.98 3.39 5.93 chr6qtel1M 640988 641488 (358512) L1ME2_3end#LINE/L1 164 652 (259) m_b315s551i4 13179 chr6qtel1M 640988 AAATGCAAAG-GAAACAACTATAAAGTACCACCTTATACTC-CTCACAAA 641035 v-i v v i ii i?i i i - ------ L1ME2_3end#LI 164 AAATGCAAATTAAAACCACAATGAGATACCACTNCACACCCACT------ 207 chr6qtel1M 641036 AGGAGATTAACTAAGATAACAGAAAAAGACAGA-AAT--CAA-TGTTGGA 641081 --- v ii i ----v v - -- - v L1ME2_3end#LI 208 ---AGAATGGCTAAAAT----TAAAAAGACTGACAATACCAAATGTTGGC 250 chr6qtel1M 641082 GAAGGTGATGGAAAAACTGTGACACTAATGCATTGTTGGGGGACTTATGA 641131 i i - iv vi v v i i v ivv i i L1ME2_3end#LI 251 GAGGATG-TGGAGCAACTGGAACTCTCATACATTGCTGGTGGGAGTGTAA 299 chr6qtel1M 641132 AATGATTCAACAATTTTGGAGAACAATCAGAAACTATGCCCAAAGGACTA 641181 i v v i i ?i iv iv v - v ii v iiii L1ME2_3end#LI 300 AATGGTACAACCACTTTGGAAAACNGTTTGGCAGT-TTCTTATAAAGTTA 348 chr6qtel1M 641182 TAACATTGTATATGCTCTTTTCACCCAGCAATTGCATTACTGGATCTGTG 641231 - -ii iv i i v -v v i v i i v v i L1ME2_3end#LI 349 -AACAT-ACACCTACCCTAT-GACCCAGCAATTCCACTCCTAGGTATTTA 395 chr6qtel1M 641232 TTCCAAGA-AAATCATAAAGGACGT----AAAAGGAACCATATAGGCAAA 641276 i- - v v viv i ---- i -- v i -- ?i L1ME2_3end#LI 396 C-CCAAGAGAAATGAAAACATATGTCCACAAAAAGA--CTTGTA--CANG 440 chr6qtel1M 641277 AATGTTTGGAGCAGCTCCCTTTTTTTTAGTAGCAACAAATCAGAAAATGA 641326 iiv --- v iv i v- v v i ii L1ME2_3end#LI 441 AATGTTCATAGCAGCT---TTATTCATAATAGCC-CAAAACTGGAAACAA 486 chr6qtel1M 641327 GTAGAAAATCCATGTATTAGGGAATGGCTGGACAAGTTGTGGTATATATA 641376 vivi vi vv ivi ? v ii i vi L1ME2_3end#LI 487 CCCAAATGTCCATCAACAGGNGAATGGATAAACAAATTGTGGTATATTCA 536 chr6qtel1M 641377 AGGAATAGAATATGATTATTCTATACAAAGGGATAAACAAGCTGATTTTA 641426 viv i iv i vvv v v i ii v - vivv L1ME2_3end#LI 537 TACAATGGAATACTACTCAGCAATAAAAAGGAACGAACTA-CTGATACAC 585 chr6qtel1M 641427 G--AAAGCCTGGAATGATTTACACATAC-TAATACTGAGTGAAACAA-TC 641472 -- v i v - v iv v v - v i i v -i L1ME2_3end#LI 586 GCAACAACATGG-ATGAATCTCAAAAACATTATGCTGAGCGAAAGAAGCC 634 chr6qtel1M 641473 AGAACC--AAGAATACAT 641488 vv -- i L1ME2_3end#LI 635 AGACACAAAAGAGTACAT 652 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 40.33 CpG sites = 77, Kimura (unadjusted) = 41.09 Transitions / transversions = 1.12 (77/69) Gap_init rate = 0.08 (40 / 500), avg. gap size = 1.15 (46 / 40) 524 33.73 0.74 4.08 chr6qtel1M 640988 641392 (358608) L1ME4c_3end#LINE/L1 164 555 (275) m_b315s551i3 13179 chr6qtel1M 640988 AAATGCAAAGGAAA-CAACTATAAAGTACCACCTTATACTCCTCACAAAA 641036 vv - v i ii -- v v ------ L1ME4c_3end#L 164 AAATGCAAATTAAAGCAACAATGAGATACCA--TTTTACGCCT------A 205 chr6qtel1M 641037 GGAGATTAACTAAGATAACAGAAAAAGACAGAAATCAATGTTGGAGAAGG 641086 vv i i v i vvv i vv i iv vi i v i ? L1ME4c_3end#L 206 TTAAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGCTGGCGAGGN 255 chr6qtel1M 641087 TGATGGAAAAACTGTGACACTAATGCATTGTTGGGGGACTTATGAAATGA 641136 -i vi vv ? v i i v vv? i i v i L1ME4c_3end#L 256 TG-CGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGG 304 chr6qtel1M 641137 TTCAACAATTTTGGAGAACAATCAGAAACTATGCCCAAAGGACTATAACA 641186 v vv i i iv iv v i iviv ii i v L1ME4c_3end#L 305 TACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAAA 354 chr6qtel1M 641187 TTGTATATGCTCTTTTCACCCAGCAATTGCATTACTGGATCTGTGTTCCA 641236 v vi i i -v i v i v ivv v i i i L1ME4c_3end#L 355 ATGTTCATACCCTTT-GACCCAGTAATTCCACTTCTGGGAATTTATCCTA 403 chr6qtel1M 641237 AGAAAATCAT--AAAGGACGTAAAAGGAACCATATAGGCAAAAATGTTTG 641284 i v -- i v v i -- i ivi i i ii L1ME4c_3end#L 404 AGGAAATAATTCAAAAGAAGGAAAAAG--CTATATGCACGAAGATGTTCA 451 chr6qtel1M 641285 GAGCAGCTCCCTTTTTTTTAGTAGCAACAAATCAGAAAATGAGTAGAAAA 641334 vv ---v v v i i v ii -ii vivi vi L1ME4c_3end#L 452 TTGCAGC---GTTATTTATAATAGCGAAAAATTGGAAA-CAACCTAAATG 497 chr6qtel1M 641335 TCCATGTATTAGGGAATGGCTGGACAAGTTGTGGTATATATAAGGAATAG 641384 vvv vi i iiii i i i v? vvvi i L1ME4c_3end#L 498 TCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGG 547 chr6qtel1M 641385 AATATGAT 641392 v L1ME4c_3end#L 548 AATATTAT 555 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 43.92 CpG sites = 68, Kimura (unadjusted) = 46.29 Transitions / transversions = 1.08 (68/63) Gap_init rate = 0.04 (18 / 404), avg. gap size = 1.06 (19 / 18) 27 15.62 2.00 0.00 chr6qtel1M 641789 641838 (358162) (TA)n#Simple_repeat 1 51 (0) m_b315s252i5 13180 chr6qtel1M 641789 TATATATATATAAATGTATAT-TATATACACATAAATATATATATGTAAA 641837 v i - i i v i v (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr6qtel1M 641838 T 641838 (TA)n#Simple_ 51 T 51 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.02 (1 / 49), avg. gap size = 1.00 (1 / 1) 945 40.63 3.38 2.67 chr6qtel1M 645210 646362 (353638) C L2#LINE/L2 (68) 3014 1854 m_b315s601i4 13181 chr6qtel1M 645210 TGTTCAAGGAACATCAAGAAAGCCAATTTTCCTTCCTTGCAGGCTATATG 645259 i v i i i v vv vvv-- i iv ivii C L2#LINE/L2 3014 TGTTCGAGGAACAGCAAGGAGGCCAGTGTGGCTGGA--GCGGAGTGAGCG 2967 chr6qtel1M 645260 GTGACGGATATGGTTTAAGA--AAACTGGAAGTGTTAGGAGGGGCCAGAT 645307 iv iv iivi vvi -- iiiii iiv v v i i C L2#LINE/L2 2966 AGGGGGAGAGTGGTAGGAGATGAGGTCAGAGAGGTAACGGGGGACCAGAT 2917 chr6qtel1M 645308 TATGAAGGGATTTG-AATTAAAAATATGAATTTTGTATTTT--CCTGAAT 645354 i v vi - iviv vvi v i i vv --i i C L2#LINE/L2 2916 CATGTAGGGCCTTGTAGGCCATTGTAAGGACTTTGGCTTTTACTCTGAGT 2867 chr6qtel1M 645355 GGAATAAAACGTAATTGTACCTTACTGAAAAGGAGAGTTGATAACATTAG 645404 ii iii v iv v vvv vi iv ii - i vv iv C L2#LINE/L2 2866 GAGATGGGAAGCCATTGGAGGGTTTTGAGCAGAGGAGT-GACATGATCTG 2818 chr6qtel1M 645405 ATCAACACTGTAGAAAGGTCAATTTGACAGGTGAGTGGAAGAAGAACTAA 645454 iiv ii v i i i v i i v v v v ii vii i? C L2#LINE/L2 2817 ACTTACGTTTTAAAAGGATCACTCTGGCTGCTGTGTTGAGAATAGACTGN 2768 chr6qtel1M 645455 ACTAGAGAGAGATTGAATTCAGAGAGACGATCTAGCAGTCTGCAACATTT 645504 vvi i vi iv i vv i v vi v v iivi v v C L2#LINE/L2 2767 AGGGGGGCAAGGGTGGAAGCAGGGAGACCAGTTAGGAGGCTATTGCAGTA 2718 chr6qtel1M 645505 ATTTGGGCATGAGATAATGAAATCCTGCACCAGGGTCATCATAATGTCAG 645554 iii iv i iviv i v vi vii i vvi C L2#LINE/L2 2717 ATCCAGGCGAGAGATGATGGTGGCTTGGACCAGGGTGGTGGCAGTGGAGG 2668 chr6qtel1M 645555 AGA-GAAAAGTGCC---ATGTAAGACATGATATAAATATAAAATTAAGAG 645600 v i- i vi--- vivi i iv v i vi i iiii v C L2#LINE/L2 2667 TGGTGAGAAGTGGTCGGATTCTGGATATATTTTGAAGGTAGAGCCGACAG 2618 chr6qtel1M 645601 TATTTGGCAACAAAATGATCATGGG-TGTTAGAATGGGAAAAGAACTCAT 645649 v vii iii v ivii - v ivii i i i- v C L2#LINE/L2 2617 GATTTGCTGATGGATTGGATGTGGGGTGTGAGAGAAAGAGAGGAG-TCAA 2569 chr6qtel1M 645650 GAATAAATGGCATGTTTCAAGTCAAAGTGACAAAAAAAA-GATGTTGGCA 645698 i i v vvv v ivi i vi ii vii ii - iv v C L2#LINE/L2 2568 GGATGACTCCAAGGTTTTTGGCCTGAGCAACTGGAAGGATGGAGTTGCCA 2519 chr6qtel1M 645699 ATATTAACAGGAATAAGGAAATATGAAAGAGAAA-AGTTTTTGAGAGAAA 645747 --- ? v ii ii ivv vii i i- v vii i i C L2#LINE/L2 2518 ---TTNACTGAGATGGGGAAGACTGCGGGAGGAGCAGGTTTGAGGGGGAA 2472 chr6qtel1M 645748 GATAATAAATTAAGCCTTTTAAATATTAATTTTAAGACAGCTATGGAACA 645797 v vi i v ii vv v i v i iiv vii C L2#LINE/L2 2471 GATCAGGAGTTCAGTTTTGGACATGTTAAGTTTGAGATGCCTATTAGACA 2422 chr6qtel1M 645798 TTCATTATGAGATGTAGGAAATTCAGTTATGGATGTAAGAA--TGGCAGT 645845 i vvvv v iiv vv -- i v i-- viv C L2#LINE/L2 2421 TCCAAGTGGAGATGTCGAGTAGGCAGT--TGGATATACGAGTCTGGAGTT 2374 chr6qtel1M 645846 CAGGAAAGAGTTT--AGCTCCAGGTTAATAGATTTT---ATAATCAATAT 645890 ii v i--i vv i -- i v---i v ii C L2#LINE/L2 2373 CAGGGGAGAGGTCCGGGCTGGAGAT--ATAAATTTGGGAGTCATCAGCAT 2326 chr6qtel1M 645891 AGAGATAATTCTTGTATTCATGGAAT--GATAATGAT--TTCAGCAAAT- 645935 v ii vi iv vi ii i-- i - --ii? vi i - C L2#LINE/L2 2325 ATAGATGGTATTTAAAGCCATGAGACTGGATGA-GATCACCNAGGGAGTG 2277 chr6qtel1M 645936 AGAATACTATAGAGAAAAAGAAAAGCCCTAGCA-TAAGAAGTGGGAAGCA 645984 vi v- i ii i i i v v - i vvv -- - C L2#LINE/L2 2276 AGTGTAG-ATAGAGAAGAGAAGAGGTCCAAGGACTGAGCCCTGGG--GC- 2231 chr6qtel1M 645985 TACATCAACCATCCAAGGCTGGATTGTGAGATAAATTAAGATCCAGCAAA 646034 - vi vv ?vi ii i---- i i-v i v C L2#LINE/L2 2230 -ACTCCAACGTTNAGAGGTCGGG----GAGATGAG-GAGGAACCAGCAAA 2187 chr6qtel1M 646035 GGAGACTCAGAAGTAGCAGTCAAATTAGCAGGAGAAGAACCA--AGACTA 646082 v v i i ivvvi i i i -- v i C L2#LINE/L2 2186 GGAGACTGAGAAGGAGCGGCCAGTGAGGTAGGAGGAAAACCAGGAGAGTG 2137 chr6qtel1M 646083 TA--GCCGTGAAAATCAAGAATGTAAACAGAAT-----AAACTAAATGGT 646125 i-- i v i ii -- v i v vi -----i vv iivi C L2#LINE/L2 2136 TGGTGTCCTGGAAGCCAAG--TGAAGAAAGTGTTTCAAGAAGGAGGGAGT 2089 chr6qtel1M 646126 AATCAACAGTTCCAGAAGCAATAGATAAATACCAATGA-ATGAGGGCTGA 646174 i v vi i v viiv ? ii - v i i - i C L2#LINE/L2 2088 GATCAACTGTGTCAAATGCTGCTGANAGGT-CAAGTAAGATGAGGACTGA 2040 chr6qtel1M 646175 AAAGAGGCCATAAGAGTGAGCATTTAGGAGACCATTAGTAAATTTGTACA 646224 i vv i vi v v vivv ii i i vi - C L2#LINE/L2 2039 GAATTGACCATTGGATTTAGCAACGTGGAGGTCATTGGTGACCTTG-ACA 1991 chr6qtel1M 646225 CCAA-AGTTCTAGTTGA---ATAGAAACTAATCATATTGTTCAGTGTTAA 646270 vv i- iii v ---i i ii v -- vvi v ii v --- C L2#LINE/L2 1990 AGAGCAGTTTCGGTGGAGTGGTGGGGACGAA--AGCCTGATTGGAGT--- 1946 chr6qtel1M 646271 GAATATAAGAAGAAATAAGAAGAAATAAAGGGAAGGCACTAATTGTATAA 646320 ii vi iii ii i i vi vv i i vii v i v v C L2#LINE/L2 1945 GGGTTCAAGAGAGAATGGGAGGAGAGGAATTGGAGACAGCGAGTATAGAC 1896 chr6qtel1M 646321 GATCTTTTCAAGGAATTGAGACATAAAAAGAAGAGGAGATAT 646362 i iii i i vv vii ii i vi v C L2#LINE/L2 1895 AACTCTTTCGAGGAGTTTTGCTGTAAAGGGGAGCAGAGAAAT 1854 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 59.47 CpG sites = 267, Kimura (unadjusted) = 62.43 Transitions / transversions = 1.41 (267/189) Gap_init rate = 0.05 (52 / 1152), avg. gap size = 1.35 (70 / 52) 12 0.00 8.00 3.85 chr6qtel1M 648594 648618 (351382) (ATA)n#Simple_repeat 1 26 (0) m_b315s252i6 13182 chr6qtel1M 648594 ATATATAATAATAATAAT-ATAA-AAT 648618 - - - (ATA)n#Simple 1 ATA-ATAATAATAATAATAATAATAAT 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.12 (3 / 24), avg. gap size = 1.00 (3 / 3) 25 9.18 0.00 0.00 chr6qtel1M 649646 649680 (350320) (AT)n#Simple_repeat 1 35 (0) m_b315s252i7 13183 chr6qtel1M 649646 ATATACAAATATACATATATATATATATATATATA 649680 i v i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATA 35 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 19 28.07 0.00 5.19 chr6qtel1M 650625 650705 (349295) (TATATG)n#Simple_repeat 1 77 (0) m_b315s252i8 13184 chr6qtel1M 650625 TAAATGTATATGAATGTATTTATGTCTATGAGTATAGGTAGCTATTTATA 650674 v v i i v v -- v -- v (TATATG)n#Sim 1 TATATGTATATGTATATGTATATGTATAT--GTATATGTA--TATGTATA 46 chr6qtel1M 650675 TGGATGTGTGTGTGTGTATACATATACATAT 650705 v i i i i ii ii (TATATG)n#Sim 47 TGTATATGTATATGTATATGTATATGTATAT 77 Matrix = Unknown Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.05 (4 / 80), avg. gap size = 1.00 (4 / 4) 13 39.42 2.08 1.03 chr6qtel1M 651318 651413 (348587) (ATAC)n#Simple_repeat 1 97 (0) m_b315s252i9 13185 chr6qtel1M 651318 ATATACACTTACATATATGCATGCATGTCTATGTGCCTACATATGCACAA 651367 i i v i i i iiv ii i v iii - (ATAC)n#Simpl 1 ATACATACATACATACATACATACATACATACATACATACATACATAC-A 49 chr6qtel1M 651368 TCTATGCATATA-AGA-AGATATAGACATTTAAACATACAAACATACA 651413 vi i i - v - v i v vi v v (ATAC)n#Simpl 50 TACATACATACATACATACATACATACATACATACATACATACATACA 97 Matrix = Unknown Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.03 (3 / 95), avg. gap size = 1.00 (3 / 3) 62 1.78 0.00 0.00 chr6qtel1M 651621 651677 (348323) (AT)n#Simple_repeat 1 57 (0) c_b315s251i1 13186 chr6qtel1M 651621 ATATATATATATATATATATATATATATATATATATATATATATATATAT 651670 (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr6qtel1M 651671 TTATATA 651677 v (AT)n#Simple_ 51 ATATATA 57 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0) 35 0.00 0.00 0.00 chr6qtel1M 651686 651715 (348285) (GT)n#Simple_repeat 1 30 (0) c_b315s251i2 13187 chr6qtel1M 651686 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 651715 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 30 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 24 27.37 2.41 2.41 chr6qtel1M 651773 651855 (348145) (AT)n#Simple_repeat 1 83 (0) m_b315s252i10 13188 chr6qtel1M 651773 ATAGATGTATAGGAATGTGTATATCATATATGTACATGAT-TATAGATAT 651821 v i viv i i - i i - - v (AT)n#Simple_ 1 ATATATATATATATATATATATAT-ATATATATATAT-ATATATATATAT 48 chr6qtel1M 651822 CTATATGTGTATATATA-AAACATATTTACATTTA 651855 v i i - v i v i v (AT)n#Simple_ 49 ATATATATATATATATATATATATATATATATATA 83 Matrix = Unknown Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.05 (4 / 82), avg. gap size = 1.00 (4 / 4) 13 11.18 0.00 6.45 chr6qtel1M 652092 652124 (347876) (ATTTTT)n#Simple_repeat 1 31 (0) m_b315s252i11 13189 chr6qtel1M 652092 ATTTTTATTTTTATTTTTTGTATTTAACTTTTA 652124 - i - v i (ATTTTT)n#Sim 1 ATTTTTATTTTTA-TTTTTAT-TTTTATTTTTA 31 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.06 (2 / 32), avg. gap size = 1.00 (2 / 2) 233 23.33 0.00 0.00 chr6qtel1M 653356 653415 (346585) L1ME3Cz_3end#LINE/L1 489 548 (449) m_b315s551i5 13190 chr6qtel1M 653356 TATCCTTCATTTGGGGAATGGCTGAATAAATGATGATATATGAAGGTAAT 653405 i v v v v i vi i vv vii L1ME3Cz_3end# 489 TGTCCATCAATAGGGGAATGGATAAATAAATTGTGGTATATTCATACAAT 538 chr6qtel1M 653406 GGAATACTAT 653415 L1ME3Cz_3end# 539 GGAATACTAT 548 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 28.03 CpG sites = 6, Kimura (unadjusted) = 28.03 Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0) 12 24.95 5.77 0.00 chr6qtel1M 653683 653734 (346266) (TTTTG)n#Simple_repeat 1 55 (0) m_b315s252i12 13191 chr6qtel1M 653683 TTTTGTTGTGTTTTG-TTTCTCATAGTTT-TTCTCTTCTGTTCTG-ATTG 653729 v - v iv iv - i v i i -v (TTTTG)n#Simp 1 TTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTG 50 chr6qtel1M 653730 TTTTG 653734 (TTTTG)n#Simp 51 TTTTG 55 Matrix = Unknown Transitions / transversions = 0.83 (5/6) Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.00 (3 / 3) 11 30.18 0.00 3.70 chr6qtel1M 653816 653871 (346129) (AAAAATT)n#Simple_repeat 1 54 (0) m_b315s252i13 13192 chr6qtel1M 653816 AAAAATTAAAATTCCAAATCTTATAAAAGTGTATATGGAAAATTGAAAGT 653865 v -i vv - v iv v vi i i (AAAAATT)n#Si 1 AAAAATTAAAAAT-TAAAAATTA-AAAATTAAAAATTAAAAATTAAAAAT 48 chr6qtel1M 653866 AAAAAA 653871 v (AAAAATT)n#Si 49 TAAAAA 54 Matrix = Unknown Transitions / transversions = 0.62 (5/8) Gap_init rate = 0.04 (2 / 55), avg. gap size = 1.00 (2 / 2) 270 21.43 0.00 0.00 chr6qtel1M 653969 654038 (345962) DNM1r#Unknown 2477 2546 (2116) m_b315s502i0 13193 chr6qtel1M 653969 CATATATATATATATATATATGTGTGTATGTGTGTGTGTGTGTGTGTTTG 654018 i i i i i i i i i i v DNM1r#Unknown 2477 CGTGTATGTGTGTATATATGTGTGTATATGTGTGTATGTGTGTATATATG 2526 chr6qtel1M 654019 TATATGAATATGTATATATA 654038 i iv i ? DNM1r#Unknown 2527 TGTATATATACGTATNTATA 2546 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 23.31 CpG sites = 13, Kimura (unadjusted) = 27.52 Transitions / transversions = 6.50 (13/2) Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0) 27 12.57 2.22 0.00 chr6qtel1M 654049 654093 (345907) (TA)n#Simple_repeat 1 46 (0) m_b315s252i14 13194 chr6qtel1M 654049 TATATGTGTAT-TATATATATATACATATATATGTACATATATATA 654093 i i - i i i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATA 46 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 602 31.45 5.16 4.97 chr6qtel1M 654723 655826 (344174) L1M1_orf2#LINE/L1 27 1132 (2162) m_b315s551i6 13195 chr6qtel1M 654723 AATCACAACTGTGAATATGAATGGGATGAAATTTCTCAT-AAAACTGAAG 654771 v i vv i i iv i v i iv - -- vi L1M1_orf2#LIN 27 AATAATAACATTGAATGTAAATGGACTAAACTCTCCAATCAAAA--GACA 74 chr6qtel1M 654772 CAAAA-GGCAGAGTAGATTAAGAAA-GAGACTGGTAGAACATGTT---TA 654816 i i i- v i i v i -i ivi?v v - --- L1M1_orf2#LIN 75 TAGAGTGGCTGAATGGATGAAAAAACAAGACCCANTGATC-TGTTGCCTA 123 chr6qtel1M 654817 CAAGAAACACATTTGAA----AGAGATAAATACAGAGTAAAGATAAAAGG 654862 i v v---- i i v i i v i i i L1M1_orf2#LIN 124 CAAGAAACACACTTCACCTATAAAGACACACATAGACTGAAAATAAAGGG 173 chr6qtel1M 654863 CTGAAATAGAATTTATTATTGTACTTCAACTGAAATTGAAAAAGCAGCAC 654912 v i v ii ----- vi ivi iv iii - v L1M1_orf2#LIN 174 ATGGAAAAAGAT-----ATTCCATGCCAATGGAAACCAAAAAAG-AGCAG 217 chr6qtel1M 654913 TAGGAACT---CTGATCTCAGATAAAGCAAA----AATACAAATAGACTA 654955 v v i --- v v i ii i ---- v --i L1M1_orf2#LIN 218 GAGTAGCTATACTTATATCAGACAAAATAGATTTCAAGACAAA--AACTA 265 chr6qtel1M 654956 ATTAAAAGGGATAAGGAAGGAAAGTACATCTTGGTAAAGGA-TAAATTAA 655004 - v i i i i vv v i vv i i- v v L1M1_orf2#LIN 266 -TAAGAAGAGACAAAGAAGGTCACTATATAATGATAAAGGGGTCAATTCA 314 chr6qtel1M 655005 ACAATGAAGTAT-TAATGATATGAAATGTATATGTACCAAGTACTGGAGC 655053 i - i - - ii v?v i i v ii L1M1_orf2#LIN 315 GCAA-GAGG-ATATAACAATTNTAAATATATATGCACCCAACACTGGAGC 362 chr6qtel1M 655054 ATTCAGCTATCTAGAGAAGATGTTAAGGCAGTTACAG-GAGAAATAAATA 655102 ii v v i v i i vviv i v - i i iv L1M1_orf2#LIN 363 ACCCAGATATATAAAGCAAATATTATTAGAGCTAAAGAGAGAGATAGACC 412 chr6qtel1M 655103 GCAAAACTA-AATTACTGGGGGACCTC-ACACTTCCCCTCTCAGAATCAT 655150 v v v - vi - i i - -i v i v iiv L1M1_orf2#LIN 413 CCAATACAATAATAGCT-GGAGACTTCAACAC-CCCACTTTCAGCATTGG 460 chr6qtel1M 655151 ACCAATCT---AACCACAAAATAAACAATAAGAAATTAGGGACATTAATA 655197 vi --- iv v v -- ivvv - v L1M1_orf2#LIN 461 ACAGATCTTCCAGACAGAAAATCAACA--AAGAAACATCGGAC-TTAATC 507 chr6qtel1M 655198 GGATCCTAAAAAC---GTAGATATGATAG--ACTTATAGGAAA--AAATT 655240 v -iv v i ---i i iv i -- i i i v --vv i L1M1_orf2#LIN 508 TG-CACTATAGACCAAATGGACCTAATAGATATTTACAGAACATTTCATC 556 chr6qtel1M 655241 AAATGGAGACATAAAAGGAATATATGTTTTTTGCTTGGTACTACATGG-- 655288 v i vvi ------ i ii i v i --i vi -- L1M1_orf2#LIN 557 CAACGGCTGCA------GAATACACATTCTTTTCCT--CAGCACATGGAT 598 chr6qtel1M 655289 CACCTACAAAAAATGGACCATGTATTAGATCAATTATGCCACATGTATTA 655338 iiiv - ii i i i i vvv ---- v v L1M1_orf2#LIN 599 CATTCTC-AAGGATAGACCATATGTTAGGTCACAAA----ACAAGTCTTA 643 chr6qtel1M 655339 GGGATTATGAACATGAAAAAGAAGAAAGAGAAAAT---GCTTGCTTTTCA 655385 --------i vv i vvi i v v --- v - i v L1M1_orf2#LIN 644 --------AAACATTCAAAAAAATTGAAATAATATCAAGCAT-CTTCTCT 684 chr6qtel1M 655386 GGCCACAATATAATAAAAAACTAT-ATTCAATAAAGGGCGGA-----GAA 655429 i iv -- v- v vii v ----- i L1M1_orf2#LIN 685 GACCACAATGGAAT--AAAACTAGAAATCAATAACAAGAGGAATTTTGGA 732 chr6qtel1M 655430 AGTTAGAATAAAAAAAT-TGGAAATTGAATAATCTCAGTCTGAATAATGA 655478 ii --- v v i- i i v vvvi i iv L1M1_orf2#LIN 733 AACT---ATACAAACACATGGAAATTAAACAATATGCTCCTGAATGACCA 779 chr6qtel1M 655479 -TGGGTCACCCAACAAATCACAGAAACAA--TCATCAATTTCCTCTAAGA 655525 - viv v i - iv -- v vv i vv v L1M1_orf2#LIN 780 GTGGGTCAATGAAGAAATTA-AGAAGGAAATTGAAAAATTTCTTGAAACA 828 chr6qtel1M 655526 CAATGACAATAATGAGACAACATACCAAAAATTATGGGATGCATCTAACA 655575 - i iivi v vi i v v vi L1M1_orf2#LIN 829 -AATGATAATGGAAACACAACATACCAAAACCTATGGGATACAGCAAAAG 877 chr6qtel1M 655576 AAGT-TTTAGGGGAAATTTTATATCAATAAATAGCTACCTAAATAAAACA 655624 v -i v i i v v v i iv v v v iv L1M1_orf2#LIN 878 CAGTACTAAGAGGGAAGTTTATAGCTATAAGTGCCTACATCAAAAAAGAA 927 chr6qtel1M 655625 GAGAAAGAGAAGATCAATGAATTGGGCATGGAACT--AAAAACGTAGAA- 655671 i vvvv i v ii vi iivv v v -- i - - L1M1_orf2#LIN 928 GAAAAACTTCAAATAAACAACCTAACGATGCATCTTAAAGAAC-TAGAAA 976 chr6qtel1M 655672 --CAAGAACAACTTAAAAACCACCAATTAAATACCAAGTTAGAAATTATG 655719 -- i vii-- vvv - i vv iivv v i L1M1_orf2#LIN 977 AGCAAGAGCAAACC--AAACCCAAAATT-AGTAGAAGAAAAGAAATAATA 1023 chr6qtel1M 655720 AAACTCCAAGGCTAGATTAATAAAATTGAAACTAAGAAGACTTTTGA--- 655766 iv vi vvv i v i iv i vv vv --- L1M1_orf2#LIN 1024 AAGATCAGAGCAGAAATAAATGAAATTGAAATGAAGAAAACAATACAAAA 1073 chr6qtel1M 655767 -ACTAATCAAACTGAGAGATGATTTTATTAAAAACAATCAACAAAATAAA 655815 - ii v vi i v i - i -i? v vi L1M1_orf2#LIN 1074 GATCAATGAAACAAAAAGTTGGTTTT-TTGAAAA-GNTAAACAAAATTGA 1121 chr6qtel1M 655816 CAAACTTTTGG 655826 i i L1M1_orf2#LIN 1122 CAAACCTTTAG 1132 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 41.47 CpG sites = 170, Kimura (unadjusted) = 41.63 Transitions / transversions = 1.06 (170/160) Gap_init rate = 0.08 (84 / 1103), avg. gap size = 1.33 (112 / 84) 309 33.80 4.98 2.55 chr6qtel1M 655830 656251 (343749) L1M3_orf2#LINE/L1 2120 2551 (737) m_b315s551i7 13196 chr6qtel1M 655830 AGAATCCTATA-ACATCATCTAAAAACCGCATGGAAACAATTCACAGCTT 655878 i i v - vi i v i i- i vi vv iiv L1M3_orf2#LIN 2120 AAAACCCTAAAGACTCCACCAAAAAACTGT-TAGAACTAATAAACGAATT 2168 chr6qtel1M 655879 TAGCAGAGTTGCAAGATATAAAACAAACTCACAGAAATCATCAACATTTC 655928 i i i i i iv vi i vivi i L1M3_orf2#LIN 2169 CAGTAAAGTTGCAGGATACAAAATCAACATACAAAAATCAGTTGCGTTTC 2218 chr6qtel1M 655929 TATATATTACTGACAAAACCTAGCAGCTAGAGA---TAGAAGAGTAATTC 655975 i i vii i -- v v vv ii --- ii i ii i L1M3_orf2#LIN 2219 TATACACTAACAACGAA--CTATCCGAAAAGGAAATTAAGAAAACAATCC 2266 chr6qtel1M 655976 CATTTGAAATTACTGTTGACAA-AATAAGATGTGT-----CTATCT--GC 656017 iv - vii ii v - i iiv -----iv v --i L1M3_orf2#LIN 2267 CATTTACAA-TAGCATCAAAAAGAATAAAATACTTAGGAATAAACTTAAC 2315 chr6qtel1M 656018 CAAGAGAAACCTAAGAACTATGTGTCCATAATTAGAAAACTTT--TCATA 656065 - iiivv vi i iiiiiv v i v v -- v v L1M3_orf2#LIN 2316 CAAG-GAGGTGAAAGACTTGTACACTGAAAACTATAAAACATTGATGAAA 2364 chr6qtel1M 656066 CAAATAAAGTCAGATCTACATAA-TGGGAA--CATTATAAATTGCTCATT 656112 v v ivv ivi v - i -- ivii--- i v L1M3_orf2#LIN 2365 GAAATTAAAGAAGACACAAATAAATGGAAAGACATCCCG---TGTTCATG 2411 chr6qtel1M 656113 GGTAGGCTGAGCTAATATGATACCAATGACACAT-CTACCTAAAGCGATT 656161 i v vv ii vi vvv v - - i i L1M3_orf2#LIN 2412 GATTGGAAGAATTAATATTGTTAAAATGTC-CATACTACCCAAAGCGATC 2460 chr6qtel1M 656162 TACTTGTTCAGTGCATTATCCATCAAAATGACAA-ACCATTATTTTCTAG 656210 vvi i v vi i vv -iv - vi L1M3_orf2#LIN 2461 TACAGATTCAATGCAATCCCTATCAAAATCCCAATGGCATT-TTTTACAG 2509 chr6qtel1M 656211 --ATAGAAAAAAATAATGACAAAATTCATCTGCAGGAACAAAA 656251 -- - i vvi v v ivv L1M3_orf2#LIN 2510 AAATAG-AAAAAACAATCCTAAAATTCATATGGAACCACAAAA 2551 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 44.47 CpG sites = 78, Kimura (unadjusted) = 46.34 Transitions / transversions = 1.28 (78/61) Gap_init rate = 0.05 (22 / 421), avg. gap size = 1.45 (32 / 22) 289 36.64 4.05 1.99 chr6qtel1M 655877 656419 (343581) L1MD_orf2#LINE/L1 2173 2726 (568) m_b315s551i8 13196 chr6qtel1M 655877 TTTAGCAGAGTTGCAAGATATAAAACAAACTCACAGAAATCATCAACATT 655926 i ii i i i i i? vi i vivii L1MD_orf2#LIN 2173 TTCAGCAAGGTCGCAGGATACAAGATNAACATACAAAAATCAATTGTATT 2222 chr6qtel1M 655927 TCTATATATTACTGACAAA-ACCTAGCAGCTAGAGATAGAAGAGTAATTC 655975 i vii ii - v i v i iii iv i ivii v L1MD_orf2#LIN 2223 TCTATATACTAGCAATGAACACGTGGAAACCGAAATTAAAAATACAATAC 2272 chr6qtel1M 655976 CATTTGAAATTACTGTTGACAAAATAAGAT------GTGTCTATCTGCCA 656019 iv ii vvvi v i i ------ i vv iv L1MD_orf2#LIN 2273 CATTTACAATCGCTCAAAAAAAAATGAAATACTTAGGTATAAATCTAACA 2322 chr6qtel1M 656020 AGAGAAACCTAAGAACTATGTGTCCATAATTAGAAAACTTT--TCATACA 656067 i v viivi i vi i i iiv v i v vi -- v v v L1MD_orf2#LIN 2323 AAACATGTACAGGACTTGTATGCTGAAAACTACAAAACGCTGATGAAAGA 2372 chr6qtel1M 656068 AATAAAGTCAGATCTACAT-AATGGGAACATTATAAATTGCTCATTGGTA 656116 v ivv v - ii v -i vvv i v i v L1MD_orf2#LIN 2373 AATCAAAGAAGATCTAAATAAATGGAGAGA-CATACCGTGTTCATGGATT 2421 chr6qtel1M 656117 GGCTGAGCTAATATGATACCAATGACACATCTACCTAAAGCGATTTACTT 656166 vv vii i ii vvi v vv v i vi ? vv L1MD_orf2#LIN 2422 GGAAGACTCAACATAGTAAAGATGTCAATTCTCCCCAAATTGATNTACAG 2471 chr6qtel1M 656167 GTTCAGTGCATTATCCATCAAAATGACAA-ACCATTATTTTCTAGATAGA 656215 i ii v vi i vv i- vv - v v L1MD_orf2#LIN 2472 GTTTAACGCAATTCCTATCAAAATCCCAGCAAGATT-TTTTGTAGATATA 2520 chr6qtel1M 656216 AA-AAAATAATGACAAAATTCATCTGCAGGAACAAAAAGTCAAGCATA-T 656263 i - i? v vvi i v v iiii iiiv v v -i L1MD_orf2#LIN 2521 GACAAGNTTATTCTAAAATTTATATGGAAAGGCAAAGGAACTAGAATAGC 2570 chr6qtel1M 656264 TAAGGGAATTAATGAAAAAATAT-ATAAAGAATGGTGGCTTAG------C 656306 iiv -v iv v- viv iv iv i ?------ L1MD_orf2#LIN 2571 TAAAACAATT-TTGAAAAAGAAGAATAAAGTGGGAGGAATCANTCTACCC 2619 chr6qtel1M 656307 AGTATCAAAACCACATTATACAGCAAC-CCCATCAAAACCTTTTGGAACT 656355 ii v i i-i i i v -viv i ?v v v i L1MD_orf2#LIN 2620 GATTTCAAGACT-TACTATATAGCTACAGTAATCAAGACNGTGTGGTATT 2668 chr6qtel1M 656356 GGCTAAGGAATATAGCGC-TGGATCATTGGGATAGCTTACATACACACAA 656404 vi i v - i - i v i i v------ i v v L1MD_orf2#LIN 2669 GGCGGAGGGATAGA-CACATAGATCAATGGAACAGA------ATAGAGAA 2711 chr6qtel1M 656405 CCTAAAAATAAAACC 656419 i i i v L1MD_orf2#LIN 2712 CCCAGAAATAGACCC 2726 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 50.67 CpG sites = 107, Kimura (unadjusted) = 52.72 Transitions / transversions = 1.22 (107/88) Gap_init rate = 0.04 (22 / 542), avg. gap size = 1.50 (33 / 22) 343 24.13 3.38 4.79 chr6qtel1M 656105 656252 (343748) L1PB_orf2#LINE/L1 2410 2555 (739) m_b315s551i9 13196 chr6qtel1M 656105 TGCTCATTGGTAGGCTGAGCTAATATGATACCAATGACACAT-CTACCTA 656153 v i i iv iii vi ivv - - i v L1PB_orf2#LIN 2410 TGCTCATGGATGGGTAGAATCAATATTGTGAAAATGAC-CATACTGCCAA 2458 chr6qtel1M 656154 AAGCGATTTACTTGTTCAGTGCATTATCCATCAAAATGACAAACCATTAT 656203 i i vvi i v vi iv -- i L1PB_orf2#LIN 2459 AAGCAATCTACAAATTCAATGCAATTCCCATCAAAATACC--ACCATCAT 2506 chr6qtel1M 656204 T-TTC-TAGA--TAGAAAAAAATAATGACAAAATTCATCTGCAGGAACAA 656249 - -i -- - i vvi v --- v L1PB_orf2#LIN 2507 TCTTCACAGAACTAG-AAAAAACAATCCTAAAATTCATAT---GGAACCA 2552 chr6qtel1M 656250 AAA 656252 L1PB_orf2#LIN 2553 AAA 2555 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 29.55 CpG sites = 19, Kimura (unadjusted) = 29.55 Transitions / transversions = 1.27 (19/15) Gap_init rate = 0.07 (11 / 147), avg. gap size = 1.09 (12 / 11) 229 30.32 7.06 4.35 chr6qtel1M 656702 656970 (343030) L1M3_orf2#LINE/L1 3013 3288 (0) m_b315s551i10 13196 chr6qtel1M 656702 AAAATGGACAACTCTGATTACATTAAATTTAAAAAG-----GCAACAAAA 656746 i v vv i i i - ----- - iv L1M3_orf2#LIN 3013 AAAATAGACAAGTGGGACTACATCAAACT-AAAAAGCTTCTGCA-CAGCA 3060 chr6qtel1M 656747 AAAAAAACAAAGAAACAGAAACAAGGTTAAAAGGTGA------AAGCTGG 656790 ii -vv ------ v ii ------i iiv L1M3_orf2#LIN 3061 AAGGAAACAA-TCAACAGA------GTGAAAAGGCAACCTACGGAATGGG 3103 chr6qtel1M 656791 GGGAAATATTAACAGCTAGTGTTTCTGA-AAAGGTCTCATTTCTAAAATA 656839 i i vi ivivi i v - i vi v v i L1M3_orf2#LIN 3104 AGAAAATATTTGCAAACCATATATCTGATAAGGGGTTAATATCCAAAATA 3153 chr6qtel1M 656840 TATAAAAAACAATGTCAAATT--TATCAAAATAA-AAGTCATTCTGTAAT 656886 ii vv?vv v i-- v v - i v ii ---i L1M3_orf2#LIN 3154 TATAAGGAACTCNTACAACTCAATAGCAAAAAAACAAATAACCC---GAT 3200 chr6qtel1M 656887 TGGTAAATGCTCAGAGGATCTGAA----CAATTTTCAAATGACAAAATTA 656932 ?iv vv i i ---- v i v v vi v vv L1M3_orf2#LIN 3201 TNAAAAATGGGCAAAGGACCTGAATAGACATTTCTCCAAAGAAGACATAC 3250 chr6qtel1M 656933 AAGCCACCTATACTTATATGAAAAAATGCTCTGCATCA 656970 iivi v i vv i vi L1M3_orf2#LIN 3251 AAATGGCCAACAGGTATATGAAAAGATGCTCAACATCA 3288 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 39.26 CpG sites = 40, Kimura (unadjusted) = 39.91 Transitions / transversions = 1.05 (40/38) Gap_init rate = 0.07 (18 / 268), avg. gap size = 1.72 (31 / 18) 258 28.54 6.59 3.74 chr6qtel1M 656789 656970 (343030) L1P4_orf2#LINE/L1 3108 3294 (0) m_b315s551i11 13196 chr6qtel1M 656789 GGGGGAAATATTAACAG-CTAGTGTTTCTGA-AAAGGTCTCATTTCTAAA 656836 i i vi i- - iv i - v v i i L1P4_orf2#LIN 3108 GGAGAAAATATTCGCAAACTA-TGCATCCGACAAAGGTCTAATATCCAGA 3156 chr6qtel1M 656837 ATATATAAA------AAACAATGTCAAATTTATCAAAATAAAAGTCATTC 656880 v i------ ?- --iv v v v i v ii L1P4_orf2#LIN 3157 ATCTATAAGGAACTTAAACAAN-TCAA--CAAGCAAAAAACAAATAACCC 3203 chr6qtel1M 656881 TGTAATTGGTAAATGCTCAGAGGATCTGAACAA----TTTTCAAATGACA 656926 i--- iiv i vv i iv i---- i v vi L1P4_orf2#LIN 3204 C---ATTAAAAAGTGGGCAAAGGACATGAACAGACACTTCTCAAAAGAAG 3250 chr6qtel1M 656927 AAATTAAAGCCACCTATACTTATATGAAAAAATGCTCTGCATCA 656970 v vv vi v i vvi vi L1P4_orf2#LIN 3251 ACATACAAGCGGCCAACAAACATATGAAAAAATGCTCAACATCA 3294 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 34.97 CpG sites = 26, Kimura (unadjusted) = 36.77 Transitions / transversions = 1.08 (26/24) Gap_init rate = 0.06 (11 / 181), avg. gap size = 1.73 (19 / 11) 604 32.65 3.58 5.21 chr6qtel1M 656831 657473 (342527) L1ME4c_3end#LINE/L1 7 639 (191) m_b315s551i12 13196 chr6qtel1M 656831 TCTAAAATATATAAAAAAC-AATGTCAAATTTATCAAAATAAAAGTCATT 656879 ?v ? i i -v - v v i - ?i vv L1ME4c_3end#L 7 TCTNTANTATATAAAGAGCTCAT-TCAAATTGATAAGAA-AAANATCAAG 54 chr6qtel1M 656880 -CTGTAATTGGTAAATGCTCAGAGGATCTGAACA----ATTTTCAAATGA 656924 - ivi v i vv i iv ---- iv ? v L1ME4c_3end#L 55 ACCCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGA 104 chr6qtel1M 656925 CAAAATTAAAGCCACCTATACTTATATGAAAAAATGCTCTGCATCAGTAC 656974 vi vv ?iviivv i vvi i i i vi v iv v L1ME4c_3end#L 105 GGAAATACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTAG 154 chr6qtel1M 656975 TAATTTATTGTATTTCTCTAAAATGCAAAGGAAA-CAACTCTAAAGTACC 657023 iv ---- -------i vv - vv i ii L1ME4c_3end#L 155 TAATCAA----A-------GAAATGCAAATTAAAGCAACAATGAGATACC 193 chr6qtel1M 657024 ACCTCACACTCCTCAAAAGGAGATTAACTAAGATAACAGAAAAAGATAAA 657073 ii i i iiv i ------ i v i vvv i vv v L1ME4c_3end#L 194 ATTTTACGCCTATTAAA------TTAGCAAAAATTTAAAAAATTGATAAT 237 chr6qtel1M 657074 AATCAATGTTGGAGAAGGTTATGGAAAAACTGGGACACTAATGCATTGTT 657123 vi i v - ? ii vi v ? v i i L1ME4c_3end#L 238 ACCCAATGCTGGCGA-GGNTGCGGTGAAACTGGTACNCTCATACATTGCT 286 chr6qtel1M 657124 GGGGAACTTATGAAATGATTCAACAATTCTAGAGAACAATCAGAAACTAT 657173 v ivv? i i v i v vv i i i i iv iv v i L1ME4c_3end#L 287 GGTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATAC 336 chr6qtel1M 657174 GTCCAAAGGACTATAACACTGTTC-----CATTCACCCAGCAGTTCCATT 657218 viv ii i v v ----- v v i i i L1ME4c_3end#L 337 GTATCAAGAGCCATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACT 386 chr6qtel1M 657219 ACTGGATCTGTGTTCCAAGAAAATCAT---AAAGTAGGGAAAAGGAACCA 657265 v ivv v i i i i v --- v i --- i L1ME4c_3end#L 387 TCTGGGAATTTATCCTAAGGAAATAATTCAAAAGAAGGAAAAAG---CTA 433 chr6qtel1M 657266 TATGTGCAAAACTGTTTGTAGCAGCTCTCTTTTTTTTAGTAGCAAAGAAT 657315 ii i iv ii v ---v v v i i i L1ME4c_3end#L 434 TATGCACGAAGATGTTCATTGCAGC---GTTATTTATAATAGCGAAAAAT 480 chr6qtel1M 657316 TA-AAATGAGTAGAAAACCCATGCATTAGGG-AATGGCTGGAGAAGTTGT 657363 i- ii vivi vii -i v - i iiiv i i L1ME4c_3end#L 481 TGGAAACAACCTAAATGTCCA-ACAATAGGGGAATGGTTAAGTAAATTAT 529 chr6qtel1M 657364 GGTATACATAGGTAACACAATATGAT-----CATTATATATAAAGTGATA 657408 i iv? vvii iiv v ----- ----- i L1ME4c_3end#L 530 GGTACATCNACTCGATGGAATATTATGCAGCCATTA-----AAAATGATA 574 chr6qtel1M 657409 AACAAGCTGATTTTAGAA-AACCTGGAATGATGTGCACGAAGTAATATTG 657457 vi v vv i v iv i- v -i vi i vi i i L1ME4c_3end#L 575 ATTATGAAGACTATGTAGCAACATGGAA-AATGTTTATGATATAATGTTA 623 chr6qtel1M 657458 AGTGAAACAATCAGAA 657473 v v L1ME4c_3end#L 624 AGTGAAAAAAGCAGAA 639 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 42.64 CpG sites = 108, Kimura (unadjusted) = 44.77 Transitions / transversions = 1.19 (108/91) Gap_init rate = 0.07 (43 / 642), avg. gap size = 1.30 (56 / 43) 23 24.43 1.45 1.45 chr6qtel1M 657776 657844 (342156) (ATAA)n#Simple_repeat 1 69 (0) m_b315s252i15 13197 chr6qtel1M 657776 ATAGATATATAAATGTATATTATATACACATAAATAAATAATTTTTTAAA 657825 i v iv -v v i v v vvv (ATAA)n#Simpl 1 ATAAATAAATAAATAAATA-AATAAATAAATAAATAAATAAATAAATAAA 49 chr6qtel1M 657826 AAAATAAACAAATAAA-AAA 657844 v i - (ATAA)n#Simpl 50 TAAATAAATAAATAAATAAA 69 Matrix = Unknown Transitions / transversions = 0.40 (4/10) Gap_init rate = 0.03 (2 / 68), avg. gap size = 1.00 (2 / 2) 239 28.97 6.86 1.87 chr6qtel1M 657856 657957 (342043) L2a_3end#LINE/L2 411 517 (0) m_b315s601i5 13198 chr6qtel1M 657856 TGAGATCAGAAATCTCATGTTCTTTTTGGTCACA-----ATCACCATAGG 657900 iv ii - iv iiv v v----- v vv v L2a_3end#LINE 411 TGAGGGCAGGGA-CTTTTGTCTGTTTTGTTCACTGCTGTATCCCCAGCGC 459 chr6qtel1M 657901 TGAAAGCAATGTGTGGCACATGGTAGGGGCTTAATAAAGGTTTAATTGAA 657950 iv i i i iv i v i vi -i L2a_3end#LINE 460 CTAGAACAGTGCCTGGCACATAGTAGGCGCTCAATAAATATTT-GTTGAA 508 chr6qtel1M 657951 --AAGGAAT 657957 -- v L2a_3end#LINE 509 TGAATGAAT 517 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 37.20 CpG sites = 15, Kimura (unadjusted) = 37.20 Transitions / transversions = 1.07 (15/14) Gap_init rate = 0.04 (4 / 101), avg. gap size = 2.25 (9 / 4) 189 29.71 6.08 9.03 chr6qtel1M 660741 660888 (339112) C L2c_3end#LINE/L2 (59) 419 276 m_b315s601i6 13199 chr6qtel1M 660741 AAAGACAAA--AGACATCATT--TGCTCTCTGAGACGCTCACGGTACAAT 660786 ii -- ivi i-- i -i iv i vi i C L2c_3end#LINE 419 AAAGATGAATAAGACACGGTCCCTGCCCTC-AAGGAGCTCACAGTCTAGT 371 chr6qtel1M 660787 GGGAGAGAC-TACATGCAAACTGATATCAACAA-ATTATTTATTTACAA- 660833 ii -v ? i v i viv - iv v v v i - C L2c_3end#LINE 370 GGAGGAGACAGACANGTAAACAGACAATTACAATACAAGTTAATGATAAG 321 chr6qtel1M 660834 -ACT-TAATGAGTGATATCAACAGAGGGAAGGTGCTGTCATTTTCGAGTA 660881 -i - i v - vi ------ i vi----- i C L2c_3end#LINE 320 TGCTATAATGGGAG-TATAGACAG------GGTGCTATGG-----GAGCA 283 chr6qtel1M 660882 TAGAGAA 660888 i i C L2c_3end#LINE 282 CAGAGGA 276 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 38.47 CpG sites = 26, Kimura (unadjusted) = 39.78 Transitions / transversions = 1.86 (26/14) Gap_init rate = 0.14 (20 / 147), avg. gap size = 1.10 (22 / 20) 972 38.62 5.28 2.83 chr6qtel1M 661029 662203 (337797) C L2#LINE/L2 (68) 3014 1812 m_b315s601i7 13199 chr6qtel1M 661029 TGTTCAAGGAACATCAAAAAAGCCAGTTTTCCTGCATTGCAGGCTGTATG 661078 i v ii i v vv v -- i iv vii C L2#LINE/L2 3014 TGTTCGAGGAACAGCAAGGAGGCCAGTGTGGCTGGA--GCGGAGTGAGCG 2967 chr6qtel1M 661079 GTAAGGGATATGGTTTAAGA--AAACTGGAAGTGTTAGGAGGGGCCAGAT 661126 ivii iivi vvi -- iiiii iiv v v i i C L2#LINE/L2 2966 AGGGGGAGAGTGGTAGGAGATGAGGTCAGAGAGGTAACGGGGGACCAGAT 2917 chr6qtel1M 661127 TATGAAGGGATTTG-AATTTAAAATATGAATTTTA-TATTTAC-CTGATT 661173 i v vi - ivii vvi v i i i-iv - v C L2#LINE/L2 2916 CATGTAGGGCCTTGTAGGCCATTGTAAGGACTTTGGCTTTTACTCTGAGT 2867 chr6qtel1M 661174 AGAATAAAATGTAATTGTACTTTACTGA--AGAGGAGCTGATAACATTAG 661221 iii iii v iv v vvv vi -- - i vv iv C L2#LINE/L2 2866 GAGATGGGAAGCCATTGGAGGGTTTTGAGCAGAGGAG-TGACATGATCTG 2818 chr6qtel1M 661222 ATTACCAATGTAGAAAGATCAATTTGAGAGGTGAGTGGAAGAAGAACTAA 661271 i vv iv v i i v i ivv v v v ii vii i? C L2#LINE/L2 2817 ACTTACGTTTTAAAAGGATCACTCTGGCTGCTGTGTTGAGAATAGACTGN 2768 chr6qtel1M 661272 AGTAGAGAGAGATTTAATTCAGAGAGATGATCTAGCAGTCTGCAACATTT 661321 vi i vi iv vi vv i iv vi v v iivi v v C L2#LINE/L2 2767 AGGGGGGCAAGGGTGGAAGCAGGGAGACCAGTTAGGAGGCTATTGCAGTA 2718 chr6qtel1M 661322 ATTTGGGCATGAGATAATGAAAACCTGCACCAGGGTCATCATAATGTCAG 661371 iii iv i ivii i v vi vii i vvi C L2#LINE/L2 2717 ATCCAGGCGAGAGATGATGGTGGCTTGGACCAGGGTGGTGGCAGTGGAGG 2668 chr6qtel1M 661372 AGA-GAAAAGTGCCATGTATGTCATGATATA-----AATATAAAATTAAG 661415 v i- i vi-i v - vv ----- vi i iiii v C L2#LINE/L2 2667 TGGTGAGAAGTGGT-CGGAT-TCTGGATATATTTTGAAGGTAGAGCCGAC 2620 chr6qtel1M 661416 AGGATTTGGCAACAAAATGATTGTGGGTTGTTAGATTGGGAAGAGA--AC 661463 vii iii v iv v v --- i -- v C L2#LINE/L2 2619 AGGATTTGCTGATGGATTGGATGTGGGGTGTGAGA---GAAAGAGAGGAG 2573 chr6qtel1M 661464 TCATGAATAAATGGCATGTTTCAAGCCAAAG----TGGAAAAAAAGATAT 661509 v i i v vvv v ivi vi ---- ii vi -i C L2#LINE/L2 2572 TCAAGGATGACTCCAAGGTTTTTGGCCTGAGCAACTGGAAGGATGGA-GT 2524 chr6qtel1M 661510 TGGCGGTATTAACAGGAATAAGAAAATATGAAAGAGGAA-AGTTTTTGAG 661558 v --- ? v ii ii i ivv vii i- v vii C L2#LINE/L2 2523 TGCC---ATTNACTGAGATGGGGAAGACTGCGGGAGGAGCAGGTTTGAGG 2477 chr6qtel1M 661559 AGAAAGATAATAAATTAAGCCTTTTAAATATTAATTTTAAGACAGGTATG 661608 i i v vi i v ii vv v i v i iivv v C L2#LINE/L2 2476 GGGAAGATCAGGAGTTCAGTTTTGGACATGTTAAGTTTGAGATGCCTATT 2427 chr6qtel1M 661609 GAACATTCATTATGAGATATAGGAAATTCAGTTATGGATGTAAGAAT--G 661656 ii i vvvv i v iiv vv -- i v i -- C L2#LINE/L2 2426 AGACATCCAAGTGGAGATGTCGAGTAGGCAGTT--GGATATACGAGTCTG 2379 chr6qtel1M 661657 GCAGTCAGGAAAGAGGATAGCTCCAGGTTA-----ATAGATTTTATA--- 661698 viv ii ----- i i i----- i viv --- C L2#LINE/L2 2378 GAGTTCAGGGGAGAGG-----TCCGGGCTGGAGATATAAATTTGGGAGTC 2334 chr6qtel1M 661699 ATCAATATAGAGATAATTCTTGTATTCATGAAATGAGAATGATTTCAGCA 661748 ii v ii vi iv vi i ivi - vv v ? C L2#LINE/L2 2333 ATCAGCATATAGATGGTATTTAAAGCCATGAGACTGGA-TGAGATCACCN 2285 chr6qtel1M 661749 AATGAAATACT----ATAGAGAAAAAGAAAAGCCCTAGCA-TAAGAAGTG 661793 iv ivv v ---- i ii i i i v v - i vvv C L2#LINE/L2 2284 AGGGAGTGAGTGTAGATAGAGAAGAGAAGAGGTCCAAGGACTGAGCCCTG 2235 chr6qtel1M 661794 GGAAGCATACATCAACCATCCAAGGCTGGATTGTGAGATAAATTAAGACC 661843 -- iv -- vv ?vi ii i---- i iv- i v C L2#LINE/L2 2234 GG--GCACTC--CAACGTTNAGAGGTCGGG----GAGATGAGG-AGGAAC 2194 chr6qtel1M 661844 CAGCAAAGGAGACTAGGAAGTAGCAGTCAAATTAGCAGGAGAAGAACCA- 661892 ii v i i ivvvi i i i - C L2#LINE/L2 2193 CAGCAAAGGAGACTGAGAAGGAGCGGCCAGTGAGGTAGGAGGAAAACCAG 2144 chr6qtel1M 661893 -AGACTATAGC--CATGAAAATCTAG-AAAGTAAATATAATAAAATAAAT 661938 - v i i i-- v i ii v -i v i i vvi i vii - C L2#LINE/L2 2143 GAGAGTGTGGTGTCCTGGAAGCCAAGTGAAGAAAGTGTTTCAAGAAGGA- 2095 chr6qtel1M 661939 GGGA---ATCAACAATTCCAGAAGCAACAGATAAATACCAATGA-ATGAG 661984 --- vi vi i v vi v ? ii - v i i - C L2#LINE/L2 2094 GGGAGTGATCAACTGTGTCAAATGCTGCTGANAGGT-CAAGTAAGATGAG 2046 chr6qtel1M 661985 GGCTGAGAAGAGGCCATAAGAGTGAGTATTTAAGACACCATTAGTAAATT 662034 i vv i vi v v i vivvi vii i i vi C L2#LINE/L2 2045 GACTGAGAATTGACCATTGGATTTAGCAACGTGGAGGTCATTGGTGACCT 1996 chr6qtel1M 662035 TGTACACCAA-AGTTCTGGTTGAAT-ACAAACTCAGAAATCAGATTGTTG 662082 - vv i- ii v i -iiiiivv ii ii v -- C L2#LINE/L2 1995 TG-ACAAGAGCAGTTTCGGTGGAGTGGTGGGGACGAAAGCCTGATTG--G 1949 chr6qtel1M 662083 AGT--GTT---AAGAAAATAAGAAGAAATAAAGGGAAGGCACCCATTGTA 662127 -- ---i i ii i i vi vv i i v v v i C L2#LINE/L2 1948 AGTGGGTTCAAGAGAGAATGGGAGGAGAGGAATTGGAGACAGCGAGTATA 1899 chr6qtel1M 662128 TAAGATATTCTCAAGGAATTGAGACACAAAAAGAAGAGGAGATAT----- 662172 v vi ivi i i i vv viii ii i vi v ----- C L2#LINE/L2 1898 GACAACTCTTTCGAGGAGTTTTGCTGTAAAGGGGAGCAGAGAAATGGGGC 1849 chr6qtel1M 662173 --TTTCT----GAGGATTTGGGAGAAAAGGAAAATTT 662203 -- vv ---- i ?v ivv i i C L2#LINE/L2 1848 GGTAGCTGGAGGGGGANGTGGGGTCAAGGGAGAATTT 1812 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 54.25 CpG sites = 251, Kimura (unadjusted) = 57.23 Transitions / transversions = 1.32 (251/190) Gap_init rate = 0.05 (62 / 1174), avg. gap size = 1.55 (96 / 62) 12 21.81 2.70 0.00 chr6qtel1M 662265 662301 (337699) (TTTTTTA)n#Simple_repeat 1 38 (0) m_b315s252i16 13200 chr6qtel1M 662265 TTTTTCCTTTGTTATTATTTA-TTATAACTTTTTATTT 662301 iv v v - v v i (TTTTTTA)n#Si 1 TTTTTTATTTTTTATTTTTTATTTTTTATTTTTTATTT 38 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 20 23.89 5.63 1.35 chr6qtel1M 662411 662481 (337519) (AT)n#Simple_repeat 1 74 (0) m_b315s252i17 13201 chr6qtel1M 662411 ATACATGT-TAAATATGTTAAAATATATGT-TGAATAT-TATATATATAT 662457 i i - v i vv v i - iv - (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr6qtel1M 662458 ACACACATATATATA-AAATAGTAT 662481 i i i - v - (AT)n#Simple_ 51 ATATATATATATATATATATA-TAT 74 Matrix = Unknown Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.07 (5 / 70), avg. gap size = 1.00 (5 / 5) 283 29.16 0.00 3.80 chr6qtel1M 663560 663641 (336359) C MIRc#SINE/MIR (162) 106 28 m_b315s601i8 13202 chr6qtel1M 663560 TGACTAATCAAGCATCACACAACTAGTAAGTGTGAGAGACTGCATTTGAG 663609 vii v ivi i vv v v v i i i C MIRc#SINE/MIR 106 TGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAA 57 chr6qtel1M 663610 CTCAGATCTTCTTAACACTATGGTCAACAGTG 663641 i i i i v i -i -- C MIRc#SINE/MIR 56 CCCAGGTCTTCCTGACTCCA-AGTC--CAGTG 28 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 35.96 CpG sites = 14, Kimura (unadjusted) = 38.05 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.04 (3 / 81), avg. gap size = 1.00 (3 / 3) 12 23.27 0.00 0.00 chr6qtel1M 666426 666460 (333540) (TATATG)n#Simple_repeat 1 35 (0) m_b316s252i0 13203 chr6qtel1M 666426 TAAATGTATATGAATGTATTTATGTCTATGAATAT 666460 v v i i v v v (TATATG)n#Sim 1 TATATGTATATGTATATGTATATGTATATGTATAT 35 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 50 2.17 0.00 0.00 chr6qtel1M 666472 666518 (333482) (TG)n#Simple_repeat 1 47 (0) c_b316s251i0 13204 chr6qtel1M 666472 TGTGTGTGTGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 666518 i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 47 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 20 32.61 2.06 2.06 chr6qtel1M 667073 667169 (332831) (ATAC)n#Simple_repeat 1 97 (0) m_b316s252i1 13205 chr6qtel1M 667073 ATACACACATACATATATGCACGCATGTCTATGTGCCTACATATGCATAC 667122 i i i ii iiv ii i v -- (ATAC)n#Simpl 1 ATACATACATACATACATACATACATACATACATACATACATA--CATAC 48 chr6qtel1M 667123 AT-C-TATGTATATAAGAAGATATAGACATTTATACATACAAACATACA 667169 - - ii i viv v i v vi v (ATAC)n#Simpl 49 ATACATACATACATACATACATACATACATACATACATACATACATACA 97 Matrix = Unknown Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.04 (4 / 96), avg. gap size = 1.00 (4 / 4) 13 31.89 3.17 0.00 chr6qtel1M 667110 667172 (332828) (TACATA)n#Simple_repeat 1 65 (0) m_b316s252i2 13205 chr6qtel1M 667110 TACATATGCATACATCTATGTATATAAGAAGATATAGACATTTATACATA 667159 i i iv ii viv v i v v i i (TACATA)n#Sim 1 TACATATACATATACATATACATATACATATACATATACATATACATATA 50 chr6qtel1M 667160 CA-A-ACATACACAT 667172 - - i (TACATA)n#Sim 51 CATATACATATACAT 65 Matrix = Unknown Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.03 (2 / 62), avg. gap size = 1.00 (2 / 2) 46 0.00 0.00 0.00 chr6qtel1M 667377 667415 (332585) (AT)n#Simple_repeat 1 39 (0) c_b316s251i1 13206 chr6qtel1M 667377 ATATATATATATATATATATATATATATATATATATATA 667415 (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATA 39 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 24 23.15 2.60 3.95 chr6qtel1M 667505 667581 (332419) (TA)n#Simple_repeat 1 76 (0) m_b316s252i3 13207 chr6qtel1M 667505 TATATCATATATGTACATGAT-TATAGATATCTCTATATGTGTATATATG 667553 - i i - - v v v i i i (TA)n#Simple_ 1 TATAT-ATATATATATAT-ATATATATATATATATATATATATATATATA 48 chr6qtel1M 667554 TAGCATGTGTATATATA-AAACATATTTA 667581 -i i i - v i v (TA)n#Simple_ 49 TA-TATATATATATATATATATATATATA 76 Matrix = Unknown Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.07 (5 / 76), avg. gap size = 1.00 (5 / 5) 12 22.41 1.92 6.00 chr6qtel1M 669372 669423 (330577) (TTTTG)n#Simple_repeat 1 50 (0) m_b316s252i4 13208 chr6qtel1M 669372 TTTTGTTTTGTTTTCTTTCTCATAGTTTTCCTCTTCTGTTCTGATTT-TT 669420 v iviv v -v - - i v - (TTTTG)n#Simp 1 TTTTGTTTTGTTTTGTTTTGTTTTGTTTT-GT-TT-TGTTTTGTTTTGTT 47 chr6qtel1M 669421 TTG 669423 (TTTTG)n#Simp 48 TTG 50 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.08 (4 / 51), avg. gap size = 1.00 (4 / 4) 17 24.98 0.00 0.00 chr6qtel1M 669665 669708 (330292) (ATAT)n#Simple_repeat 1 44 (0) m_b316s252i5 13209 chr6qtel1M 669665 ATATACATATATATGTATGTATGTATGTATAAATACGTATAAAT 669708 i i i i i v ii v (ATAT)n#Simpl 1 ATATATATATATATATATATATATATATATATATATATATATAT 44 Matrix = Unknown Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 17 24.65 0.00 3.64 chr6qtel1M 669672 669728 (330272) (TATG)n#Simple_repeat 1 55 (0) m_b316s252i6 13209 chr6qtel1M 669672 TATATATGTATGTATGTATGTATAAATACGTATAAATGCATGTTGGTATA 669721 i --i i iv i vv i (TATG)n#Simpl 1 TATGTATGTATGTATGTATGTAT--GTATGTATGTATGTATGTATGTATG 48 chr6qtel1M 669722 GGTGTAT 669728 vi (TATG)n#Simpl 49 TATGTAT 55 Matrix = Unknown Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.04 (2 / 56), avg. gap size = 1.00 (2 / 2) 51 0.00 0.00 0.00 chr6qtel1M 669729 669772 (330228) (TA)n#Simple_repeat 1 44 (0) c_b316s251i2 13210 chr6qtel1M 669729 TATATATATATATATATATATATATATATATATATATATATATA 669772 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATA 44 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 500 29.68 4.51 3.84 chr6qtel1M 670406 670871 (329129) L1M1_orf2#LINE/L1 27 495 (2799) m_b316s551i0 13211 chr6qtel1M 670406 AATGACAACTGTGAATGTGAATGGGATGAAATTTCTCAT-AAAACTGAAG 670454 i i vv i iv i v i iv - -- vi L1M1_orf2#LIN 27 AATAATAACATTGAATGTAAATGGACTAAACTCTCCAATCAAAA--GACA 74 chr6qtel1M 670455 CAAAA-GGCAGAGTAGATTAAGAAA-GAGACTGGTAGAACATGTT---TA 670499 i i i- v i i v i -i ivi?v v - --- L1M1_orf2#LIN 75 TAGAGTGGCTGAATGGATGAAAAAACAAGACCCANTGATC-TGTTGCCTA 123 chr6qtel1M 670500 CAAGAAACACATTTGAC--AGAGAGATAAATACAGACTAAAGATAAAAAT 670547 i v -- v i i v i i i i iiv L1M1_orf2#LIN 124 CAAGAAACACACTTCACCTATAAAGACACACATAGACTGAAAATAAAGGG 173 chr6qtel1M 670548 CTGAAATAGAATTTATTATTGTACTTCAATTGAAATTTTAAAA-AGCAGC 670596 v i v ii ----- vi ivi v iivv - v L1M1_orf2#LIN 174 ATGGAAAAAGA-----TATTCCATGCCAATGGAAACCAAAAAAGAGCAGG 218 chr6qtel1M 670597 ACTAGGAATTCTGATCTCAGATAAAGCAAA----AATACAACTAGATCTA 670642 v vv v v v i ii i ---- v -- i - - L1M1_orf2#LIN 219 AGTAGCTATACTTATATCAGACAAAATAGATTTCAAGACAA--AAA-CT- 264 chr6qtel1M 670643 ATTAAAAGAGATAAGGAAGGAAAGTACATCTTTGTAAA-GGATAAATTAA 670691 v i i i vv v i vv vi - i v v L1M1_orf2#LIN 265 ATAAGAAGAGACAAAGAAGGTCACTATATAATGATAAAGGGGTCAATTCA 314 chr6qtel1M 670692 ACAATGAAG-TATTAATGATATTAAATGTATATGTACCAAGAACTGAAGC 670740 i - i - - ii v? i i v iv i L1M1_orf2#LIN 315 GCAA-GAGGATA-TAACAATTNTAAATATATATGCACCCAACACTGGAGC 362 chr6qtel1M 670741 ATTCAGATATCTAGAGAAGATATTAAGGCAGTTACAGGGAGAAATAGATA 670790 ii v i v i vviv i v i i iv L1M1_orf2#LIN 363 ACCCAGATATATAAAGCAAATATTATTAGAGCTAAAGAGAGAGATAGACC 412 chr6qtel1M 670791 GCAAAATTATATTA-CTGTGGGACCT-GACACTTCCCCTCTCAGAATCAT 670838 v v iv v - - i i -i -i v i v iiv L1M1_orf2#LIN 413 CCAATACAATAATAGCTG-GAGACTTCAACAC-CCCACTTTCAGCATTGG 460 chr6qtel1M 670839 ACAAATCT----AACCACAAATAAACAATAAGAAATA 670871 i ----i viv v -- i L1M1_orf2#LIN 461 ACAGATCTTCCAGACAGAAAATCAACA--AAGAAACA 495 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 38.88 CpG sites = 74, Kimura (unadjusted) = 38.88 Transitions / transversions = 1.25 (74/59) Gap_init rate = 0.06 (30 / 465), avg. gap size = 1.30 (39 / 30) 404 31.92 7.75 4.47 chr6qtel1M 670462 671481 (328519) L1MC_orf2#LINE/L1 83 1134 (2160) m_b316s551i1 13211 chr6qtel1M 670462 CAGAGTAGATTAAGAAA-GAGACTGGTAGAACATGTT---TACAAGAAAC 670507 i i i -i ivi- vv i --- L1MC_orf2#LIN 83 CAGAGTGGATCAAAAAACAAGACCCA-ACTATATGTTGTCTACAAGAAAC 131 chr6qtel1M 670508 ACATTT--GACAGAGAGATAAATACAGACTAAAGATAAAAATCTGAAATA 670555 v i --i i v i i v i i ii ?ivv i iv L1MC_orf2#LIN 132 CCACTTTAAATATAAAGACACATATAGATTAAAAGTAAANGGATGGAGAA 181 chr6qtel1M 670556 GAATTTATTATTGTA-CTTCAATTGAAATTTTAAAAAGCAGCACTAGGAA 670604 ii v ii vv - vii ii -----i ? v v vv L1MC_orf2#LIN 182 AGATATACCATGCTAACACTAATCAAAA-----GAAAGCNGGAGTAGCTA 226 chr6qtel1M 670605 TTCTGATCTCAGATAAAGCAAAAAT-ACAACTAGATCTAATTAAAAGAGA 670653 vi i i i i i vv - v i v ivv- i vv i L1MC_orf2#LIN 227 TATTAATTTCAGACAGAGCAGACTTCAGAGCAAGGAA-AGTTATCAGGGA 275 chr6qtel1M 670654 TAAGGAAGGAAAGTACATCTTTGTAAAGGA-TAAATTAAACAATGAAGTA 670702 i i iv v vv vi i- v vvv - vv L1MC_orf2#LIN 276 TAAAGAGGGGCATTACATAATGATAAAGGGGTCAATTCTCCAA-GAAGAC 324 chr6qtel1M 670703 TTAATGATATTAAATGTATATGTACC-AAGAACTGAAGCATTCAGATATC 670751 v ii vi v i i ii - v v - i iv i iv L1MC_orf2#LIN 325 ATAACAATCCTTAACGTGTATGCGCCTAACAACAGA-GCGTCAAAATACG 373 chr6qtel1M 670752 TAGAGAAGATATTAAGGCAGTTACAGGGAGAAATAGATAGCAAAATTA-T 670800 iii v i v i i viv ii i i --- i vii - L1MC_orf2#LIN 374 TGAGGCAAAAACTGATAGAACTGCAAGGAGAAATAGA---CGAATCCACT 420 chr6qtel1M 670801 ATTACTGT--GGGACCT-GACACTTCCCCTCTCAGAATCATACAAATCTA 670847 iv -- i i -i i- i v ? vi?v i i L1MC_orf2#LIN 421 ATTATAGTTGGAGACTTCAACACC-CCTCTATCAGNAATNGACAGATCCA 469 chr6qtel1M 670848 AC-CACAAATAAACAATAAGAA-ATAAACTAGGGATATTAATAGGATCCT 670895 i -vi i v v i i - i-i --- vv ? i v i v L1MC_orf2#LIN 470 GCAGGCAGAAAATCAGTAAGGACATAG-TT---GAACTNAACAGCACCAT 515 chr6qtel1M 670896 CAA-CACCTAGATATGATAGAC-----TAGAC-----------ATAAAAG 670928 - v i ? i v ----- ?----------- i v L1MC_orf2#LIN 516 CAATCAACTGGATNTAATTGACATCTATAGANTACTTCATCCAACAACAG 565 chr6qtel1M 670929 --GAATATATGTTTTTT----GCT-ACATGG--CACTTACAAAAAATGGA 670969 -- i ii i i---- - -- i i v i - i L1MC_orf2#LIN 566 CAGAATACACATTCTTCTCAAGCTCACATGGAACATTCACCAAGA-TAGA 614 chr6qtel1M 670970 CCATGTATTAGATTAATTATGCCACATGTATTAGGGCTTA-TAAATCTCA 671018 ii vi i iii -- viv i--------- -i i - L1MC_orf2#LIN 615 CCACATTCTGGGCCA--TAAAACACAC---------CTTAACAAATTT-A 652 chr6qtel1M 671019 AAAGGA-AGAAATGG-AAAATACTTGCTATTCAGGCTACAAAATAATAAA 671066 i - vi- v ?ii? -i i i viv v L1MC_orf2#LIN 653 AAAGAATAGAAATCATACAANGTNTGCT-CTCAGACCACAATGGAATTAA 701 chr6qtel1M 671067 AACTATATTCAATGAACGACAGAAAAA--GATAGAAGA-----AAA-AAT 671108 - v --- v ii i -- v i i ----- - v L1MC_orf2#LIN 702 A-CTAGA---AATCAATAACAGAAAGATAGCTGGAAAATCCCAAAATACT 747 chr6qtel1M 671109 TGGAAATTAATC----TAATTCTAAATAATG-ATGGGTCACAAAACAAAT 671153 i v ----i v ii- v i v L1MC_orf2#LIN 748 TGGAGATTAAACAACACACTTCTAAATAACACATGGGTCAAAGAAGAAAT 797 chr6qtel1M 671154 CACAGAAACAATCCTCAA----TTTCATCTAAGACAATGACAATAATGAG 671199 v ii iv iivv ---- v v ---- v i vi v L1MC_orf2#LIN 798 CTCAAGAGAAATTTAAAAATATTTTGAACTAA----ATGAAAATGAAAAT 843 chr6qtel1M 671200 ATGACATACTAAAAATTATGGGATGCAGCTAATTCAGTTTTTAGGGGAAA 671249 ii v ii v i v vv vi i i L1MC_orf2#LIN 844 ACAACTTATCAAAATTTGTGGGATGCAGCGAAAGCAGTGCTTAGAGGGAA 893 chr6qtel1M 671250 TTTTATATCAATAAATAGCTACCTAAATAAAACAG-AGAAAGA--GAAGA 671296 v v v i ivv iv --- i v - --v i L1MC_orf2#LIN 894 ATTTATAGCATTGAATGCATATAT---TAGAAAAGAAGAAAGATCTAAAA 940 chr6qtel1M 671297 TCAATGAATTGGGC---------AGGGAACTA-AAAACTTAGAACAACTT 671336 i vi ii --------- i - vvv i v L1MC_orf2#LIN 941 TCAATAATCTAAGCTTCCACCTTAGGAAACTAGAAAAAGAAGAGCAAATT 990 chr6qtel1M 671337 AAAAACCACCAATTAAACACCAAGTTAGAAATTATGAAACTCCAAGGCTA 671386 - v -- v i vv iivv v i v ivi vvv L1MC_orf2#LIN 991 -AAATCCA--AAGTAAGCAGAAGAAAAGAAATAATAAAAATTAGAGCAGA 1037 chr6qtel1M 671387 GATTAATAAAACTGAAGCTAAGAAGACTTTTG----AACTAATAAAACTA 671432 i i i i ivi i iv vv v ---- ii ii i L1MC_orf2#LIN 1038 AATCAATGAAATTGAAAACAGGAAATCAATAGAGAAAATCAACGAAACCA 1087 chr6qtel1M 671433 AGAGATGGTTGTATTAAAAACAATCAACAAAATGAACAAACTTTTGGTC 671481 i v v - i -i i vi i i i i i i L1MC_orf2#LIN 1088 AAAGCTGGTTCT-TTGAAAA-GATCAATAAAATTGATAAGCCTCTAGCC 1134 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 42.46 CpG sites = 183, Kimura (unadjusted) = 43.63 Transitions / transversions = 1.43 (183/128) Gap_init rate = 0.08 (80 / 1019), avg. gap size = 1.57 (126 / 80) 340 35.32 4.67 3.21 chr6qtel1M 671501 672635 (327365) L1M2_orf2#LINE/L1 2141 3291 (0) m_b316s551i2 13211 chr6qtel1M 671501 CTAAAAACCTAATGGAAACAATTCACAGCTTTATCAGAGTTATAAGATAT 671550 i v ?v i vii vv iiv i vi i ii i i L1M2_orf2#LIN 2141 CCAAAAAACTNTTAGAACTGATAAACGAATTCAGTAAAGTTGCAGGATAC 2190 chr6qtel1M 671551 AAAACAAACTCACAGAAATCATCAACATTTCTATATTTTACTGACAAA-- 671598 iv vi i vi i ivii vii i -- L1M2_orf2#LIN 2191 AAAATCAACATACAAAAATCAGTAGCATTTCTATACGCCAACAACGAACT 2240 chr6qtel1M 671599 ACCTTGCACTTAGAGAT--AGAAGAGAAATTCCATTTGAAAT---TACAG 671643 i viv v-- i -- - v i iv --- i L1M2_orf2#LIN 2241 ATCTGAAAA--AGAAATCAAGAA-AGCAATCCCATTTACAATAGCTACAA 2287 chr6qtel1M 671644 GTGACAAAATAAGATG--TGGGTGTCTATCTG-CCAAGAGAAACCTAAGA 671690 --- v i i-- i vi vv i i- - iiivv L1M2_orf2#LIN 2288 ---AAAAAATAAAATACCTAGGAATAAATTTAACCAAG-GAGGTGAAAGA 2333 chr6qtel1M 671691 ACTATGTGACCATAATTAGAAAACTTT--TCATACAAAT-AAAGTCAGAT 671737 v v iii ?v v i v vi -- v v v -i -- i- L1M2_orf2#LIN 2334 TCTCTACAANGAAAACTATAAAACACTGATGAAAGAAATTGAAG--AGG- 2380 chr6qtel1M 671738 CTACACAA-----TGGGAACATTATAAATTGCTCATTGGTTGACTGAGCT 671782 -- ----- i v - vvvv v i ivv ii L1M2_orf2#LIN 2381 --ACACAAANAAATGGAAAGAT-ATCCCATGCTCATGGATTGGAAGAATT 2427 chr6qtel1M 671783 AATATGATACAAACAACCAATCTACCTAAATCGATTTACTCGTTCAGTGT 671832 vi vv ii? vv i v i vvi i i L1M2_orf2#LIN 2428 AATATTGTTAAAATGNCCATACTACCCAAAGCGATCTACAGATTCAATGC 2477 chr6qtel1M 671833 ACTATGCATCAAAATGCCAA-AACCTTATTTTC-TAGATAGAAAAAATAA 671880 v vivi i -i v v iv -v i ? L1M2_orf2#LIN 2478 AATCCCTATCAAAATACCAATGACATTCTTCACAGAAATAGAAAAAANAA 2527 chr6qtel1M 671881 TGGCAGAATTCATCTGCAAGAACAAAAACACAAGCATA-TTAAGGGAATT 671929 vvi i i v v vv ivv vv v -ii i v i L1M2_orf2#LIN 2528 TCCTAAAATTCGTATGGAACCACAAAAGACCCCGAATAGCCAAAGCAATC 2577 chr6qtel1M 671930 AATGAAAAAATATATGAAGAATGGTGGCTTCGCAGTATCAAACCTAAAAC 671979 -v iv v v vv iiv v v i v i vi i v v L1M2_orf2#LIN 2578 -CTGAGCAAAAAGAACAAAGCTGGAGGCATCACACTACCTGACTTCAAAA 2626 chr6qtel1M 671980 CACATTATACAGCAACACC-ATCAAAACCTTTTGGTATTGGCTAAGAAAT 672028 i i i i v v i vi- i vviv i vv i i L1M2_orf2#LIN 2627 TATACTACAAAGCTATAGTAACCAAAACAGCATGGTACTGGCATAAAAAC 2676 chr6qtel1M 672029 ATAGTGCTGGATCATTGGGATAGATTAAATGCACACAATACATTGATAAA 672078 v vvvv i i v i i v i - v v i- v vi vv L1M2_orf2#LIN 2677 AGACACATAGACCAATGGAACAGAATAGA-GAACCCAG-AAATAAATCCA 2724 chr6qtel1M 672079 AGC--CTATAGCAGTCTAGTGTTTGATAAACCCTCAAATTCCAGCTTTTG 672126 v --i i viv ii v i i vv v v vvv vviv? L1M2_orf2#LIN 2725 CGCATTTACAGCCAACTGATTTTCGACAAAGGCGCCAAGAACATACANTG 2774 chr6qtel1M 672127 TAATAAGAACTCATTCTTTGACAAAAATTACTGGGAAAACTGGAAAATAA 672176 viiv i vvvi ii i viv i v viv L1M2_orf2#LIN 2775 GGGAAAGGACAGTCTCTTCAATAAATGGTGCTGGGAAAACTGGATATCCA 2824 chr6qtel1M 672177 TATGTCAG--GAACTCAGCATAGACCTACACTGCACACCCGACACCAAAA 672224 - -- ivv i - ivi iiv v vv i v L1M2_orf2#LIN 2825 TATG-CAGAAGAATGAAAC-TAGACCCCTATCTCTCACCATATACAAAAA 2872 chr6qtel1M 672225 TAAGGTCAAAAAGGGTACATAGTTTGAGTACAAAGGATGATACCTTAAAT 672274 v iv v i vv viii i i ii iivvi v iv v L1M2_orf2#LIN 2873 TCAACTCAAAATGGATTAAAGACTTAAATGTAAGACCCGAAACTATAAAA 2922 chr6qtel1M 672275 GAATTAG--GAGAAC-CAGGGATAATTTGTCTATGAAATC--TTTGGAGA 672319 vv i -- i -i iv iviv - v v i-- i --- L1M2_orf2#LIN 2923 CTACTAGAAGAAAACATAGGGGAAACGCTTC-AGGACATTGGTCTGG--- 2968 chr6qtel1M 672320 AGGAAGAAATTTATGAACAAA---TAAGAAATAGAGAACATTATAAAAGG 672366 - v ii v v i?i i--- v i ii v -i -- i v L1M2_orf2#LIN 2969 -GCAAAGATTTTTTGGNTAAGACCTCAAAAGCACAG-GCA--ACAAAAGC 3014 chr6qtel1M 672367 CAAAATGGACAATTCTGATTACATTAAATTATAAAAAATGCAAC-CAAAA 672415 v i v vv i i - iv v vi - iv L1M2_orf2#LIN 3015 AAAAATAGACAAATGGGATTACATCAAACTA-AAAAGCTTCTGCACAGCA 3063 chr6qtel1M 672416 AATAAAATAACAGTAACAAGATTAAAAGGTGA-----AAGCTGGG-GAAA 672459 vi i i--i iii v i iii ----- iiv - L1M2_orf2#LIN 3064 AAGGAAACAAT--CAACAGAGTGAAGAGACAACCTACAGAATGGGAGAAA 3111 chr6qtel1M 672460 ATACTTAACAACTAGTGTTTCTGA-AACGGTCTCATTTCTAAAATATATA 672508 i ivv - ?iv - v vi v v i i L1M2_orf2#LIN 3112 ATATTTGCAAACTA-TNCATCTGACAAGGGATTAATATCCAGAATATATA 3160 chr6qtel1M 672509 AAAAACAATGTCA---AATTTATC----AAAATATAAGTCATTCTGTAAC 672551 ii ---- --- i i v ---- v i i v i ---i i L1M2_orf2#LIN 3161 AGGAAC----TCAAACAACTCAACAGCAAAAAAACAAATAATCC---GAT 3203 chr6qtel1M 672552 TGATAAATGGTCAGAGGATCTGA----ACAATTTTCAAATGATAAAATTA 672597 ? v v i i ---- v i v vi v vv L1M2_orf2#LIN 3204 TNAAAAATGGGCAAAGGACCTGAATAGACATTTCTCAAAAGAAGACATAC 3253 chr6qtel1M 672598 AAGCCACCTATACTTATATGAAAAAATGCTCTAAATCA 672635 iivi v i vv v v L1M2_orf2#LIN 3254 AAATGGCCAACAGGTATATGAAAAAATGCTCAACATCA 3291 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 47.82 CpG sites = 196, Kimura (unadjusted) = 49.23 Transitions / transversions = 1.02 (196/192) Gap_init rate = 0.05 (62 / 1134), avg. gap size = 1.45 (90 / 62) 557 32.91 3.25 6.35 chr6qtel1M 672496 673079 (326921) L1MB7_3end#LINE/L1 7 573 (358) m_b316s551i4 13211 chr6qtel1M 672496 TCTAAAATATATAAAAAACAATGTCA-AATTTATCAA----AATATAAGT 672540 i i i -- v i - i i v ---- v i i L1MB7_3end#LI 7 TCCAGAATATATAAAGAAC--TCTTACAACTCAACAATAAAAAGACAAAT 54 chr6qtel1M 672541 CATTCTGTAACTGATAAATGGTCAGAGGATCTGAA----CAATTTTCAAA 672586 v ii --- i ? v v i i ---- v i v L1MB7_3end#LI 55 AACCC---AATTNAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAA 101 chr6qtel1M 672587 TGATAAAATTAAAGCCACCTATACTTATATGAAAAAATGCTCTAAATCAG 672636 v vi v vv iivi v vvi i i v v v L1MB7_3end#LI 102 AGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCAT 151 chr6qtel1M 672637 TATTATTTCATTGCATTTCTCTAAAATGCAAA-GGAAACAACTCTAAAGT 672685 v ---- ivi-------i -vi v vv i ii L1MB7_3end#LI 152 TAGT----CATTAGG-------GAAATGCAAATCAAAACCACAATGAGAT 190 chr6qtel1M 672686 ACCACCTCACACTTCCCAAAAGGACTTTAAGTAAGATAATAGAAAAAGAT 672735 i iiv i ii v i --------- ?- i L1MB7_3end#LI 191 ACCACTTCACACCCACTAGGATGGCT---------ATAATN-AAAAAGAC 230 chr6qtel1M 672736 AAA-AAT--CAAG-GTGGGAGAAAGTTATGGGAAAACTGGGACACTAATG 672781 i - -- - v v i- v i ii i i v v i L1MB7_3end#LI 231 AGACAATAACAAGTGTTGGCGAG-GATGTGGAGAAATTGGAACCCTCATA 279 chr6qtel1M 672782 CATTGTTGGGGGAGTTATGAAGTGATTCAACCATTCTGGAAAATAATTTG 672831 i v iiv i i i i v i ii i i i L1MB7_3end#LI 280 CATTGCTGGTGGGAATGTAAAATGGTGCAGCCGCTTTGGAAAACAGTTTG 329 chr6qtel1M 672832 AAACTATGCCCAAAAGGCTATAACACTGCATATTCCCTTTTCACCCAGCA 672881 iv v - v i i i - iv vi -- v v v v L1MB7_3end#LI 330 GCAGT-TCCTCAAAAAGTTA-AACATAGAGT--TACCATATGACCCAGCA 375 chr6qtel1M 672882 GTTCCATTACTGGTTCTGTGTTCCAAGAAAATCATAAA-GTATG---AAA 672927 i i v i v v i i-i i ?iiv -i --- v L1MB7_3end#LI 376 ATTCCACTCCTAGGTATATA-CCCAAGAGAANTGAAAACATATGTCCACA 424 chr6qtel1M 672928 AGGAAACATATGTACAAAAATGTTTGTAGCAGCTCTCTTTTTTTAGTAG- 672976 vii - - vi ii vi v-- iv i - L1MB7_3end#LI 425 CAAAAAC-T-TGTACACGAATGTTCATAGCAGCATTA--TTCATAATAGC 470 chr6qtel1M 672977 TAAAGAATCAAAATGAGTAGAAAACCCATGCATTAGGCAATGGCTGGACA 673026 i i i vi ii vivi vii vv i iivv v ii L1MB7_3end#LI 471 CAAAAAGTGGAAACAACCCAAATGTCCATCAACTGATGAATGGATAAACA 520 chr6qtel1M 673027 AGTTGTCCTATATATAAGTAACAGAATATAATTATTCTATACAAAGTGAT 673076 iv vv vi vii ii v vvv i v vi L1MB7_3end#LI 521 AAATGTGGTATATCCATACAATGGAATATTATTCGGCCATAAAAAGGAAT 570 chr6qtel1M 673077 AAA 673079 i L1MB7_3end#LI 571 GAA 573 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 44.37 CpG sites = 105, Kimura (unadjusted) = 45.05 Transitions / transversions = 1.40 (105/75) Gap_init rate = 0.08 (46 / 583), avg. gap size = 1.20 (55 / 46) 571 31.49 2.80 6.46 chr6qtel1M 672496 672960 (327040) L1MB8_3end#LINE/L1 7 455 (470) m_b316s551i3 13211 chr6qtel1M 672496 TCTAAAATATATAAAAAACAATGTCAAAT---TTATCAAAATATAAGTCA 672542 i i i vv vv v --- v v v i i v L1MB8_3end#LI 7 TCCAGAATATATAAAGAACTCTTACAACTCAATAATAAAAAGACAAATAA 56 chr6qtel1M 672543 TTCTGTAACTGATAAATGGTCAGAGGATCTGAA----CAATTTTCAAATG 672588 ii --- i ? v v i ---- v i v v L1MB8_3end#LI 57 CCC---AATTNAAAAATGGGCAAAGGATCTGAATAGACATTTCTCCAAAG 103 chr6qtel1M 672589 ATAAAATTAAAGCCACCTATACTTATATGAAAAAATGCTCTAAATCAGTA 672638 vi v vv iivi v vvi i i v v v L1MB8_3end#LI 104 AAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCATTA 153 chr6qtel1M 672639 TTATTTCATTGCATTTCTCTAAAATGCAAA-GGAAACAACTCTAAAGTAC 672687 v ---- iivi-------i -vi v vv i ii L1MB8_3end#LI 154 GT----CATCAGG-------GAAATGCAAATCAAAACCACAATGAGATAC 192 chr6qtel1M 672688 CACCTCACACTTCCCAAAAGGACTTTAAGTAAGATAATAGAAAAAGATAA 672737 i iiv i ii v i v vi i ------ i v L1MB8_3end#LI 193 CACTTCACACCCACTAGGATGGCTATAATCAAAA------AGACAGATAA 236 chr6qtel1M 672738 AAATCAAG-GTGGGAGAAAGTTATGGGAAAACTGGGACACTAATGCATTG 672786 v - - v v i- v i ii i i v v i i L1MB8_3end#LI 237 TAA-CAAGTGTTGGCGAG-GATGTGGAGAAATTGGAACCCTCATACACTG 284 chr6qtel1M 672787 TTGGGGGAGTTATGAAGTGATTCAACCATTCTGGAAAATAATTTGAAACT 672836 i v iiv i i i i v i ii i i i i iv v L1MB8_3end#LI 285 CTGGTGGGAATGTAAAATGGTGCAGCCGCTTTGGAAAACAGTCTGGCAGT 334 chr6qtel1M 672837 ATGCCCAAAAGGCTATAACACTGCATATTCCCTTTTCACCCAGCAGTTCC 672886 - v i i - iv vi -- v v v v i L1MB8_3end#LI 335 -TCCTCAAAAGGTTA-AACATAGAGT--TACCATATGACCCAGCAATTCC 380 chr6qtel1M 672887 ATTACTGGTTCTGTGTTCCAAGA-AAATCATAAAGTATG---AAAAGGAA 672932 i v i v v i i-i - v v vi --- v vii L1MB8_3end#LI 381 ACTCCTAGGTATATA-CCCAAGAGAAATGAAAACATATGTCCACACAAAA 429 chr6qtel1M 672933 ACATATGTACAAAAATGTTTGTAGCAGC 672960 - - vi ii L1MB8_3end#LI 430 AC-T-TGTACACGAATGTTCATAGCAGC 455 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 40.94 CpG sites = 74, Kimura (unadjusted) = 41.74 Transitions / transversions = 1.17 (74/63) Gap_init rate = 0.08 (35 / 464), avg. gap size = 1.20 (42 / 35) 367 36.74 2.59 3.39 chr6qtel1M 672754 673139 (326861) L1MC5_3end#LINE/L1 252 634 (2060) m_b316s551i5 13211 chr6qtel1M 672754 AAGTTATGGGAAAACTGGGACACTAATGCATTGTTGGGGGAGTTATGAAG 672803 i i i i v v v v i i v iiv iii i L1MC5_3end#LI 252 AGGCTGTGGGGAAACAGGCACTCTCATACATTGCTGGTGGGAATGCAAAA 301 chr6qtel1M 672804 TGATTCAACCATTCTGGAAAATAATTTGAAACTATGCC--CAAAAGGCTA 672851 i v vi v iiiv iv v - i-- vvvi L1MC5_3end#LI 302 TGGTACAACCCCTATGGAGGGGAATTTGGCAATAT-CTAGCAAAATTACA 350 chr6qtel1M 672852 TAACACTGCATATTCCCTTTTCACCCAGCAGTTCCATTACTGGTTCTGTG 672901 ---- - v i v i i i v i vvv v i L1MC5_3end#LI 351 TA----TGCAT-TTACCCTTTGACCCAGCAATCCCACTTCTAGGAATCTA 395 chr6qtel1M 672902 TTCCAAGAAAAT-----CATAAAGTATGAAAAGGAAACATATGTACAAAA 672946 i ii v i----- - i i --- i i ii L1MC5_3end#LI 396 TCCCAAAGATACACTGGCA-AAAATACGAAAAG---ACGTATGCACAAGG 441 chr6qtel1M 672947 ATGTTTGTAGCAGCTCTCTTTTTTTAGTAGT-AAAGAATCAAAATGAGTA 672995 v i ii v v v-- v i i- v vi ii viv L1MC5_3end#LI 442 CTATTCATTGCAGCACTA--TTTGTAATAGCAAAAGACTGGAAACAACCC 489 chr6qtel1M 672996 GAAAACCCATGCATTAGGCAA-TGGCTGGACAAGTTGTCCTATATATAAG 673044 i vii - v vi - i i i ii i vv i vi vi L1MC5_3end#LI 490 AAATGTCCAT-CAATAGGGGACTGGTTGAATAAACTATGGTACATCCACA 538 chr6qtel1M 673045 TAACAGAATATAATTATTCTATACAAAGTGATAAACAAGCTTATTTTAGA 673094 i ii i iv vvvv i v vi i iv vv ivi v v L1MC5_3end#LI 539 CAATGGAGTACTATGCAGCTGTAAAAAGGAATGAGGAATATCTCTATATA 588 chr6qtel1M 673095 AAGCC-TGGAATGATTTGCACGAAGCAATATTGAATGAAACAATCA 673139 vv i- i i v v vii v i i i v v L1MC5_3end#LI 589 CTGCTATGGAGTGATCTCCAGGATATATTGTTAAGTGAAAAAAGCA 634 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 51.22 CpG sites = 77, Kimura (unadjusted) = 52.34 Transitions / transversions = 1.28 (77/60) Gap_init rate = 0.05 (18 / 385), avg. gap size = 1.28 (23 / 18) 28 21.61 3.66 1.19 chr6qtel1M 673450 673531 (326469) (ATAA)n#Simple_repeat 1 84 (0) m_b316s252i7 13212 chr6qtel1M 673450 ATAGATATATACATATATAAATGTATATTATATAAACATAAATAAATATA 673499 i v v v iv -v v v v v (ATAA)n#Simpl 1 ATAAATAAATAAATAAATAAATAAATA-AATAAATAAATAAATAAATAAA 49 chr6qtel1M 673500 T-TTTAAA-AAA-AAATAAATAAACAAATAAAAAA 673531 -vv - - i v (ATAA)n#Simpl 50 TAAATAAATAAATAAATAAATAAATAAATAAATAA 84 Matrix = Unknown Transitions / transversions = 0.25 (3/12) Gap_init rate = 0.05 (4 / 81), avg. gap size = 1.00 (4 / 4) 183 23.26 2.33 0.00 chr6qtel1M 673589 673631 (326369) MIRb#SINE/MIR 213 256 (12) m_b316s601i0 13213 chr6qtel1M 673589 GCTGAACCCAATGTGTGGCATATGGTAAGGGCTTAATAAA-GGT 673631 v i v i iv i i v i - MIRb#SINE/MIR 213 GCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAAATGGT 256 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 28.41 CpG sites = 6, Kimura (unadjusted) = 28.41 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.02 (1 / 42), avg. gap size = 1.00 (1 / 1) 203 24.45 0.00 2.22 chr6qtel1M 673595 673640 (326360) L2c_3end#LINE/L2 425 469 (9) m_b316s601i1 13214 chr6qtel1M 673595 CCCAATGTGTGGCATATGGTAAGGGCTTAATAAAGGTTTAATTGAA 673640 ii iv i i i v i v -i L2c_3end#LINE 425 CCCAGCGCCTGGCACATAGTAGGCGCTCAATAAATGTTT-GTTGAA 469 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 27.66 CpG sites = 8, Kimura (unadjusted) = 31.01 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1) 217 24.98 7.25 1.37 chr6qtel1M 674725 674793 (325207) C L2c_3end#LINE/L2 (38) 440 368 m_b316s601i2 13215 chr6qtel1M 674725 TGTGCCGAGTG-TGAGGACGTAAAGA-AAGCAAAAGCACTG--CCTGCT- 674769 ii i - i iii -i ii i - v -- i- C L2c_3end#LINE 440 TGTGCCAGGCGCTGGGGATACAAAGATGAATAAGA-CACGGTCCCTGCCC 392 chr6qtel1M 674770 TCAAGAAGTTCAAAATCTAGTGGA 674793 i i v i C L2c_3end#LINE 391 TCAAGGAGCTCACAGTCTAGTGGA 368 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 30.88 CpG sites = 15, Kimura (unadjusted) = 33.32 Transitions / transversions = 7.50 (15/2) Gap_init rate = 0.07 (5 / 68), avg. gap size = 1.20 (6 / 5) 899 39.68 4.19 3.02 chr6qtel1M 677123 678268 (321732) C L2#LINE/L2 (70) 3012 1854 m_b316s601i3 13216 chr6qtel1M 677123 TTCAAGGAACATCAAGAAAGCAAGTTTTCCTGCATTGCAGGCTTTATGGT 677172 i v i i v v vv v -- i iv vvii iv C L2#LINE/L2 3012 TTCGAGGAACAGCAAGGAGGCCAGTGTGGCTGGA--GCGGAGTGAGCGAG 2965 chr6qtel1M 677173 GAGGATTGTGGTTTAAGAAAA---CAG-GAAGTGTTGGAAGAGGCCAGAT 677218 i vv vvi vi --- - i ivi ii -- C L2#LINE/L2 2964 GGGGAGAGTGGTAGGAGATGAGGTCAGAGAGGTAACGGGGGA--CCAGAT 2917 chr6qtel1M 677219 TATGAAGGGATTTGAATTTCAA-ATATGAATTTTATATTT--CCCTGAAT 677265 i v vi v vvi v-i v i i ivv -- i i C L2#LINE/L2 2916 CATGTAGGGCCTTGTAGGCCATTGTAAGGACTTTGGCTTTTACTCTGAGT 2867 chr6qtel1M 677266 AGAATAAAATGTAATAGTAGTTTATTGTAAAGATGAGTTGATAACATTAG 677315 iii iii v iv v v vv v viv v - i vv iv C L2#LINE/L2 2866 GAGATGGGAAGCCATTGGAGGGTTTTGAGCAGAGGAGT-GACATGATCTG 2818 chr6qtel1M 677316 ATCAACACTGTAGAAAGATCTGTTTGACAGGTGCGTGGAAGAAGAACTAA 677365 iiv ii v i i vv i i v v i v ii vii i? C L2#LINE/L2 2817 ACTTACGTTTTAAAAGGATCACTCTGGCTGCTGTGTTGAGAATAGACTGN 2768 chr6qtel1M 677366 AGTAGAGAGAGATTTAATTCAGAGAGACGATCTAGCAGTCTGCAACATTT 677415 vi i vi iv vi vv i v vi v v iivi v v C L2#LINE/L2 2767 AGGGGGGCAAGGGTGGAAGCAGGGAGACCAGTTAGGAGGCTATTGCAGTA 2718 chr6qtel1M 677416 ATTTGGGCATGAGATAATGAAATCCTGCACCAGGGTCATCATAATGTCAG 677465 iii iv i iviv i v vi vii i vvi C L2#LINE/L2 2717 ATCCAGGCGAGAGATGATGGTGGCTTGGACCAGGGTGGTGGCAGTGGAGG 2668 chr6qtel1M 677466 AGA-GAAAAGTGCC---ATGTAAGACATGATATAAATATAAAATTAAGAG 677511 v i- i vi--- vivi i iv v i vi i iiii v C L2#LINE/L2 2667 TGGTGAGAAGTGGTCGGATTCTGGATATATTTTGAAGGTAGAGCCGACAG 2618 chr6qtel1M 677512 TATTTGGCAACAAAATGATCATGGGTGT-TAAGAGTAGGAAGAGAACTCA 677560 v vii iii v ivii - - i v i - i v C L2#LINE/L2 2617 GATTTGCTGATGGATTGGATGTGGG-GTGTGAGAGAAAGA-GAGGAGTCA 2570 chr6qtel1M 677561 TGAATAAATGGCATGTTTCAAGCCAAAGTGACAAAAAAAA-GATGTTGGC 677609 v i i v vvv v ivi vi ii vii ii - iv v C L2#LINE/L2 2569 AGGATGACTCCAAGGTTTTTGGCCTGAGCAACTGGAAGGATGGAGTTGCC 2520 chr6qtel1M 677610 AATATTAACAGGAATAAGGAAATATGAAAGAGGAA-AGTTTTTGAGAGAA 677658 --- ? v ii ii ivv vii i- v vii i i C L2#LINE/L2 2519 A---TTNACTGAGATGGGGAAGACTGCGGGAGGAGCAGGTTTGAGGGGGA 2473 chr6qtel1M 677659 AGATAATAAATTAAGCCTTTTAAATATTAATTTTAAGACAGCTATGGAAC 677708 v vi i v ii vv v i v i iiv vii C L2#LINE/L2 2472 AGATCAGGAGTTCAGTTTTGGACATGTTAAGTTTGAGATGCCTATTAGAC 2423 chr6qtel1M 677709 ATTCATTATGAGATGTAGGAAATTCAGTTATGGATGTAAGAAT--GGCAG 677756 i vvvv v iiv vv -- i v i -- viv C L2#LINE/L2 2422 ATCCAAGTGGAGATGTCGAGTAGGCAGTT--GGATATACGAGTCTGGAGT 2375 chr6qtel1M 677757 TCAGGAAAGAGGATAGCTCCAGGTTA-----ATAGATTTTATA---ATCA 677798 ii ----- i i i----- i viv --- C L2#LINE/L2 2374 TCAGGGGAGAGG-----TCCGGGCTGGAGATATAAATTTGGGAGTCATCA 2330 chr6qtel1M 677799 ATATAGAGATAATTCTTCTATTCATGGAATGAGAAG-GATTTCAGCAAAT 677847 ii v ii vi vv vi ii ivi v - -- v ? iv C L2#LINE/L2 2329 GCATATAGATGGTATTTAAAGCCATGAGACTGGATGAGAT--CACCNAGG 2282 chr6qtel1M 677848 GAAATACTATAGAGAAA-AAGAAAAGAACTAGCAGAAGAAGTGGGA---A 677893 ivv v i v i - i i--- ivv i v i v---i C L2#LINE/L2 2281 GAGTGAGTGTAGATAGAGAAGAGAAGAG---GTCCAAGGACTGAGCCCTG 2235 chr6qtel1M 677894 GGATACATCAACAATCCAAGGGTAGATTGTGAGATAAATTAAGATCCAGC 677943 ii vi i- i? ii v --- v i iv- i v C L2#LINE/L2 2234 GGGCACTCCAACG-TTNAGAGGTCG---GGGAGATGAGG-AGGAACCAGC 2190 chr6qtel1M 677944 AAAGGAGATTAGGAAGTAGCAGTCAAATTAGTAGGAGAAGAACCAAGACC 677993 i ii v i i ivvvi i i i vv C L2#LINE/L2 2189 AAAGGAGACTGAGAAGGAGCGGCCAGTGAGGTAGGAGGAAAACCAGGAGA 2140 chr6qtel1M 677994 ATA----GCCATGAAAATCTAGAAAGTAAAGACGAT-------AAACTAA 678032 i i---- i v i ii ---- i vii -------i vv i C L2#LINE/L2 2139 GTGTGGTGTCCTGGAAGCC----AAGTGAAGAAAGTGTTTCAAGAAGGAG 2094 chr6qtel1M 678033 ATGGTAATCAACAGTTCCAGAAGCAACAGATAAATATGAATGA-ATGAGG 678081 ivi i v vi i v vi v ? ii -ii i i - C L2#LINE/L2 2093 GGAGTGATCAACTGTGTCAAATGCTGCTGANAGGT-CAAGTAAGATGAGG 2045 chr6qtel1M 678082 GCTGAGAAGAGGCCATAAGAGTGAGCATTTAAGAGTCCATTAGCAAATTT 678131 i vv i vi v v vivvi vi i ii vi C L2#LINE/L2 2044 ACTGAGAATTGACCATTGGATTTAGCAACGTGGAGGTCATTGGTGACCTT 1995 chr6qtel1M 678132 GTACACCAA-AGTTCTGGTTGAAT-ACAAACTCAGAAATCAGATTTTTGA 678179 - vv i- ii v i -iiiiivv ii ii v -- v C L2#LINE/L2 1994 G-ACAAGAGCAGTTTCGGTGGAGTGGTGGGGACGAAAGCCTGA--TTGGA 1948 chr6qtel1M 678180 GT--GTT---AAGAAAATAAGAAGAAATAAAGGGAAGGCACCAATTGTAT 678224 -- ---i i ii i i vi vv i i v i v i v C L2#LINE/L2 1947 GTGGGTTCAAGAGAGAATGGGAGGAGAGGAATTGGAGACAGCGAGTATAG 1898 chr6qtel1M 678225 AAGATATTCTCGAGGAATTGAGACACAAAAAGAAGAGGAGATAT 678268 vi ivi i i vv viii ii i vi v C L2#LINE/L2 1897 ACAACTCTTTCGAGGAGTTTTGCTGTAAAGGGGAGCAGAGAAAT 1854 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 56.56 CpG sites = 253, Kimura (unadjusted) = 59.76 Transitions / transversions = 1.35 (253/188) Gap_init rate = 0.05 (57 / 1145), avg. gap size = 1.46 (83 / 57) 12 28.01 0.00 0.00 chr6qtel1M 678361 678399 (321601) (TTT)n#Simple_repeat 1 39 (0) m_b316s252i9 13217 chr6qtel1M 678361 TTTTTTTTCTTTTTTATTATTTATTATAGATTTTTATTT 678399 i v v v v vvv v (TTT)n#Simple 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 39 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 16 15.14 2.70 0.00 chr6qtel1M 678363 678399 (321601) (TTTTTTA)n#Simple_repeat 1 38 (0) m_b316s252i10 13217 chr6qtel1M 678363 TTTTTTCTTTTTTATTATTTATTATAGA-TTTTTATTT 678399 v v v vv - (TTTTTTA)n#Si 1 TTTTTTATTTTTTATTTTTTATTTTTTATTTTTTATTT 38 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 29 0.00 0.00 0.00 chr6qtel1M 678553 678577 (321423) (TG)n#Simple_repeat 1 25 (0) c_b316s251i3 13218 chr6qtel1M 678553 TGTGTGTGTGTGTGTGTGTGTGTGT 678577 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGT 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 49 0.00 0.00 0.00 chr6qtel1M 681533 681574 (318426) (TA)n#Simple_repeat 1 42 (0) c_b316s251i4 13219 chr6qtel1M 681533 TATATATATATATATATATATATATATATATATATATATATA 681574 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATA 42 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 1169 29.71 4.66 5.06 chr6qtel1M 681844 682637 (317363) C HERVK14C#LTR/ERVK (3799) 3635 2845 m_b316s701i0 13220 chr6qtel1M 681844 ATATCTCCTATCAATTTCTGAAAATCATTTAAGGTGTTTAG-----CTTC 681888 i vi i i v i ----- i C HERVK14C#LTR/ 3635 ATATCCCCTAATAATTTTTGAAAATCATTTAAAGTTTTCAGAGAGTCTTT 3586 chr6qtel1M 681889 TCTGGTTCTTAAGGAAAGTTTTTGTACTATAA--GCAACTTAGGGTATAC 681936 vii i------i vi ?iviv -- vvi vvv v i- C HERVK14C#LTR/ 3585 TCGAATTT------GAACCTTTTGNGGCTTAATTGCCCTTTCCTGAAC-C 3543 chr6qtel1M 681937 TTCATATCCTAAATATTGAAAAGAAGCATGTCTTTGAATTTTTTCTGGAG 681986 v - i i i i v?iv v ? ? C HERVK14C#LTR/ 3542 TGCAT-TCCCAAATATTGGAAAGGAGTAGNCGTTTGAATTTTATCNGGNG 3494 chr6qtel1M 681987 CTATGTACAGTTGGTAGTTCCTTAGTGCTTTTTTGGTCTTTTGTAGACAT 682036 v? i i--i -- v ii i?vii----- i i i ii C HERVK14C#LTR/ 3493 CTATGANCAATC--CAG--CGTCGGCNACC-----GCCTTCTGTAAATGT 3453 chr6qtel1M 682037 GTTT----CTA---AAATTTATTCC-----TCAGGTGCACATCCCAATAT 682074 vv ---- i--- i vi ii ----- i vi ?--- C HERVK14C#LTR/ 3452 GAATAACACTGGATAAGTTGGTCTCGAGTTTCGGCCGCACAN---AATAT 3406 chr6qtel1M 682075 AACATCCATGTAATGTAATAACAT--TACTTTAGGAAATGCTTGTCTTAC 682122 iv i - i i --v v i i i v v i- ? C HERVK14C#LTR/ 3405 GTCATCCATATAATG-AATGATATANGAATCTGGAAACTGATC-TCTNAC 3358 chr6qtel1M 682123 TGGAGTAAGAGCAGCAGCAGCATACATTTGACACATAGTAGGGCTGTTTC 682172 v vvv v vv?vv vi ? vi v ? ? i i iv C HERVK14C#LTR/ 3357 AGGTTGAATAGCCTNCCCCACANAAGTTTGACAAATNGTNGGACTATTCA 3308 chr6qtel1M 682173 TCATTCCCTGTGGCAAAACTGTCCATTCATATCTTTTATAAGGCTCA--G 682220 v v i ? v v v ? vvivvv? i v-- C HERVK14C#LTR/ 3307 ACATGCCCTGCGGCAANACTTTCCAATGATANCTGGCTGCNGGTTCCTTG 3258 chr6qtel1M 682221 CTAAGTTAACACTGGGCACGGAAAAGGCAAATCTTTTTGTATCCC-CTCT 682269 i -- v i vii v ii v i i iviv ?v- C HERVK14C#LTR/ 3257 TT--GTTCATAGCAGGAATAGTAAAAGCAAATTTTTCAAAATCNGGCTCT 3210 chr6qtel1M 682270 ATCTGGTAGGATAGAATAGAAACAATCCTTAATGTCTATAACCCAAAGAG 682319 i- i vi i v v i i v vi ivvv i? C HERVK14C#LTR/ 3209 G-CTAGAGGAATAGTAAAGAAGCAGTCCTTCAAATCTATAACTATTAANG 3161 chr6qtel1M 682320 GCCATTCTCTAGGGAATTCA--GTAGGAGATGGAAGTCCAGGCTGAAGAG 682367 v i -- -- ii i ? v i v v ? C HERVK14C#LTR/ 3160 GCCAGTCTCTAGGAA--TCATGGCGGGGGANGGCAGCCCTGGCTGCAGNG 3113 chr6qtel1M 682368 TCCCCATAGTTTCCAT--CTGTTCT-----TTCCTAAATCAGTCAACATC 682410 i ? v v? -- ivi -----i v i i i i ? C HERVK14C#LTR/ 3112 CCCCCATNGGTTGNATGACTGCATTGACGGCTCGTAAGTCGGTTAGCATN 3063 chr6qtel1M 682411 CTCCATTTTCTAGATTTCTTTTTTACAACAAATACTGGGGAATTCCAAGG 682460 v i v ii i i ? iv i ? ? C HERVK14C#LTR/ 3062 CGCCATCTGCCGGATTTTTTCTTNATTACAAACACTGGNGAATTCCANGG 3013 chr6qtel1M 682461 ACTTAGAGAA----GGTTGTAAGTATCCTTGGTCAAGTTGCTCCTGTACT 682506 ---- i ---- i v? v i v? v i i i vv C HERVK14C#LTR/ 3012 A----GAAAATGTGGGCTCNATGTGTCCTTTNTCTAATTGTTCTTTGACT 2967 chr6qtel1M 682507 ATATCTAATAAGGCCTGAATTTTATCGCTACCTAAGGGCCACTGTTTCAT 682556 vv ivi ivv v v viv v?? iv ? i? i C HERVK14C#LTR/ 2966 AATTCCTGTAAGGCCCCCAGTTTTTCCTGAGNNAGCGGCCACTGNTCNAC 2917 chr6qtel1M 682557 CCATACTGGTATATCAGTTTTTCATTAGATAGGAATGGGTGAAAGTGTTG 682606 v ? ?v v vi i? i vv vi i -------? iv C HERVK14C#LTR/ 2916 CCAAACNGGNTTTTGGGTCNTCCATTTTAAGGGAATAGG-------NTCT 2874 chr6qtel1M 682607 GCAGGCCTTCAACAACAGCCCTGCCTAAAAA 682637 v -- iii viv C HERVK14C#LTR/ 2873 GGAGGC--TCAACAGTGGCCGCCCCTAAAAA 2845 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 38.83 CpG sites = 118, Kimura (unadjusted) = 41.01 Transitions / transversions = 1.11 (118/106) Gap_init rate = 0.07 (52 / 793), avg. gap size = 1.48 (77 / 52) 532 31.85 3.21 5.80 chr6qtel1M 684876 685405 (314595) L1ME4c_3end#LINE/L1 164 680 (150) m_b316s551i6 13221 chr6qtel1M 684876 AAATGCAAAGGAAA-CAACTATAAAGTACCACCTTATACTCCTCACAAAA 684924 vv - v i ii -- v v ------- L1ME4c_3end#L 164 AAATGCAAATTAAAGCAACAATGAGATACCA--TTTTACGCCT------- 204 chr6qtel1M 684925 GGAGATTAAGATAACAGAAA-------AA--GACAAAAATCAATGTTGGA 684965 ---- iv i i ------- -- i v vi i v L1ME4c_3end#L 205 ----ATTAAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGCTGGC 250 chr6qtel1M 684966 GAAGTTTATGGAAAAACTGGGACACTAATGCATTGTTGGGGGACTTATGA 685015 i ? -ii vi v ? v i i v vv? i i L1ME4c_3end#L 251 GAGGNT-GCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAA 299 chr6qtel1M 685016 AATGGTTCAACAATTCTGGAGAATAATCAGAAACTATGCCCAAAGGGCTA 685065 v v vv i i ii iv iv v i iviv i i L1ME4c_3end#L 300 ATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCA 349 chr6qtel1M 685066 TAACATTGTATATGCTCTTTTCACCCAGGAGTTGCATTACTGGATCTGTG 685115 v v vi i i -v v i v i v ivv v i L1ME4c_3end#L 350 TAAAAATGTTCATACCCTTT-GACCCAGTAATTCCACTTCTGGGAATTTA 398 chr6qtel1M 685116 TTCCAAGAAAATCAT---AAAGGAGGTAAAAGGAACCATATGGGCAAAAA 685162 i i i v --- i v --- i vi i i L1ME4c_3end#L 399 TCCTAAGGAAATAATTCAAAAGAAGGAAAAAG---CTATATGCACGAAGA 445 chr6qtel1M 685163 TGTTTGGAGCAGCTCTCTCTTTTTTTTTTACTAGCAAAGAATCGGAAAAT 685212 iivv v------- v v v i i i -- L1ME4c_3end#L 446 TGTTCATTGCAGCG-------TTATTTATAATAGCGAAAAATTGGAAA-- 486 chr6qtel1M 685213 GAATAGAAA-ATCCATGCATTAGGG-AATGGCTGGACAAGTTGTGGTATA 685260 v ivv -i -i v - i iiii i i i L1ME4c_3end#L 487 CAACCTAAATGTCCA-ACAATAGGGGAATGGTTAAGTAAATTATGGTACA 535 chr6qtel1M 685261 TATAAGGAATAGAATATGATTATTCTATACAAAGTGATAAACAAGCTGAT 685310 v? vvvi i v vvvv i vv i vi v vv i L1ME4c_3end#L 536 TCNACTCGATGGAATATTATGCAGCCATTAAAAATGATAATTATGAAGAC 585 chr6qtel1M 685311 TTTATAA-AGCCTGGAATGATTTACACGAACTCATACTGAGTGAAACAAT 685359 v i i- i v -i v vi i vv v ii i v v L1ME4c_3end#L 586 TATGTAGCAACATGGAA-AATGTTTATGATATAATGTTAAGTGAAAAAAG 634 chr6qtel1M 685360 CAGAAC-CAAGAATACATTGTACACAATAATAGCAAGAATGTGCAAA 685405 i- i v ii - ? i v i vi vv iv L1ME4c_3end#L 635 CAGAATACAAAATTGTA-TNTACGCTATGATTACAACTATGTAAAAA 680 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 40.60 CpG sites = 82, Kimura (unadjusted) = 42.68 Transitions / transversions = 1.06 (82/77) Gap_init rate = 0.07 (38 / 529), avg. gap size = 1.24 (47 / 38) 28 23.81 1.52 0.00 chr6qtel1M 685674 685739 (314261) (TA)n#Simple_repeat 1 67 (0) m_b316s252i11 13222 chr6qtel1M 685674 TATATATATATATATATATAAATGTATAT-TATATACGCATAAATATGTA 685722 v i - iii v i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr6qtel1M 685723 TGTGTGTGTATGTAAAT 685739 i i i i i v (TA)n#Simple_ 51 TATATATATATATATAT 67 Matrix = Unknown Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.02 (1 / 65), avg. gap size = 1.00 (1 / 1) 13 20.69 5.77 1.85 chr6qtel1M 687060 687111 (312889) (GAAAGG)n#Simple_repeat 1 54 (0) m_b316s252i12 13223 chr6qtel1M 687060 GAAAAGG-ACGTGAGAGGGCCAGAGAGAGGGGAA--GAAAGGGAAAGGGA 687106 i - v v i vv i i i -- (GAAAGG)n#Sim 1 GAAAGGGAAAGGGAAAGGGAAAGGGAAAGGGAAAGGGAAAGGGAAAGGGA 50 chr6qtel1M 687107 GAAGG 687111 - (GAAAGG)n#Sim 51 -AAGG 54 Matrix = Unknown Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.33 (4 / 3) 12 17.86 3.12 0.00 chr6qtel1M 688390 688421 (311579) (CTTTTC)n#Simple_repeat 1 33 (0) m_b316s252i13 13224 chr6qtel1M 688390 CTTTTCCTTGTCCTAATCCATTACC-TTTCCTT 688421 v vv v v - (CTTTTC)n#Sim 1 CTTTTCCTTTTCCTTTTCCTTTTCCTTTTCCTT 33 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 698 40.13 4.35 3.72 chr6qtel1M 689529 690677 (309323) C L2#LINE/L2 (68) 3014 1859 m_b316s601i4 13225 chr6qtel1M 689529 TGTTCAAGGAACATCAAGAAAGCCAATTTTCCTTCCTTGCAGGCTATATG 689578 i v i i i v vv vvv-- i iv ivii C L2#LINE/L2 3014 TGTTCGAGGAACAGCAAGGAGGCCAGTGTGGCTGGA--GCGGAGTGAGCG 2967 chr6qtel1M 689579 GTGACGGATATGGTTTAAGA--AAACTAGGAGTGTTAGGAGGGGCCAGAT 689626 iv iv iivi vvi -- iiii iiiv v v i i C L2#LINE/L2 2966 AGGGGGAGAGTGGTAGGAGATGAGGTCAGAGAGGTAACGGGGGACCAGAT 2917 chr6qtel1M 689627 TTTGAAGGGATTTG-AATTAAAGATATGAATTTTATATTTT--CCGGAAT 689673 iv v vi - iviv vvi v i i ivv --i v i C L2#LINE/L2 2916 CATGTAGGGCCTTGTAGGCCATTGTAAGGACTTTGGCTTTTACTCTGAGT 2867 chr6qtel1M 689674 GGAATAAAATGTAATTGTACCTTACTGAAAAGGAGAGTTGATAACATTAG 689723 ii iii v iv v vvv vi iv ii - i vv iv C L2#LINE/L2 2866 GAGATGGGAAGCCATTGGAGGGTTTTGAGCAGAGGAGT-GACATGATCTG 2818 chr6qtel1M 689724 ATCAACACTGTAGAAAGGTCAGTTTGACAGGTGAGTGGAAGAAGAACTAA 689773 iiv ii v i i i v i i v v v v ii vii i? C L2#LINE/L2 2817 ACTTACGTTTTAAAAGGATCACTCTGGCTGCTGTGTTGAGAATAGACTGN 2768 chr6qtel1M 689774 AGTAGAGAGAGATCTAATTCAGAGAGACGATCTAGCAGTCTGCAACATTT 689823 vi i vi ivivi vv i v vi v v iivi v v C L2#LINE/L2 2767 AGGGGGGCAAGGGTGGAAGCAGGGAGACCAGTTAGGAGGCTATTGCAGTA 2718 chr6qtel1M 689824 ATTTGGGCATGAGATAATGAAATCCTACACCAGGGTCATCATAATGTCAG 689873 iii iv i iviv i iv vi vii i -v C L2#LINE/L2 2717 ATCCAGGCGAGAGATGATGGTGGCTTGGACCAGGGTGGTGGCAGTG-GAG 2669 chr6qtel1M 689874 ATAG--AAAAGTGCC---ATTA-AGACATGACATAAATATAAAATTAAGA 689917 i i -- i vi--- v-i i iviv i vi i iiii v C L2#LINE/L2 2668 GTGGTGAGAAGTGGTCGGATTCTGGATATATTTTGAAGGTAGAGCCGACA 2619 chr6qtel1M 689918 GGATTTGGCAAAAAAATGATCATGGG-TGTTAGGATGGGAAAAGAACTCA 689966 vii vii v ivii - v iivii i i i- C L2#LINE/L2 2618 GGATTTGCTGATGGATTGGATGTGGGGTGTGAGAGAAAGAGAGGAG-TCA 2570 chr6qtel1M 689967 TGAATAAATGGCATGTTTCAAGACAAAGTGAC--AAAAAAAGATGTTGGC 690014 v i i v vvv v ivi v vi ii --i ii v iv v C L2#LINE/L2 2569 AGGATGACTCCAAGGTTTTTGGCCTGAGCAACTGGAAGGATGGAGTTGCC 2520 chr6qtel1M 690015 AATATTAACAGGAATAAGGAAATATGAAAGAGGAAAGTTTTTGA-GAGAA 690063 --- ? v ii ii ivv vii ivivv - i i C L2#LINE/L2 2519 A---TTNACTGAGATGGGGAAGACTGCGGGAGGAGCAGGTTTGAGGGGGA 2473 chr6qtel1M 690064 AGATAATAAATTAAGCCTTTTAAATATTAATTTTAAGACAGCTATGGAAC 690113 v vi i v ii vv v i v i iiv vii C L2#LINE/L2 2472 AGATCAGGAGTTCAGTTTTGGACATGTTAAGTTTGAGATGCCTATTAGAC 2423 chr6qtel1M 690114 ATTCATTATGAGATATAGGAAATTCAGTTATGGATGTAAGAA--TGGCAG 690161 i vvvv i v iiv vv -- i v i-- viv C L2#LINE/L2 2422 ATCCAAGTGGAGATGTCGAGTAGGCAGT--TGGATATACGAGTCTGGAGT 2375 chr6qtel1M 690162 TCAGGAAAGAGGATAGCTCCAGGTTA-----ATAGATTTT---ATAATCA 690203 ii ----- i i i----- i v---i v C L2#LINE/L2 2374 TCAGGGGAGAGG-----TCCGGGCTGGAGATATAAATTTGGGAGTCATCA 2330 chr6qtel1M 690204 ATATAGAGATAATTCTTGTATTCATGGAAT--GATAATGAT--TTCAGCA 690249 ii v ii vi iv vi ii i-- i - --ii? vi C L2#LINE/L2 2329 GCATATAGATGGTATTTAAAGCCATGAGACTGGATGA-GATCACCNAGGG 2281 chr6qtel1M 690250 AAT-AGAATACTATAGAGAAAAAGAAAAGCCCTAGCA-TAAGAAGTGGGA 690297 i - vi v- i ii i i i v v - i vvv - C L2#LINE/L2 2280 AGTGAGTGTAG-ATAGAGAAGAGAAGAGGTCCAAGGACTGAGCCCTGGG- 2233 chr6qtel1M 690298 AGCATACATCAACCATCCAAGGCTGGATTGTGAGATAAATTAAAATCCAG 690347 - -- vi vv ?vi ii i---- i i-v ii v C L2#LINE/L2 2232 -GC--ACTCCAACGTTNAGAGGTCGGG----GAGATGAG-GAGGAACCAG 2191 chr6qtel1M 690348 CAAAGGAGACTAGGAAGTAGCAGTCAAATTAGCAGGAGAAGAACCA--AG 690395 ii v i i ivvvi i i i -- C L2#LINE/L2 2190 CAAAGGAGACTGAGAAGGAGCGGCCAGTGAGGTAGGAGGAAAACCAGGAG 2141 chr6qtel1M 690396 ACTATAG---CCATGAA---AAATCAAGAAAGTAAAC--AGAATAAAATA 690437 v i i --- vv --- i v ivvi-- vi iiv C L2#LINE/L2 2140 AGTGTGGTGTCCTGGAAGCCAAGTGAAGAAAGTGTTTCAAGAAGGAGGGA 2091 chr6qtel1M 690438 CATGATAATCAACAGTTCCAGAAGCAACAGATAAATACCAATGA-ATGTG 690486 ----i i v vi i v vi v ? ii - v i i - v C L2#LINE/L2 2090 ----GTGATCAACTGTGTCAAATGCTGCTGANAGGT-CAAGTAAGATGAG 2046 chr6qtel1M 690487 GGCTGAAAAGAGGGCATAAGAGTGAGCATTTAAGAGACCATTAGTAAATT 690536 i i vv iv vi v v vivvi ii i i vi C L2#LINE/L2 2045 GACTGAGAATTGACCATTGGATTTAGCAACGTGGAGGTCATTGGTGACCT 1996 chr6qtel1M 690537 TGTACACCAA-AGTTCTAGTTGA---ATAGAAACTAA--TCATATTGTTG 690580 - vv i- iii v ---i i ii v --i vv -- C L2#LINE/L2 1995 TG-ACAAGAGCAGTTTCGGTGGAGTGGTGGGGACGAAAGCCTGATTG--G 1949 chr6qtel1M 690581 AGT--GTTAAGAAAATAAGAGGAAATAAGAAGAAATAAAGGGAAGGCACT 690628 -- -------i ii ii i i vi vv i i vi C L2#LINE/L2 1948 AGTGGGTT-------CAAGAGAGAATGGGAGGAGAGGAATTGGAGACAGC 1906 chr6qtel1M 690629 AATTGTATAAGATCTTCTCAAGGAATTGAGACATAAAAAGAGGAGGAGA 690677 i v i v vi iii i i i vv vii -- i v C L2#LINE/L2 1905 GAGTATAGACAACTCTTTCGAGGAGTTTTGCTGT--AAAGGGGAGCAGA 1859 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 58.02 CpG sites = 260, Kimura (unadjusted) = 61.17 Transitions / transversions = 1.41 (260/184) Gap_init rate = 0.06 (68 / 1148), avg. gap size = 1.37 (93 / 68) 12 14.94 8.11 0.00 chr6qtel1M 690771 690807 (309193) (TATTTTT)n#Simple_repeat 1 40 (0) m_b316s252i14 13226 chr6qtel1M 690771 TATTTTAT-TTTTTTATTATTTA--TTATAGCTTTTATTT 690807 v - v -- v vi (TATTTTT)n#Si 1 TATTTTTTATTTTTTATTTTTTATTTTTTATTTTTTATTT 40 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.50 (3 / 2) 14 9.66 5.71 2.78 chr6qtel1M 690774 690808 (309192) (TTTA)n#Simple_repeat 1 36 (0) m_b316s252i15 13226 chr6qtel1M 690774 TTTATTTTTTTA-TTATTTATTATAGCT-TTTATTTA 690808 v - - vi - (TTTA)n#Simpl 1 TTTATTTATTTATTTATTTATT-TATTTATTTATTTA 36 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.09 (3 / 34), avg. gap size = 1.00 (3 / 3) 21 3.96 0.00 0.00 chr6qtel1M 690949 690974 (309026) (CA)n#Simple_repeat 1 26 (0) m_b316s252i16 13227 chr6qtel1M 690949 CAGACACACACACACACACACACACA 690974 v (CA)n#Simple_ 1 CACACACACACACACACACACACACA 26 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 16 8.55 7.69 2.44 chr6qtel1M 692349 692387 (307613) (ATTT)n#Simple_repeat 1 41 (0) m_b316s252i17 13228 chr6qtel1M 692349 ATTT-TTTA-TT-TTTATTTATTTATTATAGCTTTTTATTTA 692387 - - - - vi v (ATTT)n#Simpl 1 ATTTATTTATTTATTTATTTATTTATT-TATTTATTTATTTA 41 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.11 (4 / 38), avg. gap size = 1.00 (4 / 4) 50 2.17 0.00 0.00 chr6qtel1M 692533 692579 (307421) (AT)n#Simple_repeat 1 47 (0) c_b316s251i5 13229 chr6qtel1M 692533 ATATATATATATATATATATATATATATATATATATATATACATATA 692579 i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATA 47 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 48 0.00 0.00 0.00 chr6qtel1M 693623 693663 (306337) (TA)n#Simple_repeat 1 41 (0) c_b316s251i6 13230 chr6qtel1M 693623 TATATATATATATATATATATATATATATATATATATATAT 693663 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATAT 41 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 240 34.29 0.00 0.00 chr6qtel1M 693737 693806 (306194) C MIRb#SINE/MIR (159) 109 40 m_b316s601i5 13231 chr6qtel1M 693737 TAACTAATCAAGCATCACACAATTAGTAAATGTGAGAGACTGCATTTGAG 693786 vii v ivi ii i vv v v v i i C MIRb#SINE/MIR 109 TAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAA 60 chr6qtel1M 693787 CTCAGATCTTCTTGACACTA 693806 i i vii v i C MIRb#SINE/MIR 59 CCCAGGTCTGTCTGACTCCA 40 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 44.81 CpG sites = 14, Kimura (unadjusted) = 47.55 Transitions / transversions = 1.40 (14/10) Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0) 268 31.95 0.00 1.39 chr6qtel1M 693745 693817 (306183) C MIRc#SINE/MIR (171) 97 26 m_b316s601i6 13231 chr6qtel1M 693745 CAAGCATCACACAATTAGTAAATGTGAGAGACTGCATTTGAGCTCAGATC 693794 -i ii i vv v v v i i i i i C MIRc#SINE/MIR 97 CAAG-GTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTC 49 chr6qtel1M 693795 TTCTTGACACTATGGTCAACACT 693817 i v i v vi iii C MIRc#SINE/MIR 48 TTCCTGACTCCAAGTCCAGTGCT 26 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 41.22 CpG sites = 15, Kimura (unadjusted) = 43.80 Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.01 (1 / 72), avg. gap size = 1.00 (1 / 1) 12 0.00 8.00 3.85 chr6qtel1M 694573 694597 (305403) (ATA)n#Simple_repeat 1 26 (0) m_b316s252i18 13232 chr6qtel1M 694573 ATATATAATAATAATAAT-ATAA-AAT 694597 - - - (ATA)n#Simple 1 ATA-ATAATAATAATAATAATAATAAT 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.12 (3 / 24), avg. gap size = 1.00 (3 / 3) 17 21.05 0.00 6.90 chr6qtel1M 696906 696967 (303033) (TATATG)n#Simple_repeat 1 58 (0) m_b316s252i19 13233 chr6qtel1M 696906 TAAATGTATATGAATGTATTTATGTCTATGAGTATAAGTATCTATTTATA 696955 v v i i v v -- v -- v (TATATG)n#Sim 1 TATATGTATATGTATATGTATATGTATAT--GTATATGTA--TATGTATA 46 chr6qtel1M 696956 TGGATATATATA 696967 v i (TATATG)n#Sim 47 TGTATATGTATA 58 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.07 (4 / 61), avg. gap size = 1.00 (4 / 4) 29 0.00 0.00 0.00 chr6qtel1M 698421 698445 (301555) (AC)n#Simple_repeat 1 25 (0) c_b316s251i7 13234 chr6qtel1M 698421 ACACACACACACACACACACACACA 698445 (AC)n#Simple_ 1 ACACACACACACACACACACACACA 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 242 27.11 0.00 5.41 chr6qtel1M 698446 698515 (301485) DNM1r#Unknown 2482 2547 (2115) m_b316s502i0 13235 chr6qtel1M 698446 TATATATATATATGCAACCATGTCTACATGCCTACGTATGCATACATCTG 698495 i i i ii---- v ii iv i i i i v DNM1r#Unknown 2482 TGTGTGTATATATGTG----TGTATATGTGTGTATGTGTGTATATATGTG 2527 chr6qtel1M 698496 TATATACAAGTAGATATAGA 698515 i v v? DNM1r#Unknown 2528 TATATATACGTATNTATAGA 2547 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 37.03 CpG sites = 15, Kimura (unadjusted) = 37.03 Transitions / transversions = 2.60 (13/5) Gap_init rate = 0.06 (4 / 69), avg. gap size = 1.00 (4 / 4) 476 17.02 13.48 0.00 chr6qtel1M 698746 698886 (301114) Charlie1a#DNA/hAT-Charlie 1295 1454 (1) m_b316s502i1 13236 chr6qtel1M 698746 TTTTAAATGGTCTA-CAAAT---TCAAAAAT-----AGTTTTTATTTCCC 698786 ivi -i --- i ----- v iv Charlie1a#DNA 1295 TTTTAAATGAATTAATAAATATTTTAAAAATTTCTCAGTTTTAATTTCTA 1344 chr6qtel1M 698787 ATATGGTAAATGTCTATAAATTTAATCCAGATAAACAAAA-------AGG 698829 i v i v i v -------i Charlie1a#DNA 1345 ATATGGTAAATATCGATAGATATAACCCACATAAACAAAAGCTCTTTGGG 1394 chr6qtel1M 698830 CTCCTCAATAATTTTTAATAGGATAAA--GATACTGAAAACAAAAA-TTT 698876 v v vi -- i v i v - Charlie1a#DNA 1395 GTCCTCAATAATTTTTAAGAGTGTAAAGGGGTCCTGAGACCAAAAAGTTT 1444 chr6qtel1M 698877 GAGAACCACT 698886 i Charlie1a#DNA 1445 GAGAACCGCT 1454 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 18.60 CpG sites = 13, Kimura (unadjusted) = 19.46 Transitions / transversions = 1.18 (13/11) Gap_init rate = 0.04 (6 / 140), avg. gap size = 3.17 (19 / 6) 29 25.42 3.57 0.00 chr6qtel1M 699270 699353 (300647) (AT)n#Simple_repeat 1 87 (0) m_b316s252i20 13237 chr6qtel1M 699270 ATAGATGTATATGAATGTATATAT-TCTATATATGCA-AGAT-TATAGAT 699316 v i iv i - v ii - v - v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr6qtel1M 699317 ATCTGTATATGTATATATATATAAACATCTACATTTA 699353 v i i v i v i v (AT)n#Simple_ 51 ATATATATATATATATATATATATATATATATATATA 87 Matrix = Unknown Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.04 (3 / 83), avg. gap size = 1.00 (3 / 3) 273 29.06 2.04 8.70 chr6qtel1M 700854 701049 (298951) C L1PB2_3end#LINE/L1 (659) 239 56 m_b316s551i7 13238 chr6qtel1M 700854 TTGTTTTTTGTTTTTTTTTCTTTGTTTGTTTTTGCTGAGGCAAAATTCTG 700903 vi vvi v viii i v ii i ii --- C L1PB2_3end#LI 239 TTGTTTTTTGACTTTTTAATTATGGCCATTCTTGCAGGAGTAAGGT---G 193 chr6qtel1M 700904 GTACCTCAGTGGTACCAAATTTTGTCTTAATTTGTATTTCTCTGATCAAG 700953 i v ---------- v i i i v vv C L1PB2_3end#LI 192 GTATCTCATTG----------TGGTTTTAATTTGCATTTCCCTGATAATT 153 chr6qtel1M 700954 AATGATTTAGAACATCTTTTTATATGACTAGAAATGGC--TTTA-ATTTC 701000 i v v i i i vi iv--- -- i- v C L1PB2_3end#LI 152 AGTGATGTTGAGCATTTTTTCATATGTTTGT---TGGCCGTTTGTATATC 106 chr6qtel1M 701001 TTCTTCTAAAAATTGCTTGTCCAT-TCCTTTTACCAATTATCAATTGGAT 701049 i i i ii i i - vv v v ii v C L1PB2_3end#LI 105 TTCTTTTGAGAATTGTCTATTCATGTCCTTTGCCCACTTTTTGATGGGAT 56 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 37.55 CpG sites = 31, Kimura (unadjusted) = 37.55 Transitions / transversions = 1.48 (31/21) Gap_init rate = 0.10 (19 / 195), avg. gap size = 1.05 (20 / 19) 424 22.22 2.92 1.44 chr6qtel1M 700911 701047 (298953) C L1ME5_3end#LINE/L1 (745) 196 58 m_b316s551i8 13238 chr6qtel1M 700911 AGTGGTACCAAATT-TTGTCTTAATTTGTATTTCTCTGATCAAGAATGAT 700959 i i vv - i i i vv v C L1ME5_3end#LI 196 AGTGATATCTCATTGTTGTTTTAATTTGCATTTCTCTGATTACTAATGAG 147 chr6qtel1M 700960 TTAGAACATCTTTTTATATGACTAGAAATGGCTTT--AATTTCTTCTTCT 701007 v i i i - v vv - v --ii i C L1ME5_3end#LI 146 TTTGAGCATCTCTTCATATG-CTTGTTA-GCCTTTCGGGTTTCCTCTTCT 99 chr6qtel1M 701008 AAAAATTGCTTGTCCAT-TCCTTTTACCAATTATCAATTGG 701047 iv i i - vv v v v C L1ME5_3end#LI 98 GTAAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGG 58 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 26.48 CpG sites = 14, Kimura (unadjusted) = 26.48 Transitions / transversions = 0.88 (14/16) Gap_init rate = 0.04 (5 / 136), avg. gap size = 1.20 (6 / 5) 292 28.13 12.50 1.09 chr6qtel1M 700956 701203 (298797) C L1M5_orf2#LINE/L1 (0) 3294 3019 m_b316s551i9 13238 chr6qtel1M 700956 TGATTTAGAACATCTTTTTATATGACTAGAAATGGC---TTTAATTTCTT 701002 ?v v i i i vi v--- --- v? v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTAT---TGGCCATTTGNATATCTT 3248 chr6qtel1M 701003 CTTCTAAAAATTGCTTGTCCATTCCTTTTACCAATTATCA-ATTGGAT-- 701049 i ivi v ii i vvi i v v i?- i -- C L1M5_orf2#LIN 3247 CTTTTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTG 3198 chr6qtel1M 701050 --------------AATGGCTTGTA----TTATCTATATATTTTAGAAAT 701081 -------------- v i? ---- v i i i v i C L1M5_orf2#LIN 3197 TTTGTCTTTTTNTTATTGANTTGTAGGAGTTCTTTATATATTCTGGATAC 3148 chr6qtel1M 701082 AAGGCCTTTAACAGAACCCTTGAATGTAAACATTTTCT-CCAGTTTATGG 701130 i v iv vviv vv?v i i - ? i i C L1M5_orf2#LIN 3147 GAGTCCTTTGTCAGATATATGTNTTGCAAATATTTTCTCCCANTCTGTGG 3098 chr6qtel1M 701131 CTTCCCTTCTAATTTTGT-----GTGCATTTGTGTGTACACAAATTTTTA 701175 v i v v ----- iv vvi? vi v i C L1M5_orf2#LIN 3097 CTTGCCTTTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTTTA 3048 chr6qtel1M 701176 A-ATTAATATAATCAAAATTATCCATTTT 701203 -v i i? i v v v C L1M5_orf2#LIN 3047 ATTTTGATGNAGTCCAATTTATCAATTTT 3019 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.52 CpG sites = 34, Kimura (unadjusted) = 37.26 Transitions / transversions = 0.97 (34/35) Gap_init rate = 0.04 (11 / 247), avg. gap size = 3.09 (34 / 11) 18 20.34 0.00 0.00 chr6qtel1M 702754 702788 (297212) (A)n#Simple_repeat 1 35 (0) m_b316s252i21 13239 chr6qtel1M 702754 AAAAGAAAAAAAAAAGAGGAAACAAAAAAAGAAAA 702788 i i ii v i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 35 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 12 9.03 7.69 5.00 chr6qtel1M 704785 704823 (295177) (AGTAAGA)n#Simple_repeat 1 40 (0) m_b317s252i1 13240 chr6qtel1M 704785 AGTGAGAAGGAA-AACTACAGGAAG--AGAAGTAAGAAGTAA 704823 i v - v - - -- (AGTAAGA)n#Si 1 AGTAAGAAGTAAGAAGTA-A-GAAGTAAGAAGTAAGAAGTAA 40 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.11 (4 / 38), avg. gap size = 1.25 (5 / 4) 593 36.36 6.29 4.68 chr6qtel1M 705745 706396 (293604) C L3#LINE/CR1 (461) 3638 2977 m_b317s601i0 13241 chr6qtel1M 705745 TGCCAATGATATTTTTAAAAAGTAAAATCCTT--TTGAACATAATAATCC 705792 i vivi i v iivii vv--i ii v C L3#LINE/CR1 3638 TGTCAATGTCCCTCTTAAAATGTGGCGCCCAGAACTGAACGCAATACTCC 3589 chr6qtel1M 705793 ACATAAAAACTGTCCAGTGCTGATGACAATAGGATCATGACCTCAGTTTT 705842 v iviiv v i v vv iii ii v vv v? C L3#LINE/CR1 3588 AGATGTGGTCTGACCAGCGCAGAGTACAGCGGGACTATTACCTCCCTTGN 3539 chr6qtel1M 705843 TTCAGATCCTGTTCCTCTCTTAATG-AACCTGAG-TCTCCTCAGCTTAGG 705890 iii iv i v i v - i i - iv v i vvv C L3#LINE/CR1 3538 TCTGGACACTATACTTCTATTAATGCAGCCTAAGATTGCATTAGCTTTTT 3489 chr6qtel1M 705891 AGGATGCTTCATACATAGCACTGTTGATGCTGATATTGAACATA------ 705934 v vv i---- vi -- v i v i------ C L3#LINE/CR1 3488 TGGCAGCC----ACATCACACTGTTG--GCTCATATTGAGCTTGCGGTCA 3445 chr6qtel1M 705935 ---GAAATTCCTTCCTGCAATATTTTTTTCAAA--AACCTTT-CTAGG-- 705976 ---i ii ------- vi i vi-- ivi - i -- C L3#LINE/CR1 3444 ACTAAAACCCCT-------AGGTCTTTTTCACGTGAACTGCTGCTAAGCC 3402 chr6qtel1M 705977 -AATTGCTTTTACAATAGAACCTGGTAAAGTTG---TTTTGAATCCAAAT 706022 -i ivii ii ivv iv -- v iv --- i i C L3#LINE/CR1 3401 AGATCCTCTCCATCCTGTA--CTTGTGCAGTTGATTTTTTGAACCTAAAT 3354 chr6qtel1M 706023 TT-TAACACTATCTTTACTGCTGTCCA-TTTC--CTTGCTGAATTCTGGT 706068 vi-vi vi iv iiv iv - -- i iv v vi C L3#LINE/CR1 3353 GCAGGACTTTACATTTATCCCTGTTAAATTTCATCTTGTTGGTTTCGGCC 3304 chr6qtel1M 706069 GACC----CAATCTATC-AGACTCTTTTATGGTCCAGATTGTTTATTCCA 706113 v i ---- ii i - ii? i-ii iv v v vv C L3#LINE/CR1 3303 CATCGTTCCAGCCTGTCGAGATCNTTTTG-AATCTTGATTCTGTCATCCA 3255 chr6qtel1M 706114 ATGAATTAGCTTGTCATCCTCACTTTAAATT-TTTGCAAA----ATG-GT 706157 ?i v vvi v ivi ivi i- i ---- i- i C L3#LINE/CR1 3254 NCGTATTAGCTATCCCTCCCAGCTTTGTGTCATCTGCAAATTTGATAAGC 3205 chr6qtel1M 706158 GGGACTTCAACATGCTTTTTATCTA--TGATTGAACAAAAAAAAGTCAAG 706205 iv v --i - i i i -- v v--- v ii i C L3#LINE/CR1 3204 ATGCCTTC--TATG-TCTTCATCCAAGTCATTGAT---AAAAATGTTGAA 3161 chr6qtel1M 706206 CACCATAAACCCT-GTATAGATTTATCAATCATTCCATTGGAAATCTTCC 706254 vv i iiv v- v i viiv vviv iv i i i i i C L3#LINE/CR1 3160 CAGGACAGGGCCAAGGACAGAGCCCTGTGGCACGCCACTAGAGACCTCCC 3111 chr6qtel1M 706255 TTCATGGTTAGTTTCTACCCATCAATATCAGC-CCTTTTATGTGCCATCA 706303 i - iiiv v i i -- i - iv iivi i C L3#LINE/CR1 3110 TCCA-GGTTGACATCGATCCATTAAT--CAACACCTTTTGGGTATAGTCG 3064 chr6qtel1M 706304 TTTACTCAGATTCTAAGTCACCTAACTTTATTATCACCCCATTCATAATT 706353 i vi v v v vi v i i viii - C L3#LINE/CR1 3063 TTCAACCAGCTACGAATCCACCTAACTGTACTATCATCCAGCCCAT-ATT 3015 chr6qtel1M 706354 TCTGAAACTTGCAACTCTATATGGGTTCTCATAAGTGAATGTG 706396 vv v ---- i i -i v v i v v v C L3#LINE/CR1 3014 TCTCCATCTTG----TCCACA-AGGATATCATGAGAGACTTTG 2977 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 49.43 CpG sites = 129, Kimura (unadjusted) = 52.14 Transitions / transversions = 1.33 (129/97) Gap_init rate = 0.08 (51 / 651), avg. gap size = 1.41 (72 / 51) 204 35.10 0.00 8.93 chr6qtel1M 706836 706957 (293043) MIRb#SINE/MIR 4 115 (153) m_b317s601i1 13242 chr6qtel1M 706836 AGGGACAACTAAATGAGTCAGTAGTTAGAGAACTGGCCCTCAAAACAGGA 706885 i i ---i ivv i vv v v ii vi iv iv MIRb#SINE/MIR 4 AGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGAC 50 chr6qtel1M 706886 GAACATGAGGTGAAATCTAACCTCAGACACTTAACATTTACTAGCTGAGT 706935 ii v i v vi iviv v v ------- v MIRb#SINE/MIR 51 AGACCTGGGTTCGAATCCCGGCTCTGCCACTTA-------CTAGCTGTGT 93 chr6qtel1M 706936 GGCATTGGTCAGGTCACTTGAC 706957 i v v i i i MIRb#SINE/MIR 94 GACCTTGGGCAAGTTACTTAAC 115 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 42.92 CpG sites = 20, Kimura (unadjusted) = 47.77 Transitions / transversions = 1.05 (20/19) Gap_init rate = 0.08 (10 / 121), avg. gap size = 1.00 (10 / 10) 258 31.10 0.00 7.22 chr6qtel1M 706854 706957 (293043) MIRc#SINE/MIR 16 112 (156) m_b317s601i2 13242 chr6qtel1M 706854 CAGTAGTTAGAGAACTGGCCCTCAAAACAGGAGAACATGAGGTGAAATCT 706903 i vv v v i vi iv ii v i v vi i i MIRc#SINE/MIR 16 CAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCC 65 chr6qtel1M 706904 AACCTCAGACACTTAACATTTACTAGCTGAGTGGCATTGGTCAGGTCACT 706953 viv v v ------- v i v v i MIRc#SINE/MIR 66 CGGCTCTGCCACTTA-------CTAGCTGTGTGACCTTGGGCAAGTCACT 108 chr6qtel1M 706954 TGAC 706957 i MIRc#SINE/MIR 109 TAAC 112 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 36.94 CpG sites = 14, Kimura (unadjusted) = 40.23 Transitions / transversions = 0.88 (14/16) Gap_init rate = 0.07 (7 / 103), avg. gap size = 1.00 (7 / 7) 311 29.44 16.91 2.58 chr6qtel1M 707395 707530 (292470) MIRc#SINE/MIR 4 158 (110) m_b317s601i3 13243 chr6qtel1M 707395 GGCAGCTAGGTAGTGTGGTAGATAGAGCATTAGGTCCGGAGTTAGGAAGA 707444 i--- i ii i v i i iiii i MIRc#SINE/MIR 4 GGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA 50 chr6qtel1M 707445 GTAGCATTCAAATCCAGAT------ATTT--------------TTT---T 707471 viv vi i i v ii------ i --------------i ---i MIRc#SINE/MIR 51 CCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGC 100 chr6qtel1M 707472 AAGTCACTTTACTTATTTTTTACCTCAGTATCTTCAAATGTAAAATGGAG 707521 v i -i i vvi v i vv i MIRc#SINE/MIR 101 AAGTCACTTAACCT-CTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGG 149 chr6qtel1M 707522 ATGATAATA 707530 i MIRc#SINE/MIR 150 ATAATAATA 158 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 38.61 CpG sites = 28, Kimura (unadjusted) = 39.98 Transitions / transversions = 2.55 (28/11) Gap_init rate = 0.05 (7 / 135), avg. gap size = 3.86 (27 / 7) 40 15.96 6.78 2.44 chr6qtel1M 707538 707655 (292345) (TATAA)n#Simple_repeat 1 123 (0) m_b317s252i2 13244 chr6qtel1M 707538 TATAA-ATAGTAT-A-ATCATATAATATAGTATAA-GTAGTATAAAATAG 707583 - i - - v i -i i v i (TATAA)n#Simp 1 TATAATATAATATAATATAATATAATATAATATAATATAATATAATATAA 50 chr6qtel1M 707584 TATAGTATAA-AAAGTATAAATTTAGTATAAAATAATAT-ATAGTATATA 707631 i - v i - v i v - - - (TATAA)n#Simp 51 TATAATATAATATAATAT-AATATAATATAATATAATATAATA-TA-ATA 97 chr6qtel1M 707632 TAATATAAAATAGCATAA-A-AATAT 707655 v ii - - (TATAA)n#Simp 98 TAATATAATATAATATAATATAATAT 123 Matrix = Unknown Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.09 (11 / 117), avg. gap size = 1.00 (11 / 11) 18 0.00 0.00 0.00 chr6qtel1M 711350 711369 (288631) (T)n#Simple_repeat 1 20 (0) m_b317s252i3 13245 chr6qtel1M 711350 TTTTTTTTTTTTTTTTTTTT 711369 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTT 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 519 20.85 0.00 6.60 chr6qtel1M 711382 711494 (288506) C MIRc#SINE/MIR (153) 115 10 m_b317s601i4 13246 chr6qtel1M 711382 GGGGTTAAGTGATTTGCCTAGGATTACACAGCTAGGAAGTGTTAAGTGTC 711431 i i i i i i ------- v C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGC 73 chr6qtel1M 711432 TGAGGTCAGATTTGAACTCAGGTCCTCCTGACTTCATGGCTGGTGCTCTA 711481 v vivi i i i i i v v ii v C MIRc#SINE/MIR 72 AGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTT 23 chr6qtel1M 711482 TCCACTGCACCAC 711494 C MIRc#SINE/MIR 22 TCCACTGCACCAC 10 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 22.46 CpG sites = 15, Kimura (unadjusted) = 25.01 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.06 (7 / 112), avg. gap size = 1.00 (7 / 7) 311 31.64 8.26 0.77 chr6qtel1M 711740 711860 (288140) C L2a_3end#LINE/L2 (11) 506 377 m_b317s601i5 13247 chr6qtel1M 711740 CAATAAGTATTTACTAAAG----ATTATGTGTTAGACATTAA-GTAAATG 711784 i i i i iv---- i ii i i iv-v iii C L2a_3end#LINE 506 CAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGCG 457 chr6qtel1M 711785 GTAGAGATACA--AATATATGAAAAAATTAAAAGTCTCTGCCTTCA---A 711829 v i i -- i iv ii v ivi i i --- C L2a_3end#LINE 456 CTGGGGATACAGCAGTGAACAAAACAGACAAAAGTCCCTGCCCTCATGGA 407 chr6qtel1M 711830 GATTATATTCTAATGAGGGAAAACCACACAA 711860 v i i i i i - v C L2a_3end#LINE 406 GCTTACATTCTAGTGGGGGGAGA-CAGACAA 377 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 43.25 CpG sites = 29, Kimura (unadjusted) = 44.92 Transitions / transversions = 3.22 (29/9) Gap_init rate = 0.04 (5 / 120), avg. gap size = 2.20 (11 / 5) 375 28.28 2.06 1.54 chr6qtel1M 712304 712497 (287503) L1M5_orf2#LINE/L1 3100 3294 (0) m_b317s551i1 13248 chr6qtel1M 712304 ATAAACTGGGAAAATATTTTTACAAT-CAAAAGTTCTATAAAGGCCTCAT 712352 i i ? i v v i ?- v vi iiv i v i L1M5_orf2#LIN 3100 ACAGANTGGGAGAAAATATTTGCAANACATATATCTGACAAAGGACTCGT 3149 chr6qtel1M 712353 TTCCAAAATATATAGAGAATTGACTCTAATTTA-TAAGAAATCGAGCCAT 712401 v i i i v- vi ? i - ? --i v v L1M5_orf2#LIN 3150 ATCCAGAATATATAAAGAACTC-CTACAANTCAATAANAAA--AAGACAA 3196 chr6qtel1M 712402 TC--CTCAATTGATAAATGGTCAAAGGATATGAACAGACAATTCTCAGAT 712449 v -- i v? v v i iv v v i v L1M5_orf2#LIN 3197 ACAACCCAATANAAAAATGGGCAAAAGACTTGAACAGACACTTCACAAAA 3246 chr6qtel1M 712450 GAAGAAATTAAAACTATTTCTAGCGATATAAAAAGATGCTCCAAGTCA 712497 v ?v iviiivv ivv i i v v? L1M5_orf2#LIN 3247 GAAGATATNCAAATGGCCAATAAGCACATGAAAAGATGCTCAACNTCA 3294 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.74 CpG sites = 26, Kimura (unadjusted) = 37.60 Transitions / transversions = 0.93 (26/28) Gap_init rate = 0.03 (6 / 193), avg. gap size = 1.17 (7 / 6) 394 27.63 2.58 1.92 chr6qtel1M 712304 712458 (287542) L1P3_orf2#LINE/L1 3100 3255 (39) m_b317s551i0 13248 chr6qtel1M 712304 ATAAACTGGGAAAATATTTTTACAATCAAAAGTTCT-ATAAAGGCCTCAT 712352 i i v i v i v vvvv - i v v L1P3_orf2#LIN 3100 ACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAAAGGGCTAAT 3149 chr6qtel1M 712353 TTCCAAAATATATAGAGAATTGACTCTAATTTATAAGAAAT---CGAGCC 712399 v i v i ii i v vv v i v--- i i v L1P3_orf2#LIN 3150 ATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAAAAAACAAACA 3199 chr6qtel1M 712400 ATTCCTCAATTGATAAATGGTCAAAGGATATGAACAGACAATTCTCAGAT 712449 ii --- ii v i v i v i v L1P3_orf2#LIN 3200 ACCCC---ATCAAAAAGTGGGCGAAGGATATGAACAGACACTTCTCAAAA 3246 chr6qtel1M 712450 GAAGAAATT 712458 v L1P3_orf2#LIN 3247 GAAGACATT 3255 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 33.76 CpG sites = 20, Kimura (unadjusted) = 34.75 Transitions / transversions = 0.91 (20/22) Gap_init rate = 0.03 (5 / 154), avg. gap size = 1.40 (7 / 5) 1072 25.49 1.61 1.61 chr6qtel1M 712354 712664 (287336) L1ME5_3end#LINE/L1 7 317 (624) m_b317s551i2 13248 chr6qtel1M 712354 TCCAAAATATATAGAGAATTGACTCTAATTTATAAGAAATCGA--GCCAT 712401 i i i ii i vviv v iv i vv -- ?v - L1ME5_3end#LI 7 TCTAGAATATACAAGGAACTCCTGCAAATCAACAAGAAAAAGACGGNAA- 55 chr6qtel1M 712402 TCCTCAATTGATAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGA 712451 - i v v v i iv v L1ME5_3end#LI 56 -CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGA 104 chr6qtel1M 712452 AGAAATT---AAAACTATTTCTAGCGATATAAAAAGATGCTCCAAGTCAT 712498 i ii--- ii --v v - i i v v L1ME5_3end#LI 105 GGAAACCCGAAAGGCTA--ACAAGC-ATATGAAGAGATGCTCAAACTCAT 151 chr6qtel1M 712499 TATTAATCAGAGAAATGCAAATTAAGACAACTCTGAGATACCACTACACA 712548 v i vv i vi L1ME5_3end#LI 152 TAGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACA 201 chr6qtel1M 712549 CCTGTCAGATTGGCTAGAATGACAGGGAAAGATAATGCGAAATGTTGGAG 712598 i i i v i v v ii vvi v i v L1ME5_3end#LI 202 CCTATTAGACTGGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTGGCG 251 chr6qtel1M 712599 GGGATGTGGGAAAACAGGGACATTGATACATTGTTGGTGAAATTGTGAAT 712648 i i ? i i vi v i i i ii v ii i L1ME5_3end#LI 252 AGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGAC 301 chr6qtel1M 712649 ACATCCAGCCATTCTG 712664 vvi v L1ME5_3end#LI 302 TGGTGCAGCCATTCTG 317 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 31.98 CpG sites = 44, Kimura (unadjusted) = 31.98 Transitions / transversions = 1.29 (44/34) Gap_init rate = 0.02 (7 / 310), avg. gap size = 1.43 (10 / 7) 276 30.97 5.08 3.33 chr6qtel1M 712675 712851 (287149) L1P3_orf2#LINE/L1 3108 3287 (7) m_b317s551i3 13249 chr6qtel1M 712675 GGAAAATATTTTTACATTCAAAGGTTCTGATAAAGGCCTCATTTCTAAAA 712724 i v i v v vvvv i v v v i i L1P3_orf2#LIN 3108 GGAGAAAATTTTTGCAATCTATCCATCTGACAAAGGGCTAATATCCAGAA 3157 chr6qtel1M 712725 TATATAATTGACC----CAAATTTATAAGAATT---CAAGCCATTC--TC 712765 v i vvi i---- i vv--- i v ii -- L1P3_orf2#LIN 3158 TCTACAAGGAACTTAAACAAATTTACAAGAAAAAAACAAACAACCCCATC 3207 chr6qtel1M 712766 AAAATTGATAAATGGTCAAAGGATAGGAACAGGCAATTTTCAGATGAATA 712815 ------ i v i v i v i i v v L1P3_orf2#LIN 3208 AAAA------AGTGGGCGAAGGATATGAACAGACACTTCTCAAAAGAAGA 3251 chr6qtel1M 712816 AATTGAAACTATTTCTAGCCATATGAAAAGATGCTC 712851 v v vi viiivvi iv i v L1P3_orf2#LIN 3252 CATTTATGCGGCCAACAAACATATGAAAAAAAGCTC 3287 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 39.33 CpG sites = 24, Kimura (unadjusted) = 40.28 Transitions / transversions = 0.83 (24/29) Gap_init rate = 0.05 (9 / 176), avg. gap size = 1.67 (15 / 9) 767 32.44 4.64 4.31 chr6qtel1M 712718 713342 (286658) L1MC3_3end#LINE/L1 7 633 (1899) m_b317s551i5 13249 chr6qtel1M 712718 TCTAAAATATATAATTGACCC---AAATTTA----TAAGAATTCAAGCCA 712760 i i vvi i --- i i ---- vv i v L1MC3_3end#LI 7 TCCAAAATATACAAAGAACTCTTAAAACTCAACAATAAGAAAACAAACAA 56 chr6qtel1M 712761 TTCTCAAAATTGATAAATGGTCAAAGGATAGGAACAGGCAATTTTC---- 712806 ii ---- i v v i vv i vi iv ---- L1MC3_3end#LI 57 CCC----AATTAAAAAATGGGCAAAAGATCTGAACAGACACCTCACCAAA 102 chr6qtel1M 712807 --AGATGAATAAATTGAAACTATTTCTAGCCATATGAAAAGATGCTCCAA 712854 -- iv i i v v v ----- - v v L1MC3_3end#LI 103 GAAGATATACAGATGGCAAATA-----AGC-ATATGAAAAGATGCTCAAC 146 chr6qtel1M 712855 GTCATTATTAACCAGAGAAATGCAAATTAAGACAACTCTGAGATACCACT 712904 i vv v ii i v i vv L1MC3_3end#LI 147 ATCATTTGTCATTAGGGAATTGCAAATTAAAACAACAATGAGATACCACT 196 chr6qtel1M 712905 ACATACCTCTCAGGTTGGCTAAGATGACAGGAAAA--AATAATGATGAAT 712952 i v i iv i -- vii --i i ivii ? L1MC3_3end#LI 197 ACACACCTATTAGAATGGCTAAAAT--CCAAAAAACTGACAATACCAANT 244 chr6qtel1M 712953 ATTAGAGAGGATGTGGGAAAAATGGGACATTAATACATTGTTGGTGGAAT 713002 ii i v i iiv vv i vi v v i i v L1MC3_3end#LI 245 GCTGGCGAGGATGCGGAGCAACAGGAACTCTCATTCATTGCTGGTGGGAA 294 chr6qtel1M 713003 TGTGAACAGATCCAACCATTCTGGAGGGCAATTTGGAACTATGCCCAAAG 713052 ii vv i v i i i i i i v v - v ii v i L1MC3_3end#LI 295 TGCAAAATGGTACAGCCACTTTGGAAGACAGTTTGGCAGT-TTCTTACAA 343 chr6qtel1M 713053 AGTTATCAAAC-TGTGCATATCCTTTCATCCAGCAATGTTTCTACTGGGC 713101 i --- - ivv v i v viv vviv v i i L1MC3_3end#LI 344 AGCT---AAACATAGTCTTACCATACGATCCAGCAATCGCGCTCCTAGGT 390 chr6qtel1M 713102 TAATATCACAAAGAGATCTTAAA------GGAGGGAAAGGGACCTGTATG 713145 -- v vv v vv i v ------ vvviv v iii i -- L1MC3_3end#LI 391 --ATTTACCCAACTGATTTGAAAACTTATGTCCACACAAAAACCTGCA-- 436 chr6qtel1M 713146 TGCACAAATGTTTGTGGCAGCCCTTTTTGTAGTGGCCAGAAACTGGAAAC 713195 -- i i i i ii v ii i v i i L1MC3_3end#LI 437 --CGCGAATGTTTATAGCAGCTTTATTCATAATCGCCAAAAACTGGAAGC 484 chr6qtel1M 713196 TGAGTGGATGCCCATGAATTGGAGAATGGCTGAATAAATTAAAGTACACG 713245 vivvvi i v v v v v i i i ivi iv L1MC3_3end#LI 485 AACCAAGATGTCCTTCAATAGGTGAATGGATAAACAAACTGTGGTACATC 534 chr6qtel1M 713246 AATGTTATAACATATTATTGTTCTGT---AAGAAATGA-CCAGCAGG--A 713289 v iiv iiv vvv vi --- - i v i -- L1MC3_3end#LI 535 CATACAATGGAATATTATTCAGCGATAAAAAGAAATGAGCTATCAAGCCA 584 chr6qtel1M 713290 TGATTTCAGAGTCCTGAA-GAGACTTACATGAACTGATGCTAAATGAAAT 713338 i ---- i v v i - iv v v - iv i v L1MC3_3end#LI 585 CGA----AAAGACATGGATGAATCTTAAATGCA-TATTGCTAAGTGAAAG 629 chr6qtel1M 713339 GAGC 713342 i L1MC3_3end#LI 630 AAGC 633 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 41.69 CpG sites = 102, Kimura (unadjusted) = 43.45 Transitions / transversions = 1.11 (102/92) Gap_init rate = 0.06 (38 / 624), avg. gap size = 1.47 (56 / 38) 1325 30.23 1.10 1.85 chr6qtel1M 712718 713263 (286737) L1ME3G_3end#LINE/L1 7 548 (376) m_b317s551i4 13249 chr6qtel1M 712718 TCTAAAATATATAATTGACCC----AAATTTATAAGAATTCAAGCCATTC 712763 i i vvi i ---- iv --v v vi L1ME3G_3end#L 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAA--AAAGACAACC 54 chr6qtel1M 712764 TCAAAATTGATAAATGGTCAAAGGATAGGAACAGGCAATTTTCAGATGAA 712813 i--- v v v v iv v i L1ME3G_3end#L 55 C---AATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAG 101 chr6qtel1M 712814 TAAATTGAAACTATTTCTAGCCATATGAAAAGATGCTCCAAGTCATTATT 712863 v vv iviiivv iv v vv i v L1ME3G_3end#L 102 GAAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGT 151 chr6qtel1M 712864 AACCAGAGAAATGCAAATTAAGACAACTCTGAGATACCACTACATACCTC 712913 i i i vv i vivi iv L1ME3G_3end#L 152 AATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCA 201 chr6qtel1M 712914 TCAGGTTGGCTAAGATGACAGGAAAAAATAATGATGAATATTAGAGAGGA 712963 i v i vvv iii?vvi ivi? i i i v i L1ME3G_3end#L 202 TCAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGG 251 chr6qtel1M 712964 TGTGGGAAAAATGGGACATTAATACATTGTTGGTGGAATTGTGAACAGAT 713013 i vv v vi v i i i v i iv i L1ME3G_3end#L 252 TGTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGT 301 chr6qtel1M 713014 CCAACCATTCTGGAGGGCAATTTGGAACTATGCCCAAAGAGTTATCAAAC 713063 v i ? i v v viviv i v --- v L1ME3G_3end#L 302 ACAGCCNTTTTGGAGGGCAATTTGGCAGTATCTATTAAAATTT---AAAA 348 chr6qtel1M 713064 TGTGCATATCCTTTCATCCAGCAATGTTTCTACTGGGCTAATATCACAAA 713113 i i v i viiv v ? ?vvv vi ? L1ME3G_3end#L 349 TGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANA 398 chr6qtel1M 713114 GAGAT-CTTAAAGGAG-GGAAAGGGACCTGTATGTGCACAAATGTTTGTG 713161 i - iiv viv - v v i --? i i vii ii v L1ME3G_3end#L 399 GAAATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTCATT 446 chr6qtel1M 713162 GCAGCCCTTTTTGTAGTGGCCAGAAACTGGAAACTGAGTGGATGCCCATG 713211 vi v i i v i i vivv ii i v L1ME3G_3end#L 447 GCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATC 496 chr6qtel1M 713212 AATTGGAGAATGGCTGAATAAATTAAAGTACACGAATGTTATAACATATT 713261 v i i i vi i ivv ii iiv i L1ME3G_3end#L 497 AATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACT 546 chr6qtel1M 713262 AT 713263 L1ME3G_3end#L 547 AT 548 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 39.35 CpG sites = 84, Kimura (unadjusted) = 40.01 Transitions / transversions = 1.08 (84/78) Gap_init rate = 0.02 (13 / 545), avg. gap size = 1.23 (16 / 13) 15 25.03 1.33 7.04 chr6qtel1M 713522 713596 (286404) (TTTTG)n#Simple_repeat 1 71 (0) m_b317s252i4 13250 chr6qtel1M 713522 TTTTGTTGTTCTTTGCTTGCATTTTGTTTTGCTTCTCTCTCTTTGTTTT- 713570 - v vv vii - - - v - - (TTTTG)n#Simp 1 TTTTGTT-TTGTTTTGTTTTGTTTTGTTTTG-TT-T-TGT-TTTGTTTTG 45 chr6qtel1M 713571 TACTGGTTTGATTTGATTTTTCTTGT 713596 vi v v v v i (TTTTG)n#Simp 46 TTTTGTTTTGTTTTGTTTTGTTTTGT 71 Matrix = Unknown Transitions / transversions = 0.40 (4/10) Gap_init rate = 0.08 (6 / 74), avg. gap size = 1.00 (6 / 6) 250 30.30 6.06 0.00 chr6qtel1M 714185 714283 (285717) C MIR#SINE/MIR (61) 201 97 m_b317s601i6 13251 chr6qtel1M 714185 ATCTATTATCTCATTTGATCCTT-CAAGAATTCAGGGAAGTAAGTGTTAT 714233 v v i i- v ii viv i i ii C MIR#SINE/MIR 201 ATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGGTAGGTACTAT 152 chr6qtel1M 714234 TA----CCAAAGTTCACAATTCAGGAAACTGAAAGAAATAG-TGTTACGT 714278 ---- vv v i iv v iiv v v -v v C MIR#SINE/MIR 151 TATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGT 102 chr6qtel1M 714279 GACCT 714283 i i C MIR#SINE/MIR 101 AACTT 97 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 39.33 CpG sites = 15, Kimura (unadjusted) = 39.33 Transitions / transversions = 1.00 (15/15) Gap_init rate = 0.03 (3 / 98), avg. gap size = 2.00 (6 / 3) 300 24.68 2.60 0.00 chr6qtel1M 714185 714261 (285739) C MIRb#SINE/MIR (63) 205 127 m_b317s601i7 13251 chr6qtel1M 714185 ATCTATTATCTCATTTGATCCTT-CAAGAATTCAGGGAAGTAAGTGTTAT 714233 vi i i- v ii v v i i i C MIRb#SINE/MIR 205 ATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTAT 156 chr6qtel1M 714234 TA-CCAAAGTTCACAATTCAGGAAACTGA 714261 - vv v i iv v C MIRb#SINE/MIR 155 TATCCCCATTTTACAGATGAGGAAACTGA 127 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 30.29 CpG sites = 10, Kimura (unadjusted) = 30.29 Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.03 (2 / 76), avg. gap size = 1.00 (2 / 2) 410 36.47 8.24 4.74 chr6qtel1M 715498 715946 (284054) L2c_3end#LINE/L2 8 471 (7) m_b317s601i8 13252 chr6qtel1M 715498 ATTGGACCCCTTTTTTCTCCTCTA-TCACATTTCCAGTAATTGTACACCT 715546 iv i vii v ii i -i v i -------- v ii L2c_3end#LINE 8 ATCTGGCCCCTGCCTACCTCTCCAGCCTCATCTCC--------TCCACTC 49 chr6qtel1M 715547 TTCTCCCTGCCATACCTTAAATTTAGTGACACTGGGTTCCTTACCATTCC 715596 ii ii -i iv iv- ii iv iii ? i - L2c_3end#LINE 50 CCCTCCTCGCC-CACTATGC-TCCAGCCACACTGAACTNCTTGC-ATTCC 96 chr6qtel1M 715597 ACAGACAAGATGC--TTCATCTATGAACTTCAAATAGGTTCTCTGATTGT 715644 v i v vi -- v iiv v- i i?iivvv v v vvii L2c_3end#LINE 97 CCAAACACGCCGCAGTTCTTTCCTGC-CTCCGNGCCTTTGCACATGCTGT 145 chr6qtel1M 715645 CCCCCCAGCATTAAATATTCTTCTCCCATATCCCTGCCATCTGGCT---C 715691 i i v v vi ii i v --- v i ---i L2c_3end#LINE 146 TCCCTCTGCCTGGAATGCTCTTCCCCCCT---CCTTCCACCTGGCTAACT 192 chr6qtel1M 715692 CCCAGTT-TTCTTTAGGATTCAACTAAAATTCTATCTTTTACAAGAAAC- 715739 i v i- i i i ?i i v i vii i ii v ii i - L2c_3end#LINE 193 CCTACTCATCCTTCAAGNCTCAGCTCAGATGTCACCTCCTCCGGGAAGCC 242 chr6qtel1M 715740 -------ATCTTCCAAATTT-TTTTAA------TCCTATTGGTTTTC--- 715772 ------- i ii i?i -v i i------ v vv i ii --- L2c_3end#LINE 243 TTCCCTGACCCCCCAAGNCTAGTCTAGGTGCCCTCCTCTGTGCTCCCATA 292 chr6qtel1M 715773 ---CTCTAT-TAT-TTCCTGTTAGTG-ACGTATA--TAGTTTGT-TTGTA 715813 --- i i - -i ii vv - v v-- ii - L2c_3end#LINE 293 GCACCCTGTCTATACTCCCATTATAGCACTTATCATTAACTTGTATTGTA 342 chr6qtel1M 715814 TATATTAGTTTTCTT-TTTGTCTCTCCCACCATCACCACTGCGAGTTCCT 715862 vv i iv v ? - i ii i ----v i i L2c_3end#LINE 343 ATTGTCTGTTTACNTGTCTGTCTCCTCCACTA----GACTGTGAGCTCCT 388 chr6qtel1M 715863 TGAGGGTAGAAACTGCTTTTTGCCAGTTTTTGCATACTCAACACTTAG-- 715910 i ii i iv i iiivi i i v i i i i i -- L2c_3end#LINE 389 TGAGGGCAGGGACCGTGTCTTATTCATCTTTGTATCCCCAGCGCCTGGCA 438 chr6qtel1M 715911 CATAGTGCCTGTTAATTAATAAATATTTATTGACTG 715946 ivvi i--- i i i v L2c_3end#LINE 439 CATAGTAGGCGC---TCAATAAATGTTTGTTGAATG 471 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 51.60 CpG sites = 107, Kimura (unadjusted) = 55.41 Transitions / transversions = 2.18 (107/49) Gap_init rate = 0.08 (38 / 448), avg. gap size = 1.55 (59 / 38) 400 35.94 1.30 0.65 chr6qtel1M 716029 716182 (283818) MIR1_Amn#SINE/MIR 20 174 (56) m_b317s601i9 13253 chr6qtel1M 716029 AGTGTATAAAATGTTTGGATGGGAATCCAGAAGATATGAGTTCAAATTTA 716078 v i iiii - iv i ii i i iv i ? ? iiv MIR1_Amn#SINE 20 AGTGGATAGAGCACT-GGACTGGGACTCGGGAGACCTGGGTTCNANTCCC 68 chr6qtel1M 716079 GCCTTAGGCATTTATAATCTCTATGATTCTGGACAAATTA--TAATCTCT 716126 v iv v i ?iiv?v v?i iii i i i -- ? i MIR1_Amn#SINE 69 GGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGTCACTTNACCTCT 118 chr6qtel1M 716127 ATTTAGCTCACTTTTCTCAGCAGTAAATTGGGGATAACAACATTACCTTA 716176 v v?iv v i v v v ii i i iv i v MIR1_Amn#SINE 119 CTGNGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATGATACTGACCTC 168 chr6qtel1M 716177 CCTTGT 716182 i MIR1_Amn#SINE 169 CTTTGT 174 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 54.74 CpG sites = 36, Kimura (unadjusted) = 56.35 Transitions / transversions = 1.89 (36/19) Gap_init rate = 0.01 (2 / 153), avg. gap size = 1.50 (3 / 2) 550 30.80 3.24 2.29 chr6qtel1M 716051 716266 (283734) MIR#SINE/MIR 35 252 (10) m_b317s601i10 13253 chr6qtel1M 716051 GAATCCAGAAGATATGAGTTCAAATTTAGCCTTAGGCATTTATAATCTCT 716100 i v vviiv i i iiv v iv v i iv v v MIR#SINE/MIR 35 GGAGCCAGACTGCCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGT 84 chr6qtel1M 716101 ATGATTCTGGACAAATTA--TAATCTCTATTTAGCTCACTTTTCTCAGCA 716148 i iii i i -- i v v iv v i v v MIR#SINE/MIR 85 GTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCT 134 chr6qtel1M 716149 GTAAATTGGGGATAACAACATTACCTTACCTTGTGGTGAGGGTTG-TGTT 716197 v i i v - ii ---- - v MIR#SINE/MIR 135 GTAAAATGGGGATAATAATAGTACC-TACCTCAT----AGGGTTGTTGTG 179 chr6qtel1M 716198 AGGATAGAGTGA---AATATTTATAAA-TACATAACAAAGTTCCTGTAAC 716243 vi i --- iv i -ii v iv v v vv MIR#SINE/MIR 180 AGGATTAAATGAGTTAATACATGTAAAGCGCTTAGAACAGTGCCTGGCAC 229 chr6qtel1M 716244 ATCGTGGGCTCTATAAAAATGTT 716266 v ii v vv v MIR#SINE/MIR 230 ATAGTAAGCGCTCAATAAATGTT 252 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 38.52 CpG sites = 32, Kimura (unadjusted) = 40.16 Transitions / transversions = 0.97 (32/33) Gap_init rate = 0.04 (9 / 215), avg. gap size = 1.33 (12 / 9) 839 36.85 6.47 2.11 chr6qtel1M 716582 717446 (282554) L2#LINE/L2 1260 2161 (921) m_b317s601i11 13254 chr6qtel1M 716582 TACACAGATGCTGCTGAATAAAAGTAGAGGAAATCATGTAACTGTTCTGC 716631 i vvi? v iiviiv i i v iii ii v v L2#LINE/L2 1260 TGCACCCGNGCAGCTGAACGTGGCTGGAGAAAAACACACAACCATGCTGA 1309 chr6qtel1M 716632 CTAGCCCCATTAAAATTTTATTTAACA-GAACCTCCACTAGGCACTCACA 716680 i i i i vv v i v- v -? v v i v i - L2#LINE/L2 1310 CTGGTCTCACTTTAAATTCATG-ACCACNAACCTCAAGTGGGCCCTTA-A 1357 chr6qtel1M 716681 T-CTGTTAGGTAATCTTA-TAC--TTCTCTTATCAACTAACTCACTCACT 716726 - iiv i ? - -- i vi v i v v i L2#LINE/L2 1358 TGCTGCCCGGCAATCNTACTACATTTCCCTAGTCCATTCACTCTCCCACT 1407 chr6qtel1M 716727 CTTTCATATTGCTTTTCCAA------TCCTATTTGA-CAA---TC--ACA 716764 iii v ivi v i v------ v i vv- --- -- L2#LINE/L2 1408 CTCCTAGACGACTATTTCACACCTTCTCCTCTCTCCTCAAACCTCCAACA 1457 chr6qtel1M 716765 TAATCTATCATG-GCTCCCTCTCATTTGAGAGCCTTGATTCATATAGTAC 716813 ivvi vi v i-v v vi vii v v vvi L2#LINE/L2 1458 CCTCCTCCCCTATCCTCACTCTCAGCTGATGACCTTGCTTCCTATTTCAC 1507 chr6qtel1M 716814 AGAAAAAAAATTGAGGTCGCTTAACATGAACTCCTTCTTGTCCCCTCTTC 716863 v i v -- i iviiivi viv i iv v??ii v iv L2#LINE/L2 1508 TGAGAAAATA--GAAGCAATCAGAAGAGAACTTCCACANNCTCCCACCAC 1555 chr6qtel1M 716864 CCTATCTTATATCACTCAAATGTCAGCTGT-------TACTGTGCCTTCT 716906 vi - i-i ii vv - v ------- v i L2#LINE/L2 1556 CACATCT-AC-CCACCTACCTG-CATCTGTGCCCACATACTCTGCCTTCC 1602 chr6qtel1M 716907 TTCAATCCTACCTCACTTATTGAA--GTCT-TACTCCTTATTAGGGGACA 716953 i v- vi i-- vv - -- i- i - ivii v L2#LINE/L2 1603 CTCC-TGTTACT--ACGGAT-GAACTGTCCGTGCTCCT-ATCTAAGGCCA 1647 chr6qtel1M 716954 AACC-TCTACTTAAAGAAACGATCCCATTCCATTCCATCTCCTCCAACAG 717002 v - i iviv vvv i v ii ii v v iv v L2#LINE/L2 1648 ACCCCTCCACTTGTGCACTAGATCCCATCCCCTCTCGCCTACTCAAGGAC 1697 chr6qtel1M 717003 ATTTCTCCCTCAGTGATTCCCACTTTACCATATATTTTCAACTTTTCCTA 717052 iv vv i vv i v i vi v ii iv i iv L2#LINE/L2 1698 ATCGCTCCAGCAATTCTCCCCTCTCTCTCCTGCATCATCAATTTTTCCCT 1747 chr6qtel1M 717053 GTCTACTGGCTCCTTCTCTACTACCTACAAACATGCCCATGACT-CTTCC 717101 v v v i vv vi v i-i ? i - i L2#LINE/L2 1748 CTCTACTGGATCATTCCCATCAGCATACAAACATGCT-GTNATTTCTCCC 1796 chr6qtel1M 717102 AT-TCTAAGAAA-----ATCTGCTTTTGATCTCTTCTTCTCTGCTAACTA 717145 - i i ----- iiv ii i i vi? i i iv i i L2#LINE/L2 1797 ATCTTTAAAAAACAAAAATTCTCCCTTGACCCCACNTCCCCCTCCAGCTA 1846 chr6qtel1M 717146 TTGTCCTATAATTCTTCTATTCTTTGTTACTAAATACTGTAAAATGGGAC 717195 ii i i vvi v vii iivi v iv ivii - i vi L2#LINE/L2 1847 CCGCCCCATTTCTCTGCTCCCCTTTACAGCAAAACTCCTCGAAA-GAGTT 1895 chr6qtel1M 717196 ATCTACAATAGATCCTTTCACTTTATCTTCTCGAG--CTCTTTT-AATTT 717242 i i v v v vii i v iv i vvi-- i - iii L2#LINE/L2 1896 GTCTATACTCGCTGTCTCCAATTCCTCTCCTCCCATTCTCTCTTGAACCC 1945 chr6qtel1M 717243 -CTTTATATGTGACTTCTAGCCTTAGATCATTTCACTGGAACTTCTCCTT 717291 - ii - vv i iiiv ii --i i i i i v i v L2#LINE/L2 1946 ACTCCA-ATCAGGCTTTCGTCCCCA--CCACTCCACCGAAACTGCTCTTG 1992 chr6qtel1M 717292 TCAAAGTTATCAATGACCTCTGAATTATCAAATCCAATGGCC--TTTTTA 717339 i i i iivi iii i -- i i L2#LINE/L2 1993 TCAAGGTCACCAATGACCTCCACGTTGCTAAATCCAATGGTCAATTCTCA 2042 chr6qtel1M 717340 AT----------CTTGACTTCTTTGCAATTTTTGATATAGTTGCTCATAC 717379 i ---------- i ? iv iiv i i v iv L2#LINE/L2 2043 GTCCTCATCTTACTTGACCTNTCAGCAGCATTTGACACAGTTGATCACTC 2092 chr6qtel1M 717380 TCCCCT--TTGATAGTTCTTTCT--GTGTAGTTCTTCAGGAAACAATTAC 717425 i i -- - iiv --iiv i i - i v v ivvi L2#LINE/L2 2093 CCTCCTTCTTGA-AACACTTTCTTCACTTGGCT-TCCAGGACACCACACT 2140 chr6qtel1M 717426 CTCTTAGTGTTACACCTTCCT 717446 i i v v v v L2#LINE/L2 2141 CTCCTGGTTTTCCTCCTACCT 2161 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 50.98 CpG sites = 183, Kimura (unadjusted) = 53.86 Transitions / transversions = 1.42 (183/129) Gap_init rate = 0.05 (42 / 864), avg. gap size = 1.79 (75 / 42) 13 23.66 1.89 3.85 chr6qtel1M 718620 718672 (281328) (AAAAT)n#Simple_repeat 1 52 (0) m_b317s252i5 13255 chr6qtel1M 718620 AAAAGGAAATAGAA-CAAGGAGAATACTATAACAATCATAATAAAATAAA 718668 vi i -v iv i vv - - v (AAAAT)n#Simp 1 AAAATAAAATAAAATAAAATAAAATAAAATAA-AAT-AAAATAAAATAAA 48 chr6qtel1M 718669 ATAA 718672 (AAAAT)n#Simp 49 ATAA 52 Matrix = Unknown Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.06 (3 / 52), avg. gap size = 1.00 (3 / 3) 630 33.44 4.48 6.30 chr6qtel1M 719854 720434 (279566) L2#LINE/L2 1591 2161 (921) m_b317s601i12 13256 chr6qtel1M 719854 ACTATGTCTTCCTTCAACCTTATTTC-ACATATTGAACTTGTCT-TACTC 719901 v i i ----i i v - iv - - i- i L2#LINE/L2 1591 ACTCTGCCTTCCCTC----CTGTTACTACGGAT-GAACT-GTCCGTGCTC 1634 chr6qtel1M 719902 CTTATC--AGGATTCCA--TCCTCTACCTGAAGAAACAATCCCATTCCAT 719947 - -- --- --i i i viv vvvi i v L2#LINE/L2 1635 CT-ATCTAAGG---CCAACCCCTCCACTTGTGCACTAGATCCCATCCCCT 1680 chr6qtel1M 719948 CCTATCTCCTCCCACAGACTGATCTCTT-AATAGTTT----CACTTTATC 719992 iiii v -- vi -- v i- ii i i---- v i v L2#LINE/L2 1681 CTCGCCTACTC--AAGGAC--ATCGCTCCAGCAATTCTCCCCTCTCTCTC 1726 chr6qtel1M 719993 ATACATCTTCAACTTCTCTCAATTTGCTGTTTCCTTCTTTACAGCTTACA 720042 v i v i i i vv i i vv v iivv v L2#LINE/L2 1727 CTGCATCATCAATTTTTCCCTCTCTACTGGATCATTCCCATCAGCATACA 1776 chr6qtel1M 720043 AACATGCCCAAGTCTCCTCTATCTTCAAAAAAAAAACCCAAAAAACCCAA 720092 ivv?i i ii i i ------ vi i-- L2#LINE/L2 1777 AACATGCTGTNATTTCTCCCATCTTTAAAAAA------CAAAAATTCT-- 1818 chr6qtel1M 720093 CCCTGATTTGATCTTTTCTCCCCTGCTAACTCTGGTCTTATAATTCTTCT 720142 ---- i iivi? iv i i viv i ii -- - L2#LINE/L2 1819 CCCT----TGACCCCACNTCCCCCTCCAGCTACCGCCCCAT--TTCT-CT 1861 chr6qtel1M 720143 AAAACACTTTGTGACTAAATATCTTAAAATGAGCCATCTACAATAGATGT 720192 ivvv v iiii v ivi ii - iii i v v v L2#LINE/L2 1862 GCTCCCCTTTACAGCAAAACTCCTCGAAA-GAGTTGTCTATACTCGCTGT 1910 chr6qtel1M 720193 CTTCACTTTTTTTAA-------CTCTTTT-AATTC-CTTTATATCTGACT 720233 i v ii i vv------- i - ii - ii - v i L2#LINE/L2 1911 CTCCAATTCCTCTCCTCCCATTCTCTCTTGAACCCACTCCA-ATCAGGCT 1959 chr6qtel1M 720234 TTGAACCTTGTCATTCCACTGAAATGTCTCCTTCCAAAGTTACTAATGAT 720283 viv iiii i i ivv i vi i i i i L2#LINE/L2 1960 TTCGTCCCCACCACTCCACCGAAACTGCTCTTGTCAAGGTCACCAATGAC 2009 chr6qtel1M 720284 TTCTTAATTTCTTCAAATCCAGTGACCTATTCACAGTCCTCATTCTTATT 720333 i ivvi v -- i ii v v - i L2#LINE/L2 2010 CTCCACGTTGCT--AAATCCAATGGTCAATTCTCAGTCCTCAT-CTTACT 2056 chr6qtel1M 720334 T----TCTCTGCAATCTTTTATACAGTTGATCACACTCTTTCCTT-TCAT 720378 ---- ? v iiv v i -- ii - iiv L2#LINE/L2 2057 TGACCTNTCAGCAGCATTTGACACAGTTGAT--CACTCCCTCCTTCTTGA 2104 chr6qtel1M 720379 AGTTCTTTCTATGTAGGTCTTCCAAAA-ACAATTCCCTCTTGGTTTTAAT 720427 iiv viiivv v ii - v iv i i vv L2#LINE/L2 2105 AACACTTTCTTCACTTGGCTTCCAGGACACCACACTCTCCTGGTTTTCCT 2154 chr6qtel1M 720428 CTTCCCT 720434 i v L2#LINE/L2 2155 CCTACCT 2161 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 44.14 CpG sites = 114, Kimura (unadjusted) = 46.72 Transitions / transversions = 1.68 (114/68) Gap_init rate = 0.08 (48 / 580), avg. gap size = 1.29 (62 / 48) 242 25.45 0.00 0.00 chr6qtel1M 722281 722335 (277665) DNM1r#Unknown 2477 2531 (2131) m_b317s502i0 13257 chr6qtel1M 722281 CATATATACATATACATATATGTGTATATATGTATATGTGTGTGTGTGTG 722330 i i iii i i i i i i i i DNM1r#Unknown 2477 CGTGTATGTGTGTATATATGTGTGTATATGTGTGTATGTGTGTATATATG 2526 chr6qtel1M 722331 TGTGT 722335 i DNM1r#Unknown 2527 TGTAT 2531 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 32.35 CpG sites = 14, Kimura (unadjusted) = 35.57 Transitions / transversions = 1.00 (14/0) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 35 5.41 0.00 0.00 chr6qtel1M 722337 722375 (277625) (TA)n#Simple_repeat 1 39 (0) c_b317s251i0 13258 chr6qtel1M 722337 TATATATATATATATATATATATATATATGTATGTATAT 722375 i i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATAT 39 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 266 34.62 1.28 0.00 chr6qtel1M 722668 722745 (277255) MIRb#SINE/MIR 19 97 (171) m_b317s601i13 13259 chr6qtel1M 722668 CACTGAAAAGATCACTAATTTTGGAATCAGAGA-ACCGGGGCTCAAATTT 722716 v i v viii i v - v i i ii MIRb#SINE/MIR 19 CAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCGAATCC 68 chr6qtel1M 722717 GGATTTTGCTGTTTACTTTCCAAATGACC 722745 v ii i iii vv iivi MIRb#SINE/MIR 69 CGGCTCTGCCACTTACTAGCTGTGTGACC 97 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 46.91 CpG sites = 18, Kimura (unadjusted) = 49.57 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.01 (1 / 77), avg. gap size = 1.00 (1 / 1) 181 16.67 11.11 0.00 chr6qtel1M 723546 723599 (276401) C X6B_LINE#LINE/CR1 (548) 524 465 m_b317s601i14 13260 chr6qtel1M 723546 AATGGTAGTTTG-TATTTTCCAAATTAT---CTATTTCC--CTTAATTCA 723589 i v v i- v ---?i i -- ? C X6B_LINE#LINE 524 AATGGCATTATAATATTTTCCATATTATTCTNCATTCCCTTCTTAATNCA 475 chr6qtel1M 723590 GCTTAAGATC 723599 i v C X6B_LINE#LINE 474 GCCTAACATC 465 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 19.86 CpG sites = 5, Kimura (unadjusted) = 19.86 Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.06 (3 / 53), avg. gap size = 2.00 (6 / 3) 250 30.69 4.88 1.98 chr6qtel1M 727056 727301 (272699) C L1M1_orf2#LINE/L1 (1011) 2283 2031 m_b317s551i6 13261 chr6qtel1M 727056 TATTTTAAATAGCTTTCTATTACTGTCTCCTCTTGTAGA--GTTTGCCAG 727103 v i vv viv vi vi i i vi -- ii iiv C L1M1_orf2#LIN 2283 TATTGTAAATGGGATTACTTTTTTGATTTCTTTTTCAGATTGTTCACTGT 2234 chr6qtel1M 727104 TGATATATAGAA---CTA-TGGTTAGTTTATATGCTTTTATTTTATATCC 727149 ii --- - i -- i -- v i C L1M1_orf2#LIN 2233 TGGCATATAGAAATGCTACTGATT--TTTGTATG--TTGATTTTGTATCC 2188 chr6qtel1M 727150 TACTACTTTGCTAAAATTA-TTAACTGCTTAGAGAGATTATTAATTGTAT 727198 i v i i v i- v v i ivi v v v ?i v vi C L1M1_orf2#LIN 2187 TGCAACTTTACTGAATTTGTTTATCAGTTCTAATAGTTTTTTNGTGGAGT 2138 chr6qtel1M 727199 CTCAAAGATTATCCAAGTATATTAGCATGTCATTTG-AAAAAAAGATCAT 727247 iv i v v i vv v i i - v i v C L1M1_orf2#LIN 2137 CTTTAGGTTTTTCCAAATATAAGATCATATCATCTGCAAACAAGGATAAT 2088 chr6qtel1M 727248 TTT-CTTATCCTATTGCCCATTCTGATTCCTTCAAT---TTTTTCTTCTC 727293 v- v i i- v v iv v i iv --- i v C L1M1_orf2#LIN 2087 TTGACTTCTTCC-TTTCCAATTTGGATGCCCTTTATTTCTTTCTCTTGTC 2039 chr6qtel1M 727294 TTATTGCT 727301 v C L1M1_orf2#LIN 2038 TGATTGCT 2031 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 40.26 CpG sites = 37, Kimura (unadjusted) = 40.26 Transitions / transversions = 1.00 (37/37) Gap_init rate = 0.05 (12 / 245), avg. gap size = 1.42 (17 / 12) 299 32.15 3.43 2.43 chr6qtel1M 727097 727300 (272700) C L1MD_orf2#LINE/L1 (1057) 2237 2032 m_b317s551i7 13261 chr6qtel1M 727097 TTGCCAGTGATATATAGAACTATGGTTAGTTTATATGCTTTTATTTTATA 727146 i --- v iii ii v i iiv ? i i C L1MD_orf2#LIN 2237 TTGCTAGT---ATATAGAAATACAATTGATTTTTGTATGTTNATCTTGTA 2191 chr6qtel1M 727147 TCCTACTACTTTGCTAAAATTATTAACTGCTTAGAGAGATTATTAATTGT 727196 i v i i v i i v i iv vv iii v -- C L1MD_orf2#LIN 2190 TCCTGCGACCTTGCTGAACTCACTTATTAGTTCTAGGAGTTTTT--TTGT 2143 chr6qtel1M 727197 A---TCTCAAAGATTATCCAAGTATATTAGCATGTCATTTGAAAAAAAGA 727243 --- iivii v i v v iv v i v v i i C L1MD_orf2#LIN 2142 AGATTCCTTGGGATTTTCTACGTAGACAATCATGTCATCTGCAAATAGGG 2093 chr6qtel1M 727244 TCATTTTCTTATCCTATTGCCCATTCTG-ATTCCTTCAATT---TTTTCT 727289 v v iv v i vi vi v - v iv --- C L1MD_orf2#LIN 2092 ACAGTTTTATTTCTTCCTTTCCAATCTGTATGCCTTTTATTTCCTTTTCT 2043 chr6qtel1M 727290 TCTCTTATTGC 727300 vi C L1MD_orf2#LIN 2042 TGCCTTATTGC 2032 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 43.48 CpG sites = 36, Kimura (unadjusted) = 43.48 Transitions / transversions = 1.29 (36/28) Gap_init rate = 0.04 (8 / 203), avg. gap size = 1.50 (12 / 8) 15 20.60 1.54 8.20 chr6qtel1M 727853 727917 (272083) (AAAAG)n#Simple_repeat 1 61 (0) m_b317s252i6 13262 chr6qtel1M 727853 AAATGAAAA-TAAAGAAAAGACAAACAAATTGATTTCAGAAAAATGTAGA 727901 v -v - v -v --vv iviv (AAAAG)n#Simp 1 AAAAGAAAAGAAAAGAAAAGA-AAAGAAA-AGA--AAAGAAAAGAAAAGA 46 chr6qtel1M 727902 AAAGAAAAGAAAGAGA 727917 - (AAAAG)n#Simp 47 AAAGAAAAGAAA-AGA 61 Matrix = Unknown Transitions / transversions = 0.25 (2/8) Gap_init rate = 0.09 (6 / 64), avg. gap size = 1.00 (6 / 6) 27 12.97 0.00 0.00 chr6qtel1M 730004 730045 (269955) (AT)n#Simple_repeat 1 42 (0) m_b317s252i7 13263 chr6qtel1M 730004 ATATATATATATATACATATATATATACCTATTTAAATATAT 730045 i iv v v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATAT 42 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 309 35.39 3.93 6.32 chr6qtel1M 730050 730227 (269773) L2a_3end#LINE/L2 344 517 (0) m_b317s601i15 13264 chr6qtel1M 730050 ACATATCTATATGCACATTTCATTTGTATATAATTGTTTGCAAATTATCT 730099 - ---- i i i v -- iivivi i L2a_3end#LINE 344 ACATA-CTATAT----ATTTTACTTATTTAT--TTGTTTATTGTCTGTCT 386 chr6qtel1M 730100 TAGCCATCATTGAACTGTGAACTCTTGAAAAGCAAAGATGATCTTTTCCC 730149 i-- vi i ii v i i ivvi ii ii i-- i v iv L2a_3end#LINE 387 C--CCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGAC--TTTTGTCTG 432 chr6qtel1M 730150 TTTCAATTA-------ATCTTCAAAATATAGAATAATGCCTGGCATATGA 730192 iiv i ------- ii iviiv i i i ii L2a_3end#LINE 433 TTTTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACATAG 482 chr6qtel1M 730193 TAAGCAATCAAGAATTATTTAGTAACTGAATGGAT 730227 i iv v v iv i v i L2a_3end#LINE 483 TAGGCGCTCAATAAATATTTGTTGAATGAATGAAT 517 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 49.45 CpG sites = 42, Kimura (unadjusted) = 52.11 Transitions / transversions = 2.47 (42/17) Gap_init rate = 0.07 (12 / 177), avg. gap size = 1.50 (18 / 12) 594 21.32 2.19 0.72 chr6qtel1M 731879 732015 (267985) Charlie4a#DNA/hAT-Charlie 355 493 (15) m_b317s502i1 13265 chr6qtel1M 731879 ATCTTTTGATAATTGGATTATGATACAATTGGTTTCCCTTCTAACTTCTA 731928 v i v vii i i v - i Charlie4a#DNA 355 ATATTTTGATAACTGTATTTCAATATAATTGGTTTCCTTTGTAA-TCCTA 403 chr6qtel1M 731929 TTTATTTCATTTCATTCACT-AAAAGCCTTATTCTGAGAAGGGAATTATA 731977 v i i v i - i v ivii Charlie4a#DNA 404 TGTATTTTATTTTATGCATTTAAAAACATTATTCTGAGAAGGGGTCCATA 453 chr6qtel1M 731978 --TTTCACGAGGCTGCCAAAGAGATCCATAACATAAAAAA 732015 --i v i i i ii i Charlie4a#DNA 454 GGCTTCACCAGACTGCCAAAGGGGTCCATGGCACAAAAAA 493 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 25.89 CpG sites = 20, Kimura (unadjusted) = 25.89 Transitions / transversions = 2.22 (20/9) Gap_init rate = 0.02 (3 / 136), avg. gap size = 1.33 (4 / 3) 17 18.22 0.00 0.00 chr6qtel1M 732432 732462 (267538) (A)n#Simple_repeat 1 31 (0) m_b317s252i8 13266 chr6qtel1M 732432 AAAAAAAAAAAAGAAAAAAACTAACAAATAA 732462 i vv v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 31 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 227 36.26 4.31 2.35 chr6qtel1M 732700 732908 (267092) L1HS_3end#LINE/L1 192 404 (498) m_b317s551i8 13267 chr6qtel1M 732700 TTATCTTATATACATCACAGTGGCAAAAATGTCAAAAAG--GAGAAATTA 732747 i i i ivvi i v i vv --i --ii iv L1HS_3end#LIN 192 TCATCTCACACCAGTTAGAATGGCAATCAT--TAAAAAGTCAGGAAACAA 239 chr6qtel1M 732748 TAGGTGAATTGAAAA-----CATAGAAATGGGCACACTGATACACCGTTG 732792 i --i i i ----- iv i v vv i L1HS_3end#LIN 240 CAGGTG--CTGGAGAGGATGCGGAGAAATAGGAACACTTTTACACTGTTG 287 chr6qtel1M 732793 GTAGACCCTTGAATAAATTCAACCATTGTTGACAACAATTTGA-AATGAC 732841 i iv iv i iv i v viv i v i-i vv L1HS_3end#LIN 288 GTGGGACTGTAAACTAGTTCAACCATTGTGGAAGTCAGTGTGGCGATTCC 337 chr6qtel1M 732842 ACACAAAGTTAATAACAAGTAAAATT-TTTTACTCAATTATATCACTCTT 732890 v vii vi i- v v v ii- v i iii vi i vi L1HS_3end#LIN 338 TCAGGGATCTAG-AACTAGAAATACCATTTGACCCAGCCATCCCATTACT 386 chr6qtel1M 732891 AAGCCTATACCCAAAGAA 732908 ii iv i L1HS_3end#LIN 387 GGGTATATACCCAAAGGA 404 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 50.06 CpG sites = 45, Kimura (unadjusted) = 52.14 Transitions / transversions = 1.55 (45/29) Gap_init rate = 0.04 (9 / 208), avg. gap size = 1.56 (14 / 9) 277 33.09 3.50 2.78 chr6qtel1M 732766 732908 (267092) L1PA14_3end#LINE/L1 261 404 (504) m_b317s551i9 13267 chr6qtel1M 732766 AGAAATGGGCACACTGATACACCGTTGGTAGACCCTTGAATAAATTCAAC 732815 v v v i i ivviv i v i L1PA14_3end#L 261 AGAAAAGGGAACACTTATACACTGTTGGTGGGAGTGTAAATTAGTTCAAC 310 chr6qtel1M 732816 CATTGTTGACAACAATTTGA-AATGACACACAAAGTTAATAACAAGTAAA 732864 v v i i v i-i vv v v i i ---- i i L1PA14_3end#L 311 CATTGTGGAAAGCAGTATGGCGATTCCTCAAAGAGCTAA----AAGCAGA 356 chr6qtel1M 732865 ATT----TTTTACTCAATTATATCACTCTTAAGCCTATACCCAAAGAA 732908 i ---- iv i iiv vi i vi ii iv i i L1PA14_3end#L 357 ACTACCATTCGACCCAGCAATCCCATTACTGGGTATATACCCAGAGGA 404 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 42.57 CpG sites = 27, Kimura (unadjusted) = 45.22 Transitions / transversions = 1.42 (27/19) Gap_init rate = 0.04 (6 / 142), avg. gap size = 1.50 (9 / 6) 240 35.95 4.26 2.39 chr6qtel1M 733628 734120 (265880) L1PREC2_orf2#LINE/L1 2388 2889 (405) m_b317s551i10 13268 chr6qtel1M 733628 AAACAATCAGAACAATATTA-ATGGCCAATGAATAGACTGATCTAATATG 733676 vii v i v- vi - i ivv vii v L1PREC2_orf2# 2388 AAACAAATGGAAAAACATTCCATGCTCA-TGGATAGGAAGAATCAATATC 2436 chr6qtel1M 733677 A--AAAATGACAATCGTATCTAAACTAATTTATTGATTCAGAGCCATAGT 733724 i-- i v vv ii i vi iv iv i vvi L1PREC2_orf2# 2437 GTTAAAATGGCCATACTGCCCAAAGCAATTTACAGATTCAATGCTATTCC 2486 chr6qtel1M 733725 AACAAAACCACCAA-AATTTATTTAAGAGAGCTAGAAAAA-CTAA---AA 733769 v iv i -i iv vi v v i - v--- L1PREC2_orf2# 2487 TATCAAACTACCAATGACATTCTTCACAGAACTAGAAAAAACTATTTTAA 2536 chr6qtel1M 733770 AATGTCATCTGGAA---AACAAAAGTCAAGACTATCAGAGGCA---TTAA 733813 - v --- v i i v- v v vi ---i L1PREC2_orf2# 2537 AAT-TCATATGGAACCAAAAAAGAGCCC-GAATAGCCAAGGCAATCCTAA 2584 chr6qtel1M 733814 TGGAAAAAATTACATAGAAGATGGCCTAGTAATACAAGATCTCAAACTAT 733863 -- v vv v vv iv v viiiv vv ii L1PREC2_orf2# 2585 --GCAAAAAGAACAAAGCTGGAGGCATCACGCTACCCGACTTCAAACTAT 2632 chr6qtel1M 733864 ATTATAAAGCAGAAATCATCAAAACTATCTGCTAGTAGCTAAGAAATAAA 733913 i i ii viv i v i viiv v v i ivv i i i L1PREC2_orf2# 2633 ACTACAGGGCTACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGA 2682 chr6qtel1M 733914 GTAGTGGATCAGTGAGATAAATTAGATACCCAAGACATATTAATAGATGA 733963 vvvi i i i ii i i v v v v v vviviiv iiv L1PREC2_orf2# 2683 CACATAGACCAATGGAACAGAATAGAGAGCCCAGAAATAAGGCCGCACAC 2732 chr6qtel1M 733964 CCACAATAACCTAGTGTTAGATAAACC---CAAAGACTACAGCATATGAA 734010 i iv i ii v v i v --- i --v - ii L1PREC2_orf2# 2733 CTACAACCATCTGATCTTCGACAAAGCTGACAAAAAC--AAGCA-ATGGG 2779 chr6qtel1M 734011 ATAAGAACACATTATTTGACAAAAACTGGTGAGAAAGCTGGAAAACAATA 734060 iv i v vi ii i viv v i v i vv i v L1PREC2_orf2# 2780 GAAAGGACTCCCTATTCAATAAATGGTGCTGGGATAACTGGCTAGCCATA 2829 chr6qtel1M 734061 GGGCACAAACTAGTTGAA----GACCAGCTTCTCACACCATATACCAAGA 734106 v - v i---i ---- vvi i i v i L1PREC2_orf2# 2830 TG-CAGAAG---ATTGAAACTGGACCCCTTCCTTACACCATATACAAAAA 2875 chr6qtel1M 734107 TAAGGTCAAAATGG 734120 v iv i L1PREC2_orf2# 2876 TCAACTCAAGATGG 2889 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 48.71 CpG sites = 88, Kimura (unadjusted) = 50.01 Transitions / transversions = 1.04 (88/85) Gap_init rate = 0.04 (21 / 492), avg. gap size = 1.57 (33 / 21) 258 30.83 4.10 5.18 chr6qtel1M 734301 734495 (265505) L1M4_orf2#LINE/L1 3102 3294 (0) m_b317s551i11 13269 chr6qtel1M 734301 AAAATGGGAAACAATCTTTACTGCAAGT---ATCTTTAATAAAGACCTTA 734347 i i v v --- i --- v i i i iv ?i L1M4_orf2#LIN 3102 AGAATGGGAGAAAATATTT---GCAAATCATATATCTGATAAGGGACTNG 3148 chr6qtel1M 734348 TTTCTCAGATATATAGAGAACT-----GAGTCAAGTTTAGAAGAATACAA 734392 v ivii i -----i v --iv v i v L1M4_orf2#LIN 3149 TATCCAGAATATATAAAGAACTCTTACAACTCAA--CAATAAAAAGACAA 3196 chr6qtel1M 734393 GCCATTCCCCATTTGGCAAATGGTCAAAGGATTTGACTAGTTTAAGTTTT 734442 --- vv v ?iv v v vi-- v i L1M4_orf2#LIN 3197 ---ATAACCCAATTNAAAAATGGGCAAAGGATTTGAATAGAC--ATTTCT 3241 chr6qtel1M 734443 CAGATGAATACATCTAACCTATCTATAGGCATGTGAATAAATGCTTCAAA 734492 vi v v i vi vivii v i ii v i iv v L1M4_orf2#LIN 3242 CCAAAGAAGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACA 3291 chr6qtel1M 734493 TCA 734495 L1M4_orf2#LIN 3292 TCA 3294 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 40.87 CpG sites = 29, Kimura (unadjusted) = 40.87 Transitions / transversions = 1.04 (29/28) Gap_init rate = 0.06 (12 / 194), avg. gap size = 1.50 (18 / 12) 198 31.51 5.31 1.71 chr6qtel1M 734551 734663 (265337) L2d2_3end#LINE/L2 431 547 (8) m_b317s601i16 13270 chr6qtel1M 734551 CAAGTAGAATATAAGATGTTTTATGTTAGG---TATTTTTTTCTCTTAGT 734597 v v i v vi v v vi ---i v i viv vv L2d2_3end#LIN 431 CAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACTTCTT 480 chr6qtel1M 734598 TGTA---ATCACAGGGTCTTGGCACATTTCTATGTATATAATAGGAGCTT 734644 ---vi v i -i v v iv i i i i v i L2d2_3end#LIN 481 TGTATCCCCCACAGCGCCT-AGCACAGTGCCTTGCACACAGTAGGCGCTC 529 chr6qtel1M 734645 AATAAATGCTTTTTTGATT 734663 i- v L2d2_3end#LIN 530 AATAAATA-TTTGTTGATT 547 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 41.24 CpG sites = 16, Kimura (unadjusted) = 41.24 Transitions / transversions = 0.84 (16/19) Gap_init rate = 0.04 (4 / 112), avg. gap size = 2.00 (8 / 4) 223 23.57 0.00 9.09 chr6qtel1M 734581 734664 (265336) L2d_3end#LINE/L2 431 507 (9) m_b317s601i17 13270 chr6qtel1M 734581 TATTTTTTTCTCTTAGTTGTAATCACAGGGTCTTGGCACATTTCTATGTA 734630 i ? ? --- vi--i v i -i v v iv i L2d_3end#LINE 431 TACTNTTTTNTC---GTTCC--CCACAGCGCCT-AGCACAGTGCTGAGCA 474 chr6qtel1M 734631 TATAATAGGAGCTTAATAAATGCTTTTTTGATTG 734664 i i v i i - v L2d_3end#LINE 475 CATAGTAGGCGCTCAATAAATAC-TTGTTGATTG 507 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 29.61 CpG sites = 11, Kimura (unadjusted) = 29.61 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.08 (7 / 83), avg. gap size = 1.00 (7 / 7) 375 24.80 2.04 9.49 chr6qtel1M 734976 735122 (264878) C MIR#SINE/MIR (121) 141 5 m_b317s601i18 13271 chr6qtel1M 734976 ATATCACAGATGAGAAAACTGAGGCAAACAGAG-TTAAGTAACTTGCCCA 735024 v i i v v - C MIR#SINE/MIR 141 ATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCCA 92 chr6qtel1M 735025 TGAACATACAGCTATTAACTATCTAAAGAGAGA--CAAACTCAAGAAGAT 735072 v iv i v v iv vi ivv i -- i i i v -- C MIR#SINE/MIR 91 AGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGCAG-- 44 chr6qtel1M 735073 AAATCTATATGACTCCAGTTCTGGCATGCTATCACCTAGCTATTACTATA 735122 --- ---- i vv i-- i v i v i - - i C MIR#SINE/MIR 43 ---TC----TGGCTCCAGAGCC--CGTGCTCTTAACCA-CTA-TGCTATA 5 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 28.07 CpG sites = 17, Kimura (unadjusted) = 30.17 Transitions / transversions = 1.06 (17/16) Gap_init rate = 0.10 (15 / 146), avg. gap size = 1.07 (16 / 15) 14 25.56 0.00 2.27 chr6qtel1M 737524 737568 (262432) (ATATAC)n#Simple_repeat 1 44 (0) m_b317s252i9 13272 chr6qtel1M 737524 ATAGATATATACATAGACATGTGCACATATATACACCATGTACAT 737568 v i v i i i i i - i (ATATAC)n#Sim 1 ATATACATATACATATACATATACATATACATATA-CATATACAT 44 Matrix = Unknown Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 41 0.00 0.00 0.00 chr6qtel1M 737569 737603 (262397) (AC)n#Simple_repeat 1 35 (0) c_b317s251i1 13273 chr6qtel1M 737569 ACACACACACACACACACACACACACACACACACA 737603 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACA 35 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 449 22.22 0.85 0.85 chr6qtel1M 738698 738815 (261185) C MER63D#DNA/hAT-Tip100 (589) 472 355 m_b317s502i2 13274 chr6qtel1M 738698 ACATAACAAA-TTTTAGGTTTACTATAAACGATTAAAATTGCTTTTCATC 738746 ii v - i v v iv iv v -i i i C MER63D#DNA/hA 472 ACACGACACACTTTTAAGTTTAATCTGCATTATTAACATT-TTCTCCATC 424 chr6qtel1M 738747 ATTTTCTTAAATCTAGATAAACAATAAAACAATAAATCAAACCCTTATTT 738796 i i i v i i v C MER63D#DNA/hA 423 ACTTTCTTAAGTCTAGACAATCAACAAAACAATAAATCAAGCCCTGATTT 374 chr6qtel1M 738797 GTAATGTGTGACCATTTCC 738815 ii v v v C MER63D#DNA/hA 373 GTAGCGTTTGCCGATTTCC 355 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 24.34 CpG sites = 15, Kimura (unadjusted) = 26.78 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.02 (2 / 117), avg. gap size = 1.00 (2 / 2) 233 26.42 0.00 0.00 chr6qtel1M 738874 738926 (261074) L2b_3end#LINE/L2 404 456 (10) m_b317s601i19 13275 chr6qtel1M 738874 AGCTCCTATCACAGTACCCGTCACATAATAAGCACTTAGGTAACACTTGT 738923 v v ?i i v i i i i i vv i i L2b_3end#LINE 404 AGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTTGT 453 chr6qtel1M 738924 TGA 738926 L2b_3end#LINE 454 TGA 456 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 31.53 CpG sites = 9, Kimura (unadjusted) = 34.54 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 37 0.00 0.00 0.00 chr6qtel1M 740592 740623 (259377) (CA)n#Simple_repeat 1 32 (0) c_b318s251i0 13276 chr6qtel1M 740592 CACACACACACACACACACACACACACACACA 740623 (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACA 32 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 444 17.86 1.03 7.69 chr6qtel1M 741695 741791 (258209) C MIRc#SINE/MIR (141) 127 37 m_b318s601i0 13277 chr6qtel1M 741695 CTGAGGC-AATTGAGGTTAAGTGACTTGCCCAGGATCACACAGCTAGGAA 741743 -v vv i i --- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG--- 81 chr6qtel1M 741744 GTATTAAGTGTCTGAGACCAGATTTGAACTCAGATCCTCCTGACTTCA 741791 ---- v v v vi i i i i i i C MIRc#SINE/MIR 80 ----TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCA 37 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 19.13 CpG sites = 9, Kimura (unadjusted) = 20.50 Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.08 (8 / 96), avg. gap size = 1.00 (8 / 8) 43 0.00 0.00 0.00 chr6qtel1M 742329 742365 (257635) (AT)n#Simple_repeat 1 37 (0) c_b318s251i1 13278 chr6qtel1M 742329 ATATATATATATATATATATATATATATATATATATA 742365 (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATA 37 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 20 21.09 0.00 0.00 chr6qtel1M 742674 742712 (257288) (A)n#Simple_repeat 1 39 (0) m_b318s252i1 13279 chr6qtel1M 742674 AAACACAAAAAAAGAAAAAGAAAAAGAAAGAAAAGAAAA 742712 v v i i i i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 39 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 181 23.33 10.00 0.00 chr6qtel1M 744545 744604 (255396) C MIRc#SINE/MIR (26) 242 177 m_b318s601i1 13280 chr6qtel1M 744545 TAGAATTTTAAGGTTTTCAAA------TTATATTCATGATCTTATTTTAA 744588 v i vi v ------ i i v v i v v C MIRc#SINE/MIR 242 TAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATCTCATTTGAT 193 chr6qtel1M 744589 CCTCACAACTCCCCTG 744604 vv C MIRc#SINE/MIR 192 CCTCACAACAACCCTG 177 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 27.96 CpG sites = 5, Kimura (unadjusted) = 27.96 Transitions / transversions = 0.56 (5/9) Gap_init rate = 0.02 (1 / 59), avg. gap size = 6.00 (6 / 1) 1308 31.13 3.32 5.01 chr6qtel1M 745455 746509 (253491) L1PREC2_orf2#LINE/L1 2217 3254 (40) m_b318s551i0 13281 chr6qtel1M 745455 AGCATTT-TATACATCACCAACAAAATCCAATAGCAAGAGATACA--AAG 745501 i- --- v v -iv i vi v -- i L1PREC2_orf2# 2217 AGCATTCCTATACA---CCAACAACAGCCAA-GCCGAGAGCCAAATCAGG 2262 chr6qtel1M 745502 A--GAAATTCCATTCAAAATAACTGTCAACAGCATAAAATATTTGGGAAT 745549 -- v i v vi iiiv v v ii i L1PREC2_orf2# 2263 AACGCAATCCCATTCACAATTGCCACAAAAAGAATAAAATACCTAGGAAT 2312 chr6qtel1M 745550 CTATCTA-CCAAAGGAAAGTCAGGAAT-TATATGAGCAAAATTACAAAAA 745597 vi v - -- i i v iii - v ii vv i v L1PREC2_orf2# 2313 ACAGCTAACCA--GGGAGGTGAAAGATCTCTACAATGAGAATTACAAAAC 2360 chr6qtel1M 745598 ACTTTCCACACAAATAAAATCAGACTTAAATAATTGGAAAAATATTAAGT 745647 vii v v v i vvv vi i v i vvi L1PREC2_orf2# 2361 ACTGCTCAAAGAAATCAGAGATGACACAAACAAATGGAAAAACATTCCAT 2410 chr6qtel1M 745648 GCTCTTGGATAGGCCGAGTGAATATAATAAAGATGACAATACTCCCTAAA 745697 v vv i v vi v i i v v i L1PREC2_orf2# 2411 GCTCATGGATAGGAAGAATCAATATCGTTAAAATGGCCATACTGCCCAAA 2460 chr6qtel1M 745698 CTAATCTATTTATTTAATGCTATACCAATCAGACTTCCAAGAAAATATTT 745747 vi i ivv i v v i v vi v vi L1PREC2_orf2# 2461 GCAATTTACAGATTCAATGCTATTCCTATCAAACTACCAATGACATTCTT 2510 chr6qtel1M 745748 TAATGATCTAGAAAAAATAATAACAAAATTCATATGGAAGACAAAAAAGA 745797 i vv v iv vvi v- - L1PREC2_orf2# 2511 CACAGAACTAGAAAAAACTATTTTAAAATTCATATGGAAC-CAAAAAAG- 2558 chr6qtel1M 745798 TCAAAAAAAAAATAAAAGATCGAGAATCTCAAGGGAAT--TAATGAAAAA 745845 ---------------- vi iv v - v -- vv L1PREC2_orf2# 2559 ----------------AGCCCGAATAGC-CAAGGCAATCCTAAGCAAAAA 2591 chr6qtel1M 745846 AAAAATCAAA--TGAAGGTAGTCTAGCTGTACCTGATTTAAAACTATATT 745893 i --- -- i i - vv -- i i v i L1PREC2_orf2# 2592 GAA---CAAAGCTGGAGGCA-TCACGC--TACCCGACTTCAAACTATACT 2635 chr6qtel1M 745894 ATAAAAC-AGGGTCACCAAAACCATTTGGTATTGGCTAAGAAAGAGATTA 745942 i iii - vi v viiv i ivv i v ivv L1PREC2_orf2# 2636 ACAGGGCTACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGACAC 2685 chr6qtel1M 745943 GTTGATCAGTGAAATAGGTTTAAGTTCACA-AGACAAAATAGT-CAACTA 745990 i v i i i i iv vi vv v - i i iiiv i- v L1PREC2_orf2# 2686 ATAGACCAATGGAACAGAATAGAGAGCCCAGAAATAAGGCCGCACACCTA 2735 chr6qtel1M 745991 CAGCAATCTACTGTTTGAGAAACC---CAAAGATCCTAACTTTTGGGATA 746037 i v iv v i v v --- i -- v i vv v - L1PREC2_orf2# 2736 CAACCATCTGATCTTCGACAAAGCTGACAAAAA--CAAGCAATGGGGA-A 2782 chr6qtel1M 746038 AGAATTCATTATTTGACAAAAACTGCTGGGATAACTGGAAATTAG---TA 746084 i i vi ii i viv ---i --- L1PREC2_orf2# 2783 AGGACTCCCTATTCAATAAATGGTGCTGGGATAACTGG---CTAGCCATA 2829 chr6qtel1M 746085 TGGCAGAA-ATTAGGCATGGACCCACACTTAACACCATATACTAAGATAA 746133 - - iiivv viv i v v i v L1PREC2_orf2# 2830 T-GCAGAAGATTGAAACTGGACCCCTTCCTTACACCATATACAAAAATCA 2878 chr6qtel1M 746134 GATCAAAATGGGTCCATGATTTAGGCATAAAGAACGAGATTATAAATAAA 746183 iv i i iv v i iiii ivv i i i v vv L1PREC2_orf2# 2879 ACTCAAGATGGATTAAAGACTTAAATGTAAAACCCAAAACTATAAAAACC 2928 chr6qtel1M 746184 TTAGAGG--AACATAGG--ATAGTTTATCTCTCAGACTTGTGGAGGAGGA 746229 i i i -- v -- --ii - -i v iv i v i v L1PREC2_orf2# 2929 CTGGAAGACAACCTAGGCAATA--CCAT-TCT-GGACATAGGAACGGGCA 2974 chr6qtel1M 746230 AGAAATTTGTGACCAGAGATGAACTAGAGACCATTAC----TAATCACAA 746275 ii v ii v - i -- i i ii v i ----v v - L1PREC2_orf2# 2975 AAGATTTCATGACGA-AGACG--CCAAAAGCAATTGCAACAAAAGCA-AA 3020 chr6qtel1M 746276 AATAGAAAATTTTGATTACATCAAATTAAAAAGCCTTTGT---GCAAACA 746322 v v v vv ivv i i i i i i--- vi L1PREC2_orf2# 3021 AATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAG 3070 chr6qtel1M 746323 AAACTAATGCAAACAAGATTAGAAGGGAAGCAACAAACTGGGAAAACATC 746372 ---iv iii v iv iv v v i v i v ? L1PREC2_orf2# 3071 AAACTA---TCAACAGAGTAAACAGACAACCTACAGAATGGGAGAAAATN 3117 chr6qtel1M 746373 TTCACAGTTAAAGGTTCTGATAAAGGCCTCATTTCCAAAATATATAGAGA 746422 ii iviv v vv i i v v iv v ii L1PREC2_orf2# 3118 TTTGCAAACTATGCATCTGACAAAGGTCTAATATCCAGCATCTATAAGGA 3167 chr6qtel1M 746423 ATTAACTCTAATTTAT---AAAAAATCAAGCCATTCTCCAATTGAAAAAT 746469 i v vv v i--- v i v -- i - i i L1PREC2_orf2# 3168 ACTTAAACAAATTTACAAGAAAAAAACAAACAA--CCCC-ATTAAAAAGT 3214 chr6qtel1M 746470 GGTCAAAGGATATGGACAGACACTTTTCAGATGATGAAAT 746509 v i i i v v v L1PREC2_orf2# 3215 GGGCAAAGGACATGAACAGACACTTTTCAAAAGAAGACAT 3254 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 40.06 CpG sites = 161, Kimura (unadjusted) = 40.91 Transitions / transversions = 1.07 (161/151) Gap_init rate = 0.07 (70 / 1054), avg. gap size = 1.24 (87 / 70) 1317 29.48 2.74 4.33 chr6qtel1M 746400 747055 (252945) L1ME3A_3end#LINE/L1 1 646 (274) m_b318s551i1 13281 chr6qtel1M 746400 CTCATTTCCAAAATATATAGAGAATTAACTCTAATTTATAAAAAATCAAG 746449 v i i i vviv v iv i -- L1ME3A_3end#L 1 CTCATATCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAA--AAG 48 chr6qtel1M 746450 CCATTC--TCCAATTGAAAAATGGTCAAAGGATATGGACAGACACTTTTC 746497 v vv --i v v i iv i i iv L1ME3A_3end#L 49 ACAGACAACCCAATAGAAAAATGGGCAAAAGACTTGAACAGGCACTTCAC 98 chr6qtel1M 746498 AGATGATGAAATTAAAACTATTTCCACT---CATATGAAAGAGTGTTCCA 746544 i v v v iv --- vv v --- ii i v L1ME3A_3end#L 99 AAAAGAGGATATCCAAA---TGGCCAATAAACATATGAAAAGGTGCTCAA 145 chr6qtel1M 746545 AATCACTATTGATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCAC 746594 vv i v v i i v vv i? L1ME3A_3end#L 146 CTTCATTAGTCATCAGGGAAATGCAAATTAAAACCACAATGNGATACCAC 195 chr6qtel1M 746595 TACACACCTGTCAGATTGGCTAAGATGACAGGAAAAAATAATGATGAATG 746644 iii v i v iii v i i ivii i L1ME3A_3end#L 196 TACACACCCACCAGAATGGCTAAAATGAAAAAGACAGACAATACCAAGTG 245 chr6qtel1M 746645 TTGGAGGGGATGCGGGAAAACTGGGACACTGATGCATTGTTGGTGGAGTT 746694 v i i iiv i i v v i i i iiv L1ME3A_3end#L 246 TTGGCGAGGATGTGGAGCAACCGGAACTCTCATACACTGCTGGTGGGAGT 295 chr6qtel1M 746695 GTGAATGAATCCAACCATTCTGGAGAGCAGTCTGGAATTATGCCCCAAAA 746744 i vii v i i i i v i v v - iv v L1ME3A_3end#L 296 GTAAATTGGTACAACCACTTTGGAAAACTGTTTGGCAGTAT-CTACTAAA 344 chr6qtel1M 746745 GTTATCAAAC-TGTGCATACCCTTTGATCCAGCAGTGCTTCTACTGGGCT 746793 i ---i - i v i i v iv v i iv L1ME3A_3end#L 345 GCT---GAACATATGCATACCCTATGACCCAGCAATTCCACTCCTAGGTA 391 chr6qtel1M 746794 TATAACCCAA-AGAGATAC-CAAAGAAG---GAAAAAGGACCTGTATGTG 746838 - - i i -i v v v ---ivv i ---- i L1ME3A_3end#L 392 TAT-ACCCAACAGAAATGCGTACATATGTTCACCAAAAGAC----ATGTA 436 chr6qtel1M 746839 CCAAAATGTTTGTGGAGGCCCTGTTTGTAGTGACTAGAAACTGAAAAATG 746888 v i ii i vi v i i i ii i?? i v?i L1ME3A_3end#L 437 CAAGAATGTTCATAGCAGCACTATTCGTAATAGCCNNAAACTGGAAACNA 486 chr6qtel1M 746889 AATGGATGCACATCAATTGGAGAATGGTTGGGTAAACTGTGGCATATGTA 746938 vviii iv iv v v iii i i vi L1ME3A_3end#L 487 CCCAAATGTCCATCAACAGTAGAATGGATAAATAAATTGTGGTATATTCA 536 chr6qtel1M 746939 TGTTATGGAATATTATTGTTTGTTA-AGAAATGACCAAATG-ACGAGCAG 746986 iiiv i -------- - v --i - i -- L1ME3A_3end#L 537 CACAATGGAATACTA--------TACAGCAATGA--GAATGAACGAAC-- 574 chr6qtel1M 746987 GACAAATACAGAGAGT--CTTGGA-GAGACTTACATGAAC-TGATGCTGA 747032 v v viv ii-- v - iv i -- - i i L1ME3A_3end#L 575 TACAACTACACGCAACAACATGGATGAATCTCACA--AACATAATGTTGA 622 chr6qtel1M 747033 GTGAAATGAGCAGGAC-CAGGAGA 747055 i vi vi - ii L1ME3A_3end#L 623 GCGAAAGAAGCCAGACACAAAAGA 646 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 37.80 CpG sites = 110, Kimura (unadjusted) = 38.88 Transitions / transversions = 1.47 (110/75) Gap_init rate = 0.06 (40 / 655), avg. gap size = 1.15 (46 / 40) 1485 28.92 1.47 1.47 chr6qtel1M 746411 746954 (253046) L1ME4c_3end#LINE/L1 12 555 (275) m_b318s551i2 13281 chr6qtel1M 746411 AATATATAGAGAATTAACTCTAATTTATAA----AAAATCAAGCCATTCT 746456 ? i ii v i v v ---- ? v ----i L1ME4c_3end#L 12 ANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAAGAC----C 57 chr6qtel1M 746457 CCAATTGAAAAATGGTCAAAGGATATGGACAGACACTTTTCAGATGATGA 746506 v v v i i v iv ? v v L1ME4c_3end#L 58 CCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAGGA 107 chr6qtel1M 746507 AATTAAAACTATTTC-CACTCATATGAAAGAGTGTTCCAAATCACTATTG 746555 - v ? v vv- vv i i i i v vv i v i L1ME4c_3end#L 108 AAT-ACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTAGTA 156 chr6qtel1M 746556 ATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACACCTGT 746605 i ii vv i i vi i i L1ME4c_3end#L 157 ATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCTAT 206 chr6qtel1M 746606 CAGATTGGCTAAGATGACAGGAAAAAATAATGATGAATGTTGGAGGGGAT 746655 i i i v i vvv ii vvi iviv i v i ? L1ME4c_3end#L 207 TAAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGCTGGCGAGGNT 256 chr6qtel1M 746656 GCGGGAAAACTGGGACACTGATGCATTGTTGGTGGAGTTGTGAATGAATC 746705 vi v ? v i i vi? i vii v L1ME4c_3end#L 257 GCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGTA 306 chr6qtel1M 746706 CAACCATTCTGGAGAGCAGTCTGGAATTATGCCCCAAAAGTTATCAAACT 746755 v i i i i v v i ivi i ii v v L1ME4c_3end#L 307 CAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAAAAT 356 chr6qtel1M 746756 GTGCATACCCTTTGATCCAGCAGTGCTTCTACTGGGCTTATAACCCAAAG 746805 v i i i v iv v vv v v i i L1ME4c_3end#L 357 GTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGG 406 chr6qtel1M 746806 AGATA---CCAAAGAAGGAAAAAGGACCTGTATGTGCCAAAATGTTTGTG 746852 i --- v --- i ii v i ii v L1ME4c_3end#L 407 AAATAATTCAAAAGAAGGAAAAAG---CTATATGCACGAAGATGTTCATT 453 chr6qtel1M 746853 GAGGCCCTGTTTGTAGTGACTAGAAACTGAAAAATGAATGGATGCACATC 746902 vi vi i i i ii v i i i vvivv ii iv v L1ME4c_3end#L 454 GCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAAC 503 chr6qtel1M 746903 AATTGGAGAATGGTTGGGTAAACTGTGGCATATGTATGTTATGGAATATT 746952 v i ii i i i i v? iviv L1ME4c_3end#L 504 AATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATATT 553 chr6qtel1M 746953 AT 746954 L1ME4c_3end#L 554 AT 555 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.82 CpG sites = 86, Kimura (unadjusted) = 38.05 Transitions / transversions = 1.25 (86/69) Gap_init rate = 0.02 (11 / 543), avg. gap size = 1.45 (16 / 11) 15 8.33 0.00 3.70 chr6qtel1M 747355 747382 (252618) (GGGA)n#Simple_repeat 1 27 (0) m_b318s252i2 13282 chr6qtel1M 747355 GGGAGGGGGTGGAAGGAGGGAGGGAGGG 747382 i - i (GGGA)n#Simpl 1 GGGAGGGAG-GGAGGGAGGGAGGGAGGG 27 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 520 28.29 1.48 2.49 chr6qtel1M 748335 748537 (251463) L1ME4c_3end#LINE/L1 351 551 (279) m_b318s551i3 13283 chr6qtel1M 748335 AAAAAGATTCCATACCCTTTGACCCAGCAGTACCATTACTGGGTCTGTAT 748384 vi - i i v i v vv v L1ME4c_3end#L 351 AAAAATGTTC-ATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTAT 399 chr6qtel1M 748385 CCCAAGGAAATCAT---AAAGAAGGGGAAAAGGGCCCAGATGGGAAAAAA 748431 i v --- - i --- i v vivi i L1ME4c_3end#L 400 CCTAAGGAAATAATTCAAAAGAA-GGAAAAAG---CTATATGCACGAAGA 445 chr6qtel1M 748432 TATTTGTAGCAGCTCCTTTTGTGGTAGCAAAGAATTGGAAAAGGAGTAAA 748481 i ii v viiv i ii i i viivv L1ME4c_3end#L 446 TGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAA 495 chr6qtel1M 748482 TGTCCAAAATTTGGGGAATGACTGAACGAGGTGTGGTATATGAAAGTAAT 748531 v v v ii i iii iv i i v? vvii L1ME4c_3end#L 496 TGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGAT 545 chr6qtel1M 748532 GGAATA 748537 L1ME4c_3end#L 546 GGAATA 551 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 34.17 CpG sites = 33, Kimura (unadjusted) = 36.70 Transitions / transversions = 1.43 (33/23) Gap_init rate = 0.03 (6 / 202), avg. gap size = 1.33 (8 / 6) 689 34.01 3.61 2.17 chr6qtel1M 748614 749112 (250888) L1ME1_3end#LINE/L1 122 627 (299) m_b318s551i5 13284 chr6qtel1M 748614 ATAGATATATGAAAAAATGCTCTAAATTGTTACTGAGTAAAGAAATGCAA 748663 iii i i v v ii v v v ii L1ME1_3end#LI 122 ATAAGCACATGAAAAGATGCTCAACATCATTAGTCATTAGGGAAATGCAA 171 chr6qtel1M 748664 GTTAAAACAACTCTGAGGTACCAGTTCACACCTTTCAGATTGGTT-AAGT 748712 i v vv i v v v i v i - i L1ME1_3end#LI 172 ATTAAAACCACAATGAGATACCACTACACACCTATTAGAATGGCTAAAAT 221 chr6qtel1M 748713 TGTCAGGAAAAATAATGATGAATTTTTGAGGGGTTGTGGGAAAATGGGAA 748762 ivv i vvi i ivii i v v v i v iiv iv L1ME1_3end#LI 222 TAAAAAGACTGACAATACCAAGTGTTGGCGAGGATGTGGAGCAACTGGAA 271 chr6qtel1M 748763 CAATAATGCATTGTT-GTG--------AAGTGATCCAGCCATTTTGGAGA 748803 vv v i i - -------- i i v i i L1ME1_3end#LI 272 CTCTCATACATTGCTGGTGGGAATGCAAAATGGTACAGCCACTTTGGAAA 321 chr6qtel1M 748804 GCACTTTGGAATTATGCCCAAAGGGCTATCAAGTTGTGCAC--ACCATTT 748851 i v v v - v ii ? ii i -- --ii i -- v L1ME1_3end#LI 322 ACAGTTTGGCAGT-TTCTTANAAAGTTA--AA--CATACACTTACCATAT 366 chr6qtel1M 748852 GATCCAGCAGTGTCTCTACTGGATTTGTATTCCAAAGAAATCATAAAAAA 748901 i i vi v v i i v v ii v i v v v v L1ME1_3end#LI 367 GACCCAGCAATTCCACTCCTAGGTATTTACCCAAGAGAAATGAAAACATA 416 chr6qtel1M 748902 ----GAGAAAAGGGCCTATGTGTGCAAAAATGTTTGCAGCAGTACTATTT 748947 ----v v v i i i---- i vi iii ivi i L1ME1_3end#LI 417 TGTCCACACAAAGACT----TGTACACGAATGTTCATAGCAGCTTTATTC 462 chr6qtel1M 748948 GTGGTGGCAAGTGATTGGAAATTGAGTGAATGCCCAGCACTTGGGGAATA 748997 ii i v ivi i ivivvii i v vi? v i L1ME1_3end#LI 463 GTAATAGCCAAAAACTGGAAACAACCCAAATGTCCATCAACNGGTGAATG 512 chr6qtel1M 748998 GCTGAATAAGTTCTAGTATCTGAATGCAATGGAATATTATTGTTCTATAA 749047 v i i i v i v vv i i i vvv v L1ME1_3end#LI 513 GATAAACAAATTGTGGTATATCCATACAATGGAATACTACTCAGCAATAA 562 chr6qtel1M 749048 GAAATGATGAACAGACTGAT-TTCAGAAAAGTCTAGAGAGACCTACATGA 749096 i ivi i -v -iv iv v iiv i vii i - vi L1ME1_3end#LI 563 AAAGGAACGAAC-TACTGATACACGCAACAACATGGATGAATCT-CAAAA 610 chr6qtel1M 749097 AC-TGATGCTGAGTGAA 749112 ? - v L1ME1_3end#LI 611 NCATTATGCTGAGTGAA 627 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 45.57 CpG sites = 93, Kimura (unadjusted) = 47.13 Transitions / transversions = 1.27 (93/73) Gap_init rate = 0.04 (18 / 498), avg. gap size = 1.61 (29 / 18) 951 33.10 2.93 0.66 chr6qtel1M 748614 749057 (250943) L1ME4c_3end#LINE/L1 122 575 (255) m_b318s551i4 13284 chr6qtel1M 748614 ATAGATATATGAAAAAATGCTCTAAATTGTTACTGAGTAAAGAAATGCAA 748663 i i i i i i v vv i i v i vi L1ME4c_3end#L 122 ACAAACACATGGAAAAATGTTCAACCTCGCTAGTAATCAAAGAAATGCAA 171 chr6qtel1M 748664 GTTAAAACAACTCTGAGGTACCAGTTCACACCTTTCAGATTGGTTAAGTT 748713 i i vv i v i i v i i i iv iv L1ME4c_3end#L 172 ATTAAAGCAACAATGAGATACCATTTTACGCCTATTAAATTAGCAAAAAT 221 chr6qtel1M 748714 GTCAGGAAA--AATAATGATGAATTTTTGAGGGGTTGTGGGAAAATGGGA 748761 - i ii --i iviv vi v v i ? i vi iv v L1ME4c_3end#L 222 -TTAAAAAATTGATAATACCCAATGCTGGCGAGGNTGCGGTGAAACTGGT 270 chr6qtel1M 748762 ACAATAATGCATTG---------TTGTGAAGTGATCCAGCCATTTTGGAG 748802 ?v v i ---------? i v i v i v i L1ME4c_3end#L 271 ACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAA 320 chr6qtel1M 748803 AGCACTTTGGAATTATGCCCAAAGGGCTATCAAGTTGTGCACACCATTTG 748852 v v v i iviv i i v iv v i v L1ME4c_3end#L 321 AGCAATTTGGCAATACGTATCAAGAGCCATAAAAATGTTCATACCCTTTG 370 chr6qtel1M 748853 ATCCAGCAGTGTCTCTACTGGATTTGTATTCCAAAGAAATCAT--AAAAA 748900 i i i vi v v ivv v i i i v -- i L1ME4c_3end#L 371 ACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAAG 420 chr6qtel1M 748901 AGAGAAAAGGGCCTATGTGTGCAAAAATGTTTGCAGCAGTACTATTTGTG 748950 ii i -- i ii i i iiiv iii i i L1ME4c_3end#L 421 AAGGAAAAAG--CTATATGCACGAAGATGTTCATTGCAGCGTTATTTATA 468 chr6qtel1M 748951 GTGGCAAGTGATTGGAAATTGAGTGAATGCCCAGCACTTGGGGAATAGCT 749000 i i i ivi ivivv i i i v v i i L1ME4c_3end#L 469 ATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAATGGTT 518 chr6qtel1M 749001 GAATAAGTTCTAGTATCTGAATGCAATGGAATATTATTGTTCTATAAGAA 749050 i i i v i iv v? iv i vvvv i v i L1ME4c_3end#L 519 AAGTAAATTATGGTACATCNACTCGATGGAATATTATGCAGCCATTAAAA 568 chr6qtel1M 749051 ATGATGA 749057 i L1ME4c_3end#L 569 ATGATAA 575 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 42.73 CpG sites = 90, Kimura (unadjusted) = 46.23 Transitions / transversions = 1.61 (90/56) Gap_init rate = 0.01 (6 / 443), avg. gap size = 2.67 (16 / 6) 5044 29.16 3.40 2.41 chr6qtel1M 749365 752365 (247635) L1M5_orf2#LINE/L1 265 3294 (0) m_b318s551i6 13285 chr6qtel1M 749365 ATTAAAAGAGATAAGGAAGGAAACTACATCCTGCTAAA-GGGTAGCATAA 749413 vv i i v i v vv v - vivv v L1M5_orf2#LIN 265 ATTACCAGAGATAAAGAGGGACATTTCATAATGATAAAAGGGTCAATTCA 314 chr6qtel1M 749414 ACAACGAAGCAATATCAATATTAAATATATATGCACCAAGTGGTATGGCA 749463 v - vv v vi i i v i iii vi v L1M5_orf2#LIN 315 TCAA-GAAGACATAACAATCCTAAATGTGTATGCACCTAATAACAGAGCT 363 chr6qtel1M 749464 CTCAACTTCCTAAAGGAGAAGTTAAGAGAGTTGCAAGAAGAAATAGACAA 749513 iiv v v v i v i ii i v ii iv i L1M5_orf2#LIN 364 TCAAAATACATGAAGCAAAAACTGACAGAACTAAAAGGAGAAATAGACAA 413 chr6qtel1M 749514 ---CAAAACTGTAATAGTAGGAGATCTCAACCTTGCACTCTCAG-AATTA 749559 --- v i --- ? i i vi?v v - - L1M5_orf2#LIN 414 ATCCACAATT---ATAGTNGGAGATTTTAACACNCCTCTCTCAGTAATT- 459 chr6qtel1M 749560 GACAAATCAAAC-CACAAAACAAATAAGAAAGAA-ATTAAAGAAGTAAAT 749607 i i v ii-v -- v v i - vi vv i i L1M5_orf2#LIN 460 GATAGAACAAGTAGACAAAA--AATCAGTAAGGATATAGAAGATTTGAAC 507 chr6qtel1M 749608 AGAATATTAGAAA--AATTAGGTATGTTGGATCTTTGGAGAAAATTGAAT 749655 -- i i vv -- i v iiv iv v iv iv v i ?v i L1M5_orf2#LIN 508 A--ACACTATCAACCAACTTGACCTAATTGACATTTATAGAACACTNCAC 555 chr6qtel1M 749656 GGAGATAGAAG-GGAATATACTTTCTTCTCAGCAGTTCATGGAACCTATT 749704 vv - i iv? -i i v i ivv iv v v v L1M5_orf2#LIN 556 CCA-ACAACNGCAGAATACACATTCTTTTCAAGTGCACATGGAACATTTA 604 chr6qtel1M 749705 CAAAAATTGACCATATATTAGGACATAAAGAC----CTCAAAATTAAATG 749750 v i v ?i i v - ---- --- v L1M5_orf2#LIN 605 CCAAGATAGACCATATNCTGGGCCATAAA-ACAAGTCTCAA---TAAATT 650 chr6qtel1M 749751 CAAGAAAGCAGAAATAGTAAATGCTTTCTTTTCAGATCATGATGCAATAA 749800 i? i iiiiv vi v viv v v i v i ii v v L1M5_orf2#LIN 651 TNAAAGGATTGAAATCATACAGAGTATGTTCTCTGACCACAATGGAATTA 700 chr6qtel1M 749801 AAACTACATTCAACAACAAA-------TTAGGAAATAGACCAAAAAGTAA 749843 viviv v i -------i i vv- --- v L1M5_orf2#LIN 701 AATTAGAAATCAATAACAAAAAGATANCTAGAAAATCC-CCAAA---TAT 746 chr6qtel1M 749844 TTGGAAACTAAACAATCTCATCT-TAAAGAATGATTGGGTGAAGCAGCAA 749892 i - v ii - v ivvv v iv iv L1M5_orf2#LIN 747 TTGGAAATTAAACAA-CACACTTCTAAATAACCCATGGGTCAAAGAAGAA 795 chr6qtel1M 749893 ATTATAGATACAATTAATAATTTCACTCAAGATAATGACAATGATGAGAC 749942 i i i?viv iv v vivi v vvv ? vi v L1M5_orf2#LIN 796 ATCACAANGGAAATTAGAAAATATTTTGAACTGAATGANAATGAAAATAC 845 chr6qtel1M 749943 ATCATACCAAAATTTGTGGGATGCAGCCAAAGCGGTAATAAGAGGGAATT 749992 v i i i iv v v L1M5_orf2#LIN 846 AACATATCAAAATTTGTGGGATGCAGCTAAAGCAGTGCTTAGAGGGAAAT 895 chr6qtel1M 749993 TTATATCCTTAGAGGCTTACTTGAATAAAACAGA-GAAAGAA--AAGATT 750039 v ? i v ? iv --- i v - iv-- i i L1M5_orf2#LIN 896 TTATAGCNTTAAATGCNTATAT---TAGAAAAGAAGAAAGGCTTAAAATC 942 chr6qtel1M 750040 AATGAATTGGGCTTGCAACTAAAAAA-----AATAAAAAGACCAAATTAA 750084 vi ii v v v i ----- v i v L1M5_orf2#LIN 943 AATGATCTAAGCTTCCACCTTAAGAAGCTAGAAAAAGAAGAGCAAATTAA 992 chr6qtel1M 750085 AAACCCCCAATCAAATACGAAACTGGAAATTCTAAAATTAAAAGAAGAAA 750134 --- v v? i vi iivv vv iv i v L1M5_orf2#LIN 993 A---CCCAAAGNAAGTAGAAGGAAGGAAATAATAAAGATAAGAGCAGAAA 1039 chr6qtel1M 750135 TTAAAAATATTGAAAGTAAAAAAACTATTGAACTAATTAATAAAACTAAG 750184 i vi v v ii ? ? v v ivv i ii i i i L1M5_orf2#LIN 1040 TCAATGAAATAGAAAACAAANANACAATAGAGAAAATCAACGAAGCCAAA 1089 chr6qtel1M 750185 AGTTGGTTCTATGAAAAAGCCAATAAAATAGATAAGCCTTTGGTAAATCT 750234 i v iii v i i i i? iv L1M5_orf2#LIN 1090 AGCTGGTTCTTTGAAAAGATCAATAAAATTGATAAACCTCTAGCNAGACT 1139 chr6qtel1M 750235 GATTA-GAAAAGGAG-GAGGAAATG-AAATTAGTAGTCTTAAAAATGAAA 750281 i - ii - i i ii- vi i v i ii L1M5_orf2#LIN 1140 GATCAAGAAAAAAAGAGAGAAGACACAAATTACCAATATCAGGAATGAAA 1189 chr6qtel1M 750282 A-GGAGAACTTTCCACCAATGAAGAGGAAATTAGAGAAATAATAAGGAGT 750330 - vv iv i vi vvvivi v i iii iiiv L1M5_orf2#LIN 1190 AAGGAGACATCACTACAGATCCTACAGACATTAAAAGGATAATAAGAGAA 1239 chr6qtel1M 750331 TATTTTGCTCAACTTTATGCCAATAAATTTGATAACCTAAGTGAAATGGA 750380 v vv ? i ii L1M5_orf2#LIN 1240 TATTATGAACAACTTTATGCCAATAAATTTGANAACTTAGATGAAATGGA 1289 chr6qtel1M 750381 TGACTACCTC--AAAATACAGACTTCCGAGACTAACA-GAGGAGAAGTAA 750427 ii v v i-- i i?i v i i i ?-i i i i L1M5_orf2#LIN 1290 CAAATTCCTTGAAAAACACAANTTACCAAAACTGACNCAAGAAGAAATAG 1339 chr6qtel1M 750428 ATTGTCTTGAATAGTCCCATTTC-AGAAAAGAAATAGAACAGGCAATTAA 750476 vvi - i i v - vv v ivv i L1M5_orf2#LIN 1340 AAAATCT-GAATAGCCCTATATCTATTAAAGAAATTGAATTTGTAATTAA 1388 chr6qtel1M 750477 ACAACTCCCTAAGAAAAAATCCCCAGGACCAGATGGATTTACATCCAGAT 750526 v v i i vi i v i v v i vvviii L1M5_orf2#LIN 1389 AAACCTTCCCACAAAGAAAACTCCAGGCCCAGATGGCTTCACTGGTGAAT 1438 chr6qtel1M 750527 TTTACCAAACATTTAAA-AACAATTGGCCCCAATGCTATATAAATTATTT 750575 i i- v v iiiv vi i i i v i L1M5_orf2#LIN 1439 TCTACCAAACATTTAAGGAAGAAATAATACCAATCTTACACAAACTCTTC 1488 chr6qtel1M 750576 GATCAAAATAGGGAATGAAGGAGTCCTACCAAATTCCTTCTATGACACAG 750625 v -v ii v i iiv v v i v i vi vi L1M5_orf2#LIN 1489 CA-GAAAATAGAAAAAGAGGGAACACTTCCCAACTCATTTTATGAGGCCA 1537 chr6qtel1M 750626 ACATGGTACTGATACTAAA-CCAGGTAG-GCTGAAACAGAGAAAGAAAAT 750673 i ?iiv i - ? ii i- viivv iii L1M5_orf2#LIN 1538 GCATNACCCTGATACCAAAACCNGACAAAGACATTACAAGAAAAGAAAAT 1587 chr6qtel1M 750674 TATAGACCAGTCTCC-TAATGAATATTGATGCTAAAATCTTAAATAAGAT 750722 i i v - v i v v i ? i i L1M5_orf2#LIN 1588 TACAGACCAATATCCCTCATGAACATAGATGCAAAAATCCTNAACAAAAT 1637 chr6qtel1M 750723 ATTAGCAAAAAGACTACAGAAAATCATCTCCAAGATAATACACTATGATC 750772 vv v v v vvi vvvv i ii i L1M5_orf2#LIN 1638 ATTAGCAAATCGAATCCAGCAATATATAAAAAGGATAATACATCATGACC 1687 chr6qtel1M 750773 AAGTAGGATTTATACCAGGAAT-CAGGGCATGGTTCAATATTAGGAAAAC 750821 i i v - i i- i i v i v L1M5_orf2#LIN 1688 AAGTGGGGTTTATCCCAGGAATGCAAGGT-TGGTTTAACATTCGAAAATC 1736 chr6qtel1M 750822 TATCAATATAATTGGCCATGTTAATA-ACCAAATTAACAAAACCATATGA 750870 v i vi i i - vi vv iv i L1M5_orf2#LIN 1737 AATCAATGTAATTCACCATATTAACAGAATAAAGGAGAAAAATCATATGA 1786 chr6qtel1M 750871 TCATCTCAATAGATGCAG-AAAAGCATTTGATAAAATCCAACATCCATTC 750919 - i i i L1M5_orf2#LIN 1787 TCATCTCAATAGATGCAGAAAAAGCATTTGACAAAATTCAACACCCATTC 1836 chr6qtel1M 750920 CT-ATTAAAACACTTGAGAGTATAGGAATAAATGGACTTTTCCTTAAAAT 750968 v - v v iiiv ivv i v ivvi i vv L1M5_orf2#LIN 1837 ATGATAAAAACTCTCAGCAAACTAGGAATAGAAGGGAACTTCCTCAACCT 1886 chr6qtel1M 750969 AATCAGCAGCATCTATTTAAAACCATCAGTAAGCATCATATGTAATGGAG 751018 i v ivi ivv vv i? i iv v L1M5_orf2#LIN 1887 GATAAAGGGCATCTACGAAAAACCTACAGCNAACATCATACTTAATGGTG 1936 chr6qtel1M 751019 ACAAACTCCAACCATTCCCAATAAGATC-TGAGTGAAACAAGGTTG-CCA 751066 v ? vv ?v v vv -v iii i v - i L1M5_orf2#LIN 1937 AAANACTGAANGCTTTCCCCCTAAGATCGGGAACAAGACAAGGATGTCCG 1986 chr6qtel1M 751067 CTATCACCGTTACTATTTAATATTGTATTAGAAACGCTAGCTATAGCAAC 751116 ? ii v i i i i iiiv i vv i L1M5_orf2#LIN 1987 CTNTCACCACTTCTATTCAACATTGTACTGGAGGTCCTAGCCAGTGCAAT 2036 chr6qtel1M 751117 AAGAGCTGAGAAAGAGATTAAAGGAATAAGAATAGAAGCAATGAGGAAGC 751166 ivvv i i v v ii v i -- v i ii L1M5_orf2#LIN 2037 AAGGCAAGAAAAAGAAATAAAAGGCATAAAGATTGGA--AAGGAAGAAAT 2084 chr6qtel1M 751167 CAAATTATCACTCTTTGCCGATGACATGATAGTATACTTAGAGAACCCCA 751216 v i i ?i v i v v ? v i i ? L1M5_orf2#LIN 2085 AAAACTGTCNTTATTCGCAGATGACATGATTGTNTACGTAGAAAATCCNA 2134 chr6qtel1M 751217 GAGATTCTGCTAAAAAGTTATTAGAAATAATCCACAACTTTAGCAAAGTT 751266 i v i v ? ii i v vviii v i i L1M5_orf2#LIN 2135 AAGAATCTACAAANAAACTACTAGAACTAATAAGTGAATTTAGCAAGGTC 2184 chr6qtel1M 751267 GCTGGTTATAAAATAAACCCACATAAGTCATCAGCA-TTCTATATATCAC 751315 ? v i ii v ivi v i viv i - ii v L1M5_orf2#LIN 2185 GCNGGATACAAGGTCAATATACAAAAATCAATTGTATTTCTATATACTAG 2234 chr6qtel1M 751316 TAACAA--AATCCAACAGTCAGAGTTATACAAGAGAAATTCCATTTAAAG 751363 i -- ivi v i v i v ---? i iv v v i L1M5_orf2#LIN 2235 CAACAAACAATTGGAAAATGAAATTT---NAAAAACAATACCATTTACAA 2281 chr6qtel1M 751364 TAACTACTGATAATATAAAATATTTAGGAATCTATCTGCCAAGGGAAAAT 751413 i vv vi v i ? i vv iv --- ? L1M5_orf2#LIN 2282 TAGCATCAAAAAACATNAAATACTTAGGAATAAATCTAACAA---AANAT 2328 chr6qtel1M 751414 ---CAGAAACTTTATGAGCAAAATTACAGACCACTTTTCACACAAATTAA 751460 --- ii v ? iivvv i i v i vi v v v L1M5_orf2#LIN 2329 GTGCAAGACCTNTACACTGAAAACTACAAAACATTGCTGAGAGAAATTAA 2378 chr6qtel1M 751461 GTCTGATCT-AACCAATTGAAAAATATTAAATGCTCTTGGATAGGGCGAG 751509 ivvv i - iv v i i vvv i v v iv v L1M5_orf2#LIN 2379 AGAAGACCTAAATAAATGGAGAGATATACCATGTTCATGGATTGGAAGAC 2428 chr6qtel1M 751510 TAAATATAATAAAGATGACAATATTACCTAAACTAATCTATTTATTTAGC 751559 v vi ? v vi v i i i vv i ii L1M5_orf2#LIN 2429 TCAATATTGTNAAGATGTCAATTCTCCCCAAATTGATCTATAGATTCAAT 2478 chr6qtel1M 751560 GCTATACCAATCAGACTCCCAAAAACTATTTTAATGACCTAGAAAAATAA 751609 v v i v iv iv v -- --- - v i L1M5_orf2#LIN 2479 GCAATCCCAATCAAAATCCCAGCAGGTTTTTT--TG---TAG-AAATTGA 2522 chr6qtel1M 751610 CAA--------CAAAGTTCATATGGAAA-ACAAAGAGTCAAGAAT-TTCA 751649 --------i i i -i iii ? -vi L1M5_orf2#LIN 2523 CAAGCTGATTCTAAAATTTATATGGAAATGCAAAGGACCNAGAATAGCCA 2572 chr6qtel1M 751650 AGGGAA--TTAAAGAAAAAAAATCAAATGATGGTGG-CTTAGCTGTACCA 751696 iiv -- i i i i - - v v - - vv ? L1M5_orf2#LIN 2573 AAACAATCTTGAAAAAGAAGAA-CAAA-GTTGGAGGACTTA-CACTACCN 2619 chr6qtel1M 751697 GATCT-AAAATTATATTATAAAGCAGCAGTTACCAAAACA-TTTGGTATT 751744 ? - i i - vi v i i - v L1M5_orf2#LIN 2620 GATNTCAAGACT-TATTATAAAGCTACAGTAATCAAGACAGTGTGGTATT 2668 chr6qtel1M 751745 GGC-TAAGGAATAGATTAGTTGATCAGTGGAATAGAGTAG---GTTCAAG 751790 - - iv i v i i i --- i ii L1M5_orf2#LIN 2669 GGCGTAAGG-ATAGACAAATAGATCAATGGAACAGAATAGAGAGTCCAGA 2717 chr6qtel1M 751791 GATAAAACAGTCA-ACA-ATATAGCAACCTAGTCTTTGACAAA---CCCA 751835 i i v --- - - i ?v ?i ii i ---v L1M5_orf2#LIN 2718 AATAGACC---CACACATATATGGNCANTTGATTTTTGACAAAGGTGCCA 2764 chr6qtel1M 751836 AAG--ATCCTAGCTTTTGGGATAAGAACTTACTGTTTGATAAA-ATTGCT 751882 ? -- i - ---- iv i ivvv v ii i -iv L1M5_orf2#LIN 2765 ANGCAATTC-AG----TGGGGAAAGGATAGTCTTTTCAACAAATGGTGCT 2809 chr6qtel1M 751883 GGGAAAAATTGAA-ACTAATATGGCAGAAACTTAGGCATTGATCCATACT 751931 - v i - iiv v i v v i? - i i v i L1M5_orf2#LIN 2810 -GGAACAATTGGATATCCATATGGAAAAAAATGAANC-TCGACCCCTACC 2857 chr6qtel1M 751932 TAACGCCGTACACCAAGATAAGGTCAAAATGGGTTCATGAACCTAGGCAT 751981 v i i v i v iv ? i i- ii iiii L1M5_orf2#LIN 2858 TCACACCATACACAAAAATTAATTCNAGATGGA-TCATAGACCTAAATGT 2906 chr6qtel1M 751982 AAAGAATGAAATCATTAATAAATTAGAGG--AACATAGGATAGTTTACAT 752029 ii? i ii v vvvvi i -- v ---- i L1M5_orf2#LIN 2907 AAAAGNTAAAACTATAAAACTTCTAGAAGAAAACATAGGAGA----ATAT 2952 chr6qtel1M 752030 C-TCA-GACCTGTGGA-AGGGAAGG---TCTT---TATGAC-CAAAAGCA 752069 - i- vv ?- v i --- ---i v - -- L1M5_orf2#LIN 2953 CTTCGTGACCTTGGGNTAGGCAAAGATTTCTTAAACAGGACACAAAA--A 3000 chr6qtel1M 752070 GAACTAGAGATCATACATGATCACAAAATAGA-AAATTTGATTATACC-A 752117 v ? --- i v v --- v v - v i ?i i - L1M5_orf2#LIN 3001 GCACNA---ACCATAAAAG---AAAAAATTGATAAATTGGACTNCATCAA 3044 chr6qtel1M 752118 AACTGAAAAGTTCTGTACAAACAAAACTAATGCAGACAAGATTAGAAGGG 752167 i i v iv ?vvv ivi vi ivi v i v i v L1M5_orf2#LIN 3045 AATTAAAAACTTCTGCTCNTCAAAAGACACCGTTAAGAAAATGAAAAGGC 3094 chr6qtel1M 752168 AAGCCATAAACTGGGAAAATATTTTTACAGT-CAAAGGTTCTGATAAAGG 752216 i i ? i v v i i?- v vi- i L1M5_orf2#LIN 3095 AAGCCACAGANTGGGAGAAAATATTTGCAANACATATA-TCTGACAAAGG 3143 chr6qtel1M 752217 CCTCATTTCCAAAATATATAGAGAATTAACTCTAATTT-ATAAAAATCAA 752265 v i v i i i -v vi ? i- ? -v L1M5_orf2#LIN 3144 ACTCGTATCCAGAATATATAAAGAACT-CCTACAANTCAATAANAA-AAA 3191 chr6qtel1M 752266 GTCATTC--TCCAAT-TGAAAATGGTCAAAGGATATGAACAGACAATTCT 752312 v vv --i -?i v i iv v v L1M5_orf2#LIN 3192 GACAAACAACCCAATANAAAAATGGGCAAAAGACTTGAACAGACACTTCA 3241 chr6qtel1M 752313 CAGATGAAGAAATTGAAACTATTTCTAGTCATATGAAAAGATGCTCCAAG 752362 i v v ?v iviiivv iv i v v? L1M5_orf2#LIN 3242 CAAAAGAAGATATNCAAATGGCCAATAAGCACATGAAAAGATGCTCAACN 3291 chr6qtel1M 752363 TCA 752365 L1M5_orf2#LIN 3292 TCA 3294 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 38.02 CpG sites = 457, Kimura (unadjusted) = 38.54 Transitions / transversions = 1.15 (457/397) Gap_init rate = 0.04 (135 / 3000), avg. gap size = 1.30 (175 / 135) 1558 26.97 1.29 1.48 chr6qtel1M 752224 752765 (247235) L1ME3G_3end#LINE/L1 7 547 (377) m_b318s551i7 13285 chr6qtel1M 752224 TCCAAAATATATAGAGAATTAACTCTAATTTATAAAAATCAAGTCATTCT 752273 i i i vviv v iv i -v v --vi L1ME3G_3end#L 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAA-AAAGACA--AC 53 chr6qtel1M 752274 CCAATTGAAAA-TGGTCAAAGGATATGAACAGACAATTCTCAGATGAAGA 752322 v - v i v v i L1ME3G_3end#L 54 CCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGGA 103 chr6qtel1M 752323 AATTGAAACTATTTCTAGTCATATGAAAAGATGCTCCAAGTCATTATTAA 752372 vv iviiivv iv v vv i v L1ME3G_3end#L 104 AATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTAA 153 chr6qtel1M 752373 TCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACACCTGTC 752422 i i vv i i viv ii L1ME3G_3end#L 154 TCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCATC 203 chr6qtel1M 752423 AGATTGGCTAAGA-TGACAGGAAAAATAATGATGATTGTTGGAG-GGATG 752470 v i - v v i ?vvi ivi? v v - i L1ME3G_3end#L 204 AGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGTG 253 chr6qtel1M 752471 TGGGAAAACTGGGACATTGATTCATTGTTGGTGGAGTTGTGAACAAATCC 752520 i v v vi v v i i iiv i ivii v L1ME3G_3end#L 254 TGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTAC 303 chr6qtel1M 752521 AACCATTTTGGAGAGTAGTTTGGAACTATGCTCAAAAAGTTATCAAACTG 752570 i ? i i i v v - vvv i -- i v L1ME3G_3end#L 304 AGCCNTTTTGGAGGGCAATTTGGCAGTAT-CTATTAAAAT--TTAAAATG 350 chr6qtel1M 752571 TGCATACCCTTTGATCCAGCAGTGTTACTACT-GGCTTATATCCCAAAGA 752619 i i i vii v - ?v v i ? L1ME3G_3end#L 351 CGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAGA 400 chr6qtel1M 752620 GAT-TTTAAAGAAG-GAAAAGGGACCTGTATGTGCAAGAATGTTTGTGGC 752667 i -i iiv v v - v v i --? i i i ii v L1ME3G_3end#L 401 AATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTCATTGC 448 chr6qtel1M 752668 AGCCCT-TTTGTAGTGGATAGAAACTGGAAACTGAATGGATGTCCATCAG 752716 vi - i i vv i i vivv ii i L1ME3G_3end#L 449 AGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCAA 498 chr6qtel1M 752717 TTGGAAAATGGCTGAATAAATTGTGGTATATGAAAATTATGGAATATTA 752765 v ii i i i vv v i i L1ME3G_3end#L 499 TAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACTA 547 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 33.78 CpG sites = 76, Kimura (unadjusted) = 34.40 Transitions / transversions = 1.12 (76/68) Gap_init rate = 0.03 (15 / 541), avg. gap size = 1.00 (15 / 15) 1503 25.94 3.97 3.61 chr6qtel1M 752272 752851 (247149) L1ME5_3end#LINE/L1 56 637 (304) m_b318s551i8 13285 chr6qtel1M 752272 CTCCAATTGAAAA-TGGTCAAAGGATATGAACAGACAATTCTCAGATGAA 752320 i v - v i iv v i L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chr6qtel1M 752321 GAAA-TTGAAA--CTATTTCTAGTCATATGAAAAGATGCTCCAAGTCATT 752367 -ii -- --v v - i v v L1ME5_3end#LI 106 GAAACCCGAAAGGCTA--ACAAG-CATATGAAGAGATGCTCAAACTCATT 152 chr6qtel1M 752368 ATTAATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACAC 752417 v i vv i i vi L1ME5_3end#LI 153 AGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACAC 202 chr6qtel1M 752418 CTGTCAGATTGGCTAAGATGACAGGAA---AAATAATGATGATTGTTGGA 752464 i i i v i --i i ---ii vii v v L1ME5_3end#LI 203 CTATTAGACTGGCAAAAAT--TAGAAAGCTGGATAATGCCAAGTGTTGGC 250 chr6qtel1M 752465 G-GGATGTGGGAAAACTGGGACATTGATTCATTGTTGGTGGAGTTGTGAA 752513 - i ? iv i vi v v i i iiv ii L1ME5_3end#LI 251 GAGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGA 300 chr6qtel1M 752514 CAAATCCAACCATTTTGGAGAGTAGTTTGGAACTA--TGCTCAAA--AAG 752559 vii v i i i i i v v -- iv -- L1ME5_3end#LI 301 CTGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTAAG 350 chr6qtel1M 752560 TTATCAAACTGTGCATACCCTTTGATCCAGCAGTGTTACTACTGGCT-TA 752608 - --- --- v i i viii v v - L1ME5_3end#LI 351 -TAT---AC---GCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATA 393 chr6qtel1M 752609 TATCCCAAAGAGATTTTAAAGAAGG---A-AAAGGGACCTGTATGTGCAA 752654 i i v viv --- - i ---- i i L1ME5_3end#LI 394 TATCCCAAAGAAATTCTCACACAGGTCCATAAGGGGAC----ATGTACGA 439 chr6qtel1M 752655 GAATGTTTGTGGCAGCCCT-TTTGTAGTGGATAGAAACTGGAAACTGAAT 752703 i ii v vi - i vvi i ii ii vivv L1ME5_3end#LI 440 GGATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCT 489 chr6qtel1M 752704 GGATGTCCATCAGTTGGAAAATGGCTGAATAAATTGTGGTATATGAAAAT 752753 i v v i i v iii v iv v v i L1ME5_3end#LI 490 GGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACAC 539 chr6qtel1M 752754 TATGGAATATTACTGT-TCTGTAAGAAATGACCAACAGGATGATTTCAGA 752802 i i i - i-v v v iii vi vi -- v v L1ME5_3end#LI 540 CATGGAGTACTA-TGCAGCAGTTAGAAGCAACGGACTAGATG--TACACA 586 chr6qtel1M 752803 AAG--GCCTGGAGAGA-CTTACACGAAC-TGATGCTGAGTGAAATGAGCA 752848 v --i v vi - v -- - ii vi i L1ME5_3end#LI 587 TAGCAACATGGATGGATCTTAAA--AACATAGTGCTGAGTGAAAAAAGTA 634 chr6qtel1M 752849 GGA 752851 i L1ME5_3end#LI 635 AGA 637 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 31.81 CpG sites = 86, Kimura (unadjusted) = 32.66 Transitions / transversions = 1.46 (86/59) Gap_init rate = 0.06 (36 / 579), avg. gap size = 1.22 (44 / 36) 24 12.17 0.00 0.00 chr6qtel1M 753312 753347 (246653) (A)n#Simple_repeat 1 36 (0) m_b318s252i3 13286 chr6qtel1M 753312 AAAAAAATAAAATAAAAAAATAAAAAATAAAAAAAA 753347 v v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 36 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 1871 32.39 2.53 2.04 chr6qtel1M 753348 754614 (245386) L1P3_orf2#LINE/L1 2015 3287 (7) m_b318s551i9 13287 chr6qtel1M 753348 TAGAAACGCTAGCTATAGCAATAAGAGCTGAGAAAGAGATTAAAGGAATA 753397 i iiv i i vi v ivvv i v i v v L1P3_orf2#LIN 2015 TGGAAGTTCTGGCCAGGGCAATCAGGCAAGAGAAAGAAATAAAGGGTATT 2064 chr6qtel1M 753398 AGAATAGGCAATGAGGAAGCCAAATTATCACTCTTTGCCGATGACATGAT 753447 vi v iv i i v v v L1P3_orf2#LIN 2065 CAAATAGGAAGAGAGGAAGTCAAATTGTCTCTGTTTGCAGATGACATGAT 2114 chr6qtel1M 753448 GGTATACTTAGAGAACCCCAGAGATTCTGCT-AAAAGTTATTAGAAATAA 753496 v i i vv vi v i- ?i vi vi iv i L1P3_orf2#LIN 2115 TGTATATTTAGAAAACCCCATCGTCTCAGCCCAAAANCTCCTTAAGCTGA 2164 chr6qtel1M 753497 TCCACAACTTTAGCAAAGTTGCTGGTTATAAAATAAACCCACATAAGTCA 753546 vvi i iv v v i v ivii v i L1P3_orf2#LIN 2165 TAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTGCAAAAATCA 2214 chr6qtel1M 753547 TCAGCATTCTTATATATCACTAACAAAATCCAACAGTCAGAGTTA---CA 753593 iv i i i v i i -- v -- ii --- L1P3_orf2#LIN 2215 CAAGCATTCCTATACACCAATAATAGA--CAAACAG--AGAGCCAAATCA 2260 chr6qtel1M 753594 -AAGAGAAATTCCATTTAAAGTAACTACTGATAATATAAAATATTTAGGA 753642 -i v v i i v i vi vi v iv ii L1P3_orf2#LIN 2261 TGAGTGAACTCCCATTCACAATTGCTACAAAGAGAATAAAATACCTAGGA 2310 chr6qtel1M 753643 ATCTATCTGCCAAGGGAAAATCAGAAACTTTATGAGCAAAATTACAGACC 753692 vi v vv vivvv i v i vii v i i i L1P3_orf2#LIN 2311 ATACAACTTACAAGGGATGTGAAGGACCTCTTCAAGGAGAACTACAAACC 2360 chr6qtel1M 753693 ACTTTTACACACAAATTAAGTCTGATCTAACCAATTG--AAAATATTAAA 753740 vi - viv v iivvv ivi v v -- i vv L1P3_orf2#LIN 2361 ACTGCT-CAAGGAAATAAGAGAGGACACAAACAAATGGAAAAACATTCCA 2409 chr6qtel1M 753741 TGCTCTTGGATAGGC-GAGCAAATATAATAAAGATGACATATATTACCTA 753789 v v- iiv vi i i i -i i i i L1P3_orf2#LIN 2410 TGCTCATGGATAGGAAGAATCAATATCGTGAAAATGGC-CATACTGCCCA 2458 chr6qtel1M 753790 AA-CAATCTATTTATTTAGCGCTATACCAATCAGACTCCCAAAAACTATT 753838 -i i vv i ii v v ii v vvi v i L1P3_orf2#LIN 2459 AAGTAATTTATAGATTCAATGCTATCCCCATCAAGCTACCATTGACTTTC 2508 chr6qtel1M 753839 TTAAT-GACCTAGAAAAAATAACAACAAAGTTCATATGGAAAAACAAAAG 753887 v i- vi iv vvi v vv v L1P3_orf2#LIN 2509 TTCACAGAATTAGAAAAAACTACTTTAAATTTCATATGGAACCAAAAAAG 2558 chr6qtel1M 753888 GTCAAGAAT-TTCAAGGGAAT--TAATGAAAAAAAAATCAAATGATGGTG 753934 iv vv v -vi iv -- vv i -- - v v L1P3_orf2#LIN 2559 AGCCCGTATAGCCAAGACAATCCTAAGCAAAAAGAA--CAAA-GCTGGAG 2605 chr6qtel1M 753935 GCTTAGCTGTACCAGATCTAAAATTATATTATAAAGCAGCAGTTACCAAA 753984 v vi vv v ii v i i i i vi v L1P3_orf2#LIN 2606 GCATCACGCTACCTGACTTCAAACTATACTACAAGGCTACAGTAACCAAA 2655 chr6qtel1M 753985 ACTATTTGGTATTGGTTAAGGAATAGATTAGTTGATCAGTGGAATAGATT 754034 viiv i vvvii i vvi v i i i vi L1P3_orf2#LIN 2656 ACAGCATGGTACTGGTACCAAAACAGATATATAGACCAATGGAACAGAAC 2705 chr6qtel1M 754035 AG--GTTCAAGGGATAAAACAGTCA-ACAAATATAGCAACCTAGTCTTTG 754081 -- iiiv ii -- - i - vv i i v i ii L1P3_orf2#LIN 2706 AGAGGCCTCAGAAATAA--C-GCCACACATCTACAACCATCTGATCTTTG 2752 chr6qtel1M 754082 ACAAACC---CAAAGATCCCAGCTTTTGGGATAAGAACTTACTATTTGAT 754128 --- i -- v vv v - i i iv i L1P3_orf2#LIN 2753 ACAAACCTGACAAAAA--CAAGCAATGGGGA-AAGGATTCCCTATTTAAT 2799 chr6qtel1M 754129 AAAAATTGCTGGGAAAATTGGAAACTAATATGGCAG-AAACTAGGCATTG 754177 viv i i vv viv - - iiivv v L1P3_orf2#LIN 2800 AAATGGTGTTGGGAAAACTGGCTAGCCATAT-GCAGAAAACTGAAACTGG 2848 chr6qtel1M 754178 ATCCATACTTAACACCGTACACCAAGATAAGGTCAAAATGGGTTCATGAC 754227 i v v i v v i v i v iv i i v v L1P3_orf2#LIN 2849 ACCCCTTCCTTACACCTTATACAAAAATTAACTCAAGATGGATTAAAGAC 2898 chr6qtel1M 754228 CTAGGCATAAAGAATGAAATTATTAATAAATTAGAGGAACAC--AGGATA 754275 i ii i iivv i ii v v vvi i v -- -i L1P3_orf2#LIN 2899 TTAAACGTAAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGG-CA 2947 chr6qtel1M 754276 GTTGACCTCTCA-GACCTATGGAAGGGGAAGGTCTTTATGACCAAAGCAG 754324 i -- vi - v v v v v i v i i i v L1P3_orf2#LIN 2948 AT--ACCATTCAGGACATAGGCATGGGCAAAGACTTCATGACTAAAACAC 2995 chr6qtel1M 754325 AACTAGAGATCATTACTGATCACAAAATAGAAAATTTCGATTATACCAAA 754374 v vv vi viiv vi vvv v v v vv ivv ii L1P3_orf2#LIN 2996 CAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAA 3045 chr6qtel1M 754375 CTGAAAAG-TTTTGTA---CAAACAAAACTA--ATGCAGACAAGATTAGA 754418 i i - i i --- vi -- - -iv -- v L1P3_orf2#LIN 3046 CTAAAGAGCTTCTGCACAGCAAAAGAAACTATCAT-CAGA-GTGA--ACA 3091 chr6qtel1M 754419 AGGAAGCAATAAACTGGGAAAATATTTTTACAGTCAAAGGTTCTGATAAA 754468 i v v v i i v i v i i v vvvv i L1P3_orf2#LIN 3092 GGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAAA 3141 chr6qtel1M 754469 GGCCTCATTTCCAAAATATATAGAGAATTAACTCTAATTTAT---AAAAA 754515 v v v i v i ii i v vv v i--- L1P3_orf2#LIN 3142 GGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAAAA 3191 chr6qtel1M 754516 ATCAAGCCATTCTCCAATTGAAAAATGGTCAAAGGATATGAACAGACAAT 754565 v i v -- i - ii i v i v L1P3_orf2#LIN 3192 AACAAACAA--CCCC-ATCAAAAAGTGGGCGAAGGATATGAACAGACACT 3238 chr6qtel1M 754566 TCTCAGATGAAGAAATTGAAACTATTTCTAGTCATATGAAAAGATGCTC 754614 i v v v vi viiivvi iv i v L1P3_orf2#LIN 3239 TCTCAAAAGAAGACATTTATGCGGCCAACAAACATATGAAAAAAAGCTC 3287 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 42.61 CpG sites = 197, Kimura (unadjusted) = 43.03 Transitions / transversions = 0.96 (197/205) Gap_init rate = 0.04 (45 / 1266), avg. gap size = 1.29 (58 / 45) 1218 27.74 2.01 2.96 chr6qtel1M 754478 755023 (244977) L1ME3G_3end#LINE/L1 7 547 (377) m_b318s551i10 13287 chr6qtel1M 754478 TCCAAAATATATAGAGAATTAACTCTAATTTATAAAAAATCAAGCCATTC 754527 i i i vviv v iv i -- v --v L1ME3G_3end#L 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAA--AAGACA--A 52 chr6qtel1M 754528 TCCAATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGAAG 754577 i v v i v v i L1ME3G_3end#L 53 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chr6qtel1M 754578 AAATTGAAACTATTTCTAGTCATATGAAAAGATGCTCCAAGTCATTATTA 754627 vv iviiivv iv v vv i v L1ME3G_3end#L 103 AAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTA 152 chr6qtel1M 754628 ATCAGAGAAATGCAAATTAAGACAACTCTAAGATACTCACTACACACCTG 754677 i i vv i - i viv ii L1ME3G_3end#L 153 ATCAGGGAAATGCAAATTAAAACAACAATGAGATAC-CATTTTTCACCCA 201 chr6qtel1M 754678 TCAGATTGGCTAAGA-TGACAGGAAAAATAATGATGATTGTT---GAGGG 754723 v i - v v i ?vvi ivi? v --- L1ME3G_3end#L 202 TCAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGG 251 chr6qtel1M 754724 -ATGCGGAAAACTGGGACATTGATGCATTGTTGGTGGAGTTGTAA--CGA 754770 -i - i v v vi v i i i iiv --i i L1ME3G_3end#L 252 TGTG-GGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGG 300 chr6qtel1M 754771 ATCAATCCATTTTGAGAGTAGTTTGGAACTATGCTCAAAAAGTTATCAAA 754820 vv ii ?v v i i i v v - vvv i -- i L1ME3G_3end#L 301 TACAGCCNTTTTGGAGGGCAATTTGGCAGTAT-CTATTAAAAT--TTAAA 347 chr6qtel1M 754821 CTGTGCAGCTACCCTTTGATCCAGCTAGTGTTACTACTGGGCTTATATCC 754870 v i -- i - i vii v ? ?v v L1ME3G_3end#L 348 ATGCGCA--TACCCTTTGACCCAGC-AATTCCACTTCTNGGNATCTATCC 394 chr6qtel1M 754871 CAAAGAGATTAT-AAAGAAG-GGAAAGGGACCTGTATGTGCATGAATGTT 754918 i ? i vv -iv v v - v v i --? i i v i L1ME3G_3end#L 395 TANAGAAATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTT 442 chr6qtel1M 754919 TGTGGCAGCCCT-TTTGCTAGCGGCTAGAACCTGAGAACTGAATGGATGT 754967 ii v vi - - iii v i vi ii vivv ii L1ME3G_3end#L 443 CATTGCAGCATTGTTTG-TAATAGCGAAAAATTGGAAACAACCTAAATGT 491 chr6qtel1M 754968 CCATCAGTTGGAGAATGGCTGAATAAATC-TGTGTATATGAATATTACAA 755016 i v i i i i- - vv i iii L1ME3G_3end#L 492 CCATCAATAGGGGAATGGTTAAATAAATTATG-GTATATCCATACTATGG 540 chr6qtel1M 755017 AATACTA 755023 L1ME3G_3end#L 541 AATACTA 547 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 35.18 CpG sites = 78, Kimura (unadjusted) = 35.78 Transitions / transversions = 1.13 (78/69) Gap_init rate = 0.04 (24 / 545), avg. gap size = 1.12 (27 / 24) 1028 27.87 3.99 3.63 chr6qtel1M 754529 755105 (244895) L1MC5a_3end#LINE/L1 58 636 (2141) m_b318s551i11 13287 chr6qtel1M 754529 CCAATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGAAGA 754578 v v i i v vi L1MC5a_3end#L 58 CCAATAGAAAAATGGGCAAAAGATATGAACAGACAGTTCACAGAAAAAGA 107 chr6qtel1M 754579 AATTGAAACTATTTCTAGTCATATGAAAAGATGCTCCAAGTCATTATTAA 754628 vv iviiiii iv v vv i vv L1MC5a_3end#L 108 AATGCAAATGGCCCTTAAACATATGAAAAGATGCTCAACCTCACTCATAA 157 chr6qtel1M 754629 TCAGAGAAATGCAAATTAAGACAACTCTAAGATACTCACTACACACCTGT 754678 v i v v i - i v v i L1MC5a_3end#L 158 TAAGAGAAATGCAAATTAAAACTACACTGAGATAC-CATTTCTCACCTAT 206 chr6qtel1M 754679 CAGATTGGCTAAGAT--GACAG---GA-AAAATAATGATGATTGTTGAGG 754722 v i --i v --- - v v v- - vi L1MC5a_3end#L 207 CAGATTGGCAAAAATCCAAAAGTTTGACAACATACTC-TG-TTGGCGAGG 254 chr6qtel1M 754723 G-ATGCGGAAAACTGGGACATTGATGCATTGTTGGTGGAGTTGTAACGAA 754771 v-i - i v v vi v i i iiv i -- L1MC5a_3end#L 255 CTGTG-GGGAAACAGGCACTCTCATACATTGCTGGTGGGAATGCAA--AA 301 chr6qtel1M 754772 T----CAATCCATTTTGAGAGTAGTTTGGAACTATGCTCAAAAAGTTATC 754817 ---- i v v v i v i v v - viv i - L1MC5a_3end#L 302 TGGTACAACCCCTATGGAGGGGAATTTGGCAATAT-CTAGCAAAATTA-C 349 chr6qtel1M 754818 AAACTGTGCAGCTACCCTTTGATCCAGCTAGTGTTACTACTGGGCTTATA 754867 --- i vi i - i vii v i vv v L1MC5a_3end#L 350 A---TATGCATTTACCCTTTGACCCAGC-AATCCCACTTCTAGGAATCTA 395 chr6qtel1M 754868 TCCCAAAGAGA---TTATAAAGAAGGGAAAGGGACCTGTATGTGCATGAA 754914 i v --- ?ii i viv -? -- ii v iv L1MC5a_3end#L 396 TCCCGAAGATACACTNGCAAAAATACGAAA-NGAC--GTATGCACAAGGT 442 chr6qtel1M 754915 TGTTTGTGGCAGCCCT-TTTGCTAGCGGCTAGAACCTGAGAACTGAATGG 754963 i ii v vi - - iii v i iv ii vivviii L1MC5a_3end#L 443 TATTCATTGCAGCATTATTTG-TAATAGCAAAAGACTGGAAACAACCCAA 491 chr6qtel1M 754964 ATGTCCATCAGTTGGAGAATGGCTGAATAAATCTGT-GTATATGAATATT 755012 i v i v i - i - i vv i iv L1MC5a_3end#L 492 ATGTCCATCAATAGGGGACTGGTTGAATAAA-CTATGGTACATCCACACA 540 chr6qtel1M 755013 ACAAAATACTACTGT-TCTATAAGAAATGACCATCAGGATGATTTCAAGA 755061 iii i - i-v i - v -- v v i v v L1MC5a_3end#L 541 ATGGAGTACTA-TGCAGCTGTAA-AAAGGA--ATGAGGAAGATCTCTATA 586 chr6qtel1M 755062 AA--GGCCT-GAGAGACTTACACGA---ACTGTTGAGTGAAATGAGCAGG 755105 v -- ?iv - v ii v v --- i i vi i L1MC5a_3end#L 587 TACTGNTATGGAGTGATCTCCAGGATATATTGTTAAGTGAAAAAAGCAAG 636 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 35.08 CpG sites = 82, Kimura (unadjusted) = 35.64 Transitions / transversions = 1.12 (82/73) Gap_init rate = 0.06 (33 / 576), avg. gap size = 1.33 (44 / 33) 26 0.00 0.00 0.00 chr6qtel1M 755570 755594 (244406) (AAAAT)n#Simple_repeat 1 25 (0) c_b318s251i2 13288 chr6qtel1M 755570 AAAATAAAATAAAATAAAATAAAAT 755594 (AAAAT)n#Simp 1 AAAATAAAATAAAATAAAATAAAAT 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 248 24.83 0.00 8.70 chr6qtel1M 757399 757473 (242527) C MIRb#SINE/MIR (3) 265 197 m_b318s601i2 13289 chr6qtel1M 757399 AAGAGAACAAGCATTTATTAAGTTCCTACTATTAATATGATCAAGGAACT 757448 v i v v i iv i ----i -- v v C MIRb#SINE/MIR 265 AATAGAGCTACCATTTATTGAGCGCTTACTAT----GTG--CCAGGCACT 222 chr6qtel1M 757449 GTGCTAAGTATTTTACATATAATAT 757473 iii ii v C MIRb#SINE/MIR 221 GTGCTAAGCGCTTTACATGCATTAT 197 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 26.16 CpG sites = 10, Kimura (unadjusted) = 30.49 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.08 (6 / 74), avg. gap size = 1.00 (6 / 6) 18 21.75 3.77 0.00 chr6qtel1M 757761 757813 (242187) (AAAG)n#Simple_repeat 1 55 (0) m_b318s252i4 13290 chr6qtel1M 757761 AAAGAAATAAAGAAAGAAATACA-AAATAAAATAAAAATGAGA-AAAAAA 757808 v v v - v iv i v i - i (AAAG)n#Simpl 1 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAA 50 chr6qtel1M 757809 AGAAA 757813 (AAAG)n#Simpl 51 AGAAA 55 Matrix = Unknown Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.00 (2 / 2) 306 33.64 1.85 0.92 chr6qtel1M 758145 758252 (241748) C MIRc#SINE/MIR (157) 111 3 m_b318s601i3 13291 chr6qtel1M 758145 TTAATTGACATGCCCAGAAACATACAAGTTGTGTACTGTTATAGAAGAGA 758194 v v iiiv i iv v i- v vi v vv i C MIRc#SINE/MIR 111 TTAAGTGACTTGCCCAAGGTCACACAGCTAGTA-AGTGGCAGAGCCGGGA 63 chr6qtel1M 758195 CTTGAATCCAAATTTTTCTGGTTGGAAGGACAGTCTTCTATCCACT--AG 758242 i i ii i i ii vv vv vi v -- v C MIRc#SINE/MIR 62 CTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCAC 13 chr6qtel1M 758243 CATATTGCCT 758252 i i C MIRc#SINE/MIR 12 CACACTGCCT 3 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 43.94 CpG sites = 19, Kimura (unadjusted) = 45.64 Transitions / transversions = 1.12 (19/17) Gap_init rate = 0.02 (2 / 107), avg. gap size = 1.50 (3 / 2) 231 16.28 0.00 0.00 chr6qtel1M 758261 758303 (241697) EuthAT-N1a#DNA/hAT-Tip100 100 142 (116) m_b318s502i0 13292 chr6qtel1M 758261 CTATTTAGCAAAATTAATGACTTAAGATAGGAAGCTACCAAAT 758303 v i v v v i i EuthAT-N1a#DN 100 CTAGTTAGCAAGAATAATTAGTTAAAATAGGAAGCTACCAGAT 142 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 18.38 CpG sites = 3, Kimura (unadjusted) = 18.38 Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 372 29.27 18.29 0.00 chr6qtel1M 758871 759034 (240966) C MIRc#SINE/MIR (18) 250 57 m_b318s601i4 13293 chr6qtel1M 758871 CATTTCCATAATGCTTTATGGTTTGAAAAGGACTTT-ACATATATTAATC 758919 vi iii ii iv vi - i vii C MIRc#SINE/MIR 250 CATTTGTATAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATCT 201 chr6qtel1M 758920 CAGTTTTTCCT---GACAACCATGACAGGTAGGT------GCTATTTACA 758960 v vv ---i v vv i------ v vvi C MIRc#SINE/MIR 200 CATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTA 151 chr6qtel1M 758961 TGCCTACTTTATAAATAA-------------CAAATA-------TGATTT 758990 v i i i i i ------------- i v ------- i C MIRc#SINE/MIR 150 TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTT 101 chr6qtel1M 758991 GTGCAGGGTCACACAGCTAGTATGCATCTGAGGCAGGATTTGAA 759034 iv i v iiv v v i i i C MIRc#SINE/MIR 100 GCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAA 57 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 35.14 CpG sites = 28, Kimura (unadjusted) = 38.12 Transitions / transversions = 1.40 (28/20) Gap_init rate = 0.03 (5 / 163), avg. gap size = 6.00 (30 / 5) 353 33.40 2.01 5.56 chr6qtel1M 759349 759497 (240503) C MIRb#SINE/MIR (121) 147 4 m_b318s601i7 13289 chr6qtel1M 759349 TTTTACAGATCAGAAAACTAAAG-TAAAGGGGACCAAGTGACTTGCCAAG 759397 v i i i - v ii i iii i v i C MIRb#SINE/MIR 147 TTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAA 98 chr6qtel1M 759398 GGTCGCACAGCTAATGAAGGTTTGAGGC-AGATTTGAACTTAAGAAGATA 759446 i i i iv viv v -i i ii i ------ C MIRb#SINE/MIR 97 GGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGG------ 54 chr6qtel1M 759447 AATCTTCCTGACTGTGGATCCAGTTCTCTAATCTCTGAGCC-CTCTACTC 759495 -- vi viii v v v vvi v vi - v i i C MIRb#SINE/MIR 53 --TCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCACCACGCTGCCC 6 chr6qtel1M 759496 TT 759497 i C MIRb#SINE/MIR 5 CT 4 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 45.01 CpG sites = 30, Kimura (unadjusted) = 46.39 Transitions / transversions = 1.76 (30/17) Gap_init rate = 0.07 (11 / 148), avg. gap size = 1.00 (11 / 11) 420 28.66 1.57 6.61 chr6qtel1M 759349 759475 (240525) C MIRc#SINE/MIR (124) 144 24 m_b318s601i6 13289 chr6qtel1M 759349 TTTTACAGATCAGAAAACTAAAG-TAAAGGGGACCAAGTGACTTGCCAAG 759397 v i i i - v ii i iii v i C MIRc#SINE/MIR 144 TTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAA 95 chr6qtel1M 759398 GGTCGCACAGCTAATGAAGGTTTGAGGC-AGATTTGAACTTAAGAAGATA 759446 i i i iv viv v -i i i ii i ------ C MIRc#SINE/MIR 94 GGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGG------ 51 chr6qtel1M 759447 AATCTTCCTGACTGTGGATCCAGTTCTCT 759475 -- viiii v C MIRc#SINE/MIR 50 --TCTTCCTGACTCCAAGTCCAGTGCTCT 24 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 36.86 CpG sites = 25, Kimura (unadjusted) = 38.34 Transitions / transversions = 2.78 (25/9) Gap_init rate = 0.08 (10 / 126), avg. gap size = 1.00 (10 / 10) 798 29.87 4.10 1.20 chr6qtel1M 759541 759784 (240216) MIRc#SINE/MIR 17 267 (1) m_b318s601i8 13294 chr6qtel1M 759541 AATGCATAGAGCACTGAACTTGTAGTCAGGAAAATGTGAGCTCAAATCTT 759590 i v v i v i iv i i i i ii MIRc#SINE/MIR 17 AGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCC 66 chr6qtel1M 759591 GCCTCAGATAACAC---CTAGATGCACAAGCCTATACAAATCACTTAATC 759637 v --- iv --- v iiii v i ivi i i MIRc#SINE/MIR 67 GGCTC---TGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACC 113 chr6qtel1M 759638 TTTGTCTGCCTCAATTTACTAACCTGTAAAATGGAAGTAATTATAAC--- 759684 i v vv i v v i iii v v --- MIRc#SINE/MIR 114 TCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGC 163 chr6qtel1M 759685 ---ACATATCTGCAACCATTATTATAAGGATTAATTGAGATAATCTGTGT 759731 ---i v i vvv vvi i i i i v v i MIRc#SINE/MIR 164 CCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGT 213 chr6qtel1M 759732 -AAAGTGTCTTATAAACCTTAAAGCACTATAGAAATGTGAACCATTATAA 759780 - i ii i iv ii v i iv?i v MIRc#SINE/MIR 214 GAAAGCGCTTTGTAAACTGTAAAGTGCTATACAAATGTAAGGNGTTATTA 263 chr6qtel1M 759781 TTAT 759784 MIRc#SINE/MIR 264 TTAT 267 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 37.53 CpG sites = 44, Kimura (unadjusted) = 39.66 Transitions / transversions = 1.57 (44/28) Gap_init rate = 0.03 (7 / 243), avg. gap size = 1.86 (13 / 7) 297 28.73 10.97 1.18 chr6qtel1M 760181 760335 (239665) C L1ME5_3end#LINE/L1 (617) 324 155 m_b318s551i12 13295 chr6qtel1M 760181 TGCTTTCCAGAATGGTTAGACACC--TTCACACTTTAACCAATAGTACAT 760228 i i --i -- ii iiv ii i C L1ME5_3end#LI 324 TGCTCTCCAGAATGGCT--GCACCAGTCTACACTCCCACCAGCAGTGCAT 277 chr6qtel1M 760229 TAATATACCTGCTTTTCTTCATCC-CTCCAACATTTT---TTATC----- 760269 v ivi v ii? ii iv - v i v--- ----- C L1ME5_3end#LI 276 GAGGGTTCCTATNTCCCCACATCCTCGCCAACACTTGGCATTATCCAGCT 227 chr6qtel1M 760270 -----ACCTTTGTCAGTAACATGGGTG-AGAGTGGGATCTCAAGAATGTT 760313 ----- ii i vvv i - i iv vviv C L1ME5_3end#LI 226 TTCTAATTTTTGCCAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTT 177 chr6qtel1M 760314 TTCATTTGCTTTTCACAAATTA 760335 v v v vi C L1ME5_3end#LI 176 TTAATTTGCATTTCTCTGATTA 155 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 37.62 CpG sites = 26, Kimura (unadjusted) = 37.62 Transitions / transversions = 1.44 (26/18) Gap_init rate = 0.05 (8 / 154), avg. gap size = 2.38 (19 / 8) 360 33.33 2.19 1.45 chr6qtel1M 761238 761374 (238626) C MIR#SINE/MIR (121) 141 4 m_b318s601i9 13296 chr6qtel1M 761238 ATTTTATATATGAAATGACTGAGTCAAACAG-GATTGAGTGACTTGCCCA 761286 i v iivi v v v - i i i C MIR#SINE/MIR 141 ATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCCA 92 chr6qtel1M 761287 CAGTCAAAAAACTAGTAATTATCTAATGCTGAATTTGAATTCAGG--GTT 761334 vi v v i v iv vi vv v i i ii -- i C MIR#SINE/MIR 91 AGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGCAGTC 42 chr6qtel1M 761335 TATGCTCTGTGAGTCTATCATTTTGTGTACTAAGCTATGC 761374 i- ii- i ii vv i ivvi v i C MIR#SINE/MIR 41 TG-GCTCCA-GAGCCCGTGCTCTTAACCACTATGCTATAC 4 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 42.70 CpG sites = 26, Kimura (unadjusted) = 45.58 Transitions / transversions = 1.37 (26/19) Gap_init rate = 0.03 (4 / 136), avg. gap size = 1.25 (5 / 4) 16 5.20 0.00 0.00 chr6qtel1M 761455 761474 (238526) (A)n#Simple_repeat 1 20 (0) m_b318s252i5 13297 chr6qtel1M 761455 AAAATAAAAAAAAAAAAAAA 761474 v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAA 20 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 394 27.70 1.79 6.54 chr6qtel1M 766327 766438 (233562) MIRc#SINE/MIR 11 117 (151) m_b318s601i10 13298 chr6qtel1M 766327 TAGCACCATGGACAGAGCACCAACTCTGGAGTCATGAGAACCTGAGTTCA 766376 i ii vi v iiivii v ii i i MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr6qtel1M 766377 AATCCAGTGCTAGACCCTTAACATTTACTAGCTATGTGACCCTAGGTAAA 766426 i v - ------i iv i i i i i i MIRc#SINE/MIR 61 AGTCCCG-GCT------CTGCCACTTACTAGCTGTGTGACCTTGGGCAAG 103 chr6qtel1M 766427 TCACTT--CCTATC 766438 -- v MIRc#SINE/MIR 104 TCACTTAACCTCTC 117 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 35.19 CpG sites = 22, Kimura (unadjusted) = 36.83 Transitions / transversions = 3.14 (22/7) Gap_init rate = 0.07 (8 / 111), avg. gap size = 1.12 (9 / 8) 59 1.85 0.00 0.00 chr6qtel1M 766443 766497 (233503) (CA)n#Simple_repeat 1 55 (0) c_b318s251i3 13299 chr6qtel1M 766443 CACACACACACACACACACACACACACACACACACACACACACATACACA 766492 i (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 chr6qtel1M 766493 CACAC 766497 (CA)n#Simple_ 51 CACAC 55 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 18 18.97 0.00 0.00 chr6qtel1M 766723 766760 (233240) (AGGT)n#Simple_repeat 1 38 (0) m_b318s252i6 13300 chr6qtel1M 766723 AGATAGGTAGGTAGGTAGGTAGGTGAGTAGACAGATAG 766760 i ii ii i (AGGT)n#Simpl 1 AGGTAGGTAGGTAGGTAGGTAGGTAGGTAGGTAGGTAG 38 Matrix = Unknown Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 231 8.73 0.00 6.52 chr6qtel1M 766779 766827 (233173) L1ME2z_3end#LINE/L1 1017 1062 (129) m_b318s551i13 13301 chr6qtel1M 766779 AGATGGACAGATGGATGGATAGATGACGGATGGATAGATGGATAGATGT 766827 iv ---v i L1ME2z_3end#L 1017 AGATGGATTGATGGATGGATAGA---GGGATGGATAGATGGATAGATAT 1062 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 9.26 CpG sites = 2, Kimura (unadjusted) = 9.26 Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.06 (3 / 48), avg. gap size = 1.00 (3 / 3) 389 32.00 2.00 6.25 chr6qtel1M 767809 767958 (232042) C MIRc#SINE/MIR (120) 148 5 m_b318s601i11 13302 chr6qtel1M 767809 CCAATTTTACAAATCAGGAAACTGAGGCAAAAAAGGGCT--GTGATTTGG 767856 v i v vv i ii i -- i v C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr6qtel1M 767857 TTAGGGTTACATAGCTGGTGAGTATGTTAAGTC-AGATTTTAACTCAGGA 767905 ii i i i i i i- ivi i -i i iv i - C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTG-GCAGAGCCGGGACTCGAACCCAGG- 51 chr6qtel1M 767906 AAAAGAATTTTCCTTTGTCTAAGCTCAGCACTGAATCCAATGATCCACAT 767955 ------- i vvv i ii ii vvv v vv i C MIRc#SINE/MIR 50 -------TCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACAC 8 chr6qtel1M 767956 AGC 767958 v C MIRc#SINE/MIR 7 TGC 5 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 42.05 CpG sites = 28, Kimura (unadjusted) = 43.36 Transitions / transversions = 1.65 (28/17) Gap_init rate = 0.07 (11 / 149), avg. gap size = 1.09 (12 / 11) 427 34.94 9.41 3.86 chr6qtel1M 767980 768372 (231628) L2b_3end#LINE/L2 43 456 (10) m_b318s601i12 13303 chr6qtel1M 767980 CCACTCCTACATTGTTTAATC-----CAGTGACTTCTGGTCTCCTTGCTT 768024 iiv v i i v ----- iv v- i v L2b_3end#LINE 43 CCACTCTCCCCTTGCTCACTCTGCTCCAGCCACA-CTGGCCTCCTTGCTG 91 chr6qtel1M 768025 TTCCACCAAAAAGAAATTATAGCTCTCAGATCAATG-----------GAT 768063 v v v v vv ?vv v? i ivv iv ----------- v L2b_3end#LINE 92 TTCCTCGAACACGCCANGCTCNCTCCCGCCTCAGGGCCTTTGCACNTGCT 141 chr6qtel1M 768064 GATTGCTTT-CCTGGGATGC--TTGCTC---TCCTTATTT--CTACCTCC 768105 v iv i - i i -- v i --- i iiii -- i v L2b_3end#LINE 142 GTTCCCTCTGCCTGGAACGCCCTTCCCCACCTCTTCGCCTGGCCAACTCC 191 chr6qtel1M 768106 TGACT--TCCCTCAAGTCCCAGATAAAATTTTACCTTCTACAAGAAACCT 768153 - -- i i i v v v i i v ii i i L2b_3end#LINE 192 T-ACTCATCCTTCAGGTCTCAGCTCAAATGTCACCTCCTCCGGGAAGCCC 240 chr6qtel1M 768154 TTCCCAATCCCCC---TTAATTCTAAAGCCTTCC-CTGCGCTGATTATTT 768199 i ii i ---iiiiv viiv i - v ivviivvv L2b_3end#LINE 241 TCCCTGACCCCCCAGGCCGGGTCAGGCGCCCTCCTCTGGGCCCCCCCAGT 290 chr6qtel1M 768200 TCCATT-TGCC-TTTTGTGTAGT--TTGTTTATTTGTATCATGTGTGTTG 768245 i i ii- -i i v vi -- i i? i--- ---i L2b_3end#LINE 291 CCTACCCTGCCACTCTGGGTTATNATTGTCTGNTTA---CATGT---CTG 334 chr6qtel1M 768246 TCTTCCCCAT--GATTCTGAACTCCCTGAGAGTTTTT-TTTTTTTTACCT 768292 i i-- i v i v i ivvvv-iiv?v i i-- L2b_3end#LINE 335 TCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTG--T 382 chr6qtel1M 768293 TTTGTCTTTACCTTTTGTTGTACTCCTGGCGAGTAGCACACTGGCTAACA 768342 i -- i ---- i ii ii vv v? v ii L2b_3end#LINE 383 CTTGT--TCACC----GCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCA 426 chr6qtel1M 768343 CATAGTAGACACTTAATAAATGCTAATTGA 768372 i i i i i ii vi L2b_3end#LINE 427 CACAGTAGGCGCTCAGTAAATATTTGTTGA 456 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 46.58 CpG sites = 81, Kimura (unadjusted) = 50.51 Transitions / transversions = 1.59 (81/51) Gap_init rate = 0.08 (30 / 392), avg. gap size = 1.77 (53 / 30) 504 29.55 6.25 0.00 chr6qtel1M 768398 768573 (231427) MIRc#SINE/MIR 81 267 (1) m_b318s601i13 13304 chr6qtel1M 768398 CTAAATATTTGAGCTTAAACAAATCACTTAATCTTTGTCTGTCTCAGTTT 768447 iv i v v iii i i i v vv i MIRc#SINE/MIR 81 CTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTT 130 chr6qtel1M 768448 CTTAATCTATAAGATGTAGATAATAATAAC------ACATCCCTCCAAGA 768491 i v i i vi v ------i v v vv i MIRc#SINE/MIR 131 CCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAGG 180 chr6qtel1M 768492 GGTATTATAAGAATCAAATAAGATAACCTA-G-AAAAGAAACTCGAAATC 768539 v i i i i i iv - -i vivi i v v MIRc#SINE/MIR 181 GTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTTTGTAAAC 230 chr6qtel1M 768540 CTTAAAGTACTATAGAAATG---AGAGCTATCATAAT 768573 iv i v ---i ? i i v MIRc#SINE/MIR 231 TGTAAAGTGCTATACAAATGTAAGGNGTTATTATTAT 267 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 37.89 CpG sites = 30, Kimura (unadjusted) = 38.85 Transitions / transversions = 1.36 (30/22) Gap_init rate = 0.02 (4 / 175), avg. gap size = 2.75 (11 / 4) 248 17.03 0.00 5.66 chr6qtel1M 769549 769604 (230396) DNM1r#Unknown 2498 2550 (2112) m_b318s502i1 13305 chr6qtel1M 769549 GTGAATATATGTGTATATGTGCATATATGTATATATTTAACACATATATA 769598 v i i i i --- i i ? DNM1r#Unknown 2498 GTGTATATGTGTGTATGTGTGTATATATGTGTATAT---ATACGTATNTA 2544 chr6qtel1M 769599 TGCAAC 769604 iv DNM1r#Unknown 2545 TAGAAC 2550 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 17.95 CpG sites = 7, Kimura (unadjusted) = 20.39 Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.05 (3 / 55), avg. gap size = 1.00 (3 / 3) 259 33.47 3.40 11.52 chr6qtel1M 769695 769900 (230100) C MIR1_Amn#SINE/MIR (26) 204 14 m_b318s601i14 13306 chr6qtel1M 769695 ACTCTTTGTGAATAGATTT---GGCATTTTATTGGCAAAG-ATATTATTG 769740 i ii v i i ---i i ---- - vi i v i C MIR1_Amn#SINE 204 ACTTTTCATCAGTAGATCTCAAAGCACTTTA----CAAAGGAGGTCAGTA 159 chr6qtel1M 769741 CCATT-TCTTTTTCTAATTCATTTTACAGATAAGCAA-CTCAGACAAACT 769788 i - ii--------- i v - v i ?v vv C MIR1_Amn#SINE 158 TCATTATCCC---------CATTTTACAGATGAGGAAACTGAGGCNCAGA 118 chr6qtel1M 769789 G-GCTTAAATGACTTGCCAAGGTTCATATAGTTAGTAAATGTCTTAAACA 769837 - v ? i v i v i?i i?i i? i v vv iv i C MIR1_Amn#SINE 117 GAGGTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNAGTGGCAGAGCCG 68 chr6qtel1M 769838 ACATTTGAACTTAAGAAGATGAGTCTTCCTGACTTCAAGTCTGTCACCCT 769887 iv ? ? ii --------i - i v i v iivii i C MIR1_Amn#SINE 67 GGANTNGAACCCA--------GGTC-TCCCGAGTCCCAGTCCAGTGCTCT 27 chr6qtel1M 769888 ACTAATTGTACCA 769900 iiv i iv C MIR1_Amn#SINE 26 ATCCACTAGACCA 14 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 46.73 CpG sites = 40, Kimura (unadjusted) = 49.04 Transitions / transversions = 1.90 (40/21) Gap_init rate = 0.13 (27 / 205), avg. gap size = 1.07 (29 / 27) 398 30.92 2.11 6.62 chr6qtel1M 769759 769900 (230100) C MIRc#SINE/MIR (122) 146 11 m_b318s601i15 13306 chr6qtel1M 769759 CATTTTACAGATAAGCAA-CTCAGAC--AAACTGGCTTAAATGACTTGCC 769805 i v - v i -- i vv - i C MIRc#SINE/MIR 146 CATTTTACAGATGAGGAAACTGAGGCTCAGAGAGG-TTAAGTGACTTGCC 98 chr6qtel1M 769806 AAGGTTCATATAGTTAGTAAATGTCTTAAACAACATTTGAACTTAAGAAG 769855 v i v i i i i v vv iv iiv i i ii ----- C MIRc#SINE/MIR 97 CAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCA----- 53 chr6qtel1M 769856 ATGAGTCTTCCTGACTTCAAGTCTGTCACCCTACTAATTGTACCA 769900 ---i i iivii i viiv i i C MIRc#SINE/MIR 52 ---GGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCA 11 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 39.01 CpG sites = 27, Kimura (unadjusted) = 41.71 Transitions / transversions = 1.93 (27/14) Gap_init rate = 0.08 (11 / 141), avg. gap size = 1.09 (12 / 11) 250 22.90 10.81 1.65 chr6qtel1M 771491 771601 (228399) C L2d_3end#LINE/L2 (33) 483 363 m_b318s601i17 13307 chr6qtel1M 771491 CTTGCTATG-GCCCAGAAACTATGCTAAGAAAT-TGAAATAAGAAGAAAA 771538 i i - i v - i i viv - iii- vi ? C L2d_3end#LINE 483 CCTACTATGTGCTCAGCA-CTGTGCTAGGCGCTGTGGGG-AACGANAAAA 436 chr6qtel1M 771539 GAAGA-AAAACA--GTTCCTATCCTCAAGGAGCTTACATTCTAAT--GGA 771583 ? iv - i -- i ii v i -- i C L2d_3end#LINE 435 NAGTATAAGACATGGTCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGG 386 chr6qtel1M 771584 AGA----ACTAA-ACAAAGGAAA 771601 ---- - v v C L2d_3end#LINE 385 AGACAAGACTAACACACATGAAA 363 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 26.28 CpG sites = 17, Kimura (unadjusted) = 28.97 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.08 (9 / 110), avg. gap size = 1.56 (14 / 9) 302 30.93 4.12 0.00 chr6qtel1M 771491 771587 (228413) C L2a_3end#LINE/L2 (31) 486 386 m_b318s601i16 13307 chr6qtel1M 771491 CTTGCTATGGCCCAGAAACTATGCTAAGAAATTGAAATA-AGAAGAAAAG 771539 i i vv iv i v i viv v ii - v vi v C L2a_3end#LINE 486 CCTACTATGTGCCAGGCACTGTTCTAGGCGCTGGGGATACAGCAGTGAAC 437 chr6qtel1M 771540 AAGAAAAACA---GTTCCTATCCTCAAGGAGCTTACATTCTAATGGAAGA 771586 i v i --- i ii v i ii i C L2a_3end#LINE 436 AAAACAGACAAAAGTCCCTGCCCTCATGGAGCTTACATTCTAGTGGGGGG 387 chr6qtel1M 771587 A 771587 C L2a_3end#LINE 386 A 386 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 39.45 CpG sites = 18, Kimura (unadjusted) = 41.25 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.02 (2 / 96), avg. gap size = 2.00 (4 / 2) 469 29.84 1.69 5.85 chr6qtel1M 771924 772101 (227899) C MIR3#SINE/MIR (27) 181 11 m_b318s601i18 13308 chr6qtel1M 771924 CTAGGAAAGATATTAGAGAGC--TTAGCCTTTCTCTAGCTCATTTTACAA 771971 i i ii iv v --i i ivv i i-- i C MIR3#SINE/MIR 181 CTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCC--CTCATTTTACAG 134 chr6qtel1M 771972 ATGAATAATCTGAGGTAAAGAAAGTGAAGTGAAGTGACTTATACAAGGTC 772021 iv v ivv i ---- iiv C MIR3#SINE/MIR 133 ATGAGGAAACTGAGGCCCAGAGAG----GTGAAGTGACTTGCCCAAGGTC 88 chr6qtel1M 772022 ACATAGTTAATAAGTGTCTGATACCAGATTTGAACTCATATTGTTCCTGA 772071 i i? i v v v vv vi i v i vi --i C MIR3#SINE/MIR 87 ACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGT--CTCCTGA 40 chr6qtel1M 772072 CT-ACAGTGCAGTCATTCTATCAACTGAGTC 772101 -v v - -ii v vi v i C MIR3#SINE/MIR 39 CTCCCAGTCC-GT-GCTCTCTCTGCTCAGCC 11 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 39.11 CpG sites = 28, Kimura (unadjusted) = 39.11 Transitions / transversions = 1.27 (28/22) Gap_init rate = 0.07 (12 / 177), avg. gap size = 1.08 (13 / 12) 500 25.80 0.72 4.51 chr6qtel1M 771960 772097 (227903) C MIRc#SINE/MIR (120) 148 16 m_b318s601i19 13308 chr6qtel1M 771960 CTCATTTTACAAATGAATAATCTGAGGTAAAGAAAGTGAAGTGAAGTGAC 772009 i i iv v ivv i ---- v C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAG----GTTAAGTGAC 103 chr6qtel1M 772010 TTATACAAGGTCACATAGTTAATAAGTGTCTGATACCAGATTTGAACTCA 772059 iiv i i i v v vv vi i i i C MIRc#SINE/MIR 102 TTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCA 53 chr6qtel1M 772060 TATTGTTCCTGACTAC-AGTGCAGTCATTCTATCAACTG 772097 vi i- v - v -ii v v C MIRc#SINE/MIR 52 GGTC-TTCCTGACTCCAAGTCCAGT-GCTCTTTCCACTG 16 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 30.87 CpG sites = 18, Kimura (unadjusted) = 31.98 Transitions / transversions = 1.12 (18/16) Gap_init rate = 0.05 (7 / 137), avg. gap size = 1.00 (7 / 7) 35 0.00 0.00 0.00 chr6qtel1M 774184 774215 (225785) (TATAGA)n#Simple_repeat 1 32 (0) c_b318s251i4 13309 chr6qtel1M 774184 TATAGATATAGATATAGATATAGATATAGATA 774215 (TATAGA)n#Sim 1 TATAGATATAGATATAGATATAGATATAGATA 32 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 1571 31.35 2.31 1.86 chr6qtel1M 774239 775148 (224852) C L1M5_orf2#LINE/L1 (889) 2405 1492 m_b318s551i14 13310 chr6qtel1M 774239 ATATTTCTCCAATTGTTTAAATCTCACTTTATTTGAGTAAAAAGTGTTTT 774288 i v i ii ivi v vvv v iv i C L1M5_orf2#LIN 2405 ATATCTCTCCATTTATTTAGGTCTTCTTTAATTTCTCTCAGCAATGTTTT 2356 chr6qtel1M 774289 GTAATT----GTGTTCCTATATTGTCAATACTTTGTCTTGGAGGTAGAGT 774334 i ---- v?vvi v ivv ?i -- i vv --- C L1M5_orf2#LIN 2355 GTAGTTTTCAGTGTANAGGTCTTGCACATNTTTTGT--TAGATTTA---T 2311 chr6qtel1M 774335 TCC-AAATACTTTATATTGTCTATAGTTATTTTAAAAGAAAGTTCTCTTT 774383 - i i ? i v i ivv i v v iv - v i C L1M5_orf2#LIN 2310 TCCTAAGTATTTNATGTTTTTTGATGCTATTGTAAATGGTA-TTGTTTTT 2262 chr6qtel1M 774384 CTA--TTTATTGTTGCCAGGATTTGTTGGTAATATAAAGAAATGCTGATG 774431 ?v -- i - v v vvi v i v i viv C L1M5_orf2#LIN 2261 NAAATTTCATT-TTCCAATTGTTTGTTGCTAGTATATAGAAATACAATTG 2213 chr6qtel1M 774432 ACTTATGTGGATTTATTTTATATCCAACAATTTTGCTAAA----GTTATT 774477 i v iv v ii i ?i i ii ----v C L1M5_orf2#LIN 2212 ATTTTTGTATATTGACCTTGTATCCNGCGACCTTGCTAAATTCACTTATT 2163 chr6qtel1M 774478 GTTTCAACTAGTTGGTACTTG---ATTCTCTCAGATTCTCTAAGTATATC 774524 iv v v -- ?i --- i ?i i v ? iv C L1M5_orf2#LIN 2162 AGTTCTAGTAGTT--TNTTTGTAGATTCTTTNGGATTTTCTACGTANACA 2115 chr6qtel1M 774525 ATCATATCATCCGCAGAGAGAGCCATAGCTTTGTTTACTCATTTCCTATA 774574 i i ii v i? -- i i i vi v v v C L1M5_orf2#LIN 2114 ATCATGTCATCTGCGAATAANG--ACAGTTTTATTTCTTCCTTTCCAATC 2067 chr6qtel1M 774575 CTAATTGCCTTGATTTCTATTTCTCCTATTATTGCTATACCCAGCATTTC 774624 i v vv i v v iviv vv iv i v ii C L1M5_orf2#LIN 2066 TTTATGCCTTTTATTTCTTTTTCTTGCCTTATTGCACTGGCTAGGACCTC 2017 chr6qtel1M 774625 CAGTATTAATATTGAATAATAGTGGTGATAATGGGAATCCCCGCCTCACT 774674 i- i iv ? ii iv ii i iii C L1M5_orf2#LIN 2016 CAGTAC-AATGTTGAATAGAAGTGGTGANAGCGGACATCCTTGTCTTGTT 1968 chr6qtel1M 774675 CCTGATTTTATTTGGAAGGCTTCTAGGTCATCCCTATTATAGATAATACT 774724 i i vvv i ? ii v?iv v i viv i ii C L1M5_orf2#LIN 1967 CCCGATCTTAGGGGGAAAGCNTTCAGTNTTTCACCATTAAGTATGATGTT 1918 chr6qtel1M 774725 TGCTGATGGGTTTAGATAAATACTACTTAACATGTTAAGGTAAGCTCTCT 774774 ? vv v vvi i i ivi v v i - i i C L1M5_orf2#LIN 1917 NGCTGTAGGTTTTTCGTAGATGCCCTTTATCAGGTTGAGG-AAGTTCCCT 1869 chr6qtel1M 774775 TG-ATTCTTA---TGCCATCTAGTATTTTTAATAGGAATGGGTGCTGTAT 774820 v- i --- ii--- vi vi v i v C L1M5_orf2#LIN 1868 TCTATTCCTAGTTTGCTG---AGAGTTTTTATCATGAATGGGTGTTGAAT 1822 chr6qtel1M 774821 TTTGTAAAA-GTTTTTTCTGTATCTATTGAGATAATCTTATGATTTCTGT 774869 v - i i i v i v C L1M5_orf2#LIN 1821 TTTGTCAAATGCTTTTTCTGCATCTATTGAGATGATCATATGATTTTTCT 1772 chr6qtel1M 774870 TGCTTCTGTTATTGATAGGATCTATTATTCTGATAGTTTTCCTAATACTG 774919 ivi v vi i i v i vv ivi v v i v ii i C L1M5_orf2#LIN 1771 CCTTTATTCTGTTAATATGGTGAATTACATTGATTGATTTTCGAATGTTA 1722 chr6qtel1M 774920 AACCAATCCCATATTCCCAGTATAAATCCCACCTGGTAACAGTCTATGAT 774969 i iiii ii v i i v iii v v C L1M5_orf2#LIN 1721 AACCAACCTTGCATTCCTGGGATAAACCCCACTTGGTCATGATGTATTAT 1672 chr6qtel1M 774970 CTTTGTGATATATTTCTGTAAT-GTTATTGCTAGTATTTTATTTTAAAAT 775018 i v v v v v - v - i i ?vii v C L1M5_orf2#LIN 1671 CCTTTTTATATATTGCTGGATTCGAT-TTGCTAATATTTTGTTNAGGATT 1623 chr6qtel1M 775019 TTTACATTAATATTTATTTGGGAAATTTGTCAATAGTTTTCTGTTTCTGT 775068 i iv i i vv v v vi i v ii C L1M5_orf2#LIN 1622 TTTGCATCTATGTTCATGAGGGATATTGGTCTGTAATTTTCTTTTCTTGT 1573 chr6qtel1M 775069 TTTTGCTGTTCCTGATGTAGGTATT-GCACTATACTTACATTGTGAAAGG 775117 vv vv v vi ? i v v i- vii? i vi v ii i v C L1M5_orf2#LIN 1572 AATGTCTTTGTCNGGTTTTGGTATCAGGGTNATGCTGGCCTCATAAAATG 1523 chr6qtel1M 775118 AATTTGGTAGGACTCCATCTTCAGCTATTTT 775148 i v v vii v ivv C L1M5_orf2#LIN 1522 AGTTGGGAAGTGTTCCCTCTTTTTCTATTTT 1492 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 41.49 CpG sites = 150, Kimura (unadjusted) = 42.49 Transitions / transversions = 1.15 (150/130) Gap_init rate = 0.03 (27 / 909), avg. gap size = 1.41 (38 / 27) 238 27.83 2.91 5.99 chr6qtel1M 776041 776212 (223788) L1PREC2_orf2#LINE/L1 2372 2538 (756) m_b318s551i15 13311 chr6qtel1M 776041 AAATAAATGATGAAAGAAAAATTATTGGAAAAACATTCAATGCTC-TAAA 776089 v iv v v v -- v v - ii L1PREC2_orf2# 2372 AAATCAGAGATGACACAAACA--AATGGAAAAACATTCCATGCTCATGGA 2419 chr6qtel1M 776090 CAAGGCCATGAA--AATATAATAAAAAATACTATGATGCCACTTAAATCA 776137 i i --- v -- vi v vvi i iv ---i v L1PREC2_orf2# 2420 TAGG---AAGAATCAATATCGTTAAAATGGCCATACTGCC---CAAAGCA 2463 chr6qtel1M 776138 ATTTACAGATTTAGTGTTGTGCTTGTTAACCTACTGGAGGGTA--CTTTA 776185 i i i i v i i i v i-i v ii -- i L1PREC2_orf2# 2464 ATTTACAGATTCAATGCTATTCCTATCAAACTACC-AATGACATTCTTCA 2512 chr6qtel1M 776186 TAGGGCTAGATAAAAAATATAGTAAAA 776212 i ii - v vv L1PREC2_orf2# 2513 CAGAACTAGA-AAAAACTATTTTAAAA 2538 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 34.41 CpG sites = 25, Kimura (unadjusted) = 35.38 Transitions / transversions = 1.25 (25/20) Gap_init rate = 0.08 (13 / 171), avg. gap size = 1.15 (15 / 13) 442 39.72 7.69 1.68 chr6qtel1M 776431 776937 (223063) L2#LINE/L2 2430 2966 (116) m_b318s601i20 13312 chr6qtel1M 776431 AGACATCTCAAACTCAATCTGTCTAAAACTAAAATT---ATCT----CTA 776473 i i iv i i v i--- ---- iv L2#LINE/L2 2430 AGGCATCTCAAACTTAACATGTCCAAAACTGAACTCCTGATCTTCCCCCT 2479 chr6qtel1M 776474 CAAACC--CTTTTCAGATTTTCCTCTTTATATCCAAAGCATGGG---TTA 776518 -- ii vviivv i iii v - iv?v v--- iv L2#LINE/L2 2480 CAAACCTGCTCCTCCCGCAGTCTTCCCCATCTC-AGTNAATGGCAACTCC 2528 chr6qtel1M 776519 GCACTTTCGGTCTCCAGGGTTTATAACTTCAATATTGTTCTCAATTTC-- 776566 iiv i i iv ivi iiv v i iiivi ii i ii i i -- L2#LINE/L2 2529 ATCCTTCCAGTTGCTCAGGCCAAAAACCTTGGAGTCATCCTTGACTCCTC 2578 chr6qtel1M 776567 -CTTGCCCCCAAATT-----TCCAATCAGTTGTCAAATATTACCA-TTTG 776609 - v i i v ii----- vi iiv vi ii i-i iv L2#LINE/L2 2579 TCTTTCTCTCACACCCCACATCCAATCCATCAGCAAATCCTGTCGGCTCT 2628 chr6qtel1M 776610 ACCTCCATAACATCTTTTAAATCTAACTCTTTGTCAGAAACTAGCACAAA 776659 i v i v iivi ii ivi v vv v -v vi- L2#LINE/L2 2629 ACCTTCAAAATATATCCAGAATCCGACCACTTCTCACCACCT-CCACTG- 2676 chr6qtel1M 776660 TTAACATATTAATTTAGGTATTCATGAGT----GACTAGATCTTTGCAAC 776705 ii v ivi ii ii i ivvi v vi---- v i ivi i L2#LINE/L2 2677 CCACCACCCTGGTCCAAGCCACCATCATCTCTCGCCTGGATTACTGCAAT 2726 chr6qtel1M 776706 AGCCTCCTAAATGATCCCTC-ATTTCT-------CAGTCCTCCAGTCCTT 776747 v i i i -ii i------- vvi ? iv L2#LINE/L2 2727 AGCCTCCTAACTGGTCTCCCTGCTTCCACCCTTGCCCCCCTNCAGTCTAT 2776 chr6qtel1M 776748 TTTAAATAGAGCTGCCAAAGTAATTTTCCTTAACTACA-GTTATAACCAC 776796 i v i v v i i ii ii v viii - i v v --- L2#LINE/L2 2777 TCTCAACACAGCAGCCAGAGTGATCCTTTTAAAACGTAAGTCAGATC--- 2823 chr6qtel1M 776797 ATGGCTTTCCTACTGCATCAAAGCC----AGAGGCTTCCTCTTGCCTCTA 776842 v vi - - i ---- iv iv iv viii L2#LINE/L2 2824 ATGTCACTCCT-CTGC-TCAAAACCCTCCAATGGCTTCCCATCTCACTCA 2871 chr6qtel1M 776843 GAATATAATATCAAGCCCTCAGATTTGCCTTTAAAGTCCTACACAATCTG 776892 i v vviv i i v v v vi i i ii L2#LINE/L2 2872 GAGTAAAAGCCAAAGTCCTTACAATGGCCTACAAGGCCCTACATGATCTG 2921 chr6qtel1M 776893 G-CCTCAATCAATTTTCTCAGCCTAATTAGGTGCTACTTTCTCCCT 776937 - i vi i vi i v - v ivvv i i i i L2#LINE/L2 2922 GTCCCCCGTTACCTCTCTGA-CCTCATCTCCTACCACTCTCCCCCT 2966 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 58.60 CpG sites = 124, Kimura (unadjusted) = 61.24 Transitions / transversions = 1.68 (124/74) Gap_init rate = 0.05 (23 / 506), avg. gap size = 2.09 (48 / 23) 23 14.60 0.00 0.00 chr6qtel1M 777380 777417 (222583) (A)n#Simple_repeat 1 38 (0) m_b319s252i0 13313 chr6qtel1M 777380 AAAAAAAAAAAAAAAAAAAAAAAACAGGAAAAGATAAA 777417 v ii i v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 38 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 202 24.32 0.00 0.00 chr6qtel1M 777928 777964 (222036) C L2d2_3end#LINE/L2 (12) 543 507 m_b319s601i1 13314 chr6qtel1M 777928 AACAGATATTGATTAGATACCTACTATGTGCAAGGTA 777964 i v iiiii i i C L2d2_3end#LIN 543 AACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCA 507 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 27.38 CpG sites = 8, Kimura (unadjusted) = 32.15 Transitions / transversions = 8.00 (8/1) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 449 34.55 9.11 5.74 chr6qtel1M 777993 778431 (221569) C L2b_3end#LINE/L2 (0) 466 14 m_b319s601i3 13315 chr6qtel1M 777993 ATTTATTTATTCAACAAATATTTA-TGAA-GCCTA---TGTGCCAGGAAC 778037 i i - i- --- v? C L2b_3end#LINE 466 ATTCATTCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNC 417 chr6qtel1M 778038 TGTAACTACTCTAAGTTCTGGAGATATAAAAAGAAGTAAAAAAGA----G 778083 i------ i iv i i iviivi ii i v ---- C L2b_3end#LINE 416 TGTG------CTAGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGG 373 chr6qtel1M 778084 TCCTTCTCCTCACAGAGCTTACAACCTAATGGGAGAGATA-ACCTATAAA 778132 i vi i i ii i i i - v i ? C L2b_3end#LINE 372 TCCCTGCCCTCACGGAGCTCACAGTCTAGTGGGGGAGACAGACATGTAAN 323 chr6qtel1M 778133 TAAATACAGGTATAAAAAGTAATCTA---TGCACAGGATAAATATCAAAT 778179 i i i ----- ? ---- i i --- -i i iivv viiiv C L2b_3end#LINE 322 CAGACA-----ATNA----TAACCCAGAGTG-GCAGGGTAGGACTGGGGG 283 chr6qtel1M 778180 AA-TTAAAAGCGGG-----GAAACA--CTGGGG--------AAGATTTCC 778213 ii-ii i i v ----- vv i-- -------- i ii C L2b_3end#LINE 282 GGCCCAGAGGAGGGCGCCTGACCCGGCCTGGGGGGTCAGGGAGGGCTTCC 233 chr6qtel1M 778214 TATAGAACATGATATCTTAGGTGGGACATAGAGGA--AGTTAAGAA--AA 778259 iiv i vi i i v v i v ii -- - i i--ii C L2b_3end#LINE 232 CGGAGGAGGTGACATTTGAGCTGAGACCTGAAGGATGAG-TAGGAGTTGG 184 chr6qtel1M 778260 TCA-GTAATCAGAGCAGAGGAGGGAGAGTTCTAAGTACCAAAGG---CAG 778305 i - ii -- vv i i - v i i --- i --- C L2b_3end#LINE 183 CCAGGCGA--AGAGGTGGGGAAGG-GCGTTCCAGG---CAGAGGGAACAG 140 chr6qtel1M 778306 CCAAGGAAAATACCAGGGACCAAGAAATGGATTATCTTCTTCCTGGAAAA 778355 v?iv v vi vv iiv ii i?vi v? iv v v vv v C L2b_3end#LINE 139 CANGTGCAAAGGCCCTGAGGCGGGAGNGAGCNTGGCGTGTTCGAGGAACA 90 chr6qtel1M 778356 TC-AGGAAGCCAGGGTCATTGCATTAAAGAGTACATGGTGGAAAGCAAGG 778404 v - i v vii v vi i v vi v - i i-- C L2b_3end#LINE 89 GCAAGGAGGCCAGTGTGGCTGGAGCAGAGTGAGCAAGG-GGAGAGT--GG 43 chr6qtel1M 778405 TGTAAAA--AGACTAGAAAGATGGGAAGG 778431 ivi i -- i ii i i i vii C L2b_3end#LINE 42 TAGGAGATGAGGCCGGAGAGGTAGCGGGG 14 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 46.04 CpG sites = 96, Kimura (unadjusted) = 50.81 Transitions / transversions = 2.04 (96/47) Gap_init rate = 0.10 (42 / 438), avg. gap size = 1.57 (66 / 42) 558 22.83 7.53 3.97 chr6qtel1M 777993 778138 (221862) C L2a_3end#LINE/L2 (0) 517 367 m_b319s601i2 13315 chr6qtel1M 777993 ATTTATTTATTCAACAAATATTTATGAAGC-----CTATGTGCCAGGAAC 778037 i i vi ----- v C L2a_3end#LINE 517 ATTCATTCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCAC 468 chr6qtel1M 778038 TGTAACTACTCTAAGTTCTGGAGATATAAAAAGAAGTAAAA-----AAGA 778082 ------ i iv i i iv ivi ii ----- i C L2a_3end#LINE 467 TGT------TCTAGGCGCTGGGGATACAGCAGTGAACAAAACAGACAAAA 424 chr6qtel1M 778083 GTCCTTCTCCTCACAGAGCTTACAACCTAAT-GGGAGAGATAACCTATAA 778131 i vi ii vi i - i i iv v C L2a_3end#LINE 423 GTCCCTGCCCTCATGGAGCTTACATTCTAGTGGGGGGAGACAGACAATAA 374 chr6qtel1M 778132 ATAAATA 778138 i C L2a_3end#LINE 373 ACAAATA 367 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 27.34 CpG sites = 23, Kimura (unadjusted) = 28.39 Transitions / transversions = 2.56 (23/9) Gap_init rate = 0.06 (9 / 145), avg. gap size = 1.89 (17 / 9) 254 41.16 5.02 4.04 chr6qtel1M 778275 778593 (221407) C L2#LINE/L2 (0) 3082 2761 m_b319s601i4 13315 chr6qtel1M 778275 GAGGAGGGAGAGTTCTAAGTACCAAAGG---CAGCCAAGGAAAATACCAG 778321 i iii v i i --- i --- v iv v vi vv C L2#LINE/L2 3082 GGGGGAAGAGCGTTCCAGG---CAGAGGGAACAGCAAGTGCAAAGGCCCT 3036 chr6qtel1M 778322 GGACCAAGAAATGGATTATCTTCTTCCTGGAAAATCA-GGAAGCCAGGGT 778370 iiv ii ivvv vi iv v v vv v v - i v C L2#LINE/L2 3035 GAGGCGGGAGCGTGCCTGGCGTGTTCGAGGAACAGCAAGGAGGCCAGTGT 2986 chr6qtel1M 778371 CATTGCATTAAAGAGTACATGGTGGAAAGCAAGGTGTAAAA--AGACTAG 778418 vii v viii v vi iv v i i-- ivi i -- iii C L2#LINE/L2 2985 GGCTGGAGCGGAGTGAGCGAGGGGGAGAGT--GGTAGGAGATGAGGTCAG 2938 chr6qtel1M 778419 AAAGATGG-GAAGGGTTATGTTTTAAAGGACTTTG-----AATTACAAA- 778461 i i ii- ii iii vi iv iv i i -----v ii i- C L2#LINE/L2 2937 AGAGGTAACGGGGGACCAGATCATGTAGGGCCTTGTAGGCCATTGTAAGG 2888 chr6qtel1M 778462 ---TTGGTAATTTTATTTGATCTTAGAGGTGATAGGGAATCATTGGAGTT 778508 --- i-- i ---- v v i- i i ii vv C L2#LINE/L2 2887 ACTTTGGC--TTTTACT----CTGAGTGA-GATGGGAAGCCATTGGAGGG 2845 chr6qtel1M 778509 TACCGAGTAGATGGGGTGGCATGATTAGACCCACACTTTAGGAAAACCAT 778558 vii i - i i iv ii ii ii ii i i C L2#LINE/L2 2844 TTTTGAGCAGA-GGAGTGACATGATCTGACTTACGTTTTAAAAGGATCAC 2796 chr6qtel1M 778559 TTCAGTTACTAAATGGAGAATGGTTTCAAAAGAGG 778593 iii i i ivi v i vi v? ii i C L2#LINE/L2 2795 TCTGGCTGCTGTGTTGAGAATAGACTGNAGGGGGG 2761 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 62.62 CpG sites = 84, Kimura (unadjusted) = 66.38 Transitions / transversions = 2.00 (84/42) Gap_init rate = 0.06 (20 / 318), avg. gap size = 1.45 (29 / 20) 19 10.47 3.23 0.00 chr6qtel1M 779096 779126 (220874) (AT)n#Simple_repeat 1 32 (0) m_b319s252i1 13316 chr6qtel1M 779096 ATAAATATATATA-ATATCTATATTTATATAT 779126 v - v v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATAT 32 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.03 (1 / 30), avg. gap size = 1.00 (1 / 1) 15 29.01 3.33 1.64 chr6qtel1M 779627 779686 (220314) (AT)n#Simple_repeat 1 61 (0) m_b319s252i2 13317 chr6qtel1M 779627 ATACATAGTAAACATATTAAAATATATCTTTA-AAATA-ATATATGTGTT 779674 i - v i vv v v v - v - i i v (AT)n#Simple_ 1 ATATATA-TATATATATATATATATATATATATATATATATATATATATA 49 chr6qtel1M 779675 CATATTTATATA 779686 i v (AT)n#Simple_ 50 TATATATATATA 61 Matrix = Unknown Transitions / transversions = 0.56 (5/9) Gap_init rate = 0.05 (3 / 59), avg. gap size = 1.00 (3 / 3) 15 24.40 0.00 0.00 chr6qtel1M 780347 780380 (219620) (CA)n#Simple_repeat 1 34 (0) m_b319s252i3 13318 chr6qtel1M 780347 CACACATACACTCACACGAACACCCATGCACACA 780380 i v iv v ii (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACA 34 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 383 22.47 2.91 4.95 chr6qtel1M 780546 780648 (219352) C MIRc#SINE/MIR (27) 241 141 m_b319s601i5 13319 chr6qtel1M 780546 AATACTTTAAGATTTACAAAGCTCTTTC-CATATGCCATCTCACTTGATC 780594 ii vii v - iiii i C MIRc#SINE/MIR 241 AGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATCTCATTTGATC 192 chr6qtel1M 780595 CTTACAGCAACCCTAAGAGGTACGTAATATAGGACAGG-A-TATTTTTCC 780642 i i iv v -----i i - - v i C MIRc#SINE/MIR 191 CTCACAACAACCCTGTGAGGTAGG-----CAGGGCAGGTATTATTATCCC 147 chr6qtel1M 780643 AATTCT 780648 v i C MIRc#SINE/MIR 146 CATTTT 141 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 27.80 CpG sites = 16, Kimura (unadjusted) = 27.80 Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.08 (8 / 102), avg. gap size = 1.00 (8 / 8) 866 29.42 0.83 1.67 chr6qtel1M 780689 780930 (219070) C MIR#SINE/MIR (10) 252 13 m_b319s601i6 13320 chr6qtel1M 780689 AGCATTTATTAAGTATTTACTGTGTGCCAGGTATTGGGCTAAGTACTTTA 780738 i i iii i i i vv ii C MIR#SINE/MIR 252 AACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGCGCTTTA 203 chr6qtel1M 780739 TAGATGTTATCTCATTTAGCATTCAGAATAACTTAAGGACATAGATGCTC 780788 i vi i v iivi v i iiv v vi i i v C MIR#SINE/MIR 202 CATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGGTAGGTACTA 153 chr6qtel1M 780789 TTGTTCTGCTCATTTTACAGATGGTGAAATGCAGGAAAAAGCAGAAGTTA 780838 i v v i iv ivv v v i-- i C MIR#SINE/MIR 152 TTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAG--AGAGGTTA 105 chr6qtel1M 780839 AATGACTTGTCTAGCTTCACACAGCTATTAAGTGTCAGTAGCT-ACATTT 780887 i i i i ivv v v - i-iv i C MIR#SINE/MIR 104 AGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAG-AGCCGGGATTC 56 chr6qtel1M 780888 GAACTCAAGTCATCCTGACTCCAATTCCAGCACTC-TAACCATT 780930 i i - vi i ivv v ii - i C MIR#SINE/MIR 55 GAACCCAGG-CAGTCTGGCTCCAGAGCCCGTGCTCTTAACCACT 13 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 35.79 CpG sites = 44, Kimura (unadjusted) = 38.76 Transitions / transversions = 1.69 (44/26) Gap_init rate = 0.02 (6 / 241), avg. gap size = 1.00 (6 / 6) 448 30.24 12.61 0.78 chr6qtel1M 782220 782449 (217551) MIRc#SINE/MIR 10 266 (2) m_b319s601i7 13321 chr6qtel1M 782220 GTAGTACAGTGTTA-GAGCACAGGACCTATTGTCA---AGACTTCAGTTC 782265 i i vv - v i ivv --- i vi MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr6qtel1M 782266 AAATTCTGCCTCACACACTCAATAGCTGTGTGACAT-------ATCACT- 782307 i i i i v vvv i v v -------i - MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTT 109 chr6qtel1M 782308 ---GTCTTT----CTCAAGTTCCTCAATTG-AAAATAAGAATAATGACA- 782348 ---v i ---- iv vi - ii i i i - MIRc#SINE/MIR 110 AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAC 159 chr6qtel1M 782349 -------GCATAAACCCCCAAGAGTTTTTATCATAATCAAATATGCTAAC 782391 ------- v -- i vv i v i v vi iv v i MIRc#SINE/MIR 160 CTGCCCTGCCT--ACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAAT 207 chr6qtel1M 782392 TTATAC-AAAGTATTTTGCAAAAGTTAAAGTACCATAGAAAAATTATCTA 782440 v ii- iii i vvv i i v vi v vv?i MIRc#SINE/MIR 208 GTATGTGAAAGCGCTTTGTAAACTGTAAAGTGCTATACAAATGTAAGGNG 257 chr6qtel1M 782441 TTATTAATA 782449 v MIRc#SINE/MIR 258 TTATTATTA 266 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 37.39 CpG sites = 36, Kimura (unadjusted) = 39.64 Transitions / transversions = 1.09 (36/33) Gap_init rate = 0.05 (11 / 229), avg. gap size = 2.82 (31 / 11) 260 26.22 2.80 3.77 chr6qtel1M 783043 783149 (216851) C L1MD1_3end#LINE/L1 (443) 546 441 m_b319s551i0 13322 chr6qtel1M 783043 TTCTATCACATCCATACACCATCATTTTGGTCAATCATTCCCCAGCTTAT 783092 i vii vv ii - v v i i v v i v - C L1MD1_3end#LI 546 TTCCATGGTATGGATGTACCA-CAGTTTGTTTAACCATTCACCCGTTGA- 499 chr6qtel1M 783093 AAGTAATTCCTGGATT---TCTAGTTCTTTGCTACTATGAAAAAAGATGC 783139 i vv -- i --- i i v i i v v C L1MD1_3end#LI 498 AGGACAT--CTGGGTTGTTTCCAGTTTTTGGCTATTACGAATAAAGCTGC 451 chr6qtel1M 783140 TATAAACATT 783149 C L1MD1_3end#LI 450 TATAAACATT 441 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 31.22 CpG sites = 14, Kimura (unadjusted) = 32.65 Transitions / transversions = 1.08 (14/13) Gap_init rate = 0.05 (5 / 106), avg. gap size = 1.40 (7 / 5) 286 33.31 5.50 2.43 chr6qtel1M 783159 783358 (216642) C L1ME3G_3end#LINE/L1 (556) 368 163 m_b319s551i1 13323 chr6qtel1M 783159 TGGGTCAAAGGACATG-ACAGTTTGGGGCTGGATAAGGCATTGTTCCAAA 783207 ii -i v iiivi vi - ii i -- C L1ME3G_3end#L 368 TGGGTCAAAGGGTATGCGCATTTTAAATTTTAAT-AGATACTG--CCAAA 322 chr6qtel1M 783208 --AGTTTCCAAAATAACTAGACCAATTCACAGCTCCACCAATA----ATT 783251 --ivii ?ii iv i vii ii ---- v C L1ME3G_3end#L 321 TTGCCCTCCAAAANGGCTGTACCAATTTACACTCCCACCAGCAGTGTATG 272 chr6qtel1M 783252 AACATGCCTGTTTTCTGTCAGCTTTTCCAACACTTGTAATTTTC---CTT 783298 ivi i i i ivv v i iv ? vv v --- C L1ME3G_3end#L 271 AGAGTACCCGTTTCCCCACACCCTCGCCAACACTNGATATTATCAANCTT 222 chr6qtel1M 783299 TCTATCATTTCTGCAAAGA-GGTGAGTATAACATAATGCATCATAATTCT 783347 iv -- i v vv- i i iv v ii iiv vi v C L1ME3G_3end#L 221 TTAA--ATTTTTGCCAATCTGATGGGTGAAAAATGGTATCTCATTGTTGT 174 chr6qtel1M 783348 TTTAATTTGTA 783358 i C L1ME3G_3end#L 173 TTTAATTTGCA 163 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 43.98 CpG sites = 41, Kimura (unadjusted) = 46.99 Transitions / transversions = 1.71 (41/24) Gap_init rate = 0.05 (10 / 199), avg. gap size = 1.60 (16 / 10) 28 10.57 0.00 0.00 chr6qtel1M 783391 783430 (216570) (AT)n#Simple_repeat 1 40 (3) m_b319s252i4 13324 chr6qtel1M 783391 ATATGTATGTATATGTGTATATATATATATATATATATAT 783430 i i i i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATAT 40 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 77 3.95 0.00 0.00 chr6qtel1M 783431 783509 (216491) (AG)n#Simple_repeat 1 79 (0) c_b319s251i0 13325 chr6qtel1M 783431 AGAGAGAGAGAGAGAGAGAGAGAGAGAAAGAGAGAGAGAGAGAAAGAGAG 783480 i i (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chr6qtel1M 783481 AGAGAGAGAGAGAGAGAGAGAGAAAGAGA 783509 i (AG)n#Simple_ 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGA 79 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 78), avg. gap size = 0.0 (0 / 0) 15 27.08 2.27 0.00 chr6qtel1M 783588 783631 (216369) (TA)n#Simple_repeat 1 45 (0) m_b319s252i5 13326 chr6qtel1M 783588 TATATATTCTTATATATATCT-TATTCATATCTATTCTTATATAT 783631 viv v - vi v viv (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATAT 45 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.02 (1 / 43), avg. gap size = 1.00 (1 / 1) 31 28.10 2.13 0.00 chr6qtel1M 783749 783842 (216158) (TA)n#Simple_repeat 1 96 (0) m_b319s252i6 13327 chr6qtel1M 783749 TATATACACATATATTTATACATCTTTACA-ATGTATAT-TACATATACT 783796 i i v i v v i - i - i iv (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr6qtel1M 783797 TGTATCTATATATGTAATTATAAATATAAAAATATATAGCTAAATA 783842 i v i vv v v v vv v (TA)n#Simple_ 51 TATATATATATATATATATATATATATATATATATATATATATATA 96 Matrix = Unknown Transitions / transversions = 0.69 (9/13) Gap_init rate = 0.02 (2 / 93), avg. gap size = 1.00 (2 / 2) 58 1.89 0.00 0.00 chr6qtel1M 784816 784869 (215131) (AC)n#Simple_repeat 1 54 (0) c_b319s251i1 13328 chr6qtel1M 784816 ACACACACACACACACACACACACACACACACACACACACACACACACAT 784865 i (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50 chr6qtel1M 784866 ACAC 784869 (AC)n#Simple_ 51 ACAC 54 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 304 30.77 2.83 1.87 chr6qtel1M 785007 785112 (214888) C L2b_3end#LINE/L2 (36) 430 324 m_b319s601i8 13329 chr6qtel1M 785007 TATATGCTTCAGGAAGTGTGCTAAGTAATAGTAATA-AG-GGTGAAAGCA 785054 i i -- v?v i iiv i vi - - vivi C L2b_3end#LINE 430 TGTGTGC--CAGGCNCTGTGCTAGGCGCTGGGGATACAGCGGTGAACAAG 383 chr6qtel1M 785055 TCCAAGACAGTCTCTGTCCTCATGGATCTTACATTCTAATGAAAGA-ACA 785103 v vi v? i i i i v i v i iii - C L2b_3end#LINE 382 ACAGACNCGGTCCCTGCCCTCACGGAGCTCACAGTCTAGTGGGGGAGACA 333 chr6qtel1M 785104 AAAATGTAA 785112 i v C L2b_3end#LINE 332 GACATGTAA 324 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 37.05 CpG sites = 20, Kimura (unadjusted) = 42.35 Transitions / transversions = 1.67 (20/12) Gap_init rate = 0.05 (5 / 105), avg. gap size = 1.00 (5 / 5) 24 21.28 0.00 0.00 chr6qtel1M 787257 787305 (212695) (A)n#Simple_repeat 1 49 (0) m_b319s252i7 13330 chr6qtel1M 787257 AAAAAACAAAATATAGAAAGACAGAAAAGGAAAAAAAAAAAAAAAAAAA 787305 v v v i i v i ii (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 49 Matrix = Unknown Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 50 0.00 0.00 0.00 chr6qtel1M 787546 787588 (212412) (TA)n#Simple_repeat 1 43 (0) c_b319s251i2 13331 chr6qtel1M 787546 TATATATATATATATATATATATATATATATATATATATATAT 787588 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATAT 43 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 263 21.28 0.00 8.45 chr6qtel1M 787599 787675 (212325) C DNM1r#Unknown (2117) 2545 2475 m_b319s502i0 13332 chr6qtel1M 787599 ACACATATCTATATGCACATATGTATAACTACATGCATACACACATATAT 787648 i ? iv ii i i ---- ii -- C DNM1r#Unknown 2545 ATANATACGTATATATACACATATATA----CACACATACACACA--TAT 2502 chr6qtel1M 787649 ACGCACATGTATACATATATAAACATG 787675 i i i i v i C DNM1r#Unknown 2501 ACACACATATATACACACATACACGTG 2475 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 22.90 CpG sites = 13, Kimura (unadjusted) = 27.01 Transitions / transversions = 6.50 (13/2) Gap_init rate = 0.08 (6 / 76), avg. gap size = 1.00 (6 / 6) 12 16.67 4.55 4.55 chr6qtel1M 788003 788046 (211954) (TATCC)n#Simple_repeat 1 44 (0) m_b319s252i8 13333 chr6qtel1M 788003 TAACCTATGCTATCCTTTCCT-TCCT-TCTTAATCCCTTTCCTCTC 788046 v v v - - i - - v v (TATCC)n#Simp 1 TATCCTATCCTATCCTATCCTATCCTATCCT-AT-CCTATCCTATC 44 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.09 (4 / 43), avg. gap size = 1.00 (4 / 4) 18 0.00 0.00 0.00 chr6qtel1M 788155 788174 (211826) (GT)n#Simple_repeat 1 20 (0) m_b319s252i9 13334 chr6qtel1M 788155 GTGTGTGTGTGTGTGTGTGT 788174 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGT 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 19 33.87 0.00 2.35 chr6qtel1M 788160 788246 (211754) (TGTATA)n#Simple_repeat 1 85 (0) m_b319s252i10 13334 chr6qtel1M 788160 TGTGTGTGTGTGTGTATACATACATAAATACATACATATACATATATATG 788209 i i i i ii i iv ii i i i i (TGTATA)n#Sim 1 TGTATATGTATATGTATATGTATATGTATATGTATATGTATATGTATATG 50 chr6qtel1M 788210 TATGCATGTATAAGTGTAGGTATAGTTAGATGTAAAT 788246 -- v i v vv v v (TGTATA)n#Sim 51 TAT--ATGTATATGTATATGTATATGTATATGTATAT 85 Matrix = Unknown Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.02 (2 / 86), avg. gap size = 1.00 (2 / 2) 18 26.26 0.00 0.00 chr6qtel1M 788174 788221 (211779) (TATA)n#Simple_repeat 1 48 (0) m_b319s252i11 13335 chr6qtel1M 788174 TATACATACATAAATACATACATATACATATATATGTATGCATGTATA 788221 i i v i i i i ii i (TATA)n#Simpl 1 TATATATATATATATATATATATATATATATATATATATATATATATA 48 Matrix = Unknown Transitions / transversions = 9.00 (9/1) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 18 0.00 0.00 0.00 chr6qtel1M 788155 788174 (211826) (GT)n#Simple_repeat 1 20 (0) m_b319s252i9 13334 chr6qtel1M 788155 GTGTGTGTGTGTGTGTGTGT 788174 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGT 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 19 33.87 0.00 2.35 chr6qtel1M 788160 788246 (211754) (TGTATA)n#Simple_repeat 1 85 (0) m_b319s252i10 13334 chr6qtel1M 788160 TGTGTGTGTGTGTGTATACATACATAAATACATACATATACATATATATG 788209 i i i i ii i iv ii i i i i (TGTATA)n#Sim 1 TGTATATGTATATGTATATGTATATGTATATGTATATGTATATGTATATG 50 chr6qtel1M 788210 TATGCATGTATAAGTGTAGGTATAGTTAGATGTAAAT 788246 -- v i v vv v v (TGTATA)n#Sim 51 TAT--ATGTATATGTATATGTATATGTATATGTATAT 85 Matrix = Unknown Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.02 (2 / 86), avg. gap size = 1.00 (2 / 2) 349 12.90 0.00 0.00 chr6qtel1M 791170 791231 (208769) MER63D#DNA/hAT-Tip100 410 471 (590) m_b319s502i1 13336 chr6qtel1M 791170 AGATTTAGGAAAGTGATGGAGAAAATGTTAAGAATGCAGATTAAATGTAA 791219 i i v iv MER63D#DNA/hA 410 AGACTTAAGAAAGTGATGGAGAAAATGTTAATAATGCAGATTAAACTTAA 459 chr6qtel1M 791220 AAGTGGGCCATG 791231 v i i MER63D#DNA/hA 460 AAGTGTGTCGTG 471 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 12.51 CpG sites = 5, Kimura (unadjusted) = 14.31 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0) 20 0.00 0.00 0.00 chr6qtel1M 792482 792503 (207497) (A)n#Simple_repeat 1 22 (0) m_b319s252i12 13337 chr6qtel1M 792482 AAAAAAAAAAAAAAAAAAAAAA 792503 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAA 22 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 24 21.59 5.77 3.77 chr6qtel1M 792853 792872 (207128) (AGGA)n#Simple_repeat 1 22 (84) m_b319s252i13 13338 chr6qtel1M 792853 AGG-AGAAAGGAAAGAAAG-GG 792872 - i i i -i (AGGA)n#Simpl 1 AGGAAGGAAGGAAGGAAGGAAG 22 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.11 (2 / 19), avg. gap size = 1.00 (2 / 2) 94 3.01 0.96 0.96 chr6qtel1M 792873 792976 (207024) (GGAA)n#Simple_repeat 1 104 (0) c_b319s251i3 13339 chr6qtel1M 792873 GGAAAGAAGGAAGTAGAG-AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG 792921 i v - - (GGAA)n#Simpl 1 GGAAGGAAGGAAGGA-AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG 49 chr6qtel1M 792922 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAAGAAGGA 792971 i (GGAA)n#Simpl 50 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 99 chr6qtel1M 792972 AGGAA 792976 (GGAA)n#Simpl 100 AGGAA 104 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.02 (2 / 103), avg. gap size = 1.00 (2 / 2) 24 21.59 5.77 3.77 chr6qtel1M 792977 793059 (206941) (AGGA)n#Simple_repeat 23 105 (1) m_b319s252i13 13340 chr6qtel1M 792977 AAGG--GGAGGGAATAGAAGGAAGGAAAAGGGGAGGGAATGGGAAGGAAG 793024 -- i -i iiii i -- (AGGA)n#Simpl 23 AAGGAAGGAAGGAA-GGAAGGAAGGAAGGAAGGAAGGAA--GGAAGGAAG 69 chr6qtel1M 793025 AAAGGGAGGAAGTAA-GAA-AAAGAAAGGCAGGGAAG 793059 i i v - -i i - i (AGGA)n#Simpl 70 GAAGGAAGGAAGGAAGGAAGGAAGGAAGG-AAGGAAG 105 Matrix = Unknown Transitions / transversions = 12.00 (12/1) Gap_init rate = 0.09 (7 / 82), avg. gap size = 1.14 (8 / 7) 356 33.91 7.02 4.27 chr6qtel1M 793067 793294 (206706) C MIRb#SINE/MIR (22) 246 13 m_b319s601i9 13341 chr6qtel1M 793067 GAATGTCAACTACATGCCAAGCACCATGGGAAAGACTTTATTACTATGTT 793116 ii iiv ii i ii vv ivi i---- -- C MIRb#SINE/MIR 246 GAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTAC----ATG-- 203 chr6qtel1M 793117 TTCACTATCATCTATTTGATATTCAC------CTTAT----TTTGTGTCA 793156 -- i - - i vi ------ i ii---- vv i i C MIRb#SINE/MIR 202 --CATTATC-TC-ATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTA 157 chr6qtel1M 793157 T-ATTCTCATTTTACGGATGAGAAAACTGAAGATCTTA---TTTAAGTTA 793202 - i i i i i v vv ---v v C MIRb#SINE/MIR 156 TTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAA 107 chr6qtel1M 793203 CTGTTGCAGGGTTAAAAAGCTATTCTTCGTCTGAGAATAGATTTGATTTT 793252 vviv i i v v v vvvi v v vvvi i viii C MIRb#SINE/MIR 106 CTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCC 57 chr6qtel1M 793253 --GTCTTCCTGCCTCCAGAACTAGTCCCTTAACCACTGTACCAC 793294 -- vi v i i iv v ii vv i C MIRb#SINE/MIR 56 AGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCACCAC 13 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 43.13 CpG sites = 41, Kimura (unadjusted) = 46.50 Transitions / transversions = 1.24 (41/33) Gap_init rate = 0.07 (15 / 227), avg. gap size = 1.73 (26 / 15) 382 19.97 8.11 5.26 chr6qtel1M 793456 793566 (206434) C MIRc#SINE/MIR (3) 265 152 m_b319s601i10 13342 chr6qtel1M 793456 AATAATCATAAATAACATTTATAAAGCACGTTAAGGTTTACAGAGC---- 793501 v i?vv v i v v vi i ---- C MIRc#SINE/MIR 265 AATAATAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCGCTT 216 chr6qtel1M 793502 ----ATATACTATCTCACTTGACCCTCACAGCAACCCTA-GAAGTAGATA 793546 ---- i i i i i i- i --- C MIRc#SINE/MIR 215 TCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAG--- 169 chr6qtel1M 793547 ATGTAGGACAGGATATTTTT 793566 -- i i - v C MIRc#SINE/MIR 168 --GCAGGGCAGG-TATTATT 152 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 23.97 CpG sites = 13, Kimura (unadjusted) = 23.97 Transitions / transversions = 1.62 (13/8) Gap_init rate = 0.08 (9 / 110), avg. gap size = 1.67 (15 / 9) 476 34.07 8.48 0.41 chr6qtel1M 793627 793850 (206150) C MIR#SINE/MIR (13) 249 8 m_b319s601i11 13343 chr6qtel1M 793627 ATTTATGCAATGTCAACTTTGTGCCGGGCACTGTGCTAAGTATTTTATAG 793676 vv ii iiv v i v iii i v C MIR#SINE/MIR 249 ATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGCGCTTTACAT 200 chr6qtel1M 793677 ATGTT--CTCCTTTGGTCTTCA-AAGAAT-----------AGTACTATTA 793712 i i -- v ii i - v i-----------i C MIR#SINE/MIR 199 GTATTAACTCATTTAATCCTCACAACAACCCTATGAGGTAGGTACTATTA 150 chr6qtel1M 793713 TTGTACTCATTTTCTAAATTATGAAAGCTAGGAAGGCAGAGATTAGCTGA 793762 i v i vi i v v viv v viv i iv i C MIR#SINE/MIR 149 TTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAA 100 chr6qtel1M 793763 TGTTCTGAGGGTCACACAAC---TAAGTGTCAGGAGCTACACTTGAACTC 793809 iv v iv i i --- v iiv viv i i i C MIR#SINE/MIR 99 CTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCC 50 chr6qtel1M 793810 GAGGC-TTCCGAAACCA-AGTCCAACATTCTAACCATTGTATT 793850 - -v i ivv - i ivvv ii i i ii C MIR#SINE/MIR 49 -AGGCAGTCTGGCTCCAGAGCCCGTGCTCTTAACCACTATGCT 8 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 43.75 CpG sites = 45, Kimura (unadjusted) = 47.25 Transitions / transversions = 1.45 (45/31) Gap_init rate = 0.03 (7 / 223), avg. gap size = 2.86 (20 / 7) 37 10.74 2.86 0.00 chr6qtel1M 794265 794334 (205666) (TA)n#Simple_repeat 1 72 (0) c_b319s251i4 13344 chr6qtel1M 794265 TATATATATTTGTA-ATATATATTTATTTATATAAAT-TATATATATATA 794312 v i - v v v - (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr6qtel1M 794313 TATATATATATACACATATATA 794334 i i (TA)n#Simple_ 51 TATATATATATATATATATATA 72 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.03 (2 / 69), avg. gap size = 1.00 (2 / 2) 15 8.16 0.00 3.70 chr6qtel1M 794857 794884 (205116) (TTCT)n#Simple_repeat 1 27 (0) m_b319s252i14 13345 chr6qtel1M 794857 TTGTTTCATTCTTTCTTTTCTTTCTTTC 794884 v v - (TTCT)n#Simpl 1 TTCTTTCTTTCTTTC-TTTCTTTCTTTC 27 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 44 0.00 0.00 0.00 chr6qtel1M 795356 795393 (204607) (AC)n#Simple_repeat 1 38 (0) c_b319s251i5 13346 chr6qtel1M 795356 ACACACACACACACACACACACACACACACACACACAC 795393 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACAC 38 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 302 28.00 9.00 0.00 chr6qtel1M 795531 795630 (204370) C L2a_3end#LINE/L2 (36) 481 373 m_b319s601i12 13347 chr6qtel1M 795531 TATGCTCCAGGAAGTGTGCTAAGTAATAGTAATAAGG--GTGAA---AGC 795575 iv v v v i iiv i vi vi -- --- i C L2a_3end#LINE 481 TATGTGCCAGGCACTGTTCTAGGCGCTGGGGATACAGCAGTGAACAAAAC 432 chr6qtel1M 795576 ATCCAA--GTCTCTGTCCTCATGGATCTTACATTCTAATGAAAG--AACA 795621 vv -- i i v i iii --i C L2a_3end#LINE 431 AGACAAAAGTCCCTGCCCTCATGGAGCTTACATTCTAGTGGGGGGAGACA 382 chr6qtel1M 795622 AAAAATAGA 795630 i v i C L2a_3end#LINE 381 GACAATAAA 373 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 34.32 CpG sites = 17, Kimura (unadjusted) = 36.10 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.04 (4 / 99), avg. gap size = 2.25 (9 / 4) 14 22.09 2.27 2.27 chr6qtel1M 797197 797240 (202760) (ATA)n#Simple_repeat 1 44 (0) m_b319s252i15 13348 chr6qtel1M 797197 ATAAAACATAAAAAATTTAAAAACAATAATCAT-ATAATAATAAT 797240 v - v vvv v i v - (ATA)n#Simple 1 ATAATA-ATAATAATAATAATAATAATAATAATAATAATAATAAT 44 Matrix = Unknown Transitions / transversions = 0.14 (1/7) Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2) 13 23.81 3.85 1.89 chr6qtel1M 797795 797846 (202154) (TAAAGAA)n#Simple_repeat 1 53 (0) m_b319s252i16 13349 chr6qtel1M 797795 TAAAG-TTAAATATAAAATAATAAA-AATATAGACATCCAGAAGAAAGAA 797842 -v v vv v - v - vv v (TAAAGAA)n#Si 1 TAAAGAATAAAGAATAAAGAATAAAGAATAAAGA-ATAAAGAATAAAGAA 49 chr6qtel1M 797843 AAAA 797846 v (TAAAGAA)n#Si 50 TAAA 53 Matrix = Unknown Transitions / transversions = 0.00 (0/10) Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.00 (3 / 3) 23 25.60 5.66 1.82 chr6qtel1M 798084 798189 (201811) (ATATAC)n#Simple_repeat 1 110 (0) m_b319s252i18 13350 chr6qtel1M 798084 ATATAATTATA-TTATACATAT--ATATTCACATCCGCACCCAGAGACAT 798130 vv -v -- v i v ii iv v v (ATATAC)n#Sim 1 ATATACATATACATATACATATACATATACATATACATATACATATACAT 50 chr6qtel1M 798131 ATATCTATATACACAT-CATAT-C-TATAAGCATACACATATATATGCAC 798177 - - i - - - vii i i i i (ATATAC)n#Sim 51 ATA-C-ATATACATATACATATACATATACATATACATATACATATACAT 98 chr6qtel1M 798178 ATTTATATACAT 798189 vi (ATATAC)n#Sim 99 ATACATATACAT 110 Matrix = Unknown Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.07 (7 / 105), avg. gap size = 1.14 (8 / 7) 38 24.11 0.00 1.12 chr6qtel1M 798653 798742 (201258) (AT)n#Simple_repeat 1 89 (0) m_b319s252i20 13351 chr6qtel1M 798653 ATATACATATATAGATACACATGTATATATTTGAAAAATATATATATATA 798702 i v i i i v - v v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATAT-ATATATATATATATATA 49 chr6qtel1M 798703 TATATGTACAAGTATAGATGAATGTAAGTATATATATATA 798742 i i vi v iv i vi (AT)n#Simple_ 50 TATATATATATATATATATATATATATATATATATATATA 89 Matrix = Unknown Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.01 (1 / 89), avg. gap size = 1.00 (1 / 1) 14 27.71 2.30 5.95 chr6qtel1M 799486 799572 (200428) (TCTATTT)n#Simple_repeat 1 84 (0) m_b319s252i21 13352 chr6qtel1M 799486 TCTGTTTTCCTGATTTGTTGTTTTTTCTTATTAAATGTTTC-ACATTCTC 799534 i - - vi i i v - vv - - iv v (TCTATTT)n#Si 1 TCTATTTT-CT-ATTTTCTATTTTCTATT-TTCTAT-TTTCTATTTTCTA 46 chr6qtel1M 799535 TTCTATTTTTTC-ATTTTCTATATTTTGGTTTGCTATTT 799572 i v v - - ivi v (TCTATTT)n#Si 47 TTTTCTATTTTCTATTTTCTAT-TTTCTATTTTCTATTT 84 Matrix = Unknown Transitions / transversions = 0.80 (8/10) Gap_init rate = 0.08 (7 / 86), avg. gap size = 1.00 (7 / 7) 507 38.05 3.94 5.93 chr6qtel1M 800052 800635 (199365) L2#LINE/L2 2394 2966 (116) m_b319s601i13 13353 chr6qtel1M 800052 AACTATCCATTGTACATTTCAAACTGTGTGTCCTGGAGACATCTGAAACT 800101 ii i i vv i v vi vi iviv i v L2#LINE/L2 2394 AACTGCCTACTCGACATCTCCACTTGGATGTCTAATAGGCATCTCAAACT 2443 chr6qtel1M 800102 CATTTTGTCTAAAACTTAAATCACTAGCTTTCCTTACAAACC----CTTT 800147 i viv i v v viv v i iiv ---- i i L2#LINE/L2 2444 TAACATGTCCAAAACTGAACTCCTGATCTTCCCCCTCAAACCTGCTCCTC 2493 chr6qtel1M 800148 TCAC---CTTTCCCTTTTTATAGCCAAAGTGTGGTTCAGCACTCTCCTTT 800194 i i --- i v i i -- i? ---- -- i v iv i L2#LINE/L2 2494 CCGCAGTCTTCCCCATCTCA--GTNAA----TGG--CAACTCCATCCTTC 2535 chr6qtel1M 800195 CAGTT-TTCAGGATTTATAACCTCAGCATCATCCTCAATTTCCTTCCCTC 800243 -i -iiv v ii vi ii i i ii ii L2#LINE/L2 2536 CAGTTGCTCAGG-CCAAAAACCTTGGAGTCATCCTTGACTCCTCTCTTTC 2584 chr6qtel1M 800244 ATTTCCAATCAATTGTCATTTGACAGGAATGAG-AAGTACCATTTG---- 800288 vi iv vi v ---- iii ivv-- v - i v ii iv ---- L2#LINE/L2 2585 TCTCACACCCCA----CATCCAATCC--ATCAGCAAATCCTGTCGGCTCT 2628 chr6qtel1M 800289 ACCTTCATAACACTTCTTACATCAAACTCTTTTGCTCAAAAACTA-ACTG 800337 v i iv iviv vi ivi -- vv v v- L2#LINE/L2 2629 ACCTTCAAAATATATCCAGAATCCGACCACTT--CTCACCACCTCCACTG 2676 chr6qtel1M 800338 GTACTCATAAACATATTAATTTAGGCCCTTATCACCTCTTGCCTAGACCT 800387 vi ------- ivi ii ii i vii i i i iiv L2#LINE/L2 2677 CCAC-------CACCCTGGTCCAAGCCACCATCATCTCTCGCCTGGATTA 2719 chr6qtel1M 800388 TTACAATAGTCTCCCAAACGATCCCTCTGCCTCATATCTCAGACCTC--- 800434 i i i i vi i i i i -i i iiv v i --- L2#LINE/L2 2720 CTGCAATAGCCTCCTAACTGGTCTCCCTGCTTC-CACCCTTGCCCCCCTN 2768 chr6qtel1M 800435 CAGTCCTTCCTACATAGGGCTGCTCAAGTAATTTTCCTAAAGTGCTGATA 800484 iv i vv i vi v ivi i ii ii ii ivii v L2#LINE/L2 2769 CAGTCTATTCTCAACACAGCAGCCAGAGTGATCCTTTTAAAACGTAAGTC 2818 chr6qtel1M 800485 TGACCATGTGACTCTTCTACT---GACTCAAGGCCAATTGCTTCC--TCT 800529 v i v i i ---i i ---v v -- L2#LINE/L2 2819 AGATCATGTCACTCCTCTGCTCAAAACCC---TCCAATGGCTTCCCATCT 2865 chr6qtel1M 800530 TGACTTGAGAATATAATATCAAGTCCTCTGTTTAGTCTCTAAAGTCATAT 800579 i- i- i v vviv ivvvv i i vi i i v i L2#LINE/L2 2866 C-ACTC-AGAGTAAAAGCCAAAGTCCTTACAATGGCCTACAAGGCCCTAC 2913 chr6qtel1M 800580 ACAATCTGGTATCAATCGAT-CTTCTCAGATCAATTAGATATTATGACCC 800628 ii vi --i v - i v i -- i vv vi iv i L2#LINE/L2 2914 ATGATCTGGTCCC--CCGTTACCTCTCTGACC--TCATCTCCTACCACTC 2959 chr6qtel1M 800629 CCCCCCT 800635 i L2#LINE/L2 2960 TCCCCCT 2966 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 54.64 CpG sites = 132, Kimura (unadjusted) = 56.76 Transitions / transversions = 1.71 (132/77) Gap_init rate = 0.08 (44 / 583), avg. gap size = 1.30 (57 / 44) 477 20.86 2.38 4.88 chr6qtel1M 801077 801202 (198798) C Charlie1a#DNA/hAT-Charlie (0) 1455 1333 m_b319s502i2 13354 chr6qtel1M 801077 CAGTGGTTCTCAAACCTTT-GTTCTCAGTATC--TTCATGTTGTTAAAAA 801123 i i - v v i -- i iii v C Charlie1a#DNA 1455 CAGCGGTTCTCAAACTTTTTGGTCTCAGGACCCCTTTACACTCTTAAAAA 1406 chr6qtel1M 801124 AAACTATCTAGGATCTGTTCAAAGAGTTTCTGTTCACATGGGTTATATTT 801173 ---i iv i i--- i i i ii i C Charlie1a#DNA 1405 ---TTATTGAGGACCC---CAAAGAGCTTTTGTTTATGTGGGTTATATCT 1362 chr6qtel1M 801174 ATAGCTATTTACTATATTAGAAATAAAAA 801202 v v i v C Charlie1a#DNA 1361 ATCGATATTTACCATATTAGAAATTAAAA 1333 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 24.13 CpG sites = 18, Kimura (unadjusted) = 25.29 Transitions / transversions = 2.57 (18/7) Gap_init rate = 0.06 (8 / 125), avg. gap size = 1.12 (9 / 8) 449 25.61 0.00 0.00 chr6qtel1M 801200 801281 (198719) C Charlie1b#DNA/hAT-Charlie (441) 82 1 m_b319s502i3 13354 chr6qtel1M 801200 AAAATAATTTTGAATTTGTAGACCCTCTGAAAGGGTTTCAGAGACCCCAA 801249 i vi i ii i i i i v C Charlie1b#DNA 82 AAAATAGTTTTGACCTCGCGGACCCCCTGAAAGGGTCTCGGGGACCCCCA 33 chr6qtel1M 801250 CAATTCTTTGGACTACACTTTGAGGACCACTG 801281 viiv iii i i i C Charlie1b#DNA 32 GGGGTCCCCGGACCACACTTTGAGAACCGCTG 1 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 24.20 CpG sites = 17, Kimura (unadjusted) = 33.69 Transitions / transversions = 4.25 (17/4) Gap_init rate = 0.00 (0 / 81), avg. gap size = 0.0 (0 / 0) 635 25.00 3.20 3.20 chr6qtel1M 803509 803727 (196273) C L1ME3G_3end#LINE/L1 (376) 548 330 m_b319s551i2 13355 chr6qtel1M 803509 ATAATATTCCATAATATTCATATACCACAATTTATTCAGCCATTCTCCAA 803558 i i vv i i i i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chr6qtel1M 803559 CTGATGGGCATGCCCTCA----GTTTCCAGTTTCTGGCCACTACAAAGAG 803604 i i ---- i ---- i i v i i v i C L1ME3G_3end#L 498 TTGATGGACAT----TTAGGTTGTTTCCAATTTTTCGCTATTACAAACAA 453 chr6qtel1M 803605 GGCTGCCACAAACATTCGTGCACATACAGGTCCT--TTCCCTTCTTTAAA 803652 v v ii i v i i --? -- v v v v vii i C L1ME3G_3end#L 452 TGCTGCAATGAACATCCTTGTACATGC--NTCCTTGTGCACATGTGCGAG 405 chr6qtel1M 803653 -ATCTATTTGGGATATAAGACCAGTAGTAACACTGCTGGGTCAAAGGATA 803701 - i v ? i v v?v ? v iiv i i C L1ME3G_3end#L 404 TATTTCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTA 355 chr6qtel1M 803702 TGCACAGTTTGATAATTCAATACATA 803727 i v i - v i v C L1ME3G_3end#L 354 TGCGCATTTTAA-ATTTTAATAGATA 330 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 30.30 CpG sites = 31, Kimura (unadjusted) = 31.80 Transitions / transversions = 1.41 (31/22) Gap_init rate = 0.05 (10 / 218), avg. gap size = 1.40 (14 / 10) 36 0.00 0.00 0.00 chr6qtel1M 804332 804362 (195638) (AC)n#Simple_repeat 1 31 (0) c_b319s251i6 13356 chr6qtel1M 804332 ACACACACACACACACACACACACACACACA 804362 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACA 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 244 26.53 0.00 0.00 chr6qtel1M 805745 805793 (194207) C MIRb#SINE/MIR (15) 253 205 m_b319s601i14 13357 chr6qtel1M 805745 ATTTATTAAATATCTATTTTGTGCTGGGCAGTGTGCTAAGTACTTTACA 805793 i iiiii i v ii v ii C MIRb#SINE/MIR 253 ATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACA 205 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 28.36 CpG sites = 11, Kimura (unadjusted) = 35.78 Transitions / transversions = 5.50 (11/2) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 396 31.35 0.58 4.88 chr6qtel1M 805782 805952 (194048) C MIR1_Amn#SINE/MIR (47) 183 20 m_b319s601i15 13358 chr6qtel1M 805782 AAGTACTTTACAGATTAAGAGATGGCGAGTATTGTTATCCTCATTCTAAC 805831 i ---- - - iv ii i i - C MIR1_Amn#SINE 183 AAGCACTTTACA----AAG-GA-GGTCAGTATCATTATCCCCATTTTA-C 141 chr6qtel1M 805832 AGATGTTGAGAAAGAGGAAGGCAGGAATAAGATGATTTGCCCAGAGTCCC 805881 vv i vv v?viv iii ? ii i ii v C MIR1_Amn#SINE 140 AGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGCCCAAGGTCAC 91 chr6qtel1M 805882 ATAGTTAATAAATGTCAATAGCTAC-ATGTGAACTCAGGTCTCCCTAAAC 805930 ?i i?iii? i v i- iiv- ?v? i v iv C MIR1_Amn#SINE 90 NCAGCNGGCNAGTGGCAG-AGCCGGGANTNGAACCCAGGTCTCCCGAGTC 42 chr6qtel1M 805931 TAAGTGCATCATGCTAACCATT 805952 iv v viiiv v i C MIR1_Amn#SINE 41 CCAGTCCAGTGCTCTATCCACT 20 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 43.60 CpG sites = 32, Kimura (unadjusted) = 44.95 Transitions / transversions = 1.68 (32/19) Gap_init rate = 0.05 (9 / 170), avg. gap size = 1.00 (9 / 9) 682 32.27 3.10 2.70 chr6qtel1M 806992 807249 (192751) MIRc#SINE/MIR 10 268 (0) m_b319s601i16 13359 chr6qtel1M 806992 GTGGTGCAATGAATAGAACACTAGATGTATAGTGAAGAAGACTTTTGAGT 807041 i i v i i iv iv v i i -- i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCT--GGGT 57 chr6qtel1M 807042 TTAAATCCTACCTTTGACACTCATCAGCCTTATGACCCACCACAAATTGT 807091 ii i iiv i v i ii iv i ivvvi i iii MIRc#SINE/MIR 58 TCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCAC 107 chr6qtel1M 807092 TTAACCTCTGTCTGTCTCAATTTCCTTAATTATAAAATAGGAATAATGGT 807141 v vv i i i vi i i i ii MIRc#SINE/MIR 108 TTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAAT 157 chr6qtel1M 807142 AGC------ACAAACATGCCAGAATTTTTGTAATGATCAAATCAAGATAA 807185 v ------i vv v vv ii v i v -i MIRc#SINE/MIR 158 ACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAAT-GAGATAA 206 chr6qtel1M 807186 TATATATATTAAATATTTTTCAATACTT--AAGTGGTATAAAAATGCTAT 807233 i i i-v iiii vi - v-- v v iv v MIRc#SINE/MIR 207 TGTATGTG-AAAGCGCTTTGTAA-ACTGTAAAGTGCTATACAAATGTAAG 254 chr6qtel1M 807234 ATATTATAATATGATT 807249 i?i -- v MIRc#SINE/MIR 255 GNGTTAT--TATTATT 268 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 41.92 CpG sites = 51, Kimura (unadjusted) = 44.40 Transitions / transversions = 1.70 (51/30) Gap_init rate = 0.04 (9 / 257), avg. gap size = 1.67 (15 / 9) 251 35.84 2.50 0.61 chr6qtel1M 808189 808348 (191652) C L1ME3Cz_3end#LINE/L1 (780) 217 55 m_b319s551i3 13360 chr6qtel1M 808189 ATCTTTACCAAA--GATGAGTGTAATGTGAAGCATCAGAACTGCTTTAAT 808236 i i v-- i i vi iviiv vvii? i C L1ME3Cz_3end# 217 ATTTTTGCCAATCTGATGGGTGTGAAATGGTATCTCATTGTNGTTTTAAT 168 chr6qtel1M 808237 TTGTAGTTCACTACTTATTATAAAAAATTGGATATTTTAATATATGTT-- 808284 i v v iv i -ivi ii iii i vvi -- C L1ME3Cz_3end# 167 TTGCATTTCCCTGATTACTA-GTGAGGTTGAGCATCTTTTCATATGTTTA 119 chr6qtel1M 808285 TTGACAACTTGGATTTCTTCCTTTGAGAATAACCTTTTTCTATTCTTCTA 808334 i v i i i i i i v vi v iv i ivv C L1ME3Cz_3end# 118 TTGGCCATTCGGGTTTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGC 69 chr6qtel1M 808335 CAATGTGTCCATTG 808348 v v v i C L1ME3Cz_3end# 68 CCATTTTTCTATTG 55 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 50.46 CpG sites = 35, Kimura (unadjusted) = 51.81 Transitions / transversions = 1.59 (35/22) Gap_init rate = 0.02 (3 / 159), avg. gap size = 1.67 (5 / 3) 38 0.00 0.00 0.00 chr6qtel1M 809558 809590 (190410) (CA)n#Simple_repeat 1 33 (0) c_b319s251i7 13361 chr6qtel1M 809558 CACACACACACACACACACACACACACACACAC 809590 (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACAC 33 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 12 7.81 7.41 0.00 chr6qtel1M 810083 810109 (189891) (AAAT)n#Simple_repeat 1 29 (0) m_b319s252i22 13362 chr6qtel1M 810083 AAATACAT-AATAAATGAAT-AATAAATA 810109 v - i - (AAAT)n#Simpl 1 AAATAAATAAATAAATAAATAAATAAATA 29 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.08 (2 / 26), avg. gap size = 1.00 (2 / 2) 415 36.76 4.41 5.57 chr6qtel1M 812274 812636 (187364) C L2b_3end#LINE/L2 (6) 460 102 m_b319s601i17 13363 chr6qtel1M 812274 TTATGTAACAATGATTTATCAAATCCCTAATGTGTTCTGGGAACTGTGCT 812323 i vi vv iii iiv v v ii v? C L2b_3end#LINE 460 TCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCT 411 chr6qtel1M 812324 AAGTTCTGAGGATAC-----TAAAAAAGGTTAAAATATGGGTTCTGCTCT 812368 i iv i ----- i v ii-- i i?i vii i C L2b_3end#LINE 410 AGGCGCTGGGGATACAGCGGTGAACAAGAC--AGACNCGGTCCCTGCCCT 363 chr6qtel1M 812369 CATGCCATTCACATTCCAAATGAGGGAGACAAG-----AGGCAAACTATT 812413 i vvii v i- i i ii----- i? i v ? C L2b_3end#LINE 362 CACGGAGCTCACAGTCT-AGTGGGGGAGACAGACATGTAANCAGACAATN 314 chr6qtel1M 812414 AGGTTCATTCAAAATGTGTGTGCGTATGTAAAATGGGAGGCAAAATTAGA 812463 --- v ii i i - ii- v v --- v i ---ivii C L2b_3end#LINE 313 A---TAACCCAGAGTG-GCA-GGGTAGG---ACTGGGGGG---GCCCAGA 275 chr6qtel1M 812464 GGGATGACATC-AATTAGGCATGGCAGGGGATGGAGAAGGCCTCCTATAG 812512 - v i ii -i iiv v -- vii i i i iiv C L2b_3end#LINE 274 -GGAGGGCGCCTGACCCGGCCTGG--GGGGTCAGGGAGGGCTTCCCGGAG 228 chr6qtel1M 812513 GAAGTAGGATTTGAATGGAATCTTTAAGTAAGGTAAAGAAT---CTAGGA 812559 i iiv iiv iv i v v v ivv i i --- i - C L2b_3end#LINE 227 GAGGTGACATTTGAGCTGAGACCTGAAGGATGAGTAGGAGTTGGCCAGG- 179 chr6qtel1M 812560 AGAAAGAGTGAAAGAAGGAGCTTTACAAGAAAAAG--ATAGAACCAGCTA 812607 v iii -ii - v v i v i i -- i v ?vv v C L2b_3end#LINE 178 CGAAGAGGTG-GGGAAGG-GCGTTCCAGGCAGAGGGAACAGCANGTGCAA 131 chr6qtel1M 812608 AGATACAGAATCAAGAGATAGAGTGTCAT 812636 iiv v iv ii ?v v? v i C L2b_3end#LINE 130 AGGCCCTGAGGCGGGAGNGAGCNTGGCGT 102 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 50.16 CpG sites = 80, Kimura (unadjusted) = 55.48 Transitions / transversions = 1.74 (80/46) Gap_init rate = 0.07 (25 / 362), avg. gap size = 1.44 (36 / 25) 312 24.04 0.72 10.24 chr6qtel1M 813023 813161 (186839) MIR1_Amn#SINE/MIR 3 129 (101) m_b319s601i18 13364 chr6qtel1M 813023 GGGAGGAGCAGCTAGGTGCTGCAGTGGATAGAGGCCCAGCCATGAAGTCA 813072 -- i--- v vi vv ii v vv i v - MIR1_Amn#SINE 3 GGGAGG--CAGT---GTGGTCTAGTGGATAGAGCACTGGACTGGGACTC- 46 chr6qtel1M 813073 GGGGGAGCTGAGTTCAAATCTAGTCTCAGACACTTAACACTACCTAACTG 813122 i v i ? ? iv v ------- iv ?v i?i MIR1_Amn#SINE 47 GGGAGACCTGGGTTCNANTCCCGGCTC-------TGCCACTNGCCNGCTG 89 chr6qtel1M 813123 TGTGACCCTGAGCAAGTCACTTAACCCCAAT-TGTCTCAG 813161 ? i i ? i vv -? i MIR1_Amn#SINE 90 NGTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAG 129 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 31.02 CpG sites = 15, Kimura (unadjusted) = 31.02 Transitions / transversions = 1.00 (15/15) Gap_init rate = 0.10 (14 / 138), avg. gap size = 1.00 (14 / 14) 443 22.74 0.00 6.60 chr6qtel1M 813038 813150 (186850) MIRc#SINE/MIR 10 115 (153) m_b319s601i19 13364 chr6qtel1M 813038 GTGCTGCAGTGGATAGAGGCCCAGCCATGAAGTCAGGGGGAGCTGAGTTC 813087 v v vv ii v v i ii v i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chr6qtel1M 813088 AAATCTAGTCTCAGACACTTAACACTACCTAACTGTGTGACCCTGAGCAA 813137 i i iv v v v ------- i i i MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTGACCTTGGGCAA 102 chr6qtel1M 813138 GTCACTTAACCCC 813150 i MIRc#SINE/MIR 103 GTCACTTAACCTC 115 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 25.99 CpG sites = 13, Kimura (unadjusted) = 27.28 Transitions / transversions = 1.18 (13/11) Gap_init rate = 0.06 (7 / 112), avg. gap size = 1.00 (7 / 7) 16 17.49 0.00 0.00 chr6qtel1M 814213 814245 (185755) (CACA)n#Simple_repeat 1 33 (0) m_b320s252i1 13365 chr6qtel1M 814213 CACATACACATACACACACACACATGCACAGAC 814245 i i ii v (CACA)n#Simpl 1 CACACACACACACACACACACACACACACACAC 33 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 261 24.49 0.00 0.00 chr6qtel1M 815643 815691 (184309) C MIRb#SINE/MIR (15) 253 205 m_b320s601i0 13366 chr6qtel1M 815643 ATTTATTAAATAGCTATTTTGTGCTGGGCACTGTGCTAAGTACTTTACA 815691 i iiivi i v ii ii C MIRb#SINE/MIR 253 ATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACA 205 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 25.02 CpG sites = 10, Kimura (unadjusted) = 31.93 Transitions / transversions = 5.00 (10/2) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 417 28.92 3.30 5.03 chr6qtel1M 815680 815861 (184139) C MIR1_Amn#SINE/MIR (47) 183 5 m_b320s601i1 13367 chr6qtel1M 815680 AAGTACTTTACAGATAAAGACATGGAGAGTATTGTTATCCTCATTCTAAC 815729 i --- i --- vv ii i i - C MIR1_Amn#SINE 183 AAGCACTTTACA---AAGGA---GGTCAGTATCATTATCCCCATTTTA-C 141 chr6qtel1M 815730 AGATGTTGAGAAAGAGGAAAGCAGGCATTAGATGATTTGCCCAGAGTCCC 815779 vv i vv v?viv ivi ? ii i ii v C MIR1_Amn#SINE 140 AGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGCCCAAGGTCAC 91 chr6qtel1M 815780 ATAGTTAATAAATGTCAATAGCT-ACATTTGAACTCAGCTCTCCCTGAAA 815828 ?i i?iii? i v i- i-iv ? ? i v - iv C MIR1_Amn#SINE 90 NCAGCNGGCNAGTGGCAG-AGCCGGGANTNGAACCCAGGTCTCCC-GAGT 43 chr6qtel1M 815829 CTAAGTCCATCACACTAACCATT---TCACA--GCCTC 815861 iv vii v v i ---i -- C MIR1_Amn#SINE 42 CCCAGTCCAGTGCTCTATCCACTAGACCACACTGCCTC 5 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 38.92 CpG sites = 31, Kimura (unadjusted) = 39.97 Transitions / transversions = 1.63 (31/19) Gap_init rate = 0.07 (12 / 181), avg. gap size = 1.25 (15 / 12) 472 29.22 2.52 3.16 chr6qtel1M 815697 815855 (184145) C MIRc#SINE/MIR (98) 170 13 m_b320s601i2 13367 chr6qtel1M 815697 AGACATGGAGAGTATTGTTATCCTCATTCTAACAGATGTTGAGAAAGAGG 815746 i v vii i i i - vv i vv C MIRc#SINE/MIR 170 AGGCAGGGCAGGTATTATTATCCCCATTTTA-CAGATGAGGAAACTGAGG 122 chr6qtel1M 815747 ---AAAGCAGGCATTAGATGATTTGCCCAGAGTCCCATAGTTAATAAATG 815793 --- i - -- ii i ii v i i i i C MIRc#SINE/MIR 121 CTCAGAG-AGG--TTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTG 75 chr6qtel1M 815794 TCAATAGCTAC-ATTTGAACTCAGCTCTCCCTGAAACTAAGTCCATCACA 815842 v i- iiv- i i i v i vv i vii v C MIRc#SINE/MIR 74 GCAG-AGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCT 26 chr6qtel1M 815843 CTAACCATTTCAC 815855 vv i v C MIRc#SINE/MIR 25 CTTTCCACTGCAC 13 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 36.07 CpG sites = 28, Kimura (unadjusted) = 38.36 Transitions / transversions = 1.65 (28/17) Gap_init rate = 0.04 (7 / 158), avg. gap size = 1.29 (9 / 7) 617 30.51 4.60 5.81 chr6qtel1M 816905 817165 (182835) MIRc#SINE/MIR 10 267 (1) m_b320s601i3 13368 chr6qtel1M 816905 GTGGTACAGTGAATAAAACACTAGATGTATAGTAAGGAACACTTTTGAGT 816954 i i v i i i iv iv v v i -- i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCT--GGGT 57 chr6qtel1M 816955 TCAAATCCTATCTTTGGCACTCATCAGCTATATGACCCACCACAAATCGT 817004 i i iiv i v i ii i i ivvvi i ii MIRc#SINE/MIR 58 TCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCAC 107 chr6qtel1M 817005 TTAACCTCTGTCTG---CTCAATTTCCTCAATTATAAAACAGGGATAATG 817051 -- --- i vi i ii i MIRc#SINE/MIR 108 TTAACCTC--TCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATA 155 chr6qtel1M 817052 GTAGC------ACAAATATCCCAGAGTT-TTTTAATTATCAAATCAAAAT 817094 i v ------i vv iv v i - v i vv -i i MIRc#SINE/MIR 156 ATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAAT-GAGAT 204 chr6qtel1M 817095 AATATATACATATATATATAAAGTATTTTTCAATACTT--AAGTGGTATA 817142 i iii--------- iii vi - v-- v MIRc#SINE/MIR 205 AATGTATGTG---------AAAGCGCTTTGTAA-ACTGTAAAGTGCTATA 244 chr6qtel1M 817143 AAAATGCTATATATTATGAATAT 817165 v iv vi?i v v MIRc#SINE/MIR 245 CAAATGTAAGGNGTTATTATTAT 267 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 38.76 CpG sites = 48, Kimura (unadjusted) = 41.09 Transitions / transversions = 1.78 (48/27) Gap_init rate = 0.07 (19 / 260), avg. gap size = 1.42 (27 / 19) 253 34.30 0.70 2.13 chr6qtel1M 817787 817929 (182071) C L1ME2_3end#LINE/L1 (346) 565 425 m_b320s551i0 13369 chr6qtel1M 817787 TTTTTATAGTACAGTGGT-TTCTATTGCATCTATATACCATATTTTGGTC 817835 v ivv i - i i vv i v v i C L1ME2_3end#LI 565 TTTTTATTGCTGAGTAGTATTCCATTGTATGAATATACCACAATTTGTTT 516 chr6qtel1M 817836 AGTCATTCCCCAATTTATAAGCAACTCCTTGGTTTCTGATTCCATGCTGC 817885 vi ? vi v iii vi vvv v iii iiiv ii C L1ME2_3end#LI 515 ATCCATTCNCCTGTTGATGGACATTTGGGTTGTTTCCAGTTTTGGGCTAT 466 chr6qtel1M 817886 TATGGCAGGAATTACTATGAACATTTTATATATACAGGTTTTTT 817929 ivvii ii i ---i? i i i C L1ME2_3end#LI 465 TATGAATAAAGCTGCTATGAACATT---CNTGTACAAGTCTTTT 425 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 49.20 CpG sites = 30, Kimura (unadjusted) = 49.20 Transitions / transversions = 1.67 (30/18) Gap_init rate = 0.03 (4 / 142), avg. gap size = 1.00 (4 / 4) 22 6.91 0.00 0.00 chr6qtel1M 819161 819189 (180811) (GT)n#Simple_repeat 1 29 (3) m_b320s252i2 13370 chr6qtel1M 819161 GTGTGTGTGTGCGTGTGTGTGTGTGTATG 819189 i i (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTG 29 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 41 0.00 0.00 0.00 chr6qtel1M 819190 819224 (180776) (TA)n#Simple_repeat 1 35 (0) c_b320s251i0 13371 chr6qtel1M 819190 TATATATATATATATATATATATATATATATATAT 819224 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATAT 35 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 51 0.00 0.00 0.00 chr6qtel1M 819513 819556 (180444) (AC)n#Simple_repeat 1 44 (0) c_b320s251i1 13372 chr6qtel1M 819513 ACACACACACACACACACACACACACACACACACACACACACAC 819556 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACAC 44 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 235 34.15 4.88 0.00 chr6qtel1M 821339 821502 (178498) L1MA9_3end#LINE/L1 2 173 (886) m_b320s551i1 13373 chr6qtel1M 821339 TGATATCCAACATATATAGGGAATTGATACAAC----TATCTAAAACATG 821384 i v i i v ? ---- v v v ii L1MA9_3end#LI 2 TAATATCCAAAATATATAAGGAACTCANACAACTCAATAGCAAAAAAACA 51 chr6qtel1M 821385 CATTTCTCTGTTGATTAGTGGTCAAGGGATATGAATAG----TTTTTTAA 821430 v vv i vi ? vv i v i iv ---- i ii L1MA9_3end#LI 52 AATAACCCGATTNAAAAATGGGCAAAGGACCTGAATAGACATTTCTCCAA 101 chr6qtel1M 821431 AGAGGAATTGTAAACTATAAATCACTACATTAAAATACCTTCCAAATCAC 821480 i vv ii iviiv iviv i v viivi v v L1MA9_3end#LI 102 AGAAGACATACAAATGGCCAACAGGTATATGAAAAGGTGCTCAACATCAC 151 chr6qtel1M 821481 TAATGATAAAAGAACTCTAAAT 821502 v v ii v vi L1MA9_3end#LI 152 TAATCATCAGGGAAATGCAAAT 173 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 47.15 CpG sites = 28, Kimura (unadjusted) = 47.15 Transitions / transversions = 1.00 (28/28) Gap_init rate = 0.01 (2 / 163), avg. gap size = 4.00 (8 / 2) 469 35.84 6.37 4.05 chr6qtel1M 822024 822177 (177823) C L2b_3end#LINE/L2 (6) 460 300 m_b320s601i4 13374 chr6qtel1M 822024 TCATGCAACAATGATTTATCAAATCCCTAATGTGTTCTGGGAACTGTGCT 822073 v vv iii iiv v v ii v? C L2b_3end#LINE 460 TCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCT 411 chr6qtel1M 822074 AAGTTCTGAGGATACTACGA-----AAGGTTAAAATATGGTTTCTGTTCT 822118 i iv i vi i----- ii-- i i?i ii ii C L2b_3end#LINE 410 AGGCGCTGGGGATACAGCGGTGAACAAGAC--AGACNCGGTCCCTGCCCT 363 chr6qtel1M 822119 CAAGCCATTCACATTCCAAATGAGGGAGACAAG-----AGGCAAACTATT 822163 v vvii v i- i i ii----- i? i v ? C L2b_3end#LINE 362 CACGGAGCTCACAGTCT-AGTGGGGGAGACAGACATGTAANCAGACAATN 314 chr6qtel1M 822164 AGGTTCATTCAAA---A 822177 --- v ii i ---i C L2b_3end#LINE 313 A---TAACCCAGAGTGG 300 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 49.28 CpG sites = 72, Kimura (unadjusted) = 53.81 Transitions / transversions = 2.27 (34/15) Gap_init rate = 0.06 (9 / 153), avg. gap size = 2.11 (19 / 9) 38 0.00 0.00 0.00 chr6qtel1M 822178 822210 (177790) (TG)n#Simple_repeat 1 33 (0) c_b320s251i2 13375 chr6qtel1M 822178 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 822210 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 33 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 469 35.84 6.37 4.05 chr6qtel1M 822211 822369 (177631) C L2b_3end#LINE/L2 (167) 299 141 m_b320s601i4 13374 chr6qtel1M 822211 AAAATGGGAGTCAAAA---TTAGAGAGATGGCACC-AATTAGGCATGGCA 822256 iii i v viiii---ii - v i -i iiv v -- C L2b_3end#LINE 299 AGGGTAGGACTGGGGGGGCCCAGAG-GAGGGCGCCTGACCCGGCCTGG-- 253 chr6qtel1M 822257 GGGGATTGAGAAGGCCTCCTACAGGAAGCAGGATTTGAATGGAATCTTTA 822306 viv i i i iiv i iiiv iiv iv i v C L2b_3end#LINE 252 GGGGTCAGGGAGGGCTTCCCGGAGGAGGTGACATTTGAGCTGAGACCTGA 203 chr6qtel1M 822307 AGGAAGACAAGGAAT---CTAGGAAGAAACAGTGCGAAGAAGGAGTTTTC 822353 v vv i --- i -v ivi v -- - iv C L2b_3end#LINE 202 AGGATGAGTAGGAGTTGGCCAGG-CGAAGAGGTGGG--GAAGG-GCGTTC 157 chr6qtel1M 822354 CAAGAAAAAGAGAGAG 822369 i v i i ii v C L2b_3end#LINE 156 CAGGCAGAGGGAACAG 141 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 49.28 CpG sites = 72, Kimura (unadjusted) = 53.81 Transitions / transversions = 1.81 (38/21) Gap_init rate = 0.06 (10 / 158), avg. gap size = 1.40 (14 / 10) 464 22.59 1.69 6.19 chr6qtel1M 822791 822908 (177092) MIRc#SINE/MIR 3 115 (153) m_b320s601i5 13376 chr6qtel1M 822791 AGCTAGT-TGGTGCAGTGGGTAGAG-ACCAGCCCTGAAGTCAGGAGGACC 822838 vi - iv - ii v i i i MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chr6qtel1M 822839 TGAGTTCAAATGTAGTCTCAGACACTTAACACTTCCTAGCTGTATGACCC 822888 i i i viv v v v ------- i i MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTGACCT 95 chr6qtel1M 822889 TGAGCAAATCACTTAATCCC 822908 i i i i MIRc#SINE/MIR 96 TGGGCAAGTCACTTAACCTC 115 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 26.37 CpG sites = 17, Kimura (unadjusted) = 27.66 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.08 (9 / 117), avg. gap size = 1.00 (9 / 9) 49 5.38 0.00 0.00 chr6qtel1M 823922 823979 (176021) (CACA)n#Simple_repeat 1 58 (0) c_b320s251i3 13377 chr6qtel1M 823922 CACATACACATACAAACACACACACACACACACACACACACACACACACA 823971 i i v (CACA)n#Simpl 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 chr6qtel1M 823972 CACACACA 823979 (CACA)n#Simpl 51 CACACACA 58 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0) 498 31.74 12.67 1.63 chr6qtel1M 825161 825381 (174619) C MIRb#SINE/MIR (15) 253 9 m_b320s601i6 13378 chr6qtel1M 825161 ATTTATCGAAAGTCAATTATGTGCCAAATACTATGTTAAGCTCTTTATCA 825210 i iv iiv i iii i i v ivv C MIRb#SINE/MIR 253 ATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACAT 204 chr6qtel1M 825211 CTACTATCTCATTTGATCTT--------------------GG-ATCAT-A 825238 vi i i i -------------------- - i - C MIRb#SINE/MIR 203 GCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATTA 154 chr6qtel1M 825239 TTCCCATTTTACACA--AGGATACTGAAG---AAAATGTTAGTTGAGTGA 825283 i v -- v i --- i iv --- i i C MIRb#SINE/MIR 153 TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAG---GTTAAGTAA 107 chr6qtel1M 825284 CTTGGCCAGGATCACATAATTAATCCATGTCTGAGAATAGATTTAAATTT 825333 v i i i ii i vvi v v vvvi ii iii C MIRb#SINE/MIR 106 CTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCC 57 chr6qtel1M 825334 AAATCTTCCAGACTCC-AGGCCTATCAGCTTCATCATTGTACCACTTTG 825381 ii vi v - i ii vvv i-i i i vi C MIRb#SINE/MIR 56 AGGTCTGTCTGACTCCAAAGCCCGTGCTCTTT-CCACTGCACCACGCTG 9 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 41.78 CpG sites = 46, Kimura (unadjusted) = 43.70 Transitions / transversions = 2.00 (46/23) Gap_init rate = 0.05 (10 / 220), avg. gap size = 3.20 (32 / 10) 213 33.32 4.55 1.10 chr6qtel1M 825530 825617 (174383) C MIRc#SINE/MIR (18) 250 160 m_b320s601i7 13379 chr6qtel1M 825530 CATTTATAGTATATTTTAAGGTTTACAAAACACACTT-CATAGGCTAACT 825578 i vvii i vi i i vi i- vii v C MIRc#SINE/MIR 250 CATTTGTATAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATCT 201 chr6qtel1M 825579 CAGCTGATCTTCACAGGGA---TGTAACATAGGACAGATTAG 825617 vi i ivi --- i vi - ivi C MIRc#SINE/MIR 200 CATTTGATCCTCACAACAACCCTGTGAGGTAGG-CAGGGCAG 160 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 44.39 CpG sites = 19, Kimura (unadjusted) = 46.65 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.03 (3 / 87), avg. gap size = 1.67 (5 / 3) 49 0.00 0.00 0.00 chr6qtel1M 825846 825887 (174113) (TA)n#Simple_repeat 1 42 (0) c_b320s251i4 13380 chr6qtel1M 825846 TATATATATATATATATATATATATATATATATATATATATA 825887 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATA 42 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 250 34.52 7.14 0.00 chr6qtel1M 826686 826769 (173231) C L2d2_3end#LINE/L2 (15) 540 451 m_b320s601i8 13381 chr6qtel1M 826686 AAGTATTTATTAAATATCTATTTTGTGCTGGGCACTGTGCTAAGTACTTT 826735 i i iiii i v vi i ii v C L2d2_3end#LIN 540 AAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGT 491 chr6qtel1M 826736 ACAG---ATAAAGAGATGGAGAGTATTGTC---ATCCTCA 826769 ivi --- i ii iv iiii v ---ii C L2d2_3end#LIN 490 GGGGGATACAAAGAAGTATAAGACATGGTCCCTGCCCTCA 451 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 46.22 CpG sites = 23, Kimura (unadjusted) = 52.11 Transitions / transversions = 3.83 (23/6) Gap_init rate = 0.02 (2 / 83), avg. gap size = 3.00 (6 / 2) 261 32.86 0.00 6.36 chr6qtel1M 826727 826843 (173157) C MIR1_Amn#SINE/MIR (47) 183 74 m_b320s601i9 13382 chr6qtel1M 826727 AAGTACTTTACAGATAAAGAGATGGAGAGTATTGTCATCCTCATTCTAAC 826776 i --- i i v--- ii i i i - C MIR1_Amn#SINE 183 AAGCACTTTACA---AAGGAGGTC---AGTATCATTATCCCCATTTTA-C 141 chr6qtel1M 826777 AGATGTTGAGAAAGAGGAAGGCAGGAATTGGATGTTTTGCCCAGAGTCCC 826826 vv i vv v?viv iii ?iii vi ii v C MIR1_Amn#SINE 140 AGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGCCCAAGGTCAC 91 chr6qtel1M 826827 ATAGTTAATAAATGTCA 826843 ?i i?iii? i v C MIR1_Amn#SINE 90 NCAGCNGGCNAGTGGCA 74 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 49.37 CpG sites = 25, Kimura (unadjusted) = 49.37 Transitions / transversions = 2.27 (25/11) Gap_init rate = 0.06 (7 / 116), avg. gap size = 1.00 (7 / 7) 680 31.60 3.09 3.49 chr6qtel1M 828483 828741 (171259) MIRc#SINE/MIR 10 267 (1) m_b320s601i11 13383 chr6qtel1M 828483 GTGATGCAATGAGTAAAACACTAAGTGTACAGTAAGGAAGACTTTTGAGT 828532 i i iiv i i iiiiv iv v i -- i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCT--GGGT 57 chr6qtel1M 828533 CCAAATCCTACCTTTGGCACTCACCAGCCTTATGACCCACCACAAATCGT 828582 i i i iiv i v i i iv i ivvvi i ii MIRc#SINE/MIR 58 TCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCAC 107 chr6qtel1M 828583 TTAACCTCTGTCTGTCTCAATTTCCTCAATTATAAAATAGGGATAATGGT 828632 v vv i i vi i i ii MIRc#SINE/MIR 108 TTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAAT 157 chr6qtel1M 828633 AGC--ACAAACATAC----CAGAGTTTTTGCAATGATCAAATCAAGATAA 828676 v --v vvi v ---- i v ii v -i MIRc#SINE/MIR 158 ACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAAT-GAGATAA 206 chr6qtel1M 828677 TATATACATATATAAAGTATTTTTCAATACT-TAAA-TGGCATAAAAATG 828724 i iii----- iii vi - - - vi v MIRc#SINE/MIR 207 TGTATGTG-----AAAGCGCTTTGTAA-ACTGTAAAGTGCTATACAAATG 250 chr6qtel1M 828725 CTATATATTATTAATAT 828741 iv vi?i v MIRc#SINE/MIR 251 TAAGGNGTTATTATTAT 267 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 41.05 CpG sites = 52, Kimura (unadjusted) = 43.45 Transitions / transversions = 1.93 (52/27) Gap_init rate = 0.05 (13 / 258), avg. gap size = 1.31 (17 / 13) 47 2.27 0.00 0.00 chr6qtel1M 829545 829589 (170411) (CA)n#Simple_repeat 1 45 (0) c_b320s251i5 13384 chr6qtel1M 829545 CACACACACACACACACACACACATACACACACACACACACACAC 829589 i (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACAC 45 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 465 28.49 1.65 1.65 chr6qtel1M 831307 831488 (168512) L1P3_orf2#LINE/L1 3106 3287 (7) m_b320s551i2 13385 chr6qtel1M 831307 TGGGAAAATATTTTTACAATCAAAGGTTCTGATAAAGGCCTCATTTCCAA 831356 i v i v vvvv i v v v i L1P3_orf2#LIN 3106 TGGGAGAAAATTTTTGCAATCTATCCATCTGACAAAGGGCTAATATCCAG 3155 chr6qtel1M 831357 AATATATAGAGAACTGACTCTAATTTATAA---AAAATCAAGCTATTCTC 831403 v i ii v vv v i --- v i v -- i L1P3_orf2#LIN 3156 AATCTACAAGGAACTTAAACAAATTTACAAGAAAAAAACAAACAA--CCC 3203 chr6qtel1M 831404 CAATTGATAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGAAGAG 831453 - ii v i v i v i v v L1P3_orf2#LIN 3204 CA-TCAAAAAGTGGGCGAAGGATATGAACAGACACTTCTCAAAAGAAGAC 3252 chr6qtel1M 831454 GTTGAAACTATTTCTAGCCATATGAAAAGATGCTC 831488 i v vi viiivvi iv i v L1P3_orf2#LIN 3253 ATTTATGCGGCCAACAAACATATGAAAAAAAGCTC 3287 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 35.20 CpG sites = 23, Kimura (unadjusted) = 36.05 Transitions / transversions = 0.82 (23/28) Gap_init rate = 0.02 (4 / 181), avg. gap size = 1.50 (6 / 4) 1580 27.83 3.16 3.49 chr6qtel1M 831352 831984 (168016) L1ME5_3end#LINE/L1 7 637 (304) m_b320s551i4 13385 chr6qtel1M 831352 TCCAAAATATATAGAGAACTGACTCTAATTTATAAAAAATCAAGCTATT- 831400 i i i ii vviv v iv i i -- viiv?- L1ME5_3end#LI 7 TCTAGAATATACAAGGAACTCCTGCAAATCAACAAGAAA--AAGACGGNA 54 chr6qtel1M 831401 -CTCCAATTGATAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGA 831449 - i v v v i iv v L1ME5_3end#LI 55 ACCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGA 104 chr6qtel1M 831450 AGAGG-TTGAAA--CTATTTCTAGCCATATGAAAAGATGCTCCAAGTCAT 831496 i ii-ii -- --v v - i v v L1ME5_3end#LI 105 GGAAACCCGAAAGGCTA--ACAAG-CATATGAAGAGATGCTCAAACTCAT 151 chr6qtel1M 831497 TATTGGTTAGCGAAATGCAAATTAAGACAACTCTGAGATACCACTACACA 831546 v ii i v i vv i vi L1ME5_3end#LI 152 TAGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACA 201 chr6qtel1M 831547 CCT-TCAGACTGGCTAGAATGGCAGGAAA--AGATAATGCGGAATGTTGG 831593 - i v i --i i i--i vi i L1ME5_3end#LI 202 CCTATTAGACTGGCAAAAAT--TAGAAAGCTGGATAATGCCAAGTGTTGG 249 chr6qtel1M 831594 AGGGGATATGGGAAAACAGGGACACTAATACATTGTTGGTGGAATTGTGA 831643 v i i i ? i i v v i i i i v ii L1ME5_3end#LI 250 CGAGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAG 299 chr6qtel1M 831644 ATACATCCAACCATTCTGGAGAGCAATTTGGAACTA--TGCTCAAA--AA 831689 ivvi v i i v v -- iv -- L1ME5_3end#LI 300 ACTGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTAA 349 chr6qtel1M 831690 GTTATCAAACTGTGCATACCCTTTGATGCAGCAGTGTTACTACTGGGCTT 831739 - --- --- v iv i viii v iv L1ME5_3end#LI 350 G-TAT---AC---GCATACCCTATGACCCAGCAATTCCGCTCCTGGGTAT 392 chr6qtel1M 831740 ATATCCCAAAGAAATCATAAAGAAGG----TAAAGGGACCTGTATGTGCA 831785 iv v viv ---- i ---- i i L1ME5_3end#LI 393 ATATCCCAAAGAAATTCTCACACAGGTCCATAAGGGGAC----ATGTACG 438 chr6qtel1M 831786 TGAATGTTTGTGGCAGCCCTCTTTGTAGTGGCCATAAACTGGAAACTGAG 831835 v i ii v vi v i vivi ii ii vivv L1ME5_3end#LI 439 AGGATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACC 488 chr6qtel1M 831836 TGGATGCCCATCAATTGGAGAATGGCTGAATAAATTGTGGTATATGAATA 831885 i i v v i v iii v iv v i L1ME5_3end#LI 489 TGGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACA 538 chr6qtel1M 831886 TTATGGAATATTATTGTTCGGTAAGAAATGACCAACAGGATGATTTCAGA 831935 ii i i vvvv i v iii vi vi -- v v L1ME5_3end#LI 539 CCATGGAGTACTATGCAGCAGTTAGAAGCAACGGACTAGATG--TACACA 586 chr6qtel1M 831936 AAG--GCCTGGAGAGA-CTTACACAAAC-TGATGGTAAGTGAAACAAGCA 831981 v --i v vi - -- v - ii v i v i L1ME5_3end#LI 587 TAGCAACATGGATGGATCTT--AAAAACATAGTGCTGAGTGAAAAAAGTA 634 chr6qtel1M 831982 GGA 831984 i L1ME5_3end#LI 635 AGA 637 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 34.64 CpG sites = 98, Kimura (unadjusted) = 35.74 Transitions / transversions = 1.36 (98/72) Gap_init rate = 0.05 (34 / 632), avg. gap size = 1.24 (42 / 34) 1666 27.27 0.55 1.66 chr6qtel1M 831352 831899 (168101) L1ME3G_3end#LINE/L1 7 548 (376) m_b320s551i3 13385 chr6qtel1M 831352 TCCAAAATATATAGAGAACTGACTCTAATTTATAAAAAATCAAGCTATTC 831401 i i vviv v iv i -- vi --v L1ME3G_3end#L 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAA--AAGACA--A 52 chr6qtel1M 831402 TCCAATTGATAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGAAG 831451 i v v v i v v i L1ME3G_3end#L 53 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chr6qtel1M 831452 AGGTTGAAACTATTTCTAGCCATATGAAAAGATGCTCCAAGTCATTATTG 831501 ii vv iviiivv iv v vv i v i L1ME3G_3end#L 103 AAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTA 152 chr6qtel1M 831502 GTTAGCGAAATGCAAATTAAGACAACTCTGAGATACCACTACACACCT-T 831550 i i v i vv i viv i- L1ME3G_3end#L 153 ATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCAT 202 chr6qtel1M 831551 CAGACTGGCTAGAATGGCAGGAAAAGATAATGCGGAATGTTGGAGGGGAT 831600 i v i vvv iii?vv iiv? i v i i L1ME3G_3end#L 203 CAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGT 252 chr6qtel1M 831601 ATGGGAAAACAGGGACACTAATACATTGTTGGTGGAATTGTGAATACATC 831650 i i i v v v i i i v i vvi v L1ME3G_3end#L 253 GTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTA 302 chr6qtel1M 831651 CAACCATTCTGGAGAGCAATTTGGAACTATGCTCAAAAAGTTATCAAACT 831700 i ? i i v v viviv v --- v L1ME3G_3end#L 303 CAGCCNTTTTGGAGGGCAATTTGGCAGTATCTATTAAAATTTA---AAAT 349 chr6qtel1M 831701 GTGCATACCCTTTGATGCAGCAGTGTTACTACTGGGCTTATATCCCAAAG 831750 i iv i vii v ? ?v v i ? L1ME3G_3end#L 350 GCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAG 399 chr6qtel1M 831751 AAAT-CATAAAGAAG-GTAAAGGGACCTGTATGTGCATGAATGTTTGTGG 831798 - viiv v v - i v i --? i i v i ii v L1ME3G_3end#L 400 AAATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTCATTG 447 chr6qtel1M 831799 CAGCCCTCTTTGTAGTGGCCATAAACTGGAAACTGAGTGGATGCCCATCA 831848 vi v i i v v i vivv ii i L1ME3G_3end#L 448 CAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCA 497 chr6qtel1M 831849 ATTGGAGAATGGCTGAATAAATTGTGGTATATGAATATTATGGAATATTA 831898 v i i i i vv i i L1ME3G_3end#L 498 ATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACTA 547 chr6qtel1M 831899 T 831899 L1ME3G_3end#L 548 T 548 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 34.03 CpG sites = 76, Kimura (unadjusted) = 34.93 Transitions / transversions = 1.07 (76/71) Gap_init rate = 0.02 (12 / 547), avg. gap size = 1.00 (12 / 12) 612 23.11 9.20 0.53 chr6qtel1M 833270 833443 (166557) C MIRc#SINE/MIR (3) 265 77 m_b320s601i12 13386 chr6qtel1M 833270 AATAATAATGAGTTAGCATTTTTATAGCACTTT------TATAAAGTACT 833313 i?vv - v ------ i ii C MIRc#SINE/MIR 265 AATAATAACNCCTTA-CATTTGTATAGCACTTTACAGTTTACAAAGCGCT 217 chr6qtel1M 833314 T-AACAAATATTAACTTATTTTATCCTCACAGTATCCCTAAAAGAT---- 833358 -v v i v i v ii v ivi i ---- C MIRc#SINE/MIR 216 TTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGC 167 chr6qtel1M 833359 --GGTTGCTATCATTGTCCCCATTTAACAGGTAAGAAGACTAAGGCAGGC 833406 -- iv v i i v i i i i i vviv C MIRc#SINE/MIR 166 AGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAG 117 chr6qtel1M 833407 AGAGGTCAAGTGACCT-CACAGGGT--CACAGCTCGTAAG 833443 i i - v i -- v C MIRc#SINE/MIR 116 AGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAG 77 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 27.40 CpG sites = 23, Kimura (unadjusted) = 28.31 Transitions / transversions = 1.35 (23/17) Gap_init rate = 0.04 (7 / 173), avg. gap size = 2.43 (17 / 7) 622 23.81 2.03 0.67 chr6qtel1M 833296 833443 (166557) C MIR#SINE/MIR (40) 222 73 m_b320s601i13 13386 chr6qtel1M 833296 GCACTTTTATAAAGTACTTAACAAATATTAACTTATTTTATCCTCACAGT 833345 v v - ii v vi i v ii C MIR#SINE/MIR 222 GCACTGTTCTAA-GCGCTTTACATGTATTAACTCATTTAATCCTCACAAC 174 chr6qtel1M 833346 ATCCCTAAAAGATGGTTGCTATCATTGTCCCCATTTAACAGGTAAGAAGA 833395 v vi i i v i i i v i i i i C MIR#SINE/MIR 173 AACCCTATGAGGTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAA 124 chr6qtel1M 833396 CTAAGGCAGGCAGAGGTCAAGTGACCT-CACAGGGT--CACAGCTCGTAA 833442 i viv i i i - v i -- v C MIR#SINE/MIR 123 CTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAA 74 chr6qtel1M 833443 G 833443 C MIR#SINE/MIR 73 G 73 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 28.30 CpG sites = 22, Kimura (unadjusted) = 29.40 Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.02 (3 / 147), avg. gap size = 1.33 (4 / 3) 26 25.56 2.70 0.00 chr6qtel1M 833445 833518 (166482) (AT)n#Simple_repeat 1 76 (0) m_b320s252i3 13387 chr6qtel1M 833445 ATATA-ATTTATATTTATATATAAAGAATTTTATATATATATGGAGA-AT 833492 - v v v v vv v iv v - (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr6qtel1M 833493 TTTTATATTTATATATGCGTATATAT 833518 v v v iii (AT)n#Simple_ 51 ATATATATATATATATATATATATAT 76 Matrix = Unknown Transitions / transversions = 0.33 (4/12) Gap_init rate = 0.03 (2 / 73), avg. gap size = 1.00 (2 / 2) 13 13.08 0.00 0.00 chr6qtel1M 836300 836324 (163676) (TCAA)n#Simple_repeat 1 25 (0) m_b320s252i4 13388 chr6qtel1M 836300 TCAGTGAATCAATCATTCAATCAAT 836324 i v v (TCAA)n#Simpl 1 TCAATCAATCAATCAATCAATCAAT 25 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 182 26.04 0.00 4.00 chr6qtel1M 837098 837149 (162851) C L2#LINE/L2 (954) 2128 2079 m_b320s601i14 13389 chr6qtel1M 837098 TGGGAGATCCAAGTAAAGAAAGTGTCTCCTGAAATAAGAGATTAGCAACT 837147 i -- i i vv iv i iii v v C L2#LINE/L2 2128 TGGAAG--CCAAGTGAAGAAAGTGTTTCAAGAAGGAGGGAGTGATCAACT 2081 chr6qtel1M 837148 GT 837149 C L2#LINE/L2 2080 GT 2079 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 32.81 CpG sites = 8, Kimura (unadjusted) = 32.81 Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.00 (2 / 2) 277 35.71 1.77 0.88 chr6qtel1M 837185 837297 (162703) C MIRc#SINE/MIR (151) 117 4 m_b320s601i15 13390 chr6qtel1M 837185 GAGACATCAGGTGACATTCTCAGAGAACTACAATCTGTACGGTGTCAGGG 837234 vi i i v v i ii vvvi iiiv -i v i C MIRc#SINE/MIR 117 GAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTA-AGTGGCAGAG 69 chr6qtel1M 837235 TCAGAATTTGAAGCCA--TCTCTCTGATTGGAAGAATAGTCCTCTAGCCA 837282 i i i i i v -- ii i vv vvi v vv C MIRc#SINE/MIR 68 CCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCA 19 chr6qtel1M 837283 TTGCAGCATACTGCC 837297 i v i C MIRc#SINE/MIR 18 CTGCACCACACTGCC 4 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 46.83 CpG sites = 23, Kimura (unadjusted) = 50.38 Transitions / transversions = 1.35 (23/17) Gap_init rate = 0.02 (2 / 112), avg. gap size = 1.50 (3 / 2) 247 21.15 0.00 0.00 chr6qtel1M 837305 837356 (162644) EuthAT-N1a#DNA/hAT-Tip100 98 149 (109) m_b320s502i0 13391 chr6qtel1M 837305 ACCTATTTAGCAAAAATAATGACATAAAACAGGAAGCTAGCAGACAGTGT 837354 v i v vv i v ii i i EuthAT-N1a#DN 98 ACCTAGTTAGCAAGAATAATTAGTTAAAATAGGAAGCTACCAGATGGCGC 147 chr6qtel1M 837355 GC 837356 EuthAT-N1a#DN 148 GC 149 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 20.24 CpG sites = 6, Kimura (unadjusted) = 25.13 Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 556 25.60 6.02 3.53 chr6qtel1M 837914 838079 (161921) C MIRc#SINE/MIR (66) 202 33 m_b320s601i16 13392 chr6qtel1M 837914 CTCATTTTATCT---AAACAACTATGAGAGGTGGACAC------TAATTT 837954 v i---v iv v i i v------ v v C MIRc#SINE/MIR 202 CTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTAT 153 chr6qtel1M 837955 CATTCCTATTTTATAGATGAGAAAACTGAGCCTGAGAAAGGTTAAGTGGC 838004 i i i i i v v i i C MIRc#SINE/MIR 152 TATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGAC 103 chr6qtel1M 838005 TTGCTTAGGGTGACACAGTTCTTAGGATTCTAAGCCAGAACTTAAAGTAG 838054 ii i v i vv i vvv vi i i ii ---- C MIRc#SINE/MIR 102 TTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAA---- 57 chr6qtel1M 838055 CCCCACAGTCTTCA-GACTCCAGGCC 838079 - -i v- i i C MIRc#SINE/MIR 56 -CCCA-GGTCTTCCTGACTCCAAGTC 33 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 30.08 CpG sites = 24, Kimura (unadjusted) = 32.04 Transitions / transversions = 1.41 (24/17) Gap_init rate = 0.05 (9 / 165), avg. gap size = 1.78 (16 / 9) 428 26.23 6.04 5.33 chr6qtel1M 837948 838096 (161904) C MIR3#SINE/MIR (50) 158 9 m_b320s601i17 13392 chr6qtel1M 837948 CTAATTTCATTCCT--ATTTTATAGATGAGAAAACTGAGCCTGAGAAAGG 837995 i iiv ii i-- i i v iv i C MIR3#SINE/MIR 158 CTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGG 109 chr6qtel1M 837996 TTAAGTGGCTTGCTTAGGGTGACACAGTT-CTTAG-GATTCTAAGCCAGA 838043 v i ii i v i?-v - i-- vi i i C MIR3#SINE/MIR 108 TGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGG--CAGAGCCGGG 61 chr6qtel1M 838044 ACTTAAAGTAGCCCCACAGTCTTCAGACTCC-AGGCCAAACTCC----AC 838088 vi ----- -i i v - v ivi i----i C MIR3#SINE/MIR 60 ACTAGAA-----CCCA-GGTCTCCTGACTCCCAGTCCGTGCTCTCTCTGC 17 chr6qtel1M 838089 TCAGCCAC 838096 C MIR3#SINE/MIR 16 TCAGCCAC 9 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 31.88 CpG sites = 26, Kimura (unadjusted) = 34.17 Transitions / transversions = 2.36 (26/11) Gap_init rate = 0.09 (13 / 148), avg. gap size = 1.31 (17 / 13) 251 40.31 2.69 2.69 chr6qtel1M 838236 838495 (161505) L2d2_3end#LINE/L2 21 280 (275) m_b320s601i18 13393 chr6qtel1M 838236 CCACATTTCTAGTTTTCTTGCACATTATAACCCTCC-TATACTCTTCAGT 838284 i? v i ii v iv v i vv ? -iiv i i iv L2d2_3end#LIN 21 CTNCCTTTCCAGCCTTATCTCCCACTATTCCCCTNCACGAACCCTCCGCT 70 chr6qtel1M 838285 CCAGTGACTCGGGAATCTTGGCCATTTCAAAAATAACAACATTGCATCT- 838333 iv vv v vv vi vi ii ii vvi i - iv - ii? - L2d2_3end#LIN 71 CCAGCCAAACTGGTCTACTCACTGTCCCCCGAACA-CGCC-TTGCGCNTT 118 chr6qtel1M 838334 CTTAACTCTGGGCATTT--TCACTGGAGTCTCCCATGACTGAGGTTCTCT 838381 iiiv v v -- - vv ii vi v iii v i L2d2_3end#LIN 119 CCCGCCTCTGCGCCTTTGCTCAC-GCCGTTCCCCCCGCCTGGAATGCCCT 167 chr6qtel1M 838382 CTCTTCTCATTTCTACCTTCCTTCAGGTCCTCTACTCATCCTTCAAGTCC 838431 ii iii v i i --v i ii -- i v L2d2_3end#LIN 168 TCCCCTTCCTCTCCACCT--ATCCAAATCCT--ACCCATCCTTCAAGGCC 213 chr6qtel1M 838432 CAAATAGAACTTCATCTTCCATAGGAAACCTTTCCCAATTTCTTTAATTT 838481 iv vi i?i i i iviiv i i ii iiv ii iiii L2d2_3end#LIN 214 CAGCTCAAATNCCACCTCCTCCGTGAAGCCTTCCCTGACCACTCCAGCCC 263 chr6qtel1M 838482 GAA-TG--CCTTCCCTC 838495 ? - -- ii L2d2_3end#LIN 264 GNAGTGATCTCTCCCTC 280 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 55.85 CpG sites = 67, Kimura (unadjusted) = 65.49 Transitions / transversions = 1.91 (67/35) Gap_init rate = 0.05 (12 / 259), avg. gap size = 1.17 (14 / 12) 32 21.22 6.36 0.86 chr6qtel1M 838991 839100 (160900) (ATATTA)n#Simple_repeat 1 116 (0) m_b320s252i5 13394 chr6qtel1M 838991 ATATTAATA-TAATACTAATATGAATAAT-ATGCTACT-GT-ATATT-GT 839035 - i v v - ii v -v - -i (ATATTA)n#Sim 1 ATATTAATATTAATATTAATATTAATATTAATATTAATATTAATATTAAT 50 chr6qtel1M 839036 ATTAATATATGATAGTGAT-TATATAGTATTATTAAGA-TAATATTTATA 839083 - i v i - vv v v v - v (ATATTA)n#Sim 51 ATTAATAT-TAATATTAATATTAATATTAATATTAATATTAATATTAATA 99 chr6qtel1M 839084 TTTACATTAAGATTAAT 839100 v i v (ATATTA)n#Sim 100 TTAATATTAATATTAAT 116 Matrix = Unknown Transitions / transversions = 0.54 (7/13) Gap_init rate = 0.07 (8 / 109), avg. gap size = 1.00 (8 / 8) 25 9.63 4.92 4.92 chr6qtel1M 839085 839145 (160855) (TTACA)n#Simple_repeat 1 61 (0) m_b320s252i6 13395 chr6qtel1M 839085 TTACATTAAGATTA-ATTACACTACATTACATTATTGTACATGTACATTA 839133 - v - i ivv - (TTACA)n#Simp 1 TTACATT-ACATTACATTACATTACATTACATTACATTACAT-TACATTA 48 chr6qtel1M 839134 -A-TACATATACAT 839145 - - - (TTACA)n#Simp 49 CATTACAT-TACAT 61 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.10 (6 / 60), avg. gap size = 1.00 (6 / 6) 19 21.18 0.00 0.00 chr6qtel1M 839974 840011 (159989) (T)n#Simple_repeat 1 38 (0) m_b320s252i7 13396 chr6qtel1M 839974 TTTTTATTTTATATTGTTTTTCCTTTTTTTCTTTTTTT 840011 v v v v ii i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 38 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 15 17.31 5.26 8.11 chr6qtel1M 842081 842156 (157844) (TTTCCT)n#Simple_repeat 1 74 (0) m_b320s252i8 13397 chr6qtel1M 842081 TTTCCTTTT-TATTCCCTTTTCACCTTTTTATTTGGTTCTTTTTACTTTT 842129 -iv i -- - vi -- i v (TTTCCT)n#Sim 1 TTTCCTTTTCCTTTTCCTTTT--CC-TTTTCCTT--TTCCTTTTCCTTTT 45 chr6qtel1M 842130 CTTTTTCCCTATTCC-TAT--TTTTCCTTT 842156 i - v - v -- (TTTCCT)n#Sim 46 CCTTTT-CCTTTTCCTTTTCCTTTTCCTTT 74 Matrix = Unknown Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.12 (9 / 75), avg. gap size = 1.11 (10 / 9) 360 34.40 12.08 2.45 chr6qtel1M 844665 844852 (155148) L2b_3end#LINE/L2 120 326 (140) m_b320s601i19 13398 chr6qtel1M 844665 CCTC-GGGCATTTTC--CTG--GATTCCCATGTCGGGTTCTCCCTTCTTC 844709 - v v --? -- v i iv i v vv v -- L2b_3end#LINE 120 CCTCAGGGCCTTTGCACNTGCTGTTCCCTCTGCCTGGAACGCCCTTC--C 167 chr6qtel1M 844710 TCAGTTCTACCTTCCTTCAGGTCCTCTACTCATCCTTCAAGTCCCAAATA 844759 i vi v viiivvi iv -- i i iv v L2b_3end#LINE 168 CCACCTCTTCGCCTGGCCAACTCCT--ACTCATCCTTCAGGTCTCAGCTC 215 chr6qtel1M 844760 GAACCTTATCTTCCATAGGAAATCTTTCCCATTTCTTTAATTTGAAT--- 844806 i iv i i i ivii ii i i iivii iii ivii ii --- L2b_3end#LINE 216 AAATGTCACCTCCTCCGGGAAGCCCTCCCTGACCCCCCAGGCCGGGTCAG 265 chr6qtel1M 844807 --GCCTTCC------CTCTGCCAAT--TATCT--CCAAT-----TTATC- 844838 -- i ------ i iv i -- i i-- v ----- ?- L2b_3end#LINE 266 GCGCCCTCCTCTGGGCCCCCCCAGTCCTACCCTGCCACTCTGGGTTATNA 315 chr6qtel1M 844839 TTGTATACACTTCG 844852 v i?--- ii L2b_3end#LINE 316 TTGTCTGN---TTA 326 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 46.97 CpG sites = 70, Kimura (unadjusted) = 51.57 Transitions / transversions = 2.00 (46/23) Gap_init rate = 0.09 (16 / 187), avg. gap size = 2.06 (33 / 16) 30 3.45 0.00 0.00 chr6qtel1M 844853 844882 (155118) (GT)n#Simple_repeat 1 30 (0) c_b320s251i6 13399 chr6qtel1M 844853 GTGTATGTGTGTGTGTGTGTGTGTGTGTGT 844882 i (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 30 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 360 34.40 12.08 2.45 chr6qtel1M 844883 844991 (155009) L2b_3end#LINE/L2 327 444 (22) m_b320s601i19 13398 chr6qtel1M 844883 ATA---GTCTTCCCCATTAGACCCTCAGTTTCTTGAAAGCTGGGACTGGA 844929 i--- i i iv v i i v ii v i ?i L2b_3end#LINE 327 ATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNG 376 chr6qtel1M 844930 TTTTGCCTT-----TCATTGTATCCCTAGCA--TAGCACACCAACTATCA 844972 i - i -----i ii i i-- v?iv iv L2b_3end#LINE 377 TCT-GTCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCA 425 chr6qtel1M 844973 CATAGTAGACATTCAATAA 844991 i i ii i L2b_3end#LINE 426 CACAGTAGGCGCTCAGTAA 444 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 46.97 CpG sites = 70, Kimura (unadjusted) = 51.57 Transitions / transversions = 3.43 (24/7) Gap_init rate = 0.04 (4 / 108), avg. gap size = 2.75 (11 / 4) 14 15.24 0.00 7.69 chr6qtel1M 845210 845251 (154749) (TTTTAA)n#Simple_repeat 1 39 (0) m_b320s252i9 13400 chr6qtel1M 845210 TTTTAATTTTCATTTTATTTTTTAATTGACAAGTTTTGATTT 845251 v -v -vi - i (TTTTAA)n#Sim 1 TTTTAATTTTAATTTTA-ATTTTAATT-TTAA-TTTTAATTT 39 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.07 (3 / 41), avg. gap size = 1.00 (3 / 3) 95 20.99 5.15 5.70 chr6qtel1M 845403 845790 (154210) (AT)n#Simple_repeat 1 386 (0) m_b320s252i10 13401 chr6qtel1M 845403 ATATA-ATAGTA-ATATGAATA-ATATGTGACTGTATAT-TATATTAATT 845448 - - - iv - i - - i - vv v (AT)n#Simple_ 1 ATATATATA-TATATATATATATATATAT-A-TATATATATATATATATA 47 chr6qtel1M 845449 CAT-TATAGTGAT-TATATAGTAT-TATTAATATA-ATATTTATATTTAC 845494 i - - - - - - vv - v v i (AT)n#Simple_ 48 TATATATA-T-ATATATATA-TATATATATATATATATATATATATATAT 94 chr6qtel1M 845495 ATTAACATA-ACATGAATTCCTACATGTAGGATATTAATTTA-ATGTACT 845542 vv i - i iv viv i i -v vv v - i - (AT)n#Simple_ 95 ATATATATATATATATATATATATATATA-TATATATATATATATATA-T 142 chr6qtel1M 845543 ACATGATATATATGGTATATCATA-ATACTATATGTAT-TATATGATATG 845590 i - -i - - - i - - i (AT)n#Simple_ 143 ATAT-ATATATAT-ATATAT-ATATATA-TATATATATATATAT-ATATA 187 chr6qtel1M 845591 CA-ATATATACTATATAT-TACTACATATATACTACATATAGTAAATATA 845638 i - - - - i - i - v (AT)n#Simple_ 188 TATATATATA-TATATATATA-TATATATATA-TATATATA-TATATATA 233 chr6qtel1M 845639 TATATA-ATATATACATGCATATATATCATATATCTATATATGTATGTAT 845687 - i ii - v i i (AT)n#Simple_ 234 TATATATATATATATATATATATATAT-ATATATATATATATATATATAT 282 chr6qtel1M 845688 ATATATGAGGTATGTATATATCAAATATGCA-ATATATACTATTGCTTTG 845736 - vi i - v ii - - vvv v i (AT)n#Simple_ 283 ATATAT-ATATATATATATAT-ATATATATATATATATA-TATATATATA 329 chr6qtel1M 845737 TATATAGCATAAATATA-ATA-ATATA-ACAT-TATATGTGTACACATGC 845782 -i v - - - i - i i i i ii (AT)n#Simple_ 330 TATATA-TATATATATATATATATATATATATATATATATATATATATAT 378 chr6qtel1M 845783 ATATATAT 845790 (AT)n#Simple_ 379 ATATATAT 386 Matrix = Unknown Transitions / transversions = 1.42 (37/26) Gap_init rate = 0.11 (42 / 387), avg. gap size = 1.00 (42 / 42) 30 13.65 3.75 5.06 chr6qtel1M 846574 846653 (153347) (ATTT)n#Simple_repeat 1 79 (0) m_b320s252i11 13402 chr6qtel1M 846574 ATTTCTTTA-ATATTT-TTTTTTTATTATATTGATTTAATCTAATTTATT 846621 v -v - v - v - - v (ATTT)n#Simpl 1 ATTTATTTATTTATTTATTTATTTATT-TATTTATTT-AT-TTATTTATT 47 chr6qtel1M 846622 TATTTATGAAATTATTCATTATATTTA-TTATT 846653 vv v i - - (ATTT)n#Simpl 48 TATTTATTTATTTATTTATT-TATTTATTTATT 79 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.09 (7 / 79), avg. gap size = 1.00 (7 / 7) 18 10.00 11.11 5.26 chr6qtel1M 846581 846652 (153348) (TATTA)n#Simple_repeat 1 76 (0) m_b320s252i12 13403 chr6qtel1M 846581 TAATAT-TTTTTTTTTATTATATTGAT-TTA-ATCTA-ATT-TATT-TAT 846624 v - v v v - - - - - - - (TATTA)n#Simp 1 TATTATATTATATTATATTATATT-ATATTATAT-TATATTATATTATAT 48 chr6qtel1M 846625 T-TATGAAATTATTCATTATATT-TATTAT 846652 - v v - - - (TATTA)n#Simp 49 TATATTATATTA-T-ATTATATTATATTAT 76 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.17 (12 / 71), avg. gap size = 1.00 (12 / 12) 30 0.00 0.00 0.00 chr6qtel1M 847245 847272 (152728) (TTTTGT)n#Simple_repeat 1 28 (0) c_b320s251i7 13404 chr6qtel1M 847245 TTTTGTTTTTGTTTTTGTTTTTGTTTTT 847272 (TTTTGT)n#Sim 1 TTTTGTTTTTGTTTTTGTTTTTGTTTTT 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 15 13.79 7.50 0.00 chr6qtel1M 847378 847417 (152583) (ATAAAT)n#Simple_repeat 1 43 (0) m_b320s252i13 13405 chr6qtel1M 847378 ATAGATTTAAATAT-ATTA-AAATATAAAT-TAGATACAAATA 847417 i v - v - - i i (ATAAAT)n#Sim 1 ATAAATATAAATATAAATATAAATATAAATATAAATATAAATA 43 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.08 (3 / 39), avg. gap size = 1.00 (3 / 3) 299 35.70 11.19 1.97 chr6qtel1M 849194 849613 (150387) L2#LINE/L2 2406 2863 (219) m_b320s601i20 13406 chr6qtel1M 849194 GATATTTCCTACATTGGA------ATAGGAATTTCTATACCCTAA---AT 849234 i i - - ------ v i - - v i ---i L2#LINE/L2 2406 GACATCTCC-AC-TTGGATGTCTAATAGGCATCTC-A-AACTTAACATGT 2451 chr6qtel1M 849235 CCTAAACAAAACAACTTACCTTTCCAATAAAACTTATGCCTTTCTCTTTC 849284 v vi vv v i i vv v i iiv ii v vv L2#LINE/L2 2452 CCAAAACTGAACTCCTGATCTTCCCCCTCAAACCTGCTCCTCCCGCAGTC 2501 chr6qtel1M 849285 TTTCTGAATTCTCA-TGAA-AGCAGC---A-----CAAGTCACTTCAGGC 849324 i iv -- - ? -i i --- ----- v ii - L2#LINE/L2 2502 TTCCCCA--TCTCAGTNAATGGCAACTCCATCCTTCCAGTTGCT-CAGGC 2548 chr6qtel1M 849325 TTGAAAGCTTAGAACCATTCTCAGGCCTTTTCTCACATTCATTAATCACA 849374 ivi v i ii i iiivi i i iv vi ivvvi L2#LINE/L2 2549 CAAAAACCTTGGAGTCATCCTTGACTCCTCTCTTTCTCTCACACCCCACA 2598 chr6qtel1M 849375 TATAAACTAGGTGCCAAGTCATGTCAATTTTACCTTTGTAATATTTCT-- 849422 vi v i vvv - i v iii i iiv v i-- L2#LINE/L2 2599 TCCAATCCATCAGC-AAATCCTGTCGGCTCTACCTTCAAAATATATCCAG 2647 chr6qtel1M 849423 --TATG--------TCATTCCCTTT-CTTCTAC-------ATCAAAGGCC 849454 -- vi -------- iiv ii- v i -------i v v v L2#LINE/L2 2648 AATCCGACCACTTCTCACCACCTCCACTGCCACCACCCTGGTCCAAGCCA 2697 chr6qtel1M 849455 CCAT-ACCCTATGTC-GTACTCTTGAAAAACCCTTCTTACTTGTTTCCCT 849502 - i iivi i - v i vi v v v i v v i L2#LINE/L2 2698 CCATCATCTCTCGCCTGGATTACTGCAATAGCCTCCTAACTGGTCTCCCT 2747 chr6qtel1M 849503 GACTCTAATCTT--TCCCTTACAAA--ATTGGTGAGACAGCTGCTAAATT 849548 vi i vi --i i ? iv-- vvii v v i i v L2#LINE/L2 2748 GCTTCCACCCTTGCCCCCCTNCAGTCTATTCTCAACACAGCAGCCAGAGT 2797 chr6qtel1M 849549 AATATTTTTTAGTACACA-GTCTTAAC-TGTCATTCATCTGCTCAAAATG 849596 i -ii iv ii - vv v - i v iv L2#LINE/L2 2798 GAT-CCTTTTAAAACGTAAGTCAGATCATGTCACTCCTCTGCTCAAAACC 2846 chr6qtel1M 849597 CAGCACTAGTTCTCTAT 849613 vv v i i ii i L2#LINE/L2 2847 CTCCAATGGCTTCCCAT 2863 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 48.82 CpG sites = 84, Kimura (unadjusted) = 50.80 Transitions / transversions = 1.33 (84/63) Gap_init rate = 0.06 (26 / 419), avg. gap size = 2.15 (56 / 26) 234 26.10 1.41 2.86 chr6qtel1M 849633 849703 (150297) C MIRc#SINE/MIR (141) 127 58 m_b320s601i21 13407 chr6qtel1M 849633 CTGAGGC-AATTGGGGTTAAGTGACTTGCCCAGAGCCAAACAGCCAGAAT 849681 -v vv i ii i v i v v C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAA 78 chr6qtel1M 849682 GTGTTAAATGACTGAGACTAGA 849703 vi i --i i i v C MIRc#SINE/MIR 77 GTGGCAGA--GCCGGGACTCGA 58 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 30.47 CpG sites = 10, Kimura (unadjusted) = 32.62 Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.04 (3 / 70), avg. gap size = 1.00 (3 / 3) 282 34.98 6.10 7.94 chr6qtel1M 850272 850681 (149319) C L2b_3end#LINE/L2 (6) 460 58 m_b320s601i22 13408 chr6qtel1M 850272 TCATGCAACAATGATTTATCAAATCCCTAATGTGTTCTGGGAACTGTTCT 850321 v vv iii iiv v v ii v? v C L2b_3end#LINE 460 TCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCT 411 chr6qtel1M 850322 -------GAGGATAC-----TAAGAAAGGTTAAAATATGGTTTCTGCTCT 850359 ------- i ----- i iv ii-- i i?i ii i C L2b_3end#LINE 410 AGGCGCTGGGGATACAGCGGTGAACAAGAC--AGACNCGGTCCCTGCCCT 363 chr6qtel1M 850360 CAAGCCACTCACATTCCAAATGAGGGAGACA-ACAGGCAAACTATTAGGT 850408 v vvi v i- i i - v i ? ---- i- C L2b_3end#LINE 362 CACGGAGCTCACAGTCT-AGTGGGGGAGACAGACATGTAANC----AGA- 319 chr6qtel1M 850409 TCATTGAAAATGTGTCTGTGTGTGTGTATAAAAT--GGGAGGCAAAATTA 850456 - v ? v i---i v v vvv vi ii i-- i ----ii C L2b_3end#LINE 318 -CAATNATAAC---CCAGAGTGGCAGGGTAGGACTGGGGGGGC----CCA 277 chr6qtel1M 850457 GAGGGATGGCATC-AATTAGGCATGGCAGGGGATGGAGAAGGCCTCCTAC 850505 - v ii -i iiv v -- vii i i i iiv C L2b_3end#LINE 276 GA-GGAGGGCGCCTGACCCGGCCTGG--GGGGTCAGGGAGGGCTTCCCGG 230 chr6qtel1M 850506 AGGAAGTAGGATTTGAATGGAATCTTTAAGTAAG-GCAAGAAATCTTGG- 850553 i iiv iiv iv i v v v - i i i--- - C L2b_3end#LINE 229 AGGAGGTGACATTTGAGCTGAGACCTGAAGGATGAGTAGGAG---TTGGC 183 chr6qtel1M 850554 -AAGAAATTATGAGCAGAAGGAGCTTCCCAAGAAAAAGAGAGAAGCAGTT 850602 - i vi vv v v vi ivv -- iv i i iv ?v C L2b_3end#LINE 182 CAGGCGAAGAGGTGGGGAAGGGCGTTCC--AGGCAGAGGGAACAGCANGT 135 chr6qtel1M 850603 ---AAGGTACAGAATCAAGAGCTGGAGTGTGATCCAAAATGATTAAGGAG 850649 --- iv v iv ii --? i? ii-----i v ii - C L2b_3end#LINE 134 GCAAAGGCCCTGAGGCGGGAG--NGAGCNTGGC-----GTGTTCGAGGA- 93 chr6qtel1M 850650 AAAGC--TGAAACCAGGATGACAGG-GTAAAGGGA 850681 v --v ii vi i v - i i v C L2b_3end#LINE 92 ACAGCAAGGAGGCCAGTGTGGCTGGAGCAGAGTGA 58 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 45.98 CpG sites = 79, Kimura (unadjusted) = 50.46 Transitions / transversions = 1.49 (79/53) Gap_init rate = 0.11 (43 / 409), avg. gap size = 1.33 (57 / 43) 440 30.83 8.64 5.12 chr6qtel1M 850272 850630 (149370) C L2c_3end#LINE/L2 (6) 472 102 m_b320s601i23 13408 chr6qtel1M 850272 TCATGCAACAATGATTTATCAAATCCCTAATGTGTTCTGGGAACTGTTCT 850321 v vv ii iiv v i v ii ---i -- C L2c_3end#LINE 472 TCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGG---CG--CT 428 chr6qtel1M 850322 GAGGATACTAAGAAAGGTTAAAATATGGTTTCTGCTCTCAAGCCACTCAC 850371 i v v- iv i i i ii i vvi C L2c_3end#LINE 427 GGGGATACAAAGAT-GAATAAGACACGGTCCCTGCCCTCAAGGAGCTCAC 379 chr6qtel1M 850372 ATTCCAAATGAGGGAGACA-ACAGG----CAAACTATTA-------GGTT 850409 v i i- ii - ? ---- i v -------i C L2c_3end#LINE 378 AGTCTAG-TGGAGGAGACAGACANGTAAACAGACAATTACAATACAAGTT 330 chr6qtel1M 850410 CATTGAAAATGTGTCTGTG-TGTGTGTATAAAATGGGAGGCA--AAATTA 850456 v - v - - i i- v v i vv v vi --ii vi C L2c_3end#LINE 329 AAT-GATAA-GTG-CTATAATGGGAGTATAGACAGGGTGCTATGGGAGCA 283 chr6qtel1M 850457 GAG-GGATGGCATC--AATTAGGCATGGCAGGGGATGGAGAAGGCCTCCT 850503 v - v i --i i ? v -- vii i i i C L2c_3end#LINE 282 CAGAGGAGGGCACCTAGACTAGNCTTGG--GGGGTCAGGGAAGGCTTCCC 235 chr6qtel1M 850504 ACAGGAAGTAGGATTTGAATGGAATCTTTAAGTAAG-GCAAGA---AATC 850549 iv i iiv i iiv i? v v v - i i --- ii C L2c_3end#LINE 234 GGAGGAGGTGACATCTGAGCTGAGNCTTGAAGGATGAGTAGGAGTTAGCC 185 chr6qtel1M 850550 --TTGGAAGAAATTATGAGCAGAAGGAGCTTCCCAAGAAAAAGAGAGAAG 850597 --v i ----- i vi - v i - iv i i iv C L2c_3end#LINE 184 AGGTGGAAGGA-----GGGGGGAA-GAGCATTCC-AGGCAGAGGGAACAG 142 chr6qtel1M 850598 CA---GTTAAGGTACAGAATC----AAGAGCTGGAGTGTG 850630 --- iv i? i iv ---- i vi i C L2c_3end#LINE 141 CATGTGCAAAGGCNCGGAGGCAGGAAAGAACTGCGGCGTG 102 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 38.34 CpG sites = 65, Kimura (unadjusted) = 42.05 Transitions / transversions = 1.62 (65/40) Gap_init rate = 0.09 (31 / 358), avg. gap size = 1.61 (50 / 31) 497 19.56 0.00 14.78 chr6qtel1M 851046 851177 (148823) MIRb#SINE/MIR 4 118 (150) m_b320s601i24 13409 chr6qtel1M 851046 AGGGGCAGCTAGGTGATGTAGTGGATAGAGCACCAGCCCTGAAGTCAGAA 851095 --- i i v vi ii i v MIRb#SINE/MIR 4 AGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGAC 50 chr6qtel1M 851096 GGACCTGAGTTCAAATATGACCTCAGACATATAACATTTAACATTTCCTA 851145 i i i ---- i-- i -------- i iv i v MIRb#SINE/MIR 51 AGACCTGGGTTCGAAT----CCC--GGC--------TCTGCCACTTACTA 86 chr6qtel1M 851146 GCTATGTGACCCTGGGCAAGTTACTTAACCCC 851177 i i i MIRb#SINE/MIR 87 GCTGTGTGACCTTGGGCAAGTTACTTAACCTC 118 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 20.67 CpG sites = 17, Kimura (unadjusted) = 22.98 Transitions / transversions = 3.40 (17/5) Gap_init rate = 0.13 (17 / 131), avg. gap size = 1.00 (17 / 17) 980 32.48 4.87 3.57 chr6qtel1M 851212 852319 (147681) L1PREC2_orf2#LINE/L1 2173 3294 (0) m_b321s551i0 13410 chr6qtel1M 851212 TTCAACATAAATTT----ATACAAAATAAATCCCCATAAATCCTCAGCAT 851257 i - i ---- v viv v vii L1PREC2_orf2# 2173 TTCAGCA-AAGTTTCAGGATACAAAATCAATGTACAAAAATCACTAGCAT 2221 chr6qtel1M 851258 TTTTTTTTATACATTACCAACAAAATCCAACAGCAAGAGATAAA--AAGA 851305 ii ---- --- v v -iv i vi -- i L1PREC2_orf2# 2222 TCCT----ATACA---CCAACAACAGCCAA-GCCGAGAGCCAAATCAGGA 2263 chr6qtel1M 851306 --GAAATTCCATGCAAAATAACTGTCAACAGCATAAAATATTTGGGAATC 851353 -- v i v v vi iiiv v v ii i v L1PREC2_orf2# 2264 ACGCAATCCCATTCACAATTGCCACAAAAAGAATAAAATACCTAGGAATA 2313 chr6qtel1M 851354 TATCTA-CCAAAGGAAAGTGAGGTA-CTATATGAGCAAAATTACAAAAAA 851401 i v - -- i i iiv - v ii vv i v L1PREC2_orf2# 2314 CAGCTAACCA--GGGAGGTGAAAGATCTCTACAATGAGAATTACAAAACA 2361 chr6qtel1M 851402 CTTTCCACACAAAT-AAAGTCAGATTTAAATAATTGGAAAAATATTAAGC 851450 vii v v - i vi- ivi i v i vvii L1PREC2_orf2# 2362 CTGCTCAAAGAAATCAGAGAT-GACACAAACAAATGGAAAAACATTCCAT 2410 chr6qtel1M 851451 GCTCCTGGATAGACCAAGTAAATATAATAAAGATAACAATACTCCCTGAA 851500 v ivvi i v vi v i ii v v ii L1PREC2_orf2# 2411 GCTCATGGATAGGAAGAATCAATATCGTTAAAATGGCCATACTGCCCAAA 2460 chr6qtel1M 851501 TTAATCTATTTATTTAGTGTTCTACCAATCATACTTCCAAGAAAACATTT 851550 vi i ivv i i i v v v v v vi v ivi L1PREC2_orf2# 2461 GCAATTTACAGATTCAATGCTATTCCTATCAAACTACCAATGACATTCTT 2510 chr6qtel1M 851551 TAATGAAC-AAAAAAAATAA---CAAAATTCATATGGAGAACAAAAGATG 851596 i vv - i iv ---i - v i vi L1PREC2_orf2# 2511 CACAGAACTAGAAAAAACTATTTTAAAATTCATATGGA-ACCAAAAAAGA 2559 chr6qtel1M 851597 G--AGAAT-CTCAAGGGAAT--TAATGAAAAAAAATCAAATGAAGGTGGC 851641 --v -vi v -- vv i - - vv v L1PREC2_orf2# 2560 GCCCGAATAGCCAAGGCAATCCTAAGCAAAAAGAA-CAAA-GCTGGAGGC 2607 chr6qtel1M 851642 CTAGCTATACCTGATCTAAAACTATACTATAAAGCAGCAGTCACCAAAAC 851691 v vi vv i ii v i ii vi v L1PREC2_orf2# 2608 ATCACGCTACCCGACTTCAAACTATACTACAGGGCTACAGTAACCAAAAC 2657 chr6qtel1M 851692 CCTTTGGTATTGGCTAAGAAATAGATTAGTTGATCAGTGGAATAGGTTAG 851741 vviv i ivv i i ivvi v i i i iv L1PREC2_orf2# 2658 AGCATGGTACTGGTACAAAAACAGACACATAGACCAATGGAACAGAATAG 2707 chr6qtel1M 851742 ---GTTCACAAGACAGAATAGTCAACTATAGCAATCTAGTGTTTGACAAA 851788 --- ii v ivv iviivv v i i v ii v i L1PREC2_orf2# 2708 AGAGCCCAGAAATAAGGCCGCACACCTACAACCATCTGATCTTCGACAAA 2757 chr6qtel1M 851789 CC---CAAAGATCCTTACTTTTGGGATGAGAATTCATTATTTGACAAAAA 851835 v --- i ivvvi v--- ivi i i vi ii i vi L1PREC2_orf2# 2758 GCTGACAAAAACAAGCAA---TGGGGAAAGGACTCCCTATTCAATAAATG 2804 chr6qtel1M 851836 CTGCAGGGATAACTGGAAATTAG---TATGGCAGAA-ATTAGACATGGAC 851881 v v ---i --- - - ii vv L1PREC2_orf2# 2805 GTGCTGGGATAACTGG---CTAGCCATAT-GCAGAAGATTGAAACTGGAC 2850 chr6qtel1M 851882 CCACACTTAACACCGTATACCAAGATATGATCAAAATGGGTCCATGATTT 851931 viv i v i v i vviv i i iv v i L1PREC2_orf2# 2851 CCCTTCCTTACACCATATACAAAAATCAACTCAAGATGGATTAAAGACTT 2900 chr6qtel1M 851932 A---GTCAAAAGGAATGAGATTATAAATAAATTAGAGG--AACATAGG-- 851974 --- v vvv --- i i v vvi i i -- v -- L1PREC2_orf2# 2901 AAATGTAAAACCCA---AAACTATAAAAACCCTGGAAGACAACCTAGGCA 2947 chr6qtel1M 851975 ATAGTTTATCTCTCAGATTTGTGGAGGAGGAAGAAATTTCA-----AAGA 852019 --ii - -i iv i- ivi v i i ----- L1PREC2_orf2# 2948 ATA--CCAT-TCT-GGACATA-GGAACGGGCAAAGATTTCATGACGAAGA 2992 chr6qtel1M 852020 TG----AACTAGCTACCATTACTGATCATAAAATAGAAAATTTTGATTAT 852065 i ---- vi ii i v iv --i v - v v v vv ivv L1PREC2_orf2# 2993 CGCCAAAAGCAATTGCAACAA--AAGCA-AAAATTGACAAATGGGATCTA 3039 chr6qtel1M 852066 ATCAAATTAAAAAGCCTTTGTACAAACAAAACTAA-TGCAAACAAGATTA 852114 i i i i i i - i vv - iiv iii v L1PREC2_orf2# 3040 ATTAAACTAAAGAGCTTCTGCAC-AGCAAAAGAAACTATCAACAGAGTAA 3088 chr6qtel1M 852115 GAAGGGAAGCAACAAACTGGGAAAACATCTTCACAGTTAAAGGTTGTGAT 852164 iv iv v v i v i v ? ii iviv v vv v i L1PREC2_orf2# 3089 ACAGACAACCTACAGAATGGGAGAAAATNTTTGCAAACTATGCATCTGAC 3138 chr6qtel1M 852165 AAAGGCCTCAAT-TCCAAAATATATAGAGAACTGACTCTAATTTATAAG- 852212 i - - iv v ii v vv v i - L1PREC2_orf2# 3139 AAAGGTCT-AATATCCAGCATCTATAAGGAACTTAAACAAATTTACAAGA 3187 chr6qtel1M 852213 --AAATCAAGCCATTCTCTATTTGATAAATGGTCAAAGAATATGAACAGA 852260 -- v i v -- i i - i v i v i i L1PREC2_orf2# 3188 AAAAAACAAACAA--CCCCA-TTAAAAAGTGGGCAAAGGACATGAACAGA 3234 chr6qtel1M 852261 CAATTTTCAGATGATGAAAT---TGAAACTATTACACTCATAGGAAAGAG 852307 v i v v v --- vii i -- vv v i i L1PREC2_orf2# 3235 CACTTTTCAAAAGAAGACATACATGCGGCCA--ACAAGCATATGAAAAAA 3282 chr6qtel1M 852308 TGTTCCAAATCA 852319 v i v v L1PREC2_orf2# 3283 AGCTCAACATCA 3294 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 42.08 CpG sites = 179, Kimura (unadjusted) = 43.41 Transitions / transversions = 1.07 (179/168) Gap_init rate = 0.06 (65 / 1107), avg. gap size = 1.45 (94 / 65) 1567 27.87 2.88 2.39 chr6qtel1M 852182 852806 (147194) L1ME4c_3end#LINE/L1 12 639 (191) m_b321s551i1 13410 chr6qtel1M 852182 AATATATAGAGAACTGACTCTAATTTATAAGAAA----TCAAGCCATTCT 852227 ? i i v i v v ---- v ----i L1ME4c_3end#L 12 ANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAAGAC----C 57 chr6qtel1M 852228 CTATTTGATAAATGGTCAAAGAATATGAACAGACAATTTTCAGATGATGA 852277 i v v v i i iv ? v v L1ME4c_3end#L 58 CCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAGGA 107 chr6qtel1M 852278 AATTGAAACTATTACACT--CATAGGAAAGAGTGTTCCAAATCACTAA-G 852324 -iv ? v v v-- i v i i i v vv i i-i L1ME4c_3end#L 108 AAT-ACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTAGTA 156 chr6qtel1M 852325 ATCAAAGAA-TGCAAATTAAGACAACTCTGAGATACCACTACACACCTGT 852373 - ii vv i vi i i L1ME4c_3end#L 157 ATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCTAT 206 chr6qtel1M 852374 CAGATTGGCAAAGATGACAGGAAAAAATAATGATGAT------TGTTGGA 852417 i i i i v----v -- i ------ i v L1ME4c_3end#L 207 TAAATTAGCAAAAATT----TAAAAAAT--TGATAATACCCAATGCTGGC 250 chr6qtel1M 852418 GGGGATGTGGGAAAACTGGGACACTGATGCATTGTTGGTGGAGTTGTGAA 852467 i ? i vi v ? v i i vi? i L1ME4c_3end#L 251 GAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAA 300 chr6qtel1M 852468 TGAATCCAAACATTCTGGAGAGCAATCTGGAATTATGC-CAAAAAGTTAT 852516 vii v v v i i i v v i i-iv i ii L1ME4c_3end#L 301 TTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCAT 350 chr6qtel1M 852517 CAAACTGCCCATACCCTTTGATCCAGCAGTGTTTCTACTGGGCTTATATC 852566 v v ii i i i viiv v vv v L1ME4c_3end#L 351 AAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATC 400 chr6qtel1M 852567 CCAAAGAGATA---CTAAAGAAGGGAAAGGGGCCTGTATGTGCCAAAATG 852613 i i i --- v i i --- i ii v i L1ME4c_3end#L 401 CTAAGGAAATAATTCAAAAGAAGGAAAAAG---CTATATGCACGAAGATG 447 chr6qtel1M 852614 TTTGTGGCAGCCTTGTTTGTAGCAGCTGAAAACTGGAAAATGAATGGATG 852663 ii v v i i ii vi i vvivv ii L1ME4c_3end#L 448 TTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATG 497 chr6qtel1M 852664 CCCATCAATTGGAGAATGGTTGGGTAAATTGTGGTATATGAATGTTATGG 852713 i v v i ii i i v? iviv L1ME4c_3end#L 498 TCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGG 547 chr6qtel1M 852714 AATATTATTGTTCTATAAGAAATGACCAGCAGGATGAATACGGAGAGGTT 852763 vvvv i v i iv vi v v v i v viiiv L1ME4c_3end#L 548 AATATTATGCAGCCATTAAAAATGATAATTATGAAGACTATGTAGCAACA 597 chr6qtel1M 852764 TGGAGAGACTTACATGAAGTGATGCTAAGTGAAATGAGCAGAA 852806 i ivv -i vi i i vi L1ME4c_3end#L 598 TGGAAAATGTT-TATGATATAATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 34.81 CpG sites = 96, Kimura (unadjusted) = 36.13 Transitions / transversions = 1.30 (96/74) Gap_init rate = 0.04 (22 / 624), avg. gap size = 1.50 (33 / 22) 12 9.24 0.00 4.17 chr6qtel1M 853122 853146 (146854) (GGGA)n#Simple_repeat 1 24 (0) m_b321s252i0 13411 chr6qtel1M 853122 GGGAGGGGGTGGAGGGTGGGAGGGA 853146 i - v (GGGA)n#Simpl 1 GGGAGGGAG-GGAGGGAGGGAGGGA 24 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 625 25.13 5.56 0.53 chr6qtel1M 853546 853725 (146275) C MIRc#SINE/MIR (3) 265 77 m_b321s601i3 13412 chr6qtel1M 853546 AATAATAATGAGTTAGCATTTTTATAGCACTTTAATGTTTATAAAGTA-T 853594 i?vv - v vv i ii- C MIRc#SINE/MIR 265 AATAATAACNCCTTA-CATTTGTATAGCACTTTACAGTTTACAAAGCGCT 217 chr6qtel1M 853595 TTAACAAATATTACCTTATTTTATCCTCACAGTATCCCTAAAAGATTGTT 853644 v v i i i v ii v ivi i v vi C MIRc#SINE/MIR 216 TTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGC 167 chr6qtel1M 853645 ------GCTATCATTGTCCCCATTTAACATGTAAGAAGACTAAGGCAGGC 853688 ------ v i i v vi i i i i vviv C MIRc#SINE/MIR 166 AGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAG 117 chr6qtel1M 853689 AGAAGTCAAGTGACCT-CACAGGGT--CACAGCTTGTAAG 853725 i i i - v i -- v C MIRc#SINE/MIR 116 AGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAG 77 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 30.43 CpG sites = 25, Kimura (unadjusted) = 31.35 Transitions / transversions = 1.25 (25/20) Gap_init rate = 0.03 (5 / 179), avg. gap size = 2.20 (11 / 5) 30 23.31 2.63 0.00 chr6qtel1M 853727 853802 (146198) (AT)n#Simple_repeat 1 78 (0) m_b321s252i1 13413 chr6qtel1M 853727 ATATA-ATTTATATTAATATATAAAGAATTATATATATATATATGAAGA- 853774 - v vv v v vv iv v - (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr6qtel1M 853775 ATTTTTATATTTATATATAAATAGATAT 853802 v v v v v (AT)n#Simple_ 51 ATATATATATATATATATATATATATAT 78 Matrix = Unknown Transitions / transversions = 0.07 (1/14) Gap_init rate = 0.03 (2 / 75), avg. gap size = 1.00 (2 / 2) 13 11.69 3.57 0.00 chr6qtel1M 855405 855432 (144568) (GGAA)n#Simple_repeat 1 29 (0) m_b321s252i2 13414 chr6qtel1M 855405 GGAAGG-AGGAAGCAAGAGAGGAAGGAAG 855432 - v ii (GGAA)n#Simpl 1 GGAAGGAAGGAAGGAAGGAAGGAAGGAAG 29 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 15 13.86 0.00 0.00 chr6qtel1M 855518 855541 (144459) (A)n#Simple_repeat 1 24 (0) m_b321s252i3 13415 chr6qtel1M 855518 AAAAACAAAAAAAAAAGGAAAAAA 855541 v ii (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAA 24 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 13 13.08 0.00 0.00 chr6qtel1M 856567 856591 (143409) (TCAA)n#Simple_repeat 1 25 (0) m_b321s252i4 13416 chr6qtel1M 856567 TCAGTGAATCAATCATTCAATCAAT 856591 i v v (TCAA)n#Simpl 1 TCAATCAATCAATCAATCAATCAAT 25 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 627 26.42 3.23 4.35 chr6qtel1M 858028 858213 (141787) C MIR#SINE/MIR (50) 212 29 m_b321s601i4 13417 chr6qtel1M 858028 AAGTACTTTATCCTTATCAACTGATTTTATCCT---AACAATTATGAGAA 858074 ii iviv i v v --- iiv iv i C MIR#SINE/MIR 212 AAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAG 163 chr6qtel1M 858075 GTGGGCACTATTTTCATTCCTATTTTATAGATGAGAAAACTGAGCCTGAC 858124 i i v i i i i i v vv v C MIR#SINE/MIR 162 GTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAG 113 chr6qtel1M 858125 AAAGGTTAAGTGGCTTGCTTAGGGTGACACAGCTTGTACGATTCTAAGCC 858174 i ii ii i v v v vvv vi C MIR#SINE/MIR 112 AGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCC 63 chr6qtel1M 858175 AGAACTTAAAGTAGCCCCA--CAGTCTTCAGACTCCAG-GCC 858213 i i i ii ----- -- --- i - C MIR#SINE/MIR 62 GGGATTCGAA-----CCCAGGCAGTCT---GGCTCCAGAGCC 29 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 30.72 CpG sites = 29, Kimura (unadjusted) = 33.49 Transitions / transversions = 1.61 (29/18) Gap_init rate = 0.06 (11 / 185), avg. gap size = 1.27 (14 / 11) 407 27.29 3.62 4.38 chr6qtel1M 858093 858230 (141770) C MIR3#SINE/MIR (63) 145 9 m_b321s601i5 13417 chr6qtel1M 858093 CCTATTTTATAGATGAGAAAACTGAGCCTGACAAAGGTTAAGTGGCTTGC 858142 ii i i v iv v i v i C MIR3#SINE/MIR 145 CTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGC 96 chr6qtel1M 858143 TTAGGGTGACACAGCTTGTACGATTCTAAGCCAGAACTTAAAGTAGCCCC 858192 ii i v ?v vv vvv vi i i vi ----- C MIR3#SINE/MIR 95 CCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAA-----CCC 51 chr6qtel1M 858193 ACAGTCTTCAGACT-CCAGGCCAAA----CTCCACTCAGCCAC 858230 -i i v - v ivi---- ii C MIR3#SINE/MIR 50 A-GGTCTCCTGACTCCCAGTCCGTGCTCTCTCTGCTCAGCCAC 9 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 32.54 CpG sites = 20, Kimura (unadjusted) = 34.89 Transitions / transversions = 1.25 (20/16) Gap_init rate = 0.06 (8 / 137), avg. gap size = 1.38 (11 / 8) 576 37.75 3.84 5.50 chr6qtel1M 858359 858801 (141199) L2b_3end#LINE/L2 10 445 (21) m_b321s601i6 13418 chr6qtel1M 858359 CTTACCCCTCCACATTTCTAGTTT----TCTTGCACATTATAACCCCTCC 858404 vi v i v i ii ii ---- i i - i v -- iv L2b_3end#LINE 10 CTGGCCCCGCTACCTCTCCGGCCTCATCTCCTAC-CACTCT--CCCCTTG 56 chr6qtel1M 858405 CATACTCTTCAGTCCAATGACTCAGGATTCTTGGCCATTTCAAAAATAAC 858454 vi v -- iiv v v vi i v ii i vvi i - L2b_3end#LINE 57 CTCACTCTGC--TCCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACA-C 103 chr6qtel1M 858455 AACATTGCATCTCTTAACTCTGGGCATTTTCACTGGATGTCTCCCATGAC 858504 iv ?vviv? iiiv v v v ?v v ii iv v L2b_3end#LINE 104 GCCANGCTCNCTCCCGCCTCAGGGCCTTTGCACNTGCTGTTCCCTCTGCC 153 chr6qtel1M 858505 TGAGGTTCTCTCTCTTCTCATTTCTACCTTCCTTCAGGTCCTCTACTCAT 858554 iiiiv i - ii v v i iii vv -- iv -- L2b_3end#LINE 154 TGGAACGCCCT-TCCCCACCTCTTCGCCTGGC--CAACTCCT--ACTCAT 198 chr6qtel1M 858555 CCTTGAAGTCCCAAATAGAACCTCATCTTCCAAAGGAAACCTTTCCCAAT 858604 v i i iv vi iv i i ivvi i i i ii i L2b_3end#LINE 199 CCTTCAGGTCTCAGCTCAAATGTCACCTCCTCCGGGAAGCCCTCCCTGAC 248 chr6qtel1M 858605 TTCTT----TAATTTGAATGCCTTCC-CTCTGCCAATTATCTCCAATT-T 858648 ii ii----iiiv iiiii i - vv -----i i i i- L2b_3end#LINE 249 CCCCCAGGCCGGGTCAGGCGCCCTCCTCTGGGCC-----CCCCCAGTCCT 293 chr6qtel1M 858649 ATCTTGTATAATATAGTTTGGGGTGTGTGTGTAGGGGTGTGTGTATAGTC 858698 i i i------i v i v i ?vv vv ?v iii v - L2b_3end#LINE 294 ACCCTGC------CACTCTGGGTTATNATTGTCTGNTTACATGTCT-GTC 336 chr6qtel1M 858699 TTCCCCATTAGACCCTCAGCTTTTTGAGAGCAGGGACTGGATTTTGCCTT 858748 i i iv v iiv i i ?i- i i L2b_3end#LINE 337 TCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNG-TCTGTCTT 385 chr6qtel1M 858749 -----TCATTGTATCCCTAGCA--TAGCACACCATCTAGCACATAGTAGA 858791 -----i ii i i-- v?ii i i i L2b_3end#LINE 386 GTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGG 435 chr6qtel1M 858792 CATTCAATAA 858801 ii i L2b_3end#LINE 436 CGCTCAGTAA 445 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 50.25 CpG sites = 105, Kimura (unadjusted) = 58.29 Transitions / transversions = 1.98 (105/53) Gap_init rate = 0.07 (30 / 442), avg. gap size = 1.37 (41 / 30) 371 27.67 9.92 0.70 chr6qtel1M 858685 858815 (141185) L2d_3end#LINE/L2 369 511 (5) m_b321s601i7 13418 chr6qtel1M 858685 GTGTGT--GTATAGTCTTCCCCATTAGACCCTCAGCTTTTTGAGAGCAGG 858732 -- v v i v i iiv v ii i L2d_3end#LINE 369 GTGTGTTAGTCTTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGG 418 chr6qtel1M 858733 GACTGGATTTTG---CCTTTCATTGTATCCCTA----GCATAGCACACCA 858775 iivi i i---i? i? i - i ---- v vii L2d_3end#LINE 419 GACCATGTCTTATACTNTTTTNTCGT-TCCCCACAGCGCCTAGCACAGTG 467 chr6qtel1M 858776 TCTAGCACATAGTAGACATTCAATAA----CTGGTGATTCACTG 858815 iiv i ii ----i v v i L2d_3end#LINE 468 CTGAGCACATAGTAGGCGCTCAATAAATACTTGTTGATTGATTG 511 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 34.46 CpG sites = 25, Kimura (unadjusted) = 37.08 Transitions / transversions = 2.27 (25/11) Gap_init rate = 0.04 (5 / 130), avg. gap size = 2.80 (14 / 5) 14 15.24 0.00 7.69 chr6qtel1M 859055 859096 (140904) (TTTTAA)n#Simple_repeat 1 39 (0) m_b321s252i5 13419 chr6qtel1M 859055 TTTTAATTTTCATTTTATTTTTTAATTCACAAGTTTTGATTT 859096 v -v -vi - i (TTTTAA)n#Sim 1 TTTTAATTTTAATTTTA-ATTTTAATT-TTAA-TTTTAATTT 39 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.07 (3 / 41), avg. gap size = 1.00 (3 / 3) 108 22.42 5.16 5.39 chr6qtel1M 859206 859670 (140330) (TA)n#Simple_repeat 1 464 (0) m_b321s252i6 13420 chr6qtel1M 859206 TACATATATATGTGTGTGGTTTTACAAATATATGCATGCATATCATGCCA 859255 i i i i ivv v i v ii ii - iivv (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATAT-ATATAT 49 chr6qtel1M 859256 ATATATGGCATATTAATATA-ATACTA-ATATGAATA-ATATGCTACTGT 859302 -ii vv - - - iv - -v - i (TA)n#Simple_ 50 ATATAT-ATATATATATATATATA-TATATATATATATATAT-ATA-TAT 95 chr6qtel1M 859303 ATAT-TGTATTAATATATGATAGTGAT-TATATAGTAT-TATTAATATA- 859348 - i vv - - - - - - vv - (TA)n#Simple_ 96 ATATATATATATATATAT-ATA-T-ATATATATA-TATATATATATATAT 141 chr6qtel1M 859349 ACATTTATATTTATATTAAGATA-ACATGCAT-TACTATATATAGGATAT 859396 i v v vv v - i ii - - -v (TA)n#Simple_ 142 ATATATATATATATATATATATATATATATATATA-TATATATA-TATAT 189 chr6qtel1M 859397 TAATTTA-ATGTACTATATGATGTATATAGTATATCATA-ATACTATATG 859444 vv v - i - - i - - - - i (TA)n#Simple_ 190 ATATATATATATA-TATAT-ATATATATA-TATAT-ATATATA-TATATA 234 chr6qtel1M 859445 TAT-TATATGATATGCA-ATATATACTATATAT-TACTACATATA-ATAT 859490 - - ii - - - - i - (TA)n#Simple_ 235 TATATATAT-ATATATATATATATA-TATATATATA-TATATATATATAT 281 chr6qtel1M 859491 ATATTTATATATA-ATATATACATGCATATGTACTGTGTATCTATATATG 859539 v - i ii i - i i v i (TA)n#Simple_ 282 ATATATATATATATATATATATATATATATATA-TATATATATATATATA 330 chr6qtel1M 859540 TATGTGTATATATATGAGGTATGTATATACTAAATATGCA-ATATATAT- 859587 i i - vi i - v ii - - (TA)n#Simple_ 331 TATATATATATATAT-ATATATATATATA-TATATATATATATATATATA 378 chr6qtel1M 859588 TAT-TACTTTGTATATAGCATA-AAATAGTATA-ATA-ATATA-ACAT-T 859631 - - v i -i - v - - - - i - (TA)n#Simple_ 379 TATATA-TATATATATA-TATATATATA-TATATATATATATATATATAT 425 chr6qtel1M 859632 ATATATATATATACACACATGCATATATATGTGTGTATA 859670 i i i ii i i i (TA)n#Simple_ 426 ATATATATATATATATATATATATATATATATATATATA 464 Matrix = Unknown Transitions / transversions = 1.76 (51/29) Gap_init rate = 0.11 (49 / 464), avg. gap size = 1.00 (49 / 49) 234 30.07 2.94 2.19 chr6qtel1M 859874 860009 (139991) C L1ME3G_3end#LINE/L1 (360) 564 428 m_b321s551i2 13421 chr6qtel1M 859874 TTTTTTTAGAGAATG-ATAGTATTCCATGACATTTCTATAACATAATTTT 859922 i iv?iv - iii vvv v v C L1ME3G_3end#L 564 TCTTTTTAACNGCTGCATAGTATTCCATAGTATGGATATACCATAATTTA 515 chr6qtel1M 859923 CATCAATCAGTCCCCAATT--TAGAGATACAACTTTAGTTTCTAGTTCTT 859970 i- i i v v -- i v vi iv -- i i i C L1ME3G_3end#L 514 T-TTAACCATTCCCCTATTGATGGACATTTAGGTT--GTTTCCAATTTTT 468 chr6qtel1M 859971 TGATACTATAAAAAA-GCTGTTAGAAATATTTTTATACAT 860009 i v i i v - iv vi i ii i C L1ME3G_3end#L 467 CGCTATTACAAACAATGCTGCAATGAACATCCTTGTACAT 428 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 38.80 CpG sites = 24, Kimura (unadjusted) = 40.11 Transitions / transversions = 1.50 (24/16) Gap_init rate = 0.04 (6 / 135), avg. gap size = 1.17 (7 / 6) 236 29.41 2.46 2.46 chr6qtel1M 859889 860010 (139990) C L1ME4b_3end#LINE/L1 (340) 552 431 m_b321s551i3 13421 chr6qtel1M 859889 ATAGTATTCCATGACATTTCTATAACATAATTTTCATCAATCAGTCCCCA 859938 vii vvv i v vi- i i v C L1ME4b_3end#L 552 ATAGTATTCCATTGTATGGATGTACCATAATTTAT-TTAACCAGTCCCCT 504 chr6qtel1M 859939 ATT--TAGAGATACAACTTTAGTTTCTAGTTCTTTGATACTATAAAAAA- 859985 -- i v vi iv -- i i ii v i i v - C L1ME4b_3end#L 503 ATTGATGGACATTTAGGTT--GTTTCCAATCTTTTGCTATTACAAACAAT 456 chr6qtel1M 859986 GCTGTTAGAAATATTTTTATACATA 860010 iv vi vii i C L1ME4b_3end#L 455 GCTGCAATGAATAACCTTGTACATA 431 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 38.27 CpG sites = 20, Kimura (unadjusted) = 38.27 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.04 (5 / 121), avg. gap size = 1.20 (6 / 5) 304 33.47 2.88 1.63 chr6qtel1M 860098 860340 (139660) C L1ME5_3end#LINE/L1 (665) 276 31 m_b321s551i4 13422 chr6qtel1M 860098 GAGTGGTCAGACCTTCCCTCGGTCCCTCCAACATTTTATAGTTTCCTTTT 860147 v v vv i? i v ivi i v i vii v v vvi C L1ME5_3end#LI 276 GAGGGTTCCTATNTCCCCACATCCTCGCCAACACTTGGCATTATCCAGCT 227 chr6qtel1M 860148 TTGGAATTTTT-CAAATGGTAA-GGGTGAAAGGGAAAACTTCAATATGGC 860195 vv - v i v- -i v i vi v ii v i v i C L1ME5_3end#LI 226 TTCTAATTTTTGCCAGTC-TAATAGGTGTAAAGTGATATCTCATTGTTGT 178 chr6qtel1M 860196 TTTAATATGTGTTTTGCTCATTACTAA-AAATATGAGCACTTTTTAATAC 860244 v ii iv v -i i v ii i v i C L1ME5_3end#LI 177 TTTAATTTGCATTTCTCTGATTACTAATGAGTTTGAGCATCTCTTCATAT 128 chr6qtel1M 860245 AAAGGTGGATA-CCTT--AGATTTATTCCTTTGAAAACAGCCTGGTCATA 860291 --- v v v - --i i vi i i v iv v C L1ME5_3end#LI 127 ---GCTTGTTAGCCTTTCGGGTTTCCTCTTCTGTAAATTGCCTGTTCATA 81 chr6qtel1M 860292 TTCTTCAAACATTTATCAACTGGGACTGGC-TCTTATTCTTATACATTTG 860340 i iivv v v i ii ?v - v i vv C L1ME5_3end#LI 80 TCCTTTGCCCATTTTTCTATTGGGGTTNCCGTCTTTTTCTTGTTGATTTG 31 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 44.73 CpG sites = 39, Kimura (unadjusted) = 45.48 Transitions / transversions = 0.95 (39/41) Gap_init rate = 0.04 (10 / 242), avg. gap size = 1.10 (11 / 10) 23 13.34 0.00 0.00 chr6qtel1M 860465 860505 (139495) (AGAGAC)n#Simple_repeat 1 41 (0) m_b321s252i7 13423 chr6qtel1M 860465 AGAGACAGACAGAGACACAGAGACAGAGAAAGAGATAGAGA 860505 v v v v i (AGAGAC)n#Sim 1 AGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGA 41 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 19 17.34 3.03 6.25 chr6qtel1M 860603 860668 (139332) (TTTA)n#Simple_repeat 1 64 (0) m_b321s252i8 13424 chr6qtel1M 860603 TTTATTT-TTT-TTTATTATATTGATTTAATCTAATTTATTTATGAAATT 860650 - - - v - - v -vv (TTTA)n#Simpl 1 TTTATTTATTTATTTATT-TATTTATTT-AT-TTATTTATTTAT-TTATT 46 chr6qtel1M 860651 AACATATTTATTAATATA 860668 v iv v v (TTTA)n#Simpl 47 TATTTATTTATTTATTTA 64 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.09 (6 / 65), avg. gap size = 1.00 (6 / 6) 229 31.59 4.96 5.83 chr6qtel1M 861084 861204 (138796) C L2a_3end#LINE/L2 (31) 486 367 m_b321s601i9 13425 chr6qtel1M 861084 CTTACTGTGTGCCATGAGATTTATCAAACGCTAGGGGA---AGGAATGAA 861130 i i v viv v vii ii - --- v i C L2a_3end#LINE 486 CCTACTATGTGCCAGGCACTGTTCTAGGCGCT-GGGGATACAGCAGTGAA 438 chr6qtel1M 861131 AATAAGAAAGATGA---TACTTCCCCTCAAAGAGCTTATGTTCTAATGGA 861177 --i i v ii --- v i v vi ii i i C L2a_3end#LINE 437 --CAAAACAGACAAAAGTCCCTGCCCTCATGGAGCTTACATTCTAGTGGG 390 chr6qtel1M 861178 AAAACAAAACAGATTATTACAGAAATA 861204 ii---i i -i v v v C L2a_3end#LINE 389 GG---GAGACAGA-CAATAAACAAATA 367 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 42.91 CpG sites = 23, Kimura (unadjusted) = 42.91 Transitions / transversions = 1.77 (23/13) Gap_init rate = 0.07 (9 / 120), avg. gap size = 1.44 (13 / 9) 284 31.06 3.81 1.87 chr6qtel1M 861084 861188 (138812) C L2d2_3end#LINE/L2 (31) 524 418 m_b321s601i8 13425 chr6qtel1M 861084 CTTACTGTGTGCCATGAGATTTATCAAACGCTA--GGGGAAGGAATGAAA 861131 i v v viv v iii ii i-- viv v i C L2d2_3end#LIN 524 CCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGTGGGGGATACAAAGAAG 475 chr6qtel1M 861132 -ATAAGAAAGATGATACTTCCCCTCAAAGAGCTTATGTTCTAA-TGGAAA 861179 - --v i v i v i iiv i- ii C L2d2_3end#LIN 474 TATAAGA--CATGGTCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGGA 427 chr6qtel1M 861180 AACAAAACA 861188 i i C L2d2_3end#LIN 426 GACAAGACA 418 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 41.78 CpG sites = 20, Kimura (unadjusted) = 41.78 Transitions / transversions = 1.67 (20/12) Gap_init rate = 0.05 (5 / 104), avg. gap size = 1.20 (6 / 5) 16 10.85 3.33 0.00 chr6qtel1M 864613 864642 (135358) (TAA)n#Simple_repeat 1 31 (0) m_b321s252i9 13426 chr6qtel1M 864613 TAATAATACTAATAAAACTAATAATAA-AAT 864642 v v v - (TAA)n#Simple 1 TAATAATAATAATAATAATAATAATAATAAT 31 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 701 32.11 5.46 2.77 chr6qtel1M 865267 865724 (134276) L1ME3Cz_3end#LINE/L1 60 529 (468) m_b321s551i5 13427 chr6qtel1M 865267 GATAAATGCTCAAAGACTATGAATAGGCTGTTTTCAGAAAAAGAAATGTT 865316 v vv iv i vi iv i i iviv L1ME3Cz_3end# 60 GAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGGAAACCCG 109 chr6qtel1M 865317 A-TG---AAGAGTCATATGGGAAAAAGCTCTAAACCACTATTGATTAAAG 865362 - --- v iv ii i v v vvi v i i ii L1ME3Cz_3end# 110 AATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTAATCAGGG 159 chr6qtel1M 865363 AAATGTAATTTAAAACAACTCTGAGATCCCACCTCACATTTATCAAATTG 865412 i v ? vv v ii iii i L1ME3Cz_3end# 160 AAATGCAAATTAAAACNACAATGAGATACCATTTCACACCCATCAGATTG 209 chr6qtel1M 865413 GCTCACATAACTGAAAAAG---GAAAATAAAAAATACTGGAGTAGATGTA 865459 ---- v v vv --- v vv i ii v vi i L1ME3Cz_3end# 210 G----CAAAAATTTAAAAGTCTGACAATACCAAGTGTTGGCGAGGATGTG 255 chr6qtel1M 865460 GAAAAATTGGAGCACTTTTGGTGTTGTTGGT-----TGTAAACTAGTCCA 865504 i iv i v iv -iiii i ----- i i v L1ME3Cz_3end# 256 GAGAAACGGGAACTCTCAT-ACACTGCTGGTGGGAGTGTAAATTGGTACA 304 chr6qtel1M 865505 AGCATTCAAGAAAACAATTC-----TATCCAACAGAATATAAAAC-TGCA 865548 v i ivi i i i----- i ii i i vv i i-i L1ME3Cz_3end# 305 ACCACTTTGGAGAGCAATTTGGCAATATCTAGTAAAGTTGAAGATGCGCA 354 chr6qtel1M 865549 TACCCTTTGATCCA-CAGTACCAGTACTATATCTGTATCTCAAAGAGATC 865597 vi i - i v v v vi v i i ii i i ii L1ME3Cz_3end# 355 TACCCTACGACCCAGCAATTCCACTTCTAGGTATATACCCTAGAGAAACT 404 chr6qtel1M 865598 ATAGAATATGGG--AAAGGATTTATTAATACAA-AATATTTATAGAAGCT 865644 v v v i v --v vvi --i -i i i v v v L1ME3Cz_3end# 405 CTCGCACATGTGCACAAGGAGACAT--GTACAAGGATGTTCATTGCAGCA 452 chr6qtel1M 865645 CTTTTTATGGTAGCAAAAAAAAATTAG---TAATTGAAAGGATTCTCATC 865691 i v i ii ---i i ---i iiv v -- - L1ME3Cz_3end# 453 TTGTTTGTAATAGC---GAAAAATTGGAAACAACCTAAATG--TC-CATC 496 chr6qtel1M 865692 CATCAGGGAATGGCTAAACAAGTTGTAGTATAT 865724 v vi v i i i L1ME3Cz_3end# 497 AATAGGGGAATGGATAAATAAATTGTGGTATAT 529 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 41.56 CpG sites = 85, Kimura (unadjusted) = 43.60 Transitions / transversions = 1.47 (85/58) Gap_init rate = 0.05 (23 / 457), avg. gap size = 1.65 (38 / 23) 497 28.76 1.96 0.00 chr6qtel1M 866441 866593 (133407) C Charlie4#DNA/hAT-Charlie (0) 3378 3223 m_b321s502i0 13428 chr6qtel1M 866441 CAGAACTTCCTAACTATTTCTGTGTCACAGACATCTTTTTCAATCTGATG 866490 iiv i iv i i ii vi vv i i C Charlie4#DNA/ 3378 CAGGGGTTCTTAACCTTTTTTGTGCCATGGACCCCTTTGGCAGTCTGGTG 3329 chr6qtel1M 866491 AAGCCTTTGAA---CTGTTCAGAATCATGTCTTTAAAAGTGTAAAAAAAA 866537 v i --- vi v i v ii v C Charlie4#DNA/ 3328 AAGCCTATGGACCCCTTCTCAGAATAATGTTTTTAAATGCATAAAATAAA 3279 chr6qtel1M 866538 ATGCATAGTGTTTCAAAGGGAAAAGACCCTATTAAAATGAAATTACCAAG 866587 i vi v i vvi iiv i iv i i i C Charlie4#DNA/ 3278 ATACATAGGATTACAAAGGAAACCAATTATATTGAAATATAGTTATCAAA 3229 chr6qtel1M 866588 AAATTT 866593 v C Charlie4#DNA/ 3228 ATATTT 3223 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 37.47 CpG sites = 27, Kimura (unadjusted) = 37.47 Transitions / transversions = 1.59 (27/17) Gap_init rate = 0.01 (1 / 152), avg. gap size = 3.00 (3 / 1) 672 24.87 12.39 0.41 chr6qtel1M 866954 867171 (132829) MIRc#SINE/MIR 25 268 (0) m_b321s601i10 13429 chr6qtel1M 866954 GAGCCATTGGACCTCGAATGAGGAAAACTTGAGTTCAAATACAGCCTC-- 867001 - i i v i v i i i i i v v v -- MIRc#SINE/MIR 25 GAGC-ACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTG 73 chr6qtel1M 867002 --AC--ACTATCTCTGTGACTCTGGGCAAGTCACTTAAATTCC------- 867040 -- -- v v ii vi i------- MIRc#SINE/MIR 74 CCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCC 123 chr6qtel1M 867041 ---GTTTCCTCATCTGTAAAAAGGAGTTAATAAAAGC------ACATTCC 867081 --- v i v v v ------i v v MIRc#SINE/MIR 124 TCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACC 173 chr6qtel1M 867082 TCCCAGGATTTTTACGAAGATTAAGTAAGATA---TTTGC-AACTTACTT 867127 v i v ii i i i i --- v i- vvii MIRc#SINE/MIR 174 TCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTT 223 chr6qtel1M 867128 TGTTATCC-TAAAGTGCTATGGAAATACCAACTATTATTATTATT 867171 v v i- iv iiv iv?i MIRc#SINE/MIR 224 TGTAAACTGTAAAGTGCTATACAAATGTAAGGNGTTATTATTATT 268 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 29.49 CpG sites = 30, Kimura (unadjusted) = 30.91 Transitions / transversions = 1.25 (30/24) Gap_init rate = 0.04 (9 / 217), avg. gap size = 3.11 (28 / 9) 496 28.64 1.83 2.76 chr6qtel1M 868456 868674 (131326) C L1ME1_3end#LINE/L1 (271) 655 439 m_b321s551i6 13430 chr6qtel1M 868456 AGTATATAATGATCTCCTG-GTCCTGCTCATTTCACTCAGCATCAGTTCG 868504 i ? --- ii - iv iv - i v?v C L1ME1_3end#LI 655 AGTATGTANT---CTTTTGTGTCTGGCTTCTTTCACTCAGCAT-AATGNT 610 chr6qtel1M 868505 TGTAAGTCTC-TCCAGGCCTTTCTGAAATTATC--CTGTTGGTCATTTCT 868551 v i vi - v -- vi vivv --iv v ivi i C L1ME1_3end#LI 609 TTTGAGATTCATCCATG--TTGTTGCGTGTATCAGTAGTTCGTTCCTTTT 562 chr6qtel1M 868552 TACAGAACAGTAATATTCCATAATATTCATATACCACAATTTATTCAGCC 868601 iv vvv i vi vv i i v C L1ME1_3end#LI 561 TATTGCTGAGTAGTATTCCATTGTATGGATATACCACAATTTGTTTATCC 512 chr6qtel1M 868602 ATTCTCCAACTGATGGACATCCATTCAGTTTCCAGTTTTTAGCCACTACA 868651 v ?ii iiivviv i i i i C L1ME1_3end#LI 511 ATTCACCNGTTGATGGACATTTGGGTTGTTTCCAGTTTTTGGCTATTACG 462 chr6qtel1M 868652 AAAAGGGCTGCCACAAACATTCG 868674 v ii i ii C L1ME1_3end#LI 461 AATAAAGCTGCTATGAACATTCG 439 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.00 CpG sites = 34, Kimura (unadjusted) = 37.54 Transitions / transversions = 1.26 (34/27) Gap_init rate = 0.04 (9 / 218), avg. gap size = 1.11 (10 / 9) 502 31.61 1.03 1.03 chr6qtel1M 868480 868674 (131326) C L1MD1_3end#LINE/L1 (356) 633 439 m_b321s551i7 13430 chr6qtel1M 868480 GCTCATTTCACTCAGCATCAGTTCGTGTAAGTCTCTCCAGGCCTTTCTGA 868529 iv v v iiv v ii iiv -- vi v C L1MD1_3end#LI 633 GCTTTTTTCACTCAGCATAATTCTCTGGAGATTCATCCAGG--TTGTTGC 586 chr6qtel1M 868530 AATTATC--CTGTTGGTCATTTCTTACAGAACAGTAATATTCCATAATAT 868577 ivv --iv v ivi i iv vvv i ii C L1MD1_3end#LI 585 GTGTATCAATAGTTCGTTCCTTTTTATTGCTGAGTAGTATTCCATGGTAT 536 chr6qtel1M 868578 TCATATACCACAATTTATTCAGCCATTCTCCAACTGATGGACATCCATTC 868627 vv i i i i i v vii v iivvi C L1MD1_3end#LI 535 GGATGTACCACAGTTTGTTTAACCATTCACCCGTTGAAGGACATCTGGGT 486 chr6qtel1M 868628 AGTTTCCAGTTTTTAGCCACTACAAAAAGGGCTGCCACAAACATTCG 868674 v i i i i v ii i i C L1MD1_3end#LI 485 TGTTTCCAGTTTTTGGCTATTACGAATAAAGCTGCTATAAACATTCG 439 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 39.54 CpG sites = 35, Kimura (unadjusted) = 42.25 Transitions / transversions = 1.35 (35/26) Gap_init rate = 0.02 (3 / 194), avg. gap size = 1.33 (4 / 3) 530 31.47 1.39 0.69 chr6qtel1M 871654 871797 (128203) MIRc#SINE/MIR 7 151 (117) m_b321s601i11 13431 chr6qtel1M 871654 AGCATGATGTGATGAGAAAAACACTGCATTTAGAATCAG-AAGACCAAGG 871702 ii i iii ii i i v i i i - vi MIRc#SINE/MIR 7 AGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGG 56 chr6qtel1M 871703 TATAGATTCTGGATGTGCCACATACAGACTATGTGACCTTAGCTAAGTCA 871752 viiii i i v v v vii i i vi MIRc#SINE/MIR 57 TTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCA 106 chr6qtel1M 871753 TTTTCTCTGCCCGAGCCTCAATTTCCCTAT-TGTAAAAATGGTAAT 871797 i vvi vi i i ii - - vi MIRc#SINE/MIR 107 CTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGT-AAAATGGGGAT 151 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 41.18 CpG sites = 33, Kimura (unadjusted) = 44.02 Transitions / transversions = 2.75 (33/12) Gap_init rate = 0.02 (3 / 143), avg. gap size = 1.00 (3 / 3) 484 33.33 2.11 2.11 chr6qtel1M 871663 871852 (128148) MIR3#SINE/MIR 14 203 (5) m_b321s601i12 13431 chr6qtel1M 871663 TGATGAGAAAAA-CACTGCATTTAGAATCAGAAGACCAAGGTATAGATTC 871711 vv i i - - v i vi i i vi vivii i MIR3#SINE/MIR 14 TGAGCAGAGAGAGCAC-GGACTGGGAGTCAGGAGACCTGGGTTCTAGTCC 62 chr6qtel1M 871712 TGGATGTGCCACATACAGACTATGTGACCTTAGCTAAGTCATTTTCTCTG 871761 i v v vv v?i i i vi i ivi v MIR3#SINE/MIR 63 CGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTC 112 chr6qtel1M 871762 CCCGAGCCTCAATTTCCCTAT-TGTAAAA-ATGGTAATTCAACTGGAAAG 871809 i i i i ii - -iv vii vi i vii MIR3#SINE/MIR 113 TCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGA 162 chr6qtel1M 871810 CTTTCAAGTTGCCTTCCAGATC-AACTTCACTCAATCATTCTAT 871852 ii ii v v v -i --- i v v MIR3#SINE/MIR 163 TCTCTAAGGTCCCTTCCAGCTCTGA---CATTCTATGATTCTAT 203 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 45.35 CpG sites = 38, Kimura (unadjusted) = 46.39 Transitions / transversions = 1.58 (38/24) Gap_init rate = 0.04 (8 / 189), avg. gap size = 1.00 (8 / 8) 415 23.36 1.21 14.38 chr6qtel1M 872730 872894 (127106) MIRb#SINE/MIR 4 149 (119) m_b321s601i13 13432 chr6qtel1M 872730 AAGGGCAGGCGTGGGGGGTACCACAGTGCATAGAACACTACCT--GGAAT 872777 i - v ------- v v i viv -- i MIRb#SINE/MIR 4 AGGGGCAG-CGTGGTG-------CAGTGGAAAGAGCACGGGCTTTGGAGT 45 chr6qtel1M 872778 CAAGATAATCTTCCTGAGTCCAAATCTGGCCACAGACACTTACCAGCTGT 872827 - i iv --- i i i iv v v v v i MIRb#SINE/MIR 46 CA-GACAGAC---CTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGT 91 chr6qtel1M 872828 GTGAACCCAGGCAAGTCATTTAATCCTGTTTGCTCATTTCATCCTCAGTT 872877 v iii i i - v i -------- v MIRb#SINE/MIR 92 GTGACCTTGGGCAAGTTACTTAA-CCTCTCTG--------AGCCTCAGTT 132 chr6qtel1M 872878 GCCTCATCTGTTAAATG 872894 v v MIRb#SINE/MIR 133 TCCTCATCTGTAAAATG 149 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 26.66 CpG sites = 17, Kimura (unadjusted) = 27.61 Transitions / transversions = 1.06 (17/16) Gap_init rate = 0.13 (22 / 164), avg. gap size = 1.05 (23 / 22) 471 22.67 1.41 9.92 chr6qtel1M 872753 872894 (127106) MIRc#SINE/MIR 16 146 (122) m_b321s601i14 13432 chr6qtel1M 872753 CAGTGCATAGAACACT--ACCTGGAATCAAGATAATCTTCCTGAGTCCAA 872800 v v i -- i i i vi ---- i i i MIRc#SINE/MIR 16 CAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA----CCTGGGTTCGA 61 chr6qtel1M 872801 ATCTGGCCACAGACACTTACCAGCTGTGTGAACCCAGGCAAGTCATTTAA 872850 i iv v v v v i v iii i MIRc#SINE/MIR 62 GTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAA 111 chr6qtel1M 872851 TCCTGTTTGCTCATTTCATCCTCAGTTGCCTCATCTGTTAAATG 872894 - v i -------- v v v MIRc#SINE/MIR 112 -CCTCTCTG--------AGCCTCAGTTTCCTCATCTGTAAAATG 146 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 26.02 CpG sites = 16, Kimura (unadjusted) = 27.08 Transitions / transversions = 1.23 (16/13) Gap_init rate = 0.10 (14 / 141), avg. gap size = 1.07 (15 / 14) 233 32.03 1.02 7.61 chr6qtel1M 873339 873436 (126564) C MIR1_Amn#SINE/MIR (113) 117 26 m_b321s601i16 13433 chr6qtel1M 873339 GGGGTCAAATGACTTGTCCAAAGTCACACAACTAGTAAATGTTAATTATC 873388 i ? i i i ? i ?i i? i vi ------ C MIR1_Amn#SINE 117 GAGGTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNAGTGGCA------ 74 chr6qtel1M 873389 TGAGGCCAAATTTGAAGTCAGCTC-CTTGGGTGCTTATTGGGCCCTCTA 873436 - v vii ? ? vi v - ii i v ivi ivi iv C MIR1_Amn#SINE 73 -GAGCCGGGANTNGAACCCAGGTCTCCCGAGTCCCAGTCCAGTGCTCTA 26 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 46.47 CpG sites = 20, Kimura (unadjusted) = 48.91 Transitions / transversions = 2.22 (20/9) Gap_init rate = 0.08 (8 / 97), avg. gap size = 1.00 (8 / 8) 275 27.82 0.00 10.14 chr6qtel1M 873339 873414 (126586) C MIRc#SINE/MIR (153) 115 47 m_b321s601i15 13433 chr6qtel1M 873339 GGGGTCAAATGACTTGTCCAAAGTCACACAACTAGTAAATGTTAATTATC 873388 i i i i i i i vi ------ C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCA------ 72 chr6qtel1M 873389 TGAGGCCAAATTTGAAGTCAGCTCCT 873414 - v vii i i vi v i C MIRc#SINE/MIR 71 -GAGCCGGGACTCGAACCCAGGTCTT 47 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 34.00 CpG sites = 14, Kimura (unadjusted) = 36.44 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.09 (7 / 75), avg. gap size = 1.00 (7 / 7) 416 28.62 11.67 1.01 chr6qtel1M 874023 874202 (125798) C MIRc#SINE/MIR (26) 242 44 m_b321s601i17 13434 chr6qtel1M 874023 TAATACCTTAGGGTTTGCCAAACACTTTCCCCAATGGTACTTCATTTTAT 874072 ii i vi i v i i v vv iiv ii v C MIRc#SINE/MIR 242 TAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATCTCATTTGAT 193 chr6qtel1M 874073 TCTAGCAA---------GAGGGAGAAACGT--GCTAATTTCATCTCCATT 874111 i vi --------- v iv v v-- v v v i i C MIRc#SINE/MIR 192 CCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATT 143 chr6qtel1M 874112 TTGCAGATGAGCAAACTGAAG-TGAGCAAGGTGAAGTGCTTTGCTCA--G 874158 i v i - v vi v vi i -- C MIRc#SINE/MIR 142 TTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGG 93 chr6qtel1M 874159 TCACACAGCT-----GTGTCTGAAGCCAGAATTGAAA--TAGCGTTTCCC 874201 ----- v v - i i i vi --i - i i C MIRc#SINE/MIR 92 TCACACAGCTAGTAAGTGGCAG-AGCCGGGACTCGAACCCAG-GTCTTCC 45 chr6qtel1M 874202 T 874202 C MIRc#SINE/MIR 44 T 44 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 34.15 CpG sites = 28, Kimura (unadjusted) = 36.81 Transitions / transversions = 1.22 (28/23) Gap_init rate = 0.04 (8 / 179), avg. gap size = 2.88 (23 / 8) 32 22.92 4.90 1.90 chr6qtel1M 874218 874319 (125681) (TA)n#Simple_repeat 1 105 (0) m_b321s252i10 13435 chr6qtel1M 874218 TATGTGTATACTACCATATGT-TATCTATGAATATATATACATATAT-TT 874265 i i - -i i - v iv i - v (TA)n#Simple_ 1 TATATATATA-TA-TATATATATATATATATATATATATATATATATATA 48 chr6qtel1M 874266 TATACACACATATGTAT-TGTGTA-ATATATAAGAATATATATAAATA-A 874312 i i i i - i i - viv v - (TA)n#Simple_ 49 TATATATATATATATATATATATATATATATATATATATATATATATATA 98 chr6qtel1M 874313 TATATAT 874319 (TA)n#Simple_ 99 TATATAT 105 Matrix = Unknown Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.07 (7 / 101), avg. gap size = 1.00 (7 / 7) 376 35.24 2.44 0.80 chr6qtel1M 874364 874486 (125514) MIRc#SINE/MIR 13 137 (131) m_b321s601i18 13436 chr6qtel1M 874364 GTGCAATGGATAGGATGCTAAACTTGAGAGCAGAGAAGAATTGAATTCAA 874413 i v iiii ii iiiv - vi ii i MIRc#SINE/MIR 13 GTGCAGTGGAAAGAGCACTGGACTTGGAGTCAG-GAAGACCTGGGTTCGA 61 chr6qtel1M 874414 ATCTTGATTA-GGCACCGACTAGTCCTGTAATCCCAG--AAGTCACTTAA 874460 i ii ii v- v iv iiv i i iii -- MIRc#SINE/MIR 62 GTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAA 111 chr6qtel1M 874461 TGATTCCCAACCTCAGTTTATTCATC 874486 ivvi iv i vi MIRc#SINE/MIR 112 CCTCTCTGAGCCTCAGTTTCCTCATC 137 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 48.97 CpG sites = 32, Kimura (unadjusted) = 52.66 Transitions / transversions = 2.91 (32/11) Gap_init rate = 0.02 (3 / 122), avg. gap size = 1.33 (4 / 3) 565 20.57 13.87 0.65 chr6qtel1M 874563 874699 (125301) C MIRc#SINE/MIR (22) 246 92 m_b321s601i19 13437 chr6qtel1M 874563 TGTATGGTCACTTTAAAGTTTGCAAGGCACTTT---ACAGGTTATCT--- 874606 i - v i i i --- i vi --- C MIRc#SINE/MIR 246 TGTATAG-CACTTTACAGTTTACAAAGCGCTTTCACATACATTATCTCAT 198 chr6qtel1M 874607 --GGTTTTCACAACAACTCTGTGAGGTAAAT------GCTACTATTATCC 874648 -- i ii i iii------ v i C MIRc#SINE/MIR 197 TTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCC 148 chr6qtel1M 874649 CCATTTTATAGATGAGAAAACTGAGGCTGAAAA-----AAGAGCTTTATC 874693 i i v i i----- v vi ii C MIRc#SINE/MIR 147 CCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCC 98 chr6qtel1M 874694 CAGGGT 874699 i C MIRc#SINE/MIR 97 CAAGGT 92 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 24.19 CpG sites = 22, Kimura (unadjusted) = 25.22 Transitions / transversions = 3.67 (22/6) Gap_init rate = 0.04 (6 / 136), avg. gap size = 3.33 (20 / 6) 384 20.75 16.98 0.00 chr6qtel1M 874861 874966 (125034) C MIR3#SINE/MIR (3) 205 82 m_b321s601i20 13438 chr6qtel1M 874861 TCATGGA-TCATAGT-TATCA-AGCTCAAAGAGAACTTAGA--------A 874899 i - v- i - vi i v -------- C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTA 156 chr6qtel1M 874900 G-------CCTTCGTTTTGTAGATGAGGCAGCTGAAGCCTAGAAAAGTGA 874942 ------- i i ii v i i i i i C MIR3#SINE/MIR 155 GTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGA 106 chr6qtel1M 874943 AGTTTCTTGCCCAAGATCTCATAG 874966 vv i v i C MIR3#SINE/MIR 105 AGTGACTTGCCCAAGGTCACACAG 82 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 25.01 CpG sites = 15, Kimura (unadjusted) = 25.01 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.05 (5 / 105), avg. gap size = 3.60 (18 / 5) 486 24.75 0.00 8.77 chr6qtel1M 875464 875587 (124413) MIRc#SINE/MIR 2 115 (153) m_b321s601i21 13439 chr6qtel1M 875464 GAAACAGTTAGATGGCACTATGAATAGAGCCCTGGCCTTGGAATCAGGAG 875513 ii ---i ii vi i v v v i i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chr6qtel1M 875514 GATCTGAGTTTAAATCTGGCCACAAAGAGTTGATACTTACTAGCTGTGTG 875563 i i ii i iv v v ------- vi MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTC-------TGCCACTTACTAGCTGTGTG 91 chr6qtel1M 875564 ACTTTGGGAAAGTCACTTAATCCC 875587 i v i i MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 29.40 CpG sites = 19, Kimura (unadjusted) = 30.87 Transitions / transversions = 2.11 (19/9) Gap_init rate = 0.08 (10 / 123), avg. gap size = 1.00 (10 / 10) 335 25.84 5.62 0.00 chr6qtel1M 875933 876021 (123979) MIRc#SINE/MIR 100 193 (75) m_b321s601i22 13439 chr6qtel1M 875933 CAAATGAATTAACATATATGGGTCTCAGTTTCTATATTTGTAAAATGGAA 875982 i v v v v v i i ivi i ii MIRc#SINE/MIR 100 CAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGG 149 chr6qtel1M 875983 ATGATAAGA-CTACTC--CCT--TTCACAGAATAGTTATGAGGA 876021 i v - i i -- --i ii v i MIRc#SINE/MIR 150 ATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGA 193 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 32.79 CpG sites = 15, Kimura (unadjusted) = 32.79 Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.03 (3 / 88), avg. gap size = 1.67 (5 / 3) 237 34.11 5.03 5.03 chr6qtel1M 877362 877818 (122182) L1MEj_5end#LINE/L1 857 1313 (847) m_b321s551i8 13440 chr6qtel1M 877362 AAAAACGACAGACTTGGAAAATAGATCTAGGAGACATAATCTGAGGATTA 877411 i ii v ii i v iv v i v L1MEj_5end#LI 857 AAAGATAAGAGACTTGGAGGATAGATCCAGGAGACCTAACATGCGAATAA 906 chr6qtel1M 877412 TTGGACTTTCCGAAAACTATGATGAAAAAAA--GAGCCTAGATACTATTT 877459 v v i v iivv vi v i v i -- vvv ii v v L1MEj_5end#LI 907 TAGGAGTTCCAGAAGGAGAAAAAGGAACAGATGGAGGAGAGGCAATAATT 956 chr6qtel1M 877460 TACAAGAAATCATCAAAGAGAACTGCCC--AGATGTAATAGAATCAGAAG 877507 --v v v vi i i v -- v v iv ii i v iv L1MEj_5end#LI 957 --AAACAAATAATAGAAGAAAATTTCCCTGAGCTGAAGAAAGACCTGAGT 1004 chr6qtel1M 877508 GTAAAATAGGCATTGAAAGAATTCATCGAACACCTTCTGAAAGAAACCCT 877557 v ---ii -- iii i i---i i v iv i vivv L1MEj_5end#LI 1005 CT---GCAG--ATTGAAAGGGCTCACCGAG---TTCCAGGCAGGATTGAT 1046 chr6qtel1M 877558 AAAATAAAA---ACCCCAAGGAATATTGTGGCCAAATTTCAGAACTATCA 877604 i i v i --- v v v iv iv i v viv L1MEj_5end#LI 1047 GAGAAAAGACACACACCTAGGCATATCCTGGTAAAATTCCTGAACTCCAA 1096 chr6qtel1M 877605 GATTAAGGAAAAAATTTTACAAGCAGCCA---AAAAAAAACCATTTAAAT 877651 iv i i i vv --- i i v v vv L1MEj_5end#LI 1097 GGATAAAGAGAAAATCTTACAAGCTTCCAGACAGAAAGAACAAGTTACTT 1146 chr6qtel1M 877652 ACCGAGGTGCCACAATAAGGATCACCCAAG-ATCTGGCTGCC--TCTACA 877698 vi ------ v i vv vi - v i v i-- i L1MEj_5end#LI 1147 ACAAAGG------AAAAAGAATCAGACTGGCATCGGACTTCTCATCTGCA 1190 chr6qtel1M 877699 TTAAAGGAA---AGAAGGGCCTGGAATATGATATTCCGA-----AAGGCA 877740 vi vv --- ivvv vv v v v -----i iv L1MEj_5end#LI 1191 ACACTGGAAGCTAGAAGACGGTGGAATAACATCTACAGACTACTGAGAGA 1240 chr6qtel1M 877741 CAAGAACTTGGGATGCAG-CCAAGAATAAACTACCCAGCTAAGCTGAGCA 877789 v i ------ i- vvvv i v - v L1MEj_5end#LI 1241 AAAGGAC------TGCAACCCAAGAATCCTATACCCAGCCAAGAT-ATCA 1283 chr6qtel1M 877790 TTT-TCTTCCAGGGAAGAAGATGGACATTT 877818 i-i vi vii vi i L1MEj_5end#LI 1284 TTCACCTGTCAGGGCGAAAGAAAGATATTT 1313 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 45.56 CpG sites = 69, Kimura (unadjusted) = 45.97 Transitions / transversions = 0.87 (69/79) Gap_init rate = 0.07 (33 / 456), avg. gap size = 1.39 (46 / 33) 331 25.95 5.03 7.43 chr6qtel1M 878380 878558 (121442) L1MEd_5end#LINE/L1 2049 2223 (1) m_b321s551i9 13440 chr6qtel1M 878380 AGAATAAGTA--AAGCACAATCTGGGGTTATTAGGATGGCAGGAA---AT 878424 i i -- --------- v i i i --- L1MEd_5end#LI 2049 AGAACAAATAGAAAGCACAA---------AATAAGATGGTAGAAATAAAT 2089 chr6qtel1M 878425 ACAGAT---TTAGTAATTCTAACCGTAAATGTGAATGGGATGAACTCCCC 878471 v i --- i ivi --- i iv i ? L1MEd_5end#LI 2090 CCAAATATATCAGTAATCACAA---TAAATGTAAATGGACTAAACTCNCC 2136 chr6qtel1M 878472 CATAAAGAGGAGGCAGATAG-CAGACTGGATCAAAAGTCAGAACCCTACA 878520 vi v i ivi - v - i i ivvvi i vi v L1MEd_5end#LI 2137 AGTTAAAAGACAG-AGATTGTCAGATTGGATTAAAAAAACAAATCCAGCT 2185 chr6qtel1M 878521 ATATGTTGTTTACAAGAAACACATTTAAAGCAGGGGGA 878558 i i ii i vii L1MEd_5end#LI 2186 ATATGCTGTTTACAAGAGACACACCTAAAACATAAGGA 2223 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 33.32 CpG sites = 29, Kimura (unadjusted) = 33.32 Transitions / transversions = 2.07 (29/14) Gap_init rate = 0.10 (17 / 178), avg. gap size = 1.29 (22 / 17) 442 20.68 5.33 3.27 chr6qtel1M 878409 878558 (121442) L1MEh_5end#LINE/L1 2082 2234 (1) m_b321s551i10 13440 chr6qtel1M 878409 TAGGATGGCAGGAAATA----CAGAT---TTAGTAATTCTAACCGTAAAT 878451 i - ---- ?i ---?i vi --- L1MEh_5end#LI 2082 TAAGATGGCAG-AAATAAGTCCNAATATANCAGTAATTACAA---TAAAT 2127 chr6qtel1M 878452 GTGAATGGGATGAACTCCCCCATAAAGAGGAGGCAGAT-AGCAGACTGGA 878500 i v i v v v i ivi - -?v i L1MEh_5end#LI 2128 GTAAATGGGTTAAACTCACCAATTAAAAGACAG-AGATTNTCAGATTGGA 2176 chr6qtel1M 878501 TCAAAAGTCAGAACCCTACAATATGTTGTTTACAAGAAACACATTTAAAG 878550 i? iv i i v i i i i i L1MEh_5end#LI 2177 TTNAAAAACAAAATCCAACAATATGCTGTCTACAAGAGACACACTTAAAA 2226 chr6qtel1M 878551 CAGGGGGA 878558 ?ii L1MEh_5end#LI 2227 CANAAGGA 2234 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 26.09 CpG sites = 21, Kimura (unadjusted) = 26.09 Transitions / transversions = 2.33 (21/9) Gap_init rate = 0.05 (8 / 149), avg. gap size = 1.62 (13 / 8) 6141 30.10 2.09 2.09 chr6qtel1M 878447 881703 (118297) L1M5_orf2#LINE/L1 38 3294 (0) m_b321s551i11 13440 chr6qtel1M 878447 TAAATGTGAATGGGATGAACTCCCCCATAAAGAGGAGGCAGATAG-CAGA 878495 i ?v i v i v v i vi - v - L1M5_orf2#LIN 38 TAAATGTAAATGGNCTAAACACTCCAATTAAAAGGCAG-AGATTGTCAGA 86 chr6qtel1M 878496 CTGGATCAAAAGTCAGAACCCTACAATATGTTGTTTACAAGAAACACATT 878545 v iv ii v v i i i i i L1M5_orf2#LIN 87 CTGGATAAAAAAACAAGACCCAACTATATGCTGTCTACAAGAGACGCACT 136 chr6qtel1M 878546 TAAAGCAGGGGGATACATATAGAGTAAAGGTAAAAGGCTGGAGCAAAATC 878595 v ii viii i v ? iv i i v iv i v L1M5_orf2#LIN 137 TTAAATATAAAGACACAGANAGGTTGAAAGTAAAAGGATGGAAAAAGATA 186 chr6qtel1M 878596 TATTATGCTTCAGGTGAAGTCAAA-AAAGCAGGGGTAGCCATCCTTATCT 878644 ii v-v viiv ?iv - v ? i i vi v v L1M5_orf2#LIN 187 TACCATGCA-AACACTAANCAAAAGAAAGCTGGNGTGGCTATATTAATAT 235 chr6qtel1M 878645 CAGATCAAGCA------AAAGTAAAAATTGATCTAATTAAAAGAGATAAG 878688 iv i ------ i i i --- --- vv i L1M5_orf2#LIN 236 CAGACAAAGTAGACTTCAAGGCAAGAA---AT---ATTACCAGAGATAAA 279 chr6qtel1M 878689 GAAGGAAACTACATCCTGCTAAA-GGGTAGCATAAACAACGAAGCAATAT 878737 i v i v vv v - vivv v v - vv v L1M5_orf2#LIN 280 GAGGGACATTTCATAATGATAAAAGGGTCAATTCATCAA-GAAGACATAA 328 chr6qtel1M 878738 CAATATTAAACATATATGCACCAAGTGGTATGGCACTCAACTTCCTAAAG 878787 vi ii i v i iii vi viiv v v v i L1M5_orf2#LIN 329 CAATCCTAAATGTGTATGCACCTAATAACAGAGCTTCAAAATACATGAAG 378 chr6qtel1M 878788 GAGAAGTTAAGAGAGTTGCAAGAAGAAATAGACAA---CAAAACTGTAAT 878834 v i ii i v ii iv i --- v i --- L1M5_orf2#LIN 379 CAAAAACTGACAGAACTAAAAGGAGAAATAGACAAATCCACAATT---AT 425 chr6qtel1M 878835 AGTAGGAGATCTCAACCTTGCACTCTCAG-AATTAGACAAATCAAAC-CA 878882 ? i i vi?v v - - i i v ii-v L1M5_orf2#LIN 426 AGTNGGAGATTTTAACACNCCTCTCTCAGTAATT-GATAGAACAAGTAGA 474 chr6qtel1M 878883 CAAAACAAATAAGAAAGAA-ATTAAAGAAGTAAATAGAATATTAGAAA-- 878929 -- v v i - vi vv i i -- i i vv -- L1M5_orf2#LIN 475 CAAAA--AATCAGTAAGGATATAGAAGATTTGAACA--ACACTATCAACC 520 chr6qtel1M 878930 AATTAGGTATGTTGGATCTTTGGAGAAAATTGAATGGAGATAGAAG-GGA 878978 i v iiv iv v iv iv v i ?v ivv - i iv? -i L1M5_orf2#LIN 521 AACTTGACCTAATTGACATTTATAGAACACTNCACCCA-ACAACNGCAGA 569 chr6qtel1M 878979 ATATACTTTCTTCTCAGCAGTTCATGGAACCTATTCAAAAATTGACCATA 879028 i v i ivv iv v v v v i v L1M5_orf2#LIN 570 ATACACATTCTTTTCAAGTGCACATGGAACATTTACCAAGATAGACCATA 619 chr6qtel1M 879029 TATTAGGACATAAAGAC----CTCAAAATTAAATGCAAGAAAGCAGAAAT 879074 ?i i v - ---- --- vi? i iiiiv L1M5_orf2#LIN 620 TNCTGGGCCATAAA-ACAAGTCTCAA---TAAATTTNAAAGGATTGAAAT 665 chr6qtel1M 879075 AGTAAATGCTTTCTTTTCAGATCATGATGCAATAAAAACTACATTCAA-- 879122 vi v viv v v i v i ii v v viviv v -- L1M5_orf2#LIN 666 CATACAGAGTATGTTCTCTGACCACAATGGAATTAAATTAGAAATCAATA 715 chr6qtel1M 879123 -CAAAAAGTTAGGGGGAAATAGACCAAAAAGTAATTGGAAACTAAACAAT 879171 - v ?vvi - vv v -- v i - L1M5_orf2#LIN 716 ACAAAAAGATANCTAGAAA-ATCCCCAAA--TATTTGGAAATTAAACAA- 761 chr6qtel1M 879172 CTCA-TCTTAAAGAATGATTGGGTGAAGCAGCAAATTATAGATACAATTA 879220 v - ii v ivvv v iv iv i i i?viv L1M5_orf2#LIN 762 CACACTTCTAAATAACCCATGGGTCAAAGAAGAAATCACAANGGAAATTA 811 chr6qtel1M 879221 ATAATTTCACTCAAGATAATGACAATGATGAGACATCATACCAAAATTTG 879270 iv v vivi v vvv ? vi v v i L1M5_orf2#LIN 812 GAAAATATTTTGAACTGAATGANAATGAAAATACAACATATCAAAATTTG 861 chr6qtel1M 879271 TGGGATGCAGCCAAAGCGGTAATAAGAGGGAATTTTATATCCTTAGAGGC 879320 i i iv v v v ? i v L1M5_orf2#LIN 862 TGGGATGCAGCTAAAGCAGTGCTTAGAGGGAAATTTATAGCNTTAAATGC 911 chr6qtel1M 879321 TTACTTGAATAAAACAG-AGAAAGAA--AAGATTAATGAATTGGGCTTGC 879367 ? i--- v i v - iv-- i i vi ii v L1M5_orf2#LIN 912 NTAT---ATTAGAAAAGAAGAAAGGCTTAAAATCAATGATCTAAGCTTCC 958 chr6qtel1M 879368 AACTAAAAAAACT---AAAAAAAGACCAAATTAAAAACCCCCAATCAAAT 879414 v v i i --- i v --- v v? i L1M5_orf2#LIN 959 ACCTTAAGAAGCTAGAAAAAGAAGAGCAAATTAAA---CCCAAAGNAAGT 1005 chr6qtel1M 879415 ACTAAATTGGAAATTCTAAAATTAAAAGGAGAAATTAAAAATATTGAAAG 879464 vv iivv vv iv i v i vi v v i L1M5_orf2#LIN 1006 AGAAGGAAGGAAATAATAAAGATAAGAGCAGAAATCAATGAAATAGAAAA 1055 chr6qtel1M 879465 TAAAAAAACTATTGAACTAATTAATAAAACTAAGAGTTGGTTCTATGAAA 879514 i ? ? v v ivv i ii i i i i v L1M5_orf2#LIN 1056 CAAANANACAATAGAGAAAATCAACGAAGCCAAAAGCTGGTTCTTTGAAA 1105 chr6qtel1M 879515 AAGCCAATAAAATAGATAAGCCTTTGGTAAATCTGATTAGAAAAAGGAGG 879564 iii v i i i i? iv i ii ii i L1M5_orf2#LIN 1106 AGATCAATAAAATTGATAAACCTCTAGCNAGACTGATCAAGAAAAAAAGA 1155 chr6qtel1M 879565 GAGGAAAATGAAATTAGTAGTCTTAAAAATGAAAAGGGAGAACTTTCCAC 879614 i i vvv vi i v i ii i vv iv i L1M5_orf2#LIN 1156 GAGAAGACACAAATTACCAATATCAGGAATGAAAAAGGAGACATCACTAC 1205 chr6qtel1M 879615 CAATGAAGAGGAAATTAGAGAAATAATAAGGAGTTATTTTGCTCAACTTT 879664 vi vvvivi v i iii iiiv v vv L1M5_orf2#LIN 1206 AGATCCTACAGACATTAAAAGGATAATAAGAGAATATTATGAACAACTTT 1255 chr6qtel1M 879665 ATGCCAATAAATTTGATAACCTAAGTGAAATGGATGACTACCTCCAAAAA 879714 ? i ii ii v v iv L1M5_orf2#LIN 1256 ATGCCAATAAATTTGANAACTTAGATGAAATGGACAAATTCCTTGAAAAA 1305 chr6qtel1M 879715 TATAGACTTCCCAGACTAACAGAGGAGGAAGTAAATTGCTTGAATAGTCC 879764 i i i?i v v i i ?v i i i i vviii i L1M5_orf2#LIN 1306 CACAANTTACCAAAACTGACNCAAGAAGAAATAGAAAATCTGAATAGCCC 1355 chr6qtel1M 879765 CATTTCAGAAAAAGAAATAGAACAGGCAATTAAACAACTCCCTAAGAAAA 879814 i v vivv v ivv i v v i i vi i L1M5_orf2#LIN 1356 TATATCTATTAAAGAAATTGAATTTGTAATTAAAAACCTTCCCACAAAGA 1405 chr6qtel1M 879815 AATCCCCAGGACCAGATGGATTTACATGTGAATTTTACCAAACATTTAAA 879864 v i v v i vv i i L1M5_orf2#LIN 1406 AAACTCCAGGCCCAGATGGCTTCACTGGTGAATTCTACCAAACATTTAAG 1455 chr6qtel1M 879865 GAACAATTGGCCCCAATGCTATATAAATTATTTGATAAAATAGGGAATGA 879914 v v iiiv vi i i i v iv v ii v L1M5_orf2#LIN 1456 GAAGAAATAATACCAATCTTACACAAACTCTTCCAGAAAATAGAAAAAGA 1505 chr6qtel1M 879915 AGGAGTCCTACCAAATTCCTTCTATGACACAGACATGGTACTGATACCTA 879964 i iiv v v i v i vi vii ?iiv v L1M5_orf2#LIN 1506 GGGAACACTTCCCAACTCATTTTATGAGGCCAGCATNACCCTGATACCAA 1555 chr6qtel1M 879965 AACCAGGTAGGCTGAAA--ACAGAGAAAGAAAATTATAGACCAATCTCCC 880012 ? ii ii-- v -- iii i v L1M5_orf2#LIN 1556 AACCNGACAAA--GACATTACAAGAAAAGAAAATTACAGACCAATATCCC 1603 chr6qtel1M 880013 TAATGAATATTGATGCTAAAATCTTAAATAAGATATTAGCAAAAAGACTA 880062 v i v v i ? i i vv v v L1M5_orf2#LIN 1604 TCATGAACATAGATGCAAAAATCCTNAACAAAATATTAGCAAATCGAATC 1653 chr6qtel1M 880063 CAGAAAATCATCTCCAAGATAATACACTATGATCAAGTAGGATTTATACC 880112 v vvi vvvv i ii i i i v L1M5_orf2#LIN 1654 CAGCAATATATAAAAAGGATAATACATCATGACCAAGTGGGGTTTATCCC 1703 chr6qtel1M 880113 AGGAATGCAGGGCTGGTTCAATATTAGGAAAACTATCAATATAATTGGCC 880162 i i i i v i v v i vi L1M5_orf2#LIN 1704 AGGAATGCAAGGTTGGTTTAACATTCGAAAATCAATCAATGTAATTCACC 1753 chr6qtel1M 880163 ATGTTAATA-ACCAAATTAACAAAAACCATATGATCATCTCAATAGATGC 880211 i i - vi -vi v i L1M5_orf2#LIN 1754 ATATTAACAGAATAAA-GGAGAAAAATCATATGATCATCTCAATAGATGC 1802 chr6qtel1M 880212 AGAAAAAGCATTTGATAAAATCCAACATCCATTCCTATTAAAAACACTTG 880261 i i i v iv v ii L1M5_orf2#LIN 1803 AGAAAAAGCATTTGACAAAATTCAACACCCATTCATGATAAAAACTCTCA 1852 chr6qtel1M 880262 AGAGTATAGGAATAAATGGACTTTTCCTTAAAATAATCAGCAGCATCTAT 880311 iv ivv i v ivvi i vv i v ivi i L1M5_orf2#LIN 1853 GCAAACTAGGAATAGAAGGGAACTTCCTCAACCTGATAAAGGGCATCTAC 1902 chr6qtel1M 880312 TTAAAACCATCAGTAAGCATCATATGTAATGGAGACAAACTGCAACCATT 880361 vv vv i? i iv v v ? v ?v v L1M5_orf2#LIN 1903 GAAAAACCTACAGCNAACATCATACTTAATGGTGAAANACTGAANGCTTT 1952 chr6qtel1M 880362 CCCAATAAGATCTGGAGTGAAACAAGGTTGCCCACTATCACCGTTACTAT 880411 vv v iii i v i i ? ii v L1M5_orf2#LIN 1953 CCCCCTAAGATCGGGAACAAGACAAGGATGTCCGCTNTCACCACTTCTAT 2002 chr6qtel1M 880412 TTAATATTGTATTAGAAACGCTAGCTATAGCAATAAGAGCTGAGAAAGAG 880461 i i i i iiiv i vv ivvv i i L1M5_orf2#LIN 2003 TCAACATTGTACTGGAGGTCCTAGCCAGTGCAATAAGGCAAGAAAAAGAA 2052 chr6qtel1M 880462 ATTAAAGGAATAAGAATAGGCAATGAGGAAGCCAAATTATCACTCTTTGC 880511 v v ii v v v i iiv i i ?i v i L1M5_orf2#LIN 2053 ATAAAAGGCATAAAGATTGGAAAGGAAGAAATAAAACTGTCNTTATTCGC 2102 chr6qtel1M 880512 CGATGACATGATGGTATACTTAGAGAACCCCAGAGATTCTGCTAAAAAGT 880561 v v ? v i i ? i v i v ? ii L1M5_orf2#LIN 2103 AGATGACATGATTGTNTACGTAGAAAATCCNAAAGAATCTACAAANAAAC 2152 chr6qtel1M 880562 TATTAGAAATAATCCACAACTTTAGCAAAGTTGCTGGTTATAAAATAAAC 880611 i v vviii v i i ? v i ii v i L1M5_orf2#LIN 2153 TACTAGAACTAATAAGTGAATTTAGCAAGGTCGCNGGATACAAGGTCAAT 2202 chr6qtel1M 880612 CCACATAAGTCATCAGCATTCTTATATATCACTAACAA--AATCCAACAG 880659 vi v i viv i ii ii vi -- ivi v i L1M5_orf2#LIN 2203 ATACAAAAATCAATTGTATTTCTATATACTAGCAACAAACAATTGGAAAA 2252 chr6qtel1M 880660 TCAGAGTTACAAAGAGAAATTCCATTTAAAGTAACTACTGATAATATAAA 880709 v i v --? i iv v v i i vv vi v i ? L1M5_orf2#LIN 2253 TGAAATTT--NAAAAACAATACCATTTACAATAGCATCAAAAAACATNAA 2300 chr6qtel1M 880710 ATATTTAGGAATCTATCTGCCAAGGGAAAAT---CAGAAACTTTATGAGC 880756 i vv iv --- ? --- ii v ? iivvv L1M5_orf2#LIN 2301 ATACTTAGGAATAAATCTAACAA---AANATGTGCAAGACCTNTACACTG 2347 chr6qtel1M 880757 AAAATTACAGACCACTTTTCACACAAATTAAGTCTGATCTAACCAATTGG 880806 i i v i vi v v v ivvv i vi v L1M5_orf2#LIN 2348 AAAACTACAAAACATTGCTGAGAGAAATTAAAGAAGACCTAAATAAATGG 2397 chr6qtel1M 880807 AAAAATATTAAATGCTCTTGGATAGGGCGAGCAAATATAATAAAGATGAC 880856 i i vvv i v v iv viv vi ? v L1M5_orf2#LIN 2398 AGAGATATACCATGTTCATGGATTGGAAGACTCAATATTGTNAAGATGTC 2447 chr6qtel1M 880857 AATATTACCTAAACTAATCTATTTATTTAGCGCTATACCAATCAGACTCC 880906 vi v i i i vv i ii v v i v L1M5_orf2#LIN 2448 AATTCTCCCCAAATTGATCTATAGATTCAATGCAATCCCAATCAAAATCC 2497 chr6qtel1M 880907 CAAAAAACTATTTTAATGACCTAGAAAAAATAACAACAAAGTTCATATGG 880956 iv iii v ivv vv v v iv i ivvi i i L1M5_orf2#LIN 2498 CAGCAGGTTTTTTTGTAGAAATTGACAAGCTGATTCTAAAATTTATATGG 2547 chr6qtel1M 880957 AAAAACAAAAGGTCAAGAAT-TTCAAGGGAATTAATGAAAAA-AAAATCA 881004 vi i ii ? -vi iiv i-v - i v L1M5_orf2#LIN 2548 AAATGCAAAGGACCNAGAATAGCCAAAACAATC-TTGAAAAAGAAGAACA 2596 chr6qtel1M 881005 AATGATGGTGG-CTTAGCTGTACCAGATCT-AAAATTATATTATAGAGCA 881052 - v v - - vv ? ? - i i - i v L1M5_orf2#LIN 2597 AA-GTTGGAGGACTTA-CACTACCNGATNTCAAGACT-TATTATAAAGCT 2643 chr6qtel1M 881053 GCAGTTACCAAAACTATTTGGTATTGGC-TAAGGAATAGATTAGTTGATC 881101 i v i i vi v - - iv i v L1M5_orf2#LIN 2644 ACAGTAATCAAGACAGTGTGGTATTGGCGTAAGG-ATAGACAAATAGATC 2692 chr6qtel1M 881102 AGTGGAATAGATTAG---GTTCAAGGGATAAAACAGTCA-ACAAATATAG 881147 i i v --- i - ii i v --- - v i L1M5_orf2#LIN 2693 AATGGAACAGAATAGAGAGTCC-AGAAATAGACC---CACACATATATGG 2738 chr6qtel1M 881148 CAACCTAGTCTTTGACAAA---CCCAAAG-ATCCCAGCTTTTGGGATAAG 881193 ?v ?i ii i ---v ? - vii ---- iv L1M5_orf2#LIN 2739 NCANTTGATTTTTGACAAAGGTGCCAANGCAATTCAG----TGGGGAAAG 2784 chr6qtel1M 881194 AACTTACTGTTTGATAAAAATTGCTGGGAAAATTGGAAACTAATATGGCA 881243 i ivvv v ii i viv i v v iiv v L1M5_orf2#LIN 2785 GATAGTCTTTTCAACAAATGGTGCTGGAACAATTGGATATCCATATGGAA 2834 chr6qtel1M 881244 GAAACTAGGCATTGATCCATACTTAACGCCGTACACCAAGATAAGGTCAA 881293 i v iii?v i i v i v i i v i v iv ? L1M5_orf2#LIN 2835 AAAAATGAANCTCGACCCCTACCTCACACCATACACAAAAATTAATTCNA 2884 chr6qtel1M 881294 AATGGGTTCAT-GACCTAGGCATAAAGAATGAAATTATTAATAAATTAGA 881342 i i- - iiii ii? i i v vvvvi L1M5_orf2#LIN 2885 GATGGA-TCATAGACCTAAATGTAAAAGNTAAAACTATAAAACTTCTAGA 2933 chr6qtel1M 881343 GG--AACATAGGATAGTTTACCTCTCAGACCTGTGGA-AGGGGAAGGTCT 881389 i -- v i-- i iivv vv ?- vi i i L1M5_orf2#LIN 2934 AGAAAACATAGGAGAA--TATCTTCGTGACCTTGGGNTAGGCAAAGATTT 2981 chr6qtel1M 881390 TTATGACCAAAGCAGAACTAGAGATCATTACTGATCACAAAATAGAAAAT 881439 i - i v iii v -- i -----i ?i i i v i L1M5_orf2#LIN 2982 CT-TAAACAGGACACAA--AAAG-----CACNAACCATAAAAGAAAAAAT 3023 chr6qtel1M 881440 -------TTCGATTATACCAAACTGAAAAGTTTTTGTACAAACAAAACTA 881482 ------- v i ?i i v v ii i iv ?vvv ivi L1M5_orf2#LIN 3024 TGATAAATTGGACTNCATCAAAATTAAAAACTTCTGCTCNTCAAAAGACA 3073 chr6qtel1M 881483 ATGCAGACAAGATTAGAAGGGAAGCAATAAACTGGGAAAATATTTTTACA 881532 vi ivi v i v i v v i i ? i v v i L1M5_orf2#LIN 3074 CCGTTAAGAAAATGAAAAGGCAAGCCACAGANTGGGAGAAAATATTTGCA 3123 chr6qtel1M 881533 GT-CAAAGGTTCTGATAAAGGCCTCATTTCCAAAATATATAGAGAATTAA 881581 i?- v vi- i v i v i i i -v L1M5_orf2#LIN 3124 ANACATATA-TCTGACAAAGGACTCGTATCCAGAATATATAAAGAACT-C 3171 chr6qtel1M 881582 CTCTAATTT-ATAAAAAATCAAGCCATTC--TCCAATTGAAAAATGGTCA 881628 vi ? i- ? -- v vv --i v? v L1M5_orf2#LIN 3172 CTACAANTCAATAANAAA--AAGACAAACAACCCAATANAAAAATGGGCA 3219 chr6qtel1M 881629 AAGGATATGAACAGACAATTCTCAGATGAAGAAATTGAAACTATTTCTAG 881678 i iv v v i v v ?v iviiivv i L1M5_orf2#LIN 3220 AAAGACTTGAACAGACACTTCACAAAAGAAGATATNCAAATGGCCAATAA 3269 chr6qtel1M 881679 TCATATGAAAAGATGCTCCAAGTCA 881703 v i v v? L1M5_orf2#LIN 3270 GCACATGAAAAGATGCTCAACNTCA 3294 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 39.65 CpG sites = 511, Kimura (unadjusted) = 40.19 Transitions / transversions = 1.14 (511/449) Gap_init rate = 0.03 (105 / 3256), avg. gap size = 1.30 (136 / 105) 1599 27.50 3.15 3.65 chr6qtel1M 881560 882193 (117807) L1ME5_3end#LINE/L1 7 637 (304) m_b321s551i13 13440 chr6qtel1M 881560 TCCAAAATATATAGAGAATTAACTCTAATTTATAAAAAATCAAGCCATT- 881608 i i i ii i vviv v iv i i -- v iv?- L1ME5_3end#LI 7 TCTAGAATATACAAGGAACTCCTGCAAATCAACAAGAAA--AAGACGGNA 54 chr6qtel1M 881609 -CTCCAATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGA 881657 - i v v i iv v L1ME5_3end#LI 55 ACCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGA 104 chr6qtel1M 881658 AGAAA-TTGAAA--CTATTTCTAGTCATATGAAAAGATGCTCCAAGTCAT 881704 i -ii -- --v v - i v v L1ME5_3end#LI 105 GGAAACCCGAAAGGCTA--ACAAG-CATATGAAGAGATGCTCAAACTCAT 151 chr6qtel1M 881705 TATTAATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACA 881754 v i vv i i vi L1ME5_3end#LI 152 TAGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACA 201 chr6qtel1M 881755 CCTGTCAGATTGGCTAAGATGACAGGAAA--AAATAATGATGATTGTTGG 881802 i i i v i --i i i--ii vii v L1ME5_3end#LI 202 CCTATTAGACTGGCAAAAAT--TAGAAAGCTGGATAATGCCAAGTGTTGG 249 chr6qtel1M 881803 AGGGGATGCGGGAAAACTGGGACATTGATGCATTGTTGGTGGAGTTGTGA 881852 v i i i ? iv i vi v i i iiv ii L1ME5_3end#LI 250 CGAGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAG 299 chr6qtel1M 881853 ACGAATCCAACCATTTTGGAGAGTAGTTTGGAACTA--TGCTCAAA--AA 881898 vii v i i i i i v v -- iv -- L1ME5_3end#LI 300 ACTGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTAA 349 chr6qtel1M 881899 GTTATCAAACTGTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGATT 881948 - --- --- v i i viii v vv L1ME5_3end#LI 350 G-TAT---AC---GCATACCCTATGACCCAGCAATTCCGCTCCTGGGTAT 392 chr6qtel1M 881949 ATATTCCAAAGAGATTATAAAGAAGG----GAAAGGGACCTGTATGTGCA 881994 i i v v viv ----v i ---- i i L1ME5_3end#LI 393 ATATCCCAAAGAAATTCTCACACAGGTCCATAAGGGGAC----ATGTACG 438 chr6qtel1M 881995 CGAATGTTTGTGGCAGCCCTTTTTGTAGTGGCTAGAAACTGGAAACTGAA 882044 v i ii v vi v i vi i ii ii vivv L1ME5_3end#LI 439 AGGATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACC 488 chr6qtel1M 882045 TGGATGTCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATATGAAAA 882094 i v v i v iii v iv v v L1ME5_3end#LI 489 TGGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACA 538 chr6qtel1M 882095 TTATGGAATATTACTGT-TCTGTAAGAAATGACCAACAGGATGATTTCAG 882143 ii i i - i-v v v iii vi vi -- v v L1ME5_3end#LI 539 CCATGGAGTACTA-TGCAGCAGTTAGAAGCAACGGACTAGATG--TACAC 585 chr6qtel1M 882144 AAAG--GCCTGGAGAGA-CTTACACGAAC-TGATGCTGAGTGAAATGAGC 882189 v --i v vi - v -- - ii vi i L1ME5_3end#LI 586 ATAGCAACATGGATGGATCTTAAA--AACATAGTGCTGAGTGAAAAAAGT 633 chr6qtel1M 882190 AGGA 882193 i L1ME5_3end#LI 634 AAGA 637 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 34.20 CpG sites = 99, Kimura (unadjusted) = 35.27 Transitions / transversions = 1.43 (99/69) Gap_init rate = 0.06 (35 / 633), avg. gap size = 1.23 (43 / 35) 1633 27.65 0.36 1.66 chr6qtel1M 881560 882107 (117893) L1ME3G_3end#LINE/L1 7 547 (377) m_b321s551i12 13440 chr6qtel1M 881560 TCCAAAATATATAGAGAATTAACTCTAATTTATAAAAAATCAAGCCATTC 881609 i i i vviv v iv i -- v --v L1ME3G_3end#L 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAA--AAGACA--A 52 chr6qtel1M 881610 TCCAATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGAAG 881659 i v v i v v i L1ME3G_3end#L 53 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chr6qtel1M 881660 AAATTGAAACTATTTCTAGTCATATGAAAAGATGCTCCAAGTCATTATTA 881709 vv iviiivv iv v vv i v L1ME3G_3end#L 103 AAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTA 152 chr6qtel1M 881710 ATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACACCTGT 881759 i i vv i i viv ii L1ME3G_3end#L 153 ATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCAT 202 chr6qtel1M 881760 CAGATTGGCTAAGATGACAGGAAAAAATAATGATGATTGTTGGAGGGGAT 881809 v i vvv iii?vvi ivi? v v i i L1ME3G_3end#L 203 CAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGT 252 chr6qtel1M 881810 GCGGGAAAACTGGGACATTGATGCATTGTTGGTGGAGTTGTGAACGAATC 881859 i i v v vi v i i i iiv i ivii v L1ME3G_3end#L 253 GTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTA 302 chr6qtel1M 881860 CAACCATTTTGGAGAGTAGTTTGGAACTATGCTCAAAAAGTTATCAAACT 881909 i ? i i i v v - vvv i -- i v L1ME3G_3end#L 303 CAGCCNTTTTGGAGGGCAATTTGGCAGTAT-CTATTAAAAT--TTAAAAT 349 chr6qtel1M 881910 GTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGATTATATTCCAAAG 881959 i i i vii v ? ?v v i i ? L1ME3G_3end#L 350 GCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAG 399 chr6qtel1M 881960 AGATTAT-AAAGAAG-GGAAAGGGACCTGTATGTGCACGAATGTTTGTGG 882007 i vv -iv v v - v v i --? i i v i ii v L1ME3G_3end#L 400 AAATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTCATTG 447 chr6qtel1M 882008 CAGCCCTTTTTGTAGTGGCTAGAAACTGGAAACTGAATGGATGTCCATCA 882057 vi v i i v i i vivv ii L1ME3G_3end#L 448 CAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCA 497 chr6qtel1M 882058 GTTGGAGAATGGCTGAATAAATTGTGGTATATGAAAATTATGGAATATTA 882107 i v i i i i vv v i i L1ME3G_3end#L 498 ATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACTA 547 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 35.03 CpG sites = 79, Kimura (unadjusted) = 35.62 Transitions / transversions = 1.13 (79/70) Gap_init rate = 0.02 (11 / 547), avg. gap size = 1.00 (11 / 11) 17 5.00 0.00 0.00 chr6qtel1M 882546 882566 (117434) (G)n#Simple_repeat 1 21 (0) m_b321s252i11 13441 chr6qtel1M 882546 GGGGAGGGGGGGGGGGGGGGG 882566 i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGG 21 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 278 32.45 17.75 1.53 chr6qtel1M 884071 884239 (115761) MIR1_Amn#SINE/MIR 6 201 (29) m_b321s601i23 13442 chr6qtel1M 884071 AGATAGCATGGTATAATGGGTAGAATGCCAAAT-----CCCAGGAGGATC 884115 ii ii v i i iii iii i----- i i - i MIR1_Amn#SINE 6 AGGCAGTGTGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGAG-ACC 54 chr6qtel1M 884116 TGGGTTCAAATCTCATTTCTAACA----TCAGATACATAATTGTGGGCAA 884161 ? ? i ivi iv ----i ? v i?i i iiv MIR1_Amn#SINE 55 TGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAA 104 chr6qtel1M 884162 ATCATT------------------ATTTCCTCATGTATAGAATGAATGGA 884193 i i ------------------i v i i i-- MIR1_Amn#SINE 105 GTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGG--GGA 152 chr6qtel1M 884194 T-TTGAC-TTAATGGCCTTTA-AGATTCCTTCTAGATCTACACAAGAAA 884239 -v i-i i ivv i- i v v iv vv v MIR1_Amn#SINE 153 TAATGATACTGACCTCCTTTGTAAAGTGCTTTGAGATCTACTGATGAAA 201 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 45.25 CpG sites = 39, Kimura (unadjusted) = 47.79 Transitions / transversions = 2.60 (39/15) Gap_init rate = 0.05 (9 / 168), avg. gap size = 3.67 (33 / 9) 345 30.86 17.74 0.69 chr6qtel1M 884106 884229 (115771) MIR3#SINE/MIR 41 185 (23) m_b321s601i24 13442 chr6qtel1M 884106 CAGGAGGATCTGGGTTCAAATCTCATTTCTAACATCA----GATACATAA 884151 - i v i i ivi iv ii ---- v iii i MIR3#SINE/MIR 41 CAGGAG-ACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGA 89 chr6qtel1M 884152 TTGTGGGCAAATCATT------------------ATTTCCTCATGTATAG 884183 iiv i i ------------------i v i i MIR3#SINE/MIR 90 CCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAA 139 chr6qtel1M 884184 AATGAATGGATTTGACTTAATGGCCTTTAAGATTCCTTCTAGATCT 884229 iv i v vi ii i i i i v MIR3#SINE/MIR 140 AATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCT 185 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 41.34 CpG sites = 28, Kimura (unadjusted) = 42.89 Transitions / transversions = 2.80 (28/10) Gap_init rate = 0.02 (3 / 123), avg. gap size = 7.67 (23 / 3) 32 20.23 2.53 0.00 chr6qtel1M 884242 884320 (115680) (TATTATA)n#Simple_repeat 1 81 (0) m_b321s252i12 13443 chr6qtel1M 884242 TATTCTAAATTATATTATATACATTATATTTTATATA-TATATTATATAC 884290 v v vv i v - vv i (TATTATA)n#Si 1 TATTATATATTATATATTATATATTATATATTATATATTATATATTATAT 50 chr6qtel1M 884291 ATTATACAATATATATATTATA-TACATATT 884320 i v vv - i (TATTATA)n#Si 51 ATTATATATTATATATTATATATTATATATT 81 Matrix = Unknown Transitions / transversions = 0.40 (4/10) Gap_init rate = 0.03 (2 / 78), avg. gap size = 1.00 (2 / 2) 235 34.24 6.80 5.95 chr6qtel1M 884321 884820 (115180) L1ME4a_3end#LINE/L1 56 559 (312) m_b321s551i14 13444 chr6qtel1M 884321 CCACAATAAGCAAAGTGGTCAGTGGGCATGAACA----ATTCCCAAAGAA 884366 v - v i v iv i ---- v ii L1ME4a_3end#L 56 CCCCAATA-GAAAAATGGGCAAAGGACATGAACAGACAATTCACAAAAGA 104 chr6qtel1M 884367 AGCATTGCAAA---CTAATTTTTTTTAATCCTACAAAAACATATTCCAAA 884413 v v i --- i ------- v v ii ? i - v L1ME4a_3end#L 105 AGAAATACAAATGGCCAAT-------AAACATATGAAAANATGTTC-AAC 146 chr6qtel1M 884414 TCCA-----AATAAGAGAAATTCAAAGATAAGCAACTCTAAGGCTTCACT 884458 ii ----- v i v vvv i vv i iivi i L1ME4a_3end#L 147 CTCACTAGTAATCAAAGAAATGCAAATTAAAACAACAATGAGATACCATT 196 chr6qtel1M 884459 TTACACCCTACAAATTGGCAATGATGGTCTAAAAACAACTTTATTAGTTA 884508 v ivv v --- i i------- ii v L1ME4a_3end#L 197 TTTCACCTATCAAATTGGCAAAGA---TTTAAAAG-------ATTGATAA 236 chr6qtel1M 884509 CATC---------AGAAATAATGGAAAGAAGGGCACGTGGATTCACT--T 884547 i i ---------v iivvi ?i i v vivv v -- L1ME4a_3end#L 237 TACCCAGTGTTGGCGAGGGTGTGGNGAAACGGGCACTCTCATACACTGCT 286 chr6qtel1M 884548 GGTAGAATTATGAATTATCGCATCTATTTTGGACCTCCATTTATAACTAT 884597 i i v i i ivii v iv i vvv v ivv v L1ME4a_3end#L 287 GGTGGGAGTGTAAATTGGTACAACCTTTCTGGAGGGCAATTTGGCAATAT 336 chr6qtel1M 884598 G-----AAAGACTCAAGTTAATCTC----CTCTTTGATTCAGGATTCCCA 884638 ----- v i i-- v ?---- i ii v v i L1ME4a_3end#L 337 GTATCAAAAGCCTTAAA--AATGTNCATACCCTTTGACCCAGTAATTCCA 384 chr6qtel1M 884639 CTACTAACCATATGTCCCACAAAGA-GGTCAAAG-TTTGAAGTAAGGGCC 884686 v ivv v i i vii i -ii i - v ? vv ivii L1ME4a_3end#L 385 CTTCTAGGAATTTATCCTAAGGAAATAATCAGAGATGTGNACAAAGATTT 434 chr6qtel1M 884687 AAAATGTAGCATAATATTTCTAGTGGTATTCTTTCTTGCAGCAAACAACT 884736 --- vv vi i iv v ii i v v vii i v i L1ME4a_3end#L 435 ---ATGTACAAGGATGTTCATCGCAGCATTATTTATAATAGCGAAAAATT 481 chr6qtel1M 884737 AGATGTAGCATGGATGCTGAAAAAATGGAAAATGGCTAAAAAATTTTAAT 884786 i vii i v ii iiv v vv ii ? i ----- v L1ME4a_3end#L 482 GGAAACAACCTAAATGTCCAACAATAGGGGANTGGTTAAA-----TAAAT 526 chr6qtel1M 884787 TATAATTATATGAATGTAATAGAATGTTGTGCAG 884820 ii- i vv i? i i i L1ME4a_3end#L 527 TATGG-TACATCCATANAATGGAATATTATGCAG 559 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 47.49 CpG sites = 88, Kimura (unadjusted) = 47.91 Transitions / transversions = 1.21 (88/73) Gap_init rate = 0.08 (39 / 499), avg. gap size = 1.64 (64 / 39) 758 32.13 4.29 2.37 chr6qtel1M 886794 887166 (112834) L1ME3Cz_3end#LINE/L1 169 548 (449) m_b321s551i15 13445 chr6qtel1M 886794 TTAAAATTGTAAC-AGA-ACCACTACATACTTCTCAGGTTGACTAAGATG 886841 i?ii i- - i v i iiv i i v i v L1ME3Cz_3end# 169 TTAAAACNACAATGAGATACCATTTCACACCCATCAGATTGGCAAAAATT 218 chr6qtel1M 886842 ACAGGAAAAG----ATAATGATGAATATTGGAGGGGACATGGGAAAACTG 886887 ----v ---- i ivii i i v i ii ii v L1ME3Cz_3end# 219 ----TAAAAGTCTGACAATACCAAGTGTTGGCGAGGATGTGGAGAAACGG 264 chr6qtel1M 886888 GGACACTAATACATTGTTGGTGGAGTTGTGAACTGATCCAACCATTCTGG 886937 i v v i i iiv i i i v i i L1ME3Cz_3end# 265 GAACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTACAACCACTTTGG 314 chr6qtel1M 886938 AGAACAATTTGGAACCATGCGCTAAGGGCTATCAAATTGTGCATACCAT- 886986 i v vi viiv i v--- v iv i v - L1ME3Cz_3end# 315 AGAGCAATTTGGCAATATCTAGTAAAGT---TGAAGATGCGCATACCCTA 361 chr6qtel1M 886987 TGATCCATCAGTGTCCTTTCTGGGTTCGTATCCCAAAGAGAC-CATAAAA 887035 i i v i vi vi i vii i i i i - viiv v L1ME3Cz_3end# 362 CGACCCAGCAATTCCACTTCTAGGTATATACCCTAGAGAAACTCTCGCAC 411 chr6qtel1M 887036 AAG-GGAAAAGGACCCACATGTGCAAAAATGTTTGTGTCAGCCTTTTTTA 887084 v - v v --v i ii ii vv v v i L1ME3Cz_3end# 412 ATGTGCACAAGGA--GACATGTACAAGGATGTTCATTGCAGCATTGTTTG 459 chr6qtel1M 887085 TAGTGGCAAAAAACTGGG-------TGGCTGCCCATCAGTTGGGGAATGG 887127 i i i i i------- iiv i i v L1ME3Cz_3end# 460 TAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCAATAGGGGAATGG 509 chr6qtel1M 887128 CTGAATAAGTTATGATACATGAATGTTATGGAATATTAT 887166 v i i i i i vv iiv i L1ME3Cz_3end# 510 ATAAATAAATTGTGGTATATTCATACAATGGAATACTAT 548 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 42.20 CpG sites = 76, Kimura (unadjusted) = 44.33 Transitions / transversions = 1.85 (76/41) Gap_init rate = 0.04 (16 / 372), avg. gap size = 1.56 (25 / 16) 455 33.66 5.49 3.68 chr6qtel1M 886810 887210 (112790) L1MC1_3end#LINE/L1 191 598 (482) m_b321s551i16 13445 chr6qtel1M 886810 ACCACTACATACTTCTCAGGTTGACTAAGATGACAGGAAAA--GATAATG 886857 i i v i iv i i i -- vi v -- i ii L1MC1_3end#LI 191 ACCACTACACACCTATTAGAATGGCCAAAAT--CCAGAACACTGACAACA 238 chr6qtel1M 886858 ATGAATATTGGAGGGGACATGGGAAAACTGGGACACTAATACATTGTTGG 886907 vii ii v i ii iiv v i v v v i L1MC1_3end#LI 239 CCAAATGCTGGCGAGGATGTGGAGCAACAGGAACTCTCATTCATTGCTGG 288 chr6qtel1M 886908 TGGAGTTGTGAACTGATCCAACCATTCTGGAGAACAATTTGGAACCATGC 886957 iiv ii v i v i i i ii i -- vi vi L1MC1_3end#LI 289 TGGGAATGCAAAATGGTACAGCCACTTTGGAAGACAGTTTGG--CAGTTT 336 chr6qtel1M 886958 GCTA-AGGGCTATCAAATTGTGCATACCAT-TGATCCATCAGTGTCCTTT 887005 vi - iii -- vv iiv v -i v i vv vi i L1MC1_3end#LI 337 CTTACAAAACTA--AACATACTCTTACCATACGATCCAGCAATCGCGCTC 384 chr6qtel1M 887006 CTGGGTTCGTATCCCAAAGAGACCATAAAAA---AGG----GAAAAGGAC 887048 v viv i v i ---v i --- v ----v v ii L1MC1_3end#LI 385 CTTGGTATTTACCCAAAGGAG---TTGAAAACTTATGTCCACACAAAAAC 431 chr6qtel1M 887049 CCACATGTGCAAAAATGTTTGTGTCAGCCTTTTTTATAGTGGCAAAAAAC 887098 ---- ii vii i iv i v i i v v vi L1MC1_3end#LI 432 C----TGCACACGGATGTTTATAGCAGCTTTATTCATAATTGCCAAAACT 477 chr6qtel1M 887099 TGGGTG-------GCTGCCCATCAGTTGGGGAATGGCTGAATAAGTTATG 887141 iv ------- v i v v v v i ii i L1MC1_3end#LI 478 TGGAAGCAACCAAGATGTCCTTCAGTAGGTGAATGGATAAATAAACTGTG 527 chr6qtel1M 887142 ATACATGAATGTTATGGAATATTATTGTTCTCT---AAGAAATGATC-AG 887187 i vv viiv vvv v --- v - v L1MC1_3end#LI 528 GTACATCCAGACAATGGAATATTATTCAGCGCTAAAAAGAAATGAGCTAT 577 chr6qtel1M 887188 CAAGATTATCAGAAAGACCTGAA 887210 -ii v - v i L1MC1_3end#LI 578 CAAG-CCATGA-AAAGACATGGA 598 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 45.09 CpG sites = 73, Kimura (unadjusted) = 46.07 Transitions / transversions = 1.28 (73/57) Gap_init rate = 0.06 (23 / 400), avg. gap size = 1.61 (37 / 23) 903 29.94 3.16 0.62 chr6qtel1M 886851 887166 (112834) L1ME4c_3end#LINE/L1 232 555 (275) m_b321s551i17 13445 chr6qtel1M 886851 GATAATGATGAATATTGGAGGGGACATGGGAAAACTGGGACACTAATACA 886900 iviv ii v i ?iii vi v ? v L1ME4c_3end#L 232 GATAATACCCAATGCTGGCGAGGNTGCGGTGAAACTGGTACNCTCATACA 281 chr6qtel1M 886901 TTGTTGGTGGAGTTGTGAACTGATCCAACCATTCTGGAGAACAATTTGGA 886950 i vi? i i i v v i i i v L1ME4c_3end#L 282 TTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGGC 331 chr6qtel1M 886951 ACCATGCGCTAAGGGCTATCAAATTGTGCATACCA-TTGATCCATCAGTG 886999 vi i iiii i i v v v v- i vi i v L1ME4c_3end#L 332 AATACGTATCAAGAGCCATAAAAATGTTCATACCCTTTGACCCAGTAATT 381 chr6qtel1M 887000 TCCTTTCTGGGTTCGTATCCCAAAGAGACCAT--AAAAAAGGGAAAAGGA 887047 i vi vviv i i i iv -- i i i - L1ME4c_3end#L 382 CCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAAGAAGGAAAAAG- 430 chr6qtel1M 887048 CCCACATGTGCAAAAATGTTTGTGTCAGCCTTTTTTATAGTGGCAAAAAA 887097 - i i ii i i ii vv v v i i i L1ME4c_3end#L 431 -CTATATGCACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAA 479 chr6qtel1M 887098 CTGGG-------TGGCTGCCCATCAGTTGGGGAATGGCTGAATAAGTTAT 887140 i i------- iiv i v i v i i i i L1ME4c_3end#L 480 TTGGAAACAACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTAT 529 chr6qtel1M 887141 GATACATGAATGTTATGGAATATTAT 887166 i v? iviv L1ME4c_3end#L 530 GGTACATCNACTCGATGGAATATTAT 555 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 37.92 CpG sites = 62, Kimura (unadjusted) = 40.76 Transitions / transversions = 1.94 (62/32) Gap_init rate = 0.02 (5 / 315), avg. gap size = 2.40 (12 / 5) 293 37.12 1.56 3.17 chr6qtel1M 887870 887997 (112003) L2a_3end#LINE/L2 386 511 (6) m_b321s601i25 13446 chr6qtel1M 887870 TTCTCTAATTATAATGTAAATTCCTTGAGGAAATTCTGG--TTTTGTGCC 887917 i i iv i v ii v iv v--- -- viv L2a_3end#LINE 386 TCCCCCCACTAGAATGTAAGCTCCATGAGGGCAG---GGACTTTTGTCTG 432 chr6qtel1M 887918 CTTCTCCCATTTTTTATATCCTCAACACTTAACACAATTCCTAATACATA 887967 i ivii i vi -i i i i i iv i v iii L2a_3end#LINE 433 TTTTGTTCACTGCT-GTATCCCCAGCGCCTAGAACAGTGCCTGGCACATA 481 chr6qtel1M 887968 ATAAGAAGTTGATAAATGCTTGATGAGTGA 887997 i i viv ii ii v i L2a_3end#LINE 482 GTAGGCGCTCAATAAATATTTGTTGAATGA 511 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 52.21 CpG sites = 32, Kimura (unadjusted) = 55.98 Transitions / transversions = 2.29 (32/14) Gap_init rate = 0.04 (5 / 127), avg. gap size = 1.20 (6 / 5) 371 33.51 3.70 3.16 chr6qtel1M 888047 888613 (111387) L1M5_orf2#LINE/L1 1786 2355 (939) m_b321s551i18 13447 chr6qtel1M 888047 ATTATTTCTACATATCCAGATAAAGCCATTT-ACAAAATGAAACATTCAA 888095 i i v i v v v - - vv ii v L1M5_orf2#LIN 1786 ATCATCTCAATAGATGCAGAAAAAGC-ATTTGACAAAATTCAACACCCAT 1834 chr6qtel1M 888096 T-ATAA--AAAACTTTT--TAAA-TAGACTTGGAAGGGCTCTTATTTGAT 888139 - i -- i i--i - ivv i vv vi ii i L1M5_orf2#LIN 1835 TCATGATAAAAACTCTCAGCAAACTAGGAATAGAAGGGAACTTCCTCAAC 1884 chr6qtel1M 888140 ACAATCAAAAGAATATACCTAAAATCAAGAGCCAGAATTATTTGCAACAC 888189 vii v ii v v vv i v v ? iv i vivi iiv L1M5_orf2#LIN 1885 CTGATAAAGGGCATCTACGAAAAACCTACAGCNAACATCATACTTAATGG 1934 chr6qtel1M 888190 TGGACAATACTAGAATCTGTACAA-TACTATAAAGGGTAAGACTAGAATG 888238 i -- ? ii ?v v v vv- vv vii iii v i L1M5_orf2#LIN 1935 TGAA--ANACTGAANGCTTTCCCCCTAAGATCGGGAACAAGACAAGGATG 1982 chr6qtel1M 888239 CCTCCTCTTTCCTTATCATTAGTTGACA--GTACTGTAAAAATGCCAGCT 888286 -- v ? vii iivi v ii -- --i ii v i i L1M5_orf2#LIN 1983 --TCCGCTNTCACCACTTCTATTCAACATTGTACTG--GAGGTCCTAGCC 2028 chr6qtel1M 888287 ATCAAAATAAGACAATAGAAGAATACAAAAAGCATAAATATAG--ATGGG 888334 viiv i v i ii v i i v v -- v i L1M5_orf2#LIN 2029 AGTGCAATAAGGCAAGAAAAAGAAATAAAAGGCATAAAGATTGGAAAGGA 2078 chr6qtel1M 888335 GGAGACAAAGCTATCTTGGCTTGCACATGAAATAACAGAATATATCGAAA 888384 i i i i i ? vii i v v i iv v? ii v L1M5_orf2#LIN 2079 AGAAATAAAACTGTCNTTATTCGCAGATGACATGATTGTNTACGTAGAAA 2128 chr6qtel1M 888385 --CATAGAAAATCAACAAAGAAACTAATTGAGATGATTAATAACATGTTG 888432 -- v? i i v ? v -- -- i --- vi L1M5_orf2#LIN 2129 ATCCNAAAGAATCTACAAANAAACTACT--AGA--ACTAATAA---GTGA 2171 chr6qtel1M 888433 ATAATGATAAAGTTGCAGGATATAAAATCATTCCACAAAAAAGTCA---G 888479 v- iii i i ? i ii v vi -- --- L1M5_orf2#LIN 2172 ATT-TAGCAAGGTCGCNGGATACAAGGTCAATATACAAAAA--TCAATTG 2218 chr6qtel1M 888480 CATTTCTCTGCATTACTTTTAAAAAGTCAAAAAAT--AATTATATCAAAA 888527 i v ii i vivvi v i iii -- v? vv v L1M5_orf2#LIN 2219 TATTTCTATATACTAGCAACAAACAATTGGAAAATGAAATTTNAAAAACA 2268 chr6qtel1M 888528 ATTCCATTCAAAAAAATTATAAAAATACATAAAATACCTGGGAGCTAACC 888577 v i v v i-i v v ? i i iiv i L1M5_orf2#LIN 2269 ATACCATTTACAATAG-CATCAAAAAACATNAAATACTTAGGAATAAATC 2317 chr6qtel1M 888578 CATCAAGATTGAGGCAAAATTTTT-CA-TGAATATTAC 888613 i v i ?vviv i ii ? - - v i L1M5_orf2#LIN 2318 TAACAAAANATGTGCAAGACCTNTACACTGAAAACTAC 2355 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 46.06 CpG sites = 106, Kimura (unadjusted) = 47.54 Transitions / transversions = 1.36 (106/78) Gap_init rate = 0.05 (31 / 566), avg. gap size = 1.26 (39 / 31) 368 30.44 3.45 4.65 chr6qtel1M 888229 888576 (111424) L1M1_orf2#LINE/L1 1973 2316 (978) m_b322s551i5 13447 chr6qtel1M 888229 GACTAGAATGCCTCCTCTTTCCTTATCATTAGTTGACA--GTACTGTAAA 888276 v i -- v vii iii v ii -- --i L1M1_orf2#LIN 1973 GACAAGGATGCC--CACTTTCACCACTGTTATTCAACATAGTACTG--GA 2018 chr6qtel1M 888277 AATGCCAGCTATCAAAATAAGACAATAGAAGAATACAAAAAGCAT--AAA 888324 i v i vviv v v ii v i ii -- L1M1_orf2#LIN 2019 AGTCCTAGCTAGAGCAATCAGACAAGAGAAAGAAATAAAGGGCATCCAAA 2068 chr6qtel1M 888325 TATAGATGGG--GGAGACAAAGCTATCTTGGCTTGCACATGAAATAACAG 888372 - i vi -- i v -i i v i v v i ivv L1M1_orf2#LIN 2069 T-TGGAAAGGAAGAAGTCAAA-TTATCCTTGTTTGCAGATGATATGATCT 2116 chr6qtel1M 888373 AATATATCGAAA--CATAGAAAATCAACAAAGAAACTAATTGAGATGATT 888420 v v v -- v i i v v ? i v v iv v L1M1_orf2#LIN 2117 TATATTTGGAAAAACCTAAAGACTCCACNAAAAAACTATTAGAACTGATA 2166 chr6qtel1M 888421 AATAACATGTTGATAATGATAAAGTTGCAGGATATAAAATCATTCCACAA 888470 i ---i v -----i i vivi L1M1_orf2#LIN 2167 AACAA---ATTCA-----GTAAAGTTGCAGGATACAAAATCAACATACAA 2208 chr6qtel1M 888471 AAA--AGTCAGCATTTCTCTGCATTACTTTTAAAAAGTC--AAAAAATAA 888516 -- - v iiiii vivv i v i -- iv L1M1_orf2#LIN 2209 AAATCAGT-AGCATTTCTATATGCCAACAGTGAACAATCTGAAAAAGAAA 2257 chr6qtel1M 888517 TTATATCAAAAATTCCATTCAAAAAAATTATAAAAATACATAAAATACCT 888566 i v vv iv i i v v iii i v - v v L1M1_orf2#LIN 2258 TCAAAAAAGTAATCCCATTTACAATAGCCACAAATA-AAATTAAATACCT 2306 chr6qtel1M 888567 GGGAGCTAAC 888576 i ii L1M1_orf2#LIN 2307 AGGAATTAAC 2316 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.01 CpG sites = 55, Kimura (unadjusted) = 40.01 Transitions / transversions = 1.20 (55/46) Gap_init rate = 0.06 (22 / 347), avg. gap size = 1.27 (28 / 22) 312 38.40 1.60 0.00 chr6qtel1M 893461 893585 (106415) C MIRc#SINE/MIR (140) 128 2 m_b322s601i1 13448 chr6qtel1M 893461 ACTGGGGCATTAAGAGTTTAAATGGTTTCTTCAGGGTCACAAAACCAGTA 893510 i vivi v i ii vii i v i i C MIRc#SINE/MIR 128 ACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTA 79 chr6qtel1M 893511 TGTATCATA--CTGAACTTCAACCCAGGTGGTTCCAAGCCCATAGCCAGA 893558 v iv v -- v i iv vv i ii vi viv v C MIRc#SINE/MIR 78 AGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGT 29 chr6qtel1M 893559 CTTCTATTCACCATGTCAAATTGTTTC 893585 vi v i iiiii v i ii C MIRc#SINE/MIR 28 GCTCTTTCCACTGCACCACACTGCCTC 2 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 55.08 CpG sites = 29, Kimura (unadjusted) = 56.92 Transitions / transversions = 1.53 (29/19) Gap_init rate = 0.01 (1 / 124), avg. gap size = 2.00 (2 / 1) 337 21.93 7.14 2.27 chr6qtel1M 893865 893948 (106052) MIRc#SINE/MIR 39 126 (142) m_b322s601i2 13449 chr6qtel1M 893865 GGGGCAGAAAGACCTGAGTTCAAATCCA---TTTCACACTTAATAGCTAT 893911 i v i i i i v--- i vv v i MIRc#SINE/MIR 39 GAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGT 88 chr6qtel1M 893912 GTGAATCTGGCCAAGTCACTTAATC---CTAATTGCCTCA 893948 vii v i --- i -- MIRc#SINE/MIR 89 GTGACCTTGGGCAAGTCACTTAACCTCTCTGA--GCCTCA 126 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 24.83 CpG sites = 11, Kimura (unadjusted) = 26.50 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.05 (4 / 83), avg. gap size = 2.00 (8 / 4) 19 12.06 0.00 0.00 chr6qtel1M 894408 894435 (105565) (A)n#Simple_repeat 1 28 (0) m_b322s252i0 13450 chr6qtel1M 894408 AAAAAAAAAAAAAAAAAAAGAGGAAAAA 894435 i ii (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA 28 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 509 29.51 5.56 2.45 chr6qtel1M 894861 895058 (104942) C L3#LINE/CR1 (464) 3635 3432 m_b322s601i3 13451 chr6qtel1M 894861 CAATGTTCTTCTTATAAT------CTTATAAATAAA---GATACTC-ATA 894900 i i v ------ ii v v i ---i - v C L3#LINE/CR1 3635 CAATGTCCCTCTTAAAATGTGGCGCCCAGAACTGAACGCAATACTCCAGA 3586 chr6qtel1M 894901 TCTGAACTCAACACTACAAAGCAGAGTACAATGGGACCATTGCTTCTCTC 894950 v iv -i ---- iv ii i i i i i C L3#LINE/CR1 3585 TGTGGTCT-GAC----CAGCGCAGAGTACAGCGGGACTATTACCTCCCTT 3541 chr6qtel1M 894951 ATTGTGCTCACTTTTTCTTCCCCACTTGAGCCAAAG-TCATATTAGCTTT 894999 i? v vv v vii iivii v vv v - iii C L3#LINE/CR1 3540 GNTCTGGACACTATACTTCTATTAATGCAGCCTAAGATTGCATTAGCTTT 3491 chr6qtel1M 895000 CTTGGTATCCATATCACACTGTGGACTCATATTGAACTTTCAGTCCAATA 895049 i i v i v i i v i v v C L3#LINE/CR1 3490 TTTGGCAGCCACATCACACTGTTGGCTCATATTGAGCTTGCGGTCAACTA 3441 chr6qtel1M 895050 AATCCTCCA 895058 v i i C L3#LINE/CR1 3440 AAACCCCTA 3432 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.21 CpG sites = 34, Kimura (unadjusted) = 38.97 Transitions / transversions = 1.48 (34/23) Gap_init rate = 0.05 (9 / 197), avg. gap size = 1.78 (16 / 9) 770 31.35 5.21 1.18 chr6qtel1M 895190 895515 (104485) C L3#LINE/CR1 (868) 3231 2893 m_b322s601i4 13451 chr6qtel1M 895190 TTTGTTTTATTTGTAAATATGATTAGCATGTCGTGCATGTCTTTACCCAT 895239 v i i i v v i v vi i i v C L3#LINE/CR1 3231 TTTGTGTCATCTGCAAATTTGATAAGCATGCCTTCTATGTCTTCATCCAA 3182 chr6qtel1M 895240 GAAAATGATCAAAATGTTAAATAGCTTTGGTTCAAGGAGAAATGACCAGA 895289 vv v v i i vviv vi v i - v v v C L3#LINE/CR1 3181 GTCATTGATAAAAATGTTGAACAGGACAGGGCCAAGGACAGA-GCCCTGT 3133 chr6qtel1M 895290 GG-AGTTCACTGAAGAGCTCTCTCCAAGCTAAGATTAATCCATTAATTAC 895338 - vvi ii v i i i i v ii i v C L3#LINE/CR1 3132 GGCACGCCACTAGAGACCTCCCTCCAGGTTGACATCGATCCATTAATCAA 3083 chr6qtel1M 895339 TATGTTTTATGTTCCATTAATGTTCCAT--GTTATG-TTTCACCTAACTA 895385 i iv iv --- vivi v i-- i i -v i i C L3#LINE/CR1 3082 CACCTTTTGGGT---ATAGTCGTTCAACCAGCTACGAATCCACCTAACTG 3036 chr6qtel1M 895386 TATTTTAATCTAACACAAA--TCTTTAT-------AAAAGGATAACA--A 895424 i v v i i v v -- ii ------- v v -- C L3#LINE/CR1 3035 TACTATCATCCAGCCCATATTTCTCCATCTTGTCCACAAGGATATCATGA 2986 chr6qtel1M 895425 GAGCCTTTGT-AAATTATTTACCAACACCCAGGTAAATAATATTTACAGC 895473 v - vvi i ii v i i v iv? i i i C L3#LINE/CR1 2985 GAGACTTTGTCAAATGCCTTGCTGAAATCCAGATACACTNTGTCTACGGC 2936 chr6qtel1M 895474 ATTAATCTGAGTTATCAATCTAATAA-GCTGTCAACGAATGAA 895515 vvi vi i i i -v i vi v C L3#LINE/CR1 2935 ATTCCCCTGATCTACCAGTCTAGTAACCCTATCAAAAAAGGAA 2893 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.45 CpG sites = 54, Kimura (unadjusted) = 41.63 Transitions / transversions = 1.15 (54/47) Gap_init rate = 0.04 (12 / 325), avg. gap size = 1.75 (21 / 12) 213 28.32 0.00 1.89 chr6qtel1M 895605 895658 (104342) L2d2_3end#LINE/L2 457 509 (46) m_b322s601i5 13452 chr6qtel1M 895605 CAGAGAGCTCATTTTATACTCCTTCTGTATCCCTTACAGTACCTTGCAAA 895654 i v vii i i - ii ii v v L2d2_3end#LIN 457 CAGGGACCATGTCTTATACTTCTT-TGTATCCCCCACAGCGCCTAGCACA 505 chr6qtel1M 895655 ATAC 895658 i i L2d2_3end#LIN 506 GTGC 509 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.24 CpG sites = 11, Kimura (unadjusted) = 37.81 Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.02 (1 / 53), avg. gap size = 1.00 (1 / 1) 12 21.70 0.00 0.00 chr6qtel1M 896014 896045 (103955) (AAAGA)n#Simple_repeat 1 32 (0) m_b322s252i1 13453 chr6qtel1M 896014 AAATACAAAATAGGAAAAGAAAAGAAAAAAAA 896045 v v i v i i (AAAGA)n#Simp 1 AAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAA 32 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 25 14.38 0.00 0.00 chr6qtel1M 897229 897274 (102726) (AAGG)n#Simple_repeat 1 46 (0) m_b322s252i2 13454 chr6qtel1M 897229 AAGAAAGGATTCAAGGAAGGAAGGAAGGAAGGAAAGAAAGAAGGAA 897274 i vvv i i (AAGG)n#Simpl 1 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 46 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 198 20.75 0.25 0.00 chr6qtel1M 897422 897824 (102176) (CTCT)n#Simple_repeat 1 404 (0) m_b322s252i3 13455 chr6qtel1M 897422 CTCTGTCTGTCTCTGTCTCCCTCCCTCTGTCTCCCTCCCTCTGTCTCCCT 897471 v v v i i v i i v i (CTCT)n#Simpl 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chr6qtel1M 897472 CCCTCTGTCTCCTTCCCTCTGTCTCCGTCCGTCTCTCTCTCTATCTCCGT 897521 i v ii i v iv iv v iv (CTCT)n#Simpl 51 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 100 chr6qtel1M 897522 CCGTCTCTCTCTCTCTATCTCCGTCCATCTCTCTCTCTGTCCGTCTCTCT 897571 iv v iv iv v iv (CTCT)n#Simpl 101 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 150 chr6qtel1M 897572 CTATCTCTCTCTGTCCGTCTCTCTCTATCTCTGTCTGTCCGTCTCTCTCT 897621 v v iv v v v iv (CTCT)n#Simpl 151 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 200 chr6qtel1M 897622 CTCTCCGTCTCTCTCTCTCTCTCTCCGTCCCTCTCTCTCTCTCTCTCCGT 897671 iv iv i iv (CTCT)n#Simpl 201 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 250 chr6qtel1M 897672 CTCTCTCTCTCTCTGTCCGTCTCTCTCTCTCTGTCCGTCTCTCTCTCTCT 897721 v iv v iv (CTCT)n#Simpl 251 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 300 chr6qtel1M 897722 GTCCGTCTCTCTCTCTCTGTC-CTCTCTCTATCTCTGTCCGTCTCTCTCT 897770 v iv v - v v iv (CTCT)n#Simpl 301 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 350 chr6qtel1M 897771 CTCTGTCCGTCTCTCTCTCTCTGTCCGTCTCTCTCTATCTCTGTCCGTCT 897820 v iv v iv v v iv (CTCT)n#Simpl 351 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 400 chr6qtel1M 897821 CTCT 897824 (CTCT)n#Simpl 401 CTCT 404 Matrix = Unknown Transitions / transversions = 0.66 (29/44) Gap_init rate = 0.00 (1 / 402), avg. gap size = 1.00 (1 / 1) 271 11.60 1.28 6.04 chr6qtel1M 897825 897980 (102020) C HERV17#LTR/ERV1 (7774) 852 704 m_b322s701i0 13456 chr6qtel1M 897825 CTATCTCTGTCCGTCTCTCTCTATCTCTGTCCGTCTCTCTCTATCTCTGT 897874 i ? iv i i v i v -- v - v C HERV17#LTR/ER 852 CTATTTCTNTCTCTTTCTTTCTCTCTTTGAC--TCTCTCTCTCTC-CTCT 806 chr6qtel1M 897875 CCGTCTCTCTCTATCTCTGTCCGTCTCTGTC-TGTCTCTCTCTCTCTGTC 897923 i -- - v - - v C HERV17#LTR/ER 805 CTGTCTCTCTCT--CTCT-TCCGTCTCTCTCCTGTCTCTCTCTC-CTCTC 760 chr6qtel1M 897924 TGTCTCTCTCTCTCTCTCTGTCTGTCTCTCTCTCTCTCTGTCTGTCTCTC 897973 i- i i- C HERV17#LTR/ER 759 TGTCTCTCTCTCTCTCTCC-TCCGTCTCTCTCTCTCTCC-TCTGTCTCTC 712 chr6qtel1M 897974 -TCTCTCT 897980 - i C HERV17#LTR/ER 711 TTTTCTCT 704 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 11.99 CpG sites = 10, Kimura (unadjusted) = 12.74 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.07 (11 / 155), avg. gap size = 1.00 (11 / 11) 282 18.80 3.17 1.33 chr6qtel1M 897885 898105 (101895) C HERVIP10FH#LTR/ERV1 (4099) 1003 779 m_b322s701i1 13456 chr6qtel1M 897885 CTATCTCTGTCCGTCTCTGTCTGTCTCTCTCTCTCTGTCTGTCTCTCTCT 897934 ii i iv v v i vv v C HERVIP10FH#LT 1003 CTACTTCTATCTCTCTCTTTCTTTCTCTCTTTGACTTTCTGTCTCTCTCT 954 chr6qtel1M 897935 CTCTCTCTGTCTGTCTCTCTCTCTCTCTGTCTGTCTCTCTCTCTCTGTCT 897984 v vi i v -- ii i C HERVIP10FH#LT 953 CTCTCTCTGACTCCCTCTTTGTCTCTCTGTCT--CTTCCTCTCTCTGCCT 906 chr6qtel1M 897985 GTCTCTCTCTCTGTCTGTCTGTCTGTCTCTCTCTGTGTCTCTGTCTCTGT 898034 v i v vi v i v vi v v C HERVIP10FH#LT 905 CTCTCTCTCTTTGACTCCCTCTTTGTCTCTCTCTCTCCCTCTCTCTCTCT 856 chr6qtel1M 898035 CTGTCTCTCTCTCTCT--CTCTGTCTCTCTCTCTGTCTGTCTCTCTCT-C 898081 i v -- v v - i - C HERVIP10FH#LT 855 TTCTCTCTCTCTCTCTTCCTCTCTCTCTCTCTCTCTCT-TCTCTCTTTCC 807 chr6qtel1M 898082 TCTCT----GTCTCTCTCTCTCTCTGTC 898105 ---- i i vi i C HERVIP10FH#LT 806 TCTCTGCTGGTCTTTCCCTGCCTCTGCC 779 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 21.76 CpG sites = 20, Kimura (unadjusted) = 21.76 Transitions / transversions = 0.95 (20/21) Gap_init rate = 0.03 (6 / 220), avg. gap size = 1.67 (10 / 6) 280 18.24 0.86 3.52 chr6qtel1M 897934 898166 (101834) C HERVIP10FH#LTR/ERV1 (4104) 998 772 m_b322s701i2 13456 chr6qtel1M 897934 TCTCTCTCTGTCTGTCTCTCTCTCTCT--CTGTCTGTCTCTCTCTCTCTG 897981 v v v i i -- v v C HERVIP10FH#LT 998 TCTATCTCTCTCTTTCTTTCTCTCTTTGACTTTCTGTCTCTCTCTCTCTC 949 chr6qtel1M 897982 TCTGTCTCTCTCTCTGTCTGTCTGTCTGTCTCTCTCTGTGTCTCTGTCTC 898031 v i i v v ii v i v C HERVIP10FH#LT 948 TCTGACTCCCTCTTTGTCTCTCTGTCTCTTCCTCTCTCTGCCTCTCTCTC 899 chr6qtel1M 898032 TGTCTGTCTCTCTCTCTCTCTCTGTCTCTCTCTCTGTCTGTCTCTCTCTC 898081 v i v i i v -- i -- v i C HERVIP10FH#LT 898 TCTTTGACTCCCTCTTTGTCTC--TCTCTCTCCC--TCTCTCTCTCTTTC 853 chr6qtel1M 898082 TCTCTGTCTCTCTCTCTCTCTGTCTCTCTCTCTCTGTCTCTCTCTCTATC 898131 v ii v - i i- C HERVIP10FH#LT 852 TCTCTCTCTCTCTTCCTCTCTCTCTCTCTCTCTCT-TCTCTCTTTCC-TC 805 chr6qtel1M 898132 TCTGTCTGTCTCTCTCTCTATCTCTGTCTGTCTCT 898166 - -v i i ii i v i v C HERVIP10FH#LT 804 TCTG-CTG-GTCTTTCCCTGCCTCTGCCAGCCGCT 772 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 21.05 CpG sites = 22, Kimura (unadjusted) = 21.05 Transitions / transversions = 1.16 (22/19) Gap_init rate = 0.04 (9 / 232), avg. gap size = 1.11 (10 / 9) 352 18.84 1.75 2.64 chr6qtel1M 898002 898230 (101770) C HERVIP10FH#LTR/ERV1 (4104) 998 772 m_b322s701i3 13456 chr6qtel1M 898002 TCTGTCTGTCTCTCTCTGTGTCTCTGTCTCTGTCTGTCTCTCTCTCTCTC 898051 i v i v v v vv v C HERVIP10FH#LT 998 TCTATCTCTCTCTTTCTTTCTCTCTTTGACTTTCTGTCTCTCTCTCTCTC 949 chr6qtel1M 898052 TCTGTCTCTCTCTCTGTCT----GTCTCTCTCTCTCTCTGTCTCTCTCTC 898097 v i i ---- ii i C HERVIP10FH#LT 948 TCTGACTCCCTCTTTGTCTCTCTGTCTCTTCCTCTCTCTGCCTCTCTCTC 899 chr6qtel1M 898098 TCTCTGTCTCTCTCTCTCTGTCTCTCTCTCTATCTCTGTCTGTCTCTCTC 898147 i v i i v v iv v v i C HERVIP10FH#LT 898 TCTTTGACTCCCTCTTTGTCTCTCTCTCTCCCTCTCTCTCTCTTTCTCTC 849 chr6qtel1M 898148 TCTATCTCTGTCTGTCTCTCTCTCTATCTCTGTCTGTCTCTCTCTATCTC 898197 v vi v v - -- i i- C HERVIP10FH#LT 848 TCTCTCTCTTCCTCTCTCTCTCTCTCTCTCT-TC--TCTCTTTCC-TCTC 803 chr6qtel1M 898198 TGTCTGTCTCTCTCTCTATCTCTGTCTGTCTCT 898230 - -v i i ii i v i v C HERVIP10FH#LT 802 TG-CTG-GTCTTTCCCTGCCTCTGCCAGCCGCT 772 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 21.82 CpG sites = 21, Kimura (unadjusted) = 21.82 Transitions / transversions = 1.00 (21/21) Gap_init rate = 0.03 (7 / 228), avg. gap size = 1.43 (10 / 7) 282 19.75 1.73 3.52 chr6qtel1M 898042 898272 (101728) C HERVIP10FH#LTR/ERV1 (4104) 998 772 m_b322s701i4 13456 chr6qtel1M 898042 TCTCTCTCTCTCTGTCTCTCTCTCTGTCTGTCTCTCTCTCTCTCTGTCTC 898091 v v i --i v i v -- C HERVIP10FH#LT 998 TCTATCTCTCTCTTTCTTTCTCTCT--TTGACTTTCTGTCTCTCT--CTC 953 chr6qtel1M 898092 TCTCTCT--CTCTGTCTCTCTCTCTCTGTCTCTCTCTCTATCTCTGTCTG 898139 -- iv i v ii -- i v C HERVIP10FH#LT 952 TCTCTCTGACTCCCTCTTTGTCTCTCTGTCTCTTCCTC--TCTCTGCCTC 905 chr6qtel1M 898140 TCTCTCTCTCTA--TCTCTGTCTGTCTCTCTCTCTATCTCTGTCTGTCTC 898187 i i-- i v i vi v v i C HERVIP10FH#LT 904 TCTCTCTCTTTGACTCCCTCTTTGTCTCTCTCTCTCCCTCTCTCTCTCTT 855 chr6qtel1M 898188 TCTCTATCTCTGTCTGTCTCTCTCTCTATCTCTGTCTGTCTCTCTCTCTA 898237 v v vi v v - i i- C HERVIP10FH#LT 854 TCTCTCTCTCTCTCTTCCTCTCTCTCTCTCTCTCTCT-TCTCTCTTTCC- 807 chr6qtel1M 898238 TCTCTGTCTGTCTCTCTCTATCTCTGTCTGTCTCT 898272 iiv i i ii i v i v C HERVIP10FH#LT 806 TCTCTGCTGGTCTTTCCCTGCCTCTGCCAGCCGCT 772 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 23.18 CpG sites = 25, Kimura (unadjusted) = 23.18 Transitions / transversions = 1.32 (25/19) Gap_init rate = 0.04 (10 / 230), avg. gap size = 1.20 (12 / 10) 286 22.81 1.95 2.35 chr6qtel1M 898068 898323 (101677) C HERVIP10FH#LTR/ERV1 (4104) 998 744 m_b322s701i5 13456 chr6qtel1M 898068 TCTGTCTCTCTCTCTCTCTGTCTCTCTCTCTCTCTGTCTCTCTCTCTCTG 898117 i i i v i vv i v C HERVIP10FH#LT 998 TCTATCTCTCTCTTTCTTTCTCTCTTTGACTTTCTGTCTCTCTCTCTCTC 949 chr6qtel1M 898118 TCT--CTCTCTCTATCTCTGTCTGTCTCTCTCTCTATCTCTGTCTGTCTC 898165 -- i v v v ii -- i v C HERVIP10FH#LT 948 TCTGACTCCCTCTTTGTCTCTCTGTCTCTTCCTC--TCTCTGCCTCTCTC 901 chr6qtel1M 898166 TCTCTCTA--TCTCTGTCTGTCTCTCTCTATCTCTGTCTGTCTCTCTCTC 898213 i i-- i v i v i v v i C HERVIP10FH#LT 900 TCTCTTTGACTCCCTCTTTGTCTCTCTCTCTCCCTCTCTCTCTCTTTCTC 851 chr6qtel1M 898214 TATCTCTGTCTGTCTCTCTCTCTATCTCTGTCTGTCTCTCTCT-ATCTCT 898262 v v vi v v - i -v C HERVIP10FH#LT 850 TCTCTCTCTCTTCCTCTCTCTCTCTCTCTCTCT-TCTCTCTTTCCTCTCT 802 chr6qtel1M 898263 GTCTGTCTCTCTCTCTATCTCTGTCTGTCTCTCTCTATCTCTGTCTGTCT 898312 - -v i i ii i v i v - v iiiv iivi i C HERVIP10FH#LT 801 G-CTG-GTCTTTCCCTGCCTCTGCCAGCCGCT-TATGCTGCTGTTCTCCC 755 chr6qtel1M 898313 CTCTCTATCTC 898323 iv i C HERVIP10FH#LT 754 CTCTCCTTCCC 744 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 27.58 CpG sites = 32, Kimura (unadjusted) = 27.58 Transitions / transversions = 1.28 (32/25) Gap_init rate = 0.04 (9 / 255), avg. gap size = 1.22 (11 / 9) 295 21.42 2.36 4.42 chr6qtel1M 898104 898357 (101643) C HERVIP10FH#LTR/ERV1 (4104) 998 750 m_b322s701i6 13456 chr6qtel1M 898104 TCTCTCTCTCTCTGTCTCTCTCTCTATCTCTGTCTGTCTCTCTCTCTATC 898153 v v i v vv v -- C HERVIP10FH#LT 998 TCTATCTCTCTCTTTCTTTCTCTCTTTGACTTTCTGTCTCTCTCTCT--C 951 chr6qtel1M 898154 TCTGTCTGTCTCTCTCTCTATCTCTGTCTGTCTCTCTCTATCTCTGTCTG 898203 -- v i i i -- ii v i v C HERVIP10FH#LT 950 TCT--CTGACTCCCTCTTTGTCTCT--CTGTCTCTTCCTCTCTCTGCCTC 905 chr6qtel1M 898204 TCTCTCTCTCTA------TCTCTGTCTGTCTCTCTCTCTATCTCTGTCTG 898247 i i------ i v i v v v C HERVIP10FH#LT 904 TCTCTCTCTTTGACTCCCTCTTTGTCTCTCTCTCTCCCTCTCTCTCTCTT 855 chr6qtel1M 898248 TCTCTCTCTATCTCTGTCTGTCTCTCTCTCTATCTCTGTCTGTCTCTCTC 898297 v vi v v - -- i C HERVIP10FH#LT 854 TCTCTCTCTCTCTCTTCCTCTCTCTCTCTCTCTCTCT-TC--TCTCTTTC 808 chr6qtel1M 898298 TATCTCTGTCTGTCTCTCTCTATCTCTGTCTGTCTCTCTCTATCTCTGTC 898347 i- iiv i i ii i v i v - v iiiv i C HERVIP10FH#LT 807 C-TCTCTGCTGGTCTTTCCCTGCCTCTGCCAGCCGCT-TATGCTGCTGTT 760 chr6qtel1M 898348 TGTCTCTCTC 898357 ivi i C HERVIP10FH#LT 759 CTCCCCTCTC 750 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 25.52 CpG sites = 29, Kimura (unadjusted) = 25.52 Transitions / transversions = 1.26 (29/23) Gap_init rate = 0.05 (12 / 253), avg. gap size = 1.42 (17 / 12) 293 21.95 1.52 5.10 chr6qtel1M 898148 898411 (101589) C HERVIP10FH#LTR/ERV1 (4104) 998 744 m_b322s701i7 13456 chr6qtel1M 898148 TCTATCTCTGTCTGTCTCTCTCTCTATCTCTGTCTGTCTCTCTCTATCTC 898197 v v i v vv v -- C HERVIP10FH#LT 998 TCTATCTCTCTCTTTCTTTCTCTCTTTGACTTTCTGTCTCTCTC--TCTC 951 chr6qtel1M 898198 TGTCTGTCTCTCTCTCTA--TCTCTGTCTGTCTCTCTCTCTATCTCTGTC 898245 v v i i i-- v ii ii v C HERVIP10FH#LT 950 TCTCTGACTCCCTCTTTGTCTCTCTGTCTCTTCCTCTCTCTGCCTCTCTC 901 chr6qtel1M 898246 TGTCTCT--CTCTATCTCTGTCTGTCTCTCTCTCTATCTCTGTCTGTCTC 898293 v i -- iv i v i v v v C HERVIP10FH#LT 900 TCTCTTTGACTCCCTCTTTGTCTCTCTCTCTCCCTCTCTCTCTCTTTCTC 851 chr6qtel1M 898294 TCTCTATCTCTGTCTGTCTCTCTCTATCTCTGTCTGTCTCTCTCTATCTC 898343 v vi v v v - v i i- C HERVIP10FH#LT 850 TCTCTCTCTCTTCCTCTCTCTCTCTCTCTCTCT-TCTCTCTTTCC-TCTC 803 chr6qtel1M 898344 TGTCTGTCTCTCTCTCTATCTCTGTCTGTCTCTCTCTCTATCTCTGTCTG 898393 - -v i i ii i v i v ----- -v - C HERVIP10FH#LT 802 TG-CTG-GTCTTTCCCTGCCTCTGCCAGCCGCT-----TAT-GCTG-CTG 762 chr6qtel1M 898394 TCTGTCTCTCTCTCTCTC 898411 iivi i ii i C HERVIP10FH#LT 761 TTCTCCCCTCTCCTTCCC 744 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 26.13 CpG sites = 28, Kimura (unadjusted) = 26.13 Transitions / transversions = 1.04 (28/27) Gap_init rate = 0.06 (15 / 263), avg. gap size = 1.13 (17 / 15) 387 21.47 0.90 1.81 chr6qtel1M 898190 898412 (101588) C HERVIP10FH#LTR/ERV1 (4104) 998 778 m_b322s701i8 13456 chr6qtel1M 898190 TCTATCTCTGTCTGTCTCTCTCTCTATCTCTGTCTGTCTCTCTCTCTATC 898239 v v i v vv v v C HERVIP10FH#LT 998 TCTATCTCTCTCTTTCTTTCTCTCTTTGACTTTCTGTCTCTCTCTCTCTC 949 chr6qtel1M 898240 TCTGTCTGTCTCTCTCTATCTCTGTCTGTCTCTCTCTCTATCTCTGTCTG 898289 v vi i v v v ii ii v v C HERVIP10FH#LT 948 TCTGACTCCCTCTTTGTCTCTCTGTCTCTTCCTCTCTCTGCCTCTCTCTC 899 chr6qtel1M 898290 TCTCT--CTCTATCTCTGTCTGTCTCTCTCTATCTCTGTCTGTCTCTCTC 898337 i -- iv i -- vi v v i C HERVIP10FH#LT 898 TCTTTGACTCCCTCTTTGTC--TCTCTCTCTCCCTCTCTCTCTCTTTCTC 851 chr6qtel1M 898338 TATCTCTGTCTGTCTCTCTCTCTATCTCTGTCTGTCTCTCTCTCTATCTC 898387 v v vi v v - i i- C HERVIP10FH#LT 850 TCTCTCTCTCTTCCTCTCTCTCTCTCTCTCTCT-TCTCTCTTTCC-TCTC 803 chr6qtel1M 898388 TGTCTGTCTGTCTCTCTCTCTCTCA 898412 iiv v i vi vi C HERVIP10FH#LT 802 TGCTGGTCTTTCCCTGCCTCTGCCA 778 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 25.34 CpG sites = 20, Kimura (unadjusted) = 25.34 Transitions / transversions = 0.74 (20/27) Gap_init rate = 0.02 (5 / 222), avg. gap size = 1.20 (6 / 5) 389 17.82 3.37 2.22 chr6qtel1M 898234 898411 (101589) C HERVIP10FH#LTR/ERV1 (4104) 998 819 m_b322s701i9 13456 chr6qtel1M 898234 TCTATCTCTGTCTGTCTCTCTCTATCT--CTGTCTGTCTCTCTCTCTATC 898281 v v i v i -- v v C HERVIP10FH#LT 998 TCTATCTCTCTCTTTCTTTCTCTCTTTGACTTTCTGTCTCTCTCTCTCTC 949 chr6qtel1M 898282 TCTGTCTGTCTCTCTCTATCTCTGTCTGTCTCTCTCTATCTCTGTCTGTC 898331 v -- i i i -- ii v i v C HERVIP10FH#LT 948 TCTGACT--CCCTCTTTGTCTCT--CTGTCTCTTCCTCTCTCTGCCTCTC 903 chr6qtel1M 898332 TCTCTCT----ATCTCTGTCTGTCTCTCTCTCTATCTCTGTCTGTCTCTC 898377 ----v i v i vi v v i C HERVIP10FH#LT 902 TCTCTCTTTGACTCCCTCTTTGTCTCTCTCTCTCCCTCTCTCTCTCTTTC 853 chr6qtel1M 898378 TCTCTATCTCTGTCTGTCTGTCTCTCTCTCTCTC 898411 v v iiv v C HERVIP10FH#LT 852 TCTCTCTCTCTCTTCCTCTCTCTCTCTCTCTCTC 819 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 20.40 CpG sites = 14, Kimura (unadjusted) = 20.40 Transitions / transversions = 0.82 (14/17) Gap_init rate = 0.03 (6 / 177), avg. gap size = 1.67 (10 / 6) 21 7.56 0.00 0.00 chr6qtel1M 898413 898440 (101560) (CA)n#Simple_repeat 1 28 (0) m_b322s252i4 13457 chr6qtel1M 898413 CACACACAGACACACAGACACACACACA 898440 v v (CA)n#Simple_ 1 CACACACACACACACACACACACACACA 28 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 388 33.62 1.72 0.00 chr6qtel1M 898797 898912 (101088) C MIRc#SINE/MIR (149) 119 2 m_b322s601i6 13458 chr6qtel1M 898797 CAGAGAGGTAAAATGACTCATTCAGGGCCACACACCCAAGATGTGTCAAA 898846 v i iiii i i v i iv v v i C MIRc#SINE/MIR 119 CAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGA 70 chr6qtel1M 898847 TGAAGGACTTGAACCCA--TCTTCCTGGGTTTAGAGCCAGCTCTCTATTC 898894 vvvi i -- iv ii iiv iv v i C MIRc#SINE/MIR 69 GCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCC 20 chr6qtel1M 898895 ATAATACCATGTTACCTC 898912 ivii iii i C MIRc#SINE/MIR 19 ACTGCACCACACTGCCTC 2 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 44.02 CpG sites = 26, Kimura (unadjusted) = 47.43 Transitions / transversions = 2.00 (26/13) Gap_init rate = 0.01 (1 / 115), avg. gap size = 2.00 (2 / 1) 396 31.03 0.00 0.00 chr6qtel1M 898932 899047 (100953) MIR3#SINE/MIR 75 190 (18) m_b322s601i7 13459 chr6qtel1M 898932 TAACTTCCTGTGTGACTTCGAGCATCCTCTTTCAACTTTCTGGGAGTTAA 898981 ?v i i i vviivi v i vv i i MIR3#SINE/MIR 75 TAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAG 124 chr6qtel1M 898982 ATTCGTAATCTGAAAAAATACAGTGTTTGGCCAGATAACTTCTAAGGTCC 899031 v v v v vv vi v v i i i ii MIR3#SINE/MIR 125 TTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCC 174 chr6qtel1M 899032 CTCCCACTTCTAAAAT 899047 i vi i v MIR3#SINE/MIR 175 CTTCCAGCTCTGACAT 190 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.09 CpG sites = 18, Kimura (unadjusted) = 41.09 Transitions / transversions = 1.00 (18/18) Gap_init rate = 0.00 (0 / 115), avg. gap size = 0.0 (0 / 0) 692 27.06 8.64 2.58 chr6qtel1M 899217 899436 (100564) MIRb#SINE/MIR 13 245 (23) m_b322s601i8 13460 chr6qtel1M 899217 GCGACACAATGGATACAATACTAGGCT--AGAGTCAGGAAGACCTCAGTT 899264 i iii i v v ii -i --i iv vi MIRb#SINE/MIR 13 GTGGTGCAGTGGAAAGAGCAC-GGGCTTTGGAGTCAGACAGACCTGGGTT 61 chr6qtel1M 899265 CATATCCAGCTTCAGACACT--------GTGCAACTCTGGACAAGACATT 899306 iv v vi v v -------- ii ii i vi i MIRb#SINE/MIR 62 CGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACT 111 chr6qtel1M 899307 TGACCTCTGACTG--CCTCAGTTTCCCCCACTGTAAAATGCAAATAATAA 899354 i -- -- i vv vii MIRb#SINE/MIR 112 TAACCTCT--CTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAA 159 chr6qtel1M 899355 AAGCATTTTTCTCCCAGAGTTGT-------ATCAAATGAAATAATATTTG 899397 ---i ii vi v i ------- i i iiv MIRb#SINE/MIR 160 ---TACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCATG 206 chr6qtel1M 899398 TCAAGTGTTCAGCACAGTACCTTGCACATAATAAAAGCT 899436 v i i i i v i iv MIRb#SINE/MIR 207 TAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCT 245 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.82 CpG sites = 39, Kimura (unadjusted) = 35.08 Transitions / transversions = 2.05 (39/19) Gap_init rate = 0.05 (10 / 219), avg. gap size = 2.50 (25 / 10) 59 22.11 2.17 0.00 chr6qtel1M 899824 899961 (100039) (AAAT)n#Simple_repeat 1 141 (0) m_b322s252i5 13461 chr6qtel1M 899824 AAATAAATAAACAAACAAACAAATAAATGAAGAAATAGATGGATAGATAA 899873 i i i i v i ii i (AAAT)n#Simpl 1 AAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAA 50 chr6qtel1M 899874 ATAAATAAATAGATGGATGGATAAATGAATAAACAAATAAATAAATGAGT 899923 i ii ii i i i i (AAAT)n#Simpl 51 ATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAAT 100 chr6qtel1M 899924 AAATAAATGGGTGACTGAATAGAT-AA-AAATAAA-AAATA 899961 iii i v i i - - - (AAAT)n#Simpl 101 AAATAAATAAATAAATAAATAAATAAATAAATAAATAAATA 141 Matrix = Unknown Transitions / transversions = 11.50 (23/2) Gap_init rate = 0.02 (3 / 137), avg. gap size = 1.00 (3 / 3) 224 24.60 0.00 12.12 chr6qtel1M 900828 900901 (99099) MIRc#SINE/MIR 54 119 (149) m_b322s601i9 13462 chr6qtel1M 900828 GAATTCAAATCTGGCCTCAGATACTTAACATCCCCTAGCTCTGTGACCCT 900877 ii i i iv v v vi ------- v i MIRc#SINE/MIR 54 GGGTTCGAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTGACCTT 96 chr6qtel1M 900878 GAGCAAGTCACTCTACCCCTACTG 900901 i iv i - MIRc#SINE/MIR 97 GGGCAAGTCACTTAACCTCT-CTG 119 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 27.85 CpG sites = 10, Kimura (unadjusted) = 30.06 Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.11 (8 / 73), avg. gap size = 1.00 (8 / 8) 47 0.00 0.00 0.00 chr6qtel1M 900903 900942 (99058) (CA)n#Simple_repeat 1 40 (0) c_b322s251i0 13463 chr6qtel1M 900903 CACACACACACACACACACACACACACACACACACACACA 900942 (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACA 40 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 312 32.76 4.13 1.61 chr6qtel1M 901155 901275 (98725) MIRb#SINE/MIR 25 148 (120) m_b322s601i10 13464 chr6qtel1M 901155 AAAAAAGATTGACTTTAGGGTCAGA-GGACTTAAGTTAAAATGCTGCATC 901203 i iv iv i i i -i i ii vi v i vv MIRb#SINE/MIR 25 AAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTC 74 chr6qtel1M 901204 TGCCCTTTACTACATGAGTGACACTGCACATCATTTACTT--TCTCTCT- 901250 vi vv v vi vi -- v --i - MIRb#SINE/MIR 75 TGCCACTTACTAGCTGTGTGACCTTGGGCA--AGTTACTTAACCTCTCTG 122 chr6qtel1M 901251 -GTCTAGATCTCTTTCTCCATAAAAT 901275 - i vii i i iv ii MIRb#SINE/MIR 123 AGCCTCAGTTTCCTCATCTGTAAAAT 148 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.35 CpG sites = 24, Kimura (unadjusted) = 44.95 Transitions / transversions = 1.60 (24/15) Gap_init rate = 0.05 (6 / 120), avg. gap size = 1.17 (7 / 6) 408 33.94 2.45 0.60 chr6qtel1M 901172 901334 (98666) MIR3#SINE/MIR 37 202 (6) m_b322s601i11 13464 chr6qtel1M 901172 GGGTCAGAGGACTTAAGTTAAAATGCTGCATCTGCCCTTTACTACATGAG 901221 i ii i ii vv i v i vv vi v ?vv v MIR3#SINE/MIR 37 GAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTG 86 chr6qtel1M 901222 TGACACTGCACA--TCATTTACTTTCTCTCTGTCTAGATCTCTTTCTCCA 901269 vi vi -- i vvii vv i vii i i iv ii MIR3#SINE/MIR 87 TGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTG 136 chr6qtel1M 901270 TAAAATTAAATCATTGAGCTAAATGACCTCTGAGGTCCCTGGAAGCTCTG 901319 v iivvi ii i i i vvv MIR3#SINE/MIR 137 TAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTG 186 chr6qtel1M 901320 A-ATT-TATGAATTTTA 901334 - - - i MIR3#SINE/MIR 187 ACATTCTATG-ATTCTA 202 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 45.86 CpG sites = 31, Kimura (unadjusted) = 47.05 Transitions / transversions = 1.29 (31/24) Gap_init rate = 0.02 (4 / 162), avg. gap size = 1.25 (5 / 4) 561 25.61 5.39 4.14 chr6qtel1M 901864 902030 (97970) C MIRb#SINE/MIR (48) 220 52 m_b322s601i12 13465 chr6qtel1M 901864 TGC-AAACACAGTATAAATGTCATTTTACTTAAACCTCACAACAACACTG 901912 - i i vv i viii i i i i v v C MIRb#SINE/MIR 220 TGCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTG 171 chr6qtel1M 901913 CAAAGTAAGCCTCATTATTATCTCTACTTTACAGATAAGGAAACTGGGGC 901962 i i i i--- i i i i i C MIRb#SINE/MIR 170 CGAGGTAGGT---ATTATTATCCCCATTTTACAGATGAGGAAACTGAGGC 124 chr6qtel1M 901963 TGAAAAAGTTTAAGTGATTTGTCCAGTATCAAA----TAGTAA--GACAG 902006 v i i v i i i ivi v ---- -- i C MIRb#SINE/MIR 123 TCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAG 74 chr6qtel1M 902007 A-CCAGATTTTTGTGGAACCT-GGTC 902030 - i iv i---- i- C MIRb#SINE/MIR 73 AGCCGGGATTC----GAACCCAGGTC 52 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.30 CpG sites = 31, Kimura (unadjusted) = 33.23 Transitions / transversions = 3.10 (31/10) Gap_init rate = 0.07 (12 / 166), avg. gap size = 1.33 (16 / 12) 330 27.43 5.77 1.85 chr6qtel1M 902097 902200 (97800) C L2b_3end#LINE/L2 (43) 423 316 m_b322s601i13 13466 chr6qtel1M 902097 CAGGCCCTGTGTTAAACTTAGTGGATACAAAGACTGAAATTAAATAGCC- 902145 ? i ii viv v iv i- -iv i i v - C L2b_3end#LINE 423 CAGGCNCTGTGCTAGGCGCTGGGGATACAGCGG-TGAA-CAAGACAGACN 376 chr6qtel1M 902146 ----CCCTGCCCTTAGTGAGATTACATTCTAATGAGGGAAAT-GACATGT 902190 ---- i vv v i v i i i i- C L2b_3end#LINE 375 CGGTCCCTGCCCTCACGGAGCTCACAGTCTAGTGGGGGAGACAGACATGT 326 chr6qtel1M 902191 ATGCAAATAA 902200 v? i i C L2b_3end#LINE 325 AANCAGACAA 316 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.10 CpG sites = 17, Kimura (unadjusted) = 36.10 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.05 (5 / 103), avg. gap size = 1.60 (8 / 5) 300 27.73 1.77 7.48 chr6qtel1M 902104 902216 (97784) C L2c_3end#LINE/L2 (38) 440 334 m_b322s601i14 13466 chr6qtel1M 902104 TGTGTTAAACTTAGTGGATACAAAGACTGAAATTAAATA-GCCCCCTGCC 902152 ii ii viv v - - v i i - vi C L2c_3end#LINE 440 TGTGCCAGGCGCTGGGGATACAAAGA-TGAA-TAAGACACGGTCCCTGCC 393 chr6qtel1M 902153 CTTAGTGAGATTACATTCTAATGAGGGAAAT-GACATGTATGCAAATAAG 902201 i iv v i v i ii i i- ? vi i i v C L2c_3end#LINE 392 CTCAAGGAGCTCACAGTCTAGTGGAGGAGACAGACANGTAAACAGACAAT 343 chr6qtel1M 902202 TTTATACACAATACA 902216 ------ C L2c_3end#LINE 342 T------ACAATACA 334 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.29 CpG sites = 19, Kimura (unadjusted) = 36.29 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.09 (10 / 112), avg. gap size = 1.00 (10 / 10) 186 22.44 4.00 1.96 chr6qtel1M 902344 902393 (97607) C L2c_3end#LINE/L2 (334) 144 94 m_b322s601i15 13466 chr6qtel1M 902344 CAACATGTACAAAAGCACGGAGATAGGAAATGAA--GCCATGTGATTAGA 902391 i i i ? ii - -- vii v i i C L2c_3end#LINE 144 CAGCATGTGCAAAGGCNCGGAGGCAGGAAA-GAACTGCGGCGTGTTTGGG 96 chr6qtel1M 902392 GA 902393 C L2c_3end#LINE 95 GA 94 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.01 CpG sites = 9, Kimura (unadjusted) = 29.13 Transitions / transversions = 4.50 (9/2) Gap_init rate = 0.04 (2 / 49), avg. gap size = 1.50 (3 / 2) 216 38.25 2.97 4.74 chr6qtel1M 902415 902650 (97350) C L2#LINE/L2 (441) 2641 2410 m_b322s601i16 13466 chr6qtel1M 902415 ATGTTGTGGAGATCAAAT-GGCAATCTTTGACAAGTGATTGGGTGTGGGA 902463 i v i i vi ii- i ivv vii vv i i C L2#LINE/L2 2641 ATATTTTGAAGGTAGAGCCGACAGGATTTGCTGATGGATTGGATGTGGGG 2592 chr6qtel1M 902464 ATAGGAAAGAAGGAGAGCAAAGTCAAAAATGTCACCGAGATTTCCAACCT 902513 - iv i i --i ii v v i i iiii C L2#LINE/L2 2591 -TGTGAGAGAAAGAGAG--GAGTCAAGGATGACTCCAAGGTTTTTGGCCT 2545 chr6qtel1M 902514 TGGTGAATTTGAGAATGATAAAAT---CTTTGATGGTAATAGG---AATT 902557 vi i- i --i v ii i --- v ? iv vi i ---i i C L2#LINE/L2 2544 GAGC-AACT--GGAAGGATGGAGTTGCCATTNACTGAGATGGGGAAGACT 2498 chr6qtel1M 902558 TTAGGAAGAAGAGGTGGGTTTTGGAGGAACAGATAATGGATTATACTTTG 902607 vii i iv ----- ii iiv v v ii vvii C L2#LINE/L2 2497 GCGGGAGGAGCAGG-----TTTGAGGGGGAAGATCAGGAGTTCAGTTTTG 2453 chr6qtel1M 902608 TTCAGGTTGAATTTGAGAGGGATCTAGGGCATGCAGTTTGAGA 902650 vv v i i v vv v vi i v iv v C L2#LINE/L2 2452 GACATGTTAAGTTTGAGATGCCTATTAGACATCCAAGTGGAGA 2410 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 56.01 CpG sites = 53, Kimura (unadjusted) = 57.18 Transitions / transversions = 1.61 (53/33) Gap_init rate = 0.06 (14 / 235), avg. gap size = 1.29 (18 / 14) 13 10.81 3.12 3.12 chr6qtel1M 902754 902785 (97215) (AATTTA)n#Simple_repeat 1 32 (0) m_b322s252i6 13467 chr6qtel1M 902754 AAGTTAAATTTAAAATTTTAATTT-AATTAAAA 902785 v - v - v (AATTTA)n#Sim 1 AATTTAAATTT-AAATTTAAATTTAAATTTAAA 32 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.06 (2 / 31), avg. gap size = 1.00 (2 / 2) 243 34.04 13.88 3.03 chr6qtel1M 902787 902995 (97005) C MIRc#SINE/MIR (33) 235 5 m_b322s601i17 13468 chr6qtel1M 902787 TTAAAATTTAAAAAGCACTTTAA-AGAAATGATCTCATTTGAGTTTTGCC 902835 v i v i v - v v v vii ii - C MIRc#SINE/MIR 235 TTACAGTTTACAAAGCGCTTTCACATACATTATCTCATTTGATCCTCAC- 187 chr6qtel1M 902836 AAACAAGGCTCTGACATAGGTA----------------------TTCACA 902863 - vv v vi i ---------------------- i C MIRc#SINE/MIR 186 -AACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACA 138 chr6qtel1M 902864 GAGAAGGAAACCAAGGGTGAACATGGTTCAGTAGCAT---CATGATCAC- 902909 vi ii v v iviv v ii v --- v i - C MIRc#SINE/MIR 137 GATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACA 88 chr6qtel1M 902910 CAGAGGGTGGAT-ATAGAA-TGAGATTTGAATGCAGGGTTTTTAGGAATT 902957 vvi iii -ii i-i i i i iv vi iiv -- i C MIRc#SINE/MIR 87 CAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTG--ACT 40 chr6qtel1M 902958 GTTAGACTCTTGTATCTCTATCCATTATATCCCACTGC 902995 viv -- iv i- v i ii i v C MIRc#SINE/MIR 39 CCAAG--TCCAGTG-CTCTTTCCACTGCACCACACTGC 5 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 44.42 CpG sites = 40, Kimura (unadjusted) = 47.24 Transitions / transversions = 1.38 (40/29) Gap_init rate = 0.06 (13 / 208), avg. gap size = 2.77 (36 / 13) 395 33.36 0.00 2.90 chr6qtel1M 903121 903262 (96738) MIR3#SINE/MIR 8 145 (63) m_b322s601i18 13469 chr6qtel1M 903121 AGTGCCAGAAAGGAGAGTGTTTGAGGTGGATGAATTGGAAAATGTGAGTT 903170 v v ivi v ivi iiv -- i ii i i iv i MIR3#SINE/MIR 8 AGTGGCTGAGCAGAGAGAGCACGGACTGG--GAGTCAGGAGACCTGGGTT 55 chr6qtel1M 903171 CAAATCCTGAATCAGACAATTCCCAGGTTTATGACAACTTTCACTAGTCA 903220 v i i iv v v v vv i? v v i -- vvi v MIR3#SINE/MIR 56 CTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGAC--CTTGGGCAAGTCA 103 chr6qtel1M 903221 CCTAACTTCTCTCAGCCTCAGTTTCTTCATTTGTAAAATGGG 903262 i v i vi i i i MIR3#SINE/MIR 104 CTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAG 145 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.01 CpG sites = 25, Kimura (unadjusted) = 45.67 Transitions / transversions = 1.19 (25/21) Gap_init rate = 0.03 (4 / 141), avg. gap size = 1.00 (4 / 4) 782 24.99 4.12 1.00 chr6qtel1M 903157 903350 (96650) MIRc#SINE/MIR 45 244 (24) m_b322s601i19 13469 chr6qtel1M 903157 GGAAAATGTGAGTTCAAATCCTGAATCAGACAATTCCCAGGTTTATGACA 903206 i iv i i i i iv v v v v i v v i - MIRc#SINE/MIR 45 GGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGAC- 93 chr6qtel1M 903207 ACTTTCACTAGTCACCTAACTTCTCTCAGCCTCAGTTTCTTCATTTGTAA 903256 - vvi v i i v i i MIRc#SINE/MIR 94 -CTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAA 142 chr6qtel1M 903257 AATGGGAATAATAATA---GC---ATCCACCTCTCAGAATTGTTGTGAGA 903300 i --- ---ii i v ii i MIRc#SINE/MIR 143 AATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGG 192 chr6qtel1M 903301 ATCAAATGAAGTAACACATGT-AAGACACTCTGGGAAGC-TAAAGAGCTA 903348 ii iii - ii i i vi vi- v MIRc#SINE/MIR 193 ATCAAATGAGATAATGTATGTGAAAGCGCTTTGTAAACTGTAAAGTGCTA 242 chr6qtel1M 903349 TA 903350 MIRc#SINE/MIR 243 TA 244 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.15 CpG sites = 32, Kimura (unadjusted) = 31.51 Transitions / transversions = 2.00 (32/16) Gap_init rate = 0.03 (6 / 193), avg. gap size = 1.67 (10 / 6) 13 18.52 2.56 2.56 chr6qtel1M 903354 903392 (96608) (ATTATC)n#Simple_repeat 1 39 (0) m_b322s252i7 13470 chr6qtel1M 903354 ATTATCATTA-AATAACCAGCTATCATCATCATTATTATT 903392 -v v i -i i i (ATTATC)n#Sim 1 ATTATCATTATCATTATCA-TTATCATTATCATTATCATT 39 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2) 25 6.46 0.00 0.00 chr6qtel1M 903680 903712 (96288) (AC)n#Simple_repeat 1 33 (0) m_b322s252i8 13471 chr6qtel1M 903680 ACACATACACACACACACACACATACACACACA 903712 i i (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACA 33 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 303 32.57 0.77 3.15 chr6qtel1M 904233 904362 (95638) C MIR3#SINE/MIR (79) 129 3 m_b322s601i20 13472 chr6qtel1M 904233 GGAAGGTGATGGCAATTGGAATTAAGTGACTTGCCCAGAGAAACACAGAT 904282 iv v v v vv iii v ii vv v? C MIR3#SINE/MIR 129 GGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGCN 80 chr6qtel1M 904283 AGTAAGTGTCTGAGGCCAGATTTGAACTCAAGTTTTCCTAACT-TGAGTT 904331 v v v v vi i v i i - i i -iv i C MIR3#SINE/MIR 79 AGTTAGTGGCAGAGCCGGGACTAGAACCCAGG-TCTCCTGACTCCCAGTC 31 chr6qtel1M 904332 GATGCCCTATTCACTGAAACATCTAACTGCC 904362 vi i v iii v iv - -- C MIR3#SINE/MIR 30 CGTGCTCTCTCTGCTCAGCCA-CT--CTGCC 3 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.32 CpG sites = 20, Kimura (unadjusted) = 43.71 Transitions / transversions = 0.95 (20/21) Gap_init rate = 0.04 (5 / 129), avg. gap size = 1.00 (5 / 5) 445 24.31 1.82 2.75 chr6qtel1M 904254 904363 (95637) C MIRc#SINE/MIR (157) 111 3 m_b322s601i21 13472 chr6qtel1M 904254 TTAAGTGACTTGCCCAGAGAAACACAGATAGTAAGTGTCTGAGGCCAGAT 904303 ii vv v v v v vi i C MIRc#SINE/MIR 111 TTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGAC 62 chr6qtel1M 904304 TTGAACTCAAGTTTTCCTAACT-TGAGTTGA-TGCCCTATTCACTGAAAC 904351 i i i i i -ii iv - i v i v v C MIRc#SINE/MIR 61 TCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACC 12 chr6qtel1M 904352 ATCTAACTGCCT 904363 i--- C MIRc#SINE/MIR 11 AC---ACTGCCT 3 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.57 CpG sites = 15, Kimura (unadjusted) = 29.91 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.05 (5 / 109), avg. gap size = 1.00 (5 / 5) 483 21.70 6.60 0.00 chr6qtel1M 904362 904467 (95533) C MIRc#SINE/MIR (31) 237 125 m_b322s601i22 13473 chr6qtel1M 904362 CTTTAATTTCTAGAAAACACTCTT-CAAGTGTTATATTCTTTGATCTTCA 904410 vvv i v i i i i- viii v iv i C MIRc#SINE/MIR 237 CTTTACAGTTTACAAAGCGCTTTCACATACATTATCTCATTTGATCCTCA 188 chr6qtel1M 904411 CAACAACCCTGTAAGATAGGT------GGTGTTATTATCCCCACTTTGCA 904454 i i i------ i i i C MIRc#SINE/MIR 187 CAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACA 138 chr6qtel1M 904455 GATGAGGAAACTG 904467 C MIRc#SINE/MIR 137 GATGAGGAAACTG 125 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 25.15 CpG sites = 16, Kimura (unadjusted) = 26.48 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.02 (2 / 105), avg. gap size = 3.50 (7 / 2) 474 25.74 0.00 8.27 chr6qtel1M 904376 904519 (95481) C MIRb#SINE/MIR (52) 216 84 m_b322s601i23 13473 chr6qtel1M 904376 AAACACTCTTCAAGTGTTATATTCTTTGATCTTCACAACAACCCTGTAAG 904425 i i i v v ii v iv i i ii C MIRb#SINE/MIR 216 AAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAG 167 chr6qtel1M 904426 ATAGGTGGTGTTATTATCCCCACTTTGCAGATGAGGAAACTGGAACAGTG 904475 i --- i i i iii ---- C MIRb#SINE/MIR 166 GTA---GGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGC---- 124 chr6qtel1M 904476 TTAGAATGAATGTGAAGTCAATTCTTCCTAACTCCCACATCCAG 904519 i -- i- v - i ivi v iv v v i C MIRb#SINE/MIR 123 TCAGA--GAG-GTTAAGT-AACTTGCCCAAGGTCACACAGCTAG 84 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 30.25 CpG sites = 24, Kimura (unadjusted) = 32.72 Transitions / transversions = 2.40 (24/10) Gap_init rate = 0.08 (11 / 143), avg. gap size = 1.00 (11 / 11) 495 20.83 1.03 1.03 chr6qtel1M 904376 904472 (95528) C MIR#SINE/MIR (50) 212 116 m_b322s601i24 13473 chr6qtel1M 904376 AAACACTCTTCAAGTGTTATATTC-TTTGATCTTCACAACAACCCTGTAA 904424 i i i v v i - i - i i i i C MIR#SINE/MIR 212 AAGCGCTTTACATGTATTA-ACTCATTTAATCCTCACAACAACCCTATGA 164 chr6qtel1M 904425 GATAGGTGGTGTTATTATCCCCACTTTGCAGATGAGGAAACTGGAACA 904472 i iv i i i iii C MIR#SINE/MIR 163 GGTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCA 116 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 24.45 CpG sites = 17, Kimura (unadjusted) = 25.95 Transitions / transversions = 5.67 (17/3) Gap_init rate = 0.02 (2 / 96), avg. gap size = 1.00 (2 / 2) 272 25.55 3.36 7.89 chr6qtel1M 905190 905308 (94692) C L2b_3end#LINE/L2 (79) 387 274 m_b322s601i25 13474 chr6qtel1M 905190 ACATAACAGCATTTGGTCCCTGCCCACACGGAGCTTACAATCTA-CAAAG 905238 vi - i?i v i i -iiii C L2b_3end#LINE 387 ACAAGACAG-ACNCGGTCCCTGCCCTCACGGAGCTCACAGTCTAGTGGGG 339 chr6qtel1M 905239 CAGAATGCA-ATATGTAAACAAATAAATATAATGCAGG--AGCAGATGTA 905285 v --- - i ? i i v? iv i--i i- C L2b_3end#LINE 338 GAGA---CAGACATGTAANCAGACAATNATAACCCAGAGTGGCAGG-GTA 293 chr6qtel1M 905286 ATCAAAGTGGGAGAGAATCAGAG 905308 ---ii v - i ivi C L2b_3end#LINE 292 ---GGACTGGG-GGGGCCCAGAG 274 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.60 CpG sites = 21, Kimura (unadjusted) = 34.13 Transitions / transversions = 3.00 (21/7) Gap_init rate = 0.10 (12 / 118), avg. gap size = 1.08 (13 / 12) 218 24.33 14.05 1.47 chr6qtel1M 905205 905325 (94675) C L2a_3end#LINE/L2 (94) 423 288 m_b322s601i26 13474 chr6qtel1M 905205 GTCCCTGCCCACACGGAGCTTACAATCTA--CAAAGCAGA-ATGCAATAT 905251 v i v --viii v - vi v C L2a_3end#LINE 423 GTCCCTGCCCTCATGGAGCTTACATTCTAGTGGGGGGAGACAGACAATAA 374 chr6qtel1M 905252 GTAAACAAATAAATATA--ATGCAGGA-G-CAGAT-GTAATCAAAGTG-- 905294 ii i i v -- ii v - - - i -- -- C L2a_3end#LINE 373 ACAAATAAATAAGTAAAATATATAGTATGTCAGATGGTGAT--AAGTGCT 326 chr6qtel1M 905295 --GGAGA-----GAATCAGAGTGAAGAAGAAAGGGAAT 905325 -- -----i v i i i ii v i C L2a_3end#LINE 325 ATGGAGAAAAATAAAGCAGGGTAAGGGGGATAGGGAGT 288 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 30.42 CpG sites = 19, Kimura (unadjusted) = 30.42 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.09 (11 / 120), avg. gap size = 1.73 (19 / 11) 529 29.33 7.88 0.92 chr6qtel1M 905425 905627 (94373) MIR1_Amn#SINE/MIR 13 229 (1) m_b322s601i28 13475 chr6qtel1M 905425 GTGGCATAGTAGAGAGAGTGTTGGATCAGGAATCAGAAAAATCCAAATTC 905474 iv i v iii iii v i i i -i iiii MIR1_Amn#SINE 13 GTGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGAGA-CCTGGGTTC 61 chr6qtel1M 905475 AAATCTTGCCTCAGACACTA--C--CTATGTGACTTTGGGCAAGT-ATTT 905519 ? ? ii v v v ?-- -- i? i - i MIR1_Amn#SINE 62 NANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGTCACTT 111 chr6qtel1M 905520 GAACCTTTCTTAACATCAGTTTTCTTATCTGTAAAGTTGAAAAAAAAATA 905569 -? i v?i v i i i v ii v vi MIR1_Amn#SINE 112 -NACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATGATA 160 chr6qtel1M 905570 CTCACTTCATAT---AATTGCTTCA----CTACTTTC----AGTGTTATT 905608 v i v v --- v ii---- vvi---- i iv MIR1_Amn#SINE 161 CTGACCTCCTTTGTAAAGTGCTTTGAGATCTACTGATGAAAAGTGCTACA 210 chr6qtel1M 905609 TAAATACTGGCTATCATTA 905627 ivi i v i MIR1_Amn#SINE 211 TAAGAGCTAGGTATTATTA 229 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.83 CpG sites = 39, Kimura (unadjusted) = 40.65 Transitions / transversions = 1.95 (39/20) Gap_init rate = 0.04 (8 / 202), avg. gap size = 2.25 (18 / 8) 599 30.67 3.05 0.60 chr6qtel1M 905425 905588 (94412) MIRb#SINE/MIR 13 180 (88) m_b322s601i27 13475 chr6qtel1M 905425 GTGGCATAGTAGAGAGAGTGTTGGATCAGGAATCAGAAAAATCCAAATTC 905474 iii i i iiiv v iv i v i i iiii MIRb#SINE/MIR 13 GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTC 62 chr6qtel1M 905475 AAATCTTGCCTCAGACACT-AC---CTATGTGACTTTGGGCAAG-TATTT 905519 i ii v v v - --- i i - i MIRb#SINE/MIR 63 GAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTT 112 chr6qtel1M 905520 GAACCTTTCTTAACATCAGTTTTCTTATCTGTAAAGTTGAAAAAAAAATA 905569 - i v i v i i i v ii v v MIRb#SINE/MIR 113 -AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATA 161 chr6qtel1M 905570 CTCACTTCATATAATTGCT 905588 ii i ii vii i MIRb#SINE/MIR 162 CCTACCTCGCAGGGTTGTT 180 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.97 CpG sites = 37, Kimura (unadjusted) = 42.50 Transitions / transversions = 2.85 (37/13) Gap_init rate = 0.02 (4 / 163), avg. gap size = 1.50 (6 / 4) 29 0.00 0.00 0.00 chr6qtel1M 907012 907043 (92957) (A)n#Simple_repeat 1 32 (0) m_b322s252i9 13476 chr6qtel1M 907012 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 907043 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 32 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 180 29.55 0.00 0.00 chr6qtel1M 907599 907642 (92358) C MIRc#SINE/MIR (224) 44 1 m_b322s601i29 13473 chr6qtel1M 907599 TGAACTTAAGTTCACTGCTCTTTCCACTGCTTAATGCTGCTTTG 907642 viii i v viv ii i i C MIRc#SINE/MIR 44 TGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTGCCTCG 1 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.74 CpG sites = 9, Kimura (unadjusted) = 39.67 Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 205 23.08 0.00 0.00 chr6qtel1M 907689 907727 (92273) MIR1_Amn#SINE/MIR 91 129 (101) m_b322s601i30 13477 chr6qtel1M 907689 GTGACCTTGGGCAAATCATCTGACTTTTCAGTATCCCAG 907727 i ii ? i i v ?ii i MIR1_Amn#SINE 91 GTGACCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAG 129 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.15 CpG sites = 8, Kimura (unadjusted) = 32.15 Transitions / transversions = 8.00 (8/1) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 1164 34.61 3.58 1.44 chr6qtel1M 907850 908324 (91676) L3#LINE/CR1 3612 4096 (3) m_b322s601i31 13478 chr6qtel1M 907850 CACTATATTTTAAGAAGAAAATTGAAAAACTAGAAAGTATCTAAAGAGGG 907899 i i i i i v v i iv ii i i ii i L3#LINE/CR1 3612 CGCCACATTTTAAGAGGGACATTGACAAACTGGAGCGCGTCCAGAGGAGA 3661 chr6qtel1M 907900 GCAACCAGAACTGTGACGTGTCTTAAATGTTTGTCACATGAGGATAAGTT 907949 i i iv v v vi vviv i vvi L3#LINE/CR1 3662 GCGACCAGGATGGTGAAGGGTCTGGAAACCATGTCATATGAGGAACGGTT 3711 chr6qtel1M 907950 GAAAGAACTAGAAA---------TGGAGAAGATAAGCTTCAGGGAATATG 907990 i i ii --------- v vi i i i v ii L3#LINE/CR1 3712 GAAGGAACTGGGGATGTTTAGCCTGGAGAAGAGAAGACTTAGAGGAGACA 3761 chr6qtel1M 907991 TGTAAACTGGTTTCAAACACCTAACTGTCTGTCATGGGAAGAAGAAATTG 908040 vv i vi i ii i vv v v i ii ii i L3#LINE/CR1 3762 TGATAGCTGTCTTCAAATATTTGAAGGGCTGTCATGTGGAAGAGGGATTA 3811 chr6qtel1M 908041 GACTT-TGAGGTTTGGTTGAAAAAAGTCAGAATCAGGAGCAATGAATGAA 908089 - vvv v i vv i ii - ii v ii i L3#LINE/CR1 3812 GACTTATTCTGTGTGGCTCCAGAGGG-CAGAACTAGGACCAATGGGTGGA 3860 chr6qtel1M 908090 AACTGTAAAGATACAGATTAT-ACTTAA-GTCAAAAAAAGGTTCCTGACA 908137 ii ii ii vi vi-i i -i v ii i iv i i L3#LINE/CR1 3861 AGTTACAGGGAGGCAGATTTCGGCTCAATATAAGGAAGAACTTTCTAACA 3910 chr6qtel1M 908138 AATGGAGCTGTCC-AAGGTGGAAAAGGATGTCTCATGAAGTAATGGAGCA 908186 vii - ii vi v i i? i i - - L3#LINE/CR1 3911 ATCAGAGCTGTCCAAAAATGGAATGGGCTGCCTCGNGAGGTAGT-GAGC- 3958 chr6qtel1M 908187 TTTCCTGCCCTTCAAAGTTCTTTAAGTGTAGGTTGGCTGACCAGTTGGT- 908235 - i i i vi -ii v v i iiv i v v vi- L3#LINE/CR1 3959 -TCCCCGTCACT-GGAGGTGTTCAAGCAGAGGCTGGATGACCACTTGTCA 4006 chr6qtel1M 908236 GGGATATAACAGTGGGGATTTCTT--TTGCATGGC-GATTGTACTGGACA 908282 i vii vi i v-- v v- i v i ii L3#LINE/CR1 4007 GGGATGTTGTAGAAGGGATTCCTGCATTGGATGGGAGGTTGGACTAGATG 4056 chr6qtel1M 908283 GATGTTAAGCTCCTTTCTGACTCTTGATTTTTATGAATTTCT 908324 ivivi v i ii viiv i i -- L3#LINE/CR1 4057 ACCTCTAAGGTCCCTTCCAACTCTGAGATTCTGTGA--TTCT 4096 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 46.58 CpG sites = 108, Kimura (unadjusted) = 49.73 Transitions / transversions = 2.00 (108/54) Gap_init rate = 0.03 (14 / 474), avg. gap size = 1.71 (24 / 14) 23 19.75 4.69 0.00 chr6qtel1M 908756 908819 (91181) (AAATA)n#Simple_repeat 1 67 (0) m_b322s252i10 13479 chr6qtel1M 908756 AAATAAAAGGCTATTAAATAAAAAAAATTAAATTAAATTAAAAT-TAA-A 908803 vivv v v v v v -v - (AAATA)n#Simp 1 AAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATA 50 chr6qtel1M 908804 AAATAAAA-AAAAGAAA 908819 - v (AAATA)n#Simp 51 AAATAAAATAAAATAAA 67 Matrix = Unknown Transitions / transversions = 0.10 (1/10) Gap_init rate = 0.05 (3 / 63), avg. gap size = 1.00 (3 / 3) 18 13.01 0.00 8.70 chr6qtel1M 908771 908820 (91180) (AAATAA)n#Simple_repeat 1 46 (0) m_b322s252i11 13479 chr6qtel1M 908771 AAATAAAAAAAATTAAATTAAATTAAAATTAAAAAATAAAAAAAAGAAAT 908820 v -- v v v - v - (AAATAA)n#Sim 1 AAATAAAAATAA--AAATAAAAATAAAAAT-AAAAATAAAAATAA-AAAT 46 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.08 (4 / 49), avg. gap size = 1.00 (4 / 4) 485 28.41 3.80 4.37 chr6qtel1M 908867 909050 (90950) C MIR3#SINE/MIR (3) 205 23 m_b322s601i32 13480 chr6qtel1M 908867 TCACAGAATCATAGAAT-TTAGAACTAGAAA--ATGTTAGAAATCATCTA 908913 i - i i i i-- iv i C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTA 156 chr6qtel1M 908914 TACCAACTTCCTTCATTATACAAATAAGAAAGTCAAACCCCATA---GTG 908960 vv -i i v i i i iiii iv v --- C MIR3#SINE/MIR 155 GTCCAAC-CCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTG 107 chr6qtel1M 908961 AAGTTACTCACCCAAGGATCAGTCATATAGATAAGAAAATTACAGAATCA 909010 v ii ----- i i -i? vv i vi ii i C MIR3#SINE/MIR 106 AAGTGACTTGCCCAAG-----GTCACACAG-CNAGTTAGTGGCAGAGCCG 63 chr6qtel1M 909011 AAA-TGAAACACAGAACCTCTGACTCCAAATCCAGAACTCT 909050 ii - ii v iv ii v i - vi C MIR3#SINE/MIR 62 GGACTAGAACCCAGGTCTCCTGACTCCCAGTCC-GTGCTCT 23 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.17 CpG sites = 36, Kimura (unadjusted) = 38.17 Transitions / transversions = 2.57 (36/14) Gap_init rate = 0.07 (12 / 183), avg. gap size = 1.25 (15 / 12) 294 32.36 4.23 4.23 chr6qtel1M 908924 909065 (90935) C MIRc#SINE/MIR (119) 149 8 m_b322s601i33 13480 chr6qtel1M 908924 CTTCATTATACAAATAAGAAAGTCAAACCCCATAGTG---AAGTTACTCA 908970 ii v i i i iiii iv i v v --- v ii C MIRc#SINE/MIR 149 CCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTG 100 chr6qtel1M 908971 CCCAAGGATCAGTCATATAGATAAGAAAATTACAGAATCAAAA-TGAAAC 909019 ----- i i v - v i vi ii iii - vi C MIRc#SINE/MIR 99 CCCAAGG-----TCACACAGCTA-GTAAGTGGCAGAGCCGGGACTCGAAC 56 chr6qtel1M 909020 ACAGAACCTC-TGACTCCAAATCCAGAACTC-TGATATTGTACCACAC 909065 v iv i - i vi - vvi i i C MIRc#SINE/MIR 55 CCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACAC 8 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.22 CpG sites = 30, Kimura (unadjusted) = 45.04 Transitions / transversions = 2.14 (30/14) Gap_init rate = 0.07 (10 / 141), avg. gap size = 1.20 (12 / 10) 201 36.70 3.67 0.00 chr6qtel1M 909076 909184 (90816) C L3#LINE/CR1 (5) 4094 3982 m_b322s601i34 13481 chr6qtel1M 909076 AATCAGAGAAGCCAAAGGCTGCAAGGAACCTCAGCCACCATTTAATCTAA 909125 v v iv ii i v i i vvii i i i C L3#LINE/CR1 4094 AATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCAA 4045 chr6qtel1M 909126 T-TCAAACCCTACAAAGCAATCTCCATCATGAGATATC---CAAGTAATC 909171 i- vv i v iiv v i ivii ii v vi --- ii C L3#LINE/CR1 4044 CCTCCCATCCAATGCAGGAATCCCTTCTACAACATCCCTGACAAGTGGTC 3995 chr6qtel1M 909172 CTCAAGCCTCTGC 909184 v v C L3#LINE/CR1 3994 ATCCAGCCTCTGC 3982 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 52.92 CpG sites = 24, Kimura (unadjusted) = 52.92 Transitions / transversions = 1.50 (24/16) Gap_init rate = 0.02 (2 / 108), avg. gap size = 2.00 (4 / 2) 365 40.33 5.78 3.24 chr6qtel1M 909134 909825 (90175) MamRTE1#LINE/RTE-BovB 2493 3201 (611) m_b322s601i35 13482 chr6qtel1M 909134 CTACAAAGCAATCT---CCATCATGAGATAT---CCAAGTAATCCTCAAG 909177 v vi --- iii v vi --- -- v i MamRTE1#LINE/ 2493 CTACTAAGCAAGTTTGGCTGCCCTGAGAAGTTCACCAAG--ATCCTAAGG 2540 chr6qtel1M 909178 CCTCTGCATAATGGCATGCTTGCCCGGGTTCTAGACAAAG--AAAAATGC 909225 iv v i i vii vi v ------ i --i viii i MamRTE1#LINE/ 2541 CTACTCCATGATGGTATGGCCGGTCGCGT------CAGAGTTGACGGCGT 2584 chr6qtel1M 909226 TCT---CGAGTT-TTCCCAGTCATCAATGGAGTGATATAGAGCGGTGTGC 909271 i --- vii- vi i vii iiiv i iv MamRTE1#LINE/ 2585 CCTGTCCGACCCATTCCCCATCACCAATGGAGTGAAGCAGGATTGCGTAA 2634 chr6qtel1M 909272 TTGTTCCCATGCTTAA-CAAGATGTTTT---TAACCATGTCATCAAACAC 909317 v v vi - v- vv i ---i i i-- i iv - MamRTE1#LINE/ 2635 TAGGTCCAGT-CTTATTCAATCTATTTTATGCAGCCATGC--TCGAGGA- 2680 chr6qtel1M 909318 CTTCCATGAGGACAAACACAGAAACAAA-GTCAG--T-CACTTTACGAT- 909362 - v v ii i--- vii i vii- -- - i i- i - MamRTE1#LINE/ 2681 -TGCAACAAGGG---ACCTGGAAGCTGGTGTCAGAATACGCTTC-CGGTC 2725 chr6qtel1M 909363 ----GGTAAATTCTTCAACTTCCAAAGGCTACAAACAAAAACTAAAGTGG 909408 ---- v i v vi v v i i vv v v vv MamRTE1#LINE/ 2726 CTCTGGGAAACTCTTCCAACTCAACAGGCTACGAGCATCATCGAAAGTCC 2775 chr6qtel1M 909409 AGGGAATGCTGGTGCATGATTTTTTTT-TGTAGATGATTATGCACTCAAT 909457 vv ii iiv vi v v vi vi v - iv i i v ii v MamRTE1#LINE/ 2776 TTGAGACAGTCATCCAGGAACTGCTGTATGCCGATGACTGTGCTCTTGAA 2825 chr6qtel1M 909458 GCAGCCTCTGCA-GCTGAGATGCAACAAAGGATGAATCAATTCTCTG--- 909503 i vv v - - vv v i?vi vv i i iv iv v --- MamRTE1#LINE/ 2826 GTACACGC-GCAAGAAGACATGCAGNTGATCATGGACCGCTTTGCAGAGT 2874 chr6qtel1M 909504 CTGCTT-GTGCTAATTTTGACCTAAAAATTAATACCAAGGAAACGCAGCT 909552 v vi- i ----i iv i vi v iiviv i i vv v MamRTE1#LINE/ 2875 CAGCACAGCGCTA----CGGACTGACGATAAGCCTGAAGAAGACCGAGGT 2920 chr6qtel1M 909553 CTTTCATCAGCCAGTGCTACACCACCCATATATA-AACCATCAGTTACAA 909601 v vi i v ii i vivv v v i ii- i vvii viv MamRTE1#LINE/ 2921 CATGTACCAGCCTGCACCAGGGAAACCCTACACGCAGCCAAAGATTTTCA 2970 chr6qtel1M 909602 TAAATGGTGAAGTTCTGAATGCTGT-----GGTTCTCTTACCTTAGCAGT 909646 viiiii iv vv v -----ii vi vi i MamRTE1#LINE/ 2971 TCGGCAATACAGAGCTGAAAGCTGTCACCGAATTCTGCTACCTAGGCAGC 3020 chr6qtel1M 909647 ATACTTCCTGGGGATTCCAT-ATTGATAATGAGATTGGCATACACATTGC 909695 ii vi iiiv v vv - ? i v ii v iv vv iv iiv MamRTE1#LINE/ 3021 ACGCTGTCCAATGATGCACTGATNGACAAAGAAGTAGAAAACCGAATCAA 3070 chr6qtel1M 909696 CAGAGCTGTCTCAGCATTTGGGAGGCTC-CAAAGAAAGTGTGGAAGAGGA 909744 v ii iiv viiv v v- i v i vivviiv MamRTE1#LINE/ 3071 GAAGGCCAGCATGTCCTTTGGGAGGCTGGCAGACAGAGTGTGGCGCCAAC 3120 chr6qtel1M 909745 GAGGTATTAGACTGACTACCAACCTGAAGGTCTACAGAGCTGTCGTAAGG 909794 v i i ii vvvv v i vi v ii?v MamRTE1#LINE/ 3121 GTGGCATCAAGCTCCAGACCAAACTAAAGGTCTACAGAGCGATAGCGNTG 3170 chr6qtel1M 909795 ATCTCA-CTGTTGTATGCTTCTGAAACCTGGA 909825 - iv - vi ? i vi v i MamRTE1#LINE/ 3171 -TCCAACCTTCTNTACGGCTGTGAGACCTGGA 3201 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 54.39 CpG sites = 143, Kimura (unadjusted) = 60.55 Transitions / transversions = 1.13 (143/127) Gap_init rate = 0.06 (43 / 691), avg. gap size = 1.47 (63 / 43) 327 25.97 3.90 0.00 chr6qtel1M 910463 910539 (89461) C L3#LINE/CR1 (96) 4003 3924 m_b322s601i36 13483 chr6qtel1M 910463 CAAGTAATCATCAAGCCTTGGCTTGAAAACCTCCAATGAAGGTGACC--- 910509 ii v iv v i v v v --- C L3#LINE/CR1 4003 CAAGTGGTCATCCAGCCTCTGCTTGAACACCTCCAGTGACGGGGAGCTCA 3954 chr6qtel1M 910510 CCATCCCTCAAAGTAACTCATTCTACTTTT 910539 i i i ? i i i i i i i C L3#LINE/CR1 3953 CTACCTCNCGAGGCAGCCCATTCCATTTTT 3924 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.85 CpG sites = 14, Kimura (unadjusted) = 33.95 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.01 (1 / 76), avg. gap size = 3.00 (3 / 1) 421 31.48 0.93 0.00 chr6qtel1M 910568 910675 (89325) C MIR3#SINE/MIR (21) 187 79 m_b322s601i37 13484 chr6qtel1M 910568 TTAGAATTAAAAAG-ACTTCAGAAGCAACCTAGGCCAACCTTCCCATTTT 910616 i ii ii i - i i iiiv i v ii i C MIR3#SINE/MIR 187 TCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTT 138 chr6qtel1M 910617 ATATCTGAGGAAACTGAAGCACAAGGAGATCAAGTGAATTTTTCAAAGTC 910666 i vv i v ii i v v vii i C MIR3#SINE/MIR 137 ACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTC 88 chr6qtel1M 910667 ATACAATCA 910675 i ii? C MIR3#SINE/MIR 87 ACACAGCNA 79 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 45.18 CpG sites = 26, Kimura (unadjusted) = 45.18 Transitions / transversions = 3.25 (26/8) Gap_init rate = 0.01 (1 / 107), avg. gap size = 1.00 (1 / 1) 246 31.83 15.82 4.61 chr6qtel1M 910701 911092 (88908) L2c_3end#LINE/L2 35 468 (10) m_b322s601i38 13485 chr6qtel1M 910701 TTACCTCCTACATTCCCCTCTTTCCACCCATT---CTCCAGTGACGCCAA 910747 i i v i i -- i i --- iv i ii L2c_3end#LINE 35 TCATCTCCTCCACTCCCCTCCT--CGCCCACTATGCTCCAGCCACACTGA 82 chr6qtel1M 910748 ATTGGCTGTCTT---------------AGTCCT--CCT-CATATAAA--- 910776 i ?vi iv --------------- i -- - v vii?i--- L2c_3end#LINE 83 ACTNCTTGCATTCCCCAAACACGCCGCAGTTCTTTCCTGCCTCCGNGCCT 132 chr6qtel1M 910777 --GCA-AT-CTGTTCCCTATCTCT---ATGCAATAACTCCTCACATTCAA 910819 -- - - v vi --- vv vv i iiv v i v L2c_3end#LINE 133 TTGCACATGCTGTTCCCTCTGCCTGGAATGCTCTTCCCCCCTCCTTCCAC 182 chr6qtel1M 910820 CTCTTAAAATCCTA----TCCTTCAAGGCTCAACTCAAACACTGTCTTCT 910865 vviv v ---- ? i i iiiiii i L2c_3end#LINE 183 CTGGCTAACTCCTACTCATCCTTCAAGNCTCAGCTCAGATGTCACCTCCT 232 chr6qtel1M 910866 CCATGAAGTTTTTCCTCATCTTCC--------TCTCAGTTGC------TT 910901 iv ii i v i ii -------- - v ------i L2c_3end#LINE 233 CCGGGAAGCCTTCCCTGACCCCCCAAGNCTAGTCT-AGGTGCCCTCCTCT 281 chr6qtel1M 910902 GTGC-CTAATCTCTCCCTAAATTAT-CTTTTATC-TAGTTTTTCACATTA 910948 - iv vv v -ivi - iii i- ivi vv L2c_3end#LINE 282 GTGCTCCCATAGCACCCT-GTCTATACTCCCATTATAGCACTTATCATTA 330 chr6qtel1M 910949 TCTATG---TCTA--TGTGTATATGTGTGTATATTATCTCCACAAAAGAA 910993 v - --- v -- v i v ii? v i ivi --v v L2c_3end#LINE 331 ACT-TGTATTGTAATTGTCTGTTTACNTGTCTGTCTCCTCCAC--TAGAC 377 chr6qtel1M 910994 TATAAGCTACTCAAAGTCAATGATGGCCTTTTATTCCTATTT-----CCA 911038 i i v ii i v iv iv iv i v v ----- v L2c_3end#LINE 378 TGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTATCCCC 427 chr6qtel1M 911039 AGCACCTAGTAGAATATAAGAGCATAAAATAAGTTCTTAATAAATGTATG 911088 i i i ----------- -- i i iv i v L2c_3end#LINE 428 AGCGCCTGGCA-----------CAT--AGTAGGCGCTCAATAAATGTTTG 464 chr6qtel1M 911089 TTGA 911092 L2c_3end#LINE 465 TTGA 468 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.35 CpG sites = 71, Kimura (unadjusted) = 43.87 Transitions / transversions = 1.48 (71/48) Gap_init rate = 0.10 (38 / 391), avg. gap size = 2.16 (82 / 38) 320 35.73 6.62 7.37 chr6qtel1M 910806 911092 (88908) L2b_3end#LINE/L2 172 456 (10) m_b322s601i39 13485 chr6qtel1M 910806 CTCCTCACAT--TCAACTCTTAAAATCCTATCCTTCAAGGCTCAACTCAA 910853 i i v --i i ---- ii i v i L2b_3end#LINE 172 CTCTTCGCCTGGCCAACTCCTA----CTCATCCTTCAGGTCTCAGCTCAA 217 chr6qtel1M 910854 ACACTGTCTTCTCCATGAAGTTTTTCCTCATCTTCC---TC---TCAGTT 910897 iiiiii i iv iii i v i ii ---i --- vi L2b_3end#LINE 218 ATGTCACCTCCTCCGGGAAGCCCTCCCTGACCCCCCAGGCCGGGTCAGGC 267 chr6qtel1M 910898 GCTTGTGCCTAATCTCTCCCTAAATTATCTT-TTA-TCTAGTTTTTCACA 910945 iivivi iiv i i vivvi i i -ii - i v ----- L2b_3end#LINE 268 GCCCTCCTCTGGGCCCCCCCAGTCCTACCCTGCCACTCTGGGTT-----A 312 chr6qtel1M 910946 TTATCTATGTCTATGTGTATATGTGTGTATATTATCTCCACAAAAGAATA 910995 ? --- -- ?v i v v ----i i --v v i L2b_3end#LINE 313 TNAT---TGTC--TGNTTACATGTCTGTCT----CCCCCAC--TAGACTG 351 chr6qtel1M 910996 TAAGCTACTCAAAGTCAATGAT--GGCC--TTTTATTC----CTAT-TTC 911036 i v vii i v iv i--? i -- i i ---- i - i L2b_3end#LINE 352 TGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTGTATCC 401 chr6qtel1M 911037 CAAGCACCTAGTAGAATATAAGAGCATAAAATAAGTTCTTAATAAATGTA 911086 v i i v i?iivv - i v i i iv i i i v L2b_3end#LINE 402 CCAGCGCCTAGCACAGNGCCTG-GCACACAGTAGGCGCTCAGTAAATATT 450 chr6qtel1M 911087 TGTTGA 911092 L2b_3end#LINE 451 TGTTGA 456 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 49.86 CpG sites = 67, Kimura (unadjusted) = 54.17 Transitions / transversions = 2.39 (67/28) Gap_init rate = 0.10 (30 / 286), avg. gap size = 1.33 (40 / 30) 15 10.30 0.00 8.82 chr6qtel1M 911639 911675 (88325) (ATT)n#Simple_repeat 1 34 (0) m_b322s252i12 13486 chr6qtel1M 911639 ATTATCTTAATTATTATTATTATTCATTAATTAATTA 911675 iv v - - - (ATT)n#Simple 1 ATTATTATTATTATTATTATTATT-ATT-ATT-ATTA 34 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.08 (3 / 36), avg. gap size = 1.00 (3 / 3) 224 25.00 8.33 0.00 chr6qtel1M 911993 912052 (87948) C MIRc#SINE/MIR (134) 134 70 m_b322s601i40 13487 chr6qtel1M 911993 GGAGAAACTG-----CAGAGAAGTAAAATTACTTACCCAAGATCACACTA 912037 ii ----- i v i v i i vi C MIRc#SINE/MIR 134 GAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAG 85 chr6qtel1M 912038 ATAATAAATAGCAAA 912052 v i i i i C MIRc#SINE/MIR 84 CTAGTAAGTGGCAGA 70 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.98 CpG sites = 11, Kimura (unadjusted) = 31.98 Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.02 (1 / 59), avg. gap size = 5.00 (5 / 1) 242 15.38 3.85 0.00 chr6qtel1M 913066 913117 (86883) C DNM1r#Unknown (2134) 2528 2475 m_b322s502i0 13488 chr6qtel1M 913066 CACATATGCACAAACACACAC-CAT-TATACATATATATGCACACATACA 913113 ii v i - - i i i C DNM1r#Unknown 2528 CACATATATACACACATACACACATATACACACATATATACACACATACA 2479 chr6qtel1M 913114 TGTG 913117 i C DNM1r#Unknown 2478 CGTG 2475 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 15.62 CpG sites = 7, Kimura (unadjusted) = 18.00 Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.00 (2 / 2) 19 26.49 5.83 2.83 chr6qtel1M 913118 913220 (86780) (TGCACA)n#Simple_repeat 1 106 (0) m_b322s252i13 13489 chr6qtel1M 913118 TGCACACACACA-GTGC-TGTCACATGCACAATAACATACAAATG--TAT 913163 ii - ii - - vvv i v --i (TGCACA)n#Sim 1 TGCACATGCACATGCACATG-CACATGCACATGCACATGCACATGCACAT 49 chr6qtel1M 913164 GTGCATGCAGTCCTGCACATATACATATGCATGCATATACACAT--ACAT 913211 ii -- v ii iii i i -- (TGCACA)n#Sim 50 GCACATGCA--CATGCACATGCACATGCACATGCACATGCACATGCACAT 97 chr6qtel1M 913212 GCACATACA 913220 i (TGCACA)n#Sim 98 GCACATGCA 106 Matrix = Unknown Transitions / transversions = 3.20 (16/5) Gap_init rate = 0.07 (7 / 102), avg. gap size = 1.29 (9 / 7) 201 35.29 0.00 0.00 chr6qtel1M 913312 913379 (86621) C MIR3#SINE/MIR (3) 205 138 m_b322s601i41 13490 chr6qtel1M 913312 TCCTAGGATCAGCGAATGTTGGCATTAGGAGATACCTTAAAGTTCTTTTA 913361 v i vv ii vii i i iv i v v i C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTA 156 chr6qtel1M 913362 ATCCAAGACTTTTTTTTT 913379 i vv ii iv C MIR3#SINE/MIR 155 GTCCAACCCCCTCATTTT 138 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 49.62 CpG sites = 14, Kimura (unadjusted) = 49.62 Transitions / transversions = 1.40 (14/10) Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0) 244 29.03 0.00 0.00 chr6qtel1M 913415 913476 (86524) C MIRc#SINE/MIR (203) 65 4 m_b322s601i42 13487 chr6qtel1M 913415 GGATTTGAACTCAAGTCTTCCTAATTCTACATCCAGATATCTATCCATTG 913464 i i i i i i i vi vvv v i C MIRc#SINE/MIR 65 GGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTG 16 chr6qtel1M 913465 TTCCACTCAGCC 913476 iv v v C MIRc#SINE/MIR 15 CACCACACTGCC 4 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.92 CpG sites = 10, Kimura (unadjusted) = 37.50 Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0) 15 0.00 9.68 3.03 chr6qtel1M 913992 914022 (85978) (TAAA)n#Simple_repeat 1 33 (0) m_b322s252i15 13491 chr6qtel1M 913992 TAAA-AAAT-AAT-AATAAAGTAAATAAATAAAT 914022 - - - - (TAAA)n#Simpl 1 TAAATAAATAAATAAATAAA-TAAATAAATAAAT 33 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.13 (4 / 30), avg. gap size = 1.00 (4 / 4) 272 27.70 7.04 3.40 chr6qtel1M 914260 914401 (85599) C L2c_3end#LINE/L2 (38) 440 294 m_b322s601i43 13492 chr6qtel1M 914260 TGTTCCAGAC-TTGGT--TATAAAGATATAAAAGTATTTAGTTCCTGTCC 914306 v i -i v-- i iv v - ivii i i C L2c_3end#LINE 440 TGTGCCAGGCGCTGGGGATACAAAGATGAATAAG-ACACGGTCCCTGCCC 392 chr6qtel1M 914307 TCAAGGAACTTACAATCTATAAGTCAGAATACA-ATATATAAAAAGATAA 914355 i i i vvi -- i v - i ?i v i C L2c_3end#LINE 391 TCAAGGAGCTCACAGTCTAGTGG--AGGAGACAGACANGTAAACAGACAA 344 chr6qtel1M 914356 ATATAATGCAGCAG-CAATTATAA----TCAAATAGAAG-AGAGCCAGGA 914399 v i i -- -i v ---- vv i i - v v i C L2c_3end#LINE 343 TTACAATACA--AGTTAATGATAAGTGCTATAATGGGAGTATAGACAGGG 296 chr6qtel1M 914400 TG 914401 C L2c_3end#LINE 295 TG 294 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.67 CpG sites = 23, Kimura (unadjusted) = 35.99 Transitions / transversions = 1.53 (23/15) Gap_init rate = 0.08 (11 / 141), avg. gap size = 1.36 (15 / 11) 858 28.37 0.46 1.39 chr6qtel1M 914483 914700 (85300) MIRb#SINE/MIR 4 219 (49) m_b322s601i44 13493 chr6qtel1M 914483 AGAAACAG-GTGGCCTAAAGGAGAGAGTGCTGGATCTGGAGTCAGAAAGA 914531 iii - ivi iv i ii v v i v MIRb#SINE/MIR 4 AGGGGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGA 53 chr6qtel1M 914532 CCCAATTTCAAATCCTCCCCCAGATACTTATTACATATGTGACCCTGGGC 914581 iiiv i ivv i v vi i vv i i MIRb#SINE/MIR 54 CCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGC 103 chr6qtel1M 914582 AAGTACTTTAATCTTTCATAACATCATTTTCCTTAACTGTATAATAAAGA 914631 vvi i i vv i v v i v v iii MIRb#SINE/MIR 104 AAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGA 153 chr6qtel1M 914632 TAATAATAGAACCCACCTCACAGAGTTGTTATGAGCATGAAATGAGATGA 914681 --- i i i i v v i MIRb#SINE/MIR 154 TAATAAT---ACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAA 200 chr6qtel1M 914682 CACATGAAAATTGCTTAAC 914700 ii v vi i MIRb#SINE/MIR 201 TGCATGTAAAGCGCTTAGC 219 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.75 CpG sites = 37, Kimura (unadjusted) = 36.74 Transitions / transversions = 1.54 (37/24) Gap_init rate = 0.02 (4 / 217), avg. gap size = 1.00 (4 / 4) 833 29.53 5.12 0.00 chr6qtel1M 914484 914737 (85263) MIRc#SINE/MIR 2 268 (0) m_b322s601i45 13493 chr6qtel1M 914484 GAAACAG-GTGGCCTAAAGGAGAGAGTGCTGGATCTGGAGTCAGAAAGAC 914532 ii - ivi iv i ii ii i MIRc#SINE/MIR 2 GAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC 51 chr6qtel1M 914533 CCAATTTCAAATCCTCCCCCAGATACTTATTACATATGTGACCCTGGGCA 914582 iiiv i i ivv i v vi i vv i i MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 101 chr6qtel1M 914583 AGTACTTTAATCTTTCATAACATCATTTTCCTTAACTGTATAATAAAGAT 914632 vvi i i vv i v v i v v iii MIRc#SINE/MIR 102 AGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGAT 151 chr6qtel1M 914633 AATAATA---GA---ACCCACCTCACAGAGTTGTTATGAGCATGAAATGA 914676 --- v---i i i i v v MIRc#SINE/MIR 152 AATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGA 201 chr6qtel1M 914677 GATGACACATG-AAAATTGCTTAACCAATTTC--ATTGTTATCTAAA--- 914720 i iii -i vi viiv i vi-- v i vi --- MIRc#SINE/MIR 202 GATAATGTATGTGAAAGCGCTTTGTAAACTGTAAAGTGCTATACAAATGT 251 chr6qtel1M 914721 AACTAGTTATCATTATT 914737 vv? i MIRc#SINE/MIR 252 AAGGNGTTATTATTATT 268 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.14 CpG sites = 47, Kimura (unadjusted) = 39.16 Transitions / transversions = 1.68 (47/28) Gap_init rate = 0.02 (6 / 253), avg. gap size = 2.17 (13 / 6) 235 28.92 21.69 0.00 chr6qtel1M 914741 914823 (85177) C MIRb#SINE/MIR (161) 107 7 m_b322s601i46 13494 chr6qtel1M 914741 ATTTGCCTAAGGTCATACAACTACTAAGTAGCTTAATCAAGATT------ 914784 i i i i v i vv ii ii ------ C MIRb#SINE/MIR 107 ACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACC 58 chr6qtel1M 914785 CAGATC------------AAATCATTGTTCTGTCCATTATACCAGTCTGC 914822 i ------------ ii vv i v i ii vv C MIRb#SINE/MIR 57 CAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCACCACGCTGC 8 chr6qtel1M 914823 C 914823 C MIRb#SINE/MIR 7 C 7 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.19 CpG sites = 16, Kimura (unadjusted) = 38.24 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.02 (2 / 82), avg. gap size = 9.00 (18 / 2) 239 30.00 0.00 0.00 chr6qtel1M 914741 914790 (85210) C MIR#SINE/MIR (162) 100 51 m_b322s601i47 13494 chr6qtel1M 914741 ATTTGCCTAAGGTCATACAACTACTAAGTAGCTTAATCAAGATTCAGATC 914790 i i i i v i vv ii ii ii i C MIR#SINE/MIR 100 ACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACC 51 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.75 CpG sites = 12, Kimura (unadjusted) = 42.02 Transitions / transversions = 4.00 (12/3) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 15 6.55 5.88 2.86 chr6qtel1M 914864 914897 (85103) (ATATAC)n#Simple_repeat 1 35 (0) m_b322s252i16 13495 chr6qtel1M 914864 ATATCCATATACA-AT-CAGATACATATAACATATA 914897 v - - v - (ATATAC)n#Sim 1 ATATACATATACATATACATATACATAT-ACATATA 35 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.09 (3 / 33), avg. gap size = 1.00 (3 / 3) 372 30.17 6.03 0.00 chr6qtel1M 916530 916645 (83355) C MIR3#SINE/MIR (7) 201 79 m_b322s601i48 13496 chr6qtel1M 916530 AGAAT--TGGGAT-TTAGAACTAAAAAAGACTTTAGAGATTATCTTATTC 916576 -- i i - i i ii ii i i vi i C MIR3#SINE/MIR 201 AGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCC 152 chr6qtel1M 916577 AAACAATCTATTTTGCAGA----GAAGCTAGAGGTCAGGGAAATGAAGGG 916622 v vviii i ---- i iii vi i ii v C MIR3#SINE/MIR 151 AACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTG 102 chr6qtel1M 916623 AGATGTCCAATGTTACACAGCTA 916645 vv i v i ? C MIR3#SINE/MIR 101 ACTTGCCCAAGGTCACACAGCNA 79 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.05 CpG sites = 26, Kimura (unadjusted) = 42.05 Transitions / transversions = 2.89 (26/9) Gap_init rate = 0.03 (3 / 115), avg. gap size = 2.33 (7 / 3) 303 36.07 4.92 0.00 chr6qtel1M 917022 917204 (82796) CR1-3_Croc#LINE/CR1 2602 2793 (812) m_b322s551i6 13497 chr6qtel1M 917022 ATTTTAAGAAGGAAATTGAAAAGCTAGAAAGCGTCCAGAGAAGGACACCC 917071 i vi v i i i v iv i v v CR1-3_Croc#LI 2602 ATTTTAAAAAGGACGTGGAGAAGTTAGAGAGGGTCCAGAGGCGGGCAACA 2651 chr6qtel1M 917072 AGAATTTTAAAGAACTTTAAATGTTTGTTACATGAGGATACGTCGAAAAA 917121 ii vv ii vi v ivv i i i v v ii ii CR1-3_Croc#LI 2652 AAGATGATAAAGGGCTTGGAAGGCAAGTCATACGAGGAGAGGCTGAAGGA 2701 chr6qtel1M 917122 ACTGGAAATG--------GAGAAAAAAAAGGTTCAGTGAATATATGGAAG 917163 i i iv -------- v i iiv v v v iiv i iv CR1-3_Croc#LI 2702 GCTAGGCATGTTCAGCTTGCGGAAAAGGCGCTTAAGAGGGGACATGATAG 2751 chr6qtel1M 917164 CTGATTTCAAATATCTAAAGGTTTATCAT-GGGAAGAAGAAA 917204 v vi ii i vi ii -ii i i CR1-3_Croc#LI 2752 CAGTCTTCAAATACTTGAAGGGCTGCCATAAAGAAGAGGGAA 2793 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 49.60 CpG sites = 41, Kimura (unadjusted) = 51.92 Transitions / transversions = 1.64 (41/25) Gap_init rate = 0.01 (2 / 182), avg. gap size = 4.50 (9 / 2) 411 33.84 7.69 5.66 chr6qtel1M 917227 917486 (82514) L3#LINE/CR1 3832 4096 (3) m_b322s601i49 13498 chr6qtel1M 917227 AAAAGGCAGAATCAGGAGCGATGAATAAAAAACCATAAAGCTGCAGATTA 917276 i i ii v i ii ii i-ii i ii vv v L3#LINE/CR1 3832 AGAGGGCAGAACTAGGACCAATGGGTGGAAG-TTACAGGGAGGCAGATTT 3880 chr6qtel1M 917277 CC-CTTAATGTTAGGGAAAGGCTCCTGTTAAGGTTCCATTAAGTGGAGCT 917325 v- i i - i iii ---------- i vi vii L3#LINE/CR1 3881 CGGCTCAATAT-AAGGAAGAACT----------TTCTAACAATCAGAGCT 3919 chr6qtel1M 917326 GTCCAAGG-TGGAATA------------AAGTGGTAGACCCACTGCCCTT 917362 ii- i------------ i i iii i v i i vi L3#LINE/CR1 3920 GTCCAAAAATGGAATGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGTCACT 3969 chr6qtel1M 917363 TGGAGCTCTTTAA--AAAGGATGGCTGATCACTTGAT-GGGATGGAATAA 917409 - v v i -- i v v i vi- vvi i L3#LINE/CR1 3970 -GGAGGTGTTCAAGCAGAGGCTGGATGACCACTTGTCAGGGATGTTGTAG 4018 chr6qtel1M 917410 TGGAGATTCCTT--TTGCATAT-AGGTTGTATTAGAAAGATGTTAAGCTC 917456 vi i v-- v iv- v i viivivi v L3#LINE/CR1 4019 AAGGGATTCCTGCATTGGATGGGAGGTTGGACTAGATGACCTCTAAGGTC 4068 chr6qtel1M 917457 TCTTTTGACTCTTGAATTCTGTGAATTTCT 917486 i iii vii -- L3#LINE/CR1 4069 CCTTCCAACTCTGAGATTCTGTGA--TTCT 4096 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 47.48 CpG sites = 57, Kimura (unadjusted) = 48.33 Transitions / transversions = 2.19 (57/26) Gap_init rate = 0.08 (22 / 259), avg. gap size = 1.59 (35 / 22) 330 30.38 8.15 6.99 chr6qtel1M 917609 917792 (82208) C MIR3#SINE/MIR (21) 187 2 m_b322s601i50 13499 chr6qtel1M 917609 TCAGAGCTTAAAAAAAATATATGATAGAGATCATTTATACCAATGTCTTT 917658 -ii iii iv ---- i vv i-i ii C MIR3#SINE/MIR 187 TCAGAGCT-GGAAGGGACCT----TAGAGATCATCTAGTCCAAC-CCCCT 144 chr6qtel1M 917659 TATTATACA--TAAAGAAGTCAAGACCCAGA---GTAAAGTTTCTCACTC 917703 i v -- i i iiii i --- i vv ii i C MIR3#SINE/MIR 143 CATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCC 94 chr6qtel1M 917704 AAAGGTCAGTCACA-CAAGTTAGAAAATTACAGAGGCAAAATCA-AACAC 917751 - -- - ? ---- vi v iii ii - v C MIR3#SINE/MIR 93 -AAGGTCA--CACAGCNAGTTAG----TGGCAGAGCCGGGACTAGAACCC 51 chr6qtel1M 917752 AGAACCTTTGACTTCAAATCCAGG--------ACTCTGCCACTGTACCA 917792 iv iii i v i iv --------i v v i C MIR3#SINE/MIR 50 AGGTCTCCTGACTCCCAGTCCGTGCTCTCTCTGCTCAGCCACTCTGCCA 2 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.99 CpG sites = 38, Kimura (unadjusted) = 42.19 Transitions / transversions = 2.71 (38/14) Gap_init rate = 0.10 (18 / 183), avg. gap size = 1.56 (28 / 18) 342 29.46 4.44 4.44 chr6qtel1M 917661 917795 (82205) C MIRc#SINE/MIR (126) 142 8 m_b322s601i51 13499 chr6qtel1M 917661 TTATACATAAAGAAGTCAAGACCCAGAG---TAAAGTTTCTCACTCAAAG 917707 i v i i iiii i i --- v vv ii i i C MIRc#SINE/MIR 142 TTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGG 93 chr6qtel1M 917708 GTCAGTCACACAAGTTAGAAAATTACAGAGGCAAAA-TCAAACACAGAAC 917756 ----- - i v i vi v iii - i v iv C MIRc#SINE/MIR 92 -----TCACACA-GCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTC 49 chr6qtel1M 917757 CTT-TGACTTCAAATCCAGGACTCTG-CCACTGTACCACAC 917795 i i- i i vi v- i C MIRc#SINE/MIR 48 TTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACAC 8 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.98 CpG sites = 27, Kimura (unadjusted) = 39.72 Transitions / transversions = 2.45 (27/11) Gap_init rate = 0.07 (10 / 134), avg. gap size = 1.20 (12 / 10) 361 32.11 2.96 2.35 chr6qtel1M 917806 917974 (82026) C L3#LINE/CR1 (5) 4094 3925 m_b322s601i52 13500 chr6qtel1M 917806 AATCAGAGAAGCTGTGAGCTGCAAGGAACCTCAGCCATCATGTAATCCAA 917855 v v vv i v i i vvi v i C L3#LINE/CR1 4094 AATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCAA 4045 chr6qtel1M 917856 -CTCAGA-CCTACAAAAGAACATCTGCGATAAGACATCAG---AGTAATC 917900 - vv - v iiv i ivi v v i v ivi v --- ii C L3#LINE/CR1 4044 CCTCCCATCCAATGCAGGAATCCCTTCTACAACATCCCTGACAAGTGGTC 3995 chr6qtel1M 917901 ATTGAGTCTATGCTTGAAGACCTACAAAGAGGGGGGACCCCATCCATTGA 917950 iv i v v v iv -v v i - i ii-- C L3#LINE/CR1 3994 ATCCAGCCTCTGCTTGAACACCTCCAGTGA-CGGGGAGCTCA-CTACC-- 3949 chr6qtel1M 917951 TCTCAAAGCAACTCATTCTACTTT 917974 ? i i i i i i C L3#LINE/CR1 3948 TCNCGAGGCAGCCCATTCCATTTT 3925 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.07 CpG sites = 28, Kimura (unadjusted) = 43.14 Transitions / transversions = 1.12 (28/25) Gap_init rate = 0.04 (7 / 168), avg. gap size = 1.29 (9 / 7) 365 28.57 3.06 0.00 chr6qtel1M 918002 918099 (81901) C MIR3#SINE/MIR (31) 177 77 m_b322s601i53 13501 chr6qtel1M 918002 AAAGGACTTTAGATGCTACATAGATCAACCCTTCCATTTTATAACTCAGG 918051 i i viii iv vi iii i iv v C MIR3#SINE/MIR 177 AAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGG 128 chr6qtel1M 918052 AAACCAAG--CAAAAGGGATTAAATGATTTGATCAAGGTCACACA-CAAG 918098 ii -- v i i i v i i vi - ? C MIR3#SINE/MIR 127 AAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGCNAG 78 chr6qtel1M 918099 T 918099 C MIR3#SINE/MIR 77 T 77 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.65 CpG sites = 20, Kimura (unadjusted) = 38.65 Transitions / transversions = 2.50 (20/8) Gap_init rate = 0.02 (2 / 97), avg. gap size = 1.50 (3 / 2) 297 31.81 7.97 2.05 chr6qtel1M 918409 918546 (81454) L2d_3end#LINE/L2 367 512 (4) m_b322s601i54 13502 chr6qtel1M 918409 ATGTGTGTGTGCATTATCTTCCAAAA-GGAATATAAGCTTCTCAAAGGCA 918457 vv iv i i v v-i v i i ii i L2d_3end#LINE 367 ATGTGTGTTAGTCTTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCA 416 chr6qtel1M 918458 ATGAC--TG------ACTTTTGTCCCCATTTCCCA-AACATCTAGTACAA 918498 iv -- ------ ? - i?i i i - i ii i i L2d_3end#LINE 417 GGGACCATGTCTTATACTNTT-TTNTCGTTCCCCACAGCGCCTAGCACAG 465 chr6qtel1M 918499 TA-TAAGGACTTATAATATATTCTTAATAAATGTGTGCTAATTAGTGGA 918546 i- i v -- i viiv i iiv i i ii v L2d_3end#LINE 466 TGCTGAGCAC--ATAGTAGGCGCTCAATAAATACTTGTTGATTGATTGA 512 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.24 CpG sites = 31, Kimura (unadjusted) = 45.62 Transitions / transversions = 2.58 (31/12) Gap_init rate = 0.06 (8 / 137), avg. gap size = 1.75 (14 / 8) 221 29.09 0.00 0.00 chr6qtel1M 920647 920701 (79299) C MIR3#SINE/MIR (3) 205 151 m_b322s601i55 13503 chr6qtel1M 920647 TCCTAGAATCATCAAATGTTATTGTTGGGAAATATTTTAAAGATCTTTTA 920696 v vi i vv i i iiv ii i v i C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTA 156 chr6qtel1M 920697 GTCCA 920701 C MIR3#SINE/MIR 155 GTCCA 151 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.16 CpG sites = 10, Kimura (unadjusted) = 38.16 Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 523 22.13 1.64 0.00 chr6qtel1M 920772 920893 (79107) MER63D#DNA/hAT-Tip100 348 471 (590) m_b322s502i1 13504 chr6qtel1M 920772 ACACTTCAGAAATCAGCAAATACTCCACATCAGGGCTTAATGCATTATTT 920821 iv i i ii v v i vi i MER63D#DNA/hA 348 ACACCACGGAAATCGGCAAACGCTACAAATCAGGGCTTGATTTATTGTTT 397 chr6qtel1M 920822 TATGATTTGTCTACACGTTAGAAAATGATGG-GGACATGTTAATAATGCA 920870 i viv v v v i - i v MER63D#DNA/hA 398 TGTTGATTGTCTAGACTTAAGAAAGTGATGGAGAAAATGTTAATAATGCA 447 chr6qtel1M 920871 GATTAAA-TTAACCATGTGCCTTG 920893 - vvi i v MER63D#DNA/hA 448 GATTAAACTTAAAAGTGTGTCGTG 471 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 23.13 CpG sites = 14, Kimura (unadjusted) = 26.47 Transitions / transversions = 1.08 (14/13) Gap_init rate = 0.02 (2 / 121), avg. gap size = 1.00 (2 / 2) 324 32.39 2.80 5.00 chr6qtel1M 920944 921086 (78914) C MIR3#SINE/MIR (49) 159 20 m_b322s601i56 13503 chr6qtel1M 920944 TCTAATCCAAGTTACTGATTCTGAAGATGAGGAAGC-AAGATCTATTGAA 920992 i viiv v i iv i -i ii i vv i C MIR3#SINE/MIR 159 TCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAG 110 chr6qtel1M 920993 GTAAAATGAG-TACTT-AGGACACCTAGTTAGTTAATAGCAGAACTTGCG 921040 i i v- i ii- v vi i? i i i -i v C MIR3#SINE/MIR 109 GTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGC-CGGG 61 chr6qtel1M 921041 ACCAGAA-CAAGGTCAATCTTTCTCCATCCCAGGCCAATATCCTTTC 921086 i - v ----- i vvv v -i iii i C MIR3#SINE/MIR 60 ACTAGAACCCAGGTC-----TCCTGACTCCCAGTCC-GTGCTCTCTC 20 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.37 CpG sites = 29, Kimura (unadjusted) = 45.19 Transitions / transversions = 1.93 (29/15) Gap_init rate = 0.08 (11 / 142), avg. gap size = 1.00 (11 / 11) 263 19.64 1.75 1.75 chr6qtel1M 921557 921613 (78387) C L2d_3end#LINE/L2 (4) 512 456 m_b322s601i57 13505 chr6qtel1M 921557 TCAATCTATCAACAAGAATCTATTAAGTATCTACTATGTA-TCATTCACT 921605 v v i i iii i- -v C L2d_3end#LINE 512 TCAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCA-GCACT 464 chr6qtel1M 921606 ATGTTAGG 921613 i i C L2d_3end#LINE 463 GTGCTAGG 456 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 20.92 CpG sites = 8, Kimura (unadjusted) = 23.55 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.04 (2 / 56), avg. gap size = 1.00 (2 / 2) 13 13.24 0.00 0.00 chr6qtel1M 921811 921835 (78165) (TTTG)n#Simple_repeat 1 25 (0) m_b322s252i17 13506 chr6qtel1M 921811 TTTATTTGTTTGTTTGTTTATATGT 921835 i i v (TTTG)n#Simpl 1 TTTGTTTGTTTGTTTGTTTGTTTGT 25 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 14 18.87 0.00 2.70 chr6qtel1M 923066 923103 (76897) (AAAGAA)n#Simple_repeat 1 37 (0) m_b322s252i18 13507 chr6qtel1M 923066 AAATAAAAAGCTATTAAAAAAGAAAAAGAAAAATGAAA 923103 v vv vvi - (AAAGAA)n#Sim 1 AAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAA-GAAA 37 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 442 34.77 3.24 0.70 chr6qtel1M 924262 924539 (75461) C L1ME4c_3end#LINE/L1 (376) 454 170 m_b322s551i7 13508 chr6qtel1M 924262 CAACAAATATTTTTGTACAATGTGGGTCTTTTTCTCTTTTTTATTATCTC 924311 ii i i i i - i i v i iii vv i C L1ME4c_3end#L 454 CAATGAACATCTTCGTGCA-TATAGCTTTTTCCTTCTTTTGAATTATTTC 406 chr6qtel1M 924312 TTTGGAATACAGACCAGGTGGTGGTATTGATGGATCAAAG--TATAATAC 924359 i i i v vv vi vi v iv i -- i - C L1ME4c_3end#L 405 CTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGA-AC 357 chr6qtel1M 924360 AGTTTTATAGCCTTTTGGACAAAGTTTTAGATTGCTCTCCAAAATAAATG 924409 v i ii viv iv v vii i i viiv C L1ME4c_3end#L 356 ATTTTTATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTG 307 chr6qtel1M 924410 AATCAC----CAACTCCACTAACAATGTGCTAATGTACTAACTTTCCCAG 924455 v i v---- ?iv i i iiv i? i ii iv iv C L1ME4c_3end#L 306 TACCAATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCACCGC 257 chr6qtel1M 924456 ATCCCTTCTAAACCT---CATTTTCCTTTTCTGTCATATTAGCCAATCAG 924502 ? iiv i ivvi ---i v vv i vvv v v i ivi C L1ME4c_3end#L 256 ANCCTCGCCAGCATTGGGTATTATCAATTTTTTAAATTTTTGCTAATTTA 207 chr6qtel1M 924503 AGAGGTGTAAGATGGTACCTCAGAGTTGCTTTAATTT 924539 v i i i vv C L1ME4c_3end#L 206 ATAGGCGTAAAATGGTATCTCATTGTTGCTTTAATTT 170 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 45.89 CpG sites = 57, Kimura (unadjusted) = 49.51 Transitions / transversions = 1.46 (57/39) Gap_init rate = 0.02 (5 / 277), avg. gap size = 2.20 (11 / 5) 246 30.06 10.48 0.74 chr6qtel1M 926576 926699 (73301) MIR1_Amn#SINE/MIR 14 149 (81) m_b323s601i0 13509 chr6qtel1M 926576 TGGCTTAATG-ACAAATCATCTACATTTTGAGGTAGAAGTTCTGGGTTAG 926624 ii i - i i v - iv i vv vvii i vi v? MIR1_Amn#SINE 14 TGGTCTAGTGGATAGAGCA-CTGGACTGGGACTCGGGAGACCTGGGTTCN 62 chr6qtel1M 926625 AATCCTGA--CTGCAATTTACTATTTCTAAGACCTTTGA------ATTTC 926666 ? i i-- v i ?i i?vi v?iv v i------ i ? MIR1_Amn#SINE 63 ANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGTCACTTN 112 chr6qtel1M 926667 ACTTCTCTAGG---CAGTTTCCT-GTCAGTAAAATGG 926699 i i? --- -i v MIR1_Amn#SINE 113 ACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGG 149 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 40.04 CpG sites = 23, Kimura (unadjusted) = 43.32 Transitions / transversions = 1.64 (23/14) Gap_init rate = 0.05 (6 / 123), avg. gap size = 2.33 (14 / 6) 300 24.00 13.00 0.00 chr6qtel1M 926600 926699 (73301) MIRb#SINE/MIR 38 150 (118) m_b323s601i1 13509 chr6qtel1M 926600 TTTTGAGGTAGA-AGTTCTGGGTTAGAATCCTGA--CTGCAATTTACTAT 926646 v vi - vi v i i-- v i v MIRb#SINE/MIR 38 TTTGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAG 87 chr6qtel1M 926647 TTCTAAGACCTTTGA------ATTTCACTTCTCTAGG---CAGTTTCCT- 926686 i v iv v i------ i v i ii --- - MIRb#SINE/MIR 88 CTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTC 137 chr6qtel1M 926687 GTCAGTAAAATGG 926699 i v MIRb#SINE/MIR 138 ATCTGTAAAATGG 150 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 27.90 CpG sites = 13, Kimura (unadjusted) = 29.31 Transitions / transversions = 1.18 (13/11) Gap_init rate = 0.05 (5 / 99), avg. gap size = 2.60 (13 / 5) 232 32.01 8.65 0.89 chr6qtel1M 926680 926783 (73217) L2a_3end#LINE/L2 383 494 (23) m_b323s601i2 13510 chr6qtel1M 926680 GTTTCCTGTCAGTAAAATGGAAGCTCCCACAAGGG-AGTGACTGTTGTGT 926728 i ivi v i v - ii - v v v L2a_3end#LINE 383 GTCTCCCCCCACTAGAATGTAAGCT-CCATGAGGGCAGGGACTTTTGTCT 431 chr6qtel1M 926729 -CCTTGCT-----TTGTATCCCTAGTGTCT--AACAGCACTTTTCACTCA 926770 -ii i -----i i i i -- ii i vv vi L2a_3end#LINE 432 GTTTTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACATA 481 chr6qtel1M 926771 ACTGGTACTTAGT 926783 iiv ii i i L2a_3end#LINE 482 GTAGGCGCTCAAT 494 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 40.74 CpG sites = 23, Kimura (unadjusted) = 44.63 Transitions / transversions = 2.30 (23/10) Gap_init rate = 0.05 (5 / 103), avg. gap size = 2.00 (10 / 5) 329 21.73 7.75 12.50 chr6qtel1M 927228 927369 (72631) C Charlie4#DNA/hAT-Charlie (20) 3358 3223 m_b323s502i1 13511 chr6qtel1M 927228 TATGTCATGGATCTCTTGGGTAGCCTATTGAAGTCCTTGGAACCTTTCTC 927277 i i i i v i i iv i iv v i C Charlie4#DNA/ 3358 TGTGCCATGGACCCCTTTGGCAGTCTGGTGAAGCCTATGGACCCCTTCTC 3309 chr6qtel1M 927278 AG------GGTTATAAATATATAAAAAATAAAATATGTAAGATTATTATT 927321 ------ v v ii -- ii i i---- C Charlie4#DNA/ 3308 AGAATAATGTTTTTAAATGCATAAAA--TAAAATACATAGGATTAC---- 3265 chr6qtel1M 927322 AAAATGAAATATGTGAAATTCCATTACATTGAA----AGTTACC-AAATA 927366 - v ----------i v i ---- i - C Charlie4#DNA/ 3264 -AAAGGAAA----------CCAATTATATTGAAATATAGTTATCAAAATA 3226 chr6qtel1M 927367 TTT 927369 C Charlie4#DNA/ 3225 TTT 3223 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 26.37 CpG sites = 19, Kimura (unadjusted) = 26.37 Transitions / transversions = 2.38 (19/8) Gap_init rate = 0.14 (20 / 141), avg. gap size = 1.40 (28 / 20) 331 24.12 6.74 2.15 chr6qtel1M 927228 927316 (72684) C Charlie4a#DNA/hAT-Charlie (20) 488 396 m_b323s502i0 13511 chr6qtel1M 927228 TATGTCATGGATCTCTTGGGTAGCCTATTGAAGTCCTTGGAACCTTTCTC 927277 i i i i v i i iv i iv v i C Charlie4a#DNA 488 TGTGCCATGGACCCCTTTGGCAGTCTGGTGAAGCCTATGGACCCCTTCTC 439 chr6qtel1M 927278 AG------GGTTATAAATATATAAAAAATAAAATATGTAAGATTA 927316 ------ v v ii -- ii i C Charlie4a#DNA 438 AGAATAATGTTTTTAAATGCATAAAA--TAAAATACATAGGATTA 396 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 30.41 CpG sites = 15, Kimura (unadjusted) = 30.41 Transitions / transversions = 2.50 (15/6) Gap_init rate = 0.03 (3 / 88), avg. gap size = 2.67 (8 / 3) 420 31.32 8.00 3.28 chr6qtel1M 927411 927585 (72415) L3#LINE/CR1 3915 4097 (2) m_b323s601i3 13512 chr6qtel1M 927411 GAGTGATCCAAAAGTAGAGTAGTCAATCATGGCAGCCAGAGGGAAGAGGT 927460 ivi i i i i v vii vi ?------ v ivii i L3#LINE/CR1 3915 GAGCTGTCCAAAAATGGAATGGGCTGCCTCGN------GAGGTAGTGAGC 3958 chr6qtel1M 927461 TCTCCCTCATAATAGATCTTTGAGCAGA-----------CACTTGTCAGG 927499 i v iviv i v ii ----------- L3#LINE/CR1 3959 TCCCCGTCACTGGAGGTGTTCAAGCAGAGGCTGGATGACCACTTGTCAGG 4008 chr6qtel1M 927500 CACTTTTTAGTAAGGATTCTT-CTTCAGGTGT-AGCTTGGACTAAATGGC 927547 v iv v v i i - v ii i v- v i i L3#LINE/CR1 4009 GATGTTGTAGAAGGGATTCCTGCATTGGATGGGAGGTTGGACTAGATGAC 4058 chr6qtel1M 927548 CACTAGAGTCCCTTATAATTCTCAAATTCTGT-ATTCCA 927585 v ii vi i v i - i L3#LINE/CR1 4059 CTCTAAGGTCCCTTCCAACTCTGAGATTCTGTGATTCTA 4097 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 41.57 CpG sites = 33, Kimura (unadjusted) = 42.66 Transitions / transversions = 1.65 (33/20) Gap_init rate = 0.06 (10 / 174), avg. gap size = 2.00 (20 / 10) 465 28.45 4.31 0.00 chr6qtel1M 927671 927786 (72214) L2d2_3end#LINE/L2 433 553 (2) m_b323s601i4 13513 chr6qtel1M 927671 ATTAGACTATGAACCCCTCAAAAGCAGAGACTGACTTTTGTTTTTCTTTG 927720 i i i i i i ii ii i iivv i i vi L2d2_3end#LIN 433 ACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACTTCTTTG 482 chr6qtel1M 927721 TATCCC----AACCCTTAGCACAGTGCCTGGAATAAAGTAGATGCTTAAT 927766 ---- i v i v v i v ii i L2d2_3end#LIN 483 TATCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAGTAGGCGCTCAAT 532 chr6qtel1M 927767 AAATGTTAATTGA-TTGATCT 927786 i vi - i L2d2_3end#LIN 533 AAATATTTGTTGATTTGATTT 553 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 36.84 CpG sites = 25, Kimura (unadjusted) = 38.37 Transitions / transversions = 3.12 (25/8) Gap_init rate = 0.02 (2 / 115), avg. gap size = 2.50 (5 / 2) 19 0.00 0.00 0.00 chr6qtel1M 928171 928191 (71809) (A)n#Simple_repeat 1 21 (0) m_b323s252i0 13514 chr6qtel1M 928171 AAAAAAAAAAAAAAAAAAAAA 928191 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAA 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 261 31.36 0.00 3.61 chr6qtel1M 928303 928388 (71612) C MIRb#SINE/MIR (182) 86 4 m_b323s601i6 13515 chr6qtel1M 928303 TATTAAGTATCTGAGACTGGATTTGAATTCAGCTCCTCCTGATTTCAGGG 928352 v iv v v v i ii v ivi i i ii C MIRb#SINE/MIR 86 TAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAG 37 chr6qtel1M 928353 CCAATGCTCTATCCAGGGTGCCATCTAGTTGCCCCT 928388 vi v vv ii i--- i C MIRb#SINE/MIR 36 CCCGTGCTCTTTCCACTGCACCAC---GCTGCCCCT 4 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 35.71 CpG sites = 15, Kimura (unadjusted) = 41.76 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.04 (3 / 85), avg. gap size = 1.00 (3 / 3) 281 30.14 0.00 0.00 chr6qtel1M 928303 928375 (71625) C MIRc#SINE/MIR (185) 83 11 m_b323s601i5 13515 chr6qtel1M 928303 TATTAAGTATCTGAGACTGGATTTGAATTCAGCTCCTCCTGATTTCAGGG 928352 v iv v v v i i ii v i i i i v C MIRc#SINE/MIR 83 TAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGT 34 chr6qtel1M 928353 CCAATGCTCTATCCAGGGTGCCA 928375 i v vv ii C MIRc#SINE/MIR 33 CCAGTGCTCTTTCCACTGCACCA 11 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 37.09 CpG sites = 12, Kimura (unadjusted) = 39.35 Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.00 (0 / 72), avg. gap size = 0.0 (0 / 0) 467 33.84 1.39 3.55 chr6qtel1M 928405 928692 (71308) L1ME3Cz_3end#LINE/L1 247 528 (469) m_b323s551i1 13516 chr6qtel1M 928405 GAGGAAATTGAGAAAGAGGGACAACTTCCAACCAGTTGTTGATGGAGTTG 928454 vi v vi --- ii vv -i i i iiv L1ME3Cz_3end# 247 GAGGATGTGGAGAAACGGG---AACTCTCATACA-CTGCTGGTGGGAGTG 292 chr6qtel1M 928455 CAAAATGATCTTACCATTCTGGAGAGCACTTTGGAACTATGT-CCAAAGG 928503 i v i viv i i v v v v -vi - L1ME3Cz_3end# 293 TAAATTGGTACAACCACTTTGGAGAGCAATTTGGCAATATCTAGTAAAG- 341 chr6qtel1M 928504 GCACTTAAACTGGGTATACCCTTTGATCTAGTAATACCCCTACTAGGTCT 928553 ---i v iv v i vi i i i v v v v L1ME3Cz_3end# 342 ---TTGAAGATGCGCATACCCTACGACCCAGCAATTCCACTTCTAGGTAT 388 chr6qtel1M 928554 GTATCCCAAAGGAATTAT--AAAAAGGGGA-AAGCACTCACATGTATAAA 928600 i i i i i i v --v v v v v - v --v i i L1ME3Cz_3end# 389 ATACCCTAGAGAAACTCTCGCACATGTGCACAAGGA--GACATGTACAAG 436 chr6qtel1M 928601 AATACTTTTGGCAGTTCTTTTTGTGTTAGCAAAGAATTGGATATTGAGGG 928650 i ii iv v ivi v iv i i v ivivvvi L1ME3Cz_3end# 437 GATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTA 486 chr6qtel1M 928651 AATGCCCATTAATTAGGGAAAAGCTGAACAAGTTATGGAATA 928692 i i vi vi v i i i i v L1ME3Cz_3end# 487 AATGTCCATCAATAGGGGAATGGATAAATAAATTGTGGTATA 528 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 44.03 CpG sites = 50, Kimura (unadjusted) = 46.00 Transitions / transversions = 1.14 (50/44) Gap_init rate = 0.05 (13 / 287), avg. gap size = 1.08 (14 / 13) 523 34.68 0.80 0.40 chr6qtel1M 928440 928688 (71312) L1ME4c_3end#LINE/L1 282 531 (299) m_b323s551i2 13516 chr6qtel1M 928440 TTGTTGATGGAGTTGCAAAATGATCTTACCATTCTGGAGAGCACTTTGGA 928489 i i vi? i v i viv v i i v v L1ME4c_3end#L 282 TTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGGC 331 chr6qtel1M 928490 ACTATGTCCAAAGGGCACTTAAACTGGGTATACCCTTTGATCTAGTAATA 928539 v i viv i vv v v vvi i i v L1ME4c_3end#L 332 AATACGTATCAAGAGCCATAAAAATGTTCATACCCTTTGACCCAGTAATT 381 chr6qtel1M 928540 CCCCTACTAGGTCTGTATCCCAAAGGAATTAT--AAAAAGGGGAAAGCAC 928587 v v i vv v i i i v -- iii ivi L1ME4c_3end#L 382 CCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAAGAAGGAAAAAGC 431 chr6qtel1M 928588 TCACATGTATAAAAATACTTTTGGCAGTTCTTTTTGTGTTAGCAAAGAAT 928637 - i i ii i ii iv v ivi v i iv i i L1ME4c_3end#L 432 T-ATATGCACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAAT 480 chr6qtel1M 928638 TGGATATTGAGGGAATGCCCATTAATTAGGGAAAAGCTGAACAAGTTATG 928687 v ivivvvi i vi vi vi i i ii i L1ME4c_3end#L 481 TGGAAACAACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATG 530 chr6qtel1M 928688 G 928688 L1ME4c_3end#L 531 G 531 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 45.25 CpG sites = 49, Kimura (unadjusted) = 48.45 Transitions / transversions = 1.32 (49/37) Gap_init rate = 0.01 (2 / 248), avg. gap size = 1.50 (3 / 2) 54 0.00 0.00 0.00 chr6qtel1M 928736 928781 (71219) (GA)n#Simple_repeat 1 46 (0) c_b323s251i0 13517 chr6qtel1M 928736 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 928781 (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 46 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 12 10.73 6.67 0.00 chr6qtel1M 929341 929370 (70630) (AAAAGA)n#Simple_repeat 1 32 (0) m_b323s252i1 13518 chr6qtel1M 929341 AAAAGAAAAAGAAAAAG-CTGA-AAAAAGAAA 929370 -vvi - (AAAAGA)n#Sim 1 AAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAA 32 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.07 (2 / 29), avg. gap size = 1.00 (2 / 2) 21 17.81 0.00 0.00 chr6qtel1M 929921 929958 (70042) (T)n#Simple_repeat 1 38 (0) m_b323s252i2 13519 chr6qtel1M 929921 TTTTTTCTTTTTTTTTTTTTTGGTTGGTTTTTATTTTT 929958 i vv vv v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 38 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 30 26.41 1.28 0.00 chr6qtel1M 930581 930658 (69342) (TA)n#Simple_repeat 1 79 (0) m_b323s252i3 13520 chr6qtel1M 930581 TATATGTTAATACAT-TACATATATATTAAAATATATATACACATATGTA 930629 i vv i - i vv v i i i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr6qtel1M 930630 TACATAGACATATATGTATGTGTATATAT 930658 i v i i i i (TA)n#Simple_ 51 TATATATATATATATATATATATATATAT 79 Matrix = Unknown Transitions / transversions = 1.83 (11/6) Gap_init rate = 0.01 (1 / 77), avg. gap size = 1.00 (1 / 1) 209 25.94 11.54 1.16 chr6qtel1M 930794 930871 (69129) MIR3#SINE/MIR 120 205 (3) m_b323s601i7 13521 chr6qtel1M 930794 CTTGGTTTTGTTGATC-ATAAAATAAGGGA-TTAAATGAGATGATCTCTA 930841 ii iv i- -i i i- ii iv MIR3#SINE/MIR 120 CTCAGTTTCCTC-ATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTA 168 chr6qtel1M 930842 AGGGGACTTTCAA-------ATGCTATGTTTCTGTGA 930871 vvv i i------- v v i MIR3#SINE/MIR 169 AGGTCCCTTCCAGCTCTGACATTCTATGATTCTATGA 205 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 33.00 CpG sites = 13, Kimura (unadjusted) = 33.00 Transitions / transversions = 1.86 (13/7) Gap_init rate = 0.05 (4 / 77), avg. gap size = 2.50 (10 / 4) 13 14.35 0.00 6.06 chr6qtel1M 932479 932513 (67487) (TTGTTT)n#Simple_repeat 1 33 (0) m_b323s252i4 13522 chr6qtel1M 932479 TTGTTTCTGTTGTTATTTTTATTGTTTGTATTTTG 932513 i v i i - - (TTGTTT)n#Sim 1 TTGTTTTTGTTTTTGTTTTTGTT-TTTGT-TTTTG 33 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 13 14.35 0.00 6.06 chr6qtel1M 932784 932818 (67182) (CAAAAA)n#Simple_repeat 1 33 (0) m_b323s252i5 13523 chr6qtel1M 932784 CAAAATACAAACAATAAAAATAACAACAGAAACAA 932818 - - i i v i (CAAAAA)n#Sim 1 CAAAA-ACAAA-AACAAAAACAAAAACAAAAACAA 33 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 274 27.15 9.68 0.99 chr6qtel1M 934426 934518 (65482) C MIR3#SINE/MIR (3) 205 105 m_b323s601i8 13524 chr6qtel1M 934426 TCACAGAAACATAGCAT-------TTGAAAGTCACCTTAGAGATCATCTC 934468 i v v -------i i vv v C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTA 156 chr6qtel1M 934469 ATTTAA-TCCCTTATTTTAT-GATCAAAAAAACCAAGCTGCAGGGAGTTC 934516 i ii -i i i- -i ii ii viv i v v C MIR3#SINE/MIR 155 GTCCAACCCCCTCATTTTACAGAT-GAGGAAACTGAGGCCCAGAGAGGTG 107 chr6qtel1M 934517 AA 934518 C MIR3#SINE/MIR 106 AA 105 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 34.94 CpG sites = 16, Kimura (unadjusted) = 34.94 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.04 (4 / 92), avg. gap size = 2.50 (10 / 4) 31 24.24 1.35 0.00 chr6qtel1M 934639 934712 (65288) (AT)n#Simple_repeat 1 75 (0) m_b323s252i6 13525 chr6qtel1M 934639 ATATATACACATACATATATATGTATACATATGTGTATATATGTTTTAAT 934688 i i i i i i i i v vv (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr6qtel1M 934689 ATATATGTA-ATGTATTAATATATA 934712 i - i vv (AT)n#Simple_ 51 ATATATATATATATATATATATATA 75 Matrix = Unknown Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.01 (1 / 73), avg. gap size = 1.00 (1 / 1) 14 26.27 4.62 1.49 chr6qtel1M 935298 935362 (64638) (AAGAA)n#Simple_repeat 1 67 (0) m_b323s252i7 13526 chr6qtel1M 935298 AAGAAACAG-AACGAAAGGAAAAG-TCATAAAA-AATAAAAACCAACCAA 935344 - - v i -vv v - v i vv vvi (AAGAA)n#Simp 1 AAGAAA-AGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGA 49 chr6qtel1M 935345 AAATAAAAGAAAAGGAAA 935362 v i (AAGAA)n#Simp 50 AAAGAAAAGAAAAGAAAA 67 Matrix = Unknown Transitions / transversions = 0.40 (4/10) Gap_init rate = 0.06 (4 / 64), avg. gap size = 1.00 (4 / 4) 76 18.28 1.81 1.81 chr6qtel1M 935592 935757 (64243) (TTCC)n#Simple_repeat 1 166 (0) m_b323s252i9 13527 chr6qtel1M 935592 TTCCTTCCTCCCTTCCTCCCTCTCTCCCTTCGTT-CTTCCCTTCTTCCTT 935640 i i ii i v - i i (TTCC)n#Simpl 1 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 50 chr6qtel1M 935641 CCTCTCTCCCTTCCTTCCTTCCTCCCTTCCTTCTTTCCTCCCTTCCCTTC 935690 ii i i i i i i (TTCC)n#Simpl 51 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 100 chr6qtel1M 935691 TGCTTTCCTTCCTTCC--CCTTCTCTTTCTTCTCCTCCTTCCTTTCTTTC 935738 v i -- - i - i - i (TTCC)n#Simpl 101 TTCCTTCCTTCCTTCCTTCCTTC-CTTCCTTC-CTTCCTTCC-TTCCTTC 147 chr6qtel1M 935739 CCTGCTTCCTCCCTTTCTT 935757 i v i i (TTCC)n#Simpl 148 CTTCCTTCCTTCCTTCCTT 166 Matrix = Unknown Transitions / transversions = 7.33 (22/3) Gap_init rate = 0.03 (5 / 165), avg. gap size = 1.20 (6 / 5) 40 32.73 2.67 2.67 chr6qtel1M 935591 935777 (64223) (TTTC)n#Simple_repeat 1 187 (0) m_b323s252i8 13528 chr6qtel1M 935591 TTTCCTTCCTCCCTTC-CTCCCTCTCTCCCTTCGTTCTTCCCTTCTTCCT 935639 i i i i -i ii - i i v i i i (TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTTTCT-TTCTTTCTTTCTTTCTTTCTTTCT 49 chr6qtel1M 935640 TCCTCTC-TCCCTTCCTTCCTTCCTCCCTTCCTTCTTTCCTCCCTTCCCT 935688 i i - i i i i i i i i - ii i i (TTTC)n#Simpl 50 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT-CTTTCTTTCTT 98 chr6qtel1M 935689 TC-TGCTTTCCTTCCTTC-CCCTTCTCTTTCTTCTCCTCCTTCCTTTCTT 935736 - v i i -ii - - i i i (TTTC)n#Simpl 99 TCTTTCTTTCTTTCTTTCTTTCTT-TCTTTCTT-TCTTTCTTTCTTTCTT 146 chr6qtel1M 935737 TCCCTGCTTCCTCCCTTTCTTTTTTTC-AGCTTTTTTTCTTT 935777 - i v i ii i -vv i (TTTC)n#Simpl 147 T-CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT 187 Matrix = Unknown Transitions / transversions = 7.80 (39/5) Gap_init rate = 0.05 (10 / 186), avg. gap size = 1.00 (10 / 10) 18 4.50 0.00 0.00 chr6qtel1M 936342 936364 (63636) (CT)n#Simple_repeat 1 23 (0) m_b323s252i10 13529 chr6qtel1M 936342 CTCTCTCGCTCTCTCTCTCTCTC 936364 v (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTC 23 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 509 34.44 0.74 0.74 chr6qtel1M 936412 936683 (63317) C L1ME4a_3end#LINE/L1 (340) 531 260 m_b323s551i3 13530 chr6qtel1M 936412 CCATAACTTGTTCAGCTTTTCCCTAATTAATGGGCATTCCCTCAATATCC 936461 i i i i iv? iv iv i ivvvivi v C L1ME4a_3end#L 531 CCATAATTTATTTAACCANTCCCCTATTGTTGGACATTTAGGTTGTTTCC 482 chr6qtel1M 936462 AATTCTTTGCTAACACAAAAAGAACTGCCAAAAGCATTTTTATATATGTA 936511 i i vi i v ivi v vi i ii i i iv C L1ME4a_3end#L 481 AATTTTTCGCTATTATAAATAATGCTGCGATGAACATCCTTGTACATAAA 432 chr6qtel1M 936512 TGTGCTTTCTCCTTTTTA--TAATCCCTTTGGATACAGACCTAGTAGTGG 936559 v viv ? v v i i i-- v i v v vv v C L1ME4a_3end#L 431 TCTTTGTNCACATCTCTGATTATTTCCTTAGGATAAATTCCTAGAAGTGG 382 chr6qtel1M 936560 TATTGCTAGATCAAAGGGTATACCCAGTTTAAGTGCCCTTTGGACATAGT 936609 v i i i i?v v v iv ii viv v C L1ME4a_3end#L 381 AATTACTGGGTCAAAGGGTATGNACATTTTTAAGGCTTTTGATACATATT 332 chr6qtel1M 936610 TCCAAAGTGCTCTCCAGAATGGTAAGATCATTTTGTAACTCCATTAACAA 936659 v v i v viv i v ii vii ii i - C L1ME4a_3end#L 331 GCCAAATTGCCCTCCAGAAAGGTTGTACCAATTTACACTCCCACCAGC-A 283 chr6qtel1M 936660 GTGGTTGAAAGTTGTCCCTTTTTC 936683 vv i - i v i? C L1ME4a_3end#L 282 GTGTATGAGAG-TGCCCGTTTCNC 260 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 47.60 CpG sites = 50, Kimura (unadjusted) = 48.33 Transitions / transversions = 1.16 (50/43) Gap_init rate = 0.01 (3 / 271), avg. gap size = 1.33 (4 / 3) 261 31.36 0.00 3.61 chr6qtel1M 936711 936796 (63204) MIRb#SINE/MIR 4 86 (182) m_b323s601i9 13531 chr6qtel1M 936711 AGGGGCAACTAGATGGCACCCTGGATAGAGCATTGGCCCTGAAATCAGGA 936760 i ---i ii vv v iv ii i i iv MIRb#SINE/MIR 4 AGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGAC 50 chr6qtel1M 936761 GGAGCTGAATTCAAATCCAGTCTCAGATACTTAATA 936796 i v ii i v v v vi v MIRb#SINE/MIR 51 AGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTA 86 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 35.71 CpG sites = 15, Kimura (unadjusted) = 41.76 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.04 (3 / 85), avg. gap size = 1.00 (3 / 3) 281 30.14 0.00 0.00 chr6qtel1M 936724 936796 (63204) MIRc#SINE/MIR 11 83 (185) m_b323s601i10 13531 chr6qtel1M 936724 TGGCACCCTGGATAGAGCATTGGCCCTGAAATCAGGAGGAGCTGAATTCA 936773 ii vv v i v i i i i v ii i MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chr6qtel1M 936774 AATCCAGTCTCAGATACTTAATA 936796 i v v v vi v MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTACTA 83 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 37.09 CpG sites = 12, Kimura (unadjusted) = 39.35 Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.00 (0 / 72), avg. gap size = 0.0 (0 / 0) 16 9.71 0.00 0.00 chr6qtel1M 937006 937027 (62973) (A)n#Simple_repeat 1 22 (0) m_b323s252i11 13532 chr6qtel1M 937006 AAAAAAAAAAAAAAAAGTAAAA 937027 iv (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAA 22 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 508 27.99 3.90 2.56 chr6qtel1M 937312 937465 (62535) C L2d2_3end#LINE/L2 (2) 553 398 m_b323s601i11 13533 chr6qtel1M 937312 AGATCAA-TCAATTAACATTTATTAAGCATCTACTTTATTCCAGGCACTG 937360 i - iv i i ii v i v v C L2d2_3end#LIN 553 AAATCAAATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTG 504 chr6qtel1M 937361 TGCTAAGGGTT----GGGATACAAAGAAATACAAAAGTCAGTCTCTGCTT 937406 i v i ---- i i i vvii i ii C L2d2_3end#LIN 503 TGCTAGGCGCTGTGGGGGATACAAAGAAGTATAAGACATGGTCCCTGCCC 454 chr6qtel1M 937407 TTGAGGGGTTCACAGTCTAATATCAATGAGATAAGAAAGCCACA-GTGGC 937455 ii i i i i --i iiiv i v vvv - -- C L2d2_3end#LIN 453 TCAAGGAGCTTACAATCTA--GTTGGGGAGACAAGACATAAACACGTG-- 408 chr6qtel1M 937456 AGAAGTTGAA 937465 i i C L2d2_3end#LIN 407 AAAAGTTAAA 398 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 35.91 CpG sites = 30, Kimura (unadjusted) = 37.06 Transitions / transversions = 2.50 (30/12) Gap_init rate = 0.05 (7 / 153), avg. gap size = 1.43 (10 / 7) 370 32.63 8.18 3.61 chr6qtel1M 937515 937673 (62327) C L3#LINE/CR1 (19) 4080 3915 m_b323s601i12 13534 chr6qtel1M 937515 AGAATTATAAGGGACTCTAGTGGTCATTTAGTCCAACCT-ACACCTGAAG 937563 i iv ii v i -v i ii v C L3#LINE/CR1 4080 AGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCAACCTCCCATCCAATG 4031 chr6qtel1M 937564 -AAGAATTCTTACTAAAAAGTGCCTGACAAGTG-----------TTTGCT 937601 - i i i v v vi v ----------- i C L3#LINE/CR1 4030 CAGGAATCCCTTCTACAACATCCCTGACAAGTGGTCATCCAGCCTCTGCT 3981 chr6qtel1M 937602 CAAAGATCTATTATGAGGGAGAACCTCTTCCCTCTGGCTGCCATGATTGA 937651 ii v i vivi v i i iivi v ------? iv iiv v C L3#LINE/CR1 3980 TGAACACCTCCAGTGACGGGGAGCTCACTACCTC------NCGAGGCAGC 3937 chr6qtel1M 937652 CTACTCTACTTTTGGATCACTC 937673 i i i i ivi C L3#LINE/CR1 3936 CCATTCCATTTTTGGACAGCTC 3915 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 44.26 CpG sites = 32, Kimura (unadjusted) = 45.53 Transitions / transversions = 1.78 (32/18) Gap_init rate = 0.06 (9 / 158), avg. gap size = 2.11 (19 / 9) 329 21.73 7.75 12.50 chr6qtel1M 937715 937856 (62144) Charlie4#DNA/hAT-Charlie 3223 3358 (20) m_b323s502i2 13535 chr6qtel1M 937715 AAATATTT-GGTAACT----TTCAATGTAATGGAATTTCACATATTTCAT 937759 - i ---- i v i---------- v Charlie4#DNA/ 3223 AAATATTTTGATAACTATATTTCAATATAATTGG----------TTTCCT 3262 chr6qtel1M 937760 TTTAATAATAATCTTACATATTTTATTTTTTATATATTTATAACC----- 937804 -----i i ii -- ii v v ----- Charlie4#DNA/ 3263 TT-----GTAATCCTATGTATTTTA--TTTTATGCATTTAAAAACATTAT 3305 chr6qtel1M 937805 -CTGAGAAAGGTTCCAAGGACTTCAATAGGCTACCCAAGAGATCCATGAC 937853 - i v vi i vi i i v i i i Charlie4#DNA/ 3306 TCTGAGAAGGGGTCCATAGGCTTCACCAGACTGCCAAAGGGGTCCATGGC 3355 chr6qtel1M 937854 ATA 937856 i Charlie4#DNA/ 3356 ACA 3358 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 26.37 CpG sites = 19, Kimura (unadjusted) = 26.37 Transitions / transversions = 2.38 (19/8) Gap_init rate = 0.15 (21 / 141), avg. gap size = 1.33 (28 / 21) 331 24.12 6.74 2.15 chr6qtel1M 937768 937856 (62144) Charlie4a#DNA/hAT-Charlie 396 488 (20) m_b323s502i3 13535 chr6qtel1M 937768 TAATCTTACATATTTTATTTTTTATATATTTATAACC------CTGAGAA 937811 i ii -- ii v v ------ Charlie4a#DNA 396 TAATCCTATGTATTTTA--TTTTATGCATTTAAAAACATTATTCTGAGAA 443 chr6qtel1M 937812 AGGTTCCAAGGACTTCAATAGGCTACCCAAGAGATCCATGACATA 937856 i v vi i vi i i v i i i i Charlie4a#DNA 444 GGGGTCCATAGGCTTCACCAGACTGCCAAAGGGGTCCATGGCACA 488 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 30.41 CpG sites = 15, Kimura (unadjusted) = 30.41 Transitions / transversions = 2.50 (15/6) Gap_init rate = 0.03 (3 / 88), avg. gap size = 2.67 (8 / 3) 236 33.32 6.61 0.78 chr6qtel1M 938301 938421 (61579) C L2d2_3end#LINE/L2 (23) 532 405 m_b323s601i13 13536 chr6qtel1M 938301 ACTAAGTACCAGTTGAGTGAAAAGTGCTGT--TAGACACTA---GGGATA 938345 i i ii vii v v i ii -- i i i--- C L2d2_3end#LIN 532 ATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGTGGGGGATA 483 chr6qtel1M 938346 CAAAGCAAGGACAAAACA--ATCACTCCCTTGTGGGAGCTTATATTTTA- 938392 - v i i --i v v i vvi i v i - C L2d2_3end#LIN 482 CAAAG-AAGTATAAGACATGGTCCCTGCCCTCAAGGAGCTTACAATCTAG 434 chr6qtel1M 938393 CTGAGAGGAAACTGCCTAGAGAAGTGAAA 938421 i i ii v vvi v i v v C L2d2_3end#LIN 433 TTGGGGAGACAAGACATAAACACGTGAAA 405 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 42.86 CpG sites = 25, Kimura (unadjusted) = 46.20 Transitions / transversions = 1.67 (25/15) Gap_init rate = 0.04 (5 / 120), avg. gap size = 1.80 (9 / 5) 269 28.65 10.58 2.68 chr6qtel1M 938301 938404 (61596) C L2a_3end#LINE/L2 (23) 494 383 m_b323s601i14 13536 chr6qtel1M 938301 ACTAAGTACCAGTTGAGTGAAAAGTGCTGTT--AGACACTAGGGATACAA 938348 i i ii vii iv vv i ii -- i i i - C L2a_3end#LINE 494 ATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGCGCTGGGGATACA- 446 chr6qtel1M 938349 AGCAA-GGACAAAACAA-------TCACT-CCCTTGTGGGAGCTTATATT 938389 - i- i i------- v - ii - i C L2a_3end#LINE 445 -GCAGTGAACAAAACAGACAAAAGTCCCTGCCCTCATGG-AGCTTACATT 398 chr6qtel1M 938390 TTACTGAGAGGAAAC 938404 i v i i i C L2a_3end#LINE 397 CTAGTGGGGGGAGAC 383 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 35.59 CpG sites = 23, Kimura (unadjusted) = 39.33 Transitions / transversions = 3.83 (23/6) Gap_init rate = 0.07 (7 / 103), avg. gap size = 2.00 (14 / 7) 299 20.43 15.05 0.00 chr6qtel1M 938387 938479 (61521) C MIRb#SINE/MIR (120) 148 42 m_b323s601i15 13537 chr6qtel1M 938387 ATTTTACTGA-GAGGAAACTG---CCTAGAGAAGTGAAAT------TCAA 938426 v - --- ii i v i ------i v C MIRb#SINE/MIR 148 ATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCA 99 chr6qtel1M 938427 AGGTCTC-CAGATAGTAAATTGCAG--TCAGGATTCTAACCCAGAACT-T 938472 v - v i v --i i v iv - C MIRb#SINE/MIR 98 AGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGT 49 chr6qtel1M 938473 CTACCTC 938479 iv C MIRb#SINE/MIR 48 CTGACTC 42 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 22.68 CpG sites = 10, Kimura (unadjusted) = 24.06 Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.07 (6 / 92), avg. gap size = 2.33 (14 / 6) 13 15.86 5.71 0.00 chr6qtel1M 938940 938974 (61026) (CAA)n#Simple_repeat 1 37 (0) m_b323s252i12 13538 chr6qtel1M 938940 CAATAACAACAA-AA-AAGAAAAAAAATAACAACAAC 938974 i - - v v v i (CAA)n#Simple 1 CAACAACAACAACAACAACAACAACAACAACAACAAC 37 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 234 26.98 0.00 0.00 chr6qtel1M 940193 940255 (59745) C L1MC5_3end#LINE/L1 (2142) 552 490 m_b323s551i4 13539 chr6qtel1M 940193 ATAACATTGCATTACTTTCATATACTATAACTTATTCAACCACTCCCCAA 940242 ii i v iiv vv i i ii v v C L1MC5_3end#LI 552 ATAGTACTCCATTGTGTGGATGTACCATAGTTTATTCAACCAGTCCCCTA 503 chr6qtel1M 940243 TTGATAGGCATTT 940255 i i C L1MC5_3end#LI 502 TTGATGGACATTT 490 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 34.67 CpG sites = 11, Kimura (unadjusted) = 34.67 Transitions / transversions = 1.83 (11/6) Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0) 23 18.80 0.00 0.00 chr6qtel1M 940304 940346 (59654) (T)n#Simple_repeat 1 43 (0) m_b323s252i13 13540 chr6qtel1M 940304 TTTTTTATTTTATTTTTTTCTTTCTTTTCTTTCTTTCTTTTTT 940346 v v i i i i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 43 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 23 20.97 0.00 4.76 chr6qtel1M 940505 940570 (59430) (TTAT)n#Simple_repeat 1 63 (0) m_b323s252i14 13541 chr6qtel1M 940505 TTCTTTTTATGTTTCTTTCTTTTATTTTATTTATTTATTTATTTATTTTT 940554 v v v i v -v - v (TTAT)n#Simpl 1 TTATTTATTTATTTATTT-ATTTA-TTTATTTATTTATTTATTTATTTAT 48 chr6qtel1M 940555 AATAGCTTTTTATTTA 940570 -v vi v (TTAT)n#Simpl 49 -TTATTTATTTATTTA 63 Matrix = Unknown Transitions / transversions = 0.22 (2/9) Gap_init rate = 0.05 (3 / 65), avg. gap size = 1.00 (3 / 3) 574 32.97 1.42 1.06 chr6qtel1M 940996 941277 (58723) L1ME4c_3end#LINE/L1 170 452 (378) m_b323s551i5 13542 chr6qtel1M 940996 AAATTAAAACAACTCTGATGTATTATCTTACACCTCTCTGATTGGCTAAT 941045 i vv vi ii i i v ivi i v v L1ME4c_3end#L 170 AAATTAAAGCAACAATGAGATACCATTTTACGCCTATTAAATTAGCAAAA 219 chr6qtel1M 941046 ATGACAGAAAAGGAAAATG----AGGTTTTTAGGGGATGTGGAAAAGTTG 941091 vvv i vv v i---- v i vvi- i ? i vi ii L1ME4c_3end#L 220 ATTTAAAAAATTGATAATACCCAATGCTGGC-GAGGNTGCGGTGAAACTG 268 chr6qtel1M 941092 GTACACTAACACATTTTTGGTGGAATTATAAACTGATTCAATTATTTTGG 941141 ? v i vi v ? i i i v iiv L1ME4c_3end#L 269 GTACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGG 318 chr6qtel1M 941142 AGAGCAATCTGGAACTTTGTCTAAAAGGCTATAAAACTGGGCATTATACT 941191 i i v v vi v v ii i v vv - iv L1ME4c_3end#L 319 AAAGCAATTTGGCAATACGTATCAAGAGCCATAAAAATGTTCA-TACCCT 367 chr6qtel1M 941192 TTGATCCATCAATACTACTACCTGGTCTGTATTCCAAAGAGATAATAAAA 941241 i vi v i v iv vv v i i i i vv L1ME4c_3end#L 368 TTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAA 417 chr6qtel1M 941242 AAGAGAAAAAGACCCACATTGTACAAAAATATTTAT 941277 iii i v i i - i i i i i L1ME4c_3end#L 418 AAGAAGGAAAAAGCTATA-TGCACGAAGATGTTCAT 452 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 42.04 CpG sites = 51, Kimura (unadjusted) = 45.32 Transitions / transversions = 1.24 (51/41) Gap_init rate = 0.01 (4 / 281), avg. gap size = 1.75 (7 / 4) 36 0.00 0.00 0.00 chr6qtel1M 941505 941537 (58463) (AAC)n#Simple_repeat 1 33 (0) c_b323s251i1 13543 chr6qtel1M 941505 AACAACAACAACAACAACAACAACAACAACAAC 941537 (AAC)n#Simple 1 AACAACAACAACAACAACAACAACAACAACAAC 33 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 281 27.81 4.27 1.67 chr6qtel1M 941734 941850 (58150) L1ME2z_3end#LINE/L1 447 566 (625) m_b323s551i6 13544 chr6qtel1M 941734 CATAGTAGCTCT-TTTGTGGTGGCAAAAAATTGGAAATTGAG---GGGTG 941779 i i - ii ii i v i i-- ---i L1ME2z_3end#L 447 CATAGCAGCTTTATTCATAATAGCCAAAAACTGGAAAC--AGCCCAGGTG 494 chr6qtel1M 941780 CCCATTAA-ATGGGAATGAATGAAAAAGTTGTGGTATATAAATGTAATGA 941828 i i - v i i i v ii vv ii i L1ME2z_3end#L 495 TCCATCAACAGGAGAATGGATAAACAAACTGTGGTATATTCATACAATGG 544 chr6qtel1M 941829 ATTACTATTGTGTTATAACAAG 941850 v i vv iv v L1ME2z_3end#L 545 AATACTACTCAGCAATAAAAAG 566 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.48 CpG sites = 22, Kimura (unadjusted) = 36.48 Transitions / transversions = 2.20 (22/10) Gap_init rate = 0.04 (5 / 116), avg. gap size = 1.40 (7 / 5) 269 19.64 1.75 1.75 chr6qtel1M 943426 943482 (56518) L2d_3end#LINE/L2 456 512 (4) m_b323s601i16 13545 chr6qtel1M 943426 CCTAACATAGTGTCTGA-TACATAGTAGATACTTAATAGAATCTTGTTGA 943474 i i - -i iii i i vv L2d_3end#LINE 456 CCTAGCACAGTG-CTGAGCACATAGTAGGCGCTCAATAAATACTTGTTGA 504 chr6qtel1M 943475 TAGATTGA 943482 v L2d_3end#LINE 505 TTGATTGA 512 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 20.92 CpG sites = 8, Kimura (unadjusted) = 23.55 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.04 (2 / 56), avg. gap size = 1.00 (2 / 2) 228 37.72 2.38 3.20 chr6qtel1M 943957 944082 (55918) MIRc#SINE/MIR 21 145 (123) m_b323s601i17 13546 chr6qtel1M 943957 GAAAGGATATTGGCCTGGGATGGAAAAAGATTGACCTTGTTCTGGTTGCA 944006 iii i v v vvv ii ---- v v ii iv v v MIRc#SINE/MIR 21 GAAAGAGCACTGGACTTGGAGTCAGGAAGA----CCTGGGTTCGAGTCCC 66 chr6qtel1M 944007 AGTTCTGCTATTAACTAACTAGGTGTCCT-AAGTA-CTCATTTTACTTCA 944054 i i i i v i iv v -ii i -v i v i v MIRc#SINE/MIR 67 GGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCT 116 chr6qtel1M 944055 ATAGATCTT-GCTTCCTCATCTTCAGAAT 944082 v iiii i- i vi i MIRc#SINE/MIR 117 CTGAGCCTCAGTTTCCTCATCTGTAAAAT 145 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 51.77 CpG sites = 28, Kimura (unadjusted) = 55.38 Transitions / transversions = 1.56 (28/18) Gap_init rate = 0.06 (7 / 125), avg. gap size = 1.00 (7 / 7) 314 30.90 3.60 0.88 chr6qtel1M 943989 944099 (55901) MIR3#SINE/MIR 46 159 (49) m_b323s601i18 13546 chr6qtel1M 943989 GACCTTG-TTCTGGTTGCAAGTTCTGCTATTAACTAACTAGGTGTCCT-A 944036 v - i iv i- i i i ?i iv v -i MIR3#SINE/MIR 46 GACCTGGGTTCTAGTCCCG-GCTCTGCCACTAACTNGCTGTGTGACCTTG 94 chr6qtel1M 944037 AGTA-CTCATTTTACTTCAATAGATCTT-GCTTCCTCATCTTCAGAATCA 944084 i i -v i i i vv i ii i- i vi i v MIR3#SINE/MIR 95 GGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGA 144 chr6qtel1M 944085 GTGACTTGGATTAGA 944099 v iv i MIR3#SINE/MIR 145 GGGGGTTGGACTAGA 159 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 40.94 CpG sites = 23, Kimura (unadjusted) = 42.64 Transitions / transversions = 2.09 (23/11) Gap_init rate = 0.05 (5 / 110), avg. gap size = 1.00 (5 / 5) 269 14.29 0.00 0.00 chr6qtel1M 944112 944153 (55847) C MER63C#DNA/hAT-Tip100 (15) 915 874 m_b323s502i4 13547 chr6qtel1M 944112 AAATATTTAAGAACTGGCTCTCTGGAAAAAAAAATGTATGCA 944153 i v i ii i C MER63C#DNA/hA 915 AAATGTTTAACAACCGGCTCTCTGGGGAAAAAAATGTATGTA 874 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 13.58 CpG sites = 5, Kimura (unadjusted) = 16.40 Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 570 20.49 1.64 0.00 chr6qtel1M 944152 944273 (55727) C MER63D#DNA/hAT-Tip100 (590) 471 348 m_b323s502i5 13547 chr6qtel1M 944152 CAAGACACATGCTTAA-TTTAATCTTCATTATTAACATTTCC-CCATCAT 944199 v ivi - v i - i C MER63D#DNA/hA 471 CACGACACACTTTTAAGTTTAATCTGCATTATTAACATTTTCTCCATCAC 422 chr6qtel1M 944200 TTTCTAAGATATAGACAAATCATAAAATAATGCATTAAGCCCTGATGTGT 944249 v ii v viv i i iv i v C MER63D#DNA/hA 421 TTTCTTAAGTCTAGACAATCAACAAAACAATAAATCAAGCCCTGATTTGT 372 chr6qtel1M 944250 AGTATTTGCTGATTTCTGAGGTGT 944273 ii i i v C MER63D#DNA/hA 371 AGCGTTTGCCGATTTCCGTGGTGT 348 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 21.04 CpG sites = 15, Kimura (unadjusted) = 24.34 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.02 (2 / 121), avg. gap size = 1.00 (2 / 2) 21 22.73 0.00 0.00 chr6qtel1M 946000 946045 (53955) (AT)n#Simple_repeat 1 46 (0) m_b323s252i15 13548 chr6qtel1M 946000 ATATATGTATACATATATATACACATATATATTTTTTGAAATATAT 946045 i i i i v v vv v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATAT 46 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 208 27.96 15.56 1.96 chr6qtel1M 946248 946382 (53618) L2a_3end#LINE/L2 363 515 (2) m_b323s601i19 13549 chr6qtel1M 946248 TATTTATTTTTATATCTTCTATTTACTTCTTC----ATGTACA-TGTATG 946292 v v iv i i v ii iv ---- vi- vi L2a_3end#LINE 363 TATTTATTTGTTTATTGTCTGTCTCCCCCCACTAGAATGTAAGCTCCATG 412 chr6qtel1M 946293 AGC-CAAGTTAATTTTGGTCT-TTCTGTCTCA-------ATTTCCA---- 946329 v- i --i i v - i - ------- ii ---- L2a_3end#LINE 413 AGGGCAGG--GACTTTTGTCTGTTTTGT-TCACTGCTGTATCCCCAGCGC 459 chr6qtel1M 946330 --AGAA-AATGACTGGCACAGGGTAAACACATCACAAATGTTTGTTTATT 946376 -- - i v vi ii i viv i i v v L2a_3end#LINE 460 CTAGAACAGTGCCTGGCACATAGTAGGCGCTCAATAAATATTTGTTGAAT 509 chr6qtel1M 946377 GAATGA 946382 L2a_3end#LINE 510 GAATGA 515 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 34.84 CpG sites = 22, Kimura (unadjusted) = 36.06 Transitions / transversions = 1.47 (22/15) Gap_init rate = 0.08 (11 / 134), avg. gap size = 2.18 (24 / 11) 245 31.04 0.00 4.23 chr6qtel1M 947673 947746 (52254) C L2b_3end#LINE/L2 (71) 395 325 m_b323s601i20 13550 chr6qtel1M 947673 AATGGAGAACAGAATAGCAAACACAGTCCCTGCTCTTAAGGACCTCATAT 947722 ii v ii i --- ? i i i v v i v C L2b_3end#LINE 395 AGCGGTGAACAAGACAG---ACNCGGTCCCTGCCCTCACGGAGCTCACAG 349 chr6qtel1M 947723 TCGAATAGGGGAAGGTAACATATA 947746 v i i iivvi i C L2b_3end#LINE 348 TCTAGTGGGGGAGACAGACATGTA 325 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 38.00 CpG sites = 15, Kimura (unadjusted) = 43.18 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.04 (3 / 73), avg. gap size = 1.00 (3 / 3) 234 29.17 1.39 0.00 chr6qtel1M 948011 948082 (51918) C MIRc#SINE/MIR (20) 248 176 m_b323s601i21 13551 chr6qtel1M 948011 TTTATTTAGAACTTTAAGATTTGTAAAATATATT-ACATGTATTATCTTA 948059 i v v vii ii iiiiv - ii i C MIRc#SINE/MIR 248 TTTGTATAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATCTCA 199 chr6qtel1M 948060 TTTGATGCTCAAAATAACCTTAT 948082 v v i i i C MIRc#SINE/MIR 198 TTTGATCCTCACAACAACCCTGT 176 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 36.51 CpG sites = 15, Kimura (unadjusted) = 39.22 Transitions / transversions = 2.50 (15/6) Gap_init rate = 0.01 (1 / 71), avg. gap size = 1.00 (1 / 1) 13 18.85 2.78 0.00 chr6qtel1M 948084 948119 (51881) (AATTACT)n#Simple_repeat 1 37 (0) m_b323s252i16 13552 chr6qtel1M 948084 AATTACAAGTAACTCATTACTAATTAC-AAGTATTAA 948119 v i v v - v i (AATTACT)n#Si 1 AATTACTAATTACTAATTACTAATTACTAATTACTAA 37 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) 573 24.08 0.00 3.01 chr6qtel1M 948375 948511 (51489) C MER63D#DNA/hAT-Tip100 (589) 472 340 m_b323s502i6 13553 chr6qtel1M 948375 ATATGATGCACTTTCAAGTTTAATCTGTATAACTGACATTTTCCCAATCA 948424 i i ii i i v i i i v C MER63D#DNA/hA 472 ACACGACACACTTTTAAGTTTAATCTGCATTATTAACATTTTCTCCATCA 423 chr6qtel1M 948425 CTTTCTAAAGCCTAAAGACTCAACAAAATAATAAATTGAGTTTGTAATTC 948474 v i i v v i ii iii- i --- C MER63D#DNA/hA 422 CTTTCTTAAGTCTAGACAATCAACAAAACAATAAATCAAGCCC-TGA--- 377 chr6qtel1M 948475 TTTGGAGTGTCTGCCAATTTCTGAGGTAGAAATGCTC 948511 v i i i i v iv i C MER63D#DNA/hA 376 TTTGTAGCGTTTGCCGATTTCCGTGGTGTAAATACTC 340 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 26.06 CpG sites = 24, Kimura (unadjusted) = 30.53 Transitions / transversions = 3.00 (24/8) Gap_init rate = 0.03 (4 / 136), avg. gap size = 1.00 (4 / 4) 16 5.20 0.00 0.00 chr6qtel1M 948540 948559 (51441) (AG)n#Simple_repeat 1 20 (0) m_b323s252i17 13554 chr6qtel1M 948540 AGAGAGAGAGAGAGTGAGAG 948559 v (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAG 20 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 230 22.58 0.00 1.61 chr6qtel1M 948695 948757 (51243) L1ME4b_3end#LINE/L1 160 221 (671) m_b323s551i7 13555 chr6qtel1M 948695 AGAGATATGCAAATGAAAATTACCTTGAAATTCTCCTTTTACACCCATCA 948744 v v i vi i v - v v i L1ME4b_3end#L 160 AGAGAAATGCAAATTAAAACTACACTGAGATAC-CATTTTTCACCTATCA 208 chr6qtel1M 948745 AAATGCCAAAGGT 948757 i v v i L1ME4b_3end#L 209 GATTGGCAAAGAT 221 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 26.94 CpG sites = 6, Kimura (unadjusted) = 26.94 Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.02 (1 / 62), avg. gap size = 1.00 (1 / 1) 47 0.00 0.00 0.00 chr6qtel1M 949131 949170 (50830) (CT)n#Simple_repeat 1 40 (0) c_b323s251i2 13556 chr6qtel1M 949131 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 949170 (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 40 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 432 26.89 6.83 2.99 chr6qtel1M 950307 950467 (49533) C MIR3#SINE/MIR (5) 203 37 m_b323s601i22 13557 chr6qtel1M 950307 ATTGAAT-GTAGAATGTCATAACTATAAAGGAGTTT-GAAATCATCCAGT 950354 v -i v i iv i vi - i i C MIR3#SINE/MIR 203 ATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGT 154 chr6qtel1M 950355 -GAAACTTTTCATTTGACCAAGGAGAATAATTGAGACCCAGAAA---GAA 950400 -v v iii v vi v i - i i i --- C MIR3#SINE/MIR 153 CCAACCCCCTCATTTTACAGATGAGGA-AACTGAGGCCCAGAGAGGTGAA 105 chr6qtel1M 950401 ATGCCTTGCTCAAGATCACCCAATTA-TTCATGGTCAATATAACCAT--C 950447 i v i i v ii? - vi - i--- i iv-- C MIR3#SINE/MIR 104 GTGACTTGCCCAAGGTCACACAGCNAGTTAGTGG-CAG---AGCCGGGAC 59 chr6qtel1M 950448 TAGAATCC--GTCTCTCCATTC 950467 i -- iiv i C MIR3#SINE/MIR 58 TAGAACCCAGGTCTCCTGACTC 37 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 33.97 CpG sites = 28, Kimura (unadjusted) = 35.02 Transitions / transversions = 2.00 (28/14) Gap_init rate = 0.07 (12 / 160), avg. gap size = 1.33 (16 / 12) 470 25.47 3.68 7.63 chr6qtel1M 951167 951302 (48698) C MIRc#SINE/MIR (124) 144 14 m_b323s601i23 13558 chr6qtel1M 951167 TTTTACATCTAAGGAAACTGAGGC-----AAACTTGAGCGACTTTGCCCA 951211 vv i -----i iv i i - C MIRc#SINE/MIR 144 TTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTT-GCCCA 96 chr6qtel1M 951212 GAGTCACACAACTAGTAAGTGTCTGAGGCCAGATTTGAACTCAGAAAAAA 951261 ii i v v v vi i i i ------ C MIRc#SINE/MIR 95 AGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAG------ 52 chr6qtel1M 951262 TGAGTCTTCCTTATTTCAGGCCCACAACTTTATCCATTATA 951302 --- v i i i i vvi i v i ii C MIRc#SINE/MIR 51 ---GTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCA 14 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 30.87 CpG sites = 21, Kimura (unadjusted) = 32.09 Transitions / transversions = 1.91 (21/11) Gap_init rate = 0.08 (11 / 135), avg. gap size = 1.36 (15 / 11) 19 8.15 4.88 2.38 chr6qtel1M 951870 951910 (48090) (AAATA)n#Simple_repeat 1 42 (0) m_b323s252i18 13559 chr6qtel1M 951870 AAAT-AAA-AAACTTTAATAAAATAAAATAAAATAAAAATAAA 951910 - - v vv - (AAATA)n#Simp 1 AAATAAAATAAAATAAAATAAAATAAAATAAAAT-AAAATAAA 42 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.07 (3 / 40), avg. gap size = 1.00 (3 / 3) 211 30.00 1.43 0.00 chr6qtel1M 951912 951981 (48019) MIRc#SINE/MIR 190 260 (8) m_b323s601i24 13560 chr6qtel1M 951912 AGAATTAAATGAGATGATATATGT-AAAATGGTTTGCACATTTTAAATCA 951960 i i i i - ii v i v i v vii MIRc#SINE/MIR 190 AGGATCAAATGAGATAATGTATGTGAAAGCGCTTTGTAAACTGTAAAGTG 239 chr6qtel1M 951961 GTATGTAAATGCTAGCTATTA 951981 v ii iv v?i MIRc#SINE/MIR 240 CTATACAAATGTAAGGNGTTA 260 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 38.48 CpG sites = 14, Kimura (unadjusted) = 41.06 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.01 (1 / 69), avg. gap size = 1.00 (1 / 1) 342 28.37 14.18 2.68 chr6qtel1M 952220 952353 (47647) C MIR3#SINE/MIR (44) 164 16 m_b323s601i25 13561 chr6qtel1M 952220 GATCATCCAGTGCAACTCTTGAATTTTATTCATAATGAAACTGAGATTTA 952269 i v i iivv ivv i v iiii C MIR3#SINE/MIR 164 GATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCA 115 chr6qtel1M 952270 G----GTGTTCTAAGTGACTTGGCTAACATTACACA-------AGTAAAA 952308 ---- ---- v i vi i ------- iiv C MIR3#SINE/MIR 114 GAGAGGTG----AAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCA 69 chr6qtel1M 952309 -----GGGAC-AGAATCCAGATATTCTGATCCCAAATTCAT--TATGTCT 952350 ----- - i i v i ii v i i i -- v v C MIR3#SINE/MIR 68 GAGCCGGGACTAGAACCCAGGTCTCCTGACTCCCAGTCCGTGCTCTCTCT 19 chr6qtel1M 952351 ACT 952353 i C MIR3#SINE/MIR 18 GCT 16 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 35.96 CpG sites = 24, Kimura (unadjusted) = 37.25 Transitions / transversions = 1.85 (24/13) Gap_init rate = 0.07 (9 / 133), avg. gap size = 2.56 (23 / 9) 224 33.33 0.00 0.00 chr6qtel1M 954056 954121 (45879) L2d_3end#LINE/L2 451 516 (0) m_b323s601i26 13562 chr6qtel1M 954056 CAGCTTTGAGGATGATGTTGGGCACAGAGTAGACACATCACAAATGTTTG 954105 viiv v iii i i v i i viv i ii L2d_3end#LINE 451 CAGCGCCTAGCACAGTGCTGAGCACATAGTAGGCGCTCAATAAATACTTG 500 chr6qtel1M 954106 TTTCTTGACTGATTGA 954121 vv i L2d_3end#LINE 501 TTGATTGATTGATTGA 516 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 43.45 CpG sites = 14, Kimura (unadjusted) = 46.36 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0) 13 15.32 0.00 10.00 chr6qtel1M 955469 955512 (44488) (ATGG)n#Simple_repeat 1 40 (0) m_b323s252i19 13563 chr6qtel1M 955469 ATGGATGCATGGGCATGTGGTGGAATGGATGAAAAGATGGATGG 955512 v - - - i - i vi (ATGG)n#Simpl 1 ATGGATGGAT-GG-ATG-GATGG-ATGGATGGATGGATGGATGG 40 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.09 (4 / 43), avg. gap size = 1.00 (4 / 4) 320 26.85 5.50 0.88 chr6qtel1M 955514 955622 (44378) C L2d_3end#LINE/L2 (23) 493 380 m_b323s601i27 13564 chr6qtel1M 955514 TTATTATGTGCTAACTATGTAC--AGAACTGTGGTAAATTCTAGGATTAA 955561 iv i iv i -- v v iiiv iv ivv C L2d_3end#LINE 493 TTATTGAGCGCCTACTATGTGCTCAGCACTGTGCTAGGCGCTGTGGGGAA 444 chr6qtel1M 955562 -AACAGAATAGCA-AAAACAT--TCCCTGCTCTGAAGGAACTCACCTTCT 955607 -i ? i ? i - i -- i v i i vv C L2d_3end#LINE 443 CGANAAAANAGTATAAGACATGGTCCCTGCCCTCAAGGAGCTTACAATCT 394 chr6qtel1M 955608 AATAGGGGAAGACAA 955622 i v - C L2d_3end#LINE 393 AGTTGGGG-AGACAA 380 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 30.56 CpG sites = 17, Kimura (unadjusted) = 34.87 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.05 (5 / 108), avg. gap size = 1.40 (7 / 5) 11 25.55 1.96 4.00 chr6qtel1M 955687 955737 (44263) (AAAATT)n#Simple_repeat 1 50 (0) m_b323s252i20 13565 chr6qtel1M 955687 AAATTTAAAAGTTATAGTCACATAACAAATTAAAATT-AATTTAAGAAAT 955735 v v v v v v v v - - v - v (AAAATT)n#Sim 1 AAAATTAAAATTAAAATTAAAATTA-AAATTAAAATTAAAATTAA-AATT 48 chr6qtel1M 955736 AA 955737 (AAAATT)n#Sim 49 AA 50 Matrix = Unknown Transitions / transversions = 0.00 (0/10) Gap_init rate = 0.06 (3 / 50), avg. gap size = 1.00 (3 / 3) 304 25.68 1.35 0.00 chr6qtel1M 955864 955937 (44063) C MIRc#SINE/MIR (20) 248 174 m_b323s601i28 13566 chr6qtel1M 955864 TTTATTTAGAATTTTAAGGTTTGCAGAACATATT-ACATGCATTATCTTA 955912 i v v i vi i i i iiv - i i C MIRc#SINE/MIR 248 TTTGTATAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATCTCA 199 chr6qtel1M 955913 TTTGATCCTCAAAATAACCTTATAA 955937 v i i i i C MIRc#SINE/MIR 198 TTTGATCCTCACAACAACCCTGTGA 174 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 31.01 CpG sites = 14, Kimura (unadjusted) = 33.15 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.01 (1 / 73), avg. gap size = 1.00 (1 / 1) 230 24.34 6.25 2.41 chr6qtel1M 955885 955964 (44036) C MIRb#SINE/MIR (48) 220 138 m_b323s601i29 13566 chr6qtel1M 955885 TGCAGAACATATTACATGCATTATCTTATTTGATCCTCAAAATAACCTT- 955933 vi i iiv i i v i i - C MIRb#SINE/MIR 220 TGCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTG 171 chr6qtel1M 955934 ----ATAATTATTATAATTACTAATTATTACAAAT 955964 ----i iv v i- iv - i C MIRb#SINE/MIR 170 CGAGGTAGGTATTATTATC-CCCATT-TTACAGAT 138 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 28.66 CpG sites = 13, Kimura (unadjusted) = 30.58 Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.05 (4 / 79), avg. gap size = 1.75 (7 / 4) 216 36.06 1.14 2.30 chr6qtel1M 956081 956168 (43832) C MIRc#SINE/MIR (176) 92 6 m_b323s601i30 13567 chr6qtel1M 956081 TTACATGGCTGGCAGGTTCTGGATGCTGACATT-GAACTTGAGTACTTCC 956129 i ii i i i vvii - i iv i - iiii - C MIRc#SINE/MIR 92 TCACACAGCTAGTAAGTGGCAGA-GCCGGGACTCGAACCCAGGT-CTTCC 45 chr6qtel1M 956130 TATCTCCAAGGACATTGTTCTTTTAACCATATCACAATG 956168 iv vv v i iv iii i v C MIRc#SINE/MIR 44 TGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTG 6 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 51.11 CpG sites = 22, Kimura (unadjusted) = 53.76 Transitions / transversions = 2.44 (22/9) Gap_init rate = 0.03 (3 / 87), avg. gap size = 1.00 (3 / 3) 532 19.01 15.70 0.00 chr6qtel1M 956461 956581 (43419) C MIRc#SINE/MIR (120) 148 9 m_b323s601i31 13566 chr6qtel1M 956461 CTCATTTTACAGATGAGGAAACTGAG-CT-----AAATAAGGTGATTTGC 956504 i - ----- ii v i i C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chr6qtel1M 956505 CCACGGTCACATGGCTAGCAAGT-----------GATTGGAATTGAGGTT 956543 v ii i ----------- i v iiv i C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTC 49 chr6qtel1M 956544 TTCCTAACTCCAGGACCAATGCTCTATCTA--GCACCATA 956581 i i v i v i -- i C MIRc#SINE/MIR 48 TTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACA 9 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 22.68 CpG sites = 17, Kimura (unadjusted) = 22.68 Transitions / transversions = 2.83 (17/6) Gap_init rate = 0.03 (4 / 120), avg. gap size = 4.75 (19 / 4) 264 18.64 5.08 0.00 chr6qtel1M 956598 956656 (43344) C CR1-3_Croc#LINE/CR1 (0) 3605 3544 m_b323s551i8 13568 chr6qtel1M 956598 CATAGGATCATAAAG--CTAGTGCTGGAAGGGACC-ACAGAGACCATCCA 956644 i i --v v -v ii i C CR1-3_Croc#LI 3605 CATAGAATCATAGAGAAGTAGGGCTGGAAGGGACCTCCAGAGGTCATCTA 3556 chr6qtel1M 956645 ATCCAACTCACT 956656 i i v C CR1-3_Croc#LI 3555 GTCCAACCCCCT 3544 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 21.84 CpG sites = 7, Kimura (unadjusted) = 21.84 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.03 (2 / 58), avg. gap size = 1.50 (3 / 2) 291 31.33 2.19 4.48 chr6qtel1M 956657 956793 (43207) C MIRb#SINE/MIR (119) 149 16 m_b323s601i32 13569 chr6qtel1M 956657 CATTTTATTATTGAGGAAACTG-CCCCCAAGGAGACTACAGTAAATGACT 956705 iviv -vv i ii ii - ---- C MIRb#SINE/MIR 149 CATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTA-AGTAA----CT 105 chr6qtel1M 956706 TACCTCATGTCACACAAGTTAACAGACATCTCAGGAAATATTC-AACTCA 956754 i iv v - i ii iiiiv vv vviiv - i C MIRb#SINE/MIR 104 TGCCCAAGGTCACACA-GCTAGTAAGTGGCAGAGCCGGGATTCGAACCCA 56 chr6qtel1M 956755 GCT-TCTCTGACTCTAAAGAGAGTGTTCTTCCCTGTGCAC 956793 v - v i vvv i i vv C MIRb#SINE/MIR 55 GGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCAC 16 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 40.04 CpG sites = 22, Kimura (unadjusted) = 41.35 Transitions / transversions = 1.16 (22/19) Gap_init rate = 0.07 (9 / 136), avg. gap size = 1.00 (9 / 9) 15 19.85 0.00 0.00 chr6qtel1M 956886 956914 (43086) (A)n#Simple_repeat 1 29 (0) m_b323s252i21 13570 chr6qtel1M 956886 AAAAAAAAAAAAAAGACAGAAAAGCAAAA 956914 i v i iv (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA 29 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 14 35.18 2.44 0.00 chr6qtel1M 957128 957209 (42791) (CTTTCT)n#Simple_repeat 1 84 (0) m_b323s252i22 13571 chr6qtel1M 957128 CTTTTTATTTTACTTAATCTTTTTGTTTAT-TTTATAAAT-TCTCTCTCT 957175 i v iv vv i v v - v vvv - i (CTTTCT)n#Sim 1 CTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCT 50 chr6qtel1M 957176 TTCTCCCGCCATCTCTATCTCTCTGTCTCTTTCT 957209 iiv iv i v i v (CTTTCT)n#Sim 51 TTCTCTTTCTCTTTCTCTTTCTCTTTCTCTTTCT 84 Matrix = Unknown Transitions / transversions = 0.64 (9/14) Gap_init rate = 0.02 (2 / 81), avg. gap size = 1.00 (2 / 2) 21 21.51 0.00 0.00 chr6qtel1M 957167 957209 (42791) (TC)n#Simple_repeat 1 43 (0) m_b323s252i23 13571 chr6qtel1M 957167 TCTCTCTCTTTCTCCCGCCATCTCTATCTCTCTGTCTCTTTCT 957209 i i v iv v v i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 43 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 403 20.22 0.00 0.00 chr6qtel1M 957309 957397 (42603) C MER63D#DNA/hAT-Tip100 (589) 472 384 m_b323s502i7 13572 chr6qtel1M 957309 ATATGATGCACTTTCAAGTTTAATCTGTATTATTAACATTTTCCCACTCA 957358 i i ii i i i vv C MER63D#DNA/hA 472 ACACGACACACTTTTAAGTTTAATCTGCATTATTAACATTTTCTCCATCA 423 chr6qtel1M 957359 TTTTCTTAAGTCTAATGATTTAAATCAACAATAAATCAA 957397 i ivv v i vvv C MER63D#DNA/hA 422 CTTTCTTAAGTCTAGACAATCAACAAAACAATAAATCAA 384 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 22.39 CpG sites = 10, Kimura (unadjusted) = 23.84 Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.00 (0 / 88), avg. gap size = 0.0 (0 / 0) 15 10.04 0.00 8.57 chr6qtel1M 957398 957435 (42565) (TAAT)n#Simple_repeat 1 35 (0) m_b323s252i24 13573 chr6qtel1M 957398 TAAATAATTACATTATTTTAATTAATTACATTAAATAA 957435 v - -v - v (TAAT)n#Simpl 1 TAATTAATTA-ATTA-ATTAATTAATTA-ATTAATTAA 35 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.08 (3 / 37), avg. gap size = 1.00 (3 / 3) 330 20.93 0.00 6.94 chr6qtel1M 957440 957516 (42484) C MER63D#DNA/hAT-Tip100 (654) 407 336 m_b323s502i8 13547 chr6qtel1M 957440 ACAATAAATACAACAATAAATCAAGTTTAGTAATGCTTTGTAGTGTCTGC 957489 v i v iii----- v i i C MER63D#DNA/hA 407 ACAATCAACAAAACAATAAATCAAGCCC-----TGATTTGTAGCGTTTGC 363 chr6qtel1M 957490 CAATTTCTGAGGTGGAAATGCTCACAC 957516 i i v v i v C MER63D#DNA/hA 362 CGATTTCCGTGGTGTAAATACTCCCAC 336 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 19.50 CpG sites = 9, Kimura (unadjusted) = 24.83 Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.07 (5 / 76), avg. gap size = 1.00 (5 / 5) 256 22.54 0.00 1.41 chr6qtel1M 957689 957760 (42240) L1ME4b_3end#LINE/L1 151 221 (671) m_b323s551i10 13574 chr6qtel1M 957689 CTAATAATCAGAGAAATGCAAATGAAAATTACCTTGAAATTCTCCTTTTA 957738 v v v i vi i v - v v L1ME4b_3end#L 151 CTCATAATAAGAGAAATGCAAATTAAAACTACACTGAGATAC-CATTTTT 199 chr6qtel1M 957739 CACCAGTCAAAATGCCAAAGGT 957760 vi i v v i L1ME4b_3end#L 200 CACCTATCAGATTGGCAAAGAT 221 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 26.81 CpG sites = 6, Kimura (unadjusted) = 26.81 Transitions / transversions = 0.60 (6/10) Gap_init rate = 0.01 (1 / 71), avg. gap size = 1.00 (1 / 1) 304 17.47 0.00 1.59 chr6qtel1M 957689 957752 (42248) L1PB4_3end#LINE/L1 151 213 (690) m_b323s551i9 13574 chr6qtel1M 957689 CTAATAATCAGAGAAATGCAAATGAAAATTACCTTGAAATTCTCCTTTTA 957738 v v ii vv i v - v i L1PB4_3end#LI 151 CTAATCATCAGAGAAATGCAAATTAAAACCACAATGAGATAC-CATCTTA 199 chr6qtel1M 957739 CACCAGTCAAAATG 957752 i L1PB4_3end#LI 200 CACCAGTCAGAATG 213 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 19.93 CpG sites = 5, Kimura (unadjusted) = 19.93 Transitions / transversions = 0.83 (5/6) Gap_init rate = 0.02 (1 / 63), avg. gap size = 1.00 (1 / 1) 23 7.16 0.00 0.00 chr6qtel1M 958557 958586 (41414) (AT)n#Simple_repeat 1 30 (0) m_b323s252i25 13575 chr6qtel1M 958557 ATACATACATATATATATATATATATATAT 958586 i i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATAT 30 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 28 24.42 2.74 0.00 chr6qtel1M 959654 959726 (40274) (TA)n#Simple_repeat 1 75 (0) m_b323s252i26 13576 chr6qtel1M 959654 TAAATATATAGACA-AAATATAGCTATATGTATGTATGT-TTTATACATA 959701 v v i - v vv i i i - v i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chr6qtel1M 959702 CACATACATATATATACATATATAT 959726 i i i i (TA)n#Simple_ 51 TATATATATATATATATATATATAT 75 Matrix = Unknown Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.03 (2 / 72), avg. gap size = 1.00 (2 / 2) 12 11.65 3.33 3.33 chr6qtel1M 961209 961238 (38762) (AAG)n#Simple_repeat 1 30 (0) m_b323s252i27 13577 chr6qtel1M 961209 AATAAGATGAATGAAGATG-AGAAGAAGAAG 961238 v v - v - (AAG)n#Simple 1 AAGAAGAAGAA-GAAGAAGAAGAAGAAGAAG 30 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.07 (2 / 29), avg. gap size = 1.00 (2 / 2) 312 29.31 5.92 9.15 chr6qtel1M 961331 961499 (38501) C MIR3#SINE/MIR (8) 200 37 m_b323s601i33 13578 chr6qtel1M 961331 GAAT-GTAGAAT-TCAGTATTGGAGGGGACATATAATATAAAACATTCAA 961378 -i - vii i v ------ i i------ C MIR3#SINE/MIR 200 GAATCATAGAATGTCAGAGCTGGAAGGGACCT------TAGAG------A 163 chr6qtel1M 961379 TCATCCAGTGCAAATTTTTCATTTGATCAAAAAGGATAAACGAGACCCAG 961428 i v viiii v ivi vi - vi i C MIR3#SINE/MIR 162 TCATCTAGTCCAACCCCCTCATTTTACAGATGAGGA-AACTGAGGCCCAG 114 chr6qtel1M 961429 AAA---GAAATGCCTTGCTCAAGACCATCCAACTA-TTCATGGCCAACAA 961474 i --- i v i ii iv i ? - vi -- v i C MIR3#SINE/MIR 113 AGAGGTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGC--AGAG 66 chr6qtel1M 961475 CCAT--CTAGAATCT--GTCTCTCCATTC 961499 iv-- i i-- iiv i C MIR3#SINE/MIR 65 CCGGGACTAGAACCCAGGTCTCCTGACTC 37 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 38.23 CpG sites = 31, Kimura (unadjusted) = 39.38 Transitions / transversions = 2.21 (31/14) Gap_init rate = 0.12 (21 / 168), avg. gap size = 1.19 (25 / 21) 13 18.95 4.55 2.22 chr6qtel1M 962375 962418 (37582) (GAAGAAG)n#Simple_repeat 1 45 (0) m_b324s252i1 13579 chr6qtel1M 962375 GAA-AAGGGAGAAGGAAGAAGAAGTGAATGAA-AAGGTAAAAAGAA 962418 - i i -v v - v i i (GAAGAAG)n#Si 1 GAAGAAGGAAGAAGGAAGAAGGA-AGAAGGAAGAAGGAAGAAGGAA 45 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.07 (3 / 43), avg. gap size = 1.00 (3 / 3) 15 22.06 0.00 0.00 chr6qtel1M 962553 962589 (37411) (TATA)n#Simple_repeat 1 37 (0) m_b324s252i2 13580 chr6qtel1M 962553 TATATATTTACATATATGTATCTACATAAATATACAT 962589 v i i v i v i (TATA)n#Simpl 1 TATATATATATATATATATATATATATATATATATAT 37 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 34 11.82 0.00 0.00 chr6qtel1M 962652 962706 (37294) (ATAT)n#Simple_repeat 1 55 (0) m_b324s252i3 13581 chr6qtel1M 962652 ATATAGATATAGATATATAGATAGATAGATATATGTATATATATATATAT 962701 v v v v v i (ATAT)n#Simpl 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr6qtel1M 962702 ATATA 962706 (ATAT)n#Simpl 51 ATATA 55 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 381 30.63 4.51 3.66 chr6qtel1M 962829 963072 (36928) L1ME5_3end#LINE/L1 392 637 (304) m_b324s551i0 13582 chr6qtel1M 962829 TATATCCCAAAGAGATTATAAAGAAGG----GAAAGGGACCTGTATGTGC 962874 i v v viv ----v i ---- i L1ME5_3end#LI 392 TATATCCCAAAGAAATTCTCACACAGGTCCATAAGGGGAC----ATGTAC 437 chr6qtel1M 962875 ACGAATGTTTGTGGCAGCCCTTTTTGTAGTGGCTAGAAACTGGAAACTGA 962924 iv i ii v vi v i vi i ii ii viv L1ME5_3end#LI 438 GAGGATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAAC 487 chr6qtel1M 962925 ATGGATGTCCATCAGTTG--GAATGGCTGAATAAATTGTGGTATATGAAA 962972 v i v v -- i v iii v iv v v L1ME5_3end#LI 488 CTGGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCAC 537 chr6qtel1M 962973 ATTATGGAATATTACTGT-TCTGTAAGAAATGACCAACAGGATGATTTCA 963021 ii i i - i-v v v iii vi vi -- v L1ME5_3end#LI 538 ACCATGGAGTACTA-TGCAGCAGTTAGAAGCAACGGACTAGATG--TACA 584 chr6qtel1M 963022 GAAAG--GCCTGGAGAGA-CTTACACGAAC-TGATGCTGAGTGAAATGAG 963067 v v --i v vi - v -- - ii vi L1ME5_3end#LI 585 CATAGCAACATGGATGGATCTTAAA--AACATAGTGCTGAGTGAAAAAAG 632 chr6qtel1M 963068 CAGGA 963072 i i L1ME5_3end#LI 633 TAAGA 637 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.59 CpG sites = 40, Kimura (unadjusted) = 40.32 Transitions / transversions = 1.25 (40/32) Gap_init rate = 0.06 (15 / 243), avg. gap size = 1.33 (20 / 15) 388 25.15 4.49 3.16 chr6qtel1M 962831 962986 (37014) L1ME4c_3end#LINE/L1 397 554 (276) m_b324s551i1 13582 chr6qtel1M 962831 TATCCCAAAGAGATTAT---AAAGAAGGGAAAGGGACCTGTATGTGCACG 962877 i i i v --- i i --- i -- L1ME4c_3end#L 397 TATCCTAAGGAAATAATTCAAAAGAAGGAAAAAG---CTATATG--CACG 441 chr6qtel1M 962878 AA--TGTTTGTGGCAGCCCTTTTTGTAGTGGCTAGAAACTGGAAACTGAA 962925 -- ii v vi v i i i v i i vivv L1ME4c_3end#L 442 AAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACC 491 chr6qtel1M 962926 TGGATGTCCATCAGT--TGGAATGGCTGAATAAATTGTGGTATATGAAAA 962973 ii v i --v i i i i i v? vv L1ME4c_3end#L 492 TAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACT 541 chr6qtel1M 962974 TTATGGAATATTA 962986 iv L1ME4c_3end#L 542 CGATGGAATATTA 554 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 30.82 CpG sites = 24, Kimura (unadjusted) = 31.83 Transitions / transversions = 1.71 (24/14) Gap_init rate = 0.05 (8 / 155), avg. gap size = 1.50 (12 / 8) 398 27.83 3.52 2.49 chr6qtel1M 962870 963068 (36932) L1MC4_3end#LINE/L1 433 633 (2156) m_b324s551i3 13582 chr6qtel1M 962870 TGTGCACGAATGTTTGTGGCAGCCCTTTTTGTAGTGGCTAGAAACTGGAA 962919 i i i ii v ii i ? i i ? L1MC4_3end#LI 433 TGTACACGAATGTTTATAGCAGCTTTATTCATAATNGCCAAAANCTGGAA 482 chr6qtel1M 962920 ACTGAATGGATGTCCATCAGTTG--GAATGGCTGAATAAATTGTGGTATA 962967 vivv?i v iiv -- v i i i i L1MC4_3end#LI 483 ACAACCNAGATGTCCTTCAACAGGTGAATGGATAAACAAACTGTGGTACA 532 chr6qtel1M 962968 TGAAAATTATGGAATATTACTGTTCTGT---AAGAAATGACCAACAGGAT 963014 vv v iv i vvv vi --- i v v ---- L1MC4_3end#LI 533 TCCATACAATGGAATACTACTCAGCGATAAAAAGGAATGAACTAC----T 578 chr6qtel1M 963015 GATTT-CAGAAAGGCCTGGA-GAGACTTACACGAACTGATGCTGAGTGAA 963062 ?i- iv ?ii v - iv v i v - ?v i L1MC4_3end#LI 579 GATNCACGCAANAACATGGATGAATCTTAAATGCA-TNTTGCTAAGTGAA 627 chr6qtel1M 963063 ATGAGC 963068 vi L1MC4_3end#LI 628 AGAAGC 633 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.11 CpG sites = 30, Kimura (unadjusted) = 36.97 Transitions / transversions = 1.25 (30/24) Gap_init rate = 0.05 (9 / 198), avg. gap size = 1.33 (12 / 9) 457 25.21 1.68 0.00 chr6qtel1M 962870 962988 (37012) L1ME1_3end#LINE/L1 433 553 (373) m_b324s551i2 13582 chr6qtel1M 962870 TGTGCACGAATGTTTGTGGCAGCCCTTTTTGTAGTGGCTAGAAACTGGAA 962919 i ii i ii v i i i i i L1ME1_3end#LI 433 TGTACACGAATGTTCATAGCAGCTTTATTCGTAATAGCCAAAAACTGGAA 482 chr6qtel1M 962920 ACTGAATGGATGTCCATCAGTTG--GAATGGCTGAATAAATTGTGGTATA 962967 vivviii ii? -- v i i L1ME1_3end#LI 483 ACAACCCAAATGTCCATCAACNGGTGAATGGATAAACAAATTGTGGTATA 532 chr6qtel1M 962968 TGAAAATTATGGAATATTACT 962988 vv v iv i L1ME1_3end#LI 533 TCCATACAATGGAATACTACT 553 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 31.11 CpG sites = 21, Kimura (unadjusted) = 32.44 Transitions / transversions = 2.33 (21/9) Gap_init rate = 0.01 (1 / 118), avg. gap size = 2.00 (2 / 1) 211 34.38 0.00 0.00 chr6qtel1M 963752 963815 (36185) L2a_3end#LINE/L2 452 515 (2) m_b324s601i1 13583 chr6qtel1M 963752 CCCAGCTTCCAAGATGATGACTGGAACAGGGTAAACACATCACAAATGTT 963801 vi i ii iii v v vi ii i viv i i L2a_3end#LINE 452 CCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGGCGCTCAATAAATATT 501 chr6qtel1M 963802 TGTTTATTGAATGA 963815 v v L2a_3end#LINE 502 TGTTGAATGAATGA 515 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 45.41 CpG sites = 14, Kimura (unadjusted) = 48.53 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0) 28 39.69 0.00 0.00 chr6qtel1M 965133 965268 (34732) (GGAT)n#Simple_repeat 1 136 (0) m_b324s252i5 13584 chr6qtel1M 965133 GGATGCATGGATGTATGGAGGGACAGAGTGATAGATGGAAGGATGGATAA 965182 v v v ii vv i v ii (GGAT)n#Simpl 1 GGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGG 50 chr6qtel1M 965183 ATATACTGATGCATAAATGCATGGACATGTGAATTAATAGAAGTATGGAT 965232 iv iv v ii v iivi i vi i v v (GGAT)n#Simpl 51 ATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGAT 100 chr6qtel1M 965233 AGATAAATGAAGAAATAAATGTATGGATGATTGGAT 965268 i ii i vii ii v iv (GGAT)n#Simpl 101 GGATGGATGGATGGATGGATGGATGGATGGATGGAT 136 Matrix = Unknown Transitions / transversions = 1.41 (24/17) Gap_init rate = 0.00 (0 / 135), avg. gap size = 0.0 (0 / 0) 289 34.77 2.84 2.11 chr6qtel1M 965269 965409 (34591) C L2d2_3end#LINE/L2 (12) 543 402 m_b324s601i3 13585 chr6qtel1M 965269 AAAAAATACTTATTAAGTGCTTTCTATGTACAAAATTTTGTAAT--GTGT 965316 v i i i i v i i iiivi iv -- i i C L2d2_3end#LIN 543 AACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGC 494 chr6qtel1M 965317 TCTAGGAT-TAGAATAGAATACCAAGA-ACAGCCCTTGCTCTCAAGGAAG 965364 v i iv- v vii i i- - ii i i i iv C L2d2_3end#LIN 493 TGTGGGGGATACAAAGAAGTAT-AAGACATGGTCCCTGCCCTCAAGGAGC 445 chr6qtel1M 965365 TCACATTCTAATAGGTGAAAATAACATATAGCAAGCTTTAAAAGT 965409 i v i v - i i i v i i- vi v v C L2d2_3end#LIN 444 TTACAATCTAGTTGG-GGAGACAAGACATAA-ACACGTGAAAAGT 402 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 47.28 CpG sites = 33, Kimura (unadjusted) = 50.34 Transitions / transversions = 2.20 (33/15) Gap_init rate = 0.04 (6 / 140), avg. gap size = 1.17 (7 / 6) 305 36.13 4.20 0.00 chr6qtel1M 965269 965387 (34613) C L2a_3end#LINE/L2 (12) 505 382 m_b324s601i2 13585 chr6qtel1M 965269 AAAAAATACTTATTAAGTGCTTTCTATGTACAAAATTTTGTAATGTGTTC 965318 v i i i i v i v iiivi vv iv iv C L2a_3end#LINE 505 AACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGCGC 456 chr6qtel1M 965319 TAGGATTAGAATAG-----AATACCAAGAACAGCCCTTGCTCTCAAGGAA 965363 i iv v ii ----- v vi v v i i i v i C L2a_3end#LINE 455 TGGGGATACAGCAGTGAACAAAACAGACAAAAGTCCCTGCCCTCATGGAG 406 chr6qtel1M 965364 GTCACATTCTAATAGGTGAAAATA 965387 v i i i v i i i C L2a_3end#LINE 405 CTTACATTCTAGTGGGGGGAGACA 382 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 48.29 CpG sites = 26, Kimura (unadjusted) = 51.77 Transitions / transversions = 1.53 (26/17) Gap_init rate = 0.01 (1 / 118), avg. gap size = 5.00 (5 / 1) 256 21.71 1.94 6.06 chr6qtel1M 965829 965931 (34069) C MIRc#SINE/MIR (0) 268 170 m_b324s601i4 13586 chr6qtel1M 965829 AATAATAGTTACCATTTAAATGGATTTTATTTCAAATTTTAAAGTTTGCA 965878 i v ?vi v --- v vv --i v i C MIRc#SINE/MIR 268 AATAATAATAACNCCTTACAT---TTGTATAGCA--CTTTACAGTTTACA 224 chr6qtel1M 965879 AAATATATT-ACATGCATTTATCTCATTTGATCCTCAAAAGAA-CCTATG 965926 iiiiv - i - v v - i C MIRc#SINE/MIR 223 AAGCGCTTTCACATACATT-ATCTCATTTGATCCTCACAACAACCCTGTG 175 chr6qtel1M 965927 AGTTA 965931 v C MIRc#SINE/MIR 174 AGGTA 170 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 24.49 CpG sites = 10, Kimura (unadjusted) = 26.01 Transitions / transversions = 0.91 (10/11) Gap_init rate = 0.08 (8 / 102), avg. gap size = 1.00 (8 / 8) 322 30.34 1.11 1.11 chr6qtel1M 966100 966189 (33811) C MIRc#SINE/MIR (173) 95 6 m_b324s601i5 13586 chr6qtel1M 966100 AAGTCACACAGCTGGTAGGT-CTGGAGGCTGACCTTGAACTTAAGCATCT 966148 i i i -vii v v iv i ii i iv - C MIRc#SINE/MIR 95 AGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCT-T 47 chr6qtel1M 966149 CCTAACGTCAAGGCCATTGCTCTTTCAACCATATCACATTG 966189 i vi v v v iii i i C MIRc#SINE/MIR 46 CCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTG 6 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.87 CpG sites = 18, Kimura (unadjusted) = 40.87 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.02 (2 / 89), avg. gap size = 1.00 (2 / 2) 486 25.65 3.68 4.32 chr6qtel1M 966451 966613 (33387) C MIR#SINE/MIR (96) 166 5 m_b324s601i6 13587 chr6qtel1M 966451 TGGAGTGGTGTGCTATTTCCTTCTCCAGTTCATTTTATAGATGGGGAAAC 966500 ii i - i --v v ---i i i C MIR#SINE/MIR 166 TGAGGTAG-GTACTATT--ATTATCC---CCATTTTACAGATGAGGAAAC 123 chr6qtel1M 966501 TGAGGCAAACA-AGG----GTGATTTGTCCAGGGTCACATGGCTAGCAAG 966545 v v - ---- i i i i ii i C MIR#SINE/MIR 122 TGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAG 73 chr6qtel1M 966546 TTTCTCAGACTAGAGTGGAATTCAGGTTTTCCTAACTCCAGGCCCCGTGC 966595 vv vv v vi v v ii ivv - ii iv C MIR#SINE/MIR 72 TGGCAGAGCCGGGATTCGAACCCAGGCAGT-CTGGCTCCAGAGCCCGTGC 24 chr6qtel1M 966596 TC-TATCCACTGTACCATA 966613 - v i i i C MIR#SINE/MIR 23 TCTTAACCACTATGCTATA 5 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.14 CpG sites = 24, Kimura (unadjusted) = 32.14 Transitions / transversions = 1.50 (24/16) Gap_init rate = 0.06 (10 / 162), avg. gap size = 1.30 (13 / 10) 616 23.31 3.76 0.00 chr6qtel1M 966481 966613 (33387) C MIRc#SINE/MIR (122) 146 9 m_b324s601i7 13587 chr6qtel1M 966481 CATTTTATAGATGGGGAAACTGAGGC--AAACAAG---GGTGATTTGTCC 966525 i i -- i v i ---i i i C MIRc#SINE/MIR 146 CATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCC 97 chr6qtel1M 966526 AGGGTCACATGGCTAGCAAGTTTCTCAGACTAGAGTGGAATTCAGGTTTT 966575 i ii i vv vv v vi v v ii i C MIRc#SINE/MIR 96 AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTT 47 chr6qtel1M 966576 CCTAACTCCAGGCCCCGTGCTCTATCCACTGTACCATA 966613 i i i v v i i C MIRc#SINE/MIR 46 CCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACA 9 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.70 CpG sites = 20, Kimura (unadjusted) = 28.70 Transitions / transversions = 1.82 (20/11) Gap_init rate = 0.02 (2 / 132), avg. gap size = 2.50 (5 / 2) 434 26.05 2.33 4.76 chr6qtel1M 966623 966751 (33249) C MIR3#SINE/MIR (0) 208 83 m_b324s601i8 13588 chr6qtel1M 966623 GGATCATAGCATAATAAA--GCTAATGCTGGAAGGGATCACAGAGACCAT 966670 i v v i -- ii iv i vi i C MIR3#SINE/MIR 208 GAATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCAT 159 chr6qtel1M 966671 CTAATGCAACTCACCCCTTTCATTGTTGAGGAAACTGGTACCCAAGGAGA 966720 i v i v i v i iv v ivi ii - C MIR3#SINE/MIR 158 CTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAG- 110 chr6qtel1M 966721 CTACAGT-AAGTGACTTACCTCATGTCTCACA 966751 ----- - i iv v v C MIR3#SINE/MIR 109 -----GTGAAGTGACTTGCCCAAGGTCACACA 83 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.71 CpG sites = 19, Kimura (unadjusted) = 32.71 Transitions / transversions = 1.46 (19/13) Gap_init rate = 0.06 (8 / 128), avg. gap size = 1.12 (9 / 8) 282 31.56 4.38 5.15 chr6qtel1M 966684 966820 (33180) C MIRc#SINE/MIR (120) 148 13 m_b324s601i9 13588 chr6qtel1M 966684 CCCCTTTCATTGTTGAGGAAACTGGTACCCAAGGAGACTACAGTAAGTGA 966733 v i iv v ivi i ii ii----- C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGT-----TAAGTGA 104 chr6qtel1M 966734 CTTACCTCATGTCTCACAAATAAAAAGCATTTCAGGAAAGGTTC-AGCTC 966782 i iv v v iv iv iivivv vvii ii - i i C MIRc#SINE/MIR 103 CTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCC 54 chr6qtel1M 966783 AG--CTTCTCTGACTCTAGAG---AGTGTTCTTCCCTATGCAC 966820 -- - i - --- i i vv C MIRc#SINE/MIR 53 AGGTCTTC-CTGACTCCA-AGTCCAGTGCTCTTTCCACTGCAC 13 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.11 CpG sites = 25, Kimura (unadjusted) = 42.50 Transitions / transversions = 1.56 (25/16) Gap_init rate = 0.07 (10 / 136), avg. gap size = 1.30 (13 / 10) 17 21.18 4.55 0.00 chr6qtel1M 967201 967244 (32756) (TC)n#Simple_repeat 1 46 (0) m_b324s252i6 13589 chr6qtel1M 967201 TCTCATTCTCTCTCTC-CTATCTCCCTCTC-CCCATTCTCTCTTTC 967244 vi - v i - i vi i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 46 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2) 449 24.75 0.00 8.77 chr6qtel1M 967551 967674 (32326) MIRb#SINE/MIR 1 114 (154) m_b324s601i10 13590 chr6qtel1M 967551 CAATGGGGCAGCTAAGTGGTGCAGTGTATAGAGCATCAATCCTGAAGTCA 967600 iv --- v v iviiiii i MIRb#SINE/MIR 1 CAGAGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCA 47 chr6qtel1M 967601 GAAGGAGCTGAGTTCAAATCTGTCCTCAGACACTTAATATGTCCTAGCTA 967650 vi v i i ivvv v v ------- i MIRb#SINE/MIR 48 GACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTA-------CTAGCTG 90 chr6qtel1M 967651 TGTGACCCTGGGCAAGTCATTCAA 967674 i i i i MIRb#SINE/MIR 91 TGTGACCTTGGGCAAGTTACTTAA 114 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 27.92 CpG sites = 17, Kimura (unadjusted) = 30.46 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.08 (10 / 123), avg. gap size = 1.00 (10 / 10) 16 5.20 0.00 0.00 chr6qtel1M 967685 967704 (32296) (A)n#Simple_repeat 1 20 (0) m_b324s252i7 13591 chr6qtel1M 967685 AAAACAAAAAAAAAAAAAAA 967704 v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAA 20 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 271 30.44 5.62 2.17 chr6qtel1M 967873 968050 (31950) L1ME5_3end#LINE/L1 152 335 (606) m_b324s551i4 13592 chr6qtel1M 967873 TATTGATCAGAGAAAAGCAAATGAAAATAACCTTGAAATTCTCCCTTTAC 967922 v i v v i vv i - v v L1ME5_3end#LI 152 TAGTAATCAGAGAAATGCAAATTAAAACAACAATGAGA-TATCACTTTAC 200 chr6qtel1M 967923 ACCCATCAAAATGCCAAAGATAACATGAAAGC---ACAAATTCAA-TG-A 967967 i i i v v i v --- --- i vvi - -v L1ME5_3end#LI 201 ACCTATTAGACTGGCAAAAATTA---GAAAGCTGGATAATGCCAAGTGTT 247 chr6qtel1M 967968 GGTTTGAATATAAGTAAAAAAGAA--ATCA---GCTGTTGGCAGAGCTCT 968012 ivv i i ii v ? v i --v ---i i ii iiv v L1ME5_3end#LI 248 GGCGAGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGT 297 chr6qtel1M 968013 GGATAGGTTCAAGCTTTTTGGAAAGCAACCTGACATTA 968050 i iv v iv v i i i i v L1ME5_3end#LI 298 AGACTGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTA 335 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.13 CpG sites = 28, Kimura (unadjusted) = 40.10 Transitions / transversions = 1.12 (28/25) Gap_init rate = 0.05 (9 / 177), avg. gap size = 1.56 (14 / 9) 31 11.61 1.75 0.00 chr6qtel1M 968303 968359 (31641) (AT)n#Simple_repeat 1 58 (0) c_b324s251i0 13593 chr6qtel1M 968303 ATATATATATATATACATATGTGTATCTAT-TATGTATATGTATATATAT 968351 i i i v - i i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr6qtel1M 968352 ATATATAT 968359 (AT)n#Simple_ 51 ATATATAT 58 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.02 (1 / 56), avg. gap size = 1.00 (1 / 1) 336 30.72 9.88 1.61 chr6qtel1M 969273 969444 (30556) C MIR3#SINE/MIR (17) 191 6 m_b324s601i11 13594 chr6qtel1M 969273 AATGTCATAACTTTAAAGGATTTT-GAGGTCATCCAGTGCAACTTTC-CA 969320 v i vv i ii - i i v iii - C MIR3#SINE/MIR 191 AATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCA 142 chr6qtel1M 969321 TTTGACTAAAGAGAATAAATAAGACTCCAAAA---GAAATGCCTTACTCA 969367 v vi v i - v i i i vi i --- i v i i C MIR3#SINE/MIR 141 TTTTACAGATGAGGA-AACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCA 93 chr6qtel1M 969368 AGACCACCCAACTA-TTCATGGTCAACAACCAT--CTAGAATCT--GTCT 969412 ii v i ? - vi - i- i iv-- i i-- C MIR3#SINE/MIR 92 AGGTCACACAGCNAGTTAGTGG-CAG-AGCCGGGACTAGAACCCAGGTCT 45 chr6qtel1M 969413 C------TCCATTCAATACCCTTTCCACT-AGACAGTCT 969444 ------i v vi i i i ii - v v C MIR3#SINE/MIR 44 CCTGACTCCCAGTCCGTGCTCTCTCTGCTCAGCCACTCT 6 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.95 CpG sites = 35, Kimura (unadjusted) = 42.13 Transitions / transversions = 2.06 (35/17) Gap_init rate = 0.06 (11 / 171), avg. gap size = 1.82 (20 / 11) 387 23.12 4.76 7.32 chr6qtel1M 970104 970229 (29771) C MIR#SINE/MIR (96) 166 44 m_b324s601i12 13595 chr6qtel1M 970104 TGAAGTAGTCTGCTATT-TTCTCCTCTAGCTCACTTTTACATGTGAGGAA 970152 i v- i - v i -------v vi C MIR#SINE/MIR 166 TGAGGTAGG-TACTATTATTATCCCC-------ATTTTACAGATGAGGAA 125 chr6qtel1M 970153 ACTGAGGCA-----AAGTTGATTGATTTTGCCCAAGGTCACAAAACTAGG 970197 ----- i i v i i - v i v C MIR#SINE/MIR 124 ACTGAGGCACAGAGAGGTTAAGTAACTT-GCCCAAGGTCACACAGCTAGT 76 chr6qtel1M 970198 AAGTTTTTGAGGCCAGATTTGAACTCAGAAAG 970229 vviv v vi i i iv C MIR#SINE/MIR 75 AAGTGGCAGAGCCGGGATTCGAACCCAGGCAG 44 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.68 CpG sites = 14, Kimura (unadjusted) = 27.85 Transitions / transversions = 1.08 (14/13) Gap_init rate = 0.09 (11 / 125), avg. gap size = 1.36 (15 / 11) 456 24.45 3.31 10.64 chr6qtel1M 970137 970287 (29713) C MIRc#SINE/MIR (124) 144 4 m_b324s601i13 13595 chr6qtel1M 970137 TTTTACATGTGAGGAAACTGAGGC-----AAAGTTGATTGATTTTGCCCA 970181 vi -----i i i v i - C MIRc#SINE/MIR 144 TTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTT-GCCCA 96 chr6qtel1M 970182 AGGTCACAAAACTAGGAAGTTTTTGAGGCCAGATTTGAACTCAGAAAGAT 970231 v i v vviv v vi i i i ------ C MIRc#SINE/MIR 95 AGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAG------ 52 chr6qtel1M 970232 GAGTATTCCTTATTTCAGGTCTACTGCTTTATGCACTAGGGCATCATCTA 970281 -- v v i i i i v i v v --- i i--- C MIRc#SINE/MIR 51 --GTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACT---GCACCAC--- 10 chr6qtel1M 970282 GCTGCC 970287 i C MIRc#SINE/MIR 9 ACTGCC 4 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.79 CpG sites = 19, Kimura (unadjusted) = 29.85 Transitions / transversions = 1.36 (19/14) Gap_init rate = 0.11 (16 / 150), avg. gap size = 1.25 (20 / 16) 16 18.86 0.00 0.00 chr6qtel1M 971811 971840 (28160) (A)n#Simple_repeat 1 30 (0) m_b324s252i8 13596 chr6qtel1M 971811 AAAAAAAAATGAATAAAAAAACAAAAAGAA 971840 vi v v i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 30 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 237 26.67 3.33 0.00 chr6qtel1M 972139 972228 (27772) L1PA15-16_5end#LINE/L1 2200 2292 (670) m_b324s551i5 13597 chr6qtel1M 972139 AATCTAAGGATTATTGGACTTCCTGCAAGCCATGATGAAAAA---AAGAA 972185 i v i vv vi vv v iv --- ? L1PA15-16_5en 2200 AACCTACGAATTATTGGCGTTCCTGAGAGAGAAGGAGAAAAAGTAAANAA 2249 chr6qtel1M 972186 CCTAGACATTATCTTACAGGAAATCATAAAGGAAAACTTCCCT 972228 i i v vi v vv i v vv L1PA15-16_5en 2250 CTTGGAAAACATATTTGAGGGAATAATTCAGGAAAACTTCCCT 2292 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.42 CpG sites = 8, Kimura (unadjusted) = 33.42 Transitions / transversions = 0.50 (8/16) Gap_init rate = 0.01 (1 / 89), avg. gap size = 3.00 (3 / 1) 566 25.96 0.35 4.36 chr6qtel1M 972828 973113 (26887) L1MC4_5end#LINE/L1 2258 2532 (23) m_b324s551i6 13598 chr6qtel1M 972828 TTTAGACTGGATTAAAAGCCAGAATCCTACAATATGCTGTTTCCAAAAAA 972877 i i?i ? ? ? iv ii i v v ? v -- i L1MC4_5end#LI 2258 TTCAANTTGGNTNANAAAGCAAGACCCAACTATATGCTGTNTAC--AAGA 2305 chr6qtel1M 972878 AACATATTTAAAGAAAAGTGATACATACAGAGTGAAGGTAAAGGGTTGGA 972927 i i ii - v v v iv ii v L1MC4_5end#LI 2306 GACACACCTAAA-AAAAGTGATTCAGAAAGGCTGAAAATAAAGGGATGGA 2354 chr6qtel1M 972928 GCAGAATATATTATGCTTCAGGTGAAAGGGGA-AAAAAACAGGGGTAGCA 972976 ?v ii -------i ii v ii - v i v L1MC4_5end#LI 2355 NAAAGATATA-------CCAGGCAAATGGAAACAAAAAAGAAGGGTTGCA 2397 chr6qtel1M 972977 ATCCTGATCTCAGATCAAGTAAAAGCAATGATAAATCTAATTAAAAGAGA 973026 ?i ? v iv i ?viv v ?i vvvv ? L1MC4_5end#LI 2398 ATNTTNATATCAGACAAAGTAGANTTCAAGNCAAAAAGCATTAAANGAGA 2447 chr6qtel1M 973027 TAAGGAGGGAAACTATATCTTACTAAAGATTACCATAGATAATGAAGCAA 973076 i i i ?v i v vv i? i??? v vv i vv L1MC4_5end#LI 2448 CAAAGAAGGNCATTTTATAATGNTAAAGGNNNCAATTCACAATGAAGATA 2497 chr6qtel1M 973077 TATCAATACCAAACATATATATGCACCAAGTAACATA 973113 v --i v v ? i ? L1MC4_5end#LI 2498 TAACAAT--TATAAATATNTATGCACCAAATAACANA 2532 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.12 CpG sites = 37, Kimura (unadjusted) = 35.12 Transitions / transversions = 1.09 (37/34) Gap_init rate = 0.05 (13 / 285), avg. gap size = 1.00 (13 / 13) 13 21.67 2.63 0.00 chr6qtel1M 973240 973277 (26723) (TAAA)n#Simple_repeat 1 39 (0) m_b324s252i9 13599 chr6qtel1M 973240 TAAATAAA-AATTTTTTATTTAAAAAAATAAATAAATAA 973277 - v vvv vv v (TAAA)n#Simpl 1 TAAATAAATAAATAAATAAATAAATAAATAAATAAATAA 39 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 344 28.64 3.70 6.87 chr6qtel1M 973506 973640 (26360) MIRb#SINE/MIR 1 131 (137) m_b324s601i14 13600 chr6qtel1M 973506 CAGAAGGTT-GCGGAATA-AGTGGATAGAGAACTAGCCCTGAAGTCAGGA 973553 i vi- vii i- v v vi ii i iv MIRb#SINE/MIR 1 CAGAGGGGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGAC 50 chr6qtel1M 973554 GGACCTGAGTTCAAATTTGGCCTTAGACAATAAACACTTCCCAGCTGTGT 973603 i i i iiv v iv - ------ v i MIRb#SINE/MIR 51 AGACCTGGGTTCGAATCCCGGCTCTG-C------CACTTACTAGCTGTGT 93 chr6qtel1M 973604 GACTCCAAGGAAGTCACTTAA---CTCCAATTGCCTCAGT 973640 iiiii v i --- ii -- MIRb#SINE/MIR 94 GACCTTGGGCAAGTTACTTAACCTCTCTGA--GCCTCAGT 131 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.53 CpG sites = 25, Kimura (unadjusted) = 37.89 Transitions / transversions = 2.27 (25/11) Gap_init rate = 0.09 (12 / 134), avg. gap size = 1.17 (14 / 12) 399 23.96 2.54 8.04 chr6qtel1M 973523 973640 (26360) MIRc#SINE/MIR 17 128 (140) m_b324s601i15 13600 chr6qtel1M 973523 AGTGGATAGAGAACTAGCCCTGAAGTCAGGAGGACCTGAGTTCAAATTTG 973572 v v i v i i i i i i iiv MIRc#SINE/MIR 17 AGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCC 66 chr6qtel1M 973573 GCCTTAGACAATAAACACTTCCCAGCTGTGTGACTCCAAGGAAGTCACTT 973622 v iv - ------ v i iiiii v MIRc#SINE/MIR 67 GGCTCTG-C------CACTTACTAGCTGTGTGACCTTGGGCAAGTCACTT 109 chr6qtel1M 973623 AA---CTCCAATTGCCTCAGT 973640 --- ii -- MIRc#SINE/MIR 110 AACCTCTCTGA--GCCTCAGT 128 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.45 CpG sites = 18, Kimura (unadjusted) = 29.82 Transitions / transversions = 2.25 (18/8) Gap_init rate = 0.09 (10 / 117), avg. gap size = 1.20 (12 / 10) 198 37.67 0.00 2.35 chr6qtel1M 974263 974349 (25651) MIR3#SINE/MIR 111 195 (13) m_b324s601i16 13601 chr6qtel1M 974263 TCCTTGTGTTTCAACTTCCTCATCTGAAAAAATGCAAGGATTTAATTGAA 974312 ii v ii ii -v vii i vi i ii MIR3#SINE/MIR 111 TCTCTGGGCCTCAGTTTCCTCATCTG-TAAAATGAGGGGGTTGGACTAGA 159 chr6qtel1M 974313 TGGCATCTAAATTTCCATTTGAATCTAGATTTTTTAT 974349 iiv iv i v iiiiv - iv i MIR3#SINE/MIR 160 TGATCTCTAAGGTCCCTTCCAGCTCT-GACATTCTAT 195 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 58.02 CpG sites = 23, Kimura (unadjusted) = 58.02 Transitions / transversions = 2.56 (23/9) Gap_init rate = 0.02 (2 / 86), avg. gap size = 1.00 (2 / 2) 337 32.65 1.39 4.29 chr6qtel1M 974533 974676 (25324) L3#LINE/CR1 3850 3989 (110) m_b324s601i17 13602 chr6qtel1M 974533 CAATACATGGAAATTGCAGAGATGTGGATTCAGGCTTGATATAAAAAATA 974582 ivi i i i v ii iv ii ii v L3#LINE/CR1 3850 CAATGGGTGGAAGTTACAGGGAGGCAGATTTCGGCTCAATATAAGGAAGA 3899 chr6qtel1M 974583 --TTCCTAATAAATAGCAAAATTCAAAATTTTAAATGGGCTGCCCAGGGA 974630 -- i i vi vivvi i -v vi iv ? L3#LINE/CR1 3900 ACTTTCTAACAATCAGAGCTGTCCAAAA-ATGGAATGGGCTGCCTCGNGA 3948 chr6qtel1M 974631 GATGGTAGAATTGTTTTCCATCTCAGGGAGGTAATAAAATAGTGGC 974676 i i - --- i ii i v -v iv v ii v L3#LINE/CR1 3949 GGTAGT-GA---GCTCCCCGTCAC-TGGAGGTGTTCAAGCAGAGGC 3989 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 44.08 CpG sites = 29, Kimura (unadjusted) = 45.49 Transitions / transversions = 1.81 (29/16) Gap_init rate = 0.05 (7 / 143), avg. gap size = 1.14 (8 / 7) 225 31.10 5.49 1.05 chr6qtel1M 976102 976192 (23808) L2b_3end#LINE/L2 370 464 (2) m_b324s601i18 13603 chr6qtel1M 976102 GAACCAAGTAAATTTTGGTCTTTG-TGT---CCCAGCTTTTAAGATGATG 976147 i i? vvi i v vii - --- vii iv iii? L2b_3end#LINE 370 GGACCGNGTCTGTCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNG 419 chr6qtel1M 976148 ACTGGCACAGGGTAAACACATCA-CAAATGTTTGTTTATTGAATGA 976192 v vi ii i - -i i v v L2b_3end#LINE 420 CCTGGCACACAGTAGGCGC-TCAGTAAATATTTGTTGAATGAATGA 464 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.38 CpG sites = 18, Kimura (unadjusted) = 43.43 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.04 (4 / 90), avg. gap size = 1.50 (6 / 4) 238 30.38 5.06 0.00 chr6qtel1M 976114 976192 (23808) L2a_3end#LINE/L2 433 515 (2) m_b324s601i19 13603 chr6qtel1M 976114 TTTTGGTCTTTG-TGT---CCCAGCTTTTAAGATGATGACTGGCACAGGG 976159 v vi - --- vii ii iii v vi L2a_3end#LINE 433 TTTTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACATAG 482 chr6qtel1M 976160 TAAACACATCACAAATGTTTGTTTATTGAATGA 976192 ii i viv i i v v L2a_3end#LINE 483 TAGGCGCTCAATAAATATTTGTTGAATGAATGA 515 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.29 CpG sites = 15, Kimura (unadjusted) = 40.49 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.03 (2 / 78), avg. gap size = 2.00 (4 / 2) 270 24.34 1.35 5.63 chr6qtel1M 977500 977573 (22427) C L2b_3end#LINE/L2 (71) 395 325 m_b324s601i20 13604 chr6qtel1M 977500 AACGGATAACAGAATAGCAAACACAGTCCCTGCTCTCAAGAAGCTCACAT 977549 i vv ii i --- ? i i v i v C L2b_3end#LINE 395 AGCGGTGAACAAGACAG---ACNCGGTCCCTGCCCTCACGGAGCTCACAG 349 chr6qtel1M 977550 TCTAATAAGGAAAGATAG-CATATA 977573 i -i ii i - i C L2b_3end#LINE 348 TCTAGT-GGGGGAGACAGACATGTA 325 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.35 CpG sites = 13, Kimura (unadjusted) = 31.61 Transitions / transversions = 3.25 (13/4) Gap_init rate = 0.07 (5 / 73), avg. gap size = 1.00 (5 / 5) 277 21.57 1.47 4.55 chr6qtel1M 977511 977578 (22422) C L2c_3end#LINE/L2 (65) 413 348 m_b324s601i21 13604 chr6qtel1M 977511 GAATAGCAAACACAGTCCCTGCTCTCAAGAAGCTCACATTCTAATAAGGA 977560 -- i i i i v i -i ii C L2c_3end#LINE 413 GAATA--AGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAGT-GGAG 367 chr6qtel1M 977561 AAGATAG-CATATAGAAAG 977578 i i - ?i i v C L2c_3end#LINE 366 GAGACAGACANGTAAACAG 348 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 25.36 CpG sites = 12, Kimura (unadjusted) = 27.68 Transitions / transversions = 6.00 (12/2) Gap_init rate = 0.06 (4 / 67), avg. gap size = 1.00 (4 / 4) 608 30.80 4.80 2.97 chr6qtel1M 978034 978595 (21405) L1MC_orf2#LINE/L1 2338 2909 (385) m_b324s551i7 13605 chr6qtel1M 978034 CTATATGAGCAAAACTACAAAACACTTTCCACACAAATAAAGTCAGATCT 978083 v v vviv v v v ivv ? L1MC_orf2#LIN 2338 CTATATGAGGAAAACTACAAAACTCTGATGAAAGAAATCAAAGAAGANCT 2387 chr6qtel1M 978084 AACCAATTGGAAAAATATTAAATGCTCTTGGATAGAGCAAAC-AAATATA 978132 vi v i i vv i v - v i -v v L1MC_orf2#LIN 2388 AAATAAATGGAGAGATATTCCATGTTCATGGATAG-GAAGACTCAATATT 2436 chr6qtel1M 978133 ATAAAGATGACAATATTACCTAAACTAATCTATTTATTTAGCGCTATTCC 978182 i v v i vi v i vi i vv i ii v i L1MC_orf2#LIN 2437 GTCAAGATGTCAGTTCTTCCCAACTTGATCTATAGATTCAATGCAATCCC 2486 chr6qtel1M 978183 AGTCAGACTCCCAAAAAACTATTTTCTG---ACCTAAAAAAATAACAACA 978229 i i v iv ii v --- i -i v v i ivvi L1MC_orf2#LIN 2487 AATCAAAATCCCAGCAAGTTATTTTGTGGATATC-GACAAACTGATTCTA 2535 chr6qtel1M 978230 AA-TTCATATGGAAAAACAAAAGGTCAAGAAT-TTCAAGGGA--ACTAAT 978275 - i i ii ii v -vi viv -- i i v L1MC_orf2#LIN 2536 AAGTTTATATGGAGAGGCAAAAGACCCAGAATAGCCAACACAATATTGAA 2585 chr6qtel1M 978276 GAAAAAAATCAAATGAAGATGGCCTAGCTGTACCAGA-TCTAAAATTATA 978324 i i i v vvvi - v ii vv v - ii i i - L1MC_orf2#LIN 2586 GGAGAAGAACAAAGTCGGA-GGACTGACACTACCCGACTTCAAGACT-TA 2633 chr6qtel1M 978325 TTATAAAGCAGCAGCTACCAAAACCATCTGCTATTGGCTAAGAAAGAGAC 978374 i vi iv i i vi v v v ii v L1MC_orf2#LIN 2634 CTATAAAGCTACAGTAATCAAGACAGTGTGGTATTGGCGAAAGAATAGAC 2683 chr6qtel1M 978375 TAGTTGTTCAGTGGAATAGGTTAGGTTCAAAGGACA-AAATAG--TCA-A 978420 v i v v i i iv ---- i vv - --i - L1MC_orf2#LIN 2684 AAATAGATCAATGGAACAGAATAG----AGAGCCCAGAAATAGACCCACA 2729 chr6qtel1M 978421 TAACTTTAATAATCTAGTGTTTGACAAAC--CCAAAGAC--CCCAGCTTT 978466 v v i v v ii v v--v i --i? i--- L1MC_orf2#LIN 2730 TAAATATAGTCAACTGATCTTTGACAAAGGAGCAAAGGCAATNCAA---T 2776 chr6qtel1M 978467 TGGGATAAGA-ACTCACTGTTTGACAAAAACTGCTGGGAAAATTGGAAAT 978515 v i v - v -- v ii viv i v i v L1MC_orf2#LIN 2777 GGAGAAAAGATAGT--CTTTTCAACAAATGGTGCTGGAACAACTGGACAT 2824 chr6qtel1M 978516 TAGTATGGCAGAAA-------CTAGGCATTGATG-CACACACTTAACACC 978557 ivii - i ------- i iv iv-i v -- v L1MC_orf2#LIN 2825 CCACAT-GCAAAAAAATGAATCTAGACACAGACCTTACACCCTT--CACA 2871 chr6qtel1M 978558 AAGATAAGGTCAAAATGGGCTCAT-GACCTAGACATAAA 978595 i v iv i- - i ii L1MC_orf2#LIN 2872 AAAATTAACTCAAAATGGA-TCATAGACCTAAATGTAAA 2909 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.94 CpG sites = 87, Kimura (unadjusted) = 40.57 Transitions / transversions = 1.07 (87/81) Gap_init rate = 0.06 (32 / 561), avg. gap size = 1.38 (44 / 32) 613 30.59 4.70 3.59 chr6qtel1M 978044 978511 (21489) L1PREC2_orf2#LINE/L1 2348 2820 (474) m_b324s551i8 13605 chr6qtel1M 978044 AAAACTACAAAACACTTTCCACACAAATAAAGTCAGATCTAAC-----CA 978088 i i ----i v v - vv i ----- L1PREC2_orf2# 2348 AGAATTACAAAACACT----GCTCAAAGAAA-TCAGAGATGACACAAACA 2392 chr6qtel1M 978089 ATTGGAAAAATATTAAATGCTCTTGGATAGAGCAAACAAATATAATAAAG 978138 v i vv v iivi iv vi v i L1PREC2_orf2# 2393 AATGGAAAAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTTAAA 2442 chr6qtel1M 978139 ATGACAATATTACCTAAACTAATCTATTTATTTAGCGCTATTCCAGTCAG 978188 i v i i i vi i ivv i ii vi i L1PREC2_orf2# 2443 ATGGCCATACTGCCCAAAGCAATTTACAGATTCAATGCTATTCCTATCAA 2492 chr6qtel1M 978189 ACTCCCAA-AAAACTATTTTCTGACCTAAAAAAATAACAAC----AAATT 978233 v -i v i v iv v v i -- v i---- L1PREC2_orf2# 2493 ACTACCAATGACATTCTTCACAGAACTAGAAAA--AACTATTTTAAAATT 2540 chr6qtel1M 978234 CATATGGAAAAACAAAAGGTCAAGAAT-TTCAAGGGAA--CTAATGAAAA 978280 vv v iv vv -vi v -- vv L1PREC2_orf2# 2541 CATATGGAACCAAAAAAGAGCCCGAATAGCCAAGGCAATCCTAAGCAAAA 2590 chr6qtel1M 978281 AAATCAAA--TGAAGATGGCCTAGCTGTACCAGATCTAAAATTATATTAT 978328 i v -- i --- v vi vv v ii v i i i L1PREC2_orf2# 2591 AGAACAAAGCTGGA---GGCATCACGCTACCCGACTTCAAACTATACTAC 2637 chr6qtel1M 978329 AAAGCAGCAGCTACCAAAACCATCTGCTATTGGCTAAGAAAGAGACTAGT 978378 ii vi iv viiv v i ivv i v vvi L1PREC2_orf2# 2638 AGGGCTACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGACACAT 2687 chr6qtel1M 978379 TGTTCAGTGGAATAGGTTAGGTTCAAAGGACA-AAATA--GTCA-ATAAC 978424 v vi i i iv ---- i vv - -- i i- i v L1PREC2_orf2# 2688 AGACCAATGGAACAGAATAG----AGAGCCCAGAAATAAGGCCGCACACC 2733 chr6qtel1M 978425 TTTAATAATCTAGTGTTTGACAAACC---CAAAGACCCCAGCTTTTGGGA 978471 vi iv ii v i v --- i -- v vv v L1PREC2_orf2# 2734 TACAACCATCTGATCTTCGACAAAGCTGACAAAAA--CAAGCAATGGGGA 2781 chr6qtel1M 978472 TAAGAACTCACTGTTTGACAAAAACTGCTGGGAAAATTGG 978511 - i v i ii i viv v i L1PREC2_orf2# 2782 -AAGGACTCCCTATTCAATAAATGGTGCTGGGATAACTGG 2820 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.75 CpG sites = 69, Kimura (unadjusted) = 39.85 Transitions / transversions = 1.00 (69/69) Gap_init rate = 0.06 (27 / 467), avg. gap size = 1.44 (39 / 27) 454 29.14 4.13 3.56 chr6qtel1M 978971 979333 (20667) L1M5_orf2#LINE/L1 2930 3294 (0) m_b324s551i9 13606 chr6qtel1M 978971 TAGAAGAA--CATAAGATAGTTTACCTCA-GACCTGTAGAAGAGGAAGGA 979017 -- i v i v - i i- - i i?v v iii L1M5_orf2#LIN 2930 TAGAAGAAAACATAGGAGAATAT-CTTCGTGACCT-TGGGNTAGGCAAAG 2977 chr6qtel1M 979018 ATTTATGACCTAAAAAGAAC-TAGAGATCATTATTGATCACAAAATAGAA 979066 ---- i v i -i i i v i? --- i i v i L1M5_orf2#LIN 2978 ATTT----CTTAAACAGGACACAAAAAGCACNA---ACCATAAAAGAAAA 3020 chr6qtel1M 979067 AATT-------TTGATTATATCAAATTGAAACGTTTTTGTACAAACAAAA 979109 ------- v i ?i v v vii i iv ?vvv i L1M5_orf2#LIN 3021 AATTGATAAATTGGACTNCATCAAAATTAAAAACTTCTGCTCNTCAAAAG 3070 chr6qtel1M 979110 CTAATGCAGACAAGATTAGAAGGGAAGCAATAAACTGGGAAAATATTTTT 979159 vi vi ivi v i v i v v i i ? i v v L1M5_orf2#LIN 3071 ACACCGTTAAGAAAATGAAAAGGCAAGCCACAGANTGGGAGAAAATATTT 3120 chr6qtel1M 979160 ACAGTCAAAGGT-TCTGGTAAAGGCCTCATTTCCAAAATATATAGAGAAT 979208 i i?- v vi - ii v i v i i i L1M5_orf2#LIN 3121 GCAAN-ACATATATCTGACAAAGGACTCGTATCCAGAATATATAAAGAAC 3169 chr6qtel1M 979209 TAACTCTAATTTA-TAAAAAATCAAGCCATTC--TCCAATTGAAAAATGG 979255 v- vi ? i - ? -- v vv --i v? L1M5_orf2#LIN 3170 TC-CTACAANTCAATAANAAA--AAGACAAACAACCCAATANAAAAATGG 3216 chr6qtel1M 979256 TCAAAGGATATGAACAGACAATTCTCAGATGAAGAAATTGAAACTATTTC 979305 v i iv v v i v v ?v iviiivv L1M5_orf2#LIN 3217 GCAAAAGACTTGAACAGACACTTCACAAAAGAAGATATNCAAATGGCCAA 3266 chr6qtel1M 979306 TAGTCATATGAAAAGATGCTCCAAGTCA 979333 iv i v v? L1M5_orf2#LIN 3267 TAAGCACATGAAAAGATGCTCAACNTCA 3294 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.76 CpG sites = 55, Kimura (unadjusted) = 39.22 Transitions / transversions = 1.17 (55/47) Gap_init rate = 0.06 (20 / 362), avg. gap size = 1.40 (28 / 20) 479 28.73 2.97 2.97 chr6qtel1M 979058 979326 (20674) L1M3_orf2#LINE/L1 3013 3281 (7) m_b324s551i10 13606 chr6qtel1M 979058 AAAATAGAAAATTTTGATTATATCAAATTGAAACGTTTTTGTACA---AA 979104 v v vv i i i i v i i i --- L1M3_orf2#LIN 3013 AAAATAGACAAGTGGGACTACATCAAACTAAAAAGCTTCTGCACAGCAAA 3062 chr6qtel1M 979105 CAAAACTAATGCAGACAAGATTAGAAGGGAAGCAATAAACTGGGAAAATA 979154 vi - - - iii v i v v v iii v i v L1M3_orf2#LIN 3063 GGAAAC-AAT-CA-ACAGAGTGAAAAGGCAACCTACGGAATGGGAGAAAA 3109 chr6qtel1M 979155 TTTTTACAGTCAAAGGTTCTGGTAAAGGCCTCATTTCCAAAATATATAGA 979204 v i iv v vivv i i vi v v ii L1M3_orf2#LIN 3110 TATTTGCAAACCATATATCTGATAAGGGGTTAATATCCAAAATATATAAG 3159 chr6qtel1M 979205 GAATT-----AACTCTAATTTATAAAAAATCAAGCCATTCTCCAATTGAA 979249 i ----- - v-ii v --- vvi i ? L1M3_orf2#LIN 3160 GAACTCNTACAACTC-AATA-GCAAAAAAACAA---ATAACCCGATTNAA 3204 chr6qtel1M 979250 AAATGGTCAAAGGATATGAACAGACAATTCTCAGATGAAGAAATTGAAAC 979299 v iv i v vi v v vv i L1M3_orf2#LIN 3205 AAATGGGCAAAGGACCTGAATAGACATTTCTCCAAAGAAGACATACAAAT 3254 chr6qtel1M 979300 TATTTCTAGTCATATGAAAAGATGCTC 979326 viiivvi vi L1M3_orf2#LIN 3255 GGCCAACAGGTATATGAAAAGATGCTC 3281 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.61 CpG sites = 38, Kimura (unadjusted) = 36.89 Transitions / transversions = 1.03 (38/37) Gap_init rate = 0.04 (10 / 268), avg. gap size = 1.60 (16 / 10) 1503 28.98 1.28 2.58 chr6qtel1M 979190 979738 (20262) L1ME3Cz_3end#LINE/L1 7 548 (449) m_b324s551i11 13606 chr6qtel1M 979190 TCCAAAATATATAGAGAATTAACTCTAATTTATAAAAAATCAAGCCATTC 979239 i i i vviv v iv i -- v --v L1ME3Cz_3end# 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAA--AAGACA--A 52 chr6qtel1M 979240 TCCAATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGAAG 979289 i v v i v v i L1ME3Cz_3end# 53 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chr6qtel1M 979290 AAATTGAAACTATTTCTAGTCATATGAAAAGATGCTCCAAGTCATTATTA 979339 iivi iviiivv iv v vv i v L1ME3Cz_3end# 103 AAACCCGAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTA 152 chr6qtel1M 979340 ATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACACCTGT 979389 i i ? vv i i v ii L1ME3Cz_3end# 153 ATCAGGGAAATGCAAATTAAAACNACAATGAGATACCATTTCACACCCAT 202 chr6qtel1M 979390 CAGATTGGCTAAGATGACAGGAAAA----AATAATGATGATTGTTGGAGG 979435 v i ----vv ----i i ivii v v i L1ME3Cz_3end# 203 CAGATTGGCAAAAAT----TTAAAAGTCTGACAATACCAAGTGTTGGCGA 248 chr6qtel1M 979436 GGATGTGGGAAAACTGGGACATTGATTCATTGTTGGTGGAGTTGTGAACG 979485 ii v i vi v v i i iiv i iv L1ME3Cz_3end# 249 GGATGTGGAGAAACGGGAACTCTCATACACTGCTGGTGGGAGTGTAAATT 298 chr6qtel1M 979486 AATCCAACCATTTTGGAGAGTAGTTTGGAACTATGCTCAAAAAGTTATCA 979535 ii v i i i v v - viv i-- L1ME3Cz_3end# 299 GGTACAACCACTTTGGAGAGCAATTTGGCAATAT-CTAGTAAAGTTG--A 345 chr6qtel1M 979536 AACTCTGCATACTCTTTGATCCAGCAGTGTTACTACGGGGCTTATACCCC 979585 iv vi i vi i i vii v vi iv i L1ME3Cz_3end# 346 AGATGCGCATACCCTACGACCCAGCAATTCCACTTCTAGGTATATACCCT 395 chr6qtel1M 979586 AAAGAGA---TCAAAAAGAAGGGAAAGGGATCTGTATGTGCACGAATGCT 979632 i i --- iv v viv viv iiv --- i v i i L1ME3Cz_3end# 396 AGAGAAACTCTCGCACATGTGCACAAGGAGAC---ATGTACAAGGATGTT 442 chr6qtel1M 979633 TGTGACAACCCTCTTTGTAGTGGCCAGAAACTGGAAAGTGAGTGGATGCC 979682 ii vi i vi v i i v i i vvivv ii i L1ME3Cz_3end# 443 CATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTC 492 chr6qtel1M 979683 CATCAATTGGAGAATGGCTGAATAAATTGTGGTATATGAATGTTATGGAA 979732 v i v i vv iiv L1ME3Cz_3end# 493 CATCAATAGGGGAATGGATAAATAAATTGTGGTATATTCATACAATGGAA 542 chr6qtel1M 979733 TATTAT 979738 i L1ME3Cz_3end# 543 TACTAT 548 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.31 CpG sites = 87, Kimura (unadjusted) = 37.53 Transitions / transversions = 1.28 (87/68) Gap_init rate = 0.03 (16 / 548), avg. gap size = 1.31 (21 / 16) 526 22.28 1.61 5.88 chr6qtel1M 980055 980178 (19822) MIRc#SINE/MIR 9 127 (141) m_b324s601i22 13607 chr6qtel1M 980055 TATGGAGCAGTGGATAGAGCACCAGCCCTGAAGTCAGGAGGACCTGAGTT 980104 i v v ii v i i i i MIRc#SINE/MIR 9 TGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTT 58 chr6qtel1M 980105 CAAATCTAGTCTCAGACACTTCACACGTCCTAGCTATGTGATCCTGGGCA 980154 i i iv v v v ------- v i i i MIRc#SINE/MIR 59 CGAGTCCCGGCTCTGCCACT-------TACTAGCTGTGTGACCTTGGGCA 101 chr6qtel1M 980155 AGTTACTTAAC--CCCAAAGTCTCAG 980178 i -- i vi i MIRc#SINE/MIR 102 AGTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 25.88 CpG sites = 17, Kimura (unadjusted) = 27.08 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.07 (8 / 123), avg. gap size = 1.12 (9 / 8) 330 33.77 4.64 1.94 chr6qtel1M 980494 980644 (19356) C L2a_3end#LINE/L2 (1) 516 362 m_b324s601i23 13608 chr6qtel1M 980494 TCCATTTAATCCACAAATATTAATCAATTACCTACTGTGTATCAGACAGT 980543 i i v v v ii vii i ii i v C L2a_3end#LINE 516 TTCATTCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACT 467 chr6qtel1M 980544 GTACTGGGCTCTTGT------GCCCTAAAGATAA-AAACAGAAGCCTTTA 980586 v i v v v------ vv i v v - i i i ii i C L2a_3end#LINE 466 GTTCTAGGCGCTGGGGATACAGCAGTGAACAAAACAGACAAAAGTCCCTG 417 chr6qtel1M 980587 ACCTCAAGGATTTTGCATTAATTAGTGGTAAATAATATGACCCCAGACAA 980636 v v vi i --i viiivi i - vvi i C L2a_3end#LINE 416 CCCTCATGGAGCTTACATT--CTAGTGGGGGGAGACA-GACAATAAACAA 370 chr6qtel1M 980637 GTAAACAA 980644 i i C L2a_3end#LINE 369 ATAAATAA 362 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 45.31 CpG sites = 30, Kimura (unadjusted) = 46.76 Transitions / transversions = 1.50 (30/20) Gap_init rate = 0.03 (5 / 150), avg. gap size = 2.00 (10 / 5) 15 29.69 1.67 1.67 chr6qtel1M 981255 981314 (18686) (ATT)n#Simple_repeat 1 60 (0) m_b324s252i10 13609 chr6qtel1M 981255 ATT-TTATTAATAATATGTATTTTGATAATTAATGTTAATAATAATAGAA 981303 - v v - v v v v i v v v vv (ATT)n#Simple 1 ATTATTATTATTATTAT-TATTATTATTATTATTATTATTATTATTATTA 49 chr6qtel1M 981304 TAATTAATATT 981314 v v (ATT)n#Simple 50 TTATTATTATT 60 Matrix = Unknown Transitions / transversions = 0.08 (1/13) Gap_init rate = 0.03 (2 / 59), avg. gap size = 1.00 (2 / 2) 336 17.74 1.61 0.00 chr6qtel1M 981995 982056 (17944) MIR#SINE/MIR 116 178 (84) m_b324s601i24 13607 chr6qtel1M 981995 TGCCTCAGTTTCCCAATCTATGAAGTGGGAATAATAATAGCATCTACCAC 982044 iv i i i i i i v MIR#SINE/MIR 116 TGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTC 165 chr6qtel1M 982045 CAAGGG-TGTTGT 982056 vv - MIR#SINE/MIR 166 ATAGGGTTGTTGT 178 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 20.60 CpG sites = 7, Kimura (unadjusted) = 20.60 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.02 (1 / 61), avg. gap size = 1.00 (1 / 1) 241 30.77 1.54 0.00 chr6qtel1M 985817 985881 (14119) MIR3#SINE/MIR 30 95 (113) m_b324s601i25 13610 chr6qtel1M 985817 GGACTGAAAGCCAAGTCATATGGGTTTTAATCTTAGCCCTGCAATGCACT 985866 ii i i vv iv i i iii i v ivv MIR3#SINE/MIR 30 GGACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACT 79 chr6qtel1M 985867 TG-TGTGTGACTCTGG 985881 ? - ii MIR3#SINE/MIR 80 NGCTGTGTGACCTTGG 95 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.85 CpG sites = 14, Kimura (unadjusted) = 43.08 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.02 (1 / 64), avg. gap size = 1.00 (1 / 1) 502 26.72 3.82 0.00 chr6qtel1M 986344 986474 (13526) MIRc#SINE/MIR 13 148 (120) m_b324s601i26 13611 chr6qtel1M 986344 GTGGAGCAGGGTGAGCATTGGGCATAGGATCAGGAGAACTTCAGTTCAAA 986393 v ii iiv i i v i ii ii i vi i i MIRc#SINE/MIR 13 GTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAG 62 chr6qtel1M 986394 TATGGCCTCAGA----TACTAGCTGGGTGACCCTGGGCAAGTCACTTGAC 986439 viv v v v---- v i i MIRc#SINE/MIR 63 TCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAAC 112 chr6qtel1M 986440 C-CTGTTTGGTTCAATTTCCTCATCTGTAAAATGAG 986474 - v vv vi i i MIRc#SINE/MIR 113 CTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.71 CpG sites = 21, Kimura (unadjusted) = 33.90 Transitions / transversions = 1.50 (21/14) Gap_init rate = 0.02 (2 / 130), avg. gap size = 2.50 (5 / 2) 216 26.67 0.00 0.00 chr6qtel1M 986785 986829 (13171) C L2d_3end#LINE/L2 (13) 503 459 m_b324s601i27 13612 chr6qtel1M 986785 CAATAAGCATTTATTTAGCACTTACAATGTACTTGGCAATGCACT 986829 i i v i i v i ii v ii C L2d_3end#LINE 503 CAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTGTGCT 459 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.39 CpG sites = 9, Kimura (unadjusted) = 35.01 Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 889 36.11 3.89 0.95 chr6qtel1M 987064 987474 (12526) L3#LINE/CR1 2659 3081 (1018) m_b324s601i28 13613 chr6qtel1M 987064 GAAAACAAGAGAGGTACTCCAGAACTGGAAAGGGATGAATGTA-CCCTTG 987112 i iii i ivv ii i v iii ?-i? i i L3#LINE/CR1 2659 GAGAACGGAAGAGGTGCCAGAAGACTGGAGACGGGCAAATGTNGTNCCTA 2708 chr6qtel1M 987113 TTCAGAGAAAGGGATTGGAAA-GTAATCAGAAAACCATTCACTAGTGAAT 987161 ? ivv i vvii i - v v v ? i ivv ii i ii L3#LINE/CR1 2709 NTTTTAAAAAGGGAAAAAAGATGGATTCTGNAAACTACAGACCGGTAAGC 2758 chr6qtel1M 987162 TGGACTTCAATCTTTGGAATAATTCTCAAAGATATGATGAGGTGGAAGTT 987211 v v i iii v v vi viv v v iiii v v L3#LINE/CR1 2759 TTGACGTCGATCCCCGGCAAAATTCTAGAACGGATTATTAAACAGATGGT 2808 chr6qtel1M 987212 TTGATATGTGTTTATAAAAGGGAAAAGCAATTGCTAAATGCCAGCATGAC 987261 - iv iii v i ivi ii ii iiv iv L3#LINE/CR1 2809 TTG-TGAGCACTTAGAAAAGGAAGCGGTGATCACTAGGAGCCAGCATGGG 2857 chr6qtel1M 987262 TTCAGCAGGCACAGATTATACCAGATTGACTTCCTTTCTTTTTTGTAACA 987311 vi i v ii i i i i i i v i - i i L3#LINE/CR1 2858 TTCACTAAGAACAAGTCATGCCAAACTAACCTCATTTCCTTTTT-TGATA 2906 chr6qtel1M 987312 GGGTTACTAGACTAATGTCAGCCAGGGAGAT---GTAGCCATGGAATACT 987358 i-- viii ii --- v ?i vi ii L3#LINE/CR1 2907 GGGTTACTAGACTG--GTAGATCAGGGGAATGCCGTAGACANAGTGTATC 2954 chr6qtel1M 987359 TAGATTTTTCCAAAGCATTTTA-AAAATCTTT--TGACA-------GAGT 987398 i ivv i v - i i -- i ------- iii L3#LINE/CR1 2955 TGGATTTCAGCAAGGCATTTGACAAAGTCTCTCATGATATCCTTGTGGAC 3004 chr6qtel1M 987399 AAAGAGAATAGATATTGGCTAGATGATCATA-AATTAACCAGGTTCAGAA 987447 iiv i v i v i vi - i ivii i iv i L3#LINE/CR1 3005 AAGATGGAGAAATATGGGCTGGATGATAGTACAGTTAGGTGGATTCGTAG 3054 chr6qtel1M 987448 CTGTTTGAATGACCTGATTCAAAAGAT 987474 v i ivv ii i L3#LINE/CR1 3055 CTGGTTGAACGACTATACCCAAAAGGT 3081 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 49.94 CpG sites = 101, Kimura (unadjusted) = 54.47 Transitions / transversions = 2.20 (101/46) Gap_init rate = 0.03 (11 / 410), avg. gap size = 1.82 (20 / 11) 13 17.09 2.33 4.76 chr6qtel1M 987593 987635 (12365) (TTTTTAA)n#Simple_repeat 1 42 (0) m_b324s252i11 13614 chr6qtel1M 987593 TTTTCACATTCTGTCATTTCTTATTTTT-ATTTTTAATTTTGAA 987635 i - - v v i v - v (TTTTTAA)n#Si 1 TTTTTA-ATT-TTTAATTTTTAATTTTTAATTTTTAATTTTTAA 42 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.07 (3 / 42), avg. gap size = 1.00 (3 / 3) 43 0.00 2.50 0.00 chr6qtel1M 987964 988003 (11997) (TA)n#Simple_repeat 1 41 (0) c_b324s251i1 13615 chr6qtel1M 987964 TATATAT-TATATATATATATATATATATATATATATATAT 988003 - (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATAT 41 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1) 387 24.21 7.97 4.20 chr6qtel1M 988699 988836 (11164) C MIRc#SINE/MIR (120) 148 6 m_b324s601i29 13616 chr6qtel1M 988699 CTCATTTTACAGATGGAGGAAATCGAGGGCAAAATAGGGTCAAGTGACTC 988748 i - ii viv i v - i - C MIRc#SINE/MIR 148 CCCATTTTACAGAT-GAGGAAACTGAGGCTCAGAGA-GGTTAAGTGACT- 102 chr6qtel1M 988749 TGCCCAGGGTTACATGG-------GTATCTGAGACCAGATTTGAATTCAA 988791 i i ii ------- iv v v vi i i ii -- C MIRc#SINE/MIR 101 TGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCC-- 54 chr6qtel1M 988792 GAGATCTT-CTGAC-CCAGGCCCAGCACTC-ATCCACTGTGGCAC-CTG 988836 - i - - i i ii -v iiv - C MIRc#SINE/MIR 53 -AGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTG 6 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.46 CpG sites = 23, Kimura (unadjusted) = 30.61 Transitions / transversions = 2.56 (23/9) Gap_init rate = 0.08 (11 / 137), avg. gap size = 1.55 (17 / 11) 502 33.27 10.42 2.11 chr6qtel1M 989125 989431 (10569) L3#LINE/CR1 3092 3423 (676) m_b324s601i30 13613 chr6qtel1M 989125 GAAACAACGTCAACTTGAAGAGAAGTCTCTAAAGAAGTGCCCCAAATATC 989174 i v i i i i i i iv iv v iivv L3#LINE/CR1 3092 GGATCGATGTCAACCTGGAGGGAGGTCTCTAGTGGCGTGCCACAGGGCTC 3141 chr6qtel1M 989175 TATTTTTTACCCAAGGTTATTAAATATCTTTGC-----ACTTAGTACAAA 989219 i ii vi vivvi i v i i ii----- i - ii L3#LINE/CR1 3142 TGTCCTTGGCCCTGTCCTGTTCAACATTTTTATCAATGACTTGG-ATGAA 3190 chr6qtel1M 989220 GTCAGAGATAGCATGCTTATCAGATGTGCAGATG--GTAACGT------- 989260 v v vi i v --ii v i------- L3#LINE/CR1 3191 GACATAGAAGGCATGCTTATCAAATTTGCAGATGACACAAAGCTGGGAGG 3240 chr6qtel1M 989261 ----GCTTGT-CGGCAGATGACAG--TTCAGCCTCAAAA--------ACA 989295 ---- vi - ?ii -- iv vi -------- L3#LINE/CR1 3241 GATAGCTAATACGNTGGATGACAGAATCAAGATTCAAAANGATCTCGACA 3290 chr6qtel1M 989296 AGCTAG-TCCATGGAAGCAGAATCAAATAAGATTAAATTTTAC--GTATA 989342 i i -v v -- v v v i v v -- v L3#LINE/CR1 3291 GGCTGGAACGATGG--GCCGAAACCAACAAGATGAAATTTAACAGGGATA 3338 chr6qtel1M 989343 TTTATTATAAAATTCCACATCAGGGTTTAGAAAACCAAATTCAAAAAGTA 989392 --- v i i i ii ivi i i i v v - v L3#LINE/CR1 3339 ---AATGTAAAGTCCTGCATTTAGGTTCAAAAAATCAACTGC-ACAAGTA 3384 chr6qtel1M 989393 TGGTTTGAGGTGGACTAGACATTGGAACCATTCTCATAA 989431 ii vv ii v iiv i v v v i vi v i i L3#LINE/CR1 3385 CAGGATGGAGAGGATCTGGCTTAGCAGCAGTTCACGTGA 3423 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 44.68 CpG sites = 59, Kimura (unadjusted) = 45.95 Transitions / transversions = 1.44 (59/41) Gap_init rate = 0.05 (16 / 306), avg. gap size = 2.44 (39 / 16) 243 20.00 0.00 0.00 chr6qtel1M 989673 989737 (10263) DNM1r#Unknown 2481 2545 (2117) m_b324s502i0 13617 chr6qtel1M 989673 TATGTGTGTACATATGTGTGTATGTTTATAGATATCTATGTATATGTGTA 989722 i i v i iv i v i i DNM1r#Unknown 2481 TATGTGTGTATATATGTGTGTATATGTGTGTATGTGTGTATATATGTGTA 2530 chr6qtel1M 989723 TATGTTTGTATATAT 989737 i vi ? DNM1r#Unknown 2531 TATATACGTATNTAT 2545 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 22.30 CpG sites = 9, Kimura (unadjusted) = 24.40 Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0) 252 20.86 3.52 3.08 chr6qtel1M 989983 990693 (9307) (AAGG)n#Simple_repeat 1 714 (0) m_b324s252i12 13618 chr6qtel1M 989983 AAGAAAGGAAGAAAGG--GGAAAGGATGAAGGAAGGAAGGAAGAAAGAGA 990030 i i -- i i v i - (AAGG)n#Simpl 1 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG-GA 49 chr6qtel1M 990031 GAGAGAAGGAAGGAAGGAA--AAGAGAAGGAAGGAA-GATCAAAGGAAGG 990077 - - -- - - vvi (AAGG)n#Simpl 50 -AG-GAAGGAAGGAAGGAAGGAAG-GAAGGAAGGAAGGAAGGAAGGAAGG 96 chr6qtel1M 990078 AGGGAAGGAGATATGCTAAGTGAGAGAGAAAGGAGGAAAGTAAGAAAAGA 990127 i iiv v -v vi ii i i i v i i (AAGG)n#Simpl 97 AAGGAAGGAAGGAAG-GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 145 chr6qtel1M 990128 AAGAAAGAAAGAAAGTAGTGAAAGAAAGAA--AAGAAAGAAAGAAAGAAA 990175 i i i i v - i i -- i i i i (AAGG)n#Simpl 146 AGGAAGGAAGGAAGGAAG-GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 194 chr6qtel1M 990176 GGAAGGAA-TAA-GAAGTTAGTACAAGGAAGGAAGTAA-TAA-GAAGGAA 990221 -v - vv --v v -v - (AAGG)n#Simpl 195 GGAAGGAAGGAAGGAAGGAAG--GAAGGAAGGAAGGAAGGAAGGAAGGAA 242 chr6qtel1M 990222 TAGAA-GAAGAAAGAAAGAAAAGGAA-GAA-GAAGAAAAGAAAGAAAGAA 990268 -i - i i -i - - i i i i (AAGG)n#Simpl 243 -GGAAGGAAGGAAGGAAG-GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 290 chr6qtel1M 990269 AGAAAG-AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGGAAAGAAAG 990317 i i - i i i i i i i i - i (AAGG)n#Simpl 291 GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG-AAGGAAG 339 chr6qtel1M 990318 AAAAGAAGGAAGGAAGGAAGGAAGCAAAGGAAGGGAAGGAAGGAAGGAAG 990367 i i -i - (AAGG)n#Simpl 340 GAAGGAAGGAAGGAAGGAAGGAAG-GAAGGAA-GGAAGGAAGGAAGGAAG 387 chr6qtel1M 990368 GAAGAAAGAAAAGAAAGAAAGAAAGAAAGAAAGAAAG-TGAAAGAGAAGA 990416 i i i i i i i i i -v i - i (AAGG)n#Simpl 388 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG-GAAGG 436 chr6qtel1M 990417 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAGAAGGGTGCTG 990466 i i i i i i i i i i iv -- (AAGG)n#Simpl 437 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG--G 484 chr6qtel1M 990467 AAGG-AGGAGAGGAAGGAAGG--GGAAGGAAGGAAGG-GTGAAGGAAGGA 990512 - - -- -iv (AAGG)n#Simpl 485 AAGGAAGGA-AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 533 chr6qtel1M 990513 AGGAAGGAAGGAAGGAAGGAAGGAA-GAAGGAAAGAAAGAAAGGAAAGAA 990561 - - i i i (AAGG)n#Simpl 534 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG-AAGGAAGGAAGGAAGGAA 582 chr6qtel1M 990562 GAAAGAAAGAAAGAAAGAAAGAGAAAGAAAGAAAGAAAGAA--AAGAAAG 990609 i i i i i - i i i i -- i (AAGG)n#Simpl 583 GGAAGGAAGGAAGGAAGGAAG-GAAGGAAGGAAGGAAGGAAGGAAGGAAG 631 chr6qtel1M 990610 AAAGAAAAGAAAGAAAGAGAAAGAAAGAAAGAAGGAGGGGAGAGAAGGAA 990659 i -i i i - i i i i i - (AAGG)n#Simpl 632 GAAG-GAAGGAAGGAAG-GAAGGAAGGAAGGAAGGAAGGAAG-GAAGGAA 678 chr6qtel1M 990660 GGAACGAAGGAACGAA-GAAGAAACCAA-GAAGCAA 990693 v v - i vv - v (AAGG)n#Simpl 679 GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 714 Matrix = Unknown Transitions / transversions = 4.13 (95/23) Gap_init rate = 0.06 (42 / 710), avg. gap size = 1.12 (47 / 42) 24 8.91 2.78 0.00 chr6qtel1M 990913 990948 (9052) (AT)n#Simple_repeat 1 37 (0) m_b324s252i13 13619 chr6qtel1M 990913 ATATATATACATATATATATATATAT-TACATATTTA 990948 i - i v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATA 37 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) 218 34.11 4.59 8.57 chr6qtel1M 991058 991384 (8616) C L2#LINE/L2 (1182) 1900 1586 m_b324s601i31 13620 chr6qtel1M 991058 TGGATAGATCTTT-AAGAAATTTAGCAGTGAAG---AATAGGAAGATGAT 991103 i i iv -i i i v v i --- ii ii i i- C L2#LINE/L2 1900 TAGACAACTCTTTCGAGGAGTTTTGCTGTAAAGGGGAGCAGAGAAATGG- 1852 chr6qtel1M 991104 GATTGTATAATGGAGTGGAA----GAATCAAAGAAAGCCTTTTG------ 991143 iiv -iv v i ---- ii i i iivi ------ C L2#LINE/L2 1851 GGCGGTA-GCTGGAGGGGGANGTGGGGTCAAGGGAGAATTTTTGTTTTTT 1803 chr6qtel1M 991144 GGAGGCAATGGGGAACACTGAATGCATAATCATGTATAAGGATCATATAC 991193 ii --- ii v - ? vv iv -- ivv viv - i C L2#LINE/L2 1802 AAAG---ATGGGAGAAA-TNACAGCATGTT--TGTATGCTGATGGGA-AT 1760 chr6qtel1M 991194 AATCTGATAGAGAAGGAAAGACTGACAGATGAAAACTGAATAGAGGAGGC 991243 i iii i i i i- v ---- i v - - C L2#LINE/L2 1759 GATCCAGTAGAGAGGGAAAAATTGAT-GATGCA----GGAGAGAG-AGG- 1717 chr6qtel1M 991244 AGCAGAACAGAAGGCCACTGGAGCAATCCCTTGGAATAGGCAGGAGGAAA 991293 - v iv ------- i vi i v i ii ii C L2#LINE/L2 1716 -GGAGAATTG-------CTGGAGCGATGTCCTTGAGTAGGCGAGAGGGGA 1675 chr6qtel1M 991294 CGTGATCAAAGGCACAGAGCTAGGGGGTGGGTTTAAGGAACAGAAGTTTG 991343 i v v iv - ivii v ii v -- i i ivi C L2#LINE/L2 1674 TGGGATCTAGTGCACA-AGTGGAGGGGTTGGCCTTAG--ATAGGAGCACG 1628 chr6qtel1M 991344 GTCATTTCTTTTGTGG-AATAGGAGGGAAAGAGAAGAAAGTG 991384 v v v ii i - i i vii v v C L2#LINE/L2 1627 GACAGTTCATCCGTAGTAACAGGAGGGAAGGCAGAGTATGTG 1586 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 44.46 CpG sites = 68, Kimura (unadjusted) = 48.48 Transitions / transversions = 2.00 (68/34) Gap_init rate = 0.10 (32 / 326), avg. gap size = 1.31 (42 / 32) 243 35.10 4.17 5.04 chr6qtel1M 991570 991689 (8311) MIRc#SINE/MIR 3 121 (147) m_b324s601i32 13621 chr6qtel1M 991570 AAGCAGAATGGCATCGTAGAGAGAGAGCTTAATGGTATCGGCATCAGGAA 991619 i vi iiiv i i ----i v vv i vi MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAG----CACTGGACTTGGAGTCAGGAA 48 chr6qtel1M 991620 AGCTTTGATTCACATCCTATAGCTGTCACCTACTGGCTATAGAACCCTGT 991669 ii i v i ivi iivvv i i i i ivi i v MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 98 chr6qtel1M 991670 ----GTC-CCCAACAACTCTCTGAG 991689 ---- - ii -- MIRc#SINE/MIR 99 GCAAGTCACTTAAC--CTCTCTGAG 121 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 46.89 CpG sites = 27, Kimura (unadjusted) = 50.77 Transitions / transversions = 2.08 (27/13) Gap_init rate = 0.07 (8 / 119), avg. gap size = 1.38 (11 / 8) 12 18.29 0.00 3.12 chr6qtel1M 991714 991746 (8254) (AAAAAG)n#Simple_repeat 1 32 (0) m_b324s252i14 13622 chr6qtel1M 991714 AAAAAGAGAGAGAAAATGAAAAATATAGAAGAA 991746 i i v v - i (AAAAAG)n#Sim 1 AAAAAGAAAAAGAAAAAGAAAAAGA-AAAAGAA 32 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 332 33.35 2.05 3.47 chr6qtel1M 991821 991966 (8034) MIRb#SINE/MIR 73 216 (52) m_b324s601i33 13623 chr6qtel1M 991821 TTTACTATTCACTACATATGTGATTCTGAGGAAGCCATTTCATCTCCCCT 991870 i i i i i vv i iii i v ii i v i i - MIRb#SINE/MIR 73 TCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTC-T 121 chr6qtel1M 991871 CACCTTTACTTTTCCCTTCTATAAAATGGGTATTATAATAACAACATCAT 991920 v v i i v i i v i v v v v v i- MIRb#SINE/MIR 122 GAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTACCTCG- 170 chr6qtel1M 991921 TAAATGGGTTTTTATGAAAGTTAAAT---ACAATGTTTCTAATGTACTT 991966 i --- v i iii --- i iv v v ii MIRb#SINE/MIR 171 CA---GGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTT 216 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.51 CpG sites = 30, Kimura (unadjusted) = 46.39 Transitions / transversions = 1.76 (30/17) Gap_init rate = 0.04 (6 / 145), avg. gap size = 1.33 (8 / 6) 16 23.81 5.48 2.67 chr6qtel1M 992000 992072 (7928) (TGTATA)n#Simple_repeat 1 75 (0) m_b324s252i15 13624 chr6qtel1M 992000 TGTGATATGGA-AT-AATAGGCATATTATATATGTATACAT-TAT-AATA 992045 - v - -v v i - i ii - -v (TGTATA)n#Sim 1 TGT-ATATGTATATGTATATGTATA-TGTATATGTATATGTATATGTATA 48 chr6qtel1M 992046 GGCATATATATATATATATATATAGGT 992072 v i i i i v (TGTATA)n#Sim 49 TGTATATGTATATGTATATGTATATGT 75 Matrix = Unknown Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.08 (6 / 72), avg. gap size = 1.00 (6 / 6) 27 10.94 6.00 0.00 chr6qtel1M 992020 992069 (7931) (AT)n#Simple_repeat 1 53 (0) m_b324s252i16 13625 chr6qtel1M 992020 ATAT-TATATATGTATACAT-TATA-ATAGGCATATATATATATATATAT 992066 - i i - - vii (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chr6qtel1M 992067 ATA 992069 (AT)n#Simple_ 51 ATA 53 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.06 (3 / 49), avg. gap size = 1.00 (3 / 3) 183 27.58 3.39 1.67 chr6qtel1M 995423 995481 (4519) C MIR3#SINE/MIR (86) 122 63 m_b324s601i34 13626 chr6qtel1M 995423 GAAGCTTA-AGACGAGCCGCGACTTGCTCAAGATCACGTAG-GAGTTCAG 995470 i ii - v v vv i i i ii -? - C MIR3#SINE/MIR 122 GAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGCNAGTT-AG 74 chr6qtel1M 995471 TGACAAAGTTG 995481 i i ii C MIR3#SINE/MIR 73 TGGCAGAGCCG 63 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.56 CpG sites = 12, Kimura (unadjusted) = 37.57 Transitions / transversions = 3.00 (12/4) Gap_init rate = 0.05 (3 / 58), avg. gap size = 1.00 (3 / 3) 15 18.25 8.00 0.00 chr6qtel1M 996122 996171 (3829) (ATTG)n#Simple_repeat 1 54 (0) m_b324s252i17 13627 chr6qtel1M 996122 ATTGACT-ATCAATTTATTGATTG-TTGATT-A-TAATTAATAGATTGAT 996167 i - ii v - - - i i v (ATTG)n#Simpl 1 ATTGATTGATTGATTGATTGATTGATTGATTGATTGATTGATTGATTGAT 50 chr6qtel1M 996168 TTAT 996171 v (ATTG)n#Simpl 51 TGAT 54 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.08 (4 / 49), avg. gap size = 1.00 (4 / 4) 328 25.55 13.08 0.68 chr6qtel1M 996990 997119 (2881) MIRc#SINE/MIR 3 148 (120) m_b324s601i35 13628 chr6qtel1M 996990 AGGCAGTGAG---CAGTGGATAGGTTACCCAA---AAGATCAGGAAGACC 997033 v --- v ivi ivi ---iiii MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chr6qtel1M 997034 -------AAATATGGCCTCAGATACTGAA-GGCTG-GTGACCCTGGGCAA 997074 -------i i viv v v vi v v-i - i MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 102 chr6qtel1M 997075 GTCATCAGAATCTGTTTG--CCTCAATTTCCTCATGTGTAAAATGAG 997119 - vv i v i -- i v i MIRc#SINE/MIR 103 GTCA-CTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 30.63 CpG sites = 18, Kimura (unadjusted) = 31.77 Transitions / transversions = 1.20 (18/15) Gap_init rate = 0.05 (7 / 129), avg. gap size = 2.57 (18 / 7) 12 18.42 0.00 7.50 chr6qtel1M 997472 997514 (2486) (TAAAAA)n#Simple_repeat 1 40 (0) m_b324s252i18 13629 chr6qtel1M 997472 TAAATATACACATATAAAAATAAATAATATTAATATAAATTAA 997514 v - - v - vv v v (TAAAAA)n#Sim 1 TAAAAATA-A-AAATAAAAATAAA-AATAAAAATAAAAATAAA 40 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.07 (3 / 42), avg. gap size = 1.00 (3 / 3) 316 31.06 12.56 6.16 chr6qtel1M 997672 998069 (1931) L3#LINE/CR1 2660 3081 (1018) m_b324s601i36 13630 chr6qtel1M 997672 AGAAACAAAGAGGTACCTGTGAACTGGAAAAGGATGAATGTAA---CT-- 997716 vvi i v vii i v iii ?i--- -- L3#LINE/CR1 2660 AGAACGGAAGAGGTGCCAGAAGACTGGAGACGGGCAAATGTNGTNCCTAN 2709 chr6qtel1M 997717 TTGTGCATAG-----AAAGATGAATT--GGAAAGTAATCAGAAACCATGA 997759 v iv v ----- i -- ? v -- -- ivv L3#LINE/CR1 2710 TTTTAAAAAGGGAAAAAAGATGGATTCTGNAAACTA--CAGA--CCGGTA 2755 chr6qtel1M 997760 ATTCACTAGGTGAATTGATCTCCAA------TCT-GAA---ATAATTCCA 997799 ---i v ii -- i i ii------ - --- v vv L3#LINE/CR1 2756 A---GCTTGACG--TCGATCCCCGGCAAAATTCTAGAACGGATTATTAAA 2800 chr6qtel1M 997800 AAGATAGGGGTTTTTGATATGTACTTGAAAGGAAAAGCAACG----CTAA 997845 v --- v --- i ii iiii iii ---- i L3#LINE/CR1 2801 CAGAT---GGTTTGTGA---GCACTTAGAAAAGGAAGCGGTGATCACTAG 2844 chr6qtel1M 997846 ACGCCAGAATGAATTT-CAGAGACACAGATTATACCAGATTGAT-TC-TT 997892 iv v ii i- vi - ii i i i i i i- - L3#LINE/CR1 2845 GAGCCAGCATGGGTTCACTAAGA-ACAAGTCATGCCAAACTAACCTCATT 2893 chr6qtel1M 997893 TCCTTTTTATAACAGGGTTACTGTGATCAATGTCAGCCAGGAAGATGTA- 997941 - i i i- iii-- viii iii iv- L3#LINE/CR1 2894 TCCTTTTT-TGATAGGGTTACTA-GACTG--GTAGATCAGGGGAATGCCG 2939 chr6qtel1M 997942 -AAACAGA-TGTATTTAGATTT---TAAAGCATTTTA-AAAATTT----T 997981 - i ? - i i ---i i v - i i ---- L3#LINE/CR1 2940 TAGACANAGTGTATCTGGATTTCAGCAAGGCATTTGACAAAGTCTCTCAT 2989 chr6qtel1M 997982 GA------GGTAGATTAAA-AGAGAATAGATATTGGTT-GATGAT--CAT 998021 ------v i iv i -i --- v i - --i i L3#LINE/CR1 2990 GATATCCTTGTGGACAAGATGGAGAA---ATATGGGCTGGATGATAGTAC 3036 chr6qtel1M 998022 AATTAGCCAGGCTCAGAAATTATATTTGAATGGCCTGATTCAAAAGAT 998069 i vii ii iv i---v iv i i ivv ii i L3#LINE/CR1 3037 AGTTAGGTGGATTCGTAG---CTGGTTGAACGACTATACCCAAAAGGT 3081 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.21 CpG sites = 84, Kimura (unadjusted) = 43.81 Transitions / transversions = 2.62 (84/32) Gap_init rate = 0.12 (47 / 397), avg. gap size = 1.62 (76 / 47) 12 11.45 0.00 9.38 chr6qtel1M 998080 998114 (1886) (CTTCCC)n#Simple_repeat 1 32 (0) m_b324s252i19 13631 chr6qtel1M 998080 CTTTCCCTCCACCCTTCCCTTTCCTCACTTCCCCT 998114 i i - i - - (CTTCCC)n#Sim 1 CTTCCCCTTC-CCCTTCCCCTTCC-C-CTTCCCCT 32 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.09 (3 / 34), avg. gap size = 1.00 (3 / 3) 188 15.08 0.00 7.50 chr6qtel1M 999270 999312 (688) C MIR#SINE/MIR (118) 144 105 m_b324s601i37 13632 chr6qtel1M 999270 CTCATTTTATAGATGAGGTAAAACTGAGGGCAAACAGGGGTCA 999312 i i -- - v v i i C MIR#SINE/MIR 144 CCCATTTTACAGATGAGG--AAACTGA-GGCACAGAGAGGTTA 105 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 17.02 CpG sites = 4, Kimura (unadjusted) = 17.02 Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.07 (3 / 42), avg. gap size = 1.00 (3 / 3) 245 26.39 11.11 5.26 chr6qtel1M 999462 999605 (395) L2a_3end#LINE/L2 364 515 (2) m_b324s601i38 13633 chr6qtel1M 999462 ATATATTTGCTTATACGTTT-TCTCTTCCTCATT-----GTAACTTTCTT 999505 v i -i i - ii - i ----- vi i v L2a_3end#LINE 364 ATTTATTTGTTTAT-TGTCTGTCTCCCCC-CACTAGAATGTAAGCTCCAT 411 chr6qtel1M 999506 GAAAACAG--ACTTGTTTTTGCCTTTATT------TTTATGCCTAATGCT 999547 iii -- v v i i- i ------ v v i ii i L2a_3end#LINE 412 GAGGGCAGGGACTTTTGTCTGT-TTTGTTCACTGCTGTATCCCCAGCGCC 460 chr6qtel1M 999548 TAGTACAATGCAGGAGGATACATAGTAGGTGCTTAATTGATATTAATGTT 999597 v i vv i---i i i vi -- L2a_3end#LINE 461 TAGAACAGTGCCTGG---CACATAGTAGGCGCTCAATAAATATT--TGTT 505 chr6qtel1M 999598 G--TGACTGA 999605 -- v L2a_3end#LINE 506 GAATGAATGA 515 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.64 CpG sites = 24, Kimura (unadjusted) = 33.95 Transitions / transversions = 2.00 (24/12) Gap_init rate = 0.09 (13 / 143), avg. gap size = 1.85 (24 / 13) 266 26.57 7.02 4.27 chr6qtel1M 999492 999605 (395) L2d_3end#LINE/L2 396 512 (4) m_b324s601i39 13633 chr6qtel1M 999492 ATTGTAACTTTCTTGAAAACAG--ACT-TGTTTTTGCCTTTATTTTTATG 999538 vi i iii -- i- i vvv ? v ? ii v L2d_3end#LINE 396 ATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACTNTTTTNTCGTT 445 chr6qtel1M 999539 CCT---AATGCTTAGTACAATGCAGGAGGATACATAGTAGGTGCTTAATT 999585 i--- ii i i i -v --i i i v L2d_3end#LINE 446 CCCCACAGCGCCTAGCACAGTGC-TGAG--CACATAGTAGGCGCTCAATA 492 chr6qtel1M 999586 GATATTAATGTTG--TGACTGA 999605 i i -- -- i L2d_3end#LINE 493 AATACT--TGTTGATTGATTGA 512 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 30.85 CpG sites = 21, Kimura (unadjusted) = 35.54 Transitions / transversions = 2.62 (21/8) Gap_init rate = 0.08 (9 / 113), avg. gap size = 1.44 (13 / 9) 219 29.88 4.55 1.10 chr6qtel1M 999577 999664 (336) L3b_3end#LINE/CR1 141 231 (975) m_b324s601i40 13630 chr6qtel1M 999577 TGCTTAATT-GATATTAAT-GTTG--TGACTGACCTGACCCAAAAAGCCA 999622 v i i - i v? - i -- vii v? iii vv L3b_3end#LINE 141 TGGTCAGTTAGACATTCNTAGCTGGTTGAACAACCGNACCCAAAGGACGT 190 chr6qtel1M 999623 CCACTAATGAAACAACGTCAACTTGAAGAGAAGTCTCTAATG 999664 iv i? i?v i i i i - i i L3b_3end#LINE 191 TGATNAATGGNTCGATGTCAACCTGGAG-GGAGTCTCTAGTG 231 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.86 CpG sites = 18, Kimura (unadjusted) = 43.12 Transitions / transversions = 2.25 (18/8) Gap_init rate = 0.05 (4 / 87), avg. gap size = 1.25 (5 / 4) 268 32.63 17.60 1.29 chr6qtel1M 999599 999865 (135) L3#LINE/CR1 3060 3369 (730) m_b324s601i41 13630 chr6qtel1M 999599 TGACTGACCTGACCCAAAAAGCCACCACTAATGAAACAACGTCAACTTGA 999648 vi ivv i ivviv i i v i i i i L3#LINE/CR1 3060 TGAACGACTATACCCAAAAGGTGTTGATTAATGGATCGATGTCAACCTGG 3109 chr6qtel1M 999649 AGAGAAGTCTCTAATGAAAT----CAA-----TACCTTTAACCAGGACTA 999689 i i i ivi ---- i----- ii i ii vv v iv L3#LINE/CR1 3110 AGGGAGGTCTCTAGTGGCGTGCCACAGGGCTCTGTCCTTGGCCCTGTCCT 3159 chr6qtel1M 999690 TTTAAACATCTTTAGCAA----TTCAATACAGTC--AGATAGCATGCTTA 999733 v v i v ---- vi iv v -- vi L3#LINE/CR1 3160 GTTCAACATTTTTATCAATGACTTGGATGAAGACATAGAAGGCATGCTTA 3209 chr6qtel1M 999734 ----------ATATGA-GC-AAGATGGAA---------AATGTGTCATAT 999762 ---------- v -i - v i --------- ii ?iiv L3#LINE/CR1 3210 TCAAATTTGCAGATGACACAAAGCTGGGAGGGATAGCTAATACGNTGGAT 3259 chr6qtel1M 999763 TACAG--TCTAGATCTGTAAA-------ACAAGCTAAACCAATGGATAGA 999803 v -- v iiiv ?------- i ii v i iiv L3#LINE/CR1 3260 GACAGAATCAAGATTCAAAANGATCTCGACAGGCTGGAACGATGGGCCGA 3309 chr6qtel1M 999804 ATCAAATAAGATTAAATTTAAT--GTATATTTTTTTATAAAATTCCACAT 999851 v v i v i-- v ----vv i i i ii L3#LINE/CR1 3310 AACCAACAAGATGAAATTTAACAGGGATA----AATGTAAAGTCCTGCAT 3355 chr6qtel1M 999852 CAGCGTTCAAAAAA 999865 iviv L3#LINE/CR1 3356 TTAGGTTCAAAAAA 3369 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.51 CpG sites = 51, Kimura (unadjusted) = 45.02 Transitions / transversions = 1.46 (51/35) Gap_init rate = 0.06 (15 / 266), avg. gap size = 3.40 (51 / 15) 15 15.66 0.00 10.64 chrXptel1M 1626 1677 (998323) (AAGG)n#Simple_repeat 1 47 (0) m_b325s252i0 13634 chrXptel1M 1626 AAGGAAGGAAGTATAGGAGGAGAAGGATGGAGAGAAAGATTAGGAAGGGA 1675 v - i - v - i -vv - (AAGG)n#Simpl 1 AAGGAAGGAAGGA-AGGAAG-GAAGGAAGGA-AGGAAG-GAAGGAA-GGA 45 chrXptel1M 1676 AG 1677 (AAGG)n#Simpl 46 AG 47 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.10 (5 / 51), avg. gap size = 1.00 (5 / 5) 12 25.56 0.00 0.00 chrXptel1M 4452 4488 (995512) (AAAAGA)n#Simple_repeat 1 37 (0) m_b325s252i1 13635 chrXptel1M 4452 AAAAGTAAGAGTTTAAGAAAAAGAAAACAAAATAGAA 4488 v i vvv vi v (AAAAGA)n#Sim 1 AAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAA 37 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 21 13.40 0.00 0.00 chrXptel1M 4806 4838 (995162) (T)n#Simple_repeat 1 33 (0) m_b325s252i2 13636 chrXptel1M 4806 TTTTTTTTTTGTTTTGTTTTTGTTTGTTTTTTT 4838 v v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 33 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 13 15.42 0.00 3.33 chrXptel1M 4847 4877 (995123) (AATT)n#Simple_repeat 1 30 (0) m_b325s252i3 13637 chrXptel1M 4847 AATATAAAAAATTAATGAATGAATTAATTAA 4877 - vv v v (AATT)n#Simpl 1 AAT-TAATTAATTAATTAATTAATTAATTAA 30 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.03 (1 / 30), avg. gap size = 1.00 (1 / 1) 18 12.17 0.00 0.00 chrXptel1M 5224 5250 (994750) (T)n#Simple_repeat 1 27 (0) m_b325s252i4 13638 chrXptel1M 5224 TTTTTGTTTTTGTTTTTTTGTTTTTTT 5250 v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTT 27 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 1337 28.51 4.26 4.74 chrXptel1M 9034 9902 (990098) HERVK14C#LTR/ERVK 2856 3720 (3714) m_b325s701i0 13639 chrXptel1M 9034 GGCTGCTGTTGAAGGCCTGCCAACACTTTCACCTGTTCCTGTCCAATGGA 9083 ii -- - iv? ------ i iv vv HERVK14C#LTR/ 2856 GGCCACTGTTGA--GCCT-CCAGANC------CTATTCCCTTAAAATGGA 2896 chrXptel1M 9084 AAACTGATACACCAGTGTGGATAGAGCAGTGGCCCTTAAGTAACGATAAA 9133 ?i iv v v? ? v i ? ? vi ??v v v v HERVK14C#LTR/ 2897 NGACCCAAAANCCNGTTTGGGTNGANCAGTGGCCGCTNNCTCAGGAAAAA 2946 chrXptel1M 9134 ATTCAGGCCTTATTAGATATAGTACAGGAGCAGCTTGACCAAGGACACTT 9183 v vvi ivi vv vv i i ii v ?v v HERVK14C#LTR/ 2947 CTGGGGGCCTTACAGGAATTAGTCAAAGAACAATTAGANAAAGGACACAT 2996 chrXptel1M 9184 AAAACC----TTCTCTAAGTCCTTGAATTC-CCAGTGTTTGTTGTGAAAA 9228 ?i i ---- i ---i ? v - vi ? i HERVK14C#LTR/ 2997 NGAGCCCACATTTTCT---CCNTGGAATTCNCCAGTGTTTGTAATNAAGA 3043 chrXptel1M 9229 ACAAATCTGGAAAATGGAGGATGTTAACGGATTTAAGAAAAGTGAATGAA 9278 v i v i v ? i v i v ivv v -- HERVK14C#LTR/ 3044 AAAAATCCGGCAGATGGCGNATGCTAACCGACTTACGAGCCGTCAATG-- 3091 chrXptel1M 9279 CAG--ATGGAAACTATGGGAACTCTTCAGCCTGGACTTCCATCTCCTACT 9326 -- ?v v ? ii ? v v i v ? i ii i HERVK14C#LTR/ 3092 CAGTCATNCAACCNATGGGGGCNCTGCAGCCAGGGCTGCCNTCCCCCGCC 3141 chrXptel1M 9327 CAGTTGCCTAGAGAATGGCCTCT-TTGGTCATAGATATTAAGGATTGTTT 9375 vv v v v ?i -v i i v v i i HERVK14C#LTR/ 3142 ATGATTCCTAGAGACTGGCCNTTAATAGTTATAGATTTGAAGGACTGCTT 3191 chrXptel1M 9376 CTATTCTATCCCTCTGGACAAGGAGGATATGAAAAGATTTGCCTTTTCAG 9425 v v i i vvi vv? v vi i i v vi HERVK14C#LTR/ 3192 CTTTACTATTCCTCTAGCAGAGCCNGATTTTGAAAAATTTGCTTTTACTA 3241 chrXptel1M 9426 TGCCCAGCGTTAAC--TTAGCTGAGCCT-TATAAAGATATGAATGGACAG 9472 v iivii v --iv -- i ?-i vvv ? v v v HERVK14C#LTR/ 3242 TTCCTGCTATGAACAACAAG--GAACCNGCAGCCAGNTATCATTGGAAAG 3289 chrXptel1M 9473 TTTTACCACAGGGAATG-AAAACAGCCCTACTATGTGTCAAATGTATGTT 9521 ? i i v -vi i i ? ? v iv ? v HERVK14C#LTR/ 3290 TNTTGCCGCAGGGCATGTTGAATAGTCCNACNATTTGTCAAACTTNTGTG 3339 chrXptel1M 9522 GCTGCTGCTCTTGCTCCAGTAAGAAAAGCATTCCCAAA-AGTTATGCTAT 9570 vv?vv v vvv v ? i vvvi i i -vv? iii HERVK14C#LTR/ 3340 GGGNAGGCTATTCAACCTGTNAGAGATCAGTTTCCAGATTCNTATATCAT 3389 chrXptel1M 9571 TACATTACATGGATGACATTTTGGGATGTGCACCTGA------GGAACA- 9613 - i v ---? iv i ------i v - HERVK14C#LTR/ 3390 T-CATTATATGGATGACATATT---NTGTGCGGCCGAAACTCGAGACCAA 3435 chrXptel1M 9614 -------AATGTTAGAAGCATGTCTACAAAAGACCATAG-AAACACTAAG 9655 ------- i v--v ii i i i vi ? -vi i --- HERVK14C#LTR/ 3436 CTTATCCAGTGTTAT--TCACATTTACAGAAGGCGGTNGCCGACGCT--- 3480 chrXptel1M 9656 GAATTAGAAAGTATACATAGCACCAGAAAAAATTCAAAGACATGCTCCTT 9705 i ----i? --- ? ? v vi?v i HERVK14C#LTR/ 3481 GGATT----GNT---CATAGCNCCNGATAAAATTCAAACGNCTACTCCTT 3523 chrXptel1M 9706 TTCAATATTTAGGATATG-AAGTGTATCCTAAGGTACTTACAGGTCAAAA 9754 i i - - i vi vvvv i i v vivv? HERVK14C#LTR/ 3524 TCCAATATTTGGGA-ATGCAGGTTCAGGAAAGGGCAATTAAGCCNCAAAA 3572 chrXptel1M 9755 ACTGTCCTTAAGAACAGAGAAG-----CTAAACACATTGAATGATTTTCA 9799 i-- i --- i viv i ----- i v v i HERVK14C#LTR/ 3573 G--GTTC---AAATTCGAAAAGACTCTCTGAAAACTTTAAATGATTTTCA 3617 chrXptel1M 9800 GAAATTGATAGGAGATATCCAATGGATGCGACCAGTGTTAGACTTGACTA 9849 i iv i iv v v viiv i v vv HERVK14C#LTR/ 3618 AAAATTATTAGGGGATATTAATTGGATTCGACCTACTTTAGGCATTCCTA 3667 chrXptel1M 9850 TCTAT--CA-GTTACAACTGTTATATGACATTTTAAGGGGAGACAGTGCT 9896 i -- - ivv v v v --- i i ivv ? HERVK14C#LTR/ 3668 CCTATGCCATGTCTAATCTGTTCTCT---ATCTTAAGAGGAGATCCTGNT 3714 chrXptel1M 9897 TTAAAT 9902 i v HERVK14C#LTR/ 3715 CTCAAT 3720 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.68 CpG sites = 110, Kimura (unadjusted) = 38.29 Transitions / transversions = 0.87 (110/126) Gap_init rate = 0.07 (57 / 868), avg. gap size = 1.37 (78 / 57) 604 24.06 8.49 4.65 chrXptel1M 10855 11290 (988710) HERVK14C#LTR/ERVK 4660 5111 (2323) m_b325s701i1 13639 chrXptel1M 10855 GTAAAAGCC--TGTACGGC-TTGCCTTCCTTTCCATGCTCCTACA-CTGC 10900 i? i ? -- ? ii - i ??v v v - v - HERVK14C#LTR/ 4660 GCNAAGGNCATTGTNCAACATTGCCCTNNGTGCCAGG-TGCTACAACTGC 4708 chrXptel1M 10901 C---TCCAGGGA----AG--AACCCTCGTGGTTTGAGACCCAATGAAATC 10941 --- v ----? -- ? v v iv? i ?viv ? HERVK14C#LTR/ 4709 CACATCAAGGGACTGGNGTTAACCCNCGAGGATTGGCNCCTAATNCGCTN 4758 chrXptel1M 10942 TGGCAAATGGATGTGACCCATTATAAATCT-TTTGGTCGTCTGTCTTTCA 10990 i ? -i vv ?i- vviv ? ? v i HERVK14C#LTR/ 4759 TGGCAAATGGACGTNACCCAT-GTACCTNCATTTGGGAAACTNTCNTACG 4807 chrXptel1M 10991 TCCACGTTGTGGTAGACACCTTTTCAGGATTCACTTTT-----GCAA--T 11033 i ?iiv i ----- i v----- ? -- HERVK14C#LTR/ 4808 TCCATGTNACTGTAGATACCTTTTC-----TCATTTTGTNTGGGCNACTT 4852 chrXptel1M 11034 GCCAGCAGCAAAAGAGACAGC--CT-GAGT----GGTCACTGAATTCCTC 11076 -- i ii? i ? -- - v ----i v i viv i ii HERVK14C#LTR/ 4853 GCCA--AACAGGNGAGGCNGCTGCTCGTGTTAAAAGACATTTGCTTTCCT 4900 chrXptel1M 11077 ATACAAGCATTTGCCATTATGGGTGTGCCACAAACAATAAAAACAGACAA 11126 i ------- i ?i i ii v v? v ? HERVK14C#LTR/ 4901 GT-------TTCGCNGTCATGGGCATTCCACAAAANATTAAAACNGACAA 4943 chrXptel1M 11127 TGGTCCTGCTTATACT-TTGAAACATTTTGCACACTTTTGTGCA-CAGTA 11174 i v vi i?? -v i ? -- i? ?i v iv v - i i HERVK14C#LTR/ 4944 TGGCCCAGGCTACNNTAGTAAANC--TTTANANGCGTTCCTTCAACAATG 4991 chrXptel1M 11175 TAAGATTTTACACACCACGGGCATACCTTTTAATCCTCAAGGACAGGCAA 11224 v? v vv ?i v ? v i v i ? i v HERVK14C#LTR/ 4992 GNACATTAAACACANTACTGGNATCCCCTATAATTCTCAAGGNCAAGCCA 5041 chrXptel1M 11225 TAGTGGAGAGGAGA-AACAGAGATATTAAGACGCTC--CTCCAAAAACAA 11271 v v - v v- iv - iv i ?- --i v HERVK14C#LTR/ 5042 TTGTTGA-ACGAGCTAATCGA-ACCTTAAAAN-CTCAATTACAAAAACAA 5088 chrXptel1M 11272 A----AGAAAGGGGGAGCCACAG 11290 ---- i i v HERVK14C#LTR/ 5089 AAGACAGAAGGGGGGAACCAGAG 5111 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 30.90 CpG sites = 53, Kimura (unadjusted) = 32.43 Transitions / transversions = 1.13 (53/47) Gap_init rate = 0.09 (38 / 435), avg. gap size = 1.53 (58 / 38) 497 29.18 8.22 4.06 chrXptel1M 10890 11339 (988661) HERVK#LTR/ERVK 4796 5263 (2273) m_b325s701i2 13639 chrXptel1M 10890 TCCTACAC-TGCC---TCCAG-GGAAG-----AACCCTCGTGGTTTGAGA 10929 - --- v - v ----- i iv v i v v HERVK#LTR/ERV 4796 TCCTACACCTGCCCACTCAAGAGGCAGGAGTTAATCCCAGAGGTCTGTGT 4845 chrXptel1M 10930 CCCAATGAAATCTGGCAAATGGATGTGACCCATTATAAAT-CTTTTGGTC 10978 i viv v v v -i vv - v vv HERVK#LTR/ERV 4846 CCTAATGCGTTATGGCAAATGGATGTCACGCAT-GTACCTTCATTTGGAA 4894 chrXptel1M 10979 GTCTGTCTTTCATCCACGTTGTGGTAGACACCTTTTCAGGATTCACTTTT 11028 vi v ?ii i viii v i i v viv iv vv HERVK#LTR/ERV 4895 GATTGTCATNTGTCCATGTAACAGTTGATACTTATTCACATTTCATATGG 4944 chrXptel1M 11029 GCAA--TGCCAG-CAGCAAAAGAGACAGCCTGAGT----GGTCACTGAAT 11071 -- - v i iiv vv iiv ----iiv i v v HERVK#LTR/ERV 4945 GCAACCTGCCAGACAGGAGAAAGTACTTCCCATGTTAAAAAACATTTATT 4994 chrXptel1M 11072 TCCTCATACAAGCATTTGCCATTATGGGTGTGCCACAAACAATAAAAACA 11121 vi ii ------- ii i v v v v v v HERVK#LTR/ERV 4995 ATCTTGT-------TTTGCTGTCATGGGAGTTCCAGAAAAAATTAAAACT 5037 chrXptel1M 11122 GACAATGGTCCTGCTTATACTTTG---AAACATTTTGCACACTTTTGTGC 11168 v v v-- v i--- i ? iiiv v i i ivii HERVK#LTR/ERV 5038 GACAATGGGCCAGG--ATACTGTAGTAAAGCNTTCCAAAAATTCTTAAAT 5085 chrXptel1M 11169 ACAGTATAAGATTTTACACACCACGGGCATACCTTTTAATCCTCAAGGAC 11218 - iv i vi i v i v v v i i HERVK#LTR/ERV 5086 -CAGTGGAAAATTACACATACAACAGGAATTCCTTATAATTCCCAAGGAC 5134 chrXptel1M 11219 AGGCAATAGTGGAGAGGAGAAACAGAGATATTAAGACGCTCCTCCAA--A 11266 v v i i vv i - i i v i - vviiii-- HERVK#LTR/ERV 5135 AGGCCATAGTTGAAAGAACTAATAGA-ACACTCAAA-GCTCAATTGGTTA 5182 chrXptel1M 11267 AACAAAAGAAAGGGGGAGCCACAG--------GTAA----CCCTAGA-G- 11302 ii -- -------- ?---- i - - HERVK#LTR/ERV 5183 AACAAAAAGAAGGGGGAG--ACAGTAAGGAGTGTANCACTCCCCAGATGC 5230 chrXptel1M 11303 AACTTCTAAATCTAGCTCTTTATACTATTAACTTCTT 11339 --- v i - v i HERVK#LTR/ERV 5231 AACTT---AATCTAGCACTCTATACT-TTAAATTTTT 5263 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.48 CpG sites = 63, Kimura (unadjusted) = 37.85 Transitions / transversions = 1.00 (63/63) Gap_init rate = 0.07 (33 / 449), avg. gap size = 1.70 (56 / 33) 15 20.03 0.00 0.00 chrXptel1M 13745 13773 (986227) (A)n#Simple_repeat 1 29 (0) m_b325s252i6 13640 chrXptel1M 13745 AAAAAAATAAATAAATAAATATAAAAAAA 13773 v v v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA 29 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 14 5.00 0.00 0.00 chrXptel1M 14433 14453 (985547) (CCCA)n#Simple_repeat 1 21 (0) m_b325s252i7 13641 chrXptel1M 14433 CCCACTCACCCACCCACCCAC 14453 i (CCCA)n#Simpl 1 CCCACCCACCCACCCACCCAC 21 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 274 27.88 1.92 0.00 chrXptel1M 15329 15432 (984568) L1MC4a_3end#LINE/L1 459 564 (2065) m_b325s551i0 13642 chrXptel1M 15329 TTTTAACTGTAAAAC--TGGAAACTGAATGGATGTCCATCAGTTGGAGAA 15376 v i i i-- vivv ii i ??i v ? L1MC4a_3end#L 459 TTGTAATTGCAAAATATTGGAAACAACCTAAATGCCCATNNATAGGAGAN 508 chrXptel1M 15377 TGGCTGAATAAATTGTGGTATATGAATATTATGGAATATTATTGTTCTGT 15426 i i i i vv i iv i i vvvv L1MC4a_3end#L 509 TGGTTGAATAAACTATGGTACATCCACACAATGGAGTACTATGCAGCTGT 558 chrXptel1M 15427 AAGAAA 15432 i L1MC4a_3end#L 559 AAAAAA 564 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.17 CpG sites = 17, Kimura (unadjusted) = 37.17 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.01 (1 / 103), avg. gap size = 2.00 (2 / 1) 354 21.25 0.00 0.00 chrXptel1M 15339 15418 (984582) L1ME3G_3end#LINE/L1 469 548 (376) m_b325s551i1 13642 chrXptel1M 15339 AAAACTGGAAACTGAATGGATGTCCATCAGTTGGAGAATGGCTGAATAAA 15388 i vivv ii i v i i i L1ME3G_3end#L 469 AAAATTGGAAACAACCTAAATGTCCATCAATAGGGGAATGGTTAAATAAA 518 chrXptel1M 15389 TTGTGGTATATGAATATTATGGAATATTAT 15418 i vv i i L1ME3G_3end#L 519 TTATGGTATATCCATACTATGGAATACTAT 548 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 25.60 CpG sites = 11, Kimura (unadjusted) = 25.60 Transitions / transversions = 1.83 (11/6) Gap_init rate = 0.00 (0 / 79), avg. gap size = 0.0 (0 / 0) 323 22.06 4.90 4.90 chrXptel1M 15357 15499 (984501) L1MC1_3end#LINE/L1 491 633 (447) m_b325s551i2 13642 chrXptel1M 15357 GATGTCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATATGAATATT 15406 v v v v i i i vv v iv L1MC1_3end#LI 491 GATGTCCTTCAGTAGGTGAATGGATAAATAAACTGTGGTACATCCAGACA 540 chrXptel1M 15407 ATGGAATATTATT--GTTCT-GTAAGAAATGACCCA-CAGG--ATGATTT 15450 -- iv -iv v i - i -- --- L1MC1_3end#LI 541 ATGGAATATTATTCAGCGCTAAAAAGAAATGAGCTATCAAGCCATGA--- 587 chrXptel1M 15451 CAGAAAGGCCTGGA-GAGACTTATGTGAACTGATACTGAGTGAAACGAGC 15499 --- i v - i vi v - iv i vi L1MC1_3end#LI 588 ---AAAGACATGGAGGAAACTTAAATGCA-TATTACTAAGTGAAAGAAGC 633 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 25.28 CpG sites = 14, Kimura (unadjusted) = 26.25 Transitions / transversions = 0.88 (14/16) Gap_init rate = 0.08 (12 / 142), avg. gap size = 1.17 (14 / 12) 19 0.00 0.00 0.00 chrXptel1M 15971 15991 (984009) (AG)n#Simple_repeat 1 21 (0) m_b325s252i10 13643 chrXptel1M 15971 AGAGAGAGAGAGAGAGAGAGA 15991 (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGA 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 16 26.23 0.00 2.08 chrXptel1M 15962 16010 (983990) (AAAG)n#Simple_repeat 1 48 (0) m_b325s252i9 13644 chrXptel1M 15962 AAATAAAAAAGAGAGAGAGAGAGAGAGAGAAAAAAACAAAAAAAAAAAG 16010 v i - i i i i i v i i (AAAG)n#Simpl 1 AAAGAAAGAA-AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG 48 Matrix = Unknown Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.02 (1 / 48), avg. gap size = 1.00 (1 / 1) 14 12.68 0.00 0.00 chrXptel1M 16112 16137 (983863) (TTA)n#Simple_repeat 1 26 (0) m_b325s252i11 13645 chrXptel1M 16112 TTATCATTATTATTGTTATTATTTTT 16137 i i v (TTA)n#Simple 1 TTATTATTATTATTATTATTATTATT 26 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 16 13.08 0.00 0.00 chrXptel1M 16935 16959 (983041) (T)n#Simple_repeat 1 25 (0) m_b325s252i12 13646 chrXptel1M 16935 TTTTTTCTTTGTTTTTTGTTTTTTT 16959 i v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 16 9.71 0.00 0.00 chrXptel1M 17361 17382 (982618) (T)n#Simple_repeat 1 22 (0) m_b325s252i13 13647 chrXptel1M 17361 TTTTTTTTGCTTTTTTTTTTTT 17382 vi (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTT 22 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 253 28.46 4.29 2.10 chrXptel1M 17477 17616 (982384) L1M1_orf2#LINE/L1 1148 1290 (2004) m_b325s551i3 13648 chrXptel1M 17477 AAAAAGGAAAGAAGAACCTAAAATTGTTAATCTCAGAAATGACAAA---- 17522 i i v -- viv vv i v ---- L1M1_orf2#LIN 1148 AAAAAAGAGAGAAGACCC--AAATAAATAAAATCAGAGATGAAAAAGGAG 1195 chrXptel1M 17523 -CATTCCA-CTAATGAAGAGGACATTAGAATAATAATTAGGAGTTATTTT 17570 - v - i ivv vi v vi vi v vi i i v L1M1_orf2#LIN 1196 ACATTACAACTGATACCGCAGAAATTCAAAGGATCATTAGTGGCTACTAT 1245 chrXptel1M 17571 GCCTAATTATATGTCAATAAATCGAATAATCTAAGGAAAAGTGGAC 17616 vvi i i i i v - i i i L1M1_orf2#LIN 1246 GAGCAACTATATGCCAATAAATTGGAAAATCT-AGAAGAAATGGAC 1290 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.29 CpG sites = 20, Kimura (unadjusted) = 36.29 Transitions / transversions = 1.05 (20/19) Gap_init rate = 0.04 (6 / 139), avg. gap size = 1.50 (9 / 6) 231 30.24 1.50 3.05 chrXptel1M 17881 18013 (981987) L1MC_orf2#LINE/L1 1148 1278 (2016) m_b325s551i4 13649 chrXptel1M 17881 AAAAAGGAAAGAACATAATAAAATTGTTAATCTCAGAAATGAA--ATGGG 17928 i i v i v-- ii v -- v L1MC_orf2#LIN 1148 AAAAAAGAGAGAAGACAC--AAATTACTAATATCAGAAATGAAAGAGGGG 1195 chrXptel1M 17929 ACAACTTTCGACCAATTTAGAGGAAATTAGAACAATAATTAGGAGTTATT 17978 -- iv v ?i iiviv v i vi v i iiv i L1MC_orf2#LIN 1196 ACA--TCACTACNGATCCCATGGACATTAAAAGGATAATAAAGGAATACT 1243 chrXptel1M 17979 TTGCCTAACTAGATGTCAATAAATCTGATAATCTA 18013 v vvi vv i v i i i L1MC_orf2#LIN 1244 ATGAACAACTCTATGCCCACAAATTTGATAACCTA 1278 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.88 CpG sites = 21, Kimura (unadjusted) = 39.88 Transitions / transversions = 1.17 (21/18) Gap_init rate = 0.04 (5 / 132), avg. gap size = 1.20 (6 / 5) 11 24.76 0.00 2.56 chrXptel1M 18908 18947 (981053) (GGGGGAA)n#Simple_repeat 1 39 (0) m_b325s252i14 13650 chrXptel1M 18908 GGGGGATGGGGGTAACCAAGAAGGAGGAATGGGGAAAGGG 18947 v - vvii i v i (GGGGGAA)n#Si 1 GGGGGAAGGGGG-AAGGGGGAAGGGGGAAGGGGGAAGGGG 39 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1) 16 5.20 0.00 0.00 chrXptel1M 18952 18971 (981029) (T)n#Simple_repeat 1 20 (0) m_b325s252i15 13651 chrXptel1M 18952 TTTTTTTTTTTTTATTTTTT 18971 v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTT 20 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 16 14.07 5.13 0.00 chrXptel1M 19505 19543 (980457) (AGAGATT)n#Simple_repeat 1 41 (0) m_b325s252i16 13652 chrXptel1M 19505 AGATATTAGAAAAT-GAGAGCAG-GATTAGAGATTAGAGAT 19543 v i v - vi - (AGAGATT)n#Si 1 AGAGATTAGAGATTAGAGATTAGAGATTAGAGATTAGAGAT 41 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2) 13 14.15 3.03 3.03 chrXptel1M 21294 21326 (978674) (AGC)n#Simple_repeat 1 33 (0) m_b325s252i17 13653 chrXptel1M 21294 AGCAGCAG-AGCAGCAGTGGAAAGCAGCAGCCGC 21326 - ii -v v (AGC)n#Simple 1 AGCAGCAGCAGCAGCAGCAG-CAGCAGCAGCAGC 33 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.06 (2 / 32), avg. gap size = 1.00 (2 / 2) 42 8.76 2.60 2.60 chrXptel1M 26365 26441 (973559) (TTTTTG)n#Simple_repeat 1 77 (0) m_b325s252i18 13654 chrXptel1M 26365 TTTTTG-TTTTG-TTTTGGTTTGGTTTTTGATTTTGGTTTTGGTTTTGGT 26412 - - v v - v v v (TTTTTG)n#Sim 1 TTTTTGTTTTTGTTTTTGTTTTTGTTTTTG-TTTTTGTTTTTGTTTTTGT 49 chrXptel1M 26413 TTTGGTTTTTTGTTTTTGTTTTTGTTTTT 26441 v - (TTTTTG)n#Sim 50 TTTTG-TTTTTGTTTTTGTTTTTGTTTTT 77 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.05 (4 / 76), avg. gap size = 1.00 (4 / 4) 1335 30.12 2.85 3.66 chrXptel1M 26831 27602 (972398) L1M5_orf2#LINE/L1 1075 1840 (1454) m_b325s551i5 13655 chrXptel1M 26831 ATGAACAAAACTAAGAATTGGTTTTATGGGAAAAT-ACCAAAATAGATCA 26879 v i i i i ii i v ii i - vi v v L1M5_orf2#LIN 1075 ATCAACGAAGCCAAAAGCTGGTTCTTTGAAAAGATCAATAAAATTGATAA 1124 chrXptel1M 26880 GCTTTTATTTAGGGTTTTATTTAATTTGATTAG--AAAAAGGAAAGAAGA 26927 i i i vi? i------------i i i-- i i L1M5_orf2#LIN 1125 ACCTCTAGCNAGA------------CTGATCAAGAAAAAAAGAGAGAAGA 1162 chrXptel1M 26928 AAATCTAATT--TAGTCTCAAAAATGAAAAGGGAGAACTTTCCACCAATG 26975 v -- v --i i v ii i vv iv i vi v L1M5_orf2#LIN 1163 CA--CAAATTACCAATATCAGGAATGAAAAAGGAGACATCACTACAGATC 1210 chrXptel1M 26976 A-AGAGAAAATTAGATCAATAATTGGGAGTTATTTTGCCTAACTATATGT 27024 v- v v - i vvi vi iiiv v vvi v i L1M5_orf2#LIN 1211 CTACAGACA-TTAAAAGGATAATAAGAGAATATTATGAACAACTTTATGC 1259 chrXptel1M 27025 TGATAAATCTGATGATCTAAGTGAAATGGAGAAATACTTAGAAAAATATA 27074 ii i ?i ii ii v v i v i i L1M5_orf2#LIN 1260 CAATAAATTTGANAACTTAGATGAAATGGACAAATTCCTTGAAAAACACA 1309 chrXptel1M 27075 GATTGTCCAGATTAATAGAAGAAGAAATAAATTACCT-AGT-GCCGT--- 27119 i? ii v i i i i?v i vv i - i - v --- L1M5_orf2#LIN 1310 ANTTACCAAAACTGACNCAAGAAGAAATAGAAAATCTGAATAGCCCTATA 1359 chrXptel1M 27120 TTTAGAAAAAGAAATTGAACAGGCTATTAATTAACAATTAATCAATTAAG 27169 i vv - ivv ---- v iivvi v iv L1M5_orf2#LIN 1360 TCTATTAAA-GAAATTGAATTTG----TAATTAAAAACCTTCCCACAAAG 1404 chrXptel1M 27170 AAAAAATCTCAAGGGCCAAATGGATTTGCATGTGAATTCTACCAAATATT 27219 --- v v i v ii vv i L1M5_orf2#LIN 1405 AAAA---CTCCAGGCCCAGATGGCTTCACTGGTGAATTCTACCAAACATT 1451 chrXptel1M 27220 TAAAGAACAATTAATTTCATTATTATGCAAATTATTTGGAAAAATAGGAA 27269 i v v vi v v ii i v ivii -- L1M5_orf2#LIN 1452 TAAGGAAGAAATAATACCAATCTTACACAAACTCTTCCAGAAAATAG--A 1499 chrXptel1M 27270 AAAAAAAAGAGTCCTATCAAATTCCTTTTATGACAC-AGATATATGGTGC 27318 i ii iiv vi v i v vi - ---i ?iiv L1M5_orf2#LIN 1500 AAAAGAGGGAACACTTCCCAACTCATTTTATGAGGCCAG---CATNACCC 1546 chrXptel1M 27319 TGATAGCTAAACCAGGTAGGGTCAAAACATAGAAAGAAAATAATAGACCA 27368 v v ? ii ii v vv vii v i L1M5_orf2#LIN 1547 TGATACCAAAACCNGACAAAGACATTACAAGAAAAGAAAATTACAGACCA 1596 chrXptel1M 27369 ATTTCCCTAATTAATATTGATACAAAAATCTTAAAAAAAATATTAGCAAA 27418 v v v i v i i ? v L1M5_orf2#LIN 1597 ATATCCCTCATGAACATAGATGCAAAAATCCTNAACAAAATATTAGCAAA 1646 chrXptel1M 27419 GAGATTACAGCAAGTCAT----------CTCCATGATGACCAAGTAGGAT 27458 vv v v vvi ----------v v v i i L1M5_orf2#LIN 1647 TCGAATCCAGCAATATATAAAAAGGATAATACATCATGACCAAGTGGGGT 1696 chrXptel1M 27459 TTATAACAGGCATGCTGGGCTGGCTCAGTATTAGGAAAACAATTAGCATA 27508 vv v vi i i i ii v i v i iii L1M5_orf2#LIN 1697 TTATCCCAGGAATGCAAGGTTGGTTTAACATTCGAAAATCAATCAATGTA 1746 chrXptel1M 27509 ATGGACTATATCAATAACAAAACTAACAAACATCATATGATTATATCAGC 27558 vv i i i iv v vvi v v i v ii L1M5_orf2#LIN 1747 ATTCACCATATTAACAGAATAAAGGAGAAAAATCATATGATCATCTCAAT 1796 chrXptel1M 27559 AGATGCAGAAAAAAAAATTGACAAAATCCAGTACCTATTTTTGA 27602 iv v i ii i iv L1M5_orf2#LIN 1797 AGATGCAGAAAAAGCATTTGACAAAATTCAACACCCATTCATGA 1840 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.67 CpG sites = 125, Kimura (unadjusted) = 39.90 Transitions / transversions = 1.26 (125/99) Gap_init rate = 0.05 (37 / 771), avg. gap size = 1.35 (50 / 37) 511 20.70 0.00 8.93 chrXptel1M 27627 27748 (972252) C MIRc#SINE/MIR (153) 115 4 m_b325s601i0 13656 chrXptel1M 27627 GGGGTTAAGTGACTTGCCCAGGGTCACACAACTAGGAAGTGTTAACTGTC 27676 i i i v vi ------ C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCA------ 72 chrXptel1M 27677 CGAGGCCAGATTTGAACTGAGGTCCTCCTAACTTCAGGGCTGGTGCTCTA 27726 - v vi i i iv i i i i v ii v C MIRc#SINE/MIR 71 -GAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTT 23 chrXptel1M 27727 TCCACTGTACCACCTAGCTGCC 27748 i ---i C MIRc#SINE/MIR 22 TCCACTGCACCAC---ACTGCC 4 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 23.52 CpG sites = 16, Kimura (unadjusted) = 24.74 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.08 (10 / 121), avg. gap size = 1.00 (10 / 10) 1199 32.34 2.80 2.03 chrXptel1M 27750 28677 (971323) L1M5_orf2#LINE/L1 1823 2757 (537) m_b325s551i6 13655 chrXptel1M 27750 TCCAGTACCTATT-ATTATAATAAGCACCAGAGAATATGGGAATAAATGG 27798 i ii i - v v vivi vi i- i i v L1M5_orf2#LIN 1823 TTCAACACCCATTCATGATAAAAACTCTCAGCAAAC-TAGGAATAGAAGG 1871 chrXptel1M 27799 AGTTTTCCTTAACATGACCAGTAGCATCTATTTAAAACAT-CAGCAAGTA 27847 iivi i v iv ivi ivv v - ? ii L1M5_orf2#LIN 1872 GAACTTCCTCAACCTGATAAAGGGCATCTACGAAAAACCTACAGCNAACA 1921 chrXptel1M 27848 TCATATGTAATAAGGGCAAACTAGAACCATTCCCCAATAACATCAGGGGT 27897 iv iiv iv ? ii ?v v v- v i iii L1M5_orf2#LIN 1922 TCATACTTAATGGTGAAANACTGAANGCTTTCCCCC-TAAGATCGGGAAC 1970 chrXptel1M 27898 GAAACAAGATTGCTCACTATCACCATTACTATTCAATATTTCGTTAGAGA 27947 i i iv ii i ? i v i viii i i L1M5_orf2#LIN 1971 AAGACAAGGATGTCCGCTNTCACCACTTCTATTCAACATTGTACTGGAGG 2020 chrXptel1M 27948 TGTTAGCTTTAGCAATAATAGAGGAAAATTTGCTTAAAGGAATTAGGGTA 27997 vi ivvv viv i vvviv v v v i i v L1M5_orf2#LIN 2021 TCCTAGCCAGTGCAATAAGGCAAGAAAAAGAAATAAAAGGCATAAAGATT 2070 chrXptel1M 27998 AGTAATGAGAAAACCAAATTATTACTCTTTGCAGATGATATGATGGTATA 28047 i v v ii iv i i i?i v i i v ? L1M5_orf2#LIN 2071 GGAAAGGAAGAAATAAAACTGTCNTTATTCGCAGATGACATGATTGTNTA 2120 chrXptel1M 28048 CTTAGAGAACCCTAGAGAATCAACTAAAAAAATACTAGAAAAAATTCACA 28097 v i i ? i v v ? v vv vviii L1M5_orf2#LIN 2121 CGTAGAAAATCCNAAAGAATCTACAAANAAACTACTAGAACTAATAAGTG 2170 chrXptel1M 28098 ACTTTAGCAAAGTGGCAGGATACAAAATAAATCCACATTAATCATTAGCA 28147 v i v ? ii v vi vv v v i L1M5_orf2#LIN 2171 AATTTAGCAAGGTCGCNGGATACAAGGTCAATATACAAAAATCAATTGTA 2220 chrXptel1M 28148 TTTTTACATATTACCAACAAAGTCTAGCAGTAAGC---ACCCAAAAAAAA 28194 i i i v -- v vii v ii--- iii? v L1M5_orf2#LIN 2221 TTTCTATATACTAGCAACAAA--CAATTGGAAAATGAAATTTNAAAAACA 2268 chrXptel1M 28195 ATACCATTTAAAATAACCATAGGTAATATAAAATATTTGGGAGTCTACAT 28244 v i vvi iiv i ? i i i vv iv L1M5_orf2#LIN 2269 ATACCATTTACAATAGCATCAAAAAACATNAAATACTTAGGAATAAATCT 2318 chrXptel1M 28245 TCCAAAGCAT-TGTCAGGAACTATA---TGAACACAATTACAAAACACTT 28290 vv i? - - i v ? --- --- i i v L1M5_orf2#LIN 2319 AACAAAANATGTG-CAAGACCTNTACACTGAA---AACTACAAAACATTG 2364 chrXptel1M 28291 TCCACACAAATAAAGTCAGATCTAATCAAGTGGAAAAA-ATATCAAGTGC 28339 iiv v v v ivv i vi i i i - i -- i L1M5_orf2#LIN 2365 CTGAGAGAAATTAAAGAAGACCTAAATAAATGGAGAGATATACCA--TGT 2412 chrXptel1M 28340 TCATGGGTCATCTGAGTGAATATAATAAAGATGATAATACAATCTCAATT 28389 i iivvv v v vi ? vi v vvi iv L1M5_orf2#LIN 2413 TCATGGATTGGAAGACTCAATATTGTNAAGATGTCAATTCTCCCCAAATT 2462 chrXptel1M 28390 AATCTACTCATTCAGTGGCATAACAATCAAATTCCCAAGAAATTATTTCA 28439 i ivv i vv vv v iv ii v ii L1M5_orf2#LIN 2463 GATCTATAGATTCAATGCAATCCCAATCAAAATCCCAGCAGGTTTTTTTG 2512 chrXptel1M 28440 CAGAGCTAGAAAAAA-AATAATAAACTTCATCTGGAAGAACAAAAGTTTA 28488 i iv v v iv-i vv v i v ivi i vii? L1M5_orf2#LIN 2513 TAGAAATTGACAAGCTGATTCTAAAATTTATATGGAAATGCAAAGGACCN 2562 chrXptel1M 28489 AGAAT-TTTAAGGGAATT-----AATGAAAAATGCAAA--TGGAAATAGC 28530 -vii iiv i----- v i -- -- i--ii L1M5_orf2#LIN 2563 AGAATAGCCAAAACAATCTTGAAAAAGAAGAA--CAAAGTTGGAG--GAC 2608 chrXptel1M 28531 CTACTTGTGCCTGACCT--AAACTATATTGTGAAGCAGCTGCCATCAAAA 28578 i vi- i ? i? -- i - i i vi v iv i L1M5_orf2#LIN 2609 TTACAC-TACCNGATNTCAAGACT-TATTATAAAGCTACAGTAATCAAGA 2656 chrXptel1M 28579 TCTTTTGGTACTGGC-TAAGAAACAGAGTAGTGGATCAGTGAAATAGGAT 28627 ivv v i - -i i vv i i i i i i L1M5_orf2#LIN 2657 CAGTGTGGTATTGGCGTAAG-GATAGACAAATAGATCAATGGAACAGAAT 2705 chrXptel1M 28628 AG-GATCACAGGACAAAACAAGCA-ATAACTATAGCAATTCG--TTTTGA 28673 - viv i vv i vvi - -- i ?v ? i -- L1M5_orf2#LIN 2706 AGAGAGTCCAGAAATAGACCCACACATA--TATGGNCANTTGATTTTTGA 2753 chrXptel1M 28674 CAAA 28677 L1M5_orf2#LIN 2754 CAAA 2757 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.95 CpG sites = 164, Kimura (unadjusted) = 44.78 Transitions / transversions = 1.26 (164/130) Gap_init rate = 0.04 (34 / 927), avg. gap size = 1.32 (45 / 34) 1108 31.91 4.79 3.21 chrXptel1M 27839 28819 (971181) L1M2_orf2#LINE/L1 1910 2905 (386) m_b325s551i7 13655 chrXptel1M 27839 CAGCAAGTATCATATGTAATAAGGGCAAACTAGAA-CCATTCCCCAATAA 27887 v ii ivv ii iv ii ii - v i -- L1M2_orf2#LIN 1910 CAGCTAACATCATACTGAATGGGGAAAAGTTGAAAGCCTTTCCTC--TAA 1957 chrXptel1M 27888 CATCAGGGGTGAAACAAGATTGCTCACTATCACCATTACTATTCAATATT 27937 v ? v iiii i iv i v i v i v L1M2_orf2#LIN 1958 GANCTGGAACAAGACAAGGATGCCCACTTTCACCACTTCTATTCAACATA 2007 chrXptel1M 27938 TCGTTAGAGATGTTAGCTTTAGCAAT-----AATAGAGGAAAATTTGCTT 27982 viii i ii vi ivv ----- v iii v----- L1M2_orf2#LIN 2008 GTACTGGAAGTCCTAGCCAGAGCAATTAGGCAAGAGAAAGAAATA----- 2052 chrXptel1M 27983 AAAGGAATTAGGGTAAGTAATGAGAAAACCAAATTATTACTCTTTGCAGA 28032 v iviii vi v v i ii i iv v L1M2_orf2#LIN 2053 AAAGGCATCCAAATTGGAAAGGAGGAAGTCAAATTGTCCCTGTTTGCAGA 2102 chrXptel1M 28033 TGATATGATGGTATACTTAGAGAACCCTAGAGAATCAACTAAAAAAATAC 28082 i vv i? i ? i v v i v ?i L1M2_orf2#LIN 2103 TGACATGATCTTATATNTAGAAAANCCTAAAGACTCCACCAAAAAACTNT 2152 chrXptel1M 28083 TAGAAAAAATTCACAACTTTAGCAAAGTGGCAGGATACAAAATAAATCCA 28132 vvi vv i v i i v v ivi L1M2_orf2#LIN 2153 TAGAACTGATAAACGAATTCAGTAAAGTTGCAGGATACAAAATCAACATA 2202 chrXptel1M 28133 CATTAATCATTAGCATTTTTACATATTACCAACAAAGTCTAGC--AGTAA 28180 vv v i i iiii v i -- v -- iv L1M2_orf2#LIN 2203 CAAAAATCAGTAGCATTTCTATACGCCAACAACGAA--CTATCTGAAAAA 2250 chrXptel1M 28181 GCACCCAAAAAAA-AATACCATTTAAAATAACCATAGGTAATATAAAATA 28229 v vi i i- v v i i i iiv v L1M2_orf2#LIN 2251 GAAATCAAGAAAGCAATCCCATTTACAATAGCTACAAAAAAAATAAAATA 2300 chrXptel1M 28230 TTTGGGAGTCTACATT---CCAAAGCATTGTCAGGAACTATATGAACACA 28276 ii i i-- v --- i viv -v i v v ii ?v v L1M2_orf2#LIN 2301 CCTAGGAA--TAAATTTAACCAAGGAGGTG-AAAGATCTCTACAANGAAA 2347 chrXptel1M 28277 ATTACAAAACACTTTCCACACAAATAAAGTCAGATCTAATCAAGTGGAAA 28326 i i vviv v v vi ivvi ivi v? i - L1M2_orf2#LIN 2348 ACTATAAAACACTGATGAAAGAAATTGAAGAGGACACAAANAAATGG-AA 2396 chrXptel1M 28327 AAATATCAAGTGCTCATGGGTCATCTGAGTGAATATAATAAAGATGATAA 28376 i vvi i iivvv i v vi v i ?iv L1M2_orf2#LIN 2397 AGATATCCCATGCTCATGGATTGGAAGAATTAATATTGTTAAAATGNCCA 2446 chrXptel1M 28377 TACAATCTCAATTAATCTACTCATTCAGTGGCATAACAATCAAATTCCCA 28426 v i iv vii vv i vv vv v v v L1M2_orf2#LIN 2447 TACTACCCAAAGCGATCTACAGATTCAATGCAATCCCTATCAAAATACCA 2496 chrXptel1M 28427 A-GAAATTATTTCACAGAGCTAGAAAAAA-AATAATAAACTTCATCTGGA 28474 - v -i iv - vv v i v L1M2_orf2#LIN 2497 ATGACATT-CTTCACAGAAATAGAAAAAANAATCCTAAAATTCGTATGGA 2545 chrXptel1M 28475 AGAACAAAAGTTTAAGAAT-TTTAAGGGAATT---AATGAAAAATGCAAA 28520 vv viivv -vii i v i--- iii ivi L1M2_orf2#LIN 2546 ACCACAAAAGACCCCGAATAGCCAAAGCAATCCTGAGCAAAAAGAACAAA 2595 chrXptel1M 28521 --TGGAAATAGCCTACTTGTGCCTGACCT-AAACTATATTGTGAAGCAGC 28567 -- iii v vi --- i i - v i iii vii L1M2_orf2#LIN 2596 GCTGGAGGCATCACAC---TACCTGACTTCAAAATATACTACAAAGCTAT 2642 chrXptel1M 28568 TGCCATCAAAATCTTTTGGTACTGGCTAAGAAACAGAGTAGTGGATCAGT 28617 v iv i ivviv vv i vvvi i i i L1M2_orf2#LIN 2643 AGTAACCAAAACAGCATGGTACTGGCATAAAAACAGACACATAGACCAAT 2692 chrXptel1M 28618 GAAATAGGATAG-GATCACAGGACAAAA--CAAGCAATAACTATAG-CAA 28663 i i i - v v i vv -- v v --- i - L1M2_orf2#LIN 2693 GGAACAGAATAGAGAACCCAGAAATAAATCCACGCATT---TACAGCCAA 2739 chrXptel1M 28664 TTCGTTTT-GACAAA--C-CCAA------ATTTTGGCATAAAAAC--TCA 28701 i vi - -- - ------ iv? viv ii -- v L1M2_orf2#LIN 2740 CTGATTTTCGACAAAGGCGCCAAGAACATACANTGGGGAAAGGACAGTCT 2789 chrXptel1M 28702 CT--AACAAAAATTGTTGGGAAAATTAG-------TATGGCAGAAACTAG 28742 -- i viv i i i ------- - ivvv L1M2_orf2#LIN 2790 CTTCAATAAATGGTGCTGGGAAAACTGGATATCCATAT-GCAGAAGAATG 2838 chrXptel1M 28743 GCACT-GACCCACACTTAACACACACTTAACACCATATACCAAGATAAGG 28791 iv - vi ii -------- --- v i v iv L1M2_orf2#LIN 2839 AAACTAGACCCCTATCT--------CT---CACCATATACAAAAATCAAC 2877 chrXptel1M 28792 TCAAAATGGGTTTATGATTTAGACATAA 28819 i v v i i ii L1M2_orf2#LIN 2878 TCAAAATGGATTAAAGACTTAAATGTAA 2905 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 42.06 CpG sites = 164, Kimura (unadjusted) = 43.04 Transitions / transversions = 1.18 (164/139) Gap_init rate = 0.06 (54 / 980), avg. gap size = 1.46 (79 / 54) 267 32.80 0.00 4.17 chrXptel1M 28858 29032 (970968) L1ME4c_3end#LINE/L1 414 581 (249) m_b325s551i8 13655 chrXptel1M 28858 TTAAAGGAGGGAAAGGAACCCACATGTGCAAAATATGTTAGCGGCAGCAC 28907 i i i -- v i i ii i i- viiv i- L1ME4c_3end#L 414 TCAAAAGAAGGAAA--AAGCTATATGCACGAAG-ATGTTCATTGCAGCG- 459 chrXptel1M 28908 TTTTTTTTTGTAGTGTAAAGAAACTGGAAACTGAGTGGATGTCTATCAAT 28957 v v vi i --- i i vivv ii i v L1ME4c_3end#L 460 TTATTTATAATAGCG---AAAAATTGGAAACAACCTAAATGTCCAACAAT 506 chrXptel1M 28958 TGGAAAATGGCTGAATAAGTTATGGTATATGAATGTTATAGGATATTATT 29007 v ii i i i i i v? iviv i i v L1ME4c_3end#L 507 AGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATATTATG 556 chrXptel1M 29008 GTTCTATAAGAAATGATGAGCATGA 29032 vvv i v i i vi L1ME4c_3end#L 557 CAGCCATTAAAAATGATAATTATGA 581 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.09 CpG sites = 35, Kimura (unadjusted) = 45.55 Transitions / transversions = 1.75 (35/20) Gap_init rate = 0.04 (7 / 174), avg. gap size = 1.00 (7 / 7) 325 28.74 0.00 4.10 chrXptel1M 28880 29006 (970994) L1ME3G_3end#LINE/L1 427 548 (376) m_b325s551i9 13655 chrXptel1M 28880 CATGTGCAAAATATGTTAGCGGCAGCACTTTTTTTTTGTAGTGTAAAGAA 28929 i ii- viiv ---- v i ivvi i L1ME3G_3end#L 427 CATGTACAAGG-ATGTTCATTGCAGCA----TTGTTTGTAATAGCGAAAA 471 chrXptel1M 28930 ACTGGAAACTGAGTGGATGTCTATCAATTGGAAAATGGCTGAATAAGTTA 28979 i vivv ii i v ii i i i L1ME3G_3end#L 472 ATTGGAAACAACCTAAATGTCCATCAATAGGGGAATGGTTAAATAAATTA 521 chrXptel1M 28980 TGGTATATGAATGTTATAGGATATTAT 29006 vv ii i i i L1ME3G_3end#L 522 TGGTATATCCATACTATGGAATACTAT 548 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.61 CpG sites = 24, Kimura (unadjusted) = 38.02 Transitions / transversions = 2.18 (24/11) Gap_init rate = 0.04 (5 / 126), avg. gap size = 1.00 (5 / 5) 215 17.65 0.00 0.00 chrXptel1M 29522 29555 (970445) C L2a_3end#LINE/L2 (17) 500 467 m_b325s601i1 13657 chrXptel1M 29522 ATATTTATTAAGTACCTATTCTGTGTCAGGCACT 29555 i ii i v i C L2a_3end#LINE 500 ATATTTATTGAGCGCCTACTATGTGCCAGGCACT 467 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 16.89 CpG sites = 5, Kimura (unadjusted) = 21.06 Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 21 26.90 4.95 1.92 chrXptel1M 29558 29658 (970342) (TATT)n#Simple_repeat 1 104 (0) m_b325s252i19 13658 chrXptel1M 29558 TATTT-TTT-TTTCTTTGTTTCTTTGTTTAGCAATTTATTTTTTTATTTT 29605 - - v i v i viv v - (TATT)n#Simpl 1 TATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTA-TTT 49 chrXptel1M 29606 CCAAAAATATTTCTTT-TTT-TTTCTTT-TTTGTTTAATAATTATAACTT 29652 vivv vv v - - v - i v v - vi v (TATT)n#Simpl 50 ATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATT-TATTTA 98 chrXptel1M 29653 TTTATT 29658 (TATT)n#Simpl 99 TTTATT 104 Matrix = Unknown Transitions / transversions = 0.38 (6/16) Gap_init rate = 0.07 (7 / 100), avg. gap size = 1.00 (7 / 7) 12 4.75 0.00 8.33 chrXptel1M 29718 29743 (970257) (CCCT)n#Simple_repeat 1 24 (0) m_b325s252i20 13659 chrXptel1M 29718 CCCTCCCTCCCTCCACCCCCTTCCCT 29743 - i - (CCCT)n#Simpl 1 CCCTCCCTCCCTCC-CTCCC-TCCCT 24 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.08 (2 / 25), avg. gap size = 1.00 (2 / 2) 1519 27.87 3.55 2.86 chrXptel1M 30049 30639 (969361) C L1ME5_3end#LINE/L1 (291) 650 56 m_b325s551i10 13660 chrXptel1M 30049 ATCTC---CTGGTTCT-ACTCATTTCACTCAGCATCA-GTTCATGTAAG- 30092 --- v - iv ii - -- v - C L1ME5_3end#LI 650 ATCTCATTCTGTTTCTTACTTTTTTCACTCAGCACTATGTT--TTTAAGA 603 chrXptel1M 30093 TCCCTCCAAGCCTCTCTGTATTCATCCTGCTGGTCATTTCTTACAGAACA 30142 v v iiv v i v iv iiv iii v v vvvv C L1ME5_3end#LI 602 TCCATCCATGTTGCTATGTGTACATCTAGTCCGTTGCTTCTAACTGCTGC 553 chrXptel1M 30143 ATAATATTCCATAACATTCATATACCACAATTTACCCAACCATTCTCCAA 30192 i i iiii v vi v i v i v C L1ME5_3end#LI 552 ATAGTACTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCA 503 chrXptel1M 30193 TTGATGGGCATCTCATTT---TCCAGCTTCTAGCCACTATAAACAGGGCT 30239 v i i iviv --- i i iv i i iv C L1ME5_3end#LI 502 GTGATGGACACCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCT 453 chrXptel1M 30240 GACACAAACATTTTGGCACATACAGGTCCCTTTC----CCTTCTTTAGTA 30285 vv ii ii ---- i v i v---- viv v v C L1ME5_3end#LI 452 GCAATGAACATCCT----CGTACATGTCCCCTTATGGACCTGTGTGAGAA 407 chrXptel1M 30286 TTTCTTTGGGGTATAAGCCCAGTAGTAACACTGCTGGATCAAAGGGTATG 30335 i vi v iiiv i i v C L1ME5_3end#LI 406 TTTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATG 357 chrXptel1M 30336 CACAGTTTGATAACTT--TTGGGGCATAATTCCAGAATGCTCTCCAGAAT 30383 ii vvi -- i --i ii --- v v v C L1ME5_3end#LI 356 CGTATACT--TAATTTGACTAAG---TACTGCCAGATTGCTCTCCAGAAT 312 chrXptel1M 30384 GGTTGAATTCGTTCACAACTCTACCAACAATGCATCAGTGACCCAGTTTT 30433 i v iiv ii vii i i i v v vi vi ? i C L1ME5_3end#LI 311 GGCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATNTC 262 chrXptel1M 30434 CCCGAATCCCCTCCAACATTTATCATTA---ATTTTTCCTGTCACCTTAG 30480 iv i v i iv --- vi --- v ii v C L1ME5_3end#LI 261 CCCACATCCTCGCCAACACTTGGCATTATCCAGCTTTC---TAATTTTTG 215 chrXptel1M 30481 CCAATCTAACAGGTGTGTAGTGGTATCTCAAAGTTGTCTTAATTTGCATT 30530 i i iv i vv i C L1ME5_3end#LI 214 CCAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATT 165 chrXptel1M 30531 TCTCTGATCAATAGTGATTTGGAACACTCTTTCATATGAGTGGAAATAG- 30579 i v i v v i iiii vv v--- - C L1ME5_3end#LI 164 TCTCTGATTACTAATGAGTTTGAGCATCTCTTCATATGCTTGT---TAGC 118 chrXptel1M 30580 -TTTCAA-TTTCATCATCTGAAAATTGTCTGTTCATATCCTTTGACCATT 30627 - ii- v v v i v C L1ME5_3end#LI 117 CTTTCGGGTTTCCTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCCATT 68 chrXptel1M 30628 TATAAATTGGAG 30639 v vv i C L1ME5_3end#LI 67 TTTCTATTGGGG 56 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.46 CpG sites = 88, Kimura (unadjusted) = 35.59 Transitions / transversions = 1.22 (88/72) Gap_init rate = 0.05 (28 / 590), avg. gap size = 1.36 (38 / 28) 1546 27.90 1.85 1.29 chrXptel1M 30143 30683 (969317) C L1ME4c_3end#LINE/L1 (275) 555 12 m_b325s551i11 13660 chrXptel1M 30143 ATAATATTCCATAACATTCATATACCACAATTTACCCAACCATTCTCCAA 30192 vivi ?v i i ii i v C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chrXptel1M 30193 TTGATGGGCATCTCATTT---TCCAGCTTCTAGCCACTATAAACAGGGCT 30239 v i i viv --- ii i v i i i iv C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCT 456 chrXptel1M 30240 GACACAAACATTTTGGCACATACAGGTCCCTTTCCCTTCTTTAG---TAT 30286 vv ii i v ii i --- i i v --- C L1ME4c_3end#L 455 GCAATGAACATCTTCGTGCATATAG---CTTTTTCCTTCTTTTGAATTAT 409 chrXptel1M 30287 TTCTTTGGGGTATAAGCCCAGTAGTAACACTGCTGGATCAAAGGGTATGC 30336 i i i v vv v iiv i i i v C L1ME4c_3end#L 408 TTCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGA 359 chrXptel1M 30337 ACAGTTTGATAACTTTTGGGGCATAATTCCAGAATGCTCTCCAGAATGGT 30386 v v ii i ivi i v v i v i i v C L1ME4c_3end#L 358 ACATTTTTATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGT 309 chrXptel1M 30387 TGAATTCGTTCACAACTCTACCAACAATGCATCAGTGACCCAGTTTTCCC 30436 v iivi i ?iv i i i v ? vv iv C L1ME4c_3end#L 308 TGTACCAATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCACC 259 chrXptel1M 30437 GAATCCCCTCCAACATT---TATCATTAATTTTTCCTGTCACCTTAGCCA 30483 v ? i v i --- i i iv---v ii v i C L1ME4c_3end#L 258 GCANCCTCGCCAGCATTGGGTATTATCAATTTTTTA---AATTTTTGCTA 212 chrXptel1M 30484 ATCTAACAGGTGTGTAGTGGTATCTCAAAGTTGTCTTAATTTGCATTTCT 30533 i i i iv i vv ii C L1ME4c_3end#L 211 ATTTAATAGGCGTAAAATGGTATCTCATTGTTGCTTTAATTTGCATTTCT 162 chrXptel1M 30534 CTGATCAATAGTGATTTGGAACACTCTTTCATATGAGTGGAAATAGTTTC 30583 i i v i vv v i i i i vv vvv ivi? v C L1ME4c_3end#L 161 TTGATTACTAGCGAGGTTGAACATTTTTCCATGTGTTTGTTTACTANTTG 112 chrXptel1M 30584 AATTTCATCATCTGAAAATTGTCTGTTCATATCCTTTGACCATTTATAAA 30633 v v v ? vi i v vv C L1ME4c_3end#L 111 TATTTCCTCTTNTGTGAATTGTCTGTTCATGTCCTTTGCCCATTTATCTA 62 chrXptel1M 30634 TTGGAG-ATTGGTTTGATTTCTCATAAATTAGAGTCAATTCTCTATGTAT 30682 i -v i ? v- i v v i v ii i i ? C L1ME4c_3end#L 61 TTGGGGTCTTGATNTT-TTTCTTATCAATTTGAATGAGCTCTTTATATAN 13 chrXptel1M 30683 T 30683 C L1ME4c_3end#L 12 T 12 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.18 CpG sites = 85, Kimura (unadjusted) = 36.40 Transitions / transversions = 1.33 (85/64) Gap_init rate = 0.02 (11 / 540), avg. gap size = 1.55 (17 / 11) 689 30.13 5.03 4.62 chrXptel1M 30545 31299 (968701) C L1M5_orf2#LINE/L1 (0) 3294 2537 m_b325s551i12 13660 chrXptel1M 30545 TGATTTGGAACACTCTTTCATATG---AGTGGAAATAGTTTCAATTTCAT 30591 ?v v i iii i --- v vv --- v? v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCAT---TTGNATATCTT 3248 chrXptel1M 30592 CATCTGAAAATTGTCTGTTCATATCCTTTGACCATTTATAAATTGGA--G 30639 v i vi v vi i v v ?v i-- C L1M5_orf2#LIN 3247 CTTTTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTG 3198 chrXptel1M 30640 ATTGGTTTGATTTCTCAT-AAATTAGAGTCAATTCTCTATGTATTTTGGA 30688 v vi -- ? i -i ? iv v- i i i i C L1M5_orf2#LIN 3197 TTTGTCTT--TTTNTTATTGANTTGTAGG-AGTTCTTTATATATTCTGGA 3151 chrXptel1M 30689 AATGAGGCCTTTATCAGAACCTTTAACTGTG----AAAT-TTTTTTCCCA 30733 v i v i ----- vv ?---- - i C L1M5_orf2#LIN 3150 TACGAGTCCTTTGTCAGA-----TATATGTNTTGCAAATATTTTCTCCCA 3106 chrXptel1M 30734 GTTTGTTGCTTCCCTTCTAATATTGTTTGCATTAGTTTTGTTTGTACAGA 30783 ? i v v i v v v vi iv ivi vvv? vi C L1M5_orf2#LIN 3105 NTCTGTGGCTTGCCTTTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGA 3056 chrXptel1M 30784 GGCTTTTAATTT-AATATAATCAAA-------ATTTTCTATTTTGGGATC 30825 i i -i i? i v ------- i v iv i - C L1M5_orf2#LIN 3055 AGTTTTTAATTTTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGGT- 3007 chrXptel1M 30826 AATAATGATCTCTAGTTCATCTTTGGTTACAAATTTCTTCCTCCTCCAAA 30875 -- ?i v i i ivv v v i--- v i i v v?i i C L1M5_orf2#LIN 3006 --TNGTGCTTTTTGTGTCCTGTTTA---AGAAATCTTTGCCTANCCCAAG 2962 chrXptel1M 30876 AGTCTGAGAGGTAAATTATCCTATATT--CCTCTAATTTATTTATAATCT 30923 - vvii i -- v i -- i ivvvv i i C L1M5_orf2#LIN 2961 -GTCACGAAGATA--TTCTCCTATGTTTTCTTCTAGAAGTTTTATAGTTT 2915 chrXptel1M 30924 TGTTCTTTATGCCTAAATCACGGACCCATTTTAATCTTATCTTGGTGTAT 30973 i?ii iiii ii vvv i i ?i vi v i v C L1M5_orf2#LIN 2914 TANCTTTTACATTTAGGTCTATGATCCATCTNGAATTAATTTTTGTGTAT 2865 chrXptel1M 30974 GGTGTTAAGTGTGGGTCCATGCCTAATTTCTGCCATACAAATTTCCAGTT 31023 v i iv v v?iii v i v iii v i C L1M5_orf2#LIN 2864 GGTGTGAGGTAGGGGTCGAGNTTCATTTTTTTCCATATGGATATCCAATT 2815 chrXptel1M 31024 TTCCCAGCAGTTTTTGTCAAATAATGAATTCTTATCCCA--AAA----GT 31067 v i viv ii v ivvv i vi --i ----? C L1M5_orf2#LIN 2814 GTTCCAGCACCATTTGTTGAAAAGACTATCCTTTCCCCACTGAATTGCNT 2765 chrXptel1M 31068 TAGTATCTTTGGTTTGGTCAAACACTAGATCACTATAGCTGACTAT---T 31114 i i i ------ v ii i? v? i vv -- i --- C L1M5_orf2#LIN 2764 TGGCACCTTTG------TCAAAAATCAANTGNCCATATATG--TGTGGGT 2723 chrXptel1M 31115 TTGTCTTGTGAAC-----ATAACTTTTCCACTGATCAACTAATCTATTTC 31159 i i - v i ----- v- v i v i vi i- C L1M5_orf2#LIN 2722 CTAT-TTCTGGACTCTCTATT-CTGTTCCATTGATCTATTTGTCTATC-C 2676 chrXptel1M 31160 TTA-GCCAATACCAAATGGTTTTGGTGACTGCTGCTTTATAATATAGTTT 31208 - v iv i i v iv - i C L1M5_orf2#LIN 2675 TTACGCCAATACCACACTGTCTTGATTACTGTAGCTTTATAATA-AGTCT 2627 chrXptel1M 31209 T-AGATCAGGTACAACTAGACCACCTTCATTTGATTTTTTTTTTTCATTA 31257 - ? ? vviiv v v vv - - i i -vi C L1M5_orf2#LIN 2626 TGANATCNGGTAGTGTAAGTCCTCCAAC-TTTG-TTCTTCTTTTTCA-AG 2580 chrXptel1M 31258 ATTCCCTTGAG-ATTCTTGACCTTTTGTTCTTCCATATGAATT 31299 vii iv- ? ii i ivi i C L1M5_orf2#LIN 2579 ATTGTTTTGGCTATTCTNGGTCCTTTGCATTTCCATATAAATT 2537 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.17 CpG sites = 119, Kimura (unadjusted) = 40.91 Transitions / transversions = 1.21 (119/98) Gap_init rate = 0.07 (50 / 754), avg. gap size = 1.46 (73 / 50) 291 22.81 0.00 0.00 chrXptel1M 31424 31480 (968520) C L1ME5_3end#LINE/L1 (531) 410 354 m_b325s551i13 13661 chrXptel1M 31424 AAAGTTTCTTTGGAATATAAACCTAGTAGTGGTATTGCTGGATCAAAGGA 31473 i i i v i v i v i v i C L1ME5_3end#LI 410 AGAATTTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGG 361 chrXptel1M 31474 CATGCAT 31480 i i C L1ME5_3end#LI 360 TATGCGT 354 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 23.27 CpG sites = 9, Kimura (unadjusted) = 28.17 Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0) 498 34.21 3.52 5.69 chrXptel1M 31725 32065 (967935) L3#LINE/CR1 2793 3126 (973) m_b325s601i2 13662 chrXptel1M 31725 TCATTAAAAAGAGTGATTAATGCATACCTAGATAAAGAGACTGGGATCCC 31774 i v - i vi vii i v i ii v v v L3#LINE/CR1 2793 TTATTAAACAGA-TGGTTTGTGAGCACTTAGAAAAGGAAGCGGTGATCAC 2841 chrXptel1M 31775 ----AACTA-CATGACTTTATAAGGAACAGATT-TGCTGGATTAATCTCA 31818 ---- i i - iv i iv i ii i- iii i i L3#LINE/CR1 2842 TAGGAGCCAGCATGGGTTCACTAAGAACAAGTCATGCCAAACTAACCTCA 2891 chrXptel1M 31819 TTTCC-TTTTTAATAGGGTTACAAAACACATTGCTCAAAAGCAATGGAAA 31867 - i v i ---- v -- i v i- i L3#LINE/CR1 2892 TTTCCTTTTTTGATAGGGTTACTAGAC----TGGT--AGATCAG-GGGAA 2934 chrXptel1M 31868 TACTTTGGAAACTGTGGAAGTATTTTATTTGTATTTTTGGAAAGCAATTT 31917 i iv i v ?v --------- i v iv v i v v L3#LINE/CR1 2935 TGCCGTAGACANAGTG---------TATCTGGATTTCAGCAAGGCATTTG 2975 chrXptel1M 31918 ACAAATCATCATAAGTTATGTATGTAAACAAGATTGAGAAAGAAATGCTT 31967 viv vi v v viv ii v v viv - L3#LINE/CR1 2976 ACAAAGTCTCTCATGATATCCTTGTGGACAAGATGGAGAAATATGGGC-T 3024 chrXptel1M 31968 AGATAATGGCCCAATAAAGGGGAATGGATACTATTTGAA-AAGTAGGCTC 32016 i i i iv i v i v v v vvi iv -i v vi i L3#LINE/CR1 3025 GGATGATAGTACAGTTAGGTGGATTCGTAGCTGGTTGAACGACTATACCC 3074 chrXptel1M 32017 --CTGGTAGTTATTAGTAGGCCATTGTC--TCTGAGGAGAAAATCTGTAG 32062 --vv iv v i i ii iv --i - ii i ii v L3#LINE/CR1 3075 AAAAGGTGTTGATTAATGGATCGATGTCAACCTG-GAGGGAGGTCTCTAG 3123 chrXptel1M 32063 TGG 32065 L3#LINE/CR1 3124 TGG 3126 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 45.58 CpG sites = 63, Kimura (unadjusted) = 47.37 Transitions / transversions = 1.34 (63/47) Gap_init rate = 0.08 (26 / 340), avg. gap size = 1.19 (31 / 26) 397 33.32 4.35 2.63 chrXptel1M 32087 32385 (967615) Plat_L3#LINE/CR1 2633 2936 (637) m_b325s551i14 13663 chrXptel1M 32087 ATTGAATGTCTTTATCGGTGACATAGATAAAG-AATTGATAGCACAATTG 32135 v i i v i ii - i v iiv ii Plat_L3#LINE/ 2633 ATTCAATATCTTTATCGATGACCTGGACGAAGGAATCGAGAGCATGCTCA 2682 chrXptel1M 32136 TCAAATTTACAGATGACATAAAGCTAAGAGGGATACCTAACAG---GGAA 32182 i i iv ii ii v i vv v--- Plat_L3#LINE/ 2683 TCAAATTTGCAGATGATACTAAATTGGGCGGGGTTGCTAACACTTTGGAA 2732 chrXptel1M 32183 TGGCAGAGTTAGGAGCCAGAGAATTGGTGATAGATTAGAGCATTGAAACA 32232 - i iiv ii vi i vivivv? i i i -----i ii Plat_L3#LINE/ 2733 -GACAGGAATAAAATTCAAAGTGACCTNGACAAATTGGA-----AAAATG 2776 chrXptel1M 32233 AATCTC---AAATTG--TGAAATTCAATGGAAAAAAATGTAAAGTTTTGT 32277 ivi ?--- iv -- i ii v i i i vv i Plat_L3#LINE/ 2777 GTCCTNCAAAAACAGGATGAAATTCAATAGGGACAAGTGCAAGGTAGTGC 2826 chrXptel1M 32278 ACTAGAGTATGAGAAATCAACTCCACAGGTACGAGA--AGGAAAGTGTGA 32325 vii v i i iv iv ii ii --i vv i Plat_L3#LINE/ 2827 ACTTAGGGACGAAAAACAAACCGCACAAATACAGGATGGGGAAAGACTGG 2876 chrXptel1M 32326 TGAGGCCACAA-TCTGTCTGAAAAATATTTGGCGGTTTCAGT-GACTAAT 32373 iv - - viiv v v ii v ivi - i- ? Plat_L3#LINE/ 2877 CTAGG-CACAAGTACAGCAGAAAAAGACCTGGGGGTCATAGTCGACC-AN 2924 chrXptel1M 32374 AAGCTAAATATG 32385 i Plat_L3#LINE/ 2925 AAGCTGAATATG 2936 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 44.61 CpG sites = 64, Kimura (unadjusted) = 47.45 Transitions / transversions = 1.94 (64/33) Gap_init rate = 0.05 (15 / 298), avg. gap size = 1.40 (21 / 15) 215 22.03 10.00 3.53 chrXptel1M 32386 32465 (967535) L3#LINE/CR1 3470 3554 (545) m_b325s601i3 13662 chrXptel1M 32386 CAGTGTGATGTGGC------AAATTTAACTAATGAAACCTTAGGTTGGTT 32429 ------ --- i v i i vv L3#LINE/CR1 3470 CAGTGTGATGTGGCTGCCAAAAA---AGCTAATGCAATCTTAGGCTGCAT 3516 chrXptel1M 32430 TAAGAGAGGTATA--GTTGAGAGCAGCCAAGATGATGG 32465 v i -- iv ? ivvi i i i L3#LINE/CR1 3517 TAATAGAAGTATAGTGTCCAGANCAAGGGAGGTAATAG 3554 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 27.04 CpG sites = 10, Kimura (unadjusted) = 27.04 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.06 (5 / 79), avg. gap size = 2.20 (11 / 5) 233 31.01 3.81 4.81 chrXptel1M 33281 33385 (966615) L2d_3end#LINE/L2 146 249 (267) m_b325s601i4 13664 chrXptel1M 33281 TTCCCCCAGCATCTGG----TCCTTGCTGTATGCTTGGTGCCTTTAGTGA 33326 v -- ----i v iv - v i-- vi i viv L2d_3end#LINE 146 TTCCCCCCGC--CTGGAATGCCCTTCCCCT-TCCTC--TCTCTCTATCCA 190 chrXptel1M 33327 ATTCCTTCCCATCTTTTAAAGCTCAATTCAAATACTATCTTCTTTAGGAA 33376 v v i i i i ii i v i i i ii v L2d_3end#LINE 191 AATCCTACCCATCCTTCAAGGCCCAGCTCAAGTCCCACCTCCTCCACGAA 240 chrXptel1M 33377 ACCTTTCCT 33385 i i L2d_3end#LINE 241 GCCTTCCCT 249 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.88 CpG sites = 20, Kimura (unadjusted) = 41.88 Transitions / transversions = 1.82 (20/11) Gap_init rate = 0.06 (6 / 104), avg. gap size = 1.50 (9 / 6) 252 28.33 0.00 0.00 chrXptel1M 33326 33385 (966615) L2d2_3end#LINE/L2 190 249 (306) m_b325s601i5 13664 chrXptel1M 33326 AATTCCTTCCCATCTTTTAAAGCTCAATTCAAATACTATCTTCTTTAGGA 33375 v v i i i i ii ? i i i iiiv L2d2_3end#LIN 190 AAATCCTACCCATCCTTCAAGGCCCAGCTCAAATNCCACCTCCTCCGTGA 239 chrXptel1M 33376 AACCTTTCCT 33385 i i L2d2_3end#LIN 240 AGCCTTCCCT 249 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.50 CpG sites = 14, Kimura (unadjusted) = 39.95 Transitions / transversions = 4.67 (14/3) Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0) 249 23.59 10.20 4.85 chrXptel1M 33515 33612 (966388) C L2d2_3end#LINE/L2 (31) 524 422 m_b325s601i6 13665 chrXptel1M 33515 CTTTCTATGTAGTAGGCATGGTGCTAAGCACTACAG---ATACAAATCCA 33561 i v i ivv iv i i iii --- ---- C L2d2_3end#LIN 524 CCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGTGGGGGATACAAA---- 479 chrXptel1M 33562 GCAAGTAGAAGA----GTGCCTGACCTCAAGGAATTT--AGCCT-GATGG 33604 - v ---- v v ii -- ii - v C L2d2_3end#LIN 478 G-AAGTATAAGACATGGTCCCTGCCCTCAAGGAGCTTACAATCTAGTTGG 430 chrXptel1M 33605 GGAGATAA 33612 i C L2d2_3end#LIN 429 GGAGACAA 422 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 27.64 CpG sites = 14, Kimura (unadjusted) = 29.20 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.09 (9 / 97), avg. gap size = 1.67 (15 / 9) 15 22.82 1.75 5.45 chrXptel1M 35125 35181 (964819) (TCC)n#Simple_repeat 1 55 (0) m_b325s252i21 13666 chrXptel1M 35125 TCCTTCTCTCCCTCCT-GTCCTCCCTCATCCTCTCTATGTCTCCTCCTCC 35173 i ii -v - v - vivi (TCC)n#Simple 1 TCCTCCTCCTCCTCCTCCTCCT-CCTCCTCCTC-CTCCTCCTCCTCCTCC 48 chrXptel1M 35174 TGCCCCCT 35181 - i (TCC)n#Simple 49 T-CCTCCT 55 Matrix = Unknown Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.07 (4 / 56), avg. gap size = 1.00 (4 / 4) 206 17.60 11.27 3.95 chrXptel1M 35508 35578 (964422) C L3#LINE/CR1 (7) 4092 4017 m_b325s601i7 13667 chrXptel1M 35508 TCACAG--TCTCAGACTTGAAAGGGACTT---AAGCCACCT--TCCAGAT 35550 -- v i i --- i i i -- - i C L3#LINE/CR1 4092 TCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCA-AC 4044 chrXptel1M 35551 GCTCCC-TGAAATGTAGGTGATTCCTTCT 35578 - - vv i -i i C L3#LINE/CR1 4043 -CTCCCATCCAATGCAGG-AATCCCTTCT 4017 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 20.78 CpG sites = 9, Kimura (unadjusted) = 20.78 Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.10 (7 / 70), avg. gap size = 1.57 (11 / 7) 1199 28.54 3.73 1.28 chrXptel1M 36089 36624 (963376) C L1ME4c_3end#LINE/L1 (275) 555 7 m_b325s551i15 13668 chrXptel1M 36089 ATAATATTCCATTATTTTAATATGCCATAATTTAGTCAGCCATTCTCCAA 36138 iivv ?i i i v i i i v C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chrXptel1M 36139 CAGATGGGAATCTACTCATTTTCCAATTTTTC--CACCACAAAAAAAGCT 36186 iv v iv i vvivv --i ii i v v C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCT 456 chrXptel1M 36187 GCGACAAACGTTTTTGCACATGTGGATCTTTTCCCCTCTTT---GTGATT 36233 i ii i i i ii i i -- i i ---i v C L1ME4c_3end#L 455 GCAATGAACATCTTCGTGCATATAG--CTTTTTCCTTCTTTTGAATTATT 408 chrXptel1M 36234 TCTTTGCGATATAGACCTAGTAGTGGCGCCGCTGCATCAAAGAGTAT-AC 36282 i iv v vv i v viiii vi i - v C L1ME4c_3end#L 407 TCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAA 358 chrXptel1M 36283 TAGTTTTATAGCCCTTTGGACACAGTTCCAAATTACTCTCCAGAAAGGTT 36332 i v i i viv ii v v i i i i C L1ME4c_3end#L 357 CATTTTTATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTT 308 chrXptel1M 36333 GGATCATTTCACAACTCCACCAACAATGCATTAGTATCCCAGTTTTCCCA 36382 v i v i ?iv i i v ?i v iv i C L1ME4c_3end#L 307 GTACCAATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCACCG 258 chrXptel1M 36383 CATCC-CTCCAGCATT---TATCATC---TTTTTATGTCATCTTAGCCTA 36425 ? - v --- i --- ---v i v iv C L1ME4c_3end#L 257 CANCCTCGCCAGCATTGGGTATTATCAATTTTTTA---AATTTTTGCTAA 211 chrXptel1M 36426 TTTGAAAAATGTGAGGTGGTACTTCAGAGTTGTTTTAATTTGCATTTCTC 36475 i v iii i ii ii vv i i C L1ME4c_3end#L 210 TTTAATAGGCGTAAAATGGTATCTCATTGTTGCTTTAATTTGCATTTCTT 161 chrXptel1M 36476 TAATCAATAGTGACTTAGATCATTTTT--ATGACTATAGATGATAGCTTT 36523 i i v i vv v v -- vv v ivv iv ?i v C L1ME4c_3end#L 160 TGATTACTAGCGAGGTTGAACATTTTTCCATGTGTTTGTTTACTANTTGT 111 chrXptel1M 36524 AATTTCTTCATCTGAAAAT----TGTTCATATTCTTTCACCATTTATCAA 36569 - i v ? vi ---- i i vv v C L1ME4c_3end#L 110 -ATTTCCTCTTNTGTGAATTGTCTGTTCATGTCCTTTGCCCATTTATCTA 62 chrXptel1M 36570 TTAAGG-AATGACTTGCATTCTTATAAATTTGATTCACTTTTTTATATAT 36618 ii -vv i? vi- v v v vi i ? C L1ME4c_3end#L 61 TTGGGGTCTTGATNTTT-TTCTTATCAATTTGAATGAGCTCTTTATATAN 13 chrXptel1M 36619 TTTAGA 36624 v? C L1ME4c_3end#L 12 TANAGA 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.70 CpG sites = 86, Kimura (unadjusted) = 37.61 Transitions / transversions = 1.32 (86/65) Gap_init rate = 0.03 (16 / 535), avg. gap size = 1.69 (27 / 16) 240 30.99 6.67 3.90 chrXptel1M 36524 36748 (963252) C L1P3_orf2#LINE/L1 (39) 3255 3025 m_b325s551i16 13668 chrXptel1M 36524 AATTTCTTCATCTGAAAA----TTGTTCATATTCTTTCACCATTTATCAA 36569 v v i i ----i i ivv i v ii C L1P3_orf2#LIN 3255 AATGTCTTCTTTTGAGAAGTGTCTGTTCATATCCTTCGCCCACTTTTTGA 3206 chrXptel1M 36570 TTAAGGAATGACTTG---CATTCTTATAAATTTGATTCACTTTTTTATAT 36616 --- ii vii ---iv i v v v ii i v C L1P3_orf2#LIN 3205 T---GGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTAAGTTCCTTGTAG 3159 chrXptel1M 36617 ATTTTAGAAAATAGGCCTTTATCAAAAACACTGGCTGTAAAAATATTTTC 36666 i i v v v i i viv iv ii i v i C L1P3_orf2#LIN 3158 ATTCTGGATATTAGCCCTTTGTCAGATGGATAGATTGCAAAAATTTTCTC 3109 chrXptel1M 36667 CCAAATTTCTGC---TTCCCT-TCTAATCT--TGGCTGTGTGGGGTTTT- 36709 --- i--- v - ii v -- iiv v ---v - C L1P3_orf2#LIN 3108 CCA---TTCTGTAGGTTGCCTGTTCACTCTGATGATAGTTT---CTTTTG 3065 chrXptel1M 36710 -CATGCAAAAACATTTTAATTTAATGTAATCTAATTTGTC 36748 -ii i i vi i vvi iv C L1P3_orf2#LIN 3064 CTGTGCAGAAGCTCTTTAGTTTAATTAGATCCCATTTGTC 3025 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.57 CpG sites = 40, Kimura (unadjusted) = 41.39 Transitions / transversions = 1.48 (40/27) Gap_init rate = 0.07 (16 / 224), avg. gap size = 1.50 (24 / 16) 276 28.56 4.58 3.90 chrXptel1M 36525 36677 (963323) C L1PREC2_orf2#LINE/L1 (40) 3254 3101 m_b325s551i17 13668 chrXptel1M 36525 ATTTCTTCATCTGAAAA----TTGTTCATATTCTTTCACCATTTATCAAT 36570 v v i ----i i i vv i v i C L1PREC2_orf2# 3254 ATGTCTTCTTTTGAAAAGTGTCTGTTCATGTCCTTTGCCCACTTTTTAAT 3205 chrXptel1M 36571 TAAGGAATGACTTGCATT---CTTATAAATTTGATTCACTTTTTTATATA 36617 --- ii vii iv --- i v v v ii v C L1PREC2_orf2# 3204 ---GGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTAAGTTCCTTATAGA 3158 chrXptel1M 36618 TTTTAGAAAATAGGCCTTTATCAAAAACACTGGCTGTAAAAATATTTTCC 36667 vi i v v i i i vi iv vi i ? v i C L1PREC2_orf2# 3157 TGCTGGATATTAGACCTTTGTCAGATGCATAGTTTGCAAANATTTTCTCC 3108 chrXptel1M 36668 CAAATTTCTG 36677 --- C L1PREC2_orf2# 3107 CA---TTCTG 3101 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.16 CpG sites = 24, Kimura (unadjusted) = 37.16 Transitions / transversions = 1.33 (24/18) Gap_init rate = 0.05 (8 / 152), avg. gap size = 1.62 (13 / 8) 26 0.00 0.00 0.00 chrXptel1M 37629 37653 (962347) (GGGTTA)n#Simple_repeat 1 25 (0) c_b325s251i0 13669 chrXptel1M 37629 GGGTTAGGGTTAGGGTTAGGGTTAG 37653 (GGGTTA)n#Sim 1 GGGTTAGGGTTAGGGTTAGGGTTAG 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 329 40.11 4.97 1.53 chrXptel1M 37677 38119 (961881) MamRTE1#LINE/RTE-BovB 3138 3595 (217) m_b326s601i0 13670 chrXptel1M 37677 ATCAAATTGAAGGCCTAAAGAGCCGTTGTGTTGACCTCATTGTTGTACAC 37726 i i i i v vi v i ? v vvvi vi ? iv MamRTE1#LINE/ 3138 ACCAAACTAAAGGTCTACAGAGCGATAGCGNTGTCCAACCTTCTNTACGG 3187 chrXptel1M 37727 CTGTGAAATCTGGA--TAGTACAGCAACACCATGACAAGAAACTGAATCA 37774 i i -- ivi -- ii iiv vi vvv vi v MamRTE1#LINE/ 3188 CTGTGAGACCTGGACCTGCCACAG--ACGTCACATCCGGCTTCTTGAGCA 3235 chrXptel1M 37775 CTTCCATTTGAATTGCCTTAGGAAGATCTTGAAGATCACCTGGCAAGATA 37824 v i iv vi ii vv iivv vi v v i vv i MamRTE1#LINE/ 3236 GTTTCATCAGCGTCACCTACGAGCCATACTTAACATTAAATGGCAAGACA 3285 chrXptel1M 37825 AGGT-ACCAGAAACTGAGATCCTTTCTCG-AATTAAACTGCCAAGCATTC 37872 i i - iv - i vvvv - iii iv i - i v MamRTE1#LINE/ 3286 GGATCACCAACAAC-GAGGTCCTGGAACGCAGCCAGTCTACC-AGCACTG 3333 chrXptel1M 37873 AGACTGTA-TTGCAGAGAGCACAACTCTATTGGACTGACCTTATTGTTCA 37921 ii vi i- i v -v i i i iii i iv v i- ivv MamRTE1#LINE/ 3334 AAGCGATGCTCGCCG-CAACGCAGCTCCGCTGGGCTGGACATG-TGCGGA 3381 chrXptel1M 37922 -AATACCAAACATATGCTTGCCAAAAGGACTACTTCACGAATAACTCACA 37970 - ivvvi vvv vv i v ivii i vi ivv i v vi MamRTE1#LINE/ 3382 GAATGGATGACAGCAGGATACCCAAGCAGCTGCTGTACGGTGAGCTGAAG 3431 chrXptel1M 37971 CAGGGGAAGAGCTCACAGGGAGGTCAGAAAAAGTGATACGTGAACATTCT 38020 ii v vv vvi v i ii v viiv i i?iv MamRTE1#LINE/ 3432 TGGGGCAACCGCAAGCAGGGAGGGCAGAAGAAACGCTTTAAGGATNCACT 3481 chrXptel1M 38021 CAAGGTCCCTTTTAAGAACTTTAGAACAGACTGTGGGACA-TGGCAGACT 38069 v vv vvi i iv v vii v i - ivii- v i v MamRTE1#LINE/ 3482 GAAGCACAGCTTCAAACAATGCGGCATAG-CTGTGGACTGCTGGGAAACA 3530 chrXptel1M 38070 CTAGCA-CAG---GACCA-CCCAGCA-----CAATCAGAGA--AGGTG-- 38105 vi - --- - ii ----- ii --i -- MamRTE1#LINE/ 3531 ACAGCAGCAGACAGACCAGCCTGGCATGCAGCAATCAGGAACGGGGTGGC 3580 chrXptel1M 38106 -CTCTATGAGCAAAG 38119 - i v MamRTE1#LINE/ 3581 TCTTTTTGAGCAAAG 3595 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 54.37 CpG sites = 93, Kimura (unadjusted) = 60.14 Transitions / transversions = 1.13 (93/82) Gap_init rate = 0.05 (20 / 442), avg. gap size = 1.45 (29 / 20) 52 2.08 0.00 0.00 chrXptel1M 38925 38973 (961027) (GT)n#Simple_repeat 1 49 (0) c_b326s251i1 13671 chrXptel1M 38925 GTGTGTGTGTGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 38973 i (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 49 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 455 30.55 11.45 8.52 chrXptel1M 39808 40104 (959896) C L3#LINE/CR1 (15) 4084 3780 m_b326s601i1 13672 chrXptel1M 39808 TTTCTGTGTTGGGAGGGACCTCAGAAGTTACCTTGTCAG-----TGAGCA 39852 i v v i i i i i v vi-----iv v v C L3#LINE/CR1 4084 TCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCAACCTCCCATCC 4035 chrXptel1M 39853 AATGAA------CTCTCTGTACCAACCCTAACAAAT--------AGAATC 39888 v ------ ii ii v v i i -------- vv C L3#LINE/CR1 4034 AATGCAGGAATCCCTTCTACAACATCCCTGACAAGTGGTCATCCAGCCTC 3985 chrXptel1M 39889 TGCTTG--------CAATGATGGGCAGCTCACTACCCTCTTGAAGCAA-A 39929 -------- i i v - ?i i i-v C L3#LINE/CR1 3984 TGCTTGAACACCTCCAGTGACGGGGAGCTCACTA-CCTCNCGAGGCAGCC 3936 chrXptel1M 39930 CATTTCCGTTTTAAACAA--CTGATT-CCAGGAAGTTCTTTCTGACATTG 39976 i vv ii i-- -ii i i v i C L3#LINE/CR1 3935 CATTCCATTTTTGGACAGCTCTGATTGTTAGAAAGTTCTTCCTTATATTG 3886 chrXptel1M 39977 GTCCTAAATCATTTAGGATTAGGGTAACTCTAAATGCTTGCTCTGCTGCT 40026 iv v ------------------------ i - i ivi C L3#LINE/CR1 3885 AGCCGAAATC------------------------TGCCT-CCCTGTAACT 3861 chrXptel1M 40027 TTCCCTCAGGGATCTTTGTTCCAACCTTTGGGACTAAGCAAAATA---TT 40073 i v i vv i i v iiv i ii i vi i ---i C L3#LINE/CR1 3860 TCCACCCATTGGTCCTAGTTCTGCCCTCTGGAGCCACACAGAATAAGTCT 3811 chrXptel1M 40074 AAGTTGTTTTCCTTGTCTCTGCCCTTCAAAT 40104 viiv i vii vv v C L3#LINE/CR1 3810 AATCCCTCTTCCACATGACAGCCCTTCAAAT 3780 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.75 CpG sites = 51, Kimura (unadjusted) = 41.05 Transitions / transversions = 1.59 (51/32) Gap_init rate = 0.11 (34 / 296), avg. gap size = 1.76 (60 / 34) 348 36.46 6.67 2.97 chrXptel1M 40132 40326 (959674) C MIRc#SINE/MIR (46) 222 21 m_b326s601i2 13673 chrXptel1M 40132 AACATTTTCATATATTGCATTATCTTGCTGAGTCC-CAAAACAATCCCAT 40180 i ii i --- iii vii - v i ii C MIRc#SINE/MIR 222 AGCGCTTTCACATA---CATTATCTCATTTGATCCTCACAACAACCCTGT 176 chrXptel1M 40181 GGCATAAGTTTCTCAGGTCTTGTTATTTCCATGTCACA-AGGAAGAAACC 40229 ivi i ivvvv v i ii v i - v i i C MIRc#SINE/MIR 175 GAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACT 126 chrXptel1M 40230 AAAATTTAGAG--------CTACTTGCCTGTGCTTACCCAACGAATGAGT 40271 i iii i --------iv iiv v i v i v i i C MIRc#SINE/MIR 125 GAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGT 76 chrXptel1M 40272 AGAAGAGACAAGGGACAAATTT-CTTCTTTCTGGGTTCTCC--TTCCAAG 40318 i v v ii ivv i iii-vv i i--- --v iv C MIRc#SINE/MIR 75 GGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGA---CTCCAAGTCCAGT 29 chrXptel1M 40319 GCTCTCTC 40326 i C MIRc#SINE/MIR 28 GCTCTTTC 21 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 50.33 CpG sites = 46, Kimura (unadjusted) = 53.86 Transitions / transversions = 2.00 (46/23) Gap_init rate = 0.06 (11 / 194), avg. gap size = 1.73 (19 / 11) 637 30.76 7.45 2.04 chrXptel1M 41327 41930 (958070) L1ME4c_3end#LINE/L1 4 639 (191) m_b326s551i0 13674 chrXptel1M 41327 ATATCTCAAATTTTTAAGGACTTTTTATCAAATTTATAA---AAATGTGA 41373 ?v ? v v i vi iv - v --- ?i v L1ME4c_3end#L 4 ATATCTNTANTATATAAAGAGCTCAT-TCAAATTGATAAGAAAAANATCA 52 chrXptel1M 41374 AGTCATTCTTCTATTGATAAATGCACAAAGGATATGGACAGGTATATTTT 41423 -- ii -- v v vi i i ii - iv L1ME4c_3end#L 53 AG--ACCC--CAATAGATAAATGGGCAAAGGACATGAACAGACA-ATTCA 97 chrXptel1M 41424 CTGATGAAGAAATCAAAACAATTAAGC---CACAT--AAAAATGTTCTAA 41468 v? v i - v ?v v i --- -- v v L1ME4c_3end#L 98 CANAAGAGGAAAT-ACAANTAGTAAACAAACACATGGAAAAATGTTCAAC 146 chrXptel1M 41469 ATAACTATTGATTAGAAAAATGCAAATTAAA------ATGA--------- 41503 v vi v i i i i ------ --------- L1ME4c_3end#L 147 CTCGCTAGTAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATT 196 chrXptel1M 41504 -----CCTATCAGATTGACCAAAATTATAAAAGGGGAAAGTGACAAATGC 41548 ----- i i ii v vv ivv v i iv v L1ME4c_3end#L 197 TTACGCCTATTAAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGC 246 chrXptel1M 41549 -------AATGTGGAAAAATTGGGACCTTAATTTATTGTTGGTGGATCTG 41591 -------i? i vi i v ?i v vi i vv? L1ME4c_3end#L 247 TGGCGAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTG 296 chrXptel1M 41592 TGAGCTGATCCAACCATTTTGGAGAGATATCTGTAATTATGCCCAAAGAG 41641 i ii i v v i vv i vv v i iviv L1ME4c_3end#L 297 TAAATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAG 346 chrXptel1M 41642 TTATTAAACTGCCTATATTCTCTGATCCAGCAATACCATTATTAGGTATG 41691 ii v v iii ii i i i v i vi i v v L1ME4c_3end#L 347 CCATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATT 396 chrXptel1M 41692 TTTCCCAAGAAG----TTTAGGAAAAATGGAAAAGAATTTATATGTTCTA 41737 v i i i---- i -- i v -- vi iv v L1ME4c_3end#L 397 TATCCTAAGGAAATAATTCA--AAAGAAGGAAAA--AGCTATATGCACGA 442 chrXptel1M 41738 AAGTATTTGGTGCATCTTTATT----ATGTCAAAGAACTAAAATTTGCAG 41783 ii i iiv v v ---- iv i i i ii vivi vv L1ME4c_3end#L 443 AGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCT 492 chrXptel1M 41784 GGATGTCTATCAATTGGGAAATAGCTAAACAAATTGTGGCATATGTTCAT 41833 ii i v v i i i ii i i i v?v vi L1ME4c_3end#L 493 AAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTC 542 chrXptel1M 41834 GATGGAATATTATACTACTATAAGAAATGATGAATTCAATGACTTTAAAA 41883 i vi i v i i v vii v v iv i L1ME4c_3end#L 543 GATGGAATATTATGCAGCCATTAAAAATGATAATTATGAAGACTATGTAG 592 chrXptel1M 41884 AAGCATGGAGGAACCTCCATGAAATAATG--AAGAGCAAAATGGCAGAA 41930 v i -i iv ii v -- v v -i L1ME4c_3end#L 593 CAACATGGA-AAATGTTTATGATATAATGTTAAGTGAAAAA-AGCAGAA 639 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.02 CpG sites = 102, Kimura (unadjusted) = 41.51 Transitions / transversions = 1.27 (102/80) Gap_init rate = 0.04 (23 / 603), avg. gap size = 2.52 (58 / 23) 26 18.85 0.00 0.00 chrXptel1M 43761 43808 (956192) (A)n#Simple_repeat 1 48 (0) m_b326s252i0 13675 chrXptel1M 43761 AAACAAAACAAAACAAAAAAAAAAAAAAAAAGAAAAACTAGAAGAAAA 43808 v v v i vv i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 48 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 463 25.01 3.33 4.03 chrXptel1M 45308 45457 (954543) C MIRb#SINE/MIR (91) 177 29 m_b326s601i3 13676 chrXptel1M 45308 AACCC--AGAGGTAAAAATGACTTCTCCAGCTCATTATACAGAAAAGGAA 45355 --v iiv v - v ---i v vi C MIRb#SINE/MIR 177 AACCCTGCGAGGTAGGTATTA-TTATCC---CCATTTTACAGATGAGGAA 132 chrXptel1M 45356 ACTAAGGCAATCAG-GAGG--AAGTGAGTTTTCCAGGGTCACACAGGTAG 45402 i -- - -- i v vi i v C MIRb#SINE/MIR 131 ACTGAGGC--TCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAG 84 chrXptel1M 45403 GAAGTATCTGAGGGCAGATTTGAACTCAGGTCCTCCTGACTCCAGGCCCT 45452 v iv v vvvi i i ivi iiv i C MIRb#SINE/MIR 83 TAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCC 34 chrXptel1M 45453 GCACT 45457 ii C MIRb#SINE/MIR 33 GTGCT 29 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.81 CpG sites = 19, Kimura (unadjusted) = 30.79 Transitions / transversions = 1.12 (19/17) Gap_init rate = 0.06 (9 / 149), avg. gap size = 1.22 (11 / 9) 512 22.50 2.46 1.63 chrXptel1M 45336 45457 (954543) C MIRc#SINE/MIR (120) 148 26 m_b326s601i4 13676 chrXptel1M 45336 CTCATTATACAGAAAAGGAAACTAAGGCAATCAG-GAGG--AAGTGAGTT 45382 i v vi i -- - -- v C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGC--TCAGAGAGGTTAAGTGACTT 101 chrXptel1M 45383 TTCCAGGGTCACACAGGTAGGAAGTATCTGAGGGCAGATTTGAACTCAGG 45432 vi i v v iv v vvvi i i i C MIRc#SINE/MIR 100 GCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGG 51 chrXptel1M 45433 TCCTCCTGACTCCAGGCCCTGCACT 45457 i i i v ii C MIRc#SINE/MIR 50 TCTTCCTGACTCCAAGTCCAGTGCT 26 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.98 CpG sites = 15, Kimura (unadjusted) = 27.12 Transitions / transversions = 1.25 (15/12) Gap_init rate = 0.03 (4 / 121), avg. gap size = 1.25 (5 / 4) 246 15.25 0.00 0.00 chrXptel1M 45559 45617 (954383) HSAT5v1#Satellite 5222 5280 (618) m_b326s502i0 13677 chrXptel1M 45559 TGTGTGTGTGCGCGCGCGTGCGTGCATGTATGTGTGTGTGTGTGTGTGTG 45608 i i i i ?ii i HSAT5v1#Satel 5222 TGTGTGTGTGCACGCGCGTGCGCGCGTGTGTGTGTGTGNACGCGTGTGTG 5271 chrXptel1M 45609 TGTGTGTGT 45617 i i HSAT5v1#Satel 5272 CGCGTGTGT 5280 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 6.63 CpG sites = 9, Kimura (unadjusted) = 18.58 Transitions / transversions = 1.00 (9/0) Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.0 (0 / 0) 570 32.54 4.76 2.75 chrXptel1M 46607 46963 (953037) C L2#LINE/L2 (697) 2385 2022 m_b326s601i5 13678 chrXptel1M 46607 GAGCTCTGAGT-CAGGAGAAAGGT-------GGATAAGCAGACTTGGGGG 46648 iiiv - i i ------- v vii i i i C L2#LINE/L2 2385 GAGTCTGGAGTTCAGGGGAGAGGTCCGGGCTGGAGATATAAATTTGGGAG 2336 chrXptel1M 46649 TCATCAAGCGTAGAGATGATCATTGAAATCCATG-GACATTGATTTGATC 46697 - i v i - v v - - v vv C L2#LINE/L2 2335 TCATC-AGCATATAGATGGT-ATTTAAAGCCATGAGAC-TGGATGAGATC 2289 chrXptel1M 46698 ACCA---CAACAAAAATACCTAGGAGAGGAAGTGGGCTCAAGG-TGGAGC 46743 ?---v iii ivi vv iii ii ivi ii -iv C L2#LINE/L2 2288 ACCNAGGGAGTGAGTGTAGATAGAGAAGAGAAGAGGTCCAAGGACTGAGC 2239 chrXptel1M 46744 CTTTGGTAGACCCCTGTAACTACTGGGTATGGTGGAGCCTTGGAGGTAGA 46793 -i viv i --- vvi?i ivi v v vi--- vi C L2#LINE/L2 2238 C-CTGGGGCACTCC---AACGTTNAGAGGTCGGGGAGAT---GAGGAGGA 2196 chrXptel1M 46794 ATCAGCACAGGGAACTTAGAAGGAGCT----GTTAGATCAGAGGAGAACC 46839 i v ii v v---- v i vi i C L2#LINE/L2 2195 ACCAGCAAAGGAGACTGAGAAGGAGCGGCCAGTGAGGTAGGAGGAAAACC 2146 chrXptel1M 46840 AGGAGAGAGTAGTGCCAGGAAAACCTAGGGAGAAGAGAGTATCAGGGAAA 46889 v i i vv i i v v ii i v v i i ii C L2#LINE/L2 2145 AGGAGAGTGTGGTGTCCTGGAAGCCAAGTGAAGAAAGTGTTTCAAGAAGG 2096 chrXptel1M 46890 ATAGGGTGCTTGTCAGGGTCAAAACCTACAGGGAGGTCAAGGAGAATGAA 46939 vi i v iiv v v vv i v i? v ii i C L2#LINE/L2 2095 AGGGAGTGATCAACTGTGTCAAATGCTGCTGANAGGTCAAGTAAGATGAG 2046 chrXptel1M 46940 GATTCAGAAAAAGCCATTGGATTT 46963 i v vvii C L2#LINE/L2 2045 GACTGAGAATTGACCATTGGATTT 2022 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.61 CpG sites = 65, Kimura (unadjusted) = 44.61 Transitions / transversions = 1.35 (65/48) Gap_init rate = 0.04 (16 / 356), avg. gap size = 1.69 (27 / 16) 782 25.12 0.91 0.55 chrXptel1M 46965 48886 (951114) (GA)n#Simple_repeat 1 1929 (54) m_b326s252i1 13679 chrXptel1M 46965 GAGGGAGGGAGAGAGAGA-AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 47013 i i - (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chrXptel1M 47014 GAGAGAGAGACAAAGACAGAGAGATACAGAGAAAGAGACAGAGAGAGACA 47063 v i v v v i v v (GA)n#Simple_ 51 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 100 chrXptel1M 47064 AAGTCATAGAAAGAGACAGA-AAAAAGAG-GGGGGAGGGAGAGACAGAGA 47111 i vv v i v - i i - i i i v (GA)n#Simple_ 101 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 150 chrXptel1M 47112 GAAACAGAGAAAGAAAGAGTGATAAAGAAAGAGAGAGAGAAAGAAATGGA 47161 i v i i v v i i i i vi (GA)n#Simple_ 151 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 200 chrXptel1M 47162 AATAAAGAGAGAAAATGAGATAGAGAAAGAGAAAGGGAAAGAGAGA-AAA 47210 i v i i iv v i i i i - i (GA)n#Simple_ 201 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 250 chrXptel1M 47211 CGGGGAGGAAAAGGAAAAGACAGAGAGAAACAGATTCAGAGACAGGGACA 47260 vi i ii i ii i v i v vvv v i v (GA)n#Simple_ 251 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 300 chrXptel1M 47261 CATAACAACAGAGACAGAAAAACAGAGAGACACAGAGACA-AGAGAGAGA 47309 v v ivi v v i i v v v v - (GA)n#Simple_ 301 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 350 chrXptel1M 47310 CAGAGAGTGAGACAGAG-GAGAAAGAGAAAGACAGAGACAGAGAGAGTAA 47358 v v v - i i v v vi (GA)n#Simple_ 351 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 400 chrXptel1M 47359 GACAGAGAAAAGGAGAGAGACAGAGATAGAGACAAAGAGAGAGATAGAGA 47408 v i ii v v v i v (GA)n#Simple_ 401 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 450 chrXptel1M 47409 CAGAGAAAGAGTCAGAGATAGAGAAACAGAGACAGATAGAAAAAGAACGG 47458 v i vv v i v v v i i iv i (GA)n#Simple_ 451 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 500 chrXptel1M 47459 GAGACAAAGAAAGAGCATGGCAGAGAGAGACAGATGGGAAAGAGACAGAC 47508 v i i - - iv v - i i v v (GA)n#Simple_ 501 GAGAGAGAGAGAGAG-A-GAGAGAGAGAGAGAGA-GAGAGAGAGAGAGAG 547 chrXptel1M 47509 AGAGACAAAGACAGAGAGACAAATGA-AGAGAAAGACAGAGATAGAGACA 47557 v i v v i - - i v v v (GA)n#Simple_ 548 AGAGAGAGAGAGAGAGAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGA 596 chrXptel1M 47558 GAGACAGAGAAAGAGACAAAGAGACATACAAAGAACAAAAGACAGAG-GA 47606 v i v i v v v i ivi i v - (GA)n#Simple_ 597 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 646 chrXptel1M 47607 GAGAGAGAGA-AGAGAGACAGAGACAAAGAGAGAGAAAGAGAAAAAGTCA 47655 - v v i i i i vv (GA)n#Simple_ 647 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 696 chrXptel1M 47656 GAGACAGAGAGACAGAGAGAGAGA-AGAGAGAGACAGAGAGATAGAGACA 47704 v v - v v v (GA)n#Simple_ 697 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 746 chrXptel1M 47705 GAAAGAGACAGAGGCAGAAATAAAGAGACAGAGACACAGACAGACACTGA 47754 i v iv i v i v v v v v vv (GA)n#Simple_ 747 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 796 chrXptel1M 47755 CAGAGAGAGAAACAGAAAGAGACAGAGAGAGAGAGAGAGAGAGAGAGAGA 47804 v i v i v (GA)n#Simple_ 797 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 846 chrXptel1M 47805 GAGAGAGAGAGA-ACAGAGATATGA-AGACATACAGAGAGACAGAGACAG 47852 - v v - - v v v v v (GA)n#Simple_ 847 GAGAGAGAGAGAGAGAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGAG 895 chrXptel1M 47853 AGCAAGAGTAAGAGAAAGAGAGACAGAGACAGAGGGAGAGACAGCTGGGA 47902 vi vi i v v i v -v i (GA)n#Simple_ 896 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG-AGAGA 944 chrXptel1M 47903 GAGAGAGAGAGAGAGAGAGAGAGAGAAAGAGCAAAAGACAGAGAGAGAGA 47952 i vi i v (GA)n#Simple_ 945 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 994 chrXptel1M 47953 GAGAGAGACAAAGAAAGAGAGAAACAGAGAGAAAGAGAAAAAGACAGAGA 48002 v i i i v i i i v (GA)n#Simple_ 995 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 1044 chrXptel1M 48003 CAGAAAGGGACAGAGGCAGAAATAAAGAGACAGAGACACAGACAAACACT 48052 v i i v iv i v i v v v v i v vv (GA)n#Simple_ 1045 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 1094 chrXptel1M 48053 GACAGAGAGAAAAAGACACCGAGAGAGTGAGATAGAGAAACTGAAATATG 48102 v i i v vv v v i vv i v vi (GA)n#Simple_ 1095 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 1144 chrXptel1M 48103 GAGACATACAGAGAGACAGAGAAAGACAGAGAGAAAGAGTAAGAGAAAGA 48152 v v v v i v i vi i (GA)n#Simple_ 1145 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 1194 chrXptel1M 48153 GAGACAGAGAGATAAACAGAGACAGAGAGACAGCTAGAGAGAGAGAGACA 48202 v v i v v v vv v (GA)n#Simple_ 1195 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 1244 chrXptel1M 48203 AAGAGAGAGATAGAGAGACACACAAAGAGCAAAAGAGAGAGACAGAGAGA 48252 i v v v v i vi i v (GA)n#Simple_ 1245 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 1294 chrXptel1M 48253 AAAAGAGACAGAGACAGAAGGAGAGACAGAGACAGATGA-AGAGAGAAAG 48301 i i v v ii v v - - i (GA)n#Simple_ 1295 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA-GAGAGAGAGAGAG 1343 chrXptel1M 48302 ACAGAGACAGAGCGAGAGAGAAATTAGAGAAAGAAAGATAGTGAGAGAGA 48351 v v v i -v i i v v (GA)n#Simple_ 1344 AGAGAGAGAGAGAGAGAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGA 1392 chrXptel1M 48352 GAGAAACAGAGGCAGAAATAAAGAGACAGCAGCACAGTGACATAGAGAGA 48401 i v iv i v i v - - v v v v (GA)n#Simple_ 1393 GAGAGAGAGAGAGAGAGAGAGAGAGAGAG-AG-AGAGAGAGAGAGAGAGA 1440 chrXptel1M 48402 AAGAGAAAGAAAGAAACCGAAAGA-AAAGAGAGAGACAGAGAGACAGAGA 48450 i i i i vv i - i v v (GA)n#Simple_ 1441 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 1490 chrXptel1M 48451 GAGAGAATGAGACAGAGACAGACACAAAGAGAGAAAGAGAGACAGAGACA 48500 iv v v v v i i v v (GA)n#Simple_ 1491 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 1540 chrXptel1M 48501 GAGAGAGAGAAACAGAAAGACAGAGACAGAGAAAGAGAGA-AGAGACAAA 48549 i v i v v i - v i (GA)n#Simple_ 1541 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 1590 chrXptel1M 48550 GAGACAAAGATACACAGAGAGATAGAAAGACATTGAGAGAGAGAGAGATA 48599 v i v v v v i v vv v (GA)n#Simple_ 1591 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 1640 chrXptel1M 48600 GCGAGAGACAGAGAGTGTGAGAAAGAGTGCGAAAGAGAGAGACCAAGAGA 48649 v v v v i v v i vvi (GA)n#Simple_ 1641 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 1690 chrXptel1M 48650 GAGAAAAAAAGAGAAAGACAGAGAGATGGAGAGAGAGAGATGGACAGAGA 48699 i i i i v vi vi v (GA)n#Simple_ 1691 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 1740 chrXptel1M 48700 AAGAGACATAGACACAGAGAGAGACAGAGACAGAGAG-GAGAGATAAAGA 48748 i v v v v v v - v i (GA)n#Simple_ 1741 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 1790 chrXptel1M 48749 AACAGAGAGTGACAGAGACACTGTGAAAGAAACAGAGAGAAATAAAACTA 48798 i v v v v vv v i i v i v i ivv (GA)n#Simple_ 1791 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 1840 chrXptel1M 48799 CAGAGAGAGAAAGAGAGAGACAGAGACAGATACACAGAGACATAGACACA 48848 v i v v v v v v v v v (GA)n#Simple_ 1841 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 1890 chrXptel1M 48849 CAGAGAGAAAGAGAGATAGACACACACACACACACA-AC 48886 v i v v v v v v v v v - v (GA)n#Simple_ 1891 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 1929 Matrix = Unknown Transitions / transversions = 0.65 (159/246) Gap_init rate = 0.01 (27 / 1921), avg. gap size = 1.00 (27 / 27) 44 0.00 0.00 0.00 chrXptel1M 48887 48924 (951076) (AG)n#Simple_repeat 1 38 (0) c_b326s251i2 13680 chrXptel1M 48887 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 48924 (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 38 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 782 25.12 0.91 0.55 chrXptel1M 48925 48977 (951023) (GA)n#Simple_repeat 1930 1982 (1) m_b326s252i1 13681 chrXptel1M 48925 GCACAGAGAGAAATATA-ACAGAGAGATGGAGAGAGACAGAGTTTGAAAG 48973 - v i v v - v vi v vvv i (GA)n#Simple_ 1930 G-AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 1978 chrXptel1M 48974 AGAG 48977 (GA)n#Simple_ 1979 AGAG 1982 Matrix = Unknown Transitions / transversions = 0.33 (3/9) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.00 (2 / 2) 27 3.42 0.00 0.00 chrXptel1M 49654 49683 (950317) (AGAGAC)n#Simple_repeat 1 30 (0) c_b326s251i3 13682 chrXptel1M 49654 AGAGAGAGAGACAGAGACAGAGACAGAGAC 49683 v (AGAGAC)n#Sim 1 AGAGACAGAGACAGAGACAGAGACAGAGAC 30 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 12 15.89 5.71 0.00 chrXptel1M 49694 49728 (950272) (AGAGAC)n#Simple_repeat 1 37 (0) m_b326s252i3 13682 chrXptel1M 49694 AGAGACATAGA-A-AAAGAGAGACAGAGACACACACA 49728 v - - i v v v (AGAGAC)n#Sim 1 AGAGACAGAGACAGAGACAGAGACAGAGACAGAGACA 37 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 16 23.31 0.00 0.00 chrXptel1M 49686 49720 (950280) (AG)n#Simple_repeat 1 35 (0) m_b326s252i2 13683 chrXptel1M 49686 AGAGCAAGAGAGACATAGAAAAAGAGAGACAGAGA 49720 vi v v i i v (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 35 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 27 3.42 0.00 0.00 chrXptel1M 49654 49683 (950317) (AGAGAC)n#Simple_repeat 1 30 (0) c_b326s251i3 13682 chrXptel1M 49654 AGAGAGAGAGACAGAGACAGAGACAGAGAC 49683 v (AGAGAC)n#Sim 1 AGAGACAGAGACAGAGACAGAGACAGAGAC 30 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 12 15.89 5.71 0.00 chrXptel1M 49694 49728 (950272) (AGAGAC)n#Simple_repeat 1 37 (0) m_b326s252i3 13682 chrXptel1M 49694 AGAGACATAGA-A-AAAGAGAGACAGAGACACACACA 49728 v - - i v v v (AGAGAC)n#Sim 1 AGAGACAGAGACAGAGACAGAGACAGAGACAGAGACA 37 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 13 12.41 8.57 0.00 chrXptel1M 49736 49770 (950230) (TTA)n#Simple_repeat 1 38 (0) m_b326s252i4 13684 chrXptel1M 49736 TTATT-TT-TTGTTATTATTATTATT-TTAAAAATATT 49770 - - i - vv v (TTA)n#Simple 1 TTATTATTATTATTATTATTATTATTATTATTATTATT 38 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.09 (3 / 34), avg. gap size = 1.00 (3 / 3) 23 14.04 2.70 8.57 chrXptel1M 50660 50733 (949267) (TTA)n#Simple_repeat 1 70 (0) m_b326s252i5 13685 chrXptel1M 50660 TTATTTTCTATATCTTATTATTATTATTATTATATATTA-TGTTA-TATA 50707 v - - v - - i - - (TTA)n#Simple 1 TTATTAT-TAT-TATTATTATTATTATTATTAT-TATTATTATTATTAT- 46 chrXptel1M 50708 TGTTATAGATATTATATATCTACTAT 50733 i viv - - i (TTA)n#Simple 47 TATTATTATTATTAT-TAT-TATTAT 70 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.11 (8 / 73), avg. gap size = 1.00 (8 / 8) 706 36.68 5.17 1.42 chrXptel1M 50739 51280 (948720) L2#LINE/L2 2521 3082 (0) m_b326s601i6 13686 chrXptel1M 50739 GCAGCACCACCCTCCCAGTCTCTCTGACTCCCATCCCAGAGATCATACTG 50788 i v i i iv v i ivvv v iv iii v v L2#LINE/L2 2521 GCAACTCCATCCTTCCAGTTGCTCAGGCCAAAAACCTTGGAGTCATCCTT 2570 chrXptel1M 50789 GACTCCTTACTATCTCTCACTGTCTATATCCAAGCTCTTGCCAAGGCCTG 50838 iv v vvi i i v iv iiv iv L2#LINE/L2 2571 GACTCCTCTCTTTCTCTCACACCCCACATCCAATCCATCAGCAAATCCTG 2620 chrXptel1M 50839 TTGATCACACCTTT--GACTTCTCCCTTATATGCCCTCTTCT------CT 50880 i iiivi i--i iv v vvv vi v v ------ L2#LINE/L2 2621 TCGGCTCTACCTTCAAAATATATCCAGAATCCGACCACTTCTCACCACCT 2670 chrXptel1M 50881 CCTCTG---ACACCCTAGTGCAAGTCTTCATCACTTCATGCCTTGATTAT 50927 v ---v i v i vi ii vi v i L2#LINE/L2 2671 CCACTGCCACCACCCTGGTCCAAGCCACCATCATCTCTCGCCTGGATTAC 2720 chrXptel1M 50928 TACAGCAGTCTGCTGGAGGGTCTGCATGCCTTGACATTT-TACCCCTCCA 50976 i ii i v iivv v v i iv vi -iv ? L2#LINE/L2 2721 TGCAATAGCCTCCTAACTGGTCTCCCTGCTTCCACCCTTGCCCCCCTNCA 2770 chrXptel1M 50977 G--GATTT------CAGCTGTCAAAGTGACTTTTCTAAAGCACAAGTCTG 51018 --v i------ v i i iii i i ii v L2#LINE/L2 2771 GTCTATTCTCAACACAGCAGCCAGAGTGATCCTTTTAAAACGTAAGTCAG 2820 chrXptel1M 51019 TTCCTGTTAC-ACACAGCAAACTGAATAAACTTCAATGACTCCCTATC-C 51066 v v i -v v v ---- v v vv i i i i - L2#LINE/L2 2821 ATCATGTCACTCCTCTG----CTCAAAACCCTCCAATGGCTTCCCATCTC 2866 chrXptel1M 51067 TCCATGAGCAAAAGCAAAATGTTC-TAT-TTGGCATTTAAAGCCTTTTAT 51114 v ivv i v - i - i-v v vi i i vi L2#LINE/L2 2867 ACTCAGAGTAAAAGCCAAA-GTCCTTACAATGGCCTACAAGGCCCTACAT 2915 chrXptel1M 51115 AACTTAGCCCTATTCTACCTTTCTAG--TTGTCTTACTTCTCATTTGCCA 51162 i ii i i ivivi i ii-- ii -- i vi i iv v L2#LINE/L2 2916 GATCTGGTCCCCCGTTACCTCTCTGACCTCATCT--CCTACCACTCTCCC 2963 chrXptel1M 51163 CCAAGTATTGTTCAAC-ACAGTGACCCCGGCCTCCCAGCTGTTCCATCAA 51211 vv i- iii vi -v iv v i iv viv L2#LINE/L2 2964 CCTCGC-TCACTCCGCTCCAGCCACACTGGCCTCCTTGCTGTTCCTCGAA 3012 chrXptel1M 51212 CAAGACACTCCATCTTTTAGCTCTGGGCATTCTTTCTAGCTG-TCTCCAT 51260 v v vv vvv iiiiv v v iviv v - i iv L2#LINE/L2 3013 CACGCCAGGCACGCTCCCGCCTCAGGGCCTTTGCACTTGCTGTTCCCTCT 3062 chrXptel1M 51261 GCCTGGAATTCTCTCCTTTC 51280 iv i iii L2#LINE/L2 3063 GCCTGGAACGCTCTTCCCCC 3082 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 48.68 CpG sites = 106, Kimura (unadjusted) = 52.11 Transitions / transversions = 1.18 (106/90) Gap_init rate = 0.04 (21 / 541), avg. gap size = 1.71 (36 / 21) 584 33.54 7.28 5.88 chrXptel1M 51113 51565 (948435) L2b_3end#LINE/L2 5 463 (3) m_b326s601i7 13686 chrXptel1M 51113 ATAACTTAGCCCTATTCTACCTTTCTAG--TTGTCTT-----ACTTCTCA 51155 ii ii i ii-- i ii -- ii i----- iii v L2b_3end#LINE 5 ACGATCTGGCCCCG--CTACCTCTCCGGCCTCATCTCCTACCACTCTCCC 52 chrXptel1M 51156 TTTGC-CACCAAGTATTGTTCAACACAGTGACCCCGGCCTCCCAGCTGTT 51204 i - i-----i i ---- iv v i iv L2b_3end#LINE 53 CTTGCTCACT-----CTGCTC----CAGCCACACTGGCCTCCTTGCTGTT 93 chrXptel1M 51205 CCATCAACAAGACACTCCATCTTTTAGCTCTGGGCATTCTTTCTAGCTGT 51254 viv v v ?v iv? iiiiv v v iviv ?v L2b_3end#LINE 94 CCTCGAACACGCCANGCTCNCTCCCGCCTCAGGGCCTTTGCACNTGCTGT 143 chrXptel1M 51255 CTCC-ATGCCTGGAATTCTCT--CCTTTCTCTGC-TCTGACCA-CTGGCC 51299 ii -v iv i -- ivi v -i i - -- L2b_3end#LINE 144 TCCCTCTGCCTGGAACGCCCTTCCCCACCTCTTCGCCTGGCCAACT--CC 191 chrXptel1M 51300 TCCCTGGCTTCCTTTAA-TTTCTGAATAAATCTCAGCTTCTCCAGAAAGC 51348 v i--- v i i- i v vvi v v i i i L2b_3end#LINE 192 TACT---CATCCTTCAGGTCTCAGCTCAAATGTCACCTCCTCCGGGAAGC 238 chrXptel1M 51349 CTTAGTCAACCCCTCTTATATTCCAG--TACTTGTCCTCTGTTAATTATT 51396 i vviii i ---- vv i --i vvi i ivi iivivii L2b_3end#LINE 239 CCTCCCTGACCCCCC----AGGCCGGGTCAGGCGCCCTCCTCTGGGCCCC 284 chrXptel1M 51397 TACAG-CTTATCTGGATAT----GATTTTCTTTGTCTTTGTTTGCATGTC 51441 iv - i i iv vi i---- i v ?v -- ? i L2b_3end#LINE 285 CCCAGTCCTACCCTGCCACTCTGGGTTATNATTGTCT--GNTTACATGTC 332 chrXptel1M 51442 -ATCTCCACCATTAGATTGTAATAAGCTCCTTAAAGACAGG---CAGGTT 51487 -i v i i i --- v i i i --- i? i L2b_3end#LINE 333 TGTCTCCCCCACTAGACTGTGA---GCTCCGTGAGGGCAGGGACCGNGTC 379 chrXptel1M 51488 GTTATCTCTTTCG-----GTATCCCTATCACTTAACACAGTGCTTGGCAC 51532 -- i iv i----- i v i i i ? i L2b_3end#LINE 380 --TGTCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCAC 427 chrXptel1M 51533 ATGGTAGATACT---TAAATGTTTATTGCTTGATTG 51565 ii iii --- i i vv v L2b_3end#LINE 428 ACAGTAGGCGCTCAGTAAATATTTGTTGAATGAATG 463 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.59 CpG sites = 95, Kimura (unadjusted) = 48.47 Transitions / transversions = 1.98 (95/48) Gap_init rate = 0.09 (42 / 452), avg. gap size = 1.43 (60 / 42) 499 25.00 5.88 0.00 chrXptel1M 51569 51704 (948296) C MIRc#SINE/MIR (14) 254 111 m_b326s601i8 13687 chrXptel1M 51569 CTAATATTTATGAAGCATTTTAAAGTTTACAAATTGCTTTC-CATATATT 51617 v i i iv i v vi - i C MIRc#SINE/MIR 254 CTTACATTTGTATAGCACTTTACAGTTTACAAAGCGCTTTCACATACATT 205 chrXptel1M 51618 TCTTCATT-GGCATTCACAAAAAGCCAGTGAAATAGAT---GC---TATT 51660 vii - iivi v v v ii ii--- --- C MIRc#SINE/MIR 204 ATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATT 155 chrXptel1M 51661 ATTATTTCCATTTTGCAAATGAGGAAAAGGAGGTTGAAAGGGGT 51704 ii i i vv i v i i C MIRc#SINE/MIR 154 ATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGT 111 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.27 CpG sites = 22, Kimura (unadjusted) = 31.39 Transitions / transversions = 1.83 (22/12) Gap_init rate = 0.03 (4 / 135), avg. gap size = 2.00 (8 / 4) 52 2.08 0.00 0.00 chrXptel1M 52066 52114 (947886) (TC)n#Simple_repeat 1 49 (0) c_b326s251i4 13688 chrXptel1M 52066 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTTCTCTCT 52114 i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 49 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 876 32.46 1.05 0.54 chrXptel1M 52133 53873 (946127) (TCTCTC)n#Simple_repeat 1 1753 (1398) m_b326s252i6 13689 chrXptel1M 52133 TCTCTGTCTCTTTTTCTTCCTCTGTTTCTGTCTCTGTCTCT-TTTTTGTT 52181 v i i ii v i v v - i i v i (TCTCTC)n#Sim 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chrXptel1M 52182 TCTCTCTGTGTGTTTTTCTCT-TCTCTCTCACTCTTTCTGTCTCTCCATC 52230 v v v i i - v i v iv (TCTCTC)n#Sim 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chrXptel1M 52231 TGTTTCTCTTTTTATATCTATGTACT-TGTCTCTTTATATCTATCTATAT 52279 v i i i v v v v - - v i v v v v v (TCTCTC)n#Sim 101 TCTCTCTCTCTCTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCT 149 chrXptel1M 52280 CTTTCTCTATCAGTCTGTATCTCTCTCTGGTTCACTTTATGTCTCTGTCT 52329 i v vv v v vvi v i v v v (TCTCTC)n#Sim 150 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 199 chrXptel1M 52330 CTCACTCTCTGAATATGTCTTTCTGTGTATTTCTCTATCTCTCTTTCTCT 52379 v vvv v v i v v v i v i (TCTCTC)n#Sim 200 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 249 chrXptel1M 52380 ATGTCTGTCTCTGGGTCTCTTTCTCTAATTGTCTGTCTGTCTTTCTCTCT 52429 v v v vvv i vvi v v v i (TCTCTC)n#Sim 250 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 299 chrXptel1M 52430 TCCTCTCTGTCTCACTCTTTCTGTCTTTGTCTCTATTTCTCTGTCTCTCT 52479 ii v v i v i v v i v (TCTCTC)n#Sim 300 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 349 chrXptel1M 52480 CTCTCACTCTGCT-TCTCTGTCTCTCTCTTTCTC-CCCAATCTTTCTCCC 52527 v - - v i - i vv i i (TCTCTC)n#Sim 350 CTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 398 chrXptel1M 52528 TCTTTAACTTTCTCTCATTCCCTATCTCATTTTCTCTTGTTATATCCACC 52577 i vv i vi i v vi i ivi v v ivi (TCTCTC)n#Sim 399 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 448 chrXptel1M 52578 TATTTGTCCCTCTACCTTGCCTTGTCTCTTTCTCTGT-TTTTTCTCTGTC 52626 v i v i vi iv ii v i v - i i v (TCTCTC)n#Sim 449 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 498 chrXptel1M 52627 TGTCTCTGTCTTTATCTCTGTTTCT-TTTCTCTCTCTCTCTCTTTCT-TC 52674 v v i v v i - i i - (TCTCTC)n#Sim 499 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 548 chrXptel1M 52675 TATTTCTCTTTTAATCTTTCT-TTTTTCTCTCTTTCTCTTTATCTCTGTC 52723 v i i ivv i - i i i i v v (TCTCTC)n#Sim 549 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 598 chrXptel1M 52724 TCTCT-TCCTTTTCTCTCTATTTCTGTCTCTCTCTCTGTCTATCTATCTT 52772 - ii i v i v v v v i (TCTCTC)n#Sim 599 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 648 chrXptel1M 52773 TGCCTGTCACTCACTCTCTTTTTC-CTTTTTCTCTCTGTCTTACTCTTTC 52821 vi v v v i i - i i v iv i (TCTCTC)n#Sim 649 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 698 chrXptel1M 52822 CATCACTCTCTGCCTCACACTTTCCATCTCTCTGTCACTCTTTCTCTCTC 52871 iv v vi v v i iv v v i (TCTCTC)n#Sim 699 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 748 chrXptel1M 52872 TGTCTCTCTCTTTCTCTTGCTCTTTCTGTTGATCT-TGGCT-TCTGTTTC 52919 v i iv i v ivv - vv - v i (TCTCTC)n#Sim 749 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 798 chrXptel1M 52920 TCTGTCTCTCTGTCTCTGTCTCTGTTTCTCCCTCCCTTTTCCTTCCTCCC 52969 v v v v i i i i ii ii i (TCTCTC)n#Sim 799 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 848 chrXptel1M 52970 TCTCTCTCTGTATTGCTGTCTCCCT-TTTCATCTCTCTCT-TTTGCCTTT 53017 v v iv v i - i - - i vi i (TCTCTC)n#Sim 849 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TCTCTCTCTCTCTCTCTCT 897 chrXptel1M 53018 CTCTCTAACTCTCATTATCTCATTTTCTCTTTATTTTTATCTCTTTGTCT 53067 vv vi v vi i i v i i v i v (TCTCTC)n#Sim 898 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 947 chrXptel1M 53068 CTGTCTTTCTCTACCTCTTTCTCTGTTTCTCTCTGTCTCTTCCTTTGTTT 53117 v i vi i v i v ii i v i (TCTCTC)n#Sim 948 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 997 chrXptel1M 53118 CTGTCTCTATCTCTTTGTGCCTTTGT-TGTTTTTCTGTCCATCTTGCTTT 53166 v v i v vi i v - v i i v iv iv i (TCTCTC)n#Sim 998 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 1047 chrXptel1M 53167 CTCTCTTTCT-TCTGTCTTTCTGTGTCTTTCTCTCTTGCTCTCTCTCTCT 53215 i - v i v v i iv (TCTCTC)n#Sim 1048 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 1097 chrXptel1M 53216 ATTTGTGTATCTCTGTGTCTGTCTGTCTGTCTCTGTCTCTATCCCTCTCT 53265 v i v v v v v v v v v v i (TCTCTC)n#Sim 1098 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 1147 chrXptel1M 53266 CTGTGTATATCTGTCTCTGTCACTCTTTCTCTCTCTGTCTGTCTCTTTCT 53315 v v v v v v v i v v i (TCTCTC)n#Sim 1148 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 1197 chrXptel1M 53316 CTTGCTCCTTCTGTTGATCTTTGCT-TCTGTTTCTCTGTCTCTCTCTGTC 53364 iv ii v ivv i - - v i v v (TCTCTC)n#Sim 1198 CTCTCTCTCTCTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTC 1246 chrXptel1M 53365 TCACTTTCTCTTTGTCTGCCTGTCTGTCAGTCTCCCCCCCTTGTTCTCAC 53414 v i i v vi v v vv i i i ivi v (TCTCTC)n#Sim 1247 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 1296 chrXptel1M 53415 TCTTGCTCTCTTGCTCTTTCTCTCGTTCTGTCTTTCTGTCTCTCTAATAC 53464 iv iv i vi v i v -v - (TCTCTC)n#Sim 1297 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT-CT-C 1344 chrXptel1M 53465 TCTCATTTTCTATCT-TCTGTCCATCTCTTTGTCTGTCTGTCTGTCTGTC 53513 vi i v - v iv i v v v v v (TCTCTC)n#Sim 1345 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 1394 chrXptel1M 53514 TCTGTCTCTGTCTCTCTGTCTCTCTCTCTCTCTGTCTCTATTTCCATCTC 53563 v v v v v i iv (TCTCTC)n#Sim 1395 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 1444 chrXptel1M 53564 TCTCTCTTTGCCTGTTTCTTTCTCTCTGTCTCTCTCACCCTTTCTCATTC 53613 i vi v i i v v i i vi (TCTCTC)n#Sim 1445 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 1494 chrXptel1M 53614 ATCTCTCACTCTTTCCATATCTCTGTCTCTTTCTATTTTTCTGTCTCTCT 53663 - v i iv v v i v i i v (TCTCTC)n#Sim 1495 -TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 1543 chrXptel1M 53664 GTCATTCTCTTGCTCTTTGTCTCTCTATTTCTCTCCCTTTCTTTTTCTCT 53713 v vi iv i v v i i i i i (TCTCTC)n#Sim 1544 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 1593 chrXptel1M 53714 CTGTCTCTCTGTCCCTGTCTCTATTTCCATCACTTTCTATTTGCCTCTCT 53763 v v i v v i iv v i v i vi (TCTCTC)n#Sim 1594 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 1643 chrXptel1M 53764 TTGTCTCTTTCTTTCCCT-TCTCTCTAACTTTCTCTCATTTC-CTATCTC 53811 i v i i i - vv i - i - v (TCTCTC)n#Sim 1644 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TCTCTCTCTCTC 1692 chrXptel1M 53812 ATTTTTTCTCTTTATACCCATCTATTTGTCTCTCTATCTTTCCCTGTCTC 53861 vi i i i v - i - v i v v i i v (TCTCTC)n#Sim 1693 TCTCTCTCTCTCTCT-CTC-TCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 1740 chrXptel1M 53862 TCTCAGT-TTTTT 53873 vv - i i (TCTCTC)n#Sim 1741 TCTCTCTCTCTCT 1753 Matrix = Unknown Transitions / transversions = 0.82 (200/244) Gap_init rate = 0.02 (32 / 1740), avg. gap size = 1.00 (32 / 32) 27 8.35 0.00 0.00 chrXptel1M 53874 53912 (946088) (TCTGTC)n#Simple_repeat 1 39 (0) c_b326s251i5 13690 chrXptel1M 53874 TCTGTCTCTGTTTCTGTCTCTGTCTTTATCTCTGTCTCT 53912 i i i (TCTGTC)n#Sim 1 TCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCT 39 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 876 32.46 1.05 0.54 chrXptel1M 53913 55305 (944695) (TCTCTC)n#Simple_repeat 1754 3150 (1) m_b326s252i6 13691 chrXptel1M 53913 TTTCTCTCACTTTCTTTAGACT-TCTCTTTTAACCTGTTTTTCTCTTTCT 53961 i v i i -vv - i ivvi v i i i (TCTCTC)n#Sim 1754 TCTCTCTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 1802 chrXptel1M 53962 TTCTATTTCTGTTTCTCTCTCCTTTTTTCTCTCTATTTCTGTCTCTCTTT 54011 i v i v i ii i i v i v i (TCTCTC)n#Sim 1803 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 1852 chrXptel1M 54012 CTCTATCCATCTATCTTTCCCTGTCATTCTTTCTTTTTCTCTCTCTTTAT 54061 v iv v i i v vi i i i i v (TCTCTC)n#Sim 1853 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 1902 chrXptel1M 54062 CTCATTCTTTCTCTCTCTCTCTCTCTTTCTCTCTCTCTCTCTTTCTATCT 54111 vi i i i v (TCTCTC)n#Sim 1903 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 1952 chrXptel1M 54112 GTCTCTCTTTCTAAATCTATCTCTCATTCTCTATATCATTTTCTCTCTAT 54161 v i vvv v vi v v vi i v (TCTCTC)n#Sim 1953 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 2002 chrXptel1M 54162 GTCCATCTCTTTGTCTCTCTATCTTTCTCTGTGTCTCTCTCTTTCTCTCT 54211 v iv i v v i v v i (TCTCTC)n#Sim 2003 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 2052 chrXptel1M 54212 GTTCCTCTCTTTGTCTGTCTCTATAAGTATCTCTCTCGTCTGTCTTTGTC 54261 v ii i v v v vvv v - v i v (TCTCTC)n#Sim 2053 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TCTCTCTCTCTC 2101 chrXptel1M 54262 TATCTCCCTCTCTTTCTAATCTCTCTCATTTTCTCTTTTTGTCTGTCTCT 54311 v i i -v vi i i i v v (TCTCTC)n#Sim 2102 TCTCTCTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 2150 chrXptel1M 54312 GTCTCTCTACCTTTCCCTGTGTCTGTCTGTCTTTTTTTCTCTCTCTCCTT 54361 v vi i i v v v v i i i ii (TCTCTC)n#Sim 2151 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 2200 chrXptel1M 54362 TTATCTCTGTCTCTTTGTGTCTCCATTTCTTTCTCTCACACTGTGTTTGT 54411 i v v i v v iv i i v v v v i v (TCTCTC)n#Sim 2201 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 2250 chrXptel1M 54412 CTTTATCTCTGTCTGTCTCTCTATGTCTCTGTCTCTCTCTCCCCATCGTT 54461 i v v v v v v i iv vi (TCTCTC)n#Sim 2251 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 2300 chrXptel1M 54462 CTGTCTCTGCCTCTCTGTTTCTCTCTGACTTTCTCTTTCTCTCTCTTTCC 54511 v vi v i vv i i i i (TCTCTC)n#Sim 2301 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 2350 chrXptel1M 54512 ATCTTTCTTTGTCACTCTCTGTCTCTGTCTCTCTCTCTGTTTCTCTCTCC 54561 v i i v v v v v i i (TCTCTC)n#Sim 2351 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 2400 chrXptel1M 54562 CTTTCTCTTTC-CTAACCCTAACCCTAACCCTAAATACCTCCCGC-CTCC 54609 i i - vv i vv i vv i vvv vi i v - i (TCTCTC)n#Sim 2401 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 2450 chrXptel1M 54610 CGACTCTCTAACTTTATATCATTTTCTTTTTCTCTCTTTATCTCCCTGCC 54659 -v vv i v v vi i i i i v i vi (TCTCTC)n#Sim 2451 C-TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 2499 chrXptel1M 54660 TTTCCCTACCTATCATTCTTTCTCTGTGCT-TCTCTCTATGTATCTTCCT 54708 i i vi v vi i v - - v v v ii (TCTCTC)n#Sim 2500 TCTCTCTCTCTCTCTCTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCT 2548 chrXptel1M 54709 CTGTTTCTGTCTCTGTTTCTCTATCTCGCTTTCTCTCTCTCT-TCTCTCT 54757 v i v v i v v i - (TCTCTC)n#Sim 2549 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 2598 chrXptel1M 54758 GTCTCTATCTTTCTGTCTCTTTCTCTCT-TCTGTCTTTCTCT-TTTCATC 54805 v v i v i - v i - i - (TCTCTC)n#Sim 2599 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TC 2647 chrXptel1M 54806 TATTTCTACCTGTCTATCTTCCTATCTCTGTATCTGTCTCGCTCTCTCAC 54855 v i vi v v ii v v v v v v (TCTCTC)n#Sim 2648 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 2697 chrXptel1M 54856 TCTGTCTTGCATTGTCTCTTTACCTCTGTCTCTGTATCTCTTTTACTCAG 54905 v iv vi v i vi v v v i iv vv (TCTCTC)n#Sim 2698 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 2747 chrXptel1M 54906 TCTGTCTCTCTGTCTCCGTGTTTCTGTCTCCGTGTGTCTGTCTCTCTGTG 54955 v v iv v i v iv v v v v v (TCTCTC)n#Sim 2748 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 2797 chrXptel1M 54956 TGTCTATGTGTGTGTATGTATGTCTCTCTTGATTTATCTCTTTGTGTCTC 55005 v v v v v v v v v v ivv i v i v v (TCTCTC)n#Sim 2798 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 2847 chrXptel1M 55006 T-TTTTTATATTTCTATCTCACTCTCAGTCTCTTTCTCTCTTTTTCTCTC 55054 - i i v v i v v vv i i i (TCTCTC)n#Sim 2848 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 2897 chrXptel1M 55055 TGTCTCTCTCTGAATGGCTGTGTCTCCTTCTCTGTCTCTCTGTCTTTCTA 55104 v vvv vv v v ii v v i v (TCTCTC)n#Sim 2898 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 2947 chrXptel1M 55105 TATCTCTGTCTCTCTCGTTCTCTTTCTCTTTTTCTCTGCCTCTATTTTTG 55154 v v vi i i i vi v i i v (TCTCTC)n#Sim 2948 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 2997 chrXptel1M 55155 TCTCTCCTTGTTTCTGTTTGTCTTTATGTCTCTTGCTCTGTCTCTGTCTC 55204 ii v i v i v i v v iv v v (TCTCTC)n#Sim 2998 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 3047 chrXptel1M 55205 AAAGTGTCT-TCATCTCTTGATTTCCATCTCCCTGTCTCT-TTTTTCTCT 55252 vvvv v - - ivv i iv i v - i i (TCTCTC)n#Sim 3048 TCTCTCTCTCTC-TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 3096 chrXptel1M 55253 CTCTCATTCTCTGTCTTTCTTGCTCTTTTGTTCT-TTTTTCTCTGTGTCT 55301 vi v i iv i ivi - i i v v (TCTCTC)n#Sim 3097 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 3146 chrXptel1M 55302 GTCT 55305 v (TCTCTC)n#Sim 3147 CTCT 3150 Matrix = Unknown Transitions / transversions = 0.74 (158/213) Gap_init rate = 0.01 (18 / 1392), avg. gap size = 1.00 (18 / 18) 55 0.00 0.00 0.00 chrXptel1M 55314 55360 (944640) (TC)n#Simple_repeat 1 47 (0) c_b326s251i6 13692 chrXptel1M 55314 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 55360 (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 47 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 14 13.19 2.86 2.86 chrXptel1M 55896 55930 (944070) (GTAT)n#Simple_repeat 1 35 (0) m_b326s252i7 13693 chrXptel1M 55896 GTCTGTATTTATGTATGTTATGTA-ATATGTATTTA 55930 v v - -i v (GTAT)n#Simpl 1 GTATGTATGTATGTATG-TATGTATGTATGTATGTA 35 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 698 28.62 5.98 1.14 chrXptel1M 55953 56203 (943797) C MIRc#SINE/MIR (2) 266 4 m_b326s601i9 13694 chrXptel1M 55953 TAATAACTAATGC-TAACAGCTAGATGGCACTTTCAGGTTTTCAGAGTAC 56001 - i? - v vi iv i vvi v i ii C MIRc#SINE/MIR 266 TAATAA-TAACNCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCGC 218 chrXptel1M 56002 TT-CACATG--TTAGCTACCATAATTCTTCCAATAATCTTGTGAGGCAGG 56048 - i-- v vviv i i iv i i i i C MIRc#SINE/MIR 217 TTTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGG 168 chrXptel1M 56049 T---GC---TGTAATTATCTCCATTTTTTAAAATGAGGAAACTGAAGCTA 56092 i--- --- i v i vi i - i v C MIRc#SINE/MIR 167 CAGGGCAGGTATTATTATCCCCATTTTACAGA-TGAGGAAACTGAGGCTC 119 chrXptel1M 56093 ACAAGGGGTAAAGTGACTTGCCTATGACTATACAGATACATAGTGTCTGA 56142 -i i v i v iii i v vvv v v C MIRc#SINE/MIR 118 A-GAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGA 70 chrXptel1M 56143 GGCAGAATTTAAACCCAGGTCTCCCTCACTAAAGGTGCAG----CATTTC 56188 v i i i ii i v vv i v ---- v i C MIRc#SINE/MIR 69 GCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCC 20 chrXptel1M 56189 AGT-CACTATGATGCC 56203 v - i iiv C MIRc#SINE/MIR 19 ACTGCACCACACTGCC 4 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.06 CpG sites = 41, Kimura (unadjusted) = 37.16 Transitions / transversions = 1.37 (41/30) Gap_init rate = 0.04 (10 / 250), avg. gap size = 1.80 (18 / 10) 222 23.92 2.70 9.62 chrXptel1M 57231 57341 (942659) C L2b_3end#LINE/L2 (296) 170 67 m_b326s601i10 13695 chrXptel1M 57231 TGAGGAGAAGGCATTATAGGTGTGGGGAACAACTGGTAAAAAG---TTGA 57277 i - i i vi iivi i v? iv ---i C L2b_3end#LINE 170 TGGGGA-AGGGCGTTCCAGGCAGAGGGAACAGCANGTGCAAAGGCCCTGA 122 chrXptel1M 57278 GGAATCAGGAGATGGCGGTGGTGGATGGTGTTGGAGGAACAGGAAGGAGC 57327 --- i ?vi ?- i ----- v v v C L2b_3end#LINE 121 GG---CGGGAGNGAGCN-TGGCG-----TGTTCGAGGAACAGCAAGGAGG 81 chrXptel1M 57328 TCAGCATGGCTGGA 57341 i ii C L2b_3end#LINE 80 CCAGTGTGGCTGGA 67 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.23 CpG sites = 16, Kimura (unadjusted) = 30.68 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.10 (11 / 110), avg. gap size = 1.18 (13 / 11) 998 34.15 6.80 2.53 chrXptel1M 57476 58196 (941804) C L2#LINE/L2 (195) 2887 2137 m_b326s601i11 13695 chrXptel1M 57476 ACTTTATATTTCATCTCGAAGGTTATAGGGCTCTATTGAAGTTTATTAAA 57525 ivv i iiii iv vv i ivv i i vv v i i C L2#LINE/L2 2887 ACTTTGGCTTTTACTCTGAGTGAGATGGGAAGCCATTGGAGGGTTTTGAG 2838 chrXptel1M 57526 CAGAGAGGTGACATGGTCAGAC----------GATAGATGATGTTGACAG 57565 ii i v ----------i vi v ivi i v C L2#LINE/L2 2837 CAGAGGAGTGACATGATCTGACTTACGTTTTAAAAGGATCACTCTGGCTG 2788 chrXptel1M 57566 CTGAGTGGAAGATGGCCTG-------GCAAC--TTGAGGCAGGGAGACAA 57606 v v ii i v ------- v-- v i v C L2#LINE/L2 2787 CTGTGTTGAGAATAGACTGNAGGGGGGCAAGGGTGGAAGCAGGGAGACCA 2738 chrXptel1M 57607 ACCAGAAATCTCTTGCAATAGTCCAGGC-------TATGGGGGCTTGGAC 57649 iii i iv v i i -------v v C L2#LINE/L2 2737 GTTAGGAGGCTATTGCAGTAATCCAGGCGAGAGATGATGGTGGCTTGGAC 2688 chrXptel1M 57650 CAGGGTGGTTCCTGTAGGGAT-TCGAGAAGGGG--GAATAAATAATAAAT 57696 vv v i i i -vi v -- i vvvvi -- C L2#LINE/L2 2687 CAGGGTGGTGGCAGTGGAGGTGGTGAGAAGTGGTCGGATTCTGGAT--AT 2640 chrXptel1M 57697 GTTGTGAAGGTACAAAAGATGAGACTTGGCAACAGATCGGATTGTGAG-- 57744 i v v ivv iii i vii ii i - i -- C L2#LINE/L2 2639 ATTTTGAAGGTAGAGCCGACAGGATTTGCTGATGGATTGGA-TGTGGGGT 2591 chrXptel1M 57745 GCAAGTATAAATGAGGAGTCAAGGATGGTAGCAAGGTTTTAAGCTAATGT 57794 ii viv iv iivv vi i-- v C L2#LINE/L2 2590 GTGAGAGAAAGAGAGGAGTCAAGGATGACTCCAAGGTTTTTGGCC--TGA 2543 chrXptel1M 57795 GGAGTGGGAAGAA-GGTGACATCCTTGAAAGAAATAGGGAAG--TTCAGA 57841 v iiv i - v viii v ? vv i i -- v i i C L2#LINE/L2 2542 GCAACTGGAAGGATGGAGTTGCCATTNACTGAGATGGGGAAGACTGCGGG 2493 chrXptel1M 57842 AGAAGGGGGAATTAAGAGCAAAAATAATGAATTTGCTTTTGAACATGTTA 57891 i vi -v i i vi i v v i iiv i C L2#LINE/L2 2492 AGGAGCAGG-TTTGAGGGGGAAGATCAGGAGTTCAGTTTTGGACATGTTA 2444 chrXptel1M 57892 AAATTGAGATGTCTAGGGGGCATCAAATTCAGGATGTCTAATGGACAATT 57941 iv i vvi i v v vii v i i i i C L2#LINE/L2 2443 AGTTTGAGATGCCTATTAGACATCCAAGTGGAGATGTCGAGTAGGCAGTT 2394 chrXptel1M 57942 GGAAGTGAAAGACTGGAGGACAACCAACAGCTTAGGGCTTG-GATGAAAA 57990 vi ivi v vv ivvi v v iv v - iv C L2#LINE/L2 2393 GGATATACGAGTCTGGAGTTCAGGGGAGAGGTCCGGGCTGGAGATATAAA 2344 chrXptel1M 57991 GGTTTTTTTGGGACT-ATCTGCACAGAGACAATACTGGGA-TCATGGAAG 58038 ------ v - v i v iii i vii -i ii v C L2#LINE/L2 2343 ------TTTGGGAGTCATCAGCATATAGATGGTATTTAAAGCCATGAGAC 2300 chrXptel1M 58039 CTGATAAGGATCTCCAAGTGAGATAATTT------AGAGGAAATGAGATA 58082 iv i - v ? v vv i v ------ i i v i v C L2#LINE/L2 2299 TGGATGA-GATCACCNAGGGAGTGAGTGTAGATAGAGAAGAGAAGAGGTC 2251 chrXptel1M 58083 CCAAGAGAGACCCCTAAGGTACACTAGTAGTTACATGTAG-TGTCTGGAG 58131 v i vv v ii i v i ------ i v? -v v ii C L2#LINE/L2 2250 CAAGGACTGAGCCCTGGGGCACTCCA------ACGTTNAGAGGTCGGGGA 2207 chrXptel1M 58132 GATCTG--GGGACCAGCCTTGATCTCAGTGAAGGGGTG--CAG-GAGGCA 58176 vv -- i vvv ivvv v v i i -- - i C L2#LINE/L2 2206 GATGAGGAGGAACCAGCAAAGGAGACTGAGAAGGAGCGGCCAGTGAGGTA 2157 chrXptel1M 58177 GGAGAGACACCAGGAAGATG 58196 ii v iii C L2#LINE/L2 2156 GGAGGAAAACCAGGAGAGTG 2137 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 46.00 CpG sites = 129, Kimura (unadjusted) = 47.08 Transitions / transversions = 1.16 (129/111) Gap_init rate = 0.05 (36 / 720), avg. gap size = 1.89 (68 / 36) 360 29.89 6.91 9.24 chrXptel1M 58459 58834 (941166) C L2#LINE/L2 (879) 2203 1836 m_b326s601i12 13695 chrXptel1M 58459 GAGGAAGATGAAGCAAAGAAGGCT---AAGGAGTGGTCCAATAAA-TAGG 58504 i vvv i i --- i - i i i- C L2#LINE/L2 2203 GAGGAGGAACCAGCAAAGGAGACTGAGAAGGAGCGG-CCAGTGAGGTAGG 2155 chrXptel1M 58505 ATAAAAATGAGGAGAGAGGAGTGTCATTAAAAACCT-GTGGAGGACAGTG 58553 vi iv v vi -i ii i v- i i - C L2#LINE/L2 2154 AGGAAAACCAGGAGAGTGTGGTGTC-CTGGAAGCCAAGTGAAGAA-AGTG 2107 chrXptel1M 58554 TACATAGGAGAGGAGGGCTCGTGGTTAGACAGTGGGTTAGAAATGGAATT 58603 vi-i i - ------------- -------- v- i C L2#LINE/L2 2106 TTT-CAAGA-AGGAGGG-------------AGTG--------ATC-AACT 2081 chrXptel1M 58604 AGGGTGTTGAAAGCCAAAGAGAGGCCAAAAGAGATGAGGACTGAAAAAAA 58653 --- ii v iivv ? i ivi i vv- C L2#LINE/L2 2080 ---GTGTCAAATGCTGCTGANAGGTCAAGTAAGATGAGGACTGAGAATT- 2035 chrXptel1M 58654 GTCCATT--ATTT-TCGAAGTAA---TTATTGGTGACTTTGGAGAAAGCA 58697 v -- -v i v ii--- i i ivi i C L2#LINE/L2 2034 GACCATTGGATTTAGCAACGTGGAGGTCATTGGTGACCTTGACAAGAGCA 1985 chrXptel1M 58698 GATTCAATTGAATGATGATGA------TTTGATTGGATGATGGATGC-AG 58740 v ii v i i iv ------ii --i i v - C L2#LINE/L2 1984 GTTTCGGTGGAGTGGTGGGGACGAAAGCCTGATTGGA--GTGGGTTCAAG 1937 chrXptel1M 58741 AGAGTTTAGAAGGAAAGGA-----AGATAGTG---GTAAACCACTTTCTG 58782 vv i i i ----- i i ---i i v i i v C L2#LINE/L2 1936 AGAGAATGGGAGGAGAGGAATTGGAGACAGCGAGTATAGACAACTCTTTC 1887 chrXptel1M 58783 AAGGAGTTTATCTGCAAGATCTAAGAGAGACATAAGATGATCAGGTGAGG 58832 i vv i iivvv iv v ii ii i - v ii C L2#LINE/L2 1886 GAGGAGTTTTGCTGTAAAGGGGAGCAGAGAAATGGGGCGGT-AGCTGGAG 1838 chrXptel1M 58833 GG 58834 C L2#LINE/L2 1837 GG 1836 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.32 CpG sites = 66, Kimura (unadjusted) = 39.86 Transitions / transversions = 1.83 (66/36) Gap_init rate = 0.12 (44 / 375), avg. gap size = 1.36 (60 / 44) 120 12.40 1.04 0.00 chrXptel1M 58927 59119 (940881) (AGAG)n#Simple_repeat 1 195 (0) m_b326s252i8 13696 chrXptel1M 58927 AGAGAG-GGGGGAG-GAGGGAGGGAGGGAGACAAGGAAAGAGACAGAGAC 58974 - i i - i i i v ii i v v (AGAG)n#Simpl 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chrXptel1M 58975 AATGACAGAGAGAGAGACAGAGAGAGACAAAGAGAGAGAGAGAGAGAGAG 59024 iv v v v i (AGAG)n#Simpl 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 100 chrXptel1M 59025 AGACAGAGAGAGACAGAGAGAAAGAGAGAGAGAGACAGAGAGAGAGAGAC 59074 v v i v v (AGAG)n#Simpl 101 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 150 chrXptel1M 59075 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 59119 (AGAG)n#Simpl 151 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 195 Matrix = Unknown Transitions / transversions = 1.00 (11/11) Gap_init rate = 0.01 (2 / 192), avg. gap size = 1.00 (2 / 2) 41 33.82 1.23 0.00 chrXptel1M 58953 59115 (940885) (AGACAA)n#Simple_repeat 1 165 (0) m_b326s252i9 13697 chrXptel1M 58953 AGACAAGGAAAGAGACAGAGACAATGACAGAGAGAGAGAC--AGAGAGAG 59000 i v i i v i v i -- v i (AGACAA)n#Sim 1 AGACAAAGACAAAGACAAAGACAAAGACAAAGACAAAGACAAAGACAAAG 50 chrXptel1M 59001 ACAAAGAGAGAGAGAGAGAGAGAGAGACAGAGAGAGACAGAGAGAAAGAG 59050 v i v i v i v v v i i v v (AGACAA)n#Sim 51 ACAAAGACAAAGACAAAGACAAAGACAAAGACAAAGACAAAGACAAAGAC 100 chrXptel1M 59051 AGAGAGAGACAGAGAGAGAGAGACAGAGAGAGAGAGAGAGAGAGAGAGAG 59100 i v i v v i v i i v i v i v i v i (AGACAA)n#Sim 101 AAAGACAAAGACAAAGACAAAGACAAAGACAAAGACAAAGACAAAGACAA 150 chrXptel1M 59101 AGAGAGAGAGAGAGA 59115 v i v i (AGACAA)n#Sim 151 AGACAAAGACAAAGA 165 Matrix = Unknown Transitions / transversions = 1.00 (22/22) Gap_init rate = 0.01 (1 / 162), avg. gap size = 2.00 (2 / 1) 223 39.93 0.45 5.66 chrXptel1M 60103 60325 (939675) C L2#LINE/L2 (1713) 1369 1158 m_b326s601i13 13695 chrXptel1M 60103 TGCCTTGCTTCAGTGAGGGCCCAATTGATATTATTCAACATAAGCTTGAA 60152 vv vv v i v vi ?v viv i ii i C L2#LINE/L2 1369 TGCCGGGCAGCATTAAGGGCCCACTTGAGGTTNGTGGTCATGAATTTAAA 1320 chrXptel1M 60153 GTCGAAGTACT-GGCATATTTTTTGTGACTCCCCCTAGTTCTATTCAGCA 60201 vii vi v -i i-v v vi ii i i iivii v C L2#LINE/L2 1319 GTGAGACCAGTCAGCATG-GTTGTGTGTTTTTCTCCAGCCACGTTCAGCT 1271 chrXptel1M 60202 CCATATGGCCAAGAACAAAGTGAGCAGCTGATGGGAGTTGTTCAAGGCTG 60251 v ?iiv vv i vi ii ii i vvii v v ivi i i C L2#LINE/L2 1270 GCNCGGGTGCAGGCGCGGAGTAGGCGGAGAGTTGGATTTAACCAGGGTTG 1221 chrXptel1M 60252 GGCAAGGTCTTGAGCGAGGCATGTGGGATGGGCAAGTGAGATAAGTGGGC 60301 ----? i -- v iv iv i --- i -i - C L2#LINE/L2 1220 ----NGGTTTT--GCCAGGCGAGTACGACG---AAGCGAGA-GAG-GGGC 1182 chrXptel1M 60302 AAAATGTTTTAGTATAGAAACAAG 60325 iiviv v vi v vi C L2#LINE/L2 1181 AAGGGAGTTGAGGGTATATGCAAG 1158 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 51.89 CpG sites = 47, Kimura (unadjusted) = 60.68 Transitions / transversions = 1.27 (47/37) Gap_init rate = 0.06 (13 / 222), avg. gap size = 1.00 (13 / 13) 557 33.13 9.23 2.11 chrXptel1M 60587 61030 (938970) L2#LINE/L2 1911 2385 (697) m_b326s601i14 13698 chrXptel1M 60587 CTTCACTTCTTC--CTCTCAATCTTTTC---ATTCTTTTTGATCTGGTAT 60631 i v i -- i v i ii--- ii vi iii v iv L2#LINE/L2 1911 CTCCAATTCCTCTCCTCCCATTCTCTCTTGAACCCACTCCAATCAGGCTT 1960 chrXptel1M 60632 TTGGCCTCATCATTTCAGTTAAACTG-----GTC----TCTCCAGAGAC- 60671 i v i i i i viv ----- ---- v iv - L2#LINE/L2 1961 TCGTCCCCACCACTCCACCGAAACTGCTCTTGTCAAGGTCACCAATGACC 2010 chrXptel1M 60672 -------------ATCCAATGGCTTTTTCTGAATCTTCATTCTCCTTGAC 60708 ------------- iivv v i i ii v L2#LINE/L2 2011 TCCACGTTGCTAAATCCAATGGTCAATTCTCAGTCCTCATCTTACTTGAC 2060 chrXptel1M 60709 CTCCCTGTAGGTTTTGACCCTGACAAGCACCCTATTTTCCCTGATACTCT 60758 ?i v i vv v v vii v i iv ii i i v v L2#LINE/L2 2061 CTNTCAGCAGCATTTGACACAGTTGATCACTCCCTCCTTCTTGAAACACT 2110 chrXptel1M 60759 CTTCTCCCTAGGTTTTCCTGGCACTACTCTCTCCTGGTTCTCCTCTGAT- 60807 i ii v v i i vv i i v i iv i- L2#LINE/L2 2111 TTCTTCACTTGGCTTCCAGGACACCACACTCTCCTGGTTTTCCTCCTACC 2160 chrXptel1M 60808 ---CTAACAGCTCCTTCTAAGTTCCCTGTGCTGATTCTACCTCCAAGGCT 60854 --- ii v v ii v i iv ---iv L2#LINE/L2 2161 TCACTGGCCGCTCCTTCTCAGTCTCCTTTGCTGGTTCCTCCTC---ATCT 2207 chrXptel1M 60855 CCACCATACCCAGTAGTTACAGGGGTCTACCAAAGGCTCCA-CCTTGAGC 60903 v v ivi i?ivv --- i vi- v i vi- ii L2#LINE/L2 2208 CCCCGACCTCTNAACGTT---GGAGTGC-CCCAGGGCTCAGTCCTTGGAC 2253 chrXptel1M 60904 CCACTTCCTCTCCTAGGTATTTTTTTTTGTTGTGGTGATCAAATCAATGT 60953 ivi ii iii vv ivi ivi ivi -? vv v - L2#LINE/L2 2254 CTCTTCTCTTCTCTATCTACACTCACTCCCT-NGGTGATCTCATCCA-GT 2301 chrXptel1M 60954 C-CATGGATTCAATGATCATCTCTACGCTGATGACCCCCAAGTCTG---C 60999 - v i vv i v i i i i i--- L2#LINE/L2 2302 CTCATGGCTTTAAATACCATCTATATGCTGATGACTCCCAAATTTATATC 2351 chrXptel1M 61000 T-TATCCC--ACCTTTCTCCTG-ACTCGAGAGCTC 61030 -i v -- i i - v - L2#LINE/L2 2352 TCCAGCCCGGACCTCTCCCCTGAACTCCAGA-CTC 2385 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.09 CpG sites = 86, Kimura (unadjusted) = 45.98 Transitions / transversions = 1.48 (86/58) Gap_init rate = 0.05 (24 / 443), avg. gap size = 2.12 (51 / 24) 246 15.25 0.00 0.00 chrXptel1M 62017 62075 (937925) C HSAT5v1#Satellite (618) 5280 5222 m_b326s502i1 13699 chrXptel1M 62017 ACACACACACACACACACACACACACACATACATGCACGCACGCGCGCGC 62066 i i i ii? i i i i C HSAT5v1#Satel 5280 ACACACGCGCACACACGCGTNCACACACACACACGCGCGCACGCGCGTGC 5231 chrXptel1M 62067 ACACACACA 62075 C HSAT5v1#Satel 5230 ACACACACA 5222 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 6.63 CpG sites = 9, Kimura (unadjusted) = 18.58 Transitions / transversions = 1.00 (9/0) Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.0 (0 / 0) 476 22.68 3.31 1.63 chrXptel1M 62177 62297 (937703) MIRc#SINE/MIR 26 148 (120) m_b326s601i15 13700 chrXptel1M 62177 AGTGCAGGGCCTG-AGTCAGGAGGACCTGAGTTCAAATCTGCCCTCAGAT 62225 ii v i i - i i i i ivvv v vi MIRc#SINE/MIR 26 AGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCC 75 chrXptel1M 62226 ACTTCCTACCTGTGTGACCCTGGAAAACTCACTT--CCTC-CTGATTGCC 62272 v v i iv v -- - -- MIRc#SINE/MIR 76 ACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGA--GCC 123 chrXptel1M 62273 TTAGTTTCCTTTTCTGTATAATGAG 62297 i iv v i MIRc#SINE/MIR 124 TCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.24 CpG sites = 15, Kimura (unadjusted) = 27.40 Transitions / transversions = 1.25 (15/12) Gap_init rate = 0.04 (5 / 120), avg. gap size = 1.20 (6 / 5) 20 8.88 0.00 5.26 chrXptel1M 63001 63040 (936960) (GGAG)n#Simple_repeat 1 38 (0) m_b326s252i10 13701 chrXptel1M 63001 GGAGGGGCGGGGGTGGAGGGAGGGAGGGAGGAAGGGAGGG 63040 - v i - i (GGAG)n#Simpl 1 GGA-GGGAGGGAG-GGAGGGAGGGAGGGAGGGAGGGAGGG 38 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 12 4.77 4.55 0.00 chrXptel1M 63138 63159 (936841) (AAAG)n#Simple_repeat 1 23 (0) m_b326s252i11 13702 chrXptel1M 63138 AAAAAAAGAAA-AAAGAAAGAAA 63159 i - (AAAG)n#Simpl 1 AAAGAAAGAAAGAAAGAAAGAAA 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.05 (1 / 21), avg. gap size = 1.00 (1 / 1) 247 16.22 0.00 0.00 chrXptel1M 63207 63243 (936757) C MIR3#SINE/MIR (59) 149 113 m_b326s601i16 13703 chrXptel1M 63207 CCCCTTCATTCTACAGATGAGGAAACTAAGTTTCAGA 63243 i i i vii C MIR3#SINE/MIR 149 CCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGA 113 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 19.03 CpG sites = 5, Kimura (unadjusted) = 19.03 Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 210 34.40 11.38 0.74 chrXptel1M 63210 63332 (936668) C MIRc#SINE/MIR (119) 149 14 m_b326s601i17 13704 chrXptel1M 63210 CTTCATTCTACAGATGAGGAAACTAAGTTTCAGACA-------CAACACA 63252 ii i i vi v -------ii vii C MIRc#SINE/MIR 149 CCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTG 100 chrXptel1M 63253 CACATATACACACAG-----AAATAGCAGAACTAAGAGTGAACCCCAAAT 63297 v vivv ----- i i i iii v vi v ii C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGT 50 chrXptel1M 63298 ATT--TGAAATCTAAACCAAATATTCCTTCTACAACA 63332 v -- - v i ii v i ii i i vi C MIRc#SINE/MIR 49 CTTCCTG-ACTCCAAGTCCAGTGCTCTTTCCACTGCA 14 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.63 CpG sites = 28, Kimura (unadjusted) = 49.16 Transitions / transversions = 2.00 (28/14) Gap_init rate = 0.03 (4 / 122), avg. gap size = 3.75 (15 / 4) 53 5.36 0.00 0.00 chrXptel1M 63431 63489 (936511) (CT)n#Simple_repeat 1 59 (0) c_b326s251i7 13705 chrXptel1M 63431 CTCTCTCTCTCTCTCTCTCTCTCTCTCTTTCTCTCTCTCTCTCTCTCCCT 63480 i i (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chrXptel1M 63481 CTCCCTCTC 63489 i (CT)n#Simple_ 51 CTCTCTCTC 59 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.0 (0 / 0) 13 21.75 0.00 2.63 chrXptel1M 63490 63528 (936472) (CCTCTC)n#Simple_repeat 1 38 (0) m_b326s252i12 13706 chrXptel1M 63490 CCTTTCAGTCTCCTTCTCTCTGTCACTCTCCCTCCTCCC 63528 i vv i i v v - (CCTCTC)n#Sim 1 CCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCT-CTCCC 38 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.03 (1 / 38), avg. gap size = 1.00 (1 / 1) 285 25.82 3.09 4.17 chrXptel1M 63538 63634 (936366) MIR3#SINE/MIR 110 205 (3) m_b326s601i18 13707 chrXptel1M 63538 CTCTCTCTGCCT--GCT-CTTCACCTGTCAAAGGATGTGGTTGAGTGAAA 63584 vv -- i - i i v v v v iiiv i MIR3#SINE/MIR 110 CTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGA 159 chrXptel1M 63585 TGAGCTCTAAGATCCCTTCCATCTTGGATGATCTTATGGGCCTTCTGTGA 63634 v i v iv i- ii i--- i MIR3#SINE/MIR 160 TGATCTCTAAGGTCCCTTCCAGCTCTGAC-ATTCTATGA---TTCTATGA 205 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.32 CpG sites = 14, Kimura (unadjusted) = 32.32 Transitions / transversions = 1.40 (14/10) Gap_init rate = 0.06 (6 / 96), avg. gap size = 1.17 (7 / 6) 285 32.18 12.82 2.80 chrXptel1M 63705 63899 (936101) C L2b_3end#LINE/L2 (13) 453 240 m_b326s601i19 13708 chrXptel1M 63705 ACAAAT--TTATTAAGCGCTTAATATGTTCTAAGCTGTGTGCTAAGTGCT 63752 -- i i i v i v i i ?v i i C L2b_3end#LINE 453 ACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCT 404 chrXptel1M 63753 GGGAATACAAATTCATGTAAA-AAGGAAGACA-------TTCCTTCAATG 63794 i i--- i- i - iv ?------- v i vv C L2b_3end#LINE 403 GGGGATACAG---CG-GTGAACAAGACAGACNCGGTCCCTGCCCTCACGG 358 chrXptel1M 63795 TGTTTAAATTTGAATGGGGTCAATA-ATACATAAAAAAAGAA-------- 63835 v i i v v iv i vvi i - i ii ?v i v -------- C L2b_3end#LINE 357 AGCTCACAGTCTAGTGGGGGAGACAGACATGTAANCAGACAATNATAACC 308 chrXptel1M 63836 CTGAGAAGCAAGGAAG---TGGTGGGGCGCA---ATGGGTACCCTGCTGG 63879 v vi i v --- v v ---iv ii ivi iv C L2b_3end#LINE 307 CAGAGTGGCAGGGTAGGACTGGGGGGGCCCAGAGGAGGGCGCCTGACCCG 258 chrXptel1M 63880 GCCTTGGTAAAATCCAGGAG 63899 v --iii vi C L2b_3end#LINE 257 GCCTGGG--GGGTCAGGGAG 240 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.63 CpG sites = 36, Kimura (unadjusted) = 44.68 Transitions / transversions = 1.44 (36/25) Gap_init rate = 0.07 (13 / 194), avg. gap size = 2.38 (31 / 13) 397 33.05 0.85 0.00 chrXptel1M 64616 64733 (935267) MIRc#SINE/MIR 11 129 (139) m_b326s601i20 13709 chrXptel1M 64616 TGGGGCAGCT-AAATAGTGATGTGCCTAGCATCGGGAAGATCCAAGTTCA 64664 v iv- v iiv vi i i vi i i iii i MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chrXptel1M 64665 AGTCTAGCCTCAAACATATACTAGCTATGTAATCCTGGGCCAGTCACTTC 64714 iv v viv iv i i i i v v MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTA 110 chrXptel1M 64715 ACTGCTCTTTGCCTTAATT 64733 iv vv i i MIRc#SINE/MIR 111 ACCTCTCTGAGCCTCAGTT 129 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.59 CpG sites = 23, Kimura (unadjusted) = 45.18 Transitions / transversions = 1.44 (23/16) Gap_init rate = 0.01 (1 / 117), avg. gap size = 1.00 (1 / 1) 13 14.73 3.33 0.00 chrXptel1M 64882 64911 (935089) (CCTC)n#Simple_repeat 1 31 (0) m_b326s252i13 13710 chrXptel1M 64882 CCTCCCTCCCTTCC-CCCTACACCCCTCCCT 64911 i - v vi (CCTC)n#Simpl 1 CCTCCCTCCCTCCCTCCCTCCCTCCCTCCCT 31 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 332 31.14 5.59 3.74 chrXptel1M 65130 65576 (934424) L1M5_orf2#LINE/L1 2840 3294 (0) m_b326s551i1 13711 chrXptel1M 65130 TGAATCCATTGATCCACACTTAACACCGTACACCAAGATAAGGTCAAAAT 65179 ? -- i i vi i v i v i v iv ? i L1M5_orf2#LIN 2840 TGAANC--TCGACCCCTACCTCACACCATACACAAAAATTAATTCNAGAT 2887 chrXptel1M 65180 GGGTTCAT-GACCTAGGCATAAAGAATGAAATTATTAATAAATTAGAGGA 65228 i - - iiii ii? i i v vvvvi i L1M5_orf2#LIN 2888 GGAT-CATAGACCTAAATGTAAAAGNTAAAACTATAAAACTTCTAGAAGA 2936 chrXptel1M 65229 A--CACAGGATAGTTTACCTCTCAGACCTGTGGAAGGGGAAGGACTTTAT 65276 -- i v i -- i iivv vv ?vi v i i iv L1M5_orf2#LIN 2937 AAACATAGGAGAAT--ATCTTCGTGACCTTGGGNTAGGCAAAGATTTCTT 2984 chrXptel1M 65277 GACCAAAGCAGAAC-TAGAGATCATTATTGATCACAAAATAGAAAATT-- 65323 ----- i i -i i i v i? --- i i v i -- L1M5_orf2#LIN 2985 -----AAACAGGACACAAAAAGCACNA---ACCATAAAAGAAAAAATTGA 3026 chrXptel1M 65324 -----TCGATTATACCAAACTGAAAAGTTTTTGTACAAACAAAACTAATG 65368 ----- v i ?i i v v ii i iv ?vvv ivi vi L1M5_orf2#LIN 3027 TAAATTGGACTNCATCAAAATTAAAAACTTCTGCTCNTCAAAAGACACCG 3076 chrXptel1M 65369 CAGACAAGATTAGAAGGGAAGCAATAAACTGGGAAAATATTTTTACAGTC 65418 ivi v i v i v v i i ? i v v i i?- L1M5_orf2#LIN 3077 TTAAGAAAATGAAAAGGCAAGCCACAGANTGGGAGAAAATATTTGCAAN- 3125 chrXptel1M 65419 AAAGGT-TCTGATAAAGGCCTCATTTCCAAAATATATAGAGAATTAACTC 65467 v vi - i v i v i i i -v v L1M5_orf2#LIN 3126 ACATATATCTGACAAAGGACTCGTATCCAGAATATATAAAGAACT-CCTA 3174 chrXptel1M 65468 TAATTT-ATAAAAAATCAAGCCATTC--TCCAAT----------TCAAAG 65504 i ? i- ? -- v vv --i ----------v i L1M5_orf2#LIN 3175 CAANTCAATAANAAA--AAGACAAACAACCCAATANAAAAATGGGCAAAA 3222 chrXptel1M 65505 GATATAAACAGACAATTCTCAGATGAAGAAATTGGAACTATTTCTAGTCA 65554 iv i v v i v v ?vi iviiivv iv L1M5_orf2#LIN 3223 GACTTGAACAGACACTTCACAAAAGAAGATATNCAAATGGCCAATAAGCA 3272 chrXptel1M 65555 TATGAAAAGATGCTCCAAGTCA 65576 i v v? L1M5_orf2#LIN 3273 CATGAAAAGATGCTCAACNTCA 3294 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.46 CpG sites = 76, Kimura (unadjusted) = 43.17 Transitions / transversions = 1.31 (76/58) Gap_init rate = 0.06 (25 / 446), avg. gap size = 1.68 (42 / 25) 1040 27.55 5.16 3.99 chrXptel1M 65443 66062 (933938) L1MC4_3end#LINE/L1 7 633 (2156) m_b326s551i3 13711 chrXptel1M 65443 TCCAAAATATATAGAGAA---TTAACTCTAATTTATAAAAAATCAAGCCA 65489 i i --- vv v viv v i v L1MC4_3end#LI 7 TCCAGAATATATAAAGAACTCTTAAAACTCAACAATAAAAAAACAAACAA 56 chrXptel1M 65490 TTCTCCAATT----------CAAAGGATATAAACAGACAATTCTCAGATG 65529 i--- ---------- i v i v v vi v L1MC4_3end#LI 57 C---CCAATTAAAAAATGGGCAAAAGATTTGAACAGACATTTCACCAAAG 103 chrXptel1M 65530 AAGAAAT-----TGG-AACTATTTCTAGTCATATGAAAAGATGCTCCAAG 65573 v ----- - v ----- - i v vi L1MC4_3end#LI 104 AAGATATACAGATGGCAAATA-----AG-CACATGAAAAGATGCTCAACA 147 chrXptel1M 65574 TCATTATTAGTCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTA 65623 ?v vi i i i v vv i L1MC4_3end#LI 148 TCATTNGTCATTAGGGAAATGCAAATTAAAACCACAATGAGATACCACTA 197 chrXptel1M 65624 CACACCTGTCAGATTGGCTAAGATGACAGGAAAA--AATAATCATGAGTG 65671 i i v i -- ii ? --i i vvii i L1MC4_3end#LI 198 CACACCTATTAGAATGGCTAAAAT--CAAAAANACTGACAATACCAAATG 245 chrXptel1M 65672 TTGGAGGGGATGCGGGAAAACTGGGACATTGATGCATTGTTGGTGGAGTT 65721 i v i i iiv ? i vi v i i iiv L1MC4_3end#LI 246 CTGGCGAGGATGTGGAGCAACNGGAACTCTCATACATTGCTGGTGGGAAT 295 chrXptel1M 65722 GTGAACGAATCCAACCATTTTGGAGAGTAGTTTGGAACTATGCTCAAAAA 65771 ii vvii v i i i ii v v - v i ? L1MC4_3end#LI 296 GCAAAATGGTACAGCCACTTTGGAAAACAGTTTGGCAGT-TTCTTANAAA 344 chrXptel1M 65772 GTTATCAAACTGTGCA--TACCCTTTGATCCAGCAGTGTTACTACTGGGC 65819 i --- -i i -- v v i i v?i v i i L1MC4_3end#LI 345 GCT---AAAC-ATACANTTACCATATGACCCAGCAATCNCACTCCTAGGT 390 chrXptel1M 65820 TTATATCCCAAAGAGATCATAAAGAAGG----GAAAGGGACCTGTATGTG 65865 v v i v i? i? v v v?v v ----v v iii ---- L1MC4_3end#LI 391 ATTTACCCAAGNGAANTGAAAACNTATGTCCACACAAAAACCTGTA---- 436 chrXptel1M 65866 CACGAATGTTTGTGGCAGCCCTTTTTGTAGTGGCTGGAAACTGGAAACTG 65915 i i ii v ii i ? iii ? vi L1MC4_3end#LI 437 CACGAATGTTTATAGCAGCTTTATTCATAATNGCCAAAANCTGGAAACAA 486 chrXptel1M 65916 AATGGATATCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATATGAA 65965 vv?i i v iiv v v i i i i vv L1MC4_3end#LI 487 CCNAGATGTCCTTCAACAGGTGAATGGATAAACAAACTGTGGTACATCCA 536 chrXptel1M 65966 TATTATGGAATATTATTGTTTGGT---AAGAAATGACCCACAGGATGATT 66012 iv i i vvvi i --- i v i ---- ? L1MC4_3end#LI 537 TACAATGGAATACTACTCAGCGATAAAAAGGAATGAACTAC----TGATN 582 chrXptel1M 66013 T-CAGAAAGACCTGGA-GAGACTTACACGAACTGATGCTGAGTGAAATGA 66060 i- iv ?i v - iv v i v - ?v i vi L1MC4_3end#LI 583 CACGCAANAACATGGATGAATCTTAAATGCA-TNTTGCTAAGTGAAAGAA 631 chrXptel1M 66061 GC 66062 L1MC4_3end#LI 632 GC 633 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.65 CpG sites = 93, Kimura (unadjusted) = 36.21 Transitions / transversions = 1.31 (93/71) Gap_init rate = 0.06 (35 / 619), avg. gap size = 1.63 (57 / 35) 1343 28.05 3.34 2.77 chrXptel1M 65443 65981 (934019) L1ME3Cz_3end#LINE/L1 7 548 (449) m_b326s551i2 13711 chrXptel1M 65443 TCCAAAATATATAGAGAATTAACTCTAATTTATAAAAAATCAAGCCATTC 65492 i i i vviv v iv i -- v --v L1ME3Cz_3end# 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAA--AAGACA--A 52 chrXptel1M 65493 TCCAAT----------TCAAAGGATATAAACAGACAATTCTCAGATGAAG 65532 i ----------v i i v v i L1ME3Cz_3end# 53 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chrXptel1M 65533 AAATTGGAACTATTTCTAGTCATATGAAAAGATGCTCCAAGTCATTATTA 65582 iiv iviiivv iv v vv i v L1ME3Cz_3end# 103 AAACCCGAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTA 152 chrXptel1M 65583 GTCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACACCTGT 65632 i i i ? vv i i v ii L1ME3Cz_3end# 153 ATCAGGGAAATGCAAATTAAAACNACAATGAGATACCATTTCACACCCAT 202 chrXptel1M 65633 CAGATTGGCTAAGATGACAGGAAAAA----ATAATCATGAGTGTTGGAGG 65678 v i v----v i---- i vvii v i L1ME3Cz_3end# 203 CAGATTGGCAAAAATT----TAAAAGTCTGACAATACCAAGTGTTGGCGA 248 chrXptel1M 65679 GGATGCGGGAAAACTGGGACATTGATGCATTGTTGGTGGAGTTGTGAACG 65728 i ii v i vi v i i i iiv i iv L1ME3Cz_3end# 249 GGATGTGGAGAAACGGGAACTCTCATACACTGCTGGTGGGAGTGTAAATT 298 chrXptel1M 65729 AATCCAACCATTTTGGAGAGTAGTTTGGAACTATGCTCAAAAAGTTATCA 65778 ii v i i i v v - viv i-- L1ME3Cz_3end# 299 GGTACAACCACTTTGGAGAGCAATTTGGCAATAT-CTAGTAAAGTTG--A 345 chrXptel1M 65779 AACTGTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGCTTATATCCC 65828 iv i vi i i vii v i iv i i L1ME3Cz_3end# 346 AGATGCGCATACCCTACGACCCAGCAATTCCACTTCTAGGTATATACCCT 395 chrXptel1M 65829 AAAGAGA---TCATAAAGAAGGGAAAGG-GACCTGTATGTGCACGAATGT 65874 i i --- ii v viv viv - ---- i v i L1ME3Cz_3end# 396 AGAGAAACTCTCGCACATGTGCACAAGGAGAC----ATGTACAAGGATGT 441 chrXptel1M 65875 TTGTGGCAGCCCTTTTTGTAGTGGCTGGAAACTGGAAACTGAATGGATAT 65924 ii v vi v i i vii i vivv ii i L1ME3Cz_3end# 442 TCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGT 491 chrXptel1M 65925 CCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATATGAATATTATGGA 65974 i v i v i vv iv L1ME3Cz_3end# 492 CCATCAATAGGGGAATGGATAAATAAATTGTGGTATATTCATACAATGGA 541 chrXptel1M 65975 ATATTAT 65981 i L1ME3Cz_3end# 542 ATACTAT 548 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.20 CpG sites = 86, Kimura (unadjusted) = 36.13 Transitions / transversions = 1.41 (86/61) Gap_init rate = 0.04 (19 / 538), avg. gap size = 1.74 (33 / 19) 280 30.79 0.00 2.56 chrXptel1M 66704 66823 (933177) C L1MC5_3end#LINE/L1 (2129) 565 449 m_b326s551i4 13712 chrXptel1M 66704 TTCTTACAGAACAATAATATTCCATAATATTCATATACCACAATTTATTC 66753 i vvvv i i vi i vv i i i C L1MC5_3end#LI 565 TTTTTACAGCTGCATAGTACTCCATTGTGTGGATGTACCATAGTTTATTC 516 chrXptel1M 66754 AGCCATTCTCCAACTGATGGGCATCCATTCAGTTTCCAGGTCCTTGCCAC 66803 i v i v i i iiivviv viii i i C L1MC5_3end#LI 515 AACCAGTCCCCTATTGATGGACATTTGGGTTGTTTCCAGTCTTTTGCTAT 466 chrXptel1M 66804 TACAAAAACAAGTGCTACAA 66823 ---v i C L1MC5_3end#LI 465 TACAAA---TAGTGCTGCAA 449 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.07 CpG sites = 22, Kimura (unadjusted) = 41.07 Transitions / transversions = 1.57 (22/14) Gap_init rate = 0.03 (3 / 119), avg. gap size = 1.00 (3 / 3) 349 24.05 0.00 2.88 chrXptel1M 66717 66823 (933177) C L1ME3G_3end#LINE/L1 (376) 548 445 m_b326s551i5 13712 chrXptel1M 66717 ATAATATTCCATAATATTCATATACCACAATTTATTCAGCCATTCTCCAA 66766 i i vv i i i i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chrXptel1M 66767 CTGATGGGCATCCATTCAGTTTCCAGGTCCTTGCCACTACAAAAACAAGT 66816 i i ii vviv iv ii i i i -- - C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTAC--AAACAA-T 452 chrXptel1M 66817 GCTACAA 66823 i C L1ME3G_3end#L 451 GCTGCAA 445 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 28.84 CpG sites = 18, Kimura (unadjusted) = 30.29 Transitions / transversions = 2.57 (18/7) Gap_init rate = 0.03 (3 / 106), avg. gap size = 1.00 (3 / 3) 199 27.78 1.85 0.00 chrXptel1M 66967 67020 (932980) MIRc#SINE/MIR 7 61 (207) m_b326s601i21 13713 chrXptel1M 66967 AGTATTATGTATTAGAAAGAAAGGTGGATCTGGAGACA-GAAGACCTGAG 67015 i vi i v i iviv ii v - i MIRc#SINE/MIR 7 AGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGG 56 chrXptel1M 67016 TTCAA 67020 i MIRc#SINE/MIR 57 TTCGA 61 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.19 CpG sites = 10, Kimura (unadjusted) = 36.20 Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.02 (1 / 53), avg. gap size = 1.00 (1 / 1) 30 0.00 0.00 0.00 chrXptel1M 67389 67414 (932586) (AC)n#Simple_repeat 1 26 (0) c_b326s251i8 13714 chrXptel1M 67389 ACACACACACACACACACACACACAC 67414 (AC)n#Simple_ 1 ACACACACACACACACACACACACAC 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 512 32.10 3.20 2.79 chrXptel1M 68505 68754 (931246) L2#LINE/L2 1270 1520 (1562) m_b326s601i22 13715 chrXptel1M 68505 CAACTGTAGCCTGGAACTTGAGAAATTCAGAAACCCACGCTGACTGGGCC 68554 i - i v -- v vv v v v i v i L2#LINE/L2 1270 CAGCTG-AACGTGG--CTGGAGAAAAACACACAACCATGCTGACTGGTCT 1316 chrXptel1M 68555 CACTCCATTTTTAT-ATTACATAATCTCAACTGAGCCTTCAGTGC---AT 68600 ii vv i - ii ?- i v i i i i ---vi L2#LINE/L2 1317 CACTTTAAATTCATGACCACN-AACCTCAAGTGGGCCCTTAATGCTGCCC 1365 chrXptel1M 68601 GGCAATCCTTTTAAACATTTCTGATGGATTCATTCTCCCACTCACTATAG 68650 ? vi v iv ii ii vv i v i- L2#LINE/L2 1366 GGCAATCNTACTACATTTCCCTAGTCCATTCACTCTCCCACTCTCC-TAG 1414 chrXptel1M 68651 CTGA-TACTCCAAATCCTTTTACCCCTCTTCAAATCTCACAAGGCTCCCT 68699 vi - i i v i i i ivi i i i - vi ii L2#LINE/L2 1415 ACGACTATTTCACACCTTCTCCTCTCTCCTCAAACCTC-CAACACCTCCT 1463 chrXptel1M 68700 CTTCTGACAATGGTCT--ACTGA-GACTCTTGCCTCGGATTTTATTGGGG 68746 ii iv vviiv --i - - i vv i i i i L2#LINE/L2 1464 CCCCTATCCTCACTCTCAGCTGATGAC-CTTGCTTCCTATTTCACTGAGA 1512 chrXptel1M 68747 AAAAAAAA 68754 v i L2#LINE/L2 1513 AAATAGAA 1520 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.76 CpG sites = 49, Kimura (unadjusted) = 44.31 Transitions / transversions = 1.69 (49/29) Gap_init rate = 0.05 (12 / 249), avg. gap size = 1.25 (15 / 12) 463 27.87 9.29 0.00 chrXptel1M 72324 72506 (927494) MIRc#SINE/MIR 34 233 (35) m_b326s601i23 13716 chrXptel1M 72324 ACATGGA-TCAAAAAAACCCGAGTTCAAA---CA--TCAGAAATTTACTA 72367 v - ii i i i i i--- i-- v vv i MIRc#SINE/MIR 34 ACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTA 83 chrXptel1M 72368 ACTGTATGACATTTAGCAAGGC-TGTCACCTCTATTTACTTCAGTTCCCT 72416 i i v vi v -iv v v vvi i i MIRc#SINE/MIR 84 GCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCT 133 chrXptel1M 72417 AATCTGCAAAA--GTGATAATTGTAGTTAG--TACCCACCTCCCAGGGTA 72462 v i -- v vi vi iv-- i i v v MIRc#SINE/MIR 134 CATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTT 183 chrXptel1M 72463 GTAGTGAGAATTATATGAT----TGTA-AAGTAAGCACTATGT-AACTGT 72506 v i i v v---- -iv v i v - MIRc#SINE/MIR 184 GTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTTTGTAAACTGT 233 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.80 CpG sites = 26, Kimura (unadjusted) = 35.28 Transitions / transversions = 1.04 (26/25) Gap_init rate = 0.05 (9 / 182), avg. gap size = 1.89 (17 / 9) 40 4.88 0.00 0.00 chrXptel1M 74025 74067 (925933) (TG)n#Simple_repeat 1 43 (0) c_b326s251i9 13717 chrXptel1M 74025 TGTGTATGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 74067 i i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 43 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 442 34.26 1.57 3.74 chrXptel1M 74943 75133 (924867) L1ME5_3end#LINE/L1 366 552 (389) m_b327s551i0 13718 chrXptel1M 74943 TGAACCAGCAGTGTTTCTACTGGACCTGTATCCCAAATAGATCTTAAAGC 74992 v i viiv v iiv i v i ii v vi L1ME5_3end#LI 366 TGACCCAGCAATTCCGCTCCTGGGTATATATCCCAAAGAAATTCTCACAC 415 chrXptel1M 74993 AGG---GAAAGGGACCCACATGTACAAGAATGTTTGTGGCAGCCCTTTTT 75039 ---iv i--- i i ii v v---- L1ME5_3end#LI 416 AGGTCCATAAGGGG---ACATGTACGAGGATGTTCATTGCAGCG----TT 458 chrXptel1M 75040 TTTCATAGTGGCAAGAAACTGGAAACTGAGTGGATGCCCATCAGTTGGGG 75089 v ii i ii i ii ii vivv i i v v i L1ME5_3end#LI 459 GTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGGGTGTCCATCACTGGGAG 508 chrXptel1M 75090 AATGGATGAATAAGTTATGGTATATGAATGTTATGGAATATTAT 75133 i iii iv i iv v iiii i i L1ME5_3end#LI 509 AGTGGATAGGTAAAATGTGGTGGATGCACACCATGGAGTACTAT 552 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 45.69 CpG sites = 43, Kimura (unadjusted) = 49.04 Transitions / transversions = 2.15 (43/20) Gap_init rate = 0.04 (8 / 190), avg. gap size = 1.25 (10 / 8) 230 33.85 0.68 4.20 chrXptel1M 75006 75153 (924847) L1PA4_3end#LINE/L1 429 571 (331) m_b327s551i1 13718 chrXptel1M 75006 CACATGTACAAGAATGTTTGTGGCAGCCCTTTTTTTTCATAGTGGCAAGA 75055 i v v i v i v v ---- i i i - L1PA4_3end#LI 429 CACATGCACACGTATGTTTATTGCGGCACTATT----CACAATAGCAA-A 473 chrXptel1M 75056 AACTGGAAACTGAGT-GGATGCCCATCAGTTGGGGAATGGATGAATAAGT 75104 i v i ii vi-ii i v i vivi v v v iv L1PA4_3end#LI 474 GACTTGGAACCAACCCAAATGTCCAACAATGATAGACTGGATTAAGAAAA 523 chrXptel1M 75105 TATGGTATATGAATGTTATGGAATATTATTGTTCTATAAGAAACTGATG 75153 i i i iv iiii i vvvv i i - L1PA4_3end#LI 524 TGTGGCACATATACACCATGGAATACTATGCAGCCATAAAAAA-TGATG 571 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 45.49 CpG sites = 29, Kimura (unadjusted) = 46.86 Transitions / transversions = 1.53 (29/19) Gap_init rate = 0.05 (7 / 147), avg. gap size = 1.00 (7 / 7) 478 25.23 0.00 3.25 chrXptel1M 75007 75133 (924867) L1ME3F_3end#LINE/L1 430 552 (438) m_b327s551i2 13718 chrXptel1M 75007 ACATGTACAAGAATGTTTGTGGCAGCCCTTTTTTTTCATAGTGGCAAGAA 75056 ii i v v ---- i i i i L1ME3F_3end#L 430 ACATGTACAAGAATGTTCATAGCAGCACTGTT----CGTAATAGCAAAAA 475 chrXptel1M 75057 ACTGGAAACTGAGTGGATGCCCATCAGTTGGGGAATGGATGAATAAGTTA 75106 vivviii i iiiv i i i i L1ME3F_3end#L 476 ACTGGAAACAACCCAAATGTCCATCGACAGGAGAATGGATAAATAAATTG 525 chrXptel1M 75107 TGGTATATGAATGTTATGGAATATTAT 75133 vv iiiv L1ME3F_3end#L 526 TGGTATATTCACACAATGGAATATTAT 552 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 29.63 CpG sites = 22, Kimura (unadjusted) = 32.14 Transitions / transversions = 2.44 (22/9) Gap_init rate = 0.03 (4 / 126), avg. gap size = 1.00 (4 / 4) 1295 30.89 1.83 3.53 chrXptel1M 75366 75912 (924088) C L1ME5_3end#LINE/L1 (397) 544 7 m_b327s551i3 13719 chrXptel1M 75366 CCATAACATTCACATACCACAACTTATTCAGCCATTCTCCAATTAATGGG 75415 iiii v ivi vi iii v i v v i i C L1ME5_3end#LI 544 CCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCAGTGATGGA 495 chrXptel1M 75416 CATCCACTCAGTTTCCAGTTTCTGGCCACTACAAAGAGAGCTGCCACAAA 75465 i vviv ii ii i iv i v iv v ii C L1ME5_3end#LI 494 CACCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCTGCAATGAA 445 chrXptel1M 75466 CATTTTTGCACCAAGTCCCTTTC----CCTTCATTAGTATCTCTTTGGAA 75511 ii i i - v i v---- vii v v i i C L1ME5_3end#LI 444 CATCCTCGTAC-ATGTCCCCTTATGGACCTGTGTGAGAATTTCTTTGGGA 396 chrXptel1M 75512 TACAAGCCCACTGCTTAACACTGCTGGATCAAAGGATATGCACAGTTTGA 75561 i vi v- vviiiv i i v i --- --- C L1ME5_3end#LI 395 TATATACCCAG-GAGCGGAATTGCTGGGTCATAGGGTATGC---GT---A 353 chrXptel1M 75562 TAACTT--TTTGGGCA--TAATTCCAGATTGCTCTCCAGAATGGTTGGAT 75607 - -- ivi -- v v i v i C L1ME5_3end#LI 352 TA-CTTAATTTGACTAAGTACTGCCAGATTGCTCTCCAGAATGGCTGCAC 304 chrXptel1M 75608 CCATTCATAACTCCACCAACAATGCATCAATGTCCCAGTTTTCCTGCATC 75657 vi ii i vii i i v iv i vi ? i ii C L1ME5_3end#LI 303 CAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATC 254 chrXptel1M 75658 CCCTCCAACATTCATCATTATGTTTTTTTCTGTCATCTTAGCCAATCTGA 75707 i v i iiv vivvi i-- i v i i C L1ME5_3end#LI 253 CTCGCCAACACTTGGCATTATCCAGCTTTCTA--ATTTTTGCCAGTCTAA 206 chrXptel1M 75708 CAGGTGTGTAGTGGTATCTCAGAATTGTCTTAATTTGCATTTCTCTGATC 75757 i iv i vvi i i C L1ME5_3end#LI 205 TAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATTTCTCTGATT 156 chrXptel1M 75758 AATAATGATTTGGAACACTCTTTCATATGAGTGGAAATGGTTTCAATTTC 75807 v v v i iiii vv vv iivv ivii C L1ME5_3end#LI 155 ACTAATGAGTTTGAGCATCTCTTCATATGCTTGTTAGCCTTTCGGGTTTC 106 chrXptel1M 75808 ATCATCTGAAAATTGTCTGACCATTATCATATCCTTTGACCATTTATCAA 75857 v v v i ---- -- v v v C L1ME5_3end#LI 105 CTCTTCTGTAAATTGCCTG----T--TCATATCCTTTGCCCATTTTTCTA 62 chrXptel1M 75858 TTGGAG--AATGGCTTGATTTCTTATAAATTAGAGTCAATTCTCTATATA 75905 i --?vi v -- i vi v vivv i ii i C L1ME5_3end#LI 61 TTGGGGTTNCCGTCTT--TTTCTTGTTGATTTGCAGGAGTTCCTTGTATA 14 chrXptel1M 75906 TTTTGGA 75912 i i C L1ME5_3end#LI 13 TTCTAGA 7 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 40.00 CpG sites = 98, Kimura (unadjusted) = 41.38 Transitions / transversions = 1.51 (98/65) Gap_init rate = 0.04 (23 / 546), avg. gap size = 1.26 (29 / 23) 3612 30.02 2.69 2.32 chrXptel1M 75763 77655 (922345) C L1M5_orf2#LINE/L1 (0) 3294 1395 m_b327s551i4 13719 chrXptel1M 75763 TGATTTGGAACACTCTTTCATATG---AGTGGAAATGGTTTCAATTTCAT 75809 ?v v i iii i --- v vv --- v? v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCAT---TTGNATATCTT 3248 chrXptel1M 75810 CATCTGAAAATTGTCTGACCATTATCATATCCTTTGACCATTTATCAATT 75859 v i vi v ----- - vi i v v ?v C L1M5_orf2#LIN 3247 CTTTTGTGAAGTGTCTG-----T-TCAAGTCTTTTGCCCATTTTTNTATT 3204 chrXptel1M 75860 GGA--GAATGGCTTGATTTCTTAT-AAATTAGAGTCAATTCTCTATATAT 75906 i-- vv v -- ? -i ? iv -v i i C L1M5_orf2#LIN 3203 GGGTTGTTTGTCTT--TTTNTTATTGANTTGTAG-GAGTTCTTTATATAT 3157 chrXptel1M 75907 TTTGGAAATGAGGCCTTTATCAGA---ACCTTTCACCATAAAAATGTTTT 75953 i v i v i --- iv ? ii --- v v i C L1M5_orf2#LIN 3156 TCTGGATACGAGTCCTTTGTCAGATATATGTNTTGC---AAATATTTTCT 3110 chrXptel1M 75954 CCCAGTTTATTGCTCCCCTTCTAATCTTGTTTGCATTAGTTTTGTTTGTA 76003 ? i i v iv i v i v vi iv ivi vvv? vi C L1M5_orf2#LIN 3109 CCCANTCTGTGGCTTGCCTTTTCATTTTCTTAACGGTGTCTTTTGANGAG 3060 chrXptel1M 76004 CAAAGGCTTTTAAATTTGATGTAATCAAAATTGTGTATTTTGTGACCAAT 76053 i i i v ? i v v i vv v --- vv C L1M5_orf2#LIN 3059 CAGAAGTTTTTAATTTTGATGNAGTCCAATTTATCAATTTTTT---CTTT 3013 chrXptel1M 76054 AATGATCTCTAGTTCTTCTTTGGTC-------ACAAATTCCTTCCTCCTC 76096 v i --- ? v i vv ------- v iii v v?i C L1M5_orf2#LIN 3012 TATGGT---TNGTGCTTTTTGTGTCCTGTTTAAGAAATCTTTGCCTANCC 2966 chrXptel1M 76097 CACAAGTCTGAGAGGTAAACTATCCTATGTT--CCTCTAATTTATTTATA 76144 - i vvii i --i v -- i ivvvv C L1M5_orf2#LIN 2965 CA-AGGTCACGAAGATA--TTCTCCTATGTTTTCTTCTAGAAGTTTTATA 2919 chrXptel1M 76145 ATCTTGTTCTTTATGCCTAAATC-ATGGACCCATTTTGATCTTATCTTGG 76193 i i i?ii iiii ii - - i i ? vi v i v C L1M5_orf2#LIN 2918 GTTTTANCTTTTACATTTAGGTCTATG-ATCCATCTNGAATTAATTTTTG 2870 chrXptel1M 76194 TAAATGGCATTAAGTGTGGGTCCATGTCTAGTTTCTGCCATACTAATTTC 76243 iv ii v i iv v v? ii v i v ivi v C L1M5_orf2#LIN 2869 TGTATGGTGTGAGGTAGGGGTCGAGNTTCATTTTTTTCCATATGGATATC 2820 chrXptel1M 76244 CAGTTTTCCCAGCAGTTTTTGTCAAATA-ATGATTTTTTATCCCCAAAGT 76292 i v i viv ii v - iv ii vi v vi i C L1M5_orf2#LIN 2819 CAATTGTTCCAGCACCATTTGTTGAAAAGACTATCCTTTCCCCACTGAAT 2770 chrXptel1M 76293 TGGGATCTTTGAG---TTTGTCAAACATTGGATTGCTATAGTTATC---G 76336 ---- ? iv--- v iii? v? i vv i v--- C L1M5_orf2#LIN 2769 TG----CNTTGGCACCTTTGTCAAAAATCAANTGNCCATATATGTGTGGG 2724 chrXptel1M 76337 CCTATTT--------TGTAACCTATTCCACTGATCAACTAATCTATTTCT 76378 i -------- v vi i i v i vi i- C L1M5_orf2#LIN 2723 TCTATTTCTGGACTCTCTATTCTGTTCCATTGATCTATTTGTCTATC-CT 2675 chrXptel1M 76379 TA-GCCAATACCAAATGGTTTTGGTGATTGTTGCTTTATAATATAGTTTT 76427 - v iv i i v i v - i C L1M5_orf2#LIN 2674 TACGCCAATACCACACTGTCTTGATTACTGTAGCTTTATAATA-AGTCTT 2626 chrXptel1M 76428 G-GATCAGGTA---CAACTAGACCACCTTCATTTGATTTTTTTTCATTAA 76473 -? ? ---i v vvv v ii i-- i -- i C L1M5_orf2#LIN 2625 GANATCNGGTAGTGTAAGTCCTCCAACTTTGTTC--TTCTTTTTCA--AG 2580 chrXptel1M 76474 TTCCCTTTAA--ATTCTCGACCTTTTGTTCTTCCATATGAGTTTTGTTGT 76521 v ivi ii-- ? ii i ivi i i ivvi C L1M5_orf2#LIN 2579 ATTGTTTTGGCTATTCTNGGTCCTTTGCATTTCCATATAAATTTTAGAAT 2530 chrXptel1M 76522 TATTTTTCCAGGTCAT-TAAAATATTTTCTTTGAAGTCTGATTGGTATAG 76570 i vi vi iv iv -i v vii vi v i v i v v C L1M5_orf2#LIN 2529 CAGCTTGTCAATTTCTACAAAAAAACCTGCTGGGATTTTGATTGGGATTG 2480 chrXptel1M 76571 TACTAAATAAATAGATTGGTTTAGGGAATATTGTCATCTTTATTATATTC 76620 i i i vv iii i iv v ? iv v C L1M5_orf2#LIN 2479 CATTGAATCTATAGATCAATTTGGGGAGAATTGACATCTTNACAATATTG 2430 chrXptel1M 76621 ACACGGCCTACCCAAGAGCACTTAATATTTTTCCAATTATTTAAATCTGA 76670 vv vv v i v i ivvv i i v ii vv C L1M5_orf2#LIN 2429 AGTCTTCCAATCCATGAACATGGTATATCTCTCCATTTATTTAGGTCTTC 2380 chrXptel1M 76671 CTTTATTTGTGTGGAAAGTGTTTTGTAATTTTGCTCACATAATTCCTGAC 76720 i v v v viiv i i vvviii ? iv i vv C L1M5_orf2#LIN 2379 TTTAATTTCTCTCAGCAATGTTTTGTAGTTTTCAGTGTANAGGTCTTGCA 2330 chrXptel1M 76721 TTTCCTTTGGTAGATAGATTCCCAAATATTTTATGCTATT-GACAGTTAT 76769 iv ?i v vv i i ? i v - i- i C L1M5_orf2#LIN 2329 CATNTTTTGTTAGATTTATTCCTAAGTATTTNATGTTTTTTGAT-GCTAT 2281 chrXptel1M 76770 TCTGAATGGAATTTCTCTTTGTATCTC---TTGCTGTTGGATTTTGTTGG 76816 v i v vi i ?iv i --- v vi --- v C L1M5_orf2#LIN 2280 TGTAAATGGTATTGTTTTTNAAATTTCATTTTCCAATTG---TTTGTTGC 2234 chrXptel1M 76817 TGATGTATAAAAATGCTGAGGATTTATGGGGATTTATTTTATAACCTGCA 76866 ii i i i vivv v viv v ii i v ? i C L1M5_orf2#LIN 2233 TAGTATATAGAAATACAATTGATTTTTGTATATTGACCTTGTATCCNGCG 2184 chrXptel1M 76867 ACTTTGCTAAAGTTGTGAATTATTTCTAATAGCTTTTTAGTAGAACCCCT 76916 i v iiivv v i i ? v vi ii C L1M5_orf2#LIN 2183 ACCTTGCTAAATTCACTTATTAGTTCTAGTAGTTTNTTTGTAGATTCTTT 2134 chrXptel1M 76917 GGGGTTCTCTAAGTATACCATCATATCATCTGCAAAGAGTGATAATTTGG 76966 ? i i v ? v i i v i? i i vi C L1M5_orf2#LIN 2133 NGGATTTTCTACGTANACAATCATGTCATCTGCGAATAANGACAGTTTTA 2084 chrXptel1M 76967 TTTCCTCATTACCTACTTTAATTCCTTT-ATT-CTCATTCTTGACTCTTA 77014 i v v v ii v v - - iv --i C L1M5_orf2#LIN 2083 TTTCTTCCTTTCCAATCTTTATGCCTTTTATTTCTTTTTCTTG--CCTTA 2036 chrXptel1M 77015 TTGCCTAGGCGAGTGTTTCTAATACAATACTGAGTAATCATGGTGATAGT 77064 viv v viii i i ii i ivvi ? i C L1M5_orf2#LIN 2035 TTGCACTGGCTAGGACCTCCAGTACAATGTTGAATAGAAGTGGTGANAGC 1986 chrXptel1M 77065 GGGCAACCTTGTTTCACTCCTGATCTTACTGGGAAAGGTTCCAGTTTATT 77114 i v i iii i vv v? i ? v i C L1M5_orf2#LIN 1985 GGACATCCTTGTCTTGTTCCCGATCTTAGGGGGAAAGCNTTCAGTNTTTC 1936 chrXptel1M 77115 CCCATTACATATGATGCTTACTGACGGTTGTAAATATATGCTCCTGACTA 77164 v vi i ?i vv v vvi v i i v ii C L1M5_orf2#LIN 1935 ACCATTAAGTATGATGTTNGCTGTAGGTTTTTCGTAGATGCCCTTTATCA 1886 chrXptel1M 77165 TTTTAAGGAAAAGCCCACTTATTCCTATACTCTCAAGTGTTTTTATTATG 77214 vv i ivv vii vvi viii v i C L1M5_orf2#LIN 1885 GGTTGAGGAAGTTCCCTTCTATTCCTAGTTTGCTGAGAGTTTTTATCATG 1836 chrXptel1M 77215 AATGGATATTGGATTTTATCAAATGCTTTTTCTGCACATATTGAGATGAT 77264 i i i i iv C L1M5_orf2#LIN 1835 AATGGGTGTTGAATTTTGTCAAATGCTTTTTCTGCATCTATTGAGATGAT 1786 chrXptel1M 77265 CATATGGTTTTTGTTAATTTGGT-TATTAATATGGCCAATTATACTGATA 77313 i v iv- iv - i iv i i v C L1M5_orf2#LIN 1785 CATATGATTTTTCTCC-TTTATTCTGTTAATATGGTGAATTACATTGATT 1737 chrXptel1M 77314 GTTATCCTAATATTGAACCAGCCCTGCATTCCTGGTATAAATCCTACTTG 77363 v v i v i i i i v i i C L1M5_orf2#LIN 1736 GATTTTCGAATGTTAAACCAACCTTGCATTCCTGGGATAAACCCCACTTG 1687 chrXptel1M 77364 GTCATAGTGTATTATCCTGGGGATGATTTTCTGTAATCTTTTTGCTAATA 77413 ii vvvv ivv v v v vv C L1M5_orf2#LIN 1686 GTCATGATGTATTATCCTTTTTATATATTGCTGGATTCGATTTGCTAATA 1637 chrXptel1M 77414 TTTTATTTAAGATTTTAGCATCAATATTCATTAGGGAGATTGGTCTATAA 77463 i ? i v v i v v i C L1M5_orf2#LIN 1636 TTTTGTTNAGGATTTTTGCATCTATGTTCATGAGGGATATTGGTCTGTAA 1587 chrXptel1M 77464 TTTTCTTTTTCTGT--TTTCAACCTATCTCTTTTAGGCATCAGTACCATG 77511 ii -- v --ii i ?vv v i vii? C L1M5_orf2#LIN 1586 TTTTCTTTTCTTGTAATGTC--TTTGTCNGGTTTTGGTATCAGGGTNATG 1539 chrXptel1M 77512 TCTGTGTCATAAAAAGAATTTGGTAGGGGGCCTTCATTCCCTATTTTTTC 77561 iiv iv v i v v v vv i v ii i v C L1M5_orf2#LIN 1538 CTGGCCTCATAAAATGAGTTGGGAAGTGTTCCCTCTTTTTCTATTTTCTG 1489 chrXptel1M 77562 AAATAGTTTATATAGCATTGGGGTTCATTGTTCTTTAAATGTTTGGTAGA 77611 i v i i iv vi vv v i C L1M5_orf2#LIN 1488 GAAGAGTTTGTGTAAGATTGGTATTATTTCTTCCTTAAATGTTTGGTAGA 1439 chrXptel1M 77612 ATTCACATATAAATCCATCTGGTCCTGGGGACTTTTTTTAGGGA 77655 vvi i v v i vi i vv C L1M5_orf2#LIN 1438 ATTCACCAGTGAAGCCATCTGGGCCTGGAGTTTTCTTTGTGGGA 1395 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 39.37 CpG sites = 295, Kimura (unadjusted) = 40.11 Transitions / transversions = 1.13 (295/260) Gap_init rate = 0.03 (66 / 1892), avg. gap size = 1.44 (95 / 66) 1405 29.53 1.29 1.66 chrXptel1M 77733 78276 (921724) C L1ME3G_3end#LINE/L1 (376) 548 7 m_b327s551i5 13720 chrXptel1M 77733 ATAATATTCCATAACATTCATATACCATAACTTATACAGCCATTCTCCAA 77782 i ii vv i vi i i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chrXptel1M 77783 CTAATGGGCATTCACTCACTTTCCACTTTCTAGACACTACAAAAAGGGCT 77832 i i i i vvivv v i v vi i v iv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chrXptel1M 77833 GCCACAAACATTTTTGCACATGTGGGTCCCTTTCC-CTCCTTTAAG-ATC 77880 v ii ii i i?-- i v v - viv vii - i C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATT 401 chrXptel1M 77881 TCTTTGGGATATAAGCCCAGTAGTAACACTGCTAGA-GAAAGAGTATGCA 77929 ? i v v? ? v iiv i i i-v i i C L1ME3G_3end#L 400 TCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCG 351 chrXptel1M 77930 CAGTTGGATAACTTTTGGGGCATAATTCCAGATTGCTCTCCAGAATGATT 77979 v --- v iiviv v v i i i ? ii C L1ME3G_3end#L 350 CATTT---TAAATTTTAATAGATACTGCCAAATTGCCCTCCAAAANGGCT 304 chrXptel1M 77980 GGATCCATTCACAGTTCTACCAACAATGTATCAGTGTCCCAGTTTTCCCA 78029 v i v i v i i i i v v v v i C L1ME3G_3end#L 303 GTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCA 254 chrXptel1M 78030 AATTCCCTCCAACATTTGTCATTATCTTTTCCTGTCATCTTAGCCAATCT 78079 v ii i v i ? vi vv?iii vvv i v C L1ME3G_3end#L 253 CACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATCT 204 chrXptel1M 78080 GACAGGTGTGTAGTGGTATCTCACAGTTGTCTTGATTTGCATTTCTCTAA 78129 ii viv i iv i i i i C L1ME3G_3end#L 203 GATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGA 154 chrXptel1M 78130 TCAAAAGTGATTTAGAGCACCTTTTCATGTGGCTACAAATAGTTTCAATT 78179 i vv vv v i i vi iviiivi vv C L1ME3G_3end#L 153 TTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGTATT 104 chrXptel1M 78180 TCTTCATCTGAAAAT----TGTTCATATCCTTTGGCCATTTATGAATTGG 78225 i v vi ---- v v vv C L1ME3G_3end#L 103 TCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGG 54 chrXptel1M 78226 AGAATGGTTTGATTTCTTATAAATTAGAGTCAATTCTCTATATATTTTGG 78275 iv-- vi -- vi v vivv i i i C L1ME3G_3end#L 53 GT--TGTCTT--TTTCTTATTGATTTGTAGGAGTTCTTTATATATTCTGG 8 chrXptel1M 78276 A 78276 C L1ME3G_3end#L 7 A 7 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 38.30 CpG sites = 86, Kimura (unadjusted) = 38.97 Transitions / transversions = 1.19 (86/72) Gap_init rate = 0.02 (13 / 543), avg. gap size = 1.23 (16 / 13) 343 26.97 5.58 4.00 chrXptel1M 78137 78333 (921667) C L1MC_orf2#LINE/L1 (0) 3294 3095 m_b327s551i6 13720 chrXptel1M 78137 TGATTTAGAGCACCTTTTCATGTGGCTACAAATAGTTTCAATTTCTTCAT 78186 v ? i i vi ivviivi i vv v - C L1MC_orf2#LIN 3294 TGATGTNGAGCATCTTTTCATATGCTTATTTGCCATCTGTATATCTTC-T 3246 chrXptel1M 78187 CTGA--AAAT---TGTTCATATCCTTTGGCCATTTATGAATTGGAGAATG 78231 i i-- ii --- vi i v v ? i i--- v C L1MC_orf2#LIN 3245 TTGGTGAGGTGTCTGTTCAGGTCTTTTGCCCATTTTTNAATCGGG---TT 3199 chrXptel1M 78232 GTTTGATTTCTTATAAATTAGAGTCAA---TTCTCTATATATTTTGGAAA 78278 v viv v vv i --- i i v C L1MC_orf2#LIN 3198 GTTTGTTTTCTTATTGTTGAGTTTTAAGAGTTCTTTGTATATTTTGGATA 3149 chrXptel1M 78279 ATGAGACCTTTATGAGA---ACCTTTGACTGTAAAAATGTTTTCCCAGTT 78325 i- v v ---ii --- i v v i i C L1MC_orf2#LIN 3148 AC-AGTCCTTTATCAGATATGTCTTT---TGCAAATATTTTCTCCCAGTC 3103 chrXptel1M 78326 TATTGCTT 78333 i v C L1MC_orf2#LIN 3102 TGTGGCTT 3095 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 33.58 CpG sites = 27, Kimura (unadjusted) = 34.40 Transitions / transversions = 1.12 (27/24) Gap_init rate = 0.06 (12 / 196), avg. gap size = 1.58 (19 / 12) 17 0.00 4.00 0.00 chrXptel1M 79047 79071 (920929) (AAAC)n#Simple_repeat 1 26 (0) m_b327s252i0 13721 chrXptel1M 79047 AAACAAACAAACAAACAAA-AAACAA 79071 - (AAAC)n#Simpl 1 AAACAAACAAACAAACAAACAAACAA 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 16 23.02 0.00 0.00 chrXptel1M 79753 79793 (920207) (TATA)n#Simple_repeat 1 41 (0) m_b327s252i1 13722 chrXptel1M 79753 TATATGTATGTACATAGCTACATATATATACATAAATATAT 79793 i i i vv i i v (TATA)n#Simpl 1 TATATATATATATATATATATATATATATATATATATATAT 41 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 38 0.00 8.77 1.64 chrXptel1M 80192 80248 (919752) (TTTTCA)n#Simple_repeat 1 61 (0) c_b327s251i1 13723 chrXptel1M 80192 TTTTCATTTTTCATTTTCATTTTCA-TTTCA-TTT--TTTTCATTTTCA- 80236 - - - -- - (TTTTCA)n#Sim 1 TTTTCA-TTTTCATTTTCATTTTCATTTTCATTTTCATTTTCATTTTCAT 49 chrXptel1M 80237 TTTCATTTTCAT 80248 (TTTTCA)n#Sim 50 TTTCATTTTCAT 61 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.09 (5 / 56), avg. gap size = 1.20 (6 / 5) 308 31.09 7.27 3.51 chrXptel1M 80935 81044 (918956) MIRb#SINE/MIR 5 118 (150) m_b327s601i0 13724 chrXptel1M 80935 GGGGCAATTAGATGGCACACTGGATAAAGTATTAGCTGTGGAATCAGGAA 80984 ii---i ii v v i i ivi v i iv MIRb#SINE/MIR 5 GGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACA 51 chrXptel1M 80985 GACTTGAATTCAAATACTACCTCAGACACAACACTTACTGTG-------- 81026 i ii i v iiv v v v-i vi -------- MIRb#SINE/MIR 52 GACCTGGGTTCGAATCCCGGCTCTGCCACT-TACTAGCTGTGTGACCTTG 100 chrXptel1M 81027 GGTAAGTTACTTAACTCC 81044 i ii MIRb#SINE/MIR 101 GGCAAGTTACTTAACCTC 118 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 35.45 CpG sites = 22, Kimura (unadjusted) = 42.40 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.05 (5 / 109), avg. gap size = 2.40 (12 / 5) 41 12.89 2.44 2.44 chrXptel1M 81057 81138 (918862) (AAAG)n#Simple_repeat 1 82 (0) m_b327s252i2 13725 chrXptel1M 81057 AAAAAAAGGAAGGAAGAAAGGAAAGAAAAAAGGAAAGAAGCAAAGAAAGA 81106 i i i - i i iv (AAAG)n#Simpl 1 AAAGAAAGAAAGAAAGAAA-GAAAGAAAGAAAGAAAGAAAGAAAGAAAGA 49 chrXptel1M 81107 AAGAAA-AAAGAAAAGAAA-AGAAAAAGAAAGAA 81138 - - - i i (AAAG)n#Simpl 50 AAGAAAGAAAG-AAAGAAAGAAAGAAAGAAAGAA 82 Matrix = Unknown Transitions / transversions = 8.00 (8/1) Gap_init rate = 0.05 (4 / 81), avg. gap size = 1.00 (4 / 4) 413 32.13 7.83 6.48 chrXptel1M 81139 81534 (918466) C L1MD1_3end#LINE/L1 (531) 458 58 m_b327s551i7 13726 chrXptel1M 81139 AGAGCTGCTATAAATACTTTTATACATATAGGTGCTTTTCTTT---TTTA 81185 i i i iv i ---- -- v v ---iv C L1MD1_3end#LI 458 AAAGCTGCTATAAACATTCGTGTACA----GGT--TTTTGTGTGAACATA 415 chrXptel1M 81186 AAATTTTATCCCGTTGGGATACAGATCTAATGGTACTATTTTTGGGTCAA 81235 iv i ii vi v vii i ivi i v vi iv C L1MD1_3end#LI 414 AGTTTTCATTTCTCTGGGATAAATGCCCAGGAGTGCAATTGCTGGGTCGT 365 chrXptel1M 81236 ATGGT---TGACCA-----AGTTCCTTGAGCATAGTTCCAAATTGTGCTC 81277 --- -- ----- ii i v - v v i vi C L1MD1_3end#LI 364 ATGGTAGTTG--CATGTTTAGTTTTTTAAGAA-ACTGCCAAACTGTTTTC 318 chrXptel1M 81278 TGGAATTGTCAGATCAGTTCACAATTCTATCAACAGTACATTA------- 81320 ii i v iiiv i v i v i i i i i ii v ------- C L1MD1_3end#LI 317 CAGAGTGGCTGTACCATTTTACATTCCCACCAGCAATGTATGAGTGATCC 268 chrXptel1M 81321 -------TCAAATCCACTCAAACAT--GACATTTTC-CTCTTTTTTATAT 81360 -------i iv v v v i -- iii v - v v C L1MD1_3end#LI 267 AGTTTCTCCGCATCCTCGCCAGCATTTGGTGTTGTCACTATTTTTTATTT 218 chrXptel1M 81361 TAGCCAACCTGATAGGTATGAGGTTACCATAAAGTCTACCACAACCTACA 81410 vi i vi v ---------- i v --i --- C L1MD1_3end#LI 217 TAGCCATTCTGATAGGTGTGTAGTGA----------TATCTCA--TT--- 183 chrXptel1M 81411 AGTTGGTTTAATTTACATTTCTCTAAGCAGTAGTAATTTAGAACATTTT- 81459 - v v i i vviv i i v v i - C L1MD1_3end#LI 182 -GTGGTTTTAATTTGCATTTCCCTAATGGCTAATGATGTTGAACATCTTT 134 chrXptel1M 81460 --ATATGACTATAAATAAACTTGATGTCTTCTTCTAAAAAAATGCCTCTT 81507 -- i vi vviiv v vv i i -iivi i C L1MD1_3end#LI 133 TCATGTGCTTATTTGCCATCTGTATATCCTCTTC-GGTGAAATGTCTCTT 85 chrXptel1M 81508 CATATCCTTTGACCATTTATCAATTGG 81534 i i v vii C L1MD1_3end#LI 84 CATGTCTTTTGCCCATTTTCTAATTGG 58 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 41.49 CpG sites = 70, Kimura (unadjusted) = 43.44 Transitions / transversions = 1.43 (70/49) Gap_init rate = 0.09 (34 / 395), avg. gap size = 1.68 (57 / 34) 397 30.35 7.64 5.97 chrXptel1M 81142 81586 (918414) C L1ME4c_3end#LINE/L1 (372) 458 7 m_b327s551i8 13726 chrXptel1M 81142 GCTGCTATAAATACTTTTATACATATAGGTGCTTTTCTTTTTTAAAATTT 81191 v i i ii ii i v -i i i vi v C L1ME4c_3end#L 458 GCTGCAATGAACATCTTCGTGCATATAGCT-TTTTCCTTCTTTTGAATTA 410 chrXptel1M 81192 TATCCCGTTGGGATACAGATCTAATGGTACTATTTTTGGGTCAAATGGT- 81240 v -- i v vvi i ivi ivv vi v - C L1ME4c_3end#L 409 TTTCC--TTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTA 362 chrXptel1M 81241 TGACCAAGTTC------CTTGA-GCATAGTTCCAAATTGTGCTCTGGAAT 81283 v vv i------ -i i v v ivi iii v C L1ME4c_3end#L 361 TGAACATTTTTATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAG 312 chrXptel1M 81284 TGTCAGATCAGTTCACAATTCTATCAACAGTACAT-----TATCAAATCC 81328 v iiv i i i ? v i i i i ii ----- i iv i C L1ME4c_3end#L 311 GGTTGTACCAATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTTTC 262 chrXptel1M 81329 ACT---------CAAACAT--GACATTTTCCTCTTTTTTA-TATTAGCCA 81366 i--------- v i -- ii v vvi v - v v i C L1ME4c_3end#L 261 ACCGCANCCTCGCCAGCATTGGGTATTATCAATTTTTTAAATTTTTGCTA 212 chrXptel1M 81367 ACCTGATAGGTATGAGGTTACCATAAAGTC-TACCACAACCTACAAGTTG 81415 ii i ----------- i i v- i v --i ---- C L1ME4c_3end#L 211 ATTTAATAGG-----------CGTAAAATGGTATCTCA--TT----GTTG 179 chrXptel1M 81416 GTTTAATTTACATTTCTCTAAGCAGTAGTAATTTAGAACATTTT---ATA 81462 v i i i vi v ii vv v --- i C L1ME4c_3end#L 178 CTTTAATTTGCATTTCTTTGATTACTAGCGAGGTTGAACATTTTTCCATG 129 chrXptel1M 81463 TGACTATAAATAAACTTGATGTCTTCTTCTAAAAAAATGCCTCTTCATAT 81512 vi i vv iv ?i vv v i ? ivi v- i v i C L1ME4c_3end#L 128 TGTTTGTTTACTANTTGTATTTCCTCTTNTGTGAAT-TGTCTGTTCATGT 80 chrXptel1M 81513 CCTTTGACCATTTATCAATTGGGGAACAACTTG----TATTCTTATAAA- 81557 v v ----v ---- v v - C L1ME4c_3end#L 79 CCTTTGCCCATTTATCTATTGGGG----TCTTGATNTTTTTCTTATCAAT 34 chrXptel1M 81558 TTGATTCAGTTCTCTTTATACATTTGAGA 81586 v v -- i ? v? C L1ME4c_3end#L 33 TTGAATGAG--CTCTTTATATANTANAGA 7 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 38.35 CpG sites = 70, Kimura (unadjusted) = 40.48 Transitions / transversions = 1.23 (70/57) Gap_init rate = 0.09 (38 / 444), avg. gap size = 1.61 (61 / 38) 475 29.34 7.85 5.97 chrXptel1M 81188 81582 (918418) C L1MA8_3end#LINE/L1 (626) 412 11 m_b327s551i9 13726 chrXptel1M 81188 ATTTTATCCCGTTGGGATACAGATCTAATGGTACTATTTTTGGGTCAAAT 81237 i ii v v i v i i i i ivv vi i v C L1MA8_3end#LI 412 ATTTCATTTCCTTTGGATATATACCCAGTAGTGGGATTGCTGGATCATAT 363 chrXptel1M 81238 GGTTGACC-A-----AGTTCCTTGAGCATAGTTCCAAATTGTGCTCTGGA 81281 v vi - ----- i ii v - vi v i vi iiv C L1MA8_3end#LI 362 GGTAGTTCTATTTTTAATTTTTTGAGGA-ACCTCCATACTGTTTTCCATA 314 chrXptel1M 81282 ATTGTCAGATCAGTTCACAATTCTATCAACAGTA--CA-----------T 81318 v iiiv ii i i v i i i i-- ----------- C L1MA8_3end#LI 313 ATGGCTGTACTAATTTACATTCCCACCAACAGTGTGCAAGGGTTCCCTTT 264 chrXptel1M 81319 TATCAA-ATCCACTCAAACA--TGACAT-TTTCCTCTTTTTTATATTAGC 81364 v v - v v v -- vi - v v v C L1MA8_3end#LI 263 TCTCCACATCCTCGCCAACACTTGTTATCTTTCGTCTTTTTGATAATAGC 214 chrXptel1M 81365 CAACCTGATAGGTATGAGGTTACCATAAAGTCTACCACAACCTACAAGTT 81414 vi i i i v ---------- i v --i ---- v C L1MA8_3end#LI 213 CATTCTAACAGGTGTGAGGTGA----------TATCTCA--TT----GTG 180 chrXptel1M 81415 GGTTTAATTTACATTTCTCTAAGCAGTAGTAATTTAGAACATTTT---AT 81461 v i i i vv v i v v i --- C L1MA8_3end#LI 179 GTTTTAATTTGCATTTCCCTGATGATTAGTGATGTTGAGCATTTTTTCAT 130 chrXptel1M 81462 ATGACTATAAATAAACTTG-ATGTCTTCTTCTAAAAAAATGCCTCTTCAT 81510 iv i viii-v i - i -i i i v v C L1MA8_3end#LI 129 ATACCTGTTGGC-CATTTGTATGTCTTCTTTT-GAGAAATGTCTATTCAG 82 chrXptel1M 81511 ATCCTTTGACCATTTATCAATTGGGGAACAACTTGTATTCTTA----TAA 81556 i v v ? i ---iv i v i---- i C L1MA8_3end#LI 81 GTCCTTTGCCCATTTTTNAATCGGG---TTATTTGTTTTCTTGCTATTGA 35 chrXptel1M 81557 ATTGATTCAGTTCTCTTTATACATTT 81582 i v v -- i i C L1MA8_3end#LI 34 GTTGTTTGAGT--TCCTTATATATTT 11 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 37.89 CpG sites = 62, Kimura (unadjusted) = 38.34 Transitions / transversions = 1.32 (62/47) Gap_init rate = 0.09 (34 / 394), avg. gap size = 1.62 (55 / 34) 490 26.56 8.46 7.27 chrXptel1M 81265 81536 (918464) C L1ME5_3end#LINE/L1 (611) 330 56 m_b327s551i10 13726 chrXptel1M 81265 CCAAATTGTGCTCTGGAATTGTCAGATCAGTTCACAATTCTATCAACAGT 81314 i iv ii v iiiv i ii v i i i i C L1ME5_3end#LI 330 CCAGATTGCTCTCCAGAATGGCTGCACCAGTCTACACTCCCACCAGCAGT 281 chrXptel1M 81315 ACAT---------TAT-----CAAATCCACTCAAACA--TGACATTTTCC 81348 i --------- ----- v v v v -- i v C L1ME5_3end#LI 280 GCATGAGGGTTCCTATNTCCCCACATCCTCGCCAACACTTGGCATTATCC 231 chrXptel1M 81349 -TCTTTTTTATATTAGCCAACCTGATAGGTATGAGGTTACCATAAAGTCT 81397 -v i v v v ii i i i i v ---------- C L1ME5_3end#LI 230 AGCTTTCTAATTTTTGCCAGTCTAATAGGTGTAAAGTGA----------T 191 chrXptel1M 81398 ACCACAACCTACAAGTTGGTTTAATTTACATTTCTCTAAGCAGTAGTAAT 81447 i v --i ---- v i i vi v i i v C L1ME5_3end#LI 190 ATCTCA--TT----GTTGTTTTAATTTGCATTTCTCTGATTACTAATGAG 147 chrXptel1M 81448 TTAGAACAT---TTTATATGACTATAAATAAACTT---GATGTCTTCTTC 81491 v i --- i vi i --- iv --- i v i C L1ME5_3end#LI 146 TTTGAGCATCTCTTCATATGCTTGT---TAGCCTTTCGGGTTTCCTCTTC 100 chrXptel1M 81492 TAAAAAAATGCCTCTTCATATCCTTTGACCATTTATCAATTGGGG 81536 iv v- v v v v C L1ME5_3end#LI 99 TGTAAAT-TGCCTGTTCATATCCTTTGCCCATTTTTCTATTGGGG 56 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 33.49 CpG sites = 38, Kimura (unadjusted) = 33.49 Transitions / transversions = 1.31 (38/29) Gap_init rate = 0.10 (26 / 271), avg. gap size = 1.65 (43 / 26) 289 28.01 4.62 5.51 chrXptel1M 81481 81718 (918282) C L1M2_orf2#LINE/L1 (40) 3251 3016 m_b327s551i11 13726 chrXptel1M 81481 ATGTCTTCTTCTAAAAAAATGCCTCTTCATATCCTTTGACCATTTATCAA 81530 i -i i i v vi v v ? C L1M2_orf2#LIN 3251 ATGTCTTCTTTT-GAGAAATGTCTATTCAGGTCCTTTGCCCATTTTTNAA 3203 chrXptel1M 81531 TTGGGGAACAACTTGTATTCTTA----TAAATTGATTCAGTTCTCTTTAT 81576 i --- iv i v i i---- i i v v -- i C L1M2_orf2#LIN 3202 TCGG---ATTATTTGTTTTTTTGCTGTTGAGTTGTTTGAGT--TCCTTAT 3158 chrXptel1M 81577 ACATTTGAGAAATAAGGACTTTATTAGA-GA--AACTTGCTGTATATCTT 81623 i ivi v v ivv i i i - ?-- ii -iv - C L1M2_orf2#LIN 3157 ATATTCTGGATATTAATCCCTTGTCAGATGNATAGTTTGC-AAATAT-TT 3110 chrXptel1M 81624 TCCCCCAGTTTTCT--GCTTTCCTTTTAATCTTGGCAGAATTGGTTTTGT 81671 i - i v -- i v ii i v -- iv - v iiv C L1M2_orf2#LIN 3109 TCTCCCA-TTCTGTAGGTTGTCTCTTCACTCT--GTTG-ATTGTTTCCTT 3064 chrXptel1M 81672 T--TGTGCAAAACCTTTTTTAATTTAATGTAATTAGAATCATCCATTTT 81718 -- i v - i i ivv v ii i C L1M2_orf2#LIN 3063 TGCTGTGCAGAAGC-TTTTTAGTTTGATGTAATCCCATTTGTCTATTTT 3016 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 35.89 CpG sites = 39, Kimura (unadjusted) = 36.63 Transitions / transversions = 1.62 (39/24) Gap_init rate = 0.08 (18 / 237), avg. gap size = 1.33 (24 / 18) 496 31.90 4.11 4.11 chrXptel1M 81838 82056 (917944) L2#LINE/L2 2287 2505 (577) m_b327s601i1 13727 chrXptel1M 81838 GTGATCTT-TTTAGTTGTCATGGATTCAATTATCAGTTCT-TGAAGAGGA 81885 i- ii i- v i v i vi v - vv v L2#LINE/L2 2287 GTGATCTCATCCAGTC-TCATGGCTTTAAATACCATCTATATGCTGATGA 2335 chrXptel1M 81886 GTTTTAAATTTACTTATCCAAGCCTAACCTCTCTGCTGACATCTAGTGTC 81935 v iii iv v iv vi iv vv i vv L2#LINE/L2 2336 CTCCCAAATTTATATCTCCAGCCCGGACCTCTCCCCTGAACTCCAGACTC 2385 chrXptel1M 81936 CCATCTTCAAATGTCTATTAAACATTTCAAACTGG-------ATAGCCAT 81978 vi v i v i i vi i v vi ------- v L2#LINE/L2 2386 GTATATCCAACTGCCTACTCGACATCTCCACTTGGATGTCTAATAGGCAT 2435 chrXptel1M 81979 CTTAAATTTAACATGTTCAAAACCAAATTTATTATCTTTTCACCCCTCCC 82028 i i i ii i iv v ------- i L2#LINE/L2 2436 CTCAAACTTAACATGTCCAAAACTGAACTCCTGATCTT-------CCCCC 2478 chrXptel1M 82029 CCAAGTCCTTTCCTCTTTCTAATTTTCC 82056 i ii ivi iiv - i i L2#LINE/L2 2479 TCAAACCTGCTCCTCCCGC-AGTCTTCC 2505 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 41.19 CpG sites = 39, Kimura (unadjusted) = 42.89 Transitions / transversions = 1.39 (39/28) Gap_init rate = 0.06 (12 / 218), avg. gap size = 1.50 (18 / 12) 617 40.26 3.65 2.08 chrXptel1M 82101 82456 (917544) C L2#LINE/L2 (131) 2951 2596 m_b327s601i2 13728 chrXptel1M 82101 GGGAATGAGGTATAAGAAGACTGGTAGGAGGAAGCCAAATTATG-AGGAC 82149 ii vvi ----- ivi iii i i - i C L2#LINE/L2 2951 GGAGATGAGGTCAGAGA-----GGTAACGGGGGACCAGATCATGTAGGGC 2907 chrXptel1M 82150 TTCACAAATCAAAGAGAGAAATTTATATTTTATCTTGAAGGTAATAGGGA 82199 i iii iii vv vi i v ivv iii iv vi i i C L2#LINE/L2 2906 CTTGTAGGCCATTGTAAGGACTTTGGCTTTTACTCTGAGTGAGATGGGAA 2857 chrXptel1M 82200 GGCACTGTAACTGATTAAGTAGGAAGATTACAAGATTAAATGTAC--TTT 82247 v i v ivvvv i i iiiii v v ivi iv -- C L2#LINE/L2 2856 GCCATTGGAGGGTTTTGAGCAGAGGAGTGACATGATCTGACTTACGTTTT 2807 chrXptel1M 82248 AGAAAGATCACTTTGTTAGCTGAGTGGAAGATGGACTAAAGTGGGCAGAG 82297 i i i viv v v ii i i? v vvi C L2#LINE/L2 2806 AAAAGGATCACTCTGGCTGCTGTGTTGAGAATAGACTGNAGGGGGGCAAG 2757 chrXptel1M 82298 ACTTATGGCAGAGAAGCCAATTAGCAGATTATCACAAT--TCCAGGCATG 82345 iv vivi i ii i v ii ii i -- iv C L2#LINE/L2 2756 GGTGGAAGCAGGGAGACCAGTTAGGAGGCTATTGCAGTAATCCAGGCGAG 2707 chrXptel1M 82346 AAGTGGTAAAGGTTTGTGCCACAGTGGCACAGCACCAAAAG-AGAGAAAA 82394 ii i iiv i vi vi --ii viii i -i v i C L2#LINE/L2 2706 AGATGATGGTGGCTTGGACCAGGGTGG--TGGCAGTGGAGGTGGTGAGAA 2659 chrXptel1M 82395 GAGAACC--TTCAAAGGACATTATCAAGGTAATATCAATAGGTCTCAGAA 82442 v iv v-- viiiv i v v ivii i i vi iivvi C L2#LINE/L2 2658 GTGGTCGGATTCTGGATATATTTTGAAGGTAGAGCCGACAGGATTTGCTG 2609 chrXptel1M 82443 ATAAATTAGATACT 82456 ii i i- C L2#LINE/L2 2608 ATGGATTGGATG-T 2596 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 61.26 CpG sites = 132, Kimura (unadjusted) = 63.34 Transitions / transversions = 1.96 (96/49) Gap_init rate = 0.04 (13 / 355), avg. gap size = 1.23 (16 / 13) 43 2.31 0.00 0.00 chrXptel1M 82457 82500 (917500) (G)n#Simple_repeat 1 44 (0) c_b327s251i2 13729 chrXptel1M 82457 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCGGGGGGGG 82500 v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 44 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 617 40.26 3.65 2.08 chrXptel1M 82501 82663 (917337) C L2#LINE/L2 (487) 2595 2425 m_b327s601i2 13728 chrXptel1M 82501 AAA---GAGAGATAGTGAGGACTCTAGGATGACAGCCAGGTTGAGAACTT 82547 iii--- v v v v vv v vvvii i C L2#LINE/L2 2595 GGGTGTGAGAGAAAGAGAGGAGTCAAGGATGACTCCAAGGTTTTTGGCCT 2546 chrXptel1M 82548 GATTGACTGGGAAGATAATGATGCCCTAGAC---AATAGAGCAGTTTG-A 82593 vii i i iiv v v v? ---i i i v vi -i C L2#LINE/L2 2545 GAGCAACTGGAAGGATGGAGTTGCCATTNACTGAGATGGGGAAGACTGCG 2496 chrXptel1M 82594 AAAGAGGAAGAGTTTAGGGGGAA---CAATAATT-ATTTTCACTGTATAT 82639 ii ii v iv v --- iv i - v --- v i C L2#LINE/L2 2495 GGAGGAGCAGGTTTGAGGGGGAAGATCAGGAGTTCAGTTT---TGGACAT 2449 chrXptel1M 82640 ATTGAGGTTAGAGTGTTCACTGGA 82663 i i v iiii iii i i C L2#LINE/L2 2448 GTTAAGTTTGAGATGCCTATTAGA 2425 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 61.26 CpG sites = 132, Kimura (unadjusted) = 63.34 Transitions / transversions = 1.50 (36/24) Gap_init rate = 0.05 (8 / 162), avg. gap size = 1.75 (14 / 8) 440 30.62 0.50 1.52 chrXptel1M 84132 84330 (915670) L1P3_orf2#LINE/L1 3091 3287 (7) m_b327s551i12 13730 chrXptel1M 84132 AGGGAACCAAAAAACTGGAAAAATATTTTTACAGTCAAAGGTTCTGATAA 84181 v v v i v i i v i i v vvvv i L1P3_orf2#LIN 3091 AGGCAACCTACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAA 3140 chrXptel1M 84182 AGGCCTCATTTCCAAAATATATAGAGAATTAACTTTAATTTATAA-AAAA 84230 v v v i v i ii i v vviv i - L1P3_orf2#LIN 3141 AGGGCTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAAA 3190 chrXptel1M 84231 AATCAAGCCATTCTCCAATTGAAAAATGGTCAAAGAATATGAACAGACAA 84280 v i v -- i - ii i v i i v L1P3_orf2#LIN 3191 AAACAAACAA--CCCCA-TCAAAAAGTGGGCGAAGGATATGAACAGACAC 3237 chrXptel1M 84281 TTCTCAGATGAAGAAATTGGAACTATTTCTAGTCATATGAAAAGATGCTC 84330 i v v vivi viiivvi iv i v L1P3_orf2#LIN 3238 TTCTCAAAAGAAGACATTTATGCGGCCAACAAACATATGAAAAAAAGCTC 3287 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 38.94 CpG sites = 29, Kimura (unadjusted) = 39.77 Transitions / transversions = 0.94 (29/31) Gap_init rate = 0.02 (4 / 198), avg. gap size = 1.00 (4 / 4) 1609 28.48 2.23 2.41 chrXptel1M 84243 84825 (915175) L1ME5_3end#LINE/L1 56 637 (304) m_b327s551i13 13730 chrXptel1M 84243 CTCCAATTGAAAAATGGTCAAAGAATATGAACAGACAATTCTCAGATGAA 84292 i v v i i iv v i L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chrXptel1M 84293 GAAATTGGAACTATTTCTAGTCATATGAAAAGATGCTCCAAGTCATTATG 84342 iiv vvii vvi iv i v v vv L1ME5_3end#LI 106 GAAACCCGAAAGGCTAACAAGCATATGAAGAGATGCTCAAACTCATTAGT 155 chrXptel1M 84343 AATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACACCTG 84392 i vv i i vi i L1ME5_3end#LI 156 AATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCTA 205 chrXptel1M 84393 TCAGATTGGCTAAGATGACAGGAAA--AAATAATCATGAGTGTTGGAGGG 84440 i i v i --i i i--ii vvii v i L1ME5_3end#LI 206 TTAGACTGGCAAAAAT--TAGAAAGCTGGATAATGCCAAGTGTTGGCGAG 253 chrXptel1M 84441 GATGTGGGAAAACTGGGACATTGATGCATTGTTGGTGGAGTTGTGAACGA 84490 i ? iv i vi v i i iiv ii vi L1ME5_3end#LI 254 GATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACTG 303 chrXptel1M 84491 ATCCAACCATTTTGGAGAGTAGTTTGGAACTA--TGCTCAAAGTTATCAA 84538 i v i i i i i v v -- iv v v vi v L1ME5_3end#LI 304 GTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTAAGTAT 353 chrXptel1M 84539 ACTGTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGATTATATCCCA 84588 --- v i i viii v vv L1ME5_3end#LI 354 AC---GCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATATCCCA 400 chrXptel1M 84589 AAGAGATTATAAAGAAGG----GAAAGGGACCTGTATGTGCACGAATGTT 84634 i v v viv ----v i ---- i iv i L1ME5_3end#LI 401 AAGAAATTCTCACACAGGTCCATAAGGGGAC----ATGTACGAGGATGTT 446 chrXptel1M 84635 TGTGGCAGCCCTTTTTGTAGTGGCTGGAAACTGGAAACTGAATGGATGTC 84684 ii v vi v i v i ii ii vivv i L1ME5_3end#LI 447 CATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGGGTGTC 496 chrXptel1M 84685 CATCAGTTGGAGAATGGCTGAATAAATTGTGGTTTATGAAAATTATGGAA 84734 v v i v iii v vv v v ii i L1ME5_3end#LI 497 CATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACACCATGGAG 546 chrXptel1M 84735 TATTACTGT-TCTGTAAGAAATGACCAACAGGATGATTTCAGAAAG--GC 84781 i - i-v v v iii vi vi -- v v v --i L1ME5_3end#LI 547 TACTA-TGCAGCAGTTAGAAGCAACGGACTAGATG--TACACATAGCAAC 593 chrXptel1M 84782 CTGGAGAGA-CTTACACGAAC-TGATGCTGAGTGAAATGAGCAGGA 84825 v vi - v -- - ii vi i i L1ME5_3end#LI 594 ATGGATGGATCTTAAA--AACATAGTGCTGAGTGAAAAAAGTAAGA 637 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.03 CpG sites = 90, Kimura (unadjusted) = 36.63 Transitions / transversions = 1.25 (90/72) Gap_init rate = 0.04 (21 / 582), avg. gap size = 1.29 (27 / 21) 13 29.72 0.00 0.00 chrXptel1M 85241 85285 (914715) (AGGG)n#Simple_repeat 1 45 (0) m_b327s252i3 13731 chrXptel1M 85241 AGGGATGGAGGGAGGAAGGGTAGTCGGGGGGGGGGGGGGCAGTGA 85285 v i vi vv i i i v v (AGGG)n#Simpl 1 AGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGA 45 Matrix = Unknown Transitions / transversions = 0.83 (5/6) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 1067 28.82 1.59 3.44 chrXptel1M 87162 87664 (912336) HERVK14C#LTR/ERVK 2845 3338 (4096) m_b327s701i0 13732 chrXptel1M 87162 TTTTTAGGAAGGGCTGCTGTTGAAGGCCTGCCAACACTTCCACCTGTTCC 87211 iiv ii -- v vi ?------- i HERVK14C#LTR/ 2845 TTTTTAGGGGCGGCCACTGTTGA--GCCTCCAGAN-------CCTATTCC 2885 chrXptel1M 87212 TGTCCAATGGAAAACTGATACACCAGTGTGGATAGAGCAGTGGCCCTTAG 87261 iv vv ?i iv v v? ? v i ? ? vi ?? HERVK14C#LTR/ 2886 CTTAAAATGGANGACCCAAAANCCNGTTTGGGTNGANCAGTGGCCGCTNN 2935 chrXptel1M 87262 GTAACGATAAAATTCAGGCCTCATTAGATATAGTACAGGAGCAGCTTCAC 87311 v v v v v vvi i ivi vv vv i i ii vv ? HERVK14C#LTR/ 2936 CTCAGGAAAAACTGGGGGCCTTACAGGAATTAGTCAAAGAACAATTAGAN 2985 chrXptel1M 87312 CAAGGACACTTAAAACC----TTCTCTAAGTCCTTGGAATTCCCCAGTGT 87357 v v ?i i ---- i ---- ? ? HERVK14C#LTR/ 2986 AAAGGACACATNGAGCCCACATTTTCT----CCNTGGAATTCNCCAGTGT 3031 chrXptel1M 87358 TTGTTGTGAAAAACAAATCTGGAAAATGGAGGATGTTAACGGATTTAAGA 87407 vi ? i v i v i v ? i v i v HERVK14C#LTR/ 3032 TTGTAATNAAGAAAAAATCCGGCAGATGGCGNATGCTAACCGACTTACGA 3081 chrXptel1M 87408 AAAGTGAATGAACAG--ATGGAAACTATAGGAACTCTTCAGCCTGGACTT 87455 ivv v -- -- ?v v ? i ii ? v v i v HERVK14C#LTR/ 3082 GCCGTCAATG--CAGTCATNCAACCNATGGGGGCNCTGCAGCCAGGGCTG 3129 chrXptel1M 87456 CCATCTCCTACTCAGTTGCCTAGAGAATGGCCTCTTTGGGTCATAGGTAT 87505 ? i ii ivv v v v ?i vvvi i i v HERVK14C#LTR/ 3130 CCNTCCCCCGCCATGATTCCTAGAGACTGGCCNTTAATAGTTATAGATTT 3179 chrXptel1M 87506 TAAGGATTGTTTCTATTCTATCCCTCTGGACAAGGAGGATATGAAAATAT 87555 v i i v v i i vvi vv? v vi v HERVK14C#LTR/ 3180 GAAGGACTGCTTCTTTACTATTCCTCTAGCAGAGCCNGATTTTGAAAAAT 3229 chrXptel1M 87556 TTGCCTTTTCAGTGCCCAGCGTTAACTTAGC--TGAGCCTTATAAAAGAT 87603 i v vi v iivii v -- i --v i ?vvvivv ? HERVK14C#LTR/ 3230 TTGCTTTTACTATTCCTGCTATGAAC--AACAAGGAACCNGCAGCCAGNT 3277 chrXptel1M 87604 ATGAATGGACAGTTTTGCCACAGGGAATGAAAAACAGCCCTACTATGTGT 87653 v v v ? i v vvi i i ? ? v HERVK14C#LTR/ 3278 ATCATTGGAAAGTNTTGCCGCAGGGCATGTTGAATAGTCCNACNATTTGT 3327 chrXptel1M 87654 CAAATGTATGT 87664 iv ? HERVK14C#LTR/ 3328 CAAACTTNTGT 3338 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 38.17 CpG sites = 61, Kimura (unadjusted) = 39.24 Transitions / transversions = 0.77 (61/79) Gap_init rate = 0.04 (20 / 502), avg. gap size = 1.25 (25 / 20) 367 14.02 1.64 18.10 chrXptel1M 87702 87823 (912177) L1ME5_3end#LINE/L1 138 242 (699) m_b327s551i14 13733 chrXptel1M 87702 ATGCTCCAAATCATTATTAATCAGAGAAATGCAAATTAAGACAACTCTGA 87751 v v v i vv L1ME5_3end#LI 138 ATGCTCAAACTCATTAGTAATCAGAGAAATGCAAATTAAAACAACAATGA 187 chrXptel1M 87752 GATACCACTACATTCAGAGGCACACC--TCAGATTGGCTAGAATGACAGG 87799 i --- ------- -- i i v i v ---- L1ME5_3end#LI 188 GATATCACT---TT-------ACACCTATTAGACTGGCAAAAATTA---- 223 chrXptel1M 87800 GAAATGTTGGAATCCTAGTGCCAA 87823 - i ---- i L1ME5_3end#LI 224 GAAA-GCTGGA----TAATGCCAA 242 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 15.05 CpG sites = 7, Kimura (unadjusted) = 15.05 Transitions / transversions = 1.00 (7/7) Gap_init rate = 0.17 (20 / 121), avg. gap size = 1.05 (21 / 20) 962 28.89 3.35 3.10 chrXptel1M 88504 88921 (911079) L1ME5_3end#LINE/L1 232 650 (291) m_b327s551i15 13734 chrXptel1M 88504 GAAAATGCGGGATGTTGGAGGGAATGTGGGAAAACAGGGACACTGATACA 88553 v viii v i i i ? i i v v i L1ME5_3end#LI 232 GATAATGCCAAGTGTTGGCGAGGATGTGGGGANATAGGAACCCTCATGCA 281 chrXptel1M 88554 TTGTTGGTGGAACTGTGAATACATCCAGCCATTCTGGAGAGCAATTTGGA 88603 i i i v ii ivvi v i v L1ME5_3end#LI 282 CTGCTGGTGGGAGTGTAGACTGGTGCAGCCATTCTGGAGAGCAATCTGGC 331 chrXptel1M 88604 ACTA--TGCTCAAA--AAGTTATCAAACTGTGCATATCCTTTGATCCAGC 88649 v -- iv -- - --- --- i v i L1ME5_3end#LI 332 AGTACTTAGTCAAATTAAGT-AT---AC---GCATACCCTATGACCCAGC 374 chrXptel1M 88650 AGTGCTACTACTGGGCTTATATCCCTAAGAGATACTAAAGAAGGG----A 88695 i v ii v iv v i v v viv v---- L1ME5_3end#LI 375 AATTCCGCTCCTGGGTATATATCCCAAAGAAATTCTCACACAGGTCCATA 424 chrXptel1M 88696 AAGGGACCTGTAGGTGCCAAAATGTTTATGGCAGACCTGTTTGTAGTGGC 88745 i v v ---- ii i v vvi i L1ME5_3end#LI 425 AGGGGACATGTACG----AGGATGTTCATTGCAGCGTTGTTTGTGGTGGC 470 chrXptel1M 88746 TAGAAGCTGGAAAATGAATGGATGCCCATCAATTGGAGAATAGTTGAGTA 88795 vi i i iivvivv i i v v i i v ii L1ME5_3end#LI 471 GGGGAGTTGGAGGCAACCTGGGTGTCCATCACTGGGAGAGTGGATAGGTA 520 chrXptel1M 88796 AATTGTGGTATATGAATGTTATGGAATATTATTGTTCTGTAAGAAATGAC 88845 v iv v iiii i i vvvv v v iii L1ME5_3end#LI 521 AAATGTGGTGGATGCACACCATGGAGTACTATGCAGCAGTTAGAAGCAAC 570 chrXptel1M 88846 CAGCAGGATGAATACAGAGAGGCTTGGAGGGA-CTTACATGAAC-TGATG 88893 vii vi v i v vii v v - v -- - ii L1ME5_3end#LI 571 GGACTAGATGTACACATAGCAACATGGATGGATCTTAAA--AACATAGTG 618 chrXptel1M 88894 CTGAGTGAAATGAGT-AGAACCAG---GAGAT 88921 vi - v --- L1ME5_3end#LI 619 CTGAGTGAAAAAAGTAAGAAACAGAATGAGAT 650 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.82 CpG sites = 63, Kimura (unadjusted) = 37.26 Transitions / transversions = 1.17 (63/54) Gap_init rate = 0.05 (20 / 417), avg. gap size = 1.35 (27 / 20) 18 8.72 0.00 0.00 chrXptel1M 89278 89302 (910698) (A)n#Simple_repeat 1 25 (0) m_b327s252i4 13735 chrXptel1M 89278 AAAAAAAAAAAAGAAAGAAAAAAAA 89302 i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAA 25 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 512 26.50 4.71 4.71 chrXptel1M 89311 89607 (910393) HERVK14#LTR/ERVK 3129 3425 (2671) m_b327s701i1 13736 chrXptel1M 89311 AAAAGTTATGCTATTACATTACATGGATGATATATTGGGATGTGCACCTG 89360 v ii i- vi --- v HERVK14#LTR/E 3129 AAATGTTATATTATC-CATTACATGGATGATATTCTG---TGTGCAGCTG 3174 chrXptel1M 89361 AGGAACACATGTTAGAAGC-ATGT----CTATAAAAGACCATGGAAACAC 89405 -- -i v vv vi- ---- i viiii - i vi HERVK14#LTR/E 3175 A--AAC-TAGGGAAGAATTGATGTTGTGCTACAAACAGTTA-GAAAAGGC 3220 chrXptel1M 89406 TA-AGATACAGCAAA-TTGCACATAGCTCCAGAAAAAATTCAAAGACATG 89453 i- i i i ii- ivvi i v v i vviv i HERVK14#LTR/E 3221 TGTAAATGCGGCAGGGTTAATTATAGCCCCCGATAAAATCCAAACTTCTA 3270 chrXptel1M 89454 CTCCTTTTCAATATTTAGGATATGAAG-CATTCCTAAGGTGTTCAC--AG 89500 i i - -i vvv - i i - i-- HERVK14#LTR/E 3271 CTCCCTTTCAATATCTAGGA-ATGAAGGTAGAAC-AAAGTGCT-ATTAAG 3317 chrXptel1M 89501 TATAAAAACTTTCCTTAA----GAACAGAAAAGTTAAACACCTTAAATGA 89546 iv v vv --- ---- v v v v HERVK14#LTR/E 3318 CCTCAAAAGGTTC---AAATTCGAAGAGATAATTTAAAAACCTTAAATGA 3364 chrXptel1M 89547 TTTTCAGAAATTGATAGGAGATATCTAATGGATGCGATCAATGTTAGGCT 89596 i i iv i iv v v vi iv v HERVK14#LTR/E 3365 TTTCCAAAAATTATTAGGAGACATTAATTGGATTCGTCCAACTTTAGGCA 3414 chrXptel1M 89597 TGACTACCTAT 89607 vv HERVK14#LTR/E 3415 TTCCTACCTAT 3425 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 32.59 CpG sites = 39, Kimura (unadjusted) = 33.12 Transitions / transversions = 1.08 (39/36) Gap_init rate = 0.07 (21 / 296), avg. gap size = 1.33 (28 / 21) 495 28.27 5.08 4.67 chrXptel1M 89426 89681 (910319) HERVK3#LTR/ERVK 3295 3551 (3651) m_b327s701i2 13736 chrXptel1M 89426 ATAGCTCCAGAAAAAATTCAAAGACATGCTCCTTTTCAATATTTAGGA-- 89473 ? i ii v v vv v i v vi ? i -- HERVK3#LTR/ER 3295 ATNGCTCCAGAGAAGGTGCAAACAACTTCCCCATACCANTACTTAGGAAC 3344 chrXptel1M 89474 TATGAAGCATTCCTAAG----GTGTTCACAGTATAAAAA-----CTTTCC 89514 ----ii v vi ---- -- i iv v i -----i i HERVK3#LTR/ER 3345 TAT----TGTTACGGAGAGAAGTGT--ACGGCCTCAGAAAGTAGTTCTCC 3388 chrXptel1M 89515 TTAAGAACAGAAAAGTTAAACACCTTAAATGATTTTCAGAAATTGATAGG 89564 v ii ---- v v i iv iv HERVK3#LTR/ER 3389 GTAAAGACAG----GTTACAGACTTTAAATGATTTTCAACAATTATTAGG 3434 chrXptel1M 89565 AGATATCTAATGGATGCGATCAATGTTAGGCTTGACTACCTATCAA-TTG 89613 i iv v v vi i i iv vi - i HERVK3#LTR/ER 3435 GGATATTAATTGGCTGCGCCCGATGCTAGGTATTGCTACCTATCAACTTA 3484 chrXptel1M 89614 CA-ACCATTATATGACATTTTAAGGGGAGACAGTGCTTTAAATTCACCAC 89662 - i v ivvi vi vi i vv -- v ? v i HERVK3#LTR/ER 3485 CACATCTTTACCAAACCCTGCAAGGAGATTC--TTCNTTAAATTCCCCGC 3532 chrXptel1M 89663 GCCAGCTTACAAAAGAAGC 89681 v i ? v i HERVK3#LTR/ER 3533 GGCAACTNACTAAAGAGGC 3551 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 34.85 CpG sites = 36, Kimura (unadjusted) = 36.81 Transitions / transversions = 1.09 (36/33) Gap_init rate = 0.07 (17 / 255), avg. gap size = 1.47 (25 / 17) 366 30.59 6.71 9.47 chrXptel1M 90598 91312 (908688) HERVK3#LTR/ERVK 4478 5174 (2028) m_b327s701i3 13736 chrXptel1M 90598 AAGCCAGGAGCATAGTAAAAGCCTGTATGGCTTGCCTTCCTTTCCACGCT 90647 i ivi ? v vivi vv v v vi v? HERVK3#LTR/ER 4478 AAGCTAGGGCTATNGTACAAGCCTGTCCTACTTGCCAGCATGTCCCTGGN 4527 chrXptel1M 90648 CCTACACTGCCTCCAG--GGAAG-AACCCTTGTGGTTTGAGACCCAATAA 90694 v ii --- vi -- ?v - vi v ivv v i HERVK3#LTR/ER 4528 GCCGCAC---CTGTAGAAGGNTGTAACCCACGAGGTTTGGCTCCAAATGA 4574 chrXptel1M 90695 AATCTGGCAAATGGATGTGACCCATTATAA-ATCTTTTGGTCGTCTGTCT 90743 v v i- i- v i ---- viv HERVK3#LTR/ER 4575 AATCTGGCAAATGGATGTTACACAC-ATAGCAGCCTTTGG----CAAGCT 4619 chrXptel1M 90744 TTCATCCATGTTGTG------GTAGACACCTTTTCGGGATTCAC-TTTTG 90786 -- v i v ------i i v ----- i- vi HERVK3#LTR/ER 4620 T--AGCTATGTTCTGTGANCTATAGACACTTATTC-----TCATATGCTG 4662 chrXptel1M 90787 CA----ACATCAGC--AGCAAAAGAGACAGCCCGAGTGGTCAC------T 90824 ---- -- -- i iiv ----- i------i HERVK3#LTR/ER 4663 CATGCTACAT--GCCAAACAGGTGAGACAGC-----TGGTCATGTACGGC 4705 chrXptel1M 90825 GAATTCCTCATACAAGCATTTGCCATTATGGATGTGCCACAAGCAAT-AA 90873 vv iv - iiv v ivv ivi i -i i - HERVK3#LTR/ER 4706 GACATTGTC-TGTCATCATTTGCTCATATGGGGATACC-TAAACAATTAA 4753 chrXptel1M 90874 AAACAGATAATGGACCTGCATATACTTCTAAACAT--TTTGCACACTTTT 90921 v i i v --- iv -- v v v i HERVK3#LTR/ER 4754 AAACTGACAATGGACCCGCTTATACT---AGTCATGCTTTTCAAAATTTC 4800 chrXptel1M 90922 GTTCACAGTATTAGATTTTA---CACACCACTGACATACCCTTTAATCCT 90968 -- i iv i ii v --- i vv v iv v i v HERVK3#LTR/ER 4801 --TTACAGCTTTGGGCTATAACCCATAAAACAGGAATTCCTTATAATCCT 4848 chrXptel1M 90969 CAAGGATA-GGCAATAGTAGAGAGGAGAAACA-GAGATATTAAGAGGC-T 91015 vi i - v - v -- iv -v i i vi v - HERVK3#LTR/ER 4849 AGAGGACAAGGCATTA-TAGAGCG--GGCACATCAAACATTACAACGCAT 4895 chrXptel1M 91016 CCTCCAAAAACAAAAGAAAGGG----GGAGCCACAGGTA--ACCCTAG-- 91057 vi vv iiii? ---- v - iv -- ii i-- HERVK3#LTR/ER 4896 GTTGAAAAAACAAAAAGGGNGGTATAGGAGGC-CAACTACCACCTCAATC 4944 chrXptel1M 91058 AGAACTTCTAAATCTAGGCCTTTATATTATTAACTTCTT-GATTTTTGAC 91106 i v --- i v i v v i v v i i - i ii ii HERVK3#LTR/ER 4945 AAAACTAC---ATTTAGCCTTATTTACTTTAAATTTTTTNGACTCCTGGT 4991 chrXptel1M 91107 AAAGATGCACTGGCTCCGGCAGACAGGTTTTATAACCCACCGGAAGGGCA 91156 vi vvvv i i v iiv --------------- HERVK3#LTR/ER 4992 ACGGATGGTAAGACTCCAGCAGAAAGACATT---------------GGCA 5026 chrXptel1M 91157 GGGTCCAGTG----AGAGCAACTCCACTATCTTTAGATAATCGCCAGGTG 91202 i vvii v ---- v ------------- v v vvv i HERVK3#LTR/ER 5027 AGTGTTAGAGGAAAAGAGGAA-------------AGTTTATCCGAAAGTG 5063 chrXptel1M 91203 ATGTGGAGAGACCCAGAAACTGGTGA--ATGGAAAGGACCAGATAGGCTA 91250 v i i vv i iv-i ? -- v - i i ii v HERVK3#LTR/ER 5064 TTATGGAAATCCCCGGAAGA-AGNGACAATGGAAAGGTCC-GGTGGATTT 5111 chrXptel1M 91251 ACTGCTTTGGGGA-GAGGGTTTGCTTGTATCTCTACAGGTGGAGAAGGAA 91299 viv - v i i i v iv i vi HERVK3#LTR/ER 5112 ACTGACGTGGGGANGAGGGTATGCTTGTGTTTTTACAGGAGATGGACAAA 5161 chrXptel1M 91300 TCAGATGGGTGCC 91312 i ivi HERVK3#LTR/ER 5162 CCGTGTGGGTGCC 5174 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 38.10 CpG sites = 101, Kimura (unadjusted) = 40.17 Transitions / transversions = 1.04 (101/97) Gap_init rate = 0.12 (87 / 714), avg. gap size = 1.31 (114 / 87) 585 26.71 6.68 3.47 chrXptel1M 90629 91047 (908953) HERVK14C#LTR/ERVK 4680 5111 (2323) m_b327s701i4 13736 chrXptel1M 90629 TTGCCTTCCTTTCCACGCTCCTACA-CTGCC---TCCAGGGA----AG-- 90668 i ??v v v - v - --- v ----? -- HERVK14C#LTR/ 4680 TTGCCCTNNGTGCCAGG-TGCTACAACTGCCACATCAAGGGACTGGNGTT 4728 chrXptel1M 90669 AACCCTTGTGGTTTGAGACCCAATAAAATCTGGCAAATGGATGTGACCCA 90718 ?i v v iv? i ?viv ? i ? HERVK14C#LTR/ 4729 AACCCNCGAGGATTGGCNCCTAATNCGCTNTGGCAAATGGACGTNACCCA 4778 chrXptel1M 90719 TTATAAATCT-TTTGGTCGTCTGTCTTTCATCCATGTTGTGGTAGACACC 90767 -i vv ?i- vviv ? ? v i ?iiv i HERVK14C#LTR/ 4779 T-GTACCTNCATTTGGGAAACTNTCNTACGTCCATGTNACTGTAGATACC 4827 chrXptel1M 90768 TTTTCGGGATTCACTTTTGCAACATCAGC--AGCAAAAGAGACAGCC--- 90812 vviv iii? vv ? v -- -- i ii? i ? i--- HERVK14C#LTR/ 4828 TTTTCTCATTTTGTNTGGGCNACTT--GCCAAACAGGNGAGGCNGCTGCT 4875 chrXptel1M 90813 CGAGT----GGTCACTGAATTCCTCATACAAGCATTTGCCATTATGGATG 90858 v ----i v i viv i iii ------- i ?i i iii HERVK14C#LTR/ 4876 CGTGTTAAAAGACATTTGCTTTCCTGT-------TTCGCNGTCATGGGCA 4918 chrXptel1M 90859 TGCCACAAGCAATAAAAACAGATAATGGACCTGCATATACTTCTAAACAT 90908 v iv? v ? i v v vv i?? vv ?-i HERVK14C#LTR/ 4919 TTCCACAAAANATTAAAACNGACAATGGCCCAGGCTACNNTAGTAAAN-C 4967 chrXptel1M 90909 TTTGCACACTTTTGTTCA-CAGTATTAGATTTTACACACCACTGACATAC 90957 i? ?i v iv - i iv? v vv ?i i? v HERVK14C#LTR/ 4968 TTTANANGCGTTCCTTCAACAATGGNACATTAAACACANTACTGGNATCC 5017 chrXptel1M 90958 CCTTTAATCCTCAAGGATAGGCAATAGTAGAGAGGAGA-AACAGAGATAT 91006 v i ?i i v v v - v v- iv - iv HERVK14C#LTR/ 5018 CCTATAATTCTCAAGGNCAAGCCATTGTTGA-ACGAGCTAATCGA-ACCT 5065 chrXptel1M 91007 TAAGAGGCTC--CTCCAAAAACAAA----AGAAAGGGGGAGCCACAG 91047 i ?- --i v ---- i i v HERVK14C#LTR/ 5066 TAAAAN-CTCAATTACAAAAACAAAAGACAGAAGGGGGGAACCAGAG 5111 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 34.74 CpG sites = 55, Kimura (unadjusted) = 36.82 Transitions / transversions = 1.04 (55/53) Gap_init rate = 0.06 (27 / 418), avg. gap size = 1.59 (43 / 27) 502 21.92 2.59 1.71 chrXptel1M 92788 92903 (907097) MIRc#SINE/MIR 30 146 (122) m_b327s601i3 13737 chrXptel1M 92788 CTGGTCT-GAACTCAGGAAGACCTGAGTTCAAAGTTGAGCTGAGACGTTT 92836 v - i v i i iviivi vv v ii MIRc#SINE/MIR 30 CTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTT 79 chrXptel1M 92837 ATTAGTTCTGTGTCCTTAAGGCAAGTCACTTAATCTTGTTT--GCCTCAG 92884 i i v v -i i i- i -- MIRc#SINE/MIR 80 ACTAGCTGTGTGACCTT-GGGCAAGTCACTTAACCTC-TCTGAGCCTCAG 127 chrXptel1M 92885 TTTCCTCAACTGTAAAATG 92903 v MIRc#SINE/MIR 128 TTTCCTCATCTGTAAAATG 146 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 24.05 CpG sites = 15, Kimura (unadjusted) = 26.43 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.03 (4 / 115), avg. gap size = 1.25 (5 / 4) 227 25.46 6.96 3.05 chrXptel1M 92973 93130 (906870) L1M5_orf2#LINE/L1 1214 1377 (1917) m_b327s551i16 13738 chrXptel1M 92973 CAGACACAACTGAAAACAATGAATAACAAAATTTTGTC--CAATTATATG 93020 ---- v vi - v i v i v-- i v L1M5_orf2#LIN 1214 CAGACA----TTAAAAGGAT-AATAAGAGAATATTATGAACAACTTTATG 1258 chrXptel1M 93021 CCAATAAATCT----ATTTATTTGAAATGTATGAA-TCTATG-AAAATGT 93064 i ---- i vv v ii - iv - iii L1M5_orf2#LIN 1259 CCAATAAATTTGANAACTTAGATGAAATGGACAAATTCCTTGAAAAACAC 1308 chrXptel1M 93065 AAATTGCCTAGATTGACAAAAGAGGAAGT--AAGATAAAAAAGACCCTAT 93112 ? i v i i ?v i i -- i vvi vii L1M5_orf2#LIN 1309 AANTTACCAAAACTGACNCAAGAAGAAATAGAAAATCTGAATAGCCCTAT 1358 chrXptel1M 93113 CTTTA-AAAAGAAATTGAA 93130 v i -v L1M5_orf2#LIN 1359 ATCTATTAAAGAAATTGAA 1377 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 32.25 CpG sites = 22, Kimura (unadjusted) = 32.25 Transitions / transversions = 1.29 (22/17) Gap_init rate = 0.07 (11 / 157), avg. gap size = 1.45 (16 / 11) 40 0.00 2.63 0.00 chrXptel1M 93176 93213 (906787) (TG)n#Simple_repeat 1 39 (0) c_b327s251i3 13739 chrXptel1M 93176 TGTG-GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 93213 - (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 39 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 23 19.60 5.17 0.00 chrXptel1M 93467 93524 (906476) (TA)n#Simple_repeat 1 61 (0) m_b327s252i5 13740 chrXptel1M 93467 TATAAATATGTATACATATAT-TGGATTTA-ATATATATTTTAATATAT- 93513 v i i - iv v - v vv - (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chrXptel1M 93514 TTTATATATAT 93524 v (TA)n#Simple_ 51 TATATATATAT 61 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.05 (3 / 57), avg. gap size = 1.00 (3 / 3) 600 26.31 17.09 1.10 chrXptel1M 93931 94322 (905678) L1M5_orf2#LINE/L1 1397 1850 (1444) m_b327s551i17 13738 chrXptel1M 93931 CCACAAATGGGGTCCCAGGATCAAATGAATTCACAAGTGAATTCTTTTGA 93980 viiiiii vi i iv vi viii L1M5_orf2#LIN 1397 CCACAAAGAAAACTCCAGGCCCAGATGGCTTCACTGGTGAATTCTACCAA 1446 chrXptel1M 93981 ACATTTAAAGAATAAAGCAATA---ATC---------------------- 94005 i v -i --- ---------------------- L1M5_orf2#LIN 1447 ACATTTAAGGAAGAAA-TAATACCAATCTTACACAAACTCTTCCAGAAAA 1495 chrXptel1M 94006 -----AAAGAAGAAGTCCTACCGAAATCCCTATATGTCTCAAATATGGTG 94050 ----- i i iiv v v v vi v vvv v ii ?iiv L1M5_orf2#LIN 1496 TAGAAAAAGAGGGAACACTTCCCAACTCATTTTATGAGGCCAGCATNACC 1545 chrXptel1M 94051 CTGATATCTAAACCAGA-AAGAACAAAAACAGAAAAAGAAAACTATAGGT 94099 i v ? - ii vv - ii i i ii L1M5_orf2#LIN 1546 CTGATACCAAAACCNGACAAAGACATTA-CAAGAAAAGAAAATTACAGAC 1594 chrXptel1M 94100 CAATTTTCCTAATGAATATTGATGCAAAAAAAAATAAATAAAATAATAGC 94149 v i v i v vvv- ? i v L1M5_orf2#LIN 1595 CAATATCCCTCATGAACATAGATGCAAAAATCC-TNAACAAAATATTAGC 1643 chrXptel1M 94150 AA---GACTGCAGTAAAATCAAACAAAGATAA------------------ 94178 --- v v i v vv v i ------------------ L1M5_orf2#LIN 1644 AAATCGAATCCAGCAATATATAAAAAGGATAATACATCATGACCAAGTGG 1693 chrXptel1M 94179 GGT--------AGAATTCAGGGCTGGTTCAATATTAAAGAAACAAGCAGC 94220 --------i v i i i i vi i v v ii L1M5_orf2#LIN 1694 GGTTTATCCCAGGAATGCAAGGTTGGTTTAACATTCGAAAATCAATCAAT 1743 chrXptel1M 94221 ATAATTGATCATATCAATA--ATAAA----AAAAATTCTATGATTACCTC 94264 i v i i i -- ---- iv i i L1M5_orf2#LIN 1744 GTAATTCACCATATTAACAGAATAAAGGAGAAAAATCATATGATCATCTC 1793 chrXptel1M 94265 AATTGATACAGAAACAGCTTTTGACAAAATGCTCTACA-CCATTCCTCTT 94313 v i v v -- v - v vv L1M5_orf2#LIN 1794 AATAGATGCAGAAAAAGCATTTGACAAAAT--TCAACACCCATTCATGAT 1841 chrXptel1M 94314 AAAAACACT 94322 v L1M5_orf2#LIN 1842 AAAAACTCT 1850 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 32.91 CpG sites = 55, Kimura (unadjusted) = 33.30 Transitions / transversions = 1.17 (55/47) Gap_init rate = 0.04 (15 / 391), avg. gap size = 4.80 (72 / 15) 434 23.69 1.75 7.41 chrXptel1M 94324 94437 (905563) MIRc#SINE/MIR 21 128 (140) m_b327s601i4 13741 chrXptel1M 94324 GAGAGCAGCACCAGCCCTGAAGTCAGAAAGACCTGAGTTCAAATTTGATC 94373 i - ii v i i i i i i iiviv MIRc#SINE/MIR 21 GAAAG-AGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGC 69 chrXptel1M 94374 TCAAACACTTAACACTTCCTAGCTGTGTGACTCTGGGCAAATCACTTAAC 94423 ------- iv v ii i MIRc#SINE/MIR 70 TC-------TGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAAC 112 chrXptel1M 94424 CCAATT--GCCTCAGT 94437 ivvi -- MIRc#SINE/MIR 113 CTCTCTGAGCCTCAGT 128 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 26.78 CpG sites = 18, Kimura (unadjusted) = 29.56 Transitions / transversions = 2.57 (18/7) Gap_init rate = 0.08 (9 / 113), avg. gap size = 1.11 (10 / 9) 17 18.53 0.00 0.00 chrXptel1M 94438 94468 (905532) (A)n#Simple_repeat 1 31 (0) m_b327s252i6 13742 chrXptel1M 94438 AAAATAAATAAATAAAAATAAAAATAAAAAA 94468 v v v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 31 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 16 10.47 3.23 0.00 chrXptel1M 94439 94469 (905531) (AAAT)n#Simple_repeat 1 32 (0) m_b327s252i7 13742 chrXptel1M 94439 AAATAAATAAATAAAAATAAAAATAAA-AAAT 94469 v v v - (AAAT)n#Simpl 1 AAATAAATAAATAAATAAATAAATAAATAAAT 32 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.03 (1 / 30), avg. gap size = 1.00 (1 / 1) 24 17.89 0.00 0.00 chrXptel1M 94532 94575 (905425) (A)n#Simple_repeat 1 44 (0) m_b327s252i8 13742 chrXptel1M 94532 AAAAACAAACAAAATAATAGAAAAAAAACAAAAAAAGAAAAAAA 94575 v v v v i v i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 44 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 14 4.94 0.00 0.00 chrXptel1M 95395 95415 (904585) (TAGA)n#Simple_repeat 1 21 (0) m_b327s252i9 13743 chrXptel1M 95395 TATATAGATAGATAGATAGAT 95415 v (TAGA)n#Simpl 1 TAGATAGATAGATAGATAGAT 21 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 14 15.91 7.14 0.00 chrXptel1M 95706 95747 (904253) (TATCTTA)n#Simple_repeat 1 45 (0) m_b327s252i10 13744 chrXptel1M 95706 TATCTTATA--TT-TATCTTGGATCTTATATGTCAAATTTTATAT 95747 -- - iv v i v i (TATCTTA)n#Si 1 TATCTTATATCTTATATCTTATATCTTATATCTTATATCTTATAT 45 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.05 (2 / 41), avg. gap size = 1.50 (3 / 2) 274 28.44 2.83 3.81 chrXptel1M 95798 96009 (903991) C L1MEi_5end#LINE/L1 (693) 1519 1310 m_b327s551i18 13745 chrXptel1M 95798 AATGTCT--ATTTTTTTTTCACTCAGGATTGTGCTTAGCTTTGCTGGGTA 95845 -- viii vv v v--- i v C L1MEi_5end#LI 1519 AATGTCTTTATTTTGCCCTCACTCTTGAATGA---TAGTTTAGCTGGGTA 1473 chrXptel1M 95846 TAATATTTT-TGTCCACAGATCTTTTCCTTTTGCTCTTTGATATATATTG 95894 iv i -v iv v v i iv v - v i C L1MEi_5end#LI 1472 TAGAATTCTAGGTTGACAGTTATTTTCCCTCAGCACTTTGA-AGATATTA 1424 chrXptel1M 95895 CTTCA-AGAC--CTGCAATCTATTAATGTAATTGCTGCTAGGTCTTGTGT 95941 i -v v -- vv --- vii v vv i vv C L1MEi_5end#LI 1423 CTCCATTGTCTTCTGGCATCTAT---TGTTGCTGATGAGAAGTCTGCTGT 1377 chrXptel1M 95942 GATTCTAATTGTAGCTCCATTGTATTTGAATTGTTTTTTTTTTCCTTATT 95991 v v v i v vv i vi i i i - vi v C L1MEi_5end#LI 1376 CAGTCTAATTGTCGTTCCTTTGTAGGTAATCTGTCTTTTCTCT-CTGGTA 1328 chrXptel1M 95992 GCTCATAAAATTTTCTTT 96009 iv i i C L1MEi_5end#LI 1327 GCTTTTAAGATTTTCTCT 1310 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 35.84 CpG sites = 24, Kimura (unadjusted) = 35.84 Transitions / transversions = 0.71 (24/34) Gap_init rate = 0.06 (12 / 211), avg. gap size = 1.17 (14 / 12) 243 32.60 2.89 3.64 chrXptel1M 97494 97770 (902230) L1MC4_5end#LINE/L1 1208 1482 (1073) m_b327s551i19 13746 chrXptel1M 97494 TGGAAAATAGATCTAGGAGAGATAACCTGAGGATCATTGGACTACCTGAA 97543 i i iivv i ii? v ?v v v v v L1MC4_5end#LI 1208 TGGAAGACAGGCAAAGAAGGANTAACATNCGTATAATTGGAGTCCCTGAA 1257 chrXptel1M 97544 AATTATGATGAAAAAAAGAGCCTAGA--TACTATTTTACATGAAATCATC 97591 i vv vi vv v vi vvi -- v v v iv -- v L1MC4_5end#LI 1258 GAAGAAAAACAAAACAATGGAACAGAACTAATATTTAAAACTA--TAATC 1305 chrXptel1M 97592 AAAGAGAACTACCCAGAAGTAATAGAACTGGAAGG--TAAA-ATAGGTGT 97638 v i vi i i v ---i i-- i -v vi i L1MC4_5end#LI 1306 CAAGAAAACTTTCCGGAAATAAAAGAA---AAAGACCTGAATCTACATAT 1352 chrXptel1M 97639 TGAAAGAATCCATCGAACACCTTCTGAAAAA--GACCCTAAAATAAAGAC 97686 iii i ?ii v-- i -- vi vv vvi L1MC4_5end#LI 1353 TGAAAGGGCCCACCGNGTACCTG--GGAAAATTGACCCGGAACGATCAAC 1400 chrXptel1M 97687 TCCGAGGAATATTGTGACCAAACT-TCAGAACTTTCAGACTAAAGAAAAA 97735 iv iv iiiv - i - v iiv L1MC4_5end#LI 1401 TCCGAGACATATCCTAGTAAAACTATTAGA-CTTTAAAGATAAAGAAAAA 1449 chrXptel1M 97736 ATTTTACAAGCAGTCAGGAAAAAACAGTTCAAATA 97770 ii vvii vvi v v -- L1MC4_5end#LI 1450 ATCCTCAGGGCCTCCAGGCAAAAAGA--TCAAATA 1482 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 43.37 CpG sites = 43, Kimura (unadjusted) = 44.04 Transitions / transversions = 0.98 (43/44) Gap_init rate = 0.05 (15 / 276), avg. gap size = 1.20 (18 / 15) 248 31.30 2.61 0.00 chrXptel1M 97695 97809 (902191) L1M6_5end#LINE/L1 1521 1638 (877) m_b327s551i20 13746 chrXptel1M 97695 ATATTGTGACCAAACTTCAGAACTTTCAGACTAAAGAAAAAATTTTACAA 97744 iv i v i iv i ?iv iv ii L1M6_5end#LIN 1521 ATATCCTGGCAAAATTTTTGAATTNCAAGGATAAAGAAAAAATCCTACAA 1570 chrXptel1M 97745 GCAGTCAG---GAAAAAACAGTTCAAATACCAAGGTGCCACAATAAGGAT 97791 vi --- v i vv v viiv v v v L1M6_5end#LIN 1571 GCATCCAGGCAGAAAAAACAGGTTACCTACAAAGGAATAAAAATCAGGCT 1620 chrXptel1M 97792 CACCCAAGATCTGGCTGC 97809 vi iv ii vv L1M6_5end#LIN 1621 GGCCTCAGACTTCTCTGC 1638 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 41.40 CpG sites = 17, Kimura (unadjusted) = 41.40 Transitions / transversions = 0.89 (17/19) Gap_init rate = 0.01 (1 / 114), avg. gap size = 3.00 (3 / 1) 17 16.25 3.85 3.85 chrXptel1M 98316 98367 (901633) (AGGAAA)n#Simple_repeat 1 52 (0) m_b327s252i11 13747 chrXptel1M 98316 AGGAAAAGGAAAAGGAAAAAGTAATAAGG-AAGGGTACAAG-AAAGGGGA 98363 - v - - i v v i - ii (AGGAAA)n#Sim 1 AGGAAAAGGAAAAGG-AAAAGGAA-AAGGAAAAGGAAAAGGAAAAGGAAA 48 chrXptel1M 98364 AGGA 98367 (AGGAAA)n#Sim 49 AGGA 52 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.08 (4 / 51), avg. gap size = 1.00 (4 / 4) 16 25.27 5.56 1.33 chrXptel1M 98671 98742 (901258) (AACA)n#Simple_repeat 1 75 (0) m_b327s252i12 13748 chrXptel1M 98671 AACAAAAAAAAAATCAATTTAA-AAATAAGAAAAACACAC-CCCTAA-AA 98717 v v v viv - i - v v -vv v - (AACA)n#Simpl 1 AACAAACAAACAAACAAACAAACAAACAA-ACAAACAAACAAACAAACAA 49 chrXptel1M 98718 ACAACGAAGCAAACAAA-AAACAAAC 98742 vv i - (AACA)n#Simpl 50 ACAAACAAACAAACAAACAAACAAAC 75 Matrix = Unknown Transitions / transversions = 0.25 (3/12) Gap_init rate = 0.07 (5 / 71), avg. gap size = 1.00 (5 / 5) 20 27.96 0.00 0.00 chrXptel1M 98836 98895 (901105) (AAAA)n#Simple_repeat 1 60 (0) m_b327s252i13 13749 chrXptel1M 98836 AAAACAAAAAGAAAGAAATTAAAAAAGGTAAAAAAATTAAATAGCCAAAA 98885 v i i vv iiv vv v ivv (AAAA)n#Simpl 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chrXptel1M 98886 AAAAAAAAAA 98895 (AAAA)n#Simpl 51 AAAAAAAAAA 60 Matrix = Unknown Transitions / transversions = 0.56 (5/9) Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0) 19 12.18 2.70 0.00 chrXptel1M 100842 100878 (899122) (AAAAGG)n#Simple_repeat 1 38 (0) m_b327s252i14 13750 chrXptel1M 100842 AAAGGGGAGAGGAAAAGGAAAA-GAAAAAGAAAAGGAA 100878 i i i - i (AAAAGG)n#Sim 1 AAAAGGAAAAGGAAAAGGAAAAGGAAAAGGAAAAGGAA 38 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 225 29.27 10.47 4.91 chrXptel1M 101018 101829 (898171) L1M5_orf2#LINE/L1 38 892 (2402) m_b327s551i21 13751 chrXptel1M 101018 TAACTGTAAATTGGGGGATGAACTCCCCA--TAAAGAGAGGCAGA----- 101060 v --- ?v i v i -- --- ----- L1M5_orf2#LIN 38 TAAATGTAAAT---GGNCTAAACACTCCAATTAAA---AGGCAGAGATTG 81 chrXptel1M 101061 -TAGACTG-ATCAAAGT-CAGAACC--ACAATATGTT-TTTACAAAA-AC 101103 -i - v iv- ii -- v i - i i - L1M5_orf2#LIN 82 TCAGACTGGATAAAAAAACAAGACCCAACTATATGCTGTCTACAAGAGAC 131 chrXptel1M 101104 ACA----AAA-AGGGAGATACATATAGAGTAAAGGTAAAAGGCTGGAGCA 101148 i ---- - vii i v ? iv i i v iv L1M5_orf2#LIN 132 GCACTTTAAATATAAAGACACAGANAGGTTGAAAGTAAAAGGATGGAAAA 181 chrXptel1M 101149 AAATCTATTATGCTCAGGTGAGTCAAAACAGA----GGGTAGCCACCCTT 101194 i v ii vv viiv i? v i ---- ? i i ivi v L1M5_orf2#LIN 182 AGATATACCATGCAAACACTAANCAAAAGAAAGCTGGNGTGGCTATATTA 231 chrXptel1M 101195 ATCTCAGATCAA--------CAAAAGAAAAATTGATCTAATTAAAAGAGA 101236 v iv -------- iiv i --- --- vv L1M5_orf2#LIN 232 ATATCAGACAAAGTAGACTTCAAGGCAAGAA---AT---ATTACCAGAGA 275 chrXptel1M 101237 TAAGGAAGGAAACTACATCCTGCTAAACGGAGCA--TAAACAACGAAGCA 101284 i i v i v vv v v iv -- v v - vv L1M5_orf2#LIN 276 TAAAGAGGGACATTTCATAATGATAAAAGGGTCAATTCATCAA-GAAGAC 324 chrXptel1M 101285 ATATCAATATTAAACATATATGCACCAAGTGGTATGGCACC-AACTTCCT 101333 v vi ii i v i iii vi vi - v v v L1M5_orf2#LIN 325 ATAACAATCCTAAATGTGTATGCACCTAATAACAGAGCTTCAAAATACAT 374 chrXptel1M 101334 AAAGGAGAAGTTA--AGAGTTGCAAGAAGTA--GGACAA---CAAAACTG 101376 i v i ii i-- ii iv i v --i --- v i i L1M5_orf2#LIN 375 GAAGCAAAAACTGACAGAACTAAAAGGAGAAATAGACAAATCCACAATTA 424 chrXptel1M 101377 TAATAGTGGAGATCTCAACCTTGCACTCTCAG--ATTAGACAAACCAAAC 101424 i --? i i vi?v v -- - i i v ii L1M5_orf2#LIN 425 TAGT--NGGAGATTTTAACACNCCTCTCTCAGTAATT-GATAGAACAAGT 471 chrXptel1M 101425 CTCAAAACAAATAAGAAATAAATTAAAAAGTAAATAGAATATTAGAAAAA 101474 ---- i -------- i iv v v v v v L1M5_orf2#LIN 472 ----AGACAAA--------AAATCAGTAAGGATATAGAAGATTTGAACAA 509 chrXptel1M 101475 ----ATTAGGTATGTTG--------GATCTTTGGAGAAAATTGAATGGAG 101512 ---- i ivi vv -------- iv iv v i ?v ivv i L1M5_orf2#LIN 510 CACTATCAACCAACTTGACCTAATTGACATTTATAGAACACTNCACCCAA 559 chrXptel1M 101513 ATAGAAAGGAATATACTTTCTTCTCAGCAGTTCATGGAACCTAT-TCAAA 101561 vv v?ivi i v i ivv iv v v -i i L1M5_orf2#LIN 560 CAACNGCAGAATACACATTCTTTTCAAGTGCACATGGAACATTTACCAAG 609 chrXptel1M 101562 ATTGACCAATATTATTAGGACATAAAGAC----CTCAAATTAAATGCAA- 101606 v - - ?i i v - ---- -- vi? - L1M5_orf2#LIN 610 ATAGACC-ATA-TNCTGGGCCATAAA-ACAAGTCTCAA--TAAATTTNAA 654 chrXptel1M 101607 ------GAAAGCAGAAATAGTAAATGTTCTTTCAGATCATGATGCAA--- 101647 ------ v v v v -- i -- i ii v --- L1M5_orf2#LIN 655 AGGATTGAAATCATACAGAGT--ATGTTCTCT--GACCACAATGGAATTA 700 chrXptel1M 101648 ---TAAAAACTACATTCAACAAAAAGTTAGGTAAAGA--CCAAAAGTAAT 101692 --- i ii - -- v ?v i i -- vv i v L1M5_orf2#LIN 701 AATTAGAAATCA-AT--AACAAAAAGATANCTAGAAAATCCCCAAATATT 747 chrXptel1M 101693 TGGAAACTAAACAATTCA-TCTTAAAGAATGATTCGGT-AAACAGCAAAT 101740 i iv - ii v ivvv v - v iv L1M5_orf2#LIN 748 TGGAAATTAAACAACACACTTCTAAATAACCCATGGGTCAAAGAAGAAAT 797 chrXptel1M 101741 TATAGATACAATTAAAA-----TTTCACCAAGATAATAGACAAATGAGAC 101785 i i i?viv i ----- v v vii i ? ivv -- v L1M5_orf2#LIN 798 CACAANGGAAATTAGAAAATATTTTGAACTGAATGANAATGAAA--ATAC 845 chrXptel1M 101786 ATCATACCAAAATTT-TGGGATG-AGCCAAAG-GGTAATAAGAGGAA 101829 v i - - i -i iv v i L1M5_orf2#LIN 846 AACATATCAAAATTTGTGGGATGCAGCTAAAGCAGTGCTTAGAGGGA 892 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 38.48 CpG sites = 118, Kimura (unadjusted) = 38.69 Transitions / transversions = 1.09 (118/108) Gap_init rate = 0.09 (74 / 811), avg. gap size = 1.72 (127 / 74) 360 25.04 8.00 2.93 chrXptel1M 101018 101342 (898658) L1MC4_5end#LINE/L1 2215 2555 (0) m_b327s551i22 13751 chrXptel1M 101018 TAACTGTAAATTGGGGGATGAACTC-CCCATAAAGAGAGGCAGAT----A 101062 v --- v ? - ? v i ?iv ---- L1MC4_5end#LI 2215 TAAATGTAAAT---GGGCTNAACTCACCNATTAAAAGANAAAGATTTTCA 2261 chrXptel1M 101063 GACTGAT---CAAAGTCAGAACCA-CAATATGTT-TTTACAAAA---ACA 101104 i?i i?---? iv v - v i - ? i --- L1MC4_5end#LI 2262 ANTTGGNTNANAAAGCAAGACCCAACTATATGCTGTNTACAAGAGACACA 2311 chrXptel1M 101105 C--AAAAAGGGAGATACATATAGAGTAAAGGTAAAAGGCTGGAGCAAAAT 101152 -- ii v v v v iv i ii i v ?v i L1MC4_5end#LI 2312 CCTAAAAAAAGTGATTCAGAAAGGCTGAAAATAAAGGGATGGANAAAGAT 2361 chrXptel1M 101153 CTATTATGCTCAGGTGAGTCAAAACAGA-GGGTAGCCACCCTTATCTCAG 101201 v ii v vv v - iv v - v v i?i ? v L1MC4_5end#LI 2362 ATACCAGGCAAATG-GAAACAAAAAAGAAGGGTTGCAATNTTNATATCAG 2410 chrXptel1M 101202 ATCAA--------CAAAAGAAAAATTGATCTAATTAAAAGAGATAAGGAA 101243 iv -------- i?v vi------ ? i i L1MC4_5end#LI 2411 ACAAAGTAGANTTCAAGNCAAAAAGC------ATTAAANGAGACAAAGAA 2454 chrXptel1M 101244 GGAAACTACATCCTGCTAAACGGAGCA-TAAACAACGAAGCAATATCAAT 101292 ?v i vi vv ? v ??? - vv i vv v L1MC4_5end#LI 2455 GGNCATTTTATAATGNTAAAGGNNNCAATTCACAATGAAGATATAACAAT 2504 chrXptel1M 101293 ATTAAACATATATGCACCAAGTGGTATGGCA-CCAACTTCCTAAAGGAGA 101341 vv i ? i iii ?i - v? iv v i L1MC4_5end#LI 2505 TATAAATATNTATGCACCAAATAACANAGCANCCACNTTTATAAAGCAAA 2554 chrXptel1M 101342 A 101342 L1MC4_5end#LI 2555 A 2555 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 33.36 CpG sites = 37, Kimura (unadjusted) = 33.36 Transitions / transversions = 0.88 (37/42) Gap_init rate = 0.06 (21 / 324), avg. gap size = 1.71 (36 / 21) 627 30.75 6.99 2.68 chrXptel1M 101115 101829 (898171) L1P4_orf2#LINE/L1 148 892 (2402) m_b327s551i23 13751 chrXptel1M 101115 GATACATATAGAGTAAAGGTAAAAGGCTGGAGCAAAATCTATTATGCTCA 101164 i vi iv v i i ? v i i i vv L1P4_orf2#LIN 148 GACACCCATAGGCTCAAAGTAAAGGGNTGGAGAAAGATCTATCACGCAAA 197 chrXptel1M 101165 GGTGAGTCAAAACAGAG----GGTAGCCACCCTTATCTCAGATCAACAAA 101210 v vi iv v ---- v i ii v ---- L1P4_orf2#LIN 198 CGGAAAACAAAAAAGAGCAGGGGTCGCTATTCTTATATCAGAT----AAA 243 chrXptel1M 101211 AGAAAAATTGATCTAAT-----TAAAAGAG-ATAAGGAAGGAAACTACAT 101254 v i vv i v i i----- i - i i iv i L1P4_orf2#LIN 244 ACAGACTTTAAACCAACAACAGTAAAAAAGGACAAAGAAGGGCATTACAT 293 chrXptel1M 101255 CCTGCTAAACGGAGCA--TAAACAACGAAGCAATATCAATATTAAACATA 101302 vv v v vv -- v - vvv v v vi i L1P4_orf2#LIN 294 AATGATAAAGGGTTCAATTCAACAA-GAAGACTTAACTATCCTAAATATA 342 chrXptel1M 101303 TATGCACCAAGTGGTATGGCACC-AACTTCCTAAAGGAGAAGTTA----A 101347 i v iiiv ivi - iv v -- v ?v---- L1P4_orf2#LIN 343 TACGCACCCAACATTGGAGCACCCAGATTCATAAA--ACAAGTNCTTCTA 390 chrXptel1M 101348 GAGTTGCAAGAAG--TAGGACAACAAAACTGTAATAGTGGAG-ATCTCAA 101394 vi i i i -- vi i v v vi i - ii L1P4_orf2#LIN 391 GACCTACGAAAAGACTTAGACAGCCACACAATAATAGTGGGGGACTTCAA 440 chrXptel1M 101395 CCTTGCACTCTCAG-ATTAGACAAACCAAACCTCAAAACAAA----TAAG 101439 viiv vv -i i i ---- i ii i ---- v L1P4_orf2#LIN 441 CACCCCACTGACAGCGTTAGACAGATCA----TCGAGGCAGAAAACTAAC 486 chrXptel1M 101440 AAATAAATTA-AAAAGTAAATAGAATATTAGAAAAAATTAGGTATGTTGG 101488 v v-ii vv ivvi i i v vv - i iiv iv i L1P4_orf2#LIN 487 AAAGAAATTCTGGACTTAAACTCGACACTTGACCAA-TTGGACCTAATAG 535 chrXptel1M 101489 ATCTTTGGAGAAAATTGAATGGAGATAGAAAGGAATATACTTTCTTCTCA 101538 iv i iv v i vv ivv ?vv vv vi v L1P4_orf2#LIN 536 ACATCTACAGAATACTCCACCCANCAACCACAGAATATACATTCTTCTCA 585 chrXptel1M 101539 GCAGTTCATGGAACCTATTC-AAAATTGACCAATATTATTAGGACATAAA 101587 v v iv i v i - i i - i - ii v v L1P4_orf2#LIN 586 TCTGCACACGGAACATACTCTAAGATCGACC-ACA-TGCTCGGCCATAAA 633 chrXptel1M 101588 G---ACCTCAAATTAAATGCAAGAAAGCAGAA---ATAGTAAATGTTCTT 101631 ---ii -- v i iiv --- vi vii v i L1P4_orf2#LIN 634 GCAAGTCTCAA--TAAATTCAAAAAAATCGAAATCATACCAACCATACTC 681 chrXptel1M 101632 TCAGATCATGATGCAATAAAAACTACATTCAA---CAAAAAGTTAGGTAA 101678 i i iii ? iviv v --- i v vvv v L1P4_orf2#LIN 682 TCGGACCACAGTGNAATAAAAATAGAAATCAATACCAAGAAGATCTCTCA 731 chrXptel1M 101679 AGAC--CAAAAGTAATTGGAAACTAAACAATTCA-TCTTAAAGAATGA-- 101723 i -- v v vv i i ii- i --- -- L1P4_orf2#LIN 732 AAACCACACAATTACATGGAAATTAAACAACTTGCTCCT---GAATGACT 778 chrXptel1M 101724 -TTCGGTAAACAGC-AAATTATAGATACAATT--AAAATTTCACCAAGAT 101769 - v i - - ii v v -- v viii i L1P4_orf2#LIN 779 TTTGGGTAAACAACGAAATTA-AGGCAGAAATCAAAAAATTCTTTGAAAT 827 chrXptel1M 101770 AATAGACAAATGAGACAT--CATACCAAAAT-TTTGGGATG-AGCCAAAG 101815 ? vv v vv i-- - i - ? L1P4_orf2#LIN 828 NAATGAAAACAGAGACACAACATACCAAAATCTCTGGGATGCAGCNAAAG 877 chrXptel1M 101816 -GGTAATAAGAGGAA 101829 -i iv L1P4_orf2#LIN 878 CAGTGTTAAGAGGAA 892 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 38.55 CpG sites = 109, Kimura (unadjusted) = 40.72 Transitions / transversions = 1.04 (109/105) Gap_init rate = 0.06 (45 / 714), avg. gap size = 1.56 (70 / 45) 1649 25.57 8.50 1.15 chrXptel1M 101872 102765 (897235) L1M5_orf2#LINE/L1 1283 2241 (1053) m_b327s551i24 13751 chrXptel1M 101872 AAATGGACAA-TTACTCCAAAAATATAGACTTCCCAGACTAACAGAGGAG 101920 - v iv i i i?i v v i i ?v i i L1M5_orf2#LIN 1283 AAATGGACAAATTCCTTGAAAAACACAANTTACCAAAACTGACNCAAGAA 1332 chrXptel1M 101921 GAAGTA---AATTGTTGAATAGTCC---ATTTCAGAAAGAAATAGAACAG 101964 i --- i-- i --- i vvv v ivv L1M5_orf2#LIN 1333 GAAATAGAAAATC--TGAATAGCCCTATATCTATTAAAGAAATTGAATTT 1380 chrXptel1M 101965 GCA-TTAACAAC--TCCC-TAAGGAAAAATCCCAGGACCAGATGGATTTA 102010 i - v -- -i i v - v v i L1M5_orf2#LIN 1381 GTAATTAAAAACCTTCCCACAAAGAAAACTCC-AGGCCCAGATGGCTTCA 1429 chrXptel1M 102011 CATGTGAATTTTACCAAACATTTAAAAGAACAATTGGCCCAATG-TATAT 102059 vv i iii iv vivv v- i i L1M5_orf2#LIN 1430 CTGGTGAATTCTACCAAACATTTAAGGAAGAAATAATACCAATCTTACAC 1479 chrXptel1M 102060 AAATTATTTGATAAATTAG-GAATGAAGGAGTCCTTTCAAATTC-TTCCA 102107 i v iv v v -i v i iiv i v i - ii L1M5_orf2#LIN 1480 AAACTCTTCCAGAAAATAGAAAAAGAGGGAACACTTCCCAACTCATTTTA 1529 chrXptel1M 102108 TGACACGAACATGGTACTGGATACCTAAACCAGGT--AGGTGAAACAAGA 102155 vi v i ?iiv - v ? ii-- iiivv L1M5_orf2#LIN 1530 TGAGGCCAGCATNACCCT-GATACCAAAACCNGACAAAGACATTACAAGA 1578 chrXptel1M 102156 GAAAGAAAA----AGA-CAATCTCCCTAATG-ATAT-GATGCTAAAATCT 102198 - ---- - v v - i - v i L1M5_orf2#LIN 1579 -AAAGAAAATTACAGACCAATATCCCTCATGAACATAGATGCAAAAATCC 1627 chrXptel1M 102199 TA---AAGATATTAGCAAA--AGACACAGAAAATCATCTCCAAGATAATA 102243 ?--- i --ii iv v vvi vvvv i L1M5_orf2#LIN 1628 TNAACAAAATATTAGCAAATCGAATCCAGCAATATATAAAAAGGATAATA 1677 chrXptel1M 102244 CA-CATGATCAAGT-AGATTTATACCAAGAAT-CAGGGCTGGTTCAATAT 102290 - i -i i v i - i i i i L1M5_orf2#LIN 1678 CATCATGACCAAGTGGGGTTTATCCCAGGAATGCAAGGTTGGTTTAACAT 1727 chrXptel1M 102291 AGGAAAAC--ATCAATATAATTAGCCATGTTAAT--AACAAATTA-AAAA 102335 vv i-- i vi i i-- i vv - L1M5_orf2#LIN 1728 TCGAAAATCAATCAATGTAATTCACCATATTAACAGAATAAAGGAGAAAA 1777 chrXptel1M 102336 ACCATA-GATCATTTCAATAGATGCAGAAA----ATTTGATAAAATCCAA 102380 i - i ---- i i L1M5_orf2#LIN 1778 ATCATATGATCATCTCAATAGATGCAGAAAAAGCATTTGACAAAATTCAA 1827 chrXptel1M 102381 CATCCATTCCTATTAAAAACACTTG--AATATAGGA--AAAATGGACTTT 102426 i v iv v ii-- vv -- i v vi L1M5_orf2#LIN 1828 CACCCATTCATGATAAAAACTCTCAGCAAACTAGGAATAGAAGGGAACTT 1877 chrXptel1M 102427 CCTTAAAATAATCAGCAGCATCTATTTAAACCATCCA-TAAGCATCATAT 102475 i vv i v ivi ivv v v v -i? i i L1M5_orf2#LIN 1878 CCTCAACCTGATAAAGGGCATCTACGAAAAACCTACAGCNAACATCATAC 1927 chrXptel1M 102476 GTAATGGAGACAAACTCAAC-CATTCCCAATAAGATCTGGGA----AAAA 102520 v v v ? v ?- v vv v i ---- v L1M5_orf2#LIN 1928 TTAATGGTGAAANACTGAANGCTTTCCCCCTAAGATCGGGAACAAGACAA 1977 chrXptel1M 102521 GGTTGCCCACTATCACCGTTACTATTTAATATTGTATTGAAA--CGTA-- 102566 v i i ? ii v i i i i i-- v -- L1M5_orf2#LIN 1978 GGATGTCCGCTNTCACCACTTCTATTCAACATTGTACTGGAGGTCCTAGC 2027 chrXptel1M 102567 CA--GCAAAAAGCTGAGGAA---GAATTAAAGGAATAAGAAATAGGCAAG 102611 -- v vii i ---i v v - i v v L1M5_orf2#LIN 2028 CAGTGCAATAAGGCAAGAAAAAGAAATAAAAGGCATAA-AGATTGGAAAG 2076 chrXptel1M 102612 --AGAAAGCAAATTATCACTTTTC-CA---TACATGA-TGTATACTTAGA 102654 -- vv i i ?i v - ---v - ? v L1M5_orf2#LIN 2077 GAAGAAATAAAACTGTCNTTATTCGCAGATGACATGATTGTNTACGTAGA 2126 chrXptel1M 102655 GAACCCCAGA-ATTCTCTAAAAAAGTTATTAGAA-----AAATAAACTTT 102698 i i ? i - v vi ? ii i ----- i i --- L1M5_orf2#LIN 2127 AAATCCNAAAGAATCTACAAANAAACTACTAGAACTAATAAGTGAA---T 2173 chrXptel1M 102699 TTAGCAAAGTTGTTGGTTATAAAAAAAACCCACATAGTCATCA---GCAT 102745 i i i? v i iivv ivi v i-- --- i L1M5_orf2#LIN 2174 TTAGCAAGGTCGCNGGATACAAGGTCAATATACAAAA--ATCAATTGTAT 2221 chrXptel1M 102746 TCTTATATATCACTAACAAA 102765 ii ii vi L1M5_orf2#LIN 2222 TTCTATATACTAGCAACAAA 2241 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 31.83 CpG sites = 127, Kimura (unadjusted) = 32.53 Transitions / transversions = 1.28 (127/99) Gap_init rate = 0.06 (51 / 893), avg. gap size = 1.71 (87 / 51) 321 19.48 17.96 3.58 chrXptel1M 103529 103773 (896227) L1ME3G_3end#LINE/L1 1 279 (645) m_b327s551i25 13751 chrXptel1M 103529 TCAATTTCCAAAATATATAA-GAATTAACCTTTAA-TCAA--------AG 103568 i v i - i -- vi - -------- L1ME3G_3end#L 1 TTAATATCCAGAATATATAAAGAACT--CCTACAAATCAATAAGAAAAAG 48 chrXptel1M 103569 CCATTTCCAATTGAAAA---TGTAAAGGATATGAACAA-CAATTCTCAGA 103614 v vi- v ---v i i- v L1ME3G_3end#L 49 ACAAC-CCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGA 97 chrXptel1M 103615 -GAAGAAAGAAACATTTTTAGT---CA-ATGAAAAT---CTCCAAGTCA- 103655 - i v v v vvii i --- - v--- v vv - L1ME3G_3end#L 98 AGAGGAAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCAC 147 chrXptel1M 103656 TATTAATCAGAGAAATACAAATTAAGACAAC--TCAAATAACCA-----C 103698 v i i i -- v i - ----- L1ME3G_3end#L 148 TAGTAATCAGGGAAATGCAAATTAAAACAACAATGAGAT-ACCATTTTTC 196 chrXptel1M 103699 ACCTGTCATTGGCAGAATGGCAGAAA---AAAA---TGAT--TAT----T 103736 --- --- v i --- --- -- ---- L1ME3G_3end#L 197 ACC---CAT---CAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGT 240 chrXptel1M 103737 GTTG--GAGGGGATCGGGAAATTGGGACATTTATGCATT 103773 -- vi v iv v vi i i i L1ME3G_3end#L 241 GTTGGCGAGGGTGTGGGGAAACGGGTACTCTCATACACT 279 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 22.26 CpG sites = 22, Kimura (unadjusted) = 22.79 Transitions / transversions = 0.92 (22/24) Gap_init rate = 0.11 (26 / 244), avg. gap size = 2.08 (54 / 26) 347 23.22 14.07 0.44 chrXptel1M 103575 103773 (896227) L1ME5_3end#LINE/L1 58 283 (658) m_b327s551i26 13751 chrXptel1M 103575 CCAATTGAAAA---TGTAAAGGATATGAACAA-CAATTCTCAGA-GAAGA 103619 v ---v i i- iv - i L1ME5_3end#LI 58 CCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAGGA 107 chrXptel1M 103620 AA---GAAACATTTTTAGTCA-ATGAAAAT---CTCCAAGTCAT-ATTAA 103661 --- vii vvi iv - i v--- v v - v L1ME5_3end#LI 108 AACCCGAAAGGCTAACAAGCATATGAAGAGATGCTCAAACTCATTAGTAA 157 chrXptel1M 103662 TCAGAGAAATACAAATTAAGACAAC--TCAAATA--AC--CACACCTGTC 103705 i i -- v i -- --i i i L1ME5_3end#LI 158 TCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCTATT 207 chrXptel1M 103706 --ATTGGCAGAATGGCAGAAA-----AAAATGATTATTGTTGGAGGGGA- 103747 -- i i -ivi ----- v viv v v i - L1ME5_3end#LI 208 AGACTGGCAAAA-ATTAGAAAGCTGGATAATGCCAAGTGTTGGCGAGGAT 256 chrXptel1M 103748 -TCGGGAAATTGGGACATTTATGCATT 103773 - v ? v i vi i i L1ME5_3end#LI 257 GTGGGGANATAGGAACCCTCATGCACT 283 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 28.34 CpG sites = 25, Kimura (unadjusted) = 28.34 Transitions / transversions = 1.19 (25/21) Gap_init rate = 0.07 (14 / 198), avg. gap size = 2.07 (29 / 14) 46 3.10 4.55 0.00 chrXptel1M 104438 104503 (895497) (AAATAA)n#Simple_repeat 1 69 (0) m_b327s252i15 13752 chrXptel1M 104438 AAATAAAAATAAAAATAAAAATAAAAAT-AAAAT-AAAA-AACAATAATA 104484 - - - v v (AAATAA)n#Sim 1 AAATAAAAATAAAAATAAAAATAAAAATAAAAATAAAAATAAAAATAAAA 50 chrXptel1M 104485 ATAAAAATAAAAATAAAAA 104503 (AAATAA)n#Sim 51 ATAAAAATAAAAATAAAAA 69 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.05 (3 / 65), avg. gap size = 1.00 (3 / 3) 514 30.97 4.82 4.82 chrXptel1M 104587 105105 (894895) L1P3_orf2#LINE/L1 2733 3251 (43) m_b327s551i27 13753 chrXptel1M 104587 CTACAGCAATCTAGTGCTTGACAAACC---CAAAGACTCCAACGTTTTGG 104633 i v ii vi --- i --v i iv ---- L1P3_orf2#LIN 2733 CTACAACCATCTGATCTTTGACAAACCTGACAAAAAC--AAGCAAT---- 2776 chrXptel1M 104634 GGGGATAAGAATTGACTATTTGACAAGAACTGCTGGAAAAACTGTAAACT 104683 - i vv i i iviv i i ---i L1P3_orf2#LIN 2777 GGGGA-AAGGATTCCCTATTTAATAAATGGTGTTGGGAAAACTG---GCT 2822 chrXptel1M 104684 AG---TATGGCAGAAA-CTAGGCATTGACCCACACCTAATATCATATACC 104729 --- - - iiivv v viv v i i v v L1P3_orf2#LIN 2823 AGCCATATG-CAGAAAACTGAAACTGGACCCCTTCCTTACACCTTATACA 2871 chrXptel1M 104730 AAGATAAGATAGAAATGAATTCATGATTTAAACATAAGGAATGACATTAT 104779 i v iv vi i i v v i i ivv i v ii L1P3_orf2#LIN 2872 AAAATTAACTCAAGATGGATTAAAGACTTAAACGTAAGACCTAAAACCAT 2921 chrXptel1M 104780 AAACAAATTAGAAGAATAA---AGGATAGTTTACCTCCCAGATCTGTGGA 104826 v vvi - --- vv --- vii iv -i i i L1P3_orf2#LIN 2922 AAAAACCCTAGAAGAA-AACCTAGGCAA---TACCATTCAGGAC-ATAGG 2966 chrXptel1M 104827 GAAGGGTG--GAATTTGTGACCAAAGAACTGGAACTTAT--TATTGAACA 104872 v v ii-- v ii i iv iii viv --i vii vi L1P3_orf2#LIN 2967 CATGGGCAAAGACTTCATGACTAAAACACCAAAAGCAATGGCAACAAAAG 3016 chrXptel1M 104873 CCAAA-TAGATAATTTTGATTATATTAAGTTAAAAAGGTTTTGTACA--- 104918 - v i v vv ivv ii i v i i --- L1P3_orf2#LIN 3017 CCAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCA 3066 chrXptel1M 104919 AACAAAACTA--ATGCAGAGAAGATTAGAAGGGAAGCAATAAACTGGGAA 104966 vi -- - ---- v iv v v v i i v i L1P3_orf2#LIN 3067 AAAGAAACTATCAT-CAGAG----TGAACAGGCAACCTACAGAATGGGAG 3111 chrXptel1M 104967 AACATTTTTATATTCAAAGGTTCTGATAAAGGCCTCATTTCTA-AATATA 105015 v ii v v vvvv i v v v i - v L1P3_orf2#LIN 3112 AAAATTTTTGCAATCTATCCATCTGACAAAGGGCTAATATCCAGAATCTA 3161 chrXptel1M 105016 TAGAGAAGTGACTCAAATTTACAAG---AACTCAAGCCATTCTCCAATTC 105062 i ii v v vv --- vv i v -- i -- L1P3_orf2#LIN 3162 CAAGGAACTTAAACAAATTTACAAGAAAAAAACAAACAA--CCCCA--TC 3207 chrXptel1M 105063 ATAAA-TGGTCAAAGGATATGAACAGACAGTTTTTACATGAAGA 105105 v - v i v i i v v L1P3_orf2#LIN 3208 AAAAAGTGGGCGAAGGATATGAACAGACACTTCTCAAAAGAAGA 3251 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 39.85 CpG sites = 77, Kimura (unadjusted) = 40.52 Transitions / transversions = 1.01 (77/76) Gap_init rate = 0.07 (37 / 518), avg. gap size = 1.35 (50 / 37) 315 28.79 6.57 6.18 chrXptel1M 104875 105148 (894852) L1M1_orf2#LINE/L1 3020 3294 (0) m_b327s551i28 13753 chrXptel1M 104875 AAATAGATAATTTTGATTATATTAAGTTAAAAAGGTTTTGTA---CAAAC 104921 i i v vv i i i v i i --- v L1M1_orf2#LIN 3020 AAATGGACAAATGGGATCACATCAAGTTAAAAAGCTTCTGCACAGCAAAG 3069 chrXptel1M 104922 AAAACTAATGCAGAGAAGATTAGAAGGGAAGCAATAAACTGGGAAAACAT 104971 i - - - v ii v ii iv v v i i v i v L1M1_orf2#LIN 3070 GAAAC-AAT-CA-ACAAAGTGAAGAGACAACCCACAGAATGGGAGAAAAT 3116 chrXptel1M 104972 TTTTA-----TATTCAAAGGTTCTGATAAAGGCCTCATTTCTA-AATATA 105015 v i----- ii ----- i i vi v vv i - L1M1_orf2#LIN 3117 ATTTGCAAACTACCCA-----TCTGACAAGGGATTAATAACCAGAATATA 3161 chrXptel1M 105016 TAGAGAAGTGACTCAAATTTACAAGAACTCAAGCC--ATTCTCCAATTCA 105063 ii iv v vv v i i i --v ii -- vv i v L1M1_orf2#LIN 3162 TAAGGAGCTCAAACAACTCTATAGGAA--AAAATCTAATAATCCGATTAA 3209 chrXptel1M 105064 TAAATGGTCAAAGGATATGAACAGACAGTTTTTACATGAAGA-----AAC 105108 v v i v i v i i v v ----- v L1M1_orf2#LIN 3210 AAAATGGGCAAAAGATCTGAATAGACATTTCTCAAAAGAAGACATACAAA 3259 chrXptel1M 105109 TG--AAACCCTTTCTAATCATATGAAAAGGTGTTCCAAATCA 105148 -- ------- iv i v v L1M1_orf2#LIN 3260 TGGCAAAC-------AGGCATATGAAAAGGTGCTCAACATCA 3294 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.22 CpG sites = 38, Kimura (unadjusted) = 36.84 Transitions / transversions = 1.06 (38/36) Gap_init rate = 0.08 (23 / 273), avg. gap size = 1.52 (35 / 23) 1626 29.54 2.38 2.38 chrXptel1M 105006 105636 (894364) L1ME5_3end#LINE/L1 7 637 (304) m_b327s551i29 13753 chrXptel1M 105006 TCTA-AATATATAGAGAAGTGACTCAAATTTACAAGAACTCAAGCCATT- 105053 - i ii v vviv iv v-- v iv?- L1ME5_3end#LI 7 TCTAGAATATACAAGGAACTCCTGCAAATCAACAAGAAA--AAGACGGNA 54 chrXptel1M 105054 -CTCCAATTCATAAATGGTCAAAGGATATGAACAGACAGTTTTTACATGA 105102 - i vv v v i i vi v v L1ME5_3end#LI 55 ACCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGA 104 chrXptel1M 105103 AGAAA-CTGAAACCCTTTCTAATCATATGAAAAGGTGTTCCAAATCACTA 105151 i - i vv vv - v i i i v v i L1ME5_3end#LI 105 GGAAACCCGAAAGGCTAAC-AAGCATATGAAGAGATGCTCAAACTCATTA 153 chrXptel1M 105152 CTGATCAGAGAAATACAAATTAAGACAACTCTGAGATACCACTACACACC 105201 v i i i vv i vi L1ME5_3end#LI 154 GTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACC 203 chrXptel1M 105202 TGTCAGATTGGCTAAGATGACAGGAAA--AGATAATGATGAATGTTAGAG 105249 i i i v i --i i i--i vii i i v L1ME5_3end#LI 204 TATTAGACTGGCAAAAAT--TAGAAAGCTGGATAATGCCAAGTGTTGGCG 251 chrXptel1M 105250 AGGATGTGGAAAAACTGGAACACTGATGCATTGTTGGTGGAGTTGTGAAC 105299 ii ? iv v v i i iiv ii L1ME5_3end#LI 252 AGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGAC 301 chrXptel1M 105300 GAATCCAGCCATTCTGGAGAGCAATCTGGAATTATGCCCCAA--AAGTTA 105347 vii v v v --- ii i-- i L1ME5_3end#LI 302 TGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTA---CTTAGTCAAATTA 348 chrXptel1M 105348 TCAAACTGTGCATACCCTTTGACCCAGCAGTTTCTCTGCTGGGCCTGTAT 105397 -- ivv ii v i i v v iv i L1ME5_3end#LI 349 --AGTATACGCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATAT 396 chrXptel1M 105398 CCCAGAGATATTTTAAGA-AGG-----AAAGGGACCTGTATGTGCCAAAA 105441 i v i v v - ----- i v i ---- ii L1ME5_3end#LI 397 CCCAAAGAAATTCTCACACAGGTCCATAAGGGGACATGTACG----AGGA 442 chrXptel1M 105442 TGTTTGTGGCAGCCCTGTTTGTAGTGGCCAGAAACTGGAAACTGAGTGGA 105491 ii v vi i vi i ii ii vivv i L1ME5_3end#LI 443 TGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGGG 492 chrXptel1M 105492 TGCCCATCAGTTGGTGAATGGCTGAATAAGTTATGGTATATGAATGTTAT 105541 i v v v i v iii iv i iv v iiii L1ME5_3end#LI 493 TGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACACCAT 542 chrXptel1M 105542 GGAATCTTACTCTTCTGTAAGAAATGACCAACAGGATGATTTCAGAGAGG 105591 i vi iv vv v v iii vi vi vviv v vii L1ME5_3end#LI 543 GGAGTACTATGCAGCAGTTAGAAGCAACGGACTAGATGTACACATAGCAA 592 chrXptel1M 105592 TCTGGAAAGA-CTTATAGGAAATGATGCTGAGTGAAATGAGCAGGA 105636 iv vi - - ii v ii vi i i L1ME5_3end#LI 593 CATGGATGGATCTTA-AAAACATAGTGCTGAGTGAAAAAAGTAAGA 637 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 37.63 CpG sites = 105, Kimura (unadjusted) = 38.72 Transitions / transversions = 1.36 (105/77) Gap_init rate = 0.04 (24 / 630), avg. gap size = 1.25 (30 / 24) 13 4.70 0.00 4.35 chrXptel1M 106461 106484 (893516) (CCCT)n#Simple_repeat 1 23 (0) m_b327s252i17 13754 chrXptel1M 106461 CCCTCCCTCCCTCCATCCCCTCCC 106484 v - (CCCT)n#Simpl 1 CCCTCCCTCCCTCCCT-CCCTCCC 23 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 1443 29.01 3.15 2.97 chrXptel1M 106808 107379 (892621) C L1ME5_3end#LINE/L1 (313) 628 56 m_b327s551i30 13755 chrXptel1M 106808 TTTCACTCAGCATCA-GTTCATGTAAG-TCTCTCTAAGCCTCTCTGTCTT 106855 ii - -- v - iv i v iiv v v v C L1ME5_3end#LI 628 TTTCACTCAGCACTATGTT--TTTAAGATCCATCCATGTTGCTATGTGTA 581 chrXptel1M 106856 CATCCTGCTGGTCATTTCTTACAGAACAATAATATTCCATAACATTCATA 106905 iv iiv iii v v vvvv i i iiii v v C L1ME5_3end#LI 580 CATCTAGTCCGTTGCTTCTAACTGCTGCATAGTACTCCATGGTGTGCATC 531 chrXptel1M 106906 TATCGCAATTTACCCAACCATTCTCCAATTGATGGGCATCCATTCATTTT 106955 i i i v i v i v v i i vvivvii C L1ME5_3end#LI 530 CACCACATTTTACCTATCCACTCTCCCAGTGATGGACACCCAGGTTGCCT 481 chrXptel1M 106956 CCAGTTTCTGGCCACTACAAACAGGGCCGCCACAAACATTTAGGCACATA 107005 ii i iv i iv i v ii i---- v i C L1ME5_3end#LI 480 CCAACTCCCCGCCACCACAAACAACGCTGCAATGAACATC----CTCGTA 435 chrXptel1M 107006 CAGGTCTCTTTC----CCTTCTTTAGTATCTCTTTGGGGTATAAGCCCAG 107051 v i i v---- viv v v i i vi C L1ME5_3end#LI 434 CATGTCCCCTTATGGACCTGTGTGAGAATTTCTTTGGGATATATACCCAG 385 chrXptel1M 107052 TAGTAGCACTGCTGGATCAAAGGGTATGCACCGTTTGATAACTTTTGGGG 107101 v ii v i i v --- v iv v v --- i C L1ME5_3end#LI 384 GAGCGGAATTGCTGGGTCATAGGGTATGC---GTATACTTAATTT---GA 341 chrXptel1M 107102 C---ATAATTCCAGATTGCTCTCCAGAATGGTTGGATTCGTTCACAACTC 107148 ---i v v i v iiv ii vii C L1ME5_3end#LI 340 CTAAGTACTGCCAGATTGCTCTCCAGAATGGCTGCACCAGTCTACACTCC 291 chrXptel1M 107149 CACCAACAATGCATCAGTGTCCCAGTTTTCCCGCATCCCCTCCAACATTC 107198 i i v v i vi ? i i i v i i C L1ME5_3end#LI 290 CACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATCCTCGCCAACACTT 241 chrXptel1M 107199 ATCATTATTT--TTTCCTGTCATCTTGGCCAATCTGACAGGTGTGTAGTG 107246 iv ii--i i i-- i v i i i iv C L1ME5_3end#LI 240 GGCATTATCCAGCTTTCTA--ATTTTTGCCAGTCTAATAGGTGTAAAGTG 193 chrXptel1M 107247 GTATCTCAGAGTTGTCTTAATTTGCATTTCTCTGATCAATAGTGATTTGG 107296 i vv i i v i v v C L1ME5_3end#LI 192 ATATCTCATTGTTGTTTTAATTTGCATTTCTCTGATTACTAATGAGTTTG 143 chrXptel1M 107297 AACACTCTTTCATATAAATGGAAATAG--TTTC-AATTTCATCATCTGAA 107343 i iiii ivv v--- -- -ii v v v C L1ME5_3end#LI 142 AGCATCTCTTCATATGCTTGT---TAGCCTTTCGGGTTTCCTCTTCTGTA 96 chrXptel1M 107344 AAT----TGTTCATATCCTTTGACCATTTATCAATTGGAG 107379 ---- v v v i C L1ME5_3end#LI 95 AATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGGGG 56 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 37.04 CpG sites = 92, Kimura (unadjusted) = 37.66 Transitions / transversions = 1.33 (92/69) Gap_init rate = 0.04 (25 / 571), avg. gap size = 1.40 (35 / 25) 1458 29.45 2.04 1.29 chrXptel1M 106884 107423 (892577) C L1ME4c_3end#LINE/L1 (275) 555 12 m_b327s551i31 13755 chrXptel1M 106884 ATAATATTCCATAACATTCATATATCGCAATTTACCCAACCATTCTCCAA 106933 vivi ?v i i ii ii i v C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chrXptel1M 106934 TTGATGGGCATCCATTCATTTTCCAGTTTCTGGCCACTACAAACAGGGCC 106983 v i ii vvivv i i v i i i i iv i C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCT 456 chrXptel1M 106984 GCCACAAACATTTAGGCACATACAGGTCTCTTTCCCTTCTTTAG---TAT 107030 v ii i vv ii i v --- i v --- C L1ME4c_3end#L 455 GCAATGAACATCTTCGTGCATATAGCT---TTTTCCTTCTTTTGAATTAT 409 chrXptel1M 107031 CTCTTTGGGGTATAAGCCCAGTAGTAGCACTGCTGGATCAAAGGGTATGC 107080 i i i i v vv v i v i i i v C L1ME4c_3end#L 408 TTCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGA 359 chrXptel1M 107081 ACCGTTTGATAACTTTTGGGGCATAATTCCAGATTGCTCTCCAGAATGGT 107130 vv v ii i ivi i v v i i i v C L1ME4c_3end#L 358 ACATTTTTATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGT 309 chrXptel1M 107131 TGGATTCGTTCACAACTCCACCAACAATGCATCAGTGTCCCAGTTTTCCC 107180 v iivi i ?iv i i v ? v iv C L1ME4c_3end#L 308 TGTACCAATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCACC 259 chrXptel1M 107181 GCATCCCCTCCAACATTCATCATTATTTTTTCCTGTCATCTTGGCCAATC 107230 ? i v i vivi ivv ii vvv i v i i C L1ME4c_3end#L 258 GCANCCTCGCCAGCATTGGGTATTATCAATTTTTTAAATTTTTGCTAATT 209 chrXptel1M 107231 TGACAGGTGTGTAGTGGTATCTCAGAGTTGTCTTAATTTGCATTTCTCTG 107280 i i i iv i vv ii i C L1ME4c_3end#L 208 TAATAGGCGTAAAATGGTATCTCATTGTTGCTTTAATTTGCATTTCTTTG 159 chrXptel1M 107281 ATCAATAGTGATTTGGAACACTCTTTCATATAAATGGAAATAGTTTCAAT 107330 i v i vv v i i i i ivv vvv ivi? vv C L1ME4c_3end#L 158 ATTACTAGCGAGGTTGAACATTTTTCCATGTGTTTGTTTACTANTTGTAT 109 chrXptel1M 107331 TTCATCATCTGAAAAT----TGTTCATATCCTTTGACCATTTATCAATTG 107376 v v ? vi ---- i v v C L1ME4c_3end#L 108 TTCCTCTTNTGTGAATTGTCTGTTCATGTCCTTTGCCCATTTATCTATTG 59 chrXptel1M 107377 GAGAATGGCTTGA----TTTCTTATAAATTAAAGTCAATTGTCTATATAT 107422 i---- v ---- v vi i v ii v i ? C L1ME4c_3end#L 58 GG----GTCTTGATNTTTTTCTTATCAATTTGAATGAGCTCTTTATATAN 13 chrXptel1M 107423 T 107423 C L1ME4c_3end#L 12 T 12 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 37.69 CpG sites = 88, Kimura (unadjusted) = 38.95 Transitions / transversions = 1.28 (88/69) Gap_init rate = 0.02 (10 / 539), avg. gap size = 1.80 (18 / 10) 328 32.44 4.04 2.54 chrXptel1M 107289 107560 (892440) C L1M3_orf2#LINE/L1 (0) 3288 3013 m_b327s551i32 13755 chrXptel1M 107289 TGATTTGGAACACTCTTTCATATAAATGGAAATAGTTTCAATTTCATCAT 107338 v v i iii vv vviiivi vv v v v C L1M3_orf2#LIN 3288 TGATGTTGAGCATCTTTTCATATACCTGTTGGCCATTTGTATGTCTTCTT 3239 chrXptel1M 107339 CTGAAAATTGT----TCATATCCTTTGACCATTTATCAATTGGAGAATGG 107384 iv i v ---- vi v v ? i ivv -- C L1M3_orf2#LIN 3238 TGGAGAAATGTCTATTCAGGTCCTTTGCCCATTTTTNAATCGGGTTAT-- 3191 chrXptel1M 107385 CTTGATTTCTTA----TAAATTA-AAGTCAATTGTCTATATATTTTACAA 107429 - v i i---- i i i- ? -- i vii iv v C L1M3_orf2#LIN 3190 -TTGTTTTTTTGCTATTGAGTTGTANG--AGTTCCTTATATATTTTGGAT 3144 chrXptel1M 107430 ATGAGGCCTTTATCAGAACCTTTAACTGTGAAGATGTTTTCCCAGTTTGT 107479 v iv i vviv vivi ii v v i v ii C L1M3_orf2#LIN 3143 ATTAACCCCTTATCAGATATATGGTTTGCAAATATTTTCTCCCATTCCGT 3094 chrXptel1M 107480 TGCTTCCCTTCTAATCTTGTTTGCATTAATTTTGTT--TGTACAGAAGCT 107527 v v v i v iii --v iv iiv -- i C L1M3_orf2#LIN 3093 AGGTTGCCTTTTCACTCTGTT--GATTGTTTCCTTTGCTGTGCAGAAGCT 3046 chrXptel1M 107528 TTTTAATTTGATGTAATCAAAATTTTCTATTTT 107560 i i vv v v C L1M3_orf2#LIN 3045 TTTTAGTTTGATGTAGTCCCACTTGTCTATTTT 3013 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 42.21 CpG sites = 42, Kimura (unadjusted) = 43.53 Transitions / transversions = 0.95 (42/44) Gap_init rate = 0.04 (11 / 271), avg. gap size = 1.64 (18 / 11) 333 28.57 1.87 1.87 chrXptel1M 107347 107560 (892440) C L1M5_orf2#LINE/L1 (62) 3232 3019 m_b327s551i33 13755 chrXptel1M 107347 TGTTCATATCCTTTGACCATTTATCAATTGGA--GAATGGCTTGATTTCT 107394 vi i v v ?v i-- vv v -- ? C L1M5_orf2#LIN 3232 TGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTTGTCTT--TTTNT 3185 chrXptel1M 107395 TAT-AAATTAAAGTCAATTGTCTATATATTTTACAAATGAGGCCTTTATC 107443 -i ? iv -v i v i i iv v i v i C L1M5_orf2#LIN 3184 TATTGANTTGTAG-GAGTTCTTTATATATTCTGGATACGAGTCCTTTGTC 3136 chrXptel1M 107444 AGA-ACCTTTAACTGTGAAGATGTTTTCCCAGTTTGTTGCTTCCCTTCTA 107492 - iv v -?i ii v v i ? i v v i v C L1M5_orf2#LIN 3135 AGATATATGT-NTTGCAAATATTTTCTCCCANTCTGTGGCTTGCCTTTTC 3087 chrXptel1M 107493 ATCTTGTTTGCATTAATTTTGTTTGTACAGAAGCTTTTTAATTTGATGTA 107542 i v vi iv ivi vvv? vi i v v ? C L1M5_orf2#LIN 3086 ATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTTTAATTTTGATGNA 3037 chrXptel1M 107543 ATCAAAATTTTCTATTTT 107560 i v v v v C L1M5_orf2#LIN 3036 GTCCAATTTATCAATTTT 3019 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.23 CpG sites = 26, Kimura (unadjusted) = 37.75 Transitions / transversions = 0.76 (26/34) Gap_init rate = 0.03 (7 / 213), avg. gap size = 1.14 (8 / 7) 21 0.00 0.00 0.00 chrXptel1M 110204 110226 (889774) (T)n#Simple_repeat 1 23 (0) m_b327s252i18 13756 chrXptel1M 110204 TTTTTTTTTTTTTTTTTTTTTTT 110226 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTT 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 22 0.00 0.00 0.00 chrXptel1M 114505 114528 (885472) (T)n#Simple_repeat 1 24 (0) m_b328s252i0 13757 chrXptel1M 114505 TTTTTTTTTTTTTTTTTTTTTTTT 114528 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTT 24 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 18 23.85 2.22 0.00 chrXptel1M 115341 115385 (884615) (TG)n#Simple_repeat 1 46 (0) m_b328s252i1 13758 chrXptel1M 115341 TGTGTGT-TCTGTGTGTGAGTGCACATGTATGTGTGTGTCTGTATG 115385 - v v iiii i v i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 46 Matrix = Unknown Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 257 16.05 0.00 6.00 chrXptel1M 115402 115454 (884546) HSAT5v1#Satellite 5231 5280 (618) m_b328s502i0 13759 chrXptel1M 115402 GCATGCGTGTGCGCATATCGTGTGTATGTGTACACGCGTGTCTACACGTG 115451 i i i--- i i? v i i HSAT5v1#Satel 5231 GCACGCGCGTGCGCG---CGTGTGTGTGTGTGNACGCGTGTGTGCGCGTG 5277 chrXptel1M 115452 TGT 115454 HSAT5v1#Satel 5278 TGT 5280 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 9.71 CpG sites = 7, Kimura (unadjusted) = 19.31 Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.06 (3 / 52), avg. gap size = 1.00 (3 / 3) 24 41.64 0.62 1.90 chrXptel1M 115460 115619 (884381) (TG)n#Simple_repeat 1 158 (0) m_b328s252i2 13760 chrXptel1M 115460 TGTGGGGGTGTCGGTCTTGGTGTGCGCACGTGTGTGCAGATGTGTGTGCG 115509 v v vv v vv i iii -v - i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG-TG-TGTGTGTGTG 48 chrXptel1M 115510 CTTTTGTGTGTGCCCGCGCATGTGCGTGTGTGCGCACGTCTGTGTGTGCA 115559 iv v ivi i ii i i iii v -v (TG)n#Simple_ 49 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG-T 97 chrXptel1M 115560 CTG-GTATGGGTGCGCGCGCGTGTGCCCGCGTGTGTGCGTTGGTGCGCGC 115608 v - i v i i i i ivi i i vv i i i (TG)n#Simple_ 98 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 147 chrXptel1M 115609 GCGCGTGTGTG 115619 i i (TG)n#Simple_ 148 GTGTGTGTGTG 158 Matrix = Unknown Transitions / transversions = 1.67 (30/18) Gap_init rate = 0.03 (4 / 159), avg. gap size = 1.00 (4 / 4) 16 24.66 0.00 2.04 chrXptel1M 115759 115808 (884192) (GCGGG)n#Simple_repeat 1 49 (0) m_b328s252i3 13761 chrXptel1M 115759 GCGGTGCGGGGCTGGGGGAGGGGGCGCGGACGGGGGGCGGGGGGGGGAGG 115808 v v v i v v -v v v v (GCGGG)n#Simp 1 GCGGGGCGGGGCGGGGCGGGGCGGGGCGG-GGCGGGGCGGGGCGGGGCGG 49 Matrix = Unknown Transitions / transversions = 0.11 (1/9) Gap_init rate = 0.02 (1 / 49), avg. gap size = 1.00 (1 / 1) 37 37.47 0.00 0.00 chrXptel1M 116158 116310 (883690) (GGC)n#Simple_repeat 1 153 (0) m_b328s252i4 13762 chrXptel1M 116158 GGCGGCGGCGGCAGTAGCAGCGGTGACAGCAGCGGCTGTGGCAGAGATAG 116207 i ii i i i i i v i i v iii (GGC)n#Simple 1 GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGG 50 chrXptel1M 116208 CGGCGGCGGCAGAGACCGCGGCGGCGGCGGCAGAGACCGCGGCAGCAGAG 116257 i v i v i v i v i i v (GGC)n#Simple 51 CGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCG 100 chrXptel1M 116258 ACCGCGGCAAGAGAGATCGCCTAGGCGGCGACGACGGCGGCGGAGGAGGA 116307 i v iivi v iiv vvv i i v v v (GGC)n#Simple 101 GCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC 150 chrXptel1M 116308 GGC 116310 (GGC)n#Simple 151 GGC 153 Matrix = Unknown Transitions / transversions = 1.59 (27/17) Gap_init rate = 0.00 (0 / 152), avg. gap size = 0.0 (0 / 0) 17 15.60 0.00 0.00 chrXptel1M 117202 117230 (882770) (G)n#Simple_repeat 1 29 (0) m_b328s252i5 13763 chrXptel1M 117202 GGGGAAGGGGGGGTGGGGGAGGGGGGGGG 117230 ii v i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG 29 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 20 21.98 0.00 0.00 chrXptel1M 117252 117293 (882707) (G)n#Simple_repeat 1 42 (0) m_b328s252i6 13763 chrXptel1M 117252 GGCGGCGGTGGGGGAGGGTGGGGGGAGTGGGGAGGGGGGGGG 117293 v v v i v i v i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 42 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 48 0.00 0.00 0.00 chrXptel1M 120359 120399 (879601) (AT)n#Simple_repeat 1 41 (0) c_b328s251i0 13764 chrXptel1M 120359 ATATATATATATATATATATATATATATATATATATATATA 120399 (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATA 41 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 339 34.69 1.36 0.00 chrXptel1M 120425 120571 (879429) L3#LINE/CR1 3651 3799 (300) m_b328s601i0 13765 chrXptel1M 120425 TTTAAAGAAAATTAACCCGGATGATGGATGGACCTGAAAGTTTGTTATGG 120474 ii i i i vii v i i v v iv viv i iv L3#LINE/CR1 3651 TCCAGAGGAGAGCGACCAGGATGGTGAAGGGTCTGGAAACCATGTCATAT 3700 chrXptel1M 120475 TAGAATTGGTAAAAGGC-TTAGGTTTGTTGAGCCCAGAGAAGAGAATAAT 120523 v i vi vi v-i i vv v ii v v L3#LINE/CR1 3701 GAGGAACGGTTGAAGGAACTGGGGATGTTTAGCCTGGAGAAGAGAAGACT 3750 chrXptel1M 120524 T-GAGGGGGCTTGAGGGGAGCCTTCATCTATCTGATAGGCTGTCATATG 120571 - i i v vi vv i vv i vi i L3#LINE/CR1 3751 TAGAGGAGACATGATAGCTGTCTTCAAATATTTGAAGGGCTGTCATGTG 3799 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.02 CpG sites = 27, Kimura (unadjusted) = 47.70 Transitions / transversions = 1.12 (27/24) Gap_init rate = 0.01 (2 / 146), avg. gap size = 1.00 (2 / 2) 218 30.12 1.33 7.04 chrXptel1M 121294 121368 (878632) MIRc#SINE/MIR 3 73 (195) m_b328s601i1 13766 chrXptel1M 121294 AGGCAGTAAAGTACAGCTCAGTGAAAAGAGTGCCAAGCTTGGTGTCAGGA 121343 ivi i ----- i ii iiii v MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAG-----TGGAAAGAGCACTGGACTTGGAGTCAGGA 47 chrXptel1M 121344 A-ACCTAAGGTCAAATCTGGCCTGTG 121368 - ii v i i iv v v MIRc#SINE/MIR 48 AGACCTGGGTTCGAGTCCCGGCTCTG 73 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.23 CpG sites = 15, Kimura (unadjusted) = 40.81 Transitions / transversions = 2.50 (15/6) Gap_init rate = 0.08 (6 / 74), avg. gap size = 1.00 (6 / 6) 627 28.74 10.53 0.80 chrXptel1M 121962 122189 (877811) C MIRb#SINE/MIR (15) 253 4 m_b328s601i2 13767 chrXptel1M 121962 ATTTATTAAGAACCCACTCTGTGCCAGCTGTTGTGCTCAGTGATCGACAA 122011 i vi ii v viii v i v iv v C MIRb#SINE/MIR 253 ATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACAT 204 chrXptel1M 122012 AAATGTTCTCATTTCATCCACACAACCATCCTGTGAGGTAGGTGCTATTA 122061 iv vv v v v i i ii C MIRb#SINE/MIR 203 GCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATTA 154 chrXptel1M 122062 TCCCCTTCTTACTGTTGAGTAAAC-------------AATTGAGTAAAT- 122097 v i v v v -------------ii i v - C MIRb#SINE/MIR 153 TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTT 104 chrXptel1M 122098 ---CAGGCGTCACACAGCTTTTGAGTGTTGGAGACTAGATTTGCATTCTG 122144 --- i - vv i vii v vi i v ii v C MIRb#SINE/MIR 103 GCCCAAG-GTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAG 55 chrXptel1M 122145 GTCTTCCTGATGCTAG-------GCCCTCTCCATTATGCCACCCAGCCAC 122187 vi iv i i------- i i i iii v v - C MIRb#SINE/MIR 54 GTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCACCACGCTGCC-C 6 chrXptel1M 122188 CT 122189 C MIRb#SINE/MIR 5 CT 4 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.23 CpG sites = 36, Kimura (unadjusted) = 37.03 Transitions / transversions = 1.24 (36/29) Gap_init rate = 0.03 (6 / 227), avg. gap size = 4.33 (26 / 6) 16 14.63 6.38 2.04 chrXptel1M 122588 122634 (877366) (AGAGGA)n#Simple_repeat 1 49 (0) m_b328s252i7 13768 chrXptel1M 122588 AGAGAGCAG-GGAAGAGACAGA-GACCAAG-AGAGGAAGAGGAAGAGGAA 122634 - v - iv - vv i - (AGAGGA)n#Sim 1 AGAG-GAAGAGGAAGAGGAAGAGGAAGAGGAAGAGGAAGAGGAAGAGGAA 49 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.09 (4 / 46), avg. gap size = 1.00 (4 / 4) 206 34.65 14.33 2.22 chrXptel1M 124024 124386 (875614) C L2#LINE/L2 (357) 2725 2320 m_b328s601i3 13769 chrXptel1M 124024 TTGCAATAGCTGAAGCATGAGGTGAGGAAGGCTT--AC------GGTGCT 124065 i iiiv i iv i v iv -- ------ vi C L2#LINE/L2 2725 TTGCAGTAATCCAGGCGAGAGATGATGGTGGCTTGGACCAGGGTGGTGGC 2676 chrXptel1M 124066 AGTGAAGA----GAGAGGAG--CATATAATGGAGATGCCGGAAAAGTCAG 124109 i i---- i v -- iv vv v iiivvi i vii C L2#LINE/L2 2675 AGTGGAGGTGGTGAGAAGTGGTCGGATTCTGGATATATTTTGAAGGTAGA 2626 chrXptel1M 124110 ATCAATAATGCTTGGCAATAGATTAAATATAGGGGG-GTGAGATAGTGAG 124158 ii i i ivii vii i ii i i v - v v v C L2#LINE/L2 2625 GCCGACAGGATTTGCTGATGGATTGGATGTGGGGTGTGAGAGAAAGAGAG 2576 chrXptel1M 124159 GGGTCTGGGATAACACGTAAGTCTCAAGGATGGGGGAACTGGA-GGATGG 124207 i vi i v vv i i iv- viv i v - C L2#LINE/L2 2575 GAGTCAAGGATGACTCCAAGGTTTTT-GGCCTGAGCAACTGGAAGGATGG 2527 chrXptel1M 124208 TATCACTTTCAACAGTAATGGGGAAG---GTAAGAGG--------TGAGG 124246 vi ii iv i? v vi --- iii -------- C L2#LINE/L2 2526 AGTTGCCATTNACTGAGATGGGGAAGACTGCGGGAGGAGCAGGTTTGAGG 2477 chrXptel1M 124247 AG--AGCTTAGGAGGAAAG---AGAACCAATCTTCAGTTTAAGAAGTCTC 124291 i -- v i vvv ---v i -- v v i v i v C L2#LINE/L2 2476 GGGAAGATCAGGAGTTCAGTTTTGGAC--ATGTTAAGTTTGAGATGCCTA 2429 chrXptel1M 124292 CTGAACATCAGCAGTTAGAGAT-TTGAG-----ATTTGAAGGTAGGGACC 124335 i ii -- iv i - i ----- v i vi v iii C L2#LINE/L2 2428 TTAGACATC--CAAGTGGAGATGTCGAGTAGGCAGTTGGATATACGAGTC 2381 chrXptel1M 124336 -----TTCAAGAACCAGAAAGATTAGGGC---AGATG------TGAGAAT 124371 ----- i ----i i i iv --- i------ i i C L2#LINE/L2 2380 TGGAGTTCAGG----GGAGAGGTCCGGGCTGGAGATATAAATTTGGGAGT 2335 chrXptel1M 124372 CATCAACATGGAGAT 124386 i iv C L2#LINE/L2 2334 CATCAGCATATAGAT 2320 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 46.43 CpG sites = 77, Kimura (unadjusted) = 49.35 Transitions / transversions = 1.67 (77/46) Gap_init rate = 0.07 (24 / 362), avg. gap size = 2.54 (61 / 24) 335 31.80 4.44 2.17 chrXptel1M 124556 124690 (875310) C MIRc#SINE/MIR (120) 148 11 m_b328s601i4 13770 chrXptel1M 124556 CTCATTTTATCTAGGAAGGAAC-GAAACAAACAG-GGTGAAGTGGTGTGG 124603 i ivv v i i - ii vv v - v iiv v C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chrXptel1M 124604 CCAGGATCACACAACTAAT----GTCTGAGGCCAGACCTGAATTCAGAAA 124649 i i i i ---- v v v vi ii ii --- C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAG--- 52 chrXptel1M 124650 GGCCTCTTGACTCCAGGCCCAGCATTCTACCCACTTCCCCA 124690 v i i i i iii vi v v C MIRc#SINE/MIR 51 GTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCA 11 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.50 CpG sites = 25, Kimura (unadjusted) = 42.87 Transitions / transversions = 1.47 (25/17) Gap_init rate = 0.04 (6 / 134), avg. gap size = 1.50 (9 / 6) 473 19.32 5.65 3.97 chrXptel1M 124827 124950 (875050) MER63D#DNA/hAT-Tip100 334 459 (602) m_b328s502i1 13771 chrXptel1M 124827 TAGTATGAGTATTTATCCCTTGAAAATCAGGAAATGTTCCAAATCAGGGC 124876 i iv iv vi i i v i i v MER63D#DNA/hA 334 TGGTGGGAGTATTTACACCACGGAAATCGGCAAACGCTACAAATCAGGGC 383 chrXptel1M 124877 TTGATTGTTGCCATTGTT---TTGATTGTCTAGATT----GAAGTGATGG 124919 -----i --- i ----i MER63D#DNA/hA 384 TTGATT-----TATTGTTTTGTTGATTGTCTAGACTTAAGAAAGTGATGG 428 chrXptel1M 124920 AGAAAGTATTAATAACATAGATTACATTTAA 124950 i i iii v i MER63D#DNA/hA 429 AGAAAATGTTAATAATGCAGATTAAACTTAA 459 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 19.84 CpG sites = 17, Kimura (unadjusted) = 23.14 Transitions / transversions = 2.83 (17/6) Gap_init rate = 0.06 (7 / 123), avg. gap size = 1.71 (12 / 7) 557 29.66 5.99 4.08 chrXptel1M 125751 126351 (873649) C L1ME4c_3end#LINE/L1 (152) 678 67 m_b328s551i0 13772 chrXptel1M 125751 TTTACATTGTTGTAGTCGTTGTGTATAT-------TGTTTTCTGGGCTTT 125793 v i i v i ? ------- v -- C L1ME4c_3end#L 678 TTTACATAGTTGTAATCATAGCGTANATACAATTTTGTATTCTG--CTTT 631 chrXptel1M 125794 GCTCACTTTACTTTGCTTCGGTTCATATAGAGCTTTCCATCCTTCTCTCT 125843 vi v v iiv ----- v v -i vi v viv C L1ME4c_3end#L 630 TTTCACTTAACATTATATC-----ATAAACA-TTTTCCATGTTGCTACAT 587 chrXptel1M 125844 ATTCACTCCACA--CATCATTTCTTATGACACATGAATATTATTCCATTG 125891 v -- i i --i i v i --- v v i C L1ME4c_3end#L 586 AGTC--TTCATAATTATCATTTTTAATGGC---TGCATAATATTCCATCG 542 chrXptel1M 125892 AATTCACGTACCACAATGTGTTTAACCATTCCCCAATTG------ACT-- 125933 i ?v i i v ii v ------ i -- C L1ME4c_3end#L 541 AGTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTA 492 chrXptel1M 125934 --TTGTTTCAAATTCTTTACTATCACAAAAAAAGGAGGCTACAAATATTA 125981 -- v i ii i i v ---- v i vv -- C L1ME4c_3end#L 491 GGTTGTTTCCAATTTTTCGCTATTATAAATA----ACGCTGCAATGA--A 448 chrXptel1M 125982 TATATTTG-GAGTAT-GCACTTT-CTTCTTATTGATTATCTCCCTGAGGT 126028 i v i - vi - vi - v vi i i ii i C L1ME4c_3end#L 447 CATCTTCGTGCATATAGCTTTTTCCTTCTTTTGAATTATTTCCTTAGGAT 398 chrXptel1M 126029 ATAAGCTTAGTAATGCAATCTGTGGGTCAAAGGGTGTGGATATTTTAATC 126078 v vv ii v i v ivv i i i --- i C L1ME4c_3end#L 397 AAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTT---TT 351 chrXptel1M 126079 ATGTCATTTG---CATAACTCCACTTTGCTTTCCAAAGTAGCAATACCAT 126125 v vi --- i viv vv ivi ivi v C L1ME4c_3end#L 350 ATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAA 301 chrXptel1M 126126 GTCATAGCCCTAAAACAGCAG---ATTCATGTGCCCATCTTTCCACAGCC 126172 v i i ?iv i-- v i--- vvi? i vi i iv i ? C L1ME4c_3end#L 300 TTTACANTGCC--ACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCC 253 chrXptel1M 126173 TCCCCAACATTGTCTGTTACTATTTTTTGCCATTTTTCCCAAATTGCAGG 126222 v i vv i ii v vvv v i v ivvi C L1ME4c_3end#L 252 TCGCCAGCATTGGGTATTATCAATTTTTTAAATTTTTGCTAATTTAATAG 203 chrXptel1M 126223 GTGTGAAGTGAATCCTCA--GGTGA---GATTTGTAATTCTTTTATTATA 126267 i i i ivvi -- v v---i i v v iv C L1ME4c_3end#L 202 GCGTAAAATGGTATCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACT 153 chrXptel1M 126268 AATGATTTGGAGCATTTTTTTCATATGGTTGTGAATACCTTGCAGTT-CT 126316 ii vv v i - i i v vv ivv? i v - C L1ME4c_3end#L 152 AGCGAGGTTGAACA-TTTTTCCATGTGTTTGTTTACTANTTGTATTTCCT 104 chrXptel1M 126317 CTTA--AGAAGTGTTTGTTCATATCCTTTGATCATTT 126351 ?--v v i i vi C L1ME4c_3end#L 103 CTTNTGTGAATTGTCTGTTCATGTCCTTTGCCCATTT 67 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.69 CpG sites = 88, Kimura (unadjusted) = 38.99 Transitions / transversions = 1.06 (88/83) Gap_init rate = 0.07 (39 / 600), avg. gap size = 1.56 (61 / 39) 597 29.86 5.62 3.14 chrXptel1M 125855 126352 (873648) C L1ME4a_3end#LINE/L1 (296) 575 66 m_b328s551i1 13772 chrXptel1M 125855 ACATCATTTCTTATGACACATGAATATTATTCCATTGAATTCACGTACCA 125904 ? i v i --- v v ?v vv i C L1ME4a_3end#L 575 ACATNATTTTTAATGGC---TGCATAATATTCCATTNTATGGATGTACCA 529 chrXptel1M 125905 CAATGTGTTTAACCATTCCCCAATTG------ACTT----TGTTTCAAAT 125944 i v i ? v ------ i ---- v C L1ME4a_3end#L 528 TAATTTATTTAACCANTCCCCTATTGTTGGACATTTAGGTTGTTTCCAAT 479 chrXptel1M 125945 TCTTTACTATCACAAAAAAAGGAGGCTACAAATATTATATATTTGGAGTA 125994 i ii i i v ----v i i vv -- i vi v -i C L1ME4a_3end#L 478 TTTTCGCTATTATAAATAA----TGCTGCGATGA--ACATCCTTGTA-CA 436 chrXptel1M 125995 TGCA-CTTTCTTCTTAT---TGATTATCTCCCTGAGGTATAAGCTTAGTA 126040 iv - v ? vi --- i i ii i v vv i v C L1ME4a_3end#L 435 TAAATCTTTGTNCACATCTCTGATTATTTCCTTAGGATAAATTCCTAGAA 386 chrXptel1M 126041 ATGCAATCTGTGGGTCAAAGGGTGTGGATATTTTAATCATGTCATTTG-- 126088 i v ivv i ? i --- i v v v -- C L1ME4a_3end#L 385 GTGGAATTACTGGGTCAAAGGGTATGNACATTT---TTAAGGCTTTTGAT 339 chrXptel1M 126089 -CATAACTCCACTTTGCTTTCCAAAGTAGCAATACCATGTCATAGCCCTA 126137 - viv vv ii i ivi ivi vv i i vi i- C L1ME4a_3end#L 338 ACATATTGCCAAATTGCCCTCCAGAAAGGTTGTACCAATTTACACTCCC- 290 chrXptel1M 126138 AAACAGCAG---ATTCATGTGCCCATCTTTCCACAGCCTCCCCAACATTG 126184 - v --- vviv i i i? v v i C L1ME4a_3end#L 289 -ACCAGCAGTGTATGAGAGTGCCCGTTTCNCCACACCCTCGCCAACACTG 241 chrXptel1M 126185 TCTGTTACTATTTTTTGCCATTTTTCCCAAATTGCAGGGTGTGAAGTGAA 126234 vv i ii v i vvv i v v vvi vi i iv C L1ME4a_3end#L 240 GGTATTATCAATCTTTTAAATCTTTGCCAATTTGATAGGTGAAAAATGGT 191 chrXptel1M 126235 TCCTCA--GGTG---AGATTTGTAATTCTTTTATTATAAATGATTTGGAG 126279 vi -- v ---vi i v v iv i vv v i C L1ME4a_3end#L 190 ATCTCATTGTTGTTTTAATTTGCATTTCTTTGATTACTAGTGAGGTTGAA 141 chrXptel1M 126280 CATTTTTTTCATATGGTTGTGAATACCTTGCA---GTTCTCTTAAGAAGT 126326 - ? v i viiivvi i ---v i iv v C L1ME4a_3end#L 140 CA-TNTTTTCATATGTTTATTGGCCATTTGTATTTCTTCTTTTGTGAATT 92 chrXptel1M 126327 GTTTGTTCATATCCTTTGATCATTTT 126352 i i vi C L1ME4a_3end#L 91 GTCTGTTCATGTCCTTTGCCCATTTT 66 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.28 CpG sites = 72, Kimura (unadjusted) = 39.35 Transitions / transversions = 1.00 (72/72) Gap_init rate = 0.05 (26 / 497), avg. gap size = 1.69 (44 / 26) 580 22.55 5.97 0.71 chrXptel1M 126779 126912 (873088) C MIR#SINE/MIR (6) 256 116 m_b328s601i5 13773 chrXptel1M 126779 AACAAACATTTATGAAGTGCCTCCTCTGTGCCAGGCACTGT-----GCAC 126823 i v vi i i v v ----- i C MIR#SINE/MIR 256 AGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGCGC 207 chrXptel1M 126824 TTTACA---AATACCTCATTTGATCCTCATAATAATTCTGGGAAGTAGCT 126870 --- v v i i i ii iv i v C MIR#SINE/MIR 206 TTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGGTAGGT 157 chrXptel1M 126871 ATTTCTTTTTATTTCTGCTTTACAGATGAAGAAACCGAGGCA 126912 -i v v ii iii i i C MIR#SINE/MIR 156 A-CTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCA 116 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.53 CpG sites = 20, Kimura (unadjusted) = 27.65 Transitions / transversions = 2.00 (20/10) Gap_init rate = 0.02 (3 / 133), avg. gap size = 3.00 (9 / 3) 377 34.18 6.05 4.20 chrXptel1M 126959 127239 (872761) L2b_3end#LINE/L2 15 300 (166) m_b328s601i6 13774 chrXptel1M 126959 CCTGTTACTTTCCTATTCTTCTCACATCTTACT-TCCCTCTGCCTACTTT 127007 i i i ii iivi iv v v vii - ii ii i L2b_3end#LINE 15 CCCGCTACCTCTCCGGCCTCATCTCCTACCACTCTCCCCTTGCTCACTCT 64 chrXptel1M 127008 GGAATTCAGGGACATTGGCCTCCTTGCTGACCCTGAAACAAGTAGTAACT 127057 v-- i vv i vi vi v ivi-?i L2b_3end#LINE 65 GC--TCCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACACGCCA-NGCT 111 chrXptel1M 127058 CCATTTCTTGACTC--TGCATTTTCATTGGCTGTCTTACCTACTTCCA-- 127103 --?i ii v --v v v i?v iiivi i i vv -- L2b_3end#LINE 112 C--NCTCCCGCCTCAGGGCCTTTGCACNTGCTGTTCCCTCTGCCTGGAAC 159 chrXptel1M 127104 GTCCTATTCCCACTCCCATGCCAGGAATACTGCTCCTAACTCTTCCTTCA 127153 i - i ii ivi v ---v vi - v L2b_3end#LINE 160 GCCCT-TCCCCACCTCTTCGCCTGG---CCAACTCCT-ACTCATCCTTCA 204 chrXptel1M 127154 GGTCTCAGCTAAAAT----CCTATCTGCAAAAAATCTTGCCTGGTCCCCT 127199 v ---- -i v iii ii i v ii i L2b_3end#LINE 205 GGTCTCAGCTCAAATGTCACCT-CCTCCGGGAAGCCCTCCCTGACCCCCC 253 chrXptel1M 127200 AACGCTGG--CA-----CATTATTTGAGTTCCTCCAAT-TTGGCCTGC 127239 i- i -- ----- v iv i i ii i i -i iv L2b_3end#LINE 254 AG-GCCGGGTCAGGCGCCCTCCTCTGGGCCCCCCCAGTCCTACCCTGC 300 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.07 CpG sites = 61, Kimura (unadjusted) = 49.44 Transitions / transversions = 1.97 (61/31) Gap_init rate = 0.07 (19 / 280), avg. gap size = 1.53 (29 / 19) 848 26.31 2.83 1.40 chrXptel1M 127282 127493 (872507) C MIRb#SINE/MIR (23) 245 31 m_b328s601i7 13775 chrXptel1M 127282 AGAACCTACTACATGCCAAATGTTGTGCTAAGTACTTTACAAATACTGTC 127331 vi i ii iiiii ii vii i i C MIRb#SINE/MIR 245 AGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACATGCATTATC 196 chrXptel1M 127332 -CATTTGATTTTCACAAAAGCCCTGGGAGGTAGATACGATTCTTATCTCC 127380 - i ii v i v i --- v i C MIRb#SINE/MIR 195 TCATTTAATCCTCACAACAACCCTGCGAGGTAGGTA---TTATTATCCCC 149 chrXptel1M 127381 ACTATATAGTTGAGGAAACTGAGGCC----GGGGTACAGTAACTTTCCCA 127426 i v i v i---- i vv v C MIRb#SINE/MIR 148 ATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCA 99 chrXptel1M 127427 AGATCATACACCTACCAAATGTCTGAGGTCACATTTGAACTCAGGTCTTC 127476 i i v vi i v v viviv i i vi C MIRb#SINE/MIR 98 AGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGT 49 chrXptel1M 127477 CAGACTCC-AGGCCCATG 127493 v - i i C MIRb#SINE/MIR 48 CTGACTCCAAAGCCCGTG 31 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.85 CpG sites = 36, Kimura (unadjusted) = 33.60 Transitions / transversions = 1.89 (36/19) Gap_init rate = 0.03 (6 / 211), avg. gap size = 1.50 (9 / 6) 20 29.25 0.00 0.00 chrXptel1M 127796 127857 (872143) (AAA)n#Simple_repeat 1 62 (0) m_b328s252i8 13776 chrXptel1M 127796 AAAAAATGAAAAAGAGAATAAAAGTAAATAAACAACAACAAAAATGGTAA 127845 vi i i v iv v v v v viiv (AAA)n#Simple 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chrXptel1M 127846 AAAAAAAAAAAA 127857 (AAA)n#Simple 51 AAAAAAAAAAAA 62 Matrix = Unknown Transitions / transversions = 0.67 (6/9) Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0) 341 26.83 6.41 9.21 chrXptel1M 128052 128207 (871793) L2d_3end#LINE/L2 359 510 (6) m_b328s601i8 13774 chrXptel1M 128052 ATTAGTTCATGTGAGTCTCTCCAGTCTTTCAGAAATCATTCTGAGATTGT 128101 iv v ivv iv ii vi ------- - L2d_3end#LINE 359 ATTGTTTCATGTGTGTTAGTCTTGTCTCCCCAA-------CT-AGATTGT 400 chrXptel1M 128102 AAGTTTCTCAAGGACAGGGAT--TGTCTT-TA-TCTTTTGTCACT----- 128142 i i ii i i-- - - ? ? ii ----- L2d_3end#LINE 401 AAGCTCCTTGAGGGCAGGGACCATGTCTTATACTNTTTTNTCGTTCCCCA 450 chrXptel1M 128143 -AGAGCTTAGCACACTGCCTGGTACACAGTAGGTTCTGGGGCTTAGGAAA 128191 - v i v ivi i i i------ i iv L2d_3end#LINE 451 CAGCGCCTAGCACAGTGCTGAGCACATAGTAGGC------GCTCAATAAA 494 chrXptel1M 128192 TGCATACTGACTGACT 128207 i v ii i i L2d_3end#LINE 495 TACTTGTTGATTGATT 510 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.14 CpG sites = 27, Kimura (unadjusted) = 35.48 Transitions / transversions = 2.45 (27/11) Gap_init rate = 0.12 (19 / 155), avg. gap size = 1.26 (24 / 19) 349 18.05 11.90 1.08 chrXptel1M 128095 128178 (871822) L2d2_3end#LINE/L2 436 528 (27) m_b328s601i9 13774 chrXptel1M 128095 AGATTGTAAGTTTCTCAAGGACAGGGAT--TGTCTT-TATCT-TTTGT-- 128138 i i ii i i-- - ii - -- L2d2_3end#LIN 436 AGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACTTCTTTGTAT 485 chrXptel1M 128139 ----CACTAGAGCTTAGCACACTGCCTGGTACACAGTAGGTTCT 128178 ---- - v i v v i iv L2d2_3end#LIN 486 CCCCCAC-AGCGCCTAGCACAGTGCCTTGCACACAGTAGGCGCT 528 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 19.77 CpG sites = 11, Kimura (unadjusted) = 21.32 Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.07 (6 / 83), avg. gap size = 1.83 (11 / 6) 211 23.26 0.00 0.00 chrXptel1M 128207 128249 (871751) C MIRc#SINE/MIR (157) 111 69 m_b328s601i10 13777 chrXptel1M 128207 TCAAGAGATTTGCCCAGCGTCACATAGTTGGTAAGTGTCTGAG 128249 i v i iv i i i v v C MIRc#SINE/MIR 111 TTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAG 69 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.41 CpG sites = 6, Kimura (unadjusted) = 28.41 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 355 26.85 7.41 0.00 chrXptel1M 128668 128775 (871225) C L2d2_3end#LINE/L2 (15) 540 425 m_b328s601i11 13778 chrXptel1M 128668 AAATATTTATTAAGCACTTACTCTATGCAAAGCCTTGTACTAAGAGCT-- 128715 i i i v i i vi i i v -- C L2d2_3end#LIN 540 AAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGT 491 chrXptel1M 128716 -AAAGTTACAAA-AAGTACAACAGCT-ATCGTTG---TCAAGAAGCTCAC 128759 -iii v - i v vv -i vi --- i i C L2d2_3end#LIN 490 GGGGGATACAAAGAAGTATAAGACATGGTCCCTGCCCTCAAGGAGCTTAC 441 chrXptel1M 128760 ATTCTAACGGGGCAGA 128775 v iiv v C L2d2_3end#LIN 440 AATCTAGTTGGGGAGA 425 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.80 CpG sites = 18, Kimura (unadjusted) = 34.26 Transitions / transversions = 1.64 (18/11) Gap_init rate = 0.05 (5 / 107), avg. gap size = 1.60 (8 / 5) 204 37.72 3.51 0.00 chrXptel1M 129438 129551 (870449) C L2d2_3end#LINE/L2 (1) 554 437 m_b328s601i12 13779 chrXptel1M 129438 CAAGTCAATTCAACAAGTATTTATGAGGCATCTCTTATGAGTATACTACA 129487 i v i vii ii vi i v i vivi v C L2d2_3end#LIN 554 CAAATCAAATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACT 505 chrXptel1M 129488 CTGCTTAGCACC---AGAGATACAAAAAAAAAAAAGGCAAAAGACATCCC 129534 v vi i i---i i i iv v i viivv v v C L2d2_3end#LIN 504 GTGCTAGGCGCTGTGGGGGATACAAAGAAGTATAAGACATGGTCCCTGCC 455 chrXptel1M 129535 CCC-CGAAGCTTCTAGTC 129551 i -v i vi i C L2d2_3end#LIN 454 CTCAAGGAGCTTACAATC 437 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 51.10 CpG sites = 25, Kimura (unadjusted) = 54.87 Transitions / transversions = 1.39 (25/18) Gap_init rate = 0.02 (2 / 113), avg. gap size = 2.00 (4 / 2) 220 28.80 9.90 3.74 chrXptel1M 129445 129545 (870455) C L2a_3end#LINE/L2 (8) 509 403 m_b328s601i13 13779 chrXptel1M 129445 ATTCAACAAGTATTTATGAGGCATCTCTTATGAGTATACTA--CACTG-- 129490 i vii ii vi ---- i i -- -- C L2a_3end#LINE 509 ATTCAACAAATATTTATTGAGCGCCTACTATG----TGCCAGGCACTGTT 464 chrXptel1M 129491 CTTAGCACCAGAGATACAA----AAAAAAAAAAGGCAAAAGACATCCCCC 129536 vi i ii i i----i v v i v viiv C L2a_3end#LINE 463 CTAGGCGCTGGGGATACAGCAGTGAACAAAACAGACAAAAGTCCCTGCCC 414 chrXptel1M 129537 CC--GAAGCTT 129545 i -- i C L2a_3end#LINE 413 TCATGGAGCTT 403 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.11 CpG sites = 20, Kimura (unadjusted) = 38.65 Transitions / transversions = 2.50 (20/8) Gap_init rate = 0.08 (8 / 100), avg. gap size = 1.75 (14 / 8) 15 13.87 0.00 0.00 chrXptel1M 130216 130239 (869761) (A)n#Simple_repeat 1 24 (0) m_b328s252i9 13780 chrXptel1M 130216 AAAATAAAATAAAAAAAAACAAAA 130239 v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAA 24 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 14 4.49 0.00 4.17 chrXptel1M 130872 130896 (869104) (GTTT)n#Simple_repeat 1 24 (0) m_b328s252i10 13781 chrXptel1M 130872 GTTTTTTTGTTTGTTTGTTTTGTTT 130896 v - (GTTT)n#Simpl 1 GTTTGTTTGTTTGTTTG-TTTGTTT 24 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 13 4.13 8.00 0.00 chrXptel1M 130873 130897 (869103) (TTGTT)n#Simple_repeat 1 27 (0) m_b328s252i11 13781 chrXptel1M 130873 TTTTTTTG-TTTG-TTTGTTTTGTTTT 130897 v - - (TTGTT)n#Simp 1 TTGTTTTGTTTTGTTTTGTTTTGTTTT 27 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.08 (2 / 24), avg. gap size = 1.00 (2 / 2) 539 18.31 2.26 9.68 chrXptel1M 130900 131032 (868968) C MIRc#SINE/MIR (141) 127 4 m_b328s601i14 13782 chrXptel1M 130900 CTGAGGCAATTAG---GGTTAAGTGACTTACCCAGGGTCACACAGCTAGG 130946 -- i --- i i - C MIRc#SINE/MIR 127 CTGAGGC--TCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG- 81 chrXptel1M 130947 AAGTGTTAAGTGTCTGAGACCAGATTTGTACTCAGGTCCTCCTGACTTCA 130996 ------ v v v vi i i v i i i C MIRc#SINE/MIR 80 ------TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCA 37 chrXptel1M 130997 GGGCTAGTGCTCTATCCACTGTGCAACCTAGCTGCC 131032 i v i v ii v ---i C MIRc#SINE/MIR 36 AGTCCAGTGCTCTTTCCACTGCACCAC---ACTGCC 4 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 20.15 CpG sites = 14, Kimura (unadjusted) = 21.20 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.10 (13 / 132), avg. gap size = 1.15 (15 / 13) 12 16.98 0.00 5.71 chrXptel1M 136895 136931 (863069) (TGTATC)n#Simple_repeat 1 35 (0) m_b328s252i12 13783 chrXptel1M 136895 TGTACCTGTATCTGTATACATATTTGTGTATCTATAT 136931 i - - i v v i (TGTATC)n#Sim 1 TGTATCTGTATCTGTAT-C-TGTATCTGTATCTGTAT 35 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 500 21.10 0.00 4.39 chrXptel1M 136958 137076 (862924) C MIRb#SINE/MIR (87) 181 68 m_b328s601i15 13784 chrXptel1M 136958 CAATATTTCTGGGGAGGTGAGTGGTATTATTATCCCCATTTTACAAATGA 137007 i vii v - i--- i C MIRb#SINE/MIR 181 CAACAACCCTGCG-AGGTA---GGTATTATTATCCCCATTTTACAGATGA 136 chrXptel1M 137008 GAAAACTGAGGCAACCAGTAGTAAAGTAACTTGCCCAGGATCATACAGAT 137057 i vvvv vi v i i i v C MIRb#SINE/MIR 135 GGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCT 86 chrXptel1M 137058 AGTGAGAGTCTGAGGCCAG 137076 i v v v - i C MIRb#SINE/MIR 85 AGTAAGTGGCAGA-GCCGG 68 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 23.74 CpG sites = 12, Kimura (unadjusted) = 24.88 Transitions / transversions = 1.00 (12/12) Gap_init rate = 0.04 (5 / 118), avg. gap size = 1.00 (5 / 5) 533 20.00 0.00 0.95 chrXptel1M 136971 137076 (862924) C MIR#SINE/MIR (97) 165 61 m_b328s601i16 13784 chrXptel1M 136971 GAGGTGAGTGGTATTATTATCCCCATTTTACAAATGAGAAAACTGAGGCA 137020 ii iv i i C MIR#SINE/MIR 165 GAGGTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCA 116 chrXptel1M 137021 ACCAGTAGTAAAGTAACTTGCCCAGGATCATACAGATAGTGAGAGTCTGA 137070 vvv vi v i i i v i v v v C MIR#SINE/MIR 115 CAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGA 66 chrXptel1M 137071 GGCCAG 137076 - i C MIR#SINE/MIR 65 -GCCGG 61 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 22.24 CpG sites = 11, Kimura (unadjusted) = 23.46 Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.01 (1 / 105), avg. gap size = 1.00 (1 / 1) 195 29.66 10.19 5.49 chrXptel1M 137525 137681 (862319) C MIRb#SINE/MIR (66) 202 39 m_b328s601i17 13785 chrXptel1M 137525 CACCATCTCATTTA---CTTTCAACTCCCCTGTCGGGATTATTACCCTGC 137571 ii --- iv vv - i i ---- ---- v C MIRb#SINE/MIR 202 CATTATCTCATTTAATCCTCACAACAACCCTG-CGAGGT----A----GG 162 chrXptel1M 137572 TATTATTATCTCCCTTTTATAGTTAAAGAAAC----AATAAAAAATATTA 137617 i v i v i i ----iv v i i vi C MIRb#SINE/MIR 161 TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTA 112 chrXptel1M 137618 AGTTAGTTCTCTAGAGAAAAATAG--GATCTGAGGCA---CC--GATTC- 137659 v v vi i ii vv v i --ii vv v --- -- - C MIRb#SINE/MIR 111 AGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCG 62 chrXptel1M 137660 AATTTAGGTCT-TCTTAATTCAA 137681 iii - v v i C MIRb#SINE/MIR 61 AACCCAGGTCTGTCTGACTCCAA 39 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.64 CpG sites = 24, Kimura (unadjusted) = 38.64 Transitions / transversions = 1.20 (24/20) Gap_init rate = 0.10 (16 / 156), avg. gap size = 1.56 (25 / 16) 13 13.72 0.00 0.00 chrXptel1M 137770 137794 (862206) (TAAA)n#Simple_repeat 1 25 (0) m_b328s252i13 13786 chrXptel1M 137770 TAAATAAATAAGTAAATGAATGAAT 137794 i i i (TAAA)n#Simpl 1 TAAATAAATAAATAAATAAATAAAT 25 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 15 13.87 0.00 0.00 chrXptel1M 139027 139050 (860950) (A)n#Simple_repeat 1 24 (0) m_b328s252i14 13787 chrXptel1M 139027 AAAAATAAACAAACAAAAAAAAAA 139050 v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAA 24 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 454 18.52 10.19 0.00 chrXptel1M 139198 139305 (860695) MIRc#SINE/MIR 37 155 (113) m_b328s601i18 13788 chrXptel1M 139198 TGGAATCAGGAAAAC--GAGTTCAAATCCAGCCTCAGAT-CTT-----CT 139239 i i -- i i i v v v vi- ----- MIRc#SINE/MIR 37 TGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCT 86 chrXptel1M 139240 CTGTGATGCTGGGCAAGTCACTTAAA-TCTGTTGGTCTCAGTTTCCTCAT 139288 v ivi v- v vi i MIRc#SINE/MIR 87 GTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCAT 136 chrXptel1M 139289 CTGTATAAT--GGATAATA 139305 v -- MIRc#SINE/MIR 137 CTGTAAAATGGGGATAATA 155 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 20.25 CpG sites = 10, Kimura (unadjusted) = 21.39 Transitions / transversions = 1.00 (10/10) Gap_init rate = 0.05 (5 / 107), avg. gap size = 2.20 (11 / 5) 13 15.96 9.30 0.00 chrXptel1M 139312 139354 (860646) (AGAGAG)n#Simple_repeat 1 47 (0) m_b328s252i15 13789 chrXptel1M 139312 AGAGAGAGAGAGAG-GAGGGAG-GAG-GTGAAGGAGAAGGAGA-AGA 139354 - i - - v ii ii - (AGAGAG)n#Sim 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 47 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.10 (4 / 42), avg. gap size = 1.00 (4 / 4) 292 19.20 14.88 5.30 chrXptel1M 139955 140075 (859925) MER63D#DNA/hAT-Tip100 336 467 (594) m_b328s502i2 13790 chrXptel1M 139955 GTGTGAACATTTATATTCTCAGAAATCAGCAAAGGCTGAAGGAAATCATT 140004 v ii i i- v i i v iv --- -- MER63D#DNA/hA 336 GTGGGAGTATTTACAC-CACGGAAATCGGCAAACGCTACA---AATCA-- 379 chrXptel1M 140005 GGGGCTCGATTCATTGTTTTGTTTATTGT-----CTTAAGAAAACTA--- 140046 - i i v ----- iiv --- MER63D#DNA/hA 380 -GGGCTTGATTTATTGTTTTGTTGATTGTCTAGACTTAAGAAAGTGATGG 428 chrXptel1M 140047 ---------TAATAATGCAAATCCAATTTAAAGG-GTGT 140075 --------- i iv i i - MER63D#DNA/hA 429 AGAAAATGTTAATAATGCAGATTAAACTTAAAAGTGTGT 467 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 20.61 CpG sites = 15, Kimura (unadjusted) = 22.90 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.08 (10 / 120), avg. gap size = 2.50 (25 / 10) 463 27.23 0.00 8.78 chrXptel1M 140393 140553 (859447) MIRb#SINE/MIR 4 151 (117) m_b328s601i19 13791 chrXptel1M 140393 AGGGGCAGCTAGGGGTTGCCAGGAGGCATGAGAACCAGGCCTGAAGTTAG 140442 -- v - --i v v v v vi vii i i MIRb#SINE/MIR 4 AGGGGCAGC--GTGGT-GC--AGTGGAAAGAGCACGGGCTTTGGAGTCAG 48 chrXptel1M 140443 AAAGACTTCTCTTCCTGAATTCAAATCTGGCCCCGGACACTTACTAGTCA 140492 v -------- ii i iv v i v v iii MIRb#SINE/MIR 49 ACAGAC--------CTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTG 90 chrXptel1M 140493 TGTGCCCCTAGGCTGATCATCTCACCTCTATCTGCCTCAGTTTCCTCATC 140542 v i i vii i ii v v vv MIRb#SINE/MIR 91 TGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATC 140 chrXptel1M 140543 TGTAAAATGAG 140553 i MIRb#SINE/MIR 141 TGTAAAATGGG 151 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.08 CpG sites = 22, Kimura (unadjusted) = 34.11 Transitions / transversions = 1.22 (22/18) Gap_init rate = 0.08 (13 / 160), avg. gap size = 1.00 (13 / 13) 499 27.54 0.00 6.45 chrXptel1M 140422 140553 (859447) MIRc#SINE/MIR 25 148 (120) m_b328s601i20 13791 chrXptel1M 140422 GAGAACCAGGCCTGAAGTTAGAAAGACTTCTCTTCCTGAATTCAAATCTG 140471 v ii i i i i i -------- ii i i iv MIRc#SINE/MIR 25 GAGCACTGGACTTGGAGTCAGGAAGAC--------CTGGGTTCGAGTCCC 66 chrXptel1M 140472 GCCCCGGACACTTACTAGTCATGTGCCCCTAGGCTGATCATCTCACCTCT 140521 v i v v iii v i i vii ii v MIRc#SINE/MIR 67 GGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCT 116 chrXptel1M 140522 ATCTGCCTCAGTTTCCTCATCTGTAAAATGAG 140553 v vv i MIRc#SINE/MIR 117 CTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.34 CpG sites = 23, Kimura (unadjusted) = 35.66 Transitions / transversions = 2.09 (23/11) Gap_init rate = 0.06 (8 / 131), avg. gap size = 1.00 (8 / 8) 264 31.72 14.66 5.17 chrXptel1M 141495 141760 (858240) L2#LINE/L2 2672 2961 (121) m_b328s601i21 13792 chrXptel1M 141495 CACTACCCACACTCTAGAGTAGGCCCTGAT--------GCCTGGACTATA 141536 i vv i i vvi i viv -------- i iv L2#LINE/L2 2672 CACTGCCACCACCCTGGTCCAAGCCACCATCATCTCTCGCCTGGATTACT 2721 chrXptel1M 141537 GTAATAGC-TACTGATGGGACTGCCTGCTTCAAGCTGCTCCCCACTCCAG 141585 i - v i iv v v v v iviv v ? L2#LINE/L2 2722 GCAATAGCCTCCTAACTGGTCTCCCTGCTTCCACCCTTGCCCCCCTNCAG 2771 chrXptel1M 141586 TC----------------ACCAAAGTGATTTTCCTAACATAAATAAATCC 141619 ----------------i i ii ii v i--i i v L2#LINE/L2 2772 TCTATTCTCAACACAGCAGCCAGAGTGATCCTTTTAAAAC--GTAAGTCA 2819 chrXptel1M 141620 AACCGTGGCACACCTCCCCCTACTCCACTATAAA---CTTCAATGGCTCC 141666 i i i v v ---- i ------ --- i i L2#LINE/L2 2820 GATCATGTCACTCCT----CTGCTC------AAAACCCTCCAATGGCTTC 2859 chrXptel1M 141667 CTATGGCCTCCAGA--AATACCTAATGCAGTC-------TGGTATTCAGA 141707 i vv vii -- v v i --- ------- iv v ii L2#LINE/L2 2860 CCATCTCACTCAGAGTAAAAGCCAA---AGTCCTTACAATGGCCTACAAG 2906 chrXptel1M 141708 GCCTTTCATAACCTAGCCCTGCCCTACCTTCCTCA-TTCCTTTCCTG-TA 141755 i v i i i i iv vi ii v -i v i i-i L2#LINE/L2 2907 GCCCTACATGATCTGGTCCCCCGTTACCTCTCTGACCTCATCTCCTACCA 2956 chrXptel1M 141756 CTCTC 141760 L2#LINE/L2 2957 CTCTC 2961 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.45 CpG sites = 48, Kimura (unadjusted) = 43.26 Transitions / transversions = 1.50 (48/32) Gap_init rate = 0.09 (23 / 265), avg. gap size = 2.35 (54 / 23) 290 37.89 8.90 1.22 chrXptel1M 141713 142094 (857906) L2b_3end#LINE/L2 33 443 (23) m_b328s601i22 13792 chrXptel1M 141713 TCATAACCTAGCCCTGCCCTACCTTCCTCATTCCTTTCCTGTACTCTCTG 141762 vv v v vi -- v i ivi v i- v v L2b_3end#LINE 33 TCATCTCCTACCACTCTCC--CCTTGCTCACTCTGCTCCAGC-CACACTG 79 chrXptel1M 141763 ATCCAGTGGCT--TCAACAAACAAGACACTCCATCTCTTGGCTTCAGGCA 141810 ii ivv v -- vv i v v ?v iv? ii - i vv L2b_3end#LINE 80 GCCTCCTTGCTGTTCCTCGAACACGCCANGCTCNCTCCCG-CCTCAGGGC 128 chrXptel1M 141811 CTTTTT-TCTGCTTGTCCCCCACTTCTGGAATGTAGT-------CTCTCT 141852 vi-i? - i ivivi i ivv ------- ii L2b_3end#LINE 129 CTTTGCACNTGCT-GTTCCCTCTGCCTGGAACGCCCTTCCCCACCTCTTC 177 chrXptel1M 141853 TCCTTTCTAACTCTGAC-CGTCCT---GGCTTC-CTTTAAAT--CCCCTT 141895 v vv i iv - i --- ii -vi i -- v i L2b_3end#LINE 178 GCCTGGCCAACTCCTACTCATCCTTCAGGTCTCAGCTCAAATGTCACCTC 227 chrXptel1M 141896 CTACAGGAAGTCTTTCACAACTCCTC---TTAATTCCAGGGTCTTGTT-T 141941 v i i i i vii i i ---iiiiv vi v i i vi - L2b_3end#LINE 228 CTCCGGGAAGCCCTCCCTGACCCCCCAGGCCGGGTCAGGCGCCCTCCTCT 277 chrXptel1M 141942 G-------TTAATTATTTTCTCTTTATCTGATCTCTAATC-TGTACCTAA 141983 -------ii i iv vii viivv ivi v ? i- v i?i v L2b_3end#LINE 278 GGGCCCCCCCAGTCCTACCCTGCCACTCTGGGTTATNATTGTCTGNTTAC 327 chrXptel1M 141984 TTGTTTGTGGCTCTCA---GGCTGTGAGCCCCTTGAAGACAAGGA--GTG 142028 v i vv i i --- i i v i i i -- ? L2b_3end#LINE 328 ATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNG 377 chrXptel1M 142029 CTTATCTTTCCCTCTTCTTTATCTCCAGCACTTAGTTCAAGGCCTGGGAT 142078 ii i vii v iv v i i i iv i? v i L2b_3end#LINE 378 TCTGTCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCAC 427 chrXptel1M 142079 GAAGTAGGAGTTGAAT 142094 iv v i v i L2b_3end#LINE 428 ACAGTAGGCGCTCAGT 443 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 52.16 CpG sites = 83, Kimura (unadjusted) = 56.99 Transitions / transversions = 1.38 (83/60) Gap_init rate = 0.05 (18 / 381), avg. gap size = 2.17 (39 / 18) 257 30.02 9.04 2.12 chrXptel1M 141943 142119 (857881) L2d_3end#LINE/L2 328 516 (0) m_b328s601i23 13792 chrXptel1M 141943 TTAATTATTT--TCTCTT-TATCTGATCTCTAATCTGTACC-TAATTGTT 141988 v -- v - - v - vi - ivv L2d_3end#LINE 328 TTAATTATATACTGTCTTGTAT-TGTTCTCTAAT-TGTTTCATGTGTGTT 375 chrXptel1M 141989 TGT---GGCTCTC-----AGGCTGTGAGCCCCTTGAAGACAAGGA--GTG 142028 v --- v i ----- ii i i i i i --i L2d_3end#LINE 376 AGTCTTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATG 425 chrXptel1M 142029 -CTTAT-CTTTCCCTCTTCTTTATCTCCAGCACTTAGTTCAAGGCCTGGG 142076 - - ? i-- i? v vi iv i i iv iv ivi v L2d_3end#LINE 426 TCTTATACTNTT--TTNTCGTTCCCCACAGCGCCTAGCACAGTGCTGAGC 473 chrXptel1M 142077 ATGAAGTAGGAGTTGAATGGGTGCTTATCAGTTGACTTATTGA 142119 iiv v i v iii i i iii i v L2d_3end#LINE 474 ACATAGTAGGCGCTCAATAAATACTTGTTGATTGATTGATTGA 516 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.61 CpG sites = 33, Kimura (unadjusted) = 40.65 Transitions / transversions = 1.74 (33/19) Gap_init rate = 0.07 (12 / 176), avg. gap size = 1.67 (20 / 12) 11 22.96 1.72 7.27 chrXptel1M 142483 142540 (857460) (TTTATTA)n#Simple_repeat 1 55 (0) m_b328s252i17 13793 chrXptel1M 142483 TTGATCATGTA-TATTTATTGTCTATTTAATTTATTCTTTAACCTATTTA 142531 v i v - i i - - v - -i (TTTATTA)n#Si 1 TTTATTATTTATTATTTATTATTTA-TT-ATTTATTATTT-A-TTATTTA 46 chrXptel1M 142532 AAATGTATT 142540 vv v (TTTATTA)n#Si 47 TTATTTATT 55 Matrix = Unknown Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.09 (5 / 57), avg. gap size = 1.00 (5 / 5) 494 40.72 4.57 1.33 chrXptel1M 144052 144489 (855511) C L2b_3end#LINE/L2 (1) 465 14 m_b328s601i24 13794 chrXptel1M 144052 TCCATTAATT-AATAAACATTTATTCAGCACTT-TTTCCCCCCAGGCACC 144099 i v - i i i v i i -i viviv ? i C L2b_3end#LINE 465 TTCATTCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCT 416 chrXptel1M 144100 TTGCTAAGTACCAGGGATACA-----AAAAGAGGCAAAAATGATCCCCGA 144144 v i ii ii -----i vi i i v?i i i v C L2b_3end#LINE 415 GTGCTAGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGC 366 chrXptel1M 144145 TTTCAAGGAAGTCACAATCTAAT-GGGAACACA-AC-TGCAAAGAAATAT 144191 ii v iv i i - i v - - i ?v i i v C L2b_3end#LINE 365 CCTCACGGAGCTCACAGTCTAGTGGGGGAGACAGACATGTAANCAGACAA 316 chrXptel1M 144192 AAACAAGGCAAACTCTAGACAGAAATAAATAGAAGATAATTAAGGGAAGG 144241 v? i vv i v --- i iivvii iv ii ivivii ii i C L2b_3end#LINE 315 TNATAACCCAGAGT---GGCAGGGTAGGACTGGGGGGGCCCAGAGGAGGG 269 chrXptel1M 144242 AAGGTATCACAATTAGGAGAG--ATTGA-GGCCTCCCATCAAAGATGGGA 144288 vivv iv v iiiiv i i -- vv - i ivvii i iv C L2b_3end#LINE 268 CGCCTGACCCGGCCTGGGGGGTCAGGGAGGGCTTCCCGGAGGAGGTGACA 219 chrXptel1M 144289 CTTTAGTTGGACCTTGAAGGAGGTCAGGGAGATCAATGGGCAGAGATGAG 144338 i v i iiv i v vvvi v vivii ii - iv C L2b_3end#LINE 218 TTTGAGCTGAGACCTGAAGGATGAGTAGGAGTTGGCCAGGCGAAGA-GGT 170 chrXptel1M 144339 AAGGAAGAACATTCCATGTCTGGAGGACAGCCAGAGCAAACTTCCTGAGC 144388 ii ii i v ivvi i i v? v vvi v C L2b_3end#LINE 169 GGGGAAGGGCGTTCCAGGCAGAGGGAACAGCANGTGCAAAGGCCCTGAGG 120 chrXptel1M 144389 CAGAAATGAA-GTATCTCATTTGTAGAACAGTCAGAGGGC----ATCACT 144433 i i i? i-? iv vii i vi iv ii ----i vi C L2b_3end#LINE 119 CGGGAGNGAGCNTGGCGTGTTCGAGGAACAGCAAGGAGGCCAGTGTGGCT 70 chrXptel1M 144434 GGA-CAGAA-GAGTTTGAGGGGGGAATAACACATGAGAAGACTGGCAAGG 144481 - i- --ii i i iii viv vi i i vi C L2b_3end#LINE 69 GGAGCAGAGTGAG--CAAGGGGAGAGTGGTAGGAGATGAGGCCGGAGAGG 22 chrXptel1M 144482 TAAGAGAG 144489 ivi i C L2b_3end#LINE 21 TAGCGGGG 14 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 58.48 CpG sites = 114, Kimura (unadjusted) = 65.97 Transitions / transversions = 1.84 (114/62) Gap_init rate = 0.04 (18 / 437), avg. gap size = 1.44 (26 / 18) 252 35.41 4.72 3.64 chrXptel1M 144210 144590 (855410) C AmnL2-1#LINE/L2 (85) 2528 2144 m_b328s601i25 13794 chrXptel1M 144210 ACAGAAATAAATAGAAGATAATTAAGGGAAGGAAGGTATCACAATTAGGA 144259 iv iv i -- vii i iv --iv i C AmnL2-1#LINE/ 2528 ACAGAGTTAAATAATAAATAAT--AGCAGAGGGAGAGA--GAAATTAAGA 2483 chrXptel1M 144260 GAGATTGAGGCCTCCCATCAAAGATGGGACTTTAGTTGGACCTTGAA-GG 144308 iv -- vvvvv vv iv vi i ? iivi -? C AmnL2-1#LINE/ 2482 GGTAT--AGGCAAGGGAGAAAAGATATGTTTTCAGNTGAGATTTGAAANG 2435 chrXptel1M 144309 AGGTCAGGGAGA-TCAATG-GGCAGAGATGAGA-AGGAAGAACATTCCA- 144354 i --- - i - i - v - ivii - C AmnL2-1#LINE/ 2434 AGAT---GGAGAGTCGATGAGGCGGAGA-GATACAGGAAGGCTGTTCCAG 2389 chrXptel1M 144355 -TGTCTGGAGG-ACAGCCAGAGCAAACTTCCTGAGCCAGAAATGAAGTAT 144402 - v v v-i -- iiv ivi ii vi iv i iv - v C AmnL2-1#LINE/ 2388 ATGGCAGGAGCTGCAG--AGGAGAAGGCTCTCGCACCAACAGTGGCG-AG 2342 chrXptel1M 144403 CTCATTTGTAGA-ACAGTCAG-AGGGCATCACTGGACA---GAAGAGTTT 144447 v ii v v i- vv - v ivii i i--- i i vvi C AmnL2-1#LINE/ 2341 ATTGTGTGAAGGGACAGAGAGGAGGCCGGTGCTAGACGAGCGGAGGGAGC 2292 chrXptel1M 144448 GAGG-GGGGAATAACACATGAGAAGACTGGCAAGGTAAGAGAGAGCTAAG 144496 i - i iviviv v iiiv ii i vvi - C AmnL2-1#LINE/ 2291 GGGGAGGGGAGTAGAGAGAGACAAGGTCCGTGAGGTAGGCTGGAGC-AAG 2243 chrXptel1M 144497 TTT-TGAAGGGCTTTGAATGCCAAACAG-CA-TCGTGTGTTTGATCTTGG 144543 ii- i i i vi v iiv - - iv vii v i i C AmnL2-1#LINE/ 2242 TCCATGGAGGGTTTTAAAAACAAGGAAGGCAATTTTGAACTGGATCCTGA 2193 chrXptel1M 144544 AGGCAA--GAGTGTCACTGGAGCTTATTGAGGAGGGAGGTGATGTGGTC 144590 ivv -- i v i v i vv v i C AmnL2-1#LINE/ 2192 AATGAATGGGGAGCCAGTGGAGTTGTTTGAGGATGGGGGTGATGTGGTC 2144 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 46.84 CpG sites = 74, Kimura (unadjusted) = 50.09 Transitions / transversions = 1.32 (74/56) Gap_init rate = 0.08 (29 / 380), avg. gap size = 1.10 (32 / 29) 690 39.55 8.51 0.15 chrXptel1M 144338 144960 (855040) C L2#LINE/L2 (0) 3082 2408 m_b328s601i26 13794 chrXptel1M 144338 GAAGGAAGAACATTCCATGTCTGGAGGACAGCCAGAGCAAACTTCCTGAG 144387 ii i i v ivvi i i v v vvi C L2#LINE/L2 3082 GGGGGAAGAGCGTTCCAGGCAGAGGGAACAGCAAGTGCAAAGGCCCTGAG 3033 chrXptel1M 144388 CCAGAAATG-AAGTATCTCATTTGTAGAACAGTCAGAGGGC----ATCAC 144432 v i i ii -ivv iv vii i vi iv ii ----i vi C L2#LINE/L2 3032 GCGGGAGCGTGCCTGGCGTGTTCGAGGAACAGCAAGGAGGCCAGTGTGGC 2983 chrXptel1M 144433 TGGACAGAAGAGTTTGAGGGGG-GAATAACACATGAGAAGACTGGCAAGG 144481 vv i v vvi - i iii viv vi iiii vi C L2#LINE/L2 2982 TGGAGCGGAGTGAGCGAGGGGGAGAGTGGTAGGAGATGAGGTCAGAGAGG 2933 chrXptel1M 144482 TAAGAGAGAGCTAAGTTTTGAAGGGCTTTGAATGCCA--AACAGCATCGT 144529 vi i ii i ii iv v i v v --ivv v iiv C L2#LINE/L2 2932 TAACGGGGGACCAGATCATGTAGGGCCTTGTAGGCCATTGTAAGGACTTT 2883 chrXptel1M 144530 GTGTTTGATCTTG---GAGGCAAGAGTGTCACTGGAGCTTATTGAGGAGG 144576 vv v iii --- iiii i- i i vv v v i C L2#LINE/L2 2882 GGCTTTTACTCTGAGTGAGATGGGAA-GCCATTGGAGGGTTTTGAGCAGA 2834 chrXptel1M 144577 GAGGTGATGTGGTCAGATCTGTGCTTCAGGAAAATCATTCTGGTGGCCAA 144626 ii ii i v ii ii i i ii ii i iv iiv C L2#LINE/L2 2833 GGAGTGACATGATCTGACTTACGTTTTAAAAGGATCACTCTGGCTGCTGT 2784 chrXptel1M 144627 AAGGGGGATGGACTGGAGGGGGA-AAGACTTGAGGCAGGCAAACATTTCA 144675 ivv i i i ? i- iv v i v i vvv i C L2#LINE/L2 2783 GTTGAGAATAGACTGNAGGGGGGCAAGGGTGGAAGCAGGGAGACCAGTTA 2734 chrXptel1M 144676 TCCAACTATTGTGATACTCCAGGTTTAAGAT------------GACAAGG 144713 vvvii iii v ivvi ------------ v C L2#LINE/L2 2733 GGAGGCTATTGCAGTAATCCAGGCGAGAGATGATGGTGGCTTGGACCAGG 2684 chrXptel1M 144714 GT-ATAA----GGAGAAAAAGAGACAT--TT---TTCAAGAGACATTGCA 144753 -i ii---- iviiv vi -- i--- vi v i vii C L2#LINE/L2 2683 GTGGTGGCAGTGGAGGTGGTGAGAAGTGGTCGGATTCTGGATATATTTTG 2634 chrXptel1M 144754 GAGATTAAGTTGACAGACCTAGGCAAAAGCTTGAATCTGGGG-------- 144795 i i vi ii ivi v vii vi v i v -------- C L2#LINE/L2 2633 AAGGTAGAGCCGACAGGATTTGCTGATGGATTGGATGTGGGGTGTGAGAG 2584 chrXptel1M 144796 --AATGAGGAATCCAGTATTACACCTAGGTTGTGAGCCTGAGGGCCTGCA 144843 -- iv i v v v v v v vi viv v C L2#LINE/L2 2583 AAAGAGAGGAGTCAAGGATGACTCCAAGGTTTTTGGCCTGAGCAACTGGA 2534 chrXptel1M 144844 AAGATGCTATTGCCCTCTATAATAATGGGGAAGGTAGTAG--GGAGAAGG 144891 i vvi v i? ivivi iiv ii -- v C L2#LINE/L2 2533 AGGATGGAGTTGCCATTNACTGAGATGGGGAAGACTGCGGGAGGAGCAGG 2484 chrXptel1M 144892 TGCAGAAAAGAAGAT---GAGTTATATTTTGAAGATTTTGGATTTCAGAT 144938 viiiiiii --- vvi i v v iii v C L2#LINE/L2 2483 TTTGAGGGGGAAGATCAGGAGTTCAGTTTTGGACATGTTAAGTTTGAGAT 2434 chrXptel1M 144939 GGCTGAAAAGCTTC----TGGAGATG 144960 v ivv ii v ---- C L2#LINE/L2 2433 GCCTATTAGACATCCAAGTGGAGATG 2408 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 55.63 CpG sites = 147, Kimura (unadjusted) = 59.86 Transitions / transversions = 1.48 (147/99) Gap_init rate = 0.03 (17 / 622), avg. gap size = 3.18 (54 / 17) 326 25.61 9.24 1.56 chrXptel1M 145312 145430 (854570) C MIR1_Amn#SINE/MIR (101) 129 2 m_b328s601i28 13795 chrXptel1M 145312 CTGAGGCA-ATTGGGGTTAAGTGACTTGCCCAGGGTTACATAGCGAAGAA 145360 ?- vv i ? i i ?i ?iiv? C MIR1_Amn#SINE 129 CTGAGGCNCAGAGAGGTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNA 80 chrXptel1M 145361 GTATTAA-----GTATCTGAAACCAGATTT---GAACTCAGGTCC--TTC 145400 ivi i----- v ?i? v i i --- iii vi -- v C MIR1_Amn#SINE 79 GTGGCAGAGCCGGGANTNGAACCCAGGTCTCCCGAGTCCCAGTCCAGTGC 30 chrXptel1M 145401 TGACTATCCACTGGACCACCCAGCTGCTCT 145430 -- i v v iv i C MIR1_Amn#SINE 29 T--CTATCCACTAGACCACACTGCCTCCCT 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.06 CpG sites = 19, Kimura (unadjusted) = 35.06 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.05 (6 / 118), avg. gap size = 2.17 (13 / 6) 371 23.12 1.06 7.95 chrXptel1M 145312 145405 (854595) C MIRc#SINE/MIR (141) 127 40 m_b328s601i27 13795 chrXptel1M 145312 CTGAGGC-AATTGGGGTTAAGTGACTTGCCCAGGGTTACATAGCGAAGAA 145360 -v vv i i i i ------ C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGC------ 84 chrXptel1M 145361 GTATTAAGTATCTGAAACCAGATTTGAACTCAGGTCCTTCTGACT 145405 - v iv v iv vi i i i i i C MIRc#SINE/MIR 83 -TAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACT 40 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.40 CpG sites = 12, Kimura (unadjusted) = 28.01 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.09 (8 / 93), avg. gap size = 1.00 (8 / 8) 268 26.03 8.53 7.69 chrXptel1M 145726 145742 (854258) C MIR3#SINE/MIR (56) 152 136 m_b328s601i29 13796 chrXptel1M 145726 CAACCCCTTTGCGTTCC 145742 i iiiv v C MIR3#SINE/MIR 152 CAACCCCCTCATTTTAC 136 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.49 CpG sites = 20, Kimura (unadjusted) = 33.83 Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 31 0.00 0.00 0.00 chrXptel1M 145743 145771 (854229) (T)n#Simple_repeat 1 29 (0) c_b328s251i1 13797 chrXptel1M 145743 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 145771 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 268 26.03 8.53 7.69 chrXptel1M 145772 145882 (854118) C MIR3#SINE/MIR (73) 135 24 m_b328s601i29 13796 chrXptel1M 145772 GGCTGAGGCAATTGCGGTT-----------AGTGACTTACCCAGGGTCAC 145810 i- v i v ii----------- i i C MIR3#SINE/MIR 135 GA-TGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCAC 87 chrXptel1M 145811 ACACACTAGGAGGTTTAAGTGTCTGAGACCAGATTTGAACTTGGGTCCTC 145860 -i ? ---- -- v v v vi i v iii - C MIR3#SINE/MIR 86 ACA-GCNA----GTT--AGTGGCAGAGCCGGGACTAGAACCCAGGT-CTC 45 chrXptel1M 145861 CTGACTTCAGGGCTGGTACTCT 145882 i vi v i- i C MIR3#SINE/MIR 44 CTGACTCCCAGTCC-GTGCTCT 24 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.49 CpG sites = 20, Kimura (unadjusted) = 33.83 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.10 (11 / 110), avg. gap size = 1.91 (21 / 11) 470 20.94 1.63 6.84 chrXptel1M 145774 145896 (854104) C MIRc#SINE/MIR (141) 127 11 m_b328s601i30 13796 chrXptel1M 145774 CTGAGGC-AATTGCGGTTA-GTGACTTACCCAGGGTCACACACACTAGGA 145821 -v vv v - i i -i -- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACA-GCTAG-- 81 chrXptel1M 145822 GGTTTAAGTGTCTGAGACCAGATTTGAACTTGGGTCCTCCTGACTTCAGG 145871 ---- v v v vi i i iii i i i C MIRc#SINE/MIR 80 ----TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chrXptel1M 145872 GCTGGTACTCTTATCCACTGCACCA 145896 v ii i - C MIRc#SINE/MIR 34 TCCAGTGCTCTT-TCCACTGCACCA 11 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 23.80 CpG sites = 15, Kimura (unadjusted) = 24.97 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.08 (10 / 122), avg. gap size = 1.00 (10 / 10) 49 7.59 2.82 0.00 chrXptel1M 146170 146240 (853760) (CA)n#Simple_repeat 1 73 (0) c_b328s251i2 13798 chrXptel1M 146170 CACACACACATACACATACACATACACATGCACACAC-CACACACAC-CA 146217 i i i ii - - (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 chrXptel1M 146218 CACACACACACACACACACACAC 146240 (CA)n#Simple_ 51 CACACACACACACACACACACAC 73 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.03 (2 / 70), avg. gap size = 1.00 (2 / 2) 16 21.70 0.00 0.00 chrXptel1M 147231 147262 (852738) (A)n#Simple_repeat 1 32 (0) m_b328s252i18 13799 chrXptel1M 147231 AAAAAAAAAAAAAAAGTAAAATAAGTAAAGAA 147262 iv v iv i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 32 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 chrXptel1M 147493 147509 (852491) (A)n#Simple_repeat 1 17 (0) m_b328s252i19 13800 chrXptel1M 147493 AAAAAAAAAAAAAAAAA 147509 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 736 30.06 9.46 3.13 chrXptel1M 147720 149072 (850928) L1M5_orf2#LINE/L1 806 2241 (1053) m_b328s551i2 13801 chrXptel1M 147720 AAATTAGAAAACAATAAATTTAAGGGAAAGAAAGTGATAATGAAACAACA 147769 i v --- v vv v ? i v --- L1M5_orf2#LIN 806 AAATTAGAAAATATT---TTGAACTGAATGANAATGAAAAT---ACAACA 849 chrXptel1M 147770 TATCAAAATTTCTGGGATGTAGCTAATACAGTCCTCA-AGTGAAAATCGT 147818 v i vi v i - v v ii L1M5_orf2#LIN 850 TATCAAAATTTGTGGGATGCAGCTAAAGCAGTGCTTAGAGGGAAATTTAT 899 chrXptel1M 147819 TTCATTACAAACATATATTAACAAAACAAAAAG-------ATTAATGAAC 147861 vv ? v vi ? iv iv i ------- i v L1M5_orf2#LIN 900 AGCNTTAAATGCNTATATTAGAAAAGAAGAAAGGCTTAAAATCAATGATC 949 chrXptel1M 147862 TGAGTATGCA--TTAAAAAATTATAAAATCAA---CAAATAAAAC----A 147902 i iv v -- i ii v vv --- v ---- L1M5_orf2#LIN 950 TAAGCTTCCACCTTAAGAAGCTAGAAAAAGAAGAGCAAATTAAACCCAAA 999 chrXptel1M 147903 ATAAGCAAAAAAGAGAAGATATTAAAAATTAAATGGGGAATAAATTGGAA 147952 i? i i iii i i v i v i vvi i v -- L1M5_orf2#LIN 1000 GNAAGTAGAAGGAAGGAAATAATAAAGATAAGAGCAGAAATCAAT--GAA 1047 chrXptel1M 147953 ACAAAAAGCATAAGTATGACAAATAAAA---------CTAAAAGTTGGTT 147993 i i i v ?i? ii i i v --------- i i L1M5_orf2#LIN 1048 ATAGAAAACAAANANACAATAGAGAAAATCAACGAAGCCAAAAGCTGGTT 1097 chrXptel1M 147994 CTTTAAAAAAGT-AATAAAATTGATAAACCTTTGAT----CTGATTAATA 148038 i ii - i iii---- i v L1M5_orf2#LIN 1098 CTTTGAAAAGATCAATAAAATTGATAAACCTCTAGCNAGACTGATCAAGA 1147 chrXptel1M 148039 AGAAAATCAATA------AAATTA--AATAACA--AATGTACAAGATGAA 148078 i vvi v ------ -- v -- v v iv v L1M5_orf2#LIN 1148 AAAAAAGAGAGAAGACACAAATTACCAATATCAGGAATGAAAAAGGAGAC 1197 chrXptel1M 148079 ATCATAGCAAAACCAGAAGAAATAAAAAGAATAATCAAACTAA----ATC 148124 ivi i v viv v v i - ivv ---- v L1M5_orf2#LIN 1198 ATCACTACAGATCCTACAGACATTAAAAGGATAAT-AAGAGAATATTATG 1246 chrXptel1M 148125 AAGAACTCAAAGCACACAGG-ATGAGAACACAAAAGAAAAAAAAGAATAT 148173 v iv v vv i ii-v ? vi i v vii vi vi L1M5_orf2#LIN 1247 AACAACTTTATGCCAATAAATTTGANAACTTAGATGAAATGGACAAATTC 1296 chrXptel1M 148174 TTTCAAAAATATAAGATACCCACATTATCAGAAGACTAGACACAG---AT 148220 i v i i ?v v v i iv ?v -- v i --- L1M5_orf2#LIN 1297 CTTGAAAAACACAANTTACCAAAACTGACNCAAGA--AGAAATAGAAAAT 1344 chrXptel1M 148221 CTTAAATAGTTCAATCTCTGAAAAGGAAATAGACCTAGATGTAA--AGAA 148268 - i ii v v ivv i v vi --- -- i L1M5_orf2#LIN 1345 C-TGAATAGCCCTATATCTATTAAAGAAATTGAATT---TGTAATTAAAA 1390 chrXptel1M 148269 A----CTAACAAAAGCAGGAAAAATAAAATTTCTGGACCCAG-TGAATTC 148313 ---- iv ----- -------i ii i - iv L1M5_orf2#LIN 1391 ACCTTCCCACAAA-----GAAAA-------CTCCAGGCCCAGATGGCTTC 1428 chrXptel1M 148314 ACAGGAGAATTCTACCATACTTTTAGAGAACAGTTAGGACCATGCTT-CA 148362 v v v v ii v iv iv vv - L1M5_orf2#LIN 1429 ACTGGTGAATTCTACCAAACATTTAAGGAAGAAATAATACCAATCTTACA 1478 chrXptel1M 148363 GAAATTATTCTCAAAAATTGAGAAAGAAAACACCCTTAGTAGAATCTATT 148412 v i v ivi v i iiiv v --ivv iii L1M5_orf2#LIN 1479 CAAACTCTTCCAGAAAATAGAAAAAGAGGGAACACTT--CCCAACTCATT 1526 chrXptel1M 148413 TTA-AAAACAAATAGAATATTAATACCTAAACAAGGGAAAGA-GTTAAAA 148460 -i ii v ii v? ivi i v v? iv -i v L1M5_orf2#LIN 1527 TTATGAGGCCAGCATNACCCTGATACCAAAACCNGACAAAGACATTACAA 1576 chrXptel1M 148461 AAACAGAAATAAAACTATATGCCAACATCATTAATGAGCATTGACTTTAA 148510 i v ---- i i vi i vi v i v iviv L1M5_orf2#LIN 1577 GAAAAG----AAAATTACAGACCAATATCCCTCATGAACATAGATGCAAA 1622 chrXptel1M 148511 AATGTTTAATAAAATCCT----------ATACAATGATTTATCCACAAAA 148550 vi ? i vi ---------- v iii v vv v ii L1M5_orf2#LIN 1623 AATCCTNAACAAAATATTAGCAAATCGAATCCAGCAATATATAAAAAGGA 1672 chrXptel1M 148551 TATTTTATGTTAATCAAGTAGAATTTATTCCAGGGATGTAAGAATGATTA 148600 v vi vv i i i ii i i i iv i v L1M5_orf2#LIN 1673 TAATACATCATGACCAAGTGGGGTTTATCCCAGGAATGCAAGGTTGGTTT 1722 chrXptel1M 148601 ATCAGTAGGAAAACAATCAACATAATCAATCATATTAA-AAACTAAAATA 148649 v v v i v ii iv i - i v iv L1M5_orf2#LIN 1723 AACATTCGAAAATCAATCAATGTAATTCACCATATTAACAGAATAAAGGA 1772 chrXptel1M 148650 TCTAAAATCTCATGATCATCTC---AGATCCAAAAAAAGC-CTTGTCCAT 148695 vv- vi --- v i -i v v v L1M5_orf2#LIN 1773 GA-AAAATCATATGATCATCTCAATAGATGCAGAAAAAGCATTTGACAAA 1821 chrXptel1M 148696 ATACAACACTCGTTTATGATTAAAAAAAAAAAGTCT--ACAAAGTCAAGG 148743 v i i i ------- v --i v -- L1M5_orf2#LIN 1822 ATTCAACACCCATTCATGAT-------AAAAACTCTCAGCAAACT--AGG 1862 chrXptel1M 148744 CATA-AAGGGACCTTTTTTCGTATCATAAAAAGCAATCTGAAATAAA--- 148789 v - v ii iviiv v ii - ivi v --- L1M5_orf2#LIN 1863 AATAGAAGGGAACTTCCTCAACCTGATAAAGGGC-ATCTACGAAAAACCT 1911 chrXptel1M 148790 AAAACAAGCATCACGTATAATGGGGATACAATGGAACATTTCCCATTGA- 148838 v i ? i iiiv v v ? v i ?vv vi i - L1M5_orf2#LIN 1912 ACAGCNAACATCATACTTAATGGTGAAANACTGAANGCTTTCCCCCTAAG 1961 chrXptel1M 148839 ATATGG--TAAAGTGAGAATGTCTAATCTCCCTCCTATTATTTGACATGG 148886 vv --i iiii i iiv ? v iv vi ii v L1M5_orf2#LIN 1962 ATCGGGAACAAGACAAGGATGTCCGCTNTCACCACTTCTATTCAACATTG 2011 chrXptel1M 148887 TACTAGAAATGTTAG--------------------AAAGGAATTAAAGGA 148916 i ii vi -------------------- i v v L1M5_orf2#LIN 2012 TACTGGAGGTCCTAGCCAGTGCAATAAGGCAAGAAAAAGAAATAAAAGGC 2061 chrXptel1M 148917 ATAAAGATT---------------AAAC--TCTTTCTTAGCTGATGCTTT 148949 --------------- -- ? v v v viv L1M5_orf2#LIN 2062 ATAAAGATTGGAAAGGAAGAAATAAAACTGTCNTTATTCGCAGATGACAT 2111 chrXptel1M 148950 GAAGATTTCCTTGGAAAACATCAGGGATTCAGCAAAGAGTCC----GAGG 148995 vvi ? v v i ivi? ii v vi ? iv i---- iv L1M5_orf2#LIN 2112 GATTGTNTACGTAGAAAATCCNAAAGAATCTACAAANAAACTACTAGAAC 2161 chrXptel1M 148996 CGATACT----TTTAGCAAAGTTGTGGACTGCAAAGTAAATCCTCAAAAA 149041 ii vv---- i i i? iv i i v viv L1M5_orf2#LIN 2162 TAATAAGTGAATTTAGCAAGGTCGCNGGATACAAGGTCAATATACAAAAA 2211 chrXptel1M 149042 TCAACAGCATTTCTACATATATAATAACAAA 149072 iv i i i- ii L1M5_orf2#LIN 2212 TCAATTGTATTTCTATATAC-TAGCAACAAA 2241 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.73 CpG sites = 212, Kimura (unadjusted) = 40.14 Transitions / transversions = 1.16 (212/182) Gap_init rate = 0.06 (79 / 1352), avg. gap size = 2.19 (173 / 79) 593 31.01 6.34 3.17 chrXptel1M 147893 148901 (851099) L1MD_orf2#LINE/L1 987 2026 (1268) m_b329s551i1 13801 chrXptel1M 147893 AAATAAAAC---AATAAGCAAAAAAGAGAAGATATTAAAAATTAAATGGG 147939 v --- ii i iii i i v i v i vvi L1MD_orf2#LIN 987 AAATAAACCCAAAGCAAGCAGAAGGAAGGAAATAATAAAGATAAGAGCAG 1036 chrXptel1M 147940 GAAT-----AAATTGGAAACA-AAAAGCA-TAAGTATGACAAATAAAACT 147982 i ----- i - i - iiv vi iv i v L1MD_orf2#LIN 1037 AAATCAATGAAATTGAAAACAGAAAAACAATAGAGAAAATCAATGAAACA 1086 chrXptel1M 147983 AAAAGTTGGTTCTTTAAAAAAGT-AATAAAATTGATAAACCTTTGAT--- 148028 i i ii - i i iii--- L1MD_orf2#LIN 1087 AAAAGCTGGTTCTTTGAAAAGATCAATAAAATTGACAAACCTCTAGCAAG 1136 chrXptel1M 148029 -CTGATTAATAAGAAAATCAATAA------AATTA--AATAACA--AATG 148067 - iv v i vvi v ------ -- v -- L1MD_orf2#LIN 1137 ACTGACAAAGAAAAAAAGAGAGAAGACACAAATTACCAATATCAGGAATG 1186 chrXptel1M 148068 TACAAGATGAAATCATAGCAAAACCAGAAGAAATAAAAAGAATAATCAA- 148116 v vv iv v ivi i v v v v v i v i- L1MD_orf2#LIN 1187 AAACAGGGGATATCACTACAGACCCTGCAGACATCAAAAGGATAATAAGG 1236 chrXptel1M 148117 ----ACTAAATCAAGAACTCAAAGCACACAGGAT-GAGAACACAAAAGAA 148161 ---- vi-- v v v i iiv - v vi i v L1MD_orf2#LIN 1237 GAATACTACG--AACAACTCTACGCACATAAATTTGACAACTTAGATGAA 1284 chrXptel1M 148162 AAAAAAGAATATTTTCAAAAATATAAGATACCCACATTATCAGAAGACTA 148211 vii vv vii iv i i iv v?v i vv vv ? i-- L1MD_orf2#LIN 1285 ATGGACCAATTCCTCGAAAAACACAAACTACCANAACTCACCCAANAT-- 1332 chrXptel1M 148212 GACACAGAT--CTTAAATAGTTCAATCTCTGAAAAGGAAATAGACCTAG- 148258 v i --i i ii v vv ivv v vi v - L1MD_orf2#LIN 1333 GAAATAGATAATTTGAATAGCCCTATAACTATTAAGGAAATTGAATTCGT 1382 chrXptel1M 148259 -ATGTAAAGAAACTAACAAAAGCAGGAAAAATAAAATTTCTGGACCCAG- 148306 - v ? -- vv v -------- -i i ii i - L1MD_orf2#LIN 1383 AATTTNAA--AACTCCCCAAA--------AA-GAAATCTCCAGGCCCAGA 1421 chrXptel1M 148307 TGAATTCACAGGAGAATTCTACCATACTTTTAGAGAACAGTTAGGACCA- 148355 iv v v v i v i iv - L1MD_orf2#LIN 1422 TGGTTTCACTGGAGAATTCTACCAAACGTTTAAAGAAGAATTAACACCAA 1471 chrXptel1M 148356 TGCTTCAGAAATTATTCTCAAAAATTGAGAAAGAAAACACCCTTAGTAGA 148405 v v v vi v ivi v ii i iiiv v vvi -- L1MD_orf2#LIN 1472 TTCTACACAATCTCTTCCAGAAAATAGAAGAGGAGGGAACACTTCCCA-- 1519 chrXptel1M 148406 ATCTATTTTA-AAAACAAATAGAATATTAATACCTAAACAAGGGAAAGA- 148453 iii -i ii v i vv ivi i v v iv - L1MD_orf2#LIN 1520 ACTCATTTTATGAGGCCAGTATTACCCTGATACCAAAACCAGACAAAGAC 1569 chrXptel1M 148454 GTTAAAAAAACAGAAATAAAACTATATGCCAACATCATTAATGAGCATTG 148503 iv v v ---- i vi i vi v i v L1MD_orf2#LIN 1570 AGTACAAAAAAAGAAA----ACTACAGACCAATATCCCTCATGAACATAG 1615 chrXptel1M 148504 ACTTTAAAATGTTTAATAAAATCCTATACAATG--ATT------TATCCA 148545 viv vi i i vi vvv ?-- ------ vi L1MD_orf2#LIN 1616 ACGCAAAAATCCTCAACAAAATATTAGCAAATNGAATTCAGCAATATATA 1665 chrXptel1M 148546 CAAAATATTTTATGTTA--ATCAAGTAGAATTTATTCCAGGGATGTAAGA 148593 v iv v iiii -- i i ii ? i i L1MD_orf2#LIN 1666 AAAAGAATTATACACCATGACCAAGTGGGGTTTATTCCAGGNATGCAAGG 1715 chrXptel1M 148594 ATGATTAATCAGTAGGAAAACAATCAACATAATCAATCATATTAA-AAAC 148642 v i v vi v v i v ii v i - ii L1MD_orf2#LIN 1716 CTGGTTCAATATTCGAAAATCAATCAATGTAATCCACCATATTAACAGGC 1765 chrXptel1M 148643 TAAAATATCTAAAATCTCATGATCATCTCA---GATCCAAAAAAAGC-CT 148688 iv vv- v v --- v i -i L1MD_orf2#LIN 1766 TAAAGAAGA-AAAATCACATGATCATATCAATTGATGCAGAAAAAGCATT 1814 chrXptel1M 148689 TGTCCATATACAACACTCGTTTATGATTAAAAAAAAAAAGTCTACAAAGT 148738 v v v v i i i ------- v vvi? iv L1MD_orf2#LIN 1815 TGACAAAATTCAACACCCATTCATGAT-------AAAAACTCTCAGNAAA 1857 chrXptel1M 148739 CAAGGCATA-AAGGGACCTTTTTTCGTATCATAAAAAGCAATCTGAAATA 148787 v v - i v ii iviiv v i - --- i L1MD_orf2#LIN 1858 CTAGGAATAGAGGGGAACTTCCTCAACTTGATAAAGAGC-ATCT---ACA 1903 chrXptel1M 148788 AAAAA---ACA---AGCATCACGTATAATGGGGATACAATGGAACATTTC 148831 --- --- i iiiv v v v v i vvv L1MD_orf2#LIN 1904 AAAAACCTACAGCTAACATCATACTTAATGGTGAAAGACTGAATGCTTTC 1953 chrXptel1M 148832 CCATTGA-ATATGG--TAAAGTGAGAATGTCTAATCTCCCTCCTATTATT 148878 vi i - vv --i i ii i iiv v iv v L1MD_orf2#LIN 1954 CCCCTAAGATCGGGAACAAGGCAAGGATGTCCGCTCTCACCACTCTTATT 2003 chrXptel1M 148879 TGACATGGTACTAGAAATGTTAG 148901 ii i i i vi L1MD_orf2#LIN 2004 CAACATAGTACTGGAAGTTCTAG 2026 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.58 CpG sites = 158, Kimura (unadjusted) = 41.12 Transitions / transversions = 1.09 (158/145) Gap_init rate = 0.06 (63 / 1008), avg. gap size = 1.54 (97 / 63) 637 30.52 5.60 3.19 chrXptel1M 148286 148928 (851072) L1M4_orf2#LINE/L1 1401 2058 (1236) m_b329s551i2 13801 chrXptel1M 148286 AAATAAAATTTCTGGACCCAGTGAATTCACAGGAGAATTCTACCATACTT 148335 v vii v ? vii iv v v v v L1M4_orf2#LIN 1401 AAAGAAAAGCCCAGGNCCAGATGGCTTCACTGGTGAATTCTACCAAACAT 1450 chrXptel1M 148336 TTAGAGAACAGTTAGGACCA-TGCTTCAGAAATTATTCTCAAAAATTGAG 148384 i v i iv - v v i v iv v i L1M4_orf2#LIN 1451 TTAAAGAAGAATTAACACCAATCCTTCACAAACTCTTCCAAAAAATAGAA 1500 chrXptel1M 148385 AAAGAAAACACCCTTAGTAGAATCTATTTTA-AAAACAAATAGAATATTA 148433 i i iiiv v vvi -- iii i -i ii v i vv ivi i L1M4_orf2#LIN 1501 GAGGAGGGAACACTTCCCA--ACTCATTCTATGAGGCCAGTATTACCCTG 1548 chrXptel1M 148434 ATACCTAAACAAGGGAAAGAGTTAAAAAAACAGAAATAAAACTATATGCC 148483 v v iv vv v v i --- v i vi L1M4_orf2#LIN 1549 ATACCAAAACCAGACAAAGACATCACAAGA---AAAGAAAACTACAGACC 1595 chrXptel1M 148484 AACATCATTAATGAGCATTGACTTTAAAATGTTTAATAAAATCCTATACA 148533 i vi v ii v iviv vi i i v -i L1M4_orf2#LIN 1596 AATATCCCTTATGAATATAGATGCAAAAATCCTCAACAAAATACTA-GCA 1644 chrXptel1M 148534 A--TGATTTATCCA-CAAAATATT-------TTATGT----TAATCAAGT 148569 --i --- - v v------- ii---- i i L1M4_orf2#LIN 1645 AACCGA---ATCCAGCAACATATAAAAAGGATTATACACCATGACCAAGT 1691 chrXptel1M 148570 AGAATTTATTCCAGGGATGTAAGAATGATTAATCAGTAGGAAAACAATCA 148619 i i i i i iv i v v v?v i v L1M4_orf2#LIN 1692 GGGATTTATCCCAGGAATGCAAGGTTGGTTCAACATNCGAAAATCAATCA 1741 chrXptel1M 148620 ACATAATCAATCATATTAA-AAACTAAAATATCTAAAATCTCATGATCAT 148668 ii vv i - i v iv - v i v L1M4_orf2#LIN 1742 ATGTAATACACCATATTAATAGAATAAAGGA-CAAAAACCACATGATCAT 1790 chrXptel1M 148669 CTC---AGATCCAAAAAAAGC-CTTGTCCATATACAACACTCGTTTATGA 148714 --- iv i -i v v v v i v i L1M4_orf2#LIN 1791 CTCAATAGACGCAGAAAAAGCATTTGACAAAATCCAACACCCTTTCATGA 1840 chrXptel1M 148715 TTAAAAAAAAAAAGTCTACAAAGTCAAGGCATA-AAGGGACCTTTTTTCG 148763 ----- v v v v -- v - v ii ivi L1M4_orf2#LIN 1841 T-----AAAAACACTCAACAAACT--AGGAATAGAAGGGAACTTCCTCAA 1883 chrXptel1M 148764 TATCATAAAAAGCAATCTGAAATAAAAAA---ACA---AGCATCACGTAT 148807 iv v ii - --- ii --- --- i iiiv L1M4_orf2#LIN 1884 CCTGATAAAGGGC-ATCT---ACGAAAAACCCACAGCTAACATCATACTT 1929 chrXptel1M 148808 AATGGGGATACAATGGAACATTTCCCATTGA-ATATGG--TAAAGTGAGA 148854 v v v v i ?vv vi i - vv --i iiii i L1M4_orf2#LIN 1930 AATGGTGAAAGACTGAANGCTTTCCCCCTAAGATCAGGAACAAGACAAGG 1979 chrXptel1M 148855 ATGTCTAATCTCCCTCCTATTATTTGACATGGTACTAGAAATGTTAGAAA 148904 iiv v iv vi ii v i ii vi vv L1M4_orf2#LIN 1980 ATGTCCGCTCTCGCCACTTCTATTCAACATTGTACTGGAGGTTCTAGCCA 2029 chrXptel1M 148905 GG--AATTA---AAGGAATAAAGATTAAA 148928 -- --- i v i i v L1M4_orf2#LIN 2030 GGGCAATTAGGCAAGAAAAAGAAATAAAA 2058 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.09 CpG sites = 101, Kimura (unadjusted) = 40.23 Transitions / transversions = 1.13 (101/89) Gap_init rate = 0.06 (37 / 642), avg. gap size = 1.54 (57 / 37) 258 30.91 7.33 2.81 chrXptel1M 149344 149616 (850384) L1MC_orf2#LINE/L1 2537 2821 (473) m_b329s551i4 13801 chrXptel1M 149344 AATTCATGTAGAAAAACAACAGATCTAGAATA-TCAACAGAAATGATGAG 149392 i i i i i ii v i i -i v - iv i L1MC_orf2#LIN 2537 AGTTTATATGGAGAGGCAAAAGACCCAGAATAGCCAACACAA-TATTGAA 2585 chrXptel1M 149393 ATGTAAGAACAAAG--GGA-GATTAGCACTTCTAGATCTAAAAGTATATT 149439 iviv -- - i ii v iv ii v iiiv i L1MC_orf2#LIN 2586 GGAGAAGAACAAAGTCGGAGGACTGACACTACCCGACTTCAAGACTTACT 2635 chrXptel1M 149440 ATAAAG---CAGTCATCAAAGTCATCTGTTATTGGTTAAATAATAGAG-- 149484 --- v iiivi v v iv v v-- L1MC_orf2#LIN 2636 ATAAAGCTACAGTAATCAAGACAGTGTGGTATTGGCGAAAGAATAGACAA 2685 chrXptel1M 149485 --AGATCAAAGGAACAGACTGGACAAGGGAGACTCAGAAACA-------A 149525 -- v v ----- i - i i ------- L1MC_orf2#LIN 2686 ATAGATCAATGGAACAGAAT-----AGAGAG-CCCAGAAATAGACCCACA 2729 chrXptel1M 149526 TAGAAGGCAGTAACCCAATGTTTGACAAAGTG--AAAAACAAAATATTGA 149573 - vii v v ii v vi-- ii v?i v i L1MC_orf2#LIN 2730 TA-AATATAGTCAACTGATCTTTGACAAAGGAGCAAAGGCAATNCAATGG 2778 chrXptel1M 149574 GGGAAAAATTCCCTATTTCATAAAAATTTCTGGGAAAACTGGA 149616 i i i vvi v iv i viv v i v L1MC_orf2#LIN 2779 AGAAAAGATAGTCTTTTCAACAAATGGTGCTGGAACAACTGGA 2821 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.80 CpG sites = 49, Kimura (unadjusted) = 41.47 Transitions / transversions = 1.48 (49/33) Gap_init rate = 0.06 (16 / 272), avg. gap size = 1.75 (28 / 16) 310 23.54 6.59 4.30 chrXptel1M 149344 149525 (850475) L1M3_orf2#LINE/L1 2531 2716 (572) m_b329s551i3 13801 chrXptel1M 149344 AATTCATGTAGAAAAACAACAGATCTAGAATATCAACAGAAATGATGAGA 149393 i i vv v i iv v v v v vv L1M3_orf2#LIN 2531 AATTCATATGGAACCACAAAAGACCCCGAATAGCCAAAGCAATCTTGAGA 2580 chrXptel1M 149394 TGTAAGAACAAAG--GGAG--ATTAGCACTTCTAGATCTAAAAGTATATT 149439 viv -- -- i - iv i v i L1M3_orf2#LIN 2581 AAGAAGAACAAAGCTGGAGGCATCA-CACTTCCTGATTTCAAAATATATT 2629 chrXptel1M 149440 ATAAAG---CAGTCATCAAAGTCATCTGTTATTGGT-TAAATAATAGAG- 149484 i --- v iivi v v i i- - i v- L1M3_orf2#LIN 2630 ACAAAGCTACAGTAATCAAAACAGTATGGTACTGGCATAAA-AACAGACA 2678 chrXptel1M 149485 ---AGATCAAAGGAACAGACTGGACAAGGGAGACTCAGAAACAA 149525 --- i v v ----- i - i i L1M3_orf2#LIN 2679 TATAGACCAATGGAACAGAAT-----AGAGAG-CCCAGAAATAA 2716 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 28.49 CpG sites = 20, Kimura (unadjusted) = 28.49 Transitions / transversions = 0.95 (20/21) Gap_init rate = 0.08 (14 / 181), avg. gap size = 1.43 (20 / 14) 274 26.13 9.59 3.90 chrXptel1M 149397 149615 (850385) L1P1_orf2#LINE/L1 2590 2820 (474) m_b329s551i5 13801 chrXptel1M 149397 AAGAACAAAG--GGAG--ATTAGCACTTCTAGATCTAAAAGTATATTATA 149442 -- -- i - i v iv ii v v i i L1P1_orf2#LIN 2590 AAGAACAAAGCTGGAGGCATCA-CGCTACCTGACTTCAAACTATACTACA 2638 chrXptel1M 149443 AAGC---AGTCATCAAAGTCATCTGTTATTGGTTAAATAATAGAGA---- 149485 i --- v i iiviiv v i vvv v i ---- L1P1_orf2#LIN 2639 AGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATA 2688 chrXptel1M 149486 GATCAAAGGAACAGACTGGACAAGGGAGAC-TCAGAAACAATA--GAAGG 149532 v ---- --- v - i ii-- v vi L1P1_orf2#LIN 2689 GATCAATGGAACAGA----ACA---GAGCCCTCAGAAATAACGCCGCATA 2731 chrXptel1M 149533 ----CAGTAACCCAATGTTTGACAAA---GTGAAAAACAAAATATTGAGG 149575 ---- iiv i ii v --- v i-i v i L1P1_orf2#LIN 2732 TCTACAACTATCTGATCTTTGACAAACCTGAGAAAAACAAG-CAATGGGG 2780 chrXptel1M 149576 GAAAAATTCCCTATTTCATAAAAATTTCTGGGAAAACTGG 149615 i ii v viv v L1P1_orf2#LIN 2781 AAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGG 2820 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 31.32 CpG sites = 31, Kimura (unadjusted) = 32.83 Transitions / transversions = 1.29 (31/24) Gap_init rate = 0.08 (17 / 218), avg. gap size = 1.76 (30 / 17) 15 12.03 5.56 0.00 chrXptel1M 149784 149819 (850181) (ATAAAAG)n#Simple_repeat 1 38 (0) m_b329s252i0 13802 chrXptel1M 149784 ATAAAAGATAAAAGAT--ATTATGAAAGATAAAACATA 149819 -- vv i v (ATAAAAG)n#Si 1 ATAAAAGATAAAAGATAAAAGATAAAAGATAAAAGATA 38 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.03 (1 / 35), avg. gap size = 2.00 (2 / 1) 25 2.85 0.00 5.26 chrXptel1M 149944 149983 (850017) (AAGAA)n#Simple_repeat 1 38 (0) m_b329s252i1 13803 chrXptel1M 149944 AAAAAAAGAAAAGAAAAGAAAAGAAAAGGAAAAGGAAAAG 149983 i - - (AAGAA)n#Simp 1 AAGAAAAGAAAAGAAAAGAAAAGAAAA-GAAAA-GAAAAG 38 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 25 32.16 0.98 1.98 chrXptel1M 150639 150715 (849285) (AT)n#Simple_repeat 1 77 (24) m_b329s252i2 13804 chrXptel1M 150639 ATATATATCATATATTCATAAACCCAATTATATACATGTATACATATACA 150688 - vi v ivi vv i i i i (AT)n#Simple_ 1 ATATATAT-ATATATATATATATATATATATATATATATATATATATATA 49 chrXptel1M 150689 CATGTATATGTATGCATATATGTGTA-A 150715 i i i ii i i - (AT)n#Simple_ 50 TATATATATATATATATATATATATATA 77 Matrix = Unknown Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.03 (2 / 76), avg. gap size = 1.00 (2 / 2) 31 12.06 0.00 0.00 chrXptel1M 150716 150769 (849231) (AT)n#Simple_repeat 1 54 (0) c_b329s251i0 13804 chrXptel1M 150716 ATATATATATCTATATATCTATATCTATATGTAGATATATAGATATATAT 150765 v v v i v v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chrXptel1M 150766 ATAT 150769 (AT)n#Simple_ 51 ATAT 54 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 25 32.16 0.98 1.98 chrXptel1M 150770 150793 (849207) (AT)n#Simple_repeat 78 100 (1) m_b329s252i2 13804 chrXptel1M 150770 CTGGCTATATATATCAGATAGATA 150793 v ivv - v v (AT)n#Simple_ 78 ATATATATATATAT-ATATATATA 100 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 19 3.70 0.00 3.45 chrXptel1M 152343 152372 (847628) (AAGAA)n#Simple_repeat 1 29 (0) m_b329s252i3 13805 chrXptel1M 152343 AAAAAAAGAAAAGAAAAGAAAAGGAAAAGA 152372 i - (AAGAA)n#Simp 1 AAGAAAAGAAAAGAAAAGAAAA-GAAAAGA 29 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 371 19.87 10.20 10.96 chrXptel1M 153099 153245 (846755) MIRb#SINE/MIR 6 151 (117) m_b329s601i0 13806 chrXptel1M 153099 GGCCAGCAAGTGGCGCAGTGGACGGA--ATGGA---TGGA---AGACTCA 153140 v -- i vi -- i i--- --- vv MIRb#SINE/MIR 6 GGGCAGC--GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGA 53 chrXptel1M 153141 TTTTCTTGAGTTTAAATCTCAGA-----CACTTAACTGTTTGTGTGATCC 153185 ---- i i ii i i v----- - ivi i i MIRb#SINE/MIR 54 ----CCTGGGTTCGAATCCCGGCTCTGCCACTTA-CTAGCTGTGTGACCT 98 chrXptel1M 153186 TGGGTAAGTCACTCATAACTTTAACCCCATCTG--CCTCAGTTTCCTCTT 153233 i i -------- i - -- v MIRb#SINE/MIR 99 TGGGCAAGTTACT--------TAACCTC-TCTGAGCCTCAGTTTCCTCAT 139 chrXptel1M 153234 CTGTAAAACGAG 153245 i i MIRb#SINE/MIR 140 CTGTAAAATGGG 151 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 20.71 CpG sites = 19, Kimura (unadjusted) = 23.87 Transitions / transversions = 2.71 (19/7) Gap_init rate = 0.14 (21 / 146), avg. gap size = 1.48 (31 / 21) 722 28.70 2.07 6.03 chrXptel1M 153332 153572 (846428) C MIR#SINE/MIR (10) 252 21 m_b329s601i1 13807 chrXptel1M 153332 AACATTTACCAGATACCTACTATGTGCCAGGCACTGTGCCAAGTGCTTTA 153381 iiiiiii i v i i C MIR#SINE/MIR 252 AACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGCGCTTTA 203 chrXptel1M 153382 CATTTATCATGCCATTTTAGCTTCACAACAACCCACAACAACCCAACATG 153431 v i vvi v v i -------ivii vi i C MIR#SINE/MIR 202 CATGTATTAACTCATTTAATCCTCACAACAACCC-------TATGAGGTA 160 chrXptel1M 153432 GGTACTATTATCACCCCAATTTTTGAGAAATTTTGAGGAAATTTAGG-AT 153480 i i v vv ----- i v - i C MIR#SINE/MIR 159 GGTACTATTATTATCCCCATTTTACAGA-----TGAGGAAACTGAGGCAC 115 chrXptel1M 153481 GGCAAAAGCTAAGTGACTTGCCCAGCATCATATAGTT----CGTGGCTGA 153526 i - i i i i ivi i i i ----v v C MIR#SINE/MIR 114 AG-AGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGA 66 chrXptel1M 153527 GACTTGACTTGAACCTGGGCTTCCTGATCCCGCTGCTCTGTGCTTT 153572 v vv i i ii vvi iii ivv - i i C MIR#SINE/MIR 65 GCCGGGATTCGAACCCAGGCAGTCTGGCTCCAGAGC-CCGTGCTCT 21 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.66 CpG sites = 43, Kimura (unadjusted) = 37.68 Transitions / transversions = 1.95 (43/22) Gap_init rate = 0.07 (16 / 240), avg. gap size = 1.19 (19 / 16) 349 28.22 4.27 4.91 chrXptel1M 153431 153594 (846406) C MIR1_Amn#SINE/MIR (64) 166 4 m_b329s601i2 13807 chrXptel1M 153431 GGGTACTATTATCACCCCAATTTTTGAGAAATTTTGAGGAAATTTAGGAT 153480 vi v i i i v vv ----- i v v? C MIR1_Amn#SINE 166 GGTCAGTATCATTATCCCCATTTTACAGA-----TGAGGAAACTGAGGCN 122 chrXptel1M 153481 GGCAAAAGCTAAGTGACTTGCCCAGCATCATATAGTT--C--GTGGCTGA 153526 viv i i i? ivi i?i i?-- -- v C MIR1_Amn#SINE 121 CAGAGAGGTNAAGTGACTTGCCCAAGGTCACNCAGCNGGCNAGTGGCAGA 72 chrXptel1M 153527 GACTTGACTTGAACCTGGGCTTCCTGA-TCCCGCTGCTCTGTGCTTTGT- 153574 v vv ? ? ii ii i - i-- ii v i i - C MIR1_Amn#SINE 71 GCCGGGANTNGAACCCAGGTCTCCCGAGTCCCA--GTCCAGTGCTCTATC 24 chrXptel1M 153575 -AGTGTTCCTTCACTGCCTCC 153594 - v ivv -v C MIR1_Amn#SINE 23 CACTAGACC-ACACTGCCTCC 4 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.01 CpG sites = 25, Kimura (unadjusted) = 38.11 Transitions / transversions = 1.32 (25/19) Gap_init rate = 0.08 (13 / 163), avg. gap size = 1.15 (15 / 13) 729 26.59 6.39 0.43 chrXptel1M 153891 154109 (845891) MIRb#SINE/MIR 34 265 (3) m_b329s601i3 13808 chrXptel1M 153891 GGGATTTGGAATCAGGAAAGTCTGAGCTCAAATTCTGCTTCAGACACTT- 153939 v i iv iii i i i i i vi v v - MIRb#SINE/MIR 34 GGGCTTTGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTA 83 chrXptel1M 153940 -TACCTGTATGTCCCTGGGTAAGTTACTTCACATTT----GCCTCAAGTT 153984 - v i v i i v v i ---- iv MIRb#SINE/MIR 84 CTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTT 133 chrXptel1M 153985 GGCCATCAGTAAAATGGGAATATTAATAGC-ACC----AGAGTCGC-ACC 154028 vvi v i v v - ---- i i i-iiv MIRb#SINE/MIR 134 CCTCATCTGTAAAATGGGGATAATAATACCTACCTCGCAGGGTTGTTGTG 183 chrXptel1M 154029 AG-ATCAAATGAGGTGGT-CATTGTAAAACATTTACCACGGTGCCTGACA 154076 - i i ii - - i ii v i i MIRb#SINE/MIR 184 AGGATTAAATGAGATAATGCAT-GTAAAGCGCTTAGCACAGTGCCTGGCA 232 chrXptel1M 154077 CACATTAAGAACTAAATAAATGTTATTTCTTTT 154109 i v vi v v vi v MIRb#SINE/MIR 233 CATAGTAAGCGCTCAATAAATGGTAGCTCTATT 265 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.93 CpG sites = 35, Kimura (unadjusted) = 33.73 Transitions / transversions = 1.52 (35/23) Gap_init rate = 0.04 (9 / 218), avg. gap size = 1.67 (15 / 9) 192 25.72 26.71 0.99 chrXptel1M 154537 154697 (845303) L2c_3end#LINE/L2 201 402 (76) m_b329s601i4 13809 chrXptel1M 154537 TCCTTCATGTCTCAGGTAAAATCCCATATTCTGCAAGAAGCTTCTCTGGA 154586 v ? v v i vi iv i v ii i ii iv L2c_3end#LINE 201 TCCTTCAAGNCTCAGCTCAGATGTCACCTCCTCCGGGAAGCCTTCCCTGA 250 chrXptel1M 154587 TCCTGCTTAATGCTA----AAGT---CTTCTCTCTG-------AG-ACCC 154621 i -- ii v? ---- i --- i v ------- - L2c_3end#LINE 251 CCC--CCCAAGNCTAGTCTAGGTGCCCTCCTCTGTGCTCCCATAGCACCC 298 chrXptel1M 154622 T--C----CTCCT------GCAATT-----TATCTTGT-CTACA-TTGT- 154651 -- ---- i------ v ----- v -i ii - - L2c_3end#LINE 299 TGTCTATACTCCCATTATAGCACTTATCATTAACTTGTATTGTAATTGTC 348 chrXptel1M 154652 TGTTTAC-----TG---CCTCCATCAGATCATGAGCTCCTTTAAGACAGA 154693 ----- --- ii iii v i i i L2c_3end#LINE 349 TGTTTACNTGTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGG 398 chrXptel1M 154694 AATC 154697 i i L2c_3end#LINE 399 GACC 402 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.64 CpG sites = 29, Kimura (unadjusted) = 33.66 Transitions / transversions = 2.42 (29/12) Gap_init rate = 0.09 (15 / 160), avg. gap size = 3.00 (45 / 15) 257 22.93 12.50 3.54 chrXptel1M 157969 158072 (841928) L2b_3end#LINE/L2 293 405 (61) m_b329s601i5 13810 chrXptel1M 157969 TACTCT-CCACTTTG-----CAATTTCTTTTTTATGCG-CTATCTTCTCC 158011 i - i -----i? vii v? iii - i i - L2b_3end#LINE 293 TACCCTGCCACTCTGGGTTATNATTGTCTGNTTACATGTCTGTCTCC-CC 341 chrXptel1M 158012 CATTAGACTTTGAGCCCCTTGAGGAGAGGGACCG-GTTTATACCCTTGCT 158060 i v i v iv - i i --- i L2b_3end#LINE 342 CACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGT---CTTGTT 388 chrXptel1M 158061 -----TTGTATCCTCAG 158072 -----i i L2b_3end#LINE 389 CACCGCTGTATCCCCAG 405 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.79 CpG sites = 18, Kimura (unadjusted) = 29.79 Transitions / transversions = 3.60 (18/5) Gap_init rate = 0.09 (9 / 103), avg. gap size = 1.89 (17 / 9) 329 21.12 2.15 3.26 chrXptel1M 157980 158072 (841928) L2c_3end#LINE/L2 338 429 (49) m_b329s601i6 13810 chrXptel1M 157980 TTGCAATTTCTTTTTTATGCG-CTATCTTCTCCCATTAGACTTTGAGCCC 158028 i vii v i?i - i i - i v i L2c_3end#LINE 338 TTGTAATTGTCTGTTTACNTGTCTGTCTCCTCC-ACTAGACTGTGAGCTC 386 chrXptel1M 158029 CTTGAGGAGAGGGACCG-GTTTATACCCTTGCTTTGTATCCTCAG 158072 iv - i - ii v - i L2c_3end#LINE 387 CTTGAGGGCAGGGACCGTGTCT-TATTCAT-CTTTGTATCCCCAG 429 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.14 CpG sites = 14, Kimura (unadjusted) = 26.14 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.05 (5 / 92), avg. gap size = 1.00 (5 / 5) 426 26.10 0.00 8.93 chrXptel1M 158163 158284 (841716) MIRc#SINE/MIR 2 113 (155) m_b329s601i7 13811 chrXptel1M 158163 GGGGCAGCTAGATGGCGCGGGAGATAGAGCACCAGCCCTGAAGCTAGGAG 158212 i i---i i i vi v ii v i i ii i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chrXptel1M 158213 GACCTGAGTTCAAATCTGCCCTCAGACCCATAACTTGTACTAGCTGTGTA 158262 i i i i----- i vi iiiv -- i MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCC-----CGGCTCTGCCACTT--ACTAGCTGTGTG 91 chrXptel1M 158263 ACCCTGGGCAAGTCACTTAACC 158284 i MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACC 113 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.42 CpG sites = 24, Kimura (unadjusted) = 34.39 Transitions / transversions = 4.80 (24/5) Gap_init rate = 0.08 (10 / 121), avg. gap size = 1.00 (10 / 10) 366 32.21 0.00 1.69 chrXptel1M 159414 159533 (840467) L2a_3end#LINE/L2 400 517 (0) m_b329s601i8 13812 chrXptel1M 159414 TGTATGGTCCATGGGGTCACAAAGAGTTGGATATGACTGAACAACAACAG 159463 v v i --i ii v vvi v vi viviv vi v L2a_3end#LINE 400 TGTAAGCTCCATGAGG--GCAGGGACTTTTGTCTGTTTTGTTCACTGCTG 447 chrXptel1M 159464 TATCTCCAGCATTTGGCACATTGCCTAGAACATAGTAGGTGCTTAATAAA 159513 i iii i v v i v i i L2a_3end#LINE 448 TATCCCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGGCGCTCAATAAA 497 chrXptel1M 159514 TGTTTATTGTCTGACTAAAT 159533 i i vv v i L2a_3end#LINE 498 TATTTGTTGAATGAATGAAT 517 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.00 CpG sites = 20, Kimura (unadjusted) = 42.92 Transitions / transversions = 1.11 (20/18) Gap_init rate = 0.02 (2 / 119), avg. gap size = 1.00 (2 / 2) 16 0.00 0.00 0.00 chrXptel1M 159892 159908 (840092) (G)n#Simple_repeat 1 17 (0) m_b329s252i4 13813 chrXptel1M 159892 GGGGGGGGGGGGGGGGG 159908 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGG 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 19 3.42 3.33 0.00 chrXptel1M 160135 160164 (839836) (ATTAA)n#Simple_repeat 1 31 (0) m_b329s252i5 13814 chrXptel1M 160135 ATTTAATT-AATTAAATTAAATTAAATTAAA 160164 v - (ATTAA)n#Simp 1 ATTAAATTAAATTAAATTAAATTAAATTAAA 31 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 378 35.75 9.60 5.64 chrXptel1M 160364 161030 (838970) L2#LINE/L2 2391 3082 (0) m_b329s601i9 13815 chrXptel1M 160364 TCCAATTGTCTTTCAAACATCTTAAACTATATAGCCATCAGA-ATTTGAA 160412 i i viivi iv vi iv iv i vi i- i v L2#LINE/L2 2391 TCCAACTGCCTACTCGACATCTCCACTTGGATGTCTAATAGGCATCTCAA 2440 chrXptel1M 160413 ACTCAGTATGTCCAATAACAGAACTCATTATCTTTTCCCCTAA-----CC 160457 i ii - v v v ii ii ----- i L2#LINE/L2 2441 ACTTAACATGTCCAA-AACTGAACTCCTGATCTTCCCCCTCAAACCTGCT 2489 chrXptel1M 160458 CCTAACCCGC---CT--CCTATTACTGGAGGTGGCAACAATATTCTCTCA 160502 -- --- -- i iv v v?ii vvi i ii L2#LINE/L2 2490 CCT--CCCGCAGTCTTCCCCATCTCAGTNAATGGCAACTCCATCCTTCCA 2537 chrXptel1M 160503 CTCCCTCAGGCTCACAACCTAGGAGTCATCCAGAACT-CTCACTATCTTT 160551 v iv iv v v vvi - v v i L2#LINE/L2 2538 GTTGCTCAGGCCAAAAACCTTGGAGTCATCCTTGACTCCTCTCTTTCTCT 2587 chrXptel1M 160552 TGCCTCCAATATCCAAGCTGTTGCCAAGGCCTATCAATCTCACTTTTGCA 160601 ii vi v i v ii iiv iv i iiiiii i iiv L2#LINE/L2 2588 CACACCCCACATCCAATCCATCAGCAAATCCTGTCGGCTCTACCTTCAAA 2637 chrXptel1M 160602 GCTTCTCTCACATAGACCCCCTCCTCTCTGACAAACA----CACACATCT 160647 iiv v iviv vviv v i v i- vvv ---- - i i L2#LINE/L2 2638 ATATATCCAGAATCCGACCACTTCTCACC-ACCTCCACTGCCAC-CACCC 2685 chrXptel1M 160648 TGGTTCAGGGGATGACATCAACATATGCTTGAATTTTTGT-ACAG-CTGG 160695 i i vv i-- v vivi i i vi i- i - vv L2#LINE/L2 2686 TGGTCCAAGCCAC--CATCATCTCTCGCCTGGATTACTGCAATAGCCTCC 2733 chrXptel1M 160696 TGGTGGATCTGATTGGCTCCAGTCT--CCCCACTCTAGTTCATCCTCTAC 160743 iiiv i vvi vi vi -- v ?i ii i v L2#LINE/L2 2734 TAACTGGTCTCCCTGCTTCCACCCTTGCCCCCCTNCAGTCTATTCTCAAC 2783 chrXptel1M 160744 TCA------------ATCTTCCTAAAACACAGATTGAACCATGACAATCC 160781 v ------------ i ii ii ii iii i v v L2#LINE/L2 2784 ACAGCAGCCAGAGTGATCCTTTTAAAACGTAAGTCAGATCATGTCACTCC 2833 chrXptel1M 160782 CTTGCGC--------CCAGTAA-----AATCT-----AGAAGCAAATACA 160813 ii v -------- i ii-----v ----- ivv vv L2#LINE/L2 2834 TCTGCTCAAAACCCTCCAATGGCTTCCCATCTCACTCAGAGTAAAAGCCA 2883 chrXptel1M 160814 GAATGCTGTGC-TTGGCATTCTGAGCCCT-CATAACCCTGCCTCCTCCTA 160861 i i v - i -v v v vii - i i iv i i ivi L2#LINE/L2 2884 AAGTCCT-TACAATGGCCTACAAGGCCCTACATGATCTGGTCCCCCGTTA 2932 chrXptel1M 160862 CCTTTCTCAACCCTAAC-CCTAACCCTAACTGTAAATTCGTGTAAACATT 160910 i -i ii v - v v vv ivi---i i------- i L2#LINE/L2 2933 CCTCTCT-GACCTCATCTCCTACCACTCTCCCC---CTCGC-------TC 2971 chrXptel1M 160911 ACTCCGTGACATGTACTCTTCCAGCCAGTGACACTGGTCTCCTAGATGTT 160960 ------------i ---- i v v L2#LINE/L2 2972 ACTCCG------------CTCCAGCC----ACACTGGCCTCCTTGCTGTT 3005 chrXptel1M 160961 CTACCAAACA------AAACGCTCCATCTCTCAAATTCTCT---CTGGTT 161001 i-i i ------iv vv - iivi i --- v i L2#LINE/L2 3006 CC-TCGAACACGCCAGGCACGCTCCCGC-CTCAGGGCCTTTGCACTTGCT 3053 chrXptel1M 161002 G-TCCCAGT-CTTGGAATGGTCTCATTCCTC 161030 - vv - i i v -- i i L2#LINE/L2 3054 GTTCCCTCTGCCTGGAACGCTCT--TCCCCC 3082 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 48.63 CpG sites = 135, Kimura (unadjusted) = 51.27 Transitions / transversions = 1.50 (135/90) Gap_init rate = 0.09 (59 / 666), avg. gap size = 1.75 (103 / 59) 233 33.64 16.51 2.80 chrXptel1M 160925 161239 (838761) L2b_3end#LINE/L2 60 416 (50) m_b329s601i10 13815 chrXptel1M 160925 ACTCT--TCCAGCCAGTGACACTGGTCTCCTAGATGTTCTACCAA-ACAA 160971 -- ---- i v v iv v - iv L2b_3end#LINE 60 ACTCTGCTCCAGCCA----CACTGGCCTCCTTGCTGTTCCTCGAACACGC 105 chrXptel1M 160972 AACGCTCCATCTC---TCAAATTCTCT---CTGGTTGT-CCCAGT-CTTG 161013 v ? ?v i --- iivi i --- ?v i - vv - i L2b_3end#LINE 106 CANGCTCNCTCCCGCCTCAGGGCCTTTGCACNTGCTGTTCCCTCTGCCTG 155 chrXptel1M 161014 GAATGGTCT----CATTCCTCTGTT---CCAACT---ACTGACC------ 161047 i vi ---- iii ii ii--- --- v i ------ L2b_3end#LINE 156 GAACGCCCTTCCCCACCTCTTCGCCTGGCCAACTCCTACTCATCCTTCAG 205 chrXptel1M 161048 -TCTC----------CCACTTTCTAGCAGAAGTCTTCCCCAACCCCTC-- 161084 - ----------i i i vvvi i i ii i -- L2b_3end#LINE 206 GTCTCAGCTCAAATGTCACCTCCTCCGGGAAGCCCTCCCTGACCCCCCAG 255 chrXptel1M 161085 -CTAATGTTAGTGTTTCCCCTTTATTATTTACTATT--TATTTTGTGTAT 161131 - iii- i vvvii i i ivvviiiv i v -- iii i---i L2b_3end#LINE 256 GCCGG-GTCAGGCGCCCTCCTCTGGGCCCCCCCAGTCCTACCCTGC---C 301 chrXptel1M 161132 AGCTTATGTGTTCATACCATTTGCT--CAT---TGTCTCTCCTATTAGAT 161176 - i- v vv? iii i ? -- --- i i i i L2b_3end#LINE 302 A-CTC-TGGGTTATNATTGTCTGNTTACATGTCTGTCTCCCCCACTAGAC 349 chrXptel1M 161177 TGTAAAGTCTTTGAGGGTAAGGACTGTATTTGGCCTTTTTG----TGTGT 161222 i iv iv i i i ?i i v i v ii---- i L2b_3end#LINE 350 TGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTGTAT 399 chrXptel1M 161223 CCCCAACACTTAGCTCA 161239 i i i v L2b_3end#LINE 400 CCCCAGCGCCTAGCACA 416 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.75 CpG sites = 71, Kimura (unadjusted) = 49.63 Transitions / transversions = 2.22 (71/32) Gap_init rate = 0.09 (27 / 314), avg. gap size = 2.30 (62 / 27) 292 28.03 5.22 6.82 chrXptel1M 161106 161239 (838761) L2d2_3end#LINE/L2 374 505 (50) m_b329s601i11 13815 chrXptel1M 161106 TATTATTTACTATTTATTTTGT-GTATAGCTT---ATGTGTTCATACCAT 161151 i vvvi i v -i v i --- i i ii -- L2d2_3end#LIN 374 TGTTATTTAAATCTTGTATTGTTATTTAACTTTTCACGTGTTTATGTC-- 421 chrXptel1M 161152 TTGCTCATTGTCTCTCCTATTAGATTGTAAAGTCTTTGAGGGTAAGGAC- 161200 ------- i v i iv i i i - L2d2_3end#LIN 422 -------TTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACC 464 chrXptel1M 161201 -TGTATTTGGCCTTTTTGTGTGTCCC-CAACACTTAGCTCA 161239 - v vvi i i i vi - i i i v L2d2_3end#LIN 465 ATGTCTTATACTTCTTTGTATCCCCCACAGCGCCTAGCACA 505 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.89 CpG sites = 23, Kimura (unadjusted) = 36.51 Transitions / transversions = 1.92 (23/12) Gap_init rate = 0.10 (13 / 133), avg. gap size = 1.23 (16 / 13) 314 35.48 1.08 0.00 chrXptel1M 161148 161240 (838760) L2c_3end#LINE/L2 348 441 (37) m_b329s601i12 13815 chrXptel1M 161148 CCATTTGCTCAT-TGTCTCTCCTATTAGATTGTAAAGTCTTTGAGGGTAA 161196 ii i ?ii - ii i i i i iv i i i L2c_3end#LINE 348 CTGTTTACNTGTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAG 397 chrXptel1M 161197 GGACTGTATTTGGCCTTTTTGTGTGTCCCCAACACTTAGCTCAT 161240 i i i viiiiv i v i i i i i v L2c_3end#LINE 398 GGACCGTGTCTTATTCATCTTTGTATCCCCAGCGCCTGGCACAT 441 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 51.77 CpG sites = 28, Kimura (unadjusted) = 57.27 Transitions / transversions = 5.60 (28/5) Gap_init rate = 0.01 (1 / 92), avg. gap size = 1.00 (1 / 1) 15 12.76 2.78 2.78 chrXptel1M 161241 161276 (838724) (TAATTA)n#Simple_repeat 1 36 (0) m_b329s252i6 13816 chrXptel1M 161241 TAATAATAATTATAACATATAACAATAA-TATAATTA 161276 v -v iv - (TAATTA)n#Sim 1 TAATTATAATTATAA-TTATAATTATAATTATAATTA 36 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 14 17.86 0.00 0.00 chrXptel1M 163277 163308 (836692) (CCCCCA)n#Simple_repeat 1 32 (0) m_b329s252i7 13817 chrXptel1M 163277 CCGCCTCCCCCCCCCCCACCCCCACACGCACC 163308 v v v v v (CCCCCA)n#Sim 1 CCCCCACCCCCACCCCCACCCCCACCCCCACC 32 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 19 12.20 6.25 2.00 chrXptel1M 163632 163679 (836321) (CTAACC)n#Simple_repeat 1 50 (0) m_b329s252i8 13818 chrXptel1M 163632 CTAACCCTAATCCT---CCTGACTCTAACCCCCAACTCTAACCCTAACCC 163678 i --- i i - i i (CTAACC)n#Sim 1 CTAACCCTAACCCTAACCCTAACCCTAA-CCCTAACCCTAACCCTAACCC 49 chrXptel1M 163679 T 163679 (CTAACC)n#Sim 50 T 50 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.04 (2 / 47), avg. gap size = 2.00 (4 / 2) 12 30.44 1.92 0.00 chrXptel1M 165066 165117 (834883) (AAAAC)n#Simple_repeat 1 53 (0) m_b329s252i9 13819 chrXptel1M 165066 AAATCAAGAAACAATAAAACAAAACTAAA-AGAATGAAAAAATAGAAAAA 165114 v i v v i v - i ii v v v v (AAAAC)n#Simp 1 AAAACAAAACAAAACAAAACAAAACAAAACAAAACAAAACAAAACAAAAC 50 chrXptel1M 165115 AAA 165117 (AAAAC)n#Simp 51 AAA 53 Matrix = Unknown Transitions / transversions = 0.62 (5/8) Gap_init rate = 0.02 (1 / 51), avg. gap size = 1.00 (1 / 1) 292 31.54 4.19 2.05 chrXptel1M 166296 166486 (833514) L1ME4c_3end#LINE/L1 342 536 (294) m_b329s551i6 13820 chrXptel1M 166296 AAGGGTCATAAAATCGTGCATACTCTTTGACCTAA-----GCACTACTAG 166340 i i vi v i i i-----v v i L1ME4c_3end#L 342 AAGAGCCATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGG 391 chrXptel1M 166341 GCATGTATGCCCAAAGAGAT--TTAAGAAAAAAGGACAAGAATCTATATG 166388 v v - i i i -- v - i -- i v L1ME4c_3end#L 392 GAATTTAT-CCTAAGGAAATAATTCA-AAAGAAGG--AAAAAGCTATATG 437 chrXptel1M 166389 CACTAAAATATATATAATAGCTCT-TTTGCTAGGGCAAAGAATTGGAAAT 166437 v i i vi vii vi - iiv vi i i i L1ME4c_3end#L 438 CACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAAC 487 chrXptel1M 166438 TAAGGGGATGCTCAGTAAATGGGGACTAGCTGAATAAACTGAGGTATAT 166486 v vvvii ii ii vv v i i i i i iv i L1ME4c_3end#L 488 AACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACAT 536 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.74 CpG sites = 37, Kimura (unadjusted) = 42.72 Transitions / transversions = 1.68 (37/22) Gap_init rate = 0.04 (7 / 190), avg. gap size = 1.71 (12 / 7) 41 0.00 0.00 0.00 chrXptel1M 168327 168361 (831639) (TG)n#Simple_repeat 1 35 (0) c_b329s251i1 13821 chrXptel1M 168327 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 168361 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 35 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 13 15.85 0.00 7.89 chrXptel1M 168598 168638 (831362) (TTTTCTA)n#Simple_repeat 1 38 (0) m_b329s252i10 13822 chrXptel1M 168598 TTTTTTATTTTTCTGTTTTATTCTCTTTGTATTTTCTATTT 168638 i - i -i v - v (TTTTCTA)n#Si 1 TTTTCTA-TTTTCTATTTT-CTAT-TTTCTATTTTCTATTT 38 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.07 (3 / 40), avg. gap size = 1.00 (3 / 3) 16 0.00 0.00 0.00 chrXptel1M 168651 168668 (831332) (A)n#Simple_repeat 1 18 (0) m_b329s252i11 13823 chrXptel1M 168651 AAAAAAAAAAAAAAAAAA 168668 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAA 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 199 23.53 0.00 0.00 chrXptel1M 169579 169629 (830371) L2b_3end#LINE/L2 332 382 (84) m_b329s601i13 13824 chrXptel1M 169579 CTGTCACCCCCAAAAGAATGGAAGCCCCTTGGGGGCAGGGACTGGCTATG 169628 v vv v vi i v i i ?v v L2b_3end#LINE 332 CTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTG 381 chrXptel1M 169629 T 169629 L2b_3end#LINE 382 T 382 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.35 CpG sites = 4, Kimura (unadjusted) = 28.92 Transitions / transversions = 0.50 (4/8) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 42 0.00 0.00 0.00 chrXptel1M 170436 170471 (829529) (TG)n#Simple_repeat 1 36 (0) c_b329s251i2 13825 chrXptel1M 170436 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 170471 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 36 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 224 18.18 0.00 0.00 chrXptel1M 172879 172922 (827078) MIR3#SINE/MIR 165 208 (0) m_b329s601i14 13826 chrXptel1M 172879 TCTAAGGTGCCTCCAAGCTCTGACATTCTGTGTTTCAAGGATCC 172922 v i v i v v v i MIR3#SINE/MIR 165 TCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTATGATTC 208 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 20.83 CpG sites = 3, Kimura (unadjusted) = 20.83 Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 645 28.90 7.47 2.56 chrXptel1M 172999 173520 (826480) L1M5_orf2#LINE/L1 1469 2015 (1279) m_b329s551i7 13827 chrXptel1M 172999 CAATTTTACACAAACTCTTT--GCAAAAAGACAAAAGAG----TCCTGCC 173042 i i-- v v - ----iv v L1M5_orf2#LIN 1469 CAATCTTACACAAACTCTTCCAGAAAATAGA-AAAAGAGGGAACACTTCC 1517 chrXptel1M 173043 GAAGTACTTCTATAATACAAAAATGGTCTTGATACTTAAATTACAGAAAG 173092 v v vv i i vi v iv ?ii i iv ii?v v L1M5_orf2#LIN 1518 CAACTCATTTTATGAGGCCAGCATNACCCTGATACCAAAACCNGACAAAG 1567 chrXptel1M 173093 TCAAAACAGAAAAAGAAAATTACAAACCAACATCCCTAATGGATACCCAT 173142 v vv ii i i v i i ivv L1M5_orf2#LIN 1568 ACATTACAAGAAAAGAAAATTACAGACCAATATCCCTCATGAACATAGAT 1617 chrXptel1M 173143 GCAAACATTTTAAATAAAATAGTAACAAAAAGCTTATAGCAATATATACA 173192 v ii ? i v i vv vv vi v L1M5_orf2#LIN 1618 GCAAAAATCCTNAACAAAATATTAGCAAATCGAATCCAGCAATATATAAA 1667 chrXptel1M 173193 TATCATTAAGATGCTATACCATGACCAGGTTGAATTTATACCAGCAATGA 173242 - ----- i iv i i i v ii v v v L1M5_orf2#LIN 1668 -A-----AGGATAATACATCATGACCAAGTGGGGTTTATCCCAGGAATGC 1711 chrXptel1M 173243 AGTAGTGGTCTAATATAAAGAAAATT-ATCAATGTCATTGCCTATATCAA 173291 iviv i i -vv i- v vv i i L1M5_orf2#LIN 1712 AAGGTTGGTTTAACAT-TCGAAAATCAATCAATGTAATTCACCATATTAA 1760 chrXptel1M 173292 TAA---CAAGAATAAAAATCATGTGATTATGTCAA---AT---------- 173325 i i---v i v i i v --- ---------- L1M5_orf2#LIN 1761 CAGAATAAAGGAGAAAAATCATATGATCATCTCAATAGATGCAGAAAAAG 1810 chrXptel1M 173326 --TCTGACAAAATTCAACA--TATTTCTGCTTACAAAAAAT---AGAAAA 173368 -- i --i iv --- i v --- v L1M5_orf2#LIN 1811 CATTTGACAAAATTCAACACCCATTCATG---ATAAAAACTCTCAGCAAA 1857 chrXptel1M 173369 CACAGCAATATATGTAATTTTCCTTATCATGGTAAATAGACTGCATGGAA 173418 -i v v v vi vi i v v i vi vv vi i i L1M5_orf2#LIN 1858 C-TAGGAATAGAAGGGAACTTCCTCAACCTGATAAAGGGCATCTACGAAA 1906 chrXptel1M 173419 AACA-AAACCCAACATTGTG--TA-----GATAAACTAGTATCTTTTATC 173460 v- v v ? ii i-- ----- v ? iiv?v ivi L1M5_orf2#LIN 1907 AACCTACAGCNAACATCATACTTAATGGTGAAANACTGAANGCTTTCCCC 1956 chrXptel1M 173461 AGTTAAGATCAGGGTTAATTCAAGGATGCCCAGTATTATCATTGCTGTTT 173510 --i i ivi vv i iv ? i i i v i i L1M5_orf2#LIN 1957 --CTAAGATCGGGAACAAGACAAGGATGTCCGCTNTCACCACTTCTATTC 2004 chrXptel1M 173511 -GTATTGTGCT 173520 -ii i L1M5_orf2#LIN 2005 AACATTGTACT 2015 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.90 CpG sites = 78, Kimura (unadjusted) = 37.87 Transitions / transversions = 1.13 (78/69) Gap_init rate = 0.05 (27 / 521), avg. gap size = 1.96 (53 / 27) 14 7.68 3.33 3.33 chrXptel1M 174032 174061 (825939) (GGAA)n#Simple_repeat 1 30 (0) m_b329s252i12 13828 chrXptel1M 174032 GGAA-GAAGGAAGGAAGGGAAGGAGGGAGGG 174061 - - i i (GGAA)n#Simpl 1 GGAAGGAAGGAAGGAA-GGAAGGAAGGAAGG 30 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.07 (2 / 29), avg. gap size = 1.00 (2 / 2) 386 29.10 8.21 0.00 chrXptel1M 174065 174198 (825802) C MIR#SINE/MIR (10) 252 108 m_b329s601i15 13829 chrXptel1M 174065 AACATTTATTAAGCACTTACAATATGCTATGCACTATACTA----TTTTG 174110 i i v i i v i v ----i i C MIR#SINE/MIR 252 AACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGCGCTTTA 203 chrXptel1M 174111 CA---ATTAATTCATCTGGTTCTTACAACCATTC---AAGTTACCT-CTA 174153 --- i i ii i i v ii ---i v vv - C MIR#SINE/MIR 202 CATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGGTAGGTACTA 153 chrXptel1M 174154 AAATTATCCTTCTTTTGAAATTGAAGAAACTGAAGTGGATGGAGG 174198 vv iiv iv iv i i iiv vi C MIR#SINE/MIR 152 TTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGG 108 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.06 CpG sites = 25, Kimura (unadjusted) = 38.33 Transitions / transversions = 1.79 (25/14) Gap_init rate = 0.03 (4 / 133), avg. gap size = 2.75 (11 / 4) 187 17.65 0.00 0.00 chrXptel1M 174195 174228 (825772) C MIRc#SINE/MIR (134) 134 101 m_b329s601i16 13830 chrXptel1M 174195 GAGGAAACTGAAGTTGAGGGAGATTAAATGACTT 174228 i i v i i i C MIRc#SINE/MIR 134 GAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTT 101 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 21.06 CpG sites = 5, Kimura (unadjusted) = 21.06 Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 213 33.33 4.55 0.00 chrXptel1M 174625 174690 (825310) C L2d2_3end#LINE/L2 (15) 540 472 m_b329s601i17 13831 chrXptel1M 174625 AAGTACTCATTAAGTACCTAATCTATGTGAGACATCATGCTAAGATCTG- 174673 i i i i ii v v i ii i iii i vv - C L2d2_3end#LIN 540 AAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGT 491 chrXptel1M 174674 --GGGATATAAGGAAAGAT 174690 -- i i iv C L2d2_3end#LIN 490 GGGGGATACAAAGAAGTAT 472 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.23 CpG sites = 17, Kimura (unadjusted) = 48.80 Transitions / transversions = 3.40 (17/5) Gap_init rate = 0.03 (2 / 65), avg. gap size = 1.50 (3 / 2) 43 0.00 0.00 0.00 chrXptel1M 174910 174946 (825054) (AC)n#Simple_repeat 1 37 (0) c_b329s251i3 13832 chrXptel1M 174910 ACACACACACACACACACACACACACACACACACACA 174946 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACA 37 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 27 20.13 5.77 3.77 chrXptel1M 175784 175887 (824113) (ATA)n#Simple_repeat 1 106 (0) m_b329s252i13 13833 chrXptel1M 175784 ATTATAATAGCTGATAA-AACCAAAATAA-AATAA-ATTAATAAGAA-AG 175829 v -v i - iv v - - v v - i (ATA)n#Simple 1 ATAATAATA-ATAATAATAATAATAATAATAATAATAATAATAATAATAA 49 chrXptel1M 175830 TATTATTAATATATTATATTAATAAGTATTAA-AAT-ATATTAATAACTA 175877 v v - v v - v - - v - (ATA)n#Simple 50 TAATAATAATA-ATAATAATAATAA-TAATAATAATAATAATAATAA-TA 96 chrXptel1M 175878 TTATTAATAA 175887 v v (ATA)n#Simple 97 ATAATAATAA 106 Matrix = Unknown Transitions / transversions = 0.21 (3/14) Gap_init rate = 0.10 (10 / 103), avg. gap size = 1.00 (10 / 10) 214 27.75 12.41 2.67 chrXptel1M 176977 177113 (822887) C L3b_3end#LINE/CR1 (114) 1092 943 m_b329s601i18 13834 chrXptel1M 176977 TTCTATTTTTAA-GATTC----AAGAATGGGAATTTAACG-TCTCCCCCA 177020 - ?i ----i - ii ivi i-i i i C L3b_3end#LINE 1092 TTCTATTTTTAAAGNCTCTCCAGAGAA-GGAGATTCCGCAACCTCCCTCG 1044 chrXptel1M 177021 A-AATCCATTCCAGTATTTAATAAATTTTATTTCAAGAAAATTC-----T 177064 i- i i i v i i i viv i i ----- C L3b_3end#LINE 1043 GTAACCCATTCCAGTGTTTAACAACTCTCACTGTCAGGAAGTTCTTCCTT 994 chrXptel1M 177065 ACACCCCACC-AAATCCTCACCATGTTCC---CTAAACACCA-TCCCATT 177109 i i iv - i--i i v ---i i - - i vi C L3b_3end#LINE 993 ATATCTAACCTAAATCCC--TCATGCTGCAGTTTAAGC-CCATTTCCTCT 947 chrXptel1M 177110 TGTT 177113 C L3b_3end#LINE 946 TGTT 943 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.53 CpG sites = 30, Kimura (unadjusted) = 38.22 Transitions / transversions = 4.29 (30/7) Gap_init rate = 0.09 (12 / 136), avg. gap size = 1.75 (21 / 12) 247 36.57 11.74 1.47 chrXptel1M 177079 177325 (822675) L2#LINE/L2 1826 2097 (985) m_b329s601i19 13835 chrXptel1M 177079 CCTCACCATGTTCCCTAAACACCATCCCATTTGTTTCTCTGCTTTCTT-- 177126 i ?vivii i i ivi ii ---- ii i -- L2#LINE/L2 1826 CCCCACNTCCCCCTCCAGCTACCGCCCCATTT----CTCTGCTCCCCTTT 1871 chrXptel1M 177127 --AGCCAAACTTCTTAAAAATGCTTTTTACATTAGATAT-TAAAA----- 177168 -- v i ii iv i v i i i v v i - vv ----- L2#LINE/L2 1872 ACAGCAAAACTCCTCGAAAGAGTTGTCTATACTCGCTGTCTCCAATTCCT 1921 chrXptel1M 177169 -----CTGATACTCTCTTCTTCCTTTTATAATGTGACTTCTGACCCTATC 177213 ----- iv v vvv ivi vi vv i ii v i i L2#LINE/L2 1922 CTCCTCCCATTCTCTCTTGAACCCACTCCAATCAGGCTTTCGTCCCCACC 1971 chrXptel1M 177214 AATCAATGGAAATTGTTCTTCCCAAAGTTATTA--GACATC--------- 177252 v v iv i i vi i i ii -- v --------- L2#LINE/L2 1972 ACTCCACCGAAACTGCTCTTGTCAAGGTCACCAATGACCTCCACGTTGCT 2021 chrXptel1M 177253 AAATCAAATGGATTCTTCCCTATCCCCATTCTTCTTGAC---TCTGCTAT 177299 v vivv i vi i ii v --- v vii L2#LINE/L2 2022 AAATCCAATGGTCAATTCTCAGTCCTCATCTTACTTGACCTNTCAGCAGC 2071 chrXptel1M 177300 TTTTGATATTGTTGACTAAACTCTCC 177325 v i iv ii vv i L2#LINE/L2 2072 ATTTGACACAGTTGATCACTCCCTCC 2097 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 50.12 CpG sites = 52, Kimura (unadjusted) = 52.82 Transitions / transversions = 1.41 (52/37) Gap_init rate = 0.04 (11 / 246), avg. gap size = 3.00 (33 / 11) 13 20.84 4.35 2.13 chrXptel1M 177852 177897 (822103) (TGTA)n#Simple_repeat 1 47 (0) m_b329s252i14 13836 chrXptel1M 177852 TGCATGCTATGGTTTTATGTA--TATGTATTTACATATGTATATATGT 177897 i - vv v -- v ii i (TGTA)n#Simpl 1 TGTATG-TATGTATGTATGTATGTATGTATGTATGTATGTATGTATGT 47 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.04 (2 / 45), avg. gap size = 1.50 (3 / 2) 15 17.99 6.82 0.00 chrXptel1M 178120 178163 (821837) (TTA)n#Simple_repeat 1 47 (0) m_b329s252i15 13837 chrXptel1M 178120 TTATTATTTCAATGAATATTATTATAAAT-TTATTATT-TTA-TATT 178163 viv v v v v - - - (TTA)n#Simple 1 TTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATT 47 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.07 (3 / 43), avg. gap size = 1.00 (3 / 3) 378 36.44 5.36 2.23 chrXptel1M 178712 178972 (821028) C L2b_3end#LINE/L2 (10) 456 188 m_b329s601i20 13838 chrXptel1M 178712 TCAAGAAACATTTAATAAATGCTTAATATGTGCCAAACAATGTCATAAAG 178761 v i v i ii i v i ii ?v vv iiv C L2b_3end#LINE 456 TCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGC 407 chrXptel1M 178762 GCAGGGCATAGAAAGA-GAAGCACACA---TCAATTCCTGTTCTTGAGGA 178807 v v v iv i- vv v ---? ii i ii iiv C L2b_3end#LINE 406 GCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGGA 357 chrXptel1M 178808 GCTTT--GTCTAAATGGAAGAGAC-CACGTGCAAAT-GATTATGTATAAA 178853 iv-- i- ii -v i i ?i- iv ?- v C L2b_3end#LINE 356 GCTCACAGTCTAG-TGGGGGAGACAGACATGTAANCAGACAATN-ATAAC 309 chrXptel1M 178854 C--AAACCACAGAAAAGATCAATTGGAAATAATTAGAGGGAAGGCAGC-A 178900 --i iivi iiv i--- i iiivivii - i iv -i C L2b_3end#LINE 308 CCAGAGTGGCAGGGTAGG---ACTGGGGGGGCCCAGAGG-AGGGCGCCTG 263 chrXptel1M 178901 ACATTAA--GAGAGGTTAAGAAAGACTTCCTGTAGAAGGTAAGATTTTTG 178948 viviv-- i i i i i i i i v i i v vv C L2b_3end#LINE 262 ACCCGGCCTGGGGGGTCAGGGAGGGCTTCCCGGAGGAGGTGACATTTGAG 213 chrXptel1M 178949 CTATGATCTGAAGAGTCAG-AGGAG 178972 iv i ii v - C L2b_3end#LINE 212 CTGAGACCTGAAGGATGAGTAGGAG 188 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 50.26 CpG sites = 60, Kimura (unadjusted) = 54.65 Transitions / transversions = 1.82 (60/33) Gap_init rate = 0.06 (15 / 260), avg. gap size = 1.33 (20 / 15) 223 31.06 8.00 1.25 chrXptel1M 179001 179150 (820850) L2#LINE/L2 2139 2298 (784) m_b329s601i21 13835 chrXptel1M 179001 CTCTCTTAGTTCTTCTGCTACCTATCTGACCACTCC-TCT--GTCTCATT 179047 i i i i v vv i i - -- v L2#LINE/L2 2139 CTCTCCTGGTTTTCCTCCTACCTCACTGGCCGCTCCTTCTCAGTCTCCTT 2188 chrXptel1M 179048 TGCTGGATGCTTCTCA------AGAATCCTCTAGTCATAGGTGCCCCTCA 179091 v v i ------v -- ?iv i v v iv i L2#LINE/L2 2189 TGCTGGTTCCTCCTCATCTCCCCGA--CCTCTNAACGTTGGAGTGCCCCA 2236 chrXptel1M 179092 TCATTATATCCTGTGCCTTCTTTTCTCCT---TCTCAACTATTTTACTGG 179138 vvii vvi vv v i i i --- vv vvi iv ? L2#LINE/L2 2237 GGGCTCAGTCCTTGGACCTCTTCTCTTCTCTATCTACACTCACTCCCTNG 2286 chrXptel1M 179139 GTGATTTTACTC 179150 i i ii L2#LINE/L2 2287 GTGATCTCATCC 2298 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.17 CpG sites = 23, Kimura (unadjusted) = 41.45 Transitions / transversions = 1.00 (23/23) Gap_init rate = 0.04 (6 / 149), avg. gap size = 2.33 (14 / 6) 431 32.54 14.84 0.85 chrXptel1M 179324 179633 (820367) L2b_3end#LINE/L2 110 462 (4) m_b329s601i22 13835 chrXptel1M 179324 CTCCCTACC-CCTCCAGTCTTCTG-ACATCTTACTTCCCTC------ATA 179365 ? v - vi v i i - ? vi i- ------iv L2b_3end#LINE 110 CTCNCTCCCGCCTCAGGGCCTTTGCACNTGCTG-TTCCCTCTGCCTGGAA 158 chrXptel1M 179366 TACTCTTCCACACAGTGAC-CCTGGCC--TTCCTGC-CACAGCTCAAATC 179411 ii i v vvivv - --i i - ivvi ii L2b_3end#LINE 159 CGCCCTTCCCCACCTCTTCGCCTGGCCAACTCCTACTCATCCTTCAGGTC 208 chrXptel1M 179412 CCAGCTCAAGTCGCACTTTCTTCAAGAAGCCTTTCCCAGCTTTCC----- 179456 i i vv i i i ii i i iii iii ----- L2b_3end#LINE 209 TCAGCTCAAATGTCACCTCCTCCGGGAAGCCCTCCCTGACCCCCCAGGCC 258 chrXptel1M 179457 ---TTAATCTGTTCTCCAA-AATTACTCCCAATTC-ATCCT----CTCTA 179497 --- i iv - ii vv-iiviv i i i - i ---- i L2b_3end#LINE 259 GGGTCAGGC-GCCCTCCTCTGGGCCCCCCCAGTCCTACCCTGCCACTCTG 307 chrXptel1M 179498 TGTT-TTATTGTTTG----CATGT-TGTCTCCTTCATTAGACTG--AGTT 179539 v - ? i ---- - ii i -- i L2b_3end#LINE 308 GGTTATNATTGTCTGNTTACATGTCTGTCTCCCCCACTAGACTGTGAGCT 357 chrXptel1M 179540 CGTTGGAAGCAGTGGCTTC--CTTTCTT---------TGTATGCCCAATG 179578 vv iii v i iv?-- v --------- v ii L2b_3end#LINE 358 CCGTGAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTGTATCCCCAGCG 407 chrXptel1M 179579 TTCA-TATGGTGCTCGACATATAGTAAGTACTTTACAAATATTTGTTGAC 179627 iii -i ii ? ii i i i i ii ivii v L2b_3end#LINE 408 CCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTTGTTGAA 457 chrXptel1M 179628 TTGAAT 179633 - L2b_3end#LINE 458 -TGAAT 462 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.78 CpG sites = 72, Kimura (unadjusted) = 47.27 Transitions / transversions = 2.57 (72/28) Gap_init rate = 0.07 (21 / 309), avg. gap size = 2.33 (49 / 21) 311 28.33 8.55 2.48 chrXptel1M 179717 179868 (820132) MIRc#SINE/MIR 40 200 (68) m_b329s601i23 13839 chrXptel1M 179717 AGTCAG-AAGAGCTAAGTCTAAACCTCAGCTCAACCAGTT-CT-GATCTG 179763 - v ii iii ii i i vi v - - v v MIRc#SINE/MIR 40 AGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTG 89 chrXptel1M 179764 TAAGCTTAGA-AAGTCATTT--CATCTCTGAGATTCGGTC-ACTCAT--G 179807 i v i i- i -- v vi i i-v -- MIRc#SINE/MIR 90 TGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTG 139 chrXptel1M 179808 CAAAATGGAGATGACTACGCATATGTTCCCT-CCT-CTCCTCTGGGCCTT 179855 i i i - --- iv v - - ii v v iiv MIRc#SINE/MIR 140 TAAAATGGGGATAA-TA---ATACCTGCCCTGCCTACCTCACAGGGTTGT 185 chrXptel1M 179856 TACAAGG--CAAATG 179868 iii -- MIRc#SINE/MIR 186 TGTGAGGATCAAATG 200 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.89 CpG sites = 28, Kimura (unadjusted) = 37.27 Transitions / transversions = 2.00 (28/14) Gap_init rate = 0.09 (14 / 151), avg. gap size = 1.21 (17 / 14) 258 32.93 15.74 1.44 chrXptel1M 180140 180444 (819556) C L2c_3end#LINE/L2 (2) 476 129 m_b329s601i24 13840 chrXptel1M 180140 TCAATCAATCAGGAAGTCTTTATTTAAAATATACTTGATGCCAGGCTGTG 180189 v v iv iiv v iviiv vvi vv C L2c_3end#LINE 476 TCATTCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTG 427 chrXptel1M 180190 GGGAATACAAAGA-------------GTACCTG---TCAAGGAGCTTAC- 180222 - ------------- v --- i - C L2c_3end#LINE 426 GGGA-TACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACA 378 chrXptel1M 180223 CTCT-GAGCAGGAGA-AACCAC----ATGGATGCGTACAACATAGGT--- 180263 v - v v - iv ?---- ii iivv i i i --- C L2c_3end#LINE 377 GTCTAGTGGAGGAGACAGACANGTAAACAGACAATTACAATACAAGTTAA 328 chrXptel1M 180264 --ACAAA----GTAAT-GGAGCATA------ATG-TAAAGTAAT-TAGAA 180298 -- i i----i - i ------i - vi v ii-i i C L2c_3end#LINE 327 TGATAAGTGCTATAATGGGAGTATAGACAGGGTGCTATGGGAGCACAGAG 278 chrXptel1M 180299 GCTGGCA-CTAG----GAGTTGGAGGGATCCCAAAGGCTTCCTATAGAAA 180343 vv - ---- ?v i vivvvi iiv i i C L2c_3end#LINE 277 GAGGGCACCTAGACTAGNCTTGGGGGGTCAGGGAAGGCTTCCCGGAGGAG 228 chrXptel1M 180344 TTTCCAGTTAAATTGAATTTTGAGGGA-AATTAAGGATT-TCAAGAGTAG 180391 v vv vi i ii i?i i -i v i ii -v v - i C L2c_3end#LINE 227 GTGACATCTGAGCTGAGNCTTGAAGGATGAGTAGGAGTTAGCCAG-GTGG 179 chrXptel1M 180392 AGGAAAAAGAGGACTACATTCTAAGCATGAGACATTTCAACCAATGCAAA 180441 i i iii i i vvi i i - iv --v i vvi C L2c_3end#LINE 178 AAGGAGGGGGGAAGAGCATTCCAGGCA-GAGGGA--ACAGCATGTGCAAA 132 chrXptel1M 180442 GGC 180444 C L2c_3end#LINE 131 GGC 129 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.34 CpG sites = 58, Kimura (unadjusted) = 45.68 Transitions / transversions = 1.41 (58/41) Gap_init rate = 0.07 (22 / 304), avg. gap size = 2.41 (53 / 22) 252 34.93 5.56 4.59 chrXptel1M 180441 180548 (819452) MIRc#SINE/MIR 3 111 (157) m_b329s601i25 13841 chrXptel1M 180441 AGGCATCATGATGGAAATTAGTGAAAAGAACGTTGCTCCTGGCATTGGGA 180490 vii i -----i i i ii vv i vi ii MIRc#SINE/MIR 3 AGGCAGTGTGGTG-----CAGTGGAAAGAGCACTGGACTTGGAGTCAGGA 47 chrXptel1M 180491 -GATCTGGTCTCAAACTCT-----TGATGCTTCCTAAACATGTGATCTTG 180534 - i vi i iii i----- vii v ivii i MIRc#SINE/MIR 48 AGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTG 97 chrXptel1M 180535 GCCAAGTCAATTGA 180548 v v i MIRc#SINE/MIR 98 GGCAAGTCACTTAA 111 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 47.25 CpG sites = 26, Kimura (unadjusted) = 51.46 Transitions / transversions = 2.60 (26/10) Gap_init rate = 0.07 (7 / 107), avg. gap size = 1.57 (11 / 7) 204 20.71 3.28 5.00 chrXptel1M 180703 180763 (819237) C L2b_3end#LINE/L2 (14) 452 393 m_b329s601i26 13842 chrXptel1M 180703 CAGATCTTTATGAAGTGCCTTTTCTGTGTGCCAGGCA--GAGCTGGACAC 180750 i v ivi i v-- ?-- v i i i C L2b_3end#LINE 452 CAAATATTTACTGAGCGCCTA--CTGTGTGCCAGGCNCTGTGCTAGGCGC 405 chrXptel1M 180751 TGGGGAAACCAGC 180763 v - C L2b_3end#LINE 404 TGGGGATA-CAGC 393 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 20.57 CpG sites = 7, Kimura (unadjusted) = 25.10 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.07 (4 / 60), avg. gap size = 1.25 (5 / 4) 16 24.17 3.33 1.64 chrXptel1M 182232 182291 (817709) (AAAAGAA)n#Simple_repeat 1 61 (0) m_b329s252i16 13843 chrXptel1M 182232 AAAACAATCAAATCAAAGAGAAAAAACGAGAAAGAAAAAAG--TAAACAA 182279 v -v vv i vi i --v v (AAAAGAA)n#Si 1 AAAAGAA-AAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAA 49 chrXptel1M 182280 ACAACAAAAAAG 182291 v v (AAAAGAA)n#Si 50 AAAAGAAAAAAG 61 Matrix = Unknown Transitions / transversions = 0.33 (3/9) Gap_init rate = 0.03 (2 / 59), avg. gap size = 1.50 (3 / 2) 16 21.13 3.45 3.45 chrXptel1M 182233 182290 (817710) (AAAC)n#Simple_repeat 1 58 (0) m_b329s252i17 13843 chrXptel1M 182233 AAACAATCAAATCAAAGAGAAAAAAC-GAGAAAGAAAAAAGTAAACAAAC 182281 v - v - v -i v v v ii (AAAC)n#Simpl 1 AAACAAACAAA-CAAACA-AACAAACAAACAAACAAACAAACAAACAAAC 48 chrXptel1M 182282 -AACAAAAAA 182290 - v (AAAC)n#Simpl 49 AAACAAACAA 58 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.07 (4 / 57), avg. gap size = 1.00 (4 / 4) 962 30.50 3.46 2.87 chrXptel1M 182435 182954 (817046) C L1ME5_3end#LINE/L1 (275) 666 144 m_b329s551i8 13844 chrXptel1M 182435 TGGTGTTGTGT-ATAATGGTCTC---CTGTTTCT-GCTCATTTCACTGAG 182479 i - ?--i --- -i iv v C L1ME5_3end#LI 666 TGGTATTGTGTTATAN--ATCTCATTCTGTTTCTTACTTTTTTCACTCAG 619 chrXptel1M 182480 CATCA-GTTCATTTGAG-TCTCTCCAAGCCTCTCTGTATTCACCCTGCTG 182527 ii - -- i - iv v iiv v i v i iv iiv C L1ME5_3end#LI 618 CACTATGTT--TTTAAGATCCATCCATGTTGCTATGTGTACATCTAGTCC 571 chrXptel1M 182528 GTCATTTCTTACAGAACAATAATATTCCATAACATGCATATACCACAATT 182577 iii v v vvvv i i iiii vi v C L1ME5_3end#LI 570 GTTGCTTCTAACTGCTGCATAGTACTCCATGGTGTGCATCCACCACATTT 521 chrXptel1M 182578 TATTCAGCCATTCTCCAACTGATGGGCATCCACTCAGTTTCCAGTTCCTT 182627 iii v i v v i i vviv ii ii ii C L1ME5_3end#LI 520 TACCTATCCACTCTCCCAGTGATGGACACCCAGGTTGCCTCCAACTCCCC 471 chrXptel1M 182628 GTCACTACAAACAGGGCTGCCTCAAACATTTTTACACATGTGGGTCCCTT 182677 i i iv vvii ii iii ---- i C L1ME5_3end#LI 470 GCCACCACAAACAACGCTGCAATGAACATCCTCGTACATGT----CCCCT 425 chrXptel1M 182678 TCT---CTCATTTAAGA-TCTCTTTGGGTTATAAGTCCAGTAGACACACT 182723 v --- iii v i - i v vii v vviv i C L1ME5_3end#LI 424 TATGGACCTGTGTGAGAATTTCTTTGGGATATATACCCAGGAGCGGAATT 375 chrXptel1M 182724 GCTAGATCAAAGGGTATGCATAGTGTGATAGCCCTTTGGGCA--TAGTTA 182771 i i v i vvv -- i--- ivi -- v vv C L1ME5_3end#LI 374 GCTGGGTCATAGGGTATGCGTATACT--TAA---TTTGACTAAGTACTGC 330 chrXptel1M 182772 CAAATTGTTCTCCAGAATGGTTGGCTCAGTTTACAACTCCACCAATAATG 182821 i i i vvi i vii ii i C L1ME5_3end#LI 329 CAGATTGCTCTCCAGAATGGCTGCACCAGTCTACACTCCCACCAGCAGTG 280 chrXptel1M 182822 TATTAGTGTCCCCATTGTCCCACATCTCCTCCAACATTTATCATTATTT- 182870 i v v i i ?vi ii v i iv ii- C L1ME5_3end#LI 279 CATGAGGGTTCCTATNTCCCCACATCCTCGCCAACACTTGGCATTATCCA 230 chrXptel1M 182871 -TTTCCTATCATCTTAGCAAATCTG--AGGTATGTTGTGGTACCTCAGAG 182917 -i i -- i v v i i-- i ivv i i vv C L1ME5_3end#LI 229 GCTTTCTA--ATTTTTGCCAGTCTAATAGGTGTAAAGTGATATCTCATTG 182 chrXptel1M 182918 TTGTATTAATTTGCA-TTCTCTAATTAATAATTAATTT 182954 v - i v v i C L1ME5_3end#LI 181 TTGTTTTAATTTGCATTTCTCTGATTACTAATGAGTTT 144 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.76 CpG sites = 95, Kimura (unadjusted) = 40.85 Transitions / transversions = 1.61 (95/59) Gap_init rate = 0.05 (27 / 519), avg. gap size = 1.22 (33 / 27) 1186 30.01 4.16 5.66 chrXptel1M 183162 184362 (815638) L1M5_orf2#LINE/L1 1516 2699 (595) m_b329s551i9 13845 chrXptel1M 183162 CCAAATTCCTTCTATGACACAAATATGTTATTGATACCTAAACCAGGAAG 183211 v i v i vi v ii ?vivi v ? iv i L1M5_orf2#LIN 1516 CCCAACTCATTTTATGAGGCCAGCATNACCCTGATACCAAAACCNGACAA 1565 chrXptel1M 183212 AGCCA--------AAAGAAAATTACATACCAATCTCCCTAATGAATATTA 183253 v -------- v v v i vi L1M5_orf2#LIN 1566 AGACATTACAAGAAAAGAAAATTACAGACCAATATCCCTCATGAACATAG 1615 chrXptel1M 183254 ATGCAAAAATATTAGATAAAATATTGACAAAGAGATTATAACAACTTATC 183303 vi ?i i ii vv v vi i iv v L1M5_orf2#LIN 1616 ATGCAAAAATCCTNAACAAAATATTAGCAAATCGAATCCAGCAATATATA 1665 chrXptel1M 183304 AGCAGGATAATACAATATAACTAACTAGGATTTATACCAGGAGATATCAG 183353 iv vi i i v i i v - iiv L1M5_orf2#LIN 1666 AAAAGGATAATACATCATGACCAAGTGGGGTTTATCCCAGGA-ATGCAAG 1714 chrXptel1M 183354 G---------------AAAATTG-TTGCTATGAT-GACCAATATCATAAC 183386 --------------- ii- iiv i i -v - -- L1M5_orf2#LIN 1715 GTTGGTTTAACATTCGAAAATCAATCAATGTAATTCACCA-TAT--TAAC 1761 chrXptel1M 183387 AAAAC---CCAGAGAAATTATATTTTAATCTCAATAGATACAAAAAAAAA 183433 i i---vv i i vv v i i -- L1M5_orf2#LIN 1762 AGAATAAAGGAGAAAAATCATATGATCATCTCAATAGATGCAGAAAAA-- 1809 chrXptel1M 183434 GTTTTTGACAAAATACAGCACTTTTTCCTATTAAACATTCTTATTAAAAC 183483 iv v i iiv v iv v i i vi v- L1M5_orf2#LIN 1810 GCATTTGACAAAATTCAACACCCATTCATGATAAAAACTCTCAGCAAAC- 1858 chrXptel1M 183484 ATTAGAGAACATAGGAATGGAAGGAGTTTTCCTTAAAATGATAAGCAGCA 183533 ----------- i iivi i vv ivi L1M5_orf2#LIN 1859 -----------TAGGAATAGAAGGGAACTTCCTCAACCTGATAAAGGGCA 1897 chrXptel1M 183534 TCTACCTAAAACCATTAGCAAATATTATTTGTAATGGAGAGAAACTGGAT 183583 vv vvi ? i i viv v i ? i ? L1M5_orf2#LIN 1898 TCTACGAAAAACCTACAGCNAACATCATACTTAATGGTGAAANACTGAAN 1947 chrXptel1M 183584 GCATTCCCAATAAAATTGGGG-TAAAAGTAGGATGCTCATTATCACCATT 183632 v vv i i i-i i vv ii ii ? i L1M5_orf2#LIN 1948 GCTTTCCCCCTAAGATCGGGAACAAGACAAGGATGTCCGCTNTCACCACT 1997 chrXptel1M 183633 ATTATTTGATGTTGTACTAGAAATGTTTGCTTTAGCAATAAGAAAAGACA 183682 vi ii ii i ii vi v ivvv iv v L1M5_orf2#LIN 1998 TCTATTCAACATTGTACTGGAGGTCCTAGCCAGTGCAATAAGGCAAGAAA 2047 chrXptel1M 183683 AATAAATTAAAGAAATTACAGTAGGCAATGAGGAAATAAAACTATCACTA 183732 v v iv v vii v v v i i ?i L1M5_orf2#LIN 2048 AAGAAATAAAAGGCATAAAGATTGGAAAGGAAGAAATAAAACTGTCNTTA 2097 chrXptel1M 183733 TTTGTAGATGATATGATGATATACTTAGAGAATCATCCAAA-AACCTATT 183781 i i i vi ? v i -- ? - i i- L1M5_orf2#LIN 2098 TTCGCAGATGACATGATTGTNTACGTAGAAAATC--CNAAAGAATCTAC- 2144 chrXptel1M 183782 TGAAACAATTAACAGTTTTAGCAAACTATGAAATAAAATGGGTTTTATTA 183831 -- ? ----- v vi -- vv i i ------ vi L1M5_orf2#LIN 2145 --AAANAA-----ACTACTAG--AACTAATAAGTGAA------TTTAGCA 2179 chrXptel1M 183832 TGGGTTGTTATGGGTTATTGTGAGTTATATAAAATAAACCCACAAAATCA 183881 v ---- iii? ------------ i ii v ivi -- L1M5_orf2#LIN 2180 AG----GTCGCNGG------------ATACAAGGTCAATATACAAAA--A 2211 chrXptel1M 183882 TCA---GCATTTCTACATATTACTGGC-ATAGACTAGTAGCAA--GAGAT 183925 --- i i i --- - i i v v i v -- i L1M5_orf2#LIN 2212 TCAATTGTATTTCTATATACTA---GCAACAAACAATTGGAAAATGAAAT 2258 chrXptel1M 183926 AGAAAGAGAAATCCCATTTCAAATAACTGTAGACAAAATTAAATATTTGG 183975 vv? i iv v vv i vvi i v v ? i i L1M5_orf2#LIN 2259 TTNAAAAACAATACCATTTACAATAGCATCAAAAAACATNAAATACTTAG 2308 chrXptel1M 183976 GTGTCTAACTGCCAGGACAAATCCAGGAACTGTAC---GAACACAATTAC 184022 vi vv v iv ii ? vi v i v ? --- --- i L1M5_orf2#LIN 2309 GAATAAATCTAACAAAANATGTGCAAGACCTNTACACTGAA---AACTAC 2355 chrXptel1M 184023 AAAACACTTCTCACACGA--TAAAGTCAGATCTAAACAATTAGATCTGAA 184070 i v v v vi -- -v i i v i --- i L1M5_orf2#LIN 2356 AAAACATTGCTGAGAGAAATTAAAG-AAGACCTAAATAAATGGA---GAG 2401 chrXptel1M 184071 A-ATGTCAGTTGTTCATGGGTAGGCTGAGCTAATATAAGAAAAATGACAA 184119 - ii -- i v vv vii viv? i v L1M5_orf2#LIN 2402 ATATACCA--TGTTCATGGATTGGAAGACTCAATATTGTNAAGATGTCAA 2449 chrXptel1M 184120 TTATGCCTAAATTTGTCTACTTGTTCAGTGCAATAATATTCAATTTGCCA 184169 v v i vi ivvi i vvi v vv v L1M5_orf2#LIN 2450 TTCTCCCCAAATTGATCTATAGATTCAATGCAATCCCAATCAAAATCCCA 2499 chrXptel1M 184170 A-AAATGATTTTATAGAGCGAGATAAA--AATAACAAAATTTATCTGAAA 184216 i- ii vv i ivvv i i--i vvi v i L1M5_orf2#LIN 2500 GCAGGTTTTTTTGTAGAAATTGACAAGCTGATTCTAAAATTTATATGGAA 2549 chrXptel1M 184217 GAAGAAAAAGGCAAGAAT--TCAAGCAAATTTATGAAAAAAATGCA-AAG 184263 iviv iiiv ? --i ivv i - i v v - i L1M5_orf2#LIN 2550 ATGCAAAGGACCNAGAATAGCCAAAACAATCT-TGAAAAAGAAGAACAAA 2598 chrXptel1M 184264 GATGGTGGGCTAGAAGGATGAGACCTAAAATGATATTATAAAGCAGCAGC 184313 v v i viv vv iv? i? v ivvv vi i L1M5_orf2#LIN 2599 GTTGGAGGACTTACACTACCNGATNTCAAGACTTATTATAAAGCTACAGT 2648 chrXptel1M 184314 CACCAAAACCATTTGTTACTGGC-TAAGAA-ACAGAGATAGATCAATAGA 184361 v i i vi v v i - i - v v i i L1M5_orf2#LIN 2649 AATCAAGACAGTGTGGTATTGGCGTAAGGATAGACAAATAGATCAATGGA 2698 chrXptel1M 184362 A 184362 L1M5_orf2#LIN 2699 A 2699 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.29 CpG sites = 180, Kimura (unadjusted) = 39.91 Transitions / transversions = 1.12 (180/160) Gap_init rate = 0.07 (86 / 1200), avg. gap size = 1.36 (117 / 86) 442 29.48 1.57 1.57 chrXptel1M 184697 184951 (815049) L1PB_orf2#LINE/L1 3040 3294 (0) m_b329s551i10 13845 chrXptel1M 184697 ATTAAATTCAAAAGTTTTTGCACAAGCAAAACCAACAGAAACCAGATTAG 184746 i v i i i i- vv vv v v i L1PB_orf2#LIN 3040 ATTAAACTAAAGAGCTTCTGCACG-GCAAAAGGAACAGTCAGCAGAGTAA 3088 chrXptel1M 184747 A-AGGGAAGT-ACAACGCTGAGAAAGAATCTTTCCAGCCAGTATTTCTGA 184794 - iv vi- iv - i i i iv ii vi iv L1PB_orf2#LIN 3089 ACAGACAACCCACAGAG-TGGGAGAAAATCTTCACAATCTATACATCTGA 3137 chrXptel1M 184795 TAAAGGCCTCATTTGTAAAATATATAAAGAACTGTGTCAAATTTGTAAGA 184844 i v v v vi i v i ? vviv iv i L1PB_orf2#LIN 3138 CAAAGGACTAATATCCAGAATCTACAANGAACTCAAACAAATCAGCAAGA 3187 chrXptel1M 184845 ATACAACT--CATTCCTCAGTTGATAAATGGTCAAAGAATACGAACAGAC 184892 v v v-- v - - ii v i v v i i i i L1PB_orf2#LIN 3188 AAAAAACAAACAATCC-CA-TCAAAAAGTGGGCTAAGGACATGAATAGAC 3235 chrXptel1M 184893 AATTTTCAGATGAAGAAATTAAAGTCGTCTATAATCATATGAAAAAATGC 184942 i i v v vv i v i v i v L1PB_orf2#LIN 3236 AATTCTCAAAAGAAGATATACAAATGGCCAACAAACATATGAAAAAATGC 3285 chrXptel1M 184943 TCTAAATCA 184951 v v L1PB_orf2#LIN 3286 TCAACATCA 3294 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.41 CpG sites = 36, Kimura (unadjusted) = 38.05 Transitions / transversions = 0.95 (36/38) Gap_init rate = 0.03 (7 / 254), avg. gap size = 1.14 (8 / 7) 637 25.84 0.00 1.44 chrXptel1M 184811 185022 (814978) L1ME3C_3end#LINE/L1 10 218 (652) m_b329s551i11 13845 chrXptel1M 184811 AAAATATATAAAGAACTGTGTCAAATTTGTAAGAATACAACTCATTCCTC 184860 i vivv ivi v iviv --- i L1ME3C_3end#L 10 AGAATATATAAAGAACTCCTACAAATCAATAAGAAAACAGACAA---CCC 56 chrXptel1M 184861 AGTTGATAAATGGTCAAAGAATACGAACAGACAATTTTCAGATGAAGAAA 184910 i v v v ii i i iv v i L1ME3C_3end#L 57 AATAGAAAAATGGGCAAAAGATATGAACAGGCAATTCACAGAAGAGGAAA 106 chrXptel1M 184911 TTAAAGTCGTCTATAATCATATGAAAAAATGCTCTAAATCACTATTGACT 184960 i?vi i v i v v i v vv v i ii L1ME3C_3end#L 107 CNCGAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTAATC 156 chrXptel1M 184961 AGAGAAATGCAAATTTAAAAAACTCTGAGTTACCACCTCACACCTCTCAG 185010 i v v? vv v ii iv L1ME3C_3end#L 157 AGGGAAATGCAAATTAAAACNACAATGAGATACCATTTCACACCCATCAG 206 chrXptel1M 185011 ATTGGTTAAAAT 185022 iv L1ME3C_3end#L 207 ATTGGCAAAAAT 218 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 31.67 CpG sites = 27, Kimura (unadjusted) = 32.38 Transitions / transversions = 1.00 (27/27) Gap_init rate = 0.01 (3 / 211), avg. gap size = 1.00 (3 / 3) 374 35.07 9.50 4.54 chrXptel1M 185146 185608 (814392) C L2#LINE/L2 (240) 2842 2358 m_b329s601i27 13846 chrXptel1M 185146 TTGGGGAAAAGGGTGACA----CAGACCTCCATTTTAG--GGAAACTTTT 185189 i v i i i ---- v i v i i-- vvvi i C L2#LINE/L2 2842 TTGAGCAGAGGAGTGACATGATCTGACTTACGTTTTAAAAGGATCACTCT 2793 chrXptel1M 185190 GGTGGTTGAATGGAGGGTAGACAGAAGTAGGGAGAGACTTGAGGCAGGCA 185239 iv i vi v ii v ? vi vi iv v i v C L2#LINE/L2 2792 GGCTGCTGTGTTGAGAATAGACTGNAGGGGGGCAAGGGTGGAAGCAGGGA 2743 chrXptel1M 185240 GACCCTCCAACAAACTACTGTAGGAGTACAGTGTG--------TGGTG-- 185279 vvii iv ii i i v i v - i -------- -- C L2#LINE/L2 2742 GACCAGTTAGGAGGCTATTGCAGTAATCCAG-GCGAGAGATGATGGTGGC 2694 chrXptel1M 185280 -----TCAGAG-GATGGAAGGGAAAGTACTTAAGAG-------ATGCTGC 185316 -----i i - i v v i i iv v ii ------- v v C L2#LINE/L2 2693 TTGGACCAGGGTGGTGGCAGTGGAGGTGGTGAGAAGTGGTCGGATTCTGG 2644 chrXptel1M 185317 A---------AAGGTGAAGTCAAGAAATCTTGGCAACAGCTTGGACAAGG 185357 --------- ii i i v iivi vii ii v iiv C L2#LINE/L2 2643 ATATATTTTGAAGGTAGAGCCGACAGGATTTGCTGATGGATTGGATGTGG 2594 chrXptel1M 185358 GG---GAGAGGTAAGAGAGAGAAAGTGAGGGTTATGCTCTTAGGTTGGAT 185404 --- --- i i ivii i v -- iv vvvv C L2#LINE/L2 2593 GGTGTGAGAG---AAAGAGAGGAGTCAAGGATGA--CTCCAAGGTTTTTG 2549 chrXptel1M 185405 GCCTGAAAGACTGAGAAGATGGTAGTGCTCTCCACAGTAAGAAGGAAGAT 185454 ivi ii i viv iv i? v vi vii i C L2#LINE/L2 2548 GCCTGAGCAACTGGAAGGATGGAGTTGCCATTNACTGAGATGGGGAAGAC 2499 chrXptel1M 185455 AGGAAGGGGAGAAGGCTGGGAAGAGCTTAGAGGAGGGGAAAGAAATCACC 185504 v vii i v i v -------------- i -- vv C L2#LINE/L2 2498 TGCGGGAGGAGCAGGTTTG--------------AGGGGGAAGA--TCAGG 2465 chrXptel1M 185505 TCATCAGTTTTGAA--TGTTGAATT-GGGATCCCTAAGAGATATCCTCTT 185551 vvv i -- i i - i v vv i vvv C L2#LINE/L2 2464 AGTTCAGTTTTGGACATGTTAAGTTTGAGATGCCTATTAGACATCCAAGT 2415 chrXptel1M 185552 TTAGATATCTAATAAACAGGTGGAGATCTGAAAGTGGAGGTCAGGGGAGA 185601 vv i v i ii v v vi ivv v C L2#LINE/L2 2414 GGAGATGTCGAGTAGGCAGTTGGATATACGAGTCTGGAGTTCAGGGGAGA 2365 chrXptel1M 185602 TGGCCAG 185608 v v i C L2#LINE/L2 2364 GGTCCGG 2358 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 46.45 CpG sites = 84, Kimura (unadjusted) = 49.08 Transitions / transversions = 1.18 (84/71) Gap_init rate = 0.07 (33 / 462), avg. gap size = 2.00 (66 / 33) 259 22.81 0.00 0.00 chrXptel1M 185600 185656 (814344) L2#LINE/L2 2420 2476 (606) m_b329s601i28 13847 chrXptel1M 185600 GATGGCCAGTAGGCATCTGAAGCTCACCATGTCCAAAGCAGAATTCATTA 185649 v i i v i i v i v i v v L2#LINE/L2 2420 GATGTCTAATAGGCATCTCAAACTTAACATGTCCAAAACTGAACTCCTGA 2469 chrXptel1M 185650 TCTCCCC 185656 i L2#LINE/L2 2470 TCTTCCC 2476 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.52 CpG sites = 7, Kimura (unadjusted) = 27.52 Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0) 36 34.11 3.14 2.22 chrXptel1M 186496 186718 (813282) (CTCT)n#Simple_repeat 1 225 (0) m_b330s252i0 13848 chrXptel1M 186496 CTTTCTTTTTC-CTGTTTCTCTCCCTCCGAAGCTCTCCATCTCTATATCT 186544 i i i - v i i ivvvv iv v v (CTCT)n#Simpl 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chrXptel1M 186545 GTCTTCCGCCCTCCCTACCGTCTTTTTCT-TCTGACTCTTTCT-TCTGTT 186592 v ii v i i - iv i i - vv i - v i (CTCT)n#Simpl 51 CTCTCTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 99 chrXptel1M 186593 TTTGTCTCTGTCCCCCTCCCTCATCTCTGT-TCATCTTCCTCTGTCTTTC 186641 i v v i i i - v - - ii v i (CTCT)n#Simpl 100 TCTCTCTCTCTCTCTCTCTCTC-TCTCTCTCTC-TCTCTCTCTCTCTCTC 147 chrXptel1M 186642 TCTTTCTGTCTCCCTCCCTTGCTCT-TCTCTTTCT-TCGTCTCATCT-TG 186688 i v i i iv - i - - - - v (CTCT)n#Simpl 148 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TCTC-TCTCTC 195 chrXptel1M 186689 CCTGTCTGTCACCATCTCTGTCTTTCTATC 186718 i v v v iv v i v (CTCT)n#Simpl 196 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 225 Matrix = Unknown Transitions / transversions = 1.15 (31/27) Gap_init rate = 0.05 (12 / 222), avg. gap size = 1.00 (12 / 12) 38 24.96 4.35 4.92 chrXptel1M 186528 186711 (813289) (TCTCTG)n#Simple_repeat 1 183 (0) m_b330s252i1 13849 chrXptel1M 186528 TCTCCATCTCTATATCTGTCTTCCG-CCCTCCCTACCGTCTTTTTCTTCT 186576 ii i v - i - i vi - i i v - (TCTCTG)n#Sim 1 TCTCTGTCTCTGTCTCTGTC-TCTGTCTCTGTCT-CTGTCTCTGTC-TCT 47 chrXptel1M 186577 GACTCTTTCTTCTGTTTTTGTCTCTGTCCCCCTCCCTCATCTCTGTTCAT 186626 v v - i i i iv i -i - - (TCTCTG)n#Sim 48 GTCTCTGTC-TCTGTCTCTGTCTCTGTCTCTGTCTCT-GTCTCTG-TC-T 93 chrXptel1M 186627 CTTCCTCTGTCT-T-TCTCT-T-TCTGTCTCCCTCCCTTGCTCT-TCTCT 186671 vi - - - - iv i vv - (TCTCTG)n#Sim 94 CTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCT 143 chrXptel1M 186672 TTCTTCGTCTC-ATCT-TGCCTGTCTGTCACCATCTCTGTCT 186711 v ii -i - -- v v ii (TCTCTG)n#Sim 144 GTCTCTGTCTCTGTCTCTG--TCTCTGTCTCTGTCTCTGTCT 183 Matrix = Unknown Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.09 (17 / 183), avg. gap size = 1.00 (17 / 17) 36 34.11 3.14 2.22 chrXptel1M 186496 186718 (813282) (CTCT)n#Simple_repeat 1 225 (0) m_b330s252i0 13848 chrXptel1M 186496 CTTTCTTTTTC-CTGTTTCTCTCCCTCCGAAGCTCTCCATCTCTATATCT 186544 i i i - v i i ivvvv iv v v (CTCT)n#Simpl 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chrXptel1M 186545 GTCTTCCGCCCTCCCTACCGTCTTTTTCT-TCTGACTCTTTCT-TCTGTT 186592 v ii v i i - iv i i - vv i - v i (CTCT)n#Simpl 51 CTCTCTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 99 chrXptel1M 186593 TTTGTCTCTGTCCCCCTCCCTCATCTCTGT-TCATCTTCCTCTGTCTTTC 186641 i v v i i i - v - - ii v i (CTCT)n#Simpl 100 TCTCTCTCTCTCTCTCTCTCTC-TCTCTCTCTC-TCTCTCTCTCTCTCTC 147 chrXptel1M 186642 TCTTTCTGTCTCCCTCCCTTGCTCT-TCTCTTTCT-TCGTCTCATCT-TG 186688 i v i i iv - i - - - - v (CTCT)n#Simpl 148 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TCTC-TCTCTC 195 chrXptel1M 186689 CCTGTCTGTCACCATCTCTGTCTTTCTATC 186718 i v v v iv v i v (CTCT)n#Simpl 196 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 225 Matrix = Unknown Transitions / transversions = 1.15 (31/27) Gap_init rate = 0.05 (12 / 222), avg. gap size = 1.00 (12 / 12) 15 13.67 0.00 0.00 chrXptel1M 187498 187521 (812479) (T)n#Simple_repeat 1 24 (0) m_b330s252i2 13850 chrXptel1M 187498 TTTTTTTTTTTTTGCTTTTTATTT 187521 vi v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTT 24 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 13 14.67 8.51 2.00 chrXptel1M 187641 187687 (812313) (AATATAT)n#Simple_repeat 1 50 (0) m_b330s252i3 13851 chrXptel1M 187641 AATATGTTAAAGTATAA-GT-TAA-ATAAAATATATAATATAT-ATACAT 187686 -v vi -i - - v - i (AATATAT)n#Si 1 AATAT-ATAATATATAATATATAATATATAATATATAATATATAATATAT 49 chrXptel1M 187687 A 187687 (AATATAT)n#Si 50 A 50 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.11 (5 / 46), avg. gap size = 1.00 (5 / 5) 940 30.70 2.55 2.88 chrXptel1M 187972 188598 (811402) C L1MC5a_3end#LINE/L1 (2141) 636 12 m_b330s551i1 13852 chrXptel1M 187972 CCTGCTCATTTCACTCAACATCAGTTCATGTAAGTCTCTCCAAGGCTTTC 188021 i iv i vi vv v v ii v vi? vv v C L1MC5a_3end#L 636 CTTGCTTTTTTCACTTAACAATATATCCTGGAGATCACTCCATANCAGTA 587 chrXptel1M 188022 T---GAAATCATCCTGTTGGTCATTTCTTACAGA-ACAGTAATATTCCAT 188067 --- i v vv -- v - v-i - i i C L1MC5a_3end#L 586 TATAGAGATCTTCCTCAT--TCCTTT-TTACAGCTGCA-TAGTACTCCAT 541 chrXptel1M 188068 AATATTCATATACCATCACTTATTCAGCCATTCTCCAATTGATGGGCATC 188117 vi i vv i vii i v i v i i C L1MC5a_3end#L 540 TGTGTGGATGTACCATAGTTTATTCAACCAGTCCCCTATTGATGGACATT 491 chrXptel1M 188118 CACTCAGTTTCCAGTTTCTGGCCACCTCAAACAGGGCTGCCACAAACATT 188167 iivviv i i v i iiv i iv v ii i vi C L1MC5a_3end#L 490 TGGGTTGTTTCCAGTCTTTTGCTATTACAAATAATGCTGCAATGAATAAC 441 chrXptel1M 188168 TTGGCACATACGGGTCCCTTCCCCTTCTT--TAGTATCTCTATGGGGTAT 188215 i v ii -- ?i viv i --? i v vi i v C L1MC5a_3end#L 440 CTTGTGCATACG--TCNTTTCGTATTTTTGCNAGTGTATCTTCGGGATAG 393 chrXptel1M 188216 AAGCCCAGTAGTAGCACTGCTGGATCAAAGGGT--ATGCACCGTTTGATA 188263 vv i v i v i i -- --- v - C L1MC5a_3end#L 392 ATTCCTAGAAGTGGGATTGCTGGGTCAAAGGGTAAATGCA---TATG-TA 347 chrXptel1M 188264 ACTTTTGGGGCATAATTCCAGATTGCTCTCCAGAATGGTTGGATTCGTTC 188313 - vviv v v i v i v iv v iivv i C L1MC5a_3end#L 346 A-TTTTGCTAGATATTGCCAAATTCCCCTCCATAGGGGTTGTACCATTTT 298 chrXptel1M 188314 ACAACTCCACCAACAATGCATCAGTGTCCCAGTTTTCCCACATCCCCTCC 188363 i vii i i v v v v i v i v C L1MC5a_3end#L 297 GCATTCCCACCAGCAATGTATGAGAGTGCCTGTTTCCCCACAGCCTCGCC 248 chrXptel1M 188364 AACATTCATCATTATTTTTTC---CTGTC--ATCTTAGTCAATCTGAAAG 188408 -----v v v v --- v i-- i v i v C L1MC5a_3end#L 247 AACA-----GAGTATGTTGTCAAACTTTTGGATTTTTGCCAATCTGATAG 203 chrXptel1M 188409 GTGTGTAGTGATATCTCATTGTTGTCTTCATTTGCATTTCTCTGATCAAT 188458 v v i i v v i v v i vv C L1MC5a_3end#L 202 GTGAGAAATGGTATCTCAGTGTAGTTTTAATTTGCATTTCTCTTATTATG 153 chrXptel1M 188459 ACTGATTTGGAACACTCTTTCATATGAGTGGAAATAGTTTCAATTTCATC 188508 v vv v i iii vv iiiiiivi vv v i C L1MC5a_3end#L 152 AGTGAGGTTGAGCATCTTTTCATATGTTTAAGGGCCATTTGCATTTCTTT 103 chrXptel1M 188509 ATCTGAAAATTGTCTGTCCATATCCTTTGACCATTTATCAATTGGAGAAT 188558 v vi i i i v v v ivvi C L1MC5a_3end#L 102 TTCTGTGAACTGTCTGTTCATATCTTTTGCCCATTTTTCTATTGGGTTGT 53 chrXptel1M 188559 GGCTTGATTTCTTATAAA---TTAGAGTCACTCTCTATATATT 188598 v v ivv v v --- i--i i C L1MC5a_3end#L 52 TGGTCTTTTTCTTCTCAATTTTTAGAA--GCTCTTTATATATT 12 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.91 CpG sites = 90, Kimura (unadjusted) = 40.19 Transitions / transversions = 0.93 (90/97) Gap_init rate = 0.04 (25 / 626), avg. gap size = 1.36 (34 / 25) 1369 26.88 1.65 2.77 chrXptel1M 188057 188603 (811397) C L1ME3G_3end#LINE/L1 (377) 547 7 m_b330s551i2 13852 chrXptel1M 188057 TAATATTCCATAATATTCATATACCATCACTTATTCAGCCATTCTCCAAT 188106 i i vv v i i i i v C L1ME3G_3end#L 547 TAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTAT 498 chrXptel1M 188107 TGATGGGCATCCACTCAGTTTCCAGTTTCTGGCCACCTCAAACAGGGCTG 188156 i ii vviv i i v i iiv iv C L1ME3G_3end#L 497 TGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCTG 448 chrXptel1M 188157 CCACAAACATTTTGGCACATACGGGTCCCT-TCCCCTTCTTT-AGTATCT 188204 v ii ii v i i ?-- i - v v v v vi- i C L1ME3G_3end#L 447 CAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATTT 400 chrXptel1M 188205 CTATGGGGTATAAGCCCAGTAGTAGCACTGCTGGATCAAAGGGTATGCAC 188254 ? i i v v? ? v i v i i i C L1ME3G_3end#L 399 CTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGC 350 chrXptel1M 188255 CGTTTGATAACTTTTGGGGCATAATTCCAGATTGCTCTCCAGAATGGTTG 188304 -i -- v iiviv v v i i i ? i C L1ME3G_3end#L 349 -ATTT--TAAATTTTAATAGATACTGCCAAATTGCCCTCCAAAANGGCTG 303 chrXptel1M 188305 GATTCGTTCACAACTCCACCAACAATGCATCAGTGTCCCAGTTTTCCCAC 188354 v iivi i vii i i i v v v v i C L1ME3G_3end#L 302 TACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCAC 253 chrXptel1M 188355 ATCCCCTCCAACATTCATCATTATTTTTTCCTGTCATCTTAGTCAATCTG 188404 i i v i ?ivi ivv?iii vvv i v i C L1ME3G_3end#L 252 ACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATCTG 203 chrXptel1M 188405 AAAGGTGTGTAGTGATATCTCATTGTTGTCTTCATTTGCATTTCTCTGAT 188454 vi viv i i i v i C L1ME3G_3end#L 202 ATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGAT 153 chrXptel1M 188455 CAATACTGATTTGGAACACTCTTTCATATG---AGTGGAAATAGTTTCAA 188501 i v v vv v i iii --- v vv --- vv C L1ME3G_3end#L 152 TACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCAT---TTGTA 106 chrXptel1M 188502 TTTCATCATCTGAAAATTGTCTGTCCATATCCTTTGACCATTTATCAATT 188551 v v vi i i v v v C L1ME3G_3end#L 105 TTTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATT 56 chrXptel1M 188552 GGAGAATGGCTTGATTTCTTATAAATT----AGAGTCACTCTCTATATAT 188597 iv-- v -- vi ----i --- i C L1ME3G_3end#L 55 GGGT--TGTCTT--TTTCTTATTGATTTGTAGGAGT---TCTTTATATAT 13 chrXptel1M 188598 TTTGGA 188603 i C L1ME3G_3end#L 12 TCTGGA 7 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 33.88 CpG sites = 79, Kimura (unadjusted) = 34.47 Transitions / transversions = 1.23 (79/64) Gap_init rate = 0.03 (19 / 546), avg. gap size = 1.26 (24 / 19) 180 31.74 1.57 5.74 chrXptel1M 189554 189680 (810320) C L2d2_3end#LINE/L2 (292) 263 142 m_b330s601i2 13853 chrXptel1M 189554 GGGCTAGAAGTAGGAGGTCAAGAAAGACTTACTGTAGAAAATGGAATCTC 189603 i - ---- i i i vvi v i ii ? i v C L2d2_3end#LIN 263 GGGCTGGA-GT----GGTCAGGGAAGGCTTCACGGAGGAGGTGGNATTTG 219 chrXptel1M 189604 ACCTGGGGCATGAAGGATGCCAAGGA--AGCAAAAGGGGTGATGAAGGGT 189651 v v v vvv --v v v i v v v v C L2d2_3end#LIN 218 AGCTGGGCCTTGAAGGATGGGTAGGATTTGGATAGGTGGAGAGGAAGGGG 169 chrXptel1M 189652 GAGAATATTGAAGGTGCTGGGTAGATGGC 189680 i iii vv i -- vii i C L2d2_3end#LIN 168 AAGGGCATTCCAGGCG--GGGGGAACGGC 142 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.93 CpG sites = 18, Kimura (unadjusted) = 42.04 Transitions / transversions = 0.90 (18/20) Gap_init rate = 0.06 (8 / 126), avg. gap size = 1.12 (9 / 8) 186 34.23 1.80 0.00 chrXptel1M 189555 189665 (810335) C L2c_3end#LINE/L2 (212) 266 154 m_b330s601i3 13853 chrXptel1M 189555 GGCTAGAAGTAGGAGGTCAAGAAAGACTTACTGTAGAAAATGGAATCTCA 189604 i ?vv i i i i i v i v i ii iv v C L2c_3end#LINE 266 GACTAGNCTTGGGGGGTCAGGGAAGGCTTCCCGGAGGAGGTGACATCTGA 217 chrXptel1M 189605 CCTGGGGCATGAAGGATGCCAAGGAAGCAA-AAGGGGTGATGAAGGGTG- 189652 v i ? v vvv ivi i-v v vi v i v - C L2c_3end#LINE 216 GCTGAGNCTTGAAGGATGAGTAGGAGTTAGCCAGGTGGAAGGAGGGGGGA 167 chrXptel1M 189653 AGAATATTGAAGG 189665 ii vv C L2c_3end#LINE 166 AGAGCATTCCAGG 154 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 46.02 CpG sites = 19, Kimura (unadjusted) = 47.72 Transitions / transversions = 1.00 (19/19) Gap_init rate = 0.02 (2 / 110), avg. gap size = 1.00 (2 / 2) 194 32.58 7.87 0.00 chrXptel1M 189564 189652 (810348) C L2b_3end#LINE/L2 (212) 254 159 m_b330s601i4 13853 chrXptel1M 189564 TAGGAGGTCAAGAAAGACTTACTGTAGAAAATGGAATCTCACCTGGGGCA 189613 i i i i i i v i v i ii iv i v v i i v C L2b_3end#LINE 254 TGGGGGGTCAGGGAGGGCTTCCCGGAGGAGGTGACATTTGAGCTGAGACC 205 chrXptel1M 189614 TGAAGGATGCCAAGGA---AGCAA----AAGGGGTGATGAAGGGTG 189652 vvv ---i v ---- i iv i C L2b_3end#LINE 204 TGAAGGATGAGTAGGAGTTGGCCAGGCGAAGAGGTGGGGAAGGGCG 159 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.54 CpG sites = 18, Kimura (unadjusted) = 44.65 Transitions / transversions = 1.64 (18/11) Gap_init rate = 0.02 (2 / 88), avg. gap size = 3.50 (7 / 2) 473 26.90 3.52 5.76 chrXptel1M 191336 191477 (808523) MIRc#SINE/MIR 10 148 (120) m_b330s601i5 13854 chrXptel1M 191336 GTGGCACAATAAATAGAGCCTTAGACTTGGAATCTGGAAGGCTCATCTCA 191385 ii i ii v vi i i v i -------- MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC-------- 51 chrXptel1M 191386 CTGAGATTATATCTGGCCTCAGACACTGGCTAGCTGTATGGCCCTGGCCA 191435 i v iivi iv v v v vi i i i v MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 101 chrXptel1M 191436 AGTCACTTCA-CTCT----GCCTCAGTTCACTCAGCTATAAAATAAG 191477 v - ---- iv v i ii MIRc#SINE/MIR 102 AGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.92 CpG sites = 22, Kimura (unadjusted) = 34.22 Transitions / transversions = 1.57 (22/14) Gap_init rate = 0.07 (10 / 141), avg. gap size = 1.30 (13 / 10) 301 26.58 11.82 0.82 chrXptel1M 191628 191737 (808263) L2b_3end#LINE/L2 332 453 (13) m_b330s601i6 13855 chrXptel1M 191628 CTGCCTCCCC--------TGTTAGCACTG-AAGGGCAGGAACTTTCTTTG 191668 i -------- v v i -i i iv?v i L2b_3end#LINE 332 CTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTG 381 chrXptel1M 191669 ACTTGGT----GTTGGTATTCCTAGTGCTTAGGACAGTGCCTGGCTCAAA 191714 v v ---- i - i i i i v ? v v L2b_3end#LINE 382 TCTTGTTCACCGCTG-TATCCCCAGCGCCTAGCACAGNGCCTGGCACACA 430 chrXptel1M 191715 GGAAGCTCTGACCAAATGCTTAT 191737 v i v v vi ii i L2b_3end#LINE 431 GTAGGCGCTCAGTAAATATTTGT 453 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.07 CpG sites = 16, Kimura (unadjusted) = 34.24 Transitions / transversions = 1.23 (16/13) Gap_init rate = 0.04 (4 / 109), avg. gap size = 3.50 (14 / 4) 17 4.94 0.00 0.00 chrXptel1M 192103 192123 (807877) (AT)n#Simple_repeat 1 21 (0) m_b330s252i4 13856 chrXptel1M 192103 ATATATATATATATATATTTA 192123 v (AT)n#Simple_ 1 ATATATATATATATATATATA 21 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 335 31.53 0.76 3.91 chrXptel1M 195388 195519 (804481) MIRb#SINE/MIR 3 130 (138) m_b330s601i7 13857 chrXptel1M 195388 GAGGGGCAGCTAGTTGATGTACTGGATAGAGTATCAGCTCTAAAGTCAGG 195437 -- - i i v v i ivi i ii i MIRb#SINE/MIR 3 GAGGGGCAGC--GT-GGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGA 49 chrXptel1M 195438 AGGACCCGAGTTCAAATGTGACCTCAGACACTTAACAGGGAAACATAGCC 195487 vi i i i viviv v v vi vv--iii ii MIRb#SINE/MIR 50 CAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCT--GTGTGACC 97 chrXptel1M 195488 CTGGGCAAGTGGCTTAACCCCAATT-GCCTCAG 195519 i vi i vv v- MIRb#SINE/MIR 98 TTGGGCAAGTTACTTAACCTCTCTGAGCCTCAG 130 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.20 CpG sites = 24, Kimura (unadjusted) = 42.31 Transitions / transversions = 1.50 (24/16) Gap_init rate = 0.05 (6 / 131), avg. gap size = 1.00 (6 / 6) 16 16.52 0.00 0.00 chrXptel1M 196040 196066 (803934) (A)n#Simple_repeat 1 27 (0) m_b330s252i6 13858 chrXptel1M 196040 AAAAAAAAAGAACAAAACAAAACAAAA 196066 i v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAA 27 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 187 24.98 8.79 7.61 chrXptel1M 196534 196624 (803376) MIRb#SINE/MIR 133 224 (44) m_b330s601i8 13857 chrXptel1M 196534 TCCCCATATGCACAAGGGGAATAAGACATATCTACATCTGTTTCCTAGGG 196583 i v i v v i v - i ------i vi MIRb#SINE/MIR 133 TCCTCATCTGTAAAATGGGGATAATA-ATACCTAC------CTCGCAGGG 175 chrXptel1M 196584 GTGTTGGGAG----AAAC-ACACAGTG---ATAAAGTCCTTAACACAGT 196624 v v ---- i- v i i ---i iv i MIRb#SINE/MIR 176 TTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAGT 224 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.24 CpG sites = 12, Kimura (unadjusted) = 30.98 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.11 (10 / 90), avg. gap size = 1.50 (15 / 10) 26 0.00 0.00 0.00 chrXptel1M 197057 197081 (802919) (ATA)n#Simple_repeat 1 25 (0) c_b330s251i0 13859 chrXptel1M 197057 ATAATAATAATAATAATAATAATAA 197081 (ATA)n#Simple 1 ATAATAATAATAATAATAATAATAA 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 24 26.48 3.00 3.00 chrXptel1M 199264 199363 (800637) (ATAT)n#Simple_repeat 1 100 (0) m_b330s252i7 13860 chrXptel1M 199264 ATTTATCGATACAAAT-TATTTAT-TATGTATTTATATTTATTTTTAGCA 199311 v vv i v - v - i v v v v -i (ATAT)n#Simpl 1 ATATATATATATATATATATATATATATATATATATATATATATATA-TA 49 chrXptel1M 199312 TCACTTTAT-TTTATATATTTGTATATAAATTTATATTTATTTATAAATA 199360 - - v - v v i v v v v v (ATAT)n#Simpl 50 T-A-TATATATATATATATATATATATATATATATATATATATATATATA 97 chrXptel1M 199361 TAT 199363 (ATAT)n#Simpl 98 TAT 100 Matrix = Unknown Transitions / transversions = 0.24 (4/17) Gap_init rate = 0.06 (6 / 99), avg. gap size = 1.00 (6 / 6) 733 29.24 1.55 1.55 chrXptel1M 200508 200830 (799170) L1ME4c_3end#LINE/L1 232 554 (276) m_b330s551i3 13861 chrXptel1M 200508 GATAATGACGAATGTTGGAGGGGA-GTGGGGAAGACTGGGACACTGATGC 200556 iv v i v i ?- i v - v ? v i L1ME4c_3end#L 232 GATAATACCCAATGCTGGCGAGGNTGCGGTGAA-ACTGGTACNCTCATAC 280 chrXptel1M 200557 ATTGTTGGTGGAGTTGTGAACAGAGCCAACCATTCTGGAGAGCAGTTTGG 200606 i vi? i iv ivv v i i i L1ME4c_3end#L 281 ATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGG 330 chrXptel1M 200607 AACTATGC-TCAAAAGGTTATCAAACTCTGCATACCCTTTGATCCAGCAG 200655 v v i i- i -ii v v v v i i i L1ME4c_3end#L 331 CAATACGTATCAAGAG-CCATAAAAATGTTCATACCCTTTGACCCAGTAA 379 chrXptel1M 200656 TGTTACTACTGGGATTATATCCCAAAGAGATCAT---AAAGAAGAGAAAG 200702 vii v v v i i i v --- ii i L1ME4c_3end#L 380 TTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAAGAAGGAAAAA 429 chrXptel1M 200703 GGACCTGTATGTGCACAGATGCTTGCGGCAGCCCTCTTTGTAGTGGCTAG 200752 --- i ii iv i iiiv vi v i i i v i L1ME4c_3end#L 430 G---CTATATGCACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAA 476 chrXptel1M 200753 AAACTGGAAACTGAGAGGATGCCCATCAGTTGGAGAATGGCTGAATAAAT 200802 i vivvvii i v i v i i i i L1ME4c_3end#L 477 AAATTGGAAACAACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAAT 526 chrXptel1M 200803 GGTGGTATATGAAAATTATGGAATATTA 200830 vi i v? vviv L1ME4c_3end#L 527 TATGGTACATCNACTCGATGGAATATTA 554 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.68 CpG sites = 55, Kimura (unadjusted) = 38.80 Transitions / transversions = 1.45 (55/38) Gap_init rate = 0.02 (8 / 322), avg. gap size = 1.25 (10 / 8) 12 26.09 6.78 0.00 chrXptel1M 201706 201764 (798236) (AAAT)n#Simple_repeat 1 63 (0) m_b330s252i8 13862 chrXptel1M 201706 AAATGAA-AAAT-TATTATTAAGAAAATAAA-ACATGAAGACA-GTTTAA 201751 i - -v v v iv - v i v v -ivv (AAAT)n#Simpl 1 AAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAA 50 chrXptel1M 201752 ATAAATAAATAAA 201764 (AAAT)n#Simpl 51 ATAAATAAATAAA 63 Matrix = Unknown Transitions / transversions = 0.44 (4/9) Gap_init rate = 0.07 (4 / 58), avg. gap size = 1.00 (4 / 4) 35 0.00 0.00 0.00 chrXptel1M 202470 202499 (797501) (TA)n#Simple_repeat 1 30 (0) c_b330s251i1 13863 chrXptel1M 202470 TATATATATATATATATATATATATATATA 202499 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATA 30 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 63 1.66 0.00 0.00 chrXptel1M 204250 204310 (795690) (AAGA)n#Simple_repeat 1 61 (0) c_b330s251i2 13864 chrXptel1M 204250 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAATAAAGAAAGAAAGAAA 204299 v (AAGA)n#Simpl 1 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 50 chrXptel1M 204300 GAAAGAAAGAA 204310 (AAGA)n#Simpl 51 GAAAGAAAGAA 61 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 18 12.03 0.00 0.00 chrXptel1M 206153 206179 (793821) (C)n#Simple_repeat 1 27 (0) m_b330s252i9 13865 chrXptel1M 206153 CCCCCCTCCCCGCCCCCCCACCCCCCC 206179 i v v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCC 27 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 16 9.55 0.00 0.00 chrXptel1M 206579 206601 (793399) (G)n#Simple_repeat 1 23 (0) m_b330s252i10 13866 chrXptel1M 206579 GGGGGGGGAGGGGGGGAGGGGGG 206601 i i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGG 23 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 534 31.64 2.22 1.66 chrXptel1M 207157 207336 (792664) C MIRb#SINE/MIR (23) 245 65 m_b330s601i9 13867 chrXptel1M 207157 AGTGCCCGCTATGTGCCAGGCACCGTGCTAGTGGCTTTCAAAATACCATC 207206 i iii i ivv vv vii ii C MIRb#SINE/MIR 245 AGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACATGCATTATC 196 chrXptel1M 207207 TCCTGGGATGCTGGCAACAATCCTGGGAGATAGGTGCTATTGTGATTCCC 207256 v vvi v vi i v i ii --- i C MIRb#SINE/MIR 195 TCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATT---ATCCCC 149 chrXptel1M 207257 ATTTTCTGGATGATGAGACTGAGGC----AGAAATCAAGGGAAGTATCTA 207302 vii v i ---- ii i vi vv ii i C MIRb#SINE/MIR 148 ATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCA 99 chrXptel1M 207303 AAGTCACCTCGATAGAAAAAGTCTAAGGCAGGAT 207336 i viv v v iv v vi v i C MIRb#SINE/MIR 98 AGGTCACACAGCTAGTAAGTGGCAGAGCCGGGAT 65 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.30 CpG sites = 32, Kimura (unadjusted) = 42.28 Transitions / transversions = 1.33 (32/24) Gap_init rate = 0.02 (4 / 179), avg. gap size = 1.75 (7 / 4) 185 13.09 4.00 8.33 chrXptel1M 207611 207660 (792340) C MIR3#SINE/MIR (59) 149 102 m_b330s601i10 13868 chrXptel1M 207611 CCCCAGTTCATTTTATAGACGAGG-AACTGA-GCCCACATAGCTAGGAAG 207658 --i i i - - v v v -- C MIR3#SINE/MIR 149 CCCC--CTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGT--GAAG 104 chrXptel1M 207659 TG 207660 C MIR3#SINE/MIR 103 TG 102 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 14.38 CpG sites = 3, Kimura (unadjusted) = 14.38 Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.12 (6 / 49), avg. gap size = 1.00 (6 / 6) 246 30.09 0.00 5.56 chrXptel1M 207637 207731 (792269) C MIRc#SINE/MIR (170) 98 9 m_b330s601i11 13869 chrXptel1M 207637 CTGAGCCCACATAGCTAGGAAGTGTCAGAGGATATATTTGCACTCTCAGA 207686 ii vi i v v vvviv i i v -- i i C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAA--CCCAGG 51 chrXptel1M 207687 TTTTCCTGACTCCAGGCAGCAGTGCCACCTACTCACTCCAGCACA 207731 i i i-v --i vii v v C MIRc#SINE/MIR 50 TCTTCCTGACTCCAAGT-CCAGTGC--TCTTTCCACTGCACCACA 9 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.34 CpG sites = 15, Kimura (unadjusted) = 39.18 Transitions / transversions = 1.25 (15/12) Gap_init rate = 0.05 (5 / 94), avg. gap size = 1.00 (5 / 5) 180 39.02 7.17 1.60 chrXptel1M 207763 207999 (792001) L2#LINE/L2 2833 3082 (0) m_b330s601i12 13870 chrXptel1M 207763 CCCTGTTCAAGTAACGCCAGTGGCTCCCTATTTCTCT-AGGATCAA--CT 207809 i i ivvv v i i i i v - ii v -- i L2#LINE/L2 2833 CTCTGCTCAAAACCCTCCAATGGCTTCCCATCTCACTCAGAGTAAAAGCC 2882 chrXptel1M 207810 AGGAAATCTCTG-ATTGGCTTTCAAATTCCTTCATAACCT--TCCTCCCT 207856 -- i ii i- v i v ivi v i i -- i v L2#LINE/L2 2883 A--AAGTCCTTACAATGGCCTACAAGGCCCTACATGATCTGGTCCCCCGT 2930 chrXptel1M 207857 C-CCACTTT--TCCAGTCTTTGAAAACTTTTCTTCCTCCACTTCCTCTGA 207903 i- v i --i ivi iiv vv i i -- ii i iv i v L2#LINE/L2 2931 TACCTCTCTGACCTCATCTCCTACCACTCTCC--CCCTCGCTCACTCCGC 2978 chrXptel1M 207904 CCCAGTGACACTAATTTCTTTGCTATTTCTTA------CCTGAAACACTC 207947 i iv iiii i i i ii------ v iv i L2#LINE/L2 2979 TCCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACACGCCAGGCACGCTC 3028 chrXptel1M 207948 CATCTCCAGACCTCCCGCACTTG--GAACTCTCTTCCTCATCTGTTCTTC 207995 vv ii iv iiii -- vv i v vivvi i L2#LINE/L2 3029 CCGCCTCAGGGCCTTTGCACTTGCTGTTCCCTCTGCCTGGAACGCTCTTC 3078 chrXptel1M 207996 TTTC 207999 iii L2#LINE/L2 3079 CCCC 3082 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 54.89 CpG sites = 61, Kimura (unadjusted) = 60.27 Transitions / transversions = 2.03 (61/30) Gap_init rate = 0.05 (12 / 236), avg. gap size = 1.75 (21 / 12) 188 37.07 17.07 0.00 chrXptel1M 207853 208057 (791943) L2b_3end#LINE/L2 14 253 (213) m_b330s601i13 13870 chrXptel1M 207853 CCCTCCCACTTTTCCAGTCT--TTGAAAACTTTTCTTCCTCCACTTCCTC 207900 iv i i i i i -- ivvvv ivi i iiii iv L2b_3end#LINE 14 CCCCGCTACCTCTCCGGCCTCATCTCCTACCACTCTCCCCTTGCTCACTC 63 chrXptel1M 207901 TGACCCAGTGACACTAATTTCTTTGCTATTTCTT--ACCTGAAACACTC- 207947 vi iv iiii i i i i-- vi vv ?i - L2b_3end#LINE 64 TGCTCCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACACGCCANGCTCN 113 chrXptel1M 207948 ----CATCTCCAGACCT--------------CCCGC-ACTTGGAACTCTC 207978 ---- ii vi i -------------- v -i i v i L2b_3end#LINE 114 CTCCCGCCTCAGGGCCTTTGCACNTGCTGTTCCCTCTGCCTGGAACGCCC 163 chrXptel1M 207979 TTCCTCATCTGTTCTTCT------TTCTT-----TCCATCATATTTCAAC 208017 i i v vi ------i i ----- v vi i i L2b_3end#LINE 164 TTCCCCACCTCTTCGCCTGGCCAACTCCTACTCATCCTTCAGGTCTCAGC 213 chrXptel1M 208018 TAAAATCCCACATTCTGTAAGAAGCATTTCCTGGTCCCTC 208057 v vi v i viii vi i ii i L2b_3end#LINE 214 TCAAATGTCACCTCCTCCGGGAAGCCCTCCCTGACCCCCC 253 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 49.32 CpG sites = 52, Kimura (unadjusted) = 56.08 Transitions / transversions = 2.17 (52/24) Gap_init rate = 0.04 (8 / 204), avg. gap size = 4.38 (35 / 8) 291 26.09 9.57 0.00 chrXptel1M 208492 208606 (791394) L2b_3end#LINE/L2 308 433 (33) m_b330s601i14 13870 chrXptel1M 208492 GGTTGTTTTTGTCT---TACAAGTG-ATTTTCCACATTGGACAATGAGCT 208537 i ?v --- v v-i i i v i i vi L2b_3end#LINE 308 GGTTATNATTGTCTGNTTACATGTCTGTCTCCCCCACTAGACTGTGAGCT 357 chrXptel1M 208538 CCTTGAAAGCAAGGAGTGC-TTTG-CTT-TTC-CTG--GTATCCCTGG-A 208580 v ii i vi ?- i - - - i -- ii -i L2b_3end#LINE 358 CCGTGAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTGTATCCCCAGCG 407 chrXptel1M 208581 ATTACCACAGGGCCTGGCCTATATTA 208606 vi v ? vi i v L2b_3end#LINE 408 CCTAGCACAGNGCCTGGCACACAGTA 433 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.12 CpG sites = 19, Kimura (unadjusted) = 34.24 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.07 (8 / 114), avg. gap size = 1.38 (11 / 8) 398 27.92 4.35 2.67 chrXptel1M 210973 211156 (788844) C L1ME4c_3end#LINE/L1 (275) 555 369 m_b330s551i4 13871 chrXptel1M 210973 ATAATATTCCATAACATTCATATACCACAATTTACCCAACCATTCTCCAA 211022 vivi ?v i i ii i v C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chrXptel1M 211023 TGCATGGGCATCCATTCATTTTTCAGTTTCTGGCCACTACAAAGAGGGCT 211072 vvv i ii vvivv i i i v i i i v iv C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCT 456 chrXptel1M 211073 GCCACAAACA--TTCGTGCACATAGAGGTCCCTTTCCCTTCTTT---AGT 211117 v ii -- i ----- i i --- v C L1ME4c_3end#L 455 GCAATGAACATCTTCGTGCATATAG-----CTTTTTCCTTCTTTTGAATT 411 chrXptel1M 211118 ATCTCTTTAGGGTATAAGCCCAGTAGTAG---CACTGAATCA 211156 i i i v vv v i ---i ii C L1ME4c_3end#L 410 ATTTCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCA 369 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.29 CpG sites = 30, Kimura (unadjusted) = 36.20 Transitions / transversions = 1.50 (30/20) Gap_init rate = 0.04 (8 / 183), avg. gap size = 1.62 (13 / 8) 277 24.66 4.11 0.00 chrXptel1M 213553 213625 (786375) L1ME5_3end#LINE/L1 255 330 (611) m_b330s551i5 13872 chrXptel1M 213553 ATATGGGAAAAGTGGGACACTAATGTACTATTGGTGGAGTTGTGAACTGA 213602 i i ? vv i v v i ii iiv ii i L1ME5_3end#LI 255 ATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACTGG 304 chrXptel1M 213603 TGC---CATTCTGGAGAACAATTTGG 213625 --- i i L1ME5_3end#LI 305 TGCAGCCATTCTGGAGAGCAATCTGG 330 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 31.89 CpG sites = 13, Kimura (unadjusted) = 31.89 Transitions / transversions = 2.60 (13/5) Gap_init rate = 0.01 (1 / 72), avg. gap size = 3.00 (3 / 1) 229 27.03 0.00 0.00 chrXptel1M 213770 213843 (786157) L1ME1_3end#LINE/L1 492 565 (361) m_b330s551i6 13872 chrXptel1M 213770 ATACCCATCAATTGGGAAAAGGCTGAACAAGTTGTGGTATATGAAGGTAA 213819 ii i? vi v v i i vv vii L1ME1_3end#LI 492 ATGTCCATCAACNGGTGAATGGATAAACAAATTGTGGTATATCCATACAA 541 chrXptel1M 213820 TGAAATACTATTGTGCTATAAGAA 213843 i i vv v i L1ME1_3end#LI 542 TGGAATACTACTCAGCAATAAAAA 565 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.72 CpG sites = 11, Kimura (unadjusted) = 34.72 Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.00 (0 / 73), avg. gap size = 0.0 (0 / 0) 50 0.00 0.00 0.00 chrXptel1M 214094 214136 (785864) (TG)n#Simple_repeat 1 43 (0) c_b330s251i3 13873 chrXptel1M 214094 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 214136 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 43 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 992 31.87 1.37 4.02 chrXptel1M 216191 216700 (783300) L1ME5_3end#LINE/L1 56 552 (389) m_b330s551i7 13874 chrXptel1M 216191 CTCCAACTGACAAATGGTCAAAGGATACGAACAGATAATTTTCAGATGAA 216240 i iv v v i ii v v i L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chrXptel1M 216241 GAAATT--AAAGTCATTTCTAGTCATATGAAAAATTGTTTTAAATCACTA 216288 ii-- v - vv v - i iv i iv v i L1ME5_3end#LI 106 GAAACCCGAAAGGC-TAACAAG-CATATGAAGAGATGCTCAAACTCATTA 153 chrXptel1M 216289 TTGATTAGAGAAATGCAAATTAAGACAACTCCAAGGTATTATTTCTTACC 216338 v i i i vvii i i i ivi L1ME5_3end#LI 154 GTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACC 203 chrXptel1M 216339 TCTCAGATGGACTAAATTGATAGGAAA--AGATAACGAAGAATATTGGAG 216386 v i iv i v v -- i i--i i vvi i i v L1ME5_3end#LI 204 TATTAGACTGGCAAAAAT--TAGAAAGCTGGATAATGCCAAGTGTTGGCG 251 chrXptel1M 216387 AGGATGTAGGACAATTAGGACATGCATACATCATTGG-GGGAGTTGTGAA 216435 i iv? vi i viv i iiii - - ii L1ME5_3end#LI 252 AGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAG-TGTAGA 300 chrXptel1M 216436 CTGATCCAACCATTCTGAAGAGGAATTTAGAACTA--TACCCAAAGAGCT 216483 i v i i v i i v v -- vi ---i L1ME5_3end#LI 301 CTGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAA---TT 347 chrXptel1M 216484 ATGCAACTATGCATACCCTTTGATCCAGCAGTGTTTCTACTAGGCCTGTA 216533 v i -- i v i i viiv v i iv i L1ME5_3end#LI 348 AAGTA--TACGCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATA 395 chrXptel1M 216534 TCCCAAAGAGATCAAAAAAAAAAAAAAAAAGGGAAAAAGGATCCACATGT 216583 i ivvv v v iivvv v i---------- L1ME5_3end#LI 396 TCCCAAAGAAATTCTCACACAGGTCCATAAGGGG----------ACATGT 435 chrXptel1M 216584 GCAAATATGTTTGTGGCAGCCCTTTTTGTAGAGACAAGGAACTGGAAACT 216633 i i iv ii v vi v i v i ii ii ii v L1ME5_3end#LI 436 ACGAGGATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCA 485 chrXptel1M 216634 GAGTGGATGCCCATCAATTGGAGAATGGCTGAATAAATTGTGGTATATGA 216683 ivv i i v v i v iii v iv v L1ME5_3end#LI 486 ACCTGGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGC 535 chrXptel1M 216684 GTGTTATGGAATATTAT 216700 iiiii i i L1ME5_3end#LI 536 ACACCATGGAGTACTAT 552 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.69 CpG sites = 95, Kimura (unadjusted) = 43.18 Transitions / transversions = 1.56 (95/61) Gap_init rate = 0.05 (24 / 509), avg. gap size = 1.12 (27 / 24) 22 10.38 0.00 0.00 chrXptel1M 216850 216881 (783119) (T)n#Simple_repeat 1 32 (0) m_b330s252i11 13875 chrXptel1M 216850 TTTTCTTTTCCTTTTTTTTTTTTTTTTTTTTT 216881 i ii (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 32 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 439 21.12 2.21 9.45 chrXptel1M 216885 217020 (782980) C MIRc#SINE/MIR (141) 127 1 m_b330s601i15 13876 chrXptel1M 216885 CTGAGGC-AATTGGGGTT--GTGACTTGCCCAAGGTCACACAGCCAGGAA 216931 -v vv i -- i --- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG--- 81 chrXptel1M 216932 GTGTTAAGTGTCTGAGACCAGACACTTGAACTCAGGTCCTCCCAACTTCA 216981 ---- v v - i i- i i i ii i C MIRc#SINE/MIR 80 ----TAAGTGGCAGAG-CCGGG-ACTCGAACCCAGGTCTTCCTGACTCCA 37 chrXptel1M 216982 GGGCTGGTGCTCTAGCCACTGTGTCACCTAGCTGCCCCG 217020 i v ii vv iii ---i i C MIRc#SINE/MIR 36 AGTCCAGTGCTCTTTCCACTGCACCAC---ACTGCCTCG 1 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 23.17 CpG sites = 18, Kimura (unadjusted) = 25.37 Transitions / transversions = 2.25 (18/8) Gap_init rate = 0.10 (14 / 135), avg. gap size = 1.07 (15 / 14) 13 13.57 0.00 8.57 chrXptel1M 217140 217177 (782823) (TTG)n#Simple_repeat 1 35 (0) m_b330s252i12 13877 chrXptel1M 217140 TTGTTGTTAATGTTGTTGTTTGCTTGCTTGTTTTTTTT 217177 iv - - - v v (TTG)n#Simple 1 TTGTTGTTGTTGTTGTTG-TTG-TTG-TTGTTGTTGTT 35 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.08 (3 / 37), avg. gap size = 1.00 (3 / 3) 197 41.65 0.35 7.20 chrXptel1M 218632 218913 (781087) L2d2_3end#LINE/L2 15 278 (277) m_b330s601i16 13878 chrXptel1M 218632 CCTAATCTGTCTGGTTTTCTGATGTATTTGCCATCACTCCTCTTCATTTC 218681 i i ?i --- i v viv i v ii i i ? ---- L2d2_3end#LIN 15 CCCAACCTNCCT---TTCCAGCCTTATCTCCCACTATTCCCCTNCA---- 57 chrXptel1M 218682 TTCTATATCTTGGCTATATCCCAGCCAAAGCATTCTTCTTGTTCTTCCCC 218731 -- v vvi iv ----- viiv v iii v i L2d2_3end#LIN 58 --CGAACCCTCCGCT-----CCAGCCAAACTGGTCTACTCACTGTCCCCC 100 chrXptel1M 218732 AAGCTTGCAGTTTTCTCTCTCGCTCCCATGACTTGGCTCAGGCAATAAAT 218781 i i vi vv viv ?i i ii iii v v v vi --- L2d2_3end#LIN 101 GAACACGCCTTGCGCNTTCCCGCCTCTGCGCCTTTGCTCACGCCGT---T 147 chrXptel1M 218782 CTCCTGTGCTTCAAGTACACTCTCTCCTCACCTCTTTGTCTTAGAATCTG 218831 i i-i i vi i i v ii i i vi iviv v ivi i- L2d2_3end#LIN 148 CCCCC-CGCCTGGAATGCCCTTCCCCTTCCTCTCCACCTATCCAAATCC- 195 chrXptel1M 218832 TGGTT-TCCTTCAGGACTCGGTTTACAGACTGCTACCTCCAGGAAGCTCC 218880 ivii- i i i i i i v v? ii iv iv iii L2d2_3end#LIN 196 TACCCATCCTTCAAGGCCCAGCTCAAATNCCACCTCCTCCGTGAAGCCTT 245 chrXptel1M 218881 TCCTGATTCCCCCAGTGTTTAATGCTCTCTTTC 218913 i iiv i iviv? i v ii L2d2_3end#LIN 246 CCCTGACCACTCCAGCCCGNAGTGATCTCTCCC 278 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 60.34 CpG sites = 72, Kimura (unadjusted) = 68.91 Transitions / transversions = 1.95 (72/37) Gap_init rate = 0.07 (20 / 281), avg. gap size = 1.00 (20 / 20) 268 37.67 5.58 2.71 chrXptel1M 218661 218911 (781089) L2b_3end#LINE/L2 18 275 (191) m_b330s601i17 13878 chrXptel1M 218661 GCCATCACTCCT-CTTCATTTCTT----CTATATCTTGGCTA----TATC 218701 i i v v- i i i ---- v vi i v v---- iii L2b_3end#LINE 18 GCTACCTCTCCGGCCTCATCTCCTACCACTCTCCCCTTGCTCACTCTGCT 67 chrXptel1M 218702 CCAGCCAAAGCATTCTTCTTGTTCTTCCCCAAGCTTGCAGTTTTCTCTCT 218751 v viivi i i v i i i vi vi?vi ? i L2b_3end#LINE 68 CCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACACGCCANGCTCNCTCC 117 chrXptel1M 218752 CGCTCCCATGACTTGGCTCAGGCAATAAATCTCCTGTGCTTCAAGTACAC 218801 ii viv v v v ?v vi --- - v i vi -- i L2b_3end#LINE 118 CGCCTCAGGGCCTTTGCACNTGCTGT---TC-CCTCTGCCTGGA--ACGC 161 chrXptel1M 218802 TCTCTCCTCACCTCTTTGTCTTAGAATCTGTGGTT--TCCTTCAGGACTC 218849 i - i i i vivv v vivii -- v L2b_3end#LINE 162 CCT-TCCCCACCTCTTCGCCTGGCCAACTCCTACTCATCCTTCAGGTCTC 210 chrXptel1M 218850 GGTTTACAGACTGCTACCTCCAGGAAGCTCCTCCTGATTCCCC---CAGT 218896 i i i v viiii iv i i ii ii --- v v L2b_3end#LINE 211 AGCTCAAATGTCACCTCCTCCGGGAAGCCCTCCCTGACCCCCCAGGCCGG 260 chrXptel1M 218897 GTTTAATGCTCTCTT 218911 iviii i i L2b_3end#LINE 261 GTCAGGCGCCCTCCT 275 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 51.18 CpG sites = 57, Kimura (unadjusted) = 56.73 Transitions / transversions = 1.63 (57/35) Gap_init rate = 0.05 (12 / 250), avg. gap size = 1.75 (21 / 12) 275 25.47 0.00 7.04 chrXptel1M 220051 220126 (779874) L2a_3end#LINE/L2 429 499 (18) m_b330s601i18 13879 chrXptel1M 220051 TCAGTTTTGCTTGTTATTCTGTATTCCCGTTGCTTAATACTGATATGCTT 220100 v i iii i-- i ivi i iv v --- i L2a_3end#LINE 429 TCTGTTTTGTTCACTG--CTGTATCCCCAGCGCCTAGAACAG---TGCCT 473 chrXptel1M 220101 TACACATAGTAGGTGCTCAATAAATA 220126 vi i L2a_3end#LINE 474 GGCACATAGTAGGCGCTCAATAAATA 499 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.18 CpG sites = 13, Kimura (unadjusted) = 32.49 Transitions / transversions = 2.60 (13/5) Gap_init rate = 0.07 (5 / 75), avg. gap size = 1.00 (5 / 5) 260 22.22 4.00 4.00 chrXptel1M 221577 221651 (778349) C MIR#SINE/MIR (120) 142 68 m_b330s601i19 13880 chrXptel1M 221577 CATTT--CAGATGAGGAAATCAAAGCAAACAG-GATTAAATGACTTGCCT 221623 -- iii i v v - i i i i C MIR#SINE/MIR 142 CATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCC 93 chrXptel1M 221624 GTGAGCACACTGCTTAGATTAGGTGGCA 221651 iv iv v - -- i C MIR#SINE/MIR 92 AAGGTCACACAGC-TAG--TAAGTGGCA 68 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.24 CpG sites = 11, Kimura (unadjusted) = 27.24 Transitions / transversions = 2.20 (11/5) Gap_init rate = 0.07 (5 / 74), avg. gap size = 1.20 (6 / 5) 213 31.65 6.73 2.78 chrXptel1M 222808 222911 (777089) C MIRc#SINE/MIR (71) 197 90 m_b331s601i0 13881 chrXptel1M 222808 TTGTTTCTTACAACATCACATTTGTAAG-TAGA---GGCGAATGTTATTG 222853 v i i v v --- i - i--- iii i i C MIRc#SINE/MIR 197 TTGATCCTCACAACAACCC---TGTGAGGTAGGCAGGGCAGGTATTATTA 151 chrXptel1M 222854 TTCCCATTCTGGGGATCAGGAATCAAAAACT--GTCACTTCAAGTGAC-A 222900 i i ivi v v vi ii -- vv vv i -v C MIRc#SINE/MIR 150 TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTT 101 chrXptel1M 222901 ATCCAAAGTCA 222911 ii i C MIRc#SINE/MIR 100 GCCCAAGGTCA 90 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.95 CpG sites = 20, Kimura (unadjusted) = 42.95 Transitions / transversions = 1.67 (20/12) Gap_init rate = 0.07 (7 / 103), avg. gap size = 1.43 (10 / 7) 731 34.46 5.96 3.27 chrXptel1M 223046 223582 (776418) L2#LINE/L2 2464 3014 (68) m_b331s601i1 13882 chrXptel1M 223046 TTCTCATATTGATTCTCATATCCCCCCGCCCCCGCACT-TTCCCTACTAC 223094 i v v vvii v i iv i - i v - i iiv L2#LINE/L2 2464 TCCTGATCTTCCCCCTCAAACCTGCTC-CTCCCGCAGTCTTCCCCATCTC 2512 chrXptel1M 223095 TTTCAAGGGCACCTCC------CCAGGTCCT---------AACATATGAG 223129 vv ? v v ------ v v --------- v vv L2#LINE/L2 2513 AGTNAATGGCAACTCCATCCTTCCAGTTGCTCAGGCCAAAAACCTTGGAG 2562 chrXptel1M 223130 TCAGCCTAGAGTCTTCGCTCTCTTTCACCATTCTCCCCTGCCTCCCATAT 223179 v v v ---- ----- ----i vi i L2#LINE/L2 2563 TCATCCTTGACTC----CTCTCTTTC-----TCTC----ACACCCCACAT 2599 chrXptel1M 223180 CCAAGCGGTTGTCAAGATCTGCCAATTCTACCTTTACAACATCTCTCTAA 223229 v vi iiv ivi i iii i v i v ivv L2#LINE/L2 2600 CCAATCCATCAGCAAATCCTGTCGGCTCTACCTTCAAAATATATCCAGAA 2649 chrXptel1M 223230 TATATCCCCTTCTCTCCTCTGACATTGTCACC-CCTTGGTGTAGTCCCTG 223278 viiv v v v ivv i i - i vi iv viv L2#LINE/L2 2650 TCCGACCACTTCTCACCACCTCCACTGCCACCACCCTGGTCCAAGCCACC 2699 chrXptel1M 223279 GTCACCTCACAACTGGATTGTTGCAATGGCC-ATTAGTGGGTCTGTCTGC 223327 i i v iv ii i -vi iiv vi L2#LINE/L2 2700 ATCATCTCTCGCCTGGATTACTGCAATAGCCTCCTAACTGGTCTCCCTGC 2749 chrXptel1M 223328 TTCAAGTCTCTCCACGCTCCAGTCCACCTTCCATTTAGCCACTTA---GA 223374 v vi iv v v ? i iii v ivi vi ivi--- L2#LINE/L2 2750 TTCCACCCTTGCCCCCCTNCAGTCTATTCTCAACACAGCAGCCAGAGTGA 2799 chrXptel1M 223375 TTCCCCTAAAACACAGGTCTGATTATG--ACCCC---ACTCAAGAAAGTC 223419 i iii ii i v i -- i ---i i vvv L2#LINE/L2 2800 TCCTTTTAAAACGTAAGTCAGATCATGTCACTCCTCTGCTCAAAACCCTC 2849 chrXptel1M 223420 CAGTGGCTCCCTATCACCTCCAGGATCAAATACAAAATGTTGTT----TG 223465 i i i v vii ii v vv -- iv ---- L2#LINE/L2 2850 CAATGGCTTCCCATCTCACTCAGAGTAAAAGCCAAA--GTCCTTACAATG 2897 chrXptel1M 223466 ACATTCTAAGCTCTTTATAGCCTAGCCCCTTTTTACCTTTCCAGTCT--T 223513 i v v v i i vi iii i i iiv i iiii -- L2#LINE/L2 2898 GCCTACAAGGCCCTACATGATCTGGTCCCCCGTTACCTCTCTGACCTCAT 2947 chrXptel1M 223514 CTTTCACCTTACTCCTCAATACTCCCTCTTCAGTCCAGTAACACTGACCT 223563 iii viv i vvii v iv -- iv i L2#LINE/L2 2948 CTCCTACCACTCTCCCCCTCGCTCACTCCGC--TCCAGCCACACTGGCCT 2995 chrXptel1M 223564 CCTGGCTGTTCCACAAACA 223582 v v i L2#LINE/L2 2996 CCTTGCTGTTCCTCGAACA 3014 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.95 CpG sites = 101, Kimura (unadjusted) = 47.98 Transitions / transversions = 1.29 (101/78) Gap_init rate = 0.05 (28 / 536), avg. gap size = 1.79 (50 / 28) 251 27.04 3.45 4.35 chrXptel1M 223487 223602 (776398) L2b_3end#LINE/L2 10 124 (342) m_b331s601i2 13882 chrXptel1M 223487 CTAGCCCCTTTTTACCTTTCCAGTCT--TCTTTCACCTTACTCCTCAATA 223534 i vi -- i i i -- iii viv i v- i L2b_3end#LINE 10 CTGGCCCCGCT--ACCTCTCCGGCCTCATCTCCTACCACTCTCCCCT-TG 56 chrXptel1M 223535 CTCCCTCTTCAGTCCAGTAACACTGACCTCCTGGCTGTTCCACAAACAAG 223584 v v -- iv i v v i v L2b_3end#LINE 57 CTCACTCTGC--TCCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACACG 104 chrXptel1M 223585 --ACGCTTCATCTGGGCTTA 223602 -- ? i?v iv v i L2b_3end#LINE 105 CCANGCTCNCTCCCGCCTCA 124 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.20 CpG sites = 17, Kimura (unadjusted) = 35.02 Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.06 (7 / 115), avg. gap size = 1.29 (9 / 7) 12 35.79 2.25 2.25 chrXptel1M 225566 225654 (774346) (ATATAC)n#Simple_repeat 1 89 (0) m_b331s252i0 13883 chrXptel1M 225566 ATATGCATATACGTATTAGCACATA-GTATGTATATAGAGAGAAAGAGA- 225613 i i - - i -i ii v v v v v v - (ATATAC)n#Sim 1 ATATACATATACATA-TA-CATATACATATACATATACATATACATATAC 48 chrXptel1M 225614 AGACAACCATACACATCCATATGTATGTAAATATATATATA 225654 v i vvi i v ii i v i (ATATAC)n#Sim 49 ATATACATATACATATACATATACATATACATATACATATA 89 Matrix = Unknown Transitions / transversions = 1.18 (13/11) Gap_init rate = 0.05 (4 / 88), avg. gap size = 1.00 (4 / 4) 15 34.97 0.00 0.00 chrXptel1M 225632 225685 (774315) (AT)n#Simple_repeat 1 54 (0) m_b331s252i1 13884 chrXptel1M 225632 ATATGTATGTAAATATATATATAGAGAGAGAGAGAGAGAGATGGAGATAT 225681 i i v v v v v v v v v v iv v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chrXptel1M 225682 ATAT 225685 (AT)n#Simple_ 51 ATAT 54 Matrix = Unknown Transitions / transversions = 0.25 (3/12) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 235 35.71 0.00 0.00 chrXptel1M 225725 225794 (774206) L2b_3end#LINE/L2 397 466 (0) m_b331s601i3 13882 chrXptel1M 225725 TACTCTTGGTATCTAGCACTTGGCTTGCTACACAGGAAGTACTCAATAGG 225774 ii iii iii vv? i vi v i ii i ii L2b_3end#LINE 397 TATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAA 446 chrXptel1M 225775 TATATGAGAAATAAATGAAT 225794 v vvi i L2b_3end#LINE 447 TATTTGTTGAATGAATGAAT 466 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 47.31 CpG sites = 18, Kimura (unadjusted) = 54.47 Transitions / transversions = 2.57 (18/7) Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0) 477 23.49 3.65 3.65 chrXptel1M 225834 225970 (774030) MIR3#SINE/MIR 10 146 (62) m_b331s601i4 13885 chrXptel1M 225834 TAGCTAAATCAGGTAGGGGGCACTTGGTTTGGAATCAGGAAGGCCTGAGT 225883 i i i- -- i i v- ii v i - i i MIR3#SINE/MIR 10 TGGCTGAG-CAG--AGAGAGCACG-GACTGGGAGTCAGGA-GACCTGGGT 54 chrXptel1M 225884 TCAAATGTGACCTCAGATACTTGCTAGCTGTTTAACCCTGG-CAAGTCTC 225932 v i viviv v vi vi ? v i i - v MIR3#SINE/MIR 55 TCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCAC 104 chrXptel1M 225933 TTCACCTCT----GCCTCAATTTCCTCATCTCTAAAATGGGG 225970 ---- i v i MIR3#SINE/MIR 105 TTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGG 146 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.00 CpG sites = 19, Kimura (unadjusted) = 29.10 Transitions / transversions = 1.58 (19/12) Gap_init rate = 0.05 (7 / 136), avg. gap size = 1.43 (10 / 7) 810 25.71 2.34 1.86 chrXptel1M 225851 226064 (773936) MIRb#SINE/MIR 28 242 (26) m_b331s601i5 13885 chrXptel1M 225851 GGGCACTTGGTTTGGAATCAGGAAGGCCTGAGTTCAAATGTGACCTCAGA 225900 i vv v i iv i i i viviv v v MIRb#SINE/MIR 28 GAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTCTGC 77 chrXptel1M 225901 TACTTGCTAGCTGTTTAACCCT-GGCAAGTCTCTTCACCTCT----GCCT 225945 i i v i i - iv v ---- MIRb#SINE/MIR 78 CACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCT 127 chrXptel1M 225946 CAATTTCCTCATCTCTAAAATGGGGATCATCACAGCACCTCTCTCCCATG 225995 i v v --- ii vi v v MIRb#SINE/MIR 128 CAGTTTCCTCATCTGTAAAATGGGGATAAT---AATACCTACCTCGCAGG 174 chrXptel1M 225996 GTTGATGTGGGAAATCGGATGAAATAATAATTGGAAAGCCCTTAGTACAC 226045 v i -i iii i ivv v v i v MIRb#SINE/MIR 175 GTTGTTGTGAG-GATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAG 223 chrXptel1M 226046 TATCCGGCACACAGTGGGC 226064 ii i i ii MIRb#SINE/MIR 224 TGCCTGGCACATAGTAAGC 242 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.70 CpG sites = 31, Kimura (unadjusted) = 32.12 Transitions / transversions = 1.35 (31/23) Gap_init rate = 0.03 (6 / 213), avg. gap size = 1.50 (9 / 6) 183 31.34 1.49 0.00 chrXptel1M 226185 226251 (773749) C MIR3#SINE/MIR (0) 208 141 m_b331s601i6 13886 chrXptel1M 226185 GAATCATCCAATCTTTGCATCTCAGTATCAGAAGGGACCTCCAAGGTAAT 226234 vv v v v v viiii ivi i v C MIR3#SINE/MIR 208 GAATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCAT 159 chrXptel1M 226235 GTAG-GTAACCCCTACAT 226251 v -vi iv C MIR3#SINE/MIR 158 CTAGTCCAACCCCCTCAT 141 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.78 CpG sites = 9, Kimura (unadjusted) = 40.78 Transitions / transversions = 0.75 (9/12) Gap_init rate = 0.02 (1 / 66), avg. gap size = 1.00 (1 / 1) 557 20.36 5.76 8.09 chrXptel1M 226449 226587 (773413) C MIRc#SINE/MIR (123) 145 10 m_b331s601i7 13887 chrXptel1M 226449 ATTTTACAGATGAGGAAATCAAGGC----AAAC----AATAACTTGCACA 226490 iii ---- i v---- i i v C MIRc#SINE/MIR 145 ATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCA 96 chrXptel1M 226491 GAGTCACACAGCTATTATGTGTCTGAGGCTGGATTTGAACCCAGGTCTTC 226540 ii v v v v v v i i C MIRc#SINE/MIR 95 AGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTC 46 chrXptel1M 226541 CTGGGAGTTAGCTGACTCCAGGCCTAGCACTCTATCCACTGTATCAC 226587 ----------- i i i ii v i i C MIRc#SINE/MIR 45 -----------CTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 23.21 CpG sites = 17, Kimura (unadjusted) = 24.26 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.09 (13 / 138), avg. gap size = 1.46 (19 / 13) 12 4.75 0.00 8.33 chrXptel1M 230115 230140 (769860) (TCCC)n#Simple_repeat 1 24 (0) m_b331s252i2 13888 chrXptel1M 230115 TCCCTTCCCTCCCTCCACCCCCTCCC 230140 - - i (TCCC)n#Simpl 1 TCCC-TCCCTCCCTCC-CTCCCTCCC 24 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.08 (2 / 25), avg. gap size = 1.00 (2 / 2) 1374 30.11 1.11 1.27 chrXptel1M 230459 231087 (768913) C L1ME4c_3end#LINE/L1 (191) 639 12 m_b331s551i0 13889 chrXptel1M 230459 TTCTGCTCATTTCACTTACCATCAGCTCATGTAAGTGTCTCCAAGCCTCT 230508 iv v i vv iv vi - i v iiv C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATAAACAT-TTTCCATGTTGCT 591 chrXptel1M 230509 CTGTATTCATCCTGCTGGTCATTTCTTACAGAACAATAATATTCCATAAC 230558 vii v v v iv vi i v ii vvvv viv C L1ME4c_3end#L 590 ACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCGA 541 chrXptel1M 230559 ATTCATATACCACAATTTACCCAACCATTCTCCAATTGATGGGCATCCAT 230608 i ?v i i ii i v v i ii v C L1ME4c_3end#L 540 GTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAG 491 chrXptel1M 230609 TCATTTTCCAGTTTCTGGCCACTACAAACAGGGCTACCACAAACATTTTG 230658 vivv i i v i i i i iv i v ii i v C L1ME4c_3end#L 490 GTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTC 441 chrXptel1M 230659 GCACATACAGGTCCCTTTCCCTTCTTT--AAG-ATTTCTTTGGGTTATAA 230705 ii i --- i i -- v- i i v v v C L1ME4c_3end#L 440 GTGCATATAG---CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAAT 394 chrXptel1M 230706 GCCAAGTCGTAGCACTGCTGGATCAAAGGGTATGCACAGTTTGATAACTT 230755 v v vv i v i i i v v v ii i C L1ME4c_3end#L 393 TCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTC 344 chrXptel1M 230756 TTGGGGCATAATTCCAGATTGCTCTCCAGAATGGCTGGATTCGTTCACAA 230805 ivi i v v i i i v i v iivi i ? C L1ME4c_3end#L 343 TTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACAN 294 chrXptel1M 230806 CTCCACCAACAATGCATCAGTGTCCCAGTTTTCCCATATCCCCTCCAACA 230855 iv i i v ? v iv ii ? i v i C L1ME4c_3end#L 293 TGCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGCA 244 chrXptel1M 230856 TTCATCATTATCTTTTCCTGTCATCTTAGCCAATCTGACAGGTGTGTAGT 230905 vivi vv ii vvv i v i i i i i iv i C L1ME4c_3end#L 243 TTGGGTATTATCAATTTTTTAAATTTTTGCTAATTTAATAGGCGTAAAAT 194 chrXptel1M 230906 GGTATCTCAGAGTTGTCTTAATTTGCATTTCTCTGATCAATAGTGATTTG 230955 vv ii i i v i vv v C L1ME4c_3end#L 193 GGTATCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACTAGCGAGGTT 144 chrXptel1M 230956 GAGCACTCTTTCATATGAGTGGTAATAGTTTCAATTTCATCATCTGAAAA 231005 i i i i i vv v v ivi? vv v v ? vi C L1ME4c_3end#L 143 GAACATTTTTCCATGTGTTTGTTTACTANTTGTATTTCCTCTTNTGTGAA 94 chrXptel1M 231006 TTGTCTGTTCATATCCTTTGACCATTTATCAATTGGAGAATGGCTTGA-- 231053 i v v i---- v -- C L1ME4c_3end#L 93 TTGTCTGTTCATGTCCTTTGCCCATTTATCTATTGGG----GTCTTGATN 48 chrXptel1M 231054 --TTTCTTATAAATTACAGTCAATTCTCTATATATT 231087 -- v vv i v ii i ? C L1ME4c_3end#L 47 TTTTTCTTATCAATTTGAATGAGCTCTTTATATANT 12 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.47 CpG sites = 100, Kimura (unadjusted) = 39.83 Transitions / transversions = 1.15 (100/87) Gap_init rate = 0.02 (12 / 628), avg. gap size = 1.25 (15 / 12) 1461 27.65 0.55 1.85 chrXptel1M 230544 231092 (768908) C L1ME3G_3end#LINE/L1 (376) 548 7 m_b331s551i1 13889 chrXptel1M 230544 ATAATATTCCATAACATTCATATACCACAATTTACCCAACCATTCTCCAA 230593 i ii vv i iii i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chrXptel1M 230594 TTGATGGGCATCCATTCATTTTCCAGTTTCTGGCCACTACAAACAGGGCT 230643 i ii vvivv i i v i i iv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chrXptel1M 230644 ACCACAAACATTTTGGCACATACAGGTCCCTTTCC-CTTCTTTAAG-ATT 230691 i v ii ii v i i ?-- i v v - v v vii - C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATT 401 chrXptel1M 230692 TCTTTGGGTTATAAGCCAAGTCGTAGCACTGCTGGATCAAAGGGTATGCA 230741 ? i v v v? ? vv i v i i i C L1ME3G_3end#L 400 TCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCG 351 chrXptel1M 230742 CAGTTTGATAACTTTTGGGGCATAATTCCAGATTGCTCTCCAGAATGGCT 230791 v --- v iiviv v v i i i ? C L1ME3G_3end#L 350 CATTTT---AAATTTTAATAGATACTGCCAAATTGCCCTCCAAAANGGCT 304 chrXptel1M 230792 GGATTCGTTCACAACTCCACCAACAATGCATCAGTGTCCCAGTTTTCCCA 230841 v iivi i vii i i i v v v v i C L1ME3G_3end#L 303 GTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCA 254 chrXptel1M 230842 TATCCCCTCCAACATTCATCATTATCTTTTCCTGTCATCTTAGCCAATCT 230891 i i i v i ?ivi vv?iii vvv i v C L1ME3G_3end#L 253 CACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATCT 204 chrXptel1M 230892 GACAGGTGTGTAGTGGTATCTCAGAGTTGTCTTAATTTGCATTTCTCTGA 230941 ii viv i vv i i C L1ME3G_3end#L 203 GATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGA 154 chrXptel1M 230942 TCAATAGTGATTTGGAGCACTCTTTCATATGAGTGGTAATAGTTTCAATT 230991 i v vv v iii vv iv iiivi vv C L1ME3G_3end#L 153 TTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGTATT 104 chrXptel1M 230992 TCATCATCTGAAAATTGTCTGTTCATATCCTTTGACCATTTATCAATTGG 231041 v v vi i v v v C L1ME3G_3end#L 103 TCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGG 54 chrXptel1M 231042 AGAATGGCTTGATTTCTTA-TAAATTACAGTCAATTCTCTATATATTTTG 231090 iv-- v -- - i v ii -v i i i C L1ME3G_3end#L 53 GT--TGTCTT--TTTCTTATTGATTTGTAG-GAGTTCTTTATATATTCTG 9 chrXptel1M 231091 GA 231092 C L1ME3G_3end#L 8 GA 7 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.10 CpG sites = 82, Kimura (unadjusted) = 35.73 Transitions / transversions = 1.22 (82/67) Gap_init rate = 0.02 (13 / 548), avg. gap size = 1.00 (13 / 13) 893 33.11 4.11 2.98 chrXptel1M 230949 232044 (767956) C L1PREC2_orf2#LINE/L1 (0) 3294 2187 m_b331s551i2 13889 chrXptel1M 230949 TGATTTGGAGCACTCTTTCATATGAGTGGTAATAGTTTCAATTTCATCAT 230998 v v vi i vv v iiiv iv vv v v v C L1PREC2_orf2# 3294 TGATGTTGAGCTTTTTTTCATATGCTTGTTGGCCGCATGTATGTCTTCTT 3245 chrXptel1M 230999 CTGAAAATTGTCTGTTCATATCCTTTGACCATTTATCAATTGGAGAATGG 231048 i v i v i v i v i--- v C L1PREC2_orf2# 3244 TTGAAAAGTGTCTGTTCATGTCCTTTGCCCACTTTTTAATGGGG---TTG 3198 chrXptel1M 231049 CTTGATTT---CTTATAAATTACAGTCAATTCTCTATATATTTTGGAAAT 231095 i v --- i vvvv v i ii v vi v C L1PREC2_orf2# 3197 TTTGTTTTTTTCTTGTAAATTTGTTTAAGTTCCTTATAGATGCTGGATAT 3148 chrXptel1M 231096 GAGGCCTTTATCAGAACCTTCGACTGTAAAAATGTTTTCCCAGTTTGTTG 231145 v i i vv v v vi i ? v i v i v C L1PREC2_orf2# 3147 TAGACCTTTGTCAGATGCATAGTTTGCAAANATTTTCTCCCATTCTGTAG 3098 chrXptel1M 231146 TTTCCCTTCTAATCTTGTCTGCATTAGTTTTGTTTG---TACAAAAACTT 231192 v vi vi v iii - v-- iv --- i i i i C L1PREC2_orf2# 3097 GTTGTCTGTTTACTCTGT-TGA--TAGTTTCTTTTGCTGTGCAGAAGCTC 3051 chrXptel1M 231193 TTCAATTTGAT-ATAATCAA------AATTTTCTATTTTGTAGTCAATAG 231235 i i i - v vi v ------ ivv v - -- C L1PREC2_orf2# 3050 TTTAGTTTAATTAGATCCCATTTGTCAATTTTTGCTTTTGTTG-CAAT-- 3004 chrXptel1M 231236 TGATCTCTAGT-TCTTCTTTGGTCATAAATTCCTTCTCAGGTC---TG-- 231279 v i - i i- ---- i v i vi v v --- -- C L1PREC2_orf2# 3003 TGCTTT-TGGCGTCTTC----GTCATGAAATCTTTGCCCGTTCCTATGTC 2959 chrXptel1M 231280 -AGA--GGTAAACTATCCTATGCT--CTTCCAATTTATTTATAATCTCAT 231324 - -- --- vv v i -- ivv v i i iiv C L1PREC2_orf2# 2958 CAGAATGGTA---TTGCCTAGGTTGTCTTCCAGGGTTTTTATAGTTTTGG 2912 chrXptel1M 231325 TCTTTATGCCTAGGTCATGAACCCATTTTGACCTTATCTTGATGTATGGT 231374 vi iiii i v v i i vi v i vi i C L1PREC2_orf2# 2911 GTTTTACATTTAAGTCTTTAATCCATCTTGAGTTGATTTTTGTATATGGT 2862 chrXptel1M 231375 GTTAAGTGTGGGTC-AATGCCTACTTTCTGCCATA---CTAATTTCCAAT 231420 v i viv - i vi v ii - --- i--- i C L1PREC2_orf2# 2861 GTAAGGAAGGGGTCCAGTTTCAATCTTCTGC-ATATGGCTAG---CCAGT 2816 chrXptel1M 231421 TTTCCCAGCAATTTTTGTCAAATAATGCACTCTTATCCCAAAAACTGGGG 231470 v viv i ii iv - v i v v vvi v -- C L1PREC2_orf2# 2815 TATCCCAGCACCATTTATTGAATAGGG-AGTCCTTTCCCCATTGCTTG-- 2769 chrXptel1M 231471 TCTTTG---GGTTTGTCAAACACTAGATTATTAAAGTTATTGGCTGTTTT 231517 i --- v i v ii vi iv v i -- v ii C L1PREC2_orf2# 2768 TTTTTGTCAGCTTTGTCGAAGATCAGATGGTTGTAGGTGT--GCGGCCTT 2721 chrXptel1M 231518 GTACTTTGAAC---CTAACCTATTCTATTGATCAACTAGTCTATTTCTTA 231564 i -i i ii --- vi i i i v ivv i i vv C L1PREC2_orf2# 2720 AT-TTCTGGGCTCTCTATTCTGTTCCATTGGTCTATGTGTCTGTTTTTGT 2672 chrXptel1M 231565 GCCAATAACAAATGGTTTTGGTAACTGCTGCTTTATAATATAATTTTAGA 231614 i i v viiv v iv ii i i i v ii C L1PREC2_orf2# 2671 ACCAGTACCATGCTGTTTTGGTTACTGTAGCCCTGTAGTATAGTTTGAAG 2622 chrXptel1M 231615 TCTGGTACAGCTAGGCC---ACCTTCATTTTTTTTTCATTA--ATTCCCT 231659 v vv iv v --- v ii i v - -- v C L1PREC2_orf2# 2621 TCGGGTAGCGTGATGCCTCCAGCTTTGTTCTTTTTGC-TTAGGATTGCCT 2573 chrXptel1M 231660 TGAA-ATTCTTGACCTTTTGTTTTTCCATATGAACTTTGTTGTTATTTTT 231708 iv- vv vi v vv i ivvi vi C L1PREC2_orf2# 2572 TGGCTATTCGGGCTCTTTTTTGGTTCCATATGAATTTTAAAATAGTTTTT 2523 chrXptel1M 231709 TCTAGGTCATCAAAATAGTTTTTTGGGACTCTGATTGGTATAGCGCTAAA 231758 v vvii iv vv iv v v i v v ii i C L1PREC2_orf2# 2522 TCTAGTTCTGTGAAGAATGTCATTGGTAGTTTGATAGGAATAGCATTGAA 2473 chrXptel1M 231759 TAAATAGATTAGTTTAGGTAATATTGCCATCTTTATTATATTTGCCCACC 231808 vvi i iv i i i v i v iv viii vi C L1PREC2_orf2# 2472 TCTGTAAATTGCTTTGGGCAGTATGGCCATTTTAACGATATTGATTCTTC 2423 chrXptel1M 231809 CTATCCAAGAGCATTTAATATTTTTCCAATTGGTTAGATTAGACTAAATT 231858 v vv i v v ivi i vviivi C L1PREC2_orf2# 2422 CTATCCATGAGCATGGAATGTTTTTCCATTTGTTTGTGTCATCTCTGATT 2373 chrXptel1M 231859 TGGGTGAAAAGTGGTCTGTAATTTTGCTCATAAAG---TTTCGGTTTTTC 231905 vvv iv v i i vv ii i --- i---ii C L1PREC2_orf2# 2372 TCTTTGAGCAGTGTTTTGTAATTCTCATTGTAGAGATCTTTCA---CCTC 2326 chrXptel1M 231906 CCTTGGCAGATAGATTCCTAAGTATTTTATACAACCAGTAGTTACATTAA 231955 v vi v iv i v vviiv i iv ivv i C L1PREC2_orf2# 2325 CCTGGTTAGCTGTATTCCTAGGTATTTTATTCTTTTTGTGGCAATTGTGA 2276 chrXptel1M 231956 ATGGGATTTCTCTTTGTAACTCTGACTATTGGATT--TTGTTAGTGATAT 232003 v v- iv i i - i v i v --i iv i i C L1PREC2_orf2# 2275 ATGGGATTGCG-TTCCTGATT-TGGCTCTCGGCTTGGCTGTTGTTGGTGT 2228 chrXptel1M 232004 ATAAGAATGCTGATGACTTATGTGGGTTTATTTTGTATCCT 232044 i ii i v ivi v C L1PREC2_orf2# 2227 ATAGGAATGCTAGTGATTTTTGTACATTGATTTTGTATCCT 2187 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 43.86 CpG sites = 180, Kimura (unadjusted) = 44.54 Transitions / transversions = 1.05 (180/172) Gap_init rate = 0.05 (52 / 1095), avg. gap size = 1.50 (78 / 52) 236 14.63 0.00 0.00 chrXptel1M 232869 232909 (767091) C MIR#SINE/MIR (124) 138 98 m_b331s601i8 13890 chrXptel1M 232869 TCACAGATGAGAAAACAGAGGCACAGAGAGACTAAGTGACT 232909 i i v ii i C MIR#SINE/MIR 138 TTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACT 98 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 16.87 CpG sites = 5, Kimura (unadjusted) = 16.87 Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 18 0.00 0.00 4.00 chrXptel1M 233186 233211 (766789) (TTA)n#Simple_repeat 1 25 (0) m_b331s252i3 13891 chrXptel1M 233186 TTATTTATTATTATTATTATTATTAT 233211 - (TTA)n#Simple 1 TTA-TTATTATTATTATTATTATTAT 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.04 (1 / 25), avg. gap size = 1.00 (1 / 1) 13 20.48 7.69 2.94 chrXptel1M 233802 233866 (766134) (GTCTCT)n#Simple_repeat 1 68 (0) m_b331s252i4 13892 chrXptel1M 233802 GTCTGTGCACTCTTTCTCT-CCTC-CTCTTCTCTCCCT-TCTC-CCCCCT 233847 v -v v -i -v - v i - -vi i (GTCTCT)n#Sim 1 GTCTCTG-TCTCTGTCTCTGTCTCTGTC-TCTGTCTCTGTCTCTGTCTCT 48 chrXptel1M 233848 CTC-CTGTCTCTGTCTCTGT 233866 v - (GTCTCT)n#Sim 49 GTCTCTGTCTCTGTCTCTGT 68 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.11 (7 / 64), avg. gap size = 1.00 (7 / 7) 12 19.28 0.00 7.50 chrXptel1M 233815 233857 (766143) (TTCTCCC)n#Simple_repeat 1 40 (0) m_b331s252i6 13893 chrXptel1M 233815 TTCTCTCCTCCTCTTCTCTCCCTTCTCCCCCCTCTCCTGTCTC 233857 - i iii ii - - (TTCTCCC)n#Si 1 TTCTC-CCTTCTCCCTTCTCCCTTCTCCCTTCTC-CCT-TCTC 40 Matrix = Unknown Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.07 (3 / 42), avg. gap size = 1.00 (3 / 3) 22 12.16 11.11 0.00 chrXptel1M 233811 233864 (766136) (CT)n#Simple_repeat 1 60 (0) m_b331s252i5 13894 chrXptel1M 233811 CTCTTTCTCTC-CTC-CTCT-TCTCTCCCT-TCTC-CCCCCTCTC-CTGT 233854 i - - - i - - i i - v (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chrXptel1M 233855 CTCTGTCTCT 233864 v (CT)n#Simple_ 51 CTCTCTCTCT 60 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.11 (6 / 53), avg. gap size = 1.00 (6 / 6) 29 6.13 0.00 0.00 chrXptel1M 233872 233905 (766095) (TC)n#Simple_repeat 1 34 (0) c_b331s251i0 13895 chrXptel1M 233872 TCTCTCTCTGTCTCTCTCTCTCTCTCTCTTTCTC 233905 v i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 34 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 286 13.73 1.96 0.00 chrXptel1M 236502 236552 (763448) MIR#SINE/MIR 72 123 (139) m_b331s601i9 13896 chrXptel1M 236502 ACTTCCTAGCTGTGTGACTCTGGGCAAGTGACTTAACCCCAAT-TGCCTC 236550 v ii v i vv - MIR#SINE/MIR 72 ACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTC 121 chrXptel1M 236551 AG 236552 MIR#SINE/MIR 122 AG 123 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 15.18 CpG sites = 3, Kimura (unadjusted) = 15.18 Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.02 (1 / 50), avg. gap size = 1.00 (1 / 1) 321 30.80 3.70 2.08 chrXptel1M 236870 237058 (762942) L1ME4c_3end#LINE/L1 325 516 (314) m_b331s551i3 13897 chrXptel1M 236870 ATTTGGAGCTATGTCCAAAGGGCTATAAAGCTGTGCCCACCCTTTGACCC 236919 viv i viv i i iv v vi L1ME4c_3end#L 325 ATTTGGCAATACGTATCAAGAGCCATAAAAATGTTCATACCCTTTGACCC 374 chrXptel1M 236920 AACAATACCACTGCTAAG--TCTGTCTCCCTGAGATCAT---AAAAAAGG 236964 ii v v ii -- i i iivvv i v --- i L1ME4c_3end#L 375 AGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAAGAAGG 424 chrXptel1M 236965 AAAAGGACTCACATTTACAAATATATTTATAGCA--GTTCTTTCAGTGGA 237012 i - - i vi i v i i v -- v --i iiv L1ME4c_3end#L 425 AAAAAG-CT-ATATGCACGAAGATGTTCATTGCAGCGTTATTT--ATAAT 470 chrXptel1M 237013 GGCAAAGAATTGGAAATCAAGGGGATGTCTATCAATTGGGGAATGG 237058 i i i iv vvvii i v v L1ME4c_3end#L 471 AGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAATGG 516 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.07 CpG sites = 33, Kimura (unadjusted) = 40.83 Transitions / transversions = 1.38 (33/24) Gap_init rate = 0.04 (7 / 188), avg. gap size = 1.57 (11 / 7) 343 30.02 6.60 1.94 chrXptel1M 236895 237091 (762909) L1ME3Cz_3end#LINE/L1 343 548 (449) m_b331s551i4 13897 chrXptel1M 236895 TAAAGCTGTGCCCACCCTTTGACCCAACAATACCACTGCTAAGTCTGTCT 236944 i v i vi vi i v v i v i vi L1ME3Cz_3end# 343 TGAAGATGCGCATACCCTACGACCCAGCAATTCCACTTCTAGGTATATAC 392 chrXptel1M 236945 CCCTGAGA-----TCATAAAAAAGGAAAAGGACTCACATTTACAAATATA 236989 iv ----- ii v viv v v v-- v iv i L1ME3Cz_3end# 393 CCTAGAGAAACTCTCGCACATGTGCACAAGGAG--ACATGTACAAGGATG 440 chrXptel1M 236990 TTTATAGCAG--TTCTTTCAGTGGAGGCAAAGAATTGGAAATCAAGGGGA 237037 i v -- v -- iivi i i iv vvvii L1ME3Cz_3end# 441 TTCATTGCAGCATTGTTT--GTAATAGCGAAAAATTGGAAACAACCTAAA 488 chrXptel1M 237038 TGTCTATCAATTGGGGAATGGATGAACAA------GTATATGAGTGTAAC 237081 i v i i ------ vvi ii i L1ME3Cz_3end# 489 TGTCCATCAATAGGGGAATGGATAAATAAATTGTGGTATATTCATACAAT 538 chrXptel1M 237082 AGAATAGTAT 237091 i v L1ME3Cz_3end# 539 GGAATACTAT 548 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.77 CpG sites = 31, Kimura (unadjusted) = 39.12 Transitions / transversions = 1.15 (31/27) Gap_init rate = 0.04 (7 / 196), avg. gap size = 2.43 (17 / 7) 513 32.71 12.48 2.81 chrXptel1M 237856 238440 (761560) L2#LINE/L2 2442 3081 (1) m_b331s601i10 13898 chrXptel1M 237856 CTTAATGTTTCCAAAAACTGAATTCATTATCTTCCCCCC----CCCACTA 237901 ii v - i v v i---- ii - L2#LINE/L2 2442 CTTAACATGTCCAAAA-CTGAACTCCTGATCTTCCCCCTCAAACCTGCT- 2489 chrXptel1M 237902 CCACCCTC--TCTT-CCCATTACTGTCAAGTGTGCTGCCATTCTCCCA-- 237946 v v -- - iv v ? vv iiviv i i -- L2#LINE/L2 2490 CCTCCCGCAGTCTTCCCCATCTCAGTNAATGGCAACTCCATCCTTCCAGT 2539 chrXptel1M 237947 TGCTTGG------AACCT---AGACATCCTT--CTCCACTC-TCGTCTCA 237984 ii ------ --- v -- v - iv L2#LINE/L2 2540 TGCTCAGGCCAAAAACCTTGGAGTCATCCTTGACTCCTCTCTTTCTCTCA 2589 chrXptel1M 237985 CTTCCCCATGTCCATTCTGTTGCTAAGTCCTGTTATTTTCCCCTTTGTA- 238033 -v ii v ii iivi i iivi iiv iiv - L2#LINE/L2 2590 C-ACCCCACATCCAATCCATCAGCAAATCCTGTCGGCTCTACCTTCAAAA 2638 chrXptel1M 238034 -ATATCC------------CTTCTCTCCTCTGACACTACCACTGCCCTG- 238069 - ------------ v v ivv i ii - L2#LINE/L2 2639 TATATCCAGAATCCGACCACTTCTCACCACCTCCACTGCCACCACCCTGG 2688 chrXptel1M 238070 -----------ATCATCTC---CTTGGACTATTGAAAAAAGCTACTGATA 238105 ----------- --- i i i v v iv v i iv L2#LINE/L2 2689 TCCAAGCCACCATCATCTCTCGCCTGGATTACTGCAATAGCCTCCTAACT 2738 chrXptel1M 238106 TGTCTTCCGGCTCCAAATTTTTCCCCATTCTAGTCCATCCTCCACTCAG- 238154 v i v i v vii v vi ?i i i v v - L2#LINE/L2 2739 GGTCTCCCTGCTTCCACCCTTGCCCCCCTNCAGTCTATTCTCAACACAGC 2788 chrXptel1M 238155 ----AGAACA--------AAAGTACAAATGGGACCATGAAATCACACTAT 238192 ---- iii-------- iiii i vi i vv iiv v ii L2#LINE/L2 2789 AGCCAGAGTGATCCTTTTAAAACGTAAGTCAGATCATGTCACTCCTCTGC 2838 chrXptel1M 238193 TCAATCAA--TTCCAGCGCCTCCTTTCAACTC---CAAAATCAAATATAT 238237 -- --i ii v -- ii v --- i i v vvi v L2#LINE/L2 2839 TCAA--AACCCTCCAATGGCT--TCCCATCTCACTCAGAGTAAAAGCCAA 2884 chrXptel1M 238238 ATTTCTCTCTTTGGACTTTGAAATCCTTCATAATCTGACCTTTTTGCACC 238287 v i iv vv v vii iii v i ii iiiivvi L2#LINE/L2 2885 AGTCCTTACAATGGCCTACAAGGCCCTACATGATCTGGTCCCCCGTTACC 2934 chrXptel1M 238288 CTTCCAGACTTCTTATCCCTTAGTCA-TCCCACCCAAACATTCTCTTCTA 238336 ii i- -- i i i -i - i v --v ii v i vv L2#LINE/L2 2935 TCTCT-GAC--CTCATCTCCTA-CCACTCTCCCCC--TCGCTCACTCCGC 2978 chrXptel1M 238337 TCCAGGGACCCTGACCTCCTGGCAACATGTTCATCACACACGACATTC-C 238385 vv v i v ---- v iv v vv - L2#LINE/L2 2979 TCCAGCCACACTGGCCTCCTTGC----TGTTCCTCGAACACGCCAGGCAC 3024 chrXptel1M 238386 ACTTCCTGAATCTAGGTCTTTTCATTGGCTGTTCATT---CCTGGAATGT 238432 i - i vv vi i v i v vi --- i i L2#LINE/L2 3025 GC-TCCCGCCTCAGGGCCTTTGCACTTGCTGTTCCCTCTGCCTGGAACGC 3073 chrXptel1M 238433 CCTTGCTC 238440 i v i L2#LINE/L2 3074 TCTTCCCC 3081 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.15 CpG sites = 108, Kimura (unadjusted) = 44.81 Transitions / transversions = 1.38 (108/78) Gap_init rate = 0.07 (39 / 584), avg. gap size = 2.33 (91 / 39) 337 31.25 11.03 4.35 chrXptel1M 238266 238546 (761454) L2b_3end#LINE/L2 4 302 (164) m_b331s601i11 13898 chrXptel1M 238266 CATAATCTGACCTTTTTGCACCCTTCCAGACTTCTTATCCCTTAGTCATC 238315 ii i iivi -- ii i ---i i i i -i ii L2b_3end#LINE 4 CACGATCTGGCCCCGCT--ACCTCTCCGG---CCTCATCTCCTA-CCACT 47 chrXptel1M 238316 CCACCCAAACATTCTCTTCTATCCAGGGACCCTGACCTCCTGGCAACATG 238365 iv vvi viv v -- vv v i v ---- L2b_3end#LINE 48 CTCCCCTTGCTCACTCTGCT--CCAGCCACACTGGCCTCCTTGC----TG 91 chrXptel1M 238366 TTCATCACACACGACATTCCACTTCCTGAATCTAGGTCTTTTCATTGGCT 238415 v iv v ?v iv?i i vv vi i v i?v L2b_3end#LINE 92 TTCCTCGAACACGCCANGCTCNCTCCCGCCTCAGGGCCTTTGCACNTGCT 141 chrXptel1M 238416 GTTCATT---CCTGGAATGTCCTT-----GCTCTT--------CAGCTCT 238449 vi --- i i -----v -------- i i L2b_3end#LINE 142 GTTCCCTCTGCCTGGAACGCCCTTCCCCACCTCTTCGCCTGGCCAACTCC 191 chrXptel1M 238450 --GTC-TCCTTTGAGTTCCAGCTAAAGTTTCACCTTCTGCAGGAACCCTT 238496 --v - iii ii v i v i v i v i L2b_3end#LINE 192 TACTCATCCTTCAGGTCTCAGCTCAAATGTCACCTCCTCCGGGAAGCCCT 241 chrXptel1M 238497 TTTTGAACCTCCC--------TCAAA---CTTCCTAT-GGCTCCCCCTCT 238534 iii - i -------- ii--- i v - i vv L2b_3end#LINE 242 CCCTG-ACCCCCCAGGCCGGGTCAGGCGCCCTCCTCTGGGCCCCCCCAGT 290 chrXptel1M 238535 CTCACCCTATCA 238546 ii ii L2b_3end#LINE 291 CCTACCCTGCCA 302 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.28 CpG sites = 53, Kimura (unadjusted) = 43.05 Transitions / transversions = 1.71 (53/31) Gap_init rate = 0.07 (21 / 280), avg. gap size = 2.10 (44 / 21) 574 33.88 14.80 1.27 chrXptel1M 238513 239343 (760657) L2#LINE/L2 1534 2475 (607) m_b331s601i12 13899 chrXptel1M 238513 AACTTCCTATGGCTCCCCCTCTCTCACC---CTATCAGCCTTCATTTTTT 238559 vvv?? v ivi v i --- i i vi v i v v L2#LINE/L2 1534 AACTTCCACANNCTCCCACCACCACATCTACCCACCTACCTGCATCTGTG 1583 chrXptel1M 238560 TTTACTGAACTC---CTTCTCTCCC-TTCTCAC--ATGAACTATCTACCT 238603 iii -iv --- i i- vii -- i iiivi L2#LINE/L2 1584 CCCAC-ATACTCTGCCTTCCCTCCTGTTACTACGGATGAACTGTCCGTGC 1632 chrXptel1M 238604 TTCTCTCTA----C--CTCTTTTACTCTT-CTCT---TCTTCATACCCAT 238643 i v ---- -- i i ii iv - v --- i- v - L2#LINE/L2 1633 TCCTATCTAAGGCCAACCCCTCCACTTGTGCACTAGATCC-CATCCCC-T 1680 chrXptel1M 238644 CTCACCTGCTGAAATGGCTTTATTCC-TCA--CCTCCTATCATTGCCACT 238690 i i v i- i v iii -v --i iv - iv iv L2#LINE/L2 1681 CTCGCCTACTCAAG-GACATCGCTCCAGCAATTCTCCCCTC-TCTCTCCT 1728 chrXptel1M 238691 CTTTAAGTAATCTCTCCCCATCTCCTGGTTACTTCCC-------TGCAAT 238733 viv v vi i i iv v v vv ------- i v L2#LINE/L2 1729 GCATCATCAATTTTTCCCTCTCTACTGGATCATTCCCATCAGCATACAAA 1778 chrXptel1M 238734 TATGCTTACATCTTCTTCATTCTCAAAAACC------CCTCATTTGGTCC 238777 i vv? i iiii ii i v ------i vi ii L2#LINE/L2 1779 CATGCTGTNATTTCTCCCATCTTTAAAAAACAAAAATTCTCCCTTGACCC 1828 chrXptel1M 238778 ----TTTCCTGGCAGGTATTGTCACATATCTG-GCCATCCTTGTGTGGCT 238822 ---- ii ivv v ii i v v v- ivi - iii v L2#LINE/L2 1829 CACNTCCCCCTCCAGCTACCGCCCCATTTCTCTGCTCCCCTT-TACAGCA 1877 chrXptel1M 238823 AGACTCCTTGAGAAGATCATCTCCAACTGGTGACTTGACTTCCTTTTCCT 238872 i i i iii ii vi vii v v iv v i - L2#LINE/L2 1878 AAACTCCTCGAAAGAGTTGTCTATACTCGCTGTCTCCAATTCCTCT-CCT 1926 chrXptel1M 238873 ATCATTGTCTTCTTACTTCTCTGCAATC----TTCTGACCTCATTCTTCA 238918 vi v ii v vii v v ---- ii v i iivi v L2#LINE/L2 1927 CCCATTCTCTCTTGAACCCACTCCAATCAGGCTTTCGTCCCCACCACTCC 1976 chrXptel1M 238919 ACTGAAGCTACTCTC--CAAAGTTACCAGTGATCTA---GTTGTCAAATA 238963 i i i i-- i i i i v--- ii v L2#LINE/L2 1977 ACCGAAACTGCTCTTGTCAAGGTCACCAATGACCTCCACGTTGCTAAATC 2026 chrXptel1M 238964 CAATGACCTTTTCTCAATCCTT------CTCGACCTCTCGGCAACCTCTG 239007 ii vv i i------ i ? i i v i L2#LINE/L2 2027 CAATGGTCAATTCTCAGTCCTCATCTTACTTGACCTNTCAGCAGCATTTG 2076 chrXptel1M 239008 ACA-----------------CTACTTGATGC----TCTTC-------TCC 239029 ----------------- v vi ---- ------- i L2#LINE/L2 2077 ACACAGTTGATCACTCCCTCCTTCTTGAAACACTTTCTTCACTTGGCTTC 2126 chrXptel1M 239030 TAAGATAC-----TTTCCTGGTT---CTTCTACCCGTCTGATCATTCCCT 239071 i i i ----- i --- i ivv ii ii i L2#LINE/L2 2127 CAGGACACCACACTCTCCTGGTTTTCCTCCTACCTCACTGGCCGCTCCTT 2176 chrXptel1M 239072 CTCAGTCTCCTTTGCTGGATCTTCATC--CAGGGCAAACACAATAATTGT 239119 v i v -- vvvv i v v -- ? vi L2#LINE/L2 2177 CTCAGTCTCCTTTGCTGGTTCCTCCTCATCTCCCCGACCTC--TNAACGT 2224 chrXptel1M 239120 GGATGACCTCTACAGTCCTGTCCCAGG---TCTTCTC-CCTCTGTGC-CA 239164 v iv vv i i vi ii v iv --- -i i vi- L2#LINE/L2 2225 TGGAGTGCCCCAGGGCTCAGTCCTTGGACCTCTTCTCTTCTCTATCTACA 2274 chrXptel1M 239165 TTC-CCCCATGGG--------TCCA-----ATGA----ACATATC----- 239191 i - i v ? -------- ----- i---- v i ----- L2#LINE/L2 2275 CTCACTCCCTNGGTGATCTCATCCAGTCTCATGGCTTTAAATACCATCTA 2324 chrXptel1M 239192 TATGCTGGTGATTCTGAGACATATCCATCTAGCCCTAACTTTTTCCCATG 239241 i i iv i iv viv i vi i i i - L2#LINE/L2 2325 TATGCTGATGACTCCCAAATTTATATCTCCAGCCCGGACCTCTCCCC-TG 2373 chrXptel1M 239242 AACTCTAG--TTTTACAACAGCAATTACCTCTTAAATATTTTGAACTGGA 239289 i -- iv i v -- i i vi vi i i iv vi L2#LINE/L2 2374 AACTCCAGACTCGTATATC--CAACTGCCTACTCGACATCTCCACTTGGA 2421 chrXptel1M 239290 TGTTCCACAGACGTCTTAAATTTAACCTTTCCAACACTGACCTTGCTATG 239339 iiv i i i i i v v v v iviv v L2#LINE/L2 2422 TGTCTAATAGGCATCTCAAACTTAACATGTCCAAAACTGAACTCCTGATC 2471 chrXptel1M 239340 TTCC 239343 L2#LINE/L2 2472 TTCC 2475 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.65 CpG sites = 171, Kimura (unadjusted) = 47.82 Transitions / transversions = 1.60 (171/107) Gap_init rate = 0.05 (45 / 830), avg. gap size = 3.00 (135 / 45) 977 27.16 2.03 1.21 chrXptel1M 239350 239595 (760405) MIRb#SINE/MIR 13 260 (8) m_b331s601i13 13900 chrXptel1M 239350 GTGGTGCAATGGATAGAGAACCGGGTATGGTGTCAGAAAGACCTAAATTC 239399 i v v v v v v v iii MIRb#SINE/MIR 13 GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTC 62 chrXptel1M 239400 AAATTTGACCTCAGACACTCATCAGTTATGTTATTCTGGACAAGTCACTT 239449 i iiviv v v i ii i i v iii i i MIRb#SINE/MIR 63 GAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTT 112 chrXptel1M 239450 CATTTGTTT--GCCTCGATTTCCTGGCCTGTAAAATGAGGAGAATAATCA 239497 v ii v i -- ii vii i v v- MIRb#SINE/MIR 113 AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATA- 161 chrXptel1M 239498 CTCCTACCTCTCAAGCTTGTTGTGAGGATCAAATGAGATAAT---TGTAA 239544 -- v i v i --- MIRb#SINE/MIR 162 --CCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAA 209 chrXptel1M 239545 TCCATTTAGTGCAATGCCCGGCACGTGGCTGGTACTATCTAAATGTTAGC 239594 vv ii ii i i i i ivi ii vvv v MIRb#SINE/MIR 210 AGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAAATGGTAGC 259 chrXptel1M 239595 T 239595 MIRb#SINE/MIR 260 T 260 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.04 CpG sites = 40, Kimura (unadjusted) = 34.67 Transitions / transversions = 1.54 (40/26) Gap_init rate = 0.02 (5 / 245), avg. gap size = 1.60 (8 / 5) 24 12.25 4.26 2.08 chrXptel1M 240571 240617 (759383) (GA)n#Simple_repeat 1 48 (0) m_b331s252i7 13901 chrXptel1M 240571 GAGAGAAAGAGAGAAAG-GAGAGGGAGAGAAAGAG-GAGCAGAGAGTGA 240617 i i - i i - - v (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG-AGAGAGAGA 48 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.07 (3 / 46), avg. gap size = 1.00 (3 / 3) 14 18.72 2.17 4.44 chrXptel1M 240690 240735 (759265) (TAGGTT)n#Simple_repeat 1 45 (0) m_b331s252i8 13902 chrXptel1M 240690 TAGGATTTAGGCGTATGGTTAGAGTTGA-ATTTAGGTTTAGGGTTAG 240735 - iv v v - v -i v (TAGGTT)n#Sim 1 TAGG-TTTAGGTTTAGGTTTAG-GTTTAGGTTTAGGTTTAGGTTTAG 45 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.07 (3 / 45), avg. gap size = 1.00 (3 / 3) 44 0.00 0.00 0.00 chrXptel1M 241160 241197 (758803) (AG)n#Simple_repeat 1 38 (0) c_b331s251i1 13903 chrXptel1M 241160 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 241197 (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 38 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 367 18.29 2.41 1.19 chrXptel1M 241265 241347 (758653) U6#snRNA 24 107 (0) m_b331s502i0 13904 chrXptel1M 241265 ACTAAAATT--AAGTACACAGGAGCAGATTAGCGTAACCCCAGTGCAAGG 241312 -- vv i - v i ii v i U6#snRNA 24 ACTAAAATTGGAACGATACAG-AGAAGATTAGCATGGCCCCTGCGCAAGG 72 chrXptel1M 241313 ATGACACTCAGATATGTGAAGTGTTCCATAGTTTT 241347 v i vi i v U6#snRNA 73 ATGACACGCAAATTCGTGAAGCGTTCCATATTTTT 107 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 16.76 CpG sites = 8, Kimura (unadjusted) = 21.14 Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.02 (2 / 82), avg. gap size = 1.50 (3 / 2) 17 21.80 2.08 0.00 chrXptel1M 241741 241788 (758212) (TACACA)n#Simple_repeat 1 49 (0) m_b331s252i9 13905 chrXptel1M 241741 TACAGATACAGAGGCACATTCACATACACATATATAT-CATATGCACAT 241788 v v vi v i i - i i (TACACA)n#Sim 1 TACACATACACATACACATACACATACACATACACATACACATACACAT 49 Matrix = Unknown Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.02 (1 / 47), avg. gap size = 1.00 (1 / 1) 15 26.69 1.79 1.79 chrXptel1M 241743 241798 (758202) (CACATG)n#Simple_repeat 1 56 (0) m_b331s252i10 13905 chrXptel1M 241743 CAGATACAGAGGCACATTCACATACACATATATAT-CATATGCACATGTA 241791 v i v v v i ii i - i i (CACATG)n#Sim 1 CACATGCACATGCACATGCACATGCACATGCACATGCACATGCACATGCA 50 chrXptel1M 241792 TCAGGCA 241798 - v (CACATG)n#Sim 51 -CATGCA 56 Matrix = Unknown Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.04 (2 / 55), avg. gap size = 1.00 (2 / 2) 474 25.39 3.42 5.59 chrXptel1M 241803 241948 (758052) MIRc#SINE/MIR 6 148 (120) m_b331s601i14 13906 chrXptel1M 241803 CGGGGTGCTGCAGTAAGTACAGGGCCAGCCCTGGAGTCAGGAAGATTCAT 241852 i v v iiiv v vi ii v i ----- MIRc#SINE/MIR 6 CAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA----- 50 chrXptel1M 241853 CTTCCTGAATTCAAATTGAGCCTCAGAAACTT-C---CTGTGTGACCCTG 241898 --- ii i i ivv v v vv - --- i MIRc#SINE/MIR 51 ---CCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTG 97 chrXptel1M 241899 GGTAAGTCACTTCACCCCATTTA-CCTCAGTTTCCCCATCTGTAAAATAA 241947 i v i vi v - i ii MIRc#SINE/MIR 98 GGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGG 147 chrXptel1M 241948 G 241948 MIRc#SINE/MIR 148 G 148 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.48 CpG sites = 20, Kimura (unadjusted) = 31.55 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.08 (11 / 145), avg. gap size = 1.18 (13 / 11) 884 33.41 6.22 3.62 chrXptel1M 242393 243248 (756752) L2#LINE/L2 2055 2933 (149) m_b331s601i15 13907 chrXptel1M 242393 CTTGATCCCTCTGCAGCCTCCAACAC------TC--TCTCTCCTCCTGGA 242434 i i? v v iii ------ -- i i v L2#LINE/L2 2055 CTTGACCTNTCAGCAGCATTTGACACAGTTGATCACTCCCTCCTTCTTGA 2104 chrXptel1M 242435 TCCCCTCTTCTCTCTAGGTTTCTGGGA-GCCTT-CTGCTCTGGGTCTGCT 242482 vv v i ii v v i ii -i vi- vii v i v L2#LINE/L2 2105 AACACTTTCTTCACTTGGCTTCCAGGACACCACACTCTCCTGGTTTTCCT 2154 chrXptel1M 242483 CCTCCCTCTCGGGCTGCTCCTTCTCGGTCTCCTTTACTGGACCCTCCTCC 242532 v v v i i i vi - L2#LINE/L2 2155 CCTACCTCACTGGCCGCTCCTTCTCAGTCTCCTTTGCTGGTTCCTCCTC- 2203 chrXptel1M 242533 AGATCACTCC-----CCCAACTGTAGGTGTCCCTCAGGGCTCTGCCCTGG 242577 -- v i ----- i? - v v v i v i v L2#LINE/L2 2204 --ATCTCCCCGACCTCTNAAC-GTTGGAGTGCCCCAGGGCTCAGTCCTTG 2250 chrXptel1M 242578 GCTCTCTGC-GTTCTCCCTCTCCACTCCTTCACTAGGAGGGCTCATCAAC 242626 vi v -v iv v vi v ? v iv v v L2#LINE/L2 2251 GACCTCTTCTCTTCTCTATCTACACTCACTCCCTNGGTGATCTCATCCAG 2300 chrXptel1M 242627 CCCCAGAAATTCCCTTCTTCTCTGGATGCTGATGATTCTCAGCCCTACCC 242676 i i viiv ivvv viiv iv i i ivii --i L2#LINE/L2 2301 TCTCATGGCTTTAAATACCATCTATATGCTGATGACTCCCAAATTTA--T 2348 chrXptel1M 242677 ATGCTCC--CCCTAA-CTCTGCC--GACCTCCACTCCCTCGGCTCTGACT 242721 - -- vi - v -- v vv i viivv ii L2#LINE/L2 2349 AT-CTCCAGCCCGGACCTCTCCCCTGAACTCCAGACTCGTATATCCAACT 2397 chrXptel1M 242722 GACTTTCCCACGGCTTCACCTGGATGGCCGGCAGCCATCGGAAATGGAGC 242771 v vii v iv i i v iiii v vv ivv i L2#LINE/L2 2398 GCCTACTCGACATCTCCACTTGGATGTCTAATAGGCATCTCAAACTTAAC 2447 chrXptel1M 242772 ---TCCAGCATGGAA------GTCTTTCCCCTCGAGC---CTCCCCAGAC 242809 --- iv iv ------i i i i --- i vvi L2#LINE/L2 2448 ATGTCCAAAACTGAACTCCTGATCTTCCCCCTCAAACCTGCTCCTCCCGC 2497 chrXptel1M 242810 CAACTTCCCGATGACTGAG-----GGCAACACCCTTC-TCCTGCCCCTCA 242853 viv v -- v ----- v v i - v iiv L2#LINE/L2 2498 AGTCTTCCCCAT--CTCAGTNAATGGCAACTCCATCCTTCCAGTTGCTCA 2545 chrXptel1M 242854 GGCTCACAAGCTAGAAGTTGTGCTGGA-TCCTCCCATTACCTCTCGCCCC 242902 iv v v v i ii v v - i v -- i v L2#LINE/L2 2546 GGCCAAAAACCTTGGAGTCATCCTTGACTCCTCTCTTT--CTCTCACACC 2593 chrXptel1M 242903 CCAGATCCAGGCTGTTGCCAAGGCCTGTCCATCCCACCTCTGCAGCATCT 242952 v iv ii iiv iv viii i iiiv ii v L2#LINE/L2 2594 CCACATCCAATCCATCAGCAAATCCTGTCGGCTCTACCTTCAAAATATAT 2643 chrXptel1M 242953 CTTGGATACATCCCCTCCTCTTCCCCTGACGCTGCCCCCACCCTGGGACA 243002 iv i v iv v i vi v -v i v vv L2#LINE/L2 2644 CCAGAATCCGACCACTTCTCACCACCT-CCACTGCCACCACCCTGGTCCA 2692 chrXptel1M 243003 GCCCCTCATCGCCTCATGTCCAGACTATGGTAATAGCGTGCTAGGGGCGG 243052 iv vi ii vi i ii i iv i v v ---i -v L2#LINE/L2 2693 AGCCACCATCATCTCTCGCCTGGATTACTGCAATAGCCTCCTA---AC-T 2738 chrXptel1M 243053 GGTCTGCCTG---CCACA--TGTCTCTCTTTAGTCCAATTCGTCCTCCAT 243097 v --- v-- i i i ?i i ----- i v i L2#LINE/L2 2739 GGTCTCCCTGCTTCCACCCTTGCCCCCCTNCAGTCTA-----TTCTCAAC 2783 chrXptel1M 243098 TCAGACACCAAAGTGACTTTGCTAAAATGCAGATCTCATCACGTCACCCT 243147 v vvi i iii vi i i ii vv i i-- L2#LINE/L2 2784 ACAGCAGCCAGAGTGATCCTTTTAAAACGTAAGTCAGATCATGTCACT-- 2831 chrXptel1M 243148 CCACACCTCTGCTTAATACTTTCTCTTGG-TTCCC-TCTTACCTCCAGGA 243195 ----- i v ii ivv - - i --i ii L2#LINE/L2 2832 -----CCTCTGCTCAAAACCCTCCAATGGCTTCCCATCTCAC--TCAGAG 2874 chrXptel1M 243196 AGAAATATAAAATGCTTTGCTTGGCGTTCAAAGCCCTTTAAAACCT-ATC 243244 vi vvi i v vvvv v v i vi vi i -i L2#LINE/L2 2875 TAAAAGCCAAAGTCCTTACAATGGCCTACAAGGCCCTACATGATCTGGTC 2924 chrXptel1M 243245 C-----TAT 243248 ----- i L2#LINE/L2 2925 CCCCGTTAC 2933 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.72 CpG sites = 171, Kimura (unadjusted) = 45.63 Transitions / transversions = 1.16 (148/128) Gap_init rate = 0.06 (51 / 855), avg. gap size = 1.63 (83 / 51) 33 0.00 0.00 0.00 chrXptel1M 243249 243276 (756724) (AC)n#Simple_repeat 1 28 (0) c_b331s251i2 13908 chrXptel1M 243249 ACACACACACACACACACACACACACAC 243276 (AC)n#Simple_ 1 ACACACACACACACACACACACACACAC 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 884 33.41 6.22 3.62 chrXptel1M 243277 243416 (756584) L2#LINE/L2 2934 3075 (7) m_b331s601i15 13907 chrXptel1M 243277 TTCC--AC----TCTTCTAACACCTGACTCCCCAAAATATACTATTGTAT 243320 ii -- ---- i v i--- vvviivi -ii i- L2#LINE/L2 2934 TCTCTGACCTCATCTCCTACCACT---CTCCCCCTCGCTCACT-CCGC-T 2978 chrXptel1M 243321 CTAGTGACCCTGGCCTCCTGGCTGTCCCATGAACAAG--AGCCTCCATTT 243368 i iv v v i vi v -- v v --vi L2#LINE/L2 2979 CCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACACGCCAGGCAC--GCT 3026 chrXptel1M 243369 CTCAGCTGTGGATATTCTCCCTGGCTATGCTC-ATGCCTGGAATGCTCT 243416 i iv vv iiv iv v v i v i -v i L2#LINE/L2 3027 CCCGCCTCAGGGCCTTTGCACTTGCTGTTCCCTCTGCCTGGAACGCTCT 3075 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.72 CpG sites = 171, Kimura (unadjusted) = 45.63 Transitions / transversions = 1.05 (23/22) Gap_init rate = 0.08 (11 / 139), avg. gap size = 1.45 (16 / 11) 194 36.49 8.28 1.10 chrXptel1M 243320 243488 (756512) L2a_3end#LINE/L2 70 250 (267) m_b331s601i16 13907 chrXptel1M 243320 TCTAGTGACCCTGGCCTCCTGGCTGTCCCATGAACAAG--AGCCTCCATT 243367 i iv v v i vi v -- v v --vi L2a_3end#LINE 70 TCCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACACGCCAGGCAC--GC 117 chrXptel1M 243368 TCTCAGCTGTGGATATTCTCCCTGGCTATGCTC-ATGCCTGGAATGCTCT 243416 i iv vv iiv iv v v i v i -v i L2a_3end#LINE 118 TCCCGCCTCAGGGCCTTTGCACTTGCTGTTCCCTCTGCCTGGAACGCTCT 167 chrXptel1M 243417 GTTC-----TGTCTACTTGAC---CTCCCTGTCTCCCTGGGAGTTCTTAT 243458 vii ----- i ii v i --- vv ii vvii ii ii L2a_3end#LINE 168 TCCCCCAGATATCCGCATGGCTCGCTCCCTCACCTCCTTCAGGTCTTTGC 217 chrXptel1M 243459 TAAAATCT---TTTCCCAAACTGGTTTTCTTTG 243488 v v ---i i i?vv ii ii L2a_3end#LINE 218 TCAAATGTCACCTTCTCAGNGAGGCCTTCCCTG 250 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 47.35 CpG sites = 34, Kimura (unadjusted) = 52.30 Transitions / transversions = 1.26 (34/27) Gap_init rate = 0.04 (7 / 168), avg. gap size = 2.29 (16 / 7) 26 8.91 0.00 0.00 chrXptel1M 243839 243874 (756126) (T)n#Simple_repeat 1 36 (0) m_b331s252i11 13909 chrXptel1M 243839 TTTTTTGTTGTTTTTTTTTGTTTTTTTTTTTTTTTT 243874 v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 36 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 36 0.00 0.00 0.00 chrXptel1M 244635 244665 (755335) (AC)n#Simple_repeat 1 31 (0) c_b331s251i3 13910 chrXptel1M 244635 ACACACACACACACACACACACACACACACA 244665 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACA 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 893 32.41 6.71 1.60 chrXptel1M 245772 246188 (753812) L3#LINE/CR1 2914 3351 (748) m_b331s601i17 13911 chrXptel1M 245772 TAGACTCAGAGATTAGGAGAATGACAGGAACAGAGACCACCTTGATTCCT 245821 viv i i v ivii ? vvi i v i v L3#LINE/CR1 2914 TAGACTGGTAGATCAGGGGAATGCCGTAGACANAGTGTATCTGGATTTCA 2963 chrXptel1M 245822 CTAAAATATTTGA--AAGTCTC--ATTGTATCCTTGTATCCAAGATAGAG 245867 vi iii -- -- vi ivv i L3#LINE/CR1 2964 GCAAGGCATTTGACAAAGTCTCTCATGATATCCTTGTGGACAAGATGGAG 3013 chrXptel1M 245868 AAATGTGGA----GTGAT--TATAGTTAAAGAGATGTGTAGTTGTTTAAT 245911 i i----i -- i iivi vi i v i v L3#LINE/CR1 3014 AAATATGGGCTGGATGATAGTACAGTTAGGTGGATTCGTAGCTGGTTGAA 3063 chrXptel1M 245912 CAATTAAATGCAAAGGCTATAAATCAATGTTTTAATT---ATCTAAAAGG 245958 i i v iv i v i vi i vv ii v--- i ii i L3#LINE/CR1 3064 CGACTATACCCAAAAGGTGTTGATTAATGGATCGATGTCAACCTGGAGGG 3113 chrXptel1M 245959 AGATCTTTAGTCATGTATTATAGGATGTTGATATTAGCCTTTTCCTATTG 246008 i i vii iii i iivi viv i i v i v L3#LINE/CR1 3114 AGGTCTCTAGTGGCGTGCCACAGGGCTCTGTCCTTGGCCCTGTCCTGTTC 3163 chrXptel1M 246009 GATACTTTTATAAATGA--------AAG-CATAAAATGCCTGATTATCAT 246049 i i i v -------- - i v v v v L3#LINE/CR1 3164 AACATTTTTATCAATGACTTGGATGAAGACATAGAAGGCATGCTTATCAA 3213 chrXptel1M 246050 ACTTGCCAATG--ACGGTGCTGGGAAGGATATTTAATATTTAATGCTGTT 246097 i vi -- iiv i vi --ii? -- v L3#LINE/CR1 3214 ATTTGCAGATGACACAAAGCTGGGAGGGATAGCTAATA--CGNTG--GAT 3259 chrXptel1M 246098 GACAGGATTACAATTCTAAA--ATTTGAACA-GCTGAAATTGTTAAAATA 246144 i i vi v -- i vi - i -i v iiivii L3#LINE/CR1 3260 GACAGAATCAAGATTCAAAANGATCTCGACAGGCTGGAA-CGATGGGCCG 3308 chrXptel1M 246145 TAATT-ACAAGGGGATTAATTAAATGGGAATAAATCTAAAATCTT 246188 v ii- iv -- v ii i v i i L3#LINE/CR1 3309 AAACCAACAAGATGA--AATTTAACAGGGATAAATGTAAAGTCCT 3351 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.76 CpG sites = 86, Kimura (unadjusted) = 45.02 Transitions / transversions = 1.83 (86/47) Gap_init rate = 0.04 (18 / 416), avg. gap size = 1.94 (35 / 18) 253 18.60 0.00 0.00 chrXptel1M 246360 246402 (753598) L3#LINE/CR1 4050 4092 (7) m_b331s601i18 13912 chrXptel1M 246360 CTAGGTGATCTCTAAGGTACCTTCAGATTCAAAGATTCTGTGA 246402 i i v vi i vi L3#LINE/CR1 4050 CTAGATGACCTCTAAGGTCCCTTCCAACTCTGAGATTCTGTGA 4092 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 21.76 CpG sites = 5, Kimura (unadjusted) = 21.76 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 541 33.32 6.09 0.83 chrXptel1M 246887 247116 (752884) L3#LINE/CR1 3501 3742 (357) m_b331s601i19 13911 chrXptel1M 246887 CAATTTGGGTGCCATATTCACAAAGACATAGT-TCCAGAACAAGTACAAT 246935 i vi - iii v i i iii - ? vivii L3#LINE/CR1 3501 CAATCTTAG-GCTGCATTAATAGAAGTATAGTGTCCAGANCAAGGGAGGT 3549 chrXptel1M 246936 GATCATTTGGTTATACTATGACCTGAGGAGCCCACACCGGAAGTAATGGG 246985 i vi iiv i i v vv ivv v i v i v v L3#LINE/CR1 3550 AATAGTCCCGCTGTACTCTGCGCTGGTCAGACCACATCTGGAGTATTGCG 3599 chrXptel1M 246986 CCCAGTTCTGGGTGCCATCACTTACAAAGGATATTAA-------GGGTTA 247028 ii i ivvi vi i i i ------- i ivv L3#LINE/CR1 3600 TTCAGTTCTGGGCGCCACATTTTAAGAGGGACATTGACAAACTGGAGCGC 3649 chrXptel1M 247029 GTT----GGA-AGTGATCAAGATGGCCAAGGAACTTGAAACTATGCCATA 247073 i---- - i i i iv iv v i i L3#LINE/CR1 3650 GTCCAGAGGAGAGCGACCAGGATGGTGAAGGGTCTGGAAACCATGTCATA 3699 chrXptel1M 247074 TGGGGATGGGTGAAAGGAACTGCAAATAATTTAG-ATGGAAAGG 247116 i vv vi vii -i -v i i L3#LINE/CR1 3700 TGAGGAACGGTTGAAGGAACTGGGGAT-GTTTAGCCTGGAGAAG 3742 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.04 CpG sites = 48, Kimura (unadjusted) = 46.59 Transitions / transversions = 1.71 (48/28) Gap_init rate = 0.03 (7 / 229), avg. gap size = 2.29 (16 / 7) 344 37.79 0.78 0.78 chrXptel1M 247129 247256 (752744) MIRc#SINE/MIR 19 146 (122) m_b331s601i20 13913 chrXptel1M 247129 TAGGAAAAACTCTGGACTTCAAGTCAGATAAACTAGGGTGTGAATTCTAC 247178 i i i i v vi iv i iv vi i i iiv MIRc#SINE/MIR 19 TGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGG 68 chrXptel1M 247179 CTCAAATGTTTTCTAACTATGTGAACCCTAATAAATCAGCTAAATTGTCT 247228 viviii v i i v iiviii i vi vi v MIRc#SINE/MIR 69 CTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCT 118 chrXptel1M 247229 GGGTTTCAGTTATCTTATC-ATAGAAATG 247256 i ii vi i -i - MIRc#SINE/MIR 119 GAGCCTCAGTTTCCTCATCTGTA-AAATG 146 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 53.55 CpG sites = 33, Kimura (unadjusted) = 57.51 Transitions / transversions = 2.20 (33/15) Gap_init rate = 0.02 (2 / 127), avg. gap size = 1.00 (2 / 2) 307 22.81 0.00 0.00 chrXptel1M 247668 247724 (752276) L2b_3end#LINE/L2 400 456 (10) m_b331s601i21 13914 chrXptel1M 247668 CCCCAGTGCTTAGCAGAGTGCCTGACAAAGAGTAGCCACTTAATAAGTGT 247717 i i v ? i v v v i i i i i L2b_3end#LINE 400 CCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATAT 449 chrXptel1M 247718 TTATTGA 247724 i L2b_3end#LINE 450 TTGTTGA 456 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 23.77 CpG sites = 9, Kimura (unadjusted) = 28.80 Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0) 257 36.66 1.65 0.82 chrXptel1M 248921 249041 (750959) MIR3#SINE/MIR 4 125 (83) m_b331s601i22 13915 chrXptel1M 248921 GTAGAGAGGGAAGGCACAGATAGCACAGCACCTGGAGTTGAAAAGCTAGG 248970 i v vvii v v i - iv iiii ii iv MIR3#SINE/MIR 4 GCAGAGTGGCTGAGCAGAGAGAGCACGG-ACTGGGAGTCAGGAGACCTGG 52 chrXptel1M 248971 AGTTTAA-ATTGG-TCTGACACTCATTAGCTCAATGACTCCATGCAAGTC 249018 iv i i-vii - v v i ? vvi iiiiv MIR3#SINE/MIR 53 GTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTC 102 chrXptel1M 249019 TCATCACCTCGGTTTGCCTTAGT 249041 v v vv vv i MIR3#SINE/MIR 103 ACTTCACCTCTCTGGGCCTCAGT 125 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 49.20 CpG sites = 24, Kimura (unadjusted) = 52.61 Transitions / transversions = 1.20 (24/20) Gap_init rate = 0.03 (3 / 120), avg. gap size = 1.00 (3 / 3) 452 29.94 1.59 17.51 chrXptel1M 248942 249192 (750808) MIRb#SINE/MIR 29 245 (23) m_b331s601i23 13915 chrXptel1M 248942 AGCACAGCACCTGGAGTTGAAAAGCTAGGAGTTTAAATT--GG-TCTGAC 248988 i vvii iii v vivv i ii i-- - v MIRb#SINE/MIR 29 AGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTCTGCC 78 chrXptel1M 248989 ACTCATTAGCTCAATGACTCCATGCAAGTCTCATCACCTCGGTTTGCCTT 249038 i i vvi iiiiv iv v v vv vv i MIRb#SINE/MIR 79 ACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTC 128 chrXptel1M 249039 AGTAAAAAATCTGTTGTGGATTTTACTCAGTAAAATCATCTGGAAAATAG 249088 ------------------- v --------- v i MIRb#SINE/MIR 129 AG-------------------TTTCCTC---------ATCTGTAAAATGG 150 chrXptel1M 249089 GGATCATAATAGCCTCTACCTCACATAGCAGGGTTGTTGTGA-AACCCAA 249137 v ---i ----- -i iiv MIRb#SINE/MIR 151 GGATAATAATA---CCTACCTC-----GCAGGGTTGTTGTGAGGATTAAA 192 chrXptel1M 249138 TGAGATCACATCTGTAAAAATCATCTCTCAAAGTACCTGGCACACAGTAG 249187 v iiiv i-- iii vv v i i i MIRb#SINE/MIR 193 TGAGATAATGCATGTAAAG--CGCTTAGCACAGTGCCTGGCACATAGTAA 240 chrXptel1M 249188 GCACT 249192 i MIRb#SINE/MIR 241 GCGCT 245 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.70 CpG sites = 36, Kimura (unadjusted) = 37.82 Transitions / transversions = 1.38 (36/26) Gap_init rate = 0.16 (41 / 250), avg. gap size = 1.02 (42 / 41) 248 21.30 11.81 7.58 chrXptel1M 249320 249446 (750554) L2c_3end#LINE/L2 345 476 (2) m_b331s601i24 13916 chrXptel1M 249320 TATTTCTTTACATCT-TGTCTCCTCCA---------AAG-TCTTTA---- 249354 i i v ? v - ---------i - i i---- L2c_3end#LINE 345 TGTCTGTTTACNTGTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGG 394 chrXptel1M 249355 CAGGGACTGGTTTTTTTTTTCTTCCTTTGAATTCCCAAGACATAGTTCCT 249404 i -- v i v v - v i ------- iv L2c_3end#LINE 395 CAGGGACCG--TGTCTTATTCATC-TTTGTATCCCCA-------GCGCCT 434 chrXptel1M 249405 AGTACATAGTATGCATTCACTAAATGTTTGTTTATTGATTGA 249446 i i v ii v v v v L2c_3end#LINE 435 GGCACATAGTAGGCGCTCAATAAATGTTTGTTGAATGAATGA 476 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 22.29 CpG sites = 13, Kimura (unadjusted) = 25.64 Transitions / transversions = 1.08 (13/12) Gap_init rate = 0.11 (14 / 126), avg. gap size = 1.79 (25 / 14) 265 26.09 7.61 0.00 chrXptel1M 249355 249446 (750554) L2a_3end#LINE/L2 417 515 (2) m_b331s601i25 13916 chrXptel1M 249355 CAGGGACTGGTTTTTTTTTTCTTC-CT-TTGAATTCCCAAGAC-----AT 249397 vv v i v v - -i v i ivi ----- i L2a_3end#LINE 417 CAGGGACTTTTGTCTGTTTTGTTCACTGCTGTATCCCCAGCGCCTAGAAC 466 chrXptel1M 249398 AGTTCCTAGTACATAGTATGCATTCACTAAATGTTTGTTTATTGATTGA 249446 v i i v ii v i v v v L2a_3end#LINE 467 AGTGCCTGGCACATAGTAGGCGCTCAATAAATATTTGTTGAATGAATGA 515 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.18 CpG sites = 11, Kimura (unadjusted) = 32.24 Transitions / transversions = 0.85 (11/13) Gap_init rate = 0.03 (3 / 91), avg. gap size = 2.33 (7 / 3) 13 5.20 0.00 0.00 chrXptel1M 249769 249788 (750212) (TTA)n#Simple_repeat 1 20 (0) m_b331s252i12 13917 chrXptel1M 249769 TTTTTATTATTATTATTATT 249788 v (TTA)n#Simple 1 TTATTATTATTATTATTATT 20 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 303 23.96 11.11 1.80 chrXptel1M 250076 250228 (749772) L1P1_orf2#LINE/L1 1665 1831 (1463) m_b331s551i5 13918 chrXptel1M 250076 CAAAAAGGTTA--AACTATGATCAGATTGGACTTTTATTC--AGAATCCA 250121 v --v i - v i i- i --i i v L1P1_orf2#LIN 1665 CAAAAAGCTTATCCACCATGATCA-AGTGGGCTTC-ATCCCTGGGATGCA 1712 chrXptel1M 250122 GGGTTGATTCAAC-TGTAGGAATACTATAAATGT---------TAAAAAC 250161 i i i - iiivi - v i --------- v L1P1_orf2#LIN 1713 AGGCTGGTTCAACATACGCAAAT-CAATAAACGTAATCCAGCATATAAAC 1761 chrXptel1M 250162 AAGAACAA---TAAAAAGCACATGATTATAGTAATAGATGCAGAAAAATC 250208 ii v ---i v vvi iv L1P1_orf2#LIN 1762 AGAACCAAAGACAAAAACCACATGATTATCTCAATAGATGCAGAAAAGGC 1811 chrXptel1M 250209 TTTTGAGAAAACTCAATAGC 250228 i v i i i L1P1_orf2#LIN 1812 CTTTGACAAAATTCAACAAC 1831 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 27.70 CpG sites = 23, Kimura (unadjusted) = 29.75 Transitions / transversions = 1.77 (23/13) Gap_init rate = 0.05 (8 / 152), avg. gap size = 2.50 (20 / 8) 243 30.36 7.39 5.64 chrXptel1M 250085 250625 (749375) L1MD_orf2#LINE/L1 1676 2225 (1069) m_b331s551i6 13918 chrXptel1M 250085 TAAACTATGATCAGATTGGACTTTTATTC--AGAATCCAGGGTTGATTCA 250132 v i i ii v i-- --i ? v i i i L1MD_orf2#LIN 1676 TACACCATGACCAAGTGGGG--TTTATTCCAGGNATGCAAGGCTGGTTCA 1723 chrXptel1M 250133 ACTGTAGGAATACTATAAATGT---------TAAAAACAAG---AACAAT 250170 ivv v i vv v v --------- vv i --- v v L1MD_orf2#LIN 1724 ATATTCGAAAATCAATCAATGTAATCCACCATATTAACAGGCTAAAGAAG 1773 chrXptel1M 250171 AAAAAGCACATGATTATAGTAATAGATGCAGAAAAATCTTTTGAGAAAAC 250220 v i vi v v v v i L1MD_orf2#LIN 1774 AAAAATCACATGATCATATCAATTGATGCAGAAAAAGCATTTGACAAAAT 1823 chrXptel1M 250221 TCAATA-GCAGTC----------CTCTTAGAACACC-CAAATGCAGAGGA 250258 i -v v ---------- i ? v i-vi iv i L1MD_orf2#LIN 1824 TCAACACCCATTCATGATAAAAACTCTCAGNAAACTAGGAATAGAGGGGA 1873 chrXptel1M 250259 ATTTATAGATCTTTCCTTAATATGATAGAG-TCATAAAAATAAAATGTTT 250307 ----------i i iv i -v vv v v ----i L1MD_orf2#LIN 1874 A----------CTTCCTCAACTTGATAAAGAGCATCTACAAAAAA----C 1909 chrXptel1M 250308 CTAAAACCAAGAACTGGAATATGTTATGG-GAATAAATCAGTCCTTT-GC 250355 v i i v v ---- iv v - vi v v i v -v L1MD_orf2#LIN 1910 CTACAGCTAACATC----ATACTTAATGGTGAAAGACTGAATGCTTTCCC 1955 chrXptel1M 250356 AATAAGCTCAGTGATAAATAAAGGGTGTTCGTTATTAGTACAATTATTTG 250405 vv v i vi i ivv i i i v i vi vv ii L1MD_orf2#LIN 1956 CCTAAGATCGGGAACAAGGCAAGGATGTCCGCTCTCACCACTCTTATTCA 2005 chrXptel1M 250406 ATGTAGTATTAGAAATGCTTTATGAAAATATGAATATCATTATGAAAAGA 250455 ii i i i -- i - vv i ii- -vivi v i L1MD_orf2#LIN 2006 ACATAGTACTGGAAGT--TCTA-GCCAGTGC-AATA-AGGCAAGAAAAGG 2050 chrXptel1M 250456 AAATAATGTGAAGGAAAAAACCTAGGCAAAGAGGAATT---ACTG---CC 250499 ---- v v v vv v v i i v --- --- i L1MD_orf2#LIN 2051 AAATAA----AAGGCATACAGATTGGAAAGGAAGAAATAAAACTGTCCCT 2096 chrXptel1M 250500 ATTTTCAGATTATCTGATTGTTTATTTAGAGAACCCTAGAGAGT-TACAT 250548 v v iv i iv i i i ii i - - L1MD_orf2#LIN 2097 ATTTGCAGATGACATGATTGTCTACGTAGAAAATCCCAAGGAATCTACA- 2145 chrXptel1M 250549 AAAAAATTATTTGAAATAA----TGACTTCAACAAAGTTTAAGGATATCC 250594 i vi v v ---- v i i ivv - v L1MD_orf2#LIN 2146 AAAAAACTCCTAGAACTAATAAGTGAGTTCAGCAAGGTCGCAGGATA-CA 2194 chrXptel1M 250595 AAATAAATCCAGATAAATCATTGGTGTTTCT 250625 i ? ivi v v v v i L1MD_orf2#LIN 2195 AGATNAACATACAAAAATCAATTGTATTTCT 2225 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.74 CpG sites = 75, Kimura (unadjusted) = 39.70 Transitions / transversions = 0.94 (75/80) Gap_init rate = 0.08 (44 / 540), avg. gap size = 1.61 (71 / 44) 274 26.11 7.41 0.69 chrXptel1M 250480 250614 (749386) L1PB_orf2#LINE/L1 2071 2214 (1080) m_b331s551i7 13918 chrXptel1M 250480 GGCAAAGAGGAATT---ACTGCCA---TTTTCAGATTATCTGATTGTTTA 250523 i v --- i i--- v v v v i ? L1PB_orf2#LIN 2071 GGTAAAGAGGAAGTCAAACTGTCGCTGTTTGCTGATGATATGATCGTNTA 2120 chrXptel1M 250524 TTTAGAGAACCCTAGAGAGTTACATAAAAAATTATTTGAAAT----AATG 250569 ii i i v ivivi i ii vi v v ---- ? L1PB_orf2#LIN 2121 CCTAGAAAACCCTAAAGACTCCTCCAGAAAGCTCCTAGAACTGATAAANG 2170 chrXptel1M 250570 ACTTCAACAAAGTTTAAGGATATCCAAATAAATCCAGATAAATCA 250614 v i v? - v v vi v i L1PB_orf2#LIN 2171 AATTCAGCAAAGTTTCNGGATA-CAAAATTAATGTACACAAATCA 2214 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 31.18 CpG sites = 18, Kimura (unadjusted) = 33.44 Transitions / transversions = 1.06 (18/17) Gap_init rate = 0.03 (4 / 134), avg. gap size = 2.75 (11 / 4) 298 31.18 6.06 6.06 chrXptel1M 250708 250905 (749095) C MamRTE1#LINE/RTE-BovB (1539) 2273 2076 m_b331s601i26 13919 chrXptel1M 250708 GAGCTTGCCAGCAAAGACTAAAAGAGAGACCCCTCTGTGATTGTGATAGG 250757 v v ivv iv ? iv v vi ii ivii v C MamRTE1#LINE/ 2273 GATCTTGCCAGCAATGGAGAGCAGNGAGATGCCGCGATAGTTGCCGCAGT 2224 chrXptel1M 250758 AAAATCTCTTTCTTTACCT-TTATAGATATGGACAGTGGTGGCATCCTTG 250806 v iv i iv i v i - iv ivv iii i i C MamRTE1#LINE/ 2223 CAGCTTTCTCGCCTTTCTTCTTGAAGATGGTGATGATAGTGGCATCTTTG 2174 chrXptel1M 250807 AACTCCTGGGGGATAACTTCTTC--TAG-CCATATAACCTAGAAGATTTG 250853 v v v --- i -- v- i-- - ---i C MamRTE1#LINE/ 2173 AAATCCTGCGGCAT---TTCCTCGGTACTCCATATG--CT-GAAGA---A 2133 chrXptel1M 250854 AGTCAGCTTTTGCA------TGAGCAATG--GACCCTCCCACCTTATAAA 250895 --- i v ------ i ii --vv i vv iv C MamRTE1#LINE/ 2132 A---AGCCTATGCAGACGTCTAAGCAGCGTCTCCCCTTCCTGCTTGAAAA 2086 chrXptel1M 250896 TCTCAGCTGG 250905 v C MamRTE1#LINE/ 2085 TCTCAGCAGG 2076 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.59 CpG sites = 30, Kimura (unadjusted) = 41.30 Transitions / transversions = 1.07 (30/28) Gap_init rate = 0.09 (17 / 197), avg. gap size = 1.41 (24 / 17) 17 0.00 0.00 0.00 chrXptel1M 251521 251539 (748461) (TA)n#Simple_repeat 1 19 (0) m_b331s252i13 13920 chrXptel1M 251521 TATATATATATATATATAT 251539 (TA)n#Simple_ 1 TATATATATATATATATAT 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 199 25.00 0.00 0.00 chrXptel1M 251924 251967 (748033) C MamRTE1#LINE/RTE-BovB (2206) 1606 1563 m_b331s601i27 13919 chrXptel1M 251924 AGAAGCTTCTGAATTTTCTCATCATTTTCATCAAACCAGTCTTG 251967 v v i iivvi i ii C MamRTE1#LINE/ 1606 AGTAGCTTCTTAATCTCTGAGTCATTCTCATCAAACCAGTTCTG 1563 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.32 CpG sites = 7, Kimura (unadjusted) = 31.32 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 1210 28.82 1.67 1.52 chrXptel1M 252282 252940 (747060) L1M5_orf2#LINE/L1 1764 2423 (871) m_b331s551i8 13921 chrXptel1M 252282 AATAAACAAACAAAAATCATGAGATTATTTCAATAAATGCAGAAAAAACA 252331 vi i- iv i i i i L1M5_orf2#LIN 1764 AATAAAGGAG-AAAAATCATATGATCATCTCAATAGATGCAGAAAAAGCA 1812 chrXptel1M 252332 TTTGATAAAAT-CAATACCCATTCCTATTAAAAAAAAAACACTACAGAAT 252380 i - i v iv ----- v - v v L1M5_orf2#LIN 1813 TTTGACAAAATTCAACACCCATTCATGATAAAAA-----CTCT-CAGCAA 1856 chrXptel1M 252381 ATT-GGAATAACTGAAGATTTCCTTACAATGATCAAGAGCATCTATTTAA 252429 i - ivv iii i i vvv v i ivv L1M5_orf2#LIN 1857 ACTAGGAATAGAAGGGAACTTCCTCAACCTGATAAAGGGCATCTACGAAA 1906 chrXptel1M 252430 AACTATCAGCAAGCATCATATGTAATGGGGACAAACTAGAACCATTCCCA 252479 ivv ? i iv v v ? ii ?v v v L1M5_orf2#LIN 1907 AACCTACAGCNAACATCATACTTAATGGTGAAANACTGAANGCTTTCCCC 1956 chrXptel1M 252480 AAAGGATCAGGAGTAAAACAAGGTTGCCCACTATCACTATTAATCTTCAA 252529 vv i i ii i v i i ? i i vv v L1M5_orf2#LIN 1957 CTAAGATCGGGAACAAGACAAGGATGTCCGCTNTCACCACTTCTATTCAA 2006 chrXptel1M 252530 TATTGTATTAGAAATGCTAGCTTTGGCAATAAAAGAAGAAAAAGAGATCA 252579 i i i ii v ivvv iiv i v L1M5_orf2#LIN 2007 CATTGTACTGGAGGTCCTAGCCAGTGCAATAAGGCAAGAAAAAGAAATAA 2056 chrXptel1M 252580 AAGGAATTAGAGTAGGCAATGAGGAAATCAAATTATCACTCTTTGCTGAT 252629 v v iii v v v i v i i ?i v i v L1M5_orf2#LIN 2057 AAGGCATAAAGATTGGAAAGGAAGAAATAAAACTGTCNTTATTCGCAGAT 2106 chrXptel1M 252630 GCTATGATGGTATACTTGGAGAA-CCCAGAGAATCAACTAAAAAACTACT 252678 vi v ? v i i - ? i v v ? L1M5_orf2#LIN 2107 GACATGATTGTNTACGTAGAAAATCCNAAAGAATCTACAAANAAACTACT 2156 chrXptel1M 252679 AGAAATTATCAACATCTTTAGCAAAGTGGAAGGATACAAAATAAATCCAC 252728 v v v iiivv i v v? ii v vi L1M5_orf2#LIN 2157 AGAACTAATAAGTGAATTTAGCAAGGTCGCNGGATACAAGGTCAATATAC 2206 chrXptel1M 252729 ATAAATGATAAGCATTTTTATATATTGTCAACAAAATCTAGCAGCAAGAG 252778 v v vvv i i i iv vvv v v iv v i L1M5_orf2#LIN 2207 AAAAATCAATTGTATTTCTATATACTAGCAACAAACAATTGGAAAATGAA 2256 chrXptel1M 252779 ATACAAAGAGAAATCCCATTTAATATAACTGTTGATAATAAAAAACATTT 252828 vi? i iv v vv i vvivi v i v? i i L1M5_orf2#LIN 2257 ATTTNAAAAACAATACCATTTACAATAGCATCAAAAAACATNAAATACTT 2306 chrXptel1M 252829 TGGAGTCAACCCCA-AGAGTAAGT-CAGGAACTATA---TGAACACAACT 252873 v i v i iv - i i? v - i v ? --- --- L1M5_orf2#LIN 2307 AGGAATAAATCTAACAAAANATGTGCAAGACCTNTACACTGAA---AACT 2353 chrXptel1M 252874 ACAAAACATTTCC-ACACAAA--AAGTCAGATCTAATCAATTGGAAAAAT 252920 v i- v v -- ivv i vi v i i L1M5_orf2#LIN 2354 ACAAAACATTGCTGAGAGAAATTAAAGAAGACCTAAATAAATGGAGAGAT 2403 chrXptel1M 252921 ATCAAGTGCTCATGGGTAGG 252940 vvvi i i v L1M5_orf2#LIN 2404 ATACCATGTTCATGGATTGG 2423 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.72 CpG sites = 91, Kimura (unadjusted) = 37.72 Transitions / transversions = 0.95 (91/96) Gap_init rate = 0.03 (18 / 658), avg. gap size = 1.17 (21 / 18) 994 33.21 9.55 3.74 chrXptel1M 256927 257711 (742289) C MamRTE1#LINE/RTE-BovB (2637) 1175 347 m_b331s601i28 13919 chrXptel1M 256927 TTTCCTGTGAGGTAAATGGAAGATAGTATTGGTGAT-----GGTCATGTT 256971 i i i vv iii i i ----- v v i C MamRTE1#LINE/ 1175 TCTCTTATTCGGTAGGCGGAAGATGGTGTTGGTGATTACGAGCTGATGCT 1126 chrXptel1M 256972 --------------AGCAGTAAGT-GATCATTACTATTGCTGTTTCTGAT 257006 -------------- -i - i i i ?vvv ii C MamRTE1#LINE/ 1125 TGGCACATTCGCTGAGCAG-GAGTAGACCATTGCTGTTNAGCTTTCCAAT 1077 chrXptel1M 257007 TCCATTCCTCCCAAGGACTCCCTGCCATGTCT-GGTAGTCTGGGTCTATC 257055 i i v?vvi i v iiiiv i i - i - vvv i v iv C MamRTE1#LINE/ 1076 CCCGTGNGGTCCGATGACTTTTCTCCACGTTTCGGCA-TCGCTGCCGACA 1028 chrXptel1M 257056 CTAGCATTAAAATCACACAGAATTATAAGCTTGTCTTCTTTCAGCACCTT 257105 vv i i v v ivi iv v vvv v ii i vi C MamRTE1#LINE/ 1027 CGTGCGTTGAAATCTCCCGTGACGATCAGCTTGTCAGATGTTGGTACCGC 978 chrXptel1M 257106 GGTGATAAAGGTCCCCAGGTCTTCATAAATTTTTTTTTTTTTACCTCATC 257155 v i i ivv vi i i ii i v i i i -- C MamRTE1#LINE/ 977 TGCGATGAGTCTGTCCAGATCCTTGTAGAATCTTTCTTTCT--CCTCATC 930 chrXptel1M 257156 AGGGCTCATCATGATGGGAGCATAGCCACTGATGATGGTGGTATTACACT 257205 i vii i i i vv i i i ?vi i C MamRTE1#LINE/ 929 GGTATTCGTCATGGTGGGGGCATATGCGCTGATGACGGTGGCANAGCGCT 880 chrXptel1M 257206 TCCCTACAAGTGGCAATTTCATTGTCATGAGTCCATCATTCGCTCCTTTT 257255 iiv viv v? i ivivi vv v v vi i ?iiv i v C MamRTE1#LINE/ 879 TTTGTTTCAGANGTAGGCGTAGGGTCATCAGACGGTCACTNATGCCTCTG 830 chrXptel1M 257256 GGAAAACCTATGA-ACTTGTTTACTAAATTAGT-TTTGATTTCCAAACC- 257302 v ii iv -? -vv - i v v - i v v i i- C MamRTE1#LINE/ 829 GGCAAATTTGGGAGNCTTG-AGAC-AAGTGACTGTCTGATTGCAAAGCTG 782 chrXptel1M 257303 ACACCACCTTCATGGCACTCCCTTCACTCT----------GGCCAATCCA 257342 i ------- iv --v v i ---------- i vv C MamRTE1#LINE/ 781 ACGCC-------TGAGA--GCCGTCGCTCTGAAGAGGGAAGACCTCTCCA 741 chrXptel1M 257343 GAAAAATACGGATCCAGCTCCAACTTTGAGAAGCTGGCTTTCATTTG--- 257389 i vi v ? i v viii ivivi v i iv --- C MamRTE1#LINE/ 740 GAAGAAGGCGTANCCGGCACCTGTCTCCGTGAGCTGTCCTTCATCAGGAA 691 chrXptel1M 257390 --CTTATTTCATTCAGGGCTGCTAT-TTGAATGTGATATCTCCTGATTTC 257436 -- vi ii v v v - i v vi - vvvv v C MamRTE1#LINE/ 690 GTCTGGTTTCGCTCAGTGCGGCGATGTCGACTCCG-TATCTGGACAGTTC 642 chrXptel1M 257437 TCTTGCA------GCTGTTGATCTTTCAGGTCCACTG--GATTTTGT-GT 257477 v v i------ i vv v v v -- v i i -i C MamRTE1#LINE/ 641 ACGTGCGACGAGTGCCGTTCTTCTTTCTGGACGACTGCTGTTCTCGTCAT 592 chrXptel1M 257478 TGTCTATGTGTGT--ACATTCCATGTAC-CAATGGTGAGCAGAATCATCT 257524 i iv - i vi-- ii - - v------ iv C MamRTE1#LINE/ 591 CGCATA-GCGTCCTGATGTTCCATG-ACGCAATGGTT------ATTTTCT 550 chrXptel1M 257525 TTGCAAACATTTTTGTAG-TTTCTTTTTG--TTTGGAACACAAG-GTGGG 257570 i-----?? ?v - v -- v v i -? iii C MamRTE1#LINE/ 549 TTGT-----NNTNGGTAGTTTTCTATTTGNTTTTGCACCGCAAGANTAAA 505 chrXptel1M 257571 ATTCTTACCAGCCACAATAATCAGGTTA--------TGGTTAT-ATGCAG 257611 -- ii v i i v v -------- i? v -ii vi C MamRTE1#LINE/ 504 A--CCCACCAGACGCGATAATCTGGTGAGCCAGNTTTGANTTTGGCGAGG 457 chrXptel1M 257612 CAGGCAGT-TTTAGCGCACCTTTTCTAGCCCCTTCTTCAC--------AG 257652 ii- v ? ii i-------- C MamRTE1#LINE/ 456 CAGGCAACGTTTAGGGCACCTTTTCTAGNCCCTTCCCCATTCGGAGTGAG 407 chrXptel1M 257653 CAGTTTGAGCCTTAA-AAAGCTACTCAGGCACTCAGGAGGCTGCTGAATC 257701 ivi ?v v - ii i i i ?v i iv C MamRTE1#LINE/ 406 CAGCGCGNTCCTAAACAGGGCTGCTCAGACACCCAGGNCGCTGCCGAACG 357 chrXptel1M 257702 CCACTGCTGC 257711 vii C MamRTE1#LINE/ 356 GTGCTGCTGC 347 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.27 CpG sites = 140, Kimura (unadjusted) = 46.59 Transitions / transversions = 1.26 (140/111) Gap_init rate = 0.07 (55 / 784), avg. gap size = 1.93 (106 / 55) 953 26.60 1.54 2.73 chrXptel1M 258364 258622 (741378) C MIRb#SINE/MIR (0) 268 13 m_b331s601i29 13922 chrXptel1M 258364 AATCATGATGTTACAACCTTTAAAGAGTACTCACTATGTACCTGGCACCA 258413 v iiv i -- v vv ii i i v ii C MIRb#SINE/MIR 268 AATAATAGAGCTAC--CATTTATTGAGCGCTTACTATGTGCCAGGCACTG 221 chrXptel1M 258414 TGCTAAATGCTTTATAAATGTAATCTCATTTAATCTTCATAACAAGCCTG 258463 ii i viii v i i v C MIRb#SINE/MIR 220 TGCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTG 171 chrXptel1M 258464 GGAGGAAGATGGTATCATTATCCCTATTTTTTTGATGAGGAAATGGAGGC 258513 v v --- i i viv iv C MIRb#SINE/MIR 170 CGAGGTA---GGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGC 124 chrXptel1M 258514 AGACAGAAATGAAGTGACTTGCCCAGGGATCACACAGCAAATTAGTGTAT 258563 vv v ii v i i - v i v -ii C MIRb#SINE/MIR 123 TCAGAGAGGTTAAGTAACTTGCCCAAGG-TCACACAGCTAGTAAGTG-GC 76 chrXptel1M 258564 ATGGTCATGTTTC-AACTCAGAT---TTTAACTTCAAGCTCAGTGCTCTA 258609 vi i iv v - i i --- i i i ivi v v C MIRb#SINE/MIR 75 AGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTT 26 chrXptel1M 258610 TCCACAGTGCCAC 258622 v ii C MIRb#SINE/MIR 25 TCCACTGCACCAC 13 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.77 CpG sites = 40, Kimura (unadjusted) = 33.66 Transitions / transversions = 1.48 (40/27) Gap_init rate = 0.03 (9 / 258), avg. gap size = 1.22 (11 / 9) 579 31.35 5.46 2.14 chrXptel1M 258759 259436 (740564) L1M4_orf2#LINE/L1 749 1448 (1846) m_b331s551i9 13923 chrXptel1M 258759 GAAGACTAAACAACCTAATCTCAGAGAATGA---GGAAAAGGAAGAAATC 258805 i i i vi v ii i v iv --- vv i L1M4_orf2#LIN 749 GGAAATTAAACAACACACTCCTAAATAACCAATGGGTCAAAGAAGAAATC 798 chrXptel1M 258806 ATAGAAATGATCAATAATTTCATTAAGGAGAATGATTAAAATGAGA---C 258852 i iiiivi i iv v v v i iv --- i i --- L1M4_orf2#LIN 799 ACAAGGGAAATTAGAAAATACTTTGAGATGAATGA---AAACGAAAACAC 845 chrXptel1M 258853 AATATAGCAAAACTTATGGGATGCAGCAAAAGCAGGAATCAG-GAAAAAT 258901 i v ? viv i - ii L1M4_orf2#LIN 846 AACATACCAAAACTTATGGGATGCAGCNAAAGCAGTGCTTAGAGGGAAAT 895 chrXptel1M 258902 CTAAATCTCTAAATGCTTATATCAATAA--AATCTAAATCTCTAAATGCT 258949 i v v v i i v -- vvv i v viiv L1M4_orf2#LIN 896 TTATAGCTGTAAATGCCTATATTAAAAAAGAAGAAAGATCTCAAATCAAT 945 chrXptel1M 258950 TATATCAATGTGCATTTTAA-AAGCTACAA----AAGAACAAAGTTA--C 258992 v iv v viv v ii - i v ---- i v v -- L1M4_orf2#LIN 946 AACCTAACCTTCCACCTTAAGAAACTAGAAAAAGAAGAGCAAACTAAACC 995 chrXptel1M 258993 CAATGAAATGACAAATTGGAGG---TCTTAAA-ATTAAAGGTGAGATTAA 259038 v v --i i vv i --- vv - i vv i v L1M4_orf2#LIN 996 CAAAGCAA--GCAGAAGGAAGGAAATAATAAAGATTAGAGCGGAAATAAA 1043 chrXptel1M 259039 TAAAATTGAGTGTAAGAAAACCTTTGAATTAATAAATAAACCTAGGAGTT 259088 i v vi ii vv v ivv v ii v i ii L1M4_orf2#LIN 1044 TGAAATAGAGAATAGAAAAACAATAGAGAAAATCAACGAAACCAAAAGTT 1093 chrXptel1M 259089 GGTTTCATGAAAA----AATAAAATAGATAAACCATTGGTTAATATGATT 259134 iiv ---- i v i v i i ivv -i L1M4_orf2#LIN 1094 GGTTCTTTGAAAAGATCAACAAAATTGACAAACCTTTAGCTAGACTGA-C 1142 chrXptel1M 259135 TTTTAAAAGGAGAGAAGAAAAC-CAAATCACTAGTGTTGAAAATGAAA-A 259182 ivvv ii - i - i ivi iiii - L1M4_orf2#LIN 1143 CAAGAAAAAAAGAG-AGAAGACTCAAATTACTAAAATCAGGAATGAAAGA 1191 chrXptel1M 259183 GGGTAAATATAACACTGAT----GATGATTTCAAGTAATTATAAGGAGTT 259228 v v - vi i i----v vi v vv ivi iiv L1M4_orf2#LIN 1192 GGGGACAT-TACTACCGACCTTACAGAAATAAAAAGGATTATAAGGGAAT 1240 chrXptel1M 259229 AC-ATGATCTAATTATAGGTCAATAACCTGAACACTTTAGTCAAAATGGA 259277 - v - i v i i vi ii i vii vii L1M4_orf2#LIN 1241 ACTATGAAC-AATTGTATGCCAACAAATTAGATAACCTAGATGAAATGGA 1289 chrXptel1M 259278 AGAATATTTACAAAAATATAAACTGCCTAGATTAGCTGAAGAGGAAATAC 259327 vi vii v i i i i v i i ii v i v L1M4_orf2#LIN 1290 CAAATTCCTAGAAAGACACAAACTACCGAAACTGACTCAAGAAGAAATAG 1339 chrXptel1M 259328 AATATCTAAATGGACCTATTTTGGAAAAA--AACGAAATTGAACAGGCCA 259375 v i i ----- v -- v i ivi iv L1M4_orf2#LIN 1340 AAAATCTGAATAGACCTAT-----AACAAGTAAAGAGATTGAATTAGTAA 1384 chrXptel1M 259376 T-AAAGAACTTCCT---AAGAAAAACACCAGAATCAGATGGATTTCCAAG 259421 - i i--- i - i?i v iv vi L1M4_orf2#LIN 1385 TCAAAAAACTTCCCACAAAGAAAAGC-CCAGGNCCAGATGGCTTCACTGG 1433 chrXptel1M 259422 TGAATTTTATCAAAC 259436 i i L1M4_orf2#LIN 1434 TGAATTCTACCAAAC 1448 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.10 CpG sites = 118, Kimura (unadjusted) = 41.93 Transitions / transversions = 1.31 (118/90) Gap_init rate = 0.05 (32 / 677), avg. gap size = 1.62 (52 / 32) 12 20.84 0.00 2.94 chrXptel1M 259839 259873 (740127) (AAGA)n#Simple_repeat 1 34 (0) m_b332s252i0 13924 chrXptel1M 259839 AAGAACAAAAGAAAAATTAGAAGGAAACAAAGAAA 259873 vi i -v i v (AAGA)n#Simpl 1 AAGAAAGAAAGAAAGA-AAGAAAGAAAGAAAGAAA 34 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 465 26.72 7.56 8.52 chrXptel1M 261020 261244 (738756) MIRb#SINE/MIR 13 235 (33) m_b332s601i0 13925 chrXptel1M 261020 GTGGTACCCTAGTGGGTAGAGCAGGAGAGCAGGAATCAGGAGGACCTAAA 261069 i --- iv v i vviv i ivi iii MIRb#SINE/MIR 13 GTGGTGC---AGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGG 59 chrXptel1M 261070 GTCATATCCAGCCTCAGACACT------------GACTCAGGGCAAGTCA 261107 v iv v v v v ------------ iiv i MIRb#SINE/MIR 60 TTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTA 109 chrXptel1M 261108 CTTCACTGCTGTGAACCTGATGTGAGGACCTGATGTCCTCAGCTGTGAAA 261157 v iv v i v ------------i v v i MIRb#SINE/MIR 110 CTTAACCTCTCTGAGCCTCA------------GTTTCCTCATCTGTAAAA 147 chrXptel1M 261158 TGGGGATAATACCAGCCCCTAACTCCCCAAGGTTGT-----AGATCAAAT 261202 vi --- v v - i -----i i MIRb#SINE/MIR 148 TGGGGATAATAATA---CCTACCTCGC-AGGGTTGTTGTGAGGATTAAAT 193 chrXptel1M 261203 GCGATTCTGTTTGTAAAATGCTTGGCCTAGTACCTGGCACAT 261244 v vv iv ii i vi i MIRb#SINE/MIR 194 GAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACAT 235 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 31.94 CpG sites = 28, Kimura (unadjusted) = 33.38 Transitions / transversions = 1.04 (28/27) Gap_init rate = 0.09 (21 / 224), avg. gap size = 1.71 (36 / 21) 316 26.80 2.26 4.62 chrXptel1M 262854 262986 (737014) MIR1_Amn#SINE/MIR 1 130 (100) m_b332s601i1 13926 chrXptel1M 262854 TAGGGGACAGCTAGT-TGGTGCATTGGACAGAGCACAGTCCTGA-AGTCA 262901 --- vi - vi v i v vv i- v i MIR1_Amn#SINE 1 TAGGG---AGGCAGTGTGGTCTAGTGGATAGAGCACTGGACTGGGACTCG 47 chrXptel1M 262902 GGGGAGCTGAGTTCAAATCTAACCTCAGACACTTAATATTTACTGTGTGA 262951 i v i ? ? iviv v v ?i---ii?i ? MIR1_Amn#SINE 48 GGAGACCTGGGTTCNANTCCCGGCTCTGCCACTNG---CCNGCTGNGTGA 94 chrXptel1M 262952 TTCTGGACAAGTCACTTAATCCCAGT-TGCTTCAGT 262986 iii i ? i i vv -? i MIR1_Amn#SINE 95 CCTTGGGCAAGTCACTTNACCTCTCTGNGCCTCAGT 130 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.88 CpG sites = 20, Kimura (unadjusted) = 36.53 Transitions / transversions = 1.43 (20/14) Gap_init rate = 0.07 (9 / 132), avg. gap size = 1.00 (9 / 9) 400 24.27 1.89 2.86 chrXptel1M 262869 262974 (737026) MIRc#SINE/MIR 11 115 (153) m_b332s601i2 13926 chrXptel1M 262869 TGGTGCATTGGACAGAGCAC-AGTCCTGAAGTCAGGG-GAGCTGAGTTCA 262916 v v -i v i i i- v i i MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chrXptel1M 262917 AATCTAACCTCAGACACTTAATATTTACTGTGTGATTCTGGACAAGTCAC 262966 i iviv v v v ---i iii i MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTACTA---GCTGTGTGACCTTGGGCAAGTCAC 107 chrXptel1M 262967 TTAATCCC 262974 i i MIRc#SINE/MIR 108 TTAACCTC 115 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 27.36 CpG sites = 16, Kimura (unadjusted) = 30.18 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.05 (5 / 105), avg. gap size = 1.00 (5 / 5) 328 28.44 1.90 2.88 chrXptel1M 262882 262986 (737014) MIR#SINE/MIR 21 124 (138) m_b332s601i3 13926 chrXptel1M 262882 AGAGCACAGTC-CTGAAGTCAGGGGAGCTGAGTTCAAATCTAACCTCAGA 262930 i v - i i ivviv i i iviv v v MIR#SINE/MIR 21 AGAGCACGGGCTCTGGAGCCAGACTGCCTGGGTTCGAATCCCGGCTCTGC 70 chrXptel1M 262931 CACTTAATATTTACTGTGTGATTCTGGACAAGTCACTTAATCCCAGT-TG 262979 v ---i iii i i i i vv - MIR#SINE/MIR 71 CACTTACTA---GCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTG 117 chrXptel1M 262980 CTTCAGT 262986 i MIR#SINE/MIR 118 CCTCAGT 124 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 32.27 CpG sites = 18, Kimura (unadjusted) = 36.96 Transitions / transversions = 1.64 (18/11) Gap_init rate = 0.05 (5 / 104), avg. gap size = 1.00 (5 / 5) 21 8.18 5.13 0.00 chrXptel1M 262987 263025 (736975) (AAAAG)n#Simple_repeat 1 41 (0) m_b332s252i1 13927 chrXptel1M 262987 AAAAAAAAAATAAAG-AAAGAAAAGAAAAG-AAAGAAAAGA 263025 i iv - - (AAAAG)n#Simp 1 AAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGA 41 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2) 391 30.80 10.20 0.62 chrXptel1M 264567 264713 (735287) MIR3#SINE/MIR 37 197 (11) m_b332s601i4 13928 chrXptel1M 264567 GATTCTAAAGACT--GGTTCTGGCTCTTGCTCTGCCACCA---------- 264604 v vii i-- i ii iv i ---------- MIR3#SINE/MIR 37 GAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTG 86 chrXptel1M 264605 ---CTTTGAGCAAGCTATTCAACCCTTGTGGGCTTCAGATGTGTCCTCTG 264651 --- i i ii i iv ii v i v viv v MIR3#SINE/MIR 87 TGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTG 136 chrXptel1M 264652 CAAAATGAAAGGATTGGACCGGATGACCTCCATGACCCTTTAGAGCTCCC 264701 i ii i ii i i v ii i vv - i MIR3#SINE/MIR 137 TAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCT-CT 185 chrXptel1M 264702 AAAAGTCTATGA 264713 i v v MIR3#SINE/MIR 186 GACATTCTATGA 197 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 40.81 CpG sites = 31, Kimura (unadjusted) = 42.08 Transitions / transversions = 2.21 (31/14) Gap_init rate = 0.03 (4 / 146), avg. gap size = 4.00 (16 / 4) 18 13.26 0.00 0.00 chrXptel1M 264926 264958 (735042) (GAG)n#Simple_repeat 1 33 (0) m_b332s252i3 13929 chrXptel1M 264926 GAGGAGGAGGATGAAAAGGAGGAGGTGGAGGAG 264958 v ii v (GAG)n#Simple 1 GAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG 33 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 304 28.23 8.87 0.00 chrXptel1M 265449 265572 (734428) L2d_3end#LINE/L2 380 514 (2) m_b332s601i5 13930 chrXptel1M 265449 TTGTCTCTCCCATCAGAAC-TAA----CTTGA----AAGGGCC-TGTCTT 265488 i v ii vi- ---- ---- i i - L2d_3end#LINE 380 TTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTT 429 chrXptel1M 265489 TTGC-CTTCTTTTGTTCCCCCCAGCACTTAGCACGATTCCTGGCACATAG 265537 v i -? i ? i v i i ii v ivi L2d_3end#LINE 430 ATACTNTTTTNTCGTTCCCCACAGCGCCTAGCACAGTGCTGAGCACATAG 479 chrXptel1M 265538 AAGGTGCTTAATCAACACTGACCAACTGGCTGACT 265572 v i i v i viiii i ii i L2d_3end#LINE 480 TAGGCGCTCAATAAATACTTGTTGATTGATTGATT 514 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 34.41 CpG sites = 26, Kimura (unadjusted) = 38.65 Transitions / transversions = 2.89 (26/9) Gap_init rate = 0.04 (5 / 123), avg. gap size = 2.20 (11 / 5) 267 37.56 1.65 0.54 chrXptel1M 267800 267981 (732019) C L2#LINE/L2 (341) 2741 2558 m_b332s601i6 13931 chrXptel1M 267800 ACTGGTTAGGAGACT--TGCAATAGTCCAGGCAAG-GAGGGAAGAGGTTA 267846 ii i -- i i i - v ivi v i - C L2#LINE/L2 2741 ACCAGTTAGGAGGCTATTGCAGTAATCCAGGCGAGAGATGATGGTGGCT- 2693 chrXptel1M 267847 TATTCTAGGGAAGCAGCAGAGCAAGTGGAGAGAGGAGAATGGGCCTGAGA 267896 ivv i vi ii v v i v i v ivi iiiivi C L2#LINE/L2 2692 TGGACCAGGGTGGTGGCAGTGGAGGTGGTGAGAAGTGGTCGGATTCTGGA 2643 chrXptel1M 267897 GAGATTTCAGAGGGAAAAGTAACATGACTTGGGGACTGACTGAGTCTGGG 267946 v v iii v i ivii v i vv iv i ii v C L2#LINE/L2 2642 TATATTTTGAAGGTAGAGCCGACAGGATTTGCTGATGGATTGGATGTGGG 2593 chrXptel1M 267947 GAATGACAAAAGGAAAAGAGTCCAGGGTCATTCTA 267981 vi v i i i i v i v i i C L2#LINE/L2 2592 GTGTGAGAGAAAGAGAGGAGTCAAGGATGACTCCA 2558 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 51.73 CpG sites = 43, Kimura (unadjusted) = 55.58 Transitions / transversions = 1.72 (43/25) Gap_init rate = 0.02 (3 / 181), avg. gap size = 1.33 (4 / 3) 493 24.97 7.14 2.74 chrXptel1M 268193 268332 (731668) C MIRc#SINE/MIR (120) 148 3 m_b332s601i7 13932 chrXptel1M 268193 CTTATTTTATAGATGAGGGAACTGAGGC--AAACAAGGCTAAGTGGCGTG 268240 ii i i -- i -i i i v C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGA-GAGGTTAAGTGACTTG 100 chrXptel1M 268241 GCCAGGGTCACACAGCCGAGAAGTGTCTGAGGCTGAATTTA--------T 268282 v i iiiv v v v v i i ii-------- C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGT 50 chrXptel1M 268283 CTTCCTGACTCCGGGTCTAACACTCTATCTATTGCATCACGTACCTGCCT 268332 ii i iii v i i i i--- C MIRc#SINE/MIR 49 CTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACA---CTGCCT 3 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 30.93 CpG sites = 26, Kimura (unadjusted) = 32.23 Transitions / transversions = 3.25 (26/8) Gap_init rate = 0.04 (6 / 139), avg. gap size = 2.33 (14 / 6) 319 30.83 9.67 5.90 chrXptel1M 269158 269550 (730450) L2#LINE/L2 1917 2323 (759) m_b332s601i8 13933 chrXptel1M 269158 TTCATCTCTTTCC-TCTTCTCT------CACTCC--TCAGTGCTTTGCTG 269198 v i i - ii ------ -- - --i L2#LINE/L2 1917 TTCCTCTCCTCCCATTCTCTCTTGAACCCACTCCAATCAG-GCTTT--CG 1963 chrXptel1M 269199 ACCTCATCATTCAACTGAAACTGTTCCCTCCAAAGTTAGCAATTATCTTT 269248 v i i i v i i iivi i i v v i ii L2#LINE/L2 1964 TCCCCACCACTCCACCGAAACTGCTCTTGTCAAGGTCACCAATGACCTCC 2013 chrXptel1M 269249 TAATTGCCAAACCTAATAGCCAGTTATTGTTTTTTTTTTCAATCATACTT 269298 vvi i i i i i i v iiv ii i------ v -- L2#LINE/L2 2014 ACGTTGCTAAATCCAATGGTCAATTCTCAGTCCTC------ATCTTAC-- 2055 chrXptel1M 269299 TTTATCTTCTTGCTAGCATCT------GTTGACCACTCTCTCTTCC---G 269339 v i ?iiv - i ------ i i i i ---i L2#LINE/L2 2056 TTGACCTNTCAGC-AGCATTTGACACAGTTGATCACTCCCTCCTTCTTGA 2104 chrXptel1M 269340 GACAC--TCTGCA-----TTTCTGTGGTACCACTTTGTGGTACTTGGTTT 269382 i -- v -----i iiv ii vi v ---- i L2#LINE/L2 2105 AACACTTTCTTCACTTGGCTTCCAGGACACCACACTCT----CCTGGTTT 2150 chrXptel1M 269383 GGCTCCCACCAGTC-----CCACTACTCCTCTGTTTCCTTTACTCATT-A 269426 vv i -- ----- i v i v i i vi -v L2#LINE/L2 2151 TCCTCCTACC--TCACTGGCCGCTCCTTCTCAGTCTCCTTTGCTGGTTCC 2198 chrXptel1M 269427 TCCACATCCC----ATTCCTT---GTGGGTGTCCCCCAAGGCTTCATTCT 269469 v i ---- iii ?--- v v v i ivi i L2#LINE/L2 2199 TCCTCATCTCCCCGACCTCTNAACGTTGGAGTGCCCCAGGGCTCAGTCCT 2248 chrXptel1M 269470 AACCCTTCTTCCCTTCTCCTTCTCTATTCCTTCTTTTTCTCTGAGTGACC 269519 vivv i i iv vi i v------i i ?i i L2#LINE/L2 2249 TGGACCTCTTCTCTTCTCTATCTACACTCA------CTCCCTNGGTGATC 2292 chrXptel1M 269520 TCATCCGCTCCTATGGATTTAATCATCATTT 269550 iv ii v vi i i L2#LINE/L2 2293 TCATCCAGTCTCATGGCTTTAAATACCATCT 2323 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 40.52 CpG sites = 77, Kimura (unadjusted) = 42.54 Transitions / transversions = 2.08 (77/37) Gap_init rate = 0.09 (35 / 392), avg. gap size = 1.77 (62 / 35) 207 35.05 2.06 0.00 chrXptel1M 269620 269716 (730284) L2#LINE/L2 2420 2518 (564) m_b332s601i9 13933 chrXptel1M 269620 GATATTCTGTGAGCATCTCAAACTCAACGTGGCTAGG-TAGGGCTCAGGA 269668 i iivi ii i i v i ii-iv ii vv L2#LINE/L2 2420 GATGTCTAATAGGCATCTCAAACTTAACATGTCCAAAACTGAACTCCTGA 2469 chrXptel1M 269669 TGTTTCCCCCCAAACCCGCCCTTCCTCCAAACTCTCAC-TTTCTGTCAA 269716 v i i i i i iv iv ii v - i v ? L2#LINE/L2 2470 TCTTCCCCCTCAAACCTGCTCCTCCCGCAGTCTTCCCCATCTCAGTNAA 2518 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 49.86 CpG sites = 24, Kimura (unadjusted) = 52.18 Transitions / transversions = 2.40 (24/10) Gap_init rate = 0.02 (2 / 96), avg. gap size = 1.00 (2 / 2) 20 6.76 0.00 0.00 chrXptel1M 270884 270914 (729086) (AGGGTT)n#Simple_repeat 1 31 (0) m_b332s252i4 13934 chrXptel1M 270884 AGGGTTAGGATTAGGGTTAGGGTTAGGGGTA 270914 i v (AGGGTT)n#Sim 1 AGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA 31 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 317 27.09 11.89 1.91 chrXptel1M 271020 271162 (728838) MIRc#SINE/MIR 2 158 (110) m_b332s601i10 13935 chrXptel1M 271020 GAGGCAGTTAGCTGTTACAGTGGATAGGGCAGTTGGCCTGGAGTCAGGGA 271069 -- - v i v i v v i i i MIRc#SINE/MIR 2 GAGGCAGT--G-TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chrXptel1M 271070 CATCTGACTTGAAATAC-----------------AGCTCTGGGAAACTGG 271102 v i iv vi i v ----------------- v v vvi MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 98 chrXptel1M 271103 GGGAGTCTCTTAACCTCTGTTTGCTTTTGTTTCTTTGACTGTAAAATGGA 271152 vi v v vv i iv i iiv i MIRc#SINE/MIR 99 GCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 chrXptel1M 271153 AATATTAATA 271162 i v MIRc#SINE/MIR 149 GATAATAATA 158 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 32.89 CpG sites = 18, Kimura (unadjusted) = 33.95 Transitions / transversions = 0.90 (18/20) Gap_init rate = 0.03 (4 / 142), avg. gap size = 5.00 (20 / 4) 23 25.57 0.00 0.00 chrXptel1M 272763 272822 (727178) (TTT)n#Simple_repeat 1 60 (0) m_b332s252i5 13936 chrXptel1M 272763 TTTTTGTTATTTTTTGGCTTGTTTTTTATTTTTCTTACTCATGTTTTTTT 272812 v v vvi v v i vi iv v (TTT)n#Simple 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chrXptel1M 272813 TTTTTTTTTT 272822 (TTT)n#Simple 51 TTTTTTTTTT 60 Matrix = Unknown Transitions / transversions = 0.44 (4/9) Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0) 239 12.20 0.00 0.00 chrXptel1M 272886 272926 (727074) MIRc#SINE/MIR 75 115 (153) m_b332s601i11 13937 chrXptel1M 272886 CACGTCCTGGCTGTGTGACCCTGGGCAAGTCACTTAACCCC 272926 v v i i i MIRc#SINE/MIR 75 CACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 13.42 CpG sites = 3, Kimura (unadjusted) = 13.42 Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 chrXptel1M 272938 272954 (727046) (A)n#Simple_repeat 1 17 (0) m_b332s252i6 13938 chrXptel1M 272938 AAAAAAAAAAAAAAAAA 272954 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 27 18.44 0.00 0.00 chrXptel1M 275374 275422 (724578) (A)n#Simple_repeat 1 49 (0) m_b332s252i7 13939 chrXptel1M 275374 AAGAAAAAGCAAACAACAACAACAAAAAAAAAAAAAAAAAAAAAAACAA 275422 i iv v v v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 49 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 753 32.60 1.69 2.93 chrXptel1M 277831 278244 (721756) L1ME4c_3end#LINE/L1 147 555 (275) m_b332s551i1 13940 chrXptel1M 277831 CTCCCTATTAACTGGAGGAATGCGAATTAAAACAATTCTGAGCTACTACC 277880 v v iiii i i i ivv v i ii L1ME4c_3end#L 147 CTCGCTAGTAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATT 196 chrXptel1M 277881 TCAGACCTATTAGATTGACTAATGAGCCAAAGGAG-GAAAATGACCAAAG 277929 i vi i ii v -i vii ii v- v iv v L1ME4c_3end#L 197 TTACGCCTATTAAATTAGCAAA-AATTTAAAAAATTGATAATACCCAATG 245 chrXptel1M 277930 CTGGAGGGAATGTGGGGAAAATGAGACATGAAGGCATCGTTGGGGGAACT 277979 v i i? i v v iv ?ivv vi i i v v ? L1ME4c_3end#L 246 CTGGCGAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANT 295 chrXptel1M 277980 GTGAATTGATTCAACCATTCTGGAGAACA-TTTGGAATTATGCCCAAAGG 278028 i i v v i i i - v v i iviv i L1ME4c_3end#L 296 GTAAATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGA 345 chrXptel1M 278029 GATATCAAAACATGCATACAAACCCTTTGACCTAGAAAGACCCCTACTGG 278078 vi v ii v ---- i v vv v v L1ME4c_3end#L 346 GCCATAAAAATGTTCATAC----CCTTTGACCCAGTAATTCCACTTCTGG 391 chrXptel1M 278079 GCCCGAATC---CCCAAAGAGATTTGTTTTTAAAGGGAAAACAATCTATA 278125 ---- i--- i i i --iv iv iiii v v L1ME4c_3end#L 392 G----AATTTATCCTAAGGAAAT--AATTCAAAAGAAGGAAAAAGCTATA 435 chrXptel1M 278126 TGCACAAAACTATTTATAGCAGCTCT-TTTCTCGGGGCAAAGAACTGAAA 278174 i iv i i v vi - v vivi i i i i L1ME4c_3end#L 436 TGCACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAA 485 chrXptel1M 278175 ATTGAGGGGATTCCCATCAAGTGGGAAATGGATGAATAAATTGTGGTATA 278224 ivivvvii vi v vv i v i i i i L1ME4c_3end#L 486 ACAACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACA 535 chrXptel1M 278225 T-GATTATGGTGGAATATTAT 278244 -? i -i i L1ME4c_3end#L 536 TCNACT-CGATGGAATATTAT 555 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 42.12 CpG sites = 77, Kimura (unadjusted) = 44.89 Transitions / transversions = 1.43 (77/54) Gap_init rate = 0.04 (17 / 413), avg. gap size = 1.12 (19 / 17) 290 31.88 2.84 2.11 chrXptel1M 278126 278266 (721734) L1MC3_3end#LINE/L1 433 574 (1958) m_b332s551i2 13940 chrXptel1M 278126 TGCACAAAACTATTTATAGCAGCTCTTTTC----TCGGGGCAAAGAACTG 278171 ivi v i i v ---- --- v i L1MC3_3end#LI 433 TGCACGCGAATGTTTATAGCAGCTTTATTCATAATCG---CCAAAAACTG 479 chrXptel1M 278172 AAAATTGAGGGGATTCCCATCAAGTGGGAAATGGATGAATAAATTGTGGT 278221 i iivivvii vi v vv vi i i i L1MC3_3end#LI 480 GAAGCAACCAAGATGTCCTTCAATAGGTGAATGGATAAACAAACTGTGGT 529 chrXptel1M 278222 ATATGATTATGGTGGAATATTATTGTTCTATAAGAAATGGTGAGC 278266 i vvv iii vvv v i ivii L1MC3_3end#LI 530 ACATCCATACAATGGAATATTATTCAGCGATAAAAAGAAATGAGC 574 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 39.99 CpG sites = 24, Kimura (unadjusted) = 42.50 Transitions / transversions = 1.20 (24/20) Gap_init rate = 0.03 (4 / 140), avg. gap size = 1.75 (7 / 4) 17 15.09 0.00 2.63 chrXptel1M 278713 278751 (721249) (AAAGAAA)n#Simple_repeat 1 38 (0) m_b332s252i8 13941 chrXptel1M 278713 AATGAAAAAATATAAAAGAAAAAAGAAAGAAAGTAATAA 278751 v v v - v v (AAAGAAA)n#Si 1 AAAGAAAAAAGAAAAAAGAAAAAAGAAA-AAAGAAAAAA 38 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.03 (1 / 38), avg. gap size = 1.00 (1 / 1) 284 35.23 7.39 0.00 chrXptel1M 278752 278927 (721073) C L2#LINE/L2 (1079) 2003 1815 m_b332s601i12 13942 chrXptel1M 278752 GGTAGCTTTGGAAAAAGCAGTTTCAGTGAAATGATGAAATCAGAAACCGA 278801 ii i iv i i i i i iiiv ii i vi C L2#LINE/L2 2003 GGTGACCTTGACAAGAGCAGTTTCGGTGGAGTGGTGGGGACGAAAGCCTG 1954 chrXptel1M 278802 AATGTAATGGGTTAAAAAGAGGGTAAGAGAAGA-----TGGGGAT----- 278841 v v i v i ii ii i ----- i i----- C L2#LINE/L2 1953 ATTGGAGTGGGTTCAAGAGAGAATGGGAGGAGAGGAATTGGAGACAGCGA 1904 chrXptel1M 278842 -CATAGATGGC-CTTTTAAGGGATTTAGC-ATAAATGGCAGGAGAGCTAT 278888 -i iii - ii ii v -i v v v vv C L2#LINE/L2 1903 GTATAGACAACTCTTTCGAGGAGTTTTGCTGTAAAGGGGAGCAGAGAAAT 1854 chrXptel1M 278889 CTGACAATATTTGTTGAGGATGGAAGGATCAAGTGAGAA 278927 vv i ii vi vv i iv? vi i v C L2#LINE/L2 1853 GGGGCGGTAGCTGGAGGGGGANGTGGGGTCAAGGGAGAA 1815 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 46.64 CpG sites = 42, Kimura (unadjusted) = 51.59 Transitions / transversions = 2.10 (42/20) Gap_init rate = 0.03 (5 / 175), avg. gap size = 2.60 (13 / 5) 13 18.75 6.90 3.33 chrXptel1M 279820 279877 (720123) (AATAAT)n#Simple_repeat 1 60 (0) m_b332s252i9 13943 chrXptel1M 279820 AAT-ATGATTATAATAATAACCTGCTAAAAATGA-AATAA-AACAA-AAT 279865 - i v -- iv v i - - i - (AATAAT)n#Sim 1 AATAATAATAATAATAATAA--TAATAATAATAATAATAATAATAATAAT 48 chrXptel1M 279866 AAAAATAAAAAT 279877 v v (AATAAT)n#Sim 49 AATAATAATAAT 60 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.11 (6 / 57), avg. gap size = 1.00 (6 / 6) 16 7.69 0.00 3.45 chrXptel1M 279846 279875 (720125) (AAAAT)n#Simple_repeat 1 29 (0) m_b332s252i11 13944 chrXptel1M 279846 AAAATGAAATAAAACAAAATAAAAATAAAA 279875 i i - (AAAAT)n#Simp 1 AAAATAAAATAAAATAAAAT-AAAATAAAA 29 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 16 9.78 0.00 0.00 chrXptel1M 280355 280376 (719624) (A)n#Simple_repeat 1 22 (0) m_b332s252i12 13945 chrXptel1M 280355 AAAAAAAAAAAAAAAACCAAAA 280376 vv (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAA 22 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 378 27.09 3.64 2.70 chrXptel1M 280383 280492 (719508) MIRc#SINE/MIR 2 112 (156) m_b332s601i13 13946 chrXptel1M 280383 GGGGCAGTAAGGTGGCTCACTGAATAAAGCACTGGCTCTGGAGCCAGAAG 280432 i iv --- v i v i vii i i i MIRc#SINE/MIR 2 GAGGCAGTGTGGTG---CAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chrXptel1M 280433 GGTTTGAATTCAAATCAGGGCTCAGGCACTTA----CTGTGTGATCCTGA 280478 iii ii i i vv v v ---- i i i MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 98 chrXptel1M 280479 GCAAGTCATTAAAC 280492 i v MIRc#SINE/MIR 99 GCAAGTCACTTAAC 112 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.70 CpG sites = 20, Kimura (unadjusted) = 35.22 Transitions / transversions = 2.22 (20/9) Gap_init rate = 0.04 (4 / 109), avg. gap size = 1.75 (7 / 4) 311 25.88 5.56 3.40 chrXptel1M 280925 281068 (718932) L1MEj_5end#LINE/L1 2005 2151 (9) m_b332s551i3 13947 chrXptel1M 280925 AGAAAGATGGAGAGAAATACA--TAAGTAC--TAATCATAACCCTGAATG 280970 v - i v --i i--i i i v v i L1MEj_5end#LI 2005 AGTAAGATGGA-AGGAATAAAATCAAGTATATCAGTCGTTACACTAAATG 2053 chrXptel1M 280971 TGAATAGGATGAATTCACTCAT--AAAG-CAGAAA-TGTATAGTAGAATG 281016 i iv v i -- - i - ----i v L1MEj_5end#LI 2054 TGAATGGACTGAATTCTCCCATTAAAAGACAGAGACTGT----CAGATTG 2099 chrXptel1M 281017 GATTAAAAATCAGAATCTGACAGTACCTTGTTCATAAGAAACAAATTTGA 281066 i v i i iii vi ivi i i v i i L1MEj_5end#LI 2100 GGTTAAAAAACAAAACCCAGCTATATGCTGTTTACAAGAAACACACTTAA 2149 chrXptel1M 281067 AA 281068 L1MEj_5end#LI 2150 AA 2151 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 32.06 CpG sites = 25, Kimura (unadjusted) = 33.20 Transitions / transversions = 2.27 (25/11) Gap_init rate = 0.07 (10 / 143), avg. gap size = 1.30 (13 / 10) 246 32.67 2.60 2.60 chrXptel1M 280950 281103 (718897) L1M4_orf2#LINE/L1 23 176 (3118) m_b332s551i4 13947 chrXptel1M 280950 TACTAATCATAACCCTGAATGTGAATAGGATGAA----TTCACTCATAAA 280995 ii i v v vi i i - v ---- i v v i L1M4_orf2#LIN 23 TATCAGTAATTACATTAAATGTAAAT-GGATTAAACACTCCAATCAAAAG 71 chrXptel1M 280996 GCAGAAATGTATAGTAGAATGGATTAAAAATCAGAATCTGACAGTACCTT 281045 i --- i i v v vi ii vi ivi L1M4_orf2#LIN 72 GCAGAGAT---TGGCAGAATGGATAAAAAAACATGATCCAACTATATGCT 118 chrXptel1M 281046 GTTCATAAGAAACAAATTTGAAAATGAGAAATACATACATAATTAAAATA 281095 ii i i v i v i v v i i i v i viv v i L1M4_orf2#LIN 119 GTCTACAAGAGACACACTTTAGATTCAAAGACACAAATAGGTTGAAAGTA 168 chrXptel1M 281096 AAAGGCTG 281103 v L1M4_orf2#LIN 169 AAAGGATG 176 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 44.45 CpG sites = 29, Kimura (unadjusted) = 44.45 Transitions / transversions = 1.45 (29/20) Gap_init rate = 0.03 (5 / 153), avg. gap size = 1.60 (8 / 5) 452 23.33 0.74 7.94 chrXptel1M 281106 281240 (718760) MIRc#SINE/MIR 2 127 (141) m_b332s601i14 13948 chrXptel1M 281106 GGGGCAGCTAGGTGGCGCAGTGGATAGAGCACCAGCCCTACAGTCAGGAG 281155 i i--- i v ii v i iv i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chrXptel1M 281156 AACCTGAGTTCAAATCTGAACTCAGATACTTAACACTTTTTCACTGTGTG 281205 i i i i ivii --- i ---- vi vi MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTC---TGC----CACTTACTAGCTGTGTG 91 chrXptel1M 281206 ACCCTGGGCAAGTCACTTAACCCCAGTT-GCCTCAG 281240 i i vv v- MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 26.45 CpG sites = 20, Kimura (unadjusted) = 28.77 Transitions / transversions = 2.22 (20/9) Gap_init rate = 0.08 (11 / 134), avg. gap size = 1.00 (11 / 11) 12 25.34 0.00 4.55 chrXptel1M 281246 281291 (718709) (AAAAT)n#Simple_repeat 1 44 (0) m_b332s252i13 13949 chrXptel1M 281246 AAAATGAAAGAAAATAAAATCCTTCTAACAAAAAAAGAAAAGAAAA 281291 i v -vvvv - v v v (AAAAT)n#Simp 1 AAAATAAAATAAAATAAAAT-AAAATAA-AATAAAATAAAATAAAA 44 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.04 (2 / 45), avg. gap size = 1.00 (2 / 2) 199 37.47 7.64 1.57 chrXptel1M 281319 281619 (718381) C L2#LINE/L2 (2128) 954 636 m_b332s601i15 13942 chrXptel1M 281319 TTGAACTTA--GAGGTGGTACATTTGTGGGTGAGGACAAGATTGAAGGTA 281366 iv -- v v i v i v i v i iv i C L2#LINE/L2 954 TTGAGATTATGGAGGGGTTGCAGTTATTGGTAATGACAAGGTCTAGGGTA 905 chrXptel1M 281367 TGACCGGTTTTGTGTTTAAGTGAAGTATGGTCAAGAAGAAGGTCATAGGA 281416 ivvvvv vv iiv i v vi i v i v C L2#LINE/L2 904 TGACCATGGGAGTGAGTGGCTGAGGTAGGGTGGAGGACAAGATCATTGGA 855 chrXptel1M 281417 GGTGACTCACTATTGAGTAATCTAGTGGCAAGGGTATTTGAGGAACAATC 281466 v --vivvi ii v iiv v v v i i iv C L2#LINE/L2 854 GGAGA--GGAGGTCAAGGAACTGAGAGGCCAGGGTATTGGAAGGATCATC 807 chrXptel1M 281467 GCTGTGTATGT------------------TGGCAGGAG--GTGGGGAAGA 281496 vvi v i ------------------ i -- vv i C L2#LINE/L2 806 TACGTGGATATTGAAATCACCAAGAATTATGACAGGAGTAGTGTTGGAGA 757 chrXptel1M 281497 GAAAAAAATTGGCAGCCAGGTATTGAGCTCATTGACAAAGAAAGGGAACT 281546 ivi v v -- vii i iv v ii vi vi i i v C L2#LINE/L2 756 GAGTGACAGTG--AGCCAGGAGCTAAAATCTTCAAGGAATGAGGGGGAGT 709 chrXptel1M 281547 GACTTTGGGGTCCACAAACAACAGCTACCAGGATTTTGATTGAGTGGT-T 281595 iiv i vii i ii v v v vvvvv vi i - C L2#LINE/L2 708 GACCCGGAGGTCGGTAGATGACTGCAACAAGGAGGGGTAGCGGGTGGTAT 659 chrXptel1M 281596 GATATGAATAGCATGAATTCCAAA 281619 ii v - ii iv i C L2#LINE/L2 658 AGTCTG-ATGACATGAGATTCAAA 636 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 50.99 CpG sites = 55, Kimura (unadjusted) = 53.03 Transitions / transversions = 0.98 (55/56) Gap_init rate = 0.03 (9 / 300), avg. gap size = 3.11 (28 / 9) 16 0.00 0.00 0.00 chrXptel1M 282224 282240 (717760) (A)n#Simple_repeat 1 17 (0) m_b332s252i14 13950 chrXptel1M 282224 AAAAAAAAAAAAAAAAA 282240 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 19 22.61 0.00 0.00 chrXptel1M 282766 282806 (717194) (C)n#Simple_repeat 1 41 (0) m_b332s252i15 13951 chrXptel1M 282766 CCCCCCACCCCACCCCCCTTCACTCCCCCACCCCACCCCCC 282806 v v ii v i v v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 41 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 410 30.91 5.09 4.13 chrXptel1M 284280 284495 (715505) MIRb#SINE/MIR 4 221 (47) m_b332s601i16 13952 chrXptel1M 284280 AGAGGCAGCTAGGGATGCCTCAGGATGCAAAGCAATGGGCCT-GGAGTAG 284328 i -- v i vvii i --- i -i i - v- MIRb#SINE/MIR 4 AGGGGCAGC--GTGGTGCAGTGGAA---AGAGCA-CGGGCTTTGGAGTC- 46 chrXptel1M 284329 AGAC-GACCCAAGTTCAAATATGACCTCAGACACT------CTCTGTCAC 284371 - iii i viviv v v ------ v v MIRb#SINE/MIR 47 AGACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGAC 96 chrXptel1M 284372 CC-GAACCAGTCTTTTCACTTCTGTTTGCCTCAATTTCCTCACCCATAAA 284420 i- ii v ivi v i v vv i i ii MIRb#SINE/MIR 97 CTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAA 146 chrXptel1M 284421 AGAGAAACAATAATAGCACTATTTCACGGAGTTCTTGTGGGCAGCAAATG 284470 vi ii i - - ii i i i v i v vi MIRb#SINE/MIR 147 ATGGGGATAATAATA-C-CTACCTCGCAGGGTTGTTGTGAGGATTAAATG 194 chrXptel1M 284471 AAATAGCATTTGCAAAGTGCT--GCAC 284495 i iiiiv i i -- MIRb#SINE/MIR 195 AGATAATGCATGTAAAGCGCTTAGCAC 221 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 37.59 CpG sites = 42, Kimura (unadjusted) = 41.85 Transitions / transversions = 1.91 (42/22) Gap_init rate = 0.07 (14 / 215), avg. gap size = 1.43 (20 / 14) 442 29.65 9.24 1.01 chrXptel1M 284308 284491 (715509) MIRc#SINE/MIR 24 222 (46) m_b332s601i17 13952 chrXptel1M 284308 AAAGCAATGGGCCTGGAGTAGAGACGACCCAAGTTCAAATATGACCTCAG 284357 i v i i vii v iii i i viviv v MIRc#SINE/MIR 24 AGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTG 73 chrXptel1M 284358 ACACT------CTCTGTCACCC-GAACCAGTCTTTTCACTTCTGTTTGCC 284400 v ------ v v i- ii v vi v i v vv MIRc#SINE/MIR 74 CCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCC 123 chrXptel1M 284401 TCAATTTCCTCACCCATAAAAGAGAAACAATAATA--------GCACTAT 284442 i i ii vi ii i -------- - i MIRc#SINE/MIR 124 TCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGC-CTAC 172 chrXptel1M 284443 TTCACGGAGTTCTTGTGGGCAGCAAATGAAATA--GCATTTGCAAAGTGC 284490 i i i v i v v i -- i v - i MIRc#SINE/MIR 173 CTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTG-AAAGCGC 221 chrXptel1M 284491 T 284491 MIRc#SINE/MIR 222 T 222 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 36.30 CpG sites = 33, Kimura (unadjusted) = 39.07 Transitions / transversions = 1.57 (33/21) Gap_init rate = 0.03 (6 / 183), avg. gap size = 3.17 (19 / 6) 181 29.11 3.70 2.44 chrXptel1M 288146 288226 (711774) C L2d2_3end#LINE/L2 (62) 493 412 m_b332s601i18 13953 chrXptel1M 288146 TGTGGTTGACACAAGGAAAGGCTAAAACA--GTCCCTGCTCTTGAGAAAC 288193 vv i i - vv i -- i ii i i C L2d2_3end#LIN 493 TGTGGGGGATACAAAGAA-GTATAAGACATGGTCCCTGCCCTCAAGGAGC 445 chrXptel1M 288194 TCTCTCCTTTAA-TGGGGAGGCAACAGGCAAACA 288226 - vivv i i- i v vii C L2d2_3end#LIN 444 T-TACAATCTAGTTGGGGAGACAAGACATAAACA 412 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 38.05 CpG sites = 14, Kimura (unadjusted) = 38.05 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.05 (4 / 80), avg. gap size = 1.25 (5 / 4) 20 4.35 0.00 0.00 chrXptel1M 290235 290258 (709742) (G)n#Simple_repeat 1 24 (0) m_b332s252i17 13954 chrXptel1M 290235 GGGGGGGGGGGGGGGGGGGAGGGG 290258 i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGG 24 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 252 11.87 3.51 11.32 chrXptel1M 292701 292757 (707243) C Plat_L3#LINE/CR1 (6) 3567 3515 m_b332s551i5 13955 chrXptel1M 292701 ATAATAGAATCCTAGCTCTTGAGCTGGAAGGGACCTC-AGAAGCCATCT- 292748 v ? ------ - i i - C Plat_L3#LINE/ 3567 ATCATAGAATCNTAG------AGCTGGAAGGGACCTCGAGAGGTCATCTG 3524 chrXptel1M 292749 ATCTAGTCC 292757 i i i C Plat_L3#LINE/ 3523 GTCCAGCCC 3515 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 13.44 CpG sites = 5, Kimura (unadjusted) = 13.44 Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.14 (8 / 56), avg. gap size = 1.00 (8 / 8) 421 31.93 6.56 1.17 chrXptel1M 292763 293006 (706994) C L3#LINE/CR1 (209) 3890 3634 m_b332s601i19 13956 chrXptel1M 292763 TGTTCAGCTGAATTTTGTCTTTCT--AATGGGCACCCATGGTTCCCA--- 292807 i v i v i i ii -- ivvv v v i --- C L3#LINE/CR1 3890 TATTGAGCCGAAATCTGCCTCCCTGTAACTTCCACCCATTGGTCCTAGTT 3841 chrXptel1M 292808 C--CCCCCTTGACCCAGG-AGACCAATTCTTATCCCATATCATGCATGAG 292854 -- i v v vi- vi v v viv -ii v C L3#LINE/CR1 3840 CTGCCCTCTGGAGCCACACAGAATAAGTCTAATCCCTCTTC-CACATGAC 3792 chrXptel1M 292855 GGTTGCTTTCAAATTCTCAAAGG--GTTAT-ATATCCCCTGCA--TTTTC 292899 i i-- i vi ii i-- i - i i vi -- i C L3#LINE/CR1 3791 AGC--CCTTCAAATATTTGAAGACAGCTATCATGTCTCCTCTAAGTCTTC 3744 chrXptel1M 292900 TCTTCTCCAAGAGAAACATTCCCATTTTCTTCAACCAATCTCCATATAAT 292949 i vv i v i iv ii i i C L3#LINE/CR1 3743 TCTTCTCCAGGCTAAACATCCCCAGTTCCTTCAACCGTTCCTCATATGAC 3694 chrXptel1M 292950 ATCACCTTGTGGCTTTTC-CCAATCTGATAAGTCTCCTTTG--CATACTC 292996 viii ivv i ii - vi i viv i -- iii C L3#LINE/CR1 3693 ATGGTTTCCAGACCCTTCACCATCCTGGTCGCTCTCCTCTGGACGCGCTC 3644 chrXptel1M 292997 TAGTTTGTCA 293006 i C L3#LINE/CR1 3643 CAGTTTGTCA 3634 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 39.76 CpG sites = 49, Kimura (unadjusted) = 43.60 Transitions / transversions = 1.75 (49/28) Gap_init rate = 0.05 (12 / 243), avg. gap size = 1.58 (19 / 12) 312 26.61 8.57 3.40 chrXptel1M 293408 293547 (706453) L2b_3end#LINE/L2 317 463 (3) m_b332s601i20 13957 chrXptel1M 293408 TGGTTATTTGTATGTG-GTCTCCTGCCATTATTAGACTG--AGTTCTTTG 293454 vi i? ii v- i- i --- -- i iv L2b_3end#LINE 317 TGTCTGNTTACATGTCTGTCTCCC-CCACTA---GACTGTGAGCTCCGTG 362 chrXptel1M 293455 AGTGTAGGAATTGTTTTTGTCTT--TC-------TTTCCACAGTGCTTGC 293495 v i i ii ?v i -- ------- v v i i iv L2b_3end#LINE 363 AGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTGTATCCCCAGCGCCTAG 412 chrXptel1M 293496 CATAATATCTGGCACACAGTAAGTGCTAAATAAATGCTTGTCTGACTGAC 293545 i i?ii i i v i ii - v v L2b_3end#LINE 413 CACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTTGT-TGAATGAA 461 chrXptel1M 293546 TG 293547 L2b_3end#LINE 462 TG 463 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 30.73 CpG sites = 25, Kimura (unadjusted) = 35.56 Transitions / transversions = 2.27 (25/11) Gap_init rate = 0.06 (9 / 139), avg. gap size = 1.89 (17 / 9) 350 27.23 8.00 3.05 chrXptel1M 293412 293536 (706464) L2d2_3end#LINE/L2 412 542 (13) m_b332s601i21 13957 chrXptel1M 293412 TATTTGTATGTGGTCTCCTGCCATTATTAGACTG--AGTTCTTTGAGTGT 293459 i i i v v -- -- i i -- i i v i L2d2_3end#LIN 412 TGTTTATGTCTTGTCTCC--CCA--ACTAGATTGTAAGCTCCTTGAGGGC 457 chrXptel1M 293460 AGGAATTGT-TTTTGTCTTTCTTT-------CCACAGTGCTTGCCATAAT 293501 i iii - i i vi ------- i i iv i i L2d2_3end#LIN 458 AGGGACCATGTCTTATACTTCTTTGTATCCCCCACAGCGCCTAGCACAGT 507 chrXptel1M 293502 ATCTGGCACACAGTAAGTGCTAAATAAATGCTTGT 293536 ii v i i v ii L2d2_3end#LIN 508 GCCTTGCACACAGTAGGCGCTCAATAAATATTTGT 542 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.68 CpG sites = 26, Kimura (unadjusted) = 36.51 Transitions / transversions = 3.71 (26/7) Gap_init rate = 0.06 (7 / 124), avg. gap size = 2.00 (14 / 7) 31 20.25 0.00 0.00 chrXptel1M 293591 293652 (706348) (CA)n#Simple_repeat 1 62 (0) m_b332s252i18 13958 chrXptel1M 293591 CACACCCACACCCACACATACACATGTACTCAGTCACACACACAGAGACA 293640 v v i iii v vv v v (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 chrXptel1M 293641 CACACACACACA 293652 (CA)n#Simple_ 51 CACACACACACA 62 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0) 291 35.66 10.79 0.29 chrXptel1M 293703 294017 (705983) C L3#LINE/CR1 (2988) 1111 764 m_b332s601i22 13956 chrXptel1M 293703 TCCTTCAC-TGTCAGTTTTAAAACCATCTGAATCAGATTTGTAACACCCA 293751 i v- v - ii v vi i iv ii vv i v C L3#LINE/CR1 1111 TCCCTCAAATTTCAGTTT-AAAGTCCTCTTGATCAGGTCGGCGAGTCTCC 1063 chrXptel1M 293752 AGGTCAATAT-TTTGTGATGGCGCACATTAGGTGCATTCTGTTCTTGG-- 293798 ? ?iv i i- iv vvi iviv i v i i i i i ? -- C L3#LINE/CR1 1062 NGNCAAACACGTTCTTCCCGGTCTTCGTGAGATGCACTCCGTCCCTNGCC 1013 chrXptel1M 293799 ----GC--ATCATTCCTGTATTTTCAGCCATTCTCCAGAAATCCCAGTTC 293842 ---- -- i iv i? v vv v v i i C L3#LINE/CR1 1012 AGGAGCCCATCGTTCTGGTATCNTAAGCCATGGTCCAGAAAACCAAATCC 963 chrXptel1M 293843 CGTTCTCAGACGCCATCTTCTCAGCCATCTGGTCCCTTCGTG-ATCCAAC 293891 i iv i v vi v v v vii- vv C L3#LINE/CR1 962 TGTTCTTCGACACCATCTACGTAGCCAGCTGTTCACTTCCCATATCCTCC 913 chrXptel1M 293892 TTTC----CCAG---------CTGCAGC-------AGCGATGAAAATACC 293921 ---- i--------- v i ------- v i C L3#LINE/CR1 912 TTTCTCTTCCAAAGTCACGACCTTCAACTGGAAGAAGAGATGAAAACACC 863 chrXptel1M 293922 ATGGGTGTTCTGGACATCCTCGGTCGCTTGACGGGAATTCCCCAATCCTC 293971 ivv ii ivi vvi i i iv i v vi i i i vv i vii C L3#LINE/CR1 862 ACCTGTGCCCCCAAGTCCTTCAGTTTCCTGCCCAGGACTTCAAAGTCACT 813 chrXptel1M 293972 CGTAAGGCTCTCTCCGTTCCCTCTGA---TATCACTTGTCCCCACTTGA 294017 v vi v vi ivv i i --- i i i i v C L3#LINE/CR1 812 AGAGATGCATTCCAGGTTTCTTCTGACTGTGTCATTCGTTCCCACGTGA 764 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 45.83 CpG sites = 62, Kimura (unadjusted) = 50.93 Transitions / transversions = 1.24 (62/50) Gap_init rate = 0.04 (11 / 314), avg. gap size = 3.18 (35 / 11) 365 24.68 0.00 0.00 chrXptel1M 294092 294168 (705832) MIRc#SINE/MIR 76 152 (116) m_b332s601i23 13959 chrXptel1M 294092 ACTTCCCAGCTGTGTGATCTTGGGTGAATAACTTAACTTCTCTCAATTCC 294141 v i i ii i v i v iiii MIRc#SINE/MIR 76 ACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTC 125 chrXptel1M 294142 AGTTTCCTGATCTGTGCAACGGAGACA 294168 v iv i i i MIRc#SINE/MIR 126 AGTTTCCTCATCTGTAAAATGGGGATA 152 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 31.46 CpG sites = 14, Kimura (unadjusted) = 31.46 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.00 (0 / 76), avg. gap size = 0.0 (0 / 0) 333 29.28 6.67 6.67 chrXptel1M 294194 294343 (705657) MIR3#SINE/MIR 31 180 (28) m_b332s601i24 13960 chrXptel1M 294194 GATGGAGAGGCACGTGACCTCGATTCAGATCCACTCCAAGCCCCAAGCCA 294243 iv i v v v v i -----i v vi i i-- MIR3#SINE/MIR 31 GACTGGGAGTCAGGAGACCTGGGTTC-----TAGTCCCGGCTCT--GCCA 73 chrXptel1M 294244 CTTACTACTTGTATGTCCTTGAACAAGT---------TCT-TAGGCCTCA 294283 v ?vi i v ii --------- - i MIR3#SINE/MIR 74 CTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCA 123 chrXptel1M 294284 GTTTACCCATCTATAAAATGAGAAGATTGAGCTCGACCAGGGTTTCAAAA 294333 v i i ii i ii v i--- i i v i MIR3#SINE/MIR 124 GTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGAT---GATCTCTAAG 170 chrXptel1M 294334 ACTTTTTCCA 294343 iiiii MIR3#SINE/MIR 171 GTCCCTTCCA 180 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 38.21 CpG sites = 28, Kimura (unadjusted) = 39.48 Transitions / transversions = 2.15 (28/13) Gap_init rate = 0.08 (12 / 149), avg. gap size = 1.67 (20 / 12) 204 20.98 0.00 4.65 chrXptel1M 294622 294666 (705334) L3#LINE/CR1 4038 4080 (19) m_b332s601i25 13961 chrXptel1M 294622 TGAGAAGCTTTGAACTAGTTGACTTCCAAGGGCTCTTCCAGCTCT 294666 i i -- i v i i v i i L3#LINE/CR1 4038 TGGGAGG--TTGGACTAGATGACCTCTAAGGTCCCTTCCAACTCT 4080 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 25.71 CpG sites = 7, Kimura (unadjusted) = 25.71 Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.05 (2 / 44), avg. gap size = 1.00 (2 / 2) 218 22.97 5.41 0.00 chrXptel1M 294678 294751 (705249) MIRc#SINE/MIR 173 250 (18) m_b332s601i26 13959 chrXptel1M 294678 CTCACAGGTTTATTGTGAGGAGCAAATAAG-T--TGTGTGT-AAAGTCCA 294723 v i v i - -- i - iv v MIRc#SINE/MIR 173 CTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCT 222 chrXptel1M 294724 TTACAAGCCTTAAAGGTATATAGAAATG 294751 ii i iv vvv v MIRc#SINE/MIR 223 TTGTAAACTGTAAAGTGCTATACAAATG 250 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 25.78 CpG sites = 8, Kimura (unadjusted) = 27.58 Transitions / transversions = 0.89 (8/9) Gap_init rate = 0.04 (3 / 73), avg. gap size = 1.33 (4 / 3) 462 28.17 6.32 1.00 chrXptel1M 295071 295260 (704740) MIRc#SINE/MIR 25 224 (44) m_b332s601i27 13962 chrXptel1M 295071 GATTATTGGA--TAGAATTGGGAAGAGCCAATTTCAAATTCAGCCTGAAA 295118 vi i -- i i ii v iiiv i i i v v vviv MIRc#SINE/MIR 25 GAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGC 74 chrXptel1M 295119 CACTTAGTAGTGGCATGACCCCAGG-AAGTCACTTCGGCTGCCTG--CCT 295165 v iv ii iii - viv vi -- MIRc#SINE/MIR 75 CACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCT 124 chrXptel1M 295166 CAGTTTACCCATCTGTAAACATGGGTACCATAATA---GC---ATCTACC 295209 v i - v iv --- ---ii MIRc#SINE/MIR 125 CAGTTTCCTCATCTGTAAA-ATGGGGATAATAATACCTGCCCTGCCTACC 173 chrXptel1M 295210 TCCCAGGGGTGTAGTTAGGATGGAAGGAAATGATTT-TTTGTAAAGCGCC 295258 v v v v vi v i i v - v - i MIRc#SINE/MIR 174 TCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTG-AAAGCGCT 222 chrXptel1M 295259 TT 295260 MIRc#SINE/MIR 223 TT 224 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 35.18 CpG sites = 29, Kimura (unadjusted) = 36.02 Transitions / transversions = 1.21 (29/24) Gap_init rate = 0.04 (8 / 189), avg. gap size = 1.75 (14 / 8) 383 22.85 7.44 2.36 chrXptel1M 295821 295941 (704059) MIRc#SINE/MIR 1 127 (141) m_b332s601i28 13963 chrXptel1M 295821 CAAGGCAGCTAGGTGGTGCAGTGCATAGAGCACCAGCCCTG-AGTCAGGA 295869 i i--- v v ii v i - MIRc#SINE/MIR 1 CGAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGA 47 chrXptel1M 295870 GGACCTGAATTCAAATCTGTTCTCAGACACTT-------GTGTGACCCTG 295912 i ii i i ivvv v v ------- i MIRc#SINE/MIR 48 AGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTG 97 chrXptel1M 295913 GGCAAGTCAGTCAATCCCAATT-GCCTCAG 295941 v i i i vv v- MIRc#SINE/MIR 98 GGCAAGTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 25.37 CpG sites = 15, Kimura (unadjusted) = 27.68 Transitions / transversions = 1.25 (15/12) Gap_init rate = 0.05 (6 / 120), avg. gap size = 2.00 (12 / 6) 12 9.78 0.00 0.00 chrXptel1M 295944 295965 (704035) (AAAC)n#Simple_repeat 1 22 (0) m_b332s252i20 13964 chrXptel1M 295944 AAAAAAACAAACAAACAAAAAA 295965 v v (AAAC)n#Simpl 1 AAACAAACAAACAAACAAACAA 22 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 14 24.88 0.00 0.00 chrXptel1M 295943 295980 (704020) (AAA)n#Simple_repeat 1 38 (0) m_b332s252i19 13965 chrXptel1M 295943 AAAAAAAACAAACAAACAAAAAAGTAGAAGAAGAAAAA 295980 v v v iv i i i (AAA)n#Simple 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 38 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 489 31.91 10.95 0.88 chrXptel1M 296185 296595 (703405) L2#LINE/L2 1739 2190 (892) m_b332s601i29 13966 chrXptel1M 296185 TCTTTCCCCTTCTACTGGCTCCTTCCCTATT-GTCTACAAACATGCTCAA 296233 i ii v v - i- iv vv? L2#LINE/L2 1739 TTTTTCCCTCTCTACTGGATCATTCCC-ATCAGCATACAAACATGCTGTN 1787 chrXptel1M 296234 GTCTCCCCCACCCT-AAAAATCATA----CTGACTTTGATCC---TTCCC 296275 i i i i i - v v ---- v- i i ---? L2#LINE/L2 1788 ATTTCTCCCATCTTTAAAAAACAAAAATTCTC-CCTTGACCCCACNTCCC 1836 chrXptel1M 296276 TCCCCA-CTATCATCC------TCTTCTACCCTGGGTGGCCAGATTCTTC 296318 i i - i ii ------ v v vviii v i i i L2#LINE/L2 1837 CCTCCAGCTACCGCCCCATTTCTCTGCTCCCCTTTACAGCAAAACTCCTC 1886 chrXptel1M 296319 CAAAAGGCCATTTA----CAATGACTCCATTTTCTCTCCTCTCACTCTCT 296364 v ii iii i ---- iv v v i i i L2#LINE/L2 1887 GAAAGAGTTGTCTATACTCGCTGTCTCCAATTCCTCTCCTCCCATTCTCT 1936 chrXptel1M 296365 TC---ATTCGTTATCATCCAGCTCCTGAACTCATCATTCCCATTAAACTG 296411 ii--- ii ii viv vi iii vv i i i vviv L2#LINE/L2 1937 CTTGAACCCACTCCAATCAGGCTTTCGTCCCCACCACTCCACCGAAACTG 1986 chrXptel1M 296412 TTCTGTCCAAATTTACCAACGATCTCTCAATTGGCAAATCTGATGGTGTT 296461 i vvi iv i i i ivvi vi ii vvv L2#LINE/L2 1987 CTCTTGTCAAGGTCACCAATGACCTCCACGTTGCTAAATCCAATGGTCAA 2036 chrXptel1M 296462 TTCTCAGTCCTTGATCCC-CTTGACCTTTCAGCAGTCTTGGGCCTGGTGA 296510 i- ii- ? iv v i vii vi L2#LINE/L2 2037 TTCTCAGTCCTC-ATCTTACTTGACCTNTCAGCAGCATTTGACACAGTTG 2085 chrXptel1M 296511 ATGATTCTCCCCTTT-----------------CTAGGTCTTGGGGCCATC 296543 v i i i i----------------- v ii ivi v i L2#LINE/L2 2086 ATCACTCCCTCCTTCTTGAAACACTTTCTTCACTTGGCTTCCAGGACACC 2135 chrXptel1M 296544 CTTCTCTCCTACCTCTCTTCCTA-CTCATCTGGCC---CCTCCTCTGTTT 296589 viv ivi i i - - --- i v i L2#LINE/L2 2136 ACACTCTCCTGGTTTTCCTCCTACCTCA-CTGGCCGCTCCTTCTCAGTCT 2184 chrXptel1M 296590 CCTCTG 296595 i L2#LINE/L2 2185 CCTTTG 2190 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 41.87 CpG sites = 84, Kimura (unadjusted) = 44.18 Transitions / transversions = 1.83 (84/46) Gap_init rate = 0.04 (16 / 410), avg. gap size = 3.06 (49 / 16) 330 32.97 5.83 2.83 chrXptel1M 296675 296983 (703017) L2#LINE/L2 2357 2674 (408) m_b333s601i2 13966 chrXptel1M 296675 CTCGGGCCTCCCTTTCCT--ACTCAAATCTC-TAGACCTCCAGCTGCCTT 296721 i i -- ii -- v iv - v -- i v L2#LINE/L2 2357 CCCGGACCTC--TCCCCTGAACTCCAGACTCGTATA--TCCAACTGCCTA 2402 chrXptel1M 296722 TCAGACAACTTGAAATGAAGGTCCAGCAGACATCTTAAACTTAGC----- 296766 iiv v iv vv i v i ii i i i ----- L2#LINE/L2 2403 CTCGACATCTCCACTTGGATGTCTAATAGGCATCTCAAACTTAACATGTC 2452 chrXptel1M 296767 CAAAATAGAACTCATTCTGTTCCCCCTAGATCCTTCCCCACTTCTCACCT 296816 iv v vv v vi v v i v iivivii L2#LINE/L2 2453 CAAAACTGAACTCCTGATCTTCCCCCTCAAACCTGCTCCTCCCGCAGTCT 2502 chrXptel1M 296817 TTCCTATTACCAGAGAA-GATAAGACCAGTCTCCCTGCTTCTCAGGCTCA 296865 i i i-i v? - ii vv vi i v i v iv L2#LINE/L2 2503 TCCCCATC-TCAGTNAATGGCAACTCCATCCTTCCAGTTGCTCAGGCCAA 2551 chrXptel1M 296866 CGACCTGGGAGTCATCATGGAGTCCTCAGTCCCTTCC---TCCCCCATCC 296912 vi v v v v vv ii ii ---i v L2#LINE/L2 2552 AAACCTTGGAGTCATCCTTGACTCCTCTCTTTCTCTCACACCCCACATCC 2601 chrXptel1M 296913 AA---AT--GCAATGGCCTGGCAAGTTCACCTTTGCAACATCTCTCCCCA 296957 --- -- -iv v iiv ii -- v v v vv L2#LINE/L2 2602 AATCCATCAGCAA-ATCCTGTCGGCTCTACCTT--CAAAATATATCCAGA 2648 chrXptel1M 296958 CTCCAATGCATCCTCCATC-CGTCCAC 296983 v i i- iiiii i - v L2#LINE/L2 2649 ATCCGAC-CACTTCTCACCACCTCCAC 2674 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.89 CpG sites = 53, Kimura (unadjusted) = 44.69 Transitions / transversions = 1.15 (53/46) Gap_init rate = 0.06 (17 / 308), avg. gap size = 1.59 (27 / 17) 353 31.50 4.05 3.63 chrXptel1M 296675 296921 (703079) L2#LINE/L2 2357 2604 (478) m_b332s601i30 13966 chrXptel1M 296675 CTCGGGCCTCCCTTTCCT--ACTCAAATCTC-TAGACCTCCAGCTGCCTT 296721 i i -- ii -- v iv - v -- i v L2#LINE/L2 2357 CCCGGACCTC--TCCCCTGAACTCCAGACTCGTATA--TCCAACTGCCTA 2402 chrXptel1M 296722 TCAGACAACTTGAAATGAAGGTCCAGCAGACATCTTAAACTTAGC----- 296766 iiv v iv vv i v i ii i i i ----- L2#LINE/L2 2403 CTCGACATCTCCACTTGGATGTCTAATAGGCATCTCAAACTTAACATGTC 2452 chrXptel1M 296767 CAAAATAGAACTCATTCTGTTCCCCCTAGATCCTTCCCCACTTCTCACCT 296816 iv v vv v vi v v i v iivivii L2#LINE/L2 2453 CAAAACTGAACTCCTGATCTTCCCCCTCAAACCTGCTCCTCCCGCAGTCT 2502 chrXptel1M 296817 TTCCTATTACCAGAGAA-GATAAGACCAGTCTCCCTGCTTCTCAGGCTCA 296865 i i i-i v? - ii vv vi i v i v iv L2#LINE/L2 2503 TCCCCATC-TCAGTNAATGGCAACTCCATCCTTCCAGTTGCTCAGGCCAA 2551 chrXptel1M 296866 CGACCTGGGAGTCATCATGGAGTCCTCAGTCCCTTCCTCCCCCA-TCCAA 296914 vi v v v v ---- i i i v -i v L2#LINE/L2 2552 AAACCTTGGAGTCATCCTTGACTCC----TCTCTTTCTCTCACACCCCAC 2597 chrXptel1M 296915 ATGCAAT 296921 v L2#LINE/L2 2598 ATCCAAT 2604 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 41.12 CpG sites = 39, Kimura (unadjusted) = 41.85 Transitions / transversions = 1.08 (39/36) Gap_init rate = 0.06 (14 / 246), avg. gap size = 1.36 (19 / 14) 518 21.60 7.95 1.88 chrXptel1M 297067 297217 (702783) C MIRc#SINE/MIR (64) 204 45 m_b333s601i3 13967 chrXptel1M 297067 ATCTCATCTGAGCCCCACTACCACCCTG------AGACAGGG---GTAGT 297107 i v i v v ------ i --- v C MIRc#SINE/MIR 204 ATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATT 155 chrXptel1M 297108 -CTATCTCCGTTTTACAAATGAGAAAAATGAGGCAGGCAGAGACTAAGGG 297156 -i i i i i v vviv ii v C MIRc#SINE/MIR 154 ATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTG 105 chrXptel1M 297157 ACTGCCTCAGGGTCACACAGCTCACTGAGTGACGGAG--GGTTGATTTGA 297204 vv i i - v i i i -- -- i i C MIRc#SINE/MIR 104 ACTTGCCCAAGGTCACACAGCT-AGTAAGTGGCAGAGCCGG--GACTCGA 58 chrXptel1M 297205 AAACAGGTCTTCC 297217 vv C MIRc#SINE/MIR 57 ACCCAGGTCTTCC 45 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 24.95 CpG sites = 18, Kimura (unadjusted) = 25.86 Transitions / transversions = 1.29 (18/14) Gap_init rate = 0.05 (7 / 150), avg. gap size = 2.14 (15 / 7) 284 30.22 3.70 3.70 chrXptel1M 297219 297407 (702593) L1MC1_3end#LINE/L1 445 633 (447) m_b333s551i1 13968 chrXptel1M 297219 TTTGTGGCACCCCTTTTTGTAGCGGCTAAAAACTGGAAACTGAGAGGATG 297268 i i v ii v ii iiv i vi i vivv i L1MC1_3end#LI 445 TTTATAGCAGCTTTATTCATAATTGCCAAAACTTGGAAGCAACCAAGATG 494 chrXptel1M 297269 CCCATCAGTTGGAGAATGGCTGAATAAATTATGGTATATGAATATTATGG 297318 i v v v v i i i i vv v iv L1MC1_3end#LI 495 TCCTTCAGTAGGTGAATGGATAAATAAACTGTGGTACATCCAGACAATGG 544 chrXptel1M 297319 AATATTACT--GTTCT-GGAAGAAATGA-CCAACAGG--ATGATTTCAGA 297362 i -- iv -ii - i v i -- ------ L1MC1_3end#LI 545 AATATTATTCAGCGCTAAAAAGAAATGAGCTATCAAGCCATGA------A 588 chrXptel1M 297363 AAGGCCTGGA-GAGACTGACACGAACTGATGCTGAGTGAAATGAGC 297407 i v - i v v i v - iv i i vi L1MC1_3end#LI 589 AAGACATGGAGGAAACTTAAATGCA-TATTACTAAGTGAAAGAAGC 633 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.85 CpG sites = 32, Kimura (unadjusted) = 39.79 Transitions / transversions = 1.39 (32/23) Gap_init rate = 0.06 (12 / 188), avg. gap size = 1.17 (14 / 12) 371 30.28 0.00 0.00 chrXptel1M 297219 297327 (702673) L1ME2z_3end#LINE/L1 445 553 (638) m_b333s551i0 13968 chrXptel1M 297219 TTTGTGGCACCCCTTTTTGTAGCGGCTAAAAACTGGAAACTGAGAGGATG 297268 ii i v ii v ii iii i v vvvi i L1ME2z_3end#L 445 TTCATAGCAGCTTTATTCATAATAGCCAAAAACTGGAAACAGCCCAGGTG 494 chrXptel1M 297269 CCCATCAGTTGGAGAATGGCTGAATAAATTATGGTATATGAATATTATGG 297318 i iiv v i i i i vv iv L1ME2z_3end#L 495 TCCATCAACAGGAGAATGGATAAACAAACTGTGGTATATTCATACAATGG 544 chrXptel1M 297319 AATATTACT 297327 i L1ME2z_3end#L 545 AATACTACT 553 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.75 CpG sites = 22, Kimura (unadjusted) = 40.75 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.00 (0 / 108), avg. gap size = 0.0 (0 / 0) 372 23.91 0.00 0.00 chrXptel1M 297234 297325 (702675) L1ME3G_3end#LINE/L1 456 547 (377) m_b333s551i2 13968 chrXptel1M 297234 TTTGTAGCGGCTAAAAACTGGAAACTGAGAGGATGCCCATCAGTTGGAGA 297283 iii v i vivvvii i i v i L1ME3G_3end#L 456 TTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCAATAGGGGA 505 chrXptel1M 297284 ATGGCTGAATAAATTATGGTATATGAATATTATGGAATATTA 297325 i i vv i i L1ME3G_3end#L 506 ATGGTTAAATAAATTATGGTATATCCATACTATGGAATACTA 547 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 29.60 CpG sites = 14, Kimura (unadjusted) = 29.60 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.00 (0 / 91), avg. gap size = 0.0 (0 / 0) 18 0.00 0.00 0.00 chrXptel1M 298842 298861 (701139) (T)n#Simple_repeat 1 20 (0) m_b333s252i2 13969 chrXptel1M 298842 TTTTTTTTTTTTTTTTTTTT 298861 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTT 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 354 27.44 0.76 8.20 chrXptel1M 298862 298992 (701008) C MIRb#SINE/MIR (143) 125 4 m_b333s601i4 13970 chrXptel1M 298862 GCTGAGACAA-TTGGTTGACTTGCCTAGGGTCCCACAGCTAGAAAGTATT 298910 v v i- iiv i i i v v iv- C MIRb#SINE/MIR 125 GCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGG- 77 chrXptel1M 298911 CAGTGTCTGACGGCAGATTTGAACTCAGGTGCTCCTAATTTAAGGGCTGG 298960 v i ---- -- i i vivi i i iv ii iv C MIRb#SINE/MIR 76 CAGAGCC----GG--GATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCG 33 chrXptel1M 298961 TACTCTACCCACTGTACCACCTAGCTGCCCCT 298992 i vi i --- C MIRb#SINE/MIR 32 TGCTCTTTCCACTGCACCAC---GCTGCCCCT 4 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.76 CpG sites = 21, Kimura (unadjusted) = 35.08 Transitions / transversions = 1.75 (21/12) Gap_init rate = 0.08 (11 / 130), avg. gap size = 1.00 (11 / 11) 48 2.94 6.94 1.32 chrXptel1M 299341 299412 (700588) (AT)n#Simple_repeat 1 76 (0) c_b333s251i0 13971 chrXptel1M 299341 ATAT-TATATAT-TATATATA-ATACATATATATGATA-ATATATGT-TA 299385 - - - i - - i - (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATAT-ATATATATATATATA 49 chrXptel1M 299386 TATATATATATATATATATATATATAT 299412 (AT)n#Simple_ 50 TATATATATATATATATATATATATAT 76 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.08 (6 / 71), avg. gap size = 1.00 (6 / 6) 354 34.96 4.91 3.78 chrXptel1M 299622 300171 (699829) L2#LINE/L2 1540 2095 (987) m_b333s601i5 13972 chrXptel1M 299622 CACACTCTCCTCCCATTCCTCATCTCCTCTCACTCAGGTGCCT-TCTGCC 299670 ?? iv -- v v i -- ii vv v - v L2#LINE/L2 1540 CACANNCTCCCACCA--CCACATCTACCC--ACCTACCTGCATCTGTGCC 1585 chrXptel1M 299671 T-CTTTCTCTTCCTTCAATTCTGTTTC-ATGTGAAGAAATGGCCTTACTC 299718 i- v v v vv i v - i - v v v v i L2#LINE/L2 1586 CACATACTCTGCCTTCCCTCCTGTTACTACG-GATGAACTGTCCGTGCTC 1634 chrXptel1M 299719 CGCCCCGATAACAAACCCTCTGCT-GTTCAGCTGATCCCACTGCATCCCA 299767 vvi ii viv v ii - v viv iiv v i i L2#LINE/L2 1635 CTATCTAAGGCCAACCCCTCCACTTGTGCACTAGATCCCATCCCCTCTCG 1684 chrXptel1M 299768 TCTCCTCAATGGATTACCCTCTATCA----CACCCACACTTTCCGTCACC 299813 i v - ivv v i v ----iv v v i vv i L2#LINE/L2 1685 CCTACTCAA-GGACATCGCTCCAGCAATTCTCCCCTCTCTCTCCTGCATC 1733 chrXptel1M 299814 TTCCATCTCTATCTCTCC---GGCTTTTTCC--TTAGTGCCTGCAAACAT 299858 v v i i vi i--- v iv -- i -- v i L2#LINE/L2 1734 ATCAATTTTTCCCTCTCTACTGGATCATTCCCATCAG--CATACAAACAT 1781 chrXptel1M 299859 GCCCATGTTGTCCCCATCCTT------CTAAGTCCTTCACTTGATCCTTT 299902 ivv?i vii i ------ v iviii v i ivi L2#LINE/L2 1782 GCTGTNATTTCTCCCATCTTTAAAAAACAAAAATTCTCCCTTGACCCCAC 1831 chrXptel1M 299903 CATTCCTGCTGACTATTGTTCCATATCCCTTCTGCTGTTTGGAGCTA--- 299949 ?vii iv iii ii ii v i v v iv iv v --- L2#LINE/L2 1832 NTCCCCCTCCAGCTACCGCCCCATTTCTCTGCTCCCCTTTACAGCAAAAC 1881 chrXptel1M 299950 TGCTCAAAAAGGCCGTCTACCACAGGTT-CCTTCATTTTTTCTTCCCTAA 299998 v i ii ii i- vv i -i i v ii i ----- L2#LINE/L2 1882 TCCTCGAAAGAGTTGTCTAT-ACTCGCTGTCTCCAATTCCTCTCC----- 1925 chrXptel1M 299999 TCCTACATTCCTTTGTTAATTCTTTACAGTTTAGCTTCCCAACTTCCTGA 300048 -- ii iv v ii vi v i ivi i -iv ii viv L2#LINE/L2 1926 TCC--CATTCTCTCTTGAACCCACTCCAATCAGGCTTTC-GTCCCCACCA 1972 chrXptel1M 300049 TTGCACCAAAACTGCTCTCCCCAATGTTACCGATGGTCTCTCAGTTGCTA 300098 i v i ivi v i i ii ivv L2#LINE/L2 1973 CTCCACCGAAACTGCTCTTGTCAAGGTCACCAATGACCTCCACGTTGCTA 2022 chrXptel1M 300099 AAGCTAATCAATGGCC-TTTAACAG--CT-GTTTTCTGTGACCTCTCTGC 300144 v ---- i -v vv -- -i i viv ? v L2#LINE/L2 2023 AATC----CAATGGTCAATTCTCAGTCCTCATCTTACTTGACCTNTCAGC 2068 chrXptel1M 300145 AGCCTCTGACACTGTGGATCCATCCTT 300171 v i v v vv i L2#LINE/L2 2069 AGCATTTGACACAGTTGATCACTCCCT 2095 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 46.73 CpG sites = 98, Kimura (unadjusted) = 48.92 Transitions / transversions = 1.13 (98/87) Gap_init rate = 0.06 (34 / 549), avg. gap size = 1.41 (48 / 34) 277 27.68 6.52 5.76 chrXptel1M 300692 300829 (699171) L2#LINE/L2 2066 2204 (878) m_b333s601i6 13972 chrXptel1M 300692 AACAGTTCTCAACAAATGTTGATTCACCCTCTTCTTCT-----CACTTTC 300736 i ivi ii v - - i i i ----- L2#LINE/L2 2066 AGCAGCATTTGACACA-GTTGAT-CACTCCCTCCTTCTTGAAACACTTTC 2113 chrXptel1M 300737 TTCTCTCTAGGATTTTTTGGGGCATGATTCTCTCCCAGTTCTCGATTGCT 300786 v - i ---i iii i iv iv ii i --i v L2#LINE/L2 2114 TTCACT-TGG---CTTCCAGGACACCACACTCTCCTGGTTTTC--CTCCT 2157 chrXptel1M 300787 ATCCAACTG----CTTCTTCTCAGGCTCCTTTGCCAGATCTTCTTCA 300829 i iv ---- i v ii v i i L2#LINE/L2 2158 ACCTCACTGGCCGCTCCTTCTCAGTCTCCTTTGCTGGTTCCTCCTCA 2204 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 36.87 CpG sites = 27, Kimura (unadjusted) = 36.87 Transitions / transversions = 3.00 (27/9) Gap_init rate = 0.07 (10 / 137), avg. gap size = 1.70 (17 / 10) 372 30.56 8.67 4.98 chrXptel1M 300848 301274 (698726) L2-1_AMi#LINE/L2 283 724 (511) m_b333s551i3 13973 chrXptel1M 300848 TAGGTGTCCTGTATGGCTCTCTCCTGGGTCCTCTTCCCCT-TCTCCA--- 300893 i v i iii v v v i i i - i --- L2-1_AMi#LINE 283 TGGGGGTTCCACAGGGCTCTGTCCTTGGTCCCCTTCTCTTCTCTCTACAC 332 chrXptel1M 300894 -TTA---CTTAGTGGTCTCACCAGGTTTTATGGATTTAACTACCATCTCT 300939 - --- vi ii i v vvvvi iii i v L2-1_AMi#LINE 333 CTTATCTCTGGGTAATCTCATCCGCAAACACAAATTCAACTACCATCTGT 382 chrXptel1M 300940 ATTCTGATGATTT-CAAATCTACCTATC--CTCC---CCTAACTGCTGAC 300983 ------- i i- i v -- --- iv v vvi L2-1_AMi#LINE 383 -------TGACTCACAGATCTACCTCTCTACTCCAGACCTGTCTCCTTCT 425 chrXptel1M 300984 CTCCAATCTCATAATTTCAAC-TGTATTTCAGACATCTCAAACTC---GA 301029 v v v - i ii - v i v --- --- L2-1_AMi#LINE 426 GTCCAAACTAA-AATCTCGGCCTGTCTCTCTGACATCTC---CTCGTGGA 471 chrXptel1M 301030 TGTCCAGGAGACAGCTCAAATTCAAGATGTTC-AAACCAGAATTTGTTAC 301078 i vv v ii v vi - v ii iv v i L2-1_AMi#LINE 472 TGTCTAGCCGTCAGCTCAAGCTCAACATGGCCTAAAACAGAGCTCTTAAT 521 chrXptel1M 301079 CTT--TCCCAAGCCCA---TCCATTTCC----CTC--TTACCGTCAAGAG 301117 --i i?---i i ---- -- i i vi v i L2-1_AMi#LINE 522 CTTCCCCCCAAGCCTNCTCCCCATTCCCTTTTCTCGATCACTGTGGACAA 571 chrXptel1M 301118 CAATATCATCCTCCTGGTCCCTTGGGCTCACCACGTAGGAGTCATGCTGA 301167 vi i v iv v ii i iiv v i v ------ L2-1_AMi#LINE 572 CACCACCATCCTGCCTGTCACTCAGGCCCGTAACCTGGGCGTCA------ 615 chrXptel1M 301168 TTCTTC-ACT---ATTTCTCACTGCCAGCCTCCCACATCCAAACTGTTGC 301213 - - --- ii v --- vii i ii i- i L2-1_AMi#LINE 616 -TCTTCGACTCGGACCTCTCTCT---AGGTCCTCACATCCAGGCTA-TGT 660 chrXptel1M 301214 CCAAGGC-TGTTGACCTTACCTTTGCAGCATCTCTAACATAC--CCGCTT 301260 i iv - iv iii vi viii i v -- vi i L2-1_AMi#LINE 661 CTAAATCTTGCAGATTCTTTCTGCATAACATCTCTAAGATACGGCCTTTC 710 chrXptel1M 301261 CTCTCCTTTGACAC 301274 v v iv L2-1_AMi#LINE 711 CTATCCATCCACAC 724 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.00 CpG sites = 75, Kimura (unadjusted) = 40.87 Transitions / transversions = 1.53 (75/49) Gap_init rate = 0.09 (40 / 426), avg. gap size = 1.48 (59 / 40) 219 38.55 0.00 2.46 chrXptel1M 301637 301761 (698239) L2#LINE/L2 2659 2780 (302) m_b333s601i7 13972 chrXptel1M 301637 TTGTCCTCATCATCACTGCCATCTTCCTCTTGTGAGTCTTGCATATCACC 301686 v vi i vi i vi vv vii i vi---i i L2#LINE/L2 2659 TTCTCACCACCTCCACTGCCACCACCCTGGTCCAAGCCAC---CATCATC 2705 chrXptel1M 301687 TCATACCCGGACCATCGCAATAACCTGTTGGTGAGCCTGTCTGCTTCAGA 301736 vii i ii ii i vi iiivi i vi viv L2#LINE/L2 2706 TCTCGCCTGGATTACTGCAATAGCCTCCTAACTGGTCTCCCTGCTTCCAC 2755 chrXptel1M 301737 TCTTTCCTCCTTTCAGTCCACTCTC 301761 i v i i ? i i L2#LINE/L2 2756 CCTTGCCCCCCTNCAGTCTATTCTC 2780 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 57.70 CpG sites = 32, Kimura (unadjusted) = 60.03 Transitions / transversions = 2.13 (32/15) Gap_init rate = 0.02 (3 / 124), avg. gap size = 1.00 (3 / 3) 295 28.00 0.00 0.00 chrXptel1M 302009 302083 (697917) L2#LINE/L2 2765 2839 (243) m_b333s601i8 13972 chrXptel1M 302009 CTTTCAGTCCACTCTCCATTCAGCCACCAAAGTGATTTTCCTAAAATAAA 302058 i ? i i v iv vi i ii ii iiv L2#LINE/L2 2765 CCTNCAGTCTATTCTCAACACAGCAGCCAGAGTGATCCTTTTAAAACGTA 2814 chrXptel1M 302059 GGTTTGATCATTTCACTCCCCTGCT 302083 i iv v i L2#LINE/L2 2815 AGTCAGATCATGTCACTCCTCTGCT 2839 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.18 CpG sites = 15, Kimura (unadjusted) = 37.75 Transitions / transversions = 2.50 (15/6) Gap_init rate = 0.00 (0 / 74), avg. gap size = 0.0 (0 / 0) 549 33.67 10.00 1.80 chrXptel1M 302290 302649 (697351) L2b_3end#LINE/L2 72 460 (6) m_b333s601i9 13972 chrXptel1M 302290 CCACCCTGGCTTCCTAGCTGTTCC------AC----------CTCTTGGC 302323 v i v ------ ---------- ii v L2b_3end#LINE 72 CCACACTGGCCTCCTTGCTGTTCCTCGAACACGCCANGCTCNCTCCCGCC 121 chrXptel1M 302324 TCTGGGCATTTTTGCCGTTTGTCCCCTGTTCTTGGGAT-CACTTCCTTCC 302372 v v vii ?vvi i v v i i i- v iiv L2b_3end#LINE 122 TCAGGGCCTTTGCACNTGCTGTTCCCTCTGCCTGGAACGCCCTTCCCCAC 171 chrXptel1M 302373 TTGGCTCCAGCC--ACTAATCTCCTTTGACT--TTCTTCAAATCCCAACT 302418 i -- i - --i i - --- -- i ii i i L2b_3end#LINE 172 CT--CTTC-GCCTGGCCAA-CTCCT---ACTCATCCTTCAGGTCTCAGCT 214 chrXptel1M 302419 -AAATCCCATCTTCTACAAAATACCTTTTCC-ACCACCTGTTAAAGGT-- 302464 - vi i i v iii vi i ii i- v iivvvvi -- L2b_3end#LINE 215 CAAATGTCACCTCCTCCGGGAAGCCCTCCCTGACCCCCCAGGCCGGGTCA 264 chrXptel1M 302465 AGTGCTTTCTT--GCACTATCTCATTTTCATCTT-CTATAC-AGCTTGT- 302509 i i ii i -- vi ivi i v iii i i - i iv -i v i - L2b_3end#LINE 265 GGCGCCCTCCTCTGGGCCCCCCCAGTCCTACCCTGCCACTCTGGGTTATN 314 chrXptel1M 302510 -TTGGACACTTTTCTCTTTGTCTTCTTCATTAGATTGCAAGTTACTGGAG 302558 - vvii? viv v i i ii i i ii i v vv L2b_3end#LINE 315 ATTGTCTGNTTACATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGTGAG 364 chrXptel1M 302559 GGCAGGG-CC---TTTCTTTTGCTTCTTTTTGTATCCTGAG-GCTTAGCA 302603 - --- i v i i iviivi iv - i L2b_3end#LINE 365 GGCAGGGACCGNGTCTGTCTTGTTCACCGCTGTATCCCCAGCGCCTAGCA 414 chrXptel1M 302604 CCGAGCCTAGCACACAGTAGGTGCTTAATAAATATTCATTGATTGA 302649 v ? i i i i ii v L2b_3end#LINE 415 CAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTTGTTGAATGA 460 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 44.33 CpG sites = 80, Kimura (unadjusted) = 48.34 Transitions / transversions = 2.05 (80/39) Gap_init rate = 0.06 (22 / 359), avg. gap size = 1.95 (43 / 22) 18 4.71 0.00 0.00 chrXptel1M 303627 303648 (696352) (G)n#Simple_repeat 1 22 (0) m_b333s252i3 13974 chrXptel1M 303627 GGTGGGGGGGGGGGGGGGGGGG 303648 v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGG 22 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 24 30.96 0.00 2.25 chrXptel1M 304005 304095 (695905) (GCG)n#Simple_repeat 1 89 (0) m_b333s252i4 13975 chrXptel1M 304005 GCAGCGGCGGCGGGGGCGGCGGCGGAGGAAACGGTCACTGCGCGCTTGGG 304054 i v v vii ivi v - -v v (GCG)n#Simple 1 GCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCG-GC-GGCG 48 chrXptel1M 304055 GACGCCACAGAGGCGGCGGCGGCAGCGACGACGGCGGCAGC 304095 vv vi i v i i i i (GCG)n#Simple 49 GCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC 89 Matrix = Unknown Transitions / transversions = 1.00 (11/11) Gap_init rate = 0.02 (2 / 90), avg. gap size = 1.00 (2 / 2) 18 7.86 0.00 0.00 chrXptel1M 304158 304184 (695816) (GGC)n#Simple_repeat 1 27 (0) m_b333s252i5 13976 chrXptel1M 304158 GGAGGAGGCGGCGGCGGCGGCGGCGGC 304184 v v (GGC)n#Simple 1 GGCGGCGGCGGCGGCGGCGGCGGCGGC 27 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 17 16.19 0.00 2.70 chrXptel1M 304201 304238 (695762) (GGCTC)n#Simple_repeat 1 37 (0) m_b333s252i6 13977 chrXptel1M 304201 GGCTCGGCCCCGGCTCGGCTCAGCTCGGTCCGGCCCGG 304238 - i i ii i (GGCTC)n#Simp 1 GGCTCGG-CTCGGCTCGGCTCGGCTCGGCTCGGCTCGG 37 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 15 17.14 2.22 4.55 chrXptel1M 306305 306349 (693651) (GGGGAA)n#Simple_repeat 1 44 (0) m_b333s252i7 13978 chrXptel1M 306305 GGAGAAGGGGAA-GGGAGGGGGAGGGAGAGGGAAAGAAGGGGAAGG 306349 i - i i i i --i (GGGGAA)n#Sim 1 GGGGAAGGGGAAGGGGAAGGGGAAGGGGAAGG--GGAAGGGGAAGG 44 Matrix = Unknown Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.07 (3 / 44), avg. gap size = 1.00 (3 / 3) 11 13.59 2.78 5.71 chrXptel1M 306742 306777 (693223) (AATTCA)n#Simple_repeat 1 35 (0) m_b333s252i8 13979 chrXptel1M 306742 AATTCATAAATCAAATGCAACATTCAGATT-AACTTC 306777 - v v - i - v (AATTCA)n#Sim 1 AATTCA-AATTCAAATTCAA-ATTCAAATTCAAATTC 35 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.09 (3 / 35), avg. gap size = 1.00 (3 / 3) 21 3.31 3.23 0.00 chrXptel1M 307762 307792 (692208) (AAAC)n#Simple_repeat 1 32 (0) m_b333s252i9 13980 chrXptel1M 307762 AAACAAACAAACAAACAAACAAACCAA-AAAC 307792 v - (AAAC)n#Simpl 1 AAACAAACAAACAAACAAACAAACAAACAAAC 32 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.03 (1 / 30), avg. gap size = 1.00 (1 / 1) 73 1.44 1.43 0.00 chrXptel1M 308079 308148 (691852) (CT)n#Simple_repeat 1 71 (0) c_b333s251i1 13981 chrXptel1M 308079 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 308128 (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chrXptel1M 308129 CTCTCTCTCT-TCTGTCTCTC 308148 - v (CT)n#Simple_ 51 CTCTCTCTCTCTCTCTCTCTC 71 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.01 (1 / 69), avg. gap size = 1.00 (1 / 1) 25 15.11 0.00 0.00 chrXptel1M 308152 308197 (691803) (TGCG)n#Simple_repeat 1 46 (0) m_b333s252i10 13982 chrXptel1M 308152 TGTGTGCATGCGTGCGTGCGTGCGTGCGTGTGTGTGTGTGTGTGTG 308197 i i i i i i (TGCG)n#Simpl 1 TGCGTGCGTGCGTGCGTGCGTGCGTGCGTGCGTGCGTGCGTGCGTG 46 Matrix = Unknown Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 186 21.44 0.00 2.38 chrXptel1M 308292 308334 (691666) X6A_LINE#LINE/CR1 40 81 (997) m_b333s601i10 13983 chrXptel1M 308292 AGTAGAGACAAATGGTCAATTGCTCAGCGTAGGAAGAAGCTGA 308334 ii i i - ?i i i i i X6A_LINE#LINE 40 AGTAGGAATAAATGGCCAATT-CTCAGNATGGAAAGAAGTTAA 81 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.90 CpG sites = 9, Kimura (unadjusted) = 28.90 Transitions / transversions = 1.00 (9/0) Gap_init rate = 0.02 (1 / 42), avg. gap size = 1.00 (1 / 1) 42 0.00 0.00 0.00 chrXptel1M 308466 308501 (691499) (AC)n#Simple_repeat 1 36 (0) c_b333s251i2 13984 chrXptel1M 308466 ACACACACACACACACACACACACACACACACACAC 308501 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACAC 36 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 31 23.62 2.60 0.00 chrXptel1M 308882 308958 (691042) (AT)n#Simple_repeat 1 79 (0) m_b333s252i11 13985 chrXptel1M 308882 ATAT-TTTATATATATATATATATATACACACATATGTATGGATATAT-T 308929 - v i i i i iv - (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chrXptel1M 308930 CTGCATGCATGTATGTATATATGTATATA 308958 v ii ii i i i (AT)n#Simple_ 51 ATATATATATATATATATATATATATATA 79 Matrix = Unknown Transitions / transversions = 4.00 (12/3) Gap_init rate = 0.03 (2 / 76), avg. gap size = 1.00 (2 / 2) 241 17.41 11.59 8.45 chrXptel1M 309516 309584 (690416) MIR#SINE/MIR 143 213 (49) m_b333s601i11 13986 chrXptel1M 309516 GGGATAATAATAATACTAGCATCTGCCTCCCAGTGTTGTTGGAGGAATTA 309565 i ------ i vi v vii i MIR#SINE/MIR 143 GGGATAATAATAGTAC------CTACCTCATAGGGTTGTTGTGAGGATTA 186 chrXptel1M 309566 AATGATTT--------TAAAGTGCTTA 309584 v -------- i MIR#SINE/MIR 187 AATGAGTTAATACATGTAAAGCGCTTA 213 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 18.26 CpG sites = 7, Kimura (unadjusted) = 20.22 Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.10 (7 / 68), avg. gap size = 2.00 (14 / 7) 210 31.94 11.11 0.00 chrXptel1M 309521 309592 (690408) MIRb#SINE/MIR 146 225 (43) m_b333s601i12 13986 chrXptel1M 309521 AATAATAATACTAGCATCTGCCTCCCAGTGTTGTTGGAGGAATTAAATGA 309570 iivi v ii i i v v vii i MIRb#SINE/MIR 146 AATGGGGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGA 195 chrXptel1M 309571 T--------TTTAAAGTGCTTAATATAACG 309592 v-------- v i ii i ii MIRb#SINE/MIR 196 GATAATGCATGTAAAGCGCTTAGCACAGTG 225 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.76 CpG sites = 16, Kimura (unadjusted) = 44.41 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.01 (1 / 71), avg. gap size = 8.00 (8 / 1) 24 24.89 0.00 0.00 chrXptel1M 312072 312122 (687878) (T)n#Simple_repeat 1 51 (0) m_b333s252i12 13987 chrXptel1M 312072 TTTTCTTTTTCTTTCTTCCTTTCCTTTTCTTTTTTCTTTTTTTCTTTTTT 312121 i i i ii ii i i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chrXptel1M 312122 T 312122 (T)n#Simple_r 51 T 51 Matrix = Unknown Transitions / transversions = 1.00 (10/0) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 501 21.07 0.71 8.46 chrXptel1M 312125 312264 (687736) C MIRb#SINE/MIR (138) 130 1 m_b333s601i14 13988 chrXptel1M 312125 CTGAGGC-AATTGGGGTTAAGTGACTTGCCTAGGATCACACAGCTAGGAA 312173 -v vv i i i i i --- C MIRb#SINE/MIR 130 CTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAG--- 84 chrXptel1M 312174 GTGTTAAGTGTCTGAGACCAGATTTGGACTCAGGTCCTCCTGACTTCAGG 312223 ---- v v v vi i i i ivi i ii C MIRb#SINE/MIR 83 ----TAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAA 38 chrXptel1M 312224 GCTGGTGCTCTATCCACTGCACCAGCTAGCTGTCCTGTCTG 312264 iv v - -- i i- C MIRb#SINE/MIR 37 GCCCGTGCTCTTTCCACTGCACCA-C--GCTGCCCC-TCTG 1 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 24.02 CpG sites = 17, Kimura (unadjusted) = 25.07 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.09 (12 / 139), avg. gap size = 1.00 (12 / 12) 544 19.89 0.81 5.98 chrXptel1M 312125 312247 (687753) C MIRc#SINE/MIR (141) 127 11 m_b333s601i13 13988 chrXptel1M 312125 CTGAGGC-AATTGGGGTTAAGTGACTTGCCTAGGATCACACAGCTAGGAA 312173 -v vv i i i i --- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG--- 81 chrXptel1M 312174 GTGTTAAGTGTCTGAGACCAGATTTGGACTCAGGTCCTCCTGACTTCAGG 312223 ---- v v v vi i i i i i i i C MIRc#SINE/MIR 80 ----TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chrXptel1M 312224 GCTGGTGCTCTATCCACTGCACCA 312247 v ii v C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTGCACCA 11 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 22.30 CpG sites = 14, Kimura (unadjusted) = 23.42 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.07 (8 / 122), avg. gap size = 1.00 (8 / 8) 3317 28.70 2.92 2.44 chrXptel1M 312307 314020 (685980) L1M5_orf2#LINE/L1 1573 3294 (0) m_b333s551i4 13989 chrXptel1M 312307 ACAGAGAAAGAAAATTATAGACCAATCTCCCTAATGAATATTGATGCTAA 312356 iii i v v i v v L1M5_orf2#LIN 1573 ACAAGAAAAGAAAATTACAGACCAATATCCCTCATGAACATAGATGCAAA 1622 chrXptel1M 312357 AATCTTAAATAAGATATTAGCAAA-AGACTACAGAAAATCATCTCCAAGA 312405 i ? i i -v v v v vvi vvvv i L1M5_orf2#LIN 1623 AATCCTNAACAAAATATTAGCAAATCGAATCCAGCAATATATAAAAAGGA 1672 chrXptel1M 312406 TAATACACTATGATCAAGTAGGATTTATACCAGGAATGCAGGGCTGGTTC 312455 ii i i i v i i i L1M5_orf2#LIN 1673 TAATACATCATGACCAAGTGGGGTTTATCCCAGGAATGCAAGGTTGGTTT 1722 chrXptel1M 312456 AATATTAGGAAAACTATCAATATAATTGGCCATGTCAATAACCAAATTAA 312505 i v i v v i vi i --- vi v L1M5_orf2#LIN 1723 AACATTCGAAAATCAATCAATGTAATTCACCATAT---TAACAGAATAAA 1769 chrXptel1M 312506 C---AAAAACCATATGATCATCTCAATAGATGCAGAAAAAGCATTTGATA 312552 v--- i i L1M5_orf2#LIN 1770 GGAGAAAAATCATATGATCATCTCAATAGATGCAGAAAAAGCATTTGACA 1819 chrXptel1M 312553 AAATCCAACATCCATTCCTATTAAAAACACTTGAGAGTATAGGAATAAAT 312602 i i v iv v iiiv ivv i v L1M5_orf2#LIN 1820 AAATTCAACACCCATTCATGATAAAAACTCTCAGCAAACTAGGAATAGAA 1869 chrXptel1M 312603 GGACTTTTCCTTAAAATAATCAGCAGCATCTATTTAAAACCATCAGTAAG 312652 ivvi i vv i v ivi ivv vv i? i L1M5_orf2#LIN 1870 GGGAACTTCCTCAACCTGATAAAGGGCATCTACGAAAAACCTACAGCNAA 1919 chrXptel1M 312653 CATCATATGTAATGGAGACAAACTGCAACCATTCCCAATAAGATC-TGAG 312701 iv v v ? v ?v v vv -v i L1M5_orf2#LIN 1920 CATCATACTTAATGGTGAAANACTGAANGCTTTCCCCCTAAGATCGGGAA 1969 chrXptel1M 312702 TGAAACAAGGTTGCCCACTATCACCGTTACTATTTAATATTGTATTAGAA 312751 ii i v i i ? ii v i i i i i L1M5_orf2#LIN 1970 CAAGACAAGGATGTCCGCTNTCACCACTTCTATTCAACATTGTACTGGAG 2019 chrXptel1M 312752 ACGCTAGCTATAGCAATAAGAGCTGAGAAAGAGATTAAAGGAATAAGAAT 312801 iiv i vv ivvv i i v v ii L1M5_orf2#LIN 2020 GTCCTAGCCAGTGCAATAAGGCAAGAAAAAGAAATAAAAGGCATAAAGAT 2069 chrXptel1M 312802 AGGCAATGAGGAAGCCAAATTATCACTCTTTGCCGATGACATGATGGTAT 312851 v v v i iiv i i ?i v i v v ? L1M5_orf2#LIN 2070 TGGAAAGGAAGAAATAAAACTGTCNTTATTCGCAGATGACATGATTGTNT 2119 chrXptel1M 312852 ACTTAGAGAACCCCAGA-ATTCTGCTAAAAAGTTATTAGAAATAATCCAC 312900 v i i ? i - v i v ? ii i v vvii L1M5_orf2#LIN 2120 ACGTAGAAAATCCNAAAGAATCTACAAANAAACTACTAGAACTAATAAGT 2169 chrXptel1M 312901 AACTTTAGCAAAGTTGCTGGTTATAAAATAAACCCACATAAGTCATCAGC 312950 i v i i ? v i ii v ivi v i viv i L1M5_orf2#LIN 2170 GAATTTAGCAAGGTCGCNGGATACAAGGTCAATATACAAAAATCAATTGT 2219 chrXptel1M 312951 ATTCTTATATATCACTAACAA--AATCCAACAGTCAGAGTTACAAAGAGA 312998 ii ii vi -- ivi v i v i v --? i iv L1M5_orf2#LIN 2220 ATTTCTATATACTAGCAACAAACAATTGGAAAATGAAATTT--NAAAAAC 2267 chrXptel1M 312999 AATTCCATTTAAAGTAACTACTGATAATATAAAATATTTAGGAATCTATC 313048 v v i i vv vi v i ? i vv L1M5_orf2#LIN 2268 AATACCATTTACAATAGCATCAAAAAACATNAAATACTTAGGAATAAATC 2317 chrXptel1M 313049 TGCCAAGGGAAAAT---CAGAAACTTTATGAGCAAAATTACAGACCACTT 313095 iv --- ? --- ii v ? iivvv i i v i v L1M5_orf2#LIN 2318 TAACAA---AANATGTGCAAGACCTNTACACTGAAAACTACAAAACATTG 2364 chrXptel1M 313096 TTCACACAAATTAAGTCTGATCT-AACCAATTGAAAAATATTAAATGCTC 313144 i v v v ivvv i - iv v i i vvv i L1M5_orf2#LIN 2365 CTGAGAGAAATTAAAGAAGACCTAAATAAATGGAGAGATATACCATGTTC 2414 chrXptel1M 313145 TTGGATAGGGCGAGCAAATATAATAAAGATGACAATATTACCTAAACTAA 313194 v v iv viv vi ? v vi v i i i L1M5_orf2#LIN 2415 ATGGATTGGAAGACTCAATATTGTNAAGATGTCAATTCTCCCCAAATTGA 2464 chrXptel1M 313195 TCTATTTATTTAGCGCTATACCAATCAGACTCCCAAAAACAATTTTAATG 313244 vv i ii v v i v iv --ii vv L1M5_orf2#LIN 2465 TCTATAGATTCAATGCAATCCCAATCAAAATCCCAGCA--GGTTTTTTTG 2512 chrXptel1M 313245 ACCTAGAAAAATAACAA--------CAAAGTTCATATGGAAAAACAAAAG 313286 --- - v i --------i i i vi i L1M5_orf2#LIN 2513 ---TAG-AAATTGACAAGCTGATTCTAAAATTTATATGGAAATGCAAAGG 2558 chrXptel1M 313287 GTCAAGAAT-TTCAAGGGAATTAATGAAAAAAAAT--CAAATGATGGTGG 313333 ii ? -vi iiv i-v i v-- - v v L1M5_orf2#LIN 2559 ACCNAGAATAGCCAAAACAATC-TTGAAAAAGAAGAACAAA-GTTGGAGG 2606 chrXptel1M 313334 -CTTAGCTGTACCAGATCT-AAAATTATATTATAGAGCAGCAGTTACCAA 313381 - - vv ? ? - i i - i vi v i L1M5_orf2#LIN 2607 ACTTA-CACTACCNGATNTCAAGACT-TATTATAAAGCTACAGTAATCAA 2654 chrXptel1M 313382 AACTATTTGGTATTGGC-TAAGGAATAGATTAGTTGATCAGTGGAATAGA 313430 i vi v - - iv i v i i L1M5_orf2#LIN 2655 GACAGTGTGGTATTGGCGTAAGG-ATAGACAAATAGATCAATGGAACAGA 2703 chrXptel1M 313431 TTAG---GTTCAAGGGATAAAACAGTCA-ACAAATATAGCAACCTAGTCT 313476 v --- i - ii i v --- - v i ?v ?i ii i L1M5_orf2#LIN 2704 ATAGAGAGTCC-AGAAATAGACC---CACACATATATGGNCANTTGATTT 2749 chrXptel1M 313477 TTGACAAA---CCCAAAG-ATCCCAGCTTTTGGGATAAGAACTTACTGTT 313522 ---v ? - vii ---- iv i ivvv v L1M5_orf2#LIN 2750 TTGACAAAGGTGCCAANGCAATTCAG----TGGGGAAAGGATAGTCTTTT 2795 chrXptel1M 313523 TGATAAAAATTGCTGGGAAAATTGGAAACTAATATGGCAGAAACTAGGCA 313572 ii i viv i v v iiv v i v iii?v L1M5_orf2#LIN 2796 CAACAAATGGTGCTGGAACAATTGGATATCCATATGGAAAAAAATGAANC 2845 chrXptel1M 313573 TTGATCCATACTTAACGCCGTACACCAAGATAAGGTCAAAATGGGTGCAT 313622 i i v i v i i v i v iv ? i i - L1M5_orf2#LIN 2846 TCGACCCCTACCTCACACCATACACAAAAATTAATTCNAGATGGAT-CAT 2894 chrXptel1M 313623 -GACCTAGGCATAAAGAATGAAATTATTAATAAATTAGAGG--AACATAG 313669 - iiii ii? i i v vvvvi i -- L1M5_orf2#LIN 2895 AGACCTAAATGTAAAAGNTAAAACTATAAAACTTCTAGAAGAAAACATAG 2944 chrXptel1M 313670 GATAGTTTACCTCTCAGACCTGTGGA-AGGGGAAGGTTTTTATGACCAAA 313718 v i-- i iivv vv ?- vi i i - i v ii L1M5_orf2#LIN 2945 GAGAA--TATCTTCGTGACCTTGGGNTAGGCAAAGATTTCT-TAAACAGG 2991 chrXptel1M 313719 GCAGAACTAGAGATCATTACTGATCACAAAATAGAAAAT-------TTCG 313761 i v -- i -----i ?i i i v i ------- v L1M5_orf2#LIN 2992 ACACAA--AAAG-----CACNAACCATAAAAGAAAAAATTGATAAATTGG 3034 chrXptel1M 313762 ATTATACCAAACTGAAAAGTTTTTGTACAAACAAAACTAATGCAGACAAG 313811 i ?i i v v ii i iv ?vvv ivi vi ivi v i L1M5_orf2#LIN 3035 ACTNCATCAAAATTAAAAACTTCTGCTCNTCAAAAGACACCGTTAAGAAA 3084 chrXptel1M 313812 ATTAGAAGGGAAGCAATAAACTGGGAAAATATTTTTACAGT-CAAAGGTT 313860 v i v v i i ? i v v i i?- v vi- L1M5_orf2#LIN 3085 ATGAAAAGGCAAGCCACAGANTGGGAGAAAATATTTGCAANACATATA-T 3133 chrXptel1M 313861 CTGATAAAGGCCACATTTCCAAAATATATAGAGAATTAACTCTAATTT-A 313909 i v v i v i i i -v vi ? i- L1M5_orf2#LIN 3134 CTGACAAAGGACTCGTATCCAGAATATATAAAGAACT-CCTACAANTCAA 3182 chrXptel1M 313910 TAAAAAATCAAGCCATTC--TCCAAT-TGAAAATGGTCAAAGGATATGAA 313956 ? -- v vv --i -?i v i iv L1M5_orf2#LIN 3183 TAANAAA--AAGACAAACAACCCAATANAAAAATGGGCAAAAGACTTGAA 3230 chrXptel1M 313957 CAGACAATTCTCAGATGAAGACATTGAAACTATTTCTAGTCATATGAAAA 314006 v v i v i ?v iviiivv iv i L1M5_orf2#LIN 3231 CAGACACTTCACAAAAGAAGATATNCAAATGGCCAATAAGCACATGAAAA 3280 chrXptel1M 314007 GATGCTCCAAGTCA 314020 v v? L1M5_orf2#LIN 3281 GATGCTCAACNTCA 3294 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.12 CpG sites = 261, Kimura (unadjusted) = 37.92 Transitions / transversions = 1.19 (261/219) Gap_init rate = 0.04 (67 / 1713), avg. gap size = 1.37 (92 / 67) 1453 26.77 4.12 4.12 chrXptel1M 313878 314508 (685492) L1ME5_3end#LINE/L1 7 637 (304) m_b333s551i5 13989 chrXptel1M 313878 TCCAAAATATATAGAGAATTAACTCTAATTTATAAAAAATCAAGCCATT- 313926 i i i ii i vviv v iv i i -- v iv?- L1ME5_3end#LI 7 TCTAGAATATACAAGGAACTCCTGCAAATCAACAAGAAA--AAGACGGNA 54 chrXptel1M 313927 -CTCCAATTGAAAA-TGGTCAAAGGATATGAACAGACAATTCTCAGATGA 313974 - i v - v i iv v L1ME5_3end#LI 55 ACCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGA 104 chrXptel1M 313975 AGACA-TTGAAA--CTATTTCTAGTCATATGAAAAGATGCTCCAAGTCAT 314021 i v -ii -- --v v - i v v L1ME5_3end#LI 105 GGAAACCCGAAAGGCTA--ACAAG-CATATGAAGAGATGCTCAAACTCAT 151 chrXptel1M 314022 TATTAATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACA 314071 v i vv i i vi L1ME5_3end#LI 152 TAGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACA 201 chrXptel1M 314072 CCTGTCAGATTGGCTAAGATGACAGGAAA---AAATAATGATGATTGTTG 314118 i i i v i v --- ---ii vii v L1ME5_3end#LI 202 CCTATTAGACTGGCAAAAATTA---GAAAGCTGGATAATGCCAAGTGTTG 248 chrXptel1M 314119 GAG-GGACGTGGGAAAACTGGGACATTGATTCATTGTTGGTGGAGTTGTG 314167 v - i i ? iv i vi v v i i iiv i L1ME5_3end#LI 249 GCGAGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTA 298 chrXptel1M 314168 AACGAATCCAACCATTTTGGAGAGTAGTTTGGAACTA--TGCTCAAA--A 314213 i vii v i i i i i v v -- iv -- L1ME5_3end#LI 299 GACTGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTA 348 chrXptel1M 314214 AGTTATCAAACTGTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGAT 314263 - --- --- v i i viii v vv L1ME5_3end#LI 349 AG-TAT---AC---GCATACCCTATGACCCAGCAATTCCGCTCCTGGGTA 391 chrXptel1M 314264 TATATCCCAAAGAGATTATAAAGAAGG----GAAAGGGACCTGTATGTGC 314309 i v v viv ----v i ---- i L1ME5_3end#LI 392 TATATCCCAAAGAAATTCTCACACAGGTCCATAAGGGGAC----ATGTAC 437 chrXptel1M 314310 ACGAATGTTTGTGGCAGCCCT-TTTGTAGTGGCTAGAAACTGGAAACTGA 314358 iv i ii v vi - i vi i ii ii -- L1ME5_3end#LI 438 GAGGATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGC--A 485 chrXptel1M 314359 AC--GGATGTCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATATGA 314406 -- i v v i v iii v iv v L1ME5_3end#LI 486 ACCTGGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGC 535 chrXptel1M 314407 AAATTATGGAATATTACTGT-TCTGTAAGAAATGACCAACAGGATGATTT 314455 v ii i i - i-v v v iii vi vi -- v L1ME5_3end#LI 536 ACACCATGGAGTACTA-TGCAGCAGTTAGAAGCAACGGACTAGATG--TA 582 chrXptel1M 314456 CAGAAAG--GCCTGGAGAGA-CTTACACGAAC-TGATGCTAAGTGAAATG 314501 v v --i v vi - v -- - ii i vi L1ME5_3end#LI 583 CACATAGCAACATGGATGGATCTTAAA--AACATAGTGCTGAGTGAAAAA 630 chrXptel1M 314502 AGCAGGA 314508 i i L1ME5_3end#LI 631 AGTAAGA 637 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.96 CpG sites = 94, Kimura (unadjusted) = 34.02 Transitions / transversions = 1.38 (94/68) Gap_init rate = 0.07 (42 / 630), avg. gap size = 1.24 (52 / 42) 1513 26.78 1.28 2.03 chrXptel1M 313878 314422 (685578) L1ME3G_3end#LINE/L1 7 547 (377) m_b333s551i6 13989 chrXptel1M 313878 TCCAAAATATATAGAGAATTAACTCTAATTTATAAAAAATCAAGCCATTC 313927 i i i vviv v iv i -- v --v L1ME3G_3end#L 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAA--AAGACA--A 52 chrXptel1M 313928 TCCAATTGAAAA-TGGTCAAAGGATATGAACAGACAATTCTCAGATGAAG 313976 i v - v i v v i L1ME3G_3end#L 53 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chrXptel1M 313977 ACATTGAAACTATTTCTAGTCATATGAAAAGATGCTCCAAGTCATTATTA 314026 v vv iviiivv iv v vv i v L1ME3G_3end#L 103 AAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTA 152 chrXptel1M 314027 ATCAGAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACACCTGT 314076 i i vv i i viv ii L1ME3G_3end#L 153 ATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCAT 202 chrXptel1M 314077 CAGATTGGCTAAGATGACAGGAAAAAATAATGATGATTGTTGGAG-GGAC 314125 v i vvv iii?vvi ivi? v v - ii L1ME3G_3end#L 203 CAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGT 252 chrXptel1M 314126 GTGGGAAAACTGGGACATTGATTCATTGTTGGTGGAGTTGTGAACGAATC 314175 i v v vi v v i i iiv i ivii v L1ME3G_3end#L 253 GTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTA 302 chrXptel1M 314176 CAACCATTTTGGAGAGTAGTTTGGAACTATGCTCAAAAAGTTATCAAACT 314225 i ? i i i v v - vvv i -- i v L1ME3G_3end#L 303 CAGCCNTTTTGGAGGGCAATTTGGCAGTAT-CTATTAAAAT--TTAAAAT 349 chrXptel1M 314226 GTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGATTATATCCCAAAG 314275 i i i vii v ? ?v v i ? L1ME3G_3end#L 350 GCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANAG 399 chrXptel1M 314276 AGATTAT-AAAGAAG-GGAAAGGGACCTGTATGTGCACGAATGTTTGTGG 314323 i vv -iv v v - v v i --? i i v i ii v L1ME3G_3end#L 400 AAATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTCATTG 447 chrXptel1M 314324 CAGCCCT-TTTGTAGTGGCTAGAAACTGGAAACTGAAC--GGATGTCCAT 314370 vi - i i v i i -- --ii L1ME3G_3end#L 448 CAGCATTGTTTGTAATAGCGAAAAATTGGAAAC--AACCTAAATGTCCAT 495 chrXptel1M 314371 CAGTTGGAGAATGGCTGAATAAATTGTGGTATATGAAAATTATGGAATAT 314420 i v i i i i vv v i i L1ME3G_3end#L 496 CAATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATAC 545 chrXptel1M 314421 TA 314422 L1ME3G_3end#L 546 TA 547 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.58 CpG sites = 75, Kimura (unadjusted) = 34.16 Transitions / transversions = 1.10 (75/68) Gap_init rate = 0.03 (17 / 544), avg. gap size = 1.06 (18 / 17) 12 17.70 0.00 5.88 chrXptel1M 315760 315795 (684205) (TTTG)n#Simple_repeat 1 34 (0) m_b333s252i13 13990 chrXptel1M 315760 TTTGCTTTTTTTGTTAGTTTGTTTTCTTTGATTCTT 315795 - v v - v v v (TTTG)n#Simpl 1 TTTG-TTTGTTTGTTTGTTTG-TTTGTTTGTTTGTT 34 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 395 22.21 4.43 3.12 chrXptel1M 317889 318046 (681954) L1MEh_5end#LINE/L1 2069 2228 (7) m_b333s551i7 13991 chrXptel1M 317889 AGAAAAGCAAATGCTAAAAGATGGCA--AGTAATACAGAAT----TGGTA 317932 - iv -- -- i vv v? ----ii L1MEh_5end#LI 2069 AGAAAA-CAAATAATAA--GATGGCAGAAATAAGTCCNAATATANCAGTA 2115 chrXptel1M 317933 ATTTTACCATAAATGTGAAAGGGGTAAACCCCTCA-CAAAGAGGAAGCGA 317981 -- v i v v i vi -iv i iv v L1MEh_5end#LI 2116 ATT--ACAATAAATGTAAATGGGTTAAACTCACCAATTAAAAGACAGAGA 2163 chrXptel1M 317982 TTAGCAGAATGGATTAAAAGCCAGAATCCTACAATATGTTGTTTACAGGA 318031 ?v v ? iv i v i i i L1MEh_5end#LI 2164 TTNTCAGATTGGATTNAAAAACAAAATCCAACAATATGCTGTCTACAAGA 2213 chrXptel1M 318032 AACACACCTGAAGCA 318046 i i i i L1MEh_5end#LI 2214 GACACACTTAAAACA 2228 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 27.37 CpG sites = 19, Kimura (unadjusted) = 27.37 Transitions / transversions = 1.27 (19/15) Gap_init rate = 0.05 (8 / 157), avg. gap size = 1.50 (12 / 8) 4454 29.42 3.89 3.16 chrXptel1M 317936 321175 (678825) L1M5_orf2#LINE/L1 32 3294 (0) m_b333s551i8 13991 chrXptel1M 317936 TTACCATAAATGTGAAAGGGGTAAACCCCTCA-CAAAGAGGAAGCGATTA 317984 vv i v ?v v ii -iv i v v i L1M5_orf2#LIN 32 TTACATTAAATGTAAATGGNCTAAACACTCCAATTAAAAGGCAGAGATTG 81 chrXptel1M 317985 GCAGAATGGATTAAAAGCCAGAATCCTACAATATGTTGTTTACAGGAAAC 318034 v v v iv ii i v v i i i i L1M5_orf2#LIN 82 TCAGACTGGATAAAAAAACAAGACCCAACTATATGCTGTCTACAAGAGAC 131 chrXptel1M 318035 ACACCTGAAGCAGGGAGATACATGCAGAATAAAGGTAAAAGGATGGAGCA 318084 i i v ii vii i vi? iv i i iv L1M5_orf2#LIN 132 GCACTTTAAATATAAAGACACAGANAGGTTGAAAGTAAAAGGATGGAAAA 181 chrXptel1M 318085 AAATCTACTATGCTCAGGTGAAGTCAAA---AGCAGGGGTAGCCATCCTG 318131 i v i vv viiv ?iv --- v ? i i vi i L1M5_orf2#LIN 182 AGATATACCATGCAAACACTAANCAAAAGAAAGCTGGNGTGGCTATATTA 231 chrXptel1M 318132 ATCTCAGATCAAGCA------AAAACAAAAATTGATCTAATTAAAAGAGA 318175 v iv i ------ ii i --- --- vv L1M5_orf2#LIN 232 ATATCAGACAAAGTAGACTTCAAGGCAAGAA---AT---ATTACCAGAGA 275 chrXptel1M 318176 TAAAGAAGGGCACTATATCTTACTAAA-GGGTAGCATAAATAATGAAGCA 318224 i i i vi vv iv - vi- vv v v vv L1M5_orf2#LIN 276 TAAAGAGGGACATTTCATAATGATAAAAGGGTCA-ATTCATCAAGAAGAC 324 chrXptel1M 318225 ATATCAATATTTAACATATATGCACCAAGTGGTGTAGCATCTAAATTCTT 318274 v vi v ii i v i iiiiv v v v v L1M5_orf2#LIN 325 ATAACAATCCTAAATGTGTATGCACCTAATAACAGAGCTTCAAAATACAT 374 chrXptel1M 318275 AAAAGAGAAATTAAAAGAGCTGCAAGAAGAAATAGATAG---CAAAACTA 318321 i iv i i i v i iv i i i--- v i L1M5_orf2#LIN 375 GAAGCAAAAACTGACAGAACTAAAAGGAGAAATAGACAAATCCACAATTA 424 chrXptel1M 318322 TAAGAGTGGGAGATCTCAACCTTGCATTCTTAG-AATTAGATAAATCAAA 318370 --- ? i i vi?v vi i - - i v i L1M5_orf2#LIN 425 TA---GTNGGAGATTTTAACACNCCTCTCTCAGTAATT-GATAGAACAAG 470 chrXptel1M 318371 C---CACAAAATAAATAAGAAAGAAGTCAAAGCGGTAAATAGAA-TACCA 318416 i--- v v i --- vi vi vvv i i iv - i L1M5_orf2#LIN 471 TAGACAAAAAATCAGTAAG---GATATAGAAGATTTGAACAACACTATCA 517 chrXptel1M 318417 GAAAAGTTAGATATGATAGACCTCTGGAGAAAACGAAATGGAG--ACAGA 318464 ivv v - iv i v v i iv v v?v ivv i-- ? v L1M5_orf2#LIN 518 ACCAACTT-GACCTAATTGACATTTATAGAACACTNCACCCAACAACNGC 566 chrXptel1M 318465 AAGGAGTACACTTTCTTTTCAGCAGTTCATGGAACCTATACAAAAATAGA 318514 -- i v ivv iv v v v i L1M5_orf2#LIN 567 A--GAATACACATTCTTTTCAAGTGCACATGGAACATTTACCAAGATAGA 614 chrXptel1M 318515 CCATATATTAGGACATAAAA---ACCTCAAACTCAAATGCAGTAAGGCAG 318561 ?i i v ---ii ---i vi?iv i iiv L1M5_orf2#LIN 615 CCATATNCTGGGCCATAAAACAAGTCTCAA---TAAATTTNAAAGGATTG 661 chrXptel1M 318562 AAATAGT---GAATGCATCCTTTTCAGACCACGATGCAATAAAAATTACA 318608 vi --- i iii i i --- i v v v viv L1M5_orf2#LIN 662 AAATCATACAGAGTATGTTCTCT---GACCACAATGGAATTAAATTAGAA 708 chrXptel1M 318609 CTCAACAAAAAGCCAGGGAAAAGTAGACCAAA-----AAATAATTGGAAA 318653 v i v --- ii v ?v -- ----- v L1M5_orf2#LIN 709 ATCAATAACAA---AAAGATANCTAGA--AAATCCCCAAATATTTGGAAA 753 chrXptel1M 318654 CTAAATAATCCTTATACTAAAGAATGATTGGATGAAACAGCAAATCATAG 318703 i i iv viv - v ivvv i v v iv i i L1M5_orf2#LIN 754 TTAAACAACACACTT-CTAAATAACCCATGGGTCAAAGAAGAAATCACAA 802 chrXptel1M 318704 ACATAATTAATAACTTCACCCAAGAAAATGACAATAATGAGACATCATAT 318753 ?viv iv v viviiv vvi ? i vi v v L1M5_orf2#LIN 803 NGGAAATTAGAAAATATTTTGAACTGAATGANAATGAAAATACAACATAT 852 chrXptel1M 318754 CAAAATGTGTGGGATGCAGCCAAAGCGGTAATAAG-GGGAAATTTCATAT 318802 v i i iv v - - v L1M5_orf2#LIN 853 CAAAATTTGTGGGATGCAGCTAAAGCAGTGCTTAGAGGGAAATTT-ATAG 901 chrXptel1M 318803 CTCTAGAGGCCTACTTCCAGAAAATAGAGAAAGAG--AAGGTCAACGAAT 318850 ?i i v ? iv i- v - iv-- ii i vi L1M5_orf2#LIN 902 CNTTAAATGCNTATATT-AGAAAAGA-AGAAAGGCTTAAAATCAATGATC 949 chrXptel1M 318851 TGGGCTAGCAACTAAAAATCCTAGAAAAGGAA---CAAATTAAAAACCCC 318897 ii vv v v i vv i --- --- L1M5_orf2#LIN 950 TAAGCTTCCACCTTAAGAAGCTAGAAAAAGAAGAGCAAATTAAA---CCC 996 chrXptel1M 318898 CAGTCAAACACTAAACTTGAAATTCTAAAAATAAAAGGAGAGATCAATAA 318947 v iv? ii vv iivvv vv i i v i i L1M5_orf2#LIN 997 AAAGNAAGTAGAAGGAAGGAAATAATAAAGATAAGAGCAGAAATCAATGA 1046 chrXptel1M 318948 AATTGAAATTAAAAAG-CTATTGAATTAATTAATAAAACTAAGAGTTGGT 318996 v vi ? ?- v v ivv i ii i i i i L1M5_orf2#LIN 1047 AATAGAAAACAAANANACAATAGAGAAAATCAACGAAGCCAAAAGCTGGT 1096 chrXptel1M 318997 TCTATGAAAA-ACCAACAAAATAGATAAACTTTTAGTAAATCTGATTAAA 319045 v - i i v i i i? iv i i L1M5_orf2#LIN 1097 TCTTTGAAAAGATCAATAAAATTGATAAACCTCTAGCNAGACTGATCAAG 1146 chrXptel1M 319046 AAAAGGAAAGAGGAAAATCAAATTGTTAGTCTTAA-AATGAAAAGGGAGA 319094 ii i i i vv iii i v i i- i L1M5_orf2#LIN 1147 AAAAAAAGAGAGAAGACACAAATTACCAATATCAGGAATGAAAAAGGAGA 1196 chrXptel1M 319095 ACTCACCACTGATGAAGAGGAAATTAGAGCAATAATTAGAAGTTACTTCT 319144 vv i v vvvivi v i ivi v iiv - v L1M5_orf2#LIN 1197 CATCACTACAGATCCTACAGACATTAAAAGGATAATAAGAGAATA-TTAT 1245 chrXptel1M 319145 GTCTGACTTTTATGCCAATAAATCTGATAACTTAAATGAAATGGCAGAAT 319194 vvii - i ? i vvi L1M5_orf2#LIN 1246 GAACAACTTT-ATGCCAATAAATTTGANAACTTAGATGAAATGGACAAAT 1294 chrXptel1M 319195 ATCTT-AAAAATATAGCTTGCCCAGATTAACAAAGGAAGAAGTAAATATC 319243 vi - i i i? i v i i i ?v i i i v vi L1M5_orf2#LIN 1295 TCCTTGAAAAACACAANTTACCAAAACTGACNCAAGAAGAAATAGAAAAT 1344 chrXptel1M 319244 CTAAATAATCCCATCTTAGAAAAAGAAATAGAGCAAGCTATTAA---CCT 319290 i ii i v ivivv v iivv iv --- L1M5_orf2#LIN 1345 CTGAATAGCCCTATATCTATTAAAGAAATTGAATTTGTAATTAAAAACCT 1394 chrXptel1M 319291 AACTCCCTAAGAAAAATCCCTCAGGACCAGATGGATTTAT--ATGAATTC 319338 v- i v v v --- v v i i--i L1M5_orf2#LIN 1395 T-CCCACAAAGAAAACTCC---AGGCCCAGATGGCTTCACTGGTGAATTC 1440 chrXptel1M 319339 TACCAAACATTTAAAGAACAATTAACCCCAATGCTATATAAACTATTTGA 319388 i v v iv vi i i v iv L1M5_orf2#LIN 1441 TACCAAACATTTAAGGAAGAAATAATACCAATCTTACACAAACTCTTCCA 1490 chrXptel1M 319389 AAAAATATGATT-GAAGGAGTCCTATGAAACTCCTTTTATGACACAGACA 319437 i vi vv- i iiv vivv v vi vii L1M5_orf2#LIN 1491 GAAAATAGAAAAAGAGGGAACACTTCCCAACTCATTTTATGAGGCCAGCA 1540 chrXptel1M 319438 TGGTATTGATACCTAAACCAGATAGGCTGAAA--ACAGAGAAAGAAAATT 319485 ?iivi v ? i ii-- v -- iii L1M5_orf2#LIN 1541 TNACCCTGATACCAAAACCNGACAAA--GACATTACAAGAAAAGAAAATT 1588 chrXptel1M 319486 ATAGACCAATCTCTCTAATGGATATCGATGCTAAAATCTTAAATAAAATA 319535 i v i v i i v v i ? i L1M5_orf2#LIN 1589 ACAGACCAATATCCCTCATGAACATAGATGCAAAAATCCTNAACAAAATA 1638 chrXptel1M 319536 TTAGCAAAAAGATTACAGAAA---ATCATCCCAGGATAATACACTATGAC 319582 vv v v v --- v --vv ii L1M5_orf2#LIN 1639 TTAGCAAATCGAATCCAGCAATATATAA--AAAGGATAATACATCATGAC 1686 chrXptel1M 319583 CAAGTAGGATTTATACCAGGAATGCAGGGCTGGTTCAATATTAGGAAAAC 319632 i i v i i i i v i v L1M5_orf2#LIN 1687 CAAGTGGGGTTTATCCCAGGAATGCAAGGTTGGTTTAACATTCGAAAATC 1736 chrXptel1M 319633 TATTAGTATAATTGACTATATCAATA-ACCAAATTAACAAAAACATATGA 319681 v i i i v i i i - vi vv iv v L1M5_orf2#LIN 1737 AATCAATGTAATTCACCATATTAACAGAATAAAGGAGAAAAATCATATGA 1786 chrXptel1M 319682 TCATCTCAATAGATGCATAAGAAGCATTTGATAAAATCCAACATCCCTTC 319731 v i i i i v L1M5_orf2#LIN 1787 TCATCTCAATAGATGCAGAAAAAGCATTTGACAAAATTCAACACCCATTC 1836 chrXptel1M 319732 CTAATAAAAACACTTGAGAGTATAGGAATAAATGGACTTTTCCTTAAAAT 319781 v i v iiiv ivv i v ivvi i vv L1M5_orf2#LIN 1837 ATGATAAAAACTCTCAGCAAACTAGGAATAGAAGGGAACTTCCTCAACCT 1886 chrXptel1M 319782 AGTCAGGAGCATATATTTAAAACCATCAATAACCTATTATATTCAGTGGG 319831 ii v i i v ivv vv ii? v - i i i i v L1M5_orf2#LIN 1887 GATAAAGGGCATCTACGAAAAACCTACAGCNAAC-ATCATACTTAATGGT 1935 chrXptel1M 319832 GAAA-ACTGGAACTTTTCCCAGTAAGATCTGGAGGAAG-CATAGGCTGCT 319879 - i ?vi vv v iv - - v ii L1M5_orf2#LIN 1936 GAAANACTGAANGCTTTCCCCCTAAGATCGGGAACAAGACA-AGGATGTC 1984 chrXptel1M 319880 CACTGTCACCATTATTATTCAATATTGTATTAGAAACGCTAGCTATAGCA 319929 i ? i vi i i i iiiv i vv L1M5_orf2#LIN 1985 CGCTNTCACCACTTCTATTCAACATTGTACTGGAGGTCCTAGCCAGTGCA 2034 chrXptel1M 319930 ATAAGAGCTGAGAAAAG--ATTAAAGGAATAAGAATAGGCAATGAGGAAA 319977 - viii -- v v ii v v v i L1M5_orf2#LIN 2035 ATAAG-GCAAGAAAAAGAAATAAAAGGCATAAAGATTGGAAAGGAAGAAA 2083 chrXptel1M 319978 CCAAATTATCACTCTTTGCAGATGACATGATGGTATACTTAGAGAACCCT 320027 iv i i ?i v i v ? v i i ? L1M5_orf2#LIN 2084 TAAAACTGTCNTTATTCGCAGATGACATGATTGTNTACGTAGAAAATCCN 2133 chrXptel1M 320028 AGTGGCTTCTACTAAAAAGATATTAGAAATAATTCACAACTTTAGCAAAG 320077 i-i vv v ? iv i v vviii v i L1M5_orf2#LIN 2134 AA-AGAATCTACAAANAAACTACTAGAACTAATAAGTGAATTTAGCAAGG 2182 chrXptel1M 320078 TTGCAGGATACAAAATAAATCTCCATAA--CCTTAGAATTGTTATACATC 320125 i ? ii v v v v -- vv v v vi i ii L1M5_orf2#LIN 2183 TCGCNGGATACAAGGTCAATATACAAAAATCAATTGTATTTCTATATACT 2232 chrXptel1M 320126 ATCAACAA--AATCTGACAGCAAGAGATACAAAGAGAAATTCCTATCTCA 320173 v -- iv v -- v i vi? i iv v - - i L1M5_orf2#LIN 2233 AGCAACAAACAATTGGAAA--ATGAAATTTNAAAAACAATACC-AT-TTA 2278 chrXptel1M 320174 AAATAACTGTC-GATAGCATAAAA-ATTTGGGAATCTATCTACCAAGGAA 320221 v i -i -i v i ? - i i vv v -i ? L1M5_orf2#LIN 2279 CAATAGC-ATCAAAAAACATNAAATACTTAGGAATAAATCTAACAA-AAN 2326 chrXptel1M 320222 AAGT-CAGAAACTATATGAGCAAAATTACAAAAAACGTTCC--ACA---- 320264 v - ii v ? iivvv i -- i v -- v ---- L1M5_orf2#LIN 2327 ATGTGCAAGACCTNTACACTGAAAACTAC--AAAACATTGCTGAGAGAAA 2374 chrXptel1M 320265 -CAAAGTCGATGTGAATAATTGAAA----ATATTAAGTGCTATTGATAGG 320309 -i vv iv i v i i---- ii v v - v v L1M5_orf2#LIN 2375 TTAAAGAAGACCTAAATAAATGGAGAGATATACCATGTTC-ATGGATTGG 2423 chrXptel1M 320310 CTGAGTGAATATAATAAAGATGACAATACTTCCTAAACTAATCTATTTAT 320359 vv v v vi ? v v i i i i vv L1M5_orf2#LIN 2424 AAGACTCAATATTGTNAAGATGTCAATTCTCCCCAAATTGATCTATAGAT 2473 chrXptel1M 320360 TTAATCCTATACCAATCAAACTCCCAAGAAAATATTTTAATGACCTAGAA 320409 i v v v v - v ii v -- --- - L1M5_orf2#LIN 2474 TCAATGCAATCCCAATCAAAATCCC-AGCAGGTTTTTT--TG---TAG-A 2516 chrXptel1M 320410 AAATAACAA--------CAAAATTCATATGGAAGAAGAAAAGGTCAAGAA 320451 v i --------i i iviv i ii ? L1M5_orf2#LIN 2517 AATTGACAAGCTGATTCTAAAATTTATATGGAAATGCAAAGGACCNAGAA 2566 chrXptel1M 320452 T-TTCAAGGGAATTAATGAAAAAAAATCAAATGAAGGTGG----CTTA-G 320495 -vi iiv i-v i --i ii v ---- -i L1M5_orf2#LIN 2567 TAGCCAAAACAATC-TTGAAAAAGAA--GAACAAAGTTGGAGGACTTACA 2613 chrXptel1M 320496 CTGTGCTCATCT-AAAACTATATATTATAAAG---CAGTGATCATCCCAA 320541 ii- ?v ? - i --- --- i ---vi L1M5_orf2#LIN 2614 CTAC-CNGATNTCAAGACT---TATTATAAAGCTACAGTAATCA---AGA 2656 chrXptel1M 320542 CCATTTGGTATTGGC-TAAGAAATAGATTAGTTGATCAATGGAATAGGTT 320590 vi v - -i iv i v i iv L1M5_orf2#LIN 2657 CAGTGTGGTATTGGCGTAAG-GATAGACAAATAGATCAATGGAACAGAAT 2705 chrXptel1M 320591 AGGTCTAAAGTACA-AAACAG-CCAATA-ACCT-TAATTATCTAGTGTTT 320636 ---- i v - i - v i - iv - ii?i ?i ii v L1M5_orf2#LIN 2706 AG----AGAGTCCAGAAATAGACCCACACATATATGGNCANTTGATTTTT 2751 chrXptel1M 320637 GACAAA---CCCAAAG-ACCCCAGCTTTTGGGATAAGAATCTACCTATTT 320682 ---v ? - vii ---- iv i v-ii v i L1M5_orf2#LIN 2752 GACAAAGGTGCCAANGCAATTCAG----TGGGGAAAGGATA-GTCTTTTC 2796 chrXptel1M 320683 GACAAA-ACTGTTGGAA-AATCTGAAATTAGTATGG-CAGAAATTAAGCA 320729 i -iv i - iv v ivi -v i v ? v L1M5_orf2#LIN 2797 AACAAATGGTGCTGGAACAATTGGATATCCATATGGAAAAAAATGAANCT 2846 chrXptel1M 320730 TGGATGCAACTTAACACCATACGTCAAGATAAGATCAA-ATGGTCCAT-G 320777 i iviv v i v iiv i v iv ? - vi - L1M5_orf2#LIN 2847 CGACCCCTACCTCACACCATACACAAAAATTAATTCNAGATGGATCATAG 2896 chrXptel1M 320778 ATTTAGGCATAAAGAATGAGATTATAAA-----TAAATTAGAGAAACATA 320822 ii iiii ii? i i i ----- i -- - L1M5_orf2#LIN 2897 ACCTAAATGTAAAAGNTAAAACTATAAAACTTCTAGA--AGA-AAACATA 2943 chrXptel1M 320823 AGATAGTTGAACTCTCA-GACTTGTGGAGGAGG-AAGGAATTAGTGACCA 320870 i v i --- iii i- i - i?v - i v vv ---- L1M5_orf2#LIN 2944 GGAGAAT---ATCTTCGTGACCT-TGGGNTAGGCAAAGATTTCTT----A 2985 chrXptel1M 320871 AAGAAGAACTAGAGATCATTATTGATCACAAAATAGAAAAT-------TT 320913 v i vvi i i v i? --- i i v i ------- L1M5_orf2#LIN 2986 AACAGGACACAAAAAGCACNA---ACCATAAAAGAAAAAATTGATAAATT 3032 chrXptel1M 320914 TGATTACATTAAATTAAAAGGCCTTTGTACAAACAAAACTAATGCAAACA 320963 v i ? i v v ii i i iv ?vvv ivi vi iv v L1M5_orf2#LIN 3033 GGACTNCATCAAAATTAAAAACTTCTGCTCNTCAAAAGACACCGTTAAGA 3082 chrXptel1M 320964 AGATTAGAAGGGAAGCAACAAACTGGGAAAACATTTTTACAGTTAAAGGT 321013 i v i v v i ? i v v i i-? v vi L1M5_orf2#LIN 3083 AAATGAAAAGGCAAGCCACAGANTGGGAGAAAATATTTGCAA-NACATAT 3131 chrXptel1M 321014 -TCTGATAAAGACCTCTTTGCCAAAATATATAAAGCATTGACTCTAATTT 321062 - i iv v vv i v i -v vi ? i L1M5_orf2#LIN 3132 ATCTGACAAAGGACTCGTATCCAGAATATATAAAGAACT-CCTACAANTC 3180 chrXptel1M 321063 -ATAAGAAATCAAGCCATTC--TCCAATTGATAAATGGTCAAAGGATATG 321109 - ? -- v vv --i v? v v i iv L1M5_orf2#LIN 3181 AATAANAAA--AAGACAAACAACCCAATANAAAAATGGGCAAAAGACTTG 3228 chrXptel1M 321110 AACAGAAAATTCTCAGATGAAGAAATTGAAACTATTTCTAGTCATATGAA 321159 v v v i v v ?v iviiivv iv i L1M5_orf2#LIN 3229 AACAGACACTTCACAAAAGAAGATATNCAAATGGCCAATAAGCACATGAA 3278 chrXptel1M 321160 AAGATGCTCCAAGTCA 321175 v v? L1M5_orf2#LIN 3279 AAGATGCTCAACNTCA 3294 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.51 CpG sites = 495, Kimura (unadjusted) = 39.00 Transitions / transversions = 1.16 (495/428) Gap_init rate = 0.05 (165 / 3239), avg. gap size = 1.39 (229 / 165) 1527 28.41 3.12 2.80 chrXptel1M 321033 321673 (678327) L1ME5_3end#LINE/L1 8 650 (291) m_b333s551i9 13991 chrXptel1M 321033 CCAAAATATATAAAGCATTGACTCTAATTTATAAGAAATCAAGCCATT-- 321080 i i i i v i vviv v iv i -- v iv?-- L1ME5_3end#LI 8 CTAGAATATACAAGGAACTCCTGCAAATCAACAAGAAA--AAGACGGNAA 55 chrXptel1M 321081 CTCCAATTGATAAATGGTCAAAGGATATGAACAGAAAATTCTCAGATGAA 321130 i v v v iv iv v i L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chrXptel1M 321131 GAAA-TTGAAA--CTATTTCTAGTCATATGAAAAGATGCTCCAAGTCATT 321177 -ii -- --v v - i v v L1ME5_3end#LI 106 GAAACCCGAAAGGCTA--ACAAG-CATATGAAGAGATGCTCAAACTCATT 152 chrXptel1M 321178 ATTAATCATAGAAATGCAAATTAAGACAACTCTAAGATACCACTACACAC 321227 v v i vv i i vi L1ME5_3end#LI 153 AGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACAC 202 chrXptel1M 321228 CTGTCAGATTGGCTAAAATGACAGGGAAAAATAATGATGATTGTTGGAGG 321277 i i i v v v ii vvii vii v v i L1ME5_3end#LI 203 CTATTAGACTGGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTGGCGA 252 chrXptel1M 321278 GGATGTGGGAAAACTGGGACATTGATGCATTGTTGGTGGAGTTGGGAACG 321327 i ? iv i vi v i i iiv vii v L1ME5_3end#LI 253 GGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACT 302 chrXptel1M 321328 AATCCAACCATTTTGGAGAGTAGTTTGGAACTA--TGCTCAAA--AAGTT 321373 ii v i i i i i v v -- iv -- - L1ME5_3end#LI 303 GGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTAAG-T 351 chrXptel1M 321374 ATCAAACTGTGATTACCCTTTGATCCAGCAGTGTTACTACTGGGCTTATA 321423 --- --- vv v i i viii v iv L1ME5_3end#LI 352 AT---AC---GCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATA 395 chrXptel1M 321424 TCCCAAAGAGATTATAAAGAAGG----GAAAGGGACCTGTATGTGCACGA 321469 i v v viv ----v i ---- i iv i L1ME5_3end#LI 396 TCCCAAAGAAATTCTCACACAGGTCCATAAGGGGAC----ATGTACGAGG 441 chrXptel1M 321470 ATGTTTGTGGCAGCCCT-TTTGTAGTGGCTAGAAACTGGAAACTGAATGG 321518 ii v vi - i vi i ii ii vivv L1ME5_3end#LI 442 ATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGG 491 chrXptel1M 321519 ATGTCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATATGAATGTTA 321568 i v v i v iii v iv v iiii L1ME5_3end#LI 492 GTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACACCA 541 chrXptel1M 321569 TGGAATATTATTGTTCTGTAAGAAATGACCAGCAGGATGAATACAGAGAG 321618 i i vvvv v v iii vii vi v i v vi L1ME5_3end#LI 542 TGGAGTACTATGCAGCAGTTAGAAGCAACGGACTAGATGTACACATAGCA 591 chrXptel1M 321619 GCTTGGAGGGA-CTTACACGAAC-TGATGCTAAGTGAAATGAGT-AGAAC 321665 i v v - v -- - ii i vi - v L1ME5_3end#LI 592 ACATGGATGGATCTTAAA--AACATAGTGCTGAGTGAAAAAAGTAAGAAA 639 chrXptel1M 321666 CAG---GAGAT 321673 --- L1ME5_3end#LI 640 CAGAATGAGAT 650 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.46 CpG sites = 96, Kimura (unadjusted) = 36.51 Transitions / transversions = 1.19 (96/81) Gap_init rate = 0.05 (29 / 640), avg. gap size = 1.31 (38 / 29) 12 4.75 0.00 8.33 chrXptel1M 321981 322006 (677994) (GGGA)n#Simple_repeat 1 24 (0) m_b333s252i14 13992 chrXptel1M 321981 GGGAGGGAGTGGAGGGATGGAAGGGA 322006 - - i (GGGA)n#Simpl 1 GGGAGGGAG-GGAGGGA-GGGAGGGA 24 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.08 (2 / 25), avg. gap size = 1.00 (2 / 2) 343 31.78 3.46 4.18 chrXptel1M 322304 322592 (677408) L1ME3G_3end#LINE/L1 304 590 (334) m_b333s551i10 13993 chrXptel1M 322304 AACCATTTTGGAGAGAAATATGGAACCAT--GCCAAAAGGGCTATAAAAT 322351 i ? i v v v vi --iii ---- v L1ME3G_3end#L 304 AGCCNTTTTGGAGGGCAATTTGGCAGTATCTATTAAAA----TTTAAAAT 349 chrXptel1M 322352 CCATGTATACCTTTTGATCTAGCAATATTACTATTAGGTCTATATCCCAA 322401 v -- i i i i vii vi ? ?v v i ? L1ME3G_3end#L 350 GC--GCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTAN 397 chrXptel1M 322402 AGA--TATCCAAAAAGGGAAACA-GTCCTTTTGTACAAAAATATTTATAC 322448 -- ii iv v v viv - vv?viv ii i i vv L1ME3G_3end#L 398 AGAAATACTCGCACATGTGCACAAGGANGCATGTACAAGGATGTTCATTG 447 chrXptel1M 322449 AAGTGCTTTTTATAGTGGCTAAGAACTGAAATTGAA--GGATGCCCATCA 322496 v iii v i i i v i i i vii v--ii i L1ME3G_3end#L 448 CAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATCA 497 chrXptel1M 322497 ATCTGGGAATGGCTAAACAAGTTGTAGAATAT---TATTGTGCTATAATA 322543 vv i i i i i v --- i i vv v - L1ME3G_3end#L 498 ATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACT- 546 chrXptel1M 322544 AATGACAGGACAATGTCAGAAAAATCTGAAAGACTTATATGAACTGATA 322592 - - -- ?i - v i i vv iv ii v i L1ME3G_3end#L 547 -ATG-CAG--CNGT-TAAAAAGAATGAGGTAGATCTATATGTACTGACA 590 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.26 CpG sites = 51, Kimura (unadjusted) = 43.94 Transitions / transversions = 1.38 (51/37) Gap_init rate = 0.06 (17 / 288), avg. gap size = 1.29 (22 / 17) 415 32.12 3.56 1.75 chrXptel1M 322304 322528 (677472) L1ME4c_3end#LINE/L1 308 536 (294) m_b333s551i11 13993 chrXptel1M 322304 AACCATTTTGGAGAGAAATATGGAACCATGCCAAAAGGGCTATAAAATCC 322353 v i v v v vi i ivvv i i --- L1ME4c_3end#L 308 AACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAAA--- 354 chrXptel1M 322354 ATGT--ATACCTTTTGATCTAGCAATATTACTATTAGGTCTATATCCCAA 322401 -- i i i i vii vi i vv v i L1ME4c_3end#L 355 ATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAA 404 chrXptel1M 322402 AGA--TA--TCCAAAAAGGGAAACAGTCCTTTTGTACAAAAATATTTATA 322447 i -- -- v i i v - iv v i i i i i v L1ME4c_3end#L 405 GGAAATAATTCAAAAGAAGGAAAAAG-CTATATGCACGAAGATGTTCATT 453 chrXptel1M 322448 CAAGTGCTTTTTATAGTGGCTAAGAACTGAAATTGAA--GGATGCCCATC 322495 vv i i v i i v i i i vii v--ii i v L1ME4c_3end#L 454 GCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAAC 503 chrXptel1M 322496 AATCTGGGAATGGCTAAACAAGTTGTAGAATAT 322528 vv i ii i i i v i L1ME4c_3end#L 504 AATAGGGGAATGGTTAAGTAAATTATGGTACAT 536 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.11 CpG sites = 43, Kimura (unadjusted) = 43.57 Transitions / transversions = 1.54 (43/28) Gap_init rate = 0.04 (8 / 224), avg. gap size = 1.50 (12 / 8) 237 27.48 4.00 6.43 chrXptel1M 323288 323462 (676538) L1MC1_3end#LINE/L1 463 633 (447) m_b333s551i12 13994 chrXptel1M 323288 ATAATTCCTTAAAAAGCAGAAGTAGTCAAGTGGATGCCCATCAGTTGGGG 323337 v i- vvii i ii --- i v v v L1MC1_3end#LI 463 ATAATTGCC-AAAACTTGGAAGCAACCAAG---ATGTCCTTCAGTAGGTG 508 chrXptel1M 323338 AATAGCTGAATAAGTTATGGGATATAAATGTAATGGAATATTATT--GTT 323385 i v i ii i v i vv vii -- iv L1MC1_3end#LI 509 AATGGATAAATAAACTGTGGTACATCCAGACAATGGAATATTATTCAGCG 558 chrXptel1M 323386 CT-GTAAGAAATGA-CCAACAGG--ATGATTTCAGAGAGGCCTGGA-GAG 323430 -iv - i v i -- ------ i i v - i L1MC1_3end#LI 559 CTAAAAAGAAATGAGCTATCAAGCCATGA------AAAGACATGGAGGAA 602 chrXptel1M 323431 ACTTACATGAACTGATCCTGAGTGAAATGAGC 323462 v v - iv v i vi L1MC1_3end#LI 603 ACTTAAATGCA-TATTACTAAGTGAAAGAAGC 633 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.87 CpG sites = 25, Kimura (unadjusted) = 34.82 Transitions / transversions = 1.25 (25/20) Gap_init rate = 0.09 (16 / 174), avg. gap size = 1.12 (18 / 16) 259 22.95 0.00 0.00 chrXptel1M 323321 323381 (676619) L1ME3Cz_3end#LINE/L1 488 548 (449) m_b333s551i13 13994 chrXptel1M 323321 ATGCCCATCAGTTGGGGAATAGCTGAATAAGTTATGGGATATAAATGTAA 323370 i i v i v i i i v vv ii L1ME3Cz_3end# 488 ATGTCCATCAATAGGGGAATGGATAAATAAATTGTGGTATATTCATACAA 537 chrXptel1M 323371 TGGAATATTAT 323381 i L1ME3Cz_3end# 538 TGGAATACTAT 548 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 28.14 CpG sites = 9, Kimura (unadjusted) = 28.14 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 14 5.00 0.00 0.00 chrXptel1M 324148 324168 (675832) (ATA)n#Simple_repeat 1 21 (0) m_b333s252i15 13995 chrXptel1M 324148 ATAATAATAGTAATAATAATA 324168 i (ATA)n#Simple 1 ATAATAATAATAATAATAATA 21 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 299 22.67 0.00 0.00 chrXptel1M 324274 324348 (675652) L1MEj_5end#LINE/L1 1059 1133 (1027) m_b333s551i14 13996 chrXptel1M 324274 ACTCCCAGGAATATTATGGTCAGATTCCTGAGCTCCCAGGTAAAGGAGAA 324323 v i v iv v i i v vv i L1MEj_5end#LI 1059 ACACCTAGGCATATCCTGGTAAAATTCCTGAACTCCAAGGATAAAGAGAA 1108 chrXptel1M 324324 AATATTGCAAGCAGCCAGAAAGAAA 324348 v i vv v L1MEj_5end#LI 1109 AATCTTACAAGCTTCCAGACAGAAA 1133 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 26.99 CpG sites = 6, Kimura (unadjusted) = 26.99 Transitions / transversions = 0.55 (6/11) Gap_init rate = 0.00 (0 / 74), avg. gap size = 0.0 (0 / 0) 12 18.27 5.41 0.00 chrXptel1M 325298 325334 (674666) (TATACT)n#Simple_repeat 1 39 (0) m_b333s252i16 13997 chrXptel1M 325298 TATACATATA-TTGTATTTA-ACTTATACTTTAACATAT 325334 v - i i - vv v (TATACT)n#Sim 1 TATACTTATACTTATACTTATACTTATACTTATACTTAT 39 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 227 27.27 7.78 2.27 chrXptel1M 325666 325999 (674001) L1MC4_5end#LINE/L1 2204 2555 (0) m_b333s551i16 13998 chrXptel1M 325666 AATCATAACTGTGAATATGAATGGAATGAACTCATCCATAAAATGAAAGG 325715 i ? ? vi i i i iv ? i ? v v ? i- L1MC4_5end#LI 2204 AGTNATANCAATAAATGTAAATGGGCTNAACTCACCNATTAAAAGANAA- 2252 chrXptel1M 325716 AGATAGAAGAAT-GAATTAGAAACCAGAATTCAACAAT-CATTGCTTACA 325763 vvvvi ? - i? ? ? v ii ii v -iii i? L1MC4_5end#LI 2253 AGATTTTCAANTTGGNTNANAAAGCAAGACCCAACTATATGCTGTNTACA 2302 chrXptel1M 325764 AGAAACATATTTGAAACGGAAAT-ACGCACATGGAGTTAAAAT-AAGGCA 325811 i i ii i --i i - iv v vi iv v - v L1MC4_5end#LI 2303 AGAGACACACCTAAAA--AAAGTGATTCAGAAAGGCTGAAAATAAAGGGA 2350 chrXptel1M 325812 TCGAAACAGAATATATCATGCTTCAGTTAAAGTAAAAAGGCATGGGTAGC 325861 v ? v - i v --v i vi ii i v - v L1MC4_5end#LI 2351 TGGANAAAG-ATATACCAGGC--AAATGGAAACAAAAAAGAA-GGGTTGC 2396 chrXptel1M 325862 AATTATGATTTCAGGC-----------CATGCT--AAAGCA-AAAATAGG 325897 ?v ? v i ----------- v ?i-- -v ?ii L1MC4_5end#LI 2397 AATNTTNATATCAGACAAAGTAGANTTCAAGNCAAAAAGCATTAAANGAG 2446 chrXptel1M 325898 CCTAATTAAAATATTT-----TGCTAAAAGACACCATATGCAATGAAG-T 325941 v v vv ii?i ----- ? i ??? v vii - L1MC4_5end#LI 2447 ACAAAGAAGGNCATTTTATAATGNTAAAGGNNNCAATTCACAATGAAGAT 2496 chrXptel1M 325942 AACACAAATACTAAATA--TATGTACCAAATGGAATAGCTTCCAAATTCA 325989 vv v - -- i iiv ? v? v? i L1MC4_5end#LI 2497 ATAACAATTA-TAAATATNTATGCACCAAATAACANAGCANCCACNTTTA 2545 chrXptel1M 325990 TAAAAGAAAA 325999 iv L1MC4_5end#LI 2546 TAAAGCAAAA 2555 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.05 CpG sites = 49, Kimura (unadjusted) = 38.05 Transitions / transversions = 1.23 (49/40) Gap_init rate = 0.05 (18 / 333), avg. gap size = 1.89 (34 / 18) 376 26.46 4.72 3.74 chrXptel1M 325666 325877 (674123) L1M1_orf2#LINE/L1 27 240 (3054) m_b333s551i15 13998 chrXptel1M 325666 AATCATAACTGTGAATATGAATGGAATGAACTCATCCATAAAATGAAAGG 325715 v vv i i v i - ---- v i L1M1_orf2#LIN 27 AATAATAACATTGAATGTAAATGGACTAAACTC-TCCA----ATCAAAAG 71 chrXptel1M 325716 AGATAGAA-----GAATGAATTAGAAACCAGAATTCAACAATC-ATTGCT 325759 v i----- i v i v ii ii ?ii -i i L1M1_orf2#LIN 72 ACATAGAGTGGCTGAATGGATGAAAAAACAAGACCCANTGATCTGTTGCC 121 chrXptel1M 325760 TACAAGAAACATATTTGAAACGGAAATACGCACATGGAGTTAAAAT-AAG 325808 i i v vviiv v i i v v - L1M1_orf2#LIN 122 TACAAGAAACACACTTCACCTATAAAGACACACATAGACTGAAAATAAAG 171 chrXptel1M 325809 GCATCGAAACAGAATATATCATGCTTCAGTTAAAGT--AAAAAG-GCATG 325855 v v v - vi -- i vi ii-- - v L1M1_orf2#LIN 172 GGATGGAAAAAG-ATATTCCATGC--CAATGGAAACCAAAAAAGAGCAGG 218 chrXptel1M 325856 GGTAGCAATTATGATTTCAGGC 325877 i v vv v v i L1M1_orf2#LIN 219 AGTAGCTATACTTATATCAGAC 240 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.27 CpG sites = 28, Kimura (unadjusted) = 33.27 Transitions / transversions = 1.08 (28/26) Gap_init rate = 0.06 (13 / 211), avg. gap size = 1.38 (18 / 13) 12 15.88 2.56 5.26 chrXptel1M 326358 326396 (673604) (TCTTTCT)n#Simple_repeat 1 38 (0) m_b333s252i17 13999 chrXptel1M 326358 TCTTTCTTCTTTC-TGTCCCTCCTTTCTATCTTCTCTACT 326396 - v ii i - - v (TCTTTCT)n#Si 1 TCTTTCTTCTTTCTTCTTTCTTCTTTCT-TCTT-TCTTCT 38 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.08 (3 / 38), avg. gap size = 1.00 (3 / 3) 39 25.78 3.18 3.85 chrXptel1M 326440 326596 (673404) (CTTT)n#Simple_repeat 1 156 (0) m_b333s252i18 14000 chrXptel1M 326440 CTTT-TTT-TTCCTTTCTATTTATC-TTCCTTCTTTCTTT-TCTATTTCC 326485 - - i v i v - i - i v i (CTTT)n#Simpl 1 CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 50 chrXptel1M 326486 TTGCCCCCTTCTCTCCTTCCTT-TATCTTCTCTTTCTTTCTTTGCTTCCT 326534 viii i i i i - v - - i (CTTT)n#Simpl 51 TTCTTTCTTTCTTTCTTTCTTTCTTTCTT-TCTTTCTTTCTTT-CTTTCT 98 chrXptel1M 326535 TTCCTTCTTTCCATTTTTTCTTTCCCTTATTCCCTACCTCTTCCTTCTCT 326584 i - v i - i v -i vi - i i (CTTT)n#Simpl 99 TTCTTTCTTT-CTTTCTTTCTTT-CTTTCTT-TCTTTCT-TTCTTTCTTT 144 chrXptel1M 326585 CCTTCCTACTTT 326596 i i v (CTTT)n#Simpl 145 CTTTCTTTCTTT 156 Matrix = Unknown Transitions / transversions = 2.44 (22/9) Gap_init rate = 0.07 (11 / 156), avg. gap size = 1.00 (11 / 11) 853 29.77 3.26 4.04 chrXptel1M 327070 327468 (672532) C L1ME5_3end#LINE/L1 (304) 637 242 m_b333s551i17 14001 chrXptel1M 327070 TCCTGCTCATTTCACTCAGCATCA-GTTCGTGTAAG-TCTCTCCAGGC-- 327115 i i iv ii - -- v - iv v i-- C L1ME5_3end#LI 637 TCTTACTTTTTTCACTCAGCACTATGTT--TTTAAGATCCATCCATGTTG 590 chrXptel1M 327116 CTTTCTGAAATCATCCTGTTGGTCATTTCTTACAGA-ACAGTAATATTCC 327164 v v v -- iv iv iii v v v-i - i i C L1ME5_3end#LI 589 CTATGTGTA--CATCTAGTCCGTTGCTTCTAACTGCTGCA-TAGTACTCC 543 chrXptel1M 327165 ATAATATTCATATACCACAATTTATTCAGCCATTCTCCAACTGATGGACA 327214 ii i v vi v iii v i v v C L1ME5_3end#LI 542 ATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCAGTGATGGACA 493 chrXptel1M 327215 TCCATTCAGTTTCCAGTTTTTAGCCACTACAAAAAGGGCTGCCACAAACA 327264 i vviv ii ii iiiv i v iv v ii C L1ME5_3end#LI 492 CCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCTGCAATGAACA 443 chrXptel1M 327265 TTCGTGCACGTACAGGTCCCTTTC----CCTTTTTTAAGATCTCTTTGGG 327310 i v---- v i v---- v v v ii i C L1ME5_3end#LI 442 TCCT----CGTACATGTCCCCTTATGGACCTGTGTGAGAATTTCTTTGGG 397 chrXptel1M 327311 ATATAATCCCAGTAGTAACACTGCTGGATCAAAGGGTATGCACAGTTTGA 327360 vv v iiiv i i v --- --- C L1ME5_3end#LI 396 ATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATGC---GT---A 353 chrXptel1M 327361 TAACTT--TTTGGGCA--TAGTTCCAAACTACTCTCCAAAATGGCTGTAT 327406 - -- ivi -- v v i i i i i i C L1ME5_3end#LI 352 T-ACTTAATTTGACTAAGTACTGCCAGATTGCTCTCCAGAATGGCTGCAC 304 chrXptel1M 327407 GTATTCACAATTCCACCCATAATGTATTAGTGTCCCTGTTTTCCCACATC 327456 vvi ii v i vii i i v v i i ? i C L1ME5_3end#LI 303 CAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATC 254 chrXptel1M 327457 CCTTCCAACATT 327468 iiv i C L1ME5_3end#LI 253 CTCGCCAACACT 242 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.30 CpG sites = 68, Kimura (unadjusted) = 39.24 Transitions / transversions = 1.48 (68/46) Gap_init rate = 0.06 (23 / 398), avg. gap size = 1.26 (29 / 23) 1014 26.63 0.64 1.61 chrXptel1M 327156 327468 (672532) C L1ME3G_3end#LINE/L1 (377) 547 238 m_b333s551i18 14001 chrXptel1M 327156 TAATATTCCATAATATTCATATACCACAATTTATTCAGCCATTCTCCAAC 327205 i i vv i i i i v i C L1ME3G_3end#L 547 TAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTAT 498 chrXptel1M 327206 TGATGGACATCCATTCAGTTTCCAGTTTTTAGCCACTACAAAAAGGGCTG 327255 ii vviv i v i i v iv C L1ME3G_3end#L 497 TGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCTG 448 chrXptel1M 327256 CCACAAACATTCGTGCACGTACAGGTCCCTTTCC-CTTTTTTAAG-ATCT 327303 v ii i v i i i ?-- i v v - v v vii - i C L1ME3G_3end#L 447 CAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATTT 400 chrXptel1M 327304 CTTTGGGATATAATCCCAGTAGTAACACTGCTGGATCAAAGGGTATGCAC 327353 ? i v v? ? v iiv i i i C L1ME3G_3end#L 399 CTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGC 350 chrXptel1M 327354 AGTTTGATAACTTTTTGGGCATAGTTCCAAACTACTCTCCAAAATGGCTG 327403 v --- v viviv v v i i i ? C L1ME3G_3end#L 349 ATTT---TAAATTTTAATAGATACTGCCAAATTGCCCTCCAAAANGGCTG 303 chrXptel1M 327404 TATGTATTCACAATTCCACCCATAATGTATTAGTGTCCCTGTTTTCCCAC 327453 ivv i v i vii i v v v i i C L1ME3G_3end#L 302 TACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCAC 253 chrXptel1M 327454 ATCCCTTCCAACATT 327468 i iiv i C L1ME3G_3end#L 252 ACCCTCGCCAACACT 238 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.22 CpG sites = 47, Kimura (unadjusted) = 34.30 Transitions / transversions = 1.34 (47/35) Gap_init rate = 0.02 (7 / 312), avg. gap size = 1.00 (7 / 7) 327 27.67 6.97 3.02 chrXptel1M 327483 327769 (672231) L1M2_orf2#LINE/L1 679 976 (2315) m_b333s551i19 13998 chrXptel1M 327483 TTTTGGAACCATAATGTAACAAATATTATGT-TCAATAA------AAACT 327525 v?i i v i - i viv- ------i L1M2_orf2#LIN 679 TTTTCNGACCACAATGGAATAAA-ACTAGAAATCAATAACAAGAGGAACT 727 chrXptel1M 327526 TTGAAATATAGATTTAAAATTAACTGGAAACTAAAC----TAGTCCTGAA 327571 i - i--- ? v v vv i ---- iv L1M2_orf2#LIN 728 TTGGAA-AC---TNTACAAATACATGGAAATTAAACAACATGCTCCTGAA 773 chrXptel1M 327572 GAATGAATGAGACAAAGAACACATCATAGAA--ACCTTCAATAATTTCAT 327619 vi iv i v v v v i - -- vv ? v - L1M2_orf2#LIN 774 CGACCAATGGGTCAATGAAGAAATTA-AGAAGGAAATTNAAAAATTTC-T 821 chrXptel1M 327620 TAAGATAGACAACAATGAAA---TAACATACCAGTAC-TGTGGCATGTAG 327665 i i i i ii v i ---i iv - i v ii L1M2_orf2#LIN 822 TGAAACAAATGAAAATGGAAACACAACATACCAAAACCTATGGGATACAG 871 chrXptel1M 327666 CCAAAGCAGTAATTGGGAGGAAATTTCTATCGTTAAATGCTTACATTGAT 327715 v ?v vi ii i v v iv i i ii - L1M2_orf2#LIN 872 CAAAAGCAGTNCTAAGAGGGAAGTTTATAGCAATAAACGCCTACATCAA- 920 chrXptel1M 327716 AAAAAGAGAAAGA--GCAGATCAATCAGTTAG-AATGCAACTAAGAAAAA 327762 iv --v i v iv vi i-i v v - ii L1M2_orf2#LIN 921 AAAAGTAGAAAGATTTCAAATAAACAACCTAACGATGCACCTCA-AGGAA 969 chrXptel1M 327763 CTAGAAA 327769 L1M2_orf2#LIN 970 CTAGAAA 976 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.22 CpG sites = 43, Kimura (unadjusted) = 35.94 Transitions / transversions = 1.26 (43/34) Gap_init rate = 0.06 (17 / 286), avg. gap size = 1.71 (29 / 17) 285 29.54 11.35 1.97 chrXptel1M 327542 328052 (671948) L1MC_orf2#LINE/L1 740 1297 (1997) m_b333s551i20 13998 chrXptel1M 327542 AAATTAACTGGAAACTAAAC----TAGTCCTGAAGAATGAATGAGACAAA 327587 v vi i i ----i v i i v iiv i v L1MC_orf2#LIN 740 AAAATACTTGGAGATTAAACAACACACTTCTAAATAACACATGGGTCAAA 789 chrXptel1M 327588 GAACACATC---ATAGAAACCTTCAATAATTTCATTAAGATAGACAACAA 327634 v v --- v -- i v v i- i iv i ii v L1MC_orf2#LIN 790 GAAGAAATCTCAAGAGAAA--TTTAAAAATATT-TTGAACTAAATGAAAA 836 chrXptel1M 327635 TGAAA---TAACATACCAGTACT-GTGGCATGTAGCCAAAGCAGTAATTG 327680 ---i v i iv i - v i v iv i L1MC_orf2#LIN 837 TGAAAATACAACTTATCAAAATTTGTGGGATGCAGCGAAAGCAGTGCTTA 886 chrXptel1M 327681 GGAGGAAATTTCTATCGTTAAATGCTTACATTGATAAAAAGAGAAAGAGC 327730 ii v v i i v i - v ii v L1MC_orf2#LIN 887 GAGGGAAATTTATAGCATTGAATGCATATATT-AGAAAAGAAGAAAGATC 935 chrXptel1M 327731 --AGATCAATCAGTTAGA----------ATGCAACT-----AAGAAAAAC 327763 -- i v vi ii---------- v v ----- i i L1MC_orf2#LIN 936 TAAAATCAATAATCTAAGCTTCCACCTTAGGAAACTAGAAAAAGAAGAGC 985 chrXptel1M 327764 TAG--AAATCACTGATTAAGCACCAGCATACAAATCTTAAAAATCA-AG- 327809 v i-- - vi v vv v v v vv i - - L1MC_orf2#LIN 986 AAATTAAATC-CAAAGTAAGCAGAAGAAAAGAAATAATAAAAATTAGAGC 1034 chrXptel1M 327810 AGAGGTCAATAAAA-TGA------GAGTTTAA-----AAAGTGAACTAG- 327846 ii i - ------ iv i ----- i v v i- L1MC_orf2#LIN 1035 AGAAATCAATGAAATTGAAAACAGGAAATCAATAGAGAAAATCAACGAAA 1084 chrXptel1M 327847 -TAAAA-CTTGATCT-----GAGCTTATAAAAATTAGACAAACCATTGGT 327889 -i - v v -----i v i vv - i i vi i i L1MC_orf2#LIN 1085 CCAAAAGCTGGTTCTTTGAAAAGATCAATAAAATT-GATAAGCCTCTAGC 1133 chrXptel1M 327890 TAATTTGACTTTTAAAAAGAAAGAAGAAAC-CAAATTATCAGCATCAAAA 327938 i ivi i vvv i i ii i - ii ii i L1MC_orf2#LIN 1134 CAGGCTAACTAAGAAAAAAAGAGAGAAGACACAAATTACTAATATCAGAA 1183 chrXptel1M 327939 ATTAA--AGGGCAAAT--GTACAAA-CCAGTGAAGATTAAATTAAAGTAA 327983 v -- v v --v ?i - vi i v --- i vv L1MC_orf2#LIN 1184 ATGAAAGAGGGGACATCACTACNGATCCCATGGACATTAA---AAGGATA 1230 chrXptel1M 327984 ATATTAGGAGTTATTTTGACCAATTATATACCAGCAAAACTGACAATCTA 328033 -v i- i v v i v i vi vi i i L1MC_orf2#LIN 1231 ATA-AAGGAA-TACTATGAACAACTCTATGCCCACAAATTTGATAACCTA 1278 chrXptel1M 328034 AATGAAATGGATGATTTCC 328052 i iv v L1MC_orf2#LIN 1279 GATGAAATGGACCAATTCC 1297 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.58 CpG sites = 82, Kimura (unadjusted) = 38.58 Transitions / transversions = 1.24 (82/66) Gap_init rate = 0.06 (32 / 510), avg. gap size = 2.16 (69 / 32) 410 25.67 6.82 2.62 chrXptel1M 327550 327769 (672231) L1M4_orf2#LINE/L1 748 976 (2318) m_b333s551i22 13998 chrXptel1M 327550 TGGAAACTAAAC----TAGTCCTGAAGAATGAATGAGACAAAGAACACAT 327595 i ----i v i v iv i v v v L1M4_orf2#LIN 748 TGGAAATTAAACAACACACTCCTAAATAACCAATGGGTCAAAGAAGAAAT 797 chrXptel1M 327596 CATA---GAAACCTTCAATAATTTCATTAAGATAGACAACAATGAAA--- 327639 i --- --- i iv v v v i ii ii v i --- L1M4_orf2#LIN 798 CACAAGGGAAA---TTAGAAAATACTTTGAGATGAATGAAAACGAAAACA 844 chrXptel1M 327640 TAACATACCAGTACT-GTGGCATGTAGCCAAAGCAGTAATTGGGAGGAAA 327688 i iv -i v i ? iv i ii L1M4_orf2#LIN 845 CAACATACCAAAACTTATGGGATGCAGCNAAAGCAGTGCTTAGAGGGAAA 894 chrXptel1M 327689 TTTCTATCGTTAAATGCTTACATTGATAAAAAGAGAAAGA--GCAGATCA 327736 v v vv i i i - ii --v i L1M4_orf2#LIN 895 TTTATAGCTGTAAATGCCTATATTAA-AAAAGAAGAAAGATCTCAAATCA 943 chrXptel1M 327737 ATCAGTTAGAATGCAAC--TAAGAAAAACTAGAAA 327769 v vi ivv v v -- -- L1M4_orf2#LIN 944 ATAACCTAACCTTCCACCTTAAG--AAACTAGAAA 976 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 31.45 CpG sites = 30, Kimura (unadjusted) = 32.15 Transitions / transversions = 1.20 (30/25) Gap_init rate = 0.05 (12 / 219), avg. gap size = 1.75 (21 / 12) 431 23.98 6.15 2.15 chrXptel1M 327550 327728 (672272) L1M3_orf2#LINE/L1 748 933 (2355) m_b333s551i21 13998 chrXptel1M 327550 TGGAAACTAAAC----TAGTCCTGAAGAATGAATGAGACAAAGAACACAT 327595 i ----i v v iv i v v v L1M3_orf2#LIN 748 TGGAAATTAAACAACACACTCCTGAACAACCAATGGGTCAAAGAAGAAAT 797 chrXptel1M 327596 CATA---GAAACCTTCAATAATTTCATTAAGATAGACAACAATGAAA--- 327639 v --- -- vi v v - i i i ii v --- L1M3_orf2#LIN 798 CAAAAGGGAAA--TTAGAAAATATC-TTGAGACAAATGAAAATGAAAACA 844 chrXptel1M 327640 TAACATACCAGTACT-GTGGCATGTAGCCAAAGCAGTAATTGGGAGGAAA 327688 i iv -i v i v ?v vi ii i L1M3_orf2#LIN 845 CAACATACCAAAACTTATGGGATGCAGCAAAAGCAGTNCTAAGAGGGAAG 894 chrXptel1M 327689 TTTCTATCGTTAAATGCTTACATTGATAAAAAGAGAAAGA 327728 v v v i i i - ii L1M3_orf2#LIN 895 TTTATAGCGATAAACGCCTACATTAA-AAAAGAAGAAAGA 933 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 28.73 CpG sites = 23, Kimura (unadjusted) = 29.55 Transitions / transversions = 1.21 (23/19) Gap_init rate = 0.04 (8 / 178), avg. gap size = 1.88 (15 / 8) 292 30.17 2.72 2.72 chrXptel1M 327869 328052 (671948) L1M4_orf2#LINE/L1 1114 1297 (1997) m_b333s551i23 13998 chrXptel1M 327869 AAAATTAGACAAACCATTGGTTAATTTGACTTTTAAAAAGAAAGAAGAAA 327918 - v i i ivi ivvv i i ii i L1M4_orf2#LIN 1114 AAAATT-GACAAACCTTTAGCTAGACTGACCAAGAAAAAAAGAGAGAAGA 1162 chrXptel1M 327919 C-CAAATTATCAGCATCAAAAATTAAAG--GGCAAAT--GTACAAACCAG 327963 - ii iv ii v -- v v --v vi -v L1M4_orf2#LIN 1163 CTCAAATTACTAAAATCAGGAATGAAAGAGGGGACATTACTACCGACC-T 1211 chrXptel1M 327964 TGAAGATTAAATTAAAGTAAATATTAGGAGTTATTTTGACCAATTATATA 328013 iv --- v ivi v v iiv i v v i i L1M4_orf2#LIN 1212 TACAGA---AATAAAAAGGATTATAAGGGAATACTATGAACAATTGTATG 1258 chrXptel1M 328014 CCAGCAAAACTGACAATCTAAATGAAATGGATGATTTCC 328052 i viv i i i ii v L1M4_orf2#LIN 1259 CCAACAAATTAGATAACCTAGATGAAATGGACAAATTCC 1297 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.68 CpG sites = 31, Kimura (unadjusted) = 39.63 Transitions / transversions = 1.35 (31/23) Gap_init rate = 0.04 (8 / 183), avg. gap size = 1.25 (10 / 8) 579 32.91 7.89 2.94 chrXptel1M 328290 328752 (671248) L1PREC2_orf2#LINE/L1 2100 2588 (706) m_b333s551i24 14002 chrXptel1M 328290 TGTAAAC--CATGACAATATATTTAGAGT-CCTCA-AGAATCAACTAAAA 328335 i i -- ivv i iv- i - vv ii iv L1PREC2_orf2# 2100 TGCAGACGACATGATTCTATATCTAGAAAACCCCATAGTCTCGGCCCAAA 2149 chrXptel1M 328336 GGCTACTTCAAACAATTAACAGCTTTGGCAAAATTGCAGGATATAAAAAA 328385 i v ? ivii v i ii i v i vv L1PREC2_orf2# 2150 AGCTCCTTNAGCTGATAAACAACTTCAGCAAAGTTTCAGGATACAAAATC 2199 chrXptel1M 328386 ACTCCACATAAGTCATCAGCATTTCAATATATGACCAACAA-AGCCCAGC 328434 v vi v i ii i -- i- - v L1PREC2_orf2# 2200 AATGTACAAAAATCACTAGCATTCC--TATAC-ACCAACAACAGCCAAGC 2246 chrXptel1M 328435 AGCAAAG--AGAT--AGAAAGATATTCAATTTAAAACAACTGTAGACAAT 328480 v - i -- i --i v vv i v i v ivi iii i v iv L1PREC2_orf2# 2247 CG-AGAGCCAAATCAGGAACGCAATCCCATTCACAATTGCCACAAAAAGA 2295 chrXptel1M 328481 ACAAAATAT-TGGGGGTCTATCTGCCAAGACAAACGCAGGGACTTTATGA 328529 i i- i ii vi v iv v iv iii v i iv i ii L1PREC2_orf2# 2296 ATAAAATACCTAGGAATACAGCTAACCAGGGAGGTGAAAGATCTCTACAA 2345 chrXptel1M 328530 GCAGAATTACAAAACACTTTTCACAGAAATAAAGTCAGAT--CTCAA-TA 328576 vv vi v v i--- -- v -i L1PREC2_orf2# 2346 TGAGAATTACAAAACACTGCTCAAAGAAATCAG---AGATGACACAAACA 2392 chrXptel1M 328577 ACTGGAAAAAC-TTCAATTGCTTATGGGTAGGCTGAGCTAATATAATAAA 328625 v - v - i i vv iii vi v L1PREC2_orf2# 2393 AATGGAAAAACATTCCAT-GCTCATGGATAGGAAGAATCAATATCGTTAA 2441 chrXptel1M 328626 AATGATAATTCTACCTAAATCTACTTA---ATATAACA----TACTGTGA 328668 iiv v i i v v i --- vi ii---- v i v L1PREC2_orf2# 2442 AATGGCCATACTGCCCAAAGCAATTTACAGATTCAATGCTATTCCTATCA 2491 chrXptel1M 328669 AA------ATAA-----TTTATAGAGTTAGAAAAAATCATGACAAAATTC 328707 ------ i ----- i i ii ii vvi L1PREC2_orf2# 2492 AACTACCAATGACATTCTTCACAGAACTAGAAAAAACTATTTTAAAATTC 2541 chrXptel1M 328708 ATCTGGAAGAACAAAAGGTCAAGAATATCAAGGGTA---CTAATACAT 328752 v vv v iv vv v v i i --- -i v L1PREC2_orf2# 2542 ATATGGAACCAAAAAAGAGCCCGAATAGCCAAGGCAATCCTAA-GCAA 2588 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.74 CpG sites = 195, Kimura (unadjusted) = 44.77 Transitions / transversions = 1.30 (82/63) Gap_init rate = 0.05 (24 / 462), avg. gap size = 1.83 (44 / 24) 44 6.13 0.00 0.00 chrXptel1M 328753 328803 (671197) (AC)n#Simple_repeat 1 51 (0) c_b333s251i3 14003 chrXptel1M 328753 ACACACACACACAGACACACACACAGACACACACACACACACATACACAC 328802 v v i (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50 chrXptel1M 328803 A 328803 (AC)n#Simple_ 51 A 51 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 579 32.91 7.89 2.94 chrXptel1M 328804 329441 (670559) L1PREC2_orf2#LINE/L1 2589 3253 (41) m_b333s551i24 14002 chrXptel1M 328804 GAGGAAAA---TAG-----TCTAGCTAAACCAAACCTAAAATCATACTAT 328845 i i v --- i ----- vv -- vi i v ii i L1PREC2_orf2# 2589 AAGAACAAAGCTGGAGGCATCACGCTA--CCCGACTTCAAACTATACTAC 2636 chrXptel1M 328846 ATAACAGAAGTCATCAAATCATT-TGGTGCTGACTAAGAAATAGAGTGGT 328894 vii viv v i v vi- i iivv i i vvvi L1PREC2_orf2# 2637 AGGGCTACAGTAACCAAAACAGCATGGTACTGGTACAAAAACAGACACAT 2686 chrXptel1M 328895 GGATCAGCGGAATAGATTAGATACACAAGATATAATAGTCA-ATGACTAT 328943 i i ii i v v vv v v -i i i- iiv i L1PREC2_orf2# 2687 AGACCAATGGAACAGAATAGAGAGCCCAGAAATAA-GGCCGCACACCTAC 2735 chrXptel1M 328944 AGTAATCTACTGTTTGATAAA-CTCATAGATTCCAGCTTCTGGGAAAAGA 328992 iiv iv v i i - v i i vv v v-v i i L1PREC2_orf2# 2736 AACCATCTGATCTTCGACAAAGCTGACAAAAACAAGCA-ATGGGGAAAGG 2784 chrXptel1M 328993 ACTATCTCTTTGAAAAAAAATTGCTGGGAAAACTGGAAAATAGTATGTCA 329042 vi v i- v viv v vv iivi - L1PREC2_orf2# 2785 ACTCCCTATTC-AATAAATGGTGCTGGGATAACTGGCTAGCCATATG-CA 2832 chrXptel1M 329043 GAAACTAGGCA-TAGACCAAGATCTAACACCA-----AGAGA--AGGTCA 329084 iv v iv - i vvvvi v ----- i i -- iv L1PREC2_orf2# 2833 GAAGATTGAAACTGGACCCCTTCCTTACACCATATACAAAAATCAACTCA 2882 chrXptel1M 329085 AAATGGATTCCTTATTTAAACATAGAAT--GATACTATAAGCAAATTAGG 329132 i vvvv i ii i i--i v i- viiv L1PREC2_orf2# 2883 AGATGGATTAAAGACTTAAATGTAAAACCCAAAACTATAAA-AACCCTGG 2931 chrXptel1M 329133 AAAACAAGGGATAGTTTACGTGTAAGATC--TCTGGA-----GAA-GGG- 329173 i vv-- ------- i v i -- ----- - - L1PREC2_orf2# 2932 AAGACAACC--TAG-------GCAATACCATTCTGGACATAGGAACGGGC 2972 chrXptel1M 329174 -AGGAATTTATGGCCAAAGAAGA-ACTAGAGAACATTATGA--AATGCAA 329219 - i v i i ---- -i i i iivv iii -- v L1PREC2_orf2# 2973 AAAGATTTCATGAC----GAAGACGCCAAAAGCAATTGCAACAAAAGCAA 3018 chrXptel1M 329220 TTAAATT---AAATTACATTACATTACATTAAAAGGTTTTTGCACA---A 329263 -- --- viv ivv v i ii i i --- L1PREC2_orf2# 3019 --AAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAA 3066 chrXptel1M 329264 AGGCAATG--CAGCCAAGATAGAAAGGAAAACAGTAAATTGAGAAGCAGT 329311 i v iv-- i vi - i v iv v vii i v i iiv i L1PREC2_orf2# 3067 AAGAAACTATCAACAGAG-TAAACAGACAACCTACAGAATGGGAGAAAAT 3115 chrXptel1M 329312 TTTT---AACAGTGTTTCTGATAAAAGCCTCATTTCTCAAAAATACAGAG 329358 ? --- vi iv i i i v v iviv vv i ii L1PREC2_orf2# 3116 NTTTGCAAACTATGCATCTGACAAAGGTCTAATATCCAGCATCTATAAGG 3165 chrXptel1M 329359 AACT-----AAATTTATAAGAATAC--CAGTCATTCCCCAATTGATAAAT 329401 ----- i v v-- iv vi -- i v i L1PREC2_orf2# 3166 AACTTAAACAAATTTACAAGAAAAAAACAAACAACCCC--ATTAAAAAGT 3213 chrXptel1M 329402 GGTCAAAGGACATAAACAGACAATTTTCAGATGAAGACAT 329441 v i v i v L1PREC2_orf2# 3214 GGGCAAAGGACATGAACAGACACTTTTCAAAAGAAGACAT 3253 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.74 CpG sites = 195, Kimura (unadjusted) = 44.77 Transitions / transversions = 1.20 (113/94) Gap_init rate = 0.07 (47 / 637), avg. gap size = 1.64 (77 / 47) 259 31.70 7.23 2.02 chrXptel1M 329239 329473 (670527) L1PB_orf2#LINE/L1 3040 3286 (8) m_b333s551i25 14002 chrXptel1M 329239 ATTACATTAAAAGGTTTTTGCAC----AAAGG--CAATGCAGCCAAGATA 329282 v i ii i i ---- -- i - vi - L1PB_orf2#LIN 3040 ATTAAACTAAAGAGCTTCTGCACGGCAAAAGGAACAGT-CAGCAGAG-TA 3087 chrXptel1M 329283 GAAAGGAAAACAGTAAATTGAGAAGCAGTTTTTAACAGTGT-T---TCTG 329328 i v iv v vii i v i iiv i i i - i v - --- L1PB_orf2#LIN 3088 AACAGACAACCCACAGAGTGGGAGAAAATCTTCA-CAATCTATACATCTG 3136 chrXptel1M 329329 ATAAAAGCCTCATTTCTCAAAAATACAGAGAACT-----AAATTTATAAG 329373 i i v v v ivi vv i? ----- ivii L1PB_orf2#LIN 3137 ACAAAGGACTAATATCCAGAATCTACAANGAACTCAAACAAATCAGCAAG 3186 chrXptel1M 329374 AATAC--CAGTCATTCCCCAATTGATAAATGGTCAAAGGACATAAACAGA 329421 v v-- iv v -- ii v i v v i i L1PB_orf2#LIN 3187 AAAAAAACAAACAATCCC--ATCAAAAAGTGGGCTAAGGACATGAATAGA 3234 chrXptel1M 329422 CAATTTTCAGATGAAGACATTAAAGTCATTTCTAGTCAGATGAAAAAATG 329471 i i v i vv i viiivvi iv v L1PB_orf2#LIN 3235 CAATTCTCAAAAGAAGATATACAAATGGCCAACAAACATATGAAAAAATG 3284 chrXptel1M 329472 CT 329473 L1PB_orf2#LIN 3285 CT 3286 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 42.77 CpG sites = 42, Kimura (unadjusted) = 42.77 Transitions / transversions = 1.35 (42/31) Gap_init rate = 0.05 (11 / 234), avg. gap size = 2.00 (22 / 11) 301 25.66 6.71 3.25 chrXptel1M 329325 329473 (670527) L1P1_orf2#LINE/L1 3133 3286 (8) m_b333s551i26 14002 chrXptel1M 329325 TCTGATAAAAGCCTCATTTCTCAAAAATACAGAGAACT-----AAATTTA 329369 i i v v v ivi vv iv ----- L1P1_orf2#LIN 3133 TCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTA 3182 chrXptel1M 329370 TAAGAATAC--CAGTCATTCCCCAATTGATAAATGGTCAAAGGACATAAA 329417 i v v-- iv vi -- ii v i v i i L1P1_orf2#LIN 3183 CAAGAAAAAAACAAACAACCCC--ATCAAAAAGTGGGCGAAGGACATGAA 3230 chrXptel1M 329418 CAGACAATTTTCAGATGAAGACATTAA---AGTCATTTCTAGTCAGATGA 329464 v i i v v --- i ---vv iv v L1P1_orf2#LIN 3231 CAGACACTTCTCAAAAGAAGACATTTATGCAGCCA---AAAAACACATGA 3277 chrXptel1M 329465 AAAAATGCT 329473 L1P1_orf2#LIN 3278 AAAAATGCT 3286 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 30.65 CpG sites = 17, Kimura (unadjusted) = 31.64 Transitions / transversions = 0.85 (17/20) Gap_init rate = 0.05 (8 / 148), avg. gap size = 1.88 (15 / 8) 1310 32.31 0.90 0.00 chrXptel1M 329351 329904 (670096) L1ME4c_3end#LINE/L1 15 573 (257) m_b333s551i27 14002 chrXptel1M 329351 ATACAGAGAACT-----AAATTTATAAGAATACCAGTCATTCCCCAATTG 329395 i i i ----- v v v? viv vv v L1ME4c_3end#L 15 ATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAAGACCCCAATAG 64 chrXptel1M 329396 ATAAATGGTCAAAGGACATAAACAGACAATTTTCAGATGAAGACATTAAA 329445 v i iv ? v i v vv L1ME4c_3end#L 65 ATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAGGAAATACAA 114 chrXptel1M 329446 GTCATTTCTAGTCAGATGAAAAAATGCTATAAATCACTAATGATTAGAGA 329495 ? vi vvvi iv v i i vv vv i i i i i L1ME4c_3end#L 115 NTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTAGTAATCAAAGA 164 chrXptel1M 329496 AATGCAAATTAAGACAGCATTGAGGTACCATTTTACACCTCTCAGATCAG 329545 ii i v i i v i i i L1ME4c_3end#L 165 AATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCTATTAAATTAG 214 chrXptel1M 329546 CTAAGATGAAAGGAAAAGATAATGACAAACGTTGGAGAAGATGTGGAAAA 329595 v i vv ii vv iv v i i v i ? i vi L1ME4c_3end#L 215 CAAAAATTTAAAAAATTGATAATACCCAATGCTGGCGAGGNTGCGGTGAA 264 chrXptel1M 329596 GCTGAGACACTGATATATTGTTGGTGGATTTGTGAATATATCCAGCCATT 329645 i iv ? v i i vv? i vvi v i v L1ME4c_3end#L 265 ACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACAACCCTT 314 chrXptel1M 329646 CTGGAGAGCAATATGGAACTATGCCCAAAGGGCTATCAAAATGTGCATAT 329695 i i v v v i iviv i i v v i L1ME4c_3end#L 315 TTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAAAATGTTCATAC 364 chrXptel1M 329696 CCTTGGATCCAGCAGTGTCTTTATTATGTCTGTATATCAGAGACATAGTA 329745 v i i i vi vi vi iv vv v vii ii v i v L1ME4c_3end#L 365 CCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATT 414 chrXptel1M 329746 AAGGAGAGGAAAGGATCTACATGTGCCAAAATATTTGTAGCAACTCTTTT 329795 v ii i i ii v i ii v i i ii v i vi v L1ME4c_3end#L 415 CAAAAGAAGGAAAAAGCTATATGCACGAAGATGTTCATTGCAGCGTTATT 464 chrXptel1M 329796 TGTGGTGGCAAAGAATTAAAAATTGAGTGGATGCCCAACAATTGGGAAAT 329845 i ii i i i ii ivivv ii i v i L1ME4c_3end#L 465 TATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAAT 514 chrXptel1M 329846 CACTGAGTAAGTTATGGTATATGAAGGCAATGAAATATTATTGTTCTATA 329895 vii i i i v? vv i i vvvv i v L1ME4c_3end#L 515 GGTTAAGTAAATTATGGTACATCNACTCGATGGAATATTATGCAGCCATT 564 chrXptel1M 329896 AGAAATGAT 329904 i L1ME4c_3end#L 565 AAAAATGAT 573 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 42.17 CpG sites = 99, Kimura (unadjusted) = 44.14 Transitions / transversions = 1.24 (99/80) Gap_init rate = 0.00 (1 / 553), avg. gap size = 5.00 (5 / 1) 674 27.98 4.07 0.72 chrXptel1M 330422 330691 (669309) L1M4_orf2#LINE/L1 1572 1850 (1444) m_b333s551i28 13998 chrXptel1M 330422 CAAAAAGAAACAAAATTATCAACCAATTTCTTTTATAAATATTGATACAA 330471 v ii v i ivi v ii i v i L1M4_orf2#LIN 1572 CACAAGAAAAGAAAACTACAGACCAATATCCCTTATGAATATAGATGCAA 1621 chrXptel1M 330472 AATTTCTTTTAA-AAAATTCTAGCAAAGAGACTACACTAATATATCACAA 330520 v i i-- - v vv v v vi i v v L1M4_orf2#LIN 1622 AAATCCTC--AACAAAATACTAGCAAACCGAATCCAGCAACATATAAAAA 1669 chrXptel1M 330521 AGCTCATGTA----------GTATGATTTATATCGGAAATTTGGGGATGG 330560 i v i ii ---------- iv vi i i viii v L1M4_orf2#LIN 1670 GGATTATACACCATGACCAAGTGGGATTTATCCCAGGAATGCAAGGTTGG 1719 chrXptel1M 330561 TTAAATATTAGGAAAACTATCAGCATAACTGACCATATCAATAGCAAAAA 330610 v i ?v i v v iii ivv i v v L1M4_orf2#LIN 1720 TTCAACATNCGAAAATCAATCAATGTAATACACCATATTAATAGAATAAA 1769 chrXptel1M 330611 GAACAAAAACCATATGATTATATCAATAGCTTCAGAAAAAGCTTTTGACA 330660 i i i v viv v L1M4_orf2#LIN 1770 GGACAAAAACCACATGATCATCTCAATAGACGCAGAAAAAGCATTTGACA 1819 chrXptel1M 330661 AAATATAATATGCTTTCCCATTAAAAACACT 330691 vi i iv viiv L1M4_orf2#LIN 1820 AAATCCAACACCCTTTCATGATAAAAACACT 1850 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.18 CpG sites = 40, Kimura (unadjusted) = 35.77 Transitions / transversions = 1.14 (40/35) Gap_init rate = 0.01 (4 / 269), avg. gap size = 3.25 (13 / 4) 275 24.75 4.67 13.13 chrXptel1M 330694 330800 (669200) MIRb#SINE/MIR 2 100 (168) m_b333s601i15 14004 chrXptel1M 330694 AAAGGGGCAGCTTGTTGACATAGTGGA----GT-CTGGCCCTGAAATCAG 330738 i v v ---i ---- i- v ii i i MIRb#SINE/MIR 2 AGAGGGGCAGCGTGGTG---CAGTGGAAAGAGCACGGGCTTTGGAGTCAG 48 chrXptel1M 330739 AAGGATCTGAGCTCAAATCTGGATTCAGGTACTTGACGTTTACTAGCTGT 330788 vi i i i i iv ii ------- v ii MIRb#SINE/MIR 49 ACAGACCTGGGTTCGAATCCCGGCTC-------TGCCACTTACTAGCTGT 91 chrXptel1M 330789 GTGATTGCCTTG 330800 --- MIRb#SINE/MIR 92 GTGA---CCTTG 100 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.49 CpG sites = 17, Kimura (unadjusted) = 31.13 Transitions / transversions = 2.83 (17/6) Gap_init rate = 0.14 (15 / 106), avg. gap size = 1.20 (18 / 15) 627 29.07 4.68 3.41 chrXptel1M 331336 331741 (668259) C L1MC4_3end#LINE/L1 (2156) 633 223 m_b333s551i29 14005 chrXptel1M 331336 GCTCATTTCACTCAGCATCAGTTCATGTAAGTCTC-TCCAGGCCTTTCTG 331384 iv i v? - v v vi - v ii? vi C L1MC4_3end#LI 633 GCTTCTTTCACTTAGCAANA-TGCATTTAAGATTCATCCATGTTNTTGCG 585 chrXptel1M 331385 -AAATCATCCTGCTGGTCATTCCTT---ACAGAACAGTAATATTCCATAA 331430 -i? ---- iv v --- iv vvv i vi C L1MC4_3end#LI 584 TGNATCA----GTAGTTCATTCCTTTTTATCGCTGAGTAGTATTCCATTG 539 chrXptel1M 331431 CATTCATATACCACAATTTACCCAACCATTCTCCAATTGATGGACATCCA 331480 i vv i i iiii v v vi v i? C L1MC4_3end#LI 538 TATGGATGTACCACAGTTTGTTTATCCATTCACCTGTTGAAGGACATCTN 489 chrXptel1M 331481 TTCAGTTTCCAGTTTTTAGTCACTACAAAAAGGGCTGCCACAAACATTCG 331530 vviv ? i i? i ii v ii i i C L1MC4_3end#LI 488 GGTTGTTTCCAGNTTTTGGCNATTATGAATAAAGCTGCTATAAACATTCG 439 chrXptel1M 331531 TGCACGTACAGGTCCCTTTC----CCTTCTTTATAATCTCTTTGGGATAT 331576 ---- iii v v---- v v?v v v ?i ?i v i v C L1MC4_3end#LI 438 T----GTACAGGTTTTTGTGTGGACATANGTTTTCANTTCNCTTGGGTAA 393 chrXptel1M 331577 AAGCCTAGTAGTAACACTGCTGGATCAAAGGGTA--TGCACAGTTTGATA 331624 vi v i?v i i v v -- i i- --- C L1MC4_3end#LI 392 ATACCTAGGAGTGNGATTGCTGGGTCATATGGTAANTGTAT-GTT---TA 347 chrXptel1M 331625 ACTTTTTGAGCATAGTTCCAAACTACTCTCCAAAATGCTTGGATTCGTTC 331674 i ? i v - v v ii i i vi v iivv i C L1MC4_3end#LI 346 GCTTTNTAAGAA-ACTGCCAAACTGTTTTCCAAAGTGGCTGTACCATTTT 298 chrXptel1M 331675 ACAACTCCACCAACAATGCATCAATGTCCCAGTT-TTCCGCATCC-CTCC 331722 i vii i i v iv i ? -i i - v C L1MC4_3end#LI 297 GCATTCCCACCAGCAATGTATGAGAGTTCCNGTTGCTCCACATCCTCGCC 248 chrXptel1M 331723 AACA------ATCATCATTATTTTT 331741 i ------ ii v ? C L1MC4_3end#LI 247 AGCATTTGGTATTGTCAGTNTTTTT 223 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.92 CpG sites = 64, Kimura (unadjusted) = 39.37 Transitions / transversions = 1.28 (64/50) Gap_init rate = 0.05 (22 / 405), avg. gap size = 1.50 (33 / 22) 898 26.97 2.27 1.61 chrXptel1M 331418 331726 (668274) C L1ME4c_3end#LINE/L1 (276) 554 244 m_b333s551i30 14005 chrXptel1M 331418 TAATATTCCATAACATTCATATACCACAATTTACCCAACCATTCTCCAAT 331467 vivi ?v i i ii i v C L1ME4c_3end#L 554 TAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTAT 505 chrXptel1M 331468 TGATGGACATCCATTCAGTTTCCAGTTTTTAGTCACTACAAAAAGGGCTG 331517 v ii vviv i v ii i i v iv C L1ME4c_3end#L 504 TGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCTG 455 chrXptel1M 331518 CCACAAACAT--TCGTGCACGTACAGGTCCCTTTCCCTTCTTT---ATAA 331562 v ii -- -- i --- i i --- v C L1ME4c_3end#L 454 CAATGAACATCTTCGTGCA--TATAG---CTTTTTCCTTCTTTTGAATTA 410 chrXptel1M 331563 TCTCTTTGGGATATAAGCCTAGTAGTAACACTGCTGGATCAAAGGGTATG 331612 i i i v vv i v iiv i i i C L1ME4c_3end#L 409 TTTCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATG 360 chrXptel1M 331613 CACAGTTTGATAACTTTTTGAGCATAGTTCCAAACTACTCTCCAAAATGC 331662 v v v ii i vivi i v v i i i v v C L1ME4c_3end#L 359 AACATTTTTATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAGGG 310 chrXptel1M 331663 TTGGATTCGTTCACAACTCCACCAACAATGCATCAATGTCCCAGTTTT-C 331711 v iivi i ?iv i i v i? v i- C L1ME4c_3end#L 309 TTGTACCAATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCAC 260 chrXptel1M 331712 CGCATCC-CTCCAACA 331726 ? - v i C L1ME4c_3end#L 259 CGCANCCTCGCCAGCA 244 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.85 CpG sites = 49, Kimura (unadjusted) = 34.91 Transitions / transversions = 1.48 (49/33) Gap_init rate = 0.03 (9 / 308), avg. gap size = 1.33 (12 / 9) 229 23.19 5.80 0.00 chrXptel1M 332032 332100 (667900) L1M1_orf2#LINE/L1 2157 2229 (1065) m_b333s551i31 14006 chrXptel1M 332032 AGAAACAATTAAGAATTTCAGCAAAGTTGCAAGATATAAAATAAGCCCAC 332081 vii v v v i i i v i vi L1M1_orf2#LIN 2157 AGAACTGATAAACAAATTCAGTAAAGTTGCAGGATACAAAATCAACATAC 2206 chrXptel1M 332082 ATAAATT----GCATTTCTGTAT 332100 v i---- i L1M1_orf2#LIN 2207 AAAAATCAGTAGCATTTCTATAT 2229 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 28.17 CpG sites = 9, Kimura (unadjusted) = 28.17 Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.01 (1 / 68), avg. gap size = 4.00 (4 / 1) 13 15.86 5.71 0.00 chrXptel1M 334324 334358 (665642) (AAGAA)n#Simple_repeat 1 37 (0) m_b334s252i0 14007 chrXptel1M 334324 AAGAGAAGCATA-AAAAGGCAA-AAAAGAAAAGAAAA 334358 i v v - iv - (AAGAA)n#Simp 1 AAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAA 37 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 298 27.20 8.81 0.96 chrXptel1M 334831 335023 (664977) L1MEi_5end#LINE/L1 2000 2207 (5) m_b334s551i0 14008 chrXptel1M 334831 GGGAAGGAGGGAAAGGGAAGAGAAAAA-TATAATTAGGAGCAAACA---- 334875 i i ii ? i -? i v iv v ---- L1MEi_5end#LI 2000 GGAAAGGAGAGAAAAAGNAAAGAAAAAGNATGATAAACAGAAAACACAAA 2049 chrXptel1M 334876 ---AGATGGCAGGAAATACAGAGTAATTCTATCTGTGA---------ATG 334913 --- i - - vvi v v v i --------- L1MEi_5end#LI 2050 ATAAGATGGTAG-AAATA-AGTCCAAATATATCAGTAATCACAATAAATG 2097 chrXptel1M 334914 TGAATGGAATGAACTCTCCCATAAAACGGAAGTGCATAGCAGACTGGATT 334963 i v i v i v v iv v vv v i L1MEi_5end#LI 2098 TAAATGGATTAAACTCACCTATTAAAAGACAGAGATTATCAGATTGGATT 2147 chrXptel1M 334964 AAAAGCCAGAATACTACAATGTATTGTTTACAAGAAACTCATTTAAAGCA 335013 ivv i v vi v i ii i v ii i L1MEi_5end#LI 2148 AAAAAAAAAAATCCAGCTATATGCTGTTTACAAGAGACACACCTAAAACA 2197 chrXptel1M 335014 GAGTGATACA 335023 i ii i L1MEi_5end#LI 2198 AAACGACACA 2207 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.13 CpG sites = 29, Kimura (unadjusted) = 34.95 Transitions / transversions = 1.26 (29/23) Gap_init rate = 0.03 (6 / 192), avg. gap size = 3.17 (19 / 6) 313 24.80 6.94 1.99 chrXptel1M 334872 335015 (664985) L1MEh_5end#LINE/L1 2080 2230 (5) m_b334s551i1 14008 chrXptel1M 334872 AACAAGATGGCAGGAA---------ATACAG-AGTAATTCTATCTGTGAA 334911 i i --------- i ?- vi ---i i L1MEh_5end#LI 2080 AATAAGATGGCAGAAATAAGTCCNAATATANCAGTAATTACA---ATAAA 2126 chrXptel1M 334912 TGTGAATGGAATGAACTCTCCCATAAAACGGAAGTGCATAGCAGACTGGA 334961 i iv i v v v v iv v vv ?v i L1MEh_5end#LI 2127 TGTAAATGGGTTAAACTCACCAATTAAAAGACAGAGATTNTCAGATTGGA 2176 chrXptel1M 334962 TTAAAAGCCAGAATACTACAATGTATTGTTTACAAGAAACTCATTTAAAG 335011 ? iv i v v i ii i i v i i L1MEh_5end#LI 2177 TTNAAAAACAAAATCCAACAATATGCTGTCTACAAGAGACACACTTAAAA 2226 chrXptel1M 335012 CAGA 335015 ? L1MEh_5end#LI 2227 CANA 2230 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 31.84 CpG sites = 20, Kimura (unadjusted) = 31.84 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.03 (5 / 143), avg. gap size = 2.60 (13 / 5) 616 32.02 5.46 3.53 chrXptel1M 334905 335765 (664235) L1MC_orf2#LINE/L1 35 911 (2383) m_b334s551i2 14008 chrXptel1M 334905 CTGTGAATGTGAATGGAATGAACTCTCCCATAAAACGGAAGTGCATAGCA 334954 v i ? vv i iv v v v v iv v vv iv L1MC_orf2#LIN 35 CTTTAAATGTNAATGGTCTAAATACACCAATTAAAAGACAGAGATTGTCA 84 chrXptel1M 334955 GACTGGATTAAAAGCCAGAATACTACAATGTATTGTTTACAAGAAACTCA 335004 v i iv ii iv v v i i i i L1MC_orf2#LIN 85 GAGTGGATCAAAAAACAAGACCCAACTATATGTTGTCTACAAGAAACCCA 134 chrXptel1M 335005 TTTAAAGCAGAGTGATACATTCAGAGTAAAGGTAAAAGACTAGAGCAAAA 335054 i v ii v iv i vi v i ? iv i v i L1MC_orf2#LIN 135 CTTTAAATATAAAGACACATATAGATTAAAAGTAAANGGATGGAGAAAGA 184 chrXptel1M 335055 TTTATTGTGCTTCAGCTAAGGTTAAAAAAAAAAAAAGGCAGGAGTAGCAA 335104 v iii vvvi -- i i ------ ? v L1MC_orf2#LIN 185 TATACCATGCTAACACTAA--TCAAAAGAAA------GCNGGAGTAGCTA 226 chrXptel1M 335105 TCCTCTTCTCAGGTCAAGCAAA------AGCAAAAATAGATCTAATTAAA 335148 vi vv i iivi i ------ ii v ------ vv L1MC_orf2#LIN 227 TATTAATTTCAGACAGAGCAGACTTCAGAGCAAGGAAAG------TTATC 270 chrXptel1M 335149 AGACATAAGGAAGGAAATTACATCCTGCTTAAAGGCAAAATGGATAATGA 335198 iv i i iv vv v v i vvv vvviv v L1MC_orf2#LIN 271 AGGGATAAAGAGGGGCATTACATAATGATAAAGGGGTCAATTCTCCAAGA 320 chrXptel1M 335199 AGTGATATCAATACTAAACATATATGCACCAAGTGGTATAGCATCCAAAT 335248 vv v v v i i i v iiiii v i v L1MC_orf2#LIN 321 AGACATAACAATCCTTAACGTGTATGCGCCTAACAACAGAGCGTCAAAAT 370 chrXptel1M 335249 TCCTAGAGGAAAAGTTAAGAGAACTGCAAGAAGAAATAGACAGCAAAACT 335298 v v iii v ii i v i iivvvv L1MC_orf2#LIN 371 ACGTGAGGCAAAAACTGATAGAACTGCAAGGAGAAATAGACGAATCCACT 420 chrXptel1M 335299 GTAATAGTAGGAGATCTCAACCTAGCACTCTCAGAATTAGATAAATTGAA 335348 i v v ii vivv v v ? v ? i i iv i L1MC_orf2#LIN 421 ATTATAGTTGGAGACTTCAACACCCCTCTATCAGNAATNGACAGATCCAG 470 chrXptel1M 335349 T---CACAAAATAAATAAGAAAGAAGTTAAGAAGGTAAATAGAATC-TCA 335394 i--- v v i i viv -- -v ? i v i - L1MC_orf2#LIN 471 CAGGCAGAAAATCAGTAAGGACATAGTT--GAA-CTNAACAGCACCATCA 517 chrXptel1M 335395 GAAAAGTTAGGGATGATAGACCTTTGGAAAATATTGAATGGA--GATAGA 335442 - vv ii i iv? i v v i iv i ? i vv vv --i i v L1MC_orf2#LIN 518 -ATCAACTGGATNTAATTGACATCTATAGANTACTTCATCCAACAACAGC 566 chrXptel1M 335443 AATGAATATATCTTTTTCTCAGCAGTACATGGAACCTATACAAAAACTGA 335492 -- i iv i ivvvi v vi v i iv L1MC_orf2#LIN 567 A--GAATACACATTCTTCTCAAGCTCACATGGAACATTCACCAAGATAGA 614 chrXptel1M 335493 CTATGTATTAGGGCATAAAA---ACCTCAAAATCAAACGCAGAAAGGCAG 335539 i ii vi i v --- i --- ivi i iiii L1MC_orf2#LIN 615 CCACATTCTGGGCCATAAAACACACCTTAA---CAAATTTAAAAGAATAG 661 chrXptel1M 335540 AAATAGTA-AATGCT---TCTTAGATCATAATGCAA-TAAA----AAATT 335580 vi - ? i?--- i i i v - ---- i L1MC_orf2#LIN 662 AAATCATACAANGTNTGCTCTCAGACCACAATGGAATTAAACTAGAAATC 711 chrXptel1M 335581 ATATGCAATAAAAAGACAGG-GGAAAATAGACCAAAAATTAATTGGAAAC 335629 - -- i i i v- --v -- v i i L1MC_orf2#LIN 712 A-AT--AACAGAAAGATAGCTGGAAAAT--CCCAAAA--TACTTGGAGAT 754 chrXptel1M 335630 TAAATAATCTAATCCTAAAGAAAGAGTGGGTGAAACAACAAATCACAATT 335679 i ivi v i v vivi v v v v vv L1MC_orf2#LIN 755 TAAACAACACACTTCTAAATAACACATGGGTCAAAGAAGAAATCTCAAGA 804 chrXptel1M 335680 GATAATTT-----CATT---------ACGGAG--------ACAACATACA 335707 - -----i --------- i i i-------- v iv L1MC_orf2#LIN 805 GA-AATTTAAAAATATTTTGAACTAAATGAAAATGAAAATACAACTTATC 853 chrXptel1M 335708 AAAATTTGTGGAATACAGCCAAAGTGGTTGTTAGGGGAAATTTTATATCT 335757 i i v ii vv i i v v v L1MC_orf2#LIN 854 AAAATTTGTGGGATGCAGCGAAAGCAGTGCTTAGAGGGAAATTTATAGCA 903 chrXptel1M 335758 CTAAATGC 335765 i i L1MC_orf2#LIN 904 TTGAATGC 911 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 42.43 CpG sites = 138, Kimura (unadjusted) = 43.29 Transitions / transversions = 1.08 (138/128) Gap_init rate = 0.05 (44 / 860), avg. gap size = 1.77 (78 / 44) 399 17.67 9.71 6.60 chrXptel1M 335874 335976 (664024) C MIRc#SINE/MIR (153) 115 10 m_b334s601i0 14009 chrXptel1M 335874 GGGGTTAAGTGACTTGCCCAGGGTCACACAGCCAGGAAATGTTAAGAGTC 335923 i i i v i vi- - C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGC-AGAG-C 68 chrXptel1M 335924 TGAGACCAGATTTGAACTCAGA----------TCCAGGGCTGGTGCTCTA 335963 i i ----- i i i---------- i v ii v C MIRc#SINE/MIR 67 CGGGAC-----TCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTT 23 chrXptel1M 335964 TCCACTGCACCAC 335976 C MIRc#SINE/MIR 22 TCCACTGCACCAC 10 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 18.25 CpG sites = 13, Kimura (unadjusted) = 20.91 Transitions / transversions = 3.25 (13/4) Gap_init rate = 0.08 (8 / 102), avg. gap size = 2.12 (17 / 8) 2180 27.25 6.48 2.53 chrXptel1M 336090 337309 (662691) L1M5_orf2#LINE/L1 920 2186 (1108) m_b334s551i3 14008 chrXptel1M 336090 GAAAATAGAGAAAGAG--AAGATCAATGAATTGGGCTTACAACTAAAAAA 336137 v - iv-- i vi ii v v v i L1M5_orf2#LIN 920 GAAAAGA-AGAAAGGCTTAAAATCAATGATCTAAGCTTCCACCTTAAGAA 968 chrXptel1M 336138 GCTAGAAAAAGAA---CAAATTAAAAACCCTCAATTGAATATCAAATTTG 336184 --- --- iv v?i i vv iivvv L1M5_orf2#LIN 969 GCTAGAAAAAGAAGAGCAAATTAAA---CCCAAAGNAAGTAGAAGGAAGG 1015 chrXptel1M 336185 AAATTCTGAAAATAAAAGGGGAGATTAATAAAACTGAAAGTAAGAAAACT 336234 vv i i i vi i i i iv ii i? ? v L1M5_orf2#LIN 1016 AAATAATAAAGATAAGAGCAGAAATCAATGAAATAGAAAACAAANANACA 1065 chrXptel1M 336235 ATTGAATTAAAA--AATAAAACCAAGAGTTGGTTTTATGAAAAAAACCCA 336282 v i-- -- ii i i i i v i --i L1M5_orf2#LIN 1066 ATAGAG--AAAATCAACGAAGCCAAAAGCTGGTTCTTTGAAAAGA--TCA 1111 chrXptel1M 336283 ACAAAATAGATAAACCTTTAGTTAATCTGATTA-GAAAAAGGAAAAAAGA 336331 i v i i? iv i - -- i i L1M5_orf2#LIN 1112 ATAAAATTGATAAACCTCTAGCNAGACTGATCAAGAAAAA--AAGAGAGA 1159 chrXptel1M 336332 AAAT-CAAATTGTTAGTCTCAAAAATAAAAAGGGAGAACTTTCCATCAGT 336380 i i- iii i v ii i i ------ v L1M5_orf2#LIN 1160 AGACACAAATTACCAATATCAGGAATGAAAAAGGAGA------CATCACT 1203 chrXptel1M 336381 GAAGA------GGAAATTAGAGCAATAATTAGGAGTTATTTTGCCTCATT 336424 iv ------i v i ivi v iiiv v vviv i L1M5_orf2#LIN 1204 ACAGATCCTACAGACATTAAAAGGATAATAAGAGAATATTATGAACAACT 1253 chrXptel1M 336425 ATATGTCAACAAATCTGATAA-----GTGAAATGGAGGAATACCTACAAA 336469 v i i i ? -----i vi v vv L1M5_orf2#LIN 1254 TTATGCCAATAAATTTGANAACTTAGATGAAATGGACAAATTCCTTGAAA 1303 chrXptel1M 336470 AATATAA------------------AGAGGAAATAAAATTACTTAAGTAG 336501 i i ------------------ i i v- ii i i L1M5_orf2#LIN 1304 AACACAANTTACCAAAACTGACNCAAGAAGAAATAGAAA-ATCTGAATAG 1352 chrXptel1M 336502 TCCTATTTCAGAAAAAGAAATTGAACAAGCTATTAATCAAC--TCCCTCA 336549 i v vivv ivv iv -v -- v L1M5_orf2#LIN 1353 CCCTATATCTATTAAAGAAATTGAATTTGTAATTAA-AAACCTTCCCACA 1401 chrXptel1M 336550 GAAAAAATCTCCAAGGTCAGA---------------ATTCTAGCAAATAT 336584 i i - i vi --------------- v i L1M5_orf2#LIN 1402 AAGAAAA-CTCCAGGCCCAGATGGCTTCACTGGTGAATTCTACCAAACAT 1450 chrXptel1M 336585 TTAAAGAACTATTAAGTCTAATACTATACAAACTATTTGAAAAAATAGGA 336634 i vv v vv i vi i v iv i i L1M5_orf2#LIN 1451 TTAAGGAAGAAATAATACCAATCTTACACAAACTCTTCCAGAAAATAGAA 1500 chrXptel1M 336635 ATGGAAGGAGTCCTATCAAATTCCTTTTATGACACAGACA-CATGGTACT 336683 vi i iiv vi v i v vi --- - ?iiv L1M5_orf2#LIN 1501 AAAGAGGGAACACTTCCCAACTCATTTTATGAGGC---CAGCATNACCCT 1547 chrXptel1M 336684 GATACCTAAATCAGGTAAGATGAAA--ACAGAGAAAGAAAATTATAGACC 336731 v i ? ii i-- v -- iii i L1M5_orf2#LIN 1548 GATACCAAAACCNGACAAA--GACATTACAAGAAAAGAAAATTACAGACC 1595 chrXptel1M 336732 AATCTCCCTAATGAATATTGATGCTAAAATCTTAAATAAAATATTAGCAA 336781 v v i v v i ? i L1M5_orf2#LIN 1596 AATATCCCTCATGAACATAGATGCAAAAATCCTNAACAAAATATTAGCAA 1645 chrXptel1M 336782 AGAGATCATAGAAAGTCATCTCCAGGATAATACACTATGACCAAGTAGGA 336831 vv vivi v vvi vvvv ii i i L1M5_orf2#LIN 1646 ATCGAATCCAGCAATATATAAAAAGGATAATACATCATGACCAAGTGGGG 1695 chrXptel1M 336832 TTTATACCAGGAATGCAGGGCTGGTTCAATATTAGGAAAACTGTTAGCAT 336881 v i i i i v i v vi i iii L1M5_orf2#LIN 1696 TTTATCCCAGGAATGCAAGGTTGGTTTAACATTCGAAAATCAATCAATGT 1745 chrXptel1M 336882 AACTGACTATATCATTAACCAAATTAAC---AAAAACCATATGATTGATT 336928 i v i --- vi v v--- i i---- L1M5_orf2#LIN 1746 AATTCACCATAT---TAACAGAATAAAGGAGAAAAATCATATGATC---- 1788 chrXptel1M 336929 ATCTCAATAGATGCAGAAAAAACATTTGATACAATCCAACATCCATTCCT 336978 i i v i i v L1M5_orf2#LIN 1789 ATCTCAATAGATGCAGAAAAAGCATTTGACAAAATTCAACACCCATTCAT 1838 chrXptel1M 336979 AATACAAACACTTGAAAGGATAGGAATAAATGGACTTTTCCTTAAAATAG 337028 i v v iiiv iiv i v ivvi i vv ii L1M5_orf2#LIN 1839 GATAAAAACTCTCAGCAAACTAGGAATAGAAGGGAACTTCCTCAACCTGA 1888 chrXptel1M 337029 TCAGGAGCATATATTTAAA-CCTTCAGTAAGTATCATATGTAATGGTGAT 337077 v i i v ivv - v i? ii iv v L1M5_orf2#LIN 1889 TAAAGGGCATCTACGAAAAACCTACAGCNAACATCATACTTAATGGTGAA 1938 chrXptel1M 337078 AAACTAGACCCATTCCCAGCAAGATCAGGGGTGAAATAAGGTTGCCCACT 337127 ? ii ?v v vvi i iiii i i v i i L1M5_orf2#LIN 1939 ANACTGAANGCTTTCCCCCTAAGATCGGGAACAAGACAAGGATGTCCGCT 1988 chrXptel1M 337128 ATCACCATTATTATTCAATATTATTTAAGAAATGCTAGCTTTGGCAATAA 337177 ? i vi i i vivi ii v ivvv L1M5_orf2#LIN 1989 NTCACCACTTCTATTCAACATTGTACTGGAGGTCCTAGCCAGTGCAATAA 2038 chrXptel1M 337178 GAGAAGA-----AAAT-AAAGGAATAAGAATAGGTAATGAGGAAACCAAA 337221 iv ----- - v ii v v v i iv L1M5_orf2#LIN 2039 GGCAAGAAAAAGAAATAAAAGGCATAAAGATTGGAAAGGAAGAAATAAAA 2088 chrXptel1M 337222 ---TTAGTACTCTGCAGATGAAA--------TACTTAGAGAATCCTAGAG 337260 --- i?v i - v -------- v i ? i L1M5_orf2#LIN 2089 CTGTCNTTATTC-GCAGATGACATGATTGTNTACGTAGAAAATCCNAAAG 2137 chrXptel1M 337261 AATCAACTGAAAAACTACTAGAAACAATTCACAACTTTAGCAAAGTGGC 337309 v vi ? vi vviii v i v L1M5_orf2#LIN 2138 AATCTACAAANAAACTACTAGAACTAATAAGTGAATTTAGCAAGGTCGC 2186 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.72 CpG sites = 188, Kimura (unadjusted) = 35.27 Transitions / transversions = 1.38 (188/136) Gap_init rate = 0.04 (50 / 1219), avg. gap size = 2.22 (111 / 50) 300 35.33 5.11 5.11 chrXptel1M 337696 337871 (662129) L2b_3end#LINE/L2 276 451 (15) m_b334s601i1 14010 chrXptel1M 337696 CTAGGTATCTTC-GTCTTACCTTAGCCCCCTTCCATTTTCAGCTACCT-T 337743 i ivi ii - i i - v ii vvi v ? -i ii -? L2b_3end#LINE 276 CTGGGCCCCCCCAGTCCTACCCT-GCCACTCTGGGTTATNA-TTGTCTGN 323 chrXptel1M 337744 CTATGTGT-TGTCTTCCCCATTAGAATATAAGCTTCTCGGGTATAGAGGT 337792 i ii - i i v i i i vi i vii i ii L2b_3end#LINE 324 TTACATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGAC 373 chrXptel1M 337793 TG---CTATTCTTTTTAACACAAATAAATGTATTCCCAGTGTTCTGCGAA 337839 i --- i ii v i v i ------- i i iiiv iv L2b_3end#LINE 374 CGNGTCTGTCTTGTTCACCGC-------TGTATCCCCAGCGCCTAGCACA 416 chrXptel1M 337840 GTTCATGGCACATGGTAAGCACTC---AAATACTT 337871 ?v v ii i i --- i L2b_3end#LINE 417 GNGCCTGGCACACAGTAGGCGCTCAGTAAATATTT 451 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 49.29 CpG sites = 45, Kimura (unadjusted) = 54.96 Transitions / transversions = 3.21 (45/14) Gap_init rate = 0.08 (14 / 175), avg. gap size = 1.29 (18 / 14) 302 30.88 4.39 6.25 chrXptel1M 337752 337865 (662135) L2a_3end#LINE/L2 382 493 (24) m_b334s601i2 14010 chrXptel1M 337752 TGTCTTCCCC-ATTAGAATATAAGCTTCTCGGGTATAGAGG---TTG-CT 337796 i - i i i vi i vii i i--- - L2a_3end#LINE 382 TGTCTCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTCT 431 chrXptel1M 337797 ATTCTTTTTAACACAAATAAATGTATTCCCAGTGTTCTGCGAAGTTCATG 337846 i i v i vii ------- i i iiiv viv v v L2a_3end#LINE 432 GTTTTGTTCACTGC-------TGTATCCCCAGCGCCTAGAACAGTGCCTG 474 chrXptel1M 337847 GCACATGGTAAGCACTCAA 337865 i i i L2a_3end#LINE 475 GCACATAGTAGGCGCTCAA 493 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.17 CpG sites = 24, Kimura (unadjusted) = 42.65 Transitions / transversions = 2.67 (24/9) Gap_init rate = 0.09 (10 / 113), avg. gap size = 1.20 (12 / 10) 217 23.11 0.00 3.85 chrXptel1M 337934 337987 (662013) MIRb#SINE/MIR 210 261 (7) m_b334s601i3 14011 chrXptel1M 337934 AGAGCTAAGCACAGTGCTTGGAACATAAGAAACACTTCTTAAATGCAGTA 337983 v v i v iv i i ivv -- MIRb#SINE/MIR 210 AGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAAATG--GTA 257 chrXptel1M 337984 TCTC 337987 v MIRb#SINE/MIR 258 GCTC 261 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.13 CpG sites = 5, Kimura (unadjusted) = 27.64 Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.04 (2 / 53), avg. gap size = 1.00 (2 / 2) 399 17.67 9.71 6.60 chrXptel1M 338088 338190 (661810) MIRc#SINE/MIR 10 115 (153) m_b334s601i4 14012 chrXptel1M 338088 GTGGTGCAGTGGATAGAGCACCAGCCCTGGA----------TCTGAGTTC 338127 v ii v i ----------i i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chrXptel1M 338128 AAATCTGGTCTCAGACTCTTAACATTTCCTGGCTGTGTGACCCTGGGCAA 338177 i ----- i i - -iv i v i i MIRc#SINE/MIR 60 GA-----GTCCCGG-CTCT-GCCACTTACTAGCTGTGTGACCTTGGGCAA 102 chrXptel1M 338178 GTCACTTAACCCC 338190 i MIRc#SINE/MIR 103 GTCACTTAACCTC 115 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 18.25 CpG sites = 13, Kimura (unadjusted) = 20.91 Transitions / transversions = 3.25 (13/4) Gap_init rate = 0.08 (8 / 102), avg. gap size = 2.12 (17 / 8) 13 23.57 0.00 0.00 chrXptel1M 340633 340667 (659333) (TATA)n#Simple_repeat 1 35 (0) m_b334s252i1 14013 chrXptel1M 340633 TATAAGTATATACATACATATATATGTCTATCTAT 340667 vi i i i v v (TATA)n#Simpl 1 TATATATATATATATATATATATATATATATATAT 35 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 324 27.18 2.59 1.71 chrXptel1M 347133 347248 (652752) C L1ME3G_3end#LINE/L1 (551) 373 257 m_b334s551i4 14014 chrXptel1M 347133 ATTTCCAGGTCAAAGGGTCCCCATACTTTAGTAATTTT--TGGCTGCTTC 347180 v ii viv ii i -- -- i v i v C L1ME3G_3end#L 373 ATTGCTGGGTCAAAGGGTATGCGCATTTTA--AATTTTAATAGATACTGC 326 chrXptel1M 347181 CAAATTAATATCCAGAATGGCTAGACCAATTTACAGTTTCACCAGTAATG 347230 iviv i ? iv v ii i i C L1ME3G_3end#L 325 CAAATTGCCCTCCAAAANGGCTGTACCAATTTACACTCCCACCAGCAGTG 276 chrXptel1M 347231 AATTAATGTGTCC-TTTCC 347248 v v iv ii - C L1ME3G_3end#L 275 TATGAGAGTACCCGTTTCC 257 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 33.77 CpG sites = 19, Kimura (unadjusted) = 35.18 Transitions / transversions = 1.58 (19/12) Gap_init rate = 0.03 (4 / 115), avg. gap size = 1.25 (5 / 4) 690 27.14 4.39 6.25 chrXptel1M 347634 347861 (652139) MIR#SINE/MIR 33 256 (6) m_b334s601i5 14015 chrXptel1M 347634 CTGGA--TAGAACACTGGGACTGGAATCAGAAGACTCAGACCCTTACCAG 347681 --i vii iv ii v vv-- i v v v i MIR#SINE/MIR 33 CTGGAGCCAGACTGCCTGGGTTCGAATCCC--GGCTCTGCCACTTACTAG 80 chrXptel1M 347682 GTATATGATCTTGAACAACTCTACTTTGTTTCTGTTTGCCTCAATTTATC 347731 v i i i ii v - viii v v i vii MIR#SINE/MIR 81 CTGTGTGACCTTGGGCAAGT-TACTTAACCTCTCTGTGCCTCAGTTTCCT 129 chrXptel1M 347732 CATTTATAAAATGGGGATCATGACAGCACCTCCATCTCAGGATTGTTGTG 347781 i i v i i i v v vi i MIR#SINE/MIR 130 CATCTGTAAAATGGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTG 179 chrXptel1M 347782 AGGATTAAATCATTGTAAAATGAGATAAT---TGGAAAGCATTT-----A 347823 ----------- v --- v ii ----- MIR#SINE/MIR 180 AGGATT-----------AAATGAGTTAATACATGTAAAGCGCTTAGAACA 218 chrXptel1M 347824 GTGCCTGGCATGTGGTGGGTGCTTAATAAATGCTTGTT 347861 ii i ii i i i v i MIR#SINE/MIR 219 GTGCCTGGCACATAGTAAGCGCTCAATAAATGTTAGCT 256 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.31 CpG sites = 37, Kimura (unadjusted) = 34.80 Transitions / transversions = 1.76 (37/21) Gap_init rate = 0.07 (17 / 227), avg. gap size = 1.41 (24 / 17) 228 26.71 7.58 0.71 chrXptel1M 350316 350447 (649553) C L1PREC2_orf2#LINE/L1 (764) 2530 2390 m_b334s551i5 14016 chrXptel1M 350316 TATTTTTTAATAGCTCTATAAAGTAATCT-GTTGGTAGTTTGCTTGGTAT 350364 v vv i i i - v -i v v v C L1PREC2_orf2# 2530 TAGTTTTTTCTAGTTCTGTGAAG-AATGTCATTGGTAGTTTGATAGGAAT 2482 chrXptel1M 350365 GGCACTGAATGT-TAATTTATTTTG-------TAGTCATTTTATTG-CAT 350405 i i v - v ii ------- i i vi -i C L1PREC2_orf2# 2481 AGCATTGAATCTGTAAATTGCTTTGGGCAGTATGGCCATTTTAACGATAT 2432 chrXptel1M 350406 TAGTTTAGCCTATGCATGAGCAATGAATACTTCTCCAATTAT 350447 ii ivv v vv ii i v i C L1PREC2_orf2# 2431 TGATTCTTCCTATCCATGAGCATGGAATGTTTTTCCATTTGT 2390 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 32.42 CpG sites = 19, Kimura (unadjusted) = 33.57 Transitions / transversions = 1.19 (19/16) Gap_init rate = 0.04 (5 / 131), avg. gap size = 2.20 (11 / 5) 244 30.74 9.94 1.08 chrXptel1M 350730 350900 (649100) C L1MD_orf2#LINE/L1 (1180) 2114 1929 m_b334s551i6 14017 chrXptel1M 350730 ATCATATTATTTGCAAAAAAAATCTTAATTTTGTTTTTTCTTTGCC--TC 350777 i i i v iiiv -- i i i i v -- C L1MD_orf2#LIN 2114 ATCATGTCATCTGCAAATAGGGAC--AGTTTTATTTCTTCCTTTCCAATC 2067 chrXptel1M 350778 AATGT---TTTTGTTT-------TTGTCTTACTGTTATAACTAGCATTTC 350817 vi i --- i ------- i i ivv ii v i C L1MD_orf2#LIN 2066 TGTATGCCTTTTATTTCCTTTTCTTGCCTTATTGCACTGGCTAGAACTTC 2017 chrXptel1M 350818 TAGTA---TATTGCATCATAATGGTGATAGTGAACATTCTTGCCTTAT-- 350862 i --- i v v v i v i i i i -- C L1MD_orf2#LIN 2016 CAGTACTATGTTGAATAAGAGTGGTGAGAGCGGACATCCTTGCCTTGTTC 1967 chrXptel1M 350863 CCAATTGTATTGGAAAGGAGTCTAGTGTATCTTCATTA 350900 i iv vv i i vi ii v v vi C L1MD_orf2#LIN 1966 CCGATCTTAGGGGGAAAGCATTCAGTCTTTCACCATTA 1929 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.42 CpG sites = 34, Kimura (unadjusted) = 41.54 Transitions / transversions = 1.89 (34/18) Gap_init rate = 0.04 (7 / 170), avg. gap size = 2.71 (19 / 7) 314 30.26 5.75 6.10 chrXptel1M 350985 351593 (648407) C L1M5_orf2#LINE/L1 (1465) 1829 1223 m_b334s551i7 14014 chrXptel1M 350985 TATTGATTTTTAACAAA-GATTTTTGTCCAT--ATCAATATAAGCATACA 351031 i v iv - v v v -- ii v i v ii C L1M5_orf2#LIN 1829 TGTTGAATTTTGTCAAATGCTTTTTCTGCATCTATTGAGATGATCATATG 1780 chrXptel1M 351032 ATTTTTGTTGTTCTTATTATAAATACAGTTAATTGTATCTATTCTTTTTC 351081 v iv iv vi i v ii v ii iv vv C L1M5_orf2#LIN 1779 ATTTTTCTCCTTTATTCTGTTAATATGGTGAATTACATTGATTGATTTTC 1730 chrXptel1M 351082 CCAGTACTAAACCAAACTTTTATTGCTGGTATAAACTCAATGTTGTCA-G 351130 v- i ii v vi v v i v iv v - C L1M5_orf2#LIN 1729 G-AATGTTAAACCAACCTTGCATTCCTGGGATAAACCCCACTTGGTCATG 1681 chrXptel1M 351131 AGATATTTACATCATATCTTTGATATGATGCTATGTCCGCCTTGCTAAGA 351180 vi --- v --- v iv ivi i vi v C L1M5_orf2#LIN 1680 ATGTATT---ATCCT---TTTTATATATTGCTGGATTCGATTTGCTAATA 1637 chrXptel1M 351181 TTTTATTTGAAATTTTCATGTCATTGTTCATTAGTGATATTGATCTAT-A 351229 i ?iii iiii vv v v i i - C L1M5_orf2#LIN 1636 TTTTGTTNAGGATTTTTGCATCTATGTTCATGAGGGATATTGGTCTGTAA 1587 chrXptel1M 351230 TATTCCTTATTT----TATCCTT-TCCAATTTCATAATTAAGACTAAATT 351274 v i vi ---- i i - ?ii iivv i i ii? vii C L1M5_orf2#LIN 1586 TTTTCTTTTCTTGTAATGTCTTTGTCNGGTTTTGGTATCAGGGTNATGCT 1537 chrXptel1M 351275 TGTATCAT-AAATGAAATTTGGTAAG-GTTTTTTCTTTTGTTCTTTT-TA 351321 v iv - i-- v - iii vi v - i C L1M5_orf2#LIN 1536 GGCCTCATAAAATGAG--TTGGGAAGTGTTCCCTCTTTTTCTATTTTCTG 1489 chrXptel1M 351322 AAAGTGGTTTGTACAAT-TTGGTTTTAATCATTCTTTGAATGTTTGATAA 351370 i -i ii v- v v iv i i i i C L1M5_orf2#LIN 1488 GAAG-AGTTTGTGTAAGATTGGTATTATTTCTTCCTTAAATGTTTGGTAG 1440 chrXptel1M 351371 AAT------------CCATCTGATCCCAGAGTATTTT-----GGAAGGTT 351403 ------------ iv ii v i ----- C L1M5_orf2#LIN 1439 AATTCACCAGTGAAGCCATCTGGGCCTGGAGTTTTCTTTGTGGGAAGGTT 1390 chrXptel1M 351404 TGTTTTGTAGCTTGTTTCCTGTCTTTTTTTTTTTAA-AGAAATTGGACTG 351452 ---------- iv v vivi ivv i - v v i i C L1M5_orf2#LIN 1389 T----------TTAATTACAAATTCAATTTCTTTAATAGATATAGGGCTA 1350 chrXptel1M 351453 TTTTAATGATCTATTTCTTGTTCAGTTCTTGTTCTTGT-TCAGTTAATCT 351501 ivi vv -------------- ?- -v vv C L1M5_orf2#LIN 1349 TTCAGATTTTCTATTTC--------------TTCTTGNGTCAGTT-TTGG 1315 chrXptel1M 351502 TATTTTATATTTCTAAAAAAATTCCTTTATTTTACTTAAGTTGTTGGATT 351551 v? i i i v ii iv ii i ii ? iii C L1M5_orf2#LIN 1314 TAANTTGTGTTTTTCAAGGAATTTGTCCATTTCATCTAAGTTNTCAAATT 1265 chrXptel1M 351552 TATTGGAAT--AGTTAGGCAAAACATTTTCCAATGCTATTCTTT 351593 v -- ivv v i i iv -- i C L1M5_orf2#LIN 1264 TATTGGCATAAAGTTGTTCATAATATTCTCTTAT--TATCCTTT 1223 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.38 CpG sites = 100, Kimura (unadjusted) = 40.38 Transitions / transversions = 1.37 (100/73) Gap_init rate = 0.09 (52 / 608), avg. gap size = 1.38 (72 / 52) 1047 22.72 4.45 1.98 chrXptel1M 352680 352926 (647074) C MIRb#SINE/MIR (7) 261 9 m_b334s601i6 14018 chrXptel1M 352680 GAACAAGCATTTATTAAGAATATGCTATGTGCCAAGCACTGTGATAAGTG 352729 i v v i viiv i i v i C MIRb#SINE/MIR 261 GAGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCG 212 chrXptel1M 352730 CTTTACAAATCTTATCTCATTTAATTCCTCATAATAACCCTGGGAGGAAG 352779 viiv - i i v v C MIRb#SINE/MIR 211 CTTTACATGCATTATCTCATTTAA-TCCTCACAACAACCCTGCGAGGTAG 163 chrXptel1M 352780 GTGCTAGTATTATCTTCATTTTACTGTTGAGGAAACTGAGGC-------A 352822 --- v ii v v -------i C MIRb#SINE/MIR 162 G---TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAG 116 chrXptel1M 352823 GTAAAATGACTTGTCTAAGGCCACAAAGCT----AGTGTCTGAATCTGGA 352868 v i i i i i v ---- v v ii v C MIRb#SINE/MIR 115 GTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGA 66 chrXptel1M 352869 TTTGAACTTGGGTCTTCTTGACTCCGAGTCCAGTGCTTCATGCACTGTCA 352918 i iii vii i iv v iiv v - C MIRb#SINE/MIR 65 TTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTG-CA 17 chrXptel1M 352919 CCTAGCTG 352926 vv C MIRb#SINE/MIR 16 CCACGCTG 9 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.78 CpG sites = 31, Kimura (unadjusted) = 27.48 Transitions / transversions = 1.29 (31/24) Gap_init rate = 0.03 (7 / 246), avg. gap size = 2.29 (16 / 7) 407 26.11 6.25 0.85 chrXptel1M 355102 355213 (644787) C MIRc#SINE/MIR (141) 127 10 m_b334s601i7 14019 chrXptel1M 355102 CTGAGGC-AATTGAAGTTAAGTGACTTTCCCAGGG------AAGTGTTAA 355144 -v vv i v i ------ iv iv C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAA 78 chrXptel1M 355145 GTGTCTAGAGACCAGATTTGAACTCAGGTTCTTCTGACTTCAGGGCTGCT 355194 v - v vi i i i ii i i i v iiv C MIRc#SINE/MIR 77 GTGGC-AGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGT 29 chrXptel1M 355195 GTTCTACCCACTGCACCAC 355213 i vi C MIRc#SINE/MIR 28 GCTCTTTCCACTGCACCAC 10 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.48 CpG sites = 17, Kimura (unadjusted) = 32.85 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.03 (3 / 111), avg. gap size = 2.67 (8 / 3) 14 0.00 0.00 0.00 chrXptel1M 355537 355554 (644446) (TTA)n#Simple_repeat 1 18 (0) m_b334s252i2 14020 chrXptel1M 355537 TTATTATTATTATTATTA 355554 (TTA)n#Simple 1 TTATTATTATTATTATTA 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 183 19.44 2.78 0.00 chrXptel1M 356452 356487 (643513) C Penelope1_Vert#LINE/Penelope (540) 539 503 m_b334s601i8 14021 chrXptel1M 356452 GCATCCCTTTGAATTCCAGTAG-GAGATCCGGGATTG 356487 i i v ii - v i C Penelope1_Ver 539 GCATCTCTTTGAGTTACAGCGGTGAGAGCCAGGATTG 503 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 19.22 CpG sites = 5, Kimura (unadjusted) = 23.22 Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) 388 25.27 3.30 0.00 chrXptel1M 357277 357367 (642633) MER58C#DNA/hAT-Charlie 1 94 (121) m_b334s502i0 14022 chrXptel1M 357277 CATGGATCAGCAAACTACAGCCCTTGGGCCAACTCTAGACTACAGCCTGT 357326 v i i i vi v ii v ii i MER58C#DNA/hA 1 CAGGGGTCGGCAAACTACGGCCCGCGGGCCAAATCCGGCCCGCGGCCTGT 50 chrXptel1M 357327 TTTTGTATGGTACATGAGTTCAGA---GTTTTGACATCTTGAAA 357367 i iv ii i v --- v i v MER58C#DNA/hA 51 TTTTGTACGGCCCGCGAGCTAAGAATGGTTTTTACATTTTTAAA 94 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 18.24 CpG sites = 15, Kimura (unadjusted) = 31.86 Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.01 (1 / 90), avg. gap size = 3.00 (3 / 1) 260 32.50 2.44 2.44 chrXptel1M 358873 358995 (641005) C L2d_3end#LINE/L2 (37) 479 357 m_b334s601i9 14023 chrXptel1M 358873 CTAAGTGCCTA-CTGTGTACCAGGTACTG-GGAATACAAAAAAAG-GCAC 358919 v ii - vv i i ii - iiv i ? ?- i i C L2d_3end#LINE 479 CTATGTGCTCAGCACTGTGCTAGGCGCTGTGGGGAACGANAAAANAGTAT 430 chrXptel1M 358920 AAGGATAAAACCTCTCACCTTAAGGAGCTTACATTCTAATGGGAGAAATG 358969 - i viii i vv i v i v i i ii C L2d_3end#LINE 429 AAG-ACATGGTCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGGAGACA 381 chrXptel1M 358970 GCATACAAACAAGTATGTGCCAATTA 358995 -- v v vii viv C L2d_3end#LINE 380 --AGACTAACACACATGAAACAATTA 357 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.46 CpG sites = 25, Kimura (unadjusted) = 45.86 Transitions / transversions = 1.79 (25/14) Gap_init rate = 0.05 (6 / 122), avg. gap size = 1.00 (6 / 6) 394 28.87 0.93 2.86 chrXptel1M 358874 358980 (641020) C L2c_3end#LINE/L2 (25) 453 349 m_b334s601i10 14023 chrXptel1M 358874 TAAGTGCCTACTGTGTACCAGGTACTGGGAATACAAAAAAAGGCACAAGG 358923 i i i i ii i -- i v v i - C L2c_3end#LINE 453 TGAGCGCCTACTATGTGCCAGGCGCTGGGGATAC--AAAGATGAATAA-G 407 chrXptel1M 358924 ATAAAACCTCTCACCTTAAGGAGCTTACATTCTAATGGGAGAAAT-GGCA 358972 i viii i vv i i v i ii i i- i C L2c_3end#LINE 406 ACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAGTGGAGGAGACAGACA 357 chrXptel1M 358973 TACAAACA 358980 ?ii C L2c_3end#LINE 356 NGTAAACA 349 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.83 CpG sites = 24, Kimura (unadjusted) = 40.24 Transitions / transversions = 4.00 (24/6) Gap_init rate = 0.04 (4 / 106), avg. gap size = 1.00 (4 / 4) 200 32.87 5.23 2.55 chrXptel1M 359051 359203 (640797) C L2b_3end#LINE/L2 (260) 206 50 m_b334s601i11 14023 chrXptel1M 359051 CCTATAGGAGGA--AGGAA---GTCAGGAGGCAGAGATGAGAAGGGGCAG 359095 iv v -- i--- i v i- i i i i i- C L2b_3end#LINE 206 CCTGAAGGATGAGTAGGAGTTGGCCAGGCGA-AGAGGTGGGGAAGGGCG- 159 chrXptel1M 359096 CATTCCAGGCCCGAAGAACAATCCGTGAGAATGGCCAGACTTGGGAGAT- 359144 -- vviii iiv? vi v v v vvi ?v- C L2b_3end#LINE 158 --TTCCAGGCAGAGGGAACAGCANGTGCAAAGGCCCTGAGGCGGGAGNGA 111 chrXptel1M 359145 CCAGGGATTTTTTGAGCAATAATGAGGACGTCAGTGTCACTGG-GTGGAA 359193 v ?v vv v i v i iii v i vi - ii i C L2b_3end#LINE 110 GCNTGGCGTGTTCGAGGAACAGCAAGGAGGCCAGTGTGGCTGGAGCAGAG 61 chrXptel1M 359194 -GAGCACAGGG 359203 - vi C L2b_3end#LINE 60 TGAGCAAGGGG 50 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.01 CpG sites = 27, Kimura (unadjusted) = 45.72 Transitions / transversions = 1.23 (27/22) Gap_init rate = 0.05 (8 / 152), avg. gap size = 1.50 (12 / 8) 445 33.54 13.89 2.08 chrXptel1M 359086 359560 (640440) C L2#LINE/L2 (0) 3082 2553 m_b334s601i12 14023 chrXptel1M 359086 GAAGGGGCAGCATTCCAGGCCCGAAGAACAATCCGTGAGAATGGCCAGAC 359135 ii iiv i vviii iivv vi v v v v C L2#LINE/L2 3082 GGGGGAAGAGCGTTCCAGGCAGAGGGAACAGCAAGTGCAAAGGCCCTGAG 3033 chrXptel1M 359136 TTGGGAG-ATCCAGGGATTTTTTGAGCAATAATGAGGACGTCAGTGTCAC 359184 vi -i v vv vv v i v i iii v i vi C L2#LINE/L2 3032 GCGGGAGCGTGCCTGGCGTGTTCGAGGAACAGCAAGGAGGCCAGTGTGGC 2983 chrXptel1M 359185 TGG-GTGGAA-GAGCACAGGGCTCTTGATGATGG-AAAACATAAGA--AG 359229 - i i- ivi ----- vii - ii v i i-- C L2#LINE/L2 2982 TGGAGCGGAGTGAGCGAGGGG-----GAGAGTGGTAGGAGATGAGGTCAG 2938 chrXptel1M 359230 AGTGGGAAGGCAGGA---GA----GTTGGGTTATGAATGCCAAACAGAGC 359272 v v v vi --- ---- v iiv v v vvvvi v C L2#LINE/L2 2937 AGAGGTAACGGGGGACCAGATCATGTAGGGCCTTGTAGGCCATTGTAAGG 2888 chrXptel1M 359273 AGTTTTGTATTTGATCCTGGAGGTG-GATAAGAAGCCCCTGGAG--TTGA 359319 v v i- v ii i-- - ii vi -- -- C L2#LINE/L2 2887 ACTTTGGC-TTTTACTCTGA--GTGAGATGGGAAGCCATTGGAGGGTT-- 2843 chrXptel1M 359320 CTGAGTAGAAAGATGGCATGGTAGGAACTATACTTTAGGAAGATCACT-- 359367 i i iiii i i vv vi iii ii i -- C L2#LINE/L2 2842 TTGAGCAGAGGAGTGACATGATCTGACTTACGTTTTAAAAGGATCACTCT 2793 chrXptel1M 359368 ----------TTAAGA---GACTGCAA-----------TGAAAACAGG-- 359391 ---------- i --- ? i----------- i i -- C L2#LINE/L2 2792 GGCTGCTGTGTTGAGAATAGACTGNAGGGGGGCAAGGGTGGAAGCAGGGA 2743 chrXptel1M 359392 --CTGGT---------ATAGCAATGATCTAGGTGTGAAGTGATGGGGATT 359430 -- ii --------- v i i i i v ii v ii C L2#LINE/L2 2742 GACCAGTTAGGAGGCTATTGCAGTAATCCAGGCGAGAGATGATGGTGGCT 2693 chrXptel1M 359431 TGTACCAGGGTGGGGGCAGGGTCAGAGGAGAAAAGGGGAGTGTATTCAAG 359480 v v v vvi v v i v -vi v vi C L2#LINE/L2 2692 TGGACCAGGGTGGTGGCAGTGGAGGTGGTGAGAAGTGG-TCGGATTCTGG 2644 chrXptel1M 359481 ATATGCTGCACAGGTGACACTGACAA-----GCC------TTGGATATTG 359519 ii viiv iivi i i----- i------ i v C L2#LINE/L2 2643 ATATATTTTGAAGGTAGAGCCGACAGGATTTGCTGATGGATTGGATGTGG 2594 chrXptel1M 359520 GAGGTGAGAAAGAGTGAGGAGGCCAGGATGGTTCCTAGGTT 359560 iv i i v v v ii v C L2#LINE/L2 2593 GGTGTGAGAGAAAGAGAGGAGTCAAGGATGACTCCAAGGTT 2553 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.25 CpG sites = 90, Kimura (unadjusted) = 46.28 Transitions / transversions = 1.36 (90/66) Gap_init rate = 0.06 (28 / 474), avg. gap size = 2.75 (77 / 28) 362 26.80 1.29 1.29 chrXptel1M 359641 359795 (640205) L1M5_orf2#LINE/L1 3133 3287 (7) m_b334s551i8 14024 chrXptel1M 359641 TCTGATAAAGGCCTCATTTCTAAAATATATAGAGAATTGATTCAAATTTA 359690 i v i v i i i i vv v ? iv L1M5_orf2#LIN 3133 TCTGACAAAGGACTCGTATCCAGAATATATAAAGAACTCCTACAANTCAA 3182 chrXptel1M 359691 TAAGAACTCAAGCCATTC--TCCAATTGATAAATGGTCAAAGGATATGAA 359738 ? v-- v vv --i v? v v i iv L1M5_orf2#LIN 3183 TAANAAA--AAGACAAACAACCCAATANAAAAATGGGCAAAAGACTTGAA 3230 chrXptel1M 359739 CAGACAATTCTCAGAAGAAGAAATTGAAACCATTTCTACTCATATGAAAA 359788 v v i v ?v iviiivv vv i L1M5_orf2#LIN 3231 CAGACACTTCACAAAAGAAGATATNCAAATGGCCAATAAGCACATGAAAA 3280 chrXptel1M 359789 AGTGCTC 359795 ii L1M5_orf2#LIN 3281 GATGCTC 3287 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 33.45 CpG sites = 18, Kimura (unadjusted) = 34.44 Transitions / transversions = 0.78 (18/23) Gap_init rate = 0.02 (3 / 154), avg. gap size = 1.33 (4 / 3) 1316 28.73 3.14 3.14 chrXptel1M 359659 360294 (639706) L1ME5_3end#LINE/L1 7 642 (299) m_b334s551i10 14024 chrXptel1M 359659 TCTAAAATATATAGAGAATTGATTCAAATTTATAAGAACTCAAGCCATT- 359707 i i ii i vv v iv i v-- v iv?- L1ME5_3end#LI 7 TCTAGAATATACAAGGAACTCCTGCAAATCAACAAGAAA--AAGACGGNA 54 chrXptel1M 359708 -CTCCAATTGATAAATGGTCAAAGGATATGAACAGACAATTCTCAGAAGA 359756 - i v v v i iv L1ME5_3end#LI 55 ACCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGA 104 chrXptel1M 359757 AGAAATTGAAACCATTTCTACTCATATGAAAAAGTGCTCTAAATTACTAT 359806 i iivi vvii vvi vv i ii v v i i v L1ME5_3end#LI 105 GGAAACCCGAAAGGCTAACAAGCATATGAAGAGATGCTCAAACTCATTAG 154 chrXptel1M 359807 TGATCAGAAAAATGCAAATTAAGACAACTCTGAGATACCACTACACACCT 359856 i i i vv i vi L1ME5_3end#LI 155 TAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCT 204 chrXptel1M 359857 GTCAGACTGGCTAAGATGACAGGAAAA---GACAATGATGGATGTTGGAG 359903 i i v i v --- i--- i viiii v L1ME5_3end#LI 205 ATTAGACTGGCAAAAATTA---GAAAGCTGGATAATGCCAAGTGTTGGCG 251 chrXptel1M 359904 GGGATGTGGGAAAACTGGGACACTGACGCATTGTTGGTGGAACTGTGAAT 359953 i i ? iv i v v i i i i v ii i L1ME5_3end#LI 252 AGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGAC 301 chrXptel1M 359954 ACATGCAACCATTCTGGAGAGCAATGTGGAATTA--TGCTCAAAAAGTTA 360001 vvi i v v v -- iv --- L1ME5_3end#LI 302 TGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAA---TTA 348 chrXptel1M 360002 TCAGACTGTGCATACCCT-TGATCCAGCAGTGCTACTACTGGGCTTATAC 360050 -- vv ii - i i v ii v iv i L1ME5_3end#LI 349 --AGTATACGCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATAT 396 chrXptel1M 360051 TCCAAAGAGATACTAAAGGAGG---GAAAGGGACCCACATGTGCAAAAAT 360097 i i v v viv ---iv i--- i i ii L1ME5_3end#LI 397 CCCAAAGAAATTCTCACACAGGTCCATAAGGGG---ACATGTACGAGGAT 443 chrXptel1M 360098 GTGTGTGGCAGCCCT-TTTGTAGTGGCCAGAAACTGGA---AACCGAGTG 360143 vii v vi - i vi i ii --- --- L1ME5_3end#LI 444 GTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACC---TG 490 chrXptel1M 360144 GATGCCCATCAGCTGGG-GAATGGCTGAATAAGTTATGGGATATGAATGT 360192 i i - - i v iii iv i viv v iii L1ME5_3end#LI 491 GGTGTCCATCA-CTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACAC 539 chrXptel1M 360193 TAGGGAATATTATTGTTGT-GTAAGAAATGACCAACAGGATGAATACAGA 360241 i v i i - iv i- v iii vi vi v i v L1ME5_3end#LI 540 CATGGAGTACTAT-GCAGCAGTTAGAAGCAACGGACTAGATGTACACATA 588 chrXptel1M 360242 GAGGCTTGGAGAGA-CTTACATGAACGGA-TGCCGAGTGAAATGAGC-AG 360288 vii v vi - v -- iv - i vi i- L1ME5_3end#LI 589 GCAACATGGATGGATCTTAAA--AACATAGTGCTGAGTGAAAAAAGTAAG 636 chrXptel1M 360289 AACCAG 360294 v L1ME5_3end#LI 637 AAACAG 642 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.10 CpG sites = 106, Kimura (unadjusted) = 37.47 Transitions / transversions = 1.49 (106/71) Gap_init rate = 0.05 (33 / 635), avg. gap size = 1.21 (40 / 33) 1366 27.96 1.65 2.58 chrXptel1M 359659 360205 (639795) L1ME3Cz_3end#LINE/L1 7 548 (449) m_b334s551i9 14024 chrXptel1M 359659 TCTAAAATATATAGAGAATTGATTCAAATTTATAAGAACTCAAGCCATTC 359708 i i i i vv v iv v-- v --v L1ME3Cz_3end# 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAA--AAGACA--A 52 chrXptel1M 359709 TCCAATTGATAAATGGTCAAAGGATATGAACAGACAATTCTCAGAAGAAG 359758 i v v v i v i L1ME3Cz_3end# 53 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chrXptel1M 359759 AAATTGAAACCATTTCTACTCATATGAAAAAGTGCTCTAAATTACTATTG 359808 iivi iviiivv vv ii v vv i v i L1ME3Cz_3end# 103 AAACCCGAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTA 152 chrXptel1M 359809 ATCAGAAAAATGCAAATTAAGACAACTCTGAGATACCACTACACACCTGT 359858 ii i ? vv i v ii L1ME3Cz_3end# 153 ATCAGGGAAATGCAAATTAAAACNACAATGAGATACCATTTCACACCCAT 202 chrXptel1M 359859 CAGACTGGCTAAGATGACAGGAAAA----GACAATGATGGATGTTGGAGG 359904 i v i ----vv ---- iviiii v i L1ME3Cz_3end# 203 CAGATTGGCAAAAAT----TTAAAAGTCTGACAATACCAAGTGTTGGCGA 248 chrXptel1M 359905 GGATGTGGGAAAACTGGGACACTGACGCATTGTTGGTGGAACTGTGAATA 359954 ii v i v v ii i i i v i v L1ME3Cz_3end# 249 GGATGTGGAGAAACGGGAACTCTCATACACTGCTGGTGGGAGTGTAAATT 298 chrXptel1M 359955 CATGCAACCATTCTGGAGAGCAATGTGGAATTATGCTCAAAAAGTTATCA 360004 vi i i i v v v - viv i-v L1ME3Cz_3end# 299 GGTACAACCACTTTGGAGAGCAATTTGGCAATAT-CTAGTAAAGTTG-AA 346 chrXptel1M 360005 GACTGTGCATACCCT-TGATCCAGCAGTGCTACTACTGGGCTTATACTCC 360053 - i -i i i v i v i iv i i L1ME3Cz_3end# 347 GA-TGCGCATACCCTACGACCCAGCAATTCCACTTCTAGGTATATACCCT 395 chrXptel1M 360054 AAAGAGATACT---AAAGGAGGGAAAGGGACCCACATGTGCAAAAATGTG 360100 i i iv --- v v v viv ii--- i ii v L1ME3Cz_3end# 396 AGAGAAACTCTCGCACATGTGCACAAGGAG---ACATGTACAAGGATGTT 442 chrXptel1M 360101 TGTGGCAGCCCT-TTTGTAGTGGCCAGAAACTGGAAACCGAGTGGATGCC 360149 ii v vi - i i v i i vivv ii i L1ME3Cz_3end# 443 CATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTC 492 chrXptel1M 360150 CATCAGCTGGGGAATGGCTGAATAAGTTATGGGATATGAATGTTAGGGAA 360199 iiv v i i i v vv iiv v L1ME3Cz_3end# 493 CATCAATAGGGGAATGGATAAATAAATTGTGGTATATTCATACAATGGAA 542 chrXptel1M 360200 TATTAT 360205 i L1ME3Cz_3end# 543 TACTAT 548 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.96 CpG sites = 85, Kimura (unadjusted) = 35.86 Transitions / transversions = 1.33 (85/64) Gap_init rate = 0.03 (18 / 546), avg. gap size = 1.28 (23 / 18) 446 30.92 12.99 2.35 chrXptel1M 360750 361057 (638943) C L2#LINE/L2 (624) 2458 2119 m_b334s601i13 14023 chrXptel1M 360750 GTTTTAGATATGTTGAAATTAAGATG------GGACATCCAATTCATGAT 360793 i i i iv i ------i v viv C L2#LINE/L2 2458 GTTTTGGACATGTTAAGTTTGAGATGCCTATTAGACATCCAAGTGGAGAT 2409 chrXptel1M 360794 TTCATGATATCCAAGTTAGAGATGTGAGATTGTCCCACAGAGAAGACAGA 360843 v iv - vv - i v ii vi vvviv i i vivv C L2#LINE/L2 2408 GTCGAG-TAGGCA-GTTGGATATACGAGTCTGGAGTTCAGGGGAGAGGTC 2361 chrXptel1M 360844 GGGGTTTGGGATCTGAGTGGATCTGAGA---ATCAGCACAGAAGTAATA- 360889 v i v i v i ---- i i --- i v ii ii - C L2#LINE/L2 2360 CGGGCTGGAGATATAA----ATTTGGGAGTCATCAGCATATAGATGGTAT 2315 chrXptel1M 360890 ---AGTCCATGCCATCTTATGAGGCTACCAAGT-----AGTACAGAGAGA 360931 --- iv vv iivv iii ? v----- ii v C L2#LINE/L2 2314 TTAAAGCCATGAGACTGGATGAGATCACCNAGGGAGTGAGTGTAGATAGA 2265 chrXptel1M 360932 GAAGCAAAGAACCCCGAAGGACT-------------CTCCC-CATTAGTA 360967 vi ivi - ------------- v- i ?iv C L2#LINE/L2 2264 GAAGAGAAGAGGTCC-AAGGACTGAGCCCTGGGGCACTCCAACGTTNAGA 2216 chrXptel1M 360968 GGCCTG--ACGTGAAGAT---CCAGCAAAGGAGACTGGG---GAGCCACC 361009 i v -- vi i v--- i --- vi C L2#LINE/L2 2215 GGTCGGGGAGATGAGGAGGAACCAGCAAAGGAGACTGAGAAGGAGCGGCC 2166 chrXptel1M 361010 ACATTGGGTAGGAGGAAAACCAGGAGAAAATGGTGGCACAAAAACAAA 361057 -i vi ivi v viii i v C L2#LINE/L2 2165 A-GTGAGGTAGGAGGAAAACCAGGAGAGTGTGGTGTCCTGGAAGCCAA 2119 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.64 CpG sites = 52, Kimura (unadjusted) = 41.38 Transitions / transversions = 1.27 (52/41) Gap_init rate = 0.06 (18 / 307), avg. gap size = 2.67 (48 / 18) 481 26.15 1.43 4.41 chrXptel1M 361708 361847 (638153) C MIRc#SINE/MIR (120) 148 13 m_b334s601i14 14025 chrXptel1M 361708 CTCATTGTACAGATGAGAAAACTGAGGT--AGACGGGGTGAAATGACTTG 361755 i v i i-- - i v i C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGA-GAGGTTAAGTGACTTG 100 chrXptel1M 361756 CTCAGGATCACATGGCTAGGAAGTGTCTGAGGCCAGTTTTGAACTCGGGA 361805 i i i ii v v v v vi vi i i ---- C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCC---- 54 chrXptel1M 361806 AGATGAGTCTTGACTGCAGGCCTGGTGCTCTGTGCACTGTGC 361847 i -vv i v i i ii v v ii C MIRc#SINE/MIR 53 AGGT-CTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCAC 13 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.94 CpG sites = 22, Kimura (unadjusted) = 33.09 Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.05 (7 / 139), avg. gap size = 1.14 (8 / 7) 665 36.32 9.01 3.60 chrXptel1M 361853 362829 (637171) C L2#LINE/L2 (1683) 1399 372 m_b334s601i15 14023 chrXptel1M 361853 AGTGTGTTAATTAGGGTGTCTTAAAAGGATTGCCTAGCAGCAACGAGGAT 361902 vi vi i viviv iv ? vi vii ii C L2#LINE/L2 1399 AGTGAATGGACTAGGGAAATGTAGTANGATTGCCGGGCAGCATTAAGGGC 1350 chrXptel1M 361903 ACTGTTGAGGTTATGTCA-CATAAATTTGGGGAAGGACCCAATCAGCAGA 361951 v vv ?- vi- i iii vii - i vi C L2#LINE/L2 1349 CCACTTGAGGTTN-GTGGTCATGAATTTAAAGTGAGACC-AGTCAGCATG 1302 chrXptel1M 361952 GTTTTGTGATTTTCTCCAG----GTTCCAGGCAACTTGCATGCGAGAGTG 361997 v v ---- --i vi ?i vi ii v i C L2#LINE/L2 1301 GTTGTGTGTTTTTCTCCAGCCACGTTC--AGCTGCNCGGGTGCAGGCGCG 1254 chrXptel1M 361998 AAGGCAACAGAAGATTGGAACAATTTTAA----GGT-GAGGTTTGGCAGG 362042 i vvii i iii ----- ---- - ? v vi C L2#LINE/L2 1253 GAGTAGGCGGAGAGTTGGA-----TTTAACCAGGGTTGNGGTTTTGCCAG 1209 chrXptel1M 362043 ACAAGATTGGTGATATGGATAAGGGGACAAAGAATTTAGGGAAGAGGACC 362092 i i vvi ii vii iivi vv ii i v v v v - v C L2#LINE/L2 1208 GCGAGTACGACGAAGCGAGAGAGGGGCAAGGGAGTTGAGGGTATATG-CA 1160 chrXptel1M 362093 AGGTAGAGTTGAGAGAACTGGTTCACCAAAGGAT-TAAGATGGG-AAAAA 362140 -- vivv v - i ?v vi i - v - ii C L2#LINE/L2 1159 AGG--GAGTGATTATAA-TGATNGACCATGGAATCTAAGCTGGGTAAGGA 1113 chrXptel1M 362141 GTATGATTAGTACACA-----GATGATTGCTTGGGAAGAAACAGAGAGGT 362185 vivii v v ii----- i vv viv v i iiii vii i C L2#LINE/L2 1112 GGGAAGTGAGGACATGAGGGGGGTGAGGGACAGTGAAAAGGTGGTAGGAT 1063 chrXptel1M 362186 TCAGGGTTTAGAGGTCATGGTATGG---AAGAGCAAAAAGGTTTGGGGT- 362231 iv v v i vi iv --- iivivvi iv i - C L2#LINE/L2 1062 CAATGGATTGGAGGTCCCGGTGGGGTCGAAGAATTGTTGGAGTCGGGGTA 1013 chrXptel1M 362232 -TGCAAGG-------CAGAATGACAACAGATTGTAATCAGATAGGGGAAT 362273 - iv i -------ii v i iv i v ii v v i C L2#LINE/L2 1012 CTAGAGGGAGTGAGCTGGAAAGATAGGAGGTGGTGGTCAGAGAGTGGGAT 963 chrXptel1M 362274 -TTTAGAGTTCATGAACATAGAGGTGGGTATACTTGTAAGTGATGGTAAA 362322 -i ii i v - vi i - v ii v i vi i ii i C L2#LINE/L2 962 GCTTGAAATTGA-GATTATGGAGG-GGTTGCAGTTATTGGTAATGACAAG 915 chrXptel1M 362323 ATCAAAGGTAGGACCATCTTTATGTGTGGCTG-----GGGTGGAGGTGAC 362367 i v i v vvvvi v ----- -- C L2#LINE/L2 914 GTCTAGGGTATGACCATGGGAGTGAGTGGCTGAGGTAGGGTGGAG--GAC 867 chrXptel1M 362368 AAGGTCATGGGAAG-TAGGAAGCTGAGTAGGTGGGAGGTTAGCATGTTTG 362416 i v i -v i iii v iv i ii vi i v C L2#LINE/L2 866 AAGATCATTGGAGGAGAGGAGGTCAAGGAACTGAGAGGCCAGGGTATTGG 817 chrXptel1M 362417 AAAGAGCATAGCTATGTAA--GCTGAAG----CGAG------GGAAGGA- 362453 i v -- i ii--ii i---- i ------ iv - C L2#LINE/L2 816 AAGGATCAT--CTACGTGGATATTGAAATCACCAAGAATTATGACAGGAG 769 chrXptel1M 362454 ----ATTGGAGAGAAAGATTATGAACCAGGTCCTGAACTCACTGAGGAAA 362499 ----i iv ivi i vv i v viii v C L2#LINE/L2 768 TAGTGTTGGAGAGAGTGACAGTGAGCCAGGAGCTAAAATCTTCAAGGAAT 719 chrXptel1M 362500 TAGAGGGAATGTCCTGGAGGCCCATCCACAGTAATTACCAGAATTTCAAT 362549 v i i v i ---- vii -- v iiv --- v C L2#LINE/L2 718 GAGGGGGAGTGACCCGGAGG----TCGGTAG--ATGACTGCAA---CAAG 678 chrXptel1M 362550 CAGATGGATCAAGTG----AATCTTAATGGTTACTTCACTCAAGGAAGGA 362595 v iv v v ii ---- i - i i-i ivvv i i vv i C L2#LINE/L2 677 GAGGGGTAGCGGGTGGTATAGTC-TGATGA-CATGAGATTCAAAGCTGGG 630 chrXptel1M 362596 A------AGGGA--AGGGAAG------ACTCTGAAAATGTTCAAGAGGAG 362631 i------ -- i ------iv i ii viv v C L2#LINE/L2 629 GTGTTTTAGGGAGGAGGGAGGGAGAATGGTCTGGAAGCGGCAATGAGGAG 580 chrXptel1M 362632 CAAGGAGAATTCCTACTCCTCTACCTCAAG---TAATGAACTGAGGGG-- 362676 i iv i --- v ---i i ivvi ?-- C L2#LINE/L2 579 CAAGGAGGACACCTACCCC---ACCTCCAGGCCCAGTGGTACGAGGGNTG 533 chrXptel1M 362677 -AGGAGTGAAAGTGCAGCTATTGATGGAAAGAG-----GGACCAGCACAT 362720 -i v --i i iiiv v i i ----- ivv -i C L2#LINE/L2 532 TGGGAGAGAAA--ACAGCCACCACTTGAGAGGGCTGCAGGGGAAGCA-GT 486 chrXptel1M 362721 GTCATCAAGAAGTAAACAGGTCTCAGTGAGTTCCAGAAGATGGATAGGAA 362770 v i iiiv iv i ? v vv v i i -i C L2#LINE/L2 485 GTCCTCAGGGGAGAGCCAGGTTTCNGTTAGAGCAAGAAGGTGAA-GGGAA 437 chrXptel1M 362771 AG------GAAAAGATTTACGATGAAACCAATTTTCTTGCTTATGGAGCA 362814 v ------ i i v v iviivvi vi v v i v i C L2#LINE/L2 436 CGTTCAGAGAAGAGGTTGAGGATACGGGGGATTTTGCTGATGACGGACCG 387 chrXptel1M 362815 AACATCCTAAAGAGC 362829 vivi i i i i C L2#LINE/L2 386 TGAGTTCCAGAGGGC 372 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 48.88 CpG sites = 202, Kimura (unadjusted) = 52.66 Transitions / transversions = 1.44 (202/140) Gap_init rate = 0.07 (65 / 976), avg. gap size = 1.92 (125 / 65) 32 17.78 2.82 0.00 chrXptel1M 363266 363336 (636664) (TCTC)n#Simple_repeat 1 73 (0) m_b334s252i3 14026 chrXptel1M 363266 TCTCTCTTTCCCTCCCTCCCTCCATCTGTCTGTCTCTCTCTCTCTCTCTC 363315 i i i i iv v v (TCTC)n#Simpl 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chrXptel1M 363316 CCCCTC-CTTTC-CTCTCTCTCT 363336 i i - i - (TCTC)n#Simpl 51 TCTCTCTCTCTCTCTCTCTCTCT 73 Matrix = Unknown Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.03 (2 / 70), avg. gap size = 1.00 (2 / 2) 221 37.98 2.33 0.00 chrXptel1M 364151 364279 (635721) C L2#LINE/L2 (387) 2695 2564 m_b334s601i16 14027 chrXptel1M 364151 GCTTGAATTAGGGTTGTGGCTGTGTAAGCAGAAAGGAGGAGATGCATATG 364200 i ii v v v i ii vi i vi vi v viv C L2#LINE/L2 2695 GCTTGGACCAGGGTGGTGGCAGTGGAGGTGGTGAGAAGTGGTCGGATTCT 2646 chrXptel1M 364201 AGAGACATTGTGAAGGAAGAAATCATCGG---TGTCAATGGTTTAGGTAT 364247 i v i v v iviv iv --- iii v i i i C L2#LINE/L2 2645 GGATATATTTTGAAGGTAGAGCCGACAGGATTTGCTGATGGATTGGATGT 2596 chrXptel1M 364248 GCAGAGTAAGGGAGAAAGTGGAATCAAGACTG 364279 vi v i i i i v i iv C L2#LINE/L2 2595 GGGGTGTGAGAGAAAGAGAGGAGTCAAGGATG 2564 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 52.27 CpG sites = 29, Kimura (unadjusted) = 55.68 Transitions / transversions = 1.45 (29/20) Gap_init rate = 0.01 (1 / 128), avg. gap size = 3.00 (3 / 1) 271 32.94 3.43 2.84 chrXptel1M 364299 364473 (635527) C L2#LINE/L2 (641) 2441 2266 m_b334s601i17 14027 chrXptel1M 364299 TTTGGGGTATGTCTATGAGATATCCAGTTCGAGATG-CGAAGGGTAAGTA 364347 i -- i v i iv v - --- i i C L2#LINE/L2 2441 TTTGAG--ATGCCTATTAGACATCCAAGTGGAGATGTCGA---GTAGGCA 2397 chrXptel1M 364348 AGTGGAGGTGCTAGACTGGAGATGAGAAGACAGGTTACAGAGGGCCAAAT 364397 iv vi i v v v v ii v ivvi vv vv v C L2#LINE/L2 2396 GTTGGATATACGAGTCTGGAGTTCAGGGGAGAGGTCCGGGCTGGAGATAT 2347 chrXptel1M 364398 AGATCTGAGA--CAGCTGCCTAAAGACCACAATTGAATCCACGCAAGTTG 364445 i i i -- v v v v ivii v i v i vi v v C L2#LINE/L2 2346 AAATTTGGGAGTCATCAGCATATAGATGGTATTTAAAGCCATGAGACTGG 2297 chrXptel1M 364446 ATAAGATCA--TACACAGCGAGC-TAGATGG 364473 i --? viv i i- i C L2#LINE/L2 2296 ATGAGATCACCNAGGGAGTGAGTGTAGATAG 2266 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.29 CpG sites = 27, Kimura (unadjusted) = 44.29 Transitions / transversions = 0.93 (27/29) Gap_init rate = 0.05 (9 / 174), avg. gap size = 1.22 (11 / 9) 500 25.70 5.63 1.35 chrXptel1M 364462 364603 (635397) MIRc#SINE/MIR 1 148 (120) m_b334s601i18 14028 chrXptel1M 364462 CGAGCTAG-ATGGCACAATCGGTAGAGTTCCAGATCTTGAATCAGGAAGA 364510 vi -i ii i v iv iv ii ii v i MIRc#SINE/MIR 1 CGAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA 50 chrXptel1M 364511 CCTGACTTC-AGATCTGGCATTGGACTCTTACTAGTTGTATGACC-TAGC 364558 iv - vi i - iv v v i i - i v MIRc#SINE/MIR 51 CCTGGGTTCGAGTCCCGGC-TCTGCCACTTACTAGCTGTGTGACCTTGGG 99 chrXptel1M 364559 CAAATTACTTAACACTTT----ACCTCAG-TTCCTCATGTGTAAAATGAG 364603 i i - i ----i - v i MIRc#SINE/MIR 100 CAAGTCACTTAAC-CTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.57 CpG sites = 24, Kimura (unadjusted) = 32.68 Transitions / transversions = 2.00 (24/12) Gap_init rate = 0.05 (7 / 141), avg. gap size = 1.43 (10 / 7) 237 29.41 1.18 0.00 chrXptel1M 364696 364780 (635220) C L1M3_orf2#LINE/L1 (1259) 2029 1944 m_b334s551i11 14029 chrXptel1M 364696 TTGCTGTTGCTAGCATTTGCAGAACTATATTGATGACTAGTGGGAGAAGT 364745 v v v i v v i vv vv viii C L1M3_orf2#LIN 2029 TTGCTCTGGCTAGGACTTCCAGTACTATGTTGAATAGAAGTGGCGAGAGT 1980 chrXptel1M 364746 GGGCATTCTTGCTTCAGTCTT-ATATTAGAAAAGAA 364780 i i iiv i - v ii i C L1M3_orf2#LIN 1979 GGGCATCCTTGCCTTGTTCCTGATCTTAGAGGAAAA 1944 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.04 CpG sites = 13, Kimura (unadjusted) = 37.92 Transitions / transversions = 1.08 (13/12) Gap_init rate = 0.01 (1 / 84), avg. gap size = 1.00 (1 / 1) 312 31.95 9.11 2.25 chrXptel1M 364854 365852 (634148) C L1M5_orf2#LINE/L1 (1448) 1846 781 m_b334s551i12 14029 chrXptel1M 364854 TTTTTAATATAAACG--TATTATATTTTGTGAAGTTTTTTTTTT-CATCT 364900 vi i i -- i iv v i vi i - C L1M5_orf2#LIN 1846 TTTTTATCATGAATGGGTGTTGAATTTTGTCAAATGCTTTTTCTGCATCT 1797 chrXptel1M 364901 GTTGAGATAACCATGTGATTTTT------TACACTGT-------GCTAAT 364937 i i i i ------ iv ------- iv C L1M5_orf2#LIN 1796 ATTGAGATGATCATATGATTTTTCTCCTTTATTCTGTTAATATGGTGAAT 1747 chrXptel1M 364938 TATGTTAATTATTTCCTTGATGTCAAACCATTCT--CATACCTCTCTTAT 364985 ii i iv iiivi i vi -- v vvvv v C L1M5_orf2#LIN 1746 TACATTGATTGATTTTCGAATGTTAAACCAACCTTGCATTCCTGGGATAA 1697 chrXptel1M 364986 ATTTTATCTGGTCATATTGGATGATCTCTTAGATAAATCACTATACTCTG 365035 iiii ii iv v v ii vv v ii iv i vi C L1M5_orf2#LIN 1696 ACCCCACTTGGTCATGATGTATTATCCTTTTTATATATTGCTGGATTCGA 1647 chrXptel1M 365036 TACAATGAGATTTTGTTGAAAAAGTTTGAGACAATTTTTATTAATTATAT 365085 viiv i v ? ii vv viv v v i v ivv C L1M5_orf2#LIN 1646 TTTGCTAATATTTTGTTNAGGATTTTTGCATCTATGTTCATGAGGGATAT 1597 chrXptel1M 365086 TGGCTTACAATTTCCTTTCTGTGTTTTAAATTTCCCTGGCCAA------- 365128 ii ii i iiv ---- v ii v ?ii------- C L1M5_orf2#LIN 1596 TGGTCTGTAATTTTCTTTTCTTGT----AATGTCTTTGTCNGGTTTTGGT 1551 chrXptel1M 365129 ---AGGATAAGTACTTTCTCTCATAAAAGGAGTTTGGTAGGGTGCTTTAT 365175 --- i ? - i vv - v v v v v ii v C L1M5_orf2#LIN 1550 ATCAGGGTNA-TGCTGGC-CTCATAAAATGAGTTGGGAAGTGTTCCCTCT 1503 chrXptel1M 365176 TTCTCAACTTTTGAGGATAATTTGTGAAGCATGAGTTCTAACTGTTCTTT 365225 i v i ivi i v i v iv vi vi vi v i C L1M5_orf2#LIN 1502 TTTTCTATTTTCTGGAAGAGTTTGTGTAAGATTGGTATTATTTCTTCCTT 1453 chrXptel1M 365226 AAA-GTCTGATAGAAT--ACT-GTGAATCCTTC-AGGCCTGGGAATTTTG 365270 - i i -- i- v v -i i------ C L1M5_orf2#LIN 1452 AAATGTTTGGTAGAATTCACCAGTGAAGCCATCTGGGCCTGGA------G 1409 chrXptel1M 365271 TTTTCCTT-TGGTA--GTTCCCTTAATGCTAGGTCTGTTTTCTTTTCTGA 365317 i - v -- --i vvi ii iiiv vv - C L1M5_orf2#LIN 1408 TTTTCTTTGTGGGAAGGTT--TTTAATTACAAATTCAATTTCTTTAAT-A 1362 chrXptel1M 365318 GGT-TAGG--TATTTAAAATCTTTATCTCATCTTCTGATAATCTGGGTGT 365364 i - -- i i v i i i v v? vi i i v iv C L1M5_orf2#LIN 1361 GATATAGGGCTATTCAGATTTTCTATTTCTTCTTGNGTCAGTTTTGGTAA 1312 chrXptel1M 365365 TTTATATTTTGGAAGGTATTCTTCTATTTCTTTTGTATTCTCA------- 365407 ? i i vv v iv i v i ivi ? ------- C L1M5_orf2#LIN 1311 NTTGTGTTTTTCAAGGAATTTGTCCATTTCATCTAAGTTNTCAAATTTAT 1262 chrXptel1M 365408 --GTATGTAGCTGTACATAATG-TGTCCTATTAACCTTTTAATTTCTTCA 365454 -- i iv i v i- v i v v vi C L1M5_orf2#LIN 1261 TGGCATAAAGTTGTTCATAATATTCTCTTATTATCCTTTTAATGTCTGTA 1212 chrXptel1M 365455 AGTATTGGCTGTGATGTCACCTTGCTCATATGCT-ATGCCCTTGATTTGA 365503 i - iv iv v vi - v - iiivv i - C L1M5_orf2#LIN 1211 GG-ATCTGTAGTGATGTCTCCTTTTTCAT-TCCTGATATTGGTAATTTG- 1165 chrXptel1M 365504 TTTTCTGCTCTCTTCTTTCTATTCAT-ATTAGCTTTG-TGAAGGTTTATC 365551 - v v i ---- v - i ii ? - ii C L1M5_orf2#LIN 1164 -TGTCTTCTCTCTTTTT----TTCTTGATCAGTCTNGCTAGAGGTTTATC 1120 chrXptel1M 365552 AATTTCATGAGTTTTTGCCAAGCACCAACTACTAAA--AGTTGA----AT 365595 i vii i v v v i vi iiv--v ----v C L1M5_orf2#LIN 1119 AATTTTATTGATCTTTTCAAAGAACCAGCTTTTGGCTTCGTTGATTTTCT 1070 chrXptel1M 365596 GTATCACTTCCTTGGTTTC----CCATTCATTTC----CCTA-----ATT 365632 v iii? ?i v ----i v ---- i ----- C L1M5_orf2#LIN 1069 CTATTGTNTNTTTGTTTTCTATTTCATTGATTTCTGCTCTTATCTTTATT 1020 chrXptel1M 365633 -TCTCCTCTTTTGTGCTTATTTTCGGTTTGCTTATTTGTTGATTCTTTAA 365681 - i iii v i ?i v iv vvi v vv i i i C L1M5_orf2#LIN 1019 ATTTCCTTCCTTCTACTTNCTTTGGGTTTAATTTGCTCTTCTTTTTCTAG 970 chrXptel1M 365682 TTTTAAAAAGTACA----TAGTTCATGGGTCTTCTCTTTTTCTATTTTGT 365727 i ivv i iv ---- v v i i vvvii vi vi C L1M5_orf2#LIN 969 CTTCTTAAGGTGGAAGCTTAGATCATTGATTTTAAGCCTTTCTTCTTTTC 920 chrXptel1M 365728 TAATGTATTCTTATAAGGATATGATTTTCACCTTAAGGACTATTTTAG-- 365775 i ?v v v ? v i v v ii v ii -- C L1M5_orf2#LIN 919 TAATATANGCATTTAANGCTATAAATTTCCCTCTAAGCACTGCTTTAGCT 870 chrXptel1M 365776 ---------AAATTCTGGCATATTGTTTCATCATTAACATTTTTCTTTTA 365816 --------- i ii i v iv ?v - ivv iv C L1M5_orf2#LIN 869 GCATCCCACAAATTTTGATATGTTGTATTTTCATTNTCA-TTCAGTTCAA 821 chrXptel1M 365817 CATAGTTATT-ATTTC---TACGATTTGTTCTTTGATCTA 365852 v v vi - --- ii v i i C L1M5_orf2#LIN 820 AATATTTTCTAATTTCCNTTGTGATTTCTTCTTTGACCCA 781 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 43.48 CpG sites = 175, Kimura (unadjusted) = 43.67 Transitions / transversions = 1.28 (175/137) Gap_init rate = 0.06 (56 / 998), avg. gap size = 2.05 (115 / 56) 424 32.30 6.73 3.46 chrXptel1M 364854 365581 (634419) C L1M3_orf2#LINE/L1 (1448) 1840 1090 m_b334s551i13 14029 chrXptel1M 364854 TTTTTAATATAAACG--TATTATATTTTGTGAAGTTTTTTTTTT-CATCT 364900 vi i v -- i iv v i vi i - C L1M3_orf2#LIN 1840 TTTTTATCATGAAAGGATGTTGAATTTTGTCAAATGCTTTTTCTGCATCT 1791 chrXptel1M 364901 GTTGAGATAACCATGTGATTTTT----TACACTGTGCTAAT--------- 364937 i i i ---- v i v i --------- C L1M3_orf2#LIN 1790 ATTGAGATGATCATGTGATTTTTATCCTTCATTCTGTTAATGTGGTGTAT 1741 chrXptel1M 364938 TATGTTAATT-ATTTCCTTGATGTCAAACCATTCTCATACCTCTCTTATA 364986 i ii ? - ? v - ii i iii i i vvvv C L1M3_orf2#LIN 1740 CACATTNATTGATTTNCGT-ATGTTGAACCATCCTTGCATCCCAGGGATA 1692 chrXptel1M 364987 --TTTTATCTGGTCATATTGGATGATCTCTTAGATAAATCACTATACTCT 365034 -- iii ii iv v ii vi iviiiii iv i v C L1M3_orf2#LIN 1691 AATCCCACTTGGTCATGGTGTATGATCCTTTTAATGTGCTGTTGAATTCG 1642 chrXptel1M 365035 GTACAATGAGATTTTGTTGAAAAAGTTTGAGACAATTTTTATTAATTATA 365084 viiv iiv ii vv viv v v i i ivv C L1M3_orf2#LIN 1641 GTTTGCTAGTATTTTGTTGAGGATTTTTGCATCTATGTTCATCAGGGATA 1592 chrXptel1M 365085 TTGGCTTACAATTTCCTTTCTGTGTTTTAAATTTCCCTGGCC-----A-A 365128 i ii i i iiv vv ivv vi i----- -v C L1M3_orf2#LIN 1591 TTGGCCTGTAGTTTTCTTTTCTTGTAGTGTCTTTGTCTGGCTTTGGTATC 1542 chrXptel1M 365129 AGGATAAGTACTTTCTCTCATAAAAGGAGTTTGGTAGGGTGCTTTATTTC 365178 i - i vv - v v v v ii vi ii C L1M3_orf2#LIN 1541 AGGGTAA-TGCTGGC-CTCATAAAATGAGTTTGGAAGTGTTCCCTCCTCT 1494 chrXptel1M 365179 TCAACTTTTGAGGATAATTTGTGAAGCATGAGTTCTAACTGTTCTTTAAA 365228 i vi i v i v v vi vi i v C L1M3_orf2#LIN 1493 TCAATTTTTTGGAAGAGTTTGAGAAGGATTGGTATTAATTCTTCTTTAAA 1444 chrXptel1M 365229 -GTCTGATAGAAT--ACT-GTGAATCCTTCAGGCCTGGGAATTTTGTTTT 365274 - i i -- i- v v v i iv iv v - C L1M3_orf2#LIN 1443 TGTTTGGTAGAATTCACCAGTGAAGCCATCTGGTCCTGGGCTTTTCTTT- 1395 chrXptel1M 365275 CCTTTGGTAGTTCCCTTAATGCTAGGTCTGTTTTCTT-TTCTGAGGTTA- 365322 --v v v iii v v i iiv vi i i -i ---- - C L1M3_orf2#LIN 1394 --GTTGGGAGGTTTTTGATTACTGATTCAATCTCCTTACTC----GTTAT 1351 chrXptel1M 365323 -GG--TATTTAAAATCTTTATCTCATCTTC-TGAT--AATCTGGGT--GT 365364 - -- i i i v i i i--- - -- i v -- C L1M3_orf2#LIN 1350 TGGTCTGTTCAGATTTTCTATT---TCTTCATGATTCAGTCTTGGTAGGT 1304 chrXptel1M 365365 TTTATATTTTGGAAGGTATTCTTCTATTTCTTTTG---TATTC------T 365405 v i iv-- v iv i i i--- i ------ C L1M3_orf2#LIN 1303 TGTATGTTTCT--AGGAATTTATCCATTTCTTCTAGGTTATCCAATTTGT 1256 chrXptel1M 365406 CAGTATGTAGCTGTACATAAT-GTGTCCTATTAACCTTTTAATTTCTTCA 365454 ii ii i ii v i - v i v v v vi- C L1M3_orf2#LIN 1255 TGGCGTATAATTGTTCATAGTAGTCTCTTATGATCCTTTTTATTTCTGT- 1207 chrXptel1M 365455 AGTATTGGCTGTGATGTCACCTTGCTCATATGCTATGCCCTTGATTTGAT 365504 i i ii i i v ivi v viv viiv v - C L1M3_orf2#LIN 1206 GGCATCAGTTGTAATGTCTCCTCTTTCATTTCTGATTTTATTTATTTGA- 1158 chrXptel1M 365505 TTTCTGCTCTCTTCTTTCTATTCATATTAGCTTTGTGAAGGTTTATCAAT 365554 -v v i i ii v ---- ---- i i C L1M3_orf2#LIN 1157 -GTCTTCTCTTTTTTTCTTAGTC----TAGC----TAAAGGTTTGTCAAT 1117 chrXptel1M 365555 TTCATGAGTTTTTGCCAAGCACCAACT 365581 ii vvi i v v iv C L1M3_orf2#LIN 1116 TTTGTTTATCTTTTCAAAAAACCAACT 1090 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 43.78 CpG sites = 136, Kimura (unadjusted) = 44.08 Transitions / transversions = 1.49 (136/91) Gap_init rate = 0.06 (46 / 727), avg. gap size = 1.63 (75 / 46) 343 33.25 2.17 5.86 chrXptel1M 366155 366384 (633616) C L2#LINE/L2 (601) 2481 2260 m_b334s601i19 14030 chrXptel1M 366155 TAAGGGAGAAAGT--GGAATCAAGGTTGTGAACGTTGACGAATTTGTTTT 366202 i i ii -- i iv v - i i ------i viv C L2#LINE/L2 2481 TGAGGGGGAAGATCAGGAGTTCAGTTT-TGGACAT------GTTAAGTTT 2439 chrXptel1M 366203 GGGGTATGTCTATGAGATATCCAGTTCGAGATG-CGAAGGGGTAAGTAAG 366251 i -- i v i iv v - ---- i i iv C L2#LINE/L2 2438 GAG--ATGCCTATTAGACATCCAAGTGGAGATGTCGA----GTAGGCAGT 2395 chrXptel1M 366252 TGGAGGTGCTAGACTGGAGATGAGAAGACAGGTTACAGAGGGCCAAATAG 366301 vi i v v v v ii v ivvi vv vv v i C L2#LINE/L2 2394 TGGATATACGAGTCTGGAGTTCAGGGGAGAGGTCCGGGCTGGAGATATAA 2345 chrXptel1M 366302 ATCTGAGA--CAGCTGCCTAAAGACCACAATTGAATCCACGCAAGTTGAT 366349 i i -- v v v v ivii v i v i vi v v C L2#LINE/L2 2344 ATTTGGGAGTCATCAGCATATAGATGGTATTTAAAGCCATGAGACTGGAT 2295 chrXptel1M 366350 AAGACCACCCAATGAAGGAGTATAGAGGGAGAAGA 366384 i i ? iv iv i vi C L2#LINE/L2 2294 GAGATCACCNAGGGAGTGAGTGTAGATAGAGAAGA 2260 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.04 CpG sites = 38, Kimura (unadjusted) = 45.04 Transitions / transversions = 1.12 (38/34) Gap_init rate = 0.07 (16 / 229), avg. gap size = 1.12 (18 / 16) 422 30.29 15.35 1.54 chrXptel1M 366552 366779 (633221) MIR#SINE/MIR 4 262 (0) m_b334s601i20 14031 chrXptel1M 366552 GTATAGTGGAGTGACTGCCAGACC-TGGGTTTAGGA---AGATCTTCCCA 366597 iiv ii i-- v -i i iv --- - v ii MIR#SINE/MIR 4 GTATAGCATAGTGGTTA--AGAGCACGGGCTCTGGAGCCAGA-CTGCCTG 50 chrXptel1M 366598 AATTCAAATTTAGCCTCAGGCCATT------CTG---AACTGTGATCAAG 366638 ii i iiv v -v i ------ ---i iv iv MIR#SINE/MIR 51 GGTTCGAATCCCGGCTC-TGCCACTTACTAGCTGTGTGACCTTGGGCAAG 99 chrXptel1M 366639 CCATTTAACCTTTGTCTGCTTCAGGCTCCTCATGCAGAAAATGAAAATAC 366688 ii i i v v i vi viiv iii v MIR#SINE/MIR 100 TTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAA 149 chrXptel1M 366689 TACTAATTCCTACATCCTAA---TGAAATGAGGATTAA----------AC 366725 v i v v v i--- vvi ---------- MIR#SINE/MIR 150 TAATAGTACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATAC 199 chrXptel1M 366726 ACGT-----GCTTAACACTGCGTCTGACACCTAGT----GTTATAAAAAT 366766 i ----- iv v i i i v ---- i vv v MIR#SINE/MIR 200 ATGTAAAGCGCTTAGAACAGTGCCTGGCACATAGTAAGCGCTCAATAAAT 249 chrXptel1M 366767 GTTAGCTGTTGTT 366779 i i MIR#SINE/MIR 250 GTTAGCTATTATT 262 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.69 CpG sites = 41, Kimura (unadjusted) = 40.23 Transitions / transversions = 1.52 (41/27) Gap_init rate = 0.05 (12 / 227), avg. gap size = 3.25 (39 / 12) 217 33.41 0.00 4.76 chrXptel1M 366881 366968 (633032) C L2a_3end#LINE/L2 (0) 517 434 m_b334s601i21 14032 chrXptel1M 366881 ATTCAGTCCAGTCCCTAAGTATTTATCAAAGACTTCCTATGTTCTTGGCG 366930 - i v vvi i ii ivi i v v iv i C L2a_3end#LINE 517 ATTCA-TTCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCA 469 chrXptel1M 366931 GTTTCCTAAATGCTGGGGAGAGAGGTACAATGAATCAA 366968 v v i iii v v --- i iv C L2a_3end#LINE 468 CTGTTCTAGGCGCTGGGGATACAG---CAGTGAACAAA 434 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 41.20 CpG sites = 16, Kimura (unadjusted) = 45.51 Transitions / transversions = 1.33 (16/12) Gap_init rate = 0.05 (4 / 87), avg. gap size = 1.00 (4 / 4) 15 5.56 0.00 0.00 chrXptel1M 369281 369299 (630701) (T)n#Simple_repeat 1 19 (0) m_b334s252i4 14033 chrXptel1M 369281 TTCTTTTTTTTTTTTTTTT 369299 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 416 27.24 7.19 4.93 chrXptel1M 369300 369438 (630562) C MIRc#SINE/MIR (124) 144 3 m_b334s601i22 14034 chrXptel1M 369300 TTTTCCAGCTGAGGCAATTG---------GAG-TGAAATAACTTGGCCAG 369339 v v v i --------- - v i i v i C MIRc#SINE/MIR 144 TTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAA 95 chrXptel1M 369340 GGTCACACAGCCAGAAAGCGTTAAGTGTCTGAGATCAGATTTGAACTCGG 369389 i ------- v v vivi i i i i C MIRc#SINE/MIR 94 GGTCACACAGCTAG-------TAAGTGGCAGAGCCGGGACTCGAACCCAG 52 chrXptel1M 369390 CTTCTCCTGACTTCAGGACTGGTGTCCTATCCACTCTACCAAACTAGCT 369438 v ii i i v ii ii v vi v iv C MIRc#SINE/MIR 51 GTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTGCCT 3 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.37 CpG sites = 21, Kimura (unadjusted) = 34.71 Transitions / transversions = 1.40 (21/15) Gap_init rate = 0.07 (9 / 138), avg. gap size = 1.89 (17 / 9) 416 21.85 8.03 6.47 chrXptel1M 370977 371113 (628887) MIRc#SINE/MIR 10 148 (120) m_b335s601i0 14035 chrXptel1M 370977 GTGGTGCATTG-----AGTATCAGGCCTGGAGTCAGGAAGGCTCATCTTC 371021 v ----- i iii i i i -------- MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC-------- 51 chrXptel1M 371022 CTGAGTTCAAA-CCCGGCCC---CAAACACCAGCTGTGTGACCCCAGCTG 371067 i i i- i --- vvi i iii vii MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 101 chrXptel1M 371068 AATCACTTCACCCTGTCTA--CATCAGTTTCCTCATCTGTAAAATGAG 371113 i v - v i-- v i MIRc#SINE/MIR 102 AGTCACTTAACC-TCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 25.90 CpG sites = 21, Kimura (unadjusted) = 27.02 Transitions / transversions = 3.00 (21/7) Gap_init rate = 0.10 (13 / 136), avg. gap size = 1.54 (20 / 13) 214 34.78 6.96 0.00 chrXptel1M 371242 371356 (628644) C L3#LINE/CR1 (10) 4089 3967 m_b335s601i1 14036 chrXptel1M 371242 CAGGATCTCTGAGTTGGAAGGGCCC-----GTCCATCTCATTCAG--GCC 371284 i v v ----- vi vi i i--v C L3#LINE/CR1 4089 CAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCAACCTCC 4040 chrXptel1M 371285 CACTGGAC-TATGGATCTCCTCCACCACGTTCCCAACAAGAAGTCTGCTG 371333 iivi i-i v i i i i v i i ii vi vv ii C L3#LINE/CR1 4039 CATCCAATGCAGGAATCCCTTCTACAACATCCCTGACAAGTGGTCATCCA 3990 chrXptel1M 371334 GCGACTATTTGAAGGCTTCTAGT 371356 vv ii vi i i C L3#LINE/CR1 3989 GCCTCTGCTTGAACACCTCCAGT 3967 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 49.63 CpG sites = 26, Kimura (unadjusted) = 49.63 Transitions / transversions = 1.86 (26/14) Gap_init rate = 0.03 (3 / 114), avg. gap size = 2.67 (8 / 3) 770 33.52 6.55 3.12 chrXptel1M 372807 373749 (626251) L2#LINE/L2 1957 2926 (156) m_b335s601i2 14037 chrXptel1M 372807 GCCTCTGACCTC-CCGTGCCACTAAAAGTGCCCTC-CCAAAGTCACCAGT 372854 i ii v i - iiv ii v i i-i i i L2#LINE/L2 1957 GCTTTCGTCCCCACCACTCCACCGAAACTGCTCTTGTCAAGGTCACCAAT 2006 chrXptel1M 372855 GATCTCTTAGTGGCCAAAGCCACGGGCCTTTTCTCCGTCCTCCTTCTCCT 372904 i ivv v i v vv i vv v v ii v L2#LINE/L2 2007 GACCTCCACGTTGCTAAATCCAATGGTCAATTCTCAGTCCTCATCTTACT 2056 chrXptel1M 372905 TGATCCCTCTGCAGCCTCCAACAC------TC--TCTCTCCTCCTGGATC 372946 i i? v v iii ------ -- i i v vv L2#LINE/L2 2057 TGACCTNTCAGCAGCATTTGACACAGTTGATCACTCCCTCCTTCTTGAAA 2106 chrXptel1M 372947 CCCTCTTCTCTCTAGGTTTCTGGGA-GCCTT-CTGCTCTGGGTCTGCTCC 372994 v i ii v v i ii -i vi- vii v i v L2#LINE/L2 2107 CACTTTCTTCACTTGGCTTCCAGGACACCACACTCTCCTGGTTTTCCTCC 2156 chrXptel1M 372995 TCCCTCTCAGGCTGCTCCTTCTCAGTCTCCTTTACTGGACCCTCCTCCAG 373044 v v v i i vi --- L2#LINE/L2 2157 TACCTCACTGGCCGCTCCTTCTCAGTCTCCTTTGCTGGTTCCTCCTC--- 2203 chrXptel1M 373045 ATCCTCCCCAAC-------TGTAGGTGTCCCTCAGGGCTCTGCCCTGGG- 373086 - i -------i v v v i v i v - L2#LINE/L2 2204 AT-CTCCCCGACCTCTNAACGTTGGAGTGCCCCAGGGCTCAGTCCTTGGA 2252 chrXptel1M 373087 -CTCTCTCGTTCTCCCTCTCCACTCCTTCACTAGGAGGGCTCAT-CAACC 373134 - iiiv iv v vi v ? v iv - ii L2#LINE/L2 2253 CCTCTTCTCTTCTCTATCTACACTCACTCCCTNGGTGATCTCATCCAGTC 2302 chrXptel1M 373135 CCAGAAATTCCCTTCTTCTCTGGATGCTGATGATTCTCAGCCCTACCCAT 373184 i viiv ivvv viiv iv i i ivii --i L2#LINE/L2 2303 TCATGGCTTTAAATACCATCTATATGCTGATGACTCCCAAATTTA--TAT 2350 chrXptel1M 373185 GCTCC--CCTAA--CTCTGCC--GACCTCCACTCCCTCGGCTCTGACTGA 373228 - -- iii-- v -- v vv i viivv ii -- L2#LINE/L2 2351 -CTCCAGCCCGGACCTCTCCCCTGAACTCCAGACTCGTATATCCAACT-- 2397 chrXptel1M 373229 GCTTTCCC-ACGGCTTCACCTGGATGGCCGGCAGCCATCGGAAATGGAGC 373277 i v i - iv i i v iiii v vv ivv i L2#LINE/L2 2398 GCCTACTCGACATCTCCACTTGGATGTCTAATAGGCATCTCAAACTTAAC 2447 chrXptel1M 373278 ---TCCAGCATGGAA------GTCTTTCCCCTCGAGC---CTCCCCAGAC 373315 --- iv iv ------i i i i --- i vvi L2#LINE/L2 2448 ATGTCCAAAACTGAACTCCTGATCTTCCCCCTCAAACCTGCTCCTCCCGC 2497 chrXptel1M 373316 CAACTTCCCGATGACTGAG-----GGCAACACCCTTC-TCCTGCCCCTCA 373359 viv v -- v ----- v v i - v iiv L2#LINE/L2 2498 AGTCTTCCCCAT--CTCAGTNAATGGCAACTCCATCCTTCCAGTTGCTCA 2545 chrXptel1M 373360 GGCTCACAAGCTAGAAGTTGTGCTGGA-TCCTCCCATACCTCTCGC-CCC 373407 iv v v v i ii v v - i - vi i - L2#LINE/L2 2546 GGCCAAAAACCTTGGAGTCATCCTTGACTCCTCTC-TTTCTCTCACACCC 2594 chrXptel1M 373408 CAGATCCAGGCTGTTGCCAAGGCCTGTCCGTCCCACCTCTGCAGCATCTC 373457 v iv ii iiv iv v ii i iiiv ii v L2#LINE/L2 2595 CACATCCAATCCATCAGCAAATCCTGTCGGCTCTACCTTCAAAATATATC 2644 chrXptel1M 373458 TTGGATACATCCCCTCCTCTTCCCCTGACC-CTGCC-CCACCCTGGGACA 373505 iv i v iv v i vi v -- - - vv L2#LINE/L2 2645 CAGAATCCGACCACTTCTCACCACCT--CCACTGCCACCACCCTGGTCCA 2692 chrXptel1M 373506 GCCCCTCATCGCCTCATGTCCAGACTATGGTAATAGCGTGCTAGGGGCAG 373555 iv vi ii vi i ii i iv i v v ---i -v L2#LINE/L2 2693 AGCCACCATCATCTCTCGCCTGGATTACTGCAATAGCCTCCTA---AC-T 2738 chrXptel1M 373556 GGTCTGCCTG---CCACAC--GTCTCTCTTTAGTCCAATTCGTCCTCCAT 373600 v --- v -- i i i ?i i ----- i v i L2#LINE/L2 2739 GGTCTCCCTGCTTCCACCCTTGCCCCCCTNCAGTCTA-----TTCTCAAC 2783 chrXptel1M 373601 TCAGACACCAAAGTGACTTTGCTAAAATGCAGATCTCATCACGTCACCCT 373650 v vvi i iii vi i i ii vv i i-- L2#LINE/L2 2784 ACAGCAGCCAGAGTGATCCTTTTAAAACGTAAGTCAGATCATGTCACT-- 2831 chrXptel1M 373651 CCACACCTCTGCTTAATACTTTCTCTTGG-TTCCC-TCTTACCTCCAGGA 373698 ----- i v ii ivv - - i --i ii L2#LINE/L2 2832 -----CCTCTGCTCAAAACCCTCCAATGGCTTCCCATCTCAC--TCAGAG 2874 chrXptel1M 373699 AGAAATATAAAATGCTTTGC-TTGGCGTTCAAAGCCCTTTAAAACCT-AT 373746 vi vvi i - i i -v v v i vi vi i -i L2#LINE/L2 2875 TAAAAGCCAAAGT-CCTTACAATGGCCTACAAGGCCCTACATGATCTGGT 2923 chrXptel1M 373747 CCT 373749 i L2#LINE/L2 2924 CCC 2926 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 42.83 CpG sites = 196, Kimura (unadjusted) = 46.02 Transitions / transversions = 1.35 (172/127) Gap_init rate = 0.07 (62 / 942), avg. gap size = 1.50 (93 / 62) 46 2.31 0.00 0.00 chrXptel1M 373750 373793 (626207) (AC)n#Simple_repeat 1 44 (0) c_b335s251i0 14038 chrXptel1M 373750 ACACACACACACACACACACACACACACAGACACACACACACAC 373793 v (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACAC 44 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 770 33.52 6.55 3.12 chrXptel1M 373794 373933 (626067) L2#LINE/L2 2927 3075 (7) m_b335s601i2 14037 chrXptel1M 373794 TTTT-CCACTCT-------TCTAACACCTGACTCCCCAAAATATACTATT 373835 iv - v ------- vvi vvv vvviivi -ii L2#LINE/L2 2927 CGTTACCTCTCTGACCTCATCTCCTACCACTCTCCCCCTCGCTCACT-CC 2975 chrXptel1M 373836 GTATCTAGTGACCCTAGCCTCCTGGCTA-TCCATGAACAAAGCCTCCAT- 373883 i- i iv v i v i- vi viv vvv i- L2#LINE/L2 2976 GC-TCCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACACGCCAGGCACG 3024 chrXptel1M 373884 TTCTCAGCTGTGGATATTCTCCCTAGCTATGCTC-ATGCCTGGAATGCTC 373932 i i iv vv iiv iv v v i v i -v i L2#LINE/L2 3025 CTCCCGCCTCAGGGCCTTTGCACTTGCTGTTCCCTCTGCCTGGAACGCTC 3074 chrXptel1M 373933 T 373933 L2#LINE/L2 3075 T 3075 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 42.83 CpG sites = 196, Kimura (unadjusted) = 46.02 Transitions / transversions = 0.83 (24/29) Gap_init rate = 0.05 (7 / 139), avg. gap size = 1.86 (13 / 7) 520 21.17 5.00 1.61 chrXptel1M 373953 374072 (625928) MIRc#SINE/MIR 3 126 (142) m_b335s601i3 14039 chrXptel1M 373953 AGACAG---GGTGCAGTGGATAGAGCACCAGCCCTGAAGTCAGAAGAACC 373999 i --- v ii v i i i ii MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chrXptel1M 374000 TGAGTTCAAATCTGGCCTCAGATACGTCTTAGCTGTGTGACCTTGGGTAA 374049 i i i iv v v vi v vi i MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 102 chrXptel1M 374050 GTCACTTAATC---CTAACTGCCTCA 374072 i --- i -- MIRc#SINE/MIR 103 GTCACTTAACCTCTCTGA--GCCTCA 126 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 24.47 CpG sites = 17, Kimura (unadjusted) = 25.64 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.03 (4 / 119), avg. gap size = 2.00 (8 / 4) 574 21.23 1.37 6.47 chrXptel1M 376352 376497 (623503) C MIRc#SINE/MIR (120) 148 10 m_b335s601i4 14040 chrXptel1M 376352 CTCACTTTACAGATGGGGAAACTGAGGT--GAACAGGTTGACGTGACTTG 376399 i i i i--ii v i - C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAA-GTGACTTG 100 chrXptel1M 376400 CCCAGGATCACACAGCTAGGAAGTGTCTGAGGCCAGATTTGAACTCAGGA 376449 i i v v v v vi i i i -- C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAG-- 52 chrXptel1M 376450 AAATGAGTCTTCCTGACTCCAGGCCTGGGTCTTTATCTACTCCACCAC 376497 ------ i i ii vv i v i v C MIRc#SINE/MIR 51 ------GTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 24.51 CpG sites = 19, Kimura (unadjusted) = 25.51 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.07 (10 / 145), avg. gap size = 1.10 (11 / 10) 12 20.88 3.64 5.56 chrXptel1M 377965 378019 (621981) (ATCCTTG)n#Simple_repeat 1 54 (0) m_b335s252i0 14041 chrXptel1M 377965 ATCCTCTTCTCCTGAATCCCTTGGCCCTTGATCCTGTTATCC-T-ATCAC 378012 - vv vi - ii - v - - vi (ATCCTTG)n#Si 1 ATCCT-TGATCCTTGAT-CCTTGATCCTTGATCCT-TGATCCTTGATCCT 47 chrXptel1M 378013 TGATCCT 378019 (ATCCTTG)n#Si 48 TGATCCT 54 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.09 (5 / 54), avg. gap size = 1.00 (5 / 5) 209 29.97 7.95 9.40 chrXptel1M 378336 378486 (621514) C L2c_3end#LINE/L2 (2) 476 328 m_b335s601i6 14042 chrXptel1M 378336 TCAGTTAGTCAATAAATATTTGTTAAGTGCTTACTATGTTCTGGGCATGA 378385 v i v i i i i i i ----- ---- C L2c_3end#LINE 476 TCATTCATTCAACAAACATTTATTGAGCGCCTACTATGT-----GC---- 436 chrXptel1M 378386 ACTTAAGCACTGAGGAT-TAAA-ACGGACAAAAGACAGTCATTGTTTCCA 378433 ---i i i i -i - i i i i v i vi iiii C L2c_3end#LINE 435 ---CAGGCGCTGGGGATACAAAGATGAATAAGACACGGTCCCTGCCCTCA 389 chrXptel1M 378434 ATG----CAC---CTAATGTGAAAGACGACCAAGT--ACAAATGATGCTA 378474 v ---- --- i viii iiv ? -- i ii -- C L2c_3end#LINE 388 AGGAGCTCACAGTCTAGTGGAGGAGACAGACANGTAAACAGACAAT--TA 341 chrXptel1M 378475 CAG-ACAGGATAA 378486 i- i v C L2c_3end#LINE 340 CAATACAAGTTAA 328 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 38.23 CpG sites = 33, Kimura (unadjusted) = 42.41 Transitions / transversions = 4.12 (33/8) Gap_init rate = 0.13 (20 / 150), avg. gap size = 1.30 (26 / 20) 281 26.83 13.41 0.00 chrXptel1M 378336 378417 (621583) C L2a_3end#LINE/L2 (2) 515 423 m_b335s601i5 14042 chrXptel1M 378336 TCAGTTAGTCAATAAATATTTGTTAAGTGCTTACTATGTTCTGGGCATGA 378385 v i v i i i i i v ii ivi C L2a_3end#LINE 515 TCATTCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTG 466 chrXptel1M 378386 ACTTAAGCACTGAGGAT-----------TAAAACGGACAAAAG 378417 vii i i i -----------i i C L2a_3end#LINE 465 TTCTAGGCGCTGGGGATACAGCAGTGAACAAAACAGACAAAAG 423 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 31.51 CpG sites = 17, Kimura (unadjusted) = 35.53 Transitions / transversions = 3.40 (17/5) Gap_init rate = 0.01 (1 / 81), avg. gap size = 11.00 (11 / 1) 246 35.43 4.49 3.23 chrXptel1M 379437 379681 (620319) C L2#LINE/L2 (365) 2717 2470 m_b335s601i7 14043 chrXptel1M 379437 ATCTGAGCATCAGGTAATGAGGGCCCGAAAT-GAGTGGTGACAGTAACAA 379485 iii ivv i i iv ii i vi- i i ii-- C L2#LINE/L2 2717 ATCCAGGCGAGAGATGATGGTGGCTTGGACCAGGGTGGTGGCAGTGG--A 2670 chrXptel1M 379486 GATGCAAAGGAGGGG-CAGA-----GAGAGATTAGGAAGATAAAATCAAA 379529 i vvi i v - i ----- v v vv i i ii i v C L2#LINE/L2 2669 GGTGGTGAGAAGTGGTCGGATTCTGGATATATTTTGAAGGTAGAGCCGAC 2620 chrXptel1M 379530 AGGACTTGATGTTGAAATAGATATTGGGGGAAAGGTGAAAATGAATGAGG 379579 i v v i v i i v v vi --- i v -- C L2#LINE/L2 2619 AGGATTTGCTGATGGATTGGATGTGGGGTGTGAG---AGAAAGA--GAGG 2575 chrXptel1M 379580 AGTCAGAGGTGACCCTTAAGTTGCCACCTTGGGTGACTGGGAGGATGGCA 379629 ii i i iv i viiiv i i ii i - C L2#LINE/L2 2574 AGTCAAGGATGACTCCAAGGTTTTTGGCCTGAGCAACTGGAAGGATGG-A 2526 chrXptel1M 379630 GTGACC-TTGACAGCAATAAGAAAG--TTCAGAAGAAAGA-GTTTAGGTG 379675 vi - ? v vi ii i -- v i i i iv - ii v C L2#LINE/L2 2525 GTTGCCATTNACTGAGATGGGGAAGACTGCGGGAGGAGCAGGTTTGAGGG 2476 chrXptel1M 379676 GAAAGA 379681 i C L2#LINE/L2 2475 GGAAGA 2470 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 48.13 CpG sites = 56, Kimura (unadjusted) = 51.75 Transitions / transversions = 2.00 (56/28) Gap_init rate = 0.06 (14 / 244), avg. gap size = 1.36 (19 / 14) 487 21.70 3.03 2.26 chrXptel1M 380688 380819 (619181) MIR#SINE/MIR 48 180 (82) m_b335s601i8 14044 chrXptel1M 380688 CTGTGTTCAAATTCAGCCTCAAAACACTTACTG--TGTGGAACCT--GGC 380733 v i i v v viv- i-- vi -- MIR#SINE/MIR 48 CTGGGTTCGAATCCCGGCTCTGC-CACTTACTAGCTGTGTGACCTTGGGC 96 chrXptel1M 380734 AAGTGACTTCACATGTCTGCCTGCCTAGGTTTCCTGATCTGTAAAATAGG 380783 v v v v -- vi v i MIR#SINE/MIR 97 AAGTTACTTAACCTCTCTG--TGCCTCAGTTTCCTCATCTGTAAAATGGG 144 chrXptel1M 380784 AATAGTAACAGCATCTACCTCCCAGGGTAGTTATGA 380819 i i i i i vi v i MIR#SINE/MIR 145 GATAATAATAGTACCTACCTCATAGGGTTGTTGTGA 180 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 24.79 CpG sites = 14, Kimura (unadjusted) = 25.81 Transitions / transversions = 1.00 (14/14) Gap_init rate = 0.04 (5 / 131), avg. gap size = 1.40 (7 / 5) 14 0.00 7.41 3.57 chrXptel1M 382182 382208 (617792) (TCAG)n#Simple_repeat 1 28 (0) m_b335s252i1 14045 chrXptel1M 382182 TCAGTCAGTCAGTCAG--AGTCAGTTCAG 382208 -- - (TCAG)n#Simpl 1 TCAGTCAGTCAGTCAGTCAGTCAG-TCAG 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.08 (2 / 26), avg. gap size = 1.50 (3 / 2) 236 25.47 5.71 2.78 chrXptel1M 383874 383978 (616022) L1P1_orf2#LINE/L1 2410 2517 (777) m_b335s551i0 14046 chrXptel1M 383874 TGTTCATGGTTAGGCAAAATCAATATACTTAAAAATGAGAAT-TTACCTA 383922 i v v i - v i ivv -i i i L1P1_orf2#LIN 2410 TGCTCATGGGTAGGAAGAATCAATAT-CGTGAAAATGGCCATACTGCCCA 2458 chrXptel1M 383923 AT-CAGTTTAT----TCAATGGCATCCCTATTAAATTACTAACTGTATTT 383967 v-i i ---- v i i ii i - - i L1P1_orf2#LIN 2459 AGGTAATTTATAGATTCAATGCCATCCCCATCAAGCTACCAA-TG-ACTT 2506 chrXptel1M 383968 TACTAATAGAA 383978 vi v i L1P1_orf2#LIN 2507 TCTTCACAGAA 2517 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 32.23 CpG sites = 17, Kimura (unadjusted) = 32.23 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.06 (6 / 104), avg. gap size = 1.50 (9 / 6) 18 35.74 0.00 0.00 chrXptel1M 384976 385042 (614958) (TA)n#Simple_repeat 1 67 (0) m_b335s252i2 14047 chrXptel1M 384976 TACATATGCATAAATATATGCATGTTTATAGATATCTATGTTTATAGAGA 385025 i ii v ii i v v v i v v v (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chrXptel1M 385026 GAGAGATATGTTTATAT 385042 v v v i v (TA)n#Simple_ 51 TATATATATATATATAT 67 Matrix = Unknown Transitions / transversions = 0.73 (8/11) Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.0 (0 / 0) 21 15.86 0.00 0.00 chrXptel1M 385263 385297 (614703) (T)n#Simple_repeat 1 35 (0) m_b335s252i3 14048 chrXptel1M 385263 TTTTTTTTTTTCTTTTCTTGTTTTTTATTTGTTTT 385297 i i v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 35 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 265 37.45 14.76 1.06 chrXptel1M 385408 385739 (614261) L3#LINE/CR1 379 755 (3344) m_b335s601i9 14049 chrXptel1M 385408 TTAGAGGGTAGAAGAATATGACAT-GAGGAAG----GAAAG----GAACC 385448 i v i i i i- i---- ---- v L3#LINE/CR1 379 TTGGCGAGTGGAAGAATGTGACACAGAGGAAAAGGAGAAAGAGAAGAAAC 428 chrXptel1M 385449 TCTGAACTTTTGAAACTA----------ATAAGAC-----------AGGT 385477 i v ivi i i ---------- i i ----------- v L3#LINE/CR1 429 TCCGCACCACTGGAGCTANACAACAGGTATGAGGCTCTTCCCACGGAGGG 478 chrXptel1M 385478 CAGAACTGGGCCATCTATTAAGGAAACAGGCTT--ATGCTCAA-GGAAGG 385524 iii v i i v ivvi i i vv -- v - vi L3#LINE/CR1 479 TGAATCCGGACCTTCTGAAGAAGAAGCAGCATTCCATGCTCCACGGAACA 528 chrXptel1M 385525 ATGCTT-TGATCTAAAGCTATTATCAGGTGCCATGTCCCTCAGCAATGGT 385573 ivvv-v iiiv vi i v v v vvi iiivi v ?i L3#LINE/CR1 529 ATAAGGAGGATTCGCAGGCACTAGCAGGTGCGAGGAATCCTGTTACTGNC 578 chrXptel1M 385574 CAGAATAAGAATAGACTAGATGTTCTGTCTAATGGCTCTCTGCTGAA--- 385620 vv iv i v vv vi vv vi ii i i i i--- L3#LINE/CR1 579 CCCAGGAGGAAGAGACGCGTCGTGGTGGTTGGTGACTCCCCGCTGAGGGA 628 chrXptel1M 385621 -----------CCATCTGTAGACTTTACATTAACAACCGAGACATAAACT 385659 ----------- i v i i v i vivi i i vi i--- L3#LINE/CR1 629 TACGGAGGCGGCCGTATGCAGACCTGACGTGGCTAATCGGGAGGTG---T 675 chrXptel1M 385660 ACTGTCTTCTTGGAGCAGACAACTGAGATGTGACGGAGCACTGGCCAGCA 385709 i i ivii v i i vi iv i-i L3#LINE/CR1 676 GCTGTCTTCCTGGAGCGTGTATCCGAGACGTGACGGAGAGCCTGCCAA-G 724 chrXptel1M 385710 ACTTGTC-ATCTAGTCAAATGACATCCACTC 385739 ii - v iv i i vi vi i L3#LINE/CR1 725 ACTCATCAAACCCGCCGACCGCTACCCACTC 755 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 47.28 CpG sites = 74, Kimura (unadjusted) = 55.03 Transitions / transversions = 1.51 (74/49) Gap_init rate = 0.05 (15 / 331), avg. gap size = 3.53 (53 / 15) 455 16.82 5.41 3.54 chrXptel1M 385800 385910 (614090) MER63D#DNA/hAT-Tip100 340 452 (609) m_b335s502i0 14050 chrXptel1M 385800 GAGCATTTACACCTCAGAAATCAGCTACAAAACTCCACAAA-CTGGGCTG 385848 i v i i ---- v i - v v MER63D#DNA/hA 340 GAGTATTTACACCACGGAAATCGGC----AAACGCTACAAATCAGGGCTT 385 chrXptel1M 385849 GATGGATT----TGTTGCTTGACTAGATTGGGCAAAGTGATGGAGAAAGT 385894 vv ---- v v i viiv i MER63D#DNA/hA 386 GATTTATTGTTTTGTTGATTGTCTAGACTTAAGAAAGTGATGGAGAAAAT 435 chrXptel1M 385895 GTTAA-AATGCAGATTA 385910 - MER63D#DNA/hA 436 GTTAATAATGCAGATTA 452 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 16.92 CpG sites = 8, Kimura (unadjusted) = 19.09 Transitions / transversions = 0.80 (8/10) Gap_init rate = 0.06 (7 / 110), avg. gap size = 1.43 (10 / 7) 448 20.77 0.85 5.36 chrXptel1M 385912 386028 (613972) MIRc#SINE/MIR 4 115 (153) m_b335s601i10 14051 chrXptel1M 385912 GGTAGCTGGGTTGAAAGGGATAGAGCATTGGCCTTTAAGTCAGGAGGACC 385961 i - v v v iv v i v vi i MIRc#SINE/MIR 4 GGCAG-TGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chrXptel1M 385962 TGAGTTCTAATCTGGAAGACACT-TAACACTTCCTAGATGTGTGACCCTG 386010 i v i iv i----- - iv v v i MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGG-----CTCTGCCACTTACTAGCTGTGTGACCTTG 97 chrXptel1M 386011 GGCAAGTCACTTAACCTC 386028 MIRc#SINE/MIR 98 GGCAAGTCACTTAACCTC 115 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 24.38 CpG sites = 11, Kimura (unadjusted) = 24.38 Transitions / transversions = 0.92 (11/12) Gap_init rate = 0.06 (7 / 116), avg. gap size = 1.00 (7 / 7) 568 30.68 4.43 0.47 chrXptel1M 386330 386532 (613468) C MIR#SINE/MIR (19) 243 33 m_b335s601i11 14052 chrXptel1M 386330 TAAACATTTATTATGTA------ACTACTATCAACA-TTTATAAAAGTTC 386372 i i ii i i------ ii v v i i- i vivi v C MIR#SINE/MIR 243 TGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGCGCTTTACATGTATTA 194 chrXptel1M 386373 TCTCATTTGATCCTCGAAA--ACCCTGGGAGGTGGGTGCTATTGTTATAC 386420 v i iv -- iv i i i v C MIR#SINE/MIR 193 ACTCATTTAATCCTCACAACAACCCTATGAGGTAGGTACTATTATTATCC 144 chrXptel1M 386421 TCGTTTTGCCAAAGAGGAAACTGAGGCAGACAGAGGTGAAATGACTTGCT 386470 i i i vi v v v v i i i C MIR#SINE/MIR 143 CCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCC 94 chrXptel1M 386471 CGGGGTCATATAGCCTGTTAGATGTCTAAGGCTGGATTTGAACTCGGTTT 386520 ii i i iv v - v vi v v i i i viv C MIR#SINE/MIR 93 CAAGGTCACACAGCTAGTAAG-TGGCAGAGCCGGGATTCGAACCCAGGCA 45 chrXptel1M 386521 TCTTGACTCCAG 386532 vii i C MIR#SINE/MIR 44 GTCTGGCTCCAG 33 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 38.51 CpG sites = 39, Kimura (unadjusted) = 41.12 Transitions / transversions = 1.70 (39/23) Gap_init rate = 0.02 (4 / 202), avg. gap size = 2.50 (10 / 4) 682 26.20 4.29 1.86 chrXptel1M 386360 386569 (613431) C MIRc#SINE/MIR (52) 216 2 m_b335s601i12 14052 chrXptel1M 386360 TTTATAAAAGTTCTCTCATTTGATCCTCGAAA--ACCCTGGGAGGTGGGT 386407 i i v vi v iv -- v i i C MIRc#SINE/MIR 216 TTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGC 167 chrXptel1M 386408 ---GC---TATTGTTATACTCGTTTTGCCAAAGAGGAAACTGAGGCAGAC 386451 --- --- i v i i i vi v vv v C MIRc#SINE/MIR 166 AGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAG 117 chrXptel1M 386452 AGAGGTGAAATGACTTGCTCGGGGTCATATAGCCTGTTAGATGTCTAAGG 386501 v i i ii i i iv v - v vi v C MIRc#SINE/MIR 116 AGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAG-TGGCAGAGC 68 chrXptel1M 386502 CTGGATTTGAACTC-GGTTTTCTTGACTCCAGCCTTAGCACTTTATCTAT 386550 v i i i - i i iviii ii i v i i C MIRc#SINE/MIR 67 CGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCAC 18 chrXptel1M 386551 TGTACCACATAGCTGCCTC 386569 i --- C MIRc#SINE/MIR 17 TGCACCACA---CTGCCTC 2 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 32.50 CpG sites = 34, Kimura (unadjusted) = 33.26 Transitions / transversions = 1.70 (34/20) Gap_init rate = 0.04 (8 / 209), avg. gap size = 1.62 (13 / 8) 471 29.38 0.68 2.08 chrXptel1M 386764 386909 (613091) L3#LINE/CR1 2737 2880 (1219) m_b335s601i13 14049 chrXptel1M 386764 TGCAAACTCCAGGCCCCAGTAGACTCCATTTCCATTCCTGGCAAAATTCT 386813 ? v i --i ii iv iv v i i L3#LINE/CR1 2737 TGNAAACTACAGACC--GGTAAGCTTGACGTCGATCCCCGGCAAAATTCT 2784 chrXptel1M 386814 GGGAAACATTATTAAACAGATAATTGTTCAGAACCTAGAAAGGGAAACAG 386863 i i viv ii vv v v i i i i L3#LINE/CR1 2785 AGAACGGATTATTAAACAGATGGTTTGTGAGCACTTAGAAAAGGAAGCGG 2834 chrXptel1M 386864 TGATTACCAAAAGTTAGTA-GGATATGATAAAGAATGGGTCATGCTA 386909 i i ii ii i - i - v iv iii i L3#LINE/CR1 2835 TGATCACTAGGAGCCAGCATGGGT-TCACTAAGAACAAGTCATGCCA 2880 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.95 CpG sites = 30, Kimura (unadjusted) = 40.00 Transitions / transversions = 2.50 (30/12) Gap_init rate = 0.03 (4 / 145), avg. gap size = 1.00 (4 / 4) 241 27.64 4.84 0.78 chrXptel1M 386963 387086 (612914) L1PREC2_orf2#LINE/L1 2350 2478 (816) m_b335s551i1 14053 chrXptel1M 386963 AATTACAAAATACTTTCCAACAGTAA--AGACA-GATCTAAACAATTGAG 387009 i vii - v -- v - ivi v ii L1PREC2_orf2# 2350 AATTACAAAACACTGCTCAA-AGAAATCAGAGATGACACAAACAAATGGA 2398 chrXptel1M 387010 AAGTCAAT---TGCTTATGGATAGGCTGAGCCAATATAATAAAAATGGCA 387056 iv v --- i vv ii vi v v L1PREC2_orf2# 2399 AAAACATTCCATGCTCATGGATAGGAAGAATCAATATCGTTAAAATGGCC 2448 chrXptel1M 387057 TTTCTACTTAAATTAATTTACTCATTAAAT 387086 v v i ii vi vv v L1PREC2_orf2# 2449 ATACTGCCCAAAGCAATTTACAGATTCAAT 2478 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 33.53 CpG sites = 16, Kimura (unadjusted) = 34.74 Transitions / transversions = 0.89 (16/18) Gap_init rate = 0.03 (4 / 123), avg. gap size = 1.75 (7 / 4) 38 0.00 0.00 0.00 chrXptel1M 387238 387270 (612730) (TG)n#Simple_repeat 1 33 (0) c_b335s251i1 14054 chrXptel1M 387238 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 387270 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 33 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 441 27.20 5.88 3.66 chrXptel1M 387293 387479 (612521) L1ME4c_3end#LINE/L1 346 536 (294) m_b335s551i2 14055 chrXptel1M 387293 GCTATAAAATTGTGCATATCCTTTGTCCCAGCA----CACATTTAGGGTT 387338 i v v i v i ---- v i i iv L1ME4c_3end#L 346 GCCATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAAT 395 chrXptel1M 387339 TGTATCCCAAAGAGATCAA---AGAAAAAGGAAAGAACCTATTTGTACAA 387385 - i i i - --- i i - v v i i L1ME4c_3end#L 396 T-TATCCTAAGGAAAT-AATTCAAAAGAAGGAAA-AAGCTATATGCACGA 442 chrXptel1M 387386 AAACATTTATAGCAGCAGTTTTTTGTAGGGCCAAAGAATTGGAAAT---- 387431 i ii i v - v i iviv i i i---- L1ME4c_3end#L 443 AGATGTTCATTGCAGC-GTTATTTATAATAGCGAAAAATTGGAAACAACC 491 chrXptel1M 387432 TGAGGGGACACCATCAGTTGGGGAATGACTGAACAAGTTGTGGTATAT 387479 i iv v--- v i v ii i ii i i i L1ME4c_3end#L 492 TAAATGT---CCAACAATAGGGGAATGGTTAAGTAAATTATGGTACAT 536 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 33.65 CpG sites = 34, Kimura (unadjusted) = 35.47 Transitions / transversions = 2.27 (34/15) Gap_init rate = 0.05 (10 / 186), avg. gap size = 1.80 (18 / 10) 690 29.62 6.42 1.94 chrXptel1M 388034 388329 (611671) L3#LINE/CR1 3055 3363 (736) m_b335s601i14 14049 chrXptel1M 388034 CTGTTTGAATAACTAAAATCAAAGTAGAGCT-ATTAATGGGTCAATGCCA 388082 v ii v vi i-i v i - i i i L3#LINE/CR1 3055 CTGGTTGAACGACTATACCCAAAA-GGTGTTGATTAATGGATCGATGTCA 3103 chrXptel1M 388083 ATAT--AAGGAGTTCTCCAATGGAGTATTACAGAGTTCTGTCATTGGCCT 388130 iv -- i v i i v iii i i v i L3#LINE/CR1 3104 ACCTGGAGGGAGGTCTCTAGTGGCGTGCCACAGGGCTCTGTCCTTGGCCC 3153 chrXptel1M 388131 TGTGCTATACATTAATGTTATGAATAATTCGGATAAAGACAGAGAAGGAA 388180 v i v vi v v v i i i i v v L3#LINE/CR1 3154 TGTCCTGTTCAACATTTTTATCAATGACTTGGATGAAGACATAGAAGGCA 3203 chrXptel1M 388181 TAC--------TCTGTGGCTAACACCAAACTAAGATGGACAGTT--TACA 388220 i -------- i ii v i v i ii v i i -- i L3#LINE/CR1 3204 TGCTTATCAAATTTGCAGATGACACAAAGCTGGGAGGGATAGCTAATACG 3253 chrXptel1M 388221 --GGTTAAT-GAATCAGGCTACAAAACGATCTCCATGAGCTAGAATGAT- 388266 -- v i i- i v v ? v iii i i - L3#LINE/CR1 3254 NTGGATGACAGAATCAAGATTCAAAANGATCTCGACAGGCTGGAACGATG 3303 chrXptel1M 388267 AGCCAAATCTATTTAAAAAAAGTGAAATGTAATA--CATAAATCAAGAGT 388314 i i v i----- v ii v i --v vv i L3#LINE/CR1 3304 GGCCGAAACC-----AACAAGATGAAATTTAACAGGGATAAATGTAAAGT 3348 chrXptel1M 388315 TATACACTTGGGGTC 388329 iv i i i v L3#LINE/CR1 3349 CCTGCATTTAGGTTC 3363 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 36.48 CpG sites = 55, Kimura (unadjusted) = 39.50 Transitions / transversions = 1.77 (55/31) Gap_init rate = 0.04 (13 / 295), avg. gap size = 1.92 (25 / 13) 234 24.26 16.67 0.80 chrXptel1M 388323 388430 (611570) MIRc#SINE/MIR 9 133 (135) m_b335s601i15 14056 chrXptel1M 388323 TGGGGTCCAGTGGA--------TAGTCATGGAGTCAGGGGGACCAGAGTT 388364 v v -------- i v v ii v i MIRc#SINE/MIR 9 TGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTT 58 chrXptel1M 388365 CAAATCTGGCCTCGGACACTTAACACTT------CCT--AGCAAGTCACT 388406 i i iv v v v vi vi ------ --i MIRc#SINE/MIR 59 CGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACT 108 chrXptel1M 388407 TAATCCTAATTGA--CTCACTTCCCT 388430 - vvi -- v i MIRc#SINE/MIR 109 TAA-CCTCTCTGAGCCTCAGTTTCCT 133 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 28.23 CpG sites = 12, Kimura (unadjusted) = 29.52 Transitions / transversions = 0.86 (12/14) Gap_init rate = 0.05 (5 / 107), avg. gap size = 3.80 (19 / 5) 243 29.58 19.71 2.02 chrXptel1M 388561 388981 (611019) L3b_3end#LINE/CR1 517 1010 (196) m_b335s601i16 14049 chrXptel1M 388561 CCTATAAAAAAAAGAACTAGAGGTTTTAGTTATCTGCAAAC--AAAATG- 388607 ?i ivi v i i iv i i -- v - L3b_3end#LINE 517 CNCATGTGAAAAAGACCTGGGGGTTTTAGTTGACCGCAAGCTCAATATGA 566 chrXptel1M 388608 -----------GAAGC--CT--CAAAA--GCTAATGCTATACAAGGTTA- 388639 ----------- v -- -- -- v vivi i i- L3b_3end#LINE 567 GTCAGCAGTGCGACGCGGCTGCCAAAAAAGCTAATGCGATCTTGGGCTGC 616 chrXptel1M 388640 ATTAAGAAAGACATATTTTCCAAAT---GAGAGAC-ATA---------TA 388676 v i ii? vviivv i ?--- i ii- ?--------- L3b_3end#LINE 617 ATTAACAGAAGNATCGCCGACAGANCAAGGGAGGTGATNNTCCCGCTCTA 666 chrXptel1M 388677 CTCTGCCTTGGTCAGGGCACATATGGAG-----AGTTCAGTTTAGTGCAT 388721 vi v ? ?v -----v iv v ?i L3b_3end#LINE 667 CTCTGCGCTGGTCAGGCCNCANCTGGAGTACTGCGTTCAGTTCTGGGCNC 716 chrXptel1M 388722 TATATCTTATAGAAGAGAAAGACAAGCTGGGGCTTGTTCCAAAG---GCA 388768 i i ?i v iii vivi v ?i i vvv vi i --- L3b_3end#LINE 717 CACANTTTAAAAGGGACGTGGAGAANTTGGAGAGAGTTCAGAGGAGAGCA 766 chrXptel1M 388769 ACA------AT----------GAAAATGG------TGAGAA--------- 388787 ------ ---------- ------ i --------- L3b_3end#LINE 767 ACAAAAATGATTAAAGGGCTGGAAAATGGGACCTATGAGGAAAGGTTAAA 816 chrXptel1M 388788 -GAACCGGGAATATTTAGACTTGA-AAGAG--GACTTGAAAAGGACCAAA 388833 - i v i v v - -- i viiiii? iv L3b_3end#LINE 817 GGAACTGGGATTATTCAGCCTGGAGAAGAGAAGGCTGAGGGGNGACTTAA 866 chrXptel1M 388834 TTTTGGCTGTCTTCAAGTATGTGAAGGGCTGTCATTGTGGAAGAAAGATG 388883 ---ii ? i i i i i- i i vi - L3b_3end#LINE 867 T---AACNGTCTTCAAGTATATGAAGGGTTATTAC-GTAGAGGACGG-TG 911 chrXptel1M 388884 AAAATTCAGTCTGGTT--CACCTCAA---ACAGCATAACTAGATAAAACA 388928 ----i - v i-- i v --- vii v v vi ii L3b_3end#LINE 912 A----CCAG-CTGTTCTCCATCTCCACTGAGGACAGAACAAGAGGAAATG 956 chrXptel1M 388929 GG-TGAAACTTCAGAGGGATTGTTTTAGGCCTGATAAAAACAAAAGCTTT 388977 - v v viv vv v iiv v iv i i i L3b_3end#LINE 957 GGCTTAAACTGCAGCATGAGGGATTTAGGTTAGATATAAGGAAGAACTTC 1006 chrXptel1M 388978 TTAA 388981 i i L3b_3end#LINE 1007 CTGA 1010 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 38.30 CpG sites = 73, Kimura (unadjusted) = 40.45 Transitions / transversions = 1.49 (73/49) Gap_init rate = 0.07 (31 / 420), avg. gap size = 3.00 (93 / 31) 354 29.26 17.90 1.50 chrXptel1M 388569 388797 (611203) L3#LINE/CR1 3423 3688 (411) m_b335s601i17 14049 chrXptel1M 388569 AAAAAGAACTAGAGGTTTTAGTTATCTGCAAACAAAATGGAAGCC----- 388613 v i iv i i vv ivi ----- L3#LINE/CR1 3423 AAAAAGACCTAGGGGTTTTAGTTGACCGCAAGCTCAATATGAGCCAACAG 3472 chrXptel1M 388614 -------------TCAAAA--GCTAATGCTATACAAGGTTA-ATTAAGAA 388647 -------------i -- v viv i i- v i L3#LINE/CR1 3473 TGTGATGTGGCTGCCAAAAAAGCTAATGCAATCTTAGGCTGCATTAATAG 3522 chrXptel1M 388648 AGACATATTTTCCAAAT---GAGAGACA----------TATACTCTGCCT 388684 iii v v i ?--- i ii ---------- i vi L3#LINE/CR1 3523 AAGTATAGTGTCCAGANCAAGGGAGGTAATAGTCCCGCTGTACTCTGCGC 3572 chrXptel1M 388685 TGGTCAGGGCACATATGGAG-----AGTTCAGTTTAGTGCATTATATCTT 388729 iv v -----v iv v iii i i L3#LINE/CR1 3573 TGGTCAGACCACATCTGGAGTATTGCGTTCAGTTCTGGGCGCCACATTTT 3622 chrXptel1M 388730 ATAGAAGAGAAA--GACAAGCTGGGGCTTGTTCCAAAGGCAACAATGAAA 388777 - - i v -- i i vi i vi i iv i i iv ii L3#LINE/CR1 3623 A-AG-AGGGACATTGACAAACTGGAGCGCGTCCAGAGGAGAGCGACCAGG 3670 chrXptel1M 388778 ATGGTGAGAAGAACCGGGAA 388797 -- iii v L3#LINE/CR1 3671 ATGGT--GAAGGGTCTGGAA 3688 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 36.05 CpG sites = 43, Kimura (unadjusted) = 39.08 Transitions / transversions = 1.87 (43/23) Gap_init rate = 0.05 (12 / 228), avg. gap size = 3.75 (45 / 12) 589 28.28 3.25 3.67 chrXptel1M 388772 389017 (610983) L3#LINE/CR1 3699 3943 (156) m_b335s601i18 14049 chrXptel1M 388772 ATGAA-AATGGTGAGAAGAACCGGGAATATTTAGACTTGA-AAGAG--GA 388817 i- i vii i i i i v v - -- L3#LINE/CR1 3699 ATGAGGAACGGTTGAAGGAACTGGGGATGTTTAGCCTGGAGAAGAGAAGA 3748 chrXptel1M 388818 CTTGAAAAGGACCAAATTTTGGCTGTCTTCAAGTATGTGAAGGGCTGTCA 388867 ii iii --- vv i i v L3#LINE/CR1 3749 CTTAGAGGAGAC---ATGATAGCTGTCTTCAAATATTTGAAGGGCTGTCA 3795 chrXptel1M 388868 TTGTGGAAGAAAGATGAAA---ATTCAGTCTGGTTCACCTCAAACAGCAT 388914 - ii v i --- v v i ---- i vi v L3#LINE/CR1 3796 -TGTGGAAGAGGGATTAGACTTATTCTGTGTGGCTC----CAGAGGGCAG 3840 chrXptel1M 388915 AACTAGATAAAACAGGTGAAACTT-CAGAGGGATTGTTTTAGGCCTGATA 388963 ivvv ii i v - i i iiv v v iii L3#LINE/CR1 3841 AACTAGGACCAATGGGTGGAAGTTACAGGGAGGCAGATTTCGGCTCAATA 3890 chrXptel1M 388964 AAAACAAAAGCTTTTTAATCCTTTTGAGTTGGGCCCAAATGGAATGGACT 389013 v iv i i i - vv iv i vv vv i L3#LINE/CR1 3891 TAAGGAAGAACTTTCTAA-CAATCAGAGCTGTCCAAAAATGGAATGGGCT 3939 chrXptel1M 389014 CCCT 389017 v L3#LINE/CR1 3940 GCCT 3943 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 35.70 CpG sites = 39, Kimura (unadjusted) = 36.38 Transitions / transversions = 1.39 (39/28) Gap_init rate = 0.06 (14 / 245), avg. gap size = 1.21 (17 / 14) 13 17.64 0.00 7.32 chrXptel1M 391020 391063 (608937) (CCCGGC)n#Simple_repeat 1 41 (0) m_b335s252i4 14057 chrXptel1M 391020 CCCGGCCCCGAAACCCCGGCCCCACACCCCAGCCCCTGCCGCGG 391063 --i -vi i v v (CCCGGC)n#Sim 1 CCCGGCCCCG--GCCCCGGCCCC-GGCCCCGGCCCCGGCCCCGG 41 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.07 (3 / 43), avg. gap size = 1.00 (3 / 3) 371 27.95 6.62 5.23 chrXptel1M 392933 393083 (606917) HERV4_I#LTR/ERV1 3251 3403 (3136) m_b335s701i0 14058 chrXptel1M 392933 GGGGACACACGATGGTCTCCTACTTTAGATCTTAAAGATGCTTTCTTTTG 392982 ii vi iii viiii i v i v HERV4_I#LTR/E 3251 GGGGATGCAAAATGGTTCTCAGTCCTAGACCTAAAAGATGCTTTCTTCTC 3300 chrXptel1M 392983 TGCACCATTG--CATAAAGTCACAATTTCTTTTTGCCTTTAAAGGGAGAA 393030 iiiv vi -- vi i v vi i v ii HERV4_I#LTR/E 3301 CATTCCTCTGGCCCCAGAGTCCCAATACCTTTTTGCCTTTGAATGGGAAA 3350 chrXptel1M 393031 AT-------CCAGGGGAACGTAAACCCCCACCAATGCACATGGCCAGT-C 393072 ------- i i --- ----- v i v v - HERV4_I#LTR/E 3351 ATCCTAATACCAGAGAAA---AA-----CAACAATACACTTGGACAGTGC 3392 chrXptel1M 393073 CGCCTCAGGGC 393083 iv HERV4_I#LTR/E 3393 TCCCTCAGGGC 3403 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 36.40 CpG sites = 26, Kimura (unadjusted) = 36.40 Transitions / transversions = 1.86 (26/14) Gap_init rate = 0.07 (11 / 150), avg. gap size = 1.64 (18 / 11) 311 29.16 6.06 2.34 chrXptel1M 392953 393117 (606883) MER84-int#LTR/ERV1 3088 3258 (1696) m_b335s701i1 14058 chrXptel1M 392953 TACTTTAGATCTTAAAGATGCTTTCTTTTGTGCACCATTGCATAAAGTCA 393002 -- i i i i iiiv vv i ivv vi MER84-int#LTR 3088 TACTT--GATCTTAAGGATGCCTTTTTCTGCATTCCTGTACACCCAGATA 3135 chrXptel1M 393003 --CAATTTCTTTTTGCCTTTAAAGGGAGAAATCCAGGGGAACGTAAACC- 393049 -- i v i i v vi i i iv-- vi iv- MER84-int#LTR 3136 GCCAATTTTTGTTTGCTTTTGAATGGCAAGACCCAGAT--ACTCAAATAA 3183 chrXptel1M 393050 CCCACCAATGCACATGGCCAGTCC-GCCTCAGGGCGTGAGCG-----CCC 393093 i v i vv v v i - i vv v v ----- MER84-int#LTR 3184 CTCAACAGTTAACTTGGACAGTTCTGCCCCAGGGATTCAGAGATAGCCCC 3233 chrXptel1M 393094 CACATATT-GGACAGGCCCTGGCTA 393117 v v - i MER84-int#LTR 3234 CACCTTTTTGGACAGGCCCTAGCTA 3258 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 37.49 CpG sites = 24, Kimura (unadjusted) = 37.49 Transitions / transversions = 1.04 (24/23) Gap_init rate = 0.05 (8 / 164), avg. gap size = 1.75 (14 / 8) 335 28.38 9.78 6.01 chrXptel1M 393851 394075 (605925) HERV4_I#LTR/ERV1 5079 5311 (1228) m_b335s701i2 14058 chrXptel1M 393851 TTCAACAGGTCTGCCAGGCCTGCCCAGTTTGTGC---------CCAAGTA 393891 v i i i i v v --------- v v HERV4_I#LTR/E 5079 TTAAGCAGGTCTGTCAAGCCTGCTCACTGTGTGCACTTAACAACCCAGGA 5128 chrXptel1M 393892 AATCTTGAAAAGGGCT--TTTAAACTTCCCATGTCTGTGGGAGGAGTACA 393939 i---- v v -- i vvvvv - iivi ii v v HERV4_I#LTR/E 5129 AAC----AAAATGCCTCCTCTAATAGAACCA-GTCCAGAGGAGAGGAACT 5173 chrXptel1M 393940 TACATACCTGGGGAGGACTGGCCGATT-GATTTTACACACATGCCCCTTT 393988 --- v i -i - i i v i vvi HERV4_I#LTR/E 5174 TAC---CCAGGGGAAGACTGGC-AATTAGACTTCACCCATATGCCAGCTT 5219 chrXptel1M 393989 GCAGGAACTTCAAACTGCTTTTTTCCTCGT---------CACCTTTACTA 394029 iiiv v i----- v v --------- i HERV4_I#LTR/E 5220 GCAGAGGATACAAG-----TTTTTGCTAGTACTAATAGACACCTTTACTG 5264 chrXptel1M 394030 ATTGGGGAAAAGCCTTCCCTTGTAAGACTGAAAAGGCTCA-GAGGTT 394075 ii vvi i v vvi ii v i v - HERV4_I#LTR/E 5265 GCTGGGTCGAAGCTTACCCTACCAGAACAGAGAAGGCTAATGAGGTT 5311 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.43 CpG sites = 30, Kimura (unadjusted) = 36.17 Transitions / transversions = 1.00 (30/30) Gap_init rate = 0.08 (19 / 224), avg. gap size = 1.89 (36 / 19) 401 25.38 5.34 0.73 chrXptel1M 393944 394074 (605926) HERV17#LTR/ERV1 6061 6197 (2429) m_b335s701i3 14058 chrXptel1M 393944 TACCTGGG-GAGGACTGGCCGATTGATTTTACACACATGCCCC--TTTGC 393990 ii - i viv v v v-- i - HERV17#LTR/ER 6061 TACCCAGGAGAAGACTGGCAACTAGATTTTACCCACATGCCCAAATCT-C 6109 chrXptel1M 393991 AGGAACTTCA--AACTGCT-TTTTTCCTCGTCACCTTTACTAATTGGGGA 394037 i i -- v i -v i vvv v vi i i ii vi HERV17#LTR/ER 6110 AGGGATTTCAGTATCTACTAGTCTGGGTAGATACTTTCACTGGTTGGGCG 6159 chrXptel1M 394038 AAAGCCTTCCCTTGTAAGACTGAAAAGGCTC-AGAGGT 394074 i i i v i - HERV17#LTR/ER 6160 GAGGCCTTCCCTTGTAGGACAGAAAAGGCCCAAGAGGT 6197 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 30.46 CpG sites = 19, Kimura (unadjusted) = 31.61 Transitions / transversions = 1.36 (19/14) Gap_init rate = 0.05 (6 / 130), avg. gap size = 1.33 (8 / 6) 583 21.68 4.12 2.31 chrXptel1M 395623 395792 (604208) C MIR#SINE/MIR (25) 237 65 m_b335s601i19 14059 chrXptel1M 395623 CTTATTGTGTTCCCAGAAACTATGCTAAGCTCTTT---TGTAC-AAATAA 395668 i i v - iv i v v --- i- v v C MIR#SINE/MIR 237 CTTACTATGTGCC-AGGCACTGTTCTAAGCGCTTTACATGTATTAACTCA 189 chrXptel1M 395669 ATTGATCTTCAGACCGATCCTGGGAGTTAGGTGCTGCTATTATTCCCATT 395718 v i i v v i i iv v i ii i C MIR#SINE/MIR 188 TTTAATCCTCACAACAACCCTATGAGGTAGGTACTATTATTATCCCCATT 139 chrXptel1M 395719 TTACAGATGAAGAAACTGAGGCAGGCA-ATAGGTGAAGT--CTCTGCCCA 395765 i -- - v v -- - C MIR#SINE/MIR 138 TTACAGATGAGGAAACTGAGGCA--CAGAGAGGTTAAGTAACT-TGCCCA 92 chrXptel1M 395766 GAGTCATATAGCTAAAAAGTGTCTGAG 395792 ii i i iv v v C MIR#SINE/MIR 91 AGGTCACACAGCTAGTAAGTGGCAGAG 65 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 25.93 CpG sites = 20, Kimura (unadjusted) = 25.93 Transitions / transversions = 1.25 (20/16) Gap_init rate = 0.05 (8 / 169), avg. gap size = 1.38 (11 / 8) 478 20.08 12.66 2.30 chrXptel1M 395670 395827 (604173) C MIRc#SINE/MIR (71) 197 24 m_b335s601i20 14059 chrXptel1M 395670 TTGATCTTCAGACCGATCCTGGGAGTTAGGT---GC---TGCTATTATTC 395713 i v v i i v v i--- --- ii i C MIRc#SINE/MIR 197 TTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCC 148 chrXptel1M 395714 CCATTTTACAGATGAAGAAACTGAGG--CAGGCAATAGGTGAAGT--CTC 395759 i -- --- v v -- - C MIRc#SINE/MIR 147 CCATTTTACAGATGAGGAAACTGAGGCTCAG---AGAGGTTAAGTGACT- 102 chrXptel1M 395760 TGCCCAGAGTCATATAGCTAAAAAGTGTCTGAGGCTG--TTC---C---- 395800 ii i i iv v v v v --i --- ---- C MIRc#SINE/MIR 101 TGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAG 52 chrXptel1M 395801 -TCTTCCTGACTCCACATTCAGCAATCT 395827 - vi i iiv C MIRc#SINE/MIR 51 GTCTTCCTGACTCCAAGTCCAGTGCTCT 24 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 23.77 CpG sites = 18, Kimura (unadjusted) = 23.77 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.08 (12 / 157), avg. gap size = 2.00 (24 / 12) 433 21.99 1.65 6.03 chrXptel1M 397412 397532 (602468) MIRc#SINE/MIR 12 127 (141) m_b335s601i21 14060 chrXptel1M 397412 GGTACAGTGGATAGAGCACCAGCCCTGAAGTCAAGAGGATCTGAGTT-GA 397460 i v ii v i i i i i i - MIRc#SINE/MIR 12 GGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGA 61 chrXptel1M 397461 AACCGGCCTCATACACTTAAAACTTCCTAGCTGTGTGACCCTGAGCAAGT 397510 iv v v vvv ------- i i MIRc#SINE/MIR 62 GTCCCGGCTCTGCCACTTA-------CTAGCTGTGTGACCTTGGGCAAGT 104 chrXptel1M 397511 CACTTAATCCCAATT-GCCTCAG 397532 i i vv v- MIRc#SINE/MIR 105 CACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 26.30 CpG sites = 14, Kimura (unadjusted) = 26.30 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.07 (9 / 120), avg. gap size = 1.00 (9 / 9) 13 20.41 0.00 4.88 chrXptel1M 397533 397575 (602425) (CAAAAG)n#Simple_repeat 1 41 (0) m_b335s252i5 14061 chrXptel1M 397533 CAAAAATAAATACCTAAATACATAAGCAAAAGCAAAAGGAAAA 397575 ii - v - vi v v (CAAAAG)n#Sim 1 CAAAAGCAAA-AGC-AAAAGCAAAAGCAAAAGCAAAAGCAAAA 41 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.00 (2 / 2) 12 35.27 0.00 2.99 chrXptel1M 398731 398799 (601201) (AAGAG)n#Simple_repeat 1 67 (0) m_b335s252i6 14062 chrXptel1M 398731 AAGAAAAAAGGAAAGAGGGAGAAAAAGAATACACTGGGAGAGAGGTGAAG 398780 i i i i -i - i v v vvi i i v (AAGAG)n#Simp 1 AAGAGAAGAGAAGAGA-AGAG-AAGAGAAGAGAAGAGAAGAGAAGAGAAG 48 chrXptel1M 398781 AGAATAGAAGAATGGAGAA 398799 v ivi (AAGAG)n#Simp 49 AGAAGAGAAGAGAAGAGAA 67 Matrix = Unknown Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.03 (2 / 68), avg. gap size = 1.00 (2 / 2) 13 17.47 0.00 3.03 chrXptel1M 398898 398931 (601069) (GAAAA)n#Simple_repeat 1 33 (0) m_b335s252i7 14063 chrXptel1M 398898 GAAAAGAAAAGAAAAGTATGAGAACAGGATAGAA 398931 - vi v i v (GAAAA)n#Simp 1 GAAAAGAAAAGAAAAG-AAAAGAAAAGAAAAGAA 33 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 21 17.73 0.00 0.00 chrXptel1M 399620 399657 (600343) (T)n#Simple_repeat 1 38 (0) m_b335s252i8 14064 chrXptel1M 399620 TTTTTTGCTTATGTTTTTTTTTTTTCTTATTTTTTTTT 399657 vi v v i v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 38 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 579 29.94 7.02 3.76 chrXptel1M 399879 400291 (599709) L1M4_orf2#LINE/L1 614 1039 (2255) m_b335s551i3 14065 chrXptel1M 399879 ACCATGTATTAGGC-ATAAAA-ATTTCTCAA---ACTGAAGAAAAATAAA 399923 i i - - vv --- i v i ii v i L1M4_orf2#LIN 614 ACCATATGTTAGGCCATAAAACAAGTCTCAATAAATTTAAAAGGATTGAA 663 chrXptel1M 399924 AT------AAATG-ATTTTCTGACCATAA-------ACAATAAAAAT-AA 399958 ------ i i-i i i i ------- v v i - L1M4_orf2#LIN 664 ATCATACAAAGTATGTTCTCCGACCACAATGGAATGAAATTAGAAATCAA 713 chrXptel1M 399959 TAATA-AAGGATCTCTAAAACAAATATTTAAAATTAAATAGAAAGTAAAT 400007 i - vv i iii v ---- i v v vi i v i L1M4_orf2#LIN 714 TAACAGAAGGAAATTTGGGAAA----TTCACAAATATGTGGAAATTAAAC 759 chrXptel1M 400008 AACAA--TCCTAAGAAATGAGGGGAATCAAATAACAAATCATAGAAACAA 400055 v-- iv iv iv i- v v i iiiiv L1M4_orf2#LIN 760 AACACACTCCTAAATAACCAATGGG-TCAAAGAAGAAATCACAAGGGAAA 808 chrXptel1M 400056 TAATAACTTGCCATTAAAGAT-AATGACAATTGTGATAGAACAAATCAAA 400104 v v vv i -- vi - v ivivi i v v i L1M4_orf2#LIN 809 TTAGAAAATAC--TTTGAGATGAATGAAAACGAAAACACAACATACCAAA 856 chrXptel1M 400105 ATTTATGGAATGTAGCTAAAGCAGTACCTAGGGGAAATTTTCTACTTTTA 400154 i i i ? i i i i v v vi v L1M4_orf2#LIN 857 ACTTATGGGATGCAGCNAAAGCAGTGCTTAGAGGGAAATTTATAGCTGTA 906 chrXptel1M 400155 AATACTTGTCTCAATAAAAGAAAAAAAGA--GCATATCAATGAATTGATA 400202 i i i v i - - i --v v i vi i iv L1M4_orf2#LIN 907 AATGCCTATATTAA-AAAAG-AAGAAAGATCTCAAATCAATAACCTAACC 954 chrXptel1M 400203 ATGTAACTAAAAACAACTAGAAAACCAACAGAATACACCAAATAGAAATC 400252 v vi v v i - -- iv ii v i ivv -- L1M4_orf2#LIN 955 TTCCACCTTAAGA-AACTAGAAAA--AGAAGAGCAAACTAAACCCAAA-- 999 chrXptel1M 400253 TCAAATATCAAAGGAATG-ATTAACAAAG-TT-GAAAGGAAA 400291 v ii --i v - v i - - iv L1M4_orf2#LIN 1000 GCAAGCA--GAAGGAAGGAAATAATAAAGATTAGAGCGGAAA 1039 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 38.55 CpG sites = 68, Kimura (unadjusted) = 39.40 Transitions / transversions = 1.33 (68/51) Gap_init rate = 0.07 (30 / 412), avg. gap size = 1.50 (45 / 30) 270 28.40 6.47 1.90 chrXptel1M 400329 400529 (599471) L1M4_orf2#LINE/L1 1075 1284 (2010) m_b335s551i4 14065 chrXptel1M 400329 ATAAATAAAACTAAGATCTG-TTTTTTAAACAGCACTATAAAAATATATA 400377 v ii i i vi - i i v vv v i v i- i L1M4_orf2#LIN 1075 ATCAACGAAACCAAAAGTTGGTTCTTTGAAAAGATCAACAAAATTG-ACA 1123 chrXptel1M 400378 AGCCATTAGTTAACTTGAT--GTAAAGAAAGA-AGAAAACT-AAATTACT 400423 i v i ivi i--iv i - i - L1M4_orf2#LIN 1124 AACCTTTAGCTAGACTGACCAAGAAAAAAAGAGAGAAGACTCAAATTACT 1173 chrXptel1M 400424 ACTATCATGAGTAAA---GTGAAC-TTACAACCAG---TGAAGAAAAAGA 400466 vv v i i --- v i - v ii--- iv v - L1M4_orf2#LIN 1174 AAAATCAGGAATGAAAGAGGGGACATTACTACCGACCTTACAGAAATA-A 1222 chrXptel1M 400467 AAAGGCAATTATTAAGAGCTACTTTGCCCAATTTTATGCCAACGGATCTG 400516 -- v i iiv v vv v ii iv L1M4_orf2#LIN 1223 AAAGG--ATTATAAGGGAATACTATGAACAATTGTATGCCAACAAATTAG 1270 chrXptel1M 400517 ACAACCT-GATGGA 400529 i - i L1M4_orf2#LIN 1271 ATAACCTAGATGAA 1284 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 34.86 CpG sites = 32, Kimura (unadjusted) = 36.57 Transitions / transversions = 1.33 (32/24) Gap_init rate = 0.06 (12 / 200), avg. gap size = 1.42 (17 / 12) 1442 29.13 2.66 1.55 chrXptel1M 400788 401425 (598575) C L1ME4c_3end#LINE/L1 (184) 646 2 m_b335s551i5 14066 chrXptel1M 400788 TTTTG-GTTCTGCTTGTTTTGCTCAGCATCAGTTCATGTAAATCTTTCCA 400836 -i v ii i i i vv iv v - C L1ME4c_3end#L 646 TTTTGTATTCTGCTTTTTTCACTTAACATTATATCATAAACAT-TTTCCA 598 chrXptel1M 400837 AGTCTTTCTAAAATCAGCTTGATCATCATCATTAATAGA---ATAATATT 400883 v ivi vi v i vv v i i iv i v--- C L1ME4c_3end#L 597 TGTTGCTACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATT 548 chrXptel1M 400884 CCATTGCCTGCATATATCACAACTTGTTCAGCCACTCCCCAATTAATAGG 400933 i vv ?v i i i i ii i i i v iv i i C L1ME4c_3end#L 547 CCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGA 498 chrXptel1M 400934 CACCTACTCATTTTCCAGTTCTTTGCCACCACCAAAAGAACTGCTCCAA- 400982 ii vvivv i i i i ii i-- v - v - C L1ME4c_3end#L 497 CATTTAGGTTGTTTCCAATTTTTCGCTATTAT--AAATAAC-GCTGCAAT 451 chrXptel1M 400983 --ACATTTTAGTACATGTGGGTGCTTTTCCTTTCTTTG--TGATTTTCTT 401028 -- i v i i i v -- ii -- v i C L1ME4c_3end#L 450 GAACATCTTCGTGCATATAGCT--TTTTCCTTCTTTTGAATTATTTCCTT 403 chrXptel1M 401029 GGGATACAGACCCATTAGTGGCACTGCTGGGTCAAAAAGGGTATGCAGAG 401078 i v vv vv v i i -- v v v C L1ME4c_3end#L 402 AGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAA--GGGTATGAACAT 355 chrXptel1M 401079 TTATACAGTCCTTTGGT---CAGTTCCAAATTGTCTCTCCAGAATGGTTG 401125 v ii ii - i ---i v v - i i v C L1ME4c_3end#L 354 TTTTATGGCTCTT-GATACGTATTGCCAAATTG-CTTTCCAAAAGGGTTG 307 chrXptel1M 401126 GATCGTTTCACAATTTCACCAACAATGCATTAATGTCCCAGTTTTCCCAC 401175 v i iv i ? vi i i v i? v iv i C L1ME4c_3end#L 306 TACCAATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCACCGC 257 chrXptel1M 401176 ATACCCTCTAACATT---TATAATTTTTTCCTTTCATTTTAGCCCATCTG 401222 ?v i v i i --- v ivv ii vv v iv i i C L1ME4c_3end#L 256 ANCCTCGCCAGCATTGGGTATTATCAATTTTTTAAATTTTTGCTAATTTA 207 chrXptel1M 401223 AGAGGTGTGAGGTGATACCTCAGAGTTGTTTTAATTTGCATTTCTCTAAT 401272 v i i ii i i vv i i i C L1ME4c_3end#L 206 ATAGGCGTAAAATGGTATCTCATTGTTGCTTTAATTTGCATTTCTTTGAT 157 chrXptel1M 401273 CAATAGTGATTTAGAGCATCTTTTCACATGACTATAGATGATTTTAATTT 401322 i v i vv v i i i ii vi i vv iv ? vv C L1ME4c_3end#L 156 TACTAGCGAGGTTGAACATTTTTCCATGTGTTTGTTTACTANTTGTATTT 107 chrXptel1M 401323 CCTCATCTGAAAACTGTCCGTTCATATCCTTTGACCATTTATCAAGTGAG 401372 v ? vi i i i v v v i C L1ME4c_3end#L 106 CCTCTTNTGTGAATTGTCTGTTCATGTCCTTTGCCCATTTATCTATTGGG 57 chrXptel1M 401373 G-AATGACATATTT-TTATAAATTTGACACAGTTCTTTATATATTTTAGA 401420 -vv i? v - v vvv i ? v? C L1ME4c_3end#L 56 GTCTTGATNTTTTTCTTATCAATTTGAATGAGCTCTTTATATANTANAGA 7 chrXptel1M 401421 AATTA 401425 v C L1ME4c_3end#L 6 TATTA 2 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 37.03 CpG sites = 100, Kimura (unadjusted) = 38.36 Transitions / transversions = 1.20 (100/83) Gap_init rate = 0.03 (19 / 637), avg. gap size = 1.42 (27 / 19) 365 27.57 4.78 2.82 chrXptel1M 401279 401487 (598513) C L1M3_orf2#LINE/L1 (0) 3288 3076 m_b335s551i7 14066 chrXptel1M 401279 TGATTTAGAGCATCTTTTCACATGACTATAGATGATTTTAATTTCCTCAT 401328 v v i iv i v iiv vv v i v C L1M3_orf2#LIN 3288 TGATGTTGAGCATCTTTTCATATACCTGTTGGCCATTTGTATGTCTTCTT 3239 chrXptel1M 401329 CTGAAAACTGTCCGTTCATATCCTTTGACCATTTATCAAGTGAGGAATGA 401378 iv i v ii vi v v ? vi i --- v C L1M3_orf2#LIN 3238 TGGAGAAATGTCTATTCAGGTCCTTTGCCCATTTTTNAATCGGG---TTA 3192 chrXptel1M 401379 CATATTTT-----TATAAATTTGACACAGTTCTTTATATATTTTAGAAAT 401423 iv i ----- vi v vv?v i i v C L1M3_orf2#LIN 3191 TTTGTTTTTTTGCTATTGAGTTGTANGAGTTCCTTATATATTTTGGATAT 3142 chrXptel1M 401424 TAG---ATTATCAGAAACATTGGCTATAAAAATATTTTCCCCCAGCTTTG 401470 i---v v i - i - iv i -i ii C L1M3_orf2#LIN 3141 TAACCCCTTATCAGATATA-TGGTT-TGCAAATATTTTCTCCCA-TTCCG 3095 chrXptel1M 401471 TA--TTTCCCTTTTAATCT 401487 -- v i i v C L1M3_orf2#LIN 3094 TAGGTTGCCTTTTCACTCT 3076 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 33.71 CpG sites = 28, Kimura (unadjusted) = 35.22 Transitions / transversions = 1.00 (28/28) Gap_init rate = 0.04 (9 / 208), avg. gap size = 1.78 (16 / 9) 391 27.71 2.69 1.06 chrXptel1M 401279 401464 (598536) C L1M4_orf2#LINE/L1 (0) 3294 3106 m_b335s551i6 14066 chrXptel1M 401279 TGATTTAGAGCATCTTTTCACATGACTATAGATGATTTTAATTTCCTCAT 401328 v v ii vi v iiv vv v i v C L1M4_orf2#LIN 3294 TGATGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGTATATCTTCTT 3245 chrXptel1M 401329 CTGAAAACTGTCCGTTCATATCCTTTGACCATTTATCAAGTGAGGAA--T 401376 iv i v ii v v v ? v i vv -- C L1M4_orf2#LIN 3244 TGGAGAAATGTCTATTCAAATCCTTTGCCCATTTTTNAATTGGGTTATTT 3195 chrXptel1M 401377 GACATATTTTTATAAATTTGACACAGTTCTTTATATATTTTAGAAATTAG 401426 v v v v i vi v vv v i i v i? C L1M4_orf2#LIN 3194 GTCTTTTTATTGTTGAGTTGTAAGAGTTCTTTATATATTCTGGATACNAG 3145 chrXptel1M 401427 ---ATTATCAGAAACATTGGCTATAAAAATATTTTCCCCCA 401464 ---v v i -- v v iv i C L1M4_orf2#LIN 3144 TCCCTTATCAGATATAT--GATTTGCAAATATTTTCTCCCA 3106 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.11 CpG sites = 19, Kimura (unadjusted) = 35.11 Transitions / transversions = 0.59 (19/32) Gap_init rate = 0.02 (4 / 185), avg. gap size = 1.75 (7 / 4) 746 32.08 5.28 2.89 chrXptel1M 401548 402324 (597676) L1M4_orf2#LINE/L1 1328 2122 (1172) m_b335s551i8 14065 chrXptel1M 401548 AAGAGGAAATAGAATA-CTGAA-----CTATCTTAGGAAAAGAAATTGAA 401591 i v - ----- vvi i v i L1M4_orf2#LIN 1328 AAGAAGAAATAGAAAATCTGAATAGACCTATAACAAGTAAAGAGATTGAA 1377 chrXptel1M 401592 CAAGT---CAAATGAAGTCCAAAAGGGGAAAAACAACTCCCAGGACCAGA 401638 iv --- vi vv v v ii i i------ ? L1M4_orf2#LIN 1378 TTAGTAATCAAAAAACTTCCCACAAAGAAAAG------CCCAGGNCCAGA 1421 chrXptel1M 401639 GAGATTTACAAGTGAATTCAACCAAACA----AAAAATAATTAATTCTAA 401684 vi v i vi v ---- i v iv i L1M4_orf2#LIN 1422 TGGCTTCACTGGTGAATTCTACCAAACATTTAAAGAAGAATTAACACCAA 1471 chrXptel1M 401685 TACCACATAAACTATTTGAAAATAATTGAAAAGAAGG-AACCCTACCAAA 401733 v iv i v iv - v i i - v v v L1M4_orf2#LIN 1472 TCCTTCACAAACTCTTCCAAAA-AATAGAAGAGGAGGGAACACTTCCCAA 1520 chrXptel1M 401734 TTCTTCCTATGACACAAATACAGTTTTGATATCTGA-CTAGGGAAAGCCA 401782 i v i vi v i iviiii i vi - i iv v L1M4_orf2#LIN 1521 CTCATTCTATGAGGCCAGTATTACCCTGATACCAAAACCAGACAAAGACA 1570 chrXptel1M 401783 AAACAGAGGGAAAAACCTATAGAACAACTTTCCTAATGAATATTGATACA 401832 vv iiiii i v i v iv i v v i L1M4_orf2#LIN 1571 TCACAAGAAAAGAAAACTACAGACCAATATCCCTTATGAATATAGATGCA 1620 chrXptel1M 401833 AAAGAAATTAAACAAAATACTTGCAAGGACATTGCTATAACATATCATAA 401882 - vvi v v ivvv v v vii v v L1M4_orf2#LIN 1621 AAA-ATCCTCAACAAAATACTAGCAAACCGAATCCAGCAACATATAAAAA 1669 chrXptel1M 401883 AGATCATAT-CCATATCTAGGCAGAACTTATACCAGGAATAGAGGGCCAG 401931 i i i- iv i i ii i i v iv i iii L1M4_orf2#LIN 1670 GGATTATACACCATGACCAAGTGGGATTTATCCCAGGAATGCAAGGTTGG 1719 chrXptel1M 401932 TTC--TGTACAAAGAAACCATAAGCATAATTGACTAGATTTATA------ 401973 --ii ? i - v v v iii vv i v v ------ L1M4_orf2#LIN 1720 TTCAACATNCGAA-AATCAATCAATGTAATACACCATATTAATAGAATAA 1768 chrXptel1M 401974 ---ACAAAAATAATAT---TATTTCAATGGATGCTAAAAAAGCTTTAGAC 402017 --- iv i ---i i i i vi v v L1M4_orf2#LIN 1769 AGGACAAAAACCACATGATCATCTCAATAGACGCAGAAAAAGCATTTGAC 1818 chrXptel1M 402018 AAAATACAATACCCATTCCTATTAAAAAAAA-CAATAGAAAGCATAGGAA 402066 v i v v iv v v- i i --- - L1M4_orf2#LIN 1819 AAAATCCAACACCCTTTCATGATAAAAACACTCAACAAA---C-TAGGAA 1864 chrXptel1M 402067 TA-AATGAAACTTTTCTAAAATGATAAATAGAATTTCTCTAAAACCAA-- 402113 - v i iiii vv vi v i vivv v -- L1M4_orf2#LIN 1865 TAGAAGGGAACTTCCTCAACCTGATAAAGGGCATCTACGAAAAACCCACA 1914 chrXptel1M 402114 GACAGTATTATTTTTAATAGGAACAAACTAAAAGCATATACAATAAAATT 402163 vi ii i vi i vi v i i ? v viv vv i i L1M4_orf2#LIN 1915 GCTAACATCATACTTAATGGTGAAAGACTGAANGCTTTCCCCCTAAGATC 1964 chrXptel1M 402164 GGATGCAG--CAAAGATTCCCATTATCACA----TTATTTAATAGAGCAT 402207 i ivi i-- i vi ii v i v----i i i vv i i L1M4_orf2#LIN 1965 AGGAACAAGACAAGGATGTCCGCTCTCGCCACTTCTATTCAACATTGTAC 2014 chrXptel1M 402208 TGGAAGTTCTAGTTATCGCAGTAATAACAAACACCAAAAAAGAAATTGAA 402257 i ii vv i v -ii i----- vi L1M4_orf2#LIN 2015 TGGAGGTTCTAGCCAGGGCAATTA-GGCAAG-----AAAAAGAAATAAAA 2058 chrXptel1M 402258 GTAATAAAGCAAAGAGAAAGAAGAAATAAAACCATC-ATAGTTGCAAGAT 402306 vv vv - vv ii i i i -v v i i--- L1M4_orf2#LIN 2059 GGCATCCAG-ATTGGAAAGGAAGAAGTAAAACTATCTCTATTCGCAG--- 2104 chrXptel1M 402307 ATAAAATAAACCTATATA 402324 i v i v i i L1M4_orf2#LIN 2105 ATGACATGATCTTGTATA 2122 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 41.78 CpG sites = 134, Kimura (unadjusted) = 43.20 Transitions / transversions = 1.24 (134/108) Gap_init rate = 0.05 (40 / 776), avg. gap size = 1.60 (64 / 40) 758 31.57 4.96 2.13 chrXptel1M 401617 402302 (597698) L1MD_orf2#LINE/L1 1399 2103 (1191) m_b335s551i9 14065 chrXptel1M 401617 AAAAACAACTC-CCAGGACCAGAGAGATTTACAAGTGAATTCAACCAAAC 401665 v v - v vi v i vi v v L1MD_orf2#LIN 1399 AAAAAGAAATCTCCAGGCCCAGATGGTTTCACTGGAGAATTCTACCAAAC 1448 chrXptel1M 401666 ----AAAAAATAATTAATTCTAATACCACATAAACTATTTGAAAATAATT 401711 ---- i v iv i v i i v v iv i - v L1MD_orf2#LIN 1449 GTTTAAAGAAGAATTAACACCAATTCTACACAATCTCTTCCAGAA-AATA 1497 chrXptel1M 401712 GAAAAGAAGG-AACCCTACCAAATTCTTCCTATGACACAAATACAGTTTT 401760 i i - v v v i v ii vi v i iviiii L1MD_orf2#LIN 1498 GAAGAGGAGGGAACACTTCCCAACTCATTTTATGAGGCCAGTATTACCCT 1547 chrXptel1M 401761 GATATCTGA-CTAGGGAAAGCCAAAACAGAGGGAAAAACCTATAGAACAA 401809 i vi - i iv v iv i iii i v i v L1MD_orf2#LIN 1548 GATACCAAAACCAGACAAAGACAGTACAAAAAAAGAAAACTACAGACCAA 1597 chrXptel1M 401810 CTTTCCTAATGAATATTGATACAAAAGAAATTAAACAAAATACTTGCAA- 401858 iv i v i v ii - vvi v i v - L1MD_orf2#LIN 1598 TATCCCTCATGAACATAGACGCAAAA-ATCCTCAACAAAATATTAGCAAA 1646 chrXptel1M 401859 -GGACATTGCTATAACATATCATAAAGATCATAT-CCATATCTAGGCAGA 401906 -? - - vii i v v ii i i- iv i i ii i L1MD_orf2#LIN 1647 TNGA-ATT-CAGCAATATATAAAAAGAATTATACACCATGACCAAGTGGG 1694 chrXptel1M 401907 ACTTATACCAGGAATAGAGGGCCAGTTCTGTA--CAAAGAAACCATAAGC 401954 ii v ? iv i ii vi -- i - v v v ii L1MD_orf2#LIN 1695 GTTTATTCCAGGNATGCAAGGCTGGTTCAATATTCGAA-AATCAATCAAT 1743 chrXptel1M 401955 ATAATTGACTAGATTTATA---------ACAAAAATAATATTATT---TC 401992 i iv i v v i --------- v v i v i--- L1MD_orf2#LIN 1744 GTAATCCACCATATTAACAGGCTAAAGAAGAAAAATCACATGATCATATC 1793 chrXptel1M 401993 AATGGATGCTAAAAAAGCTTTAGACAAAATACAATACCCATTCCTATTAA 402042 v vi v v v i -- v v L1MD_orf2#LIN 1794 AATTGATGCAGAAAAAGCATTTGACAAAATTCAACACCCATTC--ATGAT 1841 chrXptel1M 402043 AAAAAACAATAGAAAGCATAGGAATA-AATGAAACTTTTCTAAAATGATA 402091 vivvi ? i - - iv i iiii vv L1MD_orf2#LIN 1842 AAAAACTCTCAGNAAAC-TAGGAATAGAGGGGAACTTCCTCAACTTGATA 1890 chrXptel1M 402092 AATAGAATTTCTCTAAAACC--AAGACAGTATTATTTTTAATAGGAACAA 402139 v v i vivv --v vi ii i vi i vi v i L1MD_orf2#LIN 1891 AAGAGCATCTACAAAAAACCTACAGCTAACATCATACTTAATGGTGAAAG 1940 chrXptel1M 402140 ACTAAAAGCATATACAATAAAATTGGATGCA--GCAAAGATTCCCATTAT 402187 i v v viv vv i i ivi -- i vi ii v L1MD_orf2#LIN 1941 ACTGAATGCTTTCCCCCTAAGATCGGGAACAAGGCAAGGATGTCCGCTCT 1990 chrXptel1M 402188 CAC----ATTATTTAATAGAGCATTGGAAGTTCTAGTTATCGCAGTAATA 402233 ----v i i v i i ii vi i -i L1MD_orf2#LIN 1991 CACCACTCTTATTCAACATAGTACTGGAAGTTCTAGCCAGTGCAATAA-G 2039 chrXptel1M 402234 ACAAACACCAAAAAAGAAATTGAAGTAATAAAGCAAAGAGAAAGAAGAAA 402283 i -----i i vi vv v - vv ii i L1MD_orf2#LIN 2040 GCAA-----GAAAAGGAAATAAAAGGCATACAG-ATTGGAAAGGAAGAAA 2083 chrXptel1M 402284 TAAAACCAT-CATAGTTGCA 402302 ii - v v L1MD_orf2#LIN 2084 TAAAACTGTCCCTATTTGCA 2103 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 41.24 CpG sites = 118, Kimura (unadjusted) = 42.32 Transitions / transversions = 1.26 (118/94) Gap_init rate = 0.04 (30 / 685), avg. gap size = 1.63 (49 / 30) 21 16.52 5.56 0.00 chrXptel1M 402769 402822 (597178) (TTCTTT)n#Simple_repeat 1 57 (0) m_b335s252i10 14067 chrXptel1M 402769 TTCTTTTTC-TTTT-TTTTT-TTTTTCTTTTCCTATTTATTTAGTATTTT 402815 - - - i v v vviv (TTCTTT)n#Sim 1 TTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTT 50 chrXptel1M 402816 ATTTTTC 402822 v (TTCTTT)n#Sim 51 CTTTTTC 57 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.06 (3 / 53), avg. gap size = 1.00 (3 / 3) 28 19.30 0.00 0.00 chrXptel1M 403252 403304 (596696) (A)n#Simple_repeat 1 53 (0) m_b335s252i11 14068 chrXptel1M 403252 AAAAAAAAATAAAAAAAATAAAAATAAAAAAAAAATAAAATTGCAAAGAA 403301 v v v v vviv i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chrXptel1M 403302 AAA 403304 (A)n#Simple_r 51 AAA 53 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 23 22.39 1.61 0.00 chrXptel1M 403253 403314 (596686) (AAAAAG)n#Simple_repeat 1 63 (0) m_b335s252i12 14068 chrXptel1M 403253 AAAAAAAATAAAAAAAATAAAAATAAAAA-AAAAATAAAATTGCAAAGAA 403301 i v i v v - v vviv (AAAAAG)n#Sim 1 AAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAA 50 chrXptel1M 403302 AAAGAGCAAGAAA 403314 iv (AAAAAG)n#Sim 51 AAAGAAAAAGAAA 63 Matrix = Unknown Transitions / transversions = 0.50 (4/8) Gap_init rate = 0.02 (1 / 61), avg. gap size = 1.00 (1 / 1) 41 2.43 0.00 2.33 chrXptel1M 405266 405309 (594691) (AC)n#Simple_repeat 1 43 (0) c_b335s251i2 14069 chrXptel1M 405266 ACACACACACACACACACACATCACACACACACACACAGACACA 405309 - v (AC)n#Simple_ 1 ACACACACACACACACACACA-CACACACACACACACACACACA 43 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.02 (1 / 43), avg. gap size = 1.00 (1 / 1) 698 24.40 0.60 0.00 chrXptel1M 405914 406081 (593919) MIR#SINE/MIR 88 256 (6) m_b335s601i22 14070 chrXptel1M 405914 ACCCTGGCCAAGTCACTTAAT-TCCATTTGCCACCATTCCCTCAACTGTA 405962 i v i i- iv v v vi i v MIR#SINE/MIR 88 ACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTA 137 chrXptel1M 405963 GACTAAGGATAATAACAGCACCTACCTCCCAGAGTAGTTGTGAGGATCAA 406012 i v ii i i vi i v i MIR#SINE/MIR 138 AAATGGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGGATTAA 187 chrXptel1M 406013 ATGAGATGACAACTATAAAGTGCTTAGCATGGTGCCTGGAACATAGTAAG 406062 v i i vv i i v ii v MIR#SINE/MIR 188 ATGAGTTAATACATGTAAAGCGCTTAGAACAGTGCCTGGCACATAGTAAG 237 chrXptel1M 406063 TACTATAGAAGTGCTAGCT 406081 ii vv v i i MIR#SINE/MIR 238 CGCTCAATAAATGTTAGCT 256 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 28.30 CpG sites = 24, Kimura (unadjusted) = 30.11 Transitions / transversions = 1.41 (24/17) Gap_init rate = 0.01 (1 / 167), avg. gap size = 1.00 (1 / 1) 50 20.58 1.77 0.88 chrXptel1M 406185 406297 (593703) (CA)n#Simple_repeat 1 114 (0) m_b335s252i13 14071 chrXptel1M 406185 CACGCACAGACACACACAGAGTCACACACAGTCAGAGACACACAGTCACA 406234 i v v vv vv v v vv (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 chrXptel1M 406235 GGCACACAC-CACACACACATAGACACACACACATACAGACATACACTCA 406283 vi - i v i v i v (CA)n#Simple_ 51 CACACACACACACACACACACACACACACACACACACACACACACACACA 100 chrXptel1M 406284 CAC-CACATACTACA 406297 - i - (CA)n#Simple_ 101 CACACACACAC-ACA 114 Matrix = Unknown Transitions / transversions = 0.43 (6/14) Gap_init rate = 0.03 (3 / 112), avg. gap size = 1.00 (3 / 3) 18 3.33 6.06 2.94 chrXptel1M 407215 407247 (592753) (GAG)n#Simple_repeat 1 34 (0) m_b335s252i14 14072 chrXptel1M 407215 GAGAGAGGGGGAGGAGGAGGA-GAGGAGGA-GAGG 407247 - i - - (GAG)n#Simple 1 GAG-GAGGAGGAGGAGGAGGAGGAGGAGGAGGAGG 34 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.09 (3 / 32), avg. gap size = 1.00 (3 / 3) 12 23.91 5.36 1.72 chrXptel1M 407880 407935 (592065) (GGCGAGG)n#Simple_repeat 1 58 (0) m_b336s252i3 14073 chrXptel1M 407880 GGCGA-CGGCGGAGGGC-AGGGGCGAGGGAC-CGGAAGTAGGCAGCTAGG 407926 -v ii - i -v iivv -i v (GGCGAGG)n#Si 1 GGCGAGGGGCGAGGGGCGAGGGGCGAGGGGCGAGGGGCGAGG-GGCGAGG 49 chrXptel1M 407927 GGCGAGGGG 407935 (GGCGAGG)n#Si 50 GGCGAGGGG 58 Matrix = Unknown Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.07 (4 / 55), avg. gap size = 1.00 (4 / 4) 287 20.03 2.53 5.19 chrXptel1M 409348 409426 (590574) DNM1r#Unknown 2470 2546 (2116) m_b336s502i0 14074 chrXptel1M 409348 TCAGCCA--TACATGTGTGTATATGCAGGTATATGTGTATGTGTGTATGT 409395 i -- ii ----i i i i DNM1r#Unknown 2470 TCGGCCACGTGTATGTGTGTATAT----ATGTGTGTATATGTGTGTATGT 2515 chrXptel1M 409396 ACATATATGTGTGTGTACATATATATTTATA 409426 iii i i i ii ? DNM1r#Unknown 2516 GTGTATATATGTGTATATATACGTATNTATA 2546 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 21.85 CpG sites = 15, Kimura (unadjusted) = 25.99 Transitions / transversions = 1.00 (15/0) Gap_init rate = 0.06 (5 / 78), avg. gap size = 1.20 (6 / 5) 236 27.14 0.00 0.00 chrXptel1M 409378 409447 (590553) DNM1r#Unknown 2476 2545 (2117) m_b336s502i1 14074 chrXptel1M 409378 ATGTGTATGTGTGTATGTACATATATGTGTGTGTACATATATATTTATAC 409427 i i ii i i i i ii i i i v i DNM1r#Unknown 2476 ACGTGTATGTGTGTATATATGTGTGTATATGTGTGTATGTGTGTATATAT 2525 chrXptel1M 409428 GGGTATATGCATGTATATAT 409447 v ii i ? DNM1r#Unknown 2526 GTGTATATATACGTATNTAT 2545 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 33.20 CpG sites = 17, Kimura (unadjusted) = 38.37 Transitions / transversions = 8.50 (17/2) Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0) 289 23.19 0.00 0.00 chrXptel1M 409397 409465 (590535) DNM1r#Unknown 2475 2543 (2119) m_b336s502i2 14074 chrXptel1M 409397 CATATATGTGTGTGTACATATATATTTATACGGGTATATGCATGTATATA 409446 ii i i i i i v i v i ii DNM1r#Unknown 2475 CACGTGTATGTGTGTATATATGTGTGTATATGTGTGTATGTGTGTATATA 2524 chrXptel1M 409447 TGTGCATATGTATGTATAT 409465 i i i ? DNM1r#Unknown 2525 TGTGTATATATACGTATNT 2543 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 25.85 CpG sites = 14, Kimura (unadjusted) = 30.61 Transitions / transversions = 7.00 (14/2) Gap_init rate = 0.00 (0 / 68), avg. gap size = 0.0 (0 / 0) 29 29.62 0.00 0.00 chrXptel1M 409467 409556 (590444) (TATATA)n#Simple_repeat 1 90 (0) m_b336s252i4 14075 chrXptel1M 409467 TATATATCTGTGTTTATATTTATGTCTGTCTATATATTTCTATGTCTCTA 409516 v i i v v i v i v v v i v v (TATATA)n#Sim 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chrXptel1M 409517 TATATACATATATCTATAGCTATATATCTCTATCTATCTA 409556 i v vv v v v v (TATATA)n#Sim 51 TATATATATATATATATATATATATATATATATATATATA 90 Matrix = Unknown Transitions / transversions = 0.38 (6/16) Gap_init rate = 0.00 (0 / 89), avg. gap size = 0.0 (0 / 0) 1064 29.07 3.41 2.79 chrXptel1M 411531 412029 (587971) C L1ME5_3end#LINE/L1 (313) 628 127 m_b336s551i0 14076 chrXptel1M 411531 TTTCACTTAGCATCA-GTTCATGTAAT-TCTCTCCAAGCCTCTCTGTATT 411578 i ii - -- v v- iv v iiv v i v C L1ME5_3end#LI 628 TTTCACTCAGCACTATGTT--TTTAAGATCCATCCATGTTGCTATGTGTA 581 chrXptel1M 411579 CATCCTGCTGGTCATTTCT---TACAGAACAGTAAAATTCCATAACATAC 411625 iv iiv iii --- i v v i ---i iiii i C L1ME5_3end#LI 580 CATCTAGTCCGTTGCTTCTAACTGCTGCATAGTA---CTCCATGGTGTGC 534 chrXptel1M 411626 ATATACCACAATTTACCCA-CCATTCTCCAATTGATGGGCATCCACTCAT 411674 vi v i - i v v i i vvivv C L1ME5_3end#LI 533 ATCCACCACATTTTACCTATCCACTCTCCCAGTGATGGACACCCAGGTTG 484 chrXptel1M 411675 TTTCCAGTTTCTAGCCACTACAAACAGGGCTGCCACAAACATTTTGGCAC 411724 ii ii i iv i iv v ii ii v i C L1ME5_3end#LI 483 CCTCCAACTCCCCGCCACCACAAACAACGCTGCAATGAACATCCTCGTAC 434 chrXptel1M 411725 ATACTGGTCCCTTT-----CCTTCTTTAGTATCTCCTTGGGGTATAAGCC 411769 ---- i ----- viv v v i i i vi C L1ME5_3end#LI 433 AT----GTCCCCTTATGGACCTGTGTGAGAATTTCTTTGGGATATATACC 388 chrXptel1M 411770 CAGTAGCAACACTGCTGGGTCAAAGGGTATGCACAGTTTGGTAACTTTTG 411819 v iiv i v ii vvi -- -- C L1ME5_3end#LI 387 CAGGAGCGGAATTGCTGGGTCATAGGGTATGCGTATACT--TAA--TTTG 342 chrXptel1M 411820 AGCA--TAGTTCCAAACTGCTTCTCCAGAATGGTTGGATT-GTTCACAAC 411866 vi -- v v i i - i v ii- ii vi C L1ME5_3end#LI 341 ACTAAGTACTGCCAGATTGCT-CTCCAGAATGGCTGCACCAGTCTACACT 293 chrXptel1M 411867 TCCACCAACAATGCATCAATGTCCC-AGTTTTCCGCATCC-CTCCAACAA 411914 i i i v iv i - v? ii i - v v C L1ME5_3end#LI 292 CCCACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATCCTCGCCAACAC 243 chrXptel1M 411915 TCATCATTATTTTTCCTGTCAACTTA-GCCAATCTGACAGGTGTGTAGTG 411963 iiv iivv i vii i v- i i i iv C L1ME5_3end#LI 242 TTGGCATTATCCAGCTTTCTAATTTTTGCCAGTCTAATAGGTGTAAAGTG 193 chrXptel1M 411964 GTATCTTAGAGTTGTCTTAATTTGCATTTCTCTGATTCATAATGACTTGG 412013 i i vv i vv v v C L1ME5_3end#LI 192 ATATCTCATTGTTGTTTTAATTTGCATTTCTCTGATTACTAATGAGTTTG 143 chrXptel1M 412014 AGCATCTTTTCATGTG 412029 i i C L1ME5_3end#LI 142 AGCATCTCTTCATATG 127 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.40 CpG sites = 86, Kimura (unadjusted) = 38.10 Transitions / transversions = 1.56 (86/55) Gap_init rate = 0.05 (24 / 498), avg. gap size = 1.29 (31 / 24) 18 0.00 7.41 0.00 chrXptel1M 412169 412195 (587805) (AAC)n#Simple_repeat 1 29 (0) m_b336s252i6 14077 chrXptel1M 412169 AACAA-AACAA-AACAACAACAACAACAA 412195 - - (AAC)n#Simple 1 AACAACAACAACAACAACAACAACAACAA 29 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.08 (2 / 26), avg. gap size = 1.00 (2 / 2) 793 31.06 4.10 3.99 chrXptel1M 418411 419312 (580688) L1M5_orf2#LINE/L1 2268 3170 (124) m_b336s551i1 14078 chrXptel1M 418411 AATCCCATTTAAAGTAACTACTGATAGTATAAAATATTTGGGAATCTATC 418460 v v i i vv vi v ii ? i i vv L1M5_orf2#LIN 2268 AATACCATTTACAATAGCATCAAAAAACATNAAATACTTAGGAATAAATC 2317 chrXptel1M 418461 TGCCAAGGGAAAAT---CAGAAACTTTATGAGCAAAACTACAAAACACTT 418507 iv --- ? --- ii v ? iivvv i v L1M5_orf2#LIN 2318 TAACAA---AANATGTGCAAGACCTNTACACTGAAAACTACAAAACATTG 2364 chrXptel1M 418508 TCCACACAAATTAAGTCTGATCTAACCAACTGGAAAAATATTAGATGCTC 418557 iiv v v ivvv i vi v i i vvv i L1M5_orf2#LIN 2365 CTGAGAGAAATTAAAGAAGACCTAAATAAATGGAGAGATATACCATGTTC 2414 chrXptel1M 418558 TTGGATTGGGCGAGCAAATATAATAAAGATGACAATATTACCTAAACTAA 418607 v iv viv vi ? v vi v i i i L1M5_orf2#LIN 2415 ATGGATTGGAAGACTCAATATTGTNAAGATGTCAATTCTCCCCAAATTGA 2464 chrXptel1M 418608 TCTATTTATTTAGCGCTATACCAATCAGACTCCCAAAAAACTATTTTGAT 418657 vv i ii v v i v iv iii v -- L1M5_orf2#LIN 2465 TCTATAGATTCAATGCAATCCCAATCAAAATCCCAGCAGGTTTTTTTG-- 2512 chrXptel1M 418658 GACCTACAAAAAATAACAA--------CAAAGTTCATATGGAAAAACAAA 418699 ------i i v i --------i i i vi L1M5_orf2#LIN 2513 ------TAGAAATTGACAAGCTGATTCTAAAATTTATATGGAAATGCAAA 2556 chrXptel1M 418700 AGGTCAAGAAT-GTCAAGGGAATTAATGAAAAAAAAAATCAAA--TGAAG 418746 i ii ? - i iiv i-v i i v -- i L1M5_orf2#LIN 2557 GGACCNAGAATAGCCAAAACAATC-TTGAAAAAGAAGAACAAAGTTGGAG 2605 chrXptel1M 418747 GTGGCCTAGCTGTACCAGATCT-AAAACTATATTATAAGGC-AGGGTTAC 418794 -- i i - vv ? ? - i - i - vi v i L1M5_orf2#LIN 2606 --GACTTA-CACTACCNGATNTCAAGACT-TATTATAAAGCTACAGTAAT 2651 chrXptel1M 418795 TAAAACTATCTGGTATTGAC-TAAGAAATAGACTAG-GGATCAATGGAAT 418842 i i vi v i - -i v i-i i L1M5_orf2#LIN 2652 CAAGACAGTGTGGTATTGGCGTAAG-GATAGACAAATAGATCAATGGAAC 2700 chrXptel1M 418843 AAGTTAGGTTCAAAGGACA-AAATAG--CCA-ATAACTTTAATTATCTAG 418888 iiv ---- i vv - -- - i vv v ii?i ?i ii L1M5_orf2#LIN 2701 AGAATAG----AGAGTCCAGAAATAGACCCACACATATATGGNCANTTGA 2746 chrXptel1M 418889 TGTTTGACAAA---CCCAAAGACCCCAGTTT-TTGGGATAAGAGTGCATT 418934 v ---v ? ---- i i-v iv ii ivvi L1M5_orf2#LIN 2747 TTTTTGACAAAGGTGCCAANG----CAATTCAGTGGGGAAAGGATAGTCT 2792 chrXptel1M 418935 ATTTGACAAAAATTGCTGGGAAAATTGGAAATTAGTATGGCAGAAACTAG 418984 v ii viv i v v ivi v i v ii L1M5_orf2#LIN 2793 TTTCAACAAATGGTGCTGGAACAATTGGATATCCATATGGAAAAAAATGA 2842 chrXptel1M 418985 GCATTGACCCACACTTAAGACCATACACCAAGATAAGGTCAAAATGGGTT 419034 i?v i vi i v v v i v iv ? i i- L1M5_orf2#LIN 2843 ANCTCGACCCCTACCTCACACCATACACAAAAATTAATTCNAGATGGA-T 2891 chrXptel1M 419035 CAT-GATTTAGGCATAAAGAATGAGATCATAAATAAATTGGAAG--AGCA 419081 - ii iiii ii? i i ii vvvvi i -- i L1M5_orf2#LIN 2892 CATAGACCTAAATGTAAAAGNTAAAACTATAAAACTTCTAGAAGAAAACA 2941 chrXptel1M 419082 TAGGATACTTTACCTCTCAGACCTGTGGAAGAGGAAGGAATTTATGACCA 419131 v v-- i iivv - i?v v iii v ---i L1M5_orf2#LIN 2942 TAGGAGAA--TATCTTCGTGACCT-TGGGNTAGGCAAAGATTTCT---TA 2985 chrXptel1M 419132 AAGAAGAACTAGAGATCACTATTGACTACAAAATAGAAAAT-------TT 419174 v i vvi i i v ? --- i i v i ------- L1M5_orf2#LIN 2986 AACAGGACACAAAAAGCACNA---ACCATAAAAGAAAAAATTGATAAATT 3032 chrXptel1M 419175 TGATTATATCAAATTGAAAAGTTTTTGTACAAACAAAACTAATGCAGACA 419224 v i ?i v v ii i iv ?vvv ivi vi ivi v L1M5_orf2#LIN 3033 GGACTNCATCAAAATTAAAAACTTCTGCTCNTCAAAAGACACCGTTAAGA 3082 chrXptel1M 419225 AGATTAGAAGGGAAACAACAAACTGGGAAAACATTTTTACAGT-CAAAGG 419273 i v i v i v i ? i v v i i?- v vi L1M5_orf2#LIN 3083 AAATGAAAAGGCAAGCCACAGANTGGGAGAAAATATTTGCAANACATATA 3132 chrXptel1M 419274 TCCTGATAAAGGCCTCATTTCCAAAATATATAGAGAACT 419312 - i v i v i i L1M5_orf2#LIN 3133 T-CTGACAAAGGACTCGTATCCAGAATATATAAAGAACT 3170 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.68 CpG sites = 154, Kimura (unadjusted) = 42.52 Transitions / transversions = 1.34 (154/115) Gap_init rate = 0.06 (53 / 901), avg. gap size = 1.38 (73 / 53) 368 24.04 0.96 0.00 chrXptel1M 419338 419441 (580559) L1ME3G_3end#LINE/L1 443 547 (377) m_b336s551i2 14078 chrXptel1M 419338 CATT-CAGCCCTTTTTGTAGTGGCTAAAAACTGGAAACTGAATGGATGTC 419386 - vi v i i v i vivv ii L1ME3G_3end#L 443 CATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTC 492 chrXptel1M 419387 CATCAGTTGGAGAATGGCTGAATCAATTGTGGTATATGATTATTATGGAA 419436 i v i i i v i vvv i L1ME3G_3end#L 493 CATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAA 542 chrXptel1M 419437 TATTA 419441 i L1ME3G_3end#L 543 TACTA 547 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 29.44 CpG sites = 14, Kimura (unadjusted) = 29.44 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.01 (1 / 103), avg. gap size = 1.00 (1 / 1) 244 27.16 4.95 4.95 chrXptel1M 419342 419523 (580477) L1MC1_3end#LINE/L1 452 633 (447) m_b336s551i4 14078 chrXptel1M 419342 CAGCCCTTTTTGTAGTGGCTAAAAACTGGAAACTGAAT--GGATGTCCAT 419389 ii v ii i v i vi i -- i--i v L1MC1_3end#LI 452 CAGCTTTATTCATAATTGCCAAAACTTGGAAGC--AACCAAGATGTCCTT 499 chrXptel1M 419390 CAGTTGGAGAATGGCTGAATCAATTGTGGTATATGATTATTATGGAATAT 419439 v v v i v i i vvvv iv L1MC1_3end#LI 500 CAGTAGGTGAATGGATAAATAAACTGTGGTACATCCAGACAATGGAATAT 549 chrXptel1M 419440 TACT--GTTCT-GTAAGAAATGA-CCAACAGG--ATGATTTCAGAAAGGC 419483 i -- iv -iv - i v i -- ------ i L1MC1_3end#LI 550 TATTCAGCGCTAAAAAGAAATGAGCTATCAAGCCATGA------AAAGAC 593 chrXptel1M 419484 CTGGA-GAGACTTACACGAACTGATGCTGAGTGAAATGAGC 419523 v - i v i v - iv i i vi L1MC1_3end#LI 594 ATGGAGGAAACTTAAATGCA-TATTACTAAGTGAAAGAAGC 633 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 33.47 CpG sites = 26, Kimura (unadjusted) = 34.36 Transitions / transversions = 1.24 (26/21) Gap_init rate = 0.08 (15 / 181), avg. gap size = 1.20 (18 / 15) 275 28.60 0.00 2.68 chrXptel1M 419342 419456 (580544) L1MB8_3end#LINE/L1 452 563 (362) m_b336s551i3 14078 chrXptel1M 419342 CAGCCCTTTTTGTAGTGGCTAAAAACTGGAAACTGAATGGATGTCCATCA 419391 vi v ii i i i v vivviii L1MB8_3end#LI 452 CAGCATTATTCATAATAGCCAAAAAGTGGAAACAACCCAAATGTCCATCA 501 chrXptel1M 419392 GTTGGAGAATGGCTGAATCAATTGTGGTATATGATTATTATGGAATATTA 419441 ii iv v i v v vvv iv L1MB8_3end#LI 502 ACTGATGAATGGATAAATAAAATGTGGTATATCCATACAATGGAATATTA 551 chrXptel1M 419442 CTGTTCTGTAAGAAA 419456 --- v i v L1MB8_3end#LI 552 ---TTCGGCAATAAA 563 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.39 CpG sites = 16, Kimura (unadjusted) = 36.39 Transitions / transversions = 1.00 (16/16) Gap_init rate = 0.03 (3 / 114), avg. gap size = 1.00 (3 / 3) 20 11.25 0.00 0.00 chrXptel1M 419982 420010 (579990) (A)n#Simple_repeat 1 29 (0) m_b336s252i8 14079 chrXptel1M 419982 AAATAAAAAAAAAGAAAAAAAAAAAGAAA 420010 v i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA 29 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 1285 28.56 3.57 2.35 chrXptel1M 420021 420608 (579392) L1ME5_3end#LINE/L1 56 650 (291) m_b336s551i5 14080 chrXptel1M 420021 CTCCAGTTGATAAATGGTCAAAGGATATGAACAGACAATTTTCAGATGAT 420070 i i v v v i v v v L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chrXptel1M 420071 GAAATTGAAACTATTACTACTCATATGAAAGAGTGTTCCAAATCACTATT 420120 iivi vvii vi vv iiii i v v i v L1ME5_3end#LI 106 GAAACCCGAAAGGCTAACAAGCATATGAAGAGATGCTCAAACTCATTAGT 155 chrXptel1M 420121 GATCAGAGAAATGCAAATTAAGATAACTCTGAGATACCACTACACAGCTG 420170 i i i vv i vi v i L1ME5_3end#LI 156 AATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCTA 205 chrXptel1M 420171 TCAGATTGGCCAGAATGACAGGGAAAGATAATGCAGAATGTTGGAG-GGA 420219 i i v i v v ii vvi vi i v - L1ME5_3end#LI 206 TTAGACTGGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTGGCGAGGA 255 chrXptel1M 420220 --TGGGAAAACAGGGACACTGATACATTGTTGGTAGAATTGTGAAC-AAT 420266 -- i ? i i v v i i i i i v ii -ii L1ME5_3end#LI 256 TGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACTGGT 305 chrXptel1M 420267 CCAACCATTCTGGAGAGCAATTTGGAACTA--TGCTCAAA--AAGTTATC 420312 v i i v v -- iv -- - - L1ME5_3end#LI 306 GCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTAAG-TAT- 353 chrXptel1M 420313 AAACTGTGCATACCCTTTGATCCAGCAAGTGTTGCTACTGGGCTTATACC 420362 -- --- v i - vii v iv i L1ME5_3end#LI 354 --AC---GCATACCCTATGACCCAGCAA-TTCCGCTCCTGGGTATATATC 397 chrXptel1M 420363 TCAAAGAGATACTAAAGAAGG-----AAAGGGACCTGTATGTGCCAAAAT 420407 i i v v viv ----- i v i ---- ii L1ME5_3end#LI 398 CCAAAGAAATTCTCACACAGGTCCATAAGGGGACATGTACG----AGGAT 443 chrXptel1M 420408 GTTTGTGGCAGCCCTGTTTGTAGTGGCCAGAAACTGAAACTGA-GTGGAT 420456 ii v vi i vi i ii i ivii -v i L1ME5_3end#LI 444 GTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGGGT 493 chrXptel1M 420457 GCCCATCAAT-TGAGAATGGTTGGGTAAATTGTGGTATATGAATGTTATG 420505 i v -v i v i v iv v iiii L1ME5_3end#LI 494 GTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACACCATG 543 chrXptel1M 420506 GAATATTATTGTTCTGTAAGAAATGACCAGCAGGATGAATACAGAGAGGC 420555 i i vvvv v v iii vii vi v i v vii L1ME5_3end#LI 544 GAGTACTATGCAGCAGTTAGAAGCAACGGACTAGATGTACACATAGCAAC 593 chrXptel1M 420556 TTGGAGAGA-CTGACATGAAC-TGATGCTAAGTGAAATGAGC-AGAACCA 420602 v vi - v v -- - ii i vi i- v L1ME5_3end#LI 594 ATGGATGGATCTTAAA--AACATAGTGCTGAGTGAAAAAAGTAAGAAACA 641 chrXptel1M 420603 G---GAGAT 420608 --- L1ME5_3end#LI 642 GAATGAGAT 650 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.07 CpG sites = 94, Kimura (unadjusted) = 36.92 Transitions / transversions = 1.34 (94/70) Gap_init rate = 0.04 (26 / 587), avg. gap size = 1.35 (35 / 26) 12 9.92 7.46 10.77 chrXptel1M 421453 421519 (578481) (AGAAAC)n#Simple_repeat 1 65 (0) m_b336s252i9 14081 chrXptel1M 421453 AGAAACAGAATAATCA-AAACAGAAAGACAGAAA-AGTAATGCA-AAAC- 421498 - - - - - - - - -i - - (AGAAAC)n#Sim 1 AGAAACAG-A-AA-CAGAAACAG-AA-ACAGAAACAG-AA-ACAGAAACA 43 chrXptel1M 421499 CAAAATGAAACA-AAAGAGAAA 421519 v vv - v (AGAAAC)n#Sim 44 GAAACAGAAACAGAAACAGAAA 65 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.18 (12 / 66), avg. gap size = 1.00 (12 / 12) 24 29.19 0.98 5.10 chrXptel1M 421753 421854 (578146) (AT)n#Simple_repeat 1 98 (0) m_b336s252i10 14082 chrXptel1M 421753 ATATATTTATATATGCATATGCAGATATATACATAAAGCATATCTATACA 421802 v ii ii v i v -i v i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATA-TATATATATATA 49 chrXptel1M 421803 TATATGCTGGATATGATGCTCATACATACACACACATAGATACATA-ATA 421851 -v iv - -v - i i i i i v i - (AT)n#Simple_ 50 TATAT-ATATATAT-AT-AT-ATATATATATATATATATATATATATATA 95 chrXptel1M 421852 TAT 421854 (AT)n#Simple_ 96 TAT 98 Matrix = Unknown Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.06 (6 / 101), avg. gap size = 1.00 (6 / 6) 13 22.14 4.65 0.00 chrXptel1M 421916 421958 (578042) (ATAC)n#Simple_repeat 1 45 (0) m_b336s252i11 14083 chrXptel1M 421916 ATACATATGTAGATATATACATAC--ACACACATACTCACACACA 421958 ii v i -- i vi i (ATAC)n#Simpl 1 ATACATACATACATACATACATACATACATACATACATACATACA 45 Matrix = Unknown Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.02 (1 / 42), avg. gap size = 2.00 (2 / 1) 17 12.68 0.00 0.00 chrXptel1M 421934 421959 (578041) (AC)n#Simple_repeat 1 26 (0) m_b336s252i12 14083 chrXptel1M 421934 ACATACACACACATACTCACACACAC 421959 i i v (AC)n#Simple_ 1 ACACACACACACACACACACACACAC 26 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 39 15.19 1.25 2.53 chrXptel1M 421961 422040 (577960) (TCCT)n#Simple_repeat 1 79 (0) m_b336s252i13 14084 chrXptel1M 421961 TCCTTCCCTCTTTCTTTCTTTCTTTCCTTCCTTCCTCCCTCCCTCCCTCC 422010 i i i i i i i i i (TCCT)n#Simpl 1 TCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC 50 chrXptel1M 422011 CTTCCTTCCTTCCTTCTCTT-CTCCCTCTCC 422040 - - i - (TCCT)n#Simpl 51 CTTCCTTCCTTCCTTC-CTTCCTTCCT-TCC 79 Matrix = Unknown Transitions / transversions = 1.00 (10/0) Gap_init rate = 0.04 (3 / 79), avg. gap size = 1.00 (3 / 3) 12 22.15 3.92 3.92 chrXptel1M 422449 422499 (577501) (ATAT)n#Simple_repeat 1 51 (0) m_b336s252i14 14085 chrXptel1M 422449 ATACATGT-TAAATATGATAAAGTATATGTTTA-ATATATGTATACATAT 422496 i i - v - v - i v - i i (ATAT)n#Simpl 1 ATATATATATATATAT-ATATA-TATATATATATATATATATATATATAT 48 chrXptel1M 422497 TTA 422499 v (ATAT)n#Simpl 49 ATA 51 Matrix = Unknown Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.08 (4 / 50), avg. gap size = 1.00 (4 / 4) 12 30.06 0.00 5.08 chrXptel1M 422535 422596 (577404) (AGAA)n#Simple_repeat 1 59 (0) m_b336s252i15 14086 chrXptel1M 422535 AGAAAGAAAGTAAAATAACCTGAGAAGAAAAAAAAAAATGCAAGCAAACA 422584 v i v ivvv - i i - v - v (AGAA)n#Simpl 1 AGAAAGAAAGAAAGAAAGAAAGA-AAGAAAGAAAGAAA-GAAAG-AAAGA 47 chrXptel1M 422585 ATAACAGAAAGA 422596 vi v (AGAA)n#Simpl 48 AAGAAAGAAAGA 59 Matrix = Unknown Transitions / transversions = 0.56 (5/9) Gap_init rate = 0.05 (3 / 61), avg. gap size = 1.00 (3 / 3) 305 28.99 1.42 2.14 chrXptel1M 422848 422988 (577012) C L1ME4c_3end#LINE/L1 (275) 555 416 m_b336s551i6 14087 chrXptel1M 422848 ATAATATTCCATAACGTTCATATACCACAATTTACCCAACCGTTCTCCAA 422897 viv ?v i i ii i i v C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chrXptel1M 422898 TTGATGGGCATCCATTCAATTTCCGGTTTCTAGCCACTATAAA-AGGGTT 422946 v i ii vvivi ii i v i i - iv i C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCT 456 chrXptel1M 422947 GCCACAAACAT-TTTACACATACGGGCCGCTTTCCATTCTTTT 422988 v ii - iiii ii -- vi - C L1ME4c_3end#L 455 GCAATGAACATCTTCGTGCATATAG--CTTTTTCC-TTCTTTT 416 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.43 CpG sites = 28, Kimura (unadjusted) = 39.11 Transitions / transversions = 2.33 (28/12) Gap_init rate = 0.04 (5 / 140), avg. gap size = 1.00 (5 / 5) 454 30.48 3.11 3.11 chrXptel1M 423532 423917 (576083) C L1MC4a_3end#LINE/L1 (2003) 626 241 m_b336s551i7 14088 chrXptel1M 423532 TTTCACTCAGCATCAGTTCGTGTAAGTCTCTCCAGGCC--TTTCT-GAAA 423578 i i vi vv v v i v vii -- iv - i C L1MC4a_3end#L 626 TTTCACTTAACAATATATCCTGGAAATCACTCCATATCAGTTCATAGAGA 577 chrXptel1M 423579 TCCTCCTGCTGGTCATTTCTTACAGA-ACAGTAATATTCCATAACATTCA 423627 i vv -- - i v-i - i i viii vv C L1MC4a_3end#L 576 TCTTCCTCAT--TC-TTTTTTACAGCTGCA-TAGTACTCCATTGTGTGGA 531 chrXptel1M 423628 TATACCACCATTTATTCAGCCATTCTCC-ACTGATGGGCATCCACTCAGT 423676 i ivi i ? - i?? ii vviv C L1MC4a_3end#L 530 TGTACCATAGTTTATTCAACCANTCTCCTATNNATGGGCATTTAGGTTGT 481 chrXptel1M 423677 TTCCAGTTTCTAGCCACTACAAAGAGGGCTGCCACAAACATTTTGGCACA 423726 i v i v v i v iv v ii i vii v ii C L1MC4a_3end#L 480 TTCCAATATTTTGCAATTACAAACAATGCTGCAATGAATAACCTTGTGCA 431 chrXptel1M 423727 GACAGGTCCCTTTC--CTTCTTTATGATCT--CTTTGGGGTATAAGCCCA 423772 v i-- ?vi v-- v v viv i v -- ii v vv i C L1MC4a_3end#L 430 TAT--GTNATTTTGTACATGTTGGAGGTGTATCTTCAGGGTAAATTCCTA 383 chrXptel1M 423773 GTTGTAGCACTGCTGGGTCAAAGGGTA--TGCACAGTTTGATAACTTT-T 423819 vv i v i -- i --- - ii - C L1MC4a_3end#L 382 GAAGTGGGATTGCTGGGTCAAAGGGTAAATGCATA---TG-TAGTTTTGT 337 chrXptel1M 423820 TGGGCTTAGTTTCAAATTTCTCTCCAGAATGACTGGATGTATTCACAATT 423869 i i-- v vi i i ? v ii v ivv? ii v i C L1MC4a_3end#L 336 TAGA--TATTGCCAAATTCCCCTCCANAAGGGTTGTACCANTTTGCATTC 289 chrXptel1M 423870 TCACCAACAATGTATCAGTGTCCCTTTTTCCCCACATCCCCTCCAACA 423917 i i v v v v v i v C L1MC4a_3end#L 288 CCACCAGCAATGTATGAGAGTGCCTGTTTCCCCACAGCCTCGCCAACA 241 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.76 CpG sites = 61, Kimura (unadjusted) = 40.76 Transitions / transversions = 1.15 (61/53) Gap_init rate = 0.05 (20 / 385), avg. gap size = 1.20 (24 / 20) 761 27.96 1.93 2.26 chrXptel1M 423609 423919 (576081) C L1ME3G_3end#LINE/L1 (377) 547 238 m_b336s551i8 14088 chrXptel1M 423609 TAATATTCCATAACATTCATATACCACCATTTATTCAGCCATTCTCC-AC 423657 i ii vv iv i i i - i C L1ME3G_3end#L 547 TAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTAT 498 chrXptel1M 423658 TGATGGGCATCCACTCAGTTTCCAGTTTCTAGCCACTACAAAGAGGGCTG 423707 i ii vviv i i v i i v iv C L1ME3G_3end#L 497 TGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCTG 448 chrXptel1M 423708 CCACAAACATTTTGGCACAGACAGGTCCCTTTCCTTCTTTATGA---TCT 423754 v ii ii v i vi ?-- i v v viv v ii --- i C L1ME3G_3end#L 447 CAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATTT 400 chrXptel1M 423755 CTTTGGGGTATAAGCCCAGTTGTAGCACTGCTGGGTCAAAGGGTATGCAC 423804 ? i i v v? ? vv i v i i C L1ME3G_3end#L 399 CTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGC 350 chrXptel1M 423805 AGTTTGATAACTTTT--TGGGCTTAGTTTCAAATTTCTCTCCAGAATGAC 423852 v --- v -- i i-- v vi v i i ? i C L1ME3G_3end#L 349 ATTTT---AAATTTTAATAGA--TACTGCCAAATTGCCCTCCAAAANGGC 305 chrXptel1M 423853 TGGATGTATTCACAATTTCACCAACAATGTATCAGTGTCCCTTTTTCCCC 423902 v ivv i v ii i i v v v iv C L1ME3G_3end#L 304 TGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCC 255 chrXptel1M 423903 ACATCCCCTCCAACATT 423919 i i v i C L1ME3G_3end#L 254 ACACCCTCGCCAACACT 238 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.00 CpG sites = 49, Kimura (unadjusted) = 36.61 Transitions / transversions = 1.36 (49/36) Gap_init rate = 0.03 (10 / 310), avg. gap size = 1.30 (13 / 10) 535 25.17 3.45 1.35 chrXptel1M 425520 425664 (574336) MIR3#SINE/MIR 23 170 (38) m_b336s601i0 14089 chrXptel1M 425520 AGAGCACTGGACCAAGAGTCCAGAGAAGTGGATTTAAATCATGGTCCTGC 425569 - iii vi vv i iv i vi ii MIR3#SINE/MIR 23 AGAGCAC-GGACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGC 71 chrXptel1M 425570 TACTAACAAACTGTGTCATCTTGAGCAAGTCATT---CTTCACTGGGTCT 425616 i v?i v i i i --- i v i MIR3#SINE/MIR 72 CACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCT 121 chrXptel1M 425617 CA-TTTTCTGTCCTGTAAATTCAGAGGCTTGGAG-AGAGTTATGTCTAAG 425664 - i vvi v v i v v- - v v MIR3#SINE/MIR 122 CAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGA-TGATCTCTAAG 170 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.42 CpG sites = 20, Kimura (unadjusted) = 31.46 Transitions / transversions = 1.25 (20/16) Gap_init rate = 0.03 (5 / 144), avg. gap size = 1.40 (7 / 5) 560 26.98 4.26 5.38 chrXptel1M 425674 425861 (574139) MIR3#SINE/MIR 10 195 (13) m_b336s601i1 14090 chrXptel1M 425674 TGACCTAGTGGAGAGAAT---GACCAG-AGTCAGAGAGTTTGAATTA-AG 425718 i iv ii ii--- ii - iiiiii ii v- MIR3#SINE/MIR 10 TGGCTGAGCAGAGAGAGCACGGACTGGGAGTCAGGAGACCTGGGTTCTAG 59 chrXptel1M 425719 TCTGAACTTTGCCATTC-CTCACTCTTGTGACCTTGGGCAAAGAGCTGCC 425767 ivii i i v- ?i v - ivvi v v MIR3#SINE/MIR 60 TCCCGGCTCTGCCACTAACTNGCTGT-GTGACCTTGGGCAAGTCACTTCA 108 chrXptel1M 425768 CTTCTCTGGGCCTCAGCTTCTTCACCAACTCT-TAAAATGA-GGGGCTGG 425815 i i i ----- - - i MIR3#SINE/MIR 109 CCTCTCTGGGCCTCAGTTTCCTCA-----TCTGTAAAATGAGGGGGTTGG 153 chrXptel1M 425816 ACTAAATGATCTATTACATCTCCTCTATCGTGCTCTAACCTTCAAT 425861 i v v vi i i i ---- i v v MIR3#SINE/MIR 154 ACTAGATGATCTCTAAGGTCCCTTCCA----GCTCTGACATTCTAT 195 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.48 CpG sites = 34, Kimura (unadjusted) = 35.42 Transitions / transversions = 2.43 (34/14) Gap_init rate = 0.09 (16 / 187), avg. gap size = 1.12 (18 / 16) 469 29.13 4.69 0.75 chrXptel1M 427843 427970 (572030) C MIRc#SINE/MIR (133) 135 3 m_b336s601i2 14091 chrXptel1M 427843 TAATGAAACGGAGACTCAGGAATGCTAAATGATTTGGCTAAAGTTGCACA 427892 i v v i ii v i i i v i i ii C MIRc#SINE/MIR 135 TGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACA 86 chrXptel1M 427893 ATTAACAAGTGTCAT-----GGATTCTGAACTTAGCTTTTCCTGCCTCCA 427937 ii ii v v----- i - ii v i v C MIRc#SINE/MIR 85 GCTAGTAAGTGGCAGAGCCGGGACTC-GAACCCAGGTCTTCCTGACTCCA 37 chrXptel1M 427938 AATCCAGAACACTTTCTAATATGCCA-AATGCCT 427970 i vi v i v iii - v C MIRc#SINE/MIR 36 AGTCCAGTGCTCTTTCCACTGCACCACACTGCCT 3 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.73 CpG sites = 25, Kimura (unadjusted) = 38.73 Transitions / transversions = 2.08 (25/12) Gap_init rate = 0.02 (3 / 127), avg. gap size = 2.33 (7 / 3) 17 9.12 0.00 0.00 chrXptel1M 430105 430128 (569872) (A)n#Simple_repeat 1 24 (0) m_b336s252i16 14092 chrXptel1M 430105 AAAAAAAAAAAAAAAAAAGAAGAA 430128 i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAA 24 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 49 0.00 0.00 0.00 chrXptel1M 431479 431520 (568480) (AT)n#Simple_repeat 1 42 (0) c_b336s251i0 14093 chrXptel1M 431479 ATATATATATATATATATATATATATATATATATATATATAT 431520 (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATAT 42 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 18 19.41 0.00 0.00 chrXptel1M 434832 434872 (565128) (AAAAAG)n#Simple_repeat 1 41 (0) m_b336s252i17 14094 chrXptel1M 434832 AAAAAGAAAAAGAAAAAAGAAAGGCAAAATAAAAATTAAAA 434872 ii i v v vv (AAAAAG)n#Sim 1 AAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAA 41 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 13 10.46 6.45 0.00 chrXptel1M 434898 434928 (565072) (AGACAC)n#Simple_repeat 1 33 (0) m_b336s252i18 14095 chrXptel1M 434898 AGACACACACACAGGCACAGA-A-AAACACAGA 434928 v i - - i (AGACAC)n#Sim 1 AGACACAGACACAGACACAGACACAGACACAGA 33 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2) 20 0.00 0.00 0.00 chrXptel1M 434998 435019 (564981) (CA)n#Simple_repeat 1 22 (0) m_b336s252i19 14096 chrXptel1M 434998 CACACACACACACACACACACA 435019 (CA)n#Simple_ 1 CACACACACACACACACACACA 22 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 190 30.34 2.20 2.20 chrXptel1M 435925 436015 (563985) C L2#LINE/L2 (730) 2352 2262 m_b336s601i3 14097 chrXptel1M 435925 AGATCTAGATATCTGAGTCATCTATTAAGAGATGACAATAAAACCCATAG 435974 v i v vv viivv v ii v v v -- C L2#LINE/L2 2352 AGATATAAATTTGGGAGTCATCAGCATATAGATGGTATTTAAAGCCAT-- 2305 chrXptel1M 435975 GAGATT--ATGAAGTCACAAAAAGAATGAATGTAAAGAGAGGA 436015 i -- ii v? ii i i i v i C L2#LINE/L2 2304 GAGACTGGATGAGATCACCNAGGGAGTGAGTGTAGATAGAGAA 2262 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.11 CpG sites = 14, Kimura (unadjusted) = 40.11 Transitions / transversions = 1.08 (14/13) Gap_init rate = 0.03 (3 / 90), avg. gap size = 1.33 (4 / 3) 741 33.62 3.40 2.24 chrXptel1M 436240 437033 (562967) L1M2_orf2#LINE/L1 2133 2935 (356) m_b336s551i9 14098 chrXptel1M 436240 AGATTCTACTAAAAAGCTATTAGAAATAATTCATAACTTTAGCAAGGTTG 436289 i i i i ? v i vv ii v i i i L1M2_orf2#LIN 2133 AGACTCCACCAAAAAACTNTTAGAACTGATAAACGAATTCAGTAAAGTTG 2182 chrXptel1M 436290 CAGGATACAAAATAAACCCACATAAATCCTCAGCATTTTTATACATCACC 436339 v vi v vvi i ii v L1M2_orf2#LIN 2183 CAGGATACAAAATCAACATACAAAAATCAGTAGCATTTCTATACGCCAAC 2232 chrXptel1M 436340 AACAAA--ATCCAATAGCAAGAGATACAAAGAGAAATTCCATTCACAATA 436387 i -- ii v -- i vv i i v i i L1M2_orf2#LIN 2233 AACGAACTATCTGAAA--AAGAAATCAAGAAAGCAATCCCATTTACAATA 2280 chrXptel1M 436388 ACTGTCGACAGCATAAAATATTTGGGAATCTATCTACCAAAGGAAAGTCA 436437 i iivi v iv ii i vv i v v iivvv L1M2_orf2#LIN 2281 GCTACAAAAAAAATAAAATACCTAGGAATAAATTTAACCAAGGAGGTGAA 2330 chrXptel1M 436438 GGAATTATGTGAGCAAAATTACAAAAAACTTTCCACACAAATAAAGTCAG 436487 i vi v iii ?v i i v vviv v v vi ivvi L1M2_orf2#LIN 2331 AGATCTCTACAANGAAAACTATAAAACACTGATGAAAGAAATTGAAGAGG 2380 chrXptel1M 436488 ACTTAAATAATTGGAAAAATATCAAGTGCTCATGGGTAGGCCAAGCTAAT 436537 vi ? v i vvi i v vvi ii L1M2_orf2#LIN 2381 ACACAAANAAATGGAAAGATATCCCATGCTCATGGATTGGAAGAATTAAT 2430 chrXptel1M 436538 ATAATAAAAATGACAATATTACCTAAATTAATCTACTTATTCAGTGCCAT 436587 vi v ? v i i vii vv i v L1M2_orf2#LIN 2431 ATTGTTAAAATGNCCATACTACCCAAAGCGATCTACAGATTCAATGCAAT 2480 chrXptel1M 436588 ATCAATCAAACT-CCGAAGAAATTATTTTACAGATCTAGAATAAGTAATA 436636 vi v v - i v v -i i vv v i? v L1M2_orf2#LIN 2481 CCCTATCAAAATACCAATGACATT-CTTCACAGAAATAGAAAAAANAATC 2529 chrXptel1M 436637 ACAAACGTTATCTGGAAGAACAAAAGGTCAAGAATTTC--AAGAGAT--T 436682 vi vv ii v vv ii vv vv -- vi -- L1M2_orf2#LIN 2530 CTAAAATTCGTATGGAACCACAAAAGACCCCGAATAGCCAAAGCAATCCT 2579 chrXptel1M 436683 TAATGAAAAAAATGTAAATGAAGGTGGCCTAGTTGTAACAGACCTAAAAC 436732 v iii i iiv iv i iiv vi ---v v v i v v L1M2_orf2#LIN 2580 GAGCAAAAAGAACAAAGCTGGAGGCATCACA---CTACCTGACTTCAAAA 2626 chrXptel1M 436733 TATATTATAAAGC---AGCGGTCA------TTTGATACTGGTAAAGAAAT 436773 i i --- iiii ------iv i i v i i L1M2_orf2#LIN 2627 TATACTACAAAGCTATAGTAACCAAAACAGCATGGTACTGGCATAAAAAC 2676 chrXptel1M 436774 AGAGAAGCTAATCAGTGGACTACATTAGGTTCACAGGAC---AAAAT-AG 436819 v viivi i i vi v v ------ i ---i - i L1M2_orf2#LIN 2677 AGACACATAGACCAATGGAACAGAATAG------AGAACCCAGAAATAAA 2720 chrXptel1M 436820 TTAATGA--CTATAGCAATCTACTGTTTGACAAA---CTCAAAGACATCC 436864 iv i v--i i v v iv v i ---vi ii v L1M2_orf2#LIN 2721 TCCACGCATTTACAGCCAACTGATTTTCGACAAAGGCGCCAAGAACATAC 2770 chrXptel1M 436865 AGCTTTTGGGATAAGAACTCACTATTTGACAAAAACTGATAGGAAAACTA 436914 ----? iv i vvv v ii i viv v i i L1M2_orf2#LIN 2771 A----NTGGGGAAAGGACAGTCTCTTCAATAAATGGTGCTGGGAAAACTG 2816 chrXptel1M 436915 GAAACTAGTATG--GAAGAAATTAGGCATTGACCCACATCTAACACTGTA 436962 v iivi -- - v ii - v vi vv ii L1M2_orf2#LIN 2817 GATATCCATATGCAGAAG-AATGAAAC-TAGACCCCTATCTCTCACCATA 2864 chrXptel1M 436963 TACCAAAATAAGGTTGAAATGGGTTCATGATTTAAACATAAAGATAGATA 437012 v v iv ii i v v i ii iiviv v L1M2_orf2#LIN 2865 TACAAAAATCAACTCAAAATGGATTAAAGACTTAAATGTAAGACCCGAAA 2914 chrXptel1M 437013 TTATAAAGAAATTAGAAAAAA 437033 i ivv i i L1M2_orf2#LIN 2915 CTATAAAACTACTAGAAGAAA 2935 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 44.45 CpG sites = 140, Kimura (unadjusted) = 46.21 Transitions / transversions = 1.16 (140/121) Gap_init rate = 0.04 (29 / 793), avg. gap size = 1.55 (45 / 29) 465 25.20 0.00 0.00 chrXptel1M 437114 437236 (562764) L1ME3G_3end#LINE/L1 426 548 (376) m_b336s551i10 14099 chrXptel1M 437114 GTATGTGCAAAAATGTTTGTGGCAGCCCTTTTTGTAGTGGCAAGAAACTG 437163 i i ii ii v vi v i i i i i L1ME3G_3end#L 426 GCATGTACAAGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTG 475 chrXptel1M 437164 GAAACTGAGTGGATGCCCATCAATTGGAGAATGGTTGAATAAATTATGGT 437213 vivv ii i v i i L1ME3G_3end#L 476 GAAACAACCTAAATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGT 525 chrXptel1M 437214 ATATGAGTTTTATGGAATATTAT 437236 vvi vi i L1ME3G_3end#L 526 ATATCCATACTATGGAATACTAT 548 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 30.66 CpG sites = 21, Kimura (unadjusted) = 31.91 Transitions / transversions = 2.10 (21/10) Gap_init rate = 0.00 (0 / 122), avg. gap size = 0.0 (0 / 0) 18 17.00 2.00 4.08 chrXptel1M 437494 437543 (562457) (TTTTC)n#Simple_repeat 1 49 (0) m_b336s252i20 14100 chrXptel1M 437494 TTTTATTGTTGTTTTCTTGCATTTTATTTTCTTTTTCATTT-TTTTCTTT 437542 v - v viv v - v - (TTTTC)n#Simp 1 TTTTCTT-TTCTTTTCTTTTCTTTTCTTTTC-TTTTCTTTTCTTTTCTTT 48 chrXptel1M 437543 T 437543 (TTTTC)n#Simp 49 T 49 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.06 (3 / 49), avg. gap size = 1.00 (3 / 3) 14 5.00 0.00 0.00 chrXptel1M 439088 439108 (560892) (CAA)n#Simple_repeat 1 21 (0) m_b336s252i21 14101 chrXptel1M 439088 CAACAACGACAACAACAACAA 439108 i (CAA)n#Simple 1 CAACAACAACAACAACAACAA 21 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 250 34.65 2.54 7.08 chrXptel1M 439750 439867 (560133) C MIRc#SINE/MIR (154) 114 2 m_b336s601i4 14102 chrXptel1M 439750 AGGTTAAGTGCTTTG--CAGGGTCATAGAACTAGTCAGTGTTAAGTGTCT 439797 vi -- i i v i v vi i------ C MIRc#SINE/MIR 114 AGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAG------ 71 chrXptel1M 439798 TTGGTCCATATATGAGCTCCAGTCCTCTTGAAATCAAAACCCTTGTTCTA 439847 --i i viv ivi i i vi i i vvi iv vv i v C MIRc#SINE/MIR 70 --AGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTT 23 chrXptel1M 439848 TCCACTGTGCCAT-CTAGCTC 439867 ii i- iv C MIRc#SINE/MIR 22 TCCACTGCACCACACTGCCTC 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 46.59 CpG sites = 23, Kimura (unadjusted) = 48.39 Transitions / transversions = 1.53 (23/15) Gap_init rate = 0.09 (10 / 117), avg. gap size = 1.10 (11 / 10) 19 0.00 0.00 0.00 chrXptel1M 443559 443579 (556421) (T)n#Simple_repeat 1 21 (0) m_b336s252i22 14103 chrXptel1M 443559 TTTTTTTTTTTTTTTTTTTTT 443579 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTT 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 460 29.13 4.69 0.75 chrXptel1M 445708 445835 (554165) MIRc#SINE/MIR 3 135 (133) m_b337s601i0 14104 chrXptel1M 445708 AGGCATT-TGGCATATTAGAAAGTGTTCTGGATTTGGAGGCAGGAAAAGC 445756 v - iii v i v iv i v i v MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chrXptel1M 445757 TAAGTTCAGAATCC-----ATGACACTTGTTAATTGTGCAACTTTAGCCA 445801 ii - i -----v v ii ii ii i i v MIRc#SINE/MIR 53 TGGGTTC-GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 101 chrXptel1M 445802 AATCATTTAGCATTCCTGAGTCTCCGTTTCATTA 445835 i i i v ii i v v i MIRc#SINE/MIR 102 AGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCA 135 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.73 CpG sites = 25, Kimura (unadjusted) = 38.73 Transitions / transversions = 2.08 (25/12) Gap_init rate = 0.02 (3 / 127), avg. gap size = 2.33 (7 / 3) 596 26.84 3.70 5.38 chrXptel1M 447823 448011 (551989) C MIR3#SINE/MIR (13) 195 10 m_b337s601i1 14105 chrXptel1M 447823 ATTGAAGGTTAGAGCACGATAGAGGAGATGTAATAGATCATTTAGTCCAG 447872 v v i ---- i i i iv v v i i C MIR3#SINE/MIR 195 ATAGAATGTCAGAGC----TGGAAGGGACCTTAGAGATCATCTAGTCCAA 150 chrXptel1M 447873 CCCCCTCATTTTA-AGAGTTGGTGAAGAAGCTGAGGCCCAGAGAAGGGCA 447921 - ----- i i i v v C MIR3#SINE/MIR 149 CCCCCTCATTTTACAGA-----TGAGGAAACTGAGGCCCAGAGAGGTGAA 105 chrXptel1M 447922 GCTCTTTGCCCAAGGTCACAAGAGTGAG-GAATGGCAAAGTTCAGACT-T 447969 ivvi - v i? -v i i iivi -v C MIR3#SINE/MIR 104 GTGACTTGCCCAAGGTCAC-ACAGCNAGTTAGTGGCAGAGCCGGGACTAG 56 chrXptel1M 447970 AATTCAAACTCTCTGACT-CTGGTC---ATTCTCTCCACTAGGTCA 448011 ii iiiiii - ii ---ii ii vi i C MIR3#SINE/MIR 55 AACCCAGGTCTCCTGACTCCCAGTCCGTGCTCTCTCTGCTCAGCCA 10 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.22 CpG sites = 34, Kimura (unadjusted) = 35.15 Transitions / transversions = 2.43 (34/14) Gap_init rate = 0.08 (15 / 188), avg. gap size = 1.13 (17 / 15) 528 25.17 3.45 1.35 chrXptel1M 448021 448165 (551835) C MIR3#SINE/MIR (38) 170 23 m_b337s601i2 14106 chrXptel1M 448021 CTTAGACATAACTCTC-TCCAAGCCTCTGAATTTACAGGACAGAAAA-TG 448068 v v - v- v i v v ivv i - C MIR3#SINE/MIR 170 CTTAGAGATCA-TCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTG 122 chrXptel1M 448069 AGACCCAGTGAAG---AATGACTTGCTCAAGATGACACAGTTTGTTAGTA 448115 i v i --- i i i v i?v i C MIR3#SINE/MIR 121 AGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTG 72 chrXptel1M 448116 GCAGGACCATGATTTAAATCCACTTCTCTGGACTCTTGGTCCAGTGCTCT 448165 ii iv i vi i vv iv iii - C MIR3#SINE/MIR 71 GCAGAGCCGGGACTAGAACCCAGGTCTCCTGACTCCCAGTCC-GTGCTCT 23 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.42 CpG sites = 20, Kimura (unadjusted) = 31.46 Transitions / transversions = 1.25 (20/16) Gap_init rate = 0.03 (5 / 144), avg. gap size = 1.40 (7 / 5) 16 0.00 0.00 0.00 chrXptel1M 448617 448633 (551367) (A)n#Simple_repeat 1 17 (0) m_b337s252i1 14107 chrXptel1M 448617 AAAAAAAAAAAAAAAAA 448633 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 866 30.00 0.96 1.28 chrXptel1M 449783 450096 (549904) L1ME4c_3end#LINE/L1 242 554 (276) m_b337s551i0 14108 chrXptel1M 449783 AATGTTGGAGGGGATGTGGGGAAAAAAGGGACACTGATACATTGTTGGTG 449832 i v i ? i v vv- v ? v i L1ME4c_3end#L 242 AATGCTGGCGAGGNTGCGGTGAAACT-GGTACNCTCATACATTGCTGGTG 290 chrXptel1M 449833 AAATTGTGAATACATCCAGTCATTCTGGAGAGAAATTTGAAACTAAGCCC 449882 iv ? i vvi v ii v i i v iv v v ivi L1ME4c_3end#L 291 GCANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTAT 340 chrXptel1M 449883 AAAAAGTTATCAAACTGTGCATACCCTTTGACCCAGCAGTGCTACAACTG 449932 v i ii v v v i i v i vv L1ME4c_3end#L 341 CAAGAGCCATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTG 390 chrXptel1M 449933 GGCTTATACCCCAAAGAGATCAT---AAAGAAGGGAAAGGGACCTGTCTG 449979 vv v i i i i v --- i i --- i v L1ME4c_3end#L 391 GGAATTTATCCTAAGGAAATAATTCAAAAGAAGGAAAAAG---CTATATG 437 chrXptel1M 449980 TGCCAAAATGTTTGTGGCAGCCCTCTTTGTAGTGGCTAGAAACTGGAAAC 450029 ii v i ii v vi v i i i v i i L1ME4c_3end#L 438 CACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAAC 487 chrXptel1M 450030 TGAGTGGATGCCCATCAGTGGGAGAATGGCTGAATAAATGGTGGTATATG 450079 vivv ii i v i i i i i i vi i v L1ME4c_3end#L 488 AACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATC 537 chrXptel1M 450080 AATGTTATGGAATATTA 450096 ? iviv L1ME4c_3end#L 538 NACTCGATGGAATATTA 554 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.80 CpG sites = 52, Kimura (unadjusted) = 39.91 Transitions / transversions = 1.27 (52/41) Gap_init rate = 0.02 (5 / 313), avg. gap size = 1.40 (7 / 5) 622 30.98 3.02 4.07 chrXptel1M 449785 450181 (549819) L1MC5a_3end#LINE/L1 244 636 (2141) m_b337s551i1 14108 chrXptel1M 449785 TGTTGGAGGGGATGTGGGGAAAAAAGGGACACTGATACATTGTTGGTGAA 449834 v i v v - v v v i ii L1MC5a_3end#L 244 TGTTGGCGAGGCTGTGGGGAAACA-GGCACTCTCATACATTGCTGGTGGG 292 chrXptel1M 449835 ATTGTGAATACATCCAGTCATTCTGGAGAGAAATTTGAAACTA---AGCC 449881 v ii vvvi v ii vi v i i iv v --- - L1MC5a_3end#L 293 AATGCAAAATGGTACAACCCCTATGGAGGGGAATTTGGCAATATCTAGC- 341 chrXptel1M 449882 CAAAAAGTTATCAAACTGTGCAT--ACCCTTTGACCCAGCAGTGCTACAA 449929 --- i - --- i -- i v i vv L1MC5a_3end#L 342 ---AAAATTA-CA---TATGCATTTACCCTTTGACCCAGCAATCCCACTT 384 chrXptel1M 449930 CTGGGCTTATACCCCAAAGAGA---TCATAAAGAAGGGAAAGGGACCTGT 449976 i vv v i i v --- ?ii i viv -? -- L1MC5a_3end#L 385 CTAGGAATCTATCCCGAAGATACACTNGCAAAAATACGAAA-NGAC--GT 431 chrXptel1M 449977 CTGTGCCAAAATGTTTGTGGCAGCCCTCTTTGTAGTGGCTAGAAACTGGA 450026 v ii v iiv i ii v vi v i i v i i L1MC5a_3end#L 432 ATGCACAAGGTTATTCATTGCAGCATTATTTGTAATAGCAAAAGACTGGA 481 chrXptel1M 450027 AACTGAGTGGATGCCCATCAGTGGGAGAATGGCTGAATAAATGGTGGTAT 450076 vivviii i i i i v i ivi i L1MC5a_3end#L 482 AACAACCCAAATGTCCATCAATAGGGGACTGGTTGAATAAACTATGGTAC 531 chrXptel1M 450077 ATGAATGTTATGGAATATTACTGT-TCTGTAAGAAATGACCAGCAGGAGG 450125 vv iiiv i i - i-v - v -- vv i L1MC5a_3end#L 532 ATCCACACAATGGAGTACTA-TGCAGCTGTAA-AAAGGA--ATGAGGAAG 577 chrXptel1M 450126 ATTTC---AGAAAGGCCTGGAGAGACTTACACGAACTGATGCTGAGTGAA 450172 i --- v vv ?iv v ii v v vv iv i i L1MC5a_3end#L 578 ATCTCTATATACTGNTATGGAGTGATCTCCAGGATATATTGTTAAGTGAA 627 chrXptel1M 450173 ATGAGCAGG 450181 vi i L1MC5a_3end#L 628 AAAAGCAAG 636 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.79 CpG sites = 64, Kimura (unadjusted) = 41.25 Transitions / transversions = 1.19 (64/54) Gap_init rate = 0.05 (21 / 396), avg. gap size = 1.33 (28 / 21) 13 10.07 5.88 2.86 chrXptel1M 450467 450500 (549500) (ATTTAT)n#Simple_repeat 1 35 (0) m_b337s252i2 14109 chrXptel1M 450467 ATGTATACTTAT-TTTGTATTTA-ATTTATACTTTA 450500 v i - i - - (ATTTAT)n#Sim 1 ATTTATATTTATATTTATATTTATATTTATA-TTTA 35 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.09 (3 / 33), avg. gap size = 1.00 (3 / 3) 405 27.55 1.40 3.57 chrXptel1M 450729 450871 (549129) L1ME4c_3end#LINE/L1 416 555 (275) m_b337s551i2 14110 chrXptel1M 450729 AAAAGAATGGAAAGCGGCCCGTATGTGTAAAAATGTTTGTGGCAACCCTT 450778 - iv -- ii iiii i ii v i vi v L1ME4c_3end#L 416 AAAAGAA-GGAAAAAG--CTATATGCACGAAGATGTTCATTGCAGCGTTA 462 chrXptel1M 450779 TTTATAGTGGCTAGAAACCGGAAATTGAA--TGGATGCCCATCAATTGGA 450826 i i v i ii i-- -- ii i v v i L1ME4c_3end#L 463 TTTATAATAGCGAAAAATTGGAAAC--AACCTAAATGTCCAACAATAGGG 510 chrXptel1M 450827 GAACGGTTGGGTAAATTGTGGTATATGAACGTTATGGAATATTAT 450871 i ii i i v? viv L1ME4c_3end#L 511 GAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATATTAT 555 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 34.20 CpG sites = 28, Kimura (unadjusted) = 36.81 Transitions / transversions = 2.80 (28/10) Gap_init rate = 0.04 (6 / 142), avg. gap size = 1.17 (7 / 6) 39 15.19 1.25 2.53 chrXptel1M 451686 451765 (548235) (GGAA)n#Simple_repeat 1 79 (0) m_b337s252i3 14111 chrXptel1M 451686 GGAGAGGGA-GAAGAGAAGGAAGGAAGGAAGGGAGGGAGGGAGGGAGGAA 451734 - i - - i i i i (GGAA)n#Simpl 1 GGA-AGGAAGGAAG-GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 48 chrXptel1M 451735 GGAAGGAAAGAAAGAAAGAAAGAGGGAAGGA 451765 i i i i i (GGAA)n#Simpl 49 GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 79 Matrix = Unknown Transitions / transversions = 1.00 (10/0) Gap_init rate = 0.04 (3 / 79), avg. gap size = 1.00 (3 / 3) 17 12.68 0.00 0.00 chrXptel1M 451767 451792 (548208) (GT)n#Simple_repeat 1 26 (0) m_b337s252i4 14112 chrXptel1M 451767 GTGTGTGTGAGTATGTGTGTGTATGT 451792 v i i (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGT 26 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 13 22.14 4.65 0.00 chrXptel1M 451768 451810 (548190) (TGTA)n#Simple_repeat 1 45 (0) m_b337s252i5 14112 chrXptel1M 451768 TGTGTGTGAGTATG--TGTGTGTATGTATATATCTACATATGTAT 451810 i iv -- i i v ii (TGTA)n#Simpl 1 TGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTAT 45 Matrix = Unknown Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.02 (1 / 42), avg. gap size = 2.00 (2 / 1) 24 30.37 0.96 5.00 chrXptel1M 451875 451978 (548022) (AT)n#Simple_repeat 1 100 (0) m_b337s252i6 14113 chrXptel1M 451875 ATATAT-TATGTATCTATGTGTGTGTGTATGTATGAGCATCATATCCAGC 451923 - i v i i i i i i - -i - vi -i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATAT-A-TAT-ATATATA-T 46 chrXptel1M 451924 ATATATGTATAGATATGCTTTATGTATATATCTGCATATGCATATATAAA 451973 i v -v v i v ii ii v (AT)n#Simple_ 47 ATATATATATATATAT-ATATATATATATATATATATATATATATATATA 95 chrXptel1M 451974 TATAT 451978 (AT)n#Simple_ 96 TATAT 100 Matrix = Unknown Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.06 (6 / 103), avg. gap size = 1.00 (6 / 6) 12 10.11 7.58 10.94 chrXptel1M 452216 452281 (547719) (TTCTGT)n#Simple_repeat 1 64 (0) m_b337s252i7 14114 chrXptel1M 452216 TTCTCTTT-TGTTTC-ATTT-TGGTTTTGCATTACT-TTTCTGTCTTTCT 452261 v - -i - v i -- v - -- (TTCTGT)n#Sim 1 TTCTGTTTCTGTTTCTGTTTCTGTTTCTG--TTTCTGTTTCTG--TTTCT 46 chrXptel1M 452262 GTTT-TGATTATTCTGTTTCT 452281 - -- - (TTCTGT)n#Sim 47 GTTTCTG--T-TTCTGTTTCT 64 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.18 (12 / 65), avg. gap size = 1.00 (12 / 12) 1637 28.79 2.53 2.18 chrXptel1M 453143 453735 (546265) C L1ME5_3end#LINE/L1 (291) 650 56 m_b337s551i3 14115 chrXptel1M 453143 ATCTC---CTGGTTCT-GCTCATTTCACTTAGCATCA-GTTCATGTAAG- 453186 --- v -i iv i ii - -- v - C L1ME5_3end#LI 650 ATCTCATTCTGTTTCTTACTTTTTTCACTCAGCACTATGTT--TTTAAGA 603 chrXptel1M 453187 TCTCTCAA-GCCTCTCTGTATTCATCCTGCTGGTCATTTCTTACAGAACA 453235 iv v - iiv v i v iv iiv iii v v vvvv C L1ME5_3end#LI 602 TCCATCCATGTTGCTATGTGTACATCTAGTCCGTTGCTTCTAACTGCTGC 553 chrXptel1M 453236 ATAATATTCCATAACATTCATATACCACAATTTACCCAACCATTCTCCAA 453285 i i iiii v vi v i v i v C L1ME5_3end#LI 552 ATAGTACTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCA 503 chrXptel1M 453286 TTGATGGGCATCCACTCAGTTTCCAGTTTCTGGCCACTACAAACAGGGCT 453335 v i i vviv ii ii i iv i iv C L1ME5_3end#LI 502 GTGATGGACACCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCT 453 chrXptel1M 453336 GCCACAAACATTTTGGCACATACAGGTCCCTTTC----CCTTCTTTAGTA 453381 v ii ii ---- i v i v---- viv v v C L1ME5_3end#LI 452 GCAATGAACATCCT----CGTACATGTCCCCTTATGGACCTGTGTGAGAA 407 chrXptel1M 453382 TCTCTTTGAGGTATAAGCCCAGTAGCAACACTGCTGGATCAAAGGGTATG 453431 i i i vi v iiv i i v C L1ME5_3end#LI 406 TTTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATG 357 chrXptel1M 453432 CACAGTTTGATAACTT--TTTGAGCA--TAGTTCCAAATTGCTCTCCAGA 453477 --- --- - -- vi -- v v i C L1ME5_3end#LI 356 C---GT---ATA-CTTAATTTGACTAAGTACTGCCAGATTGCTCTCCAGA 314 chrXptel1M 453478 ATGGTTGGATGTGTTCACAATTCTACCAACAATGTATCAGTGTCCCTGTT 453527 i v ivv ii v i i i i i v v i i ? C L1ME5_3end#LI 313 ATGGCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATN 264 chrXptel1M 453528 TTCCCACATCCCCTCCAACATTCTGCATTATCTTTCCCTGTCATTCTGGC 453577 i i v i iv ivv ii v v i v C L1ME5_3end#LI 263 TCCCCACATCCTCGCCAACACTTGGCATTATCCAGCTTTCTAATTTTTGC 214 chrXptel1M 453578 CAATCTGACAGCTGTGTAGTGGTATCTCAGAGTTATCTTAATTTGCATTT 453627 i i i v iv i vv i i C L1ME5_3end#LI 213 CAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATTT 164 chrXptel1M 453628 CTCTGATCAATAGTGATTTGGAACACTCTTTCATATGAGTAGTAATAGTT 453677 i v i v v i iiii vv iv iivv C L1ME5_3end#LI 163 CTCTGATTACTAATGAGTTTGAGCATCTCTTCATATGCTTGTTAGCCTTT 114 chrXptel1M 453678 TTAATTTCATCATCTGAAAATTGTCTGTTCATATCCTTTGACCATTTATC 453727 ivii v v v i v v C L1ME5_3end#LI 113 CGGGTTTCCTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCCATTTTTC 64 chrXptel1M 453728 AACTGGAG 453735 v i i C L1ME5_3end#LI 63 TATTGGGG 56 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.38 CpG sites = 94, Kimura (unadjusted) = 37.23 Transitions / transversions = 1.29 (94/73) Gap_init rate = 0.04 (21 / 592), avg. gap size = 1.33 (28 / 21) 1108 30.35 1.77 4.93 chrXptel1M 453237 453801 (546199) C L1PA17_3end#LINE/L1 (362) 551 4 m_b337s551i4 14115 chrXptel1M 453237 TAATATTCCATAACATTCATATACCACAATTTACCCAACCATTCTCCAAT 453286 i iiii vi i v viii v v iv vi C L1PA17_3end#L 551 TAGTATTCCATGGTGTATATGTACCACATTTTCTTTATCCAATCCACCGT 502 chrXptel1M 453287 TGATGGGCATCCACTCAGTTTCCA-GTTTCTGGCCACTACAAACAGGGCT 453335 i i vviv v - i i - i i iii i v C L1PA17_3end#L 501 TGATGGGCACCTAGGTTGATTCCATGTCTTTG-CTATTGTGAATAGTGCT 453 chrXptel1M 453336 GCCACAAACATTTTGGCACATACAGGTCCCTTTCCCTT----C--TTTAG 453379 v i ----i ivi i vi iivv ---- -- v C L1PA17_3end#L 452 GCGATAAACAT----ACGAGTGCAGGTGTCTTTTTGGTAGAACGATTTAT 407 chrXptel1M 453380 TATCTCTTTGAGGTATAAGCCCAGTAGCAACACTGCTGGATCAAAGGGTA 453429 v - - vi iiiiv i i i v C L1PA17_3end#L 406 TTTC-CTTTG-GGTATATACCCAGTAATGGGATTGCTGGGTCGAATGGTA 359 chrXptel1M 453430 TGCACAGTTTGATAACTTTTTGAGCATAGTTCCAAATTGCTCTCCAGAAT 453479 vvivi v -- ii i v - vi i i v iv C L1PA17_3end#L 358 GTTCTATTTT--TAGTTCTTTGAGAA-ATCTCCAAACTGCTTTCCACAGG 312 chrXptel1M 453480 GGTTGGATGTGTTCACAATTCTACCAACAATGTATCAGTGTCCCTGTTTT 453529 i i ivvi i v i i i v i i iv i C L1PA17_3end#L 311 GGCTGAACTAATTTACATTCCCACCAACAGTGTATAAGCGTTCCCTTTTC 262 chrXptel1M 453530 CCCACATCCCCTCCAACATTCTGCATTATCTTT---CCCTGTCATTCTGG 453576 i i ? i v - -- i --- ii v v vv i C L1PA17_3end#L 261 TCCGCANCCTCGCCAACAT-CTG--TTATTTTTTGACTTTTTAATAATAG 215 chrXptel1M 453577 CCAATCTGACAGCTGTGTAGTGGTATCTCAGAGTTATCTTAATTTGCATT 453626 v v v vii vv vi i i C L1PA17_3end#L 214 CCATTCTGACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATT 165 chrXptel1M 453627 TCTCTGATCAATAGTGATTTGGAACACTCTTTCATATGAGTAGTAATAGT 453676 v v v v i i i vv iv iiiv i C L1PA17_3end#L 164 TCTCTGATGATTAGTGATGTTGAGCATTTTTTCATATGTTTGTTGGCCGC 115 chrXptel1M 453677 TTTAATTTCATCATCTGAAAATTGTCTGTTCATATCCTTTGACCATTTAT 453726 vv v v v i i v i v i v C L1PA17_3end#L 114 TTGTATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTTGCCCACTTTT 65 chrXptel1M 453727 CAACTGGAGAATGGCTTGATTTCTTTCTTTTTTTCTTTTTTTTTATTATT 453776 i - i ----------- v v v vv -- i C L1PA17_3end#L 64 TAA-TGGGG-----------TTATTTGTTTTTTTCTTGTTGAT--TTGTT 29 chrXptel1M 453777 TAATAGCCTTTTATTTACAGGATAT 453801 vvv v vv v v C L1PA17_3end#L 28 TAAGTTCCTTATAGATTCTGGATAT 4 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.10 CpG sites = 87, Kimura (unadjusted) = 39.64 Transitions / transversions = 1.14 (87/76) Gap_init rate = 0.05 (31 / 564), avg. gap size = 1.19 (37 / 31) 328 32.59 2.20 2.20 chrXptel1M 454236 454417 (545583) C L1MD1_3end#LINE/L1 (356) 633 452 m_b337s551i5 14116 chrXptel1M 454236 GCTCATTTCACTCAGCATCAGTTCGTGTAAGTCTCTCCAGGCCTTTCTGA 454285 iv v v iiv v ii iiv iiv vi v C L1MD1_3end#LI 633 GCTTTTTTCACTCAGCATAATTCTCTGGAGATTCATCCAGGTTGTTGCGT 584 chrXptel1M 454286 A-ATCATCCTGTTGGTCATTTCTTACAGAACAGTAATATTCCATAATAAT 454334 i- viv- v ivi i iv vvv i ii vv C L1MD1_3end#LI 583 GTATCAATA-GTTCGTTCCTTTTTATTGCTGAGTAGTATTCCATGGTATG 535 chrXptel1M 454335 CATATACCACAATTGATTCAGCCATTCTCCAACTGATGGACATCCA--TT 454382 v i i vi i i v vii v ii-- C L1MD1_3end#LI 534 GATGTACCACAGTTTGTTTAACCATTCACCCGTTGAAGGACATCTGGGTT 485 chrXptel1M 454383 CAGTTTCCAGTTTTATAGCCACTACAAA-AGGGCTG 454417 -- - i i i i - ii C L1MD1_3end#LI 484 --GTTTCCAGTTTT-TGGCTATTACGAATAAAGCTG 452 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.18 CpG sites = 34, Kimura (unadjusted) = 44.23 Transitions / transversions = 1.42 (34/24) Gap_init rate = 0.04 (7 / 181), avg. gap size = 1.14 (8 / 7) 374 19.80 3.85 2.86 chrXptel1M 454318 454421 (545579) C L1ME3G_3end#LINE/L1 (377) 547 443 m_b337s551i6 14116 chrXptel1M 454318 TAATATTCCATAATAATCATATACCACAATTGATTCAGCCATTCTCCAAC 454367 i i vvv i v i i i v i C L1ME3G_3end#L 547 TAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTAT 498 chrXptel1M 454368 TGATGGACATCCA--TTCAGTTTCCAGTTTTATAGCCACTACAAA-AGGG 454414 ii -- -- i - v i i - iv C L1ME3G_3end#L 497 TGATGGACATTTAGGTT--GTTTCCAATTTT-TCGCTATTACAAACAATG 451 chrXptel1M 454415 CTG-AATG 454421 - C L1ME3G_3end#L 450 CTGCAATG 443 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 23.51 CpG sites = 13, Kimura (unadjusted) = 23.51 Transitions / transversions = 1.86 (13/7) Gap_init rate = 0.06 (6 / 103), avg. gap size = 1.17 (7 / 6) 916 30.49 5.30 4.54 chrXptel1M 454446 455407 (544593) C L1M5_orf2#LINE/L1 (124) 3170 2202 m_b337s551i7 14116 chrXptel1M 454446 AGTTCTCTATATATTTTGGAAATGAGGCCTTTATCAGGACCTTTG-ACTG 454494 i i v i v i - iv v -?i C L1M5_orf2#LIN 3170 AGTTCTTTATATATTCTGGATACGAGTCCTTTGTCAG-ATATATGTNTTG 3122 chrXptel1M 454495 TAAA-ATGTTTTCCCAGTTTGTTGTTT-CCTTCTAATCTTGTCTGCATTA 454542 i - v i ? i v i - i v i v ivi iv i C L1M5_orf2#LIN 3121 CAAATATTTTCTCCCANTCTGTGGCTTGCCTTTTCATTTTCTTAACGGTG 3072 chrXptel1M 454543 GTTTTGTTTGTACAAAAACTTTTCAATTTGATATAATCAAA-------AT 454585 vi vvv? vi i ii v v i? i v ------- C L1M5_orf2#LIN 3071 TCTTTTGANGAGCAGAAGTTTTTAATTTTGATGNAGTCCAATTTATCAAT 3022 chrXptel1M 454586 TTTCTATTTTGTAGTCAATAGTGATCTCTAGTTCTTCTTTGGTCATAAAT 454635 i v i i --- ? v i i ivv i v i--- v C L1M5_orf2#LIN 3021 TTTTTCTTTTATGGT---TNGTGCTTTTTGTGTCCTGTTTA---AGAAAT 2978 chrXptel1M 454636 TCCTTCCTCTTCCACAGGTCTGAGAGGTAAAGTATCCTATGCT--CTTCC 454683 iii v v?i - vvii i --v v i -- i C L1M5_orf2#LIN 2977 CTTTGCCTANCCCA-AGGTCACGAAGATA--TTCTCCTATGTTTTCTTCT 2931 chrXptel1M 454684 AA----TTTAT--TTTGATCTCATTCTTTATGCCTTAAATC-ATGAACCC 454726 i---- -- v ? ----- iii- ii - -i C L1M5_orf2#LIN 2930 AGAAGTTTTATAGTTTTANCT-----TTTACAT-TTAGGTCTATGA-TCC 2888 chrXptel1M 454727 ATTTTGACCTTTATCTTGTGTGTATGGTCTTAAGTGTGGGTCAATGCCTA 454776 i ? v-- vi v v v i iv i v?iii C L1M5_orf2#LIN 2887 ATCTNGAA--TTAATTTTTGTGTATGGTGTGAGGTAGGGGTCGAGNTTCA 2840 chrXptel1M 454777 GTTTCTGCCATACTAATTTCCAATTTTCCCAGCAATTTTTGTCAAATAAT 454826 v i v ivi v v i viv ii v iv C L1M5_orf2#LIN 2839 TTTTTTTCCATATGGATATCCAATTGTTCCAGCACCATTTGTTGAAAAGA 2790 chrXptel1M 454827 GCACTCTTATCCCAA-AAACTGGGGTCTTTGGG---TTTGTCAAACACTA 454872 vi ii vi v-i i ---- ? v--- v ii C L1M5_orf2#LIN 2789 CTATCCTTTCCCCACTGAATTG----CNTTGGCACCTTTGTCAAAAATCA 2744 chrXptel1M 454873 GATAATTAAAGTTAT-TGG--CTATTT-TGTCCTTTGAACCTAACTTATT 454918 i? i?ii v vv i - -- - vv i ---- vii i C L1M5_orf2#LIN 2743 ANTGNCCATATATGTGTGGGTCTATTTCTGGACTCT----CTATTCTGTT 2698 chrXptel1M 454919 CCATTGATCCCCTAGTCTATTTCTTA-GTCAATACCAGATAGTTTTAGTA 454967 ivi v i- - i v iv i ii v C L1M5_orf2#LIN 2697 CCATTGATCTATTTGTCTATC-CTTACGCCAATACCACACTGTCTTGATT 2649 chrXptel1M 454968 ACCCT-GCCTTATAATATAGTTTT-AGATCTGGTACAGCTAGG----CCA 455011 iv - i - i - ? ? vv - i ---- C L1M5_orf2#LIN 2648 ACTGTAGCTTTATAATA-AGTCTTGANATCNGGTAGTG-TAAGTCCTCCA 2601 chrXptel1M 455012 CCTTCATTTGATTTTTTTTCATTAATTCCTTGAC-ATTCTTGACCTTTTG 455060 v ii i-- i vv v vii i - ? ii i C L1M5_orf2#LIN 2600 ACTTTGTTC--TTCTTTTTCAAGATTGTTTTGGCTATTCTNGGTCCTTTG 2553 chrXptel1M 455061 TTTTTCCATATGAACTTT-------GTTTGTTA-TTTTTGTAGGTCATCA 455102 iv i i ------- i i - i ii i------ C L1M5_orf2#LIN 2552 CATTTCCATATAAATTTTAGAATCAGCTTGTCAATTTCTACAA------A 2509 chrXptel1M 455103 AATAGTTTTTGGGAGTCTGATTGG-ATAGCGCTAAATAAATAGATTAGGT 455151 v vi vi v i - v ii i vv i i- C L1M5_orf2#LIN 2508 AAAACCTGCTGGGATTTTGATTGGGATTGCATTGAATCTATAGATCAA-T 2460 chrXptel1M 455152 TTAGGTAATATTGTCATCTTTATTATATTTGCTCGCCCAATCCAAGAGCA 455201 i v iv v ? iv viv vi v i C L1M5_orf2#LIN 2459 TTGGGGAGAATTGACATCTTNACAATATTGAGTCTTCCAATCCATGAACA 2410 chrXptel1M 455202 TCTAATATTT-TCCAGTTGAGTTAGATCAGACTTAATTTGTGTGGAAAGT 455250 vvv i - v - v i vvvi v v viiv i C L1M5_orf2#LIN 2409 TGGTATATCTCTCCATTT-ATTTAGGTCTTCTTTAATTTCTCTCAGCAAT 2361 chrXptel1M 455251 GTTTTGTAGTTTTGCTCATAAAGTTTCTG---ATTTTCCTTGGCAGATAG 455297 vvvii ? v ii --- ? -- vi vv C L1M5_orf2#LIN 2360 GTTTTGTAGTTTTCAGTGTANAGGTCTTGCACATNTT--TTGTTAGATTT 2313 chrXptel1M 455298 ATTCCCAAATATTTTATACTATCAGTAGTTACTTTAAATGGGATTTCTCT 455347 i i ? ii v iv vv i i v v vi i C L1M5_orf2#LIN 2312 ATTCCTAAGTATTTNATGTTTTTTGATGCTATTGTAAATGGTATTGTTTT 2263 chrXptel1M 455348 TTGTAACTCTGACTGTTGGA---TTTGTTAGTGATGTATAAGAATGCTGA 455394 --? v i v i v ivi --- iv ii i ii i viv C L1M5_orf2#LIN 2262 T--NAAATTTCATTTTCCAATTGTTTGTTGCTAGTATATAGAAATACAAT 2215 chrXptel1M 455395 TGACTTATGTGTA 455407 i v i C L1M5_orf2#LIN 2214 TGATTTTTGTATA 2202 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.63 CpG sites = 159, Kimura (unadjusted) = 41.41 Transitions / transversions = 1.31 (159/121) Gap_init rate = 0.07 (68 / 961), avg. gap size = 1.40 (95 / 68) 18 0.00 7.41 0.00 chrXptel1M 461535 461561 (538439) (TTG)n#Simple_repeat 1 29 (0) m_b337s252i9 14117 chrXptel1M 461535 TTGTTGTTGTTGTTGTT-TTGTT-TTGTT 461561 - - (TTG)n#Simple 1 TTGTTGTTGTTGTTGTTGTTGTTGTTGTT 29 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.08 (2 / 26), avg. gap size = 1.00 (2 / 2) 21 16.45 1.67 5.17 chrXptel1M 461530 461589 (538411) (TTGTT)n#Simple_repeat 1 58 (0) m_b337s252i8 14118 chrXptel1M 461530 TTGCTTTGTTGTTGTTGTTGTTTTGTTTTGTTTGGATTT-TTTTCCTATG 461578 i - - v v - vi v (TTGTT)n#Simp 1 TTGTTTTGTT-TTGTT-TTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTG 48 chrXptel1M 461579 ACTTTGTCTTG 461589 -i i (TTGTT)n#Simp 49 -TTTTGTTTTG 58 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.07 (4 / 59), avg. gap size = 1.00 (4 / 4) 1329 27.18 3.97 4.38 chrXptel1M 461705 462208 (537792) L1ME5_3end#LINE/L1 127 628 (313) m_b337s551i8 14119 chrXptel1M 461705 CACATGAAAAGATGCTCCAAGTCATTATGAATCAGAGAAATGCAAATTAA 461754 i i v v vv L1ME5_3end#LI 127 CATATGAAGAGATGCTCAAACTCATTAGTAATCAGAGAAATGCAAATTAA 176 chrXptel1M 461755 GACAACTCTAAGATACCACTACACACCTGTCAGATTGGCTAAGTTGACAG 461804 i vv i i vi i i i v iv v --- L1ME5_3end#LI 177 AACAACAATGAGATATCACTTTACACCTATTAGACTGGCAAAAATTA--- 223 chrXptel1M 461805 GAAA---AAATAATGATGATTGTTGGAGGGGATGCGGGAAAACTGGGACA 461851 ---ii vii v v i i i ? iv i v L1ME5_3end#LI 224 GAAAGCTGGATAATGCCAAGTGTTGGCGAGGATGTGGGGANATAGGAACC 273 chrXptel1M 461852 TTGATGCATTGTTGGTGGAGTTGTGAACGAATCCAACCATTCTGGAGAGC 461901 i v i i iiv ii vii v i L1ME5_3end#LI 274 CTCATGCACTGCTGGTGGGAGTGTAGACTGGTGCAGCCATTCTGGAGAGC 323 chrXptel1M 461902 AGTTTGGAACTA--TGCTCAAA--AAGT-TACCAAACTGTGCATACCCTT 461946 i i v v -- iv -- - -------- v L1ME5_3end#LI 324 AATCTGGCAGTACTTAGTCAAATTAAGTATAC--------GCATACCCTA 365 chrXptel1M 461947 TGACCCAGCAGTGTTGCTACTGGGCTTATACCCCAAGGAGATACTAAAGA 461996 i vii v iv i i i v v viv L1ME5_3end#LI 366 TGACCCAGCAATTCCGCTCCTGGGTATATATCCCAAAGAAATTCTCACAC 415 chrXptel1M 461997 AGG----GAAAGGGACCAGTATGTGCCAAAATGTTTGTGGCAGCCCTGTT 462042 ----v i ---- i v ii ii v vi L1ME5_3end#LI 416 AGGTCCATAAGGGGAC----ATGTACGAGGATGTTCATTGCAGCGTTGTT 461 chrXptel1M 462043 TGTAGTGGCTAGAAACTGGAA--AATGAGTGGATGCCCATCAATTGGAGA 462090 i vi i ii i-- i--v i i v v L1ME5_3end#LI 462 TGTGGTGGCGGGGAGTTGGAGGCAAC--CTGGGTGTCCATCACTGGGAGA 509 chrXptel1M 462091 ATGG-TGGGTAAATTGTGGTATATGTATGTTATGGAATTTTACTGTTCTG 462139 i - i v iv i iiii i--- i v v L1ME5_3end#LI 510 GTGGATAGGTAAAATGTGGTGGATGCACACCATGGAG---TACTATGCAG 556 chrXptel1M 462140 TA---AGAAATGACCAGCAGGATGAATACAGAGAGGCTTGGAGAGA-ATT 462185 i --- iii vii vi v i v vii v vi -v L1ME5_3end#LI 557 CAGTTAGAAGCAACGGACTAGATGTACACATAGCAACATGGATGGATCTT 606 chrXptel1M 462186 ACATGAAC-TGATGCTAAGTGAAA 462208 v -- - ii i L1ME5_3end#LI 607 AAA--AACATAGTGCTGAGTGAAA 628 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 34.50 CpG sites = 80, Kimura (unadjusted) = 34.83 Transitions / transversions = 1.57 (80/51) Gap_init rate = 0.06 (32 / 503), avg. gap size = 1.31 (42 / 32) 22 25.80 0.00 0.00 chrXptel1M 464182 464241 (535759) (TAGATA)n#Simple_repeat 1 60 (0) m_b337s252i10 14120 chrXptel1M 464182 TAGATAGATAGAGATATATAGCTATAGATATATGTATATATAGAGACATA 464231 v v v v v v vi v v i (TAGATA)n#Sim 1 TAGATATAGATATAGATATAGATATAGATATAGATATAGATATAGATATA 50 chrXptel1M 464232 GAAATATATA 464241 v v (TAGATA)n#Sim 51 GATATAGATA 60 Matrix = Unknown Transitions / transversions = 0.18 (2/11) Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0) 238 17.86 3.57 0.00 chrXptel1M 464253 464308 (535692) C DNM1r#Unknown (2127) 2535 2478 m_b337s502i0 14121 chrXptel1M 464253 ATATAAACACAGATATATAAATATACATACATATGCACA--TATATACAT 464300 v v i v i i i -- i C DNM1r#Unknown 2535 ATATATACACATATATACACACATACACACATATACACACATATATACAC 2486 chrXptel1M 464301 GCATATAC 464308 i i C DNM1r#Unknown 2485 ACATACAC 2478 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 20.92 CpG sites = 7, Kimura (unadjusted) = 20.92 Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.02 (1 / 55), avg. gap size = 2.00 (2 / 1) 313 23.61 0.00 0.00 chrXptel1M 464270 464341 (535659) C DNM1r#Unknown (2116) 2546 2475 m_b337s502i1 14121 chrXptel1M 464270 TAAATATACATACATATGCACATATATACATGCATATACCCGTATAAATA 464319 v ? i i i ii i v i v i C DNM1r#Unknown 2546 TATANATACGTATATATACACATATATACACACATACACACATATACACA 2497 chrXptel1M 464320 TATATGTACACACACATATATG 464341 i i i i ii C DNM1r#Unknown 2496 CATATATACACACATACACGTG 2475 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 26.36 CpG sites = 14, Kimura (unadjusted) = 30.90 Transitions / transversions = 4.67 (14/3) Gap_init rate = 0.00 (0 / 71), avg. gap size = 0.0 (0 / 0) 266 27.14 0.00 0.00 chrXptel1M 464291 464360 (535640) C DNM1r#Unknown (2117) 2545 2476 m_b337s502i2 14121 chrXptel1M 464291 ATATATACATGCATATACCCGTATAAATATATATGTACACACACATATAT 464340 ? i ii v i v i i i ii i i i i i C DNM1r#Unknown 2545 ATANATACGTATATATACACATATATACACACATACACACATATACACAC 2496 chrXptel1M 464341 GTACATACACACATACACAT 464360 i i i C DNM1r#Unknown 2495 ATATATACACACATACACGT 2476 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.20 CpG sites = 17, Kimura (unadjusted) = 38.37 Transitions / transversions = 8.50 (17/2) Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0) 244 28.57 0.00 0.00 chrXptel1M 464303 464372 (535628) C DNM1r#Unknown (2117) 2545 2476 m_b337s502i3 14121 chrXptel1M 464303 ATATACCCGTATAAATATATATGTACACACACATATATGTACATACACAC 464352 ? iv v i i i i i iii i C DNM1r#Unknown 2545 ATANATACGTATATATACACATATATACACACATACACACATATACACAC 2496 chrXptel1M 464353 ATACACATATACCTGCATAT 464372 i i i i v i ii C DNM1r#Unknown 2495 ATATATACACACATACACGT 2476 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.66 CpG sites = 17, Kimura (unadjusted) = 40.69 Transitions / transversions = 5.67 (17/3) Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0) 322 20.03 2.53 5.19 chrXptel1M 464312 464390 (535610) C DNM1r#Unknown (2116) 2546 2470 m_b337s502i4 14121 chrXptel1M 464312 TATAAATATATATGTACACACACATATATGTACATACACACATACACATA 464361 ? ii i i i iii i i C DNM1r#Unknown 2546 TATANATACGTATATATACACATATATACACACATACACACATATACACA 2497 chrXptel1M 464362 TACCTGCATATACACACATGTA--TGGCTGA 464390 i i---- ii -- i C DNM1r#Unknown 2496 CAT----ATATACACACATACACGTGGCCGA 2470 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 21.85 CpG sites = 15, Kimura (unadjusted) = 25.99 Transitions / transversions = 1.00 (15/0) Gap_init rate = 0.06 (5 / 78), avg. gap size = 1.20 (6 / 5) 15 13.04 8.82 0.00 chrXptel1M 466602 466635 (533365) (CT)n#Simple_repeat 1 37 (0) m_b337s252i11 14122 chrXptel1M 466602 CTC-CTCCCGCTCTC-CTC-CTCTCCCCCTCTCTCTC 466635 - i v - - i i (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 37 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.09 (3 / 33), avg. gap size = 1.00 (3 / 3) 49 21.05 1.83 0.00 chrXptel1M 467552 467660 (532340) (GT)n#Simple_repeat 1 111 (0) m_b337s252i12 14123 chrXptel1M 467552 GTATGTG-GTGTGAGTGTATGTCTGTATGTGTGTGTGTCTATGTGTGTGT 467600 i - v i v i v i (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50 chrXptel1M 467601 G-GTGTGTGCCTGTGACTGTGTGTCTCTGACTGTGTGTGACTCTGTGTGT 467649 - iv vv v v vv vv v (GT)n#Simple_ 51 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 100 chrXptel1M 467650 GTCTGTGCGTG 467660 v i (GT)n#Simple_ 101 GTGTGTGTGTG 111 Matrix = Unknown Transitions / transversions = 0.43 (6/14) Gap_init rate = 0.02 (2 / 108), avg. gap size = 1.00 (2 / 2) 747 24.40 0.60 0.00 chrXptel1M 467762 467929 (532071) C MIR#SINE/MIR (6) 256 88 m_b337s601i3 14124 chrXptel1M 467762 AGCTAGCACTTCTATAGTACTTACTATGTTCCAGGCACCATGCTAAGCAC 467811 i i v vv ii v ii v i C MIR#SINE/MIR 256 AGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGCGC 207 chrXptel1M 467812 TTTATAGTTGTCATCTCATTTGATCCTCACAACTACTCTGGGAGGTAGGT 467861 i vv i i v i v i iv C MIR#SINE/MIR 206 TTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGGTAGGT 157 chrXptel1M 467862 GCTGTTATTATCCTTAGTCTACAGTTGAGGGAATGGTGGCAAATGGA-AT 467910 i i ii v i v i iv v v vi -i C MIR#SINE/MIR 156 ACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGT 107 chrXptel1M 467911 TAAGTGACTTGGCCAGGGT 467929 i v i C MIR#SINE/MIR 106 TAAGTAACTTGCCCAAGGT 88 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.30 CpG sites = 24, Kimura (unadjusted) = 30.11 Transitions / transversions = 1.41 (24/17) Gap_init rate = 0.01 (1 / 167), avg. gap size = 1.00 (1 / 1) 47 2.26 0.00 0.00 chrXptel1M 468538 468582 (531418) (TG)n#Simple_repeat 1 45 (0) c_b337s251i0 14125 chrXptel1M 468538 TGTGTCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 468582 v (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 45 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 34 7.03 0.00 0.00 chrXptel1M 470534 470578 (529422) (T)n#Simple_repeat 1 45 (0) c_b337s251i1 14126 chrXptel1M 470534 TTTTATTTTTTTTTTATTTTTATTTTTTTTTTTTTTTTTTTTTTT 470578 v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 45 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 23 24.37 0.00 0.00 chrXptel1M 471009 471066 (528934) (AAAA)n#Simple_repeat 1 58 (0) m_b337s252i13 14127 chrXptel1M 471009 AAAAATAAAATACTAAATAAATAGGAAAAAAGAAGAAAAAAAAAAAAAAG 471058 v v vv v v ii i i i (AAAA)n#Simpl 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chrXptel1M 471059 AAAAAGAA 471066 i (AAAA)n#Simpl 51 AAAAAAAA 58 Matrix = Unknown Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0) 795 31.58 5.37 3.65 chrXptel1M 471512 472293 (527707) C L1M4_orf2#LINE/L1 (1172) 2122 1328 m_b337s551i9 14128 chrXptel1M 471512 TATATAGGTTTATTTTATATCTTGCAACTAT-GATGGTTTTATTTCTTCT 471560 i i v i v i ---i i v v- i i i C L1M4_orf2#LIN 2122 TATACAAGATCATGTCAT---CTGCGAATAGAGATAGTTTTACTTCTTCC 2076 chrXptel1M 471561 TTCTCTTTGCTTTATTACTTCAATTTCTTTTTTGGTGTTTGTTATTACTG 471610 ii vv - vv vv iv i----- ii- v i C L1M4_orf2#LIN 2075 TTTCCAAT-CTGGATGCCTTTTATTTCTTTTTC-----TTGCC-TAATTG 2033 chrXptel1M 471611 CGATAACTAGAACTTCCAATGCTCTATTAAATAA----TGTGATAATGGG 471656 vv ii i i i vv i i i----v i v ii i C L1M4_orf2#LIN 2032 CCCTGGCTAGAACCTCCAGTACAATGTTGAATAGAAGTGGCGAGAGCGGA 1983 chrXptel1M 471657 AATCTTTGC--TGCATCCAATTTTATTGTATATGCTTTTAGTTTGTTCCT 471704 v i i-- ivi ii i vv viv v ? i i v iv i C L1M4_orf2#LIN 1982 CATCCTTGTCTTGTTCCTGATCTTAGGGGGAAAGCNTTCAGTCTTTCACC 1933 chrXptel1M 471705 ATTAAAAATAATACTGTCTT--GGTTTTAGAGAAATTCTATTTATCATTT 471752 iv i ii iv v-- vviv i v iv vv C L1M4_orf2#LIN 1932 ATTAAGTATGATGTTAGCTGTGGGTTTTTCGTAGATGCCCTTTATCAGGT 1883 chrXptel1M 471753 TAGAAAAGTTTCATT-TATTCCTATGCTTTCT-ATTGTTTTTTTTTTAAT 471800 iiii i v - - i vi - v v i----- C L1M4_orf2#LIN 1882 TGAGGAAGTTCCCTTCTATTCCTA-GTTTGTTGAGTGTTTTTATC----- 1839 chrXptel1M 471801 AGGAATGGGTATTGTATTTTGTCTAAAGCTTTTTTAGCATCCATTGAAAT 471850 v v i v v v iv i i i C L1M4_orf2#LIN 1838 ATGAAAGGGTGTTGGATTTTGTCAAATGCTTTTTCTGCGTCTATTGAGAT 1789 chrXptel1M 471851 A---ATATTATTTTTGT---------TATAAATCTAGTCAATTATGCTTA 471888 i--- i vi --------- v v i vv iii v C L1M4_orf2#LIN 1788 GATCATGTGGTTTTTGTCCTTTATTCTATTAATATGGTGTATTACATTGA 1739 chrXptel1M 471889 TGGTTTCTTTGTACA--GAACTGGCCCTCTATTCCTGGTATAAGTTCTGC 471936 v v - i ? ii-- iii i vi v i i ii C L1M4_orf2#LIN 1738 TTGATT-TTCGNATGTTGAACCAACCTTGCATTCCTGGGATAAATCCCAC 1690 chrXptel1M 471937 CTAGATATGG-ATATGATCTTTATGATATGTTATAGCAATGTCCTTGCAA 471985 i i vi -i i i v v iiv v v vvvi v C L1M4_orf2#LIN 1689 TTGGTCATGGTGTATAATCCTTTTTATATGTTGCTGGATTCGGTTTGCTA 1640 chrXptel1M 471986 GTATTTTGTTTAATTTCTTTTGTATCAATATTCATTAGGAAAGTTGTTCT 472035 v ivv - i v v i vi v C L1M4_orf2#LIN 1639 GTATTTTGTTGAGGAT-TTTTGCATCTATATTCATAAGGGATATTGGTCT 1591 chrXptel1M 472036 ATAGGTTTTTCCCTCTGTTTTGGCTTTCCCTAG-TCAGATATCAAAACTG 472084 i v i iiiii vv v vi i - iv i iiiivi C L1M4_orf2#LIN 1590 GTAGTTTTCTTTTCTTGTGATGTCTTTGTCTGGTTTTGGTATCAGGGTAA 1541 chrXptel1M 472085 TATTTGTGTCATAGGAAGAATTTGGTAGGGTTCCTTCTTTTTCAATTATT 472134 i v iv i v i v v v i i i v - C L1M4_orf2#LIN 1540 TACTGGCCTCATAGAATGAGTTGGGAAGTGTTCCCTCCTCTTCTATT-TT 1492 chrXptel1M 472135 TTCAAATAGTTTATGTGGTATTAGAATTAATTATTTTT----TGTTTGGT 472180 vi v i vi v i vi v i ---- C L1M4_orf2#LIN 1491 TTGGAAGAGTTTGTGAAGGATTGGTGTTAATTCTTCTTTAAATGTTTGGT 1442 chrXptel1M 472181 TGAATTCACTTGTAAATCTCTCTGGTCCTGGGAGTTGTTTTTTCCCCCTT 472230 v iv i v iv ? ----- i ---- i C L1M4_orf2#LIN 1441 AGAATTCACCAGTGAAGCCATCTGGNCCTGG-----GCTTTT----CTTT 1401 chrXptel1M 472231 TTGG--ACTTCATTTG---ACTTGTTCAATTTCTTTTCCTAAGATAG--- 472272 v -- v i- --- vi i v i ivv --- C L1M4_orf2#LIN 1400 GTGGGAAGTTT-TTTGATTACTAATTCAATCTCTTTACTTGTTATAGGTC 1352 chrXptel1M 472273 --TTCAG-TATTCTATTTCCTCTT 472293 -- - v i C L1M4_orf2#LIN 1351 TATTCAGATTTTCTATTTCTTCTT 1328 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.93 CpG sites = 133, Kimura (unadjusted) = 42.34 Transitions / transversions = 1.27 (133/105) Gap_init rate = 0.06 (46 / 781), avg. gap size = 1.54 (71 / 46) 834 31.82 4.78 2.55 chrXptel1M 471534 472223 (527777) C L1MD_orf2#LINE/L1 (1191) 2103 1399 m_b337s551i10 14128 chrXptel1M 471534 TGCAACTATG-ATGGTTTTATTTCTTCTTTCTCTTTGCTTTATTACTTCA 471582 v v - ii i ii vv - v vv iv C L1MD_orf2#LIN 2103 TGCAAATAGGGACAGTTTTATTTCTTCCTTTCCAAT-CTGTATGCCTTTT 2055 chrXptel1M 471583 ATTTCTTTTTTGGTGTTTGTTATTACTGCGATAACTAGAACTTCCAATGC 471632 i i----- ii- i iv ii i i C L1MD_orf2#LIN 2054 ATTTCCTTTTC-----TTGCC-TTATTGCACTGGCTAGAACTTCCAGTAC 2011 chrXptel1M 471633 TCTATTAAATAAT----GTGATAATGGGAATCTTTGC--TGCATCCAATT 471676 v i i v---- v ii iv i -- ivi i i C L1MD_orf2#LIN 2010 TATGTTGAATAAGAGTGGTGAGAGCGGACATCCTTGCCTTGTTCCCGATC 1961 chrXptel1M 471677 TTATTGTATATGCTTTTAGTTTGTTCCTATTAAAAATAATACTGTCTT-- 471724 vv viv v v i i v iv i iv i ii iv v-- C L1MD_orf2#LIN 1960 TTAGGGGGAAAGCATTCAGTCTTTCACCATTAAGTATGATGTTAGCTGTA 1911 chrXptel1M 471725 GGTTTTAGAGAAATTCTATTTATCATTTTAGAAAAGTTTCATT-TATTCC 471773 vviv i v v vv iiii i vi - C L1MD_orf2#LIN 1910 GGTTTTTTGTAGATGCTCTTTATCAAGTTGAGGAAGTTCCCCTCTATTCC 1861 chrXptel1M 471774 TATGCTTTCT-ATTGTTTTTTTTTTAATAGGAATGGGTATTGTATTTTGT 471822 - i ? - vv v i----- v i v C L1MD_orf2#LIN 1860 TA-GTTTNCTGAGAGTTTTTATC-----ATGAATGGGTGTTGAATTTTGT 1817 chrXptel1M 471823 CTAAAGCTTTTTTAGCATCCATTGA---AATAATATTATTTTTGT----- 471864 v v iv v ---i v i v v ----- C L1MD_orf2#LIN 1816 CAAATGCTTTTTCTGCATCAATTGATATGATCATGTGATTTTTCTTCTTT 1767 chrXptel1M 471865 ----TATAAATCTAGTCAATTATGCTTATGGTTTCTTTG--TACAGAACT 471908 ---- i v v i vi iii v v v - i -- iv i C L1MD_orf2#LIN 1766 AGCCTGTTAATATGGTGGATTACATTGATTGATT-TTCGAATATTGAACC 1718 chrXptel1M 471909 GGCCCTCTATTCCTGGTATAAGTTCTGCCTAGATATGG-ATATGATCTTT 471957 i i vi ? v iii ii i i vi -i i ii C L1MD_orf2#LIN 1717 AGCCTTGCATNCCTGGAATAAACCCCACTTGGTCATGGTGTATAATTCTT 1668 chrXptel1M 471958 ATGATATGTTATAGCAATGTCC--TTGCAAGTATTTTGTTTAATTTCTTT 472005 v v i iiv - - ?-- v i v ivv - C L1MD_orf2#LIN 1667 TTTATATATTGCTG-AAT-TCNATTTGCTAATATTTTGTTGAGGAT-TTT 1621 chrXptel1M 472006 TGTATCAATATTCATTAGGAAAGTTGTTCTATAGGTTTTTCCCTCTGTTT 472055 ii v i v i vi v i v i iii i vi C L1MD_orf2#LIN 1620 TGCGTCTATGTTCATGAGGGATATTGGTCTGTAGTTTTCTTTTTTTGTAC 1571 chrXptel1M 472056 TGGCTTTCCCTAG-TCAGATATCAAAACTGTATTTGTGTCATAGGAAGAA 472104 v vi i - iv i iiiivi i v iv ii v i C L1MD_orf2#LIN 1570 TGTCTTTGTCTGGTTTTGGTATCAGGGTAATACTGGCCTCATAAAATGAG 1521 chrXptel1M 472105 TTTGGTAGGGTTCCTTCTTTTTCAATTATTTTCAAATAGTTTATGTGGTA 472154 v v v i i i v - i vi v v i i v C L1MD_orf2#LIN 1520 TTGGGAAGTGTTCCCTCCTCTTCTATT-TTCTGGAAGAGATTGTGTAGAA 1472 chrXptel1M 472155 TTAGAATTAATTATTTTTT----GTTTGGTTGAATTCACTTGTAAATCTC 472200 i vi v i ---- v v iv i v iv C L1MD_orf2#LIN 1471 TTGGTGTTAATTCTTCTTTAAACGTTTGGTAGAATTCTCCAGTGAAACCA 1422 chrXptel1M 472201 TCTGGTCCTGGGAGTTGTTTTTT 472223 v iii vi C L1MD_orf2#LIN 1421 TCTGGGCCTGGAGATTTCTTTTT 1399 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.82 CpG sites = 122, Kimura (unadjusted) = 42.92 Transitions / transversions = 1.33 (122/92) Gap_init rate = 0.05 (32 / 689), avg. gap size = 1.59 (51 / 32) 386 27.57 4.78 2.82 chrXptel1M 472354 472562 (527438) L1M3_orf2#LINE/L1 3076 3288 (0) m_b337s551i11 14129 chrXptel1M 472354 AGATTAAAAGGGAAA--TACAAAGCTGGGGGAAAATATTTTTATAGCCAA 472401 v i i v -- ii i- i vi - i - L1M3_orf2#LIN 3076 AGAGTGAAAAGGCAACCTACGGAA-TGGGAGAAAATATTTGCA-AACCA- 3122 chrXptel1M 472402 TGTTTCTGATAAT---CTAATTTCTAAAATATATAAAGAACTGTGTCAAA 472448 i v v---i v i i v?vv v L1M3_orf2#LIN 3123 TATATCTGATAAGGGGTTAATATCCAAAATATATAAGGAACTCNTACAAC 3172 chrXptel1M 472449 TTTATA-----AAAATATGTCATTCCTCACTTGATAAATGGTCAAAGGAT 472493 iv ----- i vi v --- i iv ? v v i L1M3_orf2#LIN 3173 TCAATAGCAAAAAAACAAATAA---CCCGATTNAAAAATGGGCAAAGGAC 3219 chrXptel1M 472494 ATGAACGGACAGTTTTCAGATGAGGAAATTAAAATCATCTATAGTCATGT 472543 v ii v i vi v i v vv vii v i vi i L1M3_orf2#LIN 3220 CTGAATAGACATTTCTCCAAAGAAGACATACAAATGGCCAACAGGTATAT 3269 chrXptel1M 472544 GAAAAGATGCTCTAAATCA 472562 v v L1M3_orf2#LIN 3270 GAAAAGATGCTCAACATCA 3288 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.71 CpG sites = 28, Kimura (unadjusted) = 35.22 Transitions / transversions = 1.00 (28/28) Gap_init rate = 0.04 (9 / 208), avg. gap size = 1.78 (16 / 9) 410 27.71 2.69 1.06 chrXptel1M 472377 472562 (527438) L1M4_orf2#LINE/L1 3106 3294 (0) m_b337s551i12 14129 chrXptel1M 472377 TGGGGGAAAATATTTTTATAGCCAATGTTTCTGATAAT---CTAATTTCT 472423 i vi v v -- i v v--- ?i v i L1M4_orf2#LIN 3106 TGGGAGAAAATATTTGCAAATC--ATATATCTGATAAGGGACTNGTATCC 3153 chrXptel1M 472424 AAAATATATAAAGAACTGTGTCAAATTTATAAAAATATGTCA--TTCCTC 472471 i v vv v iv i v v v v -- vv i L1M4_orf2#LIN 3154 AGAATATATAAAGAACTCTTACAACTCAACAATAAAAAGACAAATAACCC 3203 chrXptel1M 472472 ACTTGATAAATGGTCAAAGGATATGAACGGACAGTTTTCAGATGAGGAAA 472521 v ? v v v ii v i vi v i v L1M4_orf2#LIN 3204 AATTNAAAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATA 3253 chrXptel1M 472522 TTAAAATCATCTATAGTCATGTGAAAAGATGCTCTAAATCA 472562 vv vii v iv ii v v L1M4_orf2#LIN 3254 TACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCA 3294 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 35.11 CpG sites = 19, Kimura (unadjusted) = 35.11 Transitions / transversions = 0.59 (19/32) Gap_init rate = 0.02 (4 / 185), avg. gap size = 1.75 (7 / 4) 1505 29.14 2.67 1.40 chrXptel1M 472416 473052 (526948) L1ME4c_3end#LINE/L1 2 646 (184) m_b337s551i13 14129 chrXptel1M 472416 TAATTTCTAAAATATATAAAGAACTGTGTCAAATTTATAA-AAATATGTC 472464 v ?v ? i vvv v - v ?i L1ME4c_3end#L 2 TAATATCTNTANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATC 51 chrXptel1M 472465 ATT-CCTCACTTGATAAATGGTCAAAGGATATGAACGGACAGTTTTCAGA 472513 vv- i v v v i i i iv ? L1ME4c_3end#L 52 AAGACCCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANA 101 chrXptel1M 472514 TGAGGAAATTAAAATCATCTATAGTCATGTGAAAAGATGCTCTAAATCAC 472563 v vv ? vi vv i iv ii i i i v vv i L1ME4c_3end#L 102 AGAGGAAATACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGC 151 chrXptel1M 472564 TATTGATTAGAGAAATGCAAATTAAAACAACTCTGAGGTATCACCTCACA 472613 v i i i i vv i i ii i i L1ME4c_3end#L 152 TAGTAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACG 201 chrXptel1M 472614 CCTCTCAGATGGGCTAAAATGAAAGGAAAAAATTATA---AATGTTAGAG 472660 v i i vi v vv ii vvi v --- i i v L1ME4c_3end#L 202 CCTATTAAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGCTGGCG 251 chrXptel1M 472661 GGTATGTGGGAAAACTGGGACATTAATGCATTGTTGGTGAAATTGTGAAA 472710 i v? i vi v ?i v i i iv ? i v L1ME4c_3end#L 252 AGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAAT 301 chrXptel1M 472711 CGATCCAACCATTCTGGAGAGCAATTTGGAACTG---ACCAAAGGACTGT 472757 i i v v i i v v i--- i ii - ii L1ME4c_3end#L 302 TGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAG-CCAT 350 chrXptel1M 472758 ATAACTCTGCATACCCTTTTTGACCCAGCAGTGCCACTAATGGGTCTGTA 472807 v v v v -- i i v vv vv v L1ME4c_3end#L 351 AAAAATGTTCATACCCTTT--GACCCAGTAATTCCACTTCTGGGAATTTA 398 chrXptel1M 472808 TCCCAAGAAAATCA--CAAAGAAAGGAAAAGCACCCACATGTACTAAAAT 472855 i i v -- ii -- v i i i v i L1ME4c_3end#L 399 TCCTAAGGAAATAATTCAAAAGAAGGAAAA--AGCTATATGCACGAAGAT 446 chrXptel1M 472856 GTT---TGGAGCAGTTCTTTTGGTGGTGGCAAAGAACTGGAAAATGAGTA 472902 --- v - v --i ii i i i i vvivv L1ME4c_3end#L 447 GTTCATTGCAGC-GTTATTT--ATAATAGCGAAAAATTGGAAACAACCTA 493 chrXptel1M 472903 GGTGCCTATTAATTGGGGAGTGGCTGAACAAGTTGTGATATATGCAGGCA 472952 ii i i vi v i i i ii i i i i v? vv i L1ME4c_3end#L 494 AATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCG 543 chrXptel1M 472953 ATGGAATATTAT---TCTATTAATGATGATGATCAAGCTGATTTTAGAAA 472999 ---v i vi i i v vv i v iv iv L1ME4c_3end#L 544 ATGGAATATTATGCAGCCATTAAAAATGATAATTATGAAGACTATGTAGC 593 chrXptel1M 473000 GACTTGGAAAGATTTACATGAACTGATGCTGAGCAAAACAAGCAGAAC-C 473048 i v - v vi vv i i i ii v i- L1ME4c_3end#L 594 AACATGGAAA-ATGTTTATGATATAATGTTAAGTGAAAAAAGCAGAATAC 642 chrXptel1M 473049 AAAA 473052 L1ME4c_3end#L 643 AAAA 646 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.03 CpG sites = 100, Kimura (unadjusted) = 38.36 Transitions / transversions = 1.20 (100/83) Gap_init rate = 0.03 (17 / 636), avg. gap size = 1.53 (26 / 17) 300 30.46 7.37 4.17 chrXptel1M 473312 473962 (526038) C L1M4_orf2#LINE/L1 (2010) 1284 614 m_b337s551i14 14128 chrXptel1M 473312 TCCATC-AGGTTGTCAGATCCGTTGGCATAAAATTGGGCAAAGTAGCTCT 473360 i - i vi ii v vv v vii i C L1M4_orf2#LIN 1284 TTCATCTAGGTTATCTAATTTGTTGGCATACAATTGTTCATAGTATTCCC 1235 chrXptel1M 473361 TAATAATTGCCTTTTCTTTTTCTTCA---CTGGTTGTAA-GTTCACTTT- 473405 v -- - v vi ---ii v - i v i - C L1M4_orf2#LIN 1234 TTATAAT--CCTTTT-TATTTCTGTAAGGTCGGTAGTAATGTCCCCTCTT 1188 chrXptel1M 473406 --ACTCATGATAGTAGTAATTT-AGTTTTCT-TCTTTCTTTAC--ATCAA 473449 -- i v vv - i - i vi--i i C L1M4_orf2#LIN 1187 TCATTCCTGATTTTAGTAATTTGAGTCTTCTCTCTTTTTTTCTTGGTCAG 1138 chrXptel1M 473450 GTTAACTAATGGCTTATATATTTTTATAGTGCTGTTTAAAAAACAGA-TC 473498 vi i v i i -i v i v vv v i i vi - i C L1M4_orf2#LIN 1137 TCTAGCTAAAGGTTTGT-CAATTTTGTTGATCTTTTCAAAGAACCAACTT 1089 chrXptel1M 473499 TTAGTTTTATTTATAAATTTAGTGGGGGGGTCTTGAAGGAGTCGTGTAGT 473548 i ii ----i vv vvivv v i vv ---- iv v v C L1M4_orf2#LIN 1088 TTGGTTTCGTT----GATTTTCTCTATTGTTTTTCTA----TTCTCTATT 1047 chrXptel1M 473549 T------TTTCCTTTC-AA-CTTTGTTAAT-CATTCCTTTGATATTTGAG 473589 ------ vi - - i v - v i-- ii v- C L1M4_orf2#LIN 1046 TCATTTATTTCCGCTCTAATCTTTATTATTTCCTTCCTTC--TGCTTGC- 1000 chrXptel1M 473590 ATTTCTATTTGGTGTATTCTGTTGGTTTTCTAGTTGTTTTTAGTTACATT 473639 - vvi i v ii vi -- - i v v iv vv C L1M4_orf2#LIN 999 -TTTGGGTTTAGTTTGCTCTTCT--TTTTCTAGTT-TCTTAAGGTGGAAG 954 chrXptel1M 473640 ATCAATTCATTGATATGC--TCTTTTTTTCTTTTATTGAGACAAGTATTT 473687 i i iv i v v-- i - - i v i i i C L1M4_orf2#LIN 953 GTTAGGTTATTGATTTGAGATCTTTCTT-CTTTT-TTAATATAGGCATTT 906 chrXptel1M 473688 AAAAGTAGAAAATTTCCCCTAGGTACTGCTTTAGCTACATTCCATAAATT 473737 v iv v v i i i i ? i i i C L1M4_orf2#LIN 905 ACAGCTATAAATTTCCCTCTAAGCACTGCTTTNGCTGCATCCCATAAGTT 856 chrXptel1M 473738 TTGATTTGTTCTATCACAATTGTCATT-ATCTTTAATGGCAAGTTATTAT 473786 i v v i ivivi v - iv -- i vv v v C L1M4_orf2#LIN 855 TTGGTATGTTGTGTTTTCGTTTTCATTCATCTCAAA--GTATTTTCTAAT 808 chrXptel1M 473787 TGTTTCTATGATTTGTTATTTGATTCCCCTCATTTCTTAGGA--TTGTTA 473834 viiii i v v -i vi vi vi --v i C L1M4_orf2#LIN 807 TTCCCTTGTGATTTCTTCTTTGA-CCCATTGGTTATTTAGGAGTGTGTTG 759 chrXptel1M 473835 TTTACTTTCTATTTAATTTTAAATATTTGTTTTAGAGATCCTT-TATTAT 473883 v i iv v v i ---- v iii i vv - i C L1M4_orf2#LIN 758 TTTAATTTCCACATATTTGTGAA----TTTCCCAAATTTCCTTCTGTTAT 713 chrXptel1M 473884 T-ATTTTTATTGT-------TTATGGTCAGAAAAT-CATTT------ATT 473918 - i v v ------- i i i i-i i ------ C L1M4_orf2#LIN 712 TGATTTCTAATTTCATTCCATTGTGGTCGGAGAACATACTTTGTATGATT 663 chrXptel1M 473919 TTATTTTTCTTCAGT---TTGAGAAAT-TTTTAT-GCCTAATACATGGT 473962 i v ii i v i --- vv - - i i C L1M4_orf2#LIN 662 TCAATCCTTTTAAATTTATTGAGACTTGTTTTATGGCCTAACATATGGT 614 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.97 CpG sites = 104, Kimura (unadjusted) = 40.09 Transitions / transversions = 1.21 (104/86) Gap_init rate = 0.08 (52 / 650), avg. gap size = 1.46 (76 / 52) 20 18.27 0.00 0.00 chrXptel1M 474185 474221 (525779) (A)n#Simple_repeat 1 37 (0) m_b337s252i15 14130 chrXptel1M 474185 AAAAAAAAATAAGAAAAAAAAAACATAAGCAAAAAAA 474221 v i v v iv (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 37 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 229 29.41 1.92 1.92 chrXptel1M 474699 474802 (525198) C L1P3_orf2#LINE/L1 (3046) 248 145 m_b337s551i15 14131 chrXptel1M 474699 TTTGTCTTGTCTGAGATTATGATTGCTACCCCTGCCCTTTTT--ATTTTG 474746 i i i v i v v ii --v iv C L1P3_orf2#LIN 248 TCTGTTTTATCAGAGACTAGGATTGCAACCCCTGCTTTTTTTTGCTTTCC 199 chrXptel1M 474747 ACTGAAGCATAATCAGTTATGCTTCAATCCCTTATTTTAATTCTATGTAT 474796 i v-- v ii v i ?v v i vi i i vi i C L1P3_orf2#LIN 198 ATTT--GCTTGGTAAATNTTCCTCCATCCCTTTATTTTGAGCCTATGTGT 151 chrXptel1M 474797 ATCTTT 474802 i C L1P3_orf2#LIN 150 GTCTTT 145 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.02 CpG sites = 18, Kimura (unadjusted) = 39.02 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.03 (3 / 103), avg. gap size = 1.33 (4 / 3) 13 20.37 0.00 4.88 chrXptel1M 476076 476118 (523882) (TTTTGC)n#Simple_repeat 1 41 (0) m_b337s252i16 14132 chrXptel1M 476076 TTTTCCTTTTGCTTTTGCTTATGTATTTAGGTATTTATTTTTG 476118 v v -v v v - ii (TTTTGC)n#Sim 1 TTTTGCTTTTGCTTTTGCTTTTG-CTTTTGCT-TTTGCTTTTG 41 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.00 (2 / 2) 502 22.68 0.82 6.03 chrXptel1M 476119 476240 (523760) C MIRc#SINE/MIR (141) 127 12 m_b337s601i4 14133 chrXptel1M 476119 CTGAGGC-AATTGGGATTAAGTGACTTGCTCAGGGTCACACAGCTAGGAA 476167 -v vv i i i i --- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG--- 81 chrXptel1M 476168 GTTTTAAGTGTATGAGGCCGGATTTCAACTCAGATCCTCTTGACTTCAGG 476217 ---- vvv v v i iv i i i i i i C MIRc#SINE/MIR 80 ----TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chrXptel1M 476218 GCTGGTGCTCTATCCACTGTACC 476240 v ii v i C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTGCACC 12 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 26.15 CpG sites = 15, Kimura (unadjusted) = 27.35 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.07 (8 / 121), avg. gap size = 1.00 (8 / 8) 505 20.08 12.58 2.87 chrXptel1M 477827 477985 (522015) MIRc#SINE/MIR 24 197 (71) m_b337s601i5 14134 chrXptel1M 477827 AGATTGCTGAATGTGGAGTCAGGAAGA-----G---GAA--CAGCCTCAG 477866 vii i iv ----- --- i-- v v v MIRc#SINE/MIR 24 AGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTG 73 chrXptel1M 477867 ACACTTTTTTAGCTATATGACTCTGGGCAGAG--ACTTCACCTATTGCCT 477914 v vi - i i ii - -- v v --- MIRc#SINE/MIR 74 CCACTTACT-AGCTGTGTGACCTTGGGCA-AGTCACTTAACCTCT---CT 118 chrXptel1M 477915 G--CCTCAGTTTCTTCATCTGTAAAATGGGAATAATAGCA---GC---AC 477956 -- i i ii --- ---i MIRc#SINE/MIR 119 GAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGC 168 chrXptel1M 477957 CTAACTCCCAGGATCGGTCTGAAGATCAA 477985 v v i i v v i MIRc#SINE/MIR 169 CTACCTCACAGGGTTGTTGTGAGGATCAA 197 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 23.77 CpG sites = 18, Kimura (unadjusted) = 23.77 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.08 (12 / 158), avg. gap size = 2.08 (25 / 12) 610 21.68 4.09 2.89 chrXptel1M 477862 478032 (521968) MIR#SINE/MIR 65 237 (25) m_b337s601i6 14134 chrXptel1M 477862 CTCAGACACTTTTTTAGCTATATGACTCTGGGCAGAG--ACTTCACCTAT 477909 v v vi - i i ii - -- v v MIR#SINE/MIR 65 CTCTGCCACTTACT-AGCTGTGTGACCTTGGGCA-AGTTACTTAACCTCT 112 chrXptel1M 477910 -TGCCTGCCTCAGTTTCTTCATCTGTAAAATGGGAATAATAGCAGCACCT 477958 - -- i i ii i MIR#SINE/MIR 113 CTG--TGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCT 160 chrXptel1M 477959 AACTCCCAGGATCGGTCTGAAGATCAATTTATTT-GTACA---AAAGAGC 478004 v vi i i v v i i v v v -i --- v MIR#SINE/MIR 161 ACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATACATGTAAAGCGC 210 chrXptel1M 478005 TTAGCATAGTTTCTGGGAACACAATAAG 478032 v i vi - v i i MIR#SINE/MIR 211 TTAGAACAGTGCCT-GGCACATAGTAAG 237 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 25.93 CpG sites = 20, Kimura (unadjusted) = 25.93 Transitions / transversions = 1.25 (20/16) Gap_init rate = 0.05 (9 / 170), avg. gap size = 1.33 (12 / 9) 381 25.13 7.98 2.33 chrXptel1M 479582 479744 (520256) C HERV30#LTR/ERV1 (2639) 5618 5447 m_b337s701i0 14135 chrXptel1M 479582 CTTTAGCCAAACCTCT-GAGCCTTTTCAGTCTTACAAGGGAAGGCTTTTC 479630 i -- i - i i vi ii iiv C HERV30#LTR/ER 5618 CTTTAACCA--CTTCTTGGGCCTTCTCTATTCTACAAGGGAAGGCTTCCA 5571 chrXptel1M 479631 CCCAATTAGTAAAGGTG-----ACGGGAAAAAAAGCAGTTTGAAGTTC-C 479674 v i----- i ivv v i -- i i - C HERV30#LTR/ER 5570 CCCAATTTGTAAAGGTATCAACACAGACCAATAAGTA--TTGAAATCCTC 5523 chrXptel1M 479675 TGCAAAGGGGCATGTGTGTAAAATCAATCGGCCAGTCCTCCCCCAGGT-A 479723 vv vvvv i v v v v i vi i - C HERV30#LTR/ER 5522 TTGACTTTGGCATATGGGTAAAATCTAACTGCCAGTCCTCTCCGGGATAA 5473 chrXptel1M 479724 TGT-ATGTAC----TCCTCCCACAGA 479744 -v v ---- iv C HERV30#LTR/ER 5472 TGTCCTGTTCTTTGTCCTCCCGGAGA 5447 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 30.03 CpG sites = 20, Kimura (unadjusted) = 30.93 Transitions / transversions = 1.00 (20/20) Gap_init rate = 0.06 (10 / 162), avg. gap size = 1.70 (17 / 10) 317 28.38 9.73 6.44 chrXptel1M 479591 479816 (520184) C HERV4_I#LTR/ERV1 (1228) 5311 5079 m_b337s701i1 14135 chrXptel1M 479591 AACCTC-TGAGCCTTTTCAGTCTTACAAGGGAAGGCTTTTCCCCAATTAG 479639 - v i v ii ivv v i ivv iii C HERV4_I#LTR/E 5311 AACCTCATTAGCCTTCTCTGTTCTGGTAGGGTAAGCTTCGACCCAGCCAG 5262 chrXptel1M 479640 TAAAGGTG---------ACGGGAAAAAAAGCAGTTTGAAGTTCCTGCAAA 479680 --------- vi v -----i v viii i C HERV4_I#LTR/E 5261 TAAAGGTGTCTATTAGTACTAGCAAAAA-----CTTGTATCCTCTGCAAG 5217 chrXptel1M 479681 GGGGCATGTGTGTAAAATC-AATCGGCCAGTCCTCCCCCAGGTATGTATG 479729 vv i v i i - i- i ii v - v C HERV4_I#LTR/E 5216 CTGGCATATGGGTGAAGTCTAATT-GCCAGTCTTCCCCTGGGTAAGT-TC 5169 chrXptel1M 479730 TACTCCTCCCACAGACATGGGAAGTTTAAA--AGCCCTTTTCAAGATTTA 479777 iv ---ii - vvvvv i -- v v ----i v C HERV4_I#LTR/E 5168 CTCTCCTC---TGGAC-TGGTTCTATTAGAGGAGGCATTTT----GTTTC 5127 chrXptel1M 479778 CTTGG---------GCACAAACTGGGCAGGCCTGGCAGACCTGTTGAA 479816 v --------- v v i i i i v C HERV4_I#LTR/E 5126 CTGGGTTGTTAAGTGCACACAGTGAGCAGGCTTGACAGACCTGCTTAA 5079 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 35.51 CpG sites = 31, Kimura (unadjusted) = 36.25 Transitions / transversions = 1.07 (31/29) Gap_init rate = 0.09 (20 / 225), avg. gap size = 1.85 (37 / 20) 405 24.78 6.06 2.19 chrXptel1M 479592 479723 (520277) C HERV17#LTR/ERV1 (2429) 6197 6061 m_b337s701i2 14135 chrXptel1M 479592 ACCTCT-GAGCCTTTTCAGTCTTACAAGGGAAGGCTTTTCCCCAATTAGT 479640 - i v i i iiv ii C HERV17#LTR/ER 6197 ACCTCTTGGGCCTTTTCTGTCCTACAAGGGAAGGCCTCCGCCCAACCAGT 6148 chrXptel1M 479641 AAAGGTG---ACGGGAAAAAAAGCAGTT--TGAAGTTCCTGCAAA--GGG 479683 i i i--- vv-- i vv i v -- i i - i --v C HERV17#LTR/ER 6147 GAAAGTATCTACCC--AGACTAGTAGATACTGAAATCCCTG-AGATTTGG 6101 chrXptel1M 479684 GCATGTGTGTAAAATCAATCGGCCAGTCCTCCCCCAGGTA 479723 v v viv i i ii C HERV17#LTR/ER 6100 GCATGTGGGTAAAATCTAGTTGCCAGTCTTCTCCTGGGTA 6061 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 29.79 CpG sites = 20, Kimura (unadjusted) = 30.95 Transitions / transversions = 1.67 (20/12) Gap_init rate = 0.05 (7 / 131), avg. gap size = 1.57 (11 / 7) 397 29.91 7.03 4.21 chrXptel1M 480568 480752 (519248) C HERV4_I#LTR/ERV1 (3099) 3440 3251 m_b337s701i3 14135 chrXptel1M 480568 CCAGGGCCTGTCCAAATATGTGGGGGCCGTCACG----CCCTGAGGCGGG 480613 i i ii vv v vi ii v ---- vi v C HERV4_I#LTR/E 3440 CTAAGGCTCGGGCAAAGAAATGGGGGCTATCCCGAAAGCCCTGAGGGAGC 3391 chrXptel1M 480614 ACTGGCCATGTGCATTGGTGGGGGTTTACGTTCCCCTGG-------ATTT 480656 v v i v ----- --- i i ------- C HERV4_I#LTR/E 3390 ACTGTCCAAGTGTATTGTTG-----TT---TTTCTCTGGTATTAGGATTT 3349 chrXptel1M 480657 CTCCCTTTAAAGGCAAAAAGAAATTGTGACTTTATG--CAATGGTGCACA 480704 ii v i iv v i iv -- iv viiiv C HERV4_I#LTR/E 3348 TCCCATTCAAAGGCAAAAAGGTATTGGGACTCTGGGGCCAGAGGAATGGA 3299 chrXptel1M 480705 AAAGAAAGCATCTTTAAGATCTAAAGTAGGAGACCATCGTGTGTCCCC 480752 i v i iiiiv iii iv ii C HERV4_I#LTR/E 3298 GAAGAAAGCATCTTTTAGGTCTAGGACTGAGAACCATTTTGCATCCCC 3251 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.69 CpG sites = 33, Kimura (unadjusted) = 39.67 Transitions / transversions = 1.65 (33/20) Gap_init rate = 0.06 (11 / 184), avg. gap size = 1.91 (21 / 11) 575 27.86 3.24 4.08 chrXptel1M 484711 484957 (515043) C L3#LINE/CR1 (156) 3943 3699 m_b338s601i0 14136 chrXptel1M 484711 AGGGAGTCCATTCCATTTGGGCCCAACTCAAAAGGATTAAAAAGCTTTTT 484760 v i vv vv i vi vv - i - i C L3#LINE/CR1 3943 AGGCAGCCCATTCCATTTTTGGACAGCTCTGATTG-TTAGAAAG-TTCTT 3896 chrXptel1M 484761 GTTTTTATCAGGCCTAAAACAATCCCTCTG-AAGTTTCACCTGTTTTATC 484809 vi v iii v v vii i i - v i ii vvvi C L3#LINE/CR1 3895 CCTTATATTGAGCCGAAATCTGCCTCCCTGTAACTTCCACCCATTGGTCC 3846 chrXptel1M 484810 TAGTTATGCTGTTTGAGGTGAACCAGACTGAAT---TTTCATCTTTCTTC 484856 v iv i ---- i v v --- i v ii C L3#LINE/CR1 3845 TAGTTCTGCCCTCTG----GAGCCACACAGAATAAGTCTAATCCCTCTTC 3800 chrXptel1M 484857 CACAATGACAGCCCTTCACATACTTGAAGACAGCCAAAATTTGGTCCTTT 484906 - v i i vv --- iii C L3#LINE/CR1 3799 CACA-TGACAGCCCTTCAAATATTTGAAGACAGCTATCAT---GTCTCCT 3754 chrXptel1M 484907 TCAAGTC--CTCTT-TCAAGTCTAAATATTCCCGGTTCTTCTCACCATT- 484952 ii -- - v v i i i i iiv i - C L3#LINE/CR1 3753 CTAAGTCTTCTCTTCTCCAGGCTAAACATCCCCAGTTCCTTCAACCGTTC 3704 chrXptel1M 484953 TTCAT 484957 i C L3#LINE/CR1 3703 CTCAT 3699 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 34.95 CpG sites = 38, Kimura (unadjusted) = 35.62 Transitions / transversions = 1.36 (38/28) Gap_init rate = 0.06 (15 / 246), avg. gap size = 1.20 (18 / 15) 366 28.81 17.90 1.50 chrXptel1M 484932 485160 (514840) C L3#LINE/CR1 (411) 3688 3423 m_b338s601i1 14136 chrXptel1M 484932 TTCCCGGTTCTTCTCACCATTTTCATTGCTGCCTTTGGAACAAGCCCCAG 484981 v iii -- ii vi i vi i iv i iv i C L3#LINE/CR1 3688 TTCCAGACCCTTC--ACCATCCTGGTCGCTCTCCTCTGGACGCGCTCCAG 3641 chrXptel1M 484982 CTTGTC--TTTCTCTTCTATAAGATATAATGCACTAAACTGAACT----- 485024 i -- v i - - i i iii v vi v----- C L3#LINE/CR1 3640 TTTGTCAATGTCCCT-CT-TAAAATGTGGCGCCCAGAACTGAACGCAATA 3593 chrXptel1M 485025 CTCCATATGTGCCCTGACCAAGGCAGAGTATA----------TGTCTCTC 485064 v vi iv i ---------- ii i C L3#LINE/CR1 3592 CTCCAGATGTGGTCTGACCAGCGCAGAGTACAGCGGGACTATTACCTCCC 3543 chrXptel1M 485065 ---ATTTGGAAAATATGTCTTTCTTAAT-TAACCTTGTATAGCATTAGC- 485109 ---? i v v iii i v -i i viv v - C L3#LINE/CR1 3542 TTGNTCTGGACACTATACTTCTATTAATGCAGCCTAAGATTGCATTAGCT 3493 chrXptel1M 485110 -TTTTGA------------------GGCTTCCATTTTGTTTGCAGATAAC 485140 - i------------------ ivi vv i i vi C L3#LINE/CR1 3492 TTTTTGGCAGCCACATCACACTGTTGGCTCATATTGAGCTTGCGGTCAAC 3443 chrXptel1M 485141 TAAAACCTCTAGTTCTTTTT 485160 i v C L3#LINE/CR1 3442 TAAAACCCCTAGGTCTTTTT 3423 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 35.23 CpG sites = 42, Kimura (unadjusted) = 38.22 Transitions / transversions = 1.83 (42/23) Gap_init rate = 0.05 (11 / 228), avg. gap size = 4.09 (45 / 11) 225 24.50 16.82 0.81 chrXptel1M 485312 485418 (514582) C MIRc#SINE/MIR (136) 132 9 m_b338s601i2 14137 chrXptel1M 485312 GGGAAGTGAG--TCAATTAGGATTAAGTGACTTGCT--AGG------AAG 485351 i v -- ivv - i-- ------ iv C MIRc#SINE/MIR 132 GGAAACTGAGGCTCAGAGAGG-TTAAGTGACTTGCCCAAGGTCACACAGC 84 chrXptel1M 485352 TGTTAAGTGTCCGAGGCCAGATTTGAACTCTGGTCCCCCTGACTCCATGA 485401 iv v v v vi i i i v ii v v C MIRc#SINE/MIR 83 TAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGT 34 chrXptel1M 485402 CTA--------TCCACTGGACCCCA 485418 i -------- v v C MIRc#SINE/MIR 33 CCAGTGCTCTTTCCACTGCACCACA 9 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 28.56 CpG sites = 12, Kimura (unadjusted) = 29.86 Transitions / transversions = 0.86 (12/14) Gap_init rate = 0.05 (5 / 106), avg. gap size = 3.80 (19 / 5) 678 29.63 6.38 2.59 chrXptel1M 485412 485709 (514291) C L3#LINE/CR1 (736) 3363 3055 m_b338s601i3 14136 chrXptel1M 485412 GACCCCAAGTGTATAACTCTTGATTTATG--TATTACATTTCACTTTTTT 485459 v i i i vi i vv v-- i v ii v C L3#LINE/CR1 3363 GAACCTAAATGCAGGACTTTACATTTATCCCTGTTAAATTTCATCTTGTT 3314 chrXptel1M 485460 TTTAAATAGATTTGGCT-ATCATTCTAGCTCATGGAGATCGTTTTGTAGC 485508 -------i v i i- i i iii v ? v v C L3#LINE/CR1 3313 -------GGTTTCGGCCCATCGTTCCAGCCTGTCGAGATCNTTTTGAATC 3271 chrXptel1M 485509 CTGATTC-ATTAACC--TGTA--AACTGTCCATCTTAGTTTGGTGTTAGC 485553 i -i i v --i -- i i v ii i v i v C L3#LINE/CR1 3270 TTGATTCTGTCATCCANCGTATTAGCTATCCCTCCCAGCTTTGTGTCATC 3221 chrXptel1M 485554 CACAGA--------GTATTCCTTCTCTGTCTTTATCCGAATTATTCATAA 485595 ii i -------- i v v i i i i v C L3#LINE/CR1 3220 TGCAAATTTGATAAGCATGCCTTCTATGTCTTCATCCAAGTCATTGATAA 3171 chrXptel1M 485596 CATTAATGTATAGCACAAGGCCAATGACAGAACTCTGTAATACTCCATTG 485645 v v iv v i v i v i i iii v i i C L3#LINE/CR1 3170 AAATGTTGAACAGGACAGGGCCAAGGACAGAGCCCTGTGGCACGCCACTA 3121 chrXptel1M 485646 GAGAACTCCTT--ATATTGGCATTGACCCATTAAT-AGCTCTACTTTGAT 485692 v i -- vi i i i - i v i-i iv C L3#LINE/CR1 3120 GAGACCTCCCTCCAGGTTGACATCGATCCATTAATCAACACC-TTTTGGG 3072 chrXptel1M 485693 TTTAGTTATTCAAACAG 485709 v ii v C L3#LINE/CR1 3071 TATAGTCGTTCAACCAG 3055 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 36.48 CpG sites = 55, Kimura (unadjusted) = 39.50 Transitions / transversions = 1.77 (55/31) Gap_init rate = 0.05 (16 / 297), avg. gap size = 1.69 (27 / 16) 424 30.59 4.26 2.62 chrXptel1M 486269 486456 (513544) C L1ME4c_3end#LINE/L1 (294) 536 346 m_b338s551i0 14138 chrXptel1M 486269 ATATACCACAACTTGTTCAGTCATTCCCCAACTGATGGTGTCCCCTCA-- 486316 i i i ii i ii v i v ---v vi i -- C L1ME4c_3end#L 536 ATGTACCATAATTTACTTAACCATTCCCCTATTGTTGG---ACATTTAGG 490 chrXptel1M 486317 --ATTTCCAATTCTTTGGCCCTACAAAAAACTGCTGCTATAAATGTTTTT 486364 --i i i vivi i v - v i ii i i C L1ME4c_3end#L 489 TTGTTTCCAATTTTTCGCTATTATAAATAAC-GCTGCAATGAACATCTTC 441 chrXptel1M 486365 GTACAAATAGGTTCTTTCCCTTTTTCTTTGATCTCTTTGGGATACAAACC 486414 i v v i i iii vvv v i i i - vi C L1ME4c_3end#L 440 GTGCATATAGCTTTTTCCTTCTTTTGAATTATTTCCTTAGGATA-AATTC 392 chrXptel1M 486415 CTAAATGTG----TGCTGGGACAAAGGATATGCACAATTTTATAGC 486456 i i v ---- i v i v v i C L1ME4c_3end#L 391 CCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGC 346 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 39.34 CpG sites = 37, Kimura (unadjusted) = 41.30 Transitions / transversions = 1.95 (37/19) Gap_init rate = 0.04 (8 / 187), avg. gap size = 1.62 (13 / 8) 38 0.00 0.00 0.00 chrXptel1M 486479 486511 (513489) (AC)n#Simple_repeat 1 33 (0) c_b338s251i0 14139 chrXptel1M 486479 ACACACACACACACACACACACACACACACACA 486511 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACA 33 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 258 26.00 4.80 1.55 chrXptel1M 486664 486788 (513212) C L1PREC2_orf2#LINE/L1 (816) 2478 2350 m_b338s551i1 14140 chrXptel1M 486664 ATTTAATGAGTAAATTAATTTAAGTAGAAATGCCATTTTTATTATATTGG 486713 v vv iv ii i v vv v iv i C L1PREC2_orf2# 2478 ATTGAATCTGTAAATTGCTTTGGGCAGTATGGCCATTTTAACGATATTGA 2429 chrXptel1M 486714 CTCAGCCTATCCATAAGCAATTGA---CTTCTCCAATTGTTTAGATC-TG 486759 i vv i - v ---i i v ivi - v C L1PREC2_orf2# 2428 TTCTTCCTATCCATGAGC-ATGGAATGTTTTTCCATTTGTTTGTGTCATC 2380 chrXptel1M 486760 TCT--TTACTGTTGGAAAGTATTTTGTAATT 486788 -- v - iiv i C L1PREC2_orf2# 2379 TCTGATTTCT-TTGAGCAGTGTTTTGTAATT 2350 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 30.99 CpG sites = 15, Kimura (unadjusted) = 32.16 Transitions / transversions = 0.88 (15/17) Gap_init rate = 0.04 (5 / 124), avg. gap size = 1.60 (8 / 5) 270 26.37 2.17 1.08 chrXptel1M 486673 486764 (513236) C L1MD_orf2#LINE/L1 (825) 2469 2377 m_b338s551i2 14140 chrXptel1M 486673 GTAAATTAATTTAAGTAGAAATGCCATTTTTATTATATTGGCTCAGCCTA 486722 ? i ii v v v i i i iv vv v C L1MD_orf2#LIN 2469 GTANATCAATTTGGGGAGAATTGACATCTTTACTATGTTGAGTCTTCCAA 2420 chrXptel1M 486723 TCCATAAGCA--ATTGACTTCTCCAATTGTTTAGATCTGTCTTT 486764 i i --i vviii v i - C L1MD_orf2#LIN 2419 TCCATGAACACGGTATGTCTCTCCATTTATTTAGATCT-TCTTT 2377 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 33.71 CpG sites = 14, Kimura (unadjusted) = 33.71 Transitions / transversions = 1.40 (14/10) Gap_init rate = 0.02 (2 / 91), avg. gap size = 1.50 (3 / 2) 471 29.38 0.68 2.08 chrXptel1M 486842 486987 (513013) C L3#LINE/CR1 (1219) 2880 2737 m_b338s601i4 14136 chrXptel1M 486842 TAGCATGACCCATTCTTTATCATATCC-TACTAACTTTTGGTAATCACTG 486890 i iii vi v - i - i ii ii i i i C L3#LINE/CR1 2880 TGGCATGACTTGTTCTTAGTGA-ACCCATGCTGGCTCCTAGTGATCACCG 2832 chrXptel1M 486891 TTTCCCTTTCTAGGTTCTGAACAATTATCTGTTTAATAATGTTTCCCAGA 486940 i i i v v vv ii viv i i C L3#LINE/CR1 2831 CTTCCTTTTCTAAGTGCTCACAAACCATCTGTTTAATAATCCGTTCTAGA 2782 chrXptel1M 486941 ATTTTGCCAGGAATGGAAATGGAGTCTACTGGGGCCTGGAGTTTGCA 486987 i i v vi vi ii i-- i v ? C L3#LINE/CR1 2781 ATTTTGCCGGGGATCGACGTCAAGCTTACC--GGTCTGTAGTTTNCA 2737 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 33.95 CpG sites = 30, Kimura (unadjusted) = 40.00 Transitions / transversions = 2.50 (30/12) Gap_init rate = 0.03 (4 / 145), avg. gap size = 1.00 (4 / 4) 754 26.31 2.82 1.86 chrXptel1M 487183 487395 (512605) MIRc#SINE/MIR 2 216 (52) m_b338s601i5 14141 chrXptel1M 487183 GAGGCAGCTATGTGGTACAATAGATAAAGTGCTAAGGCTGGAGTCAAGAA 487232 --- i i i v i ii iiivi i MIRc#SINE/MIR 2 GAGGCAG---TGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chrXptel1M 487233 AACCCGAGTTCAAATCCAGCCTTAGACATCTAACAGGCTATATGACCCCG 487282 i i i i i v v iv v - v vi i i ii MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCCA-CTTACTAGCTGTGTGACCTTG 97 chrXptel1M 487283 AGCAAGTCATTTCACCTCTGTCTGCCTCAGTTTCCTCTTTGGCAAAACGA 487332 i i v v vv v iv i i i MIRc#SINE/MIR 98 GGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGG 147 chrXptel1M 487333 GTATAACAATA---GC---ACCCACCTCCCAGGGTTTTTGCGAGGATCAA 487376 v i --- ---i i v v i MIRc#SINE/MIR 148 GGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAA 197 chrXptel1M 487377 ATGAGAGAACTTTTATAAA 487395 v iv v i i MIRc#SINE/MIR 198 ATGAGATAATGTATGTGAA 216 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 32.72 CpG sites = 35, Kimura (unadjusted) = 33.47 Transitions / transversions = 1.75 (35/20) Gap_init rate = 0.03 (6 / 212), avg. gap size = 1.67 (10 / 6) 640 28.91 3.40 0.95 chrXptel1M 487220 487425 (512575) MIR#SINE/MIR 33 243 (19) m_b338s601i6 14141 chrXptel1M 487220 CTGGAGTCAAGAAAACCCGAGTTCAAATCCAGCCTTAGACATCTAACAGG 487269 i - vvi i i i v v iv v - v vi MIR#SINE/MIR 33 CTGGAGCCA-GACTGCCTGGGTTCGAATCCCGGCTCTGCCA-CTTACTAG 80 chrXptel1M 487270 CTATATGACCCCGAGCAAGTCATTTCACCTCTGTCTGCCTCAGTTTCCTC 487319 i i ii i i i v v v MIR#SINE/MIR 81 CTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTC 130 chrXptel1M 487320 TTTGGCAAAACGAGTATAACAATAGCACCCACCTCCCAGGGTTTTTGCGA 487369 v iv i i i v i i i vi v i MIR#SINE/MIR 131 ATCTGTAAAATGGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTGA 180 chrXptel1M 487370 GGATCAAATGAGAGAACTTTTATAAA-TGTTGATAGTAGT------TACA 487412 i vv iviv i -i i v v ii ------i MIR#SINE/MIR 181 GGATTAAATGAGTTAATACATGTAAAGCGCTTAGAACAGTGCCTGGCACA 230 chrXptel1M 487413 TAATAAATGTTTA 487425 i ii i i MIR#SINE/MIR 231 TAGTAAGCGCTCA 243 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 35.43 CpG sites = 37, Kimura (unadjusted) = 37.87 Transitions / transversions = 1.68 (37/22) Gap_init rate = 0.02 (4 / 205), avg. gap size = 2.25 (9 / 4) 446 21.29 0.84 5.26 chrXptel1M 487729 487847 (512153) C MIRc#SINE/MIR (153) 115 2 m_b338s601i7 14142 chrXptel1M 487729 GAGGTTAAGTGACTTGCCCAGGGTCACACATCTAGGAAGTGTTA-AGTGT 487777 i v v vi - --- C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAG--- 69 chrXptel1M 487778 CTTCCAGATTAGAACTCAGGTCCTCCTGACTTAAAGGCCAATGCTCTATC 487827 --i vi i v i i iv v i v C MIRc#SINE/MIR 68 --CCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTC 21 chrXptel1M 487828 CCTTTCAACCCAGCTACCCC 487847 vi v v v - i i C MIRc#SINE/MIR 20 CACTGCACCACA-CTGCCTC 2 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 25.15 CpG sites = 12, Kimura (unadjusted) = 25.15 Transitions / transversions = 1.00 (12/12) Gap_init rate = 0.06 (7 / 118), avg. gap size = 1.00 (7 / 7) 467 17.58 4.46 3.54 chrXptel1M 487848 487959 (512041) C MER63D#DNA/hAT-Tip100 (609) 452 340 m_b338s502i0 14143 chrXptel1M 487848 TAATCTGCATTTTTAACACTTTCTCCATCACTTTGCCCAATCTAGTCAAG 487897 v i viiv i v v C MER63D#DNA/hA 452 TAATCTGCATTATTAACATTTTCTCCATCACTTTCTTAAGTCTAGACAAT 403 chrXptel1M 487898 CAACA----AATCCATCCAGCCCAG-TTTGTGGAGTTTTGTAGCTGATTT 487942 ---- vv v v - i v ---- i C MER63D#DNA/hA 402 CAACAAAACAATAAATCAAGCCCTGATTTGTAGCGTTT----GCCGATTT 357 chrXptel1M 487943 CTGAGGTGTAAATGCTC 487959 i v i C MER63D#DNA/hA 356 CCGTGGTGTAAATACTC 340 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 17.90 CpG sites = 8, Kimura (unadjusted) = 20.08 Transitions / transversions = 0.73 (8/11) Gap_init rate = 0.05 (6 / 111), avg. gap size = 1.50 (9 / 6) 298 37.34 14.41 1.06 chrXptel1M 488020 488352 (511648) C L3#LINE/CR1 (3344) 755 379 m_b338s601i8 14136 chrXptel1M 488020 GAGTGGATGTCATTTGACTAGAT-GACAAGTTGCTGGCCAGTGCTCCGTC 488068 i iv iv i i vi v - ii i-i vi iv C L3#LINE/CR1 755 GAGTGGGTAGCGGTCGGCGGGTTTGATGAGTC-TTGGCAGGCTCTCCGTC 707 chrXptel1M 488069 ACATCTCAGTTGTCTGCTCCAAGAAGACAGTAGTTTATGTCTCGGTTGTT 488118 i i v iivi i i ---i iv i i ivi C L3#LINE/CR1 706 ACGTCTCGGATACACGCTCCAGGAAGACAGCA---CACCTCCCGATTAGC 660 chrXptel1M 488119 AATGTAAAGTCTACAGATGG--------------TTCAGCAGAGAGCCAT 488154 v i v i i v i --------------i i i i i C L3#LINE/CR1 659 CACGTCAGGTCTGCATACGGCCGCCTCCGTATCCCTCAGCGGGGAGTCAC 610 chrXptel1M 488155 TAGACAGAACATCTAGTCTATTCTTATTCTGACCATTGCTGAGGGACATG 488204 i iv vv iv vv v i vi vv i? v iviii ivv v v C L3#LINE/CR1 609 CAACCACCACGACGCGTCTCTTCCTCCTGGGGNCAGTAACAGGATTCCTC 560 chrXptel1M 488205 GCACCTGATAATAGCTTTAGATCCAAAGCATCCTTCC-TTGAGCAT--AA 488251 v i iv viii vvvvi iv - v -- C L3#LINE/CR1 559 GCACCTGCTAGTGCCTGCGAATCCTCCTTATTGTTCCGTGGAGCATGGAA 510 chrXptel1M 488252 GCCTGTTTCCTTAATAGATGGCCCAGTTCTGACCT-----------GTCT 488290 vv i i ivvi v i i v iiiv ----------- i C L3#LINE/CR1 509 TGCTGCTTCTTCTTCAGAAGGTCCGGATTCACCCTCCGTGGGAAGAGCCT 460 chrXptel1M 488291 TAT----------TAGTTTCAAAAGTTCAGAGGTTC----CTTTC----C 488322 i ---------- i i ivi v i v ---- ----i C L3#LINE/CR1 459 CATACCTGTTGTNTAGCTCCAGTGGTGCGGAGTTTCTTCTCTTTCTCCTT 410 chrXptel1M 488323 TTCCTC-ATGTCATATTCTTCTACCCTCTAA 488352 -i i i i v i C L3#LINE/CR1 409 TTCCTCTGTGTCACATTCTTCCACTCGCCAA 379 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 47.07 CpG sites = 74, Kimura (unadjusted) = 54.76 Transitions / transversions = 1.51 (74/49) Gap_init rate = 0.04 (13 / 332), avg. gap size = 4.00 (52 / 13) 20 16.38 0.00 0.00 chrXptel1M 488465 488498 (511502) (A)n#Simple_repeat 1 34 (0) m_b338s252i0 14144 chrXptel1M 488465 AAAACAAATAAAAAACAAGAAAAGAAAAAAAAAA 488498 v v v i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 34 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 236 25.47 5.71 2.78 chrXptel1M 489791 489895 (510105) C L1P1_orf2#LINE/L1 (777) 2517 2410 m_b338s551i3 14145 chrXptel1M 489791 TTCTATTAGTAAAATACAGTTAGTAATTTAATAGGGATGCCATTGA---- 489836 i v iv i - - i ii i i v ---- C L1P1_orf2#LIN 2517 TTCTGTGAAGAAAGT-CA-TTGGTAGCTTGATGGGGATGGCATTGAATCT 2470 chrXptel1M 489837 ATAAACTG-ATTAGGTAA-ATTCTCATTTTTAAGTATATTGATTTTGCCT 489884 i i-v i i i- vvi i v - i v C L1P1_orf2#LIN 2469 ATAAATTACCTTGGGCAGTATGGCCATTTTCACG-ATATTGATTCTTCCT 2421 chrXptel1M 489885 AACCATGAACA 489895 v i C L1P1_orf2#LIN 2420 ACCCATGAGCA 2410 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 32.23 CpG sites = 17, Kimura (unadjusted) = 32.23 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.06 (6 / 104), avg. gap size = 1.50 (9 / 6) 228 25.25 11.11 0.00 chrXptel1M 490198 490296 (509704) C L1MEj_5end#LINE/L1 (1) 2159 2050 m_b338s551i4 14146 chrXptel1M 490198 TCATTTTGTT------GTGTTTTTTGAAAGCAGGATATTGTTGAATTTAG 490241 i ------ i v i v v i ii v C L1MEj_5end#LI 2159 TCACTTTGTTTTAAGTGTGTTTCTTGTAAACAGCATATAGCTGGGTTTTG 2110 chrXptel1M 490242 ATTTTTAGTCCG--CTACCCATTTCC--CTTTTA-TGGTTAAATTCATCC 490286 v ii i-- iv vi i i-- - vvi vi C L1MEj_5end#LI 2109 TTTTTTAACCCAATCTGACAGTCTCTGTCTTTTAATGGGAGAATTCAGTC 2060 chrXptel1M 490287 CATTCACATT 490296 C L1MEj_5end#LI 2059 CATTCACATT 2050 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 31.52 CpG sites = 15, Kimura (unadjusted) = 31.52 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.04 (4 / 98), avg. gap size = 2.75 (11 / 4) 14 0.00 7.41 3.57 chrXptel1M 491567 491593 (508407) (CTGA)n#Simple_repeat 1 28 (0) m_b338s252i1 14147 chrXptel1M 491567 CTGAACTGACT--CTGACTGACTGACTGA 491593 - -- (CTGA)n#Simpl 1 CTG-ACTGACTGACTGACTGACTGACTGA 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.08 (2 / 26), avg. gap size = 1.50 (3 / 2) 496 21.55 2.24 3.01 chrXptel1M 492969 493102 (506898) C MIR#SINE/MIR (82) 180 48 m_b338s601i9 14148 chrXptel1M 492969 TCATAACTACCCTGGGAGGTAGATGCTGTTACTATTCCTATTTTACAGAT 493018 i v iv i i i i i i C MIR#SINE/MIR 180 TCACAACAACCCTATGAGGTAGGTACTATTATTATCCCCATTTTACAGAT 131 chrXptel1M 493019 CAGGAAACCTAGGCAGGCAGACATGTGAAGTCACTTGCCC-AGGTTCCAC 493067 v iv -- v v v v - iv C MIR#SINE/MIR 130 GAGGAAACTGAGGCA--CAGAGAGGTTAAGTAACTTGCCCAAGGTCACAC 83 chrXptel1M 493068 A--CAGTAAGTGTTTTTGAGGCTGAATTTGAACACAG 493102 --i --viv v v i i v C MIR#SINE/MIR 82 AGCTAGTAAGTG--GCAGAGCCGGGATTCGAACCCAG 48 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 24.56 CpG sites = 14, Kimura (unadjusted) = 25.57 Transitions / transversions = 1.00 (14/14) Gap_init rate = 0.05 (6 / 133), avg. gap size = 1.17 (7 / 6) 246 35.43 4.49 3.23 chrXptel1M 494114 494358 (505642) L2#LINE/L2 2470 2717 (365) m_b338s601i10 14149 chrXptel1M 494114 TCTTTCCACCTAAAC-TCTTTCTTCTGAA--CTTTCTTATTGCTGTCAA- 494159 i v ii - vi i i i v -- i ii iv v ? - L2#LINE/L2 2470 TCTTCCCCCTCAAACCTGCTCCTCCCGCAGTCTTCCCCATCTCAGTNAAT 2519 chrXptel1M 494160 GGTCACTGCCATCCTCCCAGTCACCCAAGGTGGCAACTTAAGGGTCACCT 494209 iv - i ii i i viiiv i vi i i i L2#LINE/L2 2520 GGCAACT-CCATCCTTCCAGTTGCTCAGGCCAAAAACCTTGGAGTCATCC 2568 chrXptel1M 494210 CTGACTCCTCATTCATTTTCACCTTTCCCCCAATATCTATTTCAACATCA 494259 i -- v i --- iv v v i i v i v v L2#LINE/L2 2569 TTGACTCCTC--TCTTTCT---CTCACACCCCACATCCAATCCATCAGCA 2613 chrXptel1M 494260 AGTCCTTTTGATTTTATCTTCCTAATCTCTC-----TCTG-CCCCTCCTT 494303 i v i ii i i vv v v ----- i - v i i L2#LINE/L2 2614 AATCCTGTCGGCTCTACCTTCAAAATATATCCAGAATCCGACCACTTCTC 2663 chrXptel1M 494304 TGCATCTTGTTACTGTCACCACTC-ATTTCGGGCCCTCATTACCTGATGC 494352 vv i --ii i i -iv i ii vi i i vvi L2#LINE/L2 2664 ACCACCT--CCACTGCCACCACCCTGGTCCAAGCCACCATCATCTCTCGC 2711 chrXptel1M 494353 TCAGAT 494358 iii L2#LINE/L2 2712 CTGGAT 2717 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 48.13 CpG sites = 56, Kimura (unadjusted) = 51.75 Transitions / transversions = 2.00 (56/28) Gap_init rate = 0.06 (14 / 244), avg. gap size = 1.36 (19 / 14) 232 30.50 7.24 9.40 chrXptel1M 495314 495465 (504535) L2c_3end#LINE/L2 328 476 (2) m_b338s601i11 14149 chrXptel1M 495314 TTATCCTGT-CTGTAGCATCATTTGT--ACTTGGTCGTCTTTCACATTAG 495360 v i -i -- ii i -- ? vii iiiv i L2c_3end#LINE 328 TTAACTTGTATTGTA--ATTGTCTGTTTACNTGTCTGTCTCCTCCACTAG 375 chrXptel1M 495361 ---GTG----CATTGGAAACAATGACTGTCTTTTGTCCGTTTTTA-ATCC 495402 --- ---- v iiii iv i v i i i i i i- L2c_3end#LINE 376 ACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTATCC 425 chrXptel1M 495403 TCAGTGCTTAAGTTCATGCCCAGAACATAGTAAGCACTTAACAAATATTT 495452 i i i i------- ----- i i i i i L2c_3end#LINE 426 CCAGCGCCTG-------GC-----ACATAGTAGGCGCTCAATAAATGTTT 463 chrXptel1M 495453 ATTGACTAACTGA 495465 i v i v L2c_3end#LINE 464 GTTGAATGAATGA 476 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 39.32 CpG sites = 34, Kimura (unadjusted) = 43.56 Transitions / transversions = 4.25 (34/8) Gap_init rate = 0.13 (19 / 151), avg. gap size = 1.32 (25 / 19) 242 29.98 5.94 0.94 chrXptel1M 495366 495466 (504534) L2d_3end#LINE/L2 408 513 (3) m_b338s601i12 14149 chrXptel1M 495366 TTGGAAACAATGAC--TGTCTTTTGTCCGTTTTTAAT---CCTCAGTGCT 495410 iiii iv -- v iii?v ? vi --- v i i L2d_3end#LINE 408 TTGAGGGCAGGGACCATGTCTTATACTNTTTTNTCGTTCCCCACAGCGCC 457 chrXptel1M 495411 TAAGTTCA-TGCCCAGAACATAGTAAGCACTTAACAAATATTTATTGACT 495459 - iv - iv v i i i i i i i L2d_3end#LINE 458 TA-GCACAGTGCTGAGCACATAGTAGGCGCTCAATAAATACTTGTTGATT 506 chrXptel1M 495460 AACTGAT 495466 i i L2d_3end#LINE 507 GATTGAT 513 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 36.72 CpG sites = 22, Kimura (unadjusted) = 42.27 Transitions / transversions = 2.75 (22/8) Gap_init rate = 0.04 (4 / 100), avg. gap size = 1.75 (7 / 4) 283 30.23 3.49 0.00 chrXptel1M 495380 495465 (504535) L2a_3end#LINE/L2 427 515 (2) m_b338s601i13 14149 chrXptel1M 495380 TGTCT--TTTGTCCGTTTTTA-ATCCTCAGTGCTTAAGTTCATGCCCAGA 495426 -- i ii vi i- i i i iivivi ii v L2a_3end#LINE 427 TGTCTGTTTTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGC 476 chrXptel1M 495427 ACATAGTAAGCACTTAACAAATATTTATTGACTAACTGA 495465 i i i i i v i v L2a_3end#LINE 477 ACATAGTAGGCGCTCAATAAATATTTGTTGAATGAATGA 515 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 37.72 CpG sites = 20, Kimura (unadjusted) = 42.03 Transitions / transversions = 3.33 (20/6) Gap_init rate = 0.02 (2 / 85), avg. gap size = 1.50 (3 / 2) 574 21.23 1.37 6.47 chrXptel1M 497318 497463 (502537) MIRc#SINE/MIR 10 148 (120) m_b338s601i14 14150 chrXptel1M 497318 GTGGTGGAGTAGATAAAGACCCAGGCCTGGAGTCAGGAAGACTCATTTTC 497367 v i v i vv ii i i -------- MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC-------- 51 chrXptel1M 497368 CTGAGTTCAAATCTGGCCTCAGACACTTCCTAGCTGTGTGATCCTGGGCA 497417 i i i iv v v v v i i MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 101 chrXptel1M 497418 AGTCACGTCAACCTGTTC--ACCTCAGTTTCCCCATCTGTAAAGTGAG 497463 - i v ii--i i i i MIRc#SINE/MIR 102 AGTCAC-TTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 24.51 CpG sites = 19, Kimura (unadjusted) = 25.51 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.07 (10 / 145), avg. gap size = 1.10 (11 / 10) 520 21.17 5.00 1.61 chrXptel1M 499763 499882 (500118) C MIRc#SINE/MIR (142) 126 3 m_b338s601i15 14151 chrXptel1M 499763 TGAGGCAGTTAG---GATTAAGTGACTTACCCAAGGTCACACAGCTAAGA 499809 -- i --- i i iv C MIRc#SINE/MIR 126 TGAGGC--TCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTA 79 chrXptel1M 499810 CGTATCTGAGGCCAGATTTGAACTCAGGTTCTTCTGACTTCAGGGCTGGT 499859 v iv v v vi i i i ii i i i v ii C MIRc#SINE/MIR 78 AGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGT 29 chrXptel1M 499860 GCTCTATCCACTGCACC---CTGTCT 499882 v --- i C MIRc#SINE/MIR 28 GCTCTTTCCACTGCACCACACTGCCT 3 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 24.47 CpG sites = 17, Kimura (unadjusted) = 25.64 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.03 (4 / 119), avg. gap size = 2.00 (8 / 4) 866 33.43 5.67 3.21 chrXptel1M 499903 500044 (499956) C L2#LINE/L2 (6) 3076 2928 m_b338s601i16 14152 chrXptel1M 499903 AGAGCATTCCAGGCAT-GAGCATAGCCAGGGAGAATATCCACAGCTGAGA 499951 i v- i v i v v vi vii vv vi i C L2#LINE/L2 3076 AGAGCGTTCCAGGCAGAGGGAACAGCAAGTGCAAAGGCCCTGAGGCGGGA 3027 chrXptel1M 499952 AATGGAGGCT--CTTGTTCATGGGACAGCCAGGAGGCCAGGGTCACTAGA 499999 iv-- v v -- v iv i v v vi i C L2#LINE/L2 3026 GC--GTGCCTGGCGTGTTCGAGGAACAGCAAGGAGGCCAGTGTGGCTGGA 2979 chrXptel1M 500000 TACAATAGTATATTTTGGGGAGTCAGGTGTTAGA-------AGAGTGG-A 500041 -i ii- iviivvv vvv ivv ------- v - C L2#LINE/L2 2978 -GCGG-AGTGAGCGAGGGGGAGAGTGGTAGGAGATGAGGTCAGAGAGGTA 2931 chrXptel1M 500042 AAA 500044 vi C L2#LINE/L2 2930 ACG 2928 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 43.39 CpG sites = 189, Kimura (unadjusted) = 45.65 Transitions / transversions = 0.75 (21/28) Gap_init rate = 0.06 (8 / 141), avg. gap size = 1.88 (15 / 8) 46 2.31 0.00 0.00 chrXptel1M 500045 500088 (499912) (GT)n#Simple_repeat 1 44 (0) c_b338s251i1 14153 chrXptel1M 500045 GTGTGTGTGTGTGTCTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 500088 v (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 44 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 866 33.43 5.67 3.21 chrXptel1M 500089 501039 (498961) C L2#LINE/L2 (155) 2927 1958 m_b338s601i16 14152 chrXptel1M 500089 AGGAT-AGGTTTTAAAGGGCTTTGAACGCCAA-GCAAAGCATTTTATATT 500136 i i- i iv iv i v v v- i i - i ivv C L2#LINE/L2 2927 GGGACCAGATCATGTAGGGCCTTGTAGGCCATTGTAAGG-ACTTTGGCTT 2879 chrXptel1M 500137 TCTTCCTGGAGGTAAGA-GGGAA-CCAAGAGAAAGTATTAAGCAGAGGTG 500184 ivii i-- i - - vvi ii v i -- C L2#LINE/L2 2878 TTACTCTGA--GTGAGATGGGAAGCCATTGGAGGGTTTTGAGCAGAGG-- 2833 chrXptel1M 500185 TGGAGGGTGACGTGATGAGATCTGCATTTTAGCAAAGTCACTTTGGTGTC 500234 -----i i vv ii i i iv iii i ivv C L2#LINE/L2 2832 -----AGTGACATGATCTGACTTACGTTTTAAAAGGATCACTCTGGCTGC 2788 chrXptel1M 500235 TGAATGGAGGACGAATTGGACTAAAGAGAGAC--GTGTGG---CAGGCAG 500279 vi v i ----- i i? i i i -- v --- v C L2#LINE/L2 2787 TGTGTTGAGAA-----TAGACTGNAGGGGGGCAAGGGTGGAAGCAGGGAG 2743 chrXptel1M 500280 ACCCCGCCCCTAGCACGCTATTACCATAGTCTGGACATGAGGCGATGAGG 500329 v- i--- v v i vi i ii i iv ii iv C L2#LINE/L2 2742 ACCA-GT---TAGGAGGCTATTGCAGTAATCCAGGCGAGAGATGATGGTG 2697 chrXptel1M 500330 GGCTGTCCCAGGGTGGGGGCAG-GGTCAGGGGAAGAGGAGGGGATGTATC 500378 vi vv v - -- v iv i v vi v i C L2#LINE/L2 2696 GCTTGGACCAGGGTGGTGGCAGTGG--AGGTGGTGAGAAGTGGTCGGATT 2649 chrXptel1M 500379 CAAGAGATGCTGCAGAGGTGGGACGGACAGGCCTTGGCAACAGCCTGGAT 500428 vi v ii viii i ii v vi vii ii vi C L2#LINE/L2 2648 CTGGATATATTTTGAAGGTAGAGCCGACAGGATTTGCTGATGGATTGGAT 2599 chrXptel1M 500429 CTGGGGGGCGAGAGGTAATGGGAGGA-TCCAGCACAACTTCTAGCTTGTG 500477 v v i -- v i - v v ii i v v v v C L2#LINE/L2 2598 GTGGGGTGTGAGAG--AAAGAGAGGAGTCAAGGATGACTCCAAGGTTTTT 2551 chrXptel1M 500478 AGCCTGAGGGGCAGGA-GAAGGGTGTTGCC-----CTCAGTCATCGGGAA 500521 i vii v - i v v ----- v -- v C L2#LINE/L2 2550 GGCCTGAGCAACTGGAAGGATGGAGTTGCCATTNACTGAG--ATGGGGAA 2503 chrXptel1M 500522 GTTGGTCTGGGGAG---GCTCGAGGGGAAAGAC------TTCCATGCTGG 500562 viv ivv i --- i i i i------ vi vi C L2#LINE/L2 2502 GACTGCGGGAGGAGCAGGTTTGAGGGGGAAGATCAGGAGTTCAGTTTTGG 2453 chrXptel1M 500563 A---GCTCCATTTCCGATGGCTGCCGGCCATCCAGGTGAAGCCGTGGGAA 500609 --- i vvi vv v iiii v i i vi v iiv C L2#LINE/L2 2452 ACATGTTAAGTTTGAGATGCCTATTAGACATCCAAGTGGAGATGTCGAGT 2403 chrXptel1M 500610 AGTCAGTCAGAGCCGAGGGAGTGGAGGTC--GGCAGAG-TTAGGG--GGA 500654 v ii vviiv i vv v -- v - iv -- C L2#LINE/L2 2402 AGGCAGTTGGATATACGAGTCTGGAGTTCAGGGGAGAGGTCCGGGCTGGA 2353 chrXptel1M 500655 GCATGGGTAGGGCTGAGAATCATCAGCATCCAGAGAAGAAGGGAATTTCT 500704 - i-- iivi i i vi viiv vvvi viiv C L2#LINE/L2 2352 G-ATA--TAAATTTGGGAGTCATCAGCATATAGATGGTATTTAAAGCCAT 2306 chrXptel1M 500705 GGGGGTTGATGAGCCCTCCTAGTGAAGGAGTGGAGAGGGAGAAC-GCAGA 500753 i iv v vi v ? v iv v vi v- v C L2#LINE/L2 2305 GAGACTGGATGAGATCACCNAGGGAGTGAGTGTAGATAGAGAAGAGAAGA 2256 chrXptel1M 500754 GAGCCCAGGGCAGAGCCCTGAGGGACACCTACAGTTGGG-----GGAGTG 500798 iv v i v i v v v - ?i ----- i v C L2#LINE/L2 2255 GGTCCAAGGACTGAGCCCTGGGGCACTCCAAC-GTTNAGAGGTCGGGGAG 2207 chrXptel1M 500799 ATCTGGAGGAGGGTCCAGTAAAGGAGACCGAGAAGGAGCAGCCCGAGAGG 500848 --- iv i i i v v C L2#LINE/L2 2206 AT---GAGGAGGAACCAGCAAAGGAGACTGAGAAGGAGCGGCCAGTGAGG 2160 chrXptel1M 500849 GAGGAGCAGACCCAGAGCAG-AAGGC-TCCCAGAAACCTAGAGAGAAGAG 500896 v v i v iiv -iv i- ii i v v ii i C L2#LINE/L2 2159 TAGGAGGAAAACCAGGAGAGTGTGGTGTCCTGGAAGCCAAGTGAAGAAAG 2110 chrXptel1M 500897 GGGATCCAGGAGGAGAGA--GA------GTGTTGGAGGCTGCAGAGGGAT 500938 v vv v i i -- ------ iii v v ?i i C L2#LINE/L2 2109 TGTTTCAAGAAGGAGGGAGTGATCAACTGTGTCAAATGCTGCTGANAGGT 2060 chrXptel1M 500939 CAAGGAGAAGGAGGACGGAGAAAAGGCCCGTGGCTTTGGCCACTAAGAGA 500988 v ii v v vv i vv v i v vvi i C L2#LINE/L2 2059 CAAGTAAGATGAGGACTGAGAATTGACCATTGGATTTAGCAACGTGGAGG 2010 chrXptel1M 500989 TCACTGGTGACTTTGG-GAGGGCACTTTTAGTGGCACGGCGAGGTCAGAG 501037 i i i-i i v ii vii i i v ii i C L2#LINE/L2 2009 TCATTGGTGACCTTGACAAGAGCAGTTTCGGTGGAGTGGTGGGGACGAAA 1960 chrXptel1M 501038 GC 501039 C L2#LINE/L2 1959 GC 1958 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 43.39 CpG sites = 189, Kimura (unadjusted) = 45.65 Transitions / transversions = 1.23 (168/137) Gap_init rate = 0.06 (55 / 950), avg. gap size = 1.51 (83 / 55) 214 34.78 6.96 0.00 chrXptel1M 502498 502612 (497388) L3#LINE/CR1 3967 4089 (10) m_b338s601i17 14154 chrXptel1M 502498 ACTAGAAGCCTTCAAATAGTCGCCAGCAGACTTCTTGTTGGGAACGTGGT 502547 i i iv ii vv ii vv iv ii i i v L3#LINE/CR1 3967 ACTGGAGGTGTTCAAGCAGAGGCTGGATGACCACTTGTCAGGGATGTTGT 4016 chrXptel1M 502548 GGAGGAGATCCATA-GTCCAGTGGGC--CTGAATGAGATGGAC-----GG 502589 i i i i v i-i ivii v--i i iv iv ----- L3#LINE/CR1 4017 AGAAGGGATTCCTGCATTGGATGGGAGGTTGGACTAGATGACCTCTAAGG 4066 chrXptel1M 502590 GCCCTTCCAACTCAGAGATCCTG 502612 v v i L3#LINE/CR1 4067 TCCCTTCCAACTCTGAGATTCTG 4089 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 49.63 CpG sites = 26, Kimura (unadjusted) = 49.63 Transitions / transversions = 1.86 (26/14) Gap_init rate = 0.03 (3 / 114), avg. gap size = 2.67 (8 / 3) 416 21.85 8.03 6.47 chrXptel1M 502741 502877 (497123) C MIRc#SINE/MIR (120) 148 10 m_b338s601i18 14155 chrXptel1M 502741 CTCATTTTACAGATGAGGAAACTGATG--TAGACAGGGTGAAGTGATTCA 502788 i v --i v - v i ii C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGA-GGTTAAGTGACTTG 100 chrXptel1M 502789 GCTGGGGTCACACAGCTGGTGTTTG---GGGCCGGG-TTTGAACTCAGGA 502834 v iii i ivv --- i -i i i -- C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAG-- 52 chrXptel1M 502835 AGATGAGCCTTCCTGACTCCAGGCCTGATACT-----CAATGCACCAC 502877 ------ i i i iii i ----- v C MIRc#SINE/MIR 51 ------GTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 25.90 CpG sites = 21, Kimura (unadjusted) = 27.02 Transitions / transversions = 3.00 (21/7) Gap_init rate = 0.10 (13 / 136), avg. gap size = 1.54 (20 / 13) 372 28.33 2.26 7.09 chrXptel1M 504423 504555 (495445) MIRc#SINE/MIR 3 129 (139) m_b338s601i19 14156 chrXptel1M 504423 AGCTAGTTTGGTAGAGTGGATAGGACACCAGTCCTGAAGTCAGGAGAAGC 504472 vi v iv v ii ii v i i ii v MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chrXptel1M 504473 CGAGTTCAAATCTGATCTCAGACACTTAACGCTTTCTGGCTGTGTGACCC 504522 i i i i iviv v v ------- i i MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTGACCT 95 chrXptel1M 504523 TGGCCAAGTTATTTCA---CTCCAATTGCCTCAGCT 504555 v i i v --- ii -- i MIRc#SINE/MIR 96 TGGGCAAGTCACTTAACCTCTCTGA--GCCTCAGTT 129 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 34.25 CpG sites = 23, Kimura (unadjusted) = 36.91 Transitions / transversions = 1.92 (23/12) Gap_init rate = 0.08 (10 / 132), avg. gap size = 1.20 (12 / 10) 21 4.17 0.00 0.00 chrXptel1M 504558 504582 (495418) (A)n#Simple_repeat 1 25 (0) m_b338s252i2 14157 chrXptel1M 504558 AAAAAAAAAAAAAAAAAAAAAAGAA 504582 i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAA 25 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 210 30.09 4.81 0.93 chrXptel1M 507065 507168 (492832) C MIR#SINE/MIR (63) 199 92 m_b338s601i20 14158 chrXptel1M 507065 GTGTTACACGTGTTTAATCCTCATTTCA---TTAGGATGTAGGAATTAGT 507111 i - vii ivv ---i v v v i v C MIR#SINE/MIR 199 GTATTA-ACTCATTTAATCCTCACAACAACCCTATGAGGTAGGTACTATT 151 chrXptel1M 507112 AGTATTTC-ATTTTCTGCATGAGGAGCCTGAAG-AGACAAAGGTTAAATG 507159 v ii - viiv iv i - v v i i i C MIR#SINE/MIR 150 ATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTA 101 chrXptel1M 507160 GCTTGATCA 507168 i vi C MIR#SINE/MIR 100 ACTTGCCCA 92 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 39.30 CpG sites = 17, Kimura (unadjusted) = 39.30 Transitions / transversions = 1.21 (17/14) Gap_init rate = 0.04 (4 / 103), avg. gap size = 1.50 (6 / 4) 280 31.38 12.41 2.76 chrXptel1M 508168 509029 (490971) L1M2_orf2#LINE/L1 1090 2032 (1259) m_b338s551i5 14159 chrXptel1M 508168 AGTTGGTGCTTGGCAAAAACTCATGAAATTGATAAACCTTCACAAAGCTA 508217 vi v v i ivv ii i i ? i ---- L1M2_orf2#LIN 1090 AGTTGGTTTTTTGAAAAGATAAACAAAATCGACAAACCNTTA----GCTA 1135 chrXptel1M 508218 ATATGAATA-GAAAGAAGAGAGAGAAAA-TCAAATCAAGGGA--TAGATA 508263 ---- v - i i i -i v vii --i v L1M2_orf2#LIN 1136 ----GACTAAGAAAAAAAAGAGAGAAGACCCAAATAAATAAAATCAGAAA 1181 chrXptel1M 508264 TGAGCAAGGTGACATCA-AGCCAATACTTGAAGAAATTAAAAGGTTAATA 508312 iv v i - i ii -iiv vv v v ? L1M2_orf2#LIN 1182 TGAAAAAGGAGACATTACAACTGATAC-CACAGAAATACAAAGGATCATN 1230 chrXptel1M 508313 GGACAC-ATTATGTACAGCTACATACTGA-------GAATAC--AAAAGA 508352 i v - v i i ii ii ------- v -- i L1M2_orf2#LIN 1231 AGAGACTATTATGAACAACTATACGCCAACAAATTGGAAAACCTAGAAGA 1280 chrXptel1M 508353 AATAGAAGAATACCTTCCAAAATATAA---AACAAGATT--ATCAGAAGA 508397 i vi v vvvv v i --- v -- i -- ? L1M2_orf2#LIN 1281 AATGGATAAATTCCTGGACACATACAACCTACCAAGATTGAACC--ANGA 1328 chrXptel1M 508398 TGAGATA-AAGATTTTAAT--ACC--TAACCTCAGAAAAGAAAACAGACC 508442 v i - i ii v i-- -- --v v v i viii i L1M2_orf2#LIN 1329 AGAAATAGAAAACCTGAACAGACCAATAAC--GAGTAACGAGATTGAATC 1376 chrXptel1M 508443 TAGCATTAAGGGAACTACCAAAGGAAAAAATTCCTAGGCCTGAAGGATC- 508491 - i v iiiiv v ?vii i vi vi i ? v v i- L1M2_orf2#LIN 1377 -AGTAATAAAAAGTCTCCCANCAAAGAAAAGCCCAGGACCNGATGGCTTC 1425 chrXptel1M 508492 ----CTGTATTCTATCAGAC-TTTAAAGAACAGTTAGAACTCA-TGTTCA 508535 ---- v i i - v ii iv iv - v v L1M2_orf2#LIN 1426 ACTGCTGAATTCTACCAAACATTTAAAGAAGAACTAATACCAATTCTTCT 1475 chrXptel1M 508536 CAAATTATCCTCAAAAGTTGAGAAAAAAAGCA-CCTACCAAACTCCTTTT 508584 i i iv i ii ii ii v -? v v i L1M2_orf2#LIN 1476 CAAACTATTCCAAAAAATTGAAGAGGAGGGAATNCTTCCAAACTCATTCT 1525 chrXptel1M 508585 ATGGAGAGAAAGTATTATCCT----------TTGGCCAGGAAATTTAAAA 508624 i- - vv i i ----------iii v i i ---i v L1M2_orf2#LIN 1526 AC-GAG-GCCAGCATTACCCTGATACCAAAACCAGACAAGGA---CACAA 1570 chrXptel1M 508625 CACAGAAAGGAAATTGTAAGCCAATATAATTAATAA--ATTG-TCTCAAA 508671 v i i i ii i vvi i i -- v - viv L1M2_orf2#LIN 1571 CAAAAAAAGAAAACTACAGGCCAATATCCCTGATGAACATAGATGCAAAA 1620 chrXptel1M 508672 CTTTTCAACAAAATCTCATTGTAATAGAGTATAGTGATTTATCTAAGAGA 508721 v ii vii vii- iv i vi iiiiivi iv i L1M2_orf2#LIN 1621 ATCCTCAACAAAATACTAGCA-AACCGAATTCAACAGCACATTAAAAAGA 1669 chrXptel1M 508722 TCATCCAATATGACCAGATAAAATATA----AGAGAGGTATGAGAATGGT 508767 ? ? vi i ii iii v ---- i v i -- i L1M2_orf2#LIN 1670 TNATNCACCATGATCAAGTGGGATTTATCCCAGGGATGCA--AGGATGGT 1717 chrXptel1M 508768 T---------TGAATCAAGGAA----ATA-ATTAAATAATTAG--TACAG 508801 ---------ii vi ---- - i v v vi -- iv L1M2_orf2#LIN 1718 TCAACATACGCAAATCAATAAACGTGATACATCACATCAACAGAATGAAG 1767 chrXptel1M 508802 TGTAAAAATCACATGGTTATCTCAA-AGATG-AAAAAAAAC--TTCACAA 508847 vii i i i i - - i i -- v i L1M2_orf2#LIN 1768 GACAAAAACCATATGATCATCTCAATAGATGCAGAAAAAGCATTTGATAA 1817 chrXptel1M 508848 AATATAAATTACGTTTATATTAAAAAAATCCTCA--AAAGTAG------- 508888 vi vv v v i i-- v ii -- v ------- L1M2_orf2#LIN 1818 AATTCAACATCCCTTCATG--ATAAAAACTCTCAACAAATTAGGTATAGA 1865 chrXptel1M 508889 AGGGACTT--TTTAA------AAATATCATA----ACAAGCACTTTTCTA 508926 i v --i i ------ vii ---- i v vivv L1M2_orf2#LIN 1866 AGGAACGTACCTCAACACAATAAAGGCCATATATGACAAACCCACAGCTA 1915 chrXptel1M 508927 AAACCAAAAAGAATT-----ATGTT-----CTTTTCTAATATAAGA-CTG 508965 v i v vv v----- v ----- i i-- v - L1M2_orf2#LIN 1916 ACATCATACTGAATGGGGAAAAGTTGAAAGCCTTTCC--TCTAAGANCTG 1963 chrXptel1M 508966 AAGCAAGA-----ATGCCCACTTCTCCCACTAGTCATCAATATAGTTCTG 509010 i i ----- iiv vv vv i v L1M2_orf2#LIN 1964 GAACAAGACAAGGATGCCCACTTTCACCACTTCTATTCAACATAGTACTG 2013 chrXptel1M 509011 CAAATGCTAGCAACAGCAA 509029 v i v v v L1M2_orf2#LIN 2014 GAAGTCCTAGCCAGAGCAA 2032 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 42.02 CpG sites = 155, Kimura (unadjusted) = 42.70 Transitions / transversions = 1.44 (155/108) Gap_init rate = 0.07 (62 / 861), avg. gap size = 2.15 (133 / 62) 269 25.14 12.69 2.03 chrXptel1M 509118 509251 (490749) C MIRc#SINE/MIR (120) 148 1 m_b338s601i21 14160 chrXptel1M 509118 CTCATTTT-CACATGAGGAA-CTGAGGT----AAAGTGTTATAATA--TT 509159 i - v - i---- i - - i i-- C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAG-GTTA-AGTGACTT 101 chrXptel1M 509160 -----AGGTCACA--ACTAGTAAGAGTCCAATGCCAGATCT-GAAGTCAG 509201 ----- --i v v vi - i iv - vi C MIRc#SINE/MIR 100 GCCCAAGGTCACACAGCTAGTAAGTGGCAGA-GCCGGGACTCGAACCCAG 52 chrXptel1M 509202 GTCTTCCTGATTCAAGATCTGGAACTCTACCGATTGTGCCAT-CTAGCTC 509250 i v ii ii vi vi v i ii i- iv C MIRc#SINE/MIR 51 GTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTGCCTC 2 chrXptel1M 509251 G 509251 C MIRc#SINE/MIR 1 G 1 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 30.65 CpG sites = 22, Kimura (unadjusted) = 31.82 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.08 (11 / 133), avg. gap size = 1.82 (20 / 11) 746 28.52 4.78 5.22 chrXptel1M 509295 509775 (490225) L1MC4a_3end#LINE/L1 154 632 (1997) m_b338s551i7 14161 chrXptel1M 509295 ATTAGAGAATTGCACCTTAAAACAACAATGAGATACCCATATCACACCTA 509344 v v vv v v - v v L1MC4a_3end#L 154 ATAAGAGAAATGCAAATTAAAACTACACTGAGATACC-ATTTCTCACCTA 202 chrXptel1M 509345 TT-GATTTAGCTAATATGACAGAAAAGGAAAA---TGATAAAA------A 509384 i- ---------- i i vvv --- i v ------i L1MC4a_3end#L 203 TCAGATT----------GGCAAAAATTCAAAAGTTTGACAACACACTCTG 242 chrXptel1M 509385 TGGAAGGGGATGTGGGAAAACTGGGGCACTGATACATTGTTGGTGGAGTT 509434 v iv i v i v vi v v i iiv L1MC4a_3end#L 243 TTGGCGAGGCTGTGGGGAAACAGGCACTCTCATACATTGCTGGTGGGAAT 292 chrXptel1M 509435 GTGAACTGACCCAACCCTTCTGGAGAGCAATTTGGAACTATACTCA-AAA 509483 ii ? iiv ? i v v v - v - L1MC4a_3end#L 293 GCAAANTGGTACAACCCTTNTGGAGGGGAATTTGGCAATAT-CTAACAAA 341 chrXptel1M 509484 GTTATCAAACTGTGCA--TACCCTTTGACCCAGCAGTGTTGCTACTGGGC 509531 ii - --- i -- i viii v i v L1MC4a_3end#L 342 ACTA-CA---TATGCATTTACCCTTTGACCCAGCAATCCCACTTCTAGGA 387 chrXptel1M 509532 TTATATCCCAAAG--AGATCATAAAGAAG-GGAAAGGGACCTGTATGTGC 509578 v v i ii -- v i viv v v -iv iv? --i ii L1MC4a_3end#L 388 ATTTACCCTGAAGATACACCTCCAACATGTACAAAATNAC--ATATGCAC 435 chrXptel1M 509579 ACGGATGTTTGTGGCAGCCCTTTTTGTAGTGGCCAGAAACTGG----AAC 509624 v v i ii v vi v i v v i v i ---- L1MC4a_3end#L 436 AAGGTTATTCATTGCAGCATTGTTTGTAATTGCAAAATATTGGAAACAAC 485 chrXptel1M 509625 CTGAGTGGATGCCCATCAGGTGGAGAATGGCTGAATAAATTGTGGTATAT 509674 i ---- ??ivv ? i i i i L1MC4a_3end#L 486 CTAA----ATGCCCATNNATAGGAGANTGGTTGAATAAACTATGGTACAT 531 chrXptel1M 509675 GAATATTATGGAATATTATTGTTCTGTAGGAAATGACCAACAGGATGATT 509724 vv i iv i i vvvv ii - -- vv v i L1MC4a_3end#L 532 CCACACAATGGAGTACTATGCAGCTGTAAAAAA-GA--ATGAGGAAGATC 578 chrXptel1M 509725 TC-AGAAA--GGCCTGGAGAGACTTACACGAACCGATGCTGAGTGAAACG 509771 - vi -- iiv v i v v vviiv i i vi L1MC4a_3end#L 579 TCTATGAACTGATATGGAGTGATTTCCAGGATATATTGTTAAGTGAAAAA 628 chrXptel1M 509772 AGCA 509775 L1MC4a_3end#L 629 AGCA 632 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 36.88 CpG sites = 64, Kimura (unadjusted) = 36.88 Transitions / transversions = 0.97 (64/66) Gap_init rate = 0.07 (35 / 480), avg. gap size = 1.37 (48 / 35) 1205 24.54 4.01 4.01 chrXptel1M 509295 509693 (490307) L1ME4c_3end#LINE/L1 157 555 (275) m_b338s551i6 14161 chrXptel1M 509295 ATTAGAGAATTGCACCTTAAAACAACAATGAGATACCCATATCACACCTA 509344 i i v vv i - v i i L1ME4c_3end#L 157 ATCAAAGAAATGCAAATTAAAGCAACAATGAGATACC-ATTTTACGCCTA 205 chrXptel1M 509345 TTGATTTAGCTAATATGACAGAAAAGGAAAATGATAA----AAATG--GA 509388 i v v v v---v --- v ----v -- i L1ME4c_3end#L 206 TTAAATTAGCAAAAATT---TAAAA---AATTGATAATACCCAATGCTGG 249 chrXptel1M 509389 AGGGGATGTGGGAAAACTGGGGCACTGATACATTGTTGGTGGAGTTGTGA 509438 v i ? i vi vi ? v i vi? i L1ME4c_3end#L 250 CGAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAA 299 chrXptel1M 509439 ACTGACCCAACCCTTCTGGAGAGCAATTTGGAACTATAC---TCAAAAGT 509485 i iiv i i v -- --- i i L1ME4c_3end#L 300 ATTGGTACAACCCTTTTGGAAAGCAATTTGGCA--ATACGTATCAAGAGC 347 chrXptel1M 509486 TATCAAACTGTGCATACCCTTTGACCCAGCAGTGTTGCTACTGGGCTTAT 509535 i v v v i i viii v vv v L1ME4c_3end#L 348 CATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTT 397 chrXptel1M 509536 ATCCCAAAGAGATCAT---AAAGAAGGGAAAGGGACCTGTATGTGCACGG 509582 i i i v --- i i --- i ii ivi L1ME4c_3end#L 398 ATCCTAAGGAAATAATTCAAAAGAAGGAAAAAG---CTATATGCACGAAG 444 chrXptel1M 509583 ATGTTTGTGGCAGCCCTTTTTGTAGTGGCCAGAAACTGG----AACCTGA 509628 ii v vi v i i i v i i ---- i L1ME4c_3end#L 445 ATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAA 494 chrXptel1M 509629 GTGGATGCCCATCAGGTGGAGAATGGCTGAATAAATTGTGGTATATGAAT 509678 ---- i v ivv i i i i i i v? i L1ME4c_3end#L 495 ----ATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNAC 540 chrXptel1M 509679 ATTATGGAATATTAT 509693 viv L1ME4c_3end#L 541 TCGATGGAATATTAT 555 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 29.24 CpG sites = 56, Kimura (unadjusted) = 30.79 Transitions / transversions = 1.47 (56/38) Gap_init rate = 0.05 (21 / 398), avg. gap size = 1.52 (32 / 21) 207 33.58 6.57 0.00 chrXptel1M 511538 511674 (488326) L2a_3end#LINE/L2 52 197 (320) m_b338s601i22 14162 chrXptel1M 511538 CCCCTCCACACACTAGGATCCAGCCACAATGGCAGACTTGTTGTTCCTT- 511586 ii i v vv v v vvv i i- L2a_3end#LINE 52 CCCCCTCGCTCACTCCGCTCCAGCCACACTGGCCTCCTTGCTGTTCCTCG 101 chrXptel1M 511587 -ACATGCT--GCA-GCTCCTGAAGCCGTGCACTTGCGCTGGGCGACCTAC 511632 - i i-- - i vvv v v vi i v vi vi ivi L2a_3end#LINE 102 AACACGCCAGGCACGCTCCCGCCTCAGGGCCTTTGCACTTGCTGTTCCCT 151 chrXptel1M 511633 ATGCTCAAAGCACT-TTCCCT---ATCTCCACATGGCCAGTTTCCT 511674 v iiii i i - i--- v i iv i i L2a_3end#LINE 152 CTGCCTGGAACGCTCTTCCCCCAGATATCCGCATGGCTCGCTCCCT 197 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 38.09 CpG sites = 25, Kimura (unadjusted) = 45.67 Transitions / transversions = 1.19 (25/21) Gap_init rate = 0.04 (6 / 136), avg. gap size = 1.50 (9 / 6) 207 26.58 1.52 3.08 chrXptel1M 512435 512500 (487500) C L2a_3end#LINE/L2 (21) 496 432 m_b338s601i23 14163 chrXptel1M 512435 TTATTAAGTACCTACCACGTGCCAGGTACTA-TAGAGGCAGCTAGGGGAC 512483 i ii i i i i- vv - - i C L2a_3end#LINE 496 TTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGC-GCT-GGGGAT 449 chrXptel1M 512484 ACCACAACGGACAGAGC 512500 vi ii i i i C L2a_3end#LINE 448 ACAGCAGTGAACAAAAC 432 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 32.64 CpG sites = 14, Kimura (unadjusted) = 35.58 Transitions / transversions = 4.67 (14/3) Gap_init rate = 0.05 (3 / 65), avg. gap size = 1.00 (3 / 3) 560 25.44 12.43 0.00 chrXptel1M 512488 512656 (487344) MIRc#SINE/MIR 16 205 (63) m_b338s601i24 14164 chrXptel1M 512488 CAACGGACAGAGCTCCAGTCCGAGAGTCAGGAAGATCTGAATTCAAGTCT 512537 ii v v ii v ivi i ii i i MIRc#SINE/MIR 16 CAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCC 65 chrXptel1M 512538 AGCCTCAGCCCCTT--------TGTG-------GCAAGTCACTCCATCTC 512572 v v v v -------- ------- iv i MIRc#SINE/MIR 66 CGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 chrXptel1M 512573 CTTTTACCTCAGTTTCCCCACTTGTAAAATGGGAATAATAGTA---GC-- 512617 ii vvi i ii i i --- -- MIRc#SINE/MIR 116 TCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCC 165 chrXptel1M 512618 -ATCTATGTCAAGAGCTTGTTAGGAGGATTAAATGAGATA 512656 -ii iv vii v iv i MIRc#SINE/MIR 166 TGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATA 205 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 31.22 CpG sites = 28, Kimura (unadjusted) = 32.13 Transitions / transversions = 1.87 (28/15) Gap_init rate = 0.03 (5 / 168), avg. gap size = 4.20 (21 / 5) 426 24.32 0.00 8.62 chrXptel1M 512666 512791 (487209) MIRb#SINE/MIR 3 118 (150) m_b338s601i25 14165 chrXptel1M 512666 GGGGGGCAGCTCGGTGGTACAGTAGATAGAGCATCAGCCCTGAAGTCTGA 512715 i --- i i v ivi ii i v MIRb#SINE/MIR 3 GAGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGA 49 chrXptel1M 512716 AGGACCCGAGTTCAAATCTGACCTCAGACACTTAACATTTCCTAGCTGAG 512765 vi i i i iviv v v ------- v MIRb#SINE/MIR 50 CAGACCTGGGTTCGAATCCCGGCTCTGCCACTTA-------CTAGCTGTG 92 chrXptel1M 512766 TGACCCTGGGCAGATCACTTAACCCC 512791 i ii i i MIRb#SINE/MIR 93 TGACCTTGGGCAAGTTACTTAACCTC 118 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 26.42 CpG sites = 19, Kimura (unadjusted) = 30.19 Transitions / transversions = 2.11 (19/9) Gap_init rate = 0.08 (10 / 125), avg. gap size = 1.00 (10 / 10) 302 21.67 0.00 0.00 chrXptel1M 512838 512897 (487103) MIR#SINE/MIR 203 262 (0) m_b338s601i26 14165 chrXptel1M 512838 TAAAGCACTTAACCTAGTACCTGGCATATAGTAGGTGCCATACAAATGTT 512887 i ivvi i i i i ivv i MIR#SINE/MIR 203 TAAAGCGCTTAGAACAGTGCCTGGCACATAGTAAGCGCTCAATAAATGTT 252 chrXptel1M 512888 AGCTATTATT 512897 MIR#SINE/MIR 253 AGCTATTATT 262 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 21.89 CpG sites = 9, Kimura (unadjusted) = 26.42 Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0) 269 16.56 1.38 3.52 chrXptel1M 513577 514156 (485844) (AAGG)n#Simple_repeat 1 568 (0) m_b338s252i3 14166 chrXptel1M 513577 AAAGAAGAAAGGAAGGGAAGCAGGAAAGAA-GAAAAAAGAAAGGAGAGAA 513625 i i i i v i - ii i ii (AAGG)n#Simpl 1 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 50 chrXptel1M 513626 GG-AGGAAGGGATGAAAGGGAAGGAGGAAAGGAAGGAAGGAAGAAAGGAA 513674 - - v i - i i i (AAGG)n#Simpl 51 GGAAGGAA-GGAAGGAA-GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 98 chrXptel1M 513675 GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG 513724 (AAGG)n#Simpl 99 GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG 148 chrXptel1M 513725 AAGGAAAGGAAGAAAGAAAGG-AGGGAGAAAGG-GGGAAAGGAGGGAGGA 513772 - i i - i i -i i i i (AAGG)n#Simpl 149 AAGG-AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 197 chrXptel1M 513773 AGGAGGGAAGGAAAGAAGGAGGGAAGGGAAGAAAGAAGGAGGGAAGGAGA 513822 i i i i i i i - (AAGG)n#Simpl 198 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA-A 246 chrXptel1M 513823 GTGAAAGTGTGAGGAAAAGAAGGAAGGAGAGAGAGGCAGGAAAGGAGGGA 513872 - i viv i i i - ii v - i (AAGG)n#Simpl 247 G-GAAGGAAGGAAGGAAGGAAGGAAGGA-AGGAAGGAAGG-AAGGAAGGA 293 chrXptel1M 513873 AAGAAGGAAGAAAGGAA--AAGAGAA-AAAGGACAGAGGGAAGGAGTAGG 513919 i i -- - -i vi i -- (AAGG)n#Simpl 294 AGGAAGGAAGGAAGGAAGGAAG-GAAGGAAGGAAGGAAGGAAGGA--AGG 340 chrXptel1M 513920 AAGGGAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGGAAGAAAGAT 513969 i i i i v (AAGG)n#Simpl 341 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 390 chrXptel1M 513970 GGAGGGAGGGAGAGAGAAAGTGTGAGGGAAAGAAGGAAGGAGAGAGAGGC 514019 i i - - i viv i i - ii v (AAGG)n#Simpl 391 GGAAGGAAGGA-AG-GAAGGAAGGAAGGAAGGAAGGAAGGA-AGGAAGGA 437 chrXptel1M 514020 AGGAAAGGAGGGAAAGAAGGAAGAAAGGAAAAGAGAGAAAAGGACAGAGG 514069 - i i i - i - -i vi i (AAGG)n#Simpl 438 AGG-AAGGAAGGAAGGAAGGAAGGAAGG-AAGGA-AG-GAAGGAAGGAAG 483 chrXptel1M 514070 GAAGGAGTAGGAAGGGAGGAAGGAAGGAAGGAAGGAAAGAAGGAAGAGAA 514119 -- i i - (AAGG)n#Simpl 484 GAAGGA--AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG-GAA 530 chrXptel1M 514120 GG-AGGAAGGAAGGAAGGGAGGGAGGGAGGGAGGAAGG 514156 - i i i i (AAGG)n#Simpl 531 GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG 568 Matrix = Unknown Transitions / transversions = 6.09 (67/11) Gap_init rate = 0.05 (27 / 579), avg. gap size = 1.04 (28 / 27) 250 25.64 13.51 1.61 chrXptel1M 514593 514703 (485297) MIRc#SINE/MIR 75 198 (70) m_b338s601i27 14167 chrXptel1M 514593 CATTTTCTAATTGTGTGATGCCGAGGAAGTCAC---AGCACT-----CAT 514634 i v ii ivii i v --- v v ----- v MIRc#SINE/MIR 75 CACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCT 124 chrXptel1M 514635 CAGTTCCTTCCCACCTATAAAA-GGGGATAACAATG---GCCCCGC---C 514677 -- i i i i - i i--- i --- MIRc#SINE/MIR 125 CAGTT--TCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTAC 172 chrXptel1M 514678 CTGAAAAGTTTGCGGTAAGAATCAAA 514703 v v i v iv i i MIRc#SINE/MIR 173 CTCACAGGGTTGTTGTGAGGATCAAA 198 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 32.48 CpG sites = 18, Kimura (unadjusted) = 32.48 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.06 (7 / 110), avg. gap size = 2.43 (17 / 7) 186 19.20 2.00 6.25 chrXptel1M 515793 515842 (484158) C L2d2_3end#LINE/L2 (90) 465 418 m_b338s601i28 14168 chrXptel1M 515793 TGGTCC-TGCCCTCAAGGAGCATGCAATTGAATGGGGAAAAGAACAAAAC 515841 - v i iv i v i ---i i C L2d2_3end#LIN 465 TGGTCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGGA---GACAAGAC 419 chrXptel1M 515842 A 515842 C L2d2_3end#LIN 418 A 418 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 22.63 CpG sites = 6, Kimura (unadjusted) = 22.63 Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.08 (4 / 49), avg. gap size = 1.00 (4 / 4) 216 30.32 7.42 3.38 chrXptel1M 516354 516609 (483391) C L2#LINE/L2 (2562) 520 255 m_b338s601i29 14169 chrXptel1M 516354 CAGCCAGGACTGGAAAGAGTGGCGGGAGAAGCTGCGCCATCAGGGGAGAG 516403 vv v i i iv i i v i i v C L2#LINE/L2 520 CAGCCACCACTTGAGAGGGCTGCAGGGGAAGCAGTGTCCTCAGGGGAGAG 471 chrXptel1M 516404 GCAGGTTTCAGTGATTGCTAGAAGGT---GGGAAGGTGGAGAGAGGAAAA 516450 v ? v vv v --- v vv --- i C L2#LINE/L2 470 CCAGGTTTCNGTTAGAGCAAGAAGGTGAAGGGAACGTTCAGA---GAAGA 424 chrXptel1M 516451 GATTCAGGATGAAGGCAAGTTCATT-ATCTCAGGAAAAGGCTTTCCATAA 516499 i v ivi vi v iii - vv - vviv vv v i C L2#LINE/L2 423 GGTTGAGGATACGGGGGATTTTGCTGATGAC-GGACCGTGAGTTCCAGAG 375 chrXptel1M 516500 GGCCCAGGAGAAGCAGAGGTT---AGAATTTGATTGGGATTGG-GATGAG 516545 v vi ---- ---i i v ivv i v - i C L2#LINE/L2 374 GGCACAGTGGAAG----GGTTTCAGGAGTTGGGGAGGGGTGGGAGATGGG 329 chrXptel1M 516546 ATAACAAGAGGGAGGAGTGAGGAAC----TGGAAGTGAGGGT--GGGAAA 516589 i v v ? - iv ivi i ---- iii ? i -- ii C L2#LINE/L2 328 GTCAGAANA-GGAGATGTACAGAGCCGTATGGGGATNAGAGTCCGGGGGA 280 chrXptel1M 516590 T-AG----GATTTGGAGGCCTTGGG 516609 - ---- ii ii i C L2#LINE/L2 279 TGAGGGATGACCTGGGAGTCTTGGG 255 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 38.86 CpG sites = 39, Kimura (unadjusted) = 40.22 Transitions / transversions = 1.08 (39/36) Gap_init rate = 0.07 (17 / 255), avg. gap size = 1.65 (28 / 17) 12 34.03 0.00 1.85 chrXptel1M 517326 517380 (482620) (TATTG)n#Simple_repeat 1 54 (0) m_b338s252i4 14170 chrXptel1M 517326 TATGTGTATTGTTTTGAGTTGTGTGGTGCTGCATTACTCTGTATTGTACT 517375 - v vi i v ii i iivi i (TATTG)n#Simp 1 TAT-TGTATTGTATTGTATTGTATTGTATTGTATTGTATTGTATTGTATT 49 chrXptel1M 517376 ATATT 517380 i (TATTG)n#Simp 50 GTATT 54 Matrix = Unknown Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1) 20 22.23 0.00 0.00 chrXptel1M 517937 517975 (482025) (A)n#Simple_repeat 1 39 (0) m_b338s252i5 14171 chrXptel1M 517937 AAAAAAAAAAAGAAAAGGAAAGGAAAAAAAAAGAAAGAA 517975 i ii ii i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 39 Matrix = Unknown Transitions / transversions = 1.00 (7/0) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 331 21.73 9.77 6.57 chrXptel1M 518097 518229 (481771) C MIRc#SINE/MIR (122) 146 10 m_b338s601i30 14172 chrXptel1M 518097 CATTTTACAAATGAGGGAAACTGAGG-TAAAAAGGGTTAAGTGACCTACC 518145 i - - v i ii i i C MIRc#SINE/MIR 146 CATTTTACAGATGAGG-AAACTGAGGCTCAGAGAGGTTAAGTGACTTGCC 98 chrXptel1M 518146 TGCTCGTGTCACACTGCTAGCATCTGAAGGCAGA-TTGGAACTCGA---- 518190 ii---iv v i vv --- -ii i ---- C MIRc#SINE/MIR 97 CA---AGGTCACACAGCTAGTAAGTG---GCAGAGCCGGGACTCGAACCC 54 chrXptel1M 518191 -GAT------GAGTCTGCGTCCAGCACTCTAGATGCACTGCACCAC 518229 - i ------ v iiv ii v-- v C MIRc#SINE/MIR 53 AGGTCTTCCTGACTCCAAGTCCAGTGCTCTT--TCCACTGCACCAC 10 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 25.34 CpG sites = 18, Kimura (unadjusted) = 26.46 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.11 (14 / 132), avg. gap size = 1.57 (22 / 14) 193 23.33 6.67 0.00 chrXptel1M 518339 518398 (481602) MIRc#SINE/MIR 6 69 (199) m_b338s601i31 14173 chrXptel1M 518339 CAGTCTGATCC---GGGAAGAGCACTGGCCTGGGAGTCA-GAAGACCGAG 518384 v i v --- i v v - vi MIRc#SINE/MIR 6 CAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGG 55 chrXptel1M 518385 ATTCAGGGCTTGGC 518398 i ii v ii MIRc#SINE/MIR 56 GTTCGAGTCCCGGC 69 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 23.89 CpG sites = 8, Kimura (unadjusted) = 28.42 Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.03 (2 / 59), avg. gap size = 2.00 (4 / 2) 260 26.06 19.85 1.24 chrXptel1M 518343 518478 (481522) MIR3#SINE/MIR 13 173 (35) m_b339s601i1 14173 chrXptel1M 518343 CTGATCCGGGAAGAGCACTGGCCTGGGAGTCAGAAGACCGAGATTC-AG- 518390 v v i - - v i vi i - - MIR3#SINE/MIR 13 CTGAGCAGAGA-GAGCAC-GGACTGGGAGTCAGGAGACCTGGGTTCTAGT 60 chrXptel1M 518391 ---GGCT-TGGCACCGA-------TGTGGCCCTG--------ACATTAAC 518421 --- - v ii ------- i i -------- v i v MIR3#SINE/MIR 61 CCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACC 110 chrXptel1M 518422 TCTCTGGGGCT--GTTTTC----CTATGGAACCAAGGAACTAGATGAGAT 518465 v -- i ---- i ii iv i iii i iv MIR3#SINE/MIR 111 TCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGAT 160 chrXptel1M 518466 GATGTTCAAAATC 518478 v ii ii MIR3#SINE/MIR 161 GATCTCTAAGGTC 173 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.50 CpG sites = 24, Kimura (unadjusted) = 33.50 Transitions / transversions = 2.18 (24/11) Gap_init rate = 0.07 (10 / 135), avg. gap size = 2.90 (29 / 10) 19 20.42 6.45 0.00 chrXptel1M 525184 525245 (474755) (TGTTATG)n#Simple_repeat 1 66 (0) m_b339s252i1 14174 chrXptel1M 525184 TGGTATGTGTTATATGTT-TGT-TTA-ATGTTGTG-ACTGTGTGTTCTGT 525229 v i - - -i i -ii i v (TGTTATG)n#Si 1 TGTTATGTGTTATGTGTTATGTGTTATGTGTTATGTGTTATGTGTTATGT 50 chrXptel1M 525230 GTTCTGTGTGATTTGT 525245 v v v (TGTTATG)n#Si 51 GTTATGTGTTATGTGT 66 Matrix = Unknown Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.07 (4 / 61), avg. gap size = 1.00 (4 / 4) 22 0.00 0.00 0.00 chrXptel1M 533587 533610 (466390) (A)n#Simple_repeat 1 24 (0) m_b339s252i2 14175 chrXptel1M 533587 AAAAAAAAAAAAAAAAAAAAAAAA 533610 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAA 24 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 385 33.38 6.15 3.39 chrXptel1M 538805 539666 (460334) L1P1_orf2#LINE/L1 1674 2558 (736) m_b339s551i0 14176 chrXptel1M 538805 TATACATTATGACTAAGCAGGATTTGTACCAGGAATGAAGGGATGATTTA 538854 v ii ii ii v ii v v i v i v i i L1P1_orf2#LIN 1674 TATCCACCATGATCAAGTGGGCTTCATCCCTGGGATGCAAGGCTGGTTCA 1723 chrXptel1M 538855 ACATAAAGAAAATTATTAACATAATTGATCATATAAATA--ATAAAAGTA 538902 viv viv v i iv v i -- iv -- L1P1_orf2#LIN 1724 ACATACGCAAATCAATAAACGTAATCCAGCATATAAACAGAACCAAAG-- 1771 chrXptel1M 538903 ACAAAA-TCAC-TGATAATGTAAATAGATGCAGAATAAGCTTTTAATAAA 538950 -i - v v v v i i i i L1P1_orf2#LIN 1772 ACAAAAACCACATGATTATCTCAATAGATGCAGAAAAGGCCTTTGACAAA 1821 chrXptel1M 538951 GTACAATATTCGTTTCTATTAAAAAC----AATGAA---AGTATATGTAG 538993 i v i vi v iv ii ---- i ---i - vv L1P1_orf2#LIN 1822 ATTCAACAACCCTTCATGCTAAAAACTCTCAATAAATTAGGTAT-TGATG 1870 chrXptel1M 538994 AAATGAATTTTTCCTTAAATAAATAAAAGGTGTTTATCTAAAACCATTAG 539043 ii i v ----- i vv i v i i vvv vvi L1P1_orf2#LIN 1871 GGACGTAT-----CTCAAAATAATAAGAGCTATCTATGACAAACCCACAG 1915 chrXptel1M 539044 CAAGCATTATTTCTAATATG---AATC----AGCTTTACCAGT-AAATCA 539085 v ii i viiv iv --- v ---- v v vv - v v L1P1_orf2#LIN 1916 CCAATATCATACTGAATGGGCAAAAACTGGAAGCATTCCCTTTGAAAACT 1965 chrXptel1M 539086 GGTGTGAAACAGAAATGCACATCATCACAAATATTATTCAATATTACATT 539135 iiii i ii v viiv v v vi i viii L1P1_orf2#LIN 1966 GGCACAAGACAGGGATGCCCTCTCTCACCACTCCTATTCAACATAGTGTT 2015 chrXptel1M 539136 GGAAATCCTAGCAATAGCAAAAAGAGATGAAAAAGAAATAGAAGGAATCA 539185 i i i v vi vv iv v i i i i v iv L1P1_orf2#LIN 2016 GGAAGTTCTGGCCAGGGCAATCAGGCAGGAGAAGGAAATAAAGGGTATTC 2065 chrXptel1M 539186 GAATAAGAAAAGAGGTAATAAAATTATCTCTTTTTGCAA--GATATGGTG 539233 i v i v i v i i v i-- i i v L1P1_orf2#LIN 2066 AATTAGGAAAAGAGGAAGTCAAATTGTCCCTGTTTGCAGACGACATGATT 2115 chrXptel1M 539234 ATATAATCAAAAAATCCTAAAAACTCAA-CTAAAATGTTATTTGAAAC-A 539281 i vii i i i vviv i- i v iv -- i -i L1P1_orf2#LIN 2116 GTATATCTAGAAAACCCCATCGTCTCAGCCCAAAATCTCCTT--AAGCTG 2163 chrXptel1M 539282 ATTAGTAATTTTAGCAAAATAGGCAGACATAATGTAAATCTACCTAATTC 539331 v i i i i vvvvi i i vi v v i vv v L1P1_orf2#LIN 2164 ATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTGCAAAAATC 2213 chrXptel1M 539332 ATCAGCATTCCTATATATCACAAATAAAAGCCTAAAAGA-----AGATAG 539376 iv i --- v v v v v ----- i vi L1P1_orf2#LIN 2214 ACAAGCATTCTTATA---CACCAATAACAGACAAACAGAGAGCCAAATCA 2260 chrXptel1M 539377 TAAGAGAAACCCCACTTAAAAATAATTCTAGACAGTCTAAAATAACTGGG 539426 i v vi i i v v iv - i v vv v i L1P1_orf2#LIN 2261 TGAGTGAACTCCCATTCACAATTGCTTC-AAAGAGAATAAAATACCTAGG 2309 chrXptel1M 539427 GCTATACCTGCCAAAAAACACATAAAGTATGTGAACAAAATTATTAAAGA 539476 iv --- -------- vi i i v vi vv iv i i L1P1_orf2#LIN 2310 AAT---CC--------AACTTACAAGGGATGTGAAGGACCTCTTCAAGGA 2348 chrXptel1M 539477 AA-----AAAT--CTTCTTATACAAATAAAATCAAATTTAATTAATTGGG 539519 i ----- i-- v i v?v vvii vi vi v i L1P1_orf2#LIN 2349 GAACTACAAACCACTGCTCAANGAAATAAAAGAGGATACAAACAAATGGA 2398 chrXptel1M 539520 A------------TTCATGAGTATGCAGGGCCAATATAAT-ACAATGG-- 539554 ------------i i v v iii vi - v -- L1P1_orf2#LIN 2399 AGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAATGGCC 2448 chrXptel1M 539555 GGACTTTCCA---TAAACTATACATTCAATGCCCTTCCAATTAAATCACC 539601 iv vi --- vi v v i v i iii L1P1_orf2#LIN 2449 ATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGCTACC 2498 chrXptel1M 539602 AAAAATACATATTTTTTACTGAGTTTGAAAAAAATAATAAAAAATTCCAT 539651 --- i- iv i i v i v v v vv i - L1P1_orf2#LIN 2499 ---AATG-ACTTTCTTCACAGAATTGGAAAAAACTACTTTAAAGTT-CAT 2543 chrXptel1M 539652 TTGGAATAACAAAAG 539666 v iv v L1P1_orf2#LIN 2544 ATGGAACCAAAAAAG 2558 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 44.15 CpG sites = 146, Kimura (unadjusted) = 45.25 Transitions / transversions = 1.11 (146/132) Gap_init rate = 0.06 (48 / 861), avg. gap size = 1.73 (83 / 48) 860 30.91 3.07 0.71 chrXptel1M 538806 539359 (460641) L1M5_orf2#LINE/L1 1675 2241 (1053) m_b339s551i1 14176 chrXptel1M 538806 ATACATTATGACTAAGCAGGATTTGTACCAGGAATGAAGGGATGATTTAA 538855 i i ii i i v v i v i L1M5_orf2#LIN 1675 ATACATCATGACCAAGTGGGGTTTATCCCAGGAATGCAAGGTTGGTTTAA 1724 chrXptel1M 538856 CATAAAGAAAATTA-TTAACATAATTGATCATATAAATA--ATAAAAGTA 538902 vv- i - i ii v i v i -- i - L1M5_orf2#LIN 1725 CATTC-GAAAATCAATCAATGTAATTCACCATATTAACAGAATAAAGG-A 1772 chrXptel1M 538903 ACAAAATCAC-TGATAATGTAAATAGATGCAGAATAAGCTTTTAATAAAG 538951 iv i- v v v v v i i i L1M5_orf2#LIN 1773 GAAAAATCATATGATCATCTCAATAGATGCAGAAAAAGCATTTGACAAAA 1822 chrXptel1M 538952 TACAATATTCGTTTCTATTAAAAAC---AATGAAAGTATATGTAGAAATG 538998 v i ii i iv iv ---v vv v vivi iv L1M5_orf2#LIN 1823 TTCAACACCCATTCATGATAAAAACTCTCAGCAAACTAGGAATAGAAGGG 1872 chrXptel1M 538999 AATTTTTCCTTAAATAAATAAAAGGTGTTTATCTAAAACCATTAGCAAGC 539048 i -- i vivi i ii i ivv vvi ? i L1M5_orf2#LIN 1873 AACTT--CCTCAACCTGATAAAGGGCATCTACGAAAAACCTACAGCNAAC 1920 chrXptel1M 539049 ATTATTTCTAATA-TGAATCA------GCTTTACCAGTAA-ATCAGGTGT 539090 i vii i- v? ------ v vv - i vii L1M5_orf2#LIN 1921 ATCATACTTAATGGTGAAANACTGAANGCTTTCCCCCTAAGATCGGGAAC 1970 chrXptel1M 539091 GAAACAGAAATGCACATCATCACAAATATTATTCAATATTACATTGGAAA 539140 i i iii iv iii? v v vi i ii i ii L1M5_orf2#LIN 1971 AAGACAAGGATGTCCGCTNTCACCACTTCTATTCAACATTGTACTGGAGG 2020 chrXptel1M 539141 TCCTAGCAATAGCAAAAAGAGATGAAAAAGAAATAGAAGGAATCAGAATA 539190 v vv v iv v i v v ii v L1M5_orf2#LIN 2021 TCCTAGCCAGTGCAATAAGGCAAGAAAAAGAAATAAAAGGCATAAAGATT 2070 chrXptel1M 539191 AGAAAAGAGGTAATAAAATTATCTCTTTTTGCAA--GATATGGTGATATA 539238 i i i v i i ?i v i i-- i i vi ? L1M5_orf2#LIN 2071 GGAAAGGAAGAAATAAAACTGTCNTTATTCGCAGATGACATGATTGTNTA 2120 chrXptel1M 539239 ATCAAAAAATCCTAAAAACTCAACTAAAATGTTATTTGAAACAATTAGTA 539288 vvi i ? i v v v ? vii i v vi v i L1M5_orf2#LIN 2121 CGTAGAAAATCCNAAAGAATCTACAAANAAACTACTAGAACTAATAAGTG 2170 chrXptel1M 539289 ATTTTAGCAAAATAGGCAGACATAATGTAAATCTACCTAATTCATCAGCA 539338 v ii v v?i i i v v v vv v viv i L1M5_orf2#LIN 2171 AATTTAGCAAGGTCGCNGGATACAAGGTCAATATACAAAAATCAATTGTA 2220 chrXptel1M 539339 TTCCTATATATCACAAATAAA 539359 i ii vv i L1M5_orf2#LIN 2221 TTTCTATATACTAGCAACAAA 2241 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.48 CpG sites = 97, Kimura (unadjusted) = 41.77 Transitions / transversions = 1.33 (97/73) Gap_init rate = 0.02 (12 / 553), avg. gap size = 1.75 (21 / 12) 246 28.83 11.33 1.06 chrXptel1M 540019 540274 (459726) L1PREC2_orf2#LINE/L1 2352 2633 (661) m_b339s551i2 14177 chrXptel1M 540019 TTACAAAACACTTTTCACATAAA-GACAGATG---CATGCAAATGGTGAA 540064 vi v v -v v --- vi vi L1PREC2_orf2# 2352 TTACAAAACACTGCTCAAAGAAATCAGAGATGACACAAACAAATGGAAAA 2401 chrXptel1M 540065 ATATTAATTACTCATGGGCAGAGCAAGCCAATATCCATAAAAATGACAAT 540114 i vvv i ii iivi ii -i v i v L1PREC2_orf2# 2402 ACATTCCATGCTCATGGATAGGAAGAATCAATATC-GTTAAAATGGCCAT 2450 chrXptel1M 540115 TCTATCAAATG-----TATGTATTTAGTGTGATAGCTTTCAAACCACCAA 540159 v ii v v ----- iiv i i iv vv v i L1PREC2_orf2# 2451 ACTGCCCAAAGCAATTTACAGATTCAATGCTATTCCTATCAAACTACCAA 2500 chrXptel1M 540160 AAATAATTTT-ATGGAACTAGGAAAA--TAAT--GACGTTCATGTGCAAG 540204 vi i v i - ii i -- v --i vi i v v L1PREC2_orf2# 2501 TGACATTCTTCACAGAACTAGAAAAAACTATTTTAAAATTCATATGGAAC 2550 chrXptel1M 540205 AGCAAAATGGCAAGAATATCCAGGG-------AAGCAATGAAAGAA-AAA 540246 viv vi vv v i ------- -- - L1PREC2_orf2# 2551 CAAAAAAGAGCCCGAATAGCCAAGGCAATCCTAAGCAA--AAAGAACAAA 2598 chrXptel1M 540247 GCCA-AG------TGCTTCCAGACTTCAAACTGTA 540274 ii- ------i v v i L1PREC2_orf2# 2599 GCTGGAGGCATCACGCTACCCGACTTCAAACTATA 2633 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.72 CpG sites = 38, Kimura (unadjusted) = 36.98 Transitions / transversions = 1.09 (38/35) Gap_init rate = 0.05 (13 / 255), avg. gap size = 2.46 (32 / 13) 257 31.72 0.65 9.93 chrXptel1M 540404 540557 (459443) C MIRc#SINE/MIR (124) 144 4 m_b339s601i2 14178 chrXptel1M 540404 TTTTACTGACGAGGAAACACAGGCAAATAG-GGTGTAGTGATGTGACTAG 540452 v i vv vv v - vv iv v i i C MIRc#SINE/MIR 144 TTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAA 95 chrXptel1M 540453 GAAAAAACAGGTAACAAGCATCTAAGGCCTGATTTGCACTGAGAAAGCAA 540502 ivv v v ii iiv vi v vv i i v iv ------- C MIRc#SINE/MIR 94 GGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAG------- 52 chrXptel1M 540503 AGTCTTTCTGACTCCACAGCCAACAACACTCCATCCAAGGCACCACTTAG 540552 - i - i -- iii iv vv ---i C MIRc#SINE/MIR 51 -GTCTTCCTGACTCCA-AGTC--CAGTGCTCTTTCCACTGCACCAC---A 9 chrXptel1M 540553 CTGCC 540557 C MIRc#SINE/MIR 8 CTGCC 4 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.87 CpG sites = 20, Kimura (unadjusted) = 41.04 Transitions / transversions = 0.83 (20/24) Gap_init rate = 0.10 (15 / 153), avg. gap size = 1.00 (15 / 15) 225 36.60 2.09 1.88 chrXptel1M 541024 541502 (458498) L1ME4c_3end#LINE/L1 7 486 (344) m_b339s551i3 14176 chrXptel1M 541024 TCTCCAGGACATAGGGAACTGAGTCAAAT-GTTAAAAAGAAGAACCCTTC 541072 ?i ?v i ii i v v - v i i ? v vvvv L1ME4c_3end#L 7 TCTNTANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAAGAC 56 chrXptel1M 541073 TTCAGCTGATAAAGGGTCAAAAGATAGCAACAGGCAGATTGAGAAAAAA- 541121 ii iiv v v i i vv i - v v ? i - L1ME4c_3end#L 57 CCCAATAGATAAATGGGCAAAGGACATGAACAGACA-ATTCACANAAGAG 105 chrXptel1M 541122 --AATCAAAGAAATCAAGAGTGACTTGAGAAAAATGGTGTAAGTCACCAA 541169 -- vv ?v i v v ivv v - v vv vv i i i L1ME4c_3end#L 106 GAAATACAANTAGTAAACAAACACATG-GAAAAATGTTCAACCTCGCTAG 154 chrXptel1M 541170 CCCTTAAAGGAATGCAAATTTAAAAAATTCTGAGATACCGCTTCACACTT 541219 ivv i i v iv ivv ii i i i L1ME4c_3end#L 155 TAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCT 204 chrXptel1M 541220 TTGGGACTGACTCAAATGACAGAAAAAGAAT-ATGACAAACGCTGGAAAG 541268 v vii i ii vv v-i i vvi - iv v i vi L1ME4c_3end#L 205 ATTAAATTAGCAAAAATT-TAAAAAATTGATAATACCCAATGCTGGCGAG 253 chrXptel1M 541269 AATGGGGGAAAGGTAGGACGCTAATGCATCATTATTGGAGCCGTGAAGTT 541318 i? v vi iv i v ? v i iii iv vi?i i v v L1ME4c_3end#L 254 GNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTG 303 chrXptel1M 541319 GTTCTGCCGTTCCAAAGAACAGTTT-GCAATTATATCTCCCAAAGCATAA 541367 v vi v iiii i i i - - ii v vvi iv L1ME4c_3end#L 304 GTACAACCCTTTTGGAAAGCAATTTGGCAA-TACGTATCAAGAGCCATAA 352 chrXptel1M 541368 AACTATGTACCACCTTTGACCTAGGAAATACAACTGCTAGCTCTGTATCC 541417 v i vi ivv i v- v v v i vvv v L1ME4c_3end#L 353 AAATGTTCATACCCTTTGACCCAGT-AATTCCACTTCTGGGAATTTATCC 401 chrXptel1M 541418 CAAAGAGATGA---AAGGAAAGGGAAAGGAACTTGTTGATACAAAAATAT 541464 i i i i --- iii i i ---i i vvii i i i L1ME4c_3end#L 402 TAAGGAAATAATTCAAAAGAAGGAAAAAG---CTATATGCACGAAGATGT 448 chrXptel1M 541465 TTATAGCAGCTGTT-TTTGTGCTGGCAAAGGGTTAGAAA 541502 i v - - i iv i i iii i L1ME4c_3end#L 449 TCATTGCAGC-GTTATTTATAATAGCGAAAAATTGGAAA 486 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 50.52 CpG sites = 95, Kimura (unadjusted) = 53.26 Transitions / transversions = 1.23 (95/77) Gap_init rate = 0.03 (16 / 478), avg. gap size = 1.19 (19 / 16) 292 34.27 3.11 4.04 chrXptel1M 541080 541529 (458471) L1ME5_3end#LINE/L1 64 509 (432) m_b339s551i4 14176 chrXptel1M 541080 GATAAAGGGTCAAAAGATAGCAACAGGCAGATTG-AGAAAAA-AAATCAA 541127 v v v i vv iv i- i i- i vi L1ME5_3end#LI 64 GAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAGGAAACCCG 113 chrXptel1M 541128 AGAAATCAAGAGTGACTTGAGAAAAATGGTGTAAGTCACCAACCCTTAAA 541177 i iiii v ivv iv - i i v vv v ii iivv i i L1ME5_3end#LI 114 AAAGGCTAACAAGCATATGA-AGAGATGCTCAAACTCATTAGTAATCAGA 162 chrXptel1M 541178 GGAATGCAAATTTAAAAAATTCTGAGATACCGCTTCACACTTTTGGGACT 541227 i v v ivv i i i i v vi L1ME5_3end#LI 163 GAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCTATTAGACT 212 chrXptel1M 541228 GACTCAAATGACAGAAAAA-GAAT-ATGACAAACGCTGGAAAGAATG-GG 541274 i vv --i iv- i - v ii i vi i - L1ME5_3end#LI 213 GGCAAAAAT--TAGAAAGCTGGATAATGCCAAGTGTTGGCGAGGATGTGG 260 chrXptel1M 541275 GGAAAGGTAGG-ACGCTAATGCATCATTATTGGAGCCGTGAAGTTGTTCT 541323 ? -- - v v iiii iv iivi ii v v v v L1ME5_3end#LI 261 GGANA--TAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACTGGTGCA 308 chrXptel1M 541324 GCCGTTCCAAAGAACAGTTTGCAATTATATCTCCCAAAGCATAAAACTAT 541373 i iii i i i vv v i- ivvi v-- ivv i L1ME5_3end#LI 309 GCCATTCTGGAGAGCAATCTGGCAGTAC-TTAGTCAAAT--TAAGTATAC 355 chrXptel1M 541374 GTACCACCTTTGACCTAGGAAATACAACTGCTAGCTCTGTATCCCAAAGA 541423 i ivv v i - v v vi v i v v i L1ME5_3end#LI 356 GCATACCCTATGACCCA-GCAATTCCGCTCCTGGGTATATATCCCAAAGA 404 chrXptel1M 541424 GATGAAAGGAAAGG----GAAAGGAACTTGTTGATACAAAAATATTTATA 541469 i vvvviv v ----v i i v ---- i ii i i v L1ME5_3end#LI 405 AATTCTCACACAGGTCCATAAGGGGACATG----TACGAGGATGTTCATT 450 chrXptel1M 541470 GCAGCTGTT-TTTGTGCTGGCAAAGGGTTAGAAAGCGA---GGGAACATC 541515 - - v iii i - i i i --- --ii L1ME5_3end#LI 451 GCAGC-GTTGTTTGTGGTGGCGGGGAGTT-GGAGGCAACCTGGG--TGTC 496 chrXptel1M 541516 CATCAAGTGGGAGA 541529 - v L1ME5_3end#LI 497 CATC-ACTGGGAGA 509 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 44.81 CpG sites = 84, Kimura (unadjusted) = 47.45 Transitions / transversions = 1.31 (84/64) Gap_init rate = 0.06 (27 / 449), avg. gap size = 1.19 (32 / 27) 321 34.69 2.58 3.93 chrXptel1M 541163 541549 (458451) L1ME1_3end#LINE/L1 148 529 (397) m_b339s551i6 14176 chrXptel1M 541163 TCACCAACCCTTAAAGGAATGCAAATTTAAAAAATTCTGAGATACCGCTT 541212 ii ii v ii i v vv ivv i v L1ME1_3end#LI 148 TCATTAGTCATTAGGGAAATGCAAATTAAAACCACAATGAGATACCACTA 197 chrXptel1M 541213 CACACTTTTGGGACTGACTCAAATGACAGAAAAAGAATATGACAAACGCT 541262 i v vi v i v v v i i vv vv iv ii i L1ME1_3end#LI 198 CACACCTATTAGAATGGCTAAAATTAAAAAGACTGACAATACCAAGTGTT 247 chrXptel1M 541263 GGAAAGAATGGGGGAAAGGTAGGACGCTAATGCATCATTATTGGAGCCGT 541312 vi i v iiv iv i i v v i iii iv iivi i L1ME1_3end#LI 248 GGCGAGGATGTGGAGCAACTGGAACTCTCATACATTGCTGGTGGGAATGC 297 chrXptel1M 541313 GAAGTTGTTCTGCCGTTCCAAAGAACAGTTT-GCAATTATATCTCCCAAA 541361 i i v v v ii iiii i - i --- iv? L1ME1_3end#LI 298 AAAATGGTACAGCCACTTTGGAAAACAGTTTGGCAGTT---TCTTANAAA 344 chrXptel1M 541362 GCATAAAACTATG--TACCACCTTTGACCTAGGAAATACAACTGCTAGCT 541409 i- vv ii-- -- v i - v v v v v L1ME1_3end#LI 345 GT-TAAACATACACTTACCA--TATGACCCA-GCAATTCCACTCCTAGGT 390 chrXptel1M 541410 CTGTATCCCAAAGAGATGAAAGGAAAGG------GAAAGGAACTTGTTGA 541453 v v i v i i iv v v ------v -- ---- L1ME1_3end#LI 391 ATTTACCCAAGAGAAATGAAAACATATGTCCACACAAAG--ACTTG---- 434 chrXptel1M 541454 TACAAAAATATTTATAGCAGCTGTTTTTGTGCTGGCAAAGGGTTAGAAAG 541503 vi i i v v i iv i v iiii i - L1ME1_3end#LI 435 TACACGAATGTTCATAGCAGCTTTATTCGTAATAGCCAAAAACTGGAAA- 483 chrXptel1M 541504 CGA-GGGAACATCCATCAAGTGGGAGATAGCCCCAACAAGTTGTGGT 541549 i -vvi ii v? vii i -viv i L1ME1_3end#LI 484 CAACCCAAATGTCCATCAACNGGTGAATGG-ATAAACAAATTGTGGT 529 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 46.91 CpG sites = 73, Kimura (unadjusted) = 48.49 Transitions / transversions = 1.30 (73/56) Gap_init rate = 0.05 (19 / 386), avg. gap size = 1.32 (25 / 19) 385 32.35 3.53 4.87 chrXptel1M 541163 541474 (458526) L1MB4_3end#LINE/L1 148 455 (472) m_b339s551i5 14176 chrXptel1M 541163 TCACCAACCCTTAAAGGAATGCAAATTTAAAAAATTCTGAGATACCGCTT 541212 i ii v ii i iv vv ivv i L1MB4_3end#LI 148 TCACTAGTCATTAGGGAAATGCAAATCAAAACCACAATGAGATACCACTT 197 chrXptel1M 541213 CACACTT-TTGGGACTGACTCAAATGACAGAAAAAGAATATGACAAACGC 541261 ii-i i - i vv? v v i vi v i ii i L1MB4_3end#LI 198 CACACCCACTAGGA-TGGCTATNATCAAAAAAACGGAAAATAACAAGTGT 246 chrXptel1M 541262 TGGAAAGAATGGGGGAAAGGTAGGACGCTAATGCATCATTATTGGAGCCG 541311 vi i v ii iv i i v vi iii iv iivi L1MB4_3end#LI 247 TGGCGAGGATGTGGAGAAATTGGAACCCTCGTGCATTGCTGGTGGGAATG 296 chrXptel1M 541312 TGAAGTTGTTCTGCCGTTCCAAAGAACAGTTT-GCAATTATATCTCCCAA 541360 i i v v v i viii i - ii ---i vv L1MB4_3end#LI 297 TAAAATGGTGCAGCCGCTGTGGAAAACAGTTTGGCGGTT---CCTCAAAA 343 chrXptel1M 541361 AG-----CATAAAACTATGTACCACCTTTGACCTAGGAAATACAACTGCT 541405 ----- i i---- -- v i - v v v v L1MB4_3end#LI 344 AGTTAAACATAGAAT----TACCA--TATGACCCA-GCAATTCCACTCCT 386 chrXptel1M 541406 AGCTCTGTATCCCAAAGAGATGAAAGGAAAGG---GAAAGGA-ACTTGTT 541451 v v i i v iv v ii i---i vi - -- L1MB4_3end#LI 387 AGGTATATACCCAAAAGAATTGAAAGCAGGGACTCAAACAGATACTTG-- 434 chrXptel1M 541452 GATACAAAAATATTTATAGCAGC 541474 -- vv i i L1MB4_3end#LI 435 --TACACCAATGTTCATAGCAGC 455 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.67 CpG sites = 58, Kimura (unadjusted) = 44.14 Transitions / transversions = 1.53 (58/38) Gap_init rate = 0.06 (20 / 311), avg. gap size = 1.30 (26 / 20) 13 24.01 0.00 0.00 chrXptel1M 541820 541858 (458142) (TTTTTAT)n#Simple_repeat 1 39 (0) m_b339s252i3 14179 chrXptel1M 541820 TTTATATTTTGTTTTTTTCATGTTTTTTTTTTTCCTTTT 541858 v v v i v v vi (TTTTTAT)n#Si 1 TTTTTATTTTTTATTTTTTATTTTTTATTTTTTATTTTT 39 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 42 0.00 0.00 0.00 chrXptel1M 541911 541946 (458054) (TA)n#Simple_repeat 1 36 (0) c_b339s251i0 14180 chrXptel1M 541911 TATATATATATATATATATATATATATATATATATA 541946 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATA 36 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 30 23.27 0.00 0.00 chrXptel1M 542064 542128 (457872) (A)n#Simple_repeat 1 65 (0) m_b339s252i4 14181 chrXptel1M 542064 AAAAAAATAAAATACTTTTAAAAATCAAAAAAAAAAAGAAAAGAAAAAAG 542113 v v vvvvv vv i i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chrXptel1M 542114 AAAAAAAAAAAGAAA 542128 i (A)n#Simple_r 51 AAAAAAAAAAAAAAA 65 Matrix = Unknown Transitions / transversions = 0.44 (4/9) Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0) 21 15.12 5.77 0.00 chrXptel1M 542084 542135 (457865) (AAAAG)n#Simple_repeat 1 55 (0) m_b339s252i5 14181 chrXptel1M 542084 AAAATCAAA-AAAA-AAAAGAAAAGAAAA-AAGAAAAAAAAAAAGAAAGG 542130 vv - - - i i i i (AAAAG)n#Simp 1 AAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAG 50 chrXptel1M 542131 AAGAG 542135 i (AAAAG)n#Simp 51 AAAAG 55 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.00 (3 / 3) 13 21.42 4.35 2.13 chrXptel1M 542791 542836 (457164) (TTCC)n#Simple_repeat 1 47 (0) m_b339s252i6 14182 chrXptel1M 542791 TTCTTGCCTTCTTTCACCTCCTTCCTTCCCCCCGT-TTTCCTT-CTTC 542836 i v i - i ii v -i - (TTCC)n#Simpl 1 TTCCTTCCTTCCTTC-CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC 47 Matrix = Unknown Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.07 (3 / 45), avg. gap size = 1.00 (3 / 3) 474 31.25 4.97 0.60 chrXptel1M 546908 547068 (452932) MIR3#SINE/MIR 38 205 (3) m_b339s601i3 14183 chrXptel1M 546908 AGCCATAAAAACTG----CTCATCCCACTACTGATCATTA-CTAACCCTA 546952 i vi i v ---- vi iviv -i i - ?i iv i MIR3#SINE/MIR 38 AGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTG-CCACTAACTNGCTGTG 86 chrXptel1M 546953 TAACCTTGACCACATTATTTAAACTTCCTGA-CCTCAGTTGCCTCATATC 547001 i iv vi i i v v ii i- v v v MIR3#SINE/MIR 87 TGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTG 136 chrXptel1M 547002 TAAAATGAAGGGGTTGATCCAGATGGCTTCTGGAGTCCCTTCTAACTTTA 547051 i iv i iii iii i i i i MIR3#SINE/MIR 137 TAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTG 186 chrXptel1M 547052 AA--TCCATGATCCTGTGA 547068 v-- i i i MIR3#SINE/MIR 187 ACATTCTATGATTCTATGA 205 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.27 CpG sites = 35, Kimura (unadjusted) = 43.47 Transitions / transversions = 2.33 (35/15) Gap_init rate = 0.03 (5 / 160), avg. gap size = 1.80 (9 / 5) 519 32.85 5.75 1.58 chrXptel1M 549381 549745 (450255) C L1ME4c_3end#LINE/L1 (294) 536 157 m_b339s551i7 14184 chrXptel1M 549381 ATATACCAAAACTTATTCAGCCATTCTCCAGCTGATGGGCATCCACTCAT 549430 i v i i i i i vii v i ii v--i C L1ME4c_3end#L 536 ATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAG--GT 489 chrXptel1M 549431 TCAGTTTCCAGTTTCTTGGCACTACAAAAAAGGCTGCCACAAACCTTTTT 549480 -- i i i vi i i v v v ii v i i C L1ME4c_3end#L 488 T--GTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTC 441 chrXptel1M 549481 GCACATGAAGGTCCCTTTCCCTCCTTTAACTT--CTCTTTGAGATATAAA 549528 ii iv -- ii i i i v --i i ii v vv C L1ME4c_3end#L 440 GTGCATATAG--CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAATT 393 chrXptel1M 549529 CCCGGTAGAAAAATAGCTGGGCCAAAGGATATGCACAGTTTGATAGCCCC 549578 i v vii vi i i v v v i i i C L1ME4c_3end#L 392 CCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTCT 343 chrXptel1M 549579 TGGGCCATAGTTTCAAATTGCTCTCCAGAAG------------TCACAAT 549616 ivv i v vi i i ------------ i ? C L1ME4c_3end#L 342 TGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACANT 293 chrXptel1M 549617 TTCAACAACAAGGTACTAGT------GTTCCACTA-ATCCCCTCCCACAT 549659 vi v i v iv ?------ i ii- ? i v vi C L1ME4c_3end#L 292 GCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGCAT 243 chrXptel1M 549660 CTGGCATCATCTTTTTCTGTCATCTTGGCCTATCTCAGTGATGGGTAGTG 549709 iv i i vv i vvv i v iv i v vv ii viv i C L1ME4c_3end#L 242 TGGGTATTATCAATTTTTTAAATTTTTGCTAATTTAATAGGCGTAAAATG 193 chrXptel1M 549710 GTATCTCAGAATGGTCTTAATTTGCATTTCTCTGAT 549745 vvi v ii i C L1ME4c_3end#L 192 GTATCTCATTGTTGCTTTAATTTGCATTTCTTTGAT 157 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 42.92 CpG sites = 72, Kimura (unadjusted) = 45.62 Transitions / transversions = 1.57 (72/46) Gap_init rate = 0.03 (10 / 364), avg. gap size = 2.70 (27 / 10) 266 31.75 8.15 3.18 chrXptel1M 549515 549784 (450216) C L1HS_3end#LINE/L1 (500) 402 120 m_b339s551i8 14184 chrXptel1M 549515 CTTTGAGATATAAACCCGGTAGAAAAATAGCTGGGCCAAAGGATATGCAC 549564 i - v i iviii i i v i vivi C L1HS_3end#LIN 402 CTTTGGG-TATATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCT 354 chrXptel1M 549565 AGTTTGATAG-CCCCTGGGCCATAGTTTCAAATTGCTCTCCAGAA----- 549608 i-- -i i vv v i-- v i vii v ----- C L1HS_3end#LIN 353 AGTTC--TAGATCCCTGAGGAATCGC--CACACTGACTTCCACAATGGTT 308 chrXptel1M 549609 ------GTC-ACAATTTCAACAACAAGGTACTAGTGTTCC-ACTAATCCC 549650 ------ i- i ii v iv vv - i vv v C L1HS_3end#LIN 307 GAACTAGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCG 258 chrXptel1M 549651 CTCCCACATCTGGCATC-ATCTTTTTCTGTCATCTTG------GCCTATC 549693 vi v - ii i -i iv i v v i i------ vv C L1HS_3end#LIN 257 CATCCTC-TCCAGCACCTGTTGTTTCCTGACTTTTTAATGATTGCCATTC 209 chrXptel1M 549694 TCAGTGATGGGTAGTGGTATCTCAGAATGGTCTTAATTTGCATTTCTCTG 549743 v v i v vii i v i i i C L1HS_3end#LIN 208 TAACTGGTGTGAGATGATATCTCATAGTGGTTTTGATTTGCATTTCTCTG 159 chrXptel1M 549744 ATCAATCTATATTTGAATGGGTA-TTCTTCATGTAATTTCTG 549784 -iii vi iv --i i i - iv i C L1HS_3end#LIN 158 AT-GGCCAGTGAT--GATGAGCATTTCTTCATGTGTTTTTTG 120 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 42.91 CpG sites = 50, Kimura (unadjusted) = 42.91 Transitions / transversions = 1.52 (50/33) Gap_init rate = 0.06 (17 / 269), avg. gap size = 1.82 (31 / 17) 321 34.80 4.85 4.22 chrXptel1M 551018 551182 (448818) C MIR3#SINE/MIR (2) 206 41 m_b339s601i4 14185 chrXptel1M 551018 ATTATGGAATTATTACAGAACATATTTGGAGCTAAAGTGGAGCTCATAAA 551067 i i i --- ii ---ii ii iv v i v i C MIR3#SINE/MIR 206 ATCATAGAATCAT---AGAATGT---CAGAGCTGGAAGGGACCTTAGAGA 163 chrXptel1M 551068 CGAGCTAGGACAGTCTTTTAATTTTAGAGAAGAGGACAAAAAGTCCCAGA 551117 iv v vv ii iii v v v v vvi v C MIR3#SINE/MIR 162 TCATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGA 113 chrXptel1M 551118 GCATGTAAAG-GACTTATCAAAGGTCACACA-------AGTAACATGGTT 551159 - v i - ii v ------- ii vi ii C MIR3#SINE/MIR 112 G-AGGTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCC 64 chrXptel1M 551160 GAAATTTGAATATACATCCTCTG 551182 ii i v ivi vi ii C MIR3#SINE/MIR 63 GGGACTAGAACCCAGGTCTCCTG 41 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 48.15 CpG sites = 35, Kimura (unadjusted) = 49.45 Transitions / transversions = 1.75 (35/20) Gap_init rate = 0.05 (9 / 164), avg. gap size = 1.67 (15 / 9) 268 28.82 7.30 11.36 chrXptel1M 551088 551224 (448776) C MIRb#SINE/MIR (120) 148 17 m_b339s601i5 14185 chrXptel1M 551088 ATTTTAGAGAAGAGGACAAAAAGTCCCAGAGCATGTAAAG-GACTTATCA 551136 v v v vvi v i - v v -i ii v C MIRb#SINE/MIR 148 ATTTTACAGATGAGGAAACTGAGGCTCAGAG-AGGTTAAGTAACTTGCCC 100 chrXptel1M 551137 AAGGTCACAC-------AAGTAACATGGTTGAAATTTGAATATACATCCT 551179 ------- ii vi ii ii i ---------i C MIRb#SINE/MIR 99 AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAA---------C 59 chrXptel1M 551180 CTGGGTACCGATTGTCT--TTCCAAATCTCATGTTATTTCTGCTGCA 551224 ii -----i --i v i i i v ii C MIRb#SINE/MIR 58 CCAGGT-----CTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCA 17 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.68 CpG sites = 23, Kimura (unadjusted) = 37.73 Transitions / transversions = 1.92 (23/12) Gap_init rate = 0.13 (18 / 136), avg. gap size = 1.39 (25 / 18) 22 0.00 0.00 0.00 chrXptel1M 551495 551518 (448482) (AT)n#Simple_repeat 1 24 (0) m_b339s252i7 14186 chrXptel1M 551495 ATATATATATATATATATATATAT 551518 (AT)n#Simple_ 1 ATATATATATATATATATATATAT 24 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 184 22.22 12.70 0.00 chrXptel1M 551927 551989 (448011) L3#LINE/CR1 4026 4096 (3) m_b339s601i6 14187 chrXptel1M 551927 TCCTTTCTTTGATGGG--GTTGGACTGGA---CTGCTAAGATCCCTTTCA 551971 viv v -- i --- iv i i L3#LINE/CR1 4026 TCCTGCATTGGATGGGAGGTTGGACTAGATGACCTCTAAGGTCCCTTCCA 4075 chrXptel1M 551972 AGGCCAAG--TCTATG-TTCT 551989 vv ii -- i - L3#LINE/CR1 4076 ACTCTGAGATTCTGTGATTCT 4096 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.76 CpG sites = 8, Kimura (unadjusted) = 26.76 Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.06 (4 / 62), avg. gap size = 2.00 (8 / 4) 438 31.24 10.00 1.20 chrXptel1M 552856 553085 (446915) C MIRc#SINE/MIR (17) 251 2 m_b339s601i7 14188 chrXptel1M 552856 ACGTTTGTAGAGC----TG-AGTTT-CAAAGCTCTGTCACGGACAGTTGC 552899 i v ---- i- - v v iv - ii C MIRc#SINE/MIR 251 ACATTTGTATAGCACTTTACAGTTTACAAAGCGCTTTCACATACA-TTAT 203 chrXptel1M 552900 CTTACCGGGCCTCTGCAAGAAGCCTGGAAGGTAGGCAGGAC---CATTGT 552946 i iiv ii iiii v v vi i ---i i C MIRc#SINE/MIR 202 CTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTAT 153 chrXptel1M 552947 TCTCTCCACCTTGTCCAGATGAGGATACTGAGGCTAAGAGCAGTTGGTTG 552996 v i ii i-- v v vi iiv C MIRc#SINE/MIR 152 TATCCCCATTTTA--CAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTG 105 chrXptel1M 552997 ACGTGGACAAG--------GCTAGGAACTGGGAAAGAGAAGATCAGATTG 553038 v vv -------- v v v i vvii iiv viv C MIRc#SINE/MIR 104 ACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACC 55 chrXptel1M 553039 CAGGT----CTGACCTCAGAACCAGTGGCC--TCCATAATAGCATCCTCC 553082 ---- ii iiv vi -- ivii v iv v C MIRc#SINE/MIR 54 CAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTGC 5 chrXptel1M 553083 TTC 553085 i C MIRc#SINE/MIR 4 CTC 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.90 CpG sites = 41, Kimura (unadjusted) = 41.67 Transitions / transversions = 1.37 (41/30) Gap_init rate = 0.04 (10 / 229), avg. gap size = 2.60 (26 / 10) 292 26.82 10.00 6.80 chrXptel1M 553519 553618 (446382) MIRc#SINE/MIR 42 144 (124) m_b339s601i8 14189 chrXptel1M 553519 TCAGGAGGATCTGAGTTCAAATCTAACTTCAGACGCTTAACATTTCCTAA 553568 i i i i i ivivi v v i ------- i MIRc#SINE/MIR 42 TCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTA-------CTAG 84 chrXptel1M 553569 CTGTGTGACCCCGAACGAGCCACTTAA----------CCCCAGTTGCCTC 553608 ii ii i i ---------- i v MIRc#SINE/MIR 85 CTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTC 134 chrXptel1M 553609 ATCCAAAAAA 553618 iiv MIRc#SINE/MIR 135 ATCTGTAAAA 144 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.95 CpG sites = 19, Kimura (unadjusted) = 35.49 Transitions / transversions = 3.17 (19/6) Gap_init rate = 0.08 (8 / 99), avg. gap size = 2.12 (17 / 8) 214 37.52 0.00 6.59 chrXptel1M 553648 553744 (446256) MIRc#SINE/MIR 11 101 (167) m_b339s601i9 14190 chrXptel1M 553648 TGGCAGAGTGGAGAGAATCCCGACCCCGCATTCAGGAGGATCTGAGTTCA 553697 iiv i iiv i iv ii v v i i i i MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chrXptel1M 553698 AATCTGACCTCAGACATTTAATACTTTCTACGGGGTGATTCTGAGCA 553744 i iviv v v i v ------i v v iii i MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTACTA------GCTGTGTGACCTTGGGCA 101 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 50.53 CpG sites = 22, Kimura (unadjusted) = 55.43 Transitions / transversions = 1.83 (22/12) Gap_init rate = 0.06 (6 / 96), avg. gap size = 1.00 (6 / 6) 32 0.00 0.00 0.00 chrXptel1M 556502 556531 (443469) (T)n#Simple_repeat 1 30 (0) c_b340s251i0 14191 chrXptel1M 556502 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 556531 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 30 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 541 24.47 3.45 1.35 chrXptel1M 558095 558239 (441761) MIR3#SINE/MIR 23 170 (38) m_b340s601i0 14192 chrXptel1M 558095 AGAGCACTGGACCAAGAGTCCAGAGAAGTGGATTTAAATCATGGTCCTGC 558144 - iii vi vv i iv i vi ii MIR3#SINE/MIR 23 AGAGCAC-GGACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGC 71 chrXptel1M 558145 CACTAACAAACTGTGTCATCTTGAGCAAGTCATT---CTTCACTGGGTCT 558191 v?i v i i i --- i v i MIR3#SINE/MIR 72 CACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCT 121 chrXptel1M 558192 CA-TTTTCTGTCCTGTAAATTCAGAGGCTTGGAG-AGAGTTATGTCTAAG 558239 - i vvi v v i v v- - v v MIR3#SINE/MIR 122 CAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGA-TGATCTCTAAG 170 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.30 CpG sites = 19, Kimura (unadjusted) = 30.31 Transitions / transversions = 1.19 (19/16) Gap_init rate = 0.03 (5 / 144), avg. gap size = 1.40 (7 / 5) 247 32.11 9.15 1.31 chrXptel1M 558249 558390 (441610) MIR3#SINE/MIR 10 162 (46) m_b340s601i1 14193 chrXptel1M 558249 TGACCTAGTGGAGAGAAT---GACCAG-AGTCAGAGAGTTTGAATTA-AG 558293 i iv ii ii--- ii - iiiiii ii v- MIR3#SINE/MIR 10 TGGCTGAGCAGAGAGAGCACGGACTGGGAGTCAGGAGACCTGGGTTCTAG 59 chrXptel1M 558294 TCTGAACTTTGCCATTC-CTCACTCTTGTGACCTTGGGCAAAGAGGTGTC 558342 ivii i i v- ?i v - ivviv viv MIR3#SINE/MIR 60 TCCCGGCTCTGCCACTAACTNGCTGT-GTGACCTTGGGCAAGTCACTTCA 108 chrXptel1M 558343 CATTTTGGGGCCTCAG---CTGCA-CT---AAGTGAGGGAGGTGGGCCTA 558385 v i iv --- iv - --- i - v v MIR3#SINE/MIR 109 CCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGG-GGTTGGACTA 157 chrXptel1M 558386 AATGA 558390 i MIR3#SINE/MIR 158 GATGA 162 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.47 CpG sites = 30, Kimura (unadjusted) = 44.86 Transitions / transversions = 2.00 (30/15) Gap_init rate = 0.06 (9 / 141), avg. gap size = 1.67 (15 / 9) 12 15.98 2.56 5.26 chrXptel1M 559587 559625 (440375) (CAAATA)n#Simple_repeat 1 38 (0) m_b340s252i0 14194 chrXptel1M 559587 CAATTAAAAATCCTAATACAAATAAAAATCAGCAAA-ACA 559625 v v v v v - - - (CAAATA)n#Sim 1 CAAATACAAATACAAATACAAATACAAAT-A-CAAATACA 38 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.08 (3 / 38), avg. gap size = 1.00 (3 / 3) 384 27.48 10.74 0.75 chrXptel1M 560124 560244 (439756) C MIRc#SINE/MIR (133) 135 3 m_b340s601i2 14195 chrXptel1M 560124 TAATGAAACTGAGCCTCAGGAATGCTAAATGATTTGGCTAAAGTTGCACA 560173 i v v ii v i i i v i i ii C MIRc#SINE/MIR 135 TGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACA 86 chrXptel1M 560174 ATTAACAAGTGTCA-----TGGATTCTGAA-------CTTCATGCCTCCA 560211 ii ii v -----v i - ------- v v C MIRc#SINE/MIR 85 GCTAGTAAGTGGCAGAGCCGGGACTC-GAACCCAGGTCTTCCTGACTCCA 37 chrXptel1M 560212 AATCCAGAACACTTTCTAATATGCCA-AATGCCT 560244 i vi v i v iii - v C MIRc#SINE/MIR 36 AGTCCAGTGCTCTTTCCACTGCACCACACTGCCT 3 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.47 CpG sites = 21, Kimura (unadjusted) = 35.47 Transitions / transversions = 1.75 (21/12) Gap_init rate = 0.03 (4 / 120), avg. gap size = 3.50 (14 / 4) 38 0.00 0.00 0.00 chrXptel1M 561093 561125 (438875) (TA)n#Simple_repeat 1 33 (0) c_b340s251i1 14196 chrXptel1M 561093 TATATATATATATATATATATATATATATATAT 561125 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATAT 33 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 15 23.20 1.92 1.92 chrXptel1M 561256 561307 (438693) (AATTTGT)n#Simple_repeat 1 52 (0) m_b340s252i1 14197 chrXptel1M 561256 AATTTATACATTTGCAGTTTGTAAATTCTGATTT-TAATTTTTCATTACT 561304 i - i i v v i - v v vv (AATTTGT)n#Si 1 AATTTGTA-ATTTGTAATTTGTAATTTGTAATTTGTAATTTGTAATTTGT 49 chrXptel1M 561305 AAT 561307 (AATTTGT)n#Si 50 AAT 52 Matrix = Unknown Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.00 (2 / 2) 11 21.63 0.00 5.13 chrXptel1M 562151 562191 (437809) (TTTATTT)n#Simple_repeat 1 39 (0) m_b340s252i2 14198 chrXptel1M 562151 TTTACTTTTTAGAATTTTTATTATCTGTTATTTATGTTTTA 562191 - -v v v i i v v (TTTATTT)n#Si 1 TTTA-TTTTT-TATTTTTTATTTTTTATTTTTTATTTTTTA 39 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 17 13.78 2.27 4.65 chrXptel1M 563030 563073 (436927) (AAAAT)n#Simple_repeat 1 43 (0) m_b340s252i3 14199 chrXptel1M 563030 AAAATACTAAGAAAA-AATTTAAAATAAAATAAAAATAACATAAA 563073 -v v - vv - v (AAAAT)n#Simp 1 AAAATA-AAATAAAATAAAATAAAATAAAAT-AAAATAAAATAAA 43 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.07 (3 / 43), avg. gap size = 1.00 (3 / 3) 368 26.53 2.72 0.00 chrXptel1M 564351 564497 (435503) L1M2_orf2#LINE/L1 1668 1818 (1473) m_b340s551i0 14200 chrXptel1M 564351 GATCATACATTATGACCAAACAGGATTTATACCGGGAATGAAGTGATGAT 564400 ? ? ii i iii v i i v iv i L1M2_orf2#LIN 1668 GATNATNCACCATGATCAAGTGGGATTTATCCCAGGGATGCAAGGATGGT 1717 chrXptel1M 564401 TTAACATAGAGAAAATTATAAAC--TATTGATTATATCAATA-ATTAAAG 564447 i viv viv --v vv i i i - v i L1M2_orf2#LIN 1718 TCAACATACGCAAATCAATAAACGTGATACATCACATCAACAGAATGAAG 1767 chrXptel1M 564448 TAACAAAATCA-ATGATTATATTAATAGATGCATAAAAATCTTTTCATAA 564496 v vv i - i v i v v v v L1M2_orf2#LIN 1768 GACAAAAACCATATGATCATCTCAATAGATGCAGAAAAAGCATTTGATAA 1817 chrXptel1M 564497 A 564497 L1M2_orf2#LIN 1818 A 1818 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.68 CpG sites = 20, Kimura (unadjusted) = 33.72 Transitions / transversions = 1.05 (20/19) Gap_init rate = 0.02 (3 / 146), avg. gap size = 1.33 (4 / 3) 16 24.87 0.00 0.00 chrXptel1M 564528 564570 (435430) (AAAT)n#Simple_repeat 1 43 (0) m_b340s252i4 14201 chrXptel1M 564528 AAATAGATTAATCCTTAAATAAATAAATTTATATTTAAATAAA 564570 i v vvv vv vv (AAAT)n#Simpl 1 AAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAA 43 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 510 32.99 1.36 1.36 chrXptel1M 564610 564904 (435096) L1MC_orf2#LINE/L1 1947 2241 (1053) m_b340s551i1 14202 chrXptel1M 564610 AGCTTTGCCAGTAAAATCAGGTGTGAAACAGAGATGCCCATTATCACCAA 564659 v iv i viii ii ii i vi v v L1MC_orf2#LIN 1947 AGCTTTCCCGCTAAGATCAGGAACAAGGCAAGGATGTCCCCTCTCACCAC 1996 chrXptel1M 564660 TATTATTCAATATTACATTAGAAATCTTAG-TAATTAGCAATAAGAGACG 564708 vi v i iii i i i i - -- v v L1MC_orf2#LIN 1997 TCCTTTTCAACATCGTACTGGAAGTCCTAGCTAAT--GCAATAAGACAAG 2044 chrXptel1M 564709 CAAAAGAAATAGAAGG-ATTCAGAATAACAATTAAAGTAATAAAACTATC 564757 v i i - v v iiv -vi v i L1MC_orf2#LIN 2045 AAAAGGAAATAAAAGGTATACAGATTGGGAA-GGAAGAAATAAAACTGTC 2093 chrXptel1M 564758 TCCTTTTGCAA--GATATGGTGACATATTCTCAAAATCCTGAAGGCTCAA 564805 iiv i i-- i i viiv vivv vi iv i L1MC_orf2#LIN 2094 TTTGTTCGCAGATGACATGATTGTCTATGTAGAAAATCCGAAAGAATCGA 2143 chrXptel1M 564806 CTAAAAAAGTTAGTTGAAATCATTAGTAATTTTAGCAAAATAGCCAGATA 564855 - ii vv v v v v ii v ii v vi L1MC_orf2#LIN 2144 C-AAAAAAACTCCTGGAACTAATAAGCGATTATAGCAAGGTTGCAGGATA 2192 chrXptel1M 564856 TAATGTAAATCCACCTAATTCACCAGCATTCCGAAATATCACAAATAAA 564904 i v v vi vv v viv v v v i vv i L1MC_orf2#LIN 2193 CAAGGTTAATATACAAAAGTCAATCGCTTTCCTATATACCAGCAATGAA 2241 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.19 CpG sites = 50, Kimura (unadjusted) = 44.33 Transitions / transversions = 1.09 (50/46) Gap_init rate = 0.02 (7 / 294), avg. gap size = 1.14 (8 / 7) 524 32.41 0.78 0.78 chrXptel1M 564611 564865 (435135) L1M5_orf2#LINE/L1 1948 2202 (1092) m_b340s551i2 14202 chrXptel1M 564611 GCTTTGCCAGTAAAATCAGGTGTGAAACAGAGATGCCCATTATCACCAAT 564660 v vv i i viii i ii i ii ? v L1M5_orf2#LIN 1948 GCTTTCCCCCTAAGATCGGGAACAAGACAAGGATGTCCGCTNTCACCACT 1997 chrXptel1M 564661 ATTATTCAATATTACATTAGAAATCTTAGTAATTAGCAATAAGAGACGCA 564710 vi i ii i i ii i iv v - iv v v L1M5_orf2#LIN 1998 TCTATTCAACATTGTACTGGAGGTCCTAGCCAGT-GCAATAAGGCAAGAA 2046 chrXptel1M 564711 AAAGAAATAGAAGGATTCAGAATAACAATTAAAGTAATAAAACTATCTCC 564760 i vv v ii viv vvi v i ?ii L1M5_orf2#LIN 2047 AAAGAAATAAAAGGCATAAAGATTGGAAAGGAAGAAATAAAACTGTCNTT 2096 chrXptel1M 564761 TTTTGCAA--GATATGGTGACATATTCTCAAAATCCTGAAGGCTCAACTA 564808 v i i-- i i vii? ivivv ?i iv v - L1M5_orf2#LIN 2097 ATTCGCAGATGACATGATTGTNTACGTAGAAAATCCNAAAGAATCTAC-A 2145 chrXptel1M 564809 AAAAAGTTAGTTGAAATCATTAGTAATTTTAGCAAAATAGCCAGATATAA 564858 ? ii v v v v v i v ii v ?i i L1M5_orf2#LIN 2146 AANAAACTACTAGAACTAATAAGTGAATTTAGCAAGGTCGCNGGATACAA 2195 chrXptel1M 564859 TGTAAAT 564865 v v L1M5_orf2#LIN 2196 GGTCAAT 2202 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 42.30 CpG sites = 47, Kimura (unadjusted) = 45.27 Transitions / transversions = 1.34 (47/35) Gap_init rate = 0.01 (3 / 254), avg. gap size = 1.33 (4 / 3) 285 29.22 11.33 1.06 chrXptel1M 565546 565801 (434199) L1PREC2_orf2#LINE/L1 2352 2633 (661) m_b340s551i3 14203 chrXptel1M 565546 TTACAAAACACTTTTCACATAAA-GACAGATG---CATGCAAATGGTGAA 565591 vi v v -v v --- vi vi L1PREC2_orf2# 2352 TTACAAAACACTGCTCAAAGAAATCAGAGATGACACAAACAAATGGAAAA 2401 chrXptel1M 565592 ATATTAATTACTCATGGGCAGAGCAAGCCAATATCCATAAAAATGACAAT 565641 i vvv i ii iivi ii -i v i v L1PREC2_orf2# 2402 ACATTCCATGCTCATGGATAGGAAGAATCAATATC-GTTAAAATGGCCAT 2450 chrXptel1M 565642 TCTATCAAATG-----TATGTATTTAGTGTGATAGCTTTCAAACCACCAA 565686 v ii v v ----- iiv i i iv vv v i L1PREC2_orf2# 2451 ACTGCCCAAAGCAATTTACAGATTCAATGCTATTCCTATCAAACTACCAA 2500 chrXptel1M 565687 AAATAATTTT-ATGGAACTAGGAAAA--TAAT--GACGTTCATGTGCAAG 565731 vi i v i - ii i -- v --i vi i v v L1PREC2_orf2# 2501 TGACATTCTTCACAGAACTAGAAAAAACTATTTTAAAATTCATATGGAAC 2550 chrXptel1M 565732 AGCAAAATGTCAAGAATATCCAGGG-------AAGCAATGAAAGAA-AAA 565773 viv viv vv v i ------- -- - L1PREC2_orf2# 2551 CAAAAAAGAGCCCGAATAGCCAAGGCAATCCTAAGCAA--AAAGAACAAA 2598 chrXptel1M 565774 GCCA-AG------TGCTTCCAGACTTCAAACTGTA 565801 ii- ------i v v i L1PREC2_orf2# 2599 GCTGGAGGCATCACGCTACCCGACTTCAAACTATA 2633 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.34 CpG sites = 38, Kimura (unadjusted) = 37.60 Transitions / transversions = 1.06 (38/36) Gap_init rate = 0.05 (13 / 255), avg. gap size = 2.46 (32 / 13) 251 32.29 0.69 8.15 chrXptel1M 565931 566075 (433925) C MIRc#SINE/MIR (124) 144 10 m_b340s601i3 14204 chrXptel1M 565931 TTTTACTGACGAGGAAACACAGGCAAATAG-GGTGTAGTGATGTGACTAG 565979 v i vv vv v - vv iv v i i C MIRc#SINE/MIR 144 TTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAA 95 chrXptel1M 565980 GAAAAAACAGGTAACAAGCATCTAAGGCCTGATTTGCACTGAGAAGGCAA 566029 ivv v v ii iiv vi v vv i i v iv ------- C MIRc#SINE/MIR 94 GGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAG------- 52 chrXptel1M 566030 AGTCTTTCTGACTCCACAGCCAACAACACTCCATCCAAGGCACCAC 566075 - i - i -- iii iv vv C MIRc#SINE/MIR 51 -GTCTTCCTGACTCCA-AGTC--CAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.91 CpG sites = 19, Kimura (unadjusted) = 42.15 Transitions / transversions = 0.79 (19/24) Gap_init rate = 0.08 (12 / 144), avg. gap size = 1.00 (12 / 12) 190 30.00 3.46 1.76 chrXptel1M 566099 566802 (433198) (AGAGAC)n#Simple_repeat 1 714 (137) m_b340s252i5 14205 chrXptel1M 566099 AGAGACAGACCGAGAGAGAAAAAGAGGGACAAAGAGATAGACACAGAGAC 566148 -- v v i vi v v i v (AGAGAC)n#Sim 1 AGAGACAGA--GACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGAC 48 chrXptel1M 566149 AGACAGACAGACAGAGA-A-AGAGAGAGACAGAGACAGAGATGACAGACA 566196 v v v - - v -v v (AGAGAC)n#Sim 49 AGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGA-CAGAGACA 97 chrXptel1M 566197 GAGAGATAGTGAGAACCAGAAATAGAGACAGTCACA-A-AAAGAAACAGA 566244 v v vv iv i i vv - - v i (AGAGAC)n#Sim 98 GAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGA 147 chrXptel1M 566245 GAGAGAGAAAGAGA-AAAGATAGAAAAAGACAAAGATAAAGAGAGTGAGG 566293 v v - i i i v v v v v vv i (AGAGAC)n#Sim 148 GACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGA 197 chrXptel1M 566294 GAGATACAGACAGAGAAACAGAGACAGAGAGAGATAGAGAAACAGA-AAA 566342 v v v v i v v v i - v (AGAGAC)n#Sim 198 CAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACA 247 chrXptel1M 566343 G-GAGAGAGATAGAGTCAGAGAGTTAGAAAGGTACAGA-A-AAAGGCAGA 566389 - v i v vvv v iv - - i i (AGAGAC)n#Sim 248 GAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGA 297 chrXptel1M 566390 CAATTGGACTGACAGAGAGAGACATACACAAAGAGATCGACTGAG-C-GA 566437 v vvvi -- v v v v i v vv v - - (AGAGAC)n#Sim 298 GACAGAGAC--AGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGA 345 chrXptel1M 566438 GAAAAAAATAGAAAAAGAGA-A-AAACAGGGAGAGGTTGGGAAAGAGGGA 566485 v i i i i v - - i i v ivvvi i v i (AGAGAC)n#Sim 346 GACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGA 395 chrXptel1M 566486 AGGAGAGAGAGACAGAGACAGAG--AGAGATAGAGAAAGAAATAGACACA 566533 vi v -- i v i i v (AGAGAC)n#Sim 396 CAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACA 445 chrXptel1M 566534 GAGACAAAAAGACAGGCA-AGGC-GATAGTAAGACAGATAGAGAGACA-A 566580 i i v v i - i - v vvi v v - (AGAGAC)n#Sim 446 GAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGA 495 chrXptel1M 566581 GACTCATAAAGAAAGATGATGACAGATGGAAAGATAGAGATATAAAGACA 566630 vv v v i v - - -- v v v v i i (AGAGAC)n#Sim 496 GACAGAGACAGAGACA-GA-GACAGA--GACAGAGACAGAGACAGAGACA 541 chrXptel1M 566631 CACAGAGAAAAAGATAGAGAGACAGAGAGAAACACAGTGTGACTAATAAA 566680 v v v i v v v v i v -- v vi v v (AGAGAC)n#Sim 542 GAGACAGAGACAGAGACAGAGACAGAGACAGAGACA--GAGACAGAGACA 589 chrXptel1M 566681 GAGAAACGGACA-AAAAATAGACTGAG--AGAGACAGAGATGTAGATAGA 566727 v vi - i v v v -- iiv i (AGAGAC)n#Sim 590 GAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGA 639 chrXptel1M 566728 GAAACAGAGCA-AGA-A-ATGTAGAGACTGACTGAAAGAAAGAGCAAGGG 566774 v v - - - - vii v vvv i v vv i (AGAGAC)n#Sim 640 GACAGAGA-CAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAG 688 chrXptel1M 566775 ACACAGTCAGAGAGAGAGAGACAGTGAA 566802 v -- v v v v (AGAGAC)n#Sim 689 ACAGAG--ACAGAGACAGAGACAGAGAC 714 Matrix = Unknown Transitions / transversions = 0.46 (53/116) Gap_init rate = 0.05 (36 / 703), avg. gap size = 1.06 (38 / 36) 36 0.00 0.00 0.00 chrXptel1M 566803 566833 (433167) (AC)n#Simple_repeat 1 31 (0) c_b340s251i2 14206 chrXptel1M 566803 ACACACACACACACACACACACACACACACA 566833 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACA 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 190 30.00 3.46 1.76 chrXptel1M 566834 566965 (433035) (AGAGAC)n#Simple_repeat 715 850 (1) m_b340s252i5 14207 chrXptel1M 566834 GAGAGA-AAATAGAGCAAAAGAGAGAG-CA-AAAAAGAGACAGAGGGATA 566880 v - i i vv i v - - i v iv v (AGAGAC)n#Sim 715 GAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGA 764 chrXptel1M 566881 GAGAGATAAAGA-AAAG-TAGAGATACAGATAAAGAGAAAGACAGACAGA 566928 v v v - v -v v v v v v v v v (AGAGAC)n#Sim 765 GACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGA 814 chrXptel1M 566929 CAGAGAAAGAGACAGAAAGAGAGAGACAGAAAGGAGA 566965 v i v v v v - (AGAGAC)n#Sim 815 CAGAGACAGAGACAGAGACAGAGACAGAGACA-GAGA 850 Matrix = Unknown Transitions / transversions = 0.24 (6/25) Gap_init rate = 0.05 (6 / 131), avg. gap size = 1.00 (6 / 6) 157 28.83 2.70 2.38 chrXptel1M 567479 568107 (431893) (ACAGAG)n#Simple_repeat 1 631 (0) m_b340s252i6 14208 chrXptel1M 567479 ACAGAGACAGAGA-A-AGAAAGAGACAGAGAATCAGAGAAACAGAGACAG 567526 - - v - - -- (ACAGAG)n#Sim 1 ACAGAGACAGAGACAGAGACAGAGACAGAG-A-CAGAG--ACAGAGACAG 46 chrXptel1M 567527 AAAGAGAGACAGAGAGAGACAAAGAGAAAGAAAAAGACACAAAGAGATAG 567576 i v v v v v i v v i v v (ACAGAG)n#Sim 47 AGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAG 96 chrXptel1M 567577 AAAAAAAAACACAGAGATGA-AGAGACAGAG--AGAGACAGGTAAAAAGA 567623 v i i v v v v - - -- iv v i (ACAGAG)n#Sim 97 ACAGAGACAGAGACAGA-GACAGAGACAGAGACAGAGACAGAGACAGAGA 145 chrXptel1M 567624 AAGAGATAGACAAAGAGA-A-ATAGAGAGAAAGAGACAGAAAGACAGAGT 567671 v i v v - - v v v -- v (ACAGAG)n#Sim 146 CAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAG--AGACAGAGA 193 chrXptel1M 567672 CAGAGATATACA-AAATA-AGAGAAAAAGAGAAAGACAGAGACAGA-A-A 567717 i v v - i v - v i v i - - (ACAGAG)n#Sim 194 CAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACA 243 chrXptel1M 567718 GACACAGAAAGAGAGACAGGTAAAGACAAAGATAAACAGAAAGGGGGAGG 567767 v i v iv v v v v v v v i iv i (ACAGAG)n#Sim 244 GAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGA 293 chrXptel1M 567768 GAGGGAGGGAAGGAAGGAGAGAGAGGCAGAGGCAGAAACAGAGATAGAGG 567817 vi iv ii vi v i i i i i (ACAGAG)n#Sim 294 GACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGA 343 chrXptel1M 567818 CAGAGACATAGAGAGACTGACAGACAGAGAGCACA-AGGGAGAAAGAGAG 567866 v v -- v v - - iv i v (ACAGAG)n#Sim 344 CAGAGACAGAGACAGA--GACAGAGACAGAG-ACAGAGACAGAGACAGAG 390 chrXptel1M 567867 AATGAGAAAGAGAGAGAGACAGAAAAAACCAAAGAGACAGAAAGACAGAT 567916 vv v v i v ivv v i v v i (ACAGAG)n#Sim 391 ACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGAC 440 chrXptel1M 567917 AGAGGTAGAAAGTGAGAGAAAGTGATAGACAGATGGACA-A-AAAGAGAT 567964 ii i vv v i vv v -- - - v i (ACAGAG)n#Sim 441 AGAGACAGAGACAGAGACAGAGACAGAGACAGA--GACAGAGACAGAGAC 488 chrXptel1M 567965 AGATTGAGAAAGTTATATACAAAAATCA-AGAGCTTGACAGAGACAGA-A 568012 -- v i vi v v i i - - vvvv - (ACAGAG)n#Sim 489 AGA--GACAGAGACAGAGACAGAGA-CAGAGACAGAGACAGAGACAGAGA 535 chrXptel1M 568013 -AGAGACAGAGGCAGAGAGATAGGAAAAGTAAAAGAGAAAAAGAGGTATA 568061 - i v v iv i vv i v i i v iv i (ACAGAG)n#Sim 536 CAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACA 585 chrXptel1M 568062 ATGACACAGACAGTGACAGAGATAGACAAACAGACAGAAATAAAGA 568107 iv v v i v v v i i i (ACAGAG)n#Sim 586 GAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGA 631 Matrix = Unknown Transitions / transversions = 0.62 (55/89) Gap_init rate = 0.05 (31 / 628), avg. gap size = 1.03 (32 / 31) 361 19.99 3.37 1.42 chrXptel1M 568115 568322 (431678) HERVIP10FH#LTR/ERV1 788 999 (4103) m_b340s701i0 14209 chrXptel1M 568115 AGAGAAAGATATATAGAGAGAAAAATAGAGACAGAGAGACGGTGAGACAA 568164 i ivvii i i- - vi v v i HERVIP10FH#LT 788 AGGGAAAGACCAGCAGAGAGGAAAG-AGAGA-AGAGAGAGAGAGAGAGAG 835 chrXptel1M 568165 AGACAGAGAAATAGAGACAGAAAGAGAGAGACAGAGAGAGAGAGACAAAG 568214 iv i v v i i vi HERVIP10FH#LT 836 AGGAAGAGAGAGAGAGAGAAAGAGAGAGAGAGGGAGAGAGAGAGACAAAG 885 chrXptel1M 568215 AGACAG--AGAGAGACAGACAGACAGACAGAAGAAGAGTCAGAGAGACAT 568262 iv -- i v v i v i v v HERVIP10FH#LT 886 AGGGAGTCAAAGAGAGAGAGAGGCAGAGAGAGGAAGAGACAGAGAGACAA 935 chrXptel1M 568263 AAA--GAGTGAGAGACAAAGAGAAAGACAGAAAG---AGGAGAGAAAAGA 568307 i -- v v i i --- i - HERVIP10FH#LT 936 AGAGGGAGTCAGAGAGAGAGAGAGAGACAGAAAGTCAAAGAGAG-AAAGA 984 chrXptel1M 568308 CAAAGAGAGACAGAA 568322 v i i HERVIP10FH#LT 985 AAGAGAGAGATAGAA 999 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 23.54 CpG sites = 23, Kimura (unadjusted) = 23.54 Transitions / transversions = 1.28 (23/18) Gap_init rate = 0.03 (6 / 207), avg. gap size = 1.67 (10 / 6) 268 31.94 1.16 0.63 chrXptel1M 568323 568966 (431034) (AG)n#Simple_repeat 1 650 (0) m_b340s252i7 14210 chrXptel1M 568323 AGACAGAGAGAGAGAAAGACAAAAAGACAGAGAGAGACAGAGAAAGACAG 568372 v i v i i v v i v (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chrXptel1M 568373 AGAAAGAGAGAGAG-GAGAGAGAGGGGGAGGGGGCGACAGAGACACAAAA 568421 i - i i i i v v v v i i (AG)n#Simple_ 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 100 chrXptel1M 568422 AGAAAGAAAGAGAGACTCAGGGAGCAAGAGACAGAGAGAGCAACAGAAAA 568471 i i vvv i vi v vi v i i (AG)n#Simple_ 101 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 150 chrXptel1M 568472 ATAGTGAGACACAGATAGAGATAGAGAAACAGA-ACAGAGTTAGGGAAAT 568520 v v v v v v i v - v vv i i v (AG)n#Simple_ 151 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 200 chrXptel1M 568521 AAACATATAGAGTTAGAGAGATAGAGTGAGAAAAAGAGACCGAGAGATAC 568570 i v v v vv v v i i vv v v (AG)n#Simple_ 201 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 250 chrXptel1M 568571 AGACAGACATCCACTGACACAAACACATTGACAGAAAGTAATTGAGAGCA 568620 v v vvv vv v v i v v vv v i vi vv - (AG)n#Simple_ 251 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG-A 299 chrXptel1M 568621 CAGAGAGAGCAAAAGAAAGAGAGAGAGAGAGGGACAGAGAGACAGAGAAA 568670 v vi i i i v v i (AG)n#Simple_ 300 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 349 chrXptel1M 568671 GAAAGACAGAGATACTAAAAGAGAAAAAGAGGTAGAGAGAGGAACAGAGA 568720 i v v vvi i i i iv ii v (AG)n#Simple_ 350 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 399 chrXptel1M 568721 GAGAGA-AGAGAGAAACAGA-AGAGAGAGAGGTAGAAAGAAACAGAGAGA 568768 - i v - iv i i v (AG)n#Simple_ 400 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 449 chrXptel1M 568769 CACATAGAGACAGAGAGGTAGAAAGAAACAGAGAGACACATAGAGACAGA 568818 v v v v iv i i v v v v v (AG)n#Simple_ 450 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 499 chrXptel1M 568819 GAGACTTAGAGAGACAAAGAG-GAGAGAGTGAGACAGAGAAAGTCAGAGA 568867 vvv v i - v v i vv (AG)n#Simple_ 500 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 549 chrXptel1M 568868 GAGAAAGAG-GAGAGACAGAGAGAGA-AAAAAGAGGGAGGGAGGGAGGGA 568915 i - v - i i i i i i (AG)n#Simple_ 550 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 599 chrXptel1M 568916 GGGAGGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGGGA 568965 i i i (AG)n#Simple_ 600 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 649 chrXptel1M 568966 G 568966 (AG)n#Simple_ 650 G 650 Matrix = Unknown Transitions / transversions = 0.68 (59/87) Gap_init rate = 0.01 (8 / 643), avg. gap size = 1.00 (8 / 8) 268 31.94 1.16 0.63 chrXptel1M 569034 569251 (430749) (AG)n#Simple_repeat 715 933 (0) m_b340s252i8 14211 chrXptel1M 569034 GGAGAGACACAGAGACAGAGAGAGGGAGACTGAGTGAAAAAGCAACACAG 569083 i v v v i vv v i i vi v v (AG)n#Simple_ 715 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 764 chrXptel1M 569084 TGAGAGAGACAGAGAGAAACAGAGAGACAGAAAGAGATAGAAAAAATGTG 569133 v v i v v i v i i iv v (AG)n#Simple_ 765 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 814 chrXptel1M 569134 AGAGATATTGATA-AAAAAGAGATGCAAAGGGAAAGATATATAGA-AAAA 569181 v vv v - i i - - i i i v v v - i i (AG)n#Simple_ 815 AGAGAGAGAGAGAGAGAGAGAGA-G-AGAGAGAGAGAGAGAGAGAGAGAG 862 chrXptel1M 569182 AGATAGAGACAGAAAGAGAAAGAGAGATAGAGAGA-AGAGAGATAGACAA 569230 v v i i v - v v i (AG)n#Simple_ 863 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 912 chrXptel1M 569231 ACACAGAGATAGAAAGACAGA 569251 v v v i v (AG)n#Simple_ 913 AGAGAGAGAGAGAGAGAGAGA 933 Matrix = Unknown Transitions / transversions = 0.66 (21/32) Gap_init rate = 0.02 (5 / 217), avg. gap size = 1.00 (5 / 5) 34 0.00 0.00 0.00 chrXptel1M 569794 569822 (430178) (AC)n#Simple_repeat 1 29 (0) c_b340s251i3 14212 chrXptel1M 569794 ACACACACACACACACACACACACACACA 569822 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACA 29 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 300 20.30 3.91 5.75 chrXptel1M 570221 570450 (429550) HERVIP10FH#LTR/ERV1 771 996 (4106) m_b340s701i1 14213 chrXptel1M 570221 AAGTGG--GGCATAGACAGCTAGAGACACAA-AGAGAGGGAGAGAAAGAG 570267 i -- v i vv i - i- ----- HERVIP10FH#LT 771 AAGCGGCTGGCAGAGGCAGGGAAAGAC-CAGCAGAGAGG-----AAAGAG 814 chrXptel1M 570268 AAATAGAGACAGAGAGAGAAACAGATACAGAGGCAAAGAGACAGAGACAG 570317 i - v i v iv v iv i v v HERVIP10FH#LT 815 AGA-AGAGAGAGAGAGAGAGAGAGGAAGAGAGAGAGAGAGAAAGAGAGAG 863 chrXptel1M 570318 AGAGCAAGAGACAGAGACAAAGAAATAG----AGAGACGGAGAGAAAGAG 570363 vi v iiv ---- vi iv HERVIP10FH#LT 864 AGAGGGAGAGAGAGAGACAAAGAGGGAGTCAAAGAGAGAGAGAGGCAGAG 913 chrXptel1M 570364 AAAGACAGATACAGAGAGACAAAGAGAGA--CAGAGAAAGAGAGCTGTAA 570411 i iv v i -- i ------ HERVIP10FH#LT 914 AGAGGAAGAGACAGAGAGACAAAGAGGGAGTCAGAGAGAGAGAG------ 957 chrXptel1M 570412 AGACACAGCAATATAAAGAGAGAGACAAAGACAGAGACA 570450 v v vvi i v v i HERVIP10FH#LT 958 AGAGACAGAAAGTCAAAGAGAGAAAGAAAGAGAGAGATA 996 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 23.17 CpG sites = 21, Kimura (unadjusted) = 23.76 Transitions / transversions = 0.91 (21/23) Gap_init rate = 0.07 (17 / 229), avg. gap size = 1.29 (22 / 17) 64 33.03 0.43 0.87 chrXptel1M 570452 570683 (429317) (AG)n#Simple_repeat 1 231 (0) m_b340s252i9 14214 chrXptel1M 570452 AGAGAGAAACATAGAGAGACAGCGAGTGGGAGACAAAGAGAAAAAGTGAC 570501 i v v v v v i v i i i v v (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chrXptel1M 570502 AGAGAGACTGACCAAGAGAAAAAGAGATATGCAGAGAGAGATATGGAGAG 570551 vv vvi i i v - - v vi (AG)n#Simple_ 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGA-G-AGAGAGAGAGAGAGAGAG 98 chrXptel1M 570552 CCAAAAAACCAGAGAGTGGCAAAAAGACATAAAGACATAGAGAGAGACAG 570601 vv i i ivv v iv i i v v i v v v (AG)n#Simple_ 99 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 148 chrXptel1M 570602 ACACAGAGAGATAGAAACAGAGAGAGAGAGA-AGAGAGAGATATAGAAAA 570650 v v v i v - v v i i (AG)n#Simple_ 149 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 198 chrXptel1M 570651 AGAATTTGAGAGATAGAGATAAGGAGACAGTGA 570683 ivvv v v ii v v (AG)n#Simple_ 199 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 231 Matrix = Unknown Transitions / transversions = 0.56 (22/39) Gap_init rate = 0.01 (3 / 231), avg. gap size = 1.00 (3 / 3) 12 19.96 5.00 0.00 chrXptel1M 571828 571867 (428133) (AGGAGAG)n#Simple_repeat 1 42 (0) m_b340s252i10 14215 chrXptel1M 571828 AGGAG-GAGAAGGGTTGGGA-AGCAGAGTGGAGAGAGGAGAG 571867 - i i vv i - v v (AGGAGAG)n#Si 1 AGGAGAGAGGAGAGAGGAGAGAGGAGAGAGGAGAGAGGAGAG 42 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 12 26.57 1.96 1.96 chrXptel1M 571852 571902 (428098) (AGGGGAA)n#Simple_repeat 1 51 (0) m_b340s252i11 14216 chrXptel1M 571852 AGTGGAGAGAGGAGAGGCGCCACGTGGCATGGGGGAAGGGGAAA-GGGAA 571900 v i i i - vv v v v v i - (AGGGGAA)n#Si 1 AGGGGAAAGGGGAAAGG-GGAAAGGGGAAAGGGGAAAGGGGAAAGGGGAA 49 chrXptel1M 571901 AG 571902 (AGGGGAA)n#Si 50 AG 51 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.04 (2 / 50), avg. gap size = 1.00 (2 / 2) 250 20.00 4.29 0.00 chrXptel1M 574007 574076 (425924) MER50-int#LTR/ERV1 7104 7176 (29) m_b340s701i2 14217 chrXptel1M 574007 CAACGTCCAT-TCTCAGCAGGAAGTAGTTTCAGAAGA-TGAAATTGCTCC 574054 v i v - v i v - vv vv MER50-int#LTR 7104 CACCGCCCCTCTGTCAGCAGGAAGCAGTTACAGAAGACTGACCTTCGTCC 7153 chrXptel1M 574055 A-TATCCCAAAAGACTTGGGGCC 574076 - v v v i MER50-int#LTR 7154 ATTTTCCCCAAAGAATTGGGGTC 7176 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 23.34 CpG sites = 3, Kimura (unadjusted) = 23.34 Transitions / transversions = 0.27 (3/11) Gap_init rate = 0.04 (3 / 69), avg. gap size = 1.00 (3 / 3) 263 19.99 3.28 1.61 chrXptel1M 574970 575030 (424970) HERVI#LTR/ERV1 6947 7008 (776) m_b340s701i3 14218 chrXptel1M 574970 CCAAG--ACCTGAGTGGACACCGGGGCACTGACCCAATTGGCTATTCCTT 575017 -- iv i - iv v v i i i i HERVI#LTR/ERV 6947 CCAAGTAACTGGAGCGGA-ACTTGCGCTCTAATCCAATTGGCCATCCCTT 6995 chrXptel1M 575018 TTACCCTGGCATT 575030 i HERVI#LTR/ERV 6996 TCACCCTGGCATT 7008 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 21.65 CpG sites = 8, Kimura (unadjusted) = 23.85 Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.03 (2 / 60), avg. gap size = 1.50 (3 / 2) 315 32.26 0.00 0.00 chrXptel1M 575155 575278 (424722) HERVIP10FH#LTR/ERV1 4562 4685 (417) m_b340s701i4 14219 chrXptel1M 575155 TACACCAGAAAAGCAGGGAAGTGAATAACAGAATAATGAGATGCTGCCAG 575204 i i v v vv iv i v ii v iv i i HERVIP10FH#LT 4562 TACACTAGAGATGCTGTTAAAGGAATAGCTGAGCAATTAGGGGCTACTAG 4611 chrXptel1M 575205 CAGAATGGCATGAGAAAATAAGATGACTCTAGAAAGGTTATGGGCAGGAA 575254 vii v i i ii ii v v v vi i HERVIP10FH#LT 4612 CCAGATGGCTTGGGAAAATAGGATAGCCTTAGACATGATATTAGCAGAAA 4661 chrXptel1M 575255 GAGGAGGAATATTTGTTACAATTA 575278 i v vi i ii HERVIP10FH#LT 4662 GAGGAGGAGTTTGCGTCATGATTA 4685 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 42.28 CpG sites = 24, Kimura (unadjusted) = 43.76 Transitions / transversions = 1.50 (24/16) Gap_init rate = 0.00 (0 / 123), avg. gap size = 0.0 (0 / 0) 43 0.00 0.00 0.00 chrXptel1M 575663 575699 (424301) (TG)n#Simple_repeat 1 37 (0) c_b340s251i4 14220 chrXptel1M 575663 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 575699 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 37 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 18 7.71 0.00 0.00 chrXptel1M 578271 578298 (421702) (TCT)n#Simple_repeat 1 28 (0) m_b340s252i12 14221 chrXptel1M 578271 TCTCCTTCTTCTTCTTCTTCTTCTTTTT 578298 i i (TCT)n#Simple 1 TCTTCTTCTTCTTCTTCTTCTTCTTCTT 28 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 1720 34.68 2.39 1.42 chrXptel1M 578319 579365 (420635) HERVP71A#LTR/ERV1 3239 4295 (3295) m_b340s701i5 14222 chrXptel1M 578319 TATTGTAGAACCTGGATTGATGAATATGCATTATTAACTAAGGCTTTAGA 578368 i iviv ivv viv vvi v ii i iv HERVP71A#LTR/ 3239 TACTGTAGGTTATGGATTGACTCATATGCTCAAAAGACAAAGATTCTGTA 3288 chrXptel1M 578369 TACTCA-TTTGTTAGAAGAGAAACCAGATATAGTGCAATGGGATCCAGAA 578417 - -v ii i v vivv vvi i HERVP71A#LTR/ 3289 T-CTCAAGTTACTAGAAGAGGAACCCGATCCCTTGCAATGGTCCCCAGAG 3337 chrXptel1M 578418 GGAGAACAGTT-TTGAACAACTTAATG--GGCATTGAGGTCAGCCCCTGT 578464 i ivv vi-v vi vi v -- vi v vvv v HERVP71A#LTR/ 3338 GAAATTCAGGCAGTGAAAGAGCTAAAGCAGGCCCTCATTACAGCCCCGGT 3387 chrXptel1M 578465 ATT----TTGCCATCTTTAGAAAAGCCTGTTCATTTATATGTAAATACGG 578510 vi ----i v i i vv i i i v --- i HERVP71A#LTR/ 3388 CCTGGCCCTCCCATCTTTAGAGAAACCATTCCATCTGTTTGTAA---CAG 3434 chrXptel1M 578511 TAAAT--GGGT-TGGCTTTAGGAGTATTGGCACAATTAAGGGGAGGGCAG 578557 i i-- i- ii v i ii vi v vivv v HERVP71A#LTR/ 3435 TAGACCAGGGCGTGGCCCTTGGGGTGCTCACTCAAACCTGGGGAGGGAAG 3484 chrXptel1M 578558 TGACACCCAGTAGCCTTT-TGTCAAAAATGTAAGACCCAGTGGCAAAGGG 578606 v i v v v i - v v iv vivv i v vv vvi HERVP71A#LTR/ 3485 AGGCAACCTGTTGCTTTTGTCTCCAAGCTTCTCGATCCTGTCTCTCGGGG 3534 chrXptel1M 578607 ATGGCCTGTTTGTATTCAAGCAGTGGCAGCCACTGCACTTTTGGTAGAAG 578656 i i vv i v i v v v vi i HERVP71A#LTR/ 3535 GTGGCCCGAATGTGTGCAAGCAGTAGCTGCCACAGCCCTGCTGGTAGAGG 3584 chrXptel1M 578657 AAAGTCGGAAGTTAACCTTTGGGGGCAGTTTAATAGTGAGTGTCCCGCAC 578706 i i i v vivii i iii i HERVP71A#LTR/ 3585 AGAGTCGAAAGCTAACCTTTGGCGGGGCCCTAATAGTAAGCACCCCACAC 3634 chrXptel1M 578707 CAAGTTCGATCAATTCTGAATCAAAGGGCCGGGAGGTGGCTAACTGATTC 578756 i iv ivvv vi i ii i i v HERVP71A#LTR/ 3635 CAGGTCAGGAATATATTAAATCAAAAAGCCGGGAGATGGTTAACGGATTC 3684 chrXptel1M 578757 AAGGATTTTAAAATATGAGGCAATCTTACTGGAAAGAGATGATTTGGTTC 578806 vvi i i v v i i iv HERVP71A#LTR/ 3685 TCAGATTCTAAAATATGAAGCCATATTACTAGAAAAAGATGATTTGGTCG 3734 chrXptel1M 578807 TCTCACCAGACCATGACCTTAATCCAGCCACGTTCTTATCTGCTTCCCCT 578856 vv v i ivv vi v vv i -v vvvvvvvv HERVP71A#LTR/ 3735 TAACAACAAATACTTGCCTGAATCCAGCCAGTTTCCTAT-GGAAAGGAGA 3783 chrXptel1M 578857 GGGGAAC-ATGTGTCCCCTGAACATGATGGTCTAAATGTGATTGATTATA 578905 i - v v v vi v v i iv ii i i v v v iv HERVP71A#LTR/ 3784 GGAGAACGAAGAGGCATCAGACCATAACTGCTTAGATATCATAGAATACC 3833 chrXptel1M 578906 AAACTAAGATTAGGGAAGATTTGCAGGAGGCCCCTTTGTTAAAAGGTGCT 578955 i ii ivv ii vvi i i ---ii v v i vv HERVP71A#LTR/ 3834 AAACCAAAGTTAGACCAGACCTTAGGGAAGCTCC---ACTACATGATGGG 3880 chrXptel1M 578956 CAATGGC---TCATAGACAGATCCTCACGAGTAGTTAATGGGAAAAGGAA 579002 vv v --- ii i ii i v v ii vi v i iv HERVP71A#LTR/ 3881 ATAAGGCTGTTTGTGGATGGGTCGTCCCGAGTGATAGATGGCAAGAGACA 3930 chrXptel1M 579003 AAATGGGATATGCTATTGTTGATGGGGAGGA-----CTTGACTGGTTCAA 579047 v - v i ii ii vi ----- i v ivv vvv HERVP71A#LTR/ 3931 TAAT-GGCTATGCTGTCATTGATGGAAATAAACANTCCTTATGTGAGAAA 3979 chrXptel1M 579048 GCTGGAT--CCTTGCGAAAAGAGTGGTCAGCTCAAACTTGTGAATTAAAT 579095 v i -- ----- v iv i i i v HERVP71A#LTR/ 3980 GGTAGATTACCT-----AATGGCTGGTCGGCCCAAACCTGTGAATTATAT 4024 chrXptel1M 579096 GCATTAAATCAAGCCCTAAAATTGCTTGAAGG-AAAGAATGGAACCGTAT 579144 vi v i i ii v -v - v ii HERVP71A#LTR/ 4025 GCTCTTAACCAGGCCCTAAAGCTCCTTGAAGGCCAAGAA-GGCACTATAT 4073 chrXptel1M 579145 ATATGGATTCAAAATATGCCTGGGGAGTGGTTCATGTATTTGGGAAAATA 579194 iv v iv i v iiiv i v HERVP71A#LTR/ 4074 ATACTGATTCCAAATATGCCTATGGGGTGGTACACACTTTTGGAAAAATC 4123 chrXptel1M 579195 TGGG-AGGAAAGGGAATGGTAAATAGTAAAGGTAAGGGATTGGCACACAG 579243 i- iivi vv ii i ii v i i i ii HERVP71A#LTR/ 4124 TGGACAGAGCGGGGCCTAATAAATAGCAGGGGAAAAGAATTGGTACATGG 4173 chrXptel1M 579244 GGCATTGGTCACTGAAATTTTAACCAGTCTTATGTTACCTAAGAATGTTG 579293 v i vvv ii ivv i iv i v vivii v v HERVP71A#LTR/ 4174 GGAACTGGTCAAACAGGTTTTAGAAAGCCTCCTGCTTCCAGCAGAGGTAG 4223 chrXptel1M 579294 CAGTGATTCGTGTGCAGGGTCACCAAAGAGAAGATTCATTTGAGGCAAGG 579343 vi ii i iv v i i i i iii iv vv v i vivi HERVP71A#LTR/ 4224 CCATAGTTCATGTAAATGGCCATCAGAAAGGGAACACTATAGAAGCTGTA 4273 chrXptel1M 579344 GGAAACTGCTTTGCAGATGAGG 579365 v vi i i HERVP71A#LTR/ 4274 GGAAACAGGCTTGCGGATGAAG 4295 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 46.26 CpG sites = 184, Kimura (unadjusted) = 47.52 Transitions / transversions = 1.06 (184/174) Gap_init rate = 0.03 (28 / 1046), avg. gap size = 1.43 (40 / 28) 2617 32.72 3.96 3.30 chrXptel1M 578457 580504 (419496) HERVIP10B3#LTR/ERV1 3538 5598 (2005) m_b340s701i6 14222 chrXptel1M 578457 GCCCCTGT----ATTTTGCCATCTTTAGAAAAGCCTGTTCATTTATATGT 578502 ----ii v ii v vv i ii v v HERVIP10B3#LT 3538 GCCCCTGTTCTAGCTTTGCCCTCCCTAGAACAGCCATTCCACCTTTTTGT 3587 chrXptel1M 578503 AAATACGGTAAAT---GGGTTGGCTTTAGGAGTATTGGCACAATTAAGGG 578549 v i--- i--- v i i i i vi v vv viv HERVIP10B3#LT 3588 CAAC---GTAAACAAGGGGGTAGCCTTAGGGGTACTTACCCAAGAACACG 3634 chrXptel1M 578550 GAGGGCAGTGACACCCAGTAGCCTTT-TGTCAAAAATGTAAGACCCAGTG 578598 v vi i v v i- i viv? i HERVIP10B3#LT 3635 GAGGCCACCGGCAACCCGTAGCCTTCCTATCAAAAATTCTNGACCCAGTA 3684 chrXptel1M 578599 GCAAAGGGATGGCCTGTTTGTATTCAAGCAGTGGCAGCCACTGCACTTTT 578648 i vviv i vv i v v i i v i vi vi HERVIP10B3#LT 3685 ACCCGTGGATGGCCCGAATGTGTTCAATCCGTAGCGGCAACCGCCTTGCT 3734 chrXptel1M 578649 GGTAGAAGAAAGTCGGAAGTTAACCTTTGGGGGCAGTTTAATAGTGAGTG 578698 iii iv i i? v iii vi v i ii HERVIP10B3#LT 3735 AACAGAAGAAAGCAGAAAANTAACCTTTGGGGGAAACCTCGTCGTAAGCA 3784 chrXptel1M 578699 TCCCGCACCAAGTTCGATCAATTCTGAATCAAAGGGCCGGGAGGTGGCTA 578748 iv v i i iv v v i ? i i v i v HERVIP10B3#LT 3785 CGCCTCATCAGGTCAGAACTATCCTNAATCAGAAGGCAGGAAGGTGGCTT 3834 chrXptel1M 578749 ACTGATTCAAGGATTTTAAAATATGAGGCAATCTTACTGGAAAGAGATGA 578798 i i i i v i ii i HERVIP10B3#LT 3835 ACTGACTCAAGAATTTTAAAGTATGAAGCTATCCTGTTAGAAAGAGATGA 3884 chrXptel1M 578799 TTTGGTTCTCTCACCA--GACCATGACCTTAATCCAGCCACGTTCTTATC 578846 ii-- v v -- iv vvv i ? ii v i v HERVIP10B3#LT 3885 TTTAA--CACTAACCACTGATAATTCACTTAACCCNGCTGCTTTCCTAAC 3932 chrXptel1M 578847 TGC---TTC---CCCTGGGGAACATGTGTCCCCTGAACATGATGGTCTAA 578890 v v--- i --- v ii --------- i i vv i i HERVIP10B3#LT 3933 AGGAAATCCAAACCCAGAAGAA---------CCTGAGCATAAATGTTTAG 3973 chrXptel1M 578891 ATGTGATTGATTATAAAACTAAGATTAGGGAAGATTTGCAGGAGGCCCCT 578940 v i i i v ? ? ii ivv? iviv i HERVIP10B3#LT 3974 ATCTAATCGGTTATCANACNAAAGTTAGACCNGATTTAAGCGAGACCCCT 4023 chrXptel1M 578941 TTGTTAAAAGGTGC-TCAATGGCTCATAGACAGATCCTCACGAGTAGTTA 578989 -ii v v -? vivvi i ii v i v i i i HERVIP10B3#LT 4024 TT-CCAAACGGGGCGNCACCTCTTTATAGATGGCTCTTCCCGGGTAATTG 4072 chrXptel1M 578990 ATGGGAAAAGGAAAAATGGGATATGCTATTGTTGATGGGGAGGACTTGAC 579039 v i v v i - iv ?i v ? ?iv i vi HERVIP10B3#LT 4073 AAGGAAAAAGGCATAACGGG-TACTCNGTAGTNGATGGGGANACCCTCGC 4121 chrXptel1M 579040 TG--GTTCAAGCTGGATCCTTGCGAAAAGAGTGGTCAGCTCAAACTTGTG 579087 v -- vv iv v vvvi v vi v v i v HERVIP10B3#LT 4122 AGAAGTAGAGTCAGGAAGACTGCCAAATAACTGGTCCGCCCAAACATGTG 4171 chrXptel1M 579088 AATTAAATGCATTAAATCAAGCCCTAAAATTGCTTGAAGGAAAGAATGGA 579137 i ivv i ?v vv iivv i v i HERVIP10B3#LT 4172 AACTGTTTGCATTAAATCAAGCCTTAAAATNCCTGCAAAACCAGGAAGGG 4221 chrXptel1M 579138 ACCGTATATATGGATTCAAAATATGCCTGGGGAGTGGTTCATGTATTTGG 579187 ii v iv i v i vv i i iiiv HERVIP10B3#LT 4222 ACTATTTATACTGACTCCAAGTATGCCTTCGGAGTAGTCCACACCTTTGG 4271 chrXptel1M 579188 GAAAATATGGGAGGAAAG-GGAATGGTAAATAGTAAAGGTAAGGGATTGG 579236 i v ivv v - vv vi v iv i ivi HERVIP10B3#LT 4272 AAAAATTTGGACTGAACGAGGCCTCATTAATAGTAAAGGCCAAGACCTGG 4321 chrXptel1M 579237 CACACAGGGCATTGGTCACTGAAATTTTAACCAGTCTTATGTTACC-TAA 579285 iv ii v ii ? i?v i v iv? ii ?vv i i -v HERVIP10B3#LT 4322 TCCACAAAGAATTAATNATNCAAGTATTAGANAACCTNCAGCTGCCAGAA 4371 chrXptel1M 579286 GAATGTTGCAGTGATTCGTGTGCAGGGTCACCAAAGAGAA-GATTCATTT 579334 -i v ? vi i i v vi v - -vv? v HERVIP10B3#LT 4372 GAA-ATAGCNGTTGTCCATGTCCCAGGACACCAAA-AGAACCCNTCTTTT 4419 chrXptel1M 579335 GAGGCAAGGGGAAACTGCTTTGCAGATGAGGAGGCGAA--AAG--G--TC 579378 iivvv ivi i ? ? v iivi v -- -- -- HERVIP10B3#LT 4420 GAAAGCCGGGGAAATAACCTNGCNGATCAAATAGCCAAGCAAGCTGCCTC 4469 chrXptel1M 579379 TGGAGAAGAGGAATCTAAGTATGGAGGAGATGGAGCTAA-TTCTGGCATT 579427 vvvv vii i-- v -------- vv v -ii v iv HERVIP10B3#LT 4470 TTCCCAAGAGGCGCCC--GTTT--------TCCACCTAACCCCTTGTCTT 4509 chrXptel1M 579428 TCTGCCTCAGATGC---CTCCACTTTCCCTTACCCCAGAAGAGAACCAGG 579474 i iv ii v --- i ii i --- ? - v --- i HERVIP10B3#LT 4510 CCCCCTCCAGCTGCAATCCCCATCTTCTC---CCNC-GCAG---ACCAAG 4552 chrXptel1M 579475 AAATCC---AAAGCCTTGGTGCTCAGGAGGATCAAGAGGGGCACTGGCTC 579521 vv --- ivv v v v ii i v iv v v v HERVIP10B3#LT 4553 AAAAACTAAAAAAAATAGGAGCTAAGGAAAACCCAGAGGGAAAGTGGGTA 4602 chrXptel1M 579522 CTCCCTAACGGCAGAGAGGTGCTGACCACAGCGGGTATGGGACATGTGCT 579571 i v vi v v i ii i v v v vvvi i iv vi i HERVIP10B3#LT 4603 TTACCAGACCGAAGGGAAATGTTGTCCAAACCCCTCATGAGGGAAATACT 4652 chrXptel1M 579572 CCCACATTTACATCAGGGCAGTCCTTGGTGTGGCCAAGACCTGTGTGACG 579621 vi ? vi ? i v v vi v ?vvi viv i HERVIP10B3#LT 4653 GTCNCAGCTNCATCAAGGAACTCACTGGGGNCCTCAAGCTATGTGTGATG 4702 chrXptel1M 579622 TGGTGCTGACCAAGTTTGTG---GCACTGGTTTGTACACAATAGC-AGGC 579667 ii v -- vi i i --- i iv vv ? i vv ? - HERVIP10B3#LT 4703 CAGTCCT--CAGAGTCTATGGGTGTATAGGAATNTATACCCTNGCNAGGC 4750 chrXptel1M 579668 AACTGGCCAGCGGGTGTCC--TGTGAAG-AGGACGAATAGAGC-AGCCC- 579712 v v viiii v i?i-- v - ii v - - i - HERVIP10B3#LT 4751 AAGTTGCGGATAGTTGCNTAGTGTGCAGAAAAACTAATA-AGCAAACCCT 4799 chrXptel1M 579713 -----AGTGACAAGTCCAGAAAGGAGGAAGGCCCCCTGGTATCAGGCCTT 579757 ----- i? --v v iii i i --- vv - v v HERVIP10B3#LT 4800 AAAGAAGCNAC--CTCCCGGGGGAAGAAA---CCCAGGGT-TAAGGCCGT 4843 chrXptel1M 579758 TCCAAAGCATACAGGTGGACTTTACTGAACTGCCACTAGTGTGGTGTCTC 579807 ii v i v vi i v v i i iv vi i ? HERVIP10B3#LT 4844 TCCAAAGTGTCCAAGTTGACTACACCGAAATGCCCCCAATAGGCCGCCTN 4893 chrXptel1M 579808 AAATACCTGTT-GTCTTAGTGGACCATCTGAGCTCA-TGAGTTGAGGCCT 579855 i ii ii - vv i i v - i - i v i v HERVIP10B3#LT 4894 AAGTATTTACTAGTAATAGTAGACCACCTCA-CCCACTGGGTAGAAGCCA 4942 chrXptel1M 579856 TCCCCCTTGCCCGGGCAACTGCCTCGGCA--GCCGTAAAAGTCCTCCTTG 579903 i iv vv v ? -- i i -- iv v iv -v HERVIP10B3#LT 4943 TCCCCTTCCCAAGCGCAACNGC--CAGTAATGTAGTCAAAGCACT-GTTG 4989 chrXptel1M 579904 CGCATATATCATTCCAGGGTATGGGATGGTGGAGCAGGTAGATTCAGACC 579953 - v ? v vi v iv ii i iv vi v v HERVIP10B3#LT 4990 -GAANATATCATACCCAGGTTTGGACTAATAGAAAACATTGATTCAGACA 5038 chrXptel1M 579954 AAGGCACCCATTTCACAGCTAAGATCCTC--TGATCTGTGGCCGTGCTCT 580001 v v i v vv vi v i--v iv i- v iv v HERVIP10B3#LT 5039 ATGGGACCCACTTCACTGCACACGTCATTAAGGGGCTA-GCCCAAGCACT 5087 chrXptel1M 580002 AGA-----------AATATCATACCCCATGGCATCTGCCCTCATCAGGTA 580040 ----------- i v i ii v HERVIP10B3#LT 5088 AGANATAAAATGGGAATACCATACCCCCTGGCACCCACCCTCATCAGGGA 5137 chrXptel1M 580041 AAGTGGAAAGGATGGATAAGG----AAATTAAACAG--TAACTAAATTGG 580084 i i i i v i---- -- vi-- i ii HERVIP10B3#LT 5138 GAGTAGAAAGAATGAATCAGACTCTAAA--AAACCACCTAACCAAATTAA 5185 chrXptel1M 580085 -CT--GAGACACAATTGCCCTGGACCAAGTGCCTTCCTCTTGCCTTATTA 580131 - -- i v ii i v ? i iv ii HERVIP10B3#LT 5186 TCTTAGAAACCCGGTTACCATGGACNAAATGCCTTCCCATTGCCTTGCTA 5235 chrXptel1M 580132 AG-ATTAGAATAAAACCCCAAAGGGATGTGGGATTATCACTTTATGAATT 580180 - iv ivivv i ii ii v vi v i v HERVIP10B3#LT 5236 AGAATCCGAACTGCCCCTCGGAAAGATGTCGGCCTATCCCCTTATGAAAT 5285 chrXptel1M 580181 ATTGTATGGTCACCCTTATCCAAAAGGGATTCAAAATTCTTCCTTGGATC 580230 ii ? vivv i -----? i -v v v vv ? --- HERVIP10B3#LT 5286 GCTNTATGGGTTGCCTTATCTA-----NACTC-CACTACTGACNT---TC 5326 chrXptel1M 580231 CAATATTTGAGACCAAGGATTTGTTTTTAAGGAA--ATATGTCAGGTCTT 580278 v ii i v i iv i v ii -- iiiv v HERVIP10B3#LT 5327 CTACGTTTGAAACAAAAGATCAGTTTCTCAAAAACTATATACTTGGTCTG 5376 chrXptel1M 580279 TACTGTAACATCTGAATACTTTACAATTGAAAGGGCTTATTGCTCACACT 580328 vi vi v v -vv v i i vi i -? v iv v v v ? HERVIP10B3#LT 5377 TCTTCCACCTTCT-CCTCCCTCAGGACT-NAAGGCCTCCTAGCACAGACN 5424 chrXptel1M 580329 CTTCCCTTAGGATTCACAGTGCATAAGTTCTAGCCTGGAGACTGGGGCCT 580378 iv i v i v ? iv iiv i i iiiv v HERVIP10B3#LT 5425 CCACCCCTCGAATTCCCAGTNCACCAACACCAGCCCGGAGATCACGTCCT 5474 chrXptel1M 580379 GGTTTGGACGTGGAAGGAGGACAAGC-CGACCCTGAGCTGGGAAGGATTG 580427 vi ivii vv i iv - v i -v iiv HERVIP10B3#LT 5475 CATCAAAAGTTGGAAAGAGGGAAAGCTCGAACCCG-CCTGGGAAGGACCT 5523 chrXptel1M 580428 TTCCAGATCCTGTTGACTTCAGATACGGCGATAC--ACAGCAAAGAGAGA 580475 v vii v vi i ?v v v ? ii v -- ? ----v i HERVIP10B3#LT 5524 TACCTAGTGCTCCTAACNACTGAGACNGCAGTCCGAACNGC----CGAAA 5569 chrXptel1M 580476 GAGGTTGGACACATCACACTGGAGTCAAA 580504 i v v iv HERVIP10B3#LT 5570 AAGGATGGACCCATCACACCCGAGTCAAA 5598 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.17 CpG sites = 336, Kimura (unadjusted) = 45.12 Transitions / transversions = 1.08 (336/312) Gap_init rate = 0.05 (105 / 2047), avg. gap size = 1.42 (149 / 105) 14 12.39 5.41 2.63 chrXptel1M 581240 581276 (418724) (ATGT)n#Simple_repeat 1 38 (0) m_b340s252i13 14223 chrXptel1M 581240 ATTTATGTATGTATGTA-GTATAAATGTA-GTCATGCAT 581276 v - iv - - i (ATGT)n#Simpl 1 ATGTATGTATGTATGTATGTATGTATGTATGT-ATGTAT 38 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.08 (3 / 36), avg. gap size = 1.00 (3 / 3) 726 32.73 3.07 2.84 chrXptel1M 581772 582227 (417773) HERVH48#LTR/ERV1 5847 6303 (351) m_b340s701i7 14222 chrXptel1M 581772 TATATGATAATCTAAAAAGAGAAGAACAAGGCTTA--GATTGTTCCCTAA 581819 i v i i vv -- i v v----- i HERVH48#LTR/E 5847 TATATGATAACCTAAACAGAGAAAAACGATCCTTAAAGGTAGG-----AG 5891 chrXptel1M 581820 CTAGCATAGATACTTCTCTGACTCAAACAGGTGATGCTAATGGATGGGGA 581869 vv -i i ?? v? ----i?????? i?????i ??i -i i ii HERVH48#LTR/E 5892 GAAGC-CAAANNCGNC----GNNNNNNCGNNNNNCGNNGATGG-CGAGAG 5935 chrXptel1M 581870 AATACATGCCCCCCAGAAAGAATCATCAAAGGATATGGGCCAGCCACATG 581919 i iiv v i iv v i i viv i v v v HERVH48#LTR/E 5936 GACGAATGGCCTCCGCAACGGATCATCGAATATTACGGTCCTGCCACTTG 5985 chrXptel1M 581920 GGCTCAGGATGAAAGCTGGGGGTATAGGACCCTAATATATATATATTAAA 581969 v ivvvv v v v i i--i ii HERVH48#LTR/E 5986 GGCTGAGGATGGTTCATGGGGTTATCGCACTCC--CATATATATGCTAAA 6033 chrXptel1M 581970 TAGGCTAATTAGACTACAAGCAGTTCTGGAGATAA------------CTG 582007 iv i v i ------------ i HERVH48#LTR/E 6034 TAGAATAATTAGACTACAGGCTGTTCTAGAGATAATCACTAACCAAACCG 6083 chrXptel1M 582008 TTCAAGCTCTTGATTTGCTAGCTGATCAAGCCACTCAAACACAAGAAGCT 582057 iiiv i v vv v vv v vvv vi ii iv vi v HERVH48#LTR/E 6084 CCTCAGCCCTGGAAATGCTCGCGCAACAACAAAACCAAATGCGCGCGGCA 6133 chrXptel1M 582058 GTTTAACAGCATCGACTAGGCTTAGATTATTTGCTAGCAGAGGAAGGAGG 582107 i v iv iv i vvi i i ii i i v HERVH48#LTR/E 6134 ATTTATCAAAACAGGCTAGCACTAGACTACTTATTAGCAGAAGAGGGTGG 6183 chrXptel1M 582108 GGTCTGTGGAAAATTAAATTTGTCCACTTGTTGCATGCAAATTGATGATA 582157 v i v v v v i iv vv v v i HERVH48#LTR/E 6184 GGTCTGTGGTAAGTTTAATATCTCCAATTGCTGTCTTAACATAGACGATA 6233 chrXptel1M 582158 ATGGGCGAGTGGTAAAAGAAATTACAAAAGGCATTCGCAGAATAGTTCAT 582207 i ivi i vvv ii vvv ii iv v i i ii HERVH48#LTR/E 6234 ACGGAAAAGCGGTTCTAGAAATCGCTTCAAACATCAGAAAAGTAGCCCAT 6283 chrXptel1M 582208 GTGCCTGTACAGGAGTGGAA 582227 i v v iivv HERVH48#LTR/E 6284 GTACCAGTCCAAACCTGGAA 6303 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.50 CpG sites = 74, Kimura (unadjusted) = 46.07 Transitions / transversions = 1.04 (74/71) Gap_init rate = 0.03 (15 / 455), avg. gap size = 1.80 (27 / 15) 927 30.74 3.43 0.56 chrXptel1M 581870 582219 (417781) HERV1_I#LTR/ERV1 8127 8486 (315) m_b340s701i8 14222 chrXptel1M 581870 AATACATGCCCCCCAGAAAGAATCATCAAAGGATATGGGCCAGCCACATG 581919 iv v i v i viv i ? HERV1_I#LTR/E 8127 AATGAATGGCCTCCTGAAAGAATTATCAAATACTATGGGCCAGCTACNTG 8176 chrXptel1M 581920 GGCTCAGGATGAAAGCTGGGGGTATAGGACCCTAATATATATATATTAAA 581969 ? i iivvv ? iv v i i-- v i i HERV1_I#LTR/E 8177 GGCNCAAGATGGGTCATGGGGNTACCGTACTCC--TATTTACATGTTAAA 8224 chrXptel1M 581970 TAGGCTAATTAGACTACAAGCAGTTCTGGAGAT------------AACTG 582007 iv iv v v i i v i i ------------ v HERV1_I#LTR/E 8225 CCGAATCATAAGATTGCAAGCAGTACTAGAAATCATAGTCAATGAAACAG 8274 chrXptel1M 582008 TTCAAGCTCTTGATTTGCTAGCTGATCAAGCCACTCAAACACAAGAAGCT 582057 ii i ii v iivv i ? i i iivi v i HERV1_I#LTR/E 8275 CCCGAGCCTTGGATTTGCTAGCCATACAGGCNACCCAGATGAGAGATGCC 8324 chrXptel1M 582058 GTTTAACAGCATCGACTAGGCTTAGATTATTTGCTAGCAGAGGAAGGAGG 582107 i v v iv v i vv i i v vvvi HERV1_I#LTR/E 8325 ATATATCAAAATAGGCTAGCATTAGACTATCTCCTAGCCTCAGAAGGAGG 8374 chrXptel1M 582108 GGTCTGTGGAAAATTAAATTTGTCCACTTGTTGCATGCAAATTGATGATA 582157 i i ? i v v ? vi i v i i i HERV1_I#LTR/E 8375 AGTTTGTGGNAAACTTAATTTGACNAACTGCTGCTTACAAATCGATGACA 8424 chrXptel1M 582158 ATGGGCGAGTGGTAAAAGAAATTACAAAAGGCATTCGCAGAATAGTTCAT 582207 iv iv v vi i vivvi v v v iiv ii HERV1_I#LTR/E 8425 ATGGAAGAGCTGTCATGGAAATCACTGCCAGGATGCGGAAGTTAGCCCAT 8474 chrXptel1M 582208 GTGCCTGTACAG 582219 v v v HERV1_I#LTR/E 8475 GTCCCGGTCCAG 8486 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.30 CpG sites = 57, Kimura (unadjusted) = 41.30 Transitions / transversions = 1.14 (57/50) Gap_init rate = 0.01 (3 / 349), avg. gap size = 4.67 (14 / 3) 202 25.49 1.96 0.00 chrXptel1M 583084 583134 (416866) L2a_3end#LINE/L2 373 424 (93) m_b340s601i4 14224 chrXptel1M 583084 TTTCCTGTTACTTTCCCCTC-CTAAAATGGAAACTCCTTTAAGGCAGGGA 583132 vi ivv i i - i v i v v i L2a_3end#LINE 373 TTTATTGTCTGTCTCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGA 422 chrXptel1M 583133 CT 583134 L2a_3end#LINE 423 CT 424 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.60 CpG sites = 7, Kimura (unadjusted) = 31.60 Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.02 (1 / 50), avg. gap size = 1.00 (1 / 1) 237 25.63 0.00 9.52 chrXptel1M 583169 583237 (416763) LTR71A#LTR/ERV1 256 318 (141) m_b340s502i0 14225 chrXptel1M 583169 TGTAACTTCCGTAACACCCAATTAATGTGGAATCAGGGGAGGGACTTGTG 583218 i- i ii i i ii v iii i LTR71A#LTR/ER 256 TGTAACC-CCATAGTACTCGACCAATGAGGAACTGGGGGAGGGACTTGCG 304 chrXptel1M 583219 CTTCAGGATAGGAAATAAA 583237 i----- v i LTR71A#LTR/ER 305 T-----GCTAGGAGATAAA 318 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 28.79 CpG sites = 14, Kimura (unadjusted) = 33.97 Transitions / transversions = 7.00 (14/2) Gap_init rate = 0.09 (6 / 68), avg. gap size = 1.00 (6 / 6) 14 32.91 5.81 0.00 chrXptel1M 584580 584665 (415335) (GAA)n#Simple_repeat 1 91 (0) m_b340s252i14 14226 chrXptel1M 584580 GAAGAAGGAGGGGAGGAAG-AGAAGGGGAA-AGGGGGTAG-GGAATGAGA 584626 i ii i - ii - i ii v -i vi (GAA)n#Simple 1 GAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA 50 chrXptel1M 584627 GTAAGAA-AAAAAAAAAAAGAAGAAGCA-AACAACAAAAAG 584665 iv - i i i v - v v i (GAA)n#Simple 51 AGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAG 91 Matrix = Unknown Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.06 (5 / 85), avg. gap size = 1.00 (5 / 5) 17 22.79 0.00 0.00 chrXptel1M 584629 584664 (415336) (A)n#Simple_repeat 1 36 (0) m_b340s252i15 14227 chrXptel1M 584629 AAGAAAAAAAAAAAAAGAAGAAGCAAACAACAAAAA 584664 i i i iv v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 36 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 1491 26.25 3.28 4.23 chrXptel1M 584926 585474 (414526) C L1ME5_3end#LINE/L1 (391) 550 7 m_b340s551i4 14228 chrXptel1M 584926 AATATTCCATAA----CATTCACATACATAATTTATTCAGCCATTCTCCA 584971 i i ii---- i -i -- iii v i v C L1ME5_3end#LI 550 AGTACTCCATGGTGTGCATCCAC-CACAT--TTTACCTATCCACTCTCCC 504 chrXptel1M 584972 ACTGATGGGCATCCACTCAATTTCCAGTTTCTAGCCACTACAAAAAGGGC 585021 v i i vviviii ii i iv i v iv C L1ME5_3end#LI 503 AGTGATGGACACCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGC 454 chrXptel1M 585022 TGCCACAAACATTCTTGCACATAAAGGTCCCTTTC----CCTTCTTTAGT 585067 v ii i i i ---- i v---- viv v v C L1ME5_3end#LI 453 TGCAATGAACATCCTCGTACAT----GTCCCCTTATGGACCTGTGTGAGA 408 chrXptel1M 585068 ATCTTCTTGGGGTATAAGCCCAGTAGAGACACTGCTGGATCAAAGGGTAT 585117 i ii i vi v v iv i i v C L1ME5_3end#LI 407 ATTTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTAT 358 chrXptel1M 585118 GCACAGTTTGATAACTT--TTTGGGCA--TAATTCCAGATTGCTCTCCAG 585163 --- --- - -- ivi -- v v C L1ME5_3end#LI 357 GC---GT---ATA-CTTAATTTGACTAAGTACTGCCAGATTGCTCTCCAG 315 chrXptel1M 585164 AATGGTTGGAT--GTTATCACAGTTCCACCAGTAATGCATCAGTGTCCCT 585211 i v i-- i--i v i i i v v i C L1ME5_3end#LI 314 AATGGCTGCACCAGTC--TACACTCCCACCAGCAGTGCATGAGGGTTCCT 267 chrXptel1M 585212 GTTTTCCCACATCCCCTCTAACATTCATCATTATTTTTTTTCCTGTCATC 585261 i ? i i v i i iiv iivvi i i-- i C L1ME5_3end#LI 266 ATNTCCCCACATCCTCGCCAACACTTGGCATTATCCAGCTTTCTA--ATT 219 chrXptel1M 585262 TTAGCCAATCTGACAGGTGTGTAGTGGTATCTCAAAGTTGTTTTAATTTG 585311 v i i i iv i vv C L1ME5_3end#LI 218 TTTGCCAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTG 169 chrXptel1M 585312 CATTTCTCTAATTAATAATGATTTAGAGTATGTTTTCATATGACTAGAAA 585361 i v v v i v i - v vv C L1ME5_3end#LI 168 CATTTCTCTGATTACTAATGAGTTTGAGCATCTCTTCATATG-CTTGTTA 120 chrXptel1M 585362 TGGCTTTCA--TTTCTTCATTTGAAAATTGTCTGTTCATATCCTTTGACC 585409 - v i-- i v i v i v C L1ME5_3end#LI 119 -GCCTTTCGGGTTTCCTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCC 71 chrXptel1M 585410 ACTTATCAAATTGGAG--AATGGCTTGAATTCTTATAAATTTGAGTCAAT 585457 i v -v i --?vi v v-- i vi vivv i C L1ME5_3end#LI 70 ATTTTTC-TATTGGGGTTNCCGTCTTT--TTCTTGTTGATTTGCAGGAGT 24 chrXptel1M 585458 TCTTTATATATTTTAAA 585474 i i i i C L1ME5_3end#LI 23 TCCTTGTATATTCTAGA 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.40 CpG sites = 83, Kimura (unadjusted) = 33.28 Transitions / transversions = 1.51 (83/55) Gap_init rate = 0.05 (30 / 548), avg. gap size = 1.37 (41 / 30) 2626 30.43 5.50 2.31 chrXptel1M 585330 587384 (412616) C L1M5_orf2#LINE/L1 (0) 3294 1176 m_b340s551i5 14228 chrXptel1M 585330 TGATTTAGAGTATGTTTTCATATGACTAGAAATGGC---TTTCATTTCTT 585376 ?v v i v i vi v--- --- v? v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTAT---TGGCCATTTGNATATCTT 3248 chrXptel1M 585377 CATTTGAAAATTGTCTGTTCATATCCTTTGACCACTTATCAAATTGGA-- 585424 v vi v vi i v i - i?v i-- C L1M5_orf2#LIN 3247 CTTTTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTT-TTNTATTGGGTT 3199 chrXptel1M 585425 GAATGGCTTGAATTCTTATAAATTTGAGTCAATTCTTTATATATTTTAAA 585474 vv v v-- ? vi ? vivv i i ii C L1M5_orf2#LIN 3198 GTTTGTCTTT--TTNTTATTGANTTGTAGGAGTTCTTTATATATTCTGGA 3151 chrXptel1M 585475 AATAAGGTCTTTATCACCCTTACATGT-----AAACATTTT-TCCCAGCT 585518 v ii vi i vv-- i ----- i - ?ii C L1M5_orf2#LIN 3150 TACGAGTCCTTTGTCAGA--TATATGTNTTGCAAATATTTTCTCCCANTC 3103 chrXptel1M 585519 TTCTGCTTCCCTTCTAATCTTGGCTGCATTGGGGTTTTGTTTTATAAA-- 585566 viv v i v i -- -i vi v i -- v ?i i-- C L1M5_orf2#LIN 3102 TGTGGCTTGCCTTTTCATTTT--CT-TAACGGTGTCTT--TTGANGAGCA 3058 chrXptel1M 585567 -AACTTTTTAATTC-AATATAATCAAAATTATCAATTTTGCATTTTAT-- 585612 - v i-i i? i v v viv -- C L1M5_orf2#LIN 3057 GAAGTTTTTAATTTTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGG 3008 chrXptel1M 585613 --AATATTCTCTA-GTTCTTTTTTAGCCACAAATTCCTTCCTTTTTCACA 585659 --?i ii i i i- i v v ---- iii v v?ii - C L1M5_orf2#LIN 3007 TTNGTGCTTTTTGTGTCCTGTTTAAG----AAATCTTTGCCTANCCCA-A 2963 chrXptel1M 585660 GATCTGAAAGGTAGACTATCCTTTGTT--CTTCTA--ATTTGCTTATAAT 585705 i vvi i --i v v -- -- v -- i C L1M5_orf2#LIN 2962 GGTCACGAAGATA--TTCTCCTATGTTTTCTTCTAGAAGTT--TTATAGT 2917 chrXptel1M 585706 ATCTATCACTTTTTATGTCTAAATC-ATGAACTCATTTTGATCTTATTCT 585754 - i ? --- ii i ii - v - i ? vi v i C L1M5_orf2#LIN 2916 -TTTANC---TTTTACATTTAGGTCTATGATC-CATCTNGAATTAATTTT 2872 chrXptel1M 585755 GATATAGGGTGTTAGGTGTTATTCAATGCTTAATTTTTGCCATACTATTT 585804 vi i v v ivviv i v?i i v v iviv v C L1M5_orf2#LIN 2871 TGTGTATGGTGTGAGGTAGGGGTCGAGNTTCATTTTTTTCCATATGGATA 2822 chrXptel1M 585805 TCCAATTTTTCCAGCAATTTTTGTCAAAAAGTAAGTTCTTATCCCAGAAG 585854 v viv ii vvvi i vi ---- C L1M5_orf2#LIN 2821 TCCAATTGTTCCAGCACCATTTGTTGAAAAGACTATCCTTTCCCCA---- 2776 chrXptel1M 585855 CTGGAGT-CTTT---AAGTTTATCAAACACTAGATTACTATA-AT-CATT 585898 i v - ? --- vv i v ii i? v? i - -ii v C L1M5_orf2#LIN 2775 CTGAATTGCNTTGGCACCTTTGTCAAAAATCAANTGNCCATATATGTGTG 2726 chrXptel1M 585899 GAT-TATTTT--GTCTTATGACCCTAACCCATTGCACTGATCTACTACTT 585945 i - i-- v ----- i vi ii v i i vv i C L1M5_orf2#LIN 2725 GGTCTATTTCTGGACT-----CTCTATTCTGTTCCATTGATCTATTTGTC 2681 chrXptel1M 585946 CATTTCT----TAGTACCAAATCATTTTGATGACCTCTGCTTTATAATAT 585991 i iii ----i i v iii i v iviv - C L1M5_orf2#LIN 2680 TATCCTTACGCCAATACCACACTGTCTTGATTACTGTAGCTTTATAATA- 2632 chrXptel1M 585992 AGT-TTGAGATCTGGTAC----AGTCTTCA---TTTGCATTTTTCTAATT 586033 - ? ? v---- i v--- -- i vv C L1M5_orf2#LIN 2631 AGTCTTGANATCNGGTAGTGTAAGTCCTCCAACTTTG--TTCTTCTTTTT 2584 chrXptel1M 586034 ---AATTTTCTTGAA-ATTCTTGACCTTTTGTTCTTTTAAATGAATTT-- 586077 ---i v i iv- ? ii i ivi ii v i -- C L1M5_orf2#LIN 2583 CAAGATTGTTTTGGCTATTCTNGGTCCTTTGCATTTCCATATAAATTTTA 2534 chrXptel1M 586078 --ATT--TTTTTCTAGCTCCATAAAGTAATATTTTAGAAGTTTGATTGGT 586123 -- i--i v v vi i i iv iv vi i i v v C L1M5_orf2#LIN 2533 GAATCAGCTTGTCAATTTCTACAAAAAAACCTGCTGGGATTTTGATTGGG 2484 chrXptel1M 586124 ATGGCACTAAATAAGTAGATTAATTTTCATAGAATTATCATTTTTATTAT 586173 v i i vvi i vviv iv i ? iv C L1M5_orf2#LIN 2483 ATTGCATTGAATCTATAGATCAATTTGGGGAGAATTGACATCTTNACAAT 2434 chrXptel1M 586174 ATTAGTTCAGCCTACCCGTGAGCACTTAATATTCTTCCAATTGTTTAGAT 586223 iiv vv v i i i ivvv iii v i i C L1M5_orf2#LIN 2433 ATTGAGTCTTCCAATCCATGAACATGGTATATCTCTCCATTTATTTAGGT 2384 chrXptel1M 586224 GTGATTTTATTGTTTGTAA-AGCACTTTGTAATTGTGTTCA---TATAGT 586269 v vv v vi ivi i- iiii i --- --- ? v C L1M5_orf2#LIN 2383 CTTCTTTAATTTCTCTCAGCAATGTTTTGTAGTT---TTCAGTGTANAGG 2337 chrXptel1M 586270 CCCTGTCTTTGTCTTGGCAGGTAGACTCTCAAATATTTTATATTATCTAC 586319 i i iviv ? i vi i vv i ii i ? i v i iv C L1M5_orf2#LIN 2336 TCTTGCACATNTTTTGTTAGATTTATTCCTAAGTATTTNATGTTTTTTGA 2287 chrXptel1M 586320 AGTTATTTTAAATGGGATTTCTCT----ATTTC---TTGCTGTTGGACTT 586362 v i v v vi i ---- --- v vi --- C L1M5_orf2#LIN 2286 TGCTATTGTAAATGGTATTGTTTTTNAAATTTCATTTTCCAATTG---TT 2240 chrXptel1M 586363 TGTTGGTAACATATAGAAATGTTGATGACTTATGTGGATTTATCTTATAT 586412 v ii iiviv i v iv v i i C L1M5_orf2#LIN 2239 TGTTGCTAGTATATAGAAATACAATTGATTTTTGTATATTGACCTTGTAT 2190 chrXptel1M 586413 CCTGCAACTTTGA-----------ATTATTTTTAGTAGTTTTTTAGTTGA 586451 ? i i v----------- v i ? v v C L1M5_orf2#LIN 2189 CCNGCGACCTTGCTAAATTCACTTATTAGTTCTAGTAGTTTNTTTGTAGA 2140 chrXptel1M 586452 TTCTTTAGGATTCTCTAAGGAAAC---CAT--CATCTGCAAAGAATAATA 586496 ? i v v ? --- -- i v ?i i C L1M5_orf2#LIN 2139 TTCTTTNGGATTTTCTACGTANACAATCATGTCATCTGCGAATAANGACA 2090 chrXptel1M 586497 ATTTTATTTCCTCATTACC--TCTCTAATTCCTTCAATTTATTTTTCTTC 586544 i i v v -- i - v iv v v C L1M5_orf2#LIN 2089 GTTTTATTTCTTCCTTTCCAATCTTTA-TGCCTTTTATTTCTTTTTCTTG 2041 chrXptel1M 586545 CCTTATTTTTAAAGCGAACATTTCTAATAAAATATTGAAAAGTAATGGTA 586594 vivvvi v iv ii i i v i v v i i C L1M5_orf2#LIN 2040 CCTTATTGCACTGGCTAGGACCTCCAGTACAATGTTGAATAGAAGTGGTG 1991 chrXptel1M 586595 ATAGCAAGCAATCTTATTTCACCCCTGATCTCATTGGGAATGGTTTTCAC 586644 ? iii vi i i iiii i i vv -i i? v C L1M5_orf2#LIN 1990 ANAGCGGACATCCTTGTCTTGTTCCCGATCTTAGGGGGAA-AGCNTTCAG 1942 chrXptel1M 586645 T-TATCCCTATTACATATG---TTTGCTGATGGTTTTAGATAGATGCTAC 586690 - v v i vi --- ? vv vvi ivi C L1M5_orf2#LIN 1941 TNTTTCACCATTAAGTATGATGTTNGCTGTAGGTTTTTCGTAGATGCCCT 1892 chrXptel1M 586691 CTATAATTTAAAGGAAAATTCCATTTATTCCTATGCTCTTTAGTGTTTTT 586740 i v vv vi iv i v i vvi vi v v C L1M5_orf2#LIN 1891 TTATCAGGTTGAGGAAGTTCCCTTCTATTCCTAGTTTGCTGAGAGTTTTT 1842 chrXptel1M 586741 AATAGGAATGGGTGTAGTATTTTGTCAAATACTTTTTCTGCATCTATCGA 586790 vi v v v i i C L1M5_orf2#LIN 1841 ATCATGAATGGGTGTTGAATTTTGTCAAATGCTTTTTCTGCATCTATTGA 1792 chrXptel1M 586791 TAAAATCATAAGATTTCTGTTAGTTTGGTTATTGATAGAGTCAATTATGC 586840 v vi v i v ivv vvvi i i vi v iii C L1M5_orf2#LIN 1791 GATGATCATATGATTTTTCTCCTTTATTCTGTTAATATGGTGAATTACAT 1742 chrXptel1M 586841 TAATAGTTTTCCTGATATTCCAACAGTCCTGCATTCCTAGTATAAATCTT 586890 i v v i vi i vv v ii i i v i ii C L1M5_orf2#LIN 1741 TGATTGATTTTCGAATGTTAAACCAACCTTGCATTCCTGGGATAAACCCC 1692 chrXptel1M 586891 AC---------------TATCCTGGTGATAACTTGCTGTAATCTCTTTGC 586925 --------------- vv v vv v v vv C L1M5_orf2#LIN 1691 ACTTGGTCATGATGTATTATCCTTTTTATATATTGCTGGATTCGATTTGC 1642 chrXptel1M 586926 TAATATTT-----AAGATTTTTGCCTCAATATTCATTAGGGAAATTGGTC 586970 ----- i v v i v v C L1M5_orf2#LIN 1641 TAATATTTTGTTNAGGATTTTTGCATCTATGTTCATGAGGGATATTGGTC 1592 chrXptel1M 586971 TATAATTGCCTTTCTCTGTTTTGGCTTTTCGTGGTTTTGGTATCAGCACC 587020 i vi iii vv v viv? vii? C L1M5_orf2#LIN 1591 TGTAATTTTCTTTTCTTGTAATGTCTTTGTCNGGTTTTGGTATCAGGGTN 1542 chrXptel1M 587021 ATATCTGTGTTATAAAAAGAATTTGGCAAAAGTCCTTC---TTCTATTTT 587067 iiiv iv i v i v v iviv i --- C L1M5_orf2#LIN 1541 ATGCTGGCCTCATAAAATGAGTTGGGAAGTGTTCCCTCTTTTTCTATTTT 1492 chrXptel1M 587068 TCCAAATAGATTGTATAGTATTGGAATTAATTGTTCTTTAAATATTTGTT 587117 iivi v v i iv v v v i i v C L1M5_orf2#LIN 1491 CTGGAAGAGTTTGTGTAAGATTGGTATTATTTCTTCCTTAAATGTTTGGT 1442 chrXptel1M 587118 AAAATTCACATGCAAATCC-TTTGGTGCTGGAGATTTTTTCTTAGGGAGT 587166 i vv ii v - i vv v i iv i i v C L1M5_orf2#LIN 1441 AGAATTCACCAGTGAAGCCATCTGGGCCTGGAGTTTTCTTTGTGGGAAGG 1392 chrXptel1M 587167 TAATCAATAACTTGTTCAATTTCTTTTCCTAAAATGGGACTATTTAAGTA 587216 vv i v vvi vvivi v i i i ii v C L1M5_orf2#LIN 1391 TTTTTAATTACAAATTCAATTTCTTTAATAGATATAGGGCTATTCAGATT 1342 chrXptel1M 587217 ATTTATTTCCTCTACTGTTAATCTGGGCAACCTATATTTTTTGTAGGTAT 587266 v i i vv? i i i v i ?i i i ii- v C L1M5_orf2#LIN 1341 TTCTATTTCTTCTTGNGTCAGTTTTGGTAANTTGTGTTTTTCA-AGGAAT 1293 chrXptel1M 587267 TCATCCACTTCACTTAGATTATCAGATCTATTGGCATACAGTAAGGACAA 587316 ii i ii ii ? i i v -v vv v C L1M5_orf2#LIN 1292 TTGTCCATTTCATCTAAGTTNTCAAATTTATTGGCATAAAGT-TGTTCAT 1244 chrXptel1M 587317 AATAGTTCCTAATTATTGCTTTAATTTCCTTTTCATTGGTAGTGAGTTCA 587366 v ii v ivi v iv vvv iv vv v C L1M5_orf2#LIN 1243 AATATTCTCTTATTATCCTTTTAATGTCTGTAGGATCTGTAGTGATGTCT 1194 chrXptel1M 587367 CCCTTTTCATTTTTTATA 587384 i ii v C L1M5_orf2#LIN 1193 CCTTTTTCATTCCTGATA 1176 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.04 CpG sites = 327, Kimura (unadjusted) = 40.83 Transitions / transversions = 1.15 (327/284) Gap_init rate = 0.04 (89 / 2054), avg. gap size = 1.82 (162 / 89) 519 29.67 6.70 0.98 chrXptel1M 587600 587793 (412207) C MIRb#SINE/MIR (62) 206 2 m_b340s601i5 14229 chrXptel1M 587600 CATTCATGACCTCAACTGATCTCCAGAACT-CCCTAGGAGGCAG----TA 587644 v v i vi i ii v v- iv i ---- C MIRb#SINE/MIR 206 CATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTA 157 chrXptel1M 587645 TTATCCCTATTTTGTTGGTGAG-AATCTGAGGCTCAGAAAGCTTAAATGA 587693 i iiv i - v i v i i C MIRb#SINE/MIR 156 TTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAA 107 chrXptel1M 587694 TGTACTCATGGAAGCATAGCT----AATGTCAGAG--GTAATTCCAAGCT 587737 iv i i v vvi i ---- i v -- vi v v i C MIRb#SINE/MIR 106 CTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCC 57 chrXptel1M 587738 ATATTTCTTTAGACTCC-AAGTCTGTCATTCTGTCCATTAAACCACTATG 587786 vi i v i - - i i -ii v i iv vv C MIRb#SINE/MIR 56 AGGTCTGTCT-GACTCCAAAGCCCGT-GCTCTTTCCACTGCACCACGCTG 9 chrXptel1M 587787 CTACTTT 587793 iv i C MIRb#SINE/MIR 8 CCCCTCT 2 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.94 CpG sites = 33, Kimura (unadjusted) = 38.82 Transitions / transversions = 1.38 (33/24) Gap_init rate = 0.04 (8 / 193), avg. gap size = 1.88 (15 / 8) 257 23.40 0.00 0.00 chrXptel1M 588633 588679 (411321) C MIR3#SINE/MIR (41) 167 121 m_b340s601i6 14230 chrXptel1M 588633 AGAGGCTATCTAGTTCACTCTCTTCATTCTACTGATAAGGAAACTGA 588679 iii i vi i i i v i C MIR3#SINE/MIR 167 AGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGA 121 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.94 CpG sites = 9, Kimura (unadjusted) = 29.94 Transitions / transversions = 4.50 (9/2) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 270 32.17 1.74 0.00 chrXptel1M 589336 589450 (410550) L1M5_orf2#LINE/L1 1240 1356 (1938) m_b340s551i6 14231 chrXptel1M 589336 TATTTTGCTCAATTACATGCCAGTAAAAATGACAATTTAAGCAAAATGGA 589385 v vv i vi i vv ? i iiii L1M5_orf2#LIN 1240 TATTATGAACAACTTTATGCCAATAAATTTGANAACTTAGATGAAATGGA 1289 chrXptel1M 589386 TGAATGTTTTAAAAAATGTAAATTGCCCAGGTTA--GCAGAAAAAAATAG 589433 ii vii i iii ? i v iii i--? ii i L1M5_orf2#LIN 1290 CAAATTCCTTGAAAAACACAANTTACCAAAACTGACNCAAGAAGAAATAG 1339 chrXptel1M 589434 AATACTTAAATAACCCT 589450 v ii i i L1M5_orf2#LIN 1340 AAAATCTGAATAGCCCT 1356 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 47.80 CpG sites = 28, Kimura (unadjusted) = 47.80 Transitions / transversions = 3.11 (28/9) Gap_init rate = 0.01 (1 / 114), avg. gap size = 2.00 (2 / 1) 13 13.25 0.00 0.00 chrXptel1M 590514 590538 (409462) (AACA)n#Simple_repeat 1 25 (0) m_b340s252i16 14232 chrXptel1M 590514 AACAATCAAACAAACAAAAAAAGAA 590538 v v v (AACA)n#Simpl 1 AACAAACAAACAAACAAACAAACAA 25 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 26 33.25 0.00 0.00 chrXptel1M 590749 590834 (409166) (AA)n#Simple_repeat 1 86 (0) m_b340s252i18 14233 chrXptel1M 590749 AAAAAAAACATCAACAACACAGCAAAAAAAAAAAAAAAGAAAAAACCACA 590798 v vv v v v iv i vv v (AA)n#Simple_ 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chrXptel1M 590799 GACACACAAAAATTGAAAAAAGACATACAAAAAAAA 590834 i v v v vvi i v v v (AA)n#Simple_ 51 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 86 Matrix = Unknown Transitions / transversions = 0.28 (5/18) Gap_init rate = 0.00 (0 / 85), avg. gap size = 0.0 (0 / 0) 33 9.25 0.00 0.00 chrXptel1M 591009 591054 (408946) (A)n#Simple_repeat 1 46 (0) m_b340s252i19 14234 chrXptel1M 591009 AAAAAAGAAACAAACCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 591054 i v vv (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 46 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 15 7.22 3.23 3.23 chrXptel1M 591178 591208 (408792) (ATAGAA)n#Simple_repeat 1 31 (0) m_b340s252i20 14235 chrXptel1M 591178 ATAGAAATAGAAGGTA-AAATAGAAATTGAAA 591208 -i - v (ATAGAA)n#Sim 1 ATAGAAATAGAA-ATAGAAATAGAAATAGAAA 31 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2) 20 0.00 0.00 0.00 chrXptel1M 591762 591783 (408217) (A)n#Simple_repeat 1 22 (0) m_b340s252i21 14236 chrXptel1M 591762 AAAAAAAAAAAAAAAAAAAAAA 591783 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAA 22 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 418 23.80 4.70 1.30 chrXptel1M 592121 592269 (407731) L1MEj_5end#LINE/L1 2003 2156 (4) m_b340s551i7 14237 chrXptel1M 592121 AAAATATGATGGAGGAGAATATGGTTAAGT-TATCA-----TACCTATAA 592164 i v i - vii i - ----- vi- L1MEj_5end#LI 2003 AAAGTAAGATGGAAG-GAATAAAATCAAGTATATCAGTCGTTACAC-TAA 2050 chrXptel1M 592165 ATGTGAATGGGATGAACTTGCCTATAAAATGGAAGAGGATAGCAGAATGG 592214 iv i iv i v v iv iv iv v L1MEj_5end#LI 2051 ATGTGAATGGACTGAATTCTCCCATTAAAAGACAGAGACTGTCAGATTGG 2100 chrXptel1M 592215 ATTAAAAA-CAGAATCCTACAATATGCTGTTTACAAGAAGCAAATTTGAA 592263 i - i i vi v i v i i L1MEj_5end#LI 2101 GTTAAAAAACAAAACCCAGCTATATGCTGTTTACAAGAAACACACTTAAA 2150 chrXptel1M 592264 ACACAG 592269 v L1MEj_5end#LI 2151 ACAAAG 2156 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 29.14 CpG sites = 20, Kimura (unadjusted) = 29.14 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.03 (5 / 148), avg. gap size = 1.80 (9 / 5) 267 27.15 11.50 1.16 chrXptel1M 592153 592465 (407535) L1MC4_5end#LINE/L1 2206 2550 (5) m_b341s551i2 14237 chrXptel1M 592153 TCATACCTATAAATGTGAATGGGATGAACTTGCCTATAAAATGGAAGAGG 592202 ? ? v i v ? ii ? v v i? i i L1MC4_5end#LI 2206 TNATANCAATAAATGTAAATGGGCTNAACTCACCNATTAAAAGANAAAGA 2255 chrXptel1M 592203 ATAGCAGAATGGATTAAAAA-CAGAATCCTACAATATGCTGTTTACAAGA 592251 v vv i?v ? ? ? - ii i v v ? L1MC4_5end#LI 2256 TTTTCAANTTGGNTNANAAAGCAAGACCCAACTATATGCTGTNTACAAGA 2305 chrXptel1M 592252 AGCAAATTTGAAACACAGAAAAATACAAAGAGCAAAGGT-CAGGACTGGA 592300 ii v ii i - v vi vvi v ivii ii -v iv L1MC4_5end#LI 2306 GACACACCTAAAA-AAAGTGATTCAGAAAGGCTGAAAATAAAGGGATGGA 2354 chrXptel1M 592301 GTAGAATCTATTATGCTTCAGCTGAAGTTCAAAAGCAA--GTAGCAAT-- 592346 ?v ii v ii v --- iv i iviv iv -- v -- L1MC4_5end#LI 2355 NAAAGATATACCAGG---CAAATGGAAACAAAAAAGAAGGGTTGCAATNT 2401 chrXptel1M 592347 ---------------TAGGGTGTGAGAC-AAAAGC---AAATGCAA-AAA 592376 --------------- i? vii ? - --- ? vi - L1MC4_5end#LI 2402 TNATATCAGACAAAGTAGANTTCAAGNCAAAAAGCATTAAANGAGACAAA 2451 chrXptel1M 592377 GAA----ATTGTATCTTGCTAAAAGGTAC----CACAATGAAGTAATATT 592418 ---- v vv ? i ??? ---- vv vi L1MC4_5end#LI 2452 GAAGGNCATTTTATAATGNTAAAGGNNNCAATTCACAATGAAGATATAAC 2501 chrXptel1M 592419 AATAGTAAACATATATGTATAAA--AATATAGCATTTAAATTTTTAAAG 592465 vi i ? i iv -- i ? ?ii v? v L1MC4_5end#LI 2502 AATTATAAATATNTATGCACCAAATAACANAGCANCCACNTTTATAAAG 2550 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 37.77 CpG sites = 45, Kimura (unadjusted) = 37.77 Transitions / transversions = 1.15 (45/39) Gap_init rate = 0.05 (15 / 312), avg. gap size = 2.67 (40 / 15) 299 31.11 1.63 2.19 chrXptel1M 592159 592342 (407658) L1MC_orf2#LINE/L1 35 217 (3077) m_b340s551i8 14237 chrXptel1M 592159 CTATAAATGTGAATGGGATGAACTTGCCTATAAAATGGAAGAGGATAGCA 592208 v ? vv i ivii v v v iv iv iv L1MC_orf2#LIN 35 CTTTAAATGTNAATGGTCTAAATACACCAATTAAAAGACAGAGATTGTCA 84 chrXptel1M 592209 GAATGGATTAAAAA-CAGAATCCTACAATATGCTGTTTACAAGAAGCAAA 592257 i i - ii i v v i i i vv L1MC_orf2#LIN 85 GAGTGGATCAAAAAACAAGACCCAACTATATGTTGTCTACAAGAAACCCA 134 chrXptel1M 592258 TTTGAAACACAGAAAAATACAAAGAGCAAAGGTCA--GGACTGGAGTAGA 592305 i v i i i i v i i v vi i v -- - v ii L1MC_orf2#LIN 135 CTTTAAATATAAAGACACATATAGATTAAAAGTAAANGGA-TGGAGAAAG 183 chrXptel1M 592306 ATCTATTATGCTTCAGCTGAAGTTCAAAAGCAAGTAG 592342 v ii vvvi i --- v i? L1MC_orf2#LIN 184 ATATACCATGCTAACACTAA---TCAAAAGAAAGCNG 217 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.79 CpG sites = 31, Kimura (unadjusted) = 41.79 Transitions / transversions = 1.24 (31/25) Gap_init rate = 0.03 (6 / 183), avg. gap size = 1.17 (7 / 6) 431 20.37 0.93 0.00 chrXptel1M 592161 592268 (407732) L1MEh_5end#LINE/L1 2122 2230 (5) m_b340s551i9 14237 chrXptel1M 592161 ATAAATGTGAATGGGATGAACTTGCCTATAAAATGGAAGAGGATAGCAGA 592210 i v i ii v v v iv iv ?v L1MEh_5end#LI 2122 ATAAATGTAAATGGGTTAAACTCACCAATTAAAAGACAGAGATTNTCAGA 2171 chrXptel1M 592211 ATGGATT-AAAAACAGAATCCTACAATATGCTGTTTACAAGAAGCAAATT 592259 v - i v i ii v i L1MEh_5end#LI 2172 TTGGATTNAAAAACAAAATCCAACAATATGCTGTCTACAAGAGACACACT 2221 chrXptel1M 592260 TGAAACACA 592268 i ? L1MEh_5end#LI 2222 TAAAACANA 2230 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 24.57 CpG sites = 12, Kimura (unadjusted) = 24.57 Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.01 (1 / 107), avg. gap size = 1.00 (1 / 1) 331 25.84 0.82 1.65 chrXptel1M 592162 592283 (407717) L1M4_orf2#LINE/L1 38 158 (3136) m_b340s551i10 14237 chrXptel1M 592162 TAAATGTGAATGGGATGAACTTGCCTATAAAATGGAAGAGGATAGCAGAA 592211 i iv i viv v v v v iv i L1M4_orf2#LIN 38 TAAATGTAAATGGATTAAACACTCCAATCAAAAGGCAGAGATTGGCAGAA 87 chrXptel1M 592212 TGGAT-TAAAAACAGAATCCTACAATATGCTGTTTACAAGAAGCAAATTT 592260 -v vi v v i ii v i L1M4_orf2#LIN 88 TGGATAAAAAAACATGATCCAACTATATGCTGTCTACAAGAGACACACTT 137 chrXptel1M 592261 GAAACACAGAAAAATACAAAGAG 592283 v i iv -- i i v L1M4_orf2#LIN 138 TAGATTC--AAAGACACAAATAG 158 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 31.93 CpG sites = 15, Kimura (unadjusted) = 31.93 Transitions / transversions = 0.94 (15/16) Gap_init rate = 0.02 (3 / 121), avg. gap size = 1.00 (3 / 3) 235 28.46 8.13 0.00 chrXptel1M 592627 592749 (407251) L1MD_orf2#LINE/L1 1366 1498 (1796) m_b341s551i6 14237 chrXptel1M 592627 AAGAAAACTGAATTGG-AAT---AGGATTCAC----AAGAA-TCCTCAAG 592667 i i v - --- ii i v ---- - ii i L1MD_orf2#LIN 1366 AAGGAAATTGAATTCGTAATTTNAAAACTCCCCAAAAAGAAATCTCCAGG 1415 chrXptel1M 592668 ACCAGATGGGCTCACAAGTGCATTTTACTAAACATTTAAA-AACTATTAA 592716 v vi vi v v i i i - vv L1MD_orf2#LIN 1416 CCCAGATGGTTTCACTGGAGAATTCTACCAAACGTTTAAAGAAGAATTAA 1465 chrXptel1M 592717 CTGCAATACTATCTAAACCATTTGGAAAAATAG 592749 vv v ivi v iv ivii L1MD_orf2#LIN 1466 CACCAATTCTACACAATCTCTTCCAGAAAATAG 1498 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 35.15 CpG sites = 19, Kimura (unadjusted) = 36.44 Transitions / transversions = 1.19 (19/16) Gap_init rate = 0.04 (5 / 122), avg. gap size = 2.00 (10 / 5) 252 24.07 0.00 0.00 chrXptel1M 592653 592706 (407294) L1MC_orf2#LINE/L1 1401 1454 (1840) m_b341s551i7 14237 chrXptel1M 592653 ACAAGAATCCTCAAGACCAGATGGGCTCACAAGTGCATTTTACTAAACAT 592702 ii v vi i v i vi v i i L1MC_orf2#LIN 1401 ACAGAAAGCACCAGGCCCAGATGGGTTCACTGGTGAATTCTACCAAACAT 1450 chrXptel1M 592703 TTAA 592706 L1MC_orf2#LIN 1451 TTAA 1454 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 29.74 CpG sites = 8, Kimura (unadjusted) = 29.74 Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 291 26.14 1.14 0.00 chrXptel1M 592662 592749 (407251) L1M4_orf2#LINE/L1 1410 1498 (1796) m_b341s551i8 14237 chrXptel1M 592662 CTCAAGACCAGATGGGCTCACAAGTGCATTTTACTAAACATTTAAA-AAC 592710 i i ? vi vi v i i - v L1M4_orf2#LIN 1410 CCCAGGNCCAGATGGCTTCACTGGTGAATTCTACCAAACATTTAAAGAAG 1459 chrXptel1M 592711 TATTAACTGCAATACTATCTAAACCATTTGGAAAAATAG 592749 v vv v vivi iv ivi L1M4_orf2#LIN 1460 AATTAACACCAATCCTTCACAAACTCTTCCAAAAAATAG 1498 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 32.85 CpG sites = 11, Kimura (unadjusted) = 32.85 Transitions / transversions = 0.92 (11/12) Gap_init rate = 0.01 (1 / 87), avg. gap size = 1.00 (1 / 1) 489 26.13 2.82 0.55 chrXptel1M 593327 593503 (406497) L1MD_orf2#LINE/L1 1518 1698 (1596) m_b341s551i9 14237 chrXptel1M 593327 CAACACCTTTTATGTCACAAAAATGGTGCTGATACCTAAACAAGA----G 593372 v v vvi v iv viiv v v ---- L1MD_orf2#LIN 1518 CAACTCATTTTATGAGGCCAGTATTACCCTGATACCAAAACCAGACAAAG 1567 chrXptel1M 593373 TCAAAAGAGAAAAAGAAAACTGTAGACCAAATTCCCTAAAGAATATTGAT 593422 v iv v i ii vv v v i v i L1MD_orf2#LIN 1568 ACAGTACAAAAAAAGAAAACTACAGACCAATATCCCTCATGAACATAGAC 1617 chrXptel1M 593423 GTAAAAAACTTAAATAAAATATTAG-AAAGGAAATTACAGCAATATAGCA 593471 i v i v i - v?i - vv L1MD_orf2#LIN 1618 GCAAAAATCCTCAACAAAATATTAGCAAATNGAATT-CAGCAATATATAA 1666 chrXptel1M 593472 TAAGGATCATATACTATGACTAGGTAGGATTT 593503 v i i i i i i i i L1MD_orf2#LIN 1667 AAAGAATTATACACCATGACCAAGTGGGGTTT 1698 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 31.78 CpG sites = 22, Kimura (unadjusted) = 32.61 Transitions / transversions = 0.92 (22/24) Gap_init rate = 0.02 (3 / 176), avg. gap size = 2.00 (6 / 3) 274 26.92 0.00 0.00 chrXptel1M 594223 594300 (405700) C L1MC_orf2#LINE/L1 (3099) 195 118 m_b341s551i10 14238 chrXptel1M 594223 AGCATAATAGATTCTGCTTTACCCCATTACTTTTGTTCTATATGTGTCTC 594272 ii v ii v ii i ?v iv i C L1MC_orf2#LIN 195 AGCATGGTATATCTTTCTCCATCCNTTTACTTTTAATCTATATGTGTCTT 146 chrXptel1M 594273 TCTGCTTCAGGAGTGTTTCTTGTAAACA 594300 v ii v i v v i C L1MC_orf2#LIN 145 TATATTTAAAGTGGGTTTCTTGTAGACA 118 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 34.95 CpG sites = 13, Kimura (unadjusted) = 34.95 Transitions / transversions = 1.62 (13/8) Gap_init rate = 0.00 (0 / 77), avg. gap size = 0.0 (0 / 0) 267 23.12 5.69 1.56 chrXptel1M 594265 594387 (405613) C L1MEi_5end#LINE/L1 (5) 2207 2080 m_b341s551i11 14238 chrXptel1M 594265 TGTGTCTCTCTGCTTCAGGAGTGTTTCTTGTAAA---CATGTTGCAAGAT 594311 vi i i i v i --- i v vi C L1MEi_5end#LI 2207 TGTGTCGTTTTGTTTTAGGTGTGTCTCTTGTAAACAGCATATAGCTGGAT 2158 chrXptel1M 594312 TTTTGTTCTGAATAC-ATTTGCCTATTCACTTCCTATTT--TATTTGAGT 594358 v i v v - i -v v v vi - -- vv C L1MEi_5end#LI 2157 TTTTTTTTTTAATCCAATCTG-ATAATCTCTGTCT-TTTAATAGGTGAGT 2110 chrXptel1M 594359 TCATTCCACTTACA-TTGTTATGATTACTG 594387 i v i - i i C L1MEi_5end#LI 2109 TTAATCCATTTACATTTATTGTGATTACTG 2080 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 27.90 CpG sites = 14, Kimura (unadjusted) = 27.90 Transitions / transversions = 1.00 (14/14) Gap_init rate = 0.05 (6 / 122), avg. gap size = 1.50 (9 / 6) 18 10.11 6.25 0.00 chrXptel1M 594412 594443 (405557) (TC)n#Simple_repeat 1 34 (0) m_b341s252i1 14239 chrXptel1M 594412 TCTCTCTCTCT-TCTCTCACTCTTTCCCTC-CTC 594443 - v i i - (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 34 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.06 (2 / 31), avg. gap size = 1.00 (2 / 2) 895 28.68 10.41 2.33 chrXptel1M 596483 597039 (402961) L1M4_orf2#LINE/L1 1686 2286 (1008) m_b341s551i12 14240 chrXptel1M 596483 CCAGGTAAGATTTATGCCAGAAGTGCAGGGCTGGTTCAATATTAGGAAAA 596532 i ii v i i i i i ?v i v L1M4_orf2#LIN 1686 CCAAGTGGGATTTATCCCAGGAATGCAAGGTTGGTTCAACATNCGAAAAT 1735 chrXptel1M 596533 CTATCAGTCTAATAGATCATATAAATAAAACCAA---CTGAAAC-ATATG 596578 v i v v i v i iv --- vi - i L1M4_orf2#LIN 1736 CAATCAATGTAATACACCATATTAATAGAATAAAGGACAAAAACCACATG 1785 chrXptel1M 596579 ATTATTTCAACAGAGGCAGGAAAGGCTTTTGACAAAATACAACACTCATT 596628 i i i v i i v v i v L1M4_orf2#LIN 1786 ATCATCTCAATAGACGCAGAAAAAGCATTTGACAAAATCCAACACCCTTT 1835 chrXptel1M 596629 CCTAGTTAAAAAAAACACTAAAGAGCATAGAA--AGAATAGAGCTTACTT 596676 v ii ---- v v ivv i -- vi i - i L1M4_orf2#LIN 1836 CATGAT----AAAAACACTCAACAAACTAGGAATAGAAGGGAACTT-CCT 1880 chrXptel1M 596677 TAAAATGATGAATAATATTTATCTAAAATCATCAGGAATCATTATCAGTA 596726 i vv i viii i ivv i vv vv v i vvv L1M4_orf2#LIN 1881 CAACCTGATAAAGGGCATCTACGAAAAACCCACAGCTAACATCATACTTA 1930 chrXptel1M 596727 ATCTCTATTACAGAAGTTAGAAGCCTTCCCAATAACATAAGGGATGGATC 596776 v---i v v --i ii ? i vv v v i iiiiv L1M4_orf2#LIN 1931 ATG---GTGAAAGA--CTGAANGCTTTCCCCCTAAGATCAGGAACAAGAC 1975 chrXptel1M 596777 AAGGAT----------GCCA---------------------GAAATGCTA 596795 ---------- --------------------- ii v L1M4_orf2#LIN 1976 AAGGATGTCCGCTCTCGCCACTTCTATTCAACATTGTACTGGAGGTTCTA 2025 chrXptel1M 596796 GCTATAGCAATAAGGGAAGAAAAAGAAATTAAAGG------AATTAGAAC 596839 i vi v v v ------i i - L1M4_orf2#LIN 2026 GCCAGGGCAATTAGGCAAGAAAAAGAAATAAAAGGCATCCAGATTGGAA- 2074 chrXptel1M 596840 AGGCAGGAAAGAAAACTATCACTCCTTGTAG--GATATG--TTGGAATAC 596885 - i iv v vi i i -- i --i v v i L1M4_orf2#LIN 2075 AGG-AAGAAGTAAAACTATCTCTATTCGCAGATGACATGATCTTGTATAT 2123 chrXptel1M 596886 TCAGAGTCCTAAAGAATCAATTAAAAAACTACTTGAAATAATTAACAACT 596935 vv i i i v i? i v v v i v L1M4_orf2#LIN 2124 AGAAAATCCTAAGGAATCCACNAAAAAACTATTAGAACTAATAAACGAGT 2173 chrXptel1M 596936 TTAACACAGT-------TATAAAATAAGCCTACATAAGTCATCAGCATTT 596978 i i vi ------- i i v iiv v i viv i L1M4_orf2#LIN 2174 TCAGCAAGGTTGCAGGATACAAGATCAATATACAAAAATCAATTGTATTT 2223 chrXptel1M 596979 TTATATATTACCAATAAAGCCCAGCAGCAA--GACATAAAGAGA--AATT 597024 i i i v i -- v v v v -- v v i -- L1M4_orf2#LIN 2224 CTATACACTAGCAATGAA--CAATCCGAAAATGAAATTAAGAAAACAATT 2271 chrXptel1M 597025 CCATTCATAGTAACA 597039 i i i i L1M4_orf2#LIN 2272 CCATTTACAATAGCA 2286 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.33 CpG sites = 86, Kimura (unadjusted) = 37.23 Transitions / transversions = 1.23 (86/70) Gap_init rate = 0.04 (25 / 556), avg. gap size = 2.88 (72 / 25) 354 32.49 9.69 0.96 chrXptel1M 596782 597070 (402930) L1PB_orf2#LINE/L1 2012 2325 (969) m_b341s551i13 14240 chrXptel1M 596782 TGCCAGAAATGCTAGCTATAGCAATAAGGGAAGAAAAAGAAATTAAAGGA 596831 i ii i v i v v iv i v i v L1PB_orf2#LIN 2012 TACTGGAAGTCCTAGCCAGAGCAATCAGACAAGAGAAAGAAATAAAGGGC 2061 chrXptel1M 596832 ATTAGAACAGGC----AGGAAAGAAAACTATCACTCCTTGTAG--GATAT 596875 ivi iv i---- ivv i i vi iv -- L1PB_orf2#LIN 2062 ATCCAAATCGGTAAAGAGGAAGTCAAACTGTCGCTGTTTGCTGATGATAT 2111 chrXptel1M 596876 GTTGGAATACTCAG--AGTCCTAAAGAATCAATTAAAAAACTACTTGAAA 596923 v v v? ii -- ii v vvii i i v v v L1PB_orf2#LIN 2112 GATCGTNTACCTAGAAAACCCTAAAGACTCCTCCAGAAAGCTCCTAGAAC 2161 chrXptel1M 596924 TAATTAACAACTTTAACACAGT-------TATAAAATAAGCCTACATAAG 596966 i v ?i v i i v ------- i v iiv i i L1PB_orf2#LIN 2162 TGATAAANGAATTCAGCAAAGTTTCNGGATACAAAATTAATGTACACAAA 2211 chrXptel1M 596967 TCATCAGCATTTTTATATATTACCA---ATAAAGCCCAGCAGCAAGACAT 597013 vi vi ?i i ii v --- iv iv v v --- L1PB_orf2#LIN 2212 TCAGTAGCTCTNCTATACACCAACAGCGACCAAGCTGAGAATCAA---AT 2258 chrXptel1M 597014 AAAGAG--AAATTCCATTCATAGTAACAGTAG-------ACAATACTTGG 597054 v i--v ii v i i i i v i i------- v i L1PB_orf2#LIN 2259 CAAGAACTCAACCCCTTTTACAATAGCTGCAAAAAAAATAAAATACTTAG 2308 chrXptel1M 597055 GAGTCTACCT-GCCAAG 597070 i v -i L1PB_orf2#LIN 2309 GAATATACCTAACCAAG 2325 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 44.04 CpG sites = 54, Kimura (unadjusted) = 44.70 Transitions / transversions = 1.38 (54/39) Gap_init rate = 0.04 (11 / 288), avg. gap size = 2.82 (31 / 11) 331 29.48 6.37 2.16 chrXptel1M 597072 597338 (402662) L1PB_orf2#LINE/L1 2430 2707 (587) m_b341s551i14 14240 chrXptel1M 597072 CAATATAATAAAAATAACAGTTCTGTGTAAATTATTCTACTTATTCAGTG 597121 vi i i vi v ivv vi v vv i L1PB_orf2#LIN 2430 CAATATTGTGAAAATGACCATACTGCCAAAAGCAATCTACAAATTCAATG 2479 chrXptel1M 597122 CCATACAAACTAAAA-------ATTATTCTTTA--GAGCTAGAAAAAATA 597162 v v vv ii ------- i i -- i i L1PB_orf2#LIN 2480 CAATTCCCATCAAAATACCACCATCATTCTTCACAGAACTAGAAAAAACA 2529 chrXptel1M 597163 AT------ATTACTCTGGAAGAACTAAAGGGCAAGAATATCAAGGGAATC 597206 ------ vv v vv vv i vv v v v --- v L1PB_orf2#LIN 2530 ATCCTAAAATTCATATGGAACCAAAAAAGAGCCCGCATAGCCA---AAGC 2576 chrXptel1M 597207 AATAATAATAATAAAAGATAAAGTAAGGTAGCCTTGACAT-ACCAGATAT 597255 v v vv - vv i vv - v v v - v iv L1PB_orf2#LIN 2577 AAGACTAAGCA-AAAAGAACAAATCTGG-AGGCATCACATTACCCGACTT 2624 chrXptel1M 597256 CAAACTGTATTATAAAGCAGTAATTATCAAAACTATCTGGTACTGGTTAA 597305 i i i vi i i i viiv vv L1PB_orf2#LIN 2625 CAAACTATACTATAAGGCCATAGTCACCAAAACAGCATGGTACTGGTATA 2674 chrXptel1M 597306 AAAATAAAGTGCAGA-ATCAGTGGAATAGATTAG 597338 - i ii v - i i i v L1PB_orf2#LIN 2675 AAAAT-AGGCACATAGACCAATGGAACAGAATAG 2707 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 37.57 CpG sites = 31, Kimura (unadjusted) = 37.57 Transitions / transversions = 0.67 (31/46) Gap_init rate = 0.04 (11 / 266), avg. gap size = 2.09 (23 / 11) 47 0.00 2.27 0.00 chrXptel1M 597427 597470 (402530) (TG)n#Simple_repeat 1 45 (0) c_b341s251i0 14241 chrXptel1M 597427 TGTGTGTGTG-GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 597470 - (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 45 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.02 (1 / 43), avg. gap size = 1.00 (1 / 1) 17 11.13 0.00 0.00 chrXptel1M 597475 597503 (402497) (ACAT)n#Simple_repeat 1 29 (0) m_b341s252i2 14242 chrXptel1M 597475 ACACACATACATACAAACATACATCCATA 597503 i v v (ACAT)n#Simpl 1 ACATACATACATACATACATACATACATA 29 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 13 14.35 0.00 6.06 chrXptel1M 597560 597594 (402406) (CCTAAC)n#Simple_repeat 1 33 (0) m_b341s252i3 14243 chrXptel1M 597560 CCTAACCCTAACCCTAAATGCCCGACTCTAACCCT 597594 - -v ii i (CCTAAC)n#Sim 1 CCTAACCCTAACCCT-AA-CCCTAACCCTAACCCT 33 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 12 4.77 4.55 0.00 chrXptel1M 597725 597746 (402254) (AAAG)n#Simple_repeat 1 23 (0) m_b341s252i4 14244 chrXptel1M 597725 AAAAAAAGAAA-AAAGAAAGAAA 597746 i - (AAAG)n#Simpl 1 AAAGAAAGAAAGAAAGAAAGAAA 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.05 (1 / 21), avg. gap size = 1.00 (1 / 1) 45 2.37 0.00 0.00 chrXptel1M 597751 597793 (402207) (TA)n#Simple_repeat 1 43 (0) c_b341s251i1 14245 chrXptel1M 597751 TATATATATATATATATATATATATATATATATATTTATATAT 597793 v (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATAT 43 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 19 8.18 0.00 0.00 chrXptel1M 599035 599060 (400940) (A)n#Simple_repeat 1 26 (0) m_b341s252i5 14246 chrXptel1M 599035 AAAAAAAAAAACAAAAAACAAAAAAA 599060 v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAA 26 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 46 0.00 0.00 0.00 chrXptel1M 599718 599756 (400244) (AC)n#Simple_repeat 1 39 (0) c_b341s251i2 14247 chrXptel1M 599718 ACACACACACACACACACACACACACACACACACACACA 599756 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACA 39 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 314 27.76 4.62 3.03 chrXptel1M 602993 603122 (396878) MIR1_Amn#SINE/MIR 14 145 (85) m_b341s601i0 14248 chrXptel1M 602993 TGGCACAGCAGCTAGAGCATTGGGCTTGGACTC---AGACTCATCTTCCC 603039 ivi ii v i i v --- iiivv ?- MIR1_Amn#SINE 14 TGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGAGACCTGGGTTCN- 62 chrXptel1M 603040 GACTTCAAATTTGGCC-CAGGACAAAGCTATATGACCCTGAGCAAATCAC 603088 - ? i viii iv - v? v ?-- i?i i i i MIR1_Amn#SINE 63 -ANTCCCGGCTCTGCCACTNGCCN--GCTGNGTGACCTTGGGCAAGTCAC 109 chrXptel1M 603089 TTAATGTTGCT-TGCCTTTG-TTCCTCATCTATAAA 603122 ? iv iv -? iv - i MIR1_Amn#SINE 110 TTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAA 145 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 37.59 CpG sites = 23, Kimura (unadjusted) = 39.04 Transitions / transversions = 1.92 (23/12) Gap_init rate = 0.06 (8 / 129), avg. gap size = 1.25 (10 / 8) 435 19.33 0.00 9.57 chrXptel1M 604650 604752 (395248) MIRc#SINE/MIR 14 107 (161) m_b341s601i1 14249 chrXptel1M 604650 TGCAGTGGATAGAGCACTGGCCATGAAGTCAGGAGTATCAGAGTTCAATT 604699 v v v i iv i v i i v MIRc#SINE/MIR 14 TGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGT 63 chrXptel1M 604700 CTGGACTCAGGACACTTAAACACTTACTAGCTGTGTGACCTTATGCAAGT 604749 iv i v v--------- iv MIRc#SINE/MIR 64 CCCGGCTCTGC---------CACTTACTAGCTGTGTGACCTTGGGCAAGT 104 chrXptel1M 604750 CAC 604752 MIRc#SINE/MIR 105 CAC 107 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 20.86 CpG sites = 8, Kimura (unadjusted) = 22.17 Transitions / transversions = 0.80 (8/10) Gap_init rate = 0.09 (9 / 102), avg. gap size = 1.00 (9 / 9) 326 23.70 3.45 9.09 chrXptel1M 604653 604768 (395232) MIR#SINE/MIR 13 122 (140) m_b341s601i2 14249 chrXptel1M 604653 AGTGGATA-GAGCACTGGCCATGAAGTCAGGAGTATCAGAGTTCAATTCT 604701 v - v iv i i - v ii v i i v i MIR#SINE/MIR 13 AGTGGTTAAGAGCACGGGCTCTGGAGCCA-GACTGCCTGGGTTCGAATCC 61 chrXptel1M 604702 GGACTCAGGACACTTAAACACTTACTAGCTGTGTGACCTTATGCAAGTCA 604751 v i v v--------- iv i MIR#SINE/MIR 62 CGGCTCTGC---------CACTTACTAGCTGTGTGACCTTGGGCAAGTTA 102 chrXptel1M 604752 C--AAACTCAAT-TGCCTTA 604768 -- v vv - i MIR#SINE/MIR 103 CTTAACCTCTCTGTGCCTCA 122 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 27.21 CpG sites = 12, Kimura (unadjusted) = 28.50 Transitions / transversions = 0.92 (12/13) Gap_init rate = 0.11 (13 / 115), avg. gap size = 1.08 (14 / 13) 17 0.00 0.00 0.00 chrXptel1M 604907 604925 (395075) (A)n#Simple_repeat 1 19 (0) m_b341s252i6 14250 chrXptel1M 604907 AAAAAAAAAAAAAAAAAAA 604925 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAA 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 20 7.03 0.00 0.00 chrXptel1M 605482 605511 (394489) (AACA)n#Simple_repeat 1 30 (0) m_b341s252i7 14251 chrXptel1M 605482 AAAAAACAAACAAACAAACAAACAAAAAAA 605511 v v (AACA)n#Simpl 1 AACAAACAAACAAACAAACAAACAAACAAA 30 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 1287 28.67 1.07 1.95 chrXptel1M 605659 606124 (393876) L1ME3G_3end#LINE/L1 87 548 (376) m_b341s551i15 14252 chrXptel1M 605659 CAATTTTCAGATGAAGAAATTGAAACCATCTTTAGCCATATGAAAAGGTG 605708 iv v i vv ivii vv iv i L1ME3G_3end#L 87 CAATTCACAGAAGAGGAAATACAAATGGCCAATAAACATATGAAAAGATG 136 chrXptel1M 605709 CTCTAAATTACAACAGGTCAGAGAAATGCAAATTAAGACAATTCTGAGGT 605758 v vv i v vvii i i ivv i L1ME3G_3end#L 137 CTCAACCTCACTAGTAATCAGGGAAATGCAAATTAAAACAACAATGAGAT 186 chrXptel1M 605759 ACCCCTACACACCTGTCAGATTGGCTAAGATGATGGAAAAA--GATAATG 605806 vi viv ii v i -- vi i?-- i L1ME3G_3end#L 187 ACCATTTTTCACCCATCAGATTGGCAAAAAT--TTAAAAGNTTGATAATA 234 chrXptel1M 605807 ATGAAAGTTAGAGGGGATGTGGGAAAACTGGGACACTGATACATTGTTGG 605856 vi? iv i v i i i v v v v i i L1ME3G_3end#L 235 TCNAGTGTTGGCGAGGGTGTGGGGAAACGGGTACTCTCATACACTGCTGG 284 chrXptel1M 605857 TGGAACTGTGAACGGATCCAGCCATTCTGGAGAGCAGTTTGGAACTATGT 605906 i v i iv i v ? i i i v v v L1ME3G_3end#L 285 TGGGAGTGTAAATTGGTACAGCCNTTTTGGAGGGCAATTTGGCAGTATCT 334 chrXptel1M 605907 TCAAAAAAATTATCAAACTGCACATACCCTTTGACCCAGCAGCGTTTTTA 605956 -- vv -- i v i iiviivi v L1ME3G_3end#L 335 --ATTAAAAT--TTAAAATGCGCATACCCTTTGACCCAGCAATTCCACTT 380 chrXptel1M 605957 CTGAGCTTATATCCCAAAGAGATCATTAAAAAA---GGAAAAGAACTCAC 606003 ?i ?v v i ? i - i viv v --- v v i --?i L1ME3G_3end#L 381 CTNGGNATCTATCCTANAGAAAT-ACTCGCACATGTGCACAAGGA--NGC 427 chrXptel1M 606004 ATGTGCAAAAATGTTTGTGGCAGCCCTTTTCATAGTGGCAAGAAACTGGA 606053 i ii ii v vi v ii i i i i i L1ME3G_3end#L 428 ATGTACAAGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGA 477 chrXptel1M 606054 AACAGAATGGATGCCCATCAGTTGGGGAATAGATGAATAAGTTATGGTAT 606103 ivv ii i i v i v i i L1ME3G_3end#L 478 AACAACCTAAATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGTAT 527 chrXptel1M 606104 ATGAATGTTATGGAATATTAT 606124 vv ii i L1ME3G_3end#L 528 ATCCATACTATGGAATACTAT 548 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 36.66 CpG sites = 75, Kimura (unadjusted) = 37.76 Transitions / transversions = 1.34 (75/56) Gap_init rate = 0.02 (11 / 465), avg. gap size = 1.27 (14 / 11) 1090 27.83 4.74 5.58 chrXptel1M 605695 606200 (393800) L1MD1_3end#LINE/L1 127 628 (361) m_b341s551i16 14252 chrXptel1M 605695 CATATGAAAAGGTGCTCTAAATTACAACAGGTCAGAGAAATGCAAATTAA 605744 i i i v v i iv vvvi i i L1MD1_3end#LI 127 CACATGAAAAGATGTTCAACATCATTAGCCATTAGGGAAATGCAAATTAA 176 chrXptel1M 605745 GACAATTCTGAGGTACCCCTACACACCTGTCAGATTGGCTAAGATGATGG 605794 i v ivv i i v i v i ----- L1MD1_3end#LI 177 AACCACAATGAGATATCACTACACACCTATCAGAATGGCTAAAAT----- 221 chrXptel1M 605795 AAAAAGATAATGATGAAA------GTTAGAGGGGATGTGGGAAAACTGGG 605838 - i i ii v ------ i i v i i ii i L1MD1_3end#LI 222 -AAAAAATAGTGACAACACCAAATGCTGGCGAGGATGCGGAGAAACTGGA 270 chrXptel1M 605839 ACACTGATACATTGTTGGTGGAACTGTGAACGGATCCAGCCATTCTGGAG 605888 v v i i v i vv i v i i L1MD1_3end#LI 271 TCACTCATACATTGCTGGTGGGAATGTAAAATGGTACAGCCACTCTGGAA 320 chrXptel1M 605889 AGCAGTTTGGAACTATGTTCAAAAAAATTATCAAAC-TGCACATACCCTT 605937 i v v v v -- i --- - vv v v L1MD1_3end#LI 321 AACAGTTTGGCAGTTTCTT--AAAAAACT---AAACATGCAACTACCATA 365 chrXptel1M 605938 TGACCCAGCA---GCGTTTTTACTGAGCTTATATCCCAAAGAGATCATTA 605984 i --- ii i--- i v v i i ---- i L1MD1_3end#LI 366 CGACCCAGCAATTGCACTC---CTGGGCATTTATCCCAGAGAAA----TG 408 chrXptel1M 605985 AAAA---AGG-----AAAAGAACTCACATGTGCAAAAATGTTTGTGGCAG 606026 --- v ----- v i i---- i vi i i L1MD1_3end#LI 409 AAAACTTATGTTCACACAAAAACC----TGTACACGAATGTTTATAGCAG 454 chrXptel1M 606027 CCCTTTTCATAGTGGCAAGAAACTGGAAACAGAATGGATGCCCATCAGTT 606076 ii v i i i v i ivvii i v iiv L1MD1_3end#LI 455 CTTTATTCGTAATAGCCAAAAACTGGAAACAACCCAGATGTCCTTCAACG 504 chrXptel1M 606077 GGGGAATAGATGAATAAGTTATGGTATATGAATGTTATGGAATATTATTG 606126 v i v i i ii i i vv iii i --- L1MD1_3end#LI 505 GGTGAATGGTTAAACAAACTGTGGTACATCCATACCATGGAATACTA--- 551 chrXptel1M 606127 TTCTGTAATAAATAATCAACAGGATGATTT-----CAGAAAGGCCTGGA- 606170 i v i - vv - i iv v----- iv vii - L1MD1_3end#LI 552 CTCAGCAATAAA-AAGGAAC-GAACTATTGATACACGCAACAACCTGGAT 599 chrXptel1M 606171 GAGACTTATGTGAACTGATGCTGAGTGAAA 606200 iv ivv v i - L1MD1_3end#LI 600 GAATCTCCAGAGAATT-ATGCTGAGTGAAA 628 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 33.76 CpG sites = 80, Kimura (unadjusted) = 35.76 Transitions / transversions = 1.51 (80/53) Gap_init rate = 0.07 (35 / 505), avg. gap size = 1.49 (52 / 35) 12 19.72 6.25 2.00 chrXptel1M 606381 606428 (393572) (TTTTCCTT)n#Simple_repeat 1 50 (0) m_b341s252i8 14253 chrXptel1M 606381 TTTTCACCTTTTT-GTTGTTTGCTTGTTT-GTTTTTTCC-TTTCTCATTT 606427 - i -v v v v -v - i v (TTTTCCTT)n#S 1 TTTTC-CTTTTTTCCTTTTTTCCTTTTTTCCTTTTTTCCTTTTTTCCTTT 49 chrXptel1M 606428 T 606428 (TTTTCCTT)n#S 50 T 50 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.09 (4 / 47), avg. gap size = 1.00 (4 / 4) 13 8.48 4.00 0.00 chrXptel1M 606391 606415 (393585) (TTTG)n#Simple_repeat 1 26 (0) m_b341s252i9 14254 chrXptel1M 606391 TTTG-TTGTTTGCTTGTTTGTTTTTT 606415 - i v (TTTG)n#Simpl 1 TTTGTTTGTTTGTTTGTTTGTTTGTT 26 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 12 19.72 6.25 2.00 chrXptel1M 606381 606428 (393572) (TTTTCCTT)n#Simple_repeat 1 50 (0) m_b341s252i8 14253 chrXptel1M 606381 TTTTCACCTTTTT-GTTGTTTGCTTGTTT-GTTTTTTCC-TTTCTCATTT 606427 - i -v v v v -v - i v (TTTTCCTT)n#S 1 TTTTC-CTTTTTTCCTTTTTTCCTTTTTTCCTTTTTTCCTTTTTTCCTTT 49 chrXptel1M 606428 T 606428 (TTTTCCTT)n#S 50 T 50 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.09 (4 / 47), avg. gap size = 1.00 (4 / 4) 240 32.79 0.81 0.81 chrXptel1M 608993 609115 (390885) L1ME4b_3end#LINE/L1 444 566 (326) m_b341s551i17 14255 chrXptel1M 608993 ATTTATATCAGCATGTTTTGTGGTAATAAAGACATGGAGAGAAAGTGAGT 609042 i vv vv ii ii iivv i v vv i i L1ME4b_3end#L 444 ATTCATTGCAGCATTGTTTGTAATAGCAAAAGATTGGAAACAACCTAAAT 493 chrXptel1M 609043 CCTCATGGATTGGGGAATGGTTAAACAAATTATGGCACATGAATATGAGA 609092 vii vi v v i i vv ii vi L1ME4b_3end#L 494 GTCCATCAATAGGGGACTGGTTAAATAAATTATGGTACATCCATACAATG 543 chrXptel1M 609093 GACCATTATTGCAA-TGTAAGAAA 609115 vi i - i-i i L1ME4b_3end#L 544 GAATACTA-TGCAGCCGTAAAAAA 566 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 42.99 CpG sites = 23, Kimura (unadjusted) = 44.49 Transitions / transversions = 1.35 (23/17) Gap_init rate = 0.02 (2 / 122), avg. gap size = 1.00 (2 / 2) 505 28.17 10.81 4.06 chrXptel1M 609430 609799 (390201) L1ME4c_3end#LINE/L1 242 635 (195) m_b341s551i18 14256 chrXptel1M 609430 AATGTTGA-GGTGATAAGGAAAAACTGGGACACTAATCCATTGTCGATAG 609478 i i- iv ? iv vi v ? v v ii i i L1ME4c_3end#L 242 AATGCTGGCGAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGG 291 chrXptel1M 609479 AACTTTGAACTGATCCAACCACTTTGGAAAGCAATCTGGAATTATG-GCC 609527 v ? v i i i v vi i v v i -ii L1ME4c_3end#L 292 CANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATC 341 chrXptel1M 609528 AAGAGTTATAAAG-----------CTTTGACCCAGAAATATCCCAATTAG 609566 ii i----------- v vi v vvi i L1ME4c_3end#L 342 AAGAGCCATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGG 391 chrXptel1M 609567 GCCTGTTTCCCAAGG----------AGAGCAGAGAAAA-----ATGAA-- 609599 vv v v i ---------- i v ii ----- v -- L1ME4c_3end#L 392 GAATTTATCCTAAGGAAATAATTCAAAAGAAGGAAAAAGCTATATGCACG 441 chrXptel1M 609600 AAGA-ACTTATAGCAGCTCTCTTTGTGAGGGCAAAGACCTGGA---AATT 609645 -ii i v vi v i i vi i i vi --- ii L1ME4c_3end#L 442 AAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACC 491 chrXptel1M 609646 TAAAGGATACCCATCAATTAGGAAATGGCTAAACAAGTTGTGGTATAT-A 609694 --- ii v vi i i ii i i i -? L1ME4c_3end#L 492 TAA---ATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCN 538 chrXptel1M 609695 ATTGTGATGGAATACTACTGT-GCTATAAGAAATGA----TGTGCAGGCT 609739 i -i i - i- i v i ---- i v i L1ME4c_3end#L 539 ACT-CGATGGAATATTA-TGCAGCCATTAAAAATGATAATTATGAAGACT 586 chrXptel1M 609740 GATTTTAGCAAAAACATGGAAACACTTGAATGAAATAATGAAGAGTTAAA 609789 i-- v --- - iv vv v ----- i L1ME4c_3end#L 587 A--TGTAGC---AACATGGAAA-ATGTTTATGATATAAT-----GTTAAG 625 chrXptel1M 609790 TGAAGAGAAC 609799 i i i L1ME4c_3end#L 626 TGAAAAAAGC 635 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 35.86 CpG sites = 63, Kimura (unadjusted) = 37.28 Transitions / transversions = 1.70 (63/37) Gap_init rate = 0.07 (27 / 369), avg. gap size = 2.07 (56 / 27) 50 0.00 0.00 0.00 chrXptel1M 609974 610016 (389984) (AC)n#Simple_repeat 1 43 (0) c_b341s251i3 14257 chrXptel1M 609974 ACACACACACACACACACACACACACACACACACACACACACA 610016 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACA 43 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 442 30.93 3.09 0.00 chrXptel1M 610309 610502 (389498) L2#LINE/L2 1309 1508 (1574) m_b341s601i3 14258 chrXptel1M 610309 ACTGGGCCAACTATAGATTTATCACAA--AACCTCAACAGGGCCTTCAAT 610356 v iv v i i v v -- vv i i L2#LINE/L2 1309 ACTGGTCTCACTTTAAATTCATGACCACNAACCTCAAGTGGGCCCTTAAT 1358 chrXptel1M 610357 A--GCAGAACAATCATTTCACATTTCCCTAATCGATTTGCTCTCCCATTC 610404 i-- vvii ? vii i v ii i L2#LINE/L2 1359 GCTGCCCGGCAATCNTACTACATTTCCCTAGTCCATTCACTCTCCCACTC 1408 chrXptel1M 610405 CCCACCACAATTATTCCACATCTTTTCATCATTCTTCCCGTCATCCACAG 610454 i vvv i i i i i v vi i vvii vi v v L2#LINE/L2 1409 TCCTAGACGACTATTTCACACCTTCTCCTCTCTCCTCAAACCTCCAACAC 1458 chrXptel1M 610455 CTCCCTTCCC-TCCCCACTC-CAGCTGAGGATCTCATCTCATCCTTCACT 610502 iii i- i - v i iiii v vi L2#LINE/L2 1459 CTCCTCCCCTATCCTCACTCTCAGCTGATGACCTTGCTTCCTATTTCACT 1508 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 39.73 CpG sites = 36, Kimura (unadjusted) = 41.55 Transitions / transversions = 1.50 (36/24) Gap_init rate = 0.02 (4 / 193), avg. gap size = 1.50 (6 / 4) 13 15.72 0.00 7.89 chrXptel1M 610535 610575 (389425) (TCCTCA)n#Simple_repeat 1 38 (0) m_b341s252i10 14259 chrXptel1M 610535 TCCTCTTTCTCACCCTTTCCTCCTCATCCTCATGCCACATC 610575 v i i -- v - v (TCCTCA)n#Sim 1 TCCTCATCCTCATCC--TCATCCTCATCCTCAT-CCTCATC 38 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.07 (3 / 40), avg. gap size = 1.00 (3 / 3) 397 32.63 11.46 2.64 chrXptel1M 610635 611018 (388982) L2#LINE/L2 1633 2049 (1033) m_b341s601i4 14258 chrXptel1M 610635 TCTTTTCCAAGGCAAATCCTTATACCCTTGAGTCTACTACAATCCTGTCT 610684 i v i v i i vi -- -- vi -i ii i L2#LINE/L2 1633 TCCTATCTAAGGCCAACCCCTCCAC--TTG--TGCACTA-GATCCCATCC 1677 chrXptel1M 610685 TTTCTGGC----------ACACTGTCCC-----TTCTCTCATCATCATTC 610719 ii v ---------- ii ii ----- i v - vi L2#LINE/L2 1678 CCTCTCGCCTACTCAAGGACATCGCTCCAGCAATTCTCCCCTC-TCTCTC 1726 chrXptel1M 610720 CCTAATGTTCAATGTCTCCTTCTCTACTG--------CTATC----TACA 610757 ivv vv v i i -------- i ---- L2#LINE/L2 1727 CTGCATCATCAATTTTTCCCTCTCTACTGGATCATTCCCATCAGCATACA 1776 chrXptel1M 610758 A-CATGCCCGTGTTTCCCTCATCCTTAAAATGC------CTTCATTTAAT 610800 - ivv?i i i i vi ------ii vi i i L2#LINE/L2 1777 AACATGCTGTNATTTCTCCCATCTTTAAAAAACAAAAATTCTCCCTTGAC 1826 chrXptel1M 610801 GTTCCCATC-CCTTCTCC--CTAACAATCCATAACACTTCACCTTTTCCT 610847 --- i?- ii -- v ivi vv v v v ii ivi L2#LINE/L2 1827 ---CCCACNTCCCCCTCCAGCTACCGCCCCATTTCTCTGCTCCCCTTTAC 1873 chrXptel1M 610848 AGTTATACTCCTTGAAGAAAAAATTTATGCT-----TCTGC--TGCTTCT 610890 iv v i ii ivvi i i ----- v -- v i L2#LINE/L2 1874 AGCAAAACTCCTCGAAAGAGTTGTCTATACTCGCTGTCTCCAATTCCTCT 1923 chrXptel1M 610891 CGTCACACTTGATTCTAAATCCACTGCAATCTCACTTTCAACCTCACTAT 610940 v v i ivv ii i i v vvi iv i i i L2#LINE/L2 1924 CCTCCCATTCTCTCTTGAACCCACTCCAATCAGGCTTTCGTCCCCACCAC 1973 chrXptel1M 610941 TCAACTAAATCTGTTCTTTCTAAAGTCACCTTTGTCACCTCTTAATTGTC 610990 v ii v i vii i vv -- ivvi ii L2#LINE/L2 1974 TCCACCGAAACTGCTCTTGTCAAGGTCACCAATG--ACCTCCACGTTGCT 2021 chrXptel1M 610991 AAATCCAATGATCCTTTCCCAATCCTCA 611018 i vv i i L2#LINE/L2 2022 AAATCCAATGGTCAATTCTCAGTCCTCA 2049 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 42.10 CpG sites = 75, Kimura (unadjusted) = 45.16 Transitions / transversions = 1.60 (75/47) Gap_init rate = 0.05 (21 / 383), avg. gap size = 2.62 (55 / 21) 486 27.85 3.50 2.07 chrXptel1M 612000 612142 (387858) MIRc#SINE/MIR 4 148 (120) m_b341s601i5 14260 chrXptel1M 612000 GGCAGCTAGGTGGCTCAGTGGATAGAGGGCCAGGCTTCAAGTTAGGAAGG 612049 i--- iv v vi ii i vi i i MIRc#SINE/MIR 4 GGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA 50 chrXptel1M 612050 TCTGAGTTTAAATATGGCCTCAGACACTTGCTAGCTAAGTGATTCTAGGC 612099 i i ii i viv v v v i iv iii i MIRc#SINE/MIR 51 CCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGC 100 chrXptel1M 612100 AAGTCATTTCACC-CTGTTTGCCTCA----CTGCATCTGTAAAATGAG 612142 i v - v vv ---- iv i MIRc#SINE/MIR 101 AAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 34.64 CpG sites = 24, Kimura (unadjusted) = 35.92 Transitions / transversions = 1.60 (24/15) Gap_init rate = 0.04 (5 / 142), avg. gap size = 1.60 (8 / 5) 13 4.76 0.00 4.35 chrXptel1M 613517 613540 (386460) (GGGA)n#Simple_repeat 1 23 (0) m_b341s252i11 14261 chrXptel1M 613517 GGGAGGGGGTGGAGGGAGGGAGGG 613540 i - (GGGA)n#Simpl 1 GGGAGGGAG-GGAGGGAGGGAGGG 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 17 11.64 2.44 5.00 chrXptel1M 613607 613647 (386353) (AATA)n#Simple_repeat 1 40 (0) m_b341s252i12 14262 chrXptel1M 613607 AATAAAAAGTTATAATAAA-AAATAAATAAATAAACAATATA 613647 v iv - - i - (AATA)n#Simpl 1 AATAAATAAATA-AATAAATAAATAAATAAATAAATAA-ATA 40 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.07 (3 / 40), avg. gap size = 1.00 (3 / 3) 12 16.31 2.78 2.78 chrXptel1M 613884 613919 (386081) (ATTTCAT)n#Simple_repeat 1 36 (0) m_b341s252i13 14263 chrXptel1M 613884 ATTT-ATATTTCATATTTCCTTTTTTGTAATTGCATA 613919 - v v ii - v (ATTTCAT)n#Si 1 ATTTCATATTTCATATTTCATATTTCAT-ATTTCATA 36 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 16 24.35 3.51 3.51 chrXptel1M 614044 614100 (385900) (TA)n#Simple_repeat 1 57 (0) m_b341s252i14 14264 chrXptel1M 614044 TAT-TATACACATATATTCACATATATGTA-AAATCATACTATATATACT 614091 - i i vi i i - v - - iv (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATAT-ATA-TATATATATA 48 chrXptel1M 614092 TCTATTTAT 614100 v v (TA)n#Simple_ 49 TATATATAT 57 Matrix = Unknown Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.07 (4 / 56), avg. gap size = 1.00 (4 / 4) 342 30.40 7.08 2.25 chrXptel1M 614348 614559 (385441) C L1ME4a_3end#LINE/L1 (335) 536 315 m_b341s551i19 14265 chrXptel1M 614348 ATATATCACAACTTGTTTAGCCATTCCCCAATTGATGGGCATCCCTGCAT 614397 i i i i i i ? v v i iivv ivv C L1ME4a_3end#L 536 ATGTACCATAATTTATTTAACCANTCCCCTATTGTTGGACATTTAGGTTG 487 chrXptel1M 614398 TTTCCAATTCTTTGTCACCACAAAGAGATG-TGCTCTAAATATTTTAGAA 614446 i i ii ii i v - - vv i i ii v v C L1ME4a_3end#L 486 TTTCCAATTTTTCGCTATTATAAATA-ATGCTGCGATGAACATCCTTGTA 438 chrXptel1M 614447 CATACAGGTTTCTTTTCCTTTTTCCCTGAACAT---CTTGAGAAAGACAG 614493 v ---- vi?iviv i vi --- ii v i ivv C L1ME4a_3end#L 437 CATAAA----TCTTTGTNCACATCTCTGATTATTTCCTTAGGATAAATTC 392 chrXptel1M 614494 CTAATAGTAGTATTGCTGGGTCAAA-GGTATA--------TAACTCTTTG 614534 iv i v i - i-------- vv v C L1ME4a_3end#L 391 CTAGAAGTGGAATTACTGGGTCAAAGGGTATGNACATTTTTAAGGCTTTT 342 chrXptel1M 614535 GGTACA-ATT-CCAGATTGTCTCCCAG 614559 i - - i i ii C L1ME4a_3end#L 341 GATACATATTGCCAAATTGCCCTCCAG 315 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 40.22 CpG sites = 39, Kimura (unadjusted) = 41.08 Transitions / transversions = 1.62 (39/24) Gap_init rate = 0.05 (11 / 211), avg. gap size = 1.82 (20 / 11) 395 30.36 2.31 2.91 chrXptel1M 614348 614520 (385480) C L1MC5_3end#LINE/L1 (2161) 533 362 m_b341s551i20 14265 chrXptel1M 614348 ATATATCACAACTTGTTTAGCCATTCCCCAATTGATGGGCATCCCTGCAT 614397 i i i ii i i i v v i iivv ivv C L1MC5_3end#LI 533 ATGTACCATAGTTTATTCAACCAGTCCCCTATTGATGGACATTTGGGTTG 484 chrXptel1M 614398 TTTCCAATTCTTTGTCACCACAAAGAGATG-TGCTCTAAATATTTTAGAA 614446 i ii ii ii v - - vv i vii v vi C L1MC5_3end#LI 483 TTTCCAGTCTTTTGCTATTACAAATAG-TGCTGCAATGAATAGCCTTGTG 435 chrXptel1M 614447 CATACAGGTTTCTTTTCC--TTTTTCCCTGAACATC-TTGAGAAAGACAG 614493 i---- v-- v v vii - i v ivv C L1MC5_3end#LI 434 CATACG----TCTTTTCGTATTTTTGCCAGTGTATCTTTGGGATAGATTC 389 chrXptel1M 614494 CTAATAGTAGTATTGCTGGGTCAAAGG 614520 iv i v C L1MC5_3end#LI 388 CTAGAAGTGGGATTGCTGGGTCAAAGG 362 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 39.07 CpG sites = 30, Kimura (unadjusted) = 40.09 Transitions / transversions = 1.43 (30/21) Gap_init rate = 0.05 (8 / 172), avg. gap size = 1.12 (9 / 8) 578 31.47 1.45 3.32 chrXptel1M 614554 614829 (385171) C L1ME3_3end#LINE/L1 (638) 271 1 m_b341s551i21 14265 chrXptel1M 614554 TCCCAGTTTTCCCATATTCCTTCCAACATTTGTTACTTTC--CCCTTGTA 614601 i vii i i iiv i v i v --i i v C L1ME3_3end#LI 271 TTCCAGTTGCTCCACATCCTCGCCAACACTTGGTATTGTCAGTCTTTTTA 222 chrXptel1M 614602 TCATTTCAGCCACTCTGAAAGATGTAAATCTGTATCTCAACATTGTTTTA 614651 -- i i ivi i iv viv vii v C L1ME3_3end#LI 221 --ATTTTAGCCATTCTGGTGGGTGTGTAGTGGTATCTCATTGTGGTTTTA 174 chrXptel1M 614652 ATTTTCACTTCTCTAATAAATACAGATTTAGAGCATTTTCTTTCCATATG 614701 v i i i i v vv v v ---i i C L1ME3_3end#LI 173 ATTTGCATTTCCCTGATGACTAATGATGTTGAGCA---CCTTTTCATATG 127 chrXptel1M 614702 TCTATAAATTGCTTTGATGTCTTCACTAGCAAAAGTGCTTATTCACATCT 614751 ii viiiiii v i i vi v i-i i i vi C L1ME3_3end#LI 126 CTTATTGGCCATTTGGATATCCTCTTTTGT-GAAGTGCCTGTTCAAGTCT 78 chrXptel1M 614752 TTTGACCATTTATCAATTGGGGATTG--AGTCATATTTGTCATAGATTTG 614799 v v i -- --v - v v i v C L1ME3_3end#LI 77 TTTGCCCATTTTTTAATTGGG--TTGTTTGTC-TTTTTCTTATTGATTTG 31 chrXptel1M 614800 ACAAAGTTTTTTGCATACTTGAGATATGAG 614829 vvii i ii i ivi i C L1ME3_3end#LI 30 TAGGAGTTCTTTATATATTCTGGATACGAG 1 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 41.23 CpG sites = 53, Kimura (unadjusted) = 42.59 Transitions / transversions = 1.71 (53/31) Gap_init rate = 0.04 (11 / 275), avg. gap size = 1.18 (13 / 11) 311 31.78 10.96 4.54 chrXptel1M 614676 615733 (384267) C L1P4_orf2#LINE/L1 (1) 3293 2171 m_b341s551i22 14265 chrXptel1M 614676 GATTTAGAGCATTTTCTTTCCATATGTCTATAAATTGCTTTGATGTCTTC 614725 v v i --- i i viiii vv C L1P4_orf2#LIN 3293 GATGTTGAGCATTTTTT---CATATGTTTGTTGGCCGCTTGTATGTCTTC 3247 chrXptel1M 614726 ACTAGCAAAAGTGCTTATTCACATCTTTTGACCATTTATCAATTGGGGAT 614775 vi v - i ii i ii i v i v i -- i C L1P4_orf2#LIN 3246 TTTTG-AGAAGTGTCTGTTCATGTCCTTTGCCCACTTTTTAAT--GGGGT 3200 chrXptel1M 614776 TGAGTCATATTTG-TCATAGATTTGACAAAGTTTTTTGCATACTTGAGAT 614824 ivv vv v - ii v ? viv ii ii v i ivi C L1P4_orf2#LIN 3199 TATTTGTTTTTTGCTTGTTGANTTGTTTAAGTTCCTTATAGATTCTGGAT 3150 chrXptel1M 614825 ATGAGACTTTTATCTGAAAAACTGTTCATAAA---TTTCCCCC-TTCC-- 614868 v i i v viv iv iiii --- i - i-- C L1P4_orf2#LIN 3149 ATTAGACCTTTGTCGGATGCATAGTTTGCGAATATTTTCTCCCATTCTGT 3100 chrXptel1M 614869 -AATTTTCTGCTTTACT-TATGGCTACATTGGTTTTATTTCTACAAACAA 614916 -ii v - - i v v -i vv i-i v i i viv C L1P4_orf2#LIN 3099 AGGTTGTCTG-TTTACTCTGTTGATA-GTTTCTTTTG-CTGTGCAGAAGC 3053 chrXptel1M 614917 TTTTAAATTTAATTTAATTGAAATTATCCACTTTATACTCT-----CTAT 614961 i v i vii ivv v i v i - ii i ----- v C L1P4_orf2#LIN 3052 TCTTTAGTTTAATTAGGTCCCACTTGTCAATTTT-TGTTTTTGTTGCAAT 3004 chrXptel1M 614962 --CTCTTG----TTTGTTCATAAATTATTCACCTATCCATAAGTTTGATA 615005 -- i ----i iv v ii ------- vii i C L1P4_orf2#LIN 3003 TGCTTTTGAGGACTTAGTCATAAATTCTTTGCC-------AAGGCCGATG 2961 chrXptel1M 615006 --CATAAA--TATCTTCCATG-----TTCTA--ATTTTCTTA---TGATG 615041 -- v ?-- i i i v ----- -- iv --- v C L1P4_orf2#LIN 2960 TCCAGAANGGTATTTCCTAGGTTTTCTTCTAGGATTTTTATAGTTTGAGG 2911 chrXptel1M 615042 TCTCCCTACATATCTAGGTCATGTATCCATTCTGACCTTATTTTAGTAAA 615091 --- -- i i v vv ii vi v v v C L1P4_orf2#LIN 2910 TCT---TAC--ATTTAAGTCTTTAATCCATCTTGAGTTAATTTTTGTATA 2866 chrXptel1M 615092 TGCTATAAAATATTGGTCTATGCCTAAATGC----CAGGCTGCTTGCCAG 615137 v iv ii vv i - ii v v vi---- viiv v C L1P4_orf2#LIN 2865 TGGTGAAAGGTAGGGGTCCA-GTTTCATTCTTCTGCATATGGCTAGCCAG 2817 chrXptel1M 615138 CTTTCCCAACAATTTTTTTAAATTAAATAACGAATTCTTATCCCCAAAAC 615187 i v i viv ---- i iv i i - vvi C L1P4_orf2#LIN 2816 TTATCCCAGCACCATTT----ATTGAATAGGGAGTCCTT-TCCCCATTGC 2772 chrXptel1M 615188 TTAAGTTTTTACATGA----GTCAAACATAAGGTTATTATAG-------- 615225 -- ii-i ---- i v v i vi i -------- C L1P4_orf2#LIN 2771 TTA--TTTTTGT-CGACTTTGTCGAAGATCAGATGGTTGTAGGTGTGCGG 2725 chrXptel1M 615226 --TTATTTGCT--GCTGTATACTCTATTTC-TTAG-CTA----------- 615258 -- - -- i v v i i i - i - ----------- C L1P4_orf2#LIN 2724 CTTTATTT-CTGGGTTCTCTATTCTGTTCCATTGGTCTATGTGTCTGTTT 2676 chrXptel1M 615259 --GTATCAG----ATA--GTTTTGATAATTACTGCCTTATAACATAGTTT 615300 -- i ---- i-- i v i iiv i ii C L1P4_orf2#LIN 2675 TTGTACCAGTACCATGCTGTTTTGGTTACTGTAGCCTTGTAGTATAGTTT 2626 chrXptel1M 615301 AA------TTAATAT----CTTTC--CTTTACATTCTTTTTTCATTAG-- 615336 i ------v i ---- i i -- --i v - -- C L1P4_orf2#LIN 2625 GAAGTCGGGTAATGTGATGCCTCCGGCTTT--GTTCTTTTTGC-TTAGGA 2579 chrXptel1M 615337 TTTCTTTAAC-ATTCTTGATCTTATGTTCTTCCAAATGACTTTTGTTATT 615385 v ii - vv v v v vv v v ivv v C L1P4_orf2#LIN 2578 TTGCTTTGGCTATTCGGGCTCTTTTTTGGTTCCATATGAATTTTAGAATA 2529 chrXptel1M 615386 ATTTTATTTTTCTAACTCAGTAAAATAAAACTGTGGTAATTTAATTGGGA 615435 i ---- i v i v vi vv i i v i C L1P4_orf2#LIN 2528 GT----TTTTTCTAATTCTGTGAAAAATGACGTTGGTAGTTTGATAGGAA 2483 chrXptel1M 615436 TGGCATTGAA----TAGATTA----GGTTAA-ATTGTCATTTTTATTATA 615476 i i ---- i---- vi i- v i v iv C L1P4_orf2#LIN 2482 TAGCGTTGAATCTGTAGATTGCTTTGGGCAGTATGGCCATTTTAACGATA 2433 chrXptel1M 615477 TTGGCCCTGCCTACCCATGAACTAT-TAATATTCATTCAATTATTTAAAT 615525 iii v v i i - -v i iv i v i ivi C L1P4_orf2#LIN 2432 TTGATTCTTCCAATCCATGAGC-ATGGAATGTTTTTCCATTTGTTTGTGT 2384 chrXptel1M 615526 TTGAATTT---ATTTGTATATAAAGTTTTTTATGATTTTATTCATAAAAT 615572 i--- i --- v v vviv v i ii i vi ii i iv C L1P4_orf2#LIN 2383 C---ATCTNTGATTTCTTTCAGCAGTGTTTTGTAGTTCTCCTTGTAGAGA 2337 chrXptel1M 615573 TCCTGGGTTTCCTTTGGTCAC-TGTATTCCCACGTATTTCCTACTATCTA 615621 i vviii - i v- i v iv vi v i i C L1P4_orf2#LIN 2336 TCTTTCACCTCC-TTGGTTAGATGTATTCCTAGGTATTTTATTTTTTTTG 2288 chrXptel1M 615622 CAATTATTTTAAATTAAAATTAC-----TAA-------CTCATCTTGCAG 615659 iiii v - iii i ----- i ------- v v v C L1P4_orf2#LIN 2287 TGGCTATTGTAAA-TGGGATTGCGTTCTTGATTTGGCTCTCAGCTTGAAC 2239 chrXptel1M 615660 GGTTTTGTTGGTGATATATAGAAATGCTGATAATTTATGTGGTTTTGCTT 615709 --- i --- iv i v ivv vii C L1P4_orf2#LIN 2238 G---TTATTGGTG---TATAGAAATGCTACTGATTTTTGTACATTGATTT 2195 chrXptel1M 615710 TATATCCTGCTACTTTGTTAAAAT 615733 i vv ii i i C L1P4_orf2#LIN 2194 TGTATCCTGAAACTTTACTGAAGT 2171 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 41.72 CpG sites = 188, Kimura (unadjusted) = 42.99 Transitions / transversions = 1.41 (188/133) Gap_init rate = 0.08 (88 / 1057), avg. gap size = 1.90 (167 / 88) 365 31.61 7.38 2.75 chrXptel1M 615244 615731 (384269) C L1M1_orf2#LINE/L1 (612) 2682 2173 m_b341s551i23 14265 chrXptel1M 615244 TCTATTTCTTAGCTAGTATCAGATAGTTTTGATAATTACTGCCTTATAAC 615293 i i vv i i viiv i v i iv ii i ii C L1M1_orf2#LIN 2682 TCTGTTTTTATGCCAGTACCATGCTGTTTTGGTTACTATAGCTCTGTAGT 2633 chrXptel1M 615294 ATAGTTTAA------TTAATATCTTTCCTTTA----CATTCTTTTTTCAT 615333 i i ------v i vv ii ----ii v - C L1M1_orf2#LIN 2632 ATAATTTGAAGTCAGGTAATGTGATTCCTCCAGTTTTGTTCTTTTTGC-T 2584 chrXptel1M 615334 TAGTTT--CTTTAAC-ATTCTTGATCTTATGTTCTTCCAAATGACTTTTG 615380 i vv -- ii - v i v vv v i v i C L1M1_orf2#LIN 2583 CAGGATAGCTTTGGCTATTCTGGGTCTTTTGTGGTTCCATATAAATTTTA 2534 chrXptel1M 615381 TTATTATTTTATTTTTCTAACTCAGTAAAATAAAACTGTGGTAATTTAAT 615430 vv i ---- vi v i iv viv vv v i C L1M1_orf2#LIN 2533 GGATTGTTTT----TTCTATTTCTGTGAAGAATGTCATTGGTATTTTGAT 2488 chrXptel1M 615431 TGGGATGGCATTGAA----TAGATTA----GGTTAA-ATTGTCATTTTTA 615471 v v ---- i---- v i- v v v C L1M1_orf2#LIN 2487 AGGGATTGCATTGAATCTGTAGATTGCTTTGGGTAGTATGGACATTTTAA 2438 chrXptel1M 615472 TTATATTGGCCCTGCCTACCCATGAACTAT-TAATATTCATTCAATTATT 615520 iv iii v v i - -v - v v v C L1M1_orf2#LIN 2437 CAATATTGATTCTTCCAATCCATGAAC-ATGGAATA-TCTTTCCATTTTT 2390 chrXptel1M 615521 TAA-AT----TTGAATTTATTTGTATATAAAGTTTTTTATGATTTTATTC 615565 ii-i ---- v v -i ---v v ii vv i C L1M1_orf2#LIN 2389 TGGTGTCCTCTTCAATTTCTTT-CAT---CAGTGTTTTATAGTTTTCATT 2344 chrXptel1M 615566 ATAAAATTCCTGGGTTTCCTTTGGTCACTGT--ATTCCCACGTATTTCCT 615613 i i iv i vvii - i v- -- i v vv C L1M1_orf2#LIN 2343 GTAGAGATCTTTCACTT-CTTTGGTTAA-GTTAATTCCTAGGTATTTAAT 2296 chrXptel1M 615614 ACTATCTACAATTATTTTAAATTAAAATTAC-----TAACTCATCTTGCA 615658 vi i iiiii v - iii ----- i i iv i v C L1M1_orf2#LIN 2295 TTTATTTGTGGCTATTGTAAA-TGGGATTACTTTTTTGATTTCTTTTTCA 2247 chrXptel1M 615659 GGGT-TTTGTTGGTGATATATAGAAATGCTGATAATTTATGTGGTTTTGC 615707 iv - iii v ii iv i v ivv vii C L1M1_orf2#LIN 2246 GATTGTTCACTGTTGGCATATAGAAATGCTACTGATTTTTGTATGTTGAT 2197 chrXptel1M 615708 TTTATATCCTGCTACTTTGTTAAA 615731 i v ii i C L1M1_orf2#LIN 2196 TTTGTATCCTGCAACTTTACTGAA 2173 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 42.19 CpG sites = 84, Kimura (unadjusted) = 42.19 Transitions / transversions = 1.27 (84/66) Gap_init rate = 0.06 (27 / 487), avg. gap size = 1.85 (50 / 27) 419 30.27 1.60 1.60 chrXptel1M 615746 615933 (384067) L1P3_orf2#LINE/L1 3100 3287 (7) m_b341s551i24 14266 chrXptel1M 615746 ATAAACTGGGAAAACATTTTTACAGTCAAAGGTTCTGATAAAGGCCTCAT 615795 i i v i v i i v vvvv i v v L1P3_orf2#LIN 3100 ACAGAATGGGAGAAAATTTTTGCAATCTATCCATCTGACAAAGGGCTAAT 3149 chrXptel1M 615796 TTCCAAAATATACAGAGAATTAACTCTAATTTATAA---AAAATCAAGCC 615842 v i v ii i v vv v i --- v i v L1P3_orf2#LIN 3150 ATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAAAAAACAAACA 3199 chrXptel1M 615843 ATTCTCCAATTGATAAATGGTCAAAGGATATGAACAGACAATTTTCAGAT 615892 -- i - ii v i v i v i i v L1P3_orf2#LIN 3200 A--CCCCA-TCAAAAAGTGGGCGAAGGATATGAACAGACACTTCTCAAAA 3246 chrXptel1M 615893 GATGAAATTGAAACTATTACCACTCATATGAAAGAGTGTTC 615933 v v v vi viii v vv i iv i L1P3_orf2#LIN 3247 GAAGACATTTATGCGGCCAACAAACATATGAAAAAAAGCTC 3287 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 38.22 CpG sites = 26, Kimura (unadjusted) = 39.08 Transitions / transversions = 0.87 (26/30) Gap_init rate = 0.02 (4 / 187), avg. gap size = 1.50 (6 / 4) 1615 29.23 2.80 2.64 chrXptel1M 615797 616439 (383561) L1ME5_3end#LINE/L1 7 650 (291) m_b341s551i25 14266 chrXptel1M 615797 TCCAAAATATACAGAGAATTAACTCTAATTTATAAAAAATCAAGCCATT- 615845 i i ii i vviv v iv i i -- v iv?- L1ME5_3end#LI 7 TCTAGAATATACAAGGAACTCCTGCAAATCAACAAGAAA--AAGACGGNA 54 chrXptel1M 615846 -CTCCAATTGATAAATGGTCAAAGGATATGAACAGACAATTTTCAGATGA 615894 - i v v v i v v L1ME5_3end#LI 55 ACCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGA 104 chrXptel1M 615895 TGAAATTGAAACTATTACCACTCATATGAAAGAGTGTTCCAAATCACTAT 615944 v iivi vvii v vv iiii i v v i v L1ME5_3end#LI 105 GGAAACCCGAAAGGCTAACAAGCATATGAAGAGATGCTCAAACTCATTAG 154 chrXptel1M 615945 TGATCAGAGAAATGCAAATTAAGACAACTCTGAGATACCACTACACACCT 615994 i i vv i vi L1ME5_3end#LI 155 TAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCT 204 chrXptel1M 615995 GTCAGATTGGCTAAGATGACAGGAAA--AAATAATGATGATTGTTGGAGG 616042 i i i v i --i i i--ii vii v v i L1ME5_3end#LI 205 ATTAGACTGGCAAAAAT--TAGAAAGCTGGATAATGCCAAGTGTTGGCGA 252 chrXptel1M 616043 GGATGTGGGAAAACAGGGACACTGATACATTGTTGGTGGAATTGTGAATA 616092 i ? i i v v i i i i v ii iv L1ME5_3end#LI 253 GGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACT 302 chrXptel1M 616093 CATCCAGCCATTCTGGAGAGCAATTTGGAACTA--TGCCCAAA--AAGTT 616138 vi v i v v -- ivi -- - L1ME5_3end#LI 303 GGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTAAG-T 351 chrXptel1M 616139 ATCAAACTGTGCATACCCTTTGATCCAGCAGTGTCTCTACTGGGCTTATA 616188 --- --- v i i vi v v iv L1ME5_3end#LI 352 AT---AC---GCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATA 395 chrXptel1M 616189 CCCCAAGGAGATACTAAAGAAGG----GAAAGGGACCTGTCTGTGCCAAA 616234 i i i v v viv ----v i v vi ---- ii L1ME5_3end#LI 396 TCCCAAAGAAATTCTCACACAGGTCCATAAGGGGACATGTACG----AGG 441 chrXptel1M 616235 ATGTTTGTGGCAGCCCTGTTTGTAGTGGCCAGAAGCTGGAAAATGAATGG 616284 ii v vi i vi i i iivvivv L1ME5_3end#LI 442 ATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGG 491 chrXptel1M 616285 ATGCCCATCAATTGGAGAATGGTTGAGTAAACTGTGGTATATGAATGTTA 616334 i i v v i v ii v iv v iiii L1ME5_3end#LI 492 GTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACACCA 541 chrXptel1M 616335 TGGAATATTATTGTTCTGTAAGAAATGACCAGCAGGACGAATACAGAG-A 616383 i i vvvv v v iii vii vi i v i v - L1ME5_3end#LI 542 TGGAGTACTATGCAGCAGTTAGAAGCAACGGACTAGATGTACACATAGCA 591 chrXptel1M 616384 GGATTGGCGAGACTTACAGGAAC-TGATGCTGAGTGAAATGAGC-AGAAC 616431 iv v ii iiv v -- - ii vi i- v L1ME5_3end#LI 592 ACATGGATGGATCTTAAA--AACATAGTGCTGAGTGAAAAAAGTAAGAAA 639 chrXptel1M 616432 CAG---GAGAT 616439 --- L1ME5_3end#LI 640 CAGAATGAGAT 650 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 37.31 CpG sites = 104, Kimura (unadjusted) = 38.10 Transitions / transversions = 1.32 (104/79) Gap_init rate = 0.04 (27 / 642), avg. gap size = 1.30 (35 / 27) 16 9.15 5.41 2.63 chrXptel1M 616838 616874 (383126) (AATA)n#Simple_repeat 1 38 (0) m_b341s252i15 14267 chrXptel1M 616838 AATAAA-AAATTATTTAAT-AATAAATAAATAAAATAAA 616874 - v v v - - (AATA)n#Simpl 1 AATAAATAAATAAATAAATAAATAAATAAAT-AAATAAA 38 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.08 (3 / 36), avg. gap size = 1.00 (3 / 3) 1322 31.62 6.18 3.00 chrXptel1M 616883 618144 (381856) C L1M5_orf2#LINE/L1 (1134) 2160 860 m_b341s551i26 14265 chrXptel1M 616883 TTCAACTAACTTTTTAGTTG--TCTTTAGGATTTTCCAAGTATATCATCA 616930 v v ii ? v v -- ? i v ? iv C L1M5_orf2#LIN 2160 TTCTAGTAGTTTNTTTGTAGATTCTTTNGGATTTTCTACGTANACAATCA 2111 chrXptel1M 616931 TATTCTCTAC--ACAA--ACAGTTTTACAACCTCACTACCTATTCTGACA 616976 i iv i -- i -- ivv i vi v v ii v ii C L1M5_orf2#LIN 2110 TGTCATCTGCGAATAANGACAGTTTTATTTCTTCCTTTCCAATCTTTATG 2061 chrXptel1M 616977 TCTTCTATTTCTTTTTCTTCTCTTATTGTTTTTGCTAGTATTTCCAATAC 617026 i i vi ivi v v ii i C L1M5_orf2#LIN 2060 CCTTTTATTTCTTTTTCTTGCCTTATTGCACTGGCTAGGACCTCCAGTAC 2011 chrXptel1M 617027 AACA--AAATAATTCTGATGACGAAGAGCATCCTTGGTTCACTCCAGATC 617074 ii--i ivvv i ?iiv ii vi iii v C L1M5_orf2#LIN 2010 AATGTTGAATAGAAGTGGTGANAGCGGACATCCTTGTCTTGTTCCCGATC 1961 chrXptel1M 617075 TAACTAAGAAGGCTTTTAGTTTATTCCCATTACAAATAATGCTTGTTGAT 617124 v vvii i ? i ? v iv viv i i ? i vv C L1M5_orf2#LIN 1960 TTAGGGGGAAAGCNTTCAGTNTTTCACCATTAAGTATGATGTTNGCTGTA 1911 chrXptel1M 617125 GGTTTTAGGTAAATACTTCTTATCAATTTAAGGAGAAAAAAAAATT---- 617170 vv i i iii iv i -------- i ---- C L1M5_orf2#LIN 1910 GGTTTTTCGTAGATGCCCTTTATCAGGTTGAGGA--------AGTTCCCT 1869 chrXptel1M 617171 --TATACCTTATACTGTCAAGTATTTTTAGTAGGAATGAGTGTTG----- 617213 -- v vi -i iii vi vi v i ----- C L1M5_orf2#LIN 1868 TCTATTCCTAGT-TTGCTGAGAGTTTTTATCATGAATGGGTGTTGAATTT 1820 chrXptel1M 617214 -------TGGCTTTTCTGCATCTAATGAAATAATCAT--GATTTTTGTTA 617254 ------- vi v i i -- v -- C L1M5_orf2#LIN 1819 TGTCAAATGCTTTTTCTGCATCTATTGAGATGATCATATGATTTTTCT-- 1772 chrXptel1M 617255 CTTTTATTTTG--GATACAATCAATTATCTTAATACTTTTCCTTAAGCTA 617302 i i --i iii v iv i vvv i vv v i C L1M5_orf2#LIN 1771 CCTTTATTCTGTTAATATGGTGAATTACATTGATTGATTTTCGAATGTTA 1722 chrXptel1M 617303 AACTATCTCTGTATTATTGGTATAACTCTCACCTGATCACAATGTATAAT 617352 i v ii i vi v vi i i i ii v C L1M5_orf2#LIN 1721 AACCAACCTTGCATTCCTGGGATAAACCCCACTTGGTCATGATGTATTAT 1672 chrXptel1M 617353 CTTTGTTATAT-TTGCTGA---CG-TCTCCTAGGTATTTTATTTAGAATT 617397 i v - i--- - i v -i i ? i C L1M5_orf2#LIN 1671 CCTTTTTATATATTGCTGGATTCGATTTGCTA-ATATTTTGTTNAGGATT 1623 chrXptel1M 617398 TTTGTATCCATATTCATTAATGGAAAAGAGTCTATA------TTTTTTTG 617441 i i i - i v v vvi i ------ i C L1M5_orf2#LIN 1622 TTTGCATCTATGTTCA-TGAGGGATATTGGTCTGTAATTTTCTTTTCTTG 1574 chrXptel1M 617442 TTTTGGCTCTTCCTGGTTTGGATACCAATACCATATTTATTTCATAAAAG 617491 vv v i vi ? v i i ivii? ii viii v C L1M5_orf2#LIN 1573 TAATGTCTTTGTCNGGTTTTGGTATCAGGGTNATGCTGGCCTCATAAAAT 1524 chrXptel1M 617492 TAGTTTGATAG-GACCTATTTTTTTGCCTATTATTCCAAATAATTTACTT 617540 v v iv - vi iv i -- v iivi v i iiv C L1M5_orf2#LIN 1523 GAGTTGGGAAGTGTTCCCTCTTTTT--CTATTTTCTGGAAGAGTTTGTGT 1476 chrXptel1M 617541 AATATTGGAATTAGTTGGCGTTTAAATGTTTAGTAGAAT------GTAAA 617584 v v v vvivi i ------ i C L1M5_orf2#LIN 1475 AAGATTGGTATTATTTCTTCCTTAAATGTTTGGTAGAATTCACCAGTGAA 1426 chrXptel1M 617585 TCTGTGTAGTCCTGATGCTTTTCTTTTTCTCAGAAAGCTCATTTATGGC- 617633 v ii v i v iv - v ---i i v iv v vi - C L1M5_orf2#LIN 1425 GCCATCTGGGCCTGGAG-TTTTCTTTGT---GGGAAGGTTTTTAATTACA 1380 chrXptel1M 617634 -ATTTGACTTTTTCTTT-CCAAA-ATAGGTTTATTTAGACATTCTACTGT 617680 - ii --- -vi i - vi i iv i vi C L1M5_orf2#LIN 1379 AATTCAA---TTTCTTTAATAGATATAGGGCTATTCAGATTTTCTATTTC 1333 chrXptel1M 617681 GTCTTCTGCCAAATCTAGGCAATTTACATTTGTGTAAATATTTTTCCATT 617730 v v? i - i i v i ? iii v vv iiv v C L1M5_orf2#LIN 1332 TTCTTGNGTC-AGTTTTGGTAANTTGTGTTTTTCAAGGAATTTGTCCATT 1284 chrXptel1M 617731 TAAAC--AGTTC---AATTTATTAGCATATAACTGGGCAAAATAAT-TTT 617774 v v -- ?--- i v ii vv v v - i C L1M5_orf2#LIN 1283 TCATCTAAGTTNTCAAATTTATTGGCATAAAGTTGTTCATAATATTCTCT 1234 chrXptel1M 617775 TA-TATTGCTTTGAT---TTTATCTTCATTAGTGGGATATTTACTCTTTG 617820 - ivi i --- v vvv vv -- i i v i - C L1M5_orf2#LIN 1233 TATTATCCTTTTAATGTCTGTAGGATCTGTAGT--GATGTCTCCTTTTT- 1187 chrXptel1M 617821 CATTTTTAATATTTAT-CTTAGTAT-TTAGTTTTATTTTTAAAAATCACA 617868 ii i vi -v v i - vvi i v vvvi vv C L1M5_orf2#LIN 1186 CATTCCTGATATTGGTAATTTGTGTCTTCTCTCTTTTTTTCTTGATCAGT 1137 chrXptel1M 617869 TTAACTAATTATTTACCTACTTTACTATTTTTCCCATAAAACTAACTCCT 617918 i ?i ivvi i v i i iv i ii v i i i ii C L1M5_orf2#LIN 1136 CTNGCTAGAGGTTTATCAATTTTATTGATCTTTTCAAAGAACCAGCTTTT 1087 chrXptel1M 617919 AGTCTTGTTTATTACTTCAATT-----CTTACTTTCAATTTTATTAATTT 617963 i ii i v vii v -----i ii v i i C L1M5_orf2#LIN 1086 GGCTTCGTTGATTTTCTCTATTGTNTNTTTGTTTTCTATTTCATTGATTT 1037 chrXptel1M 617964 -TGCCTTTAGTTTTAAGGAATTCCAGTTCA--GTATTTAACTAGAGTTTT 618010 - ii vi - vv v -- v--v i ?vi v i -- C L1M5_orf2#LIN 1036 CTGCTCTTATCTTT-ATTATTTCC--TTCCTTCTACTTNCTTTGGG--TT 992 chrXptel1M 618011 TAATTTG---TTCTTTTTCTAGTTTTTTTTTTTTAATTGCATATCCAGTC 618057 --- -----i i v iv v viiii vi C L1M5_orf2#LIN 991 TAATTTGCTCTTCTTTTTCTAG-----CTTCTTAAGGTGGAAGCTTAGAT 947 chrXptel1M 618058 CACTGGTCT---GCTCATTGTCTAATTTATTAATATAAATATGTAAAGTG 618104 i i i --- ---i v vv vi ?ii v ? iv C L1M5_orf2#LIN 946 CATTGATTTTAAGC---CTTTCTTCTTTTCTAATATANGCATTTAANGCT 900 chrXptel1M 618105 ATAAATTTTCCTCTGGTTACTGCTTTTGCTATATCTCATA 618144 i iivi v ii i i C L1M5_orf2#LIN 899 ATAAATTTCCCTCTAAGCACTGCTTTAGCTGCATCCCACA 860 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 43.08 CpG sites = 225, Kimura (unadjusted) = 43.23 Transitions / transversions = 1.39 (225/162) Gap_init rate = 0.06 (70 / 1261), avg. gap size = 1.67 (117 / 70) 261 34.72 4.33 3.69 chrXptel1M 618313 618635 (381365) C L1MC_orf2#LINE/L1 (2596) 698 374 m_b341s551i27 14265 chrXptel1M 618313 ATTGCATTGTGATCTGAAAAGGATGCATTA-ACTATTTCTGCTTTTCTG- 618360 v i i - v ?i ? i- iv ii i i i- C L1MC_orf2#LIN 698 ATTCCATTGTGGTCTGAGA-GCANACNTTGTATGATTTCTATTCTTTTAA 650 chrXptel1M 618361 -CTCACTTAACTATAAAATTTTTATTTCATAATATATGATTGATCTTTGT 618409 -i iii v iv i i---- vv vi iv i i iv v C L1MC_orf2#LIN 649 ATTTGTTAAGGTGTG----TTTTATGGCCCAGAATGTGGTCTATCTTGGT 604 chrXptel1M 618410 AAA-GTTACTATGTGCTGCTGAGGAAAAAGGTGTATTCTTTTCTATTCCC 618458 i - - i v- vii i v vi v vv ivv C L1MC_orf2#LIN 603 GAATGTT-CCATGTGA-GCTTGAGAAGAATGTGTATTCTGCTGTTGTTGG 556 chrXptel1M 618459 ATCCAGTTCTCTCCAGATATCTATGACATCTGGCCTATCTAAAACTCTAT 618508 vv v? vi i v v ? ii iiv iv viiiv i C L1MC_orf2#LIN 555 ATGAAGTANTCTATAGATGTCAATTANATCCAGTTGATTGATGGTGCTGT 506 chrXptel1M 618509 TCACCTCTTTGACTTCTTCCTTATTTATTTTTTG---GTTAGATTCATCT 618555 ? vi ---i viv i v i --- i i iii ? C L1MC_orf2#LIN 505 TNAGTTC---AACTATGTCCTTACTGATTTTCTGCCTGCTGGATCTGTCN 459 chrXptel1M 618556 ACTTTTGAGAGGGGAAGAGTAAAGTCCCCACTATTATAATACTA------ 618599 i ?i v i iiviv i i -- i v i------ C L1MC_orf2#LIN 458 ATTNCTGATAGAGGGGTGTTGAAGTCTCCA--ACTATAATAGTGGATTCG 411 chrXptel1M 618600 TCTATTTCTACCTGTAATTCATTTAACTTTT-CCTTA 618635 v i i i vv i ii - i C L1MC_orf2#LIN 410 TCTATTTCTCCTTGCAGTTCTATCAGTTTTTGCCTCA 374 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 50.72 CpG sites = 67, Kimura (unadjusted) = 50.72 Transitions / transversions = 1.63 (67/41) Gap_init rate = 0.06 (19 / 322), avg. gap size = 1.37 (26 / 19) 325 33.46 3.12 1.93 chrXptel1M 618379 618634 (381366) C L1M4_orf2#LINE/L1 (2660) 634 376 m_b341s551i28 14265 chrXptel1M 618379 TTTTATTTCATAATATATGATTGATCTTTGTAAA-GTTACTATGTGCTGC 618427 vv v i i iv i v vi - - i vvi C L1M4_orf2#LIN 634 TTTTATGGCCTAACATATGGTCTATCCTGGAGAATGTT-CCATGTGCACT 586 chrXptel1M 618428 TGAGGAAAAAGGTGTATTCTTTTCTATTCCCATCCAGTTCTCTCCAGATA 618477 - i v vi v vv ivvi vv vi vi i C L1M4_orf2#LIN 585 TGAG-AAGAATGTGTATTCTGCTGTTGTTGGGTGGAGTGTTCTATAGATG 537 chrXptel1M 618478 TCTATGACATCTGGCCTATCTAAAACTCTATTCACCTCTTTGACTTCTTC 618527 i v vi i iivi i v iivi i vv --- vi C L1M4_orf2#LIN 536 TCTGTTAGGTCTAGTTGGTTTATAGTGTTGTTCAAGTCTT---CTATTTC 490 chrXptel1M 618528 CTTATTTATTTTTTGGTTAG--ATTC-ATCTACTTTTGAGAGGGGAAGAG 618574 i v i i vi --i - i i v i v iiv v C L1M4_orf2#LIN 489 CTTGTTGATCTTCTGTCTAGTTGTTCTATCCATTATTGAAAGTGGGGTAT 440 chrXptel1M 618575 TAAAGTCCCCA-CTATTATAAT---ACTATCTATTTCTACCTGTAATTCA 618620 i i - vi --- i i v vi v C L1M4_orf2#LIN 439 TGAAGTCTCCAACTATTATTGTTGAATTGTCTATTTCTCCCTTCAATTCT 390 chrXptel1M 618621 TTTAACTTTTCCTT 618634 v i ii v C L1M4_orf2#LIN 389 GTCAGTTTTTGCTT 376 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 45.38 CpG sites = 45, Kimura (unadjusted) = 45.38 Transitions / transversions = 1.15 (45/39) Gap_init rate = 0.04 (10 / 255), avg. gap size = 1.30 (13 / 10) 426 31.10 7.34 2.63 chrXptel1M 618642 618968 (381032) L1PREC2_orf2#LINE/L1 363 704 (2590) m_b341s551i29 14268 chrXptel1M 618642 ATCCAAATTCCTAGAG-AAGTTAT--GAGAGCTGCAAGAAGA----AACT 618684 i i v i - v -- v ? ii ----i L1PREC2_orf2# 363 ACCCAGATTCATAAAGCAAGTTCTTAGAGACCTNCAAAGAGACTTAGACT 412 chrXptel1M 618685 --------ATACCAGTGGGGGATCTCAACCTTGCTCTCTCAGAACTAGAT 618726 -------- vi i ii viiv v vv v i i L1PREC2_orf2# 413 CCCACACAATAATAGTGGGAGACTTCAACACCCCACTGACAGTATTAGAC 462 chrXptel1M 618727 AAATC---GAACCACAAAATAAATAAGAAAGAAGTTAAGGAGGTAAACCA 618773 i --- iv v --- v vi v vv i iv L1PREC2_orf2# 463 AGATCATCGAGGCAGAAAAT---TAACAAAGATATTCAGGACCTGAACTC 509 chrXptel1M 618774 AATTTTAGAAAAGTTAGATATGATAGACCTCTGTAGAAAACTGAATGGAC 618823 ivi i vv iv i iv v ii vv vv ivv?v L1PREC2_orf2# 510 AACACTGGACCAAATGGACCTGATAGACATCTACAGAACTCTCCACCCNA 559 chrXptel1M 618824 ACAGAAAGGAATATATCTTTTTCTCCATGATACATGGAACCTACACAAAA 618873 v v vi iv i vvi vi v v v v L1PREC2_orf2# 560 AAACAACAGAATATACATTCTTCTCATCGCCACATGGCACATACTCTAAA 609 chrXptel1M 618874 ATTGACCCTGTATTAGGGCATAAAAA---CCTCAAAATCAAATGCAGATA 618920 i vii v v i v--- i--- i vi L1PREC2_orf2# 610 ATCGACCACATAATCGGACATAAAACAATCCTCAG---CAAATGCAAAAG 656 chrXptel1M 618921 GGCAGAA---ATACTAAATGCATCTTTTTCAGATAACAATGCAACAAAAA 618967 ii v --- i -- - ?i i i iv ii i L1PREC2_orf2# 657 AACCGAAATCATACCAAA--CA-CNCTCTCGGACCACAGCGCAATAAAAA 703 chrXptel1M 618968 T 618968 L1PREC2_orf2# 704 T 704 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 39.22 CpG sites = 50, Kimura (unadjusted) = 41.35 Transitions / transversions = 1.02 (50/49) Gap_init rate = 0.05 (16 / 326), avg. gap size = 2.06 (33 / 16) 1237 28.85 5.48 3.04 chrXptel1M 619551 620097 (379903) C L1ME5_3end#LINE/L1 (313) 628 69 m_b341s551i30 14269 chrXptel1M 619551 TTTCACTCAGCATCA-ATTCATTTAAG-TCTCTCCAGGC--CTTTCTGAA 619596 ii -i -- - iv v i-- v v v C L1ME5_3end#LI 628 TTTCACTCAGCACTATGTT--TTTAAGATCCATCCATGTTGCTATGTGTA 581 chrXptel1M 619597 ATCATCCTGCTGGTCATTTCTTACAGAACAATAATATTCCATAATATTCA 619646 -- iv iiv iii v v vvvv i i ii i v C L1ME5_3end#LI 580 --CATCTAGTCCGTTGCTTCTAACTGCTGCATAGTACTCCATGGTGTGCA 533 chrXptel1M 619647 TATACCACAATTTATTCAGCCATTCTCCAACTGATGGGCATCCATTCAGT 619696 vi v iii v i v v i i vviv i C L1ME5_3end#LI 532 TCCACCACATTTTACCTATCCACTCTCCCAGTGATGGACACCCAGGTTGC 483 chrXptel1M 619697 TTCCAGTTTCTGGTCACTACAAAGAGGGCTGCCACAAACATTCGTGCACA 619746 i ii i iv i i v iv v ii i vi i C L1ME5_3end#LI 482 CTCCAACTCCCCGCCACCACAAACAACGCTGCAATGAACATCCTCGTACA 433 chrXptel1M 619747 TACAGGTCCCTTTC----CCTTCTTTATAATCTCTTTGGGGTATAAGCCC 619792 ---- i v---- viv v v i i vi C L1ME5_3end#LI 432 T----GTCCCCTTATGGACCTGTGTGAGAATTTCTTTGGGATATATACCC 387 chrXptel1M 619793 AGTAGAGACACTGCTGGATCAAAGGGTATGCACAGTTTGATAACTT--TT 619840 v v iv i i v --- --- - -- C L1ME5_3end#LI 386 AGGAGCGGAATTGCTGGGTCATAGGGTATGC---GT---ATA-CTTAATT 344 chrXptel1M 619841 TGAGCA--TAGTTCCAAATTGCTCTCCAGAATGGTTGGATGCATTCACAA 619888 vi -- v v i i v ivvi ii v C L1ME5_3end#LI 343 TGACTAAGTACTGCCAGATTGCTCTCCAGAATGGCTGCACCAGTCTACAC 294 chrXptel1M 619889 TTGCACCAACAATGTATCAGTGTCCCAATTTTCCCACATCCCCTCTCACA 619938 iv i i i v v i v ? i i v iv C L1ME5_3end#LI 293 TCCCACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATCCTCGCCAACA 244 chrXptel1M 619939 TTCATCGTTATTT--TTTCCTGTCATCTCAGCCAATTTGACAAGTGTGTA 619986 i iiv i ii--i i i-- i iv i i i i i iv C L1ME5_3end#LI 243 CTTGGCATTATCCAGCTTTCTA--ATTTTTGCCAGTCTAATAGGTGTAAA 196 chrXptel1M 619987 GTGGTATCTCAGAGTTGTCTTAATTTGCATTTCTCTGATCAACAGTGATT 620036 i vv i i vi i v C L1ME5_3end#LI 195 GTGATATCTCATTGTTGTTTTAATTTGCATTTCTCTGATTACTAATGAGT 146 chrXptel1M 620037 TGGAACA-CT-TTCATATG---ATTAGAAAT---AGTTTTA--------A 620070 v i - - ---i vvv ---i iv-------- C L1ME5_3end#LI 145 TTGAGCATCTCTTCATATGCTTGTTAGCCTTTCGGGTTTCCTCTTCTGTA 96 chrXptel1M 620071 AATTGTCTGTTCATATCCTTTAACTAT 620097 i iv i C L1ME5_3end#LI 95 AATTGCCTGTTCATATCCTTTGCCCAT 69 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 37.24 CpG sites = 90, Kimura (unadjusted) = 37.55 Transitions / transversions = 1.43 (90/63) Gap_init rate = 0.05 (29 / 546), avg. gap size = 1.62 (47 / 29) 1267 27.97 4.88 2.07 chrXptel1M 619627 620097 (379903) C L1ME3Cz_3end#LINE/L1 (449) 548 65 m_b341s551i31 14269 chrXptel1M 619627 ATAATATTCCATAATATTCATATACCACAATTTATTCAGCCATTCTCCAA 619676 i vi vv i v i v C L1ME3Cz_3end# 548 ATAGTATTCCATTGTATGAATATACCACAATTTATTTATCCATTCCCCTA 499 chrXptel1M 619677 CTGATGGGCATCCATTCAGTTTCCAGTTTCTGGTCACTACAAAGAGGGCT 619726 i i ii vviv i i v ii i v iv C L1ME3Cz_3end# 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chrXptel1M 619727 GCCACAAACATTCGTGCACATACAGGTCCCTTT---CCCTTCTTT-ATAA 619772 v ii i v i ---- i i --- v v v vi- v i C L1ME3Cz_3end# 448 GCAATGAACATCCTTGTACAT----GTCTCCTTGTGCACATGTGCGAGAG 403 chrXptel1M 619773 TCTCTTTGGGGTATAAGCCCAGTAGAGACACTGCTGGATCAAAGGGTATG 619822 i i i vi i v v iv i i iv C L1ME3Cz_3end# 402 TTTCTCTAGGGTATATACCTAGAAGTGGAATTGCTGGGTCGTAGGGTATG 353 chrXptel1M 619823 CACAGTTTGATAACTTTTTGAGCATAGTTCCAAATTGCTCTCCAGAATGG 619872 i vi --i viv - v v i i C L1ME3Cz_3end# 352 CGCATCTT--CAACTTTACTAG-ATATTGCCAAATTGCTCTCCAAAGTGG 306 chrXptel1M 619873 TTGGATGCATTCACAATTGCACCAACAATGTATCAGTGTCCCAATTTTCC 619922 v ivv i v iv i i v v i vi ii C L1ME3Cz_3end# 305 TTGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTTCCCGTTTCTC 256 chrXptel1M 619923 CACATCCCCTCTCACATTC---ATCGTTATTTTTTCCTGTCATCTCAGCC 619969 i v iv i i--- i i vvi iv---v i iv C L1ME3Cz_3end# 255 CACATCCTCGCCAACACTTGGTATTGTCAGACTTTTA---AATTTTTGCC 209 chrXptel1M 619970 AATTTGACAAGTGTGTAGTGGTATCTCAGAGTTGTCTTAATTTGCATTTC 620019 i iii v i vv ? i C L1ME3Cz_3end# 208 AATCTGATGGGTGTGAAATGGTATCTCATTGTNGTTTTAATTTGCATTTC 159 chrXptel1M 620020 TCTGATCAACAGTGATTTGGAACA--CTTTCATATG---ATTAGAAAT-- 620062 i i vi vv v i --i --- i vv -- C L1ME3Cz_3end# 158 CCTGATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTC 109 chrXptel1M 620063 -AGTTTTA--------AAATTGTCTGTTCATATCCTTTAACTAT 620097 -i iv--------i i iv i C L1ME3Cz_3end# 108 GGGTTTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCAT 65 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 34.61 CpG sites = 75, Kimura (unadjusted) = 35.99 Transitions / transversions = 1.39 (75/54) Gap_init rate = 0.04 (18 / 470), avg. gap size = 1.83 (33 / 18) 323 30.81 3.41 9.64 chrXptel1M 620317 620668 (379332) C L1M5_orf2#LINE/L1 (348) 2946 2615 m_b341s551i32 14269 chrXptel1M 620317 TCCTATGTT--CTTCTAATTTATTTATAATCTCACTCTTTATGCCTAAAT 620364 -- ivvvv i i i ?ii iiii ii C L1M5_orf2#LIN 2946 TCCTATGTTTTCTTCTAGAAGTTTTATAGTTTTANCTTTTACATTTAGGT 2897 chrXptel1M 620365 C-ATGAACCCATTTCAACCTTATCTTGGTATATGGTATTAGGTGTGGTTC 620413 - -i i ?i vi v i v i i v iv v C L1M5_orf2#LIN 2896 CTATGA-TCCATCTNGAATTAATTTTTGTGTATGGTGTGAGGTAGGGGTC 2848 chrXptel1M 620414 AATGTCTAGTTTCTGCCTTACTAGTTTCCAATTTTCCCTGCAGTTTTTGT 620463 i v? ii v i v v ivii v v i v viv C L1M5_orf2#LIN 2847 GAGNTTCATTTTTTTCCATATGGATATCCAATTGTTCCAGCACCATTTGT 2798 chrXptel1M 620464 CAAATAGTGAATTCTTATCCCAAAAGCTGGGGT-CTTTGGG---TTTGTC 620509 ii v vvv i vi ---- iiv - ? v--- C L1M5_orf2#LIN 2797 TGAAAAGACTATCCTTTCCCCA----CTGAATTGCNTTGGCACCTTTGTC 2752 chrXptel1M 620510 AAACACTAGATTGCTATAGTCATTAACTAGATTAT-TATAGTCATTGACT 620558 v ii i? v? i -------------- - i i ----- v C L1M5_orf2#LIN 2751 AAAAATCAANTGNCCATA--------------TATGTGTGG-----GTCT 2721 chrXptel1M 620559 ATTTTCTCCTATAAAC---CTAACCTATTCCACTGATTGACTACTCTATT 620605 i------ ii --- vi i i iv i vv i C L1M5_orf2#LIN 2720 ATTTC------TGGACTCTCTATTCTGTTCCATTGATCTATTTGTCTATC 2677 chrXptel1M 620606 TCTTA-GCCAGTACCAAATGATTTTGATGATTGCTGCTTTATAATACAGT 620654 - - i v ivi i v i iv - C L1M5_orf2#LIN 2676 -CTTACGCCAATACCACACTGTCTTGATTACTGTAGCTTTATAATA-AGT 2629 chrXptel1M 620655 TTTAAGGTCTGGCA 620668 i i ?i ? i C L1M5_orf2#LIN 2628 CTTGANATCNGGTA 2615 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 41.70 CpG sites = 60, Kimura (unadjusted) = 42.28 Transitions / transversions = 1.58 (60/38) Gap_init rate = 0.11 (39 / 351), avg. gap size = 1.13 (44 / 39) 353 31.15 2.93 2.93 chrXptel1M 620324 620528 (379472) C L1P3_orf2#LINE/L1 (357) 2937 2733 m_b341s551i33 14269 chrXptel1M 620324 TTCTTCTAATTTATTTATAATCTCACTCTTTATGCCTAAATCATGAACCC 620373 ivv v ii i i vvii i ii i v v i C L1P3_orf2#LIN 2937 TTCTTCTAGGGTTTTTATGGTTTTAGGTCTTACGTTTAAGTCTTTAATCC 2888 chrXptel1M 620374 ATTTCAACCTTATCTTGGTATATGGTATTAGGT-GTGGTTCAATGTCTAG 620422 i ii vi v i v v i v v- v i i v viv C L1P3_orf2#LIN 2887 ATCTTGAGTTAATTTTTGTATAAGGTGTAAGGAAGGGGTCCAGTTTCAGT 2838 chrXptel1M 620423 TTTCTGCCT--TACTAGTTTCCAATTTTCCCTGCAGTTTTTGTCAAATAG 620470 v --vi --- i vi viv i i C L1P3_orf2#LIN 2837 TTTCTGCATATGGCTAG---CCAGTTTTCCCAACACCATTTATTAAATAG 2791 chrXptel1M 620471 TGAATTCTTATCCCAAAAGCTGGGGTCTTTG---GGTTTGTCAAACACTA 620517 v i - v vv v -- i --- v ii C L1P3_orf2#LIN 2790 GGAATCCTT-TCCCCATTGCTTG--TTTTTGTCAGGTTTGTCAAAGATCA 2744 chrXptel1M 620518 GATTGCTATAG 620528 v i i C L1P3_orf2#LIN 2743 GATGGTTGTAG 2733 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 40.20 CpG sites = 33, Kimura (unadjusted) = 41.06 Transitions / transversions = 1.14 (33/29) Gap_init rate = 0.04 (9 / 204), avg. gap size = 1.33 (12 / 9) 349 32.82 2.95 2.05 chrXptel1M 620691 621029 (378971) L1M5_orf2#LINE/L1 755 1096 (2198) m_b341s551i34 14268 chrXptel1M 620691 TAAATAATCTAATCCTAAAGAATGAATGGATAAAACAACAAATCAAAGAC 620740 i ivi v i v ivv i v v v v i?v L1M5_orf2#LIN 755 TAAACAACACACTTCTAAATAACCCATGGGTCAAAGAAGAAATCACAANG 804 chrXptel1M 620741 ACAATCAATAATTTTATCCAAGAGAATGACAATTATGAGACAGCATACCA 620790 iv i iv v v v iv vv ? v vi v i i L1M5_orf2#LIN 805 GAAATTAGAAAATATTTTGAACTGAATGANAATGAAAATACAACATATCA 854 chrXptel1M 620791 AAATTTATGGGATACAGCCAAAGCAATTCTTGGGGGAACTTTTATATCTC 620840 i i i i v i i i vv v ?i L1M5_orf2#LIN 855 AAATTTGTGGGATGCAGCTAAAGCAGTGCTTAGAGGGAAATTTATAGCNT 904 chrXptel1M 620841 TAGATGCTTACTTGCATAAAATAGAGAAAGAG---AAGATCAATGAATTG 620887 i ? iv --- i v ii ii --- i vi i L1M5_orf2#LIN 905 TAAATGCNTATAT---TAGAAAAGAAGAAAGGCTTAAAATCAATGATCTA 951 chrXptel1M 620888 GG--TACATGACTAAAAAAGCTATTAAAAAAATTAAAAACC--ACCCACA 620933 i -- v i-- v i vv i vviv ii-- - L1M5_orf2#LIN 952 AGCTTCCAC--CTTAAGAAGCTAGAAAAAGAAGAGCAAATTAAACCCA-A 998 chrXptel1M 620934 ATTAAATACCAAATTTGAAATTCTGAAAATAAAAAGGGAGATTAATAAAA 620983 v? i vv iivvv vv i i i ivi i i i L1M5_orf2#LIN 999 AGNAAGTAGAAGGAAGGAAATAATAAAGATAAGAGCAGAAATCAATGAAA 1048 chrXptel1M 620984 TTATAAGAGAAA---ACTATTGAACAAATAAACACAATTAAGAGTTGGT 621029 - v i v --- v v iv v iv iii i i L1M5_orf2#LIN 1049 -TAGAAAACAAANANACAATAGAGAAAATCAACGAAGCCAAAAGCTGGT 1096 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 44.53 CpG sites = 58, Kimura (unadjusted) = 45.09 Transitions / transversions = 1.14 (58/51) Gap_init rate = 0.03 (11 / 338), avg. gap size = 1.55 (17 / 11) 373 27.44 2.21 3.35 chrXptel1M 620691 620871 (379129) L1P4_orf2#LINE/L1 755 933 (2361) m_b341s551i36 14268 chrXptel1M 620691 TAAATAATCTAATCCTAAAGAATGAAT---GGATAAAACAACAAATCAAA 620737 i ii iv --- v --- i - i viv L1P4_orf2#LIN 755 TAAACAACTTGCTCCT---GAATGACTTTTGGGTAAA-CAACGAAATTAA 800 chrXptel1M 620738 GACACAA-TCAATAATTTTATCCAAGAGAATGACAATTATGAGACAGCAT 620786 i v - v v iv iv iv? v iviv v i L1P4_orf2#LIN 801 GGCAGAAATCAAAAAATTCTTTGAAATNAATGAAAACAGAGACACAACAT 850 chrXptel1M 620787 ACCAAAATTTATGGGATACAGCCAAAGCAATTCTTGGGGGAACTTTTATA 620836 i v i ? i vi vi i vv L1P4_orf2#LIN 851 ACCAAAATCTCTGGGATGCAGCNAAAGCAGTGTTAAGAGGAAAGTTTATA 900 chrXptel1M 620837 TCTCTAGATGCTTACTTGCATAAAATAGAGAAAGA 620871 v v i i i v - v i -v L1P4_orf2#LIN 901 GCGCTAAACGCCTACAT-CAAAAAGT-TAGAAAGA 933 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 33.28 CpG sites = 24, Kimura (unadjusted) = 35.03 Transitions / transversions = 1.00 (24/24) Gap_init rate = 0.04 (8 / 180), avg. gap size = 1.25 (10 / 8) 408 28.93 1.24 1.24 chrXptel1M 620691 620851 (379149) L1PB_orf2#LINE/L1 755 915 (2379) m_b341s551i35 14268 chrXptel1M 620691 TAAATAATCTAATCCTAAAGAATGAATGGATAAAACAACAAATCAAAGAC 620740 i iv i vi v v i v ?v vv - i L1PB_orf2#LIN 755 TAAATAACCTGCTCCTGAATGATCATTGGGTCAANAATGAAATCAA-GAT 803 chrXptel1M 620741 ACAA--TCAATAATTTTATCCAAGAGAATGACAATTATGAGACAGCATAC 620788 iv -- ? v i - v vv i vi v i v i L1PB_orf2#LIN 804 GGAAATTNAAAAATTCT-TCGAACTGAACGACAATAGTGACACAACCTAT 852 chrXptel1M 620789 CAAAATTTATGGGATACAGCCAAAGCAATTCTTGGGGGAACTTTTATATC 620838 ii v v i ii v vi i vv i v L1PB_orf2#LIN 853 CAAAACCTCTGGGATACAGCAAAGGCGGTGCTAAGAGGAAAGTTCATAGC 902 chrXptel1M 620839 TCTAGATGCTTAC 620851 i i i L1PB_orf2#LIN 903 CCTAAATGCCTAC 915 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 35.61 CpG sites = 23, Kimura (unadjusted) = 37.61 Transitions / transversions = 1.00 (23/23) Gap_init rate = 0.02 (3 / 160), avg. gap size = 1.33 (4 / 3) 1708 29.30 5.95 1.14 chrXptel1M 621465 622220 (377780) L1M4_orf2#LINE/L1 1092 1883 (1411) m_b341s551i37 14268 chrXptel1M 621465 TTGGTTTTATGGAAAAA---ACAAAA----CATACTTCTTTAGTTAATTT 621507 i v i i --- ---- v -- i ivi L1M4_orf2#LIN 1092 TTGGTTCTTTGAAAAGATCAACAAAATTGACAAAC--CTTTAGCTAGACT 1139 chrXptel1M 621508 GATTAGAAAAAGACAAGAAAA---TCAA-CTGTTAGTATCAAAAATGAAA 621553 ii ii i vi i --- -i ii iv ii L1M4_orf2#LIN 1140 GACCAAGAAAAAAAGAGAGAAGACTCAAATTACTAAAATCAGGAATGAAA 1189 chrXptel1M 621554 AGGGTGA-ACTCTCACCAATGAAGAGGAAATTAGAGTAATAATTAGGAGT 621602 ii v - i vii i ivvvivi v i ivi v v iiv L1M4_orf2#LIN 1190 GAGGGGACATTACTACCGACCTTACAGAAATAAAAAGGATTATAAGGGAA 1239 chrXptel1M 621603 TATTTTGCCCAAATGTATGTCAATAAATTTGATAACCTAAGTGAAATGGA 621652 i v vv v i i v ii L1M4_orf2#LIN 1240 TACTATGAACAATTGTATGCCAACAAATTAGATAACCTAGATGAAATGGA 1289 chrXptel1M 621653 GTAATACCTATAAAAATATAGGCTGCCCAGATTAACAGAGGAGGAAGTAA 621702 vv v v i i i ii i v i i i vv i i i i L1M4_orf2#LIN 1290 CAAATTCCTAGAAAGACACAAACTACCGAAACTGACTCAAGAAGAAATAG 1339 chrXptel1M 621703 ATTGCTTGAATAGTCCCATTTTAGAAAAAGAAAGTGAACAAGCTATTAAC 621752 vviii v i vvi iiv i v iv iv i v L1M4_orf2#LIN 1340 AAAATCTGAATAGACCTATAACAAGTAAAGAGATTGAATTAGTAATCAAA 1389 chrXptel1M 621753 CGACTCCCTAAGAAAAAATCCCCAGGACCAGATGGATTTACATGTGAATT 621802 vi i i vi i vv ? v i vv L1M4_orf2#LIN 1390 AAACTTCCCACAAAGAAAAGCCCAGGNCCAGATGGCTTCACTGGTGAATT 1439 chrXptel1M 621803 CTACCAAACATTTAAAGAACAATTACTTCCAATACTATGCAAACTATTTA 621852 v viv v vii v iv L1M4_orf2#LIN 1440 CTACCAAACATTTAAAGAAGAATTAACACCAATCCTTCACAAACTCTTCC 1489 chrXptel1M 621853 GAAAAATAGGGAATGAAGGAGT-CCTACCAACTTCCTTTTATGACACAGA 621901 i iii v i ii- i v - v i vi vii L1M4_orf2#LIN 1490 AAAAAATAGAAGAGGAGGGAACACTTCCCAAC-TCATTCTATGAGGCCAG 1538 chrXptel1M 621902 TATGATGCTGATACCTAAAGGGTCAGA----------ACAGAGAAAGAAA 621941 v iv v ---i ---------- iii L1M4_orf2#LIN 1539 TATTACCCTGATACCAAAA---CCAGACAAAGACATCACAAGAAAAGAAA 1585 chrXptel1M 621942 ATTACAGACCAATTTCCCTAATGAATATTGATGCAAAAATCTTAAATAAA 621991 i v v v i v i L1M4_orf2#LIN 1586 ACTACAGACCAATATCCCTTATGAATATAGATGCAAAAATCCTCAACAAA 1635 chrXptel1M 621992 ATATTAGCAAAGAGATTACAGCAA------------GTCATCCCCATGAT 622029 i vv v v ------------i i --v iv L1M4_orf2#LIN 1636 ATACTAGCAAACCGAATCCAGCAACATATAAAAAGGATTAT--ACACCAT 1683 chrXptel1M 622030 GACCAAGTAGGATCTATACCAGG-----AAGGCTGGTTCACTATTAGGAA 622074 i i v ----- i vi ?v i L1M4_orf2#LIN 1684 GACCAAGTGGGATTTATCCCAGGAATGCAAGGTTGGTTCAACATNCGAAA 1733 chrXptel1M 622075 AAC--TTAGCATAATTGAC--TATCAATA-ACCAAACTAACAGAAATCAT 622119 v -- i iii vv -- i - vi v-i i i i L1M4_orf2#LIN 1734 ATCAATCAATGTAATACACCATATTAATAGAATAAAG-GACAAAAACCAC 1782 chrXptel1M 622120 ATGATTACCTTAATAGATGCAGAAAAGTCATTTGATCAAAACTAACATCT 622169 i i i i iv iv v i i i L1M4_orf2#LIN 1783 ATGATCATCTCAATAGACGCAGAAAAAGCATTTGACAAAATCCAACACCC 1832 chrXptel1M 622170 ATTCCTATTAAAAACACTAGAGAATGTAGGATTTAATGGAGTTTTCCTTA 622219 v v iv vi v vv v vi v iivi i L1M4_orf2#LIN 1833 TTTCATGATAAAAACACTCAACAAACTAGGAATAGAAGGGAACTTCCTCA 1882 chrXptel1M 622220 A 622220 L1M4_orf2#LIN 1883 A 1883 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 37.86 CpG sites = 127, Kimura (unadjusted) = 38.31 Transitions / transversions = 1.38 (127/92) Gap_init rate = 0.03 (21 / 755), avg. gap size = 2.57 (54 / 21) 427 25.72 0.72 7.69 chrXptel1M 623796 623934 (376066) MIRb#SINE/MIR 1 130 (138) m_b341s601i6 14270 chrXptel1M 623796 CAGGGGGGCAGCTAGGTGGCACAGTGGATAGAGCACCAGCCCTAAAATCA 623845 i --- ii v vi ii ii i MIRb#SINE/MIR 1 CAGAGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCA 47 chrXptel1M 623846 GGAGGACCTGAGTTCAAATTTGATCTCAGACACTTAATACTTCCTGGCTG 623895 ivi i i iiviv v v ------- i MIRb#SINE/MIR 48 GACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTA-------CTAGCTG 90 chrXptel1M 623896 TATGACCCGGGGCAAGTCACTTACCCCCAATT-GCCTCAG 623934 i iv i v i vv v- MIRb#SINE/MIR 91 TGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAG 130 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 29.92 CpG sites = 21, Kimura (unadjusted) = 32.26 Transitions / transversions = 1.75 (21/12) Gap_init rate = 0.08 (11 / 138), avg. gap size = 1.00 (11 / 11) 469 22.10 0.00 8.77 chrXptel1M 623962 624085 (375915) MIRc#SINE/MIR 2 115 (153) m_b341s601i7 14271 chrXptel1M 623962 GGGGCAGCTAGATGGCTCAGTGGATAGAGTGCTGACCCTGAAGTCAGGAG 624011 i i---i iv v ii iv i i i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chrXptel1M 624012 GGCCTGAGTTCAAATCCTGCCCCAGACACTTAATACTTCCTAGCTGTGTG 624061 i i i i i v i v v ------- MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTG 91 chrXptel1M 624062 ACCCTAGGCAAGTCACTTAACCCC 624085 i i i MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 24.66 CpG sites = 19, Kimura (unadjusted) = 27.17 Transitions / transversions = 3.17 (19/6) Gap_init rate = 0.08 (10 / 123), avg. gap size = 1.00 (10 / 10) 21 22.29 5.17 0.00 chrXptel1M 626256 626313 (373687) (AG)n#Simple_repeat 1 61 (0) m_b341s252i16 14272 chrXptel1M 626256 AGAGAG-GGGGGAGA-AGAGA-AGAAGGAGAGAGACAGAGAGAAAGAGGC 626302 - i i - - ii v i iv (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chrXptel1M 626303 AGGTAGACAGA 626313 iv v (AG)n#Simple_ 51 AGAGAGAGAGA 61 Matrix = Unknown Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.05 (3 / 57), avg. gap size = 1.00 (3 / 3) 231 24.39 3.66 0.00 chrXptel1M 626818 626899 (373101) L1MEc_5end#LINE/L1 2385 2469 (58) m_b341s551i38 14273 chrXptel1M 626818 AAAACCCTACAATCTTTTTCTTACAAGAAATTCA--TTAAAAATGAAGAC 626865 i v v v vi v i i? -- v i L1MEc_5end#LI 2385 AAGACCCAACTATATGCTGCCTACAAGAAACNCACTTTAAATATAAAGAC 2434 chrXptel1M 626866 ATAAACAAAATAAAAGT-AGGGGCTGGAAAAAAAT 626899 i i iiv - ii v i L1MEc_5end#LI 2435 ACAAATAGGTTAAAAGTAAAAGGATGGAAAAAGAT 2469 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 30.63 CpG sites = 12, Kimura (unadjusted) = 30.63 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.02 (2 / 81), avg. gap size = 1.50 (3 / 2) 232 33.01 0.00 2.00 chrXptel1M 627058 627159 (372841) L1PB_orf2#LINE/L1 343 442 (2852) m_b341s551i39 14274 chrXptel1M 627058 TATGCTCCAAATGCCTTAGTGTCCAAATTTATAAAACAAATATCACTAAG 627107 v v ii ivv ivi v ii ? ii L1PB_orf2#LIN 343 TATGCACCTAACACTGGAGCTCCCAAATTTATAAAACAATTACTANTAGA 392 chrXptel1M 627108 CTGCTACACAGAGATATAGAGAGTAATGCAACAATGACCAGAGATTTCAA 627157 -- viv iv v v i ii i iiivi i i L1PB_orf2#LIN 393 C--CTAAGAAATGAGATAGACAGCAACACAATAATAGTGGGGGACTTCAA 440 chrXptel1M 627158 TA 627159 L1PB_orf2#LIN 441 TA 442 Matrix = 20p35g.matrix Kimura (with divCpGMod) = 46.36 CpG sites = 21, Kimura (unadjusted) = 46.36 Transitions / transversions = 1.75 (21/12) Gap_init rate = 0.02 (2 / 101), avg. gap size = 1.00 (2 / 2) 19 12.06 0.00 0.00 chrXptel1M 627688 627715 (372285) (A)n#Simple_repeat 1 28 (0) m_b341s252i17 14275 chrXptel1M 627688 AAAAAAAAAAAAAAAGAAAGAAAGAAAA 627715 i i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA 28 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 234 33.85 1.53 0.76 chrXptel1M 629083 629213 (370787) AmnL2-1#LINE/L2 2361 2492 (121) m_b341s601i8 14276 chrXptel1M 629083 GAGCATTTTCATATCCTATCTCCGAACTGCTGGAATAGTCTCCCTCTTCA 629132 v i v v v - v viv vv i i i v viv AmnL2-1#LINE/ 2361 GAGCCTTCTCCTCTGC-AGCTCCTGCCATCTGGAACAGCCTTCCTGTATC 2409 chrXptel1M 629133 TCTCTACCTCTTAGATTTCTTAACTTCTTTCAAATCTCAGCTAAAATCCT 629182 ii v v i iiii v i? ? i v v AmnL2-1#LINE/ 2410 TCTCCGCCTCATCGACTCTCCATCTCNTTTCAAATCTCANCTGAAAACAT 2459 chrXptel1M 629183 A-CTTTCTTTTTTTAAA-ATAGCTTTTTGTTTC 629213 - ii iii ivv- v i vi AmnL2-1#LINE/ 2460 ATCTTTTCTCCCTTGCCTATACCTCTTAATTTC 2492 Matrix = 25p35g.matrix Kimura (with divCpGMod) = 45.39 CpG sites = 23, Kimura (unadjusted) = 47.00 Transitions / transversions = 1.10 (23/21) Gap_init rate = 0.02 (3 / 130), avg. gap size = 1.00 (3 / 3) 886 29.38 6.45 2.41 chrXptel1M 629616 630173 (369827) C L1MC5a_3end#LINE/L1 (2140) 637 58 m_b342s551i0 14277 chrXptel1M 629616 CCTGGTTCTTCTCACTTA-CAGT---TCCTGTAAGTCTCTCCAGGCCTCT 629661 v i i i - i --- v ii v vi? vv C L1MC5a_3end#L 637 CCTTGCTTTTTTCACTTAACAATATATCCTGGAGATCACTCCATANCAGT 588 chrXptel1M 629662 CTAAAATCATCCTCCTGATCGTTTCTTATAGAACAATAATATTCCATAAC 629711 v v ivv i v ivi i i vvvv i i vii C L1MC5a_3end#L 587 ATATAGAGATCTTCCTCATTCCTTTTTACAGCTGCATAGTACTCCATTGT 538 chrXptel1M 629712 ATTCATATACCACCACTTATTCAACCATTTTCC-ATTCA----------- 629749 i vv i ivii v ii - v ----------- C L1MC5a_3end#L 537 GTGGATGTACCATAGTTTATTCAACCAGTCCCCTATTGATGGACATTTGG 488 chrXptel1M 629750 ---GTTTCCAGTTTCTAGCCACTACAAACAGGGCTGCCACAAATCTCCGT 629796 --- i i v i i i iv v ii vv v C L1MC5a_3end#L 487 GTTGTTTCCAGTCTTTTGCTATTACAAATAATGCTGCAATGAATAACCTT 438 chrXptel1M 629797 GCACATACAGGTCCCTTTCCCTTCTTTATGA---TCTCTTTGGGGTATAA 629843 ii -- ?- viv i ii? --- v i i v v C L1MC5a_3end#L 437 GTGCATAC--GTCN-TTTCGTATTTTTGCNAGTGTATCTTCGGGATAGAT 391 chrXptel1M 629844 GCCCAGGAGTAACACTGCTGGATCAAAGGGTA--TGCACAGTTTGATAAC 629891 v i i iiv i i -- i --- - i C L1MC5a_3end#L 390 TCCTAGAAGTGGGATTGCTGGGTCAAAGGGTAAATGCATA---TG-TAAT 345 chrXptel1M 629892 TTTTTAAGCATAGTTTCAAATTGCTCTCCAGAATGGCTGGATGTATTCAC 629941 viv - v vi v i v iv i v ivvv ii C L1MC5a_3end#L 344 TTTGCTAG-ATATTGCCAAATTCCCCTCCATAGGGGTTGTACCATTTTGC 296 chrXptel1M 629942 AATTCCACCAACAATGCATCAGTGTCCCAGTTTCC--ACATCCCCTCCAA 629989 v i i i v v v v -- v i v C L1MC5a_3end#L 295 ATTCCCACCAGCAATGTATGAGAGTGCCTGTTTCCCCACAGCCTCGCCAA 246 chrXptel1M 629990 CAA------TTGTCATTATCTTTTCCTGTCACCTTAACCAATCTGAGAGG 630033 i------ -- v vv---- ii vi v C L1MC5a_3end#L 245 CAGAGTATGTTGTCA--AACTTTTGG----ATTTTTGCCAATCTGATAGG 202 chrXptel1M 630034 TGTATAGTGGTATTTCAGAGTTATCTTAATTTGCATTTCTCTGATCAAGA 630083 viv i i v vi i v i v C L1MC5a_3end#L 201 TGAGAAATGGTATCTCAGTGTAGTTTTAATTTGCATTTCTCTTATTATGA 152 chrXptel1M 630084 GTGATTTAGAGCACTTTTTCATATGACCAGAAATGGCTTTCATTTCTTCG 630133 vv v ii vii iiiiivii v iv C L1MC5a_3end#L 151 GTGAGGTTGAGCATCTTTTCATATGTTTAAGGGCCATTTGCATTTCTTTT 102 chrXptel1M 630134 TCTGAAAA----CTGTTCATATCCTCTGACCATTTATCAATTGG 630173 vi ---- i i v v v C L1MC5a_3end#L 101 TCTGTGAACTGTCTGTTCATATCTTTTGCCCATTTTTCTATTGG 58 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.97 CpG sites = 85, Kimura (unadjusted) = 38.27 Transitions / transversions = 1.13 (85/75) Gap_init rate = 0.04 (24 / 557), avg. gap size = 2.08 (50 / 24) 1125 26.43 5.45 1.62 chrXptel1M 629697 630173 (369827) C L1ME3G_3end#LINE/L1 (376) 548 54 m_b342s551i1 14277 chrXptel1M 629697 ATAATATTCCATAACATTCATATACCACCACTTATTCAACCATTTTCC-- 629744 i ii vv iv i i ii -- C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chrXptel1M 629745 ---------ATTCAG----TTTCCAGTTTCTAGCCACTACAAACAGGGCT 629781 --------- i ---- i i v i i iv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chrXptel1M 629782 GCCACAAATCTCCGTGCACATACAGGTCCCTTTCC-CTTCTTTATG-ATC 629829 v ii iv v i i ?-- i v v - v v viiv - i C L1ME3G_3end#L 448 GCAATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATT 401 chrXptel1M 629830 TCTTTGGGGTATAAGCCCAGGAGTAACACTGCTGGATCAAAGGGTATGCA 629879 ? i i v v? ? i iiv i i i C L1ME3G_3end#L 400 TCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCG 351 chrXptel1M 629880 CAGTTTGATAACTTTTTAAGCATAGTTTCAAATTGCTCTCCAGAATGGCT 629929 v --- v v viv v vi i i ? C L1ME3G_3end#L 350 CATTTT---AAATTTTAATAGATACTGCCAAATTGCCCTCCAAAANGGCT 304 chrXptel1M 629930 GGATGTATTCACAATTCCACCAACAATGCATCAGTGTCCCAGTTTCC--A 629977 v ivv i v i i i i v v v v -- C L1ME3G_3end#L 303 GTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCA 254 chrXptel1M 629978 CATCCCCTCCAACAATTGTCATTATCTTTTCCTGTCACCTTAACCAATCT 630027 i i v v ? vi vv?iii vvv ii vi C L1ME3G_3end#L 253 CACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATCT 204 chrXptel1M 630028 GAGAGGTGTATAGTGGTATTTCAGAGTTATCTTAATTTGCATTTCTCTGA 630077 vi v v i i vv i i i C L1ME3G_3end#L 203 GATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGA 154 chrXptel1M 630078 TCAAGAGTGATTTAGAGCACTTTTTCATATGACCAGAAATGGC---TTTC 630124 i vv vv v ii vii v--- --- vi C L1ME3G_3end#L 153 TTACTAGTGAGGTTGAGCATCTTTTCATATGTTTAT---TGGCCATTTGT 107 chrXptel1M 630125 ATTTCTTCGTCTGAAAA----CTGTTCATATCCTCTGACCATTTATCAAT 630170 i v vi ---- i v v v C L1ME3G_3end#L 106 ATTTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTAT 57 chrXptel1M 630171 TGG 630173 C L1ME3G_3end#L 56 TGG 54 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 32.99 CpG sites = 65, Kimura (unadjusted) = 33.68 Transitions / transversions = 1.10 (65/59) Gap_init rate = 0.03 (16 / 476), avg. gap size = 2.12 (34 / 16) 212 25.67 14.08 1.25 chrXptel1M 631113 631183 (368817) L2c_3end#LINE/L2 390 469 (9) m_b342s601i1 14278 chrXptel1M 631113 GATGGCAGGAACTTTTGTCTTA---ATCT------CTCCAGC-CCTGATA 631152 v i iv - --- ------ i - ii L2c_3end#LINE 390 GAGGGCAGGGACCGT-GTCTTATTCATCTTTGTATCCCCAGCGCCTGGCA 438 chrXptel1M 631153 TACAGTAGGTACTGAAGAACTGCTTACTAAA 631183 i i ii v v v i ii i L2c_3end#LINE 439 CATAGTAGGCGCTCAATAAATGTTTGTTGAA 469 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.45 CpG sites = 13, Kimura (unadjusted) = 33.10 Transitions / transversions = 2.60 (13/5) Gap_init rate = 0.06 (4 / 70), avg. gap size = 2.75 (11 / 4) 513 22.67 4.08 6.99 chrXptel1M 631667 631813 (368187) MIRc#SINE/MIR 5 147 (121) m_b342s601i2 14279 chrXptel1M 631667 GCAGTGGCAGCACAGTGCCCAGAGTACCAGACCTGGAGTCAGGAAGACTC 631716 -ii ii vvv i ii i -- MIRc#SINE/MIR 5 GCAGTG-TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA--C 51 chrXptel1M 631717 CTCTTTGAGAGTTCAAATCCTGTCTCAGATACTTA----CTGTGTGATCC 631762 ------ i i i i v v vi ---- i i MIRc#SINE/MIR 52 CT------GGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCT 95 chrXptel1M 631763 TAGCCAAGTCACTTATCCTTGTTT--GCCTCAGTGTCCTCATCTACAACA 631810 i v v i- i -- v ii v MIRc#SINE/MIR 96 TGGGCAAGTCACTTAACCTC-TCTGAGCCTCAGTTTCCTCATCTGTAAAA 144 chrXptel1M 631811 TAG 631813 i MIRc#SINE/MIR 145 TGG 147 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 25.74 CpG sites = 21, Kimura (unadjusted) = 27.81 Transitions / transversions = 2.10 (21/10) Gap_init rate = 0.08 (12 / 146), avg. gap size = 1.33 (16 / 12) 295 29.69 5.52 3.24 chrXptel1M 632170 632531 (367469) L1PB_orf2#LINE/L1 2458 2827 (467) m_b342s551i2 14280 chrXptel1M 632170 AAATTAATTTAAACTTTTAATGCTATTCTGATCAAGATATCAAAA-AATA 632218 vi i v vv i v iv i i vv -v - L1PB_orf2#LIN 2458 AAAGCAATCTACAAATTCAATGCAATTCCCATCAAAATACCACCATCAT- 2506 chrXptel1M 632219 TCTATCACAAAACTTGAAAAAATAAT---AAAATTCTTTTGGAAAAAGTG 632265 - i v i --- v v vv ivi L1PB_orf2#LIN 2507 TCT-TCACAGAACTAGAAAAAACAATCCTAAAATTCATATGGAACCAAAA 2555 chrXptel1M 632266 AAGATGTAGAATATCAAGAG-AAGTTTGA--AAAGGGTAGCGAAACAGAG 632312 vviv v v v i - vi i -- ii - i i v v ii L1PB_orf2#LIN 2556 AAGAGCCCGCATAGCCAAAGCAAGACTAAGCAAAAAG-AACAAATCTGGA 2604 chrXptel1M 632313 GGAATAACAATTATA-GACCTTAAACTATATTATGAAGCAGAAATTCTCA 632361 v v - iv- i i i i i viv i ivi L1PB_orf2#LIN 2605 GGCATCACA-TTACCCGACTTCAAACTATACTATAAGGCCATAGTCACCA 2653 chrXptel1M 632362 AAACTGTTTGGTATTGGC-TAAAAATTGG---GTAGGTCAATGGAACAGA 632407 v iv i i- v ---i ii L1PB_orf2#LIN 2654 AAACAGCATGGTACTGGTATAAAAATAGGCACATAGACCAATGGAACAGA 2703 chrXptel1M 632408 CTAGACAAAGCAGAGTCAGAAGCAAAGGAACT--CAATAAACCAGTGCTG 632455 v v vv ivi i vv v-- -- iiv iii vi v L1PB_orf2#LIN 2704 ATAGAGAACCCAGAAATAAACCCAAAT--ACTTACAGCCAACTGATCTTC 2751 chrXptel1M 632456 GGTAAATCA---GAAAACATAAATTAATTAGGAAAGAACTCCCTATTTGA 632502 ii v ---i --- i vi i v ii L1PB_orf2#LIN 2752 GACAAAGCAAACAAAAACATAA---AGTGGGGAAAGGACACCCTATTCAA 2798 chrXptel1M 632503 CTATAAAT--TTCTGGGAAAACT-GCAAGGCA 632531 --- -- v v i - v L1PB_orf2#LIN 2799 C---AAATGGTGCTGGGATAATTGGCAAGCCA 2827 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.43 CpG sites = 54, Kimura (unadjusted) = 38.43 Transitions / transversions = 1.08 (54/50) Gap_init rate = 0.06 (23 / 361), avg. gap size = 1.39 (32 / 23) 20 16.41 0.00 0.00 chrXptel1M 632606 632639 (367361) (A)n#Simple_repeat 1 34 (0) m_b342s252i0 14281 chrXptel1M 632606 AAAAATAAAATTTGAAAAAAAAAAAAAAAAAAAA 632639 v vvvi (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 34 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 495 22.26 0.00 7.96 chrXptel1M 633369 633490 (366510) MIRc#SINE/MIR 1 113 (155) m_b342s601i3 14282 chrXptel1M 633369 CAAGGCAGCCAGGTGGTGCAGTGAATAGAGCAGCAGCCCTGAAGTCAGAA 633418 i i--- i v vii v i i i MIRc#SINE/MIR 1 CGAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGA 47 chrXptel1M 633419 GGATCTGAGTACAAATCTGGCCTCAGACACTAATACTTCCTAGCTGTATG 633468 i i i v i i iv v v v ------ v i MIRc#SINE/MIR 48 AGACCTGGGTTCGAGTCCCGGCTCTGCC------ACTTACTAGCTGTGTG 91 chrXptel1M 633469 ACCCTGGGCAAGTCACTTAACC 633490 i MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACC 113 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.43 CpG sites = 16, Kimura (unadjusted) = 26.87 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.07 (9 / 121), avg. gap size = 1.00 (9 / 9) 24 27.34 0.00 1.39 chrXptel1M 633553 633625 (366375) (ATAT)n#Simple_repeat 1 72 (0) m_b342s252i2 14283 chrXptel1M 633553 ATCTACATATACATATATATGTAAATTTATAAATATATGTGTGTATGTAT 633602 v i i i v v v i i i i (ATAT)n#Simpl 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chrXptel1M 633603 ATACATAAATACATTTCACATAT 633625 i v i v - i (ATAT)n#Simpl 51 ATATATATATATATAT-ATATAT 72 Matrix = Unknown Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.01 (1 / 72), avg. gap size = 1.00 (1 / 1) 22 25.17 1.19 4.94 chrXptel1M 633551 633634 (366366) (ACATAT)n#Simple_repeat 1 81 (0) m_b342s252i1 14284 chrXptel1M 633551 ACATCTACATATACATATATATGTAAATTTATAAATATATGTGTGTATGT 633600 v i i v v i v i i iii ii (ACATAT)n#Sim 1 ACATATACATATACATATACATATACATATACATATACATATACATATAC 50 chrXptel1M 633601 ATATACATAAATACATTTCACATATGGCA-ATACA 633634 -- v - -i - (ACATAT)n#Sim 51 ATATACAT--ATACATAT-ACATAT-ACATATACA 81 Matrix = Unknown Transitions / transversions = 2.20 (11/5) Gap_init rate = 0.06 (5 / 83), avg. gap size = 1.00 (5 / 5) 312 26.67 3.70 0.00 chrXptel1M 634732 634866 (365134) L1MD3_3end#LINE/L1 430 569 (2173) m_b342s551i4 14285 chrXptel1M 634732 ACATATACCAGAAT-CTTATAGCAGCATTTTTCGTGATGGCAAAGACTTG 634780 v i vv -i v v i i ? v i ?i L1MD3_3end#LI 430 ACCTGTACACGAATGTTTATAGCAGCTTTATTCATAATNGCCAAAANCTG 479 chrXptel1M 634781 GAAACAAAGTGGATATCCGTGGATTGGGGAATGGGCAAAC--ACTGTGGT 634828 vv?i i ? vi iv v ii -- L1MD3_3end#LI 480 GAAACAACCNAGATGTCCNTCAACAGGTGAATGGATAAACAAACTGTGGT 529 chrXptel1M 634829 CCAT--GTGTAATGGAATATGAGTATACTGTAAAAAGAAA 634866 v --i ii iv v vvi vi i L1MD3_3end#LI 530 ACATCCATACAATGGAATACTATTCAGCAATAAAAAGGAA 569 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.74 CpG sites = 19, Kimura (unadjusted) = 34.74 Transitions / transversions = 1.12 (19/17) Gap_init rate = 0.02 (3 / 134), avg. gap size = 1.67 (5 / 3) 332 26.96 4.35 0.00 chrXptel1M 634732 634846 (365154) L1ME3F_3end#LINE/L1 430 549 (441) m_b342s551i3 14285 chrXptel1M 634732 ACATATACCAGAATCTT-ATAGCAGCATTTTTCGTGATGGCAAAGACTTG 634780 i v v - i v i i i vi L1ME3F_3end#L 430 ACATGTACAAGAATGTTCATAGCAGCACTGTTCGTAATAGCAAAAAACTG 479 chrXptel1M 634781 GAAACAAAGTGGATATCCGTGGATTGGGGAATGGGCAAAC--ACTGTGGT 634828 vviii i i v iv i ii i-- i L1ME3F_3end#L 480 GAAACAACCCAAATGTCCATCGACAGGAGAATGGATAAATAAATTGTGGT 529 chrXptel1M 634829 CCAT--GTGTAATGGAATAT 634846 vi --iiii L1ME3F_3end#L 530 ATATTCACACAATGGAATAT 549 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.15 CpG sites = 22, Kimura (unadjusted) = 35.15 Transitions / transversions = 2.44 (22/9) Gap_init rate = 0.03 (3 / 114), avg. gap size = 1.67 (5 / 3) 202 33.33 11.73 0.00 chrXptel1M 635839 636000 (364000) C L2#LINE/L2 (318) 2764 2584 m_b342s601i4 14286 chrXptel1M 635839 GGGTGAAGACTGGAGGCAGGGAGACCCACTAGGAGGCTATTCCGATATTC 635888 vv iv i vii v ii v C L2#LINE/L2 2764 GGGGCAAGGGTGGAAGCAGGGAGACCAGTTAGGAGGCTATTGCAGTAATC 2715 chrXptel1M 635889 CTGGTGAAAAGGGATGATG--TTGGA---------TGAC--TGGAGA-GC 635924 v i i iiv i -- --------- i -- i- v C L2#LINE/L2 2714 CAGGCGAGAGATGATGGTGGCTTGGACCAGGGTGGTGGCAGTGGAGGTGG 2665 chrXptel1M 635925 TGCGGA--GATAGG---CCAGAGACGTTGTGTGGATGACAACGACAGGGC 635969 v i -- i v --- ii v ii v vi i iiviv ii C L2#LINE/L2 2664 TGAGAAGTGGTCGGATTCTGGATATATTTTGAAGGTAGAGCCGACAGGAT 2615 chrXptel1M 635970 TCGGCAACTGATTGAACATGGGGGCTGAGGG 636000 i vii iv i ii vv i C L2#LINE/L2 2614 TTGCTGATGGATTGGATGTGGGGTGTGAGAG 2584 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.06 CpG sites = 34, Kimura (unadjusted) = 46.27 Transitions / transversions = 1.70 (34/20) Gap_init rate = 0.04 (6 / 161), avg. gap size = 3.17 (19 / 6) 41 22.70 3.36 4.05 chrXptel1M 636099 636247 (363753) (GAGA)n#Simple_repeat 1 148 (0) m_b342s252i3 14287 chrXptel1M 636099 GAGAGACAGAGAGAGACAGACAGACAAAGAAACAGATGAGAAATGAGATA 636148 v v v v i i v - i - v (GAGA)n#Simpl 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA-GAGAGA-GAGAGA 48 chrXptel1M 636149 GAGACA-AGCGCGGGGGCAGATGAGGGAGAGACAGGGAGGGAGGGAGATG 636197 v - v v i i - - i v i i i - (GAGA)n#Simpl 49 GAGAGAGAGAGAGAGAG-AGA-GAGAGAGAGAGAGAGAGAGAGAGAGA-G 95 chrXptel1M 636198 AGAAAG-GAGACAGACAGACAGAGACAGAGACA-AGA-AGCACGGAGA-A 636243 i - v v v v v - - - vi - (GAGA)n#Simpl 96 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG-AGAGAGAGA 144 chrXptel1M 636244 GAGA 636247 (GAGA)n#Simpl 145 GAGA 148 Matrix = Unknown Transitions / transversions = 0.69 (11/16) Gap_init rate = 0.07 (11 / 148), avg. gap size = 1.00 (11 / 11) 13 11.70 3.57 0.00 chrXptel1M 636356 636383 (363617) (GGGGC)n#Simple_repeat 1 29 (0) m_b342s252i4 14288 chrXptel1M 636356 GGGCCGCGGCGGGGC-GGGAGGGGCGGGG 636383 v v - v (GGGGC)n#Simp 1 GGGGCGGGGCGGGGCGGGGCGGGGCGGGG 29 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 356 20.31 0.99 7.37 chrXptel1M 637733 637833 (362167) MIRc#SINE/MIR 32 126 (142) m_b342s601i5 14289 chrXptel1M 637733 GGCCCTGGAGTCAGGAGGGCCCGAGTTCGAATCCAGCCTCAGACACTTAA 637782 v i i i i i i v v v v - MIRc#SINE/MIR 32 GGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTA- 80 chrXptel1M 637783 CGCTTCCTAGCTGCGGGACCCTGGGCAGGTCACTTAA-CTCCCATTGCCT 637831 ------ i v i i - i vvv MIRc#SINE/MIR 81 ------CTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCT 124 chrXptel1M 637832 CA 637833 MIRc#SINE/MIR 125 CA 126 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 23.76 CpG sites = 10, Kimura (unadjusted) = 23.76 Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.08 (8 / 100), avg. gap size = 1.00 (8 / 8) 462 21.26 2.24 8.73 chrXptel1M 638079 638212 (361788) MIRc#SINE/MIR 2 127 (141) m_b342s601i6 14290 chrXptel1M 638079 GGGGCAGCCGGGTGATGCAGTGGTTAGAGCGCCAGCCCTGAAGTCAGGAG 638128 i i--- i vv i ii v i i i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chrXptel1M 638129 GATCTGAGTTCAAATGTGATCTCAGACACTTAACACCGCCTA-CTGTGTG 638177 i i i i viviv v v ------- - MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTG 91 chrXptel1M 638178 ACCCTGGGCAAGTCACTTAACCCCAACT--GCCTCAG 638212 i i -v -- MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACCTC-TCTGAGCCTCAG 127 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 23.26 CpG sites = 17, Kimura (unadjusted) = 25.46 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.10 (13 / 133), avg. gap size = 1.08 (14 / 13) 16 0.00 0.00 0.00 chrXptel1M 643063 643080 (356920) (T)n#Simple_repeat 1 18 (0) m_b342s252i5 14291 chrXptel1M 643063 TTTTTTTTTTTTTTTTTT 643080 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTT 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 20 0.00 6.67 0.00 chrXptel1M 644609 644638 (355362) (AGGC)n#Simple_repeat 1 32 (0) m_b342s252i6 14292 chrXptel1M 644609 AGGCAGGCA-GCAGGCAGGCAGGCAGG-AGGC 644638 - - (AGGC)n#Simpl 1 AGGCAGGCAGGCAGGCAGGCAGGCAGGCAGGC 32 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.07 (2 / 29), avg. gap size = 1.00 (2 / 2) 48 0.00 0.00 0.00 chrXptel1M 645695 645738 (354262) (TCTACAA)n#Simple_repeat 1 44 (0) c_b342s251i0 14293 chrXptel1M 645695 TCTACAATCTACAATCTACAATCTACAATCTACAATCTACAATC 645738 (TCTACAA)n#Si 1 TCTACAATCTACAATCTACAATCTACAATCTACAATCTACAATC 44 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 16 16.64 0.00 4.76 chrXptel1M 646002 646045 (353955) (GAAAGAA)n#Simple_repeat 1 42 (0) m_b342s252i7 14294 chrXptel1M 646002 GAAATACAAAAGAAGAAAGAATAGAAAGAACAGAGAACAAAGAA 646045 v vi - - v i v (GAAAGAA)n#Si 1 GAAAGAAGAAAGAAGAAAG-A-AGAAAGAAGAAAGAAGAAAGAA 42 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2) 14 0.00 0.00 0.00 chrXptel1M 646538 646555 (353445) (TTA)n#Simple_repeat 1 18 (0) m_b342s252i8 14295 chrXptel1M 646538 TTATTATTATTATTATTA 646555 (TTA)n#Simple 1 TTATTATTATTATTATTA 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 1217 27.26 4.61 0.81 chrXptel1M 647089 647565 (352435) C L1ME3G_3end#LINE/L1 (376) 548 54 m_b342s551i5 14296 chrXptel1M 647089 ATAATATTCCATAACATTCATATACCACAATTTATTCAGCCATTCTCCAG 647138 i ii vv i i i i vi C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chrXptel1M 647139 TTGATGGGCATCCTCTCAGTTTCCAGTTTCTGGCTGCCACAAACATTCGT 647188 i iivvviv i i v iii v vv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 449 chrXptel1M 647189 GCACATACAGGTCCCTTTCC---CTTCTTTATG-------------ATCT 647222 - iv vi i v v --- ? i i ------------- i C L1ME3G_3end#L 448 GCA-ATGAACATCCTTGTACATGCNTCCTTGTGCACATGTGCGAGTATTT 400 chrXptel1M 647223 CTTTGGGGTATAAGTCCAGTAGTAGCACTGCTGGATCAAAGGGTATGCAC 647272 ? i i v v?i ? v i v i i i C L1ME3G_3end#L 399 CTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGC 350 chrXptel1M 647273 AGTTTGATAACTTTTTGAGCATAATTCCAAATCGCTCTCCAGAATGGTTG 647322 v i -- i vvv - v v i i i ? i C L1ME3G_3end#L 349 ATTTTAA--ATTTTAATAG-ATACTGCCAAATTGCCCTCCAAAANGGCTG 303 chrXptel1M 647323 GATGTATTCACAGTTCCACCAACAATGTATCAGTGTCCCTGTTTTCCCAC 647372 v ivv i v i i i v v v i i C L1ME3G_3end#L 302 TACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCAC 253 chrXptel1M 647373 ATCCCTTCCAACATTCTGCATTATCTTTCCCTGTCATTCTAGCCAGTCTG 647422 i iiv i ?vii vv? ii vvv i v i C L1ME3G_3end#L 252 ACCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATCTG 203 chrXptel1M 647423 ACAAGTG------TGTGTCTCAGAGTTGTCTTAATTTGCATTTCTCTGAT 647466 iii ------v i vv i i C L1ME3G_3end#L 202 ATGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGAT 153 chrXptel1M 647467 TAATAATGACTTAGAGCATCTTTTCCTATGGCTAGAAATAGTTTCAATTT 647516 v i vv v v vi vviiivi vv C L1ME3G_3end#L 152 TACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGTATTT 103 chrXptel1M 647517 CTTCATGTGAAAATTGTCTGTTCATATCCTTTGACCATTTACCAATTGG 647565 i v v vi i v vi v C L1ME3G_3end#L 102 CCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGG 54 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.11 CpG sites = 69, Kimura (unadjusted) = 35.10 Transitions / transversions = 1.15 (69/60) Gap_init rate = 0.01 (7 / 476), avg. gap size = 3.71 (26 / 7) 675 19.22 1.32 6.99 chrXptel1M 647789 647939 (352061) MIRc#SINE/MIR 6 148 (120) m_b342s601i7 14297 chrXptel1M 647789 CAGTAGTGGTGCAGTGAATAGAGTTCCAGGCCTGAAGTCAGGAATACTCA 647838 - i v iv ii i i i v --- MIRc#SINE/MIR 6 CAGT-GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC--- 51 chrXptel1M 647839 TCTTCCTGAATTCAAATCTGGCCTCAGACACATACTAGCTATGTGACCCT 647888 ----- ii i i iv v v v v i i MIRc#SINE/MIR 52 -----CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTT 96 chrXptel1M 647889 GGACAAGTCACTTCATCCTGTTT--GCCTCAGTTTCCTCATCTGTAAAAT 647936 i v - v i -- MIRc#SINE/MIR 97 GGGCAAGTCACTTAA-CCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAAT 145 chrXptel1M 647937 GAG 647939 i MIRc#SINE/MIR 146 GGG 148 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 21.61 CpG sites = 17, Kimura (unadjusted) = 22.53 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.07 (11 / 150), avg. gap size = 1.09 (12 / 11) 301 32.56 3.03 2.26 chrXptel1M 649946 650077 (349923) C L3#LINE/CR1 (127) 3972 3840 m_b342s601i8 14298 chrXptel1M 649946 TCCAATAACAGGAAACTCATTATTTACATCAAG-ATCACATGATCCATTG 649994 i i i i i i ii - ?iv i - v v -- v C L3#LINE/CR1 3972 TCCAGTGACGGGGAGCTCACTACCT-CNCGAGGCAGCCCAT--TCCATTT 3926 chrXptel1M 649995 CTCAATCACTTAGATCATTTGAAA---CATCTTAATATTGAGCAGAAATG 650041 i vi ivi iv ii v --- v i v v v C L3#LINE/CR1 3925 TTGGACAGCTCTGATTGTTAGAAAGTTCTTCCTTATATTGAGCCGAAATC 3876 chrXptel1M 650042 TGCACTCCTAAAACTCCCACTCACTCATTATAGTTC 650077 vii iv i i i vi iv C L3#LINE/CR1 3875 TGCCTCCCTGTAACTTCCACCCATTGGTCCTAGTTC 3840 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.16 CpG sites = 26, Kimura (unadjusted) = 45.08 Transitions / transversions = 1.62 (26/16) Gap_init rate = 0.04 (5 / 131), avg. gap size = 1.40 (7 / 5) 271 31.06 1.91 15.94 chrXptel1M 650163 650319 (349681) C L3#LINE/CR1 (280) 3819 3682 m_b342s601i9 14298 chrXptel1M 650163 AACAAATCTAATTTTTCTTCCTCATGTTGGACCTTCAGAAACTGAAAAAT 650212 i i iii v vii v i v i vi i i C L3#LINE/CR1 3819 AATAAGTCTAATCCCTCTTCCACATGACAGCCCTTCAAATATTTGAAGAC 3770 chrXptel1M 650213 TATCATTCTTGCATCCCTCCTTACACTCCACCCCTATACAATGTCTTCCC 650262 viii ----- vi ------------ ---- - i C L3#LINE/CR1 3769 AGCTAT-----CATGTCTCCT------------CTA----A-GTCTTCTC 3742 chrXptel1M 650263 TACTTCAAGCTAAGTGTTCCCAATTTCTTCAACTGACCCTTGTATTA--- 650309 v i i iii i i i i vi ii v --- C L3#LINE/CR1 3741 TTCTCCAGGCTAAACATCCCCAGTTCCTTCAACCGTTCCTCATATGACAT 3692 chrXptel1M 650310 GATTTCTAGA 650319 i i C L3#LINE/CR1 3691 GGTTTCCAGA 3682 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.71 CpG sites = 31, Kimura (unadjusted) = 42.12 Transitions / transversions = 3.10 (31/10) Gap_init rate = 0.15 (23 / 156), avg. gap size = 1.09 (25 / 23) 818 21.66 4.37 1.60 chrXptel1M 651262 651444 (348556) MIRb#SINE/MIR 42 229 (39) m_b342s601i10 14299 chrXptel1M 651262 GATTCCAACAGAC-----TTCAAATTTGGCCTCAGT-ACTCACTAGCTGT 651305 v vi ----- i iiv v v i- i MIRb#SINE/MIR 42 GAGTCAGACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGT 91 chrXptel1M 651306 ATCACCTTGGACAAGTTATTTAACCTGTTTT--CCTCAGTTTCCTCAACT 651353 i v i i v i v-- v MIRb#SINE/MIR 92 GTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCT 141 chrXptel1M 651354 ATAAAATGGTGATAATAAAAGTAGCCATTTCCCAGGGTTATGATGAGGAT 651403 i v --- v i ii v i vi MIRb#SINE/MIR 142 GTAAAATGGGGATAATAA---TACCTACCTCGCAGGGTTGTTGTGAGGAT 188 chrXptel1M 651404 CAAATAAGATAATATTTGTAAAATGGTTAGCACAGTAGCTG 651444 i i iiv ii v iv MIRb#SINE/MIR 189 TAAATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTG 229 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.50 CpG sites = 23, Kimura (unadjusted) = 26.01 Transitions / transversions = 1.44 (23/16) Gap_init rate = 0.03 (6 / 182), avg. gap size = 1.83 (11 / 6) 269 38.06 2.22 0.73 chrXptel1M 651474 651608 (348392) C L3#LINE/CR1 (410) 3689 3553 m_b342s601i11 14298 chrXptel1M 651474 TTTCCATTCCCATTCCCTCACTGATTATACTTTCCCAGACACACTATGGC 651523 vv v iv viv i iiiv iii ii i i vii - C L3#LINE/CR1 3689 TTTCCAGACCCTTCACCATCCTGGTCGCTCTCCTCTGGACGCGCTCCAG- 3641 chrXptel1M 651524 TTTGCCAATGTCTTTCCTATAATGTGGTGCTGAAATCTGAATCTGA-AGT 651572 i ii i v i iv i v ivii - v C L3#LINE/CR1 3640 TTTGTCAATGTCCCTCTTAAAATGTGGCGCCCAGAACTGAACGCAATACT 3591 chrXptel1M 651573 CAGAATCT-GTCTGATT-GAGTTGAGTTCAGTGTAACT 651608 vii v - ii- v iv v i vi C L3#LINE/CR1 3590 CCAGATGTGGTCTGACCAGCGCAGAGTACAGCGGGACT 3553 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 46.87 CpG sites = 32, Kimura (unadjusted) = 56.64 Transitions / transversions = 1.68 (32/19) Gap_init rate = 0.03 (4 / 134), avg. gap size = 1.00 (4 / 4) 235 32.53 1.63 5.04 chrXptel1M 651682 651804 (348196) X6A_LINE#LINE/CR1 632 750 (328) m_b342s601i12 14300 chrXptel1M 651682 ATGTCCAGAGGTATGCAAGTGGCTCCACGCCACATAAAGATAGATTTAAA 651731 vi v v i vivi i -----i i ? v X6A_LINE#LINE 632 ATGGTCAGAGGAATGGAGGGACTTCCGCGC-----GAGGANAGATTGAAA 676 chrXptel1M 651732 AGATGAGGATTCCCATATCTGGAATGGTAAAGGATGAAAAG-GACATGAT 651780 v i iivvi v ivi vi i i - i i X6A_LINE#LINE 677 AGATTAGGACTCTTTAGTCTGGAAAGAGGAAGGCCGAGAGGAGATACGAT 726 chrXptel1M 651781 -CAAGCACAGAAAATCATGAAATGG 651804 -v i iii vi v - X6A_LINE#LINE 727 AGAGGTGTACGAAATAATG-AATGG 750 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 37.22 CpG sites = 23, Kimura (unadjusted) = 44.79 Transitions / transversions = 1.53 (23/15) Gap_init rate = 0.07 (8 / 122), avg. gap size = 1.00 (8 / 8) 488 19.89 3.08 7.20 chrXptel1M 651808 651937 (348063) MIRc#SINE/MIR 3 127 (141) m_b342s601i13 14301 chrXptel1M 651808 AGTTAGT-TGGAGCAGTGGATAGAGCACCAGGCCTGAAGTCATGAGGACC 651856 vi - v v ii i i i v i MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chrXptel1M 651857 TGAGTTCAAATCTGGCCTCAGACACTTAACACTTCCTAGCTGTGTGACCC 651906 i i i iv v v v ------- i MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTGACCT 95 chrXptel1M 651907 TGGGCAAGAAACTTAATGCCAATC---GCCTCAG 651937 vv -- vv --- MIRc#SINE/MIR 96 TGGGCAAGTCACTTAA--CCTCTCTGAGCCTCAG 127 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 22.14 CpG sites = 12, Kimura (unadjusted) = 23.18 Transitions / transversions = 1.00 (12/12) Gap_init rate = 0.09 (11 / 129), avg. gap size = 1.18 (13 / 11) 261 32.41 0.68 0.68 chrXptel1M 652502 652647 (347353) L1ME3A_3end#LINE/L1 429 574 (346) m_b342s551i6 14302 chrXptel1M 652502 GACCTGTACAAAAATATTTATAGCACCTCTTTTTGTGCTGACAAAGAATT 652551 v i i i v v v i iv ii v??i i L1ME3A_3end#L 429 GACATGTACAAGAATGTTCATAGCAGCACTATTCGTAATAGCCNNAAACT 478 chrXptel1M 652552 GGAAATTAAAGGGATGCCTCCCAATTAAGAAATGGCTGAATAAGCTGTGG 652601 i? vvvii i ivi ivivii v i ii L1ME3A_3end#L 479 GGAAACNACCCAAATGTCCATCAACAGTAGAATGGATAAATAAATTGTGG 528 chrXptel1M 652602 CATATGATTATAATGGAATAATACTGTGCCATGAGACATGAA-GAAC 652647 i vvvi i v ivvv v - - L1ME3A_3end#L 529 TATATTCACACAATGGAATACTATACAGCAATGAGA-ATGAACGAAC 574 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 43.56 CpG sites = 26, Kimura (unadjusted) = 44.85 Transitions / transversions = 1.24 (26/21) Gap_init rate = 0.01 (2 / 145), avg. gap size = 1.00 (2 / 2) 309 32.26 0.00 0.00 chrXptel1M 652503 652626 (347374) L1MC4_3end#LINE/L1 430 553 (2236) m_b342s551i7 14302 chrXptel1M 652503 ACCTGTACAAAAATATTTATAGCACCTCTTTTTGTGCTGACAAAGAATTG 652552 vi i v i v ii iv ?i v i ?i L1MC4_3end#LI 430 ACCTGTACACGAATGTTTATAGCAGCTTTATTCATAATNGCCAAAANCTG 479 chrXptel1M 652553 GAAATTAAAGGGATGCCTCCCAATTAAGAAATGGCTGAATAAGCTGTGGC 652602 iv vv?i i iii iviivi v i i i i L1MC4_3end#LI 480 GAAACAACCNAGATGTCCTTCAACAGGTGAATGGATAAACAAACTGTGGT 529 chrXptel1M 652603 ATATGATTATAATGGAATAATACT 652626 i vvv i v L1MC4_3end#LI 530 ACATCCATACAATGGAATACTACT 553 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 44.06 CpG sites = 25, Kimura (unadjusted) = 45.65 Transitions / transversions = 1.67 (25/15) Gap_init rate = 0.00 (0 / 123), avg. gap size = 0.0 (0 / 0) 16 27.77 1.12 7.14 chrXptel1M 653216 653304 (346696) (CTTT)n#Simple_repeat 1 84 (0) m_b342s252i9 14303 chrXptel1M 653216 CTTTCTTCCCTTCTCTCTTTCCTTCTATTATTCCAATTAAACTCTTTCTC 653265 i i i i - v i -- vvvi - (CTTT)n#Simpl 1 CTTTCTTTCTTTCTTTCTTTCTTTCT-TTCTTTC--TTTCTTTCTTTCT- 46 chrXptel1M 653266 TTCCTACTATCTTTTTGATCCATTCTAT-GTTCTTTCTTT 653304 i v v i -- i v v -v (CTTT)n#Simpl 47 TTCTTTCTTTCTTTCT--TTCTTTCTTTCTTTCTTTCTTT 84 Matrix = Unknown Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.08 (7 / 88), avg. gap size = 1.00 (7 / 7) 621 18.77 2.67 7.69 chrXptel1M 653410 653559 (346441) C MIRc#SINE/MIR (123) 145 3 m_b342s601i14 14304 chrXptel1M 653410 ATTTTACAGATGAGGAAACTGAGGCAAACAG-GGTGAAGTGACTTGCCCA 653458 vv v - v C MIRc#SINE/MIR 145 ATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCA 96 chrXptel1M 653459 GGGTTGCACAGCTAGTAAGTGTCTGAGGACAGATTTGGCCTCTTGAAGAA 653508 i ii v v vvvi i i iv i ---- -- C MIRc#SINE/MIR 95 AGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCC----AG-- 52 chrXptel1M 653509 AAAGAGTCTTCTTAACTCTAGGTCCA--GCTCTTTACACTGTACT-CACT 653555 ----- i i i i -- v i i- C MIRc#SINE/MIR 51 -----GTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACT 7 chrXptel1M 653556 ACCT 653559 i C MIRc#SINE/MIR 6 GCCT 3 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 20.87 CpG sites = 15, Kimura (unadjusted) = 21.78 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.09 (14 / 149), avg. gap size = 1.07 (15 / 14) 721 33.21 5.42 6.98 chrXptel1M 653774 654456 (345544) L2#LINE/L2 2060 2732 (350) m_b342s601i15 14305 chrXptel1M 653774 CCTCTTTGAGGTTTTTAACACTGTTGATTCCCCTTTCCTTTTTGAGACTC 653823 ? iv vi iv i v iv i ii i i v L2#LINE/L2 2060 CCTNTCAGCAGCATTTGACACAGTTGATCACTCCCTCCTTCTTGAAACAC 2109 chrXptel1M 653824 TCGGCTCTCTAGGTTTTTGGGTTATCAG--TCTCTGGGTTGTCTTCCTAC 653871 ivvi v v i iii vi i v-- iv v i L2#LINE/L2 2110 TTTCTTCACTTGGCTTCCAGGACACCACACTCTCCTGGTTTTCCTCCTAC 2159 chrXptel1M 653872 CTATGTGACCACTTTTTCCCTTTTCCCTTTGCAGAAACCTCCTCCAGCTC 653921 vvv i i ii i vv ii v ivv - v L2#LINE/L2 2160 CTCACTGGCCGCTCCTTCTCAGTCTCCTTTGCTGGTTCCTCCT-CATCTC 2208 chrXptel1M 653922 ATTG-CCTCTGACCACAGGTATCCCTCAGAGTTCTGTCC-TGGGTTTCCT 653969 vii - ? v iiv vi v i i i v - iii -- L2#LINE/L2 2209 CCCGACCTCTNAACGTTGGAGTGCCCCAGGGCTCAGTCCTTGGACCTC-- 2256 chrXptel1M 653970 TTCACTTTTCCCTCTATA--CACTGTACTTGATGATTTCAACAGTTCTCA 654017 v i iv i -- -iv ? i i v viv L2#LINE/L2 2257 TTCTCTTCTCTATCTACACTCACT-CCCTNGGTGATCTCATCCAGTCTCA 2305 chrXptel1M 654018 TGGATTTAATGACCATGCCTAAGCTGATGATTCTCAGTCTAGCTTTTCTA 654067 v vv viv v i i i--- --- v L2#LINE/L2 2306 TGGCTTTAAATACCATCTATATGCTGATGACTCCCAA---A---TTTATA 2349 chrXptel1M 654068 GCTAAAGCTCCCATCATCAGGTCTTTT---TTCTAGCCTTCCCCTTTCTG 654114 v vv i vv i - --- iii ---i i v iviviv i vi L2#LINE/L2 2350 TCTCCAGCCCGGACC-TC---TCCCCTGAACTCCAGACTCGTATATCCAA 2395 chrXptel1M 654115 CTGCCCTCTACTCTCACATTTTTATCTGCCCTTCAGACATCTTGAACTAA 654164 --- -v i ii ii ------- ii ------- L2#LINE/L2 2396 CTGC---CTACTC-GACATCTCCACTTG-------GATGTCT-------A 2427 chrXptel1M 654165 ATATCTAGCAGACATCTTAAACCTGATATGTCTAAAATGGAATTCATAAT 654214 ---i ---- i i i i i iv i v i L2#LINE/L2 2428 ATA---GGCA----TCTCAAACTTAACATGTCCAAAACTGAACTCCTGAT 2470 chrXptel1M 654215 CTTTCACCCTAAACTTTCTC------CA----TCACTATTGCCATAGAGG 654254 i v ii i v ------ ---- v i iv vi ?i v L2#LINE/L2 2471 CTTCCCCCTCAAACCTGCTCCTCCCGCAGTCTTCCCCATCTCAGTNAATG 2520 chrXptel1M 654255 GCAATGCTATTCTCTCAGTCCCTCAGTCTTGTAACCTAAGAGTCATGCTG 654304 iv i i ii iv v iviv vi v v L2#LINE/L2 2521 GCAACTCCATCCTTCCAGTTGCTCAGGCCAAAAACCTTGGAGTCATCCTT 2570 chrXptel1M 654305 GACCCTTGACTGTCTTTTAT-CCCTCCATCCCAATAC-TC-----ACCCT 654347 i i vv v i i i- iv - v - ----- i L2#LINE/L2 2571 GACTCCTCTCTTTCTCTCACACCCCACAT-CCAATCCATCAGCAAATCCT 2619 chrXptel1M 654348 GTTGCCAAGGCCT---GGCGATCTC----ATGCCACCTCTGCTCATT-TC 654389 i v vvvi ---iivv v ---- v v v v ii-i L2#LINE/L2 2620 GTCGGCTCTACCTTCAAAATATATCCAGAATCCGACCACTTCTCACCACC 2669 chrXptel1M 654390 TCCCCTTTGAGCCCAACTTATCCTAGTACAA--CACTATCGACTTGTGCC 654437 v ---- -- -i i i v -- i iv ivi L2#LINE/L2 2670 TCCACT----GCC--AC-CACCCTGGTCCAAGCCACCATCATCTCTCGCC 2712 chrXptel1M 654438 TGAACTATGACAA-ACCCTC 654456 i i ivi - v L2#LINE/L2 2713 TGGATTACTGCAATAGCCTC 2732 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.82 CpG sites = 120, Kimura (unadjusted) = 45.58 Transitions / transversions = 1.32 (120/91) Gap_init rate = 0.09 (62 / 682), avg. gap size = 1.35 (84 / 62) 194 42.76 0.72 0.72 chrXptel1M 654530 654668 (345332) L2d_3end#LINE/L2 1 139 (377) m_b342s601i16 14305 chrXptel1M 654530 CTTCAAAATTTAGTTCCCTCCTACCTGTTCAGTCCTCTTATACCTTATCT 654579 i vi i i ii vi ? i i i v iviv vi iii L2d_3end#LINE 1 CTCCACGATCTGGCCCCACCCTACCTNTCCAGCCTTATCTCCCACTACTC 50 chrXptel1M 654580 CCTGACATGTACTCTTCAATCTAGTGATCCTGGCCTTTTGGCTGGTCTAC 654629 iii i v i i iv i v vv i i i vi vi iv L2d_3end#LINE 51 CCCAGCACGAACCCTCCGCTCCAGTCAGGCCGGTCTCTTCACTGTCCCCC 100 chrXptel1M 654630 GAGCCTGGCCCTCCAT-CTCTCAGCTTTGAGCGTTTTCTC 654668 i vi- i v ii-i i iv i v v v L2d_3end#LINE 101 GAACAC-GCCTTGCGCATTCCCGCCTCTGCGCCTTTGCTC 139 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 57.45 CpG sites = 39, Kimura (unadjusted) = 71.45 Transitions / transversions = 1.95 (39/20) Gap_init rate = 0.01 (2 / 138), avg. gap size = 1.00 (2 / 2) 37 5.13 0.00 0.00 chrXptel1M 654898 654938 (345062) (GT)n#Simple_repeat 1 41 (0) c_b342s251i1 14306 chrXptel1M 654898 GTGTGCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGTGTG 654938 i i (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 41 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 273 27.27 7.95 0.00 chrXptel1M 655098 655185 (344815) MIR3#SINE/MIR 110 204 (4) m_b342s601i17 14307 chrXptel1M 655098 CTTTATGGGTCT--GTTTCTTCAATTATAAATGAAAAGAGTTGGACCAGA 655145 i v i -- i vi i vvi ii i i MIR3#SINE/MIR 110 CTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGA 159 chrXptel1M 655146 TGG-CT-TGAGGTCTGTTCCAGCCATAA-AT--CATAATCCTATG 655185 i- - i iv iv i - --i i i MIR3#SINE/MIR 160 TGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTATGATTCTATG 204 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.10 CpG sites = 18, Kimura (unadjusted) = 36.10 Transitions / transversions = 3.00 (18/6) Gap_init rate = 0.06 (5 / 87), avg. gap size = 1.40 (7 / 5) 343 36.15 0.00 1.68 chrXptel1M 655470 655590 (344410) C L3#LINE/CR1 (156) 3943 3825 m_b342s601i18 14308 chrXptel1M 655470 AGGCAGAGTGCATTCTACTTTTCAATAGTTCTAATTGTTAGCAAGTTTTT 655519 --iv i i vi i i i v i C L3#LINE/CR1 3943 AGGCAG--CCCATTCCATTTTTGGACAGCTCTGATTGTTAGAAAGTTCTT 3896 chrXptel1M 655520 CTGGATACTAAACCTTAACTTGACTATTTGCAACTTGCACTTCCTATCAC 655569 ivv i i i vv ii v vii i v iivi iviv C L3#LINE/CR1 3895 CCTTATATTGAGCCGAAATCTGCCTCCCTGTAACTTCCACCCATTGGTCC 3846 chrXptel1M 655570 TGGTTCTATTTTCAAGAGCTA 655590 i iiii vi i C L3#LINE/CR1 3845 TAGTTCTGCCCTCTGGAGCCA 3825 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 53.16 CpG sites = 29, Kimura (unadjusted) = 53.16 Transitions / transversions = 2.07 (29/14) Gap_init rate = 0.02 (2 / 120), avg. gap size = 1.00 (2 / 2) 361 25.92 10.61 3.55 chrXptel1M 656324 656455 (343545) C L3#LINE/CR1 (419) 3680 3540 m_b342s601i19 14308 chrXptel1M 656324 CCTCTACCCTGTCTGCCTCGATCTCCTCTAGACACTCTCCAGCTTGTTAA 656373 ii v -i v- v i i v i i C L3#LINE/CR1 3680 CCTTCACCAT-CCTGG-TCGCTCTCCTCTGGACGCGCTCCAGTTTGTCAA 3633 chrXptel1M 656374 TGT--------------GGCACTCCGAATGGAACACATTAACCCAGATGT 656409 -------------- i i v iv i v vi C L3#LINE/CR1 3632 TGTCCCTCTTAAAATGTGGCGCCCAGAACTGAACGCAATACTCCAGATGT 3583 chrXptel1M 656410 GGTCTCGCCACACCAGAAGACAAAGGGATCATAATCCTGTCCCTTG 656455 vi vvv iv iv ii v i --- C L3#LINE/CR1 3582 GGTCTGACCAGCGCAGAGTACAGCGGGACTATTACC---TCCCTTG 3540 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 28.98 CpG sites = 18, Kimura (unadjusted) = 32.41 Transitions / transversions = 1.20 (18/15) Gap_init rate = 0.05 (6 / 131), avg. gap size = 3.17 (19 / 6) 286 27.90 5.26 2.56 chrXptel1M 656490 656603 (343397) C L3#LINE/CR1 (562) 3537 3421 m_b342s601i20 14308 chrXptel1M 656490 CTGGAAGCTGTGATTCTTCTGT-GACCCAAGGTAACATT-CATTAGCTTT 656537 vi --- v i -i iv ivv v - C L3#LINE/CR1 3537 CTGGACACT---ATACTTCTATTAATGCAGCCTAAGATTGCATTAGCTTT 3491 chrXptel1M 656538 TCTGACTACCACATCATACT----GCTCAAATTGAAGTTGAAATCTCTTA 656583 i i vi i ---- v iv vii vvi C L3#LINE/CR1 3490 TTTGGCAGCCACATCACACTGTTGGCTCATATTGAGCTTGCGGTCAACTA 3441 chrXptel1M 656584 AAAATCCAAGCTCCTTTTTA 656603 vi v v i i C L3#LINE/CR1 3440 AAACCCCTAGGTCTTTTTCA 3421 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.02 CpG sites = 16, Kimura (unadjusted) = 35.41 Transitions / transversions = 1.07 (16/15) Gap_init rate = 0.05 (6 / 113), avg. gap size = 1.50 (9 / 6) 30 0.00 0.00 0.00 chrXptel1M 657459 657486 (342514) (TTAGGG)n#Simple_repeat 1 28 (0) c_b342s251i2 14309 chrXptel1M 657459 TTAGGGTTAGGGTTAGGGTTAGGGTTAG 657486 (TTAGGG)n#Sim 1 TTAGGGTTAGGGTTAGGGTTAGGGTTAG 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 585 35.15 11.50 1.20 chrXptel1M 657687 658138 (341862) C L3#LINE/CR1 (693) 3406 2909 m_b342s601i21 14308 chrXptel1M 657687 AAGCTATACCATATCAATTTTATATTTATGAAGTTGGCTTTTTAAATTCG 657736 i v i v v v ii i i i v ii i iiii C L3#LINE/CR1 3406 AAGCCAGATCCTCTCCATCCTGTACTTGTGCAGTTGATTTTTTGAACCTA 3357 chrXptel1M 657737 AGTTGTAAAAGCGTACATTTATCCCTTCTGAACTTCATCTCATTCAATTT 657786 i - i ii viv vi i i ii viv i C L3#LINE/CR1 3356 AAT-GCAGGACTTTACATTTATCCCTGTTAAATTTCATCTTGTTGGTTTC 3308 chrXptel1M 657787 AGCCCAATGTTCCA----ATCAAA--------GAAT-TTGATTGGATCAT 657823 i vi ----i i i-------- - vvi C L3#LINE/CR1 3307 GGCCCATCGTTCCAGCCTGTCGAGATCNTTTTGAATCTTGATTCTGTCAT 3258 chrXptel1M 657824 TTCTTATTTCAGGTGT------CAA--TTATCTCAGCTG-GCCTTTAATA 657864 iiv?ii v i v i ------ i-- i v v -ivv i C L3#LINE/CR1 3257 CCANCGTATTAGCTATCCCTCCCAGCTTTGTGTCATCTGCAAATTTGATA 3208 chrXptel1M 657865 ACTCTGTTTTCAAAAGTATTATCCAGGTCACTGACACAAATATT---CAG 657911 viv ii v viviv i i i i v i --- C L3#LINE/CR1 3207 AGCATGCCTTCTATGTCTTCATCCAAGTCATTGATAAAAATGTTGAACAG 3158 chrXptel1M 657912 --CAGTG-------CAGATCCCAGTGGTACAACTCTGAAGACCTTCTGTC 657952 -- v ------- v v i iv v ii i ivi C L3#LINE/CR1 3157 GACAGGGCCAAGGACAGAGCCCTGTGGCACGCCACTAGAGACCTCCCTCC 3108 chrXptel1M 657953 AAGCAGA----GAACCATTAATGACTA--TTCAGAGTCCAACCATTCAAT 657996 i iv ---- v v vi -- iv i vi ii i i C L3#LINE/CR1 3107 AGGTTGACATCGATCCATTAATCAACACCTTTTGGGTATAGTCGTTCAAC 3058 chrXptel1M 657997 ACATTCTAAATGTCGCCT---TGTGCTACTGTCTACTTCCCATCTCTCCA 658043 vvii vii -i i --- i iii i vii vi i C L3#LINE/CR1 3057 CAGCTACGAAT-CCACCTAACTGTACTATCATCCAGCCCATATTTCTCCA 3009 chrXptel1M 658044 TCATTCCCCACAAAGATAATATGGCTAAAATCTAGGTTAACTAGATT--T 658091 - vi i vi --- i iv vv i v ivv -- C L3#LINE/CR1 3008 TC-TTGTCCACAAGGATATCATG---AGAGACTTTGTCAAATGCCTTGCT 2963 chrXptel1M 658092 AAAA-CTAGAT----TTAATC-AAAACATT-CTTTGACTTGCCACTTTAG 658134 i - i ---- ?vi - vii - ii ii i v i C L3#LINE/CR1 2962 GAAATCCAGATACACTNTGTCTACGGCATTCCCCTGATCTACCAGTCTAG 2913 chrXptel1M 658135 TAAC 658138 C L3#LINE/CR1 2912 TAAC 2909 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 46.99 CpG sites = 102, Kimura (unadjusted) = 50.89 Transitions / transversions = 1.85 (102/55) Gap_init rate = 0.05 (23 / 451), avg. gap size = 2.52 (58 / 23) 247 30.95 0.00 0.00 chrXptel1M 658140 658223 (341777) C CR1-3_Croc#LINE/CR1 (1716) 1889 1806 m_b342s551i8 14310 chrXptel1M 658140 GTCACAAAAGATGATAAGGCTAGTCTGTCATGATTGGTTCTCCATAAAGC 658189 v i iv v i i v i v i v i i i v C CR1-3_Croc#LI 1889 GTCAAAGAAGGAGATCAAGTTTGTTTGACACGATTTGTTTTTCGTAAATC 1840 chrXptel1M 658190 TCTGCTGGTTCTTTGTGATCATCATTTCTTTTTC 658223 iv i vi v v i ii C CR1-3_Croc#LI 1839 CATGCTGGCTGCTTGTGATCAGCCTTTCCTCCTC 1806 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.05 CpG sites = 15, Kimura (unadjusted) = 41.07 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.00 (0 / 83), avg. gap size = 0.0 (0 / 0) 404 33.08 1.08 6.86 chrXptel1M 658261 658445 (341555) C L3#LINE/CR1 (1419) 2680 2506 m_b342s601i22 14308 chrXptel1M 658261 TTCTCTTATCTCTCCTGTTCTCTAGGATCTTTTACAGATCACAGGCAAAT 658310 vvi i i i iiv i i i v i v i i-i C L3#LINE/CR1 2680 TTCTGGCACCTCTTCCGTTCTCCGTGATTTCTCAAAGATTACCGACAG-C 2632 chrXptel1M 658311 CACTTAACATTCACA-ATGACTGTTTTTCCAATGATGCAACCCAAAGATG 658359 vii ivi iv -v vvv i i i ------ vii C L3#LINE/CR1 2631 GGTTCCGCGATCACATCTGCAAGTTCTTTCAGT------ACCCTGGGATG 2588 chrXptel1M 658360 CAGTTCATCTGGGCCAACTGACTAGGATTCATTCTGGAACTGA-AAGCAC 658408 i i i vivv v i i - ii i v v- i ii C L3#LINE/CR1 2587 TAATTCGTCTGGGCCTGGAGACTTGAACTCATT-TAAAGCGGCTAGGTGC 2539 chrXptel1M 658409 TCTTACTCTTACTATCTCCTCATTTATCTTAGGCTTC 658445 ---- ii i C L3#LINE/CR1 2538 TCT----CTTACTATCTCCTCACCTATCTTGGGCTTC 2506 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.43 CpG sites = 38, Kimura (unadjusted) = 46.03 Transitions / transversions = 2.00 (38/19) Gap_init rate = 0.08 (14 / 184), avg. gap size = 1.00 (14 / 14) 376 33.76 2.27 4.05 chrXptel1M 658857 659032 (340968) C L3#LINE/CR1 (2668) 1431 1259 m_b342s601i23 14308 chrXptel1M 658857 CTATTTCTTTTGAATAAGCTATTCAATATGAGCCAGAGCCATAATGCAAG 658906 i i v ? v vv ----v vv i v v iv C L3#LINE/CR1 1431 CTGTTTCTTTTGAACAAGGTNTACCCT----TCCATCGCCGTATTCCAGT 1386 chrXptel1M 658907 TATATGTTTCACCCCACTAAGTCTCAGTGCTACCCACAAAGCTAAATTTG 658956 i iv ii i i i v i ii iiiiiv i C L3#LINE/CR1 1385 CATGAGTCCCATCCCACCAAGTCTCGGTGATACCTATGAGATCGTATTTA 1336 chrXptel1M 658957 CCTCTTTGAATTAGAATT----GTTGATTTAATACTTGATGTCTGAAGTT 659002 i vi i ---- ? i -- ?i iv ii i- vii C L3#LINE/CR1 1335 CCTCCTTGTGTTAAAATTTCAAGTTNACTT--TNTTTATTACCC-ATACT 1289 chrXptel1M 659003 GGGGGCATTAGTGAGTAGACACATGAGTCC 659032 vv v i ivi iv v C L3#LINE/CR1 1288 CTGTGCATTGGTATATAGACATCTGAGGCC 1259 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 44.45 CpG sites = 35, Kimura (unadjusted) = 48.10 Transitions / transversions = 1.59 (35/22) Gap_init rate = 0.05 (8 / 175), avg. gap size = 1.38 (11 / 8) 274 24.36 7.06 3.41 chrXptel1M 659970 660054 (339946) MIR3#SINE/MIR 97 184 (24) m_b342s601i24 14311 chrXptel1M 659970 CAAGTCACTTAACC---AAAGGCCAGAGAGGTCTCCTCATCTCTAAAATG 660016 v ---vvi vv --- i v MIR3#SINE/MIR 97 CAAGTCACTTCACCTCTCTGGGCCTCA---GTTTCCTCATCTGTAAAATG 143 chrXptel1M 660017 AGAGGATTTGATT---CAACTTATTAGATCCCTTTCAGCTC 660054 i i v i ---ii ii v v i i MIR3#SINE/MIR 144 AGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTC 184 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 29.94 CpG sites = 11, Kimura (unadjusted) = 29.94 Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.06 (5 / 84), avg. gap size = 1.80 (9 / 5) 16 21.67 0.00 0.00 chrXptel1M 661355 661392 (338608) (GAGA)n#Simple_repeat 1 38 (0) m_b342s252i10 14312 chrXptel1M 661355 GAGAGACTGAGAGAGACAGACAGACAGAGTCAGAGAGA 661392 vv v v v vv (GAGA)n#Simpl 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 38 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 15 30.48 0.00 0.00 chrXptel1M 662599 662640 (337360) (AT)n#Simple_repeat 1 42 (0) m_b342s252i11 14313 chrXptel1M 662599 ATATGTATATACATAAACATTTGTATGCATATGTGTATATAT 662640 i i v i v i ii i i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATAT 42 Matrix = Unknown Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 195 25.76 14.29 1.41 chrXptel1M 662688 662750 (337250) C MIRc#SINE/MIR (188) 80 10 m_b342s601i25 14314 chrXptel1M 662688 TAAGTATCTGATGCCAG-ATTCGAACTTAG--------GACTGCAAGCCC 662728 iv v - i - i ii -------- v i C MIRc#SINE/MIR 80 TAAGTGGCAGA-GCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCC 32 chrXptel1M 662729 AGCACTCTATCTACTGTGCTAC 662750 ii v i ii i C MIRc#SINE/MIR 31 AGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.91 CpG sites = 12, Kimura (unadjusted) = 33.49 Transitions / transversions = 3.00 (12/4) Gap_init rate = 0.05 (3 / 62), avg. gap size = 3.33 (10 / 3) 229 30.72 4.04 2.20 chrXptel1M 662795 663017 (336983) L1PB_orf2#LINE/L1 124 350 (2944) m_b342s551i9 14315 chrXptel1M 662795 CAAAAGACACAATTGAAACAGAAACACACACACCAAGTTAACATAAAGAA 662844 i v vi i v v iv v iv v vi ii L1PB_orf2#LIN 124 CAAGAGACTCACCTAACACATAAGGACTCACATAAACTTAAGGTAAAGGG 173 chrXptel1M 662845 CTGGAGCAGAATATATTCTTTTCAAATGAA-ATTAAAATGT---CGGGGG 662890 v -- i v i iv v i - ii - i--- i i L1PB_orf2#LIN 174 GTGGA--AAAAGACATTCCATGCAAATGGACACCAAAA-GCGAGCAGGAG 220 chrXptel1M 662891 TAGCAATC--TATCTCAGACAAAGCAAAAGTAAAAATAGACCTAATTAAA 662938 v i-- v i vv v ii ivvvi i L1PB_orf2#LIN 221 TAGCTATTCTTATATCAGACAAAACAAACTTTAAAGCAACAGCAGTTAAA 270 chrXptel1M 662939 AGAGATAAGGAAGGAAACTACATTTTGCTAAAAGGTATTATAGACACCGA 662988 i i i i v i i vv v ?v ?i vv - v i L1PB_orf2#LIN 271 AAAGACAAAGAGGGACATTATATAATGATAAAAGGNCTNGTCCA-ACAGG 319 chrXptel1M 662989 AGTAATATTATA---CTAAATATATGTACTCC 663017 i- i i --- i i v L1PB_orf2#LIN 320 AA-AATATCACAATCCTAAATATATATGCACC 350 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.18 CpG sites = 37, Kimura (unadjusted) = 40.97 Transitions / transversions = 1.23 (37/30) Gap_init rate = 0.04 (9 / 222), avg. gap size = 1.56 (14 / 9) 17 9.75 2.86 2.86 chrXptel1M 663352 663386 (336614) (TTG)n#Simple_repeat 1 35 (0) m_b342s252i12 14316 chrXptel1M 663352 TTGTTGTTGTTGTTGTT-TTCTTGCTTGTTTTTTTT 663386 - v - v v (TTG)n#Simple 1 TTGTTGTTGTTGTTGTTGTTGTTG-TTGTTGTTGTT 35 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 522 21.58 0.73 8.66 chrXptel1M 663589 663725 (336275) MIRb#SINE/MIR 4 130 (138) m_b342s601i26 14317 chrXptel1M 663589 AGGGGCAGCTAGGTGGCACAGTGGATAGAGTACTAACCCTGAAGTCAGAA 663638 --- ii v i vii ii i v MIRb#SINE/MIR 4 AGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGAC 50 chrXptel1M 663639 GGACCTGAGTTCAAATGTGATCTCAGACACTTAACACTTCCTAGCTGTGT 663688 i i i viviv v v ------- MIRb#SINE/MIR 51 AGACCTGGGTTCGAATCCCGGCTCTGCCACTTA-------CTAGCTGTGT 93 chrXptel1M 663689 GATCCTTGGGCAAGTCATTTAACCCCAATT-GCCTCAG 663725 - i i i vv v- MIRb#SINE/MIR 94 GA-CCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAG 130 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 23.55 CpG sites = 16, Kimura (unadjusted) = 25.67 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.09 (12 / 136), avg. gap size = 1.00 (12 / 12) 298 28.20 3.70 3.70 chrXptel1M 664738 664899 (335101) L1PREC2_orf2#LINE/L1 3133 3294 (0) m_b342s551i10 14318 chrXptel1M 664738 TCTGATAAAGGCCTCATTTCTAAAATATATAGAGAATTGACTCAAATTTA 664787 i i v v i iv v ii i v vv L1PREC2_orf2# 3133 TCTGACAAAGGTCTAATATCCAGCATCTATAAGGAACTTAAACAAATTTA 3182 chrXptel1M 664788 TAAGAATT---CAAGCCATTCTCCAATTGATAAATGGTCAAAGGATATGA 664834 i vv--- i v i--- v i v i v i L1PREC2_orf2# 3183 CAAGAAAAAAACAAACAAC---CCCATTAAAAAGTGGGCAAAGGACATGA 3229 chrXptel1M 664835 ACAGACAATTTCCAGATGATGAAAT---TGAAATTAATACCACTCATATG 664881 v i i v v v --- viiii --- vv L1PREC2_orf2# 3230 ACAGACACTTTTCAAAAGAAGACATACATGCGGCCAA---CAAGCATATG 3276 chrXptel1M 664882 AAAGAGGGCTCCAAATCA 664899 i ii v v L1PREC2_orf2# 3277 AAAAAAAGCTCAACATCA 3294 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.80 CpG sites = 22, Kimura (unadjusted) = 35.79 Transitions / transversions = 1.00 (22/22) Gap_init rate = 0.05 (8 / 161), avg. gap size = 1.50 (12 / 8) 1375 27.17 3.53 1.46 chrXptel1M 664756 665293 (334707) L1ME4c_3end#LINE/L1 7 555 (275) m_b342s551i11 14318 chrXptel1M 664756 TCTAAAATATATAGAGAATTGACTCAAATTTATAAGAAT----TCAAGCC 664801 ?v ? i ii v i v v---- v L1ME4c_3end#L 7 TCTNTANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAAGAC 56 chrXptel1M 664802 ATTCTCCAATTGATAAATGGTCAAAGGATATGAACAGACAATTTCCAGAT 664851 ----i v v i iv ? v L1ME4c_3end#L 57 ----CCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAA 102 chrXptel1M 664852 GATGAAATTGAAATTAATAC-CACTCATATGAAAGAGGGCTCCAAATCAC 664900 v -iv ? i v- vv i i i iv i v vv i L1ME4c_3end#L 103 GAGGAAAT-ACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGC 151 chrXptel1M 664901 TATTGATCAGAGAAATGCAAATTAAGACAACTCTGAGATACCACTCCACA 664950 v i i ii vv i ii i L1ME4c_3end#L 152 TAGTAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACG 201 chrXptel1M 664951 CCTGTCAGATTGGCTAAAATGACAGGAAAAAATAATGATGAATGTTGG-- 664998 i i i i v vvv ii vvi iviv i -- L1ME4c_3end#L 202 CCTATTAAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGCTGGCG 251 chrXptel1M 664999 -GGATGTGGGAAAACTGGGACACTGATACATTGTTGGTGGA---GTAA-- 665042 - ? i vi v ? v i v--- -- L1ME4c_3end#L 252 AGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAAT 301 chrXptel1M 665043 ---TCCAACCATTCTGAAGAGCAATCTGGAATTATGCCCCAAAAGTTATC 665089 --- v v i i i i v v i ivi i ii v L1ME4c_3end#L 302 TGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATA 351 chrXptel1M 665090 AAACTGTGCATATCCTTTGATCCAGCAGTGCTACGACTGGGCTTATACCC 665139 v v i i i i v i vv vv v i L1ME4c_3end#L 352 AAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCC 401 chrXptel1M 665140 CAAAGAGATA---CTAAAGAAGGGAAAGGGACCTGTCTGTGCCAAAATGT 665186 i i i --- v i i --- i v ii v i L1ME4c_3end#L 402 TAAGGAAATAATTCAAAAGAAGGAAAAAG---CTATATGCACGAAGATGT 448 chrXptel1M 665187 TTGTGGCAGCCCTCTTTGTAGTGGCTAGAAACTGGAAACTGAGTGGATGC 665236 ii v vi v i i i v i i vivv ii i L1ME4c_3end#L 449 TCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGT 498 chrXptel1M 665237 CCATCAATTGGAGAATGGCTGAATAAATTGTGCTATATGAATGTTATGGA 665286 v v i i i i i v i v? iviv L1ME4c_3end#L 499 CCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGA 548 chrXptel1M 665287 ATATTAT 665293 L1ME4c_3end#L 549 ATATTAT 555 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 33.53 CpG sites = 81, Kimura (unadjusted) = 35.02 Transitions / transversions = 1.29 (81/63) Gap_init rate = 0.03 (15 / 537), avg. gap size = 1.80 (27 / 15) 1005 29.11 4.22 2.77 chrXptel1M 664807 665375 (334625) L1MC5a_3end#LINE/L1 58 634 (2143) m_b342s551i12 14318 chrXptel1M 664807 CCAATTGATAAATGGTCAAAGGATATGAACAGACAATTTCCAGATGATGA 664856 v v v i i iv vi v L1MC5a_3end#L 58 CCAATAGAAAAATGGGCAAAAGATATGAACAGACAGTTCACAGAAAAAGA 107 chrXptel1M 664857 AATTGAAATTAATACCACTCATATGAAAGAGGGCTCCAAATCACTATTGA 664906 vv vivivii vv iiiv v vv vv i L1MC5a_3end#L 108 AATGCAAATGGCCCTTAAACATATGAAAAGATGCTCAACCTCACTCATAA 157 chrXptel1M 664907 TCAGAGAAATGCAAATTAAGACAACTCTGAGATACCACTCCACACCTGTC 664956 v i v v i i v i L1MC5a_3end#L 158 TAAGAGAAATGCAAATTAAAACTACACTGAGATACCATTTCTCACCTATC 207 chrXptel1M 664957 AGATTGGCTAAAAT--GACAG---GAAAAAATAATGATGAATGTTGG--- 664998 v --i v --- v v v -----v --- L1MC5a_3end#L 208 AGATTGGCAAAAATCCAAAAGTTTGACAACATACT-----CTGTTGGCGA 252 chrXptel1M 664999 GGATGTGGGAAAACTGGGACACTGATACATTGTTGGTGG--------AGT 665040 v i v v v v i -------- i L1MC5a_3end#L 253 GGCTGTGGGGAAACAGGCACTCTCATACATTGCTGGTGGGAATGCAAAAT 302 chrXptel1M 665041 AATCCAACCATTCTGAAGAGCAATCTGGAATTATGCCCCAAAAGTTATCA 665090 ii v vi v i i v i v v vivv - - L1MC5a_3end#L 303 GGTACAACCCCTATGGAGGGGAATTTGGCAATATCTAGCAAAA-TTA-CA 350 chrXptel1M 665091 AACTGTGCA--TATCCTTTGATCCAGCAGTGCTACGACTGGGCTTATACC 665138 --- i -- i i i v i vv i vv v i L1MC5a_3end#L 351 ---TATGCATTTACCCTTTGACCCAGCAATCCCACTTCTAGGAATCTATC 397 chrXptel1M 665139 CCAAAGAGATACTA--AAGAAGGGAAAGGGACCTGTCTGTGCCAAAATGT 665186 i v i ?-- i vivi i? -- v ii v iiv i L1MC5a_3end#L 398 CCGAAGATACACTNGCAAAAATACGAAANGAC--GTATGCACAAGGTTAT 445 chrXptel1M 665187 TTGTGGCAGCCCTCTTTGTAGTGGCTAGAAACTGGAAACTGAGTGGATGC 665236 ii v vi v i i v i i vivviii i L1MC5a_3end#L 446 TCATTGCAGCATTATTTGTAATAGCAAAAGACTGGAAACAACCCAAATGT 495 chrXptel1M 665237 CCATCAATTGGAGAATGGCTGAATAAATTGTGCTATATGAATGTTATGGA 665286 v i v i i i v i vv iiiv L1MC5a_3end#L 496 CCATCAATAGGGGACTGGTTGAATAAACTATGGTACATCCACACAATGGA 545 chrXptel1M 665287 ATATTATTGTTCTATAAGAAACAA-GCAGCAGGAAGATCTC---ACAAAG 665332 i i vvvv i i iv - ---- --- i vv L1MC5a_3end#L 546 GTACTATGCAGCTGTAAAAAGGAATG----AGGAAGATCTCTATATACTG 591 chrXptel1M 665333 GCCTGGAGAGACTTACACGAACTGATGCTGAGTGAAATGAGCA 665375 ?iv v ii v v vv iv i i vi L1MC5a_3end#L 592 NTATGGAGTGATCTCCAGGATATATTGTTAAGTGAAAAAAGCA 634 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.91 CpG sites = 78, Kimura (unadjusted) = 37.49 Transitions / transversions = 0.94 (78/83) Gap_init rate = 0.04 (24 / 568), avg. gap size = 1.67 (40 / 24) 12 24.76 0.00 2.56 chrXptel1M 665967 666006 (333994) (AAAAC)n#Simple_repeat 1 39 (0) m_b342s252i13 14319 chrXptel1M 665967 AAGACAAAGCAATAACAAAACAGAATATAAAAAATGAAAA 666006 i i - i i v v vv (AAAAC)n#Simp 1 AAAACAAAACAA-AACAAAACAAAACAAAACAAAACAAAA 39 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1) 13 25.67 2.08 2.08 chrXptel1M 666401 666448 (333552) (AAG)n#Simple_repeat 1 48 (0) m_b343s252i1 14320 chrXptel1M 666401 AAGGAGAACAATTAGAAGAATTAGAAG-GGATAGTAGAAGAATTAGAAG 666448 i v vv vv -i - v vv (AAG)n#Simple 1 AAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA-AGAAGAAGAAGAAGAAG 48 Matrix = Unknown Transitions / transversions = 0.25 (2/8) Gap_init rate = 0.04 (2 / 47), avg. gap size = 1.00 (2 / 2) 273 22.87 0.00 2.86 chrXptel1M 666583 666654 (333346) DNM1r#Unknown 2476 2545 (2117) m_b343s502i0 14321 chrXptel1M 666583 ATGCATATTTACATATATATAAATGCATATGTGTGTATGTATGTAGCTGT 666632 i ii v iii ivi i i -- i DNM1r#Unknown 2476 ACGTGTATGTGTGTATATATGTGTGTATATGTGTGTATGTGTGTA--TAT 2523 chrXptel1M 666633 GTGTGTATATATACACATATAT 666654 i ii ? DNM1r#Unknown 2524 ATGTGTATATATACGTATNTAT 2545 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 25.61 CpG sites = 14, Kimura (unadjusted) = 30.02 Transitions / transversions = 7.00 (14/2) Gap_init rate = 0.03 (2 / 71), avg. gap size = 1.00 (2 / 2) 15 28.75 1.82 0.00 chrXptel1M 666784 666838 (333162) (CTTTT)n#Simple_repeat 1 56 (0) m_b343s252i2 14322 chrXptel1M 666784 CTTTGCTTTTTTTTTTTTAATTTTTCTTTT-TTGTATTTCTTTTTCTATT 666832 v i i vvi - v v ii v (CTTTT)n#Simp 1 CTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTT 50 chrXptel1M 666833 TTTCTC 666838 i i (CTTTT)n#Simp 51 CTTTTC 56 Matrix = Unknown Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1) 24 19.79 0.00 0.00 chrXptel1M 666790 666835 (333165) (T)n#Simple_repeat 1 46 (0) m_b343s252i3 14323 chrXptel1M 666790 TTTTTTTTTTTTAATTTTTCTTTTTTGTATTTCTTTTTCTATTTTT 666835 vv i v v i i v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 46 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 15 12.41 5.71 0.00 chrXptel1M 666848 666882 (333118) (ATAAA)n#Simple_repeat 1 37 (0) m_b343s252i4 14324 chrXptel1M 666848 ATTAAATAAAA-AAGA-AAAAAATAATAAAATAAAAT 666882 v - i - v v (ATAAA)n#Simp 1 ATAAAATAAAATAAAATAAAATAAAATAAAATAAAAT 37 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 17 18.22 0.00 0.00 chrXptel1M 666851 666881 (333119) (A)n#Simple_repeat 1 31 (0) m_b343s252i5 14324 chrXptel1M 666851 AAATAAAAAAGAAAAAAATAATAAAATAAAA 666881 v i v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 31 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 949 32.19 4.83 0.85 chrXptel1M 667106 667788 (332212) L1M4_orf2#LINE/L1 1025 1734 (1560) m_b343s551i0 14325 chrXptel1M 667106 AAATTAAAGTAGAAATTCATAAATTTG-GAA--GAAAAA--ATTGAATTA 667150 i i ii vv i v v - -- -- v ivv L1M4_orf2#LIN 1025 AGATTAGAGCGGAAATAAATGAAATAGAGAATAGAAAAACAATAGAGAAA 1074 chrXptel1M 667151 TTAAATGAAATTATGAGCTGATTATATTTAAAAATT--TAAAATAGATAA 667198 v v i ii vi i i v v vv i i--i v i L1M4_orf2#LIN 1075 ATCAACGAAACCAAAAGTTGGTTCTTTGAAAAGATCAACAAAATTGACAA 1124 chrXptel1M 667199 GCCACCAGTTAATTTGATTAA--ATGAAAGAAAAAA-ACT-AAATTACCA 667244 i vii i ivi ii -- vi i i - - i L1M4_orf2#LIN 1125 ACCTTTAGCTAGACTGACCAAGAAAAAAAGAGAGAAGACTCAAATTACTA 1174 chrXptel1M 667245 GAATAAAAAATGAATAGGGTGA-ATGCACGGTCAAGAT----GAAATTAA 667289 i v ii vii v - -i vii i vv ---- v L1M4_orf2#LIN 1175 AAATCAGGAATGAAAGAGGGGACAT-TACTACCGACCTTACAGAAATAAA 1223 chrXptel1M 667290 AGCCATTATTAGGATGCATTTTGTTCAATAATATGCTAATAACAGT-GAC 667338 ivv v ivii i v vv vi i i - v - i L1M4_orf2#LIN 1224 AAGGATTATAAGGGAATACTATGAACAATTGTATGCCAACAA-ATTAGAT 1272 chrXptel1M 667339 AATCTAAATTAAATATATGA----CTAAAAA-ATGTAAAATGTCCAGATT 667383 i i v iv ii ---- i - iii v ii v i i L1M4_orf2#LIN 1273 AACCTAGATGAAATGGACAAATTCCTAGAAAGACACAAACTACCGAAACT 1322 chrXptel1M 667384 AACAGAAAAAGAAATAGAGTACTTAAATAATTCTATTTTAGGAAAAAAAA 667433 i vv i iv ii i ivi vvi i v i i L1M4_orf2#LIN 1323 GACTCAAGAAGAAATAGAAAATCTGAATAGACCTATAACAAGTAAAGAGA 1372 chrXptel1M 667434 ATTGAATAAAACATAGATGAGATCCCCA-AGAAAAAAACCCACGACCAGA 667482 - v ivv vi vi iv i - i i i v ? L1M4_orf2#LIN 1373 -TTGAATTAGTAATCAAAAAACTTCCCACAAAGAAAAGCCCAGGNCCAGA 1421 chrXptel1M 667483 TGAATTTACAAGCAAATTCTACCA--CACTTAAAGAATAATTAATTCCAA 667530 iv i vi ii -- i v iv L1M4_orf2#LIN 1422 TGGCTTCACTGGTGAATTCTACCAAACATTTAAAGAAGAATTAACACCAA 1471 chrXptel1M 667531 TCTTTTCTAAGCTATTTTGAAAAAGAGGTAAAGGAG------TTACAAAA 667574 i ivi i v iii v i- i ------i v vv L1M4_orf2#LIN 1472 TCCTTCACAAACTCTTCCAAAAAATAGA-AGAGGAGGGAACACTTCCCAA 1520 chrXptel1M 667575 TTCCTTCTGTGACTCAAATATGATTTTATTACCTAAACCAAGGAGAAAAA 667624 i v i vv v i v iii iv v -- v i L1M4_orf2#LIN 1521 CTCATTCTATGAGGCCAGTATTACCCTGATACCAAAACCA--GACAAAGA 1568 chrXptel1M 667625 CA--ACAGAGAAAGAAAACTTCAAATCAATTTCTCTAATGAACATTGATG 667672 -- iii v i i v i v i v L1M4_orf2#LIN 1569 CATCACAAGAAAAGAAAACTACAGACCAATATCCCTTATGAATATAGATG 1618 chrXptel1M 667673 TGAAAAGTTTTTATAAAATACTAATAAGGAGACTACAAAAATATATCACA 667722 ii vii iv i ii ivv v v iv i v v L1M4_orf2#LIN 1619 CAAAAATCCTCAACAAAATACTAGCAAACCGAATCCAGCAACATATAAAA 1668 chrXptel1M 667723 AAGCTCATGTTCCATGACCAGGTGGGATTTATCCCAGGAATGCAGGGCTG 667772 i v i iiv i i i L1M4_orf2#LIN 1669 AGGATTATACACCATGACCAAGTGGGATTTATCCCAGGAATGCAAGGTTG 1718 chrXptel1M 667773 GTTCCATATTAGGAAA 667788 v i ?v i L1M4_orf2#LIN 1719 GTTCAACATNCGAAAA 1734 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 42.99 CpG sites = 131, Kimura (unadjusted) = 43.84 Transitions / transversions = 1.51 (131/87) Gap_init rate = 0.03 (22 / 682), avg. gap size = 1.77 (39 / 22) 988 29.01 2.78 0.00 chrXptel1M 667458 667781 (332219) L1M1_orf2#LINE/L1 1395 1727 (1567) m_b343s551i1 14325 chrXptel1M 667458 CCCA--AGAAAAAAACCCACGACCAGATGAATTTACAAGCAAATTCTACC 667505 -- i i i iv v iv i vivii L1M1_orf2#LIN 1395 CCCAGTAAAGAAAAGCCCGGGACCCGATGGCTTCACTGCTGAATTCTACC 1444 chrXptel1M 667506 A--CACTTAAAGAATAATTAATTCCAATCTTTTCTAAGCTATTTTGAAAA 667553 -- i v i v i viii i ii L1M1_orf2#LIN 1445 AAACATTTAAAGAAGAACTAATACCAATCCTACTCAAACTATTCCGAAAA 1494 chrXptel1M 667554 A--GAGGTAAAGGAGTTAC---AAAATTCCTTCTGTGACTCAAATATGAT 667598 -- vii iiv ---v i v ii vv v i v i L1M1_orf2#LIN 1495 ATAGAGGAGGAGGGAATACTTCCAAACTCATTCTACGAGGCCAGTATTAC 1544 chrXptel1M 667599 TTTATTACCTAAACCAAGGAGAAAAACAACAGAGAAAGAAAACTTCAAAT 667648 ii iv v iiv i i v v i i v iii L1M1_orf2#LIN 1545 CCTGATACCAAAACCAGACAAAGACACATCAAAAAAAGAAAACTACAGGC 1594 chrXptel1M 667649 CAATTTCTCTAATGAACATTGATGTGAAAAGTTTTTATAAAATACTAATA 667698 v i i ii vii iv i ii L1M1_orf2#LIN 1595 CAATATCTCTGATGAATATTGATGCAAAAATCCTCAACAAAATACTAGCA 1644 chrXptel1M 667699 AGGAGACTACAAAAATATATCACAAAGCTCATGTTCCATGACCAGGTGGG 667748 ivv v v v i i v v vivi i L1M1_orf2#LIN 1645 AACCGAATTCAACAATACATTAAAAAGATCATTCATCATGACCAAGTGGG 1694 chrXptel1M 667749 ATTTATCCCAGGAATGCAGGGCTGGTTCCATAT 667781 ? i i v v i L1M1_orf2#LIN 1695 ATTTATCCCNGGGATGCAAGGATGGTTCAACAT 1727 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.55 CpG sites = 58, Kimura (unadjusted) = 38.10 Transitions / transversions = 1.61 (58/36) Gap_init rate = 0.01 (4 / 323), avg. gap size = 2.25 (9 / 4) 801 33.15 2.60 1.28 chrXptel1M 667464 667848 (332152) L1P4_orf2#LINE/L1 1403 1792 (1502) m_b343s551i2 14325 chrXptel1M 667464 AAAAAAACCCACGACCAGATGAATTTACAAGCAAATTCTACCACACTTA- 667512 i vv i i iv i v v - L1P4_orf2#LIN 1403 AAAAAAGCCCCGGACCAGATGGATTCACAGCCGAATTCTACCAGACGTAC 1452 chrXptel1M 667513 -AAGAATAATTAATTCCAATCTTTTCTAAGCTATTTTGAAAAA--GAGGT 667559 - v ii ii v i viiv i iii -- v L1P4_orf2#LIN 1453 AAAGAAGAGCTGGTACCAATCCTACTGAAACTATTCCAAAAAATCGAGGA 1502 chrXptel1M 667560 AAAGGAGTTACAA---AATTCCTTCTGTGACTCAAATATGATTTTATTAC 667606 ii iii v vv--- i v ii vv v ii v iii iv L1P4_orf2#LIN 1503 GGAGGGACTCCTCCCTAACTCATTCTACGAAGCCAGCATCACCCTGATAC 1552 chrXptel1M 667607 CTAAACCAAGGAGAAAAACAACAGAGAAAGAAAACTTCAAATCAATTTCT 667656 v vi v i i v ii i ? iii v i L1P4_orf2#LIN 1553 CAAAACCTGGCAAAGACACAACGAAAAAAGAAAACTNCAGGCCAATATCC 1602 chrXptel1M 667657 CTAATGAACATTGATGTGAAAAGTTTTTATAAAATACTAATAAGGAGACT 667706 i v i ii vii iv i ii ivv v L1P4_orf2#LIN 1603 CTGATGAACATAGACGCAAAAATCCTCAACAAAATACTAGCAAACCGAAT 1652 chrXptel1M 667707 ACAAAAATATATCACAAAGCTCATGTTCCATGACCAGGTGGGATTTATCC 667756 v iv ii i v i v viv i i i i v i L1P4_orf2#LIN 1653 CCAGCAGCACATCAAAAAGTTAATTCACCACGATCAAGTAGGCTTTATTC 1702 chrXptel1M 667757 CAGGAATGCAGGGCTGGTTCCATATTAGGAAAGTTTTAAGTCTAATTGAC 667806 v i i i v i vv v vivv i v i v L1P4_orf2#LIN 1703 CTGGGATGCAAGGTTGGTTCAACATACGCAAATCAATAAATGTGATTCAC 1752 chrXptel1M 667807 TGTTTTAACAA---CAACAATAAAAACCAACTATCTAAATCATCT 667848 iiiv v i---i v i -- ---i L1P4_orf2#LIN 1753 CACATAAACAGAATTAAAAACAAAAACCA--TAT---GATCATCT 1792 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.25 CpG sites = 76, Kimura (unadjusted) = 45.73 Transitions / transversions = 1.52 (76/50) Gap_init rate = 0.03 (10 / 384), avg. gap size = 1.50 (15 / 10) 391 23.12 10.98 7.69 chrXptel1M 667928 668091 (331909) C MIR1_Amn#SINE/MIR (55) 175 7 m_b343s601i0 14326 chrXptel1M 667928 TACAAAGGGGGGTTTTTTTCCATTTCCTTCTCCAGATCATTTTATAGATG 667977 i ------- vi v v v ---i i C MIR1_Amn#SINE 175 TACAAAGGAGG-------TCAGTATCATTATCC---CCATTTTACAGATG 136 chrXptel1M 667978 AGGAAACTGAGGCA-AACGGGGTTAAATGACTTG-ACAAAACTGCACA-- 668023 ?- iv i ? i -v iiiii ? -- C MIR1_Amn#SINE 135 AGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGCCCAAGGTCACNCAGC 86 chrXptel1M 668024 --GCTAGTATCTGAGGCCTGATTTAAACTCAGGTCT------------TT 668059 -- ? iv v v vv ? ?i i ------------ i C MIR1_Amn#SINE 85 NGGCNAGTGGCAGAGCCGGGANTNGAACCCAGGTCTCCCGAGTCCCAGTC 36 chrXptel1M 668060 TAGCACTCTAACCACTGCACCATCTAGCTGCC 668091 i ii v iv i---i C MIR1_Amn#SINE 35 CAGTGCTCTATCCACTAGACCAC---ACTGCC 7 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.91 CpG sites = 22, Kimura (unadjusted) = 29.91 Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.11 (18 / 163), avg. gap size = 1.72 (31 / 18) 438 24.18 6.35 1.52 chrXptel1M 667965 668090 (331910) C MIRc#SINE/MIR (122) 146 15 m_b343s601i1 14326 chrXptel1M 667965 CATTTTATAGATGAGGAAACTGAGGC-AAACGGGGTTAAATGACTTG-AC 668012 i -v iv i i -v C MIRc#SINE/MIR 146 CATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCC 97 chrXptel1M 668013 AAAACTGCACAGCTAGTA----TCTGAGGCCTGATTTAAACTCAGGTCTT 668058 iiiii ----v v v vv i ii i C MIRc#SINE/MIR 96 AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTT 47 chrXptel1M 668059 TTAGCACTCTAA--CCACTGCACCATCTAGCTGC 668090 iiv - i -- v v iv i - C MIRc#SINE/MIR 46 CCTG-ACTCCAAGTCCAGTGCTCTTTCCA-CTGC 15 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.56 CpG sites = 18, Kimura (unadjusted) = 29.86 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.05 (6 / 125), avg. gap size = 1.67 (10 / 6) 323 20.99 2.83 10.10 chrXptel1M 668092 668197 (331803) L1MC_orf2#LINE/L1 1782 1880 (1414) m_b343s551i3 14327 chrXptel1M 668092 CATGATTATATCAATAGATGCAGGAAAAGCTTTCAAGAAAATACAATAAC 668141 i i v ii v v i v L1MC_orf2#LIN 1782 CATGATCATATCAATAGATGCAGAAAAAGCATTTGACAAAATCCAACACC 1831 chrXptel1M 668142 CATTCCTATTGGAAATACTTTCTAGTGTTTAGCA---TGGGAATAAATGG 668188 v iv -- v i -------- --- i i v L1MC_orf2#LIN 1832 CATTCATGAT--AAAAACTCTC--------AGCAAACTAGGAATAGAGGG 1871 chrXptel1M 668189 GACTTTTCT 668197 vi i L1MC_orf2#LIN 1872 GAACTTCCT 1880 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 24.69 CpG sites = 11, Kimura (unadjusted) = 24.69 Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.10 (11 / 105), avg. gap size = 1.18 (13 / 11) 29 0.00 0.00 0.00 chrXptel1M 668278 668302 (331698) (AT)n#Simple_repeat 1 25 (0) c_b343s251i0 14328 chrXptel1M 668278 ATATATATATATATATATATATATA 668302 (AT)n#Simple_ 1 ATATATATATATATATATATATATA 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 289 24.99 2.70 2.70 chrXptel1M 669380 669490 (330510) C L1ME3C_3end#LINE/L1 (706) 164 54 m_b343s551i4 14329 chrXptel1M 669380 ATTTCTCTAATCAACAGTGATTTAAAGCATTTTTTCAAACAGCTATCAAT 669429 i i i vi vv vi i v iivi --- C L1ME3C_3end#L 164 ATTTCCCTGATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTAT---T 118 chrXptel1M 669430 GGGC-TT--AATTTAATTATCTGTAAATTGTCTGTTCATATCTTTTGAAC 669476 v - --?i vv iv i i vv C L1ME3C_3end#L 117 GGCCATTCGNGTTTCCTCTTCTGTGAATTGCCTGTTCATATCTTTTGCCC 68 chrXptel1M 669477 ATTTATCAATTGGG 669490 v v C L1ME3C_3end#L 67 ATTTTTCTATTGGG 54 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 30.99 CpG sites = 13, Kimura (unadjusted) = 30.99 Transitions / transversions = 0.93 (13/14) Gap_init rate = 0.05 (5 / 110), avg. gap size = 1.20 (6 / 5) 269 23.13 5.42 11.46 chrXptel1M 670032 670197 (329803) C L1M3_orf2#LINE/L1 (126) 3162 3006 m_b343s551i5 14329 chrXptel1M 670032 TTCTTTATATATTTTAGAGATGAGATCTTTATCAGAAATACTGACT---A 670078 i i v v ivi i v - ii --- C L1M3_orf2#LIN 3162 TTCCTTATATATTTTGGATATTAACCCCTTATCAGATATA-TGGTTTGCA 3114 chrXptel1M 670079 AAGATTTTTTCCCAGCTTTGTA-----CTTTTAAATTTTGTTTTGGTTGT 670123 v i -i ii ----- i vv i i -- i C L1M3_orf2#LIN 3113 AATATTTTCTCCCA-TTCCGTAGGTTGCCTTTTCACTCTG--TTGATTGT 3067 chrXptel1M 670124 TTTTTTGTGTGTGTGTGCGTGTGTGTGCAAAATCTTTTTAATTTAATGTA 670173 ii --------- ----- i v i i C L1M3_orf2#LIN 3066 TTCCTT---------TGC-----TGTGCAGAAGCTTTTTAGTTTGATGTA 3031 chrXptel1M 670174 ATCAGAGTTGTCCA-TTTTGCCTTT 670197 i vv v i - i C L1M3_orf2#LIN 3030 GTCCCACTTGTCTATTTTTGCTTTT 3006 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 27.36 CpG sites = 23, Kimura (unadjusted) = 28.34 Transitions / transversions = 2.09 (23/11) Gap_init rate = 0.13 (21 / 165), avg. gap size = 1.29 (27 / 21) 15 19.46 0.00 0.00 chrXptel1M 670696 670730 (329270) (TCTGTC)n#Simple_repeat 1 35 (0) m_b343s252i6 14330 chrXptel1M 670696 TCTTTCTCAGGCTCTGCCTGTGTCTCTATCTCTGT 670730 v v v i v i (TCTGTC)n#Sim 1 TCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGT 35 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 198 30.31 1.27 8.11 chrXptel1M 671551 671629 (328371) C MamTip2b#DNA/hAT-Tip100 (344) 105 32 m_b343s601i2 14331 chrXptel1M 671551 CAGGTGAGAGGGGGAGAGATTTAGGATGATGGCAGTGAACACCTTTTG-T 671599 ivi v v v ----- v ii-i i -i C MamTip2b#DNA/ 105 CAGGCCGGTGGGGGAGATATTTTGG-----GGCAGGGGG-GCCTTTCGGC 62 chrXptel1M 671600 GTCCCTTAAATTACTCTTTGTAGGCATCTG 671629 i i i v ivi iv i C MamTip2b#DNA/ 61 GCCCCTCAAATCACACCACGTAGGCGGCCG 32 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 27.36 CpG sites = 14, Kimura (unadjusted) = 40.16 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.09 (7 / 78), avg. gap size = 1.00 (7 / 7) 23 22.31 1.69 1.69 chrXptel1M 672612 672670 (327330) (AT)n#Simple_repeat 1 59 (0) m_b343s252i7 14332 chrXptel1M 672612 ATATATATATATATTTATAAAAAGATAGATACATACATACACATATGTA- 672660 v v v v v i i i i i - (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chrXptel1M 672661 ATGAAATATA 672670 - v (AT)n#Simple_ 51 AT-ATATATA 59 Matrix = Unknown Transitions / transversions = 0.83 (5/6) Gap_init rate = 0.03 (2 / 58), avg. gap size = 1.00 (2 / 2) 310 31.10 3.48 2.15 chrXptel1M 672826 673055 (326945) L2#LINE/L2 2044 2276 (806) m_b343s601i3 14333 chrXptel1M 672826 TCCTCATTCTCCTCCATCTCTCTGTAGGCTTTGACACTGTTGCTCACCCT 672875 ii v iv i ? v i vv v v i i L2#LINE/L2 2044 TCCTCATCTTACTTGACCTNTCAGCAGCATTTGACACAGTTGATCACTCC 2093 chrXptel1M 672876 CTTCTCCTT--AAT-CTCTCCTCTCTAGATTTTCTGATGGTATCTACTCT 672922 i i -- i- i i v v ii i -- v ii - i v L2#LINE/L2 2094 CTCCTTCTTGAAACACTTTCTTCACTTGGCTTCC--AGGACA-CCACACT 2140 chrXptel1M 672923 CTCCTAGATCTCCTCCTATCTATCTGAGCA---CTTCTCTGTCTTCTTTG 672969 i v i i vv iv i--- v i L2#LINE/L2 2141 CTCCTGGTTTTCCTCCTACCTCACTGGCCGCTCCTTCTCAGTCTCCTTTG 2190 chrXptel1M 672970 CAGGATCCTCATTCAGATCAC--ACTCTCTAACCTCTCTAATCCTAGAGG 673017 v v -i vv v -- - ? v vi vv i v ivv L2#LINE/L2 2191 CTGGTTCCTC-CTCATCTCCCCGAC-CTCTNAACGTTGGAGTGCCCCAGG 2238 chrXptel1M 673018 GTTTTGACCTGGCCCCTCTTCTTTTTTTCCTTTATACT 673055 i iv v v vv i i iiv i i L2#LINE/L2 2239 GCTCAGTCCTTGGACCTCTTCTCTTCTCTATCTACACT 2276 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.58 CpG sites = 36, Kimura (unadjusted) = 41.34 Transitions / transversions = 1.06 (36/34) Gap_init rate = 0.04 (9 / 229), avg. gap size = 1.44 (13 / 9) 18 16.64 4.08 2.00 chrXptel1M 674419 674467 (325533) (TTG)n#Simple_repeat 1 50 (0) m_b343s252i8 14334 chrXptel1M 674419 TTGATCTTAGTTGTT-TGGTTATTGTT-TTTTGGTTGTTGTTGTTGTAGT 674466 v v - - v i - v v v (TTG)n#Simple 1 TTGTTGTT-GTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGT 49 chrXptel1M 674467 T 674467 (TTG)n#Simple 50 T 50 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.06 (3 / 48), avg. gap size = 1.00 (3 / 3) 503 32.07 11.35 1.05 chrXptel1M 675117 675636 (324364) C L1ME4c_3end#LINE/L1 (257) 573 1 m_b343s551i6 14335 chrXptel1M 675117 ATCATTTCTTACAGCACAATAATATTTCATCATAATC-ACATGGTACAAT 675165 i v ii vvv i i- i ?- ii ivi i C L1ME4c_3end#L 573 ATCATTTTTAATGGCTGCATAATATTCCATCG-AGTNGATGTACCATAAT 525 chrXptel1M 675166 TTGTTCAGCCATTTCTCAATTGATGGGCACCTCTCAAATT----CCAATT 675211 ii i i i i v v i ii --- ii ---- C L1ME4c_3end#L 524 TTACTTAACCATTCCCCTATTGTTGGACATTT---AGGTTGTTTCCAATT 478 chrXptel1M 675212 ---CACAATCAGAAA-AGAGCTTCTATACATAATTTTACACCTATAGGTC 675257 --- i v i v - iv v v iv i vi iiii v v i C L1ME4c_3end#L 477 TTTCGCTATTATAAATAACGCTGCAATGAACATCTTCGTGCATATAGCTT 428 chrXptel1M 675258 CTTTCCCTTTTTGTAATCCCTTTTTAGAAACAAAT--CTAGTAATGGTAT 675305 i i iii v v vii ii i -i -- i v i v C L1ME4c_3end#L 427 TTTCCTTCTTTTGAATTATTTCCTTAGGA-TAAATTCCCAGAAGTGGAAT 379 chrXptel1M 675306 TGCTAGGTCAAAGAGTATGCATGGTTTCATG---CTT-----------CC 675341 i i i v iiv i --- ----------- C L1ME4c_3end#L 378 TACTGGGTCAAAGGGTATGAACATTTTTATGGCTCTTGATACGTATTGCC 329 chrXptel1M 675342 AAACTGCTGTACAGAA----TGTGACAGTACACAATCCTACCAACTGTTC 675387 i v v i ---- iv i vi ? v i i vi vi C L1ME4c_3end#L 328 AAATTGCTTTCCAAAAGGGTTGTACCAATTTACANTGCCACCAGCAATGT 279 chrXptel1M 675388 ACTAATGTCTCATTTTTCTCACATCCTTGCACA--ATTTGTCATTTTCCT 675435 iv i? vi v ivi i ? i - -- v vi v vv C L1ME4c_3end#L 278 ATGAGNGTACCAGTTTCACCGCANCCTCGC-CAGCATTGGGTATTATCAA 230 chrXptel1M 675436 TTTCTGTCCTATTAGCTAATCTAATAGGTATGAAAGAGTAGCTCAGAATT 675485 i vvvv v v i ii i vi v vvi C L1ME4c_3end#L 229 TTTTTTAAATTTTTGCTAATTTAATAGGCGTAAAATGGTATCTCATTGTT 180 chrXptel1M 675486 GTTTTAATTTGCAATTCTACAATCAATAGTGAGTTACATCATTTTTACAC 675535 i v vii i v i v vv v v i C L1ME4c_3end#L 179 GCTTTAATTTGCATTTCTTTGATTACTAGCGAGGTTGAACATTTTTCCAT 130 chrXptel1M 675536 ATG---G----------GTA--------TAGATAACTT-------CATAT 675557 i --- ---------- -------- ?vi i v ------- i C L1ME4c_3end#L 129 GTGTTTGTTTACTANTTGTATTTCCTCTTNTGTGAATTGTCTGTTCATGT 80 chrXptel1M 675558 CTCTTGACCATTTATCAATTAGGGAATGGCTCTTAATTTTATAAATTTGA 675607 ii v v i vv v v ? vv i v C L1ME4c_3end#L 79 CCTTTGCCCATTTATCTATTGGGGTCTTGATNTTTTTCTTATCAATTTGA 30 chrXptel1M 675608 CTCAGTTCTCTATATGTTTGAGAAATTAA 675636 v v i i i? v? v C L1ME4c_3end#L 29 ATGAGCTCTTTATATANTANAGATATTAA 1 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.47 CpG sites = 93, Kimura (unadjusted) = 44.03 Transitions / transversions = 1.29 (93/72) Gap_init rate = 0.04 (19 / 519), avg. gap size = 3.42 (65 / 19) 527 29.36 7.66 1.14 chrXptel1M 675291 675538 (324462) C L1ME5_3end#LINE/L1 (551) 390 127 m_b343s551i7 14335 chrXptel1M 675291 ATCTAGTAATGGTATTGCTAGGTCAAAGAGTATGCATG------GTTTCA 675334 i i v ii v i v i i i------i v C L1ME5_3end#LI 390 ACCCAGGAGCGGAATTGCTGGGTCATAGGGTATGCGTATACTTAATTTGA 341 chrXptel1M 675335 -----TGCTTCCAAACTGCTGTACAGAATG--TGA--CAGTACACAATCC 675375 ----- i v i i v v -- v-- vi v C L1ME5_3end#LI 340 CTAAGTACTGCCAGATTGCTCTCCAGAATGGCTGCACCAGTCTACACTCC 291 chrXptel1M 675376 TACCAACTGTTCACTAATGTCTCATTTTTCTCACATCCTTGCACAAT--T 675423 i i v v iv iv ii vv ? i i i - i-- C L1ME5_3end#LI 290 CACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATCCTCGC-CAACACT 242 chrXptel1M 675424 TGTCATTTTCC--TTTTCTGTCCTATTAGCTAATCTAATAGGTATGAAAG 675471 v v --i i--v v v i i i i iv C L1ME5_3end#LI 241 TGGCATTATCCAGCTTTCTA--ATTTTTGCCAGTCTAATAGGTGTAAAGT 194 chrXptel1M 675472 AGTAGCTCAGAATTGTTTTAATTTGCAATTCTACAATCAATAGTGAGTTA 675521 ii v vvi v vii i v i v C L1ME5_3end#LI 193 GATATCTCATTGTTGTTTTAATTTGCATTTCTCTGATTACTAATGAGTTT 144 chrXptel1M 675522 CATCATTTTTACACATG 675538 v v i i v i C L1ME5_3end#LI 143 GAGCATCTCTTCATATG 127 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.32 CpG sites = 40, Kimura (unadjusted) = 38.32 Transitions / transversions = 1.25 (40/32) Gap_init rate = 0.04 (9 / 247), avg. gap size = 2.44 (22 / 9) 13 28.94 0.00 3.57 chrXptel1M 676636 676693 (323307) (AAAAC)n#Simple_repeat 1 56 (0) m_b343s252i9 14336 chrXptel1M 676636 AATACATAATAGAAGAAAGAAAAACAGAAAAGGAAAATAACACAAACAAA 676685 v v i i v iv - vii v v - (AAAAC)n#Simp 1 AAAACAAAACAAAACAAAACAAAACA-AAACAAAACAAAACA-AAACAAA 48 chrXptel1M 676686 ACAGAACA 676693 i (AAAAC)n#Simp 49 ACAAAACA 56 Matrix = Unknown Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.04 (2 / 57), avg. gap size = 1.00 (2 / 2) 15 15.50 6.98 0.00 chrXptel1M 676649 676691 (323309) (AGAAAC)n#Simple_repeat 1 46 (0) m_b343s252i10 14336 chrXptel1M 676649 AGAAAGAAAAACAGAAA-AGGAA-AATAACACAAACA-AAACAGAA 676691 v i - i - iv v - (AGAAAC)n#Sim 1 AGAAACAGAAACAGAAACAGAAACAGAAACAGAAACAGAAACAGAA 46 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.07 (3 / 42), avg. gap size = 1.00 (3 / 3) 14 24.28 2.86 5.88 chrXptel1M 676794 676863 (323137) (TTTC)n#Simple_repeat 1 68 (0) m_b343s252i11 14337 chrXptel1M 676794 TTTCCATCTTTATTTCCTTGTAGTTATTCTGTTCTTTGCTGT-GTACTTT 676842 iv v i v -v iv - - v -v v (TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCT-TTCTTTCT-TTCTTT-CTTTCTTTCTTT 47 chrXptel1M 676843 TTTTACTTT-ATTCTTTCTTTC 676863 i - -v (TTTC)n#Simpl 48 CTTT-CTTTCTTTCTTTCTTTC 68 Matrix = Unknown Transitions / transversions = 0.44 (4/9) Gap_init rate = 0.09 (6 / 69), avg. gap size = 1.00 (6 / 6) 41 0.00 2.56 0.00 chrXptel1M 676929 676967 (323033) (TA)n#Simple_repeat 1 40 (0) c_b343s251i1 14338 chrXptel1M 676929 TATATATATATATATATATATATATATATATATA-ATATA 676967 - (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATA 40 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.03 (1 / 38), avg. gap size = 1.00 (1 / 1) 16 19.85 4.69 4.69 chrXptel1M 676984 677047 (322953) (ACAT)n#Simple_repeat 1 64 (0) m_b343s252i12 14339 chrXptel1M 676984 ACATACATAGA-GCA-ACATGCATACATATTTACATATACTCAGATACAT 677031 v -i - i iv i - - v (ACAT)n#Simpl 1 ACATACATACATACATACATACATACATACATACATACA-T-ACATACAT 48 chrXptel1M 677032 GTATATATA-ATCACAT 677047 ii i - - (ACAT)n#Simpl 49 ACATACATACAT-ACAT 64 Matrix = Unknown Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.10 (6 / 63), avg. gap size = 1.00 (6 / 6) 1040 30.61 3.96 2.67 chrXptel1M 678270 678749 (321251) L1ME5_3end#LINE/L1 156 641 (300) m_b343s551i8 14340 chrXptel1M 678270 AATTAGAAAAATTAAAATTAAAACA-CTCTAAGATACCACCTCACACTTC 678318 i i vv - vv i i i i i v L1ME5_3end#LI 156 AATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCTA 205 chrXptel1M 678319 TCAGATTGACTAAGATGACAGAAAA--AGATAAT---AAATGTTGGAGGA 678363 i i i v i --i i--i --- i v ii L1ME5_3end#LI 206 TTAGACTGGCAAAAAT--TAGAAAGCTGGATAATGCCAAGTGTTGGCGAG 253 chrXptel1M 678364 GAGGTAGGAAAACTGGGACACTAATGTA-------TAAGAGTTGTGAAAT 678406 v i i ? iv i v v i ------- ii - ii v L1ME5_3end#LI 254 GATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGT-GTAGACT 302 chrXptel1M 678407 GATCCAACCATTCTGGAGAGCAATTTGGAGCTATGCTCAA-GAAGTTAAG 678455 i v i i -- vi i i i-v i L1ME5_3end#LI 303 GGTGCAGCCATTCTGGAGAGCAATCTGG--CAGTACTTAGTCAAATTAAG 350 chrXptel1M 678456 CTGATCATACATACTCTTTGATCCAGCCATGTTACTACTGGGCTTATATC 678505 i-- - ii i v i v viii v iv L1ME5_3end#LI 351 T--AT-ACGCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATATC 397 chrXptel1M 678506 CCAAAGAGATCTTAAAGAAGG---GAAAGGGACCCACATGTGCAAAAATG 678552 i ii v viv ---iv i--- i i ii L1ME5_3end#LI 398 CCAAAGAAATTCTCACACAGGTCCATAAGGGG---ACATGTACGAGGATG 444 chrXptel1M 678553 TTTGTGGCAGCCCTCTTTGTTGTGGCAAGAAACTGGAAACTGAGTGGATG 678602 ii v vi v v ii i ii ii vivv i L1ME5_3end#LI 445 TTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGGGTG 494 chrXptel1M 678603 CCCATCAGCTGGAGAATGGCTGAATAAATTGTGGTACATGAATATTATGG 678652 i viv i v iii v iv v i ii L1ME5_3end#LI 495 TCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACACCATGG 544 chrXptel1M 678653 AATATTATTGTTCTGTAAGAAACAACCAACAGGATGATTTCAGAGAAGCC 678702 i i vvvv v v i vi vi vviv v v i v L1ME5_3end#LI 545 AGTACTATGCAGCAGTTAGAAGCAACGGACTAGATGTACACATAGCAACA 594 chrXptel1M 678703 TGAAGAGA-CTTACATGAAC-TGATGCTGAGTGAAACAAGCAGAAAACA 678749 i vi - v -- - ii v i ii L1ME5_3end#LI 595 TGGATGGATCTTAAA--AACATAGTGCTGAGTGAAAAAAGTAAGAAACA 641 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.44 CpG sites = 89, Kimura (unadjusted) = 41.03 Transitions / transversions = 1.65 (89/54) Gap_init rate = 0.04 (21 / 479), avg. gap size = 1.52 (32 / 21) 240 19.11 1.04 12.79 chrXptel1M 679304 679399 (320601) C L1M4a2_5end#LINE/L1 (910) 1746 1661 m_b343s551i9 14341 chrXptel1M 679304 TTTTTTTCTTGTTTCTTGCAAAATTTTCTCTTTGATCTGGGGGTTTCAA- 679352 i i v v i - vv v - C L1M4a2_5end#L 1746 TTTTTCTCTTGCTGCTTTCAAGATTTTCTCTTTG-TCTTTGGCTTTCAAC 1698 chrXptel1M 679353 AATTTGGCAATAATATTTTTATGTGTTTCCCACAAAGGATCTCTTTG 679399 i i v i i v i v ---------- C L1M4a2_5end#L 1697 AGTTTGACTATGATGTGTCTAGGTGT----------GGATCTCTTTG 1661 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 21.80 CpG sites = 8, Kimura (unadjusted) = 21.80 Transitions / transversions = 1.00 (8/8) Gap_init rate = 0.13 (12 / 95), avg. gap size = 1.00 (12 / 12) 12 28.14 3.85 0.00 chrXptel1M 680033 680084 (319916) (AATATAA)n#Simple_repeat 1 54 (0) m_b343s252i13 14342 chrXptel1M 680033 AATAGAAAATTTAACATATAAAA-A-CCAATATTAAAGATTAATTTCAAA 680080 v v v - -vv v v v v vi (AATATAA)n#Si 1 AATATAAAATATAAAATATAAAATATAAAATATAAAATATAAAATATAAA 50 chrXptel1M 680081 AGAT 680084 v (AATATAA)n#Si 51 ATAT 54 Matrix = Unknown Transitions / transversions = 0.09 (1/11) Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.00 (2 / 2) 37 0.00 0.00 2.86 chrXptel1M 680359 680394 (319606) (AC)n#Simple_repeat 1 35 (0) c_b343s251i2 14343 chrXptel1M 680359 ACACTACACACACACACACACACACACACACACACA 680394 - (AC)n#Simple_ 1 ACAC-ACACACACACACACACACACACACACACACA 35 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) 21 0.00 0.00 0.00 chrXptel1M 680395 680417 (319583) (TA)n#Simple_repeat 1 23 (0) m_b343s252i14 14344 chrXptel1M 680395 TATATATATATATATATATATAT 680417 (TA)n#Simple_ 1 TATATATATATATATATATATAT 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 49 22.92 4.93 0.68 chrXptel1M 680751 680892 (319108) (AT)n#Simple_repeat 1 148 (0) m_b343s252i15 14345 chrXptel1M 680751 ATATATATATATATATATATATGGAGGGTATGTATGTATGCATGTAGATA 680800 iv -vi i i ii i v (AT)n#Simple_ 1 ATATATATATATATATATATATATA-TATATATATATATATATATATATA 49 chrXptel1M 680801 TATGTATGTGTGTATATAGATATATGTGTGGATGTGAATATATATCTAT- 680849 i i i i v i i iv i iv v - (AT)n#Simple_ 50 TATATATATATATATATATATATATATATATATATATATATATATATATA 99 chrXptel1M 680850 TACAT-TATAT-TATATATCT-TAT-TGTATATGT-TATATAT-TATAT 680892 i - - v - - i i - - (AT)n#Simple_ 100 TATATATATATATATATATATATATATATATATATATATATATATATAT 148 Matrix = Unknown Transitions / transversions = 2.38 (19/8) Gap_init rate = 0.06 (8 / 141), avg. gap size = 1.00 (8 / 8) 24 14.26 3.57 1.75 chrXptel1M 680839 680894 (319106) (TATAT)n#Simple_repeat 1 57 (0) m_b343s252i16 14346 chrXptel1M 680839 TATATATCTATTACATTATATTATA-TATCTTATTGTATATGTTA-TATA 680886 - v i - v vv vv - (TATAT)n#Simp 1 TATAT-TATATTATATTATATTATATTATATTATATTATATTATATTATA 49 chrXptel1M 680887 TTATATTA 680894 (TATAT)n#Simp 50 TTATATTA 57 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.05 (3 / 55), avg. gap size = 1.00 (3 / 3) 18 20.51 1.92 1.92 chrXptel1M 681112 681163 (318837) (TTTTC)n#Simple_repeat 1 52 (0) m_b343s252i17 14347 chrXptel1M 681112 TTTTGTTTTGTTTTCCTTTTC-TGTATTTCTTTTTCTATTTTGTTCTTTT 681160 v v - - v v ii v i v (TTTTC)n#Simp 1 TTTTCTTTTCTTTT-CTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTT 49 chrXptel1M 681161 CTT 681163 (TTTTC)n#Simp 50 CTT 52 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.00 (2 / 2) 19 13.65 3.85 3.85 chrXptel1M 681123 681174 (318826) (TTTCTTA)n#Simple_repeat 1 52 (0) m_b343s252i18 14347 chrXptel1M 681123 TTTCCT-TTTCTGTATTTCTT-TTTCTATTTTGTTCTTTTCTTATTTCAT 681170 i - - - vv v -v v (TTTCTTA)n#Si 1 TTTCTTATTTCT-TATTTCTTATTTCTTATTTCTT-ATTTCTTATTTCTT 48 chrXptel1M 681171 ATTT 681174 (TTTCTTA)n#Si 49 ATTT 52 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.08 (4 / 51), avg. gap size = 1.00 (4 / 4) 214 34.18 1.27 0.00 chrXptel1M 681901 681979 (318021) C MIRb#SINE/MIR (187) 81 2 m_b343s601i5 14348 chrXptel1M 681901 AGTAGTTGAGTAAGAATTCTA-CTTTGGTGTTTCTGACTCTAATCCTAGT 681949 i iv ivi i v - iiv v v i vv iv C MIRb#SINE/MIR 81 AGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGT 32 chrXptel1M 681950 GGTCTTGCCATTGGACCATGTTTTCCATCT 681979 v v i v i i vi v C MIRb#SINE/MIR 31 GCTCTTTCCACTGCACCACGCTGCCCCTCT 2 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.82 CpG sites = 13, Kimura (unadjusted) = 46.23 Transitions / transversions = 0.93 (13/14) Gap_init rate = 0.01 (1 / 78), avg. gap size = 1.00 (1 / 1) 219 32.84 1.49 0.00 chrXptel1M 681901 681967 (318033) C MIRc#SINE/MIR (190) 78 11 m_b343s601i4 14348 chrXptel1M 681901 AGTAGTTGAGTAAGAATTCTA-CTTTGGTGTTTCTGACTCTAATCCTAGT 681949 i iv ivi i i v - iiv v i i vi i C MIRc#SINE/MIR 78 AGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGT 29 chrXptel1M 681950 GGTCTTGCCATTGGACCA 681967 v v i v C MIRc#SINE/MIR 28 GCTCTTTCCACTGCACCA 11 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.03 CpG sites = 13, Kimura (unadjusted) = 44.77 Transitions / transversions = 1.44 (13/9) Gap_init rate = 0.02 (1 / 66), avg. gap size = 1.00 (1 / 1) 25 8.61 3.77 3.77 chrXptel1M 682014 682066 (317934) (TCTCTG)n#Simple_repeat 1 53 (0) m_b343s252i20 14349 chrXptel1M 682014 TCTCTCTGTGTGTCTCTGTTTCTG-C-CTGTCTCTGTCTCTGTCTGTCTG 682061 v v v i - - -- (TCTCTG)n#Sim 1 TCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTC--TCTG 48 chrXptel1M 682062 TCTCT 682066 (TCTCTG)n#Sim 49 TCTCT 53 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.08 (4 / 52), avg. gap size = 1.00 (4 / 4) 24 23.09 0.00 1.61 chrXptel1M 682014 682076 (317924) (TCTG)n#Simple_repeat 1 62 (0) m_b343s252i19 14350 chrXptel1M 682014 TCTCTCTGTGTGTCTCTGTTTCTGCCTGTCTCTGTCTCTGTCTGTCTGTC 682063 v v v v v i v v v (TCTG)n#Simpl 1 TCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTC 50 chrXptel1M 682064 TCTCCTTTCAGTC 682076 v - v v (TCTG)n#Simpl 51 TGT-CTGTCTGTC 62 Matrix = Unknown Transitions / transversions = 0.09 (1/11) Gap_init rate = 0.02 (1 / 62), avg. gap size = 1.00 (1 / 1) 12 21.84 2.70 0.00 chrXptel1M 682935 682971 (317029) (AGATCTG)n#Simple_repeat 1 38 (0) m_b343s252i21 14351 chrXptel1M 682935 AGATATGAGATCTGAGAGC-AAGATTAGAGATTGGAGA 682971 v v -i iv iv (AGATCTG)n#Si 1 AGATCTGAGATCTGAGATCTGAGATCTGAGATCTGAGA 38 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 272 29.20 1.81 3.05 chrXptel1M 683625 683790 (316210) L1ME1_3end#LINE/L1 492 655 (271) m_b343s551i11 14352 chrXptel1M 683625 ATGCCCGTCAACTGGAGAATGGCTGAATAAATTGTGGTATATGATTGTTA 683674 i i ? v v i i vvv iiv L1ME1_3end#LI 492 ATGTCCATCAACNGGTGAATGGATAAACAAATTGTGGTATATCCATACAA 541 chrXptel1M 683675 TGGAATATTACTGTTCTGTAAGAAATGACCAACAGGATGAT-TTCAGAAA 683723 i vvv vi i ivi v -viv -iv iv v L1ME1_3end#LI 542 TGGAATACTACTCAGCAATAAAAAGGAACGAAC-TACTGATACACGCAAC 590 chrXptel1M 683724 GGCCTGGA-GAGACTTACAAGAACTGATGCTGAGTGAAATGAGCAGGAC- 683771 ii v - iv i v ?v i - vi vi - L1ME1_3end#LI 591 AACATGGATGAATCTCAAAANCATT-ATGCTGAGTGAAAGAAGCCAGACA 639 chrXptel1M 683772 CAGGAGATCATTATATACT 683790 ii --- ? i L1ME1_3end#LI 640 CAAAAG---ANTACATACT 655 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.41 CpG sites = 24, Kimura (unadjusted) = 38.44 Transitions / transversions = 1.04 (24/23) Gap_init rate = 0.05 (8 / 165), avg. gap size = 1.00 (8 / 8) 282 19.67 0.00 0.00 chrXptel1M 683625 683685 (316315) L1ME3_3end#LINE/L1 492 552 (357) m_b343s551i10 14352 chrXptel1M 683625 ATGCCCGTCAACTGGAGAATGGCTGAATAAATTGTGGTATATGATTGTTA 683674 i i v ? v i vvv iiv L1ME3_3end#LI 492 ATGTCCATCAACAGNAGAATGGATAAATAAATTGTGGTATATTCATACAA 541 chrXptel1M 683675 TGGAATATTAC 683685 i L1ME3_3end#LI 542 TGGAATACTAC 552 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 23.41 CpG sites = 6, Kimura (unadjusted) = 23.41 Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 13 17.73 5.26 0.00 chrXptel1M 684058 684095 (315905) (TTATAC)n#Simple_repeat 1 40 (0) m_b343s252i22 14353 chrXptel1M 684058 TTATACATATA-TTGTATTTA-ACTTATACTTTAACATAT 684095 v - i i - vv v (TTATAC)n#Sim 1 TTATACTTATACTTATACTTATACTTATACTTATACTTAT 40 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 27 11.21 0.00 0.00 chrXptel1M 684353 684391 (315609) (A)n#Simple_repeat 1 39 (0) m_b343s252i23 14354 chrXptel1M 684353 AAAAAAAAAAAAAAAAAAAGAAAGAAAAAGAAAAACAAA 684391 i i i v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 39 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 43 2.31 0.00 0.00 chrXptel1M 684542 684585 (315415) (AAAC)n#Simple_repeat 1 44 (0) c_b343s251i3 14355 chrXptel1M 684542 AAACAAACAAACAAACAAACAAACAAACAAACAAACAAAAAAAC 684585 v (AAAC)n#Simpl 1 AAACAAACAAACAAACAAACAAACAAACAAACAAACAAACAAAC 44 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 496 20.70 1.63 9.65 chrXptel1M 684588 684710 (315290) MIRc#SINE/MIR 2 115 (153) m_b343s601i6 14356 chrXptel1M 684588 GAGGCAGCTAGGTGATACAGTGTATAGAACACCAGCCCTGAAGTCGGGAG 684637 i--- i i v v i ii v i i i i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chrXptel1M 684638 GACCTGAGTTCAAATCT--GCTCTCAGACACTTACCCTTCCTATCTGTGT 684685 i i i i-- -- v ------ v MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCT--GCCACTTA------CTAGCTGTGT 90 chrXptel1M 684686 GATTCTGGGCAAGTCACTTAACTTC 684710 iii i MIRc#SINE/MIR 91 GACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 23.88 CpG sites = 18, Kimura (unadjusted) = 25.13 Transitions / transversions = 3.60 (18/5) Gap_init rate = 0.10 (12 / 122), avg. gap size = 1.08 (13 / 12) 35 0.00 0.00 0.00 chrXptel1M 684743 684774 (315226) (AAC)n#Simple_repeat 1 32 (0) c_b343s251i4 14357 chrXptel1M 684743 AACAACAACAACAACAACAACAACAACAACAA 684774 (AAC)n#Simple 1 AACAACAACAACAACAACAACAACAACAACAA 32 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 48 0.00 0.00 0.00 chrXptel1M 684835 684875 (315125) (TG)n#Simple_repeat 1 41 (0) c_b343s251i5 14358 chrXptel1M 684835 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 684875 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 41 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 13 4.76 0.00 4.35 chrXptel1M 688820 688843 (311157) (CCCT)n#Simple_repeat 1 23 (0) m_b343s252i24 14359 chrXptel1M 688820 CCCTCCCTCCCTCCACCCCCTCCC 688843 - i (CCCT)n#Simpl 1 CCCTCCCTCCCTCC-CTCCCTCCC 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 17 0.00 0.00 0.00 chrXptel1M 689471 689489 (310511) (A)n#Simple_repeat 1 19 (0) m_b343s252i25 14360 chrXptel1M 689471 AAAAAAAAAAAAAAAAAAA 689489 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAA 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 18 3.57 3.23 3.23 chrXptel1M 690555 690585 (309415) (ATA)n#Simple_repeat 1 31 (0) m_b343s252i26 14361 chrXptel1M 690555 ATAATAATAAT-ATAATAATACATAACAATAA 690585 - - i (ATA)n#Simple 1 ATAATAATAATAATAATAATA-ATAATAATAA 31 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2) 17 15.30 0.00 0.00 chrXptel1M 694464 694492 (305508) (G)n#Simple_repeat 1 29 (0) m_b343s252i27 14362 chrXptel1M 694464 GGTGGGGGGGGAGGTGGGGGGGGGGGAGG 694492 v i v i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG 29 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 332 31.86 5.56 1.18 chrXptel1M 696492 696653 (303347) L2d2_3end#LINE/L2 374 542 (13) m_b343s601i7 14363 chrXptel1M 696492 TGTTGTATAGATCTTGTAT----ATATCGCGTTTGTACAGAATGTATATA 696537 i v i ---- v vi v -i - vi v i v L2d2_3end#LIN 374 TGTTATTTAAATCTTGTATTGTTATTTAACTTTT-CAC-GTGTTTATGTC 421 chrXptel1M 696538 TTGTCTCCTATATTAGAGTATGCACTTCTTGGGAGTAGATGC--TGCCTT 696585 ivv i v i ivi i i i i ivi -- i L2d2_3end#LIN 422 TTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTT 471 chrXptel1M 696586 ATTCTTTTCTGTGTAGACC-CAGAACTTA-C-CAGTGCCTGACCCATTGT 696632 v i i i vvv - vi i - - vi v iv L2d2_3end#LIN 472 ATACTTCTTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAGT 521 chrXptel1M 696633 AGATGATTAATAAATGTCTGT 696653 ii v i i i L2d2_3end#LIN 522 AGGCGCTCAATAAATATTTGT 542 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.67 CpG sites = 30, Kimura (unadjusted) = 42.90 Transitions / transversions = 1.43 (30/21) Gap_init rate = 0.04 (7 / 161), avg. gap size = 1.57 (11 / 7) 18 17.84 5.88 0.00 chrXptel1M 696665 696715 (303285) (TATC)n#Simple_repeat 1 54 (0) m_b343s252i28 14364 chrXptel1M 696665 TATCTATCTATCT-TCTATCTACCTATC-ATGTCCTTATTTGTC-ATCTC 696711 - i - v vii i i - v (TATC)n#Simpl 1 TATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTA 50 chrXptel1M 696712 TCTA 696715 (TATC)n#Simpl 51 TCTA 54 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.06 (3 / 50), avg. gap size = 1.00 (3 / 3) 343 33.82 4.48 0.72 chrXptel1M 697006 697139 (302861) L2a_3end#LINE/L2 373 511 (6) m_b343s601i8 14365 chrXptel1M 697006 TTTAATGT--GTCTTTTGCCATGAAAATGGCAGTTCCATTAGAAAGAGTC 697053 v -- iiiv iv i vv i v iivii vv L2a_3end#LINE 373 TTTATTGTCTGTCTCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGA 422 chrXptel1M 697054 CCTTTCTTTCTACTTGT--ATTG--ATATTCCCAATGATTAGCACGGTGC 697099 i v i v -i -- i --i i ii vi v i L2a_3end#LINE 423 CTTTTGTCTGT-TTTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGC 471 chrXptel1M 697100 CTGAAACATAGAAAGTGCTTACCAAATGCTTGTTAAGTGA 697139 iv v i i i vi ii i i L2a_3end#LINE 472 CTGGCACATAGTAGGCGCTCAATAAATATTTGTTGAATGA 511 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 44.56 CpG sites = 29, Kimura (unadjusted) = 47.52 Transitions / transversions = 1.81 (29/16) Gap_init rate = 0.03 (4 / 133), avg. gap size = 1.75 (7 / 4) 184 30.58 0.00 2.78 chrXptel1M 697286 697359 (302641) L2c_3end#LINE/L2 2 73 (405) m_b343s601i9 14366 chrXptel1M 697286 TTCATAACCTGGTTCCCCACCTACCTTTCTAGCATTCACATCTTCTCATC 697335 ? ii i i- ii i i -i iv i ivv L2c_3end#LINE 2 TNCACGATCTGGC-CCCTGCCTACCTCTCCAGC-CTCATCTCCTCCACTC 49 chrXptel1M 697336 TCCTCCAAGGACACTGTGGTCCAG 697359 i vv vv i v L2c_3end#LINE 50 CCCTCCTCGCCCACTATGCTCCAG 73 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 38.97 CpG sites = 14, Kimura (unadjusted) = 41.75 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.03 (2 / 73), avg. gap size = 1.00 (2 / 2) 257 34.08 0.00 2.20 chrXptel1M 697924 698016 (301984) L2c_3end#LINE/L2 383 473 (5) m_b343s601i10 14366 chrXptel1M 697924 GTTCCTTTTGTGGCAGGAGCTATAAAACTTTTGTCCTTGTCTCTCCAGCC 697973 i vv - ii ii ivvviv ii i v i v L2c_3end#LINE 383 GCTCCTTGAG-GGCAGGGACCGTGTCTTATTCATCTTTGTATCCCCAGCG 431 chrXptel1M 697974 CTTAGCACATTGTAGGTGCTGGAAAAAATGCTCATTAAACAAA 698016 i i v i -v v i ii i ii L2c_3end#LINE 432 CCTGGCACATAGTAGGCGCT-CAATAAATGTTTGTTGAATGAA 473 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.48 CpG sites = 20, Kimura (unadjusted) = 48.02 Transitions / transversions = 1.82 (20/11) Gap_init rate = 0.02 (2 / 92), avg. gap size = 1.00 (2 / 2) 16 13.24 0.00 0.00 chrXptel1M 698636 698660 (301340) (A)n#Simple_repeat 1 25 (0) m_b343s252i29 14367 chrXptel1M 698636 AAAATAGAAAAAAAAAAGAAAAAAA 698660 v i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAA 25 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 15 19.67 2.00 4.08 chrXptel1M 699085 699134 (300866) (AAATA)n#Simple_repeat 1 49 (0) m_b343s252i30 14368 chrXptel1M 699085 AAATAAACTCAAGT-CAATAATAGAAAATGAAATACAATTTAAAATAAAA 699133 v v i -v v v i - -v (AAATA)n#Simp 1 AAATAAAATAAAATAAAATAAAATAAAATAAAATA-AA-ATAAAATAAAA 48 chrXptel1M 699134 T 699134 (AAATA)n#Simp 49 T 49 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.06 (3 / 49), avg. gap size = 1.00 (3 / 3) 14 21.19 0.00 6.52 chrXptel1M 699490 699538 (300462) (AACA)n#Simple_repeat 1 46 (0) m_b343s252i31 14369 chrXptel1M 699490 AAAAAATAAACAGATCAAACAGACCAAACAAGGGAAAATAACAAACAAA 699538 v i - v - v -iv vv (AACA)n#Simpl 1 AACAAACAAACA-AACAAACA-AACAAACAA-ACAAACAAACAAACAAA 46 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.06 (3 / 48), avg. gap size = 1.00 (3 / 3) 19 4.50 0.00 0.00 chrXptel1M 699597 699619 (300381) (A)n#Simple_repeat 1 23 (0) m_b343s252i32 14370 chrXptel1M 699597 AAAAAAAACAAAAAAAAAAAAAA 699619 v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAA 23 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 447 31.65 7.48 3.74 chrXptel1M 700193 700553 (299447) L1ME5_3end#LINE/L1 277 650 (291) m_b343s551i12 14371 chrXptel1M 700193 ATGCATTGTTGGTGGAGTCATGAATGGATCCAACCATTCTGGAGATCCAT 700242 i i iivii ii iv i v i v v L1ME5_3end#LI 277 ATGCACTGCTGGTGGGAGTGTAGACTGGTGCAGCCATTCTGGAGAGCAAT 326 chrXptel1M 700243 TTGGAACTA--TGCTCAAAGTTATCAAACCGTGCATACCCTTTGACCCAG 700290 i v v -- iv v v vi v --- v L1ME5_3end#LI 327 CTGGCAGTACTTAGTCAAATTAAGTATAC---GCATACCCTATGACCCAG 373 chrXptel1M 700291 CAGTGCTACTACTGGGCTTATACCCCAAGGAGGTACTAAAGAAGG----- 700335 i v ii v iv i i ii v v viv ----- L1ME5_3end#LI 374 CAATTCCGCTCCTGGGTATATATCCCAAAGAAATTCTCACACAGGTCCAT 423 chrXptel1M 700336 AAAAGGACCTGTATGTCAAAAGAATG--GATTGGGCAGCCCT-TTTATAA 700382 ii v i ----- i --v -- vi - i ii L1ME5_3end#LI 424 AAGGGGACATGTACG-----AGGATGTTCATT--GCAGCGTTGTTTGTGG 466 chrXptel1M 700383 -GGC-CAAAACTGGAAACTGAGTGGATGCCCATCAATTGGAGAATGGCTG 700430 - -vii ii ii vivv i i v v i v i L1ME5_3end#LI 467 TGGCGGGGAGTTGGAGGCAACCTGGGTGTCCATCACTGGGAGAGTGGATA 516 chrXptel1M 700431 AATAAATTGGTATTAGAT-----TTATGGAATATTTTGT----TCTTGAA 700471 ii v - iv i -----ii i i v i----vi v L1ME5_3end#LI 517 GGTAAAAT-GTGGTGGATGCACACCATGGAGTACTATGCAGCAGTTAGAA 565 chrXptel1M 700472 ATGACCAACAGGATGAATACAGAGAGGCCCTGGAGAGA-CTTACATGAAC 700520 iii vi vi v i v vii- v vi - v -- L1ME5_3end#LI 566 GCAACGGACTAGATGTACACATAGCAA-CATGGATGGATCTTAAA--AAC 612 chrXptel1M 700521 -TGATGCTGAGTGAAATGAGC-AGAACCAG---GAGAT 700553 - ii vi i- v --- L1ME5_3end#LI 613 ATAGTGCTGAGTGAAAAAAGTAAGAAACAGAATGAGAT 650 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.51 CpG sites = 65, Kimura (unadjusted) = 42.60 Transitions / transversions = 1.44 (65/45) Gap_init rate = 0.07 (26 / 360), avg. gap size = 1.58 (41 / 26) 651 25.55 5.17 1.79 chrXptel1M 700193 700463 (299537) L1ME4c_3end#LINE/L1 277 556 (274) m_b343s551i13 14371 chrXptel1M 700193 ATGCATTGTTGGTGGAGTCATGAATGGATCCAACCATTCTGGAGATCCAT 700242 i i vi?ii i v i v v i i v v L1ME4c_3end#L 277 ATACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGCAAT 326 chrXptel1M 700243 TTGGAACTATGC-TCAA-AGTTATCAAACCGTGCATACCCTTTGACCCAG 700290 v v i i- - ii v vi v L1ME4c_3end#L 327 TTGGCAATACGTATCAAGAGCCATAAAAATGTTCATACCCTTTGACCCAG 376 chrXptel1M 700291 CAGTGCTACTACTGGGCTTATACCCCAAGGAGGTA---CTAAAGAAGGAA 700337 i i v i v vv v i i ii --- v L1ME4c_3end#L 377 TAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAAGAAGGAA 426 chrXptel1M 700338 AAGGACCTGTATGTCAAAAGAATG--GATTGGGCAGCCCT-TTTATAA-G 700383 i -- i - vi ii --v -- vi - -i L1ME4c_3end#L 427 AAAG--CTATATG-CACGAAGATGTTCATT--GCAGCGTTATTTATAATA 471 chrXptel1M 700384 GCC-AAAACTGGAAACTGAGTGGATGCCCATCAATTGGAGAATGGCTGAA 700432 v- i vivv ii i v v i i i i L1ME4c_3end#L 472 GCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAATGGTTAAG 521 chrXptel1M 700433 TAAAT--TGGTAT-TAGATTT-ATGGAATATTTTG 700463 -- i- v? i i- v L1ME4c_3end#L 522 TAAATTATGGTACATCNACTCGATGGAATATTATG 556 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 30.56 CpG sites = 40, Kimura (unadjusted) = 32.26 Transitions / transversions = 1.43 (40/28) Gap_init rate = 0.06 (15 / 270), avg. gap size = 1.27 (19 / 15) 201 29.37 10.26 6.17 chrXptel1M 702759 702914 (297086) C L2a_3end#LINE/L2 (12) 505 344 m_b343s601i11 14372 chrXptel1M 702759 AAAAAAAATTTATTAACAGCCTATT-----CCTGATACTGAGCTAAGTG- 702802 v v i vv i ----- v ii vv i i - C L2a_3end#LINE 505 AACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGCGC 456 chrXptel1M 702803 -GGGGTTTACAA-ATTAAGGAAAAGTGGGTGTGGGGGAAGGAATCGCTGT 702850 - v - i- v i iv -------ii ivi -- i v i C L2a_3end#LINE 455 TGGGGAT-ACAGCAGTGAACAAAA-------CAGACAAA--AGTCCCTGC 416 chrXptel1M 702851 TCTCAAAGAGCTCATATTCTA--AAGGGAA---AGATAACAGGCAAATAA 702895 i vi i i --ii i --- i i ii C L2a_3end#LINE 415 CCTCATGGAGCTTACATTCTAGTGGGGGGAGACAGACAATAAACAAATAA 366 chrXptel1M 702896 CTATGTAAAA---ATAAGATGT 702914 v v --- iv C L2a_3end#LINE 365 ATAAGTAAAATATATAGTATGT 344 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.66 CpG sites = 27, Kimura (unadjusted) = 38.83 Transitions / transversions = 1.69 (27/16) Gap_init rate = 0.11 (17 / 155), avg. gap size = 1.53 (26 / 17) 651 35.87 5.05 3.37 chrXptel1M 703109 703662 (296338) C L2#LINE/L2 (86) 2996 2434 m_b344s601i2 14372 chrXptel1M 703109 GAAGTCAGTGTCATTGAATCATAAAGTAC-ATGGAGTGTATGATATAAAA 703157 i i vii i v iv iv vi - v i v vi i vi i C L2#LINE/L2 2996 GAGGCCAGTGTGGCTGGAGCGGAGTGAGCGAGGGGGAGAGTGGTAGGAGA 2947 chrXptel1M 703158 --AGACTGGAAAGGTAA-GAAGGAACA-ATTGTGAAGGACA--------- 703194 -- iiii i - ii v - ii v i v--------- C L2#LINE/L2 2946 TGAGGTCAGAGAGGTAACGGGGGACCAGATCATGTAGGGCCTTGTAGGCC 2897 chrXptel1M 703195 -----AAAAAATTTATATTTGACCCTGGAAGTGTTAGGTAG--AGCCACG 703237 ----- ii v ivv v i -- -- i i -- iv C L2#LINE/L2 2896 ATTGTAAGGACTTTGGCTTTTACTCTG--AGTG--AGATGGGAAGCCATT 2851 chrXptel1M 703238 GCAATTTATTGAGGAGACAAGCTGATGTGGTCAGACCTGTACTTTGGGGA 703287 v ivv v v vi - ii i v i iiii iii- C L2#LINE/L2 2850 GGAGGGTTTTGAGCAGAGGAG-TGACATGATCTGACTTACGTTTTAAA-A 2803 chrXptel1M 703288 AAATCCATTGGACAGCTAAGTGAAGGATGGACTGGAGTGAAAATAAATAA 703337 ii vv iv i v iv vi i i ? - iiiii iviv C L2#LINE/L2 2802 GGATCACTCTGGCTGCTGTGTTGAGAATAGACTGNAG-GGGGGCAAGGGT 2754 chrXptel1M 703338 AGAGGGCAGAAAGATCAACCAGAAGATTAATGTAACCATCCAGGTGTGAG 703387 i i - ii i iii i ii v i iiv i v C L2#LINE/L2 2753 GGAAG-CAGGGAGACCAGTTAGGAGGCTATTGCAGTAATCCAGGCGAGAG 2705 chrXptel1M 703388 GTAATGAAGGTCTCC-CTAGGATGGTGGCAAGGTCAGAGGAGAGAAGGGG 703436 i i iv ii vv- i i iv vvi v v v C L2#LINE/L2 2704 ATGATGGTGGCTTGGACCAGGGTGGTGGCAGTGGAGGTGGTGAGAAGTGG 2655 chrXptel1M 703437 TCTG--CCAAGAGATTCTGTGAAGTTAGAAACAACAGGACCTGGTGACAG 703484 v --i vi v vi v v iv i ii v ii C L2#LINE/L2 2654 TCGGATTCTGGATATATTTTGAAGGTAGAGCCGACAGGATTTGCTGATGG 2605 chrXptel1M 703485 TCCTGGTTATGATGGGAGGACAGTGGGAAGTGAGGAGTCAATGCTTTCTC 703534 -vi -- - iv vv -i i v v v vv C L2#LINE/L2 2604 -ATTGG--ATG-TGGGGTGTGAG-AGAAAGAGAGGAGTCAAGGATGACTC 2560 chrXptel1M 703535 CTAGGTTTGTAAGTCTGGGCGACTGGGAGGACGATGGTCCTCTTGACAGG 703584 v v i- i i i i i iv v v iv ? v i C L2#LINE/L2 2559 CAAGGTTTTTG-GCCTGAGCAACTGGAAGGATGGAGTTGCCATTNACTGA 2511 chrXptel1M 703585 AACAAGGA----TGTTAGGACAAGGAGGTATTTGGGTGAGGGGAAATAAT 703630 i iii ---- i-i vi v -- i --i i i v v C L2#LINE/L2 2510 GATGGGGAAGACTGC-GGGAGGAGCAGGT--TTGAG--GGGGAAGATCAG 2466 chrXptel1M 703631 GAGTTCAGTGCTGGACTTGTTGAGTTTAAGAT 703662 vi v i i C L2#LINE/L2 2465 GAGTTCAGTTTTGGACATGTTAAGTTTGAGAT 2434 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 49.64 CpG sites = 118, Kimura (unadjusted) = 51.70 Transitions / transversions = 1.59 (118/74) Gap_init rate = 0.05 (28 / 553), avg. gap size = 1.68 (47 / 28) 226 36.85 4.97 1.06 chrXptel1M 703728 703908 (296092) C L2#LINE/L2 (937) 2145 1958 m_b344s601i3 14372 chrXptel1M 703728 AGGAGAAAGTAGAATCTGAAAAACCTAGAGAGAAGAGAAAATCA--AAGG 703775 iv i vi ivii i v v ii i vivv -- C L2#LINE/L2 2145 AGGAGAGTGTGGTGTCCTGGAAGCCAAGTGAAGAAAGTGTTTCAAGAAGG 2096 chrXptel1M 703776 TAAGAGTCTGATTGACTATGGCAAAAGCTACAGAGAAGTCGAG------A 703819 vii -- ii i v v i v ? i i ------i C L2#LINE/L2 2095 AGGGAG--TGATCAACTGTGTCAAATGCTGCTGANAGGTCAAGTAAGATG 2048 chrXptel1M 703820 AGGATTGAGAAGACACTAATAGAGTTGTCAATGAAGATGTCGTTGCTAAG 703869 i vvv i v i v iv i vi v i v i v C L2#LINE/L2 2047 AGGACTGAGAATTGACCATTGGATTTAGCAACGTGGAGGTCATTGGTGAC 1998 chrXptel1M 703870 TTTGGAGAGAGC-TTTTCAATGGTGGGATCAGAATAAAGG 703908 i ivi -v ii v v i vi i ii i C L2#LINE/L2 1997 CTTGACAAGAGCAGTTTCGGTGGAGTGGTGGGGACGAAAG 1958 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 49.91 CpG sites = 39, Kimura (unadjusted) = 53.60 Transitions / transversions = 1.44 (39/27) Gap_init rate = 0.03 (5 / 180), avg. gap size = 2.20 (11 / 5) 305 36.55 3.76 3.76 chrXptel1M 704555 705006 (294994) C L2#LINE/L2 (1395) 1687 1236 m_b344s601i4 14372 chrXptel1M 704555 AGATGGGATGGAACGGGACCCCTTGTGCATGGAGAGGGATTTCCCTTGCC 704604 ii i v i i i ivv ii v vi i vv ivv C L2#LINE/L2 1687 AGGCGAGAGGGGATGGGATCTAGTGCACAAGTGGAGGGGTTGGCCTTAGA 1638 chrXptel1M 704605 GAGGAGAAGGGCCGACTCTTCATGT-GAGATAGGAATGAAGGAGGAAATA 704653 v v v v iii v -i - vi i iv vi i- C L2#LINE/L2 1637 TAGGAGCACGGACAGTTCATC-CGTAGTAACAGGAGGGAAGGCAGAG-TA 1590 chrXptel1M 704654 GTGGAGGCAGAGTTTTCATTAATGTG---AGATAAGGATGACGGGCAAAA 704700 - vi v v viviv i- --- iv - ii - i?? C L2#LINE/L2 1589 -TGTGGGCACAGATGCAGGTAG-GTGGGTAGATGTGG-TGGTGGG-AGNN 1544 chrXptel1M 704701 AGGGGAATGGTTGATTGGTTAATGGTCTCAACTGTTTTTCAGTAAAACAT 704750 v v -- v- ivvi i v ii v i -- i i i v C L2#LINE/L2 1543 TGTGGAA--GTTC-TCTTCTGATTGCTTCTATT--TTCTCAGTGAAATAG 1499 chrXptel1M 704751 GAGGCAAGATTCTTTGTTGAAAG----GCCATGA-AGGCCATG--GGAGT 704793 i i iv iv i i ---- vi v i- vvi -- v C L2#LINE/L2 1498 GAAGCAAGGTCATCAGCTGAGAGTGAGGATAGGGGAGGAGGTGTTGGAGG 1449 chrXptel1M 704794 TTGGAGAAGGCACAGAAAGGTTTGGAAATGGT-GTTGTGGTGAGTAGACA 704842 v i iv viii v - i - ivv v i ivi C L2#LINE/L2 1448 TTTGAGGAGAGAGGAGAAGGTGTG-AAATAGTCGTCTAGGAGAGTGGGAG 1400 chrXptel1M 704843 CATGAACCAGTCAGGGAGAGGTAAAAGGGATTGACTTCTTAG-ACTGAGG 704891 vi iviiii i v iv ? - - ivvvi - i i C L2#LINE/L2 1399 AGTGAATGGACTAGGGAAATGTAGTANG-ATTG-CCGGGCAGCATTAAGG 1352 chrXptel1M 704892 GTCTAGTTGAGATTGTGTAA-CATAGACGCATAGTGGACCCAGTCAGCAC 704940 i i v i ?- ii- ii ivi v iiv i C L2#LINE/L2 1351 GCCCACTTGAGGTTN-GTGGTCATGAATTTAAAGTGAGACCAGTCAGCAT 1303 chrXptel1M 704941 GGTTTGGTGGCTTCTGACAGCCTCGTTCATCTAGGTGAATG-AAGT-CGG 704988 vv vi iivv v v iv?i ii - i i- C L2#LINE/L2 1302 GGTTGTGTGTTTTTCTCCAGCCACGTTCAGCTGCNCGGGTGCAGGCGCGG 1253 chrXptel1M 704989 AGCCAAGGCAGA-AGATGG 705006 i-- i - v C L2#LINE/L2 1252 AGT--AGGCGGAGAGTTGG 1236 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 50.23 CpG sites = 92, Kimura (unadjusted) = 53.16 Transitions / transversions = 1.37 (92/67) Gap_init rate = 0.06 (28 / 451), avg. gap size = 1.21 (34 / 28) 190 35.17 5.50 0.88 chrXptel1M 705309 705417 (294583) C L2#LINE/L2 (2158) 924 811 m_b344s601i5 14372 chrXptel1M 705309 TAATGGCAAGGTCCCGGATGAAGCTACCTCTGTGTGTAGCTGAAATTAGG 705358 i iv i ivii i ivvvv v i ii vi C L2#LINE/L2 924 TAATGACAAGGTCTAGGGTATGACCATGGGAGTGAGTGGCTGAGGTAGGG 875 chrXptel1M 705359 TGGAGGAGTAGGTCCTCAGA----AAGCAGCTGAAAAATTGAGAGG-TAG 705403 vv i v ii ---- i vi iii ii i -i C L2#LINE/L2 874 TGGAGGACAAGATCATTGGAGGAGAGGAGGTCAAGGAACTGAGAGGCCAG 825 chrXptel1M 705404 AG-GTTGTGAAGGAT 705417 i -i - C L2#LINE/L2 824 GGTATTG-GAAGGAT 811 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 51.18 CpG sites = 26, Kimura (unadjusted) = 51.18 Transitions / transversions = 2.17 (26/12) Gap_init rate = 0.04 (4 / 108), avg. gap size = 1.75 (7 / 4) 429 35.20 5.15 6.63 chrXptel1M 705563 706067 (293933) C L2#LINE/L2 (1) 3081 2584 m_b344s601i6 14373 chrXptel1M 705563 GGGGGAGAGCAGTCCAAGTATGTGAGAGAGCCAAAGAAAATGCAAACAGA 705612 i iv i i --- i i --- v i -i v C L2#LINE/L2 3081 GGGGAAGAGCGTTCCAGGCA---GAGGGAAC---AGCAAGTGCAAA-GGC 3039 chrXptel1M 705613 CAAGTGACGGAA---TGTCT--TATGCTTGA--AACAGTGACGGGATCGG 705655 vv v i i --- i --ii i i -- ii v i ii i C L2#LINE/L2 3038 CCTGAGGCGGGAGCGTGCCTGGCGTGTTCGAGGAACAGCAAGGAGGCCAG 2989 chrXptel1M 705656 TGTCAGTGGATTAAAGAGGGTATGTCAGAGAA--GTATGAGA--AGACCG 705701 viv viii v i iiv vvi i-- v -- ii i C L2#LINE/L2 2988 TGTGGCTGGAGCGGAGTGAGCGAGGGGGAGAGTGGTAGGAGATGAGGTCA 2939 chrXptel1M 705702 GAAAGGCAGGAGGGGACTAGTTTGTG-AGACCCTTCCAATGCCAG-ACAG 705749 i i ivi i v ii - iv vi i- v-ii i C L2#LINE/L2 2938 GAGAGGTAACGGGGGACCAGATCATGTAGGGCCTTGTAG-GCCATTGTAA 2890 chrXptel1M 705750 AGGGTTTAGTATTTGATCACTGAG-GCAATGAGGGGCAACTGGAGTTTAC 705798 i iv i iv iv -- - vi i ii v i vv vi C L2#LINE/L2 2889 GGACTTTGGCTTTTACTC--TGAGTGAGATGGGAAGCCATTGGAGGGTTT 2842 chrXptel1M 705799 TGAGTAGGGGAGTGACATCACTGGGCCTGTGCTTCAGTAAACTCATGTTG 705848 i i v iiv i i ii i i iv iiv --i v C L2#LINE/L2 2841 TGAGCAGAGGAGTGACATGATCTGACTTACGTTTTAAAAGGATCA--CTC 2794 chrXptel1M 705849 TGGCTGAAATGAAATGAAATGAAATATGGAATGGAGCGGGGAGAGACTTG 705898 vvi --- ---- i - i v ? v vi iv v C L2#LINE/L2 2793 TGGCTGCTGTG---T----TGAGA-ATAGACTGNAGGGGGGCAAGGGTGG 2752 chrXptel1M 705899 AGGCAGGGAGAGCCCA--CAGTAGGCTCTTGTAATAGTCTAAGTGTGAGG 705946 i -- --i v v i i i i i i v i C L2#LINE/L2 2751 AAGCAGGGAGA--CCAGTTAGGAGGCTATTGCAGTAATCCAGGCGAGAGA 2704 chrXptel1M 705947 GGATGAGCCCCTAGACTAGAGTGCTTGGCGGTGTCACAGGAGAGAAAATA 705996 v ivvv i i i i -v i vvivv v i--- C L2#LINE/L2 2703 TGATGGTGGCTTGGACCAGGGTG-GTGGCAGTGGAGGTGGTGAGAAG--- 2658 chrXptel1M 705997 CCTAGTC--ATTCAATGG--------TGAAATGGTGAAACTGGCAACCTT 706036 -- i -- -- -------- -- ii i i i ivv C L2#LINE/L2 2657 --TGGTCGGATTC--TGGATATATTTTGAA--GGTAGAGCCGACAGGATT 2614 chrXptel1M 706037 TGGCAATGGATGAGTTATGAGTGTTTGGGGG 706067 vii vi v i i - v i i C L2#LINE/L2 2613 TGCTGATGGATTGGATGTGGG-GTGTGAGAG 2584 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 46.47 CpG sites = 107, Kimura (unadjusted) = 50.54 Transitions / transversions = 1.81 (107/59) Gap_init rate = 0.09 (44 / 504), avg. gap size = 1.34 (59 / 44) 250 29.40 9.29 8.51 chrXptel1M 706072 706491 (293509) C L2-1_AMi#LINE/L2 (615) 620 198 m_b344s551i0 14374 chrXptel1M 706072 GAGGATGACACTT-GGTAGCCAGCCTGAAGGACTGGCAGGAGGGTGTTGC 706120 i i ii- vi vi iv v v v i C L2-1_AMi#LINE 620 GAAGATGACGCCCAGGTTACGGGCCTGAGTGACAGGCAGGATGGTGGTGT 571 chrXptel1M 706121 CTCCCACAGTAAT------AAGGAAA--GGGAGAAGCTTTCAAGGGGAAA 706162 ivi i ------ i -- ? vi -ii i C L2-1_AMi#LINE 570 TGTCCACAGTGATCGAGAAAAGGGAATGGGGAGNAGGCTT-GGGGGGAAG 522 chrXptel1M 706163 ATCACAGAGTTTGATTTGTTTTAGT-----TTGACTTTTAGCTACCTACT 706207 i - i i---- v----- vi v iv vi C L2-1_AMi#LINE 521 ATTA-AGAGCTC----TGTTTTAGGCCATGTTGAGCTTGAGCTGACGGCT 477 chrXptel1M 706208 GTACACCCAGTTTGAGGTATCTGAAAGGTAGTTAAAAGGGTGAGTTTGGG 706257 iv i vvvv i i v i ii vivi iivv v i C L2-1_AMi#LINE 476 AGACATCCACGAGGAGATGTCAGAGAGACAGGCCGAGATTTTAGTTTGGA 427 chrXptel1M 706258 GTTCAGC-GCAG---GGTTTAGGG---AAAAATAGATTTGAAAACTATTA 706300 --- v- v --- i i i --- i ii i vi i--- i C L2-1_AMi#LINE 426 ---CAGAAGGAGACAGGTCTGGAGTAGAGAGGTAGATCTGTGAG---TCA 383 chrXptel1M 706301 GCATTGAGATCATAATTAAAGTCGCGGGAGCTGATGAGATCACCAAGTGA 706350 i ---- vi i i v i i vvv v i v -- C L2-1_AMi#LINE 382 ACA----GATGGTAGTTGAATTTGTGTTTGCGGATGAGATTACCCA--GA 339 chrXptel1M 706351 AATAATACTTAGTG-AAAGAGAAGAGAAAG----CAAGG-CAGAATTATG 706394 i -----i - i i ---- - iiiv C L2-1_AMi#LINE 338 GATAA-----GGTGTAGAGAGAAGAGAAGGGGACCAAGGACAGAGCCCTG 294 chrXptel1M 706395 TGAGGCAGCTATGGTAAGACAGT-GGAGTCTGGAGAAAGAA---CCAGTG 706440 iii vv i i---- v - --- i i --- i- C L2-1_AMi#LINE 293 TGGAACCCCCAC----AGAAAGTGGGAG---GAAGGAAGAATTGCCAA-G 252 chrXptel1M 706441 GA--------AGAGGCTGAGAGGAAGCAGAGAGATAGGTAGCCGTGGAAG 706482 -------- - ii ii i - i -- i ii C L2-1_AMi#LINE 251 GAGCGATTAGAGAGG-TAGGAGGAGACGGAG-GACAG--AGTCACGGAAG 206 chrXptel1M 706483 CCAGAGGGA 706491 - C L2-1_AMi#LINE 205 CCA-AGGGA 198 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.47 CpG sites = 75, Kimura (unadjusted) = 39.28 Transitions / transversions = 1.97 (75/38) Gap_init rate = 0.12 (49 / 419), avg. gap size = 1.53 (75 / 49) 379 34.80 4.95 4.46 chrXptel1M 706493 706916 (293084) C L2#LINE/L2 (946) 2136 1711 m_b344s601i7 14373 chrXptel1M 706493 TGGTGCGCCGACAACCTAGAGA-GAAGGTAT--CAGGGAGGGGAGGCTGA 706539 iv i iv i v v - i i -- i i i i iv C L2#LINE/L2 2136 TGGTGTCCTGGAAGCCAAGTGAAGAAAGTGTTTCAAGAAGGAGGGAGTGA 2087 chrXptel1M 706540 TTTACAACCCTGAGGTACATA-TACAGTGAGGCCA-GTGAGAGTGAGGAT 706587 --- -- v vi v i- i v v? i - i - i C L2#LINE/L2 2086 T---CAAC--TGTGTCAAATGCTGCTGANAGGTCAAGTAAGA-TGAGGAC 2043 chrXptel1M 706588 TGAGACCAGACAATTCAGTTCATCAACTGAGAGATCACTGGCAACCTTAG 706637 viv v vii i v vvi i i ii ii C L2#LINE/L2 2042 TGAGAATTGACCATTGGATTTAGCAACGTGGAGGTCATTGGTGACCTTGA 1993 chrXptel1M 706638 AGAGAGCCCTTGGGATGAAAAGGTGAGATTG-GAGCCAGCTTGGGAGGAG 706686 vi vv vv i i iv i ivi -i v v iiv i C L2#LINE/L2 1992 CAAGAGCAGTTTCGGTGGAGTGGTGGGGACGAAAGCCTGATTGGAGTGGG 1943 chrXptel1M 706687 TTAAGGAAAGAATGATGGAAGAGAATGTGGAGGATGC-AGGATAGATTAC 706735 v i i ivi i i vv ivv - v iv C L2#LINE/L2 1942 TTCAAGAGAGAATGGGAGGAGAGGAATTGGAGACAGCGAGTATAGACAAC 1893 chrXptel1M 706736 GTTTCCAAGG-GTTTGGGTACAACGGCA---AAAGAGATGTGGCATTAGA 706781 vi i i - v v ii v vi--- i i v iv - C L2#LINE/L2 1892 TCTTTCGAGGAGTTTTGCTGTAAAGGGGAGCAGAGAAATGGGGCGGTAG- 1844 chrXptel1M 706782 ATTATCGACAGGAAACTGAGA--AAGCAAGGACTTTTG------AGCGTG 706823 -i i-- vi i ?v i i-- vi i i ------ iv vv C L2#LINE/L2 1843 -CTG--GAGGGGGANGTGGGGTCAAGGGAGAATTTTTGTTTTTTAAAGAT 1797 chrXptel1M 706824 AGGAGACATAAAAAC--TTTTGTTTGTTGACAGGAGAGAAAATGTCAACA 706871 i v ? v i --v v i ii --- vi -i ii C L2#LINE/L2 1796 GGGAGAAATNACAGCATGTTTGTATGCTGATGGGA---ATGAT-CCAGTA 1751 chrXptel1M 706872 GACAGACATTGAAAATAAATAATAAATAGGAGGAAAGGGGGATAA 706916 v iv --- vi i --ii ii ii v C L2#LINE/L2 1750 GAGAGGGA---AAAATTGATGAT--GCAGGAGAGAGAGGGGAGAA 1711 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 47.85 CpG sites = 84, Kimura (unadjusted) = 49.35 Transitions / transversions = 1.47 (84/57) Gap_init rate = 0.07 (30 / 423), avg. gap size = 1.33 (40 / 30) 233 23.66 9.76 4.65 chrXptel1M 707021 707184 (292816) L1MEh_5end#LINE/L1 2036 2207 (28) m_b344s551i1 14375 chrXptel1M 707021 GAAGGAACAGGATAAAAAA--GATGAGA-----AGAGAAACAATAAAACA 707063 ii ? i vi -- i ----- - - v i L1MEh_5end#LI 2036 GAAAAAANAGAAAGAAAAACAGATGGGACAAATAGA-AAACAA-ATAATA 2083 chrXptel1M 707064 GGGTGGCAGGAA---GCGCACAC---TTAGTCATTATAACTGTGAATGTG 707107 i i i --- iv ?v i---?i v i --- i i L1MEh_5end#LI 2084 AGATGGCAGAAATAAGTCCNAATATANCAGTAATTACAA---TAAATGTA 2130 chrXptel1M 707108 AAGAGGATAAATTCACCCTTAATACAGAAGCAGACAG---CAGAATGGAT 707154 vi v i --- vv i ii v v--- v L1MEh_5end#LI 2131 AATGGGTTAAACTCACC---AATTAAAAGACAGAGATTNTCAGATTGGAT 2177 chrXptel1M 707155 TAAAAATCAGAATCTCACAATATGCTGTTT 707184 ? v i iv i L1MEh_5end#LI 2178 TNAAAAACAAAATCCAACAATATGCTGTCT 2207 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 30.19 CpG sites = 23, Kimura (unadjusted) = 30.19 Transitions / transversions = 1.64 (23/14) Gap_init rate = 0.08 (13 / 163), avg. gap size = 1.85 (24 / 13) 16 11.66 5.13 2.50 chrXptel1M 711971 712009 (287991) (TTA)n#Simple_repeat 1 40 (0) m_b344s252i0 14376 chrXptel1M 711971 TTATGATT-TCATAATTATTATTA-TGTTATCTATTATTAT 712009 v - i v - i - (TTA)n#Simple 1 TTATTATTATTATTATTATTATTATTATTAT-TATTATTAT 40 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.08 (3 / 38), avg. gap size = 1.00 (3 / 3) 770 33.20 9.91 2.00 chrXptel1M 716069 716532 (283468) C HERVP71A#LTR/ERV1 (2365) 5225 4726 m_b344s701i0 14377 chrXptel1M 716069 AGGACACCGCCAGTATATAATT-CTTAAAACTTTATTCTTTGTTTCAA-- 716115 i iv - i v vi i v v -- C HERVP71A#LTR/ 5225 AGGATATGGCCAGTATATAATTTCTTAAGAATTGGTCCTTGGTTTCCATA 5176 chrXptel1M 716116 --AGGAGGTATTATTTCTCTTTTC-----------CCTCTAT-----CTC 716147 -- i vvi i vv i vii ----------- iv ----- C HERVP71A#LTR/ 5175 GTAGGAAGATCTGTAGCCCTGCCCAAATATGGGAGCCCATATAATAACTC 5126 chrXptel1M 716148 ATATGGGGAAAGCTCCCGATCTCTTGTGGGAACAGTTCTAATTCATTAAC 716197 i v v iii vii i v v ii v i i -- v C HERVP71A#LTR/ 5125 GTAGGGGGACAATCCCAAGTCTTTTCTTGGGGCTGTCCTAATCC--TAAG 5078 chrXptel1M 716198 AAA-GCAACAGGCAAACATTTGGTCCAAAATAATTTAGTATCTGACATCA 716246 i i- v iv v i iii v v i v i C HERVP71A#LTR/ 5077 GAGTGCTATTGGGAGACATTTGGTCCAAGGCATTTTAGTTTCTAAGATTA 5028 chrXptel1M 716247 ATTCAGTAATCTGTTTTTTAAAAACCTGACTTATTCTTTTCATTTTCCCT 716296 i ii i v i i i iii i i ii ii i v C HERVP71A#LTR/ 5027 GTTTGGTGATATGCTTTTTGAGAGTTTGATTCATTCTTTCTACCTTTCCA 4978 chrXptel1M 716297 GATGAGGACAGATG-------------------CACTCAATTTGCAGCCG 716327 v i ivi ------------------- iii i i--- C HERVP71A#LTR/ 4977 GAGGAAGGGGGATGCCAAGGGGTGTGATAATCCCATCTAATTTGTAA--- 4931 chrXptel1M 716328 CCCCTTTCCTTAGCTCTTA-TAAAACCTTAGAAGGAAAGTGTGTTCCATT 716376 --v i v ii iiv- v i v i v vv i C HERVP71A#LTR/ 4930 --ACCTTCCATAATTCCCCTTAACACCCTTGAGGTAAAGTGGCTCCCATT 4883 chrXptel1M 716377 ATCAGAATACAATAGTCTCTAGCAATCCATACCTAAGCATAATTTATTCC 716426 i v - v i i v iv v i i i i i i i C HERVP71A#LTR/ 4882 GTCTGAAT-CAATATTTTCCACCAGGCCAAATCTAGGTACAATCTGTTCT 4834 chrXptel1M 716427 AATGTCATTTTACTAATGTCTTCAAC-GTAGCAGAGTT--CAGGGGAAA- 716472 i i iviv ii iii ii - i --v --v - C HERVP71A#LTR/ 4833 AATATTATTTTGACCACATTCCCGGCGGTGGC--TGTTGGGAGGGGAAAG 4786 chrXptel1M 716473 GCATCCACCCTGTCTATCAAATAGTCCACTATCACCAATAAATACCTCAG 716522 v v i vivv ii ii i v i i i C HERVP71A#LTR/ 4785 GCTTCCACCCAGCCGGAAAGGTGATCTACGATCACCAGTAAATACTTTAG 4736 chrXptel1M 716523 TTTTCCTGCT 716532 i i C HERVP71A#LTR/ 4735 TCTTCCTACT 4726 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 45.73 CpG sites = 100, Kimura (unadjusted) = 46.61 Transitions / transversions = 1.96 (100/51) Gap_init rate = 0.05 (21 / 463), avg. gap size = 2.67 (56 / 21) 513 32.07 2.07 4.24 chrXptel1M 716620 716860 (283140) C HERVP71A#LTR/ERV1 (4917) 2673 2438 m_b344s701i1 14377 chrXptel1M 716620 TTTACTGCCCCTAAATCTTGTATTAATCCATAAATCTTGTCTGACTTCTT 716669 iv i i i ii i viv iii v i C HERVP71A#LTR/ 2673 TTTATAGCCCTTAGATCTTGCACCAATCTATACGACCCATCAGGCTTCTT 2624 chrXptel1M 716670 GAGGACCCTCTTGAGGA---GGGGTAATGAAAGAGGACATACAAAATTTT 716716 ------- v ii --- i v v v iv i iii i C HERVP71A#LTR/ 2623 GA-------CTGGGAGAATTGGAGTATTGTATGGTGACATGCAGGGTTCT 2581 chrXptel1M 716717 AATGGCCCATCCTTCACGAGTCCCTTTATTACTGATTGCAAGCTTATTTT 716766 i i i v iv i i i i v ii i - i C HERVP71A#LTR/ 2580 AATAGTCCATCTTTAATCAATCCCTCTATTACCGGTTGGAGACCT-TTTC 2532 chrXptel1M 716767 TCCCTTCAAT-GATTTAGGGTATTGTTTAACACACACACCACATCCTCTG 716815 - vv i i --ivii v i v ii C HERVP71A#LTR/ 2531 TCCCTTCAATGGAAATGGGATATTGTTT--TCTGCAAACTACTTCTCCTG 2484 chrXptel1M 716816 GATTTTTCATATGGATTT-TAAGTGGGGAATTTTTCAATCTCCCTT 716860 v v i vv vi i - v v vi v vi i C HERVP71A#LTR/ 2483 GTTGTTTTAGTTCAATCTGTAAGGGTGTGATTTTTAACCCTCCCCT 2438 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 42.14 CpG sites = 47, Kimura (unadjusted) = 43.75 Transitions / transversions = 1.74 (47/27) Gap_init rate = 0.05 (13 / 240), avg. gap size = 1.15 (15 / 13) 12 20.98 2.44 2.44 chrXptel1M 717729 717769 (282231) (AACACAG)n#Simple_repeat 1 41 (0) m_b344s252i1 14378 chrXptel1M 717729 AACACAGAACACAGAGTGCAAAGCACACATCCACAG-ACACA 717769 iii i i v -v - (AACACAG)n#Si 1 AACACAGAACACAGAACACAGAACACAGA-ACACAGAACACA 41 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 19 21.99 1.28 6.76 chrXptel1M 719623 719700 (280300) (AAGGGAG)n#Simple_repeat 1 74 (0) m_b344s252i2 14379 chrXptel1M 719623 AATGGGGAAGGGGCAGAAGAGGAGAAATGGGAAGGGAGGGTGGAGAAGGA 719672 v i - - - iv i iiv i (AAGGGAG)n#Si 1 AAGGGAGAA-GGG-AGAAG-GGAGAAGGGAGAAGGGAGAAGGGAGAAGGG 47 chrXptel1M 719673 CGAATGG-GAAGGGGGAATAGGGAGTAGG 719700 v v - i - - v (AAGGGAG)n#Si 48 AGAAGGGAGAAGGGAG-A-AGGGAGAAGG 74 Matrix = Unknown Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.08 (6 / 77), avg. gap size = 1.00 (6 / 6) 37 33.07 2.83 5.82 chrXptel1M 721179 721461 (278539) (AGAAAG)n#Simple_repeat 1 275 (0) m_b344s252i3 14380 chrXptel1M 721179 AGGAAGAGGAAGGAGAAAGAAGAATGGGAAAGAGGAATGGGGAGGAGGAA 721228 i - i - v i - v i i i - (AGAAAG)n#Sim 1 AGAAAGA-GAAAGAGAAAG-AGAAAGAGAAAGA-GAAAGAGAAAGA-GAA 46 chrXptel1M 721229 TGGGGGAAG-GGTGGCTGGAGAGACAGAGGAATAGGGAGAGAAGGATAGA 721277 -i i i - ivi vvii v i v ii i v - (AGAAAG)n#Sim 47 -AGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGA-A 94 chrXptel1M 721278 GGAGAAAGGAGAAGGAGTGGGGGAGGGACAAAGGGGGAG-GGATGGGAAA 721326 i - i vii i ii v i ii - i v i (AGAAAG)n#Sim 95 AGAGAAA-GAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAAA 143 chrXptel1M 721327 -AG-GGGAGAAA-AGGAGGAGGAATAGGAAAG-GAACAGAGGAAGAGAGA 721372 - -ii - i i i v - - - i - (AGAAAG)n#Sim 144 GAGAAAGAGAAAGAGAAAGAGAAAGA-GAAAGAGAA-AGAGAAAGAGA-A 190 chrXptel1M 721373 GGAAAAAGAAATAAGAGAAGGTGAGGGGAGAAATGAGAAAGGGGGAATAA 721422 i i i - i v -ii - -- i vi (AGAAAG)n#Sim 191 AGAGAAAGAGA-AAGAGAAAGAGA-AAGAGAAA-GAGAAA--GAGAAAGA 235 chrXptel1M 721423 GAAGGAG-AAG-GAAAGAGGAGAGGGATGGGAAAAGGGAAA 721461 i - - - i i vi ii i (AGAAAG)n#Sim 236 GAAAGAGAAAGAGAAAGA-GAAAGAGAAAGAGAAAGAGAAA 275 Matrix = Unknown Transitions / transversions = 3.33 (50/15) Gap_init rate = 0.09 (24 / 282), avg. gap size = 1.00 (24 / 24) 13 0.00 0.00 0.00 chrXptel1M 725342 725358 (274642) (GAA)n#Simple_repeat 1 17 (0) m_b344s252i4 14381 chrXptel1M 725342 GAAGAAGAAGAAGAAGA 725358 (GAA)n#Simple 1 GAAGAAGAAGAAGAAGA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 19 9.88 0.00 10.42 chrXptel1M 725710 725762 (274238) (TTTTAAT)n#Simple_repeat 1 48 (0) m_b344s252i5 14382 chrXptel1M 725710 TTTTAATTTTTAATTTTTCAAATTTTGCCAAGTTTTTGAAATTTAATTTT 725759 -- --i - i vv (TTTTAAT)n#Si 1 TTTTAATTTTTAATTTTT--AATTTT--TAA-TTTTTAATTTTTAATTTT 45 chrXptel1M 725760 TAA 725762 (TTTTAAT)n#Si 46 TAA 48 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.10 (5 / 52), avg. gap size = 1.00 (5 / 5) 19 15.00 0.00 6.38 chrXptel1M 725770 725819 (274181) (TTTTC)n#Simple_repeat 1 47 (0) m_b344s252i6 14383 chrXptel1M 725770 TTTTATTTTGCTTTTCTTTTTTTCTCCATTTTCTTTACTTTCATTTTCTT 725819 v - i - i - v iv (TTTTC)n#Simp 1 TTTTCTTTT-CTTTTCTTTTCTT-TTC-TTTTCTTTTCTTTTCTTTTCTT 47 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.06 (3 / 49), avg. gap size = 1.00 (3 / 3) 16 13.08 0.00 0.00 chrXptel1M 727128 727152 (272848) (T)n#Simple_repeat 1 25 (0) m_b344s252i7 14384 chrXptel1M 727128 TTTTTTTTTATTATTTTTTTTCTTT 727152 v v i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 262 25.40 1.59 0.00 chrXptel1M 727155 727217 (272783) C MIR#SINE/MIR (3) 259 196 m_b344s601i8 14385 chrXptel1M 727155 AAAAACAAGTATTTATTAAACATCTACTATGTGCCAGGCAC-ATGGTAAG 727203 v i v ii i i iii -i vv C MIR#SINE/MIR 259 AATAGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAG 210 chrXptel1M 727204 TGCTTTACAAATAT 727217 i vi C MIR#SINE/MIR 209 CGCTTTACATGTAT 196 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.54 CpG sites = 11, Kimura (unadjusted) = 32.30 Transitions / transversions = 2.20 (11/5) Gap_init rate = 0.02 (1 / 62), avg. gap size = 1.00 (1 / 1) 299 15.79 7.02 0.00 chrXptel1M 727165 727221 (272779) C MIRb#SINE/MIR (15) 253 193 m_b344s601i9 14385 chrXptel1M 727165 ATTTATTAAACATCTACTATGTGCCAGGCAC-ATGGTAAGTGCTTTACA- 727212 i i iii -i v i - C MIRb#SINE/MIR 253 ATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACAT 204 chrXptel1M 727213 --AATATCTCA 727221 -- v C MIRb#SINE/MIR 203 GCATTATCTCA 193 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 14.08 CpG sites = 7, Kimura (unadjusted) = 18.29 Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.05 (3 / 56), avg. gap size = 1.33 (4 / 3) 363 16.64 14.29 0.97 chrXptel1M 727333 727423 (272577) MER63D#DNA/hAT-Tip100 365 467 (594) m_b344s502i0 14386 chrXptel1M 727333 AAATAATACAAATCCGGGTTTGATT-------------ATTCTCTAGACT 727369 iiv v i ------------- v - MER63D#DNA/hA 365 AAACGCTACAAATCAGGGCTTGATTTATTGTTTTGTTGATTGTCTAGAC- 413 chrXptel1M 727370 TTAAAAAAATGTTGGAGAAAATGTTAAAAATGCAGATTAACTATAAAAGC 727419 i i v v viv i MER63D#DNA/hA 414 TTAAGAAAGTGATGGAGAAAATGTTAATAATGCAGATTAAACTTAAAAGT 463 chrXptel1M 727420 ATGT 727423 i MER63D#DNA/hA 464 GTGT 467 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 17.51 CpG sites = 8, Kimura (unadjusted) = 18.98 Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.02 (2 / 90), avg. gap size = 7.00 (14 / 2) 458 30.78 7.96 1.40 chrXptel1M 727591 727791 (272209) C L3#LINE/CR1 (108) 3991 3778 m_b344s601i10 14387 chrXptel1M 727591 CAGATTCTTCTAAAAGACTTTCAAAGAGGTGGGACATACCACTTCTCCAG 727640 vi v vi v i i iv v v ii vi i i ? v C L3#LINE/CR1 3991 CAGCCTCTGCTTGAACACCTCCAGTGACGGGGAGCTCACTACCTCNCGAG 3942 chrXptel1M 727641 GAAGCCCAGTCCAT------ATAGAACTAATTTTTTAGGAAGTTTTTA-T 727683 v v ------ i vv i v - i i v- C L3#LINE/CR1 3941 GCAGCCCATTCCATTTTTGGACAGCTCTGATTGTT-AGAAAGTTCTTCCT 3893 chrXptel1M 727684 GATA--GACACCAAGGCTTAAATTGCT---ACTTTCATCCATT---CCCA 727725 v -- -i i iiii ivv iv --- i i --- i C L3#LINE/CR1 3892 TATATTGA-GCCGAAATCTGCCTCCCTGTAACTTCCACCCATTGGTCCTA 3844 chrXptel1M 727726 ATTCTGCCCTCTGGAACTAGATAGAATGAATTGAATTACCTCTTCTG-AG 727774 i i i v i i i iv i- ii- v C L3#LINE/CR1 3843 GTTCTGCCCTCTGGAGCCACACAGAATAAGTCTAATC-CCTCTTCCACAT 3795 chrXptel1M 727775 AACAACCTTTAAAATAT 727791 i i i v C L3#LINE/CR1 3794 GACAGCCCTTCAAATAT 3778 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 40.65 CpG sites = 38, Kimura (unadjusted) = 41.56 Transitions / transversions = 1.65 (38/23) Gap_init rate = 0.04 (9 / 200), avg. gap size = 2.11 (19 / 9) 11 29.94 0.00 0.00 chrXptel1M 728301 728339 (271661) (ATATAT)n#Simple_repeat 1 39 (0) m_b344s252i8 14388 chrXptel1M 728301 ATACATGCATGTATATGTATATATGCATACATAAATATA 728339 i ii i i ii i v (ATATAT)n#Sim 1 ATATATATATATATATATATATATATATATATATATATA 39 Matrix = Unknown Transitions / transversions = 8.00 (8/1) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 14 21.11 10.26 1.18 chrXptel1M 729664 729741 (270259) (ATAGAT)n#Simple_repeat 1 85 (0) m_b344s252i9 14389 chrXptel1M 729664 ATAGTTTTA-ATA-AGAT-TAGGTA-A-TTTTAGGTATAG-TATAAGTAT 729707 v v - - - i - -v v i - ii (ATAGAT)n#Sim 1 ATAGATATAGATATAGATATAGATATAGATATAGATATAGATATAGATAT 50 chrXptel1M 729708 A-ATATAGATACTG-TTTGGTAATAGGATATAGATA 729741 - iv - v i vv - (ATAGAT)n#Sim 51 AGATATAGATATAGATATAGATATA-GATATAGATA 85 Matrix = Unknown Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.12 (9 / 77), avg. gap size = 1.00 (9 / 9) 13 13.32 9.76 0.00 chrXptel1M 729673 729713 (270287) (ATAAGT)n#Simple_repeat 1 45 (0) m_b344s252i10 14390 chrXptel1M 729673 ATAAG-ATTAG-GTAATTTTAGGTAT-AGTATAAGTATAA-TATA 729713 - v -i v v i - - (ATAAGT)n#Sim 1 ATAAGTATAAGTATAAGTATAAGTATAAGTATAAGTATAAGTATA 45 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.10 (4 / 40), avg. gap size = 1.00 (4 / 4) 14 21.11 10.26 1.18 chrXptel1M 729664 729741 (270259) (ATAGAT)n#Simple_repeat 1 85 (0) m_b344s252i9 14389 chrXptel1M 729664 ATAGTTTTA-ATA-AGAT-TAGGTA-A-TTTTAGGTATAG-TATAAGTAT 729707 v v - - - i - -v v i - ii (ATAGAT)n#Sim 1 ATAGATATAGATATAGATATAGATATAGATATAGATATAGATATAGATAT 50 chrXptel1M 729708 A-ATATAGATACTG-TTTGGTAATAGGATATAGATA 729741 - iv - v i vv - (ATAGAT)n#Sim 51 AGATATAGATATAGATATAGATATA-GATATAGATA 85 Matrix = Unknown Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.12 (9 / 77), avg. gap size = 1.00 (9 / 9) 14 33.20 0.00 0.00 chrXptel1M 732175 732230 (267770) (ATC)n#Simple_repeat 1 56 (0) m_b344s252i11 14391 chrXptel1M 732175 ATGATGATGATGATAATTATCATCATCATCAACAACAACAACAACTTTAC 732224 v v v v v i v v v v v v i i (ATC)n#Simple 1 ATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCAT 50 chrXptel1M 732225 CATTAT 732230 i (ATC)n#Simple 51 CATCAT 56 Matrix = Unknown Transitions / transversions = 0.36 (4/11) Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0) 249 22.07 1.43 2.90 chrXptel1M 732632 732701 (267299) C DNM1r#Unknown (2119) 2543 2475 m_b344s502i1 14392 chrXptel1M 732632 ATATAGGTATATATACATATACATACATGTACA-ACACACATATGCATAT 732680 ? v i i --i - i i i C DNM1r#Unknown 2543 ANATACGTATATATACACATATATACA--CACATACACACATATACACAC 2496 chrXptel1M 732681 AGATATGTTCATTTACATATG 732701 v iiv iv ii C DNM1r#Unknown 2495 ATATATACACACATACACGTG 2475 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 25.35 CpG sites = 11, Kimura (unadjusted) = 27.73 Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.04 (3 / 69), avg. gap size = 1.00 (3 / 3) 235 29.58 1.41 0.00 chrXptel1M 732639 732709 (267291) C DNM1r#Unknown (2116) 2546 2475 m_b344s502i2 14392 chrXptel1M 732639 TATATATACATATACATACATGTACA-ACACACATATGCATATAGATATG 732687 ? i i ii i - ii i v i ii C DNM1r#Unknown 2546 TATANATACGTATATATACACATATATACACACATACACACATATACACA 2497 chrXptel1M 732688 TTCATTTACATATGTGCACATG 732709 ivi v i ii i i C DNM1r#Unknown 2496 CATATATACACACATACACGTG 2475 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.47 CpG sites = 18, Kimura (unadjusted) = 42.97 Transitions / transversions = 6.00 (18/3) Gap_init rate = 0.01 (1 / 70), avg. gap size = 1.00 (1 / 1) 13 17.47 0.00 3.03 chrXptel1M 732718 732751 (267249) (ATACAT)n#Simple_repeat 1 33 (0) m_b344s252i12 14393 chrXptel1M 732718 ATACACATACATATATTTATAGATAAGACATATA 732751 i iv v - v (ATACAT)n#Sim 1 ATACATATACATATACATATACAT-ATACATATA 33 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 390 26.46 13.33 2.00 chrXptel1M 732817 732951 (267049) C MIRc#SINE/MIR (116) 152 3 m_b344s601i11 14394 chrXptel1M 732817 TATCCTT-TTTTATAGATGAAAAAACTGAAAACTAGAGAAGTTAAAGGA- 732864 ii- i ii iivii i iv - C MIRc#SINE/MIR 152 TATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGAC 103 chrXptel1M 732865 TTACCCAAACTCTCATACAACAACATAAGGAGCAG-------------AC 732901 i i--v i i v -i vi ------------- C MIRc#SINE/MIR 102 TTGCCCAAG--GTCACACAGCTA-GTAAGTGGCAGAGCCGGGACTCGAAC 56 chrXptel1M 732902 ACAAGGCCCTCTGTCTCTAA---CAGAGCTCTTTCTACTGCACCATATTA 732948 v i v iii v i --- v i i i i C MIRc#SINE/MIR 55 CCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTG 6 chrXptel1M 732949 CCT 732951 C MIRc#SINE/MIR 5 CCT 3 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.67 CpG sites = 26, Kimura (unadjusted) = 34.67 Transitions / transversions = 2.89 (26/9) Gap_init rate = 0.05 (7 / 134), avg. gap size = 3.00 (21 / 7) 233 13.51 0.00 0.00 chrXptel1M 733005 733041 (266959) C L2#LINE/L2 (617) 2465 2429 m_b344s601i12 14395 chrXptel1M 733005 GAATTCAGTTTTGAACATGTTGAGTTTAAGATGGCTA 733041 i i i i v C L2#LINE/L2 2465 GAGTTCAGTTTTGGACATGTTAAGTTTGAGATGCCTA 2429 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 15.32 CpG sites = 4, Kimura (unadjusted) = 15.32 Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 1658 28.22 2.38 2.55 chrXptel1M 733570 734198 (265802) C L1ME4c_3end#LINE/L1 (191) 639 12 m_b344s551i2 14396 chrXptel1M 733570 TTCTGCTCATTTCACTTAGCATCAGTTCATGTAATTCTCTCCAAGCCTCT 733619 iv i i vv i- ivi i v iiv C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATA-AACATTTTCCATGTTGCT 591 chrXptel1M 733620 CTGTATTCATCCTGCTGGTCATTTCTTACAGA-ACAGTAATATTCCATAA 733668 vii v v v iv vi i v ii v-i - vi C L1ME4c_3end#L 590 ACATAGTCTTCATAATTATCATTTTTAATGGCTGCA-TAATATTCCATCG 542 chrXptel1M 733669 CATTCATATACCACAATTTACCCAACCATTCTCCAATTGATGGGCATCCA 733718 vi ?v i i ii i v v i ii C L1ME4c_3end#L 541 AGTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTA 492 chrXptel1M 733719 CTCAGTTTCCAGCTTCTAGCCACTACAAACAGGGCTGCCACAAACATTTT 733768 vviv ii i v i i i i iv v ii i C L1ME4c_3end#L 491 GGTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTT 442 chrXptel1M 733769 GGCACATACAGGTCCCTTTCCCTTCTTT---AGTATCTCCTTGGGGTATA 733815 v ii i --- i i --- v i i i - C L1ME4c_3end#L 441 CGTGCATATAG---CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATA-A 396 chrXptel1M 733816 ACTCT----AGTAGAAACTCTGCTGGATCAAAGGGTATGCACAGTTTGAT 733861 i i---- i ---i i i v v v C L1ME4c_3end#L 395 ATTCCCAGAAGTGGAA---TTACTGGGTCAAAGGGTATGAACATTTTTAT 349 chrXptel1M 733862 AACTTTTGGGGCATAATTCCAGATTGCTCTCCAGAATGGTTGGATTCGTT 733911 ii i ivi i v v i i i v v iivi C L1ME4c_3end#L 348 GGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATT 299 chrXptel1M 733912 CACAACTCCACCAACAATGCATCAGTGTCCCAGTTTTCCCGCATCCCCTC 733961 i ?iv i i v ? v iv ? i v C L1ME4c_3end#L 298 TACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGC 249 chrXptel1M 733962 CAACA------ATCATCATTATTTTTTCCTGTCATCTTAGCCAATCTGAC 734005 i ------ i -- vv---- i v i i i i C L1ME4c_3end#L 248 CAGCATTGGGTATTATCA--ATTTTTTAA----ATTTTTGCTAATTTAAT 205 chrXptel1M 734006 AGGTATGCAGTAGCATCTCAGAGTTGTCTTAATTTACATTTCTCTGTTCA 734055 ii iv i i i vv ii i i v i C L1ME4c_3end#L 204 AGGCGTAAAATGGTATCTCATTGTTGCTTTAATTTGCATTTCTTTGATTA 155 chrXptel1M 734056 ATAGTGATTTGGGACACTATTTCATATAAGTGTT-AATAGTTTTAATTTC 734104 v i vv v i i v i i ivv - v ? v - C L1ME4c_3end#L 154 CTAGCGAGGTTGAACATTTTTCCATGTGTTTGTTTACTANTTGTA-TTTC 106 chrXptel1M 734105 ATCATCTGAAAATTGTCTGTTCGTATCCTTTGACCATTTATCAATTGGAG 734154 v v ? vi i i v v i C L1ME4c_3end#L 105 CTCTTNTGTGAATTGTCTGTTCATGTCCTTTGCCCATTTATCTATTGGGG 56 chrXptel1M 734155 AATGGCTTGGTTTCTTATAAATTAGAGTCAGTTCTCTATATATT 734198 vv v v ?vv v v i v i i ? C L1ME4c_3end#L 55 TCTTGATNTTTTTCTTATCAATTTGAATGAGCTCTTTATATANT 12 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 35.89 CpG sites = 102, Kimura (unadjusted) = 36.99 Transitions / transversions = 1.44 (102/71) Gap_init rate = 0.03 (21 / 628), avg. gap size = 1.48 (31 / 21) 395 31.19 1.59 1.59 chrXptel1M 734060 734248 (265752) C L1PB_orf2#LINE/L1 (0) 3294 3106 m_b344s551i3 14396 chrXptel1M 734060 TGATTTGGGACACTATTTCATATAAGTGTTAATAGTTTTAATTTCATCAT 734109 v v ii i v ivv iiivi vv v v v C L1PB_orf2#LIN 3294 TGATGTTGAGCATTTTTTCATATGTTTGTTGGCCATTTGTATATCTTCTT 3245 chrXptel1M 734110 CTGAAAATTGTCTGTTCGTATCCTTTGACCATTTATCAATTGGAGAATGG 734159 i i i i i v v i v ii v --- v C L1PB_orf2#LIN 3244 TTGAGAATTGTCTATTCATGTCCTTAGCCCACTTTTTGATGGGA---TTG 3198 chrXptel1M 734160 CTTGGTTT---CTTATAAATTAGAGTCAGTTCTCTATATATTTTGGAAAT 734206 i v --- iivi v vv v ?i i v i v C L1PB_orf2#LIN 3197 TTTGTTTTTTTCTTGCTGATTTGTTTGAGTTCNTTGTAGATTCTGGATAT 3148 chrXptel1M 734207 AAGTCCTTTATCAGAACCTTTAACTGTGAAGATGTTTTCCCA 734248 v i vviv vi i v i C L1PB_orf2#LIN 3147 TAGTCCTTTGTCAGATGTATAGATTGTGAAGATTTTCTCCCA 3106 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.06 CpG sites = 28, Kimura (unadjusted) = 41.06 Transitions / transversions = 0.93 (28/30) Gap_init rate = 0.02 (4 / 188), avg. gap size = 1.50 (6 / 4) 348 28.06 3.54 4.59 chrXptel1M 736602 736799 (263201) C L1ME1_3end#LINE/L1 (271) 655 460 m_b344s551i4 14397 chrXptel1M 736602 AGTATATAATGATCTCCTG-GTCCTGCTCATTTCACTCAGCATCA-GTTC 736649 i ? --- ii - iv iv v - ? i C L1ME1_3end#LI 655 AGTATGTANT---CTTTTGTGTCTGGCTTCTTTCACTCAGCATAATGNTT 609 chrXptel1M 736650 GTGTAAATCTCTCCAGGCCTTTCTGAA-ATCATCTTGTTGGTCATTTCTT 736698 v - i iiv v iiv vi vi- -v v v ivi i C L1ME1_3end#LI 608 TTG-AGATTCATCCATGTTGTTGCGTGTATCA-GTAGTTCGTTCCTTTTT 561 chrXptel1M 736699 AC--CTAACAATAATATTCCATAATATTCATATACCACAATTTATTCAGC 736746 i-- i --i i vi vv i i v C L1ME1_3end#LI 560 ATTGCTGA--GTAGTATTCCATTGTATGGATATACCACAATTTGTTTATC 513 chrXptel1M 736747 CATTCTCCCACTGATGGGCATCCA--TTCAGTTTCCAGTTTCTAGCCACC 736794 v ?ii i iii-- -- i i i ii C L1ME1_3end#LI 512 CATTCACCNGTTGATGGACATTTGGGTT--GTTTCCAGTTTTTGGCTATT 465 chrXptel1M 736795 ACAAA 736799 i C L1ME1_3end#LI 464 ACGAA 460 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 35.61 CpG sites = 35, Kimura (unadjusted) = 37.42 Transitions / transversions = 1.94 (35/18) Gap_init rate = 0.07 (14 / 197), avg. gap size = 1.14 (16 / 14) 363 30.77 2.87 2.87 chrXptel1M 736626 736799 (263201) C L1MD1_3end#LINE/L1 (356) 633 460 m_b344s551i5 14397 chrXptel1M 736626 GCTCATTTCACTCAGCATCAGTTCGTGTAAATCTCTCCAGGCCTTTCTGA 736675 iv v v iiv v i iiv iiv vi v C L1MD1_3end#LI 633 GCTTTTTTCACTCAGCATAATTCTCTGGAGATTCATCCAGGTTGTTGCGT 584 chrXptel1M 736676 A-ATCATCTTGTTGGTCATTTCTTAC--CTAACAATAATATTCCATAATA 736722 i- -v v v ivi i i-- i --i i ii C L1MD1_3end#LI 583 GTATCA-ATAGTTCGTTCCTTTTTATTGCTGA--GTAGTATTCCATGGTA 537 chrXptel1M 736723 TTCATATACCACAATTTATTCAGCCATTCTCCCACTGATGGGCATCCA-- 736770 vv i i i i i v ii v i ii-- C L1MD1_3end#LI 536 TGGATGTACCACAGTTTGTTTAACCATTCACCCGTTGAAGGACATCTGGG 487 chrXptel1M 736771 TTCAGTTTCCAGTTTCTAGCCACCACAAA 736799 -- i i i ii i C L1MD1_3end#LI 486 TT--GTTTCCAGTTTTTGGCTATTACGAA 460 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.59 CpG sites = 35, Kimura (unadjusted) = 41.77 Transitions / transversions = 2.06 (35/17) Gap_init rate = 0.05 (8 / 173), avg. gap size = 1.25 (10 / 8) 394 20.88 2.15 2.15 chrXptel1M 736707 736799 (263201) C L1ME3G_3end#LINE/L1 (376) 548 456 m_b344s551i6 14397 chrXptel1M 736707 ATAATATTCCATAATATTCATATACCACAATTTATTCAGCCATTCTCCCA 736756 i i vv i i i i i C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chrXptel1M 736757 CTGATGGGCATCCA--TTCAGTTTCCAGTTTCTAGCCACCACAAA 736799 i i ii -- -- i i v i ii C L1ME3G_3end#L 498 TTGATGGACATTTAGGTT--GTTTCCAATTTTTCGCTATTACAAA 456 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 25.98 CpG sites = 16, Kimura (unadjusted) = 25.98 Transitions / transversions = 5.33 (16/3) Gap_init rate = 0.03 (3 / 92), avg. gap size = 1.33 (4 / 3) 685 26.90 10.35 5.03 chrXptel1M 736806 737259 (262741) L1ME3Cz_3end#LINE/L1 67 543 (454) m_b344s551i8 14398 chrXptel1M 736806 GGTCAAAGGAT-TAAAAAGGCAATTTGCAGAAG--GAATC---AA-GGCT 736848 v - i v ii -- v --- - - L1ME3Cz_3end# 67 GGGCAAAGGATATGAACAGGCAATTCACAGAAGAGGAAACCCGAATGGC- 115 chrXptel1M 736849 CTCAATAGTCATATAAAAA--TGCTCTGAATGCTC--TGATTATTAGAGA 736894 -- iv i -- -- i- -- ii v i i L1ME3Cz_3end# 116 --CAATAAACATATGAAAAGATGCTC--AAC-CTCACTAGTAATCAGGGA 160 chrXptel1M 736895 AATACCAATTAAAACAACTTTAAGATTCTAT-------CCATCAGATTGG 736937 i v ? vv i v i ------- L1ME3Cz_3end# 161 AATGCAAATTAAAACNACAATGAGATACCATTTCACACCCATCAGATTGG 210 chrXptel1M 736938 CTGACATGACAGAAAAG---GAAAATGACAAACGCTCTGAAGAATGTGGA 736984 vi v v---v --- v iv ii i vvvi i L1ME3Cz_3end# 211 CAAAAATT---TAAAAGTCTGACAATACCAAGTGTTGGCGAGGATGTGGA 257 chrXptel1M 736985 -AAATAGGGACTCTAAT--------GGTGGAGTTGTGAAATGGTCCAATT 737025 - ii i v -------- iiv i v v ii L1ME3Cz_3end# 258 GAAACGGGAACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTACAACC 307 chrXptel1M 737026 ATTCTGGAGAACAGTTCAGAACTA-CTCCCAAAGGACTTTAAAACTCTAC 737074 i i i i ii v v - vvi ---- i iv vii L1ME3Cz_3end# 308 ACTTTGGAGAGCAATTTGGCAATATCTAGTAAAG----TTGAAGATGCGC 353 chrXptel1M 737075 ATACCCTTTGACCCAGTAATACTGCTACTAGGTCTATACACTAAAGAGA- 737123 vi i v ii v v v i i - L1ME3Cz_3end# 354 ATACCCTACGACCCAGCAATTCCACTTCTAGGTATATACCCTAGAGAAAC 403 chrXptel1M 737124 --TCA-----GGGAAAAAGGAAAAGCACCTGTTTGTAACAAATATATTTA 737166 -- i----- v v v i---- v ----- iv i i L1ME3Cz_3end# 404 TCTCGCACATGTGCACAAGGAG----ACATGT-----ACAAGGATGTTCA 444 chrXptel1M 737167 T---AGCATCTCTTTGTGGTGGCAAAGAATTAGAAACTAGGC--GATGCC 737211 --- - v ii i i i i - iv --i i L1ME3Cz_3end# 445 TTGCAGCAT-TGTTTGTAATAGCGAAAAATTGGAAAC-AACCTAAATGTC 492 chrXptel1M 737212 CGTAAATTGGATAATAGCCGAACAGGTTA-GTTATGATCGT--AATGGAA 737258 i v v iv i vii i ii i- v iv i -- L1ME3Cz_3end# 493 CATCAATAGGGGAATGGATAAATAAATTGTGGTATATTCATACAATGGAA 542 chrXptel1M 737259 T 737259 L1ME3Cz_3end# 543 T 543 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 32.20 CpG sites = 70, Kimura (unadjusted) = 34.45 Transitions / transversions = 1.52 (70/46) Gap_init rate = 0.09 (42 / 453), avg. gap size = 1.69 (71 / 42) 705 27.67 9.87 4.83 chrXptel1M 736806 737200 (262800) L1ME5_3end#LINE/L1 71 484 (457) m_b344s551i7 14398 chrXptel1M 736806 GGTCAAAGGAT-TAAAAAGGCAATTTGCAGAAG--GAATC----AAGGCT 736848 v - i v i -- v ---- L1ME5_3end#LI 71 GGGCAAAGGATATGAACAGGCAATTTACAGAAGAGGAAACCCGAAAGGCT 120 chrXptel1M 736849 CTCAATAGTCATATAAAAA--TGCTCTGAATGCTCTGATTATTAGAGAAA 736896 --- i iv i i -- -i iv vi ii v i L1ME5_3end#LI 121 ---AACAAGCATATGAAGAGATGCTC-AAACTCATTAGTAATCAGAGAAA 166 chrXptel1M 736897 TACCAATTAAAACAACTTTAAGAT-TC------TATCCATCAGATTGGCT 736939 i v vv i - ------i i i i i v L1ME5_3end#LI 167 TGCAAATTAAAACAACAATGAGATATCACTTTACACCTATTAGACTGGCA 216 chrXptel1M 736940 GACATGACAGAAAA--GGAAAATGACAAACGCTCTGAAGAATGTGGA-AA 736986 i v --i i-- v v ii i vvvi i i- ? L1ME5_3end#LI 217 AAAAT--TAGAAAGCTGGATAATGCCAAGTGTTGGCGAGGATGTGGGGAN 264 chrXptel1M 736987 ATAGGGACTCTAATG--------GTGGAGTTGTGAAATGGTCCAATTATT 737028 i i v -------- iiv ii v v iii L1ME5_3end#LI 265 ATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACTGGTGCAGCCATT 314 chrXptel1M 737029 CTGGAGAACAGTTCAGAACTACTC--CCAAAGGACTTTAAAACTCTACAT 737076 i i iii v v i--i ----- ivv vii L1ME5_3end#LI 315 CTGGAGAGCAATCTGGCAGTACTTAGTCAAA-----TTAAGTATACGCAT 359 chrXptel1M 737077 ACCCTTTGACCCAGTAATACTGCTACTAGGTCTATACACTAAAGAGAT-- 737124 v i v i v i v iv i i -- L1ME5_3end#LI 360 ACCCTATGACCCAGCAATTCCGCTCCTGGGTATATATCCCAAAGAAATTC 409 chrXptel1M 737125 -----CAGGGAAA-AAGGAAAAGCACCTGTTTGTAACAAATATATTTATA 737168 ----- vvv - ---- v v ----- i iv i i v L1ME5_3end#LI 410 TCACACAGGTCCATAAGG----GGACATGT-----ACGAGGATGTTCATT 450 chrXptel1M 737169 GCATC--TCTTTGTGGTGGCAAAGAATTAGAAAC 737200 v -- v iii i i ii L1ME5_3end#LI 451 GCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGC 484 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.65 CpG sites = 64, Kimura (unadjusted) = 35.84 Transitions / transversions = 1.60 (64/40) Gap_init rate = 0.09 (34 / 394), avg. gap size = 1.74 (59 / 34) 19 25.58 0.00 0.00 chrXptel1M 738363 738406 (261594) (TG)n#Simple_repeat 1 44 (0) m_b344s252i13 14399 chrXptel1M 738363 TGTGTGTGTATGTGTGTGCACGAGTGTGTGTGTACATATGTGTG 738406 i iii v iii i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 44 Matrix = Unknown Transitions / transversions = 8.00 (8/1) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 17 21.80 1.96 1.96 chrXptel1M 738534 738584 (261416) (TTCCC)n#Simple_repeat 1 51 (0) m_b344s252i14 14400 chrXptel1M 738534 TTCCCTTCCC-CCCATTCTTTTACCCTTCTCTTCTCTTCCCCTCCATCCC 738582 -i v ii - i i i v i (TTCCC)n#Simp 1 TTCCCTTCCCTTCCCTTCCCTT-CCCTTCCCTTCCCTTCCCTTCCCTTCC 49 chrXptel1M 738583 CT 738584 (TTCCC)n#Simp 50 CT 51 Matrix = Unknown Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.04 (2 / 50), avg. gap size = 1.00 (2 / 2) 526 25.18 4.55 0.73 chrXptel1M 739770 739901 (260099) C MIRc#SINE/MIR (122) 146 10 m_b344s601i13 14401 chrXptel1M 739770 CATTTTGCAGATGAGAAAAGTGAGG--CAAAGAGG----GTGAAGTGCCC 739813 i i v -- i ---- vv C MIRc#SINE/MIR 146 CATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCC 97 chrXptel1M 739814 AATGTCACATAGCCTAGTGAGTGTCTGAGGCTGGTTTTGAACTCAGATCT 739863 v i - i v v v v vi i i i C MIRc#SINE/MIR 96 AAGGTCACACAG-CTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCT 48 chrXptel1M 739864 TCATAACTTCAAGCTGGGTTTTCCGTCTACTGTGTCAC 739901 v i i iivi vi iv i iii C MIRc#SINE/MIR 47 TCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.31 CpG sites = 20, Kimura (unadjusted) = 31.46 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.02 (3 / 131), avg. gap size = 2.33 (7 / 3) 1408 31.87 4.43 1.10 chrXptel1M 740507 741296 (258704) C L1MD_orf2#LINE/L1 (1053) 2241 1426 m_b345s551i0 14402 chrXptel1M 740507 TTTGTTATTATTACATAGCAACACTATTGATTTTTTGAGCATTTATTTTG 740556 ii ii v i v i v - viii ? i C L1MD_orf2#LIN 2241 TTCATTGCTAGTATATAGAAATACAATTGATTTTT-GTATGTTNATCTTG 2193 chrXptel1M 740557 TAACCTACACTTTTGCTGAAGCAATTGTCTTATTA-----------TCTT 740595 v i ivii ----i vv ----------- i C L1MD_orf2#LIN 2192 TATCCTGCGACCTTGCTGAA----CTCACTTATTAGTTCTAGGAGTTTTT 2147 chrXptel1M 740596 TTCTA-ATTCCCTAGAATTTTTTAAATAAACTATCATATCACCAGCAAAC 740644 v - i i i i vi i v i i v i C L1MD_orf2#LIN 2146 TTGTAGATTCCTTGGGATTTTCTACGTAGACAATCATGTCATCTGCAAAT 2097 chrXptel1M 740645 AGGGACAGTTTCATCATTTCTTTGCCTATCTATCTCCTTCACATTTCTTT 740694 i ivi i v v i v v i ivi i C L1MD_orf2#LIN 2096 AGGGACAGTTTTATTTCTTCCTTTCCAATCTGTATGCCTTTTATTTCCTT 2047 chrXptel1M 740695 CTCTTGTCTTATCGCTATTG--TGG--TTTTTAGAATTATATCAAATAAT 740740 i i i - i -- i --i ii v i i ii v C L1MD_orf2#LIN 2046 TTCTTGCCTTATTGC-ACTGGCTAGAACTTCCAGTACTATGTTGAATAAG 1998 chrXptel1M 740741 AATGAGAAGAATGAACATTCTTGCTTCATTCTTGTATTTATTGGAGAAAG 740790 i ivi ii i i i ii ii vvi v- i C L1MD_orf2#LIN 1997 AGTGGTGAGAGCGGACATCCTTGCCTTGTTCCCGATCTTAG-GGGGAAAG 1949 chrXptel1M 740791 TCCT-AGTAT---ACTCCTGGATATGAGGCCTACTTTTCATTTTAGATAG 740836 ivi - v --- ivi iii v iivi v vvi vvi C L1MD_orf2#LIN 1948 CATTCAGTCTTTCACCATTAAGTATGATGTTAGCTGTAGGTTTTTTGTAG 1899 chrXptel1M 740837 CTACTGTTAATCATATTAATAATGGTACATCTCTGCCTATACTTTGT--A 740884 v i v v vi i vi -i v vi iiiiv v ?i-- C L1MD_orf2#LIN 1898 ATGCTCTTTATCAAGTTGAGGA-AGTTCCCCTCTATTCCTAGTTTNCTGA 1850 chrXptel1M 740885 GGGTATTTAGCATAAAAGAGTTTTGTAGTTTGTCAAAAGCTTTTTCTACA 740934 i v v i v i v v v v i C L1MD_orf2#LIN 1849 GAGTTTTTATCATGAATGGGTGTTGAATTTTGTCAAATGCTTTTTCTGCA 1800 chrXptel1M 740935 TCTATTGACATGATCATGTGGTTTCAGATAGTTTGGCCT-TTGCTATA-- 740981 v i i i-vv vv i - iv i-- C L1MD_orf2#LIN 1799 TCAATTGATATGATCATGTGATTTT-TCTTCTTTAGCCTGTTAATATGGT 1751 chrXptel1M 740982 --ATTATGTTGATTGTTTTCCTTATGCTGAGCCATCCTTGCATCCCTGGA 741029 -- ii v i vv ii i v ? C L1MD_orf2#LIN 1750 GGATTACATTGATTGATTTTCGAATATTGAACCAGCCTTGCATNCCTGGA 1701 chrXptel1M 741030 ATATATTCCAATTAGGCAAAATGAATAAATTCTTGGATAAATTGCTGTAG 741079 v ii v i v vii v v ii vv v v v C L1MD_orf2#LIN 1700 ATAAACCCCACTTGGTCATGGTGTATAATTCTTTTTATATATTGCTGAAT 1651 chrXptel1M 741080 TCCATATGATAAGGTTCTGTTGAAATTTTTTGAGTAAATATTCATTAATT 741129 ? v v vi i iiv v vv i v ivv C L1MD_orf2#LIN 1650 TCNATTTGCTAATATTTTGTTGAGGATTTTTGCGTCTATGTTCATGAGGG 1601 chrXptel1M 741130 ATGTTGTTCT-TGATTCTATGTTTCT------TCTTTCTACAACTTAGAT 741172 i v - ii i v v i ------ v viiii v i C L1MD_orf2#LIN 1600 ATATTGGTCTGTAGTTTTCTTTTTTTGTACTGTCTTTGTCTGGTTTTGGT 1551 chrXptel1M 741173 ATTAGGACTATATTTGTCTTATAAGAGGCTTTGGGGAG-GAGGGCGCTTT 741221 i iiv i v i i i v vv i - vvvv v i i C L1MD_orf2#LIN 1550 ATCAGGGTAATACTGGCCTCATAAAATGAGTTGGGAAGTGTTCCCTCCTC 1501 chrXptel1M 741222 TTTGATTTTTAAGAATAATTTGCGAAGAATGGGCGTTCATTGTTCTTTAA 741271 iv ivi v iv i v v i v v C L1MD_orf2#LIN 1500 TTCTATTTTCTGGAAGAGATTGTGTAGAATTGGTGTTAATTCTTCTTTAA 1451 chrXptel1M 741272 AAGTTGGATAGAATTCCCCTTTGAA 741296 v v i i vv C L1MD_orf2#LIN 1450 ACGTTTGGTAGAATTCTCCAGTGAA 1426 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 42.03 CpG sites = 140, Kimura (unadjusted) = 42.95 Transitions / transversions = 1.28 (140/109) Gap_init rate = 0.03 (22 / 789), avg. gap size = 2.00 (44 / 22) 17 13.69 0.00 0.00 chrXptel1M 741932 741963 (258037) (AACAAA)n#Simple_repeat 1 32 (0) m_b345s252i1 14403 chrXptel1M 741932 AACCAAAAAACAAACAAAAACAAAAACGAAAA 741963 v v v i (AACAAA)n#Sim 1 AACAAAAACAAAAACAAAAACAAAAACAAAAA 32 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 16 18.91 0.00 0.00 chrXptel1M 741936 741965 (258035) (A)n#Simple_repeat 1 30 (0) m_b345s252i2 14403 chrXptel1M 741936 AAAAAACAAACAAAAACAAAAACGAAAAAA 741965 v v v vi (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 30 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 255 30.30 7.37 0.99 chrXptel1M 741967 742156 (257844) L1ME4c_3end#LINE/L1 475 676 (154) m_b345s551i1 14404 chrXptel1M 741967 AAAACTGGGAACCGAAGTAGATATGCATCAACTAGGGGAA-AGCTAACCA 742015 v v v i vv i i v v - -i i vi L1ME4c_3end#L 475 AAAAATTGGAAACAACCTAAATGTCCAACAA-TAGGGGAATGGTTAAGTA 523 chrXptel1M 742016 AATTGTGGTCCATGGATGCGATGGAAGATTATTGTGCTATGAGGAATGAT 742065 i v v? iv v vvv i v ii L1ME4c_3end#L 524 AATTATGGTACATCNACTCGATGGAATATTATGCAGCCATTAAAAATGAT 573 chrXptel1M 742066 GAAGATAAAGG------------ATGGAAAGTGTTACATGAACTGACACA 742103 i vv i i------------ i -i vv i iiiv L1ME4c_3end#L 574 AATTATGAAGACTATGTAGCAACATGGAAAATGTT-TATGATATAATGTT 622 chrXptel1M 742104 GAGTGAAATAAGCAGAGC-CAAGAAAACACATAGACTATGATGACAGCAA 742152 i v ii- i vvii i? vi v i v L1ME4c_3end#L 623 AAGTGAAAAAAGCAGAATACAAAATTGTATNTACGCTATGATTACAACTA 672 chrXptel1M 742153 TATA 742156 i L1ME4c_3end#L 673 TGTA 676 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 39.20 CpG sites = 30, Kimura (unadjusted) = 40.10 Transitions / transversions = 1.11 (30/27) Gap_init rate = 0.03 (5 / 189), avg. gap size = 3.20 (16 / 5) 13 21.75 0.00 2.63 chrXptel1M 742562 742600 (257400) (AAAAAC)n#Simple_repeat 1 38 (0) m_b345s252i3 14405 chrXptel1M 742562 AAAGACTAATAATAAAAACAAAAAGAAAACCATAAATAA 742600 i - v i v v v i (AAAAAC)n#Sim 1 AAAAAC-AAAAACAAAAACAAAAACAAAAACAAAAACAA 38 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.03 (1 / 38), avg. gap size = 1.00 (1 / 1) 293 31.22 0.00 7.76 chrXptel1M 743357 743481 (256519) C MIRc#SINE/MIR (37) 231 116 m_b345s601i1 14406 chrXptel1M 743357 AATTTACCACCAGCACTGTCTTTATCTATGTTATCTTATTTGATCTTCAC 743406 i v -- i --- i iv ii i i C MIRc#SINE/MIR 231 AGTTTACAA--AGCGCT---TTCACATACATTATCTCATTTGATCCTCAC 187 chrXptel1M 743407 AATAACTCTGGAAGTTAGGTTGAACAAGCAACTGCTTTCTCCATCTAGAA 743456 i i vi v iv ii i i- i ii v i i ---v C MIRc#SINE/MIR 186 AACAACCCTGTGAGGTAGGCAGGGCAGGT-ATTATTATCCCCATTT---T 141 chrXptel1M 743457 AAAAAAAAAAAAACTGGAGCTCAGA 743481 v i vi ii ii C MIRc#SINE/MIR 140 ACAGATGAGGAAACTGAGGCTCAGA 116 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 41.71 CpG sites = 27, Kimura (unadjusted) = 43.38 Transitions / transversions = 3.00 (27/9) Gap_init rate = 0.07 (9 / 124), avg. gap size = 1.00 (9 / 9) 245 30.82 2.82 13.18 chrXptel1M 743376 743517 (256483) C MIRb#SINE/MIR (57) 211 83 m_b345s601i2 14406 chrXptel1M 743376 CTTTATCTATGTTATCTTATTTGATCTTCACAATAACTCTGGAAGTTAGG 743425 iv iii i i i i i vi v C MIRb#SINE/MIR 211 CTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGG 162 chrXptel1M 743426 TTGAACAAGCAACTGCTTTCTCCATCTAGAAAAAAAAAAAAAAACTGGAG 743475 ---------- i ii v i i ---v v i vi ii ii C MIRb#SINE/MIR 161 T----------ATTATTATCCCCATTT---TACAGATGAGGAAACTGAGG 125 chrXptel1M 743476 CTCAGAACAAAGGTATAATAGTTAGGCCTAAG----CACAGTCAGT 743517 --- i vv i ii -v i ---- ii C MIRb#SINE/MIR 124 CTCAG---AGAGGTTAAGTAACT-TGCCCAAGGTCACACAGCTAGT 83 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 40.40 CpG sites = 28, Kimura (unadjusted) = 41.90 Transitions / transversions = 2.80 (28/10) Gap_init rate = 0.13 (18 / 141), avg. gap size = 1.17 (21 / 18) 247 23.00 24.11 2.96 chrXptel1M 743640 743751 (256249) C MIR#SINE/MIR (120) 142 8 m_b345s601i3 14407 chrXptel1M 743640 CATTTTACAAATGAGGAAACTGAGA---AAAG-----------------C 743669 i i--- i ----------------- C MIR#SINE/MIR 142 CATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCC 93 chrXptel1M 743670 AGGACTACATAGCTAGTAAGTGTCTAGGGCC-AGATTTGAACTT------ 743712 i iii i v - i -i i ii------ C MIR#SINE/MIR 92 AAGGTCACACAGCTAGTAAGTGGC-AGAGCCGGGATTCGAACCCAGGCAG 44 chrXptel1M 743713 CCTGACTCCAAGTCTTGATGCTCTGATAAGAACTGTACT 743751 i i iiv ii - -- vv i i C MIR#SINE/MIR 43 TCTGGCTCCAGAGCCCG-TGCTCT--TAACCACTATGCT 8 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 26.85 CpG sites = 21, Kimura (unadjusted) = 29.67 Transitions / transversions = 5.25 (21/4) Gap_init rate = 0.07 (8 / 111), avg. gap size = 3.88 (31 / 8) 303 15.72 28.87 1.63 chrXptel1M 743640 743736 (256264) C MIRc#SINE/MIR (122) 146 24 m_b345s601i4 14407 chrXptel1M 743640 CATTTTACAAATGAGGAAACTGAGA-----AAAG---------------C 743669 i i----- i --------------- C MIRc#SINE/MIR 146 CATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCC 97 chrXptel1M 743670 AGGACTACATAGCTAGTAAGTGTCTAGGGCC-AGATTTGAA-------CT 743711 i iii i v - i -i i i ------- C MIRc#SINE/MIR 96 AAGGTCACACAGCTAGTAAGTGGC-AGAGCCGGGACTCGAACCCAGGTCT 48 chrXptel1M 743712 TCCTGACTCCAAGTCTTGATGCTCT 743736 iv - C MIRc#SINE/MIR 47 TCCTGACTCCAAGTCCAG-TGCTCT 24 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 17.21 CpG sites = 13, Kimura (unadjusted) = 18.53 Transitions / transversions = 6.50 (13/2) Gap_init rate = 0.06 (6 / 96), avg. gap size = 5.00 (30 / 6) 16 8.35 0.00 0.00 chrXptel1M 745877 745902 (254098) (GGAT)n#Simple_repeat 1 26 (0) m_b345s252i4 14408 chrXptel1M 745877 GGATGGATGGATGGGTGAATGGATGG 745902 i i (GGAT)n#Simpl 1 GGATGGATGGATGGATGGATGGATGG 26 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 26 10.96 8.47 0.00 chrXptel1M 745962 746020 (253980) (TTA)n#Simple_repeat 1 64 (0) m_b345s252i5 14409 chrXptel1M 745962 TTTTTATT-TTA-TATT-TCATTATTATTATTATTATTATTGTT-TTTTT 746007 v - - - i i - v (TTA)n#Simple 1 TTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATT 50 chrXptel1M 746008 A-CATTTTTATTAT 746020 -i v (TTA)n#Simple 51 ATTATTATTATTAT 64 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.09 (5 / 58), avg. gap size = 1.00 (5 / 5) 15 22.54 7.25 1.37 chrXptel1M 745964 746032 (253968) (TTTATA)n#Simple_repeat 1 73 (0) m_b345s252i6 14409 chrXptel1M 745964 TTTAT-TTTATATTTCATTATTATTATTATTATTAT-TGTTTTTTTACAT 746011 - - vv vv vv - v v v i (TTTATA)n#Sim 1 TTTATATTTATATTT-ATATTTATATTTATATTTATATTTATATTTATAT 49 chrXptel1M 746012 TTTTA-TTATAGCT-T-TTTATAT 746032 v - vi - - (TTTATA)n#Sim 50 TTATATTTATATTTATATTTATAT 73 Matrix = Unknown Transitions / transversions = 0.18 (2/11) Gap_init rate = 0.09 (6 / 68), avg. gap size = 1.00 (6 / 6) 1207 28.66 3.43 3.63 chrXptel1M 746263 746787 (253213) L1ME5_3end#LINE/L1 127 650 (291) m_b345s551i2 14410 chrXptel1M 746263 CATATGAAAGAGTGTTCCAAATCACTATTGATCAGAGAAATGCAAATTGA 746312 iiii i v v i v i i L1ME5_3end#LI 127 CATATGAAGAGATGCTCAAACTCATTAGTAATCAGAGAAATGCAAATTAA 176 chrXptel1M 746313 GACATCTCTAAGATATCACCATATACCTTTCAGATTGGCTAAGATGACAG 746362 i v vv i iv i v i i v i v v i L1ME5_3end#LI 177 AACAACAATGAGATATCACTTTACACCTATTAGACTGGCAAAAATTAGAA 226 chrXptel1M 746363 AGAAAGGTAATGACGAGTGTTGGAGGGGATGTGGGAAAACTGGGACACTG 746412 vvi i v i v i i ? iv i v v L1ME5_3end#LI 227 AGCTGGATAATGCCAAGTGTTGGCGAGGATGTGGGGANATAGGAACCCTC 276 chrXptel1M 746413 ATACATTGTTAGT-GGAGTGGTGAACTGATGCAAACCATTCTGGAGAGTG 746461 i i i i - - ii i - i ii L1ME5_3end#LI 277 ATGCACTGCTGGTGGGAGT-GTAGACTGGTGC-AGCCATTCTGGAGAGCA 324 chrXptel1M 746462 ATTT-GCA--ACTATGCTCAAA--AAGTTATCAAACTTTGCATATCCTTT 746506 i - -- - iv -- - --- --- i v L1ME5_3end#LI 325 ATCTGGCAGTACT-TAGTCAAATTAAG-TAT---AC---GCATACCCTAT 366 chrXptel1M 746507 GATTCAGCAGCGTTTCTACTGGGCTTGTATCTCAAAGAGATCTTAAAAGA 746556 ii iiviiv v iv i i i ii v v v L1ME5_3end#LI 367 GACCCAGCAATTCCGCTCCTGGGTATATATCCCAAAGAAATTCTCACACA 416 chrXptel1M 746557 AG---GGAAAGGGACCTGTATGTGCACGAATGTTTGTGGCAGGTCTCTTT 746603 i ---iv i ---- i iv i ii v vvi v L1ME5_3end#LI 417 GGTCCATAAGGGGAC----ATGTACGAGGATGTTCATTGCAGCGTTGTTT 462 chrXptel1M 746604 GTAGTGGCCAGAAACTGGAAACTGAGTGGATGCCCATCAGTTGGAGAATG 746653 i vi i ii ii vivv i i v v i L1ME5_3end#LI 463 GTGGTGGCGGGGAGTTGGAGGCAACCTGGGTGTCCATCACTGGGAGAGTG 512 chrXptel1M 746654 GCTGAATAAATTGTGGTATATGAATATTATGGAATATTACTGT-TCCGTT 746702 v iii v iv v i ii i i - i-v v L1ME5_3end#LI 513 GATAGGTAAAATGTGGTGGATGCACACCATGGAGTACTA-TGCAGCAGTT 561 chrXptel1M 746703 AGAAATGACCAACAGGATAATTTCAGAAAG--GCCTGGAGAGA-CTTACA 746749 iii vi vi i-- v v v --i v vi - v L1ME5_3end#LI 562 AGAAGCAACGGACTAGATG--TACACATAGCAACATGGATGGATCTTAAA 609 chrXptel1M 746750 TGAAC-TGATGCTGAGTGAAATGAGC-AGAACCAG---GAGAT 746787 -- - ii vi i- v --- L1ME5_3end#LI 610 --AACATAGTGCTGAGTGAAAAAAGTAAGAAACAGAATGAGAT 650 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 36.79 CpG sites = 90, Kimura (unadjusted) = 37.45 Transitions / transversions = 1.64 (90/55) Gap_init rate = 0.06 (30 / 524), avg. gap size = 1.23 (37 / 30) 24 6.91 0.00 0.00 chrXptel1M 747080 747110 (252890) (A)n#Simple_repeat 1 31 (0) m_b345s252i7 14411 chrXptel1M 747080 AAAAAAAAAAAAAAAAAAAAAAAGAAAGAAA 747110 i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 31 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 12 15.85 0.00 3.45 chrXptel1M 747325 747354 (252646) (CAATA)n#Simple_repeat 1 29 (0) m_b345s252i8 14412 chrXptel1M 747325 CAATACAATGACAGCACAATACATGACAAT 747354 - ii vv (CAATA)n#Simp 1 CAATACAAT-ACAATACAATACAATACAAT 29 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 217 19.44 0.00 0.00 chrXptel1M 747562 747597 (252403) C MIRb#SINE/MIR (21) 247 212 m_b345s601i5 14413 chrXptel1M 747562 TAAGTTCCTACTATGTGCCAGACACTGTGCTAAATG 747597 i iv i i ii C MIRb#SINE/MIR 247 TGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCG 212 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 16.56 CpG sites = 6, Kimura (unadjusted) = 23.83 Transitions / transversions = 6.00 (6/1) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 214 27.28 0.00 1.52 chrXptel1M 747837 747903 (252097) L2a_3end#LINE/L2 193 258 (259) m_b345s601i6 14414 chrXptel1M 747837 TCCCTGGATTCCTTCAGGTCTTGGCTAACATCTCACCTTCTACAGGAAGA 747886 vivi v v v v - ?i i L2a_3end#LINE 193 TCCCTCACCTCCTTCAGGTCTTTGCTCAAATGTCACCTTCT-CAGNGAGG 241 chrXptel1M 747887 CTTTTCCCAATTCCTCT 747903 i i ii iiv i L2a_3end#LINE 242 CCTTCCCTGACCACCCT 258 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 35.61 CpG sites = 11, Kimura (unadjusted) = 35.61 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.02 (1 / 66), avg. gap size = 1.00 (1 / 1) 12 9.71 0.00 0.00 chrXptel1M 748013 748034 (251966) (ATCT)n#Simple_repeat 1 22 (0) m_b345s252i9 14415 chrXptel1M 748013 ATTTATCTATCTAGCTATCTAT 748034 i v (ATCT)n#Simpl 1 ATCTATCTATCTATCTATCTAT 22 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 25 12.18 0.00 0.00 chrXptel1M 748520 748556 (251444) (T)n#Simple_repeat 1 37 (0) m_b345s252i10 14416 chrXptel1M 748520 TTTCTTTTTTTCTTTTTTTTTTCTTTTCTTTTTTTTT 748556 i i i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 37 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 451 22.82 1.54 5.60 chrXptel1M 748558 748687 (251313) C MIRc#SINE/MIR (141) 127 3 m_b345s601i7 14417 chrXptel1M 748558 CTGAGGC-AATTGGGGTTAAGTGACTTGCCCAGGGTCACACAGCCAAAAA 748606 -v vv i i i i--- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG--- 81 chrXptel1M 748607 GCATTAAGTGTGTGAGGCCACATTTGAACTCAGGTCCTCCTGACTTCAGG 748656 ---- vvv v viv i i i i i i C MIRc#SINE/MIR 80 ----TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chrXptel1M 748657 GCTGGTGCTCTATACACTATACCAC-CTGGCT 748687 v ii v v ii - v C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTGCACCACACTGCCT 3 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 26.33 CpG sites = 15, Kimura (unadjusted) = 27.44 Transitions / transversions = 1.15 (15/13) Gap_init rate = 0.07 (9 / 129), avg. gap size = 1.00 (9 / 9) 519 18.64 7.25 2.78 chrXptel1M 749289 749426 (250574) L2b_3end#LINE/L2 317 460 (6) m_b345s601i8 14414 chrXptel1M 749289 TGTC-GTTTTCATGT-TGTCTCACC-ATTGGACTAGGAACTTT-TGAGAG 749334 - ? v - v - i i iv i ii- i L2b_3end#LINE 317 TGTCTGNTTACATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGG 366 chrXptel1M 749335 CAGGGACCGTATGTTTTGCCTTTGTTCA------TATCCCCAACATTTAG 749378 ?i ---i i - ------ i iii L2b_3end#LINE 367 CAGGGACCGNGT---CTGTCTT-GTTCACCGCTGTATCCCCAGCGCCTAG 412 chrXptel1M 749379 CACAGAGCCTGGAACACAGCAGGAGCTCAATAAACATTTATTCACTGA 749426 ? v i v i i i v v L2b_3end#LINE 413 CACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTTGTTGAATGA 460 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 20.71 CpG sites = 18, Kimura (unadjusted) = 22.72 Transitions / transversions = 2.57 (18/7) Gap_init rate = 0.07 (9 / 137), avg. gap size = 1.56 (14 / 9) 11 6.92 2.63 11.43 chrXptel1M 749724 749761 (250239) (AGTAAC)n#Simple_repeat 1 35 (0) m_b345s252i11 14418 chrXptel1M 749724 AGTGAACAGTATCAG-AACATTGTATACAGTAACAGCAA 749761 - v - -- - i (AGTAAC)n#Sim 1 AGT-AACAGTAACAGTAACA--GTA-ACAGTAACAGTAA 35 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.14 (5 / 37), avg. gap size = 1.00 (5 / 5) 12 13.05 0.00 3.70 chrXptel1M 750027 750054 (249946) (AGGG)n#Simple_repeat 1 27 (0) m_b345s252i12 14419 chrXptel1M 750027 AGGGAAGGGAGGGAGGGAAAAAGGGAGG 750054 - iii (AGGG)n#Simpl 1 AGGG-AGGGAGGGAGGGAGGGAGGGAGG 27 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 1208 30.15 3.54 2.73 chrXptel1M 751479 751986 (248014) L1ME5_3end#LINE/L1 127 638 (303) m_b345s551i3 14420 chrXptel1M 751479 CATATGAAAGAGGGTTCCAAATCACTATTCATCAGAGAAATGCAAATTAA 751528 iiiiv i v v i v v L1ME5_3end#LI 127 CATATGAAGAGATGCTCAAACTCATTAGTAATCAGAGAAATGCAAATTAA 176 chrXptel1M 751529 GACAACTCTGAGATACCACTACACACCTGTCAGATTGGCTAAGATGACAG 751578 i vv i vi i i i v i v --- L1ME5_3end#LI 177 AACAACAATGAGATATCACTTTACACCTATTAGACTGGCAAAAATTA--- 223 chrXptel1M 751579 GAAA---AGACAAGGATGAACTTTGGAGGGGATGTGGGAAAACCGGGACA 751625 ---i i v vii iiv v i i ? iv i v L1ME5_3end#LI 224 GAAAGCTGGATAATGCCAAGTGTTGGCGAGGATGTGGGGANATAGGAACC 273 chrXptel1M 751626 CCGGTGCATTGTTGGTGGAGTTGTGAACGGATCCAACCATTCTGGAGAGC 751675 ivi i i iiv ii v i v i L1ME5_3end#LI 274 CTCATGCACTGCTGGTGGGAGTGTAGACTGGTGCAGCCATTCTGGAGAGC 323 chrXptel1M 751676 AATCTGGAATTATGCCCCAA--AAGTTATCAAACTGTGCATACCCTTTGA 751723 v v --- ii i-- i -- ivv ii v L1ME5_3end#LI 324 AATCTGGCAGTA---CTTAGTCAAATTA--AGTATACGCATACCCTATGA 368 chrXptel1M 751724 CCCAGCAGTGCTACTGCTGGGCTTGTCCCCCAAAGAGATACTAAAGAAGG 751773 i v ii v iv i vi i v v viv L1ME5_3end#LI 369 CCCAGCAATTCCGCTCCTGGGTATATATCCCAAAGAAATTCTCACACAGG 418 chrXptel1M 751774 ----GAAAGGGACCCGTATGTGCCAAAATGTCTGTGGCGGCCCCGTTTGT 751819 ----v i ---- i v ii iii v i vii L1ME5_3end#LI 419 TCCATAAGGGGAC----ATGTACGAGGATGTTCATTGCAGCGTTGTTTGT 464 chrXptel1M 751820 AGTGGCCAGAAACTGGAG------TGGATGCCCATTTGTTGGAGAATGGT 751863 i vi i ii ------ i i ivv v i v L1ME5_3end#LI 465 GGTGGCGGGGAGTTGGAGGCAACCTGGGTGTCCATCACTGGGAGAGTGGA 514 chrXptel1M 751864 TGGGTAAATTGTGGTATGTGAATATTATGGAATATTATTGTTTGGTAAGA 751913 i v ivi v i ii i i vvvvii v L1ME5_3end#LI 515 TAGGTAAAATGTGGTGGATGCACACCATGGAGTACTATGCAGCAGTTAGA 564 chrXptel1M 751914 AATGACCAGCAGGATGAACACAGAGAGGCTTGGAGAGA-CTTACATGAAC 751962 iii vii vi v v vii v vi - v -- L1ME5_3end#LI 565 AGCAACGGACTAGATGTACACATAGCAACATGGATGGATCTTAAA--AAC 612 chrXptel1M 751963 -TGATGCTGAGTGAAGTGAG-AAGAA 751986 - ii ivi - L1ME5_3end#LI 613 ATAGTGCTGAGTGAAAAAAGTAAGAA 638 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 39.26 CpG sites = 90, Kimura (unadjusted) = 40.00 Transitions / transversions = 1.53 (90/59) Gap_init rate = 0.04 (21 / 507), avg. gap size = 1.52 (32 / 21) 12 22.91 6.90 1.64 chrXptel1M 752232 752289 (247711) (TATA)n#Simple_repeat 1 61 (0) m_b345s252i13 14421 chrXptel1M 752232 TATAAATATGTATACATATAT-TGTATTTA-ACATATACTTTA-ACATAT 752278 v i i - i v - i - v - i (TATA)n#Simpl 1 TATATATATATATATATATATATATATATATATATATA-TATATATATAT 49 chrXptel1M 752279 TTA-ACATTTAT 752289 v - i v (TATA)n#Simpl 50 ATATATATATAT 61 Matrix = Unknown Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.09 (5 / 57), avg. gap size = 1.00 (5 / 5) 573 22.30 1.44 0.00 chrXptel1M 753153 753291 (246709) C MIRc#SINE/MIR (118) 150 10 m_b345s601i9 14422 chrXptel1M 753153 TTCTCATTTTACA-ATGAGGAAACTGAGGCAAACAG-GGTTAGATGACTA 753200 i i - vv v - ii v C MIRc#SINE/MIR 150 TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTT 101 chrXptel1M 753201 GGCTAGAGAAACACAGCTAGTAAGTGTCTGAGGCCAGATTTAAACCCAGG 753250 v i ii vv v v v vi i ii C MIRc#SINE/MIR 100 GCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGG 51 chrXptel1M 753251 GCTTGCTGACTGGAGGCCCAGTGCTCTATCCACTGAGCCAC 753291 v v vv i i v vi C MIRc#SINE/MIR 50 TCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 25.52 CpG sites = 14, Kimura (unadjusted) = 26.57 Transitions / transversions = 0.82 (14/17) Gap_init rate = 0.01 (2 / 138), avg. gap size = 1.00 (2 / 2) 276 32.87 8.41 0.41 chrXptel1M 754025 754250 (245750) L2#LINE/L2 2429 2672 (410) m_b345s601i10 14423 chrXptel1M 754025 TAGGCAGCTTAAAATTCAACATTTCCAAAACT-AACT----ATCCCCCCC 754069 v i v - v - ---- ii L2#LINE/L2 2429 TAGGCATCTCAAACTT-AACATGTCCAAAACTGAACTCCTGATCTTCCCC 2477 chrXptel1M 754070 CCCCAAGCCACTCC-CCTGTCAACTTCCCTGTTATTGTCAAGGACATCAC 754118 i v v ii - i iviv ii iviv ? v i v v L2#LINE/L2 2478 CTCAAACCTGCTCCTCCCGCAGTCTTCCCCATCTCAGTNAATGGCAACTC 2527 chrXptel1M 754119 CATTCTCCCCATCTC-CAGGCTCACAACCTCGGAGTCA---------CTT 754158 i i vi iv - iv v i --------- i L2#LINE/L2 2528 CATCCTTCCAGTTGCTCAGGCCAAAAACCTTGGAGTCATCCTTGACTCCT 2577 chrXptel1M 754159 CCCA--CTCTTACTCCTCAGATCCAAATTGTTGCCAAGGCCTCTTGATTT 754206 i v-- i v i v viii iiv iv v i ii i L2#LINE/L2 2578 CTCTTTCTCTCACACCCCACATCCAATCCATCAGCAAATCCTGTCGGCTC 2627 chrXptel1M 754207 CACCTTTGCGATGTCTCTCAAATGTACCCTCCTCTC-TCACCTCC 754250 i iivi i v ivi viiv v i -i L2#LINE/L2 2628 TACCTTCAAAATATATCCAGAATCCGACCACTTCTCACCACCTCC 2672 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 42.78 CpG sites = 45, Kimura (unadjusted) = 45.38 Transitions / transversions = 1.55 (45/29) Gap_init rate = 0.04 (8 / 225), avg. gap size = 2.50 (20 / 8) 62 0.00 0.00 0.00 chrXptel1M 754407 754459 (245541) (AT)n#Simple_repeat 1 53 (0) c_b345s251i0 14424 chrXptel1M 754407 ATATATATATATATATATATATATATATATATATATATATATATATATAT 754456 (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chrXptel1M 754457 ATA 754459 (AT)n#Simple_ 51 ATA 53 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 35 2.50 2.44 0.00 chrXptel1M 755912 755952 (244048) (AACAAATG)n#Simple_repeat 1 42 (0) c_b345s251i1 14425 chrXptel1M 755912 AACAAATGAACAAAT-AACAAATGAACGAATGAACAAATGAA 755952 - i (AACAAATG)n#S 1 AACAAATGAACAAATGAACAAATGAACAAATGAACAAATGAA 42 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 13 3.22 11.76 2.70 chrXptel1M 756890 756923 (243077) (CCTCT)n#Simple_repeat 1 37 (0) m_b345s252i14 14426 chrXptel1M 756890 CCT-TCC-CTCCTCT-C-CTCCTTTCCTTCTCCTCTCC 756923 - - - - i - (CCTCT)n#Simp 1 CCTCTCCTCTCCTCTCCTCTCCTCTCC-TCTCCTCTCC 37 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.15 (5 / 33), avg. gap size = 1.00 (5 / 5) 486 21.97 3.65 3.65 chrXptel1M 757121 757257 (242743) C MIRc#SINE/MIR (119) 149 13 m_b345s601i11 14427 chrXptel1M 757121 CCCGATTTTACAGATGAGGAAACTGAGGCAAACAG-GGTGAAGTGACTTG 757169 v vv v - v C MIRc#SINE/MIR 149 CCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTG 100 chrXptel1M 757170 CCCAGGATCAAACA--TA--AAGTGTTTGAGGCTGGATTGGAATTCAAGC 757215 i i v -- -- viv v v i v ii --- C MIRc#SINE/MIR 99 CCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCA--- 53 chrXptel1M 757216 TGAGTCTTCCTGACTCCAGGCCTTGCATTCTGTGCACTGTGC 757257 --i i i iv iii v v ii C MIRc#SINE/MIR 52 --GGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCAC 13 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 26.23 CpG sites = 15, Kimura (unadjusted) = 26.23 Transitions / transversions = 1.07 (15/14) Gap_init rate = 0.06 (8 / 136), avg. gap size = 1.25 (10 / 8) 12 19.34 6.06 6.06 chrXptel1M 761230 761295 (238705) (TCCTCT)n#Simple_repeat 1 66 (0) m_b345s252i15 14428 chrXptel1M 761230 TCCTCTTCAGTC-TCCTCTTCCCCAACC-CTACCCGCTTTCCTTTTCCTC 761277 -v - i vv - -i v - i (TCCTCT)n#Sim 1 TCCTCTTC-CTCTTCCTCTTCCTCTTCCTCT-TCCTC-TTCCTCTTCCTC 47 chrXptel1M 761278 -T-CTATTCCCTCTGCCCCT 761295 - - v - v i (TCCTCT)n#Sim 48 TTCCTCTT-CCTCTTCCTCT 66 Matrix = Unknown Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.12 (8 / 65), avg. gap size = 1.00 (8 / 8) 259 25.71 0.00 0.00 chrXptel1M 761821 761890 (238110) C DNM1r#Unknown (2117) 2545 2476 m_b345s502i0 14429 chrXptel1M 761821 ATACATACATACATTGATACATCTATACAAACACACATGCATATACACAT 761870 ? i i vv i v v i ii i C DNM1r#Unknown 2545 ATANATACGTATATATACACATATATACACACATACACACATATACACAC 2496 chrXptel1M 761871 ATACCTGCATGCACACATGT 761890 iv i ii i i C DNM1r#Unknown 2495 ATATATACACACATACACGT 2476 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 29.21 CpG sites = 13, Kimura (unadjusted) = 33.74 Transitions / transversions = 2.60 (13/5) Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0) 17 9.89 6.38 4.17 chrXptel1M 761899 761945 (238055) (ATACAT)n#Simple_repeat 1 48 (0) m_b345s252i17 14430 chrXptel1M 761899 ATACATACCAACATATACATATACCTAT--A-ATACACACACATATACAT 761945 --v v -- - i i (ATACAT)n#Sim 1 ATACATA--TACATATACATATACATATACATATACATATACATATACAT 48 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.09 (4 / 46), avg. gap size = 1.25 (5 / 4) 226 32.20 0.00 0.00 chrXptel1M 761953 762011 (237989) C DNM1r#Unknown (2126) 2536 2478 m_b345s502i1 14431 chrXptel1M 761953 TATATGCAAACATATATACACATGTGCATATATGCATGTACACATGTGCA 762002 ii v ii i i i ii iii i i i C DNM1r#Unknown 2536 TATATATACACATATATACACACATACACACATATACACACATATATACA 2487 chrXptel1M 762003 CGTATGCAC 762011 ii i C DNM1r#Unknown 2486 CACATACAC 2478 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 50.19 CpG sites = 18, Kimura (unadjusted) = 50.19 Transitions / transversions = 18.00 (18/1) Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.0 (0 / 0) 259 29.03 0.00 9.59 chrXptel1M 761970 762049 (237951) C HSAT5v1#Satellite (618) 5280 5208 m_b345s502i2 14432 chrXptel1M 761970 ACACATGTGCATATATGCATGTACACATGTGCACGTATGCACAAACATAT 762019 i i i i i i ?i iiii iii ivi ---- C HSAT5v1#Satel 5280 ACACACGCGCACACACGCGTNCACACACACACACGCGCGCACGCGC---- 5235 chrXptel1M 762020 AGTACACATACACACAATGCATGCATACAT 762049 - i -- v ii C HSAT5v1#Satel 5234 -GTGCACA--CACACATTGCATGCACGCAT 5208 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 21.08 CpG sites = 19, Kimura (unadjusted) = 41.98 Transitions / transversions = 9.50 (19/2) Gap_init rate = 0.09 (7 / 79), avg. gap size = 1.00 (7 / 7) 22 15.01 6.02 6.02 chrXptel1M 762052 762134 (237866) (ATACAT)n#Simple_repeat 1 83 (0) m_b345s252i18 14433 chrXptel1M 762052 ATATATATGCA-ATACATGCATCACATGTACATATACATA-A-ATATCTA 762098 i i - -- - i - - vi (ATACAT)n#Sim 1 ATACATATACATATACAT--AT-ACATATACATATACATATACATATACA 47 chrXptel1M 762099 TAACCATATACATAT--ATACAAATCTACACTCATACA 762134 vv -- i v v - - (ATACAT)n#Sim 48 TATACATATACATATACATATACATATACA-T-ATACA 83 Matrix = Unknown Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.11 (9 / 82), avg. gap size = 1.11 (10 / 9) 1260 31.83 5.03 2.71 chrXptel1M 762751 763725 (236275) L1P4_orf2#LINE/L1 1896 2892 (402) m_b345s551i4 14434 chrXptel1M 762751 CATCTATT-TAAAGCTATCAGCAGGTATCAGATGTAATGGGGATAAACAA 762799 v-i v i - viii v ivv i v v i vi L1P4_orf2#LIN 1896 CATCTATGACAAACCCA-CAGCCAACATCATACTGAACGGGCAAAAGCTG 1944 chrXptel1M 762800 GAAACATCCCCAATAAGA-CTGAGGTGAAACAAAGTTGCCCACTATCACC 762848 i i vv i - iiiii i i v v L1P4_orf2#LIN 1945 GAAGCATTCCCCTTGAGAACTGGAACAAGACAAGGATGCCCACTCTCACC 1994 chrXptel1M 762849 ATTA--ATTCAATAT-----TCAATATGTTAGCTTTGGCAATAAGAGCAG 762891 i v-- i ----- vi vi vi ivvi v ivv L1P4_orf2#LIN 1995 ACTCCTATTCAACATAGTACTGGAAGTCCTAGCCAGAGCAATCAGGCAAG 2044 chrXptel1M 762892 AAAAAGAGATTAAAGGAATTAGAGTAGG----TCATAAGGCAAATTATCA 762937 i i v v ivi i ----vv v v i v L1P4_orf2#LIN 2045 AGAAAGAAATAAAAGGCATCCAAATAGGAAAAGAAGAAGTCAAACTATCT 2094 chrXptel1M 762938 CTCTTTGTAGTTGATACAATGATACACTTAAAGAATCCTAGAGAATCAAC 762987 i iv vi ii vv i i i i i i v vi L1P4_orf2#LIN 2095 CTCTTCGCTGACGATATGATTCTATACCTAGAAAACCCTAAAGACTCCGC 2144 chrXptel1M 762988 TAAAAAACTACTGGAAATAATTCACAACTTTAGCAAAGTTGCAGGATACA 763037 i ii v i v i vv i i i v L1P4_orf2#LIN 2145 CAAAAGGCTCCTAGAACTGATAAACGACTTCAGTAAAGTTTCAGGATACA 2194 chrXptel1M 763038 AAATAAATCCACAGAAATCATCAACATTTGTACATATTATCAACA---AA 763084 v vi i vi i v i i ii vi i--- L1P4_orf2#LIN 2195 AAATCAATGTACAAAAATCAGTAGCATTTCTATACACCAATAACGTTCAA 2244 chrXptel1M 763085 GCAGCAAGAGATATAAAGA--GAAATTCCATTTAAAAGAACTGTAGATAA 763132 v vi vv v v -- v i v v i i---- i L1P4_orf2#LIN 2245 GCTGAGAGCCAAATCAAGAACGCAATCCCATTTACAATAGCC----ACAA 2290 chrXptel1M 763133 ATAATATAAAATATTTGGGAGTCTACCT-GTGAAGGCAAAGTCAGAAA-- 763179 v v ii i i vi i -iiv -- i v i i -- L1P4_orf2#LIN 2291 AAAAAATAAAATACCTAGGAATACATCTAACCAAGG--AGGTGAAAGATC 2338 chrXptel1M 763180 -CTATGAACACAACTACAAAACAGTTTCCACACAAAT---AGAT--C-TA 763222 - ii iv v v viiv v v --- -- -i L1P4_orf2#LIN 2339 TCTACAAGGAGAACTACAAAACACTGCTGAAAGAAATCANAGATGACACA 2388 chrXptel1M 763223 ACCACCTGGAAAAATATCAAGTGCTCTTGGATAGGCCGAGTAAGTATAAC 763272 v vv i ivvi v v vv i v i -- L1P4_orf2#LIN 2389 AACAAATGGAAAAACATTCCATGCTCATGGATTGGAAGAATCAATAT--C 2436 chrXptel1M 763273 AAAAAAATGGCAATATTACCTAAACTAATTTATTTATTTTGTGCTATACC 763322 ivv v i i i vi i ivv ivii v L1P4_orf2#LIN 2437 GTTAAAATGGCCATACTGCCCAAAGCAATCTACAGATTCAACGCTATTCC 2486 chrXptel1M 763323 AATCAAACTCCCAA-GAAATTATTTTACAGA---AAAAAAAATAATAACA 763368 v v - vv - i --- i iv vvi L1P4_orf2#LIN 2487 TATCAAACTACCAACGTCATT-TTTCACAGAATTAGAAAAAACTATTCTA 2535 chrXptel1M 763369 AAGTTCATCTGGAAGAACAAAAG-GTC--AAGAACTTCAAGGGAAT--TA 763413 i v vv v - i -- v i -- i v -- L1P4_orf2#LIN 2536 AAATTCATATGGAACCAAAAAAGAGCCCGAATAGC--CAAAGCAATCCTA 2583 chrXptel1M 763414 ATGAAAAAAAATGCCAATGAAGGTGGCCTCACTGTGGCAGACCTAAAACT 763463 vv i --- v vv v v vv iv v i v L1P4_orf2#LIN 2584 AGCAAAAAGAA---CAAAGCCGGAGGCATCACATTACCCGACTTCAAACT 2630 chrXptel1M 763464 ATATTATAAAGCAGTGATTATCAAAACCATTTGGTACTGGCTAAGAAACA 763513 i i i viiii v i viiv ivv i L1P4_orf2#LIN 2631 ATACTACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACAAAAACA 2680 chrXptel1M 763514 GA-ATAGTTGATCAGTGGAATAGGTTAGGTTTACAGGAC---AAAAT--A 763557 - i - v i i i iv ------ i ---i -- L1P4_orf2#LIN 2681 GACACA-TAGACCAATGGAACAGAATAG------AGAACCCAGAAATAAA 2723 chrXptel1M 763558 GTCA-ATAACTATAGCAAGCTAGTGTTTGACAAACCCAAAGACCCCAACT 763606 i i- i v i i v v ii v i vi i vi vvvi vi L1P4_orf2#LIN 2724 GCCGCACACCTACAACCATCTGATCTTCGACAAAGTCGACAAAAATAAGC 2773 chrXptel1M 763607 TTTGGGATAAGAATTCACTATTTGACAAAAACTGCTGGGAAAATTGGAAA 763656 vv iv i i v ii i viv v i --- L1P4_orf2#LIN 2774 AATGGGGAAAGGACTCCCTATTCAATAAATGGTGCTGGGATAACTGG--- 2820 chrXptel1M 763657 CTAG---TATGGCAGA--AATGAGACATGGAACCACACCTAATACCATAT 763701 --- - -- i - v vi vvi L1P4_orf2#LIN 2821 CTAGCCATAT-GCAGAAGAATGAAAC-TGGACCCCTACCTTTCACCATAT 2868 chrXptel1M 763702 ACCAAGATAAGGTTGAAATGGGTT 763725 v i v iv ii i i L1P4_orf2#LIN 2869 ACAAAAATTAACTCAAGATGGATT 2892 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 40.31 CpG sites = 160, Kimura (unadjusted) = 42.31 Transitions / transversions = 1.13 (160/142) Gap_init rate = 0.05 (51 / 974), avg. gap size = 1.49 (76 / 51) 1127 31.52 6.90 3.30 chrXptel1M 762785 764103 (235897) L1M2_orf2#LINE/L1 1927 3291 (0) m_b345s551i5 14434 chrXptel1M 762785 AATGGGGATAAACAAGAAACATCCCCAATAAGA-CTGAGGTGAAACAAAG 762833 v iivii i v ii vv - iiiii i i L1M2_orf2#LIN 1927 AATGGGGAAAAGTTGAAAGCCTTTCCTCTAAGANCTGGAACAAGACAAGG 1976 chrXptel1M 762834 TTGCCCACTATCACCATTA--ATTCAATAT-----TCAATATGTTAGCTT 762876 v v i v-- i ----- vi vi vi iv L1M2_orf2#LIN 1977 ATGCCCACTTTCACCACTTCTATTCAACATAGTACTGGAAGTCCTAGCCA 2026 chrXptel1M 762877 TGGCAATAAGAGCAGAAAAAGAGATTAAAGG------AATTAGA--GTAG 762918 vi v ivv i i v ------ i -- v L1M2_orf2#LIN 2027 GAGCAATTAGGCAAGAGAAAGAAATAAAAGGCATCCAAATTGGAAAGGAG 2076 chrXptel1M 762919 GTCATAAGGCAAATTATCACTCTTTGTAGTTGATACAATGATACACTTAA 762968 ---- v i v v i v i ii vv i i? i L1M2_orf2#LIN 2077 G----AAGTCAAATTGTCCCTGTTTGCAGATGACATGATCTTATATNTAG 2122 chrXptel1M 762969 AGAATCCTAGAGAATCAACTAAAAAACTACTGGAAATAATTCACAACTTT 763018 i ? i v v i ?i i v i vv i v i L1M2_orf2#LIN 2123 AAAANCCTAAAGACTCCACCAAAAAACTNTTAGAACTGATAAACGAATTC 2172 chrXptel1M 763019 AGCAAAGTTGCAGGATACAAAATAAATCCACAGAAATCATCAACATTTGT 763068 i v ivi i vi i v L1M2_orf2#LIN 2173 AGTAAAGTTGCAGGATACAAAATCAACATACAAAAATCAGTAGCATTTCT 2222 chrXptel1M 763069 ACATATTATCAACAAAGCA---GCAAGAGATATAAAGAGA--AATTCCAT 763113 i iiii v i vi --- v i v v i -- i L1M2_orf2#LIN 2223 ATACGCCAACAACGAACTATCTGAAAAAGAAATCAAGAAAGCAATCCCAT 2272 chrXptel1M 763114 TTAAAAGAACTGTAGATAAATAATATAAAATATTTGGGAGTCTACCT-GT 763162 v v i ---- i v v ii i i vv ii -ii L1M2_orf2#LIN 2273 TTACAATAGCT----ACAAAAAAAATAAAATACCTAGGAATAAATTTAAC 2318 chrXptel1M 763163 GAAGGCAAAGTCAGAAA---CTATGAACACAACTACAAAACAGTTTCCAC 763209 v -- i v i i --- ii ?v v i v vviv v L1M2_orf2#LIN 2319 CAAGG--AGGTGAAAGATCTCTACAANGAAAACTATAAAACACTGATGAA 2366 chrXptel1M 763210 ACAAAT------AGATCTAACCACCTGGAAAAATATCAAGTGCTCTTGGA 763253 v ------i ivi v? vv i vvi v L1M2_orf2#LIN 2367 AGAAATTGAAGAGGACACAAANAAATGGAAAGATATCCCATGCTCATGGA 2416 chrXptel1M 763254 TAGGCCGAGTAAGTATAACAAAAAAATGGCAATATTACCTAAACTAATTT 763303 v vv i v i --iivv ? v i i vii i L1M2_orf2#LIN 2417 TTGGAAGAATTAATAT--TGTTAAAATGNCCATACTACCCAAAGCGATCT 2464 chrXptel1M 763304 ATTTATTTTGTGCTATACCAATCAAACTCCCAA-GAAATTATTTTACAGA 763352 ivv ivi v v v v v - v -i i L1M2_orf2#LIN 2465 ACAGATTCAATGCAATCCCTATCAAAATACCAATGACATT-CTTCACAGA 2513 chrXptel1M 763353 AA---AAAAAATAATAACAAAGTTCATCTGGAAGAACAAAAGGTCAAGAA 763399 --- ? vvi i i v vv ii vv L1M2_orf2#LIN 2514 AATAGAAAAAANAATCCTAAAATTCGTATGGAACCACAAAAGACCCCGAA 2563 chrXptel1M 763400 C-TTCAAGGGAATTAATGAAAAAAAATGCCAATGAAGGTGGCCTCACTGT 763448 i-vi i v i-v iv viv v vv v v vv L1M2_orf2#LIN 2564 TAGCCAAAGCAATC-CTGAGCAAAAAGAACAAAGCTGGAGGCATCACACT 2612 chrXptel1M 763449 GGCAGACCTAAAACTATATTATAAAGCAGTGATTATCAAAACCATTTGGT 763498 iv v i v v i i vi ii v i viiv L1M2_orf2#LIN 2613 ACCTGACTTCAAAATATACTACAAAGCTATAGTAACCAAAACAGCATGGT 2662 chrXptel1M 763499 ACTGGCTAAGAAACAGA-ATAGTTGATCAGTGGAATAGGTTAGGTTTACA 763547 vv i - i - v i i i iv ------ L1M2_orf2#LIN 2663 ACTGGCATAAAAACAGACACA-TAGACCAATGGAACAGAATAG------A 2705 chrXptel1M 763548 GGAC---AAAAT-AGTCAA--TAACTATAGCAAGCTAGTGTTTGACAAA- 763590 i ---i - i v --i vi i v i ii v i - L1M2_orf2#LIN 2706 GAACCCAGAAATAAATCCACGCATTTACAGCCAACTGATTTTCGACAAAG 2755 chrXptel1M 763591 -CCCAAAGACCCCAACTTTTGGGATAAGAATTCACTATTTGACAAAAACT 763639 - v v v vi- v? v - i ivvv v ii i viv L1M2_orf2#LIN 2756 GCGCCAAGAACAT-ACANTGGGGA-AAGGACAGTCTCTTCAATAAATGGT 2803 chrXptel1M 763640 GCTGGGAAAATTGGAAACTAGTATGGCAGA--AATGAGACATGGAACCAC 763687 i v iivi - -- i - i v vi L1M2_orf2#LIN 2804 GCTGGGAAAACTGGATATCCATAT-GCAGAAGAATGAAAC-TAGACCCCT 2851 chrXptel1M 763688 ACCTAATACCATATACCAAGATAAGGTTGAAATGGGTTCATGATACAGGC 763737 i vvi v i v iv ii i v v ivi iii L1M2_orf2#LIN 2852 ATCTCTCACCATATACAAAAATCAACTCAAAATGGATTAAAGACTTAAAT 2901 chrXptel1M 763738 ATAAAGAGGGATATGATAAGCAA--ATTAGAAG--AACAAAGGATATTTT 763783 i iivvv v iv -- -- i -- v iv ---v L1M2_orf2#LIN 2902 GTAAGACCCGAAACTATAA--AACTACTAGAAGAAAACATAGGGGA---A 2946 chrXptel1M 763784 ACCTCTCAGATCTGTGGAGAAGG-AAGGAATTTCTGACCAA------AGA 763826 vii iv vv vvvi - i v i i?i ------ i L1M2_orf2#LIN 2947 ACGCTTCAGGACATTGGTCTGGGCAAAGATTTTTTGGNTAAGACCTCAAA 2996 chrXptel1M 763827 AGAACTGAAGGTCATTATTGATCATGAAATAGATAATTTTAATTATATTA 763876 v --- iv iv --i v vi - i v vvi i i L1M2_orf2#LIN 2997 AGCAC---AGGCAACAA--AAGCAAAAA-TAGACAAATGGGATTACATCA 3040 chrXptel1M 763877 AGTTAAAAAGTTTTTGTAC--CAACAAAACCAATGCAGACTAGATTAGAA 763924 ii i i i -- vii v - - - v - L1M2_orf2#LIN 3041 AACTAAAAAGCTTCTGCACAGCAAAGGAAACAAT-CA-AC-AGAGT-GAA 3086 chrXptel1M 763925 GGGA-AACA-ATAAATTGGGAAAACATTTTTACATTTAAGGGTTCTAATC 763972 i - v- i i v i v v i --- vvi ? -- L1M2_orf2#LIN 3087 GAGACAACCTACAGAATGGGAGAAAATATTTGCA---AACTATNC--ATC 3131 chrXptel1M 763973 T-ATAGAGAACTGAC-TCC--AATTTATAA-GAATTCAAGCCATTC---- 764013 - i ii i i i i- -- v - i i v i ---- L1M2_orf2#LIN 3132 TGACAAGGGATTAATATCCAGAATATATAAGGAACTCAAACAACTCAACA 3181 chrXptel1M 764014 ----------------TCCAATTGATAAATGCTCAAAGGATATGA----A 764043 ---------------- i ? v vv iv ---- L1M2_orf2#LIN 3182 GCAAAAAAACAAATAATCCGATTNAAAAATGGGCAAAGGACCTGAATAGA 3231 chrXptel1M 764044 CAATTTTCAGATGAAGAAATTAAAACCATTTCTAGTCATATGAAAAAGTG 764093 v i i v v vv iviiivvi vi i L1M2_orf2#LIN 3232 CATTTCTCAAAAGAAGACATACAAATGGCCAACAGGTATATGAAAAAATG 3281 chrXptel1M 764094 CTCCAAATCA 764103 v v L1M2_orf2#LIN 3282 CTCAACATCA 3291 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 41.27 CpG sites = 213, Kimura (unadjusted) = 42.26 Transitions / transversions = 1.13 (213/189) Gap_init rate = 0.06 (79 / 1318), avg. gap size = 1.72 (136 / 79) 1343 31.90 3.75 0.95 chrXptel1M 763966 764579 (235421) L1ME4c_3end#LINE/L1 9 639 (191) m_b345s551i6 14434 chrXptel1M 763966 TCTAATCTATAGAGAACTGACTCCAATTTATAAGAAT----TCAAGCCAT 764011 ? ? v i i v i v v v---- v -- L1ME4c_3end#L 9 TNTANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAAGAC-- 56 chrXptel1M 764012 TCTCCAATTGATAAATGCTCAAAGGATATGAACA----ATTTTCAGATGA 764057 --i v vv i ---- iv ? v L1ME4c_3end#L 57 --CCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGA 104 chrXptel1M 764058 AGAAATTAAAACCATTTCTAGTCATATGAAAAAGTGCTCCAAATCACTAT 764107 i vv ?ivi vvvi iv i i i i v vv i v L1ME4c_3end#L 105 GGAAATACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTAG 154 chrXptel1M 764108 TTATCAAAGAAATGCAAATTAAGACAACTCTGAGATACCACTACACACCT 764157 v ii vv i vi i L1ME4c_3end#L 155 TAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCT 204 chrXptel1M 764158 GTCAGATTGGCTAAGATGGCAGGAAAAGATCATGACGAATATTGGAGGGG 764207 i i i i v i vvv ii vv v iv v ii v i L1ME4c_3end#L 205 ATTAAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGCTGGCGAGG 254 chrXptel1M 764208 ATGTGGGAAAATTGGGA------TACATCGTTGATGGAATTGTGAACGAA 764251 ? i vi i v ------ i i i v ? i ivii L1ME4c_3end#L 255 NTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGG 304 chrXptel1M 764252 TCCAGCCATTCTGGAGAGTAGTTTGGAACTATGCCCAAAAAGTTATCAAA 764301 v i v i i i i v v i iviv i ii v L1ME4c_3end#L 305 TACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAAA 354 chrXptel1M 764302 CTGTGCATCCCCTTTGATCCAGCAGGGTTACTACTGGGCTTATACCCCAA 764351 v v v i i ivvii v vv v i i L1ME4c_3end#L 355 ATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAA 404 chrXptel1M 764352 AAAGATCAT--AAAGGAGGGAAAGGGACCCGTACGTGCACAAATGTTTGT 764399 ii i v -- i i ii -- ii i ii iv i ii L1ME4c_3end#L 405 GGAAATAATTCAAAAGAAGGAAAAAG--CTATATGCACGAAGATGTTCAT 452 chrXptel1M 764400 GGCAGCCCTTTTCGTAGTGGCCAGAAACTGGAAACTGAGTGGATGCCCAT 764449 v vi v ii i i v i i vivv ii i v L1ME4c_3end#L 453 TGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAA 502 chrXptel1M 764450 CAATTGGAGAATGGCTGAATAAATTATGGTATATGAATATTATGGAATAT 764499 v i i i i i v? iviv L1ME4c_3end#L 503 CAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATAT 552 chrXptel1M 764500 TATTGTTCTGTAAGAAATGACCAGCAGGATGATTTTAGAGCGGTCTGGA- 764548 vvvv ii v i iv vi v v i v iv iiiv - L1ME4c_3end#L 553 TATGCAGCCATTAAAAATGATAATTATGAAGACTATGTAGCAACATGGAA 602 chrXptel1M 764549 ------CATGAACTGATGCTGAGTGAAATGAGCAGAA 764579 ------i vv i i i vi L1ME4c_3end#L 603 AATGTTTATGATATAATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 41.61 CpG sites = 109, Kimura (unadjusted) = 43.39 Transitions / transversions = 1.28 (109/85) Gap_init rate = 0.02 (12 / 613), avg. gap size = 2.42 (29 / 12) 1375 27.46 3.75 3.17 chrXptel1M 763969 764502 (235498) L1ME3G_3end#LINE/L1 12 548 (376) m_b345s551i7 14434 chrXptel1M 763969 AATCTATAGAGAACTGACTCCAATTTATAAGAATTCAAGCCATTCTCCAA 764018 v i vviv v iv --v v --vi L1ME3G_3end#L 12 AATATATAAAGAACTCCTACAAATCAATAAGAA--AAAGACA--ACCCAA 57 chrXptel1M 764019 TTGATAAATGCTCAAAGGATATGAACA----ATTTTCAGATGAAGAAATT 764064 v v vv ---- iv v i v L1ME3G_3end#L 58 TAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGGAAATA 107 chrXptel1M 764065 AAAACCATTTCTAGTCATATGAAAAAGTGCTCCAAATCACTATTTATCAA 764114 v iviiivv iv ii v vv v v i L1ME3G_3end#L 108 CAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTAATCAG 157 chrXptel1M 764115 AGAAATGCAAATTAAGACAACTCTGAGATACCACTACACACCTGTCAGAT 764164 i i vv i viv ii L1ME3G_3end#L 158 GGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCATCAGAT 207 chrXptel1M 764165 TGGCTAAGATGGCAGGAAAAG----ATCATGACGAATATTGGAGGGGATG 764210 v i vv---- ---- v iv ? i i v i i L1ME3G_3end#L 208 TGGCAAAAATTT----AAAAGNTTGATAATATCNAGTGTTGGCGAGGGTG 253 chrXptel1M 764211 TGGGAAAATTGGG-------ATACATCGTTGATGGAATTGTGAACGAATC 764253 i i- ------- ii i i i v i ivii v L1ME3G_3end#L 254 TGGGGAAAC-GGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTA 302 chrXptel1M 764254 CAGCCATTCTGGAGAGTAGTTTGGAACTATGCCCA--AAAAGTTATCAAA 764301 ? i i i i v v -- i -- v --- L1ME3G_3end#L 303 CAGCCNTTTTGGAGGGCAATTTGGCAGTAT--CTATTAAAATTTA---AA 347 chrXptel1M 764302 CTGTGCATCCCCTTTGATCCAGCAGGGTTACTACTGGGCTTATACCCCAA 764351 v i v i ivvii v ? ?v v i i ? L1ME3G_3end#L 348 ATGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTAN 397 chrXptel1M 764352 AAAGAT---CATAAAGGAGGGAAAGGGACCCGTACGTGCACAAATGTTTG 764398 i i --- ii v v v viv i?--- i i i vii ii L1ME3G_3end#L 398 AGAAATACTCGCACATGTGCACAAGGAN---GCATGTACAAGGATGTTCA 444 chrXptel1M 764399 TGGCAGCCCTTTTCGTAGTGGCCAGAAACTGGAAACTGAGTGGATGCCCA 764448 v vi v i i i v i i vivv ii i L1ME3G_3end#L 445 TTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCA 494 chrXptel1M 764449 TCAATTGGAGAATGGCTGAATAAATTATGGTATATGAATATTATGGAATA 764498 v i i i vv i L1ME3G_3end#L 495 TCAATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATA 544 chrXptel1M 764499 TTAT 764502 i L1ME3G_3end#L 545 CTAT 548 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 34.40 CpG sites = 77, Kimura (unadjusted) = 35.32 Transitions / transversions = 1.18 (77/65) Gap_init rate = 0.04 (22 / 533), avg. gap size = 1.68 (37 / 22) 233 30.47 0.00 15.84 chrXptel1M 765500 765616 (234384) C L2c_3end#LINE/L2 (14) 464 364 m_b345s601i12 14435 chrXptel1M 765500 CAAGCATTTATTAAGTGTACACTATCTGTATGCCAGGCCCTGGGGACACA 765549 i i i i--- - i i v i C L2c_3end#LINE 464 CAAACATTTATTGAGCGC---CTA-CTATGTGCCAGGCGCTGGGGATACA 419 chrXptel1M 765550 AATACAATTTTTCAAAGCTTCTGTCAAGAGAATCCACTATTGAGGGGCTT 765599 v ii v ----- viv v -------i ii iv ii i i C L2c_3end#LINE 418 AAGATGAAT-----AAGACACGGTC-------CCTGCCCTCAAGGAGCTC 381 chrXptel1M 765600 ATAGTCCAATGGCGGGG 765616 i i i v i C L2c_3end#LINE 380 ACAGTCTAGTGGAGGAG 364 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 38.67 CpG sites = 22, Kimura (unadjusted) = 40.48 Transitions / transversions = 2.75 (22/8) Gap_init rate = 0.14 (16 / 116), avg. gap size = 1.00 (16 / 16) 289 31.99 0.00 3.09 chrXptel1M 765825 765924 (234076) MIRc#SINE/MIR 15 111 (157) m_b345s601i13 14436 chrXptel1M 765825 GTAGTAGATGGAGGGCTACGCTTAAAGCCAAGAAGTCCTGAGTTCAAATC 765874 i i vi vi ivi ii i i v i i i MIRc#SINE/MIR 15 GCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTC 64 chrXptel1M 765875 CCACTTCAGACCCTTCAGACTAGTGGGCTGACCCTTTGTAAGTCACTTAA 765924 ivi v v v --- iv vv i vv i MIRc#SINE/MIR 65 CCGGCTCTGCCACTT---ACTAGCTGTGTGACCTTGGGCAAGTCACTTAA 111 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 39.36 CpG sites = 18, Kimura (unadjusted) = 42.98 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.03 (3 / 99), avg. gap size = 1.00 (3 / 3) 49 9.90 1.30 0.00 chrXptel1M 766952 767028 (232972) (TG)n#Simple_repeat 1 78 (0) c_b345s251i2 14437 chrXptel1M 766952 TGTGTGTGTGTGTGTGTATGTGTGTGTGTG-GTATGTATGTATGTATGTA 767000 i - i i i i i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chrXptel1M 767001 TGTGTGTGAGTGTGTGTGTGTGTGTGTG 767028 v (TG)n#Simple_ 51 TGTGTGTGTGTGTGTGTGTGTGTGTGTG 78 Matrix = Unknown Transitions / transversions = 6.00 (6/1) Gap_init rate = 0.01 (1 / 76), avg. gap size = 1.00 (1 / 1) 49 18.20 4.35 2.86 chrXptel1M 767144 767281 (232719) (TAATA)n#Simple_repeat 1 140 (0) m_b345s252i19 14438 chrXptel1M 767144 TAATATAAT-TAATATAATTCAATATAATGTTAT-TAGAATAATACAAT- 767190 - vi i v - iv i - (TAATA)n#Simp 1 TAATATAATATAATATAATATAATATAATATAATATAATATAATATAATA 50 chrXptel1M 767191 TGTAATAATAAACTATAATACTAATGATATTAT-GTATAATATGATATGA 767239 ivv v v - - v -i i i (TAATA)n#Simp 51 TAATATAATATAATATAATA-TAAT-ATAATATAATATAATATAATATAA 98 chrXptel1M 767240 CATAATAGAATATGTCATGTAATATAATAT--TATAATATAGTA 767281 i v -- v i -- i (TAATA)n#Simp 99 TATAATATAATA--TAATATAATATAATATAATATAATATAATA 140 Matrix = Unknown Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.07 (9 / 137), avg. gap size = 1.11 (10 / 9) 412 24.16 0.83 3.42 chrXptel1M 767386 767505 (232495) MIRb#SINE/MIR 2 118 (150) m_b345s601i14 14439 chrXptel1M 767386 AGAGGGGCAGCTAGGAGGTGCTGTGGATAGAGCCCCAGCCCGGAAGTCAA 767435 --- v v v v vi iiv i i MIRb#SINE/MIR 2 AGAGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAG 48 chrXptel1M 767436 GAAGGCCTGAGTTCAAATCT-GACACTTAACACTCCCTAGCTGTGTGATC 767484 iv i i i i- i v -iv iv i MIRb#SINE/MIR 49 ACAGACCTGGGTTCGAATCCCGGCTCT-GCCACTTACTAGCTGTGTGACC 97 chrXptel1M 767485 CTGGGCAAGTCTCTTAACCCC 767505 i iv i MIRb#SINE/MIR 98 TTGGGCAAGTTACTTAACCTC 118 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 28.55 CpG sites = 17, Kimura (unadjusted) = 29.80 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.04 (5 / 119), avg. gap size = 1.00 (5 / 5) 413 24.27 0.96 0.96 chrXptel1M 767402 767505 (232495) MIRc#SINE/MIR 12 115 (153) m_b345s601i15 14439 chrXptel1M 767402 GGTGCTGTGGATAGAGCCCCAGCCCGGAAGTCAAGAAGGCCTGAGTTCAA 767451 v v v ii v iv i i i i i MIRc#SINE/MIR 12 GGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGA 61 chrXptel1M 767452 ATCT-GACACTTAACACTCCCTAGCTGTGTGATCCTGGGCAAGTCTCTTA 767500 i i- i v -iv iv i i v MIRc#SINE/MIR 62 GTCCCGGCTCT-GCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTA 110 chrXptel1M 767501 ACCCC 767505 i MIRc#SINE/MIR 111 ACCTC 115 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 28.75 CpG sites = 16, Kimura (unadjusted) = 30.18 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.02 (2 / 103), avg. gap size = 1.00 (2 / 2) 105 2.00 0.98 0.00 chrXptel1M 768060 768161 (231839) (GA)n#Simple_repeat 1 103 (0) c_b345s251i3 14440 chrXptel1M 768060 GAGAGAGAGAGAAAGAGAGAGAGAAAGAGAGAGAGA-AGAGAGAGAGAGA 768108 i i - (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chrXptel1M 768109 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 768158 (GA)n#Simple_ 51 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 100 chrXptel1M 768159 GAG 768161 (GA)n#Simple_ 101 GAG 103 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.01 (1 / 101), avg. gap size = 1.00 (1 / 1) 504 27.08 0.00 2.26 chrXptel1M 768559 768694 (231306) MIR#SINE/MIR 49 181 (81) m_b345s601i16 14441 chrXptel1M 768559 TGAGTTCCAATTCAGCTTCAGACACTTCCTAGCTATGTGATCCTAAGCAA 768608 i v i v vi v v v i i i ii MIR#SINE/MIR 49 TGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 98 chrXptel1M 768609 ATCATTGAATATCTATATGCTTCAGTTTCCTCAAGTGTAAAGGGGGGGGG 768658 i i i v iv v i i vv iv i-- MIR#SINE/MIR 99 GTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGA-- 146 chrXptel1M 768659 CTAATAGTAGCACCCACCTCTGAGAGTTGTTTTAAG 768694 - i i i vv i v i MIR#SINE/MIR 147 -TAATAATAGTACCTACCTCATAGGGTTGTTGTGAG 181 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 34.37 CpG sites = 21, Kimura (unadjusted) = 34.37 Transitions / transversions = 1.40 (21/15) Gap_init rate = 0.02 (3 / 135), avg. gap size = 1.00 (3 / 3) 183 21.06 0.00 10.42 chrXptel1M 768992 769044 (230956) C L2a_3end#LINE/L2 (84) 433 386 m_b345s601i17 14442 chrXptel1M 768992 ACAGACAAAAGTGAGATCCCAACCATCAAGGGGCTTCTATCCTAATGGGG 769041 ----- vi v v i vi i i C L2a_3end#LINE 433 ACAGACAAAAGT-----CCCTGCCCTCATGGAGCTTACATTCTAGTGGGG 389 chrXptel1M 769042 GAA 769044 i C L2a_3end#LINE 388 GGA 386 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 24.83 CpG sites = 6, Kimura (unadjusted) = 24.83 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.10 (5 / 52), avg. gap size = 1.00 (5 / 5) 272 20.10 2.53 2.53 chrXptel1M 769275 769947 (230053) (AGGA)n#Simple_repeat 1 673 (0) m_b345s252i20 14443 chrXptel1M 769275 AGGAGAGAAGGAAAGAAGGAAGGAAGGAAGGAAGGAAGAGAGGGAGGAAG 769324 ii i ii i (AGGA)n#Simpl 1 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG 50 chrXptel1M 769325 GGAGGGAGGCAGGGAGGCAGAGAAAGAAAGAAGGAAGGAAGGAAAGAAGG 769374 i i v i v - i i i (AGGA)n#Simpl 51 GAAGGAAGGAAGGAAGGAAG-GAAGGAAGGAAGGAAGGAAGGAAGGAAGG 99 chrXptel1M 769375 AAGGAAGGAGAGAAAGG-AGAAAGGAGGGAA-GAAGGAAGGAAGAGAAGG 769422 - i - i i - - (AGGA)n#Simpl 100 AAGGAAGGA-AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG-GAAGG 147 chrXptel1M 769423 AAGGAAGGAAAGAAGAGAAAGAA-GAAGGGAGGGAGGAAGGAAGAAAAGG 769471 i - i - i i -i (AGGA)n#Simpl 148 AAGGAAGGAAGGAAG-GAAGGAAGGAAGGAAGGAAGGAAGGAAG-GAAGG 195 chrXptel1M 769472 AGGGAAGGAGGGAAAG-AGGGAGGAAGATAAGGAGAAAAAGGAAAGGAGA 769520 i i i - i -v - ii - ii (AGGA)n#Simpl 196 AAGGAAGGAAGGAAGGAAGGAAGGAAG-GAAGGA-AGGAAGG-AAGGAAG 242 chrXptel1M 769521 CAAAGAAGAAAAGAGGGAAGG-AGGAGCAAATGAAAGTAAGAAGGTAGGA 769569 v i i i i - ivi v i v i v (AGGA)n#Simpl 243 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 292 chrXptel1M 769570 AGGAAAAAAGGAAAGAAGAGAAGGAA-AAAGAGAAGGAAGAAAGGAAGGA 769618 ii i - -i - i (AGGA)n#Simpl 293 AGGAAGGAAGGAAGGAAG-GAAGGAAGGAAG-GAAGGAAGGAAGGAAGGA 340 chrXptel1M 769619 AGG-A-GAAAAAAGAAAGGAAAGAAAGAAGAAAGGGAAGAAGGAAGGCAC 769666 - - ii i i i i i i v v (AGGA)n#Simpl 341 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG 390 chrXptel1M 769667 AAAAGTAAGAAGATAGGAAGGAAGAAAGGAGGAAAGGAAGGAAGAAAGGA 769716 i i v i iv i i i i (AGGA)n#Simpl 391 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 440 chrXptel1M 769717 A-GAA-AAAGGAGGGAAAGAA-AAAGGAAGGAAGGAGAAAAAGAAAAGGA 769763 - -i i i -i - ii -i (AGGA)n#Simpl 441 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA-AGGAAG-GAAGGA 488 chrXptel1M 769764 GAGAGAAGAAAGGGAAGAAGGGAGGAACGAAAATAAGAAGGTAGGAAGGA 769813 - - i i i i v iiv i v (AGGA)n#Simpl 489 -AG-GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 536 chrXptel1M 769814 AGAAAGG-AGGAAAGGAGGAGGGTAGGAAGGAAGGAAGAACAGAAAGAAA 769862 i - i i i v i vi i i (AGGA)n#Simpl 537 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG 586 chrXptel1M 769863 GAAGGAAGG-AGAGAGGAAGGAAGG-AGAACAGGAATGGAA-G-AGGAA- 769907 - ii - i - - - - - (AGGA)n#Simpl 587 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGA-AGGAA-GGAAGGAAGGAAG 634 chrXptel1M 769908 GAAAAAAGCAAGGAGAGAAGAGGAGAAAAAAAGGGAGGAA 769947 ii v ii - i i ii i (AGGA)n#Simpl 635 GAAGGAAGGAAGGAAGGAAG-GAAGGAAGGAAGGAAGGAA 673 Matrix = Unknown Transitions / transversions = 5.06 (91/18) Gap_init rate = 0.05 (34 / 672), avg. gap size = 1.00 (34 / 34) 672 21.96 4.60 0.55 chrXptel1M 769951 770124 (229876) C MIR#SINE/MIR (10) 252 72 m_b345s601i18 14444 chrXptel1M 769951 AGCATATATGAATCATGCATCATGTGCCAGGCA-TGTGATA---GCTTTC 769996 i v vi v iivi ii - vv --- v C MIR#SINE/MIR 252 AACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGCGCTTTA 203 chrXptel1M 769997 CAACTGTAATCTCATCTGATCTTCACAACCATCCTAAAAAAGTAGGTACT 770046 vv i v v i i i v i vi i- C MIR#SINE/MIR 202 CATGTATTAACTCATTTAATCCTCACAACAACCCTATGAG-GTAGGTACT 154 chrXptel1M 770047 ATTACTATCTCCATTTTACAGTTGAGGAAACTGAGGTAC--ACAGGT--A 770092 i i v i -- v -- C MIR#SINE/MIR 153 ATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAA 104 chrXptel1M 770093 GTGACTTACCCAGGATCACACAGCTAATAAAT 770124 i i i i i i C MIR#SINE/MIR 103 GTAACTTGCCCAAGGTCACACAGCTAGTAAGT 72 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 25.70 CpG sites = 23, Kimura (unadjusted) = 26.50 Transitions / transversions = 1.53 (23/15) Gap_init rate = 0.03 (5 / 173), avg. gap size = 1.80 (9 / 5) 201 27.66 5.88 10.20 chrXptel1M 770568 770720 (229280) L2c_3end#LINE/L2 319 465 (13) m_b345s601i19 14445 chrXptel1M 770568 CATTTATT-TTGACTCGCATCTGAAACTTCCTA-----ATGTACCGTCTC 770611 i i- i i i - v i vi i-----? - i L2c_3end#LINE 319 CACTTATCATTAACTTGTAT-TGTAATTGTCTGTTTACNTGT-CTGTCTC 366 chrXptel1M 770612 CTTT-TTAGAAAGTGAACTCCTTGAAAGCAAA-ACC-TGCCTTCGTTTGC 770658 ii-i vv i ii ii- - i -i ii- L2c_3end#LINE 367 CTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTT-ATTCA- 414 chrXptel1M 770659 TATTTGGGTCCCAGCACTTAGCACCATGCTTCACACATAGTAAGCACCCC 770708 v vi ------i i - ----i i i i v L2c_3end#LINE 415 TCTTTGTATCCC------CAGCGCC-TG----GCACATAGTAGGCGCTCA 453 chrXptel1M 770709 AAAAATGCTCGT 770720 v i i L2c_3end#LINE 454 ATAAATGTTTGT 465 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 34.86 CpG sites = 30, Kimura (unadjusted) = 37.40 Transitions / transversions = 3.75 (30/8) Gap_init rate = 0.13 (20 / 152), avg. gap size = 1.20 (24 / 20) 261 31.15 4.92 0.00 chrXptel1M 770607 770728 (229272) L2d_3end#LINE/L2 382 509 (7) m_b345s601i20 14445 chrXptel1M 770607 GTCTCCTTT-TTAGAAAGTGAACTCCTTGAAAGCAAA-ACC-TGCCTTCG 770653 iiv-i vv i i ii ii- - i vv L2d_3end#LINE 382 GTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTAT 431 chrXptel1M 770654 TTTGCTATTTGGGTCCC---AGCACTTAGCACCATGCTTCACACATAGTA 770700 vi ?i v ? v v --- i i vi vvi L2d_3end#LINE 432 ACTNTTTTNTCGTTCCCCACAGCGCCTAGCACAGTGCTGAGCACATAGTA 481 chrXptel1M 770701 AGCACCCCAAAAATGCTCGTCCATTCAT 770728 i i i v v i i iv v L2d_3end#LINE 482 GGCGCTCAATAAATACTTGTTGATTGAT 509 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 39.50 CpG sites = 22, Kimura (unadjusted) = 42.41 Transitions / transversions = 1.38 (22/16) Gap_init rate = 0.03 (4 / 121), avg. gap size = 1.50 (6 / 4) 307 24.76 17.14 0.00 chrXptel1M 770854 770958 (229042) C MIR3#SINE/MIR (11) 197 75 m_b345s601i21 14446 chrXptel1M 770854 TCACAGCATTTTAGAGCTG--AGGGACTCCCAAAATC--------CAACC 770893 i v v i -- iiivi i -------- C MIR3#SINE/MIR 197 TCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACC 148 chrXptel1M 770894 C--TCATTTCATAAATGAAGAAACTGAGACC------GGAGCAATAACTT 770935 -- i i i i i ------ v v i i C MIR3#SINE/MIR 147 CCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTT 98 chrXptel1M 770936 GTTTAAGATCCCATAGCTTGTTA 770958 iii i v i ?v C MIR3#SINE/MIR 97 GCCCAAGGTCACACAGCNAGTTA 75 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 31.96 CpG sites = 19, Kimura (unadjusted) = 31.96 Transitions / transversions = 2.71 (19/7) Gap_init rate = 0.04 (4 / 104), avg. gap size = 4.50 (18 / 4) 415 22.81 13.16 0.00 chrXptel1M 770981 771094 (228906) MIRb#SINE/MIR 92 220 (48) m_b345s601i22 14447 chrXptel1M 770981 GTAGCTCTGGACAAGTGACTCAACCCCACTGAGCCTCAGTTTCCTCATCT 771030 ii ii i v i i v MIRb#SINE/MIR 92 GTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCT 141 chrXptel1M 771031 -TCAAACGGGGA--------------TCACAGGACTATTAGGAGTATCGA 771065 - v i -------------- i ii i iv v ii MIRb#SINE/MIR 142 GTAAAATGGGGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAA 191 chrXptel1M 771066 ATGAGTTGAACCATGTAAAGTGCTTTGCA 771094 v i vv i v MIRb#SINE/MIR 192 ATGAGATAATGCATGTAAAGCGCTTAGCA 220 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 25.50 CpG sites = 17, Kimura (unadjusted) = 27.97 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.02 (2 / 113), avg. gap size = 7.50 (15 / 2) 30 10.03 0.00 0.00 chrXptel1M 771740 771783 (228217) (AT)n#Simple_repeat 1 44 (0) c_b345s251i4 14448 chrXptel1M 771740 ATATATATATATATGTATATATGTGCATATATATATATATATAT 771783 i i ii (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATAT 44 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 16 16.12 0.00 0.00 chrXptel1M 772210 772237 (227763) (T)n#Simple_repeat 1 28 (0) m_b345s252i21 14449 chrXptel1M 772210 TTTTTTTTTTTTTTTTTAAATTTTATTT 772237 vvv v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 28 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 28 3.10 0.00 2.94 chrXptel1M 774223 774257 (225743) (CGC)n#Simple_repeat 1 34 (0) c_b345s251i5 14450 chrXptel1M 774223 CGCCGCCCGCCGCGGCCGCCGCCGCCGCCGCCGCC 774257 - v (CGC)n#Simple 1 CGCCG-CCGCCGCCGCCGCCGCCGCCGCCGCCGCC 34 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 92 15.96 0.00 0.00 chrXptel1M 774259 774418 (225582) (GAG)n#Simple_repeat 1 160 (0) m_b345s252i22 14451 chrXptel1M 774259 GAGGAGAAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA 774308 i (GAG)n#Simple 1 GAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA 50 chrXptel1M 774309 GGAGGTGGAGGAAGAGGAGCAGCAGCAGCAGCAGCAGGAGGAGGAGGAGG 774358 v i v v v v v v (GAG)n#Simple 51 GGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGG 100 chrXptel1M 774359 AGGAAGAGCAGGAGCTGCGGCGGGAGCAGGAGAAGGACCAGGAGGAAGAG 774408 i v vv vi vi v i vv i (GAG)n#Simple 101 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG 150 chrXptel1M 774409 CAGGAGGAGG 774418 v (GAG)n#Simple 151 GAGGAGGAGG 160 Matrix = Unknown Transitions / transversions = 0.44 (7/16) Gap_init rate = 0.00 (0 / 159), avg. gap size = 0.0 (0 / 0) 11 27.68 0.00 0.00 chrXptel1M 774492 774530 (225470) (GGGGTGG)n#Simple_repeat 1 39 (0) m_b345s252i23 14452 chrXptel1M 774492 GGGGTGGGGGTTGGGCGGGGGGAGGCCAGGGGAGGGAGG 774530 v v v i ivi v i (GGGGTGG)n#Si 1 GGGGTGGGGGGTGGGGGGTGGGGGGTGGGGGGTGGGGGG 39 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 16 18.66 3.23 6.67 chrXptel1M 774493 774554 (225446) (GGGA)n#Simple_repeat 1 60 (0) m_b345s252i24 14452 chrXptel1M 774493 GGGTGGG-GGTTGGGCGGG-GGGAGGCCAGGGGAGGGAGGGGAGAGAGGG 774540 v - vv v - -v - - i (GGGA)n#Simpl 1 GGGAGGGAGGGAGGGAGGGAGGGAGG-GA-GGGAGGGA-GGGAGGGAGGG 47 chrXptel1M 774541 CGAGCGCGGAGGGA 774554 v i v - (GGGA)n#Simpl 48 AGGGAG-GGAGGGA 60 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.10 (6 / 61), avg. gap size = 1.00 (6 / 6) 17 14.43 2.50 2.50 chrXptel1M 774586 774625 (225375) (CGG)n#Simple_repeat 1 40 (0) m_b345s252i25 14453 chrXptel1M 774586 CGGCGGCGGC-GCGGCGGCGGCCGAGGGAGGGGGCGACGGC 774625 - - iv v v i (CGG)n#Simple 1 CGGCGGCGGCGGCGGCGGCGG-CGGCGGCGGCGGCGGCGGC 40 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 26 14.84 1.92 0.00 chrXptel1M 774608 774659 (225341) (GAGG)n#Simple_repeat 1 53 (0) m_b345s252i26 14454 chrXptel1M 774608 GAGGGAGGGGGCGACGG-CCGAGGGAGGGAGGGAGGGAGAGAGGGAGCGA 774656 i v v -vv i v (GAGG)n#Simpl 1 GAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGA 50 chrXptel1M 774657 GGG 774659 (GAGG)n#Simpl 51 GGG 53 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.02 (1 / 51), avg. gap size = 1.00 (1 / 1) 14 24.65 2.00 2.00 chrXptel1M 774815 774864 (225136) (GGCGG)n#Simple_repeat 1 50 (0) m_b345s252i27 14455 chrXptel1M 774815 GGAGGGGCTGCG-GGGGCGGGGGCTTGAGGGACGGGGGCGGGGCGGGGAG 774863 v v v - vvvv v i - v (GGCGG)n#Simp 1 GGCGGGGCGGGGCGGGGCGGGGCGGGGCGGGGC-GGGGCGGGGCGGGGCG 49 chrXptel1M 774864 G 774864 (GGCGG)n#Simp 50 G 50 Matrix = Unknown Transitions / transversions = 0.11 (1/9) Gap_init rate = 0.04 (2 / 49), avg. gap size = 1.00 (2 / 2) 17 3.21 2.63 8.33 chrXptel1M 774824 774861 (225139) (GCGGGG)n#Simple_repeat 1 36 (0) m_b345s252i28 14456 chrXptel1M 774824 GCGGGGGCGGGGGCTTGAGGGACGGGGGC-GGGGCGGGG 774861 -- - i - (GCGGGG)n#Sim 1 GCGGGGGCGGGGGC--G-GGGGCGGGGGCGGGGGCGGGG 36 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.11 (4 / 37), avg. gap size = 1.00 (4 / 4) 183 26.32 18.95 0.00 chrXptel1M 775107 775201 (224799) MIR#SINE/MIR 138 250 (12) m_b345s601i23 14457 chrXptel1M 775107 AAACGGGGAGAACCAGGGTCCCCACCTCCCAGGATCG--GGGAGAA---- 775150 i v iv vi v i vi i i -- v i ---- MIR#SINE/MIR 138 AAATGGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGGATTAA 187 chrXptel1M 775151 -------AATAACCGTAAAGCGCT-----CACTGCTTAGCACATAGTAGG 775188 ------- vvi ----- v i i i MIR#SINE/MIR 188 ATGAGTTAATACATGTAAAGCGCTTAGAACAGTGCCTGGCACATAGTAAG 237 chrXptel1M 775189 TGCCCTTTAAATG 775201 i i vv MIR#SINE/MIR 238 CGCTCAATAAATG 250 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 31.43 CpG sites = 14, Kimura (unadjusted) = 33.01 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.04 (4 / 94), avg. gap size = 4.50 (18 / 4) 199 21.43 8.93 0.00 chrXptel1M 775146 775201 (224799) MIRb#SINE/MIR 194 254 (14) m_b345s601i24 14457 chrXptel1M 775146 GAGAAAATAACCGTAAAGCGCT---CAC--TGCTTAGCACATAGTAGGTG 775190 v ivvi --- -- i i i i MIRb#SINE/MIR 194 GAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCG 243 chrXptel1M 775191 CCCTTTAAATG 775201 i vv MIRb#SINE/MIR 244 CTCAATAAATG 254 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 23.26 CpG sites = 7, Kimura (unadjusted) = 25.64 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.04 (2 / 55), avg. gap size = 2.50 (5 / 2) 192 20.93 0.00 0.00 chrXptel1M 775165 775207 (224793) L2d_3end#LINE/L2 460 502 (14) m_b345s601i25 14458 chrXptel1M 775165 GCTCACTGCTTAGCACATAGTAGGTGCCCTTTAAATGCCTGTT 775207 v v v i i vv i i L2d_3end#LINE 460 GCACAGTGCTGAGCACATAGTAGGCGCTCAATAAATACTTGTT 502 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 21.70 CpG sites = 4, Kimura (unadjusted) = 24.62 Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 259 21.43 13.10 0.00 chrXptel1M 775240 775323 (224677) MIRc#SINE/MIR 63 157 (111) m_b345s601i26 14459 chrXptel1M 775240 TCCCTCCTTTCTCCCTTCCT-GCTGCTTGACCGTAGGCAAGTCACTTAA- 775287 vv i vi v v - iv v i - MIRc#SINE/MIR 63 TCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAAC 112 chrXptel1M 775288 ---------CCTCAATTTGCTCACCGGTAAAATGGGGGAAATCAT 775323 --------- i v i v iv v MIRc#SINE/MIR 113 CTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAAT 157 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 25.26 CpG sites = 7, Kimura (unadjusted) = 25.26 Transitions / transversions = 0.64 (7/11) Gap_init rate = 0.04 (3 / 83), avg. gap size = 3.67 (11 / 3) 42 0.00 0.00 0.00 chrXptel1M 775369 775404 (224596) (GT)n#Simple_repeat 1 36 (0) c_b345s251i6 14460 chrXptel1M 775369 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 775404 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 36 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 268 24.63 2.65 13.97 chrXptel1M 775527 775677 (224323) MIR3#SINE/MIR 9 144 (64) m_b345s601i27 14461 chrXptel1M 775527 GCAGCTGGGTGGATAGAGCACGGCCGGGGAACCAAGACTGATTTTCCCAA 775576 ii i ii v v v ii i -- ---- iii MIR3#SINE/MIR 9 GTGGCTGAGCAGAGAGAGCACGGACTGGGAGTCAGGA--GA----CCTGG 52 chrXptel1M 775577 GTTCAAATCAAGCCTCAGACACTTCCTAGCTGGGTTAGGAAGTCACTTCA 775626 v i vv v v v vv ? v ------ -- i -- MIR3#SINE/MIR 53 GTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGT------G--ACCT-- 92 chrXptel1M 775627 CCTGGGCAAATCACTTCACCCCGTTTG---CTCCGTTTCCT-GTCTGCAA 775672 -- i i - i --- v -i i MIR3#SINE/MIR 93 --TGGGCAAGTCACTTCACCTC-TCTGGGCCTCAGTTTCCTCATCTGTAA 139 chrXptel1M 775673 AGTGA 775677 i MIR3#SINE/MIR 140 AATGA 144 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 30.19 CpG sites = 19, Kimura (unadjusted) = 30.19 Transitions / transversions = 1.46 (19/13) Gap_init rate = 0.14 (21 / 150), avg. gap size = 1.10 (23 / 21) 192 20.93 0.00 0.00 chrXptel1M 775958 776000 (224000) MamTip2#DNA/hAT-Tip100 114 156 (149) m_b345s601i28 14462 chrXptel1M 775958 GTCAGAAATTTCACTATTAGAATTTCATGGCTTTGGGTGTTGA 776000 i v i i iv vv v MamTip2#DNA/h 114 GCCTGAAATTCCACCATTAGAGATTCATTCCTTTGGGTCTTGA 156 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 24.62 CpG sites = 4, Kimura (unadjusted) = 24.62 Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 17 9.12 0.00 0.00 chrXptel1M 776922 776945 (223055) (T)n#Simple_repeat 1 24 (0) m_b345s252i29 14463 chrXptel1M 776922 TTTCTTTCTTTTTTTTTTTTTTTT 776945 i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTT 24 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 248 17.98 16.85 0.00 chrXptel1M 777799 777887 (222113) C MIR1_Amn#SINE/MIR (80) 150 47 m_b346s601i0 14464 chrXptel1M 777799 CTCATTTTCCAGATGAGGAATCT----CAC---GAGG-CAAGCGG----- 777835 i v v ---- ? --- -? i i----- C MIR1_Amn#SINE 150 CCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGC 101 chrXptel1M 777836 --AGGGTCACCCAGCTGGGAAGTGCCTGAGGCTGGCTTTGAATTCGGGTC 777883 -- i ? ? v? v v v v v? ? ii i C MIR1_Amn#SINE 100 CCAAGGTCACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAACCCAGGTC 51 chrXptel1M 777884 TTCC 777887 i C MIR1_Amn#SINE 50 TCCC 47 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 22.74 CpG sites = 8, Kimura (unadjusted) = 22.74 Transitions / transversions = 1.00 (8/8) Gap_init rate = 0.06 (5 / 88), avg. gap size = 3.00 (15 / 5) 389 25.48 0.85 10.19 chrXptel1M 778295 778412 (221588) C MIRc#SINE/MIR (153) 115 8 m_b346s601i1 14465 chrXptel1M 778295 GAGGTTAAATGACTTGCCCAGAATCACCCAGCTTGTAAGTGTTA-AGTGT 778343 i iii v v vi - --- C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAG--- 69 chrXptel1M 778344 CTGATGTTGGATTTGAACTCAGATCCTCCTGACTCTGGCTTGTCTGCTGC 778393 i ----- i i i i i iii--- iiv C MIRc#SINE/MIR 68 CCG-----GGACTCGAACCCAGGTCTTCCTGACTCCAA---GTCCAGTGC 27 chrXptel1M 778394 CCTCTCCAATTTACTTCAC 778412 i i v vi iv C MIRc#SINE/MIR 26 TCTTTCCACTGCACCACAC 8 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.52 CpG sites = 20, Kimura (unadjusted) = 32.43 Transitions / transversions = 2.86 (20/7) Gap_init rate = 0.10 (12 / 117), avg. gap size = 1.00 (12 / 12) 321 28.21 0.00 0.00 chrXptel1M 778419 778496 (221504) MIRb#SINE/MIR 83 160 (108) m_b346s601i2 14466 chrXptel1M 778419 ACTTGCTATGGAATCACAGGCAAGTTGCTTTAGCTCTCAGAAACTCAGTT 778468 v i vi i vii i v v v iv MIRb#SINE/MIR 83 ACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTT 132 chrXptel1M 778469 TTCTTACCTGTAAAAAGAGAATCATAGT 778496 i i i v i i v i MIRb#SINE/MIR 133 TCCTCATCTGTAAAATGGGGATAATAAT 160 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.33 CpG sites = 13, Kimura (unadjusted) = 36.33 Transitions / transversions = 1.44 (13/9) Gap_init rate = 0.00 (0 / 77), avg. gap size = 0.0 (0 / 0) 244 22.92 0.00 0.00 chrXptel1M 779206 779253 (220747) Charlie4a#DNA/hAT-Charlie 460 507 (1) m_b346s502i0 14467 chrXptel1M 779206 ATCAGATTACCAAAGGGGAACATGATACATAAAAGGTTAAAAATTCCT 779253 i i i vv ii v i ii Charlie4a#DNA 460 ACCAGACTGCCAAAGGGGTCCATGGCACAAAAAAGGTTAAGAACCCCT 507 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 28.53 CpG sites = 8, Kimura (unadjusted) = 28.53 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 549 20.75 0.81 5.98 chrXptel1M 779396 779518 (220482) C MIRc#SINE/MIR (141) 127 11 m_b346s601i3 14468 chrXptel1M 779396 CTGAGGC-AATTGGGGTTAAGTGACTTGTCCAGGGTCACACAGCCAGGAA 779444 -v vv i i i i --- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG--- 81 chrXptel1M 779445 ATGTTAAGTGTCTGAGGCCAGATTTGAACTCAGGTCTTCCTGACTTCAGA 779494 ---- v v v vi i i i i ii C MIRc#SINE/MIR 80 ----TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chrXptel1M 779495 GCTGGTACTCTATCCACCGCACCA 779518 v ii i v i C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTGCACCA 11 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 23.55 CpG sites = 15, Kimura (unadjusted) = 24.70 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.07 (8 / 122), avg. gap size = 1.00 (8 / 8) 375 21.83 5.68 1.09 chrXptel1M 779557 779644 (220356) MER63D#DNA/hAT-Tip100 347 438 (623) m_b346s502i1 14469 chrXptel1M 779557 TACACCTCAGAAGCTGGCAAATGCTCCAGAATCAGTCTTTGTTTTGTCAT 779606 v i iii i v - vvi v i ii MER63D#DNA/hA 347 TACACCACGGAAATCGGCAAACGCTACA-AATCAGGGCTTGATTTATTGT 395 chrXptel1M 779607 CTTGTTATCTGTCTAAACTTA-----GTGATGGAGAAAATGTT 779644 i ivi i ----- MER63D#DNA/hA 396 TTTGTTGATTGTCTAGACTTAAGAAAGTGATGGAGAAAATGTT 438 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 21.96 CpG sites = 13, Kimura (unadjusted) = 26.64 Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.02 (2 / 87), avg. gap size = 3.00 (6 / 2) 311 36.17 14.53 0.75 chrXptel1M 780153 780386 (219614) L2b_3end#LINE/L2 195 460 (6) m_b346s601i4 14470 chrXptel1M 780153 TCTTCTTTCCAGGCTCAGTTCCAATTCCATCTTC-CCG---ATTCCTCT- 780197 v i vi v i v vi i i - --- vi i- L2b_3end#LINE 195 TCATCCTTCAGGTCTCAGCTCAAATGTCACCTCCTCCGGGAAGCCCTCCC 244 chrXptel1M 780198 TGGCCACC------------AGTGCCTTCC------CTCCCCAAACTAGA 780229 i v ------------i i i ------ i v iiivv L2b_3end#LINE 245 TGACCCCCCAGGCCGGGTCAGGCGCCCTCCTCTGGGCCCCCCCAGTCCTA 294 chrXptel1M 780230 CTGTGTGAATTTTGGACATACTTACCCATGTACACGTCT------CCTTT 780273 iv iv v i v vi ?v ii ii?v i ------ ivi L2b_3end#LINE 295 CCCTGCCACTCTGGGTTATNATTGTCTGNTTACATGTCTGTCTCCCCCAC 344 chrXptel1M 780274 GAGACAATAGAAATCCCTTGAGACCAGGTACTG-GCTTGCTCTGTTT--- 780319 v -- ivi iii v iv v i - ii iii i--- L2b_3end#LINE 345 TAGAC--TGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCTTGTTCACC 392 chrXptel1M 780320 -CTTTATCCCCAGAGTTTAGCGTAGTACCTAACAAATGGTAGCCACATAA 780368 - v v ii ii ?i ii v ii v i vi i L2b_3end#LINE 393 GCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAG 442 chrXptel1M 780369 TAAATGTTTATCGAGTGA 780386 i i i i L2b_3end#LINE 443 TAAATATTTGTTGAATGA 460 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 51.32 CpG sites = 56, Kimura (unadjusted) = 54.27 Transitions / transversions = 2.00 (56/28) Gap_init rate = 0.05 (11 / 233), avg. gap size = 3.27 (36 / 11) 333 32.41 5.56 0.00 chrXptel1M 780279 780386 (219614) L2a_3end#LINE/L2 398 511 (6) m_b346s601i5 14470 chrXptel1M 780279 AATAGAAATCCCTTGAGACCAGGTACTG--GCTTGCTCTGTTT----CTT 780322 iv iii v iv v v-- ii i i i---- v L2a_3end#LINE 398 AATGTAAGCTCCATGAGGGCAGGGACTTTTGTCTGTTTTGTTCACTGCTG 447 chrXptel1M 780323 TATCCCCAGAGTTTAGCGTAGTACCTAACAAATGGTAGCCACATAATAAA 780372 v ii vii i ii v i v i vi L2a_3end#LINE 448 TATCCCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGGCGCTCAATAAA 497 chrXptel1M 780373 TGTTTATCGAGTGA 780386 i i i i L2a_3end#LINE 498 TATTTGTTGAATGA 511 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 43.41 CpG sites = 24, Kimura (unadjusted) = 45.21 Transitions / transversions = 2.18 (24/11) Gap_init rate = 0.02 (2 / 107), avg. gap size = 3.00 (6 / 2) 565 20.55 0.78 5.69 chrXptel1M 780512 780640 (219360) MIRc#SINE/MIR 5 127 (141) m_b346s601i6 14471 chrXptel1M 780512 GCAAGGTGGCACAATGGATAGAGCACCAGCCCTGAAGTCAGGAGGACCTG 780561 iv ii i v ii v i i i MIRc#SINE/MIR 5 GCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTG 54 chrXptel1M 780562 AGTTCAAGTCTGGTCTCAGACACTTAACACTCCCTAGCCGTGTGACCCTG 780611 i i iv v v v ------- i i MIRc#SINE/MIR 55 GGTTCGAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTGACCTTG 97 chrXptel1M 780612 GGCAAGTCACTTAACCCCAATT-GCCTCAG 780640 i vv v- MIRc#SINE/MIR 98 GGCAAGTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 23.26 CpG sites = 15, Kimura (unadjusted) = 24.34 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.06 (8 / 128), avg. gap size = 1.00 (8 / 8) 354 31.65 6.25 2.79 chrXptel1M 781791 781998 (218002) L2d2_3end#LINE/L2 54 268 (287) m_b346s601i7 14472 chrXptel1M 781791 TTCACGTGCTCTATCTTCCAGCCAAACTTGCCTATCTTCCATATTCCCC- 781839 ? vi i vivi v i - iv - i i - L2d2_3end#LIN 54 TNCACGAACCCTCCGCTCCAGCCAAACTGGTCTA-CTCAC-TGTCCCCCG 101 chrXptel1M 781840 -ATATTCTATGTGC-----CATCTCTGCGCCTTTGCGTATGCTGT-ATTC 781882 - i iv iv i ----- ii vi i i -vii L2d2_3end#LIN 102 AACACGCCTTGCGCNTTCCCGCCTCTGCGCCTTTGCTCACGCCGTTCCCC 151 chrXptel1M 781883 ATGACTGAACTCCGTACCTTCCTCA-CCTCGGCCTCCTA---AAGTCCTA 781928 vi v i v v --- i v- v- v --- i L2d2_3end#LIN 152 CCGCCTGGAATGC---CCTTCCCCTTCCTCT-CCACCTATCCAAATCCTA 197 chrXptel1M 781929 AAC-TCCTTCAAGGCTCAGCTCAAGTGCCGTCTCCCACACCAGACCCTTC 781977 vv - i i ? ii iv iiv ii i i L2d2_3end#LIN 198 CCCATCCTTCAAGGCCCAGCTCAAATNCCACCTCCTCCGTGAAGCCTTCC 247 chrXptel1M 781978 CTGGTCTCCTTAGTTGGGAAT 781998 ii v iii iiv ? i L2d2_3end#LIN 248 CTGACCACTCCAGCCCGNAGT 268 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.08 CpG sites = 42, Kimura (unadjusted) = 44.28 Transitions / transversions = 1.91 (42/22) Gap_init rate = 0.06 (13 / 207), avg. gap size = 1.46 (19 / 13) 187 26.39 13.33 2.59 chrXptel1M 782004 782108 (217892) L2c_3end#LINE/L2 353 468 (10) m_b346s601i8 14472 chrXptel1M 782004 TACATAT-TGTTTGGCCCCAGGAGAATATAAAGTTCCT-----GCAGGAA 782047 ? i - i v- i vv v i i - i ----- i L2c_3end#LINE 353 TACNTGTCTGTCTC-CTCCACTAGACTGTGA-GCTCCTTGAGGGCAGGGA 400 chrXptel1M 782048 CTG-GT-TCATTTGCTTTTTTTATCCCC------TGGCATGCAGTTGGCA 782089 i - - i ii- i v ------ iii v i L2c_3end#LINE 401 CCGTGTCTTATTCA-TCTTTGTATCCCCAGCGCCTGGCACATAGTAGGCG 449 chrXptel1M 782090 ATTAAGAAATGCTTTTTGA 782108 v i v i v L2c_3end#LINE 450 CTCAATAAATGTTTGTTGA 468 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.28 CpG sites = 18, Kimura (unadjusted) = 34.40 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.08 (8 / 104), avg. gap size = 2.12 (17 / 8) 193 30.35 2.86 5.88 chrXptel1M 782086 782190 (217810) C AmnL2-1#LINE/L2 (137) 2476 2375 m_b346s601i9 14473 chrXptel1M 782086 GGCAATTAAGAAATGCTTTTTGATTTGAGCCGAATCTTTAAAAGTGGCTA 782135 vvi v v v v -- v ?i ivi v ? v iivi C AmnL2-1#LINE/ 2476 GGCAAGGGAGAAAAGATATGT--TTTCAGNTGAGATTTGAAANGAGATGG 2429 chrXptel1M 782136 AGAGTTGATGAGGCGGAAA---ACAGAGAAAGTCATCCCCAGAGAGGGAA 782182 i i --- - i iii i --- v v C AmnL2-1#LINE/ 2428 AGAGTCGATGAGGCGGAGAGATACAG-GAAGGCTGTTCC---AGATGGCA 2383 chrXptel1M 782183 AGAGTTAC 782190 i i i C AmnL2-1#LINE/ 2382 GGAGCTGC 2375 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.17 CpG sites = 17, Kimura (unadjusted) = 40.94 Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.07 (7 / 104), avg. gap size = 1.29 (9 / 7) 207 34.67 2.67 0.00 chrXptel1M 782108 782182 (217818) C L2b_3end#LINE/L2 (247) 219 143 m_b346s601i10 14473 chrXptel1M 782108 ATTTGAGCCGAATCTTTAAAAGTGGCTAAGAGTTGATGAGGCGGA-AAAC 782156 i iv i v iii iv i iiv i - iii C L2b_3end#LINE 219 ATTTGAGCTGAGACCTGAAGGATGAGTAGGAGTTGGCCAGGCGAAGAGGT 170 chrXptel1M 782157 AGAGAAAGTCATCCCCAG-AGAGGGAA 782182 i i i v i i vi - C L2b_3end#LINE 169 GGGGAAGGGCGTTCCAGGCAGAGGGAA 143 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 48.86 CpG sites = 20, Kimura (unadjusted) = 51.87 Transitions / transversions = 3.33 (20/6) Gap_init rate = 0.03 (2 / 74), avg. gap size = 1.00 (2 / 2) 22 19.04 0.00 0.00 chrXptel1M 782931 782972 (217028) (T)n#Simple_repeat 1 42 (0) m_b346s252i1 14474 chrXptel1M 782931 TTTTCTTTTTTTCTTTTCTTTTTTCTTTTTATTTATTTATTT 782972 i i i i v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 42 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 17 16.41 0.00 6.82 chrXptel1M 782932 782978 (217022) (TTTA)n#Simple_repeat 1 44 (0) m_b346s252i2 14474 chrXptel1M 782932 TTTCTTTTTTTCTTTTCTTTTTTCTTTTTATTTATTTATTTAATTTA 782978 v v -v v v - v - (TTTA)n#Simpl 1 TTTATTTATTT-ATTTATTTATT-TATTTATTTATTTATTT-ATTTA 44 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.07 (3 / 46), avg. gap size = 1.00 (3 / 3) 12 18.65 5.41 0.00 chrXptel1M 782957 782993 (217007) (TTTAA)n#Simple_repeat 1 39 (0) m_b346s252i3 14475 chrXptel1M 782957 TTTTATTT-ATTT-ATTTAATTTAATAGCCTTTTATTTA 782993 v - - vvvv v (TTTAA)n#Simp 1 TTTAATTTAATTTAATTTAATTTAATTTAATTTAATTTA 39 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 1293 26.57 4.78 3.83 chrXptel1M 783456 783999 (216001) C L1ME5_3end#LINE/L1 (389) 552 4 m_b346s551i0 14476 chrXptel1M 783456 ATAATATTCCATAAAATTCA-ATACCACAATTTTAT-TA-CCATTCTCC- 783501 i i iivi v -vi - i- - i - C L1ME5_3end#LI 552 ATAGTACTCCATGGTGTGCATCCACCACA-TTTTACCTATCCACTCTCCC 504 chrXptel1M 783502 AGTTATGG-CATCCAC-TCAGTTTCAGTTTTTTAGCCACTACAAAGACAC 783549 v - i v- iivi i ii iiii- i v - C L1ME5_3end#LI 503 AGTGATGGACACCCAGGTTGCCTCCAACTCCCC-GCCACCACAAACA-AC 456 chrXptel1M 783550 CCCACAA---ACATTCATTTTATACAGGTCCCTTT-----CCTTCTTTAA 783591 v ii --- i --- ii v i ----- viv v i C L1ME5_3end#LI 455 GCTGCAATGAACATCC---TCGTACATGTCCCCTTATGGACCTGTGTGAG 409 chrXptel1M 783592 GATCTCTTTGGGATATA-AGCCAGTAGAGACACTGCTGGATCAAAAGGGT 783640 i i - v v v iv i i v i vv C L1ME5_3end#LI 408 AATTTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTA 359 chrXptel1M 783641 TGCACGGTTT-TGTAACGGTTTGAGCA--TAGTTCCAAATTGCTCTTCAG 783687 --- v -iv --- vi -- v v i i C L1ME5_3end#LI 358 TGC---GTATACTTAA---TTTGACTAAGTACTGCCAGATTGCTCTCCAG 315 chrXptel1M 783688 AATGGTTGGAGGTATTCACAACTCCACCAACAATGCATCAATGTCCCAGT 783737 i v vvvi ii vii i i v iv i vi C L1ME5_3end#LI 314 AATGGCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTAT 265 chrXptel1M 783738 TTTCCCACATCCCCTCCAACAATCATCATTATTT---TTTCCTGTCATCT 783784 ? i i v v iiv ii--- --- v i C L1ME5_3end#LI 264 NTCCCCACATCCTCGCCAACACTTGGCATTATCCAGCTTTC---TAATTT 218 chrXptel1M 783785 TAGCCAATCTGACAGGTGTGTAGTGGTATCTCAGAGTTGTCTTAATTTGC 783834 v i i i iv i vv i C L1ME5_3end#LI 217 TTGCCAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGC 168 chrXptel1M 783835 ATTTCTCTAATTAATAATGACTTGGAGCATCTTTTCATATGGTTAGAAAT 783884 i v v v i v iv--- C L1ME5_3end#LI 167 ATTTCTCTGATTACTAATGAGTTTGAGCATCTCTTCATATGCTTGT---T 121 chrXptel1M 783885 AG--TTTCAA-TTTCTTCATCTGAGAATTGTCTGTTCATATCCTTTGACC 783931 -- ii- i v vi i v C L1ME5_3end#LI 120 AGCCTTTCGGGTTTCCTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCC 71 chrXptel1M 783932 ATTTATCAATTGGAG--AATGGCTTGATTTTTTTATAAATTAAAGTTAAT 783979 v v i --?vi v -- i vv i v iv -v i C L1ME5_3end#LI 70 ATTTTTCTATTGGGGTTNCCGTCTT--TTTCTTGTTGATTTGCAG-GAGT 24 chrXptel1M 783980 TCTCTATATATTTTGGAAAT 783999 ii i i i v C L1ME5_3end#LI 23 TCCTTGTATATTCTAGATAT 4 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 32.51 CpG sites = 81, Kimura (unadjusted) = 33.73 Transitions / transversions = 1.40 (81/58) Gap_init rate = 0.07 (36 / 543), avg. gap size = 1.31 (47 / 36) 548 26.67 2.17 2.54 chrXptel1M 783852 784128 (215872) C L1M5_orf2#LINE/L1 (0) 3294 3019 m_b346s551i1 14476 chrXptel1M 783852 TGACTTGGAGCATCTTTTCATATGGTTAGAAATAGTTTCAATTTCTTCAT 783901 ?v v i v vviiivi v? v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chrXptel1M 783902 CTGAGAATTGTCTGTTCATATCCTTTGACCATTTATCAATTGGAGAATGG 783951 i v v vi i v v ?v i--- v C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGG---TTG 3198 chrXptel1M 783952 CTTGA--TTTTTTTAT-AAATTAAAGTTAATTCTCTATATATTTTGGAAA 783998 i v-- ? -i ? iv v- i i i v C L1M5_orf2#LIN 3197 TTTGTCTTTTTNTTATTGANTTGTAGG-AGTTCTTTATATATTCTGGATA 3149 chrXptel1M 783999 TGAGGCCTTTATCAGA-ACCTTTGACTGTAAAAATGTTTTCCCAGTTTAT 784047 i v i - iv v -?i i v v i ? i i C L1M5_orf2#LIN 3148 CGAGTCCTTTGTCAGATATATGT-NTTGCAAATATTTTCTCCCANTCTGT 3100 chrXptel1M 784048 TGCTTCCCTTCTAATCTTGTCTGCATTAGTTTTGTTG--GTACAAAAACT 784095 v v i v i v ivi iv - i - -- vi i ii C L1M5_orf2#LIN 3099 GGCTTGCCTTTTCATTTTCTTAACGGT-GTCTT-TTGANGAGCAGAAGTT 3052 chrXptel1M 784096 TTTCAGTTTGATATAGTCGAAATTTTCTATTTT 784128 v v i? v v v v C L1M5_orf2#LIN 3051 TTTAATTTTGATGNAGTCCAATTTATCAATTTT 3019 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.35 CpG sites = 34, Kimura (unadjusted) = 34.49 Transitions / transversions = 0.89 (34/38) Gap_init rate = 0.04 (11 / 276), avg. gap size = 1.18 (13 / 11) 438 26.54 0.80 9.57 chrXptel1M 784346 784470 (215530) MIRb#SINE/MIR 4 118 (150) m_b346s601i11 14477 chrXptel1M 784346 AGGGGCAGCTGGATGGCACAGTGGATAAAGCATCAGCTCTGAAATCAAGA 784395 ---i ii v i ivi i i i iiv MIRb#SINE/MIR 4 AGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGAC 50 chrXptel1M 784396 GGACCCAAGTTTAAA-CCTGGCCTTAAACACTTAACACGTCTTGGCTGTG 784444 i iii ii - i ii iv- -------i i MIRb#SINE/MIR 51 AGACCTGGGTTCGAATCCCGGCTCTGC-CACTTA-------CTAGCTGTG 92 chrXptel1M 784445 TGACCTTGGGCAAGTCACTTAAACCC 784470 i v i MIRb#SINE/MIR 93 TGACCTTGGGCAAGTTACTTAACCTC 118 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.32 CpG sites = 25, Kimura (unadjusted) = 35.23 Transitions / transversions = 5.00 (25/5) Gap_init rate = 0.10 (12 / 124), avg. gap size = 1.00 (12 / 12) 202 24.14 8.62 0.00 chrXptel1M 785790 785847 (214153) MIR3#SINE/MIR 139 201 (7) m_b346s601i12 14478 chrXptel1M 785790 AGATAAGGG---TGAACTAGATGACTTGGAAAGCCGCTTCTAGTTCT-AT 785835 i i --- i ii vv i i v i i - i MIR3#SINE/MIR 139 AAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGAC 188 chrXptel1M 785836 A-TCTATGAATCT 785847 - v MIR3#SINE/MIR 189 ATTCTATGATTCT 201 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.41 CpG sites = 10, Kimura (unadjusted) = 30.41 Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.05 (3 / 57), avg. gap size = 1.67 (5 / 3) 26 18.25 5.26 1.27 chrXptel1M 786148 786223 (213777) (AGAGAG)n#Simple_repeat 1 79 (0) m_b346s252i4 14479 chrXptel1M 786148 AGTGAAAGAG-GGGAGAGACGGAGAGACAGATAGAGAGA-AGA-AGAGAG 786194 v i - i vi v v - - (AGAGAG)n#Sim 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chrXptel1M 786195 AGAGAAAGCAGA-AGGGAGCTAGAGATAGA 786223 i - - i vv v (AGAGAG)n#Sim 51 AGAGAGAG-AGAGAGAGAGAGAGAGAGAGA 79 Matrix = Unknown Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.07 (5 / 75), avg. gap size = 1.00 (5 / 5) 18 15.81 2.70 0.00 chrXptel1M 786229 786245 (213755) (TA)n#Simple_repeat 1 18 (20) m_b346s252i5 14480 chrXptel1M 786229 TATATAT-TCCATATATA 786245 - vi (TA)n#Simple_ 1 TATATATATATATATATA 18 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.06 (1 / 16), avg. gap size = 1.00 (1 / 1) 31 0.00 0.00 0.00 chrXptel1M 786246 786272 (213728) (TG)n#Simple_repeat 1 27 (0) c_b346s251i0 14481 chrXptel1M 786246 TGTGTGTGTGTGTGTGTGTGTGTGTGT 786272 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGT 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 18 15.81 2.70 0.00 chrXptel1M 786273 786291 (213709) (TA)n#Simple_repeat 19 37 (1) m_b346s252i5 14482 chrXptel1M 786273 ATACACATACATATATATA 786291 i i i (TA)n#Simple_ 19 ATATATATATATATATATA 37 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 347 28.34 10.44 3.08 chrXptel1M 786333 786514 (213486) L2d_3end#LINE/L2 322 516 (0) m_b346s601i13 14483 chrXptel1M 786333 TAACATTTA--TATAAAC-ATTTTATATAATCATATCCTCTAATTTATTT 786379 i i -- v -i i i ----- i i -i L2d_3end#LINE 322 TAGCACTTAATTATATACTGTCTTGTAT-----TGTTCTCTAATT-GTTT 365 chrXptel1M 786380 CATGTAATATATACATGTGTA------TAGACCCCAAACTTCTTGAAGGC 786423 ivvv vv v v v------ iivi i i i L2d_3end#LINE 366 CATGTGTGTTAGTCTTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGC 415 chrXptel1M 786424 AGGGAC--TGTTTAAT----TTTTGTCA---CCC-CAGTGTCTGATAGAG 786463 -- i v ---- ? i--- - i i iii v L2d_3end#LINE 416 AGGGACCATGTCTTATACTNTTTTNTCGTTCCCCACAGCGCCTAGCACAG 465 chrXptel1M 786464 TACTTGACACATATTAGACAGTTAATTAATGCTTTTTGATTAACTAACTG 786513 i vii v i iv i v i v i i i i L2d_3end#LINE 466 TGCTGAGCACATAGTAGGCGCTCAATAAATACTTGTTGATTGATTGATTG 515 chrXptel1M 786514 A 786514 L2d_3end#LINE 516 A 516 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.70 CpG sites = 33, Kimura (unadjusted) = 37.55 Transitions / transversions = 1.94 (33/17) Gap_init rate = 0.07 (13 / 181), avg. gap size = 1.92 (25 / 13) 229 14.29 2.38 0.00 chrXptel1M 786572 786613 (213387) C L2d2_3end#LINE/L2 (88) 467 425 m_b346s601i14 14484 chrXptel1M 786572 CATAGTCCCTGCCC-CAAGGAGCTTCCATTCTAGAAGGGGAAA 786613 i - v v vv i C L2d2_3end#LIN 467 CATGGTCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGGAGA 425 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 15.85 CpG sites = 2, Kimura (unadjusted) = 15.85 Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.02 (1 / 41), avg. gap size = 1.00 (1 / 1) 214 13.68 2.13 6.67 chrXptel1M 786575 786621 (213379) C L2a_3end#LINE/L2 (93) 424 380 m_b346s601i15 14484 chrXptel1M 786575 AGTCCCTGCCC-CAAGGAGCTTCCATTCTAGAAGGGGAAAGTAACAGA 786621 - v v vi i ---i C L2a_3end#LINE 424 AGTCCCTGCCCTCATGGAGCTTACATTCTAGTGGGGGGA---GACAGA 380 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 15.11 CpG sites = 3, Kimura (unadjusted) = 15.11 Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.09 (4 / 46), avg. gap size = 1.00 (4 / 4) 201 19.51 2.44 0.00 chrXptel1M 786687 786727 (213273) C L2d2_3end#LINE/L2 (92) 463 422 m_b346s601i16 14485 chrXptel1M 786687 GTCCC-GCCTCCAGGGAGCTTATAGTCTTTTTGGGGAGAAAA 786727 - ii i i i vv v C L2d2_3end#LIN 463 GTCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGGAGACAA 422 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 23.02 CpG sites = 5, Kimura (unadjusted) = 23.02 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 236 27.80 6.16 6.16 chrXptel1M 789589 789864 (210136) C L1M2_orf2#LINE/L1 (2377) 914 639 m_b346s551i2 14486 chrXptel1M 789589 TAAGCATTTGTAAATATAAAGGTTTCTCTAATCACTGCTTTTGTTGTATC 789638 i i i viv vv ii v v? i C L1M2_orf2#LIN 914 TAGGCGTTTATTGCTATAAACTTCCCTCTTAGNACTGCTTTTGCTGTATC 865 chrXptel1M 789639 TCATA-GTTTTGATATGCTGTCACATTATTGTCATTTTCTTTAATGAAAG 789687 i - i i vvivii v vi i - v C L1M2_orf2#LIN 864 CCATAGGTTTTGGTATGTTGTGTTTCCATTTTCATTTGTTTCAA-GAAAT 816 chrXptel1M 789688 TTTTA-------TGATTAAAGAACACCTTAAGCCACTTATTCCTTAAGAC 789730 ?------- vv vvvviv v i v - iv v v i- C L1M2_orf2#LIN 815 TTTTNAATTTCCTTCTTAATTTCTTCATTGACCCA-TTGGTCGTTCAGG- 768 chrXptel1M 789731 TATCAGGTTGTTTAATCTCTACTTCATTTTTAATCTGTTTTTAA---TCT 789777 - v v i i - vi v --?v ii --- i C L1M2_orf2#LIN 767 -AGCATGTTGTTTAATTTCCA-TGTATTTGTA--NAGTTTCCAAAGTTCC 722 chrXptel1M 789778 TCTGTGTCTTTATTAAATGGT--TTTTATTGCATTATGATTTGAAAAGGA 789825 - --- i v vv -- v i i i? - C L1M2_orf2#LIN 721 TCT-TG---TTATTGATTTCTAGTTTTATTCCATTGTGGTCNGAAAA-GA 677 chrXptel1M 789826 TCCTTTGAATAATAAAATTTTAATGT----AAAACTATTGAGA 789864 v ----- i vi ii v ---- vi i C L1M2_orf2#LIN 676 TACT-----TGATATGATTTCGATTTTTTNAAATTTGTTGAGA 639 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 34.50 CpG sites = 35, Kimura (unadjusted) = 35.77 Transitions / transversions = 0.95 (35/37) Gap_init rate = 0.08 (22 / 275), avg. gap size = 1.55 (34 / 22) 323 26.47 0.97 0.97 chrXptel1M 789589 789691 (210309) C L1M1_orf2#LINE/L1 (2380) 914 812 m_b346s551i3 14486 chrXptel1M 789589 TAAGCATTTGTAAATATAAAGGTTTCTCTAATCACTGCTTTTGTTGTATC 789638 i i i iv vv ii v vi i C L1M1_orf2#LIN 914 TAGGCACTTATAGCTATAAACTTCCCTCTTAGTACTGCTTTTGCTGTATC 865 chrXptel1M 789639 TCATA-GTTTTGATATGCTGTCACATTATTGTCATTTTCTTTAATGAAAG 789687 i - i i vvivii i vi i - v C L1M1_orf2#LIN 864 CCATAGGTTTTGGTATGTTGTGTTTCCATTATCATTTGTTTCAA-GAAAT 816 chrXptel1M 789688 TTTT 789691 C L1M1_orf2#LIN 815 TTTT 812 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.68 CpG sites = 17, Kimura (unadjusted) = 33.68 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.02 (2 / 102), avg. gap size = 1.00 (2 / 2) 227 23.36 11.21 0.00 chrXptel1M 792205 792311 (207689) C L1M8_5end#LINE/L1 (9) 2346 2228 m_b346s551i4 14487 chrXptel1M 792205 TTTCAGAAGTGTGTATTGTAAACAACATTGTGTTAGACT--GGTTTGTAA 792252 i iv v v v i v v i i -- v ? C L1M8_5end#LIN 2346 TTTTAGGTGTGTCTCTTGTATACAGCATAGAGTTGGATTTTGCTTTGTNA 2297 chrXptel1M 792253 TCCTTTCT-----TGTTTTGCTTTTG---GATGATTTCATCCCATTTACA 792294 v vv ----- v v i--- i v v v C L1M8_5end#LIN 2296 GCCAATCTGAAAATCTTTTTCTTTTAATAGGTGAGTTAAGCCCATTTACA 2247 chrXptel1M 792295 TTCAGT--TATGATTGATA 792311 i v -- i C L1M8_5end#LIN 2246 TTTATTGATATGATCGATA 2228 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 27.09 CpG sites = 9, Kimura (unadjusted) = 28.32 Transitions / transversions = 0.56 (9/16) Gap_init rate = 0.04 (4 / 106), avg. gap size = 3.00 (12 / 4) 356 27.50 1.25 0.00 chrXptel1M 792330 792409 (207591) MIRc#SINE/MIR 24 104 (164) m_b346s601i17 14488 chrXptel1M 792330 AGAACACTGGGGCAGAAGTCAGGAAGACCTGAGTTCACAT-GTGATCCCA 792378 i iviv i i ivi -vi iii ii MIRc#SINE/MIR 24 AGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTG 73 chrXptel1M 792379 ACATTTACTAGTTGTGAGACCTTGGGTAAGT 792409 v i i v i MIRc#SINE/MIR 74 CCACTTACTAGCTGTGTGACCTTGGGCAAGT 104 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.17 CpG sites = 16, Kimura (unadjusted) = 36.28 Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.01 (1 / 79), avg. gap size = 1.00 (1 / 1) 25 26.33 5.49 1.05 chrXptel1M 792426 792516 (207484) (AG)n#Simple_repeat 1 95 (0) m_b346s252i6 14489 chrXptel1M 792426 AGAGAGAAATGGGAGAGAGAAAAGGGGACAGAAAG-GGGGGAGAGAGA-A 792473 i - i i ii i v i - i i - (AG)n#Simple_ 1 AGAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 49 chrXptel1M 792474 GA-AGAGAAAG-GGGAGACAGTGACAGAGAG-GGGGGAAGGAGAGA 792516 - i - i v v v - i i ii (AG)n#Simple_ 50 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 95 Matrix = Unknown Transitions / transversions = 3.75 (15/4) Gap_init rate = 0.07 (6 / 90), avg. gap size = 1.00 (6 / 6) 14 11.93 0.00 10.00 chrXptel1M 793634 793677 (206323) (AAATTAA)n#Simple_repeat 1 40 (0) m_b346s252i7 14490 chrXptel1M 793634 AAATTAAAAATTAAAAGTAATTAAAAGTAATCAATTAAACAATT 793677 - -- i v vv - (AAATTAA)n#Si 1 AAATTAAAAATT-AAA--AATTAAAAATTAAAAATTAAA-AATT 40 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.09 (4 / 43), avg. gap size = 1.00 (4 / 4) 63 29.06 3.11 5.85 chrXptel1M 793635 794020 (205980) (AATT)n#Simple_repeat 1 376 (0) m_b346s252i8 14490 chrXptel1M 793635 AATTAA-AAATTAA--AAGTAATTAA--AAGTAATCAATTAAACAATTGA 793679 -v -- v -- v i vi i (AATT)n#Simpl 1 AATTAATTAATTAATTAATTAATTAATTAATTAATTAATTAATTAATTAA 50 chrXptel1M 793680 TTAACCGATAAAATTATGTGAATAAGGCAATATATTTATTTAA--AATGA 793727 iii -v -i v v ivi - v v -- v (AATT)n#Simpl 51 TTAATTAAT-TAATTA-ATTAATTAATTAAT-TAATTAATTAATTAATTA 97 chrXptel1M 793728 ATCAATTAATTAAAAGGTCAATTAAATAATGAAATGACATGAA-TAATAC 793776 i vvii i v -v v - v - -i (AATT)n#Simpl 98 ATTAATTAATTAATTAATTAATTAATTAAT-TAATTA-ATTAATTAAT-T 144 chrXptel1M 793777 AATATAATATAATTAATTACAATCACTCAACTAATTAGATAAGCAATGGA 793826 - - -- i v i i iv vi -v (AATT)n#Simpl 145 AAT-TAAT-TAATTAATT--AATTAATTAATTAATTAATTAATTAAT-TA 189 chrXptel1M 793827 TTTGCATAGATGAGATAATATAATTATTTAGTTATTCAGTTAATTGATAA 793876 v -v vi v iv - v i v i i i -v (AATT)n#Simpl 190 ATT-AATTAATTAATTAAT-TAATTAATTAATTAATTAATTAATTAAT-T 236 chrXptel1M 793877 AATTAATTGACTGA-TAAACAGTGCAATTGCATGAATAAGGTAATATAAT 793925 i i i - vi i -i -v v v iv - (AATT)n#Simpl 237 AATTAATTAATTAATTAATTAAT-TAATT-AATTAATTAATTAAT-TAAT 283 chrXptel1M 793926 TATTTAA--AATTAATCAATTAGTTAA-AGATAAACTAAATAATAAAATT 793972 v -- i i -vi v i v -v (AATT)n#Simpl 284 TAATTAATTAATTAATTAATTAATTAATTAATTAATTAATTAAT-TAATT 332 chrXptel1M 793973 GCACAAATAATATAATATAATTAATTGAAATTGATTGCTTAATTAATT 794020 ivvi v - - -- i iv (AATT)n#Simpl 333 AATTAATTAAT-TAAT-TAATTAATT--AATTAATTAATTAATTAATT 376 Matrix = Unknown Transitions / transversions = 0.93 (40/43) Gap_init rate = 0.08 (30 / 385), avg. gap size = 1.13 (34 / 30) 19 21.10 6.90 3.33 chrXptel1M 793911 793997 (206003) (ATAAT)n#Simple_repeat 1 90 (0) m_b346s252i9 14491 chrXptel1M 793911 ATAAGGTAATATAAT-T-ATTTAAAATTAAT-CAAT-TAGTTAAAGATAA 793956 vi - - v v - -i - i vv v (ATAAT)n#Simp 1 ATAATATAATATAATATAATATAATA-TAATATAATATAATATAATATAA 49 chrXptel1M 793957 ACTAA-ATAATAAAATTGCACAAATAATATAATATAAT-TAAT 793997 vv - v - ii - v - (ATAAT)n#Simp 50 TATAATATAATATAA-TATA-ATATAATATAATATAATATAAT 90 Matrix = Unknown Transitions / transversions = 0.50 (5/10) Gap_init rate = 0.10 (9 / 86), avg. gap size = 1.00 (9 / 9) 14 11.93 0.00 10.00 chrXptel1M 793634 793677 (206323) (AAATTAA)n#Simple_repeat 1 40 (0) m_b346s252i7 14490 chrXptel1M 793634 AAATTAAAAATTAAAAGTAATTAAAAGTAATCAATTAAACAATT 793677 - -- i v vv - (AAATTAA)n#Si 1 AAATTAAAAATT-AAA--AATTAAAAATTAAAAATTAAA-AATT 40 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.09 (4 / 43), avg. gap size = 1.00 (4 / 4) 63 29.06 3.11 5.85 chrXptel1M 793635 794020 (205980) (AATT)n#Simple_repeat 1 376 (0) m_b346s252i8 14490 chrXptel1M 793635 AATTAA-AAATTAA--AAGTAATTAA--AAGTAATCAATTAAACAATTGA 793679 -v -- v -- v i vi i (AATT)n#Simpl 1 AATTAATTAATTAATTAATTAATTAATTAATTAATTAATTAATTAATTAA 50 chrXptel1M 793680 TTAACCGATAAAATTATGTGAATAAGGCAATATATTTATTTAA--AATGA 793727 iii -v -i v v ivi - v v -- v (AATT)n#Simpl 51 TTAATTAAT-TAATTA-ATTAATTAATTAAT-TAATTAATTAATTAATTA 97 chrXptel1M 793728 ATCAATTAATTAAAAGGTCAATTAAATAATGAAATGACATGAA-TAATAC 793776 i vvii i v -v v - v - -i (AATT)n#Simpl 98 ATTAATTAATTAATTAATTAATTAATTAAT-TAATTA-ATTAATTAAT-T 144 chrXptel1M 793777 AATATAATATAATTAATTACAATCACTCAACTAATTAGATAAGCAATGGA 793826 - - -- i v i i iv vi -v (AATT)n#Simpl 145 AAT-TAAT-TAATTAATT--AATTAATTAATTAATTAATTAATTAAT-TA 189 chrXptel1M 793827 TTTGCATAGATGAGATAATATAATTATTTAGTTATTCAGTTAATTGATAA 793876 v -v vi v iv - v i v i i i -v (AATT)n#Simpl 190 ATT-AATTAATTAATTAAT-TAATTAATTAATTAATTAATTAATTAAT-T 236 chrXptel1M 793877 AATTAATTGACTGA-TAAACAGTGCAATTGCATGAATAAGGTAATATAAT 793925 i i i - vi i -i -v v v iv - (AATT)n#Simpl 237 AATTAATTAATTAATTAATTAAT-TAATT-AATTAATTAATTAAT-TAAT 283 chrXptel1M 793926 TATTTAA--AATTAATCAATTAGTTAA-AGATAAACTAAATAATAAAATT 793972 v -- i i -vi v i v -v (AATT)n#Simpl 284 TAATTAATTAATTAATTAATTAATTAATTAATTAATTAATTAAT-TAATT 332 chrXptel1M 793973 GCACAAATAATATAATATAATTAATTGAAATTGATTGCTTAATTAATT 794020 ivvi v - - -- i iv (AATT)n#Simpl 333 AATTAATTAAT-TAAT-TAATTAATT--AATTAATTAATTAATTAATT 376 Matrix = Unknown Transitions / transversions = 0.93 (40/43) Gap_init rate = 0.08 (30 / 385), avg. gap size = 1.13 (34 / 30) 24 16.28 0.00 0.00 chrXptel1M 801084 801124 (198876) (AC)n#Simple_repeat 1 41 (0) m_b346s252i10 14492 chrXptel1M 801084 ACACAGACACACAGACACACACGGACACACACGGACACACA 801124 v v iv iv (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACA 41 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 13 28.86 0.00 6.06 chrXptel1M 801182 801251 (198749) (ACAAAAC)n#Simple_repeat 1 66 (0) m_b346s252i11 14493 chrXptel1M 801182 ACAAAAGAGACAGACAAATCACACAGAACACAGAACACACAGTCACAACA 801231 v v - i v vv i i - iv - (ACAAAAC)n#Si 1 ACAAAACACA-AAACACAAAACACAAAACACAAAACACA-AAACACAA-A 47 chrXptel1M 801232 TTAAACAAACATATAACACA 801251 vi v - i v (ACAAAAC)n#Si 48 ACACA-AAACACAAAACACA 66 Matrix = Unknown Transitions / transversions = 0.67 (6/9) Gap_init rate = 0.06 (4 / 69), avg. gap size = 1.00 (4 / 4) 18 19.28 6.78 0.00 chrXptel1M 801195 801253 (198747) (ACACATA)n#Simple_repeat 1 63 (0) m_b346s252i12 14493 chrXptel1M 801195 ACAAATCACACAGAACACAGAACACA-CAGTCACAACA-TTAA-ACA-AA 801240 v v v v -v vv i -v - - (ACACATA)n#Si 1 ACACATAACACATAACACATAACACATAACACATAACACATAACACATAA 50 chrXptel1M 801241 CATATAACACATA 801253 i (ACACATA)n#Si 51 CACATAACACATA 63 Matrix = Unknown Transitions / transversions = 0.25 (2/8) Gap_init rate = 0.07 (4 / 58), avg. gap size = 1.00 (4 / 4) 12 23.27 0.00 0.00 chrXptel1M 805587 805621 (194379) (TTTCTA)n#Simple_repeat 1 35 (0) m_b346s252i13 14494 chrXptel1M 805587 TTTCTATTGATTTTTTAATTTCTATTTTTCTTTCT 805621 vv v iv i v (TTTCTA)n#Sim 1 TTTCTATTTCTATTTCTATTTCTATTTCTATTTCT 35 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 15 5.56 0.00 0.00 chrXptel1M 805712 805730 (194270) (T)n#Simple_repeat 1 19 (0) m_b346s252i14 14495 chrXptel1M 805712 TTTCTTTTTTTTTTTTTTT 805730 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 15 27.04 1.35 5.63 chrXptel1M 806394 806467 (193533) (GTATAG)n#Simple_repeat 1 71 (0) m_b346s252i15 14496 chrXptel1M 806394 GTATATGTGTATATTTATAGACGTCTCTGTATAGCT-TAGCTCTATGTGT 806442 - - vv -- v vv v - v v v i (GTATAG)n#Sim 1 GTATA-G-GTATAGGTATAG--GTATAGGTATAGGTATAGGTATAGGTAT 46 chrXptel1M 806443 AGCTATCGGTATAGGTACATCTATA 806467 v v i vv (GTATAG)n#Sim 47 AGGTATAGGTATAGGTATAGGTATA 71 Matrix = Unknown Transitions / transversions = 0.15 (2/13) Gap_init rate = 0.07 (5 / 73), avg. gap size = 1.00 (5 / 5) 266 26.06 19.85 1.24 chrXptel1M 807977 808112 (191888) C MIR3#SINE/MIR (35) 173 13 m_b346s601i18 14497 chrXptel1M 807977 GATTTTGAACATCATCTCATCTAGTTCCTTGGTTCCATAG----GAAAAC 808022 ii ii v vi i iii i vi ii i ---- i C MIR3#SINE/MIR 173 GACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAAC 124 chrXptel1M 808023 --AGCCCCAGAGAGTTAATGT--------CAGGGCCACA-------TCGG 808055 -- v v i v -------- i i ------- ii C MIR3#SINE/MIR 123 TGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAG 74 chrXptel1M 808056 TGCCA-AGCC----CT-GAATCTCGGTCTTCTGACTCCCAGGCCAGTGCT 808099 v - ---- - i iv i v - C MIR3#SINE/MIR 73 TGGCAGAGCCGGGACTAGAACCCAGGTCTCCTGACTCCCAGTCC-GTGCT 25 chrXptel1M 808100 CTTCCCGGATCAG 808112 - i v v C MIR3#SINE/MIR 24 C-TCTCTGCTCAG 13 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.50 CpG sites = 24, Kimura (unadjusted) = 33.50 Transitions / transversions = 2.18 (24/11) Gap_init rate = 0.07 (9 / 135), avg. gap size = 3.22 (29 / 9) 373 21.73 9.77 6.57 chrXptel1M 808226 808358 (191642) MIRc#SINE/MIR 10 146 (122) m_b346s601i19 14498 chrXptel1M 808226 GTGGTGCAGTGCATCTAGAGTGCTGGACGCAGACTC------ATC----- 808264 v --v ii vii v ------ i ----- MIRc#SINE/MIR 10 GTGGTGCAGTGGA--AAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGT 57 chrXptel1M 808265 TCGAGTTCCAA-TCTGCCTTCAGATGCTAGCAGTGTGACACGAGCAGGTA 808313 i ii- --- vv i v vi---ii i MIRc#SINE/MIR 58 TCGAGTCCCGGCTCTGC---CACTTACTAGCTGTGTGACCT---TGGGCA 101 chrXptel1M 808314 GGTCACTTAACCCTTTTTA-CCTCAGTTTCCCTCATTTGTAAAATG 808358 i ii i v - - i MIRc#SINE/MIR 102 AGTCACTTAACCTCTCTGAGCCTCAGTTT-CCTCATCTGTAAAATG 146 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 25.34 CpG sites = 18, Kimura (unadjusted) = 26.46 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.10 (13 / 132), avg. gap size = 1.69 (22 / 13) 21 21.54 0.00 0.00 chrXptel1M 808480 808519 (191481) (T)n#Simple_repeat 1 40 (0) m_b346s252i16 14499 chrXptel1M 808480 TTCTTTCTTTTTTTTTCCTTTCCTTTTCTTTTTTTTTTTT 808519 i i ii ii i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 40 Matrix = Unknown Transitions / transversions = 1.00 (7/0) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 12 34.03 0.00 1.85 chrXptel1M 809076 809130 (190870) (AATAC)n#Simple_repeat 1 54 (0) m_b346s252i17 14500 chrXptel1M 809076 AATATAGTACAATACAGAGTAATGCAGCACCACACAACTCAAAACAATAC 809125 i i ivii i ii v i iv v (AATAC)n#Simp 1 AATACAATACAATACAATACAATACAATACAATACAATACAATACAATAC 50 chrXptel1M 809126 ACATA 809130 - (AATAC)n#Simp 51 A-ATA 54 Matrix = Unknown Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1) 204 26.06 5.50 8.49 chrXptel1M 809144 809252 (190748) C L2d2_3end#LINE/L2 (49) 506 401 m_b346s601i20 14501 chrXptel1M 809144 CTGTGCTAAGTGC---AAAGGATACACAGAAGAAAAGTA-AAGACA--AT 809187 i i ---iii v ----- - --i C L2d2_3end#LIN 506 CTGTGCTAGGCGCTGTGGGGGATACAAAG-----AAGTATAAGACATGGT 462 chrXptel1M 809188 TCCTCCCTTTGAGGGTTATAAAAGCTAACAGGGAAAGACAACACACAAAA 809237 i v i ii iviv v v iiv -i v i - C L2d2_3end#LIN 461 CCCTGCCCTCAAGGAGCTTACAATCTAGTTGGG-GAGACAAGACATAAA- 414 chrXptel1M 809238 GCAAGCTAAAAAGTT 809252 - v - i C L2d2_3end#LIN 413 -CACG-TGAAAAGTT 401 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.51 CpG sites = 17, Kimura (unadjusted) = 33.07 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.11 (12 / 108), avg. gap size = 1.25 (15 / 12) 11 9.73 8.57 2.70 chrXptel1M 809869 809903 (190097) (TCCTCAC)n#Simple_repeat 1 37 (0) m_b346s252i18 14502 chrXptel1M 809869 TCC-CAC-CCTCACTTC-CAGTTCCTCACTCCTCCCTC 809903 - - i - -i v (TCCTCAC)n#Si 1 TCCTCACTCCTCACTCCTCA-CTCCTCACTCCTCACTC 37 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.12 (4 / 34), avg. gap size = 1.00 (4 / 4) 89 39.37 1.32 3.08 chrXptel1M 812206 812465 (187535) (TCCC)n#Simple_repeat 1 259 (261) m_b346s252i19 14503 chrXptel1M 812206 TCCCTGCCTCTCTTTTCCCCTCCCATTCCTCCCTCCCCTCCCTCCCTTCC 812255 v i iiii - i - i (TCCC)n#Simpl 1 TCCCTCCCTCCCTCCCTCCCTCCC-TCCCTCCCT-CCCTCCCTCCCTCCC 48 chrXptel1M 812256 CCTTTCCTTCTCT-TTTCTTTCCTTCCTTTTCCTTCCTCCCTTCCTCTCC 812304 i ii i i -ii ii i -i i i i i i (TCCC)n#Simpl 49 TCCCTCCCTCCCTCCCTCCCTCCCTCC-CTCCCTCCCTCCCTCCCTCCCT 97 chrXptel1M 812305 CCCTCTGTCCTTTTCTCTCT-TTTCCTTTCTTCCTTCTTTCCCTCCTTTC 812353 iv i ii i -ii i i i i ii i i (TCCC)n#Simpl 98 CCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCC 147 chrXptel1M 812354 CTGCCCTCTCTCCTTCCTTCTTTTCCTCCACCTTTCCCACTCTCCC-CCC 812402 - i i i ii i vi ii v i - (TCCC)n#Simpl 148 CT-CCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCC 196 chrXptel1M 812403 TTCTTTCTTCCCTTCCCTCCCT-TCTTTTTCCCCCTCCTTCCTCCCTCCC 812451 i i i i - -i iii i - i (TCCC)n#Simpl 197 TCCCTCCCTCCC-TCCCTCCCTCCCTCCCTCCCTC-CCTCCCTCCCTCCC 244 chrXptel1M 812452 TTTC-CCCTTTCTCC 812465 ii - ii (TCCC)n#Simpl 245 TCCCTCCCTCCCTCC 259 Matrix = Unknown Transitions / transversions = 15.50 (62/4) Gap_init rate = 0.04 (11 / 259), avg. gap size = 1.00 (11 / 11) 86 5.21 2.36 2.36 chrXptel1M 812466 812592 (187408) (TCCT)n#Simple_repeat 1 127 (0) c_b346s251i1 14504 chrXptel1M 812466 TCCTTTCTTTCTTCCTTTCCTTCCTTCCTTCCTTCCTTCCTTCCCTTCCT 812515 i i - - (TCCT)n#Simpl 1 TCCTTCCTTCCTTCC-TTCCTTCCTTCCTTCCTTCCTTCCTT-CCTTCCT 48 chrXptel1M 812516 TCCTTCCCTTCCTTCC-TCCCTCCTTCCTTTCTTCCTTTCTTCCTTCCTT 812564 - - i i i (TCCT)n#Simpl 49 TCCTT-CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 97 chrXptel1M 812565 CCTTCCTTCCCTCCTT-C-TCCTTCCTTCC 812592 i - - (TCCT)n#Simpl 98 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 127 Matrix = Unknown Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.05 (6 / 126), avg. gap size = 1.00 (6 / 6) 89 39.37 1.32 3.08 chrXptel1M 812593 812843 (187157) (TCCC)n#Simple_repeat 260 504 (16) m_b346s252i19 14505 chrXptel1M 812593 CTTCTTTCTTCCCTCTCTTCTTTTTTTACCTTCTTTTCTTCCTTTCATCC 812642 i i i i - i ii iii v i i ii i ii vi (TCCC)n#Simpl 260 CTCCCTCCCTCCCTC-CCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCC 308 chrXptel1M 812643 TTTTACCCTCTCTCCC-ACCTCCTCCCCTCCCTCCTTCCTTTTCTCTTTT 812691 iiiv i -v ii i i ii ii i (TCCC)n#Simpl 309 TCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTC 358 chrXptel1M 812692 CCTTTCTTCTTTCCATCCTCATTCCCTCCCTCCCT-ACTCCTCTCTCCCC 812740 ii i i i vi vi -v - i i (TCCC)n#Simpl 359 CCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCC-CTCCCTCC 407 chrXptel1M 812741 CTTTTTCTCTCTTTTCCTTTCTTCCATCTCTCCCTGCTTCCCTGCCTCGC 812790 iii i -ii i i i v i v i v - (TCCC)n#Simpl 408 CTCCCTCCCTC-CCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTC-C 455 chrXptel1M 812791 TCTCATTTCCTCTTTCCCTCACACTTTCTCTCTCCCTCCCTCCATCTTTC 812840 - vi i ii - - ii i v ii (TCCC)n#Simpl 456 -CTCCCTCCCTCCCTCCCTC-C-CTCCCTCCCTCCCTCCCTCCCTCCCTC 502 chrXptel1M 812841 TTC 812843 -i (TCCC)n#Simpl 503 -CC 504 Matrix = Unknown Transitions / transversions = 5.08 (61/12) Gap_init rate = 0.04 (10 / 250), avg. gap size = 1.00 (10 / 10) 71 0.00 1.41 1.41 chrXptel1M 812844 812914 (187086) (CCTT)n#Simple_repeat 1 71 (0) c_b346s251i2 14506 chrXptel1M 812844 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 812893 (CCTT)n#Simpl 1 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 50 chrXptel1M 812894 TT-CTTCCTTCCCTTCCTTCCT 812914 - - (CCTT)n#Simpl 51 TTCCTTCCTT-CCTTCCTTCCT 71 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.03 (2 / 70), avg. gap size = 1.00 (2 / 2) 89 39.37 1.32 3.08 chrXptel1M 812915 812930 (187070) (TCCC)n#Simple_repeat 505 519 (1) m_b346s252i19 14507 chrXptel1M 812915 CCCTCTCCCCCATCCC 812930 - i v (TCCC)n#Simpl 505 CCCTC-CCTCCCTCCC 519 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.07 (1 / 15), avg. gap size = 1.00 (1 / 1) 22 16.17 4.00 1.96 chrXptel1M 813206 813255 (186745) (AT)n#Simple_repeat 1 51 (0) m_b346s252i20 14508 chrXptel1M 813206 ATATATAT-TAAATATGATAAATGT-TAAATATAAATATATATACATATT 813253 - v - v i - v v i v (AT)n#Simple_ 1 ATATATATATATATAT-ATATATATATATATATATATATATATATATATA 49 chrXptel1M 813254 TA 813255 (AT)n#Simple_ 50 TA 51 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.06 (3 / 49), avg. gap size = 1.00 (3 / 3) 309 31.40 0.00 0.00 chrXptel1M 813628 813713 (186287) C L1ME2z_3end#LINE/L1 (673) 518 433 m_b346s551i5 14509 chrXptel1M 813628 TTTCCCCATTCTCCAATTGATGGGCATCCATTCAGTTTCTGGTTTCTAGC 813677 vi vi i i iivv v ii i i C L1ME2z_3end#L 518 TTTATCCATTCTCCTGTTGATGGACACCTGGGCTGTTTCCAGTTTTTGGC 469 chrXptel1M 813678 CACTATAAAAAGGGCTGCCACAAACATTTTTACACA 813713 i i i v ii i ii i ii C L1ME2z_3end#L 468 TATTATGAATAAAGCTGCTATGAACATTCTTGTACA 433 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 44.60 CpG sites = 21, Kimura (unadjusted) = 44.60 Transitions / transversions = 3.50 (21/6) Gap_init rate = 0.00 (0 / 85), avg. gap size = 0.0 (0 / 0) 1629 27.08 1.88 3.34 chrXptel1M 814281 814918 (185082) C L1ME3G_3end#LINE/L1 (292) 632 4 m_b347s551i1 14510 chrXptel1M 814281 CCTGCTCGTTTCACTCAGCATCAGTTCGTGTAAGTCTCTCCAGGCCTTTC 814330 i iv i vi vv v v ii i v i vv v C L1ME3G_3end#L 632 CTTGCTTTTTTCACTCAACAATATGTCTTGGAGATCTTTCCATGTCAGTA 583 chrXptel1M 814331 TATAT---TCGTCCTGATGGTCATTTCTTACAGA-ACACTAATATTCCAT 814376 i --- vv v -- - i v ? v-i - i C L1ME3G_3end#L 582 CATATAGATCTACCTCAT--TC-TTTTTAACNGCTGCA-TAGTATTCCAT 537 chrXptel1M 814377 AAAATTCATATACCATAATTTATTCAGCCATTCTCCAATTGATGGGCATC 814426 iv vv i i i v i i C L1ME3G_3end#L 536 AGTATGGATATACCATAATTTATTTAACCATTCCCCTATTGATGGACATT 487 chrXptel1M 814427 CAT-TCATTGTCCAGTTTCTAGCCACTACAAACAGGGCTGCCACAAACAT 814475 i v- ii - i i v i i iv v ii C L1ME3G_3end#L 486 TAGGTTGTT-TCCAATTTTTCGCTATTACAAACAATGCTGCAATGAACAT 438 chrXptel1M 814476 TCTTGCACATGTGGGTCCCT-TACCCTTCTTT-AGTATCTCTTTGGGGTA 814523 i i i?-- i - i v v v vi- i ? i i C L1ME3G_3end#L 437 CCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATTTCTNTAGGATA 390 chrXptel1M 814524 TAAGCCCAGTAGAAACAGTGCTGGGTCAAAGGGTATGCACAGTTTGATAA 814573 v v? ? v viiv v i v --- C L1ME3G_3end#L 389 GATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGCATTT---TAA 343 chrXptel1M 814574 CTTTTTGAGCATAGTTCCAAATTGCTCTCCAGAATGACTAGGTGTATTCA 814623 v viviv v v i i ? i iviivv i C L1ME3G_3end#L 342 ATTTTAATAGATACTGCCAAATTGCCCTCCAAAANGGCTGTACCAATTTA 293 chrXptel1M 814624 CAATTCCACTAACAATGTATTAGTGTCCCTGTTTTCCTGCATCCCCTCCA 814673 v i i i i v v v i i ii i i v C L1ME3G_3end#L 292 CACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCACACCCTCGCCA 243 chrXptel1M 814674 ACATTCATCATTAT--GTTTTTTTCTGTCATTCTAGCCAATCTGACAGGT 814721 i ?ivi --i?i ----vv i v ii C L1ME3G_3end#L 242 ACACTNGATATTATCAANCTTTT----AAATTTTTGCCAATCTGATGGGT 197 chrXptel1M 814722 GTGTAGTGGTATCTCAGAGTTGTCTTAATTTGCATTTCTCTGATCAATAG 814771 viv i vv i i i v C L1ME3G_3end#L 196 GAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGATTACTAG 147 chrXptel1M 814772 TGATTTGGACCACCTGTTCATATG---AGTGGAAATAATTTCAGTTTTAT 814818 vv v v i v --- v ---iv vvi iv C L1ME3G_3end#L 146 TGAGGTTGAGCATCTTTTCATATGTTTATTGG---CCATTTGTATTTCCT 100 chrXptel1M 814819 CATCTGAAAATTGTCTGTTCATAACTTTTGACCATTTGTCAGTTGAAGAA 814868 v vi i v i v v vi -- iv C L1ME3G_3end#L 99 CTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTG--GGT 52 chrXptel1M 814869 TGGCTTGATTTCTTATAAATTAGAGTCAATTCTCTATATATTTTGGAAAT 814918 v -- vi v vivv i i i v C L1ME3G_3end#L 51 TGTCTT--TTTCTTATTGATTTGTAGGAGTTCTTTATATATTCTGGATAT 4 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.82 CpG sites = 86, Kimura (unadjusted) = 34.58 Transitions / transversions = 1.06 (86/81) Gap_init rate = 0.04 (28 / 637), avg. gap size = 1.18 (33 / 28) 604 29.01 5.34 5.84 chrXptel1M 814818 815454 (184546) C L1M5_orf2#LINE/L1 (46) 3248 2615 m_b347s551i2 14510 chrXptel1M 814818 TCATCTGAAAATTGTCTGTTCATAACTTTTGACCATTTGTCAGTTGAA-- 814865 v i vi v viv v v ?vi ii-- C L1M5_orf2#LIN 3248 TCTTTTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTT 3199 chrXptel1M 814866 GAATGGCTTGATTTCTTAT-AAATTAGAGTCAATTCTCTATATATTTTGG 814914 vv v -- ? -i ? iv -v i i i C L1M5_orf2#LIN 3198 GTTTGTCTT--TTTNTTATTGANTTGTAG-GAGTTCTTTATATATTCTGG 3152 chrXptel1M 814915 AAATGAGGCCTTTTTCAGA---ACCTTTAGCTGTAAAAATGTTTTCCCAT 814961 v i v v --- iv ? --- i v v i ? C L1M5_orf2#LIN 3151 ATACGAGTCCTTTGTCAGATATATGTNT---TGCAAATATTTTCTCCCAN 3105 chrXptel1M 814962 T-TATTGCTTCCCTTCTAATCCTGTATGCATTACGCATTAGTTTTATTTG 815010 - i v v i v ii v ----- v ----- v iv C L1M5_orf2#LIN 3104 TCTGTGGCTTGCCTTTTCATTTTCT-----TAACG-----GTGTCTTTTG 3065 chrXptel1M 815011 TA---CAAAAGCTTTTTAACTTAATATAATCAAA-------ACTTTCTAT 815050 v?--- i i v vi i i? i v ------- i i v C L1M5_orf2#LIN 3064 ANGAGCAGAAGTTTTTAATTTTGATGNAGTCCAATTTATCAATTTTTTCT 3015 chrXptel1M 815051 TTTGTGATCAGTAATGACCTGTAGTTCT-TTGGTCACAAATTTCTTCCTC 815099 i i i? iv v-ii - i - -- v v i i v v C L1M5_orf2#LIN 3014 TTTATGGTTNGTGCTT-TTTGT-GTCCTGTT--TAAGAAATCTTTGCCTA 2969 chrXptel1M 815100 CTCCACAGGT-GTGAGAGGTAAACTATCCTATGTT--CTTCTA--ATTTA 815144 ?i - -ii - i --i v -- -- v - C L1M5_orf2#LIN 2968 NCCCA-AGGTCACGA-AGATA--TTCTCCTATGTTTTCTTCTAGAAGTT- 2924 chrXptel1M 815145 TTTATAATTTCATTCTTTATGCCTAGATC-ATGACCCCATTTTCATCTTA 815193 - i i ?ii iiii i - i - i ?v vi v C L1M5_orf2#LIN 2923 -TTATAGTTTTANCTTTTACATTTAGGTCTATGATCC-ATCTNGAATTAA 2876 chrXptel1M 815194 TCTTGATGTACGGTGTTAAGTGTGGGTCAATGCCTAGTTTCTGCCATACT 815243 i vi i v i iv i v?iii v i v iv C L1M5_orf2#LIN 2875 TTTTTGTGTATGGTGTGAGGTAGGGGTCGAGNTTCATTTTTTTCCATATG 2826 chrXptel1M 815244 AATTTCCAATTTTCCCAGTAATTTTTGTCAAACAGTGAGTTCTTATCCCA 815293 i v v i i viv ii v vvvi i vi C L1M5_orf2#LIN 2825 GATATCCAATTGTTCCAGCACCATTTGTTGAAAAGACTATCCTTTCCCCA 2776 chrXptel1M 815294 --AAACTTGGGGTTTTGGGG--TTTGTCAAACACTAGATTATTAAAGTTA 815339 --i i ---- i? vi-- v ii i? v?ii v -- C L1M5_orf2#LIN 2775 CTGAATT----GCNTTGGCACCTTTGTCAAAAATCAANTGNCCATA--TA 2732 chrXptel1M 815340 TTGACTGTTTTGTCTTTTGAAA---CTAACCTATTCCACTGATCTACTAG 815386 vviiv v i i - i i v--- vi i i i v C L1M5_orf2#LIN 2731 TGTGTGGGTCTAT-TTCTGGACTCTCTATTCTGTTCCATTGATCTATTTG 2683 chrXptel1M 815387 TCTATTTCTTA-GCCAATACCAAATGGTTTTGGTAACCACTGCTTTATAA 815435 i- - v iv i i v iiiv - C L1M5_orf2#LIN 2682 TCTATC-CTTACGCCAATACCACACTGTCTTGATTACTGTAGCTTTATA- 2635 chrXptel1M 815436 TATAAGTTT--AGATCTGGTA 815454 - i -- ? ? C L1M5_orf2#LIN 2634 -ATAAGTCTTGANATCNGGTA 2615 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.24 CpG sites = 101, Kimura (unadjusted) = 39.11 Transitions / transversions = 1.38 (101/73) Gap_init rate = 0.08 (53 / 636), avg. gap size = 1.34 (71 / 53) 15 24.85 1.85 1.85 chrXptel1M 815866 815919 (184081) (AAAATG)n#Simple_repeat 1 54 (0) m_b347s252i1 14511 chrXptel1M 815866 AAAATGAGAAAGAAAA-CAAAATGCAAGTAAACATTAACAAAAAGAATGA 815914 i v -v v i i v v - vi i (AAAATG)n#Sim 1 AAAATGAAAATGAAAATGAAAATGAAAATGAAAATGAA-AATGAAAATGA 49 chrXptel1M 815915 AAATG 815919 (AAAATG)n#Sim 50 AAATG 54 Matrix = Unknown Transitions / transversions = 0.83 (5/6) Gap_init rate = 0.04 (2 / 53), avg. gap size = 1.00 (2 / 2) 323 31.93 2.55 2.55 chrXptel1M 816074 816269 (183731) C L1MC4a_3end#LINE/L1 (2003) 626 431 m_b347s551i3 14512 chrXptel1M 816074 TTTCACTCAGCATCAGTTCGTGTAAGTCTCTCCAGACC---TCTCTGAAA 816120 i i vi vv v v i v v i --- viv i C L1MC4a_3end#L 626 TTTCACTTAACAATATATCCTGGAAATCACTCCATATCAGTTCATAGAGA 577 chrXptel1M 816121 TCATCCTGTTGATCATTTCTTATAGACCAATAATATTCCATAACATTCAT 816170 v v--- iv i i vivv i i viii vv C L1MC4a_3end#L 576 TCTTCCTC---ATTCTTTTTTACAGCTGCATAGTACTCCATTGTGTGGAT 530 chrXptel1M 816171 ATACCATCACTTATTCAGCCATTCTCCAACTGATGGGCATTCA--TTCAA 816218 i vii i ? v i?? i -- --i C L1MC4a_3end#L 529 GTACCATAGTTTATTCAACCANTCTCCTATNNATGGGCATTTAGGTT--G 482 chrXptel1M 816219 TTTCCAGTTTCTTGCCACAACAAAAAGGGCTGCCACAAACATTTTTGCAC 816268 i v i v iv v iv v ii i vii ii C L1MC4a_3end#L 481 TTTCCAATATTTTGCAATTACAAACAATGCTGCAATGAATAACCTTGTGC 432 chrXptel1M 816269 A 816269 C L1MC4a_3end#L 431 A 431 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 43.66 CpG sites = 34, Kimura (unadjusted) = 43.66 Transitions / transversions = 1.26 (34/27) Gap_init rate = 0.04 (7 / 195), avg. gap size = 1.43 (10 / 7) 359 28.68 1.45 1.45 chrXptel1M 816132 816269 (183731) C L1ME4a_3end#LINE/L1 (298) 573 436 m_b347s551i4 14512 chrXptel1M 816132 ATCATTTCTTATAGACCAATAATATTCCATAACATTCATATACCATCACT 816181 ? i v i vivv v?i vv i v i C L1ME4a_3end#L 573 ATNATTTTTAATGGCTGCATAATATTCCATTNTATGGATGTACCATAATT 524 chrXptel1M 816182 TATTCAGCCATTCTCCAACTGATGGGCATTCA--TTCAATTTCCAGTTTC 816229 i i ? i v i v i i -- --i i i C L1ME4a_3end#L 523 TATTTAACCANTCCCCTATTGTTGGACATTTAGGTT--GTTTCCAATTTT 476 chrXptel1M 816230 TTGCCACAACAAAAAGGGCTGCCACAAACATTTTTGCACA 816269 i i iv i v iv v ii ii i C L1ME4a_3end#L 475 TCGCTATTATAAATAATGCTGCGATGAACATCCTTGTACA 436 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.43 CpG sites = 25, Kimura (unadjusted) = 38.72 Transitions / transversions = 1.79 (25/14) Gap_init rate = 0.02 (3 / 137), avg. gap size = 1.33 (4 / 3) 384 30.17 0.00 2.21 chrXptel1M 816150 816288 (183712) C L1ME3A_3end#LINE/L1 (368) 552 417 m_b347s551i6 14512 chrXptel1M 816150 ATAATATTCCATAACATTCATATACCATCACTTATTCAGCCATTCTCCAA 816199 i viii vv iv i i v v vi C L1ME3A_3end#L 552 ATAGTATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTACTG 503 chrXptel1M 816200 CTGATGGGCATTCATTCAATTTCCAGTTTCTTGCCACAACAAAAAGGGCT 816249 i i iivvi?i ??v i iv i v v C L1ME3A_3end#L 502 TTGATGGACATTTGGGTNGTTTCCAGTTTNNGGCTATTACGAATAGTGCT 453 chrXptel1M 816250 GCCACAAACATTTTTGCACACTCTATTTCTTAGTCAATA 816288 i ii i i --- i i i i v i C L1ME3A_3end#L 452 GCTATGAACATTCTTGTACA---TGTCTTTTGGTGAACA 417 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.34 CpG sites = 27, Kimura (unadjusted) = 41.71 Transitions / transversions = 1.93 (27/14) Gap_init rate = 0.02 (3 / 138), avg. gap size = 1.00 (3 / 3) 438 25.42 1.67 1.67 chrXptel1M 816150 816269 (183731) C L1ME3G_3end#LINE/L1 (376) 548 429 m_b347s551i5 14512 chrXptel1M 816150 ATAATATTCCATAACATTCATATACCATCACTTATTCAGCCATTCTCCAA 816199 i ii vv v i i i i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chrXptel1M 816200 CTGATGGGCATTCA--TTCAATTTCCAGTTTCTTGCCACAACAAAAAGGG 816247 i i i -- --i i i i i iv v iv C L1ME3G_3end#L 498 TTGATGGACATTTAGGTT--GTTTCCAATTTTTCGCTATTACAAACAATG 451 chrXptel1M 816248 CTGCCACAAACATTTTTGCACA 816269 v ii ii i C L1ME3G_3end#L 450 CTGCAATGAACATCCTTGTACA 429 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 31.35 CpG sites = 22, Kimura (unadjusted) = 32.69 Transitions / transversions = 2.75 (22/8) Gap_init rate = 0.03 (3 / 119), avg. gap size = 1.33 (4 / 3) 1213 30.05 4.86 4.40 chrXptel1M 816271 817175 (182825) C L1M5_orf2#LINE/L1 (612) 2682 1774 m_b347s551i7 14512 chrXptel1M 816271 TCTATTTCTTA-GTCAATACCAAATGGTTTTGATGACTGCTGTTTTATAT 816319 i- - i v iv i v iv i v C L1M5_orf2#LIN 2682 TCTATC-CTTACGCCAATACCACACTGTCTTGATTACTGTAGCTTTATAA 2634 chrXptel1M 816320 TATAGTTTT-AGATCTGACACATTTAGG----CCATCTTCATTGGCATTT 816364 - i - ? ? ii -i v i ---- v ii -- v i C L1M5_orf2#LIN 2633 TA-AGTCTTGANATCNGGTA-GTGTAAGTCCTCCAACTTTGTT--CTTCT 2588 chrXptel1M 816365 TTTCCCATTAATTCCCTTGAA-ATTCTTGA-CCTTTG-ATTCTTGGGTGA 816411 i v --i vii iv- ? i- - iiiivi i C L1M5_orf2#LIN 2587 TTTTCAA--GATTGTTTTGGCTATTCTNGGTCCTTTGCATTTCCATATAA 2540 chrXptel1M 816412 ATTTTGTTATTATTTTTTTCTAGGTCTGTATAATAAATTCTTGGGAGTTT 816461 ivv i vi v - v vv ii v v vi vi v C L1M5_orf2#LIN 2539 ATTTTAGAATCAGCTTGT-CAATTTCTACAAAAAAACCTGCTGGGATTTT 2491 chrXptel1M 816462 GATTGGTATGGCATTGAATAAGTAGATTAATTTAGGGAGATTTGTTATTT 816511 v v vvi i i v vi i C L1M5_orf2#LIN 2490 GATTGGGATTGCATTGAATCTATAGATCAATTTGGGGAGAATTGACATCT 2441 chrXptel1M 816512 TTATTATATCTGTTCAGCCTACCCATGAGCATTTGATATTTTCCCAAGTG 816561 ? iv iviv vv v i i vvv i ii vv i C L1M5_orf2#LIN 2440 TNACAATATTGAGTCTTCCAATCCATGAACATGGTATATCTCTCCATTTA 2391 chrXptel1M 816562 ATTAGATCTGACTT--TTTGTGTGGAAAGTGTTTTGTAGTT--------- 816600 v i vvi -- v v viiv i --------- C L1M5_orf2#LIN 2390 TTTAGGTCTTCTTTAATTTCTCTCAGCAATGTTTTGTAGTTTTCAGTGTA 2341 chrXptel1M 816601 ---GTGTT-CATATAGTTCCT--GACTT-TTCC-AAATATTTTATACTAT 816642 --- v - i ?v iv -- i - - i ? ii v C L1M5_orf2#LIN 2340 NAGGTCTTGCACATNTTTTGTTAGATTTATTCCTAAGTATTTNATGTTTT 2291 chrXptel1M 816643 CGACAATTCTTTTG--AATGGAATTTCTCTTTGTATTTCTTCTTGCTGGA 816690 i--ii v v -- v vi i ?iv v i v vivv C L1M5_orf2#LIN 2290 T--TGATGCTATTGTAAATGGTATTGTTTTTNAAATTTCATTTTCCAATT 2243 chrXptel1M 816691 GTTTGTTGGTAGGATATAAAAATGCTGATGATTTTGTTGGATTTATTTTG 816740 v v i i viv vv iv v ii C L1M5_orf2#LIN 2242 GTTTGTTGCTAGTATATAGAAATACAATTGATTTTTGTATATTGACCTTG 2193 chrXptel1M 816741 CATCCTGAAACTTTGCGAAAGTTGTGGATTGTTTCTAGTAGGTTTTTTTT 816790 i ? vi i v v iiivv iv - ? v C L1M5_orf2#LIN 2192 TATCCNGCGACCTTGCTAAATTCACTTATTAGTTCTAGTAG-TTTNTTTG 2144 chrXptel1M 816791 TAAGCTGATTCTCTAAGGTTCTCTAAATATACCATTTCTCATGGTCCTAT 816840 ---- i ?i i i vi ? v ---- ------ C L1M5_orf2#LIN 2143 TA----GATTCTTTNGGATTTTCTACGTANACAAT----CATG------T 2108 chrXptel1M 816841 CATCTAAGTATACCATCTCAAAAGAATGATGATTTGGCTTTCTCATTACC 816890 iv ------------- v ? iii vii ii v v C L1M5_orf2#LIN 2107 CATCTGCG-------------AATAANGACAGTTTTATTTCTTCCTTTCC 2071 chrXptel1M 816891 TCCTCTAATTCCTTTAATCTCTTTTTCTTCTCTCATTG-ACAAATCTAAC 816939 vviii v v v i vi i - vii- iv C L1M5_orf2#LIN 2070 AATCTTTATGCCTTTTATTTCTTTTTCTTGCCTTATTGCACTGG-CTAGG 2022 chrXptel1M 816940 ATTTCTAATACAATACTGAATAGCAATGGCAGTAGTGGGCAACCTTGTGT 816989 ii i i ii v i iii? i i v v C L1M5_orf2#LIN 2021 ACCTCCAGTACAATGTTGAATAGAAGTGGTGANAGCGGACATCCTTGTCT 1972 chrXptel1M 816990 CACACTTGACCTTATTGGGAATGATTGTAGTTTGTCCCCAATACATACAA 817039 iiiv ii i vv v v? vi ? v v v vi ii C L1M5_orf2#LIN 1971 TGTTCCCGATCTTAGGGGGAAAGCNTTCAGTNTTTCACCATTAAGTATGA 1922 chrXptel1M 817040 TGCTTGCTGATGGTTTTAAATAGATGTTCCTGATCATTTTAAAGAAAAGT 817089 i ? vv vvi ii i v vv i i ivvi C L1M5_orf2#LIN 1921 TGTTNGCTGTAGGTTTTTCGTAGATGCCCTTTATCAGGTTGAGGAAGTTC 1872 chrXptel1M 817090 ACATTTATTCCTATACTCTCAAGTGTTTT-------AATAGGGTATTGAA 817132 v v i vvi viii v ------- - i C L1M5_orf2#LIN 1871 CCTTCTATTCCTAGTTTGCTGAGAGTTTTTATCATGAAT-GGGTGTTGAA 1823 chrXptel1M 817133 TTTTATCAAATGCTTTTTCTGCATCTATTGAG------ATATGGTTTTT 817175 i ------ i C L1M5_orf2#LIN 1822 TTTTGTCAAATGCTTTTTCTGCATCTATTGAGATGATCATATGATTTTT 1774 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.17 CpG sites = 140, Kimura (unadjusted) = 40.16 Transitions / transversions = 1.17 (140/120) Gap_init rate = 0.06 (57 / 904), avg. gap size = 1.47 (84 / 57) 12 24.12 0.00 0.00 chrXptel1M 817196 817229 (182771) (TTAA)n#Simple_repeat 1 34 (0) m_b347s252i2 14513 chrXptel1M 817196 TTAATTTATTAAGTTATCTGCTAATTAATTAATT 817229 v v v ivii (TTAA)n#Simpl 1 TTAATTAATTAATTAATTAATTAATTAATTAATT 34 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 436 23.12 0.00 7.00 chrXptel1M 817268 817374 (182626) C MIRc#SINE/MIR (153) 115 16 m_b347s601i0 14514 chrXptel1M 817268 GGGGTTAAGTGAATTGCCCAGTGTTACACAGGTAGGAAGTGTTAAGTGTC 817317 i v iv i v ------- v C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGC 73 chrXptel1M 817318 TGAAGCCAGATTTGAACTCAGGTCCTCCTGACTTCAGGGCTGGAGCTCTA 817367 v iv vi i i i i i i v ii v v C MIRc#SINE/MIR 72 AGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTT 23 chrXptel1M 817368 TCCACTG 817374 C MIRc#SINE/MIR 22 TCCACTG 16 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 26.51 CpG sites = 13, Kimura (unadjusted) = 27.89 Transitions / transversions = 1.30 (13/10) Gap_init rate = 0.07 (7 / 106), avg. gap size = 1.00 (7 / 7) 1157 24.80 5.76 2.46 chrXptel1M 817385 817749 (182251) C L1M4_orf2#LINE/L1 (1519) 1775 1399 m_b347s551i8 14512 chrXptel1M 817385 TTGCCCTTAGTTTGCTTATTGATATGATCAATTATGCTAATAGTTTTCCT 817434 i vi i--- i i vv iii i v v i v C L1M4_orf2#LIN 1775 TTGTCCTTTATTC---TATTAATATGGTGTATTACATTGATTGATTTTCG 1729 chrXptel1M 817435 AATATTGAACCAGCCCTGTATTTCTGGTATAAATCCTACTTGGTCATGGT 817484 ? i i i i i v i C L1M4_orf2#LIN 1728 NATGTTGAACCAACCTTGCATTCCTGGGATAAATCCCACTTGGTCATGGT 1679 chrXptel1M 817485 ATATTACCC--TGGAGATGATTTTCTGTAATCGCTTTGCTAATATTTTTA 817532 i v i -- vv v -- v v v v i -- C L1M4_orf2#LIN 1678 GTATAATCCTTTTTATATG--TTGCTGGATTCGGTTTGCTAGTATTTT-- 1633 chrXptel1M 817533 ATTG-GGATTTTTGCATCAATATTCATTAGAGGAATTAGCCTATAATTTT 817581 i - v v i iv i i i i C L1M4_orf2#LIN 1632 GTTGAGGATTTTTGCATCTATATTCATAAGGGATATTGGTCTGTAGTTTT 1583 chrXptel1M 817582 C-TTTCTTTTCAT-CCTT--CCTTGTTTAGGTATTAGCACCATATCTGCG 817627 - v v -i --i v v i viiv iiv v C L1M4_orf2#LIN 1582 CTTTTCTTGTGATGTCTTTGTCTGGTTTTGGTATCAGGGTAATACTGGCC 1533 chrXptel1M 817628 TCATAAAAGGAATTTTGGTAGGAGTCCTTCTTTCCCTATTTTTTCAAATA 817677 i v i- v v viv i i iii vi v C L1M4_orf2#LIN 1532 TCATAGAATGAG-TTGGGAAGTGTTCCCTCCTCTTCTATTTTTTGGAAGA 1484 chrXptel1M 817678 GTTTATATAGTATTAG----AATTGTTCTTTGAATGTTTGGTAGAATTCA 817723 i iv v i ---- v i C L1M4_orf2#LIN 1483 GTTTGTGAAGGATTGGTGTTAATTCTTCTTTAAATGTTTGGTAGAATTCA 1434 chrXptel1M 817724 CGTGTAAATCCATCTGGCCCTGGA---------GA 817749 vv i v ? i--------- v C L1M4_orf2#LIN 1433 CCAGTGAAGCCATCTGGNCCTGGGCTTTTCTTTGT 1399 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 30.89 CpG sites = 58, Kimura (unadjusted) = 30.89 Transitions / transversions = 1.20 (48/40) Gap_init rate = 0.04 (15 / 364), avg. gap size = 1.87 (28 / 15) 28 0.00 0.00 0.00 chrXptel1M 817750 817776 (182224) (T)n#Simple_repeat 1 27 (0) c_b347s251i0 14515 chrXptel1M 817750 TTTTTTTTTTTTTTTTTTTTTTTTTTT 817776 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTT 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 1157 24.80 5.76 2.46 chrXptel1M 817777 817844 (182156) C L1M4_orf2#LINE/L1 (1896) 1398 1329 m_b347s551i8 14512 chrXptel1M 817777 AGGAG----TTGATTAGTAACTGTACTATTTTTTTTC-TAAAATGGTTCT 817821 i i ---- v i --- v i i v - ivv i v C L1M4_orf2#LIN 1398 GGAAGTTTTTTGATTACTAATT---CAATCTCTTTACTTGTTATAGGTCT 1352 chrXptel1M 817822 ATTTAGATATTTTATTTCCTCTT 817844 i v i i C L1M4_orf2#LIN 1351 ATTCAGATTTTCTATTTCTTCTT 1329 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 30.89 CpG sites = 58, Kimura (unadjusted) = 30.89 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.07 (5 / 67), avg. gap size = 1.60 (8 / 5) 970 31.53 3.11 3.69 chrXptel1M 818289 818996 (181004) C L1M4_orf2#LINE/L1 (1978) 1316 613 m_b347s551i9 14512 chrXptel1M 818289 GGCAATCTATATTTTTTGTAGGTATTCCTCCAATTCACTTAGATTATCCA 818338 i i i i i i i- v iv v ii i i C L1M4_orf2#LIN 1316 GGTAGTTTGTGTCTTTC-TAGGAATTTGTCCATTTCATCTAGGTTATCTA 1268 chrXptel1M 818339 ATTTATTGGCATATACTTGGGCAAAAAACTTCTAATTATTGCCCTACTTT 818388 i i v vv v iv i i i-- vii -- C L1M4_orf2#LIN 1267 ATTTGTTGGCATACAATTGTTCATAGTATTCCC--TTATAATCCT--TTT 1222 chrXptel1M 818389 CCTCTTCCT------TTGGTGGAAAGTTCTCCCTTTTCATTTTTAAGACT 818432 -- v i ------ i i v vv i ii ii i vvi C L1M4_orf2#LIN 1221 --TATTTCTGTAAGGTCGGTAGTAATGTCCCCTCTTTCATTCCTGATTTT 1174 chrXptel1M 818433 AACAATTTGATTTTCCTCTTTCCTTTTTCTAATCAAATTGACTAAAGTTT 818482 ii v i i i ii ii ii ivi ii v C L1M4_orf2#LIN 1173 AGTAATTTGAGTCTTCTCTCTTTTTTTCTTGGTCAGTCTAGCTAAAGGTT 1124 chrXptel1M 818483 TATCTATTTTCTTGTTTTTTTTTCCATACAATCAACTCTTTGTTTTATT- 818531 i v v v i --- v v i i v ii - C L1M4_orf2#LIN 1123 TGTCAATTTTGTTGATCTTTT---CAAAGAACCAACTTTTGGTTTCGTTG 1077 chrXptel1M 818532 -TTTTAATTCAATAGTTTTCTTACTTTCAATTTTATTAATCTCTCCTTTT 818580 - --i v v ii i i v i v i iv i v C L1M4_orf2#LIN 1076 ATTTT--CTCTATTGTTTTTCTATTCTCTATTTCATTTATTTCCGCTCTA 1029 chrXptel1M 818581 ATTTTCAGAATTTCAAATTTGGTATTTAATTGGTTTTTGATTTGTTCTT- 818629 i i vv vvvii vv ii iv v vv ii i - C L1M4_orf2#LIN 1028 ATCTTTATTATTTCCTTCCTTCTGCTTGCTTTGGGTTTAGTTTGCTCTTC 979 chrXptel1M 818630 -TTTTCTAGCTTTTTTAGTTGTAAGCCCAATTCACTGATCTTC--TCTTT 818676 - i i v v v vii iv i i i vv-- C L1M4_orf2#LIN 978 TTTTTCTAGTTTCTTAAGGTGGAAGGTTAGGTTATTGATTTGAGATCTTT 929 chrXptel1M 818677 CT-CTATTTTATGCAAGTAAGCATCTTAGAGATATAAAATTTCCCCTAAT 818725 - v --- vi i - v v v i i v C L1M4_orf2#LIN 928 CTTCTTTTTTA---ATATAGGCAT-TTACAGCTATAAATTTCCCTCTAAG 883 chrXptel1M 818726 AACCACTTTGGCTGCATCTCATAAATTTTGGCATGTTGTCTCATTACTGT 818775 v ii ? i i i v iv iii v C L1M4_orf2#LIN 882 CACTGCTTTNGCTGCATCCCATAAGTTTTGGTATGTTGTGTTTTCGTTTT 833 chrXptel1M 818776 CATTC-TCTTGGATGAATTTATTGATTGTTACTATGATTTGCTGTTTCAC 818824 - iii - v vi i viivi i vi v v C L1M4_orf2#LIN 832 CATTCATCTCAAA-GTATTTTCTAATTTCCCTTGTGATTTCTTCTTTGAC 784 chrXptel1M 818825 CCATTCATTCTTTAGGATTAGGATATTTAGTTTCCAATTAATTCTTGGTC 818874 vi v v iv v i i vv v v vii i C L1M4_orf2#LIN 783 CCATTGGTTATTTAGGAGTGTGTTGTTTAATTTCCACATATTTGTGAATT 734 chrXptel1M 818875 T-----ATTTCCCCCTGATGTTTTATTGCATGTGATTTTTATTGCATCAT 818919 ----- ii ----- vv viv v i v ii C L1M4_orf2#LIN 733 TCCCAAATTTCCTTCTG-----TTATTGATTTCTAATTTCATTCCATTGT 689 chrXptel1M 818920 GATCTGAAAAAAATGCATTTAACTATTTCTGTCTTTCTGCATTTAATTTT 818969 i - i i v i v vv iv vi i i iv --- C L1M4_orf2#LIN 688 GGTC-GGAGAACATACTTTGTATGATTTCAATCCTTTTAAATTTA---TT 643 chrXptel1M 818970 GAGG---GTTTTATGCCCTAATACATGGTC 818996 i--- v i i C L1M4_orf2#LIN 642 GAGACTTGTTTTATGGCCTAACATATGGTC 613 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.20 CpG sites = 126, Kimura (unadjusted) = 42.31 Transitions / transversions = 1.42 (126/89) Gap_init rate = 0.05 (36 / 707), avg. gap size = 1.33 (48 / 36) 805 32.22 5.37 4.11 chrXptel1M 818307 819387 (180613) C L1M1_orf2#LINE/L1 (1995) 1299 206 m_b347s551i10 14512 chrXptel1M 818307 TAGGTATTCCTCCAATTCACTTAGATTATCCAATTTATTGGCATATACTT 818356 v iv v vii v v C L1M1_orf2#LIN 1299 TAGGAATTTGTCCATTTCTTCTAGATTTTCCAATTTATTGGCATATAGTT 1250 chrXptel1M 818357 GGGCAAAA-AACTTCTAATTATTGCCCT--ACTTTCCTCTTCCTTTGGTG 818403 vv v i- i iv v -- i -- v iv vviv iv v C L1M1_orf2#LIN 1249 GCTCATAGTAGCCACTAATGAT--CCTTTGAATTTCTGCGGTATCAGTTG 1202 chrXptel1M 818404 GAAAGTTCTCCCTTTTCATTTTTAAGACTAACAATTTGATTTTCCTCTTT 818453 v v - i i i i vvi viv iv i i i C L1M1_orf2#LIN 1201 TAATGT-CTCCTTTTTCATCTCTGATTTTATTTATTTGGGTCTTCTCTCT 1153 chrXptel1M 818454 CCTTTTTCTAATCAAATTGACTAAAGTTTTATCTATTTTCTTGTTTTTTT 818503 ii ii ?? i ivi i v i v --- v?i C L1M1_orf2#LIN 1152 TTTTTTCTTNNTTAGTCTGGCTAAAGGTTTGTCAATTTT---GTTTANCT 1106 chrXptel1M 818504 TTCCATACAATCAACTCTTTGTTTTATT--TTTTAATTCAATAGTTTTCT 818551 i v v i i i -- i -- vv v C L1M1_orf2#LIN 1105 TTTCAAAAAACCAACTTTTTGTTTCATTGATCTT--TTGTATTGTTTTCT 1058 chrXptel1M 818552 TACTTTCAATTTTATTAATCTCTCCTTTTATTTTCAGAATTTCAAATTTG 818601 vv i v i v i v i i vv vvv i v C L1M1_orf2#LIN 1057 TCATTTCAATTTCATTTATTTCTGCTCTGATCTTTATTATTTCTTTTCTT 1008 chrXptel1M 818602 GTATTTAATTGGTTTTTGATTTGTTCTT--TTTTCTAGCTTTTTTAG--- 818646 v i v v v vv i i -- i i v --- C L1M1_orf2#LIN 1007 CTACTAATTTTGGGTTTGGTTTGCTCTTGCTTTTCTAGTTCTTTAAGATG 958 chrXptel1M 818647 --TTGTAAGCCCAATTCACTGATCTTCTCTTTCTCTATTTTATGCAAGTA 818694 -- i v viiiv vvi vv i ii i - v ---- C L1M1_orf2#LIN 957 CATCGTTAGGTTGTTTATTTGAAGTTTTTCTTCTTT-TTTGAT----GTA 913 chrXptel1M 818695 AGCATCTTAGAGATATAAAATTTCCCCTAATAACCACTTTGGCTGCATCT 818744 i - v v v i i v vv ii v i i C L1M1_orf2#LIN 912 GGCA-CTTATAGCTATAAACTTCCCTCTTAGTACTGCTTTTGCTGTATCC 864 chrXptel1M 818745 CATAAATTTTGGCATGTTGTCTCATTACTGTCATTCTCTTGGATGAATTT 818794 ii i v ivii i i ivi vi vi C L1M1_orf2#LIN 863 CATAGGTTTTGGTATGTTGTGTTTCCATTATCATTTGTTTCAAGAAATTT 814 chrXptel1M 818795 ATTGA-TTGTTACTATGATTTGCTGTTTCACCCATTCATTCTTTAGGATT 818843 v ii - vi v - i vi vv v i vi iv i vi C L1M1_orf2#LIN 813 TTCAATTTCCTTCT-TAATTTCTTCATTGACCCACTGGTCATTCAGGAGC 765 chrXptel1M 818844 AGGATATTTAGTTTCCAATTAATTCT-TGGTCT----ATTTCCCCCTGAT 818888 viv i i vv iv v - i i ---- v i i -- C L1M1_orf2#LIN 764 ATATTGTTTAATTTCCATGTGTTTGTATAGTTTCCAAAATTCCTCTTG-- 717 chrXptel1M 818889 GTTTTATTGCATGTGATTTTTATTGCATCATGATCTGAAAAAAATGCATT 818938 --- vv viv v v ii i v - i i - C L1M1_orf2#LIN 716 ---TTATTGATTTCTAGTTTTATTCCATTGTGGTCAG-AGAAGATGC-TT 672 chrXptel1M 818939 TA-ACTATTTCTGTCTTTCTGCATTTAATTTTGAGG---GTTTTATGCCC 818984 v - i vi i i v ---i i i--- i v C L1M1_orf2#LIN 671 GATATTATTTCAATTTTTTTGAAT---GTTTTAAGACTTGTTTTGTGACC 625 chrXptel1M 818985 TAATACATGGTC--------AACATGAACC----GCTGAGGAAAAAAA-A 819021 i i -------- iv v ---- i -i C L1M1_orf2#LIN 624 TAACATATGGTCTATCCTTGAGAATGATCCATGTGCTGAGGAAAAGAATG 575 chrXptel1M 819022 AGTAAACTCCTTTCTGTCTCCATTC-----AATTTTCTCCCAAAATTTAT 819066 v ------- ivv i v----- v viv v i C L1M1_orf2#LIN 574 TGTA-------TTCTGCAGCCGTTGGATGAAATGTTCTGTAAATATCTAT 532 chrXptel1M 819067 CATACTTAACTTTCCTAAAATTCTATTTTCCTCTTTAA---CG-TGGTTC 819112 i viiii -- ------iv vv v vvv --- - v C L1M1_orf2#LIN 531 TAGGTCCA--TTT------GGTCTATAGTGCAGATTAAGTCCGATGTTTC 490 chrXptel1M 819113 -TTATTTATTTTGTGGTTC---GATTTATCTAGTTATGAGAGAGCGAGGT 819158 - i v v vi v--- i i i i vv i v v iv C L1M1_orf2#LIN 489 TTTGTTGATTTTCTGTCTGGAAGATCTGTCCAATGCTGAAAGTGGGGTGT 440 chrXptel1M 819159 TGAGATGCCCCACTGGTATAGTTTTGTTGTCTATTTTTTCTTGCAGTTCT 819208 ii vi vi iv v v vv i i iii vi i C L1M1_orf2#LIN 439 TGAAGTCTCCAGCTATTATTGTATTGGGGTCTATCTCTCTCTTTAGCTCT 390 chrXptel1M 819209 CTTAA---CTTCTTTAGGAAGTTAGATACTATACCACTTGGTGCATATAT 819255 vv ---i v viv vi i i i vi viii v C L1M1_orf2#LIN 389 AATAATATTTGCTTTATATATCTGGGTGCTCCAGTGTTGGGTGCATATAT 340 chrXptel1M 819256 GTTTAGCAGTGTTATAGCTTCATTATCTATGGTACCCTTTATCAAGATAT 819305 i ?v v v i v vv vv v vv vv C L1M1_orf2#LIN 339 ATTTANAATTGTTATATCCTCTTGCTGAATTGACCCCTTTATCATTATAT 290 chrXptel1M 819306 AATTTCCTTCCTTATCTCTTTTAATTAGATCAAATTTGCTTT------TG 819349 i vv i i i v - v ---- ii ------ i C L1M1_orf2#LIN 289 AGTGACCTTCTTTGTCTCTTCTTA-TAGTT----TTTGTCTTGAAATCTA 245 chrXptel1M 819350 CTTCATCTGAGATCAGGATGGCTG-TGGTGTTCTTTTCT 819387 i ii v v v i i- vv i i C L1M1_orf2#LIN 244 TTTTGTCTGATATAAGTATAGCTACTCCTGCTCTTTTTT 206 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 42.66 CpG sites = 167, Kimura (unadjusted) = 43.00 Transitions / transversions = 1.00 (167/167) Gap_init rate = 0.06 (67 / 1080), avg. gap size = 1.54 (103 / 67) 363 29.13 0.49 6.70 chrXptel1M 819915 820120 (179880) C L1MC_orf2#LINE/L1 (3067) 227 34 m_b347s551i11 14512 chrXptel1M 819915 ATGGCTACCCCTGCTTTTTTTTTTTTTTTTTTACTTCACCTGAAGCATAA 819964 i i ? i vv vv v ----------- ii C L1MC_orf2#LIN 227 ATAGCTACTCCNGCTTTCTTTTGATTAGTGTTA-----------GCATGG 189 chrXptel1M 819965 TAGATTCTTCGCCAGCCTTTTACCTTTACTGTGTATGTATCACTCTACTT 820014 v ii v v ? i v v i i vi v i C L1MC_orf2#LIN 188 TATATCTTTCTCCATCCNTTTACTTTTAATCTATATGTGTCTTTATATTT 139 chrXptel1M 820015 TAAATGTGTTTCTTGTAAATAACAAATGGTAGGATTGTGGCTTTTAATCC 820064 v i v i i v i v i iv vi i C L1MC_orf2#LIN 138 AAAGTGGGTTTCTTGTAGACAACATATAGTTGGGTCTTGTTTTTTGATCC 89 chrXptel1M 820065 AGTTCTG-CTATCCGTTCCTGTTTTGTGGAAGAGTTCATCCCATTCATAT 820113 -i - v iv vi - vi v iv vi i vv ? i C L1MC_orf2#LIN 88 A-CTCTGACAATCTCTGTCT-TTTAATTGGTGTATTTAGACCATTNACAT 41 chrXptel1M 820114 TTACAGT 820120 v C L1MC_orf2#LIN 40 TTAAAGT 34 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.91 CpG sites = 28, Kimura (unadjusted) = 37.91 Transitions / transversions = 1.00 (28/28) Gap_init rate = 0.07 (14 / 205), avg. gap size = 1.00 (14 / 14) 276 29.16 2.65 5.94 chrXptel1M 819932 820157 (179843) C L1MC4_5end#LINE/L1 (166) 2389 2171 m_b347s551i12 14512 chrXptel1M 819932 TTTTTTTTTTTTTTTACTTCACCTGAAGCATAATAGATTCTTCGCCAGCC 819981 i v ii i -i i------- v ii ?v v C L1MC4_5end#LI 2389 TTCTTTTTTGTTTCCATTT-GCCTGG-------TATATCTTTNTCCATCC 2348 chrXptel1M 819982 TTTTACCTTTACTGTGTATGTATCACTCTACTTTAAATGTGTTTCTTGTA 820031 i ii i viv v v v i -i ii i C L1MC4_5end#LI 2347 CTTTATTTTCAGCCTTTCTGAATCACTTT-TTTTAGGTGTGTCTCTTGTA 2299 chrXptel1M 820032 AATAACAAATGGTAGGATTGTGGCTTTTAATCCAGTTCTGCTATCCGTTC 820081 ? i i v i v i iv vi ? ? ? i? ivivv iv ?i C L1MC4_5end#LI 2298 NACAGCATATAGTTGGGTCTTGCTTTNTNANCCAANTTGAAAATCTTTNT 2249 chrXptel1M 820082 CTGTTTTGTGGAAGAGTTCATCCCATTCATATTTACAGTTAGAGTAACTA 820131 - vi ? iv ? v i i iv ? --- ? i C L1MC4_5end#LI 2248 CT-TTTAATNGGTGAGTTNAGCCCATTTACATTTATTGNTA---TNACTG 2203 chrXptel1M 820132 A----TTCTGTATT--TCCTGCCATCTTATTT 820157 ---- iv v -- i i v C L1MC4_5end#LI 2202 ATATGTTTGGTCTTAATTCTGTCATATTATTT 2171 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 40.95 CpG sites = 38, Kimura (unadjusted) = 40.95 Transitions / transversions = 1.58 (38/24) Gap_init rate = 0.07 (15 / 225), avg. gap size = 1.27 (19 / 15) 315 28.17 8.06 4.11 chrXptel1M 820000 820210 (179790) C L1MEi_5end#LINE/L1 (5) 2207 1989 m_b347s551i13 14512 chrXptel1M 820000 TGTATCACTCTACTTTAAATGTGTTTCTTGTAAATAACAAATGGTAGGAT 820049 i ii i ii ii i i i v i iv C L1MEi_5end#LI 2207 TGTGTCGTTTTGTTTTAGGTGTGTCTCTTGTAAACAGCATATAGCTGGAT 2158 chrXptel1M 820050 TGTGGCTTTTAATCCAGTTCTGCTATCCGTTCCTGTTTT---GTGGAAGA 820096 v vvi i- v ---i ii i ---i i iv C L1MEi_5end#LI 2157 TTTTTTTTTTAATCCAA-TCTGATA---ATCTCTGTCTTTTAATAGGTGA 2112 chrXptel1M 820097 GTTCATCCCATTCATATTTACAGTTAGAGTAACTAAT---TCTG----TA 820139 i vi i i iv -- v - i --- i ---- C L1MEi_5end#LI 2111 GTTTAATCCATTTACATTTATTGT--GATT-ACTGATATATTTGGACTTA 2065 chrXptel1M 820140 TTTCCTGCCATCTTATT---TATCTCCAGTTT----TGCTTTTCTCTTTC 820182 - i --- i i i v ---- ? - ? C L1MEi_5end#LI 2064 TTT-CTACCATCTTATTTTGTGTTTTCTGTTTATCATNCTTTT-TCTTTN 2017 chrXptel1M 820183 CCCCATCCCTTCTCCCCAGTATTTTGCT 820210 iiiv i i ii v iv i i C L1MEi_5end#LI 2016 CTTTTTCTCTCCTTTCCTGCCTTCTGTT 1989 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.54 CpG sites = 43, Kimura (unadjusted) = 38.43 Transitions / transversions = 3.07 (43/14) Gap_init rate = 0.07 (14 / 210), avg. gap size = 1.86 (26 / 14) 413 24.38 7.82 3.76 chrXptel1M 820003 820181 (179819) C L1MEj_5end#LINE/L1 (0) 2160 1975 m_b347s551i14 14512 chrXptel1M 820003 ATCACTCTACTTTAAATGTGTTTCTTGTAAATAACAAATGGTAGGATTGT 820052 i ii i i i v i iv i v C L1MEj_5end#LI 2160 ATCACTTTGTTTTAAGTGTGTTTCTTGTAAACAGCATATAGCTGGGTTTT 2111 chrXptel1M 820053 GGCTTTTAATCCAGTTCTGCTATCCGTTCCTGTTTT---GTGGAAGAGTT 820099 vi i i- vi --- ii i ---i i i C L1MEj_5end#LI 2110 GTTTTTTAACCCAA-TCTGACA---GTCTCTGTCTTTTAATGGGAGAATT 2065 chrXptel1M 820100 CATCCCATTCATATTTACAGTTA-GAGTAA-----CTAATTCTGTATTTC 820143 vi i vv v - v i -----i i i i--- C L1MEj_5end#LI 2064 CAGTCCATTCACATTTAGTGTAACGACTGATATACTTGATTTTA---TTC 2018 chrXptel1M 820144 CTGCCATCTTA-TTTA-TCTCCA---GTTTTGCTTTTCTCTTT 820181 v - - ? ii ---i i i ? C L1MEj_5end#LI 2017 CTTCCATCTTACTTTATTNTTTATTTATTTTGTTTTTTTNTTT 1975 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 31.52 CpG sites = 31, Kimura (unadjusted) = 31.52 Transitions / transversions = 2.82 (31/11) Gap_init rate = 0.07 (13 / 178), avg. gap size = 1.62 (21 / 13) 12 15.04 8.11 0.00 chrXptel1M 820310 820346 (179654) (TTCCCCT)n#Simple_repeat 1 40 (0) m_b347s252i3 14516 chrXptel1M 820310 TTACCCTTT--CTTTTCCCCTTTCCCC-TCCCATTTTCCC 820346 v -- i - i vi (TTCCCCT)n#Si 1 TTCCCCTTTCCCCTTTCCCCTTTCCCCTTTCCCCTTTCCC 40 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.50 (3 / 2) 185 25.00 4.17 0.00 chrXptel1M 823454 823501 (176499) C MIR3#SINE/MIR (8) 200 151 m_b347s601i1 14517 chrXptel1M 823454 GGATCAAAGA--TTTAGAGCTGAAAGACATCTTTGAGATGATCTGGCCCA 823501 i v --v i i iv i v v i i C MIR3#SINE/MIR 200 GAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCA 151 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.04 CpG sites = 7, Kimura (unadjusted) = 31.04 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.02 (1 / 47), avg. gap size = 2.00 (2 / 1) 201 24.00 2.00 0.00 chrXptel1M 823550 823599 (176401) C MIR3#SINE/MIR (96) 112 62 m_b347s601i2 14517 chrXptel1M 823550 GGGCTGAAGTGACTTGTGCAGGATCACACAGCTAGGAAGTATTA-AGCCA 823598 i v iv i i ? vv ivi - i C MIR3#SINE/MIR 112 GAGGTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCG 63 chrXptel1M 823599 G 823599 C MIR3#SINE/MIR 62 G 62 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.32 CpG sites = 7, Kimura (unadjusted) = 30.24 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.02 (1 / 49), avg. gap size = 1.00 (1 / 1) 222 20.45 2.27 0.00 chrXptel1M 823556 823599 (176401) C MIRc#SINE/MIR (159) 109 65 m_b347s601i3 14517 chrXptel1M 823556 AAGTGACTTGTGCAGGATCACACAGCTAGGAAGTATTA-AGCCAG 823599 iv i i v ivi - i C MIRc#SINE/MIR 109 AAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGG 65 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 21.50 CpG sites = 6, Kimura (unadjusted) = 24.51 Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.02 (1 / 43), avg. gap size = 1.00 (1 / 1) 17 9.12 0.00 0.00 chrXptel1M 823608 823631 (176369) (T)n#Simple_repeat 1 24 (0) m_b347s252i4 14518 chrXptel1M 823608 TTTTCTTCTTTTTTTTTTTTTTTT 823631 i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTT 24 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 23 13.32 0.00 0.00 chrXptel1M 824422 824462 (175538) (AAGGCG)n#Simple_repeat 1 41 (0) m_b347s252i5 14519 chrXptel1M 824422 AAGGGGAAGGTGAAGGAGAAGGTGAAGGCGCAGGCGAAGGC 824462 v i v i v (AAGGCG)n#Sim 1 AAGGCGAAGGCGAAGGCGAAGGCGAAGGCGAAGGCGAAGGC 41 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 16 5.27 0.00 0.00 chrXptel1M 825310 825329 (174671) (T)n#Simple_repeat 1 20 (0) m_b347s252i6 14520 chrXptel1M 825310 TTTCTTTTTTTTTTTTTTTT 825329 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTT 20 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 248 31.94 0.00 8.54 chrXptel1M 825798 825886 (174114) MIRc#SINE/MIR 34 115 (153) m_b347s601i4 14521 chrXptel1M 825798 ATTTGAAGACCAAAGGAGCTGAGTTCAAATGCTACCTCAGAGACTTGGTA 825847 i i v vii i v i i i v iiv ------- vi MIRc#SINE/MIR 34 ACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTC-------TGCCA 76 chrXptel1M 825848 CTTCCTAACAATGTAACATTGGGCAAGGCACTTTACCCC 825886 v i vi i v v v i MIRc#SINE/MIR 77 CTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.03 CpG sites = 15, Kimura (unadjusted) = 42.47 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.08 (7 / 88), avg. gap size = 1.00 (7 / 7) 266 27.78 0.00 0.00 chrXptel1M 827884 827955 (172045) C HERV17#LTR/ERV1 (2233) 6393 6322 m_b347s701i0 14522 chrXptel1M 827884 TTGCTTGAGGTTTTGGTTCATTTTCTTCACTTTTCCAGAAGATTGAGAAT 827933 i i vv v iv v i v ivi C HERV17#LTR/ER 6393 TCGTTTGAGTGTTTCGTTCATTTTCTCGACTTTTCCTGAGGATTGTGGCC 6344 chrXptel1M 827934 GCTAGCCAGAGTGGAAATGATA 827955 v i v iv v i C HERV17#LTR/ER 6343 TCCAGGCGCAGTGTAAGTGATA 6322 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 28.97 CpG sites = 9, Kimura (unadjusted) = 34.89 Transitions / transversions = 0.82 (9/11) Gap_init rate = 0.00 (0 / 71), avg. gap size = 0.0 (0 / 0) 32 7.72 3.51 1.72 chrXptel1M 828039 828095 (171905) (TG)n#Simple_repeat 1 58 (0) c_b347s251i1 14523 chrXptel1M 828039 TGTGTGTGTGTGTGTGTGTGTG-GTGTCATGTGTATCTGTG-GTGTATGT 828086 - -i i v - i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGT-GTGTGTGTGTGTGTGTGTGTGT 49 chrXptel1M 828087 GTGTGTGTG 828095 (TG)n#Simple_ 50 GTGTGTGTG 58 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.05 (3 / 56), avg. gap size = 1.00 (3 / 3) 307 26.31 1.04 1.04 chrXptel1M 828420 828515 (171485) C PRIMA41-int#LTR/ERV1 (3340) 4416 4321 m_b347s701i1 14524 chrXptel1M 828420 AGAGAGCCTGAGACTTTGG-AAACCTCCCACTAGCAAGCCACTGATGATC 828468 ? i v i ?i - ?iv v iv ?- i vi C PRIMA41-int#L 4416 ANAAAGCCTGATATTTNAGTAANTGTCCCCCTGTCAN-CCACTGGTGTCC 4368 chrXptel1M 828469 TTTGGCTTCTAGGGTGCTCTGATCCTAGTGGGAAGTTAAGACCTCCA 828515 ? iiv i vv i i ? ii i i i C PRIMA41-int#L 4367 TTTNGCTTCTAGGACCCCCTGTACTTGGTGNGGGGTCAAAACCTCTA 4321 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.88 CpG sites = 17, Kimura (unadjusted) = 36.88 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.02 (2 / 95), avg. gap size = 1.00 (2 / 2) 19 14.21 0.00 0.00 chrXptel1M 828755 828785 (171215) (C)n#Simple_repeat 1 31 (0) m_b347s252i7 14525 chrXptel1M 828755 CCTCCCCTCCCAACCCCCCCCCCCCCCCCCC 828785 i i vv (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 31 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 281 19.49 16.13 0.70 chrXptel1M 830708 830831 (169169) L1PA17_3end#LINE/L1 61 203 (710) m_b347s551i15 14526 chrXptel1M 830708 ATTAGAAAT--GGCAGACGGACA-----AGA-AGTTTTCCAAAGAAGAGA 830749 i v-- i - ----- - v i v v L1PA17_3end#L 61 ATTAAAAAGTGGGCAAA-GGACATGAACAGACACTTCTCAAAAGAAGACA 109 chrXptel1M 830750 T-CA-GTTATCAATAGTCATATGAAAA--TGCTC----TCAGAAAT---- 830787 - - ivii i iv -- ---- vv ---- L1PA17_3end#L 110 TACAAGCGGCCAACAAACATATGAAAAAATGCTCAACATCACTAATCATC 159 chrXptel1M 830788 AAAGAAATGCAAATTAAAACAACCCTGAGGTACCAACTCACATC 830831 i i v vv i v i L1PA17_3end#L 160 AGAGAAATGCAAATCAAAACCACAATGAGATACCATCTCACACC 203 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 21.72 CpG sites = 12, Kimura (unadjusted) = 22.74 Transitions / transversions = 1.00 (12/12) Gap_init rate = 0.07 (9 / 123), avg. gap size = 2.33 (21 / 9) 333 27.53 14.24 3.44 chrXptel1M 830722 831037 (168963) L1ME4c_3end#LINE/L1 86 434 (396) m_b347s551i16 14526 chrXptel1M 830722 ACGGACAAGAAGTTTTCCAAAGAAGAGAT-CAGTTA-TCAATAGTCATAT 830769 i ---- iv v? i i - i? - v i iv i L1ME4c_3end#L 86 ACAGACAA----TTCACANAAGAGGAAATACAANTAGTAAACAAACACAT 131 chrXptel1M 830770 G--AAAATGCTC----TC---AGAAAT-AAAGAAATGCAAATTAAAACAA 830809 -- i ---- --- v - i L1ME4c_3end#L 132 GGAAAAATGTTCAACCTCGCTAGTAATCAAAGAAATGCAAATTAAAGCAA 181 chrXptel1M 830810 CCCTGAGGTACCAACTCACATCTATTGGCTAATCTGACAGAG----AAGG 830855 vv i vi i ii i--- - ii i i---- ii L1ME4c_3end#L 182 CAATGAGATACCATTTTACGCCTATTA---AAT-TAGCAAAAATTTAAAA 227 chrXptel1M 830856 AAT--ATAAC------TGCTGGAGAGAAGGAACAGAAATAGGTACA---- 830893 -- i------ v i?v vivv iv ?---- L1ME4c_3end#L 228 AATTGATAATACCCAATGCTGGCGAGGNTGCGGTGAAACTGGTACNCTCA 277 chrXptel1M 830894 -GCG--GTTGATGGAGTTG-----TGAT----CTCTTCCACAGTGCTATT 830931 -i i-- i i vi? ----- i ---- i iiiv iv v L1ME4c_3end#L 278 TACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGCAATT 327 chrXptel1M 830932 TAGAACTATGC-CCACAGGGCTATAAGACTATTCATACCTTTTGTTCCAT 830980 i v v i i-i - i i i v i i vi v L1ME4c_3end#L 328 TGGCAATACGTATCA-AGAGCCATAAAAATGTTCATACCCTTTGACCCAG 376 chrXptel1M 830981 CAGTACTCCTTACTGGATCTGTATCCCAAAGAAA----CCAAAGGGAAAG 831026 i i v iv - ivv v i i ----i i -- L1ME4c_3end#L 377 TAATTCCACTT-CTGGGAATTTATCCTAAGGAAATAATTCAAAAG--AAG 423 chrXptel1M 831027 GAAAAGGCTAT 831037 i L1ME4c_3end#L 424 GAAAAAGCTAT 434 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 35.09 CpG sites = 56, Kimura (unadjusted) = 36.76 Transitions / transversions = 2.00 (56/28) Gap_init rate = 0.09 (28 / 315), avg. gap size = 2.04 (57 / 28) 397 25.29 13.93 2.57 chrXptel1M 830734 831013 (168987) L1PA4_3end#LINE/L1 94 404 (498) m_b347s551i17 14526 chrXptel1M 830734 TTTTCCAAAGAAGAGATCAGTTAT-----CAATAGTCATATGAAAA--TG 830776 i v v --- ----- v v i -- L1PA4_3end#LI 94 TTCTCAAAAGAAGACAT---TTATGCAGCCAAAAGACACATGAAAAAATG 140 chrXptel1M 830777 CTC----TCA---GAAAT-AAAGAAATGCAAATTAAAACAACCCTGAGGT 830818 ---- --- vv - i i v vv i L1PA4_3end#LI 141 CTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGAT 190 chrXptel1M 830819 ACCAACTCACATCTAT-----TGGCTAATC-TGACAGAG-AAGGAATATA 830861 v i vi ----- -i - v v i -v - i L1PA4_3end#LI 191 ACCATCTCACACCAGTTAGAATGGC-GATCATTAAAAAGTCAGGAA-ACA 238 chrXptel1M 830862 AC---TGCTGGAGAGAAGGAACAGAAATAGGTACA-------GCGGTTGA 830901 --- i v viv v -------i v i L1PA4_3end#LI 239 ACAGGTGCTGGAGAGGATGTGGAGAAATAGGAACACTTTTACACTGTTGG 288 chrXptel1M 830902 TGGAGTTGTGATCTCTTCCA--CA--GTGCTATTTAG---AACTATGCCC 830944 iii i v vv i -- -- vv v i ---ii v v i L1PA4_3end#LI 289 TGGGACTGTAAACTAGTTCAACCATTGTGGAAGTCAGTGTGGCGATTCCT 338 chrXptel1M 830945 ACAGGGCTATAAGACTATTCATACCTTTTGTTCCATCAGTACTCCTTACT 830994 - v v ii vvv v vi v vi - i v L1PA4_3end#LI 339 -CAGGGATCTAGAACTAGAAATACCATTTGACCCAGCCAT-CCCATTACT 386 chrXptel1M 830995 GGATCTGTATCCCAAAGAA 831013 i v i - i L1PA4_3end#LI 387 GGGTATATA-CCCAAAGGA 404 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 30.59 CpG sites = 31, Kimura (unadjusted) = 31.11 Transitions / transversions = 0.82 (31/38) Gap_init rate = 0.08 (21 / 279), avg. gap size = 2.24 (47 / 21) 197 22.47 1.96 4.00 chrXptel1M 831466 831516 (168484) C L3#LINE/CR1 (7) 4092 4043 m_b347s601i5 14527 chrXptel1M 831466 TCACCAAACCTCAGGGTTGGAAGGCAGATCATAGCAGTCATCCA-TCCAG 831514 vi i i -- i v vi i - i C L3#LINE/CR1 4092 TCACAGAATCTCAGAGTTGGAAGG--GACCTTAGAGGTCATCTAGTCCAA 4045 chrXptel1M 831515 TC 831516 i C L3#LINE/CR1 4044 CC 4043 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.80 CpG sites = 8, Kimura (unadjusted) = 27.80 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.06 (3 / 50), avg. gap size = 1.00 (3 / 3) 256 30.15 0.93 4.81 chrXptel1M 832226 832333 (167667) L2c_3end#LINE/L2 153 256 (222) m_b347s601i6 14528 chrXptel1M 832226 GTCTGGAACGCATTTCCTTCTTACTACTGCCTCATAAAATCTCTTGTTT- 832274 i i vi ii i v v ii viiv -- i ii i- L2c_3end#LINE 153 GCCTGGAATGCTCTTCCCCCCTCCTTCCACCTGGCTAA--CTCCTACTCA 200 chrXptel1M 832275 TCTTTGGAAGCTCAGCTCAGCTGCCACCTCCTCTGTGCAAACTTGCTTCT 832324 i vi i? v i i - v i i v -i L2c_3end#LINE 201 TCCTTCAAGNCTCAGCTCAGATGTCACCTCCTCCG-GGAAGCCTTC-CCT 248 chrXptel1M 832325 GCACCCCCC 832333 - L2c_3end#LINE 249 G-ACCCCCC 256 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.71 CpG sites = 22, Kimura (unadjusted) = 41.51 Transitions / transversions = 2.44 (22/9) Gap_init rate = 0.06 (6 / 107), avg. gap size = 1.00 (6 / 6) 212 18.92 28.38 0.00 chrXptel1M 832554 832627 (167373) L2a_3end#LINE/L2 386 480 (37) m_b347s601i7 14528 chrXptel1M 832554 TCTGCCCAATACAATGTAAGCTTCTTGAGGG------CTTTTTTC---TT 832594 iv v v i v ------ v --- L2a_3end#LINE 386 TCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTCTGTTT 435 chrXptel1M 832595 TGTT------------CCTAGTGCCTGGCAGAATGCCTGGCAAAT 832627 ------------ i i i v v i v L2a_3end#LINE 436 TGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACAT 480 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 20.21 CpG sites = 6, Kimura (unadjusted) = 21.84 Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.04 (3 / 73), avg. gap size = 7.00 (21 / 3) 31 0.00 0.00 0.00 chrXptel1M 833376 833402 (166598) (TG)n#Simple_repeat 1 27 (0) c_b347s251i2 14529 chrXptel1M 833376 TGTGTGTGTGTGTGTGTGTGTGTGTGT 833402 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGT 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 204 27.18 3.12 4.21 chrXptel1M 833789 833884 (166116) C L2d2_3end#LINE/L2 (268) 287 193 m_b347s601i8 14530 chrXptel1M 833789 TTCAGAATGGAGAGAGGGCTCA--GCAAGTTGGGTTAGTCAAGGAAGGAT 833836 -- i i v --? ii i iv i i v C L2d2_3end#LIN 287 TTCAGA--GGAGGGAGAGATCACTNCGGGCTGGAGTGGTCAGGGAAGGCT 240 chrXptel1M 833837 TGCA-AGAGGAGATGTTAGTAAAGTTGGACCCTGGAGAAGAAGGTGGGA 833884 - -i i v? v vi i i i i i v-i i C L2d2_3end#LIN 239 T-CACGGAGGAGGTGGNATTTGAGCTGGGCCTTGAAGGAT-GGGTAGGA 193 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.02 CpG sites = 18, Kimura (unadjusted) = 36.71 Transitions / transversions = 2.57 (18/7) Gap_init rate = 0.06 (6 / 95), avg. gap size = 1.17 (7 / 6) 183 30.76 3.03 1.49 chrXptel1M 834279 834344 (165656) C L2d2_3end#LINE/L2 (10) 545 479 m_b347s601i9 14531 chrXptel1M 834279 TCAACAAACTCCT-TTGGACACATACTGTGTGGAAGG-GTTGTACTAGAT 834326 ivii - ii i v v -ii i ii C L2d2_3end#LIN 545 TCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGC 496 chrXptel1M 834327 AGTGCAGTGAGATAGAAA 834344 iv ii - i v C L2d2_3end#LIN 495 GCTGTGG-GGGATACAAA 479 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.87 CpG sites = 15, Kimura (unadjusted) = 42.84 Transitions / transversions = 3.00 (15/5) Gap_init rate = 0.05 (3 / 65), avg. gap size = 1.00 (3 / 3) 44 7.52 0.00 0.00 chrXptel1M 834412 834467 (165533) (AT)n#Simple_repeat 1 56 (0) c_b347s251i3 14532 chrXptel1M 834412 ATATATAAATTTATATATATATATATATATATATATACGTATATATATAT 834461 v v ii (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chrXptel1M 834462 ATATAT 834467 (AT)n#Simple_ 51 ATATAT 56 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0) 17 25.80 1.92 0.00 chrXptel1M 834470 834521 (165479) (ACAT)n#Simple_repeat 1 53 (0) m_b347s252i8 14533 chrXptel1M 834470 ACACATATAAATATGTATACACAGGCATACATACATATATACATA-ATAA 834518 i i v ii i i vi i - v (ACAT)n#Simpl 1 ACATACATACATACATACATACATACATACATACATACATACATACATAC 50 chrXptel1M 834519 ATA 834521 (ACAT)n#Simpl 51 ATA 53 Matrix = Unknown Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.02 (1 / 51), avg. gap size = 1.00 (1 / 1) 231 15.49 30.00 3.17 chrXptel1M 834768 834867 (165133) MIRb#SINE/MIR 5 130 (138) m_b347s601i10 14534 chrXptel1M 834768 GGGGCAGCCAGGTGGCGCAGTGGAGAGAGCAC------------CAG-CA 834804 --- i i ------------ - MIRb#SINE/MIR 5 GGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACA 51 chrXptel1M 834805 AATATGG-------TCTCAGATC---------CTAGCTGTGTGACCCTGG 834838 i iv ------- i i v --------- i MIRb#SINE/MIR 52 GACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 101 chrXptel1M 834839 GCAAAGTCACTTAAGCCCAATT-GCCTCAG 834867 - i v i vv v- MIRb#SINE/MIR 102 GC-AAGTTACTTAACCTCTCTGAGCCTCAG 130 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 16.49 CpG sites = 9, Kimura (unadjusted) = 17.72 Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.09 (9 / 99), avg. gap size = 3.78 (34 / 9) 234 13.05 2.13 2.13 chrXptel1M 834821 834867 (165133) MIR#SINE/MIR 77 123 (139) m_b347s601i11 14534 chrXptel1M 834821 CTAGCTGTGTGACCCTGGGCAAAGTCACTTAAGCCCAAT-TGCCTCAG 834867 i - i v i vv - MIR#SINE/MIR 77 CTAGCTGTGTGACCTTGGGC-AAGTTACTTAACCTCTCTGTGCCTCAG 123 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 14.38 CpG sites = 3, Kimura (unadjusted) = 14.38 Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.04 (2 / 46), avg. gap size = 1.00 (2 / 2) 200 33.84 12.71 2.50 chrXptel1M 834923 835213 (164787) C L2c_3end#LINE/L2 (37) 441 122 m_b347s601i12 14531 chrXptel1M 834923 ATGGGCCAGGTGCCGAAGAAACAAATGCAAAGAATGAAACGATCCCTACT 834972 v i i ii v viii v - v i i i C L2c_3end#LINE 441 ATGTGCCAGGCGCTGGGGATACAAAGATGAATAA-GACACGGTCCCTGCC 393 chrXptel1M 834973 CCAAAAGAGCCTGCCTTCTA-TGGGGGAAAGCAG-TAGTCAGACGTATAA 835020 iv i iii vv - i i - -i ?vi i iv i C L2c_3end#LINE 392 CTCAAGGAGCTCACAGTCTAGTGGAGGAGA-CAGACANGTAAACAGACAA 344 chrXptel1M 835021 GTAAATTTGAAATGAATATAAAGTG-GATAAGTATGTGGTTGTTAAGAGG 835069 v v v vv i v ivv -v --- v iv i vi v C L2c_3end#LINE 343 TTACAATACAAGTTAATGATAAGTGCTATA---ATGGGAGTATAGACAGG 297 chrXptel1M 835070 G----AGGTGATTATTGAGGGAGG--CCTCCATTA-------GGGGTCAG 835106 ---- v v vi iv ii -- vv i ------- C L2c_3end#LINE 296 GTGCTATGGGAGCACAGAGGAGGGCACCTAGACTAGNCTTGGGGGGTCAG 247 chrXptel1M 835107 GAAGGACTTCAAACGGATGGTGTG---------------CTTGAAGAAAG 835141 i i i --v v iv --------------- i v C L2c_3end#LINE 246 GGAAGGCTTC--CCGGAGGAGGTGACATCTGAGCTGAGNCTTGAAGGATG 199 chrXptel1M 835142 AG-AGGAATTCTGTGAGGTGCAGAGAAGGAGGGAGTATATTTTGGTCTGG 835190 - i v- iv v ii i i i vii iii v v i C L2c_3end#LINE 198 AGTAGGAGTTA-GCCAGGTGGAAGGAGGGGGGAAGAGCATTCCAGGCAGA 150 chrXptel1M 835191 AG-----GCTTGACCAAAGGGTCAAAGG 835213 i ----- v vv v? ii C L2c_3end#LINE 149 GGGAACAGCATGTGCAAAGGCNCGGAGG 122 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 45.57 CpG sites = 53, Kimura (unadjusted) = 46.91 Transitions / transversions = 1.23 (53/43) Gap_init rate = 0.06 (17 / 290), avg. gap size = 2.65 (45 / 17) 194 26.28 1.43 7.58 chrXptel1M 835333 835402 (164598) C AmnL2-1#LINE/L2 (354) 2259 2194 m_b347s601i13 14535 chrXptel1M 835333 AGGTAGGTTGGGGGCAAATGGA-GGAGGGCTTTAAAAGCCAAAAAGAGAT 835381 i i - i vv - i i v ii ---- C AmnL2-1#LINE/ 2259 AGGTAGGCTGGAG-CAAGTCCATGGAGGGTTTTAAAAACAAGGAAG---- 2215 chrXptel1M 835382 GCATCTTTGACTTAAATTCTG 835402 vi vi ii i C AmnL2-1#LINE/ 2214 GCAATTTTGAACTGGATCCTG 2194 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.72 CpG sites = 12, Kimura (unadjusted) = 33.72 Transitions / transversions = 2.40 (12/5) Gap_init rate = 0.09 (6 / 69), avg. gap size = 1.00 (6 / 6) 205 30.03 12.42 4.24 chrXptel1M 835699 835851 (164149) C L2b_3end#LINE/L2 (10) 456 292 m_b347s601i14 14536 chrXptel1M 835699 TCAATAAAC-CTTAATAAAGGC-TATTAAGCACC---TTCTGTGCCAGGG 835743 i i-i v i iv - i iv ii ---i? i v C L2b_3end#LINE 456 TCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGC 407 chrXptel1M 835744 ACTGG--ATTCA------AATAGAAGGAATGTGATGATCTTGACTCTCAA 835785 i -- v ------ i ii vii i?i i --i i - i v C L2b_3end#LINE 406 GCTGGGGATACAGCGGTGAACAAGACAGACNCGGT--CCCTG-CCCTCAC 360 chrXptel1M 835786 GTAGCTCACAGTTGTAGTGGGGAAGGCAGTAAATACATAAAGCGACTA-- 835833 v i- i i --- i ii ?vv v -- C L2b_3end#LINE 359 GGAGCTCACAGTC-TAGTGGGGGAGACAG---ACATGTAANCAGACAATN 314 chrXptel1M 835834 --AATCAAGATTA--AGGGTAG 835851 -- i v v i-- C L2b_3end#LINE 313 ATAACCCAGAGTGGCAGGGTAG 292 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 39.60 CpG sites = 31, Kimura (unadjusted) = 42.18 Transitions / transversions = 2.38 (31/13) Gap_init rate = 0.10 (15 / 152), avg. gap size = 1.73 (26 / 15) 316 24.77 6.87 4.48 chrXptel1M 835720 835850 (164150) C L2c_3end#LINE/L2 (22) 456 323 m_b347s601i15 14536 chrXptel1M 835720 TATTAAGCACCTTCT--GTGCCAGGGACTGG--ATTCAAATAGAAGGAAT 835765 i i v -- vi -- v ---i v C L2c_3end#LINE 456 TATTGAGCGCCTACTATGTGCCAGGCGCTGGGGATACAAA---GATGAAT 410 chrXptel1M 835766 GTGAT--GATCTTGACTCTCAAGTAGCTCACAGTTGTAGTGGGGAAGGCA 835813 iv i-- i iivi i v i- i i i C L2c_3end#LINE 409 AAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTC-TAGTGGAGGAGACA 361 chrXptel1M 835814 G-TAAATACATAAAGCGACTA-AAT-CAAGATTAAGGGTA 835850 -i ?i v i i - i i - - - v i C L2c_3end#LINE 360 GACANGTAAACAGA-CAATTACAATACAAG-TTAATGATA 323 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 29.33 CpG sites = 22, Kimura (unadjusted) = 31.80 Transitions / transversions = 2.44 (22/9) Gap_init rate = 0.09 (12 / 130), avg. gap size = 1.25 (15 / 12) 181 28.64 8.15 4.29 chrXptel1M 835733 835867 (164133) C L2d2_3end#LINE/L2 (49) 506 367 m_b347s601i16 14536 chrXptel1M 835733 CTGTGCCAGGGACTG-----GATTCAAATAGAAGGA-ATGTGATGATCTT 835776 i vi ----- v -- v - v vv i ii C L2d2_3end#LIN 506 CTGTGCTAGGCGCTGTGGGGGATACAAA--GAAGTATAAGACATGGTCCC 459 chrXptel1M 835777 GACTCTCAAGTAGCTCACAGTTGTAGT-GGGG----AAGGCAGTAAATAC 835821 vi i v i i i- - ---- i - i C L2d2_3end#LIN 458 TGCCCTCAAGGAGCTTACAATC-TAGTTGGGGAGACAAGACA-TAAACAC 411 chrXptel1M 835822 ATAAAGCGACTAAATCAAGATTAAGGGTAGAGAGAACCAATTCAAG 835867 i i iv -i v vi vv i i vv i v - i C L2d2_3end#LIN 410 GTGAAAAG-TTAAATAACAATACAAGATTTAAATAA-CAGTTCAAG 367 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.51 CpG sites = 21, Kimura (unadjusted) = 36.98 Transitions / transversions = 1.31 (21/16) Gap_init rate = 0.07 (10 / 134), avg. gap size = 1.70 (17 / 10) 1634 25.42 3.02 3.57 chrXptel1M 836688 837250 (162750) C L1ME5_3end#LINE/L1 (314) 627 68 m_b347s551i18 14537 chrXptel1M 836688 TTCACTCAGCATCA-GTTCGTGTAAG-TCTCTCCAGGC--CTTTCTGAAA 836733 ii - -- v - iv v i-- v v v - C L1ME5_3end#LI 627 TTCACTCAGCACTATGTT--TTTAAGATCCATCCATGTTGCTATGTGTA- 581 chrXptel1M 836734 TCATCCTGTTGGTCATTTCTTACAGA-ACAGTAATATTCCATAATATTCA 836782 - iv iv iii v v v-i - i i ii i v C L1ME5_3end#LI 580 -CATCTAGTCCGTTGCTTCTAACTGCTGCA-TAGTACTCCATGGTGTGCA 533 chrXptel1M 836783 TATACCACAATTTATTCAGCCATTCTCCCACTGATGGACATCCA--TTCA 836830 vi v iii v i v i -- -- C L1ME5_3end#LI 532 TCCACCACATTTTACCTATCCACTCTCCCAGTGATGGACACCCAGGTT-- 485 chrXptel1M 836831 GTTTCCAGTTTCTGGCCACTGCAAAAAGGGCTGCCACAAACATTCTTGCA 836880 ii ii i iv ii v iv v ii i i i C L1ME5_3end#LI 484 GCCTCCAACTCCCCGCCACCACAAACAACGCTGCAATGAACATCCTCGTA 435 chrXptel1M 836881 CATACAGGCCCCTTTC---CCTTCTTTAGTATCTCTTTGGGATATAATCC 836927 --- v vi--- viv v v i vv C L1ME5_3end#LI 434 CAT---GTCCCCTTATGGACCTGTGTGAGAATTTCTTTGGGATATATACC 388 chrXptel1M 836928 CAGTAGTAACACTGCTGGATCAAAGGGTATGCACAGTTTGATAACTT--T 836975 v iiiv i i v --- --- - -- C L1ME5_3end#LI 387 CAGGAGCGGAATTGCTGGGTCATAGGGTATGC---GT---ATA-CTTAAT 345 chrXptel1M 836976 TTGAGCA--TAGTTCCAAATTGCTCTCCAGAATGGCTGGATGTGTTCACA 837023 vi -- v v i v ivv ii C L1ME5_3end#LI 344 TTGACTAAGTACTGCCAGATTGCTCTCCAGAATGGCTGCACCAGTCTACA 295 chrXptel1M 837024 ATTCCACTAACAATGTATCAGTGTCCCTGTTTTCCCACATCCCCTCCAAC 837073 v i i i i i v v i i ? i i v C L1ME5_3end#LI 294 CTCCCACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATCCTCGCCAAC 245 chrXptel1M 837074 ATTCTGCATTATCTTTCCCTGTCATTCTAGACAATCTGACAGGTGTGTAG 837123 i iv ivv ii v v i v v i i i iv C L1ME5_3end#LI 244 ACTTGGCATTATCCAGCTTTCTAATTTTTGCCAGTCTAATAGGTGTAAAG 195 chrXptel1M 837124 TGGTATCTCAGAGTTGTCTTAATTTGAATTTCTCTGATCAATAGTGATTT 837173 i vv i v i v i v C L1ME5_3end#LI 194 TGATATCTCATTGTTGTTTTAATTTGCATTTCTCTGATTACTAATGAGTT 145 chrXptel1M 837174 GGAGCCCTCTTTCATATGACTAGAAATAG--TTTCAG-TTTCTTCTTCTG 837220 v viiii - v v-- -- i - i C L1ME5_3end#LI 144 TGAGCATCTCTTCATATG-CTTGT--TAGCCTTTCGGGTTTCCTCTTCTG 98 chrXptel1M 837221 AAAATTGTCTGTTCATATCCTTTGACCATT 837250 v i v C L1ME5_3end#LI 97 TAAATTGCCTGTTCATATCCTTTGCCCATT 68 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 30.82 CpG sites = 78, Kimura (unadjusted) = 31.67 Transitions / transversions = 1.30 (78/60) Gap_init rate = 0.05 (30 / 562), avg. gap size = 1.23 (37 / 30) 14 0.00 0.00 0.00 chrXptel1M 838452 838469 (161531) (AGC)n#Simple_repeat 1 18 (0) m_b347s252i9 14538 chrXptel1M 838452 AGCAGCAGCAGCAGCAGC 838469 (AGC)n#Simple 1 AGCAGCAGCAGCAGCAGC 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 15 18.85 0.00 0.00 chrXptel1M 838971 839006 (160994) (GGGACAG)n#Simple_repeat 1 36 (0) m_b347s252i10 14539 chrXptel1M 838971 GGGGCAGGGGGCAGGGGCCAGCGCACAGGGCACAGG 839006 i i v v v v (GGGACAG)n#Si 1 GGGACAGGGGACAGGGGACAGGGGACAGGGGACAGG 36 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 33 0.00 0.00 0.00 chrXptel1M 839705 839732 (160268) (GT)n#Simple_repeat 1 28 (0) c_b347s251i4 14540 chrXptel1M 839705 GTGTGTGTGTGTGTGTGTGTGTGTGTGT 839732 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGT 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 14 12.03 0.00 0.00 chrXptel1M 840775 840801 (159199) (AATGA)n#Simple_repeat 1 27 (0) m_b347s252i12 14541 chrXptel1M 840775 AATGAAAAAAAATTAAATGAAATGAAA 840801 vi v (AATGA)n#Simp 1 AATGAAATGAAATGAAATGAAATGAAA 27 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 624 29.59 1.53 0.00 chrXptel1M 842430 842625 (157375) C L1ME4c_3end#LINE/L1 (400) 430 232 m_b347s551i19 14542 chrXptel1M 842430 CTTTTTCCTCCTTT---ATGATTTCCTTGGGGTGCAAGTGCAATAGAAAA 842476 i --- v i i iv vviv iv vii C L1ME4c_3end#L 430 CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAATTCCCAGAAGTGGA 381 chrXptel1M 842477 ACTGCTGGATCAAAGGGCATGCACAGTTTGATAACTTTTTGGGCATAGTT 842526 i i i i v v v ii i vivi i v v C L1ME4c_3end#L 380 ATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTCTTGATACGTATTG 331 chrXptel1M 842527 CCAAATTGCTCTCCAGAATGGCTGGATCCATTCACAAGTCCACCAACGAT 842576 i i v i v i v i ?vv i i C L1ME4c_3end#L 330 CCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACANTGCCACCAGCAAT 281 chrXptel1M 842577 GTATTAGTGTCCCAGTTTTCCCACACCCCCCCTGACATTTACCATTATC 842625 v ? v iv i ? i v iii vivi C L1ME4c_3end#L 280 GTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGCATTGGGTATTATC 232 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.65 CpG sites = 33, Kimura (unadjusted) = 39.38 Transitions / transversions = 1.32 (33/25) Gap_init rate = 0.01 (1 / 195), avg. gap size = 3.00 (3 / 1) 907 25.37 2.82 2.82 chrXptel1M 843169 843452 (156548) L1ME4c_3end#LINE/L1 271 554 (276) m_b347s551i20 14543 chrXptel1M 843169 ACATTGATGCATTGTTGGTGGAGTTGTGAATGAATCCAACCATTTTGGAG 843218 ?i v i i vi? i vii v v i L1ME4c_3end#L 271 ACNCTCATACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAA 320 chrXptel1M 843219 AGTAGTTTGGAACTATA-ATCAAAAAGTTATCAAACTGTGCATACCCTTT 843267 i i v v ii- i - ii v v v L1ME4c_3end#L 321 AGCAATTTGGCAATACGTATCAAGA-GCCATAAAAATGTTCATACCCTTT 369 chrXptel1M 843268 GATCCAGCAGTGTTACTACTGGGCTTATATCCCAAAGAGATTAT---AAA 843314 i i i vii v vv v i i i v --- L1ME4c_3end#L 370 GACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAA 419 chrXptel1M 843315 GAAGGGAAAGGGACCTGTATGTGCACGA--ATGTTTGTGGCAGCCCTTTT 843362 i i -----v i -- ii v vi v L1ME4c_3end#L 420 GAAGGAAAAAG-----CTATATGCACGAAGATGTTCATTGCAGCGTTATT 464 chrXptel1M 843363 TGTAGTGGCTAAAAACTGGAAACTGAA--TGGATGTCCATCAGTTGGAGA 843410 i i i v i -- -- ii v i v i L1ME4c_3end#L 465 TATAATAGCGAAAAATTGGAAAC--AACCTAAATGTCCAACAATAGGGGA 512 chrXptel1M 843411 ATGGCTGAATAAATTGTGGTATATGAATATTATGGAATATTA 843452 i i i i i v? iviv L1ME4c_3end#L 513 ATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATATTA 554 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 31.13 CpG sites = 44, Kimura (unadjusted) = 32.31 Transitions / transversions = 1.69 (44/26) Gap_init rate = 0.04 (12 / 283), avg. gap size = 1.33 (16 / 12) 790 27.67 4.49 7.16 chrXptel1M 843175 843575 (156425) L1ME5_3end#LINE/L1 277 667 (274) m_b347s551i21 14543 chrXptel1M 843175 ATGCATTGTTGGTGGAGTTGTGAATGAATCCAACCATTTTGGAGAGTAGT 843224 i i iiv ii ivii v i i i i L1ME5_3end#LI 277 ATGCACTGCTGGTGGGAGTGTAGACTGGTGCAGCCATTCTGGAGAGCAAT 326 chrXptel1M 843225 TTGGAACTA--TAATCAAA--AAGTTATCAAACTGTGCATACCCTTTGAT 843270 i v v -- i -- - --- --- v i L1ME5_3end#LI 327 CTGGCAGTACTTAGTCAAATTAAGT-AT---AC---GCATACCCTATGAC 369 chrXptel1M 843271 CCAGCAGTGTTACTACTGGGCTTATATCCCAAAGAGATTATAAAGAAGGG 843320 i viii v iv i v v viv v L1ME5_3end#LI 370 CCAGCAATTCCGCTCCTGGGTATATATCCCAAAGAAATTCTCACACAGGT 419 chrXptel1M 843321 ----AAAGGGACCTGTATGTGCACGAATGTTTGTGGCAGCCCTTTTTGTA 843366 ---- i ---- i iv i ii v vi v i L1ME5_3end#LI 420 CCATAAGGGGAC----ATGTACGAGGATGTTCATTGCAGCGTTGTTTGTG 465 chrXptel1M 843367 GTGGCTAAAAACTGGAAACTGAA--TGGATGTCCATCAGTTGGAGAATGG 843414 viii ii ii -- -- i v v i L1ME5_3end#LI 466 GTGGCGGGGAGTTGGAGGC--AACCTGGGTGTCCATCACTGGGAGAGTGG 513 chrXptel1M 843415 CTGAATAAATTGTGGTATATGAATATTATGGAATATTACTGT-TCTGTAA 843463 v iii v iv v i ii i i - i-v v v L1ME5_3end#LI 514 ATAGGTAAAATGTGGTGGATGCACACCATGGAGTACTA-TGCAGCAGTTA 562 chrXptel1M 843464 GAAATGACCAACAGGATAATTTCAGAAAG--GCCTGGAGAGA-CTTACAC 843510 iii vi vi i-- v v v --i v vi - v - L1ME5_3end#LI 563 GAAGCAACGGACTAGATG--TACACATAGCAACATGGATGGATCTTAAA- 609 chrXptel1M 843511 GAAC-TGATGCTGAGTGAAATGAGCAGGGACCAG---GAGATCATTATAT 843556 - - ii vi i i i v --- --? - L1ME5_3end#LI 610 -AACATAGTGCTGAGTGAAAAAAGTAAGAAACAGAATGAGAT--NTATA- 655 chrXptel1M 843557 ACTTCAACAACAATACTAT 843575 ------- i L1ME5_3end#LI 656 AC-------ACAATACCAT 667 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 34.83 CpG sites = 65, Kimura (unadjusted) = 35.75 Transitions / transversions = 1.71 (65/38) Gap_init rate = 0.09 (37 / 400), avg. gap size = 1.24 (46 / 37) 24 17.89 0.00 0.00 chrXptel1M 843983 844026 (155974) (A)n#Simple_repeat 1 44 (0) m_b347s252i13 14544 chrXptel1M 843983 AAATAAAAAAAATTAAATTAAAAAAAAAAAGAAAAAAAAGAAAA 844026 v vv vv i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 44 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 288 28.37 5.16 4.49 chrXptel1M 844163 844317 (155683) C L1ME4a_3end#LINE/L1 (651) 220 65 m_b347s551i22 14545 chrXptel1M 844163 TCCTAGCCAATTTGATAGGTATGAAATGATACCTCATGGTTACTTTAACC 844212 i v ivi i i v ii ii C L1ME4a_3end#L 220 TCTTTGCCAATTTGATAGGTGAAAAATGGTATCTCATTGTTGTTTTAATT 171 chrXptel1M 844213 TGCATTTCACTAAGCAATAATGA--TTTAATGCAATTTTAAAAGTATA-- 844258 vi i vi v i -- v iii?v i v v v -- C L1ME4a_3end#L 170 TGCATTTCTTTGATTACTAGTGAGGTTGAACATNTTTTCATATGTTTATT 121 chrXptel1M 844259 -ACTATAAATTGTCTTGATTATTGCATTGGAAAACTGT---TTCATATCC 844304 -i i --- ---- vi v v v vi i --- i C L1ME4a_3end#L 120 GGCCAT---TTGT----ATTTCTTCTTTTGTGAATTGTCTGTTCATGTCC 78 chrXptel1M 844305 TTTGACTATCTTT 844317 v i i C L1ME4a_3end#L 77 TTTGCCCATTTTT 65 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.00 CpG sites = 25, Kimura (unadjusted) = 37.00 Transitions / transversions = 1.47 (25/17) Gap_init rate = 0.07 (11 / 154), avg. gap size = 1.36 (15 / 11) 340 23.53 0.00 0.00 chrXptel1M 844168 844235 (155765) C L1ME3Cz_3end#LINE/L1 (786) 211 144 m_b347s551i23 14545 chrXptel1M 844168 GCCAATTTGATAGGTATGAAATGATACCTCATGGTTACTTTAACCTGCAT 844217 i i i i i v ?ii ii C L1ME3Cz_3end# 211 GCCAATCTGATGGGTGTGAAATGGTATCTCATTGTNGTTTTAATTTGCAT 162 chrXptel1M 844218 TTCACTAAGCAATAATGA 844235 v i vi v i C L1ME3Cz_3end# 161 TTCCCTGATTACTAGTGA 144 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 30.24 CpG sites = 12, Kimura (unadjusted) = 30.24 Transitions / transversions = 3.00 (12/4) Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0) 13 19.20 0.00 6.82 chrXptel1M 844728 844774 (155226) (TTTTACA)n#Simple_repeat 1 44 (0) m_b347s252i14 14546 chrXptel1M 844728 TTTAAAATTTTAGTGTTATTACAATTATACATTTTACATTTAACTTT 844774 v v -ii - - v v v (TTTTACA)n#Si 1 TTTTACATTTTA-CATT-TTAC-ATTTTACATTTTACATTTTACATT 44 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.07 (3 / 46), avg. gap size = 1.00 (3 / 3) 11 18.65 0.00 7.69 chrXptel1M 844746 844787 (155213) (TTACAT)n#Simple_repeat 1 39 (0) m_b347s252i15 14546 chrXptel1M 844746 TTACAATTATACATTTTACATTTAACTTTGCTCTTTCATTTA 844787 - - - vv i vi v (TTACAT)n#Sim 1 TTAC-ATT-TACA-TTTACATTTACATTTACATTTACATTTA 39 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.07 (3 / 41), avg. gap size = 1.00 (3 / 3) 289 30.40 1.34 0.67 chrXptel1M 845010 845158 (154842) C L1P4_orf2#LINE/L1 (753) 2541 2392 m_b347s551i24 14547 chrXptel1M 845010 GAATTTTGTTATTGTCTTTTCTAATTCAGTAAAAAAAAAAATGGGTAATT 845059 ivv v i v i vi vi v i C L1P4_orf2#LIN 2541 GAATTTTAGAATAGTTTTTTCTAATTCTGTGAAAAATGACGTTGGTAGTT 2492 chrXptel1M 845060 TAATTGACCTGGCTTTGAATATATAAATTAGTTTGGACAAAACTGTCATT 845109 i v ivv i v v i i iv i iv iv i C L1P4_orf2#LIN 2491 TGATAGGAATAGCGTTGAATCTGTAGATTGCTTTGGGCAGTATGGCCATT 2442 chrXptel1M 845110 TTTATTATAAT-ATCCTTCCCTTGTCATGAACAATTAATATTTCT-CATT 845157 v iv v - i vv -i i vvv i i - C L1P4_orf2#LIN 2441 TTAACGATATTGATTCTTCCAAT-CCATGAGCATGGAATGTTTTTCCATT 2393 chrXptel1M 845158 T 845158 C L1P4_orf2#LIN 2392 T 2392 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.27 CpG sites = 22, Kimura (unadjusted) = 39.44 Transitions / transversions = 0.96 (22/23) Gap_init rate = 0.02 (3 / 148), avg. gap size = 1.00 (3 / 3) 285 30.11 5.06 1.08 chrXptel1M 845023 845200 (154800) C L1P1_orf2#LINE/L1 (766) 2528 2344 m_b347s551i25 14547 chrXptel1M 845023 GTCTTTTCTAATTCAGTAAAAAAAAAAATGGGTAATTTAATTGACCTGGC 845072 i i v i i ivv v ii i v ivv C L1P1_orf2#LIN 2528 GTTTTTTCCAATTCTGTGAAGAAAGTCATTGGTAGCTTGATGGGGATGGC 2479 chrXptel1M 845073 TTTGAATATATAAATTAGTTTGGACAAAACTGTCATTTTTATTATAAT-A 845121 v v vi i iv iv i i iv v - C L1P1_orf2#LIN 2478 ATTGAATCTATAAATTACCTTGGGCAGTATGGCCATTTTCACGATATTGA 2429 chrXptel1M 845122 TCCTTCCCTTGTCATGAACAATTAATATTTCTC-----ATTTAAATCTAA 845166 i - vvi i vvv i ii -----i iv ivv C L1P1_orf2#LIN 2428 TTCTT-CCTACCCATGAGCATGGAATGTTCTTCCATTTGTTTGTATCCTC 2380 chrXptel1M 845167 TTTTATTTGTATGAAAA---GTTTTTAGCTTCTTCTT 845200 v?v iv --- v - i C L1P1_orf2#LIN 2379 TTTTATTTCNTTGAGCAGTGGTTTGTAG-TTCTCCTT 2344 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.42 CpG sites = 27, Kimura (unadjusted) = 39.36 Transitions / transversions = 1.04 (27/26) Gap_init rate = 0.03 (5 / 177), avg. gap size = 2.20 (11 / 5) 46 1.59 0.00 8.57 chrXptel1M 845201 845276 (154724) (CTT)n#Simple_repeat 1 70 (0) m_b347s252i16 14548 chrXptel1M 845201 CTTCTTCTTCCTCCTTCTTCCTTCTTCTTCTTTCTTCTTTCTTCTTCTTT 845250 - i - - - - (CTT)n#Simple 1 CTTCTTCTT-CTTCTTCTT-CTTCTTCTTC-TTCTTC-TTCTTCTTC-TT 45 chrXptel1M 845251 CTTCTTCTTTCTTCTTCTTCTTCTTC 845276 - (CTT)n#Simple 46 CTTCTTC-TTCTTCTTCTTCTTCTTC 70 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.08 (6 / 75), avg. gap size = 1.00 (6 / 6) 24 3.57 0.00 0.00 chrXptel1M 845387 845415 (154585) (AT)n#Simple_repeat 1 29 (0) m_b347s252i17 14549 chrXptel1M 845387 ATATATATATATATACATATATATATATA 845415 i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATA 29 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 507 28.98 5.71 4.09 chrXptel1M 845422 845806 (154194) C L1M1_orf2#LINE/L1 (1064) 2230 1840 m_b347s551i26 14550 chrXptel1M 845422 CATATATATATGCTAAAGATTTATGAA----AACTTTATATCCTAGTATT 845467 v v vv v v ----i i i ivv i C L1M1_orf2#LIN 2230 CATATAGAAATGCTACTGATTTTTGTATGTTGATTTTGTATCCTGCAACT 2181 chrXptel1M 845468 TTGATAAA---GTTTAGTTGTTTCAACTAATATTTTAGTTGAGTCT--GG 845512 iv i --- viv ii - i v ? v --i C L1M1_orf2#LIN 2180 TTACTGAATTTGTTTATCAGTTCTAA-TAGTTTTTTNGTGGAGTCTTTAG 2132 chrXptel1M 845513 GATTTTCCAAGAATATCACCATATCATCTG---ACAAGAGATAGTTTTGT 845559 v iv vv i --- - i vii C L1M1_orf2#LIN 2131 GTTTTTCCAAATATAAGATCATATCATCTGCAAACAAG-GATAATTTGAC 2083 chrXptel1M 845560 TACATCATTCTCTATTCTGAT---TTCAATTTCTTCTTCTT-TTTAAAAA 845605 v v v ii v iv ---i iv ii - i ----i C L1M1_orf2#LIN 2082 TTCTTCCTTTCCAATTTGGATGCCCTTTATTTCTTTCTCTTGTCT----G 2037 chrXptel1M 845606 ATTGTTATTGCTAAGATTTCCAAAGCAATACTGACTAACACTGTTGACAG 845655 i v v i i ivi v ii v v v v C L1M1_orf2#LIN 2036 ATTGCTCTAGCTAGGACTTCCAGTACTATGTTGAATAACAGTGGTGAAAG 1987 chrXptel1M 845656 TGGGTATCTTTGT----TTCACAG-TCTTACAGGGAAGGCTTCAAGCTTA 845700 i i ---- - - v i iv i v C L1M1_orf2#LIN 1986 TGGGCATCCTTGTCGTGTTC-CAGATCTTAGAGGAAAGGCTTTCAGTTTT 1938 chrXptel1M 845701 TTCCTGTTACATAATAAAATTAGCTGATGGTTTTAGATAAATGCGTTTTT 845750 i ii - vv i v i - v i i-------v v v C L1M1_orf2#LIN 1937 TCCCCATT-CAGTATGATACTAGCTG-TGGGTCTG-------TCGTATAT 1897 chrXptel1M 845751 TTTTTTTATCAATTTAAGGGAAAGTCTGTTTATA-CCAATGTTTTCAGTT 845799 vvi i vv i v viv iv i - i v v vv C L1M1_orf2#LIN 1896 GGCTTTTATTATGTTGAGGTATGTTCCTTCTATACCCAGTTTTTTGAGGG 1847 chrXptel1M 845800 TTTTTGT 845806 i C L1M1_orf2#LIN 1846 TTTTTAT 1840 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.21 CpG sites = 53, Kimura (unadjusted) = 37.21 Transitions / transversions = 0.98 (53/54) Gap_init rate = 0.07 (25 / 384), avg. gap size = 1.52 (38 / 25) 15 5.48 0.00 0.00 chrXptel1M 845809 845827 (154173) (T)n#Simple_repeat 1 19 (0) m_b347s252i18 14551 chrXptel1M 845809 TTGTTTTTTTTTTTTTTTT 845827 v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 22 7.25 0.00 0.00 chrXptel1M 847308 847336 (152664) (A)n#Simple_repeat 1 29 (0) m_b347s252i19 14552 chrXptel1M 847308 AAAAGTAAAAAAAAAAAAAAAAAAAAAAA 847336 iv (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA 29 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 208 34.29 8.09 1.38 chrXptel1M 847427 847562 (152438) C MIR3#SINE/MIR (57) 151 7 m_b347s601i17 14553 chrXptel1M 847427 AACCAGCTCATTTTATAAATGAGGAAACTGAA--TCAAACAGGATAAAGC 847474 vv i i i--i i v - i i C MIR3#SINE/MIR 151 AACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGG-TGAAGT 103 chrXptel1M 847475 AAAAGTATCTAAGGCCAGAT-TTGAATCAAT--CA-AATTGAGTCTTGAT 847520 -i vv ii i i v i-vi? i i i -- - iii i v v v C MIR3#SINE/MIR 102 -GACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAA 54 chrXptel1M 847521 TTCAGA-CTC--AACGTTTGGTCCA-ACT-TCACCAGTCAGCCACTC 847562 ii i- --i viiii i-i - v iiv C MIR3#SINE/MIR 53 CCCAGGTCTCCTGACTCCCAGTCCGTGCTCTCTCTGCTCAGCCACTC 7 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 47.28 CpG sites = 33, Kimura (unadjusted) = 50.51 Transitions / transversions = 2.54 (33/13) Gap_init rate = 0.07 (10 / 135), avg. gap size = 1.30 (13 / 10) 20 25.03 0.00 0.00 chrXptel1M 848648 848694 (151306) (AT)n#Simple_repeat 1 47 (0) m_b347s252i20 14554 chrXptel1M 848648 ATATATAGAGATCTAGATACACACAAATATATAAATATATTTATATA 848694 v v v v i i i v v v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATA 47 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 12 18.24 4.26 4.26 chrXptel1M 850855 850901 (149099) (CCCGGC)n#Simple_repeat 1 47 (0) m_b347s252i21 14555 chrXptel1M 850855 CCCGGCCCCGAAACCCCGGCCCC-ACACC-CCCCCAGCCCCTGCCGCGG 850901 --i -i v -v i v v (CCCGGC)n#Sim 1 CCCGGCCCCG--GCCCCGGCCCCGGCCCCGGCCCCGGCCCCGGCCCCGG 47 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.09 (4 / 46), avg. gap size = 1.00 (4 / 4) 385 29.91 7.03 4.21 chrXptel1M 852824 853008 (146992) HERV4_I#LTR/ERV1 3251 3440 (3099) m_b348s701i0 14556 chrXptel1M 852824 GGGGACACACGATGGTCTCCTACTTTAGATCTTAAAGATGCTTTCTTTTG 852873 ii vi iii viiii i v i v HERV4_I#LTR/E 3251 GGGGATGCAAAATGGTTCTCAGTCCTAGACCTAAAAGATGCTTTCTTCTC 3300 chrXptel1M 852874 TGCACCATTG--CATAAAGTCACAATTTCTTTTTGCCTTTAAAGGGAGAA 852921 iiiv vi -- vi i v vi i v ii HERV4_I#LTR/E 3301 CATTCCTCTGGCCCCAGAGTCCCAATACCTTTTTGCCTTTGAATGGGAAA 3350 chrXptel1M 852922 AT-------CCAGGGGAACGTAAACCCCCACCAATGCACATGGCCAGTCC 852964 ------- i i --- ----- v i v v v HERV4_I#LTR/E 3351 ATCCTAATACCAGAGAAA---AA-----CAACAATACACTTGGACAGTGC 3392 chrXptel1M 852965 CGCCTCAGGG----CGTGACGGCCCCCACATATTTGGACAGGCCCTGG 853008 iv ---- v ii iv v vv ii i i HERV4_I#LTR/E 3393 TCCCTCAGGGCTTTCGGGATAGCCCCCATTTCTTTGCCCGAGCCTTAG 3440 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.69 CpG sites = 33, Kimura (unadjusted) = 39.67 Transitions / transversions = 1.65 (33/20) Gap_init rate = 0.06 (11 / 184), avg. gap size = 1.91 (21 / 11) 1364 29.61 4.83 4.94 chrXptel1M 853150 854101 (145899) PRIMA41-int#LTR/ERV1 4054 5004 (2752) m_b348s701i1 14556 chrXptel1M 853150 CAGTCTCTTGAGACCCTGAAAGCTAAAC--GGACC-TCTCCTCCACCTTA 853196 ?v i i v ? vv -- ? -v ?--i i PRIMA41-int#L 4054 CANACTTTTAATACCCTNAAAGAGAAACTGGGANCAGCTCCN--GCCTTG 4101 chrXptel1M 853197 GCCCTCCCTAG--------AGCCTTTT-----ATG-------AAAGCCAG 853226 vv? i i-------- ? ----- ------- i v PRIMA41-int#L 4102 GGANTCCCCAANTTNGANAAGCCNTTTCCTTTATGTGGCTGAAAAACAAG 4151 chrXptel1M 853227 GGCCAGGTCCTAGGGGTCTCGACTCAGTCCCTGGGACCCGATCTCAGACC 853276 v -- i i v ii?i i ivvv vvi- i v PRIMA41-int#L 4152 GGAC--GCCCTGGGTGTCCTNGCCCAAAGGCTGGGAAAT-ATCCCCGACC 4198 chrXptel1M 853277 TCTTGCTTCTTTCTCAAAGAAACTGGACTCAGTTTCCCTAGAATAGCCCT 853326 vv v ? v i v v i i ivi vv ?iii ii i ?v PRIMA41-int#L 4199 AGTGGCNTATTTTTCTAAGCAGCTAGACCAGGTGGCNTCGGGGTGGCCNG 4248 chrXptel1M 853327 CCAGCCTTAGAATGGTGACTGCCATGGCCCTTTTAATTGAAGAAGCCTA- 853375 vvv ? iii? ?i ? ? iv i ? ii v ? vi- PRIMA41-int#L 4249 GATGCCTNAGGGCNGTNGCNGCNACCGCTCTNTTGGTAGANGAAGCCAGT 4298 chrXptel1M 853376 AAACTCACCCTAGGACAGCTATTGGAGGTTTTAACCTTCTCCCCTCCTCC 853425 ? ?i i i v?i i i i----------- ? PRIMA41-int#L 4299 AAACTNACNTTGGGACAACANCTAGAGGTTTTGACCC-----------CN 4337 chrXptel1M 853426 CACCCTGCCTTGGGTTCAGAGCATTCTAGAAGCCAAAGGGCATCAATGGC 853475 -------ii v i vi i ? i i i ? PRIMA41-int#L 4338 CACC-------AAGTACAGGGGGTCCTAGAAGCNAAAGGACACCAGTGGN 4380 chrXptel1M 853476 TAGCGAGTGGGAGGCTTACT-AGATATCCGGCTCTCCTACTAGACACCCC 853524 ii - v vi? - i v i ?i i PRIMA41-int#L 4381 TGAC-AGGGGGACANTTACTNAAATATCAGGCTTTNTTGCTAGACACCCC 4429 chrXptel1M 853525 GACTTGATTATCCTGGTGTGTCCCACTCTTAATCCTGCCAACCTGCTC-C 853573 iv i i v ivvi i i vv i v i v i - ?i i- PRIMA41-int#L 4430 GATGTAACTCTTAAAGTATGCCAAACTTTGAACCCAGCTA-CCTNTTTGC 4478 chrXptel1M 853574 CTGATAGATAGCACTCAGTCAGG------AGATGTCATTCATAATTGTGA 853617 ? -------- i -- ------ -- ---- iv PRIMA41-int#L 4479 CNGA--------ACCCA--CAGGCACCCTAGAT--CATTC----TTGTAT 4512 chrXptel1M 853618 GGAAGCTTTAGATTG--TCTACTCCAGCAGATTG-ACCTGAGGGATATTC 853664 iv i v i vii-- i ? iii - i i i ivv PRIMA41-int#L 4513 ACAAGTTATGGAGCAAATTTACTCCAGCNGGCCGGACTTAAAGGATGAGC 4562 chrXptel1M 853665 CTCTTGACAACCCAGATGGT-GAATGGTTTACAGATGGGTCAAGTTTTCT 853713 i v i i v - - --- vvii PRIMA41-int#L 4563 CCCTAGATAATCCCGA-GGTAGAATGGTTTACAGATGG---AAGTAGCTT 4608 chrXptel1M 853714 TG-AAAATAGGGCA--AGAAAGGCAGGTTATTCTGTGGTGACTCTCAATG 853760 -iv v? v -- ? v v ? v vi vvv ? PRIMA41-int#L 4609 TGTGCACNAGGGAAACAGAAAGGCNGGGTATGCTGTNGTTAGCCAACANG 4658 chrXptel1M 853761 GCACCTTGGAAGCTGAGCCACTACCTCCTGTGACTTCTGCCCAGAAAGCT 853810 ivii?v v i ?? v vi vv vi? i v i i i v PRIMA41-int#L 4659 AGGTNATCGAGGCNNAGGCCTTACCGGCTTCNACCTCAGCTCAAAAGGCG 4708 chrXptel1M 853811 GAACTCATTGTCCTAACCAGAGTTTTGGAACTGGGGAAGGGAATAAGAGT 853860 i v ? ii ? ii i iii ?v i i ivv PRIMA41-int#L 4709 GAATTAATNGCTCTNATTAGGGCCCTNCAATTGGGAAAGGACTTAAGAGT 4758 chrXptel1M 853861 GAACATGTCCACCAATTCCATGTCTGCTTTTC--ATGTTT--TGCTCATG 853906 v ? ? ii v v ?? --i i i-- PRIMA41-int#L 4759 CAACATNTNCACTGATTCCAAGTATGNNTTTCTGGTGCTCCATGCTCATG 4808 chrXptel1M 853907 GGACTAGATGGAAAGAAAGGGGACTTTTGACAGCAAAGAATCCTCTTATT 853956 v?i i v? i ? ?i i ? v ii?i i ii v PRIMA41-int#L 4809 CNGCCATNTGGAAGGAANGGGGACTNCTAACNGCTAAGGGNTCCCCCATA 4858 chrXptel1M 853957 AAATATGCAA-GAGAAATTCAACAGTTACTACAAGGTGTCCACAAACCCA 854005 i - v-v viv vi ?i v v v ii?vvvi PRIMA41-int#L 4859 AAACAT-CACTCAGAAATTCTGAATCTNTTAGATGCTGTTTNGCTGCCCA 4907 chrXptel1M 854006 GAGAGGTTTCAGTCAT--ATTCTTAAAGGACACCAGAAAAGAGATTCACT 854053 ii i vv ? ? -- -vi i i i i i i vv? PRIMA41-int#L 4908 AGGAAGTAGCNGTNATTCATT-GCAGAGGACATCAAAAAGGGGACTCCAN 4956 chrXptel1M 854054 TCAGGCCAAGGGGAATAGGTCTGCAGATTCAGCTGCTATAGCTGCTGC 854101 vv?i i i ivvvii? iv? v vi i v PRIMA41-int#L 4957 TGTNACTAAGGGAAACTCCCTNGCAGACGNAGCAGCTAAGGCCGCAGC 5004 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.46 CpG sites = 156, Kimura (unadjusted) = 42.33 Transitions / transversions = 1.39 (156/112) Gap_init rate = 0.07 (65 / 951), avg. gap size = 1.43 (93 / 65) 571 34.91 5.03 2.81 chrXptel1M 854372 854928 (145072) HERV4_I#LTR/ERV1 5078 5646 (893) m_b348s701i2 14556 chrXptel1M 854372 GCTAAACAGATCTGTCAGGTCTGCCCAGTTTGTGC---------CCAAGT 854412 i i i i i i v v --------- v v HERV4_I#LTR/E 5078 GTTAAGCAGGTCTGTCAAGCCTGCTCACTGTGTGCACTTAACAACCCAGG 5127 chrXptel1M 854413 AAATTCTGAGGGGCTGTTCAACCCCTGATCCTGAAGCCTATATGGAGGAG 854462 -- vi iv v ------ i i v-- - vi vii HERV4_I#LTR/E 5128 AAA--CAAAATGCCT------CCTCTAATA--GAA-CCAGTCCAGAGGAG 5166 chrXptel1M 854463 GCCCACCTATTTAGGGGAGGACTGGCAGATGGATTTTAC--ACATGCCTC 854510 ivvv i iii i iv i i i -- i vv HERV4_I#LTR/E 5167 AGGAACTTACCCAGGGGAAGACTGGCAATTAGACTTCACCCATATGCCAG 5216 chrXptel1M 854511 CTCTCAGGGCCTTCAGACTGCTTTG---GTCTCGGTCGTCACCTTTACTA 854557 iv i vv v iii -- --- viiii v v i HERV4_I#LTR/E 5217 CTTGCAGAGGATACAAGTT--TTTGCTAGTACTAATAGACACCTTTACTG 5264 chrXptel1M 854558 ACTGGGGAGAAGCCCTCCCTTGCAAGACTGAAAAGGCTCGGGAGGT-ATC 854606 i vv iiv vv ii v i viv - v HERV4_I#LTR/E 5265 GCTGGGTCGAAGCTTACCCTACCAGAACAGAGAAGGCTAATGAGGTTATA 5314 chrXptel1M 854607 AAAGTGCTTGCTAA--GAGATCATACCTCGGTCTGGCCTGCCC-AGCTCC 854653 i v i-i -- i v v i i vi i - vv HERV4_I#LTR/E 5315 AAGGTTCTC-TTAAAGGAAATAATCCCCCGGTTTGGGTTACCCCAGAGCC 5363 chrXptel1M 854654 TTGCAGAGTGACAGTGGCCCAGCCTCCACTTCTCAAATAACTCCAAGGGT 854703 i- i i ii iv ii ii i v i HERV4_I#LTR/E 5364 TC-CAAAGTGATAACGGCCCGTCCTTTATCTCCCAAATAACTCAAGGGGT 5412 chrXptel1M 854704 GGCCCGGGCTCTGAAGGTC-------ATCCCCACCCTGCCTGGCAGCCTC 854746 v ivi viiii ------- iiv ii v v vi HERV4_I#LTR/E 5413 TGCTAAGGCTCTCGGAATCAAATACTATTTACATTCAGCATGGAGGCCTC 5462 chrXptel1M 854747 AGTCTTCTGGGAAGGTGGAGAAAATGACTCACACCCTCAAGCGAGTCCTT 854796 i i i i i i iiiiv v v i v i i ivi v HERV4_I#LTR/E 5463 AATCCTCCGGGAAAGTAGAAAGGGCTAATCAAACTCTAAAACGGGCGTTA 5512 chrXptel1M 854797 ACTAAACTGTGCCTGGAGAC--CAGAGCATTGGGGGAAGAATGTT-CTCT 854843 i i i i v i -- i- i v vv vv ii - i v HERV4_I#LTR/E 5513 GCTAAGCTATGTCAGGAAACATCAGAA-ACTTGGGTCAGCTTACTGCCCA 5561 chrXptel1M 854844 TAGGACTTTGTGGAGTCCACCTTACACCTGGGGAGAACATTGAGTTGAGC 854893 vv i vvi ii iivv ? v i i vi v i vv HERV4_I#LTR/E 5562 TAGCCCTCTTAAGGATCCGTAATNCCCCTAGAGCAAAAATTAATATGAGC 5611 chrXptel1M 854894 CCCTTTGAACTTCGGTATGGGAGGCCCTTCTTAAC 854928 v v v vivi i i v i HERV4_I#LTR/E 5612 CCATATGAAATGTTATACGGAAGGCCATTTTTAAC 5646 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 46.58 CpG sites = 112, Kimura (unadjusted) = 49.15 Transitions / transversions = 1.45 (112/77) Gap_init rate = 0.04 (25 / 556), avg. gap size = 1.76 (44 / 25) 634 32.10 4.47 1.92 chrXptel1M 854476 855034 (144966) PRIMA41-int#LTR/ERV1 5387 5959 (1797) m_b348s701i3 14556 chrXptel1M 854476 GGGGAGGACTGGCAGATGGATTTTACACA--TGCCTCCTCTCAGGGCCTT 854523 ? i i i i v -- i vivi i vv PRIMA41-int#L 5387 GGNGAAGACTGGCAAATAGACTTTACTCAGATGCCCCCATGTAGAGGGTT 5436 chrXptel1M 854524 CAGAC---TGCTTTGGTCTCGGTCGTCACCTTTACTAACTGGGGAGAAGC 854570 i i i--- --i v iv ? v i iii? iv? i PRIMA41-int#L 5437 TAAATATTTGCT--AGTATTCGTNGACACCTTCACCGGNTGGATNGAGGC 5484 chrXptel1M 854571 CCTCCCTTGCAAGACTGAAAAGGCTCGGGAGGTATCAAAGTGCTTGCTAA 854620 ii i ivv ?i ? ? vvvv ? v iiv i i PRIMA41-int#L 5485 TTTTCCCACCNGGNCNGAAAAGGCAATTGAGGTNTCTAAACTCCTACTAA 5534 chrXptel1M 854621 --GAGATCATACCTCGGTCTGGCCTGCCCAGCTCCTTGCAGAGTGACAGT 854668 -- i v v v i v i ivvv i i PRIMA41-int#L 5535 AGGAAATAATTCCTAGGTTTGGGCTGCCTAAGAGCTTGCAGAGTGATAAT 5584 chrXptel1M 854669 GGCCCAGCCTCCACTTCTCAAATAACTCCAAGGGTGGCCCGGGCTCT--G 854716 v i i vv ?v? i ? i v iv ?v iivi i -- PRIMA41-int#L 5585 GGCCCATCTTTCACAGCNANAGTNACCCAAAACGTNTCTTCAGCCCTAGG 5634 chrXptel1M 854717 AA---GGT--CATCCCCACCCTGCCTGGCAGCCTCAGTCTTCTGGGAAGG 854761 ---i -- ii ii i i ? vi v i v ? i PRIMA41-int#L 5635 AATTCAGTACCGCCTTCACTCCGCNTGGAGGCCACAGTCCTCAGGNAAAG 5684 chrXptel1M 854762 TGGAGAAAATGACTCACACCCTCAAGCGAGTCCTTACTAAACTGTGCCTG 854811 i i i iiv v v i v iv iiii ?i ? i v PRIMA41-int#L 5685 TAGAAAGAGCTAATCAAACTCTAAAAAGGACTCTNGCNAAACTATGCCAG 5734 chrXptel1M 854812 GAGAC--CAGAGCATTGGGGGAAGAATGT-TCTCTTA-----GGACTTTG 854853 -- vvi -------? - v -----i v ?v PRIMA41-int#L 5735 GAGACNTCAGAGACCTGG-------NTGTCTCTATTACCCGTAGCCTTNT 5777 chrXptel1M 854854 TG-GAGTCCACCTTACACCTGGGGAGAACATTGAGTTGAGCCCCTTTGAA 854902 i- i ? ivv vi v ?ii ii iv v? i v i PRIMA41-int#L 5778 TACGGGTNCGAATGGCCCCNAAGGGAAATCTGNAGCTCAGCCCTTTTGAA 5827 chrXptel1M 854903 CTTCGGTATGGGAGGCCCTTCTTAACCTCTAACATTCTTGTAGACCCACA 854952 v vvv i i i? vi v i vi v? -i PRIMA41-int#L 5828 ATGACGTATGGAAGGCCTTTCTTAACTNCAGACCTCCTAATAGACGNA-G 5876 chrXptel1M 854953 ACAGCATCGGGTCACTCAGTT-TGCCACACAGCTCGGTGCA-GTCCAGAA 855000 i viv ii ii vv i - i? i- i ii v? - ? i PRIMA41-int#L 5877 ATACTTTCAAGCTACAGAATTATGTNAT-CAACTTAGGNCAGGTNCAAAA 5925 chrXptel1M 855001 AGCCCTTTCTGAACACGCAAGGGAACATCTCCCT 855034 i ? ii? i i v iv? viv ? PRIMA41-int#L 5926 GGCNCTCCNTGAATATGGAAATNAAAGACTNCCT 5959 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 45.64 CpG sites = 106, Kimura (unadjusted) = 47.18 Transitions / transversions = 1.51 (106/70) Gap_init rate = 0.04 (23 / 558), avg. gap size = 1.57 (36 / 23) 238 21.46 16.05 2.17 chrXptel1M 856066 856146 (143854) C L1ME3A_3end#LINE/L1 (698) 222 131 m_b348s551i0 14557 chrXptel1M 856066 CATCTCAGTCAATCTGAAAGGTGTGTAG-----------TGTTGTTTTAA 856104 i i i v ivi ----------- v C L1ME3A_3end#L 222 CATTTTAGCCATTCTGGTGGGTGTGTAGTGGTATCNCATTGTGGTTTTAA 173 chrXptel1M 856105 ATTGTATTTCCTTGAT--CAAAGGAAATTTAGGGCACTTCTTCA 856146 v i i -- v v i -- i i i C L1ME3A_3end#L 172 TTTGCATTTCCCTGATGACTAATGAAGTT--GAGCACCTTTTCA 131 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 26.00 CpG sites = 11, Kimura (unadjusted) = 26.00 Transitions / transversions = 1.83 (11/6) Gap_init rate = 0.05 (4 / 80), avg. gap size = 3.75 (15 / 4) 287 31.01 10.98 1.68 chrXptel1M 856375 856538 (143462) C MIRc#SINE/MIR (60) 208 30 m_b348s601i0 14558 chrXptel1M 856375 CACCATCTCATTTA---CTTTCAACTCCCCTGTCGGGATTATTACC-CTG 856420 ii i--- iv vv - i i vivi vv- v C MIRc#SINE/MIR 208 CATTATCTCATTTGATCCTCACAACAACCCTGT-GAGGTAGGCAGGGCAG 160 chrXptel1M 856421 CTATTATTATCTCCATTTTATAGTTAAAGAAACAATAA-----AAAAAGA 856465 v i i v i i -- i ----- i i i C MIRc#SINE/MIR 159 GTATTATTATCCCCATTTTACAGATGAGGAAAC--TGAGGCTCAGAGAGG 112 chrXptel1M 856466 TTAAGTTAGTTCTCTAGAGAAAAATAG--GATCTGAGGCA---CC--GAT 856508 v v vi i ii vv v i --ii vv v --- -- i C MIRc#SINE/MIR 111 TTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGAC 62 chrXptel1M 856509 TC-AATTTAGGTCTTCTTAA-TTCAAGTCTAG 856538 - iii i i - i i C MIRc#SINE/MIR 61 TCGAACCCAGGTCTTCCTGACTCCAAGTCCAG 30 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.70 CpG sites = 31, Kimura (unadjusted) = 41.70 Transitions / transversions = 1.63 (31/19) Gap_init rate = 0.07 (11 / 163), avg. gap size = 1.91 (21 / 11) 13 13.72 0.00 0.00 chrXptel1M 856621 856645 (143355) (TAAA)n#Simple_repeat 1 25 (0) m_b348s252i1 14559 chrXptel1M 856621 TAAATAAATAAGTAAATGAATGAAT 856645 i i i (TAAA)n#Simpl 1 TAAATAAATAAATAAATAAATAAAT 25 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 60 20.78 1.94 2.60 chrXptel1M 856928 857082 (142918) (AGGA)n#Simple_repeat 1 154 (0) m_b348s252i2 14560 chrXptel1M 856928 AGGACAGAAGGGGGGCAGGGAAGGAAGAAAGGGAGAGAGGGAAAG-AGGG 856976 vi ii - i i i - i i - i (AGGA)n#Simpl 1 AGGAAGGAAGGAAGG-AAGGAAGGAAGGAAGGAAG-GAAGGAAGGAAGGA 48 chrXptel1M 856977 AGGAAGGAAGGAAGGAGGGAAAAGAA-GAAGTGAGGAAGGAAGGAAAGAA 857025 i - i - vi i (AGGA)n#Simpl 49 AGGAAGGAAGGAAGGAAGG-AAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 97 chrXptel1M 857026 GGATGATATGGAGGGAA-GAATGAAAGAAGGAAGGGAGGGAGGGAAGAAG 857074 v -v v i - v i i i i i (AGGA)n#Simpl 98 GGAAG-GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG 146 chrXptel1M 857075 GAAGAAAG 857082 i (AGGA)n#Simpl 147 GAAGGAAG 154 Matrix = Unknown Transitions / transversions = 3.33 (20/6) Gap_init rate = 0.05 (7 / 154), avg. gap size = 1.00 (7 / 7) 259 22.89 0.00 0.00 chrXptel1M 857118 857200 (142800) C L1ME4c_3end#LINE/L1 (741) 89 7 m_b348s551i1 14561 chrXptel1M 857118 CTGTTCATATTCTTTCACCATTTATCATTTGGGGAATAGTTTGTATTCTT 857167 i i vv vv vv v v ?v v C L1ME4c_3end#L 89 CTGTTCATGTCCTTTGCCCATTTATCTATTGGGGTCTTGATNTTTTTCTT 40 chrXptel1M 857168 ATAAATTTGACTCAGTTCTCTACATATTTGAGA 857200 v v v i i i ? v? C L1ME4c_3end#L 39 ATCAATTTGAATGAGCTCTTTATATANTANAGA 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 28.60 CpG sites = 5, Kimura (unadjusted) = 28.60 Transitions / transversions = 0.36 (5/14) Gap_init rate = 0.00 (0 / 82), avg. gap size = 0.0 (0 / 0) 225 27.14 6.15 3.26 chrXptel1M 857363 857541 (142459) C L1PREC2_orf2#LINE/L1 (2910) 384 201 m_b348s551i2 14562 chrXptel1M 857363 AACTT-CTTTAAGAATCTGAATACTATACCACTTGATGCATATATCTTTA 857411 - v ii i vivviii v i v C L1PREC2_orf2# 384 AACTTGCTTTATGAATCTGGGTGCTCCTGTGTTGGGTGCATATATATTTA 335 chrXptel1M 857412 GGACTAATATTGCTTCATTATCTG--TTG-TTCCTTTAGCAAGATATAAT 857458 iviv vvv - i - -- -vi v vv i C L1PREC2_orf2# 334 GGATAGTTAGGTCTTC-TTGT-TGAATTGAACCCTTTACCATTATGTAAT 287 chrXptel1M 857459 TTCCTTCCTTATCTCTTTTAAATAATTTTT-TTGCTTT------TGCTTC 857501 vi i i i ---- i i - v ------ i i C L1PREC2_orf2# 286 GCCCTTCTTTGTCTTTTT----TGATCTTTGTTGGTTTAAAGTCTGTTTT 241 chrXptel1M 857502 TTGTGAAATCAGGATTGCTACCTCTTATTTTTTTTCTTTT 857541 v v i v i vv i v C L1PREC2_orf2# 240 GTCTGAAATTAGGATTGCAACCCCTGCTTTTTTCTGTTTT 201 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.14 CpG sites = 24, Kimura (unadjusted) = 34.14 Transitions / transversions = 1.04 (24/23) Gap_init rate = 0.06 (11 / 178), avg. gap size = 1.55 (17 / 11) 421 17.92 5.61 0.89 chrXptel1M 858431 858537 (141463) C Charlie4#DNA/hAT-Charlie (44) 3334 3223 m_b348s502i0 14563 chrXptel1M 858431 CTAGTAAAGCCTCTGAACCC----TCAGAATA--CTTTTTAAATACATAA 858474 i i v i ---- --v i C Charlie4#DNA/ 3334 CTGGTGAAGCCTATGGACCCCTTCTCAGAATAATGTTTTTAAATGCATAA 3285 chrXptel1M 858475 AAGTAAAAAGCCTAGAATTTCAAAAGAAATCAACCAAACTGAAATATAGT 858524 - vi v i v i i ii v i C Charlie4#DNA/ 3284 AA-TAAAATACATAGGATTACAAAGGAAACCAATTATATTGAAATATAGT 3236 chrXptel1M 858525 TGTCAAAATACTT 858537 i i C Charlie4#DNA/ 3235 TATCAAAATATTT 3223 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 20.97 CpG sites = 13, Kimura (unadjusted) = 20.97 Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.03 (3 / 106), avg. gap size = 2.33 (7 / 3) 277 31.19 2.75 0.00 chrXptel1M 858606 858714 (141286) LTR90A#LTR 863 974 (2) m_b348s502i1 14564 chrXptel1M 858606 GATCACTTTCTTGTGACTCATATCTTAATCGGAAATCTCTGAATAATTGG 858655 iv i i i i iv vi i ii iv vvi LTR90A#LTR 863 GATTCCTTCCCTGTGATTCACACATTACCCAGAAGCCTCTGGCTTCCTGG 912 chrXptel1M 858656 AATTCTTAATAAATCTTAAAAATACTTCCATAATAGCTTTAAAA---TAT 858702 vv vv vii vii i v ---i i LTR90A#LTR 913 AATTCTTAATAAAAATTCCAAATCTCTCGGCAATAACTTTCAAACACCAC 962 chrXptel1M 858703 AATTTTCACCAA 858714 i i LTR90A#LTR 963 AATTTTCGCTAA 974 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.29 CpG sites = 21, Kimura (unadjusted) = 41.93 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.01 (1 / 108), avg. gap size = 3.00 (3 / 1) 634 26.29 9.79 0.00 chrXptel1M 859214 859407 (140593) C MIRb#SINE/MIR (14) 254 42 m_b348s601i1 14565 chrXptel1M 859214 CATTTATTTAGTTCCTGTTATGTTCCAGGAACTGTCCTAAGTACTTTACA 859263 v iv i ii v v v ii C MIRb#SINE/MIR 254 CATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACA 205 chrXptel1M 859264 AATATTAACTCATTTGATTCTGACA--TGCTCTGCAAAGAAGGGTTTATT 859311 vii v i i v --vi i i i v vv C MIRb#SINE/MIR 204 TGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATT 155 chrXptel1M 859312 ---TACATTTTATAGTTGGAGAAACTGAGGCAAATAAACGTTAAGTAATT 859358 ---iv i v ii vv v i v i C MIRb#SINE/MIR 154 ATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACT 105 chrXptel1M 859359 TGCT----------CAGCTAGT--GTCTTAG-GCT-GGATTTGAACTCAA 859394 i---------- -- vvi - i- i i i C MIRb#SINE/MIR 104 TGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAG 55 chrXptel1M 859395 GACTTCCCGATTC 859407 v vi i i C MIRb#SINE/MIR 54 GTCTGTCTGACTC 42 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.13 CpG sites = 29, Kimura (unadjusted) = 33.01 Transitions / transversions = 1.32 (29/22) Gap_init rate = 0.03 (6 / 193), avg. gap size = 3.17 (19 / 6) 306 27.17 14.78 0.76 chrXptel1M 859314 859428 (140572) C MIR3#SINE/MIR (65) 143 13 m_b348s601i2 14565 chrXptel1M 859314 CATTTTATAGTTGGAGAAACTGAGGCAAATAAACGTTAAGTAATTTGCTC 859363 i v ii vv v i v v i i i C MIR3#SINE/MIR 143 CATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCC 94 chrXptel1M 859364 --------------AGCTAGTGTCTTAGGCTGGATTTGAACTCAAGACTT 859399 -------------- i v vv v v i v i i v - C MIR3#SINE/MIR 93 AAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGTC-T 45 chrXptel1M 859400 CCCGATTCTC--TCTCT-CTCTCTCTGTTGAG 859428 i i i -- iv - i v C MIR3#SINE/MIR 44 CCTGACTCCCAGTCCGTGCTCTCTCTGCTCAG 13 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.88 CpG sites = 16, Kimura (unadjusted) = 34.21 Transitions / transversions = 1.07 (16/15) Gap_init rate = 0.04 (4 / 114), avg. gap size = 4.50 (18 / 4) 12 30.77 1.92 0.00 chrXptel1M 859644 859695 (140305) (TAAAT)n#Simple_repeat 1 53 (0) m_b348s252i3 14566 chrXptel1M 859644 TAAAGT-ACTTAAATCAAATAAAAATAAAATATATTATACGAACGTATAT 859692 v - v i v v v v v iv vv v (TAAAT)n#Simp 1 TAAATTAAATTAAATTAAATTAAATTAAATTAAATTAAATTAAATTAAAT 50 chrXptel1M 859693 TAA 859695 (TAAAT)n#Simp 51 TAA 53 Matrix = Unknown Transitions / transversions = 0.18 (2/11) Gap_init rate = 0.02 (1 / 51), avg. gap size = 1.00 (1 / 1) 16 6.64 2.78 5.71 chrXptel1M 860952 860987 (139013) (ATTCT)n#Simple_repeat 1 35 (0) m_b348s252i4 14567 chrXptel1M 860952 ATTCTATTCCATTCTATTCT-TTCTTATTTTATATCT 860987 i - - i - (ATTCT)n#Simp 1 ATTCTATTCTATTCTATTCTATTC-TATTCTAT-TCT 35 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.09 (3 / 35), avg. gap size = 1.00 (3 / 3) 215 26.94 9.35 6.36 chrXptel1M 860992 861098 (138902) C L2a_3end#LINE/L2 (5) 512 403 m_b348s601i3 14568 chrXptel1M 860992 TTTATTCAGGCCTAAATACATCTATTAAGCACTTTAGATGT-CCAGG--- 861037 i i---i -- i i i i vvv - --- C L2a_3end#LINE 512 TTCATTCAA---CAAATA--TTTATTGAGCGCCTACTATGTGCCAGGCAC 468 chrXptel1M 861038 -GCTCTAAGCATTAGGGATAAAGGGG-AAAAAAAACAGAGCCA----TCA 861081 - i i ii i v vi -i v -- ---- v C L2a_3end#LINE 467 TGTTCTAGGCGCTGGGGATACAGCAGTGAACAAAACAGA--CAAAAGTCC 420 chrXptel1M 861082 TTGTCCTTGAGTAGCTT 861098 i i iiv v C L2a_3end#LINE 419 CTGCCCTCATGGAGCTT 403 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.68 CpG sites = 18, Kimura (unadjusted) = 34.85 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.11 (12 / 106), avg. gap size = 1.42 (17 / 12) 1305 28.73 2.52 3.33 chrXptel1M 861112 861626 (138374) L1ME5_3end#LINE/L1 127 637 (304) m_b348s551i3 14569 chrXptel1M 861112 CATATGAAAAAATGTTCTAAATTTCTATTGATCAGAAAAATGCAAAATAA 861161 i i i v v ivi v i i v L1ME5_3end#LI 127 CATATGAAGAGATGCTCAAACTCATTAGTAATCAGAGAAATGCAAATTAA 176 chrXptel1M 861162 GACAACTCTGAGGTACCACTACACACCTGTCAGACTGGCTAAGATGACAG 861211 i vv i i vi i i v i v --- L1ME5_3end#LI 177 AACAACAATGAGATATCACTTTACACCTATTAGACTGGCAAAAATTA--- 223 chrXptel1M 861212 GAAAA---GATAATGATGAATGTTGGAGGGGATGTGGGAAAACTGGGGAC 861258 i--- vii i v i i ? - i i L1ME5_3end#LI 224 GAAAGCTGGATAATGCCAAGTGTTGGCGAGGATGTGGGGANA-TAGGAAC 272 chrXptel1M 861259 ACTGATGCATTGTTGGTGGAATTGTGAATGGATCCAACCATTCTGGAGAG 861308 v v i i i v ii iv i v i L1ME5_3end#LI 273 CCTCATGCACTGCTGGTGGGAGTGTAGACTGGTGCAGCCATTCTGGAGAG 322 chrXptel1M 861309 CAATTTGGAACTA--TAGCCTAAGGGTTATCAAACTGTGCATACCCTTTG 861356 i v v -- i v --- -- ivv ii v L1ME5_3end#LI 323 CAATCTGGCAGTACTTAGTCAAA---TTA--AGTATACGCATACCCTATG 367 chrXptel1M 861357 ATCCAGCAGTGTTACTACCGGGATTATATCCCAAAGAGATTATAAAGAAG 861406 i i viii v i vv i v v viv L1ME5_3end#LI 368 ACCCAGCAATTCCGCTCCTGGGTATATATCCCAAAGAAATTCTCACACAG 417 chrXptel1M 861407 G----GAAAGGGACCTGTATGTGCACGAATGTTTGCGGCAGCCCTCTTTG 861452 ----v i ---- i iv i iiiv vi v L1ME5_3end#LI 418 GTCCATAAGGGGAC----ATGTACGAGGATGTTCATTGCAGCGTTGTTTG 463 chrXptel1M 861453 TAGTGGCTAGAAACTGGAAACTGAATGGATGTCCATCAGTGGGAGAATGG 861502 i vi i ii ii vivv i v i L1ME5_3end#LI 464 TGGTGGCGGGGAGTTGGAGGCAACCTGGGTGTCCATCACTGGGAGAGTGG 513 chrXptel1M 861503 CTGAATAAATTGTGGTATATGAATATTATGGAATATTATTGTTCTGTAAG 861552 v iii v iv v i ii i i vvvv v v L1ME5_3end#LI 514 ATAGGTAAAATGTGGTGGATGCACACCATGGAGTACTATGCAGCAGTTAG 563 chrXptel1M 861553 AAATGACCAACAGAATGATTTCAGAAAG--GCCTGGAGAGA-CTTACACG 861599 iii vi vii -- v v v --i v vi - v -- L1ME5_3end#LI 564 AAGCAACGGACTAGATG--TACACATAGCAACATGGATGGATCTTAAA-- 609 chrXptel1M 861600 AAC-TGATGCTGAGTGAAATGAGCAGGA 861626 - ii vi i i L1ME5_3end#LI 610 AACATAGTGCTGAGTGAAAAAAGTAAGA 637 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.21 CpG sites = 83, Kimura (unadjusted) = 37.23 Transitions / transversions = 1.38 (83/60) Gap_init rate = 0.04 (23 / 514), avg. gap size = 1.30 (30 / 23) 12 4.75 0.00 8.33 chrXptel1M 861943 861968 (138032) (GGGA)n#Simple_repeat 1 24 (0) m_b348s252i5 14570 chrXptel1M 861943 GGGAGGGGGTGGAGGGAGGGAAGGGA 861968 i - - (GGGA)n#Simpl 1 GGGAGGGAG-GGAGGGAGGG-AGGGA 24 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.08 (2 / 25), avg. gap size = 1.00 (2 / 2) 426 27.16 0.00 8.70 chrXptel1M 862067 862191 (137809) MIRc#SINE/MIR 1 115 (153) m_b348s601i4 14571 chrXptel1M 862067 CAGGGCAGCTAGGTGGCACAGTAGATAGAACATCAGCCCTCAAGTCAGGA 862116 ii i--- ii i v i iii v i vi MIRc#SINE/MIR 1 CGAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGA 47 chrXptel1M 862117 GGACCTGAGTTCAAATGTGACCTCAGACACTTAATGCTTCCTGGCTGTGT 862166 i i i i viviv v v ------- i MIRc#SINE/MIR 48 AGACCTGGGTTCGAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGT 90 chrXptel1M 862167 GACCCTGAGCAAGTCACTTAACTCC 862191 i i ii MIRc#SINE/MIR 91 GACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.21 CpG sites = 23, Kimura (unadjusted) = 35.45 Transitions / transversions = 2.88 (23/8) Gap_init rate = 0.08 (10 / 124), avg. gap size = 1.00 (10 / 10) 421 27.57 10.86 0.52 chrXptel1M 862312 862486 (137514) C L2#LINE/L2 (580) 2502 2310 m_b348s601i5 14568 chrXptel1M 862312 AGCCTG-GAGATGGGAAGGGCTTAGGAGCAAAGATAATGAGTTCA----- 862355 v - i v i v vi v i -i v v ----- C L2#LINE/L2 2502 AGACTGCGGGAGGAGCAGGTTTGAGGGG-GAAGATCAGGAGTTCAGTTTT 2454 chrXptel1M 862356 --AGATG---AGTTTAAGATGTCTACTGAACATCCAGGTCAAGA------ 862394 -- v --- i i i ii i vi ------ C L2#LINE/L2 2453 GGACATGTTAAGTTTGAGATGCCTATTAGACATCCAAGTGGAGATGTCGA 2404 chrXptel1M 862395 --AGGCTATTGGAAATGCTACATTGGAGGTCAGCAGAGAGGTTAGGGCAA 862442 -- vi v i v vvi v vi iv vi C L2#LINE/L2 2403 GTAGGCAGTTGGATATACGAGTCTGGAGTTCAGGGGAGAGGTCCGGGCTG 2354 chrXptel1M 862443 GATTTGTAGATCTGAGAATCATCAACAGAGAGATGATAATTAAA 862486 vv i i i i i i v v i v C L2#LINE/L2 2353 GAGATATAAATTTGGGAGTCATCAGCATATAGATGGTATTTAAA 2310 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.87 CpG sites = 25, Kimura (unadjusted) = 34.87 Transitions / transversions = 1.09 (25/23) Gap_init rate = 0.03 (6 / 174), avg. gap size = 3.33 (20 / 6) 189 30.67 13.33 0.00 chrXptel1M 862545 862619 (137381) L2a_3end#LINE/L2 421 505 (12) m_b348s601i6 14572 chrXptel1M 862545 GGTTTTCGTTTGTTGTATT------TGTATCCTTAGCAACCAGCATAGTT 862588 ii i i v i ------ ii iv i v i v L2a_3end#LINE 421 GACTTTTGTCTGTTTTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTG 470 chrXptel1M 862589 CAGGGTGCATAGAA----TTTAATAAATACTTGCT 862619 vv ii v ----i i i i L2a_3end#LINE 471 CCTGGCACATAGTAGGCGCTCAATAAATATTTGTT 505 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.42 CpG sites = 16, Kimura (unadjusted) = 41.86 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.03 (2 / 74), avg. gap size = 5.00 (10 / 2) 204 27.67 6.06 1.45 chrXptel1M 862569 862634 (137366) L2d_3end#LINE/L2 448 516 (0) m_b348s601i7 14572 chrXptel1M 862569 CCTTAGCAACCAGCATAGTTCAGGGTGCATAGAA----TTTAATAAATAC 862614 vi iv i i v v i ii v ----i i L2d_3end#LINE 448 CCACAGCGCCTAGCACAGTGCTGAGCACATAGTAGGCGCTCAATAAATAC 497 chrXptel1M 862615 TTGCTTCTTGATTGGACTGA 862634 i vv - i L2d_3end#LINE 498 TTGTTGATTGATT-GATTGA 516 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.17 CpG sites = 11, Kimura (unadjusted) = 35.61 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.03 (2 / 65), avg. gap size = 2.50 (5 / 2) 566 32.23 0.54 2.21 chrXptel1M 863122 863305 (136695) MIR3#SINE/MIR 3 183 (25) m_b348s601i8 14573 chrXptel1M 863122 GGTAGCGTGTTACAAAGCATAGGTAG-ATGGACTTTGAGCCTGGAGAGGC 863170 i v --i vi v iv - i vv i v -- MIR3#SINE/MIR 3 GGCAGAGTG--GCTGAGCAGAGAGAGCACGGACTGGGAGTCAGGAGA--C 48 chrXptel1M 863171 CTAAGTTTGAATTGTGACTCAGATGCTTACCAGTTATGTGATCCTAGACA 863220 ii iv i ivi i v vii v i? i i i i i i MIR3#SINE/MIR 49 CTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCA 98 chrXptel1M 863221 TGTCACCTAAATTTTTTGTGCCTCGATTTCCTTTTCTATAAAATGAGAGG 863270 v i v vi i i v ii iv i i MIR3#SINE/MIR 99 AGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGG 148 chrXptel1M 863271 GATGGACTTGATTACCATTATGGTCTCTTTCTGCT 863305 v v v i vi v i i v MIR3#SINE/MIR 149 GTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCT 183 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.03 CpG sites = 35, Kimura (unadjusted) = 44.08 Transitions / transversions = 1.52 (35/23) Gap_init rate = 0.03 (5 / 183), avg. gap size = 1.00 (5 / 5) 4869 30.27 2.85 2.46 chrXptel1M 864177 867329 (132671) L1M5_orf2#LINE/L1 130 3294 (0) m_b348s551i4 14574 chrXptel1M 864177 ACACACCTGAAGCAGGGAGATACATACAGAGTAAAGGTAAAAGGTTGGAG 864226 i i v ii vii i v ? iv i i v i L1M5_orf2#LIN 130 ACGCACTTTAAATATAAAGACACAGANAGGTTGAAAGTAAAAGGATGGAA 179 chrXptel1M 864227 CAGAATCTACTATGCTTCAGGTGAATTTAAAAAAGCAGGGGTAGCCATCC 864276 v ii v i vvvviv i ?ivv i v ? i i vi L1M5_orf2#LIN 180 AAAGATATACCATGCAAACACTAANCAAAAGAAAGCTGGNGTGGCTATAT 229 chrXptel1M 864277 TGATCTCAGATCAAGCA------AAAGCAAAAATTGATCTAATTAAAAGA 864320 i v iv i ------ i i --- --- vv L1M5_orf2#LIN 230 TAATATCAGACAAAGTAGACTTCAAGGCAAGAA---AT---ATTACCAGA 273 chrXptel1M 864321 GATAAGGAAGGGCACTATATCTTGCTAAA-GGGTAGCATAAATAATGAAG 864369 i i i i vi vv v - vi- vv v v L1M5_orf2#LIN 274 GATAAAGAGGGACATTTCATAATGATAAAAGGGTCA-ATTCATCAAGAAG 322 chrXptel1M 864370 CAATATCAATATTTAACATATATGCACCAAGTGGTGTAGCATCTAAATTC 864419 vv v vi v ii i v i iiiiv v v v L1M5_orf2#LIN 323 ACATAACAATCCTAAATGTGTATGCACCTAATAACAGAGCTTCAAAATAC 372 chrXptel1M 864420 TTAAAAGAGAAATTAAGAGAGCTGCAAGAAGAAATAGATAGCAAAACTAT 864469 v i iv i i i v i iv i --- v i i L1M5_orf2#LIN 373 ATGAAGCAAAAACTGACAGAACTAAAAGGAGAAATAGA---CAAATCCAC 419 chrXptel1M 864470 AAT---AGTGGGAGATCTCAACCTTGCACTCTCAG-AATTAGATAAATCA 864515 --- ? i i vi?v v - - i v L1M5_orf2#LIN 420 AATTATAGTNGGAGATTTTAACACNCCTCTCTCAGTAATT-GATAGAACA 468 chrXptel1M 864516 AAC---CACAAAATAAATAAGAAAGAAGTCAAAGAGGCAAATAAAA-TAT 864561 ii--- v v i --- vi vi vvii i v - L1M5_orf2#LIN 469 AGTAGACAAAAAATCAGTAAG---GATATAGAAGATTTGAACAACACTAT 515 chrXptel1M 864562 TAGAAAAATTAGGTATGATAGATCTTTGGAGAAAAATGAATGGAG--ACA 864609 i - vv i v iiv i v iv iv v v ?v ivv i-- ? L1M5_orf2#LIN 516 CA-ACCAACTTGACCTAATTGACATTTATAGAACACTNCACCCAACAACN 564 chrXptel1M 864610 GAAAGGAGTATACTTTCTTCTCAGCAGTTCATGGAACCTATACAAAAATA 864659 v -- i i v i ivv iv v v v i L1M5_orf2#LIN 565 GCA--GAATACACATTCTTTTCAAGTGCACATGGAACATTTACCAAGATA 612 chrXptel1M 864660 GACCATATATTAGGACATAAAA---ACCTCAAACTCAAGTGCAGTAAGG- 864705 ?i i v ---ii -- v v v? -- - L1M5_orf2#LIN 613 GACCATATNCTGGGCCATAAAACAAGTCTCAA--TAAATTTNA--AAGGA 658 chrXptel1M 864706 CAGAAATAGTA-AATGCATCCTTTTCAGACCACGATGCAATGAAAATTAC 864754 iv vi - iv i v- i v i v v v viv L1M5_orf2#LIN 659 TTGAAATCATACAGAGTATG-TTCTCTGACCACAATGGAATTAAATTAGA 707 chrXptel1M 864755 ATTCAA---CAAAAAGCCAGG-GGAAAGTAGACCAAAAAATAATTGGAAA 864800 v --- vi ?v-i i vv- --- v L1M5_orf2#LIN 708 AATCAATAACAAAAAGATANCTAGAAAATCC-CCAAA---TATTTGGAAA 753 chrXptel1M 864801 CTAAATAATCTCACG-CTAAAGAATGATTGGGTGATACAGCAAATCATAG 864849 i i - v v- v ivvv v v v iv i i L1M5_orf2#LIN 754 TTAAACAA-CACACTTCTAAATAACCCATGGGTCAAAGAAGAAATCACAA 802 chrXptel1M 864850 ACATAATTAATAACTTCACCCAAGAAAATAACAATAATGAGACAACCTAC 864899 ?viv iv v viviiv vvi i ? i vi v v i L1M5_orf2#LIN 803 NGGAAATTAGAAAATATTTTGAACTGAATGANAATGAAAATACAACATAT 852 chrXptel1M 864900 CAAAATGTGTGGGATGCAGCCAAAGCGATAATAAG-GGGAAATTTCATAT 864948 v i ii iv v - - v L1M5_orf2#LIN 853 CAAAATTTGTGGGATGCAGCTAAAGCAGTGCTTAGAGGGAAATTT-ATAG 901 chrXptel1M 864949 CTCTAGAGGCTTACTTGCATAAAATAGA-GAAAGAG--AAGGTCAATGAA 864995 ?i i v ? iv --- i v - iv-- ii v L1M5_orf2#LIN 902 CNTTAAATGCNTATAT---TAGAAAAGAAGAAAGGCTTAAAATCAATGAT 948 chrXptel1M 864996 TTGGGCTTGCAACTAAAAATGCTAGAAAAGTAA---CAAATTAAAAACTC 865042 i ii v v v i v iv --- ---i L1M5_orf2#LIN 949 CTAAGCTTCCACCTTAAGAAGCTAGAAAAAGAAGAGCAAATTAAA---CC 995 chrXptel1M 865043 CCAGTCAAACATTAAACATGAAATTCTAAAAATAAAAGGAGAGATCAATA 865092 v iv? ii vv iiv v vv i i v i i L1M5_orf2#LIN 996 CAAAGNAAGTAGAAGGAAGGAAATAATAAAGATAAGAGCAGAAATCAATG 1045 chrXptel1M 865093 AAATTGAAAGTAAAAAAAAACTATTGAA--TTAATAAAACTAATACTTGG 865140 v ii ? ? v v vv -- i ii i i v vi L1M5_orf2#LIN 1046 AAATAGAAAACAAANANACAATAGAGAAAATCAACGAAGCCAAAAGCTGG 1095 chrXptel1M 865141 TTCTATGAAAAAACCAACAAAATAGACAAACCCTTAGTAAATCTGATTAA 865190 v i i i v i ii i? iv i L1M5_orf2#LIN 1096 TTCTTTGAAAAGATCAATAAAATTGATAAACCTCTAGCNAGACTGATCAA 1145 chrXptel1M 865191 AAAAGGAAAGAG-GAAAAT-CAAATTGTTAGTCTTAAAAATTAAAAGGGA 865238 i i- - i i- iii i v i ii v i L1M5_orf2#LIN 1146 GAAAA-AAAGAGAGAAGACACAAATTACCAATATCAGGAATGAAAAAGGA 1194 chrXptel1M 865239 GAACTTGCCACTGATGAAGAGGAAATTAGAGCAATAATTAGAAGTTACTT 865288 vv ii i v vvvivi v i ivi v iiv i v L1M5_orf2#LIN 1195 GACATCACTACAGATCCTACAGACATTAAAAGGATAATAAGAGAATATTA 1244 chrXptel1M 865289 TGCCCAACTTTATGCCAATAAATTCGACAACTTAAATGAAATGGAAGAAT 865338 vv i ? i vi L1M5_orf2#LIN 1245 TGAACAACTTTATGCCAATAAATTTGANAACTTAGATGAAATGGACAAAT 1294 chrXptel1M 865339 ACCTTCAAAAATATAGCTTGCCCAGATTAACAAAGGAAGAAGTAAATATC 865388 v v i i i? i v i i i ?v i i i v vi L1M5_orf2#LIN 1295 TCCTTGAAAAACACAANTTACCAAAACTGACNCAAGAAGAAATAGAAAAT 1344 chrXptel1M 865389 CTAAACAGTCCCATCT-TGGAAAAAAAATAGAACAAGCTATTAACCAATT 865437 i i i i v - ivv i v ivv iv vv vi L1M5_orf2#LIN 1345 CTGAATAGCCCTATATCTATTAAAGAAATTGAATTTGTAATTAAAAACCT 1394 chrXptel1M 865438 CCCTAAGAAAAAATCCTCAGGACCAGATGGATTTACATGTGAATTCTACC 865487 i i vi i v ii v v i vv L1M5_orf2#LIN 1395 TCCCACAAAGAAAACTCCAGGCCCAGATGGCTTCACTGGTGAATTCTACC 1444 chrXptel1M 865488 AAACATTTAAAGAACAATTAACTCCAATGCTATATAAACTATTTGAAAAA 865537 i v v iv vi i i v iv i L1M5_orf2#LIN 1445 AAACATTTAAGGAAGAAATAATACCAATCTTACACAAACTCTTCCAGAAA 1494 chrXptel1M 865538 ATAGGGATTGAAGGAGTCCTAACAAACTGTTTTTACGACACAGACATAGT 865587 ii vv i iiv vv v vv i vi vii ?ii L1M5_orf2#LIN 1495 ATAGAAAAAGAGGGAACACTTCCCAACTCATTTTATGAGGCCAGCATNAC 1544 chrXptel1M 865588 ACCGATACCTAAACCAGGTAGGCTGAAA--ACAGAGAAAAAAAATTATAG 865635 v i v ? ii ii-- v -- iii i i L1M5_orf2#LIN 1545 CCTGATACCAAAACCNGACAAA--GACATTACAAGAAAAGAAAATTACAG 1592 chrXptel1M 865636 ACCAATCTCCCTAGTGAATATTGATGTTAAAATCTTAAATAAAATATTAG 865685 v vi i v iv i ? i L1M5_orf2#LIN 1593 ACCAATATCCCTCATGAACATAGATGCAAAAATCCTNAACAAAATATTAG 1642 chrXptel1M 865686 TAAAAAGATTACAGAAAATCATACTCAGGATAATACACTATGACGAAGTA 865735 i vv v v v vvi vvv ii v i L1M5_orf2#LIN 1643 CAAATCGAATCCAGCAATATATAAAAAGGATAATACATCATGACCAAGTG 1692 chrXptel1M 865736 GGATTTATACCAGGAATGCAGGGCTGGTTCAATATTAGGAAAACTATTAG 865785 i v i i i i v i v v i i L1M5_orf2#LIN 1693 GGGTTTATCCCAGGAATGCAAGGTTGGTTTAACATTCGAAAATCAATCAA 1742 chrXptel1M 865786 CATCATTGACTATATCAATAACCAAACTAATAAAAACCATATGATCATCT 865835 ii v v i i i ivvv vvi v i L1M5_orf2#LIN 1743 TGTAATTCACCATATTAACAGAATAAAGGAGAAAAATCATATGATCATCT 1792 chrXptel1M 865836 CAATAGATGCAGAAAAAGCATTTGATAAAATCCAACATCCATTCCTAATA 865885 i i i v i L1M5_orf2#LIN 1793 CAATAGATGCAGAAAAAGCATTTGACAAAATTCAACACCCATTCATGATA 1842 chrXptel1M 865886 AAAACATTTAAGAGTATAGGAATAAATGGACTTTTCCTTAAAATAGTCAG 865935 vi i iv ivv i v ivvi i vv ii v i L1M5_orf2#LIN 1843 AAAACTCTCAGCAAACTAGGAATAGAAGGGAACTTCCTCAACCTGATAAA 1892 chrXptel1M 865936 GAGCATATATTTAAAACCATCAGTAAGCATCATATGCAATGGGGAAAAAC 865985 i v ivv vv i? i ivi v ? L1M5_orf2#LIN 1893 GGGCATCTACGAAAAACCTACAGCNAACATCATACTTAATGGTGAAANAC 1942 chrXptel1M 865986 TGGAATCTTTCCCAATAAGATCTGGAGTGAAGCAAGGTTGCTCACTGTCA 866035 i ?v vv v iii ii v ii i ? L1M5_orf2#LIN 1943 TGAANGCTTTCCCCCTAAGATCGGGAACAAGACAAGGATGTCCGCTNTCA 1992 chrXptel1M 866036 CCATTATTATTCAATATTTTATTAGAAACACTAGCCTTGGCAATAAGAGT 866085 i vi i v i i iiiv vvv ivv L1M5_orf2#LIN 1993 CCACTTCTATTCAACATTGTACTGGAGGTCCTAGCCAGTGCAATAAGGCA 2042 chrXptel1M 866086 AGAAAAAGAGATTAAAGGAATTAGAGTAGGTAAAGAGGAAACCAAACTAT 866135 i v v v iii v v i i iv i L1M5_orf2#LIN 2043 AGAAAAAGAAATAAAAGGCATAAAGATTGGAAAGGAAGAAATAAAACTGT 2092 chrXptel1M 866136 CACTCTTTGCAGATGATATGATGGTATACTTAGAGGACCCCAGAGATTCT 866185 ?i v i i v ? v ii i ? i v L1M5_orf2#LIN 2093 CNTTATTCGCAGATGACATGATTGTNTACGTAGAAAATCCNAAAGAATCT 2142 chrXptel1M 866186 ACTAAAAAGATATTAGAAATAATTCACAAATTTAGCAAAGTTGCAGGATA 866235 v ? iv i v vviii i i ? L1M5_orf2#LIN 2143 ACAAANAAACTACTAGAACTAATAAGTGAATTTAGCAAGGTCGCNGGATA 2192 chrXptel1M 866236 CAAAAAAAAATCCACATAAATCCTCAGCATTTTTATACATCACCAACAAA 866285 iivv - vi v vviv i i i ii v L1M5_orf2#LIN 2193 CAAGGTCAA-TATACAAAAATCAATTGTATTTCTATATACTAGCAACAAA 2241 chrXptel1M 866286 ATCCAACAGCAA---GAGATACAAAGAGAAATTCCATTCAAAATAACTGT 866332 --- iv v --- i vi? i iv v i v i -i L1M5_orf2#LIN 2242 ---CAATTGGAAAATGAAATTTNAAAAACAATACCATTTACAATAGC-AT 2287 chrXptel1M 866333 CGACAG-CATAAAATATTTGGGAATCTATCTACCAAAGGAAAGTCAGGAA 866381 i v i- ? i i vv v i? vivv i v L1M5_orf2#LIN 2288 CAAAAAACATNAAATACTTAGGAATAAATCTAACAAAANATGTGCAAGAC 2337 chrXptel1M 866382 TTATA---TGAGCTAAATTACAAAAAACTTTCCACACAAATAAAGTCAGA 866428 i ? --- --- i v i viiv v v v ivv L1M5_orf2#LIN 2338 CTNTACACTGA---AAACTACAAAACATTGCTGAGAGAAATTAAAGAAGA 2384 chrXptel1M 866429 CCTAAATTATTGGAAAAATATTAAATGCTCTTGGATAGGCCGAGTGAATA 866478 v v i i vvv i v v vv v v L1M5_orf2#LIN 2385 CCTAAATAAATGGAGAGATATACCATGTTCATGGATTGGAAGACTCAATA 2434 chrXptel1M 866479 TAATAAAGATGACAATACTCCCTAG-----TCTATTTATTTAGTGCTATA 866523 vi ? v v i i----- vv i i v v L1M5_orf2#LIN 2435 TTGTNAAGATGTCAATTCTCCCCAAATTGATCTATAGATTCAATGCAATC 2484 chrXptel1M 866524 CCAATCAGATTTCCAAGAAAATATTTTAATGACCTAGAAAAAATAACAAC 866573 i v i iv iiv v ivv vv v v iv i ivvi L1M5_orf2#LIN 2485 CCAATCAAAATCCCAGCAGGTTTTTTTGTAGAAATTGACAAGCTGATTCT 2534 chrXptel1M 866574 AAAATTCATATGGAAGAACAAAAGGTCAAGAAT-CTCAAGGGAATTAATG 866622 i ivi i ii ? -vi iiv iv- L1M5_orf2#LIN 2535 AAAATTTATATGGAAATGCAAAGGACCNAGAATAGCCAAAACAATCT-TG 2583 chrXptel1M 866623 AAAAAAAAT--CAAA--TGAAGGTAGCCTAGCTGTACCTGATCT-AAAAT 866667 i v-- -- i --i i - vv ? ? - i i L1M5_orf2#LIN 2584 AAAAAGAAGAACAAAGTTGGAGG--ACTTA-CACTACCNGATNTCAAGAC 2630 chrXptel1M 866668 TATATTATAGAGCAGCAGTCACCAAAACCATTTAGTATTGGC-TAAGAAA 866716 - i vi v i i vi v i - -i L1M5_orf2#LIN 2631 T-TATTATAAAGCTACAGTAATCAAGACAGTGTGGTATTGGCGTAAG-GA 2678 chrXptel1M 866717 TAGATTAGTTGATCAGTGGAACAGGTTAG---GTTTACAAGACAGA---A 866760 iv i v i iv --- ii v - i --- L1M5_orf2#LIN 2679 TAGACAAATAGATCAATGGAACAGAATAGAGAGTCCAGAA-ATAGACCCA 2727 chrXptel1M 866761 TAGTCAACTATAGCAATATAGTGTCTGAAAAACCCAAAGATCCTAAC--- 866807 i -- vv i ?v ?v ii v i ------ i v i ?--- L1M5_orf2#LIN 2728 CA--CATATATGGNCANTTGATTTTTGA------CAAAGGTGCCAANGCA 2769 chrXptel1M 866808 -TTT--TGGGATAAGAATTCATTATTTGACAAAAACTGCTGGGATAACTG 866854 - i-- iv i vvvi v ii viv i i i L1M5_orf2#LIN 2770 ATTCAGTGGGGAAAGGATAGTCTTTTCAACAAATGGTGCTGGAACAATTG 2819 chrXptel1M 866855 GAAATTAGTATGGCAGAAATTAGGCATGGACCCACACTTAACACCATATA 866904 v ivi v i v iii?v v vi i v i L1M5_orf2#LIN 2820 GATATCCATATGGAAAAAAATGAANCTCGACCCCTACCTCACACCATACA 2869 chrXptel1M 866905 CCAACATAAGATCAAAATGAGTCCAT-GATTTAGGCAGAAAGAATGAGAT 866953 v v v iv ? i ii - - ii iiiiv ii? i i i L1M5_orf2#LIN 2870 CAAAAATTAATTCNAGATGGAT-CATAGACCTAAATGTAAAAGNTAAAAC 2918 chrXptel1M 866954 TATAAA---TAAAGTAAAGGAACATCGGATAGTTTATCTCTCAGAATTGT 867000 --- vv - iii v v i-- - ivi iiv L1M5_orf2#LIN 2919 TATAAAACTTCTAG-AAGAAAACATAGGAGAA--TATCT-TCGTGACCTT 2964 chrXptel1M 867001 GGAGAAGGAAGATATTTGTGACCAAAGATGAACTAGAGACCATTATTGAT 867050 i?v v i v v ---i v v vvi i i v i? --- i L1M5_orf2#LIN 2965 GGGNTAGGCAAAGATTTCT---TAAACAGGACACAAAAAGCACNA---AC 3008 chrXptel1M 867051 CACAAAATAGAAAAT-------TTTGATTACATCAAATTAAAAAGCCTTT 867093 i v i ------- v i ? v v i i i L1M5_orf2#LIN 3009 CATAAAAGAAAAAATTGATAAATTGGACTNCATCAAAATTAAAAACTTCT 3058 chrXptel1M 867094 GTACAAACAAAACTAATGCAAACAAAATTAGAAGGGAAGCAACAAACTAG 867143 iv ?vvv ivi vi iv v v i v v i ? i L1M5_orf2#LIN 3059 GCTCNTCAAAAGACACCGTTAAGAAAATGAAAAGGCAAGCCACAGANTGG 3108 chrXptel1M 867144 GAAAACATCTTCACAGTTAAAGGT-TCTGATAAAGGCCTCATTTCCAAAA 867192 i v v ii i-? v vi - i v i v i L1M5_orf2#LIN 3109 GAGAAAATATTTGCAA-NACATATATCTGACAAAGGACTCGTATCCAGAA 3157 chrXptel1M 867193 TACATAGAGAATTGACTCTAATTT-ATAAGAAATCAAGCCATTC--TCCA 867239 i i i -v vi ? i- ? -- v vv --i L1M5_orf2#LIN 3158 TATATAAAGAACT-CCTACAANTCAATAANAAA--AAGACAAACAACCCA 3204 chrXptel1M 867240 ATTGATAAATGGTCAAAGGATATGAATAGACAATTTTCAGATGATGAAAT 867289 v? v v i iv i v iv i v v v L1M5_orf2#LIN 3205 ATANAAAAATGGGCAAAAGACTTGAACAGACACTTCACAAAAGAAGATAT 3254 chrXptel1M 867290 TGAAATTATTTCCACT---CATATGAAAGAGTGTTCCAAATCA 867329 ?v vi--- v --- i iii i v v? L1M5_orf2#LIN 3255 NCAAATGG---CCAATAAGCACATGAAAAGATGCTCAACNTCA 3294 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.99 CpG sites = 493, Kimura (unadjusted) = 40.51 Transitions / transversions = 1.13 (493/438) Gap_init rate = 0.04 (121 / 3152), avg. gap size = 1.39 (168 / 121) 1237 27.30 2.88 3.56 chrXptel1M 867186 867637 (132363) L1ME5_3end#LINE/L1 7 455 (486) m_b348s551i5 14574 chrXptel1M 867186 TCCAAAATACATAGAGAATTGACTCTAATTTATAAGAAATCAAGCCATT- 867234 i i i i ii i vviv v iv i -- v iv?- L1ME5_3end#LI 7 TCTAGAATATACAAGGAACTCCTGCAAATCAACAAGAAA--AAGACGGNA 54 chrXptel1M 867235 -CTCCAATTGATAAATGGTCAAAGGATATGAATAGACAATTTTCAGATGA 867283 - i v v v i i v v L1ME5_3end#LI 55 ACCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGA 104 chrXptel1M 867284 TGAAATTGAAATTATTTCCACTCATATGAAAGAGTGTTCCAAATCACTAT 867333 v iivi vvii vv vv iiii i v v i v L1ME5_3end#LI 105 GGAAACCCGAAAGGCTAACAAGCATATGAAGAGATGCTCAAACTCATTAG 154 chrXptel1M 867334 TGATCAGAGAAATGCAAATTAAGACAACTCTGAGATACCACTATACACCT 867383 i i vv i v L1ME5_3end#LI 155 TAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCT 204 chrXptel1M 867384 GTCAGATTGGCTAAGATGACAGGAAA---AAATAATGATGATTGTTGGAG 867430 i i i v i v --- ---ii vii v v L1ME5_3end#LI 205 ATTAGACTGGCAAAAATTA---GAAAGCTGGATAATGCCAAGTGTTGGCG 251 chrXptel1M 867431 GGGATGTGGGAAAACTGGGACATTGATGCATTGTTGGTGGAGCTGTGAAC 867480 i i ? iv i vi v i i iiv ii L1ME5_3end#LI 252 AGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGAC 301 chrXptel1M 867481 GAATTCAACCATTCTGGAGACCAATCTAGAATTA--TGCCCAAA--AAGT 867526 vii v i v i v v -- ivi -- - L1ME5_3end#LI 302 TGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTAAG- 350 chrXptel1M 867527 TATCAAACTGTGCATACCCTTTGACCCAGCAGTGTTTCTACTGGGCTTAT 867576 --- --- v i viiv v iv L1ME5_3end#LI 351 TAT---AC---GCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATAT 394 chrXptel1M 867577 ACCCCAAGGAGATACTAAAGAAGG----TAAAGGGACCAGTATGTGCCAA 867622 i i i v v viv ---- i ---- i v i L1ME5_3end#LI 395 ATCCCAAAGAAATTCTCACACAGGTCCATAAGGGGAC----ATGTACGAG 440 chrXptel1M 867623 AATGTTTGTGGCAGC 867637 i ii v L1ME5_3end#LI 441 GATGTTCATTGCAGC 455 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.75 CpG sites = 67, Kimura (unadjusted) = 34.83 Transitions / transversions = 1.29 (67/52) Gap_init rate = 0.05 (22 / 451), avg. gap size = 1.32 (29 / 22) 15 15.30 1.61 10.53 chrXptel1M 869741 869802 (130198) (AAATAAT)n#Simple_repeat 1 57 (0) m_b348s252i6 14575 chrXptel1M 869741 AAATGAATAAGATAATATATCCATATAAGTATTTGAATATTGAATAATAA 869790 - - v -- - i -v i v i (AAATAAT)n#Si 1 AAAT-AATAA-ATAATAAAT--A-ATAAATA-ATAAATAATAAATAATAA 44 chrXptel1M 869791 AT-ATCAATAATA 869802 - v (AAATAAT)n#Si 45 ATAATAAATAATA 57 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.11 (7 / 61), avg. gap size = 1.00 (7 / 7) 643 29.79 3.59 4.53 chrXptel1M 870118 870451 (129549) C L1ME5_3end#LINE/L1 (304) 637 307 m_b348s551i6 14576 chrXptel1M 870118 TCCTGCTCATTTCACTCAGCATCA-GTTCATGTAAG-TCTCTCCAGGC-- 870163 i i iv ii - -- v - iv v i-- C L1ME5_3end#LI 637 TCTTACTTTTTTCACTCAGCACTATGTT--TTTAAGATCCATCCATGTTG 590 chrXptel1M 870164 CTTTCTGAAATCATCCTGTTGGTCATTTCTTACAGAACAATAATATTCCA 870213 v v v -- iv iv iii v v vvvv i i C L1ME5_3end#LI 589 CTATGTGTA--CATCTAGTCCGTTGCTTCTAACTGCTGCATAGTACTCCA 542 chrXptel1M 870214 TAATATTCATATACCACAATTTATTCAGCCATTCTCCAACTGATGGGCAT 870263 ii i v vi v iii v i v v i i C L1ME5_3end#LI 541 TGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCAGTGATGGACAC 492 chrXptel1M 870264 CCACTCAGTTTCCAGTTTCTAGCCACTACAAACAGGGCTGCCACAAACAT 870313 vviv ii ii i iv i iv v ii C L1ME5_3end#LI 491 CCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCTGCAATGAACAT 442 chrXptel1M 870314 TTGTGCACATACTGGTCCCTTT----CCCTTCTTTATGATCTCTTTGGGG 870359 iivi i ---- i ----v viv v vi i i C L1ME5_3end#LI 441 CCTCGTACAT----GTCCCCTTATGGACCTGTGTGAGAATTTCTTTGGGA 396 chrXptel1M 870360 TATAAGCCCAGTAGTAGCACTGCTGGTTCAAAGGACATGCCCAGTTTGAT 870409 vi v ii v i v v ii --- --- C L1ME5_3end#LI 395 TATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATGC---GT---AT 352 chrXptel1M 870410 AACTT--TTTGAGCA--TAGTTCCAAATTGCTCTCCAGAATCGTTG 870451 - -- vi -- v v i v i C L1ME5_3end#LI 351 -ACTTAATTTGACTAAGTACTGCCAGATTGCTCTCCAGAATGGCTG 307 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.72 CpG sites = 53, Kimura (unadjusted) = 38.82 Transitions / transversions = 1.26 (53/42) Gap_init rate = 0.06 (21 / 333), avg. gap size = 1.29 (27 / 21) 708 28.36 1.53 2.71 chrXptel1M 870203 870463 (129537) C L1ME3C_3end#LINE/L1 (321) 549 292 m_b348s551i7 14576 chrXptel1M 870203 ATAATATTCCATAATATTCATATACCACAATTTATTCAGCCATTCTCCAA 870252 i vi vv i v vi C L1ME3C_3end#L 549 ATAGTATTCCATTGTATGAATATACCACAATTTATTTATCCATTCTCCTG 500 chrXptel1M 870253 CTGATGGGCATCCACTCAGTTTCCAGTTTCTAGCCACTACAAACAGGGCT 870302 i i ii vviv i i v i i iv C L1ME3C_3end#L 499 TTGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCT 450 chrXptel1M 870303 GCCACAAACATTTGTGCACATACTGGTC-CCTTTCCCTTCTTTATGA--- 870348 v ii iv i ---- - viv viviv ii --- C L1ME3C_3end#L 449 GCAATGAACATTCTTGTACAT----GTCTCCTTGTGCACACGTGCGAGAG 404 chrXptel1M 870349 TCTCTTTGGGGTATAAGCCCAGTAGTAGCACTGCTGGTTCAAAGGACATG 870398 i i i vi i v i v i v iv ii C L1ME3C_3end#L 403 TTTCTCTAGGGTATATACCTAGGAGTGGAATTGCTGGGTCGTAGGGTATG 354 chrXptel1M 870399 CCCAGTTTGATAACTTTTTGAGCATAGTTCCAAATTGCTCTCCAGAATCG 870448 v vi --i viv - v v i i v C L1ME3C_3end#L 353 CGCATCTT--CAACTTTACTAG-ATATTGCCAAATTGCTCTCCAAAGTGG 307 chrXptel1M 870449 TTGGATGTATTCACA 870463 v ivv i C L1ME3C_3end#L 306 TTGTACCAATTTACA 292 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.47 CpG sites = 40, Kimura (unadjusted) = 36.33 Transitions / transversions = 1.25 (40/32) Gap_init rate = 0.03 (9 / 260), avg. gap size = 1.22 (11 / 9) 559 21.15 5.67 2.76 chrXptel1M 871079 871219 (128781) MIRc#SINE/MIR 7 151 (117) m_b348s601i9 14577 chrXptel1M 871079 AGTGTGAT--AGTA-AAAGATTTATATATTTGGGGTCAG-AAGAGATGGG 871124 i -- i- vivv iv i i - vv MIRc#SINE/MIR 7 AGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGG 56 chrXptel1M 871125 TTCAAGACC----TTTACCCTTTACTAGCTATGTGACTGTGGGCAAGTCA 871170 i v ---- i i vi i iv MIRc#SINE/MIR 57 TTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCA 106 chrXptel1M 871171 CTTCATCTCTCTGGGCTACAGTTTCCTTACCTGTTGAAATGATGAGGAT 871219 v i i iv i i -- -- i MIRc#SINE/MIR 107 CTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGT--AAA--ATGGGGAT 151 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 24.39 CpG sites = 18, Kimura (unadjusted) = 25.38 Transitions / transversions = 1.64 (18/11) Gap_init rate = 0.06 (8 / 140), avg. gap size = 1.50 (12 / 8) 690 23.03 3.27 0.64 chrXptel1M 871103 871255 (128745) MIR3#SINE/MIR 32 188 (20) m_b348s601i10 14577 chrXptel1M 871103 ATTTGGGGTCAGAAGAGATGGGTTCAAGACC----TTTACCCTTTACTAG 871148 i v i i vv v v ---- i i vi v ? MIR3#SINE/MIR 32 ACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNG 81 chrXptel1M 871149 CTATGTGACTGTGGGCAAGTCACTTCATCTCTCTGGGCTACAGTTTCCTT 871198 i iv i iv i MIR3#SINE/MIR 82 CTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTC 131 chrXptel1M 871199 ACCTGTTGAAATGATGAGGATGGACAAGATGACTTCCAAGAT-CTTTCTA 871247 i - i v i v v ii i i - i i MIR3#SINE/MIR 132 ATCTG-TAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCA 180 chrXptel1M 871248 GTTCTAGC 871255 i ii MIR3#SINE/MIR 181 GCTCTGAC 188 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 28.56 CpG sites = 23, Kimura (unadjusted) = 28.56 Transitions / transversions = 1.92 (23/12) Gap_init rate = 0.02 (3 / 152), avg. gap size = 2.00 (6 / 3) 232 36.11 1.39 0.00 chrXptel1M 871277 871348 (128652) C MIRc#SINE/MIR (182) 86 14 m_b348s601i11 14578 chrXptel1M 871277 AGCTGCTTAGTATCTAAGTCAGATTTTGAATTCAAACCTTTCTGACT-CA 871325 iv v iv vi i i ivi i ii iii i - C MIRc#SINE/MIR 86 AGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCA 37 chrXptel1M 871326 AGTTCAACATTCTATCCACTACA 871348 i iiii v i C MIRc#SINE/MIR 36 AGTCCAGTGCTCTTTCCACTGCA 14 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 49.00 CpG sites = 20, Kimura (unadjusted) = 55.49 Transitions / transversions = 3.33 (20/6) Gap_init rate = 0.01 (1 / 71), avg. gap size = 1.00 (1 / 1) 607 31.66 10.36 0.41 chrXptel1M 871866 872087 (127913) C MIRc#SINE/MIR (17) 251 8 m_b348s601i12 14579 chrXptel1M 871866 ATAGTTATAGAGTTCTCTAAAGTTTCCAAGGGACTTT-ACATACATCATC 871914 i v i v iv i v v i vi - i C MIRc#SINE/MIR 251 ACATTTGTATAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATC 202 chrXptel1M 871915 ATCTTTGAGTCTTACAGCAAGCTCATAA------------------TGTT 871946 viv vi i i v iii i ------------------ i C MIRc#SINE/MIR 201 TCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATT 152 chrXptel1M 871947 ATTCCCATTTTCCAGGCAAAGAAAATG--TTTCAGTGGGATTAAGTGATT 871994 i v iii i v --vi v i i i C MIRc#SINE/MIR 151 ATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACT 102 chrXptel1M 871995 TGCCTAAGGTCACACATTTGGTAAATATCAAAGGCAGAATTCCAA--TGG 872042 i vi i i iv i v i i i v --ii C MIRc#SINE/MIR 101 TGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAG 52 chrXptel1M 872043 GTCTTTTTGACATCACCTCCTGTACTCCATATCATTTCATCATGC 872087 ii vi vv v i i- vi i v i ii C MIRc#SINE/MIR 51 GTCTTCCTGACTCCAAGTCCAGTGCTCT-TTCCACTGCACCACAC 8 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 41.65 CpG sites = 46, Kimura (unadjusted) = 43.33 Transitions / transversions = 1.92 (46/24) Gap_init rate = 0.02 (5 / 221), avg. gap size = 4.80 (24 / 5) 371 22.98 10.43 1.60 chrXptel1M 872852 872966 (127034) MIRc#SINE/MIR 3 127 (141) m_b348s601i13 14580 chrXptel1M 872852 AGGTAG-GTGTTGCAGTGGATAGAGCACCAGCCCTGAAGTCAAGAGGACC 872900 i - v v ii v i i i i MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chrXptel1M 872901 TGACTTCAAATCTGGCCTCAGACACTTGAC----------ACTTCTGGGC 872940 iv i i iv v v v - ---------- i - MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCACTT-ACTAGCTGTGTGACCT-TGGGC 100 chrXptel1M 872941 AAGTCAGTTAATCCCAATT-GCCTCAG 872966 v i i vv v- MIRc#SINE/MIR 101 AAGTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 26.60 CpG sites = 14, Kimura (unadjusted) = 27.82 Transitions / transversions = 1.17 (14/12) Gap_init rate = 0.04 (5 / 114), avg. gap size = 2.80 (14 / 5) 16 4.50 0.00 0.00 chrXptel1M 872969 872991 (127009) (AAAC)n#Simple_repeat 1 23 (0) m_b348s252i7 14581 chrXptel1M 872969 AAACAAACAAACAAACAAAAAAA 872991 v (AAAC)n#Simpl 1 AAACAAACAAACAAACAAACAAA 23 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 26 17.58 2.04 8.70 chrXptel1M 873682 873779 (126221) (ATTGAT)n#Simple_repeat 1 92 (0) m_b348s252i8 14582 chrXptel1M 873682 ATTGATAGAGACAATAATTATTGATATTGTTTTTGATATTGATATATCAA 873731 vv i v i - v v - -i (ATTGAT)n#Sim 1 ATTGATATTGATATTGA-TATTGATATTGATATTGATATTGATAT-T-GA 47 chrXptel1M 873732 TATTGATATCATTATATCATGATATCAATATATCA-AAT-ATATTGATAT 873779 -- v -- ii - v - v - (ATTGAT)n#Sim 48 TATTGATAT--TGATAT--TGATATTGATAT-TGATATTGATATTGATAT 92 Matrix = Unknown Transitions / transversions = 0.62 (5/8) Gap_init rate = 0.10 (10 / 97), avg. gap size = 1.00 (10 / 10) 13 18.20 2.56 2.56 chrXptel1M 876565 876603 (123397) (TGTA)n#Simple_repeat 1 39 (0) m_b348s252i9 14583 chrXptel1M 876565 TGT-TGTATGTATGTGCTTATGTATTTTATGTAATTATGT 876603 - iiv - v vv (TGTA)n#Simpl 1 TGTATGTATGTATGTATGTATGTA-TGTATGTATGTATGT 39 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2) 220 21.75 0.00 2.17 chrXptel1M 879152 879198 (120802) C L2d2_3end#LINE/L2 (1) 554 509 m_b348s601i14 14584 chrXptel1M 879152 CAAATTAAATTCAACAATCATTTATTAAGTGCCTGCTATATACAAAG 879198 i - vi i i i i i i i C L2d2_3end#LIN 554 CAAATCAAAT-CAACAAATATTTATTGAGCGCCTACTGTGTGCAAGG 509 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 24.52 CpG sites = 9, Kimura (unadjusted) = 27.75 Transitions / transversions = 9.00 (9/1) Gap_init rate = 0.02 (1 / 46), avg. gap size = 1.00 (1 / 1) 285 28.36 0.00 0.00 chrXptel1M 880216 880282 (119718) L2a_3end#LINE/L2 446 512 (5) m_b348s601i15 14585 chrXptel1M 880216 TGTATAACTGGGGCATAGTACAGTACCTTATACATAGTGGGCATTTAACA 880265 vv ii v v v i vii i ii i i L2a_3end#LINE 446 TGTATCCCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGGCGCTCAATA 495 chrXptel1M 880266 AACATTCGTTGAATTAA 880282 i i v L2a_3end#LINE 496 AATATTTGTTGAATGAA 512 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 34.48 CpG sites = 12, Kimura (unadjusted) = 36.92 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.0 (0 / 0) 233 29.06 0.00 3.23 chrXptel1M 880228 880291 (119709) L2d_3end#LINE/L2 455 516 (0) m_b348s601i16 14585 chrXptel1M 880228 GCATAGTACAGTACCTTATACATAGTGGGCATTTAACAAACATTCGTTGA 880277 v i i ivvii i ii i i i i i - L2d_3end#LINE 455 GCCTAGCACAGTGCTGAGCACATAGTAGGCGCTCAATAAATACTTGTTG- 503 chrXptel1M 880278 ATTAAATTGATTAA 880291 -i i L2d_3end#LINE 504 ATT-GATTGATTGA 516 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.53 CpG sites = 15, Kimura (unadjusted) = 40.54 Transitions / transversions = 5.00 (15/3) Gap_init rate = 0.03 (2 / 63), avg. gap size = 1.00 (2 / 2) 12 17.67 2.38 4.88 chrXptel1M 880755 880796 (119204) (TATAAA)n#Simple_repeat 1 41 (0) m_b348s252i10 14586 chrXptel1M 880755 TACAAATATAAATGCTAAA-ATAAAGTATAATTTAAAAAATAA 880796 i -v - - v vv v (TATAAA)n#Sim 1 TATAAATATAAAT-ATAAATATAAA-TATAAATATAAATATAA 41 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.07 (3 / 41), avg. gap size = 1.00 (3 / 3) 236 28.92 1.52 13.56 chrXptel1M 880998 881129 (118871) MIR3#SINE/MIR 90 207 (1) m_b348s601i17 14587 chrXptel1M 880998 CCATAAGCAAATCATTTGTTCTTCTTGAGTCACAGTTTTCTTGTTTTCTT 881047 v ii i i vvi iii i i v i ii i ---- MIR3#SINE/MIR 90 CCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCT---- 135 chrXptel1M 881048 GTAAA-TGAGGGATTTGGATTAGATG-TCATTATGATATTTCTTCTAGAT 881095 - iv i - vi -- vi ii i v MIR3#SINE/MIR 136 GTAAAATGAGGGGGTTGGACTAGATGATCTCTA--AGGTCCCTTCCAGCT 183 chrXptel1M 881096 GTAGAGACATGAGTTATGAGTCATAAGTATGATT 881129 v --- --vi v ----- MIR3#SINE/MIR 184 CT---GACAT--TCTATGATTC-----TATGATT 207 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.39 CpG sites = 22, Kimura (unadjusted) = 37.39 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.14 (18 / 131), avg. gap size = 1.00 (18 / 18) 13 14.50 7.89 0.00 chrXptel1M 881278 881315 (118685) (TTAAAAA)n#Simple_repeat 1 41 (0) m_b348s252i11 14588 chrXptel1M 881278 TTAAAAATTAAAGA--AATTTTTAAAAATT-AAATTTAAAA 881315 i -- vvv - v (TTAAAAA)n#Si 1 TTAAAAATTAAAAATTAAAAATTAAAAATTAAAAATTAAAA 41 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.50 (3 / 2) 375 28.60 3.20 4.88 chrXptel1M 881511 881635 (118365) C MIRc#SINE/MIR (144) 124 2 m_b348s601i18 14589 chrXptel1M 881511 AGGCAATCAG---GATTAAATGATTCATCCAGGGTCACAAAGCTAATAGG 881557 -- --- i i i iii i v i i C MIRc#SINE/MIR 124 AGGC--TCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAG 77 chrXptel1M 881558 TGTCTGCAGCT-GGATTTCAACTAAGATCCCACTGATATCAGGCCTGATG 881606 v v - i- i iv iv i iiv ivi i i iii C MIRc#SINE/MIR 76 TGGCAG-AGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTG 28 chrXptel1M 881607 CGCTATACACTGTACCACCTAACTGCCTC 881635 v v v i --- C MIRc#SINE/MIR 27 CTCTTTCCACTGCACCAC---ACTGCCTC 2 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 35.15 CpG sites = 24, Kimura (unadjusted) = 38.01 Transitions / transversions = 2.40 (24/10) Gap_init rate = 0.06 (8 / 124), avg. gap size = 1.25 (10 / 8) 438 27.94 1.34 6.34 chrXptel1M 882076 882224 (117776) C MIRc#SINE/MIR (122) 146 5 m_b348s601i19 14590 chrXptel1M 882076 CATTTTGTAGAGGAGGAAATCAAGGC--AAATGGGATAAAGTGATTTGCC 882123 ii v iii -- i - i i v i C MIRc#SINE/MIR 146 CATTTTACAGATGAGGAAACTGAGGCTCAGA-GAGGTTAAGTGACTTGCC 98 chrXptel1M 882124 CAAGGTTACCCAGCAAGTAAGAACCTGAGGCCATATATGAACTTAGGAAT 882173 i v v viv v - i----- i i-- i C MIRc#SINE/MIR 97 CAAGGTCACACAGCTAGTAAGTGGCAGA-GCCG-----GGACTC--GAAC 56 chrXptel1M 882174 ATGGGTGTTTCTGACCTGAAGCTCAGTGCTCTATCAACTGAACTGACCTG 882223 vii v i iiv ii v v v iivv C MIRc#SINE/MIR 55 CCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTG 6 chrXptel1M 882224 C 882224 C MIRc#SINE/MIR 5 C 5 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 33.64 CpG sites = 24, Kimura (unadjusted) = 35.92 Transitions / transversions = 1.60 (24/15) Gap_init rate = 0.07 (10 / 148), avg. gap size = 1.10 (11 / 10) 248 35.10 0.68 5.67 chrXptel1M 883397 883544 (116456) UCON86#LINE/L2 140 280 (402) m_b348s502i2 14591 chrXptel1M 883397 GAAGTGCAGTTCTAACCACGGTATTCCTGCACTCAATAAACTCCAATGGT 883446 i------ ivi ii iiiv vv v i UCON86#LINE/L 140 GAAGTGCG------ACCACATCACCCCCATCCTCAAACAACTCCACTGGC 183 chrXptel1M 883447 TTCCTGTTTCCTCTAGGATCCAATAT-AAATTCCTCTATTTAGCTTTTAA 883495 i ii ivi ii i vi- v i vi - i UCON86#LINE/L 184 TCCCCATTCATTTCAGGATCCAGTTCAAAATTGCCCTCCTT-GTTTTTAA 232 chrXptel1M 883496 AGCCTTAAATAACATTGCCCTTTCCCACCTCATGAGCCATTACTTCTCT 883544 i i vv iivv i ivv i i ii - iii UCON86#LINE/L 233 AACCCTCCATGGACTTGCTCCAGCCTACCTCACGGACC-TTGTCTCTCT 280 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 47.90 CpG sites = 34, Kimura (unadjusted) = 50.96 Transitions / transversions = 2.27 (34/15) Gap_init rate = 0.06 (9 / 147), avg. gap size = 1.00 (9 / 9) 463 30.44 2.42 2.42 chrXptel1M 886442 886606 (113394) L1ME5_3end#LINE/L1 387 551 (390) m_b348s551i8 14592 chrXptel1M 886442 GGGCTTATATCCCAAAGAGATTTTAAAGAAGG----GAAAGGGACCTGTA 886487 iv i i v viv ----v i ---- L1ME5_3end#LI 387 GGGTATATATCCCAAAGAAATTCTCACACAGGTCCATAAGGGGAC----A 432 chrXptel1M 886488 TGTGCACGAATGTTTGGGGCAGCCCTGTTTGTAGTGGCCAGAAACTGGAA 886537 i iv i iivv vi i vi i ii i L1ME5_3end#LI 433 TGTACGAGGATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAG 482 chrXptel1M 886538 ACTGAGTGGATGCCCATCAGTGGGAGAATGGCTGAATAAATTGTGGTATA 886587 i vivv i i v i v iii v iv L1ME5_3end#LI 483 GCAACCTGGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGA 532 chrXptel1M 886588 TGAATATTATGGAATATTA 886606 v i ii i i L1ME5_3end#LI 533 TGCACACCATGGAGTACTA 551 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.58 CpG sites = 31, Kimura (unadjusted) = 40.68 Transitions / transversions = 1.72 (31/18) Gap_init rate = 0.03 (5 / 164), avg. gap size = 1.60 (8 / 5) 502 26.45 0.00 0.00 chrXptel1M 886488 886608 (113392) L1MD1_3end#LINE/L1 433 553 (436) m_b348s551i9 14592 chrXptel1M 886488 TGTGCACGAATGTTTGGGGCAGCCCTGTTTGTAGTGGCCAGAAACTGGAA 886537 i ivi ii i i i i i L1MD1_3end#LI 433 TGTACACGAATGTTTATAGCAGCTTTATTCGTAATAGCCAAAAACTGGAA 482 chrXptel1M 886538 ACTGAGTGGATGCCCATCAGTGGGAGAATGGCTGAATAAATTGTGGTATA 886587 vivvii i v ii v i i i i i L1MD1_3end#LI 483 ACAACCCAGATGTCCTTCAACGGGTGAATGGTTAAACAAACTGTGGTACA 532 chrXptel1M 886588 TGAATATTATGGAATATTACT 886608 vv ii i L1MD1_3end#LI 533 TCCATACCATGGAATACTACT 553 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 31.92 CpG sites = 24, Kimura (unadjusted) = 34.62 Transitions / transversions = 3.00 (24/8) Gap_init rate = 0.00 (0 / 120), avg. gap size = 0.0 (0 / 0) 396 26.53 0.64 3.95 chrXptel1M 886506 886662 (113338) L1MC4a_3end#LINE/L1 449 600 (2029) m_b348s551i10 14592 chrXptel1M 886506 GCAGCCCTGTTTGTAGTGGCCAGAAACTGGAAACTGAGTGGATGCCCATC 886555 vi i v v i v i vivv ii ? L1MC4a_3end#L 449 GCAGCATTGTTTGTAATTGCAAAATATTGGAAACAACCTAAATGCCCATN 498 chrXptel1M 886556 AGTGGGAGAATGGCTGAATAAATTGTGGTATATGAATATTATGGAATATT 886605 ?i i ? i i i i vv i iv i i L1MC4a_3end#L 499 NATAGGAGANTGGTTGAATAAACTATGGTACATCCACACAATGGAGTACT 548 chrXptel1M 886606 ACTGT-TCTGTAAGAAATGACCAACAGGGAGAGACTTACATGAACTGATT 886654 - i-v i - --- iii - ii vi v L1MC4a_3end#L 549 A-TGCAGCTGTAAAAAA-G---AATGAGGA-AGATCTCTATGAACTGATA 592 chrXptel1M 886655 CTGAGTGA 886662 iv L1MC4a_3end#L 593 TGGAGTGA 600 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.77 CpG sites = 26, Kimura (unadjusted) = 34.77 Transitions / transversions = 1.86 (26/14) Gap_init rate = 0.04 (7 / 156), avg. gap size = 1.00 (7 / 7) 15 11.10 0.00 3.33 chrXptel1M 887117 887147 (112853) (TAAA)n#Simple_repeat 1 30 (0) m_b348s252i12 14593 chrXptel1M 887117 TAAATAAAAAGCTATAATAAATAAATAAATA 887147 v iv - (TAAA)n#Simpl 1 TAAATAAATAAATA-AATAAATAAATAAATA 30 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.03 (1 / 30), avg. gap size = 1.00 (1 / 1) 260 33.94 2.42 4.96 chrXptel1M 887171 887294 (112706) C L2d2_3end#LINE/L2 (46) 509 389 m_b348s601i20 14594 chrXptel1M 887171 GCACTATGCTAAGCACTG---AGAATATAAATAAGAGCAAAAGGAATCAA 887217 i i i ---i i i v vii i ----- v C L2d2_3end#LIN 509 GCACTGTGCTAGGCGCTGTGGGGGATACAAAGAAGTATAAGA-----CAT 465 chrXptel1M 887218 GGTACTTGCCCTCAAGGAATTGAAATTCTAATGAAGGAAATAAAAAGTGA 887267 v i ii v v v i vii i i i vi i C L2d2_3end#LIN 464 GGTCCCTGCCCTCAAGGAGCTTACAATCTAGTTGGGGAGACAAGACATAA 415 chrXptel1M 887268 GGGCATAAGGGGTTGAGATAAAAGTAC 887294 ivi i i iii - i v i C L2d2_3end#LIN 414 ACACGTGAAAAGTT-AAATAACAATAC 389 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 45.56 CpG sites = 29, Kimura (unadjusted) = 49.10 Transitions / transversions = 2.64 (29/11) Gap_init rate = 0.06 (7 / 123), avg. gap size = 1.29 (9 / 7) 284 30.61 0.00 6.10 chrXptel1M 887175 887261 (112739) C L2c_3end#LINE/L2 (38) 440 359 m_b348s601i21 14594 chrXptel1M 887175 TATGCTAAGCACTGAGAATATAAATAAGAGCAAAAGGAATCAAGGTACTT 887224 i i i i i i i v v ii i ----- v v i C L2c_3end#LINE 440 TGTGCCAGGCGCTGGGGATACAAAGATGAATAAGA-----CACGGTCCCT 396 chrXptel1M 887225 GCCCTCAAGGAATTGAAATTCTAATGAAGGAAATAAA 887261 ii v v v i i i i i C L2c_3end#LINE 395 GCCCTCAAGGAGCTCACAGTCTAGTGGAGGAGACAGA 359 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.58 CpG sites = 18, Kimura (unadjusted) = 41.84 Transitions / transversions = 2.57 (18/7) Gap_init rate = 0.06 (5 / 86), avg. gap size = 1.00 (5 / 5) 16 8.83 8.33 0.00 chrXptel1M 887706 887741 (112259) (TTTCATT)n#Simple_repeat 1 39 (0) m_b348s252i13 14595 chrXptel1M 887706 TTTC-TTTCTCATTTTTCCTTTTTGA-TTTT-ATTTTTC 887741 - i v v - - (TTTCATT)n#Si 1 TTTCATTTTTCATTTTTCATTTTTCATTTTTCATTTTTC 39 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.09 (3 / 35), avg. gap size = 1.00 (3 / 3) 12 18.44 0.00 3.12 chrXptel1M 887943 887975 (112025) (AATAAA)n#Simple_repeat 1 32 (0) m_b348s252i14 14596 chrXptel1M 887943 AATAAAAATAATAAATACATTTAAAAAGACAAA 887975 - v vv v v (AATAAA)n#Sim 1 AATAAAAATAA-AAATAAAAATAAAAATAAAAA 32 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 258 20.91 18.23 4.90 chrXptel1M 888267 888447 (111553) C L2d_3end#LINE/L2 (6) 510 307 m_b349s601i2 14597 chrXptel1M 888267 AGTCAGTCAATCGAGCATTTATTAAGCTCTTACTATGTGTTAAGCA---- 888312 i i - i i i v i i v ---- C L2d_3end#LINE 510 AATCAATCAA-CAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTGT 462 chrXptel1M 888313 -----------TGGGGAATACAGATATAAACAG-A-AAGACA--GCCCTT 888347 ----------- i--- ? - ? - - -- i i C L2d_3end#LINE 461 GCTAGGCGCTGTGGGGAAC---GANA-AAANAGTATAAGACATGGTCCCT 416 chrXptel1M 888348 TCCCTCCAGAAGC-----ATGTTGTTTTGGGGAAAAG-CAAACACTCA-- 888389 v v i ----- v v vv i v - v v -- C L2d_3end#LINE 415 GCCCTCAAGGAGCTTACAATCTAGTTGGGGAGACAAGACTAACACACATG 366 chrXptel1M 888390 AAACAAACCCATAAAAGCTACCCAAGACATGGTACAGA---AAGTCCCAA 888436 --ii v i - v iv -- i v --- v i C L2d_3end#LINE 365 AAACAA--TTAGAGAA-CAATACAAGACA--GTATATAATTAAGTGCTAA 321 chrXptel1M 888437 ATT---CAGTACAG 888447 ---ii C L2d_3end#LINE 320 ATTGCGTGGTACAG 307 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.58 CpG sites = 20, Kimura (unadjusted) = 25.37 Transitions / transversions = 1.25 (20/16) Gap_init rate = 0.11 (20 / 180), avg. gap size = 2.15 (43 / 20) 400 30.96 0.78 2.36 chrXptel1M 888269 888397 (111603) C L2c_3end#LINE/L2 (6) 472 346 m_b349s601i3 14597 chrXptel1M 888269 TCAGTCAATCGAGCATTTATTAAGCTCTTACTATGTGTTAAGCATGGGGA 888318 v - i i i v i ii i iiv i C L2c_3end#LINE 472 TCATTCAA-CAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGG 424 chrXptel1M 888319 ATACAGATATAAACAGAAAGACAGCCCTTTCCCTCCAGAAGCATGTTGTT 888368 i v i i - i v i i i v v i viiiv i C L2c_3end#LINE 423 ATACAAAGATGAATA-AGACACGGTCCCTGCCCTCAAGGAGCTCACAGTC 375 chrXptel1M 888369 TTGGGGAAAAG-CAAACACTCAAAACAAAC 888397 v v ii - i ?vi- i C L2c_3end#LINE 374 TAGTGGAGGAGACAGACANGT-AAACAGAC 346 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.91 CpG sites = 27, Kimura (unadjusted) = 42.87 Transitions / transversions = 2.25 (27/12) Gap_init rate = 0.03 (4 / 128), avg. gap size = 1.00 (4 / 4) 262 33.60 4.44 5.22 chrXptel1M 888791 888925 (111075) C L2a_3end#LINE/L2 (11) 506 373 m_b349s601i4 14598 chrXptel1M 888791 CAGCAAACATTTATGAAACAATTACTGTGTGCTG---ACTGTT---GGAG 888834 i i vi i ivi i ii--- --- v C L2a_3end#LINE 506 CAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGCG 457 chrXptel1M 888835 ATAAAAATATAGTAATAGTAATAATAATAAAGAAGGTTAGCCTTTGTGTT 888884 v iiii i i i i-- i - i i v i--- i ii ivi C L2a_3end#LINE 456 CTGGGGATACAGCAGTG--AACAA-AACAGACAAA---AGTCCCTGCCCT 413 chrXptel1M 888885 CAAGGAGCTTCTACTCTAATCGGAGAAGATAAAACAAAAAA 888925 v vi i i v i i i- i v C L2a_3end#LINE 412 CATGGAGCTTACATTCTAGTGGGGGGAGAC-AGACAATAAA 373 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 47.59 CpG sites = 33, Kimura (unadjusted) = 49.29 Transitions / transversions = 3.30 (33/10) Gap_init rate = 0.07 (9 / 134), avg. gap size = 1.44 (13 / 9) 312 27.06 15.15 2.01 chrXptel1M 889268 889399 (110601) C MIRb#SINE/MIR (117) 151 3 m_b349s601i6 14599 chrXptel1M 889268 CTTATCTGACAGATGAGGAA-CTGGGGC--AGACAGG------------- 889301 ii i v - i -- v ------------- C MIRb#SINE/MIR 151 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGC 102 chrXptel1M 889302 ---ATGTCACACAGCTGGGAAGTATCTGAAGCTGAATTTGAACTCAGTTC 889348 --- v i v iv v iv v i i i v C MIRb#SINE/MIR 101 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTC 52 chrXptel1M 889349 CTCCTGACTCTACCG-CTGTATTTCTATCCACTGAACCGTGTAGCTACCT 889397 ivi i vv - i i-i v v ii iv -- i C MIRb#SINE/MIR 51 TGTCTGACTCCAAAGCCCGTG-CTCTTTCCACTGCACCACGCTGC--CCC 5 chrXptel1M 889398 TC 889399 C MIRb#SINE/MIR 4 TC 3 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.88 CpG sites = 20, Kimura (unadjusted) = 34.40 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.06 (8 / 131), avg. gap size = 2.88 (23 / 8) 321 23.39 18.64 2.19 chrXptel1M 889268 889385 (110615) C MIRc#SINE/MIR (120) 148 12 m_b349s601i5 14599 chrXptel1M 889268 CTTATCTGACAGATGAGGAA-CTGGGGC--AGACAGG------------- 889301 ii i v - i -- v ------------- C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chrXptel1M 889302 ---ATGTCACACAGCTGGGAAGTATCTGAAGCTGAATTTGAACTCAGTTC 889348 --- v i v iv v iv v i i i i v C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTC 49 chrXptel1M 889349 CTCCTGACTCTA---CCGCTGTATTTCTATCCACTGAACC 889385 i i --- iv ---i v v C MIRc#SINE/MIR 48 TTCCTGACTCCAAGTCCAGTG---CTCTTTCCACTGCACC 12 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 27.36 CpG sites = 15, Kimura (unadjusted) = 28.58 Transitions / transversions = 1.25 (15/12) Gap_init rate = 0.07 (8 / 117), avg. gap size = 3.12 (25 / 8) 11 9.94 5.56 5.56 chrXptel1M 889716 889751 (110249) (TCTTTGC)n#Simple_repeat 1 36 (0) m_b349s252i3 14600 chrXptel1M 889716 TCTTT-CTGCTGTGCTTTTTGGCT-TTTGCTCTTTCCT 889751 - - v i - - v (TCTTTGC)n#Si 1 TCTTTGCT-CTTTGCTCTTT-GCTCTTTGCTCTTTGCT 36 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.11 (4 / 35), avg. gap size = 1.00 (4 / 4) 238 10.42 12.50 0.00 chrXptel1M 891490 891537 (108463) MIR#SINE/MIR 70 123 (139) m_b349s601i7 14601 chrXptel1M 891490 CCACTT-----CTGTGTGACCCTGGGCAAGTCACTTAACCCCAAT-TGCC 891533 ----- i i i vv - MIR#SINE/MIR 70 CCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCC 119 chrXptel1M 891534 TCAG 891537 MIR#SINE/MIR 120 TCAG 123 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 11.29 CpG sites = 3, Kimura (unadjusted) = 11.29 Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.04 (2 / 47), avg. gap size = 3.00 (6 / 2) 366 27.23 4.98 4.98 chrXptel1M 893615 893815 (106185) C L1MC3_3end#LINE/L1 (1899) 633 433 m_b349s551i0 14602 chrXptel1M 893615 GCTCATTTCACTCAGCATCAGTTCGTGTAAGTCTC-TCCAGGCCTTTCTG 893663 iv i vi - v i v vi - v i ii C L1MC3_3end#LI 633 GCTTCTTTCACTTAGCAATA-TGCATTTAAGATTCATCCATGTCTTTTCG 585 chrXptel1M 893664 AAATTATCCTGTTGG-TCATTTCTT------ACAGAACAGTAATATTCCA 893706 ---- iv i v i - ------i v --- C L1MC3_3end#LI 584 ----TGGCTTGATAGCTCATTTCTTTTTATCGCTGAA---TAATATTCCA 542 chrXptel1M 893707 TAATATTCACATACCATAATTTATTCAGCCATTCTCCAACTGATGGACAT 893756 vi vv ii i i i i v v v i v C L1MC3_3end#LI 541 TTGTATGGATGTACCACAGTTTGTTTATCCATTCACCTATTGAAGGACAT 492 chrXptel1M 893757 CC--ATTCAGTTTCCAGTTTTTAGCCACTACAAAAAGGGCTGCCACAAAC 893804 i--i -- i i v i ii v ii i i C L1MC3_3end#LI 491 CTTGGTT--GCTTCCAGTTTTTGGCGATTATGAATAAAGCTGCTATAAAC 444 chrXptel1M 893805 ATTCGTGCACA 893815 i ii C L1MC3_3end#LI 443 ATTCGCGTGCA 433 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 32.63 CpG sites = 34, Kimura (unadjusted) = 35.14 Transitions / transversions = 1.89 (34/18) Gap_init rate = 0.07 (14 / 200), avg. gap size = 1.43 (20 / 14) 384 27.50 0.00 2.29 chrXptel1M 893682 893815 (106185) C L1MB8_3end#LINE/L1 (362) 563 433 m_b349s551i1 14602 chrXptel1M 893682 TTTCTTACAGAACAGTAATATTCCATAATATTCACATACCATAATTTATT 893731 v i v --- vi vv i i v C L1MB8_3end#LI 563 TTTATTGCCGAA---TAATATTCCATTGTATGGATATACCACATTTTATT 517 chrXptel1M 893732 CAGCCATTCTCCAACTGATGGACATCCATTCAGTTTCCAGTTTTTAGCCA 893781 i v vi ii iiivviv v i i C L1MB8_3end#LI 516 TATCCATTCATCAGTTGATGGACATTTGGGTTGTTTCCACTTTTTGGCTA 467 chrXptel1M 893782 CTACAAAAAGGGCTGCCACAAACATTCGTGCACA 893815 i ii v iv i ii i C L1MB8_3end#LI 466 TTATGAATAATGCTGCTATGAACATTCGTGTACA 433 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.25 CpG sites = 22, Kimura (unadjusted) = 35.25 Transitions / transversions = 1.57 (22/14) Gap_init rate = 0.02 (3 / 133), avg. gap size = 1.00 (3 / 3) 474 24.85 1.20 1.20 chrXptel1M 893697 893863 (106137) C L1ME3G_3end#LINE/L1 (377) 547 381 m_b349s551i2 14602 chrXptel1M 893697 TAATATTCCATAATATTCACATACCATAATTTATTCAGCCATTCTCCAAC 893746 i i vv i i i i v i C L1ME3G_3end#L 547 TAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTAT 498 chrXptel1M 893747 TGATGGACATCCATTCAGTTTCCAGTTTTTAGCCACTACAAAAAGGGCTG 893796 ii vviv i v i i v iv C L1ME3G_3end#L 497 TGATGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCTG 448 chrXptel1M 893797 CCACAAACATTCGTGCACATACAGGTCCCTTTCC-CTTCT-TTAGTATCT 893844 v ii i v i i --? i v v - v v -iv i C L1ME3G_3end#L 447 CAATGAACATCCTTGTACATGC--NTCCTTGTGCACATGTGCGAGTATTT 400 chrXptel1M 893845 CTTTGGGATATAATCCCAG 893863 ? i v v? ? C L1ME3G_3end#L 399 CTNTAGGATAGATNCCNAG 381 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 30.74 CpG sites = 23, Kimura (unadjusted) = 31.66 Transitions / transversions = 1.28 (23/18) Gap_init rate = 0.02 (4 / 166), avg. gap size = 1.00 (4 / 4) 13 16.28 7.32 0.00 chrXptel1M 894785 894825 (105175) (TTAAAA)n#Simple_repeat 1 44 (0) m_b349s252i4 14603 chrXptel1M 894785 TTAAAACT-AAA-TAAGAAAAAAATTCAAATTAAAA-AAAAATT 894825 i - - i vv v -v (TTAAAA)n#Sim 1 TTAAAATTAAAATTAAAATTAAAATTAAAATTAAAATTAAAATT 44 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.07 (3 / 40), avg. gap size = 1.00 (3 / 3) 17 5.00 0.00 0.00 chrXptel1M 896483 896503 (103497) (TC)n#Simple_repeat 1 21 (0) m_b349s252i5 14604 chrXptel1M 896483 TCTCCCTCTCTCTCTCTCTCT 896503 i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCT 21 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 228 22.03 0.00 0.00 chrXptel1M 896943 897001 (102999) L1ME3Cz_3end#LINE/L1 485 543 (454) m_b349s551i3 14605 chrXptel1M 896943 TAAATGCCCATCAATTGAGGAATGGCAAAATAGATGGTGCTGTGTGAATA 896992 i v i vv i v v i i vv L1ME3Cz_3end# 485 TAAATGTCCATCAATAGGGGAATGGATAAATAAATTGTGGTATATTCATA 534 chrXptel1M 896993 TAATGGAAT 897001 i L1ME3Cz_3end# 535 CAATGGAAT 543 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 26.20 CpG sites = 6, Kimura (unadjusted) = 26.20 Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.0 (0 / 0) 362 27.27 2.48 0.00 chrXptel1M 897972 898092 (101908) C L1MC3_3end#LINE/L1 (1960) 572 449 m_b349s551i4 14606 chrXptel1M 897972 TCATTTCTT---ACCGAACAATAATATTCCATAACATTCATATACCACAA 898018 --- i vvv vii vv i i C L1MC3_3end#LI 572 TCATTTCTTTTTATCGCTGAATAATATTCCATTGTATGGATGTACCACAG 523 chrXptel1M 898019 TTTATTCAGCCATTCTCCCACTGATGGGCGTCCATGCAGTTTCCAGTTTC 898068 i i v v i i v i i ivv iv i i C L1MC3_3end#LI 522 TTTGTTTATCCATTCACCTATTGAAGGACATCTTGGTTGCTTCCAGTTTT 473 chrXptel1M 898069 TGGCCACTATAAAGAGGGCTGCTA 898092 v i i v ii C L1MC3_3end#LI 472 TGGCGATTATGAATAAAGCTGCTA 449 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.66 CpG sites = 19, Kimura (unadjusted) = 34.66 Transitions / transversions = 1.36 (19/14) Gap_init rate = 0.01 (1 / 120), avg. gap size = 3.00 (3 / 1) 586 27.63 5.56 2.15 chrXptel1M 897989 898258 (101742) C L1ME4c_3end#LINE/L1 (275) 555 277 m_b349s551i5 14606 chrXptel1M 897989 ATAATATTCCATAACATTCATATACCACAATTTATTCAGCCATTCTCCCA 898038 vivi ?v i i i i i i i C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chrXptel1M 898039 CTGATGGGCGTCCATGCAGTTTCCAGTTTCTGGCCACTATAAAGAGGGCT 898088 i v i i ii v iv i i v i i v iv C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCT 456 chrXptel1M 898089 GC--T--ACATTTTTGTACGTATGGGTCCCTTTTCC-TCTTTTAAG--AT 898131 -- -- i i i i i --- i - i i-- C L1ME4c_3end#L 455 GCAATGAACATCTTCGTGCATATAG---CTTTTTCCTTCTTTTGAATTAT 409 chrXptel1M 898132 CT-CTTGGGATATAGGGCC---AGTAGAAACACTGTCAAGTCCAAAGGTA 898177 i - i v vvv --- i vi ---i v i C L1ME4c_3end#L 408 TTCCTTAGGATAAATTCCCAGAAGTGGAATTACTG---GGTCAAAGGGTA 362 chrXptel1M 898178 TGCACAGTTTGATAGCCATTTGGGCATAGTTC----TTGCTCTCCAGAAT 898223 v v v i iv vivi i v v ---- i i v C L1ME4c_3end#L 361 TGAACATTTTTATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAG 312 chrXptel1M 898224 GGCTGGATCAATTCACAACTCCACCAACGATGTAT 898258 i v i i ?iv i i C L1ME4c_3end#L 311 GGTTGTACCAATTTACANTGCCACCAGCAATGTAT 277 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 34.29 CpG sites = 47, Kimura (unadjusted) = 36.16 Transitions / transversions = 1.81 (47/26) Gap_init rate = 0.05 (13 / 269), avg. gap size = 1.62 (21 / 13) 312 23.38 0.00 0.00 chrXptel1M 898490 898566 (101434) C L1ME5_3end#LINE/L1 (726) 215 139 m_b349s551i6 14606 chrXptel1M 898490 GCCAATCTGAGAGGTATGAAGTGGTACCTCAAAGTTGTCTTAATTAGCAT 898539 i i v i i i i vv i v C L1ME5_3end#LI 215 GCCAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCAT 166 chrXptel1M 898540 TTCTGTAATCAATAATGATTTAGGGCA 898566 v i i v v v i C L1ME5_3end#LI 165 TTCTCTGATTACTAATGAGTTTGAGCA 139 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 28.42 CpG sites = 10, Kimura (unadjusted) = 28.42 Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.00 (0 / 76), avg. gap size = 0.0 (0 / 0) 28 28.31 4.65 2.27 chrXptel1M 899569 899697 (100303) (GA)n#Simple_repeat 1 132 (0) m_b349s252i6 14607 chrXptel1M 899569 GAGAGACAGAGAGAGACAGACAGACAAAGAAACAGATGAGAAATGAGATA 899618 v v v v i i v - i - v (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA-GAGAGA-GAGAGA 48 chrXptel1M 899619 GAGACA-AGCGCG-GGGGGGGGGGGGGGGGGGGAAAG-GAGACAGACAGA 899665 v - v v - i i i i i i i i i i - v v (GA)n#Simple_ 49 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 98 chrXptel1M 899666 CAGAGACAGAGACA-AGA-AGCACGGAGA-AGAGA 899697 v v v - - - vi - (GA)n#Simple_ 99 GAGAGAGAGAGAGAGAGAGAG-AGAGAGAGAGAGA 132 Matrix = Unknown Transitions / transversions = 0.93 (14/15) Gap_init rate = 0.07 (9 / 128), avg. gap size = 1.00 (9 / 9) 18 0.00 0.00 0.00 chrXptel1M 899630 899649 (100351) (G)n#Simple_repeat 1 20 (0) m_b349s252i7 14608 chrXptel1M 899630 GGGGGGGGGGGGGGGGGGGG 899649 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGG 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 28 28.31 4.65 2.27 chrXptel1M 899569 899697 (100303) (GA)n#Simple_repeat 1 132 (0) m_b349s252i6 14607 chrXptel1M 899569 GAGAGACAGAGAGAGACAGACAGACAAAGAAACAGATGAGAAATGAGATA 899618 v v v v i i v - i - v (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA-GAGAGA-GAGAGA 48 chrXptel1M 899619 GAGACA-AGCGCG-GGGGGGGGGGGGGGGGGGGAAAG-GAGACAGACAGA 899665 v - v v - i i i i i i i i i i - v v (GA)n#Simple_ 49 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 98 chrXptel1M 899666 CAGAGACAGAGACA-AGA-AGCACGGAGA-AGAGA 899697 v v v - - - vi - (GA)n#Simple_ 99 GAGAGAGAGAGAGAGAGAGAG-AGAGAGAGAGAGA 132 Matrix = Unknown Transitions / transversions = 0.93 (14/15) Gap_init rate = 0.07 (9 / 128), avg. gap size = 1.00 (9 / 9) 13 11.70 3.57 0.00 chrXptel1M 899806 899833 (100167) (GGGGC)n#Simple_repeat 1 29 (0) m_b349s252i8 14609 chrXptel1M 899806 GGGCCGCGGCGGGGC-GGGAGGGGCGGGG 899833 v v - v (GGGGC)n#Simp 1 GGGGCGGGGCGGGGCGGGGCGGGGCGGGG 29 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 12 18.36 5.41 0.00 chrXptel1M 900486 900522 (99478) (TTAAT)n#Simple_repeat 1 39 (0) m_b349s252i9 14610 chrXptel1M 900486 TTAAATT-ATTTAATTT-ACTAAATTAAAATTAATTAAA 900522 v - - i v v v v (TTAAT)n#Simp 1 TTAATTTAATTTAATTTAATTTAATTTAATTTAATTTAA 39 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 289 30.74 8.02 7.71 chrXptel1M 901295 901643 (98357) C L2#LINE/L2 (1428) 1654 1305 m_b349s601i8 14611 chrXptel1M 901295 GAGGAATTCTGGTCTTAGATAGGGAGCATGCTGGCTTGAGTCCCCATCAG 901344 ii -- i - i -- i --- i -- v C L2#LINE/L2 1654 GAGGGGTT--GGCCTTAGATAGG-AGCACG--GAC---AGTTC--ATCCG 1615 chrXptel1M 901345 TAGGAGACAGGGATAAAGG---AGGATGTAATGGCACAAGATGTGATGTG 901391 v - iivi --- v i-- - i- v - C L2#LINE/L2 1614 TAGTA-ACAGGAGGGAAGGCAGAGTATGTG--GGCACA-GATGC-AGGT- 1571 chrXptel1M 901392 AGATGAGGAGA----GAAGAGAAAACTCATAGCAAATCGCCTCC-ATTTT 901436 i i v ---- vi v ii i??ii i v iv v i i- vi C L2#LINE/L2 1570 AGGTGGGTAGATGTGGTGGTGGGAGNNTGTGGAAGTTCTCTTCTGATTGC 1521 chrXptel1M 901437 TTCCAGTAATTTTTCTCAGTTA--TATGAGGCGAGATTCTCAGGTGAGAC 901484 i ----- v -- v i i i iv v - C L2#LINE/L2 1520 TTCTA-----TTTTCTCAGTGAAATAGGAAGCAAGGTCATCAGCTGAGA- 1477 chrXptel1M 901485 AGCGGTGAGCAT---GGAGG-CGTACTAGTGAATCCA--AGAGATGAAAC 901528 ---- v --- -v ii i v iv iv -- v i v C L2#LINE/L2 1476 ----GTGAGGATAGGGGAGGAGGTGTTGGAGGTTTGAGGAGAGAGGAGAA 1431 chrXptel1M 901529 CATTTGGAAAAGCC-TC-------GTGGGCTAATGAGATGG--TAAGGCA 901568 vi v i v i - ------- vv i - -- i v C L2#LINE/L2 1430 GGTGTGAAATAGTCGTCTAGGAGAGTGGGAGAGTGA-ATGGACTAGGGAA 1382 chrXptel1M 901569 GTGTAAAAGAATGGCTCAGCAGCAGGGAGGTTTCAGTTGAAATCA--AGT 901616 i iv ?i v ivi vvi vii v ii i?--i C L2#LINE/L2 1381 ATGTAGTANGATTGCCGGGCAGCATTAAGGGCCCACTTGAGGTTNGTGGT 1332 chrXptel1M 901617 AAAATATTCAAAGTCAGCTCAATAAAC 901643 v viv i v vi i v i C L2#LINE/L2 1331 CATGAATTTAAAGTGAGACCAGTCAGC 1305 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.29 CpG sites = 57, Kimura (unadjusted) = 41.39 Transitions / transversions = 1.36 (57/42) Gap_init rate = 0.11 (38 / 348), avg. gap size = 1.45 (55 / 38) 29 0.00 3.23 0.00 chrXptel1M 901816 901846 (98154) (AAAACA)n#Simple_repeat 1 32 (0) c_b349s251i0 14612 chrXptel1M 901816 AAAAC-AAAACAAAAACAAAAACAAAAACAAA 901846 - (AAAACA)n#Sim 1 AAAACAAAAACAAAAACAAAAACAAAAACAAA 32 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.03 (1 / 30), avg. gap size = 1.00 (1 / 1) 837 30.88 6.26 1.08 chrXptel1M 903278 903804 (96196) C L1ME4c_3end#LINE/L1 (275) 555 2 m_b349s551i7 14613 chrXptel1M 903278 ATAATATTCCATAACATTCCTATACCATAACTTAATCCGGCCATTCCCCA 903327 vivi ?vv i i v i-ii v C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTT-AACCATTCCCCT 507 chrXptel1M 903328 ACTGATGGGCGTCCCCTCAGCTTCCAGTTCCTTGACATTACAAAAAGGGC 903377 i v i i iivvviv i i ii i vi i v iv C L1ME4c_3end#L 506 ATTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGC 457 chrXptel1M 903378 TGCCACAAACATTTTTGCACATCTGGGTCCTTTTCTTTCTTTT--ATGAT 903425 v ii i i ii v i -- i i -- v C L1ME4c_3end#L 456 TGCAATGAACATCTTCGTGCATATAG--CTTTTTCCTTCTTTTGAATTAT 409 chrXptel1M 903426 CTCTCTGGGATACAGGCCCAGTAGAAACACTCCTGGATCAAAAGAGATGC 903475 i ii i v vv v viiv i v i i iv v C L1ME4c_3end#L 408 TTCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGA 359 chrXptel1M 903476 ACAGTTTGGTAGCCCTTTGGAC-CGTAGTTCCAATTTGCTCTCCTGAAGG 903524 v vi i i -- i- v v v i vi C L1ME4c_3end#L 358 ACATTTTTATGGCTCTT--GATACGTATTGCCAAATTGCTTTCCAAAAGG 311 chrXptel1M 903525 GTTAGATCAGGTCACGAGTCCACCAACGATGTATTAGTGTCCCAGTTTTC 903574 iv i iv i i?vv i i v ? v iv C L1ME4c_3end#L 310 GTTGTACCAATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCA 261 chrXptel1M 903575 CCACATCCCCTCTAATATTGG------TCA---TCTTA-------GCCAA 903608 i ? i v i ii ------ --- i ------- i C L1ME4c_3end#L 260 CCGCANCCTCGCCAGCATTGGGTATTATCAATTTTTTAAATTTTTGCTAA 211 chrXptel1M 903609 TCTGAGAGGTGT---GTGG--------TGATACCTTAATTTGCATTTCTC 903647 i i v i ---i -------- v i i i C L1ME4c_3end#L 210 TTTAATAGGCGTAAAATGGTATCTCATTGTTGCTTTAATTTGCATTTCTT 161 chrXptel1M 903648 TGATCAGTAGTGATTTAGAACACCTTTTCATATGGCTAGAAATGGTTTCA 903697 i v i vv v ii i i vi ivvv ivi? vv C L1ME4c_3end#L 160 TGATTACTAGCGAGGTTGAACATTTTTCCATGTGTTTGTTTACTANTTGT 111 chrXptel1M 903698 ATTTCATC---TGAAAATTATCTCTTCATATTCTTTGACCATTTATCAAT 903744 v --- vi i v i i v v C L1ME4c_3end#L 110 ATTTCCTCTTNTGTGAATTGTCTGTTCATGTCCTTTGCCCATTTATCTAT 61 chrXptel1M 903745 TATAGAATGGCTTAAATTCTTGATAGTTTCAAGGTAATTCTCTATATATT 903794 ivi vv v v ?vvv ivi i v v - ii i ? C L1ME4c_3end#L 60 TGGGGTCTTGATNTTTTTCTTATCAATTTGAATG-AGCTCTTTATATANT 12 chrXptel1M 903795 TTAGAAATTA 903804 v? v C L1ME4c_3end#L 11 ANAGATATTA 2 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.68 CpG sites = 90, Kimura (unadjusted) = 41.70 Transitions / transversions = 1.27 (90/71) Gap_init rate = 0.03 (14 / 526), avg. gap size = 2.79 (39 / 14) 1137 30.30 2.25 5.10 chrXptel1M 904648 905534 (94466) C L1P4_orf2#LINE/L1 (481) 2813 1951 m_b349s551i8 14614 chrXptel1M 904648 TCCCAGCAATTTTTGGCAAATAGTGAGTTCTTGTCCCCAAACCTGGGATC 904697 viv ivii v i - vvv v-- i C L1P4_orf2#LIN 2813 TCCCAGCACCATTTATTGAATAGGGAGTCCTT-TCCCCATTGCTT--ATT 2767 chrXptel1M 904698 TTTG---GCTCCGTCAAATAGCACATTGCTATAGTTATTGACTATTTTGT 904744 ---i ii i v v v v i i v i --i vii i C L1P4_orf2#LIN 2766 TTTGTCGACTTTGTCGAAGATCAGATGGTTGTAGGTGT--GCGGCTTTAT 2719 chrXptel1M 904745 CTTGTGAGT---CTAATCTATTCCACGGATCAACTACTCTGTTTCTTAGC 904791 - v i --- v i iv i v ivvv i vvi C L1P4_orf2#LIN 2718 -TTCTGGGTTCTCTATTCTGTTCCATTGGTCTATGTGTCTGTTTTTGTAC 2670 chrXptel1M 904792 CAGTACCAAATAGTTTTGATGACTGTTGCTTTATAATATAGTTTTCTATC 904841 viiv i v v i i i vvvi C L1P4_orf2#LIN 2669 CAGTACCATGCTGTTTTGGTTACTGTAGCCTTGTAGTATAGTTTGAAGTC 2620 chrXptel1M 904842 TGGTTTACAATATAGTTTTAGGTCTGGTACAGCTAGGCCACCTTTGTTTG 904891 v ---- i ii ----- i ------------ iv -- C L1P4_orf2#LIN 2619 GGGT----AATGTGAT-----GCCT------------CCGGCTTTGTT-- 2593 chrXptel1M 904892 CATCTTTTTTCATTA--ATTCCCTTGAA-ATTCTTGTGCTATTATTGTTC 904938 --- v - -- v i iv- -- v v - v vv C L1P4_orf2#LIN 2592 ---CTTTTTGC-TTAGGATTGCTTTGGCTATTC--GGGCTCTT-TTTTGG 2550 chrXptel1M 904939 TTTCAGATAAACTTTGTTATTATTTTTTCTAGCTCTGCAAAATAATTTC- 904987 i v i i ivv vi ii ii - vv - C L1P4_orf2#LIN 2549 TTCCATATGAATTTTAGAATAGTTTTTTCTAATTCTGTGAAA-AATGACG 2501 chrXptel1M 904988 TTGGGAGTTTGATTGGTATGGCACTAAATAAGCAGATTAATTTAGGTAGA 905037 v v v i ii i vv i iv i i v C L1P4_orf2#LIN 2500 TTGGTAGTTTGATAGGAATAGCGTTGAATCTGTAGATTGCTTTGGGCAGT 2451 chrXptel1M 905038 ATTGTTATTTTTATTATATTTGTTTGGCCTATCCATGAGCAATTGATATT 905087 v ii v iv vi ivv v vvvi i C L1P4_orf2#LIN 2450 ATGGCCATTTTAACGATATTGATTCTTCCAATCCATGAGCATGGAATGTT 2401 chrXptel1M 905088 TTTCCAGTTGATTAGCTCTGACTTGATTTTTATAAAAAGTGTTTTGTAGT 905137 v v ivv vvvi? i v v iv C L1P4_orf2#LIN 2400 TTTCCATTTGTTTGTGTCATCTNTGATTTCTTTCAGCAGTGTTTTGTAGT 2351 chrXptel1M 905138 TGTGTTCATATACCTCTT-GACTTTCCCTTGGC-AGATAGATTCC-AAAT 905184 v vi ii v vv -v i -- i- iv - ii C L1P4_orf2#LIN 2350 TCTCCTTGTAGAGATCTTTCACCT--CCTTGGTTAGATGTATTCCTAGGT 2303 chrXptel1M 905185 CTTTTATATTATC-ACAGTTATTTTAAATGGAATTTC--TCTT--TGTAT 905229 v v v i-iii i v i v -- -- v iv C L1P4_orf2#LIN 2302 ATTTTATTTTTTTTGTGGCTATTGTAAATGGGATTGCGTTCTTGATTTGG 2253 chrXptel1M 905230 CTCTT-GTTGCTGGACTTTGTTGGTAATATATAAAAACGCTGATCATTTC 905278 i- i -- i v i i--- i i iv v i C L1P4_orf2#LIN 2252 CTCTCAGCT--TGAACGTTATTGGTG---TATAGAAATGCTACTGATTTT 2208 chrXptel1M 905279 TGTGGATTTATTTTGTATTCTGCCACTTTGCTAAAGTTGTGAATTGTTTC 905328 iv v i vv i i i vv iiv C L1P4_orf2#LIN 2207 TGTACATTGATTTTGTATCCTGAAACTTTACTGAAGTCGTTTATCAGTTC 2158 chrXptel1M 905329 TGATAGCTTTTTAGTTGATTCTCTAGGGTCCTCTAAGTATACCATCATAT 905378 iiv i i iv v i ii i vv C L1P4_orf2#LIN 2157 TAGGAGCCTTTTGGCGGAGTCTTTAGGGTTTTCTAGGTATAGAATCATAT 2108 chrXptel1M 905379 -ATCCACAAAGAGTGATAGTTTGGTTTCCTCATTACCTACTCTAATTCCT 905427 -i vi i v ii i v v i ivi v C L1P4_orf2#LIN 2107 CGTCAGCGAAGAGAGATAGTTTGACTTCTTCTTTTCCTATTTGGATGCCT 2058 chrXptel1M 905428 TTAATTTCTTTCTCAACTCTTATTGCTGAAGCTAGCATATCTCCTACAAT 905477 v vvvi v vvi v iv ivv v C L1P4_orf2#LIN 2057 TTTATTTCTTTCTCTTGCCTGATTGCTCTGGCTAGGACTTCCAGTACTAT 2008 chrXptel1M 905478 ATTGAATAGTCACGGTGATAGTGGGCAACCTTGTTTTCCCCCTGATCTTA 905527 i vvii v v i vii v v i C L1P4_orf2#LIN 2007 GTTGAATAGGAGTGGTGAGAGTGGGCATCCTTGTCTTGTTCCAGTTCTCA 1958 chrXptel1M 905528 TTGGGAA 905534 vv C L1P4_orf2#LIN 1957 AGGGGAA 1951 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.73 CpG sites = 126, Kimura (unadjusted) = 39.27 Transitions / transversions = 0.98 (126/129) Gap_init rate = 0.06 (57 / 886), avg. gap size = 1.12 (64 / 57) 323 29.65 4.61 3.65 chrXptel1M 906916 907132 (92868) C L1PB1_3end#LINE/L1 (449) 449 231 m_b349s551i9 14615 chrXptel1M 906916 ATAAACATATATACGTA--TATCTGTATTCTTTTAA-AACATCT----CT 906958 iii ii i -- v - v v -i v ---- C L1PB1_3end#LI 449 ATAAACATGCGTGTGCAAGTATCTTT-TTCGTATAATGACTTCTTTTCCT 401 chrXptel1M 906959 TTGGGATAGAGAACTAAGAGTGCTGTTGCTGGGTCAAAGAATATGCACCG 907008 i - v v i iv vvi i vii - iv ii C L1PB1_3end#LI 400 CTGGG-TAGATACCCAGTAGTGGGATTGCTGGATCAAATGGTA-GTTCTA 353 chrXptel1M 907009 TTTTATAACTCTTTGGGAACAGCTACAAATTATTTTCCAGAATGGTTAGA 907058 i - ii ii i - v v v i i v i iv C L1PB1_3end#LI 352 CTTT-TAGTTCTTTAAGGA-ATCTCCACACTGTTTTCCATAGTGGTTGTA 305 chrXptel1M 907059 TAAGTTCACAATTCCATCAGCAGTGCATTAGT-TTCCCAGTTTTTCA--A 907105 iv i v i i i vv - --- --i C L1PB1_3end#LI 304 CTAGTTTACATTCCCACCAGCAGTGTAGAAGTGTTCCC---TTTTCACCG 258 chrXptel1M 907106 TACCCCCTGCAGCATTTATCATTTCTT 907132 i i v vv i i i i C L1PB1_3end#LI 257 CATCCACGCCAACATCTATTATTTTTT 231 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.50 CpG sites = 39, Kimura (unadjusted) = 39.22 Transitions / transversions = 1.70 (39/23) Gap_init rate = 0.06 (13 / 216), avg. gap size = 1.38 (18 / 13) 454 30.16 1.10 1.10 chrXptel1M 906941 907121 (92879) C L1ME4c_3end#LINE/L1 (408) 422 242 m_b349s551i10 14615 chrXptel1M 906941 TTCTTTTAAAACATCTCTTTGGGATAGAGAACTAAGAGTGCTGTTGCTGG 906990 i vi i i i i vvv i ii vvi i C L1ME4c_3end#L 422 TTCTTTTGAATTATTTCCTTAGGATAAATTCCCAGAAGTGGAATTACTGG 373 chrXptel1M 906991 GTCAAAGAATATGCACCGTTTTATAACTCTT--TGGGAACAGCTACAAAT 907038 ii v vv ii -- iv v iv -- C L1ME4c_3end#L 372 GTCAAAGGGTATGAACATTTTTATGGCTCTTGATACGTATTGC--CAAAT 325 chrXptel1M 907039 TATTTTCCAGAATGGTTAGATAAGTTCACAATTCCATCAGCAGTGCATTA 907088 ii i v iv iv i i ? v i i i v C L1ME4c_3end#L 324 TGCTTTCCAAAAGGGTTGTACCAATTTACANTGCCACCAGCAATGTATGA 275 chrXptel1M 907089 GTTTCCCAGTTTTTCAATACCCCCTGCAGCATT 907121 ?v v iv vii ? i vv C L1ME4c_3end#L 274 GNGTACCAGTTTCACCGCANCCTCGCCAGCATT 242 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.58 CpG sites = 31, Kimura (unadjusted) = 40.55 Transitions / transversions = 1.35 (31/23) Gap_init rate = 0.02 (3 / 180), avg. gap size = 1.33 (4 / 3) 14 27.96 2.70 4.11 chrXptel1M 907166 907239 (92761) (ATTT)n#Simple_repeat 1 73 (0) m_b349s252i10 14616 chrXptel1M 907166 ATTTATTTATTTATTTATGGTATGTGTGTGTGTGTGTGTGTGTGTTTAAC 907215 -v - - i v i v i v i v i vi (ATTT)n#Simpl 1 ATTTATTTATTTATTTAT-TTAT-T-TATTTATTTATTTATTTATTTATT 47 chrXptel1M 907216 T-GTAATTTTATTATTTATTT-TTTA 907239 -v v vv - (ATTT)n#Simpl 48 TATTTATTTATTTATTTATTTATTTA 73 Matrix = Unknown Transitions / transversions = 0.60 (6/10) Gap_init rate = 0.07 (5 / 73), avg. gap size = 1.00 (5 / 5) 21 4.00 0.00 0.00 chrXptel1M 907185 907210 (92790) (GT)n#Simple_repeat 1 26 (0) m_b349s252i11 14617 chrXptel1M 907185 GTATGTGTGTGTGTGTGTGTGTGTGT 907210 i (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGT 26 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 14 27.96 2.70 4.11 chrXptel1M 907166 907239 (92761) (ATTT)n#Simple_repeat 1 73 (0) m_b349s252i10 14616 chrXptel1M 907166 ATTTATTTATTTATTTATGGTATGTGTGTGTGTGTGTGTGTGTGTTTAAC 907215 -v - - i v i v i v i v i vi (ATTT)n#Simpl 1 ATTTATTTATTTATTTAT-TTAT-T-TATTTATTTATTTATTTATTTATT 47 chrXptel1M 907216 T-GTAATTTTATTATTTATTT-TTTA 907239 -v v vv - (ATTT)n#Simpl 48 TATTTATTTATTTATTTATTTATTTA 73 Matrix = Unknown Transitions / transversions = 0.60 (6/10) Gap_init rate = 0.07 (5 / 73), avg. gap size = 1.00 (5 / 5) 555 31.17 4.30 3.53 chrXptel1M 907387 908061 (91939) L1M5_orf2#LINE/L1 2615 3294 (0) m_b349s551i11 14618 chrXptel1M 907387 TACCTGATCT-AAAACTATATTATAAAGCAGCAGTCACCAAAACCATTTG 907435 ? ? - i - vi v i i vi v L1M5_orf2#LIN 2615 TACCNGATNTCAAGACT-TATTATAAAGCTACAGTAATCAAGACAGTGTG 2663 chrXptel1M 907436 GTATTGG-GTAAGAATTAGATTAGTTGATCAGTGGAATAGGTTAG---GT 907481 - i - iv i v i i iv --- L1M5_orf2#LIN 2664 GTATTGGCGTAAGGA-TAGACAAATAGATCAATGGAACAGAATAGAGAGT 2712 chrXptel1M 907482 TAAAAGGATAAAACAGTCAATAATTTTAATAATCTAGTGTTTGACCAA-- 907529 iv i -i i v viivv -- v ii?v ?i ii v v -- L1M5_orf2#LIN 2713 CCAGA-AATAGACCCACACATA--TATGGNCANTTGATTTTTGACAAAGG 2759 chrXptel1M 907530 -CCCAAAGACCCCAACTT-TTGGGATAAGAATTCACTATTTGACAAAAAC 907577 -v ? ---- i i-v iv i vvv v ii viv L1M5_orf2#LIN 2760 TGCCAANG----CAATTCAGTGGGGAAAGGATAGTCTTTTCAACAAATGG 2805 chrXptel1M 907578 TGCTGGGAAAATTGGAAATTAGTATGGCAGAAACTAGGCATGGACCCACA 907627 i v v ivi v i v iii?v v vi L1M5_orf2#LIN 2806 TGCTGGAACAATTGGATATCCATATGGAAAAAAATGAANCTCGACCCCTA 2855 chrXptel1M 907628 CTTAACACTGTACACCAAGATAAGGTCAAAATGGGTTCAT-GATCTAGTC 907676 i v ii v i v iv ? i i- - i ivi L1M5_orf2#LIN 2856 CCTCACACCATACACAAAAATTAATTCNAGATGGA-TCATAGACCTAAAT 2904 chrXptel1M 907677 ATAAAAAATGAGATTATAAAGAAATTAGAAG--AACATAGGATCGTTTAC 907724 i i? i i i ivvvi -- -- vv i L1M5_orf2#LIN 2905 GTAAAAGNTAAAACTATAAAACTTCTAGAAGAAAACATAGGA--GAATAT 2952 chrXptel1M 907725 CTCTCAGACTTGTGGGGGAGGAAGGAATTTGTGACCAAAGAAGAACTAGA 907774 iivv i - ?v v iii v ---i v i vvi i L1M5_orf2#LIN 2953 CTTCGTGACCT-TGGGNTAGGCAAAGATTTCT---TAAACAGGACACAAA 2998 chrXptel1M 907775 GATCATTATTGATCACAAAATAGAAAAT-------TTTGATTATATCAAG 907817 i v i? --- i i v i ------- v i ?i i L1M5_orf2#LIN 2999 AAGCACNA---ACCATAAAAGAAAAAATTGATAAATTGGACTNCATCAAA 3045 chrXptel1M 907818 TTAAAAAGCTTTTGTACAAACAAAACTAATGCAGACAAGATTAGAAGGGA 907867 v v i i iv ?vvv ivi vi ivi v i v i v L1M5_orf2#LIN 3046 ATTAAAAACTTCTGCTCNTCAAAAGACACCGTTAAGAAAATGAAAAGGCA 3095 chrXptel1M 907868 AGCAATAAACTGGGGAAACATCTTTACATTTAAAGGT---TCTGATAAAG 907914 v i i ? ii v v i --- ? vi --- i L1M5_orf2#LIN 3096 AGCCACAGANTGGGAGAAAATATTTGCA---ANACATATATCTGACAAAG 3142 chrXptel1M 907915 ACCTCATTTCCAAAATAGAGAGAGAATT-----GACTCTATAAGAAATCA 907959 iv i v i v v i i -----i ? v ? -- L1M5_orf2#LIN 3143 GACTCGTATCCAGAATATATAAAGAACTCCTACAANTCAATAANAAA--A 3190 chrXptel1M 907960 AGCCATCC--TCCAATTGATAAATGGTTAAAGGATAGGAACAGATAATTT 908007 v vv --i v? v vi i ivv i v i L1M5_orf2#LIN 3191 AGACAAACAACCCAATANAAAAATGGGCAAAAGACTTGAACAGACACTTC 3240 chrXptel1M 908008 TCAGATGATGAAATTGAAACGATTTCTACTCATATGAAAAGATGCTCCAA 908057 v i v v v ?v i iiivv vv i v v L1M5_orf2#LIN 3241 ACAAAAGAAGATATNCAAATGGCCAATAAGCACATGAAAAGATGCTCAAC 3290 chrXptel1M 908058 ATCA 908061 ? L1M5_orf2#LIN 3291 NTCA 3294 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.98 CpG sites = 108, Kimura (unadjusted) = 42.81 Transitions / transversions = 1.14 (108/95) Gap_init rate = 0.05 (36 / 674), avg. gap size = 1.47 (53 / 36) 1384 28.54 1.61 2.22 chrXptel1M 907967 908464 (91536) L1ME5_3end#LINE/L1 56 550 (391) m_b349s551i12 14618 chrXptel1M 907967 CTCCAATTGATAAATGGTTAAAGGATAGGAACAGATAATTTTCAGATGAT 908016 i v v vi v ii v v v L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chrXptel1M 908017 GAAATTGAAACGATTTCTACTCATATGAAAAGATGCTCCAAATCATTATT 908066 iivi v ii vvi vv i v v v L1ME5_3end#LI 106 GAAACCCGAAAGGCTAACAAGCATATGAAGAGATGCTCAAACTCATTAGT 155 chrXptel1M 908067 GATCGGAGAAATGCAAATTAAGACAACTCTGTGATACCACTACACACCTG 908116 i i i vv v i vi i L1ME5_3end#LI 156 AATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCTA 205 chrXptel1M 908117 TCAGATTGGCTAGAATGACAGGAAA---AGATAATGACGAATGTTGGAGG 908163 i i v i v --- ---i v i i v i L1ME5_3end#LI 206 TTAGACTGGCAAAAATTA---GAAAGCTGGATAATGCCAAGTGTTGGCGA 252 chrXptel1M 908164 GGAGGTGGGAAAACTGGGATACTGATGCATTGTTGGTGGAATTGTGAATA 908213 v i ? iv i iv v i i i v ii iv L1ME5_3end#LI 253 GGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACT 302 chrXptel1M 908214 CATCCAGCCATTCTGGAGAGCAATTTGAAACTATGCTTAA-AAAGTTATC 908262 vi v i iv v -- i-v i -- L1ME5_3end#LI 303 GGTGCAGCCATTCTGGAGAGCAATCTGGCAGTA--CTTAGTCAAATTA-- 348 chrXptel1M 908263 AAACTGTGCACACCCTTTGATCCAGCAGTGTTACTCCTGGGCTTATATCC 908312 ivv ii i v i i viii iv L1ME5_3end#LI 349 AGTATACGCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATATCC 398 chrXptel1M 908313 CAAAGAGATTATAAAGAAGG----GAAAGGGACCTGTTTGTGCCAGAATG 908358 i v v viv ----v i v vi ---- i L1ME5_3end#LI 399 CAAAGAAATTCTCACACAGGTCCATAAGGGGACATGTACG----AGGATG 444 chrXptel1M 908359 TTTGTGGCAACTCTCTTTGTAGTGGCCAGAAACTGGAAACTGAGTGGATG 908408 ii v i vi v i vi i ii ii vivv i L1ME5_3end#LI 445 TTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGGGTG 494 chrXptel1M 908409 CCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATATGAATGTTATGG 908458 i v v i v iii v iv v iiii L1ME5_3end#LI 495 TCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACACCATGG 544 chrXptel1M 908459 AATATT 908464 i i L1ME5_3end#LI 545 AGTACT 550 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.49 CpG sites = 79, Kimura (unadjusted) = 36.85 Transitions / transversions = 1.32 (79/60) Gap_init rate = 0.03 (14 / 497), avg. gap size = 1.36 (19 / 14) 356 20.31 0.99 7.37 chrXptel1M 909402 909502 (90498) MIRc#SINE/MIR 32 126 (142) m_b349s601i9 14619 chrXptel1M 909402 GGCCCTGGAGTCAGGAGGGCCCGAGTTCGAATCCAGCCTCAGACACTTAA 909451 v i i i i i i v v v v - MIRc#SINE/MIR 32 GGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTA- 80 chrXptel1M 909452 CGCTTCCTAGCTGCGGGACCCTGGGCAGGTCACTTAA-CTCCCATTGCCT 909500 ------ i v i i - i vvv MIRc#SINE/MIR 81 ------CTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCT 124 chrXptel1M 909501 CA 909502 MIRc#SINE/MIR 125 CA 126 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 23.76 CpG sites = 10, Kimura (unadjusted) = 23.76 Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.08 (8 / 100), avg. gap size = 1.00 (8 / 8) 34 0.00 0.00 0.00 chrXptel1M 911607 911638 (88362) (C)n#Simple_repeat 1 32 (0) c_b349s251i1 14620 chrXptel1M 911607 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 911638 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 32 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 19 23.87 4.88 2.38 chrXptel1M 912265 912346 (87654) (CTCTGT)n#Simple_repeat 1 84 (0) m_b349s252i12 14621 chrXptel1M 912265 CTCTGTCTCCATCAGAG-CTCCAGTCT-TGTCTCTGTCGGTTCCTCTAAA 912312 ii vvv - - v - vv vi ivv (CTCTGT)n#Sim 1 CTCTGTCTCTGTCTCTGTCT-CTGTCTCTGTCTCTGTCTCTGTCTCTGTC 49 chrXptel1M 912313 TGAGTACTC-GTC-CAGTCTCTGTCTCTGTCTCTGT 912346 vv - - - v (CTCTGT)n#Sim 50 TCTGT-CTCTGTCTCTGTCTCTGTCTCTGTCTCTGT 84 Matrix = Unknown Transitions / transversions = 0.33 (4/12) Gap_init rate = 0.07 (6 / 81), avg. gap size = 1.00 (6 / 6) 40 8.35 0.00 0.00 chrXptel1M 912432 912483 (87517) (AT)n#Simple_repeat 1 52 (0) c_b349s251i2 14622 chrXptel1M 912432 ATATATATATATATACATGTGTGTATATATATATATATATATATATATAT 912481 i i i i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chrXptel1M 912482 AT 912483 (AT)n#Simple_ 51 AT 52 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 18 28.59 1.49 3.03 chrXptel1M 912559 912625 (87375) (AT)n#Simple_repeat 1 66 (0) m_b349s252i13 14623 chrXptel1M 912559 ATATATTCATATATAGATCCTCATAT-TCTCTCTCTATGTATATATACAT 912607 vi v -v - - v v v v i i (AT)n#Simple_ 1 ATATATATATATATATAT-AT-ATATATATATATATATATATATATATAT 48 chrXptel1M 912608 ATGGACATATATGTACAT 912625 iv i i i (AT)n#Simple_ 49 ATATATATATATATATAT 66 Matrix = Unknown Transitions / transversions = 0.88 (7/8) Gap_init rate = 0.05 (3 / 66), avg. gap size = 1.00 (3 / 3) 55 0.00 0.00 0.00 chrXptel1M 913818 913864 (86136) (TA)n#Simple_repeat 1 47 (0) c_b349s251i3 14624 chrXptel1M 913818 TATATATATATATATATATATATATATATATATATATATATATATAT 913864 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATAT 47 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 16 32.37 4.76 1.15 chrXptel1M 913979 914062 (85938) (AG)n#Simple_repeat 1 87 (0) m_b349s252i14 14625 chrXptel1M 913979 AGAGAAAAAAAGAGGGTGAGGGGCATAGAGAG-GAGGGAGGAACAGAAAA 914027 i i i i v i iv v - i ii v i i (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chrXptel1M 914028 GGAG-GAGAG-GTGCGCAGAGA-AAAGAGAAACAGAGA 914062 i - - v v - - i i v (AG)n#Simple_ 51 AGAGAGAGAGAGAGAG-AGAGAGAGAGAGAGAGAGAGA 87 Matrix = Unknown Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.06 (5 / 83), avg. gap size = 1.00 (5 / 5) 12 27.79 1.59 4.92 chrXptel1M 914005 914067 (85933) (AGAGAGG)n#Simple_repeat 1 61 (0) m_b349s252i15 14625 chrXptel1M 914005 AGAGAGGAGGGAGGA-ACAGAAAAGGAGGAGAGGTGCGCAGAGAAAAGAG 914053 i - v i i - iv v - i i (AGAGAGG)n#Si 1 AGAGAGGAGAGAGGAGAGAGGAGA-GAGGAGAGAGGAG-AGAGGAGAGAG 48 chrXptel1M 914054 AAACAGAGAAGGGA 914067 -i v i i (AGAGAGG)n#Si 49 -GAGAGAGGAGAGA 61 Matrix = Unknown Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.06 (4 / 62), avg. gap size = 1.00 (4 / 4) 214 28.31 0.85 7.21 chrXptel1M 915425 915542 (84458) C L3#LINE/CR1 (99) 4000 3890 m_b349s601i10 14626 chrXptel1M 915425 GTGTCCATCACAGCACGCTGACCTGATGATCTCCAA-GGTGGGAGCCCCA 915473 vi - - v - i vv i i- ii iiv i C L3#LINE/CR1 4000 GTGGTCATC-CAGC-CTCTG-CTTGAACACCTCCAGTGACGGGGAGCTCA 3954 chrXptel1M 915474 CCCCCTCCACTACTGAGGTGGTCCTTGCCACTTTGGGGCAGCTCTGGTTG 915523 iv ?-----i ii i v v i v i i C L3#LINE/CR1 3953 CTACCTCN-----CGAGGCAGCCCATTCCATTTTTGGACAGCTCTGATTG 3909 chrXptel1M 915524 TCAGGAAGCTGTTCCTGAT 915542 i i i v v C L3#LINE/CR1 3908 TTAGAAAGTTCTTCCTTAT 3890 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.17 CpG sites = 20, Kimura (unadjusted) = 37.18 Transitions / transversions = 1.82 (20/11) Gap_init rate = 0.08 (9 / 117), avg. gap size = 1.00 (9 / 9) 181 36.32 7.10 2.26 chrXptel1M 916487 916655 (83345) C L2c_3end#LINE/L2 (149) 329 153 m_b349s601i11 14627 chrXptel1M 916487 AATGACAAGTACAA-AAGAAAAGTCTAAACAAAATCC--------CTCTG 916527 i i v - viii v i iii v -------- v v C L2c_3end#LINE 329 AATGATAAGTGCTATAATGGGAGTATAGACAGGGTGCTATGGGAGCACAG 280 chrXptel1M 916528 AGGGGGCTCACTTTGAGCTGCTGTGAGCAGATAGGCGGGGCTTCATGGAG 916577 i v- i v viv ?iv i vi vi vii vi C L2c_3end#LINE 279 AGGAGGG-CACCTAGACTAGNCTTGGGGGGTCAGGGAAGGCTTCCCGGAG 231 chrXptel1M 916578 AAGGTGGCACCAGAGCTGGACTTTCAATCCTCA--AGGGATTTCAGTCA- 916624 i i i v ii?i v vvv v -- ii -- i - C L2c_3end#LINE 230 GAGGTGACATCTGAGCTGAGNCTTGAAGGATGAGTAGGAGTT--AGCCAG 183 chrXptel1M 916625 GTAGAGCTGGTGGGAAAGTCCATTGCTAGAC 916655 i ivvi v i vv - i i C L2c_3end#LINE 182 GTGGAAGGAGGGGGGAAGAGCATT-CCAGGC 153 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 51.30 CpG sites = 34, Kimura (unadjusted) = 52.59 Transitions / transversions = 1.31 (34/26) Gap_init rate = 0.05 (8 / 168), avg. gap size = 2.00 (16 / 8) 254 34.72 0.78 4.00 chrXptel1M 916527 916655 (83345) C L2d2_3end#LINE/L2 (277) 278 154 m_b349s601i12 14627 chrXptel1M 916527 GAGGGGGCTCACTTTGAGCTGCTGTGAGCAGATAGGCGGGGCTTCATGGA 916576 i i i v ?i i ---- ii vi vii i C L2d2_3end#LIN 278 GGGAGAGATCACTNCGGGCTG----GAGTGGTCAGGGAAGGCTTCACGGA 233 chrXptel1M 916577 GAAGGTGGCACCAGAGCTGGACTTTCAATCCTCAA-GGGATTTCAGTCAG 916625 i ? iiv i i v vvv vii-i vii vi C L2d2_3end#LIN 232 GGAGGTGGNATTTGAGCTGGGCCTTGAAGGATGGGTAGGATTTGGATAGG 183 chrXptel1M 916626 TAGAGCTGGTGGGAAAGTCCATTGCTAGAC 916655 i vv iv i vv - i i C L2d2_3end#LIN 182 TGGAGAGGAAGGGGAAGGGCATT-CCAGGC 154 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 46.90 CpG sites = 27, Kimura (unadjusted) = 50.24 Transitions / transversions = 1.69 (27/16) Gap_init rate = 0.05 (6 / 128), avg. gap size = 1.00 (6 / 6) 356 31.10 8.47 3.02 chrXptel1M 916653 916841 (83159) C MIR3#SINE/MIR (0) 208 10 m_b349s601i13 14628 chrXptel1M 916653 GACTCACAGA-TCAGAAAACTT--GCATTTGAAGGGACCTTAGACAAAGT 916699 v i - v i iv -- vii v v --- C MIR3#SINE/MIR 208 GAATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGA---T 162 chrXptel1M 916700 CATCTAATCCCAAACTGTCATTTT-CAAA------------GGCCCACAG 916736 i v vv iv - i ------------ v C MIR3#SINE/MIR 161 CATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAG 112 chrXptel1M 916737 AGCTAATATGACTTATTCCAAAGTCACAGGGGTGGGCACGGTCTCAGCCA 916786 v i vi i-i i vi v?i vi vv v vv i C MIR3#SINE/MIR 111 AGGTGAAGTGACTTG-CCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCG 63 chrXptel1M 916787 GAATTTATACCCAGGCCTTCCTGACTTCAAATCTAATATTCTACCCACTG 916836 i i viv i - i v i i-i ii vi ii v C MIR3#SINE/MIR 62 GGACTAGAACCCAGGTC-TCCTGACTCCCAGTCC-GTGCTCTCTCTGCTC 15 chrXptel1M 916837 AACCA 916841 i C MIR3#SINE/MIR 14 AGCCA 10 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 39.47 CpG sites = 31, Kimura (unadjusted) = 41.45 Transitions / transversions = 1.19 (31/26) Gap_init rate = 0.05 (10 / 188), avg. gap size = 2.20 (22 / 10) 372 33.33 0.00 0.81 chrXptel1M 916727 916850 (83150) C MIRc#SINE/MIR (144) 124 2 m_b349s601i14 14628 chrXptel1M 916727 AGGCCCACAGAGCTAATATGACTTATTCCAAAGTCACAGGGGTGGGCACG 916776 i v v v vi ii- i vi v i vv vv C MIRc#SINE/MIR 124 AGGCTCAGAGAGGTTAAGTGACTTGC-CCAAGGTCACACAGCTAGTAAGT 76 chrXptel1M 916777 GTCTCAGCCAGAATTTATACCCAGGCCTTCCTGACTTCAAATCTAATATT 916826 v vv i i i iiv i i i i i ii C MIRc#SINE/MIR 75 GGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCT 26 chrXptel1M 916827 CTACCCACTGAACCAGGCCGCTCC 916850 vi v vi i ii C MIRc#SINE/MIR 25 CTTTCCACTGCACCACACTGCCTC 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.50 CpG sites = 24, Kimura (unadjusted) = 45.68 Transitions / transversions = 1.41 (24/17) Gap_init rate = 0.01 (1 / 123), avg. gap size = 1.00 (1 / 1) 430 25.24 10.17 5.98 chrXptel1M 917025 917201 (82799) C MIRc#SINE/MIR (75) 193 10 m_b349s601i15 14629 chrXptel1M 917025 TCTTGGCAAAGACACTG-GAGG--GGTTGGCCA--TTTTTTTGTCAGTTC 917069 i vi vi v - -- iv v -- v v i --ii C MIRc#SINE/MIR 193 TCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATC--CCC 146 chrXptel1M 917070 ATTTTACAGACAAGGAAACTGAGG-TAAATGGGGTTAAATGACTTTC--- 917115 ii - v iv i i v --- C MIRc#SINE/MIR 145 ATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCA 96 chrXptel1M 917116 --------CAGCTAGTAAGTGTCTAGGGCC-AGATTTGAACCCAGGAAGA 917156 -------- v - i -i i i ----- C MIRc#SINE/MIR 95 AGGTCACACAGCTAGTAAGTGGC-AGAGCCGGGACTCGAACCCAG----- 52 chrXptel1M 917157 TGAGCCTTCTTAACTCTCAGCCTGCCCCTTTATCCGCTGAACCAC 917201 --- i i i iv i iiviv i v i v C MIRc#SINE/MIR 51 ---GTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.79 CpG sites = 26, Kimura (unadjusted) = 31.70 Transitions / transversions = 1.62 (26/16) Gap_init rate = 0.10 (18 / 176), avg. gap size = 1.61 (29 / 18) 508 31.69 3.88 5.94 chrXptel1M 918416 918982 (81018) C L1MB7_3end#LINE/L1 (359) 572 17 m_b349s551i13 14630 chrXptel1M 918416 TCATCATTTCTCATAGCCCAATGGTGTTCCATTAGT---CATATACCACA 918462 ivi i i i v ii i - ---v C L1MB7_3end#LI 572 TCATTCCTTTTTATGGCCGAATAATATTCCATT-GTATGGATATACCACA 524 chrXptel1M 918463 AT--GTTCAGCCATTCCCCAAATGATGGGCAACCATTCAGTTTCCAATTC 918510 v -- i v vi iv i viiivviv v i C L1MB7_3end#LI 523 TTTTGTTTATCCATTCATCAGTTGATGGACATTTGGGTTGTTTCCACTTT 474 chrXptel1M 918511 GTTGCCATCATAAAAGGAACAGCTATAAGTATTT---------TTTTTAT 918551 v v i i i viivi v i ii i--------- i C L1MB7_3end#LI 473 TTGGCTATTATGAATAATGCTGCTATGAACATTCGTGTACAAGTTTTTGT 424 chrXptel1M 918552 TT--ATATAAGTTCTTTTTCTTAAAAAAAATCTCATTTGGATACAGAACT 918599 v -- i v ---- ------- ?v -- i i v v C L1MB7_3end#LI 423 GTGGACATATGTT----TTC-------ANTTCTC--TTGGGTATATACCT 387 chrXptel1M 918600 AGTAGTAGTATTGCTGGGTCAAAGGGCATATATAATTTGTTATAGCTCTT 918649 v i v v v i vv v --- - i i C L1MB7_3end#LI 386 AGGAGTGGAATTGCTGGGTCATATGGTAACTCTA---TGTT-TAACTTTT 341 chrXptel1M 918650 TG-GGAATAGTTGCATATTGATTTCCAAAATGGTTGGATCAGTTCACAAC 918698 - iv i-- v i v ii i v i v i vi C L1MB7_3end#LI 340 TGAGGAACTGC--CAAACTGTTTTCCAAAGCGGCTGCACCATTTTACATT 293 chrXptel1M 918699 TCCACTAACCGTGCTTTAGTGTCCTGATTTTCCCACATTTTCTACAACAC 918748 i i i vi iv v v i ii ii ii vv C L1MB7_3end#LI 292 CCCACCAGCAATGTATGAGGGTTCCAATTTCTCCACATCCTCGCCAACAC 243 chrXptel1M 918749 TTGTAAT----TTTTTTTTCTATCAT-GCTATCCAATCTGTTGCCATAAG 918793 v ---- v i i? i - i v --- v vii i i C L1MB7_3end#LI 242 TTGTTATTGTCTGTCTTTTTNATTATAGCCATCCTA---GTGGGTGTGAA 196 chrXptel1M 918794 GTGGTACTTTAGAGTTGTTTAAATTTTAATTTGTCTAATCCATAGTGATT 918843 ii i vv v vi vv vi vvv i v C L1MB7_3end#LI 195 GTGGTATCTCATTGTGGTTTTGATTTGCATTTCCCTAATGACTAATGATG 146 chrXptel1M 918844 TAGAGCTTTTTTTTTTTCATTTGACAATAGATAGCTTCAATCTCTTCTTT 918893 v ----v i v viv v iivii vv v C L1MB7_3end#LI 145 TTGAGC----ATCTTTTCATGTGCTTATTGGCCATTTGTATATCTTCTTT 100 chrXptel1M 918894 GAAAAACTGCCTGTTCATATATTTTTTTTACCACTTATCAGTTGGGGAAT 918943 i i v i i --- v ii vv i v ? i --- C L1MB7_3end#LI 99 GGAGAAATGTCTATTCA---AATCCTTTGCCCATTTTTNAATTGGG---T 56 chrXptel1M 918944 GACTCGTATTCTTTTTTTTAAATTTTAATAGCTTTTTAT 918982 v i i v i v v i i v v i i C L1MB7_3end#LI 55 TATTTGTCTTTTTATTGTTGAGTTGTAAGAGTTCTTTAT 17 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.67 CpG sites = 91, Kimura (unadjusted) = 42.33 Transitions / transversions = 1.17 (91/78) Gap_init rate = 0.07 (40 / 566), avg. gap size = 1.38 (55 / 40) 557 30.30 1.55 5.36 chrXptel1M 918582 918968 (81032) C L1PA5_3end#LINE/L1 (497) 404 32 m_b349s551i14 14630 chrXptel1M 918582 TCATTTGGATACAGAACTAGTAGTAGTATTGCTGGGTCAAAGGGCATATA 918631 v i i v v i i i v v v i v v C L1PA5_3end#LI 404 TCCTTTGGGTATATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTC 355 chrXptel1M 918632 TAATTTGTTATAGCTCTTTG-GGAATAGTTGCATATTGATTTCCAAAATG 918680 ---- v v i - v i-- i i vi v C L1PA5_3end#LI 354 TA----GTTCTAGATCCTTGAGGAATCGC--CACACTGTCTTCCACAATG 311 chrXptel1M 918681 GTTGGATCAGTTCACAACTCCACTAACCGTGCTTTAGTGTCCTGATTTTC 918730 i ii i iii i v ivvv i iv ii C L1PA5_3end#LI 310 GTTGAACTAGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCT 261 chrXptel1M 918731 CCACATTTTCTACAACACTTGTAATTTTTT---TTTCT-ATCAT-GCTAT 918775 ii v i i vi ii --- i - v - i C L1PA5_3end#LI 260 CCACATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGATCGCCAT 211 chrXptel1M 918776 CCAATCTGTTGCCATAAGGTGGTACTTTAGAGTTGTTTAAATTTTAATTT 918825 i v v v --- i i ii i vv v vi vv C L1PA5_3end#LI 210 TCTAACTGGTG---TGAGATGGTATCTCATTGTGGTTTTGATTTGCATTT 164 chrXptel1M 918826 GTCTAATCCATAGTGATTTAGAGCTTTTTTTTTTTCATTTGACAATAGAT 918875 v i vvvi vvv ----v v v vi v ii C L1PA5_3end#LI 163 CTCTGATGGCCAGTGATGATGAGC----ATTTTTTCATGTGTCTGTTGGC 118 chrXptel1M 918876 AGCTTCAATCTCTTCTTTGAAAAACTGCCTGTTCATATATTTTTTTTACC 918925 v v v v vi i v i --- ii ivv C L1PA5_3end#LI 117 TGCATAAATGTCTTCTTTTGAGAAGTGTCTGTTCATA---TCCTTCGCCC 71 chrXptel1M 918926 ACTTATCAGTTGGGGAATGACTCGTATTCTTTTTTTTAAATTT 918968 - iv v -- vii i - i i v C L1PA5_3end#LI 70 ACTT-TTTGATGGGG--TTGTTTGT-TTTTTTCTTGTAAATTT 32 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.87 CpG sites = 57, Kimura (unadjusted) = 39.32 Transitions / transversions = 1.06 (57/54) Gap_init rate = 0.06 (24 / 386), avg. gap size = 1.08 (26 / 24) 18 4.71 0.00 0.00 chrXptel1M 919594 919615 (80385) (TC)n#Simple_repeat 1 22 (0) m_b349s252i16 14631 chrXptel1M 919594 TCTCTCTGTCTCTCTCTCTCTC 919615 v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTC 22 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 599 31.47 3.21 3.21 chrXptel1M 920941 921439 (78561) C L1ME4a_3end#LINE/L1 (317) 554 56 m_b349s551i15 14632 chrXptel1M 920941 TAAAATCCCTTTACATTCACATACTACAATTTGTGTAGTCATTTCAC-AG 920989 v i v ?i vv ii i i i v ii ? i v - v C L1ME4a_3end#L 554 TAATATTCCATTNTATGGATGTACCATAATTTATTTAACCANTCCCCTAT 505 chrXptel1M 920990 TAATGGGCTTCTACTTTATTTCCAATTCTTAGCTAGTACAAAAAGTGCTG 921039 iv i v i vv i i v v i v i C L1ME4a_3end#L 504 TGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAATGCTG 455 chrXptel1M 921040 TGATAAATA--ATTGGA---GAATATGGGGATATTTTTCTTAGAAATAGT 921084 i i i --v v ---i v vv v?i iv i ----i vi C L1ME4a_3end#L 454 CGATGAACATCCTTGTACATAAATCTTTGTNCACATCTCT----GATTAT 409 chrXptel1M 921085 TTCCTTGGGGTGTAAGCCCAGTAATTGAATCTCTGGTTCAAAGAGTATGG 921134 i i iv vv i v i v iv v i ? C L1ME4a_3end#L 408 TTCCTTAGGATAAATTCCTAGAAGTGGAATTACTGGGTCAAAGGGTATGN 359 chrXptel1M 921135 AAATTTT--AGCCCTTTTATTTGCAAAATTTCAAATTGCTTTCTATAATG 921182 v -- v i v --i v v vi ii i v v C L1ME4a_3end#L 358 ACATTTTTAAGGCTTTTGAT--ACATATTGCCAAATTGCCCTCCAGAAAG 311 chrXptel1M 921183 ATTATGCCATGTCATTAACTTC-ACCAATAATGTTTTAGGTGTGTCCATC 921231 i i i vv i i-- i - ii i v v i- i i i C L1ME4a_3end#L 310 GTTGTACCAATTTAC--ACTCCCACCAGCAGTGTATGAGA-GTGCCCGTT 264 chrXptel1M 921232 TTTCCACAGCCACTTTATCATTTAATACTGCCATTTTCTGTCATTT---T 921278 i? v v vii v i vii i ii v i ------ --- C L1ME4a_3end#L 263 TCNCCACACCCTCGCCAACACTGGGTATTATCAATCT------TTTAAAT 220 chrXptel1M 921279 TTTTCCCAATTTGCAGGGTGTCAAGTCAGACCTTAGGGTTGTTTTGATTT 921328 i v vvi vv i viv i i vv i C L1ME4a_3end#L 219 CTTTGCCAATTTGATAGGTGAAAAATGGTATCTCATTGTTGTTTTAATTT 170 chrXptel1M 921329 TCATTTCTCTTCTTATTAGTGATTTGAAACATTTTTTCATATG-TTATGA 921377 v i vv i vv vi ? - vi C L1ME4a_3end#L 169 GCATTTCTTTGATTACTAGTGAGGTTGAACATNTTTTCATATGTTTATTG 120 chrXptel1M 921378 ATATTTTG---TTGTTCTTTTGAGAACTGTTTTGAGCATATCTTTTGACC 921424 iivv --- v v i - i vv i i v C L1ME4a_3end#L 119 GCCATTTGTATTTCTTCTTTTGTGAATTG-TCTGTTCATGTCCTTTGCCC 71 chrXptel1M 921425 ATTTATCTGTTGAGG 921439 v i i C L1ME4a_3end#L 70 ATTTTTCTATTGGGG 56 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.62 CpG sites = 81, Kimura (unadjusted) = 42.35 Transitions / transversions = 1.14 (81/71) Gap_init rate = 0.05 (24 / 498), avg. gap size = 1.33 (32 / 24) 17 17.73 0.00 0.00 chrXptel1M 921572 921609 (78391) (TTTGTTT)n#Simple_repeat 1 38 (0) m_b349s252i17 14633 chrXptel1M 921572 TTTGTTGTTTTTTGTTTGTTTGTTGTTTTTTATCTTTT 921609 v v v v i i (TTTGTTT)n#Si 1 TTTGTTTTTTGTTTTTTGTTTTTTGTTTTTTGTTTTTT 38 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 262 29.59 8.51 3.66 chrXptel1M 922692 922926 (77074) C L1PA14_3end#LINE/L1 (536) 372 127 m_b349s551i16 14634 chrXptel1M 922692 TGAGTCGAATAATAAA---GGTTTAATAACTCTTTGGGCATAATTGC-AG 922737 i ii iv--- v -- i i v -- i - v C L1PA14_3end#L 372 TGGGTCGAATGGTAGTTCTGCTTT--TAGCTCTTTGAGGA--ATCGCCAT 327 chrXptel1M 922738 ATTACTCTCCGAAAAATTCTTCA--TAGTTCATAGATCCATCAACGATAA 922785 i i i -- v vv v -- i i i vvi i ii iv C L1PA14_3end#L 326 ACTGCTTTCC--ACAATGGTTGAACTAATTTACACTCCCACCAACAGTGT 279 chrXptel1M 922786 ATTAGTGTCCCATTTTTTCTACATCCCTTCCAACATTTTTTTCCATTC-- 922833 v i v i ii v iiv i i v viiv i-- C L1PA14_3end#L 278 ATAAGTGTTCCCTTTTCTCCGCAACCTCGCCAGCATCTGTTATTTTTTGA 229 chrXptel1M 922834 CTTTTCAATCGTTTTAGCCAATCTGATAGATATAAAATGTT--------- 922874 i vi --- v iv i i i i v --------- C L1PA14_3end#L 228 CTTTTTAATAAT---AGCCATTCTGACTGGTGTGAGATGGTATCTCATTG 182 chrXptel1M 922875 --GTTTTAATTTACATTTCTCTAATCAACAATGATTTAGAG-TATTTTTC 922921 -- i i v v i v v - v C L1PA14_3end#L 181 TGGTTTTGATTTGCATTTCTCTAATGATCAGTGATATTGAGCTTTTTTTC 132 chrXptel1M 922922 ACATG 922926 i C L1PA14_3end#L 131 ATATG 127 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.60 CpG sites = 40, Kimura (unadjusted) = 38.90 Transitions / transversions = 1.48 (40/27) Gap_init rate = 0.07 (16 / 234), avg. gap size = 1.81 (29 / 16) 325 25.89 9.38 3.45 chrXptel1M 922735 922926 (77074) C L1ME5_3end#LINE/L1 (612) 329 127 m_b349s551i17 14634 chrXptel1M 922735 CAGATTACTCTCCGAAAAATT-CTTCAT-AGTTCATAGATCCATCAACGA 922782 i -- i v- v i- ii i vvi i i ii C L1ME5_3end#LI 329 CAGATTGCTCTCC--AGAATGGCTGCACCAGTCTACACTCCCACCAGCAG 282 chrXptel1M 922783 TAAATTAGTGTCCCATTTTTTCTACATCCCTTCCAACATTT----TTTTC 922828 iv v v i vv ? ii i iiv i ---- v C L1ME5_3end#LI 281 TGCATGAGGGTTCCTATNTCCCCACATCCTCGCCAACACTTGGCATTATC 232 chrXptel1M 922829 CATTCCTTTTCAATCGTTTTAGCCAATCTGATAGATATAAAATG------ 922872 v-- ii -- - i i i i i ------ C L1ME5_3end#LI 231 CAG--CTTTCTAAT--TTTT-GCCAGTCTAATAGGTGTAAAGTGATATCT 187 chrXptel1M 922873 -----TTGTTTTAATTTACATTTCTCTAATCAACAATGATTTAGAGTAT- 922916 ----- i i i vi v v i - C L1ME5_3end#LI 186 CATTGTTGTTTTAATTTGCATTTCTCTGATTACTAATGAGTTTGAGCATC 137 chrXptel1M 922917 TTTTCACATG 922926 i i C L1ME5_3end#LI 136 TCTTCATATG 127 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 32.59 CpG sites = 33, Kimura (unadjusted) = 33.46 Transitions / transversions = 2.20 (33/15) Gap_init rate = 0.06 (12 / 191), avg. gap size = 2.08 (25 / 12) 277 30.55 3.42 1.34 chrXptel1M 923517 923662 (76338) L1MEj_5end#LINE/L1 2005 2153 (7) m_b349s551i18 14635 chrXptel1M 923517 AATAAGATAGGGGAGAATA----CACAGT-TAGCAATCATAACTATGAAT 923561 i i ii - ---- - - v i i v vv i L1MEj_5end#LI 2005 AGTAAGATGGAAG-GAATAAAATCA-AGTATATCAGTCGTTACACTAAAT 2052 chrXptel1M 923562 ATGAATCAGATGAACTCACTCATAAAATGGTTGAGGATATTAGAATGGAT 923611 i viiv i v i v v iiv iv i i v i L1MEj_5end#LI 2053 GTGAATGGACTGAATTCTCCCATTAAAAGACAGAGACTGTCAGATTGGGT 2102 chrXptel1M 923612 TAGGAAACAGAATTCAATAACATGTTGCTTACAAGAAACATACTTGAAAT 923661 ii i ii iiv i i i i i i L1MEj_5end#LI 2103 TAAAAAACAAAACCCAGCTATATGCTGTTTACAAGAAACACACTTAAAAC 2152 chrXptel1M 923662 A 923662 L1MEj_5end#LI 2153 A 2153 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.48 CpG sites = 31, Kimura (unadjusted) = 41.76 Transitions / transversions = 2.38 (31/13) Gap_init rate = 0.03 (4 / 145), avg. gap size = 1.75 (7 / 4) 230 30.45 5.83 3.29 chrXptel1M 923541 923866 (76134) L1M1_orf2#LINE/L1 22 355 (2939) m_b349s551i19 14635 chrXptel1M 923541 TTAGCAATCATAACTATGAATATGAATCAGATGAACTCACTCATAAAATG 923590 v v vv i i viiv i v iv v v L1M1_orf2#LIN 22 TTATCAATAATAACATTGAATGTAAATGGACTAAACTCTCCAATCAAAAG 71 chrXptel1M 923591 GTTGAGGATATTAGAATGGATTAGGAAACAGAATTCAATAACATGTTGCT 923640 iivv ii iviv v ii ii ii ? i iv i L1M1_orf2#LIN 72 ACATAGAGTGGCTGAATGGATGAAAAAACAAGACCCANTGATCTGTTGCC 121 chrXptel1M 923641 TACAAGAAACATACTTGAAATAGAAAAATGCACACAG--TTAAAATAAGG 923688 i v vv v i ii i -- v i L1M1_orf2#LIN 122 TACAAGAAACACACTTCACCTATAAAGACACACATAGACTGAAAATAAAG 171 chrXptel1M 923689 GGCTAG-AGTAGA-ATCTCA-GCTAAAGTTAAAACAAGCAAAACAAACCA 923735 v i - iv - ii - i -- vi --- v i v L1M1_orf2#LIN 172 GGATGGAAAAAGATATTCCATGCCAA--TGGAAAC---CAAAAAAGAGCA 216 chrXptel1M 923736 GGGGTAGCAATCATGATCTTGGGGAAAATA------AAAGCAAAAAT--- 923776 i v vv v v ii iv ------ ii i--- L1M1_orf2#LIN 217 GGAGTAGCTATACTTATATCAGACAAAATAGATTTCAAGACAAAAACTAT 266 chrXptel1M 923777 -AGACCTAATTAAAAAAGGGAAACTACATTTAACCATAAAGTA--CCAT- 923822 - vvvi i-- i i vv i -- iv vi-- v - L1M1_orf2#LIN 267 AAGAAGAGAC--AAAGAAGGTCACTATA--TAATGATAAAGGGGTCAATT 312 chrXptel1M 923823 -AGATAAAGAATTAATATCGATATTAAATATATATGCACCAAACA 923866 - vv i i -- v i v? v L1M1_orf2#LIN 313 CAGCAAGAGGAT--ATAACAATTNTAAATATATATGCACCCAACA 355 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.19 CpG sites = 51, Kimura (unadjusted) = 40.19 Transitions / transversions = 1.13 (51/45) Gap_init rate = 0.06 (20 / 325), avg. gap size = 1.50 (30 / 20) 305 30.66 1.49 1.49 chrXptel1M 923542 923743 (76257) L1MC_orf2#LINE/L1 23 224 (3070) m_b349s551i20 14635 chrXptel1M 923542 TAGCAATCATAACTATGAATATGAATCAGATGAACTCACTCATAAAATGG 923591 v v v v i i ? vivv i iv iv v v i L1MC_orf2#LIN 23 TATCAATAATCACTTTAAATGTNAATGGTCTAAATACACCAATTAAAAGA 72 chrXptel1M 923592 TTGAGGATATTAGAATGGATTAGGAAACAGAATTCAATAACATGTTGCTT 923641 iv iv i i i i ii ii ii iv i ii L1MC_orf2#LIN 73 CAGAGATTGTCAGAGTGGATCAAAAAACAAGACCCAACTATATGTTGTCT 122 chrXptel1M 923642 ACAAGAAACATACTTGAAATAGAAAAATGCACACAG-TTAAAA-TAAGGG 923689 vi v v i ii i i - - i? L1MC_orf2#LIN 123 ACAAGAAACCCACTTTAAATATAAAGACACATATAGATTAAAAGTAAANG 172 chrXptel1M 923690 GCTAGAGTAGAATCTCAGCTAAAGTTAAAAC-AAGCAAAACAAACCAGGG 923738 v i v ii v - v -- v i v - v v v ? i L1MC_orf2#LIN 173 GATGGAGAAAGATAT-ACC--ATGCTAACACTAATCAAAAGAAAGCNGGA 219 chrXptel1M 923739 GTAGC 923743 L1MC_orf2#LIN 220 GTAGC 224 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.35 CpG sites = 35, Kimura (unadjusted) = 41.35 Transitions / transversions = 1.35 (35/26) Gap_init rate = 0.03 (6 / 201), avg. gap size = 1.00 (6 / 6) 185 28.29 0.00 8.77 chrXptel1M 924305 924366 (75634) Tigger19b#DNA/TcMar-Tigger 296 352 (198) m_b349s601i16 14636 chrXptel1M 924305 GAGGAGTCTGGGAAGATGGTGGGATAAGGTAGGAAATTATCTGGCTTCCC 924354 - v iv ii i ---- i ivvii Tigger19b#DNA 296 GAGGAGT-TGGGCAGGAGGCAGGATGAGG----AAACTGGACAGCTTCCC 340 chrXptel1M 924355 AGATTCCCCTAA 924366 v i i i Tigger19b#DNA 341 AGCTCCTCCTGA 352 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.92 CpG sites = 11, Kimura (unadjusted) = 36.92 Transitions / transversions = 2.20 (11/5) Gap_init rate = 0.08 (5 / 61), avg. gap size = 1.00 (5 / 5) 18 14.87 2.63 0.00 chrXptel1M 925004 925041 (74959) (AAT)n#Simple_repeat 1 39 (0) m_b349s252i19 14637 chrXptel1M 925004 AATAA-AATAATAATAACAATAAGAGCAATGATAATAAT 925041 - i v ii i (AAT)n#Simple 1 AATAATAATAATAATAATAATAATAATAATAATAATAAT 39 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 15 24.65 3.23 3.23 chrXptel1M 925004 925065 (74935) (AATAAC)n#Simple_repeat 1 62 (0) m_b349s252i18 14638 chrXptel1M 925004 AATAA-AATAATAATAACAATAAGAGCAATGATAATAATTAAGCAA-GAG 925051 - i v ii ii i - - -i v (AATAAC)n#Sim 1 AATAACAATAACAATAACAATAACAATAACAATAACAA-TAA-CAATAAC 48 chrXptel1M 925052 AGAAAGAATAACAA 925065 iv v (AATAAC)n#Sim 49 AATAACAATAACAA 62 Matrix = Unknown Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.07 (4 / 61), avg. gap size = 1.00 (4 / 4) 14 13.53 2.08 8.89 chrXptel1M 925972 926019 (73981) (AAGAA)n#Simple_repeat 1 45 (0) m_b350s252i3 14639 chrXptel1M 925972 AAG-AAATAAAATAAAATCAAAAGAACGAAGAAAAGAAAAAGGAGAGAA 926019 - v v -v -- - i i (AAGAA)n#Simp 1 AAGAAAAGAAAAGAAAA-GAAAAGAA--AAGAAAAG-AAAAGAAAAGAA 45 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.11 (5 / 47), avg. gap size = 1.00 (5 / 5) 231 33.13 4.70 4.90 chrXptel1M 927995 928505 (71495) L1M4_orf2#LINE/L1 290 799 (2495) m_b350s551i0 14640 chrXptel1M 927995 TTATGATAAAAAAAGGTCCCATAGATAATGAGGAAATATCAATACTAAAC 928044 i i v vi v vv v v i v v vv L1M4_orf2#LIN 290 TTATAATGATAAAAGGGTCAATCCATCAGGAAGATATAACAATTATAAAC 339 chrXptel1M 928045 CTATGTGCACC-------AAAGCTTATATAATTCATATTTTAAAAGGAAA 928087 v i ------- i ii-i v v i------ v L1M4_orf2#LIN 340 ATATATGCACCTAACAACAGAGCCC-CAAAATACATG------AAGCAAA 382 chrXptel1M 928088 AACTAAACAAATTACAGAGAGAAATGGGTAGCAAAACAAGCTATAATAGT 928137 i vvi iv i i ii iivv ---- L1M4_orf2#LIN 383 AACTGACAGAATTGAAGGGAGAAATAGACAATTCAACAA----TAATAGT 428 chrXptel1M 928138 GGGGGACTACAA-ACTTC--TTTCAGAACTAGATA-AAT--CTAAACAAA 928181 v i v - ii -- iv v i - i-- i i L1M4_orf2#LIN 429 TGGAGACTTCAATACCCCACTTTCAATAATGGATAGAACAACTAGACAGA 478 chrXptel1M 928182 AGATAAATAAGAAAGAAGTCAAGGAGATGAATAGAAACT-TAGATAAGCT 928230 v i --- i vi i vv i - v - i iv i L1M4_orf2#LIN 479 AGATCAACAAG---GAAATAGAAGACTTGAACA-ACACTATAAACCAACT 524 chrXptel1M 928231 TAGATATGATCACTATCTGGGGAGAACTGAAT--GGGAATGGAAAGGAAT 928278 - iv i ivivi ivi iv vv i--iiv ii v -- L1M4_orf2#LIN 525 -AGACCTAACAGACATCTATAGAACACTCCACCCAACAACAGCA--GAAT 571 chrXptel1M 928279 ACATCTTTTTCTCAGCAGTATTTGGTACTTTTGCAAAAACTGACCATATA 928328 iv i ivv i iv v v iv v ii iv i L1M4_orf2#LIN 572 ACACATTCTTCTCAAGTGCACATGGAACATTCTCCAGGATAGACCATATG 621 chrXptel1M 928329 TTAAGGCATAAA--GACTTTACAGTTAAATGCAGAAAAATAGAAATATTA 928376 i v --i v i - i- vi i ii v vv L1M4_orf2#LIN 622 TTAGGCCATAAAACAAGTCT-CAA-TAAATTTAAAAGGATTGAAATCATA 669 chrXptel1M 928377 AAATAATATCCTTTTCAGATCACAGTGTAACAAAATTAC-ATTTAAT--- 928422 v - i -v i v i i v ii v- v i --- L1M4_orf2#LIN 670 CAA-AGTAT-GTTCTCCGACCACAATGGAATGAAATTAGAAATCAATAAC 717 chrXptel1M 928423 --AAGGGAACATGGAAACAGATTAAAAATTAATTGGAGGCTAAATAATCT 928470 -- i iv i --- v v v vv iii i ivi L1M4_orf2#LIN 718 AGAAGGAAATTTGGGAA---ATTCACAAATATGTGGAAATTAAACAACAC 764 chrXptel1M 928471 AGTATCAAAGAATGAACAGATTAAAGAACAAATCA 928505 v vii v iv ii i i v L1M4_orf2#LIN 765 ACTCCTAAATAACCAATGGGTCAAAGAAGAAATCA 799 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 44.90 CpG sites = 89, Kimura (unadjusted) = 44.90 Transitions / transversions = 1.24 (89/72) Gap_init rate = 0.07 (36 / 510), avg. gap size = 1.36 (49 / 36) 272 25.93 6.10 3.57 chrXptel1M 928275 928438 (71562) L1M2_orf2#LINE/L1 568 735 (2556) m_b350s551i1 14640 chrXptel1M 928275 GAATACATCTTTTTCTCAGCAGTATTTGGTACTTTTGCAAAAACTGACCA 928324 iv i v i iv v v iv v ii iv L1M2_orf2#LIN 568 GAATACACATTCTTCTCATCAGCACATGGAACATTCTCCAGGATAGACCA 617 chrXptel1M 928325 TATATTAAGGCATA----AAGACTTTACAGTTAAATGCAGAAAAATAGAA 928370 i i v i ---- v iv ---- vi?i v L1M2_orf2#LIN 618 TATGTTAGGCCACAAAACAAGTCTCAAC----AAATTTNAAAAAATCGAA 663 chrXptel1M 928371 ATATTAAAATAATATCCTTTTCAGATCACAGTGTAACAAAATTAC--ATT 928418 vv vv - i - ? i i v i i v-- i L1M2_orf2#LIN 664 ATCATATCA-AGTAT-CTTTTCNGACCACAATGGAATAAAACTAGAAATC 711 chrXptel1M 928419 --TAATAAG-GGAAC-ATGGAAAC 928438 -- i - -v L1M2_orf2#LIN 712 AATAACAAGAGGAACTTTGGAAAC 735 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 32.73 CpG sites = 21, Kimura (unadjusted) = 32.73 Transitions / transversions = 1.05 (21/20) Gap_init rate = 0.07 (11 / 163), avg. gap size = 1.45 (16 / 11) 304 30.67 0.71 2.17 chrXptel1M 928275 928414 (71586) L1P3_orf2#LINE/L1 568 705 (2589) m_b350s551i2 14640 chrXptel1M 928275 GAATACATCTTTTTCTCAGCAGTATTTGGTACTTTTGCAAAAACTGACCA 928324 i iv i ivi iv v i v v v i L1P3_orf2#LIN 568 GAATATACATTCTTCTCAGCGCCACATCGCACTTATTCTAAAATTGACCA 617 chrXptel1M 928325 TATATTAAGGCATAAAG-ACTTTACAGTTAAATGCAGAAAAATAGAAATA 928373 i v vi ivi i- iiv -i i i ii v L1P3_orf2#LIN 618 CATAATTGGAAGTAAAACACTCCTCAG-CAAATGCAAAAGAACGGAAATC 666 chrXptel1M 928374 TTAAAATAATATCCTTTTCAGATCACAGTGTAACAAAATTA 928414 v v - i vi - i i i iv L1P3_orf2#LIN 667 ATAACA-AACAGTC-TCTCAGACCACAGTGCAATCAAATTA 705 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.26 CpG sites = 26, Kimura (unadjusted) = 40.94 Transitions / transversions = 1.62 (26/16) Gap_init rate = 0.03 (4 / 139), avg. gap size = 1.00 (4 / 4) 17 21.21 3.39 3.39 chrXptel1M 928698 928756 (71244) (TATG)n#Simple_repeat 1 59 (0) m_b350s252i4 14641 chrXptel1M 928698 TATATGTGTGTGTATGTATGTATGCATGTGGATTTATCTCTACATG--TG 928745 i i i i -- v v v ii -- (TATG)n#Simpl 1 TATGTATGTATGTATGTATGTATGTATGT--ATGTATGTATGTATGTATG 48 chrXptel1M 928746 TGTGTATGTAT 928756 i (TATG)n#Simpl 49 TATGTATGTAT 59 Matrix = Unknown Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.05 (3 / 58), avg. gap size = 1.33 (4 / 3) 281 31.80 5.51 7.26 chrXptel1M 928937 929916 (70084) C L1P3_orf2#LINE/L1 (1762) 1532 569 m_b350s551i4 14642 chrXptel1M 928937 TCATAAAAGGAATTTGGTAGAATTTCTTTTTTGCTCTTTTCCCTAAAATA 928986 v i v v i v i i i -i v vii ii C L1P3_orf2#LIN 1532 TCATAAAATGAGTTAGGGAGGAGTCCCTCTTT-TTCTATTGTTTGGAATA 1484 chrXptel1M 928987 GTTT-ATATAGTTTATATTGGAATTAGTTGTTCTTTAAATGTTTGTTAGA 929035 - v vi ----- v v ii i vi iv iv i v C L1P3_orf2#LIN 1483 GTTTCAGAAGG-----AATGGTACCAGCTCCTCTTTGTACCTCTGGTAGA 1439 chrXptel1M 929036 ATTCATTTGTGAATTCATTTGGTCCTGGGGACTTGTTCCTAA--GGTAGC 929083 ivi i i i -- - ii ii-- v C L1P3_orf2#LIN 1438 ATTCGGCTGTGAATCCGTCTGGTCCTGGG--CTT-TTTTTGGTTGGTAGG 1392 chrXptel1M 929084 TAATTTATGGCTTGCTCAATTTC----TTTTTTCTAAGATAGGATTATTT 929129 iv v vi vv ----i v ----- v vi i C L1P3_orf2#LIN 1391 CTATTAATTACTGCCTCAATTTCAGAACTTGTT-----ATTGGTCTATTC 1347 chrXptel1M 929130 AAATATTATAGTTCTTCTTCTGTTAATGT--AAACAATTTATATTTTTGT 929177 iiv vv v i vvv i v --ii vii v i v iiiv C L1P3_orf2#LIN 1346 AGGGATTCGACTTCTTCCTGGTTTAGTCTTGGGAGGGTGTATGTGTCCAG 1297 chrXptel1M 929178 AAATGTCCATCCATTTCATTTAGAATGTCAGATTTATTGGCATGTAATTG 929227 i v -- v i v v vii v i iv iv C L1P3_orf2#LIN 1296 GAATTT--ATCCATTTCTTCTAGATTTTCTAGTTTATTTGCGTAGAGGTG 1249 chrXptel1M 929228 GGCAAAAGTAGCTTCTAATAATTGCTT-TAATTTTGTCTTCATTTGTGGT 929276 vvi v - vii i ii v i - v i vvv- iv C L1P3_orf2#LIN 1248 TTTATA-GTATTCTCTGATGGTAGTTTGTATTTCTGTGGG-ATCAGTGGT 1201 chrXptel1M 929277 GA-ATGCATCCTTT-TCATTTTTTGATACTAGTAATTTGGTT-TTCTTTC 929323 - v -- - - vv iviv i - i C L1P3_orf2#LIN 1200 GATATCC--CCTTTATCATTTTTT-ATTGTGTCTATTTGATTCTTCTCTC 1154 chrXptel1M 929324 TTTT-----TTAAAAATCAAGCTAACCAAAGATCTATCTATTTTATTGAT 929368 ----- vv i vi i ---- i i i C L1P3_orf2#LIN 1153 TTTTCTTCTTTATTAGTCTGGCTAGC----GGTCTATCTATTTTGTTAAT 1108 chrXptel1M 929369 TTTTTTAATAAAACCAGCTTCTAGTTTTATTTATTAGTTCAA---TTTAT 929415 i i - i i v i v vv v --- - C L1P3_orf2#LIN 1107 CTTTTCAA-AAAACCAGCTCCTGGATTCATTGATTTTTTGAAGGGTTT-T 1060 chrXptel1M 929416 TCTTTTACTTTTTTACTTTTACTTTTATTAACATATCTTTTGGTTTTTAC 929465 v v - i v iv i i v i ii -- vv --i v v C L1P3_orf2#LIN 1059 TCGTGT-CTCTATCTCCTTCAGTTCTGCT--CTGATCTT--AGTTATTTC 1015 chrXptel1M 929466 CTGTTCCAATTTAGTGTTTAATCGGAGATTTTTAAGTTGTT--CTTTTTC 929513 i i---- i-- i ------- v v v -- i v C L1P3_orf2#LIN 1014 TTGTC----TTC--TGCT-------AGCTTTTGAATTTGTTTGCTCTTGC 978 chrXptel1M 929514 TGTTTT--TTTTTTTAATTGC-ATG-------ATCTGTTTT------TTT 929547 vi i -- i i- -------i vi ------ i C L1P3_orf2#LIN 977 TTCTCTAGTTCTTTTAATTGTGATGTTAGGGTGTCGATTTTAGATCTTTC 928 chrXptel1M 929548 CTGTATTTTGTTGATCTGAGCATTCAGAAATATAAATTT-TCTCTAAAGT 929596 i iv i v? --- i i viv -i -i C L1P3_orf2#LIN 927 CCGCTTTCTCNTG---TGGGCATTTAGTGCTATAAATTTCCCTCTAAA-C 882 chrXptel1M 929597 ACTACTTTGGTTGCATCCCATAAATTTTGACATGTTCTTTCATTGTTATC 929646 i i i ii v i i ii i v v v v C L1P3_orf2#LIN 881 ACTGCTTTAGCTGTGTCCCAGAGATTCTGGTACGTTGTGTCTTTGTTCTC 832 chrXptel1M 929647 ATTCACTTTAATGAAAATATTTATTGTTTCTAT-GTCTTGTTCTTTGACC 929695 vii i v vv ? vi v iv -i i i v - C L1P3_orf2#LIN 831 ATTGGTTTCAAAGAACTTNTTTATTTCTGCCTTAATTTCGTTATTT-ACC 783 chrXptel1M 929696 CAGTCATTCTTTAAAATTAAATTACTTAGATTCC---TATT-----AATT 929737 vi iv i ii vi ii ii i v --- v -----ii C L1P3_orf2#LIN 782 CAGTAGTCATTCAGGAGCAGGTTGTTCAGTTTCCATGTAGTTGTGCGGTT 733 chrXptel1M 929738 TTAATTTATCCTTTCATGGTCCTTAATTAAATTAAACTAAATTTTTGTTG 929787 i v v --v v ii v i -------- -- vi C L1P3_orf2#LIN 732 TTGAGTGA--GTTTCTTAATCCTGAGTT--------CTAA--TTTGATTG 695 chrXptel1M 929788 CATTAGTTTCTATATAAAAAAGAAGCAGTTAAT----ATTTCTGCTTTTC 929833 i ivvv --------i ii v vi ---- i i i i C L1P3_orf2#LIN 694 CACTGTGGTCT--------GAGAGACTGTTTGTTATGATTTCCGTTCTTT 653 chrXptel1M 929834 TGGATTTGGTTATAAGGCTTTTATACACAA-TACATGATCAATTTATGCA 929882 v v v vi vv iviv - ii i vv v C L1P3_orf2#LIN 652 TGCATTTGCTGAGGAGTGTTTTACTTCCAATTATGTGGTCAATTTTAGAA 603 chrXptel1M 929883 TAGGAGCAATGTATCACTGAGAAAAAGGTATATT 929916 i v i iv i i v C L1P3_orf2#LIN 602 TAAGTGCGATGTGGCGCTGAGAAGAATGTATATT 569 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.54 CpG sites = 160, Kimura (unadjusted) = 42.47 Transitions / transversions = 1.24 (160/129) Gap_init rate = 0.09 (91 / 979), avg. gap size = 1.36 (124 / 91) 917 28.46 4.41 5.61 chrXptel1M 928937 929729 (70271) C L1M5_orf2#LINE/L1 (1762) 1532 749 m_b350s551i3 14642 chrXptel1M 928937 TCATAAAAGGAATTTGGTAGAATTTCTTTTTTGCTCTTTTCCCTAAAATA 928986 v i v v vi i i i -i v ii ii v C L1M5_orf2#LIN 1532 TCATAAAATGAGTTGGGAAGTGTTCCCTCTTT-TTCTATTTTCTGGAAGA 1484 chrXptel1M 928987 GTTTATATAGTTTATATTGGAATTAGTTGTTCTTTAAATGTTTGTTAGAA 929036 i i ---- v v v v i v C L1M5_orf2#LIN 1483 GTTTGTGTA----AGATTGGTATTATTTCTTCCTTAAATGTTTGGTAGAA 1438 chrXptel1M 929037 TTCATTTGTGAATTCATTTGGTCCTGGGGACTTGTTCCT---AAGGTAGC 929083 iiv vi i v i vi v iv --- vvi C L1M5_orf2#LIN 1437 TTCACCAGTGAAGCCATCTGGGCCTGGAGTTTTCTTTGTGGGAAGGTTTT 1388 chrXptel1M 929084 TAATTTATGGCTTGCTCAATTTCTTTTTTCTAAGATAGGATTATTTAAAT 929133 - iiiv --- vv v-i v ii i i C L1M5_orf2#LIN 1387 TAA-TTACAAAT---TCAATTTCTTTAATA-GATATAGGGCTATTCAGAT 1343 chrXptel1M 929134 ATTATAGTTCTTCTTCTGTTAATGTAAACAATTTATATTTTTGTAAATGT 929183 v v v v? i i v viii ? i i vv iivi C L1M5_orf2#LIN 1342 TTTCTATTTCTTCTTGNGTCAGTTTTGGTAANTTGTGTTTTTCAAGGAAT 1293 chrXptel1M 929184 CCATCCATTTCATTTAGAATGTCAGATTTATTGGCATGTAATTGGGCAAA 929233 iii i iiv ? i iv i vv v C L1M5_orf2#LIN 1292 TTGTCCATTTCATCTAAGTTNTCAAATTTATTGGCATAAAGTTGTTCATA 1243 chrXptel1M 929234 AGTAGCTTCTAATAATTGCTTTAATTTTGTCTTC---ATTTGTGGTGAAT 929280 - vii v v ivi --- vi--- i i - C L1M5_orf2#LIN 1242 A-TATTCTCTTATTATCCTTTTAA---TGTCTGTAGGATCTGTAGTG-AT 1198 chrXptel1M 929281 GCATCCTTTTCATTTTTTGATACTAGTAATTTG-GTTTTCTTTC-TTTTT 929328 iv ivv ii i i - i i - C L1M5_orf2#LIN 1197 GTCTCCTTTTTCATTCCTGATATTGGTAATTTGTGTCTTCTCTCTTTTTT 1148 chrXptel1M 929329 TAAAAATCAAGCTAACCAAAGATCTATCTATTTTATTGATTTTTTTAATA 929378 vvvi iv ?i i i i i v i i - C L1M5_orf2#LIN 1147 TCTTGATCAGTCTNGCTAGAGGTTTATCAATTTTATTGATCTTTTCAA-A 1099 chrXptel1M 929379 AAACCAGCTTCTAGTTTTATTTATTAGTTCAATT---TATTCTTTTACT- 929424 i i i i ii v vvi v --- ? iv v - C L1M5_orf2#LIN 1098 GAACCAGCTTTTGGCTTCGTTGATTTTCTCTATTGTNTNTTTGTTTTCTA 1049 chrXptel1M 929425 ---------TTTTTACTTTTACTTTTATTAACATATCTTTTGGTTTTTAC 929465 --------- i i i ii --- v i i--i i C L1M5_orf2#LIN 1048 TTTCATTGATTTCTGCTCTTATCTTTATT---ATTTCCTTC--CTTCTAC 1004 chrXptel1M 929466 CTGTTCCAATTTAGTGTTTAATCGGAGATTTTTAAGTTGTTCTTTTTCTG 929515 --- ? -- i - ------ ----- i v i C L1M5_orf2#LIN 1003 ---TTNC--TTTGG-GTTTAAT------TT-----GCTCTTCTTTTTCTA 971 chrXptel1M 929516 TTTTTTT---TTTTAA--TTGCATGATCTGTTTT-----TTTCTGTATTT 929555 vi i ---v vv -- iv v ivi ----- - v C L1M5_orf2#LIN 970 GCTTCTTAAGGTGGAAGCTTAGATCATTGATTTTAAGCCTTTCT-TCTTT 922 chrXptel1M 929556 TGTTGATCTGAGCATTCAGAAATATAAATTTTCTCTAAAGTACTACTTTG 929605 -i i v i? i i?iv i iiiv i i i C L1M5_orf2#LIN 921 T-CTAATATANGCATTTAANGCTATAAATTTCCCTCTAAGCACTGCTTTA 873 chrXptel1M 929606 GTTGCATCCCATAAATTTTGACATGTTCTTTCATTGTTATCATTCACTTT 929655 i i i v v iv ii ? v i C L1M5_orf2#LIN 872 GCTGCATCCCACAAATTTTGATATGTTGTATTTTCATTNTCATTCAGTTC 823 chrXptel1M 929656 AATGAAAATATTT----ATTGTTTCTATGTCTTGTTCTTTGACCCAGTCA 929701 ---- ---- vii?i i vi v vvvi C L1M5_orf2#LIN 822 ----AAAATATTTTCTAATTTCCNTTGTGATTTCTTCTTTGACCCATGGG 777 chrXptel1M 929702 TTCTTTAAAATTAAATTACTTAGATTCC 929729 v i v ivi ii iv C L1M5_orf2#LIN 776 TTATTTAGAAGTGTGTTGTTTAATTTCC 749 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.26 CpG sites = 129, Kimura (unadjusted) = 37.52 Transitions / transversions = 1.54 (129/84) Gap_init rate = 0.07 (55 / 792), avg. gap size = 1.44 (79 / 55) 12 28.67 0.00 2.13 chrXptel1M 930132 930179 (69821) (GAAAAAT)n#Simple_repeat 1 47 (0) m_b350s252i5 14643 chrXptel1M 930132 GAAGAATGAAAAGTCAAGAATTTCAAGGGAATTAATGAAAAATGCAAA 930179 i i v i vvv iv -v v (GAAAAAT)n#Si 1 GAAAAATGAAAAATGAAAAATGAAAAATGAA-AAATGAAAAATGAAAA 47 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.02 (1 / 47), avg. gap size = 1.00 (1 / 1) 301 28.66 7.03 7.41 chrXptel1M 930197 930765 (69235) L1M5_orf2#LINE/L1 2615 3181 (113) m_b350s551i5 14640 chrXptel1M 930197 TACCAGATCT-AAAACTATATTATAAAGCAGCAGTAATCAAAACCATTTT 930245 ? ? - i - vi i vi v v L1M5_orf2#LIN 2615 TACCNGATNTCAAGACT-TATTATAAAGCTACAGTAATCAAGACAGTGTG 2663 chrXptel1M 930246 GTATTGGT-TAAGAAATAGAGTAGTGGATCAATGGATGAGATTAG---GT 930291 i- -i vv i i vv v --- L1M5_orf2#LIN 2664 GTATTGGCGTAAG-GATAGACAAATAGATCAATGGAACAGAATAGAGAGT 2712 chrXptel1M 930292 TCACAAGACATCACAAGACCCAATAGTCA-ATGACTATAGTAATCTAGTA 930340 i --- v ---- ----- - i-- i ?v ?i ii v L1M5_orf2#LIN 2713 CC---AGAAAT----AGACCCA-----CACATA--TATGGNCANTTGATT 2748 chrXptel1M 930341 TTTGAT--AGATGCAAA---AATTCCAGCTTCTGGGATAAGAACTCAGTA 930385 i-- i v --- - ---- iv i --i v L1M5_orf2#LIN 2749 TTTGACAAAGGTGCCAANGCAATT-CAG----TGGGGAAAGGA--TAGTC 2791 chrXptel1M 930386 CCT--GACAAAAATTTTTAGGAAAATTGGAAAATAGTATGGCAAAAACTG 930433 ii --i viv vi i i v v vivi v v L1M5_orf2#LIN 2792 TTTTCAACAAATGGTGCTGGAACAATTGGATATCCATATGGAAAAAAATG 2841 chrXptel1M 930434 GGCATTGACCACACCCTATGCCACAACCCTATGCCAAAATAAGGTCAAAA 930483 ii?v i ---- ivi - v ii v v iv ? i L1M5_orf2#LIN 2842 AANCTCGAC----CCCTACCTCAC-ACCATACACAAAAATTAATTCNAGA 2886 chrXptel1M 930484 TGGGTTCAT-GATTTAAACATGAAGCATGATACTATAAGCAAATT----A 930528 i- - ii ii i iv? i v -- v ---- L1M5_orf2#LIN 2887 TGGA-TCATAGACCTAAATGTAAAAGNTAAAACTATAA--AACTTCTAGA 2933 chrXptel1M 930529 GGAGAACA-AGGAATAGTTTAGCTCTCAGATCTGTGGAGAAGGGAGGAAT 930577 i i - iv --- v iivv i - i?v v iii L1M5_orf2#LIN 2934 AGAAAACATAGGAGAA---TATCTTCGTGACCT-TGGGNTAGGCAAAGAT 2979 chrXptel1M 930578 TAATGGCCAAAGAAGAACTAGAAAACA-----CATGGAAATGCAAAATGG 930622 vv ---i v i vvi i i ----- -i viv v L1M5_orf2#LIN 2980 TTCT---TAAACAGGACACAAAAAGCACNAACCAT-AAAAGAAAAAATTG 3025 chrXptel1M 930623 ATAATTTTGATTATATTAAATTTAAAAAGTTTTGT----------ACAAA 930662 v v i ?i i v v i i---------- vv L1M5_orf2#LIN 3026 ATAAATTGGACTNCATCAAAATTAAAAACTTCTGCTCNTCAAAAGACACC 3075 chrXptel1M 930663 GCTAAG---ATTAGAAAGGAAGCAGAAAACTGAAGGAAAATTTTT---AT 930706 i --- v i i v viv i ? iii v --- ? L1M5_orf2#LIN 3076 GTTAAGAAAATGAAAAGGCAAGCCACAGANTGGGAGAAAATATTTGCAAN 3125 chrXptel1M 930707 ATCTAAAGGTTTTGATAAAAGCCTAATTTCTAAAATATATAGAGAATTTA 930756 iv v --- i i i v vi v i i i i iv L1M5_orf2#LIN 3126 ACATATA---TCTGACAAAGGACTCGTATCCAGAATATATAAAGAACTCC 3172 chrXptel1M 930757 TAAAATTTA 930765 v ? i L1M5_orf2#LIN 3173 TACAANTCA 3181 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.82 CpG sites = 86, Kimura (unadjusted) = 38.10 Transitions / transversions = 1.32 (86/65) Gap_init rate = 0.10 (56 / 568), avg. gap size = 1.46 (82 / 56) 977 30.08 4.17 3.04 chrXptel1M 930807 931262 (68738) L1ME3Cz_3end#LINE/L1 88 548 (449) m_b350s551i6 14640 chrXptel1M 930807 AATTTTCAGACAAAGAAATTTAAA--ACCATTTCTAATTATATGAAAAAA 930854 iv vi i iiii --i ---v vi i L1ME3Cz_3end# 88 AATTCACAGAAGAGGAAACCCGAATGGCCA---ATAAACATATGAAAAGA 134 chrXptel1M 930855 TGCTCTAAATCACAACTGATTAGAGAAATGCAAATTAAGACAACTCTAAG 930904 v vv v v i i i i ? vv i L1ME3Cz_3end# 135 TGCTCAACCTCACTAGTAATCAGGGAAATGCAAATTAAAACNACAATGAG 184 chrXptel1M 930905 ATACCACTACACACCTGTCAGATTGGCTAAGATGACAGGAAAG---GATA 930951 i v ii v i v---vi --- i L1ME3Cz_3end# 185 ATACCATTTCACACCCATCAGATTGGCAAAAATT---TAAAAGTCTGACA 231 chrXptel1M 930952 AGGATGGATATTGGAGGAGATGTGGGAAAACTGGGACATTAATGCATTGT 931001 viviiii i v ii ii v i vi v i i i L1ME3Cz_3end# 232 ATACCAAGTGTTGGCGAGGATGTGGAGAAACGGGAACTCTCATACACTGC 281 chrXptel1M 931002 TGGTGGAGTTGTGAATTGATCCCAACCATTCTGGAGAGCAATTTGGAACT 931051 iiv i i -v i i v v L1ME3Cz_3end# 282 TGGTGGGAGTGTAAATTGGT-ACAACCACTTTGGAGAGCAATTTGGCAAT 330 chrXptel1M 931052 GTGCCCAA-AGGGCTATCAAATTGTGCATGCCCAG-----CAGTGTTTCT 931095 i -- i i- ii i i-- iv i i vi----- iiv i L1ME3Cz_3end# 331 AT--CTAGTAAAGTTG--AAGATGCGCATACCCTACGACCCAGCAATTCC 376 chrXptel1M 931096 ACTGCT---TATATACCAAAGAGA-----TCTTAAAGGAGGGAAAGGGAC 931137 v --- vv ----- vi v v v viv ii- L1ME3Cz_3end# 377 ACTTCTAGGTATATACCCTAGAGAAACTCTCGCACATGTGCACAAGGAG- 425 chrXptel1M 931138 CCACATGTGCAAAGATGTTTGTGGCAGCCCTCTTTGTAATGGTAAAGAAC 931187 -- i i ii v vi v i ii i i L1ME3Cz_3end# 426 --ACATGTACAAGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAAT 473 chrXptel1M 931188 TGGAAACTGAATGGATCCCCATCAATTAGAAAATGGCTGAATATGTCATG 931237 vivv ii vi vi ii v i vi ii L1ME3Cz_3end# 474 TGGAAACAACCTAAATGTCCATCAATAGGGGAATGGATAAATAAATTGTG 523 chrXptel1M 931238 GTATATGAATATTATGGAATAGTAT 931262 vv iv v L1ME3Cz_3end# 524 GTATATTCATACAATGGAATACTAT 548 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.73 CpG sites = 82, Kimura (unadjusted) = 40.00 Transitions / transversions = 1.61 (82/51) Gap_init rate = 0.04 (20 / 455), avg. gap size = 1.65 (33 / 20) 750 30.72 5.07 4.09 chrXptel1M 930813 931345 (68655) L1MC5_3end#LINE/L1 98 635 (2059) m_b350s551i7 14640 chrXptel1M 930813 CAGACAAAGAAATTTAAAACCATTTCTAATTATATGAAAAAATGCTCTAA 930862 v vi -ivii ii ?i i v v L1MC5_3end#LI 98 CAGAAAAAGAAATGCAAA-TGGCTCTTAANCATATGAAAAGATGCTCAAC 146 chrXptel1M 930863 ATCACAACTGATTAGAGAAATGCAAATTAAGACAACTCTAAGATACCACT 930912 v i vvv i v i v v i i L1MC5_3end#LI 147 CTCGCTCATAATAAGAGAAATGCAAATTAAAACTACACTGAGATACCATT 196 chrXptel1M 930913 ACACACCTGTCAGATTGGCTAAGATGACAGGAAAGGATAAGGATGGA--- 930959 v v i v i -v -- vv i vi iiv --- L1MC5_3end#LI 197 TCTCACCTATCAGATTGGCAAAAAT-CCA--AAAGTTTGACAACATACTC 243 chrXptel1M 930960 TATTGGAGGAGATGTGGGAAAACTGGGACATTAATGCATTGTTGGTGGAG 931009 i v ii v i v v vi v i i ii L1MC5_3end#LI 244 TGTTGGCGAGGCTGTGGGGAAACAGGCACTCTCATACATTGCTGGTGGGA 293 chrXptel1M 931010 TTGTGAATTGATCCCAACCATTCTGGAGAGCAATTTGGAACTGTGCC--C 931057 v ii v i -v vi v i v v v i - i-- L1MC5_3end#LI 294 ATGCAAAATGGT-ACAACCCCTATGGAGGGGAATTTGGCAATAT-CTAGC 341 chrXptel1M 931058 AAAGGGCTATCAAATTGTGCAT----------GCCCAGCAGTGTTTCTAC 931097 ----- i v - i ----------i i--- i i L1MC5_3end#LI 342 AAA-----ATTACA-TATGCATTTACCCTTTGACCCAGCAA---TCCCAC 382 chrXptel1M 931098 TGCT-----TATATACCAAAGAGATCTT----AAAGGAGGGAAAGGGACC 931138 v ----- v v v ivi ---- iv v i i---- L1MC5_3end#LI 383 TTCTAGGAATCTATCCCAAAGATACACTGGCAAAAATACGAAAAGA---- 428 chrXptel1M 931139 CACATGTGCAAAGATGTTTGTGGCAGCCCTCTTTGTAATGGTAAAGAACT 931188 ii ii i v i ii v v v i i ii L1MC5_3end#LI 429 CGTATGCACAAGGCTATTCATTGCAGCACTATTTGTAATAGCAAAAGACT 478 chrXptel1M 931189 GGAAACTGAATGGATCCCCATCAATTAGAAAATGGCTGAATATGTCATGG 931238 vivviii vi vi ii v i viii L1MC5_3end#LI 479 GGAAACAACCCAAATGTCCATCAATAGGGGACTGGTTGAATAAACTATGG 528 chrXptel1M 931239 TATATGAATATTATGGAATAGTATTGTTCTGTAAGAAACGATTAGCAGGA 931288 i vv i iv i v vvvv - v v i-- L1MC5_3end#LI 529 TACATCCACACAATGGAGTACTATGCAGCTGTAA-AAAGGAATG--AGGA 575 chrXptel1M 931289 TGATTTC-AGAGAG-GCT-TGGAGAGACTTACATGAACTGATGCTAAGTG 931335 vv i - v v v- - v ii v v vv iv i L1MC5_3end#LI 576 ATATCTCTATATACTGCTATGGAGTGATCTCCAGGATATATTGTTAAGTG 625 chrXptel1M 931336 AAATGGGCAA 931345 vii L1MC5_3end#LI 626 AAAAAAGCAA 635 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.66 CpG sites = 82, Kimura (unadjusted) = 40.32 Transitions / transversions = 1.09 (82/75) Gap_init rate = 0.06 (30 / 532), avg. gap size = 1.63 (49 / 30) 16 0.00 0.00 0.00 chrXptel1M 931481 931500 (68500) (TTG)n#Simple_repeat 1 20 (0) m_b350s252i6 14644 chrXptel1M 931481 TTGTTGTTGTTGTTGTTGTT 931500 (TTG)n#Simple 1 TTGTTGTTGTTGTTGTTGTT 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 335 27.64 1.29 1.95 chrXptel1M 931852 932006 (67994) C L1MC_orf2#LINE/L1 (3046) 248 95 m_b350s551i8 14645 chrXptel1M 931852 TTTGCTTTGTCTGAGATCGTGATTGCTCCATCTGCTTTTTTTTTTCCTCA 931901 i i i iivv v v vi ? i v--v i C L1MC_orf2#LIN 248 TCTGCTCTGTCTGAAATTAATATAGCTACTCCNGCTTTCTTTTG--ATTA 201 chrXptel1M 931902 GGGGAAGCATAATAGAGTCTACTCCTGCCCTTTA--TTTAAACTCTGTAT 931949 v vv ii v vii v vv ? -- v v i i C L1MC_orf2#LIN 200 GTGTTAGCATGGTATATCTTTCTCCATCCNTTTACTTTTAATCTATATGT 151 chrXptel1M 931950 GTCTTTCTGTTTCAAGTATGTTTCTTGTAAAGAACATATTATTGGATTCT 931999 v i v iv i v vi i- C L1MC_orf2#LIN 150 GTCTTTATATTTAAAGTGGGTTTCTTGTAGACAACATATAGTTGGG-TCT 102 chrXptel1M 932000 AGTTTTT 932006 v C L1MC_orf2#LIN 101 TGTTTTT 95 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.26 CpG sites = 19, Kimura (unadjusted) = 35.26 Transitions / transversions = 0.83 (19/23) Gap_init rate = 0.03 (4 / 154), avg. gap size = 1.25 (5 / 4) 16 24.73 0.00 7.58 chrXptel1M 932629 932699 (67301) (TTTTC)n#Simple_repeat 1 66 (0) m_b350s252i7 14646 chrXptel1M 932629 TTCTCTTTCCTATTTACCTTTTTGTCCTTTTCTTGTCTTTTATTTGAATT 932678 i i - - i i v i v v vvv (TTTTC)n#Simp 1 TTTTCTTTTCT-TTT-CTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTT 48 chrXptel1M 932679 TCAGATTTTCTTTTCAGTTCT 932699 --- vv (TTTTC)n#Simp 49 TC---TTTTCTTTTCTTTTCT 66 Matrix = Unknown Transitions / transversions = 0.62 (5/8) Gap_init rate = 0.07 (5 / 70), avg. gap size = 1.00 (5 / 5) 460 31.00 3.39 3.39 chrXptel1M 932838 933221 (66779) L1PREC2_orf2#LINE/L1 2860 3243 (51) m_b350s551i9 14647 chrXptel1M 932838 ACACCGTATACCAAGATAAGATCAAAATGGGTCCATGATTTAGACATAAA 932887 i v i v iv i i iv v i i ii L1PREC2_orf2# 2860 ACACCATATACAAAAATCAACTCAAGATGGATTAAAGACTTAAATGTAAA 2909 chrXptel1M 932888 GAACGAGATTATAAACAAATTGGAGGA--ACATAGG--ATAGTTTATCTC 932933 ivv i i i v vvi i -- v -- --ii - L1PREC2_orf2# 2910 ACCCAAAACTATAAAAACCCTGGAAGACAACCTAGGCAATA--CCAT-TC 2956 chrXptel1M 932934 TCAGACTTGTGGAAGAGGAAGAAATTT-GTGACCAAAGACAAACTAGAGA 932982 -i v i- vi v i i -i -i i-- i i ii L1PREC2_orf2# 2957 T-GGACATA-GGAACGGGCAAAGATTTCATGAC-GAAGACG--CCAAAAG 3001 chrXptel1M 932983 CCATTATTG----ATCACAAAATAGAAAATTTTGATTACATCAAATTAAA 933028 v iivi---- v - v v v vv ivv i i L1PREC2_orf2# 3002 CAATTGCAACAAAAGCA-AAAATTGACAAATGGGATCTAATTAAACTAAA 3050 chrXptel1M 933029 AAGCTTCTGTACAAACAAAACTAA-TGTAAACAAGATTAGAAGGGAAGCA 933077 i i i- vv - i v iii v iv iv v v L1PREC2_orf2# 3051 GAGCTTCTGCACAG-CAAAAGAAACTATCAACAGAGTAAACAGACAACCT 3099 chrXptel1M 933078 ACAAACTGGGAAAACATCTTCACAGTTAAAGGTTCTGATAAAGGCCTCAT 933127 i v i v ? ii iviv v vv i i v L1PREC2_orf2# 3100 ACAGAATGGGAGAAAATNTTTGCAAACTATGCATCTGACAAAGGTCTAAT 3149 chrXptel1M 933128 TTCCAAAATATATAGAGAGCTGACTCTAATTTATAAGAAAC---CAAGCC 933174 v iv v ii i v vv v i v--- i v L1PREC2_orf2# 3150 ATCCAGCATCTATAAGGAACTTAAACAAATTTACAAGAAAAAAACAAACA 3199 chrXptel1M 933175 ATTCTCCAATTGATAAATGGTCAAAGGATATGAACAGACAATTTTCA 933221 -- i - i v i v i v L1PREC2_orf2# 3200 A--CCCCA-TTAAAAAGTGGGCAAAGGACATGAACAGACACTTTTCA 3243 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.66 CpG sites = 63, Kimura (unadjusted) = 41.05 Transitions / transversions = 1.21 (63/52) Gap_init rate = 0.05 (19 / 383), avg. gap size = 1.37 (26 / 19) 399 33.10 3.23 3.23 chrXptel1M 932839 933272 (66728) L1M2_orf2#LINE/L1 2858 3291 (0) m_b350s551i10 14647 chrXptel1M 932839 CACCGTATACCAAGATAAGATCAAAATGGGTCCATGATTTAGACATAAAG 932888 i v i v iv i iv v i i ii ii L1M2_orf2#LIN 2858 CACCATATACAAAAATCAACTCAAAATGGATTAAAGACTTAAATGTAAGA 2907 chrXptel1M 932889 AACGAGATTATAAACAAATTGGAGGAA--CATAGGATAGTTTATCTCTCA 932936 vv i i vvv i i i -- iv i--- ivii L1M2_orf2#LIN 2908 CCCGAAACTATAAAACTACTAGAAGAAAACATAGGGGAA---ACGCTTCA 2954 chrXptel1M 932937 G-ACTTGTGGAAGAGGAAGAAATTTGTGACCAAAGAC----AAACTAGAG 932981 - v - vvvi v i i v viv?v ---- vi v L1M2_orf2#LIN 2955 GGACAT-TGGTCTGGGCAAAGATTTTTTGGNTAAGACCTCAAAAGCACAG 3003 chrXptel1M 932982 ACCATTATTGATCACAAAATAGAAAATTTTGATTACATCAAATTAAAAAG 933031 i v iv --i v - v v vv i L1M2_orf2#LIN 3004 GCAACAA--AAGCA-AAAATAGACAAATGGGATTACATCAAACTAAAAAG 3050 chrXptel1M 933032 CTTCTGTA---CAAACAAAACTAATGTAAACAAGATTAGAAGGGAAGCAA 933078 i --- vi - -- v iii v ii iv v v L1M2_orf2#LIN 3051 CTTCTGCACAGCAAAGGAAAC-AA--TCAACAGAGTGAAGAGACAACCTA 3097 chrXptel1M 933079 CAAACTGGGAAAACATCTTCACAGTTAAAGGTTCTGATAAAGGCCTCATT 933128 i v i v v ii iviv v?vv i i vi v v L1M2_orf2#LIN 3098 CAGAATGGGAGAAAATATTTGCAAACTATNCATCTGACAAGGGATTAATA 3147 chrXptel1M 933129 TCCAAAATATATAGAGAGCTGACTCTAATTTA----TAAGAAACCAAGCC 933174 i ii i v vv - i i ----i i v --- L1M2_orf2#LIN 3148 TCCAGAATATATAAGGAACTCAAAC-AACTCAACAGCAAAAAAACAA--- 3193 chrXptel1M 933175 ATTCTCCAATTGATAAATGGTCAAAGGATATGAACAGACAATTTTCAGAC 933224 vv i ? v v iv i v i i v L1M2_orf2#LIN 3194 ATAATCCGATTNAAAAATGGGCAAAGGACCTGAATAGACATTTCTCAAAA 3243 chrXptel1M 933225 AATGAAACTGAAACTATTACCACTCATATGAAAGAGTGTTTCAAATCA 933272 i v v ivv iviii v vvi i i i iv v L1M2_orf2#LIN 3244 GAAGACATACAAATGGCCAACAGGTATATGAAAAAATGCTCAACATCA 3291 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 44.02 CpG sites = 71, Kimura (unadjusted) = 44.89 Transitions / transversions = 1.04 (71/68) Gap_init rate = 0.04 (19 / 433), avg. gap size = 1.47 (28 / 19) 429 32.10 1.81 1.81 chrXptel1M 932997 933272 (66728) L1M1_orf2#LINE/L1 3019 3294 (0) m_b350s551i11 14647 chrXptel1M 932997 AAAATAGAAAATTTTGATTACATCAAATTAAAAAGCTTCTGTA---CAAA 933043 i v v vv i i i --- L1M1_orf2#LIN 3019 AAAATGGACAAATGGGATCACATCAAGTTAAAAAGCTTCTGCACAGCAAA 3068 chrXptel1M 933044 CAAAACTAATGTAAACAAGATTAGAAGGGAAGCAACAAACTGGGAAAACA 933093 vi - -- v ii v ii iv v v i v i v L1M1_orf2#LIN 3069 GGAAAC-AA--TCAACAAAGTGAAGAGACAACCCACAGAATGGGAGAAAA 3115 chrXptel1M 933094 TCTTCACAGTTAAAGGTTCTGATAAAGGCCTCATTTCCAAAATATATAGA 933143 v ii iviv vvvv i i vi v vv i ii L1M1_orf2#LIN 3116 TATTTGCAAACTACCCATCTGACAAGGGATTAATAACCAGAATATATAAG 3165 chrXptel1M 933144 GAGCTGACTCTAATTTATAAGAAACCAAGCC--ATTCTCCAATTGATAAA 933191 v vv v v i i -- ii -- vv i i v L1M1_orf2#LIN 3166 GAGCTCAAACAACTCTATAGGAAA--AAATCTAATAATCCGATTAAAAAA 3213 chrXptel1M 933192 TGGTCAAAGGATATGAACAGACAATTTTCAGACAATGAAACTGAAACTAT 933241 v i v i v i i vi v v ivv ivii L1M1_orf2#LIN 3214 TGGGCAAAAGATCTGAATAGACATTTCTCAAAAGAAGACATACAAATGGC 3263 chrXptel1M 933242 TACCACTCATATGAAAGAGTGTTTCAAATCA 933272 v v vv ii i iv v L1M1_orf2#LIN 3264 AAACAGGCATATGAAAAGGTGCTCAACATCA 3294 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.71 CpG sites = 41, Kimura (unadjusted) = 42.33 Transitions / transversions = 0.89 (41/46) Gap_init rate = 0.03 (7 / 275), avg. gap size = 1.43 (10 / 7) 1574 29.37 1.88 4.34 chrXptel1M 933129 933765 (66235) L1ME5_3end#LINE/L1 7 628 (313) m_b350s551i12 14647 chrXptel1M 933129 TCCAAAATATATAGAGAGCTGACTCTAATTTATAAGAAACCAAGCCATT- 933177 i i i ii i vviv v iv i -- v iv?- L1ME5_3end#LI 7 TCTAGAATATACAAGGAACTCCTGCAAATCAACAAGAAA--AAGACGGNA 54 chrXptel1M 933178 -CTCCAATTGATAAATGGTCAAAGGATATGAACAGACAATTTTCAGACAA 933226 - i v v v i v vi L1ME5_3end#LI 55 ACCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGA 104 chrXptel1M 933227 TGAAACTGAAACTATTACCACTCATATGAAAGAGTGTTTCAAATCATTAT 933276 v ivi vvii v vv iiii i iv v v L1ME5_3end#LI 105 GGAAACCCGAAAGGCTAACAAGCATATGAAGAGATGCTCAAACTCATTAG 154 chrXptel1M 933277 TGATCAGAGAAATGCAAATTAAGACAACTCTGAGATACCCCTCTACACCT 933326 i i vv i v i L1ME5_3end#LI 155 TAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCT 204 chrXptel1M 933327 GTCAGATTGTCTAAGATGACAGGAAA---AAATAATGATGAATGGTGGAG 933373 i i i v v i v --- ---ii vii i v v L1ME5_3end#LI 205 ATTAGACTGGCAAAAATTA---GAAAGCTGGATAATGCCAAGTGTTGGCG 251 chrXptel1M 933374 GGGATGTGGGAAAACTGGGACACTGATACATTGTTGGTGGAGCTGTGAAT 933423 i i ? iv i v v i i i iiv ii i L1ME5_3end#LI 252 AGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGAC 301 chrXptel1M 933424 GAATTGAACCATTCTGGAGAGCAATCTGGAATTATGCCCCAAAAAGTTAT 933473 vii vv i v v ivi------- --- L1ME5_3end#LI 302 TGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTT-------AGT--- 341 chrXptel1M 933474 CATGCAAAAGTTAAAC-CGTGCATACCCTTTGACCCAGCAGTGCTACTAT 933522 ---- -- ii-iii v i v ii vi L1ME5_3end#LI 342 ----CAAA--TTAAGTATACGCATACCCTATGACCCAGCAATTCCGCTCC 385 chrXptel1M 933523 TGGGCTTATACCCCAAGGAGATACTAAAGAAGG----TAAAGGGACCAGT 933568 iv i i i v v viv ---- i ---- L1ME5_3end#LI 386 TGGGTATATATCCCAAAGAAATTCTCACACAGGTCCATAAGGGGAC---- 431 chrXptel1M 933569 ATGTGCCAAAATGTTTATGGCAGCCCTGTTTGTAGTGGCTAGAAGCTGGA 933618 i v ii i v vi i vi i i L1ME5_3end#LI 432 ATGTACGAGGATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGA 481 chrXptel1M 933619 AACTGAGTGGATGCCCATCAATTGGAGAATGGTTGAGTAAATTGTGGTAT 933668 ii vivv i i v v i v ii v iv L1ME5_3end#LI 482 GGCAACCTGGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGG 531 chrXptel1M 933669 ATGAACGTTATGGAATATTATTGTTCTGTAAGAAATGACCAGCAGGATGA 933718 v iii i i vvvv v v iii vii vi v L1ME5_3end#LI 532 ATGCACACCATGGAGTACTATGCAGCAGTTAGAAGCAACGGACTAGATGT 581 chrXptel1M 933719 AAACAGAGAAGCTTGGAGAGA-ATTACATGAAC-TGATGCTGAGTGAAA 933765 v v v i v vi -v v -- - ii L1ME5_3end#LI 582 ACACATAGCAACATGGATGGATCTTAAA--AACATAGTGCTGAGTGAAA 628 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.15 CpG sites = 101, Kimura (unadjusted) = 38.27 Transitions / transversions = 1.29 (101/78) Gap_init rate = 0.05 (34 / 636), avg. gap size = 1.15 (39 / 34) 25 24.68 6.19 1.69 chrXptel1M 934578 934690 (65310) (ATATT)n#Simple_repeat 1 118 (0) m_b350s252i8 14648 chrXptel1M 934578 ATATTATA-TA-AATATAATGTATT-TATATATGTAACATAACA-TACAT 934623 - - v v i - - i v i v i - i (ATATT)n#Simp 1 ATATTATATTATATTATATTATATTATAT-TATATTATATTATATTATAT 49 chrXptel1M 934624 TATAATATTATACATAATA-TATATAATAAAATAATATATTATATATTAT 934672 v vv i v - v vv v vv (ATATT)n#Simp 50 TATATTATATTATATTATATTATATTATATTATATTATATTATATTATAT 99 chrXptel1M 934673 GCATA-TATA-AATATAATA 934690 -i - -v v (ATATT)n#Simp 100 -TATATTATATTATATTATA 118 Matrix = Unknown Transitions / transversions = 0.44 (7/16) Gap_init rate = 0.08 (9 / 112), avg. gap size = 1.00 (9 / 9) 18 4.71 0.00 0.00 chrXptel1M 934745 934766 (65234) (TG)n#Simple_repeat 1 22 (0) m_b350s252i9 14649 chrXptel1M 934745 TGTGTTTGTGTGTGTGTGTGTG 934766 v (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTG 22 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 16 13.72 0.00 0.00 chrXptel1M 936465 936489 (63511) (T)n#Simple_repeat 1 25 (0) m_b350s252i10 14650 chrXptel1M 936465 TTTTCTTTTTTTCTTTTCTTTTTTT 936489 i i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 283 31.96 8.71 3.62 chrXptel1M 937173 937620 (62380) C L1MC_orf2#LINE/L1 (2070) 1224 755 m_b350s551i13 14651 chrXptel1M 937173 TTTAATTTCCTTTTCATTGGTGGTGAATTCGTCTTTTTCATTTTTGATAC 937222 v v vvv i? i vv vi i i i C L1MC_orf2#LIN 1224 TTTAATGTCCATGGGATCNGTAGTGATGTCCCCTCTTTCATTTCTGATAT 1175 chrXptel1M 937223 CGGATATTTG-ATTTTCTTCATTTTTTAAAAAATTAAATTAACCAATGAC 937271 ii vv -i i iiv vvvv i ivi ii i iv i C L1MC_orf2#LIN 1174 TAGTAATTTGTGTCTTCTCTCTTTTTTTCTTAGTTAGCCTGGCTAGAGGC 1125 chrXptel1M 937272 ACATCTATCCTATTGGTTTATTCAAAAAACCAGTGACTAGTTTTGCTTAT 937321 vi v ii i i v i ivvi i i i v C L1MC_orf2#LIN 1124 TTATCAATTTTATTGATCTTTTCAAAGAACCAGCTTTTGGTTTCGTTGAT 1075 chrXptel1M 937322 AAGTTCAATAGTTTTCTTATTTTCAATTTTATTAATTTCACCTTTGAATT 937371 vvvi v v v i i i i vv i i v C L1MC_orf2#LIN 1074 TTTCTCTATTGATTTCCTGTTTTCAATTTCATTGATTTCTGCTCTAATTT 1025 chrXptel1M 937372 TCAGAATTTC------------TAATTGGGAAATTTTTAACGTGTTCT-- 937407 i vv ------------ v v ---- iv i -- C L1MC_orf2#LIN 1024 TTATTATTTCTTTTCTTCTGCTTACTTTGGA----TTTAATTTGCTCTTC 979 chrXptel1M 937408 ---------TTTCCCAGGGTTCAA---TACATTGATTGGTTC----TTTT 937441 --------- i i vv --- v - i i---- i C L1MC_orf2#LIN 978 TTTTTCTAGTTTCCTAAGGTGGAAGCTTAGATT-ATTGATTTTAGATCTT 930 chrXptel1M 937442 TCCATTTTATTGATGTAAGAGTTTAGAGAATTAAAAATTT--CTTTAATT 937489 ivi vi i i v vi i iv --i v -- i vi C L1MC_orf2#LIN 929 TCTTCTTTTCTAATATATGCATTCAATG--CTATAAATTTCCCTCTAAGC 882 chrXptel1M 937490 ATTGCTCTGGCTGGCTGCATCACATAAATTTTAATATGCCATCTCACTGT 937539 i i -- -- v i i v iii------ i C L1MC_orf2#LIN 881 ACTGCTTT--C--GCTGCATCCCACAAATTTTGATAAGTTG------TAT 842 chrXptel1M 937540 TGTCATTCTCCTTAA--TGAAAGTATT----GATTGTTTCTATAATTTCT 937583 v i v v -- v i ----i vi ii ivi C L1MC_orf2#LIN 841 TTTCATTTTCATTTAGTTCAAAATATTTTTAAATTTCTCTTGAGATTTCT 792 chrXptel1M 937584 TCTTTGACCCACTTATTCTTTAAAATTACTTTATTTA 937620 iv i v i v iiv i C L1MC_orf2#LIN 791 TCTTTGACCCATGTGTTATTTAGAAGTGTGTTGTTTA 755 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 42.72 CpG sites = 79, Kimura (unadjusted) = 43.14 Transitions / transversions = 1.34 (79/59) Gap_init rate = 0.06 (26 / 447), avg. gap size = 2.15 (56 / 26) 1448 27.55 2.22 1.85 chrXptel1M 937823 938362 (61638) L1ME3G_3end#LINE/L1 7 548 (376) m_b350s551i14 14652 chrXptel1M 937823 TCGAAAATATATAGAGAATTGACTCTAAATTTATAAGAAATCAAGCCATT 937872 v i i i v- vi iv -- v -- L1ME3G_3end#L 7 TCCAGAATATATAAAGAACTC-CTACAAATCAATAAGAAA--AAGACA-- 51 chrXptel1M 937873 CTCCAATTGATAAATGATCAAAGGCTATGAACAGACAATTTTCAGATGAT 937922 vi v v iv v i iv v v L1ME3G_3end#L 52 ACCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAG 101 chrXptel1M 937923 GAAATTGAAACTATTTCTACTCATATGAAAAGG-GTTCCAAATCATTATT 937971 vv iviiivv vv i- i v vv i v L1ME3G_3end#L 102 GAAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGT 151 chrXptel1M 937972 GATCAGAGAAATGCAAATTAAGACAACTGTGAGATACCACTATACACTTC 938021 i i i vi i v v iiv L1ME3G_3end#L 152 AATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCA 201 chrXptel1M 938022 TCAGATTGGCTAAGATG-ACAGGAAAGATAATGATGAATATTGGAGGGGA 938070 v i v- v i ?vv ivi? i i v i i L1ME3G_3end#L 202 TCAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGG 251 chrXptel1M 938071 TGTGGAAAAACTGGTGC--------ATTGTTGGTGGAGTTGTGAATGGAT 938112 ii v i -------- i i iiv i v i L1ME3G_3end#L 252 TGTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGT 301 chrXptel1M 938113 CCAACCATTCTGGAGAGCAATTTGGAACTATGCTCAAAAAGTTATCAAAC 938162 v i ? i i v v viviv v --- v L1ME3G_3end#L 302 ACAGCCNTTTTGGAGGGCAATTTGGCAGTATCTATTAAAATTTA---AAA 348 chrXptel1M 938163 TGTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGATTATATCCCAAA 938212 i i i vii v ? ?v v i ? L1ME3G_3end#L 349 TGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANA 398 chrXptel1M 938213 GAGAT-CATAAAGAAG-GGAAAGGGACCTGTATGTGCCAAAATGTTTGTG 938260 i - viiv v v - v v i --? i i v ii ii v L1ME3G_3end#L 399 GAAATACTCGCACATGTGCACAAGGA--NGCATGTACAAGGATGTTCATT 446 chrXptel1M 938261 GCAGCCCTGTTTGTAGTGGCTAGAAACTGGAAACTGAGTGGATGCCCATC 938310 vi i i v i i vivv ii i L1ME3G_3end#L 447 GCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCATC 496 chrXptel1M 938311 AGTGGGAGAAAGGCTGAATAAATTGTGTTATATGAATGTTATGGAATAAT 938360 i i i v i i i v vv ii v L1ME3G_3end#L 497 AATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAATACT 546 chrXptel1M 938361 AT 938362 L1ME3G_3end#L 547 AT 548 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.85 CpG sites = 78, Kimura (unadjusted) = 35.49 Transitions / transversions = 1.15 (78/68) Gap_init rate = 0.03 (15 / 539), avg. gap size = 1.47 (22 / 15) 12 7.51 0.00 12.50 chrXptel1M 938631 938666 (61334) (TTTTTG)n#Simple_repeat 1 32 (0) m_b350s252i12 14653 chrXptel1M 938631 TTTTTGTTATTGTTTGCTTGCATTTTTGTTTTTCTT 938666 v -- -- v (TTTTTG)n#Sim 1 TTTTTGTTTTTGTTT--TTG--TTTTTGTTTTTGTT 32 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.11 (4 / 35), avg. gap size = 1.00 (4 / 4) 513 33.26 3.68 2.10 chrXptel1M 939067 939582 (60418) C L1M3_orf2#LINE/L1 (2724) 564 41 m_b350s551i15 14654 chrXptel1M 939067 TGCTGCTGAGAAAAATATTCTCCAAAGCTTCATCATATCTAACTTTTCTA 939116 i i vii i vi v vv iii i vi i vi vv C L1M3_orf2#LIN 564 TGCTGTTGGGTGGAATGTTCTGTATATGTCTGTTAGGTCCATTTGGTCTA 515 chrXptel1M 939117 AAATTTTATTCATTTCC-TTAATTTCTTGTTTCTTTTTTGGTTGGAT--- 939162 v i v i vv -i iv i i vv i vi --- C L1M3_orf2#LIN 514 TAGTGTTGTTCAAGTCCGCTGTTTCCTTATTGATTTTCTGTCTGGATGNT 465 chrXptel1M 939163 TTATCAGGTTTTGACAGGGAACAATTGAGGTCTCCCACTAGTACAGTTTT 939212 i viv v v v iivv i i v iv v C L1M3_orf2#LIN 464 CTATCCATTGTTGAAAGTGGGGTATTGAAGTCTCCTACTATTATTGTATT 415 chrXptel1M 939213 GCTATCTATTTCCTCCTGTACCTCATTTCAAT-TCTTCTTTAAAAATATG 939261 i ii vi vi - v - i v v v v i C L1M3_orf2#LIN 414 GCTGTCTATTTCTCCCTTCAGTTC-TGTCAATATTTGCTTTATATATTTA 366 chrXptel1M 939262 AATCCTATACTACTTGATGCATATATGTTTAGTATTGATATTACTTCATT 939311 ii v viiv ii v i i vv v vv v v C L1M3_orf2#LIN 365 GGTGCTCCGATGTTGGGTGCATATATATTTATAATTGTTATATCTTCTTG 316 chrXptel1M 939312 GTCTATGGTACCTTTTAGCAAGATGTAGTTTCCTTCCTTGTCTCCTTTTA 939361 ? vv v vv v vv i i v? i --- i C L1M3_orf2#LIN 315 NTGAATTGACCCTTTTATCATTATATAATGNCCTTCTTTGTCTC---TTG 269 chrXptel1M 939362 TTAGATCTATTTTTGCCTT------TGCTTTGTCTGAAATCATGATTGCT 939405 -- - vi v ------ ii v v vv v i C L1M3_orf2#LIN 268 T--GA-CAGTTTTTGACTTAAAGTCTATTTTGTCTGATATAAGTATAGCC 222 chrXptel1M 939406 ACACCTGCTAATATTTACTT-CTGCTGAAGCATAATATATTCTATTCCAG 939454 v vviv iv - iii v-- iiv ii v - C L1M3_orf2#LIN 221 ACCCCTGCTCTCTTTTGGTTACCATTT--GCATGGAATATCTTTTTCCA- 175 chrXptel1M 939455 GCTCTTTACTT------TGTGTGTATCTGTCTGTTTCAAGTGTGTTTCTT 939498 v i i ------ i i iv vvi?i v v i C L1M3_orf2#LIN 174 TCCCTTCACTTTCAGCCTATGTGTGTCCTTAAANCTAAAGTGAGTCTCTT 125 chrXptel1M 939499 GTAAACAACATATTGTAGGATTCTGGTTTTCAATCCACTCTGCTA-TCCA 939547 ii i v v ii v iv i v i - i C L1M3_orf2#LIN 124 GTAGGCAGCATATAGTTGGATCTTGTTTTTTTATCCATTCAGCCACTCTA 75 chrXptel1M 939548 CTTCTATTTTGTGAGAGAAATTATCCCATTCACAT 939582 iv - vi vi iv vi i C L1M3_orf2#LIN 74 TGTCT-TTTGATTGGAGAGTTTAATCCATTTACAT 41 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 44.60 CpG sites = 83, Kimura (unadjusted) = 44.99 Transitions / transversions = 0.98 (83/85) Gap_init rate = 0.03 (18 / 515), avg. gap size = 1.67 (30 / 18) 536 30.50 4.96 3.18 chrXptel1M 939138 939601 (60399) C L1M1_orf2#LINE/L1 (2801) 493 22 m_b350s551i16 14654 chrXptel1M 939138 TTTCTT-GTTTCTTTTTTGGTTGGA---TTTATCAGGTTTTGACAGGGAA 939183 - vv i vi --- i i vii vi v v ii C L1M1_orf2#LIN 493 TTTCTTTGTTGATTTTCTGTCTGGAAGATCTGTCCAATGCTGAAAGTGGG 444 chrXptel1M 939184 CAATTGAGGTCTCCCACTAGTACAGTTTTGCTATCTATTTCCTCCTGTAC 939233 vvi i vi v iv v vvi i iii v v C L1M1_orf2#LIN 443 GTGTTGAAGTCTCCAGCTATTATTGTATTGGGGTCTATCTCTCTCTTTAG 394 chrXptel1M 939234 CTC--ATTTCAAT-TCTTCTTTAAAAATATGAATCCTATACTACTTGATG 939280 -- --- - i v v v v ii v vi v ii v i C L1M1_orf2#LIN 393 CTCTAAT---AATATTTGCTTTATATATCTGGGTGCTCCAGTGTTGGGTG 347 chrXptel1M 939281 CATATATGTTTAGTATTGATATTACTTCATTGTCT--ATGGTACCTTTTA 939328 i ?v v vv i - - -- v vv i C L1M1_orf2#LIN 346 CATATATATTTANAATTGTTATATCCTC-TTG-CTGAATTGACCCCTTTA 299 chrXptel1M 939329 GCAAGATGTAGTTTCCTTCCTTGTCTCCTTTTATTAGATCTATTTTTGCC 939378 v vv i vv i i i - ----- i C L1M1_orf2#LIN 298 TCATTATATAGTGACCTTCTTTGTCTCTTCTTAT-AG-----TTTTTGTC 255 chrXptel1M 939379 TT------TGCTTTGTCTGAAATCATGATTGCTACACCTGCTAATATTTA 939422 ------ ii v v vv v v vv v i C L1M1_orf2#LIN 254 TTGAAATCTATTTTGTCTGATATAAGTATAGCTACTCCTGCTCTTTTTTG 205 chrXptel1M 939423 -CTTCTGCTGAAGCATAATATATTCTATTCCAGGCTCTTTACTTT----- 939466 -i iii -- iiv ii v v- i i ----- C L1M1_orf2#LIN 204 GTTTCCATTG--GCATGGAATATCTTTTTCCAT-CCCTTTATTTTCAGTC 158 chrXptel1M 939467 -GTGTGTATCTGTCTGTTTCAAGTGTGTTTCTTGTAAACAACATATTGTA 939515 -i i v v ivv v ii v ii?v C L1M1_orf2#LIN 157 TATGTGTGTCTTTATAGGTGAAGTGTGTTTCTTGTAGGCAACAGATCANT 108 chrXptel1M 939516 GGATTCTGGTTTTCAATCCACTCTGCTA-TCCACTTCTATTTTGTGAGAG 939564 i ii v iv i v i - i iv - vi vi C L1M1_orf2#LIN 107 GGGTCTTGTTTTTTCATCCATTCAGCCACTCTATGTCT-TTTGATTGGAG 59 chrXptel1M 939565 AAATTATCCCATTCACATCCACAATTATGATTACTAA 939601 iv vi i i vvi v iv C L1M1_orf2#LIN 58 AGTTTAGTCCATTTACATTCAATGTTATTATTGATAA 22 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.96 CpG sites = 69, Kimura (unadjusted) = 39.96 Transitions / transversions = 1.01 (69/68) Gap_init rate = 0.05 (24 / 463), avg. gap size = 1.58 (38 / 24) 299 26.91 5.12 3.20 chrXptel1M 939470 939684 (60316) C L1MEi_5end#LINE/L1 (5) 2207 1989 m_b350s551i17 14654 chrXptel1M 939470 TGTATCTGTCTGTTTCAAGTGTGTTTCTTGTAAACAACATATTGTAGGAT 939519 i vv i i i i i v iv C L1MEi_5end#LI 2207 TGTGTCGTTTTGTTTTAGGTGTGTCTCTTGTAAACAGCATATAGCTGGAT 2158 chrXptel1M 939520 TCTGGTTTTCAATCCACTCTGCTATCCACT-TCTATTTTGTGAGAGAAAT 939568 i vv i v v vi v - - vi ii v iv C L1MEi_5end#LI 2157 TTTTTTTTTTAATCCAATCTGATAATCTCTGTCT-TTTAATAGGTGAGTT 2109 chrXptel1M 939569 TATCCCATTCACATCCACAATTATGATTACTAAC---TCTG----TATTT 939611 vi i ii--- i i i--- i ---- C L1MEi_5end#LI 2108 TAATCCATTTACATTT---ATTGTGATTACTGATATATTTGGACTTATTT 2062 chrXptel1M 939612 CCCTCCATTTTATTT--TTTCTCCTGTTTGTTTTCCCTTTATCCTTTCCC 939659 iv- i -- v i i i iv ? i -- i ? i C L1MEi_5end#LI 2061 CTA-CCATCTTATTTTGTGTTTTCTGTTTATCATNCTTT--TTCTTTNCT 2015 chrXptel1M 939660 TTCTCACCAGTATTTTG-CTTCTGTT 939684 i v ivv v ii - C L1MEi_5end#LI 2014 TTTTCTCTCCTTTCCTGCCTTCTGTT 1989 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.85 CpG sites = 35, Kimura (unadjusted) = 34.85 Transitions / transversions = 1.67 (35/21) Gap_init rate = 0.06 (12 / 214), avg. gap size = 1.50 (18 / 12) 343 21.40 11.96 3.52 chrXptel1M 939478 939661 (60339) C L1MEh_5end#LINE/L1 (5) 2230 2032 m_b350s551i18 14654 chrXptel1M 939478 TCTGTTTCAAGTGTGTTTCTTGTAAACAACATATTGTAGGATTCTGGTTT 939527 ? i i i i v i v C L1MEh_5end#LI 2230 TNTGTTTTAAGTGTGTCTCTTGTAGACAGCATATTGTTGGATTTTGTTTT 2181 chrXptel1M 939528 TCAATCCACTCTGCTATCCACTTCTATTTTGTGA---GAGAAATTATCCC 939574 ? v v? --- ii i i v i --- v iv v C L1MEh_5end#LI 2180 TNAATCCAATCTGANA---ATCTCTGTCTTTTAATTGGTGAGTTTAACCC 2134 chrXptel1M 939575 ATTCACATCCACAATTATGATTACTA----ACTCTG---TATTTCCCTCC 939617 i ii--- i i i---- i ?v --- - iv C L1MEh_5end#LI 2133 ATTTACATTT---ATTGTAATTACTGNTATATTNGGACTTATTT-CTGCC 2088 chrXptel1M 939618 ATTTTATT-----TTTTC------TCCTGTTTGTTTTCCCTT-TATCCTT 939655 i ----- ------ ii i i i - ? ii C L1MEh_5end#LI 2087 ATCTTATTATTTGTTTTCTATTTGTCCCATCTGTTTTTCTTTCTNTTTTT 2038 chrXptel1M 939656 TCCCTT 939661 i C L1MEh_5end#LI 2037 TCCTTT 2032 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 27.29 CpG sites = 28, Kimura (unadjusted) = 27.29 Transitions / transversions = 2.80 (28/10) Gap_init rate = 0.07 (13 / 183), avg. gap size = 2.23 (29 / 13) 376 28.22 2.44 0.60 chrXptel1M 939480 939643 (60357) C L1MEj_5end#LINE/L1 (7) 2153 1987 m_b350s551i19 14654 chrXptel1M 939480 TGTTTCAAGTGTGTTTCTTGTAAACAACATATTGTAGGATTCTGGTTTTC 939529 i i v iv i i v i C L1MEj_5end#LI 2153 TGTTTTAAGTGTGTTTCTTGTAAACAGCATATAGCTGGGTTTTGTTTTTT 2104 chrXptel1M 939530 AATCCACTCTGCTATCCACT-TCTATTTTGTGAGAGAAATTATCCCATTC 939578 i v vi vi v - - vi i v i vi C L1MEj_5end#LI 2103 AACCCAATCTGACAGTCTCTGTCT-TTTAATGGGAGAATTCAGTCCATTC 2055 chrXptel1M 939579 ACATCCACAATTATGATTACTA-ACTCTGTAT--TTCCCTCCATTTTATT 939625 ii vvi v i i iv - ivi v -- i i i C L1MEj_5end#LI 2054 ACATTTAGTGTAACGACTGATATACTTGATTTTATTCCTTCCATCTTACT 2005 chrXptel1M 939626 TTTTCTCCTGTTTGTTTT 939643 v i?ii i i C L1MEj_5end#LI 2004 TTATTNTTTATTTATTTT 1987 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.95 CpG sites = 29, Kimura (unadjusted) = 36.97 Transitions / transversions = 1.71 (29/17) Gap_init rate = 0.02 (4 / 163), avg. gap size = 1.25 (5 / 4) 621 31.57 2.70 4.97 chrXptel1M 940060 940429 (59571) L1HS_3end#LINE/L1 208 569 (333) m_b350s551i20 14655 chrXptel1M 940060 AGAATTATAATTATCAAGATGACAGGAAAAAATAATGATGAATTTTGGAG 940109 vii i i i v v v i -- i ----i L1HS_3end#LIN 208 AGAATGGCAATCATTAAAAAGTCAGGAAACAACA--GGTG----CTGGAG 251 chrXptel1M 940110 AGGATGCGGGAAAACTGGGACACTGATGCATTGTTGGTGGAGCTGTGAAC 940159 ii iv i vv i i ii i L1HS_3end#LIN 252 AGGATGCGGAGAAATAGGAACACTTTTACACTGTTGGTGGGACTGTAAAC 301 chrXptel1M 940160 GAATCCAACCATTCTGGAGAGCAATATGG-AATTATGCCCAAAAAGTTAT 940208 v i i v iiv i i -i v-- i iii vi - L1HS_3end#LIN 302 TAGTTCAACCATTGTGGAAGTCAGTGTGGCGATTC--CTCAGGGATCTA- 348 chrXptel1M 940209 CAAACTGTGCCTACCCTTTGATCCAGCAGTGTTACTACTGGGATTATAT- 940257 -i ivivv v i vi vii i -- - L1HS_3end#LIN 349 -GAACTAGAAATACCATTTGACCCAGCCATCCCATTACTGGG--TATATA 395 chrXptel1M 940258 CCCAAAGAGATTATAAAGAAGG--G----AAAGGGACCTGTATGTGCACA 940301 - i vv v -- ---- iv ---- ii i L1HS_3end#LIN 396 CCCAAAG-GACTATAAATCATGCTGCTATAAAGACAC----ATGCACACG 440 chrXptel1M 940302 AATATTTGTGGCAGCCCTTTTTGTAGTGGCTAGAAACTGGAAACTGAGT- 940350 v i i v i v v iii i i - i i v i ii vi- L1HS_3end#LIN 441 TATGTTTATTGCGGCACTATTCACAATAGC-AAAGACTTGGAACCAACCC 489 chrXptel1M 940351 GGATGCCCATCAATTGGAGAATGG-TTGGTAAATTGTGGTATATGAATGT 940399 ii i v viv v - iiv v i i iv iii L1HS_3end#LIN 490 AAATGTCCAACAATGATAGACTGGATTAAGAAAATGTGGCACATATACAC 539 chrXptel1M 940400 TATGGAATATTATGGTTCTGTAAGAAATGA 940429 i i vvv ii i L1HS_3end#LIN 540 CATGGAATACTATGCAGCCATAAAAAATGA 569 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 41.48 CpG sites = 73, Kimura (unadjusted) = 43.06 Transitions / transversions = 1.92 (73/38) Gap_init rate = 0.06 (23 / 369), avg. gap size = 1.22 (28 / 23) 970 27.99 2.13 0.90 chrXptel1M 940086 940413 (59587) L1ME4c_3end#LINE/L1 225 556 (274) m_b350s551i21 14655 chrXptel1M 940086 AAAAAATAATGATG---AATTTTGGAGAGGATGCGGGAAAACTGGGACAC 940132 v i i i--- vi v ? vi v ? L1ME4c_3end#L 225 AAAAATTGATAATACCCAATGCTGGCGAGGNTGCGGTGAAACTGGTACNC 274 chrXptel1M 940133 TGATGCATTGTTGGTGGAGCTGTGAACGAATCCAACCATTCTGGAGAGCA 940182 v i i vi? i ivii v v i i L1ME4c_3end#L 275 TCATACATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGCA 324 chrXptel1M 940183 ATATGGAATTATGCCCAAAAAGTTATCAAACTGTGCCTACCCTTTGATCC 940232 v v v i iviv i ii v v v v i L1ME4c_3end#L 325 ATTTGGCAATACGTATCAAGAGCCATAAAAATGTTCATACCCTTTGACCC 374 chrXptel1M 940233 AGCAGTGTTACTACTGGGATTATATCCCAAAGAGATTAT---AAAGAAGG 940279 i i vii v v v i i i v --- L1ME4c_3end#L 375 AGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAAGAAGG 424 chrXptel1M 940280 GAAAGGGACCTGTATGTGCACAAATATTTGTGGCAGCCCTTTTTGTAGTG 940329 i i --- i ii iv i i ii v vi v i i i L1ME4c_3end#L 425 AAAAAG---CTATATGCACGAAGATGTTCATTGCAGCGTTATTTATAATA 471 chrXptel1M 940330 GCTAGAAACTGGAAACTGAGTGGATGCCCATCAATTGGAGAATGGTT-GG 940378 v i i vivv ii i v v i -i L1ME4c_3end#L 472 GCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAATGGTTAAG 521 chrXptel1M 940379 TAAATTGTGGTATATGAATGTTATGGAATATTATG 940413 i i v? iviv L1ME4c_3end#L 522 TAAATTATGGTACATCNACTCGATGGAATATTATG 556 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.09 CpG sites = 54, Kimura (unadjusted) = 36.60 Transitions / transversions = 1.46 (54/37) Gap_init rate = 0.02 (6 / 327), avg. gap size = 1.67 (10 / 6) 347 28.02 5.21 5.21 chrXptel1M 942119 942310 (57690) L1MC3_3end#LINE/L1 442 633 (1899) m_b350s551i23 14656 chrXptel1M 942119 ATGTCTGTGGCAGCCCTTTTTGTAGTGGCTAGAAACTGGAAACTGAAT-- 942166 i i i ii v ii i v i i i -- i-- L1MC3_3end#LI 442 ATGTTTATAGCAGCTTTATTCATAATCGCCAAAAACTGGAAGC--AACCA 489 chrXptel1M 942167 GGATGCCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATATGAATAT 942216 i i v i v v v i i i i vv i L1MC3_3end#LI 490 AGATGTCCTTCAATAGGTGAATGGATAAACAAACTGTGGTACATCCATAC 539 chrXptel1M 942217 TATGGAATATTACTGTTCTGT------AAGAAATGA-CCAACAGGAGGAT 942259 v --- v i------ - i v i ----i L1MC3_3end#LI 540 AATGGAATATTA---TTCAGCGATAAAAAGAAATGAGCTATCAAG----C 582 chrXptel1M 942260 TTCAGAAAGGCCTGGA-GAGACTTACACGAACTGATGCTGAGTGAAATGA 942308 iv ii i v - iv v i v - iv i vi L1MC3_3end#LI 583 CACGAAAAGACATGGATGAATCTTAAATGCA-TATTGCTAAGTGAAAGAA 631 chrXptel1M 942309 GC 942310 L1MC3_3end#LI 632 GC 633 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.66 CpG sites = 33, Kimura (unadjusted) = 36.46 Transitions / transversions = 1.83 (33/18) Gap_init rate = 0.07 (14 / 191), avg. gap size = 1.43 (20 / 14) 422 28.57 0.00 0.00 chrXptel1M 942119 942230 (57770) L1ME2z_3end#LINE/L1 442 553 (638) m_b350s551i22 14656 chrXptel1M 942119 ATGTCTGTGGCAGCCCTTTTTGTAGTGGCTAGAAACTGGAAACTGAATGG 942168 iii i ii v ii i i i i v vvii L1ME2z_3end#L 442 ATGTTCATAGCAGCTTTATTCATAATAGCCAAAAACTGGAAACAGCCCAG 491 chrXptel1M 942169 ATGCCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATATGAATATTA 942218 i i iiv v i i i vv iv L1ME2z_3end#L 492 GTGTCCATCAACAGGAGAATGGATAAACAAACTGTGGTATATTCATACAA 541 chrXptel1M 942219 TGGAATATTACT 942230 i L1ME2z_3end#L 542 TGGAATACTACT 553 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.15 CpG sites = 23, Kimura (unadjusted) = 38.15 Transitions / transversions = 2.56 (23/9) Gap_init rate = 0.00 (0 / 111), avg. gap size = 0.0 (0 / 0) 228 32.62 8.00 1.89 chrXptel1M 944025 944124 (55876) C L2a_3end#LINE/L2 (1) 516 411 m_b350s601i1 14657 chrXptel1M 944025 TTTACTCTTTTAAAAAAAAA--ATTAATAATCTAGCCTGTCTCAGGCGCT 944072 i i v i v v v-- i vvii viv vi i C L2a_3end#LINE 516 TTCATTCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACT 467 chrXptel1M 944073 GTTCTGGGCTCTGGGGATAGA------AATAGAATAAATGAAATGATCTC 944116 i v v ------ i i i i ii --i i C L2a_3end#LINE 466 GTTCTAGGCGCTGGGGATACAGCAGTGAACAAAACAGACAAAA--GTCCC 419 chrXptel1M 944117 TGTTCACA 944124 ii v C L2a_3end#LINE 418 TGCCCTCA 411 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 42.92 CpG sites = 20, Kimura (unadjusted) = 44.84 Transitions / transversions = 1.67 (20/12) Gap_init rate = 0.04 (4 / 99), avg. gap size = 2.50 (10 / 4) 199 35.72 0.00 1.43 chrXptel1M 944200 944270 (55730) MamRTE1#LINE/RTE-BovB 170 239 (3573) m_b350s601i2 14658 chrXptel1M 944200 AATGTATGCCATTGTTTGATAGCAGGGCCTGGGATGCAAGTGGGAGTGGC 944249 ii ii v i- ii vi i v viv vi v ii MamRTE1#LINE/ 170 AATGCGTGCCGCTGGTC-ACGGGGGGACCGGGCGAGAGAGTGTGGATGGC 218 chrXptel1M 944250 TCAGTGCAGCCCATCTCTGCT 944270 i i v ii MamRTE1#LINE/ 219 TCAGCGCAACCCATCACCACT 239 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 37.83 CpG sites = 17, Kimura (unadjusted) = 52.30 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.01 (1 / 70), avg. gap size = 1.00 (1 / 1) 15 19.56 0.00 0.00 chrXptel1M 945921 945955 (54045) (GAGAAA)n#Simple_repeat 1 35 (0) m_b350s252i13 14659 chrXptel1M 945921 GAGAAAGAGACAGAGACAGAGAGACAGGGAGAGAA 945955 v v i v ii (GAGAAA)n#Sim 1 GAGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGAA 35 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 16 13.72 0.00 0.00 chrXptel1M 946111 946135 (53865) (T)n#Simple_repeat 1 25 (0) m_b350s252i14 14660 chrXptel1M 946111 TTCTTTTTTTTCTTTTTTCTTTTTT 946135 i i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 428 24.66 3.05 7.14 chrXptel1M 946137 946267 (53733) C MIRc#SINE/MIR (141) 127 2 m_b350s601i3 14661 chrXptel1M 946137 CTGAGGCAATTGGAA---TTAAATGACTTGCCCAGGGTCACACAGTTAGG 946183 -- ii i--- i i i - C MIRc#SINE/MIR 127 CTGAGGC--TCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG- 81 chrXptel1M 946184 AGGAGTTAAGTGTCTGAGGCCAGATTTGAACTCAGGTCCTCCTAAATTCA 946233 ------ v v v vi i i i i i v i C MIRc#SINE/MIR 80 ------TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCA 37 chrXptel1M 946234 GGGCTGGTGCTCTACCAGCTGCCCTGCA-TGGCTC 946267 i v ii vi vi v ii - v C MIRc#SINE/MIR 36 AGTCCAGTGCTCTTTCCACTGCACCACACTGCCTC 2 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.61 CpG sites = 20, Kimura (unadjusted) = 30.84 Transitions / transversions = 2.00 (20/10) Gap_init rate = 0.08 (11 / 130), avg. gap size = 1.18 (13 / 11) 237 24.99 6.21 0.65 chrXptel1M 946904 947048 (52952) L1M2_orf2#LINE/L1 31 183 (3108) m_b350s551i24 14662 chrXptel1M 946904 ATAACTTCAAATGTATATGGATTAAAAAATTCAATT-AGAGA---AGTGT 946949 i ii v vvv i - i --- v? L1M2_orf2#LIN 31 ATAACCTTGAATGTAAATGGATTAAATTCTCCAATTAAAAGACATAGANT 80 chrXptel1M 946950 GACAGATTGGATAAGAAAACAAAACCCCAC-A-ATGTTGATTAAAATAAA 946997 i v v i i v - - i vi v v L1M2_orf2#LIN 81 GGCTGAATGGATAAAAAAACAAGACCCAACTATATGCTGCCTACAAGAAA 130 chrXptel1M 946998 --CATTTTAAAAATCAAGACATTCACACAAT-AAAGAAAAGGGACTAGAA 947044 -- i i vvvi v iv i v v - vi - i L1M2_orf2#LIN 131 CTCACTTCACCTGTAAAGACACACATAGACTGAAAGTGAAGGGA-TGGAA 179 chrXptel1M 947045 AAAG 947048 L1M2_orf2#LIN 180 AAAG 183 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 30.87 CpG sites = 17, Kimura (unadjusted) = 30.87 Transitions / transversions = 0.89 (17/19) Gap_init rate = 0.05 (7 / 144), avg. gap size = 1.43 (10 / 7) 237 25.00 5.00 0.00 chrXptel1M 946905 946984 (53016) L1HS_5end#LINE/L1 2018 2101 (35) m_b350s551i25 14662 chrXptel1M 946905 TAACTTCAAATGTATATGGATTAAAAAATTCAATTAGA-GA---AGTGTG 946950 i v i viv i i - --- vv L1HS_5end#LIN 2018 TAACTTTAAATGTAAATGGACTAAATGCTCCAATTAAAAGACACAGACTG 2067 chrXptel1M 946951 ACAGATTGGATAAGAAAACAAAACCCCACAATGT 946984 i i ii iv i vv i L1HS_5end#LIN 2068 GCAAATTGGATAAAGAGTCAAGACCCATCAGTGT 2101 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 31.12 CpG sites = 12, Kimura (unadjusted) = 31.12 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.03 (2 / 79), avg. gap size = 2.00 (4 / 2) 257 29.94 4.88 3.73 chrXptel1M 947639 948089 (51911) L1M3_orf2#LINE/L1 828 1283 (2005) m_b350s551i26 14662 chrXptel1M 947639 AAATGATAGTGCTGAAATAACATACCAATATTTCTGGGGTGCAGATAAAG 947688 v i vvi v i v i v i vv L1M3_orf2#LIN 828 AAATGAAAATGAAAACACAACATACCAAAACTTATGGGATGCAGCAAAAG 877 chrXptel1M 947689 CAGTTCACAAGGGGAAAGTCATGTACC--TAAA-ATCTGTATTAATAAAA 947735 ? -i i i i- i v -- -ii ii v i L1M3_orf2#LIN 878 CAGTNC-TAAGAGGGAAGTT-TATAGCGATAAACGCCTACATTAAAAAAG 925 chrXptel1M 947736 TAGAAAAAGGGAAGATTAATAACTTAAATATTTATTGCAA--AATAAAAA 947783 v i vvvv i v i i v v vi iiv -- iv i L1M3_orf2#LIN 926 AAGAAAGATCTCAAATAAACAACCTAACTTTACACCTCAAGGAACTAGAA 975 chrXptel1M 947784 AAAAACAAACCAAAAAATAAGCAAATCTAAAA-TACCATAAAAGAAAAGA 947832 i vi --- v ---- i i- v v iii ii i L1M3_orf2#LIN 976 AAAGAAGAAC---AAACTAAGC----CCAAAGTTAGCAGAAGGAAGGAAA 1018 chrXptel1M 947833 TATTCAAAAC--GAGGAGAAATAAAATTAAAC--------GAAAAATATA 947872 v v i i-- v - v i-------- i - L1M3_orf2#LIN 1019 TAATAAAGATTAGAGCAGAAAT-AAATGAAATAGAGANTAGAAAAACA-A 1066 chrXptel1M 947873 TAGAAATAATAAATAAAAATATAAGCTAGTTTTCTGAAAAAA-AAACCTG 947921 v v ii v vi i i i i - --- L1M3_orf2#LIN 1067 TAGAAAAAATCAACGAAACTAAGAGTTGGTTTTTTGAAAAGATAAAC--- 1113 chrXptel1M 947922 TAAAATTGATAAA-CTTTAGCCAATCTAAAAAGAGAGCAGAAAA-TCAAA 947969 - i - i iv i i i iv i - L1M3_orf2#LIN 1114 -AAAATTGACAAACCTTTAGCTAGACTAAGAAAAAAAGAGAAGACTCAAA 1162 chrXptel1M 947970 TCAACATAA-CAGCAA-AAAATTAAGGTGAAATCGCAAC-AAAACAAGAG 948016 v i v - v -i --i v v ii -i vi v v L1M3_orf2#LIN 1163 TAAATAAAATCAGAAATGAAA--GAGGAGACATTACAACTGATGCCACAG 1210 chrXptel1M 948017 GAAGAGAAAAAATAATCAGACTCTATTGTAAAGAGTTAAATGTTAACGAA 948066 i v i ii v v vv i i i v i v i ii i L1M3_orf2#LIN 1211 AAATAAAAAGGATCATAAGAGACTACTATGAACAATTATACGCCAACAAA 1260 chrXptel1M 948067 ATGGAGAAGACAAAACAAATAGA 948089 v v vvi i v i L1M3_orf2#LIN 1261 TTGGATAACCTAGAAGAAATGGA 1283 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.18 CpG sites = 75, Kimura (unadjusted) = 39.40 Transitions / transversions = 1.36 (75/55) Gap_init rate = 0.06 (29 / 450), avg. gap size = 1.34 (39 / 29) 275 24.22 2.31 1.53 chrXptel1M 948325 948454 (51546) C L1MEh_5end#LINE/L1 (1) 2234 2104 m_b350s551i27 14663 chrXptel1M 948325 TCTTTCT-TTTCAAGTGTTCGTCTTCTGAACAACATATTGTAGGATTTTG 948373 i ? - i viv v ii i v C L1MEh_5end#LI 2234 TCCTTNTGTTTTAAGTGTGTCTCTTGTAGACAGCATATTGTTGGATTTTG 2185 chrXptel1M 948374 GTTTCTAATTC-ATTTTACTGTCTGCTTGCATTTTATGAGTGAGTTCATC 948422 v i? i - i v ?vi - vv v v vi i v C L1MEh_5end#LI 2184 TTTTTNAATCCAATCTGANAATCT-CTGTCTTTTAATTGGTGAGTTTAAC 2136 chrXptel1M 948423 CCATTCAAATTCAGTTATGATTACT-ATGTATT 948454 i v i - i i -? i C L1MEh_5end#LI 2135 CCATTTACATTTA-TTGTAATTACTGNTATATT 2104 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 30.88 CpG sites = 17, Kimura (unadjusted) = 30.88 Transitions / transversions = 1.21 (17/14) Gap_init rate = 0.04 (5 / 129), avg. gap size = 1.00 (5 / 5) 14 19.66 2.78 0.00 chrXptel1M 948689 948724 (51276) (TATC)n#Simple_repeat 1 37 (0) m_b350s252i15 14664 chrXptel1M 948689 TATCTATTTATGTACCTATCTATTCATCTACCT-TCT 948724 i v i ii i - (TATC)n#Simpl 1 TATCTATCTATCTATCTATCTATCTATCTATCTATCT 37 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) 423 32.78 3.25 3.25 chrXptel1M 948832 949077 (50923) L1ME5_3end#LINE/L1 392 637 (304) m_b350s551i28 14665 chrXptel1M 948832 TATATCCCAAAGAGATTTTAAAGAAGG----GAAAGGGACCTGTATGTGC 948877 i i v viv ----v i v i v - L1ME5_3end#LI 392 TATATCCCAAAGAAATTCTCACACAGGTCCATAAGGGGACATGTACGAG- 440 chrXptel1M 948878 ACAAATGTTTGTGACAGCCCTTTTTGTAGTGGCCAGAAACTGGAAACTGA 948927 ---i ii vi vi v i vi i ii ii viv L1ME5_3end#LI 441 ---GATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAAC 487 chrXptel1M 948928 ATGGATGCCCATCAGTTGGAGAATGGCTGAATAAACTGTGGTATATGAAT 948977 v i i v v i v iii v iv v i L1ME5_3end#LI 488 CTGGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCAC 537 chrXptel1M 948978 ATTATGAAACATTATTGTTCAGTAAGAAATGACCAGCAGGATGATTTCAG 949027 ii i ii i vvvv v iii vii vi -- v v L1ME5_3end#LI 538 ACCATGGAGTACTATGCAGCAGTTAGAAGCAACGGACTAGATG--TACAC 585 chrXptel1M 949028 AAAGT--CCTGGAGAGA-CTTACACGAAC-TGATGCTGAGTGAAATGAGC 949073 v i-- v vi - v -- - ii vi i L1ME5_3end#LI 586 ATAGCAACATGGATGGATCTTAAA--AACATAGTGCTGAGTGAAAAAAGT 633 chrXptel1M 949074 AGGA 949077 i L1ME5_3end#LI 634 AAGA 637 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.71 CpG sites = 45, Kimura (unadjusted) = 44.49 Transitions / transversions = 1.36 (45/33) Gap_init rate = 0.05 (12 / 245), avg. gap size = 1.33 (16 / 12) 463 29.02 0.00 2.29 chrXptel1M 948873 949006 (50994) L1MD1_3end#LINE/L1 433 563 (426) m_b350s551i29 14665 chrXptel1M 948873 TGTGCACAAATGTTTGTGACAGCCCTTTTTGTAGTGGCCAGAAACTGGAA 948922 i i i ii ii v i i i i L1MD1_3end#LI 433 TGTACACGAATGTTTATAGCAGCTTTATTCGTAATAGCCAAAAACTGGAA 482 chrXptel1M 948923 ACTGAATGGATGCCCATCAGTTGGAGAATGGCTGAATAAACTGTGGTATA 948972 vivvii i v iiv v i i i i L1MD1_3end#LI 483 ACAACCCAGATGTCCTTCAACGGGTGAATGGTTAAACAAACTGTGGTACA 532 chrXptel1M 948973 TGAATATTATGAAACATTATTGTTCAGTAAGAAA 949006 vv ii i i i ---i i v L1MD1_3end#LI 533 TCCATACCATGGAATACTA---CTCAGCAATAAA 563 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.19 CpG sites = 28, Kimura (unadjusted) = 39.18 Transitions / transversions = 2.80 (28/10) Gap_init rate = 0.02 (3 / 133), avg. gap size = 1.00 (3 / 3) 34 21.84 0.00 0.00 chrXptel1M 950396 950417 (49583) (TA)n#Simple_repeat 1 22 (53) m_b350s252i16 14666 chrXptel1M 950396 TATATGGCTATATATAAAGCTT 950417 ivv v vv v (TA)n#Simple_ 1 TATATATATATATATATATATA 22 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 44 4.45 0.00 0.00 chrXptel1M 950418 950464 (49536) (TG)n#Simple_repeat 1 47 (0) c_b350s251i0 14667 chrXptel1M 950418 TGTGTATGTGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 950464 i i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 47 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 34 21.84 0.00 0.00 chrXptel1M 950465 950516 (49484) (TA)n#Simple_repeat 23 74 (1) m_b350s252i16 14668 chrXptel1M 950465 ATATATATATATATATATATATATATATACATACAGCTACATATGTATGT 950514 i i vv i i i (TA)n#Simple_ 23 ATATATATATATATATATATATATATATATATATATATATATATATATAT 72 chrXptel1M 950515 AT 950516 (TA)n#Simple_ 73 AT 74 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 18 33.97 0.00 0.00 chrXptel1M 950466 950528 (49472) (TATG)n#Simple_repeat 1 63 (0) m_b350s252i17 14668 chrXptel1M 950466 TATATATATATATATATATATATATATACATACAGCTACATATGTATGTA 950515 i i i i i i ii ii vv ii (TATG)n#Simpl 1 TATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTA 50 chrXptel1M 950516 TGCATGTGTGTAT 950528 i i (TATG)n#Simpl 51 TGTATGTATGTAT 63 Matrix = Unknown Transitions / transversions = 7.00 (14/2) Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0) 506 34.43 7.62 1.80 chrXptel1M 952125 952166 (47834) C L1PA8_3end#LINE/L1 (444) 475 434 m_b350s551i30 14669 chrXptel1M 952125 TCTTTGCCATCAGAGAAAGATCTACTATAAATATATATGAGT 952166 i iiv i v vv i v i ii v i C L1PA8_3end#LI 475 TCTTTGCTATTGTAAATAGTGCTGCAATAAACATACGTGTGC 434 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 45.69 CpG sites = 83, Kimura (unadjusted) = 48.10 Transitions / transversions = 1.50 (9/6) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 40 2.63 0.00 0.00 chrXptel1M 952167 952205 (47795) (AC)n#Simple_repeat 1 39 (0) c_b350s251i1 14670 chrXptel1M 952167 ACACACACACACACACACACATACACACACACACACACA 952205 i (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACA 39 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 506 34.43 7.62 1.80 chrXptel1M 952206 952582 (47418) C L1PA8_3end#LINE/L1 (486) 433 33 m_b350s551i30 14669 chrXptel1M 952206 TATCCCTTCCCCTTTAAAAAAAAAAT-----ATCTTTGGAATACAGATTT 952250 i vi ---- v iv i vi ----- i v ii i v iii C L1PA8_3end#LI 433 TGTGTCTT----TATAGTAGAATGATTTATAATCCTTTGGGTATATACCC 388 chrXptel1M 952251 AATCATGGTATTACTGGGTCAAAGGATATGCACAGTTTTATAGCCCTTTT 952300 i v v i v i vivii i v v --- C L1PA8_3end#LI 387 AGTAATGGGATTGCTGGGTCAAATGGTATTTCTGGTTCTAGATCC---TT 341 chrXptel1M 952301 GGGATAGTGCCAAGTTGTTCTTCAGAATGATTGGAGCAGTTCACAACTCC 952350 i iv vi vii ii i v i i vi i i vii C L1PA8_3end#LI 340 GAGGAATCGCCACACTGTCTTCCACAATGGTTGAACTAATTTACACTCCC 291 chrXptel1M 952351 ACTAATAATTTATTAACATACGTAGTTTTTCCTTATTGCCTCAAGCATTT 952400 i i i v vv i i v v - i vi ivi v v i C L1PA8_3end#LI 290 ACCAACAGTGTAAAAGCGTTCCTA-TTTCTCCACATCCTCGCCAGCATCT 242 chrXptel1M 952401 GTCATTTC------------TGAT--------TAAATG---TGAGGTGAT 952427 ii ------------ -------- v --- i i C L1PA8_3end#LI 241 GTTGTTTCCTGACTTTTTAATGATCGCCATTCTAACTGGCGTGAGATGGT 192 chrXptel1M 952428 TTCTCAGAATCATTTTAATTTGCATTTCTCCAAGAAATAGTAATTCAGAA 952477 v vvi vi i i vi vi i vvv i C L1PA8_3end#LI 191 ATCTCATTGTGGTTTTGATTTGCATTTCTCTAATGACCAGTGATGATGAG 142 chrXptel1M 952478 CATTTTT-CATATGACTAT-AGCTT--TGATTTTTTTCTTCTGAAAAGTA 952523 v - vi i -i iv-- i v v i i i i C L1PA8_3end#LI 141 CTTTTTTTCATATGTTTGTTGGCCGCATAAATGTCTTCTTTTGAGAAGTG 92 chrXptel1M 952524 TCTATTCATATCTTTTGGCCATTTATAAATTGGGGAATAGCTCTTATTTT 952573 i i i v i v vi v vvi vvv i v i C L1PA8_3end#LI 91 TCTGTTCATATCCTTCGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCT 42 chrXptel1M 952574 TATAAATTT 952582 i C L1PA8_3end#LI 41 TGTAAATTT 33 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 45.69 CpG sites = 83, Kimura (unadjusted) = 48.10 Transitions / transversions = 1.40 (74/53) Gap_init rate = 0.04 (15 / 376), avg. gap size = 2.67 (40 / 15) 660 28.62 8.93 1.34 chrXptel1M 952256 952602 (47398) C L1ME4c_3end#LINE/L1 (446) 384 12 m_b350s551i31 14669 chrXptel1M 952256 TGGTATTACTGGGTCAAAGGATATGCACAGTTTTATAGCCCTTTTGGGAT 952305 v i v v i i vvvivi C L1ME4c_3end#L 384 TGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTCTTGATACGT 335 chrXptel1M 952306 AGTGCCAAGTTGTTCTTCAGAATGATTGGAGCAGTTCACAACTCCACTAA 952355 v i i i i i v i v v i i ?iv i i C L1ME4c_3end#L 334 ATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACANTGCCACCAG 285 chrXptel1M 952356 TAATTTATTAACATACGTAGTTTTTCCTTATTGCCTCAAGCAT------T 952399 i v v i?i -i iv vi ?ivi v v ------ C L1ME4c_3end#L 284 CAATGTATGAGNGTAC-CAGTTTCACCGCANCCTCGCCAGCATTGGGTAT 236 chrXptel1M 952400 TGTCA-------------TTTCTGATTAAAT----GTGAGGTGATTTCTC 952432 i ------------- v i v ---- i ii i v C L1ME4c_3end#L 235 TATCAATTTTTTAAATTTTTGCTAATTTAATAGGCGTAAAATGGTATCTC 186 chrXptel1M 952433 AGAATCATTTTAATTTGCATTTCTCCAAGAAATAGTAATTCAGAACATTT 952482 vvi iii iii vv v ii vviv C L1ME4c_3end#L 185 ATTGTTGCTTTAATTTGCATTTCTTTGATTACTAGCGAGGTTGAACATTT 136 chrXptel1M 952483 TT-CATATG-------ACTATAGCTTTGATTTTTTTCTTCTGAAAAGTAT 952524 - i ------- ----? vv ii ? vi v i C L1ME4c_3end#L 135 TTCCATGTGTTTGTTTACTA----NTTGTATTTCCTCTTNTGTGAATTGT 90 chrXptel1M 952525 CTATTCATATCTTTTGGCCATTTATAAATTGGGGAATAGCTCTTATTTTT 952574 i i i v vv vv v v ? v i C L1ME4c_3end#L 89 CTGTTCATGTCCTTTGCCCATTTATCTATTGGGGTCTTGATNTTTTTCTT 40 chrXptel1M 952575 ATAAATTTTACTCAGTTCTCTACATACT 952602 v v v v i i i ? C L1ME4c_3end#L 39 ATCAATTTGAATGAGCTCTTTATATANT 12 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.70 CpG sites = 52, Kimura (unadjusted) = 37.72 Transitions / transversions = 1.13 (52/46) Gap_init rate = 0.03 (10 / 346), avg. gap size = 3.60 (36 / 10) 250 29.33 3.31 0.65 chrXptel1M 952475 952625 (47375) C L1M4_orf2#LINE/L1 (7) 3287 3133 m_b350s551i32 14669 chrXptel1M 952475 GAACAT-TTTTCATATGACTAT-AGC--TTTGATTTTTTTCTTCTGAAAA 952520 i - i vi -i -- vv v i iv i C L1M4_orf2#LIN 3287 GAGCATCTTTTCATGTGCTTATTGGCCATTTGTATATCTTCTTTGGAGAA 3238 chrXptel1M 952521 GTATCTATTCATATCTTTTGGCCATTTATAAATTGGGGAATAGCTCTTAT 952570 i i v i v v ? vv vvv v C L1M4_orf2#LIN 3237 ATGTCTATTCAAATCCTTTGCCCATTTTTNAATTGGGTTATTTGTCTTTT 3188 chrXptel1M 952571 TTTTA-TAAATTTTACTCAGTTCTCTACATACTTGAAAAATGAGGCTTTT 952619 v i- i i v v-v i i i ivii v i? v ii C L1M4_orf2#LIN 3187 TATTGTTGAGTTGTAA-GAGTTCTTTATATATTCTGGATACNAGTCCCTT 3139 chrXptel1M 952620 ATTAGA 952625 i C L1M4_orf2#LIN 3138 ATCAGA 3133 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.48 CpG sites = 23, Kimura (unadjusted) = 38.48 Transitions / transversions = 1.10 (23/21) Gap_init rate = 0.03 (5 / 150), avg. gap size = 1.20 (6 / 5) 288 28.95 4.73 1.97 chrXptel1M 952729 952876 (47124) C L1MC_orf2#LINE/L1 (3046) 248 97 m_b350s551i33 14671 chrXptel1M 952729 TTTGCTTTGTCAGAAATCATTATTGTTACACTTGCTTTTGTTTGTAACCA 952778 i i v i v v i v i? iv -- ii C L1MC_orf2#LIN 248 TCTGCTCTGTCTGAAATTAATATAGCTACTCCNGCTTTCTTTTG--ATTA 201 chrXptel1M 952779 GCTCAAACAT--TAAATTCTGCTCTAGCCCTCCA-----ACTCCATGTGT 952821 iviv i -- v ii v i v ? ii ----- v i i C L1MC_orf2#LIN 200 GTGTTAGCATGGTATATCTTTCTCCATCCNTTTACTTTTAATCTATATGT 151 chrXptel1M 952822 GTCTTTCTGGTTCAAATATGCCTCTTATAGACAATATATTGTTGGTGTCT 952871 v iv v i iv ii i i v - C L1MC_orf2#LIN 150 GTCTTTATATTTAAAGTGGGTTTCTTGTAGACAACATATAGTTGG-GTCT 102 chrXptel1M 952872 GGTTT 952876 v C L1MC_orf2#LIN 101 TGTTT 97 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.39 CpG sites = 25, Kimura (unadjusted) = 38.39 Transitions / transversions = 1.47 (25/17) Gap_init rate = 0.03 (5 / 147), avg. gap size = 2.00 (10 / 5) 231 28.55 5.84 2.84 chrXptel1M 952813 952949 (47051) C L1M1_orf2#LINE/L1 (3135) 159 19 m_b350s551i34 14671 chrXptel1M 952813 TCCATGTGTGTCTTTCTGGTTCAAATATGCCTCTTATAGACAATATATTG 952862 i v i v v i i ii i i i v ii C L1M1_orf2#LIN 159 TCTATGTGTGTCTTTATAGGTGAAGTGTGTTTCTTGTAGGCAACAGATCA 110 chrXptel1M 952863 TTGGTGTC-TGGTTTCTAATACATGTTGCTATCTGTTTCTGTTTTATGAC 952911 ? - - v i v v viv i i--- i v i v i C L1M1_orf2#LIN 109 NTGG-GTCTTGTTTTTTCATCCATTCAGCCAC---TCTATGTCTTTTGAT 64 chrXptel1M 952912 T---AAGTTCATCCCATTCACA---AA-GTTATGATTAATGTGTA 952949 ---i i vi i --- - v i iv C L1M1_orf2#LIN 63 TGGAGAGTTTAGTCCATTTACATTCAATGTTATTATTGATAAGTA 19 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.68 CpG sites = 24, Kimura (unadjusted) = 37.68 Transitions / transversions = 1.71 (24/14) Gap_init rate = 0.06 (8 / 136), avg. gap size = 1.50 (12 / 8) 274 26.86 0.92 0.92 chrXptel1M 952822 952930 (47070) C L1MEh_5end#LINE/L1 (0) 2235 2127 m_b350s551i35 14671 chrXptel1M 952822 GTCTTTCTGGTTCAAATATGCCTCTTATAGACAATATATTGTTGGTGTCT 952871 i ? v i i i i i ii vv i C L1MEh_5end#LI 2235 GTCCTTNTGTTTTAAGTGTGTCTCTTGTAGACAGCATATTGTTGGATTTT 2186 chrXptel1M 952872 GGTTTCTAATACATGTTGCT-ATCTGTTTCTGTTTTATGACTAAGTTCAT 952920 v i? v vvi v?- v v - v viv i i v C L1MEh_5end#LI 2185 GTTTTTNAATCCAATCTGANAATCTCTGTCT-TTTAATTGGTGAGTTTAA 2137 chrXptel1M 952921 CCCATTCACA 952930 i C L1MEh_5end#LI 2136 CCCATTTACA 2127 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.91 CpG sites = 15, Kimura (unadjusted) = 34.91 Transitions / transversions = 1.07 (15/14) Gap_init rate = 0.02 (2 / 108), avg. gap size = 1.00 (2 / 2) 706 15.85 1.96 7.22 chrXptel1M 956110 956313 (43687) C Charlie1a#DNA/hAT-Charlie (1) 1454 1261 m_b350s502i0 14672 chrXptel1M 956110 AGTGCTTCTCAAAGTTTTTGGTTTCACAACCCCTTTACACTTTAAACAAT 956159 i v v i vi i v v C Charlie1a#DNA 1454 AGCGGTTCTCAAACTTTTTGGTCTCAGGACCCCTTTACACTCTTAAAAAT 1405 chrXptel1M 956160 TATTTAGGA-CACAAACTGCTT---TTTAAAAAACTGTGGGTTATACCAA 956205 v - v vv --- ------ i v C Charlie1a#DNA 1404 TATTGAGGACCCCAAAGAGCTTTTGTTTA------TGTGGGTTATATCTA 1361 chrXptel1M 956206 TGGAAATTTACTACATTAGAAAAGAAATCTGATAAAATTTTAAGATATGC 956255 v v i i vv v v v i ---- C Charlie1a#DNA 1360 TCGATATTTACCATATTAGAAATTAAAACTGAGAAATTTTTAAAAT---- 1315 chrXptel1M 956256 ATTTATTAATTTATTGTAAAATGACAATGATAAACCCATTATATATTAAC 956305 i - -- i i i i C Charlie1a#DNA 1314 ATTTATTAATTCATT-TAAAA--ATAATAATAAACCCATTACATGTTAAC 1268 chrXptel1M 956306 ATCAAATA 956313 - C Charlie1a#DNA 1267 AT-AAATA 1261 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 17.15 CpG sites = 13, Kimura (unadjusted) = 17.76 Transitions / transversions = 0.76 (13/17) Gap_init rate = 0.08 (16 / 203), avg. gap size = 1.12 (18 / 16) 280 18.97 1.72 0.00 chrXptel1M 956520 956577 (43423) DNM1r#Unknown 2488 2546 (2116) m_b350s502i1 14673 chrXptel1M 956520 GTATA-ATGTGTGTATGTATGTGTGTGTATACATATATATGTATACACAC 956568 - i i i i ii i i i DNM1r#Unknown 2488 GTATATATGTGTGTATATGTGTGTATGTGTGTATATATGTGTATATATAC 2537 chrXptel1M 956569 ACATATATA 956577 ii ? DNM1r#Unknown 2538 GTATNTATA 2546 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 21.88 CpG sites = 11, Kimura (unadjusted) = 24.39 Transitions / transversions = 1.00 (11/0) Gap_init rate = 0.02 (1 / 57), avg. gap size = 1.00 (1 / 1) 273 28.57 1.43 0.00 chrXptel1M 956521 956590 (43410) C DNM1r#Unknown (2116) 2546 2476 m_b350s502i2 14673 chrXptel1M 956521 TATA-ATGTGTGTATGTATGTGTGTGTATACATATATATGTATACACACA 956569 - ii i i iiii i i i i i iii i C DNM1r#Unknown 2546 TATANATACGTATATATACACATATATACACACATACACACATATACACA 2497 chrXptel1M 956570 CATATATACATACACACACAT 956590 i i i C DNM1r#Unknown 2496 CATATATACACACATACACGT 2476 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.70 CpG sites = 20, Kimura (unadjusted) = 42.36 Transitions / transversions = 1.00 (20/0) Gap_init rate = 0.01 (1 / 69), avg. gap size = 1.00 (1 / 1) 369 14.19 0.00 8.45 chrXptel1M 956532 956608 (43392) C DNM1r#Unknown (2116) 2546 2476 m_b350s502i3 14673 chrXptel1M 956532 TATGTATGTGTGTGTATACATATATATGTATACACACACATATATACATA 956581 i? ii i i i ------ i i C DNM1r#Unknown 2546 TATANATACGTATATATACACATATAT------ACACACATACACACATA 2503 chrXptel1M 956582 CACACACATATATACACACATACACAT 956608 i i C DNM1r#Unknown 2502 TACACACATATATACACACATACACGT 2476 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 13.35 CpG sites = 10, Kimura (unadjusted) = 16.82 Transitions / transversions = 1.00 (10/0) Gap_init rate = 0.08 (6 / 76), avg. gap size = 1.00 (6 / 6) 23 3.00 5.56 2.70 chrXptel1M 956623 956658 (43342) (AT)n#Simple_repeat 1 37 (0) m_b350s252i18 14674 chrXptel1M 956623 ATATA-ATATATATATAAATATCATATATATATA-ATA 956658 - v - - (AT)n#Simple_ 1 ATATATATATATATATATATAT-ATATATATATATATA 37 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.09 (3 / 35), avg. gap size = 1.00 (3 / 3) 746 30.53 4.44 1.15 chrXptel1M 956667 957004 (42996) L1ME3Cz_3end#LINE/L1 54 402 (595) m_b350s551i36 14675 chrXptel1M 956667 CCAATAGATAAGTGGTCAAAGGATATGAACAAATGGGTCTCAAA----GA 956712 v i v iiiiiv v i ---- L1ME3Cz_3end# 54 CCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGGA 103 chrXptel1M 956713 ATTTCAAAGGATTCATAATCATATGAAAGAATGTTGAAAATCACTTATCA 956762 vii i v iiiv v ii i v vv vi v L1ME3Cz_3end# 104 AACCCGAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTAA 153 chrXptel1M 956763 AAAGAAAAATGCAAATCAAAAGGACCTTGAGGT-CC---TCACACTCTGC 956808 vv ii i v? vv i - --- i vv L1ME3Cz_3end# 154 TCAGGGAAATGCAAATTAAAACNACAATGAGATACCATTTCACACCCATC 203 chrXptel1M 956809 AAACTGAAAAAAA----AAA---TGGCAATGGTCAATGTTAAAGGGGTTG 956851 i i iv ---- --- i iviv i iiv i v L1ME3Cz_3end# 204 AGATTGGCAAAAATTTAAAAGTCTGACAATACCAAGTGTTGGCGAGGATG 253 chrXptel1M 956852 TTGATGGTTAGGCACACTAATACATTGTTGGTGGAGCTGTGAAATGGTAC 956901 v viivii v v v i i iiv i v L1ME3Cz_3end# 254 TGGAGAAACGGGAACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTAC 303 chrXptel1M 956902 CACCACTTTGGAAAGCAATTTGGAATTATGTAAAAATAGTGACTGAGATG 956951 v i v v v iv viv --- L1ME3Cz_3end# 304 AACCACTTTGGAGAGCAATTTGGCAATATCTAGTAAAGTTGA---AGATG 350 chrXptel1M 956952 TCCATAACCTTTGAACCAGAGACTTCTATTACTGGGCTCGTACCCCAGGG 957001 iv v vi v vi - i i v i ivii i i L1ME3Cz_3end# 351 CGCATACCCTACGACCCAGCAA-TTCCACTTCTAGGTATATACCCTAGAG 399 chrXptel1M 957002 AAA 957004 L1ME3Cz_3end# 400 AAA 402 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 38.12 CpG sites = 55, Kimura (unadjusted) = 40.17 Transitions / transversions = 1.17 (55/47) Gap_init rate = 0.03 (9 / 337), avg. gap size = 2.11 (19 / 9) 595 19.98 1.31 8.39 chrXptel1M 957006 957158 (42842) MIRc#SINE/MIR 4 146 (122) m_b350s601i4 14676 chrXptel1M 957006 GGCAGCGAGGTGATGCTGTGGATAGAAAGCTGGGCCTGAAGTCAGGGAGA 957055 i --- i v v ivi i i i i MIRc#SINE/MIR 4 GGCAGTG---TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA 50 chrXptel1M 957056 GTCATCTCCCTGAGTTCAACTCTGGCCTCAGATACCTCTTAGCTGCGTGA 957105 -------- i i v iv v v vi i vi i MIRc#SINE/MIR 51 --------CCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGA 92 chrXptel1M 957106 CCCTGGGCAAGTCACTTTATCCTATTT--GCCTCAGTTTCCTCATCTGTA 957153 i - v v i -- MIRc#SINE/MIR 93 CCTTGGGCAAGTCAC-TTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTA 141 chrXptel1M 957154 AAATG 957158 MIRc#SINE/MIR 142 AAATG 146 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 22.53 CpG sites = 17, Kimura (unadjusted) = 23.46 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.09 (13 / 152), avg. gap size = 1.08 (14 / 13) 398 27.12 2.33 3.53 chrXptel1M 957302 957473 (42527) L1ME3G_3end#LINE/L1 432 601 (323) m_b350s551i37 14675 chrXptel1M 957302 ACCAAAATCTTCATAGCAGCAATTTTTGTGACAGCAAAGAATTGGAAAGA 957351 v ii v v v v i i i i v L1ME3G_3end#L 432 ACAAGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACA 481 chrXptel1M 957352 AAGTAGATGCCCATCTACTGAAGAATGGTTTAACAAATTGTGATACACAA 957401 vv i i v iv ii v i i i i ivv L1ME3G_3end#L 482 ACCTAAATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGTATATCC 531 chrXptel1M 957402 ATATAATGAAAAATTACTGCACTGG--AAAAAAAATGAGG--GGTGTGAT 957447 iv i v i - vi? -- i -- i v - L1ME3G_3end#L 532 ATACTATGGAATACTA-TGCAGCNGTTAAAAAGAATGAGGTAGATCT-AT 579 chrXptel1M 957448 ACATACAGAGAAGCATGAGAAGACCT 957473 ii v ---- ii i L1ME3G_3end#L 580 ATGTACTGA----CATGGAAAGATCT 601 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.86 CpG sites = 27, Kimura (unadjusted) = 34.82 Transitions / transversions = 1.50 (27/18) Gap_init rate = 0.05 (8 / 171), avg. gap size = 1.25 (10 / 8) 423 25.18 1.47 0.73 chrXptel1M 957302 957437 (42563) L1ME3E_3end#LINE/L1 435 571 (418) m_b350s551i38 14675 chrXptel1M 957302 ACCAAAATCTTCATAGCAGCAATTTTTGTGACAGCAAAGAATTGGAAAGA 957351 v i v v v i i i i v L1ME3E_3end#L 435 ACAAGAATGTTCATAGCAGCATTGTTTGTAATAGCAAAAAACTGGAAACA 484 chrXptel1M 957352 AAGTAGATGCCCATCTACTGAAGAATGGTTTAACAAATTGTGATACACAA 957401 vvi i i v v i v v i i i ivv L1ME3E_3end#L 485 ACCCAAATGTCCATCGACAGGAGAATGGATAAATAAATTGTGGTATATTC 534 chrXptel1M 957402 ATATAATGAAAAAT--TACTGCACTGGAAAAAAAATGA 957437 i i v i-- v v - vi L1ME3E_3end#L 535 ATACAATGGAATACTATACAGCAGT-GAAAATGAATGA 571 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 30.98 CpG sites = 17, Kimura (unadjusted) = 30.98 Transitions / transversions = 1.00 (17/17) Gap_init rate = 0.01 (2 / 135), avg. gap size = 1.50 (3 / 2) 489 23.64 0.00 2.36 chrXptel1M 957876 958005 (41995) Charlie4a#DNA/hAT-Charlie 382 508 (0) m_b350s502i4 14677 chrXptel1M 957876 ATTGTTTTCCTTTGTAAGTCTTGTACATTTTATCTGATGCATTTCATAAC 957925 v - i i ii i v v v Charlie4a#DNA 382 ATTGGTTTCCTTTGTAA-TCCTATGTATTTTATTTTATGCATTTAAAAAC 430 chrXptel1M 957926 ATTATTTTGAGAAGCGGACCCCCAGGCTTCAGCAGAACTCCCCAGGGACC 957975 i - ii vi v viv vv ii Charlie4a#DNA 431 ATTATTCTGAGAAG-GGGTCCATAGGCTTCACCAGACTGCCAAAGGGGTC 479 chrXptel1M 957976 CATAGTACCACAAACAGGTAAGAGACCCTG 958005 i i - v vi v iv Charlie4a#DNA 480 CATGGCA-CAAAAAAGGTTAAGAACCCCTG 508 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 28.71 CpG sites = 16, Kimura (unadjusted) = 28.71 Transitions / transversions = 1.14 (16/14) Gap_init rate = 0.02 (3 / 129), avg. gap size = 1.00 (3 / 3) 19 6.91 6.45 0.00 chrXptel1M 960635 960665 (39335) (TC)n#Simple_repeat 1 33 (0) m_b350s252i19 14678 chrXptel1M 960635 TCTCCCTTTCT-TCTCTCTCTCTCTCT-TCTCT 960665 i i - - (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 33 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2) 14 9.32 0.00 0.00 chrXptel1M 961517 961539 (38461) (CGC)n#Simple_repeat 1 23 (0) m_b350s252i20 14679 chrXptel1M 961517 CGCCGCCGCGGCCGCCGCCTCCG 961539 v v (CGC)n#Simple 1 CGCCGCCGCCGCCGCCGCCGCCG 23 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 21 23.75 0.00 0.00 chrXptel1M 961558 961612 (38388) (GGGGAGG)n#Simple_repeat 1 55 (0) m_b350s252i21 14680 chrXptel1M 961558 GGGGAGGGGGGAGGGGGGAGGAGGGCGGGGGGGTGGGAGCTGAGGGAAAA 961607 i v iv i vv i iii (GGGGAGG)n#Si 1 GGGGAGGGGGGAGGGGGGAGGGGGGAGGGGGGAGGGGGGAGGGGGGAGGG 50 chrXptel1M 961608 GGGAG 961612 (GGGGAGG)n#Si 51 GGGAG 55 Matrix = Unknown Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 18 31.38 1.03 4.26 chrXptel1M 961741 961837 (38163) (CGC)n#Simple_repeat 1 94 (0) m_b350s252i23 14681 chrXptel1M 961741 CGCCACCGCTGCTGCCGCCACC-CTCCCGAAGCCGTCAACCTTCCCCCCC 961789 i i i i - iv vv - vi -v v v (CGC)n#Simple 1 CGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCG-CCGCC-GCCGCCGC 48 chrXptel1M 961790 CCCCCAGGCCGGGAGCTGACGCCGCCGCTCGCCGCCACCGTCGCCGCC 961837 v vvv - vv i v - i i (CGC)n#Simple 49 CGCCGCCGCC-GCCGCCGCCGCCGCCGC-CGCCGCCGCCGCCGCCGCC 94 Matrix = Unknown Transitions / transversions = 0.64 (9/14) Gap_init rate = 0.05 (5 / 96), avg. gap size = 1.00 (5 / 5) 26 0.00 0.00 0.00 chrXptel1M 962285 962309 (37691) (G)n#Simple_repeat 1 25 (0) c_b351s251i0 14682 chrXptel1M 962285 GGGGGGGGGGGGGGGGGGGGGGGGG 962309 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGG 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 242 23.66 13.98 0.00 chrXptel1M 964037 964129 (35871) MER63D#DNA/hAT-Tip100 341 446 (615) m_b351s502i0 14683 chrXptel1M 964037 AGCATTCACATTTTGAAACTGGGAAAACACTGCCTAT------TTGATTT 964080 i i iivi i v v v i i vv ------ MER63D#DNA/hA 341 AGTATTTACACCACGGAAATCGGCAAACGCTACAAATCAGGGCTTGATTT 390 chrXptel1M 964081 ATTGTTCTGCTGATT-TTGAAATTTAAGAAAGT------GAAGATGTTAA 964123 i i - iv i i ------ i MER63D#DNA/hA 391 ATTGTTTTGTTGATTGTCTAGACTTAAGAAAGTGATGGAGAAAATGTTAA 440 chrXptel1M 964124 TAATAC 964129 i MER63D#DNA/hA 441 TAATGC 446 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 26.33 CpG sites = 15, Kimura (unadjusted) = 29.44 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.03 (3 / 92), avg. gap size = 4.33 (13 / 3) 269 18.31 11.27 0.00 chrXptel1M 964576 964646 (35354) MER63D#DNA/hAT-Tip100 983 1061 (0) m_b351s502i1 14684 chrXptel1M 964576 TAAACTTGAAAATGTGT---CATACATAAATTTTTT-----AAAGAGGTG 964617 iv v i --- v ----- i vi MER63D#DNA/hA 983 TAAACTTATATATGTATATACATACATACATTTTTTCCCCCAGAGAGCCG 1032 chrXptel1M 964618 GTTATTAAACATTTACCGGCACATTCCTG 964646 i i iiv MER63D#DNA/hA 1033 GTTGTTAAACATTTACCAGCACACCACTG 1061 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 19.56 CpG sites = 8, Kimura (unadjusted) = 21.33 Transitions / transversions = 1.60 (8/5) Gap_init rate = 0.03 (2 / 70), avg. gap size = 4.00 (8 / 2) 16 21.41 2.33 0.00 chrXptel1M 964805 964847 (35153) (AAGG)n#Simple_repeat 1 44 (0) m_b351s252i4 14685 chrXptel1M 964805 AAGTAATCAAGGAAGGAAAGAATGAAGGAAGGGA-GAATTAAGG 964847 v vv i v i - vv (AAGG)n#Simpl 1 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG 44 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.02 (1 / 42), avg. gap size = 1.00 (1 / 1) 13 17.57 0.00 0.00 chrXptel1M 965379 965405 (34595) (CTC)n#Simple_repeat 1 27 (0) m_b351s252i5 14686 chrXptel1M 965379 CTCCTCCTTCTCCTCTTCTTCCTTCTC 965405 i i i i (CTC)n#Simple 1 CTCCTCCTCCTCCTCCTCCTCCTCCTC 27 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 14 16.24 0.00 0.00 chrXptel1M 965418 965445 (34555) (CTA)n#Simple_repeat 1 28 (0) m_b351s252i6 14687 chrXptel1M 965418 CTGCTGCTACTAATACTATTACTACTAC 965445 i i v i (CTA)n#Simple 1 CTACTACTACTACTACTACTACTACTAC 28 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 366 28.29 0.00 3.26 chrXptel1M 965639 965733 (34267) MIRc#SINE/MIR 3 94 (174) m_b351s601i0 14688 chrXptel1M 965639 AGCTAGGGTAACACAGTGAGTAGAACACTGGCCTTGGAATGAGGAGGACC 965688 vi v iiii iiv i v i v i MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chrXptel1M 965689 TGAATTCAAATCCAGCCTCAGACACTTAATACTACCTGTATAACC 965733 ii i i v v v v --- v i i MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCACT---TACTAGCTGTGTGACC 94 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 34.85 CpG sites = 16, Kimura (unadjusted) = 36.62 Transitions / transversions = 1.60 (16/10) Gap_init rate = 0.03 (3 / 94), avg. gap size = 1.00 (3 / 3) 340 30.22 14.89 4.25 chrXptel1M 965804 966038 (33962) L2b_3end#LINE/L2 198 456 (10) m_b351s601i1 14689 chrXptel1M 965804 TTCTTCAAAATTCAGCTAACAGGTCAACTACTCCTACAGGAGACTTTTCC 965853 i iivi v v v - -- v i ii ii i L2b_3end#LINE 198 TCCTTCAGGTCTCAGCTCAAATGTCA-C--CTCCTCCGGGAAGCCCTCCC 244 chrXptel1M 965854 TGAGAACTTCCCAAAAGGGCAGGG---AGTGCT-TCCTCTA----CCCCC 965895 --- ii ---- v ---i i i- i---- L2b_3end#LINE 245 TGA---CCCCCCA----GGCCGGGTCAGGCGCCCTCCTCTGGGCCCCCCC 287 chrXptel1M 965896 AA---------ACCGCTTGGGA--AGCATT--CTGTTT------CTATTT 965926 i---------i i iv i-- v? -- ? ------ i i L2b_3end#LINE 288 AGTCCTACCCTGCCACTCTGGGTTATNATTGTCTGNTTACATGTCTGTCT 337 chrXptel1M 965927 -----AGTACACAATCACATTTCCTG---GAAGGCACAGGGTATTTGATG 965968 ----- v v vi v -ii i v --- v v v ? v v vv L2b_3end#LINE 338 CCCCCACTAGACTGTGA-GCTCCGTGAGGGCAGGGACCGNGTCTGTCTTG 386 chrXptel1M 965969 ATTGTCTTTGTAGCCCCAGGACCTAGCCGAGGACCTAGCACATAGTAGGT 966018 v iii vi v vi vv ?i i i i L2b_3end#LINE 387 TTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGC 436 chrXptel1M 966019 ACTTAATAAATGGTTGTTAA 966038 i i i iv i L2b_3end#LINE 437 GCTCAGTAAATATTTGTTGA 456 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 38.02 CpG sites = 41, Kimura (unadjusted) = 41.25 Transitions / transversions = 1.52 (41/27) Gap_init rate = 0.09 (20 / 234), avg. gap size = 2.30 (46 / 20) 219 35.71 0.00 0.00 chrXptel1M 966693 966776 (33224) C MIRb#SINE/MIR (182) 86 3 m_b351s601i2 14690 chrXptel1M 966693 TAGTTGTTGGTCAAGCTGGGATTCAAACCTGGCTCCTCTTCCCCCCAATT 966742 viv ivi i i ii v ivii vv i vv C MIRb#SINE/MIR 86 TAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAG 37 chrXptel1M 966743 CTAGTGTTCTTTCCACTGGATCATGGTCTCCATC 966776 iv i v i i v vi v C MIRb#SINE/MIR 36 CCCGTGCTCTTTCCACTGCACCACGCTGCCCCTC 3 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 43.15 CpG sites = 16, Kimura (unadjusted) = 49.80 Transitions / transversions = 1.14 (16/14) Gap_init rate = 0.00 (0 / 83), avg. gap size = 0.0 (0 / 0) 284 30.14 0.00 0.00 chrXptel1M 966693 966765 (33235) C MIRc#SINE/MIR (185) 83 11 m_b351s601i3 14690 chrXptel1M 966693 TAGTTGTTGGTCAAGCTGGGATTCAAACCTGGCTCCTCTTCCCCCCAATT 966742 viv ivi i i i ii v i i vv i v C MIRc#SINE/MIR 83 TAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGT 34 chrXptel1M 966743 CTAGTGTTCTTTCCACTGGATCA 966765 i i v i C MIRc#SINE/MIR 33 CCAGTGCTCTTTCCACTGCACCA 11 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.52 CpG sites = 14, Kimura (unadjusted) = 40.16 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.00 (0 / 72), avg. gap size = 0.0 (0 / 0) 342 26.26 4.04 0.00 chrXptel1M 966924 967022 (32978) C MIR3#SINE/MIR (0) 208 106 m_b351s601i4 14691 chrXptel1M 966924 GGATCATAG--TCCTAGAAC--TAGAACTAAAAGGGACATCCCAGGCCAT 966969 i -- v i--i i ii v ivv ii C MIR3#SINE/MIR 208 GAATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCAT 159 chrXptel1M 966970 CTGGTCCAGCCCCCAAATTGTCCACAGGAGGAAAGTGAAACCTAGAGAGA 967019 i i vv v v v v v ii i i C MIR3#SINE/MIR 158 CTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGG 109 chrXptel1M 967020 TGA 967022 C MIR3#SINE/MIR 108 TGA 106 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 33.02 CpG sites = 15, Kimura (unadjusted) = 33.02 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.02 (2 / 98), avg. gap size = 2.00 (4 / 2) 195 31.86 8.08 4.90 chrXptel1M 969608 969706 (30294) MamTip2#DNA/hAT-Tip100 6 107 (198) m_b351s601i5 14692 chrXptel1M 969608 CCAGCCTGACCTGTAA------TAGGC--CTGCCTGTGAAGGGTGATTTT 969649 i v vi i------ -- i ii vi v v MamTip2#DNA/h 6 CCGGCCTTACGCGTAGGCAGAGTAGGCGGCCGCCTACGTGGTGTGATTTG 55 chrXptel1M 969650 AGGAAAACAGTTAAGTGTTCACTGCCATCATCCTAAATCTCTCCCCCGCT 969699 iivi v vv vv i v ----- v v i iii MamTip2#DNA/h 56 AGGGGCGCCGGGAAGGCTCCCCTGCC-----CCAAAATATCTCTCCCATC 100 chrXptel1M 969700 CACCTGT 969706 i MamTip2#DNA/h 101 CGCCTGT 107 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 32.30 CpG sites = 16, Kimura (unadjusted) = 42.45 Transitions / transversions = 1.14 (16/14) Gap_init rate = 0.07 (7 / 98), avg. gap size = 1.86 (13 / 7) 22 27.73 0.00 0.00 chrXptel1M 971714 971778 (28222) (AAAA)n#Simple_repeat 1 65 (0) m_b351s252i7 14693 chrXptel1M 971714 AAAAAAAATAAAAATAAAATAAAAATAAATAAATAAAATAGATTCAATCA 971763 v v v v v v v i vvv vv (AAAA)n#Simpl 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chrXptel1M 971764 AAAGAGAAAAAAAAA 971778 i i (AAAA)n#Simpl 51 AAAAAAAAAAAAAAA 65 Matrix = Unknown Transitions / transversions = 0.25 (3/12) Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0) 18 13.69 1.72 9.26 chrXptel1M 971998 972055 (27945) (GTAT)n#Simple_repeat 1 54 (0) m_b351s252i8 14694 chrXptel1M 971998 GTATGTTAATGTATATGTGTATG-ATGATAGATATCTATGCATATGTGTG 972046 - - i i - - vi v -- i (GTAT)n#Simpl 1 GTATG-T-ATGTATGTATGTATGTATG-TATGTATGTATG--TATGTATG 45 chrXptel1M 972047 TATGTATGT 972055 (GTAT)n#Simpl 46 TATGTATGT 54 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.11 (6 / 57), avg. gap size = 1.00 (6 / 6) 18 23.76 3.23 1.59 chrXptel1M 971999 972060 (27940) (TATGTA)n#Simple_repeat 1 63 (0) m_b351s252i9 14694 chrXptel1M 971999 TATGTTAATGTATATGTGTATG-ATGATAGATATCTATGCATATGTGTGT 972047 vv i - - iv v iii i i (TATGTA)n#Sim 1 TATGTATATGTATATGTATATGTAT-ATGTATATGTATATGTATATGTAT 49 chrXptel1M 972048 ATGTATGTGT-TAT 972060 i - (TATGTA)n#Sim 50 ATGTATATGTATAT 63 Matrix = Unknown Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.05 (3 / 61), avg. gap size = 1.00 (3 / 3) 12 24.27 3.90 6.67 chrXptel1M 972110 972186 (27814) (GAAAA)n#Simple_repeat 1 75 (0) m_b351s252i10 14695 chrXptel1M 972110 GAAAAGAGGGAAAAAAGAATAAAGAAAAAAAGTACACAGCAAAG--AACA 972157 -ii i v i i i - - v v -- v (GAAAA)n#Simp 1 GAAAAGA-AAAGAAAAGAAAAGAAAAGAAAAG-A-AAAGAAAAGAAAAGA 47 chrXptel1M 972158 AAAGAAAACCTATAAG-GAAGACAAGAAAA 972186 --v v -i v (GAAAA)n#Simp 48 AAAGAAAA--GAAAAGAAAAGAAAAGAAAA 75 Matrix = Unknown Transitions / transversions = 1.00 (7/7) Gap_init rate = 0.09 (7 / 76), avg. gap size = 1.14 (8 / 7) 225 29.91 7.78 1.57 chrXptel1M 972960 973139 (26861) L1M1_orf2#LINE/L1 31 221 (3073) m_b351s551i0 14696 chrXptel1M 972960 ATCACACTGAATGTCG-TGGATGAAAATATCCAATTTTAAAA----GAGT 973004 v i vi- iv v v ivv i ---- L1M1_orf2#LIN 31 ATAACATTGAATGTAAATGGACTAAACTCTCCAATCAAAAGACATAGAGT 80 chrXptel1M 973005 TATAGATTGGATCTGAAAAGAAAACCTCACAATCTGTTGCTTAAAGGAAA 973054 viiv v vvi v i iv?ii i v i L1M1_orf2#LIN 81 GGCTGAATGGATGAAAAAACAAGACCCANTGATCTGTTGCCTACAAGAAA 130 chrXptel1M 973055 TACTTTT------TAAAAATGTATATAGGATAAAAATGAGGGGCAAAAAA 973098 i vi ------ i iii i iv i i i vvii L1M1_orf2#LIN 131 CACACTTCACCTATAAAGACACACATAGACTGAAAATAAAGGGATGGAAA 180 chrXptel1M 973099 AACATTTGCTATGTCTCAAAT-TAATCCAAAAA--AGCAGGAGT 973139 v v v i i --- -v v -- L1M1_orf2#LIN 181 AAGATATTCCATGCC---AATGGAAACCAAAAAAGAGCAGGAGT 221 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.32 CpG sites = 29, Kimura (unadjusted) = 39.32 Transitions / transversions = 1.21 (29/24) Gap_init rate = 0.04 (8 / 179), avg. gap size = 2.12 (17 / 8) 21 20.07 0.00 0.00 chrXptel1M 973620 973659 (26341) (A)n#Simple_repeat 1 40 (0) m_b351s252i11 14697 chrXptel1M 973620 AAAAAACAAAAACAAAAACAAAATAAGAAACAAACAAAAA 973659 v v v v i v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 40 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 40 0.00 0.00 0.00 chrXptel1M 974337 974370 (25630) (GT)n#Simple_repeat 1 34 (0) c_b351s251i1 14698 chrXptel1M 974337 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 974370 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 34 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 221 24.63 0.00 5.26 chrXptel1M 976260 976319 (23681) MIRb#SINE/MIR 5 61 (207) m_b351s601i6 14699 chrXptel1M 976260 GGGGCAGCTAGGTGGCACGATCAATAGAGAACTGGCTCTGAAGTCAGGAA 976309 --- ii ii vi v v v i i iv MIRb#SINE/MIR 5 GGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACA 51 chrXptel1M 976310 GACCTGAGTT 976319 i MIRb#SINE/MIR 52 GACCTGGGTT 61 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.66 CpG sites = 9, Kimura (unadjusted) = 30.66 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.05 (3 / 59), avg. gap size = 1.00 (3 / 3) 18 25.71 0.00 0.00 chrXptel1M 977349 977391 (22609) (GA)n#Simple_repeat 1 43 (0) m_b351s252i13 14700 chrXptel1M 977349 GAGAAATAGGGAGAGAGAAAGAGAAAGGGGTGGAGAGAGAGAG 977391 i v i i i i ivi (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 43 Matrix = Unknown Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 272 0.00 0.00 0.83 chrXptel1M 977392 977633 (22367) (AGA)n#Simple_repeat 1 240 (0) c_b351s251i2 14701 chrXptel1M 977392 AGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAG 977441 (AGA)n#Simple 1 AGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAG 50 chrXptel1M 977442 AAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAA 977491 (AGA)n#Simple 51 AAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAA 100 chrXptel1M 977492 GAAGAAGAAGGAAGAAGAAGAAGAAAGAAGAAGAAGAAGAAGAAGAAGAA 977541 - - (AGA)n#Simple 101 GAAGAAGAA-GAAGAAGAAGAAG-AAGAAGAAGAAGAAGAAGAAGAAGAA 148 chrXptel1M 977542 GAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA 977591 (AGA)n#Simple 149 GAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA 198 chrXptel1M 977592 AGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA 977633 (AGA)n#Simple 199 AGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA 240 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.01 (2 / 241), avg. gap size = 1.00 (2 / 2) 1226 22.70 0.75 2.29 chrXptel1M 978321 978586 (21414) C MIRb#SINE/MIR (3) 265 4 m_b351s601i7 14702 chrXptel1M 978321 AAAAAGGCTAACATTAATATAGTGCTTACTATATGCTAGGCACTATGCTA 978370 v ii v v vv i i i i C MIRb#SINE/MIR 265 AATAGAGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTA 216 chrXptel1M 978371 AGGACTTTACAATTGTTATCTCGTTTGATCCTCACAACAACTCTGTGAAG 978420 vi vvii i i i i i C MIRb#SINE/MIR 215 AGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGG 166 chrXptel1M 978421 TAGGTGCTATTGTTTCCCCCATTTTACAGTCAAAGAAACTGAGG--TAGA 978468 ii i --- vii i --i C MIRb#SINE/MIR 165 TAGGTATTATTAT---CCCCATTTTACAGATGAGGAAACTGAGGCTCAGA 119 chrXptel1M 978469 GATGTTTAGTGACTTGCCCAAGGTCCCACAGCTAGTTAATGTCTGATACA 978518 v v i v v i v v vv i C MIRb#SINE/MIR 118 GAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 69 chrXptel1M 978519 GGATTTGAACTCAGGTCTTCCTTGATCCAGGTCTAGCACTCTATCCACTG 978568 i i vi viv iiv iv ii v C MIRb#SINE/MIR 68 GGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTG 19 chrXptel1M 978569 AGCCACTTAACTGCCCCT 978586 vi ---i C MIRb#SINE/MIR 18 CACCAC---GCTGCCCCT 4 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.39 CpG sites = 35, Kimura (unadjusted) = 27.54 Transitions / transversions = 1.46 (35/24) Gap_init rate = 0.03 (7 / 265), avg. gap size = 1.14 (8 / 7) 291 30.40 3.42 2.98 chrXptel1M 978857 979090 (20910) L1M3_orf2#LINE/L1 2482 2716 (572) m_b351s551i1 14703 chrXptel1M 978857 ATCAGATTATCAAAGGCATACTTCATAAAACTTGGCAAAATAAT---AAA 978903 i v vi v vi i i i v v iv i --- L1M3_orf2#LIN 2482 ATCAAAATCCCAATGGCATTTTTTACAGAAATAGAAAAAACAATCCTAAA 2531 chrXptel1M 978904 ATTCATTTGGAAAAATAAAACTTCTAGAATATCAAGGGAAAGGATGAAAA 978953 v vv i vvi iv v v ii v vvv i L1M3_orf2#LIN 2532 ATTCATATGGAACCACAAAAGACCCCGAATAGCCAAAGCAATCTTGAGAA 2581 chrXptel1M 978954 AGGCAGGAAGGAAG--GGGGGAATCACACATCTAGACCTCAAACTGTATC 979001 -- i vi -- i v v iv ii v i i L1M3_orf2#LIN 2582 AG--AAGAACAAAGCTGGAGGCATCACACTTCCTGATTTCAAAATATATT 2629 chrXptel1M 979002 ACGAAACAGAAGAAACCAAAATCATTTGGTGTTGGTTTAAAAATAGAG-- 979049 i i viv v i ivi v ii iv i v-- L1M3_orf2#LIN 2630 ACAAAGCTACAGTAATCAAAACAGTATGGTACTGGCATAAAAACAGACAT 2679 chrXptel1M 979050 ATAGCTCAATGGAACAGACTGGACGAGAAAG-TCAGAAACAA 979090 vi v ----- i -i i L1M3_orf2#LIN 2680 ATAGACCAATGGAACAGAAT-----AGAGAGCCCAGAAATAA 2716 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 39.64 CpG sites = 36, Kimura (unadjusted) = 39.64 Transitions / transversions = 1.09 (36/33) Gap_init rate = 0.05 (11 / 233), avg. gap size = 1.36 (15 / 11) 26 26.28 1.30 0.00 chrXptel1M 979510 979586 (20414) (TATA)n#Simple_repeat 1 78 (0) m_b351s252i14 14704 chrXptel1M 979510 TATACAAATA-ATTAATATATATTCATAAATATATGTATTTGTATGTATA 979558 i v - vv vi v i v i i (TATA)n#Simpl 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chrXptel1M 979559 GATATATTCATGTATGTATTTATATATA 979586 v vi i i v (TATA)n#Simpl 51 TATATATATATATATATATATATATATA 78 Matrix = Unknown Transitions / transversions = 0.89 (8/9) Gap_init rate = 0.01 (1 / 76), avg. gap size = 1.00 (1 / 1) 330 28.38 2.82 7.35 chrXptel1M 980418 980630 (19370) L1ME4c_3end#LINE/L1 280 483 (347) m_b351s551i2 14705 chrXptel1M 980418 CATTGTTGGTGGAACTGAGCATGAGTACCACCATTTTGGAAAGTAATTTG 980467 i v ? viv vi v v i L1ME4c_3end#L 280 CATTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTG 329 chrXptel1M 980468 GAATTATGCAAATATATGCAAATCAAGTGACTAAAATATCCATATCCTTT 980517 v v i ---- --- ---i iv iv i i i L1ME4c_3end#L 330 GCAATACG----TAT---CAA---GAGCCATAAAAATGTTCATACCCTTT 369 chrXptel1M 980518 GACCTAGAGATGCCTTTACAACACAAATGCCTCAAGAAGGTAATTGATAA 980567 i vi v vi v viviv vv ii ii i ii v v L1ME4c_3end#L 370 GACCCAGTAATTCCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAA 419 chrXptel1M 980568 GAAG---AAAGTCTTACTATATGCCC--AGAACTTTATAGTAGCACTTTT 980612 --- ----- v -- vv i v i ii v L1ME4c_3end#L 420 GAAGGAAAAAG-----CTATATGCACGAAGATGTTCATTGCAGCGTTATT 464 chrXptel1M 980613 TGTAAT-GCAAACAATTGG 980630 i - i v L1ME4c_3end#L 465 TATAATAGCGAAAAATTGG 483 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 33.89 CpG sites = 29, Kimura (unadjusted) = 36.24 Transitions / transversions = 1.07 (29/27) Gap_init rate = 0.08 (18 / 212), avg. gap size = 1.17 (21 / 18) 477 32.99 7.61 0.00 chrXptel1M 981297 981493 (18507) L3#LINE/CR1 3745 3956 (143) m_b351s601i8 14706 chrXptel1M 981297 AAGACTCAGGTGAGTCAAGAGAGATGTTTTCTAGTATTAAAGAGACCATC 981346 i iv v v v v i v i vi ii i ii L3#LINE/CR1 3745 AAGACTTAGAGGAGACATGATAGCTGTCTTCAAATATTTGAAGGGCTGTC 3794 chrXptel1M 981347 A---AGAGAAAAGATTAAAATTAAAC-----AGCCCT----GTTTAAACT 981384 ---i ii ii i v vv -----i i i---- vivi L3#LINE/CR1 3795 ATGTGGAAGAGGGATTAGACTTATTCTGTGTGGCTCCAGAGGGCAGAACT 3844 chrXptel1M 981385 TAGAACAGTGGGTGAAAGTTGCAG--AGGCAGATGCTGCCTCAATATGCA 981432 vi v i i i -- vii v ivi L3#LINE/CR1 3845 AGGACCAATGGGTGGAAGTTACAGGGAGGCAGATTTCGGCTCAATATAAG 3894 chrXptel1M 981433 GA-TAATTTCCTTACCCTTGGAGCTATCCTAAAGTAGAATGGGCTATCCA 981481 -v i i v vv ii i v i i ii iv L3#LINE/CR1 3895 GAAGAACTTTCTAACAATCAGAGCTGTCCAAAAATGGAATGGGCTGCCTC 3944 chrXptel1M 981482 GGAAAGTAATGA 981493 ?i i i L3#LINE/CR1 3945 GNGAGGTAGTGA 3956 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.16 CpG sites = 42, Kimura (unadjusted) = 46.16 Transitions / transversions = 1.83 (42/23) Gap_init rate = 0.03 (5 / 196), avg. gap size = 3.00 (15 / 5) 17 5.00 0.00 0.00 chrXptel1M 982320 982340 (17660) (T)n#Simple_repeat 1 21 (0) m_b351s252i15 14707 chrXptel1M 982320 TTTCTTTTTTTTTTTTTTTTT 982340 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTT 21 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 59 0.00 0.00 0.00 chrXptel1M 983053 983102 (16898) (TC)n#Simple_repeat 1 50 (0) c_b351s251i3 14708 chrXptel1M 983053 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 983102 (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 48 4.17 0.00 0.00 chrXptel1M 983106 983155 (16845) (CA)n#Simple_repeat 1 50 (0) c_b351s251i4 14709 chrXptel1M 983106 CACACACACACACACACACACACACACACACACACACATATACACACACA 983155 i i (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 531 32.74 12.89 3.33 chrXptel1M 985241 985597 (14403) C L2b_3end#LINE/L2 (4) 462 73 m_b351s601i9 14710 chrXptel1M 985241 ATTAATCAAATGAACATTTATTAAGCTCCTGTTATATGTCAGGCCCTGTC 985290 v iv ii i i i v ii i i i ? v C L2b_3end#LINE 462 ATTCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTG 413 chrXptel1M 985291 CCAGGTGCTGATTATATAAAG----AAAAAAT-GAAACAGCCCTTGTCCT 985335 i i ivv i iv ---- v i i- v? i i i i C L2b_3end#LINE 412 CTAGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCT 363 chrXptel1M 985336 CAAGGAGCTCACATCTTAGTGGTAG--------ATGT-AGCAGGCACATG 985376 v vii vi -------- - ? i - - C L2b_3end#LINE 362 CACGGAGCTCACAGTCTAGTGGGGGAGACAGACATGTAANCAGACA-AT- 315 chrXptel1M 985377 TATA----AGTATGTACAAAATATAAAC---AAATGCTCATTAACGATGG 985419 ? ---- vi -i iii -ii ---iiiv i --i v v C L2b_3end#LINE 314 NATAACCCAGAGTG-GCAGGGTA-GGACTGGGGGGGCCCA--GAGGAGGG 269 chrXptel1M 985420 A----GGCCTGG---GAAGGGGCAGAGATACTAAGCCTCCTATAAAAGAT 985462 v---- i i --- ii v i ----ii i iiv ii i C L2b_3end#LINE 268 CGCCTGACCCGGCCTGGGGGGTCAGGGA----GGGCTTCCCGGAGGAGGT 223 chrXptel1M 985463 GGCA-------------CTGAAGAA--ACTAGGGATTCTCAAAGTC-AGA 985496 i ------------- i -- v ii vv v i iv- C L2b_3end#LINE 222 GACATTTGAGCTGAGACCTGAAGGATGAGTAGGAGTTGGCCAGGCGAAGA 173 chrXptel1M 985497 GGTGAGGATGGAATGCACTCCAGGCATGGGGAACTGCCTTTGCAAAGGCT 985546 i v --- ii vi v v?v i C L2b_3end#LINE 172 GGTGGGGAAGG---GCGTTCCAGGCAGAGGGAACAGCANGTGCAAAGGCC 126 chrXptel1M 985547 TGCAAATGGGAAATAGTTTTACATAT--GAAATACAAGAACAAGGCCACT 985594 ivv iii i?v i? vi i i -- iiv iv vi v C L2b_3end#LINE 125 CTGAGGCGGGAGNGAGCNTGGCGTGTTCGAGGAACAGCAAGGAGGCCAGT 76 chrXptel1M 985595 TTG 985597 v C L2b_3end#LINE 75 GTG 73 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 42.52 CpG sites = 75, Kimura (unadjusted) = 47.20 Transitions / transversions = 1.97 (75/38) Gap_init rate = 0.07 (25 / 356), avg. gap size = 2.36 (59 / 25) 277 29.47 5.24 6.64 chrXptel1M 985939 986167 (13833) C L2d2_3end#LINE/L2 (329) 226 1 m_b351s601i10 14711 chrXptel1M 985939 GGTATT--AACTGGGGATTGAAGGATGCCAGGGAAG-CTAGAAGAGGCAG 985985 ? -- i vv --- v i -i v i v ii C L2d2_3end#LIN 226 GGNATTTGAGCTGGGCCTTGAAGGATG---GGTAGGATTTGGATAGGTGG 180 chrXptel1M 985986 AGATGAAGAGGGAGAACATTTCAGGCAGGGTAGACAGCCAGTGA--AAAT 986033 v i i ii i i vii i -- -- v C L2d2_3end#LIN 179 AGAGGAAGGGGAAGGGCATTCCAGGCGGGGGGAACGGC--GTGAGCAAAG 132 chrXptel1M 986034 GTCCAGAGCCGAGACAGGGAGTTTCTTGTTCCTGGAACAGGAATGAGTG- 986082 iv v i v? v vivvv v vv i --- i- C L2d2_3end#LIN 131 GCGCAGAGGCGGGAANGCGCAAGGCGTGTTCGGGGGACAG---TGAGTAG 85 chrXptel1M 986083 -CAAGGTTG-CTGGATCAAAGAATACAGAGCAGGAAA----TGAGCTATA 986126 - v v - v ii ii v - v ? ii ---- i vv C L2d2_3end#LIN 84 ACCAGTTTGGCTGGAGCGGAGGGTTC-GTGNAGGGGAATAGTGGGAGATA 36 chrXptel1M 986127 AGAAAACTGGAAAGAAAGGGAAGTGGGCTGAGGTTATGAAG 986167 i--- i? ---v viv i ii i C L2d2_3end#LIN 35 AGG---CTGGAAAGGNAGG---TTGGGGCCAGATCGTGGAG 1 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 35.15 CpG sites = 34, Kimura (unadjusted) = 39.07 Transitions / transversions = 1.17 (34/29) Gap_init rate = 0.10 (22 / 228), avg. gap size = 1.23 (27 / 22) 502 36.21 8.09 1.22 chrXptel1M 985993 986375 (13625) C L2#LINE/L2 (1) 3081 2673 m_b351s601i11 14711 chrXptel1M 985993 GAGGGAGAACATTTCAGGCAGGGTAGACAGCCAGTGAAAATGTCCAGAGC 986042 i i i i i i vii v v v i v v C L2#LINE/L2 3081 GGGGAAGAGCGTTCCAGGCAGAGGGAACAGCAAGTGCAAAGGCCCTGAGG 3032 chrXptel1M 986043 CGAGACAGGGAGTTTCTTGTTCCTGGAACAGGAATGAGTGCAAGGTTGCT 986092 i vv v vv vv v vv v v vv iv v C L2#LINE/L2 3031 CGGGAGCGTGCCTGGCGTGTTCGAGGAACAGCAAGGAGGCCAGTGTGGCT 2982 chrXptel1M 986093 GGATCAAAGAATACAGAGC-AGGAAATGAGCTATAAGAAAACTGGAAAGA 986141 v --i i --- - iiiv ivi i i vvv vv C L2#LINE/L2 2981 GGAGC--GGAGT---GAGCGAGGGGGAGAGTGGTAGGAGATGAGGTCAGA 2937 chrXptel1M 986142 AAGGGAA-GTGGGCTGAGGTTATGAAGGGCTTTAATTGCCA-AAT-AGGA 986188 i v - v viv i i v i ivvv -vi - C L2#LINE/L2 2936 GAGGTAACGGGGGACCAGATCATGTAGGGCCTTGTAGGCCATTGTAAGGA 2887 chrXptel1M 986189 TTTTGTATTTGATCTTGGAGGCAACGGGAATTCA----------TCAAGC 986228 i vv v iii iiv vi i vi ---------- ii C L2#LINE/L2 2886 CTTTGGCTTTTACTCTGAGTGAGATGGGAAGCCATTGGAGGGTTTTGAGC 2837 chrXptel1M 986229 AAGGGGGTGACACCATCAGACTTGTACTTTACAAAAACTACTCT-GTGGC 986277 ii i iv v iiii v ii ii - iv C L2#LINE/L2 2836 AGAGGAGTGACATGATCTGACTTACGTTTTAAAAGGATCACTCTGGCTGC 2787 chrXptel1M 986278 TGAATGGAAAATGCGTTGGAGCAG---------------AGAGAGACTTG 986312 vi v i ivii ? vi --------------- i iv C L2#LINE/L2 2786 TGTGTTGAGAATAGACTGNAGGGGGGCAAGGGTGGAAGCAGGGAGACCAG 2737 chrXptel1M 986313 AGATAAGGCTG-AGCAATAGGTCAAACGTGAGGCAATGAGGGACAGCACC 986361 vv vi i-v i ivi ii v iii iv viv v C L2#LINE/L2 2736 TTAGGAGGCTATTGCAGTAATCCAGGCGAGAGATGATGGTGGCTTGGACC 2687 chrXptel1M 986362 AGAGTGGTAGCAGT 986375 i i C L2#LINE/L2 2686 AGGGTGGTGGCAGT 2673 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 49.43 CpG sites = 73, Kimura (unadjusted) = 51.08 Transitions / transversions = 1.14 (73/64) Gap_init rate = 0.03 (13 / 382), avg. gap size = 2.77 (36 / 13) 514 30.60 6.26 2.54 chrXptel1M 986403 987009 (12991) L1M5_orf2#LINE/L1 2079 2707 (587) m_b351s551i3 14712 chrXptel1M 986403 AGAAATAAAACTATTACTCTTTTCAAATGATGTGATGGCATACTTAAAGA 986452 i i?i v iv i ii v i? v i i L1M5_orf2#LIN 2079 AGAAATAAAACTGTCNTTATTCGCAGATGACATGATTGTNTACGTAGAAA 2128 chrXptel1M 986453 ATTCTAGAGAATCAACTGAAAAACTATTTGGAACAATTAACAACTTTAGC 986502 i ? i v vi ? i v i vi v iii v L1M5_orf2#LIN 2129 ATCCNAAAGAATCTACAAANAAACTACTAGAACTAATAAGTGAATTTAGC 2178 chrXptel1M 986503 CAAGTTGTAGGATATAAAATAAACCTACATAAATCATCAGCATTTCTATA 986552 v i i i? i ii v iv v viv i L1M5_orf2#LIN 2179 AAGGTCGCNGGATACAAGGTCAATATACAAAAATCAATTGTATTTCTATA 2228 chrXptel1M 986553 -ATTGACCAAAAAAGCCCAGCAGCTAGAGATAGAAA---GAGAA--AAT- 986595 - i - v v ------ ii i i vv ---? i -- - L1M5_orf2#LIN 2229 TACT-AGCAACAAA------CAATTGGAAAATGAAATTTNAAAAACAATA 2271 chrXptel1M 986596 TCATTTAAAATAACTGGAGATTACATAAAATATTTGGGAGTCTACCTGCC 986645 i v i vvv i vv ? i i i vv i iv L1M5_orf2#LIN 2272 CCATTTACAATAGCATCAAAAAACATNAAATACTTAGGAATAAATCTAAC 2321 chrXptel1M 986646 AAGACAAATGCAGGAAGTATA---TGAACACAATCACAAAACATCTTTCA 986692 i ? vi i vv ? --- --- ii ivi v L1M5_orf2#LIN 2322 AAAANATGTGCAAGACCTNTACACTGAA---AACTACAAAACATTGCTGA 2368 chrXptel1M 986693 CACAGGTAAAGTCAGATCTAAATAACTGGAAA---ATAGC-------TGA 986732 v v ii v ivv i v i --- v ------- i L1M5_orf2#LIN 2369 GAGAAATTAAAGAAGACCTAAATAAATGGAGAGATATACCATGTTCATGG 2418 chrXptel1M 986733 GCTG---------ATATAATAAAAATGACAGTTCTCCCTAAATTAATCT- 986772 ii --------- vi ? i v i i i - L1M5_orf2#LIN 2419 ATTGGAAGACTCAATATTGTNAAGATGTCAATTCTCCCCAAATTGATCTA 2468 chrXptel1M 986773 ---ATCTAATGCCATATCAATAAAACTCCCAAGAAATTCTTTTATAGAGC 986819 --- ii v vi v v iv ii i i iv L1M5_orf2#LIN 2469 TAGATTCAATGCAATCCCAATCAAAATCCCAGCAGGTTTTTTTGTAGAAA 2518 chrXptel1M 986820 TAGA-AAAATAGTAACACAATTCATCTGCAAGAACAAAAGGTCAAGAATA 986868 v - iv ii vvi v i v v ivi i ii ? L1M5_orf2#LIN 2519 TTGACAAGCTGATTCTAAAATTTATATGGAAATGCAAAGGACCNAGAATA 2568 chrXptel1M 986869 TAACAGGA-AATACT-AAAAAAAATAATGCAATGGAAAGGGGCCTAGCTA 986916 -iv ii - vi - i v iiv i v i -- i i - vv L1M5_orf2#LIN 2569 -GCCAAAACAATCTTGAAAAAGAAGAACAAAGTTGGA--GGACTTA-CAC 2614 chrXptel1M 986917 TACCAAATC-AAAAACGATATTATAAAGCAGTAGTCATCAAAACCACTTG 986965 ?i ?-v i v- vii v i viiv L1M5_orf2#LIN 2615 TACCNGATNTCAAGACT-TATTATAAAGCTACAGTAATCAAGACAGTGTG 2663 chrXptel1M 986966 ATACTGGC-TAAGAAATAGAGTAGTTGATCAGTGCCACAGGTTAG 987009 i i - -i vv i v i vv iv L1M5_orf2#LIN 2664 GTATTGGCGTAAG-GATAGACAAATAGATCAATGGAACAGAATAG 2707 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.16 CpG sites = 105, Kimura (unadjusted) = 41.77 Transitions / transversions = 1.38 (105/76) Gap_init rate = 0.05 (30 / 606), avg. gap size = 1.80 (54 / 30) 479 30.36 1.89 2.67 chrXptel1M 987401 987664 (12336) L1ME4a_3end#LINE/L1 313 574 (297) m_b351s551i4 14712 chrXptel1M 987401 TTCTGGAGAGCAATTTGGAACTATGC-CCAAAGGGCATAAAACTGTGCAT 987449 i v v i-i i v v v ? L1ME4a_3end#L 313 TTCTGGAGGGCAATTTGGCAATATGTATCAAAAGCCTTAAAAATGTNCAT 362 chrXptel1M 987450 TCCCTTTGATCCAGCAAAACCACTATGAAAAATCCGTACTCCAAAGAGAA 987499 v i i vv viv ii i-- ii i i i v L1ME4a_3end#L 363 ACCCTTTGACCCAGTAATTCCACTTCTAGGAATT--TATCCTAAGGAAAT 410 chrXptel1M 987500 CATAAAAAAGGGGAA--AGGACCCATATGTGCAAAAACAGTTATAGCAGC 987547 v v i i v v ? -- i ii-- i ii iiv i v L1ME4a_3end#L 411 AATCAGAGATGTGNACAAAGATT--TATGTACAAGGATGTTCATCGCAGC 458 chrXptel1M 987548 --TCTTTGCAGTGGCAAATAATTGGAAATTGTATGGATGCTCATCAATAG 987595 -- v ii i i i v iviiv ii ii v L1ME4a_3end#L 459 ATTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAG 508 chrXptel1M 987596 GAGAATGGCTAAATAAACTGTGGCACGCGAATGTAATGACATACTACTAT 987645 i ? i i i i iivv i? iv i - ii L1ME4a_3end#L 509 GGGANTGGTTAAATAAATTATGGTACATCCATANAATGGAATATTA-TGC 557 chrXptel1M 987646 CGTTCTATAAAAAATGATG 987664 v -- i v ? L1ME4a_3end#L 558 AG--CCATTAAAAATNATG 574 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 41.16 CpG sites = 51, Kimura (unadjusted) = 41.89 Transitions / transversions = 1.89 (51/27) Gap_init rate = 0.04 (10 / 263), avg. gap size = 1.20 (12 / 10) 1008 33.75 5.99 2.66 chrXptel1M 988128 988745 (11255) C L2#LINE/L2 (447) 2635 1998 m_b351s601i12 14711 chrXptel1M 988128 TAAAAGCAAAATTGGCAGGCCTTGTCAACACAATGGATGTGGTGGATAAG 988177 i i i i iii i vi iii iiv v v vi i C L2#LINE/L2 2635 TGAAGGTAGAGCCGACAGGATTTGCTGATGGATTGGATGTGGGGTGTGAG 2586 chrXptel1M 988178 AGATACTGAGGAGTTGAGGGTAAGTCCTAGGTTGCAAGGCTGAGGTACTG 988227 v vv ii i i v v vivi v vv C L2#LINE/L2 2585 AGAAAGAGAGGAGTCAAGGATGACTCCAAGGTTTTTGGCCTGAGCAACTG 2536 chrXptel1M 988228 GGAGGATGGTGTTGGTTTCCAAAATAATAGGGACAGTAATTGGGAGAGC- 988276 i v viv i? vvivi i viiiviiv ii - C L2#LINE/L2 2535 GAAGGATGGAGTTGCCATTNACTGAGATGGGGAAGACTGCGGGAGGAGCA 2486 chrXptel1M 988277 ---CTCATAG---AGATAATGAGTTTTATTCTGGAGATATTAAGTTTAAG 988320 ---i v vi --- v v ivi i v i i C L2#LINE/L2 2485 GGTTTGAGGGGGAAGATCAGGAGTTCAGTTTTGGACATGTTAAGTTTGAG 2436 chrXptel1M 988321 ATGTTTGCTGTACTTCCAGTTCAAGATATCTG--AGACAATTGGAAAGA- 988367 ii ii iv v iv vi i vi-- i i v v - C L2#LINE/L2 2435 ATGCCTATTAGACATCCAAGTGGAGATGTCGAGTAGGCAGTTGGATATAC 2386 chrXptel1M 988368 GAGATTAGAGT-----AAAGAGGTTAGAGAAGAATATGTAAATTGGAGGA 988412 vi i -----ii iv i vv i v i v i ii C L2#LINE/L2 2385 GAGTCTGGAGTTCAGGGGAGAGGTCCGGGCTGGAGATATAAATTTGGGAG 2336 chrXptel1M 988413 TCCTCAACATAGAGCTGCTAATTAAATCCATGGGAGCTGAA-GAGAATAT 988461 v i v v v v v i - i - vi i C L2#LINE/L2 2335 TCATCAGCATATAGATGGTATTTAAAGCCATGAGA-CTGGATGAGATCAC 2287 chrXptel1M 988462 CTAAT-----ATTATGAAGAGAGAAGAGCA----CCCTATAAA-GAATCT 988501 ? iv----- v i ii v v ----i v vi v- ii i C L2#LINE/L2 2286 CNAGGGAGTGAGTGTAGATAGAGAAGAGAAGAGGTCCAAGGACTGAGCCC 2237 chrXptel1M 988502 TGTGTGATGATTC--TGGATAGAGGGTGGGATCTAGATGAAGATG---CA 988546 v vv i-- i --i vv? vi i--- i v --- C L2#LINE/L2 2236 TGGGGCAC--TCCAACGTTNAGAGGTCGGGG---AGATGAGGAGGAACCA 2192 chrXptel1M 988547 ACCAAGGAGACAAAAAAAGAAGCAGTCAAATGCTTAGATAGGATAGGAGA 988596 i v vi i i - i i i--------- ii i i C L2#LINE/L2 2191 GCAAAGGAGACTGAGAAGGA-GCGGCCAG---------TGAGGTAGGAGG 2152 chrXptel1M 988597 TAGAACTAGGAGAGAGTGCTGTCCAGAAAACCTAGAGAGAAGAGAGTACC 988646 - i i v v v i i v v ii i v vi C L2#LINE/L2 2151 -AAAACCAGGAGAGTGTGGTGTCCTGGAAGCCAAGTGAAGAAAGTGTTTC 2103 chrXptel1M 988647 AAGGAGAAAAAAGTGTTCA----TGTCAAAGGCTGCAGAGAAGTCAAGGA 988692 i i iii v ---- v v ? i v C L2#LINE/L2 2102 AAGAAGGAGGGAGTGATCAACTGTGTCAAATGCTGCTGANAGGTCAAGTA 2053 chrXptel1M 988693 AAATGAAAATTGGGAGAAG-CTA-TGGATTTACCAATTGAGAGATTATTG 988740 i ii i i ivv - i - v ivvi i i C L2#LINE/L2 2052 AGATGAGGACTGAGAATTGACCATTGGATTTAGCAACGTGGAGGTCATTG 2003 chrXptel1M 988741 GTAAC 988745 i C L2#LINE/L2 2002 GTGAC 1998 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 45.21 CpG sites = 121, Kimura (unadjusted) = 47.15 Transitions / transversions = 1.48 (121/82) Gap_init rate = 0.05 (32 / 617), avg. gap size = 1.69 (54 / 32) 569 34.92 9.55 3.80 chrXptel1M 989331 989979 (10021) C L2#LINE/L2 (1079) 2003 1319 m_b351s601i13 14711 chrXptel1M 989331 GGTAACTTTGGGGAGAGCAGTTTCATTGAAACTATAG---CAGAAACTGT 989377 i i ivi iv i iivi i --- ii i ivv C L2#LINE/L2 2003 GGTGACCTTGACAAGAGCAGTTTCGGTGGAGTGGTGGGGACGAAAGCCTG 1954 chrXptel1M 989378 ATGCTAAGGGGTT--AGAGGAAATGACA----------TGGAAGCACCTA 989415 vvv iv -- ii iv ---------- ii v v C L2#LINE/L2 1953 ATTGGAGTGGGTTCAAGAGAGAATGGGAGGAGAGGAATTGGAGACAGCGA 1904 chrXptel1M 989416 TTTTAGGCAGTCTTTTCAAGGATTTTAATCATAAAGGGCAGAAGATATGT 989465 v v i iiii i v viiii v v v vi C L2#LINE/L2 1903 GTATAGACAACTCTTTCGAGGAGTTTTGCTGTAAAGGGGAGCAGAGAAAT 1854 chrXptel1M 989466 AGAATGAAAGTTATGGTGGAA-----GATCAATGGAGGGTTGTTGTTGTT 989510 i iii iv i ivi v i ----- i v ii v --- C L2#LINE/L2 1853 GGGGCGGTAGCTGGAGGGGGANGTGGGGTCAAGGGAGAATTTTTGTT--- 1807 chrXptel1M 989511 ATTGTTGTTGTTTTCCAGAATGGGAGAGACAGGGACATATCTGTAGGAAG 989560 ----------- iv ii i i?ivii i i v vv C L2#LINE/L2 1806 -----------TTTTAAAGATGGGAGAAATNACAGCATGTTTGTATGCTG 1768 chrXptel1M 989561 -TAGGAGAGAGCCAGTAGACAGGAAAAGAATGAACATAAATGAAAGGGTA 989609 - i iv v v i i v vv iv v i i vi C L2#LINE/L2 1767 ATGGGAATGATCCAGTAGAGAGGGAAAAATTGATGATGCAGGAGAGAGAG 1718 chrXptel1M 989610 GGAATGACATGGGGGGACAGGCAATTTGTTGGAGGAACCGAGATGTATTG 989659 i - - v vv --- i v vi v v iv v viv C L2#LINE/L2 1717 GGGA-GA-ATTGCTGGA---GCGATGTCCTTGAGTAGGCGAGAGGGGATG 1673 chrXptel1M 989660 AGATGATTTAAACTAGTAGCGGAACTGGCCATT--------GTAAAGATA 989701 i vvvv iv v i v iii - -------- i vi i C L2#LINE/L2 1672 GGATCTAGTGCACAAGTGGAGGGGTTGGCC-TTAGATAGGAGCACGGACA 1624 chrXptel1M 989702 CTTCATC-------ATATGAGACAGG----AATA-------ATACATCTG 989733 v ------- i v iv i ---- i ------- i v vii C L2#LINE/L2 1623 GTTCATCCGTAGTAACAGGAGGGAAGGCAGAGTATGTGGGCACAGATGCA 1574 chrXptel1M 989734 AGT-GGTGTG-AGATGAGGAGGGGAGAAGATTCATGGCAAATGTCCT-TA 989780 i - v - v v v i i?? --i v iv v i - i C L2#LINE/L2 1573 GGTAGGTGGGTAGATGTGGTGGTGGGAGNNT--GTGGAAGTTCTCTTCTG 1526 chrXptel1M 989781 AT-------ATTTTT--GGTAACATATGAGGCAAGATTCTCAGCTGAAAG 989821 ------- i--i i v v i i iv i C L2#LINE/L2 1525 ATTGCTTCTATTTTCTCAGTGAAATAGGAAGCAAGGTCATCAGCTGAGAG 1476 chrXptel1M 989822 GGTGGGAAGAGGTCAAGCTA-TGGAAGTTTGGAAAAGAGATGAAAACATG 989870 v v iv i vvi v i- i - ii v i vi C L2#LINE/L2 1475 TGAGGATAGGGGAGGAGGTGTTGGAGGTTT-GAGGAGAGAGGAGAAGGTG 1427 chrXptel1M 989871 TAGAAGAACC-TCTGGGGAAAGTGAGATAGTGAGTTGATTACACAGATAT 989919 ii v ii - -i i i v i v i viv i i C L2#LINE/L2 1426 TGAAATAGTCGTCT-AGGAGAGTGGGAGAGTGAATGGACTAGGGAAATGT 1378 chrXptel1M 989920 ACAAAGATTTCCTAGCAGCACTGGGGGCCCAGCTGAAGTTGTGTAA-CAT 989968 vv ? v vi i ii vi i -? ii- C L2#LINE/L2 1377 AGTANGATTGCCGGGCAGCATTAAGGGCCCACTTGAGGTT-NGTGGTCAT 1329 chrXptel1M 989969 AAACTGTAAAG 989979 i i - C L2#LINE/L2 1328 GAATT-TAAAG 1319 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 47.63 CpG sites = 127, Kimura (unadjusted) = 49.57 Transitions / transversions = 1.40 (127/91) Gap_init rate = 0.07 (43 / 648), avg. gap size = 2.05 (88 / 43) 37 0.00 0.00 0.00 chrXptel1M 990331 990362 (9638) (TA)n#Simple_repeat 1 32 (0) c_b351s251i5 14713 chrXptel1M 990331 TATATATATATATATATATATATATATATATA 990362 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATA 32 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 290 17.78 0.00 4.84 chrXptel1M 990384 990448 (9552) C DNM1r#Unknown (2122) 2540 2479 m_b351s502i2 14714 chrXptel1M 990384 TACGTGTGTGTGTGTATATATACATATATACACACATATAGAATACAAAT 990433 i i i iiii i i --- i v C DNM1r#Unknown 2540 TACGTATATATACACATATATACACACATACACACATAT---ACACACAT 2494 chrXptel1M 990434 ATATACACACATACA 990448 C DNM1r#Unknown 2493 ATATACACACATACA 2479 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 21.50 CpG sites = 10, Kimura (unadjusted) = 21.50 Transitions / transversions = 10.00 (10/1) Gap_init rate = 0.05 (3 / 64), avg. gap size = 1.00 (3 / 3) 969 28.16 1.93 1.93 chrXptel1M 990852 991213 (8787) L1ME3A_3end#LINE/L1 190 551 (369) m_b351s551i5 14715 chrXptel1M 990852 TACCACTACACACCTGTCAGATTGGCTAGAATGACAGGAAAAGATAATGC 990901 iii v i v iii v i i L1ME3A_3end#L 190 TACCACTACACACCCACCAGAATGGCTAAAATGAAAAAGACAGACAATAC 239 chrXptel1M 990902 GGAATGCTGG---AGATGTGGAAAAACCGGGACACTGATGCATTGTTGGT 990948 vi i i ---i iv i v v i i i L1ME3A_3end#L 240 CAAGTGTTGGCGAGGATGTGGAGCAACCGGAACTCTCATACACTGCTGGT 289 chrXptel1M 990949 GGAATTGTGAATACATCCAGCCATTCTGGAGAGCGATTTGGAACTGTGTT 990998 i v i vvi v i i i i i vi v v i v v L1ME3A_3end#L 290 GGGAGTGTAAATTGGTACAACCACTTTGGAAAACTGTTTGGCAGTATCTA 339 chrXptel1M 990999 CAAAAACTTATCAAACGGTGCATACCCTTTGATCCAGCAGTGCTATTACT 991048 v i v v v --- v i i v i i v L1ME3A_3end#L 340 CTAAAGCTGAACATA---TGCATACCCTATGACCCAGCAATTCCACTCCT 386 chrXptel1M 991049 GGGTTTATATCCCAAAGAGAT-CTTAAAGAAG---AGAAAGGGACCTGTA 991094 i v i v v i - v v v v --- vv ii ---- L1ME3A_3end#L 387 AGGTATATACCCAACAGAAATGCGTACATATGTTCACCAAAAGAC----A 432 chrXptel1M 991095 TGTGCCAAAATGTCTGTGGCAGCCCTGTTTGTAGTGGCCAGAAACTGGAA 991144 i v i iii i v i i i i ?? L1ME3A_3end#L 433 TGTACAAGAATGTTCATAGCAGCACTATTCGTAATAGCCNNAAACTGGAA 482 chrXptel1M 991145 ACTGAGTGGATGCCCATCAATTGAAGAATGGCTGAATAAATTGTGGTATA 991194 ?ivviii i iv v v i L1ME3A_3end#L 483 ACNACCCAAATGTCCATCAACAGTAGAATGGATAAATAAATTGTGGTATA 532 chrXptel1M 991195 TGAATATTATGGAATATTA 991213 vv i iv i L1ME3A_3end#L 533 TTCACACAATGGAATACTA 551 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.14 CpG sites = 58, Kimura (unadjusted) = 36.60 Transitions / transversions = 1.38 (58/42) Gap_init rate = 0.03 (10 / 361), avg. gap size = 1.40 (14 / 10) 12 18.27 5.41 0.00 chrXptel1M 991575 991611 (8389) (TATACT)n#Simple_repeat 1 39 (0) m_b351s252i16 14716 chrXptel1M 991575 TATACATATA-TTGTATTTA-ACTTATACTTTAACATAT 991611 v - i i - vv v (TATACT)n#Sim 1 TATACTTATACTTATACTTATACTTATACTTATACTTAT 39 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 319 22.11 9.68 8.80 chrXptel1M 994078 994201 (5799) C MIRc#SINE/MIR (142) 126 2 m_b351s601i14 14717 chrXptel1M 994078 TGAGGC--AATGGGACTAAGGGACTTGCTCG----------GCTAATAAG 994115 -- iv i ii v i i---------- i C MIRc#SINE/MIR 126 TGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAG 77 chrXptel1M 994116 TGTCTGAGGCCGGATTGGAACTCGGGAAGAAGAGTCTTCCTGGATCCAAG 994165 v v v v i v i i -------- iv C MIRc#SINE/MIR 76 TGGCAGAGCCGGGACTCGAACCCAGG--------TCTTCCTGACTCCAAG 35 chrXptel1M 994166 TCCAGTGCTCTATCCACCGTGACAGCTAGCTGCCTC 994201 v i --- v vvi C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTG---CACCACACTGCCTC 2 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 26.46 CpG sites = 13, Kimura (unadjusted) = 26.46 Transitions / transversions = 1.08 (13/12) Gap_init rate = 0.11 (13 / 123), avg. gap size = 1.77 (23 / 13) 424 20.99 4.95 0.95 chrXptel1M 994658 994758 (5242) C MIR#SINE/MIR (113) 149 45 m_b351s601i15 14718 chrXptel1M 994658 TTCTCCTCATTTTACAGATGAGGAAAGTGAGGCA-----AAGTTAAGTTG 994702 v i v ----- i - i C MIR#SINE/MIR 149 TTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAG-TA 101 chrXptel1M 994703 ACTTGCCCGGGGTCACAAGGCTAGGAAGTGTCTGGGGCCAGATGGGAATT 994752 ii vi v v v i v vi vv ii C MIR#SINE/MIR 100 ACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACC 51 chrXptel1M 994753 TAGGCA 994758 i C MIR#SINE/MIR 50 CAGGCA 45 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.86 CpG sites = 11, Kimura (unadjusted) = 24.86 Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.02 (2 / 100), avg. gap size = 3.00 (6 / 2) 501 25.91 9.57 1.48 chrXptel1M 995591 995778 (4222) MIRb#SINE/MIR 48 250 (18) m_b351s601i16 14719 chrXptel1M 995591 GGCGGACCCGAGTTCCAATTTGGCGGCATAAACTAC---CTAGCTTTGTG 995637 i i i i v ii-- - vvi i --- v MIRb#SINE/MIR 48 GACAGACCTGGGTTCGAATCC--CGGC-TCTGCCACTTACTAGCTGTGTG 94 chrXptel1M 995638 ACCCTGAGCAAATACCTTAACCTGTCT--GCCT--GTTTCCTCATTTCTA 995683 i i i vv v -- -- i v MIRb#SINE/MIR 95 ACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTA 144 chrXptel1M 995684 GAGTGGGAATAAAAACA--------GCA--GCCACTCCCAGGAGTAAAGG 995723 i i i v i -------- -- iiii viv v v MIRb#SINE/MIR 145 AAATGGGGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATG 194 chrXptel1M 995724 AGAAGATGGAT-TAAAGCACTCAGCACGGTGCCCGGCACCAACGAAGTGC 995772 vi v - i i i i vv vv i MIRb#SINE/MIR 195 AGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGC 244 chrXptel1M 995773 CCATTA 995778 i v MIRb#SINE/MIR 245 TCAATA 250 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 30.92 CpG sites = 28, Kimura (unadjusted) = 32.54 Transitions / transversions = 1.40 (28/20) Gap_init rate = 0.05 (9 / 187), avg. gap size = 2.33 (21 / 9) 12 11.65 3.33 3.33 chrXptel1M 996250 996279 (3721) (CTCA)n#Simple_repeat 1 30 (0) m_b351s252i17 14720 chrXptel1M 996250 CTCAACTGACTC-CTCACTCACTCAATCTCT 996279 - v - v v (CTCA)n#Simpl 1 CTC-ACTCACTCACTCACTCACTCACTCACT 30 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.07 (2 / 29), avg. gap size = 1.00 (2 / 2) 14 13.94 2.22 6.98 chrXptel1M 996850 996894 (3106) (TAAAAA)n#Simple_repeat 1 43 (0) m_b351s252i18 14721 chrXptel1M 996850 TAAAAATTAAATAATGTAAA-ACAAATACAAAATAGAAAAAAAAAT 996894 - - iv - v - i v (TAAAAA)n#Sim 1 TAAAAA-TAAA-AATAAAAATAAAAATA-AAAATAAAAATAAAAAT 43 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.09 (4 / 44), avg. gap size = 1.00 (4 / 4) 269 22.13 1.95 9.03 chrXptel1M 998176 998329 (1671) C Charlie1a#DNA/hAT-Charlie (46) 1409 1266 m_b351s502i3 14722 chrXptel1M 998176 AAAGTTTTTGAGAACAA-AAAGAGCTTTT-TTAAAAAAAATATATGAGTT 998223 i v i vv- - -------- i i C Charlie1a#DNA 1409 AAAATTATTGAGGACCCCAAAGAGCTTTTGTT--------TATGTGGGTT 1368 chrXptel1M 998224 GTAGCATTAAATGTTTACTATAATAGAAAT-GAAGCTGAAAAACTTTTAA 998272 i v vv vi i i v -i i i i C Charlie1a#DNA 1367 ATATCTATCGATATTTACCATATTAGAAATTAAAACTGAGAAATTTTTAA 1318 chrXptel1M 998273 AATATATATTTATTAATTTACTGTAAAAGGACAATGATACTCATTATATA 998322 v v v ---- vi i i - i i i C Charlie1a#DNA 1317 AATATTTATTAATTCATTTA----AAAATAATAATAA-ACCCATTACATG 1273 chrXptel1M 998323 TCAACAT 998329 i C Charlie1a#DNA 1272 TTAACAT 1266 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 25.58 CpG sites = 19, Kimura (unadjusted) = 26.56 Transitions / transversions = 1.58 (19/12) Gap_init rate = 0.10 (16 / 153), avg. gap size = 1.00 (16 / 16) 412 25.22 0.00 2.36 chrXptel1M 998630 998759 (1241) Charlie4a#DNA/hAT-Charlie 382 508 (0) m_b351s502i4 14723 chrXptel1M 998630 ATTGTTTACCTTTGTAAGTCTTGCACATTTCATCTAATGCATTTCATAAC 998679 v v - i iiii i i v v v Charlie4a#DNA 382 ATTGGTTTCCTTTGTAA-TCCTATGTATTTTATTTTATGCATTTAAAAAC 430 chrXptel1M 998680 ATTATTTTGAGAAGGGAACCCCCAAGCTTCAGCAGAACTCCCCAGGGATC 998729 i -ii vi i v viv vv i Charlie4a#DNA 431 ATTATTCTGAGAAGGG-GTCCATAGGCTTCACCAGACTGCCAAAGGGGTC 479 chrXptel1M 998730 CATGGTACCAAAAACAGGTAAGAGGCCCCG 998759 i - vi v iv i Charlie4a#DNA 480 CATGGCA-CAAAAAAGGTTAAGAACCCCTG 508 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 31.25 CpG sites = 18, Kimura (unadjusted) = 31.25 Transitions / transversions = 1.29 (18/14) Gap_init rate = 0.02 (3 / 129), avg. gap size = 1.00 (3 / 3) 16 22.98 0.00 0.00 chrXptel1M 999167 999204 (796) (ATAC)n#Simple_repeat 1 38 (0) m_b351s252i19 14724 chrXptel1M 999167 ATACGTACATACGTACATATATATACACACACATATAT 999204 i i i i i i i (ATAC)n#Simpl 1 ATACATACATACATACATACATACATACATACATACAT 38 Matrix = Unknown Transitions / transversions = 1.00 (7/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 13 12.78 1.85 12.24 chrXptel1M 999513 999566 (434) (ATAC)n#Simple_repeat 1 49 (0) m_b351s252i20 14725 chrXptel1M 999513 ATTCATAACATTACATACATATAAAACATACATTATATATATAACATTAC 999562 v - - -v v - i i - - (ATAC)n#Simpl 1 ATACAT-ACA-TACATACATA-CATACATACA-TACATACAT-ACA-TAC 44 chrXptel1M 999563 A-ACA 999566 - (ATAC)n#Simpl 45 ATACA 49 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.13 (7 / 53), avg. gap size = 1.00 (7 / 7) 725 28.30 5.28 3.20 chrXptel1M 999571 999968 (32) C L1ME4a_3end#LINE/L1 (318) 553 148 m_b351s551i6 14726 chrXptel1M 999571 AATATTCAATTATATTCATGTGCCATAATGTGTTTAGCTATTCCCCAAAT 999620 v ? vv i v i i i ? v v C L1ME4a_3end#L 553 AATATTCCATTNTATGGATGTACCATAATTTATTTAACCANTCCCCTATT 504 chrXptel1M 999621 GATGGGCATTTGCTTTATTTCCCACTCTGTGTTACCACTTTAAAAAGTAC 999670 v i ivv i v i i vi i ii --- v i i C L1ME4a_3end#L 503 GTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTA---TAAATAATGC 457 chrXptel1M 999671 TGCTATAAAGAT--TTGGATGTTAATCAAGACTTTCTTCATATC---AAT 999715 v i v -- v ii v ----- v ? i ---i C L1ME4a_3end#L 456 TGCGATGAACATCCTTGTACATAAATC-----TTTGTNCACATCTCTGAT 412 chrXptel1M 999716 TACTTCCTTGAGGTATTAGTTTCTAAA---GGAATCATCAGGTTAAA--- 999759 i ii i -- i i i --- i iii i --- C L1ME4a_3end#L 411 TATTTCCTTAGGATA--AATTCCTAGAAGTGGAATTACTGGGTCAAAGGG 364 chrXptel1M 999760 ------CATTTTACTCACTCTATT--TGCATAATTCCAAATTGCTTTCCA 999801 ------ -- v vv v -- i v v ii C L1ME4a_3end#L 363 TATGNACATTTT--TAAGGCTTTTGATACATATTGCCAAATTGCCCTCCA 316 chrXptel1M 999802 AAATGGTTGTATCTATTTACAATTCCACCAACAATGCATTAATGTGCCTA 999851 i v i v v i i i i v iv ii C L1ME4a_3end#L 315 GAAAGGTTGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTGCCCG 266 chrXptel1M 999852 TGT-TCCACAGCCCTGCCAATACGGACTATTACC-ATCTTTTGTCATCTT 999899 v -? v ii i v iv i - i-v C L1ME4a_3end#L 265 TTTCNCCACACCCTCGCCAACACTGGGTATTATCAATCTTTTA-AATCTT 217 chrXptel1M 999900 TACTACTTTGCAGGGTTTGAGGTGAAATCTCAGAGTGACTTCAATGTGTA 999949 i i v vvi vvi ii iv vv vii i v i C L1ME4a_3end#L 216 TGCCAATTTGATAGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCA 167 chrXptel1M 999950 TTTTTCTTCTTATTAGTGA 999968 i i vv i C L1ME4a_3end#L 166 TTTCTTTGATTACTAGTGA 148 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 35.67 CpG sites = 64, Kimura (unadjusted) = 37.00 Transitions / transversions = 1.42 (64/45) Gap_init rate = 0.05 (21 / 397), avg. gap size = 1.62 (34 / 21) 15 15.26 3.45 0.00 chrXqtel1M 114 142 (999858) (TA)n#Simple_repeat 1 30 (0) m_b352s252i0 14727 chrXqtel1M 114 TAAATAAATAT-TATTTACATATATATATA 142 v v - v i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATA 30 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1) 72 1.53 0.00 0.00 chrXqtel1M 1087 1152 (998848) (AT)n#Simple_repeat 1 66 (0) c_b352s251i0 14728 chrXqtel1M 1087 ATATATATATATATATAAATATATATATATATATATATATATATATATAT 1136 v (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chrXqtel1M 1137 ATATATATATATATAT 1152 (AT)n#Simple_ 51 ATATATATATATATAT 66 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0) 12 22.42 0.00 2.70 chrXqtel1M 1785 1822 (998178) (TTTTC)n#Simple_repeat 1 37 (0) m_b352s252i1 14729 chrXqtel1M 1785 TTTTCTTTTTCCTTTGTTTTCTTTACTGTCGTTTTGTT 1822 - i v v v iv v (TTTTC)n#Simp 1 TTTTC-TTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTT 37 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1) 17 23.23 1.69 3.45 chrXqtel1M 3122 3180 (996820) (TTTTTC)n#Simple_repeat 1 58 (0) m_b352s252i2 14730 chrXqtel1M 3122 TTTTACTTATGACTTTTCGTTTTCTTTTT-TTTTTTTTTTTCATAATAGC 3170 v v vvi v - i - -v vv (TTTTTC)n#Sim 1 TTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTC-T-TTTTC 48 chrXqtel1M 3171 TTTTTATTTT 3180 v (TTTTTC)n#Sim 49 TTTTTCTTTT 58 Matrix = Unknown Transitions / transversions = 0.22 (2/9) Gap_init rate = 0.05 (3 / 58), avg. gap size = 1.00 (3 / 3) 18 12.16 0.00 0.00 chrXqtel1M 3135 3161 (996839) (T)n#Simple_repeat 1 27 (0) m_b352s252i3 14731 chrXqtel1M 3135 TTTTCGTTTTCTTTTTTTTTTTTTTTT 3161 iv i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTT 27 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 17 23.23 1.69 3.45 chrXqtel1M 3122 3180 (996820) (TTTTTC)n#Simple_repeat 1 58 (0) m_b352s252i2 14730 chrXqtel1M 3122 TTTTACTTATGACTTTTCGTTTTCTTTTT-TTTTTTTTTTTCATAATAGC 3170 v v vvi v - i - -v vv (TTTTTC)n#Sim 1 TTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTC-T-TTTTC 48 chrXqtel1M 3171 TTTTTATTTT 3180 v (TTTTTC)n#Sim 49 TTTTTCTTTT 58 Matrix = Unknown Transitions / transversions = 0.22 (2/9) Gap_init rate = 0.05 (3 / 58), avg. gap size = 1.00 (3 / 3) 16 0.00 0.00 7.69 chrXqtel1M 3247 3274 (996726) (CTCC)n#Simple_repeat 1 26 (0) m_b352s252i4 14732 chrXqtel1M 3247 CTCCCTCCCTTCCCTCCACTCCCTCCCT 3274 - - (CTCC)n#Simpl 1 CTCCCTCCC-TCCCTCC-CTCCCTCCCT 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.07 (2 / 27), avg. gap size = 1.00 (2 / 2) 17 0.00 0.00 0.00 chrXqtel1M 5871 5889 (994111) (A)n#Simple_repeat 1 19 (0) m_b352s252i5 14733 chrXqtel1M 5871 AAAAAAAAAAAAAAAAAAA 5889 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAA 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 206 32.53 6.82 2.17 chrXqtel1M 5890 5977 (994023) C L2d_3end#LINE/L2 (14) 502 411 m_b352s601i0 14734 chrXqtel1M 5890 AAGAAGCATTTATTGAGTACCCGTAATGTGTCCGTCTCTGTACCGAATAC 5939 v i ii iiiv ii iv v i iiiiii C L2d_3end#LINE 502 AACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTGTGCTAGGCGC 453 chrXqtel1M 5940 ---AGGGAATGGAATTACAAAGAATAAAACA---TCCCTGCTTT 5977 ---i i i? -- v ? v i --- ii C L2d_3end#LINE 452 TGTGGGGAACGANA--AAANAGTATAAGACATGGTCCCTGCCCT 411 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 41.20 CpG sites = 22, Kimura (unadjusted) = 49.08 Transitions / transversions = 3.67 (22/6) Gap_init rate = 0.05 (4 / 87), avg. gap size = 2.00 (8 / 4) 14 10.38 6.25 0.00 chrXqtel1M 6713 6744 (993256) (CCCTC)n#Simple_repeat 1 34 (0) m_b352s252i6 14735 chrXqtel1M 6713 CCTTCCCCT-CCCT-TTCTCCCCTCCCCTCCCCT 6744 i - -ii (CCCTC)n#Simp 1 CCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCT 34 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.06 (2 / 31), avg. gap size = 1.00 (2 / 2) 16 10.04 0.00 8.57 chrXqtel1M 6843 6880 (993120) (AAC)n#Simple_repeat 1 35 (0) m_b352s252i7 14736 chrXqtel1M 6843 AAAAACAAACAACAAGCAAACAACAACAGCAATAACAA 6880 v - - - i i (AAC)n#Simple 1 AACAAC-AACAACAA-C-AACAACAACAACAACAACAA 35 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.08 (3 / 37), avg. gap size = 1.00 (3 / 3) 426 35.71 2.72 3.86 chrXqtel1M 7125 7491 (992509) C L1ME5_3end#LINE/L1 (389) 552 190 m_b352s551i0 14737 chrXqtel1M 7125 ATAATATTCCAGAACATTCATATACCACAATTAATTCAGCCACCGTCTCA 7174 i i viiii v vi v v iii v iv i C L1ME5_3end#LI 552 ATAGTACTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCA 503 chrXqtel1M 7175 CTCATAT---TCCAATTCTTTGTCACCCCCCCCCCCCCACGCACACACTA 7221 v v iv---i iv --- i v vv i v - v v C L1ME5_3end#LI 502 GTGATGGACACCCAGGT---TGCCTCCAACTCCCCGCCAC-CACAAACAA 457 chrXqtel1M 7222 -ACTGCTAAAAACAATTTTTGCACACGTGGGTCCTTTCCCCTTTTTTGTG 7270 -i v vi - ii i i i ---i i vivvvii v C L1ME5_3end#LI 456 CGCTGCAATGAACA-TCCTCGTACATGT---CCCCTTATGGACCTGTGTG 411 chrXqtel1M 7271 A---TCTTTTTCGGATACAGGCCCAATAGTGAAACTGCTGGGTCAATGAA 7317 --- i i v i vi iv i i i vv ii C L1ME5_3end#LI 410 AGAATTTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGG 361 chrXqtel1M 7318 TCGGCACAGTTTTATGTCCCTCTGGGCATGGTTCTATATTGCTCTCTTGA 7367 vv ii vvi -i iivv ii i iv -- i v iv C L1ME5_3end#LI 360 TATGCGTATACTTA-ATTTGACTAAGTACTG--CCAGATTGCTCTCCAGA 314 chrXqtel1M 7368 ATGGCTGGATCACTTCACAACTCCACCAACAATGTATTAGTGTCCCAGTA 7417 v i v ii vii i i i v v i vi ? C L1ME5_3end#LI 313 ATGGCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATN 264 chrXqtel1M 7418 TTACCACATCCCCTCCAGCATTTCTCATGATC---TTTTCCTGTCCTCTT 7464 iv i v i i vv v ---i --- vv i C L1ME5_3end#LI 263 TCCCCACATCCTCGCCAACACTTGGCATTATCCAGCTTTC---TAATTTT 217 chrXqtel1M 7465 AACCAGTCTGAGATGTGTGAAATGGTA 7491 vi i v v i i i C L1ME5_3end#LI 216 TGCCAGTCTAATAGGTGTAAAGTGATA 190 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 48.21 CpG sites = 72, Kimura (unadjusted) = 50.50 Transitions / transversions = 1.33 (72/54) Gap_init rate = 0.05 (18 / 366), avg. gap size = 1.33 (24 / 18) 557 34.21 0.74 1.12 chrXqtel1M 7223 7491 (992509) C L1ME4c_3end#LINE/L1 (373) 457 190 m_b352s551i1 14737 chrXqtel1M 7223 CTGCTAAAAACAATTTTTGCACACGTGGGTCCTTTCCCCTTTTTTG--TG 7270 v vi - i i ii ii i -- i i i i -- v C L1ME4c_3end#L 457 CTGCAATGAACA-TCTTCGTGCATATAG--CTTTTTCCTTCTTTTGAATT 411 chrXqtel1M 7271 ATCTTTTTCGGATACAGGCCCAATAGTGAAACTGCTGGGTCAATGAATCG 7320 i ii v v vv iv i i i v ii vv C L1ME4c_3end#L 410 ATTTCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTAT 361 chrXqtel1M 7321 GCACAGTTTTATGTCCCTCTGGGCATGGTTCTATATTGCTCTCTTGAATG 7370 v v v i ivivi i iv v i v i ivi v C L1ME4c_3end#L 360 GAACATTTTTATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAGG 311 chrXqtel1M 7371 GCTGGATCACTTCACAACTCCACCAACAATGTATTAGTGTCCCAGTATTA 7420 i v i v i ?iv i v ? v v i C L1ME4c_3end#L 310 GTTGTACCAATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCA 261 chrXqtel1M 7421 CCACATCCCCTCCAGCATTTCTCATGATCTTTTCCTGTCCTCTTAACCAG 7470 i ? i v vvvi v vv ii vvvv i vi i i C L1ME4c_3end#L 260 CCGCANCCTCGCCAGCATTGGGTATTATCAATTTTTTAAATTTTTGCTAA 211 chrXqtel1M 7471 TCTGAGATGTGTGAAATGGTA 7491 i i v v i i C L1ME4c_3end#L 210 TTTAATAGGCGTAAAATGGTA 190 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 44.88 CpG sites = 50, Kimura (unadjusted) = 47.75 Transitions / transversions = 1.22 (50/41) Gap_init rate = 0.01 (4 / 268), avg. gap size = 1.25 (5 / 4) 18 12.17 0.00 0.00 chrXqtel1M 7590 7616 (992384) (T)n#Simple_repeat 1 27 (0) m_b352s252i8 14738 chrXqtel1M 7590 TTTGTTGTGTTTTTTTTTTTTTTTTTT 7616 v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTT 27 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 224 27.01 12.12 2.78 chrXqtel1M 8304 8402 (991598) MIRb#SINE/MIR 133 240 (28) m_b352s601i1 14739 chrXqtel1M 8304 TCCTTATCTATACAA-GGGGATGATATTTACAGCTATGTCCCAGGGTTGG 8352 i i v - i --- i v iv v v MIRb#SINE/MIR 133 TCCTCATCTGTAAAATGGGGATAATA---ATACCTACCTCGCAGGGTTGT 179 chrXqtel1M 8353 TGGGAGAA-------ACACAGT---TGCGAAATGTTTAGCGCAGCGCATG 8392 v i ------- v i i --- ii ii i i i v MIRb#SINE/MIR 180 TGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTG 229 chrXqtel1M 8393 GTCCGT-GTAA 8402 iv i - MIRb#SINE/MIR 230 GCACATAGTAA 240 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 33.22 CpG sites = 17, Kimura (unadjusted) = 34.89 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.07 (7 / 98), avg. gap size = 2.14 (15 / 7) 443 22.18 9.09 5.41 chrXqtel1M 8767 8909 (991091) MIRc#SINE/MIR 11 158 (110) m_b352s601i2 14740 chrXqtel1M 8767 TGGTGCAGTGGATAAAAAAACCAGCCCTGAAGTCAGGAGGACCTGAGTTC 8816 - i iv ii v i i i i MIRc#SINE/MIR 11 TGGTGCAGTGGA-AAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chrXqtel1M 8817 AAATCTGGCCTCAAACACTTAACACCTCCTAGCTGTGTGACC-TGGCCAA 8865 i i iv v viv ------- - v MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTGACCTTGGGCAA 102 chrXqtel1M 8866 GTCACTTAA----------TCCCAATTGCCTCAGC--AAAAATAAAAATA 8903 ----------i i i v v --v iiii MIRc#SINE/MIR 103 GTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATA 152 chrXqtel1M 8904 AAAATA 8909 v MIRc#SINE/MIR 153 ATAATA 158 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 25.96 CpG sites = 19, Kimura (unadjusted) = 26.99 Transitions / transversions = 1.73 (19/11) Gap_init rate = 0.08 (11 / 142), avg. gap size = 1.91 (21 / 11) 275 34.29 0.00 0.00 chrXqtel1M 9948 10052 (989948) C L1ME3F_3end#LINE/L1 (438) 552 448 m_b352s551i2 14741 chrXqtel1M 9948 ATAATATTCCAGAACATCCACATCCCATCACTTATTCAGCCATTCTCCAA 9997 vviii vv i v iv i i v vi C L1ME3F_3end#L 552 ATAATATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTCCTG 503 chrXqtel1M 9998 CCGATGGGCGTCCACTCGGTTTCCGGTTTCTGGCCACTAGAAAGAGGGCC 10047 i i i iiivviv i i v i i vi v v i C L1ME3F_3end#L 502 TCGATGGACATTTGGGTTGTTTCCAGTTTTTTGCTATTACGAACAGTGCT 453 chrXqtel1M 10048 GCTAT 10052 C L1ME3F_3end#L 452 GCTAT 448 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 45.71 CpG sites = 21, Kimura (unadjusted) = 47.55 Transitions / transversions = 1.40 (21/15) Gap_init rate = 0.00 (0 / 104), avg. gap size = 0.0 (0 / 0) 17 9.12 0.00 0.00 chrXqtel1M 12267 12290 (987710) (G)n#Simple_repeat 1 24 (0) m_b352s252i9 14742 chrXqtel1M 12267 GGGGGGGGGGGGGGAGGGGGAGGG 12290 i i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGG 24 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 12 23.96 4.55 0.00 chrXqtel1M 12638 12681 (987319) (AAGA)n#Simple_repeat 1 46 (0) m_b352s252i10 14743 chrXqtel1M 12638 AAGAAACAATAAAACAAAGTCA-AAAGAATGAAAAATAG-AAGAAA 12681 v vi v vv - v i v - (AAGA)n#Simpl 1 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 46 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2) 454 21.65 1.60 7.63 chrXqtel1M 12769 12893 (987107) MIRc#SINE/MIR 10 127 (141) m_b352s601i3 14744 chrXqtel1M 12769 GTGGTGCGGTGGCCAGAGCACCAGGCCTGAAGTCAGGAGGACCCGAGTT- 12817 i vv ii i i i i i i - MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chrXqtel1M 12818 AAATCTGACCTCAGACACTTAACGCTTCCTAGCTGTGTGACCCTGGGCAA 12867 i i iviv v v ------- i MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTGACCTTGGGCAA 102 chrXqtel1M 12868 GTCATTTAAAC-CCCCAATTGCCTCAG 12893 i v - i ii -- MIRc#SINE/MIR 103 GTCACTTAACCTCTCTGA--GCCTCAG 127 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 23.97 CpG sites = 18, Kimura (unadjusted) = 26.37 Transitions / transversions = 2.57 (18/7) Gap_init rate = 0.09 (11 / 124), avg. gap size = 1.00 (11 / 11) 16 12.89 4.35 4.35 chrXqtel1M 13386 13431 (986569) (AAGATGT)n#Simple_repeat 1 46 (0) m_b352s252i11 14745 chrXqtel1M 13386 AACATGTAAGAATGTAAGATGTAATCT-TAAGAT-TATGGATATAAGA 13431 v - vv - - -i i (AAGATGT)n#Si 1 AAGATGTAAG-ATGTAAGATGTAAGATGTAAGATGTA-AGATGTAAGA 46 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.09 (4 / 45), avg. gap size = 1.00 (4 / 4) 235 36.40 3.76 3.27 chrXqtel1M 13491 13703 (986297) L1ME2z_3end#LINE/L1 361 574 (617) m_b352s551i3 14746 chrXqtel1M 13491 CCCTTTGATCCGGCAGTCTCACTATTAGATCTGGATCCCAAAGGGATCAT 13540 v i i i ii vi i v vv i v i ii v v L1ME2z_3end#L 361 CCCTATGACCCAGCAATTCCACTCCTAGGTATTTACCCAAGAGAAATGAA 410 chrXqtel1M 13541 ACAAGAGGG----AAAAGGACCCATTTGGGAAAAAAAAGATTTATAGCAA 13586 vv v v v---- i iii ------ v i vi i i L1ME2z_3end#L 411 AACATATGTCCACAAAAAGACTTGT------ACAAGAATGTTCATAGCAG 454 chrXqtel1M 13587 CTCTTTTTGTG-TGGCCAGAGAAGTGGGAATTGAGGGGATGGCCATCAAC 13635 i v ii i- i i - v i iv vvvi i v L1ME2z_3end#L 455 CTTTATTCATAATAGCCAAA-AACTGGAAACAGCCCAGGTGTCCATCAAC 503 chrXqtel1M 13636 TGGGGAGTGCCTGAAGAAATTGGGCTACGTGAACATAACGGAATAGTGCC 13685 v i i vv i v i v v ii vv i i i v i i L1ME2z_3end#L 504 AGGAGAATGGATAAACAAACTGTGGTATATTCATACAATGGAATACTACT 553 chrXqtel1M 13686 ATGCTAT---AAGAAACGAAC 13703 vv v --- i L1ME2z_3end#L 554 CAGCAATAAAAAGGAACGAAC 574 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 51.42 CpG sites = 41, Kimura (unadjusted) = 51.42 Transitions / transversions = 1.21 (41/34) Gap_init rate = 0.05 (10 / 212), avg. gap size = 1.50 (15 / 10) 614 27.37 2.40 3.40 chrXqtel1M 14178 14385 (985615) MIR#SINE/MIR 47 252 (10) m_b352s601i4 14747 chrXqtel1M 14178 CTTGAGTTCAAATTCTGCTTCATATACTTACCACTACCTGTGTTAGCCTG 14227 i i i i i vi vvvi --- v v v i MIR#SINE/MIR 47 CCTGGGTTCGAATCCCGGCTCTGCCACTTAC---TAGCTGTGTGACCTTG 93 chrXqtel1M 14228 AGTAGGGTCACTTT-CCCCTCTATTTATCTGTTTTCTCAACTGCAAAATG 14276 i i i - i v- i i viv v i v i MIR#SINE/MIR 94 GGCAAG-TTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATG 142 chrXqtel1M 14277 GGAATAAAAACAGCACCTACCTCTTGGGGTTGTT-TCAAACTCAAATGAG 14325 i v i i v i - v iiv i MIR#SINE/MIR 143 GGGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAG 192 chrXqtel1M 14326 ATCATCTTATG-AAAATGCTTGGCGTGGTACCTGGTACATAGTAG--GTT 14372 v v v-i - ii i viii i i i-- i MIR#SINE/MIR 193 TTAATA-CATGTAAAGCGCTTAGAACAGTGCCTGGCACATAGTAAGCGCT 241 chrXqtel1M 14373 CAATATAAATGTT 14385 -- MIR#SINE/MIR 242 CA--ATAAATGTT 252 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 32.86 CpG sites = 35, Kimura (unadjusted) = 35.24 Transitions / transversions = 1.75 (35/20) Gap_init rate = 0.05 (11 / 207), avg. gap size = 1.09 (12 / 11) 20 0.00 0.00 0.00 chrXqtel1M 14501 14522 (985478) (G)n#Simple_repeat 1 22 (0) m_b352s252i12 14748 chrXqtel1M 14501 GGGGGGGGGGGGGGGGGGGGGG 14522 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGG 22 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 63 0.00 0.00 0.00 chrXqtel1M 14701 14754 (985246) (AG)n#Simple_repeat 1 54 (0) c_b352s251i1 14749 chrXqtel1M 14701 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 14750 (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chrXqtel1M 14751 AGAG 14754 (AG)n#Simple_ 51 AGAG 54 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 15 23.98 2.38 0.00 chrXqtel1M 15887 15928 (984072) (TCTC)n#Simple_repeat 1 43 (0) m_b352s252i13 14750 chrXqtel1M 15887 TCTTTC-CTTTCTCCCTCTCCCTCCTTCCCTCTCTCTTTCTCT 15928 i - i i i ii i i (TCTC)n#Simpl 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 43 Matrix = Unknown Transitions / transversions = 1.00 (8/0) Gap_init rate = 0.02 (1 / 41), avg. gap size = 1.00 (1 / 1) 240 32.08 0.00 0.00 chrXqtel1M 16675 16727 (983273) C L2d2_3end#LINE/L2 (8) 547 495 m_b352s601i5 14751 chrXqtel1M 16675 AGTCGGTAAACGCTTATTAAGCACCTACTGTGTGTCAGGCACCATACTGA 16724 i iii iii i i iv ii i ii C L2d2_3end#LIN 547 AATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAG 498 chrXqtel1M 16725 GTG 16727 i C L2d2_3end#LIN 497 GCG 495 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 41.41 CpG sites = 16, Kimura (unadjusted) = 49.69 Transitions / transversions = 16.00 (16/1) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 18 19.24 2.27 2.27 chrXqtel1M 17231 17274 (982726) (CT)n#Simple_repeat 1 44 (0) m_b352s252i14 14752 chrXqtel1M 17231 CTCTGCTCT-TCTGTATCTCTTTTTCTCCTTCTCTCTCTTTCTCT 17274 - - v v i i ii i (CT)n#Simple_ 1 CTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 44 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2) 21 17.95 4.29 4.29 chrXqtel1M 18158 18227 (981773) (GAGGG)n#Simple_repeat 1 70 (0) m_b352s252i15 14753 chrXqtel1M 18158 GATGGGATGGGGA-GGGAGGAAGGAGGGGA-GGAAGGAGATGGGGGGGGG 18205 v - - -- - i i v i i (GAGGG)n#Simp 1 GAGGGGA-GGGGAGGGGAGG--GGAGGGGAGGGGAGGGGAGGGGAGGGGA 47 chrXqtel1M 18206 GGGGA-GAGAGAGAAGGGAAGGG 18227 - i i i i (GAGGG)n#Simp 48 GGGGAGGGGAGGGGAGGGGAGGG 70 Matrix = Unknown Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.09 (6 / 69), avg. gap size = 1.00 (6 / 6) 20 21.45 1.67 3.39 chrXqtel1M 18167 18226 (981774) (GGGA)n#Simple_repeat 1 59 (0) m_b352s252i16 14753 chrXqtel1M 18167 GGGAGGGAGGAAGGAGGGGAGGAAGGAGATGG-GGGGGGGGGGGAGAGAG 18215 i ii i - v - i i i (GGGA)n#Simpl 1 GGGAGGGAGGGAGGGAGGGAGGGAGG-GAGGGAGGGAGGGAGGGAGGGAG 49 chrXqtel1M 18216 AGAAGGGAAGG 18226 - i i (GGGA)n#Simpl 50 -GGAGGGAGGG 59 Matrix = Unknown Transitions / transversions = 9.00 (9/1) Gap_init rate = 0.05 (3 / 59), avg. gap size = 1.00 (3 / 3) 21 29.62 0.00 1.52 chrXqtel1M 19789 19855 (980145) (ACAC)n#Simple_repeat 1 66 (0) m_b352s252i18 14754 chrXqtel1M 19789 ACACACGTGCACGCAAACACACAGACACATACGCTGCACACGCACGCACA 19838 iii i v v i i -i i i (ACAC)n#Simpl 1 ACACACACACACACACACACACACACACACACAC-ACACACACACACACA 49 chrXqtel1M 19839 CGTGCACACACACGCAC 19855 iii i (ACAC)n#Simpl 50 CACACACACACACACAC 66 Matrix = Unknown Transitions / transversions = 6.50 (13/2) Gap_init rate = 0.02 (1 / 66), avg. gap size = 1.00 (1 / 1) 16 14.31 4.76 2.33 chrXqtel1M 19819 19860 (980140) (ACGCGC)n#Simple_repeat 1 43 (0) m_b352s252i19 14754 chrXqtel1M 19819 ACGCTGCACACGCACGCACACGTGCA--CACACACGCACGCGCA 19860 - i i i -- i i (ACGCGC)n#Sim 1 ACGC-GCACGCGCACGCGCACGCGCACGCGCACGCGCACGCGCA 43 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.05 (2 / 41), avg. gap size = 1.50 (3 / 2) 510 25.97 7.79 0.00 chrXqtel1M 20629 20782 (979218) C MIRc#SINE/MIR (94) 174 9 m_b352s601i6 14755 chrXqtel1M 20629 AGGTAAAAGAGACAGGT----TTATCCCCATTTGACAGAGAAGGAAACTG 20674 iivii i ---- v vi C MIRc#SINE/MIR 174 AGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTG 125 chrXqtel1M 20675 AGGTTC--AGAAGCAAAAGGATTTGTTCAAAGTTCCAC-GATA--AAGTG 20719 i -- i iv iv i ii i iv - v -- C MIRc#SINE/MIR 124 AGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTG 75 chrXqtel1M 20720 G-GGAG-TGGAATTAGAACTCGGGTC-TCCTGCCTCCAAGTTCCATTTTC 20766 -i -i i i v i i - v i vi vi C MIRc#SINE/MIR 74 GCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTC 25 chrXqtel1M 20767 TTTCAGCTGCTCTGCA 20782 vi v ii C MIRc#SINE/MIR 24 TTTCCACTGCACCACA 9 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 32.15 CpG sites = 27, Kimura (unadjusted) = 33.18 Transitions / transversions = 2.08 (27/13) Gap_init rate = 0.05 (7 / 153), avg. gap size = 1.71 (12 / 7) 221 33.65 7.69 0.00 chrXqtel1M 21731 21834 (978166) L2c_3end#LINE/L2 357 468 (10) m_b352s601i7 14756 chrXqtel1M 21731 TGTTCAGCTCCCTTGTCAGAATGAAAGTTCCTTGAGGGCAGGGGCCGTG- 21779 iiiv iiiiii v vi i i - L2c_3end#LINE 357 TGTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGT 406 chrXqtel1M 21780 ----TTCCTCCCTGGGAGGTCATCTCCTGGCAC---TCAGGAGCTTAAGA 21822 ---- v ii vivvvi v v ---vi v i v L2c_3end#LINE 407 CTTATTCATCTTTGTATCCCCAGCGCCTGGCACATAGTAGGCGCTCAATA 456 chrXqtel1M 21823 ACTGCTGGCTGA 21834 v i v i L2c_3end#LINE 457 AATGTTTGTTGA 468 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 46.14 CpG sites = 20, Kimura (unadjusted) = 46.14 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.03 (3 / 103), avg. gap size = 2.67 (8 / 3) 17 20.83 5.45 0.00 chrXqtel1M 23699 23753 (976247) (CCCCAGC)n#Simple_repeat 1 58 (0) m_b352s252i20 14757 chrXqtel1M 23699 CCCCGCCCCCCCTCCCTTAGGCGCC-GCCCAC-CCCCCCA-CCCCCAGCC 23745 iv vv ii v v - v -v - (CCCCAGC)n#Si 1 CCCCAGCCCCCAGCCCCCAGCCCCCAGCCCCCAGCCCCCAGCCCCCAGCC 50 chrXqtel1M 23746 CCCAGCCC 23753 (CCCCAGC)n#Si 51 CCCAGCCC 58 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.06 (3 / 54), avg. gap size = 1.00 (3 / 3) 14 24.22 3.64 1.79 chrXqtel1M 23700 23754 (976246) (CCCG)n#Simple_repeat 1 56 (0) m_b352s252i21 14757 chrXqtel1M 23700 CCCGCCCCCCCTCCCTTAGGCGCCGCCCACCCCCCCACCC-CCAGCCC-C 23747 v v vivv - i v i - v - (CCCG)n#Simpl 1 CCCGCCCGCCCGCCCGCCCGC-CCGCCCGCCCGCCCGCCCGCCCGCCCGC 49 chrXqtel1M 23748 CAGCCCG 23754 v (CCCG)n#Simpl 50 CCGCCCG 56 Matrix = Unknown Transitions / transversions = 0.38 (3/8) Gap_init rate = 0.06 (3 / 54), avg. gap size = 1.00 (3 / 3) 13 8.48 4.00 0.00 chrXqtel1M 25199 25223 (974777) (CTTCT)n#Simple_repeat 1 26 (0) m_b352s252i22 14758 chrXqtel1M 25199 CTTC-CTACTCTTCCCTTCTCTTCTC 25223 - v i (CTTCT)n#Simp 1 CTTCTCTTCTCTTCTCTTCTCTTCTC 26 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 16 15.86 0.00 0.00 chrXqtel1M 26559 26586 (973414) (G)n#Simple_repeat 1 28 (0) m_b352s252i23 14759 chrXqtel1M 26559 GGGGGGTGGGCGGGATGGGGGGGGGGGG 26586 v v iv (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGG 28 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 42 2.37 0.00 0.00 chrXqtel1M 26814 26856 (973144) (ACCGTCCT)n#Simple_repeat 1 43 (0) c_b352s251i2 14760 chrXqtel1M 26814 ACCGGCCTACCGTCCTACCGTCCTACCGTCCTACCGTCCTACC 26856 v (ACCGTCCT)n#S 1 ACCGTCCTACCGTCCTACCGTCCTACCGTCCTACCGTCCTACC 43 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 18 25.24 1.79 0.00 chrXqtel1M 27231 27286 (972714) (CCCCG)n#Simple_repeat 1 57 (0) m_b352s252i24 14761 chrXqtel1M 27231 CCCCGCCCCGCCCCTCCCCTCCCCTCCCC-CCCAGCTCCAAGCCGGCCGG 27279 v v v - v i ivv v v (CCCCG)n#Simp 1 CCCCGCCCCGCCCCGCCCCGCCCCGCCCCGCCCCGCCCCGCCCCGCCCCG 50 chrXqtel1M 27280 TTCCGCC 27286 ii (CCCCG)n#Simp 51 CCCCGCC 57 Matrix = Unknown Transitions / transversions = 0.50 (4/8) Gap_init rate = 0.02 (1 / 55), avg. gap size = 1.00 (1 / 1) 19 12.63 0.00 0.00 chrXqtel1M 27374 27408 (972592) (TCCCCG)n#Simple_repeat 1 35 (0) m_b352s252i26 14762 chrXqtel1M 27374 TCCCCGTCCCCATCCCGGTCCCCATCCCTGTCCCC 27408 i v i i (TCCCCG)n#Sim 1 TCCCCGTCCCCGTCCCCGTCCCCGTCCCCGTCCCC 35 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 390 25.00 5.00 0.00 chrXqtel1M 28350 28449 (971551) C L2c_3end#LINE/L2 (5) 473 369 m_b352s601i8 14763 chrXqtel1M 28350 TTCAGTGAATCAGCATTTATTAAGCGACTACTATGTACT-GTAACTGGGG 28398 v v iv i i v i i- vvi C L2c_3end#LINE 473 TTCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGG 424 chrXqtel1M 28399 ATATAAAAGCAAA--AGCCA--GTTCCTGCCTTCATGGAGTTTACAATCT 28444 i iiii -- v -- i i v i i i C L2c_3end#LINE 423 ATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCT 374 chrXqtel1M 28445 AATGG 28449 i C L2c_3end#LINE 373 AGTGG 369 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 30.07 CpG sites = 17, Kimura (unadjusted) = 31.60 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.03 (3 / 99), avg. gap size = 1.67 (5 / 3) 24 23.71 5.36 4.42 chrXqtel1M 28457 28568 (971432) (TTCC)n#Simple_repeat 1 113 (0) m_b352s252i27 14764 chrXqtel1M 28457 TTCCTCGTTTCACTTCCTTTTCTCCCTCCCTCCCTTTTTTCCCTCTTTGA 28506 ivi - - i i i i ii i i vv (TTCC)n#Simpl 1 TTCCTTCCTTC-CTTCC-TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 48 chrXqtel1M 28507 TCCCCTTCTCTTTC-TCCCCCCTTCCCTCC-TCCTCCCTTCC-T-CTTCC 28552 -i - i - ii i - i - - (TTCC)n#Simpl 49 T-TCCTTC-CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 96 chrXqtel1M 28553 -TCC-TCCTTCTCCTCCT 28568 - - - i (TTCC)n#Simpl 97 TTCCTTCCTTC-CTTCCT 113 Matrix = Unknown Transitions / transversions = 5.67 (17/3) Gap_init rate = 0.10 (11 / 111), avg. gap size = 1.00 (11 / 11) 29 13.43 7.46 0.00 chrXqtel1M 28507 28573 (971427) (TCC)n#Simple_repeat 1 72 (0) m_b352s252i28 14764 chrXqtel1M 28507 TCC-CCTTCTCTTTCTCC-CC-CCTTC-CCTCCTCCTCC-CTTCCTCTTC 28551 - i i i - - i - - i i (TCC)n#Simple 1 TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC 50 chrXqtel1M 28552 CTCCTCCTTCTCCTCCTCCGCC 28573 i v (TCC)n#Simple 51 CTCCTCCTCCTCCTCCTCCTCC 72 Matrix = Unknown Transitions / transversions = 7.00 (7/1) Gap_init rate = 0.08 (5 / 66), avg. gap size = 1.00 (5 / 5) 16 13.23 3.03 0.00 chrXqtel1M 31220 31252 (968748) (GGTG)n#Simple_repeat 1 34 (0) m_b352s252i29 14765 chrXqtel1M 31220 GGTGGGTGGGTGGGTGGG-GGGGGGAATGGTGGG 31252 - v ivv (GGTG)n#Simpl 1 GGTGGGTGGGTGGGTGGGTGGGTGGGTGGGTGGG 34 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 12 18.76 2.63 2.63 chrXqtel1M 34030 34067 (965933) (TTCATT)n#Simple_repeat 1 38 (0) m_b352s252i30 14766 chrXqtel1M 34030 TTCCTTTTCTTTTTAAATTTACATTTT-GTTTTCACTTT 34067 v v -v v -i i (TTCATT)n#Sim 1 TTCATTTTCATTTT-CATTTTCATTTTCATTTTCATTTT 38 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 279 31.45 9.24 1.78 chrXqtel1M 34539 34852 (965148) C L1ME3G_3end#LINE/L1 (551) 373 37 m_b352s551i4 14767 chrXqtel1M 34539 ATTGCTGGCTCAAAGGATTCACGCGGCTTAATACCTTTTTAGGTGTAGTT 34588 v i vii ivi - ii vv i -- v v C L1ME3G_3end#L 373 ATTGCTGGGTCAAAGGGTATGCGCATTTTAA-ATTTTAATAGAT--ACTG 327 chrXqtel1M 34589 CCAAATTGCCTCTCAGACCAGTTGGATTAGTTCACAGCTCCACCTACAGT 34638 iii i v?i i v ii i i vii vi C L1ME3G_3end#L 326 CCAAATTGCCCTCCAAAANGGCTGTACCAATTTACACTCCCACCAGCAGT 277 chrXqtel1M 34639 ACATCAGAGTACTTCTTTTCTCTCAGTCCCTACAGCTTTTCATTTTTT-- 34686 ii v iiv i i v vi i vv i vi ?v v v -- C L1ME3G_3end#L 276 GTATGAGAGTACCCGTTTCCCCACACCCTCGCCAACACTNGATATTATCA 227 chrXqtel1M 34687 -TCCTTTCTATCT----CAAGCTGATGGATGTGAGGTAGGACTTTAGAGT 34731 -? i vv i ---- v i vi ii i v ii i vv C L1ME3G_3end#L 226 ANCTTTTAAATTTTTGCCAATCTGATGGGTGAAAAATGGTATCTCATTGT 177 chrXqtel1M 34732 TGTTTTAATTTGC----TTCTAATAATTAGTGATTTAGAGCATTTATTC- 34776 ----ii i v i vv v i v - C L1ME3G_3end#L 176 TGTTTTAATTTGCATTTCCCTGATTACTAGTGAGGTTGAGCATCTTTTCA 127 chrXqtel1M 34777 --TTTTTAAATATAG-CATTT-TATTT--TTTTCT---AGTTACCT-TTC 34816 -- v ---v i - - -- i --- i i - C L1ME3G_3end#L 126 TATGTTTA---TTGGCCATTTGTATTTCCTCTTCTGTGAATTGCCTGTTC 80 chrXqtel1M 34817 A-------AGACAATTTTAACATTCATTTATTTTTTTTTTATT 34852 -------v v v vvi viv i i i C L1ME3G_3end#L 79 ATATCCTTTGCCCATTTTTCTATTGGGTTGTCTTTTTCTTATT 37 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 41.96 CpG sites = 55, Kimura (unadjusted) = 42.55 Transitions / transversions = 1.31 (55/42) Gap_init rate = 0.06 (18 / 313), avg. gap size = 1.94 (35 / 18) 285 31.35 7.87 3.23 chrXqtel1M 34539 34805 (965195) C L1ME4b_3end#LINE/L1 (515) 377 99 m_b352s551i6 14767 chrXqtel1M 34539 ATTGCTGGCTCAAAGGATTCACGCGGCTTAATACCTTTT-TAGGTGTAGT 34587 v i -- i i vv vi vi v- i i -- C L1ME4b_3end#L 377 ATTGCTGGGTCAAAGGGT--ATGTGCATTTGTAATTTTGATAGATAT--T 332 chrXqtel1M 34588 TCCAAATTGCCTCTCAGACCAGTTGGATTAGTTCACAGCTCCACCTACAG 34637 v iii v vvi v ii i i vii vi i C L1ME4b_3end#L 331 GCCAAATTGCCCTCCATAGAGGTTGTACCAATTTACACTCCCACCAGCAA 282 chrXqtel1M 34638 TACATCAGAGTACTTCTTTTCTCTCAGTCCC-----TACAGCTTTTCAT- 34681 ii v i i v i i v vi i -----i iv v i - C L1ME4b_3end#L 281 TGTATGAGAGTGCCTGTTTCCCCACACCCTCGCCAACACAGTGTGTTATC 232 chrXqtel1M 34682 ---TTTTTTCCTTTCTATCTCAAGCTGATGGATGTGAGGTAGGACTTTAG 34728 ---i vv i i i--i v i i vi ii i v ii i C L1ME4b_3end#L 231 AAACTTTTTGATCTTTG--CCAATCTGATAGGTGAAAAATGGTATCTCAG 184 chrXqtel1M 34729 AGTTGTTTTAATTTGC----TTCTAATAATTAGTGATTTAGAGCATTTAT 34774 v v ----i v v v vv v i v C L1ME4b_3end#L 183 TGTAGTTTTAATTTGCATTTCTCTTATTATGAGTGAGGTTGAGCATCTTT 134 chrXqtel1M 34775 TC---TTTTTAAATATAG-CATTT-TATTT--TTTTCT 34805 --- v i--- - - -- C L1ME4b_3end#L 133 TCATATGTTTAAG---AGCCATTTGTATTTCCTTTTCT 99 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 41.92 CpG sites = 47, Kimura (unadjusted) = 41.92 Transitions / transversions = 1.38 (47/34) Gap_init rate = 0.07 (18 / 266), avg. gap size = 1.67 (30 / 18) 363 35.30 4.62 1.22 chrXqtel1M 34539 34776 (965224) C L1ME3Cz_3end#LINE/L1 (624) 373 128 m_b352s551i5 14767 chrXqtel1M 34539 ATTGCTGGCTCAAAGGATTCACGCGGCTTAATACCTTTTTAGGTGTAGTT 34588 v iv i vii iv v - i vi i i -- v C L1ME3Cz_3end# 373 ATTGCTGGGTCGTAGGGTATGCGCATCTTCA-ACTTTACTAGATAT--TG 327 chrXqtel1M 34589 CCAAATTGCCTCTCAGACCAGTTGGATTAGTTCACAGCTCCACCTACAGT 34638 iiii i vii v ii i i vii vi C L1ME3Cz_3end# 326 CCAAATTGCTCTCCAAAGTGGTTGTACCAATTTACACTCCCACCAGCAGT 277 chrXqtel1M 34639 ACATCAGAGTACTTCTTTTCTCTCAGTCCCTACAGCTTTTCATTTTTTT- 34687 ii v v iiv iii v vi i vv i vi vi v v i- C L1ME3Cz_3end# 276 GTATGAGAGTTCCCGTTTCTCCACATCCTCGCCAACACTTGGTATTGTCA 227 chrXqtel1M 34688 --CCTTTCTATCT----CAAGCTGATGGATGTGAGGTAGGACTTTAGAGT 34731 -- i vv i ---- v i ii i v ii i vv C L1ME3Cz_3end# 226 GACTTTTAAATTTTTGCCAATCTGATGGGTGTGAAATGGTATCTCATTGT 177 chrXqtel1M 34732 TGTTTTAATTTGC----TTCTAATAATTAGTGATTTAGAGCATTTATTC 34776 ? ----ii i v i vv v i v C L1ME3Cz_3end# 176 NGTTTTAATTTGCATTTCCCTGATTACTAGTGAGGTTGAGCATCTTTTC 128 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 48.54 CpG sites = 50, Kimura (unadjusted) = 50.29 Transitions / transversions = 1.52 (50/33) Gap_init rate = 0.03 (7 / 237), avg. gap size = 2.00 (14 / 7) 398 31.38 6.35 0.50 chrXqtel1M 34588 34776 (965224) C L1PA16_3end#LINE/L1 (582) 331 132 m_b352s551i7 14767 chrXqtel1M 34588 TCCAAATTGCCTCTCAGACCAGTTGGATTAGTTCACAGCTCCACCTACAG 34637 i i ii v vii i i i i i vii v C L1PA16_3end#L 331 TCCAAACTGCTTTCCACAGTGGCTGAACTAATTTACATTCCCACCAACAG 282 chrXqtel1M 34638 TACATCAGAGTACTTCTTTTCTCT-CAGTCCCTACAGC--TTTTCATTTT 34684 ii v v v i- i- i i vv --i v ii C L1PA16_3end#L 281 TGTATAAGCGTTCC-CTTTTCTCCGCAGCCTCGCCAGCATCTGTTGTTTT 233 chrXqtel1M 34685 TTTCCTTTCTATC-----TCAAGCTGATGGATGTGAGGTAGGACTTTAGA 34729 vv i vi-----i vv iv i i i v ii i vv C L1PA16_3end#L 232 TTGACTTTTTAATAATAGCCATTCTGACTGGTGTGAGATGGTATCTCATT 183 chrXqtel1M 34730 GTTGTTTTAATTTGC----TTCTAATAATTAGTGATTTAGAGCATTTATT 34775 v i ----i i i v v v C L1PA16_3end#L 182 GTGGTTTTGATTTGCATTTCTCTGATGATTAGTGATGTTGAGCATTTTTT 133 chrXqtel1M 34776 C 34776 C L1PA16_3end#L 132 C 132 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 41.25 CpG sites = 36, Kimura (unadjusted) = 42.21 Transitions / transversions = 1.57 (36/23) Gap_init rate = 0.03 (5 / 188), avg. gap size = 2.60 (13 / 5) 310 23.38 8.33 1.96 chrXqtel1M 35315 35458 (964542) C L1ME3C_3end#LINE/L1 (686) 184 32 m_b352s551i9 14768 chrXqtel1M 35315 TTATTTTAGTT---ACTTTCATTTCTCTAATCAATAGTGATTTTGAGCAT 35361 i v ? --- i v i i i v vv C L1ME3C_3end#L 184 TCATTGTNGTTTTAATTTGCATTTCCCTGATTACTAGTGAGGTTGAGCAT 135 chrXqtel1M 35362 TTTTTCATAAG-------ACCTTT--AGTTTCTTCATCCGAACACTGCCT 35402 i v -------i v --? i v i viv i C L1ME3C_3end#L 134 CTTTTCATATGTTTATTGGCCATTCGNGTTTCCTCTTCTGTGAATTGCCT 85 chrXqtel1M 35403 GTTCATATCCTTTGACCATTTAGCAATTGGGGAATGATTTGTATTTTTAT 35452 i v vv v --- vi i v i C L1ME3C_3end#L 84 GTTCATATCTTTTGCCCATTTTTCTATTGGG---TTGTCTGTTTTCTTAT 38 chrXqtel1M 35453 AAATTT 35458 vi C L1ME3C_3end#L 37 TGATTT 32 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 28.75 CpG sites = 16, Kimura (unadjusted) = 28.75 Transitions / transversions = 0.94 (16/17) Gap_init rate = 0.04 (6 / 143), avg. gap size = 2.50 (15 / 6) 402 19.64 7.50 2.38 chrXqtel1M 35315 35434 (964566) C L1ME5_3end#LINE/L1 (760) 181 56 m_b352s551i8 14768 chrXqtel1M 35315 TTATTTTAGTTACTTTCATTTCTCTAATCAATAGTGATTTTGAGCATTTT 35364 i i --- v i i v i v i i C L1ME5_3end#LI 181 TTGTTTTAATT---TGCATTTCTCTGATTACTAATGAGTTTGAGCATCTC 135 chrXqtel1M 35365 TTCATAAG-------ACCTTT--AGTTTCTTCATCCGAACACTGCCTGTT 35405 v -------i --i i v i v v i C L1ME5_3end#LI 134 TTCATATGCTTGTTAGCCTTTCGGGTTTCCTCTTCTGTAAATTGCCTGTT 85 chrXqtel1M 35406 CATATCCTTTGACCATTTAGCAATTGGGG 35434 v vv v C L1ME5_3end#LI 84 CATATCCTTTGCCCATTTTTCTATTGGGG 56 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 22.98 CpG sites = 12, Kimura (unadjusted) = 22.98 Transitions / transversions = 1.09 (12/11) Gap_init rate = 0.04 (5 / 119), avg. gap size = 2.40 (12 / 5) 309 26.05 6.63 0.57 chrXqtel1M 35324 35489 (964511) C L1ME4b_3end#LINE/L1 (716) 176 1 m_b352s551i10 14768 chrXqtel1M 35324 TTACTTT-CATTTCTCTAATCAATAGTGATTTTGAGCATTTTTTCATA-- 35370 v - v i vv vv i -- C L1ME4b_3end#L 176 TTAATTTGCATTTCTCTTATTATGAGTGAGGTTGAGCATCTTTTCATATG 127 chrXqtel1M 35371 ----AGA-CCTTTAGT--TTCTTCATCCGAACACTGCCTGTTCATATCCT 35413 ---- - v v -- i iv i viv i C L1ME4b_3end#L 126 TTTAAGAGCCATTTGTATTTCCTTTTCTGTGAACTGTCTGTTCATATCCT 77 chrXqtel1M 35414 TTGACCATTTAGCAATTGGGGAATGATTTGTATTTTTATAAATTT-CACT 35462 v vv v vvi viv iv v i vi -i vv C L1ME4b_3end#L 76 TTGCCCATTTTTCTATTGGGTTGTTGGTCTTTTTCTTATTGATTTGTAGG 27 chrXqtel1M 35463 CGCTTCTCTATATGTTTGAGAAATGAG 35489 v - i i v i v C L1ME4b_3end#L 26 AGC-TCTTTATATATTAGGGAAATTAG 1 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 32.04 CpG sites = 16, Kimura (unadjusted) = 32.04 Transitions / transversions = 0.59 (16/27) Gap_init rate = 0.04 (7 / 165), avg. gap size = 1.71 (12 / 7) 273 28.06 9.87 3.64 chrXqtel1M 35349 35581 (964419) C L1PREC2_orf2#LINE/L1 (0) 3294 3048 m_b352s551i12 14768 chrXqtel1M 35349 TGATTTTGAGCATTTTTTCATAAGACCTTTAG---------TTTCTTCAT 35389 v v v viiv i --------- v v C L1PREC2_orf2# 3294 TGATGTTGAGCTTTTTTTCATATGCTTGTTGGCCGCATGTATGTCTTCTT 3245 chrXqtel1M 35390 CCGAACACTGCCTGTTCATATCCTTTGACCATTTAGCAATTGGGGAATGA 35439 ii v v i i v i vvi v --- vi C L1PREC2_orf2# 3244 TTGAAAAGTGTCTGTTCATGTCCTTTGCCCACTTTTTAATGGGG---TTG 3198 chrXqtel1M 35440 TTTGTATTTTT---ATAAATTTCACTCGCTTCTCTATATGTTTGAGAAAT 35486 v ---i vvi viv ii vi vivi v C L1PREC2_orf2# 3197 TTTGTTTTTTTCTTGTAAATTTGTTTAAGTTCCTTATAGATGCTGGATAT 3148 chrXqtel1M 35487 GAGGTCTTTGTCAGAG--ATACTTGCTGTAAAAATTGTTTCTCA------ 35528 v ii v-- v -- i ? v i i ------ C L1PREC2_orf2# 3147 TAGACCTTTGTCAGATGCATAGTT--TGCAAANATTTTCTCCCATTCTGT 3100 chrXqtel1M 35529 --GCTTTCTGTTTTC-CAGCTAATCCTGGTTGCATTGGTTTGTGCAGAAA 35575 -- i v v - v i i --- i v v v -i i C L1PREC2_orf2# 3099 AGGTTGTCTGTTTACTCTGTTGA---TAGTTTCTTTTG-CTGTGCAGAAG 3054 chrXqtel1M 35576 CTTTTT 35581 i C L1PREC2_orf2# 3053 CTCTTT 3048 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 35.76 CpG sites = 30, Kimura (unadjusted) = 35.76 Transitions / transversions = 0.91 (30/33) Gap_init rate = 0.06 (15 / 232), avg. gap size = 2.13 (32 / 15) 281 26.49 7.41 4.10 chrXqtel1M 35349 35537 (964463) C L1M5_orf2#LINE/L1 (0) 3294 3100 m_b352s551i11 14768 chrXqtel1M 35349 TGATTTTGAGCATTTTTTCATA--------AGACCTTTAGTT-TCTTCAT 35389 ?v i i--------i v v i?v - v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chrXqtel1M 35390 CCGAACACTGCCTGTTCATATCCTTTGACCATTTAGCAATTGGGGAATGA 35439 ii viv v i vi i v vv?v --- vi C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGG---TTG 3198 chrXqtel1M 35440 TTTGTATTTTTATAAATTTCACTCGC-----TTCTCTATATGTTTGAGAA 35484 v ? v -- v ? i i----- i i ivi v C L1M5_orf2#LIN 3197 TTTGTCTTTTTNTTA--TTGANTTGTAGGAGTTCTTTATATATTCTGGAT 3150 chrXqtel1M 35485 ATGAGGTCTTTGTCAGAGATACTTGCTGTAAAAATTGTTTCTCAGCTTTC 35534 i vi v iv ?i i v v i i ---? C L1M5_orf2#LIN 3149 ACGAGTCCTTTGTCAGATATATGTNTTGCAAATATTTTCTCCCA---NTC 3103 chrXqtel1M 35535 TGT 35537 C L1M5_orf2#LIN 3102 TGT 3100 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 33.90 CpG sites = 24, Kimura (unadjusted) = 34.77 Transitions / transversions = 1.00 (24/24) Gap_init rate = 0.06 (11 / 188), avg. gap size = 2.00 (22 / 11) 380 24.81 3.05 4.65 chrXqtel1M 36272 36402 (963598) C L1ME4a_3end#LINE/L1 (316) 555 427 m_b352s551i13 14769 chrXqtel1M 36272 ATAATATTCCATAACATTCATATACCACAATTTATTCAGCCATTCCCCCA 36321 v?i vv i i i i ? i C L1ME4a_3end#L 555 ATAATATTCCATTNTATGGATGTACCATAATTTATTTAACCANTCCCCTA 506 chrXqtel1M 36322 CTGATGTGCAGACACTCA----GTTTCCAGTTTCTGGCCACTACAAAGAG 36367 i v ---- i i ---- i i v i i i v i C L1ME4a_3end#L 505 TTGTTG----GACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAA 460 chrXqtel1M 36368 GGCTGCCCCAAACATTCTTGTGTGCAGAAACTTTT 36402 v vvii i -- i v ii C L1ME4a_3end#L 459 TGCTGCGATGAACATCCT--TGTACATAAATCTTT 427 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 31.91 CpG sites = 21, Kimura (unadjusted) = 31.91 Transitions / transversions = 2.10 (21/10) Gap_init rate = 0.05 (7 / 130), avg. gap size = 1.43 (10 / 7) 447 22.13 3.42 3.42 chrXqtel1M 36272 36388 (963612) C L1ME3G_3end#LINE/L1 (376) 548 432 m_b352s551i14 14769 chrXqtel1M 36272 ATAATATTCCATAACATTCATATACCACAATTTATTCAGCCATTCCCCCA 36321 i ii vv i i i i C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chrXqtel1M 36322 CTGATGTGCAGACACTCA----GTTTCCAGTTTCTGGCCACTACAAAGAG 36367 i ---- i i ---- i i v i i v i C L1ME3G_3end#L 498 TTGATG----GACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAA 453 chrXqtel1M 36368 GGCTGCCCCAAACATTCTTGT 36388 v vvii i C L1ME3G_3end#L 452 TGCTGCAATGAACATCCTTGT 432 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 27.25 CpG sites = 18, Kimura (unadjusted) = 27.25 Transitions / transversions = 2.57 (18/7) Gap_init rate = 0.04 (5 / 116), avg. gap size = 1.60 (8 / 5) 434 24.88 0.69 10.69 chrXqtel1M 36874 37017 (962983) C MIRb#SINE/MIR (136) 132 2 m_b352s601i9 14770 chrXqtel1M 36874 AACCGAGGC-AATTGGGGTTAAATGAATTACCCAAGGTCCCACAGCTAGG 36922 i -v vv i i i v i v v C MIRb#SINE/MIR 132 AACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGT 83 chrXqtel1M 36923 CAGTGTTAAATTTCTGAGATCACATTTGAACTCAGGTCCTCCTGACTTCA 36972 v vi i v-- i i ----- i i ivi i C MIRb#SINE/MIR 82 AAGTGGCAGAG--CCGGGAT-----TCGAACCCAGGTCTGTCTGACTCCA 40 chrXqtel1M 36973 GGGCTGGTGCTCTAACCACTGCATCACCTGTGCAGCTGCCCCTTT 37017 ii iv vv i ------- i C MIRb#SINE/MIR 39 AAGCCCGTGCTCTTTCCACTGCACCAC-------GCTGCCCCTCT 2 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 28.25 CpG sites = 19, Kimura (unadjusted) = 30.48 Transitions / transversions = 1.46 (19/13) Gap_init rate = 0.10 (15 / 143), avg. gap size = 1.00 (15 / 15) 454 24.45 0.79 5.83 chrXqtel1M 36874 36999 (963001) C MIRc#SINE/MIR (139) 129 10 m_b352s601i10 14770 chrXqtel1M 36874 AACCGAGGC-AATTGGGGTTAAATGAATTACCCAAGGTCCCACAGCTAGG 36922 i -v vv i i v i v v C MIRc#SINE/MIR 129 AACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGT 80 chrXqtel1M 36923 CAGTGTTAAATTTCTGAGATCACATTTGAACTCAGGTCCTCCTGACTTCA 36972 v vi i v-- i i i----- i i i i C MIRc#SINE/MIR 79 AAGTGGCAGAG--CCGGGAC-----TCGAACCCAGGTCTTCCTGACTCCA 37 chrXqtel1M 36973 GGGCTGGTGCTCTAACCACTGCATCAC 36999 i v ii vv i C MIRc#SINE/MIR 36 AGTCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 27.66 CpG sites = 17, Kimura (unadjusted) = 30.06 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.06 (8 / 125), avg. gap size = 1.00 (8 / 8) 244 30.96 7.46 3.60 chrXqtel1M 37508 37641 (962359) C L1PREC2_orf2#LINE/L1 (385) 2909 2771 m_b352s551i15 14768 chrXqtel1M 37508 TTTATATCCAAATCATCTACCCATTTTGAGCTTACCTTGATATATGGTGT 37557 i ii i v iv i i i v ii vi C L1PREC2_orf2# 2909 TTTACATTTAAGTCTTTAATCCATCTTGAGTTGATTTTTGTATATGGTGT 2860 chrXqtel1M 37558 AAGAAAATATGCCTGGTTTCTGCCAGACTTCTTC----------CTAGTT 37597 i i-iv i ii ---- iv v ---------- i C L1PREC2_orf2# 2859 AAGGAAG-GGGTCCAGTTT----CAATCTTCTGCATATGGCTAGCCAGTT 2815 chrXqtel1M 37598 TTCCCAACGGTTTTTGTTGAATAGTGAGTACTTGCTAAGTTGCT 37641 v i iviv i v v v ivvi C L1PREC2_orf2# 2814 ATCCCAGCACCATTTATTGAATAGGGAGTCCTTTCCCCATTGCT 2771 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 41.66 CpG sites = 25, Kimura (unadjusted) = 41.66 Transitions / transversions = 1.67 (25/15) Gap_init rate = 0.05 (6 / 133), avg. gap size = 2.50 (15 / 6) 439 35.82 5.97 2.26 chrXqtel1M 37675 37768 (962232) C L1M4_orf2#LINE/L1 (591) 2703 2585 m_b352s551i16 14771 chrXqtel1M 37675 TCTATTCCAGTGA-CTAT---TCT---CTTAT--------CAAATTGTTT 37709 v - --- --- -------- v i i C L1M4_orf2#LIN 2703 TCTATTCCATTGATCTATATGTCTATCCTTATGCCAGTACCACACTGTCT 2654 chrXqtel1M 37710 TGATGATGACAACTTTGCATTACTGTTGAAAATCTGG----------CTT 37749 v ivii i i v vvv vi v ---------- i C L1M4_orf2#LIN 2653 TGATTACTGTAGCTTTGTAGTAAGTTTTGAAATCGGGAAGTGTGAGTCCT 2604 chrXqtel1M 37750 CTAGGGCTGCCTTCCCTCC 37768 i ivvi iii i i ii C L1M4_orf2#LIN 2603 CCAACTTTGTTCTTCTTTT 2585 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 49.27 CpG sites = 161, Kimura (unadjusted) = 50.50 Transitions / transversions = 1.58 (19/12) Gap_init rate = 0.05 (5 / 93), avg. gap size = 5.00 (25 / 5) 28 0.00 0.00 0.00 chrXqtel1M 37769 37795 (962205) (T)n#Simple_repeat 1 27 (0) c_b352s251i3 14772 chrXqtel1M 37769 TTTTTTTTTTTTTTTTTTTTTTTTTTT 37795 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTT 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 681 34.10 5.05 2.69 chrXqtel1M 37796 38554 (961446) C L1M5_orf2#LINE/L1 (710) 2584 1820 m_b353s551i2 14771 chrXqtel1M 37796 CATTGATTCCCTTGA-TATTCTTGACCTTTTG--TTCCTAAGAATGAATT 37842 v- vii i- ? ii i -- i i v-- i C L1M5_orf2#LIN 2584 CAA-GATTGTTTTGGCTATTCTNGGTCCTTTGCATTTCCAT--ATAAATT 2538 chrXqtel1M 37843 TTTAAATT-GTTT-CCTAGCTCTATAAAGTAAT-TCCTGATAGTTGAATT 37889 vi i- i -i v vi i iv i- v iv v vi C L1M5_orf2#LIN 2537 TTAGAATCAGCTTGTCAATTTCTACAAAAAAACCTGCTGGGATTTTGATT 2488 chrXqtel1M 37890 GATATGACACCAAATAAGTAAATTAATTTAGGTAGCTTTGTGGTTTTTAT 37939 iv vi iii vvi i i i v vv vvi i ? i C L1M5_orf2#LIN 2487 GGGATTGCATTGAATCTATAGATCAATTTGGGGAGAATTGACATCTTNAC 2438 chrXqtel1M 37940 TATGTTGACTTGGCTTACCCATGAGCAATTTATATTTCTTCAGTTATTTA 37989 v i v ivv iv i i vvv i i v C L1M5_orf2#LIN 2437 AATATTGAGTCTTCCAATCCATGAACATGGTATATCTCTCCATTTATTTA 2388 chrXqtel1M 37990 GATCTGT----ATTTGTGTGAAGACTGCTTTGAGATTCTGTTCA-TGT-- 38032 i vi---- v v v iv v i vii --- - -- C L1M5_orf2#LIN 2387 GGTCTTCTTTAATTTCTCTCAGCAATGTTTTGTAGTT---TTCAGTGTAN 2341 chrXqtel1M 38033 AGGCCCTGTGTATGCGTCTTGGCCGGTAGACTCTCAAGTACTTTATACTG 38082 i i iii --? i viv i vv i ii i ? ii v C L1M5_orf2#LIN 2340 AGGTCTTGCACAT--NTTTTGTTAGATTTATTCCTAAGTATTTNATGTTT 2293 chrXqtel1M 38083 TCTGTAGTTATTTTAAATAGAATTCTTCTTTATTCTTTTATTTGCTGAGT 38132 i vv i v i v v i ? -vv i v ii v C L1M5_orf2#LIN 2292 TTTGATGCTATTGTAAATGGTATTGTTTTTNA-AATTTCATTTTCCAATT 2244 chrXqtel1M 38133 -TTTGTTGATAACACATA-TAATGCAGATAATTTATGGACAGTTATTTGA 38180 - v ii i -v i iv i v v i v v ii vi C L1M5_orf2#LIN 2243 GTTTGTTGCTAGTATATAGAAATACAATTGATTTTTGTATATTGACCTTG 2194 chrXqtel1M 38181 TATACTGTAACTTGGCTGAAGTTGATAACTGTTTTGATTAGATTTTTAGT 38230 v ? ii i v i v iiv v i iv iv v v ? v C L1M5_orf2#LIN 2193 TATCCNGCGACCTTGCTAAATTCACTTATTAGTTCTAGTAGTTTNTTTGT 2144 chrXqtel1M 38231 TGAGTCTCTAGGGTTCTCTAAGTAAATTATTCTATCATTTGCAAGGAGTG 38280 v v i ? i i v ? iv iv i i i iv i? C L1M5_orf2#LIN 2143 AGATTCTTTNGGATTTTCTACGTANACAATCATGTCATCTGCGAATAANG 2094 chrXqtel1M 38281 ATAGTTTTGTTT-TTCCTTT---ATGCTTATTCCTTGAATTTCTTCTTTT 38326 i i - --- vi v vv i i C L1M5_orf2#LIN 2093 ACAGTTTTATTTCTTCCTTTCCAATCTTTATGCCTTTTATTTCTTTTTCT 2044 chrXqtel1M 38327 TCTCTTATTGATATAGAGTCGAGAGCTAGTATTTTCAGTCCAATATTAAT 38376 vi -i iv -------- v ii i v i i - C L1M5_orf2#LIN 2043 TGCCTTATTG-CACTG--------GCTAGGACCTCCAGTACAATGTTGA- 2004 chrXqtel1M 38377 ATAGATAAAGGTGATAATAGACATCCTTGGTTCACTCCTCATCTTACTGG 38426 - iv ? iii vi iii iv vv C L1M5_orf2#LIN 2003 ATAGA-AGTGGTGANAGCGGACATCCTTGTCTTGTTCCCGATCTTAGGGG 1955 chrXqtel1M 38427 AAAGGCTTCTAGCTTGGCCACGTTACAAATAATGCTTGCTCTTAGTTT-- 38474 i i ? ii i? vv vv i viv i i ? v vi -- C L1M5_orf2#LIN 1954 GAAAGCNTTCAGTNTTTCACCATTAAGTATGATGTTNGCTGTAGGTTTTT 1905 chrXqtel1M 38475 --TGAATAC---TAATCATTTTAATGAAAGTTCCATTTATTACTATTCTT 38519 -- ii i --- v vv i v iv i v i v v i v C L1M5_orf2#LIN 1904 CGTAGATGCCCTTTATCAGGTTGAGGAAGTTCCCTTCTATTCCTAGTTTG 1855 chrXqtel1M 38520 TCTACAATTTTAAACAGAAATGGATGGTGCATTTT 38554 iiv v i v v vi i v v C L1M5_orf2#LIN 1854 CTGAGAGTTTTTATCATGAATGGGTGTTGAATTTT 1820 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 47.42 CpG sites = 164, Kimura (unadjusted) = 48.42 Transitions / transversions = 1.25 (139/111) Gap_init rate = 0.05 (35 / 758), avg. gap size = 1.31 (46 / 35) 717 33.32 3.58 2.62 chrXqtel1M 37800 38554 (961446) C L1M5_orf2#LINE/L1 (714) 2580 1819 m_b352s551i17 14771 chrXqtel1M 37800 GATTCCCTTGA-TATTCTTGACCTTTTG--TTCCTAAGAATGAATTTTTA 37846 vii i- ? ii i -- i i v-- i vi C L1M5_orf2#LIN 2580 GATTGTTTTGGCTATTCTNGGTCCTTTGCATTTCCAT--ATAAATTTTAG 2533 chrXqtel1M 37847 AATT-GTTT-CCTAGCTCTATAAAGTAAT-TCCTGATAGTTGAATTGATA 37893 i- i -i v vi i iv i- v iv v vi iv C L1M5_orf2#LIN 2532 AATCAGCTTGTCAATTTCTACAAAAAAACCTGCTGGGATTTTGATTGGGA 2483 chrXqtel1M 37894 TGACACCAAATAAGTAAATTAATTTAGGTAGCTTTGTGGTTTTTATTATG 37943 vi iii vvi i i i v vv vvi i ? iv i C L1M5_orf2#LIN 2482 TTGCATTGAATCTATAGATCAATTTGGGGAGAATTGACATCTTNACAATA 2433 chrXqtel1M 37944 TTGACTTGGCTTACCCATGAGCAATTTATATTTCTTCAGTTATTTAGATC 37993 v ivv iv i i vvv i i v i C L1M5_orf2#LIN 2432 TTGAGTCTTCCAATCCATGAACATGGTATATCTCTCCATTTATTTAGGTC 2383 chrXqtel1M 37994 TGT----ATTTGTGTGAAGACTGCTTTGAGATTCTGTTCA-TGT--AGGC 38036 vi---- v v v iv v i vii --- - -- i C L1M5_orf2#LIN 2382 TTCTTTAATTTCTCTCAGCAATGTTTTGTAGTT---TTCAGTGTANAGGT 2336 chrXqtel1M 38037 CCTGTGTATGCGTCTTGGCCGGTAGACTCTCAAGTACTTTATACTGTCTG 38086 i iii --? i viv i vv i ii i ? ii v i C L1M5_orf2#LIN 2335 CTTGCACAT--NTTTTGTTAGATTTATTCCTAAGTATTTNATGTTTTTTG 2288 chrXqtel1M 38087 TAGTTATTTTAAATAGAATTCTTCTTTATTCTTTTATTTGCTGAGT-TTT 38135 vv i v i v v i ? -vv i v ii v - C L1M5_orf2#LIN 2287 ATGCTATTGTAAATGGTATTGTTTTTNA-AATTTCATTTTCCAATTGTTT 2239 chrXqtel1M 38136 GTTGATAACACATAT-AATGCAGATAATTTATGGACAGTTATTTGATATA 38184 v ii i v- i iv i v v i v v ii vi v C L1M5_orf2#LIN 2238 GTTGCTAGTATATAGAAATACAATTGATTTTTGTATATTGACCTTGTATC 2189 chrXqtel1M 38185 CTGTAACTTGGCTGAAGTTGATAACTGTTTTGATTAGATTTTTAGTTGAG 38234 ? ii i v i v iiv v i iv iv v v ? v v v C L1M5_orf2#LIN 2188 CNGCGACCTTGCTAAATTCACTTATTAGTTCTAGTAGTTTNTTTGTAGAT 2139 chrXqtel1M 38235 TCTCTAGGGTTCTCTAAGTAAATTATTCTATCATTTGCAAGGAGTGATAG 38284 i ? i i v ? iv iv i i i iv i? i C L1M5_orf2#LIN 2138 TCTTTNGGATTTTCTACGTANACAATCATGTCATCTGCGAATAANGACAG 2089 chrXqtel1M 38285 TTTTGTTT-TTCCTTT---ATGCTTATTCCTTGAATTTCTTCTTTTTCTC 38330 i - --- vi v vv i i vi C L1M5_orf2#LIN 2088 TTTTATTTCTTCCTTTCCAATCTTTATGCCTTTTATTTCTTTTTCTTGCC 2039 chrXqtel1M 38331 TTATTGATATAGAGTCGAGAGCTAGTATTTTCAGTCCAATATTAATATAG 38380 -i iv -------- v ii i v i i - C L1M5_orf2#LIN 2038 TTATTG-CACTG--------GCTAGGACCTCCAGTACAATGTTGA-ATAG 1999 chrXqtel1M 38381 ATAAAGGTGATAATAGACATCCTTGGTTCACTCCTCATCTTACTGGAAAG 38430 - iv ? iii vi iii iv vv i i C L1M5_orf2#LIN 1998 A-AGTGGTGANAGCGGACATCCTTGTCTTGTTCCCGATCTTAGGGGGAAA 1950 chrXqtel1M 38431 GCTTCTAGCTTGGCCACGTTACAAATAATGCTTGCTCTTAGTTT----TG 38476 ? ii i? vv vv i viv i i ? v vi ---- i C L1M5_orf2#LIN 1949 GCNTTCAGTNTTTCACCATTAAGTATGATGTTNGCTGTAGGTTTTTCGTA 1900 chrXqtel1M 38477 AATAC---TAATCATTTTAATGAAAGTTCCATT-TATTACTATTCTTTCT 38522 i i --- v vv i - i v - v v i viiv C L1M5_orf2#LIN 1899 GATGCCCTTTATCAGGTTGA-GGAAGTTCCCTTCTATTCCTAGTTTGCTG 1851 chrXqtel1M 38523 ACAATTTTAAACAGAAATGGATGGTGCATTTT 38554 v i v v vi i v v C L1M5_orf2#LIN 1850 AGAGTTTTTATCATGAATGGGTGTTGAATTTT 1819 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 45.53 CpG sites = 137, Kimura (unadjusted) = 46.63 Transitions / transversions = 1.27 (137/108) Gap_init rate = 0.05 (35 / 754), avg. gap size = 1.34 (47 / 35) 251 32.62 8.81 3.59 chrXqtel1M 38971 39129 (960871) C MIR3#SINE/MIR (19) 189 23 m_b353s601i2 14773 chrXqtel1M 38971 TGGCAAAGATACAGGAGAGCTTTGCCATTTCCTTTTCCA----TCTCATT 39016 v i v iv i i v v vv ivi vv ----i C MIR3#SINE/MIR 189 TGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATT 140 chrXqtel1M 39017 TTATAAATGTAG---CTAA--CCCAG-----CTAAGTGACTTGCCTAGGG 39056 i i vi --- i -- -----iv i i C MIR3#SINE/MIR 139 TTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGG 90 chrXqtel1M 39057 TCACATAGGTAGTGTCTAAGGTCAGATTTGAACTCATGAAGATGAGCCTT 39106 i v? --- iv v vii iivii - vviii i - C MIR3#SINE/MIR 89 TCACACAGCNAGT---TAGTGGCAGAGCCGGGACTA-GAACCCAGGTC-T 45 chrXqtel1M 39107 CCTGATTTCTAGCCCAGTGTTCT 39129 i i i i - i C MIR3#SINE/MIR 44 CCTGACTCCCAGTCC-GTGCTCT 23 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 44.00 CpG sites = 31, Kimura (unadjusted) = 45.25 Transitions / transversions = 1.63 (31/19) Gap_init rate = 0.06 (10 / 158), avg. gap size = 2.00 (20 / 10) 346 25.53 8.82 4.96 chrXqtel1M 39011 39146 (960854) C MIRc#SINE/MIR (120) 148 8 m_b353s601i3 14773 chrXqtel1M 39011 CTCATTTTATAAATGTAG---CTAA--CCCAG-----CTAAGTGACTTGC 39050 i i i vi --- i -- i -----i C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chrXqtel1M 39051 CTAGGGTCACATAGGTAGTGTCTAAG-GTCAGA-TTTGAACTCATGAAGA 39098 i i i v ---- - v -iiv i -- vv C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAG----TAAGTGGCAGAGCCGGGACTC--GAACC 55 chrXqtel1M 39099 TGAGCCTTCCTGATTTCTAGCCCAGTGTTCTATGCACCGTGCCTACAC 39146 iii i i i v i i v v i ii - C MIRc#SINE/MIR 54 CAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACC-ACAC 8 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 31.68 CpG sites = 24, Kimura (unadjusted) = 32.91 Transitions / transversions = 2.67 (24/9) Gap_init rate = 0.09 (12 / 135), avg. gap size = 1.58 (19 / 12) 18 4.50 0.00 0.00 chrXqtel1M 39147 39169 (960831) (AC)n#Simple_repeat 1 23 (0) m_b353s252i0 14774 chrXqtel1M 39147 ACACACACACACAAACACACACA 39169 v (AC)n#Simple_ 1 ACACACACACACACACACACACA 23 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 16 3.96 3.85 0.00 chrXqtel1M 39366 39391 (960609) (ATTTT)n#Simple_repeat 1 27 (0) m_b353s252i1 14775 chrXqtel1M 39366 ATTTTATTTTATTTT-TTTTAGTTTAT 39391 - v (ATTTT)n#Simp 1 ATTTTATTTTATTTTATTTTATTTTAT 27 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.04 (1 / 25), avg. gap size = 1.00 (1 / 1) 518 22.81 0.88 0.00 chrXqtel1M 40024 40137 (959863) MIR#SINE/MIR 43 157 (105) m_b353s601i4 14776 chrXqtel1M 40024 ATTATCTGGGTTCAAATTCAACCTCAAACACTAACTAGCTGTGTGACCCC 40073 i ii i i viv viv v ii MIR#SINE/MIR 43 ACTGCCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTT 92 chrXqtel1M 40074 AAAAAAGTCACTTAACCTCTGTTTGCCTCAGTTTTC-AATCTGTAAAATA 40122 iiiv i v v i -v i MIR#SINE/MIR 93 GGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATG 142 chrXqtel1M 40123 GGGATAATAATAACA 40137 ii MIR#SINE/MIR 143 GGGATAATAATAGTA 157 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 25.50 CpG sites = 17, Kimura (unadjusted) = 27.97 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.01 (1 / 113), avg. gap size = 1.00 (1 / 1) 19 24.29 1.82 1.82 chrXqtel1M 40732 40786 (959214) (AT)n#Simple_repeat 1 55 (0) m_b353s252i2 14777 chrXqtel1M 40732 ATATATGT-TAAACATGTTAAAATATATGTATATCCTATATATATATATG 40780 i - v i i vv v i -v i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATAT-ATATATATATATATA 49 chrXqtel1M 40781 TTTATA 40786 v (AT)n#Simple_ 50 TATATA 55 Matrix = Unknown Transitions / transversions = 0.83 (5/6) Gap_init rate = 0.04 (2 / 54), avg. gap size = 1.00 (2 / 2) 16 3.83 0.00 6.90 chrXqtel1M 40979 41009 (958991) (TTTGT)n#Simple_repeat 1 29 (0) m_b353s252i3 14778 chrXqtel1M 40979 TTTGTTTTTGTTCTTGTTTTGTTTCGTTTTG 41009 - - i (TTTGT)n#Simp 1 TTTG-TTTTGTT-TTGTTTTGTTTTGTTTTG 29 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2) 428 25.57 7.58 5.19 chrXqtel1M 41010 41141 (958859) C MIRc#SINE/MIR (124) 144 10 m_b353s601i5 14779 chrXqtel1M 41010 TTTTTTTGATGAGGCAATTGGGA----------TTAAGTGGCTTACCCAG 41049 viv v i i i---------- i i i C MIRc#SINE/MIR 144 TTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAA 95 chrXqtel1M 41050 GGACACACAGCCAGGAAGTGTTAAATGTCTGAGGTCACATTTGAAGTCAG 41099 v i v vi i v-- i i ----- i i vi C MIRc#SINE/MIR 94 GGTCACACAGCTAGTAAGTGGCAGAG--CCGGG-----ACTCGAACCCAG 52 chrXqtel1M 41100 GGCCTCCTGACTTCAGGGCTGGTGCTCTATTCACTGCACCAC 41141 v i i i v ii v i C MIRc#SINE/MIR 51 GTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 29.98 CpG sites = 21, Kimura (unadjusted) = 32.42 Transitions / transversions = 1.91 (21/11) Gap_init rate = 0.06 (8 / 131), avg. gap size = 2.12 (17 / 8) 48 6.75 0.00 0.00 chrXqtel1M 41151 41212 (958788) (T)n#Simple_repeat 1 62 (0) c_b353s251i1 14780 chrXqtel1M 41151 TTTTTTTTTTTTTTTTTTTTTTTATTTTTTTTTTATTTTTTTTTTTTATT 41200 v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chrXqtel1M 41201 CTTTTTTTTTTT 41212 i (T)n#Simple_r 51 TTTTTTTTTTTT 62 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0) 1652 31.48 6.30 2.90 chrXqtel1M 41656 42320 (957680) L1P1_orf2#LINE/L1 1895 2599 (695) m_b353s551i3 14781 chrXqtel1M 41656 CTATTTA----AAACCATCAGCAAGCATCATATATAATGGGAACAAACTA 41701 i ---- vv v ii ivv v v i L1P1_orf2#LIN 1895 CTATCTATGACAAACCCACAGCCAATATCATACTGAATGGGCAAAAACTG 1944 chrXqtel1M 41702 GAATCATTCCCAATAAGATCCGGAGGGAAACAAGACCGCCATTACTATCA 41751 v vv i i v i vivi i i ivi v -- v L1P1_orf2#LIN 1945 GAAGCATTCCCTTTGAAAACTGGCACAAGACAGGGATGCCCT--CTCTCA 1992 chrXqtel1M 41752 CCACTGCTATTCAACATTGTATTAGAAATGCTAGCTTTGGCAATAAG--A 41799 v v i i i v i ivv v -- L1P1_orf2#LIN 1993 CCACTCCTATTCAACATAGTGTTGGAAGTTCTGGCCAGGGCAATCAGGCA 2042 chrXqtel1M 41800 GAAGAAAGAGATTAAAGGAATTAGAGTAGGGAATGAGGAAAACAAATGAT 41849 i i i v i v vi v i v iv vi L1P1_orf2#LIN 2043 GGAGAAGGAAATAAAGGGTATTCAATTAGGAAAAGAGGAAGTCAAATTGT 2092 chrXqtel1M 41850 CACTCTTTGCAGATGACATGAAGGTATACTTAGAGAACCCTAGAGAATCA 41899 v v i vv ii i i vv vv L1P1_orf2#LIN 2093 CCCTGTTTGCAGACGACATGATTGTATATCTAGAAAACCCCATCGTCTCA 2142 chrXqtel1M 41900 ACTGAAAAAAACCCATTAGAAACAATCCACAACTTTAGCAAAGTTGTAGA 41949 i iv v-- i v - ivii vvi i ivi i L1P1_orf2#LIN 2143 GCCCAAAAT--CTCCTTA-AGCTGATAAGCAACTTCAGCAAAGTCTCAGG 2189 chrXqtel1M 41950 ATACAAAATAAATCCACAGAAATCA------TTTTTATATATTACCCACA 41993 v vii i ------ i i ii viv L1P1_orf2#LIN 2190 ATACAAAATCAATGTGCAAAAATCACAAGCATTCTTATACACCAATAACA 2239 chrXqtel1M 41994 AAGTCTAGCAGCCAGAGATACAAA------GAGAAATTCCATTCAAAATC 42037 i ------ iv vv ------ v v i v i L1P1_orf2#LIN 2240 GA------CAAACAGAGAGCCAAATCATGAGTGAACTCCCATTCACAATT 2283 chrXqtel1M 42038 ATGTCGAT-AGTATAAAATATTTGGGAAT---AGTCA----GGAAGTACA 42079 iiv i v- v ii i --- v i ---- v iv L1P1_orf2#LIN 2284 GCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACAAGGGATGTGAA 2333 chrXqtel1M 42080 ---------CAAATGCAATTACACGACACTTGCCATGCAAATAAAGTCAG 42120 --------- iviv i viv vvi v?v ivvi L1P1_orf2#LIN 2334 GGACCTCTTCAAGGAGAACTACAAACCACTGCTCAANGAAATAAAAGAGG 2383 chrXqtel1M 42121 ATCTAATCAGTTGGAAAAATATCATGTGCTCATGGGTAGGTGGAGCGAAT 42170 vi v iv i i ivii vi iiv L1P1_orf2#LIN 2384 ATACAAACAAATGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAAT 2433 chrXqtel1M 42171 ATAATAACAATGGCAACACTACCTAAACTAATCTACTTATTTAGTGCCAT 42220 vi i v v i i i iv i ivv i i L1P1_orf2#LIN 2434 ATCGTGAAAATGGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCAT 2483 chrXqtel1M 42221 ACCAATCAAACTCCCAAAAAGCTATTTCACAGATCTTGAAAAAA-TACTA 42269 v v i v vi vi vi vi v - - L1P1_orf2#LIN 2484 CCCCATCAAGCTACCAATGACTTTCTTCACAGAATTGGAAAAAACTACT- 2532 chrXqtel1M 42270 ACAAAGTTTATCTGGAAGGACAAAAG----------GTCAAG--AATTTC 42307 vi i v vv v ---------- i -- iii L1P1_orf2#LIN 2533 TTAAAGTTCATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCT 2582 chrXqtel1M 42308 AAG----GAAATTAATG 42320 ----i i vi v L1P1_orf2#LIN 2583 AAGCCAAAAGAACAAAG 2599 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 40.82 CpG sites = 201, Kimura (unadjusted) = 41.63 Transitions / transversions = 1.07 (104/97) Gap_init rate = 0.04 (24 / 664), avg. gap size = 2.67 (64 / 24) 42 0.00 2.38 0.00 chrXqtel1M 42321 42362 (957638) (AAAAC)n#Simple_repeat 1 43 (0) c_b353s251i2 14782 chrXqtel1M 42321 AAAA-AAAACAAAACAAAACAAAACAAAACAAAACAAAACAAA 42362 - (AAAAC)n#Simp 1 AAAACAAAACAAAACAAAACAAAACAAAACAAAACAAAACAAA 43 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.02 (1 / 41), avg. gap size = 1.00 (1 / 1) 1652 31.48 6.30 2.90 chrXqtel1M 42363 42998 (957002) L1P1_orf2#LINE/L1 2600 3238 (56) m_b353s551i3 14781 chrXqtel1M 42363 TGAAGGTAGCCTAGCTGTGCCAGACCTAAAACTATATTATGAAGCAGTGG 42412 i i v vi- -- i v i v i ii i viii L1P1_orf2#LIN 2600 TGGAGGCATCAC-GC--TACCTGACTTCAAACTATACTACAAGGCTACAG 2646 chrXqtel1M 42413 TCACCAAAACCATTTGGTACTGG--CTAAGAAAGAGAATGTCAATTAATG 42460 v viiv -- i i v - i vi i L1P1_orf2#LIN 2647 TAACCAAAACAGCATGGTACTGGTACCAAAACAGAG-ATATAGATCAATG 2695 chrXqtel1M 42461 GAACAGGTTAG-GTTCACAGGATAAAATA--GTCA-ATAACTTTAATAAT 42506 ivi - ii v ---- -- i i- v vi iv L1P1_orf2#LIN 2696 GAACAGAACAGAGCCCTCAG----AAATAACGCCGCATATCTACAACTAT 2741 chrXqtel1M 42507 CTAGTGTGTGACAAACCT-AAAGACCCCAGCTTTTAGGATAAGAATTCAC 42555 ii v v - i i vv v vv vi - i v L1P1_orf2#LIN 2742 CTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGA-AAGGATTCCC 2790 chrXqtel1M 42556 TCTTTGACAAAAACTGCTGGGAAAATTGGAAACTAG---TATGGCAGAAA 42602 v i i viv i --- --- - i L1P1_orf2#LIN 2791 TATTTAATAAATGGTGCTGGGAAAACTGG---CTAGCCATAT-GTAGAAA 2836 chrXqtel1M 42603 TTAGGCAC-GGACCCACACCTAACACCGTATACCAAGATAAGGTAGAAAT 42651 viv iv - i viv v v v i v iv vi i L1P1_orf2#LIN 2837 GCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGAT 2886 chrXqtel1M 42652 GGGTTCATGATTTAGACA-CAGTGCTATTA--ATAAGAAAATTAGAAGAA 42698 i v v i i i-i vv vv -- i vvi L1P1_orf2#LIN 2887 GGATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAA 2936 chrXqtel1M 42699 CAAAGTATAGTTTACC-TCCCAGACCTGTGGAAAAGGAAGGAACTTGTGG 42747 - vv vivv? - i vi v iv v vii v vi ii v L1P1_orf2#LIN 2937 -AACCTAGGCANTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGT 2985 chrXqtel1M 42748 CCAA------AGAAGAACTGGAGTTCATTCTTGAACACAAAATAGATAAT 42791 i ------ i v v viviv ------ vv v i v L1P1_orf2#LIN 2986 CTAAAACACCAAAAGCAATGGCAACAA------AAGCCAAAATTGACAAA 3029 chrXqtel1M 42792 TTTGATTATATTAAGTTAAAAAGTTTTCGTACAGACAAAACCAATGCAGA 42841 vv ivv ii i i ii i - vv ivvvv L1P1_orf2#LIN 3030 TGGGATCTAATTAAACTAAAGAGCTTCTGCACAG-CAAAAGAAACTACCA 3078 chrXqtel1M 42842 CAAGATTGGA-AGGGAAGCCATAAACTGGGGGGGAAATTT----AC--AT 42884 iv v i - v v i i i v i ii v ---- -- i L1P1_orf2#LIN 3079 TCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTAC 3128 chrXqtel1M 42885 TCAAGGTTCTGATAAAGGCCTCATTTCTAAAATATATAAAGAATTGATTC 42934 ---- i v v v i i v i v i v vv L1P1_orf2#LIN 3129 TCA----TCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAAC 3174 chrXqtel1M 42935 AAATTTATAAGAATTTAAACCATTC--TCCAATTGATAAATGGTCAAAGG 42982 i --v v vv --i v ii v i v i L1P1_orf2#LIN 3175 AAATTTACAAGAA--AAAAACAAACAACCCCATCAAAAAGTGGGCGAAGG 3222 chrXqtel1M 42983 ATATGAACAGACAGTT 42998 i v L1P1_orf2#LIN 3223 ACATGAACAGACACTT 3238 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 40.82 CpG sites = 201, Kimura (unadjusted) = 41.63 Transitions / transversions = 0.97 (97/100) Gap_init rate = 0.07 (42 / 635), avg. gap size = 1.36 (57 / 42) 327 30.29 4.41 2.90 chrXqtel1M 42780 43051 (956949) L1M3_orf2#LINE/L1 3013 3288 (0) m_b353s551i4 14781 chrXqtel1M 42780 AAAATAGATAATTTTGATTATATTAAGTTAAAAAGTTTTCGTACAGACAA 42829 i v vv i i i ii i ii i vv L1M3_orf2#LIN 3013 AAAATAGACAAGTGGGACTACATCAAACTAAAAAGCTTCTGCACAGCAAA 3062 chrXqtel1M 42830 --AACCAATGCAGACAAGATTGGAAGGGAAGCCATAAACTGGGGGGGAA- 42876 -- v - - iii vii v v i iii v i ii - L1M3_orf2#LIN 3063 GGAAACAAT-CA-ACAGAGTGAAAAGGCAACCTACGGAATGGGAGAAAAT 3110 chrXqtel1M 42877 ATTTACATTCAAGGT-TCTGATAAAGGCCTCATTTCTAAAATATATAAAG 42925 i vv v vi - i vi v v i i L1M3_orf2#LIN 3111 ATTTGCAAACCATATATCTGATAAGGGGTTAATATCCAAAATATATAAGG 3160 chrXqtel1M 42926 AATTGATTCAAATTTATAAGAATTTAAACC--ATTCTCCAATTGATAAAT 42973 i v? v v iv iv --v v -- vvi i ? v L1M3_orf2#LIN 3161 AACTCNTACAACTCAATAGCAA--AAAAACAAATAACCCGATTNAAAAAT 3208 chrXqtel1M 42974 GGTCAAAGGATATGAACAGACAGTTT------GAAGGTAAAGAAATTGAA 43017 v iv i v i------ ii v v v vv L1M3_orf2#LIN 3209 GGGCAAAGGACCTGAATAGACATTTCTCCAAAGAAGACATACAAATGGCC 3258 chrXqtel1M 43018 ACCATTTCTAGTCATGAAAAGGTGCTCTAAATCA 43051 v vv v ---- i v v L1M3_orf2#LIN 3259 AACAGGTAT----ATGAAAAGATGCTCAACATCA 3288 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 38.35 CpG sites = 39, Kimura (unadjusted) = 39.66 Transitions / transversions = 0.95 (39/41) Gap_init rate = 0.04 (12 / 271), avg. gap size = 1.67 (20 / 12) 506 26.98 1.06 0.00 chrXqtel1M 42904 43092 (956908) L1ME4b_3end#LINE/L1 1 191 (701) m_b353s551i5 14781 chrXqtel1M 42904 CTCATTTCTAAAATATATAAAGAATTGATTCAAATTTATAAGAATTTAAA 42953 v ivv ii vv v iv vvvi v L1ME4b_3end#L 1 CTAATTTCCCTAATATATAAAGAGCTCCTACAAATCAATAAGAAAAAGAC 50 chrXqtel1M 42954 CCATTCTCCAATTGATAAATGGTCAAAGGATATGAACAGACAGTTTGAAG 43003 v ivvi v v v iiv L1ME4b_3end#L 51 CAACAACCCAATAGAAAAATGGGCAAAGGATATGAACAGACAGTTCACAG 100 chrXqtel1M 43004 GTAAAGAAATTGAAACCATTTCTAGTC--ATGAAAAGGTGCTCTAAATCA 43051 iv i vv ivii ii iv -- i v vv L1ME4b_3end#L 101 AAAAGGAAATACAAATGGCTCTTAAACATATGAAAAGATGCTCAACCTCA 150 chrXqtel1M 43052 CTATTGATCAGAGAAATGCAAATTAAAACAACTCTGAGGTA 43092 vv i v v v i L1ME4b_3end#L 151 CTCATAATAAGAGAAATGCAAATTAAAACTACACTGAGATA 191 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 33.49 CpG sites = 20, Kimura (unadjusted) = 33.49 Transitions / transversions = 0.65 (20/31) Gap_init rate = 0.01 (1 / 188), avg. gap size = 2.00 (2 / 1) 228 26.88 3.12 3.12 chrXqtel1M 43558 43653 (956347) C L1M4c_5end#LINE/L1 (29) 2471 2376 m_b353s551i6 14783 chrXqtel1M 43558 TTCTAGACAACATATTATTGGATTCTGGTTTCTAAGTCAGTCTTCTATCA 43607 v i vi i? v i vi --- ?ii C L1M4c_5end#LI 2471 TTGTAGACAGCATATAGTTGGATCNTGTTTTTTAATCCA---TTCNGCCA 2425 chrXqtel1M 43608 GCTTCTGTTTT---ATGGATGAGTTTATCCCATTTACGTTCACAATTAT 43653 iii ? i --- v iv vi i i v i v C L1M4c_5end#LI 2424 ATCTNTGTCTTTTGATTGGAGAGTTTAATCCATTTACATTTAAAGTAAT 2376 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 35.98 CpG sites = 16, Kimura (unadjusted) = 35.98 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.04 (4 / 95), avg. gap size = 1.50 (6 / 4) 28 3.33 0.00 0.00 chrXqtel1M 44221 44251 (955749) (T)n#Simple_repeat 1 31 (0) c_b353s251i3 14784 chrXqtel1M 44221 TTTTCTTTTTTTTTTTTTTTTTTTTTTTTTT 44251 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 31 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 60 0.00 0.00 0.00 chrXqtel1M 44924 44974 (955026) (TA)n#Simple_repeat 1 51 (0) c_b353s251i4 14785 chrXqtel1M 44924 TATATATATATATATATATATATATATATATATATATATATATATATATA 44973 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 chrXqtel1M 44974 T 44974 (TA)n#Simple_ 51 T 51 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 50 0.00 0.00 0.00 chrXqtel1M 45619 45661 (954339) (TG)n#Simple_repeat 1 43 (0) c_b353s251i5 14786 chrXqtel1M 45619 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 45661 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 43 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 13 32.57 0.00 0.00 chrXqtel1M 46388 46440 (953560) (TTTT)n#Simple_repeat 1 53 (0) m_b353s252i4 14787 chrXqtel1M 46388 TTTTTTGTTGTTGTTTGCTTGCATTTTGTTTTCTTTCTAATTTTTTTTCT 46437 v v v vi viv v i i vv i (TTTT)n#Simpl 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 chrXqtel1M 46438 TTT 46440 (TTTT)n#Simpl 51 TTT 53 Matrix = Unknown Transitions / transversions = 0.56 (5/9) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 20 4.35 0.00 0.00 chrXqtel1M 47332 47355 (952645) (A)n#Simple_repeat 1 24 (0) m_b353s252i5 14788 chrXqtel1M 47332 AAAAAAAAAAAAAAAAAAAGAAAA 47355 i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAA 24 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 13 26.73 0.00 0.00 chrXqtel1M 47482 47522 (952478) (TTTTT)n#Simple_repeat 1 41 (0) m_b353s252i6 14789 chrXqtel1M 47482 TTATTATTATTTTCTTTCCTTCTTTCTTTTCTTTTTTTTTT 47522 v v v i ii i i i (TTTTT)n#Simp 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 41 Matrix = Unknown Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 15 11.54 0.00 3.33 chrXqtel1M 47492 47522 (952478) (TTTC)n#Simple_repeat 1 30 (0) m_b353s252i8 14789 chrXqtel1M 47492 TTTCTTTCCTTCTTTCTTTTCTTTTTTTTTT 47522 i - i i (TTTC)n#Simpl 1 TTTCTTTCTTTCTTTC-TTTCTTTCTTTCTT 30 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.03 (1 / 30), avg. gap size = 1.00 (1 / 1) 14 10.78 0.00 6.25 chrXqtel1M 47488 47521 (952479) (TTCTT)n#Simple_repeat 1 32 (0) m_b353s252i7 14790 chrXqtel1M 47488 TTATTTTCTTTCCTTCTTTCTTTTCTTTTTTTTT 47521 v i - - i (TTCTT)n#Simp 1 TTCTTTTCTTTTC-T-TTTCTTTTCTTTTCTTTT 32 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2) 12 9.24 0.00 4.17 chrXqtel1M 47611 47635 (952365) (TCCC)n#Simple_repeat 1 24 (0) m_b353s252i9 14791 chrXqtel1M 47611 TCCCTCCCACCCTCCACCCCCTCCC 47635 v - i (TCCC)n#Simpl 1 TCCCTCCCTCCCTCC-CTCCCTCCC 24 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 1487 31.03 2.23 0.79 chrXqtel1M 47933 48559 (951441) C L1ME4c_3end#LINE/L1 (191) 639 4 m_b353s551i7 14792 chrXqtel1M 47933 TTCTGCTCATTTCGCTCAGCATCAGTTCATGTAATTCTCTCCAAGCCTCT 47982 iv i i i i vv i- ivi i v iiv C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATA-AACATTTTCCATGTTGCT 591 chrXqtel1M 47983 CTGTATACATCCTGCTGGTCATTTCTTACAGAACAATGATACTCCATAAC 48032 vii vv v v iv vi i v ii vvvv i i viv C L1ME4c_3end#L 590 ACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCGA 541 chrXqtel1M 48033 ATTCATATAT-ACAATTTACCCAACCATTCTCCAATGGATGGGCATCCCT 48081 i ?v i i- i ii i v v v i iivv C L1ME4c_3end#L 540 GTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAG 491 chrXqtel1M 48082 TCATTTTCCAGTTTCTAGCCACTACAAACAGGGCTGCCACAAACATTTTG 48131 vivv i i v i i i i iv v ii i v C L1ME4c_3end#L 490 GTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTC 441 chrXqtel1M 48132 GCACATACAGGTCCCTTTGCCTTCTTT---AGTATCTCCT-AG------- 48170 ii i --- i v --- v i - ------- C L1ME4c_3end#L 440 GTGCATATAG---CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAAT 394 chrXqtel1M 48171 -CCCAGTAGTAGCACTGCTGGATCAAAGGGGATGCACAGTTTGATTACTT 48219 - v i v i i i v v v v vi i C L1ME4c_3end#L 393 TCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTC 344 chrXqtel1M 48220 TTGGGGCATAATTCCAGATTGCTCTCCATTAATGGTTGGATCCGTTCACG 48269 ivi i v v i i v- v v i vi i i C L1ME4c_3end#L 343 TTGATACGTATTGCCAAATTGCTTTCCAA-AAGGGTTGTACCAATTTACA 295 chrXqtel1M 48270 ACTCCACCAACAATGCATCAGTGTCCCAGTTTTCCCGCATCCCCTCCAAC 48319 ?iv i i v ? v iv ? i v i C L1ME4c_3end#L 294 NTGCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGC 245 chrXqtel1M 48320 ACTCATCATTATTTTTTCCTGTCATCTTAGCCAAACTGACAGGTGTGTAG 48369 i vivi ivv ii vvv i v i vi i i i iv i C L1ME4c_3end#L 244 ATTGGGTATTATCAATTTTTTAAATTTTTGCTAATTTAATAGGCGTAAAA 195 chrXqtel1M 48370 TGGTATCTCAGAGTTGTCTTAATT-GCATTTCTTTGATCAATAGTGATTT 48418 vv ii - i v i vv C L1ME4c_3end#L 194 TGGTATCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACTAGCGAGGT 145 chrXqtel1M 48419 GGAACACTCTTTCATATGAGTGGTAATGATTTCAATTTCATCATCTGAAA 48468 v i i i i vv v v iv ? vv v v ? vi C L1ME4c_3end#L 144 TGAACATTTTTCCATGTGTTTGTTTACTANTTGTATTTCCTCTTNTGTGA 95 chrXqtel1M 48469 ATTGTCTGTTCATATCCTTTGACCACTTGTCAATTGGAGAATGGCTTGGT 48518 i v i i v i vv v v ?vv C L1ME4c_3end#L 94 ATTGTCTGTTCATGTCCTTTGCCCATTTATCTATTGGGGTCTTGATNTTT 45 chrXqtel1M 48519 TTCTTATAAATTAGAGTCAGCTCTCTCTATATTTTGGAAAT 48559 v v i v i v ? v?i v C L1ME4c_3end#L 44 TTCTTATCAATTTGAATGAGCTCTTTATATANTANAGATAT 4 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 40.39 CpG sites = 99, Kimura (unadjusted) = 41.50 Transitions / transversions = 1.05 (99/94) Gap_init rate = 0.02 (11 / 626), avg. gap size = 1.73 (19 / 11) 517 35.75 1.56 1.56 chrXqtel1M 48413 48861 (951139) C L1PB_orf2#LINE/L1 (0) 3294 2846 m_b353s551i8 14792 chrXqtel1M 48413 TGATTTGGAACACTCTTTCATATGAGTGGTAATGATTTCAATTTCATCAT 48462 v v i i i vv v iiiv vv v v v C L1PB_orf2#LIN 3294 TGATGTTGAGCATTTTTTCATATGTTTGTTGGCCATTTGTATATCTTCTT 3245 chrXqtel1M 48463 CTGAAAATTGTCTGTTCATATCCTTTGACCACTTGTCAATTGGAGAATGG 48512 i i i i v v v ii v vvi vv C L1PB_orf2#LIN 3244 TTGAGAATTGTCTATTCATGTCCTTAGCCCACTTTTTGATGGGATTGTTT 3195 chrXqtel1M 48513 CTTGGTTTCTTATAAATTAGAGTCAGCTCTCTCTATATTTTGGAAATGAG 48562 v vv iivi v vv v i ?i v v i v v C L1PB_orf2#LIN 3194 GTTTTTTTCTTGCTGATTTGTTTGAGTTCNTTGTAGATTCTGGATATTAG 3145 chrXqtel1M 48563 GCCTTTATCAGAACCTTTAACTGTGAAAATGTTTTCCCAGTTTGTTGCTT 48612 v i vviv vi i i v i v i v v C L1PB_orf2#LIN 3144 TCCTTTGTCAGATGTATAGATTGTGAAGATTTTCTCCCACTCTGTGGGTT 3095 chrXqtel1M 48613 CCCTTCTAATCTTGTTTGC-ATTAGTTTTGTTTGTACAGAAGCTTTTTAA 48661 vi vi v iii i vi -i vv -ii i i i C L1PB_orf2#LIN 3094 GTCTGTTTACTCTGCTGACTGTTCCTTTTG-CCGTGCAGAAGCTCTTTAG 3046 chrXqtel1M 48662 TTTGATGTATTCAAAATTTCCTAT-TTTGTGATCA--GTAATGGTCTCTA 48708 i vv v vv ?i vii - vv ii-- i v v ii i i C L1PB_orf2#LIN 3045 TTTAATTAAGTCCCANCTATTTATCTTTGTTTTTGTTGCATTTGCTTTTG 2996 chrXqtel1M 48709 GTTCGTCTTTGGTCACAAATTTCTT-CCTCCTCCACAAGTCTGAGAGACA 48757 --- ii ii v i - vvv - v iii --i C L1PB_orf2#LIN 2995 G---GTTCTTGGTCATGAAGTCCTTGCCTAAGCCA-ATGTCTAGAAG--G 2952 chrXqtel1M 48758 AACTATCCTATGT--TCCTCCAATTTGTTTATGATCTCGTTCTTTATGTC 48805 ivi v v -- i i ivv v i i ivvii vi i C L1PB_orf2#LIN 2951 GTTTTTCCGATGTTATCTTCTAGAATTTTTATGGTTTCAGGTCTTAGATT 2902 chrXqtel1M 48806 TAGATCATGGACCCATTTTGATCTTATCTTGGTATATGGTGTTAAATGTG 48855 ii v v i i vi v i v v vv i v C L1PB_orf2#LIN 2901 TAAGTCCTTGATCCATCTTGAGTTGATTTTTGTATAAGGTGAGAGATGAG 2852 chrXqtel1M 48856 GGTCCA 48861 i C L1PB_orf2#LIN 2851 GATCCA 2846 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 49.36 CpG sites = 79, Kimura (unadjusted) = 49.80 Transitions / transversions = 1.00 (79/79) Gap_init rate = 0.03 (12 / 448), avg. gap size = 1.17 (14 / 12) 452 21.03 0.00 8.70 chrXqtel1M 49493 49617 (950383) MIRc#SINE/MIR 1 115 (153) m_b353s601i6 14793 chrXqtel1M 49493 CGGGGCAGCTAGGTAGCACGGTGGATAGAGCACCGGCCCTGAAGCCAGGA 49542 i i--- i ii i v i v i i i MIRc#SINE/MIR 1 CGAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGA 47 chrXqtel1M 49543 GGACCCGGGTTCACATGTGGTCTCAGGCACTTAACACTTCCTAGCTGTGT 49592 i i i-----i i - v -iv v MIRc#SINE/MIR 48 AGACCTGGGTTCG-----AGTCCC-GGCTCT-GCCACTTACTAGCTGTGT 90 chrXqtel1M 49593 GACCCTGGGCAAGTCACTTAGCCCC 49617 i i i MIRc#SINE/MIR 91 GACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 24.45 CpG sites = 19, Kimura (unadjusted) = 25.69 Transitions / transversions = 3.80 (19/5) Gap_init rate = 0.08 (10 / 124), avg. gap size = 1.00 (10 / 10) 21 11.73 4.17 2.04 chrXqtel1M 49627 49674 (950326) (AGAAAA)n#Simple_repeat 1 49 (0) m_b353s252i10 14794 chrXqtel1M 49627 AGAAAAAGAAAAAGAAAAAG-AAAGGAAAAA-ACTTAGATTAAAGAAAAA 49674 - i - vvv -v (AGAAAA)n#Sim 1 AGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGA-AAAAGAAAAA 49 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.06 (3 / 47), avg. gap size = 1.00 (3 / 3) 12 14.84 0.00 11.90 chrXqtel1M 49630 49676 (950324) (AAAAG)n#Simple_repeat 1 42 (0) m_b353s252i11 14794 chrXqtel1M 49630 AAAAGAAAAAGAAAAAGAAAGGAAAAAACTTAGATTAAAGAAAAAAA 49676 - - i i -vv -- i (AAAAG)n#Simp 1 AAAAG-AAAAG-AAAAGAAAAGAAAAGA-AAAGA--AAAGAAAAGAA 42 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.11 (5 / 46), avg. gap size = 1.00 (5 / 5) 16 16.80 0.00 0.00 chrXqtel1M 49790 49816 (950184) (C)n#Simple_repeat 1 27 (0) m_b353s252i12 14795 chrXqtel1M 49790 CCCCCCACCCCCACCCCCCACCCCGCC 49816 v v v v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCC 27 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 196 29.82 1.75 0.00 chrXqtel1M 50317 50373 (949627) MIR3#SINE/MIR 145 202 (6) m_b353s601i7 14796 chrXqtel1M 50317 GAAGGTTGGACTGGGTGGTCGCCAAAGCCTCTGGCGGCCCTGACCTTCTG 50366 ii i i i v i i i i vv i i v i MIR3#SINE/MIR 145 GGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTA 194 chrXqtel1M 50367 TG-TCCTA 50373 - i MIR3#SINE/MIR 195 TGATTCTA 202 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 41.14 CpG sites = 13, Kimura (unadjusted) = 41.14 Transitions / transversions = 3.25 (13/4) Gap_init rate = 0.02 (1 / 56), avg. gap size = 1.00 (1 / 1) 18 14.73 0.00 0.00 chrXqtel1M 51710 51739 (948261) (C)n#Simple_repeat 1 30 (0) m_b353s252i13 14797 chrXqtel1M 51710 CCTCCCCCCCCCCCACCCCCGCCTCCCCCC 51739 i v v i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 30 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 17 21.77 0.00 0.00 chrXqtel1M 52172 52205 (947795) (G)n#Simple_repeat 1 34 (0) m_b353s252i14 14798 chrXqtel1M 52172 GGGGGGAGGGGGGAGGGGGGAAGGGGGAAGGGGG 52205 i i ii ii (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 34 Matrix = Unknown Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 210 32.38 6.98 9.52 chrXqtel1M 52251 52465 (947535) L3#LINE/CR1 3735 3944 (155) m_b353s601i8 14799 chrXqtel1M 52251 TGGAAAAGGGAAAACTGAAGGGGGGGCCACTTGCCGAGCTGCCCTCGTTC 52300 i i i v ii i ---- v vi- i i ivvi L3#LINE/CR1 3735 TGGAGAAGAGAAGACTTAGAGGAG----ACATGAT-AGCTGTCTTCAAAT 3779 chrXqtel1M 52301 ATCCGAAGGGCAGTCGTGGACAAGAGGGTTTGG--------TGCCTG--T 52340 ii v i viv v i -------- iv -- L3#LINE/CR1 3780 ATTTGAAGGGCTGTCATGTGGAAGAGGGATTAGACTTATTCTGTGTGGCT 3829 chrXqtel1M 52341 CCAAAGACAGGGATGGGGGCCACGGGGATGGGAGGCCACAGGTGGTGGGA 52390 i ivvi i ivi i vv --v i ii -------- L3#LINE/CR1 3830 CCAGAGGGCAGAACTAGGACCAATGGG--TGGAAGTTACAGG-------- 3869 chrXqtel1M 52391 CAGAGGCACATCTAGGCTTGCAGATGTCAAGAAGAGCTTCC-----ACCC 52435 -- v i v -- - i v i i i ----- i v L3#LINE/CR1 3870 --GAGGCAGATTTCGGCT--CA-ATATAAGGAAGAACTTTCTAACAATCA 3914 chrXqtel1M 52436 CCTCTCTCCCTAAATGGAACGGGCCACCCC 52465 vvv v vv i ii i L3#LINE/CR1 3915 GAGCTGTCCAAAAATGGAATGGGCTGCCTC 3944 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 43.71 CpG sites = 37, Kimura (unadjusted) = 43.71 Transitions / transversions = 1.42 (37/26) Gap_init rate = 0.11 (23 / 214), avg. gap size = 1.52 (35 / 23) 15 5.48 0.00 0.00 chrXqtel1M 53415 53433 (946567) (C)n#Simple_repeat 1 19 (0) m_b353s252i15 14800 chrXqtel1M 53415 CCCCCCCCCCCCCCCCACC 53433 v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCC 19 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 14 32.06 1.35 2.74 chrXqtel1M 59032 59105 (940895) (GAGGAG)n#Simple_repeat 1 73 (0) m_b353s252i16 14801 chrXqtel1M 59032 GAGAAGTA-GAGGACGCTGGAGGAGGAAAAGGAGTACTGAAGAGTAGGGG 59080 i v - - vv ii v -v i v i (GAGGAG)n#Sim 1 GAGGAGGAGGAGGA-GGAGGAGGAGGAGGAGGAGGA-GGAGGAGGAGGAG 48 chrXqtel1M 59081 GCGGGGGGGGGGGGGGAGGGGAAGG 59105 v i i i i i i (GAGGAG)n#Sim 49 GAGGAGGAGGAGGAGGAGGAGGAGG 73 Matrix = Unknown Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.04 (3 / 73), avg. gap size = 1.00 (3 / 3) 18 8.48 0.00 0.00 chrXqtel1M 59077 59101 (940899) (G)n#Simple_repeat 1 25 (0) m_b353s252i17 14802 chrXqtel1M 59077 GGGGGCGGGGGGGGGGGGGGAGGGG 59101 v i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGG 25 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 15 15.01 0.00 0.00 chrXqtel1M 59078 59107 (940893) (GGGGA)n#Simple_repeat 1 30 (0) m_b353s252i18 14802 chrXqtel1M 59078 GGGGCGGGGGGGGGGGGGGAGGGGAAGGGA 59107 v i i i (GGGGA)n#Simp 1 GGGGAGGGGAGGGGAGGGGAGGGGAGGGGA 30 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 13 23.31 0.00 0.00 chrXqtel1M 59496 59530 (940470) (GAAT)n#Simple_repeat 1 35 (0) m_b353s252i19 14803 chrXqtel1M 59496 GACTGACTGAACAAATGATTGAATGAATCAGTGAA 59530 v v ii v v i (GAAT)n#Simpl 1 GAATGAATGAATGAATGAATGAATGAATGAATGAA 35 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 16 25.59 3.23 1.59 chrXqtel1M 60039 60100 (939900) (AGAAA)n#Simple_repeat 1 63 (0) m_b353s252i20 14804 chrXqtel1M 60039 AGAAAAGAAAAGAAGAG-AGACAACCG-AAACAAGATAAAAGGAAGGGAG 60086 i - i v vv - v i v - ii i (AGAAA)n#Simp 1 AGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAA-GAAAAGAA 49 chrXqtel1M 60087 AACAAATGAAAAGA 60100 v v (AGAAA)n#Simp 50 AAGAAAAGAAAAGA 63 Matrix = Unknown Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.05 (3 / 61), avg. gap size = 1.00 (3 / 3) 23 15.09 1.82 3.70 chrXqtel1M 62931 62985 (937015) (GCC)n#Simple_repeat 1 54 (0) m_b353s252i21 14805 chrXqtel1M 62931 GCCGGCCGCCGCCACCGCAGCCGCCGCCGCCGCCGCAGTCCCCTGCC-CG 62979 - i v v - v i - v (GCC)n#Simple 1 GCC-GCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCG-CCGCCGCCGCC 48 chrXqtel1M 62980 GCGGCC 62985 v (GCC)n#Simple 49 GCCGCC 54 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.06 (3 / 54), avg. gap size = 1.00 (3 / 3) 13 19.22 2.78 0.00 chrXqtel1M 63337 63372 (936628) (GGGAGG)n#Simple_repeat 1 37 (0) m_b353s252i22 14806 chrXqtel1M 63337 GGGAGGAGG-GGTGGGGGGGGGCGGGGAGGGGGAAGG 63372 i - v i iv i (GGGAGG)n#Sim 1 GGGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGGAGGG 37 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) 18 17.72 0.00 0.00 chrXqtel1M 63337 63368 (936632) (G)n#Simple_repeat 1 32 (0) m_b353s252i23 14806 chrXqtel1M 63337 GGGAGGAGGGGTGGGGGGGGGCGGGGAGGGGG 63368 i i v v i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 32 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 235 22.67 2.60 2.60 chrXqtel1M 65058 65134 (934866) Charlie1b#DNA/hAT-Charlie 31 107 (416) m_b353s502i0 14807 chrXqtel1M 65058 CCTCGGGGTCCCAGAGCCCCTTTTCAGGGGGGTCCAACAAGGCAAAACAA 65107 v v v - - ivv i v v Charlie1b#DNA 31 CCTGGGGGTCCCCGAGACCC-TTTCA-GGGGGTCCGCGAGGTCAAAACTA 78 chrXqtel1M 65108 GTCT-ACGAGAATACCGAGACATT-TTTG 65134 v i - ii v ii i - Charlie1b#DNA 79 TTTTCATAATAATACTAAGACGTTATTTG 107 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 23.66 CpG sites = 8, Kimura (unadjusted) = 27.13 Transitions / transversions = 0.89 (8/9) Gap_init rate = 0.05 (4 / 76), avg. gap size = 1.00 (4 / 4) 12 15.85 0.00 3.45 chrXqtel1M 69075 69104 (930896) (GCCCA)n#Simple_repeat 1 29 (0) m_b353s252i24 14808 chrXqtel1M 69075 GCCCGGCCCAGCCCAGTCCTGCCTCACCCC 69104 i i v - v (GCCCA)n#Simp 1 GCCCAGCCCAGCCCAGCCCAGCC-CAGCCC 29 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 277 30.39 2.91 0.95 chrXqtel1M 69614 69716 (930284) C MIRb#SINE/MIR (150) 118 14 m_b353s601i9 14809 chrXqtel1M 69614 GAGACTGAGGGACTTGCCTCAGGGCACCCAGCTGGTCC-TAACAAGAGGC 69662 ii i vi iv v v i vv- ii - v C MIRb#SINE/MIR 118 GAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCA-GAGCC 70 chrXqtel1M 69663 AGGATTTGAACCCAGGGCT-TCGGACCGTAAAGCCGAGAACCCTTCCA-T 69710 i i v - v ivi vivivi i - C MIRb#SINE/MIR 69 GGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACT 20 chrXqtel1M 69711 GTATCA 69716 i i C MIRb#SINE/MIR 19 GCACCA 14 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 35.24 CpG sites = 18, Kimura (unadjusted) = 40.09 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.04 (4 / 102), avg. gap size = 1.00 (4 / 4) 398 25.73 6.56 6.56 chrXqtel1M 71376 71558 (928442) MIR1_Amn#SINE/MIR 20 202 (28) m_b353s601i10 14810 chrXqtel1M 71376 AACGGCTAGAACAGCAGCCTGGGGATCTGCAAGACTCATCGTGGTGAGTT 71425 ii v i vii v iv v -i i-------- i MIR1_Amn#SINE 20 AGTGGATAGAGCACTGGACTGGGACTCGG-GAGACC--------TGGGTT 60 chrXqtel1M 71426 CAAATCCAACCTTGGACCCTTACTATCCGTGTGACCCTAGGCAAGTCACT 71475 ? ? viv iv v v ?i i?v i ? i i MIR1_Amn#SINE 61 CNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGTCACT 110 chrXqtel1M 71476 TCACC-CTATTTGCCTCAGTACCCTCGTCTGTAAAAGGAGCCGGAGAAGG 71524 ? - v v? vi i v i--- v v MIR1_Amn#SINE 111 TNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGG---GGATAATG 157 chrXqtel1M 71525 AAACGGTCGACC----------GCTTCGAGATCT-CTGCTGAGAA 71558 v v v vv ---------- i - v i MIR1_Amn#SINE 158 ATACTGACCTCCTTTGTAAAGTGCTTTGAGATCTACTGATGAAAA 202 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 32.57 CpG sites = 21, Kimura (unadjusted) = 33.47 Transitions / transversions = 0.91 (21/23) Gap_init rate = 0.08 (15 / 182), avg. gap size = 1.60 (24 / 15) 411 27.52 0.76 6.40 chrXqtel1M 71383 71514 (928486) MIRc#SINE/MIR 24 148 (120) m_b353s601i11 14810 chrXqtel1M 71383 AGAACAGCAGCCTGGGGATCTGCAAGACTCATCGTGGTGAGTTCAAATCC 71432 i vii v v ii v v i-------- i i i MIRc#SINE/MIR 24 AGAGCACTGGACTTGGAGTCAGGAAGACC--------TGGGTTCGAGTCC 65 chrXqtel1M 71433 AACCTTGGACCCTTACTATCCGTGTGACCCTAGGCAAGTCACTTCACC-C 71481 viv iv v v v i i i v - MIRc#SINE/MIR 66 CGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 chrXqtel1M 71482 TATTTGCCTCAGTACCCTCGTCTGTAAAAGGAG 71514 v vv vi i v i MIRc#SINE/MIR 116 TCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 32.10 CpG sites = 17, Kimura (unadjusted) = 34.50 Transitions / transversions = 1.00 (17/17) Gap_init rate = 0.07 (9 / 131), avg. gap size = 1.00 (9 / 9) 415 23.16 1.05 0.00 chrXqtel1M 71420 71514 (928486) MIR#SINE/MIR 49 144 (118) m_b353s601i12 14810 chrXqtel1M 71420 TGAGTTCAAATCCAACCTTGGACCCTTACTATCCGTGTGACCCTAGGCAA 71469 i i viv iv v v v i i i MIR#SINE/MIR 49 TGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 98 chrXqtel1M 71470 GTCACTTCACC-CTATTTGCCTCAGTACCCTCGTCTGTAAAAGGAG 71514 i v - v v vi i v i MIR#SINE/MIR 99 GTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGG 144 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 25.10 CpG sites = 11, Kimura (unadjusted) = 27.92 Transitions / transversions = 1.00 (11/11) Gap_init rate = 0.01 (1 / 94), avg. gap size = 1.00 (1 / 1) 15 5.48 0.00 0.00 chrXqtel1M 72489 72507 (927493) (C)n#Simple_repeat 1 19 (0) m_b353s252i25 14811 chrXqtel1M 72489 CCCCCCGCCCCCCCCCCCC 72507 v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCC 19 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 35 17.52 3.96 3.96 chrXqtel1M 72677 72777 (927223) (GGAA)n#Simple_repeat 1 101 (0) m_b353s252i26 14812 chrXqtel1M 72677 GGAAGGAA-GAAGGAAAGAAAGAGAGGAAAGGAGGGGGGGGGGGGAGGGA 72725 - i i - - -i ii ii i (GGAA)n#Simpl 1 GGAAGGAAGGAAGGAAGGAAGGA-AGG-AAGGA-AGGAAGGAAGGAAGGA 47 chrXqtel1M 72726 AAGAGAGGAAGCAAGGAA-GAAGGGAGG-AGGAAGGAAAAAAGGAA-GAA 72772 i - v - i - ii - (GGAA)n#Simpl 48 AGGA-AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 96 chrXqtel1M 72773 AGAAG 72777 i (GGAA)n#Simpl 97 GGAAG 101 Matrix = Unknown Transitions / transversions = 13.00 (13/1) Gap_init rate = 0.08 (8 / 100), avg. gap size = 1.00 (8 / 8) 245 27.25 0.91 9.90 chrXqtel1M 73602 73711 (926289) MIRb#SINE/MIR 162 262 (6) m_b353s601i13 14813 chrXqtel1M 73602 CCGACCTCCGAGGATGCTCGGGAGGATCGCGTGATTGGGACACGGTTACT 73651 v vv i vv i v ---- i v i i v--- i v MIRb#SINE/MIR 162 CCTACCTCGCAGGGTTGTTGTGAGGAT----TAAATGAGATAA---TGCA 204 chrXqtel1M 73652 TAGCACAGTGCCTAGCACCTAGTGCCTGGTAC-TCGCAGGCTCTTAATAA 73700 - i v i i -- i - v i i v i MIRb#SINE/MIR 205 T-GTAAAGCGCTTAGCAC--AGTGCCTGGCACATAGTAAGCGCTCAATAA 251 chrXqtel1M 73701 ATGGTTGTTCT 73711 v i MIRb#SINE/MIR 252 ATGGTAGCTCT 262 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 32.41 CpG sites = 14, Kimura (unadjusted) = 33.91 Transitions / transversions = 1.08 (14/13) Gap_init rate = 0.10 (11 / 109), avg. gap size = 1.00 (11 / 11) 251 16.99 1.82 3.70 chrXqtel1M 73655 73709 (926291) L2d2_3end#LINE/L2 490 543 (12) m_b353s601i14 14814 chrXqtel1M 73655 CACAGTGCCTAGCACCTAGTGCCTGGTACTC-GCAGGCTCTTAATAAATG 73703 i -- v i v - i v i i L2d2_3end#LIN 490 CACAGCGCCTAGCAC--AGTGCCTTGCACACAGTAGGCGCTCAATAAATA 537 chrXqtel1M 73704 GTTGTT 73709 v L2d2_3end#LIN 538 TTTGTT 543 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 17.17 CpG sites = 5, Kimura (unadjusted) = 19.43 Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.06 (3 / 54), avg. gap size = 1.00 (3 / 3) 416 24.82 2.36 4.84 chrXqtel1M 73801 73927 (926073) C L2c_3end#LINE/L2 (3) 475 352 m_b353s601i15 14815 chrXqtel1M 73801 CAGTCAGTCAACAAACATTTCTTAAGGACCTACTGTGTGCCAGGTGCTGG 73850 v v v i vi i i C L2c_3end#LINE 475 CATTCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGG 426 chrXqtel1M 73851 GGATACAAAGAAAGGCAGACCAAAGCCCCTGCCCTTGATGCGAAGGAAGA 73900 viiii iiv vi i i------ ivv C L2c_3end#LINE 425 GGATACAAAGATGAATAAGACACGGTCCCTGCCCTC------AAGGAGCT 382 chrXqtel1M 73901 AACA---CAGGGGAGGTGGCAGGCAAGGAA 73927 v ---i v v i i ? v C L2c_3end#LINE 381 CACAGTCTAGTGGAGGAGACAGACANGTAA 352 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 27.39 CpG sites = 17, Kimura (unadjusted) = 30.96 Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.06 (7 / 126), avg. gap size = 1.29 (9 / 7) 12 16.14 3.45 0.00 chrXqtel1M 74367 74395 (925605) (AAAGG)n#Simple_repeat 1 30 (0) m_b353s252i27 14816 chrXqtel1M 74367 AAGGGGAAGGAAAGG-AAGGAAAAAAAAGG 74395 i i - ii (AAAGG)n#Simp 1 AAAGGAAAGGAAAGGAAAGGAAAGGAAAGG 30 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1) 27 25.72 0.00 0.00 chrXqtel1M 74545 74606 (925394) (AA)n#Simple_repeat 1 62 (0) m_b353s252i28 14817 chrXqtel1M 74545 AAAAAAAAAATTAAGGGGGAAAAAAAAGGGAAAAGAAAAAAAAAAAATGA 74594 vv iiiii iii i vi (AA)n#Simple_ 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chrXqtel1M 74595 AAAAAAAAAAAA 74606 (AA)n#Simple_ 51 AAAAAAAAAAAA 62 Matrix = Unknown Transitions / transversions = 3.33 (10/3) Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0) 690 57.35 0.00 0.00 chrXqtel1M 75162 79092 (920908) (AA)n#Simple_repeat 1 3931 (0) m_b354s252i2 14818 chrXqtel1M 75162 AAAAAAAGGAAAAAAAAGGGAAAAAAAGGAAAAAAGGGGAAAGGAAAAGG 75211 ii iii ii iiii ii ii (AA)n#Simple_ 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chrXqtel1M 75212 GGAAAAAAAAAAAAAAAGGAAAAGAAAAGAAAAAAAAAAAAAAAAGGAAA 75261 ii ii i i ii (AA)n#Simple_ 51 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 100 chrXqtel1M 75262 GGGAAAATGGAAAATGGAAAGGGAAAAGGGAAAAGATAAAAAAAAGGGGG 75311 iii vii vii iii iii i v iiiii (AA)n#Simple_ 101 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 150 chrXqtel1M 75312 AAAAAAAAAAAAAGGGAAAAAAAAAGGGGAAAGGAAAAAGGAAAAAAAAA 75361 iii iiii ii ii (AA)n#Simple_ 151 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 200 chrXqtel1M 75362 AAGGGGGGGGAATAAAAAAAAAGGGGGAAAAAAATTTAAATTAAAAAAAT 75411 iiiiiiii v iiiii vvv vv v (AA)n#Simple_ 201 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 250 chrXqtel1M 75412 AAAAAAAGAAAAAAGAAAAAGGGGAAAAATTTGGAAAAAAGGGGGAAGGA 75461 i i iiii vvvii iiiii ii (AA)n#Simple_ 251 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 300 chrXqtel1M 75462 AAAAGAAAAAAAAAAAAAGGAAAAGAAAAAAAAAAAAAAGGCAGGAAGGA 75511 i ii i iiv ii ii (AA)n#Simple_ 301 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 350 chrXqtel1M 75512 AAAAAAGGAAATTTAAAGAATTTAAAAAAAAAAAAAAAAAAAAAGGGAAA 75561 ii vvv i vvv iii (AA)n#Simple_ 351 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 400 chrXqtel1M 75562 AAGGGAAAAGGAAAAAGGGAAAAAAAAAAAGATTAAAAAAGAAAAGGGAA 75611 iii ii iii i vv i iii (AA)n#Simple_ 401 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 450 chrXqtel1M 75612 AAAAAAAAAAAAAAAAAAAAAAAAAAGGGAAAAAAAGGGGGAAAAAAGGG 75661 iii iiiii iii (AA)n#Simple_ 451 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 500 chrXqtel1M 75662 GGAAAAGGGAAAAAGGGCCGGGGAAAAATTAAAAAAAAAAAAAGGGGGGT 75711 ii iii iiivviiii vv iiiiiiv (AA)n#Simple_ 501 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 550 chrXqtel1M 75712 TAAAAAAAAAGGAAAAAAAAAAAAAAAGGGGAAAAGGAAAAAAAAAAAGG 75761 v ii iiii ii ii (AA)n#Simple_ 551 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 600 chrXqtel1M 75762 GGGGAAATTAGGGAAAAAGGGGAAAAAAAAGAAGGGAAAGGAAAAAAAGG 75811 iiii vv iii iiii i iii ii ii (AA)n#Simple_ 601 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 650 chrXqtel1M 75812 AAAAAAGGGGAAAAGGAAAAAAAGGGGGGGGGGGAAAAGGGGAAAAAGGG 75861 iiii ii iiiiiiiiiii iiii iii (AA)n#Simple_ 651 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 700 chrXqtel1M 75862 GAAGGAAAAAAGGGAAAAAAAAAAAAAAAAATTAAAAGGGAAAAAAAAAG 75911 i ii iii vv iii i (AA)n#Simple_ 701 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 750 chrXqtel1M 75912 GGGGGAAAAAAAAAGGAAAAGGGGAAAAAAAAATAAAAAAAAAAAAAAGG 75961 iiiii ii iiii v ii (AA)n#Simple_ 751 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 800 chrXqtel1M 75962 AAAAAGGGGAAAGGAAAAGGGAAATTAAAAAAAAAGGGGAAAGGGAAAAG 76011 iiii ii iii vv iiii iii i (AA)n#Simple_ 801 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 850 chrXqtel1M 76012 GGGGAAAGGGGAATGGGAAAAAGGGGAAAGGGAAAAAAAAAAAGGGAAAC 76061 iiii iiii viii iiii iii iii v (AA)n#Simple_ 851 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 900 chrXqtel1M 76062 AAAATTTGGGAATTAAAAAAAAAATTAAAAGGGAATTTAAGAAAAAAAAA 76111 vvviii vv vv iii vvv i (AA)n#Simple_ 901 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 950 chrXqtel1M 76112 AATTGGGGGAAAAAAAAAAAACCAGGGAAAAGGGGGGAAAAAAAAAAAAA 76161 vviiiii vv iii iiiiii (AA)n#Simple_ 951 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1000 chrXqtel1M 76162 AAGAAAAAAAGGGAAAAAAAAAAGGGGGGGGTAAAAGGGGAAAAAAAAAA 76211 i iii iiiiiiiiv iiii (AA)n#Simple_ 1001 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1050 chrXqtel1M 76212 AAAAAGGAAAGGGGGGAAAAAAAAAAAGAAAAAAAGGGAAGGGGGGGGGG 76261 ii iiiiii i iii iiiiiiiiii (AA)n#Simple_ 1051 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1100 chrXqtel1M 76262 CCCGGAAAAGGATTGGGAAAGGAAAAGGAAAAAAAAAAAGGGAAAAGGGG 76311 vvvii ii vviii ii ii iii iiii (AA)n#Simple_ 1101 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1150 chrXqtel1M 76312 AAAGGGGGGAAAAAAAAAAAAAGGGGAAAAAGGGAAAAAAAAAGGGGGAA 76361 iiiiii iiii iii iiiii (AA)n#Simple_ 1151 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1200 chrXqtel1M 76362 AAAAAAGAAGGGGAAAAAAAAAAGGGGGGGAAAAAGGGGAAAAAAAAAAA 76411 i iiii iiiiiii iiii (AA)n#Simple_ 1201 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1250 chrXqtel1M 76412 AAAAGGGAAAAAGAAAGAAAAAAGGGAAAAGGAAAAAAAAGGGGGGGAAA 76461 iii i i iii ii iiiiiii (AA)n#Simple_ 1251 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1300 chrXqtel1M 76462 AAAAAAGGGGAAAATTGGGGGAAAGGGAAAAAGAAAAAAAAGGGAAAAAA 76511 iiii vviiiii iii i iii (AA)n#Simple_ 1301 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1350 chrXqtel1M 76512 AGGGGGAAAGGAAAAAAAAGGAAAAAAAGGGAAAAAAGGGGGAAAAAAAA 76561 iiiii ii ii iii iiiii (AA)n#Simple_ 1351 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1400 chrXqtel1M 76562 GGGATTAAAAAGGAAAAGGAAAAAAAGGAAAAAAAAAAATTAAAGGGGAA 76611 iii vv ii ii ii vv iiii (AA)n#Simple_ 1401 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1450 chrXqtel1M 76612 AAAAAAAAGGAAAAAGGGGAAAAAAAAAAGGGGAAAAAAAAAGGAAAGGG 76661 ii iiii iiii ii iii (AA)n#Simple_ 1451 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1500 chrXqtel1M 76662 GAAAGGAAAAAAAAAAAAAAAAAAAGGGGGAAAAAATGGGGGAAAAAAAA 76711 i ii iiiii viiiii (AA)n#Simple_ 1501 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1550 chrXqtel1M 76712 AAGGGAAATGGGGGAAAAAAGGGAAAAAAAAAAAAAAAGGGAATGGAAAA 76761 iii viiiii iii iii vii (AA)n#Simple_ 1551 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1600 chrXqtel1M 76762 GGGGAAAAGAAAAAAAAAAAAGAAAAAAAAAGGGAAAAAGGGGAAAAGGG 76811 iiii i i iii iiii iii (AA)n#Simple_ 1601 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1650 chrXqtel1M 76812 AAAAGGGGGAAAGGGGGAAAAAAAAAGGGGGGAATTGGGCCCAAAGATGG 76861 iiiii iiiii iiiiii vviiivvv i vii (AA)n#Simple_ 1651 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1700 chrXqtel1M 76862 GAAAAAAAAAAAGGGGGGGGAAGAAAAAAACCAAAAAAAAAGGGAAAATA 76911 i iiiiiiii i vv iii v (AA)n#Simple_ 1701 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1750 chrXqtel1M 76912 AAATTGGTTAAAAAAAAAAGAGGGAAAAGGAAAGGAAAAAAAAAAAAAAA 76961 vviivv i iii ii ii (AA)n#Simple_ 1751 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1800 chrXqtel1M 76962 AAAAAAAAAGGGGGAAAAAGAAAAATAAAAAAAAGGGGGGGAAAAATGAA 77011 iiiii i v iiiiiii vi (AA)n#Simple_ 1801 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1850 chrXqtel1M 77012 AAAGGGGAAAAAAAAAAAAAAAGGAAGAAAAAAACCCAAAAGGGGAAAAA 77061 iiii ii i vvv iiii (AA)n#Simple_ 1851 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1900 chrXqtel1M 77062 GGGAAAAAGGAAAAAAAAAAAAAAAAATGGAGGGGGGAAAGGGGAAAAAA 77111 iii ii vii iiiiii iiii (AA)n#Simple_ 1901 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1950 chrXqtel1M 77112 AAGGGGGAAAAGGAAAGAAAATTTTGGGGGGGAAAGGGGGGGAAAAAGGA 77161 iiiii ii i vvvviiiiiii iiiiiii ii (AA)n#Simple_ 1951 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2000 chrXqtel1M 77162 AAGGGAAAAATCAAAAAAAAAAAAAAAAAAAAAGATTGGAAAAAAAGGAA 77211 iii vv i vvii ii (AA)n#Simple_ 2001 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2050 chrXqtel1M 77212 AAAAAAGGGGAAAGGAAAAAAGAAAAAGGGGGGGGAAAAAAGGGGGGAAA 77261 iiii ii i iiiiiiii iiiiii (AA)n#Simple_ 2051 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2100 chrXqtel1M 77262 GAAGGGAAAAAAAAAGGGAAAAGGGAAAAAAAAGGGAAAAAGGGGAAAAA 77311 i iii iii iii iii iiii (AA)n#Simple_ 2101 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2150 chrXqtel1M 77312 AAAGGGGGGGAAAAAAAAGGGGCCCCGGGGGGGAAAAAAAAAAGGGGGGG 77361 iiiiiii iiiivvvviiiiiii iiiiiii (AA)n#Simple_ 2151 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2200 chrXqtel1M 77362 GGAAAAATTGGAAAAAAAAAAAAAAAAGGGGAAAAGGGAAAAAAAAAAAA 77411 ii vvii iiii iii (AA)n#Simple_ 2201 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2250 chrXqtel1M 77412 AAAAGGGGGGGGGGAAAAATAAGGAAAAGGGAAAAAAAAAAAGGGGAAAA 77461 iiiiiiiiii v ii iii iiii (AA)n#Simple_ 2251 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2300 chrXqtel1M 77462 AAAAAGGAAAAAAAAAGGAAAGGAAAAAAAGGAAAAAAGGGGGTTAAAAA 77511 ii ii ii ii iiiiivv (AA)n#Simple_ 2301 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2350 chrXqtel1M 77512 AAGAAAAAAAAAAGAAAAAAAGGGAAAAAGGGAAAAAAAAAAAAAAAAAA 77561 i i iii iii (AA)n#Simple_ 2351 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2400 chrXqtel1M 77562 AATTGGAAAAAGGGGAATAAAGGGAAAAATAAAAAAAAATAAGGAAAAAA 77611 vvii iiii v iii v v ii (AA)n#Simple_ 2401 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2450 chrXqtel1M 77612 AAAAGGGGAAAAAGGGGGGAAAAAGGGAAAAAAAAGGGGGAAAATAAAGG 77661 iiii iiiiii iii iiiii v ii (AA)n#Simple_ 2451 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2500 chrXqtel1M 77662 GGAAAGGGAAAAGGGGAAAAAAAAGGGAGGAAAAAAAAAAAATTTGGGTT 77711 ii iii iiii iii ii vvviiivv (AA)n#Simple_ 2501 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2550 chrXqtel1M 77712 CGGGCCAGGGAAAAAAAAAAAAAAGGGGGAAGGGAAAAAAAGGAAAATAA 77761 viiivv iii iiiii iii ii v (AA)n#Simple_ 2551 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2600 chrXqtel1M 77762 AAAAAAAAAGGGGGGCAAAAAAAAGGGTTAAAAGGGGTTTTTTAAAAAAA 77811 iiiiiiv iiivv iiiivvvvvv (AA)n#Simple_ 2601 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2650 chrXqtel1M 77812 AAATTTTTAAAAAAAAAAAACCGGAAAATTTAATAAAAAATTAAAGGGAA 77861 vvvvv vvii vvv v vv iii (AA)n#Simple_ 2651 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2700 chrXqtel1M 77862 AAAAAAAAAAAAAAAGGGAATGAAAGGGAAAAAAAGGAAAAAAGGGGGGG 77911 iii vi iii ii iiiiiii (AA)n#Simple_ 2701 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2750 chrXqtel1M 77912 AAAAAAAAAGGGGAAAAGGGGGAAAAAATTTAAAAAGGGAAAGGAAAAGG 77961 iiii iiiii vvv iii ii ii (AA)n#Simple_ 2751 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2800 chrXqtel1M 77962 GAAAGAAAAAAGGGGGGAAAAAAAAAAAAAAAGGGGGGGGGAAAAGGGGG 78011 i i iiiiii iiiiiiiii iiiii (AA)n#Simple_ 2801 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2850 chrXqtel1M 78012 GAAAAGGGGGGAAAAAAAAAAAAAGGGAAAAAAAAAAAACCCCAAAAAGG 78061 i iiiiii iii vvvv ii (AA)n#Simple_ 2851 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2900 chrXqtel1M 78062 AAAAAATTGGGAAAGGAAAAGGAAAAGGGTAAAAAGGGAAAAAAAAAAAA 78111 vviii ii ii iiiv iii (AA)n#Simple_ 2901 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2950 chrXqtel1M 78112 AAAAAGGGGAAAAAAAAAAAAAAAAAGGGAAAAAAGGGAAAGATTCCAAA 78161 iiii iii iii i vvvv (AA)n#Simple_ 2951 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 3000 chrXqtel1M 78162 AAAAAAAGGGGGAAAAAAAAAAAAAAAGGGAAAAAAAGAAAAAGGGGGAA 78211 iiiii iii i iiiii (AA)n#Simple_ 3001 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 3050 chrXqtel1M 78212 AAAGGGGAAAAAGGAAAGGAAAAAAAAAGGGAAAAAAAAAAAAAAGGGGG 78261 iiii ii ii iii iiiii (AA)n#Simple_ 3051 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 3100 chrXqtel1M 78262 GGGAAAAAGGGGGAAAAGGAAAAAGAAGGGGAAAAAAAAAAGAAAAAGAA 78311 iii iiiii ii i iiii i i (AA)n#Simple_ 3101 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 3150 chrXqtel1M 78312 AGGGTTTAAATTTAAACAAAAAAAAAAGGGGGAAAAAAAGGGAAATTTGG 78361 iiivvv vvv v iiiii iii vvvii (AA)n#Simple_ 3151 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 3200 chrXqtel1M 78362 AAATAAAAAGGGGGGAAAAAAAAAGGGGAAAAGGGGGGAAAAAAAAGGGG 78411 v iiiiii iiii iiiiii iiii (AA)n#Simple_ 3201 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 3250 chrXqtel1M 78412 GAAAAAAACCGGGGGGGAAAAAAAAAAAAGGAAAAGGGGGGGGGGAAAAA 78461 i vviiiiiii ii iiiiiiiiii (AA)n#Simple_ 3251 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 3300 chrXqtel1M 78462 AAAAAGGGGGAAGGGAAAAAGGGGAAAGGAAATTTAAAAAAAAAAAAAAA 78511 iiiii iii iiii ii vvv (AA)n#Simple_ 3301 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 3350 chrXqtel1M 78512 GGGGGGAAAAAAAAAATTTTAAAAAAGGGGAAAAAAAAAAAAGGAAGGAA 78561 iiiiii vvvv iiii ii ii (AA)n#Simple_ 3351 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 3400 chrXqtel1M 78562 AAAAAGGGGGAAAAAAAAAAAGGAAGGGGGGAAAAAAAAAAATTTAAAAG 78611 iiiii ii iiiiii vvv i (AA)n#Simple_ 3401 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 3450 chrXqtel1M 78612 GGAAGGAAAAAAAAAGATTAAAAAAGGGGCGGAAAAAAAAAAAAAAAAAG 78661 ii ii i vv iiiivii i (AA)n#Simple_ 3451 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 3500 chrXqtel1M 78662 GGGGGGGAAAAAAAAAAAGGGAAAAGGAAGGATTAAAAAAGGAAAGGAAA 78711 iiiiiii iii ii ii vv ii ii (AA)n#Simple_ 3501 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 3550 chrXqtel1M 78712 AAAAAAAAAAGGAAAAAAAAGGAAAAAAGGGGGGAAAAAAAAAAAATTAA 78761 ii ii iiiiii vv (AA)n#Simple_ 3551 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 3600 chrXqtel1M 78762 AAAAAGAAAAAAAAAAAGGGGGGAAAAAAAAAGGAAAAAAAAAAAAAAAG 78811 i iiiiii ii i (AA)n#Simple_ 3601 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 3650 chrXqtel1M 78812 GGCAAAAAAAGGGGGAAAAAAAAAGGGAAAAGAAGGAAAAAAAGGAAAAA 78861 iiv iiiii iii i ii ii (AA)n#Simple_ 3651 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 3700 chrXqtel1M 78862 TTAAAAGAAAAAGAAAAAAAAAAAGGGAAAAGGGAAAAAAAAAAAAAAGG 78911 vv i i iii iii ii (AA)n#Simple_ 3701 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 3750 chrXqtel1M 78912 GAAAAATGAAAAAAAAAAAAAAAAACAAAAAAAAAAAAATAAAAGGGGAA 78961 i vi v v iiii (AA)n#Simple_ 3751 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 3800 chrXqtel1M 78962 AAAAGGAAAGGAAAAAGAAGGAAAGGGGAAAGGAAACAAAAAAAAAAAAA 79011 ii ii i ii iiii ii v (AA)n#Simple_ 3801 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 3850 chrXqtel1M 79012 AAGGGAAGGGGGAAAAAAAATTTAAAAAGGGGAAAAAAAAATAAAAAAGG 79061 iii iiiii vvv iiii v ii (AA)n#Simple_ 3851 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 3900 chrXqtel1M 79062 GGAAAAAAAAAAAAAAAAAAGGGGAAAAAAA 79092 ii iiii (AA)n#Simple_ 3901 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 3931 Matrix = Unknown Transitions / transversions = 5.89 (1148/195) Gap_init rate = 0.00 (0 / 3930), avg. gap size = 0.0 (0 / 0) 690 57.35 0.00 0.00 chrXqtel1M 79968 81692 (918308) (AA)n#Simple_repeat 4807 6531 (0) m_b354s252i3 14819 chrXqtel1M 79968 GAAAAAAAAAAAAAGGGGAAAAAAAAAAAAACCCGGGGGGGAAAAAAAAA 80017 i iiii vvviiiiiii (AA)n#Simple_ 4807 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 4856 chrXqtel1M 80018 AAGAAAAAAAAAACCCAAGGGGAAAAAGGGGAAAAAAAAAAGGAAAAAAG 80067 i vvv iiii iiii ii i (AA)n#Simple_ 4857 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 4906 chrXqtel1M 80068 GGTTTTGGGAAAAAAAAAAAAAAGGGAAAAAATTGGAAATAAAATGGGGG 80117 iivvvviii iii vvii v viiiii (AA)n#Simple_ 4907 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 4956 chrXqtel1M 80118 AAAAAATTTAAAAAAGGGGGGGAAAAAAATTTTAAAAAAAAAAAAAAGGG 80167 vvv iiiiiii vvvv iii (AA)n#Simple_ 4957 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5006 chrXqtel1M 80168 GGAAAAAAAAAATGGAAAGGAAAAAAAGGGGGGAAAAAGGGGAAAAAAAA 80217 ii vii ii iiiiii iiii (AA)n#Simple_ 5007 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5056 chrXqtel1M 80218 AAAAATTTGGAAAAGGGAAAACAAAAGGAAAAAAAGGAAAAGGAAAAAAT 80267 vvvii iii v ii ii ii v (AA)n#Simple_ 5057 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5106 chrXqtel1M 80268 AAAAAAAAAAAAAAAGGAAAGGGAAAGAAAAAAAAAAGGGGGGAAAAAGA 80317 ii iii i iiiiii i (AA)n#Simple_ 5107 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5156 chrXqtel1M 80318 AAGGGGGAAAGGGGGAAAAAAAAGGGGGGAAGGAAAAAAGAAAAAAAAAG 80367 iiiii iiiii iiiiii ii i i (AA)n#Simple_ 5157 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5206 chrXqtel1M 80368 GAAAAAAAGGGAAAAAGAAAGGAAGAAAAAAAAAAAAGGGGGAAAAAGGG 80417 i iii i ii i iiiii iii (AA)n#Simple_ 5207 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5256 chrXqtel1M 80418 GAAGGGGGGGAAAAAGGGGGAAAAGGGAAAAAAAAACCAGAAAAAGGGGA 80467 i iiiiiii iiiii iii vv i iiii (AA)n#Simple_ 5257 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5306 chrXqtel1M 80468 AAAAACCGGAAAAAGGGGGGGAAAAGGAAAGGAAAAAACCAAAGGGAAAG 80517 vvii iiiiiii ii ii vv iii i (AA)n#Simple_ 5307 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5356 chrXqtel1M 80518 GAAAAAAAAAAAAAAGAAAGGGAAAGGGAAAAAATTTGGGAAAAAGGGGA 80567 i i iii iii vvviii iiii (AA)n#Simple_ 5357 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5406 chrXqtel1M 80568 AAAAAAAAAGGGGGAAAGGAAAAGGGGAAAAAAAGGGGGGGGGGGGGAAG 80617 iiiii ii iiii iiiiiiiiiiiii i (AA)n#Simple_ 5407 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5456 chrXqtel1M 80618 GAAAAGGGGGAAAAGGGAATTAAAAAAAAAAAATTTAAAAAAAAAAAGGG 80667 i iiiii iii vv vvv iii (AA)n#Simple_ 5457 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5506 chrXqtel1M 80668 GGAAAAAAAAGGGGGGGAAAAAAAAGGGAGGAAAAAGGGAAAAAAAAAAT 80717 ii iiiiiii iii ii iii v (AA)n#Simple_ 5507 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5556 chrXqtel1M 80718 GGGGAAGGAAAAAAAAAAAAAAGGGAGGGAAAAAAAAAATTTAAGGGGGG 80767 iiii ii iii iii vvv iiiiii (AA)n#Simple_ 5557 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5606 chrXqtel1M 80768 GGGGAAAAAGGGAGGAGGGTTTTGGGGGAAAAAAAAAAAAAAAAAAAAGG 80817 iiii iii ii iiivvvviiiii ii (AA)n#Simple_ 5607 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5656 chrXqtel1M 80818 AAATTAAAAATGGGGGGAAAAAGGGGGGAAAAAAGAAAGGAAAAGGAAAA 80867 vv viiiiii iiiiii i ii ii (AA)n#Simple_ 5657 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5706 chrXqtel1M 80868 AAAAAAAAAAATAAAAAAAGGGAAAAAGGGGGGGGGAAGGGGAAAGGGAA 80917 v iii iiiiiiiii iiii iii (AA)n#Simple_ 5707 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5756 chrXqtel1M 80918 AAACAAAAAAGGGCATAGTTTTTAAAAAAAAAAACCAAAAAAAGGGGGCC 80967 v iiiv v ivvvvv vv iiiiivv (AA)n#Simple_ 5757 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5806 chrXqtel1M 80968 AACCGGGGGAAAAAAAAAAAGAAAAAGGAAAAAGAAAAGGGGAAAAAAAA 81017 vviiiii i ii i iiii (AA)n#Simple_ 5807 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5856 chrXqtel1M 81018 AAAAAGGGGAAAAAAATTAAAAAAAAAGAAAAAAAAAAGGGGGAAAAAAA 81067 iiii vv i iiiii (AA)n#Simple_ 5857 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5906 chrXqtel1M 81068 AAAAAAAAGGGGGAAAAAAAAAGGAAAAGGGAAAAAAAAAAAGAAGGAAA 81117 iiiii ii iii i ii (AA)n#Simple_ 5907 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 5956 chrXqtel1M 81118 GGGGAAAAAGGAAAAAAAAGGAAAATCGAAAGGGGGGAAAAAGGGGGGGG 81167 iiii ii ii vvi iiiiii iiiiiiii (AA)n#Simple_ 5957 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6006 chrXqtel1M 81168 AAAGGGGAAAAAGGAAAAAGGGAAAAGGGGAAAAGGGGAAAAAAAGGGGG 81217 iiii ii iii iiii iiii iiiii (AA)n#Simple_ 6007 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6056 chrXqtel1M 81218 AAAAAAGAAAAAAAAAAAAAAGGGGGGAAAAAAAAAAAGGGAAGGGAAGG 81267 i iiiiii iii iii ii (AA)n#Simple_ 6057 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6106 chrXqtel1M 81268 AAGAAAGGGGGAAAAAAAAAAAAGAAATTTTAAAAAAAAATTTAAAAAAA 81317 i iiiii i vvvv vvv (AA)n#Simple_ 6107 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6156 chrXqtel1M 81318 AAGGGGGGGGGGAAAAGGGGGGGGGGGGAAAAAAAAAAATGGAAAAAAAA 81367 iiiiiiiiii iiiiiiiiiiii vii (AA)n#Simple_ 6157 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6206 chrXqtel1M 81368 AATTTAAAAAGGGAAAAGGGAAAAAAAATGAAAGGGGAAAAATGGAAAAA 81417 vvv iii iii vi iiii vii (AA)n#Simple_ 6207 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6256 chrXqtel1M 81418 AAAAAAAAGGGAAATAGGAAGGAAAGGGAAAAAAAGGGGGGGGGGGGGAA 81467 iii v ii ii iii iiiiiiiiiiiii (AA)n#Simple_ 6257 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6306 chrXqtel1M 81468 AAAAGGGGGGAAAAAAGAAAAAAATGAAAAGAAACCAAAAAATAAAAAAA 81517 iiiiii i vi i vv v (AA)n#Simple_ 6307 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6356 chrXqtel1M 81518 GGGAAAAGGGAAAAAAAAAAAGGGGGAAAAAAGGGAAAAGGGGGAATGGG 81567 iii iii iiiii iii iiiii viii (AA)n#Simple_ 6357 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6406 chrXqtel1M 81568 GGGGGGGAAAGGGGAAAAAAAGGGGGGAAAAAAAAAAAAAAAGGAAAAAA 81617 iiiiiii iiii iiiiii ii (AA)n#Simple_ 6407 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6456 chrXqtel1M 81618 AAAAAAAAGGGGAAAAAAAGGGAAAGGAAAGGGAAAAAAAGGGGGGGAAA 81667 iiii iii ii iii iiiiiii (AA)n#Simple_ 6457 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6506 chrXqtel1M 81668 AAAACCAAAAAACCGAAAAAAAAAA 81692 vv vvi (AA)n#Simple_ 6507 AAAAAAAAAAAAAAAAAAAAAAAAA 6531 Matrix = Unknown Transitions / transversions = 5.82 (547/94) Gap_init rate = 0.00 (0 / 1724), avg. gap size = 0.0 (0 / 0) 690 57.35 0.00 0.00 chrXqtel1M 82078 82919 (917081) (AA)n#Simple_repeat 6917 7758 (0) m_b354s252i4 14820 chrXqtel1M 82078 GAAAGGAAAAAAAAAACCAAAAAAAAAAAGGGAAAAAAAAGGGGGAAAAA 82127 i ii vv iii iiiii (AA)n#Simple_ 6917 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6966 chrXqtel1M 82128 AAAAAAAAAAAAGGGGGAAAAAAGGAAAAAAAAAAGGGGAAAGGGGAAAA 82177 iiiii ii iiii iiii (AA)n#Simple_ 6967 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 7016 chrXqtel1M 82178 AAAAAAAAAAAAAAAGGAAAAAAAAAAAAAGAAAAAATTTGGGGGAAAAA 82227 ii i vvviiiii (AA)n#Simple_ 7017 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 7066 chrXqtel1M 82228 AGGGAAAAGGGGAAAGAGATTAAAAAGGGAAAAAAAAAAATTAAAAAGGG 82277 iii iiii i i vv iii vv iii (AA)n#Simple_ 7067 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 7116 chrXqtel1M 82278 GAAAAAAGGAAAAAAAAAAAAAAAAGGGAAAAAAGGGGGAAAAAAAAAAT 82327 i ii iii iiiii v (AA)n#Simple_ 7117 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 7166 chrXqtel1M 82328 TGGGGAAAAAAAATTGGGGAAAGAAAAAGTTCCAAATAAAAGGAAAAGGG 82377 viiii vviiii i ivvvv v ii iii (AA)n#Simple_ 7167 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 7216 chrXqtel1M 82378 GGAAAAGGAAAAAAGGGGGGGGAAAGGGGGGAAAAAAAAAATTGGGGGGG 82427 ii ii iiiiiiii iiiiii vviiiiiii (AA)n#Simple_ 7217 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 7266 chrXqtel1M 82428 AAAAAAAAAAAAAAAAAAGGGAAAAAAAAAGGAAAAGGGGGGGGGGGGAA 82477 iii ii iiiiiiiiiiii (AA)n#Simple_ 7267 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 7316 chrXqtel1M 82478 AAAGGGGGGAAAAAAAAAATTAAAAAAATAAAAAAAAAAAAAAAAGGGGA 82527 iiiiii vv v iiii (AA)n#Simple_ 7317 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 7366 chrXqtel1M 82528 AAGGAAAAAGGAAAGGGAATTGGGGGGGGGAAAAAGGGAAAAAAAAAAAA 82577 ii ii iii vviiiiiiiii iii (AA)n#Simple_ 7367 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 7416 chrXqtel1M 82578 AAAAGGGAAAAAAAAGAAGGGGAAAAGGGGGGGAAAGGAAAGGGAAAAAA 82627 iii i iiii iiiiiii ii iii (AA)n#Simple_ 7417 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 7466 chrXqtel1M 82628 AAGAAAAAGGGAAGGGAAAAAAAGGGAAAAAAAAAGGGAAGGGGAAAAGG 82677 i iii iii iii iii iiii ii (AA)n#Simple_ 7467 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 7516 chrXqtel1M 82678 GGGGAAAGGAAAAAAAGGGGGCCCAAAGGGGGGGAAAAAAAAAAATTTGG 82727 iiii ii iiiiivvv iiiiiii vvvii (AA)n#Simple_ 7517 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 7566 chrXqtel1M 82728 GGGGGGGAAAAAAAACCAAAAAAAAAAAAAAAATTTTAAAAAAAAAGGGG 82777 iiiiiii vv vvvv iiii (AA)n#Simple_ 7567 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 7616 chrXqtel1M 82778 GGAAAAAAAAAAGGGGGGGTTTTTTAAAAAAAGAAAAAAAAAAAGGAAAA 82827 ii iiiiiiivvvvvv i ii (AA)n#Simple_ 7617 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 7666 chrXqtel1M 82828 AGGGAAAAAAAAAAGAAAAAAGGAAAGGAAGAGACAAAAAAAAAAAAAGA 82877 iii i ii ii i i v i (AA)n#Simple_ 7667 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 7716 chrXqtel1M 82878 AGAAAAAAGGGGGGAAAAAAAAAAAAAAAAAAAAAAGGAAAA 82919 i iiiiii ii (AA)n#Simple_ 7717 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 7758 Matrix = Unknown Transitions / transversions = 5.64 (248/44) Gap_init rate = 0.00 (0 / 841), avg. gap size = 0.0 (0 / 0) 356 27.37 4.73 6.16 chrXqtel1M 83611 83758 (916242) C MIR3#SINE/MIR (27) 181 36 m_b354s601i0 14821 chrXqtel1M 83611 CTGGCAGAGACTCTGGAGTGGATTGCCATTTCCTTCTCCAGCTCATTTGA 83660 v i ii i --- iii vvv vv i -- v C MIR3#SINE/MIR 181 CTGGAAGGGACCTTAGAG---ATCATCTAGTCCAACCCC--CTCATTTTA 137 chrXqtel1M 83661 CAGGTGAGGAAACTGAGG--CAGACAGGGTGAAGAGACTTGGCCAGGGTC 83708 i -- v - v v i C MIR3#SINE/MIR 136 CAGATGAGGAAACTGAGGCCCAGAGA-GGTGAAGTGACTTGCCCAAGGTC 88 chrXqtel1M 83709 ATAT-----GTCTGAGATGAAATTAGGACTCAGCAAGATGGGTCTTTCTG 83753 i i----- iv v iiii iiii - - vvii - i C MIR3#SINE/MIR 87 ACACAGCNAGTTAGTGGCAGAGCCGGGACT-AG-AACCCAGGTC-TCCTG 41 chrXqtel1M 83754 ACTCC 83758 C MIR3#SINE/MIR 40 ACTCC 36 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.87 CpG sites = 24, Kimura (unadjusted) = 35.16 Transitions / transversions = 1.71 (24/14) Gap_init rate = 0.07 (11 / 147), avg. gap size = 1.45 (16 / 11) 371 28.31 5.22 1.68 chrXqtel1M 83652 83766 (916234) C MIRc#SINE/MIR (120) 148 30 m_b354s601i1 14821 chrXqtel1M 83652 CTCATTTGACAGGTGAGGAAACTGAGGCAGACAG-GGTGAAGAGACTTGG 83700 i v i vv v - v v v C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chrXqtel1M 83701 CCAGGGTCATATGTCT-----GAGATGAAATTAGGACTCAGCAAGATGGG 83745 i i iiv ----- v iiii iiii i-- vvii C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCG--AACCCAGG 51 chrXqtel1M 83746 TCTTTCTGACTCCAGATTCAG 83766 i ii i C MIRc#SINE/MIR 50 TCTTCCTGACTCCAAGTCCAG 30 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.99 CpG sites = 21, Kimura (unadjusted) = 37.07 Transitions / transversions = 1.91 (21/11) Gap_init rate = 0.04 (4 / 114), avg. gap size = 2.00 (8 / 4) 180 20.51 2.56 0.00 chrXqtel1M 84398 84436 (915564) C Tigger19b#DNA/TcMar-Tigger (199) 351 312 m_b354s601i2 14822 chrXqtel1M 84398 CAGGGAGAGCTGGGAAGCT-CCCAGTGTCCGTTTTCTGCC 84436 ii -i v viv i C Tigger19b#DNA 351 CAGGAGGAGCTGGGAAGCTGTCCAGTTTCCTCATCCTGCC 312 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 24.45 CpG sites = 5, Kimura (unadjusted) = 24.45 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.03 (1 / 38), avg. gap size = 1.00 (1 / 1) 21 16.01 0.00 0.00 chrXqtel1M 85752 85786 (914214) (C)n#Simple_repeat 1 35 (0) m_b354s252i6 14823 chrXqtel1M 85752 CCCGCCCACCTCCTCCCCCCCCCCCCCCTCCCCCC 85786 v v i i i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 35 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 15 22.56 5.77 0.00 chrXqtel1M 85752 85803 (914197) (CCCT)n#Simple_repeat 1 55 (0) m_b354s252i5 14824 chrXqtel1M 85752 CCCGCCC-ACCT-CCTCCC-CCCCCCCCCCCTCCCCCCGTGTTCCCCTCC 85798 v -v - - i i i v viii (CCCT)n#Simpl 1 CCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCC 50 chrXqtel1M 85799 CTCCC 85803 (CCCT)n#Simpl 51 CTCCC 55 Matrix = Unknown Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.00 (3 / 3) 29 6.37 3.92 1.92 chrXqtel1M 85801 85851 (914149) (CCCGG)n#Simple_repeat 1 52 (0) m_b354s252i7 14825 chrXqtel1M 85801 CCCGGCCCGGCCCGG-CCGGCCCCGCCTGG-CCGCCCCGGCCCGGCCCGA 85848 - v i - v - (CCCGG)n#Simp 1 CCCGGCCCGGCCCGGCCCGGCCCGGCCCGGCCCGGCCCGGCCCGGCCCG- 49 chrXqtel1M 85849 GCC 85851 (CCCGG)n#Simp 50 GCC 52 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.06 (3 / 50), avg. gap size = 1.00 (3 / 3) 357 22.88 1.83 7.77 chrXqtel1M 86853 86961 (913039) C MIRc#SINE/MIR (141) 127 25 m_b354s601i3 14826 chrXqtel1M 86853 CTGAGGC--AGTTGGGGTTCAGTGACTTGCCCAGGGTCACACAGCCAGGA 86900 -- v- i v i i -- C MIRc#SINE/MIR 127 CTGAGGCTCAGA-GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG-- 81 chrXqtel1M 86901 ACTGTTAAGTGTCTGATGCTGCATTAGAACTCGGGTCCTCCCGACTTCAG 86950 ----- v v vv v v i v i i i i i i C MIRc#SINE/MIR 80 -----TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAA 36 chrXqtel1M 86951 GGCTGGGGCTC 86961 v ii v C MIRc#SINE/MIR 35 GTCCAGTGCTC 25 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.42 CpG sites = 12, Kimura (unadjusted) = 27.42 Transitions / transversions = 1.09 (12/11) Gap_init rate = 0.08 (9 / 108), avg. gap size = 1.11 (10 / 9) 447 23.30 2.22 7.81 chrXqtel1M 88746 88880 (911120) MIRb#SINE/MIR 3 130 (138) m_b354s601i4 14827 chrXqtel1M 88746 GAGGGACAGCTGGGTGGTGCAGTGGATAGAGCCCCAGCCCTGAAGTCAGG 88795 i --- v v vi ii i i MIRb#SINE/MIR 3 GAGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGA 49 chrXqtel1M 88796 AGGACCCGAGTTCAAATCCGCCCTCAGACATTTAATACTTCCTAGCTGTG 88845 vi i i i vvv v v i ------- MIRb#SINE/MIR 50 CAGACCTGGGTTCGAATCCCGGCTCTGCCACTTA-------CTAGCTGTG 92 chrXqtel1M 88846 TGACCCCAGGCAAGT--CTCAACTCCAGT-TGCCTCAG 88880 iii -- i ii vv -v MIRb#SINE/MIR 93 TGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAG 130 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.15 CpG sites = 17, Kimura (unadjusted) = 28.27 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.09 (12 / 134), avg. gap size = 1.08 (13 / 12) 429 27.70 0.70 5.93 chrXqtel1M 89212 89353 (910647) MIRc#SINE/MIR 14 148 (120) m_b354s601i5 14828 chrXqtel1M 89212 TGCAGCTGATAGGGAGGTGCTGGCCCTGGAGTCAGGGAGAGTGATCTTCC 89261 iv v i ---ii v i i vivivv - MIRc#SINE/MIR 14 TGCAGTGGAAAGAG---CACTGGACTTGGAGTCAGGAAGACCTGGGTTC- 59 chrXqtel1M 89262 CGAGTCCAAATATGACTTCACTTACTGGCTATGTCACCCTAAAGCAAATC 89311 - viiivivi -- i i v i ii- i MIRc#SINE/MIR 60 -GAGTCCCGGCTCTGC--CACTTACTAGCTGTGTGACCTTGG-GCAAGTC 105 chrXqtel1M 89312 ACATGGGC-CTGTGTGCCTCAGTTTCCTCATCTGTAAAATGAG 89353 v iiv - v v i MIRc#SINE/MIR 106 ACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.17 CpG sites = 22, Kimura (unadjusted) = 35.35 Transitions / transversions = 1.47 (22/15) Gap_init rate = 0.06 (9 / 141), avg. gap size = 1.00 (9 / 9) 264 16.36 0.00 0.00 chrXqtel1M 89413 89467 (910533) MER63D#DNA/hAT-Tip100 386 440 (621) m_b354s502i0 14829 chrXqtel1M 89413 GATTGACTGATTTGAGGTTTGCCTAGACTTAAGAAAGTGATGGAGAAAAG 89462 v i v vv v i v MER63D#DNA/hA 386 GATTTATTGTTTTGTTGATTGTCTAGACTTAAGAAAGTGATGGAGAAAAT 435 chrXqtel1M 89463 GTCAA 89467 i MER63D#DNA/hA 436 GTTAA 440 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 18.46 CpG sites = 3, Kimura (unadjusted) = 18.46 Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 24 16.57 0.00 0.00 chrXqtel1M 90309 90349 (909651) (T)n#Simple_repeat 1 41 (0) m_b354s252i8 14830 chrXqtel1M 90309 TTTTTTTTTTTTTTGTTGTTGTTGTTGGTTTTTTTTTTTTT 90349 v v v v vv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 41 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 187 33.29 7.30 3.52 chrXqtel1M 91471 91607 (908393) C MIR3#SINE/MIR (9) 199 58 m_b354s601i6 14831 chrXqtel1M 91471 AAACACAGGTTTGTGGAGCTGGAAGGAACTCTGGAGATGA---AGTCTAA 91517 v i iv vvii i ii i v --- i C MIR3#SINE/MIR 199 AATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAA 150 chrXqtel1M 91518 GCAGTTTGCTTGGCAG--GAAGAAGGTCAG---CAGAGCCCAGGTGGGAA 91562 v vvi iii vi -- i iv v --- --- iiiv C MIR3#SINE/MIR 149 CCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAG---AGGTGAAGT 103 chrXqtel1M 91563 AGCTTGTGCCCCAGGTTACAAAGGTGTTGAGTGG--AAGCTAGGCCT 91607 ii -- v i v v?iv v --i ii v C MIR3#SINE/MIR 102 GACT--TGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACT 58 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.64 CpG sites = 26, Kimura (unadjusted) = 46.25 Transitions / transversions = 1.44 (26/18) Gap_init rate = 0.07 (9 / 136), avg. gap size = 1.67 (15 / 9) 18 12.03 6.45 6.45 chrXqtel1M 91916 91977 (908023) (TATTA)n#Simple_repeat 1 62 (0) m_b354s252i9 14832 chrXqtel1M 91916 TATTACGTTATATTGAATATTATGTGTAAATGTATA-T-CATTATATTA- 91962 ii -- i - v - - -i - (TATTA)n#Simp 1 TATTATATTATATT--ATATTATAT-TATAT-TATATTATATTATATTAT 46 chrXqtel1M 91963 A-TATATTATATTTTA 91977 - v (TATTA)n#Simp 47 ATTATATTATATTATA 62 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.13 (8 / 61), avg. gap size = 1.00 (8 / 8) 15 18.86 8.00 1.89 chrXqtel1M 91924 91973 (908027) (TA)n#Simple_repeat 1 53 (0) m_b354s252i10 14833 chrXqtel1M 91924 TATAT-TGAATAT-TATGTGTAAATGTATATCAT-TATATTAATATAT-T 91969 - iv - i i v i - - vv - (TA)n#Simple_ 1 TATATATATATATATATATATATATATATAT-ATATATATATATATATAT 49 chrXqtel1M 91970 ATAT 91973 (TA)n#Simple_ 50 ATAT 53 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.10 (5 / 49), avg. gap size = 1.00 (5 / 5) 37 0.00 0.00 0.00 chrXqtel1M 92151 92184 (907816) (C)n#Simple_repeat 1 34 (0) c_b354s251i0 14834 chrXqtel1M 92151 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 92184 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 34 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 15 11.69 0.00 0.00 chrXqtel1M 94101 94128 (905872) (GGGAG)n#Simple_repeat 1 28 (0) m_b354s252i11 14835 chrXqtel1M 94101 GGGAGGGGAGGAGAAGCGAGGGGAGGGG 94128 i i v (GGGAG)n#Simp 1 GGGAGGGGAGGGGAGGGGAGGGGAGGGG 28 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 247 31.48 3.80 8.85 chrXqtel1M 96239 96475 (903525) C L2c_3end#LINE/L2 (143) 335 110 m_b354s601i7 14836 chrXqtel1M 96239 CAAGTTACTCGTAGTCAACTGTGACGATAGGATACGTAGAGACAGCTAGT 96288 v vi ---- v iv ii i --- v vvv i C L2c_3end#LINE 335 CAAGTTAATGATA----AGTGCTATAATGGGA---GTATAGACAGGGTGC 293 chrXqtel1M 96289 TACCGGAGAAAGCTAGAGG-GAGCATTTAGCACCTGC--TGACG----AG 96331 iv v ---i - i ii - iv ?-- iv ---- C L2c_3end#LINE 292 TATGGGAGCA---CAGAGGAGGGCACCTAG-ACTAGNCTTGGGGGGTCAG 247 chrXqtel1M 96332 CAATAACTTCCCAGAAAAGGCAAGATGGGAGCCAAGCCACAAAG-ACAAG 96380 vi vii i ii ii v vv ii ? vii - ii C L2c_3end#LINE 246 GGAAGGCTTCCCGGAGGAGGTGACATCTGAGCTGAGNCTTGAAGGATGAG 197 chrXqtel1M 96381 CTGAGAGACAGGAGGGAGGGGGGAGGGCGG-AGGGCGTTCCAGGCCCAGG 96429 - ii vi vvi v ii v - i i vv C L2c_3end#LINE 196 -TAGGAGTTAGCCAGGTGGAAGGAGGGGGGAAGAGCATTCCAGGCAGAGG 148 chrXqtel1M 96430 GAAAACGACAGCATCTGCAAAGGTATGGGAAGCTCAGGAAGAGATT 96475 ----- v i?i- i -- iii i C L2c_3end#LINE 147 GA-----ACAGCATGTGCAAAGGCNC-GGAGG--CAGGAAAGAACT 110 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.34 CpG sites = 42, Kimura (unadjusted) = 43.04 Transitions / transversions = 1.62 (42/26) Gap_init rate = 0.11 (25 / 236), avg. gap size = 1.16 (29 / 25) 43 0.00 0.00 0.00 chrXqtel1M 96672 96710 (903290) (G)n#Simple_repeat 1 39 (0) c_b354s251i1 14837 chrXqtel1M 96672 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 96710 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 39 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 12 15.85 9.52 0.00 chrXqtel1M 100223 100264 (899736) (GGCCAC)n#Simple_repeat 1 46 (0) m_b354s252i12 14838 chrXqtel1M 100223 GGCCACGGCCCCGCCCTCGGCC-C-ACCACAGCC-CTGCCA-GGCC 100264 v v v - -i i - v - (GGCCAC)n#Sim 1 GGCCACGGCCACGGCCACGGCCACGGCCACGGCCACGGCCACGGCC 46 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.10 (4 / 41), avg. gap size = 1.00 (4 / 4) 12 22.76 0.00 5.13 chrXqtel1M 100633 100673 (899327) (CCCTC)n#Simple_repeat 1 39 (0) m_b354s252i13 14839 chrXqtel1M 100633 CCCTCCTTTCTTCCTCCTCTCCCCGCCCCCCCTCTCTCCCT 100673 ii -i i v i i - (CCCTC)n#Simp 1 CCCTCCCCTC-CCCTCCCCTCCCCTCCCCTCCCCTC-CCCT 39 Matrix = Unknown Transitions / transversions = 6.00 (6/1) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 13 13.21 6.67 4.35 chrXqtel1M 100858 100902 (899098) (CCCCTCT)n#Simple_repeat 1 46 (0) m_b354s252i15 14840 chrXqtel1M 100858 CCCCTCTTCCTCCT-TCCCC-CGCCCCCCTCCTCGC-ACCCTCTCCCC 100902 - - - - v i i v -v (CCCCTCT)n#Si 1 CCCCTC-TCC-CCTCTCCCCTCTCCCCTCTCCCCTCTCCCCTCTCCCC 46 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.11 (5 / 44), avg. gap size = 1.00 (5 / 5) 21 10.85 0.00 0.00 chrXqtel1M 101514 101543 (898457) (C)n#Simple_repeat 1 30 (0) m_b354s252i16 14841 chrXqtel1M 101514 CCCCCCCCCCCCCACCCCCACCCCCCGCCC 101543 v v v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 30 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 13 4.76 0.00 4.35 chrXqtel1M 101857 101880 (898120) (CCCT)n#Simple_repeat 1 23 (0) m_b354s252i17 14842 chrXqtel1M 101857 CCCTCCCTCACCTCCCTTCCTCCC 101880 - i (CCCT)n#Simpl 1 CCCTCCCTC-CCTCCCTCCCTCCC 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 15 8.91 4.17 0.00 chrXqtel1M 102043 102066 (897934) (CA)n#Simple_repeat 1 25 (0) m_b354s252i20 14843 chrXqtel1M 102043 CAC-CACACACACACACACCCCCAC 102066 - v v (CA)n#Simple_ 1 CACACACACACACACACACACACAC 25 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 22 20.67 0.00 6.15 chrXqtel1M 102042 102110 (897890) (CCCCCA)n#Simple_repeat 1 65 (0) m_b354s252i19 14844 chrXqtel1M 102042 CCACCACACACACACACACCCCCACCCCCCCCCCCCGCCCCGACCCTCCC 102091 v v v v v - v i v - - (CCCCCA)n#Sim 1 CCCCCACCCCCACCCCCACCCCCA-CCCCCACCCCCACCCCCA-CC-CCC 47 chrXqtel1M 102092 ACGGACCACCCCCTCCCCC 102110 -vv v (CCCCCA)n#Sim 48 AC-CCCCACCCCCACCCCC 65 Matrix = Unknown Transitions / transversions = 0.10 (1/10) Gap_init rate = 0.06 (4 / 68), avg. gap size = 1.00 (4 / 4) 12 11.13 6.90 0.00 chrXqtel1M 102430 102458 (897542) (GGGGA)n#Simple_repeat 1 31 (0) m_b354s252i21 14845 chrXqtel1M 102430 GGGGAAGGGAGGGG-GGTG-GGGGAGGGCAG 102458 i - v - v (GGGGA)n#Simp 1 GGGGAGGGGAGGGGAGGGGAGGGGAGGGGAG 31 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.07 (2 / 28), avg. gap size = 1.00 (2 / 2) 15 28.32 0.00 0.00 chrXqtel1M 106128 106164 (893836) (GG)n#Simple_repeat 1 37 (0) m_b354s252i22 14846 chrXqtel1M 106128 GGGGGGGGGGGGGGGAAGGAAGAGGGGGAAGAGGGGG 106164 ii ii i ii i (GG)n#Simple_ 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 37 Matrix = Unknown Transitions / transversions = 1.00 (8/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 chrXqtel1M 106782 106799 (893201) (C)n#Simple_repeat 1 18 (0) m_b354s252i23 14847 chrXqtel1M 106782 CCCCCCCCCCCCCCCCCC 106799 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCC 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 16 21.70 0.00 0.00 chrXqtel1M 107151 107182 (892818) (C)n#Simple_repeat 1 32 (0) m_b354s252i24 14848 chrXqtel1M 107151 CCCCCCCTCCCCCCACATCCCCCCCCACCTCC 107182 i v vi v i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 32 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 21 11.19 8.16 0.00 chrXqtel1M 107484 107532 (892468) (GAGGA)n#Simple_repeat 1 53 (0) m_b354s252i25 14849 chrXqtel1M 107484 GAGG-GAGGA-AGGAG-GGAGGGGAGAGAAGAGGGCAGGAGAGGAG-GGG 107529 - - - i i iv - i (GAGGA)n#Simp 1 GAGGAGAGGAGAGGAGAGGAGAGGAGAGGAGAGGAGAGGAGAGGAGAGGA 50 chrXqtel1M 107530 GAG 107532 (GAGGA)n#Simp 51 GAG 53 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.08 (4 / 48), avg. gap size = 1.00 (4 / 4) 12 17.57 0.00 5.88 chrXqtel1M 108712 108747 (891253) (GGGGA)n#Simple_repeat 1 34 (0) m_b354s252i26 14850 chrXqtel1M 108712 GGGAAGGGTGAGGCGAGGCAGGGGGCAGGGGAGGGG 108747 i - v -i i v (GGGGA)n#Simp 1 GGGGAGGG-GAGGGGAGG-GGAGGGGAGGGGAGGGG 34 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 17 8.85 0.00 0.00 chrXqtel1M 110160 110183 (889817) (C)n#Simple_repeat 1 24 (0) m_b354s252i27 14851 chrXqtel1M 110160 CCCCCCCCTCCCCCCCCCCCGCCC 110183 i v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCC 24 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 457 28.31 7.14 4.48 chrXqtel1M 110658 110853 (889147) C MIRc#SINE/MIR (30) 238 38 m_b354s601i8 14852 chrXqtel1M 110658 ATCTTAAGGTCTGCAAATCAATCT-AGGAACATTACCCTCGTTTGATCCT 110706 ii vi i i v iv i - viv i - i C MIRc#SINE/MIR 238 ACTTTACAGTTTACAAAGCGCTTTCACATACATTATC-TCATTTGATCCT 190 chrXqtel1M 110707 CACAAT---CCTGGAAGGTA---AAGAC---TTACATTAGCCCCATTTTA 110747 i--- vi --- i i --- vvi v C MIRc#SINE/MIR 189 CACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTA 140 chrXqtel1M 110748 TAGCTGAAGAAACCAAGGCACAGGGAGTTGAAGCCTCTAGTTC-TGGTCA 110796 i v i ii v i v v ivv v ii -v C MIRc#SINE/MIR 139 CAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCA 90 chrXqtel1M 110797 CACAGCCAATACTGTAGGAAGGGTCCAAGGCCATATTGGAACTCG---CT 110843 -------- v v v vi v viv i v i i--- C MIRc#SINE/MIR 89 CACAGC--------TAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCT 48 chrXqtel1M 110844 TCCTGACTCC 110853 C MIRc#SINE/MIR 47 TCCTGACTCC 38 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.32 CpG sites = 28, Kimura (unadjusted) = 36.16 Transitions / transversions = 1.12 (28/25) Gap_init rate = 0.08 (15 / 195), avg. gap size = 1.53 (23 / 15) 29 0.00 0.00 0.00 chrXqtel1M 112187 112213 (887787) (AGC)n#Simple_repeat 1 27 (0) c_b355s251i0 14853 chrXqtel1M 112187 AGCAGCAGCAGCAGCAGCAGCAGCAGC 112213 (AGC)n#Simple 1 AGCAGCAGCAGCAGCAGCAGCAGCAGC 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 463 37.83 2.68 0.88 chrXqtel1M 113359 113582 (886418) C MIRc#SINE/MIR (25) 243 16 m_b355s601i0 14854 chrXqtel1M 113359 ACAGCTCCTCTTGGTCCCCAGAGCACCATTCCTTACCCTGTCCTCATCGC 113408 i v i ivii iiv i i iv iv v vi i - ivv C MIRc#SINE/MIR 243 ATAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATC-TCATTTG 195 chrXqtel1M 113409 CCCCCCACCGTCGCCCTACACTCAAAGGCAAAACAGCAGCAGTGACCCCC 113458 vi i viivi iiivv-iv iii vviivi v i C MIRc#SINE/MIR 194 ATCCTCACAACAACCCTGTGAG-GTAGGCAGGGCAGGTATTATTATCCCC 146 chrXqtel1M 113459 GTTTTACGGAGGAGGAGACTGAG---CAAAGA---TCTGGCACTTGCCCA 113502 i i v i --- i --- vv vv C MIRc#SINE/MIR 145 ATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCA 96 chrXqtel1M 113503 GGGTCAGTCAGCTAGGAAGAATCTAATGCTGAATTCGAATTCAGAGCTTC 113552 i vv v viv vi vv v i i ii iv C MIRc#SINE/MIR 95 AGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTC 46 chrXqtel1M 113553 CCGATTCCAGATCCAGAGCTCTCTGGACTG 113582 i i ii v i vv C MIRc#SINE/MIR 45 CTGACTCCAAGTCCAGTGCTCTTTCCACTG 16 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 53.75 CpG sites = 47, Kimura (unadjusted) = 54.73 Transitions / transversions = 1.27 (47/37) Gap_init rate = 0.02 (4 / 223), avg. gap size = 2.00 (8 / 4) 29 0.00 0.00 3.23 chrXqtel1M 115666 115697 (884303) (CCAGGC)n#Simple_repeat 1 31 (0) c_b355s251i1 14855 chrXqtel1M 115666 CCAGCGCCCAGGCCCAGGCCCAGGCCCAGGCC 115697 - (CCAGGC)n#Sim 1 CCAG-GCCCAGGCCCAGGCCCAGGCCCAGGCC 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 17 6.10 2.50 7.89 chrXqtel1M 116105 116144 (883856) (GCCGG)n#Simple_repeat 1 38 (0) m_b355s252i0 14856 chrXqtel1M 116105 GCCGGGGCCGGGGCCGGGGCGGAGCCAGGCC-GGCCGGGCC 116144 - - v - i - (GCCGG)n#Simp 1 GCC-GGGCC-GGGCCGGGCCGG-GCCGGGCCGGGCCGGGCC 38 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.10 (4 / 39), avg. gap size = 1.00 (4 / 4) 16 11.69 0.00 0.00 chrXqtel1M 116281 116308 (883692) (CGC)n#Simple_repeat 1 28 (0) m_b355s252i1 14857 chrXqtel1M 116281 CGCCTTCACCGCCGCCGCCGCCGCCGCC 116308 vi i (CGC)n#Simple 1 CGCCGCCGCCGCCGCCGCCGCCGCCGCC 28 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 23 10.06 9.26 0.00 chrXqtel1M 116348 116401 (883599) (GAAGA)n#Simple_repeat 1 59 (0) m_b355s252i2 14858 chrXqtel1M 116348 GAAGGGAAGAGAAGAGAAGGGAAAGGAAGA-AAG-GAAG-GACGAG-AGA 116393 i i ii - - - v - (GAAGA)n#Simp 1 GAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGA 50 chrXqtel1M 116394 GAAG-GAAG 116401 - (GAAGA)n#Simp 51 GAAGAGAAG 59 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.09 (5 / 53), avg. gap size = 1.00 (5 / 5) 17 14.38 0.00 0.00 chrXqtel1M 116753 116784 (883216) (CTTTTC)n#Simple_repeat 1 32 (0) m_b355s252i3 14859 chrXqtel1M 116753 CTTTTCCTTTTCCTTTTCCTCCTCCTCCTCCT 116784 ii ii (CTTTTC)n#Sim 1 CTTTTCCTTTTCCTTTTCCTTTTCCTTTTCCT 32 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 18 12.88 0.00 5.41 chrXqtel1M 116757 116795 (883205) (TCC)n#Simple_repeat 1 37 (0) m_b355s252i4 14859 chrXqtel1M 116757 TCCTTTTCCTTTTCCTCCTCCTCCTCCTCTCTGCCTCCT 116795 ii ii - - (TCC)n#Simple 1 TCCTCCTCCTCCTCCTCCTCCTCCTCCTC-CT-CCTCCT 37 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2) 17 3.66 0.00 6.67 chrXqtel1M 116968 116999 (883001) (CGGGG)n#Simple_repeat 1 30 (0) m_b355s252i5 14860 chrXqtel1M 116968 CGGGGCGGGGCGAAGGGCGGGGCGGGGCGCGG 116999 -- v (CGGGG)n#Simp 1 CGGGGCGGGGCG--GGGCGGGGCGGGGCGGGG 30 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.06 (2 / 31), avg. gap size = 1.00 (2 / 2) 12 4.77 4.55 0.00 chrXqtel1M 118113 118134 (881866) (CAGG)n#Simple_repeat 1 23 (0) m_b355s252i6 14861 chrXqtel1M 118113 CAGG-AGGCAGGCAAGCAGGCAG 118134 - i (CAGG)n#Simpl 1 CAGGCAGGCAGGCAGGCAGGCAG 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.05 (1 / 21), avg. gap size = 1.00 (1 / 1) 19 11.70 0.00 0.00 chrXqtel1M 120324 120351 (879649) (G)n#Simple_repeat 1 28 (0) m_b355s252i7 14862 chrXqtel1M 120324 GGCGGGGGGGGGGGGTGGGGGGGGTGGG 120351 v v v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGG 28 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 284 33.30 7.14 2.48 chrXqtel1M 121189 121342 (878658) C MIR3#SINE/MIR (29) 179 19 m_b355s601i1 14863 chrXqtel1M 121189 GGAAAAGCCATGCGTGTTCTCCAGGTCCAACCCAGACATTTTACAGAGAG 121238 ii v v vv v v vi vi vvv vii C MIR3#SINE/MIR 179 GGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGA 130 chrXqtel1M 121239 GGAAACTGAAGCCCTTACAGAGACAA---GGCTTCCTCGAGGGCACATGG 121285 i -- v iii --- i v i i v ii C MIR3#SINE/MIR 129 GGAAACTGAGGCCC--AGAGAGGTGAAGTGACTTGCCCAAGGTCACACAG 82 chrXqtel1M 121286 -GAG---GCAACAGAACCAGGTTTTCAAACTC----CCCCTGAGCCTCGG 121327 -? --- iii i i -vi vi i ---- i vi i i C MIR3#SINE/MIR 81 CNAGTTAGTGGCAGAGCCGGG-ACTAGAACCCAGGTCTCCTGACTCCCAG 33 chrXqtel1M 121328 CTTTCTCCTCTTTCT 121342 - iiv v i C MIR3#SINE/MIR 32 -TCCGTGCTCTCTCT 19 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.76 CpG sites = 30, Kimura (unadjusted) = 46.31 Transitions / transversions = 1.50 (30/20) Gap_init rate = 0.05 (8 / 153), avg. gap size = 1.88 (15 / 8) 233 32.99 10.28 0.85 chrXqtel1M 122109 122215 (877785) MIR3#SINE/MIR 71 187 (21) m_b355s601i2 14864 chrXqtel1M 122109 CCCTTAACTCCTTGTGTGACCCAGAGCAG--------AGCCCTCAGAGCC 122150 vi ?vi iv i i-------- v i v i MIR3#SINE/MIR 71 CCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCC 120 chrXqtel1M 122151 CC--TTTAATC-CCTGAGAAATGAGGGAGCTGGGTTAAGTGGCTCCCGAG 122197 i -- vv -i vi i i ii ii iiii ii MIR3#SINE/MIR 121 TCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAG 170 chrXqtel1M 122198 CCCCCTTCTGACCTTTGA 122215 vi i- v i MIR3#SINE/MIR 171 GTCCCTTCC-AGCTCTGA 187 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 47.65 CpG sites = 25, Kimura (unadjusted) = 47.65 Transitions / transversions = 2.50 (25/10) Gap_init rate = 0.04 (4 / 106), avg. gap size = 3.00 (12 / 4) 12 22.23 0.00 5.13 chrXqtel1M 123511 123551 (876449) (AGGGA)n#Simple_repeat 1 39 (0) m_b355s252i8 14865 chrXqtel1M 123511 AGGGATGGGAAGGACTAAGAGAAGGGGGGAGGAGGGAAGGG 123551 v --v i ii i i (AGGGA)n#Simp 1 AGGGAAGGGAAGG--GAAGGGAAGGGAAGGGAAGGGAAGGG 39 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2) 13 15.62 0.00 12.50 chrXqtel1M 124644 124697 (875303) (GGGGCA)n#Simple_repeat 1 48 (0) m_b355s252i9 14866 chrXqtel1M 124644 GGGGCAGGGGCAGGGACTCTGGGGTCCAGGTGGCAGCGGCCCGGGACAAG 124693 --v v -- - - v v i i (GGGGCA)n#Sim 1 GGGGCAGGGGCAGGG--GCAGGGG--CAGG-GGCAG-GGGCAGGGGCAGG 44 chrXqtel1M 124694 GGCA 124697 (GGGGCA)n#Sim 45 GGCA 48 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.11 (6 / 53), avg. gap size = 1.00 (6 / 6) 16 6.91 6.45 0.00 chrXqtel1M 124777 124807 (875193) (CTCC)n#Simple_repeat 1 33 (0) m_b355s252i10 14867 chrXqtel1M 124777 CTCCCTTCCTCCCTTCCTCCC-CCC-CCCTCCC 124807 i i - - (CTCC)n#Simpl 1 CTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCC 33 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2) 14 17.92 0.00 5.00 chrXqtel1M 124953 124994 (875006) (CCCCTCC)n#Simple_repeat 1 40 (0) m_b355s252i11 14868 chrXqtel1M 124953 CCCCTCCCCCTCTTCTGGCTCCTCCCTCCCTCCTCCCTCCCT 124994 - i ivv i i - (CCCCTCC)n#Si 1 CCCCTCCCCC-CTCCCCCCTCCCCCCTCCCCCCTCCC-CCCT 40 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.05 (2 / 41), avg. gap size = 1.00 (2 / 2) 16 13.42 7.32 0.00 chrXqtel1M 124954 124994 (875006) (CCCT)n#Simple_repeat 1 44 (0) m_b355s252i12 14868 chrXqtel1M 124954 CCCTCCCCCTCT-TCTGGCT-CCTCCCTCCCT-CCTCCCTCCCT 124994 i i -i vv - - (CCCT)n#Simpl 1 CCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCT 44 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.07 (3 / 40), avg. gap size = 1.00 (3 / 3) 12 19.31 0.00 5.41 chrXqtel1M 126851 126889 (873111) (GGGCTG)n#Simple_repeat 1 37 (0) m_b355s252i13 14869 chrXqtel1M 126851 GGGCAGGGGCTGGGGCCGGCCACAGGGCTCTGGGGCTGG 126889 v i -vi v -v (GGGCTG)n#Sim 1 GGGCTGGGGCTGGGGCTGG-GGCTGGG-GCTGGGGCTGG 37 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2) 28 3.31 0.00 0.00 chrXqtel1M 129519 129549 (870451) (C)n#Simple_repeat 1 31 (0) c_b355s251i2 14870 chrXqtel1M 129519 CCCCCCCCCCCCCCCCCCCCCCCCCCGCCCC 129549 v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 31 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 53 0.00 0.00 0.00 chrXqtel1M 130106 130153 (869847) (G)n#Simple_repeat 1 48 (0) c_b355s251i3 14871 chrXqtel1M 130106 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 130153 (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 48 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 21 4.00 0.00 0.00 chrXqtel1M 131396 131421 (868579) (GA)n#Simple_repeat 1 26 (0) m_b355s252i14 14872 chrXqtel1M 131396 GAGAGAGAAAGAGAGAGAGAGAGAGA 131421 i (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGA 26 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 34 5.48 0.00 0.00 chrXqtel1M 131422 131459 (868541) (GT)n#Simple_repeat 1 38 (0) c_b355s251i4 14873 chrXqtel1M 131422 GTGTGTGTGTGTTTCTGTGTGTGTGTGTGTGTGTGTGT 131459 v v (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 38 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 17 0.00 0.00 0.00 chrXqtel1M 132683 132701 (867299) (T)n#Simple_repeat 1 19 (0) m_b355s252i15 14874 chrXqtel1M 132683 TTTTTTTTTTTTTTTTTTT 132701 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 17 13.12 0.00 0.00 chrXqtel1M 133683 133708 (866292) (C)n#Simple_repeat 1 26 (0) m_b355s252i16 14875 chrXqtel1M 133683 CCCCCTCCCCCCTCCCCCCTCCCCCC 133708 i i i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCC 26 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 15 10.08 2.94 2.94 chrXqtel1M 133849 133882 (866118) (AAGGGG)n#Simple_repeat 1 34 (0) m_b355s252i17 14876 chrXqtel1M 133849 AAAGGGAGGGGGAAGTGGGAAGGGG-AGGGGTAGG 133882 i i - - v (AAGGGG)n#Sim 1 AAGGGGAAGGGGAAG-GGGAAGGGGAAGGGGAAGG 34 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2) 230 29.61 0.00 4.55 chrXqtel1M 134496 134587 (865413) C MIR1_Amn#SINE/MIR (52) 178 91 m_b355s601i3 14877 chrXqtel1M 134496 CTTTACAGAGGCGTCTTTGTTCCCAATTCTCCCCAACTTACAGATAAGGA 134545 i v v- iv vi -- v vi i C MIR1_Amn#SINE 178 CTTTACAAAGGAGG-TCAGTATC--ATTATCCCCATTTTACAGATGAGGA 132 chrXqtel1M 134546 AATCGAGGGGGAGAGTGGGTTGGGCCACACGGCCTTGATCAC 134587 ii v?v -i ?ii iv vi v vv i C MIR1_Amn#SINE 131 AACTGAGGCNCAGAG-AGGTNAAGTGACTTGCCCAAGGTCAC 91 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.21 CpG sites = 13, Kimura (unadjusted) = 39.21 Transitions / transversions = 1.00 (13/13) Gap_init rate = 0.04 (4 / 91), avg. gap size = 1.00 (4 / 4) 309 28.31 14.71 1.30 chrXqtel1M 135065 135200 (864800) C MIRb#SINE/MIR (114) 154 1 m_b355s601i4 14878 chrXqtel1M 135065 ACCCTCTTTTTACAGA--AGG---CCCAGGCCCAGAGAAAGGGAAGAGCA 135109 i i v -- --- iv i iivvi iv i v C MIRb#SINE/MIR 154 ATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACT 105 chrXqtel1M 135110 TGCTGAAGGTCACA------------GGCAGCAGTGAGGATTCAAACCCA 135147 iv ------------ - ivi i C MIRb#SINE/MIR 104 TGCCCAAGGTCACACAGCTAGTAAGTGGCAG-AGCCGGGATTCGAACCCA 56 chrXqtel1M 135148 GATCT---TGCCTCCAAATCTCCTGCTCTCCTTCAGCACCCTAGTTTTCT 135194 i --- v v i v -i i vii v i vvi v i C MIRb#SINE/MIR 55 GGTCTGTCTGACTCCAAAGCCCGTGCTCT-TTCCACTGCACCACGCTGCC 7 chrXqtel1M 135195 CCTCTG 135200 C MIRb#SINE/MIR 6 CCTCTG 1 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.14 CpG sites = 22, Kimura (unadjusted) = 36.51 Transitions / transversions = 1.38 (22/16) Gap_init rate = 0.04 (6 / 135), avg. gap size = 3.67 (22 / 6) 200 36.53 0.66 9.35 chrXqtel1M 135203 135353 (864647) C MIR#SINE/MIR (95) 167 29 m_b355s601i5 14879 chrXqtel1M 135203 ATGAGG-AGATATTGTCAGGTCCCCACACTCATTTCATGGATGCAGAAAA 135251 - i i i i -----ii iv i i ii - i C MIR#SINE/MIR 167 ATGAGGTAGGTACTATTA-----TTATCCCCATTTTACAGATG-AGGAAA 124 chrXqtel1M 135252 ATTACCGGCCCGAGGAGGCTTAGGGCCTTGCCTTGGGACACACGGCCCGG 135301 v v -- v iii i v viv ivi v i iv - C MIR#SINE/MIR 123 CTGA--GGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAG- 77 chrXqtel1M 135302 ATTAAGAGGAGAAAATCTTTCCCCAACCCTAAGGAGTCAGGCTTGCGGAG 135351 -- v -v i ii vvvvii i v i i v v i- i C MIR#SINE/MIR 76 --TAAGTGG-CAGAGCCGGGATTCGAACCCAGGCAGTCTGGCTC-CAGAG 31 chrXqtel1M 135352 CC 135353 C MIR#SINE/MIR 30 CC 29 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 50.71 CpG sites = 31, Kimura (unadjusted) = 52.26 Transitions / transversions = 1.63 (31/19) Gap_init rate = 0.09 (14 / 150), avg. gap size = 1.00 (14 / 14) 218 31.42 1.12 3.45 chrXqtel1M 135209 135297 (864703) C MIR3#SINE/MIR (41) 167 81 m_b355s601i6 14879 chrXqtel1M 135209 AGATATTGTCAGGTCCC-CACACTCATTTCATGGATGCAGAAAAATTACC 135257 v ii vi v- v v i ii - i v v -- C MIR3#SINE/MIR 167 AGAGATCATCTAGTCCAACCCCCTCATTTTACAGATG-AGGAAACTGA-- 121 chrXqtel1M 135258 GGCCCGAGGAGGCTTAGGGCCTTGCCTTGGGACACACGGC 135297 iii ivv v v ivi v i C MIR3#SINE/MIR 120 GGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGC 81 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.38 CpG sites = 14, Kimura (unadjusted) = 41.38 Transitions / transversions = 1.08 (14/13) Gap_init rate = 0.05 (4 / 88), avg. gap size = 1.00 (4 / 4) 208 29.04 4.04 9.57 chrXqtel1M 136901 136999 (863001) C MIR3#SINE/MIR (3) 205 112 m_b355s601i7 14880 chrXqtel1M 136901 TCCTAGAATCGGCTACTG--AGACCCGGAAGGGACTTGAGCCATCACCTC 136948 v ivvv v -- v i i v vv ---- C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCA---- 160 chrXqtel1M 136949 CGCTCTCTTCTCTCATCCCTTCGCTTTCGAGGTGAG--AACCGAGGGTCA 136996 ----- vv iv i i ii vv i -- i vi C MIR3#SINE/MIR 159 -----TCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCA 115 chrXqtel1M 136997 GAG 136999 C MIR3#SINE/MIR 114 GAG 112 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.61 CpG sites = 11, Kimura (unadjusted) = 36.61 Transitions / transversions = 0.73 (11/15) Gap_init rate = 0.11 (11 / 98), avg. gap size = 1.18 (13 / 11) 212 30.34 1.11 1.11 chrXqtel1M 136995 137084 (862916) C MIR1_Amn#SINE/MIR (131) 99 10 m_b355s601i8 14877 chrXqtel1M 136995 CAGAGTTAGAAAGCCGGCAAACGCCACGGCCGGGGCTGGCTCGTA-GTCC 137043 ii i v?v ? ? ii v vi i? ? vv vi - i C MIR1_Amn#SINE 99 CAAGGTCACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAACCCAGGTCT 50 chrXqtel1M 137044 CCCGGGACACGATCTCAGTGTTCTTTCCACCAGAGCAGGCT 137084 i v v ii - i v i v vi C MIR1_Amn#SINE 49 CCCGAGTCCCAGTC-CAGTGCTCTATCCACTAGACCACACT 10 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.07 CpG sites = 15, Kimura (unadjusted) = 43.07 Transitions / transversions = 1.25 (15/12) Gap_init rate = 0.02 (2 / 89), avg. gap size = 1.00 (2 / 2) 449 26.34 3.82 1.49 chrXqtel1M 138412 138542 (861458) L2d2_3end#LINE/L2 417 550 (5) m_b355s601i9 14881 chrXqtel1M 138412 ATGTCGATTGAGTCCCTAA-AAGACAG-AAGCTCCTTGAGGGCAGGGAC- 138458 -- vv i -v iv - - L2d2_3end#LIN 417 ATGTC--TTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACC 464 chrXqtel1M 138459 -TGACTTTCACCTCTTT-TGGCGCCTGCAGCGCTCAGCCCGGTGCCTAGT 138506 - v vi i - iv v ii ii v i v i L2d2_3end#LIN 465 ATGTCTTATACTTCTTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTGC 514 chrXqtel1M 138507 ACACAGTAGACACTTAATGTTTACTGACTGACCTAA 138542 i i i ivv i vii ii i L2d2_3end#LIN 515 ACACAGTAGGCGCTCAATAAATATTTGTTGATTTGA 550 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.21 CpG sites = 21, Kimura (unadjusted) = 33.41 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.05 (7 / 130), avg. gap size = 1.00 (7 / 7) 181 31.67 0.00 0.00 chrXqtel1M 138670 138729 (861271) C MIR3#SINE/MIR (33) 175 116 m_b355s601i10 14882 chrXqtel1M 138670 GGGACCTTCGGACTGAGCAGGTCCAACTCGCTCAGTGTTTCAAGGAGGAA 138719 v iiv v v vi i v v v vivi v C MIR3#SINE/MIR 175 GGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGAA 126 chrXqtel1M 138720 AGGGAGGCCC 138729 vv C MIR3#SINE/MIR 125 ACTGAGGCCC 116 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.15 CpG sites = 6, Kimura (unadjusted) = 41.15 Transitions / transversions = 0.46 (6/13) Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0) 12 19.97 2.27 4.65 chrXqtel1M 139349 139392 (860608) (CCCT)n#Simple_repeat 1 43 (0) m_b355s252i18 14883 chrXqtel1M 139349 CCCTCCCTTCTTTCCTTCCCTCCGCTGCC-GGTTCCCTCCCTCCC 139392 - ii i - v -vvi (CCCT)n#Simpl 1 CCCTCCC-TCCCTCCCTCCCTCC-CTCCCTCCCTCCCTCCCTCCC 43 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.07 (3 / 43), avg. gap size = 1.00 (3 / 3) 12 32.46 1.75 0.00 chrXqtel1M 139451 139507 (860493) (AGAGGGC)n#Simple_repeat 1 58 (0) m_b355s252i19 14884 chrXqtel1M 139451 AGAGGGGAGAATGGAGGGGGGGGAGGG-GGGCACCAGAGGGCTCAGGGCA 139499 v iv v i vi -i iviv vv (AGAGGGC)n#Si 1 AGAGGGCAGAGGGCAGAGGGCAGAGGGCAGAGGGCAGAGGGCAGAGGGCA 50 chrXqtel1M 139500 GAGTGCAG 139507 v (AGAGGGC)n#Si 51 GAGGGCAG 58 Matrix = Unknown Transitions / transversions = 0.67 (6/9) Gap_init rate = 0.02 (1 / 56), avg. gap size = 1.00 (1 / 1) 21 25.09 1.64 0.00 chrXqtel1M 139881 139941 (860059) (GCC)n#Simple_repeat 1 62 (0) m_b355s252i20 14885 chrXqtel1M 139881 GCTGCCGCCGCCGTTGCCGCCGCCGCCGCCACCGCTTCCGGAGGGCCCTC 139930 i ii i iv vv vvv v (GCC)n#Simple 1 GCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGC 50 chrXqtel1M 139931 CG-GGCCGCCGC 139941 -v (GCC)n#Simple 51 CGCCGCCGCCGC 62 Matrix = Unknown Transitions / transversions = 0.62 (5/8) Gap_init rate = 0.02 (1 / 60), avg. gap size = 1.00 (1 / 1) 14 22.06 0.00 0.00 chrXqtel1M 140047 140083 (859917) (GACATG)n#Simple_repeat 1 37 (0) m_b355s252i21 14886 chrXqtel1M 140047 GACATGGACACCGACATGGACGAGGACGTTGACACGG 140083 iv iv i v i (GACATG)n#Sim 1 GACATGGACATGGACATGGACATGGACATGGACATGG 37 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 18 3.29 2.86 5.88 chrXqtel1M 140147 140181 (859819) (GCCGA)n#Simple_repeat 1 34 (0) m_b355s252i22 14887 chrXqtel1M 140147 GCCG-GCCAGCAGCCGAGCCGAGCGGAGCCGAGCCG 140181 - - - v (GCCGA)n#Simp 1 GCCGAGCC-G-AGCCGAGCCGAGCCGAGCCGAGCCG 34 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.09 (3 / 34), avg. gap size = 1.00 (3 / 3) 12 15.49 3.45 0.00 chrXqtel1M 140277 140305 (859695) (CCCCT)n#Simple_repeat 1 30 (0) m_b355s252i23 14888 chrXqtel1M 140277 CCCCTCCCCTCCCCGCCAGT-CCCGCCCCT 140305 v vv - v (CCCCT)n#Simp 1 CCCCTCCCCTCCCCTCCCCTCCCCTCCCCT 30 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1) 17 4.94 0.00 0.00 chrXqtel1M 140801 140821 (859179) (G)n#Simple_repeat 1 21 (0) m_b355s252i24 14889 chrXqtel1M 140801 GGGGGGGGGGCGGGGGGGGGG 140821 v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGG 21 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 236 15.38 0.00 0.00 chrXqtel1M 141207 141245 (858755) MIR3#SINE/MIR 107 145 (63) m_b355s601i11 14890 chrXqtel1M 141207 CGCTTCTTTGGGCCTCACTTTCCTCATCTGAAAAATGGG 141245 i i i v v i MIR3#SINE/MIR 107 CACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAG 145 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 17.52 CpG sites = 4, Kimura (unadjusted) = 17.52 Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 533 33.26 3.22 3.22 chrXqtel1M 142078 142574 (857426) L1M5_orf2#LINE/L1 2791 3287 (7) m_b355s551i0 14891 chrXqtel1M 142078 CTGTTTGATAAAAATTGCTGGGAAAATTGGAAACTGATATGGCAGAAACT 142127 v ii i viv i v v iiv v i v L1M5_orf2#LIN 2791 CTTTTCAACAAATGGTGCTGGAACAATTGGATATCCATATGGAAAAAAAT 2840 chrXqtel1M 142128 AGGCATTGATCCGCACTTAACGCCGTACACCAAGATAAGGTCAAAATGGG 142177 iii?v i i vi i v i i v i v iv ? i i L1M5_orf2#LIN 2841 GAANCTCGACCCCTACCTCACACCATACACAAAAATTAATTCNAGATGGA 2890 chrXqtel1M 142178 TTCAT-GACCTAGGCATAAAGAATGAAATCATTAATAAATTAGAGGAA-- 142224 - - iiii ii? i ii v vvvvi i -- L1M5_orf2#LIN 2891 T-CATAGACCTAAATGTAAAAGNTAAAACTATAAAACTTCTAGAAGAAAA 2939 chrXqtel1M 142225 CATAGGATAGTTTACATCTC--AGACCTGTGGAAGGGGAAGGTCTTTATG 142272 v i ---- i--v vv ?vi v i vi iv i L1M5_orf2#LIN 2940 CATAGGAGAAT----ATCTTCGTGACCTTGGGNTAGGCAAAGATTTCTTA 2985 chrXqtel1M 142273 ACCAAAGCAGAACTAGAGATCATCACTGATCACAAAATAGAAAATT---- 142318 v iii v -- i ----- ?i i i v i ---- L1M5_orf2#LIN 2986 AACAGGACACAA--AAAG-----CACNAACCATAAAAGAAAAAATTGATA 3028 chrXqtel1M 142319 ---TCGATTATACCAAACTGAAAAGTTTTTGTACAAACAAAACTAATGCA 142365 --- v i ?i i v v ii i iv ?vvv ivi vi iv L1M5_orf2#LIN 3029 AATTGGACTNCATCAAAATTAAAAACTTCTGCTCNTCAAAAGACACCGTT 3078 chrXqtel1M 142366 GACAAGATTAGAAGGGAAGCAATAAACTGGGAAAATATTTTTATAGTCAA 142415 i v i v i v v i i ? i v v ii i?vv L1M5_orf2#LIN 3079 AAGAAAATGAAAAGGCAAGCCACAGANTGGGAGAAAATATTTGCAANACA 3128 chrXqtel1M 142416 AGGTTCTGATAAAGGCCTCATTTCCAAAATATAGAGAGAATTGACTCTAA 142465 vivv i v i v i v i i v- vi L1M5_orf2#LIN 3129 TATATCTGACAAAGGACTCGTATCCAGAATATATAAAGAACTC-CTACAA 3177 chrXqtel1M 142466 TTTA----TAAAAAATCAAGCCATTTTCCAATTGATAAATGGTCAAAGGA 142511 ? i ----? iv i v i--- v? v v i L1M5_orf2#LIN 3178 NTCAATAANAAAAAGACAAACAAC---CCAATANAAAAATGGGCAAAAGA 3224 chrXqtel1M 142512 TATAAACGGACAATTCCCAGATGAAGAAATTGAAACTATTTCTAGTCATA 142561 iv i i v v i v v ?v iviiivv iv i L1M5_orf2#LIN 3225 CTTGAACAGACACTTCACAAAAGAAGATATNCAAATGGCCAATAAGCACA 3274 chrXqtel1M 142562 TGAAAAGATGCTC 142574 L1M5_orf2#LIN 3275 TGAAAAGATGCTC 3287 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 45.79 CpG sites = 89, Kimura (unadjusted) = 47.01 Transitions / transversions = 1.25 (89/71) Gap_init rate = 0.04 (22 / 496), avg. gap size = 1.45 (32 / 22) 1450 31.85 0.78 0.94 chrXqtel1M 142435 143071 (856929) L1ME4c_3end#LINE/L1 4 639 (191) m_b355s551i1 14891 chrXqtel1M 142435 ATTTCCAAAATATAGAGAGAATTGACTCTAATTTATAAAAAATCAAGCCA 142484 v i?v ? v i ii v i v v i vv? v v L1ME4c_3end#L 4 ATATCTNTANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAA 53 chrXqtel1M 142485 TTTTCCAATTGATAAATGGTCAAAGGATATAAACGGACAATTCCCAGATG 142534 vvii v v i i i v ? v L1ME4c_3end#L 54 GACCCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAG 103 chrXqtel1M 142535 AAGAAATTGAAACTATTTCTAGTCATATGAAAAGATGCTCCAAGTCGTTA 142584 i vv ?ivi vvvi iv i i i i v vv i L1ME4c_3end#L 104 AGGAAATACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTA 153 chrXqtel1M 142585 TTAATCAGAGAAATGCAAATTAAGACAACTCTGAGATACCACTACACACC 142634 v i ii vv i vi i L1ME4c_3end#L 154 GTAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCC 203 chrXqtel1M 142635 TGTCAGATTGGCTAAGATGACAGGAAAACATAATGATGATTGTTGGAGGG 142684 i i i i v i vvv ii vvv iviv v i v i L1ME4c_3end#L 204 TATTAAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGCTGGCGAG 253 chrXqtel1M 142685 GATGCGGGAAAACTGGGACATTGATGCATTGTTGGTGGAGTTGTGAACGA 142734 ? vi v ?i v i i vi? i ivi L1ME4c_3end#L 254 GNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTG 303 chrXqtel1M 142735 ATCCAACCATTCTGGAGAGTAGTTTGGAACTAGGCTCAAAAAGTTATCAA 142784 i v v i i i i v v v iviv i ii v L1ME4c_3end#L 304 GTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAA 353 chrXqtel1M 142785 ACTGTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGATTATATCCCA 142834 v v i i i vii v v v i L1ME4c_3end#L 354 AATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTA 403 chrXqtel1M 142835 AAGAGATTAT---AAAGAAGGGAAAGGGACCTGTATGTGCACGAATGTTT 142881 i i v --- i i --- i ii ivii i L1ME4c_3end#L 404 AGGAAATAATTCAAAAGAAGGAAAAAG---CTATATGCACGAAGATGTTC 450 chrXqtel1M 142882 GTGGCAGCCCTTTTTGTAGTGGCTAGAAACTGGAAACTGAATGGATGTCC 142931 i v vi v i i i v i i vivv ii L1ME4c_3end#L 451 ATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCC 500 chrXqtel1M 142932 ATCAGTTGGAGAATGGCTGAATAAATTGTGGTATATGAAAATTATGGAAT 142981 v i v i i i i i i v? vviv L1ME4c_3end#L 501 AACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAAT 550 chrXqtel1M 142982 ATTACTGTT-CTGTAAGAAATGACCAACAGGATGATTTCAGAAAGGCCTG 143030 - iv- ii v i iv vi v v i viiv ivii v L1ME4c_3end#L 551 ATTA-TGCAGCCATTAAAAATGATAATTATGAAGACTATGTAGCAACATG 599 chrXqtel1M 143031 G-AGATACTGACACGAACTGATGCTGAGTGAAATGAGCAGGA 143071 - i ii --i i vv i i i vi i L1ME4c_3end#L 600 GAAAATGTT--TATGATATAATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 42.59 CpG sites = 113, Kimura (unadjusted) = 43.46 Transitions / transversions = 1.28 (113/88) Gap_init rate = 0.01 (9 / 636), avg. gap size = 1.22 (11 / 9) 284 28.12 3.88 0.75 chrXqtel1M 144054 144182 (855818) C L1MC3_3end#LINE/L1 (1960) 572 440 m_b355s551i2 14892 chrXqtel1M 144054 TCATTTCTT---ACCAAACAATAATATTCCATCACATT-ATATACCATAA 144099 --- i ivvv iii v- i i i C L1MC3_3end#LI 572 TCATTTCTTTTTATCGCTGAATAATATTCCATTGTATGGATGTACCACAG 523 chrXqtel1M 144100 CTTATTCAGCCATTCTCCAATTGATGGGCGTCC-ACTCACTTTCCAGTTT 144148 i i i v v v v i i i-iv ii - C L1MC3_3end#LI 522 TTTGTTTATCCATTCACCTATTGAAGGACATCTTGGTTGCTT-CCAGTTT 474 chrXqtel1M 144149 CTGGCCACTACAAAGACACCTGCCACAAACATTC 144182 i v i ii v v v i i C L1MC3_3end#LI 473 TTGGCGATTATGAATAAAGCTGCTATAAACATTC 440 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 35.28 CpG sites = 23, Kimura (unadjusted) = 36.57 Transitions / transversions = 1.77 (23/13) Gap_init rate = 0.03 (4 / 128), avg. gap size = 1.50 (6 / 4) 382 29.17 0.83 0.00 chrXqtel1M 144070 144189 (855811) C L1ME2z_3end#LINE/L1 (638) 553 433 m_b355s551i3 14892 chrXqtel1M 144070 AATAATATTCCATCACAT-TATATACCATAACTTATTCAGCCATTCTCCA 144118 i i iii -v i ii i i v v C L1ME2z_3end#L 553 AGTAGTATTCCATTGTATGAATATACCACAGTTTGTTTATCCATTCTCCT 504 chrXqtel1M 144119 ATTGATGGGCGTCCACTCACTTTCCAGTTTCTGGCCACTACAAAGACACC 144168 i i ii iivv vv i i i ii v v v C L1ME2z_3end#L 503 GTTGATGGACACCTGGGCTGTTTCCAGTTTTTGGCTATTATGAATAAAGC 454 chrXqtel1M 144169 TGCCACAAACATTCTTGCACA 144189 i ii i C L1ME2z_3end#L 453 TGCTATGAACATTCTTGTACA 433 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 39.22 CpG sites = 25, Kimura (unadjusted) = 39.22 Transitions / transversions = 2.50 (25/10) Gap_init rate = 0.01 (1 / 119), avg. gap size = 1.00 (1 / 1) 308 32.24 0.65 1.96 chrXqtel1M 144071 144225 (855775) C L1ME4c_3end#LINE/L1 (275) 555 403 m_b355s551i4 14892 chrXqtel1M 144071 ATAATATTCCATCACATT-ATATACCATAACTTATTCAGCCATTCTCCAA 144119 ivi ?- i i i i i i v C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chrXqtel1M 144120 TTGATGGGCGTCCACTCACTTTCCAGTTTCTGGCCACTACAAAGACACCT 144169 v i i ii vvivv i i v i i i v vvv C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCT 456 chrXqtel1M 144170 GCCACAAACATTCTTGCACACACAGGTCCCTTTCCCTTTATTTATTTTAT 144219 v ii ii i ii i i --- i i iv ivv C L1ME4c_3end#L 455 GCAATGAACATCTTCGTGCATATAG---CTTTTTCCTTCTTTTGAATTAT 409 chrXqtel1M 144220 TTATTT 144225 vi C L1ME4c_3end#L 408 TTCCTT 403 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 42.31 CpG sites = 32, Kimura (unadjusted) = 44.82 Transitions / transversions = 1.88 (32/17) Gap_init rate = 0.03 (4 / 154), avg. gap size = 1.00 (4 / 4) 294 30.85 0.00 0.00 chrXqtel1M 144774 144867 (855133) C L1ME2z_3end#LINE/L1 (638) 553 460 m_b355s551i5 14893 chrXqtel1M 144774 AGTAATATTCCATCACATTCATATCCCATAACTTACTCATCCAATCTCCA 144823 i iii vv v i ii ii i v v C L1ME2z_3end#L 553 AGTAGTATTCCATTGTATGAATATACCACAGTTTGTTTATCCATTCTCCT 504 chrXqtel1M 144824 ACTGATGGGCAGCCACTCAGGTTCCAGTTTCTGGCCACTATAAA 144867 ii i v iivv v v i i i i C L1ME2z_3end#L 503 GTTGATGGACACCTGGGCTGTTTCCAGTTTTTGGCTATTATGAA 460 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 41.71 CpG sites = 19, Kimura (unadjusted) = 41.71 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.00 (0 / 93), avg. gap size = 0.0 (0 / 0) 950 29.32 0.81 1.63 chrXqtel1M 144881 145251 (854749) C L1ME3G_3end#LINE/L1 (553) 371 4 m_b355s551i6 14894 chrXqtel1M 144881 TGCTGGATCAAAGGGGATGCACAGTTTGACAGTCTTTGGGGATAGATCCA 144930 i v i v i --i i vivi vvv C L1ME3G_3end#L 371 TGCTGGGTCAAAGGGTATGCGCATTTTAA--ATTTTAATAGATACTGCCA 324 chrXqtel1M 144931 AATTGCTCTCTAGAATGATTGTGTCAGTTTATAACTCCACCAACAATGCA 144980 i i i ? ii ii i i vii i i i C L1ME3G_3end#L 323 AATTGCCCTCCAAAANGGCTGTACCAATTTACACTCCCACCAGCAGTGTA 274 chrXqtel1M 144981 TCAGTGTCCCAGTTTTCCCACTTCCCCTCCAACATTCATCATTATCTTTT 145030 v v v v i vi i v i ?ivi vv?i C L1ME3G_3end#L 273 TGAGAGTACCCGTTTCCCCACACCCTCGCCAACACTNGATATTATCAANC 224 chrXqtel1M 145031 CCTGTTATCTCAGTTCATCTGAGGGATATGTAGTGGTATCTCAGAGTTGT 145080 ii vvv i iv iiv v i iviv i vv C L1ME3G_3end#L 223 TTTTAAATTTTTGCCAATCTGATGGGTGAAAAATGGTATCTCATTGTTGT 174 chrXqtel1M 145081 CTTAATTTGCATTTCTCTGATTAATAATGATTTGGAACACTCTTTCCTAT 145130 i i v i vv v i iii v C L1ME3G_3end#L 173 TTTAATTTGCATTTCCCTGATTACTAGTGAGGTTGAGCATCTTTTCATAT 124 chrXqtel1M 145131 GAGTGGTAATGATTTCAATTTCATCATCTGAAAATTGTCTATTCATATTC 145180 vv iv iiiv vv v v vi i i i C L1ME3G_3end#L 123 GTTTATTGGCCATTTGTATTTCCTCTTCTGTGAATTGCCTGTTCATATCC 74 chrXqtel1M 145181 TTTGACCATTTTTCAATTGGAGAATGGCTTGGTTTCCTATAAAT---GAT 145227 v v iv-- v -- i vi ---v v C L1ME3G_3end#L 73 TTTGCCCATTTTTCTATTGGGT--TGTCTT--TTTCTTATTGATTTGTAG 28 chrXqtel1M 145228 CAGTTCTTTATATATTTTGGAAAT 145251 v i v C L1ME3G_3end#L 27 GAGTTCTTTATATATTCTGGATAT 4 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 37.80 CpG sites = 57, Kimura (unadjusted) = 38.25 Transitions / transversions = 1.14 (57/50) Gap_init rate = 0.02 (7 / 370), avg. gap size = 1.29 (9 / 7) 321 31.07 3.33 1.64 chrXqtel1M 145108 145287 (854713) C L1PB_orf2#LINE/L1 (0) 3294 3112 m_b355s551i7 14894 chrXqtel1M 145108 TGATTTGGAACACTCTTTCCTATGAGTGGTAATGATTTCAATTTCATCAT 145157 v v i i i v vv v iiiv vv v v v C L1PB_orf2#LIN 3294 TGATGTTGAGCATTTTTTCATATGTTTGTTGGCCATTTGTATATCTTCTT 3245 chrXqtel1M 145158 CTGAAAATTGTCTATTCATATTCTTTGACCATTTTTCAATTGGAGAATGG 145207 i i i i v v i ii ---i i v C L1PB_orf2#LIN 3244 TTGAGAATTGTCTATTCATGTCCTTAGCCCACTTTTTGAT---GGGATTG 3198 chrXqtel1M 145208 CTTGGTTTCCTATAAATGATC------AGTTCTTTATATATTTTGGAAAT 145251 i v ii v viv i------ ? i v i v C L1PB_orf2#LIN 3197 TTTGTTTTTTTCTTGCTGATTTGTTTGAGTTCNTTGTAGATTCTGGATAT 3148 chrXqtel1M 145252 GAGGCCTTTATCAGAAGCCTTAAATGTAAAAATGTT 145287 v v i v iv vi v i i v C L1PB_orf2#LIN 3147 TAGTCCTTTGTCAGATGTATAGATTGTGAAGATTTT 3112 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 40.93 CpG sites = 27, Kimura (unadjusted) = 40.93 Transitions / transversions = 0.96 (27/28) Gap_init rate = 0.02 (4 / 179), avg. gap size = 2.25 (9 / 4) 318 32.87 3.52 2.17 chrXqtel1M 145279 145732 (854268) L1M5_orf2#LINE/L1 2835 3294 (0) m_b355s551i8 14895 chrXqtel1M 145279 AAAAATGTTGCATGGACCCACACTTAACACCACATACCAAGATAAGATCA 145328 vv? - v vi i v i i v i v iv ? L1M5_orf2#LIN 2835 AAAAATGAANC-TCGACCCCTACCTCACACCATACACAAAAATTAATTCN 2883 chrXqtel1M 145329 AAATGGGCCCATGATTTAGGCATAAAGAACAAGATTATAAATGAATTAGA 145378 i ii vvv ii iiii ii?i i i vvvvi L1M5_orf2#LIN 2884 AGATGGATCATAGACCTAAATGTAAAAGNTAAAACTATAAAACTTCTAGA 2933 chrXqtel1M 145379 GGAA--CATAGGATCGTTTACCTCTCAGACTCATGGAGGAGG-AAAGAAT 145425 i -- -- vv i iivv - v i?v - v L1M5_orf2#LIN 2934 AGAAAACATAGGA--GAATATCTTCGTGAC-CTTGGGNTAGGCAAAGATT 2980 chrXqtel1M 145426 TTGTGACCAA---AGAAGAACTAGAGACCATTATTGATCACAAAATAGAA 145472 iv i v i--- v i vi v?i v vv ---v v v L1M5_orf2#LIN 2981 TCTTAAACAGGACACAAAAAGCACNAACCATAAAAGA---AAAAATTGAT 3027 chrXqtel1M 145473 AATTTTGATTATATCAAATTAAAAAGCTTCTGTACAAACAAAATTAATGA 145522 v v i ?i v v i iv ?vvv ivi vi v L1M5_orf2#LIN 3028 AAATTGGACTNCATCAAAATTAAAAACTTCTGCTCNTCAAAAGACACCGT 3077 chrXqtel1M 145523 AAACAAGATTAGAAGGGAAGCAACAAACTGGGAG-------TTACAATTA 145565 v v i v i v v i ? ------- i ?vv L1M5_orf2#LIN 3078 TAAGAAAATGAAAAGGCAAGCCACAGANTGGGAGAAAATATTTGCAANAC 3127 chrXqtel1M 145566 AGGGTTCTGATAAAGGCCTCATTTCTAAAATATAGAGAGAATTGACTCTA 145615 vivv i v i v i i v i i v- vi L1M5_orf2#LIN 3128 ATATATCTGACAAAGGACTCGTATCCAGAATATATAAAGAACTC-CTACA 3176 chrXqtel1M 145616 ATTTA-TAAGAAATCAAGCCATTC--TCCAATTGATAAATGGTCAAAGGA 145662 ? i - ? -- v vv --i v? v v i L1M5_orf2#LIN 3177 ANTCAATAANAAA--AAGACAAACAACCCAATANAAAAATGGGCAAAAGA 3224 chrXqtel1M 145663 TACAAACAGACAATTTTCAGATGATGAAATTGAAATTATTTCCACTCATA 145712 ivii v iv i v v v ?v viiivvi vv i L1M5_orf2#LIN 3225 CTTGAACAGACACTTCACAAAAGAAGATATNCAAATGGCCAATAAGCACA 3274 chrXqtel1M 145713 TGAAAGAGTGCTCCAAGTCA 145732 iii v v? L1M5_orf2#LIN 3275 TGAAAAGATGCTCAACNTCA 3294 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 44.41 CpG sites = 67, Kimura (unadjusted) = 45.64 Transitions / transversions = 0.85 (67/79) Gap_init rate = 0.04 (16 / 453), avg. gap size = 1.62 (26 / 16) 1503 32.07 0.47 0.63 chrXqtel1M 145586 146222 (853778) L1ME4c_3end#LINE/L1 4 639 (191) m_b355s551i9 14895 chrXqtel1M 145586 ATTTCTAAAATATAGAGAGAATTGACTCTAATTTATAAGAAATCAAGCCA 145635 v ?v ? v i ii v i v v vv? v v L1ME4c_3end#L 4 ATATCTNTANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAA 53 chrXqtel1M 145636 TTCTCCAATTGATAAATGGTCAAAGGATACAAACAGACAATTTTCAGATG 145685 vv i v v i ii iv ? v L1ME4c_3end#L 54 GACCCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAG 103 chrXqtel1M 145686 ATGAAATTGAAATTATTTCCACTCATATGAAAGAGTGCTCCAAGTCATTA 145735 v vv ? vi vvv vv i i i i i v vv ii L1ME4c_3end#L 104 AGGAAATACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTA 153 chrXqtel1M 145736 TTAATCAGAGAAATGCAAATTAAGACAACTCTGAGATACCACTACACACC 145785 v i ii vv i vi i L1ME4c_3end#L 154 GTAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCC 203 chrXqtel1M 145786 TGTCAGATTGGCTAAGATGACAGGAAAAAATAATGATGAATGTTGGAGGG 145835 i i i i v i vvv ii vvi iviv i v i L1ME4c_3end#L 204 TATTAAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGCTGGCGAG 253 chrXqtel1M 145836 GATGTGGGAAAACTGGGACACTGATGCATTGTTGGTGGAGCTGTGAACGA 145885 ? i vi v ? v i i vi? i ivi L1ME4c_3end#L 254 GNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTG 303 chrXqtel1M 145886 ATCCAACCATTCTGGAGAGCAATCTGGAATTATGCCCAAAAAGTTATCAA 145935 i v v i i i v v i iviv i ii v L1ME4c_3end#L 304 GTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAA 353 chrXqtel1M 145936 ACTGTGCATCCCCTTTGATCCAGCTGTGTTACTACTGGGCTTATACTCCA 145985 v v v i ivi vii v vv v ii i L1ME4c_3end#L 354 AATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTA 403 chrXqtel1M 145986 AAGAGATACT---AAAGAAGCGAAAGGAATCTGTATGTGCCAAAATGTTT 146032 i i v --- - -- v i ii v i i L1ME4c_3end#L 404 AGGAAATAATTCAAAAGAAG-GAAA--AAGCTATATGCACGAAGATGTTC 450 chrXqtel1M 146033 GTGGCAGCCCTGTTTGTAGTGGCCAGAAGCTGGAAACTGAGTGGATGCCC 146082 i v vi i i i i v i ii vivv ii i L1ME4c_3end#L 451 ATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCC 500 chrXqtel1M 146083 ATCCATTGGAGAATGCTTGGGTAAATCGTGGTATATGAATGTTATGGAAT 146132 v v v i v ii ii i v? iviv L1ME4c_3end#L 501 AACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAAT 550 chrXqtel1M 146133 ATTATTGTTCTGTAAGAAATGACCAACAGGAGGATTTCAGAGAGGCCTGG 146182 vvvv ii v i iv vi v i i viiv vii v L1ME4c_3end#L 551 ATTATGCAGCCATTAAAAATGATAATTATGAAGACTATGTAGCAACATGG 600 chrXqtel1M 146183 AGAGACCTACATGATCTGATGCTGAGGGAAATGAGCAGGA 146222 - i iv vi v i i i v vi i L1ME4c_3end#L 601 A-AAATGTTTATGATATAATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 42.16 CpG sites = 108, Kimura (unadjusted) = 43.58 Transitions / transversions = 1.14 (108/95) Gap_init rate = 0.01 (5 / 636), avg. gap size = 1.40 (7 / 5) 12 4.75 0.00 8.33 chrXqtel1M 146537 146562 (853438) (GGGA)n#Simple_repeat 1 24 (0) m_b355s252i25 14896 chrXqtel1M 146537 GGGAGGGGGTGGAGGGAGGGAGCGGA 146562 i - - (GGGA)n#Simpl 1 GGGAGGGAG-GGAGGGAGGGAG-GGA 24 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.08 (2 / 25), avg. gap size = 1.00 (2 / 2) 1184 33.80 0.80 0.60 chrXqtel1M 147357 147859 (852141) C L1ME4c_3end#LINE/L1 (191) 639 136 m_b355s551i10 14897 chrXqtel1M 147357 TCCTGCTCGTTTCACTCAGCATCAGTTCGTGTAAGTCTCTCCAGGCCTCT 147406 i iv i i i vv i iv vi i - v iiv C L1ME4c_3end#L 639 TTCTGCTTTTTTCACTTAACATTATATCATAAACATTT-TCCATGTTGCT 591 chrXqtel1M 147407 CTGAAATCCTCCTGCTGGTCACTTCTTACAGAGCAATAATATTCCATAAC 147456 viiv i i v iv vi i i v ii vvvv viv C L1ME4c_3end#L 590 ACATAGTCTTCATAATTATCATTTTTAATGGCTGCATAATATTCCATCGA 541 chrXqtel1M 147457 ATTCATATACCACGATTTACTCAGCCATTCTCCAATTGATGGGCGTCCAC 147506 i ?v i ii i i i v v i i ii v C L1ME4c_3end#L 540 GTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGGACATTTAG 491 chrXqtel1M 147507 TCAGTTTCCAGTTTCTAGCCACTACAAACAGGGCTGCA-CAAACATTCTG 147555 viv i i v i i i i iv -ii ii v C L1ME4c_3end#L 490 GTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTC 441 chrXqtel1M 147556 GCACATACAGGTCCCTTTCCCTCCTTTAAGCT--CTCTTTGGGGTATAAG 147603 ii i -- ii i i i ii --i i i i v vv C L1ME4c_3end#L 440 GTGCATATAG--CTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAATT 393 chrXqtel1M 147604 CCCAGTAGTAACACTGCTGGATCAAAGGGGATGCACAGTTTGATAACTTT 147653 v iiv i i i v v v v ii i C L1ME4c_3end#L 392 CCCAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTCT 343 chrXqtel1M 147654 TGGGGCATAATTCCAAATTGTTCTCCAGAATGGTTGGCTCCATTCACAAC 147703 ivi i v v i i i v vvi v i ?i C L1ME4c_3end#L 342 TGATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACANT 293 chrXqtel1M 147704 TCCACCAATAATGCAGCAGTGTCCCAGTATTTCCACATCCCCTCCAACAT 147753 v ii i vv ? v v iv i ? i v i C L1ME4c_3end#L 292 GCCACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGCAT 243 chrXqtel1M 147754 TCATCATTATCTTTCCCTGGCATTCTAGCCAATGTGACAGGTGTGTAGTG 147803 vivi vv iii viv i v i v i i i iv i C L1ME4c_3end#L 242 TGGGTATTATCAATTTTTTAAATTTTTGCTAATTTAATAGGCGTAAAATG 193 chrXqtel1M 147804 GCATCTCAGAGTTGTCTTAATTTGCATTTCTCTGATCAATAGTGA-TTTG 147852 i vv ii i i v i -v C L1ME4c_3end#L 192 GTATCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACTAGCGAGGTTG 143 chrXqtel1M 147853 GATGTTT 147859 i ii C L1ME4c_3end#L 142 AACATTT 136 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 45.67 CpG sites = 105, Kimura (unadjusted) = 47.66 Transitions / transversions = 1.64 (105/64) Gap_init rate = 0.01 (6 / 502), avg. gap size = 1.17 (7 / 6) 229 35.38 2.31 0.00 chrXqtel1M 147852 147981 (852019) L1MC1_3end#LINE/L1 440 572 (508) m_b355s551i12 14898 chrXqtel1M 147852 GGATGTTTGTGGCAGGTCTCTTTGTAGTGGCCAGAAACTGGAAACTGAGT 147901 i i v i v ii i v i vi i vivvv L1MC1_3end#LI 440 GGATGTTTATAGCAGCTTTATTCATAATTGCCAAAACTTGGAAGCAACCA 489 chrXqtel1M 147902 GGACGCCCATCCATTGGAGAATGGCTGAATGGGTCCTGATATATGAATGT 147951 i i i v vi v v v i iiiiiv i i vv vii L1MC1_3end#LI 490 AGATGTCCTTCAGTAGGTGAATGGATAAATAAACTGTGGTACATCCAGAC 539 chrXqtel1M 147952 GATGGAATATTATTGTTCTCT---AAGAAATGA 147981 i vvv v --- L1MC1_3end#LI 540 AATGGAATATTATTCAGCGCTAAAAAGAAATGA 572 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 49.25 CpG sites = 25, Kimura (unadjusted) = 49.25 Transitions / transversions = 1.19 (25/21) Gap_init rate = 0.01 (1 / 129), avg. gap size = 3.00 (3 / 1) 315 35.09 0.00 0.00 chrXqtel1M 147852 147965 (852035) L1ME2z_3end#LINE/L1 440 553 (638) m_b355s551i11 14898 chrXqtel1M 147852 GGATGTTTGTGGCAGGTCTCTTTGTAGTGGCCAGAAACTGGAAACTGAGT 147901 i ii i v i v ii i i i v vvi L1ME2z_3end#L 440 GAATGTTCATAGCAGCTTTATTCATAATAGCCAAAAACTGGAAACAGCCC 489 chrXqtel1M 147902 GGACGCCCATCCATTGGAGAATGGCTGAATGGGTCCTGATATATGAATGT 147951 i ii i v iv v i iiiiiiv i vv ii L1ME2z_3end#L 490 AGGTGTCCATCAACAGGAGAATGGATAAACAAACTGTGGTATATTCATAC 539 chrXqtel1M 147952 GATGGAATATTATT 147965 i i i L1ME2z_3end#L 540 AATGGAATACTACT 553 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 51.84 CpG sites = 29, Kimura (unadjusted) = 51.84 Transitions / transversions = 2.64 (29/11) Gap_init rate = 0.00 (0 / 113), avg. gap size = 0.0 (0 / 0) 32 0.00 3.23 0.00 chrXqtel1M 148503 148533 (851467) (TA)n#Simple_repeat 1 32 (0) c_b355s251i5 14899 chrXqtel1M 148503 TATA-ATATATATATATATATATATATATATA 148533 - (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATA 32 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.03 (1 / 30), avg. gap size = 1.00 (1 / 1) 269 33.54 6.49 3.26 chrXqtel1M 148573 148988 (851012) C L1P1_orf2#LINE/L1 (388) 2906 2478 m_b355s551i13 14900 chrXqtel1M 148573 ATGTCTAAATCATGGACCTATTTCAACCTTATCTTGGTGTATTGTGTTAA 148622 i i i v vi i i i ii vi v i v i vv - C L1P1_orf2#LIN 2906 ACGTTTAAGTCTTTAATCCATCTTGAATTAATTTTTGTATAAGGTGT-AA 2858 chrXqtel1M 148623 GTGTGGG--CCAATGCCTAGTTTCTGCCATACCAGTTTGC-ACTTTTCCC 148669 viv -- i vi viv i - i-i i v - v C L1P1_orf2#LIN 2857 GGAAGGGATCCAGTTTCAGCTTTCTAC-ATAT-GGCTAGCCAGTTTTCCC 2810 chrXqtel1M 148670 AGCAGTTTTTGTCAGATGGTGATTTCTTACCCCAAAAGCTGGGGGCTTTG 148719 viv i i i i v v i v vvivi vvvvii ii C L1P1_orf2#LIN 2809 AGCACCATTTATTAAATAGGGAATCCTTTCCCCATTGCTTGTTTTTCTCA 2760 chrXqtel1M 148720 GGTTTGTCAAACACTAGATTGCTATAGTCAT-TGAC--TATTTGGTCCTG 148766 v ii v i i vi -i i -- ---- C L1P1_orf2#LIN 2759 GGTTTGTCAAAGATCAGATAGTTGTAGATATGCGGCGTTATTT----CTG 2714 chrXqtel1M 148767 TGAA-TCTGACCTATTCCACTGATGGACTGCTCTATTTCTTAGCCAGTAC 148815 v ii- vi i i vv ivv i ivvvi C L1P1_orf2#LIN 2713 AGGGCTCTGTTCTGTTCCATTGATCTATATCTCTGTTTTGGTACCAGTAC 2664 chrXqtel1M 148816 CAAATGGTTTTGGTGACCCCTGCTTTGTAATATAGTTTTAGATCTGGCAC 148865 viiv v iviv i i v ii v i v C L1P1_orf2#LIN 2663 CATGCTGTTTTGGTTACTGTAGCCTTGTAGTATAGTTTGAAGTCAGGTAG 2614 chrXqtel1M 148866 AGCTAGGCCACCTTCATTGGCATTTTTTTCATT---AATTCCCTTG--AA 148910 v iv v v vv v --- i vii ---i vv --i C L1P1_orf2#LIN 2613 CGTGATGCCTCCAGCTTTG---TTCTTTTGGCTTAGGATTGACTTGGCGA 2567 chrXqtel1M 148911 TG--------TTTTTGCTCTTCCAGATGAACCTT---GTTATTATTTTTC 148949 -------- --v v i --- vi -- C L1P1_orf2#LIN 2566 TGCGGGCTCTTTTTTG--GTTCCATATGAACTTTAAAGTAGT--TTTTTC 2521 chrXqtel1M 148950 TAGATCTGTAAACTAATTTCTTGGGA-CT---TGGGTATGGCA 148988 i iv i vv v iv v - --- v C L1P1_orf2#LIN 2520 CAATTCTGTGAAGAAAGTCATTGGTAGCTTGATGGGGATGGCA 2478 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 44.01 CpG sites = 69, Kimura (unadjusted) = 45.36 Transitions / transversions = 1.05 (69/66) Gap_init rate = 0.06 (25 / 415), avg. gap size = 1.64 (41 / 25) 540 37.81 10.01 2.70 chrXqtel1M 151447 152275 (847725) C MamRTE1#LINE/RTE-BovB (327) 3485 2598 m_b356s601i0 14901 chrXqtel1M 151447 CTTGAGAGTTTCTTTGTACCCTTTTTTCCTAGCCACCGTGTGAGCGCACG 151496 v v ?v i iv v v i - iv v v ivv vvi C MamRTE1#LINE/ 3485 CTTCAGTGNATCCTTAAAGCGTTTCTTC-TGCCCTCCCTGCTTGCGGTTG 3437 chrXqtel1M 151497 CCCTGTGTGCGTCCTCCATAAAACAGTTGTTTTAGCAAATATACGTTTGG 151546 iiiv vv ii v i v i i i vi ---- v vvi v C MamRTE1#LINE/ 3436 CCCCACTTCAGCTCACCGTACAGCAGCTGCTTGGG----TATCCTGCTGT 3391 chrXqtel1M 151547 CATTCAAACA----ATGTGGTCAGCCCACTGGAGTCG------GGC---- 151582 i vv v---- ii vi vi ii ------ ---- C MamRTE1#LINE/ 3390 CATCCATTCTCCGCACATGTCCAGCCCAGCGGAGCTGCGTTGCGGCGAGC 3341 chrXqtel1M 151583 -TCTCTGTAAGAGTTGGGATACTGGGCAGTTTAGTTCCAGAAC-TAGTGT 151630 - v - v v i v v ----i vv i - v vv C MamRTE1#LINE/ 3340 ATCGCT-TCAGTGCTGGTAGACTGG----CTGCGTTCCAGGACCTCGTTG 3296 chrXqtel1M 151631 CTGGT-ATCTTATCTTTCCAGGTGATCTTCTGAACCTTCCTAAGACAATT 151679 i - i i v vv i v vv v ivvii vv iii iv C MamRTE1#LINE/ 3295 TTGGTGATCCTGTCTTGCCATTTAATGTTAAGTATGGCTCGTAGGTGACG 3246 chrXqtel1M 151680 CAGATGGAAGCGGTTCAGTTTTCTGGCACGGCGCGGGTACGCTGTCCAGG 151729 v i vi v iv vvvi v iiii i ivv ivvvv C MamRTE1#LINE/ 3245 CTGATGAAACTGCTCAAGAAGCCGGATGTGACGTCTGTGGCAGGTCCAGG 3196 chrXqtel1M 151730 TTTCACAAGCATACA---------ACAGCG-TATGGCTCTGAAGATCTTC 151769 i iv i ? --------- ? - v v i i C MamRTE1#LINE/ 3195 TCTCACAGCCGTANAGAAGGTTGGACANCGCTATCGCTCTGTAGACCTTT 3146 chrXqtel1M 151770 ACTTTGGGAGGCAGACTAATACTTCTCTCTC-CCACACT---TCGG--AG 151813 v vvv v vi i i iv vi vv - --- v -- C MamRTE1#LINE/ 3145 AGTTTGGTCTGGAGCTTGATGCCACGTTGGCGCCACACTCTGTCTGCCAG 3096 chrXqtel1M 151814 TCTCCCAGACACTGAGCTGACTCCGGCAATTTGCGTGTCAACTTCATTTT 151863 i i viviiv i iiivvii i vv v v v v C MamRTE1#LINE/ 3095 CCTCCCAAAGGACATGCTGGCCTTCTTGATTCGGTTTTCTACTTCTTTGT 3046 chrXqtel1M 151864 CGATCTGTACGTCCCTGGAGCGTATACTGCCTAGGTAAGTGAACTGATCC 151913 ? v i i vi vv ii i ivv i viviv C MamRTE1#LINE/ 3045 CNATCAGTGCATCATTGGACAGCGTGCTGCCTAGGTAGCAGAATTCGGTG 2996 chrXqtel1M 151914 ACAGCATTTG---CTGTA--GC----------TTATGGTTCCGGGTATGG 151948 v ii--- -- ----------i v i v v v C MamRTE1#LINE/ 2995 ACAGCTTTCAGCTCTGTATTGCCGATGAAAATCTTTGGCTGCGTGTAGGG 2946 chrXqtel1M 151949 ATGCTAAGGTGCTGGCTGATGGAGCACCTGTGCCTTC-TCAGTGGTAATT 151997 v v ivv v i iv vv vv i - - v v i C MamRTE1#LINE/ 2945 TTTCCCTGGTGCAGGCTGGTACATGACCTCGGTCTTCTTCAG-GCTTATC 2897 chrXqtel1M 151998 CTTAGGCCAAAA---TGAACACAAACAGCAGAGAACTGATCCATACTTTG 152044 v i v iv i--- vi vv vv v i ---i i iv iv? C MamRTE1#LINE/ 2896 GTCAGTCCGTAGCGCTGTGCTGACTCTGCAAAG---CGGTCCATGATCAN 2850 chrXqtel1M 152045 TTGCATCTCAATTT---CAGAGGCTGCAGACAAAAAAATCACGGACCAAC 152091 i v vvi --- ivivi v - v iv v i iv i vv C MamRTE1#LINE/ 2849 CTGCATGTCTTCTTGCGCGTGTACTTCA-AGAGCACAGTCATCGGCATAC 2801 chrXqtel1M 152092 ACCCCTTCC------ACTTT-------AGTTTTGC-----CTTGTAGACT 152123 v vv ------ v ------- v i v----- i v C MamRTE1#LINE/ 2800 AGCAGTTCCTGGATGACTGTCTCAAGGACTTTCGATGATGCTCGTAGCCT 2751 chrXqtel1M 152124 -TCAAATT-GAAAAATTTACCGTTGGTTCGGCCCCG-ACTTGGATGCCAC 152170 - ii i - i i v ivv vi vvv - i iv ii v C MamRTE1#LINE/ 2750 GTTGAGTTGGAAGAGTTTCCCAGAGGACCGGAAGCGTATTCTGACACCAG 2701 chrXqtel1M 152171 ATTC---GT-CCTCATTGAAGGCGTTTGCCAACCTGGCTG---AAAACAT 152213 v --- - ii ---- i iiv v i v --- i v C MamRTE1#LINE/ 2700 CTTCCAGGTCCCTTGTT----GCATCCTCGAGCATGGCTGCATAAAATAG 2655 chrXqtel1M 152214 CATGGATAAAAACCATGGGAGCCAGCATGTGGTCTTGTTTTACTCCACTG 152263 vv i i---- iv v i vi i iii i i i i C MamRTE1#LINE/ 2654 ATTGAATAAG----ACTGGACCTATTACGCAATCCTGCTTCACTCCATTG 2609 chrXqtel1M 152264 GTGACTGGGGAA 152275 - C MamRTE1#LINE/ 2608 GTGA-TGGGGAA 2598 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 50.49 CpG sites = 141, Kimura (unadjusted) = 53.96 Transitions / transversions = 0.86 (141/164) Gap_init rate = 0.06 (50 / 828), avg. gap size = 2.14 (107 / 50) 336 34.62 5.36 2.61 chrXqtel1M 152349 152609 (847391) C MamRTE2#LINE/RTE-BovB (1278) 274 7 m_b356s551i3 14902 chrXqtel1M 152349 GATGCATTTTTCTAGGCAGCCAGATCTTGACATAATTTCCCACAAGCCCT 152398 i v vv i v v ii iiiv v iii vv i C MamRTE2#LINE/ 274 GACGAATTTTGGTGGGCATCCATACTTCAGAAGAATCCTCCACAATGCTT 225 chrXqtel1M 152399 CATGACTGACAGTATCAAAGATGTTGGTCAGATCTACAAACGTTGTATAC 152448 i vi iiv vv v ?i v vi v iii v C MamRTE2#LINE/ 224 CACGACTGACAGAGTCAAAGGCCTTCCTGANGTCGAGGAAGGCCATATAA 175 chrXqtel1M 152449 AGC--CTTACGTTCTCTGCTCCTGGCACTTCTCCTGGACTT---GAGCAG 152493 v--i i ---- i i i i ? vi --- C MamRTE2#LINE/ 174 AGAGGTTTATGT----TGTTCTTGGCATTTTTCCTGNAGCTGGCGAGCAG 129 chrXqtel1M 152494 CAAACACCTTTTCAACCATTCCCCGTCCCT--TCTGAAGCCACACTGGCT 152541 ii v v v iiiiiv i - ?vv -- i v i ivv C MamRTE2#LINE/ 128 TGAAGACCGTATCAGTTGCGCCTC-TNGATGCTCTAAACCCACGCTGAGA 80 chrXqtel1M 152542 CTCAGGTAGATG-------ACAGGTAAAGGATCAGCCTATTAAGTAGGAC 152584 i v v v -------i i --i vv i vi v v i C MamRTE2#LINE/ 79 TTCCGGGAGAAGCTCTTCAGCAAGT--GGGAGGAGTCGGTTCAGGAGGAT 32 chrXqtel1M 152585 TCTGGCAAGAATCTTGCCAGCAGTG 152609 v vi v i i C MamRTE2#LINE/ 31 TCTTGCAATGATCTTTCCGGCGGTG 7 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 44.13 CpG sites = 48, Kimura (unadjusted) = 48.62 Transitions / transversions = 1.20 (48/40) Gap_init rate = 0.04 (11 / 260), avg. gap size = 1.91 (21 / 11) 226 36.77 6.84 4.10 chrXqtel1M 152633 152822 (847178) C MamRTE1#LINE/RTE-BovB (1570) 2242 2048 m_b356s601i1 14901 chrXqtel1M 152633 CTGTGATGATCACC--AGGCAATCTATTC--TTTACTTTTATAGAGCTGA 152678 i i ii ii -- v iii vi --i v i - ii v i C MamRTE1#LINE/ 2242 CCGCGATAGTTGCCGCAGTCAGCTTTCTCGCCTTTCTTCT-TGAAGATGG 2194 chrXqtel1M 152679 --ACGTTGGCGGTGTCCTTGAACTCCTGGAGGATAACCTCTTCTTGCCAT 152726 -- i v i i ii i v vi v vv vviviv C MamRTE1#LINE/ 2193 TGATGATAGTGGCATCTTTGAAATCCTGCGGCATTTCCTCGGTACTCCAT 2144 chrXqtel1M 152727 ATGAATTTTCAGTCA-GCTTTTGTA------TGAGCAATGGACCCCCCCC 152769 ---i vv vv - i v i ------ i ii ----i i C MamRTE1#LINE/ 2143 ATG---CTGAAGAAAAGCCTATGCAGACGTCTAAGCAGCG----TCTCCC 2101 chrXqtel1M 152770 CCCCCACCTTGTAAATCTCAGCCGGAATAGAATTAGCACCAGGTGCTTTA 152819 ii vv v v v ivv i vv ii v C MamRTE1#LINE/ 2100 CTTCCTGCTTGAAAATCTCAGCAGGTATGCCATCAGGTCCGAGAGCTTTA 2051 chrXqtel1M 152820 CCA 152822 C MamRTE1#LINE/ 2050 CCA 2048 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 47.08 CpG sites = 38, Kimura (unadjusted) = 52.60 Transitions / transversions = 1.31 (38/29) Gap_init rate = 0.07 (13 / 189), avg. gap size = 1.62 (21 / 13) 322 36.47 1.64 1.09 chrXqtel1M 152847 153029 (846971) C MamRTE1#LINE/RTE-BovB (1883) 1929 1746 m_b356s601i2 14901 chrXqtel1M 152847 TGTTGAGAACATTATAGAAGTGTT-CTGCCCTCTCTCTAGGATCATGTCC 152895 ? v ii v - v iv iviv i C MamRTE1#LINE/ 1929 TGTTNAGAAGATCGTTGAAGTGTTGCTGCCATCTCCGTAGGATTCCCTTC 1880 chrXqtel1M 152896 TTAGCGCTAATCAATGTGG-GTCCTCAGCACCGAGTAATTGAGACCCAGC 152944 iiiv vv i v iv i - i v v? ivvvi iiv v -- ivv C MamRTE1#LINE/ 1879 CCGTCTGTGATGAGGGCGGAGCCATCTNCACTCCTCAGCGGTG--CCGTG 1832 chrXqtel1M 152945 ATAG-GTCCTTTGGCCCATAGGTGACCTTCAGGGCTTCATAAAAACCCTT 152993 i - viv ? vivv i i ?iv i ii C MamRTE1#LINE/ 1831 ATGGCGTGTGTTGGNCCATATAACATCTTTAGGGNCGCATAGAAGTCCTT 1782 chrXqtel1M 152994 TGTCTTTCTTCTATCAGCATAATCCTGAATTTCATC 153029 v i vviv? vi v i i i v C MamRTE1#LINE/ 1781 GGTTTGGTGNCGGTCTGCATAGTCCTGGATCTCTTC 1746 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.28 CpG sites = 33, Kimura (unadjusted) = 53.08 Transitions / transversions = 1.00 (33/33) Gap_init rate = 0.03 (5 / 182), avg. gap size = 1.00 (5 / 5) 409 25.17 7.46 5.11 chrXqtel1M 154398 154531 (845469) MIRc#SINE/MIR 10 146 (122) m_b356s601i3 14903 chrXqtel1M 154398 GCGGTGCAGTGGATAGAGTGCCAAGCCGGGAGTCAGGAGGACTTGAGTTC 154447 i v ii iiii iv i i i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chrXqtel1M 154448 AATTCCAACCTCAGAC----GCTACCTTTG------TGGGTAAGTCACTT 154487 i v viv v v ----i v v ------ i MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTT 109 chrXqtel1M 154488 CCCCCCCTCCCCCCGTTTACCTCAGTTTCCTCACCTGTGAAATG 154531 -vv i ------ vvi i i MIRc#SINE/MIR 110 -AACCTCTC------TGAGCCTCAGTTTCCTCATCTGTAAAATG 146 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.09 CpG sites = 19, Kimura (unadjusted) = 31.40 Transitions / transversions = 1.46 (19/13) Gap_init rate = 0.07 (9 / 133), avg. gap size = 1.89 (17 / 9) 538 35.04 8.15 4.37 chrXqtel1M 155086 155637 (844363) L3#LINE/CR1 906 1477 (2622) m_b356s601i4 14904 chrXqtel1M 155086 AGAGAAAAGGAGATCTGGGAAGCGGACG-------ACACAGACAGTGAGT 155128 i ii v i i i------- ii ii vvv L3#LINE/CR1 906 AGAGAAAGGAGGATATGGGAAGTGAACAGCTGGCTACGTAGATGGTGTCG 955 chrXqtel1M 155129 AAGGATCCAATGGGATCTGCGCTTTGGGATCGCAGCTGCTGTCTAATACA 155178 ----- ii i vvi iv i iii ---- v?i v L3#LINE/CR1 956 AAG-----AACAGGATTTGGTTTTCTGGACCATGGCT----TANGATACC 996 chrXqtel1M 155179 GGAATGAGAGAATGCTGG----GTGTGGAATACACGTCCCAGGGGTT--- 155221 i i vi iv v ---- vii i i iv v iii iii--- L3#LINE/CR1 997 AGAACGATGGGCTCCTGGCNAGGGACGGAGTGCATCTCACGAAGACCGGG 1046 chrXqtel1M 155222 -AAAATGGATTTGCAGGGAGACTGGCAAAGCTAATGAAATAGGCTTTAAA 155270 - i i vi ?v? v vi v i v ivi i L3#LINE/CR1 1047 AAGAACGTGTTTGNCNGGAGACTCGCCGACCTGATCAAGAGGACTTTAAA 1096 chrXqtel1M 155271 GTGAAAAG-GAGTGAGAAGGAAGTACACTGCCT--------CTGTAGATC 155311 v vv- v - iv v v i-------- i v L3#LINE/CR1 1097 CTGAAATTTGAGGGA-AAGGAAAAAAAATGCCCAGATAAAACTGTAAAAC 1145 chrXqtel1M 155312 C----CCCATAGGGAGTAGC---CATGATATCAAAAAAA----ATGAGTG 155350 ----v i i i ii ? ---i i vi i ---- vv L3#LINE/CR1 1146 CGGATACTATGGAGGATANCAGGTATGACATAGAAAGAAGAACAACAGTG 1195 chrXqtel1M 155351 G--GATACCCCCAAACCTCCTAGCCAGTACACAAAATCCGACAAATGAAT 155398 -- viiv ivvv i ?--- v v v v v ? iv - - L3#LINE/CR1 1196 GAGGAGGTGCCCAGTAATTCN---CAGGAGAAAATAACNGGAAAA-GAA- 1240 chrXqtel1M 155399 GAATGAGCAATGAAATGCATGGTATTGGTTGTCAATGCAGAAATGCACAC 155448 --iiv v ii v ivi iv ii v v ii vv v L3#LINE/CR1 1241 --GCTAGAAACAATACTTATGGCCTCAGATGTCTATATACCAATGCACAG 1288 chrXqtel1M 155449 AGTAGGGCTTGAATGAAGGAGGGGAACTAGAGATCCTAGAGCAAAGCTGC 155498 v v -- i ?i i v? v i ii ivi i vv i L3#LINE/CR1 1289 AGTATGGGT--AATAAANAAAGTNAACTTGAAATTTTAACACAAGGAGGT 1336 chrXqtel1M 155499 -----TGATCTCATGGGTGTCACTGAGATTTGGGGGGATAGAATGGGATG 155543 -----i i i i i v i i i-vv L3#LINE/CR1 1337 AAATACGATCTCATAGGTATCACCGAGACTTGGTGGGATGGGAC-TCATG 1385 chrXqtel1M 155544 AGTGGAATCAGGCTGGGGATGAGTAGATCCTACATTCACAATCAAC---T 155590 v vv viv v i ? i i --i v vv --- L3#LINE/CR1 1386 ACTGGAATACGGCGATGGAAGGGTANACCTT--GTTCAAAAGAAACAGAT 1433 chrXqtel1M 155591 CTAAGTGAGTGTGATGGCCATGGGCTTCGTGGTAGGTTAAGAAGACA 155637 ?vv iv v v ?v--- i ivv iiv v i i L3#LINE/CR1 1434 CTANTAGAAGGGGAGGNA---GAGTAGCACTGTATGTCAAGAAGATA 1477 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.85 CpG sites = 101, Kimura (unadjusted) = 50.25 Transitions / transversions = 1.20 (101/84) Gap_init rate = 0.07 (37 / 551), avg. gap size = 1.89 (70 / 37) 35 0.00 0.00 0.00 chrXqtel1M 156235 156264 (843736) (AC)n#Simple_repeat 1 30 (0) c_b356s251i1 14905 chrXqtel1M 156235 ACACACACACACACACACACACACACACAC 156264 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACAC 30 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 351 25.98 5.83 2.83 chrXqtel1M 156308 156410 (843590) MIRc#SINE/MIR 2 107 (161) m_b356s601i5 14906 chrXqtel1M 156308 GGAGCAGTGAGGTGCCACAGTGGATGGAACACTGGCCGTGGAATCAGAAA 156357 ii v --- vi i v v i i MIRc#SINE/MIR 2 GAGGCAGTGTGGTGC---AGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chrXqtel1M 156358 GACTTCTTCCTGAGT-TCAAATCTGGC-----CTAGCTGTGTGACTCTGG 156401 i vvviii -i iiv v ----- ii MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 98 chrXqtel1M 156402 ATAAGTCAC 156410 ii MIRc#SINE/MIR 99 GCAAGTCAC 107 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.01 CpG sites = 17, Kimura (unadjusted) = 33.07 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.05 (5 / 102), avg. gap size = 1.80 (9 / 5) 248 21.05 3.51 0.00 chrXqtel1M 157109 157165 (842835) MIR3#SINE/MIR 103 161 (47) m_b356s601i6 14907 chrXqtel1M 157109 ACCTC-CCCCTGCGTGTCTCAGTTTTCTCATCTGTAAAATGAGCAGG-AG 157156 i - i vi v i i vi -v MIR3#SINE/MIR 103 ACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTG 152 chrXqtel1M 157157 GAGTAAATG 157165 v i MIR3#SINE/MIR 153 GACTAGATG 161 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 25.10 CpG sites = 7, Kimura (unadjusted) = 25.10 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.04 (2 / 56), avg. gap size = 1.00 (2 / 2) 13 24.88 0.00 0.00 chrXqtel1M 158182 158219 (841781) (GGGGGTG)n#Simple_repeat 1 38 (0) m_b356s252i0 14908 chrXqtel1M 158182 GGGGGTTGGGGGTTAGGAGGGCAGAGTGGGGGGTGGGG 158219 v vi i v vi i (GGGGGTG)n#Si 1 GGGGGTGGGGGGTGGGGGGTGGGGGGTGGGGGGTGGGG 38 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 12 14.63 0.00 6.25 chrXqtel1M 158715 158748 (841252) (CCCT)n#Simple_repeat 1 32 (0) m_b356s252i1 14909 chrXqtel1M 158715 CCCTCCCTCCCTCCTTCTAATCCCCTCCCCCCCT 158748 i -vv - i (CCCT)n#Simpl 1 CCCTCCCTCCCTCCCTC-CCT-CCCTCCCTCCCT 32 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2) 16 13.24 0.00 0.00 chrXqtel1M 159120 159144 (840856) (C)n#Simple_repeat 1 25 (0) m_b356s252i2 14910 chrXqtel1M 159120 CCCCCCTCCCCCCGCCCCCCCTCCC 159144 i v i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCC 25 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 18 4.13 0.00 0.00 chrXqtel1M 160070 160094 (839906) (GGA)n#Simple_repeat 1 25 (0) m_b356s252i3 14911 chrXqtel1M 160070 GGAGGAGGAGGAGGAGGAGGAGCAG 160094 v (GGA)n#Simple 1 GGAGGAGGAGGAGGAGGAGGAGGAG 25 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 13 0.00 0.00 0.00 chrXqtel1M 161908 161924 (838076) (GCG)n#Simple_repeat 1 17 (0) m_b356s252i4 14912 chrXqtel1M 161908 GCGGCGGCGGCGGCGGC 161924 (GCG)n#Simple 1 GCGGCGGCGGCGGCGGC 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 236 23.67 13.25 3.30 chrXqtel1M 162983 163065 (836935) Charlie4a#DNA/hAT-Charlie 405 495 (13) m_b356s502i0 14913 chrXqtel1M 162983 GTGCTTTATTCTGTGCATTTAAAACCGTGATTCTTCTGAGTGGGGTTCCA 163032 ii i i v --- v vi v Charlie4a#DNA 405 GTATTTTATTTTATGCATTTAAAAAC---ATTATTCTGAGAAGGGGTCCA 451 chrXqtel1M 163033 C-----------GGCTGCCAGAGGAAGCCACGCCACCGAAAAGG 163065 i----------- i i iiv i v vi Charlie4a#DNA 452 TAGGCTTCACCAGACTGCCAAAGGGGTCCATGGCACAAAAAAGG 495 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 29.32 CpG sites = 12, Kimura (unadjusted) = 29.32 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.05 (4 / 82), avg. gap size = 3.50 (14 / 4) 14 5.00 0.00 0.00 chrXqtel1M 164279 164299 (835701) (GCG)n#Simple_repeat 1 21 (0) m_b356s252i5 14914 chrXqtel1M 164279 GCGGCGGCGGCGGCGGCAGCG 164299 i (GCG)n#Simple 1 GCGGCGGCGGCGGCGGCGGCG 21 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 20 25.88 1.52 1.52 chrXqtel1M 164478 164543 (835457) (TCTG)n#Simple_repeat 1 66 (0) m_b356s252i6 14915 chrXqtel1M 164478 TCTCTCTGTCTCTGGTTCCATCTGTCTGTCTGTCTGTCTCTCTCTCTCGC 164527 v v vvv ii v v vv (TCTG)n#Simpl 1 TCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTC 50 chrXqtel1M 164528 T-TCTCTTTTGTCTTTC 164543 - -v i v (TCTG)n#Simpl 51 TGTCT-GTCTGTCTGTC 66 Matrix = Unknown Transitions / transversions = 0.27 (3/11) Gap_init rate = 0.03 (2 / 65), avg. gap size = 1.00 (2 / 2) 15 4.71 0.00 0.00 chrXqtel1M 165476 165497 (834503) (CCCT)n#Simple_repeat 1 22 (0) m_b356s252i7 14916 chrXqtel1M 165476 CCCTCCCTCCCTCCCTCCCACC 165497 v (CCCT)n#Simpl 1 CCCTCCCTCCCTCCCTCCCTCC 22 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 527 29.87 0.69 0.69 chrXqtel1M 166355 166499 (833501) MIRc#SINE/MIR 4 148 (120) m_b356s601i7 14917 chrXqtel1M 166355 GGCTGGGTGGCACAGTGGACAGAGTACCAGGCGCTGAAGCCAGGGGGACC 166404 v v ii v i ii i -i i i ii MIRc#SINE/MIR 4 GGCAGTGTGGTGCAGTGGAAAGAGCACTGGAC-TTGGAGTCAGGAAGACC 52 chrXqtel1M 166405 CGAGTTCAAAGTCAGCCTCAGACGTTTCCTCCCCATGTGACCCTGGGCAG 166454 i i i ivi v v v v ii v vv ii i i MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 102 chrXqtel1M 166455 GTCCCTCGACC-CTGTTTACCTCAGTTTCCTCATCTGTCAGATGAG 166499 v ii - v vvi v i i MIRc#SINE/MIR 103 GTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.37 CpG sites = 27, Kimura (unadjusted) = 39.57 Transitions / transversions = 1.69 (27/16) Gap_init rate = 0.01 (2 / 144), avg. gap size = 1.00 (2 / 2) 246 29.17 2.78 0.00 chrXqtel1M 167261 167332 (832668) MIRc#SINE/MIR 159 232 (36) m_b356s601i8 14917 chrXqtel1M 167261 CCTGCCCT--CAACCTCCCAGGGTGGCTGTGAGAATCAGCTGAGGTGACG 167308 -- v v v i i iv i i i MIRc#SINE/MIR 159 CCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATG 208 chrXqtel1M 167309 CTGGGAAAAGCACTCAGCACAGTG 167332 ivv vi i iv i v v MIRc#SINE/MIR 209 TATGTGAAAGCGCTTTGTAAACTG 232 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.32 CpG sites = 11, Kimura (unadjusted) = 37.52 Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.01 (1 / 71), avg. gap size = 2.00 (2 / 1) 403 28.87 0.00 1.03 chrXqtel1M 167271 167368 (832632) MIRb#SINE/MIR 165 261 (7) m_b356s601i9 14917 chrXqtel1M 167271 ACCTCCCAGGGTGGCTGTGAGAATCAGCTGAGGTGACGCTGGGAAAAGCA 167320 v v i i i iv i i i -iv v i MIRb#SINE/MIR 165 ACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGC-ATGTAAAGCG 213 chrXqtel1M 167321 CTCAGCACAGTGCCCGGCACATAGTAGCCATTTAGTGAGTACTTGTTC 167368 i i iv ii i i i i iv v i MIRb#SINE/MIR 214 CTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAAATGGTAGCTC 261 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.11 CpG sites = 20, Kimura (unadjusted) = 38.65 Transitions / transversions = 2.50 (20/8) Gap_init rate = 0.01 (1 / 97), avg. gap size = 1.00 (1 / 1) 504 23.12 3.31 8.33 chrXqtel1M 167542 167692 (832308) C MIRc#SINE/MIR (121) 147 4 m_b356s601i10 14918 chrXqtel1M 167542 CTGTTTCACAGACGCGGAAACTGAGGC--AAACAGGGTC--TGACTGGCC 167587 ii i i v -- i v v v-- v C MIRc#SINE/MIR 147 CCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCC 98 chrXqtel1M 167588 -AGGGTCATGCAGCTAGTAAATGTCTGAGGCGGGATTTGAACTCGGGAAG 167636 - i ii i v v v i i i ------ C MIRc#SINE/MIR 97 CAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCC------ 54 chrXqtel1M 167637 AGAAGTCTTCCTGACTCCAGGTCCAGCACATTGTCGCGTTGCCCTGCCAT 167686 -- i i ii vi v - ii ---i i C MIRc#SINE/MIR 53 --AGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTC-CACTGC---ACCAC 10 chrXqtel1M 167687 GCTGCC 167692 i C MIRc#SINE/MIR 9 ACTGCC 4 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.43 CpG sites = 22, Kimura (unadjusted) = 28.47 Transitions / transversions = 2.20 (22/10) Gap_init rate = 0.10 (15 / 150), avg. gap size = 1.13 (17 / 15) 187 26.67 9.33 0.00 chrXqtel1M 167789 167863 (832137) C OldhAT1#DNA/hAT-Ac (1838) 1004 923 m_b356s601i11 14919 chrXqtel1M 167789 AGCTAGCAAA---GCAATTTGCCCAA-ATG-TATGAAGAATATGAAGTCC 167833 i i --- v ?v -i - i vvi i v i ? C OldhAT1#DNA/h 1004 AGCTGGCAGACTGGAANATTGCCCAATGTGCTGTGACTGACATGTAATCN 955 chrXqtel1M 167834 ACCGTTTG--CACTGCTCTGCCAATTTCCGGT 167863 -- v ii vv i vi C OldhAT1#DNA/h 954 ACCGTTTGACCACTGGTCCACATATCTGTGGT 923 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.72 CpG sites = 11, Kimura (unadjusted) = 34.72 Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.05 (4 / 74), avg. gap size = 1.75 (7 / 4) 241 34.74 6.16 4.38 chrXqtel1M 167846 168137 (831863) L2b_3end#LINE/L2 13 309 (157) m_b356s601i12 14920 chrXqtel1M 167846 GCTCTGCCAATT-TCCGGTCT----TCCTATGGCTTCCCTCACTTCACAA 167890 i i i vi - i ---- ivi --- v i ii vv L2b_3end#LINE 13 GCCCCGCTACCTCTCCGGCCTCATCTCCTACCACT---CTCCCCTTGCTC 59 chrXqtel1M 167891 ACTCCCTGATCTAGTAACATGCGTTCCCCTTGAAGTCCCTGGAACACGCT 167940 -- v i iv i-i vi i vv i v i L2b_3end#LINE 60 ACTC--TGCTCCAGCCACAC-TGGCCTCCTTGCTGTTCCTCGAACACGCC 106 chrXqtel1M 167941 CCTTCGTCTCTCATCTCTGTCCCTTTGCCCTTGCACCAGAGGGTCCCTAT 167990 v?viiv? i ii v v------ i ?v vv v v L2b_3end#LINE 107 ANGCTCNCTCCCGCCTCAGG------GCCTTTGCACNTGCTGTTCCCTCT 150 chrXqtel1M 167991 TCCGGGAAAGCTCTGTCTCTCCTCTCCACTT---CATTTTCTGGCCTTTT 168037 v v v i vi i v i i i --- vi i ivi v ii L2b_3end#LINE 151 GCCTGGAACGCCCTTCCCCACCTCTTCGCCTGGCCAACTCCTACTCATCC 200 chrXqtel1M 168038 TCCGAGAGTCAGCT--GACATCACAT-CTTCGGCACGATTCTCTTGCCCT 168084 i ii vv --i ii v - i v v viiii i v i L2b_3end#LINE 201 TTCAGGTCTCAGCTCAAATGTCACCTCCTCCGGGAAGCCCTCCCTGACCC 250 chrXqtel1M 168085 CTCATG--GGGAC---CTCCCTTCT-TGGGCCATCCCCTGTGCCA-CCAG 168127 i v -- v --- v i - -i v v i - v L2b_3end#LINE 251 CCCAGGCCGGGTCAGGCGCCCTCCTCTGGGCC-CCCCCAGTCCTACCCTG 299 chrXqtel1M 168128 CCTTTCTGGG 168137 vi L2b_3end#LINE 300 CCACTCTGGG 309 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.82 CpG sites = 54, Kimura (unadjusted) = 48.94 Transitions / transversions = 1.26 (54/43) Gap_init rate = 0.08 (22 / 291), avg. gap size = 1.41 (31 / 22) 196 37.54 3.09 5.26 chrXqtel1M 168275 168468 (831532) L2d2_3end#LINE/L2 41 230 (325) m_b356s601i13 14921 chrXqtel1M 168275 CCTGCTAGTCGCATTCATGCATTCTGGAGTTCTAGTCAAACCGGCTGGTT 168324 ii v v v ? i v ii vv- i i i i iivii L2d2_3end#LIN 41 CCCACTATTCCCCTNCACGAACCCTCC-GCTCCAGCCAAACTGGTCTACT 89 chrXqtel1M 168325 CATTAACTTCC---CAGGCCATCGAATATTCTACCACCTACCTCCAGTTC 168371 i iv ii --- v - i vii? -- i -- v i--i L2d2_3end#LIN 90 CACTGTCCCCCGAACACGCC-TTGCGCNTTC--CCGCCT--CTGCG--CC 132 chrXqtel1M 168372 TTTGTGTCTGCAGTTCC-CCGGTCTGGAGTGTACTCCCTCTTTACCTTTA 168420 ivivi v - v i i iv i i -- i v L2d2_3end#LIN 133 TTTGCTCACGCCGTTCCCCCCGCCTGGAATGCCCTTCCCCTT--CCTCTC 180 chrXqtel1M 168421 TACCCTTTGAAAGCTCAAATTTCCTTAAAGA--CAATTCAGGTAGCAGCT 168468 i iv iv v ii vviv v i-- ii ii ?v v L2d2_3end#LIN 181 CACCTATCCAAATCCTACCCATCCTTCAAGGCCCAGCTCAAATNCCACCT 230 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 50.56 CpG sites = 43, Kimura (unadjusted) = 56.69 Transitions / transversions = 1.65 (43/26) Gap_init rate = 0.07 (13 / 193), avg. gap size = 1.23 (16 / 13) 205 23.94 19.72 0.00 chrXqtel1M 168780 168850 (831150) MIRb#SINE/MIR 1 85 (183) m_b356s601i14 14922 chrXqtel1M 168780 CAGAGAAGCAGCCTGACTCAGTGAACATAGC-CG------------AGA- 168815 ii v iiv i v v - ------------ - MIRb#SINE/MIR 1 CAGAGGGGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGAC 50 chrXqtel1M 168816 AGACCTGAGTTCAAGTCCCAGCTATGTGACTTGCT 168850 i i i i v iv i MIRb#SINE/MIR 51 AGACCTGGGTTCGAATCCCGGCTCTGCCACTTACT 85 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 25.68 CpG sites = 11, Kimura (unadjusted) = 29.70 Transitions / transversions = 1.83 (11/6) Gap_init rate = 0.04 (3 / 70), avg. gap size = 4.67 (14 / 3) 233 24.53 3.77 0.00 chrXqtel1M 168798 168850 (831150) MIRc#SINE/MIR 28 82 (186) m_b356s601i15 14922 chrXqtel1M 168798 CAGTGAACAT--AGCCGAGAAGACCTGAGTTCAAGTCCCAGCTATGTGAC 168845 v i v -- i ii i i i v iv MIRc#SINE/MIR 28 CACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCAC 77 chrXqtel1M 168846 TTGCT 168850 i MIRc#SINE/MIR 78 TTACT 82 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 25.41 CpG sites = 9, Kimura (unadjusted) = 30.91 Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.02 (1 / 52), avg. gap size = 2.00 (2 / 1) 296 31.51 9.91 4.95 chrXqtel1M 169366 169789 (830211) L1PA6_3end#LINE/L1 12 455 (446) m_b356s551i5 14923 chrXqtel1M 169366 AGTCTCGAAGGAATAGAGTCACATTTATAAGAATAAATAAGAACCATTGC 169415 i vv i ivv iv v i v - vi v i-- L1PA6_3end#LI 12 AATCTACAAAGAACTTAAACAAATTTACAAGAAAAAA-ACAAACAAC--C 58 chrXqtel1M 169416 TCATCGATAAACAGTCAAAGGATGCGCACAGGCAGTTCAGAAAAGGATGA 169465 i i v iii v ii v i v vv i - L1PA6_3end#LI 59 CCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCTCAAAAGAA-GA 107 chrXqtel1M 169466 AAT--------CCAAT-----CTTCAAAA------------CACTA---A 169487 v -------- i----- v v ------------ i--- L1PA6_3end#LI 108 CATTTATGCAGCCAACAGACACATGAAAAAATGCTCATCATCACTGGTCA 157 chrXqtel1M 169488 CTCGAAACATGCAAATTAAAAAAACC-CAAAGTTCTAATTCATGCCCATC 169536 iiv i v i vv v-ii ii v i vi i vi i L1PA6_3end#LI 158 TCAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTCACGCCAGTT 207 chrXqtel1M 169537 AGATTGCCTAAAATGATCACCAAAAAAAAAAAAAAAAGGAAATGACAATT 169586 v v ------ ii ivv ------- ii iv L1PA6_3end#LI 208 AGAATGGC------GATCATTAAAAAGTCA-------GGAAACAACAGAT 244 chrXqtel1M 169587 GCTGGAAAGACTGTGGAAAAATAGACATTTTGTGGCTCTGTCAGTGGAGC 169636 i iv i iv ivi v vi v ii iiv L1PA6_3end#LI 245 GCTGGAGAGGATGTGGAGAAATAGGAACGCTTTTACACTGTTGGTGGGAG 294 chrXqtel1M 169637 CGGGAACAGGTTCAGCCATTCTGGAAAACAATGTTGACTATT-------A 169679 i vi vi i v i i - i v -------i L1PA6_3end#LI 295 TGTAAACTAGTTCAACCATTGTGGAAGACAGTGT-GGCGATTCCTCAAGG 343 chrXqtel1M 169680 TTCCAAAGTTAGAAA-ACC-TTTGCCCCAGGAATCCCATTTCCAGGTCTT 169727 v i i ii - - v vi v ii v v L1PA6_3end#LI 344 ATCTAGAACTAGAAATACCATTTGACCCAGCGATCCCATTACTGGGTATA 393 chrXqtel1M 169728 TGTCCCAAAGGGATCAGAAG--AAG--AGGAAAAGGACCTATATGTACAG 169773 i- - i v i-- v -- vv v i -- i i v L1PA6_3end#LI 394 TA-CCCAAA-GGATTATAAATCATGCTACTATAAAGAC--ACATGCACAC 439 chrXqtel1M 169774 AAATGTTTATAGCTGC 169789 iv v v L1PA6_3end#LI 440 GTATGTTTATTGCGGC 455 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 40.28 CpG sites = 70, Kimura (unadjusted) = 42.01 Transitions / transversions = 1.23 (70/57) Gap_init rate = 0.08 (32 / 423), avg. gap size = 2.00 (64 / 32) 320 31.56 10.19 4.85 chrXqtel1M 169366 169738 (830262) L1PA7_3end#LINE/L1 12 403 (498) m_b356s551i4 14923 chrXqtel1M 169366 AGTCTCGAAGGAATAGAGTCACATTTATAAGAATAAATAAGAACCATTGC 169415 i vv ivv iv v i v - vi v i-- L1PA7_3end#LI 12 AATCTACAAGGAACTTAAACAAATTTACAAGAAAAAA-ACAAACAAC--C 58 chrXqtel1M 169416 TCATCGATAAACAGTCAAAGGATGCGCACAGGCAGTTCAGAAAAGGATGA 169465 i i v iii v i ii v i v vv i - L1PA7_3end#LI 59 CCATCAAAAAGTGGGCGAAGGATATGAACAGACACTTCTCAAAAGAA-GA 107 chrXqtel1M 169466 AAT--------CCAA------TCTTCAAAA-----------CACTA---A 169487 v -------- ------ v vv ----------- i--- L1PA7_3end#LI 108 CATTTATGCGGCCAACAAACATATGAAAAAAAGCTCATCATCACTGGTCA 157 chrXqtel1M 169488 CTCGAAACATGCAAATTAAAAAAACC-CAAAGTTCTAATTCATGCCCATC 169536 i v i v i vv v-ii ii v i vi i vi i L1PA7_3end#LI 158 TTAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTCACGCCAGTT 207 chrXqtel1M 169537 AGATTGCCTAAAATGATCACCAAAAAAAAAAAAAAAAGGAAATGACAATT 169586 v v ------ ii ivv ------- ii iv L1PA7_3end#LI 208 AGAATGGC------GATCATTAAAAAGTCA-------GGAAACAACAGAT 244 chrXqtel1M 169587 GCTGGAAAGACTGTGGAAAAATAGACATTTTGTGGCTCTGTCAGTGGAGC 169636 i iv i iv ivi v vi v ii iiv L1PA7_3end#LI 245 GCTGGAGAGGATGTGGAGAAATAGGAACGCTTTTACACTGTTGGTGGGAG 294 chrXqtel1M 169637 CGGGAACAGGTTCAGCCATTCTGGAAAACAATGTTGACTATT-------A 169679 i vi ivi i v i i - i v -------i L1PA7_3end#LI 295 TGTAAATTAGTTCAACCATTGTGGAAGACAGTGT-GGCGATTCCTCAAGG 343 chrXqtel1M 169680 TTCCAAAGTTAGAAA-ACC-TTTGCCCCAGGAATCCCATTTCCAGGTCTT 169727 v i i iii - - v v v ii v v L1PA7_3end#LI 344 ATCTAGAACCAGAAATACCATTTGACCCAGCAATCCCATTACTGGGTATA 393 chrXqtel1M 169728 TGTCCCAAAGG 169738 i- L1PA7_3end#LI 394 TA-CCCAAAGG 403 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 40.71 CpG sites = 63, Kimura (unadjusted) = 42.20 Transitions / transversions = 1.29 (63/49) Gap_init rate = 0.07 (27 / 372), avg. gap size = 2.11 (57 / 27) 233 31.88 10.61 3.87 chrXqtel1M 169385 169893 (830107) L1ME4a_3end#LINE/L1 31 572 (299) m_b356s551i6 14923 chrXqtel1M 169385 CACATTTATAAGAATAAATAAGAACCATTGCTCATCGATAAACAGTCAAA 169434 v iv - v v - ii- iv v v ii v L1ME4a_3end#L 31 CAAATCAATAAGAA-AAAGACGAAC-ACC-CCAATAGAAAAATGGGCAAA 77 chrXqtel1M 169435 GGATGCGCACAGGCAGTTCAGAAAAGGATGAAAT--------CCAAT--- 169473 iii v i i v i - -------- --- L1ME4a_3end#L 78 GGACATGAACAGACAATTCACAAAAGAA-GAAATACAAATGGCCAATAAA 126 chrXqtel1M 169474 --CTTCAAAA------------CACTA--ACTCGAA-ACATGCAAATTAA 169506 --iv v ------------ -- v i - v L1ME4a_3end#L 127 CATATGAAAANATGTTCAACCTCACTAGTAATCAAAGAAATGCAAATTAA 176 chrXqtel1M 169507 AAAAACC-CAAAGTTCTAATTCATGCCCATCAGATTGCCTAAAATGATCA 169555 v v-ii ii v i v ivii i i v v i -- i L1ME4a_3end#L 177 AACAACAATGAGATACCATTTTTCACCTATCAAATTGGCAAAGAT--TTA 224 chrXqtel1M 169556 CCAAAAAAAAAAAAAAAAGGAAATGACAATTGCTGGAAAGACTGTGGAAA 169605 ----------- i vv iv iv v v i vi iv ?i L1ME4a_3end#L 225 -----------AAAGATTGATAATACCCAGTGTTGGCGAGGGTGTGGNGA 263 chrXqtel1M 169606 AATAGACATTTTGTGGCTCTGTCAGTGGAGCCGGGAACAGGTTCAGCCAT 169655 ii i i i vvvi v iii iivi vi iv v i v L1ME4a_3end#L 264 AACGGGCACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTACAACCTT 313 chrXqtel1M 169656 TCTGGAAAACAATGTTGACTAT-TAT-TCCAAAG--TTAGAAAA------ 169695 iii - i v - i - v -- i v------ L1ME4a_3end#L 314 TCTGGAGGGCAAT-TTGGCAATATGTATCAAAAGCCTTAAAAATGTNCAT 362 chrXqtel1M 169696 --CCTTTGCCCCAGGAATCCCATTTCCAGGTCTTTGTCCCAAAGGGAT-- 169741 -- v v i i i vv i i i ii -- L1ME4a_3end#L 363 ACCCTTTGACCCAGTAATTCCACTTCTAGGAATTTATCCTAAGGAAATAA 412 chrXqtel1M 169742 -CAGAAGAAGAGGAAAAGGACCTATATGTACAGAAATGTTTATAGCTGC- 169789 - - v v ? v i -- v iii i v v - L1ME4a_3end#L 413 TCAGA-GATGTGNACAAAGA--TTTATGTACAAGGATGTTCATCGCAGCA 459 chrXqtel1M 169790 -TATTT---CTGGCAAAAAA----AAATGAACAGGAAATTGAAAGGGAGG 169831 - ---v i i ---- ii v vii vi iv viiv L1ME4a_3end#L 460 TTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGG 509 chrXqtel1M 169832 GGAACGGATAAACAAAGTGTAGCATATGAATGTAGTTGCCCAATAGGT-G 169880 ?i v i v i i i i vv i? i v vvi v v i- L1ME4a_3end#L 510 GGANTGGTTAAATAAATTATGGTACATCCATANAATGGAATATTATGCAG 559 chrXqtel1M 169881 CCATAAGAAATGA 169893 v i ? L1ME4a_3end#L 560 CCATTAAAAATNA 572 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 42.29 CpG sites = 88, Kimura (unadjusted) = 43.44 Transitions / transversions = 1.29 (88/68) Gap_init rate = 0.07 (38 / 508), avg. gap size = 1.97 (75 / 38) 291 33.14 6.40 4.85 chrXqtel1M 169462 169867 (830133) L1MB4_3end#LINE/L1 130 541 (386) m_b356s551i7 14923 chrXqtel1M 169462 ATGAAATCCAATCTTCAA-AACACTA---ACTCGAAACATGCAAATTAAA 169507 --vi vi - v --- i v ii v i L1MB4_3end#LI 130 ATGAAA--AGATGCTCAACATCACTAGTCATTAGGGAAATGCAAATCAAA 177 chrXqtel1M 169508 AAAACC-CAAAGTTCTAATTCATGCCCATCAGATTGCCTAAAATGATCAC 169556 vv v-ii ii v i v ii ii iv v --- ? - L1MB4_3end#LI 178 ACCACAATGAGATACCACTTCACACCCACTAGGATGGCTA---TNATCA- 223 chrXqtel1M 169557 CAAAAAAAAAAAAAAAAGGAAATGACAATTGCTGGAAAGACTGTGGAAAA 169606 --------- vi i i v i vi iv i L1MB4_3end#LI 224 ---------AAAAAACGGAAAATAACAAGTGTTGGCGAGGATGTGGAGAA 264 chrXqtel1M 169607 ATAGACATTTTGTGGCTCTGTCAGTGGAGCCGGGAACAGGTTCAGCCATT 169656 v iv iii vvv vi iii iivi vi vv v ii L1MB4_3end#LI 265 ATTGGAACCCTCGTGCATTGCTGGTGGGAATGTAAAATGGTGCAGCCGCT 314 chrXqtel1M 169657 CTGGAAAACAATGTTGACTATTATTC-CAAAGTTAGAAA-------ACC- 169697 v i - i vi vi -v i v ------- - L1MB4_3end#LI 315 GTGGAAAACAGT-TTGGCGGTTCCTCAAAAAGTTAAACATAGAATTACCA 363 chrXqtel1M 169698 TTTGCCCCAGGAATCCCATTTCCAGGTCTTTGTCCCAAAGGGATCAGAAG 169747 v v v i i i i v v i- i i iii L1MB4_3end#LI 364 TATGACCCAGCAATTCCACTCCTAGGTATATA-CCCAAAAGAATTGAAAG 412 chrXqtel1M 169748 AAGAGG---AAAAGGACCTATATGTACAGAAATGTTTATAGCTGCTATTT 169794 v i i--- vi -- iv vv i v - v L1MB4_3end#LI 413 CAGGGACTCAAACAGA--TACTTGTACACCAATGTTCATAGCAGC-ATTA 459 chrXqtel1M 169795 CTGGCAAA----AAAAAATGAACAGGA---AATTGA--AAGGGAGGGGAA 169835 i vi v---- ii i v vi --- v v-- viiv iv L1MB4_3end#LI 460 TTCACAATAGCCAAAAGGTGGAAACAACCCAAGTGTCCATAACAGATGAA 509 chrXqtel1M 169836 CGGATAAACAAAGTGTAGCATATGAATGTAGT 169867 i i i i iv ii i L1MB4_3end#LI 510 TGGATAAACAAAATGTGGTATATACATACAAT 541 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 43.96 CpG sites = 74, Kimura (unadjusted) = 45.42 Transitions / transversions = 1.37 (74/54) Gap_init rate = 0.07 (30 / 405), avg. gap size = 1.53 (46 / 30) 331 31.71 7.92 2.19 chrXqtel1M 169565 169867 (830133) L1MB2_3end#LINE/L1 223 542 (376) m_b356s551i10 14923 chrXqtel1M 169565 AAAAAAAAAGGAAATGACAATTGCTGGAAAGACTGTGGAAAAATAGACAT 169614 v i i v i vi iv i v iv i L1MB2_3end#LI 223 AAAAAAACAGAAAATAACAAGTGTTGGCGAGGATGTGGAGAAATTGGAAC 272 chrXqtel1M 169615 T-TTGTGGCTCTGTCAGTGGAGCCGGGAACAGGTTCAGCCATTCTGGAAA 169663 i- - v ii iivi vi vv v ii v L1MB2_3end#LI 273 CCTTGTG-CACTGTTGGTGGGAATGTAAAATGGTGCAGCCGCTATGGAAA 321 chrXqtel1M 169664 ACAATGTTGACTATTATTC-CAAAGTTAGAAA-------ACC-TTTGCCC 169704 i i- i vi vi -v i i ------- - v vi L1MB2_3end#LI 322 ACAGTA-TGGCGGTTCCTCAAAAAATTAAAAATAGAATTACCATATGATC 370 chrXqtel1M 169705 CAGGAATCCCATTTCCAGGTCTTTGTCCCAAAGGGATCAGAAGAAGAG-- 169752 v i ii v v i - i i iii v i -- L1MB2_3end#LI 371 CAGCAATCCCACTTCTGGGTATATAT-CCAAAAGAATTGAAAGCAGGGTC 419 chrXqtel1M 169753 --GAAAAGGACCTATATGTACAGAAATGTTTATAGCTGCTATTTCTGGCA 169800 -- i i--- v i vvv i v - vi vi L1MB2_3end#LI 420 TCGAAGAGA---TATTTGCACACCCATGTTCATAGCAGC-ATTATTCACA 465 chrXqtel1M 169801 AAAA--AAAATGAACAGGAAATTGAAAGG------GAGGG--GAACGGAT 169840 v i-- i v viv i v iiv iv ------ v -- i L1MB2_3end#LI 466 ATAGCCAAGAGGTGGAAGCAACCCAAGTGTCCATCGACGGATGAATGGAT 515 chrXqtel1M 169841 AAACAAAGTGTAGCATATGAATGTAGT 169867 i i i iv ii i L1MB2_3end#LI 516 AAACAAAATGTGGTATATACATACAAT 542 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 41.54 CpG sites = 56, Kimura (unadjusted) = 42.76 Transitions / transversions = 1.47 (56/38) Gap_init rate = 0.05 (16 / 302), avg. gap size = 1.94 (31 / 16) 374 29.97 5.78 2.15 chrXqtel1M 169565 169789 (830211) L1PA4_3end#LINE/L1 223 455 (447) m_b356s551i9 14923 chrXqtel1M 169565 AAAAAAAAAGGAAATGACAATTGCTGGAAAGACTGTGGAAAAATAGACAT 169614 ivv ii iv i iv i iv i L1PA4_3end#LI 223 AAAAAGTCAGGAAACAACAGGTGCTGGAGAGGATGTGGAGAAATAGGAAC 272 chrXqtel1M 169615 TTTGTGGCTCTGTCAGTGGAGCCGGGAACAGGTTCAGCCATTCTGGAAAA 169664 vi v vi v ii ii i vi vi i v iv L1PA4_3end#LI 273 ACTTTTACACTGTTGGTGGGACTGTAAACTAGTTCAACCATTGTGGAAGT 322 chrXqtel1M 169665 CAATGTTGACTATT-------ATTCCAAAGTTAGAAA-ACC-TTTGCCCC 169705 i - i v -------iv i i ii - - v L1PA4_3end#LI 323 CAGTGT-GGCGATTCCTCAGGGATCTAGAACTAGAAATACCATTTGACCC 371 chrXqtel1M 169706 AGGAATCCCATTTCCAGGTCTTTGTCCCAAAGGGATCAGAAG--AAGAGG 169753 vv v ii v v i- - i v i-- v vv L1PA4_3end#LI 372 AGCCATCCCATTACTGGGTATATA-CCCAAA-GGATTATAAATCATGCTG 419 chrXqtel1M 169754 --AAAAGGACCTATATGTACAGAAATGTTTATAGCTGC 169789 -- v i -- i i viv v v L1PA4_3end#LI 420 CTATAAAGAC--ACATGCACACGTATGTTTATTGCGGC 455 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 38.35 CpG sites = 36, Kimura (unadjusted) = 39.11 Transitions / transversions = 1.20 (36/30) Gap_init rate = 0.04 (10 / 224), avg. gap size = 1.80 (18 / 10) 408 29.64 5.17 1.10 chrXqtel1M 169565 169738 (830262) L1PA3_3end#LINE/L1 223 403 (499) m_b356s551i8 14923 chrXqtel1M 169565 AAAAAAAAAGGAAATGACAATTGCTGGAAAGACTGTGGAAAAATAGACAT 169614 ivv ii iv i iv i iv i L1PA3_3end#LI 223 AAAAAGTCAGGAAACAACAGGTGCTGGAGAGGATGTGGAGAAATAGGAAC 272 chrXqtel1M 169615 TTTGTGGCTCTGTCAGTGGAGCCGGGAACAGGTTCAGCCATTCTGGAAAA 169664 vi v vi v ii ii i vi vi i v iv L1PA3_3end#LI 273 ACTTTTACACTGTTGGTGGGACTGTAAACTAGTTCAACCATTGTGGAAGT 322 chrXqtel1M 169665 CAATGTTGACTATT-------ATTCCAAAGTTAGAAA-ACC-TTTGCCCC 169705 i - i v -------iv i i ii - - v L1PA3_3end#LI 323 CAGTGT-GGCGATTCCTCAGGGATCTAGAACTAGAAATACCATTTGACCC 371 chrXqtel1M 169706 AGGAATCCCATTTCCAGGTCTTTGTCCCAAAGG 169738 vv v ii v v i- L1PA3_3end#LI 372 AGCCATCCCATTACTGGGTATATA-CCCAAAGG 403 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 38.83 CpG sites = 30, Kimura (unadjusted) = 38.83 Transitions / transversions = 1.43 (30/21) Gap_init rate = 0.03 (5 / 173), avg. gap size = 2.20 (11 / 5) 19 7.42 0.00 0.00 chrXqtel1M 171484 171512 (828488) (CGCCA)n#Simple_repeat 1 29 (0) m_b356s252i8 14924 chrXqtel1M 171484 CGTCATGCCACGCCACGCCACGCCACGCC 171512 i i (CGCCA)n#Simp 1 CGCCACGCCACGCCACGCCACGCCACGCC 29 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 417 28.96 13.09 2.37 chrXqtel1M 171712 171902 (828098) C MIR#SINE/MIR (19) 243 33 m_b356s601i16 14925 chrXqtel1M 171712 TAGGTGCCCACTGTGTGCCAGGCATTGGGCGAAGAGT------------- 171748 ii i ii i i vv v v i------------- C MIR#SINE/MIR 243 TGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGCGCTTTACATGTATTA 194 chrXqtel1M 171749 -CTCGATTGGCCCTCCCAAGGACGC----AGATAGCTGACAGCTATCACT 171793 - iv iii v vi v ---- i v i---- i i C MIR#SINE/MIR 193 ACTCATTTAATCCTCACAACAACCCTATGAGGTAGGTA----CTATTATT 148 chrXqtel1M 171794 GTCCCCATTTGACAGCTGAGGAAAC--AGGCAAACTGAGGTTTAGCGAC- 171840 i v v -- v vv v ii - C MIR#SINE/MIR 147 ATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACT 98 chrXqtel1M 171841 AGCCCAGGACTCACAC----AATAAGTGTCGGAAGCCGGTTTCGAACTTC 171886 v i i- ---- i v i iv v v iiv C MIR#SINE/MIR 97 TGCCCAAGG-TCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCA 49 chrXqtel1M 171887 CTCAGTCCTGATTCAG 171902 vv iv v i C MIR#SINE/MIR 48 GGCAGTCTGGCTCCAG 33 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.51 CpG sites = 29, Kimura (unadjusted) = 37.38 Transitions / transversions = 1.16 (29/25) Gap_init rate = 0.06 (11 / 190), avg. gap size = 2.73 (30 / 11) 29 0.00 0.00 0.00 chrXqtel1M 172077 172101 (827899) (CA)n#Simple_repeat 1 25 (0) c_b356s251i2 14926 chrXqtel1M 172077 CACACACACACACACACACACACAC 172101 (CA)n#Simple_ 1 CACACACACACACACACACACACAC 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 14 9.55 0.00 0.00 chrXqtel1M 173189 173211 (826789) (AAG)n#Simple_repeat 1 23 (0) m_b356s252i9 14927 chrXqtel1M 173189 AAAAAGAAGAAGAAGAAAAAGAA 173211 i i (AAG)n#Simple 1 AAGAAGAAGAAGAAGAAGAAGAA 23 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 257 34.89 1.52 2.29 chrXqtel1M 173998 174129 (825871) C L2c_3end#LINE/L2 (10) 468 338 m_b356s601i17 14928 chrXqtel1M 173998 TCAACAAGCATATACGAAGTGCCCACTCTGTGCTAAATCCTGAAGGTACA 174047 i v ivi i i v i iiiv ii i C L2c_3end#LINE 468 TCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGATACA 419 chrXqtel1M 174048 AAGAAAAACCGAAACAAAGTCCCAACTCTCTAAGAGTT--TGGTCTAATA 174095 vi -ii i vi vi i v i i --ii i i C L2c_3end#LINE 418 AAGATGAA-TAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAGTG 370 chrXqtel1M 174096 GCTAATAAAGATGAGATGGAAGAGACAGTGAAAA 174129 vvi v v i- ?i -i v i v v C L2c_3end#LINE 369 GAGGAGACAGAC-ANGT-AAACAGACAATTACAA 338 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.91 CpG sites = 30, Kimura (unadjusted) = 50.76 Transitions / transversions = 2.00 (30/15) Gap_init rate = 0.03 (4 / 131), avg. gap size = 1.25 (5 / 4) 357 28.46 15.38 0.00 chrXqtel1M 174654 174783 (825217) L3#LINE/CR1 2422 2571 (1528) m_b356s601i18 14929 chrXqtel1M 174654 CTTCTATTTAGCTGCTTTTTTCTTTACCAAAGAACATGACCT-CACAC-- 174700 i v v iv i i i i iv i - v -- L3#LINE/CR1 2422 CTCCTATTTTGCTTCCGTCTTCTCTATCAAGGAGAATGATCTTCAGACTG 2471 chrXqtel1M 174701 -----------ACAGAAATGGCTAATGGGGAGCTGATCCCTAAGAT---- 174735 ----------- i v v i vi ii vv i ---- L3#LINE/CR1 2472 GAAAGGGTAGAACAAACATCGTTAAGAGGGAATTGAAGCCCAAGATAGGT 2521 chrXqtel1M 174736 GAGGAAATAGTAGGAAAATACCAAGTCGCTCTGGATGATTTT--GTCCCC 174783 i i i ii v i i ii v i-- i L3#LINE/CR1 2522 GAGGAGATAGTAAGAGAGCACCTAGCCGCTTTAAATGAGTTCAAGTCTCC 2571 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.20 CpG sites = 25, Kimura (unadjusted) = 37.50 Transitions / transversions = 2.08 (25/12) Gap_init rate = 0.03 (4 / 129), avg. gap size = 5.00 (20 / 4) 274 39.56 2.22 9.00 chrXqtel1M 175314 175538 (824462) L3#LINE/CR1 3009 3219 (880) m_b356s601i19 14929 chrXqtel1M 175314 TGAAAAAGTTTGAGGACTAGACAATAGTCCCATTTTCAGATGGTGGATTC 175363 i i i v i -- i ii v vi v------ L3#LINE/CR1 3009 TGGAGAAATATGGG--CTGGATGATAGTACAGTTA------GGTGGATTC 3050 chrXqtel1M 175364 AGAACTAACTGGCTGGCCAGAGACAAAAATGAATCCTTTAA-GACTCAAT 175412 iv i iii ivi i i v vv i- vi ivv - iv i L3#LINE/CR1 3051 GTAGCTGGTTGAACGACTATACCCAAAAG-GTGTTGATTAATGGATCGAT 3099 chrXqtel1M 175413 GTGAGTTCGGTAGGAGGTCTTCTG-GAAGTGCTGTAGGGCTCTATGCCTA 175461 v iiii vi iiv - iv iii i v i i L3#LINE/CR1 3100 GTCAACCTGGAGGGAGGTCTCTAGTGGCGTGCCACAGGGCTCTGTCCTTG 3149 chrXqtel1M 175462 GCCATAGGCTGCTTCATCTTTTAATTTTTTCATTGGGGTGAACTGAACAA 175511 v ivv -------- i iv i i--ii vi i ii L3#LINE/CR1 3150 GCCCTGTCCTG--------TTCAACATTTTTATC--AATGACTTGGATGA 3189 chrXqtel1M 175512 AACCATCGCA---ATACTCAGTGGATCTGC 175538 iv v v --- i i viii i L3#LINE/CR1 3190 AGACATAGAAGGCATGCTTATCAAATTTGC 3219 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 57.19 CpG sites = 54, Kimura (unadjusted) = 60.86 Transitions / transversions = 2.00 (54/27) Gap_init rate = 0.10 (22 / 224), avg. gap size = 1.09 (24 / 22) 199 33.36 0.89 3.67 chrXqtel1M 175540 175651 (824349) L3b_3end#LINE/CR1 396 504 (702) m_b356s601i21 14929 chrXqtel1M 175540 TAGAGTGCTGAGCTGAAGTCA-TACGATAAAATGCGACTGGGGATGATTG 175588 ii ?i i i ?i -i v i v i -i i vi L3b_3end#LINE 396 TAGAACGNCGGGCCGAANCCAACAAGATGAAATTCAAC-AGGGATAAACG 444 chrXqtel1M 175589 GGAAACCAAACGTATGGGTTCAAATAATCAACTGGGAGTAGATGCAGATA 175638 vi ii vvi iiv v ? ii v v - - i i- L3b_3end#LINE 445 TAAAGTCCTGCACTTGGGTTCAAAAAANCAATCGCGCG-AG-TACAGG-A 491 chrXqtel1M 175639 CGGGGGCGGCCCG 175651 i v i v L3b_3end#LINE 492 TGGGGGAGACGCG 504 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.74 CpG sites = 24, Kimura (unadjusted) = 48.85 Transitions / transversions = 2.00 (24/12) Gap_init rate = 0.05 (5 / 111), avg. gap size = 1.00 (5 / 5) 218 34.14 1.20 1.20 chrXqtel1M 175540 175622 (824378) L3#LINE/CR1 3294 3376 (723) m_b356s601i20 14929 chrXqtel1M 175540 TAGAGTGCTGAGCTGAAGTCA-TACGATAAAATGCGACTGGGGATGATTG 175588 i ii v i i ii -i v i vii -i i v L3#LINE/CR1 3294 TGGAACGATGGGCCGAAACCAACAAGATGAAATTTAAC-AGGGATAAATG 3342 chrXqtel1M 175589 GGAAACCAAACGTATGGGTTCAAATAATCAACTG 175622 vi ii vvi i v i v L3#LINE/CR1 3343 TAAAGTCCTGCATTTAGGTTCAAAAAATCAACTG 3376 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.87 CpG sites = 19, Kimura (unadjusted) = 48.76 Transitions / transversions = 2.11 (19/9) Gap_init rate = 0.02 (2 / 82), avg. gap size = 1.00 (2 / 2) 245 36.90 2.94 10.53 chrXqtel1M 175697 176002 (823998) L3b_3end#LINE/CR1 661 945 (261) m_b356s601i23 14929 chrXqtel1M 175697 GCTTTACTTTGTCCTTCCTGGTCAGGCCACATCTTTGGGATCATCTCCAC 175746 i i iv ---- ? ? vvi v iiiiv i v L3b_3end#LINE 661 GCTCTACTCTGCGCT----GGTCAGGCCNCANCTGGAGTACTGCGTTCAG 706 chrXqtel1M 175747 CTTGGGGCGGTATGGTTTAAGAAGGGCTTTGGAGAAC-TGGAGAGTGTGG 175795 i iv ?vi ii? - viv ?- v v- L3b_3end#LINE 707 TTCTGGGCNCCACANTTTAA-AAGGGACGTGGAGAANTTGGAGAGAGTT- 754 chrXqtel1M 175796 AACAGGGAAGGACCTCAAATGTCTGTCATATGGGGATCAATTTAAGAAGC 175845 -- i i ii vv --------- v ------- v iivi L3b_3end#LINE 755 --CAGAGGAGAGCAACAA---------AAATG-------ATTAAAGGGCT 786 chrXqtel1M 175846 AGAGAATGTTTCGCCTGAAGGAAAAAAAAAAAAA----AAACACTGAG-- 175889 i i vvv viv i i iivv ii ----i vi i v -- L3b_3end#LINE 787 GGAAAATGGGACCTATGAGGAAAGGTTAAAGGAACTGGGATTATTCAGCC 836 chrXqtel1M 175890 GGGAGTGGGGGAGAGGTCCAGGAAAAGACTGAAAAGCTTGCTTCTC-CAC 175938 v --- ii i v iii iii? v v i ?vv vv-i i L3b_3end#LINE 837 TGGA---GAAGAGAAGGCTGAGGGGNGACTTAATAACNGTCTTCAAGTAT 883 chrXqtel1M 175939 CTGAAGGGTGACCCTGTAGAAAAC-ACAACTATTAGTTCTGTTCAGCCCC 175987 v v iivi ii -iii i viv -- i v i L3b_3end#LINE 884 ATGAAGGGTTATTACGTAGAGGACGGTGACCAGCTGTTC--TCCATCTCC 931 chrXqtel1M 175988 TCCTGAGAGCAGAAC 176002 -v ii L3b_3end#LINE 932 -ACTGAGGACAGAAC 945 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 51.49 CpG sites = 60, Kimura (unadjusted) = 54.72 Transitions / transversions = 1.46 (60/41) Gap_init rate = 0.11 (35 / 305), avg. gap size = 1.11 (39 / 35) 420 32.55 10.11 1.97 chrXqtel1M 175697 175884 (824116) L3#LINE/CR1 3559 3761 (338) m_b356s601i22 14929 chrXqtel1M 175697 GCTTTACTTTGTCCTTCCTGGTCAGGCCACATCTTTGGGATCATCTCCAC 175746 v i iv ---- i vvi v iiiv i v L3#LINE/CR1 3559 GCTGTACTCTGCGCT----GGTCAGACCACATCTGGAGTATTGCGTTCAG 3604 chrXqtel1M 175747 CTTGGGGCGGTATGGTTTAAGAAGGGCTTTGGAGAACTGGAGAGTGT--- 175793 i iv vi iiv i i v ivi v i --- L3#LINE/CR1 3605 TTCTGGGCGCCACATTTTAAGAGGGACATTGACAAACTGGAGCGCGTCCA 3654 chrXqtel1M 175794 --GGAA------CAGG-----GAAGGACCTCAAATGTCTGTCATATGGGG 175830 -- i------ ----- ii vi vviv i L3#LINE/CR1 3655 GAGGAGAGCGACCAGGATGGTGAAGGGTCTGGAAACCATGTCATATGAGG 3704 chrXqtel1M 175831 ATCAATTTAAGAAGCAGAGAATGTTTCGCCTGAAGGAAAAAAAA---AAA 175877 v ii v i i v i i v i i i i i --- i L3#LINE/CR1 3705 AACGGTTGAAGGAACTGGGGATGTTTAGCCTGGAGAAGAGAAGACTTAGA 3754 chrXqtel1M 175878 AAAAACA 175884 ii i L3#LINE/CR1 3755 GGAGACA 3761 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.03 CpG sites = 39, Kimura (unadjusted) = 45.09 Transitions / transversions = 1.86 (39/21) Gap_init rate = 0.05 (9 / 187), avg. gap size = 2.56 (23 / 9) 14 16.41 2.94 0.00 chrXqtel1M 177051 177084 (822916) (CCCT)n#Simple_repeat 1 35 (0) m_b356s252i10 14930 chrXqtel1M 177051 CCCGCCCTCAC-CGCTCCCTCCCTCCCTCTCGCCC 177084 v v - v i v (CCCT)n#Simpl 1 CCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCC 35 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 12 20.23 2.94 0.00 chrXqtel1M 177709 177742 (822258) (GCGGG)n#Simple_repeat 1 35 (0) m_b356s252i11 14931 chrXqtel1M 177709 GCCGGGCGAGGC-TGGCTGGGTAGGGCGGGGCGGG 177742 v i -v v ii (GCGGG)n#Simp 1 GCGGGGCGGGGCGGGGCGGGGCGGGGCGGGGCGGG 35 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1) 12 16.52 0.00 0.00 chrXqtel1M 178113 178139 (821861) (TTCA)n#Simple_repeat 1 27 (0) m_b356s252i12 14932 chrXqtel1M 178113 TTGATTCATTCGTTCCTTCCTTCATTC 178139 v i v v (TTCA)n#Simpl 1 TTCATTCATTCATTCATTCATTCATTC 27 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 241 18.75 10.94 0.00 chrXqtel1M 179509 179572 (820428) C MIR3#SINE/MIR (28) 180 110 m_b356s601i24 14933 chrXqtel1M 179509 TGGAGAG--CTTTAGCCAGCATCTACTCCAACCCCCA---TTTATAGCTG 179553 ii -- i vv v v v--- i v C MIR3#SINE/MIR 180 TGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATG 131 chrXqtel1M 179554 GGGAAAATGAGG--CAGAGAG 179572 i v -- C MIR3#SINE/MIR 130 AGGAAACTGAGGCCCAGAGAG 110 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 21.61 CpG sites = 5, Kimura (unadjusted) = 21.61 Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.05 (3 / 63), avg. gap size = 2.33 (7 / 3) 14 11.65 0.00 3.45 chrXqtel1M 182803 182832 (817168) (AGGGA)n#Simple_repeat 1 29 (0) m_b356s252i13 14934 chrXqtel1M 182803 AGGGAGGGGGAAGGCAAGGGGAGGGAAGGG 182832 -i v i (AGGGA)n#Simp 1 AGGGA-AGGGAAGGGAAGGGAAGGGAAGGG 29 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 27 0.00 0.00 0.00 chrXqtel1M 183071 183096 (816904) (C)n#Simple_repeat 1 26 (0) c_b356s251i3 14935 chrXqtel1M 183071 CCCCCCCCCCCCCCCCCCCCCCCCCC 183096 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCC 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 17 22.55 0.00 0.00 chrXqtel1M 183685 183720 (816280) (G)n#Simple_repeat 1 36 (0) m_b356s252i14 14936 chrXqtel1M 183685 GGGGTGGGGGAGAAGGGGCGCGCGGGGGGGGGGGGG 183720 v i ii v v v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 36 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 15 14.91 0.00 0.00 chrXqtel1M 183767 183796 (816204) (CCCGG)n#Simple_repeat 1 30 (0) m_b356s252i15 14937 chrXqtel1M 183767 CCCGGGGCGCCCCGGCCCGCCCCGGCCCGG 183796 vv v v (CCCGG)n#Simp 1 CCCGGCCCGGCCCGGCCCGGCCCGGCCCGG 30 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 56 20.03 6.02 4.09 chrXqtel1M 183960 184175 (815825) (CTCC)n#Simple_repeat 1 220 (0) m_b356s252i16 14938 chrXqtel1M 183960 CTCCCTCTCGGCCGCCCCCACCGCCCT-CCGGCCGCCAGGACTCCTCCCC 184008 i vv v i - v - vv v vvvv - i (CTCC)n#Simpl 1 CTCCCTCCCTCCCTCCCTC-CCTCCCTCCCTCCCTCCCTCCCTCC-CTCC 48 chrXqtel1M 184009 CTGCTCCTCCCT-CTTCTCCTCCCT-CCTCCCT-CCTCCCTTCCTCCTTC 184055 - - - i - - - i i - (CTCC)n#Simpl 49 CT-C-CCTCCCTCCCTC-CCTCCCTCCCTCCCTCCCTCCCTCCCTCCCT- 94 chrXqtel1M 184056 CCCTCCCTCCCTCGGTCTCCCTCCCCTCCCTCCCTCCCT--CTCCCTTCC 184103 --i - -- i (CTCC)n#Simpl 95 CCCTCCCTCCCTC--CCTCCCT-CCCTCCCTCCCTCCCTCCCTCCCTCCC 141 chrXqtel1M 184104 T-CCTCCC-CCCTCCCT-CCTGGCT-CCT-CCGGGGACCCTCTCCCTTTC 184148 - - - vv - - vvvvv i i ii (CTCC)n#Simpl 142 TCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTC 191 chrXqtel1M 184149 CCTTTC-CCCTCCCTTCC-CCCCCCATCC 184175 ii - i - i v (CTCC)n#Simpl 192 CCTCCCTCCCTCCCTCCCTCCCTCCCTCC 220 Matrix = Unknown Transitions / transversions = 0.84 (16/19) Gap_init rate = 0.10 (21 / 215), avg. gap size = 1.05 (22 / 21) 17 10.38 3.12 0.00 chrXqtel1M 184136 184167 (815833) (CCCTTT)n#Simple_repeat 1 33 (0) m_b356s252i17 14939 chrXqtel1M 184136 CCCTCTCCCTTTCCCTTTCCC-CTCCCTTCCCC 184167 i -i i (CCCTTT)n#Sim 1 CCCTTTCCCTTTCCCTTTCCCTTTCCCTTTCCC 33 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 56 20.03 6.02 4.09 chrXqtel1M 183960 184175 (815825) (CTCC)n#Simple_repeat 1 220 (0) m_b356s252i16 14938 chrXqtel1M 183960 CTCCCTCTCGGCCGCCCCCACCGCCCT-CCGGCCGCCAGGACTCCTCCCC 184008 i vv v i - v - vv v vvvv - i (CTCC)n#Simpl 1 CTCCCTCCCTCCCTCCCTC-CCTCCCTCCCTCCCTCCCTCCCTCC-CTCC 48 chrXqtel1M 184009 CTGCTCCTCCCT-CTTCTCCTCCCT-CCTCCCT-CCTCCCTTCCTCCTTC 184055 - - - i - - - i i - (CTCC)n#Simpl 49 CT-C-CCTCCCTCCCTC-CCTCCCTCCCTCCCTCCCTCCCTCCCTCCCT- 94 chrXqtel1M 184056 CCCTCCCTCCCTCGGTCTCCCTCCCCTCCCTCCCTCCCT--CTCCCTTCC 184103 --i - -- i (CTCC)n#Simpl 95 CCCTCCCTCCCTC--CCTCCCT-CCCTCCCTCCCTCCCTCCCTCCCTCCC 141 chrXqtel1M 184104 T-CCTCCC-CCCTCCCT-CCTGGCT-CCT-CCGGGGACCCTCTCCCTTTC 184148 - - - vv - - vvvvv i i ii (CTCC)n#Simpl 142 TCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTC 191 chrXqtel1M 184149 CCTTTC-CCCTCCCTTCC-CCCCCCATCC 184175 ii - i - i v (CTCC)n#Simpl 192 CCTCCCTCCCTCCCTCCCTCCCTCCCTCC 220 Matrix = Unknown Transitions / transversions = 0.84 (16/19) Gap_init rate = 0.10 (21 / 215), avg. gap size = 1.05 (22 / 21) 19 15.11 6.82 0.00 chrXqtel1M 186180 186223 (813777) (AT)n#Simple_repeat 1 47 (0) m_b357s252i0 14940 chrXqtel1M 186180 ATAAATA-ATATATCTTTCTATGGA-ATATATATATATAT-TATATA 186223 v - v v v iv - - (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATA 47 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.07 (3 / 43), avg. gap size = 1.00 (3 / 3) 66 3.46 2.06 4.21 chrXqtel1M 186420 186516 (813484) (AGAGAC)n#Simple_repeat 1 95 (0) c_b357s251i0 14941 chrXqtel1M 186420 AGAGACAGAGACAGAGACAGAGAGAAAGAGACAGAGAAAGAGAGACAGAG 186469 -- v -- v (AGAGAC)n#Sim 1 AGAGACAGAGACAGAGAC--AGAGACAGAGACAGAG--ACAGAGACAGAG 46 chrXqtel1M 186470 ACAGAGACAGAGACAGAGACAGAGACA-A-AGAGAGACAGAGACAGAGA 186516 - - v (AGAGAC)n#Sim 47 ACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGA 95 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.06 (6 / 96), avg. gap size = 1.00 (6 / 6) 17 18.36 0.00 0.00 chrXqtel1M 186527 186563 (813437) (GAGAGA)n#Simple_repeat 1 37 (0) m_b357s252i1 14942 chrXqtel1M 186527 GAGAGAGGGAGACAGAGAGACAGAGACAGAGCGTGAG 186563 i v v v v v (GAGAGA)n#Sim 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 37 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 18 24.45 1.52 3.08 chrXqtel1M 186976 187041 (812959) (CCCCCT)n#Simple_repeat 1 65 (0) m_b357s252i2 14943 chrXqtel1M 186976 CCCCTTCCCCCATCCCCTTGGGCCCTCCAGCT-CCTCTCCCCATCCAAGC 187024 i - i -vv vv - i v vvvi (CCCCCT)n#Sim 1 CCCCCTCCCCC-TCCCCCT-CCCCCTCCCCCTCCCCCTCCCCCTCCCCCT 48 chrXqtel1M 187025 CCCCCTCCCCCCCCCCC 187041 i (CCCCCT)n#Sim 49 CCCCCTCCCCCTCCCCC 65 Matrix = Unknown Transitions / transversions = 0.62 (5/8) Gap_init rate = 0.05 (3 / 65), avg. gap size = 1.00 (3 / 3) 28 23.61 1.15 3.53 chrXqtel1M 187679 187765 (812235) (GGGA)n#Simple_repeat 1 85 (0) m_b357s252i3 14944 chrXqtel1M 187679 GGGGGGCAGGGGAAGAAGGGAAGGAGGGAAGGAGAGA-GGAGGGAGGGAG 187727 i v - i i i i i - (GGGA)n#Simpl 1 GGGAGGGA-GGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAG 49 chrXqtel1M 187728 ACAGACACAGAGAGGGAGAGATGGAGGGAGGGGGAGAG 187765 --i viv i i v i i (GGGA)n#Simpl 50 --GGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAG 85 Matrix = Unknown Transitions / transversions = 3.00 (12/4) Gap_init rate = 0.05 (4 / 86), avg. gap size = 1.00 (4 / 4) 21 31.57 2.68 2.68 chrXqtel1M 187711 187822 (812178) (AGAGAC)n#Simple_repeat 1 112 (0) m_b357s252i4 14944 chrXqtel1M 187711 AGAGAGGAGGGAGGGAGACAGACACAGAGAGGGAGAGATGGAGGGAGGGG 187760 -v i vi v --v ii iv i i (AGAGAC)n#Sim 1 AGAGA-CAGAGACAGAGACAGAGACAGAGA--CAGAGACAGAGACAGAGA 47 chrXqtel1M 187761 GAGAGACAGACACAGACACACAGAC--ACACGGAAACAGAAGCCG-GGCA 187807 v v v v -- v i i ii v - i (AGAGAC)n#Sim 48 CAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACA 97 chrXqtel1M 187808 GAGATGGGGACGGAG 187822 ii i i (AGAGAC)n#Sim 98 GAGACAGAGACAGAG 112 Matrix = Unknown Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.05 (5 / 111), avg. gap size = 1.20 (6 / 5) 547 34.16 10.65 1.78 chrXqtel1M 189023 189332 (810668) L3#LINE/CR1 2979 3315 (784) m_b357s601i0 14945 chrXqtel1M 189023 AAGTTTCTCGTATTATTCTTGTGGGGAAGATGGAAAGGTTTGGG------ 189066 i i iv i iv i ii v ------ L3#LINE/CR1 2979 AAGTCTCTCATGATATCCTTGTGGACAAGATGGAGAAATATGGGCTGGAT 3028 chrXqtel1M 189067 ----------TCAGGCGG---------TGAT---ACGGC-AGGCCCAGGA 189093 ---------- i i --------- i --- i - vi ii L3#LINE/CR1 3029 GATAGTACAGTTAGGTGGATTCGTAGCTGGTTGAACGACTATACCCAAAA 3078 chrXqtel1M 189094 GCAGCCG-TTAACGGTTCACCGTCAAGTGGGCAGGAAGTCCCTACTGGAA 189142 vv ii - i v ivi viv vi i i v vi L3#LINE/CR1 3079 GGTGTTGATTAATGGATCGATGTCAACCTGGAGGGAGGTCTCTAGTGGCG 3128 chrXqtel1M 189143 TGCTCACCGGACGGGTGTC--TGGCCCCGGCCTGGGTCCTGTTTTTACCG 189190 - v i vv- -- i v vvivvii i i L3#LINE/CR1 3129 TGC-CACAGGGCTC-TGTCCTTGGCCCTGTCCTGTTCAACATTTTTATCA 3176 chrXqtel1M 189191 GGGAATTGAATAAAGGCCTAGCTGGCCTGCTTAGC-AACCTGCAGATGGT 189239 iv v i i i v vv v v - ii ii L3#LINE/CR1 3177 ATGACTTGGATGAAGACATAGAAGGCATGCTTATCAAATTTGCAGATGAC 3226 chrXqtel1M 189240 ACCGAGCTGGAAGGGCCACAGCTGACAGAGCAGACGACGGGCACTCGGGG 189289 vi i -- i i i vi?ii i i -- v ii i L3#LINE/CR1 3227 ACAAAGCTGGGAGGG--ATAGCTAATACGNTGGATGACAG--AATCAAGA 3272 chrXqtel1M 189290 TCCGCAAACGTACGGACAGGTTAGAGCCTCTGACCGAGGCTGA 189332 i iv ?vi viv i i i vviv i ii ii L3#LINE/CR1 3273 TTCAAAANGATCTCGACAGGCTGGAACGATGGGCCGAAACCAA 3315 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.62 CpG sites = 66, Kimura (unadjusted) = 48.63 Transitions / transversions = 1.74 (66/38) Gap_init rate = 0.05 (14 / 309), avg. gap size = 2.79 (39 / 14) 210 33.30 7.14 2.27 chrXqtel1M 189724 189849 (810151) C L3b_3end#LINE/CR1 (386) 820 689 m_b357s601i1 14946 chrXqtel1M 189724 TTTCTTTAACTGACCCTCAGAGGGCCTGGCTCCTCCCCATCCCCTACTCA 189773 i ivvi v v --- vii i vii ii v C L3b_3end#LINE 820 TTCCTTTAACCTTTCCTCATAGGTCC---CATTTTCCAGCCCTTTAATCA 774 chrXqtel1M 189774 G-------GCCCCCATGTGGATCCATTCCAGCTTTTCCACGTCTTTCTT- 189815 v------- i i v v i ii vi i? i ii i - C L3b_3end#LINE 773 TTTTTGTTGCTCTCCTCTGAACTCTCTCCAANTTCTCCACGTCCCTTTTA 724 chrXqtel1M 189816 ACGTCTGGTCCCCAGAGC-GGACACGGCAGTCCAG 189849 v? v ?v i - i i i i v C L3b_3end#LINE 723 AANTGTGGNGCCCAGAACTGAACGCAGTACTCCAG 689 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.38 CpG sites = 26, Kimura (unadjusted) = 48.05 Transitions / transversions = 1.73 (26/15) Gap_init rate = 0.05 (6 / 125), avg. gap size = 2.00 (12 / 6) 190 40.48 2.38 0.00 chrXqtel1M 189843 189926 (810074) C L3#LINE/CR1 (694) 3405 3320 m_b357s601i2 14947 chrXqtel1M 189843 AGTCCAGCCCTCCTCACCCTATACTTCACCAATTGACTAT--GAGCTTCG 189890 i viii ii i i vvv i i v -- i i vi C L3#LINE/CR1 3405 AGCCAGATCCTCTCCATCCTGTACTTGTGCAGTTGATTTTTTGAACCTAA 3356 chrXqtel1M 189891 GGATGAAACTTTACATCGGACCCTGTTAGTGTTCGT 189926 iviiiii iviv ivv i C L3#LINE/CR1 3355 ATGCAGGACTTTACATTTATCCCTGTTAAATTTCAT 3320 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 64.34 CpG sites = 23, Kimura (unadjusted) = 64.34 Transitions / transversions = 2.09 (23/11) Gap_init rate = 0.01 (1 / 83), avg. gap size = 2.00 (2 / 1) 191 27.78 22.22 0.00 chrXqtel1M 189948 190073 (809927) C MIR3#SINE/MIR (7) 201 48 m_b357s601i3 14948 chrXqtel1M 189948 AGGATCACTGGAT-TTAGAGGTGGAAAGGACCT--GATGTCAACCGG--- 189991 i iv i - i v i -- vi v ii --- C MIR3#SINE/MIR 201 AGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCC 152 chrXqtel1M 189992 AAGGCC----------AGAGGAGAAAACCAAGGCCTTGAGAAG-GAA--- 190027 vv ---------- v i ii iv i - --- C MIR3#SINE/MIR 151 AACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTG 102 chrXqtel1M 190028 --------AAGGTCTCACAACCACTGAACCACAGAGCTGGCATCTGAACC 190069 -------- v i ? v v iivi i v iiv C MIR3#SINE/MIR 101 ACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACC 52 chrXqtel1M 190070 CTGG 190073 v C MIR3#SINE/MIR 51 CAGG 48 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.58 CpG sites = 20, Kimura (unadjusted) = 35.85 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.06 (7 / 125), avg. gap size = 4.00 (28 / 7) 235 29.70 11.61 0.81 chrXqtel1M 189997 190108 (809892) C MIRb#SINE/MIR (126) 142 19 m_b357s601i4 14948 chrXqtel1M 189997 CAGAGGAGAAAACCAAGGCCTTGAGA-----AGGAA-------AAGGTCT 190034 v i ii iiv ----- v ------- v C MIRb#SINE/MIR 142 CAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCA 93 chrXqtel1M 190035 CACAACCACTGAACCACAGAGCTGGCATCTGAACCCTGG-CTCTGGGACG 190083 i i v i iivi i v ii v - v vv v C MIRb#SINE/MIR 92 CACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACT 43 chrXqtel1M 190084 CCAAAGCTTCTAGCTCATCACAATG 190108 iiv - v iv v C MIRb#SINE/MIR 42 CCAAAGCCCGT-GCTCTTTCCACTG 19 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.19 CpG sites = 17, Kimura (unadjusted) = 38.43 Transitions / transversions = 1.06 (17/16) Gap_init rate = 0.04 (4 / 111), avg. gap size = 3.50 (14 / 4) 23 40.41 2.24 0.74 chrXqtel1M 190575 190708 (809292) (TCTC)n#Simple_repeat 1 136 (0) m_b357s252i5 14949 chrXqtel1M 190575 TCTCTCTTTCCCTTTCCGTCTCTCTCCCTC-CGTTCTCTCCCTC-CATTC 190622 i i i iv i - vi i - vi (TCTC)n#Simpl 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chrXqtel1M 190623 CCTCCCTCCCTCCTTCCCTCCCT-TCGTTCCTTCCTTCCTTCCCTCCCTC 190671 i i i ii i i - vi ii ii ii i i (TCTC)n#Simpl 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chrXqtel1M 190672 CATTCCTCTCTCCCTCCCTCCCTCCCTTTCCCTGCTC 190708 iv ii i i i i i i - (TCTC)n#Simpl 101 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT-CTC 136 Matrix = Unknown Transitions / transversions = 6.60 (33/5) Gap_init rate = 0.03 (4 / 133), avg. gap size = 1.00 (4 / 4) 27 3.42 0.00 0.00 chrXqtel1M 192013 192042 (807958) (TCC)n#Simple_repeat 1 30 (0) c_b357s251i1 14950 chrXqtel1M 192013 TCCTCCTCCTCCTCCTCCTCCTCCTGCTCC 192042 v (TCC)n#Simple 1 TCCTCCTCCTCCTCCTCCTCCTCCTCCTCC 30 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 17 21.25 3.08 4.69 chrXqtel1M 193760 193824 (806176) (TCCCC)n#Simple_repeat 1 64 (0) m_b357s252i6 14951 chrXqtel1M 193760 TCCCCTCCCCTCCGGCTCCTTTACCTCCTGCACCCCTCTCCCCTCCAC-C 193808 -v ii - - v v i i v - (TCCCC)n#Simp 1 TCCCCTCCCCTCC-CCTCCCCT-CC-CCTCCCCTCCCCTCCCCTCCCCTC 47 chrXqtel1M 193809 CCC-CGCCGCCCCGCCC 193824 - v v v (TCCCC)n#Simp 48 CCCTCCCCTCCCCTCCC 64 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.08 (5 / 64), avg. gap size = 1.00 (5 / 5) 23 25.59 0.00 0.00 chrXqtel1M 193994 194053 (805947) (CAG)n#Simple_repeat 1 60 (0) m_b357s252i7 14952 chrXqtel1M 193994 CAGCAGCCGCCGCAGCCGCAGCCGCAGCGGGGGGAGGAGCAGAAGCAGTG 194043 v v v v i vi v v v ii (CAG)n#Simple 1 CAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA 50 chrXqtel1M 194044 GCAGCGGCAG 194053 i (CAG)n#Simple 51 GCAGCAGCAG 60 Matrix = Unknown Transitions / transversions = 0.62 (5/8) Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0) 13 25.21 2.33 0.00 chrXqtel1M 194020 194062 (805938) (GCAGGG)n#Simple_repeat 1 44 (0) m_b357s252i8 14952 chrXqtel1M 194020 GCGGGGGGAGGAGCAGAAGCAGTGGCAGCGGCA-GGACGGGGGC 194062 i v i ii v v - i i (GCAGGG)n#Sim 1 GCAGGGGCAGGGGCAGGGGCAGGGGCAGGGGCAGGGGCAGGGGC 44 Matrix = Unknown Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.02 (1 / 42), avg. gap size = 1.00 (1 / 1) 12 14.91 4.88 4.88 chrXqtel1M 194110 194150 (805850) (CCT)n#Simple_repeat 1 41 (0) m_b357s252i9 14953 chrXqtel1M 194110 CCTCCTCCTTCCGCCT-CTCGTCC-CCCCCCCCCCCTCACTCC 194150 - v - v - i i i - (CCT)n#Simple 1 CCTCCTCC-TCCTCCTCCTCCTCCTCCTCCTCCTCCTC-CTCC 41 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.10 (4 / 40), avg. gap size = 1.00 (4 / 4) 227 35.51 5.60 3.12 chrXqtel1M 195001 195125 (804875) C L3#LINE/CR1 (229) 3870 3743 m_b357s601i5 14954 chrXqtel1M 195001 CTCTGCAACTGCCATC-ACTGAACCCGCTTCTGCCCTCTGGAGCCAAACA 195049 i i v i - i iv iiv v C L3#LINE/CR1 3870 CCCTGTAACTTCCACCCATTGGTCCTAGTTCTGCCCTCTGGAGCCACACA 3821 chrXqtel1M 195050 GGTTACGGCTTTTCCTCGTCACCTTTGTGTGTCAGCTCTT------TTTC 195093 iv v v vv ---- v i iiiii v i ------ v C L3#LINE/CR1 3820 GAATAAGTCTAATCC----CTCTTCCACATGACAGCCCTTCAAATATTTG 3775 chrXqtel1M 195094 GGGTCAAATATCCCAGTTCCTTCAAACCCTTT 195125 ii v iv viivi ii ii i i C L3#LINE/CR1 3774 AAGACAGCTATCATGTCTCCTCTAAGTCTTCT 3743 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 50.88 CpG sites = 27, Kimura (unadjusted) = 50.88 Transitions / transversions = 1.69 (27/16) Gap_init rate = 0.05 (6 / 124), avg. gap size = 1.83 (11 / 6) 181 34.14 1.09 4.49 chrXqtel1M 195067 195158 (804842) C L3#LINE/CR1 (339) 3760 3672 m_b357s601i6 14954 chrXqtel1M 195067 GTCACCTTTGTGTGTCAGCTCTTTTTCGGGTCAAATATCCC-AGTTCCTT 195115 v i iv v i-- i i i ii i - C L3#LINE/CR1 3760 GTCTCCTCTAAGTCTT--CTCTTCTCCAGGCTAAACATCCCCAGTTCCTT 3713 chrXqtel1M 195116 CAAACCCTTTTCAGGGGATGTGCTTATTAATGTCCTTTTGCCA 195158 v vi ii viv ii v vii -- v i ii C L3#LINE/CR1 3712 CAACCGTTCCTCATATGACATGGTTTCCA--GACCCTTCACCA 3672 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 48.43 CpG sites = 20, Kimura (unadjusted) = 48.43 Transitions / transversions = 2.00 (20/10) Gap_init rate = 0.05 (5 / 91), avg. gap size = 1.00 (5 / 5) 185 29.17 2.08 0.00 chrXqtel1M 195085 195132 (804868) C L3b_3end#LINE/CR1 (360) 846 798 m_b357s601i7 14954 chrXqtel1M 195085 CTCTTTTTCGGGTCAAATA-TCCCAGTTCCTTCAAACCCTTTTCAGGGG 195132 i i i iii - i v ii ii vi C L3b_3end#LINE 846 CTCTTCTCCAGGCTGAATAATCCCAGTTCCTTTAACCTTTCCTCATAGG 798 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.18 CpG sites = 12, Kimura (unadjusted) = 41.18 Transitions / transversions = 6.00 (12/2) Gap_init rate = 0.02 (1 / 47), avg. gap size = 1.00 (1 / 1) 317 36.81 5.98 1.53 chrXqtel1M 195957 196207 (803793) C L2a_3end#LINE/L2 (255) 262 1 m_b357s601i8 14955 chrXqtel1M 195957 AAATAAGGGGGCATCAGAAAAGGCTGCTTTTAGAAAGCACGATTTCAGCT 196006 i v -- ii iv ?i v i iivv v v C L2a_3end#LINE 262 AAATAGGGTGG--TCAGGGAAGGCCTCNCTGAGAAGGTGACATTTGAGCA 215 chrXqtel1M 196007 GGGCCCTGAAGGAAGCCAGCAAAGTCAAG--AGGTGGTGATGAGAAGAGA 196054 ii v i iv vi i-- i -- v i vv vv ii ii C L2a_3end#LINE 214 AAGACCTGAAGGAGGTGAGGGAG--CGAGCCATGCGGATATCTGGGGGAA 167 chrXqtel1M 196055 GAGAATTTTATGTCTGGCTGGCAGCCAGTGGAAGTAGCCGGAGA-GATGG 196103 vi ii v ivvi vvii v v iviv v i- ivi C L2a_3end#LINE 166 GAGCGTTCCAGGCAGAGGGAACAGCAAGTGCAAAGGCCCTGAGGCGGGAG 117 chrXqtel1M 196104 AGTGTTT----TGTTTAAGGAAAAGCGGGGAGGTCAGTATCACC---CCG 196146 v ii ---- ii v ii i i vi i---v C L2a_3end#LINE 116 CGTGCCTGGCGTGTTCGAGGAACAGCAAGGAGGCCAGTGTGGCTGGAGCG 67 chrXqtel1M 196147 GACT----GAAGGGGAGGGAGGGAAGAAA-GAGACTGGACAGGTACTAGG 196191 v ---- i i v v i i - iiii v vii C L2a_3end#LINE 66 GAGTGAGCGAGGGGGAGAGTGGTAGGAGATGAGGTCAGAGAGGTAACGGG 17 chrXqtel1M 196192 GGACCAGGTCATGAAG 196207 i i v C L2a_3end#LINE 16 GGGCCAGATCATGTAG 1 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 49.01 CpG sites = 54, Kimura (unadjusted) = 53.46 Transitions / transversions = 1.46 (54/37) Gap_init rate = 0.04 (10 / 250), avg. gap size = 1.90 (19 / 10) 270 37.15 12.65 0.00 chrXqtel1M 196076 196328 (803672) C L2#LINE/L2 (28) 3054 2770 m_b357s601i9 14955 chrXqtel1M 196076 CAGCCAGTGGAAGTAGCCGGAGA-GATGGAGTGTTT----TGTTTAAGGA 196120 v v iviv v i- ivi v ii ---- ii C L2#LINE/L2 3054 CAGCAAGTGCAAAGGCCCTGAGGCGGGAGCGTGCCTGGCGTGTTCGAGGA 3005 chrXqtel1M 196121 AAAGCGGGGAGGTCAGTATCACCC---CGGACTGAA----GGGGAGGGAG 196163 v ii i i vi iv--- v i---- i v C L2#LINE/L2 3004 ACAGCAAGGAGGCCAGTGTGGCTGGAGCGGAGTGAGCGAGGGGGAGAGTG 2955 chrXqtel1M 196164 GGAAGAAA-GAGACTGGACAGGTACTAGGGGACCAGGTCATGAAGGGCTT 196212 v i i - iiii v vii i v i C L2#LINE/L2 2954 GTAGGAGATGAGGTCAGAGAGGTAACGGGGGACCAGATCATGTAGGGCCT 2905 chrXqtel1M 196213 TACA------TGTCAGAAC----------ATCCT-AGGATGACAGGGGGC 196245 ii ------ v i ---------- ii - viv ii ii C L2#LINE/L2 2904 TGTAGGCCATTGTAAGGACTTTGGCTTTTACTCTGAGTGAGATGGGAAGC 2855 chrXqtel1M 196246 CACAGGAGTCTATCAGGTAG-GTAGCAATACAGTTAGATCTGGGACCTAG 196294 iv vv v iii i - v ii i iii iv ii iv vii i C L2#LINE/L2 2854 CATTGGAGGGTTTTGAGCAGAGGAGTGACATGATCTGACTTACGTTTTAA 2805 chrXqtel1M 196295 GAAAAGCACTTGGGCAGCAGAGTAGAGCA-GGACT 196328 i ii v iv v v v v v -i C L2#LINE/L2 2804 AAGGATCACTCTGGCTGCTGTGTTGAGAATAGACT 2770 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 52.76 CpG sites = 60, Kimura (unadjusted) = 54.74 Transitions / transversions = 1.76 (60/34) Gap_init rate = 0.04 (10 / 252), avg. gap size = 3.20 (32 / 10) 308 29.01 1.40 3.57 chrXqtel1M 196652 196794 (803206) L1ME4c_3end#LINE/L1 416 555 (275) m_b357s551i0 14956 chrXqtel1M 196652 AAAAGAAGGGAAAGGGCCCTGTTTCTGCACGAA--TGTTTGGGGCAGGTC 196699 i i --- i --v -- iivv vvi L1ME4c_3end#L 416 AAAAGAAGGAAAAAG---CTAT--ATGCACGAAGATGTTCATTGCAGCGT 460 chrXqtel1M 196700 TCTTTGTAGTGGCCAGAAAATGGAAACAGAGTGGCTGCCCATCCATTGGA 196749 v i i i v i v ivv iiv i v v v i L1ME4c_3end#L 461 TATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAACAATAGGG 510 chrXqtel1M 196750 GAATGGTTGGGTAAATTGTAGTATATGAAGGTTATGAAATATTAT 196794 ii i i i v? vviv i L1ME4c_3end#L 511 GAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAATATTAT 555 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 36.56 CpG sites = 22, Kimura (unadjusted) = 37.75 Transitions / transversions = 1.22 (22/18) Gap_init rate = 0.04 (6 / 142), avg. gap size = 1.17 (7 / 6) 327 32.79 0.00 0.00 chrXqtel1M 196674 196795 (803205) L1ME1_3end#LINE/L1 432 553 (373) m_b357s551i1 14956 chrXqtel1M 196674 TTCTGCACGAATGTTTGGGGCAGGTCTCTTTGTAGTGGCCAGAAAATGGA 196723 v i iivi v i v i i i i v L1ME1_3end#LI 432 TTGTACACGAATGTTCATAGCAGCTTTATTCGTAATAGCCAAAAACTGGA 481 chrXqtel1M 196724 AACAGAGTGGCTGCCCATCCATTGGAGAATGGTTGGGTAAATTGTAGTAT 196773 ivviiiv i v i? v v iiii i L1ME1_3end#LI 482 AACAACCCAAATGTCCATCAACNGGTGAATGGATAAACAAATTGTGGTAT 531 chrXqtel1M 196774 ATGAAGGTTATGAAATATTATT 196795 vv viiv i i i L1ME1_3end#LI 532 ATCCATACAATGGAATACTACT 553 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 44.06 CpG sites = 25, Kimura (unadjusted) = 45.65 Transitions / transversions = 1.67 (25/15) Gap_init rate = 0.00 (0 / 121), avg. gap size = 0.0 (0 / 0) 255 33.08 2.26 0.00 chrXqtel1M 196679 196811 (803189) L1MC1_3end#LINE/L1 437 572 (508) m_b357s551i2 14956 chrXqtel1M 196679 CACGAATGTTTGGGGCAGGTCTCTTTGTAGTGGCCAGAAAATGGAAACAG 196728 i ivi v i v ii i v i vv i i L1MC1_3end#LI 437 CACGGATGTTTATAGCAGCTTTATTCATAATTGCCAAAACTTGGAAGCAA 486 chrXqtel1M 196729 AGTGGCTGCCCATCCATTGGAGAATGGTTGGGTAAATTGTAGTATATGAA 196778 vvvi v i v vi v v v iii i i i vv L1MC1_3end#LI 487 CCAAGATGTCCTTCAGTAGGTGAATGGATAAATAAACTGTGGTACATCCA 536 chrXqtel1M 196779 GGTTATGAAATATTATT--GTTCT-GTAAGAAATGA 196811 iiv i -- iv -iv L1MC1_3end#LI 537 GACAATGGAATATTATTCAGCGCTAAAAAGAAATGA 572 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 43.38 CpG sites = 24, Kimura (unadjusted) = 44.74 Transitions / transversions = 1.20 (24/20) Gap_init rate = 0.02 (2 / 132), avg. gap size = 1.50 (3 / 2) 772 36.13 9.27 1.95 chrXqtel1M 197119 197787 (802213) C L2#LINE/L2 (361) 2721 2005 m_b357s601i10 14955 chrXqtel1M 197119 AATGATCAAGGTATGAGGAGATCAGAACCTGCACCGGGACGGGGGGGGGG 197168 i i v iiv iv vivii i v i -- v v vi C L2#LINE/L2 2721 AGTAATCCAGGCGAGAGATGATGGTGGCTTGGACCAGG--GTGGTGGCAG 2674 chrXqtel1M 197169 GGGGGGTGTCGGAGGAGAAAAGGGAGTATATTTGAGAGATGTGACAAAGA 197218 v i ------ v i v iviiv ivi v i vvii i C L2#LINE/L2 2673 TGGAGGTG------GTGAGAAGTGGTCGGATTCTGGATATATTTTGAAGG 2630 chrXqtel1M 197219 TAGAAACAGCAGAACTAGGCAACAGATTGTCTATGGGAGGTGAGAGAAAA 197268 iv ii i i v vii ii vv i iv i C L2#LINE/L2 2629 TAGAGCCGACAGGATTTGCTGATGGATTGGATGTGGGGTGTGAGAGAAAG 2580 chrXqtel1M 197269 TGAGGAGTCGGGGATGACACATAGATC----------ACAAGTTGGGGAT 197308 v ii v vv i i----------i v -- i v C L2#LINE/L2 2579 AGAGGAGTCAAGGATGACTCCAAGGTTTTTGGCCTGAGCAACT--GGAAG 2532 chrXqtel1M 197309 GGTAGAAGTGCCGGGGAAAGTAACAGGGAAG-CTGCGGGGGGGGGGGGCG 197357 i i iv ivv? vv vi ii - i i vi i- C L2#LINE/L2 2531 GATGGAGTTGCCATTNACTGAGATGGGGAAGACTGCGGGAGGAGCAGGT- 2483 chrXqtel1M 197358 GATTGGGGGAAGAGCTAATGAATTCCGTTTGGAACACGTTGACTTGGAGA 197407 -- i iii v v v i v v i i i v v C L2#LINE/L2 2482 --TTGAGGGGGAAGATCAGGAGTTCAGTTTTGGACATGTTAAGTTTGAGA 2435 chrXqtel1M 197408 TGTGTA-----CAT-------GAGATTTCCGCTAGG-AGCTGAAGATGTG 197444 iv ----- ------- v viv - i i v ii C L2#LINE/L2 2434 TGCCTATTAGACATCCAAGTGGAGATGTCGAGTAGGCAGTTGGATATACG 2385 chrXqtel1M 197445 AGACTGGGGT-CAGAAGGGAGCATCGAGCTGAACAAACGGATCCGTGCCT 197493 v i - ii i vvi i i v v iii ii v vv C L2#LINE/L2 2384 AGTCTGGAGTTCAGGGGAGAGGTCCGGGCTGGAGATATAAATTTGGGAGT 2335 chrXqtel1M 197494 CATCTGTGGAGAGAC---------AAC-----GATCGGGT-------CCC 197522 v iiv v i--------- i ----- ii i ------- ? C L2#LINE/L2 2334 CATCAGCATATAGATGGTATTTAAAGCCATGAGACTGGATGAGATCACCN 2285 chrXqtel1M 197523 GGGGAGCTGAG-GCAGTCAGAGG-GAGAAGGGGGCCCGGGACAGAACCCT 197570 i - - i vi i- i v vi v i C L2#LINE/L2 2284 AGGGAG-TGAGTGTAGATAGAGAAGAGAAGAGGTCCAAGGACTGAGCCCT 2236 chrXqtel1M 197571 GGAGGAC----------AGCCGCCACCG----GATGAAGATCTAGTAAAA 197606 i v ---------- vv i ivv ---- v i v i i i C L2#LINE/L2 2235 GGGGCACTCCAACGTTNAGAGGTCGGGGAGATGAGGAGGAACCAGCAAAG 2186 chrXqtel1M 197607 GCAACTGGGGAGGAGTGCTCAGAGAAGTAGAAGGGAAACCAGAACAAAGC 197656 vi i i i vi v i i i i v iv i C L2#LINE/L2 2185 GAGACTGAGAAGGAGCGGCCAGTGAGGTAGGAGGAAAACCAGGAGAGTGT 2136 chrXqtel1M 197657 AGGGTTACGGAAACCTCTCAAGAGGAGAGTAGCAAGAAGAGAGGGATGGT 197706 i v ivi i vvvii iiii v vv iii ii i C L2#LINE/L2 2135 GGTGTCCTGGAAGCCAAGTGAAGAAAGTGTTTCAAGAAGGAGGGAGTGAT 2086 chrXqtel1M 197707 GGACAGCGCCACAGGCTGCAGAGAGATCCAAAAGGGTCACAGCTGAGAAA 197756 vi v i i v v v ? i v iv i i v vii v C L2#LINE/L2 2085 CAACTGTGTCAAATGCTGCTGANAGGTCAAGTAAGATGAGGACTGAGAAT 2036 chrXqtel1M 197757 ACGCCACTGGATTTGGCAACTAAGAGATCAT 197787 vvi i i vvi i C L2#LINE/L2 2035 TGACCATTGGATTTAGCAACGTGGAGGTCAT 2005 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 49.93 CpG sites = 139, Kimura (unadjusted) = 51.92 Transitions / transversions = 1.42 (139/98) Gap_init rate = 0.04 (27 / 668), avg. gap size = 2.81 (76 / 27) 333 24.54 8.66 6.98 chrXqtel1M 197790 197916 (802084) MIRb#SINE/MIR 2 130 (138) m_b357s601i11 14957 chrXqtel1M 197790 AGAGGGGCAGCTGGTGGCCCAGTTCA----------GCCCTGAAGTCAGG 197829 -- iv vv ---------- ii i i MIRb#SINE/MIR 2 AGAGGGGCAGC--GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGA 49 chrXqtel1M 197830 AGGACCTGAGTCCAAATCTGACCTCAGACACTCAACCCTTCCTAACTGGG 197879 vi i i i iviv v v i ------- i v MIRb#SINE/MIR 50 CAGACCTGGGTTCGAATCCCGGCTCTGCCACTTA-------CTAGCTGTG 92 chrXqtel1M 197880 TGAACCTGGGCAAGTCACTTAACCCCAAT-TGCCTCAG 197916 v i i i vv -v MIRb#SINE/MIR 93 TGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAG 130 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.83 CpG sites = 16, Kimura (unadjusted) = 30.23 Transitions / transversions = 1.23 (16/13) Gap_init rate = 0.09 (11 / 126), avg. gap size = 1.82 (20 / 11) 349 24.03 1.01 7.53 chrXqtel1M 197818 197916 (802084) MIRc#SINE/MIR 35 127 (141) m_b357s601i12 14957 chrXqtel1M 197818 CCTGAAGTCAGGAGGACCTGAGTCCAAATCTGACCTCAGACACTCAACCC 197867 i i i i i i i iviv v v i ---- MIRc#SINE/MIR 35 CTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTA---- 80 chrXqtel1M 197868 TTCCTAACTGGGTGAACCTGGGCAAGTCACTTAACCCCAAT-TGCCTCAG 197916 --- i v v i i vv -v MIRc#SINE/MIR 81 ---CTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.32 CpG sites = 13, Kimura (unadjusted) = 29.38 Transitions / transversions = 1.44 (13/9) Gap_init rate = 0.08 (8 / 98), avg. gap size = 1.00 (8 / 8) 720 25.66 11.61 0.81 chrXqtel1M 198562 198785 (801215) MIRc#SINE/MIR 3 250 (18) m_b357s601i13 14958 chrXqtel1M 198562 AGACGGTTGGCGGCACCGTGCACAGAGAACTGGGCTGAGAGGCAAGAA-- 198609 i i -- i ii v v v v i vi v i -- MIRc#SINE/MIR 3 AGGCAGT--GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGA 50 chrXqtel1M 198610 TCTGATTTTGGAT------------ACTTCCTAGCTGTGGGACCCTGGCC 198647 i iv i ii ------------ v v i v MIRc#SINE/MIR 51 CCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGC 100 chrXqtel1M 198648 AAGTCACTTAATTTCT----GCCTCAATTTCCTCCACTGTAAAATGAGAA 198693 ii ---- i vv i i MIRc#SINE/MIR 101 AAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGA 150 chrXqtel1M 198694 TAATTACAGCAG------CTACCACAAAGGGTTGTTATAAAGATGGAATG 198737 v i v v ------ v v i i i vi MIRc#SINE/MIR 151 TAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATG 200 chrXqtel1M 198738 GGATAACGTTTG-GAAAGTGCTTGGCCCATAGTAGA-CACTGTATAAATG 198785 i i v - i v ivv iv i -ii i i MIRc#SINE/MIR 201 AGATAATGTATGTGAAAGCGCTTTGTAAACTGTAAAGTGCTATACAAATG 250 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.82 CpG sites = 34, Kimura (unadjusted) = 32.18 Transitions / transversions = 1.48 (34/23) Gap_init rate = 0.04 (8 / 223), avg. gap size = 3.50 (28 / 8) 14 29.34 1.52 3.08 chrXqtel1M 199133 199198 (800802) (GTCTCT)n#Simple_repeat 1 65 (0) m_b357s252i10 14959 chrXqtel1M 199133 GTCTCTGTCTCTGTTTCTTCCACCCCTCTCT-TCGCTGTCTTTCCTCTCC 199181 i vi -i iv - v i -v i (GTCTCT)n#Sim 1 GTCTCTGTCTCTGTCTCTGTC-TCTGTCTCTGTCTCTGTCTCT-GTCTCT 48 chrXqtel1M 199182 TTCTCTTTGTCCATCTC 199198 v v v ii (GTCTCT)n#Sim 49 GTCTCTGTCTCTGTCTC 65 Matrix = Unknown Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.05 (3 / 65), avg. gap size = 1.00 (3 / 3) 241 28.04 9.89 2.04 chrXqtel1M 199687 199777 (800223) C Charlie4#DNA/hAT-Charlie (3280) 98 1 m_b357s502i0 14960 chrXqtel1M 199687 AATTGAAATGTAGTTTTCCCACCTATATGAGGTCACGGACCTCTAGTAAT 199736 vi i i ii -- i vii v i iv v v C Charlie4#DNA/ 98 AATAAAGATGTAATTTTTTC--CCATCCAAGTTCACGGACCCCCTGAATT 51 chrXqtel1M 199737 CTATCCACAGACTTCTTGAAGGTCTCT---------GTTCAGAACCCTTG 199777 i ii ii iv --------- v i C Charlie4#DNA/ 50 CTATCCACGGACCCCTTGGGGGTCCGTGGACCCCAGGTTAAGAACCCCTG 1 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 33.19 CpG sites = 17, Kimura (unadjusted) = 36.88 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.03 (3 / 90), avg. gap size = 3.67 (11 / 3) 14 20.74 2.56 0.00 chrXqtel1M 202939 202977 (797023) (GGGGA)n#Simple_repeat 1 40 (0) m_b357s252i11 14961 chrXqtel1M 202939 GGGGAGGTGAGGGAAGGGGACAGG-GAGGAAGGCAGGGGA 202977 v i vi - i i v (GGGGA)n#Simp 1 GGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGA 40 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.03 (1 / 38), avg. gap size = 1.00 (1 / 1) 15 11.53 0.00 3.45 chrXqtel1M 203693 203722 (796278) (GAG)n#Simple_repeat 1 29 (0) m_b357s252i12 14962 chrXqtel1M 203693 GAGGAGGACGAGGAGGCGGTGGGAGGAGGA 203722 v v -i (GAG)n#Simple 1 GAGGAGGAGGAGGAGGAGG-AGGAGGAGGA 29 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 13 27.52 1.85 1.85 chrXqtel1M 204626 204679 (795321) (TTCA)n#Simple_repeat 1 54 (0) m_b357s252i13 14963 chrXqtel1M 204626 TTAATTGATGCTTTCCATCAACTCCTTCA-CCCTTCACTCATTCACTCAT 204674 v v v v - iv i v -i v i i (TTCA)n#Simpl 1 TTCATTCATTCATT-CATTCATTCATTCATTCATTCATTCATTCATTCAT 49 chrXqtel1M 204675 TCATT 204679 (TTCA)n#Simpl 50 TCATT 54 Matrix = Unknown Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.04 (2 / 53), avg. gap size = 1.00 (2 / 2) 278 33.79 9.09 4.35 chrXqtel1M 204704 204901 (795099) MIR#SINE/MIR 10 216 (46) m_b357s601i14 14964 chrXqtel1M 204704 CACAATGGCTAGAACCCCGGGCTGGAATCCCAAAGCCCTGAGTGACCCAG 204753 i i i ii v v ------ iii v- v - ii MIR#SINE/MIR 10 CATAGTGGTTAAGAGCACGGGCT------CTGGAGCCA-GACTG-CCTGG 51 chrXqtel1M 204754 GTTCCAATCCAGCCTCAGACAGTTCCTGTTTGTGGGACCCGGAGTGAGCA 204803 v v v v v v v ivi v iv i ii iv MIR#SINE/MIR 52 GTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTT 101 chrXqtel1M 204804 TCT--GTCTCTGTATGC-------TCCTCAACGG------GGAGATGATC 204838 v --ii v i ------- v v ------ i i v MIR#SINE/MIR 102 ACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATA 151 chrXqtel1M 204839 CTAGCTTCCGCCTC-TCGGGTCGGTGGGAAGATGGAATGGAATCAT--TT 204885 v ivi ii - v i v v i vi iiv v --v MIR#SINE/MIR 152 ATAGTACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATACAT 201 chrXqtel1M 204886 AGAAAGTGCTCCAGAA 204901 iv i -i MIR#SINE/MIR 202 GTAAAGCGCT-TAGAA 216 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.11 CpG sites = 34, Kimura (unadjusted) = 46.09 Transitions / transversions = 1.13 (34/30) Gap_init rate = 0.07 (14 / 197), avg. gap size = 1.93 (27 / 14) 246 28.91 10.00 2.54 chrXqtel1M 205196 205305 (794695) C MIR3#SINE/MIR (20) 188 71 m_b357s601i15 14965 chrXqtel1M 205196 GTCACAGGCAGGAGGTTTGGCTTTA-AGATGATTGAGCCCGATCCTCCCA 205244 v vii i --- i i - v iv i i i i i C MIR3#SINE/MIR 188 GTCAGAGCTGGAAGG---GACCTTAGAGATCATCTAGTCCAACCCCCTCA 142 chrXqtel1M 205245 TTTTGCA--TG-------CGAGACCCAGAGCGGTGAGGGGACTTGCTCTC 205285 i -- -------i i v i v i vv C MIR3#SINE/MIR 141 TTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAA 92 chrXqtel1M 205286 GCTC-CAGAGTTGGCAAGCGG 205305 v - v i?i iv i C MIR3#SINE/MIR 91 GGTCACACAGCNAGTTAGTGG 71 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.62 CpG sites = 20, Kimura (unadjusted) = 38.62 Transitions / transversions = 1.82 (20/11) Gap_init rate = 0.06 (7 / 109), avg. gap size = 2.00 (14 / 7) 251 37.78 0.00 0.00 chrXqtel1M 208169 208258 (791742) C MIR3#SINE/MIR (10) 198 109 m_b357s601i16 14966 chrXqtel1M 208169 ATCATCAGATGGCAGAGTCGATAAGGGCCTCCGAGAACATAGAATCTCCC 208218 vii v ii iv i i iv v vv i ivv C MIR3#SINE/MIR 198 ATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAAC 149 chrXqtel1M 208219 CCCCTGGCTTTGGGGGGGGGGAAACCAGGCCTCAGAAAGG 208258 vii ivi iv i iii v i i C MIR3#SINE/MIR 148 CCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGG 109 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 55.75 CpG sites = 21, Kimura (unadjusted) = 55.75 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.00 (0 / 89), avg. gap size = 0.0 (0 / 0) 18 7.14 0.00 3.23 chrXqtel1M 208678 208709 (791291) (CCCCT)n#Simple_repeat 1 31 (0) m_b357s252i14 14967 chrXqtel1M 208678 CCCCTCCTCTCCCCTCCCCCTCCCCTCTCCTC 208709 i - i (CCCCT)n#Simp 1 CCCCTCCCCTCCCCT-CCCCTCCCCTCCCCTC 31 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 183 32.31 3.73 5.30 chrXqtel1M 210119 210252 (789748) MIRc#SINE/MIR 17 148 (120) m_b357s601i17 14968 chrXqtel1M 210119 AGCGGAAATAGC-CTGGTGCCCAGAGCCAGGCAAACGAGGGCCTTC---T 210164 i v - -i iii i v i vv -- --- MIRc#SINE/MIR 17 AGTGGAAAGAGCACTGG-ACTTGGAGTCAGGAAGACCTGGG--TTCGAGT 63 chrXqtel1M 210165 CCCGGGCCCTTTTCCCAACTTGCTGTGCCGACCTCAGTTGTGTC-CTAAG 210213 - i viiv iv v -i ii viiv - v i MIRc#SINE/MIR 64 CCCGG-CTCTGCCACTTACTAGCTGTG-TGACCTTGGGCAAGTCACTTAA 111 chrXqtel1M 210214 CCTGCACTAGGCTGGCGTTGCCCTCTTCCATTAAACGGG 210252 - v ii ivvv -i v ii v i MIRc#SINE/MIR 112 CCT-CTCTGAGCCTCAGTT-TCCTCATCTGTAAAATGGG 148 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.64 CpG sites = 24, Kimura (unadjusted) = 43.64 Transitions / transversions = 1.41 (24/17) Gap_init rate = 0.08 (10 / 133), avg. gap size = 1.20 (12 / 10) 12 24.30 0.00 0.00 chrXqtel1M 210498 210531 (789469) (GGGG)n#Simple_repeat 1 34 (0) m_b357s252i15 14969 chrXqtel1M 210498 GGAGGGGGGGGGGGGCTGGGGTGGGCCGGGCGGG 210531 i vv v vv v (GGGG)n#Simpl 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 34 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 53 2.04 0.00 0.00 chrXqtel1M 211318 211367 (788633) (GT)n#Simple_repeat 1 50 (0) c_b357s251i2 14970 chrXqtel1M 211318 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGTGT 211367 i (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 36 19.30 6.78 1.61 chrXqtel1M 213169 213286 (786714) (TTCCCTT)n#Simple_repeat 1 124 (0) m_b357s252i16 14971 chrXqtel1M 213169 TTCCCTCTTGTCTTTTTTCTTTTCCC--CT-CCTTTCCCCTTTTCCCTGC 213215 i vi ii --i - i vi (TTCCCTT)n#Si 1 TTCCCTTTTCCCTTTTCCCTTTTCCCTTTTCCCTTTTCCCTTTTCCCTTT 50 chrXqtel1M 213216 TTCCTTTT--GTTTGCCCCTCCCCCTTTTCTTCCTTTTCCCTTGT---TT 213260 i --v v i ii -- v --- (TTCCCTT)n#Si 51 TCCCTTTTCCCTTTTCCCTTTTCCCTTTTC--CCTTTTCCCTTTTCCCTT 98 chrXqtel1M 213261 TTCCCTTTTCCCTTCTCCCCCTTCCC 213286 i ii (TTCCCTT)n#Si 99 TTCCCTTTTCCCTTTTCCCTTTTCCC 124 Matrix = Unknown Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.05 (6 / 117), avg. gap size = 1.67 (10 / 6) 17 24.63 3.70 0.00 chrXqtel1M 213421 213474 (786526) (TCCC)n#Simple_repeat 1 56 (0) m_b357s252i17 14972 chrXqtel1M 213421 TCCCCCTTTCCCCCCCTTCCTCCC-GGCTCCC-CCCCCCGTCCTCCCCTC 213468 i ii i i -vv - i v ii (TCCC)n#Simpl 1 TCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTC 50 chrXqtel1M 213469 CCTCCC 213474 (TCCC)n#Simpl 51 CCTCCC 56 Matrix = Unknown Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.04 (2 / 53), avg. gap size = 1.00 (2 / 2) 16 16.31 5.66 3.70 chrXqtel1M 213423 213475 (786525) (CCCCT)n#Simple_repeat 1 54 (0) m_b357s252i18 14972 chrXqtel1M 213423 CCCCTTTCCCCCCCT-TCCTCCCGGCTCCCC-CCCCCGTCCTCCCCT-CC 213469 ii i -i -- - ivi - (CCCCT)n#Simp 1 CCCCTCCCCTCCCCTCCCCTCCC--CTCCCCTCCCCTCCCCTCCCCTCCC 48 chrXqtel1M 213470 CTCCCC 213475 (CCCCT)n#Simp 49 CTCCCC 54 Matrix = Unknown Transitions / transversions = 6.00 (6/1) Gap_init rate = 0.10 (5 / 52), avg. gap size = 1.00 (5 / 5) 16 19.60 0.00 0.00 chrXqtel1M 214123 214159 (785841) (ACTCCTG)n#Simple_repeat 1 37 (0) m_b357s252i19 14973 chrXqtel1M 214123 ACTTCTGACCCCCGACTCCTGACCCCCGACTTCTGAC 214159 i i i i i i (ACTCCTG)n#Si 1 ACTCCTGACTCCTGACTCCTGACTCCTGACTCCTGAC 37 Matrix = Unknown Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 11 16.38 5.88 0.00 chrXqtel1M 214915 214948 (785052) (CCGTGCC)n#Simple_repeat 1 36 (0) m_b357s252i20 14974 chrXqtel1M 214915 CCCTGCCCCGTGCCCC-CGCCCTG-GCCCGGAGCCC 214948 v -i i - v v (CCGTGCC)n#Si 1 CCGTGCCCCGTGCCCCGTGCCCCGTGCCCCGTGCCC 36 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2) 16 16.54 0.00 0.00 chrXqtel1M 215147 215180 (784820) (AGGAAG)n#Simple_repeat 1 34 (0) m_b357s252i21 14975 chrXqtel1M 215147 AGGAGGGAGAAGATGATGAGGAAGAGGAAGAGGA 215180 i ii v v (AGGAAG)n#Sim 1 AGGAAGAGGAAGAGGAAGAGGAAGAGGAAGAGGA 34 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 13 21.84 2.70 0.00 chrXqtel1M 215154 215190 (784810) (AGA)n#Simple_repeat 1 38 (0) m_b357s252i22 14975 chrXqtel1M 215154 AGAAGATGATGAGGAAGAGGAAG-AGGAGCAGAAGCAG 215190 v v i i - i v v (AGA)n#Simple 1 AGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAG 38 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 240 30.66 5.56 2.15 chrXqtel1M 215550 215639 (784361) L2c_3end#LINE/L2 365 457 (21) m_b357s601i18 14976 chrXqtel1M 215550 TCCCCCAGGGGACTGTAAGCTCCCTTACAGGGCAGAAACTGGATCTTGGG 215599 i vvi i - i- ii i vi ivv L2c_3end#LINE 365 TCCTCCACTAGACTGTGAGCT-CCTTG-AGGGCAGGGACCGTGTCTTATT 412 chrXqtel1M 215600 C-CCTCAGCA----CAGGGTGGGGCATACAGTAAGTGCTTAATAA 215639 -i iv i ---- v ivv i i i i i L2c_3end#LINE 413 CATCTTTGTATCCCCAGCGCCTGGCACATAGTAGGCGCTCAATAA 457 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.51 CpG sites = 18, Kimura (unadjusted) = 41.53 Transitions / transversions = 2.00 (18/9) Gap_init rate = 0.04 (4 / 89), avg. gap size = 1.75 (7 / 4) 14 29.72 0.00 0.00 chrXqtel1M 218120 218168 (781832) (TCCGCC)n#Simple_repeat 1 49 (0) m_b357s252i23 14977 chrXqtel1M 218120 TCCTCCTTAGCCTCTGCCTCCGTCTCCCCCTCAGCTTCGGCATTCTCCT 218168 v iv i i v v i v v i v (TCCGCC)n#Sim 1 TCCGCCTCCGCCTCCGCCTCCGCCTCCGCCTCCGCCTCCGCCTCCGCCT 49 Matrix = Unknown Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 253 22.88 0.00 10.71 chrXqtel1M 218847 218939 (781061) C MIRc#SINE/MIR (83) 185 102 m_b357s601i19 14978 chrXqtel1M 218847 ACAACCCTGCTTGCCGTAGTCTTTGCTTATGTACTATTATGCTGTCCCCC 218896 -- vv v vvv -- v i ----- v C MIRc#SINE/MIR 185 ACAACCCTG--TGAGGTAGGCAGGGC--AGGTATTATTAT-----CCCCA 145 chrXqtel1M 218897 TTTCACAGTTGAGGAAACTGAGGCAAGTAGATGTTAGGGGGCT 218939 i v vviv v i v i C MIRc#SINE/MIR 144 TTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACT 102 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.96 CpG sites = 5, Kimura (unadjusted) = 26.96 Transitions / transversions = 0.36 (5/14) Gap_init rate = 0.10 (9 / 92), avg. gap size = 1.00 (9 / 9) 286 16.97 0.00 3.39 chrXqtel1M 218874 218934 (781066) C MIR#SINE/MIR (101) 161 103 m_b357s601i20 14978 chrXqtel1M 218874 TATGTACTATTATGCTGTCCCCCTTTCACAGTTGAGGAAACTGAGGCAAG 218923 v -- i v i v vi C MIR#SINE/MIR 161 TAGGTACTATTAT--TATCCCCATTTTACAGATGAGGAAACTGAGGCACA 114 chrXqtel1M 218924 TAGATGTTAGG 218934 v v i C MIR#SINE/MIR 113 GAGAGGTTAAG 103 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 19.23 CpG sites = 4, Kimura (unadjusted) = 19.23 Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.03 (2 / 60), avg. gap size = 1.00 (2 / 2) 11 24.40 0.00 0.00 chrXqtel1M 222122 222155 (777845) (CCCCTC)n#Simple_repeat 1 34 (0) m_b357s252i24 14979 chrXqtel1M 222122 CCCCTCCCCCCAGGTTTCCCCCTTCCCCTCCCCC 222155 ivvvii i (CCCCTC)n#Sim 1 CCCCTCCCCCTCCCCCTCCCCCTCCCCCTCCCCC 34 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 14 31.23 0.00 4.35 chrXqtel1M 222154 222225 (777775) (CCCCAG)n#Simple_repeat 1 69 (0) m_b357s252i25 14980 chrXqtel1M 222154 CCCCAGCCAGGGCCTTCAGTCCTAGGACCCTCCCCTGCCCCAGCCAGGGC 222203 vvi -i i i vv vv v vvi (CCCCAG)n#Sim 1 CCCCAGCCCCAGCC-CCAGCCCCAGCCCCAGCCCCAGCCCCAGCCCCAGC 49 chrXqtel1M 222204 CCCGAGCCCACCGCTCCATCCC 222225 - - v i v (CCCCAG)n#Sim 50 CCC-AGCCC-CAGCCCCAGCCC 69 Matrix = Unknown Transitions / transversions = 0.55 (6/11) Gap_init rate = 0.04 (3 / 71), avg. gap size = 1.00 (3 / 3) 14 27.70 1.18 7.50 chrXqtel1M 223301 223385 (776615) (CCTC)n#Simple_repeat 1 80 (0) m_b358s252i2 14981 chrXqtel1M 223301 CCTCCGGCCCCCCCAGCCTCTCTCCACT-CATCCGTCCTCTGCTTTCTTG 223349 vv i vv i - - v v - v i i i - (CCTC)n#Simpl 1 CCTCCCTCCCTCCCTCCCTCCCTCC-CTCCCTCCCTCC-CTCCCTCCCT- 47 chrXqtel1M 223350 CCCTCACTCTTTCCTTCTTCTCCCTGCCCTCCGCTC 223385 v ii i -i - - (CCTC)n#Simpl 48 CCCTCCCTCCCTCCCTC-CCTCCCT-CCCTCC-CTC 80 Matrix = Unknown Transitions / transversions = 1.12 (9/8) Gap_init rate = 0.08 (7 / 84), avg. gap size = 1.00 (7 / 7) 12 9.29 5.00 7.69 chrXqtel1M 226556 226595 (773405) (GCCT)n#Simple_repeat 1 39 (0) m_b358s252i3 14982 chrXqtel1M 226556 GCCTACCTGGCCTGCCT--CTCCCTAGCCTGCCTGTCCTCCC 226595 i - -- v - - v (GCCT)n#Simpl 1 GCCTGCCT-GCCTGCCTGCCTGCCT-GCCTGCCTG-CCTGCC 39 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.10 (4 / 39), avg. gap size = 1.25 (5 / 4) 291 30.28 11.01 0.00 chrXqtel1M 227528 227636 (772364) C MIRc#SINE/MIR (120) 148 28 m_b358s601i0 14983 chrXqtel1M 227528 CCCATTTTACAGAGGGGGAGACTGAGGCCCAGGGAGGCGAATGGCCTCTG 227577 v i i i i iv vv v ivv C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chrXqtel1M 227578 CCAAATCCGCGCCG-------ACGGCAAAGCTGGGGTTCGACCC-----C 227615 ivi i i v -------ii i i ii v ----- C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTC 49 chrXqtel1M 227616 TTTCAGACAGCAGATCCAGCG 227636 i v vv ii i C MIRc#SINE/MIR 48 TTCCTGACTCCAAGTCCAGTG 28 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.53 CpG sites = 20, Kimura (unadjusted) = 40.11 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.02 (2 / 108), avg. gap size = 6.00 (12 / 2) 13 14.17 3.23 0.00 chrXqtel1M 227719 227749 (772251) (TAGGA)n#Simple_repeat 1 32 (0) m_b358s252i4 14984 chrXqtel1M 227719 TAGGATAGGATTGGACAGGAAAGG-TTGGATA 227749 v i v - v (TAGGA)n#Simp 1 TAGGATAGGATAGGATAGGATAGGATAGGATA 32 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.03 (1 / 30), avg. gap size = 1.00 (1 / 1) 200 32.82 1.54 1.54 chrXqtel1M 228682 228746 (771254) C MIR3#SINE/MIR (23) 185 121 m_b358s601i1 14985 chrXqtel1M 228682 AGGGTGGGGGGGTGTCCT-GAGGTTCTTTAGCCCCGCCCCATTCACTTCA 228730 i iv ii vii i - i iv i i vi -i i i C MIR3#SINE/MIR 185 AGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCC-CTCATTTTA 137 chrXqtel1M 228731 CAAATGAGGAAAGTGA 228746 i v C MIR3#SINE/MIR 136 CAGATGAGGAAACTGA 121 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 47.40 CpG sites = 16, Kimura (unadjusted) = 47.40 Transitions / transversions = 3.20 (16/5) Gap_init rate = 0.03 (2 / 64), avg. gap size = 1.00 (2 / 2) 204 32.39 2.82 0.00 chrXqtel1M 228741 228811 (771189) C MIRb#SINE/MIR (186) 82 10 m_b358s601i2 14986 chrXqtel1M 228741 AAGTGACAATGTAGGG-TTTGATCCCAGGCCC-TCCGACTCCAAAGTTGG 228788 i iv iv - i v i i- i iiv C MIRb#SINE/MIR 82 AAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCG 33 chrXqtel1M 228789 GAAGCTTCCTCTTGACCCACGCT 228811 vivv i ivi vv C MIRb#SINE/MIR 32 TGCTCTTTCCACTGCACCACGCT 10 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.13 CpG sites = 13, Kimura (unadjusted) = 43.64 Transitions / transversions = 1.30 (13/10) Gap_init rate = 0.03 (2 / 70), avg. gap size = 1.00 (2 / 2) 225 34.40 4.29 6.57 chrXqtel1M 229262 229401 (770599) C MIRc#SINE/MIR (13) 255 119 m_b358s601i3 14987 chrXqtel1M 229262 CCTTCCACCCGCCTTGCCCCTCACAG---ATAGCTCACTTCTACACTACA 229308 v iii iv v v i i --- i ivv i ii - C MIRc#SINE/MIR 255 CCTTACATTTGTATAGCACTTTACAGTTTACAAAGCGCTTTCACA-TACA 207 chrXqtel1M 229309 TTGAC-CACGTTGCTCTCACAACGGCCTTACAATAGCCCTGGGAAGG--A 229355 iv - iv viii ii i iii vi---- i v -- C MIRc#SINE/MIR 206 TTATCTCATTTGATCCTCACAACAACCCTGTGAGG----TAGGCAGGGCA 161 chrXqtel1M 229356 GGTGCCATCATGACCCCCATTTTACAGAGAAGGGAGCCCAAGGCCC 229401 --- i v i vi i i- ii i C MIRc#SINE/MIR 160 GGT---ATTATTATCCCCATTTTACAGATGAGGAAA-CTGAGGCTC 119 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 48.20 CpG sites = 32, Kimura (unadjusted) = 49.84 Transitions / transversions = 2.46 (32/13) Gap_init rate = 0.09 (12 / 139), avg. gap size = 1.25 (15 / 12) 262 24.71 0.00 6.15 chrXqtel1M 229333 229401 (770599) C MIRb#SINE/MIR (82) 186 122 m_b358s601i4 14987 chrXqtel1M 229333 CCTTACAATAGCCCTGGGAAGGAGGTGCCATCATGACCCCCATTTTACAG 229382 i i i v i v --- i v i C MIRb#SINE/MIR 186 CCTCACAACAACCCTGCGAGGTAGGT---ATTATTATCCCCATTTTACAG 140 chrXqtel1M 229383 AGAAGGGAGCCCAAGGCCC 229401 vi i i- ii i C MIRb#SINE/MIR 139 ATGAGGAAA-CTGAGGCTC 122 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.46 CpG sites = 12, Kimura (unadjusted) = 31.46 Transitions / transversions = 3.00 (12/4) Gap_init rate = 0.06 (4 / 68), avg. gap size = 1.00 (4 / 4) 291 26.67 0.00 0.00 chrXqtel1M 229333 229392 (770608) C MIR#SINE/MIR (80) 182 123 m_b358s601i5 14987 chrXqtel1M 229333 CCTTACAATAGCCCTGGGAAGGAGGTGCCATCATGACCCCCATTTTACAG 229382 i i i iv i v i i i v i C MIR#SINE/MIR 182 CCTCACAACAACCCTATGAGGTAGGTACTATTATTATCCCCATTTTACAG 133 chrXqtel1M 229383 AGAAGGGAGC 229392 vi i i C MIR#SINE/MIR 132 ATGAGGAAAC 123 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.01 CpG sites = 12, Kimura (unadjusted) = 35.01 Transitions / transversions = 3.00 (12/4) Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0) 214 22.75 7.41 2.35 chrXqtel1M 229351 229431 (770569) C MIR1_Amn#SINE/MIR (59) 171 87 m_b358s601i6 14987 chrXqtel1M 229351 AAGGAGGT-GCCATCATGACCCCCATTTTACAGAGAAGGGAGCCCAAGGC 229399 -ivi v i vi i i- ii C MIR1_Amn#SINE 171 AAGGAGGTCAGTATCATTATCCCCATTTTACAGATGAGGAAA-CTGAGGC 123 chrXqtel1M 229400 CC-----GCTACAGTGAACTTGCACTTTGTGACCCAG 229431 ? ----- v ?v - v vvv v ? C MIR1_Amn#SINE 122 NCAGAGAGGTNAAGTG-ACTTGCCCAAGGTCACNCAG 87 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.57 CpG sites = 8, Kimura (unadjusted) = 28.57 Transitions / transversions = 0.80 (8/10) Gap_init rate = 0.05 (4 / 80), avg. gap size = 2.00 (8 / 4) 237 32.99 12.10 2.21 chrXqtel1M 231026 231149 (768851) C L3#LINE/CR1 (84) 4015 3880 m_b358s601i7 14988 chrXqtel1M 231026 CAACGTGGCCAGCAAGTGGGCCTCCCGCCTCCGC----------CC---- 231061 i vv iii v v v i ---------- ---- C L3#LINE/CR1 4015 CAACATCCCTGACAAGTGGTCATCCAGCCTCTGCTTGAACACCTCCAGTG 3966 chrXqtel1M 231062 -CAAGAAGCCCATTACTTCCCTAGGCAGCCCCGTCTACTTTGGGAGAGCT 231110 - ii i i i i ? v vv i i v v C L3#LINE/CR1 3965 ACGGGGAGCTCACTACCTCNCGAGGCAGCCCATTCCATTTTTGGACAGCT 3916 chrXqtel1M 231111 CTACCCACTGATCTCAGATCTCTCTCTATCTGGGGCCAA 231149 i--- i v vvv ii iii ii v v i i C L3#LINE/CR1 3915 CTG---ATTGTTAGAAAGTTCTTCCTTATATTGAGCCGA 3880 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.75 CpG sites = 24, Kimura (unadjusted) = 45.86 Transitions / transversions = 1.50 (24/16) Gap_init rate = 0.05 (6 / 123), avg. gap size = 3.00 (18 / 6) 14 4.50 4.35 0.00 chrXqtel1M 231331 231353 (768647) (GCT)n#Simple_repeat 1 24 (0) m_b358s252i5 14989 chrXqtel1M 231331 GCTGCTGCTGCTGCT-CTGCTCCT 231353 - v (GCT)n#Simple 1 GCTGCTGCTGCTGCTGCTGCTGCT 24 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.05 (1 / 22), avg. gap size = 1.00 (1 / 1) 13 0.00 3.70 7.69 chrXqtel1M 231767 231793 (768207) (TGGG)n#Simple_repeat 1 26 (0) m_b358s252i6 14990 chrXqtel1M 231767 TGGGTTGGGATGGG-GGGTGGGTGGGTG 231793 - - - (TGGG)n#Simpl 1 TGGG-TGGG-TGGGTGGGTGGGTGGGTG 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.12 (3 / 26), avg. gap size = 1.00 (3 / 3) 26 10.85 2.44 0.00 chrXqtel1M 232445 232485 (767515) (TC)n#Simple_repeat 1 42 (0) m_b358s252i7 14991 chrXqtel1M 232445 TCTTTCTCT-TCTCTCTCTCCCTCTCTCTCTCCTTCTCTCTC 232485 i - i ii (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 42 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1) 201 33.39 1.14 4.71 chrXqtel1M 232872 232959 (767041) MIR3#SINE/MIR 31 115 (93) m_b358s601i8 14992 chrXqtel1M 232872 GACTTGAAGTTAGAA-TCACAGACTCTTGCCCTGCCTCAACTACTGACTC 232920 v i i i -v vii ii v i i v vi i i ? MIR3#SINE/MIR 31 GACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTN 80 chrXqtel1M 232921 ACTGGAGGGCGCTGGGCAAGTCGGCCCTTCCTCTGCTCT 232959 i viv i vi i--- vi - MIR3#SINE/MIR 81 GCTGTGTGACCTTGGGCAAGTCA---CTTCACCT-CTCT 115 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.91 CpG sites = 18, Kimura (unadjusted) = 47.29 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.06 (5 / 87), avg. gap size = 1.00 (5 / 5) 239 31.96 1.48 9.60 chrXqtel1M 233788 233922 (766078) MIR3#SINE/MIR 60 184 (24) m_b358s601i9 14993 chrXqtel1M 233788 TCCCAGCTTTGTGGCAGAACTAGATAGAGCATCTGATCTGCAGCAACTCT 233837 i i ivi -v ? v i----- v i vvi v - MIR3#SINE/MIR 60 TCCCGGCTCTGCCAC-TAACTNGCTG-----TGTGACCTTGGGCAAGTC- 102 chrXqtel1M 233838 AAGATTTGAC-TCTTGGGGACTTGCTTTTCTC-TGTGCTAAAGGCAGAAG 233885 --- i v - iv v iiv i - v iv v vi -- MIR3#SINE/MIR 103 ---ACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGG--G 147 chrXqtel1M 233886 GGCTGAACTAGCCAATTTCTGAGATCCCTTCTGGCTC 233922 i i vii i i i ii MIR3#SINE/MIR 148 GGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTC 184 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.61 CpG sites = 23, Kimura (unadjusted) = 43.09 Transitions / transversions = 1.44 (23/16) Gap_init rate = 0.10 (14 / 134), avg. gap size = 1.00 (14 / 14) 276 34.63 1.40 5.07 chrXqtel1M 238031 238173 (761827) MIRc#SINE/MIR 27 164 (104) m_b358s601i10 14994 chrXqtel1M 238031 GCGCTGGCTCTTGGAGCCAGGCAGACCTGGCTTGAAGAGCTGCTTCTG-- 238078 i v- i v v vi vv i vi -- MIRc#SINE/MIR 27 GCACTGGA-CTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCC 75 chrXqtel1M 238079 ACAGACTAGCTGTGCAGCCCTAGACCAGTCCCTGCCCCTCACTACATCCC 238128 vv iii i i i v v vvv v ivii i- MIRc#SINE/MIR 76 ACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCT- 124 chrXqtel1M 238129 AAAGCAATTTTCCAGCCTGCATTAGTCGGGAGAATTTCCTCTGCC 238173 ---- i i ivii i -v i v v vvivi MIRc#SINE/MIR 125 ----CAGTTTCCTCATCTGTA-AAATGGGGATAATAATACCTGCC 164 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.54 CpG sites = 24, Kimura (unadjusted) = 47.23 Transitions / transversions = 1.04 (24/23) Gap_init rate = 0.06 (8 / 142), avg. gap size = 1.12 (9 / 8) 192 31.78 9.35 0.00 chrXqtel1M 239296 239402 (760598) C MIR#SINE/MIR (100) 162 46 m_b358s601i11 14995 chrXqtel1M 239296 GTGGGAACCAGGATTGTCAGTGTT----AGGTGGGGAATCCCAGGGA-AG 239340 i v i vv i vvii ---- i i v iv v - C MIR#SINE/MIR 162 GTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAG 113 chrXqtel1M 239341 AAA----AAGTGTCT-GCTCAGGGCAGCACAGCCAGTCAGGGGCAGAGCC 239385 i ---- iv - i i ivi i v v C MIR#SINE/MIR 112 AGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCC 63 chrXqtel1M 239386 GGGCCCAGCACCCCGAC 239402 viiv v v i C MIR#SINE/MIR 62 GGGATTCGAACCCAGGC 46 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.16 CpG sites = 18, Kimura (unadjusted) = 42.16 Transitions / transversions = 1.12 (18/16) Gap_init rate = 0.04 (4 / 106), avg. gap size = 2.50 (10 / 4) 217 30.34 6.74 0.00 chrXqtel1M 239320 239408 (760592) C MIRc#SINE/MIR (130) 138 44 m_b358s601i12 14995 chrXqtel1M 239320 AGGTGGGGAATCCCAGG---GAAGAAA--AAGTGTCT-GCTCAGGGCAGC 239363 i i v iv ---ii ii-- v - i i ivi C MIRc#SINE/MIR 138 AGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCAC 89 chrXqtel1M 239364 ACAGCCAGTCAGGGGCAGAGCCGGGCCCAGCACCCCGACCTCTCT 239408 i v v v iv v v ii ii C MIRc#SINE/MIR 88 ACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCT 44 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.46 CpG sites = 17, Kimura (unadjusted) = 40.46 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.03 (3 / 88), avg. gap size = 2.00 (6 / 3) 248 25.65 1.27 1.27 chrXqtel1M 239327 239405 (760595) C MIR3#SINE/MIR (86) 122 44 m_b358s601i13 14995 chrXqtel1M 239327 GAATCCCAGGGAAGAAAAAGTGTCT-GCTCAGGGCAGCACAGCCAGTCAG 239375 iv i i vi - v - i i ivi ? i C MIR3#SINE/MIR 122 GAGGCCCAGAGAGGTGAA-GTGACTTGCCCAAGGTCACACAGCNAGTTAG 74 chrXqtel1M 239376 GGGCAGAGCCGGGCCCAGCACCCCGACCTC 239405 v v i v v ii C MIR3#SINE/MIR 73 TGGCAGAGCCGGGACTAGAACCCAGGTCTC 44 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.68 CpG sites = 12, Kimura (unadjusted) = 32.68 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.03 (2 / 78), avg. gap size = 1.00 (2 / 2) 360 25.11 7.73 5.56 chrXqtel1M 239888 240081 (759919) C L2b_3end#LINE/L2 (6) 460 263 m_b358s601i14 14996 chrXqtel1M 239888 TCAACCAAAAAGTGCTTA---AGCACTTCCTATGCTCCAGGCGTTGTTCT 239934 vi v i ii --- i i v i iv ?i --- C L2b_3end#LINE 460 TCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGT--- 414 chrXqtel1M 239935 GCTAAACGC-GAGGAGACAAGTAATAAA-AAGAAAGACA--GTCCCTGCC 239980 ii - i v - iii i - v ?-- C L2b_3end#LINE 413 GCTAGGCGCTGGGGATACA-GCGGTGAACAAGACAGACNCGGTCCCTGCC 365 chrXqtel1M 239981 CCCA--GAGCTCATAATCTAAAGGGGGAAATGACAGACA--AAAGGAGGC 240026 i -- i i iv --- --v ?v i C L2b_3end#LINE 364 CTCACGGAGCTCACAGTCTAGTGGGGGA---GACAGACATGTAANCAGAC 318 chrXqtel1M 240027 AAGAAAGCCCCAGGGGGG--AGGCAGA--TGGGACACCATCCCAGCAGGG 240072 v? viv i v --i i i-- i---viv - i C L2b_3end#LINE 317 AATNATAACCCAGAGTGGCAGGGTAGGACTGGGG---GGGCCCAG-AGGA 272 chrXqtel1M 240073 GGGCGTCCG 240081 i i C L2b_3end#LINE 271 GGGCGCCTG 263 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.88 CpG sites = 31, Kimura (unadjusted) = 32.71 Transitions / transversions = 2.07 (31/15) Gap_init rate = 0.10 (19 / 193), avg. gap size = 1.37 (26 / 19) 184 25.68 21.62 0.00 chrXqtel1M 240181 240254 (759746) MIRc#SINE/MIR 19 108 (160) m_b358s601i15 14997 chrXqtel1M 240181 TGGATAGAGCACTGGGCCTGGGGCCGG----AGCTGAGTTCAAATCCAGA 240226 v i i i i i ---- v i i i v i MIRc#SINE/MIR 19 TGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGG 68 chrXqtel1M 240227 CTAAG----------ACTGTGCTGCCC--GGCAAGTCACT 240254 vv ----------i ivi i-- MIRc#SINE/MIR 69 CTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACT 108 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.64 CpG sites = 13, Kimura (unadjusted) = 32.74 Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.04 (3 / 73), avg. gap size = 5.33 (16 / 3) 195 12.75 8.33 1.96 chrXqtel1M 240181 240228 (759772) MIR1_Amn#SINE/MIR 22 72 (158) m_b358s601i16 14997 chrXqtel1M 240181 TGGATAGAGCACTGGGCCTGGGGCC--GGAG--CTGAGTTCAAATCCAGA 240226 i- i i-- -- i ? ? v i MIR1_Amn#SINE 22 TGGATAGAGCACTGGA-CTGGGACTCGGGAGACCTGGGTTCNANTCCCGG 70 chrXqtel1M 240227 CT 240228 MIR1_Amn#SINE 71 CT 72 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 15.15 CpG sites = 5, Kimura (unadjusted) = 15.15 Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.06 (3 / 47), avg. gap size = 1.67 (5 / 3) 17 11.71 5.41 0.00 chrXqtel1M 240589 240625 (759375) (TTCCC)n#Simple_repeat 1 39 (0) m_b358s252i8 14998 chrXqtel1M 240589 TTCCC-TGACTTCCCTTCCCTTTCCTT-CCTTCCCCTCC 240625 - vv i - i (TTCCC)n#Simp 1 TTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCC 39 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 132 0.77 1.48 1.48 chrXqtel1M 241907 242041 (757959) (TTTC)n#Simple_repeat 1 135 (0) c_b358s251i0 14999 chrXqtel1M 241907 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 241956 (TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 50 chrXqtel1M 241957 TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC 242006 (TTTC)n#Simpl 51 TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC 100 chrXqtel1M 242007 --TCTTTCTTTCTTTTTTTCTTTCTTTTCTTTTCTTT 242041 -- i - - (TTTC)n#Simpl 101 TTTCTTTCTTTCTTTCTTTCTTTC-TTTC-TTTCTTT 135 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.02 (3 / 134), avg. gap size = 1.33 (4 / 3) 80 0.00 0.00 0.00 chrXqtel1M 242044 242114 (757886) (CTTC)n#Simple_repeat 1 71 (0) c_b358s251i1 15000 chrXqtel1M 242044 CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT 242093 (CTTC)n#Simpl 1 CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT 50 chrXqtel1M 242094 TCCTTCCTTCCTTCCTTCCTT 242114 (CTTC)n#Simpl 51 TCCTTCCTTCCTTCCTTCCTT 71 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0) 408 26.58 0.81 5.93 chrXqtel1M 242122 242245 (757755) C MIRc#SINE/MIR (141) 127 10 m_b358s601i17 15001 chrXqtel1M 242122 CTGAGGCA-ATTGGGGTCAAGTGCCTTGCCAGGGGTCACATGGATAGAAA 242170 v- vv i i v vii ii v v C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAA 78 chrXqtel1M 242171 GTGTGAAGTGTCTGAGGCCACATTTGAGCTCAGGTCCTCCTGACTTCAGG 242220 - v v i v i------ i i i i i i i C MIRc#SINE/MIR 77 GTG-GCAGAGCCGGG------ACTCGAACCCAGGTCTTCCTGACTCCAAG 35 chrXqtel1M 242221 GCTGGTGCTCTAACCACTGCATCAC 242245 v ii vv i C MIRc#SINE/MIR 34 TCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.11 CpG sites = 18, Kimura (unadjusted) = 33.42 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.07 (8 / 123), avg. gap size = 1.00 (8 / 8) 34 0.00 0.00 0.00 chrXqtel1M 243066 243094 (756906) (TG)n#Simple_repeat 1 29 (0) c_b358s251i2 15002 chrXqtel1M 243066 TGTGTGTGTGTGTGTGTGTGTGTGTGTGT 243094 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGT 29 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 827 31.74 8.08 1.99 chrXqtel1M 243329 243897 (756103) L2#LINE/L2 1983 2585 (497) m_b358s601i18 15003 chrXqtel1M 243329 ATTGCTCTTAT--AGAATACCGAT----TTAA--TTGCTAAATCTGAAAT 243370 i i -- ivi i ---- iv -- i-- L2#LINE/L2 1983 ACTGCTCTTGTCAAGGTCACCAATGACCTCCACGTTGCTAAATCC--AAT 2030 chrXqtel1M 243371 ATTTTTTCTCTCAGTTGTTATTCTCCTTGAGTCCTCTGCAGCCTTGGACA 243420 iv ivv - iv i ii v vii? v v v L2#LINE/L2 2031 GGTCAAT-TCTCAGTCCTCATCTTACTTGACCTNTCAGCAGCATTTGACA 2079 chrXqtel1M 243421 CTGTCTATCGTCCTTTGCTCCTGGA--TACTCTCTTCTCT------CTAG 243462 v iv iii ii v i v --i i v ------ i L2#LINE/L2 2080 CAGTTGATCACTCCCTCCTTCTTGAAACACTTTCTTCACTTGGCTTCCAG 2129 chrXqtel1M 243463 GGC----CTCTCTCTCACTTCTCCTTCTA------TGACCACTTCTT--- 243499 i ---- v iiiv i i ------ i i i --- L2#LINE/L2 2130 GACACCACACTCTCCTGGTTTTCCTCCTACCTCACTGGCCGCTCCTTCTC 2179 chrXqtel1M 243500 AGTCTTCTTTGCTGACTCTTCACCCAGATCCATG-CCTGTTAGTGGTG-A 243547 i ii i - i vv vi - v ? ii v - L2#LINE/L2 2180 AGTCTCCTTTGCTGGTTCCTC-CTCATCTCCCCGACCTCTNAACGTTGGA 2228 chrXqtel1M 243548 GTGCCCCTCAGGGCTCTGTCCC-AGTCCTTTTCT----TCCTTCTAC--- 243589 -- v i-i v i ---- iv --- L2#LINE/L2 2229 GTGCCCC--AGGGCTCAGTCCTTGGACCTCTTCTCTTCTCTATCTACACT 2276 chrXqtel1M 243590 --TTCACCGAGTGAACTTAATAACTCCTGTGGATTTCCCCACCATCTATA 243637 --i v i?i v i viv v iii v vvvi L2#LINE/L2 2277 CACTCCCTNGGTGATCTCATCCAGTCTCATGGCTTTAAATACCATCTATA 2326 chrXqtel1M 243638 CGCTAATGATTCTCAAATTTCCCTTTCCCTGCCCCTGATTCTCTGCTGAC 243687 i i i i viv i v- vvivi iv v L2#LINE/L2 2327 TGCTGATGACTCCCAAATTTATATCTCCA-GCCCGGACCTCTCCCCTGAA 2375 chrXqtel1M 243688 CTCTAATTTCTTATCTCCAGCTGCCT-TTATAGATCTTGAAATGGAAATC 243736 i ivi v v i -i vv v iv vv vi L2#LINE/L2 2376 CTCCAGACTCGTATATCCAACTGCCTACTCGACATCTCCACTTGGATGTC 2425 chrXqtel1M 243737 CCTTAAACAGCTTAAACTCAACCTGCCTGAGACTGACCTCTTTATCTCTT 243786 ivv ii v i i v i ii i v i v iii L2#LINE/L2 2426 TAATAGGCATCTCAAACTTAACATGTCCAAAACTGAACTCCTGATCTTCC 2475 chrXqtel1M 243787 CCTCTAAACCC-TTCCTCCCTTCAAAACTTCCCAATTACAGTCCAAGACA 243835 iii i-i vi-- iv v iv ?v v i L2#LINE/L2 2476 CCCTCAAACCTGCTCCTCCCGC--AGTCTTCCCCATCTCAGTNAATGGCA 2523 chrXqtel1M 243836 CCCCCTAGCCTCCTAATCCCCTAGGCTTACAATCCTT---CTCACTACTT 243882 v i - v i i i iv ii -i v v ---v - v L2#LINE/L2 2524 ACTCC-ATCCTTCCAGTTGCTCAGGC-CAAAAACCTTGGAGTCA-TCCTT 2570 chrXqtel1M 243883 ATCTCCTCTGTATCT 243897 iv v v L2#LINE/L2 2571 GACTCCTCTCTTTCT 2585 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.05 CpG sites = 102, Kimura (unadjusted) = 43.02 Transitions / transversions = 1.36 (102/75) Gap_init rate = 0.05 (29 / 568), avg. gap size = 2.00 (58 / 29) 244 24.86 3.64 8.57 chrXqtel1M 244495 244604 (755396) C L2c_3end#LINE/L2 (1) 477 373 m_b358s601i19 15004 chrXqtel1M 244495 TTCAGTTCCTTCATCAGAAAATGAATGAACGAAGCACCTACTGTGTGGGA 244544 - v v i v v v v i ----- i vv C L2c_3end#LINE 477 TTCA-TTCATTCAACAAACATTTATTGAGCG-----CCTACTATGTGCCA 434 chrXqtel1M 244545 AGCCCTGGGGATGCGAACAGAAGAGTCAG--ATGGTTCCTGTGCT-GAGA 244591 i v i i -- v i v -- i i iv -i i C L2c_3end#LINE 433 GGCGCTGGGGATACAA--AGATGAATAAGACACGGTCCCTGCCCTCAAGG 386 chrXqtel1M 244592 AGCCCCACA-TCTA 244604 - i - C L2c_3end#LINE 385 AG-CTCACAGTCTA 373 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.97 CpG sites = 13, Kimura (unadjusted) = 30.38 Transitions / transversions = 1.08 (13/12) Gap_init rate = 0.11 (12 / 109), avg. gap size = 1.08 (13 / 12) 12 17.72 3.12 0.00 chrXqtel1M 245312 245343 (754657) (TTTCTT)n#Simple_repeat 1 33 (0) m_b358s252i9 15005 chrXqtel1M 245312 TTTCTTTTTCTTGCTCATTCT-TTTTCCTTTTT 245343 vi v i - i (TTTCTT)n#Sim 1 TTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTT 33 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 12 11.20 3.23 3.23 chrXqtel1M 245434 245464 (754536) (AGGGGA)n#Simple_repeat 1 31 (0) m_b358s252i10 15006 chrXqtel1M 245434 AGGGGAAGGGGGTGGGAGAA-GGGAAGGAGAA 245464 iv - - i (AGGGGA)n#Sim 1 AGGGGAAGGGGAAGGG-GAAGGGGAAGGGGAA 31 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2) 15 5.56 0.00 0.00 chrXqtel1M 245543 245561 (754439) (A)n#Simple_repeat 1 19 (0) m_b358s252i11 15007 chrXqtel1M 245543 AAAAAAAAAAAAAAAAGAA 245561 i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAA 19 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 529 19.11 3.76 9.52 chrXqtel1M 245989 246121 (753879) MIRc#SINE/MIR 2 127 (141) m_b358s601i20 15008 chrXqtel1M 245989 GGGGCAGTTGGGTGGTGCGGTGGATAGAGCATCAGTCCTGAAGTCAGGAG 246038 i --- i v iii v i i i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chrXqtel1M 246039 AATCTGAGTTCAAATCTT--CCCTGACACTTAACATTTCCTAGCTGTGTG 246086 i i i i i ii-- i v ------- MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTG 91 chrXqtel1M 246087 ACCCTGGGCAAATCACTCAACC---CTAACTGCCTCAG 246121 i i i --- i -- MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACCTCTCTGA--GCCTCAG 127 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 20.97 CpG sites = 20, Kimura (unadjusted) = 23.23 Transitions / transversions = 6.67 (20/3) Gap_init rate = 0.11 (14 / 132), avg. gap size = 1.21 (17 / 14) 268 35.61 3.39 6.40 chrXqtel1M 246122 246298 (753702) C MIR3#SINE/MIR (8) 200 29 m_b358s601i21 15009 chrXqtel1M 246122 GAAAAATAAACAGTCAAAACAACAAAAAATCGTATTGGAGTGGTTGCCTA 246171 vv i vv i i viv iii i --- i --i iii C MIR3#SINE/MIR 200 GAATCATAGAATGTCAGAGCTGGAAGGGACC---TTAGAG--ATCATCTA 156 chrXqtel1M 246172 ATTCCTTTTCCAGCTCGAATGACAGGTGAGGAAACTGAGG--CAGA---A 246216 i i vviii --- ivv v i -- ---i C MIR3#SINE/MIR 155 GTCCAACCCCC---TCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGG 109 chrXqtel1M 246217 TGAAGTGACTTTCCCAGGGGTCACCCAGCTAGGCTGTATATGAAGTCACA 246266 v -i v ? viv i-iiii i ivi C MIR3#SINE/MIR 108 TGAAGTGACTTGCCCA-AGGTCACACAGCNAGTTAGTG-GCAGAGCCGGG 61 chrXqtel1M 246267 ATT-GAGCTCAGGCTCTCTCAAGTTCAGGCCTG 246298 i - i i - iii v i vi i i C MIR3#SINE/MIR 60 ACTAGAACCCAGG-TCTCCTGACTCCCAGTCCG 29 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 50.04 CpG sites = 41, Kimura (unadjusted) = 52.73 Transitions / transversions = 2.28 (41/18) Gap_init rate = 0.08 (14 / 176), avg. gap size = 1.21 (17 / 14) 295 29.13 4.90 6.38 chrXqtel1M 246193 246335 (753665) C MIRb#SINE/MIR (125) 143 3 m_b358s601i22 15009 chrXqtel1M 246193 ACAGGTGAGGAAACTGAGG--CAGA---ATGAAGTGACTTTCCCAGGGGT 246237 i -- ---i v i v -i C MIRb#SINE/MIR 143 ACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCA-AGGT 95 chrXqtel1M 246238 CACCCAGCTAGGCTGTATATGAAGTCACAATT-GAGCTCAGG-CTCTCTC 246285 v vvv i-iiii i ivi - i i - v - C MIRb#SINE/MIR 94 CACACAGCTAGTAAGTG-GCAGAGCCGGGATTCGAACCCAGGTCTGTCT- 47 chrXqtel1M 246286 AAGTTCAGGCCTGGCAGTCTGTTCACTGAAAGGCTCCCTAGCTGCCCCCC 246335 i v i iiv iv iiv v i v ------ vv i C MIRb#SINE/MIR 46 GACTCCAAAGCCCGTGCTCTTTCCACTGCA------CCACGCTGCCCCTC 3 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.65 CpG sites = 23, Kimura (unadjusted) = 37.88 Transitions / transversions = 1.44 (23/16) Gap_init rate = 0.09 (13 / 142), avg. gap size = 1.23 (16 / 13) 359 26.65 4.88 2.38 chrXqtel1M 246193 246315 (753685) C MIR1_Amn#SINE/MIR (88) 142 17 m_b358s601i23 15009 chrXqtel1M 246193 ACAGGTGAGGAAACTGAGG--CAGA---ATGAAGTGACTTTCCCAGGGGT 246237 i -- ---i ? v -i C MIR1_Amn#SINE 142 ACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGCCCA-AGGT 94 chrXqtel1M 246238 CACCCAGCTAGGCTGTATATGAAGTC-ACAATTGAGCTCAGGCTCTCTCA 246286 ? ?i v?v i-iiii i -iv ? ? i i - i i C MIR1_Amn#SINE 93 CACNCAGCNGGCNAGTG-GCAGAGCCGGGANTNGAACCCAGG-TCTCCCG 46 chrXqtel1M 246287 AGTTCAGGCCTGGCAGTCTGTTCACTGAA 246315 i vi i ii iiv i i ii C MIR1_Amn#SINE 45 AGTCCCAGTCCAGTGCTCTATCCACTAGA 17 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.74 CpG sites = 26, Kimura (unadjusted) = 38.32 Transitions / transversions = 4.33 (26/6) Gap_init rate = 0.05 (6 / 122), avg. gap size = 1.50 (9 / 6) 269 30.54 4.42 7.27 chrXqtel1M 246396 246508 (753492) L2b_3end#LINE/L2 321 430 (36) m_b358s601i24 15003 chrXqtel1M 246396 TGGGCACATGTCTTTTCCCTCCAGGCTCCTGCCAGACCGTGAGTTCCTTG 246445 ?vi v ii i -------- i i i v L2b_3end#LINE 321 TGNTTACATGTCTGTCTCCCCCA--------CTAGACTGTGAGCTCCGTG 362 chrXqtel1M 246446 AGGAAAGG--CTGAG---GTTCTGTTCCTATTTGTAGTGCCAATATTCAG 246490 iv -- i ? --- ii vivvi viv iiiiii L2b_3end#LINE 363 AGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTGTATCCCCAGCGCCTAG 412 chrXqtel1M 246491 CACGGAGACTGGCACATA 246508 i ? v i L2b_3end#LINE 413 CACAGNGCCTGGCACACA 430 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.34 CpG sites = 22, Kimura (unadjusted) = 43.14 Transitions / transversions = 2.20 (22/10) Gap_init rate = 0.09 (10 / 112), avg. gap size = 1.30 (13 / 10) 16 24.82 3.90 3.90 chrXqtel1M 247268 247344 (752656) (GGGAGA)n#Simple_repeat 1 77 (0) m_b358s252i12 15010 chrXqtel1M 247268 GGGACA-GGAGAAGGGTGCGGAGAGAGGGAGGGGAAGAGCAAAGAGCGGG 247316 v - - v v - i i -ii v i (GGGAGA)n#Sim 1 GGGAGAGGGAG-AGGGAGAGG-GAGAGGGAGAGGGAGAG-GGAGAGGGAG 47 chrXqtel1M 247317 AGGGA-AGGG-GAAACCGCGGGAGGGGGAG 247344 - - iivv v i (GGGAGA)n#Sim 48 AGGGAGAGGGAGAGGGAGAGGGAGAGGGAG 77 Matrix = Unknown Transitions / transversions = 1.14 (8/7) Gap_init rate = 0.08 (6 / 76), avg. gap size = 1.00 (6 / 6) 23 25.45 4.94 0.00 chrXqtel1M 247465 247545 (752455) (CTCCCT)n#Simple_repeat 1 85 (0) m_b358s252i13 15011 chrXqtel1M 247465 CTCCCTCTTTCCGTCCGTCT-CCTTTCCCT-GCCC-CTCCCCGTCCCACT 247511 ii iv v - i -v - iv v (CTCCCT)n#Sim 1 CTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCT 50 chrXqtel1M 247512 CCCCTTCTCTCTCCTCCTCCCCCTCCCT-TCTCTC 247545 ii i ii i - i (CTCCCT)n#Sim 51 CCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTC 85 Matrix = Unknown Transitions / transversions = 2.40 (12/5) Gap_init rate = 0.05 (4 / 80), avg. gap size = 1.00 (4 / 4) 17 10.71 0.00 3.23 chrXqtel1M 247943 247974 (752026) (GCC)n#Simple_repeat 1 31 (0) m_b358s252i14 15012 chrXqtel1M 247943 GCCGCCGGCTCCCGCGGCCGCCGCCGCCGCCG 247974 - iv v (GCC)n#Simple 1 GCCGCC-GCCGCCGCCGCCGCCGCCGCCGCCG 31 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 12 22.37 6.38 0.00 chrXqtel1M 248196 248242 (751758) (CCGGAG)n#Simple_repeat 1 50 (0) m_b358s252i15 15013 chrXqtel1M 248196 CCCGAGCTGG-GCCTGAGCGGGAGCC-CCCCCGGAGCGGGACCCGG-GCC 248242 v i - v v -vvv v v - (CCGGAG)n#Sim 1 CCGGAGCCGGAGCCGGAGCCGGAGCCGGAGCCGGAGCCGGAGCCGGAGCC 50 Matrix = Unknown Transitions / transversions = 0.12 (1/8) Gap_init rate = 0.07 (3 / 46), avg. gap size = 1.00 (3 / 3) 421 30.28 6.28 4.27 chrXqtel1M 249009 249215 (750785) MIR#SINE/MIR 51 261 (1) m_b358s601i25 15014 chrXqtel1M 249009 GGATGGAACACTGGCCTTCAGGCACTTACCAGTT-------CTTAA-CAA 249050 v v iv i -- v v i i ------- ii- MIR#SINE/MIR 51 GGTTCGAATCCCGGC--TCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 98 chrXqtel1M 249051 GTCTCTTAGTCTTTCAGTTGCCTCTGTTTCCTCCTCTGTGACATGGGGAC 249100 iv ii i v - v v i v - MIR#SINE/MIR 99 GTTACTTAACCTCTCTGT-GCCTCAGTTTCCTCATCTGTAAAATGGGGA- 146 chrXqtel1M 249101 TGATAAAAACATTTGCCTCCAAGG---GTGGCAAGGATCTAATGAGGTGA 249147 i v ii ii i vv --- v ii iv v i MIR#SINE/MIR 147 TAATAATAGTACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAA 196 chrXqtel1M 249148 TATCTGCCAAGCG-TTAGCA-AGCTTCAGAACGCTGTTTATAAGTGCTGG 249195 iv iv - v - ivi v --- vvv vi i -- MIR#SINE/MIR 197 TACATGTAAAGCGCTTAGAACAGTGCCTG---GCACATAGTAAGCGCT-- 241 chrXqtel1M 249196 TGATGATTGTCAGTTACTGT 249215 ii i v i i i i MIR#SINE/MIR 242 CAATAAATGTTAGCTATTAT 261 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.11 CpG sites = 34, Kimura (unadjusted) = 39.81 Transitions / transversions = 1.31 (34/26) Gap_init rate = 0.07 (14 / 206), avg. gap size = 1.57 (22 / 14) 190 24.39 0.00 0.00 chrXqtel1M 249971 250011 (749989) MIRc#SINE/MIR 3 43 (225) m_b358s601i26 15015 chrXqtel1M 249971 AGGCAGAGTGGTATAGTGCATAGAGTCCTGGCCTTAAAGTC 250011 v ii v v iv v ii MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTC 43 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.76 CpG sites = 5, Kimura (unadjusted) = 29.76 Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 183 32.20 6.59 1.04 chrXqtel1M 250698 250788 (749212) MIRb#SINE/MIR 80 175 (93) m_b358s601i27 15015 chrXqtel1M 250698 CTTATCTACCAGGGAAACTTTAGGCAGATTCCTT---CTTTCTG--TCTC 250742 - v v v vi i i ii v --- i --i MIRb#SINE/MIR 80 CTTA-CTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTC 128 chrXqtel1M 250743 ATTTTTCCTATCCTTAAAATGGGGGT-GTATTGTCAGTCTTTTAGGG 250788 v i ii iv i -i v ii vii ivi MIRb#SINE/MIR 129 AGTTTCCTCATCTGTAAAATGGGGATAATAATACCTACCTCGCAGGG 175 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.29 CpG sites = 19, Kimura (unadjusted) = 44.39 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.04 (4 / 90), avg. gap size = 1.75 (7 / 4) 204 25.69 7.04 1.33 chrXqtel1M 250698 250768 (749232) MIR#SINE/MIR 73 147 (115) m_b358s601i28 15015 chrXqtel1M 250698 CTTATCTACCAGGGAAACTTTAGGCAGATTCCTT---CTTTCTGT--CTC 250742 - v v v vi i i ii v --- i -- MIR#SINE/MIR 73 CTTA-CTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTC 121 chrXqtel1M 250743 ATTTTTCCTATCCTTAAAATGGGGGT 250768 v i ii iv i MIR#SINE/MIR 122 AGTTTCCTCATCTGTAAAATGGGGAT 147 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.32 CpG sites = 11, Kimura (unadjusted) = 32.32 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.04 (3 / 70), avg. gap size = 2.00 (6 / 3) 205 16.84 22.39 2.50 chrXqtel1M 251632 251698 (748302) C MIRb#SINE/MIR (68) 200 121 m_b358s601i29 15016 chrXqtel1M 251632 TTGTCCCGTACTTGATCCTGAC-----CCTTG-GAGGTAGGTGTGATT-- 251673 i i i -- i v ----- i - i v -- C MIRb#SINE/MIR 200 TTATCTCAT--TTAATCCTCACAACAACCCTGCGAGGTAGGTATTATTAT 153 chrXqtel1M 251674 -------TTACAAATGAGGAGACTGAGGCACA 251698 ------- i i v C MIRb#SINE/MIR 152 CCCCATTTTACAGATGAGGAAACTGAGGCTCA 121 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 19.71 CpG sites = 8, Kimura (unadjusted) = 19.71 Transitions / transversions = 2.67 (8/3) Gap_init rate = 0.09 (6 / 66), avg. gap size = 2.83 (17 / 6) 15 5.48 0.00 0.00 chrXqtel1M 252741 252759 (747241) (G)n#Simple_repeat 1 19 (0) m_b358s252i16 15017 chrXqtel1M 252741 GGGGGGGGGGGGGCGGGGG 252759 v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGG 19 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 262 23.97 5.47 5.47 chrXqtel1M 259087 259214 (740786) MIR1_Amn#SINE/MIR 1 128 (102) m_b358s601i30 15018 chrXqtel1M 259087 TAGAAAGGAAGCTTGGG--GGTAGCCAGATGCTCTGGA--GGCAGCAGGG 259132 ii v iv v--i i vi - v -- v viv MIR1_Amn#SINE 1 TAGGGAGGCAGTGTGGTCTAGTGGATAGA-GCACTGGACTGGGACTCGGG 49 chrXqtel1M 259133 ---CCTGAGTTCAAATCCAGTCTCACTCTTCACACTTCGCAGTTGTGTGA 259179 --- i ? ? v ----i v - ?vv ? i ? MIR1_Amn#SINE 50 AGACCTGGGTTCNANTCCCG----GCTCTGC-CACTNGCCNGCTGNGTGA 94 chrXqtel1M 259180 CCCTGGGCAAGGCACTTAATCCCAATTGCCCCTCA 259214 i v ? i i -vi ?v MIR1_Amn#SINE 95 CCTTGGGCAAGTCACTTNACCTC-TCTGNGCCTCA 128 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.31 CpG sites = 14, Kimura (unadjusted) = 31.31 Transitions / transversions = 0.93 (14/15) Gap_init rate = 0.08 (10 / 127), avg. gap size = 1.40 (14 / 10) 332 22.71 0.00 7.53 chrXqtel1M 259115 259214 (740786) MIR#SINE/MIR 30 122 (140) m_b358s601i31 15018 chrXqtel1M 259115 GCTCTGGAGGCAGCAGGGCCTGAGTTCAAATCCAGTCTCACTCTTCACAC 259164 v - vv i i v ----i v - MIR#SINE/MIR 30 GCTCTGGAGCCAG-ACTGCCTGGGTTCGAATCCCG----GCTCTGC-CAC 73 chrXqtel1M 259165 TTCGCAGTTGTGTGACCCTGGGCAAGGCACTTAATCCCAATTGCCCCTCA 259214 vvi i i vi i i -vi iv MIR#SINE/MIR 74 TTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTC-TCTGTGCCTCA 122 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 25.69 CpG sites = 11, Kimura (unadjusted) = 27.14 Transitions / transversions = 1.10 (11/10) Gap_init rate = 0.07 (7 / 99), avg. gap size = 1.00 (7 / 7) 332 22.88 0.00 6.33 chrXqtel1M 259119 259202 (740798) MIRc#SINE/MIR 37 115 (153) m_b358s601i32 15018 chrXqtel1M 259119 TGGAGGCAGCAGGGCCTGAGTTCAAATCCAGTCTCACTCTTCACACTTCG 259168 v v i i i i i v ----i v - vv MIRc#SINE/MIR 37 TGGAGTCAGGAAGACCTGGGTTCGAGTCCCG----GCTCTGC-CACTTAC 81 chrXqtel1M 259169 CAGTTGTGTGACCCTGGGCAAGGCACTTAATCCC 259202 i i i v i i MIRc#SINE/MIR 82 TAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 25.98 CpG sites = 11, Kimura (unadjusted) = 27.75 Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.06 (5 / 83), avg. gap size = 1.00 (5 / 5) 362 29.91 4.24 0.82 chrXqtel1M 259285 259402 (740598) MIR#SINE/MIR 90 211 (51) m_b358s601i33 15018 chrXqtel1M 259285 CCTGGATAAGTCACTAAAG---TCTCCACCT--GTTTCCTCAACTATAAA 259329 i ii i v v--- vii -- v i MIR#SINE/MIR 90 CTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAA 139 chrXqtel1M 259330 ATGAGGATATTAAAAACTCCCAATGTCCCAGGGTTGCAGTGAGGGCTGAC 259379 i v v i- v v iv vi iv ii i v MIR#SINE/MIR 140 ATGGGGATAATAATAG-TACCTACCTCATAGGGTTGTTGTGAGGATTAAA 188 chrXqtel1M 259380 CAAGCTAACAGCTGTGAAGGGCT 259402 ii i i vv i v MIR#SINE/MIR 189 TGAGTTAATACATGTAAAGCGCT 211 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.16 CpG sites = 20, Kimura (unadjusted) = 39.16 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.03 (3 / 117), avg. gap size = 2.00 (6 / 3) 304 24.66 5.48 0.00 chrXqtel1M 260358 260430 (739570) L2b_3end#LINE/L2 379 455 (11) m_b359s601i4 15019 chrXqtel1M 260358 CTGTCTAACCCACCA----GCCTCCAGTGCTTAGCACAGTGCCTGGCACA 260403 viii i----ii i i i ? L2b_3end#LINE 379 CTGTCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACA 428 chrXqtel1M 260404 CAGTAGGGGGTTAGGCAGTGTTTCTTG 260430 v v i vv i i v L2b_3end#LINE 429 CAGTAGGCGCTCAGTAAATATTTGTTG 455 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.40 CpG sites = 12, Kimura (unadjusted) = 31.51 Transitions / transversions = 2.00 (12/6) Gap_init rate = 0.01 (1 / 72), avg. gap size = 4.00 (4 / 1) 270 27.94 0.00 0.00 chrXqtel1M 260374 260441 (739559) L2d2_3end#LINE/L2 488 555 (0) m_b359s601i5 15019 chrXqtel1M 260374 CCTCCAGTGCTTAGCACAGTGCCTGGCACACAGTAGGGGGTTAGGCAGTG 260423 iv i i v v v i ivv i i L2d2_3end#LIN 488 CCCACAGCGCCTAGCACAGTGCCTTGCACACAGTAGGCGCTCAATAAATA 537 chrXqtel1M 260424 TTTCTTGCCTTCTCTTGA 260441 v vi vvi L2d2_3end#LIN 538 TTTGTTGATTTGATTTGA 555 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.04 CpG sites = 9, Kimura (unadjusted) = 35.24 Transitions / transversions = 0.90 (9/10) Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0) 474 32.93 8.11 2.56 chrXqtel1M 261315 261610 (738390) C L2b_3end#LINE/L2 (6) 460 149 m_b359s601i6 15020 chrXqtel1M 261315 TCATCCTATTAGTATTTGTTAAGCACTTAATTTCATAGCAGGCCCTGTGT 261364 i v iv i ii i i i v v -i iv ? i C L2b_3end#LINE 460 TCATTCAACAAATATTTACTGAGCGCCTACTGT-GTGCCAGGCNCTGTGC 412 chrXqtel1M 261365 TAAATGCTGGGAGT------GTGAG-AAACCACAGCTAGTCC---CCCTC 261404 iii ii ------ i- iv v v?ii --- C L2b_3end#LINE 411 TAGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGCCCTC 362 chrXqtel1M 261405 GAAGGAGCTCACAGTAAGGTCGGGGAG-CCGACAAGCAGACAGCTAGGTA 261453 - v vvi v - v v i i? vi iv? C L2b_3end#LINE 361 -ACGGAGCTCACAGTCTAGTGGGGGAGACAGACATGTAANCAGACAATNA 313 chrXqtel1M 261454 CAAACAA-----ACAGGA-AAAATTGGAGAGAATCAGCAGAGGA----AG 261493 i v v -----i i- ii i i i ivi vi i----v C L2b_3end#LINE 312 TAACCCAGAGTGGCAGGGTAGGACTGGGGGGGCCCAGAGGAGGGCGCCTG 263 chrXqtel1M 261494 ACATTGATATTAAGAGTGAGTGGGAAGGATTCCCTCTAGAAGATGGGAT- 261542 -ii iiv vii i v -- i v ---i i v v i- C L2b_3end#LINE 262 AC-CCGGCCTGGGGGGTCA--GGGAGGGCTTCCC---GGAGGAGGTGACA 219 chrXqtel1M 261543 TTTGAGTTGGAACTTGAAGGA--AGCCGGGGAGGGCCCGTGGAGGAGATG 261590 i ii i -- iv i vv v vv i i C L2b_3end#LINE 218 TTTGAGCTGAGACCTGAAGGATGAGTAGGAGTTGGCCAGGCGAAGAGGTG 169 chrXqtel1M 261591 AGGGAGACCATTCCAGCCAG 261610 i i iv i v C L2b_3end#LINE 168 GGGAAGGGCGTTCCAGGCAG 149 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.44 CpG sites = 60, Kimura (unadjusted) = 46.53 Transitions / transversions = 1.71 (60/35) Gap_init rate = 0.06 (17 / 295), avg. gap size = 1.88 (32 / 17) 185 36.78 15.83 2.58 chrXqtel1M 261457 261696 (738304) C L2d_3end#LINE/L2 (206) 310 40 m_b359s601i7 15020 chrXqtel1M 261457 ACAAACAGGAAAAATTGGAGAGAATCAGCAGAGGAAGACATTGATAT--- 261503 i viv ivii iv iiiv vii i v iii i --- C L2d_3end#LINE 310 ACAGACTATAAGTGCTATAGGAGTTCAGAGAAGGGAGAGATCAGTGTGGG 261 chrXqtel1M 261504 TAAGAGTGAGTGGGAAGGATTCCCTCTAGAAGATGGGATTTTGAGTTGGA 261553 ivi ivii i i ii i v vv i i i - i i C L2d_3end#LINE 260 CTGGAGTGGTCAGGGAAGGCTTCGTGGAGGAGGTGGGACTT-GAGCTGGG 212 chrXqtel1M 261554 ACTTGAAGGAAGCCGGGGAGGGCCCG--TGGAG-GAGATGAGGGAGAC-- 261598 v ---i v iiii -- i - v i i v-- C L2d_3end#LINE 211 CCTTGAAGGA---TGGGTAGGATTTGGATAGAGAGAGAGGAAGGGGAAGG 165 chrXqtel1M 261599 -CATTCCAGCC---------------AGTGAAGATGCTGATG-------- 261624 - v --------------- ii ii v v -------- C L2d_3end#LINE 164 GCATTCCAGGCGGGGGGAACGGCGTGAGCAAAGGCGCAGAGGCGGGAATG 115 chrXqtel1M 261625 -----GATGTGTTTAAGGAACAGC-CAGAGACCCGCATCATTAGATTGAA 261668 ----- ii iii i i-v v v v i i vi i C L2d_3end#LINE 114 CGCAAGGCGTGTTCGGGGGACAGTGAAGAGACCGGCCTGACTGGAGCGGA 65 chrXqtel1M 261669 GAGTACCTGTTTATGGGAAACAGTAGGA 261696 i v v i--- i ii i C L2d_3end#LINE 64 GGGTTCGTGC---TGGGGAGTAGTGGGA 40 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 51.49 CpG sites = 60, Kimura (unadjusted) = 55.57 Transitions / transversions = 2.31 (60/26) Gap_init rate = 0.06 (15 / 239), avg. gap size = 3.00 (45 / 15) 322 39.64 1.38 6.25 chrXqtel1M 262342 262559 (737441) L3#LINE/CR1 3034 3241 (858) m_b359s601i8 15021 chrXqtel1M 262342 TATAGTGGAGAGGATCGAGGGCT---CAGATGACCAGCCTCAGTAGAGTT 262388 i vii v ivivi ---iii i i vv i -- i v L3#LINE/CR1 3034 TACAGTTAGGTGGATTCGTAGCTGGTTGAACGACTATACCCA--AAAGGT 3081 chrXqtel1M 262389 GCTTGGTAGCAGCCCCATGTCAACATGATGAGAGGAGGTGTCCCCAGTGA 262438 i viv iii vi v v iv i ----- i i i L3#LINE/CR1 3082 GTTGATTAATGGATCGATGTCAACCTGGAGGGAGG-----TCTCTAGTGG 3126 chrXqtel1M 262439 AGTCGGACCCCAGGTATCCACACCGGGGGCCAGGCTGCTGTTTCACATTC 262488 --- vi v vv iii- vv v v v -- iv i L3#LINE/CR1 3127 ---CGTGCCACAGGGCTCTGT-CCTTGGCCCTGTC--CTGTTCAACATTT 3170 chrXqtel1M 262489 ACATCCCTAACTCGGATACAGGTATAAGCAGTCTGTTCGTCAGATGTGCA 262538 vi vv i i iv ii iivi iv i ii i v L3#LINE/CR1 3171 TTATCAATGACTTGGATGAAGACATAGAAGGCATGCTTATCAAATTTGCA 3220 chrXqtel1M 262539 GAGGATACCCAGCTAGAATGG 262559 v i vv i i v L3#LINE/CR1 3221 GATGACACAAAGCTGGGAGGG 3241 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 56.75 CpG sites = 47, Kimura (unadjusted) = 59.04 Transitions / transversions = 1.38 (47/34) Gap_init rate = 0.06 (14 / 217), avg. gap size = 1.14 (16 / 14) 230 35.03 0.00 3.00 chrXqtel1M 262988 263090 (736910) L3#LINE/CR1 3690 3789 (310) m_b359s601i9 15021 chrXqtel1M 262988 CCGAGTCATCTGGGGCCACATTGAGGGAAGTGGGATTATCTAGTCTGGAG 263037 iv v i vvvvi i v iv i i i L3#LINE/CR1 3690 CCATGTCATATGAGGAACGGTTGAAGGAACTGGGGATGTTTAGCCTGGAG 3739 chrXqtel1M 263038 AAGAAAAAAGACTCAGGAGTGTCATGGGGACTGAACTGAGGTGTCTAGAA 263087 -- i i ii v v ivii vvi v ii i i - L3#LINE/CR1 3740 AAG--AGAAGACTTAGAGGAGACATGATAGCTGTCTTCAAATATTT-GAA 3786 chrXqtel1M 263088 GAG 263090 i L3#LINE/CR1 3787 GGG 3789 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 49.26 CpG sites = 21, Kimura (unadjusted) = 49.26 Transitions / transversions = 1.50 (21/14) Gap_init rate = 0.03 (3 / 102), avg. gap size = 1.00 (3 / 3) 261 28.57 8.79 0.00 chrXqtel1M 263137 263227 (736773) L3#LINE/CR1 3998 4096 (3) m_b359s601i10 15021 chrXqtel1M 263137 CACTTGACCTGGTTGTCGTAAA--GATTTCCTTTGGTGGATG------TG 263178 v vv v i i -- iv viiv ------ L3#LINE/CR1 3998 CACTTGTCAGGGATGTTGTAGAAGGGATTCCTGCATTGGATGGGAGGTTG 4047 chrXqtel1M 263179 GCCTACATGGCCACACAGACCCCTTCCAACTTTCAAATCCTGGGATTTT 263227 v v i v vv ii i v i i v i L3#LINE/CR1 4048 GACTAGATGACCTCTAAGGTCCCTTCCAACTCTGAGATTCTGTGATTCT 4096 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.22 CpG sites = 12, Kimura (unadjusted) = 36.22 Transitions / transversions = 0.86 (12/14) Gap_init rate = 0.02 (2 / 90), avg. gap size = 4.00 (8 / 2) 310 35.11 0.00 4.27 chrXqtel1M 263882 264003 (735997) C MIRb#SINE/MIR (150) 118 2 m_b359s601i12 15022 chrXqtel1M 263882 GGGGTTAAGTGACTTGGCCTGAGTCCCATGACTAGTGAAAGTATCTGAGG 263931 i i v vii v iii -- iv v v C MIRb#SINE/MIR 118 GAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGT--AAGTGGCAGAGC 71 chrXqtel1M 263932 TTACATTTGAACTTGGGTCCTCCTGAGTGTAGGGCCAGTGCTCTAGCTCC 263981 iviv i iii ivi v vi ii v vv iv C MIRb#SINE/MIR 70 CGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCAC 21 chrXqtel1M 263982 TGTGCCACCCAACTGTTCCCCT 264003 ii ---i ii i C MIRb#SINE/MIR 20 TGCACCAC---GCTGCCCCTCT 2 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.79 CpG sites = 26, Kimura (unadjusted) = 49.91 Transitions / transversions = 1.73 (26/15) Gap_init rate = 0.04 (5 / 121), avg. gap size = 1.00 (5 / 5) 352 32.09 0.00 1.89 chrXqtel1M 263882 263989 (736011) C MIRc#SINE/MIR (153) 115 10 m_b359s601i11 15022 chrXqtel1M 263882 GGGGTTAAGTGACTTGGCCTGAGTCCCATGACTAGTGAAAGTATCTGAGG 263931 i v vii v iii -- iv v v C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGT--AAGTGGCAGAGC 68 chrXqtel1M 263932 TTACATTTGAACTTGGGTCCTCCTGAGTGTAGGGCCAGTGCTCTAGCTCC 263981 iviv i i iii i v vi i v vv iv C MIRc#SINE/MIR 67 CGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCAC 18 chrXqtel1M 263982 TGTGCCAC 263989 ii C MIRc#SINE/MIR 17 TGCACCAC 10 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.93 CpG sites = 20, Kimura (unadjusted) = 43.28 Transitions / transversions = 1.43 (20/14) Gap_init rate = 0.02 (2 / 107), avg. gap size = 1.00 (2 / 2) 284 24.05 6.33 0.00 chrXqtel1M 264385 264463 (735537) C L2c_3end#LINE/L2 (227) 251 168 m_b359s601i13 15023 chrXqtel1M 264385 GTCAGG-AAGGCTTCCCAAAGAAGATGGCATCTGACTTGTCTCTCAGAAG 264433 - ii i i i vi vv? iii i C L2c_3end#LINE 251 GTCAGGGAAGGCTTCCCGGAGGAGGTGACATCTGAGCTGAGNCTTGAAGG 202 chrXqtel1M 264434 ATGGGGAGGAAT---CCA-GTGGACAGAGGGAGG 264463 i v i --- - vi i C L2c_3end#LINE 201 ATGAGTAGGAGTTAGCCAGGTGGAAGGAGGGGGG 168 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.97 CpG sites = 14, Kimura (unadjusted) = 30.93 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.04 (3 / 78), avg. gap size = 1.67 (5 / 3) 217 32.47 1.28 1.28 chrXqtel1M 265635 265712 (734288) L3#LINE/CR1 3914 3991 (108) m_b359s601i14 15024 chrXqtel1M 265635 AGAGCTGAGCAAGGACGGAATGAGCCTTCCTTGA-AAGTAGGGGCTTCCT 265683 vv ii i i - v i ?- i v ivi i L3#LINE/CR1 3914 AGAGCTGTCCAAAAATGGAATGGG-CTGCCTCGNGAGGTAGTGAGCTCCC 3962 chrXqtel1M 265684 CCTTCCAAGAGATTTCCAAACAGTGGTTG 265712 v iv vi i v i i v i L3#LINE/CR1 3963 CGTCACTGGAGGTGTTCAAGCAGAGGCTG 3991 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.56 CpG sites = 15, Kimura (unadjusted) = 45.00 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.03 (2 / 77), avg. gap size = 1.00 (2 / 2) 487 28.76 11.11 0.00 chrXqtel1M 265950 266102 (733898) C MIR#SINE/MIR (9) 253 84 m_b359s601i15 15025 chrXqtel1M 265950 TAGCGTGCATTGATAGTCTACTATGTGCCAAACATTGTGCCATGGACTTT 265999 i i vi vv ii ii i v i v vi C MIR#SINE/MIR 253 TAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGCGCTTT 204 chrXqtel1M 266000 ACAT----------ATTTGAGACTCACAAC---TTTGGGAGGTGGGAGCA 266036 ---------- i vv ---ii iv i vi v C MIR#SINE/MIR 203 ACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGGTAGGTACT 154 chrXqtel1M 266037 ATTGTCATCTCCATTTGACAGTTGGGAAGCCTGAAAC----AGAAGTGAA 266082 i i i v v i i iv ii ---- i v C MIR#SINE/MIR 153 ATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAA 104 chrXqtel1M 266083 GTGACTTACCTAAGGTCTCA 266102 i i i v C MIR#SINE/MIR 103 GTAACTTGCCCAAGGTCACA 84 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.57 CpG sites = 28, Kimura (unadjusted) = 37.67 Transitions / transversions = 1.75 (28/16) Gap_init rate = 0.02 (3 / 152), avg. gap size = 5.67 (17 / 3) 12 11.26 7.14 4.65 chrXqtel1M 267814 267855 (732145) (CTCTTGCT)n#Simple_repeat 1 43 (0) m_b359s252i1 15026 chrXqtel1M 267814 CTCTTGCTCTCTCCTGCTCTC-GGCT-TCTTGC-CTCCTCATCTC 267855 -- -v - - i vv (CTCTTGCT)n#S 1 CTCTTGCTCTCT--TGCTCTCTTGCTCTCTTGCTCTCTTGCTCTC 43 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.12 (5 / 41), avg. gap size = 1.00 (5 / 5) 379 27.59 5.36 2.91 chrXqtel1M 267910 268069 (731931) C MIRc#SINE/MIR (4) 264 101 m_b359s601i16 15027 chrXqtel1M 267910 ACAAGAA-TCCATAC-TTTG-GTAGCACTTTTGAGACTCATAAAA-GCAT 267955 i v -? v - -i vv -i i i i- v C MIRc#SINE/MIR 264 ATAATAACNCCTTACATTTGTATAGCACTTTACAG-TTTACAAAGCGCTT 216 chrXqtel1M 267956 ATAGTGCAGACATGATTTCATTTGATTCTTAGAACAAGTCTCTGAGGTAA 268005 vi --- v v i i i v vi v i C MIRc#SINE/MIR 215 TCA---CATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAG 169 chrXqtel1M 268006 GCA---CTGTTATGATCATCTCTATTCTCTAGAGGA-GAAATTGCAGCCT 268051 --- v v v i i i i vi v - i vi ii C MIRc#SINE/MIR 168 GCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTC 119 chrXqtel1M 268052 CGA-AGGTTGTGGGGACTT 268069 v - i-i v C MIRc#SINE/MIR 118 AGAGAGGTTA-AGTGACTT 101 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.81 CpG sites = 26, Kimura (unadjusted) = 35.81 Transitions / transversions = 1.21 (23/19) Gap_init rate = 0.08 (12 / 159), avg. gap size = 1.17 (14 / 12) 43 0.00 0.00 0.00 chrXqtel1M 268070 268109 (731891) (GCCCAGCA)n#Simple_repeat 1 40 (0) c_b359s251i0 15028 chrXqtel1M 268070 GCCCAGCAGCCCAGCAGCCCAGCAGCCCAGCAGCCCAGCA 268109 (GCCCAGCA)n#S 1 GCCCAGCAGCCCAGCAGCCCAGCAGCCCAGCAGCCCAGCA 40 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 21 7.51 7.14 0.00 chrXqtel1M 269014 269055 (730945) (GACGAT)n#Simple_repeat 1 45 (0) m_b359s252i2 15029 chrXqtel1M 269014 GAGGAGGACGATGACGATGATGATGAC---GACGATGACGATGAC 269055 v v i --- (GACGAT)n#Sim 1 GACGATGACGATGACGATGACGATGACGATGACGATGACGATGAC 45 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.02 (1 / 41), avg. gap size = 3.00 (3 / 1) 183 35.98 1.09 3.33 chrXqtel1M 270215 270306 (729694) C L3#LINE/CR1 (20) 4079 3990 m_b359s601i17 15030 chrXqtel1M 270215 GAGTTAGAGGCTAA-TTAGAGCCAGTGCTCTGGCACAGCCTGACCTTGAC 270263 i i vv v- --- vv i iv i vv v iv v C L3#LINE/CR1 4079 GAGTTGGAAGGGACCTTAGAG---GTCATCTAGTCCAACCTCCCATCCAA 4033 chrXqtel1M 270264 TTGAAGCATTTCCTCTACGATATTCCCAACTAATTGTCATCCA 270306 vv i v ii i i i i ii v i v C L3#LINE/CR1 4032 TGCAGGAATCCCTTCTACAACATCCCTGACAAGTGGTCATCCA 3990 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 49.89 CpG sites = 16, Kimura (unadjusted) = 49.89 Transitions / transversions = 1.00 (16/16) Gap_init rate = 0.04 (4 / 91), avg. gap size = 1.00 (4 / 4) 367 25.00 0.00 1.09 chrXqtel1M 270954 271046 (728954) C Charlie4a#DNA/hAT-Charlie (382) 126 35 m_b359s502i0 15031 chrXqtel1M 270954 TTCAAAACTGACAGGAAGTGTTAACTTTCTGCTAGGAGGGAATGAAAAGA 271003 v i - i i v v i ii vv i v C Charlie4a#DNA 126 TTCATAATTGA-AGGAAATGCTAAATTTCAGTTAGAGGTTAGTGAAAATA 78 chrXqtel1M 271004 AAGATGTAATCTTTTCTCCAAGTCCAGTTCACAGGCCTCCTGA 271046 i ii v vi v i i i C Charlie4a#DNA 77 AAGATGTAATTTTTTTCCCCATCCAAGTTCACGGACCCCCTGA 35 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 29.56 CpG sites = 14, Kimura (unadjusted) = 31.17 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.01 (1 / 92), avg. gap size = 1.00 (1 / 1) 252 34.46 7.14 2.89 chrXqtel1M 271226 271491 (728509) C L2b_3end#LINE/L2 (2) 464 188 m_b359s601i18 15032 chrXqtel1M 271226 TCAGTCAAGCCAGTACACACTTACTAAATGCCTATTATATTCCAGACACT 271275 v -vi ii v i i i ii i i i v i ? C L2b_3end#LINE 464 TCATTCA-TTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCT 416 chrXqtel1M 271276 GTACCAAAGGCAAGGGATACAAAGGCAAA-AAAAAAAAAACAAGC----A 271320 i i iiv vi iv ii - i v i v? iiv ----v C L2b_3end#LINE 415 GTGCTAGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTGC 366 chrXqtel1M 271321 CCTCGAAGGGTGCCCAGTTTAGCGGGGGATGCTG-CATACAAACT-ACAA 271368 ivi i iv v i i vi v - ii ? v- C L2b_3end#LINE 365 CCTCACGGAGCTCACAGTCTAGTGGGGGAGACAGACATGTAANCAGACAA 316 chrXqtel1M 271369 TGGTCAAACAGGTT--CTGGCCAGGACAGCGTGGG-CGAGAGAGTAGAGG 271415 ?i v vv iv -- v vi v v v - v ---- C L2b_3end#LINE 315 TNATAACCCAGAGTGGCAGGGTAGGACTGGGGGGGCCCAGAG----GAGG 270 chrXqtel1M 271416 GCAGCC--ACTAAGATTAAGGAGACCTGGGAAGAGAAGCCAGGATGGAGT 271463 - -- ivi vi ii i v --i i i vvv v v ii C L2b_3end#LINE 269 GC-GCCTGACCCGGCCTGGGGGGTC--AGGGAGGGCTTCCCGGAGGAGGT 223 chrXqtel1M 271464 GA----TGAGGGGGGA---GAAGCTTGCCTAGGAG 271491 ---- vv i --- vv vv C L2b_3end#LINE 222 GACATTTGAGCTGAGACCTGAAGGATGAGTAGGAG 188 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.52 CpG sites = 48, Kimura (unadjusted) = 48.50 Transitions / transversions = 1.17 (48/41) Gap_init rate = 0.06 (17 / 265), avg. gap size = 1.59 (27 / 17) 446 25.99 5.83 8.46 chrXqtel1M 271647 271852 (728148) C MIRb#SINE/MIR (55) 213 13 m_b359s601i19 15033 chrXqtel1M 271647 CGTTTGAC-TCCATGACCCCATTTAGGATGTTCTTGGCAGAGATACTG-G 271694 i v - v v i i i----- i vi ivi iv - C MIRb#SINE/MIR 213 CGCTTTACATGCATTATCTCATTTAA-----TCCTCACAACAACCCTGCG 169 chrXqtel1M 271695 AGGGGTTTGCCATTGCCTTCTCCAGCTCCTTTTACATATGAGGAAACTGA 271744 --- v vi iiiv i ----- v C MIRb#SINE/MIR 168 AGG---TAGGTATTATTATCCCCA-----TTTTACAGATGAGGAAACTGA 127 chrXqtel1M 271745 GGTAGACAG-GGTTAAATGACATGCCCAGGGTCACACAGCTAGGCAGTGT 271793 ivv v - i i v i vv v C MIRb#SINE/MIR 126 GGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGG 77 chrXqtel1M 271794 CTGAGACCAGAT--GA------GTCTCCCTG-CTTTCAGGCCCAGTGGTG 271834 v v vi -- ------ vi - iiv i ---- C MIRb#SINE/MIR 76 CAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCC----GTG 31 chrXqtel1M 271835 CTCTAACCACTGCAGTAC 271852 vv vi C MIRb#SINE/MIR 30 CTCTTTCCACTGCACCAC 13 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.09 CpG sites = 24, Kimura (unadjusted) = 32.09 Transitions / transversions = 0.96 (24/25) Gap_init rate = 0.11 (23 / 205), avg. gap size = 1.26 (29 / 23) 453 24.38 8.74 5.85 chrXqtel1M 271680 271862 (728138) C MIR3#SINE/MIR (19) 189 2 m_b359s601i20 15033 chrXqtel1M 271680 TGGCAGAGATACTGGAGGGG---TTTGCCATTGCCTTCTCCAGCTCC--- 271723 v --- i --- v vv iii vv i i --- C MIR3#SINE/MIR 189 TGTCAGAG---CTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTC 143 chrXqtel1M 271724 -TTTTACATATGAGGAAACTGAGGTAGACAG-GGTTAAATGACATGCCCA 271771 - v ivv v - v i v C MIR3#SINE/MIR 142 ATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCA 93 chrXqtel1M 271772 GGGTCACACAGCTAGGCAGTGTCTGA-----GACCAGA---TGAGTCTCC 271813 i ? vi v v ----- i ---iii C MIR3#SINE/MIR 92 AGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGTCTCC 43 chrXqtel1M 271814 CTGCTTTCAGGCCCAGTGGTGCTCTAACCACTGCAGTACCACCTTGTCA 271862 ivi ii v ----- vv ii - -- ii i C MIR3#SINE/MIR 42 TGACTCCCAGTCC-----GTGCTCTCTCTGCT-CAG--CCACTCTGCCA 2 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.19 CpG sites = 23, Kimura (unadjusted) = 30.19 Transitions / transversions = 1.21 (23/19) Gap_init rate = 0.09 (17 / 182), avg. gap size = 1.59 (27 / 17) 497 21.30 6.34 4.14 chrXqtel1M 271720 271861 (728139) C MIRc#SINE/MIR (120) 148 4 m_b359s601i21 15033 chrXqtel1M 271720 CTCCTTTTACATATGAGGAAACTGAGGTAGACAG-GGTTAAATGACATGC 271768 i v v ivv v - i v C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chrXqtel1M 271769 CCAGGGTCACACAGCTAGGCAGTGTCTGAGACCAGA--TGA------GTC 271810 i vv v v v vi --i ------ C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTC 49 chrXqtel1M 271811 TCCCTGCTTTCAGGCCCAGTGGTGCTCTAACCACTGCAGTACCACCTTGT 271860 i vi i i i --- vv --- vi i C MIRc#SINE/MIR 48 TTCCTGACTCCAAGTCCA---GTGCTCTTTCCACTGC---ACCACACTGC 5 chrXqtel1M 271861 C 271861 C MIRc#SINE/MIR 4 C 4 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 24.23 CpG sites = 13, Kimura (unadjusted) = 25.17 Transitions / transversions = 0.81 (13/16) Gap_init rate = 0.06 (9 / 141), avg. gap size = 1.67 (15 / 9) 207 35.35 1.01 0.00 chrXqtel1M 272031 272129 (727871) L2d2_3end#LINE/L2 1 100 (455) m_b359s601i22 15034 chrXqtel1M 272031 CTCCACAAGCTGCTTCCCACTGGCTTATCCAGCCTCCTCTTAGGGTATTG 272080 i v vii v iv? i v iv ivviv v L2d2_3end#LIN 1 CTCCACGATCTGGCCCCAACCTNCCTTTCCAGCCTTATCTCCCACTATTC 50 chrXqtel1M 272081 CTCCTC-TGCACTCTGTGCTTGAGCCAAATGTATGTACTCTCCATCCCCC 272129 i i? -i v i vi iv ivvi v v ii L2d2_3end#LIN 51 CCCTNCACGAACCCTCCGCTCCAGCCAAACTGGTCTACTCACTGTCCCCC 100 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.53 CpG sites = 18, Kimura (unadjusted) = 50.32 Transitions / transversions = 1.06 (18/17) Gap_init rate = 0.01 (1 / 98), avg. gap size = 1.00 (1 / 1) 17 27.35 4.29 0.00 chrXqtel1M 272425 272494 (727506) (CCCTGT)n#Simple_repeat 1 73 (0) m_b359s252i4 15035 chrXqtel1M 272425 CCCTGTCCCTATCTGTCTCCGTTTCCCTGTCTATTTCCC--TCTCTGTTC 272472 i iv v v v iv v -- i i (CCCTGT)n#Sim 1 CCCTGTCCCTGTCCCTGTCCCTGTCCCTGTCCCTGTCCCTGTCCCTGTCC 50 chrXqtel1M 272473 C-ATCCATGTCCATGTGTCTGTC 272494 -i v v vi (CCCTGT)n#Sim 51 CTGTCCCTGTCCCTGTCCCTGTC 73 Matrix = Unknown Transitions / transversions = 0.78 (7/9) Gap_init rate = 0.03 (2 / 69), avg. gap size = 1.50 (3 / 2) 485 26.54 1.39 5.80 chrXqtel1M 273180 273323 (726677) C MIRc#SINE/MIR (120) 148 11 m_b359s601i23 15036 chrXqtel1M 273180 CTCGTGTGATAGATAGGGAAACTGAGGCA-AACAAGGTTAAGTGACATAT 273228 i i v v i ii v- ivi v ii C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chrXqtel1M 273229 CCAGGATCTCACAGGTAGGAAGTGTCAGAGCCTGGACTTGAACTGGGTAG 273278 i i v v v v v i i---i C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACC---CAG 52 chrXqtel1M 273279 ATGAGTCTTCCTGGCCCCAGGCTCCCATG-GCCCTCTATTACACTA 273323 ---- i i i - vi -v ii i i i i C MIRc#SINE/MIR 51 ----GTCTTCCTGACTCCAAG-TCCAGTGCTCTTTCCACTGCACCA 11 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.78 CpG sites = 24, Kimura (unadjusted) = 33.95 Transitions / transversions = 2.00 (24/12) Gap_init rate = 0.07 (10 / 143), avg. gap size = 1.00 (10 / 10) 23 17.59 5.63 2.74 chrXqtel1M 274952 275022 (724978) (AAGA)n#Simple_repeat 1 73 (0) m_b359s252i5 15037 chrXqtel1M 274952 AAGAAA-AAAG-AAGGAAGGGAGGGAGGGAGAGAGGAAGGAAAGAAAGAA 274999 - - i ii ii ii - i i (AAGA)n#Simpl 1 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA-AAGAAAGAAAGAAAGAA 49 chrXqtel1M 275000 AG-AA-AAAGAAAGGAAAGAAAAAA 275022 - - - i (AAGA)n#Simpl 50 AGAAAGAAAGAAA-GAAAGAAAGAA 73 Matrix = Unknown Transitions / transversions = 1.00 (10/0) Gap_init rate = 0.09 (6 / 70), avg. gap size = 1.00 (6 / 6) 35 0.00 0.00 0.00 chrXqtel1M 275586 275618 (724382) (T)n#Simple_repeat 1 33 (0) c_b359s251i1 15038 chrXqtel1M 275586 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 275618 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 33 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 43 0.00 0.00 0.00 chrXqtel1M 276066 276102 (723898) (TC)n#Simple_repeat 1 37 (0) c_b359s251i2 15039 chrXqtel1M 276066 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 276102 (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 37 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 14 16.62 2.27 4.65 chrXqtel1M 276241 276284 (723716) (TTTCT)n#Simple_repeat 1 43 (0) m_b359s252i6 15040 chrXqtel1M 276241 TTTCTTTT-TGTTCTTTTCTCTTTGATTTTCCTTTGGTTCCTTTT 276284 - v - -v i vv i (TTTCT)n#Simp 1 TTTCTTTTCTTTTCTTTTCT-TTT-CTTTTCTTTTCTTTTCTTTT 43 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.07 (3 / 43), avg. gap size = 1.00 (3 / 3) 535 22.09 0.00 2.60 chrXqtel1M 276583 276740 (723260) L1ME3G_3end#LINE/L1 38 191 (733) m_b359s551i0 15041 chrXqtel1M 276583 ATAAGAATTCAAGCCATCTTCCAATTGACAAATGGTCAAAGGATATGAAT 276632 --v v v -- v v v i L1ME3G_3end#L 38 ATAAGAA--AAAGACAAC--CCAATAGAAAAATGGGCAAAGGATATGAAC 83 chrXqtel1M 276633 AGGTAATTTTCCGATGAAGAAATTGAAACTATTTCTAGCCATATGGAAAG 276682 i iv v v i vv iviiivv iv i L1ME3G_3end#L 84 AGGCAATTCACAGAAGAGGAAATACAAATGGCCAATAAACATATGAAAAG 133 chrXqtel1M 276683 ATGCTCCAAGTCACTATTACTCAGAGAAATGCAAATTAAGACAACTCTGA 276732 v vv v v i i vv L1ME3G_3end#L 134 ATGCTCAACCTCACTAGTAATCAGGGAAATGCAAATTAAAACAACAATGA 183 chrXqtel1M 276733 GATACCAT 276740 L1ME3G_3end#L 184 GATACCAT 191 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 26.15 CpG sites = 12, Kimura (unadjusted) = 26.15 Transitions / transversions = 0.55 (12/22) Gap_init rate = 0.03 (4 / 157), avg. gap size = 1.00 (4 / 4) 302 31.69 13.49 1.06 chrXqtel1M 276964 277215 (722785) C L2#LINE/L2 (1585) 1497 1215 m_b359s601i24 15042 chrXqtel1M 276964 AAACAAAGTCCTCATCTGAGAGGGAGGT-----GGGGTCCTGTGGGAGGC 277008 i i v v v v----- i vvv v i C L2#LINE/L2 1497 AAGCAAGGTCATCAGCTGAGAGTGAGGATAGGGGAGGAGGTGTTGGAGGT 1448 chrXqtel1M 277009 TTGTGGAGAGAGGA-----TTTGAGGTAGCC---------AGTACG---G 277041 v ----- v ii i --------- iv --- C L2#LINE/L2 1447 TTGAGGAGAGAGGAGAAGGTGTGAAATAGTCGTCTAGGAGAGTGGGAGAG 1398 chrXqtel1M 277042 TGAATAGCATAG---AATTTATGAGGA-AGCCTTGCTGCAGTGAGGACCC 277087 i vv --- v vv ? -v vv v v i i C L2#LINE/L2 1397 TGAATGGACTAGGGAAATGTAGTANGATTGCCGGGCAGCATTAAGGGCCC 1348 chrXqtel1M 277088 A-TTGAGATTAAATACAAATTGGTGTAAGTTGGGTCCCTCTCAGCTCAGT 277136 - i -?i ivvv vii v iv i -v vv vii C L2#LINE/L2 1347 ACTTGAGGTT-NGTGGTCATGAATTTAAAGTGAG-ACCAGTCAGCATGGT 1300 chrXqtel1M 277137 TTCATGACTTTCTCCAGCTCCCTTCAACAGGTAGGATG-------GAAAG 277179 vii vi iv v i v v?v i ------- i iv C L2#LINE/L2 1299 TGTGTGTTTTTCTCCAGCCACGTTCAGCTGCNCGGGTGCAGGCGCGGAGT 1250 chrXqtel1M 277180 AGGCCAACCGGTAAGTATAATGAAGGGTTGGGGTCT 277215 vi vv v iii v i-v ? i C L2#LINE/L2 1249 AGGCGGAGAGTTGGATTTAAC-CAGGGTTGNGGTTT 1215 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.37 CpG sites = 34, Kimura (unadjusted) = 42.37 Transitions / transversions = 0.76 (34/45) Gap_init rate = 0.04 (11 / 251), avg. gap size = 3.36 (37 / 11) 255 34.45 5.71 10.17 chrXqtel1M 277741 278160 (721840) C L2#LINE/L2 (1988) 1094 692 m_b359s601i25 15042 chrXqtel1M 277741 GGGGCTGAGAGTCAGGGGGAAG-TACTGAGGGCAGGGGGACTCAAGGTTG 277789 v i v v ii - iv ii iv iv - i vi i- C L2#LINE/L2 1094 GGGGGTGAGGGACAGTGAAAAGGTGGTAGGATCAATGG-ATTGGAGGTC- 1047 chrXqtel1M 277790 GCCTGTGCCAAGGCC--AGA---GTCGGATTAGGAGTAGTAAAGCTCAGG 277834 - v ---i i -- --- i v v i v i ---i i C L2#LINE/L2 1046 -CCGGTG---GGGTCGAAGAATTGTTGGAGTCGGGGTACTAGAG---GGA 1004 chrXqtel1M 277835 GCGACATGGAATGAGAAAAGCTTATGA--AATGAA-GGAATTCCAGAGAT 277881 i vv v v ii v vi i-- iv i- i v iv i C L2#LINE/L2 1003 GTGAGCTGGAAAGATAGGAGGTGGTGGTCAGAGAGTGGGATGCTTGAAAT 954 chrXqtel1M 277882 CGCAAGCATGGAAAGGCAACACTTGTGGGT---------------GATAT 277916 i vi vi ii ivi v i v --------------- i C L2#LINE/L2 953 TGAGATTATGGAGGGGTTGCAGTTATTGGTAATGACAAGGTCTAGGGTAT 904 chrXqtel1M 277917 GACCATCCCGGGGTGATTGAGACAAGGTAGAGGAGGAGGGGGAGCTCACA 277966 v-- i v - vii - v ivi v iv C L2#LINE/L2 903 GACCATG--GGAGTGAGTG-GCTGAGGTAG-GGTGGAGGACAAGATCATT 858 chrXqtel1M 277967 GGAAGCCAGGAAGTCAACGAACTGGAAGGTAAGGGTCTTTGTGAGCACAT 278016 i vv i v ii iv v v vii vv C L2#LINE/L2 857 GGAGGAGAGGAGGTCAAGGAACTGAGAGGCCAGGGTATTGGAAGGATCAT 808 chrXqtel1M 278017 CCACATGCAACACTGAAATCAATTGGGCCATAAATGTGAACAAGAAGTCG 278066 i i -i i i ------ vi vvvi - i -- C L2#LINE/L2 807 CTACGTG-GATATTGAAATCA------CCAAGAATTATGAC-AGGAGT-- 768 chrXqtel1M 278067 CCCAGTATGAGGACAGGAGATGGTGGAGAGGGACGCTGAGGCAGATACCG 278116 --- i ------------ -i v iv v ivi ii C L2#LINE/L2 767 ---AGTGT------------TGG-AGAGAGTGACAGTGAGCCAGGAGCTA 734 chrXqtel1M 278117 AACTCCTTGAGAAAGGGGGGAGATTGGGAGCTAATGGTCATTAG 278160 v i ii i v i i -- v v iiiv iv C L2#LINE/L2 733 AAATCTTCAAGGAATGAGGGGGA--GTGACCCGGAGGTCGGTAG 692 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.91 CpG sites = 75, Kimura (unadjusted) = 47.49 Transitions / transversions = 1.36 (75/55) Gap_init rate = 0.11 (47 / 419), avg. gap size = 1.38 (65 / 47) 314 25.00 0.00 0.00 chrXqtel1M 278448 278523 (721477) L2#LINE/L2 2815 2890 (192) m_b359s601i26 15043 chrXqtel1M 278448 AGTCCTTTCATGTCATTCCCCTGCTCAGAAAGCTCTCATGGCTTCCTATT 278497 vvv i i i vv iv i i L2#LINE/L2 2815 AGTCAGATCATGTCACTCCTCTGCTCAAAACCCTCCAATGGCTTCCCATC 2864 chrXqtel1M 278498 TCAAGCAGAATCAAATCCAAAATCTT 278523 vv i v v i i L2#LINE/L2 2865 TCACTCAGAGTAAAAGCCAAAGTCCT 2890 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.61 CpG sites = 9, Kimura (unadjusted) = 30.61 Transitions / transversions = 0.90 (9/10) Gap_init rate = 0.00 (0 / 75), avg. gap size = 0.0 (0 / 0) 194 35.29 3.53 0.00 chrXqtel1M 278456 278540 (721460) AmnL2-1#LINE/L2 2147 2234 (379) m_b359s601i27 15043 chrXqtel1M 278456 CATGTCATTCCCCTGCTCAGAAAGCTCTCATGGCTTCCTATTTCAAGCAG 278505 ii ii v v i v i ivv i i ivvvv AmnL2-1#LINE/ 2147 CACATCACCCCCATCCTCAAACAACTCCACTGGCTCCCCATTCATTTCAG 2196 chrXqtel1M 278506 AATCAAATCCAAAAT---CTTGCGTGTACTTGTCACCC 278540 i v i i --- v v vi ivv AmnL2-1#LINE/ 2197 GATCCAGTTCAAAATTGCCTTCCTTGTTTTTAAAACCC 2234 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 48.57 CpG sites = 15, Kimura (unadjusted) = 48.57 Transitions / transversions = 1.00 (15/15) Gap_init rate = 0.01 (1 / 84), avg. gap size = 3.00 (3 / 1) 113 15.00 1.75 2.64 chrXqtel1M 280083 280311 (719689) (GGA)n#Simple_repeat 1 227 (0) m_b359s252i7 15044 chrXqtel1M 280083 GGGGGAGGGGGAGG-GGAGGAGGAGGAGGAGGAGGAAGAGAAGGAGGAGG 280131 i i - i i (GGA)n#Simple 1 GGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGG 50 chrXqtel1M 280132 AGGAGGAGACAGGAGGAGGAGGAGAAGGAGCTAGGGAGACAGG-GGAGGA 280180 -v i -v - -v - (GGA)n#Simple 51 AGGAGGAG-GAGGAGGAGGAGGAGGAGGAG-GA-GGAG-GAGGAGGAGGA 96 chrXqtel1M 280181 GACGGAGGAGGAGGAGGAAGAAACAGAGGAAGAAACAGGAGGAGAAAGAA 280230 iv i iivi - i iv i i i (GGA)n#Simple 97 GGAGGAGGAGGAGGAGGAGGAGGAGGAGG-AGGAGGAGGAGGAGGAGGAG 145 chrXqtel1M 280231 GA-AAGGAAGGAAGAGGAAGAAACGGAGGAGGAGGAGGAGGAGGAGGAGG 280279 -i - i i iiv (GGA)n#Simple 146 GAGGAGG-AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGG 194 chrXqtel1M 280280 AGGAGGAGGAGGAGGAGGAGAAGAAGGA-GAGG 280311 i i - (GGA)n#Simple 195 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGG 227 Matrix = Unknown Transitions / transversions = 3.14 (22/7) Gap_init rate = 0.04 (10 / 228), avg. gap size = 1.00 (10 / 10) 25 17.48 2.94 2.94 chrXqtel1M 281033 281100 (718900) (CTGT)n#Simple_repeat 1 68 (0) m_b359s252i8 15045 chrXqtel1M 281033 CTTTCT-TCTGTCTGTCT-TGTGTCTCTCGGTGTCTGTCTGCCTGCCTCT 281080 v - - v v -- i i v (CTGT)n#Simpl 1 CTGTCTGTCTGTCTGTCTGTCTGTCTGTC--TGTCTGTCTGTCTGTCTGT 48 chrXqtel1M 281081 GTGTCTGGCTGGCTGTGTGT 281100 v v v v (CTGT)n#Simpl 49 CTGTCTGTCTGTCTGTCTGT 68 Matrix = Unknown Transitions / transversions = 0.25 (2/8) Gap_init rate = 0.06 (4 / 67), avg. gap size = 1.00 (4 / 4) 16 16.93 0.00 0.00 chrXqtel1M 281419 281445 (718555) (C)n#Simple_repeat 1 27 (0) m_b359s252i9 15046 chrXqtel1M 281419 CCCCCCCCCTTCTGCCCCCCCCCCCCC 281445 ii iv (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCC 27 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 18 19.79 2.17 0.00 chrXqtel1M 281743 281788 (718212) (CCCCGC)n#Simple_repeat 1 47 (0) m_b359s252i10 15047 chrXqtel1M 281743 CCGCGCCTCCTCCCCTTCCCCCACCCCC-AGCCCGCCCCCGCCCCCG 281788 v i v iv i -vv (CCCCGC)n#Sim 1 CCCCGCCCCCGCCCCCGCCCCCGCCCCCGCCCCCGCCCCCGCCCCCG 47 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1) 21 29.83 0.00 0.00 chrXqtel1M 282112 282167 (717833) (CC)n#Simple_repeat 1 56 (0) m_b359s252i11 15048 chrXqtel1M 282112 CCCCCCCTCTTCCCCGTCCCCCTTCCTTTTCCTCCCCCCCCCCCCCCCCC 282161 i ii vi ii iiii i (CC)n#Simple_ 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 50 chrXqtel1M 282162 CCCACC 282167 v (CC)n#Simple_ 51 CCCCCC 56 Matrix = Unknown Transitions / transversions = 5.50 (11/2) Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0) 12 20.00 6.25 2.00 chrXqtel1M 282166 282213 (717787) (CCGTCT)n#Simple_repeat 1 50 (0) m_b359s252i13 15049 chrXqtel1M 282166 CCGTGCTCTG-CTCCATTTCCGTGTCCCTC-CCG-CTCTCTTTCCGTCTC 282212 - i - i i v v - - iv i (CCGTCT)n#Sim 1 CCGT-CTCCGTCTCCGTCTCCGTCTCCGTCTCCGTCTCCGTCTCCGTCTC 49 chrXqtel1M 282213 C 282213 (CCGTCT)n#Sim 50 C 50 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.09 (4 / 47), avg. gap size = 1.00 (4 / 4) 46 17.84 0.00 0.00 chrXqtel1M 282238 282319 (717681) (G)n#Simple_repeat 1 82 (0) m_b359s252i14 15050 chrXqtel1M 282238 GGGGGGGGGGGGGGGGGCCGGGGGCCCGGGCGCTGGGGGGGGGGGGGGGG 282287 vv vvv v vv (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 50 chrXqtel1M 282288 GGGGGCGGGCGGGAAGGGGGGGGGGGGGGAGG 282319 v v ii i (G)n#Simple_r 51 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 82 Matrix = Unknown Transitions / transversions = 0.30 (3/10) Gap_init rate = 0.00 (0 / 81), avg. gap size = 0.0 (0 / 0) 17 24.09 1.72 3.51 chrXqtel1M 282675 282732 (717268) (GGA)n#Simple_repeat 1 57 (0) m_b359s252i15 15051 chrXqtel1M 282675 GGGGGAGGAGGAGGAGGGAGCAGGAAGACCAGGAAGGGGGGGCGG-GAAG 282723 i - v i vv i i i v - i (GGA)n#Simple 1 GGAGGAGGAGGAGGA-GGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG 49 chrXqtel1M 282724 AAGAGAGGA 282732 i - (GGA)n#Simple 50 GAG-GAGGA 57 Matrix = Unknown Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.05 (3 / 57), avg. gap size = 1.00 (3 / 3) 84 31.54 2.96 1.16 chrXqtel1M 283021 283358 (716642) (CT)n#Simple_repeat 1 344 (0) m_b359s252i16 15052 chrXqtel1M 283021 CTCTCCATCTCTCTCTTACGTCTCCCATCTGGGTGTGTGTCCCTCACTCC 283070 iv iv - i - vvv v v v i v i (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTC-TCTCTC-TCTCTCTCTCTCTCTCTCTCTCT 48 chrXqtel1M 283071 CTAT-TCTCTCTGTCCCTGCCCTCTCTC-CTTTCTGTTTCTCTCACTCAT 283118 v - v i - i - i v i v vi (CT)n#Simple_ 49 CTCTCTCTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 97 chrXqtel1M 283119 TCTCT-TCTTTCCCCCTCTGTCCCTC-CTCTTGCTCTCT-TCCTTTTTTC 283165 - i i i v i - iv - ii i i (CT)n#Simple_ 98 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 147 chrXqtel1M 283166 ACCCTCCCTC-CTCTGTCTCTTCCTCTCTTTCCTTGTCCCTGCCTCTCTC 283214 v i i - v ii i ii v i vi (CT)n#Simple_ 148 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 197 chrXqtel1M 283215 CCAGTCTCCTTTTCTCTGTTTTTCCCTCCCTTCCTCTTTCTCT-TTTCTC 283263 i vv ii i v i i i i ii i - i (CT)n#Simple_ 198 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 247 chrXqtel1M 283264 TCTCTC-CCCTC-CTCTCTCTCCCCCTTTCCCTTCCTGTCTCTGTCTCCT 283311 - i - i i i i ii v v ii (CT)n#Simple_ 248 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 297 chrXqtel1M 283312 TCTCTCCCTCTGTCTCTCTGGTCTCTCCCT-TGCCTCTCCCTGCCTCT 283358 i v -v i - vi i vi (CT)n#Simple_ 298 TCTCTCTCTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTCT 344 Matrix = Unknown Transitions / transversions = 1.86 (54/29) Gap_init rate = 0.04 (14 / 337), avg. gap size = 1.00 (14 / 14) 24 14.70 0.00 2.17 chrXqtel1M 283536 283582 (716418) (GCC)n#Simple_repeat 1 46 (0) m_b359s252i17 15053 chrXqtel1M 283536 GCCGCCCACGACGGCCGCCGCCGCCGCCGCCGCCGCCTCCACCTCCG 283582 vv - v v i v (GCC)n#Simple 1 GCCGCCGCCG-CCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCG 46 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.02 (1 / 46), avg. gap size = 1.00 (1 / 1) 338 30.00 1.77 2.68 chrXqtel1M 286927 287039 (712961) C L2c_3end#LINE/L2 (12) 466 355 m_b359s601i28 15054 chrXqtel1M 286927 AAGAAGCATTTATTAAGCACCTATTGTGTGCCAGGACCAGGGTGTCCAGA 286976 v i i i i i vv v vi v i- C L2c_3end#LINE 466 AACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGGGATACAA- 418 chrXqtel1M 286977 CAGAAGAGTCAG--ATGGTCCCTGTTCCCAAGAAGTTTCCCTTCTAACGA 287024 - v i v -- i ii i i i iv vv ii i C L2c_3end#LINE 417 -AGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAGTGG 369 chrXqtel1M 287025 ACGGGAACACAAAGG 287039 - ii v v ? C L2c_3end#LINE 368 A-GGAGACAGACANG 355 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.00 CpG sites = 20, Kimura (unadjusted) = 40.11 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.04 (4 / 112), avg. gap size = 1.25 (5 / 4) 72 24.93 1.90 1.90 chrXqtel1M 287334 287543 (712457) (TC)n#Simple_repeat 1 210 (0) m_b359s252i18 15055 chrXqtel1M 287334 TCTCTCAGTATCTCTCTCTCTCTGTCTCTGTGTGTCTCTGTCTCTCTCTC 287383 vv v v v v v v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chrXqtel1M 287384 TCTGTTTCATCTCTCTCTCTCATCTGTCTCTGTGTGTCTTTCATCTCTAT 287433 v i - - v v v v i - v (TC)n#Simple_ 51 TCTCTCTC-TCTCTCTCTCTC-TCTCTCTCTCTCTCTCTCTC-TCTCTCT 97 chrXqtel1M 287434 CAGTCTCTGTGCCTCCCTGTGTCTGTCTCATCTCTCTGTCTCTGTCTCTC 287483 vv v vi i v v v - v v (TC)n#Simple_ 98 CTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TCTCTCTCTCTCTCTCTCTC 146 chrXqtel1M 287484 TCCCTCCCCCTC-CCCTTACTCT-TCTC-CTTCCTC-CTCTCACCCTGGC 287529 i i i - i iv - - ii - v i vv (TC)n#Simple_ 147 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 196 chrXqtel1M 287530 TCCCTGTCCTTCTC 287543 i v ii (TC)n#Simple_ 197 TCTCTCTCTCTCTC 210 Matrix = Unknown Transitions / transversions = 0.54 (15/28) Gap_init rate = 0.04 (8 / 209), avg. gap size = 1.00 (8 / 8) 12 18.23 5.45 5.45 chrXqtel1M 288586 288640 (711360) (AAGCAA)n#Simple_repeat 1 55 (0) m_b359s252i19 15056 chrXqtel1M 288586 AAGCAAAAG-AAAAAAATAAGC--CTGCACAATCAAAAGGCAAACCAACA 288632 - iv v --vv v v - -- i (AAGCAA)n#Sim 1 AAGCAAAAGCAAAAGCAAAAGCAAAAGCAAAAGCAAAA-GCAAA--AGCA 47 chrXqtel1M 288633 AAAGCAAA 288640 (AAGCAA)n#Sim 48 AAAGCAAA 55 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.09 (5 / 54), avg. gap size = 1.20 (6 / 5) 70 16.93 2.94 2.94 chrXqtel1M 289633 289802 (710198) (AAAAAG)n#Simple_repeat 1 170 (0) m_b359s252i20 15057 chrXqtel1M 289633 AAAAAGCAAAAACACAAAAACAAAGAAAAAGAAAAAGAAGAAGAATATGA 289682 - v v i v i v v - (AAAAAG)n#Sim 1 AAAAAG-AAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAG- 48 chrXqtel1M 289683 AAAAAGAAGAAGAGAAAAG-TAGAG-AAAAGAAACAAGAAAGAAAAAGAA 289730 i - -v i - - - i i (AAAAAG)n#Sim 49 AAAAAGAAAAAGA-AAAAGAAAAAGAAAAAGAAA-AAGAAA-AAGAAAAA 95 chrXqtel1M 289731 GAAGAAGAAAAAGAAAGAAAGAAAGGAAAGGAAAGAAAGAAAG-AAAAG- 289778 i i i i i i i i i - - (AAAAAG)n#Sim 96 GAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGA 145 chrXqtel1M 289779 -AAAGAAGAAGAAAAACCAAAAGAA 289802 - i vv (AAAAAG)n#Sim 146 AAAAGAAAAAGAAAAAGAAAAAGAA 170 Matrix = Unknown Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.06 (10 / 169), avg. gap size = 1.00 (10 / 10) 57 25.25 3.00 4.35 chrXqtel1M 290252 290484 (709516) (CAAAA)n#Simple_repeat 1 230 (0) m_b359s252i21 15058 chrXqtel1M 290252 CAAAACAAACAGCAGAACACAACAACCTACTAAATGCAAACACACCTACT 290301 - - i v --v - vvv v v v vv (CAAAA)n#Simp 1 CAAAACAAA-A-CAAAACAAAACAA--AAC-AAAACAAAACAAAACAAAA 45 chrXqtel1M 290302 CTAAGTAAATCTAAACACAGTGAAATGTAAAC-AAA-AAACCAAAACAAA 290349 v ii v v - ivv vvv - - v - (CAAAA)n#Simp 46 CAAAACAAAACAAAACA-AAACAAAACAAAACAAAACAAAACAAAAC-AA 93 chrXqtel1M 290350 AACATCCAAAAACAAACAAAAACAAAACAAAACAAGTAAAAAC-AAACAG 290398 vvvv vv ivv - i (CAAAA)n#Simp 94 AACAAAACAAAACAAAACAAAACAAAACAAAACAAAACAAAACAAAACAA 143 chrXqtel1M 290399 AA-AGAACAGAAAGAAAGGGCAAAACTCCAAAAAACAAAATAAAACAAAA 290447 - i - v --i vvv v i (CAAAA)n#Simp 144 AACAAAACA-AAACAAA--ACAAAACAAAACAAAACAAAACAAAACAAAA 190 chrXqtel1M 290448 TAAAA-AAAA-AACACAAAAC-ACACAAAGTAAAACAAAA 290484 i - - v - v ii (CAAAA)n#Simp 191 CAAAACAAAACAAAACAAAACAAAACAAAACAAAACAAAA 230 Matrix = Unknown Transitions / transversions = 0.35 (12/34) Gap_init rate = 0.07 (17 / 232), avg. gap size = 1.00 (17 / 17) 82 19.62 0.00 2.33 chrXqtel1M 290600 290775 (709225) (TC)n#Simple_repeat 1 172 (0) m_b359s252i22 15059 chrXqtel1M 290600 TCTCTCCCTCTCTGTGTACTGTCTCTGTCTCTTTCATGTCTCTCTCTGTC 290649 i v v - v v i - v v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCT-CTCTCTCTCTCTCTCTC-TCTCTCTCTCTCTC 48 chrXqtel1M 290650 TGTCTGTCTCTCTTTGTCTCTGACTCTCTCTCTCTCTTTCTTTGTCTCTG 290699 v v i v vv i i v v (TC)n#Simple_ 49 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 98 chrXqtel1M 290700 ACTCTCTCTGTCTCTGTCTCTCTCATCTCTGTCTCTCATCTCTCTCTCTG 290749 v v v - v - v (TC)n#Simple_ 99 TCTCTCTCTCTCTCTCTCTCTCTC-TCTCTCTCTCTC-TCTCTCTCTCTC 146 chrXqtel1M 290750 TCTCTCTGTCTCTGTGTGTGTCCCTC 290775 v v v v v i (TC)n#Simple_ 147 TCTCTCTCTCTCTCTCTCTCTCTCTC 172 Matrix = Unknown Transitions / transversions = 0.26 (6/23) Gap_init rate = 0.02 (4 / 175), avg. gap size = 1.00 (4 / 4) 61 24.75 1.79 4.61 chrXqtel1M 290835 291057 (708943) (CACAAAA)n#Simple_repeat 1 217 (0) m_b359s252i23 15060 chrXqtel1M 290835 CACAGAAAAACCTAAAAGAAAACAAGAAAAACACCACAGAAAAACAAAGA 290884 - v vv v v vi v vv -v v - (CACAAAA)n#Si 1 CACA-AAACACAAAACACAAAACACAAAACACAAAACA-CAAAACACA-A 47 chrXqtel1M 290885 AACAGAAAATAAAATAAAAATAAAACAAAATAAAATAAAACAAAACACAA 290934 v i v v v v v v i v - v - (CACAAAA)n#Si 48 AACACAAAACACAAAACACAAAACACAAAACACAA-AACACAAAACAC-A 95 chrXqtel1M 290935 GAAAAACAAGAAAACAAAGAAAC-AAA-A-AAAACACAAACAAACAAAAC 290981 - v - v - v - - - - v (CACAAAA)n#Si 96 -AAACACAA-AACACAAA-ACACAAAACACAAAACACAAA-ACACAAAAC 141 chrXqtel1M 290982 ACAAAACAAGAAACAC-ACACACAAGAAACAAAACAAGAAAAACAAACAA 291030 vi - v i v vi v - v (CACAAAA)n#Si 142 ACAAAACACAAAACACAAAACACAAAACACAAAACACAAAACACAAA-AC 190 chrXqtel1M 291031 ACAATGAAAGAAACACAAAACTTAAAA 291057 viv vi vi (CACAAAA)n#Si 191 ACAAAACACAAAACACAAAACACAAAA 217 Matrix = Unknown Transitions / transversions = 0.26 (9/34) Gap_init rate = 0.06 (14 / 222), avg. gap size = 1.00 (14 / 14) 19 23.15 5.06 2.47 chrXqtel1M 291420 291498 (708502) (AAAGCA)n#Simple_repeat 1 81 (0) m_b359s252i24 15061 chrXqtel1M 291420 AAAGCAAGAAGGAAAA-CAAAACTCCGAG-AAAA-CCTAAGCAAAACTAA 291466 - v - vivvi - - vv vi (AAAGCA)n#Sim 1 AAAGCAA-AAGCAAAAGCAAAAGCAAAAGCAAAAGCAAAAGCAAAAGCAA 49 chrXqtel1M 291467 AAGGCAAAACTAAAAGCAAAA-CTCAACCAAAA 291498 - vi - vv v (AAAGCA)n#Sim 50 AA-GCAAAAGCAAAAGCAAAAGCAAAAGCAAAA 81 Matrix = Unknown Transitions / transversions = 0.36 (4/11) Gap_init rate = 0.08 (6 / 78), avg. gap size = 1.00 (6 / 6) 12 27.41 1.79 3.64 chrXqtel1M 292088 292143 (707857) (ACACC)n#Simple_repeat 1 55 (0) m_b359s252i25 15062 chrXqtel1M 292088 ACACCCCACTACA-CACTCCATGCCACGCTACAGGCACAAACCCACCAAA 292136 v i - v ii i i -v - v v v (ACACC)n#Simp 1 ACACCACACCACACCACACCACACCACACCACA-CCAC-ACCACACCACA 48 chrXqtel1M 292137 CCCCACC 292143 v (ACACC)n#Simp 49 CCACACC 55 Matrix = Unknown Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.05 (3 / 55), avg. gap size = 1.00 (3 / 3) 13 17.81 5.26 0.00 chrXqtel1M 292486 292523 (707477) (GAAGG)n#Simple_repeat 1 40 (0) m_b359s252i26 15063 chrXqtel1M 292486 GAAGGGCA-GGAAGGG-AGGCAAGGCCCGGGAAGGGGAGG 292523 v - - v vvv i (GAAGG)n#Simp 1 GAAGGGAAGGGAAGGGAAGGGAAGGGAAGGGAAGGGAAGG 40 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 21 16.35 0.00 0.00 chrXqtel1M 293781 293821 (706179) (CTGT)n#Simple_repeat 1 41 (0) m_b359s252i27 15064 chrXqtel1M 293781 CTTTCTGTCTCTCTGTCTGTCTGTCTCTTTCTCTGTCTCTC 293821 v v v i v v (CTGT)n#Simpl 1 CTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTC 41 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 25 13.17 4.55 4.55 chrXqtel1M 295710 295775 (704225) (GGA)n#Simple_repeat 1 66 (0) m_b359s252i28 15065 chrXqtel1M 295710 GGGGGAGGGAAGAGGAGGAGGAGGGAGGA-GAGGAGG-GGAAGAGGAAGA 295757 i - i - - - i i (GGA)n#Simple 1 GGAGGA-GGAGGAGGAGGAGGA-GGAGGAGGAGGAGGAGGAGGAGGAGGA 48 chrXqtel1M 295758 GAAAAAGG-GGAGGGAGGA 295775 i ii - - (GGA)n#Simple 49 GGAGGAGGAGGA-GGAGGA 66 Matrix = Unknown Transitions / transversions = 1.00 (7/0) Gap_init rate = 0.09 (6 / 65), avg. gap size = 1.00 (6 / 6) 17 23.19 0.00 2.13 chrXqtel1M 296502 296549 (703451) (CCTGC)n#Simple_repeat 1 47 (0) m_b359s252i29 15066 chrXqtel1M 296502 CCTGCCCTTCCCTGGGCTCCGCTGCCCAGCCCCTCCCCGGCCGTGCCC 296549 v vv v v v - v v v (CCTGC)n#Simp 1 CCTGCCCTGCCCTGCCCTGCCCTGCCCTG-CCCTGCCCTGCCCTGCCC 47 Matrix = Unknown Transitions / transversions = 0.00 (0/9) Gap_init rate = 0.02 (1 / 47), avg. gap size = 1.00 (1 / 1) 92 27.73 5.60 0.28 chrXqtel1M 296710 297048 (702952) (CT)n#Simple_repeat 1 357 (0) m_b360s252i2 15067 chrXqtel1M 296710 CTCTCCCT-TCCCTCTCCTTCCCTCTCCGCCTCTCTCTCCCCCCCGC-CT 296757 i - i ii i ivi i i i v - (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chrXqtel1M 296758 CTCTCTCCCCCCCCCTCTCTCTC-CCCTC-CGCTCTC-CTCTC-CCCCCT 296803 i i i i - i - v - - i i (CT)n#Simple_ 51 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 100 chrXqtel1M 296804 GCCTCTCTCTCCCCCGC-CTCTCTCCCCCGC-CTCTCTCTCCCCCGC-CT 296850 vi i i v - i i v - i i v - (CT)n#Simple_ 101 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 150 chrXqtel1M 296851 CTCTCTC-CCCTCCCGCCCTCTCTCCCTCCCCCGCTCTCTCTCCCTCCCC 296899 - i i v i i i i v i i i (CT)n#Simple_ 151 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 200 chrXqtel1M 296900 GCCTCTCTCTCCCCCAC-CTC-CTCTCTC-CTCTCCCCCAC-CTCTCTCT 296945 vi i i v - - - i i v - (CT)n#Simple_ 201 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 250 chrXqtel1M 296946 CCCCCCGCCTCTCTCTCCCCCCCCGCCTCTCTCTC-CTCCCCCACTCTCT 296994 i i ivi i i i ivi - i i v (CT)n#Simple_ 251 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 300 chrXqtel1M 296995 CTCCCCCTCCCCCGTCTCTCTC-CCCCCACTCT-TCTCCCT-TCCCCCGC 297041 i i i i - - i i v - i - i i v (CT)n#Simple_ 301 CTCTCTCTCTCTC-TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 349 chrXqtel1M 297042 -CTCTCTC 297048 - (CT)n#Simple_ 350 TCTCTCTC 357 Matrix = Unknown Transitions / transversions = 3.41 (58/17) Gap_init rate = 0.06 (20 / 338), avg. gap size = 1.00 (20 / 20) 418 23.94 0.74 7.87 chrXqtel1M 299139 299274 (700726) C MIRb#SINE/MIR (138) 130 4 m_b360s601i0 15068 chrXqtel1M 299139 CTGAGGC-AACTGGGGTTAGGCCACTTGGCCAGGGTCACACAGCTGGGAA 299187 -v vv i i iv v i i --- C MIRb#SINE/MIR 130 CTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAG--- 84 chrXqtel1M 299188 GGGTTAAGTGTCTGAGGCCGGATTTGAACTCGGCTCCTCCTGACTTCAGG 299237 ---- v v v v i i i v ivi i ii C MIRb#SINE/MIR 83 ----TAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAA 38 chrXqtel1M 299238 GCTGCTGCTCTACCCACTACACCACCCAGCTGCCCCT 299274 ivv vi i --- C MIRb#SINE/MIR 37 GCCCGTGCTCTTTCCACTGCACCAC---GCTGCCCCT 4 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 27.88 CpG sites = 16, Kimura (unadjusted) = 29.00 Transitions / transversions = 1.14 (16/14) Gap_init rate = 0.08 (11 / 135), avg. gap size = 1.00 (11 / 11) 26 0.00 0.00 0.00 chrXqtel1M 299283 299307 (700693) (T)n#Simple_repeat 1 25 (0) c_b360s251i0 15069 chrXqtel1M 299283 TTTTTTTTTTTTTTTTTTTTTTTTT 299307 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 501 26.76 5.94 9.28 chrXqtel1M 299812 300367 (699633) C L1ME3C_3end#LINE/L1 (325) 545 7 m_b360s551i0 15070 chrXqtel1M 299812 TATTCCAT-ATATTCA-ATGCAGCAATTGTATTCAGCCATTCTCCAACCT 299859 -i vv - i vi - i v viiiv C L1ME3C_3end#L 545 TATTCCATTGTATGAATATACCACAATT-TATTTATCCATTCTCCTGTTG 497 chrXqtel1M 299860 ATGGACTCCATTCAG------TTCAGTTTTAC-CCAGCACCAGGCCTGAA 299902 --- i ------ i i v - i vi - ii ---- C L1ME3C_3end#L 496 ATGGAC---ATTTAGGTTGTTTCCAATTTTTCGCTATTAC-AAAC----A 455 chrXqtel1M 299903 GTGCTGCCCAGAACATTCGTGCACATACGGTC-CCTT-TCCTTCCTTCTG 299950 i vvv v i --- - - v viv v vi C L1ME3C_3end#L 454 ATGCTGCAATGAACATTCTTGTACAT---GTCTCCTTGTGCACACGTGCG 408 chrXqtel1M 299951 AGGTATCCTCTGGGATCTATAATCTCAGGGGCTAGTAACACTG-TGGATC 299999 ivv i i i v -- ii ---- iiv i - i C L1ME3C_3end#L 407 AGAGTTTCTCTAGGGTATATA--CCTAGG----AGTGGAATTGCTGGGTC 364 chrXqtel1M 300000 AAGGGGTCTGCACAGTTCCGATCAACGTT-TGAGCATAGTTCCAAACAGT 300048 ivi v i vi ---- v -iv - v v iv i C L1ME3C_3end#L 363 GTAGGGTATGCGCATCT----TCAACTTTACTAG-ATATTGCCAAATTGC 319 chrXqtel1M 300049 TCAGGACTGGGGTGGATTCAGTTCAAACTCC-ACCAACGAAGTGCATCGA 300097 vvv vv v v vvi i i v - i -- i - C L1ME3C_3end#L 318 TCTCCAAAGTGGTTGTACCAATTTACACTCCCACCAGC--AGTGTAT-GA 272 chrXqtel1M 300098 TATAGTCCCAGTTTTCCCGCATCC-CTTCAACAATCATCATGGTCTTTTT 300146 v -- i v vii i - vi v ----- v v i C L1ME3C_3end#L 271 GA--GTTCCCGTTGCTCCACATCCTCGCCAACACT-----TGGTATTGTC 229 chrXqtel1M 300147 ---CCTGTCATCTTTAGCCAATC-GACAGGTTGTGCCAATGCGCAGATCT 300192 --- i v v vi v - ii - v- ---iv C L1ME3C_3end#L 228 AGACTTTTAAATTTTTGCCAATCTGATGGGT-GTGA-AATG---GTATCT 184 chrXqtel1M 300193 CAG-GTTGTCTTAATTTACATTTCC-TGATTAATA-TGACTTGGAGCATC 300239 v- ? i i - v - vv v C L1ME3C_3end#L 183 CATTGTNGTTTTAATTTGCATTTCCCTGATTACTAGTGAGGTTGAGCATC 134 chrXqtel1M 300240 TTTTCAT-CGACTA--GACAAT---AGTTTCCATCTCTTTATCTACAGAT 300283 -i vi -- i v ---? - ----- iiii C L1ME3C_3end#L 133 TTTTCATATGTTTATTGGCCATTCGNGTTTCC-TCT-----TCTGTGAAT 90 chrXqtel1M 300284 TGTCTTTCCATATCCTTTGACCATTTTTTCATTGGAGAATTGGTTGATTG 300333 i v i i v ii ---i vi - v C L1ME3C_3end#L 89 TGCCTGTTCATATCTTTTGCCCATTTTTCTATTGG---GTTGTCTG-TTT 44 chrXqtel1M 300334 TTTTAT--AT---TAGGTTAATTCTCTCTATATTTTGGA 300367 i -- --- -- i i v i C L1ME3C_3end#L 43 TCTTATTGATTTGTAGG--AGTTCTTTATATATTCTGGA 7 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 32.70 CpG sites = 71, Kimura (unadjusted) = 33.60 Transitions / transversions = 1.11 (71/64) Gap_init rate = 0.13 (70 / 555), avg. gap size = 1.19 (83 / 70) 246 23.75 7.84 6.45 chrXqtel1M 300233 300385 (699615) C L1MD_orf2#LINE/L1 (7) 3287 3133 m_b360s551i1 15070 chrXqtel1M 300233 GAGCATCTTTTCATCGACTAGACAATAGTTTCCATCTCTTTA---TCTAC 300279 i vvi ------ v v v v --- v C L1MD_orf2#LIN 3287 GAACATCTTTTCATGTGCT------TATTTGCCATCTGTATATCCTCTTC 3244 chrXqtel1M 300280 AG---ATTGTCTTTCCATATCCTTTGACCATTTTTTCATTGGAGAATTGG 300326 i --- v ? i i i v i v --- v C L1MD_orf2#LIN 3243 GGTGAAATGTCTNTTCATGTCTTTTGCCCATTTTCTAATTGG---ATTGT 3197 chrXqtel1M 300327 TTGATTGTTTTA-TATTAGGTT-----AATTCTCTCTATATTTTGGAAAT 300370 - v - i ii ----- i i v i i v i C L1MD_orf2#LIN 3196 TTG-TTTTTTTACTGTTGAGTTTTGAGAGTTCTTTATATATTCTAGATAC 3148 chrXqtel1M 300371 AGGGCCTTTACCTGA 300385 ?i v ii v C L1MD_orf2#LIN 3147 NAGTCCTTTGTCGGA 3133 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 28.44 CpG sites = 18, Kimura (unadjusted) = 29.44 Transitions / transversions = 1.12 (18/16) Gap_init rate = 0.09 (14 / 152), avg. gap size = 1.57 (22 / 14) 288 33.13 12.75 0.88 chrXqtel1M 300606 300809 (699191) L3#LINE/CR1 3871 4098 (1) m_b360s601i1 15071 chrXqtel1M 300606 AGGCCGAGTGCAGCTGGATGCCAGGATAAGCCTCCTCATCACCAGAGCTG 300655 v v v i vi iiv vi i i i v iv i L3#LINE/CR1 3871 AGGCAGATTTCGGCTCAATATAAGGAAGAACTTTCTAACAATCAGAGCTG 3920 chrXqtel1M 300656 GC----GGTGGAAAGGGCCGCCTAAAGCAGCAG-GCCCTCCCCTCCTCTG 300700 v ----ii v i vi? vi i - vv vi v L3#LINE/CR1 3921 TCCAAAAATGGAATGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGTCACTG 3970 chrXqtel1M 300701 -AGACCCTCAGACGGGGCAGCTAGACGCCTGCTTGTCCA--ATATTCTAG 300747 - iivi ii i i -- i i v ii vi-- i v L3#LINE/CR1 3971 GAGGTGTTCAAGCAGAG--GCTGGATGACCACTTGTCAGGGATGTTGTAG 4018 chrXqtel1M 300748 ------TTCCTTTTGGGGATGGA---TTGGACCAAGTGGT-TCTGA---- 300783 ------ vivvv i--- i ii ii- i ---- L3#LINE/CR1 4019 AAGGGATTCCTGCATTGGATGGGAGGTTGGACTAGATGACCTCTAAGGTC 4068 chrXqtel1M 300784 ----CCCACTCTTAAGTTCTGTGATTCCAT 300809 ---- v v ii i L3#LINE/CR1 4069 CCTTCCAACTCTGAGATTCTGTGATTCTAT 4098 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 44.12 CpG sites = 41, Kimura (unadjusted) = 46.02 Transitions / transversions = 1.58 (41/26) Gap_init rate = 0.05 (10 / 203), avg. gap size = 2.80 (28 / 10) 330 29.64 4.47 3.89 chrXqtel1M 301187 301365 (698635) C L1M4_orf2#LINE/L1 (744) 2550 2371 m_b360s551i2 15070 chrXqtel1M 301187 TCTCCAGATGAATTTGCTCAGGATT--TTTATTAATTCTTTGGAATATCA 301234 i v ---i i--i i i - i v v -- C L1M4_orf2#LIN 2550 TTTCCATATGAATTT---TAGGATCAGCTTGTCAATT-TCTGCAAAA--A 2507 chrXqtel1M 301235 CGACGGC----ATTTTGATTTGTGTTGCGGGAAGTCTACAGATTAATTTA 301280 v ? i ---- vv vi vvi i ii i i C L1M4_orf2#LIN 2506 AGNCAGCTGGGATTTTGATAGGGATTGCGTTGAATCTGTAGATCAATTTG 2457 chrXqtel1M 301281 GAAAGCATTGACCTTTTT--CCACATTAGCTCAAACGGGCCACGAACAGT 301328 ii i - v i -- v i iv vvv iiv i vv C L1M4_orf2#LIN 2456 GGGAGTATTG-CCATCTTAACAATATTAAGTCTTCCAATCCATGAACATG 2408 chrXqtel1M 301329 GGATGTCTTTTCGTCCATTCGGCTCTTCTGTGATTTC 301365 i i ii ii v v i C L1M4_orf2#LIN 2407 GGATGTCTTTCCATTTATTTAGGTCTTCTTTAATTTC 2371 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.31 CpG sites = 31, Kimura (unadjusted) = 39.31 Transitions / transversions = 1.55 (31/20) Gap_init rate = 0.06 (10 / 178), avg. gap size = 1.50 (15 / 10) 27 0.00 0.00 0.00 chrXqtel1M 302051 302076 (697924) (T)n#Simple_repeat 1 26 (0) c_b360s251i1 15072 chrXqtel1M 302051 TTTTTTTTTTTTTTTTTTTTTTTTTT 302076 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 21 17.81 0.00 0.00 chrXqtel1M 304774 304811 (695189) (A)n#Simple_repeat 1 38 (0) m_b360s252i3 15073 chrXqtel1M 304774 AAGAAAAACCCAAAATAAAAAAAAAAAAAAAAAAATAA 304811 i vvv v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 38 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 84 11.94 0.00 0.00 chrXqtel1M 304988 305133 (694867) (C)n#Simple_repeat 1 146 (0) c_b360s251i2 15074 chrXqtel1M 304988 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCCCACCCCCCC 305037 v v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 50 chrXqtel1M 305038 CCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCACCACACCCCCCCCA 305087 v v v v v (C)n#Simple_r 51 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 100 chrXqtel1M 305088 CACCACCCCACTCCCCAACCCACCCCCCCCACCCCCCCCCACCCCC 305133 v v v i vv v v v (C)n#Simple_r 101 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 146 Matrix = Unknown Transitions / transversions = 0.07 (1/15) Gap_init rate = 0.00 (0 / 145), avg. gap size = 0.0 (0 / 0) 152 16.11 0.00 0.00 chrXqtel1M 305308 305564 (694436) (A)n#Simple_repeat 1 257 (0) m_b360s252i4 15075 chrXqtel1M 305308 AAAAACCCAAAAAATAAAAAACAAAAACAAAACAAAAAAAAAAAAAAAAA 305357 vvv v v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chrXqtel1M 305358 AAAAAACAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 305407 v v (A)n#Simple_r 51 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 100 chrXqtel1M 305408 AAAAAAAAAAAAAAAAAAAAAAAGTTTTAAAAAACCCAAAAAAAAAAGAA 305457 ivvvv vvv i (A)n#Simple_r 101 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 150 chrXqtel1M 305458 AAAAAAAAAAAAAAAAAAAATAAAAAGAAAAAAAAAAAAATGAAAAAAAT 305507 v i vi v (A)n#Simple_r 151 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 200 chrXqtel1M 305508 TAAAAAAAAAATTTTAAAAAATTTCCCCCAAAAATAAAAAAAAAAAAAAA 305557 v vvvv vvvvvvvv v (A)n#Simple_r 201 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 250 chrXqtel1M 305558 AAAAAAA 305564 (A)n#Simple_r 251 AAAAAAA 257 Matrix = Unknown Transitions / transversions = 0.12 (4/33) Gap_init rate = 0.00 (0 / 256), avg. gap size = 0.0 (0 / 0) 84 17.57 7.25 3.14 chrXqtel1M 305579 305854 (694146) (CCA)n#Simple_repeat 1 287 (0) m_b360s252i5 15076 chrXqtel1M 305579 CCACCCACCACC-CC-CCACC-CCACC-CCAACACCCACC-CC-CCACC- 305621 - - - - - v - - - - (CCA)n#Simple 1 CCA-CCACCACCACCACCACCACCACCACCACCA-CCACCACCACCACCA 48 chrXqtel1M 305622 CCACCCACCACCCCCACCCACCACC-CCCCCCCCACC-CCACCCCCACCA 305669 - v - - v v - v - (CCA)n#Simple 49 CCA-CCACCACCACCA-CCACCACCACCACCACCACCACCACCACCACC- 95 chrXqtel1M 305670 ACAACCACCAACCACCA-CACCA-CACCACC-CCACCACCCCCACCCACA 305716 v - - - - v vv (CCA)n#Simple 96 ACCACCACC-ACCACCACCACCACCACCACCACCACCACCACCACCACCA 144 chrXqtel1M 305717 CCACCA-CACCCCCACCCACC-CC-CCCCCCCCCCCCCCCCCAAAAAAAA 305763 - v - - - v v v v v vv vv v (CCA)n#Simple 145 CCACCACCACCACCA-CCACCACCACCACCACCACCACCACCACCACCAC 193 chrXqtel1M 305764 AAAAACCACCACCCAAAACC-CC-CCCCCACC-CCCCCACCCCCACCCAA 305810 v vv - vv - - v - v v - v (CCA)n#Simple 194 CACCACCACCA-CCACCACCACCACCACCACCACCACCACCACCA-CCAC 241 chrXqtel1M 305811 CACCCCCACACCCAAAACAAACA-AACCCCCCCAACCACC-CCACC 305854 v vv vv v v -v v v v - (CCA)n#Simple 242 CACCACCACCACCACCACCACCACCACCACCACCACCACCACCACC 287 Matrix = Unknown Transitions / transversions = 0.00 (0/40) Gap_init rate = 0.11 (29 / 275), avg. gap size = 1.00 (29 / 29) 40 21.81 0.00 0.00 chrXqtel1M 306130 306210 (693790) (A)n#Simple_repeat 1 81 (0) m_b360s252i6 15077 chrXqtel1M 306130 AAAAAAAAAAACAAAAACAAAAAAAACCCAAAAAAAAAAAAAAAACAACA 306179 v v vvv v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chrXqtel1M 306180 AAAACCCCCAAAAACCAAACAAAAAAAAAAA 306210 vvvvv vv v (A)n#Simple_r 51 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 81 Matrix = Unknown Transitions / transversions = 0.00 (0/15) Gap_init rate = 0.00 (0 / 80), avg. gap size = 0.0 (0 / 0) 26 15.69 0.00 0.00 chrXqtel1M 306329 306371 (693629) (A)n#Simple_repeat 1 43 (0) m_b360s252i7 15078 chrXqtel1M 306329 AAAAAAAAAAAAAAAAAAAAACAAACCCCAAAAAAAAAACAAA 306371 v vvvv v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 43 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 14 17.13 0.00 7.14 chrXqtel1M 306652 306696 (693304) (CCAAAAA)n#Simple_repeat 1 42 (0) m_b360s252i8 15079 chrXqtel1M 306652 CCAAAAACCAATAGCCAAAATTTACCCACAAAAAAAAACCAAAAA 306696 v i --- v v vv (CCAAAAA)n#Si 1 CCAAAAACCAAAAACCAAAA---ACCAAAAACCAAAAACCAAAAA 42 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.07 (3 / 44), avg. gap size = 1.00 (3 / 3) 15 13.87 0.00 0.00 chrXqtel1M 306681 306704 (693296) (A)n#Simple_repeat 1 24 (0) m_b360s252i9 15080 chrXqtel1M 306681 AAAAAAAAACCAAAAAAATAAAAA 306704 vv v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAA 24 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 27 3.23 0.00 0.00 chrXqtel1M 307538 307569 (692431) (A)n#Simple_repeat 1 32 (0) m_b360s252i11 15081 chrXqtel1M 307538 AAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAA 307569 i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 32 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 254 34.52 0.00 0.00 chrXqtel1M 309098 309181 (690819) L1ME3F_3end#LINE/L1 430 513 (477) m_b360s551i3 15082 chrXqtel1M 309098 ACATTTGCAAAACTGTCTATAGCAACCCTTTTTGTAGTGGTAAGGATCTG 309147 v i i v ii i v v i i i i ii v L1ME3F_3end#L 430 ACATGTACAAGAATGTTCATAGCAGCACTGTTCGTAATAGCAAAAAACTG 479 chrXqtel1M 309148 GAAACAGAGTGGACACCCATCAGCTGGGGAATGG 309181 ivviii iii ii v i L1ME3F_3end#L 480 GAAACAACCCAAATGTCCATCGACAGGAGAATGG 513 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 45.47 CpG sites = 21, Kimura (unadjusted) = 50.51 Transitions / transversions = 2.62 (21/8) Gap_init rate = 0.00 (0 / 83), avg. gap size = 0.0 (0 / 0) 13 19.31 0.00 5.41 chrXqtel1M 310256 310294 (689706) (ATT)n#Simple_repeat 1 37 (0) m_b360s252i12 15083 chrXqtel1M 310256 ATTATTATTATTATTAATGTGTTGTTAATAATAATAATA 310294 - - i i v v v v (ATT)n#Simple 1 ATTATTATTATTATT-AT-TATTATTATTATTATTATTA 37 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2) 648 30.17 8.19 0.00 chrXqtel1M 310307 310538 (689462) MIRb#SINE/MIR 2 252 (16) m_b360s601i2 15084 chrXqtel1M 310307 AGTGAAGCTGAGTGGCTCAATAGATACAGCACTGGGGACCGACTCAGGAA 310356 v ii v v iv i i v v v vvviv v iv MIRb#SINE/MIR 2 AGAGGGGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACA 51 chrXqtel1M 310357 GACTCAAGTTCAAATCCAACCTCAGACACTTA-TAA----ATGACCCTAC 310401 iiii i viv v v - i----i i iv MIRb#SINE/MIR 52 GACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 101 chrXqtel1M 310402 ACAAGTCAGTTAACTTCTCCA--CCTCCATCTT-TCA-CTGTAAAATGGG 310447 i i v i ii-- vi i i- - MIRb#SINE/MIR 102 GCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 151 chrXqtel1M 310448 GATAGTAACACTTACCTCCCAAGGTTCCGGTGAAGAT-------GAT-AT 310489 i i i v i viv i ------- - MIRb#SINE/MIR 152 GATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAAT 201 chrXqtel1M 310490 TCA--TAAAGCACTCTGCATAGTGCTGGACATGTACTAGGTACTTCATAA 310537 v -- i iv i iv i ii v i ii iv MIRb#SINE/MIR 202 GCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAA 251 chrXqtel1M 310538 A 310538 MIRb#SINE/MIR 252 A 252 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 36.88 CpG sites = 42, Kimura (unadjusted) = 39.87 Transitions / transversions = 1.50 (42/28) Gap_init rate = 0.03 (8 / 231), avg. gap size = 2.38 (19 / 8) 200 35.29 0.00 0.00 chrXqtel1M 310496 310546 (689454) L2d_3end#LINE/L2 452 502 (14) m_b360s601i3 15085 chrXqtel1M 310496 AGCACTCTGCATAGTGCTGGACATGTACTAGGTACTTCATAAACACCCAT 310545 i iiv i ii ii v ii iv i iii L2d_3end#LINE 452 AGCGCCTAGCACAGTGCTGAGCACATAGTAGGCGCTCAATAAATACTTGT 501 chrXqtel1M 310546 T 310546 L2d_3end#LINE 502 T 502 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 45.62 CpG sites = 15, Kimura (unadjusted) = 55.20 Transitions / transversions = 5.00 (15/3) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 1114 34.03 3.42 2.32 chrXqtel1M 310956 312065 (687935) C L1MD_orf2#LINE/L1 (1612) 1682 561 m_b360s551i5 15086 chrXqtel1M 310956 TGGTGTATTATCCTGGGGATGAGTTGCTGGAATCTCATTGCTAACATTTT 311005 v i vvvv ivi i v ?vv i C L1MD_orf2#LIN 1682 TGGTGTATAATTCTTTTTATATATTGCTGAATTCNATTTGCTAATATTTT 1633 chrXqtel1M 311006 ACTGAAGATTTTTGTGTCAATATTCTTTAGGGAAATTGGTCTATAATTTT 311055 ii i i v i v v v i i C L1MD_orf2#LIN 1632 GTTGAGGATTTTTGCGTCTATGTTCATGAGGGATATTGGTCTGTAGTTTT 1583 chrXqtel1M 311056 CTCTGTTTTCATCCTACCC-------GTTTTAGTCAGCAGCACCATATCT 311098 i -- ii v ii i------- i - v viiv iiv C L1MD_orf2#LIN 1582 CTTT--TTTTGTACTGTCTTTGTCTGGTTTTGGT-ATCAGGGTAATACTG 1536 chrXqtel1M 311099 ATGTCATAAAAGGAATTTGGTAGGACTCCTCCTTTCCCTAGTTTTAAAAA 311148 iiv v i v v vii ii i iii v ivii C L1MD_orf2#LIN 1535 GCCTCATAAAATGAGTTGGGAAGTGTTCCCTCCTCTTCTATTTTCTGGAA 1486 chrXqtel1M 311149 TAATTTATATAGCAGTGGAGTTAATTGTTCTTTAAATGTTTAGTAAAATT 311198 v iv i i v v v v i i i C L1MD_orf2#LIN 1485 GAGATTGTGTAGAATTGGTGTTAATTCTTCTTTAAACGTTTGGTAGAATT 1436 chrXqtel1M 311199 CACATGTAAATCCATCTAGCCCTGGAGATTTTTCTTTAGGAAGTACATTA 311248 v vv i v i v i i i i viv?v C L1MD_orf2#LIN 1435 CTCCAGTGAAACCATCTGGGCCTGGAGATTTCTTTTTGGGGAGTTTTNAA 1386 chrXqtel1M 311249 ATAGCTTATTTTATTTCTTTTTCTGAAATGCGACTATTTAAATAATTTAC 311298 vi vv iv i vviv vv iv i i v i i C L1MD_orf2#LIN 1385 ATTACGAATTCAATTTCCTTAATAGTTATAGGGCTATTCAAATTATCTAT 1336 chrXqtel1M 311299 TTCCTCTTCTGTTAACCGGAGCAATCTATATTTTTGTAGCTATTCCTCCA 311348 v ? vv v iii?vi i i i i i vv vv vv C L1MD_orf2#LIN 1335 TTCATNTTGGGTGAGTTNTGGTAGTTTGTGTTTTTCGAGGAATTGGTCCA 1286 chrXqtel1M 311349 TTTCATTTAGATTACCAAATTTAT-TGCCATATAGTCGGGCAAAATAACT 311397 i ii ii - - i v i vv iv i vii C L1MD_orf2#LIN 1285 TTTCATCTAAGTTGTCAAATTTATGTG-CGTAGAGTTGTTCGTAGTATTC 1237 chrXqtel1M 311398 CATAATTATTGCTCTAATTTCCTCTTCATTGGTGG-AAAGTTCTCT-CTT 311445 v v ivi i i v iv vvvi iv i -i vi i i -i C L1MD_orf2#LIN 1236 CCTTATTATCCTTTTGATGTCTGCAGGGTCTGTAGTGATATCCCCTGTTT 1187 chrXqtel1M 311446 CATTTTTGAGACTAACAATTTAATTTTCTTCTTTCCTTTTT--CTAATCA 311493 ii v i iii i-- v i i --i vi C L1MD_orf2#LIN 1186 CATTCCTGATATTGGTAATTTG--TGTCTTCTCTCTTTTTTTCTTTGTCA 1139 chrXqtel1M 311494 AATTAACTACAGGTTTATCTATTTTGTTGGGTTTTTCATAAAACCAACTC 311543 ivi vi v i v i ivi v i i i C L1MD_orf2#LIN 1138 GTCTTGCTAGAGGTTTGTCAATTTTATTGATCTTTTCAAAGAACCAGCTT 1089 chrXqtel1M 311544 TTACTTTTAGTTATTAATTCAATAGTTTTCATATTTTTGATTTTATTAAT 311593 vv i v v vvi v v iv i ii i i C L1MD_orf2#LIN 1088 TTTGTTTCATTGATTTTCTCTATTGTTTTTCTGTTTTCAATTTCATTGAT 1039 chrXqtel1M 311594 CTC--CCCTT---TTCAGAATTTCTAAGTTGGTATTTAATTGAGGGTTTT 311638 i -- i --- i vv ivvvi vv ii iv vi v v C L1MD_orf2#LIN 1038 TTCTGCTCTTATCTTTATTATTTCCTTCCTTCTGCTTGCTTTGGGTTTAT 989 chrXqtel1M 311639 TCATCTGTTATTTTTCTAGCTTTTTTTAGTTGTAAGCCCA-ATTCATGAT 311687 ivv v v -? i v v vi ii - vv C L1MD_orf2#LIN 988 TTTGCTCTTCTTTTTCTAG-NTTCTTGAGGTGGGAGCTTAGATTATTGAT 940 chrXqtel1M 311688 ------CTTCTCTTTATTTTATGCAAGTAATCATCTAGAGATATCAGATT 311731 ------ i i i- v i- v ?v i v v - i C L1MD_orf2#LIN 939 TTGAGACTTTTCCTC-TTTTCTA-ATGTANGCATTTAGTGCTAT-AAATT 893 chrXqtel1M 311732 TCCC-CTTATAATCACTTTGACTGCATCCCGCAAATTTTAGTATGTCGTC 311780 - i vv iii ii i i ii i v C L1MD_orf2#LIN 892 TCCCTCTCAGCACTGCTTTAGCTGCGTCCCACAAATTTTGATATGTTGTA 843 chrXqtel1M 311781 CCATTATCGTCATTCTCTTGGATGAAGTTGTCGATTGCGTCTATGATTTG 311830 iiv i iv vv vi v v v ii v vii iv i v C L1MD_orf2#LIN 842 TTTTCATTTTCATTCAGTTCAATGTATTTTTTAATTTCCCTTGAGACTTC 793 chrXqtel1M 311831 TCTTCCCACCCATTCATTCTTTAGGA-TGAGATTATTTAATTTCCAATTA 311879 iii iiv vv v i - v - i i --- C L1MD_orf2#LIN 792 CTCTTTGACCCATGGATTATTTAGAAGTGTG-TTGTTTAGTTTCCA---A 747 chrXqtel1M 311880 ATTTTTGGTCTATTTTCTCCTGGCCTTATGTTGCATGTGATTTTTA--TT 311927 i v vvvv i vi iv i v -- - i -- C L1MD_orf2#LIN 746 GTGTTTGGAGATTTTCCTGTTATCTTTCTGTT--AT-TGATTTCTAGTTT 700 chrXqtel1M 311928 G----CATAATAATCTAGAAAAAGTGCATT---TACTATTTCTGCCTTTC 311970 ---- vi ii - i --ii i --- iv viiii i C L1MD_orf2#LIN 699 GATTCCATTGTGGTC-AGAGAA--CACACTCTGTATGATTTCAATTCTTT 653 chrXqtel1M 311971 TGCCTTTGATTTTGAGGT---TTTTATGCCCTGATACGCGATCAATCTCT 312017 ivv --- --- v iiiv iii i v iv C L1MD_orf2#LIN 652 TAAATTTG---TTGAGGTTTGTTTTATGGCCCAGGATATGGTCTATCTTG 606 chrXqtel1M 312018 GTGTAGGTTTCGTGAACCGCCGAGAAAAAATGTAAACTCCTTTCTGTT 312065 i? v i ii vvii - i iv i -- v C L1MD_orf2#LIN 605 GTANATGTTCCGTGGGCACTTGA-AAAGAATGTGTATTC--TGCTGTT 561 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 46.35 CpG sites = 208, Kimura (unadjusted) = 47.25 Transitions / transversions = 1.29 (208/161) Gap_init rate = 0.04 (41 / 1109), avg. gap size = 1.56 (64 / 41) 1335 32.40 3.70 2.03 chrXqtel1M 310956 311875 (688125) C L1M4_orf2#LINE/L1 (1612) 1682 748 m_b360s551i4 15086 chrXqtel1M 310956 TGGTGTATTATCCTGGGGATGAGTTGCTGGAATCTCATTGCTAACATTTT 311005 v vvvv iv v vvv ii C L1M4_orf2#LIN 1682 TGGTGTATAATCCTTTTTATATGTTGCTGGATTCGGTTTGCTAGTATTTT 1633 chrXqtel1M 311006 ACTGAAGATTTTTGTGTCAATATTCTTTAGGGAAATTGGTCTATAATTTT 311055 ii i ii v v v v i i C L1M4_orf2#LIN 1632 GTTGAGGATTTTTGCATCTATATTCATAAGGGATATTGGTCTGTAGTTTT 1583 chrXqtel1M 311056 CTCT---------GTTTTCATCCTACCCGTTTTAGTCAGCAGCACCATAT 311096 i --------- i ii - i--- i - v viiv i C L1M4_orf2#LIN 1582 CTTTTCTTGTGATGTCTTTGTC-TG---GTTTTGGT-ATCAGGGTAATAC 1538 chrXqtel1M 311097 CTATGTCATAAAAGGAATTTGGTAGGACTCCTCCTTTCCCTAGTTTTAAA 311146 iviiv i v i v v vii ii i iii v vii C L1M4_orf2#LIN 1537 TGGCCTCATAGAATGAGTTGGGAAGTGTTCCCTCCTCTTCTATTTTTTGG 1488 chrXqtel1M 311147 AATAATTTATATAGCAGTGGAGTTAATTGTTCTTTAAATGTTTAGTAAAA 311196 v i i iv v v v v i i C L1M4_orf2#LIN 1487 AAGAGTTTGTGAAGGATTGGTGTTAATTCTTCTTTAAATGTTTGGTAGAA 1438 chrXqtel1M 311197 TTCACATGTAAATCCATCTAGCCCTGGAGATTTTTCTT--TAGGAAGTAC 311244 vv i v i ? -- ii -- i vi C L1M4_orf2#LIN 1437 TTCACCAGTGAAGCCATCTGGNCCTG--GGCTTTTCTTTGTGGGAAGTTT 1390 chrXqtel1M 311245 ATTAATAGCTTATTTTATTTCTTTTTCTGAAATGCGACTATTTAAATAAT 311294 v i vi v iv i vii vv iv v i i vv C L1M4_orf2#LIN 1389 TTTGATTACTAATTCAATCTCTTTACTTGTTATAGGTCTATTCAGATTTT 1340 chrXqtel1M 311295 TTACTTCCTCTTCTGTTAACCGGAGCAATCTATATTTTTGTAGCTATTCC 311344 i i i vv i iiivvi i i i i i i v vv iv C L1M4_orf2#LIN 1339 CTATTTCTTCTTGAGTCAGTTTCGGTAGTTTGTGTCTTTCTAGGAATTTG 1290 chrXqtel1M 311345 TCCATTTCATTTAGATTACCAAATTTATTGCCATATAGTCGGGCAAAATA 311394 i i i v i v i i i vv v i C L1M4_orf2#LIN 1289 TCCATTTCATCTAGGTTATCTAATTTGTTGGCATACAATTGTTCATAGTA 1240 chrXqtel1M 311395 ACTCATAATTATTGCTCTAATTTCCTCTTCATTGGTGG-AAAGTTCTCTC 311443 vii v v v ivi i v ivivvvi i i - v i i C L1M4_orf2#LIN 1239 TTCCCTTATAATCCTTTTTATTTCTGTAAGGTCGGTAGTAATGTCCCCTC 1190 chrXqtel1M 311444 -TTCATTTTTGAGACTAACAATTTAATTTTCTTCTTTCCTTTTTCTAATC 311492 - ii vvi ii i v i ii i ii ii ii C L1M4_orf2#LIN 1189 TTTCATTCCTGATTTTAGTAATTTGAGTCTTCTCTCTTTTTTTCTTGGTC 1140 chrXqtel1M 311493 AAATTAACTACAGGTTTATCTATTTTGTTGGGTTTTTCATAAAACCAACT 311542 ivi i v i v ivi v i C L1M4_orf2#LIN 1139 AGTCTAGCTAAAGGTTTGTCAATTTTGTTGATCTTTTCAAAGAACCAACT 1090 chrXqtel1M 311543 CTTACTTTTAGTTATTAATTCAATAGTTTTCATATTTTTGATTTTATTAA 311592 i iv iiv v vvi v v iv i iv i v C L1M4_orf2#LIN 1089 TTTGGTTTCGTTGATTTTCTCTATTGTTTTTCTATTCTCTATTTCATTTA 1040 chrXqtel1M 311593 TCTCCCC-----TTTTCAGAATTTCTAAGTTGGTATTTAATTGAGGGTTT 311637 i v ----- i i vv ivvvi vv ii iv v- C L1M4_orf2#LIN 1039 TTTCCGCTCTAATCTTTATTATTTCCTTCCTTCTGCTTGCTTT-GGGTTT 991 chrXqtel1M 311638 --TTCATCTGTTATTTTTCTAGCTTTTTTTAGTTGTAAGCCCA----ATT 311681 -- ii- v v - i v v v vii ---- C L1M4_orf2#LIN 990 AGTTTG-CTCTTCTTTTTCTAG-TTTCTTAAGGTGGAAGGTTAGGTTATT 943 chrXqtel1M 311682 CAT----GATCTTCTCTTTATTTTATGCAAGTAATCATCTAGAGATATCA 311727 v ---- iii i v --- vi iv i v v - C L1M4_orf2#LIN 942 GATTTGAGATCTTTCTTCTTTTTTA---ATATAGGCATTTACAGCTAT-A 897 chrXqtel1M 311728 GATTTCCCCTTATA-ATCACTTTGACTGCATCCCGCAAATTTTAGTATGT 311776 i ii vi- iii ?i ii i i C L1M4_orf2#LIN 896 AATTTCCCTCTAAGCACTGCTTTNGCTGCATCCCATAAGTTTTGGTATGT 847 chrXqtel1M 311777 CGTCCCATTATCG---TCATTC-TCTTGGATGAAGTTGTCGATTGCGTCT 311822 i ---i v --- - iii - v v viii v vii C L1M4_orf2#LIN 846 TGT---GTTTTCGTTTTCATTCATCTCAAA-GTATTTTCTAATTTCCCTT 801 chrXqtel1M 311823 ATGATTTGTCTTCCCACCCATTCATTCTTTAGGA-TGAGATTATTTAATT 311871 i v ii iiv vi v - v - i C L1M4_orf2#LIN 800 GTGATTTCTTCTTTGACCCATTGGTTATTTAGGAGTGTG-TTGTTTAATT 752 chrXqtel1M 311872 TCCA 311875 C L1M4_orf2#LIN 751 TCCA 748 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 43.35 CpG sites = 170, Kimura (unadjusted) = 43.98 Transitions / transversions = 1.39 (170/122) Gap_init rate = 0.03 (31 / 919), avg. gap size = 1.71 (53 / 31) 1729 30.94 6.74 2.78 chrXqtel1M 312107 313665 (686335) L1M5_orf2#LINE/L1 1669 3287 (7) m_b360s551i7 15087 chrXqtel1M 312107 AGGATAATACACCATGACCAAGCAGGATTTATAACAGGAATGCAGAGCTG 312156 i ii i vv ii i L1M5_orf2#LIN 1669 AGGATAATACATCATGACCAAGTGGGGTTTATCCCAGGAATGCAAGGTTG 1718 chrXqtel1M 312157 GTTCAATATTAGGAAAACTATTAATTAATATAATCGAGTATATCAATAGC 312206 i i v i ---- i i i iv vi i i v L1M5_orf2#LIN 1719 GTTTAACATTCGAAA----ATCAATCAATGTAATTCACCATATTAACAGA 1764 chrXqtel1M 312207 CAAACTAATAAAAATCATA-GA-----TCAATAGATGCAGAAAAAGCATC 312250 vv vvi v - ----- i L1M5_orf2#LIN 1765 ATAAAGGAGAAAAATCATATGATCATCTCAATAGATGCAGAAAAAGCATT 1814 chrXqtel1M 312251 TGATAAAACCCAACACCCATTCCTATTAAAAA--TACAAGAGATATAGAA 312298 i ii v iv --iv iv i i- i L1M5_orf2#LIN 1815 TGACAAAATTCAACACCCATTCATGATAAAAACTCTCAGCAAAC-TAGGA 1863 chrXqtel1M 312299 ATAAATGGCCTTTTCCTCAAAACAGTCAGTAGCATCTATTTAAAACCATC 312348 i v vvvi vviii v ivi ivv vv L1M5_orf2#LIN 1864 ATAGAAGGGAACTTCCTCAACCTGATAAAGGGCATCTACGAAAAACCTAC 1913 chrXqtel1M 312349 AGCAAGCATCATATGTAATGAAAACAAACTAGAACCATTCCCAGTAAGAT 312398 ? i iv ivi v ? ii ?v v vv L1M5_orf2#LIN 1914 AGCNAACATCATACTTAATGGTGAAANACTGAANGCTTTCCCCCTAAGAT 1963 chrXqtel1M 312399 -AGGAGTGAAGCAAGGTGGCCCACTATCACCATTACTATTCAGTATTGTA 312447 -i iii ii vv i i ? i v ii L1M5_orf2#LIN 1964 CGGGAACAAGACAAGGATGTCCGCTNTCACCACTTCTATTCAACATTGTA 2013 chrXqtel1M 312448 TTAGAAATGCTAGCTTTGGCGATAAGAGAAG--AAAGAGATTAAAGGAAT 312495 i i ii v ivvv i iv -- i v v L1M5_orf2#LIN 2014 CTGGAGGTCCTAGCCAGTGCAATAAGGCAAGAAAAAGAAATAAAAGGCAT 2063 chrXqtel1M 312496 TAGAGTAGGTGAAGAGGAAACCAAATTATCACTCTTTGCAGATGATATG- 312544 v iii v vi i i iv i i ?i v i i - L1M5_orf2#LIN 2064 AAAGATTGGAAAGGAAGAAATAAAACTGTCNTTATTCGCAGATGACATGA 2113 chrXqtel1M 312545 ----------GGAGAACCCTAGAGAATCAACTAAAAAACTACTAAAACCA 312584 ----------i i i ? i v v ? i i L1M5_orf2#LIN 2114 TTGTNTACGTAGAAAATCCNAAAGAATCTACAAANAAACTACTAGAACTA 2163 chrXqtel1M 312585 ATCCACAACTTTAGCAA-GTTGCAGGATATA---TAAAAATGCTGAG--- 312627 vviii v - i ? i --- v v i vi i--- L1M5_orf2#LIN 2164 ATAAGTGAATTTAGCAAGGTCGCNGGATACAAGGTCAATATACAAAAATC 2213 chrXqtel1M 312628 GATT-TATTT---TGTATTAGCAACAAAGTCCAGCAGCAA--GAGATACA 312671 i - --- i i -- v vii v -- i vi? L1M5_orf2#LIN 2214 AATTGTATTTCTATATACTAGCAACAAA--CAATTGGAAAATGAAATTTN 2261 chrXqtel1M 312672 AAGAAGAAATTCCACTTAAAATAATGTC-GATAGTATAAAATATTTGGGA 312720 - iv v i v iii -i v ii ? i i L1M5_orf2#LIN 2262 AA-AAACAATACCATTTACAATAGCATCAAAAAACATNAAATACTTAGGA 2310 chrXqtel1M 312721 CCCTATCTGCCGAGGGAAAGTTAGGATCTATA---TGAACACGACTGCAA 312767 vivv iv i ii? vivvi i i ? --- ---i i L1M5_orf2#LIN 2311 ATAAATCTAACAAAANATGTGCAAGACCTNTACACTGAA---AACTACAA 2357 chrXqtel1M 312768 AACATTTTTG---------------GATCTAATCGGTTGGAAAAATA-GC 312801 vi --------------- i viiiv i i -i L1M5_orf2#LIN 2358 AACATTGCTGAGAGAAATTAAAGAAGACCTAAATAAATGGAGAGATATAC 2407 chrXqtel1M 312802 AAGTGCTCATGGGTAGGCTGAGTGAGTATAATAAAAATGACAATACTACC 312851 v - i i v vv v v i vi ? i v v v L1M5_orf2#LIN 2408 CA-TGTTCATGGATTGGAAGACTCAATATTGTNAAGATGTCAATTCTCCC 2456 chrXqtel1M 312852 CAAATTCATCTCTTTATTTAGTGCCATGCCAATCAAACTCCCAAGAAATT 312901 v v vv i i v v v iv ii L1M5_orf2#LIN 2457 CAAATTGATCTATAGATTCAATGCAATCCCAATCAAAATCCCAGCAGGTT 2506 chrXqtel1M 312902 ATTTTACAGAGCTAGAAAAAATAA---TAAGGTTCATCCGGAAAAACAAA 312948 v ii iv v v iv i --- ii i vi vi L1M5_orf2#LIN 2507 TTTTTGTAGAAATTGACAAGCTGATTCTAAAATTTATATGGAAATGCAAA 2556 chrXqtel1M 312949 AGATCAAGAAT-TTCAAGGGAATTAGTGAAAAAAAAAATGCCAATGAAGG 312997 i i ? -vi iiv i-v i i --v v vv L1M5_orf2#LIN 2557 GGACCNAGAATAGCCAAAACAATC-TTGAAAAAGAAGA--ACAAAGTTGG 2603 chrXqtel1M 312998 TGGCCTAGCTGTGCTAGACCT-AAAACTATATTATAAAGCAGTGGTTATC 313046 v v vi vv i i? i? - i - viii v L1M5_orf2#LIN 2604 AGGACTTACACTACCNGATNTCAAGACT-TATTATAAAGCTACAGTAATC 2652 chrXqtel1M 313047 AAAGCCATTTGGTACTGGC-TAAGAA-ACAGAAGTTGATCAGTGGGATAT 313094 ii vi v i - i - v v i v i i i v L1M5_orf2#LIN 2653 AAGACAGTGTGGTATTGGCGTAAGGATAGACAAATAGATCAATGGAACAG 2702 chrXqtel1M 313095 GTTAGTTTCACAGAACA-AAACAG---TAAACGACTATAGCAATCTAGTG 313140 iv ---- v vv - i ---i v ivv i ?v ?i ii v L1M5_orf2#LIN 2703 AATAG----AGAGTCCAGAAATAGACCCACACATATATGGNCANTTGATT 2748 chrXqtel1M 313141 TTGGACAAA---CCCAAAG-ATCCCAGCTTTGGGGACTAGAACTCACTAT 313186 v ---v ? - vii --- v- i ivvv v L1M5_orf2#LIN 2749 TTTGACAAAGGTGCCAANGCAATTCAG---TGGGGAA-AGGATAGTCTTT 2794 chrXqtel1M 313187 TTGACAAAAACTGCTGGGAAAATTGAA-ATTAATACGGCAGGAACTAGGC 313235 ii viv i v i - iv i v ii v iii? L1M5_orf2#LIN 2795 TCAACAAATGGTGCTGGAACAATTGGATATCCATATGGAAAAAAATGAAN 2844 chrXqtel1M 313236 ATTGACCTACACCTAATACCATATACCAAGATAAGGTTGAGGTGGGTTCC 313285 v i ivi v i i v i v iv i? i i ivi L1M5_orf2#LIN 2845 CTCGACCCCTACCTCACACCATACACAAAAATTAATTCNAGATGGATCAT 2894 chrXqtel1M 313286 CGATTTAGAC-CAAGAG-TGATATTGTAAG-----CAAAGTAGAACACAG 313328 v ii i i-i i - i v i i i-----i i iv i i L1M5_orf2#LIN 2895 AGACCTAAATGTAAAAGNTAAAACTATAAAACTTCTAGAAGAAAACATAG 2944 chrXqtel1M 313329 GACAGTTTAACCTCTCAGATCTGGGGAGAAAGAAGGAATTTGTGTCCA-- 313376 v i --- i iivv i v ?v iiv i v iv ivv -- L1M5_orf2#LIN 2945 GAGAAT---ATCTTCGTGACCTTGGGNTAGGCAAAGATTTCTTAAACAGG 2991 chrXqtel1M 313377 ----AAGAAGAACCGGAACTCATAATTGCACACCAGATAGATAATTTTGA 313422 ---- i v --? - ---v v vv i v v v L1M5_orf2#LIN 2992 ACACAAAAAGCAC--NAAC-CATAA---AAGAAAAAATTGATAAATTGGA 3035 chrXqtel1M 313423 TTATATT-AATTTAAAAAAGTTTTTGTACAAACAAAACTAATGCAGACAA 313471 i ?i i- v --i i iv ?vvv ivi vi ivi v L1M5_orf2#LIN 3036 CTNCATCAAAATTAAAAA--CTTCTGCTCNTCAAAAGACACCGTTAAGAA 3083 chrXqtel1M 313472 GATTGGAAGGGAAG---CAAATTGG--GAAAACATTT----TACATTTAA 313512 i vii v --- i ? -- i ----? v - L1M5_orf2#LIN 3084 AATGAAAAGGCAAGCCACAGANTGGGAGAAAATATTTGCAANACATATA- 3132 chrXqtel1M 313513 GGGTTCTGATAAA-GAC-CATTTCTAAAATATATAAAAAATTGACTCAAA 313560 ---- i - - i v i i i i vviv ? L1M5_orf2#LIN 3133 ----TCTGACAAAGGACTCGTATCCAGAATATATAAAGAACTCCTACAAN 3178 chrXqtel1M 313561 TTTATAAGAATTCAAGCCATTC--TCCAATTGATAAATGGTCAGAGGATA 313608 iv ? --v v vv --i v? v v i i iv L1M5_orf2#LIN 3179 TCAATAANAA--AAAGACAAACAACCCAATANAAAAATGGGCAAAAGACT 3226 chrXqtel1M 313609 TGAACA---ATTTT-CAGATGAAGAAATTAAA---GCCATTTCTTCTGAT 313651 --- i i- i v v ?v --- v vvvi--- i L1M5_orf2#LIN 3227 TGAACAGACACTTCACAAAAGAAGATATNCAAATGGCCAATAAGC---AC 3273 chrXqtel1M 313652 ATGAAAAAGTGCTC 313665 ii L1M5_orf2#LIN 3274 ATGAAAAGATGCTC 3287 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 41.15 CpG sites = 266, Kimura (unadjusted) = 42.22 Transitions / transversions = 1.31 (266/203) Gap_init rate = 0.06 (87 / 1558), avg. gap size = 1.72 (150 / 87) 1776 30.27 6.55 2.40 chrXqtel1M 312107 313267 (686733) L1M4_orf2#LINE/L1 1669 2876 (418) m_b360s551i6 15087 chrXqtel1M 312107 AGGATAATACACCATGACCAAGCAGGATTTATAACAGGAATGCAGAGCTG 312156 v ii vv ii i L1M4_orf2#LIN 1669 AGGATTATACACCATGACCAAGTGGGATTTATCCCAGGAATGCAAGGTTG 1718 chrXqtel1M 312157 GTTCAATATTAGGAAAACTATTAATTAATATAATCGAGTATATCAATAGC 312206 i ?v i ---- i i i vv vi i v L1M4_orf2#LIN 1719 GTTCAACATNCGAAA----ATCAATCAATGTAATACACCATATTAATAGA 1764 chrXqtel1M 312207 CAAACTAATAAAAATCATA-GA-----TCAATAGATGCAGAAAAAGCATC 312250 vv vvi i i i - ----- i i L1M4_orf2#LIN 1765 ATAAAGGACAAAAACCACATGATCATCTCAATAGACGCAGAAAAAGCATT 1814 chrXqtel1M 312251 TGATAAAACCCAACACCCATTCCTATTAAAAATA--CAAGAGATATAGAA 312298 i i v v iv i -- v i i- i L1M4_orf2#LIN 1815 TGACAAAATCCAACACCCTTTCATGATAAAAACACTCAACAAAC-TAGGA 1863 chrXqtel1M 312299 ATAAATGGCCTTTTCCTCAAAACAGTCAGTAGCATCTATTTAAAACCATC 312348 i v vvvi vviii v ivi ivv vv L1M4_orf2#LIN 1864 ATAGAAGGGAACTTCCTCAACCTGATAAAGGGCATCTACGAAAAACCCAC 1913 chrXqtel1M 312349 AGCAAGCATCATATGTAATGAAAACAAACTAGAACCATTCCCAGTAAGAT 312398 v i iv ivi v i ii ?v v vv L1M4_orf2#LIN 1914 AGCTAACATCATACTTAATGGTGAAAGACTGAANGCTTTCCCCCTAAGAT 1963 chrXqtel1M 312399 -AGGAGTGAAGCAAGGTGGCCCACTATCACCATTACTATTCAGTATTGTA 312447 - iii ii vv i i v i i v ii L1M4_orf2#LIN 1964 CAGGAACAAGACAAGGATGTCCGCTCTCGCCACTTCTATTCAACATTGTA 2013 chrXqtel1M 312448 TTAGAAATGCTAGCTTTGGCGATAAGAGAAG--AAAGAGATTAAAGGAAT 312495 i i ii v ivv i v iv -- i v v L1M4_orf2#LIN 2014 CTGGAGGTTCTAGCCAGGGCAATTAGGCAAGAAAAAGAAATAAAAGGCAT 2063 chrXqtel1M 312496 -TAGAGTAGGTGAAGAGGAAACCAAATTATCACTCTTTGCAGATGATATG 312544 -i v - vi i i iiv i v v i i L1M4_orf2#LIN 2064 CCAGATT-GGAAAGGAAGAAGTAAAACTATCTCTATTCGCAGATGACATG 2112 chrXqtel1M 312545 -----------GGAGAACCCTAGAGAATCAACTAAAAAACTACTAAAACC 312583 -----------i i i ii v ? i i i L1M4_orf2#LIN 2113 ATCTTGTATATAGAAAATCCTAAGGAATCCACNAAAAAACTATTAGAACT 2162 chrXqtel1M 312584 AATCCACAACTTTAGCAA-GTTGCAGGATAT---ATAAAAATGCTGAG-- 312627 vv i v i - i--- v v i vi i-- L1M4_orf2#LIN 2163 AATAAACGAGTTCAGCAAGGTTGCAGGATACAAGATCAATATACAAAAAT 2212 chrXqtel1M 312628 -GATT-TATTT---TGTATTAGCAACAAAGTCCAGCAGCAAGAGATACAA 312672 -i - --- ii i ii -- v v v v iv v iv L1M4_orf2#LIN 2213 CAATTGTATTTCTATACACTAGCAATGAA--CAATCCGAAAATGAAATTA 2260 chrXqtel1M 312673 AGAAGA-AATTCCACTTAAAATAATGTC-GATAGTATAAAATATTTGGGA 312720 i - i v iii -i v v i i L1M4_orf2#LIN 2261 AGAAAACAATTCCATTTACAATAGCATCAAAAAGAATAAAATACTTAGGA 2310 chrXqtel1M 312721 CCCTATCTGCCGAGGGAAAGTTAGGATCTATA---TGAACACGACTGCAA 312767 vivv i iv i ii ivvi i ii i --- ---i i L1M4_orf2#LIN 2311 ATAAATTTAACAAAAGAAGTGCAAGACTTGTACACTGAA---AACTACAA 2357 chrXqtel1M 312768 AACATTTTTG---------------GATCTAATCGGTTGGAAAAATAGCA 312802 v --------------- i viiiv i i v v L1M4_orf2#LIN 2358 AACATTGTTGAAAGAAATTAAAGAAGACCTAAATAAATGGAAAGACATCC 2407 chrXqtel1M 312803 AGTGCTCATGGGTAGGCTGAGTGAGTATAATAAAAATGACAATACTACCC 312852 vi i i v vv v v i vi v i i v L1M4_orf2#LIN 2408 CATGTTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCC 2457 chrXqtel1M 312853 AAATTCATCTCTTTATTTAGTGCCATGCCAATCAAACTCCCAAGAAATTA 312902 v vivv i ii v v v v ivvi?i v L1M4_orf2#LIN 2458 AAATTGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGNCTT 2507 chrXqtel1M 312903 TTTTACAGAGCTAGAAAAAATAA---TAAGGTTCATCCGGAAAAACAAAA 312949 i iv v v iv i --- ii vi vi ii L1M4_orf2#LIN 2508 TTTTGCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGG 2557 chrXqtel1M 312950 GATCAAGAAT-TTCAAGGGAATTAGTGAAAAAAAAAATGCCAATGAAGGT 312998 i v -vi iiv i-v i i --v v vv v L1M4_orf2#LIN 2558 GACCCAGAATAGCCAAAACAATC-TTGAAAAAGAAGA--ACAAAGTTGGA 2604 chrXqtel1M 312999 GGCCTAGCTGTGCTAGACCT-AAAACTATATTATAAAGCAGTGGTTATCA 313047 v vi vv v iv ii - - i i viii v L1M4_orf2#LIN 2605 GGACTCACACTTCCCGATTTCAAAACT-TACTACAAAGCTACAGTAATCA 2653 chrXqtel1M 313048 AAGCCATTTGGTACTGGC-TAAG---AAACAGAAGTTGATCAGTGGGATA 313093 ii vi v - --- i v -- v i i L1M4_orf2#LIN 2654 AGACAGTGTGGTACTGGCATAAGGATAGACATA--TAGATCAATGGAATA 2701 chrXqtel1M 313094 ----TGTTAGTTTCACAG-AACAAAACAGTAAACGACTATAG-CAATCTA 313137 ---- vv i--- - i v v? v i--i i - - i L1M4_orf2#LIN 2702 GAATTGAGAGTC---CAGAAATAAACCCNTACAT--TTATGGTCAAT-TG 2745 chrXqtel1M 313138 GTGTTGGACAA----ACCCAAA-GATCCCAGCTTTGGGGACTAGAACTCA 313182 i v v ----i v i -? i v ---- v- ivvv L1M4_orf2#LIN 2746 ATTTTCGACAAGGGTGCCAAGACNATTCAA----TGGGGAA-AGAATAGT 2790 chrXqtel1M 313183 CTATTTGACAAAAACTGCTGGGAAAATTGAA-ATTAATACG-GCAGGAAC 313230 v ii viv v i i - iv i i -iv i i L1M4_orf2#LIN 2791 CTTTTCAACAAATGGTGCTGGGACAACTGGATATCCACATGCAAAAGAAT 2840 chrXqtel1M 313231 TAGGCATTGACCTACACCTAATACCATATACCAAGAT 313267 v i i- v ivi v i v i L1M4_orf2#LIN 2841 GAAGT-TGGACCCCTACCTCACACCATATACAAAAAT 2876 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 38.98 CpG sites = 192, Kimura (unadjusted) = 40.04 Transitions / transversions = 1.27 (192/151) Gap_init rate = 0.05 (58 / 1160), avg. gap size = 1.81 (105 / 58) 1167 29.44 3.80 4.40 chrXqtel1M 313533 314058 (685942) L1ME3Cz_3end#LINE/L1 7 529 (468) m_b360s551i8 15087 chrXqtel1M 313533 TCTAAAATATATAAAAAATTGACTCAAATTTATAAGAATTCAAGCCATTC 313582 i i i i vviv iv --v v --v L1ME3Cz_3end# 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAA--AAAGACA--A 52 chrXqtel1M 313583 TCCAATTGATAAATGGTCAGAGGATATGAACA----ATTTTCAGATGAAG 313628 i v v v i ---- iv v i L1ME3Cz_3end# 53 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chrXqtel1M 313629 AAATTAAA---GCCATTTCTTCTGATATGAAAAAGTGCTCTAAAGCACTA 313675 iivi --- v vvvi--- ii v vvv L1ME3Cz_3end# 103 AAACCCGAATGGCCAATAAAC---ATATGAAAAGATGCTCAACCTCACTA 149 chrXqtel1M 313676 TTGATCAGAGGAATGCAAATTAAGATAACTCTGAGACACCACTACACACC 313725 v i i i i i? vv i i v L1ME3Cz_3end# 150 GTAATCAGGGAAATGCAAATTAAAACNACAATGAGATACCATTTCACACC 199 chrXqtel1M 313726 TCTCCTATTGGCTAAGA--TGACAG---GAAAAGATGTCGAATGCTGGAG 313770 iv vv v i -- i v --- v -- ii i i i v L1ME3Cz_3end# 200 CATCAGATTGGCAAAAATTTAAAAGTCTGACA--ATACCAAGTGTTGGCG 247 chrXqtel1M 313771 GGCATGTGGGAAAACTGGGACGCTGACACATCGTGGGTAGAACTGTGAAT 313820 i v ii v i v v i ii iv i i v i L1ME3Cz_3end# 248 AGGATGTGGAGAAACGGGAACTCTCATACACTGCTGGTGGGAGTGTAAAT 297 chrXqtel1M 313821 AGATCCAACTACTCTGGAGAGCGATTTGGAACTATGCTCAAAAAGTTATC 313870 v i v i i i v v - viv i-- L1ME3Cz_3end# 298 TGGTACAACCACTTTGGAGAGCAATTTGGCAATAT-CTAGTAAAGTTG-- 344 chrXqtel1M 313871 AAACTGTGCATATCCTTTGACCCAGCAGTGTAACTACTGAGCTCATATCC 313920 iv i i vi i viv v ii ivi i L1ME3Cz_3end# 345 AAGATGCGCATACCCTACGACCCAGCAATTCCACTTCTAGGTATATACCC 394 chrXqtel1M 313921 CAGAAAGA---TCTTAAAGG-----AAGGAAAGGGCCCCACATGTGCAAA 313962 i i i --- vi v v ----- i-------- i --- L1ME3Cz_3end# 395 TAGAGAAACTCTCGCACATGTGCACAAGGAG--------ACATGTAC--- 433 chrXqtel1M 313963 AAAAACGTTTGCGGCAGCCCTCTTTGTATCGGCAAGGAACTGGAATCCGA 314012 ii i iiiv vi v vii i ii i v viv L1ME3Cz_3end# 434 AAGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAAC 483 chrXqtel1M 314013 ATAGACGCCCATCAGTAGGAGAATGGCTGAATAACTTGTGGTATAT 314058 v i i i i i v i v L1ME3Cz_3end# 484 CTAAATGTCCATCAATAGGGGAATGGATAAATAAATTGTGGTATAT 529 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 37.10 CpG sites = 85, Kimura (unadjusted) = 38.42 Transitions / transversions = 1.35 (85/63) Gap_init rate = 0.06 (29 / 525), avg. gap size = 1.48 (43 / 29) 13 31.04 2.90 1.43 chrXqtel1M 314580 314648 (685352) (AAAATA)n#Simple_repeat 1 70 (0) m_b360s252i13 15088 chrXqtel1M 314580 AAAATAAAAA-CTGTATAAAAATAAAAATGGCAAAAAGTATGGCAAAT-T 314627 -vviv iiv v iv -iv -v (AAAATA)n#Sim 1 AAAATAAAAATAAAAATAAAAATAAAAATAAAAATAAAAAT-AAAAATAA 49 chrXqtel1M 314628 CAGTAAAAACAAAAACAAAAA 314648 v i i i (AAAATA)n#Sim 50 AAATAAAAATAAAAATAAAAA 70 Matrix = Unknown Transitions / transversions = 0.89 (8/9) Gap_init rate = 0.04 (3 / 68), avg. gap size = 1.00 (3 / 3) 295 26.78 19.42 0.61 chrXqtel1M 315845 315983 (684017) C MIR3#SINE/MIR (2) 206 42 m_b360s601i4 15089 chrXqtel1M 315845 ATCATGGGATAGGAGA-CATCCG-GCTTGAAGGCGCCTTGGAGAGC-TTG 315891 i i viv -ii v - v vi i v - iv C MIR3#SINE/MIR 206 ATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCT 157 chrXqtel1M 315892 AG-CCAACCCTCCTCATTGT-----------------GACCCAGAGAGAT 315923 - - v ----------------- i i C MIR3#SINE/MIR 156 AGTCCAACCC-CCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGT 108 chrXqtel1M 315924 AAAGCAACTTGGTCAGGGTCACA----AAGTTGATATTTGAG--GGGATT 315967 i ii vi i ----? ii iviv -- i C MIR3#SINE/MIR 107 GAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACT 58 chrXqtel1M 315968 TGGTCCCAGATCTTTT 315983 v iv i ii C MIR3#SINE/MIR 57 AGAACCCAGGTCTCCT 42 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 34.72 CpG sites = 24, Kimura (unadjusted) = 34.72 Transitions / transversions = 1.85 (24/13) Gap_init rate = 0.06 (8 / 138), avg. gap size = 3.50 (28 / 8) 15 29.10 1.67 1.67 chrXqtel1M 316788 316847 (683153) (CCT)n#Simple_repeat 1 60 (0) m_b360s252i14 15090 chrXqtel1M 316788 CCCCCGCCT-CTCCTCCATGGGCCCCCACCTCCTCCTCCTTCCCAGTCTC 316836 i v - - vvv i v i i vvi (CCT)n#Simple 1 CCTCCTCCTCCTCCTCC-TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC 49 chrXqtel1M 316837 CGCCTTCTCCT 316847 v i (CCT)n#Simple 50 CTCCTCCTCCT 60 Matrix = Unknown Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.03 (2 / 59), avg. gap size = 1.00 (2 / 2) 424 22.13 3.62 8.33 chrXqtel1M 317607 317744 (682256) MIR#SINE/MIR 13 144 (118) m_b360s601i5 15091 chrXqtel1M 317607 AGTGGTTACAATGC-CAGGC-CTGGAGCCAGAAAGACTCCTCTTCCCAAT 317654 vi - - i - --------- v iiiv MIR#SINE/MIR 13 AGTGGTTAAGA-GCACGGGCTCTGGAGCCAGA---------CTGCCTGGG 52 chrXqtel1M 317655 TTCAAATCTGGCCACAGACACTTACTAG-TGGGCAACCCTAGGGAAGTTA 317703 i iv v v v v - v ii i i v MIR#SINE/MIR 53 TTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTA 102 chrXqtel1M 317704 CTTCACTCCGTCTGT--CTCAGTATCCTTATCTGTCAAATGAG 317744 v ii - -- v i v i MIR#SINE/MIR 103 CTTAACCTC-TCTGTGCCTCAGTTTCCTCATCTGTAAAATGGG 144 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 24.30 CpG sites = 15, Kimura (unadjusted) = 26.40 Transitions / transversions = 1.15 (15/13) Gap_init rate = 0.11 (15 / 137), avg. gap size = 1.07 (16 / 15) 26 0.00 0.00 0.00 chrXqtel1M 317882 317906 (682094) (GCT)n#Simple_repeat 1 25 (0) c_b360s251i3 15092 chrXqtel1M 317882 GCTGCTGCTGCTGCTGCTGCTGCTG 317906 (GCT)n#Simple 1 GCTGCTGCTGCTGCTGCTGCTGCTG 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 222 27.91 16.28 0.00 chrXqtel1M 318108 318193 (681807) MIRc#SINE/MIR 83 182 (86) m_b360s601i6 15093 chrXqtel1M 318108 AGCTTTGGGAACTCAGGAAAGTTGCTTCACCTC----------AGTTTCT 318147 v v v ii v ii v ---------- i MIRc#SINE/MIR 83 AGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCC 132 chrXqtel1M 318148 T-GTTGGCAAAATGGG--TG-TAATACTTGCTCTATCTGCTTTACGTGGT 318193 -i iv i -- i- i i ii i i i iv MIRc#SINE/MIR 133 TCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGT 182 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 36.83 CpG sites = 17, Kimura (unadjusted) = 36.83 Transitions / transversions = 2.43 (17/7) Gap_init rate = 0.05 (4 / 85), avg. gap size = 3.50 (14 / 4) 569 34.74 5.14 0.45 chrXqtel1M 318738 318951 (681049) C L3#LINE/CR1 (2931) 1168 945 m_b360s601i7 15094 chrXqtel1M 318738 CCTGATACTTT-----GTATCTAGTTG-AGGGTCATATATAGATACTATG 318781 ? iii ----- ii v- vi iv v i ii i - v C L3#LINE/CR1 1168 CCTGNTATCCTCCATAGTATCCGGTTTTACAGTTTTATCTGGGCATT-TT 1120 chrXqtel1M 318782 TTTCCCCTTCCCTC-----CCAGCCTAAAACCCCTTTGATTCAATTTGTA 318826 i i -----i ii ii ii ivii iv ii C L3#LINE/CR1 1119 TTTTCCTTTCCCTCAAATTTCAGTTTAAAGTCCTCTTGATCAGGTCGGCG 1070 chrXqtel1M 318827 ACACTACAGACTAATCTATTCTTTCCAAGCACTGTTAGGTGTACTCCATC 318876 vv v ? ? v ivii i iiv vii v i i i C L3#LINE/CR1 1069 AGTCTCCNGNCAAACACGTTCTTCCCGGTCTTCGTGAGATGCACTCCGTC 1020 chrXqtel1M 318877 CCTGATCAGAGACCTGTTAGTCCAATATTTTAAGCTGTGGTCCAGGAATA 318926 ?ii iii ii iiv iii i? ii i vv C L3#LINE/CR1 1019 CCTNGCCAGGAGCCCATCGTTCTGGTATCNTAAGCCATGGTCCAGAAAAC 970 chrXqtel1M 318927 CAAATCCTGTTCTCCAACACTATCT 318951 i i i C L3#LINE/CR1 969 CAAATCCTGTTCTTCGACACCATCT 945 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 43.93 CpG sites = 56, Kimura (unadjusted) = 53.79 Transitions / transversions = 3.11 (56/18) Gap_init rate = 0.02 (4 / 213), avg. gap size = 3.00 (12 / 4) 31 31.64 0.00 1.01 chrXqtel1M 318954 319053 (680947) (TC)n#Simple_repeat 1 99 (0) m_b360s252i15 15095 chrXqtel1M 318954 TCTCCCTCCTTCTCTCTGTCTCTCTGTGTCTCTCTCTGTCTCTGTGTGTG 319003 i ii v v v v v v v - (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT- 49 chrXqtel1M 319004 GTGTGTGTGTATGTGTGTGTGTCTCTGTGTCTCTCAGTCTCTCTCTCTCT 319053 v v v v v v v v v v v v v vv (TC)n#Simple_ 50 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 99 Matrix = Unknown Transitions / transversions = 0.14 (3/22) Gap_init rate = 0.01 (1 / 99), avg. gap size = 1.00 (1 / 1) 31 30.52 1.06 0.00 chrXqtel1M 318970 319063 (680937) (TG)n#Simple_repeat 1 95 (0) m_b360s252i16 15095 chrXqtel1M 318970 TGTCTCTCTGTGTCTCTCTCTGTCTCTGTGTGTG-GTGTGTGTGTATGTG 319018 v v v v v v v v v - i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chrXqtel1M 319019 TGTGTGTCTCTGTGTCTCTCAGTCTCTCTCTCTCTGTGGGTGTGT 319063 v v v v vv v v v v v v v (TG)n#Simple_ 51 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 95 Matrix = Unknown Transitions / transversions = 0.05 (1/22) Gap_init rate = 0.01 (1 / 93), avg. gap size = 1.00 (1 / 1) 12 23.23 6.25 3.03 chrXqtel1M 319063 319126 (680874) (TATATA)n#Simple_repeat 1 66 (0) m_b360s252i17 15096 chrXqtel1M 319063 TATATATATA-ATGT-TAAACATGT-TAAAGTATATGT-TAAATCAAATA 319108 - i - v i i - v - i - v - v (TATATA)n#Sim 1 TATATATATATATATATATATATATATATA-TATATATATATAT-ATATA 48 chrXqtel1M 319109 TGTATAAACATATTTATA 319126 i v i v (TATATA)n#Sim 49 TATATATATATATATATA 66 Matrix = Unknown Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.10 (6 / 63), avg. gap size = 1.00 (6 / 6) 914 36.09 1.46 1.17 chrXqtel1M 319243 319584 (680416) C L3#LINE/CR1 (3173) 926 584 m_b360s601i8 15094 chrXqtel1M 319243 TTCTTA-ATCAGTCCTTATGTTCTGAAGCCTTTGCTTCTGATTGGCAGAA 319291 ii - vvi i v v ii i vivi i iii i v C L3#LINE/CR1 926 TTCCCATATCCTCCTTTCTCTTCCAAAGTCACGACCTTCAACTGGAAGAA 877 chrXqtel1M 319292 GTTCGAAGAACAGCACCTGTACCCCTAAGGCCTTCGGTTTCTTTTCCAAC 319341 vvvvi i v i i v i i vi iv C L3#LINE/CR1 876 GAGATGAAAACACCACCTGTGCCCCCAAGTCCTTCAGTTTCCTGCCCAGG 827 chrXqtel1M 319342 GCTCAACAGTCTTTATCAGCACTTTCTAGTTTCCTTCTGGTACTATCATT 319391 i iv v vi vviiii v i v i iivv i C L3#LINE/CR1 826 ACTTCAAAGTCACTAGAGATGCATTCCAGGTTTCTTCTGACTGTGTCATT 777 chrXqtel1M 319392 TATGCCCACACAAATTGGCAA-AGTAGTTAGTACTCATCTGGTTTGACTA 319440 ii v iii ii i- i v iiv iv v iv C L3#LINE/CR1 776 CGTTCCCACGTGAATCAGCAGGAGTGGGTAGCGGTCGGCGGGTTTGATGA 727 chrXqtel1M 319441 GTCATGGGAGGTTCTTTGTCACACCCTAGATACGTGTCCTGGAAAGACAG 319490 v v i ii ii iii ii ii ii i C L3#LINE/CR1 726 GTCTTGGCAGGCTCTCCGTCACGTCTCGGATACACGCTCCAGGAAGACAG 677 chrXqtel1M 319491 TAGACATCTTTGTT-GTTA--TCGGGTAGACAGACGGTTGCCTCGGTGTC 319537 i v v iivi - ii -- i vvi v ii v i C L3#LINE/CR1 676 CACACCTCCCGATTAGCCACGTCAGGTCTGCATACGGCCGCCTCCGTATC 627 chrXqtel1M 319538 CACTCAGTGGCAAGTCATCAACCACCACACTCTGCCACTTCTTCCTC 319584 - i vi i ivivi i --- C L3#LINE/CR1 626 C-CTCAGCGGGGAGTCACCAACCACCACGACGCGTC---TCTTCCTC 584 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 43.42 CpG sites = 80, Kimura (unadjusted) = 52.66 Transitions / transversions = 1.90 (80/42) Gap_init rate = 0.02 (8 / 341), avg. gap size = 1.12 (9 / 8) 18 27.19 2.50 3.80 chrXqtel1M 319954 320033 (679967) (AAT)n#Simple_repeat 1 79 (0) m_b360s252i18 15097 chrXqtel1M 319954 AATAATTTTGATAATATTAAATGTATTGATTCAATAACAGTATTAA-ATT 320002 vv i v vvi v - v - i i v - v (AAT)n#Simple 1 AATAATAATAATAATAATAATAATAAT-AAT-AATAATAATAATAATAAT 48 chrXqtel1M 320003 ATTAATAATTAATAATAAAATTAATGA-AATA 320033 v - v v i - (AAT)n#Simple 49 AATAATAA-TAATAATAATAATAATAATAATA 79 Matrix = Unknown Transitions / transversions = 0.42 (5/12) Gap_init rate = 0.06 (5 / 79), avg. gap size = 1.00 (5 / 5) 824 31.11 9.66 1.09 chrXqtel1M 320134 320640 (679360) L1ME4c_3end#LINE/L1 6 555 (275) m_b360s551i9 15098 chrXqtel1M 320134 ATTTTTAAAATATAAGGAGA--AT--GAACTCATAAGAATACAAGCCATT 320179 i ? ?v i v-- --i i v v v? v v vv L1ME4c_3end#L 6 ATCTNTANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAAGA 55 chrXqtel1M 320180 CTCCAATCGATAAATGGTCAAAAGATGCTAATGGATAATTTTCCAAACAA 320229 i v v i iiiv ii i iv v? v i L1ME4c_3end#L 56 CCCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAG 105 chrXqtel1M 320230 -AACCATTTCTAGT-------CATATGAAAAAATGCTCCAAATCACTATT 320271 - vi ivv? ------- i i i v vv i v L1ME4c_3end#L 106 GAAATACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTAGT 155 chrXqtel1M 320272 GATTCGAGAAATGCAAATTAAGACAGCTCTGAGGTCCCACTACACACCTC 320321 i ivi ii i vv i v i vi i v L1ME4c_3end#L 156 AATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCTA 205 chrXqtel1M 320322 TCA--CTGGCTAG---TGGGAAAA--GATAATGATGAATGTTGCAGGGTA 320364 i --i i v i--- vii -- iviv i vv i v? L1ME4c_3end#L 206 TTAAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGCTGGCGAGGN 255 chrXqtel1M 320365 TGTGGGAAAACTGGGACATTAAAACATTGTCGGTGGAGTTGTAAACTGGT 320414 i vi v ?i v v ii vi? i L1ME4c_3end#L 256 TGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGGT 305 chrXqtel1M 320415 CCAACCATTCTGGAGAGCAATCTGAGACTATGCCCAAAGGGATGTCAAAC 320464 v v i i i iv v i iviv i vii v v L1ME4c_3end#L 306 ACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAAAA 355 chrXqtel1M 320465 TGTGCATCCCCTTTGATCCAGCAG---------TGGGTCTGTATCCCAAA 320505 v v i i i--------- vv v i i L1ME4c_3end#L 356 TGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAAG 405 chrXqtel1M 320506 G--ATCAT--AAAAAAGGGAAAAGGACCCACGTGTGGAAAACTGTTTGTA 320551 -- v -- i i i -- i ii iivi iv ii v L1ME4c_3end#L 406 GAAATAATTCAAAAGAAGGAAAAAG--CTATATGCACGAAGATGTTCATT 453 chrXqtel1M 320552 GCGGCCCTTTGTGTACTCGGTGGTAAAGAACTGG---------AAATG-- 320590 i vi v v i ----i i ii i i --------- -- L1ME4c_3end#L 454 GCAGCGTTATTTATA----ATAGCGAAAAATTGGAAACAACCTAAATGTC 499 chrXqtel1M 320591 ------GAGTAGAATGGCCACGTAAATTATGGCACATGAATGTGATGGAA 320634 ------v vi ii v i v? ivi L1ME4c_3end#L 500 CAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAA 549 chrXqtel1M 320635 TGTTAT 320640 i L1ME4c_3end#L 550 TATTAT 555 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.93 CpG sites = 90, Kimura (unadjusted) = 42.47 Transitions / transversions = 1.36 (90/66) Gap_init rate = 0.04 (19 / 506), avg. gap size = 2.89 (55 / 19) 834 27.60 8.23 1.72 chrXqtel1M 320180 320507 (679493) L1ME5_3end#LINE/L1 56 404 (537) m_b360s551i10 15098 chrXqtel1M 320180 CTCCAATCGATAAATGGTCAAAAGATGCTAATGGATAATTTTCCAAACA- 320228 i v v v i iiv ii ii v vi v - L1ME5_3end#LI 56 CCCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAG 105 chrXqtel1M 320229 -AAACC---ATTTCTAGT---CATATGAAAAAATGCTCCAAATCACTATT 320271 - --- vvv ii--- i i v v i v L1ME5_3end#LI 106 GAAACCCGAAAGGCTAACAAGCATATGAAGAGATGCTCAAACTCATTAGT 155 chrXqtel1M 320272 GATTCGAGAAATGCAAATTAAGACAGCTCTGAGGTCCCACTACACACCTC 320321 i iv i i vv i vi vi v L1ME5_3end#LI 156 AATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCTA 205 chrXqtel1M 320322 TCA--CTGGCTAG--TGGGAAAA---GATAATGATGAATGTTGCAGGGTA 320364 i -- v i-- vi i--- vii i vv i v L1ME5_3end#LI 206 TTAGACTGGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTGGCGAGGA 255 chrXqtel1M 320365 TGTGGGAAAACTGGGACATTAAAACATTGTCGGTGGAGTTGTAAACTGGT 320414 i ? iv i vi v vi i ii iiv i L1ME5_3end#LI 256 TGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACTGGT 305 chrXqtel1M 320415 CCAACCATTCTGGAGAGCAATCTGAGACTA--TGCCCAAAGGGATGTCAA 320462 v i iv v -- ivi ------ i L1ME5_3end#LI 306 GCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAA------TTAA 349 chrXqtel1M 320463 AC-TGTGCATCCCCTTTGATCCAGCAG---------TGGGTCTGTATCCC 320502 ii- ii v v i i--------- v i L1ME5_3end#LI 350 GTATACGCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATATCCC 399 chrXqtel1M 320503 AAAGA 320507 L1ME5_3end#LI 400 AAAGA 404 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 34.98 CpG sites = 52, Kimura (unadjusted) = 35.48 Transitions / transversions = 1.41 (52/37) Gap_init rate = 0.05 (16 / 327), avg. gap size = 2.06 (33 / 16) 672 30.91 10.04 2.60 chrXqtel1M 320182 320719 (679281) L1ME3G_3end#LINE/L1 54 630 (294) m_b360s551i11 15098 chrXqtel1M 320182 CCAATCGATAAATGGTCAAAAGATGCTAATGGATAATTTTCCAAA----- 320226 v v v i iiv ii ii iv vi ----- L1ME3G_3end#L 54 CCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGGA 103 chrXqtel1M 320227 ----CAAA--ACCATTTCTAGTCATATGAAAAAATGCTCCAAATCACTAT 320270 ---- --i ---v iv i v vv v L1ME3G_3end#L 104 AATACAAATGGCCA---ATAAACATATGAAAAGATGCTCAACCTCACTAG 150 chrXqtel1M 320271 TGATTCGAGAAATGCAAATTAAGACAGCTCTGAGGTCCCACTACACACCT 320320 i iv i i i vv i v i viv i L1ME3G_3end#L 151 TAATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCC 200 chrXqtel1M 320321 CTC--ACTGGC--TAGTGGGAAAA---GATAATGATGAATGTTGCAGGGT 320363 v -- i --v i vvi i--- ivi? i vv i v L1ME3G_3end#L 201 ATCAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGG 250 chrXqtel1M 320364 ATGTGGGAAAACTGGGACATTAAAACATTGTCGGTGGAGTTGTAAACTGG 320413 i i v v vi v v i ii iiv i L1ME3G_3end#L 251 GTGTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGG 300 chrXqtel1M 320414 TCCAACCATTCTGGAGAGCAATCTGAGACTATGCCCAAAGGGATGTCAAA 320463 v i ? i i i iv v -- i vviii - i L1ME3G_3end#L 301 TACAGCCNTTTTGGAGGGCAATTTGGCAGTAT--CTATTAAAAT-TTAAA 347 chrXqtel1M 320464 CTGTGCATCCCCTTTGATCCAGCAG---------TGGGTCTGTATCCCAA 320504 v i v i i--------- ? ?v v i ? L1ME3G_3end#L 348 ATGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTAN 397 chrXqtel1M 320505 AGATCATA-----AAAAAGGGAAAAGGACCCACGTGTGGAAAACTGTTTG 320549 -v ----- v viv v v ?v -- iv iiv ii L1ME3G_3end#L 398 AGA-AATACTCGCACATGTGCACAAGGANGCA--TGTACAAGGATGTTCA 444 chrXqtel1M 320550 TAGCGGCCCTTTGTGTACTCGGTGGTAAAGAACTGG---------AAATG 320590 v i vi v v ----i i ii i i --------- L1ME3G_3end#L 445 TTGCAGCATTGTTTGTA----ATAGCGAAAAATTGGAAACAACCTAAATG 490 chrXqtel1M 320591 --------GAGTAGAATGGCCACGTAAATTATGGCACATGAATGTGATGG 320632 --------v vi ii vi i i vv iiv L1ME3G_3end#L 491 TCCATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGG 540 chrXqtel1M 320633 AATGTTATTGTTCTGTAAGAAACAATCAGCAGGATTTCAGAGG----GGC 320678 ii vvvv ? v i v v vvi i - v v ---- i L1ME3G_3end#L 541 AATACTATGCAGCNGTTAAAAAGAATGAGGTAGATCT-ATATGTACTGAC 589 chrXqtel1M 320679 CTGGAGAGA-CTCACAGGAACTGATGCCGAGTGAAGAGAGCA 320719 v i - - i vv iv ii i i L1ME3G_3end#L 590 ATGGAAAGATCTC-CAAGACATATTGTTGAGTGAAAAAAGCA 630 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 40.82 CpG sites = 87, Kimura (unadjusted) = 41.53 Transitions / transversions = 1.16 (87/75) Gap_init rate = 0.05 (27 / 537), avg. gap size = 2.56 (69 / 27) 15 5.56 0.00 0.00 chrXqtel1M 321129 321147 (678853) (T)n#Simple_repeat 1 19 (0) m_b360s252i19 15099 chrXqtel1M 321129 TTCTTTTTTTTTTTTTTTT 321147 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 226 19.84 1.39 8.96 chrXqtel1M 321438 321509 (678491) DNM1r#Unknown 2479 2545 (2117) m_b360s502i0 15100 chrXqtel1M 321438 TGTATATGTGTATATACGTGCATACATGTATGTGTGCATATAACTGCATA 321487 i i ii ---- i i i-- i DNM1r#Unknown 2479 TGTATGTGTGTATATATGTGTGTA----TATGTGTGTATGTG--TGTATA 2522 chrXqtel1M 321488 T-TGTGTGCATATGTATATGTAT 321509 - ii iii ? DNM1r#Unknown 2523 TATGTGTATATATACGTATNTAT 2545 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 23.04 CpG sites = 13, Kimura (unadjusted) = 25.54 Transitions / transversions = 1.00 (13/0) Gap_init rate = 0.10 (7 / 71), avg. gap size = 1.00 (7 / 7) 246 23.09 3.28 7.69 chrXqtel1M 321457 321578 (678422) Tigger17#DNA/TcMar-Tigger 2283 2399 (274) m_b360s502i1 15101 chrXqtel1M 321457 GCATACATGTATGTGTGCATATAACTGCATATTGTGTGCATA-TGTA--- 321502 i - ? i vv i i i ?i - --- Tigger17#DNA/ 2283 GTATACA-GTATGTGTNCACAGTACTGCGTACTGTGCGNGTACTGTACAG 2331 chrXqtel1M 321503 TATGTATGTACATGAATGTATATGTGCATGCATGTGTGTAAATGAATGTG 321552 i i ------- i i i ii iivi v v Tigger17#DNA/ 2332 TGTGTGTGTAC-------TGTACGTGCGTGTGTGTGTACTGATGACTGAG 2374 chrXqtel1M 321553 TATATGTATGTATATAAATGTATAGT 321578 ?v v vii - ???? Tigger17#DNA/ 2375 TNAAAGTAGACA-ATNNNNGTATAGT 2399 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 25.41 CpG sites = 18, Kimura (unadjusted) = 30.91 Transitions / transversions = 2.25 (18/8) Gap_init rate = 0.09 (11 / 121), avg. gap size = 1.18 (13 / 11) 279 17.20 0.00 5.71 chrXqtel1M 321495 321568 (678432) DNM1r#Unknown 2475 2544 (2118) m_b360s502i2 15102 chrXqtel1M 321495 CATATGTATATGTATGTACATGAATGTATATGTGCATGCATGTGTGTAAA 321544 ii i i i i vi -- i v DNM1r#Unknown 2475 CACGTGTATGTGTGTATATATGTGTGTATATGTG--TGTATGTGTGTATA 2522 chrXqtel1M 321545 TGAATGTGTATATGTATGTATATA 321568 -- i i ? DNM1r#Unknown 2523 T--ATGTGTATATATACGTATNTA 2544 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 16.80 CpG sites = 10, Kimura (unadjusted) = 20.69 Transitions / transversions = 5.00 (10/2) Gap_init rate = 0.05 (4 / 73), avg. gap size = 1.00 (4 / 4) 236 23.22 1.75 1.75 chrXqtel1M 321590 321646 (678354) DNM1r#Unknown 2478 2534 (2128) m_b360s502i3 15102 chrXqtel1M 321590 GTGTGTGTGTGTACAGTA-GTATGTATATGTGTGTATGTATACACACACA 321638 i i - - i i ii i i ii DNM1r#Unknown 2478 GTGTATGTGTGTATA-TATGTGTGTATATGTGTGTATGTGTGTATATATG 2526 chrXqtel1M 321639 CATATACA 321646 ii i DNM1r#Unknown 2527 TGTATATA 2534 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 31.21 CpG sites = 13, Kimura (unadjusted) = 31.21 Transitions / transversions = 1.00 (13/0) Gap_init rate = 0.04 (2 / 56), avg. gap size = 1.00 (2 / 2) 302 23.08 17.58 0.00 chrXqtel1M 321649 321739 (678261) C MIR3#SINE/MIR (59) 149 43 m_b360s601i9 15103 chrXqtel1M 321649 CCTCCTGATTTTATAAATGAAGAAACGAAGTCCCAGAGAAGTCAAGTG-C 321697 i v i i i vi v i v - C MIR3#SINE/MIR 149 CCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGAC 100 chrXqtel1M 321698 CTG-----------ACAACG----AATGCTAGAGGCAGGATGTGAACCCA 321732 i ----------- i ?---- i vi v i ivv C MIR3#SINE/MIR 99 TTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCA 50 chrXqtel1M 321733 GGTGTCC 321739 v C MIR3#SINE/MIR 49 GGTCTCC 43 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 26.86 CpG sites = 12, Kimura (unadjusted) = 28.42 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.03 (3 / 90), avg. gap size = 5.33 (16 / 3) 276 23.44 27.59 0.68 chrXqtel1M 321651 321766 (678234) C MIRc#SINE/MIR (118) 150 4 m_b360s601i10 15103 chrXqtel1M 321651 TCCTGATTTTATAAATGAAGAAACGAAGTCCCAGAGAAGTCAAGTG-CCT 321699 iv i i i vi v i i i - i C MIRc#SINE/MIR 150 TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTT 101 chrXqtel1M 321700 G-----------ACAAC----GAATGCTAGAGGCAGGATGTGAACCCAGG 321734 ----------- i ----i i vi v i ivi C MIRc#SINE/MIR 100 GCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGG 51 chrXqtel1M 321735 T--------------GTCCA--GCTCTTTCCCAATGGCCAACGCTGCC 321766 -------------- -- - v vv v i C MIRc#SINE/MIR 50 TCTTCCTGACTCCAAGTCCAGTGCTCTTT-CCACTGCACCACACTGCC 4 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 26.42 CpG sites = 17, Kimura (unadjusted) = 28.89 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.05 (6 / 115), avg. gap size = 5.50 (33 / 6) 95 13.86 0.00 0.00 chrXqtel1M 322772 322922 (677078) (A)n#Simple_repeat 1 151 (0) m_b360s252i20 15104 chrXqtel1M 322772 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 322821 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chrXqtel1M 322822 AAAAAAAAAAAAAATAAAAAGAAAAAAAAAAAAATGAAAAAAATTAAAAA 322871 v i vi vv (A)n#Simple_r 51 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 100 chrXqtel1M 322872 AAAAATTTTAAAAAATTTCCCCCAAAAATAAAAAAAAAAAAAAAAAAAAA 322921 vvvv vvvvvvvv v (A)n#Simple_r 101 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 150 chrXqtel1M 322922 A 322922 (A)n#Simple_r 151 A 151 Matrix = Unknown Transitions / transversions = 0.12 (2/17) Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0) 84 17.57 7.25 3.14 chrXqtel1M 322937 323212 (676788) (CCA)n#Simple_repeat 1 287 (0) m_b360s252i21 15105 chrXqtel1M 322937 CCACCCACCACC-CC-CCACC-CCACC-CCAACACCCACC-CC-CCACC- 322979 - - - - - v - - - - (CCA)n#Simple 1 CCA-CCACCACCACCACCACCACCACCACCACCA-CCACCACCACCACCA 48 chrXqtel1M 322980 CCACCCACCACCCCCACCCACCACC-CCCCCCCCACC-CCACCCCCACCA 323027 - v - - v v - v - (CCA)n#Simple 49 CCA-CCACCACCACCA-CCACCACCACCACCACCACCACCACCACCACC- 95 chrXqtel1M 323028 ACAACCACCAACCACCA-CACCA-CACCACC-CCACCACCCCCACCCACA 323074 v - - - - v vv (CCA)n#Simple 96 ACCACCACC-ACCACCACCACCACCACCACCACCACCACCACCACCACCA 144 chrXqtel1M 323075 CCACCA-CACCCCCACCCACC-CC-CCCCCCCCCCCCCCCCCAAAAAAAA 323121 - v - - - v v v v v vv vv v (CCA)n#Simple 145 CCACCACCACCACCA-CCACCACCACCACCACCACCACCACCACCACCAC 193 chrXqtel1M 323122 AAAAACCACCACCCAAAACC-CC-CCCCCACC-CCCCCACCCCCACCCAA 323168 v vv - vv - - v - v v - v (CCA)n#Simple 194 CACCACCACCA-CCACCACCACCACCACCACCACCACCACCACCA-CCAC 241 chrXqtel1M 323169 CACCCCCACACCCAAAACAAACA-AACCCCCCCAACCACC-CCACC 323212 v vv vv v v -v v v v - (CCA)n#Simple 242 CACCACCACCACCACCACCACCACCACCACCACCACCACCACCACC 287 Matrix = Unknown Transitions / transversions = 0.00 (0/40) Gap_init rate = 0.11 (29 / 275), avg. gap size = 1.00 (29 / 29) 40 21.81 0.00 0.00 chrXqtel1M 323488 323568 (676432) (A)n#Simple_repeat 1 81 (0) m_b360s252i22 15106 chrXqtel1M 323488 AAAAAAAAAAACAAAAACAAAAAAAACCCAAAAAAAAAAAAAAAACAACA 323537 v v vvv v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chrXqtel1M 323538 AAAACCCCCAAAAACCAAACAAAAAAAAAAA 323568 vvvvv vv v (A)n#Simple_r 51 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 81 Matrix = Unknown Transitions / transversions = 0.00 (0/15) Gap_init rate = 0.00 (0 / 80), avg. gap size = 0.0 (0 / 0) 26 15.69 0.00 0.00 chrXqtel1M 323687 323729 (676271) (A)n#Simple_repeat 1 43 (0) m_b360s252i23 15107 chrXqtel1M 323687 AAAAAAAAAAAAAAAAAAAAACAAACCCCAAAAAAAAAACAAA 323729 v vvvv v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 43 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 14 17.13 0.00 7.14 chrXqtel1M 324010 324054 (675946) (CCAAAAA)n#Simple_repeat 1 42 (0) m_b360s252i24 15108 chrXqtel1M 324010 CCAAAAACCAATAGCCAAAATTTACCCACAAAAAAAAACCAAAAA 324054 v i --- v v vv (CCAAAAA)n#Si 1 CCAAAAACCAAAAACCAAAA---ACCAAAAACCAAAAACCAAAAA 42 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.07 (3 / 44), avg. gap size = 1.00 (3 / 3) 15 13.87 0.00 0.00 chrXqtel1M 324039 324062 (675938) (A)n#Simple_repeat 1 24 (0) m_b360s252i25 15109 chrXqtel1M 324039 AAAAAAAAACCAAAAAAATAAAAA 324062 vv v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAA 24 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 29 0.00 0.00 0.00 chrXqtel1M 324896 324927 (675073) (A)n#Simple_repeat 1 32 (0) m_b360s252i26 15110 chrXqtel1M 324896 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 324927 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 32 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 254 34.52 0.00 0.00 chrXqtel1M 326468 326551 (673449) L1ME3F_3end#LINE/L1 430 513 (477) m_b360s551i12 15111 chrXqtel1M 326468 ACATTTGCAAAACTGTCTATAGCAACCCTTTTTGTAGTGGTAAGGATCTG 326517 v i i v ii i v v i i i i ii v L1ME3F_3end#L 430 ACATGTACAAGAATGTTCATAGCAGCACTGTTCGTAATAGCAAAAAACTG 479 chrXqtel1M 326518 GAAACAGAGTGGACACCCATCAGCTGGGGAATGG 326551 ivviii iii ii v i L1ME3F_3end#L 480 GAAACAACCCAAATGTCCATCGACAGGAGAATGG 513 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 45.47 CpG sites = 21, Kimura (unadjusted) = 50.51 Transitions / transversions = 2.62 (21/8) Gap_init rate = 0.00 (0 / 83), avg. gap size = 0.0 (0 / 0) 13 25.82 0.00 0.00 chrXqtel1M 327638 327674 (672326) (ATT)n#Simple_repeat 1 37 (0) m_b360s252i27 15112 chrXqtel1M 327638 ATTATTATTATTATTAATGTGTTTAATAATAATAATA 327674 v i vv v v v v (ATT)n#Simple 1 ATTATTATTATTATTATTATTATTATTATTATTATTA 37 Matrix = Unknown Transitions / transversions = 0.14 (1/7) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 648 30.17 8.19 0.00 chrXqtel1M 327687 327918 (672082) MIRb#SINE/MIR 2 252 (16) m_b360s601i11 15113 chrXqtel1M 327687 AGTGAAGCTGAGTGGCTCAATAGATACAGCACTGGGGACCGACTCAGGAA 327736 v ii v v iv i i v v v vvviv v iv MIRb#SINE/MIR 2 AGAGGGGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACA 51 chrXqtel1M 327737 GACTCAAGTTCAAATCCAACCTCAGACACTTA-TAA----ATGACCCTAC 327781 iiii i viv v v - i----i i iv MIRb#SINE/MIR 52 GACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 101 chrXqtel1M 327782 ACAAGTCAGTTAACTTCTCCA--CCTCCATCTT-TCA-CTGTAAAATGGG 327827 i i v i ii-- vi i i- - MIRb#SINE/MIR 102 GCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 151 chrXqtel1M 327828 GATAGTAACACTTACCTCCCAAGGTTCCGGTGAAGAT-------GAT-AT 327869 i i i v i viv i ------- - MIRb#SINE/MIR 152 GATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAAT 201 chrXqtel1M 327870 TCA--TAAAGCACTCTGCATAGTGCTGGACATGTACTAGGTACTTCATAA 327917 v -- i iv i iv i ii v i ii iv MIRb#SINE/MIR 202 GCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAA 251 chrXqtel1M 327918 A 327918 MIRb#SINE/MIR 252 A 252 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 36.88 CpG sites = 42, Kimura (unadjusted) = 39.87 Transitions / transversions = 1.50 (42/28) Gap_init rate = 0.03 (8 / 231), avg. gap size = 2.38 (19 / 8) 200 35.29 0.00 0.00 chrXqtel1M 327876 327926 (672074) L2d_3end#LINE/L2 452 502 (14) m_b360s601i12 15114 chrXqtel1M 327876 AGCACTCTGCATAGTGCTGGACATGTACTAGGTACTTCATAAACACCCAT 327925 i iiv i ii ii v ii iv i iii L2d_3end#LINE 452 AGCGCCTAGCACAGTGCTGAGCACATAGTAGGCGCTCAATAAATACTTGT 501 chrXqtel1M 327926 T 327926 L2d_3end#LINE 502 T 502 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 45.62 CpG sites = 15, Kimura (unadjusted) = 55.20 Transitions / transversions = 5.00 (15/3) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 1479 31.95 3.83 3.07 chrXqtel1M 328334 329431 (670569) C L1M4_orf2#LINE/L1 (1612) 1682 577 m_b360s551i13 15115 chrXqtel1M 328334 TGGTGTATTATCCTGGGGATGAGTTGCTGGAATCTCACTGCTAACATTTT 328383 v vvvv iv v vvvi ii C L1M4_orf2#LIN 1682 TGGTGTATAATCCTTTTTATATGTTGCTGGATTCGGTTTGCTAGTATTTT 1633 chrXqtel1M 328384 ACTGAAGATTTTTGCGTCAATATTCATTAGGAA-ATTGGTCTATAATTTT 328432 ii i i v v i - i i C L1M4_orf2#LIN 1632 GTTGAGGATTTTTGCATCTATATTCATAAGGGATATTGGTCTGTAGTTTT 1583 chrXqtel1M 328433 CTCT---------GTTTTCATCCTACCCGTTTTAGTCAGCAGCACCATAT 328473 i --------- i ii - i--- i - v viiv i C L1M4_orf2#LIN 1582 CTTTTCTTGTGATGTCTTTGTC-TG---GTTTTGGT-ATCAGGGTAATAC 1538 chrXqtel1M 328474 CTATGTCATAAAAGGAATTTGGTAGGACTCCTCCTTTCCCTAGTTTTAAA 328523 iviiv i v i v v vii ii i iii v vii C L1M4_orf2#LIN 1537 TGGCCTCATAGAATGAGTTGGGAAGTGTTCCCTCCTCTTCTATTTTTTGG 1488 chrXqtel1M 328524 AATAATTTATATAGCATTGGAGTTAATTGTTCTTTAAATGTTTAGTAAAA 328573 v i i iv v v v i i C L1M4_orf2#LIN 1487 AAGAGTTTGTGAAGGATTGGTGTTAATTCTTCTTTAAATGTTTGGTAGAA 1438 chrXqtel1M 328574 TTCACATGTAAATCCATCTGGCCCTGGAGATTTTTCTT--TAGGAAGTAC 328621 vv i v ? -- ii -- i vi C L1M4_orf2#LIN 1437 TTCACCAGTGAAGCCATCTGGNCCTG--GGCTTTTCTTTGTGGGAAGTTT 1390 chrXqtel1M 328622 ATTAATAGCTTATTTTATTTCTTTTTCTAAAATGCGACTATTTAAATAAT 328671 v i vi v iv i vii ivv iv v i i vv C L1M4_orf2#LIN 1389 TTTGATTACTAATTCAATCTCTTTACTTGTTATAGGTCTATTCAGATTTT 1340 chrXqtel1M 328672 TTACTTCCTCTTCTGTTGACCCGAGCAATCTATATTTTTGTAGCTATTCC 328721 i i i vv iiiiiivi i i i i i i v vv iv C L1M4_orf2#LIN 1339 CTATTTCTTCTTGAGTCAGTTTCGGTAGTTTGTGTCTTTCTAGGAATTTG 1290 chrXqtel1M 328722 TCCATTTCATTTAGATTACCAAATTTATTGCCATATAGTCGGGCAAAATA 328771 i i i v i v i i i vv v i C L1M4_orf2#LIN 1289 TCCATTTCATCTAGGTTATCTAATTTGTTGGCATACAATTGTTCATAGTA 1240 chrXqtel1M 328772 ACTCATAATTATTGCTCTAATTTCCGCTTA---TTGGTGG-AAAGTTCTG 328817 vii v v v ivi i v i -- --- i i - v i iv C L1M4_orf2#LIN 1239 TTCCCTTATAATCCTTTTTATTTCTG--TAAGGTCGGTAGTAATGTCCCC 1192 chrXqtel1M 328818 TCTTTTCATTTTTTGATTTTCTAACAATTTGATTTTCTTCTTTCCTTTTT 328867 - - ii -- ii v i ii i ii i C L1M4_orf2#LIN 1191 TC-TTTCA-TTCCTGATTT--TAGTAATTTGAGTCTTCTCTCTTTTTTTC 1146 chrXqtel1M 328868 CTAATCAAATTAACTACAGGTTTATCTATTTTGTTGGGTTTTTCATAAAG 328917 i ii ivi i v i v ivi v i i C L1M4_orf2#LIN 1145 TTGGTCAGTCTAGCTAAAGGTTTGTCAATTTTGTTGATCTTTTCAAAGAA 1096 chrXqtel1M 328918 CCAACTCTTAGTTTTAGTTATTAATTCAATAGTTTTCATATTTTCAATTT 328967 i i iiv v vvi v v iv i v C L1M4_orf2#LIN 1095 CCAACTTTTGGTTTCGTTGATTTTCTCTATTGTTTTTCTATTCTCTATTT 1046 chrXqtel1M 328968 TATTAATCTCCCC-----TTTTCAGAATTTCTAAGTTGGTATTTAATTGA 329012 i v i v ----- i i vv ivvvi vv ii iv v- C L1M4_orf2#LIN 1045 CATTTATTTCCGCTCTAATCTTTATTATTTCCTTCCTTCTGCTTGCTTT- 997 chrXqtel1M 329013 GGGTTT--TTCATCTGTTATTTTTCTAGCTTTTTTAGTTGTAAACCCAAT 329060 -- ii- v v i i v v v ivii iv C L1M4_orf2#LIN 996 GGGTTTAGTTTG-CTCTTCTTTTTCTAGTTTCTTAAGGTGGAAGGTTAGG 948 chrXqtel1M 329061 TCATAGATCT--TCTCTTTC-TCTATTTTATGCAAGTAAGCACCTAGAGA 329107 i v i --vv - v --- vi i ii v v C L1M4_orf2#LIN 947 TTATTGATTTGAGATCTTTCTTCTTTTTTA---ATATAGGCATTTACAGC 901 chrXqtel1M 329108 TATCAGATTTCCCCTTATA-ACCACTTTGGCTGCATCCCACAAATTTTGG 329156 - i ii vi- ii ? i i C L1M4_orf2#LIN 900 TAT-AAATTTCCCTCTAAGCACTGCTTTNGCTGCATCCCATAAGTTTTGG 852 chrXqtel1M 329157 CATGTCGTCCCATTATTGTCATTC-TCTTGGATGAAGTTGTCGATTGTGT 329205 i i viiv ii v - iii - v v viii vivi C L1M4_orf2#LIN 851 TATGTTGTGTTTTCGTTTTCATTCATCTCAAA-GTATTTTCTAATTTCCC 803 chrXqtel1M 329206 CTATGATTTGTCTTCTCACCCATTCATTCTTTAGGA-TGAGATTACTTAA 329254 i i v ii i v vi v - v - ii C L1M4_orf2#LIN 802 TTGTGATTTCTTCTTTGACCCATTGGTTATTTAGGAGTGTG-TTGTTTAA 754 chrXqtel1M 329255 TTTCCA-ATTAATTTTTGG---TCT---ATTTTCTCCTGGCTTTAT--AT 329295 - -- v i--- i--- i i --- -- C L1M4_orf2#LIN 753 TTTCCACAT--ATTTGTGAATTTCCCAAATTTCCTTCTG---TTATTGAT 709 chrXqtel1M 329296 TGCATGTAATTTTTATTGCATAGTAATCTAGAAAAAGTGCATT-TACTAT 329344 v --- - i v v ii -i i vi i v - iv C L1M4_orf2#LIN 708 TTC---TAA-TTTCATTCCATTGTGGTC-GGAGAACATACTTTGTATGAT 664 chrXqtel1M 329345 TTCTGCCCTTCTGCCTTTGATTTTGAGGT---TTTTATGCCCTGATACGC 329391 vii i ivv i--- ii--- v i i iii C L1M4_orf2#LIN 663 TTCAATCCTTTTAAATTTA---TTGAGACTTGTTTTATGGCCTAACATAT 617 chrXqtel1M 329392 GATCAATCTCTGTGTAGGTTTCGTGAACCGCCGAGAAAAA 329431 i v iiv v v v i i vi vvii i C L1M4_orf2#LIN 616 GGTCTATCCTGGAGAATGTTCCATGTGCACTTGAGAAGAA 577 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 42.43 CpG sites = 205, Kimura (unadjusted) = 43.33 Transitions / transversions = 1.52 (205/135) Gap_init rate = 0.05 (52 / 1097), avg. gap size = 1.46 (76 / 52) 1730 31.11 6.61 2.66 chrXqtel1M 329493 331051 (668949) L1M5_orf2#LINE/L1 1669 3287 (7) m_b360s551i15 15116 chrXqtel1M 329493 AGGATAATACACCATGACCAAGTAGGATTTACAACAGGAATGCAGGGCTG 329542 i i i ivv i i L1M5_orf2#LIN 1669 AGGATAATACATCATGACCAAGTGGGGTTTATCCCAGGAATGCAAGGTTG 1718 chrXqtel1M 329543 GTTCAATATCAGGAAAACTATTAACATAATCGAGTATATCAATAGCCAAA 329592 i i iv i v v i ii iv vi i i vvv L1M5_orf2#LIN 1719 GTTTAACATTCGAAAATCAATCAATGTAATTCACCATATTAACAGAATAA 1768 chrXqtel1M 329593 CTAACAAAAATCATA-GA-----TCAATAGATGCCAAAAAAGCATCTGAT 329636 vvi v - ----- vi i i L1M5_orf2#LIN 1769 AGGAGAAAAATCATATGATCATCTCAATAGATGCAGAAAAAGCATTTGAC 1818 chrXqtel1M 329637 ACAACCCAATACCCATTCCTATTAAAAA--CACAAGAGATATAGGAATAA 329684 v ii i v iv -- v iv i i- i L1M5_orf2#LIN 1819 AAAATTCAACACCCATTCATGATAAAAACTCTCAGCAAAC-TAGGAATAG 1867 chrXqtel1M 329685 ATGGACTTTTCCTCAAAACACTCAGTAGCATCTATTTAAAACCATCAGCA 329734 v ivvi vviiv v ivi ivv vv ? L1M5_orf2#LIN 1868 AAGGGAACTTCCTCAACCTGATAAAGGGCATCTACGAAAAACCTACAGCN 1917 chrXqtel1M 329735 AGCATCATATGTAATGAAAACAAACTAGAACCATTCCCAGTAAGAT-AGG 329783 i iv ivi v ? ii ?v v vv -i L1M5_orf2#LIN 1918 AACATCATACTTAATGGTGAAANACTGAANGCTTTCCCCCTAAGATCGGG 1967 chrXqtel1M 329784 AGTGAAGCAAGGTGGCCCACTATCACCATTACTATTCAGTATTGTATTAG 329833 iii ii vv i i ? i v ii i i L1M5_orf2#LIN 1968 AACAAGACAAGGATGTCCGCTNTCACCACTTCTATTCAACATTGTACTGG 2017 chrXqtel1M 329834 AAATGCTAGCTTTGGCGATAAGAGAAG--AAAGAGATTAAAGGAATTAGA 329881 ii v ivvv i iv -- i v v v ii L1M5_orf2#LIN 2018 AGGTCCTAGCCAGTGCAATAAGGCAAGAAAAAGAAATAAAAGGCATAAAG 2067 chrXqtel1M 329882 GTAGGTGAAGAGGAAACCAAATTATCACTCTTTGCAGATGATATG----- 329926 i v vi i i iv i i ?i v i i ----- L1M5_orf2#LIN 2068 ATTGGAAAGGAAGAAATAAAACTGTCNTTATTCGCAGATGACATGATTGT 2117 chrXqtel1M 329927 ------GGAGAACCCTAGAGAATCAACTAAAAAACTACTAAAACCAATCC 329970 ------i i i ? i v v ? i i vv L1M5_orf2#LIN 2118 NTACGTAGAAAATCCNAAAGAATCTACAAANAAACTACTAGAACTAATAA 2167 chrXqtel1M 329971 ACAACTTTAGCAA-GTTGCAGGATATA---TAAAAATGCTGAG---GATT 330013 iii v - i ? i --- v v i vi i---i L1M5_orf2#LIN 2168 GTGAATTTAGCAAGGTCGCNGGATACAAGGTCAATATACAAAAATCAATT 2217 chrXqtel1M 330014 -TATTT---TGTATTAGCAACAAAGTCCAGCAGCAA--GAGATACAAAGA 330057 - --- i i -- v vii v -- i vi? - L1M5_orf2#LIN 2218 GTATTTCTATATACTAGCAACAAA--CAATTGGAAAATGAAATTTNAA-A 2264 chrXqtel1M 330058 AGAAATTCCACTTAAAATAATGTC-GATAGTATAAAATATTTGGGACCCT 330106 iv v i v iii -i v ii ? i i vivv L1M5_orf2#LIN 2265 AACAATACCATTTACAATAGCATCAAAAAACATNAAATACTTAGGAATAA 2314 chrXqtel1M 330107 ATCTGCCGAGGGAAAGTTAGGATCTATA---TGAACACGACTACAAAACA 330153 iv i ii? vivvi i i ? --- ---i L1M5_orf2#LIN 2315 ATCTAACAAAANATGTGCAAGACCTNTACACTGAA---AACTACAAAACA 2361 chrXqtel1M 330154 TTTTCG---------------GATCTAATCGGTTGGAAAAATA-GCAAGT 330187 vii --------------- i viiiv i i -i v - L1M5_orf2#LIN 2362 TTGCTGAGAGAAATTAAAGAAGACCTAAATAAATGGAGAGATATACCA-T 2410 chrXqtel1M 330188 GCTCATGGGTAGGTTGAGTGAGTATAATAAAAATGACAATACTACCCAAA 330237 i i v vv v v i vi ? i v v v L1M5_orf2#LIN 2411 GTTCATGGATTGGAAGACTCAATATTGTNAAGATGTCAATTCTCCCCAAA 2460 chrXqtel1M 330238 TTCATCTCTTTATTTAGTGCCATGCCAATCAAACTCCCAAGAAATTATTT 330287 v v vv i i v v v iv ii v L1M5_orf2#LIN 2461 TTGATCTATAGATTCAATGCAATCCCAATCAAAATCCCAGCAGGTTTTTT 2510 chrXqtel1M 330288 TACAGAGCTAGAAAAAATAA---TAAGGTTCATCCGGAAAAACAAAAGAT 330334 ii iv v v iv i --- ii i vi vi i i L1M5_orf2#LIN 2511 TGTAGAAATTGACAAGCTGATTCTAAAATTTATATGGAAATGCAAAGGAC 2560 chrXqtel1M 330335 CAAGAAT-TTCAAGGGAATTAGTGAAAAAAAAATGCCAA--TGAAGGTGG 330381 ? -vi iiv i-v i ivi v -- i -- i L1M5_orf2#LIN 2561 CNAGAATAGCCAAAACAATC-TTGAAAAAGAAGAACAAAGTTGGAG--GA 2607 chrXqtel1M 330382 CCTAGCTGTGCTAGACCT-AAAACTATATTATAAAGCAGTGGTTATCAAA 330430 i - vv i i? i? - i - viii v i L1M5_orf2#LIN 2608 CTTA-CACTACCNGATNTCAAGACT-TATTATAAAGCTACAGTAATCAAG 2655 chrXqtel1M 330431 GCCATTTGGTACTGGC-TAAGAAACAGAGAAGTTAATCAGTGGAATATGT 330479 i vi v i - -i i v i vi i i viv L1M5_orf2#LIN 2656 ACAGTGTGGTATTGGCGTAAG-GATAGACAAATAGATCAATGGAACAGAA 2704 chrXqtel1M 330480 TAG---GTTCACAGAACAAAACAGTAAACGACTATAGCAATCTAGTGTTG 330526 --- i v - i i v --i v ivv i ?v ?i ii v v L1M5_orf2#LIN 2705 TAGAGAGTCCAGA-AATAGACC--CACACATATATGGNCANTTGATTTTT 2751 chrXqtel1M 330527 GACAAA---CCCAAAG-ATCCCAGCTTTGGGGACTAGAACTCACTATTTG 330572 ---v ? - vii --- v- i ivvv v ii L1M5_orf2#LIN 2752 GACAAAGGTGCCAANGCAATTCAG---TGGGGAA-AGGATAGTCTTTTCA 2797 chrXqtel1M 330573 ACAAAAACTGCTGGGGAAAATTGGAAATTAATACGGCAGGAACTAGGCAT 330622 viv - i v v iv i v ii v iii?v L1M5_orf2#LIN 2798 ACAAATGGTGCT-GGAACAATTGGATATCCATATGGAAAAAAATGAANCT 2846 chrXqtel1M 330623 TGACCTACACCTAATACCATATACCAAGATAAGGTTGAGGTGGGTTCCCG 330672 i ivi v i i v i v iv i? i i iviv L1M5_orf2#LIN 2847 CGACCCCTACCTCACACCATACACAAAAATTAATTCNAGATGGATCATAG 2896 chrXqtel1M 330673 ATTTAGAC-CAAGAG-TGATATTGTAAGGC----AAAGTAGAACACAGGA 330716 ii i i-i i - i v i i ii ---- i iv i i L1M5_orf2#LIN 2897 ACCTAAATGTAAAAGNTAAAACTATAAAACTTCTAGAAGAAAACATAGGA 2946 chrXqtel1M 330717 CAGTTTAACCTCTCAGATCTGGGGAGAAAGAAGGAATTTGTGTCCA---- 330762 v i --- i iivv i v ?v iiv i v iv ivv ---- L1M5_orf2#LIN 2947 GAAT---ATCTTCGTGACCTTGGGNTAGGCAAAGATTTCTTAAACAGGAC 2993 chrXqtel1M 330763 --AAGAAGAACCGGAACTCATAATTGCACACCAGATAGATAATTTTGATT 330810 -- i v --? - ---v v vv i v v v i L1M5_orf2#LIN 2994 ACAAAAAGCAC--NAAC-CATAA---AAGAAAAAATTGATAAATTGGACT 3037 chrXqtel1M 330811 ATATT-AATTTAAAAAAGGTTTTGTACAAACAAAACTAATGCAGACAAGA 330859 ?i i- v --v i iv ?vvv ivi vi ivi v i L1M5_orf2#LIN 3038 NCATCAAAATTAAAAA--CTTCTGCTCNTCAAAAGACACCGTTAAGAAAA 3085 chrXqtel1M 330860 TTGGAAGGGAAG---CAAATTGG--GAAAACATTT----TACATTTAAGG 330900 vii v --- i ? -- i ----? v --- L1M5_orf2#LIN 3086 TGAAAAGGCAAGCCACAGANTGGGAGAAAATATTTGCAANACATATA--- 3132 chrXqtel1M 330901 GTTCTGATAAA-GAC-CATTTCTAAAATATATAAAAAATTGACTCAAATT 330948 -- i - - i v i i i i vviv ? i L1M5_orf2#LIN 3133 --TCTGACAAAGGACTCGTATCCAGAATATATAAAGAACTCCTACAANTC 3180 chrXqtel1M 330949 TATAAGAATTCAAGCCATTC--TCCAATTGATAAATGGTCAGAGGATATG 330996 v ? --v v vv --i v? v v i i iv L1M5_orf2#LIN 3181 AATAANAA--AAAGACAAACAACCCAATANAAAAATGGGCAAAAGACTTG 3228 chrXqtel1M 330997 AACA---ATTTT-CAGATGAAGAAATTAAA---GCCATTTCTTCTGATAT 331039 --- i i- i v v ?v --- v vvvi--- i L1M5_orf2#LIN 3229 AACAGACACTTCACAAAAGAAGATATNCAAATGGCCAATAAGC---ACAT 3275 chrXqtel1M 331040 GAAAAAGTGCTC 331051 ii L1M5_orf2#LIN 3276 GAAAAGATGCTC 3287 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 41.48 CpG sites = 270, Kimura (unadjusted) = 42.56 Transitions / transversions = 1.34 (270/202) Gap_init rate = 0.05 (83 / 1558), avg. gap size = 1.76 (146 / 83) 1760 30.63 6.29 2.07 chrXqtel1M 329493 330652 (669348) L1M4_orf2#LINE/L1 1669 2876 (418) m_b360s551i14 15116 chrXqtel1M 329493 AGGATAATACACCATGACCAAGTAGGATTTACAACAGGAATGCAGGGCTG 329542 v i ivv i i L1M4_orf2#LIN 1669 AGGATTATACACCATGACCAAGTGGGATTTATCCCAGGAATGCAAGGTTG 1718 chrXqtel1M 329543 GTTCAATATCAGGAAAACTATTAACATAATCGAGTATATCAATAGCCAAA 329592 i ?v i v v i ii vv vi i vvv L1M4_orf2#LIN 1719 GTTCAACATNCGAAAATCAATCAATGTAATACACCATATTAATAGAATAA 1768 chrXqtel1M 329593 CTAACAAAAATCATA-GA-----TCAATAGATGCCAAAAAAGCATCTGAT 329636 vvi i i - ----- i vi i i L1M4_orf2#LIN 1769 AGGACAAAAACCACATGATCATCTCAATAGACGCAGAAAAAGCATTTGAC 1818 chrXqtel1M 329637 ACAACCCAATACCCATTCCTATTAAAAACA--CAAGAGATATAGGAATAA 329684 v i i v v iv -- v i i- i L1M4_orf2#LIN 1819 AAAATCCAACACCCTTTCATGATAAAAACACTCAACAAAC-TAGGAATAG 1867 chrXqtel1M 329685 ATGGACTTTTCCTCAAAACACTCAGTAGCATCTATTTAAAACCATCAGCA 329734 v ivvi vviiv v ivi ivv vv v L1M4_orf2#LIN 1868 AAGGGAACTTCCTCAACCTGATAAAGGGCATCTACGAAAAACCCACAGCT 1917 chrXqtel1M 329735 AGCATCATATGTAATGAAAACAAACTAGAACCATTCCCAGTAAGAT-AGG 329783 i iv ivi v i ii ?v v vv - L1M4_orf2#LIN 1918 AACATCATACTTAATGGTGAAAGACTGAANGCTTTCCCCCTAAGATCAGG 1967 chrXqtel1M 329784 AGTGAAGCAAGGTGGCCCACTATCACCATTACTATTCAGTATTGTATTAG 329833 iii ii vv i i v i i v ii i i L1M4_orf2#LIN 1968 AACAAGACAAGGATGTCCGCTCTCGCCACTTCTATTCAACATTGTACTGG 2017 chrXqtel1M 329834 AAATGCTAGCTTTGGCGATAAGAGAAG--AAAGAGATTAAAGGAAT-TAG 329880 ii v ivv i v iv -- i v v -i L1M4_orf2#LIN 2018 AGGTTCTAGCCAGGGCAATTAGGCAAGAAAAAGAAATAAAAGGCATCCAG 2067 chrXqtel1M 329881 AGTAGGTGAAGAGGAAACCAAATTATCACTCTTTGCAGATGATATG---- 329926 v - vi i i iiv i v v i i ---- L1M4_orf2#LIN 2068 ATT-GGAAAGGAAGAAGTAAAACTATCTCTATTCGCAGATGACATGATCT 2116 chrXqtel1M 329927 -------GGAGAACCCTAGAGAATCAACTAAAAAACTACTAAAACCAATC 329969 -------i i i ii v ? i i i v L1M4_orf2#LIN 2117 TGTATATAGAAAATCCTAAGGAATCCACNAAAAAACTATTAGAACTAATA 2166 chrXqtel1M 329970 CACAACTTTAGCAA-GTTGCAGGATAT---ATAAAAATGCTGAG---GAT 330012 v i v i - i--- v v i vi i---i L1M4_orf2#LIN 2167 AACGAGTTCAGCAAGGTTGCAGGATACAAGATCAATATACAAAAATCAAT 2216 chrXqtel1M 330013 T-TATTT---TGTATTAGCAACAAAGTCCAGCAGCAAGAGATACAAAGAA 330058 - --- ii i ii -- v v v v iv v iv L1M4_orf2#LIN 2217 TGTATTTCTATACACTAGCAATGAA--CAATCCGAAAATGAAATTAAGAA 2264 chrXqtel1M 330059 GA-AATTCCACTTAAAATAATGTC-GATAGTATAAAATATTTGGGACCCT 330106 i - i v iii -i v v i i vivv L1M4_orf2#LIN 2265 AACAATTCCATTTACAATAGCATCAAAAAGAATAAAATACTTAGGAATAA 2314 chrXqtel1M 330107 ATCTGCCGAGGGAAAGTTAGGATCTATA---TGAACACGACTACAAAACA 330153 i iv i ii ivvi i ii i --- ---i L1M4_orf2#LIN 2315 ATTTAACAAAAGAAGTGCAAGACTTGTACACTGAA---AACTACAAAACA 2361 chrXqtel1M 330154 TTTTCG---------------GATCTAATCGGTTGGAAAAATAGCAAGTG 330188 v i --------------- i viiiv i i v vvi L1M4_orf2#LIN 2362 TTGTTGAAAGAAATTAAAGAAGACCTAAATAAATGGAAAGACATCCCATG 2411 chrXqtel1M 330189 CTCATGGGTAGGTTGAGTGAGTATAATAAAAATGACAATACTACCCAAAT 330238 i i v vv v v i vi v i i v L1M4_orf2#LIN 2412 TTCATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAAT 2461 chrXqtel1M 330239 TCATCTCTTTATTTAGTGCCATGCCAATCAAACTCCCAAGAAATTATTTT 330288 v vivv i ii v v v v ivvi?i v L1M4_orf2#LIN 2462 TGATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGNCTTTTTT 2511 chrXqtel1M 330289 ACAGAGCTAGAAAAAATAA---TAAGGTTCATCCGGAAAAACAAAAGATC 330335 i iv v v iv i --- ii vi vi ii i L1M4_orf2#LIN 2512 GCAGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACC 2561 chrXqtel1M 330336 AAGAAT-TTCAAGGGAATTAGTGAAAAAAAAATGCCAATGAAGGT---GG 330381 v -vi iiv i-v i i---- ii v --- L1M4_orf2#LIN 2562 CAGAATAGCCAAAACAATC-TTGAAAAAGAAG----AACAAAGTTGGAGG 2606 chrXqtel1M 330382 CCTAGCTGTGCTAGACCT-AAAACTATATTATAAAGCAGTGGTTATCAAA 330430 v vi vv v iv ii - - i i viii v i L1M4_orf2#LIN 2607 ACTCACACTTCCCGATTTCAAAACT-TACTACAAAGCTACAGTAATCAAG 2655 chrXqtel1M 330431 GCCATTTGGTACTGGC-TAAGAAACAGAGAAGTTAATCAGTGGAATATG- 330478 i vi v - -i i v vi vi i vi- L1M4_orf2#LIN 2656 ACAGTGTGGTACTGGCATAAG-GATAGACATATAGATCAATGGAATAGAA 2704 chrXqtel1M 330479 -TTAG-GTTCACAGAACAAAACAGTAAACGACTATAG-CAATCTAGTGTT 330525 - v - i v - i v v? v i--i i - - ii v L1M4_orf2#LIN 2705 TTGAGAGTCCAGA-AATAAACCCNTACAT--TTATGGTCAAT-TGATTTT 2750 chrXqtel1M 330526 GGACAA----ACCCAAA-GATCCCAGCTTTGGGGACTAGAACTCACTATT 330570 v ----i v i -? i v ---- v- ivvv v L1M4_orf2#LIN 2751 CGACAAGGGTGCCAAGACNATTCAA----TGGGGAA-AGAATAGTCTTTT 2795 chrXqtel1M 330571 TGACAAAAACTGCTGGGGAAAATTGGAAATTAATACG-GCAGGAACTAGG 330619 ii viv - v i v iv i i -iv i iv i L1M4_orf2#LIN 2796 CAACAAATGGTGCT-GGGACAACTGGATATCCACATGCAAAAGAATGAAG 2844 chrXqtel1M 330620 CATTGACCTACACCTAATACCATATACCAAGAT 330652 i- v ivi v i v i L1M4_orf2#LIN 2845 T-TGGACCCCTACCTCACACCATATACAAAAAT 2876 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.61 CpG sites = 194, Kimura (unadjusted) = 40.67 Transitions / transversions = 1.26 (194/154) Gap_init rate = 0.05 (54 / 1159), avg. gap size = 1.81 (98 / 54) 1150 29.63 3.81 4.21 chrXqtel1M 330919 331443 (668557) L1ME3Cz_3end#LINE/L1 7 529 (468) m_b360s551i16 15116 chrXqtel1M 330919 TCTAAAATATATAAAAAATTGACTCAAATTTATAAGAATTCAAGCCATTC 330968 i i i i vviv iv --v v --v L1ME3Cz_3end# 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAA--AAAGACA--A 52 chrXqtel1M 330969 TCCAATTGATAAATGGTCAGAGGATATGAACA----ATTTTCAGATGAAG 331014 i v v v i ---- iv v i L1ME3Cz_3end# 53 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chrXqtel1M 331015 AAATTAAA---GCCATTTCTTCTGATATGAAAAAGTGCTCTAAAGCACTA 331061 iivi --- v vvvi--- ii v vvv L1ME3Cz_3end# 103 AAACCCGAATGGCCAATAAAC---ATATGAAAAGATGCTCAACCTCACTA 149 chrXqtel1M 331062 TTGATCAGAGAAATGCAAATTAAGATAACTCTGAGACGCCACTACACACC 331111 v i i i i? vv ii i v L1ME3Cz_3end# 150 GTAATCAGGGAAATGCAAATTAAAACNACAATGAGATACCATTTCACACC 199 chrXqtel1M 331112 TCTCCTATTGGCTAAGA--TGACAG---GAAAAGATGTCGAATGCTGGAG 331156 iv vv v i -- i v --- v -- ii i i i v L1ME3Cz_3end# 200 CATCAGATTGGCAAAAATTTAAAAGTCTGACA--ATACCAAGTGTTGGCG 247 chrXqtel1M 331157 GGCATGTGGGAAAACTGGGACGCTGACACATCGTGGGTAGAACTGTGAAT 331206 i v ii v i v v i ii iv i i v i L1ME3Cz_3end# 248 AGGATGTGGAGAAACGGGAACTCTCATACACTGCTGGTGGGAGTGTAAAT 297 chrXqtel1M 331207 AGATCCAACTACTCTGGAGAGCGATTTGGAACTATGCTCAAAAAGTTATC 331256 v i v i i i v v - viv i-- L1ME3Cz_3end# 298 TGGTACAACCACTTTGGAGAGCAATTTGGCAATAT-CTAGTAAAGTTG-- 344 chrXqtel1M 331257 AAACTGTGCATATCCTTTGACCCAGCAGTGTAACTACTGAGCTCATATCC 331306 iv i i vi i viv v ii ivi i L1ME3Cz_3end# 345 AAGATGCGCATACCCTACGACCCAGCAATTCCACTTCTAGGTATATACCC 394 chrXqtel1M 331307 CAGAAAGA---TCTTAAAGG-----AAGGAAAGGGCCCCACATGTGCAAA 331348 i i i --- vi v v ----- i-------- i -- L1ME3Cz_3end# 395 TAGAGAAACTCTCGCACATGTGCACAAGGAG--------ACATGTAC--A 434 chrXqtel1M 331349 AAAACGTTTGCGGCAGCCCTCTTTGTATCGGCAAGGAACTGGAATCCGAA 331398 ii i iiiv vi v vii i ii i v vivv L1ME3Cz_3end# 435 AGGATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACC 484 chrXqtel1M 331399 TAGACGCCCATCAGTTGGAGAATGGCTGAATAACTTGTGGTATAT 331443 i i i i v i v i v L1ME3Cz_3end# 485 TAAATGTCCATCAATAGGGGAATGGATAAATAAATTGTGGTATAT 529 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 37.41 CpG sites = 85, Kimura (unadjusted) = 38.74 Transitions / transversions = 1.33 (85/64) Gap_init rate = 0.05 (28 / 524), avg. gap size = 1.50 (42 / 28) 16 9.32 0.00 0.00 chrXqtel1M 332022 332044 (667956) (A)n#Simple_repeat 1 23 (0) m_b360s252i28 15117 chrXqtel1M 332022 AAAAAAACAAAAAAACAAAAAAA 332044 v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAA 23 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 16 19.09 0.00 0.00 chrXqtel1M 332594 332623 (667377) (T)n#Simple_repeat 1 30 (0) m_b360s252i29 15118 chrXqtel1M 332594 TTTTCTTTTTTTCTTCAATTTTTTTTTTTT 332623 i i ivv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 30 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 15 13.67 0.00 0.00 chrXqtel1M 332718 332741 (667259) (A)n#Simple_repeat 1 24 (0) m_b360s252i30 15119 chrXqtel1M 332718 AAAAAATGAAAAAAAAAAAAACAA 332741 vi v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAA 24 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 296 25.59 16.67 5.00 chrXqtel1M 333244 333387 (666613) C MIR3#SINE/MIR (7) 201 42 m_b360s601i13 15120 chrXqtel1M 333244 AGCATCATGGGATGGGAGACATCCGGCTTGAAGGCGCCTTGGGAGAGC-T 333292 v i i vv ------ v vi i - v - C MIR3#SINE/MIR 201 AGAATCATAGAATGTCAGA------GCTGGAAGGGACCTTAG-AGATCAT 159 chrXqtel1M 333293 TGAGCCCAACCCTCCTCATTGT-----------------GACCCAGAGAG 333325 iv i - v ----------------- i C MIR3#SINE/MIR 158 CTAGTCCAACCC-CCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAG 110 chrXqtel1M 333326 ATAAAGCAACTTGGTCAGGGTCACA----AAGTTGATATTTGAG--GGGA 333369 i i ii vi i ----? ii iviv -- C MIR3#SINE/MIR 109 GTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGA 60 chrXqtel1M 333370 TTTGGTCCCAGATCTTTT 333387 i v iv i ii C MIR3#SINE/MIR 59 CTAGAACCCAGGTCTCCT 42 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 32.78 CpG sites = 22, Kimura (unadjusted) = 32.78 Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.08 (12 / 143), avg. gap size = 2.67 (32 / 12) 186 34.78 8.74 1.02 chrXqtel1M 334844 335026 (664974) C L2#LINE/L2 (73) 3009 2813 m_b361s601i1 15121 chrXqtel1M 334844 GGGGAGCAGCCAGGAACTAACTCTGAGTACATCGGGGAGAG-------GA 334886 i i v iviv v v iv iv v i v ------- C L2#LINE/L2 3009 GAGGAACAGCAAGGAGGCCAGTGTGGCTGGAGCGGAGTGAGCGAGGGGGA 2960 chrXqtel1M 334887 AAATGG-AGGA----AGCCCAGAAGGGTGGGGAGGGCCCA-CTGGGGGAG 334930 i i - ---- vi ii iiv i v -v viv v C L2#LINE/L2 2959 GAGTGGTAGGAGATGAGGTCAGAGAGGTAACGGGGGACCAGATCATGTAG 2910 chrXqtel1M 334931 GGCTCGGAAAGCC-CAGGAAGGACTTTT-CTATTGGATCCGGAAGGTGAG 334978 iiv v i -iv v v- v -- ii v iv v v C L2#LINE/L2 2909 GGCCTTGTAGGCCATTGTAAGGACTTTGGCTTTT--ACTCTGAGTGAGAT 2862 chrXqtel1M 334979 AGGGAGCCACGGGAGCTTATTGAA-AGGGGAGTGACATAGCCCCACTTA 335026 i i iv vv v i- i iii iv C L2#LINE/L2 2861 GGGAAGCCATTGGAGGGTTTTGAGCAGAGGAGTGACATGATCTGACTTA 2813 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 47.69 CpG sites = 32, Kimura (unadjusted) = 47.69 Transitions / transversions = 1.03 (32/31) Gap_init rate = 0.05 (9 / 182), avg. gap size = 2.00 (18 / 9) 217 33.74 8.00 3.18 chrXqtel1M 334879 335028 (664972) C AmnL2-1#LINE/L2 (322) 2291 2135 m_b361s601i2 15121 chrXqtel1M 334879 GGAGAGGAAAATGGAGGAAGCCCAGA----------AGGGTGGGGAGGGC 334918 i ii i i ii v v i---------- v i vii i C AmnL2-1#LINE/ 2291 GGGGAGGGGAGTAGAGAGAGACAAGGTCCGTGAGGTAGGCTGGAGCAAGT 2242 chrXqtel1M 334919 CCACTGGGGGAGGGCTCGGAAAGCCCAGGAAGG-ACTTTTCTATTGGATC 334967 i---- i ivi i v- - v vv i C AmnL2-1#LINE/ 2241 CCAT----GGAGGGTTTTAAAAACA-AGGAAGGCAATTTTGAACTGGATC 2197 chrXqtel1M 334968 CGGAAGGTGAGAGGGAGCCACGGGAGCTTATTGA-AAGGGGAGTGACATA 335016 v ivvi vi vv i vv -i v i ii i C AmnL2-1#LINE/ 2196 CTGAAATGAATGGGGAGCCAGTGGAGTTGTTTGAGGATGGGGGTGATGTG 2147 chrXqtel1M 335017 GCCCCACTTATT 335028 i v i v C AmnL2-1#LINE/ 2146 GTCGCGCTTCTT 2135 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 45.35 CpG sites = 29, Kimura (unadjusted) = 46.67 Transitions / transversions = 1.45 (29/20) Gap_init rate = 0.05 (8 / 149), avg. gap size = 2.12 (17 / 8) 410 25.66 2.17 6.82 chrXqtel1M 335090 335227 (664773) MIR#SINE/MIR 13 144 (118) m_b361s601i3 15122 chrXqtel1M 335090 AGTGGTTACAATGCCAGGC-CTGGAGCCAGAAAGACTCCTCTTCCCAATT 335138 vi vvv i - --------- v iiiv MIR#SINE/MIR 13 AGTGGTTAAGAGCACGGGCTCTGGAGCCAGA---------CTGCCTGGGT 53 chrXqtel1M 335139 TCAAATCTGGCCACAGACACTTACTAGCGG-GCAACCCTAGGGAAGTTAC 335187 i iv v v v v v - ii i i v MIR#SINE/MIR 54 TCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTAC 103 chrXqtel1M 335188 TTCAC-TCCGTCTGTCTCAGTATCCTTATCTGTCAAATGAG 335227 v - iv v i v i v i MIR#SINE/MIR 104 TTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGG 144 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.27 CpG sites = 15, Kimura (unadjusted) = 31.45 Transitions / transversions = 0.83 (15/18) Gap_init rate = 0.09 (12 / 137), avg. gap size = 1.00 (12 / 12) 30 0.00 0.00 0.00 chrXqtel1M 335366 335393 (664607) (GCT)n#Simple_repeat 1 28 (0) c_b361s251i0 15123 chrXqtel1M 335366 GCTGCTGCTGCTGCTGCTGCTGCTGCTG 335393 (GCT)n#Simple 1 GCTGCTGCTGCTGCTGCTGCTGCTGCTG 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 207 29.07 16.28 0.00 chrXqtel1M 335596 335681 (664319) MIRc#SINE/MIR 83 182 (86) m_b361s601i4 15124 chrXqtel1M 335596 AGCTTTGGGAACTCAGGAAAGTTGCTTCACCTC----------AGTTTCT 335635 v v v ii v ii v ---------- i MIRc#SINE/MIR 83 AGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCC 132 chrXqtel1M 335636 T-GTTGGCAAAATGGG---TGTAATACTTGCTCTATCTGCTTTACGTGGT 335681 -i iv i ---vi i i ii i i i iv MIRc#SINE/MIR 133 TCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGT 182 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.65 CpG sites = 17, Kimura (unadjusted) = 38.65 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.04 (3 / 85), avg. gap size = 4.67 (14 / 3) 35 0.00 0.00 0.00 chrXqtel1M 335983 336012 (663988) (CA)n#Simple_repeat 1 30 (0) c_b361s251i1 15125 chrXqtel1M 335983 CACACACACACACACACACACACACACACA 336012 (CA)n#Simple_ 1 CACACACACACACACACACACACACACACA 30 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 538 34.08 2.79 0.00 chrXqtel1M 336281 336459 (663541) C L3#LINE/CR1 (2971) 1128 945 m_b361s601i5 15126 chrXqtel1M 336281 GGTCATATGTTTCCCCTTCCCTC-----CCAGCCTAAAACCCCTTTGATT 336325 v v v i i -----i ii ii ii i C L3#LINE/CR1 1128 GGGCATTTTTTTTCCTTTCCCTCAAATTTCAGTTTAAAGTCCTCTTGATC 1079 chrXqtel1M 336326 CAATTTGTAACACTACAGACTAATCTATTCTTTCCAAGCACTGTTAGGTG 336375 vii iv ii vv v ? ? v ivii i iiv vii v i C L3#LINE/CR1 1078 AGGTCGGCGAGTCTCCNGNCAAACACGTTCTTCCCGGTCTTCGTGAGATG 1029 chrXqtel1M 336376 TACTCCATCCCTGATCAGAGACCTGTTAGTCCAATATTTTAAGCTGTGGT 336425 i i ?ii iii ii iiv iii i? ii C L3#LINE/CR1 1028 CACTCCGTCCCTNGCCAGGAGCCCATCGTTCTGGTATCNTAAGCCATGGT 979 chrXqtel1M 336426 CCAGGAATACAAATCCTGTTCTCCAACACTATCT 336459 i vv i i i C L3#LINE/CR1 978 CCAGAAAACCAAATCCTGTTCTTCGACACCATCT 945 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.75 CpG sites = 45, Kimura (unadjusted) = 51.58 Transitions / transversions = 2.81 (45/16) Gap_init rate = 0.01 (1 / 178), avg. gap size = 5.00 (5 / 1) 35 16.13 0.00 0.00 chrXqtel1M 336462 336503 (663497) (TC)n#Simple_repeat 1 42 (21) m_b361s252i1 15127 chrXqtel1M 336462 TCTCCCTCCTTCTCTCTGTCTCTCTGTGTCTCTCTCTGTCTC 336503 i ii v v v v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 42 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 40 2.61 0.00 0.00 chrXqtel1M 336504 336542 (663458) (TG)n#Simple_repeat 1 39 (0) c_b361s251i2 15128 chrXqtel1M 336504 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTCTGTGT 336542 v (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 39 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 35 16.13 0.00 0.00 chrXqtel1M 336543 336562 (663438) (TC)n#Simple_repeat 43 62 (1) m_b361s252i1 15129 chrXqtel1M 336543 CTCTCAGTCTCTCTCTCTCT 336562 vv (TC)n#Simple_ 43 CTCTCTCTCTCTCTCTCTCT 62 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 12 23.23 6.25 3.03 chrXqtel1M 336572 336635 (663365) (TATATA)n#Simple_repeat 1 66 (0) m_b361s252i2 15130 chrXqtel1M 336572 TATATATATA-ATGT-TAAACATGT-TAAAGTATATGT-TAAATCAAATA 336617 - i - v i i - v - i - v - v (TATATA)n#Sim 1 TATATATATATATATATATATATATATATA-TATATATATATAT-ATATA 48 chrXqtel1M 336618 TGTATAAACATATTTATA 336635 i v i v (TATATA)n#Sim 49 TATATATATATATATATA 66 Matrix = Unknown Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.10 (6 / 63), avg. gap size = 1.00 (6 / 6) 913 36.09 1.46 1.17 chrXqtel1M 336752 337093 (662907) C L3#LINE/CR1 (3173) 926 584 m_b361s601i6 15126 chrXqtel1M 336752 TTCTTA-ATCAGTCCTTATGTTCTGAAGCCTTTGCTTCTGATTGGCAGAA 336800 ii - vvi i v v ii i vivi i iii i v C L3#LINE/CR1 926 TTCCCATATCCTCCTTTCTCTTCCAAAGTCACGACCTTCAACTGGAAGAA 877 chrXqtel1M 336801 GTTCGAAGAACAGCACCTGTACCCCTAAGGCCTTCGGTTTCTTTTCCAGC 336850 vvvvi i v i i v i i vi v C L3#LINE/CR1 876 GAGATGAAAACACCACCTGTGCCCCCAAGTCCTTCAGTTTCCTGCCCAGG 827 chrXqtel1M 336851 GCTCAGCAGTCTTTGGCAGCACTTTCTAGTTTCCTTCTGGTACTATCATT 336900 i iviv vi i viiii v i v i iivv i C L3#LINE/CR1 826 ACTTCAAAGTCACTAGAGATGCATTCCAGGTTTCTTCTGACTGTGTCATT 777 chrXqtel1M 336901 TATGCCCACACAAATTGGCAA-AGTAGTTAGTACTCATCTGGTTTGACTA 336949 ii v iii ii i- i v iiv iv v iv C L3#LINE/CR1 776 CGTTCCCACGTGAATCAGCAGGAGTGGGTAGCGGTCGGCGGGTTTGATGA 727 chrXqtel1M 336950 GTCATGGGAGGTTCTTTGTCACACCCTAGATACGTGTCCTGGAAAGACAG 336999 v v i ii ii iii ii ii ii i C L3#LINE/CR1 726 GTCTTGGCAGGCTCTCCGTCACGTCTCGGATACACGCTCCAGGAAGACAG 677 chrXqtel1M 337000 TAGACATCTTTGTT-GTTA--TCGGGTAGACAGACGGTTGCCTCGGTGTC 337046 i v v iivi - ii -- i vvi v ii v i C L3#LINE/CR1 676 CACACCTCCCGATTAGCCACGTCAGGTCTGCATACGGCCGCCTCCGTATC 627 chrXqtel1M 337047 CACTCAGTGGCAAGTCATCAACCACCACACTCTGCCACTTCTTCCTC 337093 - i vi i ivivi i --- C L3#LINE/CR1 626 C-CTCAGCGGGGAGTCACCAACCACCACGACGCGTC---TCTTCCTC 584 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.53 CpG sites = 81, Kimura (unadjusted) = 52.84 Transitions / transversions = 1.98 (81/41) Gap_init rate = 0.02 (8 / 341), avg. gap size = 1.12 (9 / 8) 742 33.47 9.37 1.26 chrXqtel1M 337644 338230 (661770) L1ME4c_3end#LINE/L1 6 639 (191) m_b361s551i0 15131 chrXqtel1M 337644 ATTTTTAAAATATAAGAA-------TGAACTCATAAGAATACAAGCCATT 337686 i ? ?v ii -------ii i v v v? v v vv L1ME4c_3end#L 6 ATCTNTANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAAGA 55 chrXqtel1M 337687 CTCCAATCGATAAATGAGCAAAAGATGCTAATGGATAATTTTCCAAACAA 337736 i v i i iiiv ii i iv v? v i L1ME4c_3end#L 56 CCCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAG 105 chrXqtel1M 337737 -AACCATTTCTAGT-------CATATGAAAAAATGCTCCAAATCACTATT 337778 - vi ivv? ------- i i i v vv i v L1ME4c_3end#L 106 GAAATACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTAGT 155 chrXqtel1M 337779 GATCCGAGAAATGCAAATTAAGACAGCTCTGAGGTCCCACTACACACCTC 337828 i vi ii i vv i v i vi i v L1ME4c_3end#L 156 AATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCTA 205 chrXqtel1M 337829 TCA--CTGGCTAG---TGGGAAAA--GATAATGATGAACGTTGCAGGGTA 337871 i --i i v i--- vii -- iviv i i vv i v? L1ME4c_3end#L 206 TTAAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGCTGGCGAGGN 255 chrXqtel1M 337872 TGTGGGGAAAACTGGGACATTAAAACATTGTCGGTGGAGTTGTAAACTGG 337921 i v - v ?i v v ii vi? i L1ME4c_3end#L 256 TGCGGTGAAA-CTGGTACNCTCATACATTGCTGGTGGCANTGTAAATTGG 304 chrXqtel1M 337922 TCCAACCATTCTGGAGAGCAATCTGAGACTATGCCCAAAGGGATGTCAAA 337971 v v i i i iv v i iviv i vii v L1ME4c_3end#L 305 TACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAGCCATAAAA 354 chrXqtel1M 337972 CTGTGCATCCCCTTTGATCCAGCAG---------TGGGTCTGTATCCCAA 338012 v v v i i i--------- vv v i L1ME4c_3end#L 355 ATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCTAA 404 chrXqtel1M 338013 AG--ATCAT--AAAAAAGGGAAAAGGACCCACGTGTGGAAAACTGTTTGT 338058 i -- v -- i i i -- i ii iivi iv ii L1ME4c_3end#L 405 GGAAATAATTCAAAAGAAGGAAAAAG--CTATATGCACGAAGATGTTCAT 452 chrXqtel1M 338059 AGCGGCCCTTTGTGTACTCGGTGGTAAAGAACTGGAAATGG--------- 338099 v i vi v v i ----i i ii i i iii--------- L1ME4c_3end#L 453 TGCAGCGTTATTTATA----ATAGCGAAAAATTGGAAACAACCTAAATGT 498 chrXqtel1M 338100 --------AGTAGAATGGCCGCGTAAATTATGGCACATGAATGTGATGGA 338141 -------- vi iiiv i v? ivi L1ME4c_3end#L 499 CCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGA 548 chrXqtel1M 338142 ATGTTAT-TGTTCTGTAAGAA--ACAATCAGCAGGATTTCAGAGGGGCCT 338188 i -iivi vv i -- i i vv i i viiv vii v L1ME4c_3end#L 549 ATATTATGCAGCCATTAAAAATGATAATTATGAAGACTATGTAGCAACAT 598 chrXqtel1M 338189 GGAGAGACTCACAGGAACTGATGCTGAGTGAAGAGAGCAGAA 338230 - i ivivi v vv i i i i i L1ME4c_3end#L 599 GGA-AAATGTTTATGATATAATGTTAAGTGAAAAAAGCAGAA 639 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 44.90 CpG sites = 117, Kimura (unadjusted) = 47.31 Transitions / transversions = 1.52 (117/77) Gap_init rate = 0.04 (21 / 586), avg. gap size = 3.00 (63 / 21) 232 27.78 1.39 0.00 chrXqtel1M 338965 339036 (660964) DNM1r#Unknown 2476 2548 (2114) m_b361s502i0 15132 chrXqtel1M 338965 ACATGTATGTGTGCATATAACTGCATAT-TGTGTGCATATGTATATGTAT 339013 i i vv ii - i i i i DNM1r#Unknown 2476 ACGTGTATGTGTGTATATATGTGTGTATATGTGTGTATGTGTGTATATAT 2525 chrXqtel1M 339014 GTACATGAATGTATATGTGCAAA 339036 ii iv iii ? ii i DNM1r#Unknown 2526 GTGTATATATACGTATNTATAGA 2548 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 33.73 CpG sites = 17, Kimura (unadjusted) = 39.02 Transitions / transversions = 5.67 (17/3) Gap_init rate = 0.01 (1 / 71), avg. gap size = 1.00 (1 / 1) 255 25.00 0.00 0.00 chrXqtel1M 339080 339139 (660861) DNM1r#Unknown 2478 2537 (2125) m_b361s502i1 15133 chrXqtel1M 339080 GTGTGTGTGTGTACAGTAGTATGTATATGTGTGTATGTATACACACACAT 339129 i i vvv i i ii i i ii DNM1r#Unknown 2478 GTGTATGTGTGTATATATGTGTGTATATGTGTGTATGTGTGTATATATGT 2527 chrXqtel1M 339130 ATATACATAC 339139 i i DNM1r#Unknown 2528 GTATATATAC 2537 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 32.53 CpG sites = 12, Kimura (unadjusted) = 32.53 Transitions / transversions = 4.00 (12/3) Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0) 331 24.79 26.50 0.00 chrXqtel1M 339141 339257 (660743) C MIRb#SINE/MIR (115) 153 6 m_b361s601i7 15134 chrXqtel1M 339141 TCCTGATTTTATAAATGAGGAAACTAAGTCCCAGAGAAGTCAAG-----T 339185 iv i i i v i i i ----- C MIRb#SINE/MIR 153 TCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTT 104 chrXqtel1M 339186 GCCTGA-----------CAATGAATGCTAGAGGCAGGATATGAACCCAGG 339224 ii -----------i i i i vi v i vi C MIRb#SINE/MIR 103 GCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGG 54 chrXqtel1M 339225 --TGTCCAGCTC-------------TTTCCCACTGGCCCATGCTGCCC 339257 -- iii -------------i i vv i C MIRb#SINE/MIR 53 TCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCACCACGCTGCCC 6 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.88 CpG sites = 22, Kimura (unadjusted) = 31.81 Transitions / transversions = 3.14 (22/7) Gap_init rate = 0.03 (4 / 116), avg. gap size = 7.75 (31 / 4) 185 29.55 0.00 0.00 chrXqtel1M 340271 340314 (659686) L2c_3end#LINE/L2 361 404 (74) m_b361s601i8 15135 chrXqtel1M 340271 TGTCTTTCCCAACAGGCTGAGGGTTCATTCAGGGCAGAGACTGT 340314 iii vi i v i i v v i i L2c_3end#LINE 361 TGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGT 404 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.74 CpG sites = 9, Kimura (unadjusted) = 39.67 Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 190 31.91 18.09 0.00 chrXqtel1M 340677 340770 (659230) C MIR3#SINE/MIR (67) 141 31 m_b361s601i9 15136 chrXqtel1M 340677 TCTCGCACAAAAGGAAACCGAGGCCCAGAGAACCAAGGCGG--TACACAG 340724 i ii v vi i ivii i i i-- i v i C MIR3#SINE/MIR 141 TTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAA 92 chrXqtel1M 340725 GGCCATGTAGCCGGCCATT--CAAAG-------------CCAAATCTTCT 340759 i iii ?i ii v -- i ------------- ii i C MIR3#SINE/MIR 91 GGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAGGTCTCCT 42 chrXqtel1M 340760 GCCTCCCAGTC 340770 v C MIR3#SINE/MIR 41 GACTCCCAGTC 31 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.91 CpG sites = 24, Kimura (unadjusted) = 46.91 Transitions / transversions = 4.00 (24/6) Gap_init rate = 0.03 (3 / 93), avg. gap size = 5.67 (17 / 3) 18 23.65 1.75 1.75 chrXqtel1M 341337 341393 (658607) (ACACAGG)n#Simple_repeat 1 57 (0) m_b361s252i3 15137 chrXqtel1M 341337 ACAGAGAACCACAGGGCCTTGAACATAGGACACAGGACACAGAACATCGG 341386 v i - i viv i i i iv (ACACAGG)n#Si 1 ACACAGGA-CACAGGACACAGGACACAGGACACAGGACACAGGACACAGG 49 chrXqtel1M 341387 A-ACAGGA 341393 - (ACACAGG)n#Si 50 ACACAGGA 57 Matrix = Unknown Transitions / transversions = 1.75 (7/4) Gap_init rate = 0.04 (2 / 56), avg. gap size = 1.00 (2 / 2) 1832 31.89 2.36 2.14 chrXqtel1M 341492 342891 (657109) L1M5_orf2#LINE/L1 1756 3158 (136) m_b361s551i1 15138 chrXqtel1M 341492 ATAACCAAATTTAAAAAAAAAAAACATCTGATCATCTCAACAGATGCAGA 341541 v v i v v ii i v v i L1M5_orf2#LIN 1756 ATTAACAGAATAAAGGAGAAAAATCATATGATCATCTCAATAGATGCAGA 1805 chrXqtel1M 341542 AAAAGCATTTGATAAAATCCAACATCCATTCCTATTAAAAACATTAAAGA 341591 i i i v iv vi v iv L1M5_orf2#LIN 1806 AAAAGCATTTGACAAAATTCAACACCCATTCATGATAAAAACTCTCAGCA 1855 chrXqtel1M 341592 GTATAGGAATAAATGGGCTTTTTCCTTAAAATAGTTAGGAGCATCTATTT 341641 ivv i v vvi - i vv ii v i i ivv L1M5_orf2#LIN 1856 AACTAGGAATAGAAGGGAACTT-CCTCAACCTGATAAAGGGCATCTACGA 1904 chrXqtel1M 341642 AAAACTATCAGTAAGCATCATATATAATGGTGATAAACTGGAACCATTCC 341691 ivv i? i iv v ? i ?v v L1M5_orf2#LIN 1905 AAAACCTACAGCNAACATCATACTTAATGGTGAAANACTGAANGCTTTCC 1954 chrXqtel1M 341692 CAATAAGATCAGGAGTGAAACAACATTGCCCATTATCACCATTACTGTTC 341741 vv i iii i viv i ii ? i v i L1M5_orf2#LIN 1955 CCCTAAGATCGGGAACAAGACAAGGATGTCCGCTNTCACCACTTCTATTC 2004 chrXqtel1M 341742 AATATTGTATTAGAAATACTAGCTTTGGCAATAAGAGTTGAGAAAGAGAT 341791 i i i ii v ivvv ivvv i i L1M5_orf2#LIN 2005 AACATTGTACTGGAGGTCCTAGCCAGTGCAATAAGGCAAGAAAAAGAAAT 2054 chrXqtel1M 341792 TAAAGGAATTAGAGTAGGCAATGAAGAAACCAAATTATCACTCTTGGCAG 341841 v v v iii v v v iv i i ?i v v L1M5_orf2#LIN 2055 AAAAGGCATAAAGATTGGAAAGGAAGAAATAAAACTGTCNTTATTCGCAG 2104 chrXqtel1M 341842 ATCATATGATGGTATGCTTAGAGAAGCCCAGAGATTCTGCTAAAAAGCTA 341891 v i v ? i v i v ? i v i v ? i L1M5_orf2#LIN 2105 ATGACATGATTGTNTACGTAGAAAATCCNAAAGAATCTACAAANAAACTA 2154 chrXqtel1M 341892 TAAGAAATAATTCATAACTTTAGCAAAATTGCAGGATAAAAAATAAACCC 341941 iv v vvi i v ii i ? v ii v ivi L1M5_orf2#LIN 2155 CTAGAACTAATAAGTGAATTTAGCAAGGTCGCNGGATACAAGGTCAATAT 2204 chrXqtel1M 341942 ACATAAATCCTCAGCATTTTTATATGTCACTAACAA--AATCCAACAGTT 341989 v vviv i i iii vi -- ivi v i - L1M5_orf2#LIN 2205 ACAAAAATCAATTGTATTTCTATATACTAGCAACAAACAATTGGAAAAT- 2253 chrXqtel1M 341990 AGAGATACAAAGAGAAATTCCATTTAAAGTAACTGCCCTTAGTATAAAAT 342039 - i vi? i iv v v i i vv vvvv ii ? L1M5_orf2#LIN 2254 -GAAATTTNAAAAACAATACCATTTACAATAGCATCAAAAAACATNAAAT 2302 chrXqtel1M 342040 ATTTGGGAATCTATCTGCCAAGGGAAAGTCAGGAACTACATGAGCAAAAC 342089 i i vv iv ii? vivv i v ?i iivvv L1M5_orf2#LIN 2303 ACTTAGGAATAAATCTAACAAAANATGTGCAAGACCTNTACACTGAAAAC 2352 chrXqtel1M 342090 TATAAAATACTTTCCACACAAATAAAGTCAGATCTAACCAATTGGAAA-- 342137 i i i viiv v v v ivv i vi v i -- L1M5_orf2#LIN 2353 TACAAAACATTGCTGAGAGAAATTAAAGAAGACCTAAATAAATGGAGAGA 2402 chrXqtel1M 342138 -ATATCATGTGCTCCTGGACAGGTCGAGTGAATATAATAAAGATGACAAT 342186 - i -- v iv vv v v vi ? v L1M5_orf2#LIN 2403 TATACCATGT--TCATGGATTGGAAGACTCAATATTGTNAAGATGTCAAT 2450 chrXqtel1M 342187 ACTACCTAAACTAATCTATTAATTTAGTGCTATACCAATCCGACTCCCAA 342236 v v i i i vi i i v v vi v i L1M5_orf2#LIN 2451 TCTCCCCAAATTGATCTATAGATTCAATGCAATCCCAATCAAAATCCCAG 2500 chrXqtel1M 342237 GAAACTATTTTAATGACCTAGAAAAAATAACAACAAAATTCAC-TGGAAG 342285 v iii v ivv vv v v iv i ivvi i i- i L1M5_orf2#LIN 2501 CAGGTTTTTTTGTAGAAATTGACAAGCTGATTCTAAAATTTATATGGAAA 2550 chrXqtel1M 342286 AACAAAAGGTCAAAACTT-TCAAGGGAACTAATGAAAAAAATCAAATGAA 342334 vi i ii ? i v v-i iiv - vv i -- i vv L1M5_orf2#LIN 2551 TGCAAAGGACCNAGAATAGCCAAAACAA-TCTTGAAAAAGA--AGAACAA 2597 chrXqtel1M 342335 AGCTGCCTAGCTAAAAAT----GATCT-AAAACTATATTATAAAGCAGCA 342379 i vvvii v v v ---- ? - i - vi L1M5_orf2#LIN 2598 AGTTGGAGGACTTACACTACCNGATNTCAAGACT-TATTATAAAGCTACA 2646 chrXqtel1M 342380 GTTACTAAAACCATTTGGTATTGGC-TAAGAAATAGACTAGTTGATCAGT 342428 v ii i vi v - -i v i v i L1M5_orf2#LIN 2647 GTAATCAAGACAGTGTGGTATTGGCGTAAG-GATAGACAAATAGATCAAT 2695 chrXqtel1M 342429 GGAACAGGTTAG---GTTCACAGGACAAAATAG--TCA-ATAACTTTAAT 342472 iv --- i ------i --i - i vv v ii? L1M5_orf2#LIN 2696 GGAACAGAATAGAGAGTCCA------GAAATAGACCCACACATATATGGN 2739 chrXqtel1M 342473 AATCTAGTGTTTGACAAA--CCCCAAAAC--CCCAGCTTTTGGGATAAGG 342518 v ?i ii v --iv ?i --ii ---- iv L1M5_orf2#LIN 2740 CANTTGATTTTTGACAAAGGTGCCAANGCAATTCAG----TGGGGAAAGG 2785 chrXqtel1M 342519 ATTCACTGTTTGACAAAAACTGCTGGGAAAATTGGAAATTACTATGGCAG 342568 vvv v ii viv i v v ivv v i L1M5_orf2#LIN 2786 ATAGTCTTTTCAACAAATGGTGCTGGAACAATTGGATATCCATATGGAAA 2835 chrXqtel1M 342569 AAACTAGGCATTGACCAACACTTAACACCGTACACCAAGATAATGTCAAA 342618 v iii?v i vvi i v i v i v vv ? i L1M5_orf2#LIN 2836 AAAATGAANCTCGACCCCTACCTCACACCATACACAAAAATTAATTCNAG 2885 chrXqtel1M 342619 ATGGGCTCAT-GACCTCGGCATAAAGAATAAAATTATAAATAAATTAGAG 342667 i- - viiii ii? i vvvvi i L1M5_orf2#LIN 2886 ATGGA-TCATAGACCTAAATGTAAAAGNTAAAACTATAAAACTTCTAGAA 2934 chrXqtel1M 342668 G--AACATAGGATAGTTTACCTCTCAGACCTGTGGAGGAGGAAGGAATTT 342715 -- v i-- i iivv - i?v v iii L1M5_orf2#LIN 2935 GAAAACATAGGAGAA--TATCTTCGTGACCT-TGGGNTAGGCAAAGATTT 2981 chrXqtel1M 342716 ATGACTAAAAAAGAACTAGAGATCATTACTGATCACAAAATAGAAAATT- 342764 v --- v i vvi i i v i? --- i i v i - L1M5_orf2#LIN 2982 CT---TAAACAGGACACAAAAAGCACNA---ACCATAAAAGAAAAAATTG 3025 chrXqtel1M 342765 -TTAAT-----TATATCAAATTGAAAAGTTTGTGTACAAACAAAACTAAT 342808 - v ----- ?i v v ii v iv ?vvv ivi vi L1M5_orf2#LIN 3026 ATAAATTGGACTNCATCAAAATTAAAAACTTCTGCTCNTCAAAAGACACC 3075 chrXqtel1M 342809 GCAGACAAGATTAGAAGGGAAGCAATAAACTGGGAAAACATTTTTACAGT 342858 ivi v i v i v v i i ? i v v i i? L1M5_orf2#LIN 3076 GTTAAGAAAATGAAAAGGCAAGCCACAGANTGGGAGAAAATATTTGCAAN 3125 chrXqtel1M 342859 CAAGGGTTCTGATAAAGGCCTCATTTCCAAAAT 342891 vv vivv i v i v i L1M5_orf2#LIN 3126 ACATATATCTGACAAAGGACTCGTATCCAGAAT 3158 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 42.44 CpG sites = 225, Kimura (unadjusted) = 43.48 Transitions / transversions = 1.06 (225/212) Gap_init rate = 0.03 (48 / 1399), avg. gap size = 1.31 (63 / 48) 18 14.73 0.00 0.00 chrXqtel1M 342947 342976 (657024) (A)n#Simple_repeat 1 30 (0) m_b361s252i4 15139 chrXqtel1M 342947 AATAAAAAAATAGAAAAAAAAAAAAGAAAA 342976 v v i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 30 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 1350 27.46 2.40 2.40 chrXqtel1M 343098 343597 (656403) L1ME3Cz_3end#LINE/L1 7 506 (491) m_b361s551i2 15138 chrXqtel1M 343098 TCCAAAATTTCTAGAGAATTGACTCTAATTTATAAGAAATCAAGCCATTC 343147 i v v i i vviv v iv -- v --v L1ME3Cz_3end# 7 TCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAA--AAGACA--A 52 chrXqtel1M 343148 TCCAATTGATAAATGGTCAAAGAATATGAACA----ATTTTCGGATGAAG 343193 i v v v i ---- iv i v i L1ME3Cz_3end# 53 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chrXqtel1M 343194 AAATTGAAACTATTTCTAGCCATTTGAAAAGATGCTCCAAGTCATTATTA 343243 iivi iviiivv iv v v vv i v L1ME3Cz_3end# 103 AAACCCGAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTA 152 chrXqtel1M 343244 ATCAGAGGAATGCAAATTAAGACAACTCTGAGATACCACTACACACCTGT 343293 i i i ? vv i v ii L1ME3Cz_3end# 153 ATCAGGGAAATGCAAATTAAAACNACAATGAGATACCATTTCACACCCAT 202 chrXqtel1M 343294 CAGATTGGCTAAGATAAGAAAA---GATAATGCTGAATGTTGGAGGGGAT 343340 v i vvi i--- i i ii i v i L1ME3Cz_3end# 203 CAGATTGGCAAAAATTTAAAAGTCTGACAATACCAAGTGTTGGCGAGGAT 252 chrXqtel1M 343341 GTGGGAAAACTGGGACACTGATACATTGTTGGTGGAGTTGTGAA-CGATC 343389 ii v i v v i i iiv i -i i v L1ME3Cz_3end# 253 GTGGAGAAACGGGAACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTA 302 chrXqtel1M 343390 CAACCTCTCTGGAGAGCGATTTGGAACTATGCTCAAAAAGTTATCAAGCT 343439 v i i v v - viv i-- v L1ME3Cz_3end# 303 CAACCACTTTGGAGAGCAATTTGGCAATAT-CTAGTAAAGTTG--AAGAT 349 chrXqtel1M 343440 ATGCATACCCTTTGATCCAGCAGTGTTACTACTGGGTTTATATCCCCAAA 343489 ii vi i i vii v i v - i i L1ME3Cz_3end# 350 GCGCATACCCTACGACCCAGCAATTCCACTTCTAGGTATATA-CCCTAGA 398 chrXqtel1M 343490 GAGA-TCTTAAAGAAGGG---AAAGGGACCTCTATGTGCAAGAATGTTTG 343535 i - iiv v v v --- i i ---- i i ii L1ME3Cz_3end# 399 GAAACTCTCGCACATGTGCACAAGGAGAC----ATGTACAAGGATGTTCA 444 chrXqtel1M 343536 TGGCAGCACTCTTTGTAGTGGCCAGAAACTGGAAACTAAGTGGATGCCCA 343585 v i v i i v i i v vv ii i L1ME3Cz_3end# 445 TTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCA 494 chrXqtel1M 343586 TCAAGTGGAGAA 343597 vv i L1ME3Cz_3end# 495 TCAATAGGGGAA 506 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 33.70 CpG sites = 76, Kimura (unadjusted) = 35.01 Transitions / transversions = 1.31 (76/58) Gap_init rate = 0.03 (17 / 499), avg. gap size = 1.41 (24 / 17) 13 10.07 5.88 2.86 chrXqtel1M 343738 343771 (656229) (ATTTAT)n#Simple_repeat 1 35 (0) m_b361s252i5 15140 chrXqtel1M 343738 ATGTATACTTAT-TTTGTATTTA-ATTTATACTTTA 343771 v i - i - - (ATTTAT)n#Sim 1 ATTTATATTTATATTTATATTTATATTTATA-TTTA 35 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.09 (3 / 33), avg. gap size = 1.00 (3 / 3) 288 34.90 2.71 5.58 chrXqtel1M 343838 344095 (655905) L1ME2z_3end#LINE/L1 315 565 (626) m_b361s551i3 15141 chrXqtel1M 343838 TTGGAACAAAAGGTTTAGCAATTGTGAATGCTGTAAAATTACCCATGCAT 343887 -- i i i ----- vi i i vv i i L1ME2z_3end#L 315 TTGGAA--AAAGGTCTGGCAGTT-----TCTTATAAAACTAAACATACAC 357 chrXqtel1M 343888 ATATCTTGTAAATAAAAAGCTATTAAAATTTTAAAAA---ACATAAATAA 343934 v i i i i viv --- v vv v ii iiv --- vi ivi L1ME2z_3end#L 358 CTACCCTATGACCCA---GCAATTCCACTCCTAGGTATTTACCCAAGAGA 404 chrXqtel1M 343935 AAAAAAAATAAAGGG----AAAGGGACCTGTATGTGCACAAATGTCTGTG 343980 vi i v v v---- ii i ---- vi iii i L1ME2z_3end#L 405 AATGAAAACATATGTCCACAAAAAGACTTGTA----CAAGAATGTTCATA 450 chrXqtel1M 343981 GCAGCCCTCTTTGTAGTGGCCAGAAACTGGAAACTGAGTGGATGCTCATC 344030 ii v ii i i i v vvii i ii L1ME2z_3end#L 451 GCAGCTTTATTCATAATAGCCAAAAACTGGAAACAGCCCAGGTGTCCATC 500 chrXqtel1M 344031 CATTGGAGAACGGCTGAATAAATTGTGGCATATGAATGTTATGGAATGTT 344080 v iv i v i i i i vv iiv ii L1ME2z_3end#L 501 AACAGGAGAATGGATAAACAAACTGTGGTATATTCATACAATGGAATACT 550 chrXqtel1M 344081 ATTGTTCTATAAAAA 344095 i vvv v L1ME2z_3end#L 551 ACTCAGCAATAAAAA 565 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 49.29 CpG sites = 53, Kimura (unadjusted) = 49.29 Transitions / transversions = 1.66 (53/32) Gap_init rate = 0.06 (16 / 257), avg. gap size = 1.31 (21 / 16) 314 36.01 0.00 4.85 chrXqtel1M 343915 344130 (655870) L1ME4c_3end#LINE/L1 398 603 (227) m_b361s551i4 15141 chrXqtel1M 343915 ATTTTAAAAAACATAAATAAAAAAAAAATAAAGGGAAAGGGACCTGTATG 343964 ii ii - v v i ------- ii -- i L1ME4c_3end#L 398 ATCCTAAGGAA-ATAATTCAAAAGAA-------GGAAAAAG--CTATATG 437 chrXqtel1M 343965 TGCACAAATGTCTGTGGCAGCCCTCTTTGTAGTGGCCAGAAACTGGAAAC 344014 ii iv i iii v vi v i i i v i i L1ME4c_3end#L 438 CACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAAC 487 chrXqtel1M 344015 TGAGTGGATGCTCATCCATTGGAGAACGGCTGAATAAATTGTGGCATATG 344064 vivv ii ii v v v i i i i i i i i v L1ME4c_3end#L 488 AACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATC 537 chrXqtel1M 344065 AATGTTATGGAATGTTATTGTTCTATAAAAAATGACCAGCAGGAGGATTT 344114 ? iviv i vvvv i v iv vi v i i v L1ME4c_3end#L 538 NACTCGATGGAATATTATGCAGCCATTAAAAATGATAATTATGAAGACTA 587 chrXqtel1M 344115 CAGAGAAGCCTGGAGA 344130 iiv v i v i L1ME4c_3end#L 588 TGTAGCAACATGGAAA 603 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 49.92 CpG sites = 46, Kimura (unadjusted) = 51.99 Transitions / transversions = 1.64 (46/28) Gap_init rate = 0.05 (10 / 215), avg. gap size = 1.00 (10 / 10) 317 34.00 2.46 1.46 chrXqtel1M 343962 344164 (655836) L1MC4a_3end#LINE/L1 428 632 (1997) m_b361s551i5 15141 chrXqtel1M 343962 ATGTGCACAAA--TGTCTGTGGCAGCCCTCTTTGTAGTGGCCAGAAACTG 344009 i i-- i iii v vi v i v v i v i L1MC4a_3end#L 428 ATATGCACAAGGTTATTCATTGCAGCATTGTTTGTAATTGCAAAATATTG 477 chrXqtel1M 344010 GAAACTGAGTGGATGCTCATCCATTGGAGAACGGCTGAATAAATTGTGGC 344059 vivv ii i ?? v ?i i i i i L1MC4a_3end#L 478 GAAACAACCTAAATGCCCATNNATAGGAGANTGGTTGAATAAACTATGGT 527 chrXqtel1M 344060 ATATGAATGTTATGGAATGTTATTGTTCTATAAAAAATGACCAGCAGGAG 344109 i vv iiiv i ii vvvv i - -- vv i L1MC4a_3end#L 528 ACATCCACACAATGGAGTACTATGCAGCTGTAAAAAA-GA--ATGAGGAA 574 chrXqtel1M 344110 GATTTCAGAGAA---GCCTGGAGAGACTGACAGGAACTGATGCCGAGGGA 344156 i viv ---iiv v i vv vv iv iii v L1MC4a_3end#L 575 GATCTCTATGAACTGATATGGAGTGATTTCCAGGATATATTGTTAAGTGA 624 chrXqtel1M 344157 AATGAGCA 344164 vi L1MC4a_3end#L 625 AAAAAGCA 632 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 47.70 CpG sites = 38, Kimura (unadjusted) = 47.70 Transitions / transversions = 1.27 (38/30) Gap_init rate = 0.02 (5 / 202), avg. gap size = 1.60 (8 / 5) 412 31.58 0.00 0.00 chrXqtel1M 343963 344095 (655905) L1ME1_3end#LINE/L1 433 565 (361) m_b361s551i6 15141 chrXqtel1M 343963 TGTGCACAAATGTCTGTGGCAGCCCTCTTTGTAGTGGCCAGAAACTGGAA 344012 i i iii i ii v i i i i L1ME1_3end#LI 433 TGTACACGAATGTTCATAGCAGCTTTATTCGTAATAGCCAAAAACTGGAA 482 chrXqtel1M 344013 ACTGAGTGGATGCTCATCCATTGGAGAACGGCTGAATAAATTGTGGCATA 344062 vivviii ii v i? v i v i i i L1ME1_3end#LI 483 ACAACCCAAATGTCCATCAACNGGTGAATGGATAAACAAATTGTGGTATA 532 chrXqtel1M 344063 TGAATGTTATGGAATGTTATTGTTCTATAAAAA 344095 vv iiv ii i vvv v L1ME1_3end#LI 533 TCCATACAATGGAATACTACTCAGCAATAAAAA 565 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 40.92 CpG sites = 28, Kimura (unadjusted) = 43.74 Transitions / transversions = 2.00 (28/14) Gap_init rate = 0.00 (0 / 132), avg. gap size = 0.0 (0 / 0) 331 32.35 8.33 5.18 chrXqtel1M 344822 345121 (654879) C L2c_3end#LINE/L2 (4) 474 166 m_b361s601i10 15142 chrXqtel1M 344822 ATTTATTAGA-AAGCATTTATTAAGTACCTACTGGATGCCAGACTGTGGG 344870 i vi - i i ii ivi i vv C L2c_3end#LINE 474 ATTCATTCAACAAACATTTATTGAGCGCCTACTATGTGCCAGGCGCTGGG 425 chrXqtel1M 344871 GATAAGAAAGACAAAAAGAAACCTGCGGCTGCCCTCCGAGAGCTGAC-GT 344919 - v ii v ii vv v ivv vii v - C L2c_3end#LINE 424 GAT-ACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAGT 376 chrXqtel1M 344920 CTTCTAGGGGAGAT-GACCTGC--ACAAAGAA--GCACTCCA----AACG 344960 vv i i i- v? i-- i v --i v v ---- i C L2c_3end#LINE 375 CTAGTGGAGGAGACAGACANGTAAACAGACAATTACAATACAAGTTAATG 326 chrXqtel1M 344961 AT-----TTAAAAT--AAATACAGAC----TTGTATGAGAG-AGAGAACC 344998 -----i v --i i i ---- vv i - v ivv C L2c_3end#LINE 325 ATAAGTGCTATAATGGGAGTATAGACAGGGTGCTATGGGAGCACAGAGGA 276 chrXqtel1M 344999 TGGTAGCTGGAGGAGGGTGGGGATAGGGTCAAGAAAGGC--CATGTGAGG 345046 v i v i vv ?v v --- i i -- vi - C L2c_3end#LINE 275 GGGCACCTAGACTAGNCTTGGG---GGGTCAGGGAAGGCTTCCCG-GAGG 230 chrXqtel1M 345047 ACATGGCTTTGAAGGAAACAGGATCCTGAAAGATAAAGGTGAGGCAGGAG 345096 vi i v ivi ---- v ii? i i i ------- i C L2c_3end#LINE 229 AGGTGACATCTGAG----CTGAGNCTTGAAGGATGA-------GTAGGAG 191 chrXqtel1M 345097 CCGACCAGGTAACAAGACCGGAAAA 345121 iiii iiv i vv ii C L2c_3end#LINE 190 TTAGCCAGGTGGAAGGAGGGGGGAA 166 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.04 CpG sites = 53, Kimura (unadjusted) = 44.41 Transitions / transversions = 1.36 (53/39) Gap_init rate = 0.09 (27 / 299), avg. gap size = 1.52 (41 / 27) 409 39.80 2.22 2.63 chrXqtel1M 346112 347102 (652898) Cheshire#DNA/hAT-Charlie 513 1499 (921) m_b361s502i2 15143 chrXqtel1M 346112 AGAGCTGTATGTCTGATATGCCAGAATATAGTGTCTGTGCTCAAAGAATA 346161 i vv i i iv v vi i ivi iv v Cheshire#DNA/ 513 AAAGCATTGTGTTTATTATGCAATGACACTATAGCTGTGCTAAAAGAATA 562 chrXqtel1M 346162 TAATTCGTGTGGACACTATGAAACTCAACATAAAGATAAATATGATTGTT 346211 i viii v i iv i v i ivv vvvv vviiivi Cheshire#DNA/ 563 CAATATACGTCGACATTACCAGACTAAGCACTCATCACAATATTCCCAAC 612 chrXqtel1M 346212 TGGTTGGA--GCAATG---AGAAAAGATAAAATATT-AAAACTGAAAAT- 346254 viiv -- i --- iv i v - v v - Cheshire#DNA/ 613 TCACAGGAAAGCAACGGTCAGAAAAATTAGAAAATTTAAAACGGAATATC 662 chrXqtel1M 346255 ACATTGACGACTCAGCAAAATACTTTTGTGAAGCAGAAGCAGCTAAATAT 346304 v ------ v i vii iiii ivvi iv vvv iv Cheshire#DNA/ 663 TCAT------CACAGCAGAATTTCTTCACAAAAATAAAAAATGAAAATGA 706 chrXqtel1M 346305 TTCATCACTGCGAGCAAGTTTTCAAGTTGCCAAGCTAATAGC-AGGCACT 346353 vv vv vivvi i i i v iv vi iv - i v- Cheshire#DNA/ 707 GGCTGCAACCAAAGTAAGTTTCCGAGTGGCTCATTTGTTAGCCAAGCAA- 755 chrXqtel1M 346354 GGCAGACAATTCATGGAGGGAGAATTTGTTAAAGAATGCCTTCTTTCTGT 346403 v ii vi i iv v v i vi vvi ii vv v v i Cheshire#DNA/ 756 GGAAAGCCGTTTACCGATGGTGAGTTAATTAAATCGTGTTTGATTGCAGC 805 chrXqtel1M 346404 TGCCAAAGAGATGTGTCCAGAGAAGGCCAATTTACTTAGTACAGTGAGTC 346453 v i i iiiv i ii iv vi v i Cheshire#DNA/ 806 AGCCGAAGAAATGTGTCCAGAGAAAATAAACTTGTTTAAGACTATTAGCC 855 chrXqtel1M 346454 TTTCAGGACCTACAACT-CACAGAGGATTGAAAAAATGGGAAACAATCTG 346502 i vivvv ii - v ii ii ii v v i i ---- Cheshire#DNA/ 856 TTTCGGCGAGAACAGTTGCTCGAAGAGTTGAGGACATTGGGAGCAA---- 901 chrXqtel1M 346503 CATCAGCATTT--TCAAAACTCCATAAAAAAAAATTCAT---ATTTTTCT 346547 ii v i-- i vv v viv vi v iv---i i Cheshire#DNA/ 902 CATCAATAGTCAATTAAAAAACAAGGCAAATGATTTCGAGTGGTTTTCCT 951 chrXqtel1M 346548 TGGCACTCGACGAAAGCAATGATGTTTGTGATTCTGCACAACTTCTAATT 346597 v i i ivvv vv vvi v v ii------ v Cheshire#DNA/ 952 TGGCTCTTGATGAGTCGACAGATGTTACCGATACTGCTCAGT------TG 995 chrXqtel1M 346598 TTTATTCGTGGGATGAATGATTATTTTGATGTCATAGAAGAGCTTGCTGC 346647 v ii v viv v v v iv ii v iv Cheshire#DNA/ 996 TTTATTCGAGGAGTCAATGCCGAGTTTGAAGTGACTGAAGAATTAGCCTC 1045 chrXqtel1M 346648 ACTGCAAAGCATCAAAAAAAACAACTACAGGAGAGGATATCTATGAAAAG 346697 vv v v iv -ivivii v i i vii i i Cheshire#DNA/ 1046 TATGAATAGTCT-GCGTGGAACAACTACAGGCGAGAATATTTTCAAAGAA 1094 chrXqtel1M 346698 GTTTGCCAAACTATGAATGGTTTGTTGCTAGGCTGAACT-AAACTAGCCA 346746 - vv vi iv --- iiv i - iv v -i iiv i Cheshire#DNA/ 1095 G-TTGAGAAAACACTAA---TTCAGTAC-AACCTGAAGTGGAATCTGCTA 1139 chrXqtel1M 346747 ----GCGTGACCACTGATGGTGCTCCTAGGATG-GTGGGGTCTAAGAAAG 346791 ---- i v v v vvv iv - i - vi i Cheshire#DNA/ 1140 AGATGTGTTACAACTGATGGTGGTAAAAATATGTGTGGAG-CAGAAAAAG 1188 chrXqtel1M 346792 GAGTCATTGCTCGCATTAACCAAGAGATGGACAAACATAA-CCATTCTCA 346840 vv vi vv iv v v vv- viv ii -vii ivv Cheshire#DNA/ 1189 GCTTAGTTGGACAAATTTACAAAGCT-TGTGAAAATGTAAGGTGTTTAAA 1237 chrXqtel1M 346841 TTCAATAGCCATATACTGCCTCATCCACCAACAAGCGCTGTGTAGTAAAT 346890 vi v i ii vi i iv i i i i i ii v ii v Cheshire#DNA/ 1238 GCCTATGGTTATTCATTGTATTATTCATCAGCAGGTACTTTGCGGAAAAT 1287 chrXqtel1M 346891 CACTGAAGTGGGACTCTGTTATGAAAATTGTGGTATCTTGTGTTAACTTC 346940 vvi vivivvv v vi viv i i vvvv v Cheshire#DNA/ 1288 ATTTGAATCTATCATGTGTTATTGAACCAGTAGTGTCAACGGTGAACTTC 1337 chrXqtel1M 346941 ATTAGATCTAATGCACTAAATCACAGACAATTTCAGGAATTTCTGTCTGA 346990 v v vi v v i iv v i i iv i v Cheshire#DNA/ 1338 ATTCGCTCTCGTGGACTTAACCATCGTCAGTTCCGTGAATTTTTGTCAGA 1387 chrXqtel1M 346991 GCTAAATGTTGAGTATGAAGATGTTCTATATCACACACAAGTCCATTGGC 347040 iv i v i i vvv iv v iv i vv i iv Cheshire#DNA/ 1388 AATAGAAGCTGAATATCCTGACTTGCCCTACCACACAGCAGTTCGATGGC 1437 chrXqtel1M 347041 TGAGTTGAGGGAGAGTTTTGAAACGTTTCTATGA-CTTACTTCCACAGAT 347089 v iv v v i ivvi v i v - i vvv i- Cheshire#DNA/ 1438 TTAGCAGTGGTAAAGTTTTATTGCGATTTTTTGAGCTCAGGGCCG-AGAT 1486 chrXqtel1M 347090 CACAGCTTTTCTG 347102 iiv ii Cheshire#DNA/ 1487 TGAAATTTTTCTG 1499 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 53.93 CpG sites = 187, Kimura (unadjusted) = 57.91 Transitions / transversions = 0.95 (187/197) Gap_init rate = 0.04 (39 / 990), avg. gap size = 1.23 (48 / 39) 29 14.20 0.00 0.00 chrXqtel1M 347655 347701 (652299) (T)n#Simple_repeat 1 47 (0) m_b361s252i6 15144 chrXqtel1M 347655 TTTTTTTTTTGGTTTTTTGTTTTTTTATTTTTATTTTTTTTTTATTT 347701 vv v v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 47 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 283 26.97 0.00 0.00 chrXqtel1M 347764 347852 (652148) Cheshire#DNA/hAT-Charlie 2043 2131 (289) m_b361s502i3 15145 chrXqtel1M 347764 TTTGGCAGCACTTATGTCTGTGAACAGACTTTTTCTAGTATGAAACATTT 347813 i i v v v v v iv i iv Cheshire#DNA/ 2043 TTTGGCAGTACCTATCTGTGTGAAAAGACATTTTCAAAGATGAAATACGT 2092 chrXqtel1M 347814 GAAATGTCCAACCATATCAAGACTAACAGATGCACACTT 347852 i v vvvv v iv i v i Cheshire#DNA/ 2093 AAAATCTCATTACAGATCAGCATTAACAGATGAACATTT 2131 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 31.86 CpG sites = 9, Kimura (unadjusted) = 33.44 Transitions / transversions = 0.60 (9/15) Gap_init rate = 0.00 (0 / 88), avg. gap size = 0.0 (0 / 0) 15 15.85 4.55 2.22 chrXqtel1M 349305 349348 (650652) (CCCCCAG)n#Simple_repeat 1 45 (0) m_b361s252i7 15146 chrXqtel1M 349305 CCCTCAGCCCCCTCCCGCCCGCCACCCA-CCACC-GCCCCCAGCCC 349348 i vv v v - - v - (CCCCCAG)n#Si 1 CCCCCAGCCCCCAGCCCCCAGCC-CCCAGCCCCCAGCCCCCAGCCC 45 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.07 (3 / 43), avg. gap size = 1.00 (3 / 3) 20 25.94 4.60 2.25 chrXqtel1M 349489 349575 (650425) (GAAG)n#Simple_repeat 1 89 (0) m_b361s252i8 15147 chrXqtel1M 349489 GAGGGAA-GAAGGAAGAGAGGAGGGAAGTAAGACAGGAAGGGAGG--GGA 349535 i - ii i v iv i -- (GAAG)n#Simpl 1 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 50 chrXqtel1M 349536 GGGAAAGAAAGGAGGTCCTGGCA-GCAGGGAGGGAGGAAGG 349575 i - i i -vvv v - v i i (GAAG)n#Simpl 51 AGG-AAGGAAGGAAG-GAAGGAAGGAAGGAAGGAAGGAAGG 89 Matrix = Unknown Transitions / transversions = 1.57 (11/7) Gap_init rate = 0.06 (5 / 86), avg. gap size = 1.20 (6 / 5) 13 19.66 4.00 4.00 chrXqtel1M 349674 349723 (650277) (GGCAGG)n#Simple_repeat 1 50 (0) m_b361s252i10 15148 chrXqtel1M 349674 GGGAGGGGTCGGGGCTGGGG-GGGTGC-CCGGCAGGGGCAGGGGGTCAGG 349721 v iv v -i v -vv - - (GGCAGG)n#Sim 1 GGCAGGGGCAGGGGCAGGGGCAGGGGCAGGGGCAGGGGCA-GGGG-CAGG 48 chrXqtel1M 349722 GG 349723 (GGCAGG)n#Sim 49 GG 50 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.08 (4 / 49), avg. gap size = 1.00 (4 / 4) 16 19.19 1.96 4.00 chrXqtel1M 350021 350071 (649929) (GGAGG)n#Simple_repeat 1 50 (0) m_b361s252i11 15149 chrXqtel1M 350021 GGTGGGGAGGGAGGGGCGAGGGGACTGGGAAGGGA-GGAAGGGGTGGGCA 350069 v - i v -v i - i v v (GGAGG)n#Simp 1 GGAGGGGAGGG-GAGGGGAGGGGA-GGGGAGGGGAGGGGAGGGGAGGGGA 48 chrXqtel1M 350070 GG 350071 (GGAGG)n#Simp 49 GG 50 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.06 (3 / 50), avg. gap size = 1.00 (3 / 3) 238 34.16 1.81 8.01 chrXqtel1M 350493 350823 (649177) C L2#LINE/L2 (860) 2222 1911 m_b361s601i11 15150 chrXqtel1M 350493 GTCAAGGGGTCGAGAGGGGGAAGGCAGAGGGCCCAGAACAGAGCCACGGA 350542 i? i ---- ii v vi iv -- i ----- C L2#LINE/L2 2222 GTTNAGAGGTCG----GGGAGATGAGGAGGAACCAG--CAAAG-----GA 2184 chrXqtel1M 350543 GACCCCTGGGATGAGGAGGCGTGAGCTGGAGGAGGATCCAGAGGAGGAGT 350592 -------- i v i - ii v ii v ---i ii vi C L2#LINE/L2 2183 GAC--------TGAGAAGGAGCG-GCCAGTGAGGTA---GGAGGAAAACC 2146 chrXqtel1M 350593 GGAAGAGAGGGATGTCCCATAAACCTTGAGAGAATAGTCTATAAAGGGAG 350642 i i v v i iiv i vv v ii v v v v i- C L2#LINE/L2 2145 AGGAGAGTGTGGTGTCCTGGAAGCCAAGTGAAGAAAGTGTTTCAAGA-AG 2097 chrXqtel1M 350643 GAGAGAGTGATCCACGGGGTCAGAGGCCACAGGGAGGTCAAGGGGAATGA 350692 i v v v i v ii v i? viii C L2#LINE/L2 2096 GAGGGAGTGATCAACTGTGTCAAATGCTGCTGANAGGTCAAGTAAGATGA 2047 chrXqtel1M 350693 GG-CTGCAGA---GGTCAAGGGATGGGGCGATTGAGAGAAGACCGGTCAC 350738 - - --- ii vv vvi i ivvi ivv ii v C L2#LINE/L2 2046 GGACTG-AGAATTGACCATTGGATTTAGCAACGTGGAGGTCATTGGTGAC 1998 chrXqtel1M 350739 TCTGGAGGGAGTAGTTTGGGTGGGAT-ATGAGGTCGGAGGCTGGA-TGTA 350786 ii ivii i v ii -i i v i i iv - v C L2#LINE/L2 1997 CTTGACAAGAGCAGTTTCGGTGGAGTGGTGGGGACGAAAGCCTGATTGGA 1948 chrXqtel1M 350787 CAGGATGAAGAAGAGACTGTGAGGAGAGGAAGTGGGG 350823 vv i vv ii v v v i C L2#LINE/L2 1947 GTGGGTTCAAGAGAGAATGGGAGGAGAGGAATTGGAG 1911 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.04 CpG sites = 60, Kimura (unadjusted) = 47.31 Transitions / transversions = 1.36 (60/44) Gap_init rate = 0.09 (29 / 330), avg. gap size = 1.07 (31 / 29) 11 25.38 0.00 6.12 chrXqtel1M 351072 351123 (648877) (CCTTCCC)n#Simple_repeat 1 49 (0) m_b361s252i12 15151 chrXqtel1M 351072 CCTTCCCTCCTTGCTCCATGGGCCCCTTCCCCCCTCCCTGGTCCCCGTGC 351121 - - i v -vv i ivv v v (CCTTCCC)n#Si 1 CCTTCCC-CCTT-CCCCCT-TCCCCCTTCCCCCTTCCCCCTTCCCCCTTC 47 chrXqtel1M 351122 CC 351123 (CCTTCCC)n#Si 48 CC 49 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.00 (3 / 3) 204 29.31 3.45 0.00 chrXqtel1M 351321 351378 (648622) MIR3#SINE/MIR 121 180 (28) m_b361s601i12 15152 chrXqtel1M 351321 TCCATTTCCTTCTCTGTTAACTGGGGAGATGGG--TTGATGACCCTCAAG 351368 vi iv v v i i i v -- v i iii MIR3#SINE/MIR 121 TCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAG 170 chrXqtel1M 351369 GGTCCTTCCA 351378 vi MIR3#SINE/MIR 171 GTCCCTTCCA 180 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.23 CpG sites = 10, Kimura (unadjusted) = 38.23 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.02 (1 / 57), avg. gap size = 2.00 (2 / 1) 19 3.33 3.03 3.03 chrXqtel1M 352058 352090 (647910) (GGGGAA)n#Simple_repeat 1 33 (0) m_b361s252i13 15153 chrXqtel1M 352058 GGGGAA-GGGAAGGGGAAGGGAAAGGGGGAAGGG 352090 - i - (GGGGAA)n#Sim 1 GGGGAAGGGGAAGGGGAAGGGGAA-GGGGAAGGG 33 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.06 (2 / 32), avg. gap size = 1.00 (2 / 2) 186 35.94 0.00 0.00 chrXqtel1M 352563 352626 (647374) MIR3#SINE/MIR 85 148 (60) m_b361s601i13 15154 chrXqtel1M 352563 TGTGACCTTAAGGCAGCTCCTTCCCTTTTCTGATCCCCTGCCTTCTCTTC 352612 ii vv iiv v i i iv i v ii i v MIR3#SINE/MIR 85 TGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATC 134 chrXqtel1M 352613 TGACAAAAAAGAGG 352626 vv vi i MIR3#SINE/MIR 135 TGTAAAATGAGGGG 148 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 50.70 CpG sites = 13, Kimura (unadjusted) = 50.70 Transitions / transversions = 1.30 (13/10) Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0) 72 17.36 2.52 1.24 chrXqtel1M 352627 352785 (647215) (CAGAGA)n#Simple_repeat 1 161 (0) m_b361s252i15 15155 chrXqtel1M 352627 CAGAGACAGAGACAGAGAAAGAGAAACAGAGACAGAAAGAGAGAGAGAGA 352676 v -- i v v (CAGAGA)n#Sim 1 CAGAGACAGAGACAGAGACAGAG--ACAGAGACAGAGACAGAGACAGAGA 48 chrXqtel1M 352677 CAGAGAGAGAGAGAAACACAGAGACAGAGACAGTGA-A-AGAAAAATGGA 352724 v v i v v - - v i viv (CAGAGA)n#Sim 49 CAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACA 98 chrXqtel1M 352725 GAGAGGGAGACAGAGACAGA-AGAGAGACAGATACAGAGAGACAGA-AGA 352772 vi - v v v v - (CAGAGA)n#Sim 99 GAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGA 148 chrXqtel1M 352773 GAGACATAAAGAG 352785 v v v v (CAGAGA)n#Sim 149 GACAGAGACAGAG 161 Matrix = Unknown Transitions / transversions = 0.26 (5/19) Gap_init rate = 0.04 (6 / 158), avg. gap size = 1.00 (6 / 6) 196 27.59 1.72 0.00 chrXqtel1M 352917 352974 (647026) C MIRb#SINE/MIR (124) 144 86 m_b361s601i14 15156 chrXqtel1M 352917 TACAGCTGGGGACACTGAGGCTCAG-GAGGGAAGGTAGGCTACCCACAGG 352965 v i v - vv i ivi i vi v C MIRb#SINE/MIR 144 TACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGT 95 chrXqtel1M 352966 CCTCCAGCT 352974 viv C MIRb#SINE/MIR 94 CACACAGCT 86 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.54 CpG sites = 7, Kimura (unadjusted) = 34.54 Transitions / transversions = 0.78 (7/9) Gap_init rate = 0.02 (1 / 57), avg. gap size = 1.00 (1 / 1) 16 5.20 0.00 0.00 chrXqtel1M 354263 354282 (645718) (C)n#Simple_repeat 1 20 (0) m_b361s252i16 15157 chrXqtel1M 354263 CCCCCCCCCCCCCCCCGCCC 354282 v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCC 20 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 60 7.23 5.77 0.00 chrXqtel1M 354539 354642 (645358) (CT)n#Simple_repeat 1 110 (0) c_b361s251i3 15158 chrXqtel1M 354539 CTCTCTCTCCCTCCCTCCCTCCCTC-CTC-CTC-CTCCCTC-CTCTCTCT 354584 i i i i - - - i - (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chrXqtel1M 354585 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-CCCTCCCTC-CTCTCT 354632 - i i - (CT)n#Simple_ 51 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 100 chrXqtel1M 354633 CTCTCTCTCT 354642 (CT)n#Simple_ 101 CTCTCTCTCT 110 Matrix = Unknown Transitions / transversions = 1.00 (7/0) Gap_init rate = 0.06 (6 / 103), avg. gap size = 1.00 (6 / 6) 59 0.00 0.00 0.00 chrXqtel1M 355498 355547 (644453) (TC)n#Simple_repeat 1 50 (0) c_b361s251i4 15159 chrXqtel1M 355498 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 355547 (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 21 0.00 0.00 0.00 chrXqtel1M 355548 355570 (644430) (AC)n#Simple_repeat 1 23 (0) m_b361s252i17 15160 chrXqtel1M 355548 ACACACACACACACACACACACA 355570 (AC)n#Simple_ 1 ACACACACACACACACACACACA 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 25 5.18 7.50 0.00 chrXqtel1M 355571 355610 (644390) (TC)n#Simple_repeat 1 43 (0) m_b361s252i18 15161 chrXqtel1M 355571 TCTGTCTC-CTC-CTTTCTCTCTCTCTCTCTCTCTCTCT-TCT 355610 v - - i - (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 43 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.08 (3 / 39), avg. gap size = 1.00 (3 / 3) 608 33.41 14.63 0.35 chrXqtel1M 355615 356359 (643641) C L1MD_orf2#LINE/L1 (1053) 2241 1391 m_b361s551i8 15162 chrXqtel1M 355615 TTTGTTAGTAATATACAGAAATGCTGATGATTT----GTGTTTATTTTAT 355660 ii iv i i i viv ----i ? i i C L1MD_orf2#LIN 2241 TTCATTGCTAGTATATAGAAATACAATTGATTTTTGTATGTTNATCTTGT 2192 chrXqtel1M 355661 AGCCTGCAACTTTGCAAAAGTTGTTCAT-GGTTTCAATAACTTTTTT-TA 355708 v i i vi v iii i -i ii iv ii - C L1MD_orf2#LIN 2191 ATCCTGCGACCTTGCTGAACTCACTTATTAGTTCTAGGAGTTTTTTTGTA 2142 chrXqtel1M 355709 GTT-------GATTCTCCACAAACACCAATATAACATCTGCAAA--GGGT 355749 v ------- i i iv v v vi iv -- v C L1MD_orf2#LIN 2141 GATTCCTTGGGATTTTCTACGTAGACAATCATGTCATCTGCAAATAGGGA 2092 chrXqtel1M 355750 --GTTTGATTTCCATGTTACC--------TACTTTTGATGTCTTTTTCTC 355789 -- v iviv v -------- i i v v i i C L1MD_orf2#LIN 2091 CAGTTTTATTTCTTCCTTTCCAATCTGTATGCCTTTTATTTCCTTTTCTT 2042 chrXqtel1M 355790 ATCCTGTTG--------AGCATTTCGAGTAGGATATTGAATAATAGCAGC 355831 ii i i -------- v i v vv i v ii i C L1MD_orf2#LIN 2041 GCCTTATTGCACTGGCTAGAACTTCCAGTACTATGTTGAATAAGAGTGGT 1992 chrXqtel1M 355832 AATAATGGATATCTTTGC----TTCACTATCTTATCCAG---GTTTGTAG 355874 i v ii i i ---- v v vvvi --- iv vi C L1MD_orf2#LIN 1991 GAGAGCGGACATCCTTGCCTTGTTCCCGATCTTAGGGGGAAAGCATTCAG 1942 chrXqtel1M 355875 CGTATCTCCATTCCAGATAATGCTGGCTGATGGTTTT----AGATACTAC 355920 iv v v vviv i i i vv ---- i vi C L1MD_orf2#LIN 1941 TCTTTCACCATTAAGTATGATGTTAGCTGTAGGTTTTTTGTAGATGCTCT 1892 chrXqtel1M 355921 TCATCATTTGAAGGAAAGCTCCATTTAATCCTATGTTCTCT-AGCGTTTT 355969 i vv vi ivii v i v - i? - v C L1MD_orf2#LIN 1891 TTATCAAGTTGAGGAAGTTCCCCTCTATTCCTA-GTTTNCTGAGAGTTTT 1843 chrXqtel1M 355970 TAATAGGAACGAGTGCTGCGCTTTGTCAAAGGGTTTCTCTGTACCCATTG 356019 vi v i i i vii v v i i i v C L1MD_orf2#LIN 1842 TATCATGAATGGGTGTTGAATTTTGTCAAATGCTTTTTCTGCATCAATTG 1793 chrXqtel1M 356020 AGAAAATTGTACGA--TTTCCATTTTGG--TACTGACGTGGTTGGTTGTG 356065 v vi ii ii -- ivi i -- ii i ii v i iii C L1MD_orf2#LIN 1792 ATATGATCATGTGATTTTTCTTCTTTAGCCTGTTAATATGGTGGATTACA 1743 chrXqtel1M 356066 CCAAGT--TTCCCTAATATTGAACCGGACTTGCACGGCTAGTAGAAAT-- 356111 iii v -- ii v i v i?v i v v i-- C L1MD_orf2#LIN 1742 TTGATTGATTTTCGAATATTGAACCAGCCTTGCATNCCTGGAATAAACCC 1693 chrXqtel1M 356112 --GTTAG--ATAGTG--------ATTTCA-----TGCTTCAGTTGCCTTG 356144 --v i -- i --------v i ----- vv v i?vi C L1MD_orf2#LIN 1692 CACTTGGTCATGGTGTATAATTCTTTTTATATATTGCTGAATTCNATTTG 1643 chrXqtel1M 356145 CACTAGTACTTCATTGAAAACTTTTCTGTCAATATT----AAGGAAACTG 356190 -- i i ii ii i vi v i ---- i v i C L1MD_orf2#LIN 1642 --CTAATATTTTGTTGAGGATTTTTGCGTCTATGTTCATGAGGGATATTG 1595 chrXqtel1M 356191 GGCTCTAGTTTCGTTTTT--------GCTCCCCCTGGTTTCAATATCGAA 356232 v v iv --------v iivi iii iii C L1MD_orf2#LIN 1594 GTCTGTAGTTTTCTTTTTTTGTACTGTCTTTGTCTGGTTTTGGTATCAGG 1545 chrXqtel1M 356233 ACCCTATTTGTGTCCTCGAAGGCATGTGGTAGGA----CTACTCGTTGAT 356278 iivv i v iv v vi v vi vv v vi---- v v iv C L1MD_orf2#LIN 1544 GTAATACTGGCCTCATAAAATGAGTTGGGAAGTGTTCCCTCCTCTTCTAT 1495 chrXqtel1M 356279 TT-------GGGATT------------TATTA----TTCCTTAAATGTTT 356305 ------- i ------------ i ---- i i C L1MD_orf2#LIN 1494 TTTCTGGAAGAGATTGTGTAGAATTGGTGTTAATTCTTCTTTAAACGTTT 1445 chrXqtel1M 356306 GATAGAATTCACTTGTGAATTCATGTGGTTTTGGAGATGTTTTCTGAGGG 356355 i v iv vi v vii v i i vi C L1MD_orf2#LIN 1444 GGTAGAATTCTCCAGTGAAACCATCTGGGCCTGGAGATTTCTTTTTGGGG 1395 chrXqtel1M 356356 AGCT 356359 i C L1MD_orf2#LIN 1394 AGTT 1391 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 45.01 CpG sites = 147, Kimura (unadjusted) = 46.31 Transitions / transversions = 1.46 (147/101) Gap_init rate = 0.04 (29 / 744), avg. gap size = 3.86 (112 / 29) 613 32.77 10.56 0.19 chrXqtel1M 355615 356097 (643903) C L1M5_orf2#LINE/L1 (1053) 2241 1709 m_b361s551i7 15162 chrXqtel1M 355615 TTTGTTAGTAATATACAGAAATGCTGATGATTTGTGTTTATT----TTAT 355660 iv i i i viv v v ---- i C L1M5_orf2#LIN 2241 TTTGTTGCTAGTATATAGAAATACAATTGATTTTTGTATATTGACCTTGT 2192 chrXqtel1M 355661 AGCCTGCAACTTTGCAAAAGTTGTTCAT-GGTTTCAATAACTTTTTT-TA 355708 v ? i i v v iii i -i ii i ii ? - C L1M5_orf2#LIN 2191 ATCCNGCGACCTTGCTAAATTCACTTATTAGTTCTAGTAGTTTNTTTGTA 2142 chrXqtel1M 355709 GTT-------GATTCTCCACAAACACCAATATAACATCTGC----AAAGG 355747 v ------- i i iv ? v vi iv ---- ? i C L1M5_orf2#LIN 2141 GATTCTTTNGGATTTTCTACGTANACAATCATGTCATCTGCGAATAANGA 2092 chrXqtel1M 355748 GTGTTTGATTTCCATGTTACC--------TACTTTTGATGTCTTTTTCTC 355789 vv v iviv v -------- i i v v i C L1M5_orf2#LIN 2091 CAGTTTTATTTCTTCCTTTCCAATCTTTATGCCTTTTATTTCTTTTTCTT 2042 chrXqtel1M 355790 ATCCTGTTG--------AGCATTTCGAGTAGGATATTGAATAATAGCAGC 355831 ii i i -------- v ii v vi i iv ii i C L1M5_orf2#LIN 2041 GCCTTATTGCACTGGCTAGGACCTCCAGTACAATGTTGAATAGAAGTGGT 1992 chrXqtel1M 355832 AATAATGGATATCTTTGC----TTCACTATCTTATCCAG---GTTTGTAG 355874 i ? ii i i i---- v v vvvi --- i? vi C L1M5_orf2#LIN 1991 GANAGCGGACATCCTTGTCTTGTTCCCGATCTTAGGGGGAAAGCNTTCAG 1942 chrXqtel1M 355875 CGTATCTCCATTCCAGATAATGCTGGCTGATGGTTTT----AGATACTAC 355920 i? v v vviv i i ? vv ---- i ivi C L1M5_orf2#LIN 1941 TNTTTCACCATTAAGTATGATGTTNGCTGTAGGTTTTTCGTAGATGCCCT 1892 chrXqtel1M 355921 TCATCATTTGAAGGAAAGCTCCATTTAATCCTATGTTCTCT-AGCGTTTT 355969 i vv vi ivii v i v - iv - v C L1M5_orf2#LIN 1891 TTATCAGGTTGAGGAAGTTCCCTTCTATTCCTA-GTTTGCTGAGAGTTTT 1843 chrXqtel1M 355970 TAATAGGAACGAGTGCTGCGCTTTGTCAAAGGGTTTCTCTGTACCCATTG 356019 vi v i i i vii v v i i i i C L1M5_orf2#LIN 1842 TATCATGAATGGGTGTTGAATTTTGTCAAATGCTTTTTCTGCATCTATTG 1793 chrXqtel1M 356020 AGAAAATTGTACGATT----TCCATTTTGGTACTGACGTGGTTGGTTGTG 356065 vi ii i ---- v v vv ii i ii vii iii C L1M5_orf2#LIN 1792 AGATGATCATATGATTTTTCTCCTTTATTCTGTTAATATGGTGAATTACA 1743 chrXqtel1M 356066 CCAAGT--TTCCCTAATATTGAACCGGACTTGCA 356097 iii v -- ii v i i iiv C L1M5_orf2#LIN 1742 TTGATTGATTTTCGAATGTTAAACCAACCTTGCA 1709 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 44.83 CpG sites = 97, Kimura (unadjusted) = 46.05 Transitions / transversions = 1.59 (97/61) Gap_init rate = 0.03 (14 / 482), avg. gap size = 3.71 (52 / 14) 15 5.48 0.00 0.00 chrXqtel1M 356536 356554 (643446) (T)n#Simple_repeat 1 19 (0) m_b361s252i19 15163 chrXqtel1M 356536 TTTTTTTTTTTTGTTTTTT 356554 v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTT 19 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 180 17.95 2.56 0.00 chrXqtel1M 356556 356594 (643406) C MIR#SINE/MIR (139) 123 84 m_b361s601i15 15164 chrXqtel1M 356556 CTGAGGCAGTTGGAG-TTCAGTAACTCGCCCATGGTCACA 356594 vvvi - v i v C MIR#SINE/MIR 123 CTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACA 84 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 20.52 CpG sites = 2, Kimura (unadjusted) = 20.52 Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.03 (1 / 38), avg. gap size = 1.00 (1 / 1) 230 28.94 22.07 0.37 chrXqtel1M 357504 357725 (642275) L2#LINE/L2 2105 2374 (708) m_b361s601i16 15165 chrXqtel1M 357504 AGTACTCTGTTCTCTAGGTTTC-AGGACAC-----TTTCCTGGTTCTCCT 357547 ii i v v v i - ----- i i L2#LINE/L2 2105 AACACTTTCTTCACTTGGCTTCCAGGACACCACACTCTCCTGGTTTTCCT 2154 chrXqtel1M 357548 TTT--------------CCCCTCTCTGCCTCCTTTGCTGGA--------- 357574 ii --------------i i v i v--------- L2#LINE/L2 2155 CCTACCTCACTGGCCGCTCCTTCTCAGTCTCCTTTGCTGGTTCCTCCTCA 2204 chrXqtel1M 357575 -------GACCCCTCCA-----GA-TCCCCCTGGGTTCTGGCCTGGGCCC 357611 ------- i ?v ----- - v v i v v v v L2#LINE/L2 2205 TCTCCCCGACCTCTNAACGTTGGAGTGCCCCAGGGCTCAGTCCTTGGACC 2254 chrXqtel1M 357612 TCTACTCGTCCCCTGCTATACTCCTTTACTTGGTGACCCTG-CCAGCTCC 357660 v v i ivv i vi iv ? i iii- - i L2#LINE/L2 2255 TCTTCTCTTCTCTATCTACACTCACTCCCTNGGTGATCTCATCCAG-TCT 2303 chrXqtel1M 357661 CATCG-TTCGTTTGTCACCGATATGGCGATGATTTTCACATCTA-----C 357704 v - iivv ii i v vi i ii v i ----- L2#LINE/L2 2304 CATGGCTTTAAATACCATCTATATGCTGATGACTCCCAAATTTATATCTC 2353 chrXqtel1M 357705 CTGTCCTGTCTCCTTCCCTGA 357725 v i v v ii i L2#LINE/L2 2354 CAGCCCGGACCTCTCCCCTGA 2374 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.00 CpG sites = 37, Kimura (unadjusted) = 38.00 Transitions / transversions = 1.37 (37/27) Gap_init rate = 0.05 (11 / 221), avg. gap size = 4.55 (50 / 11) 15 20.36 0.00 0.00 chrXqtel1M 357875 357903 (642097) (C)n#Simple_repeat 1 29 (0) m_b361s252i20 15166 chrXqtel1M 357875 CCCCACTCCTCCCTCCTCCCCCCCCCCCC 357903 v i i i i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC 29 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 19 24.95 0.00 0.00 chrXqtel1M 360122 360173 (639827) (CCTCCT)n#Simple_repeat 1 52 (0) m_b361s252i21 15167 chrXqtel1M 360122 CCTCGGCCTCCCCTTCCTCCTCCTCTTCCTCCTCCAGCATCTCCTCTGCC 360171 vv i i i vv vi iv (CCTCCT)n#Sim 1 CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC 50 chrXqtel1M 360172 TC 360173 (CCTCCT)n#Sim 51 TC 52 Matrix = Unknown Transitions / transversions = 0.83 (5/6) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 17 20.12 0.00 0.00 chrXqtel1M 361577 361610 (638390) (C)n#Simple_repeat 1 34 (0) m_b361s252i23 15168 chrXqtel1M 361577 CCCCTCCCCTCCCCACCCCACCCCACCCCCCGCC 361610 i i v v v v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 34 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 209 27.00 19.39 1.74 chrXqtel1M 363573 363670 (636330) C MIRb#SINE/MIR (70) 198 84 m_b361s601i17 15169 chrXqtel1M 363573 ATTTCCTCGAATCCTCACAAC---TCCGTGAGGCAGGT------------ 363607 i v iv ---i i i i ------------ C MIRb#SINE/MIR 198 ATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATTATCCCC 149 chrXqtel1M 363608 ----TACCACTGGGGAAACTGAGGCAGGCAGAGGGCAAGTGTTCTGTGCC 363653 ---- viv i vviv vi i-v - C MIRb#SINE/MIR 148 ATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTA-ACT-TGCC 101 chrXqtel1M 363654 CAAGGCCTCCCGGTCAG 363670 i v v i ii C MIRb#SINE/MIR 100 CAAGGTCACACAGCTAG 84 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.75 CpG sites = 15, Kimura (unadjusted) = 34.36 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.05 (5 / 97), avg. gap size = 4.20 (21 / 5) 276 28.47 25.48 1.55 chrXqtel1M 370026 370182 (629818) C MIRc#SINE/MIR (72) 196 3 m_b361s601i18 15170 chrXqtel1M 370026 TGACCCTCCCAATAGTCCTGGGAAGTAAGTGG-----------TCATCTC 370064 i v i ii v i i ii ----------- i i C MIRc#SINE/MIR 196 TGATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCC 147 chrXqtel1M 370065 TGTTTTACCCAAGAGGAAGCTGAAG---------------------GCCC 370093 ii vv v i i --------------------- C MIRc#SINE/MIR 146 CATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCC 97 chrXqtel1M 370094 AGTATCACACAGCTCAGAAGGCCACAGTGC----ATTTGAATTCAGGGCC 370139 ivi - v i ivi v ---- i i ii v i C MIRc#SINE/MIR 96 AAGGTCACACAGCT-AGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCT 48 chrXqtel1M 370140 TCCTGACCCTAGGCTCACAGC----TCCACATGCTATCACACGGACT 370182 i i i ii vv ---- - - i v v C MIRc#SINE/MIR 47 TCCTGACTCCAAGTCCAGTGCTCTTTCCAC-TGC-ACCACACTGCCT 3 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.65 CpG sites = 30, Kimura (unadjusted) = 37.76 Transitions / transversions = 2.14 (30/14) Gap_init rate = 0.04 (7 / 156), avg. gap size = 6.14 (43 / 7) 17 0.00 0.00 0.00 chrXqtel1M 372758 372778 (627222) (GAC)n#Simple_repeat 1 21 (0) m_b362s252i0 15171 chrXqtel1M 372758 GACGACGACGACGACGACGAC 372778 (GAC)n#Simple 1 GACGACGACGACGACGACGAC 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 13 29.28 0.00 4.92 chrXqtel1M 373228 373291 (626709) (GGCCTA)n#Simple_repeat 1 61 (0) m_b362s252i1 15172 chrXqtel1M 373228 GGCCTCGGGCTTCGGCCCCGGTCCCGGCCTAGGCCTAGGTTCGAGGCCCG 373277 -i i v iv i iv -i v - v (GGCCTA)n#Sim 1 GGCCT-AGGCCTAGGCCTAGGCCTAGGCCTAGGCCTAGG-CCTAGG-CCT 47 chrXqtel1M 373278 AAGTCGAGGCCTAG 373291 i i v (GGCCTA)n#Sim 48 AGGCCTAGGCCTAG 61 Matrix = Unknown Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.05 (3 / 63), avg. gap size = 1.00 (3 / 3) 23 24.54 5.81 0.00 chrXqtel1M 373538 373623 (626377) (GCGGAC)n#Simple_repeat 1 91 (0) m_b362s252i2 15173 chrXqtel1M 373538 GCGGACGCGGGGGAGGACGCGGACGCCGACGC---CGCCGCCGCCAATGC 373584 iv v v --- v v vi i (GCGGAC)n#Sim 1 GCGGACGCGGACGCGGACGCGGACGCGGACGCGGACGCGGACGCGGACGC 50 chrXqtel1M 373585 AGACGCGGACCAGGACGAAG-CCCGG-CGCGCGCGCGTACG 373623 i vv vi - v - vi v (GCGGAC)n#Sim 51 GGACGCGGACGCGGACGCGGACGCGGACGCGGACGCGGACG 91 Matrix = Unknown Transitions / transversions = 0.50 (6/12) Gap_init rate = 0.04 (3 / 85), avg. gap size = 1.67 (5 / 3) 13 13.25 0.00 0.00 chrXqtel1M 373555 373579 (626421) (CGC)n#Simple_repeat 1 25 (0) m_b362s252i3 15174 chrXqtel1M 373555 CGCGGACGCCGACGCCGCCGCCGCC 373579 v v v (CGC)n#Simple 1 CGCCGCCGCCGCCGCCGCCGCCGCC 25 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 23 24.54 5.81 0.00 chrXqtel1M 373538 373623 (626377) (GCGGAC)n#Simple_repeat 1 91 (0) m_b362s252i2 15173 chrXqtel1M 373538 GCGGACGCGGGGGAGGACGCGGACGCCGACGC---CGCCGCCGCCAATGC 373584 iv v v --- v v vi i (GCGGAC)n#Sim 1 GCGGACGCGGACGCGGACGCGGACGCGGACGCGGACGCGGACGCGGACGC 50 chrXqtel1M 373585 AGACGCGGACCAGGACGAAG-CCCGG-CGCGCGCGCGTACG 373623 i vv vi - v - vi v (GCGGAC)n#Sim 51 GGACGCGGACGCGGACGCGGACGCGGACGCGGACGCGGACG 91 Matrix = Unknown Transitions / transversions = 0.50 (6/12) Gap_init rate = 0.04 (3 / 85), avg. gap size = 1.67 (5 / 3) 13 20.27 0.00 0.00 chrXqtel1M 373609 373638 (626362) (GCGT)n#Simple_repeat 1 30 (0) m_b362s252i4 15175 chrXqtel1M 373609 GCGCGCGCGCGTACGTGTGTGCGTGCGCGC 373638 i i i i i (GCGT)n#Simpl 1 GCGTGCGTGCGTGCGTGCGTGCGTGCGTGC 30 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 42 26.07 0.88 0.88 chrXqtel1M 373660 373773 (626227) (GCC)n#Simple_repeat 1 114 (0) m_b362s252i5 15176 chrXqtel1M 373660 GCCACCGCCGCCGCCGCCGTTGTCGCCG-CACCGCCCCTGGTCCCGACCA 373708 i ii i - i v i viv - i (GCC)n#Simple 1 GCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCG-CCG 49 chrXqtel1M 373709 CTACTGCCGCTGCCCCCGCCGCCGTCGCCGACGACGCTGCTGACGCCGCC 373758 ii i i v i v v i i v (GCC)n#Simple 50 CCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCC 99 chrXqtel1M 373759 GCCGTCGTCGCCGCC 373773 i i (GCC)n#Simple 100 GCCGCCGCCGCCGCC 114 Matrix = Unknown Transitions / transversions = 2.43 (17/7) Gap_init rate = 0.02 (2 / 113), avg. gap size = 1.00 (2 / 2) 29 0.00 0.00 0.00 chrXqtel1M 374092 374118 (625882) (GGGGCT)n#Simple_repeat 1 27 (0) c_b362s251i0 15177 chrXqtel1M 374092 GGGGCTGGGGCTGGGGCTGGGGCTGGG 374118 (GGGGCT)n#Sim 1 GGGGCTGGGGCTGGGGCTGGGGCTGGG 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 175 1.16 2.86 0.00 chrXqtel1M 374259 374433 (625567) (CT)n#Simple_repeat 1 180 (0) c_b362s251i1 15178 chrXqtel1M 374259 CTCTCCCTCTCCCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 374308 i i (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chrXqtel1M 374309 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-CTCTCTCTCTCT 374357 - (CT)n#Simple_ 51 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 100 chrXqtel1M 374358 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-CTC-CTCTC-CTCTCTCT 374404 - - - (CT)n#Simple_ 101 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 150 chrXqtel1M 374405 CTCTCTCTCTCTCTCTCTCTC-CTCTCTCT 374433 - (CT)n#Simple_ 151 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 180 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.03 (5 / 174), avg. gap size = 1.00 (5 / 5) 25 14.08 2.08 0.00 chrXqtel1M 374557 374604 (625396) (GAAT)n#Simple_repeat 1 49 (0) m_b362s252i6 15179 chrXqtel1M 374557 GACTGAA-AAATGAATGAATGAATGAACAAATGGACGAATGAATGAATG 374604 v -i ii i i (GAAT)n#Simpl 1 GAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATG 49 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.02 (1 / 47), avg. gap size = 1.00 (1 / 1) 22 10.47 0.00 0.00 chrXqtel1M 376124 376154 (623846) (T)n#Simple_repeat 1 31 (0) m_b362s252i7 15180 chrXqtel1M 376124 TTTTTTTGTTTTTTTTGTTTTTTTGTTTTTT 376154 v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 31 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 21 20.27 1.04 10.23 chrXqtel1M 376310 376405 (623595) (GGGTGGG)n#Simple_repeat 1 88 (0) m_b362s252i8 15181 chrXqtel1M 376310 GGGCGGTGGGTGGGGGGAAGGGGGGTGGGTGAATGTGGGGTGAGTGGGGT 376359 i v -v - ii v - - (GGGTGGG)n#Si 1 GGGTGGGGGGTGGGGGG-TGGGGGGTGGG-GGGTGGGGGGTG-G-GGGGT 46 chrXqtel1M 376360 ATGGGGTGAGGGCGGAGGCAGCGGT-GGGTATGAAGGGTGGGGTGGT 376405 iv - - v -- v - vi ii - (GGGTGGG)n#Si 47 GGGGGGTG-GGG-GGTGG--GGGGTGGGGGGTGGGGGGTGGGG-GGT 88 Matrix = Unknown Transitions / transversions = 1.00 (7/7) Gap_init rate = 0.11 (10 / 95), avg. gap size = 1.00 (10 / 10) 16 9.71 0.00 0.00 chrXqtel1M 376463 376484 (623516) (C)n#Simple_repeat 1 22 (0) m_b362s252i9 15182 chrXqtel1M 376463 CCCCCCCCACCCCCCCCCCTCC 376484 v i (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCC 22 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 25 23.34 0.00 0.00 chrXqtel1M 376790 376844 (623156) (G)n#Simple_repeat 1 55 (0) m_b362s252i10 15183 chrXqtel1M 376790 GGGGGGGTGGTGGGGAAGGGGGGGGTGGGGGGGTTGGGGGAAGGTGGGGA 376839 v v ii v vv ii v i (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 50 chrXqtel1M 376840 GGGGG 376844 (G)n#Simple_r 51 GGGGG 55 Matrix = Unknown Transitions / transversions = 0.83 (5/6) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 15 29.70 0.00 8.89 chrXqtel1M 376905 377002 (622998) (GGGGC)n#Simple_repeat 1 90 (0) m_b362s252i11 15183 chrXqtel1M 376905 GGGGCCGGGGGGGGTAGGGCGGGGCTAGGGTGGGGTGGTTTGGTGGGGTG 376954 v v ii -i i i --- i i (GGGGC)n#Simp 1 GGGGCGGGGCGGGGCGGGGCGGGGC-GGGGCGGGGCGG---GGCGGGGCG 46 chrXqtel1M 376955 GGGTGGTGGGAGGAGGGGACAGAGGAGGGGAAGAACGATGGGCGGGGC 377002 i v v i v - - i v vi ii -- (GGGGC)n#Simp 47 GGGCGGGGCGGGGCGGGG-C-GGGGCGGGGCGGGGCG--GGGCGGGGC 90 Matrix = Unknown Transitions / transversions = 1.86 (13/7) Gap_init rate = 0.08 (8 / 97), avg. gap size = 1.00 (8 / 8) 15 19.67 2.60 9.72 chrXqtel1M 377573 377649 (622351) (AGGAG)n#Simple_repeat 1 72 (0) m_b362s252i12 15184 chrXqtel1M 377573 AGGAG-GCAGATGGAGATG-GCGGAGGAAGAGCAAAGAGGAAGAGGAGGG 377620 - v - v - v - i vii - i (AGGAG)n#Simp 1 AGGAGAGGAGA-GGAGAGGAGAGGA-GAGGAGAGGAGAGG-AGAGGAGAG 47 chrXqtel1M 377621 AGGGAGGACTAGGAGACAGAGAGTGAGAG 377649 - i -v -i - (AGGAG)n#Simp 48 -GAGAGGA-GAGGAGA-GGAGAG-GAGAG 72 Matrix = Unknown Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.12 (9 / 76), avg. gap size = 1.00 (9 / 9) 17 23.21 0.00 6.78 chrXqtel1M 377573 377635 (622365) (AGG)n#Simple_repeat 1 59 (0) m_b362s252i13 15184 chrXqtel1M 377573 AGGAGGCAGATGGAGATGGCGGAGGAAGAGCAAAGAGGAAGAGGAGGGAG 377622 - iv iv v i -i i i - - (AGG)n#Simple 1 AGGAGG-AGGAGGAGGAGGAGGAGGAGGAG-GAGGAGGAGGAGGA-GGA- 46 chrXqtel1M 377623 GGAGGACTAGGAG 377635 vv (AGG)n#Simple 47 GGAGGAGGAGGAG 59 Matrix = Unknown Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.06 (4 / 62), avg. gap size = 1.00 (4 / 4) 259 22.41 1.12 9.76 chrXqtel1M 378372 378460 (621540) MIR3#SINE/MIR 61 142 (66) m_b362s601i1 15185 chrXqtel1M 378372 CCCGGCTCAGCCCACAACCCTGGCTGGCCTACTCAGGCTCTGAACAAGGG 378421 v vvi -- ? ------ vv i ii ii vv MIR3#SINE/MIR 61 CCCGGCTCTGCCACTAAC--TNGCTG------TGTGACCTTGGGCAAGTC 102 chrXqtel1M 378422 ACTTC-CCTCCCTGGGCCTCAGCTTCCTGCTCTATAAAAT 378460 - i i vv i MIR3#SINE/MIR 103 ACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAAT 142 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.96 CpG sites = 9, Kimura (unadjusted) = 26.96 Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.10 (9 / 88), avg. gap size = 1.00 (9 / 9) 266 32.35 3.92 0.00 chrXqtel1M 378407 378508 (621492) MIRc#SINE/MIR 91 196 (72) m_b362s601i2 15185 chrXqtel1M 378407 GGCTCTGAACAAGGGACTTC-CCTCCCTGGGCCTCAGCTTCCTGCTCTAT 378455 i ii ii vv v- i i i vv i MIRc#SINE/MIR 91 GACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGT 140 chrXqtel1M 378456 AAAAT---CATAATCTGGCCTGGATGCCCAACTTCCCTGTGCTGTCGTGA 378502 ---v vvvi vvivv v i v v v i i MIRc#SINE/MIR 141 AAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGA 190 chrXqtel1M 378503 GGGACA 378508 iv MIRc#SINE/MIR 191 GGATCA 196 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.68 CpG sites = 15, Kimura (unadjusted) = 42.68 Transitions / transversions = 0.83 (15/18) Gap_init rate = 0.02 (2 / 101), avg. gap size = 2.00 (4 / 2) 79 20.53 1.18 0.58 chrXqtel1M 378658 378827 (621173) (TC)n#Simple_repeat 1 171 (0) m_b362s252i14 15186 chrXqtel1M 378658 TCTCTGTGTCTGTCTCTCTC-CTTTTTCTCTCTCTCCCTC-CTCTCTCTG 378705 v v v - i i i - v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chrXqtel1M 378706 TTTCTCCCTCCTTCTCTCTCTGACTGTCTCTGTCTCTCTCTCTCTGTCTC 378755 i i ii vv v v v (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chrXqtel1M 378756 TCCTTCCCTCCTTCTCTCTGTCTCTCTCTCTGTCTCTCCCTCCCTCCCTC 378805 ii i ii v v i i i (TC)n#Simple_ 101 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 150 chrXqtel1M 378806 TGTCTCTGTGTTTCTCTCATCT 378827 v v v i - (TC)n#Simple_ 151 TCTCTCTCTCTCTCTCTC-TCT 171 Matrix = Unknown Transitions / transversions = 1.14 (16/14) Gap_init rate = 0.02 (3 / 169), avg. gap size = 1.00 (3 / 3) 363 34.97 16.16 0.93 chrXqtel1M 381440 382002 (617998) L2#LINE/L2 1955 2602 (480) m_b362s601i3 15187 chrXqtel1M 381440 AGGCTTCCAGCCCCACTGATCAACAGAAATGACTTTCTTCCAAGTCACCA 381489 i iv iiv v v ivi i iv v i L2#LINE/L2 1955 AGGCTTTCGTCCCCACCACTCCACCGAAACTGCTCTTGTCAAGGTCACCA 2004 chrXqtel1M 381490 CCCAGCTAC---CTGCCCA--CCCTTTGCCCCTTTTCCAGCAGCGCCCTT 381534 viv v v ---i iv -- vv v i vv i viv vv ii i v L2#LINE/L2 2005 ATGACCTCCACGTTGCTAAATCCAATGGTCAATTCTCAGTCCTCATCTTA 2054 chrXqtel1M 381535 CTTGAGCCCTCTGCAGTTCTGGACAGGGTTCACTCCCCTCCGCTCCTCCG 381584 v i? v ivi v vi v iiv i i iv i i- L2#LINE/L2 2055 CTTGACCTNTCAGCAGCATTTGACACAGTTGATCACTCCCTCCTTCTT-G 2103 chrXqtel1M 381585 CAA----TCTTTCAGTT---TTCCTAG----CATTCTTTTCTGGCT---C 381620 v ---- ii v --- vi ---- iv i i i --- L2#LINE/L2 2104 AAACACTTTCTTCACTTGGCTTCCAGGACACCACACTCTCCTGGTTTTCC 2153 chrXqtel1M 381621 TCCTACCT----GCTCGATCCTGTTCCATCTCCTC--CAGGTTACTCT-- 381662 ---- vi v vi vi i-- v v i-- L2#LINE/L2 2154 TCCTACCTCACTGGCCGCTCCTTCTCAGTCTCCTTTGCTGGTTCCTCCTC 2203 chrXqtel1M 381663 -----------CTCTAA---TTGGAGGCTTTCTAGAAAGTCAGGTCCCAG 381698 ----------- ? --- -- vi iviiiiv - iv L2#LINE/L2 2204 ATCTCCCCGACCTCTNAACGTTGGAG--TGCCCCAGGGCTCAG-TCCTTG 2250 chrXqtel1M 381699 ATCCCCTGCTCCTCTGT-CCTAC-CTCAC-----CAGGGGTCTCACCCAT 381741 iv i v i v -i - -----?i v i i v L2#LINE/L2 2251 GACCTCTTCTCTTCTCTATCTACACTCACTCCCTNGGTGATCTCATCCAG 2300 chrXqtel1M 381742 GCCCACAGATTGGCCGACCATCTCCGTGCAGATGATTCTCCTATC--TAC 381789 v i ii v vivvv vii v i i vv i-- i L2#LINE/L2 2301 TCTCATGGCTTTAAATACCATCTATATGCTGATGACTCCCAAATTTATAT 2350 chrXqtel1M 381790 TTAGAGCCCCCG-CTCTCTGCTGACCTCCATTCCCATAGCTCC-ACTGCC 381837 i vv vvi- iv v vv i i vv - L2#LINE/L2 2351 CTCCAGCCCGGACCTCTCCCCTGAACTCCAGACTCGTATATCCAACTGCC 2400 chrXqtel1M 381838 T----------------------CCCAGTGGGCATCTGCAAACTCAGCGT 381865 ----------------------i i i i - i i i L2#LINE/L2 2401 TACTCGACATCTCCACTTGGATGTCTAATAGGCATCT-CAAACTTAACAT 2449 chrXqtel1M 381866 GTGTAAAACAGAACTCATGCCCTTTCTCTGTGACCCTGCTCTGT-----G 381910 vi v v vi i i ivii v ivi----- L2#LINE/L2 2450 GTCCAAAACTGAACTCCTGATCTTCCCCCTCAAACCTGCTCCTCCCGCAG 2499 chrXqtel1M 381911 ACTGCC------------AGGACCATGCCATCCTCCCGCTTCCTCAGGCT 381948 v v ------------ v i v iv i iv v i L2#LINE/L2 2500 TCTTCCCCATCTCAGTNAATGGCAACTCCATCCTTCCAGTTGCTCAGGCC 2549 chrXqtel1M 381949 CCCCCTTTAGGAATCATTCTGGGCCTGTCGCTGTCTCTTAGCCTCCCATA 381998 vvvvvii v i i v i iiv v v i - vi i L2#LINE/L2 2550 AAAAACCTTGGAGTCATCCTTGACTCCTCTCTTTCTCTCA-CACCCCACA 2598 chrXqtel1M 381999 TCCA 382002 L2#LINE/L2 2599 TCCA 2602 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 47.88 CpG sites = 101, Kimura (unadjusted) = 48.57 Transitions / transversions = 1.07 (101/94) Gap_init rate = 0.05 (26 / 562), avg. gap size = 3.73 (97 / 26) 254 37.58 3.31 1.30 chrXqtel1M 382066 382216 (617784) L2#LINE/L2 2711 2864 (218) m_b362s601i4 15187 chrXqtel1M 382066 CCTGAACTGTTGCAGCAGC-TGCTAGGGGAGCTGTCTGCCTCTAGTCTCC 382114 i i ii ii - v ivv iv vi i i vi iv L2#LINE/L2 2711 CCTGGATTACTGCAATAGCCTCCTAACTGGTCTCCCTGCTTCCACCCTTG 2760 chrXqtel1M 382115 CCCCCCCCCATGCCATCCTCCATACGGCCACCGGTGT----TTCCTAAGA 382160 i? vv i i v i i vi i v ----i ii i L2#LINE/L2 2761 CCCCCCTNCAGTCTATTCTCAACACAGCAGCCAGAGTGATCCTTTTAAAA 2810 chrXqtel1M 382161 AACAGGTCTGATCATATGACACGTGGGGCCCAGCAAGACCCCAGGGGCTC 382210 vii i v i v v v -vv i i- vv i iv i L2#LINE/L2 2811 CGTAAGTCAGATCATGTCACTCCT-CTGCTCAA-AACCCTCCAATGGCTT 2858 chrXqtel1M 382211 CCGATC 382216 v L2#LINE/L2 2859 CCCATC 2864 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 53.79 CpG sites = 33, Kimura (unadjusted) = 55.29 Transitions / transversions = 1.43 (33/23) Gap_init rate = 0.03 (4 / 150), avg. gap size = 1.75 (7 / 4) 211 38.64 0.00 1.14 chrXqtel1M 382536 382624 (617376) L2a_3end#LINE/L2 423 510 (7) m_b362s601i5 15187 chrXqtel1M 382536 CTCTTGTCTCTTTCCCCCGGTTTTTGTATTCCTGGCCCCTGACACAGTGT 382585 i v ivii i-i vi i ii v iiv i L2a_3end#LINE 423 CTTTTGTCTGTTTTGTTCA-CTGCTGTATCCCCAGCGCCTAGAACAGTGC 471 chrXqtel1M 382586 AGAGCAAGTTGCAGGTACTCAGTTGGTATTAATTAAATG 382624 vvi vi v i ii i vii vi i L2a_3end#LINE 472 CTGGCACATAGTAGGCGCTCAATAAATATTTGTTGAATG 510 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 56.23 CpG sites = 23, Kimura (unadjusted) = 59.36 Transitions / transversions = 2.09 (23/11) Gap_init rate = 0.01 (1 / 88), avg. gap size = 1.00 (1 / 1) 232 22.73 0.00 0.00 chrXqtel1M 382606 382649 (617351) C MIR#SINE/MIR (6) 256 213 m_b362s601i7 15188 chrXqtel1M 382606 AGTTGGTATTAATTAAATGCTTGCTATATGCCAGGCACTGTTCT 382649 i iii v i ii i i C MIR#SINE/MIR 256 AGCTAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCT 213 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 25.95 CpG sites = 9, Kimura (unadjusted) = 29.43 Transitions / transversions = 9.00 (9/1) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 194 34.07 1.96 5.05 chrXqtel1M 382710 382811 (617189) C L2b_3end#LINE/L2 (240) 226 128 m_b362s601i8 15189 chrXqtel1M 382710 AGGTGACATTCGAGCTTAGCTCTGAAGGACAGCCAAGA--TGGTCAGAGG 382757 i v vi iiivi i -- i iv C L2b_3end#LINE 226 AGGTGACATTTGAGCTGAGACCTGAAGGATGAGTAGGAGTTGGCCAGGCG 177 chrXqtel1M 382758 CAATGGCAAGGAGTGAGAGCGCACCGAGTGCAGGTCACCACCGAGTTGCA 382807 v iv iii --- i iv ii iiv vv vi -- ?v C L2b_3end#LINE 176 AAGAGGTGGGGA---AGGGCGTTCCAGGCAGAGGGAACAGC--ANGTGCA 132 chrXqtel1M 382808 CAGG 382811 v C L2b_3end#LINE 131 AAGG 128 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 48.05 CpG sites = 20, Kimura (unadjusted) = 48.05 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.06 (6 / 101), avg. gap size = 1.17 (7 / 6) 240 26.23 4.88 2.38 chrXqtel1M 383008 383089 (616911) C MIR3#SINE/MIR (16) 192 109 m_b362s601i9 15190 chrXqtel1M 383008 GAACGTCTGAGTAAGATGGCCGCTTAAGGGTC-TCGGTCATTC--CCCTC 383054 i v ivi v vvv ii i - -- vi i -- i C MIR3#SINE/MIR 192 GAATGTCAGAGCTGGAAGGGACCTTAGAGATCATC--TAGTCCAACCCCC 145 chrXqtel1M 383055 TCGTTTTACAGATG-GGGAGCTGAGGGCCAGAGGGG 383089 i - i i v i C MIR3#SINE/MIR 144 TCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGG 109 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.25 CpG sites = 13, Kimura (unadjusted) = 33.25 Transitions / transversions = 1.62 (13/8) Gap_init rate = 0.06 (5 / 81), avg. gap size = 1.20 (6 / 5) 468 22.07 0.00 7.89 chrXqtel1M 383277 383399 (616601) MIRc#SINE/MIR 2 115 (153) m_b362s601i10 15191 chrXqtel1M 383277 GGGGCAGCTGGATGGTGCAGTAGATATAGCACCAGCCCTTTAGTCAGGAG 383326 i - -- i v v ii v i vv i MIRc#SINE/MIR 2 GAGGCAG-TG--TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chrXqtel1M 383327 GCCCTGAGTTCAAATCTGGTCTCAGACACTTAACACTTCTGACTGTGTGA 383376 v i i i iv v v v ------ ii MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCCACTTA------CTAGCTGTGTGA 92 chrXqtel1M 383377 CCCTGGGCAACTCATTTAACCTC 383399 i v i MIRc#SINE/MIR 93 CCTTGGGCAAGTCACTTAACCTC 115 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 25.11 CpG sites = 14, Kimura (unadjusted) = 26.30 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.07 (9 / 122), avg. gap size = 1.00 (9 / 9) 18 0.00 0.00 0.00 chrXqtel1M 383412 383431 (616569) (A)n#Simple_repeat 1 20 (0) m_b362s252i15 15192 chrXqtel1M 383412 AAAAAAAAAAAAAAAAAAAA 383431 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAA 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 14 20.85 4.55 0.00 chrXqtel1M 383915 383958 (616042) (CTCCAT)n#Simple_repeat 1 46 (0) m_b362s252i16 15193 chrXqtel1M 383915 CTCCATCTCTATCTGCTTCTACCTC-CCATGGCC-TCTCCATCCCC 383958 i v v v v - vv - i (CTCCAT)n#Sim 1 CTCCATCTCCATCTCCATCTCCATCTCCATCTCCATCTCCATCTCC 46 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2) 238 25.48 0.00 5.08 chrXqtel1M 384289 384350 (615650) L1MD1_3end#LINE/L1 426 484 (505) m_b362s551i0 15194 chrXqtel1M 384289 AAAGACCCATACGGATCAAAGGTTTATAGCAGTTCTGTTTGTGATGACCA 384338 i ii i--- i v i i i i i ii L1MD1_3end#LI 426 AAAAACCTGTACA---CGAATGTTTATAGCAGCTTTATTCGTAATAGCCA 472 chrXqtel1M 384339 AGAACTGGCAAC 384350 i v L1MD1_3end#LI 473 AAAACTGGAAAC 484 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 28.44 CpG sites = 13, Kimura (unadjusted) = 33.93 Transitions / transversions = 6.50 (13/2) Gap_init rate = 0.05 (3 / 61), avg. gap size = 1.00 (3 / 3) 356 24.76 9.52 0.00 chrXqtel1M 384487 384591 (615409) 7SLRNA#SINE/Alu 126 240 (80) m_b362s502i0 15195 chrXqtel1M 384487 CATCAACATGGCGATCGCCTGGAA-CAGGGC---------TGACCTAAGG 384526 i i i v i i - i v--------- vi 7SLRNA#SINE/A 126 CATCAATATGGTGACCTCCCGGGAGCGGGGGACCACCAGGTTGCCTAAGG 175 chrXqtel1M 384527 AGGGATGAACAAGACCAAGTCAGAAATAAAGTAGCTCAAAGCTGCCTTAC 384576 i vi v i i iii i v i v v i 7SLRNA#SINE/A 176 AGGGGTGAACCGGCCCAGGTCGGAAACGGAGCAGGTCAAAACTCCCGTGC 225 chrXqtel1M 384577 TGATCAGCAGTGGGA 384591 i 7SLRNA#SINE/A 226 TGATCAGTAGTGGGA 240 Matrix = 20p53g.matrix Kimura (with divCpGMod) = 24.26 CpG sites = 18, Kimura (unadjusted) = 31.29 Transitions / transversions = 2.25 (18/8) Gap_init rate = 0.02 (2 / 104), avg. gap size = 5.00 (10 / 2) 116 6.67 0.00 1.85 chrXqtel1M 384779 384943 (615057) (AAGG)n#Simple_repeat 1 162 (0) m_b362s252i17 15196 chrXqtel1M 384779 AAGGAAGGAAGGAAGGAAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 384828 - (AAGG)n#Simpl 1 AAGGAAGGAAGGAAGG-AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 49 chrXqtel1M 384829 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAGAGGGAGGGA 384878 - i i (AAGG)n#Simpl 50 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA-AGGAAGGAA 98 chrXqtel1M 384879 GGGAGGAAGGACAGAAGGAAGGAAGGAAGGAAAGGAAAGAAGGGAAGAAG 384928 i vi - i i i (AAGG)n#Simpl 99 GGAAGGAAGGAAGGAAGGAAGGAAGGAAGG-AAGGAAGGAAGGAAGGAAG 147 chrXqtel1M 384929 GAAGGAAGAAAGAAA 384943 i i (AAGG)n#Simpl 148 GAAGGAAGGAAGGAA 162 Matrix = Unknown Transitions / transversions = 9.00 (9/1) Gap_init rate = 0.02 (3 / 164), avg. gap size = 1.00 (3 / 3) 14 33.96 1.56 0.00 chrXqtel1M 386284 386347 (613653) (GAGGG)n#Simple_repeat 1 65 (0) m_b362s252i18 15197 chrXqtel1M 386284 GAAGGGAAAGAATGGG-GAGGAAGGCAGCCGGGGGGGGGGGGGGGAAGGG 386332 i ii i v - i i v vv i i i i (GAGGG)n#Simp 1 GAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGG 50 chrXqtel1M 386333 CAGAGGAGGGGATGG 386347 v i v (GAGGG)n#Simp 51 GAGGGGAGGGGAGGG 65 Matrix = Unknown Transitions / transversions = 1.83 (11/6) Gap_init rate = 0.02 (1 / 63), avg. gap size = 1.00 (1 / 1) 35 6.99 0.00 0.00 chrXqtel1M 386602 386647 (613353) (CCG)n#Simple_repeat 1 46 (0) c_b362s251i2 15198 chrXqtel1M 386602 CCGCCGCCGCCGCCGCCACCGCCGCTGCCGCCGCCGCCACCGCCGC 386647 i i i (CCG)n#Simple 1 CCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGC 46 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 63 6.73 0.00 0.00 chrXqtel1M 387282 387359 (612641) (CTC)n#Simple_repeat 1 78 (0) c_b362s251i3 15199 chrXqtel1M 387282 CTCCTCCTCCTCCTCCTCCTCTTCCTCCTCATCCTCCTCCTCCTCCTCGT 387331 i v v (CTC)n#Simple 1 CTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT 50 chrXqtel1M 387332 CCTCCTCTTCCTCCTCTTCCTCCTCCTC 387359 i i (CTC)n#Simple 51 CCTCCTCCTCCTCCTCCTCCTCCTCCTC 78 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 77), avg. gap size = 0.0 (0 / 0) 56 12.69 4.05 6.21 chrXqtel1M 388220 388367 (611633) (GAG)n#Simple_repeat 1 145 (0) m_b362s252i19 15200 chrXqtel1M 388220 GAGGA-GAGGA-GAGAGAGGAGGAAGGAAGGAGG-GAAGAAGCAGGGGGA 388266 - - - - - - i i v i (GAG)n#Simple 1 GAGGAGGAGGAGGAG-GAGGAGG-AGG-AGGAGGAGGAGGAGGAGGAGGA 47 chrXqtel1M 388267 GGAGGGAGGGAGGGAGGA-GAAGAGGAGGAGGAGGAGGACGCAGGAGGGA 388315 - - - - i - v - (GAG)n#Simple 48 GGA-GGA-GGA-GGAGGAGGAGGAGGAGGAGGAGGAGGA-GGAGGA-GGA 92 chrXqtel1M 388316 GCAGGGGGAGGAGGAGG-GGAGGAGAAAGGGGAGAAAGA-AAAGAGGCAG 388363 v i - i i i i i -i i - (GAG)n#Simple 93 GGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGG-AG 141 chrXqtel1M 388364 GAGG 388367 (GAG)n#Simple 142 GAGG 145 Matrix = Unknown Transitions / transversions = 4.00 (12/3) Gap_init rate = 0.10 (15 / 147), avg. gap size = 1.00 (15 / 15) 26 10.71 3.85 1.89 chrXqtel1M 389179 389230 (610770) (CCT)n#Simple_repeat 1 53 (0) m_b362s252i20 15201 chrXqtel1M 389179 CCACCT-CTCCTTCTTCCTCAT-CTCCTCCTCCTCCTCTTCCTCCTGCTC 389226 v - - i v - i v (CCT)n#Simple 1 CCTCCTCCTCC-TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC 49 chrXqtel1M 389227 CTCC 389230 (CCT)n#Simple 50 CTCC 53 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.00 (3 / 3) 376 16.08 7.95 1.06 chrXqtel1M 391409 391496 (608504) C MIRc#SINE/MIR (75) 193 100 m_b362s601i11 15202 chrXqtel1M 391409 TCCTCACAACAACCCTGTGAGGTAGGT-GGGC---TACCCGGAACCCGGA 391454 i- --- iivvv v -v C MIRc#SINE/MIR 193 TCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCC-CA 145 chrXqtel1M 391455 TTTTACAAACGCGGAGACTGAGGCTCACACAG---AAGTGACTTG 391496 i i v i v v --- C MIRc#SINE/MIR 144 TTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTG 100 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 18.14 CpG sites = 6, Kimura (unadjusted) = 18.14 Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.05 (4 / 87), avg. gap size = 2.00 (8 / 4) 19 17.90 0.00 7.41 chrXqtel1M 392315 392372 (607628) (GGGGA)n#Simple_repeat 1 54 (0) m_b362s252i21 15203 chrXqtel1M 392315 GGGGTGGGGAGGGGAGGTAAGGGGCGGGAAAGGTGAAGGGGAGTGGAGAG 392364 v vi v -i - i - - (GGGGA)n#Simp 1 GGGGAGGGGAGGGGAGGGGAGGGGAGGG-GAGG-GGAGGGGAG-GG-GAG 46 chrXqtel1M 392365 AGGTGGGG 392372 i v (GGGGA)n#Simp 47 GGGAGGGG 54 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.07 (4 / 57), avg. gap size = 1.00 (4 / 4) 110 22.53 1.77 1.41 chrXqtel1M 393232 393513 (606487) (CATC)n#Simple_repeat 1 283 (0) m_b362s252i22 15204 chrXqtel1M 393232 CAGCCAGCCATCTAT-GACCCATCTATCCATCCATCTATACCATCCATCC 393280 v v i -v i i i - (CATC)n#Simpl 1 CATCCATCCATCCATCCATCCATCCATCCATCCATCCAT-CCATCCATCC 49 chrXqtel1M 393281 ATCCATCTATCTATGGACCCATCC-TGCATTTGGACCATCCCAACCACCC 393329 i i vv i - v - iviv - v i (CATC)n#Simpl 50 ATCCATCCATCCATCCATCCATCCATCCA-TCCATCCAT-CCATCCATCC 97 chrXqtel1M 393330 ATCTATCCATCCATTCATCCATGCATCTATGGGCCCATTCAGCCAGCTAG 393379 i i v i vvii i v v i v (CATC)n#Simpl 98 ATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCAT 147 chrXqtel1M 393380 CCATCTATCCATCTATCCA-ACATCCATCCATACATCTATCCATGGACCC 393428 i i -v v i vv i (CATC)n#Simpl 148 CCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCC 197 chrXqtel1M 393429 ATCCATCCATCCATCCATCCATTGGTGGA-CCATCCATTCATCTGTCCAT 393477 ivi vv - i ii (CATC)n#Simpl 198 ATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCAT 247 chrXqtel1M 393478 CCA-CGGACCATCCCATCCATCCATCCATCTATCTAT 393513 - viv - i i (CATC)n#Simpl 248 CCATCCATCCAT-CCATCCATCCATCCATCCATCCAT 283 Matrix = Unknown Transitions / transversions = 1.21 (29/24) Gap_init rate = 0.03 (9 / 281), avg. gap size = 1.00 (9 / 9) 749 23.68 7.44 1.76 chrXqtel1M 394138 394352 (605648) C MIRb#SINE/MIR (23) 245 19 m_b362s601i12 15205 chrXqtel1M 394138 AGCACTTACTATGTATCGGGCACCGTGCTAAGAACTTTGAATAC----TT 394183 i ii i i vi iv i ---- i C MIRb#SINE/MIR 245 AGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTACATGCATTATC 196 chrXqtel1M 394184 TCTTTTGCTCCTCCCAACCACCCTGGGAGG-AGGTGCTATCACCCCCATT 394232 v iv v v v - ii i i C MIRb#SINE/MIR 195 TCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATTATCCCCATT 146 chrXqtel1M 394233 --------GAGGATACTG-GGCACATAGTTCAGTGTTCAGTGACTTTCCC 394273 -------- v - v v --- - v i v C MIRb#SINE/MIR 145 TTACAGATGAGGAAACTGAGGCTCAGAG---AG-GTTAAGTAACTTGCCC 100 chrXqtel1M 394274 AGAGTCACATAGCTAGGAGGTATCAGAGGCCAAATTTGAGCTCAGGGCT- 394322 ii i v i iv v vii i i i v - C MIRb#SINE/MIR 99 AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGTCTG 50 chrXqtel1M 394323 CCTGA-TCCCAGGCCCAGTCTCTAGCCACTG 394352 i - v i ivv vv C MIRb#SINE/MIR 49 TCTGACTCCAAAGCCCGTGCTCTTTCCACTG 19 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.29 CpG sites = 28, Kimura (unadjusted) = 28.92 Transitions / transversions = 1.27 (28/22) Gap_init rate = 0.05 (10 / 214), avg. gap size = 2.00 (20 / 10) 212 28.65 12.10 1.46 chrXqtel1M 394392 394515 (605485) C L2#LINE/L2 (151) 2931 2795 m_b362s601i13 15206 chrXqtel1M 394392 AATGGAGGATTA--TGGTAGAAGGCCTTAAATGCCAGCCCAAAGA-TTTG 394438 i i ii -- vi iv i iv v vivi i - C L2#LINE/L2 2931 AACGGGGGACCAGATCATGTAGGGCCTTGTAGGCCATTGTAAGGACTTTG 2882 chrXqtel1M 394439 TGTTTTATCCT-----AGAAGGGA-GCCACGGGAGATTTCTAAGTAGAGG 394482 vv ii ----- v - iv iv i i i C L2#LINE/L2 2881 GCTTTTACTCTGAGTGAGATGGGAAGCCATTGGAGGGTTTTGAGCAGAGG 2832 chrXqtel1M 394483 A-TGGTAAGATC-----TACGTTATTAAACGTTATCATT 394515 - ii v ----- - v -v i C L2#LINE/L2 2831 AGTGACATGATCTGACTTACGTT-TTAAAAG-GATCACT 2795 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.89 CpG sites = 21, Kimura (unadjusted) = 37.24 Transitions / transversions = 1.50 (21/14) Gap_init rate = 0.07 (8 / 123), avg. gap size = 2.12 (17 / 8) 51 29.08 2.88 1.90 chrXqtel1M 394613 394820 (605180) (ATCC)n#Simple_repeat 1 210 (0) m_b362s252i23 15207 chrXqtel1M 394613 ATCCAGCCATCCATTCATCTACTCATCCACTCAATACTTACCCATCCAGC 394662 v i i ii - v - -i i -i (ATCC)n#Simpl 1 ATCCATCCATCCATCCATCCATCCATCCA-TCCAT-C-CATCCATCCA-T 46 chrXqtel1M 394663 CCAT-AATCCATCTGCCTACCTAGCCAACCATTCATCAGTCCACCCACTG 394711 -v iii i i i v v i vi i iiv (ATCC)n#Simpl 47 CCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCC 96 chrXqtel1M 394712 AACCTTGCTTCCATCTCTCCTTCCTTCTAT-CTTCC-TAGAT-GAT-CAT 394757 v v v v iv v v i - v - vv -v - (ATCC)n#Simpl 97 ATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCAT 146 chrXqtel1M 394758 CCATCCATCCATCCATTGTTCC-TCCTTCCATCCACCTGGCCGACCATCC 394806 ivv - v i iiv iv (ATCC)n#Simpl 147 CCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCC 196 chrXqtel1M 394807 ATCCATCCATCCAT 394820 (ATCC)n#Simpl 197 ATCCATCCATCCAT 210 Matrix = Unknown Transitions / transversions = 1.09 (25/23) Gap_init rate = 0.05 (10 / 207), avg. gap size = 1.00 (10 / 10) 258 36.59 9.58 3.96 chrXqtel1M 394821 395227 (604773) C L2b_3end#LINE/L2 (35) 431 3 m_b362s601i14 15208 chrXqtel1M 394821 CTGTCCAACAAGCACCTTCCTACATGCCGAGAGCACAAAGACAAAGACCA 394870 viiv i ? iv v vii i i iii iv iii --- C L2b_3end#LINE 431 CTGTGTGCCAGGCNCTGTGCTAGGCGCTGGGGATACAGCGGTGAA---CA 385 chrXqtel1M 394871 AAACGGA----GCATCT-CCCCCGCACAACTTCCATTCTCCTAAAGGAAA 394915 i i ---- ivi - i i iv i iv v vv iii i C L2b_3end#LINE 384 AGACAGACNCGGTCCCTGCCCTCACGGAGCTCACAGTCTAGTGGGGGAGA 335 chrXqtel1M 394916 CA---ATG-GGCCA--CAAGCA--------AATGGATGAGTCAAAACGAG 394951 --- -ii? -- v? -------- i vv i vii vi i C L2b_3end#LINE 334 CAGACATGTAANCAGACAATNATAACCCAGAGTGGCAGGGTAGGACTGGG 285 chrXqtel1M 394952 ATGATTTGGAGGAGAA----AGACCTAGCAACTGGATGATCTTGGGAAGA 394997 iv iiiii ii----v ii -- iv i v- i i C L2b_3end#LINE 284 GGGGCCCAGAGGAGGGCGCCTGACCCGGC--CTGGGGGGTCA-GGGAGGG 238 chrXqtel1M 394998 CTTCCCAGAGGAGGTGGTGCCTGAGCTGAGCCTCGAAGGACTTG-AAGAA 395046 i iiiii v ii ivv - i i C L2b_3end#LINE 237 CTTCCCGGAGGAGGTGACATTTGAGCTGAGACCTGAAGGATGAGTAGGAG 188 chrXqtel1M 395047 TT--CCAAGAAACAGAGGTAAGGGCAGCAAAGAC-CCCCAGGCAATGGGG 395093 -- i vi - ii ----- i i -ii i-i C L2b_3end#LINE 187 TTGGCCAGGCGA-AGAGGTGGGG-----AAGGGCGTTCCAGGCAG-AGGG 145 chrXqtel1M 395094 GCCCACAGG-GCAA--------AGGCGGGAAATGGGATGCCAGGGCCGGG 395134 iv vi ? - -------- i?vi v? v iv vi i C L2b_3end#LINE 144 AACAGCANGTGCAAAGGCCCTGAGGCGGGAGNGAGCNTGGCGTGTTCGAG 95 chrXqtel1M 395135 AAACGGGAAGTGGCCGAGTTCGGTGCTAGTGGAGACAAGGCCAAGAG-GA 395183 i i v vi v v vi -- i v v vvii v i i - C L2b_3end#LINE 94 GAACAGCAAGGAGGCCAGTGTG--GCTGGAGCAGAGTGAGCAAGGGGAGA 47 chrXqtel1M 395184 ATGATA-AATATG-GTCTGGCGAGGCCATCTAGGGCCAGACCGGGC 395227 i i -i v - v i v ivi--ii i v C L2b_3end#LINE 46 GTGGTAGGAGATGAGGCCGGAGAGGTAG--CGGGGCCAGATCGTGC 3 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 50.86 CpG sites = 96, Kimura (unadjusted) = 55.71 Transitions / transversions = 2.04 (96/47) Gap_init rate = 0.08 (32 / 406), avg. gap size = 1.75 (56 / 32) 387 33.43 6.57 1.74 chrXqtel1M 394956 395229 (604771) C L2d2_3end#LINE/L2 (268) 287 1 m_b362s601i15 15208 chrXqtel1M 394956 TTTGGAGGAGAAAGA----CCTAGCAACTGGA-TGATCTTGGGAAGACTT 395000 ii ii ----v ?vvii - i v- i C L2d2_3end#LIN 287 TTCAGAGGAGGGAGAGATCACTNCGGGCTGGAGTGGTCA-GGGAAGGCTT 239 chrXqtel1M 395001 CCCAGAGGAGGTGGTGCCTGAGCTGAGCCTCGAAGGACTTGAAGAATTCC 395050 v i ?iii i i ivv v i iv C L2d2_3end#LIN 238 CACGGAGGAGGTGGNATTTGAGCTGGGCCTTGAAGGATGGGTAGGATTTG 189 chrXqtel1M 395051 AAGAAACAGAGGTAAGGGCAGCAAAGAC-CCCCAGGCAATGGGGGCCCAC 395099 i v iiii ivi i -- v i i -ii ii- iv vi C L2d2_3end#LIN 188 GATAGGTGGAGAGGAAGG--GGAAGGGCATTCCAGGCGG-GGGGAACGGC 142 chrXqtel1M 395100 A-GGGCAAAGGCG-GGAAATGGG-ATGC-CAGGGC-----CGGGAAACGG 395140 i- i -i iii - ? - i ----- ii i C L2d2_3end#LIN 141 GTGAGCAAAGGCGCAGAGGCGGGAANGCGCAAGGCGTGTTCGGGGGACAG 92 chrXqtel1M 395141 GAAGTGGCCGAGTTCGGTGCTAGTGGAGACAAGGCCAAGAGGAATGAT-- 395188 vi i v v i ivvv i ivvvv iv? i ii -- C L2d2_3end#LIN 91 TGAGTAGACCAGTTTGGCTGGAGCGGAGGGTTCGTGNAGGGGAATAGTGG 42 chrXqtel1M 395189 -AAATATGGTCTGGCGAGGCCATCTAGGGCCAGACCGGGCAG 395229 - i v - vi ?vivi i i v v C L2d2_3end#LIN 41 GAGATAAGG-CTGGAAAGGNAGGTTGGGGCCAGATCGTGGAG 1 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.48 CpG sites = 59, Kimura (unadjusted) = 48.24 Transitions / transversions = 1.90 (59/31) Gap_init rate = 0.05 (15 / 273), avg. gap size = 1.53 (23 / 15) 230 22.40 1.45 2.94 chrXqtel1M 396484 396552 (603448) C MIR1_Amn#SINE/MIR (80) 150 83 m_b362s601i16 15209 chrXqtel1M 396484 CCCACGTTACAGCTGAGGAAACTAAGGCA-AGACCGAGGCAGAGTGAGCG 396532 iv v i ?- -- i?i viv C MIR1_Amn#SINE 150 CCCATTTTACAGATGAGGAAACTGAGGCNCAGA--GAGGTNAAGTGACTT 103 chrXqtel1M 396533 GCTCAGAGCCACCCTGTCGG 396552 i ii i ? v i? C MIR1_Amn#SINE 102 GCCCAAGGTCACNCAGCNGG 83 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.60 CpG sites = 10, Kimura (unadjusted) = 29.60 Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.04 (3 / 68), avg. gap size = 1.00 (3 / 3) 18 33.89 3.81 1.87 chrXqtel1M 397518 397622 (602378) (GA)n#Simple_repeat 1 107 (0) m_b362s252i24 15210 chrXqtel1M 397518 GAGAGA-AGACAGAGAAATATGGGGGAGAGACAGAG-GGGATATGGAGGG 397565 - v i v - i i v - i v vi i (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAG 49 chrXqtel1M 397566 GGTGAAAGAAACCGAGAGGGAAGGAGACAGGGAGACGCG-GAGA-AGAAA 397613 i v i i vv i ii v i - v - - i (GA)n#Simple_ 50 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA-GAGAGAGAGAGAGA 98 chrXqtel1M 397614 AAAAGAAAG 397622 i i i (GA)n#Simple_ 99 GAGAGAGAG 107 Matrix = Unknown Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.06 (6 / 104), avg. gap size = 1.00 (6 / 6) 14 16.22 4.65 2.27 chrXqtel1M 398356 398398 (601602) (AGACAAG)n#Simple_repeat 1 44 (0) m_b362s252i25 15211 chrXqtel1M 398356 AGACCAGAGAAATGGACACAAGACACAA-AGAC-AGAGATAAGAG 398398 v v -i v v - - i (AGACAAG)n#Si 1 AGACAAGAGACA-AGAGACAAGAGACAAGAGACAAGAGACAAGAG 44 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.07 (3 / 42), avg. gap size = 1.00 (3 / 3) 197 32.64 2.13 5.49 chrXqtel1M 398577 398670 (601330) C Tigger19b#DNA/TcMar-Tigger (188) 362 272 m_b362s601i17 15212 chrXqtel1M 398577 AGGGCCTGGCCCAGGAGGAGCCTCCTGGG-AGCTGCTCCTCTACTTCCAG 398625 i i i i ---- - ii vvi v i - v C Tigger19b#DNA 362 AAGACCTGACTCAGGAGGAG----CTGGGAAGCTGTCCAGTTTCCT-CAT 318 chrXqtel1M 398626 CCTGTCTTTTCCTGAAC-CTGCCCCACTATTTACCCCAGGTTGGAA 398670 i ii v iv - iv ii ??iii i v i i C Tigger19b#DNA 317 CCTGCCTCCTGCCCAACTCCTCCCTGCNNCCCACTCCACGCTGGGA 272 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 47.83 CpG sites = 21, Kimura (unadjusted) = 47.83 Transitions / transversions = 2.62 (21/8) Gap_init rate = 0.08 (7 / 93), avg. gap size = 1.00 (7 / 7) 210 35.15 1.32 2.67 chrXqtel1M 398903 398978 (601022) C MIR3#SINE/MIR (22) 186 112 m_b362s601i18 15213 chrXqtel1M 398903 CGGAGCCAAGTGGGAGCTGAGAAATCATGTGACTTTCCTCTTTCCCATTC 398952 i iiiiv v v i v ii-- i vv iii i i C MIR3#SINE/MIR 186 CAGAGCTGGAAGGGACCTTAGAGATCATCTAG--TCCAACCCCCTCATTT 139 chrXqtel1M 398953 CACAGACAAG-AAACTGAGACCCTGGG 398978 i ii - i v i C MIR3#SINE/MIR 138 TACAGATGAGGAAACTGAGGCCCAGAG 112 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 52.08 CpG sites = 19, Kimura (unadjusted) = 52.08 Transitions / transversions = 2.71 (19/7) Gap_init rate = 0.04 (3 / 75), avg. gap size = 1.00 (3 / 3) 206 26.67 3.23 3.23 chrXqtel1M 399348 399409 (600591) MIR3#SINE/MIR 114 175 (33) m_b362s601i19 15214 chrXqtel1M 399348 CTGGGTCTCAGTTTCCTTCTCTGTACAAGAAACAGAAGCTGTCCTAGGT- 399396 i iv v vi --i ii i vv i - MIR3#SINE/MIR 114 CTGGGCCTCAGTTTCCTCATCTGTAAAATGA--GGGGGTTGGACTAGATG 161 chrXqtel1M 399397 -TCGCTCAAGTCCC 399409 - v v i MIR3#SINE/MIR 162 ATCTCTAAGGTCCC 175 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.59 CpG sites = 9, Kimura (unadjusted) = 33.59 Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.07 (4 / 61), avg. gap size = 1.00 (4 / 4) 13 12.12 0.00 3.57 chrXqtel1M 399654 399682 (600318) (TCCCT)n#Simple_repeat 1 28 (0) m_b362s252i26 15215 chrXqtel1M 399654 TCCCTTCCCATCCCTTCTCTCCCTCTTCC 399682 v i i - (TCCCT)n#Simp 1 TCCCTTCCCTTCCCTTCCCTTCC-CTTCC 28 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1) 441 26.65 12.31 3.79 chrXqtel1M 400325 400519 (599481) MIRc#SINE/MIR 32 242 (26) m_b362s601i20 15216 chrXqtel1M 400325 GGGCCTGGAATCAAGCAGGAAGACCCGAGGACATCTACAGCCTCGGGCAT 400374 i i i ---- i i vv ivv v v v v v i MIRc#SINE/MIR 32 GGACTTGGAGTCA----GGAAGACCTGGGTTCGAGTCCCGGCTCTGCCAC 77 chrXqtel1M 400375 TTCCTAGCCATGGAACCCAGGGCAAGTCACTTCCCTAGCCAC-CT--GCC 400421 v ii vi iv ---- i v - -- MIRc#SINE/MIR 78 TTACTAGCTGTGTGACCTTGGGCAAGTCACT----TAACCTCTCTGAGCC 123 chrXqtel1M 400422 TCAGTTTCCCCATCTGTAAAGAGCGGTTCATAACAACAGCCC------CC 400465 i iv v v v i v v ------ MIRc#SINE/MIR 124 TCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACC 173 chrXqtel1M 400466 TCACAGGGTCACTGAGAG--------------ATATTTGT-AACACACTT 400500 iii v -------------- i v - vi i MIRc#SINE/MIR 174 TCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTT 223 chrXqtel1M 400501 AGCAAAACTTAAAGCACTA 400519 v i viv ii MIRc#SINE/MIR 224 TGTAAACTGTAAAGTGCTA 242 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.83 CpG sites = 25, Kimura (unadjusted) = 33.41 Transitions / transversions = 1.00 (25/25) Gap_init rate = 0.07 (13 / 194), avg. gap size = 2.46 (32 / 13) 631 36.93 11.27 4.88 chrXqtel1M 400593 401577 (598423) C L3#LINE/CR1 (809) 3290 2246 m_b362s601i21 15217 chrXqtel1M 400593 TGCTGGGGGCCTTTTGGAGCCTGG--CTGTCATCTGCCATCCTCATTATT 400640 ii i iv ? i v i i-- ii? i vi vii i C L3#LINE/CR1 3290 TGTCGAGATCNTTTTGAATCTTGATTCTGTCATCCANCGTATTAGCTATC 3241 chrXqtel1M 400641 TCTCCCCGCTTGTCATTGCCCAAAAACCTAACAGGCAGACCCGGGCAGGC 400690 i v vvii iii iiv ii i i i vi i-vvi v i C L3#LINE/CR1 3240 CCTCCCAGCTTTGTGTCATCTGCAAATTTGATAAGCATGCCT-TCTATGT 3192 chrXqtel1M 400691 CTTCCCAGAAGTCGGATGCACAGAAACGTTCAGGCGGCGGCTCAGGGCCA 400740 vivv -- vv i i i v ----i i vv C L3#LINE/CR1 3191 CTTCATCCAAGTC--ATTGATAAAAATGTTGA----ACAGGACAGGGCCA 3148 chrXqtel1M 400741 GCCGTGGGTCCTTGCGGCCCTCTCCCAGAGCCCTCCTCCTTCAGATTAAG 400790 ivviii iv i i v v iv i v -- i i i v C L3#LINE/CR1 3147 AGGACAGAGCCCTGTGGCACGCCACTAGAGACCTC--CCTCCAGGTTGAC 3100 chrXqtel1M 400791 GT-GTTC------TCAGTGACTCTTTGGG---AGTCG-----CCATCCCC 400825 i - v ------ ii- ii --- ----- v iv C L3#LINE/CR1 3099 ATCGATCCATTAATCAAC-ACCTTTTGGGTATAGTCGTTCAACCAGCTAC 3051 chrXqtel1M 400826 GGAGCCATTCCAGAG-----CCACGTGGCCGACATCTCTCCATCCCATCC 400870 i v iiiv vv -----i ivii v i i iii C L3#LINE/CR1 3050 GAATCCACCTAACTGTACTATCATCCAGCCCATATTTCTCCATCTTGTCC 3001 chrXqtel1M 400871 CATCTCCGAGAAGGGGACGTGAGGTCCGAGCAAAGGCTCTGCTGAAATCC 400920 -----v i i vivv i v iiiiviv v ii C L3#LINE/CR1 3000 -----ACAAGGATATCATGAGAGACTTTGTCAAATGCCTTGCTGAAATCC 2956 chrXqtel1M 400921 AG--GCACCCTGTC--------TCCCATG-----CTAGTTAAGTGCCCTC 400955 --i i? -------- v ----- i iv iv ii C L3#LINE/CR1 2955 AGATACACTNTGTCTACGGCATTCCCCTGATCTACCAGTCTAGTAACCCT 2906 chrXqtel1M 400956 ATCCAAAGAGGGAACGGGCTCGGTCAGG-----CCCGCTCTCGAGGGAGG 401000 v i i i i v ii iv ----- ii i iiiv i vv C L3#LINE/CR1 2905 ATCAAAAAAGGAAATGAGGTTAGTTTGGCATGACTTGTTCTTAGTGAACC 2856 chrXqtel1M 401001 CTTTCGGACTTCCTGAAATCACCA--GCCCTTTCT--------------C 401034 v v v i i iv vi i--v i -------------- C L3#LINE/CR1 2855 CATGCTGGCTCCTAGTGATCACCGCTTCCTTTTCTAAGTGCTCACAAACC 2806 chrXqtel1M 401035 GACTGTC------TCCTCTTGGGAATTTGCCCGTGAATCCAAAATCAGAC 401078 iv i------ vi ivi vv v i - i vi ii C L3#LINE/CR1 2805 ATCTGTTTAATAATCCGTTCTAGAATTTTGCCGGGGAT-CGACGTCAAGC 2757 chrXqtel1M 401079 TTCCTAGCCCAT--TTGCCAGCAC---TCTCTCGTCCCTCTTGAAAAGT- 401122 v ii i ii -- v? v i--- i iv i v ? - C L3#LINE/CR1 2756 TTACCGGTCTGTAGTTTNCAGAATCCATCTTTTTTCCCTTTTTAAAANTA 2707 chrXqtel1M 401123 GGCAT----TCTACCATTCACCAGTCTCGCGGGCA-TGCTCCCATTTTCC 401167 ? i---- i i vv v i- v -iv i i i C L3#LINE/CR1 2706 GGNACNACATTTGCCCGTCTCCAGTCTT-CTGGCACCTCTTCCGTTCTCC 2658 chrXqtel1M 401168 ATGATCTTTCCAACGGTCCTCCACGGT-CCTCTGCAGCCCCACCTGCCTG 401216 i - ii v i ivi v i i-vi i iii v i vv C L3#LINE/CR1 2657 GTGAT-TTCTCAAAGATTACCGACAGCGGTTCCGCGATCACATCTGCAAG 2609 chrXqtel1M 401217 TTCTCTCAAGCTCCAAGGGAGACGGGAGGCTGTCCACCCCTTTTGGACCG 401266 i ivvi --------i --- -- vii v i i v C L3#LINE/CR1 2608 TTCTTTCAGTACCC--------TGGGA---TGT--AATTCGTCTGGGCCT 2572 chrXqtel1M 401267 GGTGACCTGAATTCACTTGGGGCAACCTGGGCCCCTCC--CTTCCTCCCC 401314 v i i i iii ii iv vv i i-- vi i C L3#LINE/CR1 2571 GGAGACTTGAACTCATTTAAAGCGGCTAGGTGCTCTCTTACTATCTCCTC 2522 chrXqtel1M 401315 AGC-ATC-TGAGCCGCATTT--CTCTT---GGGGCTCG----------TC 401347 v - - i iv v -- --- iv i i ---------- C L3#LINE/CR1 2521 ACCTATCTTGGGCTTCAATTCCCTCTTAACGATGTTTGTTCTACCCTTTC 2472 chrXqtel1M 401348 AGGGCCAAAGGTCGGTCATCGTCCTT---------GACGGAAGCCAGAGG 401388 vi v ii i iv ---- --------- v i vi C L3#LINE/CR1 2471 CAGTCTGAAGATCATTC----TCCTTGATAGAGAAGACGGAAGCAAAATA 2426 chrXqtel1M 401389 TGGCTCTGGCCGCCCCTCCCTGTCTCTGGTACCTGGGAATCATGGCCACA 401438 v iv ivi iv ii iv ii v vi i vv - vi vv C L3#LINE/CR1 2425 GGAGTTGAGTAGTTCTGCTTTCTCTCTGTCATCTGTTAA-CATTACGCCA 2377 chrXqtel1M 401439 TCCA-TCCAAACAGCAGTTGCATCTCTTCTTCCATTCTTGCCTTTCCCTC 401487 ii-i i i -- v v ?ii -- i v i i v ii C L3#LINE/CR1 2376 TCTGCCCCAAGCAGCGG--GCCTGTCNCTTTC--TTTTTCCTTCTGCTCC 2331 chrXqtel1M 401488 GAG---AGGTCGGCCACAAACCCTCACCTTTTTGTTGGCCTTGGC---TT 401531 i--- v iv -- v i i ---? v i --- C L3#LINE/CR1 2330 GAACATAGCTTTG--AAAAGCCTT---NTTTTTGTTGTCCTTAGCATTTT 2286 chrXqtel1M 401532 CCCCAGCCATTGTCGGCTCACTGTTCTTGACTTTTCTAGTCTTCTT 401577 iiiiv v viv i --- v i --- i i C L3#LINE/CR1 2285 TTTTTGCAAGCCTCAGCTCA---TTCTGGGCTT---TAGCCTTCCT 2246 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 51.89 CpG sites = 218, Kimura (unadjusted) = 55.05 Transitions / transversions = 1.70 (218/128) Gap_init rate = 0.08 (80 / 984), avg. gap size = 2.02 (162 / 80) 208 31.48 0.00 0.00 chrXqtel1M 401674 401727 (598273) L2b_3end#LINE/L2 200 253 (213) m_b362s601i22 15218 chrXqtel1M 401674 CTCCAAGTCTCAGGTAAAACCCCACTTTCTCCAAGGAGCTGTTCTTGATC 401723 i i v v ivi i i ii i iv i i i L2b_3end#LINE 200 CTTCAGGTCTCAGCTCAAATGTCACCTCCTCCGGGAAGCCCTCCCTGACC 249 chrXqtel1M 401724 CCCC 401727 L2b_3end#LINE 250 CCCC 253 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.94 CpG sites = 13, Kimura (unadjusted) = 44.56 Transitions / transversions = 3.25 (13/4) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 402 35.12 7.13 3.79 chrXqtel1M 401883 402317 (597683) C L3#LINE/CR1 (1834) 2265 1817 m_b362s601i23 15217 chrXqtel1M 401883 TTCTAAACTTTGGCTTTCCAGACCCCGAGTTTGCAGAACCTTGCCACGCT 401932 iii i i v v iivvi i iviiv ?i v C L3#LINE/CR1 2265 TTCTGGGCTTTAGCCTTCCTGACACTATTCTTACAGGCTTGTGNTACTCT 2216 chrXqtel1M 401933 TTGCTTGTCCTCCCTTTAGGTGGCCTGGCCTCCATCTTCTGCC-CAGGTC 401981 i vi ivv - vi v v-ii vi- v C L3#LINE/CR1 2215 CTCTTTGTCCTTGGTT-ATATGTCCTC-TTTCCATCTTCTGATACATGTC 2168 chrXqtel1M 401982 --TCTAAACTCC--CGGCTGAGGA-GCTCCCCGCA--CA-GCTG------ 402017 -- i v i-- iv v i -? ivi ? -- - i ------ C L3#LINE/CR1 2167 CTTTTAAAATCTGACATCAGAGAATNCTCTATGNAGCCACGTTGGTTTCT 2118 chrXqtel1M 402018 ----TGTCTCCTTCTTTTTCCATCTGACTGGTGGCCTCTTGTGGCT---- 402059 ---- i ii iiii ivi v i --ii vi iii ---- C L3#LINE/CR1 2117 TAAATGCCCTCCCTCTTTTCTTCCTCATTGG--ATCATTTGTAATTGTAG 2070 chrXqtel1M 402060 TCTGGATTTCCTTCTGGAGGCTGCGCCCCCCCCCCCCCGCCCCGGCTAAC 402109 v i v i vi i-- vi v? i ii ----i i v C L3#LINE/CR1 2069 TCAGAATTTCATTTTTAAGA--GCTTCCCANCCCTCTTG----AGCCATC 2026 chrXqtel1M 402110 TTGCTATTTTGCATTTTAAGTCCTTGGGATTCTACCCACCTCTTCTTTGA 402159 v - vi i i?i - v i iv i-- i i C L3#LINE/CR1 2025 TTTCT-TTTTGAGTCTCNGG-CCATGGAATCATACCT--CTTTTCTCTGA 1980 chrXqtel1M 402160 AGCCTTCAGAACCTGCTCT--CTC-CAAATCCTGGGTC-TACCTCAGACC 402205 vii iii i i -- -i vi iv - iv -i i C L3#LINE/CR1 1979 ATTTTTTGAAATCTGCTTTTCCTCGTAAAGTCTGGAACATATGT-GGACT 1931 chrXqtel1M 402206 CC--ATGTTTCCTGTACTTCTCTAGCATGCACTCTAGGGGGCAACGGGCA 402253 ii-- iv v - vv vi i v i iv vv i - C L3#LINE/CR1 1930 TTTAACTTTTCCTTT-CTTGGCTATTACGAACTCTAAGATGACATGG-CA 1883 chrXqtel1M 402254 CTTCCCCTCTGGGTTCCCACC-ATTCCCTTCCCAGGAACCAGTTCTTTCT 402302 i i i vi i i - i i viii vv i C L3#LINE/CR1 1882 CTTTCTCCCAAGGTTCCTATCGACTTCCACTTCACCAACCAGTTCTTCCT 1833 chrXqtel1M 402303 T-TGGGTGAGAATCAA 402317 - v v i C L3#LINE/CR1 1832 TGTTGGTCAGAATTAA 1817 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 50.95 CpG sites = 96, Kimura (unadjusted) = 51.47 Transitions / transversions = 1.88 (96/51) Gap_init rate = 0.07 (30 / 434), avg. gap size = 1.60 (48 / 30) 17 10.76 7.50 0.00 chrXqtel1M 402741 402780 (597220) (TGTCTC)n#Simple_repeat 1 43 (0) m_b362s252i27 15219 chrXqtel1M 402741 TGTCTCT-CATCTCTCTCTGTCTCTGTCTC--TCCCTGTCTCT 402780 -iv v -- i (TGTCTC)n#Sim 1 TGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCT 43 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.50 (3 / 2) 15 24.05 0.00 4.26 chrXqtel1M 402750 402798 (597202) (TCCC)n#Simple_repeat 1 47 (0) m_b362s252i28 15219 chrXqtel1M 402750 TCTCTCTCTGTCTCTGTCTCTCCCTGTCTCTCCCTTCCTCCCTCCCTCC 402798 i i vi iv i -- i i (TCCC)n#Simpl 1 TCCCTCCCTCCCTCCCTCCCTCCC--TCCCTCCCTCCCTCCCTCCCTCC 47 Matrix = Unknown Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.04 (2 / 48), avg. gap size = 1.00 (2 / 2) 13 11.56 3.57 0.00 chrXqtel1M 403664 403691 (596309) (CTCC)n#Simple_repeat 1 29 (0) m_b362s252i29 15220 chrXqtel1M 403664 CTCCCTCCCTCCCT-CCTCCCCCAATCCC 403691 - i vv (CTCC)n#Simpl 1 CTCCCTCCCTCCCTCCCTCCCTCCCTCCC 29 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 231 26.56 8.00 5.88 chrXqtel1M 403781 403880 (596120) C MIRc#SINE/MIR (118) 150 49 m_b362s601i24 15221 chrXqtel1M 403781 TCCTGGTCTTAAAGCCAGAGGAACTTAAGGCTGAGAAGGG------GACT 403824 ivi i v vi- vi i v ii ------ C MIRc#SINE/MIR 150 TCCCCATTTTACAGAT-GAGGAAACTGAGGCTCAGAGAGGTTAAGTGACT 102 chrXqtel1M 403825 TGCCTAAGGTCACACGACAAGGAG--GGCAGAACTGGAGGTCCGAGGCCA 403872 i ii v v i-- i i - iii ---- C MIRc#SINE/MIR 101 TGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGG-GACTCGA----A 57 chrXqtel1M 403873 CCGAGGTC 403880 v C MIRc#SINE/MIR 56 CCCAGGTC 49 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.57 CpG sites = 17, Kimura (unadjusted) = 34.27 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.08 (8 / 99), avg. gap size = 1.75 (14 / 8) 385 36.21 3.50 1.97 chrXqtel1M 405657 405856 (594144) C MIRc#SINE/MIR (6) 262 60 m_b362s601i25 15222 chrXqtel1M 405657 AATAAGCCCTT-CAATCACTTACCGTTTGCCAGGCCCTGTGCTAAGTG-T 405704 v? - v iiiv v ii vv ---- v i v i - C MIRc#SINE/MIR 262 AATAACNCCTTACATTTGTATAGCACTTTACAG----TTTACAAAGCGCT 217 chrXqtel1M 405705 TTCACAAATGCTACCTCACCGGGTCCTCCCCACACCCCTGGGCGATTGCT 405754 v iii i iiv i v v v v v i v vi C MIRc#SINE/MIR 216 TTCACATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGC 167 chrXqtel1M 405755 CG--CTACTAGGATCGGCCCCATTTTACAGCTGAGGAAAGCAAGGTGGGC 405802 v -- viv vv iiv v vii ivviv C MIRc#SINE/MIR 166 AGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAG 117 chrXqtel1M 405803 AGAGGT---GTGACTCGCTTGGGATCTCACAGTGGGTCCGGTTTAAACTC 405849 --- i iiii i v ivi vv vvvi i vi C MIRc#SINE/MIR 116 AGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCC 67 chrXqtel1M 405850 GGGGCTC 405856 i C MIRc#SINE/MIR 66 GGGACTC 60 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 49.74 CpG sites = 35, Kimura (unadjusted) = 50.74 Transitions / transversions = 0.97 (35/36) Gap_init rate = 0.04 (8 / 199), avg. gap size = 1.38 (11 / 8) 495 32.92 1.82 2.44 chrXqtel1M 405672 405836 (594164) C MIR#SINE/MIR (23) 239 76 m_b362s601i26 15222 chrXqtel1M 405672 CACTTACCGTTTGCCAGGCCCTGTGCTAAGTGTTTCACAAATGCTACCTC 405721 i ii v v v i i i vi ii v C MIR#SINE/MIR 239 CGCTTACTATGTGCCAGGCACTGTTCTAAGCGCTTTACATGTATTAACTC 190 chrXqtel1M 405722 ACCGGGTCCTCCCCACACCCCTGGGCGATTGCTCGCTACTAGGATCGGCC 405771 iivii v v v iv v i---- v v vv iiv C MIR#SINE/MIR 189 ATTTAATCCTCACAACAACCCTATGAGG----TAGGTACTATTATTATCC 144 chrXqtel1M 405772 CCATTTTACAGCTGAGGAAAGCAAGGTGGGCAGAGGT---GTGACTCGCT 405818 v vii iiviv --- i i i C MIR#SINE/MIR 143 CCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCC 94 chrXqtel1M 405819 TGGGATCTCACAGTGGGT 405836 iii i v ivi C MIR#SINE/MIR 93 CAAGGTCACACAGCTAGT 76 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.58 CpG sites = 31, Kimura (unadjusted) = 44.86 Transitions / transversions = 1.41 (31/22) Gap_init rate = 0.03 (5 / 164), avg. gap size = 1.40 (7 / 5) 251 32.78 6.11 2.21 chrXqtel1M 405770 405900 (594100) C MIR3#SINE/MIR (62) 146 11 m_b362s601i27 15222 chrXqtel1M 405770 CCCCATTTTACAGCTGAGGAAAGCAAGGTGGGCAGAGGT---GTGACTCG 405816 i v vii ivviv --- i C MIR3#SINE/MIR 146 CCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTG 97 chrXqtel1M 405817 CTTGGGATCTCACAGTGGGTCCGGTTTAAACTCGGGGCT----CCCTGAG 405862 iiii i v i?i iv vvvi i vi i ---- -- C MIR3#SINE/MIR 96 CCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCC--AG 49 chrXqtel1M 405863 GGCT-CTGTGCCCCATGATATCCCCTCGCTGCTTTAGCC 405900 v - vvi vvvii v i v - i C MIR3#SINE/MIR 48 GTCTCCTGACTCCCAGTCCGTGCTCTCTCTGC-TCAGCC 11 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.15 CpG sites = 23, Kimura (unadjusted) = 44.74 Transitions / transversions = 1.21 (23/19) Gap_init rate = 0.05 (6 / 130), avg. gap size = 1.83 (11 / 6) 14 15.99 8.82 4.23 chrXqtel1M 406040 406107 (593893) (TCCGGCCA)n#Simple_repeat 1 71 (0) m_b362s252i30 15223 chrXqtel1M 406040 TCCGGCCATCCTG-CAGCCGGCCA-CC--CCGCCCGGGAATCCGGTCGCA 406085 v - v - -- ii vv - - (TCCGGCCA)n#S 1 TCCGGCCATCCGGCCATCCGGCCATCCGGCCATCCGGCCATCCGG-C-CA 48 chrXqtel1M 406086 TCTCCTCCA-CTGGCCA-CCGGCC 406107 - vv - i - (TCCGGCCA)n#S 49 TC-CGGCCATCCGGCCATCCGGCC 71 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.12 (8 / 67), avg. gap size = 1.12 (9 / 8) 311 33.37 0.00 3.70 chrXqtel1M 406517 406628 (593372) MIR3#SINE/MIR 87 194 (14) m_b362s601i28 15224 chrXqtel1M 406517 TGCCCTTGGCCATGGCACTCTCCCTCTTGGGCTCCCACCTTCACCATCTG 406566 v v v v iiv iv vi i vi vi MIR3#SINE/MIR 87 TGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTG 136 chrXqtel1M 406567 TCAGACGAAGGTGTCGAGGCGGTGAGATGTTTGCTAAGGCTTTTTCCGGC 406616 v i i i v i ---- iiv v iv iiii i MIR3#SINE/MIR 137 TAAAATGAGGGGGTTG----GACTAGATGATCTCTAAGGTCCCTTCCAGC 182 chrXqtel1M 406617 CCTGACGCTCTA 406628 i ii MIR3#SINE/MIR 183 TCTGACATTCTA 194 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.01 CpG sites = 22, Kimura (unadjusted) = 46.01 Transitions / transversions = 1.57 (22/14) Gap_init rate = 0.04 (4 / 111), avg. gap size = 1.00 (4 / 4) 51 0.00 0.00 0.00 chrXqtel1M 407270 407313 (592687) (CA)n#Simple_repeat 1 44 (0) c_b362s251i4 15225 chrXqtel1M 407270 CACACACACACACACACACACACACACACACACACACACACACA 407313 (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACA 44 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 292 31.06 2.88 0.94 chrXqtel1M 407366 407469 (592531) C MIR3#SINE/MIR (17) 191 86 m_b362s601i29 15226 chrXqtel1M 407366 AAAGCCGAAACTGGA--GGAGCTTGCAGTTCTGTCCAATTCCTCCCCC-C 407412 v i ii i -- v iv v -i i i i vv - C MIR3#SINE/MIR 191 AATGTCAGAGCTGGAAGGGACCTTAGAGATC-ATCTAGTCCAACCCCCTC 143 chrXqtel1M 407413 ATTTTGCAGATGAAGAAGCAAAGGGGCAAAAAGGGAAAGGAGCTGGCCCG 407462 i i i vi vv i i vi vii v i C MIR3#SINE/MIR 142 ATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCA 93 chrXqtel1M 407463 AGCTCAC 407469 v C MIR3#SINE/MIR 92 AGGTCAC 86 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.45 CpG sites = 19, Kimura (unadjusted) = 41.45 Transitions / transversions = 1.46 (19/13) Gap_init rate = 0.03 (3 / 103), avg. gap size = 1.33 (4 / 3) 229 35.11 5.32 0.00 chrXqtel1M 409415 409508 (590492) C MIR3#SINE/MIR (25) 183 85 m_b363s601i1 15227 chrXqtel1M 409415 AACTGAAAGGGACCCGGGAGCTC--CCGCTCCGATCTCCTC-CTCCATTA 409461 i i ivi v -- iiv i i i -i ii ivi C MIR3#SINE/MIR 183 AGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAG 134 chrXqtel1M 409462 ATG--GAAACTGAGTCTCAAAATGGGAAACCGGCTTGTCAAAGCCCGCA 409508 -- v i i iv vi vi i i v vi i C MIR3#SINE/MIR 133 ATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACA 85 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 51.27 CpG sites = 23, Kimura (unadjusted) = 51.27 Transitions / transversions = 2.30 (23/10) Gap_init rate = 0.03 (3 / 93), avg. gap size = 1.67 (5 / 3) 63 25.55 1.22 0.00 chrXqtel1M 409890 410053 (589947) (CGG)n#Simple_repeat 1 166 (0) m_b363s252i0 15228 chrXqtel1M 409890 CGG-GGCGGCTGCGGGGGCTGCGGCTGCGGCGGTACTTGGGGGGGCTGCT 409938 - v v v v iiviv v v v v (CGG)n#Simple 1 CGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCG 50 chrXqtel1M 409939 GCGGCGCCTGGGGGGGCTGCTGCTGCTGCTGCTGCTGCGGCGGCGGCGGC 409988 v v v v v v v v v v v (CGG)n#Simple 51 GCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC 100 chrXqtel1M 409989 GGC-GCGGCGGCGGCGGAGGCTGCTGCGGCGGCGCCTGGGGGGGCTGCGG 410037 - v v v v v v v v (CGG)n#Simple 101 GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGG 150 chrXqtel1M 410038 CGGCGGGGGAGGCTGC 410053 v v v (CGG)n#Simple 151 CGGCGGCGGCGGCGGC 166 Matrix = Unknown Transitions / transversions = 0.09 (3/32) Gap_init rate = 0.01 (2 / 163), avg. gap size = 1.00 (2 / 2) 15 21.94 1.92 3.92 chrXqtel1M 410255 410306 (589694) (GGCCGC)n#Simple_repeat 1 51 (0) m_b363s252i2 15229 chrXqtel1M 410255 GGCAGCGGCGGCGGCGGCGTCCG-GTGCGAGTGCCCCGGCCGGGGCTCGC 410303 v v v v - vv v - v v - (GGCCGC)n#Sim 1 GGCCGCGGCCGCGGCCGCGGCCGCGGCCGCG-GCCGCGGCCGCGGC-CGC 48 chrXqtel1M 410304 GGC 410306 (GGCCGC)n#Sim 49 GGC 51 Matrix = Unknown Transitions / transversions = 0.00 (0/9) Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.00 (3 / 3) 27 20.78 1.47 1.47 chrXqtel1M 410645 410712 (589288) (CCT)n#Simple_repeat 1 68 (0) m_b363s252i3 15230 chrXqtel1M 410645 CCTCCTCCTCCTCCTCTTCGTCGTCGTTCTCCTCCTCCGCCGCCGCCGCC 410694 i v v v i v v v v (CCT)n#Simple 1 CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC 50 chrXqtel1M 410695 T-CTCTGTCCTCCCCCCCC 410712 - -v i i (CCT)n#Simple 51 TCCTC-CTCCTCCTCCTCC 68 Matrix = Unknown Transitions / transversions = 0.50 (4/8) Gap_init rate = 0.03 (2 / 67), avg. gap size = 1.00 (2 / 2) 21 24.29 2.74 2.74 chrXqtel1M 410817 410889 (589111) (GGAG)n#Simple_repeat 1 73 (0) m_b363s252i4 15231 chrXqtel1M 410817 GGGGGGGGGGGGGTAGATAATGCGGGAGGGA-GGAGGAAGAGGAAGAAGA 410865 i i i v iv iv v - i - i i - (GGAG)n#Simpl 1 GGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAG-GGAGGGAG- 48 chrXqtel1M 410866 GGA-GGAGGGGGGGAGGGAAGGAGG 410889 - i i (GGAG)n#Simpl 49 GGAGGGAGGGAGGGAGGGAGGGAGG 73 Matrix = Unknown Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.06 (4 / 72), avg. gap size = 1.00 (4 / 4) 24 11.64 4.00 1.96 chrXqtel1M 410841 410890 (589110) (GGA)n#Simple_repeat 1 51 (0) m_b363s252i5 15231 chrXqtel1M 410841 GGAGGGAGGAGGAAGAGGAAGAAGAGGAGGAGG-GGGGGAGG-GAAGGAG 410888 - i i i - i - i (GGA)n#Simple 1 GGA-GGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG 49 chrXqtel1M 410889 GA 410890 (GGA)n#Simple 50 GA 51 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.06 (3 / 49), avg. gap size = 1.00 (3 / 3) 78 1.17 0.00 5.49 chrXqtel1M 410925 411020 (588980) (GGCTCC)n#Simple_repeat 1 91 (0) c_b363s251i1 15232 chrXqtel1M 410925 GGCTCCGGCTCCGGGCTCCCGGCTGCCGGCTCCGGCTGCCGGCTCCGGCT 410974 - - - - (GGCTCC)n#Sim 1 GGCTCCGGCTCC-GGCT-CCGGCT-CCGGCTCCGGCT-CCGGCTCCGGCT 46 chrXqtel1M 410975 CCCGGCTCCGGCTCCGGCTCCGGCTCCGGCTCGGGCTCCGGCTCCG 411020 - v (GGCTCC)n#Sim 47 -CCGGCTCCGGCTCCGGCTCCGGCTCCGGCTCCGGCTCCGGCTCCG 91 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.05 (5 / 95), avg. gap size = 1.00 (5 / 5) 11 30.68 2.04 0.00 chrXqtel1M 411979 412027 (587973) (GGGGAG)n#Simple_repeat 1 50 (0) m_b363s252i6 15233 chrXqtel1M 411979 GGGAAGGGGAAAGAGGCAGTGGA-AGGGAGGGGCGGGGGGAGGGTAAGGG 412027 i i i i vi v -i vi vi (GGGGAG)n#Sim 1 GGGGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGGAGGG 50 Matrix = Unknown Transitions / transversions = 2.00 (8/4) Gap_init rate = 0.02 (1 / 48), avg. gap size = 1.00 (1 / 1) 474 33.94 0.42 3.03 chrXqtel1M 414678 414914 (585086) L2#LINE/L2 1830 2060 (1022) m_b363s601i2 15234 chrXqtel1M 414678 ACTGTCCCCACCCCCTACCTCAACTTTAGTTTCCTCCTTTCT-CAGCCTA 414726 ?vi v vv v vv v vv i v ii i - vv L2#LINE/L2 1830 ACNTCCCCCTCCAGCTACCGCCCCATTTCTCTGCTCCCCTTTACAGCAAA 1879 chrXqtel1M 414727 ACTCCTAGAAAAAGCTGTCTACACTTGGTGCCTCCACTTTTTCACCTCCC 414776 v i i i i v i v ii v L2#LINE/L2 1880 ACTCCTCGAAAGAGTTGTCTATACTCGCTGTCTCCAATTCCTCTCCTCCC 1929 chrXqtel1M 414777 ACTCACTTCTCAACCCCTCACAATCTGGCTAATTCCGACCTCATCACTCA 414826 i v ii v viiv v --- i v i i v L2#LINE/L2 1930 ATTCTCTCTTGAACCCACTCCAATCAGGC---TTTCGTCCCCACCACTCC 1976 chrXqtel1M 414827 ACTGAAATGGATCTCTCCAAGGTTATGAATGATCTCTTCTGAACAGCTAA 414876 i iv v ivi i iv i iv ---iiv L2#LINE/L2 1977 ACCGAAACTGCTCTTGTCAAGGTCACCAATGACCTCCAC---GTTGCTAA 2023 chrXqtel1M 414877 CCCTGGTAGCCTTTTTCTCAGCTATCACCCTGTCAGAC 414914 vi iii i i -vv iiv i i iiiv L2#LINE/L2 2024 ATCCAATGGTC-AATTCTCAGTCCTCATCTTACTTGAC 2060 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.26 CpG sites = 43, Kimura (unadjusted) = 46.70 Transitions / transversions = 1.23 (43/35) Gap_init rate = 0.03 (8 / 236), avg. gap size = 1.00 (8 / 8) 275 23.17 10.38 6.36 chrXqtel1M 414900 415005 (584995) MIR#SINE/MIR 107 216 (46) m_b363s601i3 15235 chrXqtel1M 414900 ATCACCCTGTCAGACTCAGTTTCCTCATCTATA------GTATAATAGTA 414943 i v i -- v i ------ v i MIR#SINE/MIR 107 ACCTCTCTGT--GCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATA 154 chrXqtel1M 414944 GTA---ACCTCCAGGGGTTACTGTGGGGGTATATCAAGAAAGCCAATGC- 414989 --- vvi ii i ---- i ivi ii i - MIR#SINE/MIR 155 GTACCTACCTCATAGGGTTGTTGTGAGG----ATTAAATGAGTTAATACA 200 chrXqtel1M 414990 -GTGAAGCCCTGTGGAA 415005 - i v - i MIR#SINE/MIR 201 TGTAAAGCGCT-TAGAA 216 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.85 CpG sites = 16, Kimura (unadjusted) = 28.85 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.10 (11 / 105), avg. gap size = 1.64 (18 / 11) 212 28.33 1.67 0.00 chrXqtel1M 415257 415316 (584684) L2#LINE/L2 2425 2485 (597) m_b363s601i4 15234 chrXqtel1M 415257 CTGCTGGACATCTCAA-CATGACATTTCCAAAAGAGAATTCGTGATTTTC 415305 iv i i - v i v vv i v i L2#LINE/L2 2425 CTAATAGGCATCTCAAACTTAACATGTCCAAAACTGAACTCCTGATCTTC 2474 chrXqtel1M 415306 ACCCCTAGATC 415316 v ii i i L2#LINE/L2 2475 CCCCTCAAACC 2485 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.53 CpG sites = 10, Kimura (unadjusted) = 36.53 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.02 (1 / 59), avg. gap size = 1.00 (1 / 1) 234 25.63 5.00 2.44 chrXqtel1M 415882 415961 (584039) MIR#SINE/MIR 102 183 (79) m_b363s601i5 15236 chrXqtel1M 415882 ACTTCAGCCTCTGCCT-CCTCAGTCTCCTCAACTCCGAGAT---AATAAG 415927 - i viv - i v vii i ---i v MIR#SINE/MIR 102 ACTT-AACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAAT 150 chrXqtel1M 415928 AACAGCAGCGACTTCCAAGTGGTTGTCGTGAGGA 415961 i i v v i vv - i MIR#SINE/MIR 151 AATAGTACCTACCTCATAG-GGTTGTTGTGAGGA 183 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.89 CpG sites = 11, Kimura (unadjusted) = 31.89 Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.05 (4 / 79), avg. gap size = 1.50 (6 / 4) 207 34.81 2.08 4.26 chrXqtel1M 415898 415993 (584007) MIRb#SINE/MIR 125 218 (50) m_b363s601i6 15236 chrXqtel1M 415898 CCTCAGTCTCCTCAACTCCGAGATAATAAGAACAGCAGCGACTTCCAAGT 415947 i v vii i iivi v i ii v v i vv - MIRb#SINE/MIR 125 CCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTACCTCGCAG- 173 chrXqtel1M 415948 GGTTGTCGTGAGGACCCAGGGATGGGACATCGCTAG--AAGTGTTCAG 415993 i iiv --- i i vi vv -- i i i MIRb#SINE/MIR 174 GGTTGTTGTGAGGATTAA---ATGAGATAATGCATGTAAAGCGCTTAG 218 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 47.00 CpG sites = 20, Kimura (unadjusted) = 49.20 Transitions / transversions = 1.67 (20/12) Gap_init rate = 0.05 (5 / 95), avg. gap size = 1.20 (6 / 5) 18 0.00 0.00 0.00 chrXqtel1M 416445 416464 (583536) (AC)n#Simple_repeat 1 20 (0) m_b363s252i7 15237 chrXqtel1M 416445 ACACACACACACACACACAC 416464 (AC)n#Simple_ 1 ACACACACACACACACACAC 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 13 8.48 4.00 0.00 chrXqtel1M 417021 417045 (582955) (CCTG)n#Simple_repeat 1 26 (0) m_b363s252i8 15238 chrXqtel1M 417021 CCTGCCTGCC-GCCCGCCAGCCTGCC 417045 - i v (CCTG)n#Simpl 1 CCTGCCTGCCTGCCTGCCTGCCTGCC 26 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 238 33.55 10.08 7.58 chrXqtel1M 418949 419077 (580923) MIRb#SINE/MIR 94 225 (43) m_b363s601i7 15239 chrXqtel1M 418949 GATCGTGGGCAACCCATCTCACTTCCATTTTATGCCTCAGTGGCCCGAGC 418998 i v vii ii v i --- i iv vv iv v MIRb#SINE/MIR 94 GACCTTGGGCAAGTTACTTAACCTC---TCTGAGCCTCAGTTTCCTCATC 140 chrXqtel1M 418999 TATTAACACGAGGGTCGGAGTGACAACGCCCACTCCCCAGAGTCATCATG 419048 i v -------i v ii i i ii i ii v i ii ii MIRb#SINE/MIR 141 TGTAAA-------ATGGGGATAATAATACCTACCTCGCAGGGTTGTTGTG 183 chrXqtel1M 419049 AGGATCGAATGG------------AAAGCACTTAGC-CAGTG 419077 ii i------------ i - MIRb#SINE/MIR 184 AGGATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAGTG 225 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.70 CpG sites = 29, Kimura (unadjusted) = 48.47 Transitions / transversions = 2.64 (29/11) Gap_init rate = 0.09 (12 / 128), avg. gap size = 1.92 (23 / 12) 257 37.68 0.00 6.73 chrXqtel1M 418949 419059 (580941) MIR#SINE/MIR 87 190 (72) m_b363s601i8 15239 chrXqtel1M 418949 GATCGTGGGCAACCCATCTCACTTCCATTTTATGCCTCAGTGGCCCGAGC 418998 i v vii ii v i --- i i vv iv v MIR#SINE/MIR 87 GACCTTGGGCAAGTTACTTAACCTC---TCTGTGCCTCAGTTTCCTCATC 133 chrXqtel1M 418999 TATTAACACGAGGGTCGGAGTGACAACGCCCACTCCCCAGAGTCATCATG 419048 i - v i i i --- i i i iii i ii vi i ii ii MIR#SINE/MIR 134 TGT-AAAATGGGGAT---AATAATAGTACCTACCTCATAGGGTTGTTGTG 179 chrXqtel1M 419049 AGGATCGAATG 419059 ii MIR#SINE/MIR 180 AGGATTAAATG 190 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 59.20 CpG sites = 30, Kimura (unadjusted) = 59.20 Transitions / transversions = 3.33 (30/9) Gap_init rate = 0.06 (7 / 110), avg. gap size = 1.00 (7 / 7) 207 28.07 3.51 0.00 chrXqtel1M 419798 419854 (580146) C MIR3#SINE/MIR (39) 169 111 m_b363s601i9 15240 chrXqtel1M 419798 TTAGCCATTACTTTGTTCAACCACTCCCTTTTAGAAAGAAGGAAAC--AG 419845 vv i ii v i v ii v v i vi -- C MIR3#SINE/MIR 169 TTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAG 120 chrXqtel1M 419846 GCCCGGAGA 419854 i C MIR3#SINE/MIR 119 GCCCAGAGA 111 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.91 CpG sites = 9, Kimura (unadjusted) = 35.91 Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.02 (1 / 56), avg. gap size = 2.00 (2 / 1) 16 13.24 0.00 0.00 chrXqtel1M 420435 420459 (579541) (C)n#Simple_repeat 1 25 (0) m_b363s252i9 15241 chrXqtel1M 420435 CCCCTCCCTCCCCCCCCCCCACCCC 420459 i i v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCC 25 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 206 40.13 2.65 2.65 chrXqtel1M 421635 421785 (578215) C MIR3#SINE/MIR (10) 198 48 m_b363s601i10 15242 chrXqtel1M 421635 ACCATGGGAGGTTAGACTTAAAGACAAAGACTTCCGAGGGCCATCGAGTC 421684 i i i v i vi ii --- ii i iv i-i v C MIR3#SINE/MIR 198 ATCATAGAATGTCAGAGCTGGA---AGGGACCTTAGAGA-TCATCTAGTC 153 chrXqtel1M 421685 CCAAC---TTACTGGGTAGGGGAGGGCATTGAGAGCTAGAGAGG-ACAGT 421730 v v --- i i vvii iv iv i iv i -iv C MIR3#SINE/MIR 152 CAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGT 103 chrXqtel1M 421731 GACTAGGCCAGCATGGCAAAAGCAGTCAAAGCTCTAGTCAGGATGGGATC 421780 v v ivi vi v iv? i iv vivv i i ivi v C MIR3#SINE/MIR 102 GACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAAC 53 chrXqtel1M 421781 CCAAG 421785 i C MIR3#SINE/MIR 52 CCAGG 48 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 59.88 CpG sites = 35, Kimura (unadjusted) = 61.58 Transitions / transversions = 1.46 (35/24) Gap_init rate = 0.04 (6 / 150), avg. gap size = 1.33 (8 / 6) 181 30.65 3.23 0.00 chrXqtel1M 421774 421835 (578165) MIR1_Amn#SINE/MIR 12 75 (155) m_b363s601i11 15243 chrXqtel1M 421774 TGGGATCCCAAGGCCAGAGCGCTGGACTGGGAGGTAGGAG--CCGGATCA 421821 v i iviv vi i vvii -- i i iv MIR1_Amn#SINE 12 TGTGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGAGACCTGGGTTC 61 chrXqtel1M 421822 CAGTCCCAACTCTG 421835 ? ? ii MIR1_Amn#SINE 62 NANTCCCGGCTCTG 75 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.84 CpG sites = 12, Kimura (unadjusted) = 43.00 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.02 (1 / 61), avg. gap size = 2.00 (2 / 1) 188 30.36 5.36 0.00 chrXqtel1M 421789 421844 (578156) MIRc#SINE/MIR 24 82 (186) m_b363s601i12 15243 chrXqtel1M 421789 AGAGCGCTGGACTGGGAGGTAGGAG---CCGGATCACAGTCCCAACTCTG 421835 i v vi i--- i i ivv ii MIRc#SINE/MIR 24 AGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTG 73 chrXqtel1M 421836 TTCCCTTCT 421844 iiv i v MIRc#SINE/MIR 74 CCACTTACT 82 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.57 CpG sites = 11, Kimura (unadjusted) = 40.69 Transitions / transversions = 1.83 (11/6) Gap_init rate = 0.02 (1 / 55), avg. gap size = 3.00 (3 / 1) 226 30.55 12.41 5.16 chrXqtel1M 422890 423034 (576966) C MIR3#SINE/MIR (47) 161 7 m_b363s601i13 15244 chrXqtel1M 422890 CATCTAACTCATTTCCCTTATTTTATAGAGCTGGAAACTGAGGCT----- 422934 iii vii i i vvv i----- C MIR3#SINE/MIR 161 CATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAG 112 chrXqtel1M 422935 AGAT----TGAGTTGGCTCATGTCCCATTGGAAG-GGGAGGCGGGCAACA 422979 i ---- v v iv v v iv v? -vi v -------- C MIR3#SINE/MIR 111 AGGTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGC-------- 70 chrXqtel1M 422980 AGAGCT--GACTAGAAGCTGGGCCTCC-AATTTCTGGT-----GGCTCTT 423021 i-- v ii i -i i i ii -----vv i C MIR3#SINE/MIR 69 AGAGCCGGGACTAGAACCCAGGTCTCCTGACTCCCAGTCCGTGCTCTCTC 20 chrXqtel1M 423022 TGCCCTGCTGCTC 423034 i v ii C MIR3#SINE/MIR 19 TGCTCAGCCACTC 7 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.83 CpG sites = 25, Kimura (unadjusted) = 41.12 Transitions / transversions = 1.47 (25/17) Gap_init rate = 0.10 (14 / 144), avg. gap size = 1.86 (26 / 14) 368 24.47 4.26 0.00 chrXqtel1M 423959 424052 (575948) MIRc#SINE/MIR 76 173 (95) m_b363s601i14 15243 chrXqtel1M 423959 ACCTATTAGCTGGGGGATTCTGGGCAAGTCACTTCATCTGTCT--GCCTC 424006 i i v v iii v i v -- MIRc#SINE/MIR 76 ACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTC 125 chrXqtel1M 424007 AATTTTCTCAACTGTAAAA-ATGGAGGACAGCACCT-TCCTCCCTCCC 424052 i i v -iv vi i ii -i v v MIRc#SINE/MIR 126 AGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACC 173 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.33 CpG sites = 14, Kimura (unadjusted) = 30.33 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.03 (3 / 93), avg. gap size = 1.33 (4 / 3) 194 16.68 0.00 2.78 chrXqtel1M 425778 425814 (574186) C L2b_3end#LINE/L2 (15) 451 416 m_b363s601i15 15245 chrXqtel1M 425778 AAATAATTTACCAAGTGTCCACTGTGTGCCAAGCACT 425814 - ii i i i i ? C L2b_3end#LINE 451 AAATA-TTTACTGAGCGCCTACTGTGTGCCAGGCNCT 416 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 17.23 CpG sites = 6, Kimura (unadjusted) = 20.99 Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 16 16.82 0.00 0.00 chrXqtel1M 426526 426553 (573447) (G)n#Simple_repeat 1 28 (0) m_b363s252i10 15246 chrXqtel1M 426526 GGGGGGGGGGGGGGGGAGAGAAGGGGGG 426553 i i ii (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGG 28 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 259 39.72 0.49 6.22 chrXqtel1M 428926 429129 (570871) C L2#LINE/L2 (195) 2887 2695 m_b363s601i16 15247 chrXqtel1M 428926 ACTTTATATTTGATTCTGGAGGTGTGAAGGAGCCACTGGAGCTTACTGAA 428975 ivv v i iiv v vvii i i vv vi i C L2#LINE/L2 2887 ACTTTGGCTTTTACTCTGAGTGAGATGGGAAGCCATTGGAGGGTTTTGAG 2838 chrXqtel1M 428976 GAGCGGGCACCTAGGTGGTTACACCTGTGCTTCAGGAAAATCACCTTGGT 429025 v v -- viv vi i ivv i ii i i ii ii ii i C L2#LINE/L2 2837 CAGAGG--AGTGACATGATCTGACTTACGTTTTAAAAGGATCACTCTGGC 2790 chrXqtel1M 429026 GACTGAATGGAGGATGGACTGGAGTAGGGAGAGATTTGAGGCTGGTGGAT 429075 vi vi v i i ? vi vi iv v i v vi - C L2#LINE/L2 2789 TGCTGTGTTGAGAATAGACTGNAGGGGGGCAAGGGTGGAAGCAGGGAGA- 2741 chrXqtel1M 429076 TACACCCCCCCACCCAGCA-GTGACTGCAGGGCTCCAGGCTTGAGGAGAT 429124 --------- vii v - iv i viv vv iv C L2#LINE/L2 2740 ---------CCAGTTAGGAGGCTATTGCAGTAATCCAGGCGAGAGATGAT 2700 chrXqtel1M 429125 GGAGG 429129 v C L2#LINE/L2 2699 GGTGG 2695 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 57.62 CpG sites = 41, Kimura (unadjusted) = 58.82 Transitions / transversions = 1.17 (41/35) Gap_init rate = 0.06 (13 / 203), avg. gap size = 1.00 (13 / 13) 73 29.77 1.17 1.17 chrXqtel1M 431676 431842 (568158) (CATC)n#Simple_repeat 1 166 (90) m_b363s252i11 15248 chrXqtel1M 431676 CATACCTCTAGCCAGCCAGCCATCTATGGACCCATCTATCCATCCATCTA 431725 v v i v v v i vv i i i (CATC)n#Simpl 1 CATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCA 50 chrXqtel1M 431726 TGCACCCATCCATCCATCCATCTATCTATGGACCCATCCGTGCATTGGTG 431775 v i i i vv i i v ivi v (CATC)n#Simpl 51 TCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATC 100 chrXqtel1M 431776 GA-CCATCCCAGCCACCCATCTATCCATCCATTCATCCATGCATCTATGG 431824 v - - v i i i v i vv (CATC)n#Simpl 101 CATCCAT-CCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCC 149 chrXqtel1M 431825 GCCCATTCAGCCAGCTAG 431842 ii i v v i - (CATC)n#Simpl 150 ATCCATCCATCCATCCA- 166 Matrix = Unknown Transitions / transversions = 1.00 (20/20) Gap_init rate = 0.02 (3 / 166), avg. gap size = 1.00 (3 / 3) 39 12.06 0.00 0.00 chrXqtel1M 431843 431914 (568086) (CCAT)n#Simple_repeat 1 72 (0) c_b363s251i2 15249 chrXqtel1M 431843 CCATCTATCCATCTATCCATGCATCCATCCATACATCTATCCATGGACCC 431892 i i v v i vv i (CCAT)n#Simpl 1 CCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCC 50 chrXqtel1M 431893 ATCCATCCATCCATCCATCCAT 431914 (CCAT)n#Simpl 51 ATCCATCCATCCATCCATCCAT 72 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.00 (0 / 71), avg. gap size = 0.0 (0 / 0) 73 29.77 1.17 1.17 chrXqtel1M 431915 432002 (567998) (CATC)n#Simple_repeat 167 255 (1) m_b363s252i11 15250 chrXqtel1M 431915 TGGTGGA-CCATCCATTCATCTGTCCATCCA-CGGACCATCCCATCCATC 431962 ivi vv - i ii - viv - (CATC)n#Simpl 167 CCATCCATCCATCCATCCATCCATCCATCCATCCATCCAT-CCATCCATC 215 chrXqtel1M 431963 CATCCATCTATCTATGGCCCCAGCCAGCCAGCCAGCCATC 432002 i i vvvi v v v v (CATC)n#Simpl 216 CATCCATCCATCCATCCATCCATCCATCCATCCATCCATC 255 Matrix = Unknown Transitions / transversions = 0.75 (9/12) Gap_init rate = 0.03 (3 / 87), avg. gap size = 1.00 (3 / 3) 789 25.20 4.98 2.85 chrXqtel1M 432592 432832 (567168) C MIRb#SINE/MIR (4) 264 19 m_b363s601i17 15251 chrXqtel1M 432592 ACAGAGCGGACATTTCAATAGCACCTACTATGTATCGGGCACCGTGCTAA 432641 i viv vvvv i i ii i i C MIRb#SINE/MIR 264 ATAGAGCTACCATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAA 215 chrXqtel1M 432642 GAACTTTT--TGAATACTTTC-TTTGCTCCTCCCAACCACCCTGGGAGGG 432688 vi v-- v vv i - iv v v v v C MIRb#SINE/MIR 214 GCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGT 165 chrXqtel1M 432689 AGGTGCTATTATCACCCCCATT--------GAGGATACTGAGGCACATAG 432730 ii --- -------- v v v C MIRb#SINE/MIR 164 AGGTATTATTATC---CCCATTTTACAGATGAGGAAACTGAGGCTCAGAG 118 chrXqtel1M 432731 TTCAGTGTTCAGTGACTTTCCCAGAGTCACATAGCTAGGAGGTATCAGAG 432780 --- - v i v ii i v i iv C MIRb#SINE/MIR 117 ---AG-GTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAG 72 chrXqtel1M 432781 GCCAAATTTGAGCTCAGGGCTTCCTGA-TCCCAGGCCCAGTCTCTAGCCA 432829 v vii i i i v vi - v i ivv vv C MIRb#SINE/MIR 71 CCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCA 22 chrXqtel1M 432830 CTG 432832 C MIRb#SINE/MIR 21 CTG 19 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.52 CpG sites = 27, Kimura (unadjusted) = 30.89 Transitions / transversions = 0.84 (27/32) Gap_init rate = 0.05 (11 / 240), avg. gap size = 1.73 (19 / 11) 331 32.69 5.56 1.79 chrXqtel1M 432845 433006 (566994) C L2#LINE/L2 (120) 2962 2795 m_b363s601i18 15252 chrXqtel1M 432845 GGAGAGT--CAGGAAATAAGCCTGGGAATGTAAATGGGAGGCATATGGTA 432892 --i i i viii ii v vv iiv v vi i C L2#LINE/L2 2962 GGAGAGTGGTAGGAGATGAGGTCAGAGAGGTAACGGGGGACCAGATCATG 2913 chrXqtel1M 432893 GAAGGCCTTAAATGCCAGCCCAAAGATTTCGTGTTTTATCCT-----AGA 432937 v i iv v vivi i i i vv ii ----- C L2#LINE/L2 2912 TAGGGCCTTGTAGGCCATTGTAAGGACTTTGGCTTTTACTCTGAGTGAGA 2863 chrXqtel1M 432938 AGGG-AGCCACGGGAGATTTCTAAGTAGA-GAGTGATACGGTAAGATCTA 432985 v - iv iv i i i - i i i vv ii C L2#LINE/L2 2862 TGGGAAGCCATTGGAGGGTTTTGAGCAGAGGAGTGACATGATCTGACTTA 2813 chrXqtel1M 432986 CGTTATTAAAACGTTATCATT 433006 - v -- i C L2#LINE/L2 2812 CGTT-TTAAAAGG--ATCACT 2795 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.82 CpG sites = 32, Kimura (unadjusted) = 44.82 Transitions / transversions = 1.60 (32/20) Gap_init rate = 0.04 (7 / 161), avg. gap size = 1.71 (12 / 7) 13 16.80 0.00 0.00 chrXqtel1M 433010 433036 (566964) (ATT)n#Simple_repeat 1 27 (0) m_b363s252i12 15253 chrXqtel1M 433010 ATTATTATTTTTATTATTAAAATAATT 433036 v vv v (ATT)n#Simple 1 ATTATTATTATTATTATTATTATTATT 27 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 53 29.39 2.79 1.84 chrXqtel1M 433107 433321 (566679) (ATCC)n#Simple_repeat 1 217 (0) m_b363s252i13 15254 chrXqtel1M 433107 ATCCAGCCATCCATTCATCTACTCATCCACTCAATACTTACCCATCCAGC 433156 v i i ii - v - -i i -i (ATCC)n#Simpl 1 ATCCATCCATCCATCCATCCATCCATCCA-TCCAT-C-CATCCATCCA-T 46 chrXqtel1M 433157 CCAT-AATCCATCTGCCTACCTAGCCAACCATTCATCAGTCCACCCACTG 433205 -v iii i i i v v i vi i iiv (ATCC)n#Simpl 47 CCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCC 96 chrXqtel1M 433206 AACCTTGCTTCCATCTCTCCTTCCTTCTAT-CTTCC-TAGAT-GAT-CAT 433251 v v v v iv v v i - v - vv -v - (ATCC)n#Simpl 97 ATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCAT 146 chrXqtel1M 433252 CCATCCATCCATCCATTGTTCC-TCCTTCCATCCACCTGGCCGACCATCC 433300 ivv - v i iiv iv (ATCC)n#Simpl 147 CCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCC 196 chrXqtel1M 433301 ATCCATCCATCCATCTGTCCA 433321 ii (ATCC)n#Simpl 197 ATCCATCCATCCATCCATCCA 217 Matrix = Unknown Transitions / transversions = 1.17 (27/23) Gap_init rate = 0.05 (10 / 214), avg. gap size = 1.00 (10 / 10) 221 35.07 9.36 1.74 chrXqtel1M 433450 433716 (566284) C L2d2_3end#LINE/L2 (268) 287 1 m_b363s601i19 15255 chrXqtel1M 433450 TTTGGAGGAGAAAGA----CCTAGCAACTGGA-TGATCTTGGGAAGACTT 433494 ii ii ----v ?vvii - i v- i C L2d2_3end#LIN 287 TTCAGAGGAGGGAGAGATCACTNCGGGCTGGAGTGGTCA-GGGAAGGCTT 239 chrXqtel1M 433495 CCCAGAGGGAGGTGGTGCCTGAGCTGAGCCTCGAAGGACTTGAAGAATTC 433544 v i - ?iii i i ivv v i i C L2d2_3end#LIN 238 CACGGAGG-AGGTGGNATTTGAGCTGGGCCTTGAAGGATGGGTAGGATTT 190 chrXqtel1M 433545 CAAGAAACAGAGGTAAGGGCAGCAAAGAC-CCCCAGGCAAATGGGGCCCA 433593 vi v iiii ivi i -- v i i -ii iii- iv vi C L2d2_3end#LIN 189 GGATAGGTGGAGAGGAAGG--GGAAGGGCATTCCAGGCGGG-GGGAACGG 143 chrXqtel1M 433594 CA-GGGCAAAGG----GAAATGGG-ATGC-CAGGG------CCGGAAACG 433630 i- i ---- iii - ? - i ------ v ii i C L2d2_3end#LIN 142 CGTGAGCAAAGGCGCAGAGGCGGGAANGCGCAAGGCGTGTTCGGGGGACA 93 chrXqtel1M 433631 --GAAGGGCCGAGTTCGGTGCTAGTGGAGACAAGGCCAAGAGGAATGAT- 433677 -- ivi v v i ivvv i ivvvv iv? i ii - C L2d2_3end#LIN 92 GTGAGTAGACCAGTTTGGCTGGAGCGGAGGGTTCGTGNAGGGGAATAGTG 43 chrXqtel1M 433678 --AAAT-GGTCTGGCGAGGCCATCTAGGGCCAGACCGGGCAG 433716 -- i -i v vi ?vivi i i v v C L2d2_3end#LIN 42 GGAGATAAGGCTGGAAAGGNAGGTTGGGGCCAGATCGTGGAG 1 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 47.80 CpG sites = 60, Kimura (unadjusted) = 51.92 Transitions / transversions = 1.88 (60/32) Gap_init rate = 0.06 (16 / 266), avg. gap size = 1.88 (30 / 16) 230 30.61 4.39 9.18 chrXqtel1M 433454 433658 (566342) C L2d_3end#LINE/L2 (235) 281 86 m_b363s601i20 15255 chrXqtel1M 433454 GAGGAGAAAGACC--TAGCAACTGGA-TGATCTTGGGAAGACTTCCCAGA 433500 i i i i -- ivvii - i v- i vii C L2d_3end#LINE 281 GAAGGGAGAGATCAGTGTGGGCTGGAGTGGTCA-GGGAAGGCTTCGTGGA 233 chrXqtel1M 433501 GGGAGGTGGTGCCTGAGCTGAGCCTCGAAGGACTTGAAGAATTCCA--AG 433548 - vi i i i ivv v i ivi-- C L2d_3end#LINE 232 GG-AGGTGGGACTTGAGCTGGGCCTTGAAGGATGGGTAGGATTTGGATAG 184 chrXqtel1M 433549 AAACAGAGGTAAGGGCAGCAAAGAC-CCCCAGGCAAATGGGGCCCACA-G 433596 i v v i ---- i i -ii iii- iv vi i- C L2d_3end#LINE 183 AGAGAGAGGAAGGGG----AAGGGCATTCCAGGCGGG-GGGAACGGCGTG 139 chrXqtel1M 433597 GGCAAAGGGAAATGGGATGCCAGGGCCGGAA-ACGGAAGGGCCGAGTTC- 433644 i ---------i vii v -i v -- v - C L2d_3end#LINE 138 AGCAAAGG---------CGCAGAGGCGGGAATGCGCAAGG--CGTGTTCG 100 chrXqtel1M 433645 GGTGCTAGTGGAGA 433658 v vi i C L2d_3end#LINE 99 GGGGACAGTGAAGA 86 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.29 CpG sites = 38, Kimura (unadjusted) = 41.15 Transitions / transversions = 2.00 (38/19) Gap_init rate = 0.12 (25 / 204), avg. gap size = 1.08 (27 / 25) 22 34.28 4.73 2.31 chrXqtel1M 435947 436115 (563885) (GAGAGA)n#Simple_repeat 1 173 (0) m_b363s252i14 15256 chrXqtel1M 435947 GAGAGA-AGACAGAGAAATAGGGGGAGAGACAGAGGGATATGGAGGGGGT 435995 - v i v i i v i v vi i i v (GAGAGA)n#Sim 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chrXqtel1M 435996 GAAAGAAACGAGAGGGAAGGAGACAG-GAGAGCG-GAGA-AGAAAAAGAA 436042 i i - i ii v - v - - i i i (GAGAGA)n#Sim 51 GAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 99 chrXqtel1M 436043 AGGGGGGGGGAAGGAAAGCTTAGAG-GAGATGAAGGTGGGGGCAAGAG-G 436090 i i i i ii i -vv - - ii v i i vi - (GAGAGA)n#Sim 100 AGAGAGAGAGAGAGAGAG-AGAGAGAGAGA-GAGAGAGAGAGAGAGAGAG 147 chrXqtel1M 436091 AGGGAG-GAGGGA-AGAGCAGGCAGAG 436115 i - i - - iv (GAGAGA)n#Sim 148 AGAGAGAGAGAGAGAGAG-AGAGAGAG 173 Matrix = Unknown Transitions / transversions = 2.31 (30/13) Gap_init rate = 0.07 (12 / 168), avg. gap size = 1.00 (12 / 12) 12 22.17 1.54 10.00 chrXqtel1M 435996 436060 (563940) (GAAAG)n#Simple_repeat 1 60 (0) m_b363s252i15 15257 chrXqtel1M 435996 GAAA-GAAACGAGAGGGAAGGAGACAGGAGAGCGGAGAAGAAAAAGAAAG 436044 - v i i - - - -v - i i - (GAAAG)n#Simp 1 GAAAGGAAAGGAAAGGAAAGGA-A-AGGA-A-AGGA-AAGGAAAGGAAA- 44 chrXqtel1M 436045 GGGGGGGGAAGGAAAG 436060 iii i (GAAAG)n#Simp 45 GGAAAGGAAAGGAAAG 60 Matrix = Unknown Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.11 (7 / 64), avg. gap size = 1.00 (7 / 7) 22 34.28 4.73 2.31 chrXqtel1M 435947 436115 (563885) (GAGAGA)n#Simple_repeat 1 173 (0) m_b363s252i14 15256 chrXqtel1M 435947 GAGAGA-AGACAGAGAAATAGGGGGAGAGACAGAGGGATATGGAGGGGGT 435995 - v i v i i v i v vi i i v (GAGAGA)n#Sim 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chrXqtel1M 435996 GAAAGAAACGAGAGGGAAGGAGACAG-GAGAGCG-GAGA-AGAAAAAGAA 436042 i i - i ii v - v - - i i i (GAGAGA)n#Sim 51 GAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 99 chrXqtel1M 436043 AGGGGGGGGGAAGGAAAGCTTAGAG-GAGATGAAGGTGGGGGCAAGAG-G 436090 i i i i ii i -vv - - ii v i i vi - (GAGAGA)n#Sim 100 AGAGAGAGAGAGAGAGAG-AGAGAGAGAGA-GAGAGAGAGAGAGAGAGAG 147 chrXqtel1M 436091 AGGGAG-GAGGGA-AGAGCAGGCAGAG 436115 i - i - - iv (GAGAGA)n#Sim 148 AGAGAGAGAGAGAGAGAG-AGAGAGAG 173 Matrix = Unknown Transitions / transversions = 2.31 (30/13) Gap_init rate = 0.07 (12 / 168), avg. gap size = 1.00 (12 / 12) 34 31.60 2.96 3.47 chrXqtel1M 436231 436433 (563567) (GAGACA)n#Simple_repeat 1 202 (0) m_b363s252i16 15258 chrXqtel1M 436231 GAGACAGCAGGAAGAAGCAGGGAGCAGCAGGAGGAG-GAAAGGCAGAGAC 436279 - iv ii i - - ivi -v i i (GAGACA)n#Sim 1 GAGACAG-AGACAGAGACAGAGA-CAG-AGACAGAGACAGAGACAGAGAC 47 chrXqtel1M 436280 AGAGATGGAGA-TG-G-CGAAGACAGAGACCGAGAGATGGAGCCGA-AGG 436325 ii -v - - ii v v vi - v - vi (GAGACA)n#Sim 48 AGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGA-CAGAGACA 96 chrXqtel1M 436326 GAGCCCGAGCCAGAGACACAGAGATCACAGGGAGAGAGAAACAGAGCCAG 436375 v v v v v -v v vi v i v (GAGACA)n#Sim 97 GAGACAGAGACAGAGACAGAGACA-GAGACAGAGACAGAGACAGAGACAG 145 chrXqtel1M 436376 AGCCAGAGGGAGATAGACATGGACAGAGAGATGTACAGAGAGGGA-AGGG 436424 v -- v v vi v viv vi - vi (GAGACA)n#Sim 146 AGACAGA--GACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAG 193 chrXqtel1M 436425 AGACAGGGA 436433 i (GAGACA)n#Sim 194 AGACAGAGA 202 Matrix = Unknown Transitions / transversions = 0.75 (21/28) Gap_init rate = 0.06 (13 / 202), avg. gap size = 1.00 (13 / 13) 14 16.22 4.65 2.27 chrXqtel1M 436751 436793 (563207) (AGACAAG)n#Simple_repeat 1 44 (0) m_b363s252i17 15259 chrXqtel1M 436751 AGACCAGAGAAATGGACACAAGACACAA-AGAC-AGAGATAAGAG 436793 v v -i v v - - i (AGACAAG)n#Si 1 AGACAAGAGACA-AGAGACAAGAGACAAGAGACAAGAGACAAGAG 44 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.07 (3 / 42), avg. gap size = 1.00 (3 / 3) 262 34.58 0.00 2.47 chrXqtel1M 437312 437394 (562606) C MIR3#SINE/MIR (16) 192 112 m_b363s601i21 15260 chrXqtel1M 437312 GAACGGCGGAGCCAAGTGGGAGCTGAGAAATCATGTGACTTTCCTCTTTC 437361 i v i iiiiv v v i v ii-- i vv iii C MIR3#SINE/MIR 192 GAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAG--TCCAACCCCC 145 chrXqtel1M 437362 CCATTCCACAGACAAGGAAACTGAGACCCTGGG 437394 i ii ii i v i C MIR3#SINE/MIR 144 TCATTTTACAGATGAGGAAACTGAGGCCCAGAG 112 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 50.40 CpG sites = 20, Kimura (unadjusted) = 50.40 Transitions / transversions = 2.50 (20/8) Gap_init rate = 0.02 (2 / 82), avg. gap size = 1.00 (2 / 2) 199 27.12 3.28 3.28 chrXqtel1M 437765 437825 (562175) MIR3#SINE/MIR 114 174 (34) m_b363s601i22 15261 chrXqtel1M 437765 CTGGGTCTCAGTTTCCTTCTCTGTACAAGAAACAGAAGCTGTCCTAGGT- 437813 i iv v vi --i ii i vv i - MIR3#SINE/MIR 114 CTGGGCCTCAGTTTCCTCATCTGTAAAATGA--GGGGGTTGGACTAGATG 161 chrXqtel1M 437814 -TCGCTCAAGTCC 437825 - v v i MIR3#SINE/MIR 162 ATCTCTAAGGTCC 174 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.33 CpG sites = 9, Kimura (unadjusted) = 34.33 Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.07 (4 / 60), avg. gap size = 1.00 (4 / 4) 15 16.48 0.00 2.86 chrXqtel1M 438066 438101 (561899) (CTTCC)n#Simple_repeat 1 35 (0) m_b363s252i19 15262 chrXqtel1M 438066 CTGCCCTCCCCTTCCCATCCCTTCTCTCCCTCTTCC 438101 v i v i i - (CTTCC)n#Simp 1 CTTCCCTTCCCTTCCCTTCCCTTCCCTTCC-CTTCC 35 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) 341 27.45 13.27 5.21 chrXqtel1M 438738 438933 (561067) MIRc#SINE/MIR 32 242 (26) m_b363s601i23 15263 chrXqtel1M 438738 GGGCCTGGAATCAAGCAGGAAGACCGAGGGACATCTACAGCCTCAGGCAT 438787 i i i ---- vi vv ivv v v v v v i MIRc#SINE/MIR 32 GGACTTGGAGTCA----GGAAGACCTGGGTTCGAGTCCCGGCTCTGCCAC 77 chrXqtel1M 438788 TTCCTA-CCATGGAACCCAGGGCAAGTCACTT---CCCCCTAGCCACCTG 438833 v - ii vi iv --- i i ii------ MIRc#SINE/MIR 78 TTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGA------G 121 chrXqtel1M 438834 CCTCAGTTTCCCCATCTGTAAAA----GA-AGCAGTTCCTAACACAGCC- 438877 i ---- - ii i v -i v v - MIRc#SINE/MIR 122 CCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCT-GCCCTGCCT 170 chrXqtel1M 438878 -CCTCACAGGGTCACTGAGAG--------------ATATTTGT-AACACA 438911 - iii v -------------- i v - vi i MIRc#SINE/MIR 171 ACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCG 220 chrXqtel1M 438912 CTTAGCAAAACTTAAAGCACTA 438933 v i viv ii MIRc#SINE/MIR 221 CTTTGTAAACTGTAAAGTGCTA 242 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 33.42 CpG sites = 29, Kimura (unadjusted) = 35.11 Transitions / transversions = 1.32 (29/22) Gap_init rate = 0.10 (19 / 195), avg. gap size = 1.95 (37 / 19) 598 36.20 11.27 5.23 chrXqtel1M 439007 440000 (560000) C L3#LINE/CR1 (809) 3290 2240 m_b363s601i24 15264 chrXqtel1M 439007 TGCTGGGGGCCTTTTGGAGCCTGG--CTGTCATCTGCCATCCTCATTATT 439054 ii i iv ? i v i i-- ii? i vi vii i C L3#LINE/CR1 3290 TGTCGAGATCNTTTTGAATCTTGATTCTGTCATCCANCGTATTAGCTATC 3241 chrXqtel1M 439055 TCTCCCCGCTTGTCATTGCCCAAAAACCTAACAGGCAGACCCCGGGCAGG 439104 i v vvii iii iiv ii i i i vi iiv--i v C L3#LINE/CR1 3240 CCTCCCAGCTTTGTGTCATCTGCAAATTTGATAAGCATGCCTTC--TATG 3193 chrXqtel1M 439105 CCTTCCCAGAAGTCACGGATGCACAGAAACGTTCAGCGGCGGCTCAGGGC 439154 i vivv iv ---- i i v i i vi--- C L3#LINE/CR1 3192 TCTTCATCCAAGTCATTGAT----AAAAATGTTGAACAGGA---CAGGGC 3150 chrXqtel1M 439155 CA--GCCGTGGGTCCTATGAGGCCCTCTCCCAGAGCCCTCCTCCTTCAGA 439202 -- v i- i i i -- v v iv i v -- i i C L3#LINE/CR1 3149 CAAGGACA-GAGCCCTGTG--GCACGCCACTAGAGACCTCC--CTCCAGG 3105 chrXqtel1M 439203 TTAAGGT-GTTC------TCAGTGACTCTTTGGGAGTCGCCATCCCGGAG 439245 i vi - v ------ ii- ii vi v i i i --- i C L3#LINE/CR1 3104 TTGACATCGATCCATTAATCAAC-ACCTTTTGGGTATAGTCGTTC---AA 3059 chrXqtel1M 439246 CCA--TTCAGAGCCACGTGGCCGACATCTC-TCCATCCCAT-----CCCA 439287 -- v ii v v ii i vvv v - v -----i C L3#LINE/CR1 3058 CCAGCTACGAATCCACCTAACTGTACTATCATCCAGCCCATATTTCTCCA 3009 chrXqtel1M 439288 TCTC--CGAGAAGGGGA-CGTGAG-GTCCGAGGCAAAGGCTCTGCTGAAA 439333 i-- v v iv - i - v ivv v v ii C L3#LINE/CR1 3008 TCTTGTCCACAAGGATATCATGAGAGACTTTGTCAAATGCCTTGCTGAAA 2959 chrXqtel1M 439334 TC---AGGCACCCTGTCT--------CCCATG-----CTAGTTAAGTGCC 439367 --- vi i? -------- v ----- i iv iv C L3#LINE/CR1 2958 TCCAGATACACTNTGTCTACGGCATTCCCCTGATCTACCAGTCTAGTAAC 2909 chrXqtel1M 439368 CTCATCCAAAGAGGGAACGGGCTCGGTCAGGC-----CCGCTCTCGAGGG 439412 ii v i i i i v ii iv -----ii i iiiv i C L3#LINE/CR1 2908 CCTATCAAAAAAGGAAATGAGGTTAGTTTGGCATGACTTGTTCTTAGTGA 2859 chrXqtel1M 439413 AGGCTTTCGGACTTCCTGAAATCACCA--GCCCTTTCT------------ 439448 vv v v v i i iv vi i--v i ------------ C L3#LINE/CR1 2858 ACCCATGCTGGCTCCTAGTGATCACCGCTTCCTTTTCTAAGTGCTCACAA 2809 chrXqtel1M 439449 --CGACTGTCT------CCTCTTGGGAATTTGCCCGTGAATCCAAAATCA 439490 -- iv i ------ vi ivi vv v i -i vi C L3#LINE/CR1 2808 ACCATCTGTTTAATAATCCGTTCTAGAATTTTGCCGGGGATC-GACGTCA 2760 chrXqtel1M 439491 GACTTCCTAGCCCAT--TTGCCAGCAC---TCTCTCGTCCCTCTTGAAGA 439535 ii v ii i ii -- v? v i--- i iv i v i C L3#LINE/CR1 2759 AGCTTACCGGTCTGTAGTTTNCAGAATCCATCTTTTTTCCCTTTTTAAAA 2710 chrXqtel1M 439536 GTGG------CATTCTACCATTCACCAGTCTCATGGGCATGCTCCCATTT 439579 ? i ------ - i vv v iv vvviv i i i C L3#LINE/CR1 2709 NTAGGNACNACATT-TGCCCGTCTCCAGTCTTCTGGCACCTCTTCCGTTC 2661 chrXqtel1M 439580 TCCATGATCTTTCCAACGGTCCT--CCACGGTCCTCTGCAGCC-CACCTG 439626 i i i v viv v i-- vi -- i iii - i C L3#LINE/CR1 2660 TCCGTGATTTCTCAAAGATTACCGACAGCGGT--TCCGCGATCACATCTG 2613 chrXqtel1M 439627 CCTGTTCTCTCAAGCTCCAAGGGAGACGGGAGGCTGTCCACCCCTTTTGG 439676 vv i ivvi --------i --- -- vii v i C L3#LINE/CR1 2612 CAAGTTCTTTCAGTACCC--------TGGGA---TGT--AATTCGTCTGG 2576 chrXqtel1M 439677 ACCGGGTGACCTGAATTCACTTGGGGCAACCTGGGCCCCTCC--CTTCCT 439724 i v v i i i iii ii iv vv i i-- vi C L3#LINE/CR1 2575 GCCTGGAGACTTGAACTCATTTAAAGCGGCTAGGTGCTCTCTTACTATCT 2526 chrXqtel1M 439725 CCCCAGC-ATCT-GAGCCGCATTTC--TCTT---GGGGCTCGT------- 439760 i v - - i iv v -- --- iv i i ------- C L3#LINE/CR1 2525 CCTCACCTATCTTGGGCTTCAATTCCCTCTTAACGATGTTTGTTCTACCC 2476 chrXqtel1M 439761 ---CAGGAATAAAGGTCGGTCATCGTCCTTGG---------CGGAAGCCA 439798 --- vi vv i i iv ---- i--------- v C L3#LINE/CR1 2475 TTTCCAGTCTGAAGATCATTC----TCCTTGATAGAGAAGACGGAAGCAA 2430 chrXqtel1M 439799 GAGGTGGCTCTGGCCGCCCTCTCCTGTCTCTGGTACCTGGGAATCATGGC 439848 i viv iv ivi iv ii viii v vi i vv - vi C L3#LINE/CR1 2429 AATAGGAGTTGAGTAGTTCTGCTTTCTCTCTGTCATCTGTTAA-CATTAC 2381 chrXqtel1M 439849 CACATCCATCC-AAACAGCAGTTGCATCTCTTCTTCCATTCTTGCCTTTC 439897 vv iii - i i -- v v ?ii -- i v i i v C L3#LINE/CR1 2380 GCCATCTGCCCCAAGCAGCGG--GCCTGTCNCTTTC--TTTTTCCTTCTG 2335 chrXqtel1M 439898 CCTCGGAGAGGTCGGCCACAAACCCTCACCTTTTTGTTGGCCTTGGC--- 439944 ii i v viv vviv v i i ?--- v i --- C L3#LINE/CR1 2334 CTCCGAACATAGCTTTGAAAAGCCTTN---TTTTTGTTGTCCTTAGCATT 2288 chrXqtel1M 439945 TTCCCCAGCCATTGTCGGCTCACTGTTCTTGACTTTTCTAGTCTTCTTCT 439994 iiiiv v viv i --- v i --- i -- C L3#LINE/CR1 2287 TTTTTTTGCAAGCCTCAGCTCA---TTCTGGGCTT---TAGCCTTC--CT 2246 chrXqtel1M 439995 GAGACT 440000 v C L3#LINE/CR1 2245 GACACT 2240 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 49.34 CpG sites = 206, Kimura (unadjusted) = 52.76 Transitions / transversions = 1.53 (206/135) Gap_init rate = 0.09 (88 / 993), avg. gap size = 1.90 (167 / 88) 193 36.79 5.66 0.00 chrXqtel1M 440036 440141 (559859) L2b_3end#LINE/L2 141 252 (214) m_b363s601i25 15265 chrXqtel1M 440036 TGTCCCTCCTGCC---ACCTCCTGGCTCCAGGTGTGCTCCTAGCTGTCCC 440082 i ii --- v v ivv i vv v v v i iiv i L2b_3end#LINE 141 TGTTCCCTCTGCCTGGAACGCCCTTCCCCACCTCTTCGCCTGGCCAACTC 190 chrXqtel1M 440083 CTA---GGGCTCCAAGTCTCAGGTAAAACCCCACTTTCTCCAAGGAGCTG 440129 ---ivv i i v v ivi i i ii i iv L2b_3end#LINE 191 CTACTCATCCTTCAGGTCTCAGCTCAAATGTCACCTCCTCCGGGAAGCCC 240 chrXqtel1M 440130 TTCTTGATCCCC 440141 i i i L2b_3end#LINE 241 TCCCTGACCCCC 252 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 50.94 CpG sites = 23, Kimura (unadjusted) = 52.95 Transitions / transversions = 1.44 (23/16) Gap_init rate = 0.02 (2 / 105), avg. gap size = 3.00 (6 / 2) 448 33.84 10.07 2.23 chrXqtel1M 440293 440709 (559291) C L3#LINE/CR1 (1834) 2265 1817 m_b363s601i26 15264 chrXqtel1M 440293 TTCTAAACTTTGGCTTTC-AGACCCCGAGTTTGCAGAACCTTGCCACGCT 440341 iii i i -v v iivvi i iviiv ?i v C L3#LINE/CR1 2265 TTCTGGGCTTTAGCCTTCCTGACACTATTCTTACAGGCTTGTGNTACTCT 2216 chrXqtel1M 440342 TTGCTTGTCCTCCCTTTAGGTGGCCTGGCCTCCATCTTCTGCC-CAGGTC 440390 i vi ivv - vi v v-ii vi- v C L3#LINE/CR1 2215 CTCTTTGTCCTTGGTT-ATATGTCCTC-TTTCCATCTTCTGATACATGTC 2168 chrXqtel1M 440391 --TCTAAACTCCGGCT---GAGGA-GCTCCCCACAGCTGTGT-------- 440426 -- i v i i v--- i -? ivii? iii -------- C L3#LINE/CR1 2167 CTTTTAAAATCTGACATCAGAGAATNCTCTATGNAGCCACGTTGGTTTCT 2118 chrXqtel1M 440427 --------CTCCTTCTTTTCCATCTGACTGGTGGCCTCTTGTGGCT---- 440464 -------- i ivi v i --ii vi iii ---- C L3#LINE/CR1 2117 TAAATGCCCTCCCTCTTTTCTTCCTCATTGG--ATCATTTGTAATTGTAG 2070 chrXqtel1M 440465 TCTGGATTTCCTTCTGGAG-GCT---CGCCCCCTGCCCGCTAACTTGCTA 440510 v i v i vi - --- i? iivivv i v v - C L3#LINE/CR1 2069 TCAGAATTTCATTTTTAAGAGCTTCCCANCCCTCTTGAGCCATCTTTCT- 2021 chrXqtel1M 440511 TTTTGCATTTTAAGTCCTTGGGATTCTACCCACCTCTTCTTTGAAGCCTT 440560 vi i i?i - v i iv i-- i i vii C L3#LINE/CR1 2020 TTTTGAGTCTCNGG-CCATGGAATCATACCT--CTTTTCTCTGAATTTTT 1974 chrXqtel1M 440561 CAGAACCTGCTCT--CTC-CAAATCCTGGGTC-TACCTCAGACCCC--AT 440604 iii i i -- -i vi iv - iv -i iii-- i C L3#LINE/CR1 1973 TGAAATCTGCTTTTCCTCGTAAAGTCTGGAACATATGT-GGACTTTTAAC 1925 chrXqtel1M 440605 GTTTCCTTACTTCTCTAGCATGCACTCTAGGGGCAACA-GGCACTTCCCC 440653 v v vv vi i v i i-ii - i i C L3#LINE/CR1 1924 TTTTCCTTTCTTGGCTATTACGAACTCTAAGA-TGACATGGCACTTTCTC 1876 chrXqtel1M 440654 TCTGGGTTCCCACCA--TTCCCTTCCAGGAACCAGTTCTTTCTT-TGGGT 440700 i vi i i i-- vi i vv i - v C L3#LINE/CR1 1875 CCAAGGTTCCTATCGACTTCCACTTCACCAACCAGTTCTTCCTTGTTGGT 1826 chrXqtel1M 440701 GAGAATCAA 440709 v i C L3#LINE/CR1 1825 CAGAATTAA 1817 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 47.16 CpG sites = 90, Kimura (unadjusted) = 48.69 Transitions / transversions = 1.88 (90/48) Gap_init rate = 0.06 (25 / 416), avg. gap size = 2.08 (52 / 25) 16 8.12 10.26 0.00 chrXqtel1M 441118 441156 (558844) (TGTCTC)n#Simple_repeat 1 43 (0) m_b363s252i20 15266 chrXqtel1M 441118 TGTCTCT-CATCTCTCTCTGTCTCTGTCTC--TC-CTGTCTCT 441156 -iv v -- - (TGTCTC)n#Sim 1 TGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCT 43 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.08 (3 / 38), avg. gap size = 1.33 (4 / 3) 12 25.68 0.00 4.55 chrXqtel1M 441128 441173 (558827) (CTCC)n#Simple_repeat 1 44 (0) m_b363s252i21 15266 chrXqtel1M 441128 CTCTCTCTGTCTCTGTCTCTCCTGTCTCTCCTTCCTCCCTCCCTCC 441173 i iv i vi - vi - i (CTCC)n#Simpl 1 CTCCCTCCCTCCCTCCCTC-CCTCCCTC-CCTCCCTCCCTCCCTCC 44 Matrix = Unknown Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.04 (2 / 45), avg. gap size = 1.00 (2 / 2) 14 0.00 4.76 0.00 chrXqtel1M 442014 442034 (557966) (CCTC)n#Simple_repeat 1 22 (0) m_b363s252i22 15267 chrXqtel1M 442014 CCTCCCTCCCTCCCT-CCTCCC 442034 - (CCTC)n#Simpl 1 CCTCCCTCCCTCCCTCCCTCCC 22 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.05 (1 / 20), avg. gap size = 1.00 (1 / 1) 197 26.60 7.84 7.84 chrXqtel1M 442130 442231 (557769) C MIRb#SINE/MIR (115) 153 52 m_b363s601i27 15268 chrXqtel1M 442130 TCCTGGTCTTAAAGCCAGAGGAACTTAAGGCTGAGAAGGG------GACT 442173 ivi i v vi- vi i v ii ------i C MIRb#SINE/MIR 153 TCCCCATTTTACAGAT-GAGGAAACTGAGGCTCAGAGAGGTTAAGTAACT 105 chrXqtel1M 442174 TGCCTAAGGTCACCACGACAAGGAG--GGCAGAACTGGAGGTCCGAGGGC 442221 i - ii v v i-- i i - i i ---- C MIRb#SINE/MIR 104 TGCCCAAGGTCA-CACAGCTAGTAAGTGGCAGAGCCGG-GATTCGA---- 61 chrXqtel1M 442222 CACCGAGGTC 442231 - v C MIRb#SINE/MIR 60 -ACCCAGGTC 52 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.57 CpG sites = 17, Kimura (unadjusted) = 34.27 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.10 (10 / 101), avg. gap size = 1.60 (16 / 10) 200 26.88 10.00 2.33 chrXqtel1M 442130 442209 (557791) C MIRc#SINE/MIR (118) 150 65 m_b363s601i28 15268 chrXqtel1M 442130 TCCTGGTCTTAAAGCCAGAGGAACTTAAGGCTGAGAAGGG------GACT 442173 ivi i v vi- vi i v ii ------ C MIRc#SINE/MIR 150 TCCCCATTTTACAGAT-GAGGAAACTGAGGCTCAGAGAGGTTAAGTGACT 102 chrXqtel1M 442174 TGCCTAAGGTCACCACGACAAGGAG--GGCAGAACTGG 442209 i - ii v v i-- i i C MIRc#SINE/MIR 101 TGCCCAAGGTCA-CACAGCTAGTAAGTGGCAGAGCCGG 65 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 32.67 CpG sites = 14, Kimura (unadjusted) = 34.72 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.05 (4 / 79), avg. gap size = 2.50 (10 / 4) 12 12.18 7.89 2.50 chrXqtel1M 443591 443628 (556372) (GAAGG)n#Simple_repeat 1 40 (0) m_b363s252i23 15269 chrXqtel1M 443591 GAAGGGAA-GGAAGTGGACGGG-A-GGAAGAGGAGGAAAGG 443628 - - v - - i i i (GAAGG)n#Simp 1 GAAGGGAAGGGAAG-GGAAGGGAAGGGAAGGGAAGGGAAGG 40 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.11 (4 / 37), avg. gap size = 1.00 (4 / 4) 12 16.54 5.88 0.00 chrXqtel1M 443598 443631 (556369) (AGG)n#Simple_repeat 1 36 (0) m_b363s252i24 15269 chrXqtel1M 443598 AGGAAGTGGACG-GGAGGAAGAGGAGGA-AAGGAGG 443631 i v v - i -i (AGG)n#Simple 1 AGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGG 36 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2) 495 32.92 1.82 2.44 chrXqtel1M 443982 444146 (555854) C MIR#SINE/MIR (23) 239 76 m_b363s601i29 15270 chrXqtel1M 443982 CACTTACCGTTTGCCAGGCCCTGTGCTAAGTGTTTCACAAATGCTACCTC 444031 i ii v v v i i i vi ii v C MIR#SINE/MIR 239 CGCTTACTATGTGCCAGGCACTGTTCTAAGCGCTTTACATGTATTAACTC 190 chrXqtel1M 444032 ACCGGGTCCTCCCCACACCCCTGGGCGATTGCTCGCTACTAGGATCGGCC 444081 iivii v v v iv v i---- v v vv iiv C MIR#SINE/MIR 189 ATTTAATCCTCACAACAACCCTATGAGG----TAGGTACTATTATTATCC 144 chrXqtel1M 444082 CCATTTTACAGCTGAGGAAAGCAAGGTGGGCAGAGGT---GTGACTCGCT 444128 v vii iiviv --- i i i C MIR#SINE/MIR 143 CCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCC 94 chrXqtel1M 444129 TGGGATCTCACAGTGGGT 444146 iii i v ivi C MIR#SINE/MIR 93 CAAGGTCACACAGCTAGT 76 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.58 CpG sites = 31, Kimura (unadjusted) = 44.86 Transitions / transversions = 1.41 (31/22) Gap_init rate = 0.03 (5 / 164), avg. gap size = 1.40 (7 / 5) 269 22.83 17.39 0.00 chrXqtel1M 444080 444171 (555829) C MIR1_Amn#SINE/MIR (79) 151 44 m_b363s601i30 15270 chrXqtel1M 444080 CCCCATTTTACAGCTGAGGAAAGCAAGGTGGGCAGAGGT---GTGACTCG 444126 v vii i?viv --- i C MIR1_Amn#SINE 151 CCCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTG 102 chrXqtel1M 444127 CTTGGGATCTCACAGTGGGT-----------CCGG--TTTAAACTCAGGG 444163 iiii i v ? i? i----------- --? ?i i v C MIR1_Amn#SINE 101 CCCAAGGTCACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAACCCAGGT 52 chrXqtel1M 444164 CTCCCTAG 444171 v C MIR1_Amn#SINE 51 CTCCCGAG 44 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.12 CpG sites = 14, Kimura (unadjusted) = 30.12 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.03 (3 / 91), avg. gap size = 5.33 (16 / 3) 248 30.49 2.75 3.70 chrXqtel1M 444826 444934 (555066) MIR3#SINE/MIR 87 194 (14) m_b364s601i2 15271 chrXqtel1M 444826 TGCCCTTGGCCTGG-CACTCTCCCTCT-TGGCTCCCACCTTCACCATCTG 444873 v v vi - iiv - vi i vi vi MIR3#SINE/MIR 87 TGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATCTG 136 chrXqtel1M 444874 TCAGACAGAGGTGTCGAGGCAGTGAGATGTTTGCTAAGG-CTTTTCCAGC 444922 v i iiii v i i--- v - v iv - ii MIR3#SINE/MIR 137 TAAAATGAGGGGGTTGG---ACT-AGATGATCTCTAAGGTCCCTTCCAGC 182 chrXqtel1M 444923 CCTGACGCTCTA 444934 i ii MIR3#SINE/MIR 183 TCTGACATTCTA 194 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.67 CpG sites = 20, Kimura (unadjusted) = 40.67 Transitions / transversions = 1.67 (20/12) Gap_init rate = 0.06 (7 / 108), avg. gap size = 1.00 (7 / 7) 44 0.00 0.00 0.00 chrXqtel1M 445551 445588 (554412) (CA)n#Simple_repeat 1 38 (0) c_b364s251i0 15272 chrXqtel1M 445551 CACACACACACACACACACACACACACACACACACACA 445588 (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACA 38 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 277 30.38 3.85 1.89 chrXqtel1M 445639 445742 (554258) C MIR3#SINE/MIR (17) 191 86 m_b364s601i3 15273 chrXqtel1M 445639 AAAGCCGAAACTGGA--GGAGCTTGCAGTTCTGTCCAATTC--CTCCCCC 445684 v i ii i -- v iv v -i i i i -- i i C MIR3#SINE/MIR 191 AATGTCAGAGCTGGAAGGGACCTTAGAGATC-ATCTAGTCCAACCCCCTC 143 chrXqtel1M 445685 ATTTTGCAGATGAAGAAGCAAAGGGGCAAAAAGGGAAAGGAGCTGGCCCA 445734 i i i vi vv i i vi vii v C MIR3#SINE/MIR 142 ATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCA 93 chrXqtel1M 445735 GAGCTCAC 445742 - v C MIR3#SINE/MIR 92 -AGGTCAC 86 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.73 CpG sites = 20, Kimura (unadjusted) = 40.73 Transitions / transversions = 1.82 (20/11) Gap_init rate = 0.04 (4 / 103), avg. gap size = 1.50 (6 / 4) 11 14.41 7.50 2.38 chrXqtel1M 447570 447609 (552391) (CCCCGCTC)n#Simple_repeat 1 42 (0) m_b364s252i2 15274 chrXqtel1M 447570 CCCTGC-CCACCCCTCCCACTGCT-CCCCGC-CCCCGGCTCCC 447609 i - v v - i - - v (CCCCGCTC)n#S 1 CCCCGCTCCCCCGCTCCC-CCGCTCCCCCGCTCCCCCGCTCCC 42 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.10 (4 / 39), avg. gap size = 1.00 (4 / 4) 213 34.48 6.90 0.00 chrXqtel1M 447638 447724 (552276) C MIR3#SINE/MIR (25) 183 91 m_b364s601i4 15275 chrXqtel1M 447638 AACTGAAAGGGACC---GGGAGCTCCCGCTCCGATCTCCTC-CTCCATTA 447683 i i --- i v vi iiv i i i -i ii ivi C MIR3#SINE/MIR 183 AGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAG 134 chrXqtel1M 447684 ATG--GAAACTGAGTCTCAAAATGGGAAACCGGCTTGTCAAAG 447724 -- v i i iv vi vi i i v C MIR3#SINE/MIR 133 ATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAG 91 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 49.91 CpG sites = 21, Kimura (unadjusted) = 49.91 Transitions / transversions = 2.33 (21/9) Gap_init rate = 0.03 (3 / 86), avg. gap size = 2.00 (6 / 3) 12 19.85 3.39 7.02 chrXqtel1M 447936 447994 (552006) (CCCCTGC)n#Simple_repeat 1 57 (0) m_b364s252i3 15276 chrXqtel1M 447936 CCCCCG-CCCCT-TCCCCGACCCCCAGGGCCCTGCCCCCGGCCTCCACTC 447983 i - -i vi v vv v - - - (CCCCTGC)n#Si 1 CCCCTGCCCCCTGCCCCCTGCCCCCTGCCCCCTGCCCCCTGCC-CC-CT- 47 chrXqtel1M 447984 CGCCGCCTGCC 447994 - v (CCCCTGC)n#Si 48 -GCCCCCTGCC 57 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.10 (6 / 58), avg. gap size = 1.00 (6 / 6) 26 20.91 5.00 2.94 chrXqtel1M 448094 448170 (551830) (GCGGCT)n#Simple_repeat 1 80 (22) m_b364s252i4 15277 chrXqtel1M 448094 GCGGCTGCGG--G-GGCTGCGGCTGCGGCAGTACTTGGGGCTGCTGCGGC 448140 -- - v iivi v v v (GCGGCT)n#Sim 1 GCGGCTGCGGCTGCGGCTGCGGCTGCGGCTGCGGCTGCGGCTGCGGCTGC 50 chrXqtel1M 448141 GCCTG-GGGGGCTGCTGCTGCTGCTGCTGCT 448170 v - vv v v v - (GCGGCT)n#Sim 51 GGCTGCGGCTGCGGCTGCGGCTGCGGCTGC- 80 Matrix = Unknown Transitions / transversions = 0.27 (3/11) Gap_init rate = 0.05 (4 / 76), avg. gap size = 1.25 (5 / 4) 38 6.57 0.00 0.00 chrXqtel1M 448171 448218 (551782) (GCG)n#Simple_repeat 1 48 (0) c_b364s251i1 15278 chrXqtel1M 448171 GCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGCTGCTGCGGCGGCG 448218 v v v (GCG)n#Simple 1 GCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCG 48 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 26 20.91 5.00 2.94 chrXqtel1M 448219 448240 (551760) (GCGGCT)n#Simple_repeat 81 101 (1) m_b364s252i4 15279 chrXqtel1M 448219 CCTGGGGGCT-CGGCGGCGAGCT 448240 v - v - v - (GCGGCT)n#Sim 81 GCT-GCGGCTGCGGCTGCG-GCT 101 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.14 (3 / 21), avg. gap size = 1.00 (3 / 3) 21 19.44 1.56 4.84 chrXqtel1M 448802 448865 (551135) (CCT)n#Simple_repeat 1 62 (0) m_b364s252i5 15280 chrXqtel1M 448802 CCTCCTCCTCCTCCCTCTTCGTCGTCGTTCTCCTCCTCCGCCGCCGCCCG 448851 - i v v v i v v -i v (CCT)n#Simple 1 CCTCCTCCTCCT-CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC-TCCT 48 chrXqtel1M 448852 CCT-CTCTGTCCTCC 448865 - -v (CCT)n#Simple 49 CCTCCTC-CTCCTCC 62 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.06 (4 / 63), avg. gap size = 1.00 (4 / 4) 22 7.85 2.13 6.67 chrXqtel1M 448991 449037 (550963) (GGA)n#Simple_repeat 1 45 (0) m_b364s252i6 15281 chrXqtel1M 448991 GGAGGGAGGAGGAAGAGGAAGA-GAGGAGGGAGGGGGAGGAAGGAGGA 449037 - i i - - i - (GGA)n#Simple 1 GGA-GGAGGAGGAGGAGGAGGAGGAGGA-GGAGGAGGAGG-AGGAGGA 45 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.09 (4 / 46), avg. gap size = 1.00 (4 / 4) 63 2.42 1.04 6.59 chrXqtel1M 449071 449166 (550834) (GGCTCC)n#Simple_repeat 1 91 (0) c_b364s251i2 15282 chrXqtel1M 449071 GGCTCCAGCTCCCGGGCTCCCGGCTGCCGGCTCCGGCTGCC-GCTCCGGC 449119 i - - - - - - (GGCTCC)n#Sim 1 GGCTCCGGCT-CC-GGCT-CCGGCT-CCGGCTCCGGCT-CCGGCTCCGGC 45 chrXqtel1M 449120 TCCGGCTCCGGCTCCGGCTCCGGCTCCCGGCTCGGGCTCCGGCTCCG 449166 - v (GGCTCC)n#Sim 46 TCCGGCTCCGGCTCCGGCTCCGGCT-CCGGCTCCGGCTCCGGCTCCG 91 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.07 (7 / 95), avg. gap size = 1.00 (7 / 7) 13 23.87 3.92 1.92 chrXqtel1M 450103 450153 (549847) (AGGGG)n#Simple_repeat 1 52 (0) m_b364s252i7 15283 chrXqtel1M 450103 AGGGAAGGGGA-AAGA-GGCAGTGGAAGGGAGGGGCGGGAGAGGTAAGGG 450150 i -ii - v v i v - vi (AGGGG)n#Simp 1 AGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGG-GAGGGGAGGG 49 chrXqtel1M 450151 CAG 450153 v (AGGGG)n#Simp 50 GAG 52 Matrix = Unknown Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.06 (3 / 50), avg. gap size = 1.00 (3 / 3) 184 38.92 9.62 1.18 chrXqtel1M 452176 452331 (547669) L2#LINE/L2 2419 2587 (495) m_b364s601i5 15284 chrXqtel1M 452176 GGATGGCTCTCGGGTGTTTACAGACCCAACATGT-CAAGACTGGAGTTTC 452224 v vvii ii i - i ii - i - ii i L2#LINE/L2 2419 GGATGTCTAATAGGCATCT-CAAACTTAACATGTCCAAAACT-GAACTCC 2466 chrXqtel1M 452225 ATCTCTGTTCTTCCAAGCTCACTCTTCC--CAGTATTGCTTATTT---TT 452269 vvv vii iii i iii i -- v v ii i --- ? L2#LINE/L2 2467 TGATCTTCCCCCTCAAACCTGCTCCTCCCGCAGTCTTCCCCATCTCAGTN 2516 chrXqtel1M 452270 GGTGGCAGCAACAGCCCCTCCATT-CTC--------AACCTCAAGGCCGT 452310 ii i vv v iii vi - -------- iiii i i L2#LINE/L2 2517 AATGGCAACTCCATCCTTCCAGTTGCTCAGGCCAAAAACCTTGGAGTCAT 2566 chrXqtel1M 452311 TCTCGAGTCTGCCGACTCTCT 452331 i i v iv ivvi L2#LINE/L2 2567 CCTTGACTCCTCTCTTTCTCT 2587 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 62.20 CpG sites = 43, Kimura (unadjusted) = 62.20 Transitions / transversions = 2.53 (43/17) Gap_init rate = 0.05 (7 / 155), avg. gap size = 2.43 (17 / 7) 415 34.09 0.84 3.46 chrXqtel1M 452750 452986 (547014) L2#LINE/L2 1830 2060 (1022) m_b364s601i6 15285 chrXqtel1M 452750 ACTGTCCCCACCCCCTACCTCAACTTTAGTTTCCTCCTTTCT-CAGCCTA 452798 ?vi v vv v vv v vv i v ii i - vv L2#LINE/L2 1830 ACNTCCCCCTCCAGCTACCGCCCCATTTCTCTGCTCCCCTTTACAGCAAA 1879 chrXqtel1M 452799 ACTCCTAGAAAAAGCTGTCTACACTTGGTGCCTCCACTTTTTCACCT-CC 452847 v i i i i v i v ii v - L2#LINE/L2 1880 ACTCCTCGAAAGAGTTGTCTATACTCGCTGTCTCCAATTCCTCTCCTCCC 1929 chrXqtel1M 452848 ACTCACTTCTCAACCCCTCACAATCTGGCTAATTCCGACCTCATCACTCA 452897 i v ii v viiv v --- i v i i v L2#LINE/L2 1930 ATTCTCTCTTGAACCCACTCCAATCAGGC---TTTCGTCCCCACCACTCC 1976 chrXqtel1M 452898 ACTGGAAATGGATCTCTCCAAGGTTATGAATGATCTCTTCTGAACAGCTA 452947 i- iv v ivi i iv i iv ---iiv L2#LINE/L2 1977 ACC-GAAACTGCTCTTGTCAAGGTCACCAATGACCTCCAC---GTTGCTA 2022 chrXqtel1M 452948 ACCCTGGTAGCCTTTTTCTCAGCTATCACCCTGTCAGAC 452986 vi iii i i -vv iiv i i iiiv L2#LINE/L2 2023 AATCCAATGGTC-AATTCTCAGTCCTCATCTTACTTGAC 2060 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 44.53 CpG sites = 43, Kimura (unadjusted) = 46.99 Transitions / transversions = 1.23 (43/35) Gap_init rate = 0.04 (10 / 236), avg. gap size = 1.00 (10 / 10) 275 23.17 10.38 6.36 chrXqtel1M 452972 453077 (546923) MIR#SINE/MIR 107 216 (46) m_b364s601i7 15286 chrXqtel1M 452972 ATCACCCTGTCAGACTCAGTTTCCTCATCTATA------GTATAATAGTA 453015 i v i -- v i ------ v i MIR#SINE/MIR 107 ACCTCTCTGT--GCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATA 154 chrXqtel1M 453016 GTA---ACCTCCAGGGGTTACTGTGGGGGTATATCAAGAAAGCCAATGC- 453061 --- vvi ii i ---- i ivi ii i - MIR#SINE/MIR 155 GTACCTACCTCATAGGGTTGTTGTGAGG----ATTAAATGAGTTAATACA 200 chrXqtel1M 453062 -GTGAAGCCCTGTGGAA 453077 - i v - i MIR#SINE/MIR 201 TGTAAAGCGCT-TAGAA 216 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.85 CpG sites = 16, Kimura (unadjusted) = 28.85 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.10 (11 / 105), avg. gap size = 1.64 (18 / 11) 212 28.33 1.67 0.00 chrXqtel1M 453329 453388 (546612) L2#LINE/L2 2425 2485 (597) m_b364s601i8 15285 chrXqtel1M 453329 CTGCTGGACATCTCAA-CATGACATTTCCAAAAGAGAATTCGTGATTTTC 453377 iv i i - v i v vv i v i L2#LINE/L2 2425 CTAATAGGCATCTCAAACTTAACATGTCCAAAACTGAACTCCTGATCTTC 2474 chrXqtel1M 453378 ACCCCTAGATC 453388 v ii i i L2#LINE/L2 2475 CCCCTCAAACC 2485 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.53 CpG sites = 10, Kimura (unadjusted) = 36.53 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.02 (1 / 59), avg. gap size = 1.00 (1 / 1) 234 25.63 5.00 2.44 chrXqtel1M 453955 454034 (545966) MIR#SINE/MIR 102 183 (79) m_b364s601i9 15287 chrXqtel1M 453955 ACTTCAGCCTCTGCCT-CCTCAGTCTCCTCAACTCCGAGAT---AATAAG 454000 - i viv - i v vii i ---i v MIR#SINE/MIR 102 ACTT-AACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAAT 150 chrXqtel1M 454001 AACAGCAGCGACTTCCAAGTGGTTGTCGTGAGGA 454034 i i v v i vv - i MIR#SINE/MIR 151 AATAGTACCTACCTCATAG-GGTTGTTGTGAGGA 183 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.89 CpG sites = 11, Kimura (unadjusted) = 31.89 Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.05 (4 / 79), avg. gap size = 1.50 (6 / 4) 207 34.81 2.08 4.26 chrXqtel1M 453971 454066 (545934) MIRb#SINE/MIR 125 218 (50) m_b364s601i10 15287 chrXqtel1M 453971 CCTCAGTCTCCTCAACTCCGAGATAATAAGAACAGCAGCGACTTCCAAGT 454020 i v vii i iivi v i ii v v i vv - MIRb#SINE/MIR 125 CCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTACCTCGCAG- 173 chrXqtel1M 454021 GGTTGTCGTGAGGACCCAGGGATGGGACATCGCTAG--AAGTGTTCAG 454066 i iiv --- i i vi vv -- i i i MIRb#SINE/MIR 174 GGTTGTTGTGAGGATTAA---ATGAGATAATGCATGTAAAGCGCTTAG 218 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 47.00 CpG sites = 20, Kimura (unadjusted) = 49.20 Transitions / transversions = 1.67 (20/12) Gap_init rate = 0.05 (5 / 95), avg. gap size = 1.20 (6 / 5) 16 0.00 0.00 0.00 chrXqtel1M 454514 454531 (545469) (AC)n#Simple_repeat 1 18 (0) m_b364s252i8 15288 chrXqtel1M 454514 ACACACACACACACACAC 454531 (AC)n#Simple_ 1 ACACACACACACACACAC 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 13 8.48 4.00 0.00 chrXqtel1M 455079 455103 (544897) (CCTG)n#Simple_repeat 1 26 (0) m_b364s252i9 15289 chrXqtel1M 455079 CCTGCCTGCC-GCCCGCCAGCCTGCC 455103 - i v (CCTG)n#Simpl 1 CCTGCCTGCCTGCCTGCCTGCCTGCC 26 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1) 218 31.03 10.16 6.82 chrXqtel1M 456987 457114 (542886) MIRb#SINE/MIR 94 225 (43) m_b364s601i12 15290 chrXqtel1M 456987 GATCGTGGGCAAGCCCATCTCACTTCCATTTTATGCCTCAGTGGCCCGAG 457036 i v ii- ii v i --- i iv vv iv v MIRb#SINE/MIR 94 GACCTTGGGCAAGTT-ACTTAACCTC---TCTGAGCCTCAGTTTCCTCAT 139 chrXqtel1M 457037 CTATTAACACGAGGGTCGGAGTGACAACGCCCCTCCCAGAGTCATCATGA 457086 i - v i i i --- i i i v -iv v i ii ii MIRb#SINE/MIR 140 CTGT-AAAATGGGGAT---AATAATACC-TACCTCGCAGGGTTGTTGTGA 184 chrXqtel1M 457087 GGATCGAATGG------------AAAGCACTTAGC-CAGTG 457114 ii i------------ i - MIRb#SINE/MIR 185 GGATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAGTG 225 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.22 CpG sites = 26, Kimura (unadjusted) = 42.80 Transitions / transversions = 2.36 (26/11) Gap_init rate = 0.09 (11 / 127), avg. gap size = 2.00 (22 / 11) 238 34.47 1.82 7.69 chrXqtel1M 456987 457096 (542904) MIR#SINE/MIR 87 190 (72) m_b364s601i11 15290 chrXqtel1M 456987 GATCGTGGGCAAGCCCATCTCACTTCCATTTTATGCCTCAGTGGCCCGAG 457036 i v ii- ii v i --- i i vv iv v MIR#SINE/MIR 87 GACCTTGGGCAAGTT-ACTTAACCTC---TCTGTGCCTCAGTTTCCTCAT 132 chrXqtel1M 457037 CTATTAACACGAGGGTCGGAGTGACAACGCC--CCTCCCAGAGTCATCAT 457084 i - v i i i --- i i i iii -- vi i ii ii MIR#SINE/MIR 133 CTGT-AAAATGGGGAT---AATAATAGTACCTACCTCATAGGGTTGTTGT 178 chrXqtel1M 457085 GAGGATCGAATG 457096 ii MIR#SINE/MIR 179 GAGGATTAAATG 190 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 51.07 CpG sites = 27, Kimura (unadjusted) = 51.07 Transitions / transversions = 3.38 (27/8) Gap_init rate = 0.08 (9 / 109), avg. gap size = 1.11 (10 / 9) 231 36.90 2.38 0.00 chrXqtel1M 457810 457893 (542107) C MIR3#SINE/MIR (32) 176 91 m_b364s601i13 15291 chrXqtel1M 457810 AGGACTTTTAGCCATTACTTTGTTCAACCACTCCCTTTTAGAAAGAAGGA 457859 ivii vv i ii v i v ii v v i vi C MIR3#SINE/MIR 176 AGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGA 127 chrXqtel1M 457860 AAC--AGGCCCGGAGATCCGAGGCAGCTGACTCCAG 457893 -- i vvi i iii vi i v C MIR3#SINE/MIR 126 AACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAG 91 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 53.63 CpG sites = 19, Kimura (unadjusted) = 53.63 Transitions / transversions = 1.58 (19/12) Gap_init rate = 0.01 (1 / 83), avg. gap size = 2.00 (2 / 1) 212 41.50 2.67 1.99 chrXqtel1M 459624 459773 (540227) C MIR3#SINE/MIR (10) 198 48 m_b364s601i14 15292 chrXqtel1M 459624 ACCATGGGAGGTTAGACTTAAAGACAAAGACTCTGAGGGCCATCGAGTCC 459673 i i i v i vi ii --- ii ii iii ii v C MIR3#SINE/MIR 198 ATCATAGAATGTCAGAGCTGGA---AGGGACCTTAGAGATCATCTAGTCC 152 chrXqtel1M 459674 CAAC---TTACTGGGTAGGGGAGGGCATTGAGAGCTAGAGAGG-ACAGTG 459719 v v --- i i vvii iv iv i iv i -iv C MIR3#SINE/MIR 151 AACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTG 102 chrXqtel1M 459720 ACTAGGCCAGCATGGCAAAAGCAGTCAAAGCTCTAGTCAGGATGGGATCC 459769 v v ivi vi v iv? i iv vivv i i ivi v C MIR3#SINE/MIR 101 ACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACC 52 chrXqtel1M 459770 CAAG 459773 i C MIR3#SINE/MIR 51 CAGG 48 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 64.25 CpG sites = 38, Kimura (unadjusted) = 66.13 Transitions / transversions = 1.65 (38/23) Gap_init rate = 0.03 (5 / 149), avg. gap size = 1.40 (7 / 5) 181 30.65 3.23 0.00 chrXqtel1M 459762 459823 (540177) MIR1_Amn#SINE/MIR 12 75 (155) m_b364s601i15 15293 chrXqtel1M 459762 TGGGATCCCAAGGCCAGAGCGCTGGACTGGGAGGTAGGAG--CCGGATCA 459809 v i iviv vi i vvii -- i i iv MIR1_Amn#SINE 12 TGTGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGAGACCTGGGTTC 61 chrXqtel1M 459810 CAGTCCCAACTCTG 459823 ? ? ii MIR1_Amn#SINE 62 NANTCCCGGCTCTG 75 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 36.84 CpG sites = 12, Kimura (unadjusted) = 43.00 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.02 (1 / 61), avg. gap size = 2.00 (2 / 1) 188 30.36 5.36 0.00 chrXqtel1M 459777 459832 (540168) MIRc#SINE/MIR 24 82 (186) m_b364s601i16 15293 chrXqtel1M 459777 AGAGCGCTGGACTGGGAGGTAGGAG---CCGGATCACAGTCCCAACTCTG 459823 i v vi i--- i i ivv ii MIRc#SINE/MIR 24 AGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTG 73 chrXqtel1M 459824 TTCCCTTCT 459832 iiv i v MIRc#SINE/MIR 74 CCACTTACT 82 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.57 CpG sites = 11, Kimura (unadjusted) = 40.69 Transitions / transversions = 1.83 (11/6) Gap_init rate = 0.02 (1 / 55), avg. gap size = 3.00 (3 / 1) 217 29.30 13.38 3.87 chrXqtel1M 460866 461007 (538993) C MIR3#SINE/MIR (47) 161 7 m_b364s601i17 15294 chrXqtel1M 460866 CATCTAACTCA-TTTCCTTATTTTATAGAGCTGGAAACTGAGGCT----- 460909 iii -iii i i vvv i----- C MIR3#SINE/MIR 161 CATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAG 112 chrXqtel1M 460910 AGAT----TGAGTTGGCTCATGTCCCATTGGAAGGGAGGCGGGCAACAAG 460955 i ---- v v iv v v iv v? vv --v ---- C MIR3#SINE/MIR 111 AGGTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAG--TGGC----AG 68 chrXqtel1M 460956 AGCT--GACTAGAAGCTGGGCCTCC-AATTTCTGGT---GGCTCT---TG 460996 i-- v ii i -i i i ii ---v --- C MIR3#SINE/MIR 67 AGCCGGGACTAGAACCCAGGTCTCCTGACTCCCAGTCCGTGCTCTCTCTG 18 chrXqtel1M 460997 CCCTGCTGCTC 461007 i v ii C MIR3#SINE/MIR 17 CTCAGCCACTC 7 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.64 CpG sites = 24, Kimura (unadjusted) = 38.89 Transitions / transversions = 1.50 (24/16) Gap_init rate = 0.09 (13 / 141), avg. gap size = 1.92 (25 / 13) 391 22.99 4.60 0.00 chrXqtel1M 461906 461992 (538008) MIRb#SINE/MIR 79 169 (99) m_b364s601i18 15295 chrXqtel1M 461906 ACCTATTAGCTGGGGGATTCTGGGCAAGTCACTTCATCTGTCT--GCCTC 461953 i i v v iii i v i v -- MIRb#SINE/MIR 79 ACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTC 128 chrXqtel1M 461954 AATTTTCTCAACTGTAAAATGGAG--GACAGCACCTTCCTC 461992 i i v i --i i ii v MIRb#SINE/MIR 129 AGTTTCCTCATCTGTAAAATGGGGATAATAATACCTACCTC 169 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.49 CpG sites = 14, Kimura (unadjusted) = 28.49 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.02 (2 / 86), avg. gap size = 2.00 (4 / 2) 194 16.68 0.00 2.78 chrXqtel1M 463702 463738 (536262) C L2b_3end#LINE/L2 (15) 451 416 m_b364s601i19 15296 chrXqtel1M 463702 AAATAATTTACCAAGTGTCCACTGTGTGCCAAGCACT 463738 - ii i i i i ? C L2b_3end#LINE 451 AAATA-TTTACTGAGCGCCTACTGTGTGCCAGGCNCT 416 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 17.23 CpG sites = 6, Kimura (unadjusted) = 20.99 Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 14 20.24 2.04 4.17 chrXqtel1M 465216 465264 (534736) (AGGAAGG)n#Simple_repeat 1 48 (0) m_b364s252i10 15297 chrXqtel1M 465216 AGGAAGCAGTCAGTGAGGAAGGAGGGGAGG-GGAAGAAGAAAGTAGAAAG 465264 v vv - - i - i i v i (AGGAAGG)n#Si 1 AGGAAGGAGGAAG-GAGGAAGGA-GGAAGGAGGAAGGAGGAAGGAGGAAG 48 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.06 (3 / 48), avg. gap size = 1.00 (3 / 3) 222 41.30 0.49 6.22 chrXqtel1M 466814 467017 (532983) C L2#LINE/L2 (195) 2887 2695 m_b364s601i20 15298 chrXqtel1M 466814 ACTTTATATTTGATTCTGGAGGTGTGAAGGAGCCACTG-AGCTTACTGAA 466862 ivv v i iiv v vvii i i - vv vi i C L2#LINE/L2 2887 ACTTTGGCTTTTACTCTGAGTGAGATGGGAAGCCATTGGAGGGTTTTGAG 2838 chrXqtel1M 466863 GAGCGGGCACCTAGGTGGTTACACCTGTGCTTCAGGAAAATCACCTTGGT 466912 v v -- viv vi i ivv i ii i i ii ii ii i C L2#LINE/L2 2837 CAGAGG--AGTGACATGATCTGACTTACGTTTTAAAAGGATCACTCTGGC 2790 chrXqtel1M 466913 GACTGAATGGAGGATGGACTGGAGTAGGGAGAGATTTGAGGCTGGTGGAT 466962 vi vi v i i ? vi vi iv v i v vi - C L2#LINE/L2 2789 TGCTGTGTTGAGAATAGACTGNAGGGGGGCAAGGGTGGAAGCAGGGAGA- 2741 chrXqtel1M 466963 TACACTCCCCCACCCTAGCAGTGACTGCAGGGCTCCAGGCTTGAGGAGAT 467012 --------- viivi vi iv i viv vv iv C L2#LINE/L2 2740 ---------CCAGTTAGGAGGCTATTGCAGTAATCCAGGCGAGAGATGAT 2700 chrXqtel1M 467013 GGAGG 467017 v C L2#LINE/L2 2699 GGTGG 2695 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 61.45 CpG sites = 43, Kimura (unadjusted) = 62.74 Transitions / transversions = 1.19 (43/36) Gap_init rate = 0.06 (13 / 203), avg. gap size = 1.00 (13 / 13) 211 30.00 2.82 1.39 chrXqtel1M 471362 471432 (528568) MIR3#SINE/MIR 116 187 (21) m_b364s601i21 15299 chrXqtel1M 471362 GAGCCTCAGTTTCCACAGCTG-AAAACAGGCAGAATGGCTCTTGATGGTC 471410 i v v - iii vi iv v- v i MIR3#SINE/MIR 116 GGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGA-CTAGATGATC 164 chrXqtel1M 471411 T-GAAAGTCCTCTCCAACCCCAA 471432 -v i ii i i ii MIR3#SINE/MIR 165 TCTAAGGTCCCTTCCAGCTCTGA 187 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.24 CpG sites = 14, Kimura (unadjusted) = 40.24 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.04 (3 / 70), avg. gap size = 1.00 (3 / 3) 19 28.37 2.78 0.00 chrXqtel1M 472952 473023 (526977) (CAGCCC)n#Simple_repeat 1 74 (0) m_b364s252i11 15300 chrXqtel1M 472952 CAGCCAGAGCCCAGGGCCCAGCCCCACCAGGAG-CCCA-CCCCAGTCCCA 472999 vv vi v v vvv - - i (CAGCCC)n#Sim 1 CAGCCCCAGCCCCAGCCCCAGCCCCAGCCCCAGCCCCAGCCCCAGCCCCA 50 chrXqtel1M 473000 GCGCTCGCCCGAAACCCAACCCCA 473023 v iv v iv i (CAGCCC)n#Sim 51 GCCCCAGCCCCAGCCCCAGCCCCA 74 Matrix = Unknown Transitions / transversions = 0.42 (5/12) Gap_init rate = 0.03 (2 / 71), avg. gap size = 1.00 (2 / 2) 28 21.56 0.00 10.71 chrXqtel1M 474042 474165 (525835) (GGCCGGG)n#Simple_repeat 1 112 (0) m_b364s252i12 15301 chrXqtel1M 474042 GGCCCGGGGCCGGGGGGCGGGGACCCCCTGGGTTGCTGGCCAGGGGCGGG 474091 v v --v vv ii vv i v (GGCCGGG)n#Si 1 GGCCGGGGGCCGGGGGCCGGGG--GCCGGGGGCCGGGGGCCGGGGGCCGG 48 chrXqtel1M 474092 GGGCCGGGAGGTCGGGGCCCCAGTTGCCCGGGGGGTCAGGGGATCCTGGT 474141 - i -v - vv v - - v -v - - (GGCCGGG)n#Si 49 GGGCCGGG-GGCCGGGG-GCC-GGGGGCC-GGGGG-CCGGGG-GCC-GG- 90 chrXqtel1M 474142 GTGGCCAGGGGGTCGGGGGCCGGG 474165 - - i (GGCCGGG)n#Si 91 G-GGCC-GGGGGCCGGGGGCCGGG 112 Matrix = Unknown Transitions / transversions = 0.36 (5/14) Gap_init rate = 0.10 (12 / 123), avg. gap size = 1.00 (12 / 12) 13 17.57 0.00 0.00 chrXqtel1M 497457 497483 (502517) (TCC)n#Simple_repeat 1 27 (0) m_b365s252i0 15302 chrXqtel1M 497457 TCCTCCTCTTCTTCCTCTTCCTCCCCC 497483 i i i i (TCC)n#Simple 1 TCCTCCTCCTCCTCCTCCTCCTCCTCC 27 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 20 19.98 4.35 6.67 chrXqtel1M 497526 497617 (502383) (CCCTTCT)n#Simple_repeat 1 90 (0) m_b365s252i1 15303 chrXqtel1M 497526 CCCTTCTCCCCCTTTCTCGGTTTTCCCTT-TCTCCTTC-CGCTT-TCCTT 497572 -- - vv i - - - v - -i (CCCTTCT)n#Si 1 CCCTTCT--CCC-TTCTCCCTTCTCCCTTCTC-CCTTCTCCCTTCTCC-C 45 chrXqtel1M 497573 TTTTCCCCT-TTCCTTCCGGCTTCTTCCTCCTCCCTCCCTCCCTTC 497617 i i - i ivv i i -i (CCCTTCT)n#Si 46 TTCTCCCTTCTCCCTTCTCCCTTCTCCCTTCTCCCT-TCTCCCTTC 90 Matrix = Unknown Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.11 (10 / 91), avg. gap size = 1.00 (10 / 10) 12 9.12 4.17 0.00 chrXqtel1M 497595 497618 (502382) (CTCC)n#Simple_repeat 1 25 (0) m_b365s252i2 15304 chrXqtel1M 497595 CTTCCT-CCTCCCTCCCTCCCTTCC 497618 i - i (CTCC)n#Simpl 1 CTCCCTCCCTCCCTCCCTCCCTCCC 25 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 27 6.54 1.85 5.77 chrXqtel1M 497772 497825 (502175) (CCCTT)n#Simple_repeat 1 52 (0) m_b365s252i3 15305 chrXqtel1M 497772 CCCTTCCCTTCCC-CCCTTTCCCTTCCCTTCCGTTCTCCTTCCCTTTTCC 497820 -i i v - -- (CCCTT)n#Simp 1 CCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTC-CCTTCCC--TTCC 47 chrXqtel1M 497821 CTTCC 497825 (CCCTT)n#Simp 48 CTTCC 52 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.08 (4 / 53), avg. gap size = 1.00 (4 / 4) 17 8.85 0.00 0.00 chrXqtel1M 500763 500786 (499214) (C)n#Simple_repeat 1 24 (0) m_b365s252i4 15306 chrXqtel1M 500763 CCCCCCCTCCCCCCCACCCCCCCC 500786 i v (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCC 24 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 16 23.20 1.92 1.92 chrXqtel1M 500765 500816 (499184) (CCACCT)n#Simple_repeat 1 52 (0) m_b365s252i5 15306 chrXqtel1M 500765 CCCCCTCC-CCCCCACCCCCCCCTTTGAGTTCCTCCTCCAGCTCCACCTC 500813 v - i i v - iv vi v v (CCACCT)n#Sim 1 CCACCTCCACCTCCACCTCCACC-TCCACCTCCACCTCCACCTCCACCTC 49 chrXqtel1M 500814 CAC 500816 (CCACCT)n#Sim 50 CAC 52 Matrix = Unknown Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.00 (2 / 2) 16 3.43 0.00 11.76 chrXqtel1M 501074 501111 (498889) (CCCCA)n#Simple_repeat 1 34 (0) m_b365s252i6 15307 chrXqtel1M 501074 CCCCACCCCGGACCCCACCCCACCCCCGGCCCCACCCC 501111 -- - -i (CCCCA)n#Simp 1 CCCCACCCC--ACCCCACCCCA-CCCC-ACCCCACCCC 34 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.11 (4 / 37), avg. gap size = 1.00 (4 / 4) 18 4.55 0.00 0.00 chrXqtel1M 501661 501683 (498317) (AT)n#Simple_repeat 1 23 (0) m_b365s252i7 15308 chrXqtel1M 501661 ATATATATATATGTATATATATA 501683 i (AT)n#Simple_ 1 ATATATATATATATATATATATA 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 445 32.00 0.80 0.00 chrXqtel1M 504081 504205 (495795) MIR#SINE/MIR 117 242 (20) m_b365s601i0 15309 chrXqtel1M 504081 GCCTCAGTTTCCTCAGCTGGAAAATGGGGATGATGATGGCCCCTCCCTCC 504130 v v i i i iv v v MIR#SINE/MIR 117 GCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTCA 166 chrXqtel1M 504131 CAGAGCCATCGTGAGGAACAAGAGAGGGCACATTCGCAAAA-GCTTAACA 504179 i i iii i vi iv vvv i ivi i i- iv MIR#SINE/MIR 167 TAGGGTTGTTGTGAGGATTAAATGAGTTAATACATGTAAAGCGCTTAGAA 216 chrXqtel1M 504180 TGGGGCCCGGCACAAGAGAAATGCTC 504205 ii v i viiv ii MIR#SINE/MIR 217 CAGTGCCTGGCACATAGTAAGCGCTC 242 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.08 CpG sites = 25, Kimura (unadjusted) = 43.56 Transitions / transversions = 1.67 (25/15) Gap_init rate = 0.01 (1 / 124), avg. gap size = 1.00 (1 / 1) 30 0.00 0.00 0.00 chrXqtel1M 504880 504908 (495092) (CCCAC)n#Simple_repeat 1 29 (0) c_b365s251i0 15310 chrXqtel1M 504880 CCCACCCCACCCCACCCCACCCCACCCCA 504908 (CCCAC)n#Simp 1 CCCACCCCACCCCACCCCACCCCACCCCA 29 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 180 22.22 0.00 0.00 chrXqtel1M 505911 505946 (494054) C MIR3#SINE/MIR (59) 149 114 m_b365s601i1 15311 chrXqtel1M 505911 CCCCTTCCTTTTCCAGATTGGGAAGCTGAGGCCTGG 505946 i v v vi i ii C MIR3#SINE/MIR 149 CCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAG 114 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.96 CpG sites = 5, Kimura (unadjusted) = 26.96 Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 32 0.00 3.23 0.00 chrXqtel1M 508332 508362 (491638) (TG)n#Simple_repeat 1 32 (0) c_b365s251i1 15312 chrXqtel1M 508332 TGTGTGTGTGTGTGTGTGTGTGTGTG-GTGTG 508362 - (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 32 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.03 (1 / 30), avg. gap size = 1.00 (1 / 1) 44 23.26 6.96 1.20 chrXqtel1M 508375 508532 (491468) (GA)n#Simple_repeat 1 167 (0) m_b365s252i8 15313 chrXqtel1M 508375 GAGAGAGAGAGAGAGAGAGAGAG-GAG-GGGAGGGAGGGAGGGA-AGGGG 508421 - - i i i i - i i (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chrXqtel1M 508422 GTAGAGTGAAAGGGTGGGAAAG-GACAGAAGGAGAGATGGAGTGA-AGGA 508469 - v i i v i i - v ii vi v - ii (GA)n#Simple_ 51 G-AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 99 chrXqtel1M 508470 ACAG-GAGAGAGCGAGAGA-AAAGAGAAAGAAGGATGGGGGAGGGAG-GA 508516 v - v - i i ii - i i i - (GA)n#Simple_ 100 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA-GAGAGAGAGAGAGA 148 chrXqtel1M 508517 GA-AGAG-GAG-GTGAGAG 508532 - - - v (GA)n#Simple_ 149 GAGAGAGAGAGAGAGAGAG 167 Matrix = Unknown Transitions / transversions = 2.75 (22/8) Gap_init rate = 0.08 (13 / 157), avg. gap size = 1.00 (13 / 13) 18 0.00 0.00 0.00 chrXqtel1M 510810 510829 (489171) (TG)n#Simple_repeat 1 20 (0) m_b365s252i9 15314 chrXqtel1M 510810 TGTGTGTGTGTGTGTGTGTG 510829 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTG 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 192 34.41 9.92 1.53 chrXqtel1M 514797 514917 (485083) C MIRb#SINE/MIR (92) 176 46 m_b365s601i2 15315 chrXqtel1M 514797 ATCCTGTGAG-CATGGATC-TTGGCCCCACTTAGGAGGGGAGGAAATCGA 514844 i i -i v v i- iv i viv iv ii C MIRb#SINE/MIR 176 ACCCTGCGAGGTAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGA 127 chrXqtel1M 514845 AACCCAGTGT-CTCCAGTCACATGGCCGGCTGGCCACTCAACAACTA--- 514890 ii i v v-v iv v v v ii-- i v i v v --- C MIRb#SINE/MIR 126 GGCTCAGAGAGGTTAAGTAACTTGCCCAA--GGTCACACAGCTAGTAAGT 79 chrXqtel1M 514891 -----GGCTGAGATTTGAGCTCAGGTCC-TCTG 514917 -----i i i i i i i- C MIRb#SINE/MIR 78 GGCAGAGCCGGGATTCGAACCCAGGTCTGTCTG 46 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.42 CpG sites = 25, Kimura (unadjusted) = 48.27 Transitions / transversions = 1.56 (25/16) Gap_init rate = 0.07 (8 / 120), avg. gap size = 1.75 (14 / 8) 204 34.12 10.66 1.50 chrXqtel1M 514819 514940 (485060) C MIR3#SINE/MIR (62) 146 14 m_b365s601i3 15315 chrXqtel1M 514819 CCCCACTTAGGAGGGGAGGAAATCGAAACCCAGTGT-CTCCAGTCACATG 514867 i i viv iv ii ii v v-v vv v v C MIR3#SINE/MIR 146 CCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTG 97 chrXqtel1M 514868 GCCGGCTGGCCACTCAACAA-CTAG-------GCTGAGATTTGAGCTCAG 514909 v ii-- i v i ? -i ------- i i i v i i C MIR3#SINE/MIR 96 CCCAA--GGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGAACCCAG 49 chrXqtel1M 514910 GTCCTCTG----TCATCTCTTATTCTCGCTGCTCA 514940 ii ----i vii v ii v C MIR3#SINE/MIR 48 GTCTCCTGACTCCCAGTCCGTGCTCTCTCTGCTCA 14 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.60 CpG sites = 25, Kimura (unadjusted) = 48.27 Transitions / transversions = 1.56 (25/16) Gap_init rate = 0.05 (6 / 121), avg. gap size = 2.50 (15 / 6) 13 13.12 0.00 0.00 chrXqtel1M 516061 516086 (483914) (CCCTT)n#Simple_repeat 1 26 (0) m_b365s252i10 15316 chrXqtel1M 516061 CCCCTCCCTTCCTTTCCCTCCCCTTC 516086 i i i (CCCTT)n#Simp 1 CCCTTCCCTTCCCTTCCCTTCCCTTC 26 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 541 35.96 3.07 0.00 chrXqtel1M 517386 517613 (482387) MIR#SINE/MIR 3 237 (25) m_b365s601i4 15317 chrXqtel1M 517386 AGAACAACACAATGGATGGGCAAGCTGGGCCTGG---CAGCATGAC-AAG 517431 v i i i i v ii vivi v vi --- vv v -ii MIR#SINE/MIR 3 AGTATAGCATAGTGGTTAAGAGCACGGGCTCTGGAGCCAGACTGCCTGGG 52 chrXqtel1M 517432 TTCCAATCTGGCCTTGGGTCCTTAAGAACCGTGACAGGCTAGGCAAGTCA 517481 v iv v iv viv vv i i vv vvi i i MIR#SINE/MIR 53 TTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTA 102 chrXqtel1M 517482 CTTCACGTGTCTG--CCTCAGTTTCCTCAACTGTAACATGGGAATAATAG 517529 v v v -- v v i i MIR#SINE/MIR 103 CTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAA 152 chrXqtel1M 517530 CAGCATC-AGCTGCCAGAGTTATTGTGGAGACCAAGTGAGATCCTTTTTA 517578 i i i - v vvi i i ii ii i v vv viv i MIR#SINE/MIR 153 TAGTACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATACATG 202 chrXqtel1M 517579 TACAGTGACCAGCTCGGCGTCTGGCATGGAGGAAG 517613 v i vii vv i i i iiv v MIR#SINE/MIR 203 TAAAGCGCTTAGAACAGTGCCTGGCACATAGTAAG 237 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 49.19 CpG sites = 42, Kimura (unadjusted) = 50.05 Transitions / transversions = 1.05 (42/40) Gap_init rate = 0.02 (4 / 227), avg. gap size = 1.75 (7 / 4) 552 32.60 1.09 1.09 chrXqtel1M 517431 517613 (482387) MIRb#SINE/MIR 59 241 (27) m_b365s601i5 15317 chrXqtel1M 517431 GTTCCAATCTGGCCTTGGGTCCTTAAGAACCGTGACAGGCTAGGCAAGTC 517480 v iv v iv viv vv i i vv vvi i i MIRb#SINE/MIR 59 GTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTT 108 chrXqtel1M 517481 ACTTCACGTGTCTG--CCTCAGTTTCCTCAACTGTAACATGGGAATAATA 517528 v v v -- v v i MIRb#SINE/MIR 109 ACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATA 158 chrXqtel1M 517529 GCAGCATCAGCTGCCAGAGTTATTGTGGAGACCAAGTGAGATCCTTTTTA 517578 ii v --i v vv i i ii ii i vv viv i MIRb#SINE/MIR 159 ATACC--TACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCATG 206 chrXqtel1M 517579 TACAGTGACCAGCTCGGCGTCTGGCATGGAGGAAG 517613 v i vii v i i i iiv v MIRb#SINE/MIR 207 TAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAG 241 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.40 CpG sites = 29, Kimura (unadjusted) = 43.36 Transitions / transversions = 0.97 (29/30) Gap_init rate = 0.02 (3 / 182), avg. gap size = 1.33 (4 / 3) 15 13.19 2.86 2.86 chrXqtel1M 519934 519968 (480032) (CAG)n#Simple_repeat 1 35 (0) m_b366s252i0 15318 chrXqtel1M 519934 CAG-AGGAGCAGTCACCTGCAGCAGCAGCAGCGGCA 519968 - v - v v i (CAG)n#Simple 1 CAGCAGCAGCAG-CAGCAGCAGCAGCAGCAGCAGCA 35 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 16 25.68 0.00 0.00 chrXqtel1M 523141 523186 (476814) (CATCGT)n#Simple_repeat 1 46 (0) m_b366s252i1 15319 chrXqtel1M 523141 CATCGTCATCGTCGTCCTCATCCCCCTCTTCTCCTTCCTCGTCATC 523186 i v vi v v vi v v (CATCGT)n#Sim 1 CATCGTCATCGTCATCGTCATCGTCATCGTCATCGTCATCGTCATC 46 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 12 23.51 3.33 5.08 chrXqtel1M 523189 523248 (476752) (GAGGCG)n#Simple_repeat 1 59 (0) m_b366s252i2 15320 chrXqtel1M 523189 GAGGAGGAGGCGGACCGTGTGAGG-AGAGG-GGAAGGGGAGGGGGAGGGC 523236 v -v i - -i - i v v - (GAGGCG)n#Sim 1 GAGGCGGAGGCGGA-GGCG-GAGGCGGAGGCGGAGGCGGAGGCGGA-GGC 47 chrXqtel1M 523237 TGGGCCGGACGC 523248 v i v v (GAGGCG)n#Sim 48 GGAGGCGGAGGC 59 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.08 (5 / 59), avg. gap size = 1.00 (5 / 5) 34 25.07 1.87 1.87 chrXqtel1M 523281 523387 (476613) (TCC)n#Simple_repeat 1 107 (0) m_b366s252i3 15321 chrXqtel1M 523281 TCGTCCTCCTCGTCTTCCTCCTCCTCTTCCTCCTCATCCTGACT-CTCGT 523329 v v i i v -v - v (TCC)n#Simple 1 TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT-CCTCCTCCT 49 chrXqtel1M 523330 CCTCATCCTCATTGCTACCGCTGCT-GTCCTCCTCTTGCGTGTGCTCCTC 523378 v -i v v iv v -v i v viv v (TCC)n#Simple 50 CCTCCTCCTC-CTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTC 98 chrXqtel1M 523379 CTCGTCCTC 523387 v (TCC)n#Simple 99 CTCCTCCTC 107 Matrix = Unknown Transitions / transversions = 0.38 (6/16) Gap_init rate = 0.04 (4 / 106), avg. gap size = 1.00 (4 / 4) 16 10.71 0.00 3.23 chrXqtel1M 523600 523631 (476369) (GGGGA)n#Simple_repeat 1 31 (0) m_b366s252i4 15322 chrXqtel1M 523600 GGGGAGGGGAGGGAGGTGGGTGGGGAGGGGAG 523631 - iv v (GGGGA)n#Simp 1 GGGGAGGGGAGGG-GAGGGGAGGGGAGGGGAG 31 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 25 22.94 7.38 2.34 chrXqtel1M 524586 524707 (475293) (GGGAGAGA)n#Simple_repeat 1 128 (0) m_b366s252i5 15323 chrXqtel1M 524586 GGGAG-GAGAGGAGAGATGG-GA-AGGGAGACAGGGAG-GAGGGAAAGGG 524631 - - v - - v - i i (GGGAGAGA)n#S 1 GGGAGAGAG-GGAGAGAGGGAGAGAGGGAGAGAGGGAGAGAGGGAGAGAG 49 chrXqtel1M 524632 GGCAGAAACTG-GAAAGGCA-AGACGTAG-GAGGGCAATGTGGG-GTGGG 524677 - i vv - i v - v v - - iv v - v i (GGGAGAGA)n#S 50 GG-AGAGAGGGAGAGAGGGAGAGAGGGAGAGAGGG-AGAGAGGGAGAGAG 97 chrXqtel1M 524678 GGAGAG-GAAAGAGAGGTCTGGAGGAAGAGA 524707 - ii vvvi i (GGGAGAGA)n#S 98 GGAGAGAGGGAGAGAGGGAGAGAGGGAGAGA 128 Matrix = Unknown Transitions / transversions = 0.77 (10/13) Gap_init rate = 0.10 (12 / 121), avg. gap size = 1.00 (12 / 12) 187 20.17 5.88 12.50 chrXqtel1M 525491 525575 (474425) MamTip2b#DNA/hAT-Tip100 368 447 (2) m_b366s601i1 15324 chrXqtel1M 525491 TGGGACACTTAGATGAGGGGAAAGGGAGCCTG---GGATGGTCACATCAC 525537 v i i --------- --- v v MamTip2b#DNA/ 368 TGGGCCACTCAGGTGAGGGG---------CTGTGAGGATGGTCACAACAG 408 chrXqtel1M 525538 TCTGTGAA-AGCAGGGTCCAGCTGAGG-GAAAAGCAGCAG 525575 v ii- -vvi iv - i v MamTip2b#DNA/ 409 TCTGGGGGCAGCAGGG-AGGGCCCAGGCGAAAGGCAGGAG 447 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 23.36 CpG sites = 7, Kimura (unadjusted) = 23.36 Transitions / transversions = 0.88 (7/8) Gap_init rate = 0.15 (13 / 84), avg. gap size = 1.15 (15 / 13) 246 30.11 1.06 1.06 chrXqtel1M 526167 526260 (473740) Charlie4#DNA/hAT-Charlie 3236 3329 (49) m_b366s502i0 15325 chrXqtel1M 526167 ACTATATTTGAACAGAAATGGCTTTGCTTGGCATCCTATGGA-GCTGCTT 526215 v i v v i ivi vv v -vi ii Charlie4#DNA/ 3236 ACTATATTTCAATATAATTGGTTTCCTTTGTAATCCTATGTATTTTATTT 3285 chrXqtel1M 526216 TCTGTATTTAAACACATTGTTCTAAACATGGAGTCTGCAGTCTCC 526260 v i v i i iv - i iii v i Charlie4#DNA/ 3286 TATGCATTTAAAAACATTATTCTGAGAA-GGGGTCCATAGGCTTC 3329 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 39.50 CpG sites = 16, Kimura (unadjusted) = 39.50 Transitions / transversions = 1.33 (16/12) Gap_init rate = 0.02 (2 / 93), avg. gap size = 1.00 (2 / 2) 412 32.27 12.04 3.86 chrXqtel1M 526908 527339 (472661) L2#LINE/L2 1956 2421 (661) m_b366s601i2 15326 chrXqtel1M 526908 GGCTTCTGACCTCATCATTCCGCAAAAATAACTC----CAAAGTTATCAA 526953 ii v i i i i vi ivi ---- i i i L2#LINE/L2 1956 GGCTTTCGTCCCCACCACTCCACCGAAACTGCTCTTGTCAAGGTCACCAA 2005 chrXqtel1M 526954 TTCTCTCTTAGCCAGCAAATACAAGAG-CAATTCTCA-------CCTTAC 526995 vvi ivv iiivi v vi - -------i L2#LINE/L2 2006 TGACCTCCACGTTGCTAAATCCAATGGTCAATTCTCAGTCCTCATCTTAC 2055 chrXqtel1M 526996 TCAACTTCCCTGTGGCTTTGGACACTGTCAATCATCCTCTTTTCCTC--A 527043 ii i ?i v ii v v v ii ii i ii i i-- L2#LINE/L2 2056 TTGACCTNTCAGCAGCATTTGACACAGTTGATCACTCCCTCCTTCTTGAA 2105 chrXqtel1M 527044 ATACTCCTGTCTCTGTATTTGCAGGACA--AT-CTTGGCCCTGGTTCTCC 527090 i iiiv v vvii v -- i- i--i i L2#LINE/L2 2106 ACACTTTCTTCACTTGGCTTCCAGGACACCACACTC--TCCTGGTTTTCC 2153 chrXqtel1M 527091 TTCTTCCTCTCTGAGCACTC--TCTCCATTTCC---------TCCTCCAG 527129 i v v iv i -- vi i --------- -- L2#LINE/L2 2154 TCCTACCTCACTGGCCGCTCCTTCTCAGTCTCCTTTGCTGGTTCCTCC-- 2201 chrXqtel1M 527130 ATCATACCGCCAAAC---CGACA--GGTATCCTCTGGGTGTCTGTCCTGG 527174 - vi v i v ---?i i-- vi v i ii vv v v L2#LINE/L2 2202 -TCATCTCCCCGACCTCTNAACGTTGGAGTGCCCCAGGGCTCAGTCCTTG 2250 chrXqtel1M 527175 GTCC--------------TCTGGACTTACTGCCCTGGGGGATATCCTCAG 527210 v -------------- iv i - ? v v v vi L2#LINE/L2 2251 GACCTCTTCTCTTCTCTATCTACACTCACT-CCCTNGGTGATCTCATCCA 2299 chrXqtel1M 527211 CTCCCAAGGATTGA---ACTCTTTCTATGCTGAAGATTCCCAACTCCTGC 527257 v i v v v --- iv i v v i v -- vv L2#LINE/L2 2300 GTCTCATGGCTTTAAATACCATCTATATGCTGATGACTCCCAAAT--TTA 2347 chrXqtel1M 527258 TATCTAGCTAACCTCTGGTCATTTCCACTGCCCCACAGACATCTAGTTAT 527307 -- i i -- i v v i v vv iv - -- - L2#LINE/L2 2348 TATCT--CCAGC--CCGGACCTCTCCCCTGAACTCCAGAC-TC--G-TAT 2389 chrXqtel1M 527308 GTCCAAAACAGA--ACTCAATCTCTCCCCCTAAA 527339 i -- v v-- i iv v i ii L2#LINE/L2 2390 ATCC--AACTGCCTACTCGACATCTCCACTTGGA 2421 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 41.01 CpG sites = 76, Kimura (unadjusted) = 44.05 Transitions / transversions = 1.31 (76/58) Gap_init rate = 0.07 (31 / 431), avg. gap size = 2.26 (70 / 31) 206 25.68 1.53 10.83 chrXqtel1M 527450 527580 (472420) L2#LINE/L2 2674 2793 (289) m_b366s601i3 15326 chrXqtel1M 527450 CTGCCTATTGTCCTGGTGCAGCAGG-ACC-TCATCTCTCCACACCTGGAC 527497 - iiii v -- v- - ---i i L2#LINE/L2 2674 CTGCC-ACCACCCTGGTCCA--AGCCACCATCATCTCTC---GCCTGGAT 2717 chrXqtel1M 527498 TATTCCAATACCCCACTGGTGGCCCTGCCTGCCTCAGATCCCTCCCCCTA 527547 i v v iv iiiv vi v i v- i i v -- L2#LINE/L2 2718 TACTGCAATAGCCTCCTAACTGGTCTCCCTGCTTCC-ACCCTTGCCCC-- 2764 chrXqtel1M 527548 GACCCTTCTAGTCCATTCTCAACTTAGTCGCCA 527580 --- ? - i vi iv L2#LINE/L2 2765 ---CCTNC-AGTCTATTCTCAACACAGCAGCCA 2793 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 30.86 CpG sites = 18, Kimura (unadjusted) = 32.14 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.12 (15 / 130), avg. gap size = 1.00 (15 / 15) 13 9.14 8.11 2.56 chrXqtel1M 527715 527751 (472249) (TCTCACT)n#Simple_repeat 1 39 (0) m_b366s252i6 15327 chrXqtel1M 527715 TCTCACTGTCTCA-TTCTCCCTCCTCAC--CTCACCTCTC 527751 - - v i -- i (TCTCACT)n#Si 1 TCTCACT-TCTCACTTCTCACTTCTCACTTCTCACTTCTC 39 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.08 (3 / 36), avg. gap size = 1.33 (4 / 3) 260 28.03 9.45 4.51 chrXqtel1M 527847 527973 (472027) L2d2_3end#LINE/L2 408 540 (15) m_b366s601i4 15326 chrXqtel1M 527847 CATGTGCATGATGTCTGGTGTCTTCCTGGTTAGATTATAATAAGATCCTT 527896 i i- v -- i iiii ---i v L2d2_3end#LIN 408 CACGTGT-TTATGTCT--TGTCTCCCCAACTAGATT---GTAAGCTCCTT 451 chrXqtel1M 527897 GAGGG-ACAGAC--TGTC-CACAGCGCTGGGGAT-------AGAGATAAG 527935 - vi -- -i i viv vv v ------- v viv L2d2_3end#LIN 452 GAGGGCAGGGACCATGTCTTATACTTCTTTGTATCCCCCACAGCGCCTAG 501 chrXqtel1M 527936 CA-AGTACCTGGCACAAAATAAGTGTTTAACAAATACTT 527973 - i v v i i i i i i i L2d2_3end#LIN 502 CACAGTGCCTTGCACACAGTAGGCGCTCAATAAATATTT 540 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 33.70 CpG sites = 21, Kimura (unadjusted) = 36.35 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.09 (11 / 126), avg. gap size = 1.64 (18 / 11) 16 21.74 5.66 0.00 chrXqtel1M 528890 528942 (471058) (TAAA)n#Simple_repeat 1 56 (0) m_b366s252i7 15328 chrXqtel1M 528890 TAAATAAA-AGGCTAATAAATAAAT-AAT-AATAATTTAAAAAAAAAAAA 528936 - iiiv - - v v v v v (TAAA)n#Simpl 1 TAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATA 50 chrXqtel1M 528937 AAAAAA 528942 v (TAAA)n#Simpl 51 AATAAA 56 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.06 (3 / 52), avg. gap size = 1.00 (3 / 3) 17 4.13 0.00 0.00 chrXqtel1M 528962 528986 (471014) (AAAA)n#Simple_repeat 1 25 (0) m_b366s252i8 15329 chrXqtel1M 528962 AAAAAAAAAAAAAAAAAAAAATAAA 528986 v (AAAA)n#Simpl 1 AAAAAAAAAAAAAAAAAAAAAAAAA 25 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 224 28.57 0.00 0.00 chrXqtel1M 530593 530648 (469352) MIR1_Amn#SINE/MIR 18 73 (157) m_b366s601i5 15330 chrXqtel1M 530593 CTTGTGGAGAGGACACAGGGCTTGGGCTTGAGAGACTTGGGTTTGAATTA 530642 v v ii v i v i i i i i? ? iv MIR1_Amn#SINE 18 CTAGTGGATAGAGCACTGGACTGGGACTCGGGAGACCTGGGTTCNANTCC 67 chrXqtel1M 530643 CAACTC 530648 ii MIR1_Amn#SINE 68 CGGCTC 73 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 33.52 CpG sites = 11, Kimura (unadjusted) = 39.78 Transitions / transversions = 2.20 (11/5) Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0) 12 23.47 0.00 0.00 chrXqtel1M 533881 533915 (466085) (CCAACC)n#Simple_repeat 1 35 (0) m_b366s252i9 15331 chrXqtel1M 533881 CCAAGCCCATCCCCACTGCCACCACCAACCCCAAC 533915 v v viv v v (CCAACC)n#Sim 1 CCAACCCCAACCCCAACCCCAACCCCAACCCCAAC 35 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 281 34.76 8.60 5.93 chrXqtel1M 535617 536093 (463907) L3#LINE/CR1 2240 2728 (1371) m_b366s601i6 15332 chrXqtel1M 535617 AGTGACCAGGATGCTCAGGTTCACAATGAGCTGATGATGGCCCAGGGAA- 535665 v vi i v v i ii v v v v vv iii - L3#LINE/CR1 2240 AGTGTCAGGAAGGCTAAAGCCCAGAATGAGCTGAGGCTTGCAAAAAAAAA 2289 chrXqtel1M 535666 -GCCAAGGTCAACAAAAAGGTGAGGGTTTCT---GGCTGATATCTCGAGG 535711 - i v ---? i i i ---i - i iiv v L3#LINE/CR1 2290 TGCTAAGGACAACAAAAA---NAAGGCTTTTCAAAGCT-ATGTTCGGAGC 2335 chrXqtel1M 535712 GAAAGGCAAGAATGGAAGAAGAGATGCAACTGCTGTTT-GGATGGATGTG 535760 ii v i --- ii? v v -- i i - iii vv L3#LINE/CR1 2336 AGAAGGAAAAA---GAAAGNGACAGGC--CCGCTGCTTGGGGCAGATGGC 2380 chrXqtel1M 535761 ACCATGATTCCCAGGCACCAGAGACAGGGAGGGGCGGCTAGA-------G 535803 iiv - vv iiiv v ii vi ii vi vi -------v L3#LINE/CR1 2381 GTAATG-TTAACAGATGACAGAGAGAAAGCAGAACTACTCAACTCCTATT 2429 chrXqtel1M 535804 CTGCCTCTGGCT--TCCATCAAGGACGATGACC----GACCTTTGGGATG 535847 i i i v -- i vi i ---- --- i v L3#LINE/CR1 2430 TTGCTTCCGTCTTCTCTATCAAGGAGAATGATCTTCAGAC---TGGAAAG 2476 chrXqtel1M 535848 G-----ACAAGCCTC---AAGAGAAA--CGCGGCTC-AGAT-GCTGGGGA 535885 ----- i v --- ii --i vi i - - v i L3#LINE/CR1 2477 GGTAGAACAAACATCGTTAAGAGGGAATTGAAGCCCAAGATAGGTGAGGA 2526 chrXqtel1M 535886 AGAAGGGAG-GGGC-CCAGGTTACCCCAAGTGAATTCAGGTCACCCGGTC 535933 iiv vi - i - vi iii iii i i i v v i L3#LINE/CR1 2527 GATAGTAAGAGAGCACCTAGCCGCTTTAAATGAGTTCAAGTCTCCAGGCC 2576 chrXqtel1M 535934 CAAAAGAGGTGGAGAGCCTCCCGTCTCCCTTGGAGCTTGAGAGAACCGGC 535983 i v iv -----i v i-------- ivvi i iv L3#LINE/CR1 2577 CAGACGAATT-----ACATCCCA--------GGGTACTGAAAGAACTTGC 2613 chrXqtel1M 535984 AGGTGGGGCTGCAGAG-TACCGTGGAGGACCATAGGAAAGATCATGGAAA 536032 i v iii i i-ii i v ivi i - vv i i i i L3#LINE/CR1 2614 AGATGTGATCGCGGAACCGCTGTCGGTAATC-TTTGAGAAATCACGGAGA 2662 chrXqtel1M 536033 ATGGGAGC-ATGCCCACGAGACTGGTGAATGGTAGAATG------CCACT 536075 i i v-i - vi v vv i - ------ i ? L3#LINE/CR1 2663 ACGGAAGAGGTG-CCAGAAGACTGGAGACGGGCA-AATGTNGTNCCTANT 2710 chrXqtel1M 536076 TTTCAAGAGGGATGAGAG 536093 v i vi i L3#LINE/CR1 2711 TTTAAAAAGGGAAAAAAG 2728 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 45.42 CpG sites = 100, Kimura (unadjusted) = 50.06 Transitions / transversions = 1.79 (100/56) Gap_init rate = 0.10 (46 / 476), avg. gap size = 1.52 (70 / 46) 388 29.73 1.40 3.57 chrXqtel1M 536213 536355 (463645) L3#LINE/CR1 3172 3311 (788) m_b366s601i7 15332 chrXqtel1M 536213 TATCTATGACTTCTGGA--AAGGCCTGCCTGGGATCTGTCTCTCAGATTT 536260 v -- -- i v ivvv v -- ii v i L3#LINE/CR1 3172 TATCAATGACTT--GGATGAAGACATAGAAGGCAT--GCTTATCAAATTT 3217 chrXqtel1M 536261 TCAGGTGATAAGAAGCGGGGAGAAATAATGAAGATGGTAGATGACAGAGT 536310 v i i vi v ii iiv v i ? i i L3#LINE/CR1 3218 GCAGATGACACAAAGCTGGGAGGGATAGCTAATACGNTGGATGACAGAAT 3267 chrXqtel1M 536311 TGGGGGTCTAAAAGGACCTCAACGGTCTAGAGCATTGGGCTGAAA 536355 iii iv - ? i i i v i i iv i L3#LINE/CR1 3268 CAAGATTC-AAAANGATCTCGACAGGCTGGAACGATGGGCCGAAA 3311 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 35.20 CpG sites = 26, Kimura (unadjusted) = 40.16 Transitions / transversions = 1.73 (26/15) Gap_init rate = 0.04 (6 / 142), avg. gap size = 1.17 (7 / 6) 19 0.00 0.00 0.00 chrXqtel1M 537535 537555 (462445) (T)n#Simple_repeat 1 21 (0) m_b366s252i10 15333 chrXqtel1M 537535 TTTTTTTTTTTTTTTTTTTTT 537555 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTT 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 239 23.19 7.25 0.00 chrXqtel1M 540060 540128 (459872) Charlie4a#DNA/hAT-Charlie 386 459 (49) m_b366s502i1 15334 chrXqtel1M 540060 GCTTTCTCTATAAGCCTAAGTATTGTACTTTATGCACTCAAAATCTTTCT 540109 i i i i v v v i i i v v v Charlie4a#DNA 386 GTTTCCTTTGTAATCCTATGTATTTTATTTTATGCATTTAAAAACATTAT 435 chrXqtel1M 540110 TCGGAGA-----TCTATAAGCTTC 540128 v ----- i i Charlie4a#DNA 436 TCTGAGAAGGGGTCCATAGGCTTC 459 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 28.17 CpG sites = 9, Kimura (unadjusted) = 28.17 Transitions / transversions = 1.29 (9/7) Gap_init rate = 0.01 (1 / 68), avg. gap size = 5.00 (5 / 1) 308 32.99 2.97 0.97 chrXqtel1M 542171 542271 (457729) L2d2_3end#LINE/L2 445 547 (8) m_b366s601i8 15335 chrXqtel1M 542171 GCTTCTCCAGGCCAGAGCCCAAGCCTTGCCATTCTTTGCAT---CAACAG 542217 i iv v i v v i iivv i --- v L2d2_3end#LIN 445 GCTCCTTGAGGGCAGGGACCATGTCTTATACTTCTTTGTATCCCCCACAG 494 chrXqtel1M 542218 TACTTAGCACGGTGCCACATATGTACTTAAGTGTTCAAGAAATACTTATT 542267 ii i i viii iii -v i i i v i i L2d2_3end#LIN 495 CGCCTAGCACAGTGCCTTGCACACA-GTAGGCGCTCAATAAATATTTGTT 543 chrXqtel1M 542268 GCTT 542271 v L2d2_3end#LIN 544 GATT 547 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 42.08 CpG sites = 22, Kimura (unadjusted) = 46.14 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.02 (2 / 100), avg. gap size = 2.00 (4 / 2) 338 28.80 7.74 2.84 chrXqtel1M 544146 544313 (455687) C MIR3#SINE/MIR (3) 205 30 m_b366s601i9 15336 chrXqtel1M 544146 TCCTGGGATCATAGA-T-TTAGAGCTGCAAGGGACCTTTGGAGGCCAACT 544193 v i i - - i v - i ii v C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACC-TTAGAGATCATCT 157 chrXqtel1M 544194 CCT-TAACTCC--CATTTTACAGTTCAAAAAAT--AGGTTAAGACAAACT 544238 vv -i i -- v v ii i-- iiv -i iv C MIR3#SINE/MIR 156 AGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGA-GAGGT 108 chrXqtel1M 544239 GAAG-GACTCAACTAGGAT-A---AGGTGGTTCAAAGTGTTGGAGGCAGG 544283 - iiv i i i - --- v?i --- vii v i C MIR3#SINE/MIR 107 GAAGTGACTTGCCCAAGGTCACACAGCNAGTT---AGTGGCAGAGCCGGG 61 chrXqtel1M 544284 ATTTGAACTGAGATCT-TTGACTTGAAATCC 544313 i v iv i -i ivv i C MIR3#SINE/MIR 60 ACTAGAACCCAGGTCTCCTGACTCCCAGTCC 30 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 37.09 CpG sites = 30, Kimura (unadjusted) = 38.14 Transitions / transversions = 1.76 (30/17) Gap_init rate = 0.08 (14 / 167), avg. gap size = 1.29 (18 / 14) 235 32.54 7.03 3.66 chrXqtel1M 544163 544347 (455653) C MIR1_Amn#SINE/MIR (38) 192 2 m_b366s601i10 15336 chrXqtel1M 544163 TAGAGCTGCAAGGGACCTTT----GGAGGCCAAC-TCCTTAACTCCCATT 544207 v - i v i v---- i ii- v v - C MIR1_Amn#SINE 192 TAGATCT-CAAAGCACTTTACAAAGGAGGTCAGTATCATTATC-CCCATT 145 chrXqtel1M 544208 TTACAGTTCAAAAAAT--AGGTTAAGACAAACTGAAGGACTCAACTAGGA 544255 v v ii i-- i?v v iii?i iv iiv i i i C MIR1_Amn#SINE 144 TTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTTGCCCAAGG 95 chrXqtel1M 544256 TAAGGTGGTTCA-AAGTGTTGGAGGCAGGATTTGAACTGAGATCTTTGAC 544304 v v?ii i?vi-? vii v i ? ? iv i ---- C MIR1_Amn#SINE 94 TCACNCAGCNGGCNAGTGGCAGAGCCGGGANTNGAACCCAGGTCT----C 49 chrXqtel1M 544305 TTGAAATCCCAAACCA-TG---TAT-CATGTGACCTAATTGCCTATCT 544347 ii - i iv - --- - ivv vv i vi C MIR1_Amn#SINE 48 CCG-AGTCCCAGTCCAGTGCTCTATCCACTAGACCACACTGCCTCCCT 2 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 44.83 CpG sites = 35, Kimura (unadjusted) = 47.08 Transitions / transversions = 1.52 (35/23) Gap_init rate = 0.08 (14 / 184), avg. gap size = 1.43 (20 / 14) 17 10.98 0.00 9.30 chrXqtel1M 545352 545398 (454602) (AAACATC)n#Simple_repeat 1 43 (0) m_b366s252i11 15337 chrXqtel1M 545352 AAACATTAAACATCATAAATTAAATTCATTCTAAACATCAAACATCA 545398 i v v i -- - - (AAACATC)n#Si 1 AAACATCAAACATCAAACATCAAA--CA-TC-AAACATCAAACATCA 43 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.09 (4 / 46), avg. gap size = 1.00 (4 / 4) 189 28.74 8.82 2.78 chrXqtel1M 553529 553596 (446404) C MIRc#SINE/MIR (187) 81 10 m_b366s601i11 15338 chrXqtel1M 553529 GTTAGTGTCTGAAGCTGGAATTGAATTTGGATCCTCCTGAC------TCC 553572 v v v iv v v i iiii i i ------ C MIRc#SINE/MIR 81 GTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCC 32 chrXqtel1M 553573 AGTGATCTTTATCTACTGTGTCAC 553596 v -- i iii C MIRc#SINE/MIR 31 AGTGCTCTT--TCCACTGCACCAC 10 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 35.17 CpG sites = 12, Kimura (unadjusted) = 37.68 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.04 (3 / 67), avg. gap size = 2.67 (8 / 3) 338 19.49 0.00 7.14 chrXqtel1M 553759 553863 (446137) Charlie4a#DNA/hAT-Charlie 26 123 (385) m_b366s502i2 15339 chrXqtel1M 553759 GGATACAAATCCAAAAGGGATCTATGACACTTGCACAAGAAAAAAAAATT 553808 v v --- i i ii - v iii i --- Charlie4a#DNA 26 GGATAGAATTC---AGGGGGTCCGTGA-ACTTGGATGGGGAAAAAAA--- 68 chrXqtel1M 553809 TTTCTTCTTTATTTTCAATAACCTCAAACTGATATTTAGCATTTTCTCAA 553858 v v v v v i iv Charlie4a#DNA 69 TTACATCTTTATTTTCACTAACCTCTAACTGAAATTTAGCATTTCCTTCA 118 chrXqtel1M 553859 ATTAT 553863 Charlie4a#DNA 119 ATTAT 123 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 21.19 CpG sites = 10, Kimura (unadjusted) = 22.62 Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.07 (7 / 104), avg. gap size = 1.00 (7 / 7) 305 22.47 0.00 7.06 chrXqtel1M 553862 553952 (446048) Charlie4a#DNA/hAT-Charlie 421 505 (3) m_b366s502i3 15340 chrXqtel1M 553862 ATTTAAAAGTATCATTTTGAAAAGAGTTCAGGCAGAGGGTTTCTCACATT 553911 ii i i i i v --- v v ivi v i Charlie4a#DNA 421 ATTTAAAAACATTATTCTGAGAAGGGGTC---CATAGGCTTCACCAGACT 467 chrXqtel1M 553912 GCTAAAGAGTTCCATGACTCACACAAAAAAGTTAAGAACCC 553952 i i v i-- - i Charlie4a#DNA 468 GCCAAAGGGGTCCATGG--CACA-AAAAAGGTTAAGAACCC 505 Matrix = 20p47g.matrix Kimura (with divCpGMod) = 27.42 CpG sites = 13, Kimura (unadjusted) = 27.42 Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.07 (6 / 90), avg. gap size = 1.00 (6 / 6) 14 8.35 3.85 0.00 chrXqtel1M 554090 554115 (445885) (TAAA)n#Simple_repeat 1 27 (0) m_b366s252i12 15341 chrXqtel1M 554090 TAAA-AAACAAACAAATAAATAAATAA 554115 - i i (TAAA)n#Simpl 1 TAAATAAATAAATAAATAAATAAATAA 27 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.04 (1 / 25), avg. gap size = 1.00 (1 / 1) 421 24.95 9.55 5.52 chrXqtel1M 555128 555284 (444716) C MIR#SINE/MIR (10) 252 90 m_b366s601i12 15342 chrXqtel1M 555128 AGCATTTGCATACAGTGCCTGCTTTGTGGCAGGGACTGTGCTAAGTGCTT 555177 i -- vv i i i v v v v i C MIR#SINE/MIR 252 AACATTT--ATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGCGCTT 205 chrXqtel1M 555178 T------------TTATCTGATCCTCCCAACAATCCTA--ACTTAGATGC 555213 ------------ i i i v i -- vv i i C MIR#SINE/MIR 204 TACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGGTAGGTAC 155 chrXqtel1M 555214 TGTCACTG-ACCCATTTTACAACTGAAAAAACTGAGACAAACAATCTGAC 555262 i i i i-v iv ii i -- ---- v C MIR#SINE/MIR 154 TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGC--ACA----GAG 111 chrXqtel1M 555263 AAGTGAAGTCCACTTTTTCAAG 555284 i v -v vii C MIR#SINE/MIR 110 AGGTTAAGT-AACTTGCCCAAG 90 Matrix = 25p47g.matrix Kimura (with divCpGMod) = 29.11 CpG sites = 22, Kimura (unadjusted) = 31.09 Transitions / transversions = 1.47 (22/15) Gap_init rate = 0.08 (12 / 156), avg. gap size = 2.00 (24 / 12) 28 23.30 0.00 0.00 chrXqtel1M 557141 557200 (442800) (A)n#Simple_repeat 1 60 (0) m_b367s252i0 15343 chrXqtel1M 557141 AAAAAACAAACAAACAAACAAACAAATAAATAAATAAAATAAAGAAAAAA 557190 v v v v v v v v v i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chrXqtel1M 557191 AGAAAAGAAA 557200 i i (A)n#Simple_r 51 AAAAAAAAAA 60 Matrix = Unknown Transitions / transversions = 0.33 (3/9) Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0) 22 15.61 0.00 0.00 chrXqtel1M 557323 557358 (442642) (A)n#Simple_repeat 1 36 (0) m_b367s252i1 15344 chrXqtel1M 557323 AAAAAACAAAAACAAAAAAACAAACAAATAAAAAAA 557358 v v v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 36 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 17 0.00 0.00 0.00 chrXqtel1M 557504 557522 (442478) (A)n#Simple_repeat 1 19 (0) m_b367s252i2 15345 chrXqtel1M 557504 AAAAAAAAAAAAAAAAAAA 557522 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAA 19 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 543 30.78 15.34 1.16 chrXqtel1M 559231 559608 (440392) L3#LINE/CR1 3571 4001 (98) m_b367s601i1 15346 chrXqtel1M 559231 GCTAG--AGACCAC--CCAGAATAGATGCTAGCAGTTCTCGGTACAACCG 559276 i -- -- ii i v- vvv v ii v vv L3#LINE/CR1 3571 GCTGGTCAGACCACATCTGGAGTAT-TGCGTTCAGTTCTGGGCGCCACAT 3619 chrXqtel1M 559277 GTTAAGACCAACACTGGCA---------GCAATCAGAGGAAGGCAATGAA 559317 v vvi i i --------- ivi ii i iv i L3#LINE/CR1 3620 TTTAAGAGGGACATTGACAAACTGGAGCGCGTCCAGAGGAGAGCGACCAG 3669 chrXqtel1M 559318 CAGGGTTAAGGGTCTTGAGTCCAAACCATATTTGGGTCAAGTGAAAGTAG 559367 v v v v iv vii vv iv iiv i v v L3#LINE/CR1 3670 GATGGTGAAGGGTCTGGAAACCATGTCATATGAGGAACGGTTGAAGGAAC 3719 chrXqtel1M 559368 TCAGGATTGTTTAGTCTGGAAAAGGGA----CTGGAGGAG---------- 559403 vi - i i i ----i i ---------- L3#LINE/CR1 3720 TGGGGA-TGTTTAGCCTGGAGAAGAGAAGACTTAGAGGAGACATGATAGC 3768 chrXqtel1M 559404 -----TCAAGTA---GAAAAG-------------GAGGA---AGACTTTA 559429 ----- i --- ii ------------- i--- - L3#LINE/CR1 3769 TGTCTTCAAATATTTGAAGGGCTGTCATGTGGAAGAGGGATTAGAC-TTA 3817 chrXqtel1M 559430 TGCTCAGT-ACTACA-AGG-CAGAAATCACGAACACTTGGGGAAAG--GG 559474 v vv -i v - - v - v v v v v i --iv L3#LINE/CR1 3818 TTCTGTGTGGCTCCAGAGGGCAGAACT-AGGACCAATGGGTGGAAGTTAC 3866 chrXqtel1M 559475 AAAGATATAGATTGAAACTTTAACATAAAGAAAAGCCTCCCAACAATCAG 559524 ii vii vvii - i i i i i i i i L3#LINE/CR1 3867 AGGGAGGCAGATTTCGGC-TCAATATAAGGAAGAACTTTCTAACAATCAG 3915 chrXqtel1M 559525 AACTGTCTGCAAGTGGAAGGGGTGGCCTCCAGAGGTGGT-AGATTCCCAT 559573 i iiv i v iv v? i - v i i L3#LINE/CR1 3916 AGCTGTCCAAAAATGGAATGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGT 3965 chrXqtel1M 559574 TTGTGGAGAAATTCAAATGAAGGCTGAA-GATCACT 559608 ivv ivi iiii i - i L3#LINE/CR1 3966 CACTGGAGGTGTTCAAGCAGAGGCTGGATGACCACT 4001 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.24 CpG sites = 67, Kimura (unadjusted) = 41.06 Transitions / transversions = 1.40 (67/48) Gap_init rate = 0.05 (20 / 377), avg. gap size = 3.15 (63 / 20) 204 15.15 0.00 0.00 chrXqtel1M 561149 561181 (438819) L3#LINE/CR1 4064 4096 (3) m_b367s601i2 15347 chrXqtel1M 561149 AGGTTCCTTTCAACTCTGAAAGTCTGTCATTCT 561181 i i i v v L3#LINE/CR1 4064 AGGTCCCTTCCAACTCTGAGATTCTGTGATTCT 4096 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 17.11 CpG sites = 3, Kimura (unadjusted) = 17.11 Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 199 27.99 12.63 6.19 chrXqtel1M 561253 561450 (438550) C L3b_3end#LINE/CR1 (470) 736 527 m_b367s601i3 15348 chrXqtel1M 561253 CATGGCCTTGCTAAAAAAGCGGTCCTCA-ATCCAAATGACAG--CTCCAT 561299 i v i vi ?v- i ?v i - v ii i - -- v C L3b_3end#LINE 736 CACGTCCCTTTTAAANT-GTGGNGCCCAGAACTGAACG-CAGTACTCCAG 689 chrXqtel1M 561300 GTGGGGCCTGAGGAGGACAGAGCCTAACAAAACT-CCATCTCCCT--ACC 561346 ? ? vv vi ivv i iii ??-i i --?i C L3b_3end#LINE 688 NTGNGGCCTGACCAGCGCAGAGTAGAGCGGGANNATCACCTCCCTTGNTC 639 chrXqtel1M 561347 T----------CCCCTGC-AACGTGGCCCAAAAGATCACATTTTCTTAGG 561385 ---------- ii i- i ii -- i vv --- C L3b_3end#LINE 638 TGTCGGCGATNCTTCTGTTAATGCAGCCCAA--GATCGCATTAGCTT--- 594 chrXqtel1M 561386 GGATTTCCAAGGCCAT-TC-TA-TGTCGATTCACACTGAGCTTGT----- 561427 --- ivivi ii- -i - ii i i i i----- C L3b_3end#LINE 593 ---TTTTGGCAGCCGCGTCGCACTGCTGACTCATATTGAGCTTGCGGTCA 547 chrXqtel1M 561428 ACTAAAAAGGCCCCCAGATCTTT 561450 --- i C L3b_3end#LINE 546 ACTAAAA---CCCCCAGGTCTTT 527 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 31.77 CpG sites = 37, Kimura (unadjusted) = 39.27 Transitions / transversions = 2.47 (37/15) Gap_init rate = 0.11 (22 / 197), avg. gap size = 1.73 (38 / 22) 198 28.00 3.94 12.82 chrXqtel1M 562334 562460 (437540) C MIR3#SINE/MIR (40) 168 52 m_b367s601i4 15349 chrXqtel1M 562334 TAGAATTC-TCTAACGTAACCCCAG-ACTTTTCAGACAAGAATACAGAGG 562381 iv - iivi vv- i v ii i v v C MIR3#SINE/MIR 168 TAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGG 119 chrXqtel1M 562382 TTCACCCACAAAGATGAGGTGACT---CAAATGTTTCACAGCTAACTTGC 562428 ---- v i i i --- v v iv -------- C MIR3#SINE/MIR 118 ----CCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGC-------- 81 chrXqtel1M 562429 CTTAGTTATTAGCAGATCCAGACCCCAAAACC 562460 --? v i v i i-v i i C MIR3#SINE/MIR 80 --NAGTTAGTGGCAGAGCCGGG-ACTAGAACC 52 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.18 CpG sites = 17, Kimura (unadjusted) = 35.59 Transitions / transversions = 1.21 (17/14) Gap_init rate = 0.14 (18 / 126), avg. gap size = 1.11 (20 / 18) 291 24.99 3.88 2.88 chrXqtel1M 565307 565409 (434591) MIRb#SINE/MIR 3 106 (162) m_b367s601i5 15350 chrXqtel1M 565307 GAAGGGCTAGC-TGGCACAGTAGATGGAGAGC-TGGGCCT-GTAGTCAGA 565353 i - - ii i --i -i i - v MIRb#SINE/MIR 3 GAGGGGC-AGCGTGGTGCAGTGGA--AAGAGCACGGGCTTTGGAGTCAGA 49 chrXqtel1M 565354 -AGACCCGAGTTAAAATCCAGTATCAGATACTTCCTAACTCTAGGACCCT 565402 - i i vi v vv v vi v i v iv i MIRb#SINE/MIR 50 CAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTT 99 chrXqtel1M 565403 GGGAAAG 565409 v MIRb#SINE/MIR 100 GGGCAAG 106 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.06 CpG sites = 14, Kimura (unadjusted) = 30.93 Transitions / transversions = 1.27 (14/11) Gap_init rate = 0.07 (7 / 102), avg. gap size = 1.00 (7 / 7) 306 30.43 1.09 0.00 chrXqtel1M 565318 565409 (434591) MIRc#SINE/MIR 11 103 (165) m_b367s601i6 15350 chrXqtel1M 565318 TGGCACAGTAGATGGAGAGCTGGGCCTGTAGTCAG-AAGACCCGAGTTAA 565366 ii i vi vi i i v - i i vi MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chrXqtel1M 565367 AATCCAGTATCAGATACTTCCTAACTCTAGGACCCTGGGAAAG 565409 i v vv v vi v i v iv i v MIRc#SINE/MIR 61 AGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAG 103 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 38.00 CpG sites = 15, Kimura (unadjusted) = 39.80 Transitions / transversions = 1.15 (15/13) Gap_init rate = 0.01 (1 / 91), avg. gap size = 1.00 (1 / 1) 203 29.48 7.79 8.23 chrXqtel1M 565504 565747 (434253) C L2a_3end#LINE/L2 (1) 516 274 m_b367s601i8 15351 chrXqtel1M 565504 TTCCTTTATCATCAACCAAAAGTTATGAAGTGCCTAC-ACGGGCCAGG-A 565551 v i -- v v v vi i - i v - C L2a_3end#LINE 516 TTCATTCAT--TCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCA 469 chrXqtel1M 565552 CTGTGTTTACATGCTGAGGAT------GTGAAAAGAA-----AGGGGGCC 565590 - i vii i ------ v i ----- iii v C L2a_3end#LINE 468 CTGT-TCTAGGCGCTGGGGATACAGCAGTGAACAAAACAGACAAAAGTCC 420 chrXqtel1M 565591 TTGA------GGAGCTCACAACCTAATCAGGGAAGACAATAAGAACAAAC 565634 i v------ i vi i vi i --i v i C L2a_3end#LINE 419 CTGCCCTCATGGAGCTTACATTCTAGTGGGGGGAGACA--GACAATAAAC 372 chrXqtel1M 565635 CAATCTCTAAAGACAAGGTAGAATACTAAGAATTTCAAGAGGGAAAAATT 565684 v ------ i i - i ivv v v iiv vi v v C L2a_3end#LINE 371 AAAT------AAATAA-GTAAAATATATAGTATGTCAGATGGTGATAAGT 329 chrXqtel1M 565685 TCAGTTGAGATTTCAAGGAAGCTGGGGAAAGCAGGAGGAGAGGAAGAGTT 565734 v vi v --vv vi v v ---- i v i v ? C L2a_3end#LINE 328 GCTATGGAGA--AAAATAAAGCAGGGTA----AGGGGGATAGGGAGTGNT 285 chrXqtel1M 565735 GAGAAGGTAAAGG 565747 i -- ?i i C L2a_3end#LINE 284 GGG--GGNGAGGG 274 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.98 CpG sites = 34, Kimura (unadjusted) = 38.43 Transitions / transversions = 1.06 (34/32) Gap_init rate = 0.10 (25 / 243), avg. gap size = 1.56 (39 / 25) 251 26.99 15.61 3.63 chrXqtel1M 565504 565676 (434324) C L2b_3end#LINE/L2 (1) 465 273 m_b367s601i7 15351 chrXqtel1M 565504 TTCCTTTATCATCAACCAAAAGTTATGAAGTGCCTAC-ACGGGCCAGG-A 565551 v i -- v v v ivi i -ii v -? C L2b_3end#LINE 465 TTCATTCAT--TCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCN 418 chrXqtel1M 565552 CTGTGTTTACATGCTGAGGAT------GTGAA-AAGAAAGG---GGGCCT 565591 i - vii i ------ - v i--- v i C L2b_3end#LINE 417 CTGTGCT-AGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCC 369 chrXqtel1M 565592 TGA------GGAGCTCACAACCTAATCAGGGAAGACA---ATAAGAACAA 565632 v------ ii i -i i --- ivi ? i C L2b_3end#LINE 368 TGCCCTCACGGAGCTCACAGTCTAGT-GGGGGAGACAGACATGTAANCAG 320 chrXqtel1M 565633 ACCAATC----TCTAAA--GACAAGGTAGAATACTAAGAATTTCAAGAGG 565676 - ?----i i i -- i i i-- ii iivvi v C L2b_3end#LINE 319 A-CAATNATAACCCAGAGTGGCAGGGTAGG--ACTGGGGGGGCCCAGAGG 273 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.08 CpG sites = 31, Kimura (unadjusted) = 36.10 Transitions / transversions = 2.21 (31/14) Gap_init rate = 0.09 (16 / 172), avg. gap size = 2.12 (34 / 16) 20 7.86 0.00 0.00 chrXqtel1M 566099 566125 (433875) (A)n#Simple_repeat 1 27 (0) m_b367s252i3 15352 chrXqtel1M 566099 AAAAAAAAAACAAAAAAAACAAAAAAA 566125 v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAA 27 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 442 30.92 4.57 1.48 chrXqtel1M 568698 568894 (431106) L1ME4c_3end#LINE/L1 353 555 (275) m_b367s551i0 15353 chrXqtel1M 568698 AAATATGCATACCCTTTGAGCCATCAGTGTCTGTTATGGAAA---A---- 568740 i v v vi i vi vv v i --- ---- L1ME4c_3end#L 353 AAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTTATCCT 402 chrXqtel1M 568741 AAAAAAAAAA--AAAAAAAAGGAAAAAGCACCCACACGTGCAAAAATGTT 568788 ii v --v i ---i i i ii i i L1ME4c_3end#L 403 AAGGAAATAATTCAAAAGAAGGAAAAAGC---TATATGCACGAAGATGTT 449 chrXqtel1M 568789 TGTGGCAGCCCTTTTAGTAGTGGCAAAGAACTGGAGACTGAGTAGATGCC 568838 ii v vi v vi i i i i i i vivv i i L1ME4c_3end#L 450 CATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTC 499 chrXqtel1M 568839 CATCAGTTGGAGGATAGCTGAATAAATTATGGTATATGAATGTTATAGAA 568888 v i v i i i i i i i v? iviv i L1ME4c_3end#L 500 CAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGATGGAA 549 chrXqtel1M 568889 TATTAT 568894 L1ME4c_3end#L 550 TATTAT 555 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.31 CpG sites = 39, Kimura (unadjusted) = 42.11 Transitions / transversions = 1.86 (39/21) Gap_init rate = 0.03 (6 / 196), avg. gap size = 2.00 (12 / 6) 453 29.27 0.00 0.00 chrXqtel1M 568772 568894 (431106) L1ME3F_3end#LINE/L1 430 552 (438) m_b367s551i1 15353 chrXqtel1M 568772 ACACGTGCAAAAATGTTTGTGGCAGCCCTTTTAGTAGTGGCAAAGAACTG 568821 i i i ii i v v v i i i L1ME3F_3end#L 430 ACATGTACAAGAATGTTCATAGCAGCACTGTTCGTAATAGCAAAAAACTG 479 chrXqtel1M 568822 GAGACTGAGTAGATGCCCATCAGTTGGAGGATAGCTGAATAAATTATGGT 568871 i vivvi i i iiiv i i v i i L1ME3F_3end#L 480 GAAACAACCCAAATGTCCATCGACAGGAGAATGGATAAATAAATTGTGGT 529 chrXqtel1M 568872 ATATGAATGTTATAGAATATTAT 568894 vv iiiv i L1ME3F_3end#L 530 ATATTCACACAATGGAATATTAT 552 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.75 CpG sites = 25, Kimura (unadjusted) = 39.18 Transitions / transversions = 2.27 (25/11) Gap_init rate = 0.00 (0 / 122), avg. gap size = 0.0 (0 / 0) 15 29.81 0.00 0.00 chrXqtel1M 570166 570218 (429782) (AAATAAA)n#Simple_repeat 1 53 (0) m_b367s252i4 15354 chrXqtel1M 570166 AAATCAAAAATCAAACCAATAGTTTTAAAAATAAAAAAAGAAAAATAAAG 570215 v v vvv v ivv v vi i (AAATAAA)n#Si 1 AAATAAAAAATAAAAAATAAAAAATAAAAAATAAAAAATAAAAAATAAAA 50 chrXqtel1M 570216 AAT 570218 (AAATAAA)n#Si 51 AAT 53 Matrix = Unknown Transitions / transversions = 0.30 (3/10) Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0) 596 24.14 2.07 0.00 chrXqtel1M 571583 571727 (428273) C MIR#SINE/MIR (37) 225 78 m_b367s601i9 15355 chrXqtel1M 571583 CAGTTACTGTGCTAAATA-TTTAC-TATAGTCAATGCTTTGA-CATTATG 571629 vi v iii- - i v v v vv i - v i ii C MIR#SINE/MIR 225 CAGGCACTGTTCTAAGCGCTTTACATGTATTAACTCATTTAATCCTCACA 176 chrXqtel1M 571630 ACAACCCTGAGAGGTAGGCCCTATTATTAGCCCGATTTTATAAATGAGGA 571679 iv iv v v i i C MIR#SINE/MIR 175 ACAACCCTATGAGGTAGGTACTATTATTATCCCCATTTTACAGATGAGGA 126 chrXqtel1M 571680 AACTGAGGCAAACAGAGGCTCCATGACTTGCCTCAGATCACACAGCTA 571727 v v i vvi i iv i C MIR#SINE/MIR 125 AACTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTA 78 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.35 CpG sites = 18, Kimura (unadjusted) = 29.43 Transitions / transversions = 1.06 (18/17) Gap_init rate = 0.02 (3 / 144), avg. gap size = 1.00 (3 / 3) 186 28.79 8.47 5.79 chrXqtel1M 572365 572482 (427518) L2d_3end#LINE/L2 378 498 (18) m_b367s601i10 15356 chrXqtel1M 572365 TCTTGTCTTCCC--CTTGATACTGCAAGCTCAGAGGGGGAACAGAGCAAT 572412 i -- v -- i vvv i v vi v vv L2d_3end#LINE 378 TCTTGTCTCCCCAACTAGAT--TGTAAGCTCCTTGAGGGCAGGGACCATG 425 chrXqtel1M 572413 TC----ACTCTTT----GTACTCCAATCTCTAGCACCAAGAACAAGGCCT 572454 ---- ? ---- v i -----i i v v iv iv L2d_3end#LINE 426 TCTTATACTNTTTTNTCGTTCCCCA-----CAGCGCCTAGCACAGTGCTG 470 chrXqtel1M 572455 GGCACATAGTACCTGCGTGTTAAATGCT 572482 i vvi viiv i L2d_3end#LINE 471 AGCACATAGTAGGCGCTCAATAAATACT 498 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.25 CpG sites = 14, Kimura (unadjusted) = 36.99 Transitions / transversions = 0.78 (14/18) Gap_init rate = 0.09 (10 / 117), avg. gap size = 1.70 (17 / 10) 285 28.86 4.08 0.99 chrXqtel1M 572368 572465 (427535) L2b_3end#LINE/L2 333 433 (33) m_b367s601i11 15356 chrXqtel1M 572368 TGTCTTCCCCTTGATACTGCAAGCTCAGAGGGGGAACAGAGCAATTCACT 572417 i viv v ii v v i v vi v i?v vv L2b_3end#LINE 333 TGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGT 382 chrXqtel1M 572418 CTTTGTACTCCA----ATCTCTAGCACCAAGAACAAGGCCTGGCACATAG 572463 - v v i---- i i i v v i? i L2b_3end#LINE 383 CTT-GTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAG 431 chrXqtel1M 572464 TA 572465 L2b_3end#LINE 432 TA 433 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.97 CpG sites = 13, Kimura (unadjusted) = 37.73 Transitions / transversions = 0.87 (13/15) Gap_init rate = 0.02 (2 / 97), avg. gap size = 2.50 (5 / 2) 202 27.09 0.00 2.08 chrXqtel1M 572524 572572 (427428) L2d_3end#LINE/L2 466 513 (3) m_b367s601i12 15356 chrXqtel1M 572524 TGCTGAACACGTAGTAAACACTTTACTAAACATTTACAGATTGACTGAT 572572 i i ii i - i v i i iiv i L2d_3end#LINE 466 TGCTGAGCACATAGTAGGCGC-TCAATAAATACTTGTTGATTGATTGAT 513 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 33.22 CpG sites = 11, Kimura (unadjusted) = 36.83 Transitions / transversions = 5.50 (11/2) Gap_init rate = 0.02 (1 / 48), avg. gap size = 1.00 (1 / 1) 252 27.70 7.84 0.92 chrXqtel1M 572651 572752 (427248) MIR1_Amn#SINE/MIR 22 130 (100) m_b367s601i13 15357 chrXqtel1M 572651 TAGCTAGAG----GGGCTGAA--TCAGGAGGACATTAGCACAAATCCAGG 572694 i v ---- i ii-- i - v vi iv ? ? v MIR1_Amn#SINE 22 TGGATAGAGCACTGGACTGGGACTCGGGAG-ACCTGGGTTCNANTCCCGG 70 chrXqtel1M 572695 CTCAGACACTTCCTAGCTGTGTGACCCCAGACAGGTGATTCATCCTGTTT 572744 v v ?v i? ? iii i i v i i?v v i MIR1_Amn#SINE 71 CTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGTCACTTNACCTCTCT 120 chrXqtel1M 572745 --GCCTCAAT 572752 -- i MIR1_Amn#SINE 121 GNGCCTCAGT 130 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 36.91 CpG sites = 17, Kimura (unadjusted) = 38.68 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.04 (4 / 101), avg. gap size = 2.25 (9 / 4) 337 28.41 2.27 0.00 chrXqtel1M 572665 572752 (427248) MIRc#SINE/MIR 39 128 (140) m_b367s601i14 15357 chrXqtel1M 572665 GAATCAGGAGGACATTAGCACAAATCCAGGCTCAGACACTTCCTAGCTGT 572714 i i v vi iv i i v v v v MIRc#SINE/MIR 39 GAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGT 88 chrXqtel1M 572715 GTGACCCCAGACAGGTGATTCATCCTGTTT--GCCTCAAT 572752 iii i i v i i v v i -- i MIRc#SINE/MIR 89 GTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGT 128 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.91 CpG sites = 15, Kimura (unadjusted) = 36.75 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.01 (1 / 87), avg. gap size = 2.00 (2 / 1) 12 28.45 0.00 0.00 chrXqtel1M 573738 573776 (426224) (AAA)n#Simple_repeat 1 39 (0) m_b367s252i5 15358 chrXqtel1M 573738 AAGAAAAAGAAACAAAGGGAGCATAAAAAAAAAAAAAAA 573776 i i v iii iv v (AAA)n#Simple 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 39 Matrix = Unknown Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 341 33.55 3.92 2.58 chrXqtel1M 575373 575525 (424475) MIR3#SINE/MIR 49 203 (5) m_b367s601i15 15359 chrXqtel1M 575373 CTGGATTTGGTAGCAGCAGGCCTGCC-C--ACT-GCTGTGTTGCCTTAGC 575418 i i-- ivv i vi - -- - vi i v MIR3#SINE/MIR 49 CTGGGTTC--TAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGG 96 chrXqtel1M 575419 TGAACCACCCTGGGCCACATGAGACCTCAGCTTCCCTAACTGTAAAATAT 575468 ii ii iiii-- v vivi i i ii v iv MIR3#SINE/MIR 97 CAAGTCACTTCA--CCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGA 144 chrXqtel1M 575469 AGAGACTGGACTAAATGGCCTCTAACATGACTTCCAGATTTAAC--TCTA 575516 i i ii i ii vi vv v i i -- MIR3#SINE/MIR 145 GGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCTA 194 chrXqtel1M 575517 CATTTGTAT 575525 iiv v MIR3#SINE/MIR 195 TGATTCTAT 203 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 46.16 CpG sites = 34, Kimura (unadjusted) = 47.52 Transitions / transversions = 2.12 (34/16) Gap_init rate = 0.05 (8 / 152), avg. gap size = 1.25 (10 / 8) 282 22.64 2.88 15.05 chrXqtel1M 576488 576591 (423409) L2c_3end#LINE/L2 368 460 (18) m_b367s601i16 15360 chrXqtel1M 576488 TCCACATAGACTG-GAGCTCCTGGAAAAAAGGGCCTGGCCTGTCTTGTT- 576535 - - v iiiv v i --- i - L2c_3end#LINE 368 TCCAC-TAGACTGTGAGCTCCTTGAGGGCAGGGACCG---TGTCTTATTC 413 chrXqtel1M 576536 -TTTGAAATTATACCCCAAATACTAGGCACTGACCTATAGTAGGTGCTTA 576584 - i ---- i i v iii iv ------ i i L2c_3end#LINE 414 ATCT----TTGTATCCCCAGCGCCTGGCAC------ATAGTAGGCGCTCA 453 chrXqtel1M 576585 ATAACTG 576591 v L2c_3end#LINE 454 ATAAATG 460 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 22.53 CpG sites = 14, Kimura (unadjusted) = 27.30 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.17 (17 / 103), avg. gap size = 1.00 (17 / 17) 16 22.13 0.00 0.00 chrXqtel1M 577559 577590 (422410) (A)n#Simple_repeat 1 32 (0) m_b367s252i7 15361 chrXqtel1M 577559 AAAAACCAAAACCAAAAACAAAAACAAAAAAA 577590 vv vv v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 32 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 19 11.81 2.70 0.00 chrXqtel1M 577560 577596 (422404) (AAAAAC)n#Simple_repeat 1 38 (0) m_b367s252i8 15361 chrXqtel1M 577560 AAAACCAAAACCAAAAACAAAAACAAAAA-AACCACAA 577596 v v - vv (AAAAAC)n#Sim 1 AAAAACAAAAACAAAAACAAAAACAAAAACAAAAACAA 38 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1) 31 3.01 0.00 0.00 chrXqtel1M 577847 577880 (422120) (CCCCA)n#Simple_repeat 1 34 (0) c_b367s251i0 15362 chrXqtel1M 577847 CCCCACCCCACCCCACCCCACACCACCCCACCCC 577880 v (CCCCA)n#Simp 1 CCCCACCCCACCCCACCCCACCCCACCCCACCCC 34 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 198 23.68 0.00 0.00 chrXqtel1M 580890 580927 (419073) MIRc#SINE/MIR 77 114 (154) m_b367s601i17 15363 chrXqtel1M 580890 CTTCTTAGCTATATGATCCTGGCCAGGTCATTTAACCT 580927 vi i i i i v i i MIRc#SINE/MIR 77 CTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCT 114 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.11 CpG sites = 7, Kimura (unadjusted) = 30.11 Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 184 21.88 0.00 0.00 chrXqtel1M 580940 580971 (419029) C MIRc#SINE/MIR (154) 114 83 m_b367s601i18 15364 chrXqtel1M 580940 AGGTTAAGTGACCTGGCCAGGATCATATAGTT 580971 i v i i i i i C MIRc#SINE/MIR 114 AGGTTAAGTGACTTGCCCAAGGTCACACAGCT 83 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.68 CpG sites = 6, Kimura (unadjusted) = 27.68 Transitions / transversions = 6.00 (6/1) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 339 30.13 3.52 6.52 chrXqtel1M 581264 581405 (418595) C L2d2_3end#LINE/L2 (0) 555 418 m_b367s601i19 15365 chrXqtel1M 581264 TCACAGCAGGTTAACCACCACTAATGAAGTACCCACTCTGTGCATGGCAC 581313 v v ii i v vi i v vi ii i v v C L2d2_3end#LIN 555 TCAAATCAAATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCAC 506 chrXqtel1M 581314 TATGCTCTGTGCT---GGGGATACAAAGAGGAGCCAGAACAT--TTCTTG 581358 i vv i --- i viiv - -- i i C L2d2_3end#LIN 505 TGTGCTAGGCGCTGTGGGGGATACAAAGAAGTATAAG-ACATGGTCCCTG 457 chrXqtel1M 581359 TCTTCAGGAATGTTCACGGTCTAATTAATAGAGAGGGAGAAAAGTCA 581405 i i i i - i i ii i -------i v v C L2d2_3end#LIN 456 CCCTCAAGGA-GCTTACAATCTAGTT-------GGGGAGACAAGACA 418 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.43 CpG sites = 26, Kimura (unadjusted) = 40.19 Transitions / transversions = 1.86 (26/14) Gap_init rate = 0.08 (11 / 141), avg. gap size = 1.27 (14 / 11) 18 12.06 0.00 0.00 chrXqtel1M 581841 581868 (418132) (TG)n#Simple_repeat 1 28 (0) m_b367s252i9 15366 chrXqtel1M 581841 TGTGTGTGTGTGTGTGCGCGTGCGTGTG 581868 i i i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTG 28 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 305 31.69 5.19 4.92 chrXqtel1M 582874 583258 (416742) C L1PB_orf2#LINE/L1 (1213) 2081 1696 m_b367s551i2 15367 chrXqtel1M 582874 TCTCCTTGATCCATTTGTTCATTCCCTTAATTTCTTT-TTTTGTTTCATT 582922 ii v i v --v v v - i i v C L1PB_orf2#LIN 2081 TCCTCTTTACCGATTTG--GATGCCCTTTATTTCTTTCTCTTGTCTGATT 2034 chrXqtel1M 582923 GCTGCAACTAGCACTTCATACACTAAGCCAAATAACAGTTATTAGAAGGG 582972 viii v vvii v iii ? iv vi v iv C L1PB_orf2#LIN 2033 GCTCTGGCTAGGACTTCCAGTACTATGTTGAANAGAAGTGGTGAGAGTGG 1984 chrXqtel1M 582973 TCACTCTTATTTTA-TCCAGATCTAAAAGGAAAGGGCTCAAAATTATAAC 583021 v ii i i i- v v ii i v vi iv v v vv C L1PB_orf2#LIN 1983 GCATCCTTGTCTTGTTCCAGTTCTCAGGGGGAATGCTTTCAACTTTTCCC 1934 chrXqtel1M 583022 AACTACACAATATACTGGATCTTGATTT----TAGATATGCTATTTAACA 583067 v i vvii v? ii v v v i ---- i- - vi C L1PB_orf2#LIN 1933 CATTCAGTATNATGTTGGCTGTGGGTTTGTCATAGATG-GCT-TTTATTA 1886 chrXqtel1M 583068 CAGTAAGGAAATAT-TCACTTACA--CCTATGTT--TTATGGTATTT--T 583110 ?v --- - v ?i -- v v -- v v - -- C L1PB_orf2#LIN 1885 CNTTAAGG---TATGTCCCTTNTATGCCGATTTTGCTGAGGGT-TTTAAT 1840 chrXqtel1M 583111 CAAAAAGAGAAGTGAAAGTTGTGTTGTGTCAAAGAC-TTTCCTGAATCTA 583159 v i -- ---- i vi v vi - i v C L1PB_orf2#LIN 1839 CATAAAGGGA--T----GCTGGATTTTGTCAAATGCTTTTTCTGCATCTA 1796 chrXqtel1M 583160 CTTAG----TAGTAGGATTCTCTTTGATGTT--CTCAGTATCTGTAGGGA 583203 i v ---- vi iv --- v v --i v v v i v - C L1PB_orf2#LIN 1795 TTGAGATGATCATGTGATT---TTTGTTTTTAATTCTGTTTATGTGGTG- 1750 chrXqtel1M 583204 CTGTCAGGTTTATAGTTTTCCCAACATTGAACCAACCCTGCATTTTTAGT 583253 - i vi v vi v vv ii i v iii i C L1PB_orf2#LIN 1749 -TATCACATTTATTGACTTGCGTATGTTAAACCATCCCTGCATCCCTGGT 1701 chrXqtel1M 583254 ATAAA 583258 i C L1PB_orf2#LIN 1700 ATGAA 1696 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 42.30 CpG sites = 56, Kimura (unadjusted) = 42.30 Transitions / transversions = 0.93 (56/60) Gap_init rate = 0.08 (29 / 384), avg. gap size = 1.34 (39 / 29) 361 25.99 2.29 3.08 chrXqtel1M 582876 583006 (416994) C L1M1_orf2#LINE/L1 (1216) 2078 1949 m_b367s551i3 15367 chrXqtel1M 582876 TCCTTGATCCA-TTTGTTCATTCCCTTAATTTCTTTTT-TTGTTTCATTG 582923 -- - --v v v i - i v C L1M1_orf2#LIN 2078 TCCTT--TCCAATTTG--GATGCCCTTTATTTCTTTCTCTTGTCTGATTG 2033 chrXqtel1M 582924 CTGCAACTAGCACTTCATACACTAAGCCAAATAACAGTTATTAGAAGGGT 582973 vi i v vvii v iii vi v i iv v C L1M1_orf2#LIN 2032 CTCTAGCTAGGACTTCCAGTACTATGTTGAATAACAGTGGTGAAAGTGGG 1983 chrXqtel1M 582974 CACTCTTATTTTA-TCCAGATCTAAAAGGAAAGG 583006 ii i iv i- v i C L1M1_orf2#LIN 1982 CATCCTTGTCGTGTTCCAGATCTTAGAGGAAAGG 1949 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 31.24 CpG sites = 18, Kimura (unadjusted) = 32.41 Transitions / transversions = 1.20 (18/15) Gap_init rate = 0.05 (7 / 130), avg. gap size = 1.00 (7 / 7) 285 31.20 5.23 5.52 chrXqtel1M 583331 583693 (416307) L1ME4c_3end#LINE/L1 64 425 (405) m_b367s551i4 15368 chrXqtel1M 583331 GATAAATGATCAAAAAGATACAATCAAATAAGTCACAAAAGGAAAAAATC 583380 iv i- i ii v i i v ? - ii v L1ME4c_3end#L 64 GATAAATGGGCAAAG-GACATGAACAGACAATTCACANAAG-AGGAAATA 111 chrXqtel1M 583381 CAAGGTGCCAACAAACA--TGCAAAAACTTCTCCAAACT-----ATAATT 583423 ?vv iv -- v -- v i v -----i i L1ME4c_3end#L 112 CAANTAGTAAACAAACACATGGAAAAA--TGTTCAACCTCGCTAGTAATC 159 chrXqtel1M 583424 AGAATAATAATTAGAAACATTAAAGCAACCCTGAGGTTCTATCTCA---- 583469 i iv ----- v - vv i v i i i ---- L1ME4c_3end#L 160 AAAGAAAT-----GCAA-ATTAAAGCAACAATGAGATACCATTTTACGCC 203 chrXqtel1M 583470 ----AAACCAGCACAAGGGCAAACAAAAATGGGAAATAACAAGCATTAGA 583515 ---- ii v ivvi --- v iv v v iiii i v L1ME4c_3end#L 204 TATTAAATTAGCAAAAATTTAAA---AAATTGATAATACCCAATGCTGGC 250 chrXqtel1M 583516 AGATTTGCTGGAAAACAGGC-CAATAATGCATGGTTGGTGGAGCTATGAA 583564 iiiv? v vi v i- ?v v i v i vi? i i L1ME4c_3end#L 251 GAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTGTAAA 300 chrXqtel1M 583565 TGGGTCCAGTGATTCTAGAAAGCAATTGGAAACTA--TATTCCCAAATGT 583612 v v iivv i i v iv v -- --- iv i L1ME4c_3end#L 301 TTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTAT---CAAGAGC 347 chrXqtel1M 583613 CACTAAATTGTGCATTCCCTGTGATCCAGTGATAACAC-TATGTTAAGCT 583661 iv v v v v i i vv - v vv vi L1ME4c_3end#L 348 CATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATTT 397 chrXqtel1M 583662 TAGATCCCAAAGAGATCAAAGCAAAAGGAAGA 583693 --- i i i - vv i i L1ME4c_3end#L 398 ---ATCCTAAGGAAAT-AATTCAAAAGAAGGA 425 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.31 CpG sites = 55, Kimura (unadjusted) = 41.82 Transitions / transversions = 1.06 (55/52) Gap_init rate = 0.07 (27 / 362), avg. gap size = 1.44 (39 / 27) 384 31.93 4.05 3.41 chrXqtel1M 583331 583651 (416349) L1ME4a_3end#LINE/L1 64 386 (485) m_b367s551i5 15368 chrXqtel1M 583331 GATAAATGATCAAAAAGATACAATCAAATAAGTCACAAAAGGAAAAAATC 583380 v iv i- i ii v i i v - i v L1ME4a_3end#L 64 GAAAAATGGGCAAAG-GACATGAACAGACAATTCACAAAA-GAAGAAATA 111 chrXqtel1M 583381 CAAGGTGCCAACAAACATGCAAAAACTTCTCCAA----ACTA-TAATTAG 583425 ivv i iii ?v v i ---- - i i L1ME4a_3end#L 112 CAAATGGCCAATAAACATATGAAAANATGTTCAACCTCACTAGTAATCAA 161 chrXqtel1M 583426 AATAATAATTAGAAACATTAAAGCAACCCTGAGGTTCTATCTCAAAACCA 583475 iv ----- v - i vv i v i i ivv v i L1ME4a_3end#L 162 AGAAAT-----GCAA-ATTAAAACAACAATGAGATACCATTTTTCACCTA 205 chrXqtel1M 583476 GCACAAGGGCAAAC-----AAAAATGGGAAATAACAAGCATTA--GAAGA 583518 v v vv v----- i v iv v v ii i-- i i L1ME4a_3end#L 206 TCAAATTGGCAAAGATTTAAAAGATTGATAATACCCAGTGTTGGCGAGGG 255 chrXqtel1M 583519 TTTGCTGGAAAACAGGC-CAATAATGCATGGTTGGTGGAGCTATGAATGG 583567 v -- ?i i - vv v i iv i iiv i i v L1ME4a_3end#L 256 TGTG--GNGAAACGGGCACTCTCATACACTGCTGGTGGGAGTGTAAATTG 303 chrXqtel1M 583568 GTCCAGTGATTCTAGAAAGCAATTGGAAACTATATTCCCAAATGTCACTA 583617 v iivv i ii v iv v i- vi v i viv L1ME4a_3end#L 304 GTACAACCTTTCTGGAGGGCAATTTGGCAATATG-TATCAAAAGCCTTAA 352 chrXqtel1M 583618 AATTGTGCATTCCCTGTGATCCAGTGATAACACT 583651 v ? v v i i vv L1ME4a_3end#L 353 AAATGTNCATACCCTTTGACCCAGTAATTCCACT 386 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 42.33 CpG sites = 51, Kimura (unadjusted) = 42.90 Transitions / transversions = 1.06 (51/48) Gap_init rate = 0.05 (16 / 320), avg. gap size = 1.50 (24 / 16) 13 4.76 0.00 4.35 chrXqtel1M 584471 584494 (415506) (CCCT)n#Simple_repeat 1 23 (0) m_b367s252i10 15369 chrXqtel1M 584471 CCCTCCCTCCCTCCACCCCCTCCC 584494 - i (CCCT)n#Simpl 1 CCCTCCCTCCCTCC-CTCCCTCCC 23 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (1 / 23), avg. gap size = 1.00 (1 / 1) 813 31.27 7.13 2.02 chrXqtel1M 584668 585186 (414814) L1ME3G_3end#LINE/L1 4 548 (376) m_b367s551i6 15370 chrXqtel1M 584668 ATTTCTAAAACATATAGAGAACTG--ACTCATTTATAATACAAATAATTC 584715 v i i i i v-- vv iv v v -i ivv L1ME3G_3end#L 4 ATATCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAAAA-GACAA 52 chrXqtel1M 584716 TCTAATTGATAA----TCAAAGGATATGAA--GACAATTTTCAGACAAAG 584759 i i v v ----v -- i iv vi i L1ME3G_3end#L 53 CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGG 102 chrXqtel1M 584760 AAAT-TAAA--GCCACTTCTAGTCATATGAAAAAATGCTCTAAATCACTA 584806 -i -- v --- iv i v vv L1ME3G_3end#L 103 AAATACAAATGGCCAAT---AAACATATGAAAAGATGCTCAACCTCACTA 149 chrXqtel1M 584807 -----------------AATCAATACAACTCTGAAGTACCACTTCATACC 584839 ----------------- i v vv ii i ivi L1ME3G_3end#L 150 GTAATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACC 199 chrXqtel1M 584840 TCTCAGTTTGGCTAAGATGACAGAAAAAGAAAACGACAAATACTGAATGG 584889 iv v v i vvv i i?vv v iiv ? i ii ivvi L1ME3G_3end#L 200 CATCAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAG 249 chrXqtel1M 584890 GATGTGGGAAAATTGAGATACTAATA-ATTATTGGTAGAGCTGTGAACCT 584938 i i iv iv iv v - i ii i iiv i i- L1ME3G_3end#L 250 GGTGTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAAT-T 298 chrXqtel1M 584939 GATCCTTCCATTCTGAAG---AATTTGGAACTATGCTATGGCTA----TC 584981 i v vv ? i i --- v v - --- ---- i L1ME3G_3end#L 299 GGTACAGCCNTTTTGGAGGGCAATTTGGCAGTAT-CTAT---TAAAATTT 344 chrXqtel1M 584982 AAACTGTGCATCCCCTTGGATCCAGCAGTCTCTCTACTGGAGCTGTATCC 585031 v i v v i i ii v v ? i?v v L1ME3G_3end#L 345 AAAATGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCC 394 chrXqtel1M 585032 CAAAGAGATCCTAAAAGAGG-AAAAAAGGACCCACATGTGCAAAAATGGT 585080 i ? i v viv v v -iv v ?--i i ii v L1ME3G_3end#L 395 TANAGAAATACTCGCACATGTGCACAAGGAN--GCATGTACAAGGATGTT 442 chrXqtel1M 585081 TGCAGCAGCCCTTTTTGTAGTGGCGAGGAACTGAAAACTGAGTGGATATC 585130 iiiv vi v i i ii i i vivv ii i L1ME3G_3end#L 443 CATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTC 492 chrXqtel1M 585131 CATCAGTTGGGGAGTGGCTGAATAAGTTATAATATACAAATGTAATGGAA 585180 i v i i i i ii ivv iiv L1ME3G_3end#L 493 CATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAA 542 chrXqtel1M 585181 TATTAT 585186 i L1ME3G_3end#L 543 TACTAT 548 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.30 CpG sites = 89, Kimura (unadjusted) = 42.35 Transitions / transversions = 1.27 (89/70) Gap_init rate = 0.04 (21 / 518), avg. gap size = 2.29 (48 / 21) 204 26.87 5.97 0.00 chrXqtel1M 585486 585552 (414448) L3b_3end#LINE/CR1 1128 1198 (8) m_b367s601i20 15371 chrXqtel1M 585486 TCCAGTCTGG-GCTTAGGGTGGGTATA-AC-AAATGATCACTAAGGTCCC 585532 v i i - vi ?i v i- - i i v i i L3b_3end#LINE 1128 TCCTGCCTAGAGCTAGGGGNAGGGATGGACTAGATGACCTCTGAGGTCCT 1177 chrXqtel1M 585533 TTTCAATCCT-AAATCCAATG 585552 i i - i i v L3b_3end#LINE 1178 TTCCAATTCTGAGATTCTATG 1198 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 35.82 CpG sites = 13, Kimura (unadjusted) = 35.82 Transitions / transversions = 2.60 (13/5) Gap_init rate = 0.06 (4 / 66), avg. gap size = 1.00 (4 / 4) 406 18.67 5.43 1.04 chrXqtel1M 588658 588749 (411251) MIR#SINE/MIR 93 188 (74) m_b367s601i21 15372 chrXqtel1M 588658 GGGCAAGTTACTT--CCCCTCTG--CCTCAGTTTCCTCCATC-GCAAAGC 588702 -- i -- - - i ii MIR#SINE/MIR 93 GGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCT-CATCTGTAAAAT 141 chrXqtel1M 588703 AGGGATAATTATAACACCTAACTTTCAGGATTATTCTGAGGCTCAAA 588749 i v ii v ivi i i v v i MIR#SINE/MIR 142 GGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGGATTAAA 188 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 22.10 CpG sites = 12, Kimura (unadjusted) = 22.10 Transitions / transversions = 2.40 (12/5) Gap_init rate = 0.04 (4 / 91), avg. gap size = 1.50 (6 / 4) 30 0.00 0.00 0.00 chrXqtel1M 589056 589081 (410919) (AT)n#Simple_repeat 1 26 (0) c_b367s251i1 15373 chrXqtel1M 589056 ATATATATATATATATATATATATAT 589081 (AT)n#Simple_ 1 ATATATATATATATATATATATATAT 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 186 22.27 0.00 4.44 chrXqtel1M 589338 589384 (410616) C L2c_3end#LINE/L2 (57) 421 377 m_b367s601i22 15374 chrXqtel1M 589338 ACAAAAACAAAAAACTGACACGGCTCCTGCTCTCAGGAAGCTGACAG 589384 i ii v -- ii i i i v C L2c_3end#LINE 421 ACAAAGATGAATAA--GACACGGTCCCTGCCCTCAAGGAGCTCACAG 377 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.87 CpG sites = 8, Kimura (unadjusted) = 27.87 Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.04 (2 / 46), avg. gap size = 1.00 (2 / 2) 16 0.00 0.00 0.00 chrXqtel1M 591676 591692 (408308) (A)n#Simple_repeat 1 17 (0) m_b367s252i11 15375 chrXqtel1M 591676 AAAAAAAAAAAAAAAAA 591692 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 225 27.69 1.54 0.00 chrXqtel1M 592641 592705 (407295) C L2d2_3end#LINE/L2 (296) 259 194 m_b368s601i0 15374 chrXqtel1M 592641 TGAAGCAAT-AGGAAAAACTTCTTGTAGAAGGTGTAATTTAAGCTGGGCC 592689 i iii - i ii vi v i v? i C L2d2_3end#LIN 259 TGGAGTGGTCAGGGAAGGCTTCACGGAGGAGGTGGNATTTGAGCTGGGCC 210 chrXqtel1M 592690 CTGAAGCAGGGAGAGG 592705 i v v iv C L2d2_3end#LIN 209 TTGAAGGATGGGTAGG 194 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 34.24 CpG sites = 12, Kimura (unadjusted) = 36.82 Transitions / transversions = 2.00 (12/6) Gap_init rate = 0.02 (1 / 64), avg. gap size = 1.00 (1 / 1) 433 32.08 8.02 0.00 chrXqtel1M 593059 593270 (406730) C L3b_3end#LINE/CR1 (660) 546 318 m_b368s601i2 15376 chrXqtel1M 593059 ACTAAAACTCCCTGTTCCTCTTCAA--GAGC-----CTAAAT-GTGCTTC 593100 i v v i i v-- ? ----- ii- i ii C L3b_3end#LINE 546 ACTAAAACCCCCAGGTCTTTTTCACATGNGCTGCTGCTAAGCCGCGTCTC 497 chrXqtel1M 593101 TCTTGTC-TGT----GTGCGGTTGATTTTTGGAAACCAAATTTACAACTT 593145 i iii - ---- i i ? v v i vi vi C L3b_3end#LINE 496 CCCCATCCTGTACTCGCGCGATTGNTTTTTTGAACCCAAGTGCAGGACTT 447 chrXqtel1M 593146 TCCATTTATTTCAATTACATTTTGCTTTCTTAGCCACGGCTCATCACTGT 593195 v i ii vi iv iiii v i ?iv i i? ii v C L3b_3end#LINE 446 TACGTTTATCCCTGTTGAATTTCATCTTGTTGGNTTCGGCCCGNCGTTCT 397 chrXqtel1M 593196 AGCCTGGCAACATCGTTTCGGATCCTAATCCTG---CCAACCCACTCTCT 593242 i v i v i i ii --- vi i vv i C L3b_3end#LINE 396 AGTCTGTCGAGATCGTTTTGGATCCTGATTTTGCATCCAACGTATTAGCC 347 chrXqtel1M 593243 GGCATCCCCAGAGACT-CAACTTTCAAAT 593270 v iii vvv - v ?v C L3b_3end#LINE 346 GTCGCTCCCAGCTTCTGCCACTNGCAAAT 318 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 38.48 CpG sites = 44, Kimura (unadjusted) = 45.54 Transitions / transversions = 1.83 (44/24) Gap_init rate = 0.03 (7 / 211), avg. gap size = 2.43 (17 / 7) 461 30.84 7.95 0.53 chrXqtel1M 593059 593234 (406766) C L3#LINE/CR1 (655) 3444 3256 m_b368s601i1 15376 chrXqtel1M 593059 ACTAAAACTCCCTGTTCCTCTTCAAG-------------AGCCTAAATGT 593095 i iv v i i v ------------- - i vi C L3#LINE/CR1 3444 ACTAAAACCCCTAGGTCTTTTTCACGTGAACTGCTGCTAAGCC-AGATCC 3396 chrXqtel1M 593096 GCTTC-TCTTGTCTGTGTGCGGTTGATTTTTGGAAACCAAATTTACAACT 593144 v i - i viv i v v i vi vi C L3#LINE/CR1 3395 TCTCCATCCTGTACTTGTGCAGTTGATTTTTTGAACCTAAATGCAGGACT 3346 chrXqtel1M 593145 TTCCATTTATTTCAATTACATTTTGCTTTCTTAGCCACGGCTCATCACTG 593194 v ii vi v iiii v i iiv i ii v C L3#LINE/CR1 3345 TTACATTTATCCCTGTTAAATTTCATCTTGTTGGTTTCGGCCCATCGTTC 3296 chrXqtel1M 593195 TAGCCTGGCAACATCGTTTCGGATCCTAATCCTGCCAACC 593234 i v i v ? i i i i i i v C L3#LINE/CR1 3295 CAGCCTGTCGAGATCNTTTTGAATCTTGATTCTGTCATCC 3256 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 39.72 CpG sites = 34, Kimura (unadjusted) = 41.77 Transitions / transversions = 1.70 (34/20) Gap_init rate = 0.02 (3 / 175), avg. gap size = 5.00 (15 / 3) 213 28.27 11.43 4.00 chrXqtel1M 595157 595296 (404704) L2#LINE/L2 1237 1386 (1696) m_b368s601i3 15377 chrXqtel1M 595157 CGATTTTCCTCCTTCCCCGC---TGCTCACATACAGCTGAATGGTACTGA 595203 i i i v v i --- v v i?i i vvi i L2#LINE/L2 1237 CAACTCTCCGCCTACTCCGCGCCTGCACCCGNGCAGCTGAACGTGGCTGG 1286 chrXqtel1M 595204 AGAGAGTAACTGATGAGGAT--TGAAGAGT-TCACTATAAATT------- 595243 i -- vv ii vv -- vvi - v ------- L2#LINE/L2 1287 AGAAA--AACACACAACCATGCTGACTGGTCTCACTTTAAATTCATGACC 1334 chrXqtel1M 595244 -TTAATCTCAACTGGGCCC--AATGGTGACCCCAGAGCAATCTCCTCTCA 595290 -i? i v -- v v ----i ?iviiv L2#LINE/L2 1335 ACNAACCTCAAGTGGGCCCTTAATGCTGCCC----GGCAATCNTACTACA 1380 chrXqtel1M 595291 TTTCTC 595296 i L2#LINE/L2 1381 TTTCCC 1386 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 33.70 CpG sites = 20, Kimura (unadjusted) = 37.27 Transitions / transversions = 1.11 (20/18) Gap_init rate = 0.09 (12 / 139), avg. gap size = 1.83 (22 / 12) 519 34.46 7.06 2.95 chrXqtel1M 595512 595837 (404163) L2#LINE/L2 2552 2890 (192) m_b368s601i4 15377 chrXqtel1M 595512 AAACTTAGGAGTCACCCTGAATTTCTCAATATTTCTCTCCCCTGTCCCCA 595561 i v i vi i i -- v v v--- L2#LINE/L2 2552 AAACCTTGGAGTCATCCTTGACTCCTC--TCTTTCTCTCACA---CCCCA 2596 chrXqtel1M 595562 CATCAAATC----AGC---TCCCA----CTTTATCTTTGCAACATCTC-- 595598 v ---- --- ii---- i i iiv i v -- L2#LINE/L2 2597 CATCCAATCCATCAGCAAATCCTGTCGGCTCTACCTTCAAAATATATCCA 2646 chrXqtel1M 595599 AAATTCGTCC-TTTCTGCTGACATGGCCCCCA--ACCTCCATC-TGGATT 595644 i i v -i ----- ivi i --i v i - vii L2#LINE/L2 2647 GAATCCGACCACTTCT-----CACCACCTCCACTGCCACCACCCTGGTCC 2691 chrXqtel1M 595645 AGGACTTCATCACTTTACACCTGGACTGCTGCAATAGCCTGCAGGTGAGT 595694 i v vi ii iv i i i v viiivi L2#LINE/L2 2692 AAGCCACCATCATCTCTCGCCTGGATTACTGCAATAGCCTCCTAACTGGT 2741 chrXqtel1M 595695 TTGTTTGCTCCAAGTTCCTCTTCACTTCAATCCATCCTCCATTTGGCCAC 595744 i vii i v viiiiv ii v ? i i i v ivii vi L2#LINE/L2 2742 CTCCCTGCTTCCACCCTTGCCCCCCTNCAGTCTATTCTCAACACAGCAGC 2791 chrXqtel1M 595745 TGAAGTGCTTTTTCTAAAGCACAGATCTGACCATG------CCCTGCTCA 595788 iii v ii i i ii ii v i ------ i L2#LINE/L2 2792 CAGAGTGATCCTTTTAAAACGTAAGTCAGATCATGTCACTCCTCTGCTCA 2841 chrXqtel1M 595789 ATGAACTCCAGTGGCTTCCTATCACCTCCAGGAGCAAATACAAAATCCT 595837 vivv i i v vii iivv vv i L2#LINE/L2 2842 AAACCCTCCAATGGCTTCCCATCTCACTCAGAGTAAAAGCCAAAGTCCT 2890 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 48.11 CpG sites = 72, Kimura (unadjusted) = 49.43 Transitions / transversions = 1.95 (72/37) Gap_init rate = 0.06 (18 / 325), avg. gap size = 1.83 (33 / 18) 398 24.00 4.00 0.00 chrXqtel1M 596612 596711 (403289) L2c_3end#LINE/L2 364 467 (11) m_b368s601i5 15378 chrXqtel1M 596612 CTCCCCC-TTAGACTATGAGCTCCTTAAGGACAGGAACTCTCTTTTCTT- 596659 i -i i i i i iv v i v - L2c_3end#LINE 364 CTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTC 413 chrXqtel1M 596660 -TCTTTGTA-ACACAGTGCCTGGCACAAAGCACAAACTTAACAAATGTTT 596707 - -v v i v i vivi i i L2c_3end#LINE 414 ATCTTTGTATCCCCAGCGCCTGGCACATAGTAGGCGCTCAATAAATGTTT 463 chrXqtel1M 596708 ACTG 596711 ii L2c_3end#LINE 464 GTTG 467 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 25.59 CpG sites = 16, Kimura (unadjusted) = 29.90 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.04 (4 / 99), avg. gap size = 1.00 (4 / 4) 13 13.25 0.00 0.00 chrXqtel1M 596850 596874 (403126) (ACAC)n#Simple_repeat 1 25 (0) m_b368s252i1 15379 chrXqtel1M 596850 ACAGACACACACAGACAGACACACA 596874 v v v (ACAC)n#Simpl 1 ACACACACACACACACACACACACA 25 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 13 22.57 3.64 3.64 chrXqtel1M 598985 599039 (400961) (TCCG)n#Simple_repeat 1 55 (0) m_b368s252i2 15380 chrXqtel1M 598985 TCCG-CCGTCCGTCC-TCCCTCCCGCCCTCCTGCTCGTTCGGCCTCCCGT 599032 - - v vv v - ii i v vi (TCCG)n#Simpl 1 TCCGTCCGTCCGTCCGTCCGTCCGTCCGTCC-GTCCGTCCGTCCGTCCGT 49 chrXqtel1M 599033 CCGATCC 599039 - (TCCG)n#Simpl 50 CCG-TCC 55 Matrix = Unknown Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.07 (4 / 54), avg. gap size = 1.00 (4 / 4) 14 31.16 0.00 0.00 chrXqtel1M 599107 599157 (400843) (CCC)n#Simple_repeat 1 51 (0) m_b368s252i3 15381 chrXqtel1M 599107 CCCCCCCCACCTCTCTCCGCGCCCCCCCCTCCCGCGCCGCCGCCGCCGCC 599156 v i i i v v i v v v v v v (CCC)n#Simple 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 50 chrXqtel1M 599157 C 599157 (CCC)n#Simple 51 C 51 Matrix = Unknown Transitions / transversions = 0.44 (4/9) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 57 7.37 0.00 0.00 chrXqtel1M 599916 599988 (400012) (CGC)n#Simple_repeat 1 73 (0) c_b368s251i0 15382 chrXqtel1M 599916 CGCCGCCGCCGCCGCTGTCGCCGCCGCCGCTGCCGCCGTCGTCGCCGCCG 599965 i i i i i (CGC)n#Simple 1 CGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCG 50 chrXqtel1M 599966 CCGCCGCCGCCGCCGCCGCCGCC 599988 (CGC)n#Simple 51 CCGCCGCCGCCGCCGCCGCCGCC 73 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.00 (0 / 72), avg. gap size = 0.0 (0 / 0) 219 29.37 0.00 8.33 chrXqtel1M 600610 600687 (399313) C L2#LINE/L2 (223) 2859 2788 m_b368s601i6 15383 chrXqtel1M 600610 GGAGCCACTGGGGTCTTTTGAGTAGGGGAGTGACCTCATTAGACCGGAAA 600659 i i i vv i i v v iv ------ C L2#LINE/L2 2859 GAAGCCATTGGAGGGTTTTGAGCAGAGGAGTGACATGATCTGAC------ 2816 chrXqtel1M 600660 CCACGATTTGTGAAAATCACTTTGTCTG 600687 ii v ivi ii i v C L2#LINE/L2 2815 TTACGTTTTAAAAGGATCACTCTGGCTG 2788 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 38.24 CpG sites = 13, Kimura (unadjusted) = 38.24 Transitions / transversions = 1.62 (13/8) Gap_init rate = 0.08 (6 / 77), avg. gap size = 1.00 (6 / 6) 349 30.40 2.20 4.84 chrXqtel1M 601239 601556 (398444) L1P4_orf2#LINE/L1 2985 3294 (0) m_b368s551i0 15384 chrXqtel1M 601239 GACTGAGTCATCAAAGAAGAACTGAAACTCATTATTGAACACCAAATAGA 601288 i v - iv i v vv ------ v- v L1P4_orf2#LIN 2985 GACTAAGTCCTCAAA-AGCAATTGCAACAAA------AACAA-AAATTGA 3026 chrXqtel1M 601289 TAATTTTGATTATATTAAGATAAAAAGCTTTTGTACA---AACAAAACTA 601335 i v vv iivv iv i i i --- vi L1P4_orf2#LIN 3027 CAAGTGGGACCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTA 3076 chrXqtel1M 601336 ATGCAGACAAGAGTAGGAAGG-AAGCAATAAACTGGGAAAATATTTTTAC 601384 --v - - iiv i- v v i i v i v v ii L1P4_orf2#LIN 3077 --TCA-ACA-GAGTAAACAGACAACCTACAGAATGGGAGAAAATATTCGC 3122 chrXqtel1M 601385 AGTCAAAGGTTCTGATAAAGGCCTCATTTCCAAAATATATAGAGAATTAA 601434 iv v v vv i i i v v i v ii i v L1P4_orf2#LIN 3123 AAACTATGCATCCGACAAAGGTCTAATATCCAGAATCTATAAGGAACTTA 3172 chrXqtel1M 601435 CTCTAATTTATAA---AAAATCAAGCCATTCTCCAATTGAAAAATGGTCA 601481 vv v ? iv i --- v --- vvi v i i v L1P4_orf2#LIN 3173 AACAANTCAACAAGCAAAAAACAA---ATAACCCCATTAAAAAGTGGGCA 3219 chrXqtel1M 601482 AAGGATATGAACAGACAATTCTCAGATGAAGAAATTGAAACCATTTCTAG 601531 i v i v v vv i viiivvi i L1P4_orf2#LIN 3220 AAGGACATGAACAGACACTTCTCAAAAGAAGACATACAAGCGGCCAACAA 3269 chrXqtel1M 601532 TCATATGAAAAGGTGCTCTAAATCA 601556 v ii v v L1P4_orf2#LIN 3270 ACATATGAAAAAATGCTCAACATCA 3294 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 38.26 CpG sites = 42, Kimura (unadjusted) = 39.38 Transitions / transversions = 0.84 (42/50) Gap_init rate = 0.06 (18 / 317), avg. gap size = 1.22 (22 / 18) 453 27.55 3.64 3.64 chrXqtel1M 601282 601556 (398444) L1M4_orf2#LINE/L1 3020 3294 (0) m_b368s551i1 15384 chrXqtel1M 601282 AAATAGATAATTTTGATTATATTAAGATAAAAAGCTTTTGTA---CAAAC 601328 v v i vi i i v i i--- v L1M4_orf2#LIN 3020 AAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGCTTCAAAG 3069 chrXqtel1M 601329 AAAACTAATGCAGACAAGAGTAGGAAGG-AAGCAATAAACTGGGAAAATA 601377 i v vi---- vi i iii i- v v i i v i v L1M4_orf2#LIN 3070 GACACTATC----AAGAAAGTGAAAAGACAACCCACAGAATGGGAGAAAA 3115 chrXqtel1M 601378 TTTTTAC-AGTCAAAGGTTCTGATAAAGGCCTCATTTCCAAAATATATAG 601426 v i - i v vi- i v ?i v i i L1M4_orf2#LIN 3116 TATTTGCAAATCATATA-TCTGATAAGGGACTNGTATCCAGAATATATAA 3164 chrXqtel1M 601427 AGAATT-----AACTCTAATTTATAAAAAATCAAGCCATTCTCCAATTGA 601471 i ----- -- viv iv --- vvi ? L1M4_orf2#LIN 3165 AGAACTCTTACAACTC--AACAATAAAAAGACAA---ATAACCCAATTNA 3209 chrXqtel1M 601472 AAAATGGTCAAAGGATATGAACAGACAATTCTCAGATGAAGAAATTGAAA 601521 v v i v vi v v vv L1M4_orf2#LIN 3210 AAAATGGGCAAAGGATTTGAATAGACATTTCTCCAAAGAAGATATACAAA 3259 chrXqtel1M 601522 CCATTTCTAGTCATATGAAAAGGTGCTCTAAATCA 601556 iviiivv iv i i v v L1M4_orf2#LIN 3260 TGGCCAATAAGCACATGAAAAGATGCTCAACATCA 3294 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 35.08 CpG sites = 37, Kimura (unadjusted) = 35.08 Transitions / transversions = 1.03 (37/36) Gap_init rate = 0.05 (14 / 274), avg. gap size = 1.43 (20 / 14) 978 32.70 4.72 2.06 chrXqtel1M 601407 602021 (397979) L1PB2_3end#LINE/L1 1 631 (267) m_b368s551i2 15384 chrXqtel1M 601407 CTCATTTCCAAAATATATAGAGAATTAACTCTAATTTATAAAAAATCAAG 601456 v v i v i ii i v vv v ivii i vv v L1PB2_3end#LI 1 CTAATATCCAGAATCTACAAGGAACTCAAACAAATCAGCAAGAAAAAAAC 50 chrXqtel1M 601457 CCATTCTCCAATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAG 601506 vv vv v ii i v i i i L1PB2_3end#LI 51 AAATAATCCCATCAAAAAGTGGGCAAAGGACATGAATAGACAATTCTCAA 100 chrXqtel1M 601507 ATGAAGAAATTGAAACCATTTCTAGTCATATGAAAAGGTGCTCTAAATCA 601556 v v vv viiivvi iv ii v v L1PB2_3end#LI 101 AAGAAGATATACAAACGGCCAACAAACATATGAAAAAATGCTCAACATCA 150 chrXqtel1M 601557 CTATTGATTAGAGATATGCAAATGAAGACAACTCTGAGGTACCACCACAC 601606 v v i i v v i v vv i vi L1PB2_3end#LI 151 CTAATTATCAGGGAAATGCAAATTAAAACCACAATGAGATACCACCTTAC 200 chrXqtel1M 601607 AGCTGTCAGATTGGCTAAGATGACAGGAAG--AGGTAATGATGAATGTTG 601654 vv iv v i vi v v -- -- iiv ii ii L1PB2_3end#LI 201 TCCTGCAAGAATGGCCATAATTAAA--AAGTCAAAAAACAATAGATGTTG 248 chrXqtel1M 601655 GAGGGGAGGTGGGAAGACTGGGACATTAATACATGGTTGGTGGAGCTGTG 601704 v v v vi i vv i i vv iv i iiv i L1PB2_3end#LI 249 GCGTGGATGTGGTGAAAAGGGAACACTTTTACACTGCTGGTGGGAATGTA 298 chrXqtel1M 601705 AATGGATCCAGCCATTCTGGA----AGTATG-------CTCAAAGGAATA 601743 ivii v i i v ---- ------- i i--- L1PB2_3end#LI 299 AACTAGTACAACCACTATGGAAAACAGTATGGAGATTCCTTAAAGA---A 345 chrXqtel1M 601744 TTAAACGGTGCA-TACCCTTTGATCCAGCAGTGATACTACTGGGCTTATA 601792 i v vv v - v i i vvi iv v L1PB2_3end#LI 346 CTAAAAGTAGAACTACCATTCGATCCAGCAATCCCACTACTGGGTATCTA 395 chrXqtel1M 601793 CCCCAAAGAGATGA--TAAAGAAGGGAAAGGGACCTCTATGTGCACGAAT 601840 v i i v -- v vv viv ii --vi ii v L1PB2_3end#LI 396 CCCAAAGGAAAAGAAGTCATTATATGAAAAAGAC--ACATGCACACGCAT 443 chrXqtel1M 601841 GTTTGTGGCAGCCC--TTTG----TGCAAGAAACTGGAAACTGAGTGGAT 601884 i i v -- i ---- ii vv v vivv iii L1PB2_3end#LI 444 GTTTATAGCAGCACAATTCGCAATTGCAAAGATATGGAACCAACCTAAGT 493 chrXqtel1M 601885 GTCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTCTATGGATATTATG 601934 i iiiiiv i v i v v v iv i ii L1PB2_3end#LI 494 GCCCATCAACCAACGAGTGGATAAAGAAAATGTGGTATATATACACCATG 543 chrXqtel1M 601935 GAATATTATTGTTCTGTAAGAAATGACCAACAGGATGATTT---CAGAAA 601981 i i vvv ii - v v i v vi vi --- v L1PB2_3end#LI 544 GAATACTACTCAGCCATAA-AAAGGAACGAAATAATGTCTTTTGCAGCAA 592 chrXqtel1M 601982 GGCTCGAGAGATGCACATGAA----CTGATTCTAAGTGAAGTGA 602021 -- i --- v vv i ----v v i L1PB2_3end#LI 593 --CTTG---GATGGAGCTGGAGGCCATTATTCTAAGTGAAGTAA 631 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 42.70 CpG sites = 96, Kimura (unadjusted) = 43.57 Transitions / transversions = 0.95 (96/101) Gap_init rate = 0.04 (22 / 614), avg. gap size = 1.91 (42 / 22) 1308 28.04 3.93 1.83 chrXqtel1M 601410 601943 (398057) L1ME3G_3end#LINE/L1 4 548 (376) m_b368s551i3 15384 chrXqtel1M 601410 ATTTCCAAAATATATAGAGAATTAACTCTAATTTATAAAAAATCAAGCCA 601459 v i i i vviv v iv i -- v L1ME3G_3end#L 4 ATATCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAA--AAGACA 51 chrXqtel1M 601460 TTCTCCAATTGAAAAATGGTCAAAGGATATGAACAGACAATTCTCAGATG 601509 --vi v v i v v L1ME3G_3end#L 52 --ACCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAG 99 chrXqtel1M 601510 AAGAAATTGAAACCATTTCTAGTCATATGAAAAGGTGCTCTAAATCACTA 601559 i vv iviiivv iv i v vv L1ME3G_3end#L 100 AGGAAATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTA 149 chrXqtel1M 601560 TTGATTAGAGATATGCAAATGAAGACAACTCTGAGGTACCACCACACAGC 601609 v i i i v v i vv i iiviv v L1ME3G_3end#L 150 GTAATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACC 199 chrXqtel1M 601610 TGTCAGATTGGCTAAGATGACAGGAAGAGGTAATGATGAATGTTGGAGGG 601659 ii v i vvv iii?vv i ivi? i v i L1ME3G_3end#L 200 CATCAGATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAG 249 chrXqtel1M 601660 GAGGTGGGAAGACTGGGACATTAATACATGGTTGGTGGAGCTGTGAATGG 601709 iv i i v v vi v iv i iiv i v L1ME3G_3end#L 250 GGTGTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTG 299 chrXqtel1M 601710 ATCCAGCCATTCTGGA------------AGTATGC-TCAAAGGAATATTA 601746 i v ? i ------------ vi- i --- - L1ME3G_3end#L 300 GTACAGCCNTTTTGGAGGGCAATTTGGCAGTATCTATTAAA---AT-TTA 345 chrXqtel1M 601747 AACGGTGCATACCCTTTGATCCAGCAGTGATACTACTGGGCTTATACCCC 601796 vv i i i vvi v ? ?v v i i L1ME3G_3end#L 346 AAATGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCT 395 chrXqtel1M 601797 AAAGAGATGATAA-AGAAGGGAA-AGGGACCTCTATGTGCACGAATGTTT 601844 ? i iv vi- v v v v - i ?vi-- i v i i L1ME3G_3end#L 396 ANAGAAATACTCGCACATGTGCACAAGGANGC--ATGTACAAGGATGTTC 443 chrXqtel1M 601845 GTGGCAGCCCT--TTGT----GCAAGAAACTGGAAACTGAGTGGATGTCC 601888 i v vi -- ---- i i i vivv ii L1ME3G_3end#L 444 ATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCC 493 chrXqtel1M 601889 ATCAGTTGGAGAATGGCTGAATAAATTGTGGTCTATGGATATTATGGAAT 601938 i v i i i i v vv i L1ME3G_3end#L 494 ATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGGAAT 543 chrXqtel1M 601939 ATTAT 601943 i L1ME3G_3end#L 544 ACTAT 548 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 35.34 CpG sites = 76, Kimura (unadjusted) = 36.25 Transitions / transversions = 1.07 (76/71) Gap_init rate = 0.03 (16 / 533), avg. gap size = 1.94 (31 / 16) 212 37.23 0.00 0.00 chrXqtel1M 602837 602930 (397070) L3#LINE/CR1 3233 3326 (773) m_b368s601i7 15385 chrXqtel1M 602837 CTGGGAAGGAAAGCTGACCCAACAAGGGATAGTCTCAGCATCCAATACGA 602886 i v i iv i?iiiiv i vv iv i v ? L3#LINE/CR1 3233 CTGGGAGGGATAGCTAATACGNTGGATGACAGAATCAAGATTCAAAANGA 3282 chrXqtel1M 602887 TCTTACTACACTACAACATTGGGCCAAATCAAATGCTATGAAAT 602930 iivi vi iv iv i v v iivv L3#LINE/CR1 3283 TCTCGACAGGCTGGAACGATGGGCCGAAACCAACAAGATGAAAT 3326 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 46.29 CpG sites = 20, Kimura (unadjusted) = 55.41 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.00 (0 / 93), avg. gap size = 0.0 (0 / 0) 235 34.41 0.00 1.08 chrXqtel1M 602871 602964 (397036) L3b_3end#LINE/CR1 369 461 (745) m_b368s601i8 15385 chrXqtel1M 602871 TCAGCATCCAATACGATCTTACTACACTACAACATTGGGCCAAATCAAAT 602920 v v iivi v v i?i i ? v i L3b_3end#LINE 369 TCAGGATCCAAAACGATCTCGACAGACTAGAACGNCGGGCCGAANCCAAC 418 chrXqtel1M 602921 GCTATGAAATGCTGTAGAACTACACACAGGCACCTTTCACTTGG 602964 ivv v vii iiv v ii ii-ii i v L3b_3end#LINE 419 AAGATGAAATTCAACAGGGATAAACGTAAA-GTCCTGCACTTGG 461 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 39.16 CpG sites = 19, Kimura (unadjusted) = 49.51 Transitions / transversions = 1.46 (19/13) Gap_init rate = 0.01 (1 / 93), avg. gap size = 1.00 (1 / 1) 213 33.72 2.17 3.30 chrXqtel1M 603035 603126 (396874) C MIRb#SINE/MIR (150) 118 28 m_b368s601i9 15386 chrXqtel1M 603035 GAGATTGGAAAGTATGTTCACCCATACTATACAACTAGTAAATATCAGAA 603084 i --- vv vv v viii i i i iv i C MIRb#SINE/MIR 118 GAGGTT---AAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAG 72 chrXqtel1M 603085 TCGGGATCTGAACT--GTTCTTCCCGTCTCCAAGTCCAGCACTC 603126 i ii i-- v vi i v iv v ii C MIRb#SINE/MIR 71 CCGGGATTCGAACCCAGGTCTGTCTGACTCCAAAGCCCGTGCTC 28 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 44.46 CpG sites = 18, Kimura (unadjusted) = 46.61 Transitions / transversions = 1.50 (18/12) Gap_init rate = 0.04 (4 / 91), avg. gap size = 1.25 (5 / 4) 290 25.00 3.12 0.00 chrXqtel1M 603063 603126 (396874) C MIRc#SINE/MIR (178) 90 25 m_b368s601i10 15386 chrXqtel1M 603063 ATACAACTAGTAAATATCAGAATCGGGATCTGAACT--GTTCTTCCCGTC 603110 i i i iv ii iii i-- v i v C MIRc#SINE/MIR 90 ACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGAC 41 chrXqtel1M 603111 TCCAAGTCCAGCACTC 603126 ii C MIRc#SINE/MIR 40 TCCAAGTCCAGTGCTC 25 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 30.13 CpG sites = 13, Kimura (unadjusted) = 32.64 Transitions / transversions = 4.33 (13/3) Gap_init rate = 0.02 (1 / 63), avg. gap size = 2.00 (2 / 1) 346 25.37 0.00 5.75 chrXqtel1M 603139 603230 (396770) L3b_3end#LINE/CR1 523 609 (597) m_b368s601i11 15385 chrXqtel1M 603139 TGAAAAAGATCTGGGGGTTTTAGTGGACAGCTAGCTCAATGAGCGTAAGC 603188 i v v v iv v v L3b_3end#LINE 523 TGAAAAAGACCTGGGGGTTTTAGTTGACCGCAAGCTCAATATGAGTCAGC 572 chrXqtel1M 603189 AATATGACATAATGTGGCAACCAAAGAAATCACTACGACTTT 603230 i ii ----- i vi i iii v i ii L3b_3end#LINE 573 AGTGCGAC-----GCGGCTGCCAAAAAAGCTAATGCGATCTT 609 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 28.37 CpG sites = 14, Kimura (unadjusted) = 31.78 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.05 (5 / 91), avg. gap size = 1.00 (5 / 5) 254 26.67 0.00 0.00 chrXqtel1M 603269 603328 (396672) L3#LINE/CR1 3599 3658 (441) m_b368s601i12 15387 chrXqtel1M 603269 GTTCCATTGCAGTCTCCCCATTTTAAGAAGGACATTGCCAAGCTGCAGGA 603318 vi vii v v v i v i v vi L3#LINE/CR1 3599 GTTCAGTTCTGGGCGCCACATTTTAAGAGGGACATTGACAAACTGGAGCG 3648 chrXqtel1M 603319 TGTCTAGAGG 603328 i i L3#LINE/CR1 3649 CGTCCAGAGG 3658 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 28.53 CpG sites = 8, Kimura (unadjusted) = 33.30 Transitions / transversions = 1.00 (8/8) Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0) 384 29.12 9.69 5.39 chrXqtel1M 609303 609498 (390502) C MIR#SINE/MIR (26) 236 33 m_b368s601i13 15388 chrXqtel1M 609303 TCACCATGTGCCAGGTACTGTGCCGAGCACTCTG---------------- 609336 i i i v ii i i i---------------- C MIR#SINE/MIR 236 TTACTATGTGCCAGGCACTGTTCTAAGCGCTTTACATGTATTAACTCATT 187 chrXqtel1M 609337 -AATCCTCACAACCACCCCAGGAGGCAGGGGCTCTTATTAGCATCCTATT 609385 - v i v i vi v v -- i - C MIR#SINE/MIR 186 TAATCCTCACAACAACCCTATGAGGTAGGTACTATTATTATC--CCCAT- 140 chrXqtel1M 609386 ACTTTGTTTACAAGAAAA-TGAGGTGGATGGAGAGAGATGAATGACTTGC 609434 -- iivv ii i - i-- ii - v i i i C MIR#SINE/MIR 139 --TTTACAGATGAGGAAACTGAGGC--ACAGAGAG-GTTAAGTAACTTGC 95 chrXqtel1M 609435 CCAGGAGCATTCAAATGGTTAAATGACTTTAGCT-GGATTTAATCTCAGG 609483 i iv iv iv i - i i -vv i- ii v i C MIR#SINE/MIR 94 CCAAGGTCACACAGCTAG-TAAGTGGC-AGAGCCGGGATTCGAACCCAGG 47 chrXqtel1M 609484 ACTTCTTGACTTCAG 609498 vvv - i i C MIR#SINE/MIR 46 CAGTC-TGGCTCCAG 33 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 35.87 CpG sites = 36, Kimura (unadjusted) = 38.73 Transitions / transversions = 2.00 (36/18) Gap_init rate = 0.08 (15 / 195), avg. gap size = 2.00 (30 / 15) 528 23.94 3.45 2.04 chrXqtel1M 609606 609750 (390250) C MIRc#SINE/MIR (120) 148 2 m_b368s601i14 15389 chrXqtel1M 609606 CTCATTTTACAGATGAGGAAAT---GGGTAAACAGGGTAAAGTGACTCAT 609652 i i--- v v ivii v iii C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chrXqtel1M 609653 CCAGGGTCACCCAGCTCACAAATGTCAG-GCTGG-ATTTGAACTTGGGTC 609700 i v vii i v - i - i i iii C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTC 49 chrXqtel1M 609701 TTCAGGACTCCAGGACCAGAGCTCTATCCACTGAGCCATCCAGCTGCCCC 609750 vv i v v v vi -- - i C MIRc#SINE/MIR 48 TTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCA--CA-CTGCCTC 2 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 27.52 CpG sites = 21, Kimura (unadjusted) = 29.55 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.04 (6 / 144), avg. gap size = 1.33 (8 / 6) 191 25.57 3.19 4.30 chrXqtel1M 610218 610311 (389689) C L2#LINE/L2 (1003) 2079 1987 m_b368s601i15 15390 chrXqtel1M 610218 TGGCAGAGGCTGCAGAGAGGGCAAAGAAAGTGAG-ACTGAAGAAAAGGCC 610266 v i v v ? v iv ii - - vv i C L2#LINE/L2 2079 TGTCAAATGCTGCTGANAGGTCAAGTAAGATGAGGACTGA-GAATTGACC 2031 chrXqtel1M 610267 TCGACTGGGTTGGGTAGCCAGGAGGTCACTGGTAACCT--GCAAGAG 610311 --- i i vi i i vv i i --i C L2#LINE/L2 2030 ---ATTGGATTTAGCAACGTGGAGGTCATTGGTGACCTTGACAAGAG 1987 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 32.28 CpG sites = 13, Kimura (unadjusted) = 32.28 Transitions / transversions = 1.30 (13/10) Gap_init rate = 0.06 (6 / 93), avg. gap size = 1.17 (7 / 6) 16 16.24 2.22 4.55 chrXqtel1M 610480 610524 (389476) (AAAT)n#Simple_repeat 1 44 (0) m_b368s252i4 15391 chrXqtel1M 610480 AAATAAATAAATAAATATAATAGA-AGATTGTTAACATAAAAAAAT 610524 - i - i viv - v (AAAT)n#Simpl 1 AAATAAATAAATAAATA-AATAAATAAATAAATAA-ATAAATAAAT 44 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.07 (3 / 44), avg. gap size = 1.00 (3 / 3) 25 25.83 0.00 0.00 chrXqtel1M 614743 614808 (385192) (GCCACC)n#Simple_repeat 1 66 (0) m_b368s252i5 15392 chrXqtel1M 614743 GCCACTGCTGCCGGCACCGCTGCCGGCACCGCTGCCGGCACCGCTGCCGG 614792 i ii v ii v ii v ii v (GCCACC)n#Sim 1 GCCACCGCCACCGCCACCGCCACCGCCACCGCCACCGCCACCGCCACCGC 50 chrXqtel1M 614793 CACCGCCGCCGCCACC 614808 i (GCCACC)n#Sim 51 CACCGCCACCGCCACC 66 Matrix = Unknown Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0) 346 30.73 4.59 2.90 chrXqtel1M 615915 616219 (383781) C L1ME4c_3end#LINE/L1 (139) 691 382 m_b368s551i4 15393 chrXqtel1M 615915 TGCATATTTGATGTT---AT-GTTG-AATTATTGTGTATAATGTATTCTT 615959 iv i v --- - - i v i ? - ii v i C L1ME4c_3end#L 691 TGCATACGTAATTTTTACATAGTTGTAATCATAGCGTANA-TACAATTTT 643 chrXqtel1M 615960 G-GTTCTGCTCGTTTCACTCAGCATCAGTA-CATGTAAATCTTTCCAAGC 616007 -i iv i i i - - iv v - v - C L1ME4c_3end#L 642 GTATTCTGCTTTTTTCACTTAACATTA-TATCATAAACAT-TTTCCATG- 596 chrXqtel1M 616008 CTTTCTCTAATCAAGCTTGTTCATCAT--TTTTTAATATAACAATAATAT 616055 - v vi --i iv vv v i -- ivvvvv C L1ME4c_3end#L 595 -TTGCTACA--TAGTCTTCATAATTATCATTTTTAATGGCTGCATAATAT 549 chrXqtel1M 616056 TCCATTACCTTCATATACCATGACTTGTCCAGCCATTTCCC-ATT--TGG 616102 iivv ?v i i i iiii i i - -- C L1ME4c_3end#L 548 TCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTATTGTTGG 499 chrXqtel1M 616103 GCACTTACTACATTTCCAAATCTTTGCTACTACAATAAGAGCTGTTACAA 616152 i i vvvii v i i i i vv iv iv ii C L1ME4c_3end#L 498 ACATTTAGGTTGTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGA 449 chrXqtel1M 616153 ACATTTTTGCACATGTGGGTCCTTTCCCCACCTTT--ATGATTTCCTTGA 616200 i i ii i i -- i i iv i -- v ii C L1ME4c_3end#L 448 ACATCTTCGTGCATATAG--CTTTTTCCTTCTTTTGAATTATTTCCTTAG 401 chrXqtel1M 616201 GATACAAACCCAGTAATAG 616219 v vv v i i C L1ME4c_3end#L 400 GATAAATTCCCAGAAGTGG 382 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 38.33 CpG sites = 55, Kimura (unadjusted) = 41.34 Transitions / transversions = 1.53 (55/36) Gap_init rate = 0.06 (18 / 304), avg. gap size = 1.28 (23 / 18) 14 15.45 2.63 2.63 chrXqtel1M 617133 617170 (382830) (GGGTAGA)n#Simple_repeat 1 38 (0) m_b368s252i6 15394 chrXqtel1M 617133 GGGT-GAGGGTAGAGAGTAGGGGGTAGGAGGAGACAGGG 617170 - i i - iv v (GGGTAGA)n#Si 1 GGGTAGAGGGTAGAGGGTAGAGGGTA-GAGGGTAGAGGG 38 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.00 (2 / 2) 18 22.64 1.67 3.39 chrXqtel1M 617407 617466 (382534) (CACA)n#Simple_repeat 1 59 (0) m_b368s252i7 15395 chrXqtel1M 617407 CACGCACATACACACACGCGAGCAGACACAGACATACACAGACACAGA-A 617455 i i i - - v v i v v - (CACA)n#Simpl 1 CACACACACACACACACAC-A-CACACACACACACACACACACACACACA 48 chrXqtel1M 617456 CACCAAGACAC 617466 vv v (CACA)n#Simpl 49 CACACACACAC 59 Matrix = Unknown Transitions / transversions = 0.57 (4/7) Gap_init rate = 0.05 (3 / 59), avg. gap size = 1.00 (3 / 3) 262 21.60 6.58 2.53 chrXqtel1M 617643 617718 (382282) Charlie30a#DNA/hAT-Charlie 48 126 (665) m_b368s502i0 15396 chrXqtel1M 617643 TGATTTCATCTGACCCACAGGGTACCACTGCTCTGGGCA-----GCTGGA 617687 i i vii ivi i v ----- v Charlie30a#DN 48 TGATTTCATCCGGCCCCTGGGGTGATATTGCTCTGGTCACTGCCGCTGCA 97 chrXqtel1M 617688 GCCCAGACAATCCGTTTCCCCCTTGGGTGGG 617718 v -vi i i - Charlie30a#DN 98 GCCCAGAGAAT-AATTTCTCCCCT-GGTGGG 126 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 24.23 CpG sites = 10, Kimura (unadjusted) = 26.07 Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.04 (3 / 75), avg. gap size = 2.33 (7 / 3) 16 24.28 1.92 1.92 chrXqtel1M 618493 618544 (381456) (GTCTAG)n#Simple_repeat 1 52 (0) m_b368s252i9 15397 chrXqtel1M 618493 GTC-AGGTTCTAAGTCTAAGTCTAGATCTGGATCTGCGTCCAGGTTTAGC 618541 - - i i i i i iv i i v (GTCTAG)n#Sim 1 GTCTAGG-TCTAGGTCTAGGTCTAGGTCTAGGTCTAGGTCTAGGTCTAGG 49 chrXqtel1M 618542 TCT 618544 (GTCTAG)n#Sim 50 TCT 52 Matrix = Unknown Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.00 (2 / 2) 245 19.44 8.33 0.00 chrXqtel1M 622188 622259 (377741) C MIR3#SINE/MIR (25) 183 106 m_b368s601i16 15398 chrXqtel1M 622188 AGCTGCAAGGCACCATACAGATCA---ACCCCAATGGCCTCACTTTACAG 622234 v v v v --- vi ivv i C MIR3#SINE/MIR 183 AGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAG 134 chrXqtel1M 622235 AC-AG--AACTGAGACCCAGAGTGATGA 622259 i- -- i v i C MIR3#SINE/MIR 133 ATGAGGAAACTGAGGCCCAGAGAGGTGA 106 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 22.55 CpG sites = 6, Kimura (unadjusted) = 22.55 Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.04 (3 / 71), avg. gap size = 2.00 (6 / 3) 19 23.83 0.00 0.00 chrXqtel1M 623721 623769 (376231) (TTTTT)n#Simple_repeat 1 49 (0) m_b368s252i11 15399 chrXqtel1M 623721 TTTGTTTTTTTTTTTTTTTTCTTTTTTGCTTAATTTAAATTTTCTTTTT 623769 v i vi vv vvv i (TTTTT)n#Simp 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 49 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 15 8.72 0.00 0.00 chrXqtel1M 623864 623888 (376112) (TCCC)n#Simple_repeat 1 25 (0) m_b368s252i12 15400 chrXqtel1M 623864 TCCCTCCTTCCCTCCCCCCCTCCCT 623888 i i (TCCC)n#Simpl 1 TCCCTCCCTCCCTCCCTCCCTCCCT 25 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 21 0.00 0.00 0.00 chrXqtel1M 624363 624385 (375615) (T)n#Simple_repeat 1 23 (0) m_b368s252i13 15401 chrXqtel1M 624363 TTTTTTTTTTTTTTTTTTTTTTT 624385 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTT 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 188 6.67 0.00 0.00 chrXqtel1M 624417 624446 (375554) C MIRb#SINE/MIR (125) 143 114 m_b368s601i17 15402 chrXqtel1M 624417 ACAGATGAGGAAACTAAGGGTCAGAGAGGT 624446 i v C MIRb#SINE/MIR 143 ACAGATGAGGAAACTGAGGCTCAGAGAGGT 114 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 6.99 CpG sites = 1, Kimura (unadjusted) = 6.99 Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 708 24.16 10.39 3.24 chrXqtel1M 625477 625707 (374293) C MIRb#SINE/MIR (15) 253 7 m_b368s601i18 15403 chrXqtel1M 625477 ATCTATTTGAAGGGCCTACCATCTGCCAGGCACCGTGCTAAGCACCTCAT 625526 i --i v i i v i i i i i C MIRb#SINE/MIR 253 ATTTATT--GAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTAC 206 chrXqtel1M 625527 AATTCTGATCTCATTTGATCTTCACAACAACCCTGGGAAGCAGGTGCTGT 625576 vviv v i i v i i --- i C MIRb#SINE/MIR 205 ATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGG---TAT 159 chrXqtel1M 625577 CATTGTCCTCAATGTACAGTTATGGAAACTGAGGC----GGAGGTGAAGT 625622 i i i v v v iv ----i v C MIRb#SINE/MIR 158 TATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGT 109 chrXqtel1M 625623 GACTTGCCCA-----GCACTGCAGGCAA--------------ATCTCAAC 625653 i -----i v vi i -------------- iiv C MIRb#SINE/MIR 108 AACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAAC 59 chrXqtel1M 625654 TCAGGTCT-TTTGACTCCAAGTCCAGAGCTCTATGTGCTGCCTCATCTGG 625702 i - i iv v v v vii vi i--- C MIRb#SINE/MIR 58 CCAGGTCTGTCTGACTCCAAAGCCCGTGCTCTTTCCACTGCACCAC---G 12 chrXqtel1M 625703 CTGCC 625707 C MIRb#SINE/MIR 11 CTGCC 7 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 28.00 CpG sites = 33, Kimura (unadjusted) = 29.94 Transitions / transversions = 1.57 (33/21) Gap_init rate = 0.05 (12 / 230), avg. gap size = 2.67 (32 / 12) 196 28.92 5.88 4.13 chrXqtel1M 626390 626508 (373492) C L3#LINE/CR1 (213) 3886 3766 m_b368s601i19 15404 chrXqtel1M 626390 GAACCCAAAGCAGCCTC---GCCACTTCCCCGCTGTGGCCCCTGACTTTG 626436 i v v v --- iv v v vv i i-- v -- C L3#LINE/CR1 3886 GAGCCGAAATCTGCCTCCCTGTAACTTCCACCCATTGGTCCT--AGTT-- 3841 chrXqtel1M 626437 CCTGCCCTCTGGCACCAAAAAGGACACATGGGATCTTTCAGCCA---GGC 626483 - vi v v i i vi vvi ii vv --- i C L3#LINE/CR1 3840 -CTGCCCTCTGGAGCCACACAGAATAAGTCTAATCCCTCTTCCACATGAC 3792 chrXqtel1M 626484 AACC-TTCAAACACTTGAAGACAACT 626508 i - i i i C L3#LINE/CR1 3791 AGCCCTTCAAATATTTGAAGACAGCT 3766 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 36.94 CpG sites = 16, Kimura (unadjusted) = 36.94 Transitions / transversions = 0.94 (16/17) Gap_init rate = 0.07 (8 / 118), avg. gap size = 1.50 (12 / 8) 212 24.94 16.33 1.79 chrXqtel1M 626635 626732 (373268) C L3#LINE/CR1 (902) 3197 3086 m_b368s601i20 15404 chrXqtel1M 626635 CTAAGCATTTACCCAAGTCACTCACTGATGATGCCTGA---------GGC 626675 v iv i i i v - i vi i- --------- C L3#LINE/CR1 3197 CTATGTCTTCATCCAAGTCATTGA-TAAAAATGT-TGAACAGGACAGGGC 3150 chrXqtel1M 626676 CGTGCACAGATCCCTGGGGCACTCCACTGGAGACCACC-------TAGAC 626718 iv v v v v i v ------- v C L3#LINE/CR1 3149 CAAGGACAGAGCCCTGTGGCACGCCACTAGAGACCTCCCTCCAGGTTGAC 3100 chrXqtel1M 626719 ACTGAGCTATTAAT 626732 ii v i C L3#LINE/CR1 3099 ATCGATCCATTAAT 3086 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 29.21 CpG sites = 12, Kimura (unadjusted) = 30.69 Transitions / transversions = 1.00 (12/12) Gap_init rate = 0.04 (4 / 97), avg. gap size = 4.50 (18 / 4) 578 25.44 0.68 5.76 chrXqtel1M 627976 628121 (371879) MIRc#SINE/MIR 10 148 (120) m_b368s601i21 15405 chrXqtel1M 627976 GTGGTACAGTGGATAGAGTGCCAGGCCCGGAGTCAAGGAGACTCATCTTC 628025 i v ii ii i ii i i -------- MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGAC-------- 51 chrXqtel1M 628026 CTGAGTTCAAATCTGGCCTCCGATGTTCACTAGCCATGTGACCCTCGGCA 628075 i i i iv v i viii i ii i v MIRc#SINE/MIR 52 CTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA 101 chrXqtel1M 628076 AGTCATTTCACC-CTGTTTATCTCAGTTTCCTCATCTGTAAAATGAG 628121 i v - v vvii i MIRc#SINE/MIR 102 AGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 31.51 CpG sites = 26, Kimura (unadjusted) = 32.67 Transitions / transversions = 2.89 (26/9) Gap_init rate = 0.06 (9 / 145), avg. gap size = 1.00 (9 / 9) 12 25.54 0.00 6.12 chrXqtel1M 628653 628704 (371296) (CCT)n#Simple_repeat 1 49 (0) m_b368s252i14 15406 chrXqtel1M 628653 CCTCTTCTCTCCTCCTCAGCACCTCCTATCCCATCTCCTCCTGCGCCTTC 628702 i - -- v vii vi v v i (CCT)n#Simple 1 CCTCCTC-CTCCTCCTC--CTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC 47 chrXqtel1M 628703 TC 628704 (CCT)n#Simple 48 TC 49 Matrix = Unknown Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.00 (3 / 3) 496 29.89 11.29 1.97 chrXqtel1M 628959 629330 (370670) L2#LINE/L2 1931 2336 (746) m_b368s601i22 15407 chrXqtel1M 628959 TTCTCTCCTTGACCTTTTACAATCCAGCTTCCAAACCGATGGTTTCACTG 629008 i vi ivi v vi i ivv v ivii i i L2#LINE/L2 1931 TTCTCTCTTGAACCCACTCCAATCAGGCTTTCGTCCCCACCACTCCACCG 1980 chrXqtel1M 629009 TTGGGCATCCTCTT-TGAAGTTC-TCAGAGATATCTCAGTTACCAAATCC 629056 --iii - v - v v -i iv iv ivv i i L2#LINE/L2 1981 --AAAC-TGCTCTTGTCAAGGTCACCAATGACCTCCACGTTGCTAAATCC 2027 chrXqtel1M 629057 AATAGTCTTTTCTAAGTTCTCATCT---TTGATTTCACTGTAAATTCTGA 629103 i vv v i --- ii ?v v i ivv i L2#LINE/L2 2028 AATGGTCAATTCTCAGTCCTCATCTTACTTGACCTNTCAGCAGCATTTGA 2077 chrXqtel1M 629104 CACA----------TCCTATTTTTTG--ATATTGTCT---CTGGGTTTCC 629138 ----------i vi i -- i i v --- v i L2#LINE/L2 2078 CACAGTTGATCACTCCCTCCTTCTTGAAACACTTTCTTCACTTGGCTTCC 2127 chrXqtel1M 629139 AGGACACCCCCGTTTCCTGATTCTCTGCCTCCCTCGTT-TCCGCTCCTTC 629187 v vv i i i iv v ii -v L2#LINE/L2 2128 AGGACACCACACTCTCCTGGTTTTCCTCCTACCTCACTGGCCGCTCCTTC 2177 chrXqtel1M 629188 T------------ATGGATCCTCCTCCAGATCACGCCCCCTCACCTCTGG 629225 ------------v v vvvvi v v i ? v vi L2#LINE/L2 2178 TCAGTCTCCTTTGCTGGTTCCTCCTCATCTCCCCGACCTCTNAACGTTGG 2227 chrXqtel1M 629226 GGT-CCCAGGGGCTCTGT-----GCCCTCTGTTCTTCTCCCTCTAGACTC 629269 i - vi v ----- v vi iv v L2#LINE/L2 2228 AGTGCCCCAGGGCTCAGTCCTTGGACCTCTTCTCTTCTCTATCTACACTC 2277 chrXqtel1M 629270 CTTCACTGGG-GACCTC--TCAGGCTCCCGTGATTGAAAGCCCATCTGGC 629316 vi v ? - i --i v vi - v v vv i-- L2#LINE/L2 2278 ACTCCCTNGGTGATCTCATCCAGTCTCATG-GCTTTAAATACCATCTA-- 2324 chrXqtel1M 629317 TCTATACTGAGGAC 629330 -- i v L2#LINE/L2 2325 --TATGCTGATGAC 2336 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 38.17 CpG sites = 53, Kimura (unadjusted) = 39.06 Transitions / transversions = 0.95 (53/56) Gap_init rate = 0.05 (20 / 371), avg. gap size = 2.50 (50 / 20) 208 31.34 0.00 0.00 chrXqtel1M 629427 629493 (370507) AmnL2-1#LINE/L2 2169 2235 (378) m_b369s601i1 15408 chrXqtel1M 629427 AACTCCAGTGGCTCCCTACGGCTTTCAGGAACAAATACAAAATGCTCTAT 629476 v i ivvv v v i v vvi vi AmnL2-1#LINE/ 2169 AACTCCACTGGCTCCCCATTCATTTCAGGATCCAGTTCAAAATTGCCTTC 2218 chrXqtel1M 629477 TTAGTGTTCAAAGTCCT 629493 i v v i ii AmnL2-1#LINE/ 2219 CTTGTTTTTAAAACCCT 2235 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 40.78 CpG sites = 9, Kimura (unadjusted) = 40.78 Transitions / transversions = 0.75 (9/12) Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.0 (0 / 0) 193 37.40 8.33 0.60 chrXqtel1M 629429 629584 (370416) L2#LINE/L2 2847 3014 (68) m_b369s601i2 15408 chrXqtel1M 629429 CTCCAGTGGCTCCCTACGGCTTTCAGGAACAAATACAAAATGCTCTATT- 629477 i i i ivv vi iivv vv i v - iv- L2#LINE/L2 2847 CTCCAATGGCTTCCCATCTCACTCAGAGTAAAAGCCAAAGTCCT-TACAA 2895 chrXqtel1M 629478 TAGTGTTCAAAGTCCT---------GGCCCCCTGCTCTCTGTCTGCTCTT 629518 i iv v i i --------- i i i vi v vi i L2#LINE/L2 2896 TGGCCTACAAGGCCCTACATGATCTGGTCCCCCGTTACCTCTCTGACCTC 2945 chrXqtel1M 629519 ATAT---GGCACTCCTCAGTATGTTCTCTTTGATCCAGAGACTCTGTTCT 629565 v ---iv ii vvivi i v ii v vv v vi L2#LINE/L2 2946 ATCTCCTACCACTCTCCCCCTCGCTCACTCCGCTCCAGCCACACTGGCCT 2995 chrXqtel1M 629566 CCCGGCTGTTTCCCAAACA 629584 iv i i i L2#LINE/L2 2996 CCTTGCTGTTCCTCGAACA 3014 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 48.42 CpG sites = 32, Kimura (unadjusted) = 53.67 Transitions / transversions = 1.23 (32/26) Gap_init rate = 0.03 (4 / 155), avg. gap size = 3.50 (14 / 4) 273 27.70 20.59 2.50 chrXqtel1M 629492 629865 (370135) L2b_3end#LINE/L2 10 449 (17) m_b369s601i3 15408 chrXqtel1M 629492 CTGGCCCC-CTGC-TCTCTGTCTGC-TCTTATATGGCACTCCTCAGTATG 629538 - i - i v iv - iv i-- ii vv - L2b_3end#LINE 10 CTGGCCCCGCTACCTCTCCGGCCTCATCTCCTAC--CACTCTCCCCT-TG 56 chrXqtel1M 629539 TTCTCTTTGATCCAGAGACTCTGTTCTCCCGGCTGTTTCCCAAACAAG-- 629586 i v i v vv v vi iv i i i v -- L2b_3end#LINE 57 CTCACTCTGCTCCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACACGCC 106 chrXqtel1M 629587 ATTCTGTCTCCC-CCTCAGCG--TTT---CCTGTGGA-----CGGCC-GC 629624 ?v v? - v -- --- ? iv v----- v - v L2b_3end#LINE 107 ANGCTCNCTCCCGCCTCAGGGCCTTTGCACNTGCTGTTCCCTCTGCCTGG 156 chrXqtel1M 629625 AAGGCTCCCCCTCATTTCTCCATC---CTGACTTCT--------TTCAAG 629663 v i ii i ii i ii --- ii i -------- i L2b_3end#LINE 157 AACGCCCTTCCCCACCTCTTCGCCTGGCCAACTCCTACTCATCCTTCAGG 206 chrXqtel1M 629664 GCTCGGCTCAAATTCCAC-TCTTT---AAAGCTTTTCCTG----CTCA-- 629703 v i vi - i i---i ii i ---- i -- L2b_3end#LINE 207 TCTCAGCTCAAATGTCACCTCCTCCGGGAAGCCCTCCCTGACCCCCCAGG 256 chrXqtel1M 629704 ------------CTGTCCTCAG----CAACCAAT--TATCTT-CAACTCT 629734 ------------ iv v ---- vv i -- i i - v L2b_3end#LINE 257 CCGGGTCAGGCGCCCTCCTCTGGGCCCCCCCAGTCCTACCCTGCCACTCT 306 chrXqtel1M 629735 AATTCATCCAACATCTGTTTTGTATGCAACTGTTTGCAACCCTGGCTAGC 629784 iiv i ?- vii ? -ii i-- i ---- ivi v L2b_3end#LINE 307 GGGTTATN-ATTGTCTGNTT-ACATGT--CTGTCT----CCCCCACTAGA 348 chrXqtel1M 629785 CTAAGAGCTCCTTAAG-----------AGTCTTTCTT---------TGCA 629814 iv v i -----------? v --------- i L2b_3end#LINE 349 CTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTGTA 398 chrXqtel1M 629815 GCCCCAGAACTTATCACAGTGCCTGACACACAGCAGGTGCTCAATCAATG 629864 v vi i v ? i i i i v i L2b_3end#LINE 399 TCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATA 448 chrXqtel1M 629865 T 629865 L2b_3end#LINE 449 T 449 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 34.52 CpG sites = 62, Kimura (unadjusted) = 36.79 Transitions / transversions = 1.59 (62/39) Gap_init rate = 0.09 (32 / 373), avg. gap size = 2.75 (88 / 32) 281 20.00 5.00 0.00 chrXqtel1M 629806 629865 (370135) L2d2_3end#LINE/L2 476 538 (17) m_b369s601i4 15408 chrXqtel1M 629806 TTCTTTGCAGCCCC---AGAACTTATCACAGTGCCTGACACACAGCAGGT 629852 i v --- vi i v vi i i L2d2_3end#LIN 476 TTCTTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCACACAGTAGGC 525 chrXqtel1M 629853 GCTCAATCAATGT 629865 v i L2d2_3end#LIN 526 GCTCAATAAATAT 538 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 19.39 CpG sites = 7, Kimura (unadjusted) = 23.60 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.02 (1 / 59), avg. gap size = 3.00 (3 / 1) 14 22.93 3.77 1.85 chrXqtel1M 630474 630526 (369474) (GGAGGG)n#Simple_repeat 1 54 (0) m_b369s252i1 15409 chrXqtel1M 630474 GGA-GGGGAGGCCCGAGGGGGAGGGGGA-CGCCACACGGTGGGGGAGGCG 630521 - -vv -v vv viv v v (GGAGGG)n#Sim 1 GGAGGGGGAGG-GGGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGGAGGGG 49 chrXqtel1M 630522 GAGGG 630526 (GGAGGG)n#Sim 50 GAGGG 54 Matrix = Unknown Transitions / transversions = 0.11 (1/9) Gap_init rate = 0.06 (3 / 52), avg. gap size = 1.00 (3 / 3) 20 19.79 0.00 0.00 chrXqtel1M 630833 630878 (369122) (GCCCGC)n#Simple_repeat 1 46 (0) m_b369s252i2 15410 chrXqtel1M 630833 GCCCGCGCCTGGGCCCGCGCCTCAGCCCGCTCCTGGGCCCGCGCCC 630878 i v ivv v i v (GCCCGC)n#Sim 1 GCCCGCGCCCGCGCCCGCGCCCGCGCCCGCGCCCGCGCCCGCGCCC 46 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 21 18.74 1.89 1.89 chrXqtel1M 631019 631071 (368929) (CGGTGG)n#Simple_repeat 1 53 (0) m_b369s252i3 15411 chrXqtel1M 631019 CGATGACGGCGGTGGT-GCGGCTGGTGGTGGTGGTGGCGGCGGCGGCGGC 631067 i i i i - - i i i i (CGGTGG)n#Sim 1 CGGTGGCGGTGGCGGTGGCGG-TGGCGGTGGCGGTGGCGGTGGCGGTGGC 49 chrXqtel1M 631068 GGTG 631071 (CGGTGG)n#Sim 50 GGTG 53 Matrix = Unknown Transitions / transversions = 1.00 (8/0) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.00 (2 / 2) 22 28.90 1.19 2.41 chrXqtel1M 631025 631108 (368892) (CGG)n#Simple_repeat 1 83 (0) m_b369s252i4 15411 chrXqtel1M 631025 CGGCGGTGG-TGCGGCTGGTGGTGGTGGTGGCGGCGGCGGCGGCGGTGAC 631073 i -v - i i i i i i (CGG)n#Simple 1 CGGCGGCGGCGGCGGC-GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC 49 chrXqtel1M 631074 TGAGAGCAGCGGGAGCGGTCGCAGCGCGGGGGGCG 631108 v v - i vi iv i vv v (CGG)n#Simple 50 GGCG-GCGGCGGCGGCGGCGGCGGCGGCGGCGGCG 83 Matrix = Unknown Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.04 (3 / 83), avg. gap size = 1.00 (3 / 3) 16 24.88 5.26 2.56 chrXqtel1M 631075 631150 (368850) (GAGCGC)n#Simple_repeat 1 78 (0) m_b369s252i5 15412 chrXqtel1M 631075 GAGAGC-AGCGGGAGCG-G-TCGC-AGCGCGGGGGGCGAGTGACGGGCAC 631120 v - v - -v - - i v i - i i (GAGCGC)n#Sim 1 GAGCGCGAGCGCGAGCGCGAGCGCGAGCGC-GAGCGCGAGCG-CGAGCGC 48 chrXqtel1M 631121 GAGCGTAAGCGCGAGCACGGCCACGGGCGC 631150 ii i iv i i (GAGCGC)n#Sim 49 GAGCGCGAGCGCGAGCGCGAGCGCGAGCGC 78 Matrix = Unknown Transitions / transversions = 2.00 (10/5) Gap_init rate = 0.08 (6 / 75), avg. gap size = 1.00 (6 / 6) 19 7.16 0.00 0.00 chrXqtel1M 631175 631204 (368796) (ACGTC)n#Simple_repeat 1 30 (0) m_b369s252i6 15413 chrXqtel1M 631175 ACGTCACGTTACGTCACGTTACGTCACGTC 631204 i i (ACGTC)n#Simp 1 ACGTCACGTCACGTCACGTCACGTCACGTC 30 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 45 7.18 0.00 0.00 chrXqtel1M 631267 631325 (368675) (GGCGGA)n#Simple_repeat 1 59 (0) c_b369s251i0 15414 chrXqtel1M 631267 GGCGGAGGTGGAGGCGGAGGTGGAGGCGGAGGCGGAGGCGGAGACGGAGG 631316 i i i (GGCGGA)n#Sim 1 GGCGGAGGCGGAGGCGGAGGCGGAGGCGGAGGCGGAGGCGGAGGCGGAGG 50 chrXqtel1M 631317 CGGTGGCGG 631325 v (GGCGGA)n#Sim 51 CGGAGGCGG 59 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.0 (0 / 0) 21 19.27 0.00 5.36 chrXqtel1M 631438 631496 (368504) (GCC)n#Simple_repeat 1 56 (0) m_b369s252i7 15415 chrXqtel1M 631438 GCCGCCGCCGCCGCCACTGCCGCCGTCGTTCGCGCGCCGGGGCCGCCTCT 631487 i i i -i - vv v - (GCC)n#Simple 1 GCCGCCGCCGCCGCCGCCGCCGCCGCCG-CCGC-CGCCGCCGCCGCCGC- 47 chrXqtel1M 631488 TTCCGCCGC 631496 iv (GCC)n#Simple 48 CGCCGCCGC 56 Matrix = Unknown Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.05 (3 / 58), avg. gap size = 1.00 (3 / 3) 12 11.65 3.33 3.33 chrXqtel1M 633582 633611 (366389) (TGAAC)n#Simple_repeat 1 30 (0) m_b369s252i8 15416 chrXqtel1M 633582 TGAACTGATACTGAA-GGAAATGAACAGAAC 633611 - -v v v (TGAAC)n#Simp 1 TGAACTGA-ACTGAACTGAACTGAACTGAAC 30 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.07 (2 / 29), avg. gap size = 1.00 (2 / 2) 13 29.62 0.00 0.00 chrXqtel1M 634114 634158 (365842) (AAAA)n#Simple_repeat 1 45 (0) m_b369s252i9 15417 chrXqtel1M 634114 AAAAAATAAAAAGCTTTAATTAAAAAAAAAAAGAAAGAAAAACAA 634158 v ivvvv vv i i v (AAAA)n#Simpl 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 45 Matrix = Unknown Transitions / transversions = 0.38 (3/8) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 23 15.50 2.33 0.00 chrXqtel1M 635363 635405 (364595) (CA)n#Simple_repeat 1 44 (0) m_b369s252i10 15418 chrXqtel1M 635363 CACTCAATCACAAATACA-AGACACACACACACACACACACACA 635405 v vv v i - v (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACA 44 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.02 (1 / 42), avg. gap size = 1.00 (1 / 1) 513 20.35 4.31 2.54 chrXqtel1M 636388 636503 (363497) MIRb#SINE/MIR 1 118 (150) m_b369s601i5 15419 chrXqtel1M 636388 CAGAGGGGCAGCTAGATGGTGCAATGGATAGAGCAC-----CTGAAGTCA 636432 ---i i v -----i i MIRb#SINE/MIR 1 CAGAGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCA 47 chrXqtel1M 636433 GGAGGATCTGAGTTCCAATCTGGCCTTTGACACTTCCTAGCCGTGTGACG 636482 ivi i i v iv v i v v i v MIRb#SINE/MIR 48 GACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACC 97 chrXqtel1M 636483 CTGGGCAAGTCACTTAATCCC 636503 i i i i MIRb#SINE/MIR 98 TTGGGCAAGTTACTTAACCTC 118 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 23.13 CpG sites = 15, Kimura (unadjusted) = 24.31 Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.03 (4 / 115), avg. gap size = 2.00 (8 / 4) 20 0.00 0.00 0.00 chrXqtel1M 636516 636537 (363463) (A)n#Simple_repeat 1 22 (0) m_b369s252i11 15420 chrXqtel1M 636516 AAAAAAAAAAAAAAAAAAAAAA 636537 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAA 22 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 268 29.07 7.45 8.12 chrXqtel1M 637559 637719 (362281) C L2a_3end#LINE/L2 (8) 509 350 m_b369s601i6 15421 chrXqtel1M 637559 ATTTAAGCAGCATTAATTAAGTCCTTACTACTAAACACTTAATCAGACAC 637608 i vv ii v i iv i -------- vvii i C L2a_3end#LINE 509 ATTCAACAAATATTTATTGAGCGCCTACTA--------TGTGCCAGGCAC 468 chrXqtel1M 637609 TGTGCTAAATGCTGAGGATA------TGAAGCAAGGGGA-AAATGTCTTA 637651 v iii i ------ vv ivi - v --- C L2a_3end#LINE 467 TGTTCTAGGCGCTGGGGATACAGCAGTGAACAAAACAGACAAAAGTC--- 421 chrXqtel1M 637652 CCTGCCCTAGAGGAGTTCATATTCTAACGAGGG-----AGGCAACATGCA 637696 viv i i i ii i ----- i i vi C L2a_3end#LINE 420 CCTGCCCTCATGGAGCTTACATTCTAGTGGGGGGAGACAGACAATAAACA 371 chrXqtel1M 637697 AATAACTATGGACAAATGATGTA 637719 v v v - - i C L2a_3end#LINE 370 AATAAATAAGTA-AAAT-ATATA 350 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 35.69 CpG sites = 26, Kimura (unadjusted) = 37.91 Transitions / transversions = 1.53 (26/17) Gap_init rate = 0.10 (16 / 160), avg. gap size = 1.56 (25 / 16) 291 34.78 14.20 1.31 chrXqtel1M 637587 637924 (362076) C L2b_3end#LINE/L2 (22) 444 64 m_b369s601i7 15421 chrXqtel1M 637587 TACTAAACACTTAAT------CAGACACTGTGCTAAATGCTGAGGATA-- 637628 i i i i v ------ i ? iii i -- C L2b_3end#LINE 444 TACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGGGATACA 395 chrXqtel1M 637629 ----TGAAGCAAGGGGAAAATGTCTTACCTGCCCTAGAGGAGTTCATATT 637674 ---- - i--v i i?ivv v viv i i v C L2b_3end#LINE 394 GCGGTGAA-CAAGA--CAGACNCGGTCCCTGCCCTCACGGAGCTCACAGT 348 chrXqtel1M 637675 CTAACGAGGGAGGCA-ACATG----CAAATAACTATGGACAAATGATGTA 637719 ii i i - ---- i i i? iiv v iv vv i C L2b_3end#LINE 347 CTAGTGGGGGAGACAGACATGTAANCAGACAATNATAACCCAGAGTGGCA 298 chrXqtel1M 637720 AGAAAATATCA-------CCAGAAGGAAGACACCAGGGTTGATT---GGA 637759 i iv iv iii------- - i i i v ivii iii--- i C L2b_3end#LINE 297 GGGTAGGACTGGGGGGGCCCAG-AGGAGGGCGCCTGACCCGGCCTGGGGG 249 chrXqtel1M 637760 ATAGGGAAATGTTTCTTGCAAAAGGCTGGATTTTATCTCAAATTTGAAGG 637809 i vi i iv i ii v ii iviv v v v i ii C L2b_3end#LINE 248 GTCAGGGAGGGCTTCCCGGAGGAGGTGACATTTGAGCTGAGACCTGAAGG 199 chrXqtel1M 637810 A--------AGTCAGTCAGGAAATGATGATGAGGTAGGGGG-----GACA 637846 -------- ii i vi v - i i v v ----- i C L2b_3end#LINE 198 ATGAGTAGGAGTTGGCCAGGCGAAGA-GGTGGGGAAGGGCGTTCCAGGCA 150 chrXqtel1M 637847 GC---CACTGAAAATGCAGA-GTCTGGAGATGGGATGTTGATTGG---GT 637889 v---v v v ?i i - i iv ii v?vv v? --- C L2b_3end#LINE 149 GAGGGAACAGCANGTGCAAAGGCCCTGAGGCGGGAGNGAGCNTGGCGTGT 100 chrXqtel1M 637890 TCAAGGAACAAACAGGAGGCCA-TGATACTGGATCA 637924 i ivv - vvi v C L2b_3end#LINE 99 TCGAGGAACAGCAAGGAGGCCAGTGTGGCTGGAGCA 64 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 45.21 CpG sites = 73, Kimura (unadjusted) = 50.76 Transitions / transversions = 1.70 (73/43) Gap_init rate = 0.05 (18 / 337), avg. gap size = 2.94 (53 / 18) 404 30.18 1.24 1.24 chrXqtel1M 640597 640757 (359243) L1ME3C_3end#LINE/L1 389 549 (321) m_b369s551i0 15422 chrXqtel1M 640597 TATATCCCAAAGAAA-TCTTAAAGGAGAGAA-AGGGACCCACATGTACCA 640644 i i i - iiv v v v v - i v-- v L1ME3C_3end#L 389 TATACCCTAGAGAAACTCTCGCACGTGTGCACAAGGAG--ACATGTACAA 436 chrXqtel1M 640645 AAATGTTTGTGGTGGCCCTTTTTGTAGCAGCTAGAAACTGGAAACTGAGT 640694 i ii v ii vi v ii v i i vivv L1ME3C_3end#L 437 GAATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCT 486 chrXqtel1M 640695 GGCTGCCCATCAATTGGAGACTGGCTGGGTATATTGTGGTATATGAATAT 640744 iiv i iv v v iii v vv i L1ME3C_3end#L 487 AAATGTCCATCAACAGGAGAATGGATAAATAAATTGTGGTATATTCATAC 536 chrXqtel1M 640745 TATGGAATATTAT 640757 v i L1ME3C_3end#L 537 AATGGAATACTAT 549 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 38.25 CpG sites = 26, Kimura (unadjusted) = 39.41 Transitions / transversions = 1.18 (26/22) Gap_init rate = 0.03 (4 / 160), avg. gap size = 1.00 (4 / 4) 314 35.17 2.07 2.07 chrXqtel1M 640599 640839 (359161) L1MC5a_3end#LINE/L1 394 634 (2143) m_b369s551i1 15422 chrXqtel1M 640599 TATCCCAAAGAAATCTTA--AAGGAGAGAAAGGGACCCACATGTACCAAA 640646 i v ivi ?-- ii v vi i? --ii i v ii L1MC5a_3end#L 394 TATCCCGAAGATACACTNGCAAAAATACGAAANGAC--GTATGCACAAGG 441 chrXqtel1M 640647 ATGTTTGTGGTGGCCCTTTTTGTAGCAGCTAGAAACTGGAAACTGAGTGG 640696 v i ii v ii vi v ii v i i vivviii L1MC5a_3end#L 442 TTATTCATTGCAGCATTATTTGTAATAGCAAAAGACTGGAAACAACCCAA 491 chrXqtel1M 640697 CTGCCCATCAATTGGAGACTGGCTGGGTATATTGTGGTATATGAATATTA 640746 v i v i i ii v i i i vv i iv L1MC5a_3end#L 492 ATGTCCATCAATAGGGGACTGGTTGAATAAACTATGGTACATCCACACAA 541 chrXqtel1M 640747 TGGAATATTATTGTTCTGTAAGAAATGACCAGCAGGATGATTTC---AGA 640793 i i vvvv - v -- vv v i --- v L1MC5a_3end#L 542 TGGAGTACTATGCAGCTGTAA-AAAGGA--ATGAGGAAGATCTCTATATA 588 chrXqtel1M 640794 AAGGTCTGGAGAGACTGACAGGAACTGATGCTGAGTGAAATGAGCA 640839 vv ? v v iivv vv iv i i vi L1MC5a_3end#L 589 CTGNTATGGAGTGATCTCCAGGATATATTGTTAAGTGAAAAAAGCA 634 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 47.22 CpG sites = 45, Kimura (unadjusted) = 49.72 Transitions / transversions = 1.18 (45/38) Gap_init rate = 0.03 (7 / 240), avg. gap size = 1.43 (10 / 7) 410 30.08 0.00 0.00 chrXqtel1M 640635 640757 (359243) L1ME3F_3end#LINE/L1 430 552 (438) m_b369s551i2 15422 chrXqtel1M 640635 ACATGTACCAAAATGTTTGTGGTGGCCCTTTTTGTAGCAGCTAGAAACTG 640684 v i ii i ii v v i ii v i L1ME3F_3end#L 430 ACATGTACAAGAATGTTCATAGCAGCACTGTTCGTAATAGCAAAAAACTG 479 chrXqtel1M 640685 GAAACTGAGTGGCTGCCCATCAATTGGAGACTGGCTGGGTATATTGTGGT 640734 vivviiiv i i iv v v iii v L1ME3F_3end#L 480 GAAACAACCCAAATGTCCATCGACAGGAGAATGGATAAATAAATTGTGGT 529 chrXqtel1M 640735 ATATGAATATTATGGAATATTAT 640757 vv i iv L1ME3F_3end#L 530 ATATTCACACAATGGAATATTAT 552 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 36.92 CpG sites = 22, Kimura (unadjusted) = 39.65 Transitions / transversions = 1.47 (22/15) Gap_init rate = 0.00 (0 / 122), avg. gap size = 0.0 (0 / 0) 12 7.25 10.34 0.00 chrXqtel1M 641188 641216 (358784) (AGGGG)n#Simple_repeat 1 32 (0) m_b369s252i12 15423 chrXqtel1M 641188 AGGGGA-GGG-GGTGAGGGGA-AGGAGGGGAG 641216 - - v -i (AGGGG)n#Simp 1 AGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAG 32 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.11 (3 / 28), avg. gap size = 1.00 (3 / 3) 306 34.37 5.22 2.71 chrXqtel1M 641320 641932 (358068) L1M2_orf2#LINE/L1 2028 2655 (636) m_b369s551i3 15424 chrXqtel1M 641320 AGCAATAAGACAAGAAAGAGAAATGAAGGGAATG-AGCCTAAGAAAAAGG 641368 v i i i i i v v- ivi iii ii L1M2_orf2#LIN 2028 AGCAATTAGGCAAGAGAAAGAAATAAAAGGCATCCAAATTGGAAAGGAGG 2077 chrXqtel1M 641369 AAACAAAGTTGGT--TTTTTGCAGATGACATGATGTTTTCTTTAGTGAAT 641416 iiv i vi-- v v v v ? vi ? L1M2_orf2#LIN 2078 AAGTCAAATTGTCCCTGTTTGCAGATGACATGATCTTATATNTAGAAAAN 2127 chrXqtel1M 641417 CC-----AATCAACTAAAAAACTAATTGAAACAATAAACAATTTCAGCAA 641461 ----- v v i ?v v vii i v i L1M2_orf2#LIN 2128 CCTAAAGACTCCACCAAAAAACTNTTAGAACTGATAAACGAATTCAGTAA 2177 chrXqtel1M 641462 AAATGAAAGATTCAGGAAATAAAATAAACCCACATAAATCATCAGCACAG 641511 iv ------- v i v vi v vi ivv L1M2_orf2#LIN 2178 AGTTG-------CAGGATACAAAATCAACATACAAAAATCAGTAGCATTT 2220 chrXqtel1M 641512 ATGTATTTTGCCAATGAA--ATCTGACAGGAAGAGATAGAAATAGAAATT 641559 v i iviiiv i -- v -- i vi i v v i L1M2_orf2#LIN 2221 CTATACGCCAACAACGAACTATCTGAAA--AAGAAATCAAGAAAGCAATC 2268 chrXqtel1M 641560 CCATTAAAAAAAAACCTAT-AAAAACACAAAGTATTTGAGTGTCTACCT- 641607 v v v i-- i- v i i ii ii vi vv ii - L1M2_orf2#LIN 2269 CCATTTACAATAG--CTACAAAAAAAATAAAATACCTAGGAATAAATTTA 2316 chrXqtel1M 641608 GCCAAGACACAAACAGGAACTATATGAACACAATTACAAAATAATCTTTG 641657 i i- viviv i v v ii ?v v i i i v vv vi L1M2_orf2#LIN 2317 ACCAAGG-AGGTGAAAGATCTCTACAANGAAAACTATAAAACACTGATGA 2365 chrXqtel1M 641658 TAGAAA-TGATGACTGAGCTAAATAACTGCAGAAATAGCAATTATTCATG 641706 v - v -v vvi ? v v i i v vvv ii L1M2_orf2#LIN 2366 AAGAAATTGAAGA-GGACACAAANAAATGGAAAGATATCCCATGCTCATG 2414 chrXqtel1M 641707 GGCAGGATAAGGCAATA----TAAAAAAGGCAGTCTTCCTAAACTAATTT 641752 iiv vi ivi ---- vi?v vv v i vii i L1M2_orf2#LIN 2415 GATTGGAAGAATTAATATTGTTAAAATGNCCATACTACCCAAAGCGATCT 2464 chrXqtel1M 641753 ACTTATTCAACACCATTTC---CAACCTACCAAAGG-ATTCTTTTTATAG 641798 vv ii v ii --- vv v i- -- i i L1M2_orf2#LIN 2465 ACAGATTCAATGCAATCCCTATCAAAATACCAATGACATTC--TTCACAG 2512 chrXqtel1M 641799 AGTTAAGGAAATGACCCCAACAAAATTCTTTTGGGA-AACAAAAGGTCAG 641847 iv iii v? vi --i v v i -v ii vv L1M2_orf2#LIN 2513 AAATAGAAAAAANAATCC--TAAAATTCGTATGGAACCACAAAAGACCCC 2560 chrXqtel1M 641848 AAATCA-TAAGGGAATT---AATGAAAAGGGGAAGGGGGAAGGAAGCCCA 641893 i vi-i i v i--- iii iiv i vv i v v v L1M2_orf2#LIN 2561 GAATAGCCAAAGCAATCCTGAGCAAAAAGAACAAAGCTGGAGGCATCACA 2610 chrXqtel1M 641894 ------GATCCCCAACTATACTACAAAGTAGTAATCACTAAAACA 641932 ------ iii v v ivi i v i L1M2_orf2#LIN 2611 CTACCTGACTTCAAAATATACTACAAAGCTATAGTAACCAAAACA 2655 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 46.30 CpG sites = 109, Kimura (unadjusted) = 47.95 Transitions / transversions = 1.14 (109/96) Gap_init rate = 0.05 (31 / 612), avg. gap size = 1.58 (49 / 31) 344 34.36 4.35 3.18 chrXqtel1M 641321 641849 (358151) L1M4_orf2#LINE/L1 2032 2566 (728) m_b369s551i5 15424 chrXqtel1M 641321 GCAATAAGACAAGAAAGAGAAATGAAGGGAATG-AGCCTAAGAAAAAGGA 641369 v i i i i v v- vi iii ii i L1M4_orf2#LIN 2032 GCAATTAGGCAAGAAAAAGAAATAAAAGGCATCCAGATTGGAAAGGAAGA 2081 chrXqtel1M 641370 AACAAAGTTGGTTTT--TTGCAGATGACATGATGTTTTCTTTAGTGAATC 641417 ii ii ivi i -- i v v v v vi L1M4_orf2#LIN 2082 AGTAAAACTATCTCTATTCGCAGATGACATGATCTTGTATATAGAAAATC 2131 chrXqtel1M 641418 C-----AATCAACTAAAAAACTAATTGAAACAATAAACAATTTCAGCAAA 641462 ----- v ? v v vi i v i L1M4_orf2#LIN 2132 CTAAGGAATCCACNAAAAAACTATTAGAACTAATAAACGAGTTCAGCAAG 2181 chrXqtel1M 641463 AATGAAAGATTCAGGAAATAAAATAAACCCACATAAATCATCAGCACAGA 641512 iv ------- v i i v ivi v viv i ivvv L1M4_orf2#LIN 2182 GTTG-------CAGGATACAAGATCAATATACAAAAATCAATTGTATTTC 2224 chrXqtel1M 641513 TGTATTTTGCCAATGA--AATCTGACAGGAAGAGATAGAAATAGAAATTC 641560 i ivi iv -- i v -- v i vi i v iv L1M4_orf2#LIN 2225 TATACACTAGCAATGAACAATCCGAAA--ATGAAATTAAGAAAACAATTC 2272 chrXqtel1M 641561 CATTAAAAAAAAACCTATAAAAACACAAAGTATTTGAGTGTCTACCTGCC 641610 -v v v i v vv iv i i i ii vi vv ii iv L1M4_orf2#LIN 2273 CATT-TACAATAGCATCAAAAAGAATAAAATACTTAGGAATAAATTTAAC 2321 chrXqtel1M 641611 AAGACACAAACAGGAACTATA---TGAACACAATTACAAAATAATCTTTG 641657 i v vivi i vi i --- --- i i v v vi L1M4_orf2#LIN 2322 AAAAGAAGTGCAAGACTTGTACACTGAA---AACTACAAAACATTGTTGA 2368 chrXqtel1M 641658 TAGAAATGATGACTGAGCTAAATAACTGCAGAAATAGCAATTATTCATGG 641707 v v viivv v v v i i i v vvv i L1M4_orf2#LIN 2369 AAGAAATTAAAGAAGACCTAAATAAATGGAAAGACATCCCATGTTCATGG 2418 chrXqtel1M 641708 GCAGGATAAGGCAATA---TAAAAAAGGCAGT-CTTCCTAAACTAATTTA 641753 iiv vi vvi --- v i v i - i i i i i L1M4_orf2#LIN 2419 ATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTGATCTA 2468 chrXqtel1M 641754 CTTATTCAACACCATTTC---CAACCTACCAAAGGATTCTTTTTATAG-A 641799 vv i v ii --- vv v ivv ?i - ii - L1M4_orf2#LIN 2469 CAGATTCAACGCAATCCCTATCAAAATCCCAGCTGNCT-TTTTTGCAGAA 2517 chrXqtel1M 641800 GTTAAGGAAATGACCCCAACAAAATTCTTTTGGGAA-ACAAAAGG-TCAG 641847 i i vi iv i ---i v v i -i ii i-i L1M4_orf2#LIN 2518 ATTGACAAGCTGATCC---TAAAATTCATATGGAAATGCAAGGGACCCAG 2564 chrXqtel1M 641848 AA 641849 L1M4_orf2#LIN 2565 AA 2566 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 46.03 CpG sites = 96, Kimura (unadjusted) = 47.52 Transitions / transversions = 1.20 (96/80) Gap_init rate = 0.05 (28 / 528), avg. gap size = 1.43 (40 / 28) 399 32.95 4.17 3.49 chrXqtel1M 641321 641776 (358224) L1MC_orf2#LINE/L1 2032 2490 (804) m_b369s551i4 15424 chrXqtel1M 641321 GCAATAAGACAAGAAAGAGAAATGAAGGGAATG-AGCCTAAGAAAAAGGA 641369 ii i i v i- vi ii ii i L1MC_orf2#LIN 2032 GCAATAAGACAAGAAAAGGAAATAAAAGGTATACAGATTGGGAAGGAAGA 2081 chrXqtel1M 641370 AACAAAGTTGGTTT--TTTGCAGATGACATGATGTTTTCTTTAGTGAATC 641417 i ii vi -- i vv i v v vi L1MC_orf2#LIN 2082 AATAAAACTGTCTTTGTTCGCAGATGACATGATTGTCTATGTAGAAAATC 2131 chrXqtel1M 641418 C-----AATCAACTAAAAAACTAATTGAAACAATAAACAATTTCAGCAAA 641462 ----- i v vv v vi i i vi i L1MC_orf2#LIN 2132 CGAAAGAATCGACAAAAAAACTCCTGGAACTAATAAGCGATTATAGCAAG 2181 chrXqtel1M 641463 AATGAAAGATTCAGGAAATAAAATAAACCCACATAAATCATCAGCACAGA 641512 iv ------- v i ii v ivi v i viv vivvv L1MC_orf2#LIN 2182 GTTG-------CAGGATACAAGGTTAATATACAAAAGTCAATCGCTTTCC 2224 chrXqtel1M 641513 TGTATTTTGCCAATGAAATCTGACAGGAA---GAGA-TAGAAATAGAAAT 641558 i viiiv ---ii ?v --- i - i i -v L1MC_orf2#LIN 2225 TATATACCAGCAATGAA---CAANTGGAATTTGAAATTAAAAACA-CAAT 2270 chrXqtel1M 641559 TCCA-TTAAAAAAAAACCTATAAAAACACAAAGTATTTGAGTGTCTACCT 641607 v - v vv iv ivi -- ii i i ii i vv i L1MC_orf2#LIN 2271 ACCATTTACATTAGCACCCCCAAAA--ATGAAATACTTAGGTATAAATCT 2318 chrXqtel1M 641608 GCCAAGACACAAACAGGAACTATATGAACACAATTACAAAATAATCT--T 641655 iv i i iiv i v iv v i i-- -- L1MC_orf2#LIN 2319 AACAAAATATGTACAAGATCTATATGAGGAAAACTACAAAAC--TCTGAT 2366 chrXqtel1M 641656 TGTAGAAATGATGACTGAGCTAAATAACTGCAGAAATAGCAATTATTCAT 641705 viv v viivv ? v v i vivvv i L1MC_orf2#LIN 2367 GAAAGAAATCAAAGAAGANCTAAATAAATGGAGAGATATTCCATGTTCAT 2416 chrXqtel1M 641706 GGGCAGGATAAGGCAATA---TAAAAAAGGCAG-TCTTCCTAAACTAATT 641751 ii vi vv --- v i v v - i vi i i L1MC_orf2#LIN 2417 GGATAGGAAGACTCAATATTGTCAAGATGTCAGTTCTTCCCAACTTGATC 2466 chrXqtel1M 641752 TACTTATTCAACACCATTTCCAACC 641776 ivv ii v - i i L1MC_orf2#LIN 2467 TATAGATTCAATGCAA-TCCCAATC 2490 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 43.67 CpG sites = 81, Kimura (unadjusted) = 44.92 Transitions / transversions = 1.27 (81/64) Gap_init rate = 0.05 (25 / 455), avg. gap size = 1.40 (35 / 25) 541 33.47 3.80 6.85 chrXqtel1M 642064 642589 (357411) L1ME3C_3end#LINE/L1 39 549 (321) m_b369s551i6 15424 chrXqtel1M 642064 TAAGAAAACTGGCATTCCCCAACTGATTAAAGGACAAAGTATATGAACAG 642113 v i --v iv vv v i iv L1ME3C_3end#L 39 TAAGAAAACAGACA--ACCCAATAGAAAAATGGGCAAAAGATATGAACAG 86 chrXqtel1M 642114 AAAGTTTTCAGGGAAAGAAATCCTAGTGATCAAATAGCTATATGAAAAAA 642163 iv i iv iii i i? v i ii - ivi i L1ME3C_3end#L 87 GCAATTCACAGAAGAGGAAACNCGAATGGCCAA-TAAACATATGAAAAGA 135 chrXqtel1M 642164 TACTGGAAATCACTACTGATTAGGAACACGTAAGTTTGAACCACTCTGAG 642213 i vi vv v i i i v i i i vi ? vv L1ME3C_3end#L 136 TGCTCAACCTCACTAGTAATCAGGGAAATGCAAATTAAAACNACAATGAG 185 chrXqtel1M 642214 ATTTCATCTCACAGCCATC-------CAGGAAATGACAAATGTCAGAGGA 642256 vi i v ------- ii v v v i v v v iv L1ME3C_3end#L 186 ATACCATTTCACACCCATCAGATTGGCAAAAATTTAAAAGTCTGACAATA 235 chrXqtel1M 642257 GC-TGTTTTAG---GGATATCTGAGTAGGCCTCCAATAGGTACACGGATG 642302 v -v v i --- i -v -------- ii v v vv i L1ME3C_3end#L 236 CCAAGTGTTGGCGAGGATGT-GGAG--------CAACGGGAACTCTCATA 276 chrXqtel1M 642303 CATTGTTGATGGAGCTGTGAACCCCATGTTCCAACCATTCTGGAAAGCAA 642352 i i i iiv i i---- v v i i i L1ME3C_3end#L 277 CACTGCTGGTGGGAGTGTAAAT----TGGTACAACCACTTTGGAGAGCAA 322 chrXqtel1M 642353 TTTGGAACCAGACTCTA--AAAGCTATCCAATTGTGTAGACCTCTCGACT 642400 v vi --- -- i i--v iv i i v iiv i L1ME3C_3end#L 323 TTTGGCAATA---TCTAGTAAAGTTG--AAGATGCGCATACCCTACGACC 367 chrXqtel1M 642401 CAGCTGTAATCCACTACCAGTTCCAGACACCAAAGAGA---TCAAAGAAA 642447 vi -- v i v vi v v i i i --- iv vivi L1ME3C_3end#L 368 CAGCAAT--TCCACTCCTAGGTATATACCCTAGAGAAACTCTCGCACGTG 415 chrXqtel1M 642448 GGAAAAAAAAAAGGACTCATGGATACCAAAGTATTTCCAGCAGCTTTTTC 642497 v v v ii i ----- -- v i i i iviv v v i L1ME3C_3end#L 416 TGCACAAGGAGA-----CATG--TACAAGAATGTTCATTGCAGCATTGTT 458 chrXqtel1M 642498 TGTGGGACCAAAGAATTAAAAAGTGAGAGGCTAGG----CACCCACTGGG 642543 iiv v i i ii ---- v iv ii---- i v v i L1ME3C_3end#L 459 TGTAATAGCGAAAAATTGGAA----ACAACCTAAATGTCCATCAACAGGA 504 chrXqtel1M 642544 AAATGGCTAAACCATTTGTGGTATATGAATATGATGGACTTACTAT 642589 i v iv v vv ii v- L1ME3C_3end#L 505 GAATGGATAAATAAATTGTGGTATATTCATACAATGGAA-TACTAT 549 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 43.73 CpG sites = 90, Kimura (unadjusted) = 45.65 Transitions / transversions = 1.22 (90/74) Gap_init rate = 0.08 (41 / 525), avg. gap size = 1.34 (55 / 41) 453 36.79 3.25 5.23 chrXqtel1M 642080 642664 (357336) L1ME4c_3end#LINE/L1 56 629 (201) m_b369s551i7 15424 chrXqtel1M 642080 CCCCAACTGATTAAAGGACAAAGTATATGAACAGAAAGTTTTCAGGGAAA 642129 iv v v i v i v i iv ?iii i L1ME4c_3end#L 56 CCCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAG 105 chrXqtel1M 642130 GAAATCCTAGTGATCAAATAGCTATATGAAAAAATACTGGAAATCACTAC 642179 v v ? ii - i ivi i i ii vi vv i v L1ME4c_3end#L 106 GAAATACAANTAGT-AAACAAACACATGGAAAAATGTTCAACCTCGCTAG 154 chrXqtel1M 642180 TGATTAGGAACACGTAAGTTTGAACCACTCTGAGATTTCATCTCACAGCC 642229 i i iii v i i i vi i v vv vi i i iv i L1ME4c_3end#L 155 TAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCT 204 chrXqtel1M 642230 ATCCAGGAAATGA-CAAATGTCAGAGGAGCTGTTTTAGGGATATCTGA-G 642277 i---- v - vi ivi ii ii v -----i i ii - L1ME4c_3end#L 205 ATT----AAATTAGCAAAAATTTAAAAAATTGAT-----AATACCCAATG 245 chrXqtel1M 642278 TAGGC----CTCC-----AATAGGTACACGGATGCATTGTTGATGGAGCT 642318 iv ----? v ----- iv ? vv i i i vi? L1ME4c_3end#L 246 CTGGCGAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANT 295 chrXqtel1M 642319 GTGAACCCCATGTTCCAACCATTCTGGAAAGCAATTTGGAACCAGACTCT 642368 i i---- v v v i v vi viivii L1ME4c_3end#L 296 GTAAAT----TGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATC 341 chrXqtel1M 642369 AAAAGCTATCCAATTGTGTAGACCTCTCGACTCAGCTGTAA-TCCACTAC 642417 i i vv v vi v ii i i --- - v L1ME4c_3end#L 342 AAGAGCCATAAAAATGTTCATACCCTTTGACCCA---GTAATTCCACTTC 388 chrXqtel1M 642418 CAG---TTCCAGACACCAAAGAGATCAAAGAAAGGAAAAAAAAAAGGACT 642464 ii --- i--- iv i i i v vvv i ii ---i L1ME4c_3end#L 389 TGGGAATTT---ATCCTAAGGAAATAATTCAAAAGAAGGAAAAA---GCT 432 chrXqtel1M 642465 CATGGATACCAAAGTATTTCCAGCAGCTTTTTCTGTGGGACCAAAGAATT 642514 - ivii v ii i iviv v v i i iiv v i i L1ME4c_3end#L 433 -ATATGCACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATT 481 chrXqtel1M 642515 AAAAAGTGAGAGGCTAGGCACCCACT----GGGAAATGGCTAAACCATTT 642560 ii ---- v iv iiiii vi---- i i iiv v L1ME4c_3end#L 482 GGAA----ACAACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATT 527 chrXqtel1M 642561 GTGGTATATGAATATGATGGACTTACTATGGCACTCTAAGAAATGATGAG 642610 i i v? ivi v- i vvi iv v i i v L1ME4c_3end#L 528 ATGGTACATCNACTCGATGGAA-TATTATGCAGCCATTAAAAATGATAAT 576 chrXqtel1M 642611 CAAGCTAATTTCGGAGCAACCTGGGAATACGTGTATGAATTGATATGGAG 642660 i v vvi i vi v v i - i v vv i i vi L1ME4c_3end#L 577 TATGAAGACTATGTAGCAACATGGAAA-ATGTTTATGATATAATGTTAAG 625 chrXqtel1M 642661 GGAA 642664 v L1ME4c_3end#L 626 TGAA 629 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 52.11 CpG sites = 124, Kimura (unadjusted) = 54.11 Transitions / transversions = 1.55 (124/80) Gap_init rate = 0.06 (37 / 584), avg. gap size = 1.32 (49 / 37) 243 30.31 4.32 6.29 chrXqtel1M 643338 643499 (356501) C L2#LINE/L2 (1526) 1556 1398 m_b369s601i8 15425 chrXqtel1M 643338 GGAGATAGGAGC--GAAAAGGTACTCTTAGCTAATGGTCTCAATTTTTTT 643385 v i i ?-- vii i v -- i v ii v i i C L2#LINE/L2 1556 GGTGGTGGGAGNNTGTGGAAGTTCTCTT--CTGATTGCTTCTATTTTCTC 1509 chrXqtel1M 643386 AATGAAACATGAAGCAAGGTTTTCAGGTAAATGGGTGAA-AGAGAATGAG 643434 i i v iv v i iv v v i - i i v C L2#LINE/L2 1508 AGTGAAATAGGAAGCAAGGTCATCAGCTGAGAGTGAGGATAGGGGAGGAG 1459 chrXqtel1M 643435 CCATAGGATATTTGAGGAGGGCGAGTTTAGAAG----GGAATAAAAGTCT 643480 vii v vi i v i---- ---- i ivv C L2#LINE/L2 1458 GTGTTGGAGGTTTGAGGAGAGAGG----AGAAGGTGTGAAATAGTCGTCT 1413 chrXqtel1M 643481 AGAAGAATCGCTGGAAGAG 643499 i i---- i C L2#LINE/L2 1412 AGGAGAG----TGGGAGAG 1398 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 40.48 CpG sites = 28, Kimura (unadjusted) = 40.48 Transitions / transversions = 1.56 (28/18) Gap_init rate = 0.08 (13 / 161), avg. gap size = 1.31 (17 / 13) 445 26.91 3.31 4.00 chrXqtel1M 643852 644002 (355998) L2d2_3end#LINE/L2 403 552 (3) m_b369s601i9 15426 chrXqtel1M 643852 CTTTTCAACTTCTTGTGTTTTGTCTTCCCCTGTTAGATTAGAAGCTCTTA 643901 vv vi i i - vii iv i v L2d2_3end#LIN 403 CTTTTCACGTGTTTATGTCTTGTCT-CCCCAACTAGATTGTAAGCTCCTT 451 chrXqtel1M 643902 GAGGGGAGGGATCA--TCTT-TCTTTTTTTGTATTGTGTCCCAC--CACT 643946 v i -- - vi i i---i -- i i L2d2_3end#LIN 452 GAGGGCAGGGACCATGTCTTATACTTCTTTGTATC---CCCCACAGCGCC 498 chrXqtel1M 643947 CAACACAGAGCCTGGCACATAGGAGATATTTAATAAGTGTTTACTGCCTC 643996 i i v v i v iiii i i i ii vi - L2d2_3end#LIN 499 TAGCACAGTGCCTTGCACACAGTAGGCGCTCAATAAATATTTGTTGATT- 547 chrXqtel1M 643997 CTGATT 644002 - L2d2_3end#LIN 548 -TGATT 552 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 32.54 CpG sites = 27, Kimura (unadjusted) = 34.89 Transitions / transversions = 2.25 (27/12) Gap_init rate = 0.06 (9 / 150), avg. gap size = 1.22 (11 / 9) 195 31.15 1.61 1.61 chrXqtel1M 644093 644154 (355846) C L2#LINE/L2 (626) 2456 2395 m_b369s601i10 15427 chrXqtel1M 644093 TTTGGAGCATGCCAAATTTAAGACATCTGG-GGATGTCCAGTTGGAGATG 644141 - ii i i iii iv-i ii iv C L2#LINE/L2 2456 TTTGGA-CATGTTAAGTTTGAGATGCCTATTAGACATCCAAGTGGAGATG 2408 chrXqtel1M 644142 TCCATCGGGCAAT 644154 v vii i C L2#LINE/L2 2407 TCGAGTAGGCAGT 2395 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 44.27 CpG sites = 15, Kimura (unadjusted) = 44.27 Transitions / transversions = 3.75 (15/4) Gap_init rate = 0.03 (2 / 61), avg. gap size = 1.00 (2 / 2) 181 25.71 0.00 0.00 chrXqtel1M 644152 644186 (355814) C L2c_3end#LINE/L2 (27) 451 417 m_b369s601i11 15428 chrXqtel1M 644152 AATGCTCACTGTGTGCTGAGCCCTGGGGATACAAA 644186 ii ii i iii v C L2c_3end#LINE 451 AGCGCCTACTATGTGCCAGGCGCTGGGGATACAAA 417 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 29.95 CpG sites = 8, Kimura (unadjusted) = 34.72 Transitions / transversions = 8.00 (8/1) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 516 16.59 2.42 7.63 chrXqtel1M 646249 646372 (353628) MIRc#SINE/MIR 10 127 (141) m_b369s601i12 15429 chrXqtel1M 646249 GTGGCACAGTGGATAGAGCACCGGCCCTGAAGTCAGGAGGACCTGGGTTC 646298 ii v i v i i i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chrXqtel1M 646299 AAAT-CTGGCCCTCAGACACTTAACACTTCCTAACTGTGTGATC-TGGGC 646346 i i - i i -- v ------- i i - MIRc#SINE/MIR 60 GAGTCCCGGCTCT--GCCACTTA-------CTAGCTGTGTGACCTTGGGC 100 chrXqtel1M 646347 AAGTCACTTAACCCCCATT-GCCTCAG 646372 i iv v- MIRc#SINE/MIR 101 AAGTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 17.04 CpG sites = 14, Kimura (unadjusted) = 19.18 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.10 (12 / 123), avg. gap size = 1.00 (12 / 12) 21 10.73 0.00 0.00 chrXqtel1M 646374 646403 (353597) (A)n#Simple_repeat 1 30 (0) m_b369s252i13 15430 chrXqtel1M 646374 AAAAAAAAAAAAAAAAAAAAAGATTAAAAA 646403 i vv (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 30 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 109 11.23 1.18 0.00 chrXqtel1M 646526 646694 (353306) (TCT)n#Simple_repeat 1 171 (0) m_b369s252i14 15431 chrXqtel1M 646526 TCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTC-TC 646574 - (TCT)n#Simple 1 TCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTC 50 chrXqtel1M 646575 TTCTTCTCTTTCTTCTTCTTCTTCTTCTTCTTCTTTTTCTTCTTCTTCTT 646624 ii i (TCT)n#Simple 51 TTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTT 100 chrXqtel1M 646625 C-TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCTTCT 646673 - i i i i i i i i i i i i i i (TCT)n#Simple 101 CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCT 150 chrXqtel1M 646674 TCTTCTTCTTCTTCTTCTTCT 646694 (TCT)n#Simple 151 TCTTCTTCTTCTTCTTCTTCT 171 Matrix = Unknown Transitions / transversions = 1.00 (17/0) Gap_init rate = 0.01 (2 / 168), avg. gap size = 1.00 (2 / 2) 576 32.66 3.53 8.97 chrXqtel1M 646877 647357 (352643) L1ME5_3end#LINE/L1 187 643 (298) m_b369s551i8 15432 chrXqtel1M 646877 AAACACCACTATCCACCTGTCAGATTGGCTAGAATGACAGGGAAAGATAA 646926 i i i v v i i i v i v v ii vvi L1ME5_3end#LI 187 AGATATCACTTTACACCTATTAGACTGGCAAAAATTAGAAAGCTGGATAA 236 chrXqtel1M 646927 TGAGGAATGTTGGAGGGAATGTGGGAAAACAGGGACACTGATACATTGTT 646976 vvi i v i i i ? i i v v i i i L1ME5_3end#LI 237 TGCCAAGTGTTGGCGAGGATGTGGGGANATAGGAACCCTCATGCACTGCT 286 chrXqtel1M 646977 GGTGGAGGTGTGAGCGGATCCAACCATTCTGGAGAACAATTTGG-AATAT 647025 ii iii v i v i i i - i i L1ME5_3end#LI 287 GGTGGGAGTGTAGACTGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTAC 336 chrXqtel1M 647026 ---GTCAAAGCTATCAA--ACTCCCTTACCTT-TGATCCA-CAGT---GT 647065 --- ---- i -- iv v v i - i - i --- i L1ME5_3end#LI 337 TTAGTCAA----ATTAAGTATACGCATACCCTATGACCCAGCAATTCCGC 382 chrXqtel1M 647066 TTTAAACAGGGATTATATCCCAAGGAGATACTAAAGAAGG---GAAAGGG 647112 i---- v vv i i v v viv ---iv L1ME5_3end#LI 383 TC----CTGGGTATATATCCCAAAGAAATTCTCACACAGGTCCATAAGGG 428 chrXqtel1M 647113 AGCTGACATATTTTGCATATATTTTGCACCCATATGTGCAAAAATATTTG 647162 ---- -------------------------- i i ii i ii L1ME5_3end#LI 429 ----GACAT--------------------------GTACGAGGATGTTCA 448 chrXqtel1M 647163 GGGCAGCCCTGTTTGTAGTGGCCAGAAACTGGAAACTGAGTGGACGCCCA 647212 vv vi i vi i ii ii vivv ii i L1ME5_3end#LI 449 TTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGGGTGTCCA 498 chrXqtel1M 647213 TCAGTTGGAGAATGGCTGAATAAATTGGGGTATATGAATATTATGGAATG 647262 v v i v iii v v iv v i ii i i L1ME5_3end#LI 499 TCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACACCATGGAGTA 548 chrXqtel1M 647263 TTATTGTTCTGTAAAAAATGACCCAATAGGATGATTTCAGAGAGGCCTGG 647312 i vvvv v v i iii vv v - vviv v vii v L1ME5_3end#LI 549 CTATGCAGCAGTTAGAAGCAACGGACTA-GATGTACACATAGCAACATGG 597 chrXqtel1M 647313 AGAGA-CTGACAGGAAC-TGATGCTGAGTGAAACGAG-AAGGACCAGA 647357 vi - v v -- - ii vi - i v L1ME5_3end#LI 598 ATGGATCTTAAA--AACATAGTGCTGAGTGAAAAAAGTAAGAAACAGA 643 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 43.80 CpG sites = 84, Kimura (unadjusted) = 44.22 Transitions / transversions = 1.42 (84/59) Gap_init rate = 0.11 (51 / 480), avg. gap size = 1.14 (58 / 51) 746 29.20 2.32 9.07 chrXqtel1M 646879 647266 (352734) L1ME3A_3end#LINE/L1 189 552 (368) m_b369s551i9 15432 chrXqtel1M 646879 ACACCACTATCCACCTGTCAGATTGGCTAGAATGACAGGGAAAGATAATG 646928 i iv iii v i v ii v i i L1ME3A_3end#L 189 ATACCACTACACACCCACCAGAATGGCTAAAATGAAAAAGACAGACAATA 238 chrXqtel1M 646929 AGGAATGTTGGAGGGAATGTGGGAAAACAGGGACACTGATACATTGTTGG 646978 vvi i v i i iiv v i v v i i L1ME3A_3end#L 239 CCAAGTGTTGGCGAGGATGTGGAGCAACCGGAACTCTCATACACTGCTGG 288 chrXqtel1M 646979 TGGAGGTGTGAGCGGATCCAACCATTCTGGAGAACAATTTGG-AATATGT 647027 ii i iiv i v i i i vi - i v L1ME3A_3end#L 289 TGGGAGTGTAAATTGGTACAACCACTTTGGAAAACTGTTTGGCAGTATCT 338 chrXqtel1M 647028 --CAAAGCT-ATCAAACTCCCTTACCTTTGATCCACAGTGTTTTAAACAG 647074 --i - v v - v v vv v i -----------i - L1ME3A_3end#L 339 ACTAAAGCTGAACATA-TGCATACCCTATGACCCA-----------GCA- 375 chrXqtel1M 647075 GGATTATA-TCCCAAGGAGATACTAAAGAAGGGAAAGGGAGCTGACATAT 647123 -- vi - i i v v iv v --- v ------- i - L1ME3A_3end#L 376 --ATTCCACTCCTAGGTATATACCCAACA---GAAATG-------CGTA- 412 chrXqtel1M 647124 TTTGCATATATTTTGCACCCA----TATGTGCAAAAATATTTGGGGCAGC 647169 ---- i --- v ----i i i i iivi L1ME3A_3end#L 413 ----CATATGTT---CACCAAAAGACATGTACAAGAATGTTCATAGCAGC 455 chrXqtel1M 647170 CCTGTTTGTAGTGGCCAGAAACTGGAAACTGAGTGGACGCCCATCAGTTG 647219 v i i i i ?? ?ivviii i i iiv L1ME3A_3end#L 456 ACTATTCGTAATAGCCNNAAACTGGAAACNACCCAAATGTCCATCAACAG 505 chrXqtel1M 647220 GAGAATGGCTGAATAAATTGGGGTATATGAATATTATGGAATGTTAT 647266 v v i v vv i iv ii L1ME3A_3end#L 506 TAGAATGGATAAATAAATTGTGGTATATTCACACAATGGAATACTAT 552 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 37.38 CpG sites = 63, Kimura (unadjusted) = 38.34 Transitions / transversions = 1.57 (63/40) Gap_init rate = 0.10 (38 / 387), avg. gap size = 1.11 (42 / 38) 409 28.81 6.25 2.41 chrXqtel1M 647827 647986 (352014) MIRc#SINE/MIR 37 202 (66) m_b369s601i13 15433 chrXqtel1M 647827 TGAAGTCGGGAAGGTTTGAGTTCAAGTCTC----CCGGTAGAGGTGAACC 647872 i i iii i i i ---- i vi vvviiv i i MIRc#SINE/MIR 37 TGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCT 86 chrXqtel1M 647873 GTGTGAACCACGGCAGGCCACTTAACTCCTCTCAGCAGCCTCAGTTTCCC 647922 v ivv i i -- v - i MIRc#SINE/MIR 87 GTGTGACCTTGGGCAAGTCACTTAAC--CTCTCTG-AGCCTCAGTTTCCT 133 chrXqtel1M 647923 CATCTAGAAAAGGAGAATGATAGCA-GTGCCT--CCT--CTTACA-AGTG 647966 iv v i i i ii -v i-- -- i -i v MIRc#SINE/MIR 134 CATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTT 183 chrXqtel1M 647967 ATTGTGGTAGCTCGAATGAG 647986 i i-i v i MIRc#SINE/MIR 184 GTTGTGA-GGATCAAATGAG 202 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 37.22 CpG sites = 31, Kimura (unadjusted) = 38.34 Transitions / transversions = 2.21 (31/14) Gap_init rate = 0.06 (9 / 159), avg. gap size = 1.56 (14 / 9) 385 26.93 2.96 3.73 chrXqtel1M 647869 648003 (351997) MIR#SINE/MIR 79 212 (50) m_b369s601i14 15433 chrXqtel1M 647869 AACCGTGTGAACCACGGCAGGCCACTTAACTCCTCTCAGCAGCCTCAGTT 647918 i i v ivv i ii -- v i- MIR#SINE/MIR 79 AGCTGTGTGACCTTGGGCAAGTTACTTAAC--CTCTCTGT-GCCTCAGTT 125 chrXqtel1M 647919 TCCCCATCTAGAAAAGGAGAATGATAGCAGTGCCT-CCTCTTACAAGTGA 647967 i iv v i i i ii i - v -ii vi MIR#SINE/MIR 126 TCCTCATCTGTAAAATGGGGATAATAATAGTACCTACCTCATA-GGGTTG 174 chrXqtel1M 647968 TTGTGGTAGCTCGAATGAGTCA--GCCTGTAAGG-GCTT 648003 i-i v ii i --i v i - MIR#SINE/MIR 175 TTGTGA-GGATTAAATGAGTTAATACATGTAAAGCGCTT 212 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 35.13 CpG sites = 25, Kimura (unadjusted) = 35.13 Transitions / transversions = 2.50 (25/10) Gap_init rate = 0.06 (8 / 134), avg. gap size = 1.12 (9 / 8) 673 29.00 9.37 3.09 chrXqtel1M 649063 649489 (350511) C L1ME5_3end#LINE/L1 (410) 531 79 m_b369s551i10 15434 chrXqtel1M 649063 CCATAACATTCCTAACTTATCCAGCCGTTCCCCAGCTGATGGTCATTCAC 649112 iv -- v i v--- ii - v ii v C L1ME5_3end#LI 531 CCACCACATT--TTACCTATCCAC---TCTCCCAG-TGATGGACACCCAG 488 chrXqtel1M 649113 TCAGTTTCCAGTTTCT-GCCAGCACAAA-AGGGCTGCA-CAAACATTTGT 649159 viv ii ii i i- v - iv -ii iiv- C L1ME5_3end#LI 487 GTTGCCTCCAACTCCCCGCCACCACAAACAACGCTGCAATGAACATCCT- 439 chrXqtel1M 649160 GACGTGGGCGTCCTTTTC----CCTCTTTAACGAACTCTTTGGGCTATGG 649205 -- ivii ii v---- v v i vi vi v iv C L1ME5_3end#LI 438 --CGTACATGTCCCCTTATGGACCTGTGTGAGAATTTCTTTGGGATATAT 391 chrXqtel1M 649206 GCC-AGGAGACACCGTGCTGGGTCA-AGGGTTTGCACGT--TTGATAGCC 649251 i - vvivvv - v iii -- i vvvv C L1ME5_3end#LI 390 ACCCAGGAGCGGAATTGCTGGGTCATAGGGTATGCGTATACTTAATTTGA 341 chrXqtel1M 649252 CTTGGCACAGATCCAGATTGCTCTCCAGAATGGTGGGCCTAGTTCACCGT 649301 vi i v -- iv vv i ii vv C L1ME5_3end#LI 340 CTAAGTACTG--CCAGATTGCTCTCCAGAATGGCTGCACCAGTCTACACT 293 chrXqtel1M 649302 TCCCCTGTCGATGTGTTAGTGTCCTGGTTTTCCCACATTC-CTCCAACAT 649350 i v iiv ii ii v v i ivi ? i i - v i C L1ME5_3end#LI 292 CCCACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATCCTCGCCAACAC 243 chrXqtel1M 649351 TCATCTTTATC----TTTC--------------CTGAGAGGTATGA-GTG 649381 iiv v ---- -------------- i v i i - C L1ME5_3end#LI 242 TTGGCATTATCCAGCTTTCTAATTTTTGCCAGTCTAATAGGTGTAAAGTG 193 chrXqtel1M 649382 GTACCTCA--GTTGTTTTAATTTACATTTCTCTGATCAATAGTGATTTAG 649429 i i -- i i v i v v C L1ME5_3end#LI 192 ATATCTCATTGTTGTTTTAATTTGCATTTCTCTGATTACTAATGAGTTTG 143 chrXqtel1M 649430 GGCATTTTTTCATATGACTAGAAATAGCTTT---AATTTCTTCATCTGGA 649476 i i i - v --v i ---ii i v v C L1ME5_3end#LI 142 AGCATCTCTTCATATG-CTTG--TTAGCCTTTCGGGTTTCCTCTTCTGTA 96 chrXqtel1M 649477 AAT----TGTTCATATC 649489 ---- C L1ME5_3end#LI 95 AATTGCCTGTTCATATC 79 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 37.40 CpG sites = 69, Kimura (unadjusted) = 37.80 Transitions / transversions = 1.35 (69/51) Gap_init rate = 0.07 (28 / 426), avg. gap size = 1.93 (54 / 28) 12 15.54 5.26 2.56 chrXqtel1M 654941 654978 (345022) (CAGAGAC)n#Simple_repeat 1 39 (0) m_b369s252i15 15435 chrXqtel1M 654941 CAGAGTCCAGAGAGGCACAG--CTGAGTCCAGAGACCAGA 654978 v -v v -- v v (CAGAGAC)n#Si 1 CAGAGACCAGAGA-CCAGAGACCAGAGACCAGAGACCAGA 39 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.05 (2 / 37), avg. gap size = 1.50 (3 / 2) 290 22.42 10.22 5.59 chrXqtel1M 658084 658220 (341780) MIR1_Amn#SINE/MIR 9 151 (79) m_b369s601i15 15436 chrXqtel1M 658084 CAGTGAGATAGGCTAGCTTGGCTA-AGTACTGGGCCTGGGGCCCAGTTAA 658132 --- i v -- v - i i - i i i --i MIR1_Amn#SINE 9 CAGTG---TGGTCTAG--TGGATAGAGCACTGGAC-TGGGACTCGG--GA 50 chrXqtel1M 658133 AATCTGGCTTCATAT------------ACTACCTAGCAGCGTGACCCTGG 658170 i i v ?v? ------------ ?v i? v ? i MIR1_Amn#SINE 51 GACCTGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGG 100 chrXqtel1M 658171 -CAAGTCCCTTTACCTTTGTCTGCCTCCGTTTCCCTGCTGGCAAAATGGG 658219 - v ? i v v? v iiiiiv i MIR1_Amn#SINE 101 GCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGG 150 chrXqtel1M 658220 G 658220 MIR1_Amn#SINE 151 G 151 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 28.11 CpG sites = 18, Kimura (unadjusted) = 29.30 Transitions / transversions = 1.64 (18/11) Gap_init rate = 0.08 (11 / 136), avg. gap size = 2.00 (22 / 11) 347 27.15 16.86 1.52 chrXqtel1M 658108 658279 (341721) MIRc#SINE/MIR 26 223 (45) m_b369s601i16 15436 chrXqtel1M 658108 AGTACTGGGCCTGGGGCCCAGTTAAAATCTGGCTTCA---------TATA 658148 i i i i i vi -- i i v i--------- v i MIRc#SINE/MIR 26 AGCACTGGACTTGGAGTCAGG--AAGACCTGGGTTCGAGTCCCGGCTCTG 73 chrXqtel1M 658149 CTAC---CTAGCAGCGTGACCCTGG-CAAGTCCCTTTACCTTTGTCTGCC 658194 i --- v i i - v v i v vv MIRc#SINE/MIR 74 CCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCC 123 chrXqtel1M 658195 TCCGTTTCCCTGCTGGCAAAATGGGGCT--------CTAGCATGC----- 658231 v iiiiiv i v -------- iv v ----- MIRc#SINE/MIR 124 TCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACC 173 chrXqtel1M 658232 ---CAGGACTGTTGGGAGGGTCCATTGAAATCATGTTTGTGTAAATCTCT 658278 --- ii v i v v i v v - v v MIRc#SINE/MIR 174 TCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTG-AAAGCGCT 222 chrXqtel1M 658279 T 658279 MIRc#SINE/MIR 223 T 223 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 33.48 CpG sites = 25, Kimura (unadjusted) = 34.39 Transitions / transversions = 1.19 (25/21) Gap_init rate = 0.05 (9 / 171), avg. gap size = 3.56 (32 / 9) 274 26.67 12.22 0.00 chrXqtel1M 659036 659125 (340875) C MIRc#SINE/MIR (166) 102 2 m_b369s601i17 15437 chrXqtel1M 659036 TTGCCTGGGGTTCCAAAGCTAGGGTGTGTCAGAACTAAGACATGAGCCCA 659085 iii iv v viv v i iii vi i C MIRc#SINE/MIR 102 TTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCA 53 chrXqtel1M 659086 GGTCTTCCT-----TAACTCCAGAGTTC--TCCGT----CTACACTGCCT 659124 -----i v v i -- ii---- i C MIRc#SINE/MIR 52 GGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCACACTGCCT 3 chrXqtel1M 659125 C 659125 C MIRc#SINE/MIR 2 C 2 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 30.62 CpG sites = 16, Kimura (unadjusted) = 34.28 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.03 (3 / 89), avg. gap size = 3.67 (11 / 3) 12 4.15 3.45 7.14 chrXqtel1M 659338 659366 (340634) (TTTG)n#Simple_repeat 1 28 (0) m_b369s252i16 15438 chrXqtel1M 659338 TTTGTTGTCGTTTGTTTGCTT-TTTGTTTG 659366 - - i - (TTTG)n#Simpl 1 TTTGTT-T-GTTTGTTTGTTTGTTTGTTTG 28 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.11 (3 / 28), avg. gap size = 1.00 (3 / 3) 358 33.33 1.96 0.00 chrXqtel1M 659924 660076 (339924) C L1MB3_3end#LINE/L1 (646) 284 129 m_b369s551i11 15439 chrXqtel1M 659924 CAATGCCTCAGCATCCCAACTTTCTCACCTCCCCACCAACATGCGATATT 659973 i viv vi i i iii v i i ivi v C L1MB3_3end#LI 284 CAGTGCACAAGGGTTCCAATTTCTCCACATCCTCGCCAACACTTGTTATT 235 chrXqtel1M 659974 CTCTTCTCTTGTTACCTCAGCCAATCTGAGGGGCGGGCGGTGGGACTTCA 660023 i vi i v v ivvi vi i v i v v v ii C L1MB3_3end#LI 234 TTCTGTTTTTTTGATAGTAGCCATCCTAATGGGTGTGAGGTGGTATCTCA 185 chrXqtel1M 660024 GAGTTGTCTCCATTTGCATTTCTCTGATG--CAGC-ATTTAGAGCATTTT 660070 vv v i iv i i --i i- v v i C L1MB3_3end#LI 184 TTGTGGTTTTGATTTGCATTTCCCTAATGATTAGTGATGTTGAGCATCTT 135 chrXqtel1M 660071 TTCATG 660076 C L1MB3_3end#LI 134 TTCATG 129 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 44.26 CpG sites = 29, Kimura (unadjusted) = 45.48 Transitions / transversions = 1.32 (29/22) Gap_init rate = 0.01 (2 / 152), avg. gap size = 1.50 (3 / 2) 354 30.57 7.97 2.26 chrXqtel1M 659933 660183 (339817) C L1PA6_3end#LINE/L1 (626) 275 11 m_b369s551i12 15439 chrXqtel1M 659933 AGCATCCCAACTTTCTCACCTCCCCACCAACATGCGATATTCTCTTCTCT 659982 i i v i iii v i v i vi v i - i vv C L1PA6_3end#LI 275 AGCGTTCCTATTTCTCCACATCCTCTCCAGCATCTGTTGTT-TCCTGACT 227 chrXqtel1M 659983 TGTTACC--TCAGCCAATCTGAGGGGCGGGCGGTGGGACTTCAGAGTTGT 660030 v vi-- - v i vv v v i v ii vv v C L1PA6_3end#LI 226 TTTTAATGATC-GCCATTCTAACTGGCGTGAGATGGTATCTCATTGTGGT 178 chrXqtel1M 660031 CTCCATTTGCATTTCTCTGATG--CAGCATTTA-GAGCATTTTTTCATG- 660076 i iv -- iiv v - - C L1PA6_3end#LI 177 TTTGATTTGCATTTCTCTGATGACCAGTGATGATGAGCATTTTTTCATGT 128 chrXqtel1M 660077 ----ACTAG--AAACAACAGTTTTAAGTTGTTTGAAAATCATCTG----T 660116 ----ii i --iv i vv i ---- iv i vii ---- C L1PA6_3end#LI 127 GTCTGTTGGCTGCATAAATGTCT----TCTTTTGAGAAGTGTCTGTTCAT 82 chrXqtel1M 660117 ATCCTTGGACCGTGTATTGA-GGAGTGGCTTG---TATCCTGATAAATTT 660162 v v iiv v - i v i --- v i vi C L1PA6_3end#LI 81 ATCCTTTGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCTTGTAAATTT 32 chrXqtel1M 660163 GAATCAATTCTTTATATATTC 660183 vv v i i v C L1PA6_3end#LI 31 GTTTAAGTTCTTTGTAGATTC 11 Matrix = 20p49g.matrix Kimura (with divCpGMod) = 39.24 CpG sites = 38, Kimura (unadjusted) = 39.91 Transitions / transversions = 1.03 (38/37) Gap_init rate = 0.06 (15 / 250), avg. gap size = 1.73 (26 / 15) 309 32.26 3.70 4.35 chrXqtel1M 661038 661199 (338801) C L3b_3end#LINE/CR1 (683) 523 363 m_b369s601i18 15440 chrXqtel1M 661038 ACAAATGCTGCCTGTTCAG----GTCTGTCCCACCTAATACTTGGGAGGT 661083 vi? - i v ---- vi i ivi i v v i C L3b_3end#LINE 523 ACATGNGCTGC-TGCTAAGCCGCGTCTCCCCCATCCTGTACTCGCGCGAT 475 chrXqtel1M 661084 TGATTGTT-GGGCTCAAGTGCAAGACTTCCCATTTATCCCAAGTCCAAGT 661132 ? v - ii i i iv i -v ----- C L3b_3end#LINE 474 TGNTTTTTTGAACCCAAGTGCAGGACTTTACGTTTATCCC-TGT-----T 431 chrXqtel1M 661133 GCATTTTAGCCCAGGAGGTTCTGCTCAGTGCTCTGGCCTAGCG-GATCCC 661181 v i v iiivvi ? v i i?i i i i iv - vi C L3b_3end#LINE 430 GAATTTCATCTTGTTGGNTTCGGCCCGNCGTTCTAGTCTGTCGAGATCGT 381 chrXqtel1M 661182 AGTGGATCCCAACTCTAC 661199 vv ii i i i C L3b_3end#LINE 380 TTTGGATCCTGATTTTGC 363 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 41.00 CpG sites = 32, Kimura (unadjusted) = 45.97 Transitions / transversions = 1.78 (32/18) Gap_init rate = 0.06 (10 / 161), avg. gap size = 1.30 (13 / 10) 357 23.37 0.81 6.84 chrXqtel1M 662580 662703 (337297) MIR1_Amn#SINE/MIR 13 129 (101) m_b369s601i20 15441 chrXqtel1M 662580 GTGGCACAGTGGATAGAGCAGCAGCCCTGAAGTCAGGAGGACCTGAGTTC 662629 ivi vii v iv i v i - i MIR1_Amn#SINE 13 GTGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGAG-ACCTGGGTTC 61 chrXqtel1M 662630 AAATTTGACCTCAGACATTTAATACTTCCTAGCTGTGTGACCCTGGGCAA 662679 ? ? i------ v i - i ivi ?v i? ? i MIR1_Amn#SINE 62 NANTC------CCGGC-TCTGCCACTNGCCNGCTGNGTGACCTTGGGCAA 104 chrXqtel1M 662680 GTCACTTTCCCCCAAT-CGCCTCAG 662703 ?v i vv -? MIR1_Amn#SINE 105 GTCACTTNACCTCTCTGNGCCTCAG 129 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 29.38 CpG sites = 16, Kimura (unadjusted) = 30.72 Transitions / transversions = 1.45 (16/11) Gap_init rate = 0.07 (9 / 123), avg. gap size = 1.00 (9 / 9) 460 22.11 0.00 7.00 chrXqtel1M 662580 662686 (337314) MIRc#SINE/MIR 10 109 (159) m_b369s601i19 15441 chrXqtel1M 662580 GTGGCACAGTGGATAGAGCAGCAGCCCTGAAGTCAGGAGGACCTGAGTTC 662629 ii v vii v i i i i MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chrXqtel1M 662630 AAATTTGACCTCAGACATTTAATACTTCCTAGCTGTGTGACCCTGGGCAA 662679 i i iiviv v v i ------- i MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTGACCTTGGGCAA 102 chrXqtel1M 662680 GTCACTT 662686 MIRc#SINE/MIR 103 GTCACTT 109 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 24.09 CpG sites = 15, Kimura (unadjusted) = 26.87 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.07 (7 / 106), avg. gap size = 1.00 (7 / 7) 16 0.00 0.00 0.00 chrXqtel1M 662706 662722 (337278) (A)n#Simple_repeat 1 17 (0) m_b369s252i17 15442 chrXqtel1M 662706 AAAAAAAAAAAAAAAAA 662722 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 15 13.70 7.50 0.00 chrXqtel1M 662707 662746 (337254) (AAAATC)n#Simple_repeat 1 43 (0) m_b369s252i18 15442 chrXqtel1M 662707 AAAAAAAAAAAAAAAATC-AAATC-AAATC-AAATCAGAATCA 662746 vv vv - - - i (AAAATC)n#Sim 1 AAAATCAAAATCAAAATCAAAATCAAAATCAAAATCAAAATCA 43 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.08 (3 / 39), avg. gap size = 1.00 (3 / 3) 18 0.00 0.00 3.85 chrXqtel1M 662720 662746 (337254) (AAATC)n#Simple_repeat 1 26 (0) m_b369s252i19 15442 chrXqtel1M 662720 AAATCAAATCAAATCAAATCAGAATCA 662746 - (AAATC)n#Simp 1 AAATCAAATCAAATCAAATCA-AATCA 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.04 (1 / 26), avg. gap size = 1.00 (1 / 1) 14 9.39 2.50 7.89 chrXqtel1M 663256 663295 (336705) (GGAAGAG)n#Simple_repeat 1 38 (0) m_b369s252i20 15443 chrXqtel1M 663256 GGAAGAGGGATGAGGGAAG-GGAACAGATGGGAGGCAGGGA 663295 v - i - - i - (GGAAGAG)n#Si 1 GGAAGAGGGAAGAGGGAAGAGGGA-AGA-GGGAAG-AGGGA 38 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.10 (4 / 39), avg. gap size = 1.00 (4 / 4) 181 38.38 4.04 0.00 chrXqtel1M 663638 663736 (336264) L2#LINE/L2 2408 2510 (572) m_b369s601i21 15444 chrXqtel1M 663638 CATTTCCACCTGAATGTCAGGGATGCATCTCAACGTCACCGTGCCCCAAA 663687 i i i viiv v vv i v i i v L2#LINE/L2 2408 CATCTCCACTTGGATGTCTAATAGGCATCTCAAACTTAACATGTCCAAAA 2457 chrXqtel1M 663688 GAGAGTTCTTGATTTTATTTTT----TTTAATTTTCCTTCATTTTCCCCC 663733 vv ii i i viiii ----ii iv ii iv v i i L2#LINE/L2 2458 CTGAACTCCTGATCTTCCCCCTCAAACCTGCTCCTCCCGCAGTCTTCCCC 2507 chrXqtel1M 663734 CTC 663736 v L2#LINE/L2 2508 ATC 2510 Matrix = 25p49g.matrix Kimura (with divCpGMod) = 55.15 CpG sites = 24, Kimura (unadjusted) = 57.52 Transitions / transversions = 1.71 (24/14) Gap_init rate = 0.01 (1 / 98), avg. gap size = 4.00 (4 / 1) 30 0.00 0.00 0.00 chrXqtel1M 667368 667395 (332605) (T)n#Simple_repeat 1 28 (0) c_b370s251i0 15445 chrXqtel1M 667368 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 667395 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 19 8.18 0.00 0.00 chrXqtel1M 667447 667472 (332528) (A)n#Simple_repeat 1 26 (0) m_b370s252i0 15446 chrXqtel1M 667447 AAAAAAAAAAAAAAAAAAAACCAAAA 667472 vv (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAA 26 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 13 25.80 2.17 0.00 chrXqtel1M 667451 667496 (332504) (AAAACC)n#Simple_repeat 1 47 (0) m_b370s252i1 15446 chrXqtel1M 667451 AAAAAAAAAAAAAAAACCAAAACC-AACCCCAAATAAAACCCAGAAC 667496 vv vv - v v iv v i (AAAACC)n#Sim 1 AAAACCAAAACCAAAACCAAAACCAAAACCAAAACCAAAACCAAAAC 47 Matrix = Unknown Transitions / transversions = 0.25 (2/8) Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1) 263 21.55 1.49 3.03 chrXqtel1M 670913 670979 (329021) L2a_3end#LINE/L2 433 498 (19) m_b370s601i0 15447 chrXqtel1M 670913 TTTGGTTTTCT-CTGTCTCCACGGCCAGCCCATAGCAGAGCCTGGCACAC 670961 v iv - v v i -- i v i v i L2a_3end#LINE 433 TTTTGTTCACTGCTGTATCCCCAGC--GCCTAGAACAGTGCCTGGCACAT 480 chrXqtel1M 670962 AGAAGGCACTTAATAAAT 670979 v i i L2a_3end#LINE 481 AGTAGGCGCTCAATAAAT 498 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 23.57 CpG sites = 7, Kimura (unadjusted) = 25.57 Transitions / transversions = 1.00 (7/7) Gap_init rate = 0.05 (3 / 66), avg. gap size = 1.00 (3 / 3) 72 10.99 4.62 0.00 chrXqtel1M 674023 674152 (325848) (GCTGCC)n#Simple_repeat 1 136 (0) m_b370s252i2 15448 chrXqtel1M 674023 GCTGCCACTGCCGCTGCCGCTACCGCTGCCGCT---GCTGCTGCTGCTGC 674069 i i --- i i (GCTGCC)n#Sim 1 GCTGCCGCTGCCGCTGCCGCTGCCGCTGCCGCTGCCGCTGCCGCTGCCGC 50 chrXqtel1M 674070 TGCTGCTGCTGCTGCCGCTGCCGCTACGGCTGCCGCTACGGCTGCCGCTA 674119 i i i v i v i (GCTGCC)n#Sim 51 TGCCGCTGCCGCTGCCGCTGCCGCTGCCGCTGCCGCTGCCGCTGCCGCTG 100 chrXqtel1M 674120 CCGCT---GCTGCCGCTGCTACTGCCGCTGCCGCTG 674152 --- ii (GCTGCC)n#Sim 101 CCGCTGCCGCTGCCGCTGCCGCTGCCGCTGCCGCTG 136 Matrix = Unknown Transitions / transversions = 5.50 (11/2) Gap_init rate = 0.02 (2 / 129), avg. gap size = 3.00 (6 / 2) 478 21.04 0.00 6.67 chrXqtel1M 674919 675030 (324970) MIRc#SINE/MIR 11 115 (153) m_b370s601i1 15449 chrXqtel1M 674919 TGGCCCAGTGGAGAGAGCACCAGCCCTGAAGTCAGGAGGACCTGAGTTCA 674968 iv i ii v i i i i i MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCG 60 chrXqtel1M 674969 AATGTGGCCCCACACACTTAACACTTCCTAGCTGTGTGACCTTTGGCAGG 675018 i ---- vi v --- iv v v i MIRc#SINE/MIR 61 AGT----CCCGGCTC---TGCCACTTACTAGCTGTGTGACCTTGGGCAAG 103 chrXqtel1M 675019 TCACTTAATCCC 675030 i i MIRc#SINE/MIR 104 TCACTTAACCTC 115 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 23.99 CpG sites = 15, Kimura (unadjusted) = 25.30 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.06 (7 / 111), avg. gap size = 1.00 (7 / 7) 235 27.48 1.67 15.09 chrXqtel1M 675508 675627 (324373) MIR#SINE/MIR 18 123 (139) m_b370s601i2 15450 chrXqtel1M 675508 TTAAGGGCACAG-CTAGGTGGAGTGGGTAGAGGACCTGAGCTCAAATCTG 675556 i i - v-- i---i vvi i i i iv MIR#SINE/MIR 18 TTAAGAGCACGGGCTC--TGGAGC---CAGACTGCCTGGGTTCGAATCCC 62 chrXqtel1M 675557 GTCTCAGACAGACACTTAACACTTCCTGGCTGTGAAAGCTTTGGCAAGTC 675606 v ----------- iv v i vi v v i MIR#SINE/MIR 63 GGCTC-----------TGCCACTTACTAGCTGTGTGACCTTGGGCAAGTT 101 chrXqtel1M 675607 ACCTAACCCCAAC-TGCCTCAG 675627 i i vvi- MIR#SINE/MIR 102 ACTTAACCTCTCTGTGCCTCAG 123 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 31.15 CpG sites = 16, Kimura (unadjusted) = 34.06 Transitions / transversions = 1.33 (16/12) Gap_init rate = 0.15 (18 / 119), avg. gap size = 1.00 (18 / 18) 244 24.10 1.94 15.38 chrXqtel1M 675525 675627 (324373) MIRc#SINE/MIR 37 127 (141) m_b370s601i3 15450 chrXqtel1M 675525 TGGAGTGGGTAGAGGACCTGAGCTCAAATCTGGTCTCAGACAGACACTTA 675574 vi -- i i i i i iv v ----------- i MIRc#SINE/MIR 37 TGGAGTCAG--GAAGACCTGGGTTCGAGTCCCGGCTC-----------TG 73 chrXqtel1M 675575 ACACTTCCTGGCTGTGAAAGCTTTGGCAAGTCACCTAACCCCAACT--GC 675622 v v i vi v v i i -v -- MIRc#SINE/MIR 74 CCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTC-TCTGAGC 122 chrXqtel1M 675623 CTCAG 675627 MIRc#SINE/MIR 123 CTCAG 127 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 27.23 CpG sites = 12, Kimura (unadjusted) = 28.81 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.15 (15 / 102), avg. gap size = 1.07 (16 / 15) 19 26.20 3.39 0.00 chrXqtel1M 678439 678497 (321503) (AC)n#Simple_repeat 1 61 (0) m_b370s252i3 15451 chrXqtel1M 678439 ACACACACACACACATACAGACACGCAGGGGAACACTTCCACACACATA- 678487 i v i viviv viv i - (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50 chrXqtel1M 678488 ACAGA-ACACA 678497 v - (AC)n#Simple_ 51 ACACACACACA 61 Matrix = Unknown Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.03 (2 / 58), avg. gap size = 1.00 (2 / 2) 901 30.00 7.57 2.53 chrXqtel1M 680201 680689 (319311) L1ME3G_3end#LINE/L1 9 521 (403) m_b370s551i0 15452 chrXqtel1M 680201 CAAATTATGTGCAGAATTGACTCAAATTTATAAGAATA---CAACCCATT 680247 i v i iv i vviv iv v --- v L1ME3G_3end#L 9 CAGAATATATAAAGAACTCCTACAAATCAATAAGAAAAAGACAACCCAAT 58 chrXqtel1M 680248 CTCTGAAAAATGGTTAAA----ATTAACA----ATTTCCAGATGAAGAAA 680289 v--- vi ---- v ---- iv v i L1ME3G_3end#L 59 A---GAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGGAAA 105 chrXqtel1M 680290 TTAAAGCTATTTCTAGTCATATGAAAAAATGCCCTAAATCACTATTGATC 680339 vv iiviiivv iv i i v vv v i L1ME3G_3end#L 106 TACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTAATC 155 chrXqtel1M 680340 AGAGAAATGTAAATTAAAACAAC--TGAGGTACCACTACATACCTCTCA- 680386 i i -- i i vivi iv - L1ME3G_3end#L 156 AGGGAAATGCAAATTAAAACAACAATGAGATACCATTTTTCACCCATCAG 205 chrXqtel1M 680387 ---GGAAAAGAT---AAAGAT----------GAATGTTGGAGGGAATGTG 680420 --- v i --- ? ----------? i v i ii L1ME3G_3end#L 206 ATTGGCAAAAATTTAAAAGNTTGATAATATCNAGTGTTGGCGAGGGTGTG 255 chrXqtel1M 680421 GGAAAACCAGGACACTAACACATCGACGGGGGAACGGTGAACTGAGCCCA 680470 i vi v v v i ii vi v i vv i i ivv vi L1ME3G_3end#L 256 GGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTGTAAATTGGTACAG 305 chrXqtel1M 680471 CCATTCTGGAGAGCAATCTGG----ATCTGTGCCCAAAGGGCTATCAAAC 680516 ? i i i ---- i ---i iv---- i v L1ME3G_3end#L 306 CCNTTTTGGAGGGCAATTTGGCAGTATCTAT---TAAAAT----TTAAAA 348 chrXqtel1M 680517 TGTGCAAACCCTTTGACCCAGCATGGTGTCTCCTGGGCCCATAGCCCAAA 680566 i v vvvivv i ? ?viv v i ? L1ME3G_3end#L 349 TGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTATCCTANA 398 chrXqtel1M 680567 GA---GTTCGTTAAAGAGGGAAAAGGACGCCCACGTGCACAAATGTTTGT 680613 ---ii -i v viv v v ? -- i i vii ii L1ME3G_3end#L 399 GAAATACTCG-CACATGTGCACAAGGANG--CATGTACAAGGATGTTCAT 445 chrXqtel1M 680614 GGCAGCCCTTTTTGTGCTGGCAAGAAACTGGAAACTGAGTGAATGACCAT 680663 v vi v iv i i i i vivv i v L1ME3G_3end#L 446 TGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATGTCCAT 495 chrXqtel1M 680664 CAGCTGGGGAACGGCTGGATAAGTTA 680689 iiv i i ii i L1ME3G_3end#L 496 CAATAGGGGAATGGTTAAATAAATTA 521 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 39.25 CpG sites = 78, Kimura (unadjusted) = 39.97 Transitions / transversions = 1.20 (78/65) Gap_init rate = 0.05 (23 / 488), avg. gap size = 2.17 (50 / 23) 843 31.64 8.66 2.79 chrXqtel1M 680252 680794 (319206) L1ME5_3end#LINE/L1 64 637 (304) m_b370s551i1 15452 chrXqtel1M 680252 GAAAAATGGTTAAA----ATTAACA----ATTTCCAGATGAAGAAATT-- 680291 vi ---- v ---- v v i ii-- L1ME5_3end#LI 64 GAAAAATGGGCAAAGGATATGAACAGGCAATTTACAGAAGAGGAAACCCG 113 chrXqtel1M 680292 -AAAGCTATTTCTAGTCATATGAAAAAATGCCCTAAATCACTATTGATCA 680340 - i v-- v - i i i v v i v i L1ME5_3end#LI 114 AAAGGCTAA--CAAG-CATATGAAGAGATGCTCAAACTCATTAGTAATCA 160 chrXqtel1M 680341 GAGAAATGTAAATTAAAACAAC--TGAGGTACCACTACATACCTCTCAG- 680387 i -- i i vi i v i - L1ME5_3end#LI 161 GAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCTATTAGA 210 chrXqtel1M 680388 -------------GAAA---AGATAAAGATGAATGTTGGAGGGAATGTGG 680421 ------------- ---i v vii i v i i L1ME5_3end#LI 211 CTGGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTGGCGAGGATGTGG 260 chrXqtel1M 680422 GAAAACCAGGACACTAACACATCGACGGGGGAACGGTGAACTGAGCCCAC 680471 i ? ivi i v v ii ii vi v i vv ii ivv vi L1ME5_3end#LI 261 GGANATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACTGGTGCAGC 310 chrXqtel1M 680472 CATTCTGGAGAGCAATCTGGATCTGTGCCCA---AAGGGCTATCAAAC-T 680517 -- v i ii --- ----- i ii- L1ME5_3end#LI 311 CATTCTGGAGAGCAATCTGG--CAGTACTTAGTCAA-----ATTAAGTAT 353 chrXqtel1M 680518 GTGCAAACCCTTTGACCCAGCATGGTGTCTCCTGGGCCCATAGCCCAAAG 680567 ii v v vvvivv ivi v L1ME5_3end#LI 354 ACGCATACCCTATGACCCAGCAATTCCGCTCCTGGGTATATATCCCAAAG 403 chrXqtel1M 680568 AGTTCGTTAAAGAGG----GAAAAGGACGCCCACGTGCACAAATGTTTGT 680613 iv iv i v v ----v ii ---- i i ivii ii L1ME5_3end#LI 404 AAATTCTCACACAGGTCCATAAGGGGA----CATGTACGAGGATGTTCAT 449 chrXqtel1M 680614 GGCAGCCCTTTTTGTGCTGGCAAGAAACTGGAAACTGAGTGAATGACCAT 680663 v vi v v ii i ii ii vivv ii v L1ME5_3end#LI 450 TGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACCTGGGTGTCCAT 499 chrXqtel1M 680664 CAGCTGGG-GAACGGCTGGATAA---GTTAGGAATG----TTATGGGGAA 680705 - - ii v i i --- viv i ----ii i v L1ME5_3end#LI 500 CA-CTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACACCATGGAGTA 548 chrXqtel1M 680706 TCATCGTTCTGTAAGAAATGACCGGCGGGATGATTTCAGAGAGGCCTGGA 680755 ii vvvv v v iii v i vi vviv v vii v L1ME5_3end#LI 549 CTATGCAGCAGTTAGAAGCAACGGACTAGATGTACACATAGCAACATGGA 598 chrXqtel1M 680756 GAGACTCACAGGAAC-TGATGCTGAGTGAAATGAGGAGGA 680794 vi - vi ii - ii vi v i L1ME5_3end#LI 599 TGGA-TCTTAAAAACATAGTGCTGAGTGAAAAAAGTAAGA 637 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 41.56 CpG sites = 97, Kimura (unadjusted) = 42.58 Transitions / transversions = 1.39 (97/70) Gap_init rate = 0.06 (31 / 542), avg. gap size = 2.03 (63 / 31) 452 28.54 6.67 2.67 chrXqtel1M 681769 681948 (318052) C MIRc#SINE/MIR (45) 223 37 m_b370s601i4 15453 chrXqtel1M 681769 AAGCCCTTT-ACAGGC--TGACTCATTCGAGCTACCCAACAATCACTTGT 681815 v - vi -- iv i v iv v i --i C MIRc#SINE/MIR 223 AAGCGCTTTCACATACATTATCTCATTTGATCCTCACAACAACC--CTGT 176 chrXqtel1M 681816 AAG--AGG--AGGCAC-TGCTATCATTCTCCTTTTCTAGATGGGGAAACT 681860 i -- --i v- ii i i i v vi i C MIRc#SINE/MIR 175 GAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGGAAACT 126 chrXqtel1M 681861 GAGGCTGCTGAGAGGAGTTAAGTGGCCTGCCGTGGTTCACACGGTTCACC 681910 - v -- i i vvi v i i viiv C MIRc#SINE/MIR 125 GAGGCT-CAGAGAG--GTTAAGTGACTTGCCCAAGGTCACACAGCTAGTA 79 chrXqtel1M 681911 TCTACCGG----GAGACTTGAACTCAAACCTTCCCGACTTCA 681948 vv iv i ---- i i i iii i i C MIRc#SINE/MIR 78 AGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCA 37 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 36.41 CpG sites = 32, Kimura (unadjusted) = 37.37 Transitions / transversions = 1.78 (32/18) Gap_init rate = 0.06 (11 / 179), avg. gap size = 1.55 (17 / 11) 266 34.85 10.04 1.42 chrXqtel1M 682275 682533 (317467) L2#LINE/L2 2802 3082 (0) m_b370s601i5 15454 chrXqtel1M 682275 CCTTCAAAACACAGGACTGACCATGTCACTTCCCTCCTCAAGTGAGCTTC 682324 i i ii i v v i i i v --i v i L2#LINE/L2 2802 CTTTTAAAACGTAAGTCAGATCATGTCACTCCTCTGCTCAA--AACCCTC 2849 chrXqtel1M 682325 T-GTGGCTCCCTATGGCCCCCAGGAGCAAATACGA----------AATGG 682363 i-i i i vv v i - i vi v ---------- L2#LINE/L2 2850 CAATGGCTTCCCATCTCACTCA-GAGTAAAAGCCAAAGTCCTTACAATGG 2898 chrXqtel1M 682364 CCT--------CTG---GAGCTTGCCCCCTCTTCCCTTTCCGG--TCATA 682400 -------- i--- v v i iv v i i i-- v L2#LINE/L2 2899 CCTACAAGGCCCTACATGATCTGGTCCCCCGTTACCTCTCTGACCTCATC 2948 chrXqtel1M 682401 CCTTACTTCTC-CCCAATCTGACACTTCTATCCAGGGTCACCAGCCTCCT 682449 i i iv - vv vvv i vv vvv ii L2#LINE/L2 2949 TCCTACCACTCTCCCCCTCGCTCACTCCGCTCCAGCCACACTGGCCTCCT 2998 chrXqtel1M 682450 GGCTATTCCATGAGCAAGACCCTACCTCTTCTAGCTCCTGGGATTTT-CT 682498 v i vi i v - vvi vivi iv ii v vi - v L2#LINE/L2 2999 TGCTGTTCCTCGAACACG-CCAGGCACGCTCCCGCCTCAGGGCCTTTGCA 3047 chrXqtel1M 682499 CAGGCTCTCTCCCATGCCTAGAATATTTTTGCTCC 682533 vv v ii iv i iii i v i L2#LINE/L2 3048 CTTGCTGTTCCCTCTGCCTGGAACGCTCTTCCCCC 3082 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 44.47 CpG sites = 48, Kimura (unadjusted) = 48.23 Transitions / transversions = 1.17 (48/41) Gap_init rate = 0.04 (11 / 258), avg. gap size = 2.73 (30 / 11) 300 36.36 3.31 0.00 chrXqtel1M 682616 682736 (317264) L2d2_3end#LINE/L2 420 544 (11) m_b370s601i6 15454 chrXqtel1M 682616 TCTTGGCTCTGCA-TTAGCCCG-GAGATTCTAGAAGACGGAGACTCTGTT 682663 v iv -i vii -i v i v i i i i iv i L2d2_3end#LIN 420 TCTTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTC 469 chrXqtel1M 682664 TTA--CTTTCTCCTGGTTTCCACAGGATCCAGAACAGTATCTTGTATTCA 682711 -- ii iv iviii vii i v ii i iv L2d2_3end#LIN 470 TTATACTTCTTTGTATCCCCCACAGCGCCTAGCACAGTGCCTTGCACACA 519 chrXqtel1M 682712 GAAGGTGCTTACTAAAAGTCTGTTG 682736 v i i v vi i L2d2_3end#LIN 520 GTAGGCGCTCAATAAATATTTGTTG 544 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 50.17 CpG sites = 30, Kimura (unadjusted) = 53.86 Transitions / transversions = 2.14 (30/14) Gap_init rate = 0.03 (3 / 120), avg. gap size = 1.33 (4 / 3) 477 31.34 2.08 2.94 chrXqtel1M 684921 685160 (314840) L1ME3A_3end#LINE/L1 418 655 (265) m_b370s551i2 15455 chrXqtel1M 684921 GCTCATCAGAAATTACTTGCAAAAATATTTGGGGCAGCCCTCTTTGTAGT 684970 i i i ivi iv i i i iivi v v i i L1ME3A_3end#L 418 GTTCACCAAAAGACATGTACAAGAATGTTCATAGCAGCACTATTCGTAAT 467 chrXqtel1M 684971 GGCCAGAAACTGGAAACTGAGTGGATGCCCATCAGTTGGAGAATGGCTGA 685020 i ?? ?ivviii i iiv v v i L1ME3A_3end#L 468 AGCCNNAAACTGGAAACNACCCAAATGTCCATCAACAGTAGAATGGATAA 517 chrXqtel1M 685021 ATAAATTGTGGTATATGAATGTTATGGAATATTATTGTTCTATAAGAAAT 685070 vv iiiv i vvvv v i vv L1ME3A_3end#L 518 ATAAATTGTGGTATATTCACACAATGGAATACTATACAGCAATGAGAATG 567 chrXqtel1M 685071 GACAAGCAGGAGGATTTCA--GAAAGGCCTGGA-GAGACTCACATGAAC- 685116 i i i --v vi i v --v vii v - iv -- - L1ME3A_3end#L 568 AACGAAC--TACAACTACACGCAACAACATGGATGAATCTCACA--AACA 613 chrXqtel1M 685117 TCATGCTGAGTGAAAGGAGCAGGGC-CAAGAGATCATTATATACT 685160 v i i i vi i - i --- v i L1ME3A_3end#L 614 TAATGTTGAGCGAAAGAAGCCAGACACAAAAG---AGTACATACT 655 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 40.34 CpG sites = 43, Kimura (unadjusted) = 42.65 Transitions / transversions = 1.43 (43/30) Gap_init rate = 0.05 (11 / 239), avg. gap size = 1.09 (12 / 11) 393 36.89 2.18 1.44 chrXqtel1M 684928 685202 (314798) L1ME4c_3end#LINE/L1 426 702 (128) m_b370s551i3 15455 chrXqtel1M 684928 AGAAATTACTTGCA--AAAATATTTGGGGCAGCCCTCTTTGTAGTGGCCA 684975 i ii iv -- i i iivv vi v i i i v L1ME4c_3end#L 426 AAAAGCTATATGCACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGA 475 chrXqtel1M 684976 GAAACTGGAAACTGAGTGGATGCCCATCAGTTGGAGAATGGCTGAATAAA 685025 i i vivv ii i v i v i i i i L1ME4c_3end#L 476 AAAATTGGAAACAACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAA 525 chrXqtel1M 685026 TTGTGGTATATGAATGTTATGGAATATTATTGTTCTATAAGAAATGACAA 685075 i i v? iviv vvvv i v i i L1ME4c_3end#L 526 TTATGGTACATCNACTCGATGGAATATTATGCAGCCATTAAAAATGATAA 575 chrXqtel1M 685076 GCAGGAGGATTTCAGAAAGGCCTGGAGAGACTCACATGAACTCATGCTGA 685125 vi v i i viiv ivii v - i ivivi vv v i i L1ME4c_3end#L 576 TTATGAAGACTATGTAGCAACATGGA-AAATGTTTATGATATAATGTTAA 624 chrXqtel1M 685126 GTGAAAGGAGCAGGGCCAAGAGATCAT-TATATACTTCAACAACAATACT 685174 ii ii-i vi i ii - ? ii vii iv -- L1ME4c_3end#L 625 GTGAAAAAAGCAGAA-TACAAAATTGTATNTACGCTATGATTACA--ACT 671 chrXqtel1M 685175 ATATGATGATCATTTCTG---ATGGACCAGG 685202 i i vi i iv v --- v L1ME4c_3end#L 672 ATGTAAAAATTACGTATGCATATGGACAAGG 702 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 52.03 CpG sites = 63, Kimura (unadjusted) = 54.61 Transitions / transversions = 1.70 (63/37) Gap_init rate = 0.03 (7 / 274), avg. gap size = 1.43 (10 / 7) 197 26.46 4.29 2.82 chrXqtel1M 686178 686247 (313753) C L2d2_3end#LINE/L2 (0) 555 485 m_b370s601i7 15456 chrXqtel1M 686178 TCCAGTTAAGATCAACAAATATGTACTGGGCCTTTCCTCAGTGACAATG- 686226 v i i - v i i vii v vv - v - C L2d2_3end#LIN 555 TCAAATCAA-ATCAACAAATATTTATTGAGCGCCTACTGTGTG-CAAGGC 508 chrXqtel1M 686227 --GGTTCTAGGTGCTGCAGGGGA 686247 --v v i ii C L2d2_3end#LIN 507 ACTGTGCTAGGCGCTGTGGGGGA 485 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 30.84 CpG sites = 9, Kimura (unadjusted) = 32.98 Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.06 (4 / 69), avg. gap size = 1.25 (5 / 4) 338 34.93 1.37 3.26 chrXqtel1M 686386 686604 (313396) L1ME4c_3end#LINE/L1 251 465 (365) m_b370s551i4 15457 chrXqtel1M 686386 GGGGCTGCA-TGAAGACGGGCACCCTGGTGCCTTGCGGGAGGGGAACCAT 686434 i ? i- - v i ? vi i v v --v v ?ii L1ME4c_3end#L 251 GAGGNTGCGGTGAA-ACTGGTACNCTCATACATTGCTGG--TGGCANTGT 297 chrXqtel1M 686435 GGATCGGAACAACTATTCTGGCAAGCCAATTTGGAACTGTGCAAATCAAG 686484 ii i v iv i v - v v ii i -- L1ME4c_3end#L 298 AAATTGGTACAACCCTTTTGGAAAGC-AATTTGGCAATACGTA--TCAAG 344 chrXqtel1M 686485 GG--ACCGAAATGTTCACGCCCTCTGACCTGCAGATTGCCCTACTAGGCT 686532 i -- ivi ii i iivvi v v v i vv L1ME4c_3end#L 345 AGCCATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAA 394 chrXqtel1M 686533 TCTATGCCAGGAAGGTCACTGTTGAAGAAGAAAGTCTCCATTTCCACCAC 686582 i v i i i ii v i -ivi i ivvv i v v v v L1ME4c_3end#L 395 TTTATCCTAAGGAAATAATT-CAAAAGAAGGAAAAAGCTATATGCACGAA 443 chrXqtel1M 686583 AATACTCACAGCAGCACTTTTT 686604 i ii iv ii v L1ME4c_3end#L 444 GATGTTCATTGCAGCGTTATTT 465 Matrix = 20p51g.matrix Kimura (with divCpGMod) = 46.97 CpG sites = 43, Kimura (unadjusted) = 49.82 Transitions / transversions = 1.39 (43/31) Gap_init rate = 0.04 (9 / 218), avg. gap size = 1.11 (10 / 9) 31 0.00 0.00 0.00 chrXqtel1M 688892 688918 (311082) (AC)n#Simple_repeat 1 27 (0) c_b370s251i1 15458 chrXqtel1M 688892 ACACACACACACACACACACACACACA 688918 (AC)n#Simple_ 1 ACACACACACACACACACACACACACA 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 13 14.94 0.00 3.23 chrXqtel1M 691594 691625 (308375) (CCTCCC)n#Simple_repeat 1 31 (0) m_b370s252i4 15459 chrXqtel1M 691594 CCTCCCTCTCTCCCCTCCTCCCCCCCATCCCC 691625 i - i i v (CCTCCC)n#Sim 1 CCTCCCCCTC-CCCCTCCCCCTCCCCCTCCCC 31 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 16 0.00 0.00 0.00 chrXqtel1M 695642 695659 (304341) (A)n#Simple_repeat 1 18 (0) m_b370s252i5 15460 chrXqtel1M 695642 AAAAAAAAAAAAAAAAAA 695659 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAA 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 19 14.27 3.85 3.85 chrXqtel1M 695992 696043 (303957) (AGGAGA)n#Simple_repeat 1 52 (0) m_b370s252i6 15461 chrXqtel1M 695992 AGGA-AAGGGGAAGGAGAAGGAAGGAGGGGGAGGA-AAGGCGGAAGAAGA 696039 - i - i i i - -i i (AGGAGA)n#Sim 1 AGGAGAAGGAGAAGGAGAAGG-AGAAGGAGAAGGAGAAGG-AGAAGGAGA 48 chrXqtel1M 696040 AGGA 696043 (AGGAGA)n#Sim 49 AGGA 52 Matrix = Unknown Transitions / transversions = 1.00 (6/0) Gap_init rate = 0.08 (4 / 51), avg. gap size = 1.00 (4 / 4) 25 9.96 0.00 0.00 chrXqtel1M 697191 697233 (302767) (TAGATTCTAT)n#Simple_repeat 1 43 (0) c_b370s251i2 15462 chrXqtel1M 697191 TAGATTGTATTAGATTCTTTTAGGTTCTATTAGATTCCATTAG 697233 v v i i (TAGATTCTAT)n 1 TAGATTCTATTAGATTCTATTAGATTCTATTAGATTCTATTAG 43 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 28 3.33 0.00 0.00 chrXqtel1M 698930 698960 (301040) (CTAACC)n#Simple_repeat 1 31 (0) c_b370s251i3 15463 chrXqtel1M 698930 CTAACCCTAACCCTAACCCTAACTCTAACCC 698960 i (CTAACC)n#Sim 1 CTAACCCTAACCCTAACCCTAACCCTAACCC 31 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 263 12.96 7.41 0.00 chrXqtel1M 699807 699860 (300140) C MIR#SINE/MIR (67) 195 138 m_b370s601i8 15464 chrXqtel1M 699807 TGACTCATTCAATCCTCACAACCACCTTTTGA-GCAGGTGCTATTATT-- 699853 i i v i v - i i -- C MIR#SINE/MIR 195 TAACTCATTTAATCCTCACAACAACCCTATGAGGTAGGTACTATTATTAT 146 chrXqtel1M 699854 -CCCATTT 699860 - C MIR#SINE/MIR 145 CCCCATTT 138 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 14.49 CpG sites = 5, Kimura (unadjusted) = 14.49 Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.06 (3 / 53), avg. gap size = 1.33 (4 / 3) 270 24.99 4.29 2.82 chrXqtel1M 700619 700688 (299312) C MIR3#SINE/MIR (18) 190 120 m_b370s601i9 15465 chrXqtel1M 700619 ATGTCTGTAAGCCAGAAGGGTCCTTGAAGGTCATCTCATTCAGCTTCCCC 700668 v -- ii v ii i vi i i ii i C MIR3#SINE/MIR 190 ATGTCAG--AGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTC 143 chrXqtel1M 700669 ATTTTACA---AAAGTAACTGAG 700688 ---i i v C MIR3#SINE/MIR 142 ATTTTACAGATGAGGAAACTGAG 120 Matrix = 25p51g.matrix Kimura (with divCpGMod) = 32.23 CpG sites = 13, Kimura (unadjusted) = 32.23 Transitions / transversions = 3.25 (13/4) Gap_init rate = 0.04 (3 / 69), avg. gap size = 1.67 (5 / 3) 11 16.41 5.88 0.00 chrXqtel1M 701797 701830 (298170) (TAGACA)n#Simple_repeat 1 36 (0) m_b370s252i7 15466 chrXqtel1M 701797 TAG-CATACACATA-CCAAAGGCATAGACATCGACA 701830 - v -v v i v (TAGACA)n#Sim 1 TAGACATAGACATAGACATAGACATAGACATAGACA 36 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2) 194 24.68 6.09 11.93 chrXqtel1M 703326 703440 (296560) X24_LINE#LINE/L2 30 138 (176) m_b371s601i0 15467 chrXqtel1M 703326 CATCCAGA-GTCTCGGTGGGAGCAGAAAGCTCTCCCTACAGCTGCTCTGG 703374 i i - ii i iv v --------- i v -- X24_LINE#LINE 30 CACCCGGAAGCTTCAGCTGGTGCAGAA---------TGCAGCGGCTC--G 68 chrXqtel1M 703375 TCTGCTCAGTGGCTTGAGTCTCAGGAAG-AC----CACCTGTGGTCTGTG 703419 v i? iv ? i v ? i - ---- v i ii X24_LINE#LINE 69 TCTGCTGAANGGTGTNAGCCACANGGAGCACATTACACCTGTGCTCCGCA 118 chrXqtel1M 703420 TTCCCTGTGCT-GCTACCCACT 703440 v -- ii - ? i X24_LINE#LINE 119 GT--CTGCACTGGCTACCNATT 138 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 29.32 CpG sites = 17, Kimura (unadjusted) = 32.44 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.15 (17 / 114), avg. gap size = 1.18 (20 / 17) 247 29.57 8.08 0.94 chrXqtel1M 703446 703544 (296456) L2a_3end#LINE/L2 383 488 (29) m_b371s601i1 15468 chrXqtel1M 703446 GTCTCTCACCATCAGCGTGCGAGCTCCAGGACCGCAGGGTC------CCG 703489 i v ii vi ii v vv v ------ i L2a_3end#LINE 383 GTCTCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTCTG 432 chrXqtel1M 703490 CTTTGCTTTCTGCCTCTAGCTCC--TGCTTAGCACAGGACCCCGCACCTA 703537 i i iv - v v i --i i v vi iv v L2a_3end#LINE 433 TTTTGTTCACTG-CTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACATA 481 chrXqtel1M 703538 GTAGGTG 703544 i L2a_3end#LINE 482 GTAGGCG 488 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.16 CpG sites = 16, Kimura (unadjusted) = 38.44 Transitions / transversions = 1.23 (16/13) Gap_init rate = 0.03 (3 / 98), avg. gap size = 3.00 (9 / 3) 349 28.39 5.10 5.77 chrXqtel1M 704565 704721 (295279) C L2b_3end#LINE/L2 (23) 443 288 m_b371s601i2 15469 chrXqtel1M 704565 ATTCAGCACCTACGATGTGCCAGGCCCTGGGTCAAGTGCTGAGAATGCAG 704614 i v i vi ? v ii i i i i i C L2b_3end#LINE 443 ACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGGGATACAG 394 chrXqtel1M 704615 AGGCAAAAAA-------CCAGGCCCTGACATCAAGGGGCTCCTAGGCTAA 704657 v ii v -------? i v v v v i vi v i C L2b_3end#LINE 393 CGGTGAACAAGACAGACNCGGTCCCTGCCCTCACGGAGCTCACAGTCTAG 344 chrXqtel1M 704658 TGGAGGAGACCACAAGAACCAAGCCACAAGGAGGCACT-AGAATTCAGAG 704706 i ---- -- v ---i ?v i v - v ii C L2b_3end#LINE 343 TGGGGGAGAC----AGA--CATG---TAANCAGACAATNATAACCCAGAG 303 chrXqtel1M 704707 GGGTTGGGAAAGGCT 704721 v iv v i i C L2b_3end#LINE 302 TGGCAGGGTAGGACT 288 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.19 CpG sites = 24, Kimura (unadjusted) = 37.50 Transitions / transversions = 1.33 (24/18) Gap_init rate = 0.07 (11 / 156), avg. gap size = 1.55 (17 / 11) 183 26.00 17.78 6.00 chrXqtel1M 704745 704879 (295121) L2#LINE/L2 2214 2363 (719) m_b371s601i3 15470 chrXqtel1M 704745 CCCCTCACCACAGGGGTCCCCCTGGGGCTCTGTCCTGGGCCCTTTGCTCT 704794 i ? v iiv i v -i v v v i v L2#LINE/L2 2214 CCTCTNAACGTTGGAGTGCCCC-AGGGCTCAGTCCTTGGACCTCTTCTCT 2262 chrXqtel1M 704795 TCCTGCTCTAGAC---CTCCC---------------------ATGGATCG 704820 iivv v --- --------------------- v iv L2#LINE/L2 2263 TCTCTATCTACACTCACTCCCTNGGTGATCTCATCCAGTCTCATGGCTTT 2312 chrXqtel1M 704821 AATGACCATCTAACTCTATGCTGAGGAATGATTCCCAGATCTCCCTTTCC 704870 vv ---- ---- i i i viv i L2#LINE/L2 2313 AAATACCATCTA----TATGCTG----ATGACTCCCAAATTTATATCTCC 2354 chrXqtel1M 704871 TGCCTGGGC 704879 v i i L2#LINE/L2 2355 AGCCCGGAC 2363 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.50 CpG sites = 16, Kimura (unadjusted) = 32.82 Transitions / transversions = 0.94 (16/17) Gap_init rate = 0.08 (11 / 134), avg. gap size = 3.00 (33 / 11) 181 34.61 6.25 5.47 chrXqtel1M 704859 705130 (294870) L2#LINE/L2 2409 2682 (400) m_b371s601i4 15470 chrXqtel1M 704859 ATCTCC-CTTTCCTGCCTGGGCGGCATCTGAAATGCCACCCCTCCGCCAA 704907 - vvv i iivv v iviv viv ----- L2#LINE/L2 2409 ATCTCCACTTGGATGTCTAATAGGCATCTCAAACTTAACATGTCC----- 2453 chrXqtel1M 704908 AAAAAAAGAACTCATTCTCTTTCCCCCTAAACCCTCTCTACCTCCTACCT 704957 - vv v vv i ii iv iv iv vii L2#LINE/L2 2454 -AAAACTGAACTCCTGATCTTCCCCCTCAAACCTGCTCCTCCCGCAGTCT 2502 chrXqtel1M 704958 TTCCCTTTACTGTGGAAGGTACCCCAATCCCT-CAG--ACTCC--CCAA- 705001 i v iv v ?i v i v i v i - --i v-- - L2#LINE/L2 2503 TCCCCATCTCAGTNAATGGCAACTCCATCCTTCCAGTTGCTCAGGCCAAA 2552 chrXqtel1M 705002 ---CTAGGAGTCATCCCAAACTCCTATCAGCCCCCCGC-CACAAAGTCCA 705047 --- v ivi v vvi i i i - v v vi L2#LINE/L2 2553 AACCTTGGAGTCATCCTTGACTCCTCTCTTTCTCTCACACCCCACATCCA 2602 chrXqtel1M 705048 ATATGGTGCCAAAGCCTGT-GGTTTTCACAAACCTT-----TCTCTCCTG 705091 viiviiv v - i i ----- ----- v v v L2#LINE/L2 2603 ATCCATCAGCAAATCCTGTCGGCTCT-----ACCTTCAAAATATATCCAG 2647 chrXqtel1M 705092 ATACCGCCCCTCCCTCCTGAACCACTTCAGTAGCTGCCA 705130 vv v viii ---- i viiv ii L2#LINE/L2 2648 AATCCGACCACTTCTC----ACCACCTCCACTGCCACCA 2682 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.57 CpG sites = 42, Kimura (unadjusted) = 47.28 Transitions / transversions = 0.89 (42/47) Gap_init rate = 0.09 (24 / 271), avg. gap size = 1.33 (32 / 24) 245 39.85 3.85 1.89 chrXqtel1M 705101 705256 (294744) L2#LINE/L2 2705 2863 (219) m_b371s601i5 15470 chrXqtel1M 705101 CTCCCTCCTGAACCACTTCAGTAGCTGCC-AGGGGGCTGGCCTGCCTCGA 705149 i v i ii v i iv - ivv iivv i v L2#LINE/L2 2705 CTCTCGCCTGGATTACTGCAATAGCCTCCTAACTGGTCTCCCTGCTTCCA 2754 chrXqtel1M 705150 -----GTCTCAGTCCAGTCCACCCTCCATCTGGCCATCACAGGGATTTTT 705194 ----- i i vv ? i ii v ivii vii v v ii L2#LINE/L2 2755 CCCTTGCCCCCCTNCAGTCTATTCTCAACACAGCAGCCAGAGTGATCCTT 2804 chrXqtel1M 705195 TCCCCAGAGGGTGGGTCCAACCATGTCATCCCCCAAATCAACAAACTGCA 705244 i--- i iv ii vi i ii i viv v vv v L2#LINE/L2 2805 TT---AAAACGTAAGTCAGATCATGTCACTCCTCTGCTCAAAACCCTCCA 2851 chrXqtel1M 705245 GGGACTCCCTAT 705256 iv i i i L2#LINE/L2 2852 ATGGCTTCCCAT 2863 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 61.23 CpG sites = 37, Kimura (unadjusted) = 61.23 Transitions / transversions = 1.54 (37/24) Gap_init rate = 0.03 (5 / 155), avg. gap size = 1.80 (9 / 5) 22 24.13 1.67 1.67 chrXqtel1M 705376 705435 (294565) (AG)n#Simple_repeat 1 60 (0) m_b371s252i0 15471 chrXqtel1M 705376 AGAGGGAGAGAGACAGAAACAGAGAGAAACCACACACACAGAGAGA-AGA 705424 i v i v i -v v v v v - (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGA-GAGAGAGAGAGAGAGAGAGA 49 chrXqtel1M 705425 GAGAGGGTGAG 705435 i v (AG)n#Simple_ 50 GAGAGAGAGAG 60 Matrix = Unknown Transitions / transversions = 0.50 (4/8) Gap_init rate = 0.03 (2 / 59), avg. gap size = 1.00 (2 / 2) 13 9.09 2.33 10.00 chrXqtel1M 705642 705684 (294316) (TCTTTTC)n#Simple_repeat 1 40 (0) m_b371s252i1 15472 chrXqtel1M 705642 TCATTTCTGCTTCTTC-CTCTATCTCTTTTTCGCTTTTCTCTTT 705684 v - - - - v - v (TCTTTTC)n#Si 1 TCTTTTCT-CTT-TTCTCT-TTTCTC-TTTTCTCTTTTCTCTTT 40 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.12 (5 / 42), avg. gap size = 1.00 (5 / 5) 41 37.10 1.81 3.69 chrXqtel1M 706797 707072 (292928) (CCTCCC)n#Simple_repeat 1 271 (0) m_b371s252i2 15473 chrXqtel1M 706797 CCTCCCCTACCCCATATCCAT-TCCCTCCTTCTTTTACTCCCCTTCCTCC 706845 iv v vi v -i ii iiiv i - - (CCTCCC)n#Sim 1 CCTCCCCCTCCCCCTCCCCCTCCCCCTCCCCCTCCCCCTCCCCCT-C-CC 48 chrXqtel1M 706846 CCTCCTTTTTCCCCCCAACCTTTCCC-CTCCCTCCCCTTCTCCCCTCCCT 706894 iii i i vv ii - i i - i (CCTCCC)n#Sim 49 CCTCCCCCTCCCCCTCCCCCTCCCCCTCCCCCTCCCCCTC-CCCCTCCCC 97 chrXqtel1M 706895 ACCCCCATCCCCTCTACCCCCATCCCTTTCCCTTCCTCTCCTTCCCCCCC 706944 vi v - v ivi ii i i ii i (CCTCCC)n#Sim 98 CTCCCCCTCCCC-CTCCCCCTCCCCCTCCCCCTCCCCCTCCCCCTCCCCC 146 chrXqtel1M 706945 ACCCCCTTTATCTTCTCCCTCCCCCTCCTTTGTCCCTCCCCCCCATCCAT 706994 v - ivi i i -iiv - i v -i (CCTCCC)n#Sim 147 TCCCCC-TCCCCCTCCCCCTCCCCCTCC-CCCTCCC-CCTCCCCCTCC-C 192 chrXqtel1M 706995 TTTCCCCCTCTTCC-CCTTATTTCCCTCTTCCCT-TTATTCCCCC-CCTT 707041 ii ii - iiv ii -i -iivi - ii (CCTCCC)n#Sim 193 CCTCCCCCTCCCCCTCCCCCTCCCCCTC-CCCCTCCCCCTCCCCCTCCCC 241 chrXqtel1M 707042 TTCCCCATCCCTTTCCCTCCTCCCCCTCCCC 707072 i v ii - (CCTCCC)n#Sim 242 CTCCCCCTCCCCCTCCC-CCTCCCCCTCCCC 271 Matrix = Unknown Transitions / transversions = 3.00 (54/18) Gap_init rate = 0.05 (15 / 275), avg. gap size = 1.00 (15 / 15) 201 32.00 11.00 0.00 chrXqtel1M 708875 708974 (291026) L2b_3end#LINE/L2 336 446 (20) m_b371s601i6 15474 chrXqtel1M 708875 CCCCACCGTTAAACCGTGGGCCCTTTGAGGGCAGGCGCTGG--CTGGCTT 708922 i v ii i i i i iv vi i ?-- v L2b_3end#LINE 336 CTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCTT 385 chrXqtel1M 708923 GGCCAC------ATCTCCAGGATTTAGCA---GGTTTGGCCCAGGGCACC 708963 vi ------ i viii ---? ii v vi i vv L2b_3end#LINE 386 GTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGG 435 chrXqtel1M 708964 CGCACACGAAA 708974 v vv L2b_3end#LINE 436 CGCTCAGTAAA 446 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.01 CpG sites = 19, Kimura (unadjusted) = 44.45 Transitions / transversions = 1.46 (19/13) Gap_init rate = 0.03 (3 / 99), avg. gap size = 3.67 (11 / 3) 18 0.00 0.00 0.00 chrXqtel1M 709433 709452 (290548) (T)n#Simple_repeat 1 20 (0) m_b371s252i3 15475 chrXqtel1M 709433 TTTTTTTTTTTTTTTTTTTT 709452 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTT 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 17 38.87 0.00 0.00 chrXqtel1M 709986 710046 (289954) (AA)n#Simple_repeat 1 61 (0) m_b371s252i4 15476 chrXqtel1M 709986 AAAAAAAAAAAAAATTAAAAGGGAGAAGAGAGAGGGAAAGAAAAGGAAGG 710035 vv iii i i i i iii i ii ii (AA)n#Simple_ 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chrXqtel1M 710036 AAAAAAAAAAA 710046 (AA)n#Simple_ 51 AAAAAAAAAAA 61 Matrix = Unknown Transitions / transversions = 7.50 (15/2) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 16 20.27 0.00 0.00 chrXqtel1M 710691 710720 (289280) (A)n#Simple_repeat 1 30 (0) m_b371s252i5 15477 chrXqtel1M 710691 AAGAAAAAAAAAAAAAAAAGGAGGAAAAAA 710720 i ii ii (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 30 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 14 18.78 7.81 2.99 chrXqtel1M 711313 711376 (288624) (GGTGTG)n#Simple_repeat 1 67 (0) m_b371s252i6 15478 chrXqtel1M 711313 GGTTTGGGGGTGGGTGTGGGT-TGGGAAGGGCGGTGAGGG-G-GGGAG-G 711358 v v - -v v - v - - v - (GGTGTG)n#Sim 1 GGTGTGGGTGTGGGTGTGGGTGTGGG-TGTG-GGTGTGGGTGTGGGTGTG 48 chrXqtel1M 711359 GGT-TAGGGGTGGATGAGG 711376 - i v i v (GGTGTG)n#Sim 49 GGTGTGGGTGTGGGTGTGG 67 Matrix = Unknown Transitions / transversions = 0.25 (2/8) Gap_init rate = 0.11 (7 / 63), avg. gap size = 1.00 (7 / 7) 351 29.84 2.38 1.57 chrXqtel1M 712420 712545 (287455) MIR#SINE/MIR 18 144 (118) m_b371s601i7 15479 chrXqtel1M 712420 TTAAAGACCTGGAATCAGGAGACCGCCACTCCCTGAGTTCAAAGCTGGTC 712469 iii vi iv v v v -- v i i v iv v MIR#SINE/MIR 18 TTAAGAGCACGGGCTCTGGAGCCAG--ACTGCCTGGGTTCGAATCCCGGC 65 chrXqtel1M 712470 TCACACACTTCCTAACTGTGTGACCCTGGGCAAGTCCCTGACGCAATCTG 712519 vvv v i i iv v vv vv MIR#SINE/MIR 66 TCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTG 115 chrXqtel1M 712520 C-CTTC--CTTCCTCATCACCAAAATGAG 712545 i- i --i vvi i MIR#SINE/MIR 116 TGCCTCAGTTTCCTCATCTGTAAAATGGG 144 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.75 CpG sites = 16, Kimura (unadjusted) = 38.22 Transitions / transversions = 0.76 (16/21) Gap_init rate = 0.03 (4 / 125), avg. gap size = 1.25 (5 / 4) 13 21.72 2.94 7.69 chrXqtel1M 713613 713680 (286320) (AGGG)n#Simple_repeat 1 65 (0) m_b371s252i7 15480 chrXqtel1M 713613 AGTGAGGGGGGGCGGG-GAAAGGGAGGAAGATGGAGGGGATGG-GGAACA 713660 v i v - ii -- v - v - i -i (AGGG)n#Simpl 1 AGGGAGGGAGGGAGGGAGGGAGGGAGG--GAGGGA-GGGAGGGAGGGA-G 46 chrXqtel1M 713661 GGAGGGAGGGAACGAGAGGA 713680 iv - (AGGG)n#Simpl 47 GGAGGGAGGGAGGGAG-GGA 65 Matrix = Unknown Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.10 (7 / 67), avg. gap size = 1.00 (7 / 7) 12 31.19 1.82 0.00 chrXqtel1M 713805 713859 (286141) (TCCCCC)n#Simple_repeat 1 56 (0) m_b371s252i8 15481 chrXqtel1M 713805 TCTCCCTCCCCCTCAGCC-CGCCCAGCGCTTTGTCCCCCCCCTCCCCTTC 713853 i vv - v vv v i ivi i i (TCCCCC)n#Sim 1 TCCCCCTCCCCCTCCCCCTCCCCCTCCCCCTCCCCCTCCCCCTCCCCCTC 50 chrXqtel1M 713854 CCGCTC 713859 v (TCCCCC)n#Sim 51 CCCCTC 56 Matrix = Unknown Transitions / transversions = 0.75 (6/8) Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1) 14 21.98 2.38 0.00 chrXqtel1M 714270 714311 (285689) (CCCCCT)n#Simple_repeat 1 43 (0) m_b371s252i10 15482 chrXqtel1M 714270 CCCCCTCCCCC-CGCCCCCCGCCTCCTCCTCCGCGCCGCCCTC 714311 - v i v i v vi v (CCCCCT)n#Sim 1 CCCCCTCCCCCTCCCCCTCCCCCTCCCCCTCCCCCTCCCCCTC 43 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.02 (1 / 41), avg. gap size = 1.00 (1 / 1) 19 25.68 1.67 0.00 chrXqtel1M 714278 714337 (285663) (CCTCGG)n#Simple_repeat 1 61 (0) m_b371s252i11 15482 chrXqtel1M 714278 CCCCGCCCCCCGCCTCCTCCTCCGCGCCGCCCTCGG-CTCGGCCTCAACC 714326 i v i v vv v vi v - ii (CCTCGG)n#Sim 1 CCTCGGCCTCGGCCTCGGCCTCGGCCTCGGCCTCGGCCTCGGCCTCGGCC 50 chrXqtel1M 714327 CCGGCCTCGGC 714337 i (CCTCGG)n#Sim 51 TCGGCCTCGGC 61 Matrix = Unknown Transitions / transversions = 0.86 (6/7) Gap_init rate = 0.02 (1 / 59), avg. gap size = 1.00 (1 / 1) 19 16.17 4.00 1.96 chrXqtel1M 714902 714951 (285049) (CCTCC)n#Simple_repeat 1 51 (0) m_b371s252i12 15483 chrXqtel1M 714902 CCGCCCCT-GCCGCCCCTCCCCCTTCCCTACCC-CCCCCCACCTCCCCTC 714949 v -v v - i v - i v (CCTCC)n#Simp 1 CCTCCCCTCCCCTCCCCT-CCCCTCCCCTCCCCTCCCCTCCCCTCCCCTC 49 chrXqtel1M 714950 CC 714951 (CCTCC)n#Simp 50 CC 51 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.06 (3 / 49), avg. gap size = 1.00 (3 / 3) 13 20.69 2.08 4.26 chrXqtel1M 715117 715164 (284836) (TGTCCCC)n#Simple_repeat 1 47 (0) m_b371s252i13 15484 chrXqtel1M 715117 TGTCCCC-GCACCCTGCCCCCGTTCTCCCTTTGCCCGGTTCCCCTGTCC 715164 - iv i vv - v v v - (TGTCCCC)n#Si 1 TGTCCCCTGTCCCCTGTCCCCTGTC-CCCTGTCCCCTG-TCCCCTGTCC 47 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.06 (3 / 47), avg. gap size = 1.00 (3 / 3) 60 24.39 6.15 6.15 chrXqtel1M 715180 715569 (284431) (TCTCC)n#Simple_repeat 1 390 (0) m_b371s252i14 15485 chrXqtel1M 715180 TCTCCT-TTCTC-CCCCTCCATCT-CTCTTCT-TCC-CTCCTTTTCCTCG 715224 - i - i - - i - - - i v (TCTCC)n#Simp 1 TCTCCTCTCCTCTCCTCTCC-TCTCCTCTCCTCTCCTCTCC-TCTCCTCT 48 chrXqtel1M 715225 CCTTTTTCCTTTGCCTCCACACTCCGATTTCCCCT-CTATCC-ATCCTCT 715272 -- i i - iv v -- i i - v -v (TCTCC)n#Simp 49 CC--TCTCCTCT-CCTCTCCTCTCC--TCTCCTCTCCTCTCCTCTCCTCT 93 chrXqtel1M 715273 CCCTCTTCCATCCTCCCCCTTCTCATCCCCCCTCATCTCTTCTCCTCCCT 715322 - i iv - i - v i i v i -- (TCTCC)n#Simp 94 -CCTCTCCTCTCCT-CTCC-TCTCCTCTCCTCTCCTCTCCTCTCCT--CT 138 chrXqtel1M 715323 CCTTTCCTCTTCCCATCC-ATCGTCTCC-CTTCCCTCCT-TTCTCTTCTC 715369 i - iv -v v - i i - i i (TCTCC)n#Simp 139 CCTCTCCTC-TCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTC 187 chrXqtel1M 715370 -CTTCATCC-CTTCTTTTGAGTCC-CTCCATCT-CTTTCACTCTTCTCCT 715415 - i - - i i ivvv - - - i - i - (TCTCC)n#Simp 188 TCCTC-TCCTCTCCTCTCCTCTCCTCTCC-TCTCCTCTC-CTCTCCT-CT 233 chrXqtel1M 715416 CCT-TCCACCCCGCTATCCCCCTTCCCTCTCC-CTCCTGTCC-CTATCTC 715462 - v i v vii i ii - v - -i (TCTCC)n#Simp 234 CCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCT-CCTC 282 chrXqtel1M 715463 TTCTTTCC-C-CCTTTCCTCT--TCGCCATTCCTCCTCC-CGCACTCTCC 715507 i i - - i -- v vi - - v - (TCTCC)n#Simp 283 TCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCT-CTCCTCTC-CTCTCC 330 chrXqtel1M 715508 ACCTCTTTCCACTCCGTTCTCCTC-CCTCCATCCT-TCCTCTCGACCTCT 715555 v ii i v -- - - - - vv ii (TCTCC)n#Simp 331 TCTCCTCTCCTCTCC--TCTCCTCTCCT-C-TCCTCTCCTCTCCTCTCCT 376 chrXqtel1M 715556 TTCCTTACCTCTCC 715569 i iv (TCTCC)n#Simp 377 CTCCTCTCCTCTCC 390 Matrix = Unknown Transitions / transversions = 1.73 (45/26) Gap_init rate = 0.12 (47 / 389), avg. gap size = 1.02 (48 / 47) 18 24.83 0.00 0.00 chrXqtel1M 715878 715925 (284075) (CCG)n#Simple_repeat 1 48 (0) m_b371s252i15 15486 chrXqtel1M 715878 CCGCCGCTGCCGCCGCCACTTCCTCCTCTACCGCCGGTGCCGCCGCCG 715925 i i iv v v ii vi (CCG)n#Simple 1 CCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCG 48 Matrix = Unknown Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 15 19.56 0.00 0.00 chrXqtel1M 717236 717270 (282730) (CTGCCA)n#Simple_repeat 1 35 (0) m_b371s252i16 15487 chrXqtel1M 717236 CTGCCACTGCCTCTGCCCCCACCACCGCCTCTGCC 717270 v v ii i v (CTGCCA)n#Sim 1 CTGCCACTGCCACTGCCACTGCCACTGCCACTGCC 35 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 218 30.77 0.00 0.00 chrXqtel1M 717337 717388 (282612) MIRb#SINE/MIR 53 104 (164) m_b371s601i8 15488 chrXqtel1M 717337 ATCTGGATTCACATCTCAACTCTGGTCCTCACTAAATGTGTGATCTTAGA 717386 i i iv i ii viv i iv i i i MIRb#SINE/MIR 53 ACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGG 102 chrXqtel1M 717387 CA 717388 MIRb#SINE/MIR 103 CA 104 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.85 CpG sites = 12, Kimura (unadjusted) = 42.84 Transitions / transversions = 3.00 (12/4) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 232 28.82 4.48 9.38 chrXqtel1M 717856 717989 (282011) MIR3#SINE/MIR 78 205 (3) m_b371s601i9 15489 chrXqtel1M 717856 CTTGCTGTGTCTAACGGTTTTGTGTCAGGGCA--ACATTTAACTGGGCCT 717903 ? ----- iii v - i v --v ii vv MIR3#SINE/MIR 78 CTNGCTGTGT-----GACCTTGGG-CAAGTCACTTCACCTCTCTGGGCCT 121 chrXqtel1M 717904 CC-CCTCCCCGAGTCTACAATGAGGGGGTTGGGGAAGATAGACTTTGAGT 717952 v-ii i ivv v v ivv iiv i i v MIR3#SINE/MIR 122 CAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGG 171 chrXqtel1M 717953 TCCTCCCCCCCCCCAACTCTGGC-TTCCA--ATTCTAAGA 717989 ------ ii i i - i -- v MIR3#SINE/MIR 172 T------CCCTTCCAGCTCTGACATTCTATGATTCTATGA 205 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 37.43 CpG sites = 20, Kimura (unadjusted) = 37.43 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.12 (16 / 133), avg. gap size = 1.12 (18 / 16) 194 34.02 8.25 0.00 chrXqtel1M 718275 718371 (281629) L2#LINE/L2 2729 2833 (249) m_b371s601i10 15490 chrXqtel1M 718275 CTTCCTAGTTCACTTCCTTGCTTGCATCACTGCC----TCCAGTCTATCT 718320 i ii viii i v i vi ---- ? ii L2#LINE/L2 2729 CCTCCTAACTGGTCTCCCTGCTTCCACCCTTGCCCCCCTNCAGTCTATTC 2778 chrXqtel1M 718321 TTCAAGCTGCAGCCAAAGTAATTGTCCTTACATCTGA--CAG--TGTGAC 718366 iv vi v i i iv ii v v iv i -- --ii v L2#LINE/L2 2779 TCAACACAGCAGCCAGAGTGATCCTTTTAAAACGTAAGTCAGATCATGTC 2828 chrXqtel1M 718367 ACTCC 718371 L2#LINE/L2 2829 ACTCC 2833 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.90 CpG sites = 22, Kimura (unadjusted) = 49.05 Transitions / transversions = 2.00 (22/11) Gap_init rate = 0.03 (3 / 96), avg. gap size = 2.67 (8 / 3) 201 29.59 8.11 2.56 chrXqtel1M 718418 718528 (281472) C MIR3#SINE/MIR (15) 193 77 m_b371s601i11 15491 chrXqtel1M 718418 AGATTTTCA-AGATAGAAGAAATCTTAGAAATCATGAAATT--ACATCTT 718464 v v - v i ii i i vv i i-- vi i C MIR3#SINE/MIR 193 AGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCT 144 chrXqtel1M 718465 CATTTGACAGAAAGAGGGAAAACGGATCACCGGATGGGTAGAG------G 718508 v - v -- v vvv i vi ii ------ C MIR3#SINE/MIR 143 CATTTTACAG-ATGAGG--AAACTGAGGCCCAGAGAGGTGAAGTGACTTG 97 chrXqtel1M 718509 CCCAGGTCCACATCCCCAGT 718528 i vi ivv ? C MIR3#SINE/MIR 96 CCCAAGGTCACACAGCNAGT 77 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.65 CpG sites = 16, Kimura (unadjusted) = 38.65 Transitions / transversions = 1.00 (16/16) Gap_init rate = 0.05 (6 / 110), avg. gap size = 2.00 (12 / 6) 258 30.54 7.20 3.08 chrXqtel1M 718530 718654 (281346) C MIR3#SINE/MIR (1) 207 78 m_b371s601i12 15492 chrXqtel1M 718530 AAACATAGA-TGATGGGCCAAGTTCCAGAGCTGAAAGTGACC-----AAT 718573 v - v i ---- i vi i v -----i C MIR3#SINE/MIR 207 AATCATAGAATCATAG----AATGTCAGAGCTGGAAGGGACCTTAGAGAT 162 chrXqtel1M 718574 TCTCTAGTCTGACCCCATCATTTGGGAGGAGATGATACTTAAGCCCCCTG 718623 iv ii v viv iv v v v i vvv C MIR3#SINE/MIR 161 CATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAG 112 chrXqtel1M 718624 AGAAGCAGCAGCTTA---AAAATCACAAAGTCAG 718654 iv v iii i--- ii v i? C MIR3#SINE/MIR 111 AGGTGAAGTGACTTGCCCAAGGTCACACAGCNAG 78 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.35 CpG sites = 19, Kimura (unadjusted) = 40.35 Transitions / transversions = 1.06 (19/18) Gap_init rate = 0.06 (7 / 124), avg. gap size = 1.86 (13 / 7) 188 30.36 1.79 0.00 chrXqtel1M 718751 718806 (281194) MIRb#SINE/MIR 186 242 (26) m_b371s601i13 15488 chrXqtel1M 718751 GACCAAATGAGATATT-TGTAAAAAGTATTTAACACAGTGCCTCACTTAT 718799 ii v -ii iv iii i vi vi MIRb#SINE/MIR 186 GATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACAT 235 chrXqtel1M 718800 AATAGGC 718806 i i MIRb#SINE/MIR 236 AGTAAGC 242 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 38.51 CpG sites = 13, Kimura (unadjusted) = 42.22 Transitions / transversions = 3.25 (13/4) Gap_init rate = 0.02 (1 / 55), avg. gap size = 1.00 (1 / 1) 53 0.00 0.00 0.00 chrXqtel1M 718808 718852 (281148) (AT)n#Simple_repeat 1 45 (0) c_b371s251i0 15493 chrXqtel1M 718808 ATATATATATATATATATATATATATATATATATATATATATATA 718852 (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATA 45 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 277 23.80 5.81 2.25 chrXqtel1M 720381 720466 (279534) C L2d_3end#LINE/L2 (2) 514 426 m_b371s601i14 15494 chrXqtel1M 720381 AATCCATCAATTGATCGGTAAATATTAAGTGCCTACTATGTGCA-GGCAC 720429 v ii ivi vv i i v-i C L2d_3end#LINE 514 AATCAATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCAC 465 chrXqtel1M 720430 TGTCCTAA----TGGGGGAGATGAACAAACAAGGTACAAGA 720466 v i---- v ii i ?v ? -- i C L2d_3end#LINE 464 TGTGCTAGGCGCTGTGGGGAACGANAAAANA--GTATAAGA 426 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 26.69 CpG sites = 12, Kimura (unadjusted) = 30.16 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.05 (4 / 85), avg. gap size = 1.75 (7 / 4) 304 37.34 6.02 4.51 chrXqtel1M 720561 720975 (279025) C L2#LINE/L2 (2) 3080 2660 m_b371s601i15 15495 chrXqtel1M 720561 GAGGAGAGTATTCCACAGGCAGGGGGC-CAGCTGGAGAAAACGTCC-AAA 720608 i i ii -- i v- vi v v v i -i i C L2#LINE/L2 3080 GGGAAGAGCGTTCCA--GGCAGAGGGAACAGCAAGTGCAAAGGCCCTGAG 3033 chrXqtel1M 720609 GCAAGAGAGGTAGAAGCTCTTGTTTGAGGAACTGCCAGGAGG--AAGATG 720656 ii v vvvvvi v-- i v v -- ivi C L2#LINE/L2 3032 GCGGGAGCGTGCCTGGCG--TGTTCGAGGAACAGCAAGGAGGCCAGTGTG 2985 chrXqtel1M 720657 GCCCTGGATGGAAGAGAGGCAGGCGTAAGAACACTTGAA----AGG--AA 720700 -- vv i v vv - vi iiiv v i ---- -- i C L2#LINE/L2 2984 G--CTGGAGCGGAGTGAGCGAGG-GGGAGAGTGGTAGGAGATGAGGTCAG 2938 chrXqtel1M 720701 GGAGGGAGCAG-----CAGCTTATGAAAGG-CTGGAAAGCCA--GAAATT 720742 i v i i ----- v i v i - v v i -- v vv C L2#LINE/L2 2937 AGAGGTAACGGGGGACCAGATCATGTAGGGCCTTGTAGGCCATTGTAAGG 2888 chrXqtel1M 720743 AGTTTGTCTTTGATCCTGGAGGAAATAGGGAGCCATTGGCGTTTATTTTT 720792 v v v ii iiv i i i v ----vv C L2#LINE/L2 2887 ACTTTGGCTTTTACTCTGAGTGAGATGGGAAGCCATTGGAG----GGTTT 2842 chrXqtel1M 720793 TGAGTGGGGAGGGGGCAGGTAACACAGTCAGAGCTGTACTTTGGGAAGAT 720842 i--i -----i i iii v vi iiii iii i C L2#LINE/L2 2841 TGAGC--AGAGG-----AGTGACATGATCTGACTTACGTTTTAAAAGGAT 2799 chrXqtel1M 720843 CGAGTTGACAACTGAATCGAAGACGAACTGGAGTGGGGAGAGACCCGAGG 720892 ivvi i vi vi i ii iii ? v vi iviv i C L2#LINE/L2 2798 CACTCTGGCTGCTGTGTTGAGAATAGACTGNAGGGGGGCAAGGGTGGAAG 2749 chrXqtel1M 720893 TCCGCAGATTC-TCCAAAACCTATTACAATAGTCTAGATATGAAGTAATG 720941 ivv v iiv- ivii iv i i i i iiiv ii i C L2#LINE/L2 2748 CAGGGAGACCAGTTAGGAGGCTATTGCAGTAATCCAGGCGAGAGATGATG 2699 chrXqtel1M 720942 GAGG------ACAGTGTCGGGGGCGGGGGGGAGGGCGAGA 720975 v ------v v - v i v i iv i C L2#LINE/L2 2698 GTGGCTTGGACCAGGGT-GGTGGCAGTGGAGGTGGTGAGA 2660 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 50.98 CpG sites = 87, Kimura (unadjusted) = 54.42 Transitions / transversions = 1.43 (87/61) Gap_init rate = 0.07 (29 / 414), avg. gap size = 1.52 (44 / 29) 411 33.06 1.60 0.79 chrXqtel1M 721217 721341 (278659) L2d2_3end#LINE/L2 422 547 (8) m_b371s601i16 15496 chrXqtel1M 721217 TTGCCTTCCCCATCAGACTGGGAGTTCCTTGAGGGCTGGGACTGGCTTTT 721266 i i v ii i vi i v iivv i L2d2_3end#LIN 422 TTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTT 471 chrXqtel1M 721267 GCCCTTCTTGATCTCCCCAGCGTGTATTTAGTATAGTGCCCGGCACGTAG 721316 iiv vi v vi i- iiii i i iv ii L2d2_3end#LIN 472 ATACTTCTTTGTATCCCCCACA-GCGCCTAGCACAGTGCCTTGCACACAG 520 chrXqtel1M 721317 TAGGCACTTAAT--GCTTTTATTGACT 721341 i i --iiv i i L2d2_3end#LIN 521 TAGGCGCTCAATAAATATTTGTTGATT 547 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.92 CpG sites = 30, Kimura (unadjusted) = 47.38 Transitions / transversions = 2.73 (30/11) Gap_init rate = 0.02 (2 / 124), avg. gap size = 1.50 (3 / 2) 18 25.20 0.00 0.00 chrXqtel1M 721403 721450 (278550) (GGGTC)n#Simple_repeat 1 48 (0) m_b371s252i17 15497 chrXqtel1M 721403 GGGTCGAATGGGATCGGGTCAGGTCGGGTCGGGTCAGATGGGATGGGG 721450 ii v i i i i v i v (GGGTC)n#Simp 1 GGGTCGGGTCGGGTCGGGTCGGGTCGGGTCGGGTCGGGTCGGGTCGGG 48 Matrix = Unknown Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 16 28.65 3.17 0.00 chrXqtel1M 721789 721851 (278149) (GGGA)n#Simple_repeat 1 65 (0) m_b371s252i18 15498 chrXqtel1M 721789 GGGA-GGAGGGAGGGAGCGAGCGAGCGTGAGGGGCCCGGA-AGTGGGCGG 721836 - v v v v i i vvv -i v v (GGGA)n#Simpl 1 GGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGG 50 chrXqtel1M 721837 GGGGGAGAGAGTGAG 721851 i i v (GGGA)n#Simpl 51 GAGGGAGGGAGGGAG 65 Matrix = Unknown Transitions / transversions = 0.50 (5/10) Gap_init rate = 0.03 (2 / 62), avg. gap size = 1.00 (2 / 2) 309 24.68 1.30 0.00 chrXqtel1M 723004 723080 (276920) MIR3#SINE/MIR 107 184 (24) m_b371s601i17 15499 chrXqtel1M 723004 CAATTCCCTGGTGCTGGGTTTTCTTTTCTGTTAAATAAGGGG-TTAGAGT 723052 vi i vv vi i iv v i - i v MIR3#SINE/MIR 107 CACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACT 156 chrXqtel1M 723053 AAATGATTTCTAAGGATCCTTCCAGTTC 723080 i i vi i MIR3#SINE/MIR 157 AGATGATCTCTAAGGTCCCTTCCAGCTC 184 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.51 CpG sites = 11, Kimura (unadjusted) = 30.51 Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.01 (1 / 76), avg. gap size = 1.00 (1 / 1) 526 25.43 6.47 2.84 chrXqtel1M 723387 723556 (276444) C MIRc#SINE/MIR (79) 189 14 m_b371s601i18 15500 chrXqtel1M 723387 CACAATTCCCTGGTGAAGT---CAGTGC---CATTACTATTCCCAATTTT 723430 ivv iv i --- v ---i i i - C MIRc#SINE/MIR 189 CACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCA-TTTT 141 chrXqtel1M 723431 ATATGTAAGGAAACTGAGGAT--GAGAGGTTA--TGACTTGCCCATGGTC 723476 i vi i v -- -- v C MIRc#SINE/MIR 140 ACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTC 91 chrXqtel1M 723477 ATTAAGGTAGCTAGTAAGTGTCTGAAGTGGCATGTGAACTTTGACCTTCC 723526 i----ii v v ivi v ivi iiv ii C MIRc#SINE/MIR 90 AC----ACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCC 45 chrXqtel1M 723527 TGATTCT-TGTCCAAAGCTCTATCTGCTACA 723556 i i-v iv v ii i C MIRc#SINE/MIR 44 TGACTCCAAGTCCAGTGCTCTTTCCACTGCA 14 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.13 CpG sites = 26, Kimura (unadjusted) = 31.95 Transitions / transversions = 1.62 (26/16) Gap_init rate = 0.06 (10 / 169), avg. gap size = 1.60 (16 / 10) 469 33.15 5.37 1.41 chrXqtel1M 723578 723782 (276218) C L3#LINE/CR1 (1008) 3091 2879 m_b371s601i19 15501 chrXqtel1M 723578 ATCGATGATTGCTTTTTGAATGTATTCATTAAACCGGATCCAAACCCACC 723627 ii v vii i ii i v i v i v v i i C L3#LINE/CR1 3091 ATTAATCAACACCTTTTGGGTATAGTCGTTCAACCAGCTACGAATCCACC 3042 chrXqtel1M 723628 TAGGCTATCCTGTCATCTAACGAGCATTTCTCCATCTCTTCTGTAAGAAT 723677 i- i v i i i vvii iv iii i C L3#LINE/CR1 3041 TAA-CTGTACTATCATCCAGCCCATATTTCTCCATCTTGTCCACAAGGAT 2993 chrXqtel1M 723678 AGTC--------CTCAGTCAAACGCTTTCAGGAAATCTCAGGAAACTACA 723719 - -------- iv i i vvv iviiv v ?ii C L3#LINE/CR1 2992 A-TCATGAGAGACTTTGTCAAATGCCTTGCTGAAATCCAGATACACTNTG 2944 chrXqtel1M 723720 TGCAT--TATTTCCATGATCTATTCATTGACTTAACCCCAGCAGAAAA-G 723766 vi i--i i v iivi iv -v i v i - C L3#LINE/CR1 2943 TCTACGGCATTCCCCTGATCTACCAGTCTA-GTAACCCTATCAAAAAAGG 2895 chrXqtel1M 723767 CAATGAGGCTAGTTTG 723782 v i C L3#LINE/CR1 2894 AAATGAGGTTAGTTTG 2879 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 43.56 CpG sites = 43, Kimura (unadjusted) = 46.44 Transitions / transversions = 1.79 (43/24) Gap_init rate = 0.03 (6 / 204), avg. gap size = 2.33 (14 / 6) 318 32.88 9.66 3.21 chrXqtel1M 724618 724793 (275207) C L3#LINE/CR1 (1250) 2849 2663 m_b371s601i20 15501 chrXqtel1M 724618 GACTCTTTCTGATCACTGTTTCCTCCTCTAGATTTTTAGTAATCTTGATA 724667 i i vv i i ii ii vi i vv i ------ C L3#LINE/CR1 2849 GGCTCCTAGTGATCACCGCTTCCTTTTCTAAGTGCTCACAAACC------ 2806 chrXqtel1M 724668 ACCCTTTGAAGAA---GTTCTAGAATTTTGCCAGGAATTGAGCTCAAACC 724714 i iv v v --- i i i vv i i C L3#LINE/CR1 2805 ATCTGTTTAATAATCCGTTCTAGAATTTTGCCGGGGATCGACGTCAAGCT 2756 chrXqtel1M 724715 CATTGATTT---GTTCATGCACTTCATTTCTTAGCATCTTTAGAAAGTTG 724761 i ii i i --- i?iiv v i i i vv vii vi ? v C L3#LINE/CR1 2755 TACCGGTCTGTAGTTTNCAGAATCCATCTTTTTTCCCTTTTTAAAANTAG 2706 chrXqtel1M 724762 GA-----------CCTTCTCGAGTCTCCTGGTGCTTCTTCCAT 724793 ?----------- v v i ii i i C L3#LINE/CR1 2705 GNACNACATTTGCCCGTCTCCAGTCTTCTGGCACCTCTTCCGT 2663 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 41.41 CpG sites = 37, Kimura (unadjusted) = 47.15 Transitions / transversions = 1.95 (37/19) Gap_init rate = 0.05 (9 / 175), avg. gap size = 2.56 (23 / 9) 210 19.70 23.81 3.31 chrXqtel1M 724883 725008 (274992) MIR3#SINE/MIR 13 163 (45) m_b371s601i21 15502 chrXqtel1M 724883 CTGATCAGAAAGAACA-----------TCAGTAAGACCCGAGTTTAAATC 724921 v i i ----------- -i i i iv i MIR3#SINE/MIR 13 CTGAGCAGAGAGAGCACGGACTGGGAGTCAG-GAGACCTGGGTTCTAGTC 61 chrXqtel1M 724922 CCAG-TCTGAGAC--ACTAGCTG----------GACAAGTCATTCTTAAC 724958 i - vv -- ? ---------- i -- v MIR3#SINE/MIR 62 CCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCA--CTTCAC 109 chrXqtel1M 724959 CTCTGCCTGA--CTCACTTTCCTCAAATGTAAAACATAGGGAT---ACT- 725002 -- i-- v vv iivi i --- - MIR3#SINE/MIR 110 CTCT--CTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTA 157 chrXqtel1M 725003 GATAAT 725008 i MIR3#SINE/MIR 158 GATGAT 163 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 22.62 CpG sites = 15, Kimura (unadjusted) = 23.72 Transitions / transversions = 1.67 (15/9) Gap_init rate = 0.10 (12 / 125), avg. gap size = 2.92 (35 / 12) 671 19.07 8.45 6.45 chrXqtel1M 724899 725111 (274889) MIRb#SINE/MIR 45 261 (7) m_b371s601i22 15502 chrXqtel1M 724899 TCAGTAAGACCCGAGTTTAAATCCCAG-TCTGAGAC--ACTAGCTG---- 724941 vv i i ii i - vv -- ---- MIRb#SINE/MIR 45 TCAGACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTG 94 chrXqtel1M 724942 ------GACAAGTCATTCTTAACCTCTGCCTGA--CTCACTTTCCTCAAA 724983 ------ i i -- -- -- v vv MIRb#SINE/MIR 95 ACCTTGGGCAAGTTA--CTTAACCTCT--CTGAGCCTCAGTTTCCTCATC 140 chrXqtel1M 724984 TGTAAAACATAGGGATACTGATAATAGCACCTACTTCACTGAGTGGTTGT 725033 -- i --- --- i i v i v MIRb#SINE/MIR 141 TGTAAAA--TGGGGATA---ATAATA---CCTACCTCGCAGGGTTGTTGT 182 chrXqtel1M 725034 GAGGATCAAACAAGATAATTGCA---AAAGTTGTTTAGCTTAGTGCTTGG 725080 i ii - --- -i i vi i MIRb#SINE/MIR 183 GAGGATTAAATGAGATAA-TGCATGTAAAG-CGCTTAGCACAGTGCCTGG 230 chrXqtel1M 725081 TGCACAGTAGGCCCTTAATAAACGCTTGTTC 725111 ii i i v i i v v i MIRb#SINE/MIR 231 CACATAGTAAGCGCTCAATAAATGGTAGCTC 261 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 19.88 CpG sites = 25, Kimura (unadjusted) = 22.53 Transitions / transversions = 1.92 (25/13) Gap_init rate = 0.09 (20 / 212), avg. gap size = 1.60 (32 / 20) 268 34.76 11.59 0.00 chrXqtel1M 725536 725699 (274301) C L3#LINE/CR1 (2195) 1904 1722 m_b371s601i23 15501 chrXqtel1M 725536 CAAGCTCTAGGAGGGAACGGTCATTT-------GGTTTTCATC-ATTTTT 725577 i i i v iv i ivv ------- iii - i ii C L3#LINE/CR1 1904 CGAACTCTAAGATGACATGGCACTTTCTCCCAAGGTTCCTATCGACTTCC 1855 chrXqtel1M 725578 ACTTGA---ATCAGTTTATCCCTCTAGGTTAAAATAAAATCCATAACAGT 725624 v --- i iv i v v i i v i v ii i C L3#LINE/CR1 1854 ACTTCACCAACCAGTTCTTCCTTGTTGGTCAGAATTAAGTCCAGAGTAGC 1805 chrXqtel1M 725625 AGTTTCTTTCATAATTTCCTCT--TTT-----AGTGGAAATGATTACCAA 725667 i ii i vii --i ----- vv vi i v C L3#LINE/CR1 1804 AGTTCCCCTCGTTGCTTCCTCTACCTTCTGAGAGATGAAATTGTCAGCAA 1755 chrXqtel1M 725668 AACAAGTTCCCAAACTGG-AGCTGCTTTGCTTT 725699 ii ivvv vi iv- v i C L3#LINE/CR1 1754 GGCAAGTCAAGAATTTATCAGATGCTCTGCTTT 1722 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.78 CpG sites = 36, Kimura (unadjusted) = 49.26 Transitions / transversions = 1.71 (36/21) Gap_init rate = 0.04 (6 / 163), avg. gap size = 3.17 (19 / 6) 183 25.40 5.97 5.97 chrXqtel1M 726460 726526 (273474) C L3#LINE/CR1 (3292) 807 741 m_b371s601i24 15501 chrXqtel1M 726460 TGTGTTCTAGGCTTCCTCCTCTTCACAATGTCATTTTTCCCCACA-GAAT 726508 ii i i i ---- v vi iv i i- C L3#LINE/CR1 807 TGCATTCCAGGTTTCTTC----TGACTGTGTCATTCGTTCCCACGTGAAT 762 chrXqtel1M 726509 CTCCAGAA---GGGAGCGGTC 726526 vv i --- v C L3#LINE/CR1 761 CAGCAGGAGTGGGTAGCGGTC 741 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 27.25 CpG sites = 10, Kimura (unadjusted) = 31.89 Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.09 (6 / 66), avg. gap size = 1.33 (8 / 6) 336 23.94 5.05 2.97 chrXqtel1M 726930 727028 (272972) MIRc#SINE/MIR 65 165 (103) m_b371s601i25 15503 chrXqtel1M 726930 CTGGTTCTGACATTTACCAG-TGTCAGGTGTTCTTTGGAAAATCACCTGG 726978 i i v i i - --- vi v v i i ii MIRc#SINE/MIR 65 CCGGCTCTGCCACTTACTAGCTGT---GTGACCTTGGGCAAGTCACTTAA 111 chrXqtel1M 726979 --TCTCTGGGCCT--GTTTCCTTATTTGTAAAACGAGGACAAAAATGACT 727024 -- i -- i i i i i v iv MIRc#SINE/MIR 112 CCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCT 161 chrXqtel1M 727025 TCCC 727028 v MIRc#SINE/MIR 162 GCCC 165 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 28.45 CpG sites = 16, Kimura (unadjusted) = 30.01 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.06 (6 / 98), avg. gap size = 1.33 (8 / 6) 210 31.98 4.85 2.86 chrXqtel1M 727060 727162 (272838) OldhAT1#DNA/hAT-Ac 2687 2791 (51) m_b371s601i26 15504 chrXqtel1M 727060 TGCTT--CTCAGAAGCT--GGGGGAAGGAG-AGGGGAATGGGGACACGAA 727104 -- i v -- i i i -i v iivv iv OldhAT1#DNA/h 2687 TGCTTGACTTAGAATCTTAGGAGGAGGGGGTGGGGGAAAGAATCCACGGC 2736 chrXqtel1M 727105 GAAATGAAGCATGGAGTTTTCCCAGCCTTTGTTCATCCCTGTTTTCCCTC 727154 iv i v -i ?vvv i -- ?ii i vv ii OldhAT1#DNA/h 2737 ACAGTTAAG-GTNTCTTTTTTCC--CCNCCGTTCATCTCTTATTTCCCCT 2783 chrXqtel1M 727155 CTTCTACT 727162 i ii OldhAT1#DNA/h 2784 CTCCTGTT 2791 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 42.92 CpG sites = 20, Kimura (unadjusted) = 44.84 Transitions / transversions = 1.67 (20/12) Gap_init rate = 0.06 (6 / 102), avg. gap size = 1.33 (8 / 6) 203 31.06 8.85 6.09 chrXqtel1M 727755 727946 (272054) C L3#LINE/CR1 (70) 4029 3833 m_b371s601i27 15505 chrXqtel1M 727755 AGAAACGCTTTCTG--ATTTGTTTGAGAACTGGTCTTCCAGGTT----TG 727798 i iv i i-- iv vii v v v vi ---- v C L3#LINE/CR1 4029 AGGAATCCCTTCTACAACATCCCTGACAAGTGGTCATCCAGCCTCTGCTT 3980 chrXqtel1M 727799 GAAGGCCTCCAAGGA--GGAGGCTC-CAAGCTCTCCAGGCAACAGCACAT 727845 vi iv -- ii - v v ? v --- v C L3#LINE/CR1 3979 GAACACCTCCAGTGACGGGGAGCTCACTACCTCNCGAGGCA---GCCCAT 3933 chrXqtel1M 727846 T---GTCTGGGAGAGCGATTCCGATTTCTAGGAACTCCAGCCCCCCCTC- 727891 ---v i v v --- i vi i v i vv iiviv i- C L3#LINE/CR1 3932 TCCATTTTTGGACAGC---TCTGATTGTTAGAAAGTTCTTCCTTATATTG 3886 chrXqtel1M 727892 --CC--AATCTGCAGCTTTGGAACTTCCACACCCACGGCCCTCCTCTCCA 727937 -- -- vv ii v - vvi i vv ----- C L3#LINE/CR1 3885 AGCCGAAATCTGCCTCCCTGTAACTTCCAC-CCATTGGTCCTAGT----- 3842 chrXqtel1M 727938 TCTGCCTTC 727946 i C L3#LINE/CR1 3841 TCTGCCCTC 3833 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 40.84 CpG sites = 26, Kimura (unadjusted) = 40.84 Transitions / transversions = 0.87 (26/30) Gap_init rate = 0.10 (20 / 191), avg. gap size = 1.45 (29 / 20) 265 27.18 1.37 4.23 chrXqtel1M 728322 728394 (271606) C MIR3#SINE/MIR (27) 181 111 m_b371s601i28 15506 chrXqtel1M 728322 CTGGAAGAGACTTTGGAGTCCCTGGCCCAG-CCGACTCCATCGGGTTATA 728370 i i i vi v --- i - i i v ivv i C MIR3#SINE/MIR 181 CTGGAAGGGACCTTAGAGATCAT---CTAGTCCAACCCCCTCATTTTACA 135 chrXqtel1M 728371 GATGAAGGGATTGAGGCTCAGAGA 728394 i ii i i C MIR3#SINE/MIR 134 GATGAGGAAACTGAGGCCCAGAGA 111 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 35.73 CpG sites = 14, Kimura (unadjusted) = 35.73 Transitions / transversions = 2.80 (14/5) Gap_init rate = 0.06 (4 / 72), avg. gap size = 1.00 (4 / 4) 207 27.02 11.63 1.05 chrXqtel1M 728411 728496 (271504) C MIR3#SINE/MIR (10) 198 104 m_b371s601i29 15507 chrXqtel1M 728411 ATCTGAGACTGTTAGTGCAGGACAGAACCTTAGAAACCATTGGTTCCAAA 728460 vv v i v v vi i i i iviv v C MIR3#SINE/MIR 198 ATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAAC 149 chrXqtel1M 728461 CCC------TTGC--GTGAGAGAAAC--GGGTCCAGAAATGGGAAG 728496 ------ i --i - --i i i v v C MIR3#SINE/MIR 148 CCCCTCATTTTACAGATGAG-GAAACTGAGGCCCAGAGAGGTGAAG 104 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.02 CpG sites = 12, Kimura (unadjusted) = 34.02 Transitions / transversions = 1.09 (12/11) Gap_init rate = 0.05 (4 / 85), avg. gap size = 2.75 (11 / 4) 218 33.39 1.14 4.71 chrXqtel1M 728546 728633 (271367) C MIR3#SINE/MIR (20) 188 104 m_b371s601i30 15508 chrXqtel1M 728546 GTCTGA-CTGAAACGTACTTTCTCAAAGCCGTTTAGTTCTCCCCAGCACC 728594 v - i v v i v--i iii i i i vv -- vi C MIR3#SINE/MIR 188 GTCAGAGCTGGAAGGGACCTTA--GAGATCATCTAGTCCAACCC--CCTC 143 chrXqtel1M 728595 AGTTTATAGATGGCAAAATGGAGGCCTGGAGAGATGAGG 728633 v i ivi iv ii i i C MIR3#SINE/MIR 142 ATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAG 104 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.46 CpG sites = 18, Kimura (unadjusted) = 46.46 Transitions / transversions = 1.80 (18/10) Gap_init rate = 0.06 (5 / 87), avg. gap size = 1.00 (5 / 5) 308 24.19 11.46 0.94 chrXqtel1M 728712 728807 (271193) C MIR3#SINE/MIR (18) 190 85 m_b371s601i31 15509 chrXqtel1M 728712 ATGGCAGAATTGGAGGGGACCTTGGAGAGTCAGCCAGCTCA-----CCCA 728756 v ii i i - v i ii ----- i C MIR3#SINE/MIR 190 ATGTCAGAGCTGGAAGGGACCTTAGAGA-TCATCTAGTCCAACCCCCTCA 142 chrXqtel1M 728757 TTTTACAAATGGTGAAAC--GGGC---GTGGGGC-ATGCAGCCTGCCCAA 728800 i iv --i --- v i i- v iii i C MIR3#SINE/MIR 141 TTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAA 92 chrXqtel1M 728801 AGTCACA 728807 i C MIR3#SINE/MIR 91 GGTCACA 85 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 31.03 CpG sites = 18, Kimura (unadjusted) = 31.03 Transitions / transversions = 3.60 (18/5) Gap_init rate = 0.05 (5 / 95), avg. gap size = 2.40 (12 / 5) 204 23.28 9.52 4.55 chrXqtel1M 728753 728815 (271185) C MIR#SINE/MIR (118) 144 79 m_b371s601i32 15509 chrXqtel1M 728753 CCCATTTTACAAATGGTGAAAC--GGGCGTGGGG----CATGCAGCCTGC 728796 i iv --i iii i ----i v i i i C MIR#SINE/MIR 144 CCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGC 95 chrXqtel1M 728797 CCAAAGTCACAGCACAGCT 728815 i --- C MIR#SINE/MIR 94 CCAAGGTCA---CACAGCT 79 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 30.12 CpG sites = 12, Kimura (unadjusted) = 30.12 Transitions / transversions = 6.00 (12/2) Gap_init rate = 0.08 (5 / 62), avg. gap size = 1.80 (9 / 5) 12 19.61 0.00 0.00 chrXqtel1M 729082 729110 (270890) (CTG)n#Simple_repeat 1 29 (0) m_b371s252i19 15510 chrXqtel1M 729082 CTGCTGCTATTGCAGAGGCTGCTGCTGCT 729110 ii v vv (CTG)n#Simple 1 CTGCTGCTGCTGCTGCTGCTGCTGCTGCT 29 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 443 29.98 5.26 2.19 chrXqtel1M 731355 731487 (268513) MIR3#SINE/MIR 19 155 (53) m_b371s601i33 15511 chrXqtel1M 731355 AAAAAAAGCACCCTAGGCTGTAAGCCAGGGGAGCCAGGTCCCTGCCTTGG 731404 i i i ---i i vi i i v ii i iv i ii MIR3#SINE/MIR 19 AGAGAGAGCAC---GGACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCGG 65 chrXqtel1M 731405 TCCTGTCAGTGACCTGCTGTGGGATCCCGA------CACCT-ACCTCTCT 731447 ii i v i i? v i ii i------ i - MIR3#SINE/MIR 66 CTCTGCCACTAACTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCT 115 chrXqtel1M 731448 AGGCCTCAATTTCCCCATCTCTAGAATGATGGGACTGCAC 731487 i i i v i v ii v MIR3#SINE/MIR 116 GGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGAC 155 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.46 CpG sites = 31, Kimura (unadjusted) = 42.42 Transitions / transversions = 3.88 (31/8) Gap_init rate = 0.04 (5 / 132), avg. gap size = 2.00 (10 / 5) 26 15.50 2.86 4.35 chrXqtel1M 732990 733059 (266941) (TCCA)n#Simple_repeat 1 69 (0) m_b371s252i20 15512 chrXqtel1M 732990 TCCA-CCA-CCCCCCATCCATCCACCCACCCGCATCCATCCATCTATCCA 733037 - - vi i -i - i (TCCA)n#Simpl 1 TCCATCCATCCATCCATCCATCCATCCA-TC-CATCCATCCATCCATCCA 48 chrXqtel1M 733038 TTCCTTCCAGAAATCCATCCAT 733059 - v vvv (TCCA)n#Simpl 49 -TCCATCCATCCATCCATCCAT 69 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.07 (5 / 69), avg. gap size = 1.00 (5 / 5) 16 24.84 0.00 0.00 chrXqtel1M 734787 734829 (265171) (CAC)n#Simple_repeat 1 43 (0) m_b371s252i21 15513 chrXqtel1M 734787 CAGCACCCCCTTCGCCGCCACCACCGCCACCACCGCCACCCCC 734829 v v vi i i i i v (CAC)n#Simple 1 CACCACCACCACCACCACCACCACCACCACCACCACCACCACC 43 Matrix = Unknown Transitions / transversions = 1.25 (5/4) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 18 0.00 0.00 0.00 chrXqtel1M 736336 736355 (263645) (TG)n#Simple_repeat 1 20 (0) m_b371s252i22 15514 chrXqtel1M 736336 TGTGTGTGTGTGTGTGTGTG 736355 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTG 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 219 31.03 0.00 0.00 chrXqtel1M 736517 736574 (263426) C L2d_3end#LINE/L2 (7) 509 452 m_b371s601i34 15515 chrXqtel1M 736517 ATCCATCAATTAGCATTTATTAAGTGCCAGCTGTATGCTATGTGTTGTAC 736566 v iv i i i vi i i vv iii i C L2d_3end#LINE 509 ATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTGTGC 460 chrXqtel1M 736567 TAAGGGCT 736574 i v C L2d_3end#LINE 459 TAGGCGCT 452 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 39.09 CpG sites = 12, Kimura (unadjusted) = 42.21 Transitions / transversions = 2.00 (12/6) Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0) 205 34.43 0.00 0.00 chrXqtel1M 736521 736581 (263419) C L2d2_3end#LINE/L2 (9) 546 486 m_b371s601i35 15515 chrXqtel1M 736521 ATCAATTAGCATTTATTAAGTGCCAGCTGTATGCTATGTGTTGTACTAAG 736570 iv ii i i vi i v v iii i i C L2d2_3end#LIN 546 ATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGG 497 chrXqtel1M 736571 GGCTTCGGAAG 736581 v vi ii C L2d2_3end#LIN 496 CGCTGTGGGGG 486 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 46.60 CpG sites = 15, Kimura (unadjusted) = 50.08 Transitions / transversions = 2.50 (15/6) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 14 14.38 3.12 0.00 chrXqtel1M 737379 737410 (262590) (AGAAAG)n#Simple_repeat 1 33 (0) m_b371s252i23 15516 chrXqtel1M 737379 AGAGAGAGAAAGAGAAAG-GGAGGAGGAAGAGA 737410 i - i i i (AGAAAG)n#Sim 1 AGAAAGAGAAAGAGAAAGAGAAAGAGAAAGAGA 33 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 257 23.81 13.61 0.00 chrXqtel1M 739574 739720 (260280) L2b_3end#LINE/L2 4 170 (296) m_b371s601i36 15517 chrXqtel1M 739574 CACAATCTGGCCCT-----CTCTCCAGCCT--TTTCCAACA--------- 739607 i i----- i -- i v v--------- L2b_3end#LINE 4 CACGATCTGGCCCCGCTACCTCTCCGGCCTCATCTCCTACCACTCTCCCC 53 chrXqtel1M 739608 TTACTCAGCCT--TCCGGCCAAACTGGCTCCTTTGCCGTTCCTCGAACCT 739655 i vi -- i v ii i i vi L2b_3end#LINE 54 TTGCTCACTCTGCTCCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACAC 103 chrXqtel1M 739656 GACACTCCACCTCCCGTCTCCTGGCCCTTGC-CAGGCTGTTCCC-CAACC 739703 v ?v iv? i vv i - ?v - vi L2b_3end#LINE 104 GCCANGCTCNCTCCCGCCTCAGGGCCTTTGCACNTGCTGTTCCCTCTGCC 153 chrXqtel1M 739704 CCCACCTCCCACCCCCA 739720 ivv v v vi L2b_3end#LINE 154 TGGAACGCCCTTCCCCA 170 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 25.87 CpG sites = 18, Kimura (unadjusted) = 29.68 Transitions / transversions = 1.06 (18/17) Gap_init rate = 0.04 (6 / 146), avg. gap size = 3.33 (20 / 6) 198 27.91 2.38 6.17 chrXqtel1M 740082 740165 (259835) MIR3#SINE/MIR 34 114 (94) m_b371s601i37 15518 chrXqtel1M 740082 TGGGAAGGTGAGGAGGCCGAG--TGTAGCCCCAGCTCTGCCTCAGGCTGG 740129 -- v i vi -- v i i v vii ? MIR3#SINE/MIR 34 TGGGA--GTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNG 81 chrXqtel1M 740130 CTTTGTGGTCTTGAGTCAGCCTTGGTTTCCCCCCTC 740165 v ii i iv i ---ii v i MIR3#SINE/MIR 82 CTGTGTGACCTTGGGCAAGTC---ACTTCACCTCTC 114 Matrix = 25p53g.matrix Kimura (with divCpGMod) = 34.59 CpG sites = 14, Kimura (unadjusted) = 36.69 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.07 (6 / 83), avg. gap size = 1.17 (7 / 6) 187 30.85 1.82 2.75 chrXqtel1M 741304 741413 (258587) MIR3#SINE/MIR 79 187 (21) m_b372s601i1 15519 chrXqtel1M 741304 TCGTTGTGC-ATCCTGGGCCAGGCAGGGCCCATCTCTGTGCCTCAGTTTC 741352 ? i i- i i v v vvv v v v -- MIR3#SINE/MIR 79 TNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTT-- 126 chrXqtel1M 741353 TCCTCTTCTACAAAA-GGGGAGCTTTATTTAAGGGTCCTTCAAGCTCTCC 741401 v ii - i i v vivi iiv vi ii v - MIR3#SINE/MIR 127 TCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTC-CC 175 chrXqtel1M 741402 ATCTACCTCTGA 741413 v i v MIR3#SINE/MIR 176 TTCCAGCTCTGA 187 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 40.69 CpG sites = 16, Kimura (unadjusted) = 40.69 Transitions / transversions = 0.94 (16/17) Gap_init rate = 0.05 (5 / 109), avg. gap size = 1.00 (5 / 5) 189 8.34 2.63 5.41 chrXqtel1M 741335 741372 (258628) MIR#SINE/MIR 110 146 (116) m_b372s601i2 15519 chrXqtel1M 741335 TCTCTGTGCCTCAGTTTCTCCTCTTCTACAAAA-GGGGA 741372 -- v ii - MIR#SINE/MIR 110 TCTCTGTGCCTCAGTT--TCCTCATCTGTAAAATGGGGA 146 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 8.91 CpG sites = 2, Kimura (unadjusted) = 8.91 Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.08 (3 / 37), avg. gap size = 1.00 (3 / 3) 185 28.28 10.94 2.40 chrXqtel1M 742621 742812 (257188) C L3#LINE/CR1 (484) 3615 3408 m_b372s601i3 15520 chrXqtel1M 742621 GGCCCCCAG--CTGAACG--ACCGTCTGGCTGTGG-CTGAGCCAGGGCAA 742665 v -- -- ivv ii v - - v i C L3#LINE/CR1 3615 GGCGCCCAGAACTGAACGCAATACTCCAGATGTGGTCTGA-CCAGCGCAG 3567 chrXqtel1M 742666 AGGCCGTGGGGAGCGCGCCCCTCCCTGTTGCTGCCAGACCCTGGCTCTGT 742715 vv ivv - vvviv -- ? - ii v ivvii v C L3#LINE/CR1 3566 AGTACAGCGGGA-CTATTACCTCCCT--TGNT-CTGGACACTATACTTCT 3521 chrXqtel1M 742716 ATCAGAGCAGCTTAAAA--GGAGTTGCTTTTTGGGCTGC----------T 742753 i iv i i -- v v v v v ---------- C L3#LINE/CR1 3520 ATTAATGCAGCCTAAGATTGCATTAGCTTTTTTGGCAGCCACATCACACT 3471 chrXqtel1M 742754 G--AGCTCAT--TGCACTTGTGGTCCACTCAAATCTCCAGCTCTTTTTCA 742799 --i -- vi i v v i i i v C L3#LINE/CR1 3470 GTTGGCTCATATTGAGCTTGCGGTCAACTAAAACCCCTAGGTCTTTTTCA 3421 chrXqtel1M 742800 GGAAAAGTGCAGC 742812 v vi v v C L3#LINE/CR1 3420 CGTGAACTGCTGC 3408 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 35.14 CpG sites = 22, Kimura (unadjusted) = 35.95 Transitions / transversions = 0.71 (22/31) Gap_init rate = 0.06 (12 / 191), avg. gap size = 2.17 (26 / 12) 226 15.79 0.00 0.00 chrXqtel1M 742929 742966 (257034) MIR3#SINE/MIR 116 153 (55) m_b372s601i4 15519 chrXqtel1M 742929 GGGCCTCAGTTTCTTCCCCTGGAAAATGAAGGAGTTGG 742966 i vi v i i MIR3#SINE/MIR 116 GGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGG 153 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 18.05 CpG sites = 4, Kimura (unadjusted) = 18.05 Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 61 4.88 3.45 1.12 chrXqtel1M 743363 743449 (256551) (CCT)n#Simple_repeat 1 89 (0) c_b372s251i0 15521 chrXqtel1M 743363 CCTCCTCCTCCTCCTCCTCTTCCTCCTCCTTCTCCT-CTCCTCCTCCT-G 743410 i i - -v (CCT)n#Simple 1 CCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC 50 chrXqtel1M 743411 TCCTCCTCCTCCTTCTCCT-CTCCCTCCTCCTCCTCCTCC 743449 i - - (CCT)n#Simple 51 TCCTCCTCCTCCTCCTCCTCCT-CCTCCTCCTCCTCCTCC 89 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.05 (4 / 86), avg. gap size = 1.00 (4 / 4) 21 16.61 0.00 4.08 chrXqtel1M 743575 743625 (256375) (GCCGG)n#Simple_repeat 1 49 (0) m_b372s252i0 15522 chrXqtel1M 743575 GCCGAGCCGGGCATGGCGGGGCCGGGCCTGGGGAGGGCCGGGGCCGGGGC 743624 i vv v - vv - v (GCCGG)n#Simp 1 GCCGGGCCGGGCCGGGCCGGGCCGGGCC-GGGCCGGGCC-GGGCCGGGCC 48 chrXqtel1M 743625 G 743625 (GCCGG)n#Simp 49 G 49 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.04 (2 / 50), avg. gap size = 1.00 (2 / 2) 21 3.96 0.00 0.00 chrXqtel1M 744269 744294 (255706) (GC)n#Simple_repeat 1 26 (0) m_b372s252i1 15523 chrXqtel1M 744269 GCCCGCGCGCGCGCGCGCGCGCGCGC 744294 v (GC)n#Simple_ 1 GCGCGCGCGCGCGCGCGCGCGCGCGC 26 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 200 31.25 0.00 0.00 chrXqtel1M 744661 744724 (255276) C MIR#SINE/MIR (12) 250 187 m_b372s601i6 15524 chrXqtel1M 744661 CATTTAGTAAGTACCTACTGTGCGCCAGACCCTGGGCTGAGTGCTTTAGA 744710 v i ii i i i i v vv i i v C MIR#SINE/MIR 250 CATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGCGCTTTACA 201 chrXqtel1M 744711 GTTGTGAGCTCGTT 744724 vv i v i i C MIR#SINE/MIR 200 TGTATTAACTCATT 187 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 36.24 CpG sites = 12, Kimura (unadjusted) = 41.85 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0) 226 25.00 0.00 0.00 chrXqtel1M 744661 744708 (255292) C MIRb#SINE/MIR (14) 254 207 m_b372s601i5 15524 chrXqtel1M 744661 CATTTAGTAAGTACCTACTGTGCGCCAGACCCTGGGCTGAGTGCTTTA 744708 v i ii i i i i v v i i C MIRb#SINE/MIR 254 CATTTATTGAGCGCTTACTATGTGCCAGGCACTGTGCTAAGCGCTTTA 207 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 25.52 CpG sites = 9, Kimura (unadjusted) = 32.11 Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 184 12.90 0.00 0.00 chrXqtel1M 744734 744764 (255236) C MIR#SINE/MIR (116) 146 116 m_b372s601i7 15525 chrXqtel1M 744734 TCCCCATTTTACAGGGGAGGAGACTCAGGCA 744764 iv i v C MIR#SINE/MIR 146 TCCCCATTTTACAGATGAGGAAACTGAGGCA 116 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 14.21 CpG sites = 2, Kimura (unadjusted) = 14.21 Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 413 19.79 6.25 0.00 chrXqtel1M 745961 746056 (253944) C MER63D#DNA/hAT-Tip100 (605) 456 355 m_b372s502i0 15526 chrXqtel1M 745961 AGTTTGATGGGCATTCTTGAAGTTTCCTACATCCCTTTCTTAAGTCTAGA 746010 i vv v i vi i v v C MER63D#DNA/hA 456 AGTTTAATCTGCATTATTAACATTTTCTCCATCACTTTCTTAAGTCTAGA 407 chrXqtel1M 746011 TAATC----AAACAGTAAATCAAGCCTTGATTTTTACTATCTACC--TTT 746054 i ---- i i v vii i i -- C MER63D#DNA/hA 406 CAATCAACAAAACAATAAATCAAGCCCTGATTTGTAGCGTTTGCCGATTT 357 chrXqtel1M 746055 CC 746056 C MER63D#DNA/hA 356 CC 355 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 21.80 CpG sites = 11, Kimura (unadjusted) = 23.29 Transitions / transversions = 1.38 (11/8) Gap_init rate = 0.02 (2 / 95), avg. gap size = 3.00 (6 / 2) 219 16.40 2.46 1.55 chrXqtel1M 746057 746504 (253496) (TCCT)n#Simple_repeat 1 452 (0) m_b372s252i2 15527 chrXqtel1M 746057 TCC-TCCCTCCTTCTTTCCCTCCCTCCTT-TTATCTGCTATCTTTTCCTT 746104 - i i i i -i vi v iv -i (TCCT)n#Simpl 1 TCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC-CTTCCTT 49 chrXqtel1M 746105 CCTTCCTTCCCTCCCTCCCTCCCTCCTT-TTATCTTCTATCTGTTCCTTC 746153 i i i i -i vi iv -v (TCCT)n#Simpl 50 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC-CTTCCTTC 98 chrXqtel1M 746154 CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTCTCC 746203 - (TCCT)n#Simpl 99 CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT-TCC 147 chrXqtel1M 746204 -TCCCTCCCTCCCTCCCTCCCTCCCTCCTTCCTTCCTTCCTTCCTTCCTT 746252 - i i i i i i (TCCT)n#Simpl 148 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 197 chrXqtel1M 746253 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCCTCCCTCCCTCCTT-TTATC 746301 i i i -i vi (TCCT)n#Simpl 198 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 247 chrXqtel1M 746302 TTCTATCTGTTCCTTCCTTCCTTCCTTCCTCCCTCCCTCCTCTTCCTTCC 746351 iv -v i i i - (TCCT)n#Simpl 248 TTCCTTC-CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC-CTTCCTTCC 295 chrXqtel1M 746352 -TCCCTCCCTCCCTCCTTCCTTCCTTCC-TCCCTCCCTCCCTCCTTCTTT 746399 - i i i - i i i i (TCCT)n#Simpl 296 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 345 chrXqtel1M 746400 CCTTTCTTCCTCCCTTCC-TCCCTCCCTCC-TCCTTCCTCCCTCCCTCCC 746447 i i - i i - i i i (TCCT)n#Simpl 346 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 395 chrXqtel1M 746448 TCCCTCCTTTCCTCCTCTCTCCCTCCCTCCTTCCTTCC-TCC-TCCCTCC 746495 i i i i - - i i - - i (TCCT)n#Simpl 396 TTCCTTCCTTCCTTC-CT-TCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 443 chrXqtel1M 746496 CTCCCTCCT 746504 i i (TCCT)n#Simpl 444 TTCCTTCCT 452 Matrix = Unknown Transitions / transversions = 5.89 (53/9) Gap_init rate = 0.04 (18 / 447), avg. gap size = 1.00 (18 / 18) 226 26.29 0.00 3.75 chrXqtel1M 746505 746587 (253413) C L1ME1_3end#LINE/L1 (353) 573 494 m_b372s551i0 15528 chrXqtel1M 746505 TTCCTTCCTTTTTCTTATTGCACAATACTACTTCATCACAATCATATACC 746554 v --- vv i v i i iii vvv C L1ME1_3end#LI 573 TTCGTTCCTTTTT---ATTGCTGAGTAGTATTCCATTGTATGGATATACC 527 chrXqtel1M 746555 ACAGCTTGTTCAACCATTCCCCAATTGATAGGC 746587 ii i v v ?i i i C L1ME1_3end#LI 526 ACAATTTGTTTATCCATTCACCNGTTGATGGAC 494 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 33.50 CpG sites = 12, Kimura (unadjusted) = 33.50 Transitions / transversions = 1.33 (12/9) Gap_init rate = 0.04 (3 / 82), avg. gap size = 1.00 (3 / 3) 43 0.00 0.00 0.00 chrXqtel1M 746637 746673 (253327) (TG)n#Simple_repeat 1 37 (0) c_b372s251i1 15529 chrXqtel1M 746637 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 746673 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 37 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 529 25.66 12.03 3.99 chrXqtel1M 747404 747752 (252248) C L1ME5_3end#LINE/L1 (534) 407 32 m_b372s551i1 15528 chrXqtel1M 747404 ATCTCTTTGGGATACAGATCTAGTAG-GGTATTGCTGGCTCAAAGTATAT 747452 i i v i i v - v v v vi C L1ME5_3end#LI 407 ATTTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTAT 358 chrXqtel1M 747453 GCAGTTTGATTACCCTTTGGGCCTAGTTCT-TTA---TGTTCCTCAAAAG 747498 - v iv v--- v i iv v -ii --- i ii i v C L1ME5_3end#LI 357 GC-GTATACTTAA---TTTGACTAAGTACTGCCAGATTGCTCTCCAGAAT 312 chrXqtel1M 747499 GGTTAAAACAGTTCATTACTCCAACAAACA-TGCATTAGCGTGCTGATTT 747547 i iv v ii i- v v i - v v v iv ? C L1ME5_3end#LI 311 GGCTGCACCAGTCTAC-ACTCCCACCAGCAGTGCATGAGGGTTCCTATNT 263 chrXqtel1M 747548 TCCCCTCATCC---------CTT--------CCAGTATTGCTCATTTCTG 747580 - v --------- -------- i- v v i C L1ME5_3end#LI 262 -CCCCACATCCTCGCCAACACTTGGCATTATCCAGC-TTTCTAATTTTTG 215 chrXqtel1M 747581 --AG------AGACGTGAGATGGTACCTTGGAGTTGTTCTA-TTTGCCTT 747621 -- ------ ii i ii i i iivv i - v C L1ME5_3end#LI 214 CCAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATT 165 chrXqtel1M 747622 TCTCTAATCGATAGGGATTCAGAGCATTTTTTTTCATATGCT-ATTACAT 747670 i iiv iv v iv i i -- -i --- C L1ME5_3end#LI 164 TCTCTGATTACTAATGAGTTTGAGCATCTCTT--CATATGCTTGTTA--- 120 chrXqtel1M 747671 CGCTTT---GACTTCC----CTGAAAATTGCCTGTTTATATCCTTTGACC 747713 - i --- ii ---- v i v C L1ME5_3end#LI 119 -GCCTTTCGGGTTTCCTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCC 71 chrXqtel1M 747714 ATTTATCAATTGGGGAATGGCC--CTTATTTTTATAAATTT 747752 v v -- v? -- v i i vi C L1ME5_3end#LI 70 ATTTTTCTATTGGGG--TTNCCGTCTTTTTCTTGTTGATTT 32 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 32.34 CpG sites = 48, Kimura (unadjusted) = 32.34 Transitions / transversions = 1.26 (48/38) Gap_init rate = 0.08 (28 / 348), avg. gap size = 2.04 (57 / 28) 417 26.89 5.47 1.92 chrXqtel1M 747576 747776 (252224) C L1PA11_3end#LINE/L1 (710) 211 4 m_b372s551i2 15528 chrXqtel1M 747576 TTCTGAGAGACGTGAGATGGTACCTTGGAGTTGTTCT-ATTTGCCTTTCT 747624 vv i i iivv v i - v C L1PA11_3end#L 211 TTCTGACTGGCGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCT 162 chrXqtel1M 747625 CTAATCGAT-AGGGATTCAGAGCATTTTTTTTCATATG-CTATTACATCG 747672 - - v viv -- -i i i-ii C L1PA11_3end#L 161 CTAAT-GATCAGTGATGTTGAGC--TTTTTTTCATATGTTTGTTG-GCCG 116 chrXqtel1M 747673 C---TTTGACTTC-CCTGAAAATTGCCTGTTTATATCCTTTGACCATTTA 747718 --- v v -ii i v i i i v i v C L1PA11_3end#L 115 CATGTATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTTGCCCACTTT 66 chrXqtel1M 747719 TCAATTGGGGAATGGCCCTTATTTTTATAAATTTAACTCACTTCC----A 747764 i v vvi vvvii v i i ivi v v ---- C L1PA11_3end#L 65 TTAATGGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTAAGTTCCTTGTA 16 chrXqtel1M 747765 TACTCAGAATAT 747776 v v i C L1PA11_3end#L 15 GACTCTGGATAT 4 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 33.71 CpG sites = 27, Kimura (unadjusted) = 33.71 Transitions / transversions = 1.04 (27/26) Gap_init rate = 0.05 (10 / 200), avg. gap size = 1.50 (15 / 10) 245 27.49 5.92 5.29 chrXqtel1M 747965 748133 (251867) C L1MC_orf2#LINE/L1 (3101) 193 24 m_b372s551i3 15528 chrXqtel1M 747965 CATATTAGATTCTGCTCTGGCTCTTCA-TTTTAAC---TGTGTGTCTTTC 748010 iv v ii v iiv i? i - i--- i v C L1MC_orf2#LIN 193 CATGGTATATCTTTCTCCATCCNTTTACTTTTAATCTATATGTGTCTTTA 144 chrXqtel1M 748011 TATTTCAAACGCGTCTTTTATAAACAAAATATTGTTCGATTCTGGTTTCT 748060 v ii v i i i i v v v i ii v i C L1MC_orf2#LIN 143 TATTTAAAGTGGGTTTCTTGTAGACAACATATAGTTGGGTCTTGTTTTTT 94 chrXqtel1M 748061 AATCCATTCTG-CTATCTGCTTCTGTTTTATGAATGAGCTCATCTAATTT 748109 i i - v ---- i v i v -----i v v v C L1MC_orf2#LIN 93 GATCCACTCTGACAATC----TCTGTCTTTTAATTG-----GTGTATTTA 53 chrXqtel1M 748110 GA--GTTCACAGTTA---TGATTATTAAT 748133 --i ? v --- i C L1MC_orf2#LIN 52 GACCATTNACATTTAAAGTGATTATTGAT 24 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.73 CpG sites = 26, Kimura (unadjusted) = 35.73 Transitions / transversions = 1.44 (26/18) Gap_init rate = 0.08 (14 / 168), avg. gap size = 1.36 (19 / 14) 254 24.36 8.33 0.78 chrXqtel1M 747992 748111 (251889) C L1M5_orf2#LINE/L1 (3129) 165 37 m_b372s551i4 15528 chrXqtel1M 747992 TTTTAAC---TGTGTGTCTTTCTATTTCAAACGCGTCTTTTATAAACAAA 748038 i --- v v v ii i i i iv C L1M5_orf2#LIN 165 TTTCAACCTNTCTGTGTCTTTATATTTAAAGTGCGTCTCTTGTAGACAGC 116 chrXqtel1M 748039 ATATTGTTCGATTCTGGTTTCTAATCCATTCTG-CTATCTGCTTCTGTTT 748087 v v i ii v i v v - v - v iv C L1M5_orf2#LIN 115 ATATAGTTGGGTCTTGTTTTTTTATCCAGTCTGACAATCT-CTGCCTTTT 67 chrXqtel1M 748088 TAT--GAATG---AGCTCATCTA-ATTTGA 748111 v -- i --- ?i i - i C L1M5_orf2#LIN 66 AATTGGAGTGTTTAGNCCATTTACATTTAA 37 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 30.23 CpG sites = 16, Kimura (unadjusted) = 30.23 Transitions / transversions = 1.23 (16/13) Gap_init rate = 0.05 (6 / 119), avg. gap size = 1.83 (11 / 6) 257 26.09 6.52 0.00 chrXqtel1M 747992 748083 (251917) C L1M4_orf2#LINE/L1 (3129) 165 68 m_b372s551i5 15528 chrXqtel1M 747992 TTTTAAC---TGTGTGTCTTTCTATTTCAAACGCGTCTTTTATAAACAAA 748038 i --- v vv i v ii i i i i iv C L1M4_orf2#LIN 165 TTTCAACCTATTTGTGTCTTTGAATCTAAAGTGTGTCTCTTGTAGACAGC 116 chrXqtel1M 748039 ATATTGTTCGATTCTGGTTTCTAATCCATTCTGCTA---TCTGCTTCT 748083 v v iv v i v i --- i i C L1M4_orf2#LIN 115 ATATAGTTGGATCATGTTTTTTTATCCATTCTGCCAATCTCTGCCTTT 68 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 32.77 CpG sites = 14, Kimura (unadjusted) = 32.77 Transitions / transversions = 1.40 (14/10) Gap_init rate = 0.02 (2 / 91), avg. gap size = 3.00 (6 / 2) 271 25.00 3.75 0.00 chrXqtel1M 748004 748083 (251917) C L1M4_5end#LINE/L1 (0) 2686 2604 m_b372s551i6 15528 chrXqtel1M 748004 GTCTTTCTATTTCAAACGCGTCTTTTATAAACAAAATATTGTTCGATTCT 748053 vv i v ii ? i i i iv v v iv C L1M4_5end#LIN 2686 GTCTTTGAATCTAAAGTGNGTCTCTTGTAGACAGCATATAGTTGGATCAT 2637 chrXqtel1M 748054 GGTTTCTAATCCATTCTGCTA---TCTGCTTCT 748083 v i i --- i i C L1M4_5end#LIN 2636 GTTTTTTAATCCATTCTGCCAATCTCTGCCTTT 2604 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 31.62 CpG sites = 12, Kimura (unadjusted) = 31.62 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.01 (1 / 79), avg. gap size = 3.00 (3 / 1) 14 36.66 0.00 0.00 chrXqtel1M 749634 749702 (250298) (AAAA)n#Simple_repeat 1 69 (0) m_b372s252i3 15530 chrXqtel1M 749634 AAGAAATAAAAAAAAAATTAAAAATCAAATGAGAAATATTGAGGCAAAAC 749683 i v vv vv vi i v vvi iiv v (AAAA)n#Simpl 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chrXqtel1M 749684 AAAAATAAATAAATAAAAA 749702 v v v (AAAA)n#Simpl 51 AAAAAAAAAAAAAAAAAAA 69 Matrix = Unknown Transitions / transversions = 0.43 (6/14) Gap_init rate = 0.00 (0 / 68), avg. gap size = 0.0 (0 / 0) 19 0.00 0.00 0.00 chrXqtel1M 750473 750493 (249507) (T)n#Simple_repeat 1 21 (0) m_b372s252i4 15531 chrXqtel1M 750473 TTTTTTTTTTTTTTTTTTTTT 750493 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTT 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 15 12.16 0.00 0.00 chrXqtel1M 750891 750917 (249083) (TGTA)n#Simple_repeat 1 27 (0) m_b372s252i5 15532 chrXqtel1M 750891 TGTATGTATGTATATATCTATATATGT 750917 i v i (TGTA)n#Simpl 1 TGTATGTATGTATGTATGTATGTATGT 27 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 12 23.57 0.00 0.00 chrXqtel1M 750893 750927 (249073) (TATATA)n#Simple_repeat 1 35 (0) m_b372s252i6 15532 chrXqtel1M 750893 TATGTATGTATATATCTATATATGTTTACATAAAT 750927 i i v i v i v (TATATA)n#Sim 1 TATATATATATATATATATATATATATATATATAT 35 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 21 3.81 0.00 0.00 chrXqtel1M 751089 751110 (248890) (AT)n#Simple_repeat 1 22 (6) m_b372s252i7 15533 chrXqtel1M 751089 ATATATATATATATATATATAT 751110 (AT)n#Simple_ 1 ATATATATATATATATATATAT 22 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 30 0.00 0.00 0.00 chrXqtel1M 751111 751136 (248864) (AC)n#Simple_repeat 1 26 (0) c_b372s251i2 15534 chrXqtel1M 751111 ACACACACACACACACACACACACAC 751136 (AC)n#Simple_ 1 ACACACACACACACACACACACACAC 26 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 16 23.31 0.00 0.00 chrXqtel1M 751239 751273 (248727) (A)n#Simple_repeat 1 35 (0) m_b372s252i8 15535 chrXqtel1M 751239 AAAAAAAAAAGAAACATGAAAATAATAAAAAGAAA 751273 i v vi v v i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 35 Matrix = Unknown Transitions / transversions = 0.75 (3/4) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 16 5.27 0.00 0.00 chrXqtel1M 751381 751400 (248600) (T)n#Simple_repeat 1 20 (0) m_b372s252i9 15536 chrXqtel1M 751381 TTCTTTTTTTTTTTTTTTTT 751400 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTT 20 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 11 40.53 0.00 0.00 chrXqtel1M 751523 751591 (248409) (AAAAAA)n#Simple_repeat 1 69 (0) m_b372s252i10 15537 chrXqtel1M 751523 AAAAAAAAAAAAAAAGGAAACAGCAAAAGGGGAAAAAACATGAGAAAGAA 751572 ii v iv iiii v vi i i (AAAAAA)n#Sim 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50 chrXqtel1M 751573 TAAGGTAAACAAAGACAAA 751591 v iiv v i v (AAAAAA)n#Sim 51 AAAAAAAAAAAAAAAAAAA 69 Matrix = Unknown Transitions / transversions = 1.62 (13/8) Gap_init rate = 0.00 (0 / 68), avg. gap size = 0.0 (0 / 0) 260 36.28 1.74 1.74 chrXqtel1M 751740 751969 (248031) C L1ME3F_3end#LINE/L1 (331) 659 430 m_b372s551i7 15538 chrXqtel1M 751740 ATACTGTGTCTGATGTTTTCCTGGTTCTGCTCATTTCACTTTACATCA-G 751788 i v i-- i iv? vii iv iv i i - C L1ME3F_3end#L 659 ATACTGTATGTA--GTCTTCTGNGACTTGCTTTTTTCACTCAATATTATG 612 chrXqtel1M 751789 TTCCTACAGGTCTTTCCAGGTTTTTCCAAA-ATCTGCCTGTTCATCATTT 751837 i - i iiv v v v ivi- v iv- ivv C L1ME3F_3end#L 611 TTTCTA-AGATTCATCCATGTTGTTGCGTGTAGCTGTA-GTTCATTCATT 564 chrXqtel1M 751838 TTTGTTGCCCAATAGTATT--GTTACATTCATATGCTATGCCTTCTTCAG 751885 iii ivv i --i iii vv i i iivi v i v C L1ME3F_3end#L 563 TTCACTGCTGTATAATATTCCATTGTGTGAATATACCACAATTTATTTAT 514 chrXqtel1M 751886 CCATTCCCCAATTGATGGCTATTCCCTCAATTTTTAATTCTTTGCCGCCA 751935 i vi i vi ivvvivi ii i i iiii C L1ME3F_3end#L 513 CCATTCTCCTGTCGATGGACATTTGGGTTGTTTCCAGTTTTTTGCTATTA 464 chrXqtel1M 751936 TGAAAAGGGCTGCTATAAATATTTTTGCACATGT 751969 i v v i i i i C L1ME3F_3end#L 463 CGAACAGTGCTGCTATGAACATTCTTGTACATGT 430 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 50.35 CpG sites = 53, Kimura (unadjusted) = 53.27 Transitions / transversions = 1.83 (53/29) Gap_init rate = 0.03 (7 / 229), avg. gap size = 1.14 (8 / 7) 311 30.14 4.39 2.88 chrXqtel1M 751753 751957 (248043) C L1MA4A_3end#LINE/L1 (401) 649 442 m_b372s551i8 15538 chrXqtel1M 751753 TGTTTTCCTGGTTCTG-CTCATTTCACTTTACATCAGTTCCTACAGGTCT 751801 i i vvi - i v v vvv v v i C L1MA4A_3end#L 649 TGTCTTTCTGTGCCTGGCTTATTTCACTTAACATAATGACCTCCAGTTCC 600 chrXqtel1M 751802 TTCCAGGTTTTTCCAAAATCTGCC-TG--TTCATCATTTTTTGTTGCCCA 751848 v v vi v --- v - -- iv i v v C L1MA4A_3end#L 599 ATCCATGTTGCTGCAAA---TGACATGATTTCATTCTTTTTTATGGCCGA 553 chrXqtel1M 751849 ATAGTATT--GTTACATTCATATGCTATGCCTTCTTCAGCCATTCCCCAA 751896 --i iii vi i i iiii i v vi vi C L1MA4A_3end#L 552 ATAGTATTCCATTGTGTATATATACCACATTTTCTTTATCCATTCATCCG 503 chrXqtel1M 751897 TTGATGGCTATTCCCTCAATT--TTTAAT-TCTTTGCCGCCATGAAAAGG 751943 vi i --- vii -- iv - iiiii v v C L1MA4A_3end#L 502 TTGATGGACACT---TAGGTTGATTCCATATCTTTGCTATTGTGAATAGT 456 chrXqtel1M 751944 GCTGCTATAAATAT 751957 v i C L1MA4A_3end#L 455 GCTGCAATAAACAT 442 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 38.57 CpG sites = 33, Kimura (unadjusted) = 39.41 Transitions / transversions = 1.22 (33/27) Gap_init rate = 0.06 (12 / 204), avg. gap size = 1.25 (15 / 12) 302 33.93 3.59 2.21 chrXqtel1M 751767 751989 (248011) C L1ME3G_3end#LINE/L1 (294) 630 405 m_b372s551i9 15538 chrXqtel1M 751767 TGCTCATTTCACTTTACATCAGTTCCTACAGGTCTTTCCAGGTTTTTCCA 751816 iv iv vi vv i iv i v ivv v C L1ME3G_3end#L 630 TGCTTTTTTCACTCAACAATATGTCTTGGAGATCTTTCCATGTCAGTACA 581 chrXqtel1M 751817 ---AAATCTGCCTGTTCATCATTTTTTGTTGCCCAATAGTATT--GTTAC 751861 --- i i --- iv vii? ivv --i vii C L1ME3G_3end#L 580 TATAGATCTACCT---CATTCTTTTTAACNGCTGCATAGTATTCCATAGT 534 chrXqtel1M 751862 ATTCATATGCTATGCCTTCTTCAGCCATTCCCCAATTGATGGCTATTCCC 751911 vv i i ivi v i i v vi ivv C L1ME3G_3end#L 533 ATGGATATACCATAATTTATTTAACCATTCCCCTATTGATGGACATTTAG 484 chrXqtel1M 751912 TCAATTTTTAATTCTTTGCCGCCATGAAAAGGGCTGCTATAAATATTTTT 751961 vivi ii i i iiii ii v iv v i i ii C L1ME3G_3end#L 483 GTTGTTTCCAATTTTTCGCTATTACAAACAATGCTGCAATGAACATCCTT 434 chrXqtel1M 751962 GCACATGTAGGTCCTTTTGT---TGTGGGAG 751989 i i--? v i--- v C L1ME3G_3end#L 433 GTACATGC--NTCCTTGTGCACATGTGCGAG 405 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 46.74 CpG sites = 44, Kimura (unadjusted) = 47.65 Transitions / transversions = 1.47 (44/30) Gap_init rate = 0.04 (8 / 222), avg. gap size = 1.62 (13 / 8) 315 31.78 3.23 4.58 chrXqtel1M 751827 751981 (248019) C L1ME2z_3end#LINE/L1 (617) 574 422 m_b372s551i10 15538 chrXqtel1M 751827 GTTCATCATTTTTTGTTGCCCAATAGTATT--GTTACATTCATATGCTAT 751874 i ivi i iv i --i ii vv i i i C L1ME2z_3end#L 574 GTTCGTTCCTTTTTATTGCTGAGTAGTATTCCATTGTATGAATATACCAC 525 chrXqtel1M 751875 GCCTTCTTCAGCCATTCCCCAATTGATGGCTATTCCCT---CAATTTTTA 751921 ivi v i v i vi vi --- --- vi ii C L1ME2z_3end#L 524 AGTTTGTTTATCCATTCTCCTGTTGATGGACA---CCTGGGCTGTTTCCA 478 chrXqtel1M 751922 ATTCTTTGCCGCCATGAAAAGGGCTGCTATAAATATTTTTGCACATGTAG 751971 i i v iiii v ii i i i i ---- i C L1ME2z_3end#L 477 GTTTTTGGCTATTATGAATAAAGCTGCTATGAACATTCTTGTAC----AA 432 chrXqtel1M 751972 GTCCTTTTGT 751981 i C L1ME2z_3end#L 431 GTCTTTTTGT 422 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 43.46 CpG sites = 35, Kimura (unadjusted) = 44.80 Transitions / transversions = 2.92 (35/12) Gap_init rate = 0.06 (9 / 154), avg. gap size = 1.33 (12 / 9) 432 27.23 2.56 2.04 chrXqtel1M 752344 752538 (247462) C L1PREC2_orf2#LINE/L1 (659) 2635 2440 m_b372s551i11 15538 chrXqtel1M 752344 AATATAGTTTGAGATCTGGTATTGCTAGGCCGCCTTC--CTTTGTATTTT 752391 i ii v vi i--- vi i -- vi C L1PREC2_orf2# 2635 AGTATAGTTTGAAGTCGGGTAGCGT---GATGCCTCCAGCTTTGTTCTTT 2589 chrXqtel1M 752392 TT-CTCATTAATGACCTTGA-TATTCTTGGCCTTTTTTCCTTCCAGATGG 752439 - i vv v - i- vv vi vv v i C L1PREC2_orf2# 2588 TTGCTTAGGATTG-CCTTGGCTATTCGGGCTCTTTTTTGGTTCCATATGA 2540 chrXqtel1M 752440 ATTTTGTTATTATTTCTTCTAGTTTTATTCATAATTTTGG-GGTAGTTTG 752488 ivv vi i i i vv v v iiv- C L1PREC2_orf2# 2539 ATTTTAAAATAGTTTTTTCTAGTTCTGTGAAGAATGTCATTGGTAGTTTG 2490 chrXqtel1M 752489 ATTGATATGGCACTAAATAAGTAAATTACTTTAGGCAAGATGGCCATTTT 752538 v iv i i i vv i i iv C L1PREC2_orf2# 2489 ATAGGAATAGCATTGAATCTGTAAATTGCTTTGGGCAGTATGGCCATTTT 2440 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 33.40 CpG sites = 26, Kimura (unadjusted) = 34.19 Transitions / transversions = 1.00 (26/26) Gap_init rate = 0.04 (8 / 194), avg. gap size = 1.12 (9 / 8) 39 5.11 6.56 0.00 chrXqtel1M 760749 760809 (239191) (AT)n#Simple_repeat 1 65 (0) c_b372s251i3 15539 chrXqtel1M 760749 ATATATATATATATATATATATATATATATATAAAT-TAT-TA-ATAT-T 760794 v - - - - (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chrXqtel1M 760795 AAATATATATCTATA 760809 v v (AT)n#Simple_ 51 ATATATATATATATA 65 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.07 (4 / 60), avg. gap size = 1.00 (4 / 4) 12 22.78 4.76 0.00 chrXqtel1M 761191 761232 (238768) (AGAAAGG)n#Simple_repeat 1 44 (0) m_b372s252i11 15540 chrXqtel1M 761191 AGGAAGTAGGAAGTAG-GAGGAGAAAGGGGAAA-GAAAAGGGAG 761232 i v i v -i i - i i (AGAAAGG)n#Si 1 AGAAAGGAGAAAGGAGAAAGGAGAAAGGAGAAAGGAGAAAGGAG 44 Matrix = Unknown Transitions / transversions = 3.00 (6/2) Gap_init rate = 0.05 (2 / 41), avg. gap size = 1.00 (2 / 2) 266 26.20 3.55 10.87 chrXqtel1M 761304 761500 (238500) L1MEj_5end#LINE/L1 1972 2155 (5) m_b372s551i12 15541 chrXqtel1M 761304 AAAAGAGAGAACAAAAATATATACAGGGAAGAAAATAAGATGCAGGGAAA 761353 i ? i v v v v i ii? v i v i - L1MEj_5end#LI 1972 AAAAAANAAAAAAACAAAATAAATAAANAATAAAGTAAGATGGAAGGAA- 2020 chrXqtel1M 761354 TA----CACAGATGGTAATCATAACTCTGAATGTGAATGTCATGACCTCT 761399 ---- viv ivi i i v v i vvv vi L1MEj_5end#LI 2021 TAAAATCAAGTATATCAGTCGTTACACTAAATGTGAATGGACTGAATTCT 2070 chrXqtel1M 761400 CCCATAAAACAGA-AGGGAATAGCAGAATGGATTAAGAAAC--AATCCTA 761446 v - - i v iv v i i -- i vi L1MEj_5end#LI 2071 CCCATTAAA-AGACAGAGACTGTCAGATTGGGTTAAAAAACAAAACCCAG 2119 chrXqtel1M 761447 CAATATGGTATTTTTAATTTTTTTTTTTTTAACAAGAAACATATTTGAAA 761496 v v i ------------------ i i i L1MEj_5end#LI 2120 CTATATGCTGTTT------------------ACAAGAAACACACTTAAAA 2151 chrXqtel1M 761497 CAAA 761500 L1MEj_5end#LI 2152 CAAA 2155 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 31.93 CpG sites = 24, Kimura (unadjusted) = 32.78 Transitions / transversions = 1.09 (24/22) Gap_init rate = 0.12 (23 / 196), avg. gap size = 1.17 (27 / 23) 1312 31.50 3.62 5.16 chrXqtel1M 761364 762662 (237338) L1M4_orf2#LINE/L1 28 1307 (1987) m_b372s551i13 15541 chrXqtel1M 761364 GTAATCATAACTCTGAATGTGAATGTCATGACCTCTCCCATAAAACAGAA 761413 i i ---i i i vvv i v v v v vi v L1M4_orf2#LIN 28 GTAATTACA---TTAAATGTAAATGGATTAAACACTCCAATCAAAAGGCA 74 chrXqtel1M 761414 GGGAATAGCAGAATGGATTAAGAAACA--ATCCTACAATATGGTATTTTT 761461 i v i v i -- v v v i i -- L1M4_orf2#LIN 75 GAGATTGGCAGAATGGATAAAAAAACATGATCCAACTATATGCTGTCT-- 122 chrXqtel1M 761462 AATTTTTTTTTTTTTAACAAGAAACATATTTGAAA--CAAAAAGACATAC 761509 ---------------- i i i v i -- i v v i L1M4_orf2#LIN 123 ----------------ACAAGAGACACACTTTAGATTCAAAGACACAAAT 156 chrXqtel1M 761510 AA--TGAAAGGGTCAAAGGCTGGAGCAGAATTTTTTATGCTTCAGCTGAA 761557 i-- -- v v iv ii v vii --v i --- L1M4_orf2#LIN 157 AGGTTGAAAG--TAAAAGGATGGAAAAAGATATACCATGC--AAAC---A 199 chrXqtel1M 761558 GCAAAAAAAAAAAATCAGGAATAGTCACTCTGATCTCAGAAAAAGCAAAA 761607 i vv i i v v i i ii iv i v v ii i v L1M4_orf2#LIN 200 GTAACCAAAAGAGAGCTGGAGTGGCTATACTAATATCAGACAAAATAGAC 249 chrXqtel1M 761608 GTCAAAATAGATCTAATCAAAAGAAATAAGGAAGGAAGCTACATCTTGTT 761657 v i i i i vv?vi i vv i i i vii vi vv v L1M4_orf2#LIN 250 TTTAAGACAAAAANTGTTACTAGAGACAAAGAAGGACATTTTATAATGAT 299 chrXqtel1M 761658 AAAGGGTGCCATAGACAATGAAGTTGTATTGATGCTAAATGTATATCCAC 761707 i vv v vv iv v v i vii vv ii v L1M4_orf2#LIN 300 AAAAGGGTCAATCCATCAGGAAGATATAACAATTATAAACATATATGCAC 349 chrXqtel1M 761708 CAAGTGGTAGAGCATCCAAATTCTTAAAGAAGAAGTTAAGCCACTTATAG 761757 v iiiii vi v v v i v i ii i vvv v iv L1M4_orf2#LIN 350 CTAACAACAGAGCCCCAAAATACATGAAGCAAAAACTGACAGAATTGAAG 399 chrXqtel1M 761758 GAAGAAGTAGACAG--CAA-AACCATAGCTGGGAATCTTCAGC------C 761798 i i i-- - iv i ii - ii------ L1M4_orf2#LIN 400 GGAGAAATAGACAATTCAACAATAATAGTTGGAGA-CTTCAATACCCCAC 448 chrXqtel1M 761799 TTTCTATCTTGGAAATAGATAAATCTAATCACAAAATAAACAAGAAAGAA 761848 v vv -- vv - iv v i v --- L1M4_orf2#LIN 449 TTTCAATAATGGA--TAGAACAA-CTAGACAGAAGATCAACAAG---GAA 492 chrXqtel1M 761849 ACTAATGAGGTTAATAGAATCCTAGAAAAC--TTAGATATGATAGACCTC 761896 ivi v vv v i -- iv v v --i iv i i v L1M4_orf2#LIN 493 ATAGAAGACTTGAACA--ACACTATAAACCAACTAGACCTAACAGACATC 540 chrXqtel1M 761897 TGGAGAAAACTGAAT--AGGGACAGAAAGGAATACACCCTTTTCTCAACA 761944 iv v vv i-- ivi v -- vi i vv L1M4_orf2#LIN 541 TATAGAACACTCCACCCAACAACAGCA--GAATACACATTCTTCTCAAGT 588 chrXqtel1M 761945 GTACAGGG--CAT-CTACACAAAAAATTGACCATGTATTTGAGCA-AAAA 761990 i v -- - v ----ii v i i v iv - L1M4_orf2#LIN 589 GCACATGGAACATTCTCCA----GGATAGACCATATGTTAGGCCATAAAA 634 chrXqtel1M 761991 AACCTCACAATCAAATGCAGAAAGGCAGAAATAGTAAATGCTTCCTTTTC 762040 v vv v - vi i i iiv vi v viv viv i L1M4_orf2#LIN 635 CAAGTCTCAAT-AAATTTAAAAGGATTGAAATCATACAAAGTATGTTCTC 683 chrXqtel1M 762041 AGACCATGATGCAATAAAAATTGTATTCAATAAAGGGCAAGAAAA----- 762085 v ii v i v v v v vi -- i ----- L1M4_orf2#LIN 684 CGACCACAATGGAATGAAATTAGAAATCAATAACAG--AAGGAAATTTGG 731 chrXqtel1M 762086 -AGACTGGTAATCAGTTGGAAATTAAATAAAGTAATTCTAAATAACAAGT 762134 - i i vii vi vv i vii v i v i L1M4_orf2#LIN 732 GAAATTCACAAATATGTGGAAATTAAACAACACACTCCTAAATAACCAAT 781 chrXqtel1M 762135 GGGTCAAACAATAAATCATAA----AATCATAAAAACAATAATTTAATTC 762180 v v i ---- i v --------- v i L1M4_orf2#LIN 782 GGGTCAAAGAAGAAATCACAAGGGAAATTAGAAAA---------TACTTT 822 chrXqtel1M 762181 AAGA-GAATGATGGCAATGAGACAACATACCCAAACCTATCGGATGCAGT 762229 i - vii i vi v v i v i L1M4_orf2#LIN 823 GAGATGAATGAAAACGAAAACACAACATACCAAAACTTATGGGATGCAGC 872 chrXqtel1M 762230 CAAAGCAGTTCTCAG-GGGAAATTT-TATCTCTAAATAGTTATATGAATA 762277 ? v i - - v v ivi --- L1M4_orf2#LIN 873 NAAAGCAGTGCTTAGAGGGAAATTTATAGCTGTAAATGCCTATAT---TA 919 chrXqtel1M 762278 AAATAGA-GAAAGAGG--AGATCAATGAATTTCACATGCAAC-TAAAAAA 762323 v - vv-- i - ii v v v v - v i L1M4_orf2#LIN 920 AAAAAGAAGAAAGATCTCAAATCAAT-AACCTAACCTTCCACCTTAAGAA 968 chrXqtel1M 762324 GCTAAAAAAATAA---CAAATTAAACTCTCATTAAATACCAAATAAGAAA 762370 i i v --- i i vv vi ii vv iiv i L1M4_orf2#LIN 969 ACTAGAAAAAGAAGAGCAAACTAAACCCAAAGCAAGCAGAAGGAAGGAAA 1018 chrXqtel1M 762371 TTATGAAATTCAAAGGAGAGATTAATAAAATTAAAACTAAGAAAACTATT 762420 v i iv i i vi i v i vi i v ii v v L1M4_orf2#LIN 1019 TAATAAAGATTAGAGCGGAAATAAATGAAATAGAGAATAGAAAAACAATA 1068 chrXqtel1M 762421 GAACTAATTAATTAAACTAAGAGTTGGTTTTATGAAAAAACAAACAAAAT 762470 ivv i iv i i i v i iv L1M4_orf2#LIN 1069 GAGAAAATCAACGAAACCAAAAGTTGGTTCTTTGAAAAGATCAACAAAAT 1118 chrXqtel1M 762471 AGACAAACCTTTGGTTAATTTGATC-AGAAAAAAGGAAAGGAAAAAATCA 762519 v i i ivi i - i i -- i v L1M4_orf2#LIN 1119 TGACAAACCTTTAGCTAGACTGACCAAGAAAAAAAGAGAG--AAGACTCA 1166 chrXqtel1M 762520 AATTACCAGAATCAAAAATGAAAAGGGTGAACTTACCACCAA--TGAAGA 762567 i i ii ii v vv i i -- v --- L1M4_orf2#LIN 1167 AATTACTAAAATCAGGAATGAAAGAGGGGACATTACTACCGACCTTA--- 1213 chrXqtel1M 762568 AGAAGAAATTAAAGCAATAACCAGGACCTATT-TGCCCAACTGTATGCCA 762616 --v v ivi v iv ivv i - vv i L1M4_orf2#LIN 1214 --CAGAAATAAAAAGGATTATAAGGGAATACTATGAACAATTGTATGCCA 1261 chrXqtel1M 762617 GAAAATCTGACAATCTAATTGAAATGGATGAATATTTACAAAAATA 762662 iv iv i i iv ii vii v i i L1M4_orf2#LIN 1262 ACAAATTAGATAACCTAGATGAAATGGACAAATTCCTAGAAAGACA 1307 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 41.06 CpG sites = 202, Kimura (unadjusted) = 41.62 Transitions / transversions = 1.09 (202/186) Gap_init rate = 0.07 (90 / 1298), avg. gap size = 1.26 (113 / 90) 2516 29.53 5.13 2.53 chrXqtel1M 762665 764283 (235717) L1M5_orf2#LINE/L1 1401 3060 (234) m_b372s551i14 15541 chrXqtel1M 762665 AAAAATAACTCCCGGGCCAGATGGATTTACAAGTGAATTCTACCAAACAT 762714 i v v v v i vi L1M5_orf2#LIN 1401 AAAGAAAACTCCAGGCCCAGATGGCTTCACTGGTGAATTCTACCAAACAT 1450 chrXqtel1M 762715 TTAAAGAACAATTAATTCCAATACTATGTAAACTATTTGGAAAAATAGGT 762764 i v v v vi iii v ivii iv L1M5_orf2#LIN 1451 TTAAGGAAGAAATAATACCAATCTTACACAAACTCTTCCAGAAAATAGAA 1500 chrXqtel1M 762765 GAAGAAGGAA-ACTTGCCAAATTCCTTCTATGACACAAATATGGTATTGA 762813 i i - v -i v i vi v ii ?iivi L1M5_orf2#LIN 1501 AAAGAGGGAACACTTCCCAA-CTCATTTTATGAGGCCAGCATNACCCTGA 1549 chrXqtel1M 762814 TACCTAAACCAGGAAGAGCCAAAACAGATAAAAAAAAATTACAGACCAAT 762863 v ? iv i v vv - v i L1M5_orf2#LIN 1550 TACCAAAACCNGACAAAGACATTACA-AGAAAAGAAAATTACAGACCAAT 1598 chrXqtel1M 762864 CTCCCTCATGAATATAGAAGCAAAAATTTAAAATAAAATATTAGCAAAGA 762913 v i v iiv? i vv L1M5_orf2#LIN 1599 ATCCCTCATGAACATAGATGCAAAAATCCTNAACAAAATATTAGCAAATC 1648 chrXqtel1M 762914 GATTACAACAATTTATCAACAGGATAATACACTATGACTAAGTGGGATTT 762963 v v i v v v ii i i L1M5_orf2#LIN 1649 GAATCCAGCAATATATAAAAAGGATAATACATCATGACCAAGTGGGGTTT 1698 chrXqtel1M 762964 ATACCAGGAATCCAGGACTGGTTCAGTATCAGGAAAACTATTGCCATAAT 763013 v v i ii i ii iv i v v iivii L1M5_orf2#LIN 1699 ATCCCAGGAATGCAAGGTTGGTTTAACATTCGAAAATCAATCAATGTAAT 1748 chrXqtel1M 763014 TTACCATAT---CAAAACAAAACAAACAAATCACAGGACAACTTCAATAG 763060 i --- i i iv i v i v iv ii L1M5_orf2#LIN 1749 TCACCATATTAACAGAATAAAGGAGAAAAATCATATGATCATCTCAATAG 1798 chrXqtel1M 763061 ATGCCGAAAAAGCTTTTG-CAAAATACAGCACTTATCCCTATTAAAAAC- 763108 v v - v i ii i v iv - L1M5_orf2#LIN 1799 ATGCAGAAAAAGCATTTGACAAAATTCAACACCCATTCATGATAAAAACT 1848 chrXqtel1M 763109 ATTAGAGAACACAGGAATAAACGGAGTTTTCCTTAAAATGATAAGCAACA 763158 v i vi -i i v iivi i vv ivii L1M5_orf2#LIN 1849 CTCAGCAAAC-TAGGAATAGAAGGGAACTTCCTCAACCTGATAAAGGGCA 1897 chrXqtel1M 763159 TTTATCTAAAACCATCACCAATCATTATTTGTAGTGGGGAAA-AGTGGAC 763207 i ivv vv v ? v i viv i v - v i ? L1M5_orf2#LIN 1898 TCTACGAAAAACCTACAGCNAACATCATACTTAATGGTGAAANACTGAAN 1947 chrXqtel1M 763208 ACATTCTCAGTAAGATCAGGAGTGAAACAAGGATGCCTGTTATCATCACT 763257 i v i vv i iii i i i i ? i L1M5_orf2#LIN 1948 GCTTTCCCCCTAAGATCGGGAACAAGACAAGGATGTCCGCTNTCACCACT 1997 chrXqtel1M 763258 ATTATTCAGTTTTGTACTAGAAATGTTGGCTTTAGCAATAAGAAAAGGAA 763307 vi iiv i ii vi i ivvv iv i L1M5_orf2#LIN 1998 TCTATTCAACATTGTACTGGAGGTCCTAGCCAGTGCAATAAGGCAAGAAA 2047 chrXqtel1M 763308 AAGAAATGAAAGGAATTAGAATAGGCAATGAGGTAACAAAACTATCGCTC 763357 i v v ii v v v i v i i ?i v L1M5_orf2#LIN 2048 AAGAAATAAAAGGCATAAAGATTGGAAAGGAAGAAATAAAACTGTCNTTA 2097 chrXqtel1M 763358 TTTGCAGATAATACGATGGCATACTTAG----TCCTAGAGAATTATCCCA 763403 i i i i v i? v ---- ? i ivv vv L1M5_orf2#LIN 2098 TTCGCAGATGACATGATTGTNTACGTAGAAAATCCNAAAGAATCTACAAA 2147 chrXqtel1M 763404 AAGCCTACTTGA---AACAAG-AACTTTAGCAAAGTTATAGGACATATAA 763449 ? iv v --- i -i v i iii? i i vii L1M5_orf2#LIN 2148 NAAACTACTAGAACTAATAAGTGAATTTAGCAAGGTCGCNGGATACAAGG 2197 chrXqtel1M 763450 TAAACCCACACAAATCATCAGCATTGTTATATATTATTAACAAAGCCCAT 763499 v ivi v viv i vi i vi -- v L1M5_orf2#LIN 2198 TCAATATACAAAAATCAATTGTATTTCTATATACTAGCAACAAA--CAAT 2245 chrXqtel1M 763500 T--AACAAGAAAT----AGAGAAATTCTATGTAAAATTACTGCAGACAAA 763543 -- v v ---- i iv v i v v vi vv i v v L1M5_orf2#LIN 2246 TGGAAAATGAAATTTNAAAAACAATACCATTTACAATAGCATCAAAAAAC 2295 chrXqtel1M 763544 ATAAAATACTCAGGGATCTACCTGCCAAGACAAACTCAGGAATTATA--- 763590 ? i i vv i iv i ? viiv i vi ? --- L1M5_orf2#LIN 2296 ATNAAATACTTAGGAATAAATCTAACAAAANATGTGCAAGACCTNTACAC 2345 chrXqtel1M 763591 TGAACACAATTACAAAA---TTCTCACAGAACTAAAATCAGATCTAAACA 763637 --- i --- v v v v v vv i i L1M5_orf2#LIN 2346 TGAA---AACTACAAAACATTGCTGAGAGAAATTAAAGAAGACCTAAATA 2392 chrXqtel1M 763638 ATTGGAAAAATA-GCAATTGCTCATGAGTAGGCCAAG-CT-AATATAATA 763684 v i i -i v - i ii v -- - - vi ? L1M5_orf2#LIN 2393 AATGGAGAGATATACCA-TGTTCATGGATTGG--AAGACTCAATATTGTN 2439 chrXqtel1M 763685 ATAATTTCAATTCTGCCTATACTGGTCTAGTTTTTCAAC----TGCCAAT 763730 vi v v i v i i vvvv i---- v L1M5_orf2#LIN 2440 AAGATGTCAATTCTCCCCAAATTGATCTATAGATTCAATGCAATCCCAAT 2489 chrXqtel1M 763731 --AAATT-------ATTTTATAAAGCTAGAAAAAATAACAACCAGATCC- 763770 -- i-------i v ----- iv i v i v v i - L1M5_orf2#LIN 2490 CAAAATCCCAGCAGGTTTTTT-----TGTAGAAATTGACAAGCTGATTCT 2534 chrXqtel1M 763771 ---ATCTGGATGAACA---AAAAGA-CAAGAATA-TCAAGGGAATTAATG 763812 --- i iv i v --- i - ? -i iiv i-v L1M5_orf2#LIN 2535 AAAATTTATATGGAAATGCAAAGGACCNAGAATAGCCAAAACAATC-TTG 2583 chrXqtel1M 763813 AAAAAAAATACAAAGGATAGTGGCCTACCAATTCTAGGCCT-AAAACTCT 763861 i v vv i v i v v vv v v i? ii? - i - L1M5_orf2#LIN 2584 AAAAAGAAGAACAAAGTTGGAGGACTTACACTACCNGATNTCAAGACT-T 2632 chrXqtel1M 763862 ATTATAAAGCAGAAGTCATGAAAAACATATGGTACTGGC-TAAG------ 763904 viv v v i vvi i i - ------ L1M5_orf2#LIN 2633 ATTATAAAGCTACAGTAATCAAGACAGTGTGGTATTGGCGTAAGGATAGA 2682 chrXqtel1M 763905 -AAATAGCATGGTGAATCAG--TGGAGTAGTTTAGATACAGA-TGATGCA 763950 - vviii i v -- i - ii v i -iv ii L1M5_orf2#LIN 2683 CAAATAGATCAATGGAACAGAATAGAG-AGTCCAGAAATAGACCCACACA 2731 chrXqtel1M 763951 TAATCAATGATTATAGCAATCTAGAATTTGATAAA-CCCCCAA---ATTC 763996 --------- i ?v ?i iivv i -viv --- v i L1M5_orf2#LIN 2732 TA---------TATGGNCANTTGATTTTTGACAAAGGTGCCAANGCAATT 2772 chrXqtel1M 763997 CAGCTTTTGAAATAGGAT-GTCATTATTTGACAAAAATTGCTGGGAAAAC 764045 --- v ii v - - - ii viv i v i L1M5_orf2#LIN 2773 CAG---TGGGGAAAGGATAGTC-TT-TTCAACAAATGGTGCTGGAACAAT 2817 chrXqtel1M 764046 TAGAAAATAATGTGTTAGAAACTTGGCATAGACCTACATCTTTCACCCCA 764095 i v viv i vv i v vii?v v ivi i iv vi L1M5_orf2#LIN 2818 TGGATATCCATATGGAAAAAAATGAANCTCGACCCCTACCTCACACCATA 2867 chrXqtel1M 764096 TACCAAAATAAGGTCAAAATGGGTACAT-GATTTGGGCATAAAGGGTGAT 764144 i v v iv ? i i - - ii iiiii i ? i v L1M5_orf2#LIN 2868 CACAAAAATTAATTCNAGATGGAT-CATAGACCTAAATGTAAAAGNTAAA 2916 chrXqtel1M 764145 ACCATAAGCAAAT--TAGAAG--AGCAAGGGATAATTTACCTATCA-GAC 764189 i -- v -- -- i vi v -- i - i- L1M5_orf2#LIN 2917 ACTATAA--AACTTCTAGAAGAAAACATAGGAGAA--TATCT-TCGTGAC 2961 chrXqtel1M 764190 CTTTGGAGAAGAAGGAATTTATGATCAAAGAAGAAATAGAGA--ACAA-- 764235 v ?v i v iii ---v i v i v i i i -- ? -- L1M5_orf2#LIN 2962 CTTGGGNTAGGCAAAGATTT---CTTAAACAGGACACAAAAAGCACNAAC 3008 chrXqtel1M 764236 TATGAAAGACAAAATGGACAACTT----TGTGTTAAATTAAAAAGTTTTT 764281 i i v v i v ---- ?ii i v v ii i L1M5_orf2#LIN 3009 CATAAAAGAAAAAATTGATAAATTGGACTNCATCAAAATTAAAAACTTCT 3058 chrXqtel1M 764282 GC 764283 L1M5_orf2#LIN 3059 GC 3060 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 38.59 CpG sites = 258, Kimura (unadjusted) = 39.25 Transitions / transversions = 1.24 (258/208) Gap_init rate = 0.05 (80 / 1618), avg. gap size = 1.56 (125 / 80) 15 9.71 5.71 0.00 chrXqtel1M 764336 764358 (235642) (TCTT)n#Simple_repeat 1 25 (12) m_b372s252i12 15542 chrXqtel1M 764336 TCTTTCTTTC--TCTTTCTTTCTTT 764358 -- (TCTT)n#Simpl 1 TCTTTCTTTCTTTCTTTCTTTCTTT 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.05 (1 / 22), avg. gap size = 2.00 (2 / 1) 74 1.32 2.60 0.00 chrXqtel1M 764359 764435 (235565) (CTTC)n#Simple_repeat 1 79 (0) c_b372s251i4 15543 chrXqtel1M 764359 CTTCTTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT 764408 i (CTTC)n#Simpl 1 CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT 50 chrXqtel1M 764409 TCC-TCCTTCCTTCC-TCCTTCCTTCCTT 764435 - - (CTTC)n#Simpl 51 TCCTTCCTTCCTTCCTTCCTTCCTTCCTT 79 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.03 (2 / 76), avg. gap size = 1.00 (2 / 2) 15 9.71 5.71 0.00 chrXqtel1M 764436 764446 (235554) (TCTT)n#Simple_repeat 26 36 (1) m_b372s252i12 15544 chrXqtel1M 764436 TCTTTTTTTTT 764446 i i i (TCTT)n#Simpl 26 TTTCTTTCTTT 36 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 10), avg. gap size = 0.0 (0 / 0) 1288 27.60 2.68 2.31 chrXqtel1M 764902 765461 (234539) L1ME4a_3end#LINE/L1 12 573 (298) m_b372s551i15 15541 chrXqtel1M 764902 AATATATAAAGTG-TGTCA-AAATTA-TAAGAATTTAAGTC--ATTCTCA 764946 v - v i - i - v-- v -- iv i v L1ME4a_3end#L 12 AATATATAAAGAGCTCTTACAAATCAATAAGAAA--AAGACGAACACCCC 59 chrXqtel1M 764947 AATGGATAAATGGGCAAAGGACATGAACAAACAATTTTCAGATGAAGAAA 764996 i v i iv i v L1ME4a_3end#L 60 AATAGAAAAATGGGCAAAGGACATGAACAGACAATTCACAAAAGAAGAAA 109 chrXqtel1M 764997 TTAAAGCTATCAATAGTCATATGAAAAAATGCTCTACATCACAATTGATT 765046 vv iivii iv ? i v v v v i i L1ME4a_3end#L 110 TACAAATGGCCAATAAACATATGAAAANATGTTCAACCTCACTAGTAATC 159 chrXqtel1M 765047 AGAGAAATGGAAATAAATTATAATAGCTCTGAGGTACCACTTCACACCTC 765096 i ----i v i i vv i i iv v L1ME4a_3end#L 160 AAAGAAATG----CAAATTAAAACAACAATGAGATACCATTTTTCACCTA 205 chrXqtel1M 765097 TCAGATTGGTTGAGATGACAGGAAAAGAT-AATGATA---AATGTTGGAG 765142 i ivi v----v -i i --- i v L1ME4a_3end#L 206 TCAAATTGGCAAAGATT----TAAAAGATTGATAATACCCAGTGTTGGCG 251 chrXqtel1M 765143 GGGATGTGGGAAAACTGGGATATTAATGCATTGTTGGTAGAGTTGTGAAA 765192 i i ?i v v ivi v i i i i iiv i v L1ME4a_3end#L 252 AGGGTGTGGNGAAACGGGCACTCTCATACACTGCTGGTGGGAGTGTAAAT 301 chrXqtel1M 765193 TGATCCAACCATTCTGGAGAGCAATATGGAACAATGC-CCAAAAGGCTAC 765241 i v v i v v vv i-i v -i L1ME4a_3end#L 302 TGGTACAACCTTTCTGGAGGGCAATTTGGCAATATGTATCAAAAGCCT-T 350 chrXqtel1M 765242 CACACTGTGCGTACCCTTTGATCCCATAGTGACACGTTTGGGTCTGTATC 765291 v v v ? i i vi i vv v i i vv v L1ME4a_3end#L 351 AAAAATGTNCATACCCTTTGACCCAGTAATTCCACTTCTAGGAATTTATC 400 chrXqtel1M 765292 ACAAGGAAATCATAAAGGA-G-GAAAAAAGATCCATATGTGTAAAAATGT 765339 vi v v ii - - ? v i-- ii ii L1ME4a_3end#L 401 CTAAGGAAATAATCAGAGATGTGNACAAAGATT--TATGTACAAGGATGT 448 chrXqtel1M 765340 TTATAGCAGCTCTTTTTGTGGGGGTG-AAAATTGGAAAATGAGTAGATGC 765388 i v vi v i iivi i - vvivv i i L1ME4a_3end#L 449 TCATCGCAGCATTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGT 498 chrXqtel1M 765389 TCATCAGT-TGGGAATGGCTGAATAAGTTGTGATATATGAAGATGATAGA 765437 i v i -v ? i i i i i i vv v ?i i L1ME4a_3end#L 499 CCAACAATAGGGGANTGGTTAAATAAATTATGGTACATCCATANAATGGA 548 chrXqtel1M 765438 ATATTAT-TGGTCTATAAAAATTAT 765461 -ii i vv ? L1ME4a_3end#L 549 ATATTATGCAGCCATTAAAAATNAT 573 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.36 CpG sites = 83, Kimura (unadjusted) = 35.65 Transitions / transversions = 1.22 (83/68) Gap_init rate = 0.04 (25 / 559), avg. gap size = 1.12 (28 / 25) 1593 27.57 0.73 2.03 chrXqtel1M 766008 766555 (233445) C L1ME3G_3end#LINE/L1 (380) 544 4 m_b372s551i16 15545 chrXqtel1M 766008 TATTCCATAACATTCACATACCACAGTTTACTCAACCATTCTCCAATTGA 766057 ii vv i i i i i i v C L1ME3G_3end#L 544 TATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTATTGA 495 chrXqtel1M 766058 TGGGCATCCA--TTCATTTTCCAGCTTCTGGCCACTACAAACAGGGCTGC 766105 i ii -- v-- ii i v i i iv C L1ME3G_3end#L 494 TGGACATTTAGGTTG--TTTCCAATTTTTCGCTATTACAAACAATGCTGC 447 chrXqtel1M 766106 CACAAACATTTTGGCACATACAGATCCCTTTCC-CTTCTTT-AGTATCTC 766153 v ii ii v i i ?-- i v v - v v vi- i C L1ME3G_3end#L 446 AATGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATTTC 399 chrXqtel1M 766154 CTTGGGGTATAAGCCCAGTAGAGACACTGCTGGATCAAAGGGTATGCACA 766203 i? i i v v? ? v v iv i i i C L1ME3G_3end#L 398 TNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGCA 349 chrXqtel1M 766204 GTTTGATAACTTTTTGAGCATAGTTCCAAATCGCTCTCCAGAATGGCTGG 766253 v i -- i vvv - v v i i i ? v C L1ME3G_3end#L 348 TTTTAA--ATTTTAATAG-ATACTGCCAAATTGCCCTCCAAAANGGCTGT 302 chrXqtel1M 766254 ATGTGTTCACAATTCCACCAACAATCTATCAGTGTCCCTGCTTTCCCACA 766303 ivvi i v i i i v v v v i i i C L1ME3G_3end#L 301 ACCAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCACA 252 chrXqtel1M 766304 TCCCCTCCAACAGCCTGCATTATCTTTCCCTGTCATTCTGGCCAATCTGA 766353 i i v vi?vii vv? ii vvv i v C L1ME3G_3end#L 251 CCCTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATCTGA 202 chrXqtel1M 766354 CAGGTGTGTAGTGGTATCTCAGAGTTGTCTTAATTTGCATTTCTCTGATC 766403 ii viv i vv i i i C L1ME3G_3end#L 201 TGGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGATT 152 chrXqtel1M 766404 AATAGTGATTTGGAACACTTTTTCATATGAGTAGTAATAGTTTTAATTTC 766453 v vv v i ii vv v iiivi vv C L1ME3G_3end#L 151 ACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGTATTTC 102 chrXqtel1M 766454 ATCATCTGAAAATTGTCTGTTCATATTCTTTGACCATTTATCAATTGGAG 766503 v v vi i i v v v iv C L1ME3G_3end#L 101 CTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGGGT 52 chrXqtel1M 766504 AATGGCTTGATTTCTTACAAATTAGAGTCAATTCTCTATATATTTTGGAA 766553 -- v -- ivi v vivv i i i v C L1ME3G_3end#L 51 --TGTCTT--TTTCTTATTGATTTGTAGGAGTTCTTTATATATTCTGGAT 6 chrXqtel1M 766554 AT 766555 C L1ME3G_3end#L 5 AT 4 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 34.61 CpG sites = 79, Kimura (unadjusted) = 35.50 Transitions / transversions = 1.14 (79/69) Gap_init rate = 0.03 (14 / 547), avg. gap size = 1.07 (15 / 14) 1724 32.66 2.96 2.81 chrXqtel1M 766409 767725 (232275) C L1P4_orf2#LINE/L1 (0) 3294 1976 m_b372s551i17 15545 chrXqtel1M 766409 TGATTTGGAACACTTTTTCATATGAGTAGTAATAGTTTTAATTTCATCAT 766458 v v i i vv iv iiiv i vv v v v C L1P4_orf2#LIN 3294 TGATGTTGAGCATTTTTTCATATGTTTGTTGGCCGCTTGTATGTCTTCTT 3245 chrXqtel1M 766459 CTGAAAATTGTCTGTTCATATTCTTTGACCATTTATCAATTGGAGAATGG 766508 i i v i i v i v i v ivv -- C L1P4_orf2#LIN 3244 TTGAGAAGTGTCTGTTCATGTCCTTTGCCCACTTTTTAATGGGGTTAT-- 3197 chrXqtel1M 766509 CTTGATTT---CTTACAAATTAGAGTCAATTCTCTATATATTTTGGAAAT 766555 - v --- iivi ? v vv v i ii v i v C L1P4_orf2#LIN 3196 -TTGTTTTTTGCTTGTTGANTTGTTTAAGTTCCTTATAGATTCTGGATAT 3148 chrXqtel1M 766556 GAGTCCTTTATCAGAGCCTTTAACTGTAAAAATGTTTTCCCAGTTTAT-T 766604 v v i i vv v vivi ii v v i v i i -v C L1P4_orf2#LIN 3147 TAGACCTTTGTCGGATGCATAGTTTGCGAATATTTTCTCCCATTCTGTAG 3098 chrXqtel1M 766605 GTTTTCCTTCTAATCTTGCCTGCATTAGTTTTATTTG---TACAAAAACT 766651 v iv i v - i- v-- iv --- i i i C L1P4_orf2#LIN 3097 GTTGTCTGTTTACTCT-GT-TGA--TAGTTTCTTTTGCTGTGCAGAAGCT 3052 chrXqtel1M 766652 TTTCAATTTGAT-ATATTCAA------AATTTTCAATTTTGTAGTCAATA 766694 i i i i - vi i v ------ iiv v - - C L1P4_orf2#LIN 3051 CTTTAGTTTAATTAGGTCCCACTTGTCAATTTTTGTTTTTGTTG-CAAT- 3004 chrXqtel1M 766695 ATGATGTCTAGTTCTTTGGTCATAAATTCCTT-CCTCTTCCACAGGTCT- 766742 - v v iv vv -i i - vvvv i- v i- C L1P4_orf2#LIN 3003 -TGCTTTTGAGGACTT-AGTCATAAATTCTTTGCCAAGGCCG-ATGTCCA 2957 chrXqtel1M 766743 GAGAGGTAAACTATCCTATGCT--CTTCCAATTTATTTATGATCTCATTC 766790 i? --- v v i -- i ivv v ii i v vvi C L1P4_orf2#LIN 2956 GAANGGTA---TTTCCTAGGTTTTCTTCTAGGATTTTTATAGTTTGAGGT 2910 chrXqtel1M 766791 TTTATGCCTAGATCATGAACCTATTTTGACCTTTATCTTGGTGTACGGTG 766840 i iiii ii v v i i i v- v i v i i C L1P4_orf2#LIN 2909 CTTACATTTAAGTCTTTAATCCATCTTGAG-TTAATTTTTGTATATGGTG 2861 chrXqtel1M 766841 TTAAGTGTGGGTC-AATGCCTAGTTTCTGCCATA---CTAATTTCCAATT 766886 vv i iv - i vi vvvi - --- i--- i C L1P4_orf2#LIN 2860 AAAGGTAGGGGTCCAGTTTCATTCTTCTGC-ATATGGCTAG---CCAGTT 2815 chrXqtel1M 766887 TTCCCAGAAATTTTTGTCAAATAATGCATTCTTATCTCAAAAACTGGGGT 766936 v v viv i ii iv vi i - i v vvi vivv C L1P4_orf2#LIN 2814 ATCCCAGCACCATTTATTGAATAGGGAGTCCTT-TCCCCATTGCTTATTT 2766 chrXqtel1M 766937 CT-TTGGGTTTGTCAAACACTAGATAATTAAGGTTATTGGCTGTTTTGTC 766985 i - i iv i v ii ii ivi v i -- v i i i C L1P4_orf2#LIN 2765 TTGTCGACTTTGTCGAAGATCAGATGGTTGTAGGTGT--GCGGCTTTATT 2718 chrXqtel1M 766986 CTTTGAAC---CTAACCTATTCCATTGATCAACTAGTCTATTTCTTAGCC 767032 - i iii--- vi i i v ivv i i vvi C L1P4_orf2#LIN 2717 -TCTGGGTTCTCTATTCTGTTCCATTGGTCTATGTGTCTGTTTTTGTACC 2669 chrXqtel1M 767033 AATATCAGATAGTTTTAGTAACCGCTACCTTATAATATAATTTTAGATCT 767082 i i viiv i v i ivi i i i v ii v C L1P4_orf2#LIN 2668 AGTACCATGCTGTTTTGGTTACTGTAGCCTTGTAGTATAGTTTGAAGTCG 2619 chrXqtel1M 767083 GGTACAGCTAGGCCACCTTCATTTGATTTTTTTTTCATTA--ATTCCCTT 767130 vv iv v v vv - - i v - -- v i C L1P4_orf2#LIN 2618 GGTAATGTGATGCCTCCGGC-TTTG-TTCTTTTTGC-TTAGGATTGCTTT 2572 chrXqtel1M 767131 GAA-ATTCTTGACCTTTTGTTTTTCCATATGAACTTTGTTGTTATTTTTT 767179 iv- vv vi v vv i ivvi vi C L1P4_orf2#LIN 2571 GGCTATTCGGGCTCTTTTTTGGTTCCATATGAATTTTAGAATAGTTTTTT 2522 chrXqtel1M 767180 CTAGGTC-AT-CAAAATAGTTTTGGGGAAGTCTGATTGGTATAGCGCTAA 767227 iv -i -v iiiv v-- i v v i i C L1P4_orf2#LIN 2521 CTAATTCTGTGAAAAATGACGTTGGT--AGTTTGATAGGAATAGCGTTGA 2474 chrXqtel1M 767228 ATAAATAGATAATTTTAGGTAATATTGTCATCTTTATTATATT--TTCTC 767275 vvi vii i i i v i i v iv -- - C L1P4_orf2#LIN 2473 ATCTGTAGATTGCTTTGGGCAGTATGGCCATTTTAACGATATTGATTCT- 2425 chrXqtel1M 767276 GCCCAATCCAAGAGCACTTAATATTTTTCCAGTTGGTTAGATCAGACTTT 767325 -i v ivv i v v ivi vvi? v C L1P4_orf2#LIN 2424 -TCCAATCCATGAGCATGGAATGTTTTTCCATTTGTTTGTGTCATCTNTG 2376 chrXqtel1M 767326 ATTTGTGTGGAAAGTGTTTCGTAGTTTTGCTCATAAAG-TTTCTGATTTT 767374 v v viiv i i v ii i - i i v ii - C L1P4_orf2#LIN 2375 ATTTCTTTCAGCAGTGTTTTGTAGTTCTCCTTGTAGAGATCTTTCACCT- 2327 chrXqtel1M 767375 CCCTTGG-CAGATAGATTCCTAAATATTTTATACTATCAGTAGTTACTTT 767423 - -i iv ii vi v iv i i i v C L1P4_orf2#LIN 2326 -CCTTGGTTAGATGTATTCCTAGGTATTTTATTTTTTTTGTGGCTATTGT 2278 chrXqtel1M 767424 AAATAGGATTTC--TCTT--TGTGACTCTGACTGTTGGATTTTGTTAGTG 767469 i v -- -- v i v vi- i ---i v C L1P4_orf2#LIN 2277 AAATGGGATTGCGTTCTTGATTTGGCTCTCAGC-TTGAA---CGTTATTG 2232 chrXqtel1M 767470 ATATATAAGAATGCTGATGACTTATGTGGGTTTATTTTATAACCAGCAAC 767519 i i ii iv i v ivi v i v v v C L1P4_orf2#LIN 2231 GTGTATAGAAATGCTACTGATTTTTGTACATTGATTTTGTATCCTGAAAC 2182 chrXqtel1M 767520 TTTGCTAAAATTGTGGATTATTTCTAATAACTTTTTAGTAGAATCTCTGG 767569 i i i i vv i v iv i i i ii i i i C L1P4_orf2#LIN 2181 TTTACTGAAGTCGTTTATCAGTTCTAGGAGCCTTTTGGCGGAGTCTTTAG 2132 chrXqtel1M 767570 GGTTCTCTAAGTATACCATCATATCATCAGCAAAGAGTGATAATTTGGTT 767619 i i vv i i v i ii C L1P4_orf2#LIN 2131 GGTTTTCTAGGTATAGAATCATATCGTCAGCGAAGAGAGATAGTTTGACT 2082 chrXqtel1M 767620 TCCTCATTGCCTACTCTAATTCCTTTAATCTCTTTCTCAACTCTTATTGC 767669 i v v i ivi v v i vvvi v C L1P4_orf2#LIN 2081 TCTTCTTTTCCTATTTGGATGCCTTTTATTTCTTTCTCTTGCCTGATTGC 2032 chrXqtel1M 767670 CAAAGCTAGCATATCTAATACAATATTAAATAGTAATGGTGATAGTGGGC 767719 ivvi v iv i i v i i v i v C L1P4_orf2#LIN 2031 TCTGGCTAGGACTTCCAGTACTATGTTGAATAGGAGTGGTGAGAGTGGGC 1982 chrXqtel1M 767720 AACCTT 767725 v C L1P4_orf2#LIN 1981 ATCCTT 1976 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 42.34 CpG sites = 227, Kimura (unadjusted) = 44.06 Transitions / transversions = 1.19 (227/191) Gap_init rate = 0.04 (57 / 1316), avg. gap size = 1.33 (76 / 57) 17 18.53 0.00 0.00 chrXqtel1M 768086 768116 (231884) (A)n#Simple_repeat 1 31 (0) m_b372s252i13 15546 chrXqtel1M 768086 AAAAAAATTAAAAAACAAAAAACAAAACAAA 768116 vv v v v (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 31 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 467 34.28 1.42 0.47 chrXqtel1M 768131 768341 (231659) MamRTE2#LINE/RTE-BovB 115 327 (1225) m_b372s551i18 15547 chrXqtel1M 768131 TGATATGGTTTCTACTGTCTGACAACTCCAGGAGAAATGCCAAGAGCAAA 768180 i i ii iii v i ? i i v MamRTE2#LINE/ 115 TGATACGGTCTTCACTGCTCGCCAGCTNCAGGAAAAATGCCAAGAACAAC 164 chrXqtel1M 768181 ACAGAGGTCTATTTAGAACATTTGTTTGAC-TGACCAAGGCCTTTGACAC 768229 i i vv v v vii v i-i i - v vv v MamRTE2#LINE/ 165 ATAAACCTCTTTATATGGCCTTC-CTCGACNTCAGGAAGGCCTTTGACTC 213 chrXqtel1M 768230 TGTCAATCATGCGGGTTTGTGGAAGATCATGGCAAAATTTGGTTGCTGAA 768279 i i vi vv i iv vvii i v v iv v MamRTE2#LINE/ 214 TGTCAGTCGTGAAGCATTGTGGAGGATTCTTCTGAAGTATGGATGCCCAC 263 chrXqtel1M 768280 AGAAATTCATTGATATTGTACACCAATTCCATGACAACATATTTGCAGT- 768328 vi i iivi v v i vii i iii iivv - MamRTE2#LINE/ 264 CAAAATTCGTCACCATTCTCCGCCTGCTCTATGACGGTATGCGAGCAGTG 313 chrXqtel1M 768329 TTCTTCA-TAGTGG 768341 v i - i MamRTE2#LINE/ 314 GTCCTCAGTAATGG 327 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 40.83 CpG sites = 42, Kimura (unadjusted) = 47.88 Transitions / transversions = 1.40 (42/30) Gap_init rate = 0.02 (4 / 210), avg. gap size = 1.00 (4 / 4) 266 35.77 0.81 0.00 chrXqtel1M 768894 769016 (230984) MamRTE1#LINE/RTE-BovB 3087 3210 (602) m_b372s601i8 15548 chrXqtel1M 768894 TTTGGGAAGCTCTGAAGGAAAGTGTGGAAGAAAAGAGGTATTAGACTTCC 768943 i vvv iiv i vivv v v i i ii i v MamRTE1#LINE/ 3087 TTTGGGAGGCTGGCAGACAGAGTGTGGCGCCAACGTGGCATCAAGCTCCA 3136 chrXqtel1M 768944 TAGCAAACTGAAGATCTACAGAGTTGTTGTGCTGACCTCATTGCCATATG 768993 v v i i ivi v i ? v vvvi v i? i MamRTE1#LINE/ 3137 GACCAAACTAAAGGTCTACAGAGCGATAGCGNTGTCCAACCTTCTNTACG 3186 chrXqtel1M 768994 TCTGTAAAATCTGCA-CTGTTACA 769016 v i i i v - ii MamRTE1#LINE/ 3187 GCTGTGAGACCTGGACCTGCCACA 3210 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 44.74 CpG sites = 23, Kimura (unadjusted) = 51.00 Transitions / transversions = 1.10 (23/21) Gap_init rate = 0.01 (1 / 122), avg. gap size = 1.00 (1 / 1) 294 31.69 4.19 1.75 chrXqtel1M 769604 769770 (230230) C L1MC5_3end#LINE/L1 (2164) 530 360 m_b372s551i19 15549 chrXqtel1M 769604 TACCACAGCTTGTTTAGCCATTCCCCAATGGATGT-CATGTCCTCGATTT 769652 i i i i i v v v v- v vvvivi C L1MC5_3end#LI 530 TACCATAGTTTATTCAACCAGTCCCCTATTGATGGACATTTGGGTTGTTT 481 chrXqtel1M 769653 TCAATTTTTTGCCACCTCAAAAAGAGCTGTAAC---TCTTTTTGCACATA 769699 i i i i iiv v v i i--- vvii ii C L1MC5_3end#LI 480 CCAGTCTTTTGCTATTACAAATAGTGCTGCAATGAATAGCCTTGTGCATA 431 chrXqtel1M 769700 TAGGTCCTTTTCTTATTCTTTTGA---TCTCTTTGGGATACAGGCCAAAT 769746 i-- - v i viv --- v v vv v iv C L1MC5_3end#LI 430 C--GTC-TTTTCGTATTTTTGCCAGTGTATCTTTGGGATAGATTCCTAGA 384 chrXqtel1M 769747 AGTGAGAATGATGGGTGAAAGAAT 769770 i v v v ii C L1MC5_3end#LI 383 AGTGGGATTGCTGGGTCAAAGGGT 360 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 40.77 CpG sites = 26, Kimura (unadjusted) = 41.81 Transitions / transversions = 1.00 (26/26) Gap_init rate = 0.04 (6 / 166), avg. gap size = 1.67 (10 / 6) 529 18.51 0.74 7.94 chrXqtel1M 771759 771893 (228107) MIRc#SINE/MIR 2 127 (141) m_b372s601i9 15550 chrXqtel1M 771759 GGGGCAGCTAGGTGGTGCAGTGGATAGAGCACCAGCCCTGAAGTCAGGAG 771808 i i--- v ii v i i i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chrXqtel1M 771809 GACCTGAGTTCAAATCTAGTCTCAGACACTTAACACTTCCTAGCTGTGTG 771858 i i i iv v v v ------- MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTG 91 chrXqtel1M 771859 ACCCTGGGGAAGTCACTTAACCCCAATT-GCCTCAG 771893 i v i vv v- MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAG 127 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 20.34 CpG sites = 13, Kimura (unadjusted) = 21.34 Transitions / transversions = 1.30 (13/10) Gap_init rate = 0.08 (11 / 134), avg. gap size = 1.00 (11 / 11) 368 30.46 0.57 0.57 chrXqtel1M 772017 772191 (227809) C L1ME3G_3end#LINE/L1 (294) 630 456 m_b372s551i20 15551 chrXqtel1M 772017 TGCTTGTTGAGCTCAGCA-TCTGTTTGTGTAAATCTTTCCAAGCCTTTCT 772065 v vvi i - v i - v i v i vv vi C L1ME3G_3end#L 630 TGCTTTTTTCACTCAACAATATGTCT-TGGAGATCTTTCCATGTCAGTAC 582 chrXqtel1M 772066 AAAATGAGCTTGTTCATTATTTTTAAGAGAACAATAGTACTCCATTATTT 772115 v vv v vvi v v? vvvv i vi v C L1ME3G_3end#L 581 ATATAGATCTACCTCATTCTTTTTAACNGCTGCATAGTATTCCATAGTAT 532 chrXqtel1M 772116 TAATATACCACAATTTGTTCAGCTATTCCCCAACTGATAGACATCTACTC 772165 vi i i i i i v i i i vvi C L1ME3G_3end#L 531 GGATATACCATAATTTATTTAACCATTCCCCTATTGATGGACATTTAGGT 482 chrXqtel1M 772166 ATTTTCCGATTTTTTGCTACCAAAAA 772191 vv i i ii v C L1ME3G_3end#L 481 TGTTTCCAATTTTTCGCTATTACAAA 456 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 38.66 CpG sites = 23, Kimura (unadjusted) = 39.58 Transitions / transversions = 0.77 (23/30) Gap_init rate = 0.01 (2 / 174), avg. gap size = 1.00 (2 / 2) 381 26.45 0.00 0.00 chrXqtel1M 772071 772191 (227809) C L1ME3Cz_3end#LINE/L1 (421) 576 456 m_b372s551i21 15551 chrXqtel1M 772071 GAGCTTGTTCATTATTTTTAAGAGAACAATAGTACTCCATTATTTTAATA 772120 v v vv vv vvvv i i v v C L1ME3Cz_3end# 576 GATCTAGTTCATTCATTTTAACTGCTGTATAGTATTCCATTGTATGAATA 527 chrXqtel1M 772121 TACCACAATTTGTTCAGCTATTCCCCAACTGATAGACATCTACTCATTTT 772170 i i v i v i i i vvivv C L1ME3Cz_3end# 526 TACCACAATTTATTTATCCATTCCCCTATTGATGGACATTTAGGTTGTTT 477 chrXqtel1M 772171 CCGATTTTTTGCTACCAAAAA 772191 i i ii v C L1ME3Cz_3end# 476 CCAATTTTTCGCTATTACAAA 456 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 31.51 CpG sites = 13, Kimura (unadjusted) = 32.68 Transitions / transversions = 0.68 (13/19) Gap_init rate = 0.00 (0 / 120), avg. gap size = 0.0 (0 / 0) 589 30.14 4.78 4.78 chrXqtel1M 772258 772905 (227095) L1M5_orf2#LINE/L1 2647 3294 (0) m_b372s551i22 15552 chrXqtel1M 772258 GTCATCAAAACCATTAAGTATTAGC-TAAGAA---ACAGAATACTCGATC 772303 v i vi vvi i - i --- - --- L1M5_orf2#LIN 2647 GTAATCAAGACAGTGTGGTATTGGCGTAAGGATAGACA-AATA---GATC 2692 chrXqtel1M 772304 AATGGAATAGGTTAG---GTTCACAGAACAAAATAGTTAATTAC-----T 772345 i iv --- i ------i -- vii ----- L1M5_orf2#LIN 2693 AATGGAACAGAATAGAGAGTCCA------GAAATAG--ACCCACACATAT 2734 chrXqtel1M 772346 ATAGCAATATAGTGTTTGACAAAC---CCAAAG-ACTCCAGCTTGGGGAT 772391 i ?v ?v ii v v--- ? - v i -- - L1M5_orf2#LIN 2735 ATGGNCANTTGATTTTTGACAAAGGTGCCAANGCAATTCAG--TGGGGA- 2781 chrXqtel1M 772392 AAGAATTCACTATTTGACAAAAACTTCTGGAAAAATTGGAAACTAGTATG 772441 i vvv v ii viv v v v iivi L1M5_orf2#LIN 2782 AAGGATAGTCTTTTCAACAAATGGTGCTGGAACAATTGGATATCCATATG 2831 chrXqtel1M 772442 GTAGAAATTAGGCAGTGACCCACATCTGACATCATATACCAAGATAAGGT 772491 v i v iii?vvi vi i v i i v i v iv L1M5_orf2#LIN 2832 GAAAAAAATGAANCTCGACCCCTACCTCACACCATACACAAAAATTAATT 2881 chrXqtel1M 772492 CTAAATGGGTTCAT-GATCTAGACATAAAGAATGATATTATAAACAAATT 772540 ? i i - - i i ii ii? i v i vvvvi L1M5_orf2#LIN 2882 CNAGATGGAT-CATAGACCTAAATGTAAAAGNTAAAACTATAAAACTTCT 2930 chrXqtel1M 772541 AGACGAA--CATAGGATAGTTTATCTCTCAGATTTGTGGAGGAGGAAGGA 772588 v -- v i -- iivv ii - i?v v iii L1M5_orf2#LIN 2931 AGAAGAAAACATAGGAGAAT--ATCTTCGTGACCT-TGGGNTAGGCAAAG 2977 chrXqtel1M 772589 ATTTGTGACCAAAGAAGA-ACTAGA--CATTCATTATTGATCACAAAATA 772635 v ---i v i - v i -- i?v ii vi vv v v L1M5_orf2#LIN 2978 ATTTCT---TAAACAGGACACAAAAAGCACNAACCATAAAAGAAAAAATT 3024 chrXqtel1M 772636 GAAAATTTTGATTATATCAAATTGAAAAGTTTTTGTACAAATAAAACTAA 772685 v v v i ?i v v ii i iv ?vvv ivi v L1M5_orf2#LIN 3025 GATAAATTGGACTNCATCAAAATTAAAAACTTCTGCTCNTCAAAAGACAC 3074 chrXqtel1M 772686 TGTAGACAAGATTAGAAGGGAAGCAATGAACTGGGAAAACATTTTTTACT 772735 i vi v i v i v v iii ? i v ----- i L1M5_orf2#LIN 3075 CGTTAAGAAAATGAAAAGGCAAGCCACAGANTGGGAGAAAAT-----ATT 3119 chrXqtel1M 772736 TGCAA---AGGT-TCTGATAAAGGCCTCATTTCTAAAATATATAGAGAAT 772781 --- vi - i v i v i i i i L1M5_orf2#LIN 3120 TGCAANACATATATCTGACAAAGGACTCGTATCCAGAATATATAAAGAAC 3169 chrXqtel1M 772782 TGACTCAAATTTATGAGAATTAAAGCCATTC--TCCAATTGATGAATGGT 772829 vviv ? iv i ? -- v vv --i v? vi v L1M5_orf2#LIN 3170 TCCTACAANTCAATAANAA--AAAGACAAACAACCCAATANAAAAATGGG 3217 chrXqtel1M 772830 GAAAGGACACGAACAGACAATTTTCAGATGAAGAAATTGAAA---CCATT 772876 v i vi v iv i v v ?v --- -- L1M5_orf2#LIN 3218 CAAAAGACTTGAACAGACACTTCACAAAAGAAGATATNCAAATGGCCA-- 3265 chrXqtel1M 772877 CTAGTCATATGAAAAAATGCTCTACATCA 772905 v iv i i v ? L1M5_orf2#LIN 3266 ATAAGCACATGAAAAGATGCTCAACNTCA 3294 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 39.45 CpG sites = 96, Kimura (unadjusted) = 40.57 Transitions / transversions = 1.07 (96/90) Gap_init rate = 0.07 (45 / 647), avg. gap size = 1.38 (62 / 45) 1423 31.51 1.89 1.57 chrXqtel1M 772760 773394 (226606) L1ME4c_3end#LINE/L1 4 640 (190) m_b372s551i24 15552 chrXqtel1M 772760 ATTTCTAAAATATATAGAGAATTGACTCAAATTTATGAGAATTAAAGCCA 772809 v ?v ? i ii v i v i vv ? v v L1ME4c_3end#L 4 ATATCTNTANTATATAAAGAGCTCATTCAAATTGATAAGAAAAANATCAA 53 chrXqtel1M 772810 TTCTCCAATTGATGAATGGTGAAAGGACACGAACAGACAATTTTCAGATG 772859 vv i v i vv i iv ? v L1ME4c_3end#L 54 GACCCCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAG 103 chrXqtel1M 772860 AAGAAATTGAAACCATTCTAGT-------CATATGAAAAAATGCTCTACA 772902 i ---- v ? -- ------- i i i v v L1ME4c_3end#L 104 AGGAAAT----ACAANT--AGTAAACAAACACATGGAAAAATGTTCAACC 147 chrXqtel1M 772903 TCACTACTGATCAGAGAAATGCAAATTAAGACAACTCTGAAGCACCACCC 772952 i v i i ii vv iii iii L1ME4c_3end#L 148 TCGCTAGTAATCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTT 197 chrXqtel1M 772953 ATATACTTGTCAGATTGGCTAAGATGACAGGAAAAGATAATGATGAATGT 773002 - ii i i i i i v i vvv ii vv iviv i L1ME4c_3end#L 198 -TACGCCTATTAAATTAGCAAAAATTTAAAAAATTGATAATACCCAATGC 246 chrXqtel1M 773003 TGGAGGGAATGTGGGAAAACTG--ACACTGATACATTGTTGGTGGAACTA 773050 v i i? i vi -- ? v i v ? i L1ME4c_3end#L 247 TGGCGAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGGCANTG 296 chrXqtel1M 773051 TGAATGGATCCAACCATTCTGGAGAACAATTTGGAACTGTGCTCAAAAAG 773100 i v i v v i i i v v ii iviv i L1ME4c_3end#L 297 TAAATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTATCAAGAG 346 chrXqtel1M 773101 TTGTCAAACTGTGCCCACCCTTTGAGCCAGCAATGTTACTACTGGGCTTA 773150 iii v v v vi v i vii v vv v L1ME4c_3end#L 347 CCATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGGGAATT 396 chrXqtel1M 773151 TATCCCAAAGACAT--CTTAAAGGAGGGAAAGGGACCCACATGTGCAAGA 773198 i i v --i i i i ii -- i i ii i ii L1ME4c_3end#L 397 TATCCTAAGGAAATAATTCAAAAGAAGGAAAAAG--CTATATGCACGAAG 444 chrXqtel1M 773199 ATGTTTGTGGCAGCCCTCTTTGTAGCGGC-CAGAACTGAAAACTAAGTGG 773247 ii v vi v i iii -v i i i v vv ii L1ME4c_3end#L 445 ATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACAACCTAA 494 chrXqtel1M 773248 ATGCCCATCAGTTGGAGAATGACTGAATAAATCAGGGTATATGAATGTTA 773297 i v i v i ii i i i v i v? iviv L1ME4c_3end#L 495 ATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCNACTCGA 544 chrXqtel1M 773298 TGGAATATTATTGTTCTATAAGAAATGACCAGCAGGATGCTTTCAGAGAG 773347 vvvv i v i iv vi v v vi viiv vi L1ME4c_3end#L 545 TGGAATATTATGCAGCCATTAAAAATGATAATTATGAAGACTATGTAGCA 594 chrXqtel1M 773348 GCGTAGAAAGACTTGCATGAACTGATGCGAAGTGAAATGAGCAGAAT 773394 i i i - iv vi vv i iv vi L1ME4c_3end#L 595 ACATGGAAA-ATGTTTATGATATAATGTTAAGTGAAAAAAGCAGAAT 640 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 41.23 CpG sites = 114, Kimura (unadjusted) = 43.00 Transitions / transversions = 1.37 (114/83) Gap_init rate = 0.02 (14 / 634), avg. gap size = 1.57 (22 / 14) 1474 27.40 2.19 2.94 chrXqtel1M 772760 773308 (226692) L1ME3G_3end#LINE/L1 4 548 (376) m_b372s551i23 15552 chrXqtel1M 772760 ATTTCTAAAATATATAGAGAATTGACTCAAATTTATGAGAATTAAAGCCA 772809 v i i i i vviv iv i -- v L1ME3G_3end#L 4 ATATCCAGAATATATAAAGAACTCCTACAAATCAATAAGAA--AAAGACA 51 chrXqtel1M 772810 TTCTCCAATTGATGAATGGTGAAAGGACACGAACAGACAATTTTCAGATG 772859 --vi v vi vv i i i iv v L1ME3G_3end#L 52 --ACCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAG 99 chrXqtel1M 772860 AAGAAATTGAAA---CCATTCTAGTCATATGAAAAAATGCTCTACATCAC 772906 i vv --- --v iv i v v L1ME3G_3end#L 100 AGGAAATACAAATGGCCA--ATAAACATATGAAAAGATGCTCAACCTCAC 147 chrXqtel1M 772907 TACTGATCAGAGAAATGCAAATTAAGACAACTCTGAAGCACCACCCATAT 772956 v i i i vv iii iii- vi L1ME3G_3end#L 148 TAGTAATCAGGGAAATGCAAATTAAAACAACAATGAGATACCATTT-TTC 196 chrXqtel1M 772957 ACTTGTCAGATTGGCTAAGATGACAGGAAAA----GATAATGATGAATGT 773002 iii v i ----vv ---- ivi? i L1ME3G_3end#L 197 ACCCATCAGATTGGCAAAAAT----TTAAAAGNTTGATAATATCNAGTGT 242 chrXqtel1M 773003 TGGAGGGAATGTGGGAAAACTG--ACACTGATACATTGTTGGTGGAACTA 773050 v i ii i v -- v v i i i v i L1ME3G_3end#L 243 TGGCGAGGGTGTGGGGAAACGGGTACTCTCATACACTGCTGGTGGGAGTG 292 chrXqtel1M 773051 TGAATGGATCCAACCATTCTGGAGAACAATTTGGAACTGTGCTCAAAAAG 773100 i v i v i ? i ii v v i - vvv i L1ME3G_3end#L 293 TAAATTGGTACAGCCNTTTTGGAGGGCAATTTGGCAGTAT-CTATTAAAA 341 chrXqtel1M 773101 TTGTCAAACTGTGCCCACCCTTTGAGCCAGCAATGTTACTACTGGGCTTA 773150 -- i v i vi v vii v ? ?v v L1ME3G_3end#L 342 T--TTAAAATGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATC 389 chrXqtel1M 773151 TATCCCAAAGACAT-CTTAAAGGAG-GGAAAGGGACCCACATGTGCAAGA 773198 i ? v - iiv viv - v v i --?i i i L1ME3G_3end#L 390 TATCCTANAGAAATACTCGCACATGTGCACAAGGA--NGCATGTACAAGG 437 chrXqtel1M 773199 ATGTTTGTGGCAGCCCTCTTTGTAGCGGC-CAGAACTGAAAACTAAGTGG 773247 ii v vi v iii -v i i i v vv ii L1ME3G_3end#L 438 ATGTTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAA 487 chrXqtel1M 773248 ATGCCCATCAGTTGGAGAATGACTGAATAAATCAGGGTATATGAATGTTA 773297 i i v i ii i i v vv ii L1ME3G_3end#L 488 ATGTCCATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTA 537 chrXqtel1M 773298 TGGAATATTAT 773308 i L1ME3G_3end#L 538 TGGAATACTAT 548 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 34.70 CpG sites = 83, Kimura (unadjusted) = 35.34 Transitions / transversions = 1.32 (83/63) Gap_init rate = 0.04 (22 / 548), avg. gap size = 1.27 (28 / 22) 15 20.74 5.13 0.00 chrXqtel1M 773625 773663 (226337) (TA)n#Simple_repeat 1 41 (0) m_b372s252i14 15553 chrXqtel1M 773625 TATATAAATATATATGCATATAT-TGGATTTA-ACATATAT 773663 v ii - iv v - i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATAT 41 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2) 202 24.17 3.19 3.19 chrXqtel1M 773805 773898 (226102) C L2a_3end#LINE/L2 (74) 443 350 m_b372s601i10 15554 chrXqtel1M 773805 AATTAAAAAAAAAAATTAAAAAATCTCTGTCCTCAGGGAATTTAAATTCT 773854 i v v v i i-- i i i v ii v C L2a_3end#LINE 443 AGTGAACAAAACAGAC--AAAAGTCCCTGCCCTCATGGAGCTTACATTCT 396 chrXqtel1M 773855 ACTTGGGGAGTAAGAGG-AATAAATAAACAAATA--CAAAATATATA 773898 v - i vi v i- i i --i C L2a_3end#LINE 395 AGT-GGGGGGAGACAGACAATAAACAAATAAATAAGTAAAATATATA 350 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 30.01 CpG sites = 14, Kimura (unadjusted) = 30.01 Transitions / transversions = 1.75 (14/8) Gap_init rate = 0.05 (5 / 93), avg. gap size = 1.20 (6 / 5) 596 28.70 7.87 2.62 chrXqtel1M 773909 774162 (225838) MIRc#SINE/MIR 2 268 (0) m_b372s601i11 15555 chrXqtel1M 773909 GAGGCAGCAAGGTACTACAGTGGATAGAGCATC-----TGGAGACAG-AT 773952 i--- iv i v ii----- v - v MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chrXqtel1M 773953 GCTCTGTGTTCCAATCCTGCCTCACATGTTTATAAGATGTATGGTTCTGT 774002 vi v v i i v vvviii iv v i iiii v MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 98 chrXqtel1M 774003 GAAAGTCATTTAATCCTTTCTCAACTTCAGTCTCCTCCACTCTAAAGTGG 774052 v i - i v i i i vv v i MIRc#SINE/MIR 99 GCAAGTCACTTAA-CCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGG 147 chrXqtel1M 774053 AGAAAATAACAGCACTTGTCCTG---------TAGGGCTGCTATGACAAT 774093 i v ---i i i ---------i i i i vi MIRc#SINE/MIR 148 GGATAATAA---TACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGAT 194 chrXqtel1M 774094 CAACAGAGATAGCAAATGTTGAA-TTCTTTGTAAACCCTGAAGTATTATA 774142 vv iiiv vi -iv iv i ii MIRc#SINE/MIR 195 CAAATGAGATAATGTATGTGAAAGCGCTTTGTAAACTGTAAAGTGCTATA 244 chrXqtel1M 774143 GAAATGC----TATTATTATTATT 774162 v i----?i MIRc#SINE/MIR 245 CAAATGTAAGGNGTTATTATTATT 268 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 36.24 CpG sites = 43, Kimura (unadjusted) = 37.58 Transitions / transversions = 1.54 (43/28) Gap_init rate = 0.05 (12 / 253), avg. gap size = 2.25 (27 / 12) 242 23.33 1.64 1.64 chrXqtel1M 774179 774239 (225761) L2c_3end#LINE/L2 406 466 (12) m_b372s601i12 15556 chrXqtel1M 774179 TCCCATTCAGTTTCATATTCTCCAGTGCCTTGAACATAGTAGGTGCT-AA 774227 ii vi ii i - i v v i - L2c_3end#LINE 406 TCTTATTCATCTTTGTATCC-CCAGCGCCTGGCACATAGTAGGCGCTCAA 454 chrXqtel1M 774228 TAAGTGCTTATT 774239 i i i L2c_3end#LINE 455 TAAATGTTTGTT 466 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 24.69 CpG sites = 11, Kimura (unadjusted) = 29.58 Transitions / transversions = 3.67 (11/3) Gap_init rate = 0.03 (2 / 60), avg. gap size = 1.00 (2 / 2) 1019 27.40 5.95 1.83 chrXqtel1M 774554 774973 (225027) C L1ME4c_3end#LINE/L1 (390) 440 4 m_b372s551i25 15557 chrXqtel1M 774554 GTACATATGTCCTTTTCCCTCCTTTAAG--ATTTCCACTGGATACAGACC 774601 i iv i i i i i-- viv v vv C L1ME4c_3end#L 440 GTGCATATAGCTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAATTCC 391 chrXqtel1M 774602 CAGTAATGACACTTCTGGGTCAAAGGGTACACACAGTTTTATAGCCCTTT 774651 v i iv i v iiv v i i v C L1ME4c_3end#L 390 CAGAAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTCTTG 341 chrXqtel1M 774652 GGGCATAGTTCCAGATTGCTCTCGAGAATGGTTGGATCATTTCACAACTC 774701 ivi i v v i i v i v v i v i ?iv C L1ME4c_3end#L 340 ATACGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACANTGC 291 chrXqtel1M 774702 CACCAACAATGCAT----------------CC---CCCTCCCCA-CATTT 774731 i i ---------------- ---? v - v C L1ME4c_3end#L 290 CACCAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGCATTG 241 chrXqtel1M 774732 ATCATTATCTTTTCCTGTAATCTTAGCTAATCTGAAAGGTGTGAGGTGGT 774781 ivi vv ii vv i v i i v i i ii C L1ME4c_3end#L 240 GGTATTATCAATTTTTTAAATTTTTGCTAATTTAATAGGCGTAAAATGGT 191 chrXqtel1M 774782 ACCTCAGAGCTGTCTTAATTTGCATTTCTCTGATCAATAGTGA--TTCAG 774829 i vv i ii i i v i -- -- C L1ME4c_3end#L 190 ATCTCATTGTTGCTTTAATTTGCATTTCTTTGATTACTAGCGAGGTT--G 143 chrXqtel1M 774830 AGCATTTTTTTTTTTCATATAACTATAGATGGTTTTAATTTTCTCATCTG 774879 i i----- i ivi i vv ivi? vv i v ? C L1ME4c_3end#L 142 AACATTTTTC-----CATGTGTTTGTTTACTANTTGTATTTCCTCTTNTG 98 chrXqtel1M 774880 AAAATTGTCTGTTCATACCTTTTGACCATTTATCAGTTGGAG-AATGACT 774928 vi ii i v vi i -vv i? C L1ME4c_3end#L 97 TGAATTGTCTGTTCATGTCCTTTGCCCATTTATCTATTGGGGTCTTGATN 48 chrXqtel1M 774929 TGTATTCTTATAAATTTGACACAATTCTTTATATATTTTAGAAAT 774973 v - v vvv ii ? v? v C L1ME4c_3end#L 47 TTT-TTCTTATCAATTTGAATGAGCTCTTTATATANTANAGATAT 4 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 34.38 CpG sites = 62, Kimura (unadjusted) = 35.54 Transitions / transversions = 1.22 (62/51) Gap_init rate = 0.03 (14 / 419), avg. gap size = 2.36 (33 / 14) 309 30.61 4.83 4.06 chrXqtel1M 774838 775106 (224894) C L1P3_orf2#LINE/L1 (11) 3283 3013 m_b372s551i26 15557 chrXqtel1M 774838 TTTTTTTCATATAACTATAGATGGTTTTAATTTTCTCATCTGAAAATTGT 774887 ivi i v iiv iv v v ii v i i v C L1P3_orf2#LIN 3283 TTTTTTTCATATGTTTGTTGGCCGCATAAATGTCTTCTTTTGAGAAGTGT 3234 chrXqtel1M 774888 CTGTTCATACCTTTTGACCATTTATCAGTTGGAGAATGACTTG---TATT 774934 i i i v i - iv v i -- vii --- v C L1P3_orf2#LIN 3233 CTGTTCATATCCTTCGCCCACTT-TTTGATGGGG--TTGTTTGTTTTTTT 3187 chrXqtel1M 774935 CTTATAAATTTGACACAATTCTTTATATATTTTAGAAATGAGATCTTTAT 774984 i vivv i i i v i i v v vi i C L1P3_orf2#LIN 3186 CTTGTAAATTTGTTTAAGTTCCTTGTAGATTCTGGATATTAGCCCTTTGT 3137 chrXqtel1M 774985 CAGAAACACTGGCTGTAAAGAATTTTTTCCTAGTTT-TA--CTTCCT-TT 775030 viv iv ii i - i i v i - --i v - C L1P3_orf2#LIN 3136 CAGATGGATAGATTGCAAA-AATTTTCTCCCATTCTGTAGGTTGCCTGTT 3088 chrXqtel1M 775031 TAATCTT------GTTTCTTTTGGTTTTGTTTATGCAAAACCTTTTTAAT 775074 i v v------ -------i i i v i i C L1P3_orf2#LIN 3087 CACTCTGATGATAGTTTCTTTTG-------CTGTGCAGAAGCTCTTTAGT 3045 chrXqtel1M 775075 TTAATATAATCAAAGTTGGCCATTTTGCCTTT 775106 vvi vv v v v v C L1P3_orf2#LIN 3044 TTAATTAGATCCCATTTGTCAATTTTGGCTTT 3013 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 39.54 CpG sites = 43, Kimura (unadjusted) = 40.20 Transitions / transversions = 1.19 (43/36) Gap_init rate = 0.06 (16 / 268), avg. gap size = 1.50 (24 / 16) 13 24.32 2.00 2.00 chrXqtel1M 775345 775394 (224606) (TTAAATA)n#Simple_repeat 1 50 (0) m_b372s252i15 15558 chrXqtel1M 775345 TTAACCAATAAATATTAAGTATGTTAA-AGTATATGTTAAATATAATATA 775393 vi v i - v - v v i v v (TTAAATA)n#Si 1 TTAAATATTAAATATTAAATAT-TAAATATTAAATATTAAATATTAAATA 49 chrXqtel1M 775394 T 775394 (TTAAATA)n#Si 50 T 50 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.04 (2 / 49), avg. gap size = 1.00 (2 / 2) 468 28.42 5.14 4.65 chrXqtel1M 775760 775973 (224027) C L1ME5_3end#LINE/L1 (420) 521 307 m_b372s551i27 15559 chrXqtel1M 775760 TTACCAAT--ATTCTCCAATTGATGGGCGTCCACCAGTT---TCCAGTTT 775804 v -- i v v i ii --i --- ii i C L1ME5_3end#LI 521 TTACCTATCCACTCTCCCAGTGATGGACACCCA--GGTTGCCTCCAACTC 474 chrXqtel1M 775805 CT-GTCATTA-AAAGAGGGCTGCCACAAACATTCTGGCACATGCAGGTCC 775852 i- i ii - v iv v ii i v i ---- C L1ME5_3end#LI 473 CCCGCCACCACAAACAACGCTGCAATGAACATCCTCGTACATG----TCC 428 chrXqtel1M 775853 CTTTCC---CTTCTTTAAGATCTCTTTTGGGATATAAGCCCAGTAGAAAC 775899 i vi--- i v v i vi ii vi v viiv C L1ME5_3end#LI 427 CCTTATGGACCTGTGTGAGAATTTCTTTGGGATATATACCCAGGAGCGGA 378 chrXqtel1M 775900 ACTGCTGGATCAAAGGGTATGCAGAATCTGATAACTTT-TTGAGCACAGT 775948 i i v iv vv -- i v-i i i -- C L1ME5_3end#LI 377 ATTGCTGGGTCATAGGGTATGCGTATACT--TAATTTGACTAAGTAC--T 332 chrXqtel1M 775949 TCCAAACTGCTTTCCAGAATGGCTG 775973 v i i i C L1ME5_3end#LI 331 GCCAGATTGCTCTCCAGAATGGCTG 307 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 35.48 CpG sites = 37, Kimura (unadjusted) = 37.10 Transitions / transversions = 1.76 (37/21) Gap_init rate = 0.08 (16 / 213), avg. gap size = 1.31 (21 / 16) 19 0.00 0.00 0.00 chrXqtel1M 777597 777617 (222383) (A)n#Simple_repeat 1 21 (0) m_b373s252i0 15560 chrXqtel1M 777597 AAAAAAAAAAAAAAAAAAAAA 777617 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAA 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 420 26.94 0.00 2.31 chrXqtel1M 778925 779057 (220943) C L1ME3A_3end#LINE/L1 (348) 572 443 m_b373s551i0 15561 chrXqtel1M 778925 TCATCCTTTCCCATTTCTTGAGAACAATATTCCATAATATTCATTTACCA 778974 i i v i v --- v i i vi i vv v C L1ME3A_3end#L 572 TCGTTCATTCTCATTGCT---GTATAGTATTCCATTGTGTGAATATACCA 526 chrXqtel1M 778975 CAATTTATTCAGCCATTCTCCAATGGATGGGCATCCACTCAGTTTCCAGT 779024 i v v vi v i iiivvi? C L1ME3A_3end#L 525 CAATTTATTTATCCATTCTACTGTTGATGGACATTTGGGTNGTTTCCAGT 476 chrXqtel1M 779025 TTCTGGCCACTACAAAGAGGGCTGCCACAAACA 779057 ?? i i i v v i ii C L1ME3A_3end#L 475 TTNNGGCTATTACGAATAGTGCTGCTATGAACA 443 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 32.67 CpG sites = 20, Kimura (unadjusted) = 35.11 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.02 (3 / 132), avg. gap size = 1.00 (3 / 3) 461 33.13 8.97 5.20 chrXqtel1M 780493 781272 (218728) HERVP71A#LTR/ERV1 4618 5425 (2165) m_b373s701i0 15562 chrXqtel1M 780493 TTGTCAGAGGATGAATAG---GGCGGCCCAATGACAAGCCCCAAAAAGGA 780539 i i i i--- i iiivi vi i v iii - HERVP71A#LTR/ 4618 TTGTCAAAGGATAAACAAAAAGGTGATTAGAAAACAGGCCACGGGA-GGA 4666 chrXqtel1M 780540 AGGGTCCCTGGTATCAGGCCCTTTCCAAAGCATTCAGGTGGACTT-AC-G 780587 ivii i vv v i v - i i i - - HERVP71A#LTR/ 4667 AGACCTCCCGGACTAAGACCATTTC-AAAGCATTCAAGTAGATTTCACAG 4715 chrXqtel1M 780588 AGCCGCC--AATTAGTGGGCCCTCAA--ACCTGTTGGTCGA--GTGGACC 780631 ivi -- v - iivv v -- ii ii - -- i i HERVP71A#LTR/ 4716 AAATGCCCAAAGTAG-GAAGACTAAAGTATTTACTGGT-GATCGTAGATC 4763 chrXqtel1M 780632 ATCTGACCTTTATGGGTGGAGGCCTTCCCTTTGCTTCAGCAGTCA----- 780676 i vv vvi- i i ii v -- i i ----- HERVP71A#LTR/ 4764 ACCTTTCCGGC-TGGGTGGAAGCCTTTCCCCTCC--CAACAGCCACCGCC 4810 chrXqtel1M 780677 ----------TAAAAGTACCCTTTGAGCATATCATTCC-AGGGATGGGTT 780715 ---------- v i viv v i v ii v - ivv vi HERVP71A#LTR/ 4811 GGGAATGTGGTCAAAATAATATTAGAACAGATTGTACCTAGATTTGGCCT 4860 chrXqtel1M 780716 --TGGAACAGGAAGATTTGGACCAAGGCAAACCATTTCACAGCTAAGATC 780763 -- v vivv ii - v vi i i i vv v i i - HERVP71A#LTR/ 4861 GGTGGAAAATATTGATTCAGA-CAATGGGAGCCACTTTACCTCAAGGGT- 4908 chrXqtel1M 780764 CTTTAATCCGGGGCCC------AAGCCTAAAAAATATGTTGAATTTATAT 780807 -v --- vvi------ i ii v v vi v i vvi i HERVP71A#LTR/ 4909 -GTTAA---GGGGAATTATGGAAGGTTTACAAATTAGATGGGATTATCAC 4954 chrXqtel1M 780808 ACCTCATGGCATCCCA------AAGGAAAAGTGGAAAGGATGGATAAGGA 780851 i v v------vv i i i i v iiv HERVP71A#LTR/ 4955 ACCCCTTGGCATCCCCCTTCCTCTGGAAAGGTAGAAAGAATGAATCAAAC 5004 chrXqtel1M 780852 AATTAAACAGCAACTGACTAAATTGG-CTGAGACAC--AATTGCCCTGGA 780898 vv i v vv v i i ii- v v -- v i HERVP71A#LTR/ 5005 TCTCAAAAAGCATATCACCAAACTAATCTTAGAAACTAAAATGCCTTGGA 5054 chrXqtel1M 780899 CCAAGTGCCTTCCCCTTGC-CTTATTAAGAATAGAATAAAACCCCA--AA 780945 i i i vv v - iv i v i i-- i -- HERVP71A#LTR/ 5055 CCAAATGTCTCCCAATAGCACTCCTTAGGATTAGGAC--AGCCCCAAGAA 5102 chrXqtel1M 780946 GGAATGTGGGATTATCACCCTATGAG-TATTGTATGG--TCAAATTTTAT 780992 iii iv i v i - i -- vv v -- HERVP71A#LTR/ 5103 AAGACTTGGGATTGTCCCCCTACGAGTTATTATATGGGCTCCCATAT--T 5150 chrXqtel1M 780993 TAAAAGGGATTAAAATTCTTCCTTTGGAGCCAATATTTGAGACCTAAGGA 781042 iiivi ii v iv -------- v - v i - HERVP71A#LTR/ 5151 TGGGCAGGGCTACAGATCTTCCT--------ACTA-TGGAAACC-AAGGA 5190 chrXqtel1M 781043 TTTGTTTTTAAGGAA--ATGT----GCCATGT-CTGTA--CTG-CAAATC 781082 iivi i i -- i ---- i - vi -- - vvi HERVP71A#LTR/ 5191 CCAATTCTTAAGAAATTATATACTGGCCATATCCTCCACCCTGTCATCCC 5240 chrXqtel1M 781083 TGAAAAATTTAATCCAAAGGGCTTATTGCTCAGACCTCCCCTTTAGGGAT 781132 v ii--- ---- i v vi i ii v i v i - HERVP71A#LTR/ 5241 TTAGG---TTA----AAAGGACTTCTGACTCAAACTCCGCCTCTTGAG-T 5282 chrXqtel1M 781133 TCACAGTGCATAAGTTCTAGCTT---AACCCAGTCCTGGTTCGGATGT-G 781178 i i v iv v i i ---i i i v i vi iv - HERVP71A#LTR/ 5283 TCGCGGTTCACCACTTCCAGCCTGGCGACTCGGTGCTGATTAAGACTTGG 5332 chrXqtel1M 781179 AAGGAGGATAAGCT-GACCCAACCTTGGAAAGGATTGTTCCAGATCCTCT 781227 i i i -v v - i viiv vi ii v i HERVP71A#LTR/ 5333 AAAGAAGACAAGCTCCACCCAAGC-TGGGAAGGTCCCTATCAAGTGCTCC 5381 chrXqtel1M 781228 TGATATCAGACACAGCAAGGACCG-GTGGACACCTTAA----GGTGGACT 781272 i------ v vi v i - i i v v ---- HERVP71A#LTR/ 5382 TGAC------CACTGAGACGGCCGTGCGAACAGCTGAACGGGGGTGGACT 5425 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 43.42 CpG sites = 144, Kimura (unadjusted) = 45.44 Transitions / transversions = 1.43 (144/101) Gap_init rate = 0.09 (70 / 779), avg. gap size = 1.60 (112 / 70) 474 31.60 1.49 13.61 chrXqtel1M 781653 781771 (218229) HERV1_I#LTR/ERV1 8133 8230 (571) m_b373s701i1 15563 chrXqtel1M 781653 TGGCC-CCAGCACAGATTATCAAGGAATATGGACCGGTGACATAGGCCCA 781701 - v v vii iv v i i iv ? i ? HERV1_I#LTR/E 8133 TGGCCTCCTGAAAGAATTATCAAATACTATGGGCCAGCTACNTGGGCNCA 8182 chrXqtel1M 781702 AGATGGTAGTTA--GGGATATCGGACACCAGTGTGTGTGTGTATATATAT 781749 -- i -- ? i v v ------------ v i HERV1_I#LTR/E 8183 AGATGG--GTCATGGGGNTACCGTACTCC------------TATTTACAT 8218 chrXqtel1M 781750 ATTAAACATGTGGAAAATGTAT 781771 i ----------i v HERV1_I#LTR/E 8219 GTTAAAC----------CGAAT 8230 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 41.14 CpG sites = 66, Kimura (unadjusted) = 42.70 Transitions / transversions = 1.20 (12/10) Gap_init rate = 0.22 (26 / 118), avg. gap size = 1.04 (27 / 26) 43 0.00 0.00 0.00 chrXqtel1M 781772 781808 (218192) (TA)n#Simple_repeat 1 37 (0) c_b373s251i0 15564 chrXqtel1M 781772 TATATATATATATATATATATATATATATATATATAT 781808 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATAT 37 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 474 31.60 1.49 13.61 chrXqtel1M 781809 782091 (217909) HERV1_I#LTR/ERV1 8231 8491 (310) m_b373s701i1 15563 chrXqtel1M 781809 GTATTAAACAGATTAATTCAACTGCAAGCAATCTTAGAGGTAGCAGCTAA 781858 i ------ --------- i vi ii vii ii HERV1_I#LTR/E 8231 ATA------AGATT---------GCAAGCAGTACTAGAAATCATAGTCAA 8265 chrXqtel1M 781859 CCAAACTGCTGCTCAGGCCCTTAATTTATTAGCCGATG-AAGCCACCCAG 781907 iv v i--- ii i vi ii - i- i ? HERV1_I#LTR/E 8266 TGAAACAGCC---CGAGCCTTGGATTTGCTAGCC-ATACAGGCNACCCAG 8311 chrXqtel1M 781908 ACAAGAGAAGTAGTTTTATAACCTAGATTAGTTTTAAATTATCTGTTAGC 781957 ii v ivi v vvi vv ii iv i i vi HERV1_I#LTR/E 8312 ATGAGAGATGCCATATATCAAAATAGGCTAGCATTAGACTATCTCCTAGC 8361 chrXqtel1M 781958 AGAGGAAGGAGGAAGGGTCCAGGAGAGAAAAAACTTGGTCCACTTGTTGT 782007 vvvi --- iiiv i? i vvv i ii?v - i i HERV1_I#LTR/E 8362 CTCAGAAGGAGGA---GTTTGTGGNAAACTTAATTTGACNAACT-GCTGC 8407 chrXqtel1M 782008 ATGCAACTTGATGACAATGGACAAGCAGTGAAAGAAATTACTA--AGGAT 782055 v i v i vi v v vi i i-- HERV1_I#LTR/E 8408 TTACAAATCGATGACAATGGAAGAGCTGTCATGGAAATCACTGCCAGGAT 8457 chrXqtel1M 782056 ATTCGCAGGATAGTTCATGTGACTGTACAAATTTGG 782091 i-- v i v ii vv v v i ii HERV1_I#LTR/E 8458 G--CGGAAGTTAGCCCATGTCCCGGTCCAGACCTGG 8491 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 41.14 CpG sites = 66, Kimura (unadjusted) = 42.70 Transitions / transversions = 1.59 (54/34) Gap_init rate = 0.10 (27 / 282), avg. gap size = 1.04 (28 / 27) 719 26.57 9.08 2.80 chrXqtel1M 782814 783386 (216614) C L1PREC2_orf2#LINE/L1 (928) 2366 1759 m_b373s551i1 15561 chrXqtel1M 782814 AGAAGTGTTTTGTAATTGTGTTCATAGA-ATTTCTGGGTTTTTTTGGTAG 782862 v v vv ii - i i vivi iii v v C L1PREC2_orf2# 2366 AGCAGTGTTTTGTAATTCTCATTGTAGAGATCTTTCACCTCCCTGGTTAG 2317 chrXqtel1M 782863 ----ACCCCCGGCAGTATTTTATTTTGTCTACAG-AATTTTAAAATGAAA 782907 ---- ii ii -- i v i iii - v i - ii C L1PREC2_orf2# 2316 CTGTATTCCTAG--GTATTTTATTCTTTTTGTGGCAATTGTGAA-TGGGA 2270 chrXqtel1M 782908 TTTC-TTCCTA-------TCTC---TT---TGTTGATGGGCTTTTTAGAA 782943 v - i------- --- --- v -- v v i C L1PREC2_orf2# 2269 TTGCGTTCCTGATTTGGCTCTCGGCTTGGCTGTTGTTGG--TGTATAGGA 2222 chrXqtel1M 782944 ATGTTGATGATTTGTGTGGGTTT-TTTTAAATCC-GAAACTTTTGTAAAG 782991 i ii v ivi v- iv - vv i C L1PREC2_orf2# 2221 ATGCTAGTGATTTTTGTACATTGATTTTGTATCCTGAAACTTTGCTGAAG 2172 chrXqtel1M 782992 CTGTGAATT-GTTTCAGTAGGTTTTGG---------ATGAT-TTTTCTAG 783030 i vv i- i ?v v v --------- iv- C L1PREC2_orf2# 2171 TTGTTTATCAGCTNAAGGAGCTTTTGGGCCGAGACTATGGGGTTTTCTAG 2122 chrXqtel1M 783031 -----GATTCTTTATATCATCTGCAAAGAGTGATAGTTTTATCTTTCTCA 783075 ----- v --- i i v v v - i v C L1PREC2_orf2# 2121 ATATAGAATC---ATGTCGTCTGCAAACAGGGATAGTTTGA-CTTCCTCT 2076 chrXqtel1M 783076 TTGCTTATTCTAATTCCTTTTCCTTTCTTTTTTCTTTTCTTATTGCTAAA 783125 i v i ivi v i v- i - vi v vvi C L1PREC2_orf2# 2075 CTTCCTATTTGGATGCCCTTTA-TTTCTTTCT-CTTGCCTGATTGCTCTG 2028 chrXqtel1M 783126 GCCAG-ATTTCTAGTACAAAG--GAA-AATAGTGGTGGATAATGGGAACC 783171 - i i i v v -- - iv iivi v v v C L1PREC2_orf2# 2027 GCCAGGACTTCCAATACTATGTTGAATAGGAGTGGTGAGAGAGGGCATCC 1978 chrXqtel1M 783172 TTGTTTT-CACCTTTGATCTT-ATTGGGAATACATGCAGCTTTTCTCCAT 783219 i -ii --- i i - vv i v v vi C L1PREC2_orf2# 1977 TTGTCTTGTGCC---GGTTTTCAAGGGGAATGCTTCCAGCTTTTGCCCAT 1931 chrXqtel1M 783220 TATAG-ATAATGTTTGTTG--GGTTTTAGATAGATACTGCTTATTATTTT 783266 -i - i v i -- vvv iviv C L1PREC2_orf2# 1930 T-CAGTATGATGTTGGCTGTGGGTTTGTCATAGATGGCTCTTATTATTTT 1882 chrXqtel1M 783267 AAGGAAAGCTCCTTTTATCCCTATGCTCTCTTATG--TTTTTAATAGGAA 783314 i v v i iv v - i - v iv -- i v C L1PREC2_orf2# 1881 GAGGTATGTTCCTTCAATACCTA-GTT-TATTGAGAGTTTTTAACATGAA 1834 chrXqtel1M 783315 TGGGTGTTGTATTTTGTCAAAAGCATTTTCTGCATCTATTAAGATTTTCA 783364 v i v i i v i vv C L1PREC2_orf2# 1833 GGGATGTTGAATTTTATCGAAAGCCTTTTCTGCATCTATTGAGATAATCA 1784 chrXqtel1M 783365 TATGATTTCTG---TTGGTTTTGTT 783386 i i i --- i i C L1PREC2_orf2# 1783 TGTGGTTTTTGTCTTTAGTTCTGTT 1759 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 32.90 CpG sites = 79, Kimura (unadjusted) = 33.44 Transitions / transversions = 1.14 (79/69) Gap_init rate = 0.07 (39 / 572), avg. gap size = 1.77 (69 / 39) 746 27.25 5.72 2.04 chrXqtel1M 782903 783374 (216626) C L1M5_orf2#LINE/L1 (1032) 2262 1774 m_b373s551i2 15561 chrXqtel1M 782903 TGAAATTTC---TTCCTATCTCTTTGTTGATGGGCTTTTTAGAAATGTTG 782949 ? --- v - v v i -- v v iivi C L1M5_orf2#LIN 2262 TNAAATTTCATTTTCCAAT-TGTTTGTTGCTAG--TATATAGAAATACAA 2216 chrXqtel1M 782950 ATGATTTGTGTGGGTTT-TTTTAAATCCGA-AACTTTTGTAAAGCTGTGA 782997 v v ivi v-ii iv ?i-i i vv viiiivv C L1M5_orf2#LIN 2215 TTGATTTTTGTATATTGACCTTGTATCCNGCGACCTTGCTAAATTCACTT 2166 chrXqtel1M 782998 ATT-GTTTCAGTAGGTT--TTGGATGATTTTTCTAGGATTCTTTA----- 783039 - ii v -- v - i - ? i i ----- C L1M5_orf2#LIN 2165 ATTAGTTCTAGTAGTTTNTTTGTA-GATTCTT-TNGGATTTTCTACGTAN 2118 chrXqtel1M 783040 -------TATCATCTGCAAAGAGTGATAGTTTTATCTTTCTCATTGCTTA 783082 ------- i i v i? i i i - v v iv C L1M5_orf2#LIN 2117 ACAATCATGTCATCTGCGAATAANGACAGTTTTATTTCT-TCCTTTCCAA 2069 chrXqtel1M 783083 TTCTAATTCCTTTTCCTTTCTTTTTTCTTTTCTTATTGCTAAAGCCAG-A 783131 ii v v v- - vi vvvi i - C L1M5_orf2#LIN 2068 TCTTTATGCCTTTTA-TTTCTTTTT-CTTGCCTTATTGCACTGGCTAGGA 2021 chrXqtel1M 783132 TTTCTAGTACAAAGGAAAATAGTGGTGG--ATAATGGGAA-CCTTGTTTT 783178 ii i v vvi vi -- ? ii iv - i C L1M5_orf2#LIN 2020 CCTCCAGTACAATGTTGAATAGAAGTGGTGANAGCGGACATCCTTGTCTT 1971 chrXqtel1M 783179 CACCTTTGATCTTATTGGGAATACATGCAGCTTTTCTCCATTATAGATAA 783228 -iiiiii vv vi ? v i? v viv i C L1M5_orf2#LIN 1970 -GTTCCCGATCTTAGGGGGAAAGCNTTCAGTNTTTCACCATTAAGTATGA 1922 chrXqtel1M 783229 TGTTTGTTG--GGTTTTAGATAGATACTGCTTATTATTTTAAGGAAAGCT 783276 ? i -- vvi i ivi i vv i ivii C L1M5_orf2#LIN 1921 TGTTNGCTGTAGGTTTTTCGTAGATGCCCTTTATCAGGTTGAGGAAGTTC 1872 chrXqtel1M 783277 CCTTTTATCCCTATGCTCTCTTAT-GTTTTTAATAGGAATGGGTGTTGTA 783325 i i - i iv v v- vi v v C L1M5_orf2#LIN 1871 CCTTCTATTCCTA-GTTTGCTGAGAGTTTTTATCATGAATGGGTGTTGAA 1823 chrXqtel1M 783326 TTTTGTCAAAAGCATTTTCTGCATCTATTAAGATTTTCATATGATTTCT 783374 v v i vv i C L1M5_orf2#LIN 1822 TTTTGTCAAATGCTTTTTCTGCATCTATTGAGATGATCATATGATTTTT 1774 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 33.58 CpG sites = 69, Kimura (unadjusted) = 35.29 Transitions / transversions = 1.21 (69/57) Gap_init rate = 0.05 (22 / 471), avg. gap size = 1.68 (37 / 22) 763 27.25 2.64 2.04 chrXqtel1M 783037 783377 (216623) C L1MD_orf2#LINE/L1 (1181) 2113 1771 m_b373s551i3 15561 chrXqtel1M 783037 TTATATCATCTGCAAAGAGTGATAGTTTTATCTTTCTCATTGCTTATTCT 783086 i i v v i i i ii v v -- v C L1MD_orf2#LIN 2113 TCATGTCATCTGCAAATAGGGACAGTTTTATTTCTTCCTTTCC--AATCT 2066 chrXqtel1M 783087 A-ATTCCTTTTCCTTTCTTTTTTCTTTTCTTATTGCTAAAGCCAGA-TTT 783134 i- v vi i -- vi vvvi i -i C L1MD_orf2#LIN 2065 GTATGCCTTTTATTTCCTTTT--CTTGCCTTATTGCACTGGCTAGAACTT 2018 chrXqtel1M 783135 CTAGTACAAAG--GAA-AATAGTGGTGGATAATGGGAA-CCTTGTTTTCA 783180 i v v -- - v - v ii iv - ii -i C L1MD_orf2#LIN 2017 CCAGTACTATGTTGAATAAGAGTGGTG-AGAGCGGACATCCTTGCCTT-G 1970 chrXqtel1M 783181 CCTTTGATCTTATTGGGAATACATGCAGCTTTTCTCCATTATAGATAATG 783230 iiiii vv vi v ii v viv i C L1MD_orf2#LIN 1969 TTCCCGATCTTAGGGGGAAAGCATTCAGTCTTTCACCATTAAGTATGATG 1920 chrXqtel1M 783231 TTTGTTG--GGTTTTAGATAGATACTGCTTATTATTTTAAGGAAAGCTCC 783278 v i -- vvi i vi i vv i ivii C L1MD_orf2#LIN 1919 TTAGCTGTAGGTTTTTTGTAGATGCTCTTTATCAAGTTGAGGAAGTTCCC 1870 chrXqtel1M 783279 TTTTATCCCTATGCTCTCTTAT-GTTTTTAATAGGAATGGGTGTTGTATT 783327 i i i - i i? v v- vi v v C L1MD_orf2#LIN 1869 CTCTATTCCTA-GTTTNCTGAGAGTTTTTATCATGAATGGGTGTTGAATT 1821 chrXqtel1M 783328 TTGTCAAAAGCATTTTCTGCATCTATTAAGATTTTCATATGATTTCTGTT 783377 v v v i v vv i i v C L1MD_orf2#LIN 1820 TTGTCAAATGCTTTTTCTGCATCAATTGATATGATCATGTGATTTTTCTT 1771 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 33.62 CpG sites = 49, Kimura (unadjusted) = 34.54 Transitions / transversions = 1.17 (49/42) Gap_init rate = 0.04 (14 / 340), avg. gap size = 1.14 (16 / 14) 14 26.00 1.69 3.45 chrXqtel1M 783685 783743 (216257) (TTCTT)n#Simple_repeat 1 58 (0) m_b373s252i1 15565 chrXqtel1M 783685 TTCTTTTCTTCTC-TTCCTGTTCTAGACTTTCCTGTTCTGGCTTCCTTTC 783733 i - i v vvv i v --i i (TTCTT)n#Simp 1 TTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCT--TTTCTTTTC 48 chrXqtel1M 783734 CTCTCTTTTC 783743 i i (TTCTT)n#Simp 49 TTTTCTTTTC 58 Matrix = Unknown Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.05 (3 / 58), avg. gap size = 1.00 (3 / 3) 429 25.71 3.81 0.00 chrXqtel1M 788956 789060 (210940) C L2d_3end#LINE/L2 (6) 510 402 m_b373s601i0 15566 chrXqtel1M 788956 AGTCAGTCAACAAATATTTATTAAGCATTTATTATGGGCCTGACACTGTG 789005 i i i i iii i v iiii C L2d_3end#LINE 510 AATCAATCAACAAGTATTTATTGAGCGCCTACTATGTGCTCAGCACTGTG 461 chrXqtel1M 789006 CTAA--GATCTGGGATAC-ACATAAAAGCA-AAAACCCAGCCCCTGCCTT 789051 i-- v v iv - ? v ? i - i vii i i C L2d_3end#LINE 460 CTAGGCGCTGTGGGGAACGANAAAANAGTATAAGACATGGTCCCTGCCCT 411 chrXqtel1M 789052 CAAAGAGCT 789060 i C L2d_3end#LINE 410 CAAGGAGCT 402 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 32.86 CpG sites = 21, Kimura (unadjusted) = 34.47 Transitions / transversions = 3.50 (21/6) Gap_init rate = 0.03 (3 / 104), avg. gap size = 1.33 (4 / 3) 198 20.41 12.24 0.00 chrXqtel1M 789334 789382 (210618) C L2d2_3end#LINE/L2 (2) 553 499 m_b373s601i1 15567 chrXqtel1M 789334 AAAACAATTGAACAACTA------AAGGGCCTACTATGTGCCAGGTACTG 789377 v v v v ------i v i v i C L2d2_3end#LIN 553 AAATCAAATCAACAAATATTTATTGAGCGCCTACTGTGTGCAAGGCACTG 504 chrXqtel1M 789378 TGTTA 789382 i C L2d2_3end#LIN 503 TGCTA 499 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 23.85 CpG sites = 4, Kimura (unadjusted) = 23.85 Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.02 (1 / 48), avg. gap size = 6.00 (6 / 1) 210 16.28 13.95 0.00 chrXqtel1M 789340 789382 (210618) C L2b_3end#LINE/L2 (8) 458 410 m_b373s601i2 15567 chrXqtel1M 789340 ATTGAACAACTA------AAGGGCCTACTATGTGCCAGGTACTGTGTTA 789382 v v ------i v i i? i C L2b_3end#LINE 458 ATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTA 410 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 19.04 CpG sites = 4, Kimura (unadjusted) = 19.04 Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.02 (1 / 42), avg. gap size = 6.00 (6 / 1) 275 11.46 3.33 12.73 chrXqtel1M 789353 789412 (210588) C MIRb#SINE/MIR (23) 245 191 m_b373s601i3 15568 chrXqtel1M 789353 AGGGCCTACTATGTGCCAGGTACTGTGTTAAATTCCATGCTTTACCCATG 789402 v i i i -----ii -- C MIRb#SINE/MIR 245 AGCGCTTACTATGTGCCAGGCACTGTGCTAA-----GCGCTTTA--CATG 203 chrXqtel1M 789403 CA--ATCTCATT 789412 -- C MIRb#SINE/MIR 202 CATTATCTCATT 191 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 10.49 CpG sites = 5, Kimura (unadjusted) = 12.59 Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.14 (8 / 59), avg. gap size = 1.12 (9 / 8) 214 31.88 13.57 3.54 chrXqtel1M 789541 789901 (210099) C AmnL2-1#LINE/L2 (379) 2234 1839 m_b373s601i4 15569 chrXqtel1M 789541 GAGTTTTAAAGGAGCCCAGGAAG----TTTTGAAC------CTAAAGGTC 789580 i ii--- v ---- ------ i ivvv C AmnL2-1#LINE/ 2234 GGGTTTTAAAAA---CAAGGAAGGCAATTTTGAACTGGATCCTGAAATGA 2188 chrXqtel1M 789581 CTAGGGAGCCACTAGGGTTGATTGAGTAGGAGAGTACCATGGTCACA--T 789628 v i v i i v v v i i ivii i i-- C AmnL2-1#LINE/ 2187 ATGGGGAGCCAGTGGAGTTGTTTGAGGATGGGGGTGATGTGGTCGCGCTT 2138 chrXqtel1M 789629 C----TACA-GT--GAAGGAAGATCTC----TTTTTCAGCTGGCTGGACC 789667 ---- i- -- vi iivv ---- i v vv - -- C AmnL2-1#LINE/ 2137 CTTTGTACGTGTGAGAAGGCGGGCAGCAGCATTCTGCACAT-GCTGGA-- 2091 chrXqtel1M 789668 ATCTTGGGAGAAACTTGGGAC--AGGAAGAGTACTGAGGAAGCTGTTTCA 789715 i -- i--i --i i ivi iv i i vv v C AmnL2-1#LINE/ 2090 GTCT--GGAGAG--CTGGGACTTGGGGAGGCCATAGAGAAGGGAGTTGCA 2045 chrXqtel1M 789716 GTAATTTAATGAAGAGGTGATGAGGGCCTGGGGTGAG--T----GCAGAG 789759 i i iv ivvi v i v - i -- ---- C AmnL2-1#LINE/ 2044 ATAGTCAAGGCGAGAGGAGATGAAGGCAT-GGATGAGGATTTCAGCAGAG 1996 chrXqtel1M 789760 AAGAGGTC-AGACA-TGG-A-----GGGC--T-TCCCGAAGGTAG-AAAG 789797 iv ii - i - - ----- -- - iv i i -i vi C AmnL2-1#LINE/ 1995 GTGGAGTCGAGGCAGTGGCATACACGGGCAATGTTGCGGAGGTGGTGATA 1946 chrXqtel1M 789798 GGCAAGAACTG--GCCACTGATTAGCTCTGTGGAGTGAAGAAGGATCAAG 789845 - vi -- v v i-- v v v ii v i ii iv C AmnL2-1#LINE/ 1945 GGC-AGATTTGCAGACACAGG--AGATGTGGGAGGAGAAGGAGAGTTCAG 1899 chrXqtel1M 789846 AGTCCGGGATAATGTTGAGATGATGAAC--CTGAGAC-ACTGGAAGG-AT 789891 i vi i i iii i v i i -- v i - v i -v C AmnL2-1#LINE/ 1898 GGTCAAGGATGACGCCAAGGTTACGGACAGCGGAGGCAAATGGGAGGTCT 1849 chrXqtel1M 789892 GACTCAGGGA 789901 v ii C AmnL2-1#LINE/ 1848 GAGTCGAGGA 1839 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 39.28 CpG sites = 68, Kimura (unadjusted) = 43.39 Transitions / transversions = 1.58 (68/43) Gap_init rate = 0.10 (35 / 360), avg. gap size = 1.80 (63 / 35) 414 30.50 22.65 0.97 chrXqtel1M 789582 790177 (209823) C L2#LINE/L2 (220) 2862 2139 m_b373s601i5 15569 chrXqtel1M 789582 TAGGGAGCCACT--AGGGTTGATTGAGTAGGAGAGTACCATGGTCACATC 789629 i i i -- -- i ii iv i vv ii C L2#LINE/L2 2862 TGGGAAGCCATTGGAGGGTT--TTGAGCAGAGGAGTGACATGATCTGACT 2815 chrXqtel1M 789630 TACAGTGAAGGAAGATCTCTTTTTCAGCTG-GCTG------GACCATCTT 789672 iv vv ii i v i vv v - i ------ ii?vvv C L2#LINE/L2 2814 TACGTTTTAAAAGGATCACTCTGGCTGCTGTGTTGAGAATAGACTGNAGG 2765 chrXqtel1M 789673 GGGAGAAACTTGGGA-CAGGAAGAGTACTGAGGAAGCTGTTTCAGTAATT 789721 iv ivv i - i vi v v i i v i C L2#LINE/L2 2764 GGGGCAAGGGTGGAAGCAGGGAGACCAGTTAGGAGGCTATTGCAGTAATC 2715 chrXqtel1M 789722 TAATGAAGAGGTGATGAGGGCCTGG-----GGTGAGTGCAGAGAAGA-GG 789765 i ivvi i iv i ----- ivv v i i- C L2#LINE/L2 2714 CAGGCGAGAGATGATGGTGGCTTGGACCAGGGTGGTGGCAGTGGAGGTGG 2665 chrXqtel1M 789766 TCAGACATGGAGGGCTTCC----------CGAAGGTAGAAAGGGCAAGAA 789805 v vi vv v i----------i ivv i i v C L2#LINE/L2 2664 TGAGAAGTGGTCGGATTCTGGATATATTTTGAAGGTAGAGCCGACAGGAT 2615 chrXqtel1M 789806 CTGGCCACTGATTAGCTCTGTGGAGTGA-AGAAGGATCAAGAGTCCGGGA 789854 i viv iv i v v v v - i v- i vi C L2#LINE/L2 2614 TTGCTGATGGATTGGATGTGGGGTGTGAGAGAAAGAG-AGGAGTCAAGGA 2566 chrXqtel1M 789855 TAATGTTGAGATGATGAACCTGAGACACTGGAAGGATG------------ 789892 i iviii i vv vii vv ------------ C L2#LINE/L2 2565 TGACTCCAAGGTTTTTGGCCTGAGCAACTGGAAGGATGGAGTTGCCATTN 2516 chrXqtel1M 789893 ACTCA----GGGA--ATTA----------AGGTTTGAGGGGGAATGATCG 789926 v ---- -- i i---------- - i C L2#LINE/L2 2515 ACTGAGATGGGGAAGACTGCGGGAGGAGCAGGTTTGAGGGGGAA-GATCA 2467 chrXqtel1M 789927 TTAACTTAGTTTTTTGTATATTGA--TTA-------TATT--------GA 789959 vv ii i vvii i i -- i------- --------i C L2#LINE/L2 2466 GGAGTTCAGTTTTGGACATGTTAAGTTTGAGATGCCTATTAGACATCCAA 2417 chrXqtel1M 789960 GTTGAGAT------TACTC---TGGA-ACACGTAGTTTGAAATGTTCAGT 789999 v ------ vv --- - i - i i -- v C L2#LINE/L2 2416 GTGGAGATGTCGAGTAGGCAGTTGGATATACG-AGTCTGGA--GTTCAGG 2370 chrXqtel1M 790000 ---GATGTAGAGGCTGCTTATCTAGACTTGGGAGGCTTCTGCCTAGAAGT 790046 --- v vvi vvv v i i v v v v v ii C L2#LINE/L2 2369 GGAGAGGTCCGGGCTGGAGATATAAATTTGGGAGTCATCAGCATATAGAT 2320 chrXqtel1M 790047 GACAGTTAAA-CCAT-----CGG--GAGAT-----AAGGAG-----GTAC 790078 ii v - -----i -- ----- i ----- v C L2#LINE/L2 2319 GGTATTTAAAGCCATGAGACTGGATGAGATCACCNAGGGAGTGAGTGTAG 2270 chrXqtel1M 790079 CAAGAGAAGATA---------------GAACCTTGGGG--GT---ATATT 790108 vv v --------------- i i --v --- ii C L2#LINE/L2 2269 ATAGAGAAGAGAAGAGGTCCAAGGACTGAGCCCTGGGGCACTCCAACGTT 2220 chrXqtel1M 790109 CA---GTCAGTGGGATGGAGAGAAATC-----TGGACTCTGAGGAAGGGT 790150 ? --- i v i ii i i -----v vv i i i i C L2#LINE/L2 2219 NAGAGGTCGGGGAGATGAGGAGGAACCAGCAAAGGAGACTGAGAAGGAGC 2170 chrXqtel1M 790151 CACC--T--AGTAGGAGGAGAACTAGAAGAG 790177 vi -- --i i i i C L2#LINE/L2 2169 GGCCAGTGAGGTAGGAGGAAAACCAGGAGAG 2139 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 38.57 CpG sites = 99, Kimura (unadjusted) = 40.32 Transitions / transversions = 1.22 (99/81) Gap_init rate = 0.06 (38 / 595), avg. gap size = 3.74 (142 / 38) 20 20.79 3.39 3.39 chrXqtel1M 790233 790291 (209709) (AG)n#Simple_repeat 1 59 (0) m_b373s252i2 15570 chrXqtel1M 790233 AGATGAGAGAAGGAAAGAGAGA-AGAAATTGAGAGACAGGGAGAGA-AGA 790280 - ii i - i vv v i - (AG)n#Simple_ 1 AGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 49 chrXqtel1M 790281 GACGACTGAGA 790291 - vv (AG)n#Simple_ 50 GA-GAGAGAGA 59 Matrix = Unknown Transitions / transversions = 1.00 (5/5) Gap_init rate = 0.07 (4 / 58), avg. gap size = 1.00 (4 / 4) 241 19.61 1.96 0.00 chrXqtel1M 791005 791055 (208945) C MIR#SINE/MIR (139) 123 72 m_b373s601i6 15568 chrXqtel1M 791005 CTTAGGCA-ATTGGGGTTAGGTGACTTGTCCAGGGTCACACAGCTAGAAG 791053 v - vv i i i i i v i C MIR#SINE/MIR 123 CTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAA 74 chrXqtel1M 791054 GT 791055 C MIR#SINE/MIR 73 GT 72 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 23.09 CpG sites = 6, Kimura (unadjusted) = 23.09 Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.02 (1 / 50), avg. gap size = 1.00 (1 / 1) 246 15.00 0.00 0.00 chrXqtel1M 791016 791055 (208945) C MIRc#SINE/MIR (153) 115 76 m_b373s601i7 15568 chrXqtel1M 791016 GGGGTTAGGTGACTTGTCCAGGGTCACACAGCTAGAAGGT 791055 i i i i v i C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGT 76 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 17.36 CpG sites = 5, Kimura (unadjusted) = 17.36 Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 824 26.90 7.60 1.12 chrXqtel1M 791858 792278 (207722) C L1ME4c_3end#LINE/L1 (343) 487 40 m_b373s551i4 15571 chrXqtel1M 791858 GTTTCCAGTTT----CTATTAAAAACAGGG-TGCCCCAAACATTTT-GT- 791900 i ---- v i iv - vvii i - - C L1ME4c_3end#L 487 GTTTCCAATTTTTCGCTATTATAAATAACGCTGCAATGAACATCTTCGTG 438 chrXqtel1M 791901 CACA-AACCTTTCCCTTCTTT---AGTATCTCTTTGGGGTATAAGCCCAG 791946 i - i i i --- v i i i i v vv C L1ME4c_3end#L 437 CATATAGCTTTTTCCTTCTTTTGAATTATTTCCTTAGGATAAATTCCCAG 388 chrXqtel1M 791947 TAGTAGCAT------GCGGACGCGTATGA-CAGTTTGATAACTTTTGA-G 791988 v i v ------ ivi v v - v v ii i -i C L1ME4c_3end#L 387 AAGTGGAATTACTGGGTCAAAGGGTATGAACATTTTTATGGCTCTTGATA 338 chrXqtel1M 791989 CATAGTTCCAAATCG-GTTCCAGAATGGTTGGATTG-TTCACAACTCCAC 792036 i v v i -v i v v iii- i ?iv C L1ME4c_3end#L 337 CGTATTGCCAAATTGCTTTCCAAAAGGGTTGTACCAATTTACANTGCCAC 288 chrXqtel1M 792037 CAACAATGCAT-AGTGTCCCAGTTTTCCC--AGCC-CTCCAA-ATT---C 792078 i i - ? v iv -- ? - v i- ---i C L1ME4c_3end#L 287 CAGCAATGTATGAGNGTACCAGTTTCACCGCANCCTCGCCAGCATTGGGT 238 chrXqtel1M 792079 ATCATTATTTTTCCGTCATCTAGCCAATCTA-CAGGTGTGTAGTGGT-TC 792126 i i v iiivvv i v i i -i i iv i - C L1ME4c_3end#L 237 ATTATCAATTTTTTAAATTTTTGCTAATTTAATAGGCGTAAAATGGTATC 188 chrXqtel1M 792127 TCAGAGTTGTCTTAATTTGTGTTTCTCTGATCAATAATGATTTGGAACAC 792176 vv ii ii i i v ii vv v i C L1ME4c_3end#L 187 TCATTGTTGCTTTAATTTGCATTTCTTTGATTACTAGCGAGGTTGAACAT 138 chrXqtel1M 792177 TCTTTCATATGAGTGGT-AATAGTTTTAATTTCATCATCTGAAAATTGTC 792225 i i i vv v - v ? v - v v ? vi C L1ME4c_3end#L 137 TTTTCCATGTGTTTGTTTACTANTTGTA-TTTCCTCTTNTGTGAATTGTC 89 chrXqtel1M 792226 TGTTCATATCCTTTGACCATTTATGAATTGGAGAATAGTTTGATTTCTTT 792275 i v vv i ----vi ? i C L1ME4c_3end#L 88 TGTTCATGTCCTTTGCCCATTTATCTATTGGGG----TCTTGATNTTTTT 43 chrXqtel1M 792276 TTT 792278 i C L1ME4c_3end#L 42 CTT 40 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 33.57 CpG sites = 64, Kimura (unadjusted) = 34.71 Transitions / transversions = 1.33 (64/48) Gap_init rate = 0.06 (24 / 420), avg. gap size = 1.54 (37 / 24) 551 16.73 3.08 8.06 chrXqtel1M 792285 792414 (207586) C MIRc#SINE/MIR (141) 127 4 m_b373s601i8 15572 chrXqtel1M 792285 CTGAGGCAATCGG---GGTTAAGTGACTTGCCCAGGGTCACACAGGTAGG 792331 -- i --- i v - C MIRc#SINE/MIR 127 CTGAGGC--TCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG- 81 chrXqtel1M 792332 AAGTGTTAAGTGTCTGAGACCAGATTTGAACTCAGGTCCTCCTGACTTCA 792381 ------ v v v vi i i i i i C MIRc#SINE/MIR 80 ------TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCA 37 chrXqtel1M 792382 AGGCTGGTGCTGTATCTATTGGCACCA-ACTGCC 792414 v ii v v i i - - C MIRc#SINE/MIR 36 AGTCCAGTGCTCTTTCCACT-GCACCACACTGCC 4 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 18.07 CpG sites = 12, Kimura (unadjusted) = 19.09 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.09 (12 / 129), avg. gap size = 1.17 (14 / 12) 260 27.78 3.70 0.00 chrXqtel1M 793079 793186 (206814) C L1P4_orf2#LINE/L1 (831) 2463 2352 m_b373s551i5 15573 chrXqtel1M 793079 TGGTTTAGGTAGTATTGTCATCTT---TATTTTG-CTCACCCAATCCAAG 793124 v i i v i i ---v v -i vi v C L1P4_orf2#LIN 2463 TGCTTTGGGCAGTATGGCCATTTTAACGATATTGATTCTTCCAATCCATG 2414 chrXqtel1M 793125 AGCATTTAATATTTTTCCAGTTGGTTAGATCAGACTTAATTTGTGTGGAA 793174 vv i v v ivi vvi? i v v viiv C L1P4_orf2#LIN 2413 AGCATGGAATGTTTTTCCATTTGTTTGTGTCATCTNTGATTTCTTTCAGC 2364 chrXqtel1M 793175 AGTGTTTTGTAG 793186 C L1P4_orf2#LIN 2363 AGTGTTTTGTAG 2352 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 35.26 CpG sites = 13, Kimura (unadjusted) = 35.26 Transitions / transversions = 0.76 (13/17) Gap_init rate = 0.02 (2 / 107), avg. gap size = 2.00 (4 / 2) 235 25.57 6.59 5.43 chrXqtel1M 793188 793278 (206722) C L2#LINE/L2 (2444) 638 547 m_b373s601i9 15574 chrXqtel1M 793188 AAAACTGGGTATATTTCAGAGGAGGACGGAGGGAGG-----CTGGAAATG 793232 i -i i i - v i----- ii C L2#LINE/L2 638 AAAGCTGGG-GTGTTTTAG-GGAGGAGGGAGGGAGAATGGTCTGGAAGCG 591 chrXqtel1M 793233 GCAGAGATGGGAAACAAAGATCATCCTGACTCC-CCTTGAGGACCAG 793278 --- i i i i vv iv iv i - iv v C L2#LINE/L2 590 GCA---ATGAGGAGCAAGGAGGACACCTACCCCACCTCCAGGCCCAG 547 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.76 CpG sites = 15, Kimura (unadjusted) = 32.57 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.08 (7 / 90), avg. gap size = 1.57 (11 / 7) 272 23.61 18.09 0.91 chrXqtel1M 793484 793577 (206423) C L3#LINE/CR1 (77) 4022 3913 m_b373s601i10 15575 chrXqtel1M 793484 CCCTCTATAACCCACCTGAAGAGT--TC-TTCAGTCTCTGCTTGA----- 793525 i i viv vi -- - i i ----- C L3#LINE/CR1 4022 CCTTCTACAACATCCCTGACAAGTGGTCATCCAGCCTCTGCTTGAACACC 3973 chrXqtel1M 793526 ---------GGGAAGCCCATTAACCCTCAAGGGCAGCCCATCCCATGCTG 793566 --------- i i i v i ? i - i vi v C L3#LINE/CR1 3972 TCCAGTGACGGGGAGCTCACTACCTCNCGAGG-CAGCCCATTCCATTTTT 3924 chrXqtel1M 793567 GGACAAGTTTG 793577 iv i C L3#LINE/CR1 3923 GGACAGCTCTG 3913 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 28.24 CpG sites = 15, Kimura (unadjusted) = 29.85 Transitions / transversions = 2.14 (15/7) Gap_init rate = 0.05 (5 / 93), avg. gap size = 3.60 (18 / 5) 193 23.83 0.00 2.38 chrXqtel1M 793778 793820 (206180) C MIRc#SINE/MIR (209) 59 18 m_b373s601i11 15568 chrXqtel1M 793778 GAACCTCAAGTGTCACTGACTCCAGATTCAGTACTCTGTTCAC 793820 - i v iv ii i i v i C MIRc#SINE/MIR 59 GAACC-CAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCAC 18 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.79 CpG sites = 7, Kimura (unadjusted) = 29.79 Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.02 (1 / 42), avg. gap size = 1.00 (1 / 1) 113 0.98 0.00 0.00 chrXqtel1M 794061 794163 (205837) (CTTC)n#Simple_repeat 1 103 (0) c_b373s251i1 15576 chrXqtel1M 794061 CTTCCTTCCTTCCTTCTTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT 794110 i (CTTC)n#Simpl 1 CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT 50 chrXqtel1M 794111 TCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC 794160 (CTTC)n#Simpl 51 TCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC 100 chrXqtel1M 794161 CTT 794163 (CTTC)n#Simpl 101 CTT 103 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 102), avg. gap size = 0.0 (0 / 0) 423 22.89 3.25 7.63 chrXqtel1M 794179 794301 (205699) C MIRc#SINE/MIR (141) 127 10 m_b373s601i12 15577 chrXqtel1M 794179 CTGAGGC--AGTTGGGGTT--GTGACTTGTCCAGGGTCACATTGCTTGGA 794224 -- v- i -- i i iv v v C MIRc#SINE/MIR 127 CTGAGGCTCAGA-GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTA 79 chrXqtel1M 794225 AGTGTTAAGTTGTCTGAGGTCAAATTTGAACTCGGGTCCTCCTGACTTCA 794274 vi -------- vivii i i i i i i C MIRc#SINE/MIR 78 AGTGGCA--------GAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCA 37 chrXqtel1M 794275 GGGCTGGTGCTCTATCCACTGCACCAC 794301 i v ii v C MIRc#SINE/MIR 36 AGTCCAGTGCTCTTTCCACTGCACCAC 10 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 25.50 CpG sites = 17, Kimura (unadjusted) = 27.97 Transitions / transversions = 1.89 (17/9) Gap_init rate = 0.09 (11 / 122), avg. gap size = 1.18 (13 / 11) 300 27.07 10.29 4.90 chrXqtel1M 794492 794627 (205373) C L2d2_3end#LINE/L2 (10) 545 403 m_b373s601i13 15578 chrXqtel1M 794492 TCATCAGATATTT---GAACACTTCATTGTCTATGTGCAAAGTACTGTGC 794538 v i --- i i i v----- i i i C L2d2_3end#LIN 545 TCAACAAATATTTATTGAGCGCCTA-----CTGTGTGCAAGGCACTGTGC 501 chrXqtel1M 794539 TAGGAA-TA-GAAAGATTCAAAG---TGTT-----TGCTCCCTAGTTTCA 794578 vi- i- iii v --- i v----- v ivii C L2d2_3end#LIN 500 TAGGCGCTGTGGGGGATACAAAGAAGTATAAGACATGGTCCCTGCCCTCA 451 chrXqtel1M 794579 AGGTGCTTATAATCTA-CTGGGAGGCTACAAGAAGTCAACAAGGAAACAG 794627 v i -i ii -- vi v v vi v C L2d2_3end#LIN 450 AGGAGCTTACAATCTAGTTGGGGAG--ACAAGACATAAACACGTGAAAAG 403 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 32.34 CpG sites = 22, Kimura (unadjusted) = 34.78 Transitions / transversions = 1.69 (22/13) Gap_init rate = 0.10 (13 / 135), avg. gap size = 1.62 (21 / 13) 199 38.84 6.49 3.96 chrXqtel1M 794908 795277 (204723) L2#LINE/L2 1048 1426 (1656) m_b373s601i14 15579 chrXqtel1M 794908 ACCTCTAATCCCTTAGT---------TTCTTAC-ATCACTTTCTCTGCTC 794947 i v ii --------- i i -i v iv i iv L2#LINE/L2 1048 ACCTCCAATCCATTGATCCTACCACCTTTTCACTGTCCCTCACCCCCCTC 1097 chrXqtel1M 794948 -TGATTTGATTTGTCGCTCTGCCCAATCTCAACCCCATAGTTAACTAATC 794996 - vii v i vi v ii i iii vi ii i i? ii v v L2#LINE/L2 1098 ATGTCCTCACTTCCCTCCTTACCCAGCTTAGATTCCATGGTCNATCATTA 1147 chrXqtel1M 794997 CAACTTCACCCTT-----TCTCCTCAGATCAGTTGCTTCCTTGGCCTACT 795041 i iiv v ----- vi iv vv ii ii -- iii L2#LINE/L2 1148 TAATCACTCCCTTGCATATACCCTCAACTCCCTTGCCCCTCT--CTCGCT 1195 chrXqtel1M 795042 G-GCCATGTTCAGCCCCTTGACAAA-TCCCAGCCCTG---AACTGCTGCC 795086 v- i i ii - --- i -i ? i --- v - iiv L2#LINE/L2 1196 TCGTCGTACTC-GCC---TGGCAAAACCNCAACCCTGGTTAAAT-CCAAC 1240 chrXqtel1M 795087 TTGGTCTGCCATTTCAGCTCCTGCTCCCTCATCTGGTGCTGAATACAACT 795136 i-- i vvi v v v v?iiv---- iiiii L2#LINE/L2 1241 TC--TCCGCCTACTCCGCGCCTGCACCCGNGCA----GCTGAACGTGGCT 1284 chrXqtel1M 795137 GGAGGGAATCATA-GACCTTGTTGAGTGGGGACATCTCAAATTTGTGATG 795185 ii v i -i v i v vvv ii i ii iv L2#LINE/L2 1285 GGAGAAAAACACACAACCATGCTGACTGGTCTCACTTTAAATTCATGACC 1334 chrXqtel1M 795186 TTCAAATTCAACGAGGTCCTTAACCACACCAAAGCGAACTT-TTATTCCT 795234 vi? vi vvi i ivvii -vi i v ? -i ivii L2#LINE/L2 1335 ACNAACCTCAAGTGGGCCCTTAATGCTGCC-CGGCAATCNTACTACATTT 1383 chrXqtel1M 795235 CCCTAATTACTGGCCTCTCTCATTCCTCACAGA-AACCATTCCA 795277 i ivv vvv i i - vi -i i i L2#LINE/L2 1384 CCCTAGTCCATTCACTCTCCCACT-CTCCTAGACGACTATTTCA 1426 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 56.14 CpG sites = 89, Kimura (unadjusted) = 60.50 Transitions / transversions = 1.82 (89/49) Gap_init rate = 0.07 (25 / 369), avg. gap size = 1.56 (39 / 25) 13 8.35 3.85 0.00 chrXqtel1M 795351 795376 (204624) (TCCCT)n#Simple_repeat 1 27 (0) m_b373s252i3 15580 chrXqtel1M 795351 TCCC-TCTCCTCCCTTCCCTTCCCTTC 795376 - i i (TCCCT)n#Simp 1 TCCCTTCCCTTCCCTTCCCTTCCCTTC 27 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.04 (1 / 25), avg. gap size = 1.00 (1 / 1) 195 26.93 16.67 0.96 chrXqtel1M 795518 795607 (204393) L2a_3end#LINE/L2 399 502 (15) m_b373s601i15 15581 chrXqtel1M 795518 ATATATGCACC-CGAGGGCAAAGACTCACTGTGGACTTT-----CT-CTG 795560 i v v -i ii i-i vvii ----- - L2a_3end#LINE 399 ATGTAAGCTCCATGAGGGCAGGGACTT-TTGTCTGTTTTGTTCACTGCTG 447 chrXqtel1M 795561 GATCCACAGTGCCTGGTACACTACCTGGAAC--------TGCTTCATAAA 795602 v v i i v v i v --------i iv L2a_3end#LINE 448 TATCCCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGGCGCTCAATAAA 497 chrXqtel1M 795603 TACTT 795607 i L2a_3end#LINE 498 TATTT 502 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.79 CpG sites = 14, Kimura (unadjusted) = 34.20 Transitions / transversions = 1.40 (14/10) Gap_init rate = 0.06 (5 / 89), avg. gap size = 3.20 (16 / 5) 210 29.60 12.90 1.94 chrXqtel1M 795530 795622 (204378) L2d2_3end#LINE/L2 452 554 (1) m_b373s601i16 15581 chrXqtel1M 795530 GAGGGCAAAGACT-CACTGTGGACTTTCTCTGGATCC---ACAGTGCCTG 795575 ii i-iiiiv iv - i v --- i i L2d2_3end#LIN 452 GAGGGCAGGGACCATGTCTTATACTT-CTTTGTATCCCCCACAGCGCCTA 500 chrXqtel1M 795576 GTACACTACCTGGAAC--------TGCTTCATAAATACTTCCTTGACTTG 795617 i v i v v --------i iv - iv i L2d2_3end#LIN 501 GCACAGTGCCTTGCACACAGTAGGCGCTCAATAAATA-TTTGTTGATTTG 549 chrXqtel1M 795618 GCTTG 795622 ii L2d2_3end#LIN 550 ATTTG 554 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 36.20 CpG sites = 19, Kimura (unadjusted) = 40.04 Transitions / transversions = 2.38 (19/8) Gap_init rate = 0.05 (5 / 92), avg. gap size = 2.80 (14 / 5) 195 32.89 18.79 0.00 chrXqtel1M 795577 795725 (204275) L2d_3end#LINE/L2 335 511 (5) m_b373s601i17 15581 chrXqtel1M 795577 TACACTACCTGGAACTGCTTCATAAATACTTCCT-TGACTTGG-CTTGTC 795624 i ii v v i i iiv v ii v - vv i - L2d_3end#LINE 335 TATACTGTCTTGTATTGTTCTCTAATTGTTTCATGTGTGTTAGTCTTGTC 384 chrXqtel1M 795625 TCTGCTGTCAAAACGTATACTCCCCGAGGACAGG--CAATGTT---TGCT 795669 iv viii i vi vi ii i -- v i--- i L2d_3end#LINE 385 TCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACT 434 chrXqtel1M 795670 GTCT------------------CTAGCAT--TGCCCA-CATAGAGCAGGT 795698 ? i ------------------ i-- iv - i v i i L2d_3end#LINE 435 NTTTTNTCGTTCCCCACAGCGCCTAGCACAGTGCTGAGCACATAGTAGGC 484 chrXqtel1M 795699 GCTTAACTCATGCTTGTTGATCGAGTG 795725 i ivv i i v L2d_3end#LINE 485 GCTCAATAAATACTTGTTGATTGATTG 511 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 44.83 CpG sites = 32, Kimura (unadjusted) = 46.15 Transitions / transversions = 1.88 (32/17) Gap_init rate = 0.05 (7 / 148), avg. gap size = 4.00 (28 / 7) 355 23.26 12.79 0.00 chrXqtel1M 795720 795805 (204195) C MIRc#SINE/MIR (106) 162 66 m_b373s601i18 15582 chrXqtel1M 795720 CGAGTGCTATTCTGTCCATTTTATAGATGAGTAAACTGAAGCCTAGAGAG 795769 ii ii v vi i v i ii C MIRc#SINE/MIR 162 CAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAG 113 chrXqtel1M 795770 GTCAAGT-------CCATGGTCACA----TAGGAAGTGGTCAAACTG 795805 i ------- v ---- v ivi i i C MIRc#SINE/MIR 112 GTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCG 66 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 27.21 CpG sites = 14, Kimura (unadjusted) = 28.91 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.02 (2 / 85), avg. gap size = 5.50 (11 / 2) 347 21.60 14.04 6.56 chrXqtel1M 795943 796056 (203944) MIRc#SINE/MIR 25 146 (122) m_b373s601i19 15583 chrXqtel1M 795943 GGGCACTGGGCTTAGAATCAGGGAGATTCCTCTTCCTGGGTTCAAAACCC 795992 i i i i i -------- i iv MIRc#SINE/MIR 25 GAGCACTGGACTTGGAGTCAGGAAGA--------CCTGGGTTCGAGTCCC 66 chrXqtel1M 795993 -----------TCCCTAGCCATATGACCCCGGGCAAGTCATTTCACC-CT 796030 ----------- iv ii i ii i v - MIRc#SINE/MIR 67 GGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCT 116 chrXqtel1M 796031 GTTTACCTCAG----CTCTTCTGTAGAATG 796056 v vvi ---- v i MIRc#SINE/MIR 117 CTGAGCCTCAGTTTCCTCATCTGTAAAATG 146 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 25.15 CpG sites = 16, Kimura (unadjusted) = 26.48 Transitions / transversions = 2.29 (16/7) Gap_init rate = 0.10 (11 / 113), avg. gap size = 2.18 (24 / 11) 191 25.55 13.79 1.02 chrXqtel1M 797738 797824 (202176) C AmnL2-1#LINE/L2 (354) 2259 2162 m_b373s601i20 15584 chrXqtel1M 797738 AGGCAGGGCTGGAGCAAG-CTAGGAAGGGTTTTA----TAAGTCAAACA- 797781 i - - i v i ----i vv ii - C AmnL2-1#LINE/ 2259 AGGTAGG-CTGGAGCAAGTCCATGGAGGGTTTTAAAAACAAGGAAGGCAA 2211 chrXqtel1M 797782 ----GAG--GAGTCCTGGAGGGGGTAGGGAGCCACTGGAGTTTCCTGAG 797824 ---- i-- ii i iv ii i v vii C AmnL2-1#LINE/ 2210 TTTTGAACTGGATCCTGAAATGAATGGGGAGCCAGTGGAGTTGTTTGAG 2162 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 32.91 CpG sites = 16, Kimura (unadjusted) = 32.91 Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.07 (6 / 86), avg. gap size = 2.17 (13 / 6) 208 36.05 0.00 0.00 chrXqtel1M 797935 798020 (201980) L2#LINE/L2 2316 2401 (681) m_b373s601i21 15579 chrXqtel1M 797935 TATCATCTCTTTGGAGATGGCTCTTAAATCTCCACGTTCAGCCATAGTCT 797984 i v v vv i ii i vi iv i vviii L2#LINE/L2 2316 TACCATCTATATGCTGATGACTCCCAAATTTATATCTCCAGCCCGGACCT 2365 chrXqtel1M 797985 CTCCATTGAGCCCCTGTCCCACATCACCAACTGCTT 798020 vi i i v v i ii vv i L2#LINE/L2 2366 CTCCCCTGAACTCCAGACTCGTATATCCAACTGCCT 2401 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 48.80 CpG sites = 18, Kimura (unadjusted) = 51.17 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.00 (0 / 85), avg. gap size = 0.0 (0 / 0) 12 11.51 3.33 3.33 chrXqtel1M 799007 799036 (200964) (AGG)n#Simple_repeat 1 30 (0) m_b373s252i4 15585 chrXqtel1M 799007 AGGAGGGGGAGGAGGAGGCAGCTGG-GGAGG 799036 i - vv - (AGG)n#Simple 1 AGGAGGAGGAGGAGGAGG-AGGAGGAGGAGG 30 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.07 (2 / 29), avg. gap size = 1.00 (2 / 2) 13 18.17 0.00 0.00 chrXqtel1M 799008 799038 (200962) (GGAGGG)n#Simple_repeat 1 31 (0) m_b373s252i5 15585 chrXqtel1M 799008 GGAGGGGGAGGAGGAGGCAGCTGGGGAGGGG 799038 i vi vv (GGAGGG)n#Sim 1 GGAGGGGGAGGGGGAGGGGGAGGGGGAGGGG 31 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 12 23.27 2.50 0.00 chrXqtel1M 802722 802761 (197239) (GGGGCT)n#Simple_repeat 1 41 (0) m_b373s252i6 15586 chrXqtel1M 802722 GGGGCTGGGAAGTAGGCTGGGGCTCGGGCT-GAGATGGGGC 802761 ivvvi v - i v (GGGGCT)n#Sim 1 GGGGCTGGGGCTGGGGCTGGGGCTGGGGCTGGGGCTGGGGC 41 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1) 46 0.00 0.00 0.00 chrXqtel1M 803581 803619 (196381) (TG)n#Simple_repeat 1 39 (0) c_b373s251i2 15587 chrXqtel1M 803581 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 803619 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 39 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0) 417 25.00 12.10 0.00 chrXqtel1M 803772 803895 (196105) MIRc#SINE/MIR 10 148 (120) m_b373s601i22 15588 chrXqtel1M 803772 GTGGCACAGTGGATGGAGCCCTGGGCCTGGAGACAAGAATATCTGAGTGC 803821 ii vi v i i v i v i i v MIRc#SINE/MIR 10 GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTC 59 chrXqtel1M 803822 CAATCTGGCCTCAGAAACTTCCTGGCTG--------------AGTCATTT 803857 v i iv v v vv v i -------------- i MIRc#SINE/MIR 60 GAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTT 109 chrXqtel1M 803858 TGCC-CTATTTGCCTCAGTTTCCTCATCTGGAAAATGAG 803895 vi - v vv v i MIRc#SINE/MIR 110 AACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGG 148 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.55 CpG sites = 14, Kimura (unadjusted) = 30.55 Transitions / transversions = 0.82 (14/17) Gap_init rate = 0.02 (2 / 123), avg. gap size = 7.50 (15 / 2) 486 18.51 5.26 5.26 chrXqtel1M 805379 805492 (194508) C MIRc#SINE/MIR (120) 148 35 m_b373s601i23 15589 chrXqtel1M 805379 CTCATTTTACAGATGAGGAAACTGAAGCAGACAGGGGT-AAGTGACTTGC 805427 i i vv v i - C MIRc#SINE/MIR 148 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 99 chrXqtel1M 805428 CCAGGGTCATACAGCTAATAAGG---AGGGC--ACATTTCAAGTCAGGAA 805472 i i i v--- i --iv i iv vi --- C MIRc#SINE/MIR 98 CCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAG--- 52 chrXqtel1M 805473 GATGTCTTTCTGACGCCAAG 805492 --- i v C MIRc#SINE/MIR 51 ---GTCTTCCTGACTCCAAG 35 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 20.41 CpG sites = 12, Kimura (unadjusted) = 21.58 Transitions / transversions = 1.50 (12/8) Gap_init rate = 0.08 (9 / 113), avg. gap size = 1.33 (12 / 9) 301 34.08 4.64 4.64 chrXqtel1M 805948 806227 (193773) C L1ME2z_3end#LINE/L1 (559) 632 353 m_b373s551i6 15590 chrXqtel1M 805948 CTTCTAGCTTCACTCAGCATCA-GTTCATGAGGTCTCTCTAGGGTTTTCT 805996 --- v - iv i iiv i v v v vi C L1ME2z_3end#L 632 CTTCT---TTCACTCAGCATAATGTTTTTGAGATTCATCCATGTTGTTGC 586 chrXqtel1M 805997 GAA-ATCAGCCCGCTCATCATTCGTTATAGAACAATAATATTCCATTACA 806045 vi- iv- i i ivi iv v vvv i i ii C L1ME2z_3end#L 585 GTGTATCAGTA-GTTCGTTCCTTTTTATTGCTGAGTAGTATTCCATTGTA 537 chrXqtel1M 806046 TTCAAGTAGCTCAACTTGTTCAGCCATTCCCCAAC---TGGGCATCCCTT 806092 vv vi v v ii i v i vii--- i i ivvv C L1ME2z_3end#L 536 TGAATATACCACAGTTTGTTTATCCATTCTCCTGTTGATGGACACCTGGG 487 chrXqtel1M 806093 CAATTCCCAATTCTTTGCCAGCACAAA-AAAGATCCGGTCTAAATATTTT 806141 vi i i i v i vi ii - -- i v v i i i C L1ME2z_3end#L 486 CTGTTTCCAGTTTTTGGCTATTATGAATAAAG--CTGCTATGAACATTCT 439 chrXqtel1M 806142 TATACATGAGGGTCCTTTC-------CCCCTTTTCCTGATCTCTTTGGGA 806184 i ----i i i-------iviv --- i i v i C L1ME2z_3end#L 438 TGTACA----AGTCTTTTTGTGGACATATGTTTTC---ATTTCTCTTGGG 396 chrXqtel1M 806185 TACAGACCTAGTAGTGAGACTGATGGATCAAAGGGTATGTGTA 806227 v v v ii i v i v v C L1ME2z_3end#L 395 TAAATACCTAGGAGTGGAATTGCTGGGTCATAGGGTAGGTGTA 353 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 45.55 CpG sites = 52, Kimura (unadjusted) = 46.99 Transitions / transversions = 1.33 (52/39) Gap_init rate = 0.06 (18 / 279), avg. gap size = 1.44 (26 / 18) 355 30.31 4.12 3.06 chrXqtel1M 806030 806223 (193777) C L1ME4a_3end#LINE/L1 (316) 555 360 m_b373s551i7 15590 chrXqtel1M 806030 ATAATATTCCATTACATTCAAGTAGCTCAACTTGTTCAGCCATTCCCCAA 806079 ?i vv v v vi i i i i ? v C L1ME4a_3end#L 555 ATAATATTCCATTNTATGGATGTACCATAATTTATTTAACCANTCCCCTA 506 chrXqtel1M 806080 CTG---GGCATCCC--TTCAATTCCCAATTCTTTGCCAGCACAAAAAA-G 806123 i --- i iiv-- --i i i i i vi i v - C L1ME4a_3end#L 505 TTGTTGGACATTTAGGTT--GTTTCCAATTTTTCGCTATTATAAATAATG 458 chrXqtel1M 806124 ATCCGGTCTAAATATTTTTATACATGAGGGTCCTTTCCCCCTTTTCC--T 806171 v v i --i i ii i i i-- i vi? v v i i-- C L1ME4a_3end#L 457 CTGCGAT--GAACATCCTTGTACATAAA--TCTTTGTNCACATCTCTGAT 412 chrXqtel1M 806172 GATCTCTTTGGGATACAGACCTAGTAGTGAGACTGATGGATCAAAGGGTA 806221 v i i i v vv v ii i iv i C L1ME4a_3end#L 411 TATTTCCTTAGGATAAATTCCTAGAAGTGGAATTACTGGGTCAAAGGGTA 362 chrXqtel1M 806222 TG 806223 C L1ME4a_3end#L 361 TG 360 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 40.59 CpG sites = 37, Kimura (unadjusted) = 41.57 Transitions / transversions = 1.85 (37/20) Gap_init rate = 0.05 (10 / 193), avg. gap size = 1.40 (14 / 10) 16 5.27 0.00 0.00 chrXqtel1M 806234 806253 (193747) (T)n#Simple_repeat 1 20 (0) m_b373s252i7 15591 chrXqtel1M 806234 TTCTTTTTTTTTTTTTTTTT 806253 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTT 20 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 12 13.30 4.08 8.51 chrXqtel1M 806673 806721 (193279) (TTCTCAA)n#Simple_repeat 1 47 (0) m_b373s252i8 15592 chrXqtel1M 806673 TTGTCAATCTCCTCAA--CTGACTTCTCACTTCTCAATCTCTTCAAGTCT 806720 v - - -- v v v - - v (TTCTCAA)n#Si 1 TTCTCAAT-T-CTCAATTCTCAATTCTCAATTCTCAAT-TC-TCAATTCT 46 chrXqtel1M 806721 C 806721 (TTCTCAA)n#Si 47 C 47 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.10 (5 / 48), avg. gap size = 1.20 (6 / 5) 351 31.79 4.43 3.92 chrXqtel1M 807903 808105 (191895) C L1ME3G_3end#LINE/L1 (376) 548 345 m_b373s551i8 15593 chrXqtel1M 807903 ATAATATTTCATAACATTCATAAACCATCACTTATTCAGTCATTCCCCAG 807952 i i ii vv v v i i ii vi C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chrXqtel1M 807953 CTGATGGGAGTCCACTCA----ATTTACAGTTCCTGGTCACTACAAAAAG 807998 i i---- i i ----i v i ii v ii i v i C L1ME3G_3end#L 498 TTGATGGA----CATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAA 453 chrXqtel1M 807999 GGCCGCCACAAATCTTTTTGCACACGTGGGTCCTTTTCCCCTTTT----- 808043 v i v ii iv ii i -- v? v v v v v ----- C L1ME3G_3end#L 452 TGCTGCAATGAACATCCTTGTACA--TGCNTCCTTGTGCACATGTGCGAG 405 chrXqtel1M 808044 TATGATCTTTTGACATACAGGCCCAGTAGAAACACTGCTGGGTCAAAGGA 808093 -- ii ? iiv v v? ? v viiv i i C L1ME3G_3end#L 404 TAT--TTCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGG 357 chrXqtel1M 808094 TGTGCACAGTTT 808105 i i v C L1ME3G_3end#L 356 TATGCGCATTTT 345 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 43.33 CpG sites = 38, Kimura (unadjusted) = 44.31 Transitions / transversions = 1.58 (38/24) Gap_init rate = 0.05 (10 / 202), avg. gap size = 1.70 (17 / 10) 104 7.76 4.91 0.00 chrXqtel1M 808501 808663 (191337) (GA)n#Simple_repeat 1 171 (0) m_b373s252i9 15594 chrXqtel1M 808501 GAGGGAG-GAGGGAG-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 808548 i - i - (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chrXqtel1M 808549 GAGAGAGAGAGAGAGAGAGAGAGAGAAAGAG-GAGAAAGAGAGAGAGAGA 808597 i - i (GA)n#Simple_ 51 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 100 chrXqtel1M 808598 GAGAGAGATACAGAGACACAGAAAGAGAGCGAGACAGAGAGAGAG-GAGA 808646 v v v v i v v - (GA)n#Simple_ 101 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 150 chrXqtel1M 808647 -AGA-AGA-AGA-AGAAAGAG 808663 - - - - i (GA)n#Simple_ 151 GAGAGAGAGAGAGAGAGAGAG 171 Matrix = Unknown Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.05 (8 / 162), avg. gap size = 1.00 (8 / 8) 168 15.19 4.65 3.69 chrXqtel1M 808992 809421 (190579) (AGAGAC)n#Simple_repeat 1 434 (0) m_b373s252i10 15595 chrXqtel1M 808992 AGACACAGAGACAGAGAAACAG-GAGACAAAGAGACAGAGACAGAAAGAG 809040 v v v -v v v i v (AGAGAC)n#Sim 1 AGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAG 50 chrXqtel1M 809041 AGA-AGACAGGAGAGACAGAGACAG-G-GAGACACAGAGACAGAGAGACA 809087 - v -v - -v v -- (AGAGAC)n#Sim 51 AGACAGAGA-CAGAGACAGAGACAGAGACAGAGACAGAGAC--AGAGACA 97 chrXqtel1M 809088 GAAACAGAAAACAGAGGCAGAGA-AGACAGGAGAGACAGAGACAGAGAGA 809136 i - i i - v -v -- (AGAGAC)n#Sim 98 GAGACAG-AGACAGAGACAGAGACAGAGA-CAGAGACAGAGAC--AGAGA 143 chrXqtel1M 809137 CAGAAACAGAAGACAG-G--AGAGACAGAGACAGAGAGACAGAAACAGA- 809182 i - - -- -- i - (AGAGAC)n#Sim 144 CAGAGACAG-AGACAGAGACAGAGACAGAGAC--AGAGACAGAGACAGAG 190 chrXqtel1M 809183 AGAGACACAGAAACAGAGA-AAACAGGAGAGACAGAAACAGAAAACAGAG 809231 v v i - i v -v i - i (AGAGAC)n#Sim 191 ACAGAGACAGAGACAGAGACAGAGA-CAGAGACAGAGACAG-AGACAGAG 238 chrXqtel1M 809232 CCAGAGA-AGACAGAAGAGACAGAAACAGAGA-AGACAGGAGAGACAGAG 809279 v - v -v i - v -v (AGAGAC)n#Sim 239 ACAGAGACAGAGA-CAGAGACAGAGACAGAGACAGAGA-CAGAGACAGAG 286 chrXqtel1M 809280 ACAGAGAGACAGAAACAGAGAGACAGAAACAGA-AGAGACAGAG--A-AG 809325 -- i v v v v - -- - (AGAGAC)n#Sim 287 AC--AGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAG 334 chrXqtel1M 809326 ACAG-GAGAAACAGAGAGACAGAAACAGAGGCAGAGACAGAGAGACAGAA 809374 - v i v v i i v v v (AGAGAC)n#Sim 335 ACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGAC 384 chrXqtel1M 809375 ACAGA-AGAGACACAGAAACAGAGA-AGACAG-GAGAGACAGAGAGACAG 809421 v - v v v v - - v v v (AGAGAC)n#Sim 385 AGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAGAGACAG 434 Matrix = Unknown Transitions / transversions = 0.38 (15/40) Gap_init rate = 0.08 (34 / 429), avg. gap size = 1.06 (36 / 34) 20 11.26 0.00 0.00 chrXqtel1M 809708 809736 (190264) (G)n#Simple_repeat 1 29 (0) m_b373s252i11 15596 chrXqtel1M 809708 GGGCGGGGGGGGTGGGGGGGGGTGGGGGG 809736 v v v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG 29 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 328 30.07 4.84 0.78 chrXqtel1M 809823 809946 (190054) C L2d_3end#LINE/L2 (3) 513 385 m_b373s601i24 15597 chrXqtel1M 809823 ATGAATGAATGAATAAAGTGTTTATTACGTGC-TCCCAAGTTCCAAGCTC 809871 v v v i - i iv i - v i v v iv v C L2d_3end#LINE 513 ATCAATCAATCAACAA-GTATTTATTGAGCGCCTACTATGTGCTCAGCAC 465 chrXqtel1M 809872 TATGCTAATTGCTGGGGGCCA-AAGGAAAAACTCC----CATGATCCCTG 809916 i ivi v vv -i ?i ? v vi---- i C L2d_3end#LINE 464 TGTGCTAGGCGCTGTGGGGAACGANAAAANAGTATAAGACATGGTCCCTG 415 chrXqtel1M 809917 CCCTCGAGGAGCTCCTATTCTAATGAGAGA 809946 i ivi v i vi i C L2d_3end#LINE 414 CCCTCAAGGAGCTTACAATCTAGTTGGGGA 385 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 35.91 CpG sites = 19, Kimura (unadjusted) = 39.90 Transitions / transversions = 1.06 (19/18) Gap_init rate = 0.03 (4 / 123), avg. gap size = 1.75 (7 / 4) 233 16.60 5.57 0.18 chrXqtel1M 810248 810768 (189232) (TC)n#Simple_repeat 1 549 (0) m_b373s252i12 15598 chrXqtel1M 810248 TCACTC-CTCTCTCTC-CTATCTCTCTCTGTCTC-CTGTGTCTCTGTCTC 810294 v - - v v - v v v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chrXqtel1M 810295 T-TCTTTCTCTGTCTCTGTGTCTC-CTGTCTCTCTCTCTC-CTCTCTCTC 810341 - i v v v - v - (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chrXqtel1M 810342 TGTGTCTGCTGTCT-TTTCTGTCTCT-TCTATCTCTCTGTATCTGTCTCT 810389 v v - v - i v - v v v v (TC)n#Simple_ 101 TCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 149 chrXqtel1M 810390 CT-TCTGTCTCTATCTCTCT-TTTTTCTCTCTGTCTCTGTCTCTC-CTGT 810436 - v v - i i v v - v (TC)n#Simple_ 150 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 199 chrXqtel1M 810437 CT-TACCTGTCTC-CTATGTCTCTCT-TCTGTCTGTCTCTGTCTC-CTGT 810482 - vi v - v v - v v v - v (TC)n#Simple_ 200 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 249 chrXqtel1M 810483 CTCTGTGTCT-TCTGTCT-TCTCTGTCTCTGTCTCTCT-TCTGTTTCTGT 810529 v v - v - v v - v i v (TC)n#Simple_ 250 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 299 chrXqtel1M 810530 CTCTCTGTCTCTGTCTC-CTGTCTCTCTGTGTCTCT-TGTCT-TCTCTGT 810576 v v - v v v - v - v (TC)n#Simple_ 300 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 349 chrXqtel1M 810577 CTCTCT-TCTGTTTCTGTCTCTCTGTCTCTGTC-CCCTGTCTCTCTGTGT 810624 - v i v v v - i v v v (TC)n#Simple_ 350 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 399 chrXqtel1M 810625 TTC-CTGTCT-TCTCTGTCTCTCT-TCTCTCTCTCTCTCTCTCTCTCTCT 810671 i - v - v - (TC)n#Simple_ 400 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 449 chrXqtel1M 810672 CTCTCTCTCTCTCTCTCTCTCTC-CTGTCTCTGTGCCTC-CTGTCTCTCT 810719 - v v vi - v (TC)n#Simple_ 450 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 499 chrXqtel1M 810720 CTCTGTCTCTGTCTCTCTGCCTATCCATCTCTCT-TTTCTGTCTCTCTCT 810768 v v vi v iv - i v (TC)n#Simple_ 500 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 549 Matrix = Unknown Transitions / transversions = 0.20 (13/64) Gap_init rate = 0.06 (30 / 520), avg. gap size = 1.00 (30 / 30) 227 36.26 1.10 0.00 chrXqtel1M 810980 811070 (188930) MIRb#SINE/MIR 53 144 (124) m_b373s601i25 15599 chrXqtel1M 810980 ACCCAAGTCTGAACCCTGCCTCAGAAGCTTGCGAGCCGTGTGATTCTGGT 811029 iii ii i i v v vvi i v i iii v MIRb#SINE/MIR 53 ACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGG 102 chrXqtel1M 811030 TTGGTTACTTAAGCTGCCGGAA-CTCACTTTGCTGGTCTACA 811070 ivi v vi v i- v v vi ii MIRb#SINE/MIR 103 CAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTA 144 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 47.55 CpG sites = 20, Kimura (unadjusted) = 52.08 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.01 (1 / 90), avg. gap size = 1.00 (1 / 1) 12 29.78 1.54 4.76 chrXqtel1M 811159 811223 (188777) (GGAAGGG)n#Simple_repeat 1 63 (0) m_b373s252i13 15600 chrXqtel1M 811159 GGAAAGCAGAAGAAGCAAGTGGGGAAGGGGAGAGGGAGAAGAGCAGGAA- 811207 i vi ii v - ii i - -i - (GGAAGGG)n#Si 1 GGAAGGGGGAAGGGGGAAG-GGGGAAGGGGGAAGGGGGAAG-G-GGGAAG 47 chrXqtel1M 811208 GGAGAAAGCAGAAGGG 811223 i i vi (GGAAGGG)n#Si 48 GGGGAAGGGGGAAGGG 63 Matrix = Unknown Transitions / transversions = 3.67 (11/3) Gap_init rate = 0.06 (4 / 64), avg. gap size = 1.00 (4 / 4) 343 24.05 3.80 0.00 chrXqtel1M 812542 812620 (187380) C MIR3#SINE/MIR (13) 195 114 m_b373s601i26 15601 chrXqtel1M 812542 ATAGCAT-TTAGAGTTGGAAGTCACCCCAGAGACCACCTATTCCAGTTCC 812590 v - i i vv ii i i v iii C MIR3#SINE/MIR 195 ATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCC 146 chrXqtel1M 812591 CTCATTTTATTGCCAAGGAAAC--AGACCCAG 812620 iv vii -- i C MIR3#SINE/MIR 145 CTCATTTTACAGATGAGGAAACTGAGGCCCAG 114 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.08 CpG sites = 13, Kimura (unadjusted) = 30.08 Transitions / transversions = 2.17 (13/6) Gap_init rate = 0.03 (2 / 78), avg. gap size = 1.50 (3 / 2) 327 36.43 6.20 0.00 chrXqtel1M 813988 814116 (185884) MIRc#SINE/MIR 13 149 (119) m_b373s601i27 15602 chrXqtel1M 813988 GTACAGAAGGAGATGTGTTGGACTCAGAGTCC-CAGAACCTTAATGTAAA 814036 i vi i iiv iii ii v-v ii vii vii i MIRc#SINE/MIR 13 GTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAG 62 chrXqtel1M 814037 TCTTGACTCTGACATTCACTACCTAACT-ACCCTGA------TGGTTCAC 814079 ii i v i i v ivv - i i------iiv v MIRc#SINE/MIR 63 TCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAAC 112 chrXqtel1M 814080 CTCATTGTGCTTCAGTTCCCTCATCTGCAAAATGAAG 814116 vi v i i i ii MIRc#SINE/MIR 113 CTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGG 149 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 50.78 CpG sites = 33, Kimura (unadjusted) = 54.52 Transitions / transversions = 2.36 (33/14) Gap_init rate = 0.02 (3 / 128), avg. gap size = 2.67 (8 / 3) 390 31.09 6.57 1.39 chrXqtel1M 814007 814143 (185857) MIR3#SINE/MIR 30 173 (35) m_b373s601i28 15602 chrXqtel1M 814007 GGACTCAGAGTCCCAGAACCTTAATGTAAATCTTGACTCTGACATTCACT 814056 vi vviii vii viv i ii i v i v MIR3#SINE/MIR 30 GGACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACT 79 chrXqtel1M 814057 ACCTAACTACCCTGATGG---------TTCACCTCATTGTGCTTCAGTTC 814097 ?v ivv iv -- --------- vi v i i MIR3#SINE/MIR 80 NGCTGTGTGACCT--TGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTT 127 chrXqtel1M 814098 CCTCATCTGCAAAATGAAGCCAGTGGACCAAATCACCTCTGAGGTC 814143 i i vviv i i v i i MIR3#SINE/MIR 128 CCTCATCTGTAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTC 173 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 40.43 CpG sites = 24, Kimura (unadjusted) = 41.74 Transitions / transversions = 1.33 (24/18) Gap_init rate = 0.02 (3 / 136), avg. gap size = 3.67 (11 / 3) 338 24.71 1.67 8.93 chrXqtel1M 814323 814442 (185558) MIRc#SINE/MIR 2 113 (155) m_b374s601i2 15603 chrXqtel1M 814323 GGGACAGTAGGTGGCATCTAGTCGATAGAACACTTAGCTCCTAAAGTCAG 814372 i i -- -- vi v v i vii -- ii MIRc#SINE/MIR 2 GAGGCAGT--GTGG--TGCAGTGGAAAGAGCACTGGACT--TGGAGTCAG 45 chrXqtel1M 814373 AGTGACCTGA-TTCAATGGACCTCAGACACTAACACTTCCTAGCTG-GTG 814420 iiv i- i -- v i-- i v iv v - MIRc#SINE/MIR 46 GAAGACCTGGGTTCGA--GTCCC--GGCTCTGCCACTTACTAGCTGTGTG 91 chrXqtel1M 814421 ACCCTGAGCAAGTCACTTACCC 814442 i i v MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACC 113 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 27.90 CpG sites = 17, Kimura (unadjusted) = 30.56 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.10 (12 / 119), avg. gap size = 1.00 (12 / 12) 15 12.06 0.00 0.00 chrXqtel1M 814879 814906 (185094) (GAAGA)n#Simple_repeat 1 28 (0) m_b374s252i0 15604 chrXqtel1M 814879 GAAGAGAAGAAAAGAGAAGAAAGGAGAA 814906 i i i (GAAGA)n#Simp 1 GAAGAGAAGAGAAGAGAAGAGAAGAGAA 28 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 219 27.90 25.52 1.11 chrXqtel1M 821676 821820 (178180) MIRc#SINE/MIR 24 203 (65) m_b374s601i3 15605 chrXqtel1M 821676 AGGGTGCTGGGCCTACAATCAGCAAG-TCTGAGTTTAAA--CAGTCTCTG 821722 i ii i i iv i v -i i ii i-- v v MIRc#SINE/MIR 24 AGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTG 73 chrXqtel1M 821723 TGACCCTTTTGAGCTGTGTAACA--GGGCA--------AACCTCTGCAAG 821762 i-- v viv i v-- -------- vii MIRc#SINE/MIR 74 C--CACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAG 121 chrXqtel1M 821763 CTT-----------TCTGTGAAGTGGGCAGACTAA-ATC----------A 821790 i ----------- i i v v v - i ---------- MIRc#SINE/MIR 122 CCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTA 171 chrXqtel1M 821791 TCT--TAGGCTTGTTGGGAGGATCTAGTGAAA 821820 i --i v v v i i MIRc#SINE/MIR 172 CCTCACAGGGTTGTTGTGAGGATCAAATGAGA 203 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 34.93 CpG sites = 25, Kimura (unadjusted) = 36.19 Transitions / transversions = 1.67 (25/15) Gap_init rate = 0.07 (10 / 144), avg. gap size = 3.90 (39 / 10) 229 26.70 21.71 1.29 chrXqtel1M 821692 821820 (178180) MIRb#SINE/MIR 43 197 (71) m_b374s601i4 15605 chrXqtel1M 821692 AATCAG-CAAGTCTGAGTTTAAA--CAGTCTCTGTGACCCTTTTGAGCTG 821738 i - iii i ii -- v v i-- v viv MIRb#SINE/MIR 43 AGTCAGACAGACCTGGGTTCGAATCCCGGCTCTGC--CACTTACTAGCTG 90 chrXqtel1M 821739 TGTAACA--GGGCAA--------ACCTCTGCAAGCTT-----------TC 821767 i v-- -------- vii i ----------- MIRb#SINE/MIR 91 TGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATC 140 chrXqtel1M 821768 TGTGAAGTGGGCAGACTAA-ATC-ATCTT--AGGCTTGTTGGGAGGATCT 821813 i i v v v - i - i i-- v v iv MIRb#SINE/MIR 141 TGTAAAATGGGGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTA 190 chrXqtel1M 821814 AGTGAAA 821820 i i MIRb#SINE/MIR 191 AATGAGA 197 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 31.53 CpG sites = 21, Kimura (unadjusted) = 34.10 Transitions / transversions = 1.62 (21/13) Gap_init rate = 0.08 (10 / 128), avg. gap size = 3.00 (30 / 10) 54 36.95 1.92 2.90 chrXqtel1M 822834 823146 (176854) (TG)n#Simple_repeat 1 310 (0) m_b374s252i1 15606 chrXqtel1M 822834 TGTG-GTGTGTGTGCGTGTGTGTGTGCACGTGTATATGTGTGGGTATGGA 822882 - i iii i i v i vi (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 chrXqtel1M 822883 TGTGTGTGTGAGTCTGTG-GTGTGTCTGTGTGGGCCTGTGCTTATTTGGG 822931 v v - v v iv iv i v v (TG)n#Simple_ 51 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 100 chrXqtel1M 822932 TCTGTGTG-GTGTGCATGTGTGGGCACACG-GGGTGTGCTTATGCCCGCA 822979 v - ii v iiiii - v iv i ivi ii (TG)n#Simple_ 101 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 150 chrXqtel1M 822980 CATGTGTGGGTGTGCAACACCTGTGTGTGCATGTGATGTGTGCATGTACA 823029 ii v -viiiiv ii - ii iii (TG)n#Simple_ 151 TGTGTGTGTGTGTG-TGTGTGTGTGTGTGTGTGTG-TGTGTGTGTGTGTG 198 chrXqtel1M 823030 TGTATGTGTGCTGACATGTGCATGTGTTTGGCCATGTG-GTGCAGCTACG 823078 i - -ii ii v vvii - -v - ii (TG)n#Simple_ 199 TGTGTGTGTG-TG-TGTGTGTGTGTGTGTGTGTGTGTGTGTG-TG-TGTG 244 chrXqtel1M 823079 TGTGATGTGTATAGTGTATAT-TATATGTGTGTGTGCATGTATGGGTACA 823127 - i - i i - i i ii i v iii (TG)n#Simple_ 245 TGTG-TGTGTGT-GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 292 chrXqtel1M 823128 TGTGCGCTGTGCGTGTATG 823146 i - i i (TG)n#Simple_ 293 TGTGTG-TGTGTGTGTGTG 310 Matrix = Unknown Transitions / transversions = 2.61 (60/23) Gap_init rate = 0.05 (15 / 312), avg. gap size = 1.00 (15 / 15) 333 22.68 0.90 4.67 chrXqtel1M 826730 826840 (173160) MIR3#SINE/MIR 4 110 (98) m_b374s601i5 15607 chrXqtel1M 826730 GCTGGGTGGCCTTGCAGCGGTCAGAGCACTGGTCCTGGAGTCAGGAGGAC 826779 v i ivv v --- - v iv - MIR3#SINE/MIR 4 GCAGAGTGGCTGAGCAGAG---AGAGCAC-GGACTGGGAGTCAGGAG-AC 48 chrXqtel1M 826780 CTGAGTGAAAATTCAGCTTCAGACACTTCCTAGCTGTGTGGCC-TGGGCA 826828 i vvv i i v vi v v vv ? i - MIR3#SINE/MIR 49 CTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTTGGGCA 98 chrXqtel1M 826829 AGTCACTTAACC 826840 v MIR3#SINE/MIR 99 AGTCACTTCACC 110 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 27.26 CpG sites = 8, Kimura (unadjusted) = 27.26 Transitions / transversions = 0.50 (8/16) Gap_init rate = 0.05 (6 / 110), avg. gap size = 1.00 (6 / 6) 510 19.19 1.01 0.00 chrXqtel1M 826742 826840 (173160) MIRc#SINE/MIR 14 113 (155) m_b374s601i6 15607 chrXqtel1M 826742 TGCAGCGGTCAGAGCACTGGTCCTGGAGTCAGGAGGACCTGAGTGAAAAT 826791 i vv v i i i vvi i MIRc#SINE/MIR 14 TGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGT 63 chrXqtel1M 826792 TCAGCTTCAGACACTTCCTAGCTGTGTGGCC-TGGGCAAGTCACTTAACC 826840 i v vi v v v i - MIRc#SINE/MIR 64 CCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACC 113 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 21.01 CpG sites = 9, Kimura (unadjusted) = 22.26 Transitions / transversions = 0.90 (9/10) Gap_init rate = 0.01 (1 / 98), avg. gap size = 1.00 (1 / 1) 270 31.13 1.18 5.52 chrXqtel1M 826998 827167 (172833) L1ME3G_3end#LINE/L1 54 216 (708) m_b374s551i0 15608 chrXqtel1M 826998 CCAGTGGATAAATGTTCAAAGAATTTGAACAGGCAATTTTCAAAGCAAGA 827047 i i v vv i v iv i iv i L1ME3G_3end#L 54 CCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTCACAGAAGAGGA 103 chrXqtel1M 827048 AACAGGAGCCGGCGATGACCGTATGGAAACATGGTCCAAAGTGCTAA-AA 827096 i vi iiv v i i v i i v v v vvvii i- L1ME3G_3end#L 104 AATACAAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAGTAA 153 chrXqtel1M 827097 TTA-AAACATGCCAATTAAAGCACCATTGAGCTGCCGCATCATGTTTATC 827145 i -ii v v i v v v ----- i v vv L1ME3G_3end#L 154 TCAGGGAAATGCAAATTAAAACAACAATGAGAT-----ACCATTTTTCAC 198 chrXqtel1M 827146 GTATGGACAAAGTTGGCAAAAA 827167 vi --- i - L1ME3G_3end#L 199 CCAT---CAGA-TTGGCAAAAA 216 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 40.65 CpG sites = 25, Kimura (unadjusted) = 40.65 Transitions / transversions = 1.00 (25/25) Gap_init rate = 0.07 (11 / 169), avg. gap size = 1.00 (11 / 11) 326 32.65 1.36 0.00 chrXqtel1M 826998 827144 (172856) L1ME4c_3end#LINE/L1 58 206 (624) m_b374s551i1 15608 chrXqtel1M 826998 CCAGTGGATAAATGTTCAAAGAATTTGAACAGGCAATTTTCAAAGCAAGA 827047 i i vv i iv i iv ? iv i L1ME4c_3end#L 58 CCAATAGATAAATGGGCAAAGGACATGAACAGACAATTCACANAAGAGGA 107 chrXqtel1M 827048 AACAGGAGCCGGCGATGACCGTATGGAAACATGGTCCAAAGTGCTAA-AA 827096 i vi ?iv vvi ii v ii v v v vvvi i- L1ME4c_3end#L 108 AATACAANTAGTAAACAAACACATGGAAAAATGTTCAACCTCGCTAGTAA 157 chrXqtel1M 827097 TTAAA-ACATGCCAATTAAAGCACCATTGAGCTGCCGCATCATGTTTAT 827144 i - v v v v v i iiv i i ii L1ME4c_3end#L 158 TCAAAGAAATGCAAATTAAAGCAACAATGAGATACCATTTTACGCCTAT 206 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 42.27 CpG sites = 26, Kimura (unadjusted) = 44.74 Transitions / transversions = 1.18 (26/22) Gap_init rate = 0.01 (2 / 146), avg. gap size = 1.00 (2 / 2) 486 23.25 0.00 8.55 chrXqtel1M 827176 827302 (172698) MIRb#SINE/MIR 2 118 (150) m_b374s601i7 15609 chrXqtel1M 827176 AAAGGGGCAGCTAGGGGGCGCAGTGGATAGAGCAGCAGCCCTGAAGTCAG 827225 i --- v i v vvi ii i MIRb#SINE/MIR 2 AGAGGGGCAGC---GTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAG 48 chrXqtel1M 827226 GAGGAACTGAGTTCAAATCCGGTTTCAGACACTTAATACTTCCTAGCTAT 827275 ivi v i i v vi v v ------- i MIRb#SINE/MIR 49 ACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTA-------CTAGCTGT 91 chrXqtel1M 827276 GTGACCCTGGGCAAGTCATTTAATCCC 827302 i i i i i MIRb#SINE/MIR 92 GTGACCTTGGGCAAGTTACTTAACCTC 118 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 27.05 CpG sites = 17, Kimura (unadjusted) = 28.27 Transitions / transversions = 1.70 (17/10) Gap_init rate = 0.08 (10 / 126), avg. gap size = 1.00 (10 / 10) 497 22.22 0.00 6.73 chrXqtel1M 827192 827302 (172698) MIRc#SINE/MIR 12 115 (153) m_b374s601i8 15609 chrXqtel1M 827192 GGCGCAGTGGATAGAGCAGCAGCCCTGAAGTCAGGAGGAACTGAGTTCAA 827241 i v vii v i i i v i i MIRc#SINE/MIR 12 GGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGA 61 chrXqtel1M 827242 ATCCGGTTTCAGACACTTAATACTTCCTAGCTATGTGACCCTGGGCAAGT 827291 i v vi v v ------- i i MIRc#SINE/MIR 62 GTCCCGGCTCTGCCACTTA-------CTAGCTGTGTGACCTTGGGCAAGT 104 chrXqtel1M 827292 CATTTAATCCC 827302 i i i MIRc#SINE/MIR 105 CACTTAACCTC 115 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 25.57 CpG sites = 15, Kimura (unadjusted) = 26.91 Transitions / transversions = 1.88 (15/8) Gap_init rate = 0.06 (7 / 110), avg. gap size = 1.00 (7 / 7) 231 33.51 7.84 2.48 chrXqtel1M 827314 827466 (172534) L1MB4_3end#LINE/L1 222 382 (545) m_b374s551i2 15608 chrXqtel1M 827314 CAAAAAGAGAGAGAGAGAGAAATACTGGAGAGACTGTGGGGAAATAGACG 827363 i vi i ivi v i ii v iv i v ivi L1MB4_3end#LI 222 CAAAAAAACGGAAAATAACAAGTGTTGGCGAGGATGTGGAGAAATTGGAA 271 chrXqtel1M 827364 TGTTTGTTCCCTACTGGCGTTACTGCAAATTGGTCCCGCCATTTGGGAGA 827413 ivi i v vi i i vv v i v v v ii vv i L1MB4_3end#LI 272 CCCTCGTGCATTGCTGGTGGGAATGTAAAATGGTGCAGCCGCTGTGGAAA 321 chrXqtel1M 827414 ACAGTTTGGAACTCGGACCC---AAGAGCT---------ATTGCACTGTG 827451 ---- vi --- i i --------- i vv i L1MB4_3end#LI 322 ACAGTTTGG----CGGTTCCTCAAAAAGTTAAACATAGAATTACCATATG 367 chrXqtel1M 827452 ACCCAGCATTGCCAC 827466 v v L1MB4_3end#LI 368 ACCCAGCAATTCCAC 382 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 41.98 CpG sites = 27, Kimura (unadjusted) = 45.59 Transitions / transversions = 1.17 (27/23) Gap_init rate = 0.04 (6 / 152), avg. gap size = 2.67 (16 / 6) 268 33.33 0.00 0.00 chrXqtel1M 827316 827423 (172577) L1MA1_3end#LINE/L1 224 331 (718) m_b374s551i3 15608 chrXqtel1M 827316 AAAAGAGAGAGAGAGAGAAATACTGGAGAGACTGTGGGGAAATAGACGTG 827365 v iv ivi v i v iv i vi iviiv L1MA1_3end#LI 224 AAAAGACAGGCAATAACAAATGCTGGCGAGGATGTGGAGAAAAGGGAACC 273 chrXqtel1M 827366 TTTGTTCCCTACTGGCGTTACTGCAAATTGGTCCCGCCATTTGGGAGAAC 827415 i v v ii i vv v i i v vi i vv L1MA1_3end#LI 274 CTTGTACACTGTTGGTGGGAATGTAAATTAGTACAACCACTATGGAGAAC 323 chrXqtel1M 827416 AGTTTGGA 827423 L1MA1_3end#LI 324 AGTTTGGA 331 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 44.79 CpG sites = 18, Kimura (unadjusted) = 44.79 Transitions / transversions = 1.00 (18/18) Gap_init rate = 0.00 (0 / 107), avg. gap size = 0.0 (0 / 0) 392 32.39 10.32 2.40 chrXqtel1M 827334 827643 (172357) L1ME4c_3end#LINE/L1 242 575 (255) m_b374s551i4 15608 chrXqtel1M 827334 AATACTGGAGAGACTGTGGGGAAATAGACGTGTTTGTTCCCTACTGGCGT 827383 i v i? i v iv iiii?i ii v vi i i v L1ME4c_3end#L 242 AATGCTGGCGAGGNTGCGGTGAAACTGGTACNCTCATACATTGCTGGTGG 291 chrXqtel1M 827384 TACTGCAAATTGGTCCCGCCATTTGGGAGAACAGTTTGG-AACTCGGACC 827432 i ? i v vi v v i i i - iv v -i L1ME4c_3end#L 292 CANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGGCAATACGTA-T 340 chrXqtel1M 827433 CAAGAGCTAT-----------TGCACTGTGACCCAGCATTGCCAC--CAG 827469 i ----------- i v v i v v -- v L1ME4c_3end#L 341 CAAGAGCCATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTG 390 chrXqtel1M 827470 TGAACTCA--CTGAGA-------TCAAGGAAAGAGAAAAAGGAGCCATAA 827510 v i i -- i i------- -- ii i -- i v L1ME4c_3end#L 391 GGAATTTATCCTAAGGAAATAATTCAA--AAGAAGGAAAA--AGCTATAT 436 chrXqtel1M 827511 GGACAAAACTAGTTAGGACAACTCTTTTTGTAAGAGCAAGAAACTAGAAA 827560 v i iv iv i vvi i vi v i v i i i i L1ME4c_3end#L 437 GCACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAA 486 chrXqtel1M 827561 ----CTAAAGGTTGTCTACCTGTGAAAGAATGGTGAGACACATTATGG-- 827604 ---- --- i v vi iiii v iii v -- L1ME4c_3end#L 487 CAACCTAAA---TGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTA 533 chrXqtel1M 827605 ---CGTGTGAATGGAATATTATTATATCATGAGAAATGGCAA 827643 --- ?vv vi vvvii v i ii L1ME4c_3end#L 534 CATCNACTCGATGGAATATTATGCAGCCATTAAAAATGATAA 575 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 42.63 CpG sites = 60, Kimura (unadjusted) = 45.13 Transitions / transversions = 1.58 (60/38) Gap_init rate = 0.05 (15 / 309), avg. gap size = 2.67 (40 / 15) 228 36.64 6.54 1.88 chrXqtel1M 827694 827846 (172154) C L3#LINE/CR1 (1256) 2843 2684 m_b374s601i9 15610 chrXqtel1M 827694 TAATAATCCCTGCTTCCCCTTCCAGATACCCACTAGCTCTCCCCTCAATA 827743 i i v i ii i ii i i v i iv ivi i C L3#LINE/CR1 2843 TAGTGATCACCGCTTCCTTTTCTAAGTGCTCACAAACCATCTGTTTAATA 2794 chrXqtel1M 827744 ATGCAATCTGGCCATTTTGCCAGGAACC-----CA-----ACTGGCCAAT 827783 v iv i -v i i i ----- ----- i i vi C L3#LINE/CR1 2793 ATCCGTTCTAG-AATTTTGCCGGGGATCGACGTCAAGCTTACCGGTCTGT 2745 chrXqtel1M 827784 AGGTCAAAGATTTTGTTCTCTTTCCTTTTAGGAAAATCAATTCAGCAGCT 827833 v i?v v iii ii i i vvi ? vii?v ?i vi C L3#LINE/CR1 2744 AGTTTNCAGAATCCATCTTTTTTCCCTTTTTAAAANTAGGNACNACATTT 2695 chrXqtel1M 827834 CTTCGGATCTCCA 827846 vii -- C L3#LINE/CR1 2694 GCCCG--TCTCCA 2684 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 50.92 CpG sites = 38, Kimura (unadjusted) = 57.29 Transitions / transversions = 2.24 (38/17) Gap_init rate = 0.03 (5 / 152), avg. gap size = 2.60 (13 / 5) 414 33.98 4.46 9.35 chrXqtel1M 827866 828089 (171911) C L3#LINE/CR1 (1483) 2616 2403 m_b374s601i10 15610 chrXqtel1M 827866 TCAGCCAGTTCTTTCAGTACCTCGAACAGCGATTCATCTGCATTTCAGGA 827915 v v ii iivv ii i viii vii C L3#LINE/CR1 2616 TCTGCAAGTTCTTTCAGTACCCTGGGATGTAATTCGTCTGGGCCTGGAGA 2567 chrXqtel1M 827916 CTTGAATTCAGCAAAGGCCAGCTAGGT-------TGCTCCCTACTTA--- 827955 i viv i -i ------- i vi v i --- C L3#LINE/CR1 2566 CTTGAACTCATTTAAAGC-GGCTAGGTGCTCTCTTACTATCTCCTCACCT 2518 chrXqtel1M 827956 ATCTTGGTCTTAATCTCCCTGGCAAGGGGGGTAGGGAAGAGAGCTTTGTG 828005 v v vi vvi v iv -------------- v C L3#LINE/CR1 2517 ATCTTGGGCTTCAATTCCCTCTTAACGATG--------------TTTGTT 2482 chrXqtel1M 828006 GCACTGTTCTGCCTGCTCCAAAGATTACTCTTCTGAACAGAAAAGAAAGA 828055 --- iii vi iiv ii i i i vi i i -- vi C L3#LINE/CR1 2481 ---CTACCCTTTCCAGTCTGAAGATCATTCTCCTTGATAGAGAAG--ACG 2437 chrXqtel1M 828056 GAAGCAAAAGAACGCTTGAATGATTCTGCCTTTT 828089 v iviv i ii i i C L3#LINE/CR1 2436 GAAGCAAAATAGGAGTTGAGTAGTTCTGCTTTCT 2403 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 44.51 CpG sites = 44, Kimura (unadjusted) = 47.39 Transitions / transversions = 1.76 (44/25) Gap_init rate = 0.10 (22 / 223), avg. gap size = 1.36 (30 / 22) 194 25.01 0.00 2.08 chrXqtel1M 828163 828211 (171789) L3#LINE/CR1 4043 4090 (9) m_b374s601i11 15611 chrXqtel1M 828163 GGTTGGGCTCCATGACTTTGGAAGGGGCCTTCTAACTCTGGAATTTTGT 828211 i vv i iv- vv i ii i L3#LINE/CR1 4043 GGTTGGACTAGATGACCTCT-AAGGTCCCTTCCAACTCTGAGATTCTGT 4090 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 31.04 CpG sites = 7, Kimura (unadjusted) = 31.04 Transitions / transversions = 1.40 (7/5) Gap_init rate = 0.02 (1 / 48), avg. gap size = 1.00 (1 / 1) 26 25.15 0.00 2.60 chrXqtel1M 828445 828523 (171477) (ACAGAG)n#Simple_repeat 1 77 (0) m_b374s252i2 15612 chrXqtel1M 828445 ACACACACAGAGACATAGTGTTAGAGACAGAGACAGAGACACACATGAAA 828494 v v -- v vi v v iii i (ACAGAG)n#Sim 1 ACAGAGACAGAGAC--AGAGACAGAGACAGAGACAGAGACAGAGACAGAG 48 chrXqtel1M 828495 ACAGAGATAAAGACTGAAACAGAGAGAGA 828523 i i v i v (ACAGAG)n#Sim 49 ACAGAGACAGAGACAGAGACAGAGACAGA 77 Matrix = Unknown Transitions / transversions = 1.00 (8/8) Gap_init rate = 0.03 (2 / 78), avg. gap size = 1.00 (2 / 2) 12 27.71 0.00 2.27 chrXqtel1M 830674 830718 (169282) (CAAAA)n#Simple_repeat 1 44 (0) m_b374s252i3 15613 chrXqtel1M 830674 CAAAACTAAACAAAATAAAAATAAAACCATCCAAGGAAAAAAAAA 830718 v -v i v vv iiv v (CAAAA)n#Simp 1 CAAAACAAAACAAAA-CAAAACAAAACAAAACAAAACAAAACAAA 44 Matrix = Unknown Transitions / transversions = 0.43 (3/7) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 27 33.98 1.31 3.33 chrXqtel1M 832508 832636 (167364) (ATAT)n#Simple_repeat 1 125 (25) m_b374s252i4 15614 chrXqtel1M 832508 ATATTTACATATAGGTAAATGTGTGTGTGTCAGTATATGTAGATATATAT 832557 v i vi v i i i i i - - i v (ATAT)n#Simpl 1 ATATATATATATATATATATATATATATAT-A-TATATATATATATATAT 48 chrXqtel1M 832558 GCATGT-TACTCTATGTGTGTATGTAGATATATGTACACATGAGGATCTG 832606 ii i - - v i i i i v i i i - -v v i (ATAT)n#Simpl 49 ATATATATA-TATATATATATATATATATATATATATATAT-A-TATATA 95 chrXqtel1M 832607 TGGATGGATGTGAATATATGTATATATATA 832636 iv iv i iv i (ATAT)n#Simpl 96 TATATATATATATATATATATATATATATA 125 Matrix = Unknown Transitions / transversions = 2.18 (24/11) Gap_init rate = 0.05 (6 / 128), avg. gap size = 1.00 (6 / 6) 29 30.77 1.67 2.52 chrXqtel1M 832541 832636 (167364) (TA)n#Simple_repeat 1 94 (25) m_b374s252i5 15614 chrXqtel1M 832541 TATATGTAGATATATATGCATGT-TACTCTATGTGTGTATGTAGATATAT 832589 i v ii i - - v i i i i v (TA)n#Simple_ 1 TATATATATATATATATATATATATA-TATATATATATATATATATATAT 49 chrXqtel1M 832590 GTACACATGAGGATCTGTGGATGGATGTGAATATATGTATATATATA 832636 i i i - -v v i iv iv i iv i (TA)n#Simple_ 50 ATATATAT-A-TATATATATATATATATATATATATATATATATATA 94 Matrix = Unknown Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.04 (4 / 95), avg. gap size = 1.00 (4 / 4) 29 0.00 0.00 0.00 chrXqtel1M 832637 832661 (167339) (TG)n#Simple_repeat 1 25 (0) c_b374s251i0 15615 chrXqtel1M 832637 TGTGTGTGTGTGTGTGTGTGTGTGT 832661 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGT 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 29 30.77 1.67 2.52 chrXqtel1M 832662 832684 (167316) (TA)n#Simple_repeat 95 118 (1) m_b374s252i5 15616 chrXqtel1M 832662 ATCTATATATCTAT-TACATATAT 832684 v v - i (TA)n#Simple_ 95 ATATATATATATATATATATATAT 118 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.05 (1 / 22), avg. gap size = 1.00 (1 / 1) 18 23.01 3.57 0.00 chrXqtel1M 832903 832958 (167042) (ATTTT)n#Simple_repeat 1 58 (0) m_b374s252i6 15617 chrXqtel1M 832903 ATGTTCTTTCATTTTGTTTTGTTTTATTTT-TTATCTTTT-TTCTATTCT 832950 v v i i i - v v - i i (ATTTT)n#Simp 1 ATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTT 50 chrXqtel1M 832951 GTTTTTTT 832958 i v (ATTTT)n#Simp 51 ATTTTATT 58 Matrix = Unknown Transitions / transversions = 1.20 (6/5) Gap_init rate = 0.04 (2 / 55), avg. gap size = 1.00 (2 / 2) 278 31.58 2.08 1.03 chrXqtel1M 833113 833208 (166792) MIRb#SINE/MIR 40 136 (132) m_b374s601i12 15618 chrXqtel1M 833113 TGGAGT--GCTAGGCCTGGAGTTCAAATATAGGTTCAGACACTTCCTAGT 833160 -- vi i - i viv i v v v i MIRb#SINE/MIR 40 TGGAGTCAGACAGACCTGG-GTTCGAATCCCGGCTCTGCCACTTACTAGC 88 chrXqtel1M 833161 TGTGCAATGCTGGGCAAGTCACTGGGCATACTTCTGCCCCCATTTCCT 833208 ii ivi i vii v vii vv i vi MIRb#SINE/MIR 89 TGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCT 136 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 40.29 CpG sites = 17, Kimura (unadjusted) = 42.13 Transitions / transversions = 1.31 (17/13) Gap_init rate = 0.02 (2 / 95), avg. gap size = 1.50 (3 / 2) 224 35.22 0.75 4.65 chrXqtel1M 833122 833255 (166745) MIR3#SINE/MIR 45 173 (35) m_b374s601i13 15618 chrXqtel1M 833122 AGGCCTGGAGTTCAAATATAGGTTCAGACACTTCCTAGTTGTGCAATGCT 833171 i - v i viv i v v vv ? i ii ivi MIR3#SINE/MIR 45 AGACCTGG-GTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACCTT 93 chrXqtel1M 833172 GGGCAAGTCACTGGGCATACTTCT-GCCCCCATTTCCTTTTTTTTTTTCC 833220 --v ivii - v i v i i iv i v vvvv MIR3#SINE/MIR 94 GGGCAAGTCACT--TCACCTCTCTGGGCCTCAGTTTCCTCATCTGTAAAA 141 chrXqtel1M 833221 TGAGGCAATTGGGATTAAGTGACTTTCCCAGGGTC 833255 vii - i ii -- ii i i MIR3#SINE/MIR 142 TGAGGGGGTT-GGACTAGATGA--TCTCTAAGGTC 173 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 49.83 CpG sites = 26, Kimura (unadjusted) = 49.83 Transitions / transversions = 1.37 (26/19) Gap_init rate = 0.05 (7 / 133), avg. gap size = 1.00 (7 / 7) 284 30.96 0.00 1.19 chrXqtel1M 833124 833208 (166792) MIR#SINE/MIR 46 129 (133) m_b374s601i14 15618 chrXqtel1M 833124 GCCTGGAGTTCAAATATAGGTTCAGACACTTCCTAGTTGTGCAATGCTGG 833173 - i viv i v v v i ii ivi MIR#SINE/MIR 46 GCCTGG-GTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGG 94 chrXqtel1M 833174 GCAAGTCACTGGGCATACTTCTGCCCCCATTTCCT 833208 i vii v vii v i vi MIR#SINE/MIR 95 GCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCT 129 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 39.02 CpG sites = 15, Kimura (unadjusted) = 41.07 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.01 (1 / 84), avg. gap size = 1.00 (1 / 1) 403 25.31 0.92 5.77 chrXqtel1M 833220 833328 (166672) C MIRc#SINE/MIR (141) 127 24 m_b374s601i15 15619 chrXqtel1M 833220 CTGAGGC-AATTGGGATTAAGTGACTTTCCCAGGGTCACACAGCCAGAAG 833268 -v vv i i v i i --- C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG--- 81 chrXqtel1M 833269 TGTTAAGTGTCTGAGATCACATTTGAACTCAGGTCCTGCTGACTTCAGGA 833318 --- v v viviv i i i i v i i v C MIRc#SINE/MIR 80 ---TAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGT 34 chrXqtel1M 833319 CTGATGCTCT 833328 iii C MIRc#SINE/MIR 33 CCAGTGCTCT 24 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 28.56 CpG sites = 15, Kimura (unadjusted) = 31.39 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.06 (7 / 108), avg. gap size = 1.00 (7 / 7) 205 25.98 16.84 2.78 chrXqtel1M 833365 833459 (166541) MIRb#SINE/MIR 161 268 (0) m_b374s601i16 15618 chrXqtel1M 833365 ACCTATCTCCCTGAGTTTTTTAATGCAGATCAGATGAGATAAT---TGAA 833411 i v v i v --i vi i i --- v MIRb#SINE/MIR 161 ACCTACCTCGCAGGGTTGTT--GTGAGGATTAAATGAGATAATGCATGTA 208 chrXqtel1M 833412 AAGCACT------------TGACATATAGTAAACACTTTG-AAAGAGTTA 833448 i ------------ i i i i ivi- vi vi MIRb#SINE/MIR 209 AAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAAATGGTAG 258 chrXqtel1M 833449 CTGTTATTATT 833459 -i MIRb#SINE/MIR 259 CT-CTATTATT 268 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 29.96 CpG sites = 16, Kimura (unadjusted) = 33.30 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.06 (6 / 94), avg. gap size = 3.17 (19 / 6) 16 19.86 0.00 0.00 chrXqtel1M 833465 833499 (166501) (TAG)n#Simple_repeat 1 35 (0) m_b374s252i8 15620 chrXqtel1M 833465 TAGTAATAGTACTAGTAGCATCAGCAGTAGTAGTA 833499 i v i vi i (TAG)n#Simple 1 TAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTAGTA 35 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 13 19.92 0.00 6.98 chrXqtel1M 833460 833505 (166495) (AGTAAT)n#Simple_repeat 1 43 (0) m_b374s252i7 15621 chrXqtel1M 833460 AGTCATAGTAATAGTACTAGTAGCATCAGCAGTAGTAGTATCAATA 833505 v v -- - i i i vi (AGTAAT)n#Sim 1 AGTAATAGTAATAGTAATAGTA--AT-AGTAATAGTAATAGTAATA 43 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.07 (3 / 45), avg. gap size = 1.00 (3 / 3) 493 33.04 3.39 7.65 chrXqtel1M 834731 835261 (164739) L1M3_orf2#LINE/L1 1217 1726 (1562) m_b374s551i5 15622 chrXqtel1M 834731 AAGAAATTATCAGAAACTACTTTGGCCAATTGTATTTTAACAAAACTGCT 834780 iii i v i v iv i ivii viv v L1M3_orf2#LIN 1217 AAAGGATCATAAGAGACTACTATGAACAATTATACGCCAACAAATTGGAT 1266 chrXqtel1M 834781 AA----GAAGAAATAAGTGAACACTTACCTCACTGCCCTCACAAAAGTAT 834826 ---- iii i --- ---------- --- i ii L1M3_orf2#LIN 1267 AACCTAGAAGAAATGGATAAA---TT----------CCT---AGAAACAT 1300 chrXqtel1M 834827 AGAATTCTACATTAGCAAAA---AA----GGAGAAATAGACTATTCAAGT 834869 v i- ----- i --- ---- i vv iii ii L1M3_orf2#LIN 1301 ACAAC-CTAC-----CAAGACTGAATCATGAAGAAATAGAAAATCTGAAC 1344 chrXqtel1M 834870 AACCCAGTATCAGAAAAAGAAATTGAATAAGCCATAAACGAACTACCAG- 834918 iv i v iiiv i i v iv v vi v v i- L1M3_orf2#LIN 1345 AGACCAATAACGAGTAAGGAGATTGAATCAGTAATCAAAAACCTCCCAAC 1394 chrXqtel1M 834919 -AGGAAAAGATTTTGCGACCAGATGGATTTATAAACAAATTCTAACAGAC 834967 - i --iiiiv v i iviiii v i L1M3_orf2#LIN 1395 AAAGAAAAG--CCCAGGACCAGATGGCTTCACTGGTGAATTCTACCAAAC 1442 chrXqtel1M 834968 ATTCAAAGAACAATTAATTCCATTATTCCATGAACTATTTGCAATACTAA 835017 i v v v vi i vii -i v v -- L1M3_orf2#LIN 1443 ATTTAAAGAAGAATTAATACCAATCCTTCTCAAACT-CTTCCAAAA--AA 1489 chrXqtel1M 835018 GTAAA---GAAGGCACCCTTCCAATCCTTTTCTGTGATACAAATGACACA 835064 v i --- i v v v iiv i i ------- i - L1M3_orf2#LIN 1490 TTGAAGAGGAGGGAACACTTCCAAACTCATTTTATGA-------GGC-CA 1531 chrXqtel1M 835065 GCTGTGTTCTTGATATTTAAACCCAGG-AGAAATAAAGCAAAGAAAGAGG 835113 -i vvi i -ii v i- i i i vvi ii ii L1M3_orf2#LIN 1532 GC-ATTACCCTGATA-CCAAAGCCAGACAAAGACACTACAAGAAAAGAAA 1579 chrXqtel1M 835114 ACTATAGATTAATCTCCCTAATAAACATTGATACAAACATTTAAAATAAA 835163 i iii v i i v i v iivv i- L1M3_orf2#LIN 1580 ACTACAGGCCAATATCCCTGATGAACATAGATGCAAAAATCCTCAAC-AA 1628 chrXqtel1M 835164 AATATTAGCGGGCAGGCTATAAAAACATAATAGGAAAATTTTACACTCTT 835213 i iii v iv vi v i i v ii ii iv - v L1M3_orf2#LIN 1629 AATACTAGCAAACCGAATTCAACAGCACATTAAAAGGATCATACAC-CAT 1677 chrXqtel1M 835214 GACT-GGTTAGATTTATATCAGGAATTCAGGGTTGGTTCAACATAAGGA 835261 i-i vi vi v i v i v v ? L1M3_orf2#LIN 1678 GACCAAGTGGGATTTATCCCTGGGATGCAAGGATGGTTCAACATACGNA 1726 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 44.96 CpG sites = 104, Kimura (unadjusted) = 45.76 Transitions / transversions = 1.79 (104/58) Gap_init rate = 0.09 (47 / 530), avg. gap size = 1.21 (57 / 47) 629 34.53 0.73 3.25 chrXqtel1M 834847 835256 (164744) L1M4_orf2#LINE/L1 1328 1727 (1567) m_b374s551i6 15622 chrXqtel1M 834847 AAGGAGAAATAGACTATTCAAGTAACCCAGTATCAGAAAAAGAAATTGAA 834896 i vv iii i iv vi v iiv i L1M4_orf2#LIN 1328 AAGAAGAAATAGAAAATCTGAATAGACCTATAACAAGTAAAGAGATTGAA 1377 chrXqtel1M 834897 TAAGCCATAAACGAAC-TACCA-GAGGAAAAGATTTTGCGACCAGATGGA 834944 v iv v vi - v -i i --iiiiv ? v L1M4_orf2#LIN 1378 TTAGTAATCAAAAAACTTCCCACAAAGAAAAG--CCCAGGNCCAGATGGC 1425 chrXqtel1M 834945 TTTATAAACAAATTCTAACAGACATTCAAAGAACAATTAATTCCATTATT 834994 i iviiii v i i v iv v vi L1M4_orf2#LIN 1426 TTCACTGGTGAATTCTACCAAACATTTAAAGAAGAATTAACACCAATCCT 1475 chrXqtel1M 834995 CCATGAACTATTTGCAATACTAAGTAAAGAAGGCACCCTTCCAATCCTTT 835044 i ii v ivv v v iivi i i v v v v iiv L1M4_orf2#LIN 1476 TCACAAACTCTTCCAAAAAATAGAAGAGGAGGGAACACTTCCCAACTCAT 1525 chrXqtel1M 835045 TCTGTGATACAAATGACACAGCTGTGTTCTTGATATTTAAACCCAGGAGA 835094 i vi v i ivi --------- i iiv viiv i L1M4_orf2#LIN 1526 TCTATGAGGCCAGTATTAC---------CCTGATACCAAAACCAGACAAA 1566 chrXqtel1M 835095 AATAAAGCAAAGAAAGAGGACTATAGATTAATCTCCCTAATAAACATTGA 835144 i i vvi ii ii i ii v v i i v L1M4_orf2#LIN 1567 GACATCACAAGAAAAGAAAACTACAGACCAATATCCCTTATGAATATAGA 1616 chrXqtel1M 835145 TACAAACATTTAAAATAAAAATATTAGCGGGCAGGCTATAAAAACATAAT 835194 i v iivv i- i iii v iv vi iv vv L1M4_orf2#LIN 1617 TGCAAAAATCCTCAAC-AAAATACTAGCAAACCGAATCCAGCAACATATA 1665 chrXqtel1M 835195 AGGAAAATTTTACACTCTTGACT-GGTTAGATTTATATCAGGAATTCAGG 835243 ii ii v - v i-i vi vi v i L1M4_orf2#LIN 1666 AAAAGGATTATACAC-CATGACCAAGTGGGATTTATCCCAGGAATGCAAG 1714 chrXqtel1M 835244 GTTGGTTCAACAT 835256 L1M4_orf2#LIN 1715 GTTGGTTCAACAT 1727 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 48.40 CpG sites = 82, Kimura (unadjusted) = 48.40 Transitions / transversions = 1.49 (82/55) Gap_init rate = 0.04 (16 / 409), avg. gap size = 1.00 (16 / 16) 18 12.57 0.00 0.00 chrXqtel1M 836231 836257 (163743) (A)n#Simple_repeat 1 27 (0) m_b374s252i9 15623 chrXqtel1M 836231 AAAAAAAAAAAAAAGAGAAAAAAGAAA 836257 i i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAA 27 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 36 23.30 0.91 4.72 chrXqtel1M 836384 836493 (163507) (GAGG)n#Simple_repeat 1 106 (0) m_b374s252i10 15624 chrXqtel1M 836384 GAGAGGAAGGAAGGAGGGAGGGAGGGAAGAAAAGAAAGGAGGAAGAGAGG 836433 - i i - ii i i i i i (GAGG)n#Simpl 1 GAG-GGAGGGAGGGAGGGAGGGAGGG-AGGGAGGGAGGGAGGGAGGGAGG 48 chrXqtel1M 836434 GAGGGGAAAAAAGGAGAGAGGGAGAG-GGGAGAGGAGGGAAGAGAGGAAG 836482 - iii i i i - - - i i (GAGG)n#Simpl 49 GA-GGGAGGGAGGGAGGGAGGGAGGGAGGGAG-GGAGGG-AGGGAGGGAG 95 chrXqtel1M 836483 GGATGGAGAGA 836493 v i (GAGG)n#Simpl 96 GGAGGGAGGGA 106 Matrix = Unknown Transitions / transversions = 18.00 (18/1) Gap_init rate = 0.06 (6 / 109), avg. gap size = 1.00 (6 / 6) 291 32.00 2.40 0.00 chrXqtel1M 836865 836989 (163011) L1PB_orf2#LINE/L1 2010 2137 (1157) m_b374s551i7 15625 chrXqtel1M 836865 AGTCCTAGAAGTACTAATTCTAGCAATAAGATAAGAAAGAAAAATCAAAG 836914 v i v iiivv v i i i i v i L1PB_orf2#LIN 2010 AGTACTGGAAGTCCTAGCCAGAGCAATCAGACAAGAGAAAGAAATAAAGG 2059 chrXqtel1M 836915 GAATTAATGTAGGCAGAGAAGGAA--AAATTGTGGCT-TTTGTAGATGAT 836961 v iv vi v i i i i i-- i v - iv L1PB_orf2#LIN 2060 GCATCCAAATCGGTAAAGAGGAAGTCAAACTGTCGCTGTTTGCTGATGAT 2109 chrXqtel1M 836962 ATGAGTATTCGTTTAGAACATCCTACAG 836989 vii ?iiii v i v L1PB_orf2#LIN 2110 ATGATCGTNTACCTAGAAAACCCTAAAG 2137 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 42.40 CpG sites = 25, Kimura (unadjusted) = 44.06 Transitions / transversions = 1.67 (25/15) Gap_init rate = 0.02 (2 / 124), avg. gap size = 1.50 (3 / 2) 282 29.97 8.61 1.53 chrXqtel1M 837022 837265 (162735) L1ME4a_3end#LINE/L1 307 567 (304) m_b374s551i8 15622 chrXqtel1M 837022 CAGCCATTCTGGAAAGCAATTGGTAAATATGTTT--GAAGTC------A- 837062 i v ii v vv v --i i ------ - L1ME4a_3end#L 307 CAACCTTTCTGGAGGGCAATTTGGCAATATGTATCAAAAGCCTTAAAAAT 356 chrXqtel1M 837063 --CCAAACCTTTTGATTCAGGGATGTCTCTACTAGGCCTGAATCTCAAAG 837110 --? v i ii vi vi v v vv vv ii i L1ME4a_3end#L 357 GTNCATACCCTTTGACCCAGTAATTCCACTTCTAGGAATTTATCCTAAGG 406 chrXqtel1M 837111 AAGTCAA--AGAAAGG-GAAAAAAAATTCATAGTTACAAAAATATTTATA 837157 i - -- i v - ? v i i i-- ii i i v L1ME4a_3end#L 407 AAAT-AATCAGAGATGTGNACAAAGATTTATG--TACAAGGATGTTCATC 453 chrXqtel1M 837158 GCAGC-TCAATTGTGGTTGCCCCAACTGGGAAACTAAAGGGATGTCTACT 837206 - i v i ii v vvv v v v vvvii i vi L1ME4a_3end#L 454 GCAGCATTATTTATAATAGCGAAAAATTGGAAACAACCTAAATGTCCAAC 503 chrXqtel1M 837207 TACTGGGAAATGGCAAAATA-----TGGTGGATGAATGTAATGGAATATT 837251 v iv i ? iv ----- iv vv i? L1ME4a_3end#L 504 AATAGGGGANTGGTTAAATAAATTATGGTACATCCATANAATGGAATATT 553 chrXqtel1M 837252 ATTGTA-CCATAAAA 837265 - i - v L1ME4a_3end#L 554 A-TGCAGCCATTAAA 567 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 39.69 CpG sites = 36, Kimura (unadjusted) = 39.69 Transitions / transversions = 1.00 (36/36) Gap_init rate = 0.05 (13 / 243), avg. gap size = 1.92 (25 / 13) 289 19.15 0.00 0.00 chrXqtel1M 839399 839445 (160555) L2d_3end#LINE/L2 460 506 (10) m_b374s601i17 15626 chrXqtel1M 839399 GCACAGTGCTTGGCACATAATCGGTGCTTAATAAATGCTTATTGACT 839445 vi i v i i i i i L2d_3end#LINE 460 GCACAGTGCTGAGCACATAGTAGGCGCTCAATAAATACTTGTTGATT 506 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 20.21 CpG sites = 7, Kimura (unadjusted) = 23.03 Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 42 27.59 3.80 0.61 chrXqtel1M 839446 839603 (160397) (CTCT)n#Simple_repeat 1 163 (0) m_b374s252i11 15627 chrXqtel1M 839446 CTCTCTGCCTGTCTCTCTGTCTGTCTCTCTCATGTGTCTGGCTTTCTGTC 839495 vi v v v - v v vv i v (CTCT)n#Simpl 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TCTCTCTCTCTCTCTCTC 49 chrXqtel1M 839496 TCTCCATC-CTCTCTATCTCTGTCTCTCCCTCCTTCCCTTTCTGTCCCTG 839544 iv - v v i ii i i v i v (CTCT)n#Simpl 50 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 99 chrXqtel1M 839545 TCTCT-TCCATCCCTCTCCCTC-CTGGGTCTCCCCTTGTCTC-CTC-CTC 839590 - iv i i - vvv i ii v - - (CTCT)n#Simpl 100 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 149 chrXqtel1M 839591 TGTCTGTCT-TCTC 839603 v v - (CTCT)n#Simpl 150 TCTCTCTCTCTCTC 163 Matrix = Unknown Transitions / transversions = 0.71 (15/21) Gap_init rate = 0.04 (7 / 157), avg. gap size = 1.00 (7 / 7) 244 32.35 3.92 0.00 chrXqtel1M 840164 840265 (159735) C MIR3#SINE/MIR (6) 202 97 m_b374s601i18 15628 chrXqtel1M 840164 TAGGATCCTAGGCCGTCGGGGTTG-AGCACACCTTGGGGACCCCGTAGTC 840212 i v ivi i i i - iviv i i i viv C MIR3#SINE/MIR 202 TAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTC 153 chrXqtel1M 840213 CCATCCC-GCATTTTAGAGATCAGGAAA-TG-GATTTCGAGAAGGAAAGG 840259 v i -v v v - - iiiiv i vi v C MIR3#SINE/MIR 152 CAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGT 103 chrXqtel1M 840260 GGCTTG 840265 i C MIR3#SINE/MIR 102 GACTTG 97 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 44.01 CpG sites = 20, Kimura (unadjusted) = 44.01 Transitions / transversions = 1.54 (20/13) Gap_init rate = 0.04 (4 / 101), avg. gap size = 1.00 (4 / 4) 703 25.93 15.74 0.00 chrXqtel1M 840373 840588 (159412) MIRc#SINE/MIR 17 266 (2) m_b374s601i19 15629 chrXqtel1M 840373 AATGGCTAGAACGTTGGACCTGGAGTTAGAAAGGTCTGAGTTTGAATTCA 840422 i vv i ii i i i ii i i i i v MIRc#SINE/MIR 17 AGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCC 66 chrXqtel1M 840423 ATCTCAGATGCTTCCTAGCCATGTGACCCTAGGCAAGTCACTGCATCTCT 840472 iv v vii v ii i i vv i MIRc#SINE/MIR 67 GGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCT 116 chrXqtel1M 840473 C--AGCCTCAGTTTCCTTAACTGTAAAATGGGGAT-----------CCCC 840509 -- i v ----------- i MIRc#SINE/MIR 117 CTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCT 166 chrXqtel1M 840510 ACC-------------CGTTGGGTAGA------GAGATTGCAAATGT-AA 840539 i -------------i v vi ------ viiiv - MIRc#SINE/MIR 167 GCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAA 216 chrXqtel1M 840540 AGCAC-TTGTAAGTTTTAAAGTGAGATATAAATACTAGCTGTTATGGTTA 840588 i - ii v vv i iiv v? vi MIRc#SINE/MIR 217 AGCGCTTTGTAAACTGTAAAGTGCTATACAAATGTAAGGNGTTATTATTA 266 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.92 CpG sites = 36, Kimura (unadjusted) = 33.07 Transitions / transversions = 1.80 (36/20) Gap_init rate = 0.03 (6 / 215), avg. gap size = 5.67 (34 / 6) 264 30.98 20.35 2.21 chrXqtel1M 840567 840797 (159203) C L3#LINE/CR1 (119) 3980 3709 m_b374s601i20 15630 chrXqtel1M 840567 TAAATACTAGCTGTTATGGTTACCTCATTACCTTTGAAGACATCTTGTTT 840616 i i ivv v v i vv v i i?vi i v iii i C L3#LINE/CR1 3980 TGAACACCTCCAGTGACGGGGAGCTCACTACCTCNCGAGGCAGCCCATTC 3931 chrXqtel1M 840617 -GTTTTCACACAGTCC--ATT--TAAGAAGCTTTTCCTTCTAATTA---- 840657 -i iiv ii -- -- ii i i v v v ---- C L3#LINE/CR1 3930 CATTTTTGGACAGCTCTGATTGTTAGAAAGTTCTTCCTTATATTGAGCCG 3881 chrXqtel1M 840658 -----CACCCCTTTG-AACTTCTCCCTGTTGGTCCCAATTCTTCCTTAT- 840700 -----ii i ii - iv ii i i v i v - C L3#LINE/CR1 3880 AAATCTGCCTCCCTGTAACTTCCACCCATTGGTCCTAGTTCTGCCCTCTG 3831 chrXqtel1M 840701 -AGCCA---------------ATTCCTCT---AGATAA--GT-------- 840721 - --------------- i --- v i -- i-------- C L3#LINE/CR1 3830 GAGCCACACAGAATAAGTCTAATCCCTCTTCCACATGACAGCCCTTCAAA 3781 chrXqtel1M 840722 TGTTTAAAGATGG-TGTCATGTCTTCCTGGACTCTAAATCTTCTCTTTTC 840770 i i ii - i i ------ i i C L3#LINE/CR1 3780 TATTTGAAGACAGCTATCATGTCTCC------TCTAAGTCTTCTCTTCTC 3737 chrXqtel1M 840771 TGTGGTAAGC-TCTTTAGTTTCTCCAAC 840797 iiv v i - iii i i C L3#LINE/CR1 3736 CAGGCTAAACATCCCCAGTTCCTTCAAC 3709 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 41.78 CpG sites = 51, Kimura (unadjusted) = 43.49 Transitions / transversions = 2.68 (51/19) Gap_init rate = 0.07 (17 / 230), avg. gap size = 3.12 (53 / 17) 18 0.00 0.00 0.00 chrXqtel1M 840806 840828 (159172) (ATA)n#Simple_repeat 1 23 (0) m_b374s252i12 15631 chrXqtel1M 840806 ATAATAATAATAATAATAATAAT 840828 (ATA)n#Simple 1 ATAATAATAATAATAATAATAAT 23 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 552 18.95 0.00 6.60 chrXqtel1M 840891 841003 (158997) C MIRc#SINE/MIR (153) 115 10 m_b374s601i21 15632 chrXqtel1M 840891 GGGGTTAAGTGACTTGCCCAGGGTCACACAGCTAAGAAGTGTTAAGTGTC 840940 i i i------- v C MIRc#SINE/MIR 115 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAG-------TAAGTGGC 73 chrXqtel1M 840941 TGAGACCAGATTTGAACTCAGGTCCTCCTGACTTCAGGGCTGCTGCTCTA 840990 v v vi i i i i i i v iiv v C MIRc#SINE/MIR 72 AGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTT 23 chrXqtel1M 840991 TCCACTGCGCCAC 841003 i C MIRc#SINE/MIR 22 TCCACTGCACCAC 10 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 20.97 CpG sites = 13, Kimura (unadjusted) = 22.19 Transitions / transversions = 1.86 (13/7) Gap_init rate = 0.06 (7 / 112), avg. gap size = 1.00 (7 / 7) 228 30.56 7.41 0.00 chrXqtel1M 841022 841129 (158871) C MIRc#SINE/MIR (26) 242 127 m_b374s601i22 15633 chrXqtel1M 841022 TAGTATTTTAAGGTTTACACAATGAGAT-ACAGATATGATCTAACAATAG 841070 i i vi v ii vvv - v i v v ivvv v C MIRc#SINE/MIR 242 TAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATCTCATTTGAT 193 chrXqtel1M 841071 TGTTACAACAACCCTAGGAGGAACGT---GC---TATCACGATCCCCATT 841114 iv i iv v v i--- --- i iv C MIRc#SINE/MIR 192 CCTCACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATT 143 chrXqtel1M 841115 TTACACACT-GGAAAC 841129 v iv- C MIRc#SINE/MIR 142 TTACAGATGAGGAAAC 127 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 37.95 CpG sites = 14, Kimura (unadjusted) = 39.40 Transitions / transversions = 0.74 (14/19) Gap_init rate = 0.04 (4 / 107), avg. gap size = 2.00 (8 / 4) 266 19.30 1.75 0.00 chrXqtel1M 841073 841129 (158871) C MIR#SINE/MIR (82) 180 123 m_b374s601i23 15633 chrXqtel1M 841073 TTACAACAACCCTAGGAGGAACGTGCTATCACGATCCCCATTTTACACAC 841122 i v v v i i iv v i C MIR#SINE/MIR 180 TCACAACAACCCTATGAGGTAGGTACTATTATTATCCCCATTTTACAGAT 131 chrXqtel1M 841123 T-GGAAAC 841129 v- C MIR#SINE/MIR 130 GAGGAAAC 123 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 22.38 CpG sites = 5, Kimura (unadjusted) = 22.38 Transitions / transversions = 0.83 (5/6) Gap_init rate = 0.02 (1 / 56), avg. gap size = 1.00 (1 / 1) 11 16.86 2.86 2.86 chrXqtel1M 842575 842609 (157391) (CCTCTT)n#Simple_repeat 1 35 (0) m_b374s252i13 15634 chrXqtel1M 842575 CCCCTT-CTCTTTGTCTTCCTCTTCTCTCTAGCTCT 842609 i - iv - vv (CCTCTT)n#Sim 1 CCTCTTCCTCTTCCTCTTCCTCTTC-CTCTTCCTCT 35 Matrix = Unknown Transitions / transversions = 0.67 (2/3) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 367 28.53 7.20 4.43 chrXqtel1M 843253 843516 (156484) C L1ME3G_3end#LINE/L1 (395) 529 259 m_b374s551i9 15635 chrXqtel1M 843253 ATATACCATAAGTGGATCA-CCATTCCCCAAATGATGG-CATCCCTTTGG 843300 v viv i - v v - iivvv v C L1ME3G_3end#L 529 ATATACCATAATTTATTTAACCATTCCCCTATTGATGGACATTTAGGTTG 480 chrXqtel1M 843301 TTTCCAATTTTTTTCCTACCACTAAAAA-ACTGCTATAAATATTTGTGTA 843349 iv - ii v v -i v i i iiv C L1ME3G_3end#L 479 TTTCCAATTTTTCGC-TATTACAAACAATGCTGCAATGAACATCCTTGTA 431 chrXqtel1M 843350 CATATGAGTCCTTTCCC-----------TCTTTCTTT--GATC--TCTTT 843384 -- v? viv ----------- v ? -- v-- ?ii? C L1ME3G_3end#L 430 CAT--GCNTCCTTGTGCACATGTGCGAGTATTTCTNTAGGATAGATNCCN 383 chrXqtel1M 843385 AAAACCCGA-TTTCTGGATCAAAGGGTATATAAACACAGTGCAGGAAATT 843433 i viv - v i i---- i v vi -- v C L1ME3G_3end#L 382 AGAAGTGGAATTGCTGGGTCAAAGGGTATG----CGCATTTTA--AATTT 339 chrXqtel1M 843434 TGAGGGTCATAGTTCCAAACTGCTTCCCAGAATGGCTGGACCAATTCCCA 843483 i vi -- v v i iii i ? v iv C L1ME3G_3end#L 338 TAATAG--ATACTGCCAAATTGCCCTCCAAAANGGCTGTACCAATTTACA 291 chrXqtel1M 843484 GTTAAACCAATTAGTGCACAAGGGTGCTCGATT 843516 v ivv i-i i ii i i i v C L1ME3G_3end#L 290 CTCCCACCAG-CAGTGTATGAGAGTACCCGTTT 259 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 36.22 CpG sites = 38, Kimura (unadjusted) = 37.52 Transitions / transversions = 1.12 (38/34) Gap_init rate = 0.07 (19 / 263), avg. gap size = 1.63 (31 / 19) 29 0.00 0.00 0.00 chrXqtel1M 844067 844091 (155909) (GA)n#Simple_repeat 1 25 (0) c_b374s251i1 15636 chrXqtel1M 844067 GAGAGAGAGAGAGAGAGAGAGAGAG 844091 (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAG 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 231 26.71 9.06 6.40 chrXqtel1M 844496 844815 (155185) C L1MD_orf2#LINE/L1 (112) 3182 2855 m_b374s551i10 15637 chrXqtel1M 844496 TTGAAATGTGACTGAGTTCCCTAATATATTTTAGAAATGAAACCTTTGTC 844545 iv v -- ii - i v i? iv C L1MD_orf2#LIN 3182 TTGAGTTTTGA--GAGTTCTTTA-TATATTCTAGATACNAGTCCTTTGTC 3136 chrXqtel1M 844546 AGAGAAATGTACTT--CAAA-AGTTTCCCCCAACTTTTCTGCTTTTCCTT 844592 i v -- iv -- - v i iii v v- v i C L1MD_orf2#LIN 3135 GGATA--TGTGGTTTGCAAATATTTTCTCCCAGTCTGTA-GCTTGTCTTT 3089 chrXqtel1M 844593 T-AT--TTTTACCTGCTTTGGTTTTGTTTGT---GCAAAACCTTTTTAAT 844636 - -- i v v ---- i -- i i--- v- C L1MD_orf2#LIN 3088 TCATCCTCTTAACAG----GGTCTT--TCGCAGAGCAAAAG-TTTTTAAT 3046 chrXqtel1M 844637 TTT-ATGTAATTGAAATGATCTGTTTTACCT---------CAT-CTCTTA 844675 - v i iv v v vi v --------- i - i i C L1MD_orf2#LIN 3045 TTTGATGAAGTCCAATTTATCAATTTTTCCTTTTATGGATCGTGCTTTTG 2996 chrXqtel1M 844676 CGTG----GTC-ATGAACTCTTT-CCCATCCATAGATCTGACAAGGAATC 844719 - ---- - v - i v v i-- i i v i C L1MD_orf2#LIN 2995 -GTGTCAAGTCTAAGAACTCTTTGCCTAGCCCTAGATCC--CGAAGATTT 2949 chrXqtel1M 844720 TCTTCCCTGCTCTA--CTAACTGACTTATGATATCCCCATTCATGTCTAA 844767 i iv i i v-- vv vi ii v iv vv i ii i C L1MD_orf2#LIN 2948 TCTCCTATGTTTTTTTCTAAAAGTTTTATAGTTTTACGTTTTACATTTAA 2899 chrXqtel1M 844768 ACCT-TGCACCCATTTTGAGTTTATCTTGGTATACGTGAGATGTGAGAT 844815 ii - - i v i v ---- i i C L1MD_orf2#LIN 2898 GTCTATG-ATCCATTTTGAGTTAATTTTTGTATA----AGGTGTGAGGT 2855 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 31.90 CpG sites = 46, Kimura (unadjusted) = 33.96 Transitions / transversions = 1.35 (46/34) Gap_init rate = 0.11 (34 / 319), avg. gap size = 1.47 (50 / 34) 248 24.99 3.49 2.30 chrXqtel1M 845225 845310 (154690) C L1P3_orf2#LINE/L1 (1452) 1842 1756 m_b374s551i11 15635 chrXqtel1M 845225 TAGTATAAGAACAAGTGTTATATTTGGTCAAAAGCCTTTTCTTCATTTGT 845274 i -- vii iv vi i i v i i C L1P3_orf2#LIN 1842 TAGCAT--GAAGGGGTGTTGAATTTTATCGAAGGCCTTTTCTGCATCTAT 1795 chrXqtel1M 845275 TGAAGTTATCCTGTGATTTTTGTCGT---TTTTGTTTGT 845310 ii v v i i --- i i C L1P3_orf2#LIN 1794 TGAGATAATCATGTGGTTTTTGTCATTGGTTCTGTTTAT 1756 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 29.99 CpG sites = 15, Kimura (unadjusted) = 31.83 Transitions / transversions = 2.50 (15/6) Gap_init rate = 0.04 (3 / 85), avg. gap size = 1.67 (5 / 3) 259 25.71 0.00 0.00 chrXqtel1M 845233 845302 (154698) C L1M4_orf2#LINE/L1 (1458) 1836 1767 m_b374s551i12 15635 chrXqtel1M 845233 GAACAAGTGTTATATTTGGTCAAAAGCCTTTTCTTCATTTGTTGAAGTTA 845282 vii iv v v i v i i i ii v C L1M4_orf2#LIN 1836 GAAAGGGTGTTGGATTTTGTCAAATGCTTTTTCTGCGTCTATTGAGATGA 1787 chrXqtel1M 845283 TCCTGTGATTTTTGTCGTTT 845302 v i v C L1M4_orf2#LIN 1786 TCATGTGGTTTTTGTCCTTT 1767 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 29.93 CpG sites = 10, Kimura (unadjusted) = 32.03 Transitions / transversions = 1.25 (10/8) Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0) 12 26.05 2.38 0.00 chrXqtel1M 845449 845490 (154510) (TTTATT)n#Simple_repeat 1 43 (0) m_b374s252i14 15638 chrXqtel1M 845449 TTTATTTTTA-TTTTAAAATAATAATAATTTTTCTTTTTTTTT 845490 - vvv v vv v v v (TTTATT)n#Sim 1 TTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTT 43 Matrix = Unknown Transitions / transversions = 0.00 (0/9) Gap_init rate = 0.02 (1 / 41), avg. gap size = 1.00 (1 / 1) 13 11.16 0.00 9.38 chrXqtel1M 845683 845717 (154283) (AAC)n#Simple_repeat 1 32 (0) m_b374s252i15 15639 chrXqtel1M 845683 AAAAACAATCAAGCAAATAACAACAACAACAATAA 845717 v - - - i i (AAC)n#Simple 1 AACAACAA-CAA-C-AACAACAACAACAACAACAA 32 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.09 (3 / 34), avg. gap size = 1.00 (3 / 3) 286 33.32 5.23 3.87 chrXqtel1M 845940 846245 (153755) C L1MC4a_3end#LINE/L1 (2049) 580 271 m_b374s551i13 15640 chrXqtel1M 845940 GAAATCATCCCGCTGATCATTTCTTACAGAACAATAATATTCCAT----- 845984 i v --- v iv i vvvv i i ----- C L1MC4a_3end#L 580 GAGATCTTCC---TCATTCTTTTTTACAGCTGCATAGTACTCCATTGTGT 534 chrXqtel1M 845985 -AACAT-TCATAGACCATTCAGCCATTCCCCAACTGATGGGTGTCCACTC 846032 -i ii -i vii i ? i v i?? ii ii vvi C L1MC4a_3end#L 533 GGATGTACCATAGTTTATTCAACCANTCTCCTATNNATGGGCATTTAGGT 484 chrXqtel1M 846033 AGTTTCCAGTTCCTTGCCACTATGCTACAAACATTTTTGTTTGCTACAAA 846082 v i vii v i ----- v --- i - v ii C L1MC4a_3end#L 483 TGTTTCCAATATTTTGCAATTA-----CAAACAAT---GCT-GCAATGAA 443 chrXqtel1M 846083 CATTTTTGCACATGTGGGTCCTTTTCCTTTCTTTATGT-TCTCTTTTGGA 846131 i vii ii i v?vii v v v vi vv v - v iv i C L1MC4a_3end#L 442 TAACCTTGTGCATATGTNATTTTGTACATGTTGGAGGTGTATCTTCAGGG 393 chrXqtel1M 846132 TACAGACTCAATAATGACACTGCTGGATCAAAGGATA--TCCACA---A- 846175 v vv ii iv i iv i i i -- v i --- - C L1MC4a_3end#L 392 TAAATTCCTAGAAGTGGGATTGCTGGGTCAAAGGGTAAATGCATATGTAG 343 chrXqtel1M 846176 -TTTGATAGACATT-CCAAATTATTCTTCAGAATGATTGGATCATTTCAC 846223 - v i - vii i ? v i v i ? ii C L1MC4a_3end#L 342 TTTTGTTAGATATTGCCAAATTCCCCTCCANAAGGGTTGTACCANTTTGC 293 chrXqtel1M 846224 AACTTCACCAACAATGTATTAG 846245 viii i v C L1MC4a_3end#L 292 ATTCCCACCAGCAATGTATGAG 271 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 47.14 CpG sites = 58, Kimura (unadjusted) = 47.14 Transitions / transversions = 1.45 (58/40) Gap_init rate = 0.07 (21 / 305), avg. gap size = 1.33 (28 / 21) 482 29.37 6.23 3.94 chrXqtel1M 845973 846245 (153755) C L1ME3G_3end#LINE/L1 (376) 548 270 m_b374s551i14 15640 chrXqtel1M 845973 ATAATATTCCATAACATTCATAGACCAT-------TCAGCCATTCCCCAA 846015 i ii vv v ------- i i v C L1ME3G_3end#L 548 ATAGTATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTA 499 chrXqtel1M 846016 CTGATGGGTGTCCACTCAGTTTCCAGTTCCTTGCCACTATGCTACAAACA 846065 i iii ii vviv i ii --- i -- C L1ME3G_3end#L 498 TTGATGGACATTTAGGTTGTTTCCAATTTTT---CGCTAT--TACAAACA 454 chrXqtel1M 846066 TTTTTGTTTGCTACAAACATTTTTGCACATGTGGGTCCTT-TTCCTTTCT 846114 ---v -i v ii ii i i--? - v viv v C L1ME3G_3end#L 453 ---ATG-CTGCAATGAACATCCTTGTACATGC--NTCCTTGTGCACATGT 410 chrXqtel1M 846115 TTATGT-TCTCTTTTGGATACAGACTCAATAATGACACTGCTGGATCAAA 846163 viiv - i ? v v v? i? iv i iv i i C L1ME3G_3end#L 409 GCGAGTATTTCTNTAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAA 360 chrXqtel1M 846164 GGATATCCACA----A---TTTGATAGACATT-CCAAATTATTCTTCAGA 846205 i v i ---- --- i i i - iii i i C L1ME3G_3end#L 359 GGGTATGCGCATTTTAAATTTTAATAGATACTGCCAAATTGCCCTCCAAA 310 chrXqtel1M 846206 ATGATTGGATCATTTCACAACTTCACCAACAATGTATTAG 846245 ? ii v i v i viii i i v C L1ME3G_3end#L 309 ANGGCTGTACCAATTTACACTCCCACCAGCAGTGTATGAG 270 Matrix = 20p45g.matrix Kimura (with divCpGMod) = 38.12 CpG sites = 52, Kimura (unadjusted) = 40.26 Transitions / transversions = 2.08 (52/25) Gap_init rate = 0.06 (17 / 272), avg. gap size = 1.65 (28 / 17) 267 24.07 0.00 0.00 chrXqtel1M 846893 846946 (153054) C MIR#SINE/MIR (133) 129 76 m_b374s601i24 15641 chrXqtel1M 846893 AGGGGATTAAGGCAAACAGAGGTAAAATAATTTGCCCAGGCTCACACAGT 846942 ii i i v v v i i i v i C MIR#SINE/MIR 129 AGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGC 80 chrXqtel1M 846943 TAAT 846946 i C MIR#SINE/MIR 79 TAGT 76 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 30.17 CpG sites = 9, Kimura (unadjusted) = 30.17 Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 248 27.69 1.54 0.00 chrXqtel1M 848910 848974 (151026) C L2a_3end#LINE/L2 (0) 517 452 m_b374s601i25 15642 chrXqtel1M 848910 ATTTAGTGAGTCAG-AAACACTTCTTAAGCACCTACTGTGTGCTAGGCAA 848958 i v v v i- i i v i i i i v C L2a_3end#LINE 517 ATTCATTCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCAC 468 chrXqtel1M 848959 GCTTCTAGAATCTGGG 848974 vv ivv C L2a_3end#LINE 467 TGTTCTAGGCGCTGGG 452 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 32.63 CpG sites = 9, Kimura (unadjusted) = 34.95 Transitions / transversions = 1.00 (9/9) Gap_init rate = 0.02 (1 / 64), avg. gap size = 1.00 (1 / 1) 317 32.24 8.80 0.74 chrXqtel1M 849223 849347 (150653) MIRb#SINE/MIR 3 137 (131) m_b374s601i26 15643 chrXqtel1M 849223 GAGGGGCAGAG-----CAGCTAGGAG-GCACCTGTTTCAAAGTCGGATTG 849266 v ----- iviii - vv i iii i iv MIRb#SINE/MIR 3 GAGGGGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAG 52 chrXqtel1M 849267 ACCCTAGTTCAAATGTGAACGCTTGACATTTATAAGCTATGTGACTCTGG 849316 ivi i vivii v - v i iv i ii MIRb#SINE/MIR 53 ACCTGGGTTCGAATCCCGGCTCT-GCCACTTACTAGCTGTGTGACCTTGG 101 chrXqtel1M 849317 ATAAGTCATTTAACC---CTGA--TTGACTTCCCTC 849347 ii i i --- --i v v i MIRb#SINE/MIR 102 GCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTC 137 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 41.68 CpG sites = 27, Kimura (unadjusted) = 44.74 Transitions / transversions = 2.08 (27/13) Gap_init rate = 0.04 (5 / 124), avg. gap size = 2.40 (12 / 5) 199 29.27 10.00 0.92 chrXqtel1M 849266 849365 (150635) MIR1_Amn#SINE/MIR 51 159 (71) m_b374s601i27 15643 chrXqtel1M 849266 GACCCTAGTTCAAATGTGAACGCTTGACATTTATAAGCTATGTGACTCTG 849315 ivi ? ? vivii v - v i ?iiv? i? ii MIR1_Amn#SINE 51 GACCTGGGTTCNANTCCCGGCTCT-GCCACTNGCCNGCTGNGTGACCTTG 99 chrXqtel1M 849316 GATAAGTCATTTAACC---CTGA--TTGACTTCCCTCCCCC-CAAAA--- 849356 ii i ? --- ?--i v v i vi i-i --- MIR1_Amn#SINE 100 GGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGG 149 chrXqtel1M 849357 -GATGATGAT 849365 - i MIR1_Amn#SINE 150 GGATAATGAT 159 Matrix = 25p45g.matrix Kimura (with divCpGMod) = 41.42 CpG sites = 20, Kimura (unadjusted) = 43.47 Transitions / transversions = 2.22 (20/9) Gap_init rate = 0.06 (6 / 99), avg. gap size = 1.83 (11 / 6) 12 25.05 4.26 0.00 chrXqtel1M 851930 851976 (148024) (CCTGGGG)n#Simple_repeat 1 49 (0) m_b375s252i0 15644 chrXqtel1M 851930 CCTTGGGCCTGGGG--GGGGGCCTGGGGTGTGAGGGCAGAAGACTGGGG 851976 v --v iv i v v ii v (CCTGGGG)n#Si 1 CCTGGGGCCTGGGGCCTGGGGCCTGGGGCCTGGGGCCTGGGGCCTGGGG 49 Matrix = Unknown Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.02 (1 / 46), avg. gap size = 2.00 (2 / 1) 22 19.08 7.59 1.19 chrXqtel1M 854113 854191 (145809) (TTCTG)n#Simple_repeat 1 84 (0) m_b375s252i1 15645 chrXqtel1M 854113 TTCTGATATTTTCTCTTCTTGATCTGTTCT-CT-AGATCTG-T-TGTTCT 854158 v v v v - v -i -v v - - (TTCTG)n#Simp 1 TTCTGTTCTGTTCTGTTC-TGTTCTGTTCTGTTCTGTTCTGTTCTGTTCT 49 chrXqtel1M 854159 CTTCTATTCT-TTCTGTTCTGTTTTATTAT-TTCT 854191 v i - i i v - (TTCTG)n#Simp 50 GTTCTGTTCTGTTCTGTTCTGTTCTGTTCTGTTCT 84 Matrix = Unknown Transitions / transversions = 0.44 (4/9) Gap_init rate = 0.09 (7 / 78), avg. gap size = 1.00 (7 / 7) 191 27.27 10.61 0.00 chrXqtel1M 855261 855326 (144674) C L2#LINE/L2 (1143) 1939 1867 m_b375s601i0 15646 chrXqtel1M 855261 AAGAGAGAATGG----AGAGGAAGTAGAGGTTCCGATTTTA---AGCCTT 855303 ---- v i iivv v v --- i ii C L2#LINE/L2 1939 AAGAGAGAATGGGAGGAGAGGAATTGGAGACAGCGAGTATAGACAACTCT 1890 chrXqtel1M 855304 TTCAAGGATTTTTACCACAAAAG 855326 i v i iii i C L2#LINE/L2 1889 TTCGAGGAGTTTTGCTGTAAAGG 1867 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 32.88 CpG sites = 12, Kimura (unadjusted) = 35.32 Transitions / transversions = 2.00 (12/6) Gap_init rate = 0.03 (2 / 65), avg. gap size = 3.50 (7 / 2) 380 31.81 3.09 1.69 chrXqtel1M 855583 855873 (144127) L1M2_orf2#LINE/L1 2385 2679 (612) m_b375s551i0 15647 chrXqtel1M 855583 AAAGGACTGGAAAAATATCCATTGCTCATGGTTAGGCCAAGCTAATATAA 855632 ?i v i vv v v vvi ii vi L1M2_orf2#LIN 2385 AAANAAATGGAAAGATATCCCATGCTCATGGATTGGAAGAATTAATATTG 2434 chrXqtel1M 855633 TAAAAATGAAAATTCTACTTTTATTGGTCTACTTCTTCAGTG----CCAT 855678 v ?vv v iivv vi i vvv i ---- v L1M2_orf2#LIN 2435 TTAAAATGNCCATACTACCCAAAGCGATCTACAGATTCAATGCAATCCCT 2484 chrXqtel1M 855679 ACCAAAGCGCCAAAAATCAT--GTCAGGGAGCTAGAAAAAATAATAACAA 855726 i iii vi - --v vi iv ? vvi L1M2_orf2#LIN 2485 ATCAAAATACCAATGA-CATTCTTCACAGAAATAGAAAAAANAATCCTAA 2533 chrXqtel1M 855727 AATTCATCTGTAAGAACAAAAGGACAAGAAT-GTCAAGGGAATTAATGAA 855775 i v v vv iv vv - i i v i-v i L1M2_orf2#LIN 2534 AATTCGTATGGAACCACAAAAGACCCCGAATAGCCAAAGCAATC-CTGAG 2582 chrXqtel1M 855776 AAAAAAATGCAAAGGATGGTGGCCTTGCAGTTCCATGCCTAAAACTCTAT 855825 v ivi v- v v ii v v vvi i v v v i L1M2_orf2#LIN 2583 CAAAAAGAACAAAGC-TGGAGGCATCACACTACCTGACTTCAAAATATAC 2631 chrXqtel1M 855826 TTTAAAACAGTGGTCATCAAAAC--CATTGGGAACTGGCCAAGAAATAGA 855873 vi i vi i v i -- -- v vv i i L1M2_orf2#LIN 2632 TACAAAGCTATAGTAACCAAAACAGCAT--GGTACTGGCATAAAAACAGA 2679 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.04 CpG sites = 39, Kimura (unadjusted) = 42.20 Transitions / transversions = 0.75 (39/52) Gap_init rate = 0.03 (9 / 290), avg. gap size = 1.56 (14 / 9) 843 33.42 1.96 3.08 chrXqtel1M 855880 856339 (143661) L1MD1_3end#LINE/L1 200 654 (335) m_b375s551i1 15648 chrXqtel1M 855880 CACCTGTCAGATGGGCTAGGATGGCAGGAAAAGATAATGCTGAATGTTGG 855929 i vv ii iiv iiv iv i ii ii i L1MD1_3end#LI 200 CACCTATCAGAATGGCTAAAATAAAAAATAGTGACAACACCAAATGCTGG 249 chrXqtel1M 855930 AGGGGATGTGGGAAAACTGGAACATTGATGCATTGTTGGTGGAGTTGTGA 855979 v i i ii v i v i i iiv i L1MD1_3end#LI 250 CGAGGATGCGGAGAAACTGGATCACTCATACATTGCTGGTGGGAATGTAA 299 chrXqtel1M 855980 ACGAATCCAACCATTCTGGAGAGTAGTTTGGAACTATGCTCAAAAAGTTA 856029 vvii v i i i ii v v - v i --- L1MD1_3end#LI 300 AATGGTACAGCCACTCTGGAAAACAGTTTGGCAGT-TTCTTAAAAA---A 345 chrXqtel1M 856030 TCAAACTGTGCA--TACCCTTTGATCCAGCAGTGTTATGACTGGGCTTAT 856077 ii -i -- v vi i i vvi ivv v v L1MD1_3end#LI 346 CTAAAC-ATGCAACTACCATACGACCCAGCAATTGCACTCCTGGGCATTT 394 chrXqtel1M 856078 ATCCCACGGAGATCATAAAGGAGG----GAAAGGGACCTGTATGTACACA 856123 vi i v v vvv v ----v v iii ---- i L1MD1_3end#LI 395 ATCCCAGAGAAATGAAAACTTATGTTCACACAAAAACC----TGTACACG 440 chrXqtel1M 856124 AATGTTTGTGGCAGCCCTGTTTGTAGTGGCCAGAAACTGGAAACTGAGTG 856173 i i ii i i i i i vivvii L1MD1_3end#LI 441 AATGTTTATAGCAGCTTTATTCGTAATAGCCAAAAACTGGAAACAACCCA 490 chrXqtel1M 856174 GGCGCCCATCAATTGGAGAATGGCTGAATAAATGGTGGTATATGAAAATT 856223 ii i v iv v i i i iv i vv v ii L1MD1_3end#LI 491 GATGTCCTTCAACGGGTGAATGGTTAAACAAACTGTGGTACATCCATACC 540 chrXqtel1M 856224 ATGGAATATTACTGTTCTGTAAGAAATGACCAACAGGATGAATACAGAGA 856273 i vvv vi i ivi v --v vi viv L1MD1_3end#LI 541 ATGGAATACTACTCAGCAATAAAAAGGAACGAAC--TATTGATACACGCA 588 chrXqtel1M 856274 --AGCCTGGAGAGACTTACACGAACTGATGCTAAGTGAAATGAGCAGA-A 856320 -- i vii ii v vii v v i vi vi -v L1MD1_3end#LI 589 ACAACCTGGATGAATCTCCAGAGAATTATGCTGAGTGAAAAAAGCCAATC 638 chrXqtel1M 856321 CCAAGAGATCATTATATAC 856339 i ---i i L1MD1_3end#LI 639 CCAAAAG---GTTACATAC 654 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 43.44 CpG sites = 89, Kimura (unadjusted) = 45.97 Transitions / transversions = 1.48 (89/60) Gap_init rate = 0.04 (18 / 459), avg. gap size = 1.28 (23 / 18) 944 32.35 0.73 0.98 chrXqtel1M 855912 856320 (143680) L1ME4c_3end#LINE/L1 232 639 (191) m_b375s551i2 15648 chrXqtel1M 855912 GATAATGCTGAATGTTGGAGGGGATGTGGGAAAACTGGAACATTGATGCA 855961 i iv i v i ? i vi v ?i v i L1ME4c_3end#L 232 GATAATACCCAATGCTGGCGAGGNTGCGGTGAAACTGGTACNCTCATACA 281 chrXqtel1M 855962 TTGTTGGTGGAGTTGTGAACGAATCCAACCATTCTGGAGAGTAGTTTGGA 856011 i vi? i ivii v v i i i i v L1ME4c_3end#L 282 TTGCTGGTGGCANTGTAAATTGGTACAACCCTTTTGGAAAGCAATTTGGC 331 chrXqtel1M 856012 ACTATGCTCAAAAAGTTATCAAACTGTGCATACCCTTTGATCCAGCAGTG 856061 v i iviv i ii v v v i i i v L1ME4c_3end#L 332 AATACGTATCAAGAGCCATAAAAATGTTCATACCCTTTGACCCAGTAATT 381 chrXqtel1M 856062 TTATGACTGGGCTTATATCCCACGGAGATCAT--AAAGGAGGGAAAGGGA 856109 ii ivv vv v i v i v -- i i ii - L1ME4c_3end#L 382 CCACTTCTGGGAATTTATCCTAAGGAAATAATTCAAAAGAAGGAAAAAG- 430 chrXqtel1M 856110 CCTGTATGTACACAAATGTTTGTGGCAGCCCTGTTTGTAGTGGCCAGAAA 856159 - i i iv i ii v vi i i i i v i L1ME4c_3end#L 431 -CTATATGCACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAA 479 chrXqtel1M 856160 CTGGAAACTGAGTGGGCGCCCATCAATTGGAGAATGGCTGAATAAATGGT 856209 i vivv iiii i v v i i i i vi L1ME4c_3end#L 480 TTGGAAACAACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTAT 529 chrXqtel1M 856210 GGTATATGAAAATTATGGAATATTACTGT-TCTGTAAGAAATGACCAACA 856258 i v? vviv - i-v ii v i iv vi L1ME4c_3end#L 530 GGTACATCNACTCGATGGAATATTA-TGCAGCCATTAAAAATGATAATTA 578 chrXqtel1M 856259 GGATGAATACAGAGAAGCCTGGAGAGACTTACACGAACTGATGCTAAGTG 856308 v v v iiv v i v i ivv -i i vv i i L1ME4c_3end#L 579 TGAAGACTATGTAGCAACATGGAAAATGTT-TATGATATAATGTTAAGTG 627 chrXqtel1M 856309 AAATGAGCAGAA 856320 vi L1ME4c_3end#L 628 AAAAAAGCAGAA 639 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 42.66 CpG sites = 78, Kimura (unadjusted) = 44.50 Transitions / transversions = 1.47 (78/53) Gap_init rate = 0.01 (6 / 408), avg. gap size = 1.17 (7 / 6) 281 28.21 6.73 5.71 chrXqtel1M 857087 857398 (142602) L1M2_orf2#LINE/L1 2977 3291 (0) m_b375s551i3 15647 chrXqtel1M 857087 TCTTTGCAGAAGACCAAAGAAGAACTAGAGAACATTATGCAATGCAAAA- 857135 i v?v vv i v - iv ------ v - L1M2_orf2#LIN 2977 TTTTTGGNTAAGACCTCAAAAGCAC-AGGCAACA------AAAGCAAAAA 3019 chrXqtel1M 857136 TGGACAACTTCGATTACATTAAATTTAAAAGTTCTTGCA----GAAACAA 857181 i v vv i i v i ii ----i iv L1M2_orf2#LIN 3020 TAGACAAATGGGATTACATCAAACTAAAAAGCTTCTGCACAGCAAAGGAA 3069 chrXqtel1M 857182 ACTTAATACAAGCAAGATTAAAAGGGAA-GTACAAAGCTGGGA-AAAATT 857229 -- - - iii v i iv -v i i- - v L1M2_orf2#LIN 3070 AC--AAT-CAA-CAGAGTGAAGAGACAACCTACAGAA-TGGGAGAAAATA 3114 chrXqtel1M 857230 TTTACAGCCCTTGTTTCT---AAGGGTTTCATTTCTAAAATATAAAAAGA 857276 i iv iv ?iv --- v v v i i v i L1M2_orf2#LIN 3115 TTTGCAAACTATNCATCTGACAAGGGATTAATATCCAGAATATATAAGGA 3164 chrXqtel1M 857277 ACTGTGTCAAATTTA---TAAGAATATAAGTCATTGCCCAATTGGTAAAT 857323 vviv v iv ---i i v i i v --- i ?iv L1M2_orf2#LIN 3165 ACTCAAACAACTCAACAGCAAAAAAACAAATAAT---CCGATTNAAAAAT 3211 chrXqtel1M 857324 GATCCAAAGATATGAACAGACA------ATATGCAGATAAAGAAA--GCC 857365 iv v i iv i ------ v v v i v v -- L1M2_orf2#LIN 3212 GGGCAAAGGACCTGAATAGACATTTCTCAAAAGAAGACATACAAATGGCC 3261 chrXqtel1M 857366 ATCTATAGTTATGTGAAGAAATGCTCTAAATCA 857398 --- i v i i v v L1M2_orf2#LIN 3262 A---ACAGGTATATGAAAAAATGCTCAACATCA 3291 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 35.75 CpG sites = 41, Kimura (unadjusted) = 36.28 Transitions / transversions = 0.98 (41/42) Gap_init rate = 0.08 (26 / 311), avg. gap size = 1.50 (39 / 26) 357 28.55 6.37 2.90 chrXqtel1M 857132 857398 (142602) L1M3_orf2#LINE/L1 3013 3288 (0) m_b375s551i4 15647 chrXqtel1M 857132 AAAATGGACAACTTCGATTACATTAAATTTAAAAGTTCTTGCA----GAA 857177 i v vv i i i v i ii ----i L1M3_orf2#LIN 3013 AAAATAGACAAGTGGGACTACATCAAACTAAAAAGCTTCTGCACAGCAAA 3062 chrXqtel1M 857178 ACAAACTTAATACAAGCAAGATTAAAAGGGAAG-TACAAAGCTGGGA-AA 857225 iv -- - - iii v v v- ii i- - L1M3_orf2#LIN 3063 GGAAAC--AAT-CAA-CAGAGTGAAAAGGCAACCTACGGAA-TGGGAGAA 3107 chrXqtel1M 857226 AATTTTTACAGCCCTTGTTTCT---AAGGGTTTCATTTCTAAAATATAAA 857272 v i iv v i v --- v v v i v L1M3_orf2#LIN 3108 AATATTTGCAAACCATATATCTGATAAGGGGTTAATATCCAAAATATATA 3157 chrXqtel1M 857273 AAGAACTGTGTCAAATTTATAAGAATATAAGTCATTGCCCAATTGGTAAA 857322 i v?vv v iv iv v v vvv vi i ?iv L1M3_orf2#LIN 3158 AGGAACTCNTACAACTCAATAGCAAAAAAACAAATAACCCGATTNAAAAA 3207 chrXqtel1M 857323 TGATCCAAAGATATGAACAGACAAT------ATGCAGATAAAGAAA--GC 857364 iv v i iv i v ------ v v i v v -- L1M3_orf2#LIN 3208 TGGGCAAAGGACCTGAATAGACATTTCTCCAAAGAAGACATACAAATGGC 3257 chrXqtel1M 857365 CATCTATAGTTATGTGAAGAAATGCTCTAAATCA 857398 --- i v i i i v v L1M3_orf2#LIN 3258 CA---ACAGGTATATGAAAAGATGCTCAACATCA 3288 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 35.39 CpG sites = 34, Kimura (unadjusted) = 36.58 Transitions / transversions = 0.85 (34/40) Gap_init rate = 0.05 (14 / 266), avg. gap size = 1.79 (25 / 14) 1281 30.09 3.44 3.25 chrXqtel1M 857254 857806 (142194) L1ME5_3end#LINE/L1 1 554 (387) m_b375s551i5 15647 chrXqtel1M 857254 TTCATTTCTAAAATATAAAAAGAACTGTGTCAAATTTATAAGAATATAA- 857302 v v i v i vivv iv i v vi - L1ME5_3end#LI 1 TTAATATCTAGAATATACAAGGAACTCCTGCAAATCAACAAGAAAAAGAC 50 chrXqtel1M 857303 -GTCATTGCCCAATTGGTAAATGATCCAAAGATATGAACAGACAATATGC 857351 - ?v i-- v iv iv v i i v i L1ME5_3end#LI 51 GGNAAC--CCCAATAGAAAAATGGGCAAAGGATATGAACAGGCAATTTAC 98 chrXqtel1M 857352 AGATAAAGAAAGCCA----TCTA-TAGTTATGTGAAGAAATGCTCTAAAT 857396 vi i v i----v -i ivi i i v v L1ME5_3end#LI 99 AGAAGAGGAAACCCGAAAGGCTAACAAGCATATGAAGAGATGCTCAAACT 148 chrXqtel1M 857397 CACTATTGATTAGAGAAATGTGAATTAAAACAACTCTGAGGTGTCACCTT 857446 i v i i ii vv i i i L1ME5_3end#LI 149 CATTAGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTT 198 chrXqtel1M 857447 ATATCTGTCAGATTGGCTAAGAAGACAGGAAA--GGATAATGATGAATGT 857494 i i i i i -- i ivi i i-- vii i L1ME5_3end#LI 199 ACACCTATTAGACTGGC--AAAAATTAGAAAGCTGGATAATGCCAAGTGT 246 chrXqtel1M 857495 TGGAAGGGATGTGGGAAGACTGGAACACTAAAGCATTGTTGGAGGAGTTG 857544 vii i ? iv v v v i i v iiv L1ME5_3end#LI 247 TGGCGAGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGGGAGTG 296 chrXqtel1M 857545 TGAAACTGATCCAGTCGTTCTGGAGAGCAGTTTGGAACTA--TCCCCAAA 857592 - i i v i i i i v v -- vvi - L1ME5_3end#LI 297 T-AGACTGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAA- 344 chrXqtel1M 857593 GGGCTATCAAAC-TGTGTATACTTTTTGATCTAGCTGTCTTGCTACTGAG 857641 ----- i ii- ii i ii v i i vi iii v i L1ME5_3end#LI 345 -----ATTAAGTATACGCATACCCTATGACCCAGCAATTCCGCTCCTGGG 389 chrXqtel1M 857642 TCTGTATCCCAAAAAAATTATAAAGAAAGG---AAAAGGACCCACATGTG 857688 v i i v -v v v --- v i--v i L1ME5_3end#LI 390 TATATATCCCAAAGAAATTCT-CACACAGGTCCATAAGGG--GACATGTA 436 chrXqtel1M 857689 CAAAGATGTTTGTGGCAGTCCTTTTTGTGGTGGCAAAGATTTGGAA--AA 857736 i i ii v ivi v iii v i-- L1ME5_3end#LI 437 CGAGGATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAA 486 chrXqtel1M 857737 --TGAATATTTGCCCATCAGTTGGGGAATGGCTGAAGAAGTTGTGGTATA 857784 -- ii i ---- v v i i v iiiv iv iv L1ME5_3end#LI 487 CCTGGGTGT----CCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGA 532 chrXqtel1M 857785 TGAAGATAATGGAATGTTATAC 857806 v v iv i ii i L1ME5_3end#LI 533 TGCACACCATGGAGTACTATGC 554 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.87 CpG sites = 100, Kimura (unadjusted) = 40.13 Transitions / transversions = 1.64 (100/61) Gap_init rate = 0.05 (28 / 552), avg. gap size = 1.32 (37 / 28) 835 33.44 3.91 3.57 chrXqtel1M 857260 857873 (142127) L1MD1_3end#LINE/L1 7 622 (367) m_b375s551i6 15647 chrXqtel1M 857260 TCTAAAATATAAAAAGAACTGTGTCAAATTTA----TAAGAATATAAGTC 857305 i v v -iv i i ---- i v i iiv L1MD1_3end#LI 7 TCTAGAATATATAAAGAACTCT-CAAAACTCAACAGTAAAAAAACAAACA 55 chrXqtel1M 857306 ATTGCCCAATTGGTAAATGATCCAAAGATATGAACAGACAATATGCAGA- 857354 --- i v iv v i v v vii v - L1MD1_3end#LI 56 AT---CCAATTAGAAAATGGGCAAAAGACATGAAGAGACATTTCACCGAA 102 chrXqtel1M 857355 -------TAAAGAAAGCCATCTATAGTTATGTGAAGAAATGCTCTAAATC 857397 ------- v vi v --- ivi ii i i i v v L1MD1_3end#LI 103 GAGGATATACAGATGGCAA---ATAAGCACATGAAAAGATGTTCAACATC 149 chrXqtel1M 857398 ACTATTGATTAGAGAAATGTGAATTAAAACAACTCTGAGGTGTCACCTTA 857447 i viv i ii v vv i i ivi L1MD1_3end#LI 150 ATTAGCCATTAGGGAAATGCAAATTAAAACCACAATGAGATATCACTACA 199 chrXqtel1M 857448 TATCTGTCAGATTGGCTAAGAAGACAGGAAAG-GATAATGATGAATGTTG 857496 i i i v - v v ii v - i iivii i L1MD1_3end#LI 200 CACCTATCAGAATGGCTAA-AATAAAAAATAGTGACAACACCAAATGCTG 248 chrXqtel1M 857497 GAAGGGATGTGGGAAGACTGGAACACTAAAGCATTGTTGGAGGAGTTGTG 857546 vii i ii i v v vi i v iiv i L1MD1_3end#LI 249 GCGAGGATGCGGAGAAACTGGATCACTCATACATTGCTGGTGGGAATGTA 298 chrXqtel1M 857547 AAACTGATCCAGTCGTTCTGGAGAGCAGTTTGGAACTATCCCCAAAGGGC 857596 - i v i ii i i v v - i ii iii L1MD1_3end#LI 299 AAA-TGGTACAGCCACTCTGGAAAACAGTTTGGCAGT-TTCTTAAAAAAC 346 chrXqtel1M 857597 TATCAAACTGTGTA--TACTTTTTGATCTAGCTGTCTTGCTACTGAGTCT 857644 --- -i i -- iv vi i i vi ivii v i iv L1MD1_3end#LI 347 T---AAAC-ATGCAACTACCATACGACCCAGCAATTGCACTCCTGGGCAT 392 chrXqtel1M 857645 GTATCCCAAAAAAATTATAAAGAAAGG-----AAAAGGACCCACATGTGC 857689 v i i v - vvv v ----- v ii ---- i L1MD1_3end#LI 393 TTATCCCAGAGAAATGA-AAACTTATGTTCACACAAAAACC----TGTAC 437 chrXqtel1M 857690 AAAGATGTTTGTGGCAGTCCTTTTTGTGGTGGCAAAGATTTGGAA--AAT 857737 vii i i iii v i ii i v i vi -- i L1MD1_3end#LI 438 ACGAATGTTTATAGCAGCTTTATTCGTAATAGCCAAAAACTGGAAACAAC 487 chrXqtel1M 857738 GAATATTTGCCCATCAGTTGGGGAATGGCTGAAGAAGTTGTGGTATATGA 857787 vv v -- i v iiv v i i v ii i vv L1MD1_3end#LI 488 CCAGA--TGTCCTTCAACGGGTGAATGGTTAAACAAACTGTGGTACATCC 535 chrXqtel1M 857788 AGATAATGGAATGTTATACTTCTATAAAAATG-ATGAACAGGCTGAT-TT 857835 v iv ii iv vv v v - i -vii -iv L1MD1_3end#LI 536 ATACCATGGAATACTACTCAGCAATAAAAAGGAACGAAC-TATTGATACA 584 chrXqtel1M 857836 TAGAAAGGCCTGGAAAGATTTATACAGACTTATGCTGA 857873 iiv vii vii i vi v v L1MD1_3end#LI 585 CGCAACAACCTGGATGAATCTCCAGAGAATTATGCTGA 622 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 43.51 CpG sites = 119, Kimura (unadjusted) = 46.10 Transitions / transversions = 1.51 (119/79) Gap_init rate = 0.05 (31 / 613), avg. gap size = 1.48 (46 / 31) 22 16.10 0.00 0.00 chrXqtel1M 858730 858771 (141229) (TTA)n#Simple_repeat 1 42 (0) m_b375s252i2 15649 chrXqtel1M 858730 TTTTTGTTGTTGTTGTTATTATTATTATTATTATTATTTTTA 858771 v i i i i v (TTA)n#Simple 1 TTATTATTATTATTATTATTATTATTATTATTATTATTATTA 42 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 30 17.19 2.99 1.47 chrXqtel1M 859617 859683 (140317) (AT)n#Simple_repeat 1 68 (0) m_b375s252i3 15650 chrXqtel1M 859617 ATATATGT-TAAATATGTTAAAATATTTGTCAAATATA-ACATATATATA 859664 i - v i vv v v i - v - i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATAT-ATATATATATATATATATA 49 chrXqtel1M 859665 TATATATATATATATATAT 859683 (AT)n#Simple_ 50 TATATATATATATATATAT 68 Matrix = Unknown Transitions / transversions = 0.67 (4/6) Gap_init rate = 0.05 (3 / 66), avg. gap size = 1.00 (3 / 3) 51 2.13 0.00 0.00 chrXqtel1M 859684 859731 (140269) (AG)n#Simple_repeat 1 48 (0) c_b375s251i0 15651 chrXqtel1M 859684 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAAGAGAGAG 859731 i (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 48 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 305 31.23 4.61 6.88 chrXqtel1M 859970 860251 (139749) C L1ME5_3end#LINE/L1 (274) 667 392 m_b375s551i7 15652 chrXqtel1M 859970 ATAGTATTGTTGTTGAAGTGCATAATGATCTC---CTGGTTCTT-CTCAT 860015 i - ------- ?-- --- v - iv C L1ME5_3end#LI 667 ATGGTATTGT-GTT-------ATAN--ATCTCATTCTGTTTCTTACTTTT 628 chrXqtel1M 860016 TTCACTCAGCATCA-GTTCATATAAG-TCTCTCCAAGC--CTTTCTGAAA 860061 ii - -- v - iv v i-- v v v - C L1ME5_3end#LI 627 TTCACTCAGCACTATGTT--TTTAAGATCCATCCATGTTGCTATGTGTA- 581 chrXqtel1M 860062 TCATCCTGCTAGTCATTTCTTACAGAACAATAATATTCCATAACATTCAT 860111 - iv iiv iii v v vvvv i i iiii v C L1ME5_3end#LI 580 -CATCTAGTCCGTTGCTTCTAACTGCTGCATAGTACTCCATGGTGTGCAT 532 chrXqtel1M 860112 ATACCACAATTTACCCAGCCAGTCTCCATTTGATGGGCATCCA--TTCAA 860159 vi v i v v vvv i i -- --i C L1ME5_3end#LI 531 CCACCACATTTTACCTATCCACTCTCCCAGTGATGGACACCCAGGTT--G 484 chrXqtel1M 860160 TTCTCAGTTTCTGGCTACTATGAAAAGGGCTGCCACAAATATTTTGGCAC 860209 iiii ii i iv i i ii v iv v ii i ii v i C L1ME5_3end#LI 483 CCTCCAACTCCCCGCCACCACAAACAACGCTGCAATGAACATCCTCGTAC 434 chrXqtel1M 860210 ATACAGGCCCCTTTC---CCTCCTTTAAGATCTCTCTGGGATATA 860251 --- v vi--- viv v ii i i C L1ME5_3end#LI 433 AT---GTCCCCTTATGGACCTGTGTGAGAATTTCTTTGGGATATA 392 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 41.79 CpG sites = 48, Kimura (unadjusted) = 41.79 Transitions / transversions = 1.41 (48/34) Gap_init rate = 0.09 (26 / 281), avg. gap size = 1.23 (32 / 26) 337 27.03 4.46 6.57 chrXqtel1M 860015 860216 (139784) C L1MC3_3end#LINE/L1 (1904) 628 431 m_b375s551i8 15652 chrXqtel1M 860015 TTTCACTCAGCATCAGTTCATATAAGTCTC-TCCAAGCCTTTCTGAAATC 860063 i vi - v v vi - v i ------ C L1MC3_3end#LI 628 TTTCACTTAGCAATA-TGCATTTAAGATTCATCCATGTCTTT------TC 586 chrXqtel1M 860064 AT--CCTGCTAG-TCATTTCTT---ACAGAACAATAATATTCCATAACAT 860107 i -- i v - --- iv vvv vii C L1MC3_3end#LI 585 GTGGCTTGATAGCTCATTTCTTTTTATCGCTGAATAATATTCCATTGTAT 536 chrXqtel1M 860108 TCATATACCACAATTTACCCAGCCAGTCTCCATTTGATGGGCATCCATTC 860157 vv i i iiii v v v vv v i -- v C L1MC3_3end#LI 535 GGATGTACCACAGTTTGTTTATCCATTCACCTATTGAAGGACATC--TTG 488 chrXqtel1M 860158 AATTCT--CAGTTTCTGGCTACTATGAAAAGGGCTGCCACAAATATTTTG 860205 iv v -- i v i v ii i i i --- C L1MC3_3end#LI 487 GTTGCTTCCAGTTTTTGGCGATTATGAATAAAGCTGCTATAAACATT--- 441 chrXqtel1M 860206 GCACATACAGG 860216 - i i i C L1MC3_3end#LI 440 -CGCGTGCAGG 431 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 31.56 CpG sites = 27, Kimura (unadjusted) = 33.94 Transitions / transversions = 1.12 (27/24) Gap_init rate = 0.09 (18 / 201), avg. gap size = 1.22 (22 / 18) 408 31.40 0.00 0.00 chrXqtel1M 860090 860210 (139790) C L1ME2z_3end#LINE/L1 (638) 553 433 m_b375s551i9 15652 chrXqtel1M 860090 AATAATATTCCATAACATTCATATACCACAATTTACCCAGCCAGTCTCCA 860139 i i vii vv i iiii v v v C L1ME2z_3end#L 553 AGTAGTATTCCATTGTATGAATATACCACAGTTTGTTTATCCATTCTCCT 504 chrXqtel1M 860140 TTTGATGGGCATCCATTCAATTCTCAGTTTCTGGCTACTATGAAAAGGGC 860189 v i i iivv vi ii i i v ii C L1ME2z_3end#L 503 GTTGATGGACACCTGGGCTGTTTCCAGTTTTTGGCTATTATGAATAAAGC 454 chrXqtel1M 860190 TGCCACAAATATTTTGGCACA 860210 i ii i i v i C L1ME2z_3end#L 453 TGCTATGAACATTCTTGTACA 433 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 43.16 CpG sites = 26, Kimura (unadjusted) = 43.16 Transitions / transversions = 2.17 (26/12) Gap_init rate = 0.00 (0 / 120), avg. gap size = 0.0 (0 / 0) 387 30.97 2.52 2.52 chrXqtel1M 860091 860249 (139751) C L1ME4c_3end#LINE/L1 (275) 555 397 m_b375s551i10 15652 chrXqtel1M 860091 ATAATATTCCATAACATTCATATACCACAATTTACCCAGCCAGTCTCCAT 860140 vivi ?v i i ii i v i vv C L1ME4c_3end#L 555 ATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTA 506 chrXqtel1M 860141 TTGATGGGCATCCA--TTCAATTCTCAGTTTCTGGCTACTATGAAAAGGG 860188 v i ii -- --i ii i i v i i v iv C L1ME4c_3end#L 505 TTGTTGGACATTTAGGTT--GTTTCCAATTTTTCGCTATTATAAATAACG 458 chrXqtel1M 860189 CTGCCACAAATATTTTGGCACATACAGGCCCCTTTCCCTCCTTTAAG--A 860236 v ii i i v ii i -- ii i i i i-- C L1ME4c_3end#L 457 CTGCAATGAACATCTTCGTGCATATAG--CTTTTTCCTTCTTTTGAATTA 410 chrXqtel1M 860237 TCTCTCTGGGATA 860249 i ii i C L1ME4c_3end#L 409 TTTCCTTAGGATA 397 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 42.39 CpG sites = 36, Kimura (unadjusted) = 43.66 Transitions / transversions = 3.00 (36/12) Gap_init rate = 0.04 (6 / 158), avg. gap size = 1.33 (8 / 6) 12 8.28 0.00 10.34 chrXqtel1M 860270 860301 (139699) (GGGA)n#Simple_repeat 1 29 (0) m_b375s252i4 15653 chrXqtel1M 860270 GGGAGGGAGGAGAGGTAAAGGGAAGGAGGGAG 860301 - --i i (GGGA)n#Simpl 1 GGGAGGGAGG-GAGG--GAGGGAGGGAGGGAG 29 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.10 (3 / 31), avg. gap size = 1.00 (3 / 3) 22 10.36 0.00 0.00 chrXqtel1M 860324 860354 (139646) (T)n#Simple_repeat 1 31 (0) m_b375s252i5 15654 chrXqtel1M 860324 TTTTTTTTTTTTATTTCTTTTTTTTTTATTT 860354 v i v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 31 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 545 30.20 4.83 5.64 chrXqtel1M 860817 861209 (138791) C L1MC1_3end#LINE/L1 (447) 633 244 m_b375s551i11 15655 chrXqtel1M 860817 GCTTCATTTCACTCAGCATCAGTTCAGTGTAAGTCTCT--CAGGCCTTTC 860864 - i i vi - v v - i i-- v i - C L1MC1_3end#LI 633 GCTTC-TTTCACTTAGTAATA-TGCATT-TAAGTTTCCTCCATGTCTTT- 588 chrXqtel1M 860865 TGAAATCAT--CCTGTTGG-TCATTTCTTAC-AGAAC--AGTAATATTCC 860908 ----- -- i v i - vi- vi -- i C L1MC1_3end#LI 587 -----TCATGGCTTGATAGCTCATTTCTTTTTAGCGCTGAATAATATTCC 543 chrXqtel1M 860909 ATAATTTTCATATAC-ACAATTTATTCAGCCATTCTCCAACTGATGGACA 860957 vi i vv i - i i v v v v C L1MC1_3end#LI 542 ATTGTCTGGATGTACCACAGTTTATTTATCCATTCACCTACTGAAGGACA 493 chrXqtel1M 860958 TCC--ATTCAGTTTCCAGTTTCTAGCCACTACAAAAGGGGCTGCCACAAA 861005 i--i -- i iv i i v i ii viii i i C L1MC1_3end#LI 492 TCTTGGTT--GCTTCCAAGTTTTGGCAATTATGAATAAAGCTGCTATAAA 445 chrXqtel1M 861006 CATTCGTGCACATACAGGTCCCTTTCCCTTC-----TTTATAATCTCTTT 861050 i ---- i iii v vivvv ----- vi iii C L1MC1_3end#LI 444 CATCCGTG----TGCAGGTTTTTGTGTGGACATAAGTTTTCAACTCCTTT 399 chrXqtel1M 861051 GGGATATAAGCCCAGTAGTAACACTGCTGGATCAAAGGGTATGCACAGTT 861100 - v vi v v iivv i iv v --- v v C L1MC1_3end#LI 398 GGG-TAAATACCAAGGAGCGCGATTGCTGGATCGTATGGTA---AGAGTA 353 chrXqtel1M 861101 TGATAACTTTT-TGAGCATAGAT--CCAAACTACTCTCCAAAATGGTTGG 861147 v v v - i --- i i-- iiii i i v C L1MC1_3end#LI 352 TGTTTAGTTTTGTAAG---AAACTGCCAAACTGTCTTCCAAAGTGGCTGT 306 chrXqtel1M 861148 ATTCGTTCACAACTCCACCAACAATGAATCAATGTCCCAGTTTTCCCACA 861197 iivv ii vii i v iv i v vii C L1MC1_3end#LI 305 ACCATTTTGCATTCCCACCAGCAATGAATGAGAGTTCCTGTTGCTCCACA 256 chrXqtel1M 861198 TCCCCTCCAACA 861209 i v i C L1MC1_3end#LI 255 TCCTCGCCAGCA 244 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 38.44 CpG sites = 67, Kimura (unadjusted) = 39.88 Transitions / transversions = 1.49 (67/45) Gap_init rate = 0.08 (32 / 392), avg. gap size = 1.28 (41 / 32) 872 27.72 2.58 2.25 chrXqtel1M 860900 861209 (138791) C L1ME4c_3end#LINE/L1 (276) 554 244 m_b375s551i12 15655 chrXqtel1M 860900 TAATATTCCATAATTTTCATATAC-ACAATTTATTCAGCCATTCTCCAAC 860948 vivv ?v i - i i i i i v i C L1ME4c_3end#L 554 TAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTAT 505 chrXqtel1M 860949 TGATGGACATCCA--TTCAGTTTCCAGTTTCTAGCCACTACAAAAGGGGC 860996 v ii -- -- i i v i i i viiv C L1ME4c_3end#L 504 TGTTGGACATTTAGGTT--GTTTCCAATTTTTCGCTATTATAAATAACGC 457 chrXqtel1M 860997 TGCCACAAACAT--TCGTGCACATACAGGTCCCTTTCCCTTCTTT---AT 861041 v ii -- i v----- i i --- C L1ME4c_3end#L 456 TGCAATGAACATCTTCGTGCATATAG-----CTTTTTCCTTCTTTTGAAT 412 chrXqtel1M 861042 AATCTCTTTGGGATATAAGCCCAGTAGTAACACTGCTGGATCAAAGGGTA 861091 v i i i v vv v iiv i i i C L1ME4c_3end#L 411 TATTTCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTA 362 chrXqtel1M 861092 TGCACAGTTTGATAACTTTTTGAGCATAGATCCAAACTACTCTCCAAAAT 861141 v v v ii i vivi i vvv i i i v C L1ME4c_3end#L 361 TGAACATTTTTATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAG 312 chrXqtel1M 861142 GGTTGGATTCGTTCACAACTCCACCAACAATGAATCAATGTCCCAGTTTT 861191 v iivi i ?iv i v v i? v i C L1ME4c_3end#L 311 GGTTGTACCAATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTTTC 262 chrXqtel1M 861192 CCCACATCCCCTCCAACA 861209 v i ? i v i C L1ME4c_3end#L 261 ACCGCANCCTCGCCAGCA 244 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 34.57 CpG sites = 50, Kimura (unadjusted) = 36.18 Transitions / transversions = 1.47 (50/34) Gap_init rate = 0.04 (11 / 309), avg. gap size = 1.36 (15 / 11) 583 22.58 1.61 0.00 chrXqtel1M 862372 862495 (137505) MIRc#SINE/MIR 3 128 (140) m_b375s601i1 15656 chrXqtel1M 862372 AGCTAGT-TGGTGTGGTGGGTAAAGTACCAGCCCTGAAGTCAGGAGGACC 862420 vi - ii iv i i ii v i i i MIRc#SINE/MIR 3 AGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACC 52 chrXqtel1M 862421 TGAGTTCAAGTCTGGCCTCAGACACTTCCTAGCTGTGTGACCCTGAGCAA 862470 i i iv v v v v i i MIRc#SINE/MIR 53 TGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAA 102 chrXqtel1M 862471 GTCACTTAACCCCAATT-GCCTCAGT 862495 i vv v- MIRc#SINE/MIR 103 GTCACTTAACCTCTCTGAGCCTCAGT 128 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 26.30 CpG sites = 17, Kimura (unadjusted) = 27.42 Transitions / transversions = 1.55 (17/11) Gap_init rate = 0.02 (2 / 123), avg. gap size = 1.00 (2 / 2) 564 25.29 1.13 1.70 chrXqtel1M 864564 864740 (135260) PRIMAX-int#LTR/ERV1 3005 3180 (922) m_b375s701i0 15657 chrXqtel1M 864564 CCCATTTAGCACAACAAGCCCAACTTGAGT--CAGTAGCCAGGGCTTGTC 864611 v? i v ?v -- ? -- ?v ?i i? i PRIMAX-int#LT 3005 CCANTTCAGCTCAACAAGCNGAACT--ANTAGCNTTNACTNGGGCCTGTC 3052 chrXqtel1M 864612 AGTTAGGAAAAGGAAGAAGGATTGATATCTATACTGAGAGTGGGTATATG 864661 v i v ? vvii i i v v i i iiv PRIMAX-int#LT 3053 ACTTGGCAAAAGGAANAACTGCTAATATTTATACGGACAGTAGATATGCT 3102 chrXqtel1M 864662 TTTGGGGTGGCATATCACTTTGGGATATTATGGAAGGATCGGGGGTTTCC 864711 ivi v i i ii iv vv i - i PRIMAX-int#LT 3103 TTTGGGGTGGTCCATGATTTTGGAATGCTATGGAAACAAAGAGGG-TTCT 3151 chrXqtel1M 864712 TCACCTCCTCAGGACAGCCCATTAAACAT 864740 ? i v v ii ? v PRIMAX-int#LT 3152 TNACCTCTTCTGGTCAATCCATNAAAAAT 3180 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.62 CpG sites = 25, Kimura (unadjusted) = 33.62 Transitions / transversions = 1.32 (25/19) Gap_init rate = 0.02 (4 / 176), avg. gap size = 1.25 (5 / 4) 479 28.22 1.80 2.41 chrXqtel1M 864600 864766 (135234) PRIMA4-int#LTR/ERV1 4803 4968 (3302) m_b375s701i1 15657 chrXqtel1M 864600 CCAGGGCTTGTCAGTTAGGAAAAGGAAGAAGGATTG---ATATCTATACT 864646 v i i i v -- v -i --- i i i PRIMA4-int#LT 4803 CCCGAGCTTGTCAATTGGCAAAAG--ACAAGG-CTGCGAACATTTACACT 4849 chrXqtel1M 864647 GAGAGTGGGTATATGTTTGGGGTGGCATATCACTTTGGGATATTATGGAA 864696 v iv v ii? v vi v ii PRIMA4-int#LT 4850 GACAGCCGCTATGCNTTTGGGGTTGCTCATGACTTTGGGATGCTATGGAA 4899 chrXqtel1M 864697 GGATCGGGGGTTTCCTCACCTCCTCAGGACAGCCCATTAAACATCAAAAA 864746 i vv i i v -i v i i v v vi v PRIMA4-int#LT 4900 AGAGAGAGGATAT-TTAACCTCCTCAGGGCAACCCATAAAAAATGGACAA 4948 chrXqtel1M 864747 TGGGCTTCTCAGCTATCAGA 864766 iii iv vv i i PRIMA4-int#LT 4949 CAAGTATCAGAGCTGTTAGA 4968 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.48 CpG sites = 26, Kimura (unadjusted) = 36.48 Transitions / transversions = 1.30 (26/20) Gap_init rate = 0.03 (5 / 166), avg. gap size = 1.40 (7 / 5) 682 28.77 11.78 0.68 chrXqtel1M 865289 865687 (134313) ERV24_Prim#LTR/ERV1 4987 5429 (2146) m_b375s701i2 15657 chrXqtel1M 865289 GGCCAGTTTCCTCTCCCGGATGCCCCATT-------TGGCAGATCGACTC 865331 i v i v i v v v ------- i? v i i ERV24_Prim#LT 4987 GGTCATTTTCCTTTACCAGAAGGCCCTTTCGAGGTATGGCAANTGGATTT 5036 chrXqtel1M 865332 CATTCATTTGCCACCTGCCCATGGTTACAAATATACTTTGGTTATGGTCT 865381 i vi i vv ? v v i i ii i ? ? i ERV24_Prim#LT 5037 TATTCAGCTGCCGCCATCNCAAGGATACGAGTATGTTCTNGTNATGGTTT 5086 chrXqtel1M 865382 GTATGTTTTCCTGGTGGGTGGAAGCATTCCCCT---------TCGCAGTC 865422 iiiv i i ? ---------i?i i i ERV24_Prim#LT 5087 GTATGTTTTCTCATTGGGTAGAAGCATTTCCNTGCAGAAGAGCNACGGCC 5136 chrXqtel1M 865423 TCTGGGGCAGCAAAAATCCACTTAGAAAAAATCATTCCATTATGGGGGGT 865472 iv vi i vv i v? i ??iv i ERV24_Prim#LT 5137 TTAGCAGTAGGTAAAATTCTNTTAGAAAAAATTATTCCNNCTTGGGGAGT 5186 chrXqtel1M 865473 TCCTAAAGAAATACATAATGATGGAGGTTCCCATTTCAC---AGAAGC-- 865517 vv v v i ii i? ?v i i --- v i-- ERV24_Prim#LT 5187 TCCTCTAGAACTCCACAGCGACNGAGGNACTCATTTTACTGGACAAGTAA 5236 chrXqtel1M 865518 TTCA-TTAGCT-----AAGCTGCTCTCATCCTGGTCAA-----TCATT-- 865554 ? - i i?----- v v- i i --? -----i -- ERV24_Prim#LT 5237 TNCAGTCAGTNTGTAAAATCTGG-CCCATTCT--NCAACATTTCCATTGT 5283 chrXqtel1M 865555 ---TAGCAC----------TTGGGATAATTGAACAAGTTAATGGGATACT 865591 --- v ----------i iv ii v i?iiv i v ERV24_Prim#LT 5284 GCCTATCACCCCCAGTCNTCTGGACTGGTGGAACGNACAAATGGAATAAT 5333 chrXqtel1M 865592 TACAACTTCCCTTGCTAAATTAGCTGAAGAACTAGGTATTCCTGGGCCCA 865641 ? v ivvi v v i ?i ? vvi viiv? v v ERV24_Prim#LT 5334 NAAAACTCAATTGGCAAAGTTNACNGAAGCTTTTAAANTTCCTTGGCCAA 5383 chrXqtel1M 865642 AAGCCCTGTCTTTAGCCCTACTAAGCCTTAGATCCAGACCATTTGG 865687 i i vi v i i?i i v i v ? vv ? ERV24_Prim#LT 5384 AGGCTCTTCCATTGGTNTTGCTTAACCTAAGATCNACCCCNTTTGG 5429 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.97 CpG sites = 66, Kimura (unadjusted) = 40.24 Transitions / transversions = 1.38 (66/48) Gap_init rate = 0.03 (13 / 398), avg. gap size = 3.85 (50 / 13) 321 22.54 0.00 0.00 chrXqtel1M 865919 865989 (134011) HERV-Fc2#LTR/ERV1 5294 5364 (1886) m_b375s701i3 15658 chrXqtel1M 865919 CTTTGGAGCCATGGTGGAAAGGTCCCTTTGAAGTCCTGCTCACCACCCCC 865968 i i?v ii v i i iv v v ? HERV-Fc2#LTR/ 5294 CCTTGANCCCGCGGTGGTAAGGCCCTTTCCAAGTCATCCTCACNACCCCC 5343 chrXqtel1M 865969 ACTGCAGCCAAACTCTGGGGA 865989 i ?ivi HERV-Fc2#LTR/ 5344 ACCGCAGCCAAACTNCCAGGA 5364 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 22.90 CpG sites = 10, Kimura (unadjusted) = 28.95 Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0) 471 32.33 12.15 1.69 chrXqtel1M 868317 868530 (131470) C L3#LINE/CR1 (3) 4096 3861 m_b375s601i2 15659 chrXqtel1M 868317 AGAATCCCAGTAATTCAGAGTGGAAAGAGAAAGAGCACAGGAATTATCTG 868366 v v vi v i i v---- vi iii i i C L3#LINE/CR1 4096 AGAATCACAGAATCTCAGAGTTGGAAGGGAC----CTTAGAGGTCATCTA 4051 chrXqtel1M 868367 ATTGGACT-------AAATG--GGAATCCCTT-TCTAGTGACCTTGGCAA 868406 i ivi i-------v -- - vi iiiv i i C L3#LINE/CR1 4050 GTCCAACCTCCCATCCAATGCAGGAATCCCTTCTACAACATCCCTGACAA 4001 chrXqtel1M 868407 ATGGCCACCCAATTTTCCCTGGAAGATCCCCAA------AGAGTTGG--- 868447 i i i iii iiv v v i i i------i i vi--- C L3#LINE/CR1 4000 GTGGTCATCCAGCCTCTGCTTGAACACCTCCAGTGACGGGGAGCTCACTA 3951 chrXqtel1M 868448 ----GTGAG--AGCCCATTTCACTTGGGGTCAGCTCTGATTGTTAGGAAG 868491 ----?i -- i i vv v i C L3#LINE/CR1 3950 CCTCNCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGATTGTTAGAAAG 3901 chrXqtel1M 868492 TTTTCTATGACATTAAGCTGAAGTCTACTTTTCT-CAACT 868530 i iiv v i i i i i i ii -i C L3#LINE/CR1 3900 TTCTTCCTTATATTGAGCCGAAATCTGCCTCCCTGTAACT 3861 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 44.12 CpG sites = 49, Kimura (unadjusted) = 46.04 Transitions / transversions = 2.58 (49/19) Gap_init rate = 0.06 (12 / 213), avg. gap size = 2.50 (30 / 12) 610 33.19 8.31 5.13 chrXqtel1M 868539 868935 (131065) C L2#LINE/L2 (145) 2937 2529 m_b375s601i3 15660 chrXqtel1M 868539 AAAGGTGGCCTGGGACCAGACTTTGAAGGG----GTAACCAACCTTTCTA 868584 i ii vv iiv v ---- i---i v v C L2#LINE/L2 2937 AGAGGTAACGGGGGACCAGATCATGTAGGGCCTTGTAG---GCCATTGTA 2891 chrXqtel1M 868585 ACCAGAGGAGTTTGTATTTGATCCTAGAAACAATAGAGAGTTACTGGAAA 868634 ----- v vv v ii iiivivi i ii ii i ii C L2#LINE/L2 2890 A-----GGACTTTGGCTTTTACTCTGAGTGAGATGGGAAGCCATTGGAGG 2846 chrXqtel1M 868635 ATTTTGATCAAGGGATTGATGTGATCAGATTCATACTCCAAGAATATCAC 868684 i v ii v ii v i i iii ii i iv C L2#LINE/L2 2845 GTTTTGAGCAGAGGAGTGACATGATCTGACTTACGTTTTAAAAGGATCAC 2796 chrXqtel1M 868685 TTTGGCTGCTATGTAGAAGATGGAATGAATGAGTTATAGATTTGTGGCAG 868734 i i v ii i v ? v i vvvv iv v vi C L2#LINE/L2 2795 TCTGGCTGCTGTGTTGAGAATAGACTGNAGGGGGGCAAGGGTGGAAGCAG 2746 chrXqtel1M 868735 GGAGAGCAATATGGAGGCCATTTCCATAGTCCAGATGAGAGA------TG 868778 v i vv i v vi i ii ------ C L2#LINE/L2 2745 GGAGACCAGTTAGGAGGCTATTGCAGTAATCCAGGCGAGAGATGATGGTG 2696 chrXqtel1M 868779 GCT-------ATGTGGGGGGAGAAAA-------AGAAATGGCTA----CA 868810 -------iv v v vii ------- i iii---- v C L2#LINE/L2 2695 GCTTGGACCAGGGTGGTGGCAGTGGAGGTGGTGAGAAGTGGTCGGATTCT 2646 chrXqtel1M 868811 AAATATGTTGTG--GGTTGGGAAATGACAGGAGTTGGCTAA-GAATCAAA 868857 ii i v -- --i ivi - v i - i iii C L2#LINE/L2 2645 GGATATATTTTGAAGGT--AGAGCCGACAGGA-TTTGCTGATGGATTGGA 2599 chrXqtel1M 868858 CAAGGG--GAAAGGGAAGGAGAGGGCAAAGTTGGAGTTAAGAATGACTCA 868905 iiv -- vi i i ---------- i i v C L2#LINE/L2 2598 TGTGGGGTGTGAGAGAAAGAGA----------GGAGTCAAGGATGACTCC 2559 chrXqtel1M 868906 AATGTTCCAAACCTCAGCAACTGGAAAGAT 868935 v iivii v i C L2#LINE/L2 2558 AAGGTTTTTGGCCTGAGCAACTGGAAGGAT 2529 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 44.23 CpG sites = 80, Kimura (unadjusted) = 46.42 Transitions / transversions = 1.78 (80/45) Gap_init rate = 0.07 (29 / 396), avg. gap size = 1.86 (54 / 29) 14 13.12 0.00 0.00 chrXqtel1M 869292 869317 (130683) (TCAC)n#Simple_repeat 1 26 (0) m_b375s252i6 15661 chrXqtel1M 869292 TCATTCACTTACTCACTCACTCATTC 869317 i i i (TCAC)n#Simpl 1 TCACTCACTCACTCACTCACTCACTC 26 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 35 0.00 0.00 0.00 chrXqtel1M 870405 870434 (129566) (GT)n#Simple_repeat 1 30 (0) c_b375s251i1 15662 chrXqtel1M 870405 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 870434 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 30 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 266 24.00 1.33 5.56 chrXqtel1M 870960 871034 (128966) MIR3#SINE/MIR 47 118 (90) m_b375s601i4 15663 chrXqtel1M 870960 ATCTGGGTATGAGTACAAGCTCTGTCAC-AACTTACTGTGTGACCTTTGG 871008 i viv v vi i - ?i - MIR3#SINE/MIR 47 ACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTGTGACC-TTGG 95 chrXqtel1M 871009 ACAATCCACTCATTCTTTTTTTTGGG 871034 i vi --- vii i i MIR3#SINE/MIR 96 GCAAGTCAC---TTCACCTCTCTGGG 118 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 28.14 CpG sites = 11, Kimura (unadjusted) = 30.24 Transitions / transversions = 1.83 (11/6) Gap_init rate = 0.07 (5 / 74), avg. gap size = 1.00 (5 / 5) 32 27.70 3.92 7.72 chrXqtel1M 871078 871332 (128668) (AGGAAA)n#Simple_repeat 1 246 (0) m_b375s252i7 15664 chrXqtel1M 871078 AGGAAAA-GAAGAGAAAAATG-AGAGCAAGGAGTAAAGAAGGAAGGGAAG 871125 - i i v - i v -i v - i i i - (AGGAAA)n#Sim 1 AGGAAAAGGAAAAGGAAAAGGAAAAGGAA-AAGGAAA-AGGAAAAGGAA- 47 chrXqtel1M 871126 AAGGAAAAGGGTAAGG-CAAGG-AGAGCATGAAGG-AATGAGATAGAGAA 871172 iv -v - i v -i - v ii v ii (AGGAAA)n#Sim 48 AAGGAAAAGGAAAAGGAAAAGGAAAAGGA-AAAGGAAAAGGAAAAGGAAA 96 chrXqtel1M 871173 AGG-AGAGAAGAAAGG-AAGTGAAGTTTTAAGGGTGGAAGAGAAAGGAGA 871220 - i i - - iv ivvvv i -ii ii - (AGGAAA)n#Sim 97 AGGAAAAGGA-AAAGGAAAAGGAAAAGGAAAAGG-AAAAGGAAAAGGA-A 143 chrXqtel1M 871221 AAGG-AAAGAAATGAAGGAAAATGTAAATGGAGAAAGATGAAGGAAAAAG 871269 - i -- - v v - ivi i (AGGAAA)n#Sim 144 AAGGAAAAGGAA--AAGGAAAA-GGAAAAGGA-AAAGGAAAAGGAAAAGG 189 chrXqtel1M 871270 GAAAGAAAGATAGAAAGATGGAAAA--AAGAGAAAAAGAGAGAAGGAAGG 871317 i i - - i - v -- i i - i -- (AGGAAA)n#Sim 190 AAAAGGAA-A-AGGAA-AAGGAAAAGGAAAAGGAAAAG-GAAAAGGAA-- 233 chrXqtel1M 871318 AAGGAAAGGAGGAAA 871332 -- (AGGAAA)n#Sim 234 AAGGAAA--AGGAAA 246 Matrix = Unknown Transitions / transversions = 1.94 (33/17) Gap_init rate = 0.11 (28 / 254), avg. gap size = 1.04 (29 / 28) 216 27.47 15.38 0.00 chrXqtel1M 872673 872763 (127237) C MIR3#SINE/MIR (3) 205 101 m_b375s601i5 15665 chrXqtel1M 872673 TCAGAGACTCGTAGATGATGAGAGCTGGGAAGG----------TTGTCTT 872712 v v i vvi v i i ---------- ii v C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTA 156 chrXqtel1M 872713 GTCCAACTCCTGAATTTTA-AGCTTGGATAACCAAGAACCAGAGA---GA 872758 i ivv - v vi iv ii iv --- C MIR3#SINE/MIR 155 GTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGA 106 chrXqtel1M 872759 AGTGA 872763 C MIR3#SINE/MIR 105 AGTGA 101 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.68 CpG sites = 13, Kimura (unadjusted) = 34.68 Transitions / transversions = 1.08 (13/12) Gap_init rate = 0.03 (3 / 90), avg. gap size = 4.67 (14 / 3) 34 0.00 0.00 0.00 chrXqtel1M 872835 872863 (127137) (GT)n#Simple_repeat 1 29 (0) c_b375s251i2 15666 chrXqtel1M 872835 GTGTGTGTGTGTGTGTGTGTGTGTGTGTG 872863 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTG 29 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 209 29.88 1.79 16.33 chrXqtel1M 872890 873001 (126999) C MIR3#SINE/MIR (3) 205 108 m_b375s601i6 15667 chrXqtel1M 872890 TCATGGATCCTTAGCTTGGTAAAGCTGAAATAGACTTCAGTGCTTACCTT 872939 i vi v vv vi i i vi i i v v i i v C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTA 156 chrXqtel1M 872940 ATCCAACACCCTAACCCTCTGCTCTTAGGTTCTTCCAG--GGGGAAACTG 872987 i v v ---------------- i v -- i C MIR3#SINE/MIR 155 GTCCAACCCCCTCA----------------TTTTACAGATGAGGAAACTG 122 chrXqtel1M 872988 AAGCCCACAGATGT 873001 i v v C MIR3#SINE/MIR 121 AGGCCCAGAGAGGT 108 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 37.39 CpG sites = 14, Kimura (unadjusted) = 37.39 Transitions / transversions = 1.00 (14/14) Gap_init rate = 0.15 (17 / 111), avg. gap size = 1.06 (18 / 17) 283 25.00 5.00 0.00 chrXqtel1M 873121 873200 (126800) C MIR3#SINE/MIR (12) 196 113 m_b375s601i7 15668 chrXqtel1M 873121 CATAGGATGG-AAAGCTAGTCGGCTCCTTGGAGATCGTTTAGTCCCAATC 873169 i v- i i vv vv i i i v vi C MIR3#SINE/MIR 196 CATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCC 147 chrXqtel1M 873170 CCTCA-TTGGTAGCTGAGAAAAC--AGGCTCAGA 873200 - vii v i -- i C MIR3#SINE/MIR 146 CCTCATTTTACAGATGAGGAAACTGAGGCCCAGA 113 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.88 CpG sites = 11, Kimura (unadjusted) = 30.88 Transitions / transversions = 1.22 (11/9) Gap_init rate = 0.04 (3 / 79), avg. gap size = 1.33 (4 / 3) 271 22.67 1.30 8.33 chrXqtel1M 874396 874472 (125528) HSAT5v1#Satellite 5209 5280 (618) m_b375s502i0 15669 chrXqtel1M 874396 TGTGAGCATGCA-TTTGTGTGTGCACACGTGTGAACATGTGTTTGTGTGT 874444 i v - v i i vi ii v HSAT5v1#Satel 5209 TGCGTGCATGCAATGTGTGTGTGCACGCGCGTGCGCGCGTGTGTGTGTGT 5258 chrXqtel1M 874445 ACATATGTGAGCATGTATGTACGTGTGT 874472 i? i------ i i ii HSAT5v1#Satel 5259 GNAC------GCGTGTGTGCGCGTGTGT 5280 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 12.09 CpG sites = 12, Kimura (unadjusted) = 28.58 Transitions / transversions = 3.00 (12/4) Gap_init rate = 0.09 (7 / 76), avg. gap size = 1.00 (7 / 7) 19 19.79 4.35 0.00 chrXqtel1M 875281 875326 (124674) (TC)n#Simple_repeat 1 48 (0) m_b375s252i8 15670 chrXqtel1M 875281 TCTCTCTCTCTCTCTCTCT-TCTGACTC-CTGACCCACTCCCTCTTTC 875326 - vv - vv i v i i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 48 Matrix = Unknown Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.04 (2 / 45), avg. gap size = 1.00 (2 / 2) 476 24.79 3.20 3.20 chrXqtel1M 875447 875571 (124429) C MIR3#SINE/MIR (26) 182 58 m_b375s601i8 15671 chrXqtel1M 875447 GCTGAAAGGAACTTTAGGGATCTCATCAAGTCCAATTCCTTCATTTGACA 875496 i i i i -- v ii i v C MIR3#SINE/MIR 182 GCTGGAAGGGACCTTAGAGATC--ATCTAGTCCAACCCCCTCATTTTACA 135 chrXqtel1M 875497 GATAAGGAAACCAAGG---AAACTGTGAGGAAGTGACCTGTCCAAAGTCA 875543 i ii --- i -- v iv i i i C MIR3#SINE/MIR 134 GATGAGGAAACTGAGGCCCAGA--GAGGTGAAGTGACTTGCCCAAGGTCA 87 chrXqtel1M 875544 TAGAGATACTAAGT-ACAGAGTTAGAATT 875571 i v v? v v -i iii i i C MIR3#SINE/MIR 86 CACAGCNAGTTAGTGGCAGAGCCGGGACT 58 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 30.53 CpG sites = 22, Kimura (unadjusted) = 31.98 Transitions / transversions = 2.75 (22/8) Gap_init rate = 0.05 (6 / 124), avg. gap size = 1.33 (8 / 6) 209 36.59 3.51 1.72 chrXqtel1M 876060 876173 (123827) C L3#LINE/CR1 (12) 4087 3972 m_b375s601i9 15672 chrXqtel1M 876060 GAATCTGAGAATTATGGGGGACCTTGGATGCCATGTCA-CCAAAGCCATA 876108 v i ivii i v i v vi- vvi vi C L3#LINE/CR1 4087 GAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCAACCTCCCA 4038 chrXqtel1M 876109 T---ATGACCAAGGGTCCCCTCTACAACAGACTCTATTAATCATCCTCCA 876155 --- -- i ii i vv iiv iv i vi v C L3#LINE/CR1 4037 TCCAATG--CAGGAATCCCTTCTACAACATCCCTGACAAGTGGTCATCCA 3990 chrXqtel1M 876156 GTTTATTCTCAACCATTT 876173 ii v v ii v ii C L3#LINE/CR1 3989 GCCTCTGCTTGAACACCT 3972 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 52.46 CpG sites = 24, Kimura (unadjusted) = 52.46 Transitions / transversions = 1.41 (24/17) Gap_init rate = 0.04 (4 / 113), avg. gap size = 1.50 (6 / 4) 229 36.74 0.00 2.34 chrXqtel1M 876144 876274 (123726) C L3#LINE/CR1 (220) 3879 3752 m_b375s601i10 15672 chrXqtel1M 876144 AATCATCCTCCAGTTTATTCTCAACCATTTGTTACCAATTCTGGCCCCTG 876193 vv vvv v i ii v v i- i i v i C L3#LINE/CR1 3879 AATCTGCCTCCCTGTAACTTCCACCCATTGGTC-CTAGTTCTGCCCTCTG 3831 chrXqtel1M 876194 GGATGATATAGAAAATGTTCATACCCTGTTCTGCAGGAAAAACATTCAGG 876243 iiiv i i v v ii vv v ii v v iv v ii C L3#LINE/CR1 3830 GAGCCACACAGAATAAGTCTAATCCCTCTTCCACATGACAGCCCTTCAAA 3781 chrXqtel1M 876244 CATATGTTGAAAACTCTCATGTTCATTCTCT 876274 i v vv v i v i-- i C L3#LINE/CR1 3780 TATTTGAAGACAGCTATCATGTC--TCCTCT 3752 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 51.33 CpG sites = 23, Kimura (unadjusted) = 51.33 Transitions / transversions = 0.96 (23/24) Gap_init rate = 0.02 (3 / 130), avg. gap size = 1.00 (3 / 3) 473 23.56 5.60 1.54 chrXqtel1M 876315 876439 (123561) MIR3#SINE/MIR 41 170 (38) m_b375s601i11 15673 chrXqtel1M 876315 CATGAGACGTGGATTTTCATTCTGTCTCTG------ATTCA-TGTAATAA 876357 v v i i vi i i v ------ i ?i- i- i MIR3#SINE/MIR 41 CAGGAGACCTGGGTTCTAGTCCCGGCTCTGCCACTAACTNGCTGTG-TGA 89 chrXqtel1M 876358 ACTTGGGTAGGTCCCTTTCCCTTCTCTGGGCCTCAGTTTCTGCCTCTGTA 876407 v i i v iv - iv v MIR3#SINE/MIR 90 CCTTGGGCAAGTCACTTCACCT-CTCTGGGCCTCAGTTTCCTCATCTGTA 138 chrXqtel1M 876408 AAATAAAGGGGTTGGAGTAAATTATTTGTAAG 876439 i i v i v i v MIR3#SINE/MIR 139 AAATGAGGGGGTTGGACTAGATGATCTCTAAG 170 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 27.97 CpG sites = 17, Kimura (unadjusted) = 29.14 Transitions / transversions = 1.42 (17/12) Gap_init rate = 0.03 (4 / 124), avg. gap size = 2.25 (9 / 4) 17 20.57 5.36 3.51 chrXqtel1M 876674 876729 (123271) (AG)n#Simple_repeat 1 57 (0) m_b375s252i9 15674 chrXqtel1M 876674 AGAGAGAG-GGGGGAGAGAGGGA-AGATGGGATGGGGTAG-GAGAGGGAG 876720 - i i i - - i - i iv - i (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGA-GAGA-GAGAGAGAGAGAGAGAG 48 chrXqtel1M 876721 AGAGAAAGA 876729 i (AG)n#Simple_ 49 AGAGAGAGA 57 Matrix = Unknown Transitions / transversions = 8.00 (8/1) Gap_init rate = 0.09 (5 / 55), avg. gap size = 1.00 (5 / 5) 42 2.38 0.00 0.00 chrXqtel1M 876985 877027 (122973) (CTTC)n#Simple_repeat 1 43 (0) c_b375s251i3 15675 chrXqtel1M 876985 CTTCCTTCCTTCCTTCCCTCCTTCCTTCCTTCCTTCCTTCCTT 877027 i (CTTC)n#Simpl 1 CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 43 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 386 30.18 4.36 6.98 chrXqtel1M 878288 878654 (121346) C L1PREC2_orf2#LINE/L1 (2910) 384 27 m_b375s551i13 15676 chrXqtel1M 878288 AACTT-CTCTAGGAATTTGAGTGCTATACCACTTGGCGCATATATATTTA 878336 - i v i i vivviii v i C L1PREC2_orf2# 384 AACTTGCTTTATGAATCTGGGTGCTCCTGTGTTGGGTGCATATATATTTA 335 chrXqtel1M 878337 GTAATGATA-TTA---CTTCATTATCT-ATGGTACCCTTTATCAAGTTGT 878381 ---- - --- - i iv- v v i vvv C L1PREC2_orf2# 334 G----GATAGTTAGGTCTTC-TTGTTGAATTGAACCCTTTACCATTATGT 290 chrXqtel1M 878382 AGTTTTCTTCTCTCTTTTGATTAGATCTATTTTTGCTTT------TTCTT 878425 i vii i v i v- v - v v ------ vi C L1PREC2_orf2# 289 AATGCCCTTCTTTGTCTTT-TTTGATCT-TTGTTGGTTTAAAGTCTGTTT 242 chrXqtel1M 878426 GATCTGAGATCAGTATCACTACCTCTG--TTTGTTTGTTTATTACTTCAG 878473 vi i i v ii v i -- v i vii i -- C L1PREC2_orf2# 241 TGTCTGAAATTAGGATTGCAACCCCTGCTTTTTTCTGTTTTCCATTT--G 194 chrXqtel1M 878474 CTGAAGCATAATAGATTCTGCTCCAGTCTTTTACTTTTACTCTGTATGGA 878523 ------ ii i v vi i i v vi i iv vi C L1PREC2_orf2# 193 CT------TGGTAGATTTTTCTCCATCCCTTTATTTTGAGCCTATGGGTG 150 chrXqtel1M 878524 TCATTCTCCTTTAAATATGTTTCTTGTAAAGAACATATTGTAGGATTCTG 878573 viviv v i iv i v i v i iii v i ii C L1PREC2_orf2# 149 TCATTGCATGTGAGATGGGTCTCTTGAAGACAGCATACCATTGGGTCTTG 100 chrXqtel1M 878574 ACTTCAGAATCCTAGCTTTCCAGTCTGCTATCTGCTTCCATTTTATGGGA 878623 - vvv - v v ----- i --- v v i C L1PREC2_orf2# 99 -CTTCTTTATCC-AGCTTGCCACTCTG-----TGCCT---TTTAATTGGG 60 chrXqtel1M 878624 GTATATA--CCATTCACATTCACAGTTAAAATT 878654 i v -- i vi iv C L1PREC2_orf2# 59 GCATTTAGCCCATTTACATTCAAGGTTAGTATT 27 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.30 CpG sites = 56, Kimura (unadjusted) = 39.30 Transitions / transversions = 1.19 (56/47) Gap_init rate = 0.09 (32 / 366), avg. gap size = 1.28 (41 / 32) 260 20.13 10.39 9.68 chrXqtel1M 878524 878677 (121323) C L1MEh_5end#LINE/L1 (1) 2234 2080 m_b375s551i14 15676 chrXqtel1M 878524 TCATTCTCCTTTAAATATGTTTCTTGTAAAGAACATATTGTAGGATTCTG 878573 v ? vi i i i i v i v i C L1MEh_5end#LI 2234 TCCTTNTGTTTTAAGTGTGTCTCTTGTAGACAGCATATTGTTGGATTTTG 2185 chrXqtel1M 878574 ACTTCAGAATCCTAGCTTTCCAGTCTGCT-ATCTGCTTCCATTTTA--TG 878620 vi i?i ---------- i v?- viv -- -- C L1MEh_5end#LI 2184 TTTTTNAA----------TCCAATCTGANAATCTCTGTC--TTTTAATTG 2147 chrXqtel1M 878621 G-GAGTATATACCATTCACATTCACAGTTAAAATTACT-CTAT------- 878661 - v vv i i --- iv -? ------- C L1MEh_5end#LI 2146 GTGAGTTTAACCCATTTACATTTA---TTGTAATTACTGNTATATTNGGA 2100 chrXqtel1M 878662 ----TTCCTGCCATCTTATT 878677 ---- i C L1MEh_5end#LI 2099 CTTATTTCTGCCATCTTATT 2080 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 24.61 CpG sites = 16, Kimura (unadjusted) = 24.61 Transitions / transversions = 1.33 (16/12) Gap_init rate = 0.14 (21 / 153), avg. gap size = 1.48 (31 / 21) 85 0.00 2.44 0.00 chrXqtel1M 879373 879454 (120546) (TTCT)n#Simple_repeat 1 84 (0) c_b375s251i4 15677 chrXqtel1M 879373 TTCTTTCTTTC--TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT 879420 -- (TTCT)n#Simpl 1 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT 50 chrXqtel1M 879421 CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 879454 (TTCT)n#Simpl 51 CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 84 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.01 (1 / 81), avg. gap size = 2.00 (2 / 1) 444 30.31 2.39 5.33 chrXqtel1M 879845 880095 (119905) C L1ME5_3end#LINE/L1 (274) 667 424 m_b375s551i15 15678 chrXqtel1M 879845 ACGGTATTGTTGTTGAAGTATATAATAATCTGGTTCT-GCTCATTTCACT 879893 i - i--- ? vvi v v -i iv C L1ME5_3end#LI 667 ATGGTATTGT-GTTA---TANATCTCATTCTGTTTCTTACTTTTTTCACT 622 chrXqtel1M 879894 CAGTATTA-GTTCATGTAAG-TCTCTCCAAGCCTCTCTGTATTCATTCTG 879941 i i - -- v - iv v iiv v i v iiv C L1ME5_3end#LI 621 CAGCACTATGTT--TTTAAGATCCATCCATGTTGCTATGTGTACATCTAG 574 chrXqtel1M 879942 CTGGTCATTTCTTACAG-TACGATAATATTCCATAACATTCATATACCAC 879990 iiv iii v v - i - i i iiii v vi C L1ME5_3end#LI 573 TCCGTTGCTTCTAACTGCTGC-ATAGTACTCCATGGTGTGCATCCACCAC 525 chrXqtel1M 879991 AATTTACCCAACCAATCCCCAATTGATGGGCATCCA--TTCATTTTCCAG 880038 v i v v i v v i i -- v--ii i C L1ME5_3end#LI 524 ATTTTACCTATCCACTCTCCCAGTGATGGACACCCAGGTTG--CCTCCAA 477 chrXqtel1M 880039 TTTCTAGCCACTACAAACAGGGCTGTTACAAACATTTTGGCACATACAGG 880088 i i iv i iv iv ii ii ---- i v C L1ME5_3end#LI 476 CTCCCCGCCACCACAAACAACGCTGCAATGAACATCCT----CGTACATG 431 chrXqtel1M 880089 TCCCTTT 880095 i C L1ME5_3end#LI 430 TCCCCTT 424 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 39.75 CpG sites = 45, Kimura (unadjusted) = 40.49 Transitions / transversions = 1.67 (45/27) Gap_init rate = 0.07 (18 / 250), avg. gap size = 1.06 (19 / 18) 13 25.55 1.64 5.08 chrXqtel1M 880682 880742 (119258) (AGAA)n#Simple_repeat 1 59 (0) m_b375s252i10 15679 chrXqtel1M 880682 AGAAAGAAAGAAA-AAAACCTGAGAAGAAAAACAAAAATGCAAGCAAACA 880730 - ivvv - i - i v v - v (AGAA)n#Simpl 1 AGAAAGAAAGAAAGAAAGAAAGA-AAGAAAGA-AAGAAAGAAAG-AAAGA 47 chrXqtel1M 880731 GAAACAGAAAGA 880742 i i v (AGAA)n#Simpl 48 AAGAAAGAAAGA 59 Matrix = Unknown Transitions / transversions = 0.71 (5/7) Gap_init rate = 0.07 (4 / 60), avg. gap size = 1.00 (4 / 4) 13 27.78 3.57 0.00 chrXqtel1M 880688 880743 (119257) (AAAGAA)n#Simple_repeat 1 58 (0) m_b375s252i11 15679 chrXqtel1M 880688 AAAGAAAAA-AACCTG-AGAAGAAAAACAAAAATGCAAGCAAACAGAAAC 880735 - vvv - i v viv iv v v (AAAGAA)n#Sim 1 AAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAA 50 chrXqtel1M 880736 AGAAAGAG 880743 i (AAAGAA)n#Sim 51 AGAAAAAG 58 Matrix = Unknown Transitions / transversions = 0.44 (4/9) Gap_init rate = 0.04 (2 / 55), avg. gap size = 1.00 (2 / 2) 1069 28.08 5.88 4.76 chrXqtel1M 883676 884236 (115764) C L1MA10_3end#LINE/L1 (448) 633 67 m_b375s551i16 15680 chrXqtel1M 883676 GTTCATTTCACTCAGCATCAAT-TCATGCAAGTCTCTCTAGGCCTCTCTG 883724 i i i - - v v i iiv i v i- v vv C L1MA10_3end#L 633 GCTTATTTCACTTAGCAT-AATGTCCTCCAGGTTCATCCATGT-TGTCGC 586 chrXqtel1M 883725 AAATCATCCTGGTAG-----TCTTTTCTTACAAAAC--AATAATATTCCA 883767 ------ i -----i i i vi ii -- C L1MA10_3end#L 585 AAAT------GGCAGGATTTCCTTCTTTTTTAAGGCTGAATAATATTCCA 542 chrXqtel1M 883768 TAGTATTTATATACCACAATTTACTCAGCCATTCTCCAATTGATGGGCAT 883817 v v v vi i v vi vi i i C L1MA10_3end#L 541 TTGTATGTATATACCACATTTTCTTTATCCATTCATCCGTCGATGGACAT 492 chrXqtel1M 883818 CCTCTCAG----TTTCCAGTTTCTTG-CCACTACAAACAGGGATGCCACA 883862 ---- i ---- - v - i i iii i iv v v ii C L1MA10_3end#L 491 ----TTAGGTTGTTTCCA-TATCTTGGCTATTGTGAATAATGCTGCAATG 447 chrXqtel1M 883863 AACATTTTGGCACATAGAAGTCCCTT----ATCCTTCTTTAGTATCTCTT 883908 v-- viiii vi i ---- vv --i vi C L1MA10_3end#L 446 AACATG--GGAGTGCAGATATCTCTTCGAGATCCTGATTT--CAATTCTT 401 chrXqtel1M 883909 TGGGATATAAACCCAGCAGTGACACTGCTGGATCAAAGGGGA--TTTGAG 883956 v v v iv i v v v -- i ivv C L1MA10_3end#L 400 TTGGATATATACCCAGAAGTGGGATTGCTGGATCATATGGTAGTTCTATT 351 chrXqtel1M 883957 CATAACTTTTTGAGCATAGTTCAAAATTGTTCTCCAGAATGGTTGGATC- 884005 iv i v - vi v v i i v i i v i - C L1MA10_3end#L 350 TTTAATTTTTTGAGGA-ACCTCCATACTGTTTTCCATAGTGGCTGCACCA 302 chrXqtel1M 884006 CTTCACAGTTCCACCAACAATGTATCAGTGTCCCAGTTTTCCCACATCCC 884055 ? i v i i iv v i ?? ii i C L1MA10_3end#L 301 NTTTACATTCCCACCAACAGTGTACAAGGGTTCCNNTTTCTCCACATCCT 252 chrXqtel1M 884056 CTCCGACATTCATCAT--TATCTTTTCCTGCCATCTTAGCCAATCTGAGA 884103 v i i ii i -- v v ii -- vv vi i v C L1MA10_3end#L 251 CGCCAACACTTGTTATCTTTTGTTTTTTTG--ATAATAGCCATCCTAACA 204 chrXqtel1M 884104 GGTGTGGAGTGGTACCTCAGTATTGTCTTAATTTGCATTTCTCTGATCAA 884153 ii i i v i v i i i v v C L1MA10_3end#L 203 GGTGTGAGGTGATATCTCATTGTGGTTTTGATTTGCATTTCCCTGATGAT 154 chrXqtel1M 884154 TAGTGAT---------TTTTTCATGT-CATG-TGACTAGAAATATTTTTA 884192 ---------i i - v - i ------i v - C L1MA10_3end#L 153 TAGTGATGTTGAGCACCTTTTCATATACCTGTTGGC------CATTTGT- 111 chrXqtel1M 884193 ATTTCTTCATCTAAAAATTGTCTGTCCGTATCCTTTGGCCATTT 884236 v v ivi i v i i ivi v C L1MA10_3end#L 110 ATGTCTTCTTTGGAGAAATGTCTATTCAGGTCCTTTGCCCATTT 67 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 35.72 CpG sites = 87, Kimura (unadjusted) = 36.33 Transitions / transversions = 1.38 (87/63) Gap_init rate = 0.07 (39 / 560), avg. gap size = 1.54 (60 / 39) 970 29.61 5.10 5.87 chrXqtel1M 883757 884305 (115695) C L1PA8A_3end#LINE/L1 (326) 552 8 m_b375s551i18 15680 chrXqtel1M 883757 ATAATATTCCATAGTATTTATATACCACAATTTACTCAGCCATTCTCCAA 883806 i i i v i v vi i v v viv C L1PA8A_3end#L 552 ATAGTATTCCATGGTGTATATGTACCACATTTTCTTTATCCAGTCTATCA 503 chrXqtel1M 883807 TTGATGGGCATCCTCTCAGTT---TCCAGTTTCTTGCCACTACAAACAGG 883853 i--- vi --- vv ii i i ii i v C L1PA8A_3end#L 502 TTGATGGGCATT---TGGGTTGGTTCCATGTCTTTGCTATTGTAAATAGT 456 chrXqtel1M 883854 GATGCCACAAACATTTTGGCACATAGAAGTCCCT----TATCCTTCTTTA 883899 v v i vivv ii iv-- ii ---- vvv vv C L1PA8A_3end#L 455 GCTGCAATAAACATACGTGTGCATGT--GTCTTTATAGTAGAATGATTTA 408 chrXqtel1M 883900 GTATCTCTTTGGGATATAAACCCAGCAGTGACACTGCTGGATCAAAGGGG 883949 - ii - v i i iv i i v v C L1PA8A_3end#L 407 -TATTCCTTTGGG-TATATACCCAGTAATGGGATTGCTGGGTCAAATGGT 360 chrXqtel1M 883950 ATTT--GAGCATAACTTTTTGAGCATAGTTCAAAATTGTTCTCCAGAATG 883997 -- iviv iv ii v - viv v v i ii v C L1PA8A_3end#L 359 ATTTCTGGTTCTAGATCCTTGAGGA-ATCGCCATACTGTCTTCCACAATG 311 chrXqtel1M 883998 GTTGGA-TCCTTCACAGTTCCACCAACAATGTATCAGTGTCCCAGTTTTC 884046 i - vv i v i i vv i i vi ii C L1PA8A_3end#L 310 GTTGAACTAATTTACATTCCCACCAACAGTGTAAAAGCGTTCCTATTTCT 261 chrXqtel1M 884047 CCACATCCCCTCCGACATTCATCATTATCTTTTCCTGCCATCTTA----- 884091 v i v ii i------ iv v v i ----- C L1PA8A_3end#L 260 CCACAGCCTCGCCAGCATC------TATTGTTTCCTGACTTTTTAATAAT 217 chrXqtel1M 884092 -GCCAATCTGAGAGGTGTGGAGTGGTACCTCAGTATTGTCTTAATTTGCA 884140 - v vv i iii i v i v i i C L1PA8A_3end#L 216 CGCCATTCTGACTGGCGTGAGATGGTATCTCATTGTGGTTTTGATTTGCA 167 chrXqtel1M 884141 TTTCTCTGATCAATAGTGATTTT----TTCATGTCATGTGACTAGAAATA 884186 v vi v ---- iv v i vi ivviiiv C L1PA8A_3end#L 166 TTTCTCTGATGATCAGTGATGTTGAGCTTTTTTTCATATGTTTGTTGGCC 117 chrXqtel1M 884187 TTTTTAATTTCTTCATCTAAAAATTGTCTGTCCGTATCCTTTGGCCATTT 884236 viv v v v i i i v i i v ---- C L1PA8A_3end#L 116 GCGTAAATGTCTTCTTTTGAGAAGTGTCTGTTCATATCCTTTGCCC---- 71 chrXqtel1M 884237 ACCATCAATTTTACTTTTTAA-GGAATT-----TTTTTTTCTTCAGTGAA 884280 ------------ i - ii ----- -- i C L1PA8A_3end#L 70 ------------ACTTTTTGATGGGGTTGTTTGTTTTTTTCTT--GTAAA 35 chrXqtel1M 884281 TT--TTTATGTCTCTTTTAAAATTTGG 884305 -- v ii v v i C L1PA8A_3end#L 34 TTTGTTTAAGTTCCTTGTAAATTCTGG 8 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 36.80 CpG sites = 83, Kimura (unadjusted) = 38.38 Transitions / transversions = 1.19 (83/70) Gap_init rate = 0.08 (42 / 548), avg. gap size = 1.43 (60 / 42) 1451 27.86 3.33 2.06 chrXqtel1M 883757 884236 (115764) C L1ME5_3end#LINE/L1 (389) 552 67 m_b375s551i17 15680 chrXqtel1M 883757 ATAATATTCCATAGTATTTATATACCACAATTTACTCAGCCATTCTCCAA 883806 i i i i vi vi v ii v i v C L1ME5_3end#LI 552 ATAGTACTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCA 503 chrXqtel1M 883807 TTGATGGGCATCCTCTCAGTTTCCAGTTTCTTGCCACTACAAACAGGGAT 883856 v i i vvviv ii ii i ii i iv v C L1ME5_3end#LI 502 GTGATGGACACCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCT 453 chrXqtel1M 883857 GCCACAAACATTTTGGCACATAGAAGTCCC-TTAT---CCTTCTTTAGTA 883902 v ii ii v i ---- - --- viv v v C L1ME5_3end#LI 452 GCAATGAACATCCTCGTACAT----GTCCCCTTATGGACCTGTGTGAGAA 407 chrXqtel1M 883903 TCTCTTTGGGATATAAACCCAGCAGTGACACTGCTGGATCAAAGGGGATT 883952 i v v i iv i i v v - C L1ME5_3end#LI 406 TTTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTAT- 358 chrXqtel1M 883953 TGAGCATA-ACTT--TTTGAGCA--TAGTTCAAAATTGTTCTCCAGAATG 883997 --- i - -- vi -- v v v i i C L1ME5_3end#LI 357 ---GCGTATACTTAATTTGACTAAGTACTGCCAGATTGCTCTCCAGAATG 311 chrXqtel1M 883998 GTTGGATCCTTC-ACAGTTCCACCAACAATGTATCAGTGTCCCAGTTTTC 884046 i v i vv - v i i i i v v i vi ? i C L1ME5_3end#LI 310 GCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATNTCC 261 chrXqtel1M 884047 CCACATCCCCTCCGACATTCATCATTATCT--TTTCCTGCCATCTTAGCC 884094 i v i i iiv i--i i i-- i v C L1ME5_3end#LI 260 CCACATCCTCGCCAACACTTGGCATTATCCAGCTTTCTA--ATTTTTGCC 213 chrXqtel1M 884095 AATCTGAGAGGTGTGGAGTGGTACCTCAGTATTGTCTTAATTTGCATTTC 884144 i i v ii i i v i i C L1ME5_3end#LI 212 AGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATTTC 163 chrXqtel1M 884145 TCTGATCAATAGTGATTTTT----TCATGTCATGTGACTAGAAATATTTT 884190 i v i v v---- viv i vi ivv iiv i C L1ME5_3end#LI 162 TCTGATTACTAATGAGTTTGAGCATCTCTTCATATGCTTGTTAGCCTTTC 113 chrXqtel1M 884191 TAATTTCTTCATCTAAAAATTGTCTGTCCGTATCCTTTGGCCATTT 884236 vii i v iv i i i v C L1ME5_3end#LI 112 GGGTTTCCTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCCATTT 67 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 34.59 CpG sites = 79, Kimura (unadjusted) = 35.96 Transitions / transversions = 1.52 (79/52) Gap_init rate = 0.04 (18 / 479), avg. gap size = 1.44 (26 / 18) 18 3.67 3.57 0.00 chrXqtel1M 884323 884350 (115650) (CAAA)n#Simple_repeat 1 29 (0) m_b375s252i12 15681 chrXqtel1M 884323 CAAACAAACAAACAAACAAA-AAAAAAAC 884350 - v (CAAA)n#Simpl 1 CAAACAAACAAACAAACAAACAAACAAAC 29 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1) 270 33.54 0.54 2.78 chrXqtel1M 884956 885139 (114861) C L1ME4c_3end#LINE/L1 (175) 655 476 m_b375s551i19 15682 chrXqtel1M 884956 TATGTACAATATTCTCTTGATTTTGCTCATT-CACTCAGCATCAGTTCAT 885004 ?i v v ---- i iv - i i i vv C L1ME4c_3end#L 655 TANATACAATTTTGT----ATTCTGCTTTTTTCACTTAACATTATATCAT 610 chrXqtel1M 885005 ATAAGTCTTTCCAGGCTTTTCTGAAATTTTCCTGCTGATCATTTCTTATA 885054 - vvi v i vi viiv i i v iv v i v i C L1ME4c_3end#L 609 A-AACATTTTCCATGTTGCTACATAGTCTTCATAATTATCATTTTTAATG 561 chrXqtel1M 885055 GAATAATCATATTTCATTACATTAATATACCACAACTTATTCAACCATTC 885104 vvvv v i iivi ?i i i i i i C L1ME4c_3end#L 560 GCTGCATAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTC 511 chrXqtel1M 885105 CCCAGCTGATGAGCATCCACTCAGTTTCCAGTTTT 885139 vii v ii ii vviv i C L1ME4c_3end#L 510 CCCTATTGTTGGACATTTAGGTTGTTTCCAATTTT 476 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 45.37 CpG sites = 34, Kimura (unadjusted) = 46.56 Transitions / transversions = 1.31 (34/26) Gap_init rate = 0.03 (6 / 183), avg. gap size = 1.00 (6 / 6) 300 25.89 8.04 0.00 chrXqtel1M 885064 885175 (114825) C L1ME3A_3end#LINE/L1 (372) 548 428 m_b375s551i20 15682 chrXqtel1M 885064 TATTTCATTACATTAATATACCACAACTTATTCAACCATTCCCCAGCTGA 885113 i iii v i i v iv v i C L1ME3A_3end#L 548 TATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTACTGTTGA 499 chrXqtel1M 885114 TGAGCATCCACTCAGTTTCCAGTTTTA-------ATCAATAGTGAT-TTA 885155 ii iiivvi? ??------- iv v -i C L1ME3A_3end#L 498 TGGACATTTGGGTNGTTTCCAGTTTNNGGCTATTACGAATAGTGCTGCTA 449 chrXqtel1M 885156 -GAGCATTTTTTCACATGACT 885175 - i i vi v C L1ME3A_3end#L 448 TGAACATTCTTGTACATGTCT 428 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 32.64 CpG sites = 19, Kimura (unadjusted) = 34.09 Transitions / transversions = 1.90 (19/10) Gap_init rate = 0.03 (3 / 111), avg. gap size = 3.00 (9 / 3) 302 26.32 0.00 0.00 chrXqtel1M 885064 885139 (114861) C L1ME2z_3end#LINE/L1 (643) 548 473 m_b375s551i21 15682 chrXqtel1M 885064 TATTTCATTACATTAATATACCACAACTTATTCAACCATTCCCCAGCTGA 885113 i ii v ii i i v i v i C L1ME2z_3end#L 548 TATTCCATTGTATGAATATACCACAGTTTGTTTATCCATTCTCCTGTTGA 499 chrXqtel1M 885114 TGAGCATCCACTCAGTTTCCAGTTTT 885139 ii i iivv v C L1ME2z_3end#L 498 TGGACACCTGGGCTGTTTCCAGTTTT 473 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 33.95 CpG sites = 14, Kimura (unadjusted) = 33.95 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.00 (0 / 75), avg. gap size = 0.0 (0 / 0) 278 31.91 0.70 0.70 chrXqtel1M 885137 885278 (114722) C L1ME4c_3end#LINE/L1 (668) 162 21 m_b375s551i22 15682 chrXqtel1M 885137 TTTAATCAATAGTGATTTAGAGCATTTTTTCACATGACTAGAAATGGCTT 885186 i i v i vv v i i ii vi ivvv ivi? C L1ME4c_3end#L 162 TTTGATTACTAGCGAGGTTGAACATTTTTCCATGTGTTTGTTTACTANTT 113 chrXqtel1M 885187 TAATTTCTTCATCTGAAAATTGTCTGTTTACATCTTTTGACCATTTGTCA 885236 vv i v ? vi i ii i v i v C L1ME4c_3end#L 112 GTATTTCCTCTTNTGTGAATTGTCTGTTCATGTCCTTTGCCCATTTATCT 63 chrXqtel1M 885237 ATTGGAG-AATGACTTGTACTCTTATAAATCTGAGTTAATTCT 885278 i -vv i? v -i v i i v ii C L1ME4c_3end#L 62 ATTGGGGTCTTGATNTTT-TTCTTATCAATTTGAATGAGCTCT 21 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 42.64 CpG sites = 25, Kimura (unadjusted) = 43.94 Transitions / transversions = 1.25 (25/20) Gap_init rate = 0.01 (2 / 141), avg. gap size = 1.00 (2 / 2) 333 21.78 2.88 2.88 chrXqtel1M 885139 885242 (114758) C L1MA4_3end#LINE/L1 (887) 160 57 m_b375s551i23 15682 chrXqtel1M 885139 TAATCAATAGTGATTTAGAGCATTTTTTCACATGACTAGAAATGGC--TT 885186 i v v v v i iv iv--- -- C L1MA4_3end#LI 160 TGATGATTAGTGATGTTGAGCATTTTTTCATATACCTGT---TGGCCATT 114 chrXqtel1M 885187 TA-ATTTCTTCATCTGAAAATTGTCTGTTTACATCTTTTGACCATTTGTC 885235 i- v v i i v i i v v v ? C L1MA4_3end#LI 113 TGTATGTCTTCTTTTGAGAAATGTCTATTCAGATCTTTTGCCCATTTTTN 64 chrXqtel1M 885236 AATTGGA 885242 i C L1MA4_3end#LI 63 AATCGGA 57 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 24.84 CpG sites = 10, Kimura (unadjusted) = 26.14 Transitions / transversions = 0.83 (10/12) Gap_init rate = 0.05 (5 / 103), avg. gap size = 1.20 (6 / 5) 264 29.23 3.77 7.45 chrXqtel1M 885149 885307 (114693) C L1M1_orf2#LINE/L1 (0) 3294 3142 m_b375s551i25 15682 chrXqtel1M 885149 TGATTTAGAGCATTTTTTCACATGACTAGAAATGGC--TTTA-ATTTCTT 885195 v v ii i v iv--- v -- i- v C L1M1_orf2#LIN 3294 TGATGTTGAGCACCTTTTCATATGCCTGT---TTGCCATTTGTATGTCTT 3248 chrXqtel1M 885196 CATCTGAAAATTGTCTGTTTACATCTTTTGACCATTTGTCAATTGGAGAA 885245 v i i v i i v v v i i vv C L1M1_orf2#LIN 3247 CTTTTGAGAAATGTCTATTCAGATCTTTTGCCCATTTTTTAATCGGATTA 3198 chrXqtel1M 885246 T--GACTTGTACTCTTATAAATCTGAGTTAATTCTGTCTCTCTGTATTCT 885293 -- i v -- i ----- iv vv - ii i vi C L1M1_orf2#LIN 3197 TTAGATTTTT--TCCTATA-----GAGTTGTTTGAG-CTCCTTATATATT 3156 chrXqtel1M 885294 CTCTCCCTCTCTCC 885307 vviiv ivv C L1M1_orf2#LIN 3155 CTGGTTATTAATCC 3142 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.06 CpG sites = 41, Kimura (unadjusted) = 37.65 Transitions / transversions = 0.91 (21/23) Gap_init rate = 0.09 (14 / 158), avg. gap size = 1.14 (16 / 14) 63 4.69 0.00 0.00 chrXqtel1M 885308 885374 (114626) (AT)n#Simple_repeat 1 67 (0) c_b375s251i5 15683 chrXqtel1M 885308 ATATATATATATATATATATATATATATATATATATATATATATATATAC 885357 i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50 chrXqtel1M 885358 ACACATATATATATATA 885374 i i (AT)n#Simple_ 51 ATATATATATATATATA 67 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.0 (0 / 0) 238 28.78 5.17 8.12 chrXqtel1M 885375 885543 (114457) C L1M2_orf2#LINE/L1 (152) 3139 2972 m_b375s551i24 15682 chrXqtel1M 885375 GTCTTTATCAGAAACATTGACTGTAAA-ATTGTTTCTCAGCTTTCTGC-- 885421 -- i i vi? v vi i - v i i --- i-- C L1M2_orf2#LIN 3139 --CCTTGTCAGATGNATAGTTTGCAAATATTTTCTCCCA---TTCTGTAG 3095 chrXqtel1M 885422 -TTCTCTTTTAATCTTGGCTGTATTGGTTTTGTT--TGTGTAAAACCTTT 885468 - v i v - iv i - v iiv -- i i v C L1M2_orf2#LIN 3094 GTTGTCTCTTCA-CTCTGTTG-ATTGTTTCCTTTGCTGTGCAGAAGCTTT 3047 chrXqtel1M 885469 TTAATTTAATATAATCAAAATGATCCATTTTGTGTTTTATGATGTTCTCT 885518 i i i vv v vi i - i ---- vi C L1M2_orf2#LIN 3046 TTAGTTTGATGTAATCCCATTTGTCTATTTT-TGCTTT----TGTTGCCT 3002 chrXqtel1M 885519 -TGTTCTT----TTTTGGCCATAAATTCTT 885543 - i i ---- i i? v v C L1M2_orf2#LIN 3001 GTGCTTTTGAGGTCTTANCCAAAAAATCTT 2972 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.03 CpG sites = 50, Kimura (unadjusted) = 37.58 Transitions / transversions = 1.53 (26/17) Gap_init rate = 0.10 (17 / 168), avg. gap size = 1.35 (23 / 17) 264 29.23 3.77 7.45 chrXqtel1M 885375 885506 (114494) C L1M1_orf2#LINE/L1 (153) 3141 3014 m_b375s551i25 15682 chrXqtel1M 885375 GTCTTTATCAGAAACATTGACTGTAAA-ATTGTTTCTCAGCTTTCTGC-- 885421 ---- i vivi v vi i - v i i --- i-- C L1M1_orf2#LIN 3141 ----TTGTCAGATGGGTAGTTTGCAAATATTTTCTCCCA---TTCTGTGG 3099 chrXqtel1M 885422 -TTCTCTTTTAATCTTGGCTGTATTGGTTTTGTT--TGTGTAAAACCTTT 885468 - v i v - v i - v iiv -- i i v C L1M1_orf2#LIN 3098 GTTGTCTCTTCA-CTTTGTTG-ATTGTTTCCTTTGCTGTGCAGAAGCTTT 3051 chrXqtel1M 885469 TTAATTTAATATAATCAAAATGATCCATTTTGTGTTTT 885506 i i i i vv v vi - i C L1M1_orf2#LIN 3050 TTAACTTGATGTGATCCCATTTGTCCATTTT-TGCTTT 3014 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 37.06 CpG sites = 41, Kimura (unadjusted) = 37.65 Transitions / transversions = 1.33 (20/15) Gap_init rate = 0.10 (13 / 131), avg. gap size = 1.23 (16 / 13) 264 26.61 4.04 5.10 chrXqtel1M 886146 886244 (113756) C L3#LINE/CR1 (228) 3871 3774 m_b375s601i12 15684 chrXqtel1M 886146 TCTCTG-AATTTCTACACCTCCATTGTCCCCTGGTCTTTCCCTTTGAAAG 886194 i - i i ---- vi - i ii v i i iv C L3#LINE/CR1 3871 TCCCTGTAACTTCCAC----CCATTGGTCC-TAGTTCTGCCCTCTGGAGC 3827 chrXqtel1M 886195 C---CAGGACAACTTTAAACCCTCATCCACACAACAGTGCTTCCAATACT 886241 --- i i v i v v ii iv v i C L3#LINE/CR1 3826 CACACAGAATAAGTCTAATCCCTCTTCCACATGACAGCCCTTCAAATATT 3777 chrXqtel1M 886242 TGA 886244 C L3#LINE/CR1 3776 TGA 3774 Matrix = 25p41g.matrix Kimura (with divCpGMod) = 34.27 CpG sites = 17, Kimura (unadjusted) = 34.27 Transitions / transversions = 2.12 (17/8) Gap_init rate = 0.07 (7 / 98), avg. gap size = 1.29 (9 / 7) 281 33.25 11.90 2.73 chrXqtel1M 886262 886530 (113470) C Plat_L3#LINE/CR1 (350) 3223 2931 m_b375s551i26 15685 chrXqtel1M 886262 AATCTCCTCTTCTCTAAATTCAAGGTGCCTAATCCCTTCA---TTTGCTC 886308 ii i i iii v vivv i i i --- v C Plat_L3#LINE/ 3223 AGCCTTCTCTTCTCCAGGCTAAACAACCCCAATTCCTTTAACCTTTCCTC 3174 chrXqtel1M 886309 TTATATGATACAGATTCAAAGCCTGTAGCCATTCTTGGTTGCCCTTTTAT 886358 -- v ivi vv v vv v ii i - i i i v C Plat_L3#LINE/ 3173 --ATAGGACCTATTTTCCATCCCTTTAATCATTTTT-GTCGCTCTTCTCT 3127 chrXqtel1M 886359 GAACACTTTCTGGCTCATCAATGTCCCCCTTAAAACATGATGCATAGAAC 886408 i v i ii i iv v ii iii iiii i vvi i C Plat_L3#LINE/ 3126 GGACCCTCTCCAGTTTCTCCACATCCTTTTTAAAGTGCGGTGACCAAAAC 3077 chrXqtel1M 886409 TGAACATAGAAGT-TGAGATGTGATCTGCCCAA-------------GGAA 886444 i i v v - i v v - i v i------------- C Plat_L3#LINE/ 3076 TGGACACAGTACTCTAATAAG-GGTCTGACCAGTGCAGAGTATAGCGGAA 3028 chrXqtel1M 886445 GAGATTA----TCAATCTGTTGTCTCTC---CTC------ATATACCCCA 886481 - ----i i - v iv v --- ------ i i C Plat_L3#LINE/ 3027 G-GATTACTTCCCGA-CTCTTGCATGTCATACTCCTGTTAATACATCCCA 2980 chrXqtel1M 886482 AGATGGCATTGGCTCTTTTGGT--TGGCATGGCACATTGCTGACTCATAC 886529 iv ivi i i ii --i i--i i C Plat_L3#LINE/ 2979 GTACCACGTTGGCTTTTTTAATAACGGCAC--TACATTGCTGACTCATAT 2932 chrXqtel1M 886530 T 886530 C Plat_L3#LINE/ 2931 T 2931 Matrix = 20p41g.matrix Kimura (with divCpGMod) = 43.09 CpG sites = 58, Kimura (unadjusted) = 46.83 Transitions / transversions = 2.00 (58/29) Gap_init rate = 0.06 (15 / 268), avg. gap size = 2.67 (40 / 15) 524 19.48 1.48 8.73 chrXqtel1M 889498 889632 (110368) MIRc#SINE/MIR 2 127 (141) m_b376s601i0 15686 chrXqtel1M 889498 GGGGCAGCTAGGTAGCACAGTGGTTAGAGCACCAGCCCTGAAGTCAGGAA 889547 i i--- i ii vv ii v i i MIRc#SINE/MIR 2 GAGGCAGT---GTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAA 48 chrXqtel1M 889548 GACCTGAGTTCAAATCTGGTCTCAGACACTTAGCACTTCCTAGCTGTGTG 889597 i i i iv v v v ------- MIRc#SINE/MIR 49 GACCTGGGTTCGAGTCCCGGCTCTGCCACTTA-------CTAGCTGTGTG 91 chrXqtel1M 889598 ACCCTGGGCGAGTCACTTAACCCCAACT--GCCTCAG 889632 i i i -v -- MIRc#SINE/MIR 92 ACCTTGGGCAAGTCACTTAACCTC-TCTGAGCCTCAG 127 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 21.87 CpG sites = 16, Kimura (unadjusted) = 22.93 Transitions / transversions = 2.00 (16/8) Gap_init rate = 0.09 (12 / 134), avg. gap size = 1.08 (13 / 12) 16 13.25 0.00 0.00 chrXqtel1M 889635 889659 (110341) (TA)n#Simple_repeat 1 25 (0) m_b376s252i0 15687 chrXqtel1M 889635 TATATATATATATTTATTTATTTAT 889659 v v v (TA)n#Simple_ 1 TATATATATATATATATATATATAT 25 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 15 8.53 0.00 0.00 chrXqtel1M 889637 889661 (110339) (TATT)n#Simple_repeat 1 25 (0) m_b376s252i1 15687 chrXqtel1M 889637 TATATATATATTTATTTATTTATTT 889661 v v (TATT)n#Simpl 1 TATTTATTTATTTATTTATTTATTT 25 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 624 20.93 5.43 0.00 chrXqtel1M 889828 889956 (110044) C MIRc#SINE/MIR (122) 146 11 m_b376s601i1 15688 chrXqtel1M 889828 CATTTTAGTGACAAGGAAATTGAGGCAAACAGAA-TGAAATGACTTGTCC 889876 vv ii i vv v i- v i i C MIRc#SINE/MIR 146 CATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCC 97 chrXqtel1M 889877 AGGGTCACACAACTAGTAAGTATCTGAGACTGGTTTTGAATCCAGATCTT 889926 i i iv v v v vi i i i C MIRc#SINE/MIR 96 AAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTT 47 chrXqtel1M 889927 CCTGACTCCAGCTCC------TTTTCCACTGCACCA 889956 iv ------i C MIRc#SINE/MIR 46 CCTGACTCCAAGTCCAGTGCTCTTTCCACTGCACCA 11 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 23.82 CpG sites = 15, Kimura (unadjusted) = 24.84 Transitions / transversions = 1.25 (15/12) Gap_init rate = 0.02 (2 / 128), avg. gap size = 3.50 (7 / 2) 42 0.00 0.00 0.00 chrXqtel1M 892194 892229 (107771) (TG)n#Simple_repeat 1 36 (0) c_b376s251i0 15689 chrXqtel1M 892194 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 892229 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 36 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 12 10.27 0.00 11.43 chrXqtel1M 894313 894351 (105649) (AAAAAT)n#Simple_repeat 1 35 (0) m_b376s252i2 15690 chrXqtel1M 894313 AAAAATAAAAAGCTTTAATGAAAAAAATAAAAATAAAAA 894351 ---- vi v (AAAAAT)n#Sim 1 AAAAATAAAAA----TAAAAATAAAAATAAAAATAAAAA 35 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.11 (4 / 38), avg. gap size = 1.00 (4 / 4) 394 24.72 0.00 2.35 chrXqtel1M 894472 894558 (105442) Charlie1b#DNA/hAT-Charlie 1 85 (438) m_b376s502i0 15691 chrXqtel1M 894472 CAGTGGTTCTCAAAGTATGGTCTAGAGAATCCTGGGGGATTTCTGAAACC 894521 i i ii i vi - ii i i Charlie1b#DNA 1 CAGCGGTTCTCAAAGTGTGGTCCGGGGACCCCTGGGGG-TCCCCGAGACC 49 chrXqtel1M 894522 CTTTTAAAGGGTCTACAAATTCAAAAATAGTTTTTAT 894558 i ii ii i iv v - i Charlie1b#DNA 50 CTTTCAGGGGGTCCGCGAGGTCAAAACTA-TTTTCAT 85 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 23.23 CpG sites = 18, Kimura (unadjusted) = 32.53 Transitions / transversions = 6.00 (18/3) Gap_init rate = 0.02 (2 / 86), avg. gap size = 1.00 (2 / 2) 573 14.49 5.97 2.16 chrXqtel1M 894541 894674 (105326) Charlie1a#DNA/hAT-Charlie 1317 1455 (0) m_b376s502i1 15692 chrXqtel1M 894541 TTCAAAAAT-----AGTTTTTATTTCCAATATGGTAAATGTCTATAAATA 894585 i ----- v i i v i Charlie1a#DNA 1317 TTTAAAAATTTCTCAGTTTTAATTTCTAATATGGTAAATATCGATAGATA 1366 chrXqtel1M 894586 TAATCCAGATAAACAAAAACTCTTTGGAGAGATTCTCAATAATTTTTAAT 894635 i v i --- i i v Charlie1a#DNA 1367 TAACCCACATAAACAAAAGCTCTTTGG---GGTCCTCAATAATTTTTAAG 1413 chrXqtel1M 894636 AGGATAAA--GATACTGAAAAC-AAAAGTTTGAGAACCACTG 894674 vi -- i v i v - i Charlie1a#DNA 1414 AGTGTAAAGGGGTCCTGAGACCAAAAAGTTTGAGAACCGCTG 1455 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 15.43 CpG sites = 12, Kimura (unadjusted) = 16.33 Transitions / transversions = 1.71 (12/7) Gap_init rate = 0.05 (6 / 133), avg. gap size = 1.83 (11 / 6) 250 34.96 0.00 0.00 chrXqtel1M 895429 895551 (104449) C L1MC5_3end#LINE/L1 (2119) 575 453 m_b376s551i0 15693 chrXqtel1M 895429 TCCTGATTGTTTCTTACAGAACAATGATATTCCATAACATTCATATCCCA 895478 v vi i vvvv ii i viii vv i v C L1MC5_3end#LI 575 TCCTCATTCCTTTTTACAGCTGCATAGTACTCCATTGTGTGGATGTACCA 526 chrXqtel1M 895479 TAACTTATCCAGCCGTTCTCCAACTGATAGGCATTCTCTCTGTTTCCAGT 895528 ii i i iv i v i i i ivvvi C L1MC5_3end#LI 525 TAGTTTATTCAACCAGTCCCCTATTGATGGACATTTGGGTTGTTTCCAGT 476 chrXqtel1M 895529 TTCTTGCCACTATGAAAAGGGCT 895551 i i i i ii v v C L1MC5_3end#LI 475 CTTTTGCTATTACAAATAGTGCT 453 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 49.25 CpG sites = 26, Kimura (unadjusted) = 49.25 Transitions / transversions = 1.53 (26/17) Gap_init rate = 0.00 (0 / 122), avg. gap size = 0.0 (0 / 0) 277 31.00 0.00 0.00 chrXqtel1M 895452 895551 (104449) C L1ME3F_3end#LINE/L1 (438) 552 453 m_b376s551i1 15693 chrXqtel1M 895452 ATGATATTCCATAACATTCATATCCCATAACTTATCCAGCCGTTCTCCAA 895501 i viii vv v i i ii v i vi C L1ME3F_3end#L 552 ATAATATTCCATTGTGTGAATATACCACAATTTATTTATCCATTCTCCTG 503 chrXqtel1M 895502 CTGATAGGCATTCTCTCTGTTTCCAGTTTCTTGCCACTATGAAAAGGGCT 895551 ii i i ivvvi i i i i v v C L1ME3F_3end#L 502 TCGATGGACATTTGGGTTGTTTCCAGTTTTTTGCTATTACGAACAGTGCT 453 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 38.33 CpG sites = 20, Kimura (unadjusted) = 41.88 Transitions / transversions = 1.82 (20/11) Gap_init rate = 0.00 (0 / 99), avg. gap size = 0.0 (0 / 0) 17 19.80 0.00 2.38 chrXqtel1M 896341 896383 (103617) (CTTTT)n#Simple_repeat 1 42 (0) m_b376s252i3 15694 chrXqtel1M 896341 CTCTTCTTTTGTTTATTTTTCTTTTCATTCTCTCTCCTTTTCT 896383 i v vi - i i i (CTTTT)n#Simp 1 CTTTTCTTTTCTTTTCTTTTCTTTTC-TTTTCTTTTCTTTTCT 42 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.02 (1 / 42), avg. gap size = 1.00 (1 / 1) 1019 31.27 1.83 3.35 chrXqtel1M 897631 898176 (101824) C L1ME3Cz_3end#LINE/L1 (453) 544 7 m_b376s551i2 15695 chrXqtel1M 897631 TATTCTATTACATTCATATACCACAATTTATTCAGTCATTCCCCACCTGA 897680 i ii vv i vi vvi C L1ME3Cz_3end# 544 TATTCCATTGTATGAATATACCACAATTTATTTATCCATTCCCCTATTGA 495 chrXqtel1M 897681 TGGCCCTCTACTCAATTTCCAATTCTTTGCCACTACAAAAAAGAGATTTT 897730 v v i vvivi i i i i v ----- vi C L1ME3Cz_3end# 494 TGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAA-----TGC 450 chrXqtel1M 897731 TACAA---ATAGTTTTGCACATGTGGATCCTTCCCCTCCTTT---AGGAT 897774 i --- i vii i v-- viv v v v --- ii C L1ME3Cz_3end# 449 TGCAATGAACATCCTTGTACATGTC--TCCTTGTGCACATGTGCGAGAGT 402 chrXqtel1M 897775 TTCCTTGGGACACAGGCCAAGAAATGTCACTGCTGGGTCAAAGGGCATGC 897824 ii i ii i vi v i vv i iv i C L1ME3Cz_3end# 401 TTCTCTAGGGTATATACCTAGAAGTGGAATTGCTGGGTCGTAGGGTATGC 352 chrXqtel1M 897825 AGAGTTTGATGGGCCTTAGGGCATAGTTCCAGATGGCTCTCTAGAATGGT 897874 iv vi v ---i i vviv v v i v i i i C L1ME3Cz_3end# 351 GCATCTTCA---ACTTTACTAGATATTGCCAAATTGCTCTCCAAAGTGGT 305 chrXqtel1M 897875 TGGATCATTTCACAACTCCACCAACAAAGCATCAGTAATCCAGTTTTCCC 897924 v i v i vii i iv i v viv v ii C L1ME3Cz_3end# 304 TGTACCAATTTACACTCCCACCAGCAGTGTATGAGAGTTCCCGTTTCTCC 255 chrXqtel1M 897925 ACATCCCCTCCAACATTCAGCATTATC----TTTTCCTGTCATTTTAGCC 897970 i v i ii i i ---- vv---- v C L1ME3Cz_3end# 254 ACATCCTCGCCAACACTTGGTATTGTCAGACTTTTAA----ATTTTTGCC 209 chrXqtel1M 897971 AATCTGACAGGTGTGAGTTGCTTCCTCAGAGTTATTTTAATTCACATTTC 898020 ii iv v vi vv ?i ii C L1ME3Cz_3end# 208 AATCTGATGGGTGTGAAATGGTATCTCATTGTNGTTTTAATTTGCATTTC 159 chrXqtel1M 898021 TCTAATCAATAGCGATTTAAAGCATTTGATCACATGACTATAGATGGCTT 898070 i i i v i vv vi i vv i vi v iivii i C L1ME3Cz_3end# 158 CCTGATTACTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTC 109 chrXqtel1M 898071 TAATTTCATCATCTGAAAATTGTCTGTTCATATCCTTGGACTTTTTATCC 898120 vii v v vi i v v iv v i C L1ME3Cz_3end# 108 GGGTTTCCTCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCT 59 chrXqtel1M 898121 ATTGGGCAATGACGTGTATTCTTGTAAATTTGACACAGTTCTTTATGTAT 898170 i-- v v v-- i vi vviv i C L1ME3Cz_3end# 58 ATTGGGT--TGTCTTT--TTCTTATTGATTTGTAGGAGTTCTTTATATAT 13 chrXqtel1M 898171 TTTTGA 898176 i v C L1ME3Cz_3end# 12 TCTGGA 7 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 40.14 CpG sites = 90, Kimura (unadjusted) = 41.44 Transitions / transversions = 1.20 (90/75) Gap_init rate = 0.04 (21 / 545), avg. gap size = 1.33 (28 / 21) 279 27.28 5.60 5.60 chrXqtel1M 898041 898308 (101692) C L1P4_orf2#LINE/L1 (8) 3286 3019 m_b376s551i3 15695 chrXqtel1M 898041 AGCATTTGATCACATGACTATAGATGGCTTTAATTTCATCATCTGAAAAT 898090 vv i vi i v iiv vv v v v i i v C L1P4_orf2#LIN 3286 AGCATTTTTTCATATGTTTGTTGGCCGCTTGTATGTCTTCTTTTGAGAAG 3237 chrXqtel1M 898091 TGTCTGTTCATATCCTTGG---ACTTTTTATCCATTGGGCAATGACGTGT 898137 i v --- --- v --- v iv C L1P4_orf2#LIN 3236 TGTCTGTTCATGTCCTTTGCCCACTTTTTA---ATGGGG---TTATTTGT 3193 chrXqtel1M 898138 ATT---CTTGTAAATTTGACACAGTTCTTTATGTATTTTTGAAATGAGAT 898184 v --- vi ? vivv i iv i v v v i C L1P4_orf2#LIN 3192 TTTTTGCTTGTTGANTTGTTTAAGTTCCTTATAGATTCTGGATATTAGAC 3143 chrXqtel1M 898185 CTTTATCAGAAATCTTAGCTT-CAAAGATTTTTTCCCAGCTTTGTA-CTT 898232 i i vi- v i - i v i -i i -v C L1P4_orf2#LIN 3142 CTTTGTCGGATG-CATAGTTTGCGAATATTTTCTCCCA-TTCTGTAGGTT 3095 chrXqtel1M 898233 CCCT-TTTAATGTTGTTTCTGTTG--GGTTTGTT----TGTGCAAAAACT 898275 vi - -------i --i v ---- i i C L1P4_orf2#LIN 3094 GTCTGTTTA-------CTCTGTTGATAGTTTCTTTTGCTGTGCAGAAGCT 3052 chrXqtel1M 898276 TTTTAATTGAATGTAATCAGAGTTGTCCATTTT 898308 i i v vvii vv v v C L1P4_orf2#LIN 3051 CTTTAGTTTAATTAGGTCCCACTTGTCAATTTT 3019 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 33.12 CpG sites = 32, Kimura (unadjusted) = 34.30 Transitions / transversions = 0.86 (32/37) Gap_init rate = 0.08 (22 / 267), avg. gap size = 1.36 (30 / 22) 329 25.00 5.08 5.08 chrXqtel1M 898073 898308 (101692) C L1PREC2_orf2#LINE/L1 (40) 3254 3019 m_b376s551i4 15695 chrXqtel1M 898073 ATTTCATCATCTGAAAATTGTCTGTTCATATCCTTGG---ACTTTTTATC 898119 v v v i v i v --- -- C L1PREC2_orf2# 3254 ATGTCTTCTTTTGAAAAGTGTCTGTTCATGTCCTTTGCCCACTTTTTA-- 3207 chrXqtel1M 898120 CATTGGGCAATGACGTGTATTCTTGTAAATTTGACACAGTTCTTTATGTA 898169 - v ivi vvvv v v vivv i iv C L1PREC2_orf2# 3206 -ATGGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTAAGTTCCTTATAGA 3158 chrXqtel1M 898170 TTTTTGAAATGAGATCTTTATCAGAAATCTTAGCTT-CAAAGATTTTTTC 898218 vi v v v i i vi- v i - ? i C L1PREC2_orf2# 3157 TGCTGGATATTAGACCTTTGTCAGATG-CATAGTTTGCAAANATTTTCTC 3109 chrXqtel1M 898219 CCAGCTTTGTA-CTTCCCT-TTTAATGTTGTTTCTGTTG--GGTTTGTT- 898263 -i i -v vi - -------i --i v - C L1PREC2_orf2# 3108 CCA-TTCTGTAGGTTGTCTGTTTA-------CTCTGTTGATAGTTTCTTT 3067 chrXqtel1M 898264 ---TGTGCAAAAACTTTTTAATTGAATGTAATCAGAGTTGTCCATTTT 898308 --- i i i i v vvi vv v v C L1PREC2_orf2# 3066 TGCTGTGCAGAAGCTCTTTAGTTTAATTAGATCCCATTTGTCAATTTT 3019 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 30.64 CpG sites = 23, Kimura (unadjusted) = 30.64 Transitions / transversions = 0.70 (23/33) Gap_init rate = 0.08 (19 / 235), avg. gap size = 1.26 (24 / 19) 384 27.80 15.05 3.95 chrXqtel1M 898778 898983 (101017) MamSINE1#SINE/tRNA-RTE 61 288 (2) m_b376s601i2 15696 chrXqtel1M 898778 TTCAATTTTTCCATAAGCCAGTCAACT-------GT--CATTGGCCATAA 898818 i iiiivii ii i i ------- -- - i i MamSINE1#SINE 61 TTCGATCCCCGTGTGGGCCAGTTAGCTTTGCTCTGTTCCAT-GGCCACAG 109 chrXqtel1M 898819 ATTG--------ACCACAGCCAGCGGTCTTGCAAAATGCAGGATTTTGGT 898860 i -------- v v i - iv viv MamSINE1#SINE 110 ACTGCACCCCTAACCCCAGCCAGCCGTCTCGC-AAATGCGTGCCGTTGGT 158 chrXqtel1M 898861 CACAAGGAAGGCCCAGCATCAACAAATGTGTTGACTGCT----GCAGGTC 898906 -i v i -----i iv v iv ? ---- ii MamSINE1#SINE 159 CACAAGG-GGGACCGGCA-----GAGAGTGTGGATGGNTCAGCGCAAATC 202 chrXqtel1M 898907 TCTCACCACTATTACAAAA--GACGTCAAAGGGAACATATTATTGA---T 898951 iv ? i iv --i - viv ii vi i --- MamSINE1#SINE 203 CATCNCCACTACTGGAAAAACAAC-TCAAAGCACATGTCCTACTGATAGT 251 chrXqtel1M 898952 GTGTCAGTA---TTATCTAC--ATAGAAAGGAGAACA 898983 v --- i v -- vi v i MamSINE1#SINE 252 GGGTCAGTAGCGTCATCTTCGTATACGAAGGACAGCA 288 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 31.13 CpG sites = 36, Kimura (unadjusted) = 36.85 Transitions / transversions = 1.89 (36/19) Gap_init rate = 0.08 (17 / 205), avg. gap size = 2.35 (40 / 17) 54 0.00 0.00 0.00 chrXqtel1M 899446 899491 (100509) (TC)n#Simple_repeat 1 46 (0) c_b376s251i1 15697 chrXqtel1M 899446 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 899491 (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 46 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 29 3.23 0.00 0.00 chrXqtel1M 899907 899938 (100062) (GTCT)n#Simple_repeat 1 32 (0) c_b376s251i2 15698 chrXqtel1M 899907 GTCTGTCTATCTGTCTGTCTGTCTGTCTGTCT 899938 i (GTCT)n#Simpl 1 GTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCT 32 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 33 3.10 0.00 0.00 chrXqtel1M 900789 900821 (99179) (TG)n#Simple_repeat 1 33 (0) c_b376s251i3 15699 chrXqtel1M 900789 TGTGTGTGTGTGTGTGTGTGTGTTTGTGTGTGT 900821 v (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 33 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 423 30.71 4.05 5.88 chrXqtel1M 901009 901181 (98819) C MIR3#SINE/MIR (9) 199 30 m_b376s601i3 15700 chrXqtel1M 901009 AATCACAGATTTT--GAGATGAGAGGGACCCTGGAAGTGATCTGGTAGCA 901056 i v v -- v ii i i ii v i vvv C MIR3#SINE/MIR 199 AATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAA 150 chrXqtel1M 901057 CCTCCT-ATTTTTTTCAAAATAATAAATGAAGAAAC--AGGTCTAGAGAA 901103 i - ---------- i i i -- i i i C MIR3#SINE/MIR 149 CCCCCTCATTTT----------ACAGATGAGGAAACTGAGGCCCAGAGAG 110 chrXqtel1M 901104 AGTAAATGGTTGGCTCAAG-TGACTTGG-TAGTAGATGGCAGAGCCAGGA 901151 ivv i ii v i - v vii -? vii i C MIR3#SINE/MIR 109 GTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGA 60 chrXqtel1M 901152 TTGAAATGCACGTGTTCTGATTCCTCATCC 901181 i ii iv v v i i ivi C MIR3#SINE/MIR 59 CTAGAACCCAGGTCTCCTGACTCCCAGTCC 30 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 40.67 CpG sites = 33, Kimura (unadjusted) = 41.80 Transitions / transversions = 1.94 (33/17) Gap_init rate = 0.09 (15 / 172), avg. gap size = 1.13 (17 / 15) 13 18.74 0.00 8.70 chrXqtel1M 901457 901506 (98494) (ATTTTT)n#Simple_repeat 1 46 (0) m_b376s252i4 15701 chrXqtel1M 901457 ATATTTAAATTGATTTTTGGTTAATTTATTTTGTATTTTTCTGTTTATTT 901506 v vv v -i -- - v v (ATTTTT)n#Sim 1 ATTTTTATTTTTATTTTT-ATT--TTTATTTT-TATTTTTATTTTTATTT 46 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.08 (4 / 49), avg. gap size = 1.00 (4 / 4) 20 21.76 4.11 2.70 chrXqtel1M 901580 901652 (98348) (ATTACTA)n#Simple_repeat 1 74 (0) m_b376s252i5 15702 chrXqtel1M 901580 ATTAATAAATTAATAATTA-TTATTAATAA--ATTAATTATTATGTCATT 901626 v - v - v v -- i i -i i i (ATTACTA)n#Si 1 ATTACT-AATTACTAATTACTAATTACTAATTACTAATTACTA-ATTACT 48 chrXqtel1M 901627 AATTTCTAATAATTAATTACCAATTA 901652 v v i i (ATTACTA)n#Si 49 AATTACTAATTACTAATTACTAATTA 74 Matrix = Unknown Transitions / transversions = 1.17 (7/6) Gap_init rate = 0.06 (4 / 72), avg. gap size = 1.25 (5 / 4) 15 15.31 0.00 5.26 chrXqtel1M 901852 901891 (98109) (TTTATT)n#Simple_repeat 1 38 (0) m_b376s252i6 15703 chrXqtel1M 901852 TTAATTTTATGATTCTTTTTTTTCTTTTTATGTTTATTTT 901891 v - - i v v v (TTTATT)n#Sim 1 TTTATTTT-T-ATTTTTATTTTTATTTTTATTTTTATTTT 38 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 371 31.68 6.22 1.03 chrXqtel1M 902332 902701 (97299) C L1ME3_3end#LINE/L1 (502) 407 19 m_b376s551i5 15704 chrXqtel1M 902332 ATTTC-CTTGGACACAGGCC-AGAAATGTCACTGCTGGGTCAAGGCATCA 902379 - ii i vi - i i vv i vi vi vi C L1ME3_3end#LI 407 ATTTCTCTTGGGTATATACCTAGGAGTGGAATTGCTGGGTCATAGGGTAG 358 chrXqtel1M 902380 GAGTTTGATGGGCCTTAGGGCATAGTTCCAGATGGCTTTGTAGAATGGTT 902429 v v v vi i viv v v i ii i vi i i C L1ME3_3end#LI 357 GCGTATGTTTAGCTTTAGTAGATACTGCCAAACAGTTTTCCAAAGTGGTT 308 chrXqtel1M 902430 GGA-TATTTCACAACTCC--CCAACAAAGTATCAGTATCCCAGTT--TCC 902474 v -i v i - -- i v v vi i -- C L1ME3_3end#LI 307 GTACCAATTTAC-ACTCCCACCAGCAATGTATGAGAGTTCCAGTTGCTCC 259 chrXqtel1M 902475 ACATCC-CTCC-ACATTTACCATTATC---TTTTTCCGTCATTTAGCCAA 902519 - v - i ivi i ---i ivi -- v C L1ME3_3end#LI 258 ACATCCTCGCCAACACTTGGTATTGTCAGTCTTTTTAAT--TTTAGCCAT 211 chrXqtel1M 902520 TC---CACGTGTGAGGTGACACCTCA--GAGTTTTTAAATTCACATTTCT 902564 ---iiv vi ii i -- v v - ii i C L1ME3_3end#LI 210 TCTGGTGGGTGTGTAGTGGTATCTCATTGTGGTTTT-AATTTGCATTTCC 162 chrXqtel1M 902565 CTAATCAAT-ATGATTTTAGGCA--TTTTTACATGACTATAGATGCTTTT 902611 i v v - v ii -- i i vi v iivv v C L1ME3_3end#LI 161 CTGATGACTAATGATGTTGAGCACCTTTTCATATGCTTATTGGCCATTTG 112 chrXqtel1M 902612 AATTTCATC-ACTGAAAATTGTCTGTTTGA-TCCTTTGACTATTTATTCA 902659 i v v -vi vi v i ii - i v i v v C L1ME3_3end#LI 111 GATATCCTCTTTTGTGAAGTGCCTGTTCAAGTCTTTTGCCCATTTTTTAA 62 chrXqtel1M 902660 CTGGGCAATATATTGTATTCTT-TAAATTTGACACAGTTCTTT 902701 i ivi v i iv v - vi vviv C L1ME3_3end#LI 61 TTGGGTTGTTTGTCTTTTTCTTATTGATTTGTAGGAGTTCTTT 19 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 42.20 CpG sites = 64, Kimura (unadjusted) = 42.20 Transitions / transversions = 1.23 (64/52) Gap_init rate = 0.05 (19 / 369), avg. gap size = 1.42 (27 / 19) 253 22.49 5.11 5.88 chrXqtel1M 903882 904018 (95982) C L1ME3E_3end#LINE/L1 (418) 571 436 m_b376s551i6 15705 chrXqtel1M 903882 TCATCCGTTGTCATTTCTAGAACAGTAATATTCCATAATTTTCATATACC 903931 i i v i v iv ---- i vi v vv C L1ME3E_3end#L 571 TCATTCATTTTCACTGCTGTA----TAGTATTCCATTGTATGAATATACC 526 chrXqtel1M 903932 ACAATTTATTCAGCCATTCTC--AAC-ATGGACATCCATTCAG--GTTTC 903976 i v --iv - --- vi -- C L1ME3E_3end#L 525 ACAATTTATTTATCCATTCTCCTGTCGATGGACAT---TTGGGTTGTTTC 479 chrXqtel1M 903977 CAGTTTCTAAC-ACTACAAA-AGGGCTTGCCACAAACATTCATG 904018 i vi - i - iv - i ii v C L1ME3E_3end#L 478 CAGTTTTTTGCTATTACAAACAATGC-TGCTATGAACATTCTTG 436 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 27.08 CpG sites = 16, Kimura (unadjusted) = 27.08 Transitions / transversions = 1.23 (16/13) Gap_init rate = 0.10 (13 / 136), avg. gap size = 1.15 (15 / 13) 422 25.43 10.39 1.32 chrXqtel1M 903907 904185 (95815) C L1ME4c_3end#LINE/L1 (276) 554 251 m_b376s551i7 15705 chrXqtel1M 903907 TAATATTCCATAATTTTCATATACCACAATTTATTCAGCCATTCTC--AA 903954 vivv ?v i i i i i i -- v C L1ME4c_3end#L 554 TAATATTCCATCGAGTNGATGTACCATAATTTACTTAACCATTCCCCTAT 505 chrXqtel1M 903955 CA-TGGACATCCA--TTCAGGTTTCCAGTTTCTAAC-ACTACAAA-AGGG 903999 ii- ii -- --- i i vi - i i - iv C L1ME4c_3end#L 504 TGTTGGACATTTAGGTT---GTTTCCAATTTTTCGCTATTATAAATAACG 458 chrXqtel1M 904000 CTTGCCACAAACA--TTCATGCAAAGATC-CTTTCCTTCTTT---ATAAT 904043 - v ii -- i v v v -i --- v C L1ME4c_3end#L 457 C-TGCAATGAACATCTTCGTGCATATAGCTTTTTCCTTCTTTTGAATTAT 409 chrXqtel1M 904044 CTCTTTGGGATATAATCCCAGTAGT----CTG-TGGATCAAAGGGTAT-- 904086 i i i v v v ----i i- i -- C L1ME4c_3end#L 408 TTCCTTAGGATAAATTCCCAGAAGTGGAATTACTGGGTCAAAGGGTATGA 359 chrXqtel1M 904087 -CCGTTTGATAACTTTTGA-GCATATT-CCAA----CTTCTCAAAATGGT 904129 - vv v ii i -i i - ---- ii v C L1ME4c_3end#L 358 ACATTTTTATGGCTCTTGATACGTATTGCCAAATTGCTTTCCAAAAGGGT 309 chrXqtel1M 904130 TGGATTTGTT--CAACTCCACCAACAATGCATCAATGTCCCAATTTTCCC 904177 v iivi -- ?iv i i v i? v i iv C L1ME4c_3end#L 308 TGTACCAATTTACANTGCCACCAGCAATGTATGAGNGTACCAGTTTCACC 259 chrXqtel1M 904178 GTCCCCTC 904185 iv? C L1ME4c_3end#L 258 GCANCCTC 251 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 30.38 CpG sites = 44, Kimura (unadjusted) = 32.62 Transitions / transversions = 1.69 (44/26) Gap_init rate = 0.07 (20 / 278), avg. gap size = 1.65 (33 / 20) 18 23.72 0.00 0.00 chrXqtel1M 904666 904705 (95295) (T)n#Simple_repeat 1 40 (0) m_b376s252i7 15706 chrXqtel1M 904666 TTTTATTTGCCTTTTCTTTCTTTTCTTTTTTTTTTTATTT 904705 v vii i i i v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 40 Matrix = Unknown Transitions / transversions = 1.67 (5/3) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 17 14.33 6.25 2.00 chrXqtel1M 904666 904713 (95287) (TTTTC)n#Simple_repeat 1 50 (0) m_b376s252i8 15707 chrXqtel1M 904666 TTTTATTTGCCTTTTC-TTTCTTTTCTTTT-TTTT-TTTATTTGCCTTTT 904712 v -i - - - vi vi (TTTTC)n#Simp 1 TTTTCTTT-TCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTT 49 chrXqtel1M 904713 C 904713 (TTTTC)n#Simp 50 C 50 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.09 (4 / 47), avg. gap size = 1.00 (4 / 4) 54 0.00 1.92 0.00 chrXqtel1M 904848 904899 (95101) (TTCC)n#Simple_repeat 1 53 (0) c_b376s251i4 15708 chrXqtel1M 904848 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC-TCCTTCCTTCCTT 904896 - (TTCC)n#Simpl 1 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 50 chrXqtel1M 904897 CCT 904899 (TTCC)n#Simpl 51 CCT 53 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.02 (1 / 51), avg. gap size = 1.00 (1 / 1) 54 13.88 5.88 2.86 chrXqtel1M 904900 905035 (94965) (CCTCT)n#Simple_repeat 1 140 (0) m_b376s252i9 15709 chrXqtel1M 904900 CCTCCCCTC-CCTCTCCTCTCCTCAACCTCTCCTGAACCTCTCC-CTCCC 904947 i - -v -vv - i (CCTCT)n#Simp 1 CCTCTCCTCTCCTCTCCTCTCCTC-TCCTCTCCT-CTCCTCTCCTCTCCT 48 chrXqtel1M 904948 CTCC-CTTCCCTCCCCTCCTC-ACTCTCCTTCCCTTTTCTC-CCTCTCCC 904994 - i i i -v ii i i - - (CCTCT)n#Simp 49 CTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCT-CC 97 chrXqtel1M 904995 TTTCCCCTCCTCTTCTCCTCCTCT-CTC-CCTCT-CTCTCCTCT 905035 i i i - - - - (CCTCT)n#Simp 98 TCTCCTCTCCTCTCCT-CTCCTCTCCTCTCCTCTCCTCTCCTCT 140 Matrix = Unknown Transitions / transversions = 3.00 (12/4) Gap_init rate = 0.09 (12 / 135), avg. gap size = 1.00 (12 / 12) 19 26.15 3.19 4.30 chrXqtel1M 905004 905097 (94903) (CTCTGT)n#Simple_repeat 1 93 (0) m_b376s252i10 15710 chrXqtel1M 905004 CTCT-TCTCCTCCTCTCTCCCTCTCTCT-CCTCTTGATACAATTTCTTTC 905051 - ivi v i v -i - viv vi i v (CTCTGT)n#Sim 1 CTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTC-TGTCTCTGTCTCTGTC 49 chrXqtel1M 905052 TCTG-ATCCATCTGCTTTCTCTGTACTCTGTCTCTTGTCTCTGTTTC 905097 -v ii - v - - i (CTCTGT)n#Sim 50 TCTGTCTCTGTCT-CTGTCTCTGT-CTCTGTCTC-TGTCTCTGTCTC 93 Matrix = Unknown Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.08 (7 / 93), avg. gap size = 1.00 (7 / 7) 54 0.00 0.00 0.00 chrXqtel1M 905301 905346 (94654) (TC)n#Simple_repeat 1 46 (0) c_b376s251i5 15711 chrXqtel1M 905301 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 905346 (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 46 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 35 2.76 0.00 0.00 chrXqtel1M 905796 905832 (94168) (TCTGTC)n#Simple_repeat 1 37 (0) c_b376s251i6 15712 chrXqtel1M 905796 TCTGTCTCTCTCTCTGTCTCTGTCTCTGTCTCTGTCT 905832 v (TCTGTC)n#Sim 1 TCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCT 37 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 18 14.38 3.12 0.00 chrXqtel1M 906469 906500 (93500) (AG)n#Simple_repeat 1 33 (0) m_b376s252i11 15713 chrXqtel1M 906469 AGAGGAAAAGAGAGAAAGAGAGAGA-AGAGAGA 906500 ii i i - (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 33 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 16 9.55 0.00 0.00 chrXqtel1M 906649 906671 (93329) (T)n#Simple_repeat 1 23 (0) m_b376s252i12 15714 chrXqtel1M 906649 TTTTTTTCTTTCTTTTTTTTTTT 906671 i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTT 23 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 17 24.44 0.00 7.46 chrXqtel1M 907231 907302 (92698) (TATTT)n#Simple_repeat 1 67 (0) m_b376s252i13 15715 chrXqtel1M 907231 TAATTAATTTCATGATTAATTTTAATTAAATTTGTTGAATGATTTATTTT 907280 v v i -- v v v v i vv -- (TATTT)n#Simp 1 TATTTTATTTTAT--TTTATTTTATTTTATTTTATTTTAT--TTTATTTT 46 chrXqtel1M 907281 ATTTTCTCTTTTTTTTCTTTTA 907302 v - v v (TATTT)n#Simp 47 ATTTTAT-TTTATTTTATTTTA 67 Matrix = Unknown Transitions / transversions = 0.18 (2/11) Gap_init rate = 0.07 (5 / 71), avg. gap size = 1.00 (5 / 5) 15 19.85 0.00 0.00 chrXqtel1M 907273 907301 (92699) (T)n#Simple_repeat 1 29 (0) m_b376s252i14 15716 chrXqtel1M 907273 TTTATTTTATTTTCTCTTTTTTTTCTTTT 907301 v v i i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 81 18.74 6.43 3.47 chrXqtel1M 907849 908128 (91872) (TCTCTCT)n#Simple_repeat 1 288 (0) m_b376s252i15 15717 chrXqtel1M 907849 TCTCT-TTCTCTCTTCTCT-GTCTCTCCCCTCTCCCCAC-CTTCTC-CTC 907894 - -v ii ii v - - i (TCTCTCT)n#Si 1 TCTCTCTTCTCTCTTCTCTCTTCTCTCTTCTCTCTTCTCTCTTCTCTCTT 50 chrXqtel1M 907895 CT-TCTCCTC-CTTCCCTC-TCTCACTTTCTCTCTGTCTCTCTTCTTTCC 907941 - i - i - v - - i i (TCTCTCT)n#Si 51 CTCTCTTCTCTCTTCTCTCTTCTCTC-TTCTCTCT-TCTCTCTTCTCTCT 98 chrXqtel1M 907942 TCTTTCTTTTACT-TTCTCTCTTGATC-CATTTTTCTGTCCCTGTTCTCT 907989 i i - - -v - v i i - i v (TCTCTCT)n#Si 99 TCTCTCTTCT-CTCTTCTCTCTT-CTCTCTTCTCTCT-TCTCTCTTCTCT 145 chrXqtel1M 907990 CTACTGTCTGTCTGTC-TCT-TCTTCTCCTCTT-TCTCTTTTTTACTATC 908036 v v - v - - - - i i vi v (TCTCTCT)n#Si 146 CTTCTCTCT-TCTCTCTTCTCTCTTCT-CTCTTCTCTCTTCTCTCTTCTC 193 chrXqtel1M 908037 TTTTCTCTCTTGTCTCTTTTGTTGTCT-TCTCTCTTTCTTTTCT-TGATG 908084 i v i v iv - - i i - vv v (TCTCTCT)n#Si 194 TCTTCTCTCTTCTCTCTTCTCTCTTCTCTCT-TCTCTCTTCTCTCTTCTC 242 chrXqtel1M 908085 TTTTCTGCTGTTC-CT-TTCTCTCTT-TCTCCTTCT-TCTTTCCTCTT 908128 i - v - - - - - ii (TCTCTCT)n#Si 243 TCTTCT-CTCTTCTCTCTTCTCTCTTCTCT-CTTCTCTCTTCTCTCTT 288 Matrix = Unknown Transitions / transversions = 1.39 (25/18) Gap_init rate = 0.10 (28 / 279), avg. gap size = 1.00 (28 / 28) 68 28.83 5.98 0.63 chrXqtel1M 907849 908149 (91851) (TC)n#Simple_repeat 1 317 (0) m_b376s252i16 15718 chrXqtel1M 907849 TCTCTTTCTCTCT-TCTCTGTCTCTC-CCCTCTC-CCCACCTTCTC-CTC 907894 i - v - i - i v ii - (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chrXqtel1M 907895 CTTCTC-CTCCTTCCCTCTCTCACTTTCTCTCTGTCTCTCT-TCTTTC-C 907941 ii - ii i v i v - i - (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chrXqtel1M 907942 TCTTTCTTTTACTTTCTCTCTTGATCCATTTTTCTGTCCCTGT-TCTCTC 907990 i i iv i ivv iv i i v i v - (TC)n#Simple_ 101 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 150 chrXqtel1M 907991 TACTGTCTGTCTGTCTCT-TCT-TCTC-CTCTTTCTCTTTTTTACTATCT 908037 - v v v - - - i i i iv v (TC)n#Simple_ 151 T-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 199 chrXqtel1M 908038 -TTTCTCTCT-TGTCTCTTTTGTTGTCT-TCTCTCTTTCT-TTTCTTGAT 908083 - i - v i ivi v - i - i ivv (TC)n#Simple_ 200 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 249 chrXqtel1M 908084 GT-TTTCTGCTGTTCCTTTCTCTCTTTCTCCTTCT-TCTTTC-CTCTTAG 908130 v - i - v ii i i ii - i - ivv (TC)n#Simple_ 250 CTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 298 chrXqtel1M 908131 GCTCTCTGGCTGTCCCTCT 908149 v vv v i (TC)n#Simple_ 299 TCTCTCTCTCTCTCTCTCT 317 Matrix = Unknown Transitions / transversions = 1.50 (42/28) Gap_init rate = 0.07 (20 / 300), avg. gap size = 1.00 (20 / 20) 21 7.71 0.00 0.00 chrXqtel1M 909022 909049 (90951) (T)n#Simple_repeat 1 28 (0) m_b376s252i17 15719 chrXqtel1M 909022 TTTTTTCTTTTTCTTTTTTTTTTTTTTT 909049 i i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 28 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 1151 26.43 4.43 1.02 chrXqtel1M 909718 910191 (89809) C L1ME3G_3end#LINE/L1 (380) 544 55 m_b376s551i8 15720 chrXqtel1M 909718 TATTCCATAATATTCTTATACCACAATTTACTCAGCCATTCTCCAACTGA 909767 i vvv i i i i i v i C L1ME3G_3end#L 544 TATTCCATAGTATGGATATACCATAATTTATTTAACCATTCCCCTATTGA 495 chrXqtel1M 909768 TGGACATCCATTCAGTTTCCAGTTTTTAACCACTACAAA-AGGGCTGTCA 909816 ii vviv i vi i i - iv iv C L1ME3G_3end#L 494 TGGACATTTAGGTTGTTTCCAATTTTTCGCTATTACAAACAATGCTGCAA 445 chrXqtel1M 909817 CAAACATTCGTGCACATACAGGTCCTTTCCCTTCTTTATAA---TCTCT- 909862 ii i v i i ?-- viv viv v iii --- i - C L1ME3G_3end#L 444 TGAACATCCTTGTACATGCN--TCCTTGTGCACATGTGCGAGTATTTCTN 397 chrXqtel1M 909863 TGGGATATAATCCAGTAAGTAACACT-CTGGATCAAAGGGTATGCACAGT 909911 i v v? ?iv iiv i - i i v C L1ME3G_3end#L 396 TAGGATAGATNCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGCATT 347 chrXqtel1M 909912 TTGATAACTTTTGA-GCATAGTTC--AAGTACTCTCCAAAATGGTTGGAT 909958 --- v i -iv v v -- v i i ? i v i C L1ME3G_3end#L 346 TT---AAATTTTAATAGATACTGCCAAATTGCCCTCCAAAANGGCTGTAC 300 chrXqtel1M 909959 TCATT--CACCTCCACCAACAATGCATCAATGT-CCAGTTTTCCCGCATC 910005 iv -- ii i i i v iv - v i i i C L1ME3G_3end#L 299 CAATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCACACC 250 chrXqtel1M 910006 CTC---AACAATCATCATTATTTTCCTTC---ATCTTAGCCAATCTGACA 910049 --- v ?ivi ivv? i--- i v ii C L1ME3G_3end#L 249 CTCGCCAACACTNGATATTATCAANCTTTTAAATTTTTGCCAATCTGATG 200 chrXqtel1M 910050 GGTGTGTAGTAGTATCTTAGAGTTGTCTTAATTTGCATTTCTCTGATTAA 910099 viv i i i vv i i v C L1ME3G_3end#L 199 GGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGATTAC 150 chrXqtel1M 910100 TAATGA-CTTGGGCATCTTTTCATATGACTAGAAATAGTTTCAATTTCTT 910148 i -v i vi vviiivi vv i C L1ME3G_3end#L 149 TAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGTATTTCCT 100 chrXqtel1M 910149 CATC--TAAATTGTCTGTTCATATCCTTTGACCATTTTTCAATTG 910191 v -- i i v v C L1ME3G_3end#L 99 CTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTG 55 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 32.89 CpG sites = 73, Kimura (unadjusted) = 33.93 Transitions / transversions = 1.43 (73/51) Gap_init rate = 0.04 (17 / 473), avg. gap size = 1.53 (26 / 17) 3177 28.30 6.39 2.51 chrXqtel1M 910107 913252 (86748) C L1M5_orf2#LINE/L1 (5) 3289 25 m_b376s551i9 15720 chrXqtel1M 910107 TTGGGCATCTTTTCATATGACTAGAAATAGTTTCAATTTCTTCATCTA-- 910154 i i vi vviiivi v? v v i i-- C L1M5_orf2#LIN 3289 TTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTTTTGTG 3240 chrXqtel1M 910155 AATTGTCTGTTCATATCCTTTGACCATTTTTCAATTGAA--GAATGGCGA 910202 v vi i v ?v ii-- vv v vv C L1M5_orf2#LIN 3239 AAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTTGTCTT 3190 chrXqtel1M 910203 TTT-TTAT-AAATTAGAGTTAATTCTC-ATATATTTT-------AGGCCT 910242 - -i ? iv v- i i- i ------- v C L1M5_orf2#LIN 3189 TTTNTTATTGANTTGTAGG-AGTTCTTTATATATTCTGGATACGAGTCCT 3141 chrXqtel1M 910243 TTATCA-ACCTTTGACTGTAAAAATATTTTC---CAGTTTT--GCTTCCC 910286 i - iv v v? - iv --- ? i v-- v C L1M5_orf2#LIN 3140 TTGTCAGATATATGTNT-TGCAAATATTTTCTCCCANTCTGTGGCTTGCC 3092 chrXqtel1M 910287 TTCTAATCTTGTCTGCATTGT--TTTGTTTGTCAAAACTTTTTCAGTTTG 910334 i v i v ivi iv -- v?viv i v v v C L1M5_orf2#LIN 3091 TTTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTTTAATTTTG 3042 chrXqtel1M 910335 GTATAATCAAATTT-TCTATTTTGTGATCAGTAATGATCTCTAGTTCTTC 910383 i i? i v - v v --- vv v i --- ? v i C L1M5_orf2#LIN 3041 ATGNAGTCCAATTTATCAATTTTTT---CTTTTATGGT---TNGTGCTTT 2998 chrXqtel1M 910384 TTTGGTCAT-----AAAGATCTT--CCTCTTCCACAGGTCTGAGAGGTAA 910426 vv v ----- i i -- v?i - vvii i - C L1M5_orf2#LIN 2997 TTGTGTCCTGTTTAAGAAATCTTTGCCTANCCCA-AGGTCACGAAGATA- 2950 chrXqtel1M 910427 ACTATCCTGTGTT--CCTCTA--ATTTATTAATATTTCATTCTTTTCC-- 910470 -i v i -- i -- v - vvi i ?- v -- C L1M5_orf2#LIN 2949 -TTCTCCTATGTTTTCTTCTAGAAGTT-TTATAGTTTTAN-CTTTTACAT 2903 chrXqtel1M 910471 -TAGGTC-ATGAACCCATTTTGACTTTATCTTGGTGTACGGTGTTAAGTA 910518 - - -i i ? v v i v i v i C L1M5_orf2#LIN 2902 TTAGGTCTATGA-TCCATCTNGAATTAATTTTTGTGTATGGTGTGAGGTA 2854 chrXqtel1M 910519 TGGATCAATGCCTAGTTTCTGCCATATTAGTTTCCAATT-TCCCAGCAAT 910567 v i i v?iii v i v vii v - i vi C L1M5_orf2#LIN 2853 GGGGTCGAGNTTCATTTTTTTCCATATGGATATCCAATTGTTCCAGCACC 2804 chrXqtel1M 910568 TTTTATCAAACAGTAAGTTCTTATCCCA--AAA--GC--TGGGATCTTTG 910611 v i ii v vvvi i vi --i -- -- v i C L1M5_orf2#LIN 2803 ATTTGTTGAAAAGACTATCCTTTCCCCACTGAATTGCNTTGGCACCTTTG 2754 chrXqtel1M 910612 GGTTTCAAAGACTAGAT--TCTTATTTGT-TGACTGTTTTATCCCTTGAA 910658 ---- i ii i? --i v v - --- v i ii - i C L1M5_orf2#LIN 2753 ----TCAAAAATCAANTGNCCATATATGTGTG---GGTCTATTTCT-GGA 2712 chrXqtel1M 910659 C---CTAATCTATTCCACTGATCAACTAATCTATTCTTA-GCCAATACCA 910704 --- v i i v i vi i - C L1M5_orf2#LIN 2711 CTCTCTATTCTGTTCCATTGATCTATTTGTCTATCCTTACGCCAATACCA 2662 chrXqtel1M 910705 AATGGTTTTGGTAACTGCTGGTCTATAAATATAATTTT-AGATCTGGTAC 910753 v iv i i v iv v i - - i i - ? ? v C L1M5_orf2#LIN 2661 CACTGTCTTGATTACTGTAGCTTTATAA-TA-AGTCTTGANATCNGGTAG 2614 chrXqtel1M 910754 AGCTAAG-CCACCATCATTTGATTTT---TTTCATTATTCCCTTGAA-AT 910798 v - - v v - v i --- vv vii iv- C L1M5_orf2#LIN 2613 TG-TAAGTCCTCCAAC-TTTGTTCTTCTTTTTCAAGATTGTTTTGGCTAT 2566 chrXqtel1M 910799 TCTTGATCTTTTGT-TTTCCATATGAACTTT-------GTTT--TATTTT 910838 ? i i i- i i ------- i --i v C L1M5_orf2#LIN 2565 TCTNGGTCCTTTGCATTTCCATATAAATTTTAGAATCAGCTTGTCAATTT 2516 chrXqtel1M 910839 CTAGGTCATTAAAATAGTTTTTGGGACTCTGATTGGTATAG-GCTAAATA 910887 --- -- v vi vi i i v v -ii i v C L1M5_orf2#LIN 2515 CTA---CA--AAAAAACCTGCTGGGATTTTGATTGGGATTGCATTGAATC 2471 chrXqtel1M 910888 AATAAGATTAGTT--GGTAATATTGTCATCTTTAT--TATTTGCTCGCCC 910933 v - i i -- v iv v ? i-- viv vi C L1M5_orf2#LIN 2470 TATA-GATCAATTTGGGGAGAATTGACATCTTNACAATATTGAGTCTTCC 2422 chrXqtel1M 910934 TATCCAAGG-CATT-TA-ATATTTTCAATTGGTTAGATCAGACTTAATTT 910980 v v i- v- - v i i v iv i vvvi C L1M5_orf2#LIN 2421 AATCCATGAACATGGTATATCTCTCCATTTATTTAGGTCTTCTTTAATTT 2372 chrXqtel1M 910981 GTGTGAAAAAGTGGTCTGTAATTTTGCTCATAAAGTTTCTG---ATTTTC 911027 v v v iv - v i i vvvii ? v ii --- ? - C L1M5_orf2#LIN 2371 CTCTCAGCAA-TGTTTTGTAGTTTTCAGTGTANAGGTCTTGCACATNTT- 2324 chrXqtel1M 911028 CCTTGGCAGATAGATTCCTAAATATTTTATATTATC--GTATTACTTTAA 911075 -- vi vv i ? i v i--i ii i v C L1M5_orf2#LIN 2323 --TTGTTAGATTTATTCCTAAGTATTTNATGTTTTTTGATGCTATTGTAA 2276 chrXqtel1M 911076 ATGGATTTCTCTTTTGTAACTCTGACTGTTGGATT---TGTTAGTGATAT 911122 -- vi v v? v i v i v ivi --- iv ii C L1M5_orf2#LIN 2275 ATGG--TATTGTTTTTNAAATTTCATTTTCCAATTGTTTGTTGCTAGTAT 2228 chrXqtel1M 911123 ATAGAC-TGCTGATGACTTATGTGGGTT---TTTTTAACCAGCAAC-TTG 911167 v- i viv i v ivi ---i v v ? i - C L1M5_orf2#LIN 2227 ATAGAAATACAATTGATTTTTGTATATTGACCTTGTATCCNGCGACCTTG 2178 chrXqtel1M 911168 CTAAAGTTGTGGATTA-TTCTAATAACTTTTTAGTAGAATCCCTGGGGTT 911216 v iiivv - i ii ? v v ii ? i C L1M5_orf2#LIN 2177 CTAAATTCACTTATTAGTTCTAGTAGTTTNTTTGTAGATTCTTTNGGATT 2128 chrXqtel1M 911217 CTCTAAGTATACCATCATGTCATCGGCAAGAAGTGATAATT--GGTTCCT 911264 i v ? v v i iv i? i i --iv i C L1M5_orf2#LIN 2127 TTCTACGTANACAATCATGTCATCTGCGAATAANGACAGTTTTATTTCTT 2078 chrXqtel1M 911265 CATTCCTATTCTTT--TCCTTTAATCTCTTTCTCAGCTCTTATTCTA-TA 911311 v i i v --v v i i vvvi vi - i C L1M5_orf2#LIN 2077 CCTTTCCAATCTTTATGCCTTTTATTTCTTTTTCTTGCCTTATTGCACTG 2028 chrXqtel1M 911312 GCTAGCGTTTCTAATACAATATTAAATAGTAACGGTGATAGTGGGCAACC 911361 viii i i i i v ii ? i i v C L1M5_orf2#LIN 2027 GCTAGGACCTCCAGTACAATGTTGAATAGAAGTGGTGANAGCGGACATCC 1978 chrXqtel1M 911362 TTGT-TTCCTCCAGATCTTATTGGGAATGGTTGCAGTTTGTCTCCGT-AC 911409 - vi v vv v v? v ? v v i - v C L1M5_orf2#LIN 1977 TTGTCTTGTTCCCGATCTTAGGGGGAAAGCNTTCAGTNTTTCACCATTAA 1928 chrXqtel1M 911410 ATATGATGTTA-CTGATGGTTTTAAATAGATGCTGCTGATTATTTTAAGG 911458 i ?- vv vvi ivi v i vv i C L1M5_orf2#LIN 1927 GTATGATGTTNGCTGTAGGTTTTTCGTAGATGCCCTTTATCAGGTTGAGG 1878 chrXqtel1M 911459 AAAAGTCCATTTATTCCTATACTCTCAAGTGTTTTAAT-AGGAATGGATG 911507 ivvi v i vvi viii v v - v i C L1M5_orf2#LIN 1877 AAGTTCCCTTCTATTCCTAGTTTGCTGAGAGTTTTTATCATGAATGGGTG 1828 chrXqtel1M 911508 TTGGATTTTATCAAAT--CTTTTCTGCATCTATTGAGATGATCATATGGT 911555 i i --i i C L1M5_orf2#LIN 1827 TTGAATTTTGTCAAATGCTTTTTCTGCATCTATTGAGATGATCATATGAT 1778 chrXqtel1M 911556 TTTGTTAATTTGGT-TATTAACATGGCCAATTATATTGATAGTTTTTCTA 911604 vi vv iv - i i iv i v v v C L1M5_orf2#LIN 1777 TTTTCTCCTTTATTCTGTTAATATGGTGAATTACATTGATTGATTTTCGA 1728 chrXqtel1M 911605 ATATTGAACCAGCCCTGCATTCCTGGTATAAATCCTACTTGATCATAGTG 911654 i i i i v i i i ii C L1M5_orf2#LIN 1727 ATGTTAAACCAACCTTGCATTCCTGGGATAAACCCCACTTGGTCATGATG 1678 chrXqtel1M 911655 TATTATCTTGGAGATGATTTTCTGTAGTCT-TTTGCTAATATCTTTTTA- 911702 i vvvv ivv v v v v- i v ?- C L1M5_orf2#LIN 1677 TATTATCCTTTTTATATATTGCTGGATTCGATTTGCTAATATTTTGTTNA 1628 chrXqtel1M 911703 -GATTTTAGCATCAATATTCATTAGGGAGATTGGTCTATAATTTTCTTTC 911751 - v v i v v i i C L1M5_orf2#LIN 1627 GGATTTTTGCATCTATGTTCATGAGGGATATTGGTCTGTAATTTTCTTTT 1578 chrXqtel1M 911752 TCTGT--TTTCAGCCTACCTGGTTTAGGTATCAGTACCATGTCTGTGTC- 911798 ii -- v --ii ii ? v vii? iiv iv - C L1M5_orf2#LIN 1577 CTTGTAATGTC--TTTGTCNGGTTTTGGTATCAGGGTNATGCTGGCCTCA 1530 chrXqtel1M 911799 TAGAAGGAATTTGGTGGACT--CCTTTATTCCTATTTTATCAAATAATTT 911846 i v i v vi vv -- i v i v vi v i C L1M5_orf2#LIN 1529 TAAAATGAGTTGGGAAGTGTTCCCTCTTTTTCTATTTTCTGGAAGAGTTT 1480 chrXqtel1M 911847 ATATATACATTGGGGCCAATTGTTCTTTAAATGTTTGGTAAAATTCACAT 911896 i i - v viii v v i i vv C L1M5_orf2#LIN 1479 GTGTA-AGATTGGTATTATTTCTTCCTTAAATGTTTGGTAGAATTCACCA 1431 chrXqtel1M 911897 GTAAATCCATCTGGTCCTGGGGATTTTTCT-TAGGGAGTTGTTTAATTGC 911945 i v v i v i i - i i v v i C L1M5_orf2#LIN 1430 GTGAAGCCATCTGGGCCTGGAGTTTTCTTTGTGGGAAGGTTTTTAATTAC 1381 chrXqtel1M 911946 CTGTTCTATTTCTTTTTCTGAAATGGGACTATTCAAGCAGTTTACTTCCT 911995 vvi v vviv v i i iiivv i i i C L1M5_orf2#LIN 1380 AAATTCAATTTCTTTAATAGATATAGGGCTATTCAGATTTTCTATTTCTT 1331 chrXqtel1M 911996 CCTCTGTTAGTCTGGGAAGTCTATATTTTTGGAGGTAGTCATCTATTTCA 912045 i v? i i v v i?i i i vi v v ii i C L1M5_orf2#LIN 1330 CTTGNGTCAGTTTTGGTAANTTGTGTTTTTCAAGGAATTTGTCCATTTCA 1281 chrXqtel1M 912046 CTTAGGTTATCAAATTTATTGGCATAAAGGTTGAGCAAAAATAACTCCTT 912095 ii i ? - vv v - viii C L1M5_orf2#LIN 1280 TCTAAGTTNTCAAATTTATTGGCATAAAG-TTGTTCATAA-TATTCTCTT 1233 chrXqtel1M 912096 ATTATTTCTCTAATTTCCTCTTCATTGGTGGAAAGTTCTCCCTTTTCATT 912145 iii i v ivivvv iv i vi vv i C L1M5_orf2#LIN 1232 ATTATCCTTTTAATGTCTGTAGGATCTGTAGTGATGTCTCCTTTTTCATT 1183 chrXqtel1M 912146 T-TAAGACTACTAATTTCATTTTCCTCCCTCCTTTTTCTAATCAGATTT- 912193 i- i v i iv vvv i i i ii ii i vi ?- C L1M5_orf2#LIN 1182 CCTGATATTGGTAATTTGTGTCTTCTCTCTTTTTTTCTTGATCAGTCTNG 1133 chrXqtel1M 912194 -CAAAGGCTTATCTATTTTATTGG-CTTTTCATAGAACCAACTTTTAGTT 912241 -i i i v i- v i i i C L1M5_orf2#LIN 1132 CTAGAGGTTTATCAATTTTATTGATCTTTTCAAAGAACCAGCTTTTGGCT 1083 chrXqtel1M 912242 T-ATTAATTAGTTCAATAGTTT--TTACTTTCAATATTTTTAATTTCTCC 912288 -i i vvi v v ? -- ii v v iv i v C L1M5_orf2#LIN 1082 TCGTTGATTTTCTCTATTGTNTNTTTGTTTTCTATTTCATTGATTTCTGC 1033 chrXqtel1M 912289 TTTTAATTTTAA-ATTTCCAATTTAGTATTTGATTGGGGTTTTTTAATTT 912337 i vi v- vvii vv i ?v v --- C L1M5_orf2#LIN 1032 TCTTATCTTTATTATTTCCTTCCTTCTACTTNCTTTGGGTTT---AATTT 986 chrXqtel1M 912338 GGTCTT----TTAAAATTTTTTTAGTTGCAAGCCCAATTCATTAATCTT- 912382 v ---- vv ii i v v v ii iv i i - C L1M5_orf2#LIN 985 GCTCTTCTTTTTCTAGCTTCTTAAGGTGGAAGCTTAGATCATTGATTTTA 936 chrXqtel1M 912383 -TTCTTTCTCTGTTTTTATTCAAGTAAGCCTCTAAGGATATAAAATTCCC 912431 -vi iiv i v ---i ? v i ? v v C L1M5_orf2#LIN 935 AGCCTTTCTTCTTTTCTAAT---ATANGCATTTAANGCTATAAATTTCCC 889 chrXqtel1M 912432 TCTTATTACCGCTTTGGCTGCATCCCACAAATTTTGGTATGATGTCTCAT 912481 v vi i i i v --- C L1M5_orf2#LIN 888 TCTAAGCACTGCTTTAGCTGCATCCCACAAATTTTGATATGTTGT---AT 842 chrXqtel1M 912482 CTTGTCATTATC--TTAGT-GAAATTATT----AATTGTATCTATAATTT 912524 i -- ? -- i -v v ---- viv?i i i C L1M5_orf2#LIN 841 TTT--CATTNTCATTCAGTTCAAAATATTTTCTAATTTCCNTTGTGATTT 794 chrXqtel1M 912525 GCTCTTC-ACCCAATCATTCTTTAAGA-TGAGATTGTTTAGTTTCCAATG 912572 vi i- vvvi v ii - v - i vv C L1M5_orf2#LIN 793 CTTCTTTGACCCATGGGTTATTTAGAAGTGTG-TTGTTTAATTTCCAAAT 745 chrXqtel1M 912573 CTTTTGGTCTATTTCCC--CTAACTTTTTGTTG--AATGTGT--TTTTAT 912616 v v v-- i i--? v i--i v v -- v C L1M5_orf2#LIN 744 ATTTGGGG--ATTTTCTAGNTATCTTTTTGTTATTGATTTCTAATTTAAT 697 chrXqtel1M 912617 TGCATCATGATCTGAAAAGCATTTACTATTTCTGCTTTCTTGCATTT--A 912664 v ii i v i - -- v v v v vvv v -- C L1M5_orf2#LIN 696 TCCATTGTGGTCAGAGAA-CAT--ACTCTGTATGATTTCAATCCTTTNAA 650 chrXqtel1M 912665 ATTT--TGAG----GTCTTTATGTCCTAATACATGGTCAATTTTGA-ATA 912707 -- ---- - v i i? i v i i- v C L1M5_orf2#LIN 649 ATTTATTGAGACTTGT-TTTATGGCCCAGNATATGGTCTATCTTGGTAAA 601 chrXqtel1M 912708 GGTTCCATGAACTGCTGAGAAGAAAGTATATTCCTTTCTATCTCCATTCA 912757 v vi vvi i v i ivi?v vvi vvi v? C L1M5_orf2#LIN 600 TGTTCCATGTGCACTTGAAAAGAATGTGTATTCTGCNGTTGTTGGGTGNA 551 chrXqtel1M 912758 ATTTTCTCCAAAGATCCAACATACCTAATT--TTTCTAATATTCTATTTA 912805 i v vi vi v vi vii v i -- vv i i -- i i C L1M5_orf2#LIN 550 GTGTTCTATAAATGTCAATTAGGTCAAGTTGGTTGATAGTGT--TGTTCA 503 chrXqtel1M 912806 CCTCTTTAAT-TTCTTTCTTATTTGTTTTGTG-ATTTGATTTATCTAAAT 912853 vv iv - i v v -- v- i v i -- C L1M5_orf2#LIN 502 AATCTTCTATATCCTTACTGATT--TTTTGTCTACTTGTTCTATC--AAT 457 chrXqtel1M 912854 --CTGAGAGTGCAAGATTGAGGTCTCCCGCTATTAGAGTTTTG---CTGT 912898 -- v v?ivi i ii ?i --- i v ---i C L1M5_orf2#LIN 456 TACTGAGAGAGGNGTGTTAAAATCTCCNACTAT---AATTGTGGATTTGT 410 chrXqtel1M 912899 CTATTTCTTCTTGTAACTCTCTTAACTTCTCCTTTAGGTAGTTAGATGCT 912948 i v ii v i ii i v i v v v v C L1M5_orf2#LIN 409 CTATTTCTCCTTTTAGTTCTGTCAGTTTTTGCTTCATGTATTTTGAAGCT 360 chrXqtel1M 912949 ATACCACTTGGTGCA---AAGTTTAATACTGATATCGCTTC---A----- 912987 v iii i v --- vi iv i v vv --- ----- C L1M5_orf2#LIN 359 CTGTTATTAGGTGCATACACATTTAGGATTGTTATGTCTTCTTGATGAAT 310 chrXqtel1M 912988 -------TTTAGCAAGATATAGTTTCCTTCCTTATCTCTTTTAATTAGAT 913030 ------- v vv iv i v i i vv --- C L1M5_orf2#LIN 309 TGACCCTTTTATCATTATGAAATGTCCCTCTTTATCTCTGGTAAT---AT 263 chrXqtel1M 913031 CAATTTTTGCTT-----TTTGC---GTCTGAGATAAGGATAGCTAC-CTA 913071 --- i i ----- i i --- v v iv i - i C L1M5_orf2#LIN 262 ---TTCTTGCCTTGAAGTCTACTTTGTCTGATATTAATATAGCCACNCCA 216 chrXqtel1M 913072 CTTTTGACTTCACCTGAA-----GCATAATAGA---TTTTCCAGCCTTTT 913113 vi -- ivv? v i----- ii v --- v C L1M5_orf2#LIN 215 GCTTT--CTTTTGNTTAGTGTTTGCATGGTATATCTTTTTCCATCCTTTT 168 chrXqtel1M 913114 ACCTTTACTCTAAAT-TATCTCC-TACTTTAAATGTGTTTCTT-TAAACA 913160 i i vi ?vv - i ii- i v i i i - i C L1M5_orf2#LIN 167 ACTTTCAACCTNTCTGTGTCTTTATATTTAAAGTGCGTCTCTTGTAGACA 118 chrXqtel1M 913161 ACATATTG-TAGGTTCTGACTTTTGATCCAGTCTG-CTATCTGCCTCCTC 913208 i v - i ii vi v - v -- v ii C L1M5_orf2#LIN 117 GCATATAGTTGGGTCTTGTTTTTTTATCCAGTCTGACAATCT--CTGCCT 70 chrXqtel1M 913209 TTTA--TGGGGAGTTCATCCCATTC-CATTTACTGTTAAATTACTAA 913252 -- i v i v? i- v -- i i C L1M5_orf2#LIN 69 TTTAATTGGAGTGTTTAGNCCATTTACATTTAATGT--AATTATTGA 25 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 36.45 CpG sites = 454, Kimura (unadjusted) = 36.93 Transitions / transversions = 1.10 (454/414) Gap_init rate = 0.06 (186 / 3145), avg. gap size = 1.52 (283 / 186) 228 20.02 7.79 9.21 chrXqtel1M 914174 914250 (85750) C MIR1_Amn#SINE/MIR (32) 198 123 m_b376s601i4 15721 chrXqtel1M 914174 CATTA-TAGACCTTAAAAGAGAGACTTT-----GAATGTCATGTACATCA 914217 i - i i iv ---- ----- i v - -- C MIR1_Amn#SINE 198 CATCAGTAGATCTCAAAGCA----CTTTACAAAGGAGGTCA-GTA--TCA 156 chrXqtel1M 914218 TCAGCTTCATTTTACAGATAGGAAAACTGAGGC 914250 i v ii ii i C MIR1_Amn#SINE 155 TTATCCCCATTTTACAGATGAGGAAACTGAGGC 123 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 24.33 CpG sites = 11, Kimura (unadjusted) = 24.33 Transitions / transversions = 3.67 (11/3) Gap_init rate = 0.12 (9 / 76), avg. gap size = 1.44 (13 / 9) 255 28.33 0.00 0.00 chrXqtel1M 914192 914251 (85749) C MIR3#SINE/MIR (32) 176 117 m_b376s601i5 15721 chrXqtel1M 914192 AGAGACTTTGAATGTCATGTACATCATCAGCTTCATTTTACAGATAGGAA 914241 i i ii vi v vvi v vv i ii i C MIR3#SINE/MIR 176 AGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTTACAGATGAGGA 127 chrXqtel1M 914242 AACTGAGGCC 914251 C MIR3#SINE/MIR 126 AACTGAGGCC 117 Matrix = 25p39g.matrix Kimura (with divCpGMod) = 36.53 CpG sites = 10, Kimura (unadjusted) = 36.53 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0) 30 26.98 2.04 5.63 chrXqtel1M 914914 915060 (84940) (AATT)n#Simple_repeat 1 142 (0) m_b376s252i18 15722 chrXqtel1M 914914 AATAAGTTAGTAAATTAATAAAATTTATTCAAGATAATAAAATTAATTAA 914963 v i i v -v v - -v -v (AATT)n#Simpl 1 AATTAATTAATTAATTAAT-TAATTAATT-AA-TTAAT-TAATTAATTAA 46 chrXqtel1M 914964 -TAGCAAATTGACTGGATTAATTAATAAATTGATAAAATTGAAGAATTCA 915012 - iiv - v vi v i -v i vv v (AATT)n#Simpl 47 TTAATTAATT-AATTAATTAATTAATTAATTAAT-TAATTAATTAATTAA 94 chrXqtel1M 915013 TTAATAAAGTTAA-TGATT-ACTAATTAAATTATTTTAAAAATGAATAAA 915060 v - - i - i - v v vv v v (AATT)n#Simpl 95 TTAATTAA-TTAATTAATTAATTAATT-AATTAATTAATTAATTAATTAA 142 Matrix = Unknown Transitions / transversions = 0.43 (9/21) Gap_init rate = 0.08 (11 / 146), avg. gap size = 1.00 (11 / 11) 72 32.35 1.93 4.20 chrXqtel1M 915468 915863 (84137) (CTCTTT)n#Simple_repeat 1 387 (18) m_b376s252i19 15723 chrXqtel1M 915468 CTCTTTTGCTTTCTCTTACTGTCTCTGTCTCTGTCTTTCTTATTTCCTTC 915517 iv v v i v i v i i - i i (CTCTTT)n#Sim 1 CTCTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCTT-TCTCTTTC 49 chrXqtel1M 915518 TGATTCT-TTTC-CTGTCTCTGTCTTTTTCTGTTTCTCCATCCTCTGATC 915565 vv - - v v i v - v i -v (CTCTTT)n#Sim 50 TCTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCTTTCT-CTTTCTCT-TTC 97 chrXqtel1M 915566 TTCTTCTCTTT-TCAGTCT-TTTTTCATTCTTGCTCTCTTTTCTCTGTCA 915613 ii - vv - i v ivi - v v (CTCTTT)n#Sim 98 TCTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCTTTCTC-TTTCTCTTTCT 146 chrXqtel1M 915614 CTTTCTCTGTCTCTGTCTCCATCTATCCATCTGTTTCTCTCTCTTTTTCT 915663 v v - - i v iv v i i (CTCTTT)n#Sim 147 CTTTCTCTTTCTCTTTCT-C-TTTCTCTTTCTCTTTCTCTTTCTCTTTCT 194 chrXqtel1M 915664 AAATTTCTCTAAGATTCCCTGACTTTGTTTCATTCTTTTTGTTCATATGC 915713 vvv i i vvvv i vv i v i v i -i - - v (CTCTTT)n#Sim 195 CTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCTTT-CTC-T-TTC 241 chrXqtel1M 915714 TCTTT-T-GTTCTCTTGCTCTCTTTTGCTTGCACTCTCTCTTGTTCTCTT 915761 - -v -- iv v v i - - (CTCTTT)n#Sim 242 TCTTTCTCTTTCTCTT--TCTCTTTCTCTTTCTCTTTCTC-T-TTCTCTT 287 chrXqtel1M 915762 TTGCTTGCACTCTCTCTGGATCTCATTTTCTCCCTCCCTCCCTCCCTC-A 915810 iv v v i --v v i ii ii i ii -v (CTCTTT)n#Sim 288 TCTCTTTCTCTTTCTCT--TTCTCTTTCTCTTTCTCTTTCTCTTTCTCTT 335 chrXqtel1M 915811 TATTTTTCT-TTTTTCCCTCTATATCTGTTTTCTCTGTCTCCTGTCTCTC 915859 v i - i ii v v -i v - v i (CTCTTT)n#Sim 336 TCTCTTTCTCTTTCTCTTTCTCTTTCT-CTTTCTCTTTCT-CTTTCTCTT 383 chrXqtel1M 915860 TGAG 915863 vvv (CTCTTT)n#Sim 384 TCTC 387 Matrix = Unknown Transitions / transversions = 0.81 (43/53) Gap_init rate = 0.06 (25 / 395), avg. gap size = 1.00 (25 / 25) 65 1.45 4.29 0.00 chrXqtel1M 915864 915933 (84067) (TC)n#Simple_repeat 1 73 (0) c_b376s251i7 15724 chrXqtel1M 915864 TCTCTC-CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 915912 - (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chrXqtel1M 915913 TCTCTCTCT-TTTCTC-CTCTCT 915933 - i - (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCT 73 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.04 (3 / 69), avg. gap size = 1.00 (3 / 3) 72 32.35 1.93 4.20 chrXqtel1M 915934 915950 (84050) (CTCTTT)n#Simple_repeat 388 404 (1) m_b376s252i19 15725 chrXqtel1M 915934 TCCTCCTTCCCTTCCTC 915950 i i i i (CTCTTT)n#Sim 388 TTCTCTTTCTCTTTCTC 404 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 12 11.16 6.67 0.00 chrXqtel1M 917152 917181 (82819) (TCTTCC)n#Simple_repeat 1 32 (0) m_b376s252i20 15726 chrXqtel1M 917152 TCTTTCTCTTCCT-TTTC-CTTCCTCTCCCTC 917181 i - i - i (TCTTCC)n#Sim 1 TCTTCCTCTTCCTCTTCCTCTTCCTCTTCCTC 32 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.07 (2 / 29), avg. gap size = 1.00 (2 / 2) 11 12.96 8.82 0.00 chrXqtel1M 917208 917241 (82759) (TTATTAA)n#Simple_repeat 1 37 (0) m_b376s252i21 15727 chrXqtel1M 917208 TTATTTATTATAAATT-TTAA-TA-AAATTATTCATT 917241 v v - - -v v (TTATTAA)n#Si 1 TTATTAATTATTAATTATTAATTATTAATTATTAATT 37 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.09 (3 / 33), avg. gap size = 1.00 (3 / 3) 41 23.23 1.09 0.00 chrXqtel1M 917473 917564 (82436) (TC)n#Simple_repeat 1 93 (0) m_b376s252i22 15728 chrXqtel1M 917473 TCTCTTTCTCTTCCTCCCTCCTTTTCTCTCTCTCTCTC-CCCTCCCCCCA 917521 i ii i ii i - i i i iv (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chrXqtel1M 917522 TATCTGTCTGTCTGTCTCTCTCCCTCTCTCTGTCTCTCTCTCT 917564 v v v v i v (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 93 Matrix = Unknown Transitions / transversions = 2.00 (12/6) Gap_init rate = 0.01 (1 / 91), avg. gap size = 1.00 (1 / 1) 48 0.00 0.00 0.00 chrXqtel1M 917572 917612 (82388) (TA)n#Simple_repeat 1 41 (0) c_b376s251i8 15729 chrXqtel1M 917572 TATATATATATATATATATATATATATATATATATATATAT 917612 (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATAT 41 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 284 17.79 0.00 8.82 chrXqtel1M 917613 917686 (82314) DNM1r#Unknown 2478 2545 (2117) m_b376s502i3 15730 chrXqtel1M 917613 GTGTGTGTGTGTACATATATATGTGTGTGTGTACATATATATTTTTGTAT 917662 i i i i i i ii i i ------ DNM1r#Unknown 2478 GTGTATGTGTGTATATATGTGTGTATATGTGTGTATGTGT------GTAT 2521 chrXqtel1M 917663 ATACGTGTATATATACATATATAT 917686 i i ? DNM1r#Unknown 2522 ATATGTGTATATATACGTATNTAT 2545 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 20.12 CpG sites = 12, Kimura (unadjusted) = 22.17 Transitions / transversions = 1.00 (12/0) Gap_init rate = 0.08 (6 / 73), avg. gap size = 1.00 (6 / 6) 54 17.64 0.00 0.00 chrXqtel1M 918219 918314 (81686) (CA)n#Simple_repeat 1 96 (0) m_b376s252i23 15731 chrXqtel1M 918219 CACACACACAGAGACACACACACACAATCACACACACACACAGAGACATA 918268 v v vv v v i (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50 chrXqtel1M 918269 CACACACAGAGACACACACACCCCCTCACACACACCCTCACACGCA 918314 v v v v v v v i (CA)n#Simple_ 51 CACACACACACACACACACACACACACACACACACACACACACACA 96 Matrix = Unknown Transitions / transversions = 0.15 (2/13) Gap_init rate = 0.00 (0 / 95), avg. gap size = 0.0 (0 / 0) 16 8.53 0.00 0.00 chrXqtel1M 918620 918644 (81356) (ATA)n#Simple_repeat 1 25 (0) m_b376s252i24 15732 chrXqtel1M 918620 ATAAAATTAATAATAATAATAATAA 918644 v v (ATA)n#Simple 1 ATAATAATAATAATAATAATAATAA 25 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 371 29.97 5.46 5.46 chrXqtel1M 921082 921374 (78626) C L1P4_orf2#LINE/L1 (1051) 2243 1951 m_b376s551i10 15733 chrXqtel1M 921082 TGGACTTTGTTGGTGACATAGAAATGCTGATGATTTACATGGATTCATTT 921131 i v i -i iv vii iv v C L1P4_orf2#LIN 2243 TGAACGTTATTGGTG-TATAGAAATGCTACTGATTTTTGTACATTGATTT 2195 chrXqtel1M 921132 TGCATCCTGCAACTTTGCTAAAGTTAATAGTTTGTAATCGTTTT-----C 921176 i v i i i---- i v -- i ----- C L1P4_orf2#LIN 2194 TGTATCCTGAAACTTTACTGAAGTC----GTTTATCA--GTTCTAGGAGC 2151 chrXqtel1M 921177 TTTTTAGT----TCTCTAGGATTCTCTGAGTATACCTTCTGCCCCCTTTT 921222 i i i---- i i i ii vvv ------- v v C L1P4_orf2#LIN 2150 CTTTTGGCGGAGTCTTTAGGGTTTTCTAGGTATAGAAT-------CATAT 2108 chrXqtel1M 921223 TGTTTCAT------GTCATAATTTTGTTTCCCCATTACCTGCTCTAATTC 921266 i -- v------ vv i vii ii v v ii ivi v C L1P4_orf2#LIN 2107 CG--TCAGCGAAGAGAGATAGTTTGACTTCTTCTTTTCCTATTTGGATGC 2060 chrXqtel1M 921267 CTTTAATTTCTTTTTCTTCTCTTATTGCTAAAGCCAACATTTCAAATACA 921316 v i vi v vvi i iv i v i v C L1P4_orf2#LIN 2059 CTTTTATTTCTTTCTCTTGCCTGATTGCTCTGGCTAGGACTTCCAGTACT 2010 chrXqtel1M 921317 GTATTGAATAGTAATCATGATAGTGGGCA-ACTTGATTTCATGTGGTTTT 921365 i i v i vi v -v vi vv vii i C L1P4_orf2#LIN 2009 ATGTTGAATAGGAGTGGTGAGAGTGGGCATCCTTGTCTTGTTCCAGTTCT 1960 chrXqtel1M 921366 CAAGGGAAA 921374 i C L1P4_orf2#LIN 1959 CAAGGGGAA 1951 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.40 CpG sites = 47, Kimura (unadjusted) = 39.20 Transitions / transversions = 1.31 (47/36) Gap_init rate = 0.07 (20 / 292), avg. gap size = 1.60 (32 / 20) 378 29.48 2.33 2.72 chrXqtel1M 921088 921345 (78655) C L1M5_orf2#LINE/L1 (1057) 2237 1981 m_b376s551i11 15733 chrXqtel1M 921088 TTGTTGGTGACATAGAAATGCTGATGATTTACATGGATTCATTTTGCATC 921137 i i - i i viv vii iv v ii i C L1M5_orf2#LIN 2237 TTGCTAGT-ATATAGAAATACAATTGATTTTTGTATATTGACCTTGTATC 2189 chrXqtel1M 921138 CTGCAACTTTGCTAA----AGTTAATAGTTTGTAATCGTTTTCTTTTTAG 921183 ? i i ---- v v i- i v - ? v C L1M5_orf2#LIN 2188 CNGCGACCTTGCTAAATTCACTTATTAGTTC-TAGTAG-TTTNTTTGTAG 2141 chrXqtel1M 921184 -TTCTCTAGGATTCTCTGAGTATACCTTC-TGCCCCCTTTTTGTTTCATG 921231 - i ? i iv ? vv - --i v i vi vv v ? C L1M5_orf2#LIN 2140 ATTCTTTNGGATTTTCTACGTANACAATCATG--TCATCTGCGAATAANG 2093 chrXqtel1M 921232 TCATAATTTTGTTTCCCCATTACCTGCTCTAATTCCTTTAATTTCTTTTT 921281 -- i i i ii v v viiii v v v C L1M5_orf2#LIN 2092 --ACAGTTTTATTTCTTCCTTTCCAATCTTTATGCCTTTTATTTCTTTTT 2045 chrXqtel1M 921282 CTTCTCTTATTGCTAAAGCCAACATTTCAAATACAGTATTGAATAGTAAT 921331 vi vvvi i iv ii v i i i v i C L1M5_orf2#LIN 2044 CTTGCCTTATTGCACTGGCTAGGACCTCCAGTACAATGTTGAATAGAAGT 1995 chrXqtel1M 921332 CATGATAGTGGGCA 921345 vi ? i i C L1M5_orf2#LIN 1994 GGTGANAGCGGACA 1981 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 37.69 CpG sites = 43, Kimura (unadjusted) = 39.76 Transitions / transversions = 1.39 (43/31) Gap_init rate = 0.04 (10 / 257), avg. gap size = 1.30 (13 / 10) 360 33.14 5.51 1.77 chrXqtel1M 922684 923064 (76936) MER52-int#LTR/ERV1 5758 6152 (939) m_b376s701i0 15734 chrXqtel1M 922684 GGTAGAAGCATTTCCTTCCAGGACTGAGAAGGCTCAGGAGGTG-TCACAA 922732 v viv v i iivv - v v i MER52-int#LTR 5758 GGTAGAAGCATTTCCATGTCGGACAGAGAAAGCCTCTGAGGTGATAAAAG 5807 chrXqtel1M 922733 TGCTTACTAAAAGGGATCATACCTCATTTTGACCTACTTAGCTCCTTACA 922782 i v i - v i v v ii iv v i iv v i v MER52-int#LTR 5808 TACTAATT-AATGAGATAATTCCTCGCTTTGGACTCCCTAAGTACCTCCA 5856 chrXqtel1M 922783 GAGAGACAATGGGCC---------GGCCTTTACTTCCCAG-------CCA 922816 v i v --------- vvi iiiv ------- v MER52-int#LTR 5857 GAGCGATAATGGCCCCTCGTTCAAGGCGGCTGTCACCCAGGGGGTCTCAA 5906 chrXqtel1M 922817 AAGCACTCAAAATCCCCTACCACCTGCCCTCTGCTTGTTGTCCTCAGGCT 922866 i viiv v vv i v vi v vv v v iv i MER52-int#LTR 5907 AGGCACTAGGCATACAATACCATCTTCATTGTGCTTGGAGACCACAATCC 5956 chrXqtel1M 922867 TCTGGGAAGGTGGAGAAAACGAACCACACTCTCAAGGAGT-CCTCACTAA 922915 v i i i i i iv i i v iii i- vv MER52-int#LTR 5957 TCGGGAAAGGTAGAAAAGACAAATGATATTATCAAAAGGCACCTCAGGAA 6006 chrXqtel1M 922916 ACTGTGCTTA-GAGACTGGAGAGCAATGCATAAAGAGTCTCCCATTAGGA 922964 - i - vivvvv vv v iv vvvv vv vv MER52-int#LTR 6007 ACTGT-CTCAGGAGACTCATCTCCCCTGGACTACCCTTCTCCCCATAGCC 6055 chrXqtel1M 922965 CTGCTTAGCGTCCGAATCTCCCCTTGGAAGAACATTAAG-CTGAGCCCTT 923013 i vv i iv v v vi ----i ii -i i i i MER52-int#LTR 6056 CTACTACGTGTTAGAAACACCCCTTCAAAG----CTGGGTTTAAGTCCCT 6101 chrXqtel1M 923014 TTGAACTCCTGTATGGACAGCCTTTTCTGACCACTGATATTCCTG-TAGA 923062 i v vv i v v - i - MER52-int#LTR 6102 TCGAAATGATGTATGGACGGCCTTTTCTCACCAATGAT-TTCTTGCTAGA 6150 chrXqtel1M 923063 CC 923064 MER52-int#LTR 6151 CC 6152 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 42.71 CpG sites = 55, Kimura (unadjusted) = 44.07 Transitions / transversions = 0.80 (55/69) Gap_init rate = 0.04 (14 / 380), avg. gap size = 2.00 (28 / 14) 277 10.75 20.78 3.33 chrXqtel1M 924955 925031 (74969) MER50-int#LTR/ERV1 7110 7199 (6) m_b376s701i1 15734 chrXqtel1M 924955 CCCTC-GTCAGCTCGAAGCAATTATAGAAGAATGAGACCTTCGCCCCTTT 925003 - vv i i v -- i v MER50-int#LTR 7110 CCCTCTGTCAGCAGGAAGCAGTTACAGAAGACTGA--CCTTCGTCCATTT 7157 chrXqtel1M 925004 ACCCCAAATGAATT---------------TGAGGGGGGAAATG 925031 v - --------------- MER50-int#LTR 7158 TCCCCAAA-GAATTGGGGTCTTGGACTCTTGAGGGGGGAAATG 7199 Matrix = 20p39g.matrix Kimura (with divCpGMod) = 11.68 CpG sites = 3, Kimura (unadjusted) = 11.68 Transitions / transversions = 0.60 (3/5) Gap_init rate = 0.07 (5 / 76), avg. gap size = 3.80 (19 / 5) 11 18.20 2.44 5.00 chrXqtel1M 926596 926636 (73364) (TCCCCC)n#Simple_repeat 1 40 (0) m_b377s252i0 15735 chrXqtel1M 926596 TCCCCGTCCCCCTCCCCAATCCCAGCCCCTCCTTCCCC-CCC 926636 v -v -v i i i - (TCCCCC)n#Sim 1 TCCCCCTCCCCCTCCCC-CTCCC-CCTCCCCCTCCCCCTCCC 40 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.07 (3 / 40), avg. gap size = 1.00 (3 / 3) 31 3.31 0.00 0.00 chrXqtel1M 927445 927475 (72525) (CA)n#Simple_repeat 1 31 (0) c_b377s251i0 15736 chrXqtel1M 927445 CACACACACACACACACACACACACCCACAC 927475 v (CA)n#Simple_ 1 CACACACACACACACACACACACACACACAC 31 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 13 7.56 7.14 0.00 chrXqtel1M 927560 927587 (72413) (TTAA)n#Simple_repeat 1 30 (0) m_b377s252i1 15737 chrXqtel1M 927560 TTAATTAATTAATTTA-TCATT-ATTAATT 927587 v - v - (TTAA)n#Simpl 1 TTAATTAATTAATTAATTAATTAATTAATT 30 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.07 (2 / 27), avg. gap size = 1.00 (2 / 2) 15 24.50 2.22 2.22 chrXqtel1M 927710 927754 (72246) (TA)n#Simple_repeat 1 45 (0) m_b377s252i2 15738 chrXqtel1M 927710 TAAATATGTTTAACTATATAT-TAAATACACCATATATATACATAT 927754 v i v vv - v i -i i (TA)n#Simple_ 1 TATATATATATATATATATATATATATATA-TATATATATATATAT 45 Matrix = Unknown Transitions / transversions = 0.80 (4/5) Gap_init rate = 0.05 (2 / 44), avg. gap size = 1.00 (2 / 2) 1470 27.90 3.74 3.42 chrXqtel1M 928026 928667 (71333) C L1ME5_3end#LINE/L1 (291) 650 7 m_b377s551i0 15739 chrXqtel1M 928026 ATCTC---CTGGTTCT-GCTTGTTTCACTCAGCATCA-GTTCATGTAAGG 928070 --- v -i v ii - -- v i C L1ME5_3end#LI 650 ATCTCATTCTGTTTCTTACTTTTTTCACTCAGCACTATGTT--TTTAAGA 603 chrXqtel1M 928071 CTCTCCCA-GCCTCTCTATATTCATCCTGATATATTTCTT---ACAGAAC 928116 ii vi - iiv v i i v - ii vii v --- v vvv C L1ME5_3end#LI 602 TCCATCCATGTTGCTATGTGTACATC-TAGTCCGTTGCTTCTAACTGCTG 554 chrXqtel1M 928117 CATAATATTCCATAATATTCATATACCACAATTTACCCAACCATTCTCCA 928166 i i ii i v vi v i v i v C L1ME5_3end#LI 553 CATAGTACTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCC 504 chrXqtel1M 928167 ATCGACGAGCATGCATTCAATTTCCAGTTTCTAGCCACTACAGAAATGGC 928216 vi i ii iv vviviii ii i iv i i v vv C L1ME5_3end#LI 503 AGTGATGGACACCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGC 454 chrXqtel1M 928217 TGCCACAAACATTTTTGCACATACAGGTCCCTTTC----CCTTCTTTAAT 928262 v ii ii i i ---- i v---- viv v iv C L1ME5_3end#LI 453 TGCAATGAACATCCTCGTACAT----GTCCCCTTATGGACCTGTGTGAGA 408 chrXqtel1M 928263 ATCTCTTTGGGATATAAGCCCAGTCGTAACACTGCTGGGTGAAAGGGTAT 928312 i vi vv iiiv i v v C L1ME5_3end#LI 407 ATTTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTAT 358 chrXqtel1M 928313 GCAGAGTTTGATAACTT--TTTGAGTAA--AGTTCCAAATTGCTCTCCAG 928358 --- --- - -- v -- v v i C L1ME5_3end#LI 357 GC---GT---ATA-CTTAATTTGACTAAGTACTGCCAGATTGCTCTCCAG 315 chrXqtel1M 928359 AATGGTTGGATCTGTTCACAACTCCACCAACAATGCATCAGTGTCTCAGT 928408 i v i v ii vii i i v v ii vi C L1ME5_3end#LI 314 AATGGCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTAT 265 chrXqtel1M 928409 TTTCCCACAACCCCTCCAACATTCATCATTATTT--TTTTCCTGTCATTT 928456 ? i v i v i iiv ii--i --- v C L1ME5_3end#LI 264 NTCCCCACATCCTCGCCAACACTTGGCATTATCCAGCTTTC---TAATTT 218 chrXqtel1M 928457 TAGCCAATCTGACAGGTGTGTAGTGGTATGTCAGAGTTGTCTTAATTTGC 928506 v i i i iv i v vv i C L1ME5_3end#LI 217 TTGCCAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGC 168 chrXqtel1M 928507 ATTTTTCTGATCAATAATGATTTGGAGCACCTTTTCATGTGACTAGGAAT 928556 i i v v v i i i - v v-- C L1ME5_3end#LI 167 ATTTCTCTGATTACTAATGAGTTTGAGCATCTCTTCATATG-CTTGT--T 121 chrXqtel1M 928557 AG--TTTCAG-TTTCTACATCTGAAATTTGCCTGTTCATATCCTTTGACC 928603 -- i - iv v v v v C L1ME5_3end#LI 120 AGCCTTTCGGGTTTCCTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCC 71 chrXqtel1M 928604 ATTTATC-ATTTGGA-CAATGGCTTGATTTCTTATAAATTTGAGTCAATT 928651 v - v i-i?vi v -- i vi vivv i C L1ME5_3end#LI 70 ATTTTTCTATTGGGGTTNCCGTCTT--TTTCTTGTTGATTTGCAGGAGTT 23 chrXqtel1M 928652 CTGTATATATTTTGGA 928667 iv i i i C L1ME5_3end#LI 22 CCTTGTATATTCTAGA 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.44 CpG sites = 97, Kimura (unadjusted) = 35.77 Transitions / transversions = 1.28 (97/76) Gap_init rate = 0.05 (35 / 641), avg. gap size = 1.31 (46 / 35) 455 32.10 3.59 2.98 chrXqtel1M 928524 929024 (70976) C L1M5_orf2#LINE/L1 (0) 3294 2791 m_b377s551i1 15739 chrXqtel1M 928524 TGATTTGGAGCACCTTTTCATGTGACTAGGAATAGTTTCAGTTTCTACAT 928573 ?v v i vi vviiivi v?i v v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chrXqtel1M 928574 CTGAAATTTGCCTGTTCATATCCTTTGACCATTTATCATTTGGACAA--T 928621 i vi vv i vi i v v ?vv iivi-- C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTT 3195 chrXqtel1M 928622 GGCTTGATTTCTTATAAATTTGAGTCAATTCTGTATATATTTTGGAAATG 928671 v -- ? vi ? vivv i v i v i C L1M5_orf2#LIN 3194 GTCTT--TTTNTTATTGANTTGTAGGAGTTCTTTATATATTCTGGATACG 3147 chrXqtel1M 928672 AGCTCTTTCTTAGA-ACCTTTGACTGAAAAAATGTTTTCCCAGTTTATTG 928720 ii v i - iv v -?i v v v i ? i i v C L1M5_orf2#LIN 3146 AGTCCTTTGTCAGATATATGT-NTTGCAAATATTTTCTCCCANTCTGTGG 3098 chrXqtel1M 928721 CTTCCCTTCTAA---TCTTATCTGCATTAGTTTTGTTTGTACAAAACTTT 928767 v i v --- v v ii i-- -v? vi i v C L1M5_orf2#LIN 3097 CTTGCCTTTTCATTTTCTTAACGGTGTC--TTTTG-ANGAGCAGAAGTTT 3051 chrXqtel1M 928768 TTTAACTTAATATGATCAA-------AATTTTCTATTTTGTGATCAATAA 928810 v vi i i?ii v ------- i v i i --- ?i C L1M5_orf2#LIN 3050 TTAATTTTGATGNAGTCCAATTTATCAATTTTTTCTTTTATGGT---TNG 3004 chrXqtel1M 928811 TGATCTCTATTTCTTCTTTGGCCACAATCTT--CCTCTTCCACGGGTCTG 928858 v i i i v i v ii--iv -- v?i -i vv C L1M5_orf2#LIN 3003 TGCTTTTTGTGTCCTGTTTAA--GAAATCTTTGCCTANCCCA-AGGTCAC 2957 chrXqtel1M 928859 AAAGGTAAACTGTCCTATG--TTCTTCTAATTTATTTATAATCTAATTCT 928906 i i -- i v -- ivvvv i i v ?ii C L1M5_orf2#LIN 2956 GAAGAT--ATTCTCCTATGTTTTCTTCTAGAAGTTTTATAGTTTTANCTT 2909 chrXqtel1M 928907 TTAGGCCTAGATC-ATGAACCTATTTTGAGGTTATCTTGGTGGATGGTGT 928955 viii i - v - i ? iv v i v v C L1M5_orf2#LIN 2908 TTACATTTAGGTCTATGATCC-ATCTNGAATTAATTTTTGTGTATGGTGT 2860 chrXqtel1M 928956 TAAGTGTGAGTTCATCCCTATTTTCTGCCATACTAGTCTCCAATTTTCCC 929005 v i iv i iv v?iii i v ivii v v i C L1M5_orf2#LIN 2859 GAGGTAGGGGTCGAGNTTCATTTTTTTCCATATGGATATCCAATTGTTCC 2810 chrXqtel1M 929006 AGCAGTTTTTGTCAAACAG 929024 viv ii v C L1M5_orf2#LIN 2809 AGCACCATTTGTTGAAAAG 2791 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.35 CpG sites = 82, Kimura (unadjusted) = 44.49 Transitions / transversions = 1.11 (82/74) Gap_init rate = 0.04 (22 / 500), avg. gap size = 1.50 (33 / 22) 417 32.92 4.07 3.47 chrXqtel1M 928567 929082 (70918) C L1P3_orf2#LINE/L1 (43) 3251 2733 m_b377s551i2 15739 chrXqtel1M 928567 TCTACATCTGAAATTTGCCTGTTCATATCCTTTGACCATTTATCATTTGG 928616 v v i i vv i i v i v iiv v C L1P3_orf2#LIN 3251 TCTTCTTTTGAGAAGTGTCTGTTCATATCCTTCGCCCACTTTTTGATGGG 3202 chrXqtel1M 928617 ACAATGGCTTG---ATTTCTTATAAATTTGAGTCAATTCTGTATATATTT 928663 ---i v i ---v i vv v i iv i v i C L1P3_orf2#LIN 3201 ---GTTGTTTGTTTTTTTCTTGTAAATTTGTTTAAGTTCCTTGTAGATTC 3155 chrXqtel1M 928664 TGGAAATGAGCTCTTTCTTAGAACCTTTGACTGAAAAAATGTTTTCCCAG 928713 v v i v i vvvv v i v v i v C L1P3_orf2#LIN 3154 TGGATATTAGCCCTTTGTCAGATGGATAGATTGCAAAAATTTTCTCCCAT 3105 chrXqtel1M 928714 TTTATTGCTTCCCT-TCTAATCTTATCTGCATTAGTTTTGTT---TGTAC 928759 i i v v v - ii v v ----iv iv --- i C L1P3_orf2#LIN 3104 TCTGTAGGTTGCCTGTTCACTCTGAT----GATAGTTTCTTTTGCTGTGC 3059 chrXqtel1M 928760 AAAACTTTTTTAACTTAATATGATCAAAATTTTCTATTTTGTGATCAATA 928809 i vi i ii vv vv v v v vvv ivi v C L1P3_orf2#LIN 3058 AGAAGCTCTTTAGTTTAATTAGATCCCATTTGTCAATTTTGGCTTTTGTT 3009 chrXqtel1M 928810 ATGATCTCTATTTCTTCTTTGGCCAC--AATCTT--CCTCTTCCACGGGT 928855 iiv iv v vv vi i i i-- i -- iv v vvv vi C L1P3_orf2#LIN 3008 GCCATTGCTTTTGGTGTTTTAGTCATGAAGTCTTTGCCCATGCCTATGTC 2959 chrXqtel1M 928856 CTGAAAGGTAAACTGTCCTATG--TTCTTCTAATTTATTTATAATCTAAT 928903 v -- i - v -- ivv v ii i v v C L1P3_orf2#LIN 2958 CTGAATGGT--ATTG-CCTAGGTTTTCTTCTAGGGTTTTTATGGTTTTAG 2912 chrXqtel1M 928904 TCTTTAGGCCTAGATCATGAACCTATTTTGAGGTTATCTTGGTGGATGGT 928953 vii v ii ii v v i i i v v i v iv v C L1P3_orf2#LIN 2911 GTCTTACGTTTAAGTCTTTAATCCATCTTGAGTTAATTTTTGTATAAGGT 2862 chrXqtel1M 928954 GTTAAGTGTGAGTTCA-TCCCTATTTTCTGCCATA---CTAGTCTCCAAT 928999 v i viv i i - ii vi - --- --- i C L1P3_orf2#LIN 2861 GTAAGGAAGGGGTCCAGTTTCAGTTTTCTG-CATATGGCTAG---CCAGT 2816 chrXqtel1M 929000 TTTCCCAGCAGTTTTTGTCAAACAGTGAATTCCTATTCCACA-AGCTGGG 929048 i viv i i i v - - v -v --v C L1P3_orf2#LIN 2815 TTTCCCAACACCATTTATTAAATAGGGAA-TCCT-TTCCCCATTGCT--T 2770 chrXqtel1M 929049 GTCTTTG---AGTTTGTCAAACACTAGATATCTATAG 929082 i ---i v ii ivi i C L1P3_orf2#LIN 2769 GTTTTTGTCAGGTTTGTCAAAGATCAGATGGTTGTAG 2733 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 43.51 CpG sites = 78, Kimura (unadjusted) = 43.86 Transitions / transversions = 0.91 (78/86) Gap_init rate = 0.05 (28 / 515), avg. gap size = 1.39 (39 / 28) 18 29.72 7.34 1.74 chrXqtel1M 930321 930429 (69571) (GA)n#Simple_repeat 1 115 (0) m_b377s252i3 15740 chrXqtel1M 930321 GAGAGAGAGAGACGA-AAAGACAGAGAGATAAATAAAAACAGAGGGAG-G 930368 - - i v v i v i i v i - (GA)n#Simple_ 1 GAGAGAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 49 chrXqtel1M 930369 AAAAAGAAAACTATGAGAG-GGGGGAGCAAG-GAAAAGGAG-GGGAGAGA 930415 i i i ivv - - i i vi - i ii - i (GA)n#Simple_ 50 AGAGAGAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 98 chrXqtel1M 930416 AGGAG-GAG-GAG-GAG 930429 ii - - - (GA)n#Simple_ 99 GAGAGAGAGAGAGAGAG 115 Matrix = Unknown Transitions / transversions = 2.57 (18/7) Gap_init rate = 0.09 (10 / 108), avg. gap size = 1.00 (10 / 10) 19 9.74 8.51 2.00 chrXqtel1M 930385 930431 (69569) (GAG)n#Simple_repeat 1 50 (0) m_b377s252i4 15740 chrXqtel1M 930385 GAGG-GG-GGAGCAAGGAAAAGGAGG-GGA-GAGAAGGAGGAGGAGGAGG 930430 - - -i ii - - i (GAG)n#Simple 1 GAGGAGGAGGAG-GAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGG 49 chrXqtel1M 930431 A 930431 (GAG)n#Simple 50 A 50 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.11 (5 / 46), avg. gap size = 1.00 (5 / 5) 353 33.96 2.91 4.12 chrXqtel1M 930469 930640 (69360) C MIR3#SINE/MIR (9) 199 30 m_b377s601i0 15741 chrXqtel1M 930469 AATCACAGA-TTTTA-AGGTGACAGGGACCCGGGAAGTGATCTGGTAGCA 930516 i - v i - v iv ivi ii v i ---- C MIR3#SINE/MIR 199 AATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGT---- 154 chrXqtel1M 930517 TATCCTATTTTTTTTTTTTTAAAAGAAAGAAACTGAGGTCTAGAGAAACC 930566 --- v iiiii iv vv i vi i i i iiiv C MIR3#SINE/MIR 153 ---CCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTG 107 chrXqtel1M 930567 AAAAGACTGGTTTAA-GTCACTTGG-TAGTAAATGGCAGAGCAAGGGTTC 930614 iv v iii - vii -? v i vi ii v C MIR3#SINE/MIR 106 AAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTA 57 chrXqtel1M 930615 AAATGCATGTGTCCTGA-TCCAAGGCC 930640 i iv v v - v v C MIR3#SINE/MIR 56 GAACCCAGGTCTCCTGACTCCCAGTCC 30 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 46.40 CpG sites = 34, Kimura (unadjusted) = 47.60 Transitions / transversions = 1.55 (34/22) Gap_init rate = 0.07 (12 / 171), avg. gap size = 1.00 (12 / 12) 367 33.33 3.42 1.34 chrXqtel1M 930495 930640 (69360) C MIRc#SINE/MIR (88) 180 32 m_b377s601i1 15741 chrXqtel1M 930495 CCCGGGAAGTGATCTGGTAGCATATCCTATTTTTTTTTTTTTA-AAAGAA 930543 i v i iiv v -- vi vi v iiiiv - i vi C MIRc#SINE/MIR 180 CCTGTGAGGTAGGCAGG--GCAGGTATTATTATCCCCATTTTACAGATGA 133 chrXqtel1M 930544 AGAAACTGAGGTCTAGAGAAACCAAAAGACTGGTTTAAG-TCACTTGG-T 930591 i iii iiii iv v iii - vii - C MIRc#SINE/MIR 132 GGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCT 83 chrXqtel1M 930592 AGTAAATGGCAGAGCAAGGGTTCAAATGCATGTG-TCCTGA-TCCAAGGC 930639 i vi ii i iv v v- - v C MIRc#SINE/MIR 82 AGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGACTCCAAGTC 33 chrXqtel1M 930640 C 930640 C MIRc#SINE/MIR 32 C 32 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 44.09 CpG sites = 32, Kimura (unadjusted) = 46.83 Transitions / transversions = 2.00 (32/16) Gap_init rate = 0.05 (7 / 145), avg. gap size = 1.00 (7 / 7) 89 32.05 2.43 0.00 chrXqtel1M 931567 931895 (68105) (TC)n#Simple_repeat 1 337 (0) m_b377s252i5 15742 chrXqtel1M 931567 TCTCTGT-TCTCTCTCTCTCTGTCTCTCTCCCCCTCTC-CCCACCTTCTC 931614 v - v i i - i v ii (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chrXqtel1M 931615 CCTCTCCTTCTCCCTCCTTCCCTCTCTCACTTTCTCTCTGTCTCTCT-TC 931663 i ii i ii i v i v - (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chrXqtel1M 931664 TTTCCCACTCTTTCT-TATTTTACTTTCTCTCTTGATC-CATTTTTTCTG 931711 i i v i - v i iv i ivv - vi i i v (TC)n#Simple_ 101 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 150 chrXqtel1M 931712 TCCCTGTTTCTCTCTGACTGTCTGTCTGTCTCTGTCTATGCCTCTCTTTC 931761 i v i vv v v v v v vi i (TC)n#Simple_ 151 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 200 chrXqtel1M 931762 TCTTTTACTATCTGTTTCTCTCTCTGTCTCTTTGTGTGTCTTTCTCTCT- 931810 i iv v v i v i v v v i - (TC)n#Simple_ 201 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 250 chrXqtel1M 931811 TTTCTATTTCTTGATGTTTTTCTGACTGTTCCTTTCTCTCT-TTTCTC-C 931858 i v i ivv v i i vv v ii i - i - (TC)n#Simple_ 251 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 300 chrXqtel1M 931859 TGTCTCTTTCACTCTTTGGCTCTCTGGCTCTCCCTCT 931895 v i v i vv vv i (TC)n#Simple_ 301 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 337 Matrix = Unknown Transitions / transversions = 1.07 (44/41) Gap_init rate = 0.02 (8 / 328), avg. gap size = 1.00 (8 / 8) 213 31.33 6.02 0.00 chrXqtel1M 933435 933517 (66483) C MIR3#SINE/MIR (3) 205 118 m_b377s601i2 15743 chrXqtel1M 933435 TCATCACATCATAGACCTTAAAAG-----AGAGAATCTGAATGTCATATA 933479 viv viv v i ----- i vii ii vi v C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTA 156 chrXqtel1M 933480 CAGCATCAGCTTCATTTTACAGATAAGGAAACTGAGAC 933517 vvv v vv i i i C MIR3#SINE/MIR 155 GTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGC 118 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.90 CpG sites = 12, Kimura (unadjusted) = 40.90 Transitions / transversions = 0.86 (12/14) Gap_init rate = 0.01 (1 / 82), avg. gap size = 5.00 (5 / 1) 224 17.14 0.00 0.00 chrXqtel1M 933483 933517 (66483) C MIR1_Amn#SINE/MIR (73) 157 123 m_b377s601i3 15743 chrXqtel1M 933483 CATCAGCTTCATTTTACAGATAAGGAAACTGAGAC 933517 i v ii i i C MIR1_Amn#SINE 157 CATTATCCCCATTTTACAGATGAGGAAACTGAGGC 123 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 20.34 CpG sites = 5, Kimura (unadjusted) = 20.34 Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 66 6.33 0.00 1.18 chrXqtel1M 934341 934426 (65574) (TTCT)n#Simple_repeat 1 85 (0) c_b377s251i1 15744 chrXqtel1M 934341 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT 934390 (TTCT)n#Simpl 1 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT 50 chrXqtel1M 934391 CTTTCTTCCTTCCTTCCTTCCTTCTTTTTCTTTCTT 934426 i i i i - i (TTCT)n#Simpl 51 CTTTCTTTCTTTCTTTCTTTCTT-TCTTTCTTTCTT 85 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.01 (1 / 85), avg. gap size = 1.00 (1 / 1) 119 0.00 0.00 0.00 chrXqtel1M 934452 934552 (65448) (TC)n#Simple_repeat 1 101 (0) c_b377s251i2 15745 chrXqtel1M 934452 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 934501 (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chrXqtel1M 934502 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 934551 (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 100 chrXqtel1M 934552 T 934552 (TC)n#Simple_ 101 T 101 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 100), avg. gap size = 0.0 (0 / 0) 694 29.98 6.37 5.35 chrXqtel1M 934583 935100 (64900) C L1ME3G_3end#LINE/L1 (395) 529 7 m_b377s551i3 15746 chrXqtel1M 934583 ATATGCCATAACTTATTCAGCTATTCCCCAATTGATGGGTTTCCAG---- 934628 i i i i i v iiv ii ---- C L1ME3G_3end#L 529 ATATACCATAATTTATTTAACCATTCCCCTATTGATGGACATTTAGGTTG 480 chrXqtel1M 934629 TTTCCGGGTCCTTGCCACTACAAAAGAT-CTGC--TG--CATTTTTGCAC 934673 iiv ii i i i vi - -- -- ii i C L1ME3G_3end#L 479 TTTCCAATTTTTCGCTATTACAAACAATGCTGCAATGAACATCCTTGTAC 430 chrXqtel1M 934674 CTGGGATTCCTTTTGC---TTTTTTAATGATCCCTATGGAATGAATAC-- 934718 v v?-- v --- v viv i - ii ? i i ii ? -- C L1ME3G_3end#L 429 ATGCN--TCCTTGTGCACATGTGCGAGT-ATTTCTNTAGGATAGATNCCN 383 chrXqtel1M 934719 --AAGCCTGGGAGACACCTTGCTGGGTTCAAAGATATGC-----TTGACG 934761 -- -- i ------ iv i i ----- i -- C L1ME3G_3end#L 382 AGAAG--TGGAA------TTGCTGGGTCAAAGGGTATGCGCATTTTAA-- 343 chrXqtel1M 934762 ATGGCCCTTTGG-GCATAGTTCCAAATTGCTCTTCTGATCATTTGGATCA 934810 ----- ii-iv v v i i vi v?ivi v i C L1ME3G_3end#L 342 AT-----TTTAATAGATACTGCCAAATTGCCCTCCAAAANGGCTGTACCA 298 chrXqtel1M 934811 GGTCACAACTCCACCTGTAATGTGTCAATATCCCAGTCTTCCCCCATCCC 934860 iv i vii v i i i v ivi v v i i v i i C L1ME3G_3end#L 297 ATTTACACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCCACACCCT 248 chrXqtel1M 934861 CTCTAGCATT---TATCATCAACTTTTCCTCTCATCTTAGCCCATCTGAA 934907 v i i i --- i ?i iv---v i v v v C L1ME3G_3end#L 247 CGCCAACACTNGATATTATCAANCTTTTA---AATTTTTGCCAATCTGAT 201 chrXqtel1M 934908 GGGTGTGTAGTGCTACCTCAAAATTGTCTTAATTTGCATTTCTCTGATCA 934957 viv i v i vvi i i i C L1ME3G_3end#L 200 GGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGATTA 151 chrXqtel1M 934958 GTAGTGATTTAGAGCATTTTCTC--ATGACTAGGAATGATTTTAATTTCT 935005 v vv v i i -- vi vviiiv vv i C L1ME3G_3end#L 150 CTAGTGAGGTTGAGCATCTTTTCATATGTTTATTGGCCATTTGTATTTCC 101 chrXqtel1M 935006 TCAAGTGAAAAT----TGTTCATATCCTTTGACAATTTATCAGTTGGAGA 935051 vvv vi ---- v v v vi i-- C L1ME3G_3end#L 100 TCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGGG-- 53 chrXqtel1M 935052 ATGGTTTGTATTTTTTCTA--AATATGAGGCAATTCTCTCTATATTTTAG 935099 ----- v ii --i v vi v i i v i i C L1ME3G_3end#L 52 -----TTGTCTTTTTCTTATTGATTTGTAGGAGTTCTTTATATATTCTGG 8 chrXqtel1M 935100 A 935100 C L1ME3G_3end#L 7 A 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.33 CpG sites = 87, Kimura (unadjusted) = 40.04 Transitions / transversions = 1.45 (87/60) Gap_init rate = 0.08 (41 / 517), avg. gap size = 1.49 (61 / 41) 12 8.49 0.00 7.41 chrXqtel1M 935257 935285 (64715) (TTTTA)n#Simple_repeat 1 27 (0) m_b377s252i6 15747 chrXqtel1M 935257 TTTTTTTTTATTGTGTATATTATTTTATT 935285 v - - v (TTTTA)n#Simp 1 TTTTATTTTATT-T-TATTTTATTTTATT 27 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.07 (2 / 28), avg. gap size = 1.00 (2 / 2) 15 13.86 0.00 0.00 chrXqtel1M 935471 935494 (64506) (A)n#Simple_repeat 1 24 (0) m_b377s252i7 15748 chrXqtel1M 935471 AAAAAAAAAAACAGAAAAAAGAAA 935494 v i i (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAA 24 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 60 0.00 0.00 0.00 chrXqtel1M 935622 935672 (64328) (TC)n#Simple_repeat 1 51 (0) c_b377s251i3 15749 chrXqtel1M 935622 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 935671 (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chrXqtel1M 935672 T 935672 (TC)n#Simple_ 51 T 51 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 30 0.00 0.00 6.06 chrXqtel1M 936101 936135 (63865) (TC)n#Simple_repeat 1 33 (0) c_b377s251i4 15750 chrXqtel1M 936101 TCTCTCTGCATCTCTCTCTCTCTCTCTCTCTCTCT 936135 - - (TC)n#Simple_ 1 TCTCTCT-C-TCTCTCTCTCTCTCTCTCTCTCTCT 33 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 206 33.85 3.08 0.00 chrXqtel1M 936726 936790 (63210) C MIRb#SINE/MIR (134) 134 68 m_b377s601i4 15751 chrXqtel1M 936726 GAGACTGAGGTCTGGAGAAAGTAAATAACTGGTTTAA-ATCATTTGG-TA 936773 i iiii iiv i v iii -i ivii - C MIRb#SINE/MIR 134 GAAACTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTA 85 chrXqtel1M 936774 ATAAATAGCAGAGCCAG 936790 i i i i C MIRb#SINE/MIR 84 GTAAGTGGCAGAGCCGG 68 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 48.62 CpG sites = 19, Kimura (unadjusted) = 52.24 Transitions / transversions = 6.33 (19/3) Gap_init rate = 0.03 (2 / 64), avg. gap size = 1.00 (2 / 2) 18 17.57 0.00 0.00 chrXqtel1M 937086 937117 (62883) (T)n#Simple_repeat 1 32 (0) m_b377s252i9 15752 chrXqtel1M 937086 TTTATTTTTATTTTATTTTTTTTGTTTCTTTT 937117 v v v v i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 32 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 16 25.87 1.75 1.75 chrXqtel1M 937254 937310 (62690) (TCAA)n#Simple_repeat 1 57 (0) m_b377s252i10 15753 chrXqtel1M 937254 TCAAACAATCAAT-TATCAATTCACTTTATTAATTTATCAATTAATTGAT 937302 v -v - v iv i iv i ii (TCAA)n#Simpl 1 TCAATCAATCAATCAATCAA-TCAATCAATCAATCAATCAATCAATCAAT 49 chrXqtel1M 937303 CATTCAAT 937310 v (TCAA)n#Simpl 50 CAATCAAT 57 Matrix = Unknown Transitions / transversions = 1.00 (6/6) Gap_init rate = 0.04 (2 / 56), avg. gap size = 1.00 (2 / 2) 94 4.00 0.94 0.94 chrXqtel1M 937834 937939 (62061) (CT)n#Simple_repeat 1 106 (0) c_b377s251i5 15754 chrXqtel1M 937834 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-CCCCCTCTCTCT 937882 - i i (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chrXqtel1M 937883 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCCATCTCTCTTTC 937932 i - i (CT)n#Simple_ 51 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TCTCTCTCTC 99 chrXqtel1M 937933 TCTCTCT 937939 (CT)n#Simple_ 100 TCTCTCT 106 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.02 (2 / 105), avg. gap size = 1.00 (2 / 2) 15 12.03 0.00 0.00 chrXqtel1M 938417 938443 (61557) (CTGT)n#Simple_repeat 1 27 (0) m_b377s252i11 15755 chrXqtel1M 938417 CTGTTTGTATGTCTGTCTGTCTTTCTG 938443 i v v (CTGT)n#Simpl 1 CTGTCTGTCTGTCTGTCTGTCTGTCTG 27 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 12 21.40 4.44 2.17 chrXqtel1M 938468 938512 (61488) (ACAGA)n#Simple_repeat 1 46 (0) m_b377s252i12 15756 chrXqtel1M 938468 ACAGAAAAGAGACAGAACAGAA-GGAA-AGATTTGAATGGAAAAGAA 938512 v - -i - viv ii v (ACAGA)n#Simp 1 ACAGAACAGA-ACAGAACAGAACAGAACAGAACAGAACAGAACAGAA 46 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.07 (3 / 44), avg. gap size = 1.00 (3 / 3) 15 24.42 2.00 2.00 chrXqtel1M 938662 938711 (61289) (AAT)n#Simple_repeat 1 50 (0) m_b377s252i13 15757 chrXqtel1M 938662 AATAAGAAAAATAAGAAAGAGAA-AAGGAAAATAATCATAAATAATAATA 938710 v v v vi v - vi v v - (AAT)n#Simple 1 AATAATAATAATAATAATAATAATAATAATAATAATAAT-AATAATAATA 49 chrXqtel1M 938711 A 938711 (AAT)n#Simple 50 A 50 Matrix = Unknown Transitions / transversions = 0.25 (2/8) Gap_init rate = 0.04 (2 / 49), avg. gap size = 1.00 (2 / 2) 12 20.52 5.13 0.00 chrXqtel1M 938858 938896 (61104) (GAG)n#Simple_repeat 1 41 (0) m_b377s252i14 15758 chrXqtel1M 938858 GAGAAGGAGGA-AAGTAGGAGG-GGAGCTGGTGGTGGAGGA 938896 i -i v - vv v v (GAG)n#Simple 1 GAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA 41 Matrix = Unknown Transitions / transversions = 0.40 (2/5) Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2) 18 11.69 0.00 0.00 chrXqtel1M 938932 938959 (61041) (GT)n#Simple_repeat 1 28 (0) m_b377s252i15 15759 chrXqtel1M 938932 GTGTGTGTATGTGTATGGGTGTGTGTGT 938959 i i v (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGT 28 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 47 18.65 4.20 4.20 chrXqtel1M 938970 939112 (60888) (AGAGGG)n#Simple_repeat 1 143 (0) m_b377s252i16 15760 chrXqtel1M 938970 AGAGGGAGAGAGAGAGAAAGCAAAAAGGGGCAGAGGGAGAGGGGGAGAGA 939019 i ii - iii i v i i (AGAGGG)n#Sim 1 AGAGGGAGAGGGAGAGGGAG-AGGGAGAGGGAGAGGGAGAGGGAGAGGGA 49 chrXqtel1M 939020 GAGGGAGAAGGGGAGAAGGGAGAGGGAGA--GAGATGAATA-GGAG-GGG 939065 - - - -- v i v - - (AGAGGG)n#Sim 50 GAGGGAG-A-GGGAG-AGGGAGAGGGAGAGGGAGAGGGAGAGGGAGAGGG 96 chrXqtel1M 939066 AGAAGGAGGAAAGAAATGGGAGAGGG-GAGAGAG-GGAAGAGGAGGAGG 939112 i - ii i - - i - i ii (AGAGGG)n#Sim 97 AGAGGGA-GAGGGAGA-GGGAGAGGGAGAGGGAGAGGGAGAGGGAGAGG 143 Matrix = Unknown Transitions / transversions = 6.00 (18/3) Gap_init rate = 0.08 (11 / 142), avg. gap size = 1.09 (12 / 11) 384 32.98 2.87 5.92 chrXqtel1M 939150 939323 (60677) C MIR3#SINE/MIR (9) 199 31 m_b377s601i5 15761 chrXqtel1M 939150 AATCACAGATTTT--GAGATGAGAGGGACTCTGGAAGTGATCTGGTAGCA 939197 i v v -- v ii ii i ii v i vvv C MIR3#SINE/MIR 199 AATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAA 150 chrXqtel1M 939198 CCTCCT-ATTTTTTTCAAACTAATAAATGAAGAAACTGAGGTCTAGAGAA 939246 i - ---------- i i i i i i C MIR3#SINE/MIR 149 CCCCCTCATTTT----------ACAGATGAGGAAACTGAGGCCCAGAGAG 110 chrXqtel1M 939247 AGTAAATGGTTGGCTCAA-GTGACTTGG-TAGTAGATTGCAGAGCCAGGA 939294 ivv i ii v i - v vii -? vii v i C MIR3#SINE/MIR 109 GTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGA 60 chrXqtel1M 939295 TCCAAATGCATGTGTTCTGATGCCTCATC 939323 iivi iv v v i iv ivi C MIR3#SINE/MIR 59 CTAGAACCCAGGTCTCCTGACTCCCAGTC 31 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 44.67 CpG sites = 34, Kimura (unadjusted) = 45.85 Transitions / transversions = 1.70 (34/20) Gap_init rate = 0.08 (14 / 173), avg. gap size = 1.07 (15 / 14) 358 34.07 2.17 2.17 chrXqtel1M 939219 939356 (60644) C MIRc#SINE/MIR (128) 140 3 m_b377s601i6 15761 chrXqtel1M 939219 ATAAATGAAGAAACTGAGGTCTAGAGAAAGTAAATGGTTGGCTCAA-GTG 939267 i i i iii iiv i ii v i - v C MIRc#SINE/MIR 140 ACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTC 91 chrXqtel1M 939268 ACTTGG-TAGTAGATTGCAGAGCCAGGATCCAAATGCATGTGTT-CTGAT 939315 vii - ii v i ii i iv v v - i C MIRc#SINE/MIR 90 ACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCTGAC 41 chrXqtel1M 939316 GCCTCATCTAAGGCCCATTAAGACTGTAAGTCACATTGTTT 939356 v vvi i iv i - vvv i --i i ii C MIRc#SINE/MIR 40 TCCAAGTCCAGTGCTC-TTTCCACTGCA--CCACACTGCCT 3 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 45.51 CpG sites = 31, Kimura (unadjusted) = 48.52 Transitions / transversions = 2.07 (31/15) Gap_init rate = 0.04 (6 / 137), avg. gap size = 1.00 (6 / 6) 827 31.28 4.25 4.93 chrXqtel1M 940436 941047 (58953) C L1PA6_3end#LINE/L1 (293) 608 1 m_b377s551i4 15762 chrXqtel1M 940436 TTCAGCATCAGTCCATGTCATCCTTTCCAGGCATAAGATCAGGTTATTCA 940485 i v - -- ------ v i - v v- i C L1PA6_3end#LI 608 TCCAGCTTCA-TCCATGTC--CCT------GCAAAGGA-CATGA-ACTCA 570 chrXqtel1M 940486 ACATTTTTTA-------ATGATATTCCGTAACCTACATATACCACAACTT 940528 v v ------- ii i iiiv i i i vi C L1PA6_3end#LI 569 TCCTTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCACATTTT 520 chrXqtel1M 940529 GGTCAGCCACTCCCCAGTTGATGGGCATCCACTCATTG--TCCAGTGCTT 940576 vv v v v ivivi i iiiv--i -- ivv C L1PA6_3end#LI 519 CTTAATCCAGTCTATCATTGATGGACATTTGG--GTTGGTTCCAAGTCTT 472 chrXqtel1M 940577 TGCTACCA-AAACAG--CTGCTACAAACACTCTTGCACATGTGGGTCCTT 940623 iii-i i -- i v i iv v ii -- i C L1PA6_3end#LI 471 TGCTATTGTGAATAGTGCCGCAATAAACATACGTGTGCATGTG--TCTTT 424 chrXqtel1M 940624 TT----CCATCCTCTATGATTTCCTTGGGACACAGGCCAAGAAATGTCAC 940669 v ----v vv i i -- v ii i vi v v vv i C L1PA6_3end#LI 423 ATAGTAGCATGATTTATAAT--CCTTTGGGTATATACCCAGTAATGGGAT 376 chrXqtel1M 940670 TGCTGGGTCAAAGGGCATGCAGAGTTTGATGGGCCTTAGGGCATAGTTCC 940719 i v i vivv iv - iv ii v v -- C L1PA6_3end#LI 375 CGCTGGGTCAAATGGTATTTCTAGTTCTA-GATCCTTGAGGAATCG--CC 329 chrXqtel1M 940720 AGATGGCTTTGTAGAATGGTTGGATCATTTCACAACTCCC-CCAACAAAG 940768 v iv ii vi v i ii v i - - iv C L1PA6_3end#LI 328 ACACTGTCTTCCACAATGGTTGAACTAGTTTACA-CTCCCACCAACAGTG 280 chrXqtel1M 940769 TATCAGTATCCCAGTTTTCCCACATCCCCTCCCACATTTACCATTATCTT 940818 vv ii i vi ii i vi i i--- i --- C L1PA6_3end#LI 279 TAAAAGCGTTCCTATTTCTCCACATCCTCTCCAGCATCTG---TTGT--- 236 chrXqtel1M 940819 TTCCTGTCATCTTA------GCCAATCTGACACGTGTGAGGTGACACCTC 940862 v v i ------ v i vv i i ii i C L1PA6_3end#LI 235 TTCCTGACTTTTTAATGATCGCCATTCTAACTGGCGTGAGATGGTATCTC 186 chrXqtel1M 940863 AGAGTTGTTTAAATTCACATTTCTCTAATCAATAGTGATTTAGAGCATTT 940912 vv v vi ii i v vi vvv C L1PA6_3end#LI 185 ATTGTGGTTTTGATTTGCATTTCTCTGATGACCAGTGATGATGAGCATTT 136 chrXqtel1M 940913 TATGACATGACTATAGATGGCTTTAATTTCATCATCTGAAAATTGTCTGT 940962 v v ii v i v iiv v v v v v i i v C L1PA6_3end#LI 135 TTTCATGTGTCTGTTGGCTGCATAAATGTCTTCTTTTGAGAAGTGTCTGT 86 chrXqtel1M 940963 TTGTATCCTTTGACTATTTATTCACTGGGCAATGATTTGTATT---CTTG 941009 ii v i i v v - --i vi v --- C L1PA6_3end#LI 85 TCATATCCTTTGCCCACTTTTTGA-TGGG--GTTGTTTGTTTTTTTCTTG 39 chrXqtel1M 941010 TAAATTTGACACAGTTCTTTATGTATTTTTGAAATGAG 941047 vivv i iv i v v v C L1PA6_3end#LI 38 TAAATTTGTTTAAGTTCTTTGTAGATTCTGGATATTAG 1 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.03 CpG sites = 96, Kimura (unadjusted) = 41.23 Transitions / transversions = 1.12 (96/86) Gap_init rate = 0.06 (38 / 611), avg. gap size = 1.47 (56 / 38) 1155 30.68 3.30 3.30 chrXqtel1M 940496 941041 (58959) C L1ME5_3end#LINE/L1 (389) 552 7 m_b377s551i5 15762 chrXqtel1M 940496 ATGATATTCCGTAACCTACATATACCACAACTTGGTCAGCCACTC-CCCA 940544 ii i i iiiv i vi vi ivii v - C L1ME5_3end#LI 552 ATAGTACTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCA 503 chrXqtel1M 940545 GTTGATGGGCATCCACTCATTG--TCCAGTGCTTTGCTACCA-AAACA-- 940589 - i i v--i -- iiv iii i - -- C L1ME5_3end#LI 502 GT-GATGGACACCCAG--GTTGCCTCCAACTCCCCGCCACCACAAACAAC 456 chrXqtel1M 940590 GCTGCTACAAACACTCTTGCACATGTGGGTCCTTTTCCATCCTCTATGA- 940638 v ii ii i i ---i i viviv v i - C L1ME5_3end#LI 455 GCTGCAATGAACATCCTCGTACATGT---CCCCTTATGGACCTGTGTGAG 409 chrXqtel1M 940639 --TTTCCTTGGGACACAGGCCAAGAAATGTCACTGCTGGGTCAAAGGGCA 940686 -- i i i vi v i ii vv i v i C L1ME5_3end#LI 408 AATTTCTTTGGGATATATACCCAGGAGCGGAATTGCTGGGTCATAGGGTA 359 chrXqtel1M 940687 TGCAGA-GTTTGATGGGCCTTAGGGCATAGTTCCAGATGGCTTTGTAGAA 940735 iv -ii i vv v v ---- v v v i vi C L1ME5_3end#LI 358 TGCGTATACTTAATTTGACTAAG----TACTGCCAGATTGCTCTCCAGAA 313 chrXqtel1M 940736 TGGTTGGATCATTTCACAACTCCC-CCAACAAAGTATCAGTATCCCAGTT 940784 i v i v ii - - i iv i v vi i vi ? C L1ME5_3end#LI 312 TGGCTGCACCAGTCTACA-CTCCCACCAGCAGTGCATGAGGGTTCCTATN 264 chrXqtel1M 940785 TTCCCACATCCCCTCCCACATTTACCATTATCT---TTTCCTGTCATCTT 940831 i i v v i iv i--- --- v i C L1ME5_3end#LI 263 TCCCCACATCCTCGCCAACACTTGGCATTATCCAGCTTTC---TAATTTT 217 chrXqtel1M 940832 AGCCAATCTGACACGTGTGAGGTGACACCTCAGAGTTGTTTAAATTCACA 940881 v i i i v i i i i vv v ii C L1ME5_3end#LI 216 TGCCAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCA 167 chrXqtel1M 940882 TTTCTCTAATCAATAGTGATTTAGAGCATTTTATGACATGACTATAGATG 940931 i i v i v v i iv v i vi i --- i C L1ME5_3end#LI 166 TTTCTCTGATTACTAATGAGTTTGAGCATCTCTTCATATGCTTGT---TA 120 chrXqtel1M 940932 GCTTT---AATTTCATCATCTGAAAATTGTCTGTTTGTATCCTTTGACTA 940978 i ---ii v v v i ii v i C L1ME5_3end#LI 119 GCCTTTCGGGTTTCCTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCCA 70 chrXqtel1M 940979 TTTATTCACT-GGGCAATGATTTGTATTCTTGTAAATTTGACACAGTTCT 941027 v ii i - iv?ivi i v - vi vviv i C L1ME5_3end#LI 69 TTTTTCTATTGGGGTTNCCGTCTTT-TTCTTGTTGATTTGCAGGAGTTCC 21 chrXqtel1M 941028 TTATGTATTTTTGA 941041 i i i v C L1ME5_3end#LI 20 TTGTATATTCTAGA 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.63 CpG sites = 102, Kimura (unadjusted) = 41.32 Transitions / transversions = 1.70 (102/60) Gap_init rate = 0.05 (29 / 545), avg. gap size = 1.24 (36 / 29) 263 29.94 2.76 2.20 chrXqtel1M 940898 941078 (58922) C L1P4_orf2#LINE/L1 (0) 3294 3113 m_b377s551i6 15762 chrXqtel1M 940898 TGATTTAGAGCATTTTATGACATGACTATAGATGGCTTTAATTTCATCAT 940947 v v v v i vi i v iiv vv v v v C L1P4_orf2#LIN 3294 TGATGTTGAGCATTTTTTCATATGTTTGTTGGCCGCTTGTATGTCTTCTT 3245 chrXqtel1M 940948 CTGAAAATTGTCTGTTTGTATCCTTTGACTATTTATTCACTGGGCAATGA 940997 i i v ii i v i i - i v --i v C L1P4_orf2#LIN 3244 TTGAGAAGTGTCTGTTCATGTCCTTTGCCCACTT-TTTAATGGG--GTTA 3198 chrXqtel1M 940998 TTTGTATT---CTTGTAAATTTGACACAGTTCTTTATGTATTTTTGAAAT 941044 v --- vi ? vivv i iv i v v C L1P4_orf2#LIN 3197 TTTGTTTTTTGCTTGTTGANTTGTTTAAGTTCCTTATAGATTCTGGATAT 3148 chrXqtel1M 941045 GAGATGTTTAACAGA-G-ATGGCATTATGAATATTT 941078 v iv iv i - - i i- ii C L1P4_orf2#LIN 3147 TAGACCTTTGTCGGATGCATAGT-TTGCGAATATTT 3113 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 37.13 CpG sites = 26, Kimura (unadjusted) = 38.95 Transitions / transversions = 0.96 (26/27) Gap_init rate = 0.04 (7 / 180), avg. gap size = 1.29 (9 / 7) 68 0.00 1.56 0.00 chrXqtel1M 942183 942246 (57754) (TTCC)n#Simple_repeat 1 65 (0) c_b377s251i6 15763 chrXqtel1M 942183 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC-T 942231 - (TTCC)n#Simpl 1 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 50 chrXqtel1M 942232 CCTTCCTTCCTTCCT 942246 (TTCC)n#Simpl 51 CCTTCCTTCCTTCCT 65 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.02 (1 / 63), avg. gap size = 1.00 (1 / 1) 64 17.64 1.15 6.67 chrXqtel1M 942247 942420 (57580) (CCCTC)n#Simple_repeat 1 165 (0) m_b377s252i18 15764 chrXqtel1M 942247 CCCTCCCCTCCCCTCCCCTCCCCTCTCCTCTCCTCTCCTCAACCTCTCCT 942296 i i i -v i (CCCTC)n#Simp 1 CCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTC-CCCTCCCCT 49 chrXqtel1M 942297 CAACCTTTCCCTCTCC-CCCTTCCCCTTCCCCTCCCCCTCCCCTCACTCT 942345 -- i i i - i - - - i (CCCTC)n#Simp 50 C--CCCTCCCCTCCCCTCCCCTCCCC-TCCCCT-CCCCTCCCCTC-CCCT 94 chrXqtel1M 942346 CCCCTTCCCTTCCCCTTCTTTCTCTCTCTCCCTCTCCTCCTCCCTCTTCT 942395 - i i ii - i - i i i i i i (CCCTC)n#Simp 95 CCCC-TCCCCTCCCCTCCCCTC-CCCTC-CCCTCCCCTCCCCTCCCCTCC 141 chrXqtel1M 942396 CCTCCCTCTCTCCCT-CTCTCTCCTC 942420 - - - i i (CCCTC)n#Simp 142 CCTCCC-CTC-CCCTCCCCTCCCCTC 165 Matrix = Unknown Transitions / transversions = 22.00 (22/1) Gap_init rate = 0.08 (13 / 173), avg. gap size = 1.00 (13 / 13) 65 1.70 0.00 0.00 chrXqtel1M 942700 942759 (57241) (TC)n#Simple_repeat 1 60 (0) c_b377s251i7 15765 chrXqtel1M 942700 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTTCTC 942749 i (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chrXqtel1M 942750 TCTCTCTCTC 942759 (TC)n#Simple_ 51 TCTCTCTCTC 60 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 59), avg. gap size = 0.0 (0 / 0) 16 26.14 1.75 1.75 chrXqtel1M 943025 943081 (56919) (AGACAC)n#Simple_repeat 1 57 (0) m_b377s252i19 15766 chrXqtel1M 943025 AGATACAGAAACAGTGA-AGCAGCCACACACACACAGACACACAGAGAGA 943073 i v vv - - vv v v v v v v (AGACAC)n#Sim 1 AGACACAGACACAGACACAG-ACACAGACACAGACACAGACACAGACACA 49 chrXqtel1M 943074 GACACAGA 943081 (AGACAC)n#Sim 50 GACACAGA 57 Matrix = Unknown Transitions / transversions = 0.09 (1/11) Gap_init rate = 0.04 (2 / 56), avg. gap size = 1.00 (2 / 2) 18 17.86 0.00 0.00 chrXqtel1M 943048 943079 (56921) (CA)n#Simple_repeat 1 32 (0) m_b377s252i20 15767 chrXqtel1M 943048 CACACACACACAGACACACAGAGAGAGACACA 943079 v v v v v (CA)n#Simple_ 1 CACACACACACACACACACACACACACACACA 32 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 83 35.90 1.93 0.96 chrXqtel1M 943059 943472 (56528) (AG)n#Simple_repeat 1 418 (0) m_b377s252i21 15767 chrXqtel1M 943059 AGACACACAGAGAGAGACACAGAGAGGGAAAGATTGAGTGTGAGTGGGGA 943108 v v v v v i i vv v v v i ii (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50 chrXqtel1M 943109 ATAAATGAGAAACAGAGAGCCAGAGAGATAGTGAGAGTGACAGACAGAGA 943158 v i - i v vv v v v v v (AG)n#Simple_ 51 AGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 99 chrXqtel1M 943159 -AAAGA-AAAGATATTTTCTGAGA-AAAAAGAAAGAGACAGACAGGAAAA 943205 - i - i v vvvvvv - i i i v v ii i (AG)n#Simple_ 100 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 149 chrXqtel1M 943206 AAGAGAGGCAGCTAGAAAGGGCAG-GAGAGAGATAGAGAGAAAGA-AGA- 943252 i iv vv i i - - v i - - (AG)n#Simple_ 150 GAGAGAGAGAGAGAGAGAGAG-AGAGAGAGAGAGAGAGAGAGAGAGAGAG 198 chrXqtel1M 943253 AGATATAGTCAGAGAGAAAGAGTGAAAAATAGAGGAAGAAAAAGGCATAG 943302 v v vv i v i i v ii i i iv v (AG)n#Simple_ 199 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 248 chrXqtel1M 943303 AGGAATACAGAGAGACAGA-AAAGAGAGAGAAAGAGAGGAATAAAGTCAG 943351 ii v v v - i i ii v i vv (AG)n#Simple_ 249 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 298 chrXqtel1M 943352 TAAATAAATA-ATAAAGAGACAAAGACAGTGAGACAGAGCCACAGAGAGA 943400 - i v i v - v i v i v v v vv v (AG)n#Simple_ 299 -AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 347 chrXqtel1M 943401 GAAAAAGAGAGTGACAGATATACAAAAGGAGACAGAGACAAAGACACAGA 943450 i i v v v v v i ii v v i v v (AG)n#Simple_ 348 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 397 chrXqtel1M 943451 CTGAGAGCAGACTCAGAGATAG 943472 vv - vvv v (AG)n#Simple_ 398 GAGAGAG-AGAGAGAGAGAGAG 418 Matrix = Unknown Transitions / transversions = 0.63 (45/71) Gap_init rate = 0.03 (12 / 413), avg. gap size = 1.00 (12 / 12) 44 4.40 0.00 0.00 chrXqtel1M 943515 943561 (56439) (AG)n#Simple_repeat 1 47 (0) c_b377s251i8 15768 chrXqtel1M 943515 AGAGAGAGAGATAGACAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 943561 v v (AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 47 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 18 28.84 7.48 1.77 chrXqtel1M 943804 943910 (56090) (GA)n#Simple_repeat 1 113 (0) m_b377s252i22 15769 chrXqtel1M 943804 GAGAGAGAAAGAGACGA-AAAGACAGAAACATAAAAACAGAGGGAG-GAA 943851 i - - i v i v v i i v i - i (GA)n#Simple_ 1 GAGAGAGAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 49 chrXqtel1M 943852 AAAGAAAAATATGAGAG-GGGGGAGCAAG-GAAAGGCAG-GGGAGAGAGG 943898 i i i v - - i i vi - i iv - i i (GA)n#Simple_ 50 AGAGAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 98 chrXqtel1M 943899 GAG-GAG-GAG-GAG 943910 - - - (GA)n#Simple_ 99 GAGAGAGAGAGAGAG 113 Matrix = Unknown Transitions / transversions = 2.43 (17/7) Gap_init rate = 0.09 (10 / 106), avg. gap size = 1.00 (10 / 10) 383 30.49 3.55 2.94 chrXqtel1M 943950 944118 (55882) C MIR3#SINE/MIR (9) 199 30 m_b377s601i7 15770 chrXqtel1M 943950 AATCACAGA-TCTTA-AGGTGACAGGGACTAGGGAAGTGATCTGGTAGCA 943997 i - v i - v iv ivvi ii v i vvv C MIR3#SINE/MIR 199 AATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAA 150 chrXqtel1M 943998 CCTCCT-ATTTTTTTAAAAAAAGGAAGAAACTGAGGTCTAGAGAAACCAA 944046 i - ----- v i v i i i iiiv C MIR3#SINE/MIR 149 CCCCCTCATTTT-----ACAGATGAGGAAACTGAGGCCCAGAGAGGTGAA 105 chrXqtel1M 944047 AAGACTGGTTTAA-GTCACTTGG-TAGTAAATGGCAGAGCCAGGGTTCAA 944094 iv v iii - vii -? v i i ii vi C MIR3#SINE/MIR 104 GTGACTTGCCCAAGGTCACACAGCNAGTTAGTGGCAGAGCCGGGACTAGA 55 chrXqtel1M 944095 ATGCACGTGTCCTGA-TCCAAGGCC 944118 iv v v - v v C MIR3#SINE/MIR 54 ACCCAGGTCTCCTGACTCCCAGTCC 30 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 39.37 CpG sites = 28, Kimura (unadjusted) = 40.42 Transitions / transversions = 1.27 (28/22) Gap_init rate = 0.07 (11 / 168), avg. gap size = 1.00 (11 / 11) 44 28.39 4.55 2.68 chrXqtel1M 944178 944397 (55603) (TTAA)n#Simple_repeat 1 224 (0) m_b377s252i23 15771 chrXqtel1M 944178 TTCATCAATT-TTTAGTTAATTAATT-ACCAATTAATTTTATTAACTTAC 944225 v i -v i - ii - v - v (TTAA)n#Simpl 1 TTAATTAATTAATTAATTAATTAATTAATTAATTAA-TTAATTAA-TTAA 48 chrXqtel1M 944226 CT-ATCAATTAATTTATCAGTCAATTAAAT-CCTCGTTAAGCCA-AAATA 944272 i - i v i i i v -vi vi viv -v v (TTAA)n#Simpl 49 TTAATTAATTAATTAATTAATTAATTAATTAATTAATTAATTAATTAATT 98 chrXqtel1M 944273 AGTTCTGTTGATTAATTAAATTTATTAATCAATTAATTAGTTAACTAA-G 944321 i -vi i - v i i i -v (TTAA)n#Simpl 99 AATT-AATTAATTAATT-AATTAATTAATTAATTAATTAATTAATTAATT 146 chrXqtel1M 944322 AATTGATTCAATTGATTTATCAACCCATTGA-TGATTAA-TATTGTTAGT 944369 i - i v i iiv i - i - v - v v (TTAA)n#Simpl 147 AATTAATT-AATTAATTAATTAATTAATTAATTAATTAATTAAT-TAATT 194 chrXqtel1M 944370 AATTAATTTCATGATTAATT--TTAATTAA 944397 vvv i -- (TTAA)n#Simpl 195 AATTAATTAATTAATTAATTAATTAATTAA 224 Matrix = Unknown Transitions / transversions = 1.13 (26/23) Gap_init rate = 0.07 (15 / 219), avg. gap size = 1.07 (16 / 15) 16 15.86 0.00 0.00 chrXqtel1M 944412 944439 (55561) (T)n#Simple_repeat 1 28 (0) m_b377s252i24 15772 chrXqtel1M 944412 TTTATTTTTATTTTTTTTTGTTTCTTTT 944439 v v v i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 28 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 87 32.81 2.08 0.29 chrXqtel1M 945043 945378 (54622) (CT)n#Simple_repeat 1 342 (0) m_b377s252i25 15773 chrXqtel1M 945043 CTGTCTCTGTCATATAT-TCTCTCTCTGTCTCTGTCTCTGTTTCTCTC-C 945090 v v - v v - v v v i - (CT)n#Simple_ 1 CTCTCTCTCTC-TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 49 chrXqtel1M 945091 CCCCTCCCCCTCTCCCTCTCCTTCTCCCTCCTTCCCTCTCTCACTTTCTC 945140 i i i i i ii i ii i v i (CT)n#Simple_ 50 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 99 chrXqtel1M 945141 TCTGTCTCTCT-TCTTTCTGACTCT-TTTATTTTCCTTTCTCTCTTGATC 945188 v - i vv - i v i ii i ivv (CT)n#Simple_ 100 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 149 chrXqtel1M 945189 CATTTTTTTCTGTCCCTGTTTCTCTCTGACTCTGTCTCTGTCTATGCCTC 945238 iv i i i v i v i vv v v v vi (CT)n#Simple_ 150 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 199 chrXqtel1M 945239 TCTTTCTCTTTTACTATCTGTTTCTCTCTCTGTCTCTTTGTGTGTCTTTC 945288 i i iv v v i v i v v v i (CT)n#Simple_ 200 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 249 chrXqtel1M 945289 TCTCT-TTTCTATTTCTTGATGTTTTTCTGACTGTTCCTTTCTCTCT-TT 945336 - i v i ivv v i i vv v ii i - i (CT)n#Simple_ 250 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 299 chrXqtel1M 945337 TCTC-CTGTCTCTTTCACTCTTTGGCTCTCTGGCTCTCCCTCT 945378 - v i v i vv vv i (CT)n#Simple_ 300 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 342 Matrix = Unknown Transitions / transversions = 1.05 (45/43) Gap_init rate = 0.02 (8 / 335), avg. gap size = 1.00 (8 / 8) 246 18.68 7.32 8.64 chrXqtel1M 946925 947006 (52994) C MIR1_Amn#SINE/MIR (27) 203 123 m_b377s601i8 15774 chrXqtel1M 946925 CTTTGCATCA-TAGACCTTAAAAAAGAGACTTT-----GAATGTCATGTA 946968 v - i i iv ---- ----- i v - C MIR1_Amn#SINE 203 CTTTTCATCAGTAGATCTCAAAGCA----CTTTACAAAGGAGGTCA-GTA 159 chrXqtel1M 946969 CATCATCAGCTTCATTTTAGAGATATGGAAACTGAGGC 947006 -- i v ii v iv C MIR1_Amn#SINE 158 --TCATTATCCCCATTTTACAGATGAGGAAACTGAGGC 123 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 21.72 CpG sites = 8, Kimura (unadjusted) = 21.72 Transitions / transversions = 1.33 (8/6) Gap_init rate = 0.11 (9 / 81), avg. gap size = 1.44 (13 / 9) 12 20.84 0.00 2.94 chrXqtel1M 947825 947859 (52141) (TATTT)n#Simple_repeat 1 34 (0) m_b377s252i26 15775 chrXqtel1M 947825 TATTTTATTTTATTTTTTAATTATAGCTTTTTATT 947859 v -v vviv (TATTT)n#Simp 1 TATTTTATTTTATTTTAT-TTTATTTTATTTTATT 34 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 13 0.00 0.00 0.00 chrXqtel1M 947929 947945 (52055) (ATT)n#Simple_repeat 1 17 (0) m_b377s252i27 15776 chrXqtel1M 947929 ATTATTATTATTATTAT 947945 (ATT)n#Simple 1 ATTATTATTATTATTAT 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 11 11.25 6.90 0.00 chrXqtel1M 948078 948106 (51894) (AAGTAT)n#Simple_repeat 1 31 (0) m_b377s252i28 15777 chrXqtel1M 948078 AAGTATAAGT-TAAATACAA-TATATGTATA 948106 - i i - v (AAGTAT)n#Sim 1 AAGTATAAGTATAAGTATAAGTATAAGTATA 31 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.07 (2 / 28), avg. gap size = 1.00 (2 / 2) 16 20.85 1.59 6.67 chrXqtel1M 948649 948711 (51289) (AATTTA)n#Simple_repeat 1 60 (0) m_b377s252i29 15778 chrXqtel1M 948649 AATTTAAGTTCAATTTTAAATTT-AATTCAAGTACTAACAAACACCATTT 948697 i i v - i i -i - vvi -v (AATTTA)n#Sim 1 AATTTAAATTTAAATTTAAATTTAAATTTAAAT-TTAA-ATTTA-AATTT 47 chrXqtel1M 948698 AAATTTAAATGTTA 948711 - (AATTTA)n#Sim 48 AAATTTAAAT-TTA 60 Matrix = Unknown Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.08 (5 / 62), avg. gap size = 1.00 (5 / 5) 260 33.90 1.69 1.69 chrXqtel1M 949185 949361 (50639) LSU-rRNA_Hsa#rRNA 3726 3902 (1133) m_b377s551i7 15779 chrXqtel1M 949185 AACGGCCGCAGTATCC-TGACCGTGCAAAGGTAGCATAATCACTTGTCTC 949233 v v v i- iv viv vv vv i vi LSU-rRNA_Hsa# 3726 AACGGCGGGAGTAACTATGACTCTCTTAAGGTAGCCAAATGCCTCGTCAT 3775 chrXqtel1M 949234 TTAATTGGGGACTAGTATGAATGGCAT-AACGAGGGTTCGACTGTCTCTT 949282 i i v vv i - - iv i v i v LSU-rRNA_Hsa# 3776 CTAATTAGTGACGCGCATGAATGG-ATGAACGAGATTCCCACTGTCCCTA 3824 chrXqtel1M 949283 ATTCCTAATCAGTGAAATTGACCTTCCCGTGCAGAGGC-GGGAATACTTA 949331 vi v vi i ii- vvi vv v v vi -v viv v i LSU-rRNA_Hsa# 3825 CCTACTATCCAGCGAAACC-ACAGCCAAGGGAACGGGCTTGGCGGAATCA 3873 chrXqtel1M 949332 TACAAGACGAGAAGACCCTGTGGAGCTTAA 949361 -i ii ivi v i LSU-rRNA_Hsa# 3874 -GCGGGGAAAGAAGACCCTGTTGAGCTTGA 3902 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.63 CpG sites = 26, Kimura (unadjusted) = 45.44 Transitions / transversions = 0.79 (26/33) Gap_init rate = 0.03 (6 / 176), avg. gap size = 1.00 (6 / 6) 359 17.81 2.74 0.00 chrXqtel1M 949858 949930 (50070) tRNA-Leu-TTA(m)#tRNA 1 75 (3) c_b377s355i0 15780 chrXqtel1M 949858 GTTAAG-TGGCAGAGT-TGGTAATTGCATAAAGTTTAAGCCTTTACTCCC 949905 - i- i ii ivi vvi tRNA-Leu-TTA( 1 GTTAAGATGGCAGAGCCTGGTAATCGCATAAAACTTAAAATTTTACAGTC 50 chrXqtel1M 949906 AGAGGTTCAAACCCTCTTCTTAATA 949930 vi i tRNA-Leu-TTA( 51 AGAGGTTCAACTCCTCTTCTTAACA 75 Matrix = 18p37g.matrix Kimura (with divCpGMod) = 19.10 CpG sites = 9, Kimura (unadjusted) = 20.83 Transitions / transversions = 2.25 (9/4) Gap_init rate = 0.03 (2 / 72), avg. gap size = 1.00 (2 / 2) 269 23.94 1.41 0.00 chrXqtel1M 950950 951020 (48980) C tRNA-Gln-CAA_v#tRNA (0) 72 1 c_b377s355i1 15781 chrXqtel1M 950950 CTAGGACAACAGGACTCGAACCTATACCAAAGAACTCAAAACCCTTTGTG 950999 i v i v i iv vi ii ii ii C tRNA-Gln-CAA_ 72 CTAGAACTATAGGAATTGAACCTACCCCTGAGAATCCAAAATTCTCCGTG 23 chrXqtel1M 951000 CT-CCCATTACACCACATCCTA 951020 - i i C tRNA-Gln-CAA_ 22 CTACCTATTACACCACGTCCTA 1 Matrix = 18p37g.matrix Kimura (with divCpGMod) = 26.24 CpG sites = 13, Kimura (unadjusted) = 30.44 Transitions / transversions = 3.25 (13/4) Gap_init rate = 0.01 (1 / 70), avg. gap size = 1.00 (1 / 1) 19 27.10 0.00 0.00 chrXqtel1M 953898 953943 (46057) (AC)n#Simple_repeat 1 46 (0) m_b377s252i30 15782 chrXqtel1M 953898 ACACACACGCACAGGCATACACACATGAACACACATATACGCACAC 953943 i vi i iiv i i i (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACAC 46 Matrix = Unknown Transitions / transversions = 4.00 (8/2) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 16 25.89 3.53 4.76 chrXqtel1M 954046 954130 (45870) (TATTAA)n#Simple_repeat 1 84 (0) m_b377s252i31 15783 chrXqtel1M 954046 TAGTAATA-TAATAATAGTATGTCTATCGATCATTGAT-TAAATGTGTAA 954093 v - v i vvv ii - i - v i - (TATTAA)n#Sim 1 TATTAATATTAATATTAATATTAATATTAAT-ATTAATATTAATAT-TAA 48 chrXqtel1M 954094 TATTTA-ATTAATAACTAATACTTAGCTTAATATCTAA 954130 v - - i i v vv - (TATTAA)n#Sim 49 TATTAATATTAAT-ATTAATATTAATATTAATAT-TAA 84 Matrix = Unknown Transitions / transversions = 0.70 (7/10) Gap_init rate = 0.08 (7 / 84), avg. gap size = 1.00 (7 / 7) 552 31.21 3.79 4.71 chrXqtel1M 959214 959556 (40444) C L1ME5_3end#LINE/L1 (304) 637 298 m_b377s551i8 15784 chrXqtel1M 959214 TCCTGCTCATTTCACTCAGCATCA-GTTCATGTAAG-TCTCTCCAAGTCT 959261 i i iv ii - -- v - iv v iv C L1ME5_3end#LI 637 TCTTACTTTTTTCACTCAGCACTATGTT--TTTAAGATCCATCCATGTTG 590 chrXqtel1M 959262 CTCTGTATTCATCCTGCTGGTCTCTTCTTACAGAACAATAACATTCCATA 959311 v i v iv iiv iv v v vvvv ii i i C L1ME5_3end#LI 589 CTATGTGTACATCTAGTCCGTTGCTTCTAACTGCTGCATAGTACTCCATG 540 chrXqtel1M 959312 ACATTCATATACCACAATTTACTCAGCCATTCTCCAACTGATGGACATCC 959361 iii v vi v ii v i v v i C L1ME5_3end#LI 539 GTGTGCATCCACCACATTTTACCTATCCACTCTCCCAGTGATGGACACCC 490 chrXqtel1M 959362 ATTCAGTTTCCAGTTTCTAGTCTCTACTAA-AGGGCTGCCAGAAACATTT 959410 vviv ii ii i iv i v i v - iv v vi ii C L1ME5_3end#LI 489 AGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCTGCAATGAACATCC 440 chrXqtel1M 959411 TTGCACATGTGGGTCCCTTTC---CCTTCTTTAAGATCTCTTTGGGATAT 959457 i i ---i vi--- viv v ii i C L1ME5_3end#LI 439 TCGTACATGT---CCCCTTATGGACCTGTGTGAGAATTTCTTTGGGATAT 393 chrXqtel1M 959458 AAGCCCAGTA-CAAATACGGCTGGATCAAAGGGTATGC----AC--AGTT 959500 vi v - ii - iv i v ---- -- i C L1ME5_3end#LI 392 ATACCCAGGAGCGGA-ATTGCTGGGTCATAGGGTATGCGTATACTTAATT 344 chrXqtel1M 959501 TGACAACGTTTTGAGCATAATTTCAAACTTCTCTCCAGAATGTTTGGATC 959550 v v vi ---------i i i v vi v - C L1ME5_3end#LI 343 TGACTAAGTACTG---------CCAGATTGCTCTCCAGAATGGCTGCA-C 304 chrXqtel1M 959551 CATTCT 959556 v C L1ME5_3end#LI 303 CAGTCT 298 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.21 CpG sites = 56, Kimura (unadjusted) = 41.26 Transitions / transversions = 1.22 (56/46) Gap_init rate = 0.07 (23 / 342), avg. gap size = 1.26 (29 / 23) 22 40.71 0.00 1.43 chrXqtel1M 960065 960084 (39916) (TCTC)n#Simple_repeat 1 19 (121) m_b377s252i32 15785 chrXqtel1M 960065 TCTCTGTCTCTGTCATTCAT 960084 v v vi - (TCTC)n#Simpl 1 TCTCTCTCTCTCTCTCTC-T 19 Matrix = Unknown Transitions / transversions = 0.33 (1/3) Gap_init rate = 0.05 (1 / 19), avg. gap size = 1.00 (1 / 1) 37 0.00 0.00 0.00 chrXqtel1M 960085 960116 (39884) (TC)n#Simple_repeat 1 32 (0) c_b377s251i9 15786 chrXqtel1M 960085 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 960116 (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 32 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 22 40.71 0.00 1.43 chrXqtel1M 960117 960237 (39763) (TCTC)n#Simple_repeat 20 139 (1) m_b377s252i32 15787 chrXqtel1M 960117 GCTTTTTGTCTTTGTCTCTCCCTATCTCGCTATCTCTCCTTCTATCCTTC 960166 v i i v i v i v v v ii v ii (TCTC)n#Simpl 20 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 69 chrXqtel1M 960167 CCTTCCTCCATCCCTTCCTCCTTGCCTACTCCATCTGTGTTGCTCTCTCT 960216 i ii iv i ii ii vi - iv v v iv (TCTC)n#Simpl 70 TCTCTCTCTCTCTCTCTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCT 118 chrXqtel1M 960217 CTTTTCCTCCTTCTCTCTCTC 960237 i ii ii (TCTC)n#Simpl 119 CTCTCTCTCTCTCTCTCTCTC 139 Matrix = Unknown Transitions / transversions = 1.92 (25/13) Gap_init rate = 0.01 (1 / 120), avg. gap size = 1.00 (1 / 1) 14 8.85 0.00 0.00 chrXqtel1M 960356 960379 (39621) (TGTC)n#Simple_repeat 1 24 (0) m_b377s252i33 15788 chrXqtel1M 960356 TGTCTGTCTGTCTGTCTTTCCGTC 960379 v i (TGTC)n#Simpl 1 TGTCTGTCTGTCTGTCTGTCTGTC 24 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 54 0.00 0.00 0.00 chrXqtel1M 960420 960465 (39535) (GA)n#Simple_repeat 1 46 (0) c_b377s251i10 15789 chrXqtel1M 960420 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 960465 (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 46 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 75 34.02 1.99 1.13 chrXqtel1M 960553 960903 (39097) (GAGA)n#Simple_repeat 1 354 (0) m_b377s252i34 15790 chrXqtel1M 960553 GAGA-AAAGAGAAAGAGATAGACAGGGAAAACAAGAGA-AGCCAGAGAGG 960600 - i i v v i i ivi - vv i (GAGA)n#Simpl 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chrXqtel1M 960601 GAGAGAGAGAGA-AGTAGACAGAGCCCGAGAGAAAGAGTGAAAAATAGAG 960649 - - v vvv i v i i v (GAGA)n#Simpl 51 GAGAGAGAGAGAGAG-AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 99 chrXqtel1M 960650 GAAGAAAAAGACAGAGAATTTTTGAGGAAAAGTAAAGAGAGAGAAAGAGG 960699 ii i i v ivvvvv ii i - i i i (GAGA)n#Simpl 100 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG-AGAGAGAGAGAGAGAGA 148 chrXqtel1M 960700 AATAGTGTCAGTAAACAAATA-ATAAAGAGACAAAGACAGTGATTGAGAG 960748 i v v vv - i v i v - v i v i v v vv (GAGA)n#Simpl 149 GAGAGAGAGAG-AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 197 chrXqtel1M 960749 AGAGAAAGAGAGAGAGAGAGAGAGATAGAGATCAAATA-AGAAAGAGATA 960797 i v -v i v - i v (GAGA)n#Simpl 198 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA-GAGAGAGAGAGAGAGAGA 246 chrXqtel1M 960798 AAGACAGAGCCAGAGAAAGAGAAAGAGCCAGACTGACACCCAGTCAGAGA 960847 i v vv i i vv vv v vvv vv (GAGA)n#Simpl 247 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 296 chrXqtel1M 960848 CAGACA-AGA-ACAGAGCTAGAGATAGCAAGCTAGTGAGAACCAGAGGGA 960895 v v - - v vv v vi vv v ivv i (GAGA)n#Simpl 297 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 346 chrXqtel1M 960896 AAGAGAGA 960903 i (GAGA)n#Simpl 347 GAGAGAGA 354 Matrix = Unknown Transitions / transversions = 0.62 (36/58) Gap_init rate = 0.03 (11 / 350), avg. gap size = 1.00 (11 / 11) 36 0.00 0.00 0.00 chrXqtel1M 960918 960957 (39043) (GT)n#Simple_repeat 1 40 (0) m_b377s252i35 15791 chrXqtel1M 960918 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 960957 (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 40 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 55 3.67 0.00 0.00 chrXqtel1M 960958 961013 (38987) (GA)n#Simple_repeat 1 56 (0) c_b377s251i11 15792 chrXqtel1M 960958 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGACAGAGAGACA 961007 v v (GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50 chrXqtel1M 961008 GAGAGA 961013 (GA)n#Simple_ 51 GAGAGA 56 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0) 24 29.19 2.17 2.17 chrXqtel1M 961323 961414 (38586) (TCTT)n#Simple_repeat 1 92 (0) m_b377s252i36 15793 chrXqtel1M 961323 TCTCTCTTTCTCTCCCTCCCTCCCTCCTTCCCTTCTATCCTTTATTTTTC 961372 i - i i i i i i i i i - i v i i (TCTT)n#Simpl 1 TCTTTCTTTCT-TTCTTTCTTTCTTTCTTTCTTTCT-TTCTTTCTTTCTT 48 chrXqtel1M 961373 TCCTTTTCTCTCTCTTTCTTTTTGTC-TT-TTTCTTTCTTTCTT 961414 i i i i i v - - (TCTT)n#Simpl 49 TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 92 Matrix = Unknown Transitions / transversions = 9.00 (18/2) Gap_init rate = 0.04 (4 / 91), avg. gap size = 1.00 (4 / 4) 49 3.18 6.15 0.00 chrXqtel1M 961434 961498 (38502) (TC)n#Simple_repeat 1 69 (0) c_b377s251i12 15794 chrXqtel1M 961434 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTTCTCTCCCT- 961482 i i - (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chrXqtel1M 961483 TC-CTC-CT-TCTCTCTCT 961498 - - - (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCT 69 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.06 (4 / 64), avg. gap size = 1.00 (4 / 4) 16 32.28 0.00 0.00 chrXqtel1M 961627 961687 (38313) (TCTC)n#Simple_repeat 1 61 (0) m_b377s252i37 15795 chrXqtel1M 961627 TCTCTGTCTGTCACTCTCACTATCTCCCTGGCTCTCTGTTTCTCATTATT 961676 v v v v v i vv v i vi v i (TCTC)n#Simpl 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chrXqtel1M 961677 TTTCTCACTCT 961687 i v (TCTC)n#Simpl 51 TCTCTCTCTCT 61 Matrix = Unknown Transitions / transversions = 0.45 (5/11) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 19 6.13 5.88 0.00 chrXqtel1M 961863 961896 (38104) (TTAA)n#Simple_repeat 1 36 (0) m_b377s252i38 15796 chrXqtel1M 961863 TTTATT-ATTAATTAATTAATT-ATTAATCAATTAA 961896 v - - i (TTAA)n#Simpl 1 TTAATTAATTAATTAATTAATTAATTAATTAATTAA 36 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2) 13 15.07 5.13 2.50 chrXqtel1M 962339 962377 (37623) (ATAACA)n#Simple_repeat 1 40 (0) m_b378s252i3 15797 chrXqtel1M 962339 ATAA-AATATAATTAAGAA-AACAACAAACAATAACAATAA 962377 - vv v v - -v (ATAACA)n#Sim 1 ATAACAATAACAATAACAATAACAA-TAACAATAACAATAA 40 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.08 (3 / 38), avg. gap size = 1.00 (3 / 3) 196 32.73 12.14 3.97 chrXqtel1M 962930 963069 (36931) MIRc#SINE/MIR 1 151 (117) m_b378s601i0 15798 chrXqtel1M 962930 CGAATCAGTGTGGTGCCATGAAAAGAGCAGTGCATTTTGGGATGTGAATT 962979 iv vi i v v -i ii vv i -- MIRc#SINE/MIR 1 CGAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGA-CTTGGAGTCAGGA-- 47 chrXqtel1M 962980 TAAATGTGCATTC-AGTCCTGG----G-GGCTTAGTATCTATTTAACCCT 963023 - i iv vi - i ---- -vi v v i v i i MIRc#SINE/MIR 48 -AGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTT 96 chrXqtel1M 963024 GA-----------AAATTGTCTGAAATCTGGTTTCTTTTTCTGCCAGATC 963062 i----------- vi v iviiii i iv iv i - MIRc#SINE/MIR 97 GGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAAT- 145 chrXqtel1M 963063 AGAGGAT 963069 - i MIRc#SINE/MIR 146 -GGGGAT 151 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 43.64 CpG sites = 27, Kimura (unadjusted) = 45.05 Transitions / transversions = 1.59 (27/17) Gap_init rate = 0.07 (10 / 139), avg. gap size = 2.30 (23 / 10) 205 33.32 4.88 1.18 chrXqtel1M 963032 963113 (36887) MIR3#SINE/MIR 113 197 (11) m_b378s601i1 15798 chrXqtel1M 963032 TCTGAAATCTGGTTTCTTTTTCTGCCAGATCAGAGGATTGGACTGGATGG 963081 iiviiii i iv iv i v i i i i MIR3#SINE/MIR 113 TCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTGGACTAGATGA 162 chrXqtel1M 963082 TCTTTCATGATC---TTGATTTCTAA-ATCCTATGA 963113 i v - i --- iv vi i - i MIR3#SINE/MIR 163 TCTCTAA-GGTCCCTTCCAGCTCTGACATTCTATGA 197 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 48.15 CpG sites = 20, Kimura (unadjusted) = 48.15 Transitions / transversions = 2.86 (20/7) Gap_init rate = 0.04 (3 / 81), avg. gap size = 1.67 (5 / 3) 14 22.11 2.38 0.00 chrXqtel1M 963326 963367 (36633) (AAATA)n#Simple_repeat 1 43 (0) m_b378s252i4 15799 chrXqtel1M 963326 AAATGTAATTAGA-AAAATAAAATAGTATAGAATAAATTAAAA 963367 iv v i - iv i v (AAATA)n#Simp 1 AAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAA 43 Matrix = Unknown Transitions / transversions = 1.00 (4/4) Gap_init rate = 0.02 (1 / 41), avg. gap size = 1.00 (1 / 1) 13 16.47 2.78 2.78 chrXqtel1M 963613 963648 (36352) (AAAG)n#Simple_repeat 1 36 (0) m_b378s252i5 15800 chrXqtel1M 963613 AAAGTAAGAAA-AAAAAGAAATAGAAAGAAAGGAAAG 963648 v - i i i v - (AAAG)n#Simpl 1 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA-GAAAG 36 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2) 244 23.53 0.00 0.00 chrXqtel1M 963909 963976 (36024) C DNM1r#Unknown (2119) 2543 2476 m_b378s502i0 15801 chrXqtel1M 963909 ATATAAATATCTATATACATGCATATACATATCTACATGTATACACAAAT 963958 ? vi v i ii i i vi ii v C DNM1r#Unknown 2543 ANATACGTATATATACACATATATACACACATACACACATATACACACAT 2494 chrXqtel1M 963959 ACATACAGACATACACAT 963976 i v i C DNM1r#Unknown 2493 ATATACACACATACACGT 2476 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 25.52 CpG sites = 11, Kimura (unadjusted) = 29.83 Transitions / transversions = 2.20 (11/5) Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0) 242 17.07 0.00 9.23 chrXqtel1M 963922 963992 (36008) C DNM1r#Unknown (2116) 2546 2482 m_b378s502i1 15801 chrXqtel1M 963922 TATACATGCATATACATATCTACATGTATACACAAATACATACAGACATA 963971 ? i i i i-- i v i v i i C DNM1r#Unknown 2546 TATANATACGTATATATAC--ACATATATACACACATACACACATATACA 2499 chrXqtel1M 963972 CACATATGTATTTCCACACAT 963992 i ---- C DNM1r#Unknown 2498 CACATATATA----CACACAT 2482 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 18.34 CpG sites = 9, Kimura (unadjusted) = 20.35 Transitions / transversions = 4.50 (9/2) Gap_init rate = 0.09 (6 / 70), avg. gap size = 1.00 (6 / 6) 46 2.31 0.00 0.00 chrXqtel1M 964332 964375 (35625) (GT)n#Simple_repeat 1 44 (0) c_b378s251i1 15802 chrXqtel1M 964332 GTGTGTGTGTGTGTGTGTGAGTGTGTGTGTGTGTGTGTGTGTGT 964375 v (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 44 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0) 1510 27.50 4.06 3.42 chrXqtel1M 965033 965672 (34328) C L1ME5_3end#LINE/L1 (291) 650 7 m_b378s551i0 15803 chrXqtel1M 965033 ATCTC---CTGGTTCT-ACTCACTTCACTCAGCATTA-GTTC---ATGTC 965074 --- v - ivi i - i--- vi C L1ME5_3end#LI 650 ATCTCATTCTGTTTCTTACTTTTTTCACTCAGCACTATGTTTTTAAGATC 601 chrXqtel1M 965075 TCTCCAAGCCTCTCTGTATTCATCCTGCTGGTCATTTCTTACAGAACAAT 965124 iv v iiv v i v iv iiv iii v v vvvv C L1ME5_3end#LI 600 CATCCATGTTGCTATGTGTACATCTAGTCCGTTGCTTCTAACTGCTGCAT 551 chrXqtel1M 965125 AATACTCCATAACATTCATATACCACAATTTACCCAACCATTCTTCTACT 965174 i iiii v vi v i v i i i v C L1ME5_3end#LI 550 AGTACTCCATGGTGTGCATCCACCACATTTTACCTATCCACTCTCCCAGT 501 chrXqtel1M 965175 GATGGGCATCCATTCATTTTTCAGTTTCTAGCCACTACAAACAGGGCTAC 965224 i i vvivvii i ii i iv i iv i C L1ME5_3end#LI 500 GATGGACACCCAGGTTGCCTCCAACTCCCCGCCACCACAAACAACGCTGC 451 chrXqtel1M 965225 CACACACATTTTGGCACATACAAAGTCCCCT-ATCCTTCTTTCTTG---T 965270 v iiv ii v i ----- - vvvi v v vi--- C L1ME5_3end#LI 450 AATGAACATCCTCGTACAT-----GTCCCCTTATGGACCTGTGTGAGAAT 406 chrXqtel1M 965271 CTCTTTGGGTTATTAAGCCCAGTAGTAGCACTGCTGGGTCAAAGGGTATG 965320 i v - vi v ii v i v C L1ME5_3end#LI 405 TTCTTTGGGATAT-ATACCCAGGAGCGGAATTGCTGGGTCATAGGGTATG 357 chrXqtel1M 965321 CACAGTTTGATAACTT--TTTGAGTA--TAGTTCTAAATTGCTCTTCAGA 965366 --- --- - -- v -- v v i i i C L1ME5_3end#LI 356 C---GT---ATA-CTTAATTTGACTAAGTACTGCCAGATTGCTCTCCAGA 314 chrXqtel1M 965367 ATGGCTGGATGTATTCACAATTCCACCAACAATGTATTAGTGTCCCAGTT 965416 v ivvi ii v i i i i v v i vi ? C L1ME5_3end#LI 313 ATGGCTGCACCAGTCTACACTCCCACCAGCAGTGCATGAGGGTTCCTATN 264 chrXqtel1M 965417 TTCCCACATCCCCTCCAACATTCCGCATTATCTTTCCCTGTCATTCTAGC 965466 i i v i iv ivv ii v v i v C L1ME5_3end#LI 263 TCCCCACATCCTCGCCAACACTTGGCATTATCCAGCTTTCTAATTTTTGC 214 chrXqtel1M 965467 CAATCTGACAGGTGTGTAGTGGTGTCTCAGAGTTGTTTAAATTTGCATTT 965516 i i i iv i i vv v C L1ME5_3end#LI 213 CAGTCTAATAGGTGTAAAGTGATATCTCATTGTTGTTTTAATTTGCATTT 164 chrXqtel1M 965517 CTCTGATTAATAATGACTTGGAGCATCT-TTCATATGGGTAGAAATAG-- 965563 v v v - vv iv--- -- C L1ME5_3end#LI 163 CTCTGATTACTAATGAGTTTGAGCATCTCTTCATATGCTTGT---TAGCC 117 chrXqtel1M 965564 TTTC-AATTTCTTCATCTGAGAATTGTCTGTTCATATCCTTTGACCATGT 965612 -ii i v vi i v v C L1ME5_3end#LI 116 TTTCGGGTTTCCTCTTCTGTAAATTGCCTGTTCATATCCTTTGCCCATTT 67 chrXqtel1M 965613 ATTAATTGGAG--AATGGCTTGATTTCTTATAAATT----GGAGTCCATT 965656 v iv i --?vi v -- i vi ---- ---- C L1ME5_3end#LI 66 TTCTATTGGGGTTNCCGTCTT--TTTCTTGTTGATTTGCAGGAG----TT 23 chrXqtel1M 965657 CTCTATATATTTTGGA 965672 ii i i i C L1ME5_3end#LI 22 CCTTGTATATTCTAGA 7 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.50 CpG sites = 93, Kimura (unadjusted) = 35.03 Transitions / transversions = 1.21 (93/77) Gap_init rate = 0.05 (35 / 639), avg. gap size = 1.37 (48 / 35) 2705 30.28 3.84 2.05 chrXqtel1M 965530 967353 (32647) C L1M5_orf2#LINE/L1 (0) 3294 1439 m_b378s551i1 15803 chrXqtel1M 965530 TGACTTGGAGCATCTTT-CATATGGGTAGAAATAGTTTCAATTTCTTCAT 965578 ?v v - i vv vviiivi v? v v C L1M5_orf2#LIN 3294 TGANGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGNATATCTTCTT 3245 chrXqtel1M 965579 CTGAGAATTGTCTGTTCATATCCTTTGACCATGTATTAATTGGA--GAAT 965626 i v v vi i v v v ?v i-- vv C L1M5_orf2#LIN 3244 TTGTGAAGTGTCTGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTT 3195 chrXqtel1M 965627 GGCTTGATTTCTTAT-AAATTGGAGTCCATTCTCTATATATTTTGGAAAT 965675 v -- ? -i ? v vv-i i i v i C L1M5_orf2#LIN 3194 GTCTT--TTTNTTATTGANTTGTAGGA-GTTCTTTATATATTCTGGATAC 3148 chrXqtel1M 965676 GAGGCCTTTATCAGA-ACCTTTAACTGTAAAAATGTTTTTACAGTGTATT 965724 v i - iv v ?-i i v v i iv ? v i v C L1M5_orf2#LIN 3147 GAGTCCTTTGTCAGATATATGTN-TTGCAAATATTTTCTCCCANTCTGTG 3099 chrXqtel1M 965725 GCTTATCTTCTAATCTTGTCTGCATTAGTTTTGTTTGTACAAAAACTTTT 965774 ii i v i v ivi iv ivi vvv? vi i ii C L1M5_orf2#LIN 3098 GCTTGCCTTTTCATTTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTTT 3049 chrXqtel1M 965775 CAATTTGATATAATCAAAATTTTCTATTTTGTAATCAATATGATCTCTAA 965824 v v i? i v v v v v vv i-- i i?v iv C L1M5_orf2#LIN 3048 AATTTTGATGNAGTCCAATTTATCAATTTTTTCTTT--TATGGTTNGTGC 3001 chrXqtel1M 965825 TTCTTCT---TTGGTCATAAATTCCTTCCTCTTCCCATAGGTCTGAGAGG 965871 i v ---i v i vi v i v iiv? - vvii i C L1M5_orf2#LIN 3000 TTTTTGTGTCCTGTTTAAGAAATCTTTGCCTANCCCA-AGGTCACGAAGA 2952 chrXqtel1M 965872 TAAACTATCCTATGCT--CTTCCAATTTATTTATAATCTCATTCTTTATG 965919 --i v i -- i ivvvv i i i ?ii ii C L1M5_orf2#LIN 2951 TA--TTCTCCTATGTTTTCTTCTAGAAGTTTTATAGTTTTANCTTTTACA 2904 chrXqtel1M 965920 CCTAGGTC-ATGAACCCATTTTGACCTTATTTTGTTGTACAGTGTTAAGT 965968 ii - -i i ? vi v vv ii v i C L1M5_orf2#LIN 2903 TTTAGGTCTATGA-TCCATCTNGAATTAATTTTTGTGTATGGTGTGAGGT 2855 chrXqtel1M 965969 GTGGGTCAATGCCTAGTTTCTGTCATACTAATTTACAATTTTCCCAGCAA 966018 iv i v?iii v i vi ivi v v v i v C L1M5_orf2#LIN 2854 AGGGGTCGAGNTTCATTTTTTTCCATATGGATATCCAATTGTTCCAGCAC 2805 chrXqtel1M 966019 TTTTTGTCAAATAGTGAGTTCTTATCCCAAAAACTAGGGTCTTTGGG--- 966065 iv ii v vvvi i vi vvi v v --- ? v--- C L1M5_orf2#LIN 2804 CATTTGTTGAAAAGACTATCCTTTCCCCACTGAATTG---CNTTGGCACC 2758 chrXqtel1M 966066 TTTGTCATACACTAGATTATTAAACTTAT-TGGCTGTTTTGTCCTTTGAA 966114 v v ii i? v?ii v iv i - v v v ---- i i C L1M5_orf2#LIN 2757 TTTGTCAAAAATCAANTGNCCATATATGTGTGGGTCTATT----TCTGGA 2712 chrXqtel1M 966115 C---CTAACCTATTCCATCGATCAACTAGTCTATTTCTTGGCCAATACCA 966161 --- vi i i v i v iii vv C L1M5_orf2#LIN 2711 CTCTCTATTCTGTTCCATTGATCTATTTGTCTATCCTTACGCCAATACCA 2662 chrXqtel1M 966162 AATGATTTTGGTAACCACTGCTTTGTAATATAATTTT-AGATCTGGTACA 966210 v ivi i i v iiiv i - i i - ? ? vv C L1M5_orf2#LIN 2661 CACTGTCTTGATTACTGTAGCTTTATAATA-AGTCTTGANATCNGGTAGT 2613 chrXqtel1M 966211 GCTAATTTTTCA--TTTGATTTTTTTTTTCATTAATTTCCTTGAA-ATTC 966257 iv i ii i -- v i i v-i vii iv- C L1M5_orf2#LIN 2612 GTAAGTCCTCCAACTTTGTTCTTCTTTTTCAA-GATTGTTTTGGCTATTC 2564 chrXqtel1M 966258 TTGACCGTTTGTTTTTCCATATGAACTTT-------GTTTTT----TTCT 966296 ? ii v iv i i ------- i v ---- C L1M5_orf2#LIN 2563 TNGGTCCTTTGCATTTCCATATAAATTTTAGAATCAGCTTGTCAATTTCT 2514 chrXqtel1M 966297 AGGTCATTAAAATAGTTTTTTGGGAGTCTGGTACAG--TGC--TAAATAA 966342 ------i v iii vi v i i vvi -- -- i vv C L1M5_orf2#LIN 2513 A------CAAAAAAACCTGCTGGGATTTTGATTGGGATTGCATTGAATCT 2470 chrXqtel1M 966343 ATAGATAATTTTAGGTAATATTT-CATCTTTATTATATT---TCT-CTAA 966387 v v i v iv v- ? iv --- - i C L1M5_orf2#LIN 2469 ATAGATCAATTTGGGGAGAATTGACATCTTNACAATATTGAGTCTTCCAA 2420 chrXqtel1M 966388 TCCAAGAGCATT-TA-ATATTTTCAGTTAGTTAGATCAGACTTAATTTGT 966435 v i v- - v i i v v i vvvi v C L1M5_orf2#LIN 2419 TCCATGAACATGGTATATCTCTCCATTTATTTAGGTCTTCTTTAATTTCT 2370 chrXqtel1M 966436 GTGGAAAGTGTTTTTGTAATTTTGCTCATAAAGTTTCTG-ACTTTCCTTG 966484 v viiv i - i vvvii ? v ii - v ?ii C L1M5_orf2#LIN 2369 CTCAGCAATGTTTT-GTAGTTTTCAGTGTANAGGTCTTGCACATNTTTTG 2321 chrXqtel1M 966485 C-AAATAGATTCCTGAAATATTTTATACTATCAGTAGTTACTTTAAATGG 966533 i- i vv - i ? ii v iv vv i i v C L1M5_orf2#LIN 2320 TTAGATTTATTCCT-AAGTATTTNATGTTTTTTGATGCTATTGTAAATGG 2272 chrXqtel1M 966534 AATTTCTCTTTGTAACTCTGACTTTG-----GTTTTTTAGTGATATATAA 966578 v vi i ?-- v i v i v----- v iv ii i C L1M5_orf2#LIN 2271 TATTGTTTTTN--AAATTTCATTTTCCAATTGTTTGTTGCTAGTATATAG 2224 chrXqtel1M 966579 GAATGCTGATGACTTATGTGGGTTTATTTTGTATCCA---ACTTTGCTAA 966625 i i viv i v ivi v ii ?--- i C L1M5_orf2#LIN 2223 AAATACAATTGATTTTTGTATATTGACCTTGTATCCNGCGACCTTGCTAA 2174 chrXqtel1M 966626 GGTTGG--ATT-GTTTTAATAACTT-TTAGTAAGATCTCTGGG-TTCTCT 966670 iv iiv-- - i i ii - v iiv i ? - i C L1M5_orf2#LIN 2173 ATTCACTTATTAGTTCTAGTAGTTTNTTTGTAGATTCTTTNGGATTTTCT 2124 chrXqtel1M 966671 AAATATACCATCATATCATCAGCAAAGAGTGATAATTTGGTTTCCTCATT 966720 vi ? v i v i v i? i i vi i v C L1M5_orf2#LIN 2123 ACGTANACAATCATGTCATCTGCGAATAANGACAGTTTTATTTCTTCCTT 2074 chrXqtel1M 966721 GCC--TCTCTAATTCCTTTAATCTCTTTCTCAACTCTTATTGCCAAAGCT 966768 v -- i - v v i i vvvi vvvi C L1M5_orf2#LIN 2073 TCCAATCTTTA-TGCCTTTTATTTCTTTTTCTTGCCTTATTGCACTGGCT 2025 chrXqtel1M 966769 A--ATTTCTAATACAATATTGAATAGTAATGGTGATAATGGGCAACCTTG 966816 -- ii i i i v i ? ii i v C L1M5_orf2#LIN 2024 AGGACCTCCAGTACAATGTTGAATAGAAGTGGTGANAGCGGACATCCTTG 1975 chrXqtel1M 966817 TTTCACTCCTGATCTTAATGGGAATGGTTGCAGTTTGTCCCCATTACATA 966866 i iii i iv v v? v ? v v vi C L1M5_orf2#LIN 1974 TCTTGTTCCCGATCTTAGGGGGAAAGCNTTCAGTNTTTCACCATTAAGTA 1925 chrXqtel1M 966867 TGATGCTTACTGATGGTTTTAAATAGATGCTACTGATTATTTTAAGGAAA 966916 i ?i vv vvi ivi v i vv i i C L1M5_orf2#LIN 1924 TGATGTTNGCTGTAGGTTTTTCGTAGATGCCCTTTATCAGGTTGAGGAAG 1875 chrXqtel1M 966917 AGTCCATTTATTCCTGTATTCTTGAGTGTTTTTTTTAATAGGAATGAATG 966966 vvi v i ivv vi v v i ---v ii C L1M5_orf2#LIN 1874 TTCCCTTCTATTCCTAGTTTGCTGAGAGTTTTTATCA---TGAATGGGTG 1828 chrXqtel1M 966967 TTGGATTTTTTCAAATGCTTTTTCTGCCTCTATTGAGATGATCATCTAGT 967016 i v v v ii C L1M5_orf2#LIN 1827 TTGAATTTTGTCAAATGCTTTTTCTGCATCTATTGAGATGATCATATGAT 1778 chrXqtel1M 967017 TTTTG--CTTTGGT-TATTAATATGGCCAATTATACTGATAATTTTCCTA 967063 v-- iv - i iv i i viv i v C L1M5_orf2#LIN 1777 TTTTCTCCTTTATTCTGTTAATATGGTGAATTACATTGATTGATTTTCGA 1728 chrXqtel1M 967064 ATATTTGACCAGTCCTGCATTCCTGGTATACACCCTACTTGATCATGGTG 967113 i vi ii i v v i i i C L1M5_orf2#LIN 1727 ATGTTAAACCAACCTTGCATTCCTGGGATAAACCCCACTTGGTCATGATG 1678 chrXqtel1M 967114 TATTATCCTGGGGATGATCTT-TTGTAGTCTTTTTGTTAATATCTTATTT 967162 vvvv - v -i v v vv i i i ? C L1M5_orf2#LIN 1677 TATTATCCTTTTTAT-ATATTGCTGGATTCGATTTGCTAATATTTTGTTN 1629 chrXqtel1M 967163 AAGATTTTAGCATCAATATTCATTAGGGAGATTGGTCTATAATTTTCTTT 967212 i v v i v v i C L1M5_orf2#LIN 1628 AGGATTTTTGCATCTATGTTCATGAGGGATATTGGTCTGTAATTTTCTTT 1579 chrXqtel1M 967213 CTCTGTTTTCAA---CCTACCCTGGTTTAGATATCAGTACCATGTCTGTG 967259 iii ---- --- i vvi ? v i vii? iiv iv C L1M5_orf2#LIN 1578 TCTTGT----AATGTCTTTGTCNGGTTTTGGTATCAGGGTNATGCTGGCC 1533 chrXqtel1M 967260 TTATAAAAGGAATTTGGTAGGACTCCTTCAATTTCTATTTTTCCAAATAG 967309 i v i v v vii i vv iivi v C L1M5_orf2#LIN 1532 TCATAAAATGAGTTGGGAAGTGTTCCCTCTTTTTCTATTTTCTGGAAGAG 1483 chrXqtel1M 967310 TTTATATAGCATTGGGGCTAATTGTTCTTTAAATGTTTGGTAGA 967353 i i iv vii v v i C L1M5_orf2#LIN 1482 TTTGTGTAAGATTGGTATTATTTCTTCCTTAAATGTTTGGTAGA 1439 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 39.74 CpG sites = 287, Kimura (unadjusted) = 40.61 Transitions / transversions = 1.13 (287/254) Gap_init rate = 0.04 (74 / 1823), avg. gap size = 1.46 (108 / 74) 382 28.50 4.83 2.17 chrXqtel1M 967455 967723 (32277) L1M3_orf2#LINE/L1 3013 3288 (0) m_b378s551i2 15804 chrXqtel1M 967455 AAAATAGAAAATTTTGATTACATCAAATTAAAAAGCTTCC---CTACAAA 967501 v v vv i i i--- vi L1M3_orf2#LIN 3013 AAAATAGACAAGTGGGACTACATCAAACTAAAAAGCTTCTGCACAGCAAA 3062 chrXqtel1M 967502 CAAAACTAATGTAAACAAGATTAGAAGGGAAGCAACAAACTGGGAAAACA 967551 vi - -- v iii v i v v v ii v i v L1M3_orf2#LIN 3063 GGAAAC-AA--TCAACAGAGTGAAAAGGCAACCTACGGAATGGGAGAAAA 3109 chrXqtel1M 967552 TTTTTTACAGTCAAAGGTTCTGATAAAGGCCTCATTTCCAAAATATATAA 967601 v vvv ii v vi- i vi v v L1M3_orf2#LIN 3110 TATTTGCAAACCATATA-TCTGATAAGGGGTTAATATCCAAAATATATAA 3158 chrXqtel1M 967602 ATTGACTCT---AATTTA----TAAGAAATCAACCATTCCAATTGATAAA 967644 i-vi ?--- i i ----i i v vi vi i ? v L1M3_orf2#LIN 3159 G-GAACTCNTACAACTCAATAGCAAAAAAACAAATAACCCGATTNAAAAA 3207 chrXqtel1M 967645 TGGTCAAAGGATATGAAATAGACAATTTTCAGATGATGA-ATG-AAATCA 967692 v iv - v i vi v v - i- vi L1M3_orf2#LIN 3208 TGGGCAAAGGACCTG-AATAGACATTTCTCCAAAGAAGACATACAAATGG 3256 chrXqtel1M 967693 TTACCACTCATATG-AAAGGTGTTCCAAATCA 967723 ii v vvi - i i v v L1M3_orf2#LIN 3257 CCAACAGGTATATGAAAAGATGCTCAACATCA 3288 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 35.38 CpG sites = 36, Kimura (unadjusted) = 36.57 Transitions / transversions = 0.92 (36/39) Gap_init rate = 0.04 (12 / 268), avg. gap size = 1.58 (19 / 12) 533 22.57 13.42 3.36 chrXqtel1M 967588 967885 (32115) L1ME3C_3end#LINE/L1 7 333 (537) m_b378s551i3 15804 chrXqtel1M 967588 TCCAAAATATATAAATTGACTCT----AATTTATAAGAAATCAACCATTC 967633 i v-i i---- iv v iv vi L1ME3C_3end#L 7 TCCAGAATATATAAAG-AACTCCTACAAATCAATAAGAAAACAGACAACC 55 chrXqtel1M 967634 CAATTGATAAATGGTCAAAGGATATGAAATAGACAATTTTCAGATGATGA 967683 v v v i -i i iv v v L1ME3C_3end#L 56 CAATAGAAAAATGGGCAAAAGATATGAA-CAGGCAATTCACAGAAGAGGA 104 chrXqtel1M 967684 ATGAAATC--ATTACCACT---CATATGAAAGG-TGTTCCAAATCATTAT 967727 --- v? -- vi v --- i - i v vv i v L1ME3C_3end#L 105 A---ACNCGAATGGCCAATAAACATATGAAAAGATGCTCAACCTCACTAG 151 chrXqtel1M 967728 TAATCAGAGAAATACAAATT-AAACAACTCTGAGATACCAC----CACCT 967772 i i - ? vv i---- i L1ME3C_3end#L 152 TAATCAGGGAAATGCAAATTAAAACNACAATGAGATACCATTTCACACCC 201 chrXqtel1M 967773 -TC-GATTAGCTAAGA--TGACAGGGAAAAAATAACGATGAGTGTTGGAG 967818 - - i v i -- i v vvvi v v ---i v L1ME3C_3end#L 202 ATCAGATTGGCAAAAATTTAAAAGTCTGACAATACC---AAGTGTTGGCG 248 chrXqtel1M 967819 -GGATCTG------CTGG----CATATACATTGTTGGTGGCTTGAACGT- 967856 - v ------ v ---- vi i i --- ii - L1ME3C_3end#L 249 AGGATGTGGAGCAACGGGAACTCTCATACACTGCTGGTGG---GAGTGTA 295 chrXqtel1M 967857 --------CAACCATTCTGGAG-GCGATCTGGAATTAT 967885 -------- i i - i i v v L1ME3C_3end#L 296 AATTGGTACAACCACTTTGGAGAGCAATTTGGCAATAT 333 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 27.39 CpG sites = 32, Kimura (unadjusted) = 27.39 Transitions / transversions = 0.97 (32/33) Gap_init rate = 0.08 (25 / 297), avg. gap size = 2.04 (51 / 25) 630 24.21 15.15 3.75 chrXqtel1M 967633 968160 (31840) L1ME5_3end#LINE/L1 58 643 (298) m_b378s551i4 15804 chrXqtel1M 967633 CCAATTGATAAATGGTCAAAGGATATGAAATAGACAATTTTCAGATGATG 967682 v v v -i i v v v L1ME5_3end#LI 58 CCAATAGAAAAATGGGCAAAGGATATGAA-CAGGCAATTTACAGAAGAGG 106 chrXqtel1M 967683 AA---TGAAATCATTACCACTCATATGAA-AGGTGTTCCAAATCATTATT 967728 ---i v-ii v vv - i i v v v L1ME5_3end#LI 107 AAACCCGAAAG-GCTAACAAGCATATGAAGAGATGCTCAAACTCATTAGT 155 chrXqtel1M 967729 AATCAGAGAAATACAAATT-AAACAACTCTGAGATACCAC----CACC-- 967771 i - vv i ---- -- L1ME5_3end#LI 156 AATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTACACCTA 205 chrXqtel1M 967772 TTCGATTAGCTAAGATGACAGGGAAA---AAATAACGATGAGTGTTGGAG 967818 v i i v i v ---- ---ii i vii v L1ME5_3end#LI 206 TTAGACTGGCAAAAATTA----GAAAGCTGGATAATGCCAAGTGTTGGCG 251 chrXqtel1M 967819 -GGATCTGCTGGCAT----------ATACATTGTTGGTGGCTTGAACGT- 967856 - v vv i? ---------- i i i --- ii - L1ME5_3end#LI 252 AGGATGTGGGGANATAGGAACCCTCATGCACTGCTGGTGG---GAGTGTA 298 chrXqtel1M 967857 --------CAACCATTCTGGAG-GCGATCTGGAATTAT---GCCCAA--A 967892 -------- i - i v v i--- i v -- L1ME5_3end#LI 299 GACTGGTGCAGCCATTCTGGAGAGCAATCTGGCAGTACTTAGTCAAATTA 348 chrXqtel1M 967893 AGGTTATCACTTTGCAT-CCC--TGATCCAAAGATTTT-CTACT-GGCAT 967937 -- - --- - -- i ivi ii- v - i L1ME5_3end#LI 349 AG--TAT-AC---GCATACCCTATGACCCAGCAATTCCGCTCCTGGGTAT 392 chrXqtel1M 967938 A-----CAAGGAGA-TCTAAAGAAGG-----AAAGGGACCAGTATGTGCC 967976 ----- i i - v viv ----- i ---- i v L1ME5_3end#LI 393 ATATCCCAAAGAAATTCTCACACAGGTCCATAAGGGGAC----ATGTACG 438 chrXqtel1M 967977 AAAATTTTG--TGCA-CCCTGTTTGTAATGGC-TAAAGCTGA----AACT 968018 ii v v-- - vi ii -vii i i---- i L1ME5_3end#LI 439 AGGATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAACC 488 chrXqtel1M 968019 GGTGGATGCCC-TTACT-TGAGAATGGTTTGGGTAAAT-TGGTATATGAA 968065 -- i i - i -v i v v vv - iv v L1ME5_3end#LI 489 --TGGGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCA 536 chrXqtel1M 968066 GGTTATGGAATATT-TGT-TCTGT--AAAATGACCAACAAGATGAATACA 968111 viii i i - i-v v --i iii vi v v i L1ME5_3end#LI 537 CACCATGGAGTACTATGCAGCAGTTAGAAGCAACGGACTAGATGTACACA 586 chrXqtel1M 968112 GAG-AGCTTGGA-GAATCT---GAAC---GTGCTAAGTGAAATGAAGC-A 968152 v - i v - i ---i --- i -i i- L1ME5_3end#LI 587 TAGCAACATGGATGGATCTTAAAAACATAGTGCTGAGTGAAA-AAAGTAA 635 chrXqtel1M 968153 GAACCAGA 968160 v L1ME5_3end#LI 636 GAAACAGA 643 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 29.43 CpG sites = 71, Kimura (unadjusted) = 30.00 Transitions / transversions = 1.37 (71/52) Gap_init rate = 0.11 (56 / 527), avg. gap size = 1.82 (102 / 56) 1371 28.07 7.87 3.53 chrXqtel1M 968559 969917 (30083) C L1M5_orf2#LINE/L1 (1841) 1453 38 m_b378s551i5 15803 chrXqtel1M 968559 TAAATGTTTAGTAGAATT-ACATGTAAATCCATCTGGTCCTGG-GTTTTT 968606 i - vv i v v - i C L1M5_orf2#LIN 1453 TAAATGTTTGGTAGAATTCACCAGTGAAGCCATCTGGGCCTGGAGTTTTC 1404 chrXqtel1M 968607 TT----GGGAGTTGATTAGTAACTTGTTCTATTTCTTTTTCTGAAAATGG 968652 ---- i v vv i v vvi v v-v ii v i C L1M5_orf2#LIN 1403 TTTGTGGGAAGGTTTTTAATTACAAATTCAATTTCTTTA-ATAGATATAG 1355 chrXqtel1M 968653 GACTTTTAACAATTT--ACTTCCTCCTCTGTTAATCTGGGAAACCTATAT 968700 i v v v v -- i i i v? i i i v v ?i i i C L1M5_orf2#LIN 1354 GGCTATTCAGATTTTCTATTTCTTCTTGNGTCAGTTTTGGTAANTTGTGT 1305 chrXqtel1M 968701 TTTTGGAG--ATGTCATCTATTTCACTTAGGTTATCAAATTTATTGGCAT 968748 vi -- - ii i ii i ? C L1M5_orf2#LIN 1304 TTTTCAAGGAAT-TTGTCCATTTCATCTAAGTTNTCAAATTTATTGGCAT 1256 chrXqtel1M 968749 AAAGTTGGGCAAAGTACTATTATTTCTTTTTCCTCTTCAT---TGTGGAA 968795 vv --- v v i iv v i v --- i i C L1M5_orf2#LIN 1255 AAAGTTGTTCA---TAATATTCTCTTATTATCCTTTTAATGTCTGTAGGA 1209 chrXqtel1M 968796 -----AGT----TCTCCTTTT-CATTT-TAAGACTAACAATTTGATTTTC 968834 ----- ---- - i- i v i iii vv i i C L1M5_orf2#LIN 1208 TCTGTAGTGATGTCTCCTTTTTCATTCCTGATATTGGTAATTTGTGTCTT 1159 chrXqtel1M 968835 CTCTTTCCTTTTCT-AATCAGATTTACCAAAGGTTT-------TTGTT-- 968874 i ii -i vi ?i i i ------- i -- C L1M5_orf2#LIN 1158 CTCTCTTTTTTTCTTGATCAGTCTNGCTAGAGGTTTATCAATTTTATTGA 1109 chrXqtel1M 968875 TTTTTCCATAAAATCAACTCTTAGTTTTATTTATTAGTTCAATAGTTTTT 968924 i i v i i i i i i ii v vvi v v ? ? C L1M5_orf2#LIN 1108 TCTTTTCAAAGAACCAGCTTTTGGCTTCGTTGATTTTCTCTATTGTNTNT 1059 chrXqtel1M 968925 TTTACTTTCAATATTATTAATTTCTCCTTTTAATTTTAGAATTTCAAGTT 968974 -ii v v i i v i vi vv vvvii C L1M5_orf2#LIN 1058 TT-GTTTTCTATTTCATTGATTTCTGCTCTTATCTTTATTATTTCCTTCC 1010 chrXqtel1M 968975 TAGTAATTGATTGGGATTTTTAAATTTGGTCTT---TTTCTAGCTTTTAA 969021 vv v ?v v i --- v --- i v C L1M5_orf2#LIN 1009 TTCTACTTNCTTTGGGTTT---AATTTGCTCTTCTTTTTCTAGCTTCTTA 963 chrXqtel1M 969022 AGTTGCAAGCCCAATTCACTGATCTT--TTCTTTC-TCTATTTTATGCAA 969068 v v ii iv i i --vi - v i --- v C L1M5_orf2#LIN 962 AGGTGGAAGCTTAGATCATTGATTTTAAGCCTTTCTTCTTTTCTA---AT 916 chrXqtel1M 969069 GTAAGCCTCTAAGGATATAAAATTTCCCCTTATTACTGCTTTGGCTGCAT 969118 i ? v i ? v v i i v vi i C L1M5_orf2#LIN 915 ATANGCATTTAANGCTATAAATTTCCCTCTAAGCACTGCTTTAGCTGCAT 866 chrXqtel1M 969119 C---CAAA-TTTGGCATATCAT-TTGTCATT-TC--TTGGTGGAA----- 969155 --- - ii i ii - v - -- ii vv ----- C L1M5_orf2#LIN 865 CCCACAAATTTTGATATGTTGTATTTTCATTNTCATTCAGTTCAAAATAT 816 chrXqtel1M 969156 TTATTAATTGTGTCTATAATTTGCTGTTTCACTCAATCATTCTTTA-AGA 969204 vi viv?i i i vi v v i vvvi v - ii C L1M5_orf2#LIN 815 TTTCTAATTTCCNTTGTGATTTCTTCTTTGACCCATGGGTTATTTAGAAG 766 chrXqtel1M 969205 TGAGATTATTTAGTTTCCAATTACTTTTTGGTCTATTTACCCTTAACTTT 969254 v - i i v - vv vi v i --v? v C L1M5_orf2#LIN 765 TGTG-TTGTTTAATTTCCAAATA-TTTGGGGATTTTCTA--GNTATCTTT 720 chrXqtel1M 969255 TTGTTA--AA--TGTAATATTTATTGTATCGTGATCTGAAAAGAAAGCAT 969300 --i -- v - v vi i i ----- i i - C L1M5_orf2#LIN 719 TTGTTATTGATTTCTAAT-TTAATTCCATTGTGGTC-----AGAGAACA- 677 chrXqtel1M 969301 TTACTATATTTGCCTTCCTGCATTT--AATT--TTGAG----GTCTTTAT 969342 - v i v vi vvv v -- -- ---- - C L1M5_orf2#LIN 676 -TACTCTGTATGATTTCAATCCTTTNAAATTTATTGAGACTTGT-TTTAT 629 chrXqtel1M 969343 GTCCTAATATATGGTCAATTTTTGTGTAGGTTCCATGAATTGC---TGAG 969389 v i i? v i v iv v --- --- i C L1M5_orf2#LIN 628 GGCCCAGNATATGGTCTATCTTGGTAAATGTTCCATG---TGCACTTGAA 582 chrXqtel1M 969390 AAGAAAGTATACTCCTTTCTGTCACCATT-----CAGTTTTCTCCAAAGA 969434 v i ----- i?iiii -----? v vi vi C L1M5_orf2#LIN 581 AAGAATGTGTA-----TTCTGCNGTTGTTGGGTGNAGTGTTCTATAAATG 537 chrXqtel1M 969435 TCTATCATATCTAATT--TTTCTAATATTATATTTACTTCTTTAATTTCT 969482 v i vi v i -- vv i i -- i i vv iv v i C L1M5_orf2#LIN 536 TCAATTAGGTCAAGTTGGTTGATAGTGT--TGTTCAAATCTTCTATATCC 489 chrXqtel1M 969483 TTCTTAATTGTTTTGTG-GTTTGATTTATCTAATT-CTGAGAGTGCGAGA 969530 vi i - v-ii v i - - v v?ivi C L1M5_orf2#LIN 488 TTACTGATT-TTTTGTCTACTTGTTCTATC-AATTACTGAGAGAGGNGTG 441 chrXqtel1M 969531 TTGAGATCTCCCACT---ATTATAGTTTTGCTGTCTATTTCTTCTTGCAG 969577 i i ? --- i i v --- i vi C L1M5_orf2#LIN 440 TTAAAATCTCCNACTATAATTGTGGATT---TGTCTATTTCTCCTTTTAG 394 chrXqtel1M 969578 CTCTCTTAACATCTTCTTTAGGAAGTTAGATGCTATACCACTTGGTGCAT 969627 i v i iiv i v i v v v v v v iii i v C L1M5_orf2#LIN 393 TTCTGTCAGTTTTTGCTTCATGTATTTTGAAGCTCTGTTATTAGGTGCAT 344 chrXqtel1M 969628 ATATGTTTAATATTGATATAGCTTCATTATTAAGT-ACCCTTT----AGT 969672 i ii iv v iv v v v v - ---- v C L1M5_orf2#LIN 343 ACACATTTAGGATTGTTATGTCTTCTTGATGAATTGACCCTTTTATCATT 294 chrXqtel1M 969673 AAGAATAGTTTCCTTCCTTATCTCTTTTAATTAGATCAATTTTGCTTT-- 969720 v -- i v i i vv --- i-- i i -- C L1M5_orf2#LIN 293 ATGA--AATGTCCCTCTTTATCTCTGGTAAT---ATT--TCTTGCCTTGA 251 chrXqtel1M 969721 ----TGCTTGATCTGAGATAAGGAT-GCTACCCTA-CTTTTTGACTTCAC 969764 ---- i vi v v iv - i ? i - i --- ii? C L1M5_orf2#LIN 250 AGTCTACTTTGTCTGATATTAATATAGCCACNCCAGCTTTCT---TTTGN 204 chrXqtel1M 969765 CTGA----AGCATAATAGAT-TCTGCTCAGCCTTTTACCTTTACTCTGTA 969809 i ii----v ii v - i vii v i i vi ? v C L1M5_orf2#LIN 203 TTAGTGTTTGCATGGTATATCTTTTTCCATCCTTTTACTTTCAACCTNTC 154 chrXqtel1M 969810 TGTATCTCCCTGTTTTAAATGTGTTTCCTGTAAACAACATATTGTAGGGT 969859 i iiv i v i i i i i i v v C L1M5_orf2#LIN 153 TGTGTCTTTATATTTAAAGTGCGTCTCTTGTAGACAGCATATAGTTGGGT 104 chrXqtel1M 969860 TCTGACTTTTGATTCAGTCTG----CCTCCAC--TTTA--TGGAGAGTTC 969901 ii vi v i ----i ii -- -- v i C L1M5_orf2#LIN 103 CTTGTTTTTTTATCCAGTCTGACAATCTCTGCCTTTTAATTGGAGTGTTT 54 chrXqtel1M 969902 ATCCCATTCACATTTA 969917 v? i C L1M5_orf2#LIN 53 AGNCCATTTACATTTA 38 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.42 CpG sites = 205, Kimura (unadjusted) = 36.69 Transitions / transversions = 1.26 (205/163) Gap_init rate = 0.07 (95 / 1358), avg. gap size = 1.65 (157 / 95) 263 26.26 9.64 3.35 chrXqtel1M 969810 970006 (29994) C L1MEi_5end#LINE/L1 (5) 2207 1999 m_b378s551i6 15803 chrXqtel1M 969810 TGTATCTCCCTGTTTTAAATGTGTTTCCTGTAAACAACATATTGTAGGGT 969859 i viii ii i i i v iv i C L1MEi_5end#LI 2207 TGTGTCGTTTTGTTTTAGGTGTGTCTCTTGTAAACAGCATATAGCTGGAT 2158 chrXqtel1M 969860 TCTGACTTTTGATTCAGTCTG----CCTCCA-CTTT--AT-GGAGAGTTC 969901 i vvi i i i ----i ii- -- - v i C L1MEi_5end#LI 2157 TTTTTTTTTTAATCCAATCTGATAATCTCTGTCTTTTAATAGGTGAGTTT 2108 chrXqtel1M 969902 ATCCCATTCACATTTATGGTTAAAATGACTAAT---TCTG----TATTTC 969944 vi i v ---i v i --- i ---- - C L1MEi_5end#LI 2107 AATCCATTTACATTTATTGT---GATTACTGATATATTTGGACTTATTT- 2062 chrXqtel1M 969945 CTGCCATCCTA----ATATCCCCAGATTATGCTTTTCTTTTTCTTGCCCC 969990 i i ----i i iii v v --iv ? -i? i C L1MEi_5end#LI 2061 CTACCATCTTATTTTGTGTTTTCTGTTTAT--CATNCTTTTTCTT-TNCT 2015 chrXqtel1M 969991 TCTTCTCCCCTTCCCT 970006 i i i C L1MEi_5end#LI 2014 TTTTCTCTCCTTTCCT 1999 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.98 CpG sites = 38, Kimura (unadjusted) = 34.98 Transitions / transversions = 3.17 (38/12) Gap_init rate = 0.07 (14 / 196), avg. gap size = 1.86 (26 / 14) 404 21.83 6.56 2.36 chrXqtel1M 969813 969934 (30066) C L1MEj_5end#LINE/L1 (0) 2160 2034 m_b378s551i7 15803 chrXqtel1M 969813 ATCTCCCTGTTTTAAATGTGTTTCCTGTAAACAACATATTGTAGGGTTCT 969862 v ii i i i v iv i C L1MEj_5end#LI 2160 ATCACTTTGTTTTAAGTGTGTTTCTTGTAAACAGCATATAGCTGGGTTTT 2111 chrXqtel1M 969863 GACTTTTGATTCAGTCT----GCCTCCA-CTTT--AT-GGAGAGTTCATC 969904 vi i ii i ---- i ii- -- - i vi C L1MEj_5end#LI 2110 GTTTTTTAACCCAATCTGACAGTCTCTGTCTTTTAATGGGAGAATTCAGT 2061 chrXqtel1M 969905 CCATTCACATTTATGGTTAAAATGACTAAT 969934 vv --- i i C L1MEj_5end#LI 2060 CCATTCACATTTAGTGT---AACGACTGAT 2034 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 25.68 CpG sites = 19, Kimura (unadjusted) = 26.88 Transitions / transversions = 2.71 (19/7) Gap_init rate = 0.06 (7 / 121), avg. gap size = 1.57 (11 / 7) 391 19.82 10.71 2.65 chrXqtel1M 969820 969959 (30041) C L1MEh_5end#LINE/L1 (7) 2228 2078 m_b378s551i8 15803 chrXqtel1M 969820 TGTTTTAAATGTGTTTCCTGTAAACAACATATTGTAGGGTTCTGACTTTT 969869 i i i i i v i i vi ? C L1MEh_5end#LI 2228 TGTTTTAAGTGTGTCTCTTGTAGACAGCATATTGTTGGATTTTGTTTTTN 2179 chrXqtel1M 969870 GATTCAGTCTG----CCTCCA--CTTTA--TGGAGAGTTCATCCCATTCA 969911 i i i ----i ii--i -- v i v i C L1MEh_5end#LI 2178 AATCCAATCTGANAATCTCTGTCTTTTAATTGGTGAGTTTAACCCATTTA 2129 chrXqtel1M 969912 CATTTATGGTTAAAATGACTA----ATTCTG---TATTTCCTGCCATCCT 969954 v --- v i---- ?v --- - i C L1MEh_5end#LI 2128 CATTTATTGT---AATTACTGNTATATTNGGACTTATTT-CTGCCATCTT 2083 chrXqtel1M 969955 AATAT 969959 v C L1MEh_5end#LI 2082 ATTAT 2078 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 24.20 CpG sites = 19, Kimura (unadjusted) = 24.20 Transitions / transversions = 2.38 (19/8) Gap_init rate = 0.06 (9 / 139), avg. gap size = 2.11 (19 / 9) 14 16.43 5.77 3.77 chrXqtel1M 970083 970134 (29866) (TTCCCTT)n#Simple_repeat 1 53 (0) m_b378s252i6 15805 chrXqtel1M 970083 TTCCCCTTT--CTTGTACC-CTTCCCTTATTACTCTTTTTTCTTTTCCCT 970129 i -- v v -i - - i ii (TTCCCTT)n#Si 1 TTCCCTTTTCCCTTTTCCCTTTTCCCTT-TT-CCCTTTTCCCTTTTCCCT 48 chrXqtel1M 970130 TTTCC 970134 (TTCCCTT)n#Si 49 TTTCC 53 Matrix = Unknown Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.08 (4 / 51), avg. gap size = 1.25 (5 / 4) 227 27.07 3.88 5.51 chrXqtel1M 970652 970780 (29220) C L1M6_5end#LINE/L1 (868) 1647 1521 m_b378s551i9 15803 chrXqtel1M 970652 TTTAATGTTG-AGGGCAGCCAGATGTTGAG--TGACCTTTATTGTGGCAC 970698 i - i v i v v ii- -- ii ------ C L1M6_5end#LIN 1647 TTTAGTGTTGCAGAGAAGTCTGAGGCC-AGCCTGATTTTTATT------C 1605 chrXqtel1M 970699 CTCGGTATTTGAATTGTTTTTTT--CTTGGCTGCTTGTAATATTTTTTCT 970746 iv vv i vi i-- i v iv C L1M6_5end#LIN 1604 CTTTGTAGGTAACCTGTTTTTTCTGCCTGGATGCTTGTAGGATTTTTTCT 1555 chrXqtel1M 970747 TTAGTTTGAAAATCCTGAAATTTGGCCACAATAT 970780 vii vi? i vi v vi C L1M6_5end#LIN 1554 TTATCCTTGNAATTCAAAAATTTTGCCAGGATAT 1521 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.66 CpG sites = 19, Kimura (unadjusted) = 34.66 Transitions / transversions = 1.36 (19/14) Gap_init rate = 0.08 (10 / 128), avg. gap size = 1.20 (12 / 10) 245 27.97 1.02 8.79 chrXqtel1M 972801 972898 (27102) C L1MD2_5end#LINE/L1 (653) 416 326 m_b378s551i10 15803 chrXqtel1M 972801 TGTGGTGCAAGAAAATCTGGAGAAAAGGAAAAAACAACAAAAA-GGTGAA 972849 v i i i i-- i v v - v i C L1MD2_5end#LI 416 TGGGGCGCGAGAGAAC--GGAGAAAAGAAAAAAAAAAAAAAAACGGGGGA 369 chrXqtel1M 972850 AAGTCTCTACTCTGATCCACTTTCAGCCTCCAGAGTTCTCTCTCCCGCT 972898 vvvi i i ------ i v v ivi i i i C L1MD2_5end#LI 368 TTTCCCCCACTCT------CTCTGAGCGTTAGGAGTCCCCTTTCCCGCT 326 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 30.54 CpG sites = 15, Kimura (unadjusted) = 35.67 Transitions / transversions = 1.50 (15/10) Gap_init rate = 0.09 (9 / 97), avg. gap size = 1.00 (9 / 9) 12 9.11 7.69 5.00 chrXqtel1M 973076 973114 (26886) (CCTGTC)n#Simple_repeat 1 40 (0) m_b378s252i7 15806 chrXqtel1M 973076 CCTGTGCCCATTGCCT-TCCCATG-CCC-GTCCCTGTCCCTG 973114 - vv v - - - - (CCTGTC)n#Sim 1 CCTGT-CCCTGTCCCTGTCCC-TGTCCCTGTCCCTGTCCCTG 40 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.13 (5 / 38), avg. gap size = 1.00 (5 / 5) 29 0.00 0.00 0.00 chrXqtel1M 973417 973443 (26557) (TCTCTG)n#Simple_repeat 1 27 (0) c_b378s251i2 15807 chrXqtel1M 973417 TCTCTGTCTCTGTCTCTGTCTCTGTCT 973443 (TCTCTG)n#Sim 1 TCTCTGTCTCTGTCTCTGTCTCTGTCT 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 33 0.00 0.00 0.00 chrXqtel1M 974243 974270 (25730) (AC)n#Simple_repeat 1 28 (0) c_b378s251i3 15808 chrXqtel1M 974243 ACACACACACACACACACACACACACAC 974270 (AC)n#Simple_ 1 ACACACACACACACACACACACACACAC 28 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 16 23.57 0.00 0.00 chrXqtel1M 974387 974421 (25579) (T)n#Simple_repeat 1 35 (0) m_b378s252i8 15809 chrXqtel1M 974387 TTTTATCTTCTTTTTTATCTTTTTTATTTTCTTTT 974421 v i i v i v i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 35 Matrix = Unknown Transitions / transversions = 1.33 (4/3) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 251 20.41 0.00 0.00 chrXqtel1M 975556 975604 (24396) C HERV15#LTR/ERV1 (420) 8331 8283 m_b378s701i0 15810 chrXqtel1M 975556 CACATACGCCTTCTTCAGCAGCCAAGAGATAGTCCAAAACCAATCTATT 975604 v i v vi i i i i i C HERV15#LTR/ER 8331 CACATACTCCTCCTTCTGAGGCTAAGAGGTAATCTAAAGCCAATCTATT 8283 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 24.57 CpG sites = 7, Kimura (unadjusted) = 24.57 Transitions / transversions = 2.33 (7/3) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 381 26.36 8.71 3.97 chrXqtel1M 976226 976466 (23534) C HERVK#LTR/ERVK (2283) 5253 5002 m_b378s701i1 15811 chrXqtel1M 976226 AGTATAAAGT--TAGATTTAGAAGTT-C-TCTAGGG----TTAC------ 976261 i -- --- - - i ----? ------ C HERVK#LTR/ERV 5253 AGTATAGAGTGCTAGATT---AAGTTGCATCTGGGGAGTGNTACACTCCT 5207 chrXqtel1M 976262 --CTGTGGCTCCCCCTTTCTTTTGTTT--TTGGAGGAGCATCTTAATATC 976307 -- -- ii --iiiivv - i v i i - C HERVK#LTR/ERV 5206 TACTGT--CTCCCCCTTCTTTTTGTTTAACCAATTGAGC-TTTGAGTGT- 5161 chrXqtel1M 976308 TCTGTTTCTCCTCTCTACTATTGCCTGTCCTTGAGGATTAAAAGGTATGC 976357 i vv i i v v i i v v v C HERVK#LTR/ERV 5160 TCTATTAGTTCTTTCAACTATGGCCTGTCCTTGGGAATTATAAGGAATTC 5111 chrXqtel1M 976358 CCGTGGTGTGTAAAATCTTATACTGTGCACAAAAGTGTGCTAAATGTTT- 976406 i v i iv i vi -iivi i i v vivi ? i - C HERVK#LTR/ERV 5110 CTGTTGTATGTGTAATTTTCCACTG-ATTTAAGAATTTTTGGAANGCTTT 5062 chrXqtel1M 976407 --TGAAGTATAAGCGGAACCATTGTCTGTTTTTATTGCTTATGGCACACC 976454 -- iv --v v iv v v vi v v v C HERVK#LTR/ERV 5061 ACTACAGTAT--CCTGGCCCATTGTCAGTTTTAATTTTTTCTGGAACTCC 5014 chrXqtel1M 976455 CATAATAGCAAA 976466 i i C HERVK#LTR/ERV 5013 CATGACAGCAAA 5002 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 33.52 CpG sites = 34, Kimura (unadjusted) = 33.52 Transitions / transversions = 1.26 (34/27) Gap_init rate = 0.08 (19 / 240), avg. gap size = 1.63 (31 / 19) 551 23.83 8.37 8.86 chrXqtel1M 976270 976711 (23289) C HERVK3#LTR/ERVK (2285) 4917 4478 m_b378s701i2 15811 chrXqtel1M 976270 CCCCCTTTCTTTTGTTTTTGGAGGA-GCATCTTAATATCTCTGTTTCTCC 976318 ? i -- vv iv - i iv i i v-i v vi C HERVK3#LTR/ER 4917 CCNCCCTT--TTTGTTTTTTCAACATGCGTTGTAATGTTTG-ATGTGCCC 4871 chrXqtel1M 976319 TCTCTACTATTGCCT-GTCCTTGAGGATTAAAAGGTATGCCCGTGGTGTG 976367 v - v - iv v v v i vv i C HERVK3#LTR/ER 4870 GCTCTA-TAATGCCTTGTCCTCTAGGATTATAAGGAATTCCTGTTTTATG 4822 chrXqtel1M 976368 TAAAATCTTATACTGTGCACAAAAGTGTGCTAAATGTTTTGAA------- 976410 vi----- ---- v iv ivv -- ------- C HERVK3#LTR/ER 4821 GG-----TTATA----GCCCAAAGCTGTAAGAAAT--TTTGAAAAGCATG 4783 chrXqtel1M 976411 ----GTATAAGCGGAACCATTGTCTGTTTTTA-TTGCTTATGGCACACCC 976455 ---- iv v - i - i iv C HERVK3#LTR/ER 4782 ACTAGTATAAGCGGGTCCATTGTCAGTTTTTAATTGTTTA-GGTATCCCC 4734 chrXqtel1M 976456 ATAATAGCAAATGCTTATGTGAGG-AAT-TCA------GTGACCACTCGG 976497 vv --- vv i- - i------i ----- C HERVK3#LTR/ER 4733 ATATGAGCAAATG---ATGACAGACAATGTCGCCGTACATGACCA----- 4692 chrXqtel1M 976498 GTTGTCTCTTTTGCT--GC---TAGCATTGCAAAA-GTGAATCCCGAAAA 976541 i vii i -- --- - iv -i ----- v C HERVK3#LTR/ER 4691 GCTGTCTCACCTGTTTGGCATGTAGCAT-GCAGCATATGA-----GAATA 4648 chrXqtel1M 976542 GGTGTCTAC----CACAATGTGGATGAAAGATA-GATGACCAAAAGAT-T 976585 i i---- ----- vv v v - v vi i v -i C HERVK3#LTR/ER 4647 AGTGTCTATAGNTCACA-----GAACATAGCTAAGCTTGCCAAAGGCTGC 4603 chrXqtel1M 976586 TATAATGGGTCACATCCATTTGCCAGATTTCATTGGGTCTCAAACCACGA 976635 i- v v v vvi v v C HERVK3#LTR/ER 4602 TATG-TGTGTAACATCCATTTGCCAGATTTCATTTGGAGCCAAACCTCGT 4554 chrXqtel1M 976636 GGGTT-CTTCC--CTGGAGGGAGTGTAGGAACATGGAAAGGAAGGCAAGC 976682 - v? -- iv --- ii v?v v v v vv i C HERVK3#LTR/ER 4553 GGGTTACANCCTTCTACAG---GTGCGGCNCCAGGGACATGCTGGCAAGT 4507 chrXqtel1M 976683 CGTACAGGCTTTTACTATGGTCCTAGCTT 976711 v v v ? i i C HERVK3#LTR/ER 4506 AGGACAGGCTTGTACNATAGCCCTAGCTT 4478 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 28.02 CpG sites = 40, Kimura (unadjusted) = 29.08 Transitions / transversions = 0.71 (40/56) Gap_init rate = 0.12 (55 / 441), avg. gap size = 1.38 (76 / 55) 18 0.00 0.00 0.00 chrXqtel1M 976947 976966 (23034) (AT)n#Simple_repeat 1 20 (0) m_b378s252i9 15812 chrXqtel1M 976947 ATATATATATATATATATAT 976966 (AT)n#Simple_ 1 ATATATATATATATATATAT 20 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 344 28.95 11.37 0.94 chrXqtel1M 978012 978398 (21602) C HERVK11#LTR/ERVK (4393) 3560 3134 m_b378s701i3 15811 chrXqtel1M 978012 TGACACATAGTAGGGCTGTTTT---TTCCCTGGGCAAA-ACTGTCCATT- 978056 i v v i v--- i v i- v - C HERVK11#LTR/E 3560 TGGCAGATTGTAGGGCTATTTAGCATTCCCTGAGGAAGTACTTTCCATTG 3511 chrXqtel1M 978057 ----CTATTTA-AGGCTC---AGTGTTTAACGCTGG-GCACTAAAAAAAA 978097 ---- v vi i- --- v i v vv v -i v iv C HERVK11#LTR/E 3510 ATAACGAGCTGCAGGCTCCTGATTATTGATAGATGGTACAGTAAAAGCAA 3461 chrXqtel1M 978098 TCTTTTCATATCCTCCCTTTATCCAGAGGGATA-GAATGAAACAACCTT- 978145 vi i vi - vv vi i vi - vi i - C HERVK11#LTR/E 3460 ATTTTTCACAATC-CGATTTATGTAAAGCAATATGAAAAAAACAATCTTT 3412 chrXqtel1M 978146 AATATCTATGATCCAAAGAGGCCA-TTCTCACA-ATTA--GTGGGAGATG 978191 v v i iivvi - i i vi- -- ii i vv C HERVK11#LTR/E 3411 AAGATCAATAACTATGAGAGGCCAATTTTTAGGTATTAAAGCAGGGGCAG 3362 chrXqtel1M 978192 GAA--CCAGGCTGAAAAATTCCCATAG-TTTATCT---TCATTCA---CC 978232 v -- i i i viiii - vi ---v v --- C HERVK11#LTR/E 3361 GCATGCCGGGTTGGACGGCCCCCATAGGTTTAATTACAGCATTAATGGCC 3312 chrXqtel1M 978233 TTCTTAAATCC-TTAACATCCTCTATTTTCCAGATTTCT-TTTTACAACA 978280 -- v- v v i i v v - v v C HERVK11#LTR/E 3311 --CTTAAATCGGTTACCATCCGCCACTTGCCTGATTTCTTTTTTACTAGA 3264 chrXqtel1M 978281 AAT-CTGGGGAATCCCAAGGAT-TAGA-AAGGTTTTAAGTGTCCTTGGTC 978327 i- v i i i iv-v - ii vi v vv v v C HERVK11#LTR/E 3263 AACACAGGAGAATTCCAGGGGGAAAGAGAAGGTTCCACATTTCCAAGTTG 3214 chrXqtel1M 978328 AAACCCTT-----ACCAATT---CTAAGGCCTGAATTTTATCATTACTTA 978369 v iv ----- ---i i vv v v v -vv C HERVK11#LTR/E 3213 TAACTGTTCAGAAACCAATTGAGTTAAAGCCTCCAGTTTTTCTTTA-GAA 3165 chrXqtel1M 978370 AGGGGCTACTGCT--ATCCACACTGGTGTAT 978398 v i -- v v i C HERVK11#LTR/E 3164 AGCGGCCACTGCTGAATCCAAACGGGTGTGT 3134 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 36.05 CpG sites = 50, Kimura (unadjusted) = 36.86 Transitions / transversions = 0.82 (50/61) Gap_init rate = 0.07 (28 / 386), avg. gap size = 1.71 (48 / 28) 250 25.35 0.00 0.00 chrXqtel1M 979978 980048 (19952) C HERVK11#LTR/ERVK (6683) 1270 1200 m_b378s701i4 15811 chrXqtel1M 979978 AAATTCTGTAATAGCATCTTAACATAAGCTGATGTAGCCCCATAAAGAGT 980027 v i v i vv v vv vv C HERVK11#LTR/E 1270 AAAGTTTGTAATACCATTTTAACATAAGGAGAAGTAGGACCATACTGAGT 1221 chrXqtel1M 980028 GCAAGCCTTTTTCAGGTCTTT 980048 i v ii v iv C HERVK11#LTR/E 1220 ACAAGCATCCTTAAATTCTTT 1200 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 30.94 CpG sites = 6, Kimura (unadjusted) = 30.94 Transitions / transversions = 0.50 (6/12) Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0) 256 31.03 5.75 0.00 chrXqtel1M 983371 983457 (16543) C MIR3#SINE/MIR (0) 208 117 m_b378s601i2 15813 chrXqtel1M 983371 GATTCATCACATCATAGACCTTAAAAG-----AGAGACTTTGAATGTCAT 983415 v viv viv v i ----- i i ii vi C MIR3#SINE/MIR 208 GAATCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCAT 159 chrXqtel1M 983416 GTACATCATCAGCTTCATTTTACAGATAGGAAAATTGAGGCC 983457 v vvi v vv i ii i i C MIR3#SINE/MIR 158 CTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCC 117 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.74 CpG sites = 14, Kimura (unadjusted) = 40.74 Transitions / transversions = 1.08 (14/13) Gap_init rate = 0.01 (1 / 86), avg. gap size = 5.00 (5 / 1) 33 24.72 1.97 6.90 chrXqtel1M 984150 984301 (15699) (ATTA)n#Simple_repeat 1 145 (0) m_b378s252i10 15814 chrXqtel1M 984150 ATTGAATAAGTTAGTAAATTAATAAAATCTATTTAAGATAATAAAATTAA 984199 - v i i v -v - v -v -v (ATTA)n#Simpl 1 ATT-AATTAATTAATTAATTAAT-TAAT-TAATTAA-TTAAT-TAATTAA 45 chrXqtel1M 984200 TTAATAGAGATCGCCTGAATTAATTAATAAATTAA-TAA-AAATCGAAGA 984247 -v - -vvv v v - -v ii vv (ATTA)n#Simpl 46 TTAAT-TA-AT-TAATTAATTAATTAATTAATTAATTAATTAATTAATTA 92 chrXqtel1M 984248 AGTAATTAATAAAATTAA-TGATTAATTAAATAAATTATTTTAAAAATTA 984296 v -v - i - v v v vv (ATTA)n#Simpl 93 ATTAATTAAT-TAATTAATTAATTAATT-AATTAATTAATTAATTAATTA 140 chrXqtel1M 984297 ATAAA 984301 v (ATTA)n#Simpl 141 ATTAA 145 Matrix = Unknown Transitions / transversions = 0.22 (5/23) Gap_init rate = 0.09 (13 / 151), avg. gap size = 1.00 (13 / 13) 59 38.28 2.53 1.75 chrXqtel1M 984724 985119 (14881) (CT)n#Simple_repeat 1 399 (0) m_b378s252i11 15815 chrXqtel1M 984724 CTTTCTCTTACTGTCTCTGTCTCTGTCTTTCT-TATTTC-CTTCCTGACT 984771 i iv v v v i - v i - ii vv (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 chrXqtel1M 984772 CTTTTCCTGTCTCTGTCT-TTTCTCCATTTCTCCATCTCTGATCT-TCT- 984818 i ii v v - i iv i iv -v - - (CT)n#Simple_ 51 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT-CTCTCTCTC 99 chrXqtel1M 984819 TCTCTTTTTCAGTCTTTTTCATC-CTTGCTCTCTCTTTCTCTGTCATTTT 984867 i i vv i i - - iv i v vi i (CT)n#Simple_ 100 TCTCTCTCTCTCTCTCTCTC-TCTCTCTCTCTCTCTCTCTCTCTCTCTCT 148 chrXqtel1M 984868 CTCTTTCTCTCTGTCTCCATCTATCATATCTGTTTCTCTCTCTTTTTCTA 984917 i v iv v - v v i i i v (CT)n#Simple_ 149 CTCTCTCTCTCTCTCTCTCTCTCTC-TCTCTCTCTCTCTCTCTCTCTCTC 197 chrXqtel1M 984918 AATTTCTCTAAGATTCCCTGACTTTGTTTCATTCTTTTTGT-TCATATGC 984966 vv i vvvvi i vv i v i vi i i v - - v - (CT)n#Simple_ 198 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TCT-C 245 chrXqtel1M 984967 TCTTTTGTTCTCTTGCTTGCATTCTCTCTGGATCTCATTCTCTCCCTCTC 985016 i ivi iv iv vi vvv vi i (CT)n#Simple_ 246 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 295 chrXqtel1M 985017 CCCCTCATATTTTTCT-TTTTTCCCTCTATCTGTTTTTCTCTGTCTCTGT 985065 i i - v i i - i i i v v i i v v (CT)n#Simple_ 296 TCTCTC-TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 344 chrXqtel1M 985066 CTCTCCCCCAC-CTCTTTTCCCCTCTCT-TCATCCTTCTTTTCCTCCCCC 985113 i i v - i ii i - - ii i ii i i (CT)n#Simple_ 345 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TCTCTCTCTCTCTCTCTC 393 chrXqtel1M 985114 TCTCTC 985119 (CT)n#Simple_ 394 TCTCTC 399 Matrix = Unknown Transitions / transversions = 1.31 (64/49) Gap_init rate = 0.04 (17 / 395), avg. gap size = 1.00 (17 / 17) 250 36.68 3.55 1.39 chrXqtel1M 986496 986636 (13364) L2#LINE/L2 2718 2861 (221) m_b378s601i3 15816 chrXqtel1M 986496 TATTGTAAGATTCTCCTAATCAGCAACTCTATCTCCATTC-TGCCCCACC 986544 i i v vi iii ivv i iii ii - -- L2#LINE/L2 2718 TACTGCAATAGCCTCCTAACTGGTCTCCCTGCTTCCACCCTTGCCC--CC 2765 chrXqtel1M 986545 CTCTAAACTATTCC--ACACCACTGGCAAATTGATAGCCTTGAATGACAG 986592 ?i iv i-- vi v v i v vvii i vvii i L2#LINE/L2 2766 CTNCAGTCTATTCTCAACACAGCAGCCAGAGTGATCCTTTTAAAACGTAA 2815 chrXqtel1M 986593 GTTAGAT--TGTCAGCCTCATGCTCAGGAAGCTTCAAGTGTTTCCC 986636 i -- vi iiv ii vv i vv i L2#LINE/L2 2816 GTCAGATCATGTCACTCCTCTGCTCAAAACCCTCCAATGGCTTCCC 2861 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 52.44 CpG sites = 32, Kimura (unadjusted) = 54.05 Transitions / transversions = 1.68 (32/19) Gap_init rate = 0.04 (5 / 140), avg. gap size = 1.40 (7 / 5) 557 23.25 15.59 2.87 chrXqtel1M 986914 987099 (12901) MIRc#SINE/MIR 19 227 (41) m_b378s601i4 15817 chrXqtel1M 986914 TGGATAGCATACTGCAGTGACCTGGAGGCAAGAAGACCGAAGAGCAAA-- 986961 v vii ---- i v i vii vv i i-- MIRc#SINE/MIR 19 TGGAAAGAGCACTG----GACTTGGAGTCAGGAAGACCTGGGTTCGAGTC 64 chrXqtel1M 986962 ---------ATATTTACTGGCTATGTGATCCTGGACAACTCACTTCACCT 987002 ---------vi i i i i i i v v MIRc#SINE/MIR 65 CCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCT 114 chrXqtel1M 987003 C----------AGTTTAC--AACTGTAAAATGGGGATAAATAATAT---- 987036 ---------- v -- v - i---- MIRc#SINE/MIR 115 CTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAA-TAATACCTGC 163 chrXqtel1M 987037 --TACCTGTCTCCAAGAGTTGTTGTGAAGAGCAAATGAGCTAAAATGTGT 987084 -- i ii vv i i v v vi i MIRc#SINE/MIR 164 CCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGT 213 chrXqtel1M 987085 AAAAAGCACTTTGCA 987099 -i i i MIRc#SINE/MIR 214 -GAAAGCGCTTTGTA 227 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 27.03 CpG sites = 26, Kimura (unadjusted) = 28.62 Transitions / transversions = 1.62 (26/16) Gap_init rate = 0.06 (12 / 185), avg. gap size = 2.92 (35 / 12) 676 20.99 7.50 1.78 chrXqtel1M 986964 987123 (12877) MIR#SINE/MIR 72 240 (22) m_b378s601i5 15817 chrXqtel1M 986964 ATTTACTGGCTATGTGATCCTGGACAACTCACTTCACCTC---------- 987003 i i i i i i v i v ---------- MIR#SINE/MIR 72 ACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTC 121 chrXqtel1M 987004 AGTTTAC--AACTGTAAAATGGGGATAAATAATATTACCTGTCTCCAAGA 987051 v -- v - v ii vv i MIR#SINE/MIR 122 AGTTTCCTCATCTGTAAAATGGGGATAA-TAATAGTACCTACCTCATAGG 170 chrXqtel1M 987052 GTTGTTGTGAAGAGCAAATGAGCTAAAATGTGTAAAAAGCACTTTGCACA 987101 i vi i v ii -- i v v MIR#SINE/MIR 171 GTTGTTGTGAGGATTAAATGAGTTAATACATGT--AAAGCGCTTAGAACA 218 chrXqtel1M 987102 GTACTTGGCATATTGTAGGCAC 987123 i i i v i i MIR#SINE/MIR 219 GTGCCTGGCACATAGTAAGCGC 240 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 23.51 CpG sites = 21, Kimura (unadjusted) = 25.22 Transitions / transversions = 1.75 (21/12) Gap_init rate = 0.03 (5 / 159), avg. gap size = 3.00 (15 / 5) 199 28.79 6.06 0.00 chrXqtel1M 988715 988780 (11220) C MIRc#SINE/MIR (175) 93 24 m_b378s601i6 15818 chrXqtel1M 988715 GTCACATGACCATTATGTATCAGAGGCAGTCCTTGCAGCCAGGTTTTCCT 988764 iii i v v iv v i vv i v v i C MIRc#SINE/MIR 93 GTCACACAGCTAGTAAGTGGCAGAGCCGGGACTCGAACCCAGGTCTTCCT 44 chrXqtel1M 988765 --TTC--AGTCCAGTACACT 988780 --i -- i v C MIRc#SINE/MIR 43 GACTCCAAGTCCAGTGCTCT 24 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 32.26 CpG sites = 10, Kimura (unadjusted) = 36.90 Transitions / transversions = 1.11 (10/9) Gap_init rate = 0.03 (2 / 65), avg. gap size = 2.00 (4 / 2) 24 14.38 4.35 0.00 chrXqtel1M 989490 989535 (10465) (TA)n#Simple_repeat 1 48 (0) m_b378s252i12 15819 chrXqtel1M 989490 TATATGT-TAAATACA-ATATATGTATATATATATATCTATATCTATA 989535 i - v i - i v v (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATA 48 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.04 (2 / 45), avg. gap size = 1.00 (2 / 2) 777 31.02 0.79 1.33 chrXqtel1M 989813 990191 (9809) C L1ME3G_3end#LINE/L1 (292) 632 256 m_b378s551i11 15820 chrXqtel1M 989813 CCTGCTCATTTCACTCAGCATCAGTTCCTGTAAGCCTCTCCCAGCCTCTC 989862 i iv i vi vv i v iii i vv i vv v C L1ME3G_3end#L 632 CTTGCTTTTTTCACTCAACAATATGTCTTGGAGATCTTTCCATGTCAGTA 583 chrXqtel1M 989863 TATATTCATCCTGCTTGTCATTTCTTACAGAACAATAGCATTCTATAACA 989912 i vv ivv ii iv i v ? vvvv i i ii C L1ME3G_3end#L 582 CATATAGATCTACCTCATTCTTTTTAACNGCTGCATAGTATTCCATAGTA 533 chrXqtel1M 989913 TTCATATTCCACAATTTATTCATCCATTCTCCAATTGATGGGCATCCACT 989962 vv v i i v i v i ii vv C L1ME3G_3end#L 532 TGGATATACCATAATTTATTTAACCATTCCCCTATTGATGGACATTTAGG 483 chrXqtel1M 989963 CAGTTTCCAGTTTCTGGCCAGTACAAAGAGGACTGCCCCAAACATTCTTG 990012 iv i i v i v v ivi vvii i C L1ME3G_3end#L 482 TTGTTTCCAATTTTTCGCTATTACAAACAATGCTGCAATGAACATCCTTG 433 chrXqtel1M 990013 CATATACAGGTCCCTCTCC-CTTCTTTAAG-ATTTCTTTAGGATATA-GC 990059 i i i --? i v v - v v vii - ? v -? C L1ME3G_3end#L 432 TACATGC--NTCCTTGTGCACATGTGCGAGTATTTCTNTAGGATAGATNC 385 chrXqtel1M 990060 CCAGTAGCAACAGTGCTGGATCAAAGGGGATGCACAGTTTGATAACTTTT 990109 ? v iiiv v i v i v --- v C L1ME3G_3end#L 384 CNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGCATTT---TAAATTTT 338 chrXqtel1M 990110 TGCACATAGTTCCAAATCGCTCTCCAGAATGACTGGATGTATTCACAGTT 990159 vii v v v i i i ? i v ivv i v i C L1ME3G_3end#L 337 AATAGATACTGCCAAATTGCCCTCCAAAANGGCTGTACCAATTTACACTC 288 chrXqtel1M 990160 CCACCAACAATGTATCAGTGTCCCAGTGTCCC 990191 i i v v v v v C L1ME3G_3end#L 287 CCACCAGCAGTGTATGAGAGTACCCGTTTCCC 256 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 40.45 CpG sites = 57, Kimura (unadjusted) = 41.42 Transitions / transversions = 0.97 (57/59) Gap_init rate = 0.02 (8 / 378), avg. gap size = 1.00 (8 / 8) 556 32.78 2.76 0.54 chrXqtel1M 990724 990904 (9096) C MIR3#SINE/MIR (21) 187 3 m_b378s601i7 15821 chrXqtel1M 990724 TTAGGGCTGAAAAGGATCTTGAGGATGACTGAGTCCAAACTTCTCATTTT 990773 i i i i i iii v iiv v ii C MIR3#SINE/MIR 187 TCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCTCATTTT 138 chrXqtel1M 990774 CTAGATGTAGAAACTGAGGCTCAGAAATCTTAAGTGACTTGTCGAGAGTC 990823 vi vi i i vv v i v ii C MIR3#SINE/MIR 137 ACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTC 88 chrXqtel1M 990824 ACACAGTTGATGAGTGATAA----GGAATTCAGAGCTAGAGATTTCAGCT 990869 i?ii v ii i---- i i - i ivii vi i v vi C MIR3#SINE/MIR 87 ACACAGCNAGTTAGTGGCAGAGCCGGGACT-AGAACCCAGGTCTCCTGAC 39 chrXqtel1M 990870 TCCAAGTGTGAG-TCTATCTCCTGTGCAACACTGTC 990904 v vi v - v v vv v v i C MIR3#SINE/MIR 38 TCCCAGTCCGTGCTCTCTCTGCTCAGCCACTCTGCC 3 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 44.19 CpG sites = 36, Kimura (unadjusted) = 45.25 Transitions / transversions = 1.57 (36/23) Gap_init rate = 0.02 (3 / 180), avg. gap size = 2.00 (6 / 3) 69 3.01 0.00 0.00 chrXqtel1M 991133 991200 (8800) (TC)n#Simple_repeat 1 68 (0) c_b378s251i4 15822 chrXqtel1M 991133 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCGCTCTCTCTCTCTC 991182 v (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 chrXqtel1M 991183 TCTCTCTCTCTCGCTCTC 991200 v (TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTC 68 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0) 455 24.74 0.74 7.87 chrXqtel1M 991218 991353 (8647) C MIRb#SINE/MIR (138) 130 4 m_b378s601i8 15823 chrXqtel1M 991218 CTGAGGC-AATTGGGGTTAAGTGACTTGCCTAGTGTCACATAGCTAAGAA 991266 -v vv i i i iv i iv C MIRb#SINE/MIR 130 CTGAGGCTCAGAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAA 81 chrXqtel1M 991267 GTGTTAGGTGTCTGAGGCTCGATTGGAACTCAGGTTCTCCTGACTTCAGG 991316 vi ------- v vv v i iivi i ii C MIRb#SINE/MIR 80 GTGGCAG-------AGCCGGGATTCGAACCCAGGTCTGTCTGACTCCAAA 38 chrXqtel1M 991317 GCTGGTACTCTACCCACTGTACCACCTAGCTGCCCCT 991353 iv i vi i --- C MIRb#SINE/MIR 37 GCCCGTGCTCTTTCCACTGCACCAC---GCTGCCCCT 4 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 30.40 CpG sites = 18, Kimura (unadjusted) = 30.40 Transitions / transversions = 1.38 (18/13) Gap_init rate = 0.08 (11 / 135), avg. gap size = 1.00 (11 / 11) 215 19.44 0.00 0.00 chrXqtel1M 991667 991702 (8298) C MIR3#SINE/MIR (23) 185 150 m_b378s601i9 15824 chrXqtel1M 991667 AAAGCTGAAAGGGACCCTGGGTATCATCTAGTTCAA 991702 i i i i iv i C MIR3#SINE/MIR 185 AGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAA 150 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 23.83 CpG sites = 6, Kimura (unadjusted) = 23.83 Transitions / transversions = 6.00 (6/1) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 34 18.25 3.57 2.35 chrXqtel1M 991859 991942 (8058) (TA)n#Simple_repeat 1 85 (0) m_b378s252i13 15825 chrXqtel1M 991859 TATAAATATAGCAAATATATATTTATATA-ACATATAAATATAT-TTTAC 991906 v -i v v - i v - v i (TA)n#Simple_ 1 TATATATATA-TATATATATATATATATATATATATATATATATATATAT 49 chrXqtel1M 991907 TTATACAGTATATTTATATATGT-TATATAAATATAT 991942 v i - v i - v (TA)n#Simple_ 50 ATATATA-TATATATATATATATATATATATATATAT 85 Matrix = Unknown Transitions / transversions = 0.62 (5/8) Gap_init rate = 0.06 (5 / 83), avg. gap size = 1.00 (5 / 5) 237 36.16 0.97 2.45 chrXqtel1M 992523 992729 (7271) C L1ME2z_3end#LINE/L1 (564) 627 424 m_b378s551i12 15826 chrXqtel1M 992523 TTCACTCAGCATTG-GTTCCTGTAAGTTTTCCATATTTTTGTAAA-ATCA 992570 vi- ii vi v iv i v iivi- C L1ME2z_3end#L 627 TTCACTCAGCATAATGTTTTTGAGATTCATCCATGTTGTTGCGTGTATCA 578 chrXqtel1M 992571 ACTTGTTCATTATTTCTTAAAGCACAATGATATTCCATTCCATTCATATT 992620 i- v i vi i vv vv i ii vi vv v C L1ME2z_3end#L 577 G-TAGTTCGTTCCTTTTTATTGCTGAGTAGTATTCCATTGTATGAATATA 529 chrXqtel1M 992621 CCACAAATTAATCACCCCTAGCCCAATGGATGGGCATCCCCTCAGTTTGC 992670 iv iv i i v vvi vi v i i ivvv v v C L1ME2z_3end#L 528 CCACAGTTTGTTTATCCATTCTCCTGTTGATGGACACCTGGGCTGTTTCC 479 chrXqtel1M 992671 AGCTCTTTGCCACCATAAAATGAGCCGTTGTAACTATTTTTGTATATATG 992720 i i v i ii i vvi i i i i vi i i ---- C L1ME2z_3end#L 478 AGTTTTTGGCTATTATGAATAAAGCTGCTATGAACATTCTTGTACA---- 433 chrXqtel1M 992721 GGTCTTTTT 992729 i C L1ME2z_3end#L 432 AGTCTTTTT 424 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 48.96 CpG sites = 41, Kimura (unadjusted) = 51.07 Transitions / transversions = 1.28 (41/32) Gap_init rate = 0.03 (7 / 206), avg. gap size = 1.00 (7 / 7) 400 32.53 2.37 3.59 chrXqtel1M 993146 993314 (6686) C MIR3#SINE/MIR (0) 208 42 m_b378s601i10 15827 chrXqtel1M 993146 GAACCATTAAAATCCCAGAAACCTAAAACCAGAAGCGTCTTTACCAATAG 993195 i - i vi vvii i i ii v v i vvi vi C MIR3#SINE/MIR 208 GAATCAT-AGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCA 160 chrXqtel1M 993196 TCTAGAGTGAGCCCTTCATTTCAT---TGAGGAGATTAAGGCAAAGAAAA 993242 vvii v i i i--- i i i vv i i C MIR3#SINE/MIR 159 TCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAG 110 chrXqtel1M 993243 GTGAATTT-TTTGCCTGAGGTCATACAGCTAATCAGCGGGCTGAGCTGTG 993291 v v-i ii i ? i i i- v i v C MIR3#SINE/MIR 109 GTGAAGTGACTTGCCCAAGGTCACACAGCNAGTTAGT-GGCAGAGCCGGG 61 chrXqtel1M 993292 GCGGGCAGCTCGGGTGAACTCCT 993314 i vi - i i i --- C MIR3#SINE/MIR 60 ACTAG-AACCCAGGT---CTCCT 42 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 44.26 CpG sites = 35, Kimura (unadjusted) = 45.46 Transitions / transversions = 1.94 (35/18) Gap_init rate = 0.05 (8 / 168), avg. gap size = 1.25 (10 / 8) 188 26.09 2.17 0.00 chrXqtel1M 993496 993541 (6459) C L3b_3end#LINE/CR1 (640) 566 520 m_b378s601i11 15828 chrXqtel1M 993496 TTACATTGAGTTTGCAGTTCACT-GAATCCCCATATCCTTTTCAAAT 993541 i i i i iv -i i vi i v C L3b_3end#LINE 566 TCATATTGAGCTTGCGGTCAACTAAAACCCCCAGGTCTTTTTCACAT 520 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 30.51 CpG sites = 9, Kimura (unadjusted) = 33.98 Transitions / transversions = 3.00 (9/3) Gap_init rate = 0.02 (1 / 45), avg. gap size = 1.00 (1 / 1) 275 27.38 7.14 0.00 chrXqtel1M 993633 993716 (6284) L2c_3end#LINE/L2 374 463 (15) m_b378s601i12 15829 chrXqtel1M 993633 AGAGTGAGACCTCTTTGAGAGCACGAACTGTGACTT-TTC-TACTCATAG 993680 v v v i i v i i v - - vi ii v L2c_3end#LINE 374 AGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTAT 423 chrXqtel1M 993681 CCCCAGTGCTTAGAACATAGGAAA----CAACAAATGCTT 993716 i i i v v ii---- i i L2c_3end#LINE 424 CCCCAGCGCCTGGCACATAGTAGGCGCTCAATAAATGTTT 463 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 31.37 CpG sites = 14, Kimura (unadjusted) = 35.06 Transitions / transversions = 1.56 (14/9) Gap_init rate = 0.04 (3 / 83), avg. gap size = 2.00 (6 / 3) 13 21.84 0.00 0.00 chrXqtel1M 993717 993749 (6251) (CATT)n#Simple_repeat 1 33 (0) m_b378s252i14 15830 chrXqtel1M 993717 CATTTGTTCACTCCTTCATCCATCCATTCATTC 993749 ii i v i i (CATT)n#Simpl 1 CATTCATTCATTCATTCATTCATTCATTCATTC 33 Matrix = Unknown Transitions / transversions = 5.00 (5/1) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 237 26.43 4.44 3.30 chrXqtel1M 993750 993839 (6161) L2a_3end#LINE/L2 422 512 (5) m_b378s601i13 15831 chrXqtel1M 993750 ATTCTTGTCTATTTGTCTTTGCATTCTCTTCCCCCAAGCACCTAAAAATG 993799 i i i - v ii - v v vi - i i vv L2a_3end#LINE 422 ACTTTTGTCTGTTT-TGTTCAC-TGCTGTATCCCCA-GCGCCTAGAACAG 468 chrXqtel1M 993800 TGTCTGTTGCATAGTAGATGATC----AATATTTCTTGACTGAA 993839 i vii ii v ---- v v L2a_3end#LINE 469 TGCCTGGCACATAGTAGGCGCTCAATAAATATTTGTTGAATGAA 512 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 29.82 CpG sites = 13, Kimura (unadjusted) = 33.23 Transitions / transversions = 1.30 (13/10) Gap_init rate = 0.04 (4 / 89), avg. gap size = 1.75 (7 / 4) 343 29.14 0.00 2.53 chrXqtel1M 994764 994844 (5156) C MIR3#SINE/MIR (17) 191 113 m_b378s601i14 15832 chrXqtel1M 994764 AGTGCTAGAACTAGAACAGACCTCTTAAAGATCATCTGATTCAACCTTCT 994813 i ii i i vi -- i ii i ii C MIR3#SINE/MIR 191 AATGTCAGAGCTGGAAGGGACCT--TAGAGATCATCTAGTCCAACCCCCT 144 chrXqtel1M 994814 TGTCTTTCTGAGAAGGAAACTGAGGCTTGGA 994844 ii i v v vi iii C MIR3#SINE/MIR 143 CATTTTACAGATGAGGAAACTGAGGCCCAGA 113 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 40.60 CpG sites = 19, Kimura (unadjusted) = 40.60 Transitions / transversions = 4.75 (19/4) Gap_init rate = 0.03 (2 / 80), avg. gap size = 1.00 (2 / 2) 391 35.69 9.03 6.39 chrXqtel1M 994894 995336 (4664) C L3#LINE/CR1 (70) 4029 3576 m_b378s601i15 15833 chrXqtel1M 994894 AAGAATCTTTTCTTCAGCTTTCTCAGAGAGTCAGCATTGAGTCATGGCTT 994943 i ii v i v i iiiivi viv iv i viv C L3#LINE/CR1 4029 AGGAATCCCTTCTACAACATCCCTGACAAGTGGTCATCCAGCCTCTGCTT 3980 chrXqtel1M 994944 GAAGTTCTT-GGTGACAGGGAATTGGGAACAGCTTTAACTGTTA--GCAG 994990 vvi i-i i ii ----- ---i v v?ii-- C L3#LINE/CR1 3979 GAACACCTCCAGTGACGGGGAGCT-----CA---CTACCTCNCGAGGCAG 3938 chrXqtel1M 994991 CTTGATTTGTGTTTG--TTGTTTT--TCATTTG---GTTTTTC---ACAT 995030 iiiv iii v --iv i i -- ii v --- i --- i C L3#LINE/CR1 3937 CCCATTCCATTTTTGGACAGCTCTGATTGTTAGAAAGTTCTTCCTTATAT 3888 chrXqtel1M 995031 GAAACTTTAATTTACCTTTTTGAAACT---ACC-----GTC--AATTTTT 995070 vi i ivv i i iii v --- ----- -- i i v C L3#LINE/CR1 3887 TGAGCCGAAATCTGCCTCCCTGTAACTTCCACCCATTGGTCCTAGTTCTG 3838 chrXqtel1M 995071 TCATCTGGAACCGAGCA-----------ATTTTTCTTCCATGGGACAGTC 995109 i v i ivi ----------- iii iiv i C L3#LINE/CR1 3837 CCCTCTGGAGCCACACAGAATAAGTCTAATCCCTCTTCCACATGACAGCC 3788 chrXqtel1M 995110 CTTCAAATACTTGACAATACCTATCATGACTGTCCCTTATGTCTTCTGTG 995159 i vi i v -- v ii v v - C L3#LINE/CR1 3787 CTTCAAATATTTGAAGACAGCTATCATG--TCTCCTCTAAGTCTTCTCT- 3741 chrXqtel1M 995160 TGTTGACTCTCAAC--CCCATTGATCGATTCTCTTATGTCAAACAAGTCC 995207 v iv vv v -- ------ ii - ---- v -- i C L3#LINE/CR1 3740 TCTCCAGGCTAAACATCCC------CAGTTC-CT----TCAACC--GTTC 3704 chrXqtel1M 995208 CCCTCACTGGCCCTTGAACTCAAGGTCCTCCACCTCTCTGGCCATCCTCT 995257 i vi - i v-- ivi v ii i vii i iii i C L3#LINE/CR1 3703 CTCATA-TGACA--TGGTTTCCAGACCCTTCACCATCCTGGTCGCTCTCC 3657 chrXqtel1M 995258 TCCAAACACTGTTCATATTACCACCGATTTCCTCT----GTGTGATCTTC 995303 iii i vv i vv ii vi -- i ----i iivii C L3#LINE/CR1 3656 TCTGGACGCGCTCCAGTTTGTCAATG--TCCCTCTTAAAATGTGGCGCCC 3609 chrXqtel1M 995304 TGACTTGAACACAGTAATCCAGATGTGGCCTAA 995336 v vi i i v i i C L3#LINE/CR1 3608 AGAACTGAACGCAATACTCCAGATGTGGTCTGA 3576 Matrix = 25p37g.matrix Kimura (with divCpGMod) = 48.63 CpG sites = 99, Kimura (unadjusted) = 52.34 Transitions / transversions = 2.02 (99/49) Gap_init rate = 0.09 (41 / 442), avg. gap size = 1.68 (69 / 41) 19 17.05 2.08 2.08 chrXqtel1M 995529 995576 (4424) (TATT)n#Simple_repeat 1 48 (0) m_b378s252i15 15834 chrXqtel1M 995529 TATTCTTTTTATTTATTTATTTATTT-TTTAATTAAATAACTTTTTATT 995576 - v - v vv vi v (TATT)n#Simpl 1 TATT-TATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATT 48 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.04 (2 / 47), avg. gap size = 1.00 (2 / 2) 482 25.06 11.50 1.27 chrXqtel1M 996187 996473 (3527) C L1ME4a_3end#LINE/L1 (500) 371 56 m_b378s551i13 15835 chrXqtel1M 996187 TCAAAGGGTATCAAG--TTTGACAACTTTTGGGGTATAGT-TCAAATTGC 996233 v? v-- v vii ivii v -i C L1ME4a_3end#L 371 TCAAAGGGTATGNACATTTTTAAGGCTTTTGATACATATTGCCAAATTGC 322 chrXqtel1M 996234 TCTACAGAATTGGATTTTCCAAATTCAAA----CATTATCAGT------- 996272 i v --i i v v v i v ---- ii v ------- C L1ME4a_3end#L 321 CCTCCAGAA--AGGTTGTACCAATTTACACTCCCACCAGCAGTGTATGAG 274 chrXqtel1M 996273 -GTCCCTGTTTTCCCAATCCCTCA--AACATT--CCATTATCTTTCCCT- 996316 - v i i? vv i-- i --vi vv ii - C L1ME4a_3end#L 273 AGTGCCCGTTTCNCCACACCCTCGCCAACACTGGGTATTATCAATCTTTT 224 chrXqtel1M 996317 --GTCATT-CTAATCTGACAGGTG-TTAGTGGTATCTAA--GTTGTCCTA 996360 --i v - i i i -vv i v -- ii C L1ME4a_3end#L 223 AAATCTTTGCCAATTTGATAGGTGAAAAATGGTATCTCATTGTTGTTTTA 174 chrXqtel1M 996361 ATTTGCATTTCTCTTATCAATAGTGATTTGGAACGTC-TTTCATATAGTA 996409 i v i v vv v i ?- iv - C L1ME4a_3end#L 173 ATTTGCATTTCTTTGATTACTAGTGAGGTTGAACATNTTTTCATATGTT- 125 chrXqtel1M 996410 GTAATAGT--TTT---TTTCATCATCTGAAAATTGTCTG-TCATATCCTT 996453 - v i i-- --- v v i vi - i C L1ME4a_3end#L 124 -TATTGGCCATTTGTATTTCTTCTTTTGTGAATTGTCTGTTCATGTCCTT 76 chrXqtel1M 996454 TGACCATTTATCAATTGGAG 996473 v v v i C L1ME4a_3end#L 75 TGCCCATTTTTCTATTGGGG 56 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 30.24 CpG sites = 36, Kimura (unadjusted) = 31.27 Transitions / transversions = 1.03 (36/35) Gap_init rate = 0.07 (19 / 286), avg. gap size = 1.95 (37 / 19) 533 22.42 8.70 0.90 chrXqtel1M 996267 996473 (3527) C L1ME5_3end#LINE/L1 (663) 278 56 m_b378s551i14 15835 chrXqtel1M 996267 ATCAGTGTCCCTGTTTTCCCA-ATCC-CTCAAACATTC--CATTATCTTT 996312 v v i i ? i - - v v i i-- ivv C L1ME5_3end#LI 278 ATGAGGGTTCCTATNTCCCCACATCCTCGCCAACACTTGGCATTATCCAG 229 chrXqtel1M 996313 CCCTGTCATT----CTAATCTGACAGGTGTTA-GTGGTATCTAA--GTTG 996355 ii v v ---- i i i i v - i v -- C L1ME5_3end#LI 228 CTTTCTAATTTTTGCCAGTCTAATAGGTGTAAAGTGATATCTCATTGTTG 179 chrXqtel1M 996356 TCCTAATTTGCATTTCTCTTATCAATAGTGATTTGGAACGTCT-TTCATA 996404 ii v i v i v v i i - C L1ME5_3end#LI 178 TTTTAATTTGCATTTCTCTGATTACTAATGAGTTTGAGCATCTCTTCATA 129 chrXqtel1M 996405 TAGTAGTAATAGTTTT-----TTTCATCATCTGAAAATTGTCTG-TCATA 996448 iv v -- ii ----- v v v i - C L1ME5_3end#LI 128 TGCTTGT--TAGCCTTTCGGGTTTCCTCTTCTGTAAATTGCCTGTTCATA 81 chrXqtel1M 996449 TCCTTTGACCATTTATCAATTGGAG 996473 v v v i C L1ME5_3end#LI 80 TCCTTTGCCCATTTTTCTATTGGGG 56 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 27.09 CpG sites = 24, Kimura (unadjusted) = 27.09 Transitions / transversions = 1.09 (24/22) Gap_init rate = 0.05 (11 / 206), avg. gap size = 1.82 (20 / 11) 1715 26.66 8.98 1.60 chrXqtel1M 997199 998769 (1231) C L1M5_orf2#LINE/L1 (892) 2402 718 m_b378s551i15 15835 chrXqtel1M 997199 TTTTTCCAATTAGTTAGATCAGACTTAATTTGTGTGGAAAGTGTTTTTGT 997248 i i v v i vvvi v v viiv i - C L1M5_orf2#LIN 2402 TCTCTCCATTTATTTAGGTCTTCTTTAATTTCTCTCAGCAATGTTTT-GT 2354 chrXqtel1M 997249 AGTTTTGCTCATAAAGTTTCTG---ATTTTCCCTTGGCAGATAGATTCCT 997295 vvvii ? v ii --- ? --- vi vv C L1M5_orf2#LIN 2353 AGTTTTCAGTGTANAGGTCTTGCACATNTT---TTGTTAGATTTATTCCT 2307 chrXqtel1M 997296 AAATATTTTATACTATC-GAT--TACTTTAAAAGGGTTTTTCTTTTGTAA 997342 i ? ii v i- -- i v v -- v v v? C L1M5_orf2#LIN 2306 AAGTATTTNATGTTTTTTGATGCTATTGTAAATGG--TATTGTTTTTNAA 2259 chrXqtel1M 997343 CTCTGACTGTTGGATT--TTATTAGTGATATATAAGAATGCTGATGACTT 997390 v i v i v ivi -- i iv ii ii i viv i C L1M5_orf2#LIN 2258 ATTTCATTTTCCAATTGTTTGTTGCTAGTATATAGAAATACAATTGATTT 2209 chrXqtel1M 997391 AT-TGGGTTTATTTTATA---AAAAACTTTGCTAAAATTG-----TGGAT 997431 v - ivi v ii i ---?ivi i v ii----- i v C L1M5_orf2#LIN 2208 TTGTATATTGACCTTGTATCCNGCGACCTTGCTAAATTCACTTATTAGTT 2159 chrXqtel1M 997432 CTTTTAATCTTTTTTAAAGAAT-TCTGGGGTTCTCTAAGTATA--AT-AT 997477 vv i - ? iv v - i ? i i v ? -- - C L1M5_orf2#LIN 2158 CTAGTAGT-TTNTTTGTAGATTCTTTNGGATTTTCTACGTANACAATCAT 2110 chrXqtel1M 997478 GTC---TG-GAAAGGTGAT--TTTGGTTTCCTCATTTTGCCTATTTTT-- 997519 --- - vii? i-- vi i v -- v i -- C L1M5_orf2#LIN 2109 GTCATCTGCGAATAANGACAGTTTTATTTCTTCCTTT--CCAATCTTTAT 2062 chrXqtel1M 997520 TCCTTTAATCTCTTTCTCAGCTCTTATTGCCATAGCTAGCATTTCTAATA 997569 v v i i vvvi vv i v ii i i C L1M5_orf2#LIN 2061 GCCTTTTATTTCTTTTTCTTGCCTTATTGCACTGGCTAGGACCTCCAGTA 2012 chrXqtel1M 997570 CAATATTAAATTTAAACGGTGGTAGTGGGCAACCTTGT-TTCCTCCAGAT 997618 i i vv ii i? i i v - vi v C L1M5_orf2#LIN 2011 CAATGTTGAATAGAAGTGGTGANAGCGGACATCCTTGTCTTGTTCCCGAT 1962 chrXqtel1M 997619 CTTTTGGGAA----TTTTGGTTTATC-CCATTACAT-TAATTCTTACTGT 997662 vv i ----? ii ? v - vi - i vi ?i C L1M5_orf2#LIN 1961 CTTAGGGGGAAAGCNTTCAGTNTTTCACCATTAAGTATGATGTTNGCTGT 1912 chrXqtel1M 997663 TGGTTTTAAATAGATGCTACTGTTATT---TTAAGGAAGT--CCATTTAT 997707 v vvi -- iv i--- i -- v i C L1M5_orf2#LIN 1911 AGGTTTTTCGTAGATGC--CCTTTATCAGGTTGAGGAAGTTCCCTTCTAT 1864 chrXqtel1M 997708 TCCTATAATTT--CAAGTGTTTTTAATA-GGGTGGATGTTGGA-TTTAT- 997752 -- i --ii v vi - ii i i - i - C L1M5_orf2#LIN 1863 TCC--TAGTTTGCTGAGAGTTTTTATCATGAATGGGTGTTGAATTTTGTC 1816 chrXqtel1M 997753 AAAT-CTTTTT-TGCATCTATTGA-ATGATCATATGGTTTTTTTAGTTTG 997799 - - - i i vv i C L1M5_orf2#LIN 1815 AAATGCTTTTTCTGCATCTATTGAGATGATCATATGATTTTTCTCCTTTA 1766 chrXqtel1M 997800 GT-TATTAA-ATGGCCAATTATA-TGATAG-TTTTC-AATATTAACCAAA 997844 v - i - iv i - v - - i v v C L1M5_orf2#LIN 1765 TTCTGTTAATATGGTGAATTACATTGATTGATTTTCGAATGTTAAACCAA 1716 chrXqtel1M 997845 CCC--CTTTCCTGGTATAAATCCTACTTGATCA--A---ATTATCCTGGG 997887 i-- v v i i i -- --- vvv C L1M5_orf2#LIN 1715 CCTTGCATTCCTGGGATAAACCCCACTTGGTCATGATGTATTATCCTTTT 1666 chrXqtel1M 997888 GATGATTTTTCTGG-TTCTCTTTGCTAATATTTTTTTAAG--TTTTATTA 997934 v - v v - vv v ? -- vvi C L1M5_orf2#LIN 1665 TAT-ATATTGCTGGATTCGATTTGCTAATATTTTGTTNAGGATTTTTGCA 1617 chrXqtel1M 997935 TCAATATTCATTA-GGAGATTGGTCTATAGTTTTCTTTCTCTGT--TTTC 997981 v i v - v i i iii -- v C L1M5_orf2#LIN 1616 TCTATGTTCATGAGGGATATTGGTCTGTAATTTTCTTTTCTTGTAATGTC 1567 chrXqtel1M 997982 AACCTACCTGGTTT--ATATCA-TTCCATGTCTGTGTCACAGAAGGAATT 998028 --ii ii ? --i -vvi? iiv iv i i v i C L1M5_orf2#LIN 1566 --TTTGTCNGGTTTTGGTATCAGGGTNATGCTGGCCTCATAAAATGAGTT 1519 chrXqtel1M 998029 TGGTGGGACTCCTTCATTCCCTATTTATC--AAATAATTTATATAGCATT 998076 v vi vii i v ii - --i v i i i iv C L1M5_orf2#LIN 1518 GGGAAGTGTTCCCTCTTTTTCTATTT-TCTGGAAGAGTTTGTGTAAGATT 1470 chrXqtel1M 998077 GGAATTG----TTCTTTAAATGTTTGGTAGAATTCGT---TAAATCCATC 998119 v i---- i ii--- i v C L1M5_orf2#LIN 1469 GGTATTATTTCTTCCTTAAATGTTTGGTAGAATTCACCAGTGAAGCCATC 1420 chrXqtel1M 998120 TGGTCTTGGGATTTTTTTCTTAGG--GGATTGATTAATAGC-ATTTCTAT 998166 v i ii i iv i -- v -- vi - v v C L1M5_orf2#LIN 1419 TGGGCCTGGAGTTTTCTTTGTGGGAAGGTTT--TTAATTACAAATTCAAT 1372 chrXqtel1M 998167 TTCTTTTCT-GAAATGGGACTATTTAAAACAATTC---TTCCTCCTCTGT 998212 vv - v i i i i vi-- --- i i v? C L1M5_orf2#LIN 1371 TTCTTTAATAGATATAGGGCTATTCAGATT--TTCTATTTCTTCTTGNGT 1324 chrXqtel1M 998213 TAGTCTAGGAAGTCTATATTTTT---GGGTGTCATCCATTTCAT-TAGGT 998258 i i v v i?i i i --- ivv ii - i C L1M5_orf2#LIN 1323 CAGTTTTGGTAANTTGTGTTTTTCAAGGAATTTGTCCATTTCATCTAAGT 1274 chrXqtel1M 998259 TAT-AAATTTATTGGCATAAAGCTGGGCA-AGTAACCCCTT-TTAT-TTT 998304 ? - i vv - i vi i - -i C L1M5_orf2#LIN 1273 TNTCAAATTTATTGGCATAAAGTTGTTCATAATATTCTCTTATTATCCTT 1224 chrXqtel1M 998305 TTAATTTCCTCTTCATTGGTGGAAAGTTCTCC-----CATT-TTAAGACT 998348 v ivivvv iv i vi vv ----- -i i v i C L1M5_orf2#LIN 1223 TTAATGTCTGTAGGATCTGTAGTGATGTCTCCTTTTTCATTCCTGATATT 1174 chrXqtel1M 998349 AATAATTTGATTTTCCTCTTTCCTTTTC-TAATCAGATTT--CAAAGGTT 998395 ii vv i i i ii - i vi ?--i i C L1M5_orf2#LIN 1173 GGTAATTTGTGTCTTCTCTCTTTTTTTCTTGATCAGTCTNGCTAGAGGTT 1124 chrXqtel1M 998396 TATCAATTTTATTGGTTTTCATAAAAAATC-----TTAGTTT--TTTATT 998438 i i ivi i i ----- i i -- v C L1M5_orf2#LIN 1123 TATCAATTTTATTGATCTTTTCAAAGAACCAGCTTTTGGCTTCGTTGATT 1074 chrXqtel1M 998439 AGTTCAATAGTTTTTTTAGTTTCAATATTA--AATTTC--CTTTTAATTT 998484 vvi v v ? ? iv v v i --i -- i vi C L1M5_orf2#LIN 1073 TTCTCTATTGTNTNTTTGTTTTCTATTTCATTGATTTCTGCTCTTATCTT 1024 chrXqtel1M 998485 TA--AATTTCAAGTTTATAATTATTGTGGGTTTTAATTTGGAC----TTT 998528 -- v i vvvi v v ?i v - vv ---- C L1M5_orf2#LIN 1023 TATTATTTCCTTCCTTCTACTTNCTTTGGG-TTTAATTTGCTCTTCTTTT 975 chrXqtel1M 998529 TCTAGCTTTTTAAGTTGCAAGCCCAATTCAT--ATTT-----CTTTC-TC 998570 i v v ii iv -- ----- - C L1M5_orf2#LIN 974 TCTAGCTTCTTAAGGTGGAAGCTTAGATCATTGATTTTAAGCCTTTCTTC 925 chrXqtel1M 998571 TAATTTATCAAGTAACC-TCTAAGGA-ATAAAGTTTTCCCTTATTACC-C 998617 -- v v vi ?v - i ? v- v ii i v vi i- C L1M5_orf2#LIN 924 T--TTTCTAATATANGCATTTAANGCTATAAATTTCCCTCTAAGCACTGC 877 chrXqtel1M 998618 TTTGGCT-CATCCCACAAATTTTGGTATGATGT-TTCACCTTGTCATTAT 998665 i - i v - iv v ? -- C L1M5_orf2#LIN 876 TTTAGCTGCATCCCACAAATTTTGATATGTTGTATTTTCATTNTCAT--T 829 chrXqtel1M 998666 CAG-TGAAGATAT----TAATTGTGTCTATAATTTGT--TTTCACCCAAT 998708 - v i ---- viv?i i i v -- v vv C L1M5_orf2#LIN 828 CAGTTCAAAATATTTTCTAATTTCCNTTGTGATTTCTTCTTTGACCCATG 779 chrXqtel1M 998709 CATTCTTTA-AGATGAGTTATTTAGTTTCCAATTACTTTTGGTTATTTAT 998757 vi v - ii v i i v i vv v - v C L1M5_orf2#LIN 778 GGTTATTTAGAAGTGTGTTGTTTAATTTCCAAATATTTGGGGAT-TTTCT 730 chrXqtel1M 998758 ACCTAACTTTTT 998769 v? v C L1M5_orf2#LIN 729 AGNTATCTTTTT 718 Matrix = 20p37g.matrix Kimura (with divCpGMod) = 34.03 CpG sites = 225, Kimura (unadjusted) = 34.33 Transitions / transversions = 1.20 (225/187) Gap_init rate = 0.07 (103 / 1570), avg. gap size = 1.63 (168 / 103) 13 18.15 6.25 6.25 chrXqtel1M 999486 999549 (451) (CCTT)n#Simple_repeat 1 64 (0) m_b378s252i16 15836 chrXqtel1M 999486 CCCTCCCTCCTCCCTTTGATTCCTTCC--CCTTTCTTGCTCTTCCTTATT 999533 i i i - vv -- i - - vi (CCTT)n#Simpl 1 CCTTCCTTCCTTCC-TTCCTTCCTTCCTTCCTTCCTT-C-CTTCCTTCCT 47 chrXqtel1M 999534 CTCTTTCCTT--TTCCTT 999549 - i -- (CCTT)n#Simpl 48 -TCCTTCCTTCCTTCCTT 64 Matrix = Unknown Transitions / transversions = 2.00 (6/3) Gap_init rate = 0.10 (6 / 63), avg. gap size = 1.33 (8 / 6) 16 21.27 3.85 1.89 chrXqtel1M 999508 999559 (441) (CTTCCT)n#Simple_repeat 1 53 (0) m_b378s252i17 15836 chrXqtel1M 999508 CTTCCCCTT--TCTTGCTCTTCCTTATTCTCTTTCCTTTTCCTTTTCTTC 999555 i -- v iv i - i i i (CTTCCT)n#Sim 1 CTTCCTCTTCCTCTTCCTCTTCCTCTTCCTC-TTCCTCTTCCTCTTCCTC 49 chrXqtel1M 999556 TCCC 999559 i (CTTCCT)n#Sim 50 TTCC 53 Matrix = Unknown Transitions / transversions = 3.50 (7/2) Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.50 (3 / 2)